Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_Position	End_Position	Strand	Consequence	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_File	Sequencer	t_ref_count	t_alt_count	n_ref_count	n_alt_count	HGVSc	HGVSp	HGVSp_Short	Transcript_ID	RefSeq	Protein_position	Codons	Exon_Number	ACSN.CELLULAR_FRACTION	ASCN.ASCN_INTEGER_COPY_NUMBER	ASCN.ASCN_METHOD	ASCN.CCF_EXPECTED_COPIES	ASCN.CCF_EXPECTED_COPIES_LOWER	ASCN.CCF_EXPECTED_COPIES_UPPER	ASCN.CCF_M_COPIES	ASCN.CCF_M_COPIES_LOWER	ASCN.CCF_M_COPIES_UPPER	ASCN.CLONAL	ASCN.EXPECTED_ALT_COPIES	ASCN.FACETS_QC_PASSED	ASCN.MINOR_COPY_NUMBER	ASCN.PURITY	ASCN.TOTAL_COPY_NUMBER	genomic_location_explanation	n_depth	t_depth	Annotation_Status
FAT1	2195	MSKCC	GRCh37	4	187630641	187630641	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006727-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	254	446	0	ENST00000441802.2:c.341A>T	p.Asp114Val	p.D114V	ENST00000441802	NM_005245.3	114	gAt/gTt	2/27	1	2	FACETS	0.98	0.921	1	0.98	0.921	1	CLONAL	1	TRUE	1	0.674251244783792	2		446	769	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340097	116340097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35776110	NA	P-0006727-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	270	420	3	ENST00000397752.3:c.959C>T	p.Ala320Val	p.A320V	ENST00000397752	NM_000245.2	320	gCg/gTg	2/21	0.674251244783792	3	FACETS	1	0.981	1	0.554	0.52	0.588	CLONAL	1	TRUE	1	0.674251244783792	3		423	967	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238146	133238146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006727-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	100	570	0	ENST00000320574.5:c.2831C>T	p.Ala944Val	p.A944V	ENST00000320574	NM_006231.2	944	gCc/gTc	24/49	0.162125291201358	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.674251244783792	0		570	840	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348235	89348235	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006727-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	330	846	0	ENST00000301030.4:c.4715T>C	p.Leu1572Pro	p.L1572P	ENST00000301030	NM_001256183.1	1572	cTc/cCc	9/13	0.321381354987836	3	FACETS	0.996	0.94	1			1	INDETERMINATE	1	TRUE	NA	0.674251244783792	3		846	1314	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134330	41134330	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006727-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	453	893	0	ENST00000379561.5:c.1298del	p.Pro433LeufsTer20	p.P433Lfs*20	ENST00000379561	NM_002015.3	433	cCt/ct	2/3	1	2	FACETS	0.944	0.901	0.988	0.944	0.901	0.988	CLONAL	1	TRUE	1	0.674251244783792	2		893	1423	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0011014-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	151	333	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.223720389711521	2		333	1156	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739803	41739803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011014-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1617	225	734	1	ENST00000242208.4:c.170C>T	p.Ala57Val	p.A57V	ENST00000242208	NM_002192.2	57	gCc/gTc	2/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.223720389711521	2		735	1842	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0013121-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	270	347	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.592595421042285	1	FACETS	0.98	0.926	1	0.98	0.926	1	CLONAL	1	TRUE	0	0.592595421042285	1		347	654	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846342	156846342	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746049437	NA	P-0013121-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	246	250	0	ENST00000524377.1:c.1783G>A	p.Gly595Arg	p.G595R	ENST00000524377	NM_002529.3	595	Ggg/Agg	14/17	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.592595421042285	2		250	735	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403244	213403244	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs748663394	NA	P-0013121-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	153	151	0	ENST00000342788.4:c.11C>A	p.Ala4Glu	p.A4E	ENST00000342788	NM_005235.2	4	gCg/gAg	1/28	1	2	FACETS	0.93	0.856	1	0.93	0.856	1	CLONAL	1	TRUE	1	0.592595421042285	2		151	555	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372070	55372070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013121-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	195	97	1	ENST00000297316.4:c.760G>A	p.Ala254Thr	p.A254T	ENST00000297316	NM_022454.3	254	Gcg/Acg	2/2	0.561555575153058	3	FACETS	1	0.967	1	0.536	0.497	0.576	CLONAL	1	TRUE	1	0.592595421042285	3		98	796	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882073	36882073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1372104492	NA	P-0013121-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	234	228	0	ENST00000358127.4:c.940G>A	p.Gly314Arg	p.G314R	ENST00000358127	NM_001280556.1	314	Ggg/Agg	8/10	1	2	FACETS	0.965	0.903	1	0.965	0.903	1	CLONAL	1	TRUE	1	0.592595421042285	2		228	818	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346901	89346901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1455558820	NA	P-0013121-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	69	203	0	ENST00000301030.4:c.6049G>A	p.Ala2017Thr	p.A2017T	ENST00000301030	NM_001256183.1	2017	Gcc/Acc	9/13	0.190318500055832	1	FACETS	0.605	0.532	0.681	0.605	0.532	0.681	INDETERMINATE	1	TRUE	0	0.592595421042285	1		203	271	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256445	46256445	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013121-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	217	208	0	ENST00000371998.3:c.673C>T	p.Gln225Ter	p.Q225*	ENST00000371998		225	Cag/Tag	7/23	1	2	FACETS	0.975	0.91	1	0.975	0.91	1	CLONAL	1	TRUE	1	0.592595421042285	2		208	751	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930942	39930942	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013121-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	184	181	0	ENST00000378444.4:c.2999T>C	p.Met1000Thr	p.M1000T	ENST00000378444	NM_001123385.1	1000	aTg/aCg	5/15	NA	2	FACETS	0.931	0.863	1			1	INDETERMINATE	1	TRUE	NA	0.592595421042285	2		181	667	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923000	44923000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139486036	NA	P-0013121-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	290	264	0	ENST00000377967.4:c.1861C>T	p.Arg621Cys	p.R621C	ENST00000377967	NM_021140.2	621	Cgc/Tgc	16/29	NA	2	FACETS	0.972	0.915	1			1	INDETERMINATE	1	TRUE	NA	0.592595421042285	2		264	1007	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849108	156849108	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013121-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	276	278	0	ENST00000524377.1:c.2000G>C	p.Gly667Ala	p.G667A	ENST00000524377	NM_002529.3	667	gGt/gCt	15/17	1	2	FACETS	0.921	0.866	0.978	0.921	0.866	0.978	CLONAL	1	TRUE	1	0.592595421042285	2		278	1011	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436624	52436624	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs387906848	NA	P-0017843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	157	359	0	ENST00000460680.1:c.2050C>T	p.Gln684Ter	p.Q684*	ENST00000460680	NM_004656.3	684	Cag/Tag	16/17	0.567702644457611	1	FACETS	0.945	0.875	1	0.945	0.875	1	CLONAL	1	FALSE	0	0.567702644457611	1		359	419	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549149	21549149	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1444091389	NA	P-0017843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	63	395	0	ENST00000382592.4:c.3127C>T	p.Arg1043Ter	p.R1043*	ENST00000382592	NM_014572.2	1043	Cga/Tga	8/8	0.567702644457611	1	FACETS	0.337	0.292	0.386	0.337	0.292	0.386	SUBCLONAL	1	FALSE	0	0.567702644457611	1		395	471	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038275	30038275	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0017843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	122	250	0	ENST00000338641.4:c.447+1G>T		p.X149_splice	ENST00000338641	NM_000268.3	149			0.567702644457611	1	FACETS	0.987	0.905	1	0.987	0.905	1	CLONAL	1	FALSE	0	0.567702644457611	1		250	312	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005017	150005017	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	46	247	0	ENST00000253339.5:c.1208del	p.Gly403GlufsTer7	p.G403Efs*7	ENST00000253339		403	gGa/ga	3/7	0.567702644457611	1	FACETS	0.351	0.296	0.41	0.351	0.296	0.41	SUBCLONAL	1	FALSE	0	0.567702644457611	1		247	331	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188197	10188197	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0018929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	199	598	0	ENST00000256474.2:c.341-1G>T		p.X114_splice	ENST00000256474	NM_000551.3	114			0.58385324029898	1	FACETS	0.954	0.893	1	0.954	0.893	1	CLONAL	1	TRUE	0	0.60934203207032	1		598	476	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610665	52610666	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	C	novel	NA	P-0018929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	152	596	0	ENST00000394830.3:c.3507_3508delinsG	p.Ile1170SerfsTer23	p.I1170Sfs*23	ENST00000394830	NM_018313.4	1169	ccCAtc/ccGtc	23/30	0.566624269747628	1	FACETS	0.901	0.834	0.969	0.901	0.834	0.969	CLONAL	1	TRUE	0	0.60934203207032	1		596	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	1159	1081	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.817681577355135	3	FACETS	1	0.999	1			1	CLONAL	3	TRUE	NA	0.913880254180242	3		1081	1185	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910578	32910579	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0021409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	241	663	61	ENST00000380152.3:c.2090_2091dup	p.Leu698AsnfsTer33	p.L698Nfs*33	ENST00000380152		696	gaa/gAAaa	11/27	0.918571851523191	2	FACETS	1	0.968	1	0.518	0.489	0.547	CLONAL	1	TRUE	0	0.913880254180242	2		724	509	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983722	15983722	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	445	723	0	ENST00000268712.3:c.3400G>A	p.Gly1134Ser	p.G1134S	ENST00000268712	NM_006311.3	1134	Ggt/Agt	25/46	0.817681577355135	3	FACETS	1	0.967	1			1	CLONAL	2	TRUE	NA	0.913880254180242	3		723	708	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023765	27023766	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCACCC	novel	NA	P-0021409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	148	857	0	ENST00000324856.7:c.878_883dup	p.Pro293_Thr294dup	p.P293_T294dup	ENST00000324856	NM_006015.4	293	gcc/gCCACCCcc	1/20	0.817681577355135	3	FACETS	0.51	0.465	0.557			1	SUBCLONAL	1	TRUE	NA	0.913880254180242	3		857	925	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277991	18277991	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1974	347	977	0	ENST00000222254.8:c.1611G>C	p.Glu537Asp	p.E537D	ENST00000222254	NM_005027.3	537	gaG/gaC	13/16	0.913880254180242	6	FACETS	0.925	0.872	0.98	0.231	0.218	0.246	CLONAL	1	TRUE	2	0.913880254180242	6		977	2321	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141565784	141566048	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CATTAAGGATAATTCTGAAAAACTTTAAAAAGGACCAAGGAAAGCCATTCCTTTATGAAATCTCACGTCTTTTACAGGCTCAGCCGGGAGTAGAAAGGATTCTCCTGCATGGAACACAGTCTACACCGCGGGCGATAGCTCAGAACCTGAGAGGGGTCGCAGGGCAGAGACATGCCCCGCAGCCACACGTTCCCCGCCGCCCCACACGTACCCTGCCCCCGTAGAGGATGGAGGGCGGCTGCAGCACCCGCCCAGTCACGTCTGT	CATTAAGGATAATTCTGAAAAACTTTAAAAAGGACCAAGGAAAGCCATTCCTTTATGAAATCTCACGTCTTTTACAGGCTCAGCCGGGAGTAGAAAGGATTCTCCTGCATGGAACACAGTCTACACCGCGGGCGATAGCTCAGAACCTGAGAGGGGTCGCAGGGCAGAGACATGCCCCGCAGCCACACGTTCCCCGCCGCCCCACACGTACCCTGCCCCCGTAGAGGATGGAGGGCGGCTGCAGCACCCGCCCAGTCACGTCTGT	-	novel	NA	P-0021409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2442	171	19	0	ENST00000220592.5:c.1216_1269+211del		p.X406_splice	ENST00000220592	NM_012154.3	406		10/19	0.913880254180242	7	FACETS	0.47	0.43	0.513	0.118	0.107	0.129	SUBCLONAL	1	TRUE	3	0.913880254180242	7		19	2613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021409-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	88	1081	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.402784612112039	1	FACETS	0.651	0.579	0.728	0.651	0.579	0.728	SUBCLONAL	1	TRUE	0	0.427554033235113	1		1081	497	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106203	2106209	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTCTG	CTGTCTG	-	novel	NA	P-0021409-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	148	812	0	ENST00000219476.3:c.610_616del	p.Leu204AlafsTer10	p.L204Afs*10	ENST00000219476	NM_000548.3	202	atCTGTCTG/at	7/42	0.362755719745337	1	FACETS	0.889	0.815	0.966	0.889	0.815	0.966	CLONAL	1	TRUE	0	0.427554033235113	1		812	612	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0021882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	300	732	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.523524925468285	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.523524925468285	1		732	806	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008033	29008033	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	60	480	0	ENST00000282397.4:c.736C>G	p.His246Asp	p.H246D	ENST00000282397	NM_002019.4	246	Cat/Gat	6/30	1	2	FACETS	0.344	0.296	0.397	0.344	0.296	0.397	SUBCLONAL	1	TRUE	1	0.523524925468285	2		480	666	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724664	43724664	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	318	853	0	ENST00000382044.4:c.3403G>C	p.Glu1135Gln	p.E1135Q	ENST00000382044	NM_001141980.1	1135	Gaa/Caa	17/28	0.307965993202404	0	FACETS	0.683	0.648	0.72			1	INDETERMINATE	1	TRUE	0	0.523524925468285	0		853	847	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187558017	187558017	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	169	400	0	ENST00000441802.2:c.3694A>T	p.Ile1232Phe	p.I1232F	ENST00000441802	NM_005245.3	1232	Att/Ttt	5/27	0.418965902025332	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.523524925468285	1		400	430	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349204	70349204	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	168	678	1	ENST00000374080.3:c.3616C>A	p.His1206Asn	p.H1206N	ENST00000374080		1206	Cac/Aac	26/45	NA	2	FACETS	0.696	0.64	0.755			1	INDETERMINATE	1	TRUE	NA	0.523524925468285	2		679	922	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	96	1081	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.544355429221779	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.544355429221779	2		1081	157	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76876000	76876000	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	94	241	0	ENST00000373344.5:c.5135G>T	p.Gly1712Val	p.G1712V	ENST00000373344	NM_000489.3	1712	gGc/gTc	20/35	0.544355429221779	2	FACETS	0.879	0.82	0.934			1	CLONAL	3	TRUE	NA	0.544355429221779	2		241	131	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319056	62319056	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs941024707	NA	P-0023858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	81	775	4	ENST00000360203.5:c.1414G>A	p.Val472Ile	p.V472I	ENST00000360203	NM_001283009.1	472	Gtc/Atc	17/35	0.286298458996363	4	FACETS	0.842	0.76	0.925	1	0.974	1	INDETERMINATE	3	TRUE	2	0.544355429221779	4		779	182	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468323	50468323	+	stop_lost	Nonstop_Mutation	SNP	T	T	A	novel	NA	P-0023858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	18	483	1	ENST00000331340.3:c.1558T>A	p.Ter520LysextTer29	p.*520Kext*29	ENST00000331340	NM_006060.4	520	Taa/Aaa	8/8	0.544355429221779	5	FACETS	0.89	0.676	1	0.297	0.225	0.379	CLONAL	1	TRUE	2	0.544355429221779	5		484	135	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211407	98211407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502265	NA	P-0023858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	36	689	4	ENST00000331920.6:c.3748C>T	p.Pro1250Ser	p.P1250S	ENST00000331920	NM_000264.3	1250	Cct/Tct	22/24	0.188990661552459	4	FACETS	1	0.916	1	0.587	0.488	0.694	INDETERMINATE	1	TRUE	2	0.544355429221779	4		693	174	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0024969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	241	710	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.273049369293347	2	FACETS	1	0.991	1	0.681	0.636	0.727	CLONAL	1	TRUE	0	0.35088472992725	2		710	1009	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0024969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	114	460	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	0.0827668511445996	4	FACETS	1	0.973	1	0.617	0.556	0.682	INDETERMINATE	1	TRUE	2	0.35088472992725	4		460	711	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280679	115280679	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	54	537	0	ENST00000438362.2:c.352G>C	p.Glu118Gln	p.E118Q	ENST00000438362	NM_001242891.1	118	Gaa/Caa	4/20	0.130016210953753	3	FACETS	0.497	0.423	0.578	0.248	0.211	0.289	INDETERMINATE	1	TRUE	1	0.35088472992725	3		537	728	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111097	193111099	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0024969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	74	418	0	ENST00000367435.3:c.633_635del	p.Arg211del	p.R211del	ENST00000367435	NM_024529.4	210	caGAGg/cag	7/17	0.130016210953753	3	FACETS	0.97	0.851	1	0.485	0.425	0.549	INDETERMINATE	1	TRUE	1	0.35088472992725	3		418	511	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40879689	40879692	+	frameshift_variant	Frame_Shift_Del	DEL	TGAC	TGAC	-	novel	NA	P-0024969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	229	712	0	ENST00000428826.2:c.207_210del	p.Ser70Ter	p.S70*	ENST00000428826		69	caGTCA/ca	4/21	0.230419969963754	3	FACETS	1	0.991	1	0.487	0.454	0.522	CLONAL	1	TRUE	0	0.35088472992725	3		712	1050	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0024969-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	99	509	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.825	0.736	0.92	0.825	0.736	0.92	CLONAL	1	FALSE	1	0.307292554372244	2		509	781	SUCCESS
APC	324	MSKCC	GRCh37	5	112176027	112176030	+	frameshift_variant	Frame_Shift_Del	DEL	TTAT	TTAT	-	novel	NA	P-0024969-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	124	316	0	ENST00000257430.4:c.4738_4741del	p.Ile1580LeufsTer69	p.I1580Lfs*69	ENST00000257430	NM_000038.5	1579	aTTATt/at	16/16	1	2	FACETS	0.839	0.764	0.917	1	0.988	1	CLONAL	2	FALSE	1	0.307292554372244	2		316	481	SUCCESS
APC	324	MSKCC	GRCh37	5	112174489	112174490	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0024969-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	114	341	0	ENST00000257430.4:c.3199_3200del	p.Gln1067IlefsTer13	p.Q1067Ifs*13	ENST00000257430	NM_000038.5	1066	agACaa/agaa	16/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.307292554372244	2		341	582	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469956	157469956	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024969-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	84	498	0	ENST00000346085.5:c.2750C>G	p.Thr917Ser	p.T917S	ENST00000346085	NM_020732.3	917	aCc/aGc	9/20	1	2	FACETS	0.73	0.644	0.822	0.73	0.644	0.822	SUBCLONAL	1	FALSE	1	0.307292554372244	2		498	749	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224498	108224498	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	45	296	0	ENST00000278616.4:c.8677G>C	p.Ala2893Pro	p.A2893P	ENST00000278616	NM_000051.3	2893	Gct/Cct	60/63	1	2	FACETS	0.614	0.519	0.718	0.614	0.519	0.718	SUBCLONAL	1	TRUE	1	0.5000889525942	2		296	293	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939241	76939241	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1340830235	NA	P-0025167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	84	783	0	ENST00000373344.5:c.1507C>G	p.Gln503Glu	p.Q503E	ENST00000373344	NM_000489.3	503	Caa/Gaa	9/35	1	2	FACETS	0.565	0.499	0.635	0.565	0.499	0.635	SUBCLONAL	1	TRUE	1	0.5000889525942	2		783	595	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041833	42041833	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	74	531	0	ENST00000219905.7:c.6028C>T	p.Gln2010Ter	p.Q2010*	ENST00000219905	NM_001164273.1	2010	Caa/Taa	17/24	1	2	FACETS	0.742	0.653	0.837	0.742	0.653	0.837	SUBCLONAL	1	TRUE	1	0.5000889525942	2		531	399	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622073	1622073	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	140	718	0	ENST00000344749.5:c.802C>A	p.Leu268Met	p.L268M	ENST00000344749	NM_001136139.2	268	Ctg/Atg	10/19	1	2	FACETS	0.962	0.88	1	0.962	0.88	1	CLONAL	1	TRUE	1	0.5000889525942	2		718	582	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058665	47058680	+	frameshift_variant	Frame_Shift_Del	DEL	TGTTTCACATTCTCAT	TGTTTCACATTCTCAT	-	novel	NA	P-0025167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	34	707	0	ENST00000409792.3:c.7598_7613del	p.Asn2533ThrfsTer26	p.N2533Tfs*26	ENST00000409792	NM_014159.6	2533	aATGAGAATGTGAAACAc/ac	21/21	0.5000889525942	1	FACETS	0.183	0.149	0.222	0.183	0.149	0.222	SUBCLONAL	1	TRUE	0	0.5000889525942	1		707	557	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613124	52613128	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTT	ACCTT	-	novel	NA	P-0025167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	181	504	0	ENST00000394830.3:c.3400_3404del	p.Lys1134TrpfsTer20	p.K1134Wfs*20	ENST00000394830	NM_018313.4	1134	AAGGTt/t	22/30	0.5000889525942	1	FACETS	0.961	0.892	1	0.961	0.892	1	CLONAL	1	TRUE	0	0.5000889525942	1		504	565	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821594	72821596	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs374416547	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	13	77	0	ENST00000268489.5:c.10579_10581del	p.Gly3527del	p.G3527del	ENST00000268489	NM_006885.3	3527	GGC/-	10/10	1	2	FACETS	0.653	0.469	0.874	0.653	0.469	0.874	SUBCLONAL	1	TRUE	1	0.318497170097495	2		77	125	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	203	470	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.969	0.902	1	1	0.994	1	CLONAL	2	TRUE	1	0.318497170097495	2		472	658	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	128	334	1	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.318497170097495	2		335	583	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841231	15841236	+	inframe_deletion	In_Frame_Del	DEL	AGCCGG	AGCCGG	-	rs752736259	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	63	276	5	ENST00000307771.7:c.1338_1343del	p.Ser447_Arg448del	p.S447_R448del	ENST00000307771	NM_005089.3	439	AGCCGG/-	11/11	1	2	FACETS	0.891	0.773	1	0.891	0.773	1	CLONAL	1	TRUE	1	0.318497170097495	2		281	444	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258889	16258889	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	150	573	1	ENST00000375759.3:c.6158del	p.Asn2053ThrfsTer11	p.N2053Tfs*11	ENST00000375759	NM_015001.2	2052	Aaa/aa	11/15	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.318497170097495	2		574	924	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026664	6026664	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750534	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	178	691	0	ENST00000265849.7:c.1732C>T	p.Arg578Cys	p.R578C	ENST00000265849	NM_000535.5	578	Cgt/Tgt	11/15	1	2	FACETS	0.902	0.83	0.978	0.902	0.83	0.978	CLONAL	1	TRUE	1	0.318497170097495	2		691	1239	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608237	100608237	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	140	533	0	ENST00000308731.7:c.1853G>T	p.Arg618Met	p.R618M	ENST00000308731	NM_000061.2	618	aGg/aTg	18/19	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.318497170097495	2		533	859	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435552	56435552	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs62636625	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	128	483	1	ENST00000407977.2:c.1585C>T	p.Arg529Trp	p.R529W	ENST00000407977		529	Cgg/Tgg	9/10	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.318497170097495	2		484	790	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	85	503	4	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.881	0.779	0.989	0.881	0.779	0.989	CLONAL	1	TRUE	1	0.318497170097495	2		507	606	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687471	37687472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs760014508	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	57	220	0	ENST00000447079.4:c.4382dup	p.Thr1463AsnfsTer50	p.T1463Nfs*50	ENST00000447079	NM_015083.1	1459	tgg/tGgg	14/14	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.318497170097495	2		220	358	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	12	172	1	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	2	FACETS	0.428	0.301	0.583	0.428	0.301	0.583	SUBCLONAL	1	TRUE	1	0.318497170097495	2		173	176	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	100	282	2	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.318497170097495	2		284	611	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	53	293	2	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.954	0.817	1	0.954	0.817	1	CLONAL	1	TRUE	1	0.318497170097495	2		295	349	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129329	152129329	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	116	383	4	ENST00000206249.3:c.287del	p.Gly96ValfsTer13	p.G96Vfs*13	ENST00000206249	NM_000125.3	94	ctG/ct	1/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.318497170097495	2		387	557	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675571	86675571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1561325048	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	116	280	0	ENST00000274376.6:c.2513del	p.Asn838MetfsTer4	p.N838Mfs*4	ENST00000274376	NM_002890.2	836	gAa/ga	19/25	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.318497170097495	2		280	672	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100728	8100728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs771019738	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	97	490	4	ENST00000346208.3:c.708del	p.Ser237AlafsTer28	p.S237Afs*28	ENST00000346208		234	ttC/tt	3/6	1	2	FACETS	0.937	0.836	1	0.937	0.836	1	CLONAL	1	TRUE	1	0.318497170097495	2		494	650	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739031	40739031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358914349	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	85	459	1	ENST00000373198.4:c.3253G>A	p.Val1085Ile	p.V1085I	ENST00000373198	NM_133170.3	1085	Gtc/Atc	24/32	1	2	FACETS	0.914	0.809	1	0.914	0.809	1	CLONAL	1	TRUE	1	0.318497170097495	2		460	584	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732963	30732963	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	87	286	1	ENST00000295754.5:c.1576G>T	p.Glu526Ter	p.E526*	ENST00000295754	NM_003242.5	526	Gag/Tag	7/7	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.318497170097495	2		287	505	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422384	47422384	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	63	300	1	ENST00000377045.4:c.23del	p.Pro8LeufsTer26	p.P8Lfs*26	ENST00000377045	NM_001654.4	6	ggC/gg	2/16	1	2	FACETS	0.824	0.714	0.943	0.824	0.714	0.943	CLONAL	1	TRUE	1	0.318497170097495	2		301	480	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468185	120468185	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	99	451	0	ENST00000256646.2:c.4254del	p.Ser1419AlafsTer8	p.S1419Afs*8	ENST00000256646	NM_024408.3	1418	ccC/cc	25/34	1	2	FACETS	0.862	0.77	0.96	0.862	0.77	0.96	CLONAL	1	TRUE	1	0.318497170097495	2		451	721	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272337	15272337	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs771517374	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	105	563	8	ENST00000263388.2:c.6102del	p.Gly2035ValfsTer50	p.G2035Vfs*50	ENST00000263388	NM_000435.2	2034	ccC/cc	33/33	1	2	FACETS	0.975	0.875	1	0.975	0.875	1	CLONAL	1	TRUE	1	0.318497170097495	2		571	676	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150022	202150022	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	98	461	0	ENST00000358485.4:c.1463T>C	p.Leu488Pro	p.L488P	ENST00000358485	NM_001080125.1	488	cTg/cCg	8/9	1	2	FACETS	0.77	0.687	0.859	0.77	0.687	0.859	SUBCLONAL	1	TRUE	1	0.318497170097495	2		461	799	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	97	452	5	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.318497170097495	2		457	576	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627501	37627501	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	120	432	0	ENST00000447079.4:c.1421del	p.Asn474IlefsTer8	p.N474Ifs*8	ENST00000447079	NM_015083.1	472	gtA/gt	2/14	1	2	FACETS	0.941	0.85	1	0.941	0.85	1	CLONAL	1	TRUE	1	0.318497170097495	2		432	801	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017210	31017210	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	88	288	2	ENST00000375687.4:c.541G>A	p.Gly181Arg	p.G181R	ENST00000375687	NM_015338.5	181	Ggg/Agg	7/13	1	2	FACETS	0.992	0.881	1	0.992	0.881	1	CLONAL	1	TRUE	1	0.318497170097495	2		290	557	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512377	38512377	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555574293	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	55	384	0	ENST00000254066.5:c.1293del	p.Arg432GlyfsTer211	p.R432Gfs*211	ENST00000254066	NM_000964.3	430	Ggg/gg	9/9	1	2	FACETS	0.633	0.541	0.733	0.633	0.541	0.733	SUBCLONAL	1	TRUE	1	0.318497170097495	2		384	546	SUCCESS
APC	324	MSKCC	GRCh37	5	112170772	112170772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765557332	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	153	510	0	ENST00000257430.4:c.1868G>A	p.Arg623Gln	p.R623Q	ENST00000257430	NM_000038.5	623	cGg/cAg	15/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.318497170097495	2		510	914	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356251	70356251	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	115	481	0	ENST00000374080.3:c.5146C>T	p.Arg1716Ter	p.R1716*	ENST00000374080		1716	Cga/Tga	37/45	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.318497170097495	2		481	668	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856626	111856626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1441752820	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	73	249	0	ENST00000341259.2:c.677G>A	p.Arg226Gln	p.R226Q	ENST00000341259	NM_005475.2	226	cGg/cAg	2/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.318497170097495	2		249	375	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9770535	9770535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	113	544	0	ENST00000377346.4:c.22C>T	p.Pro8Ser	p.P8S	ENST00000377346	NM_005026.3	8	Ccc/Tcc	3/24	1	2	FACETS	0.954	0.859	1	0.954	0.859	1	CLONAL	1	TRUE	1	0.318497170097495	2		544	744	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912075	50912077	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs398122386	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	116	600	0	ENST00000440232.2:c.1812_1814del	p.Ser605del	p.S605del	ENST00000440232	NM_002691.3	603	ttCTCc/ttc	15/27	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.318497170097495	2		600	694	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396590	396590	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	124	508	1	ENST00000262320.3:c.436C>T	p.Arg146Ter	p.R146*	ENST00000262320	NM_003502.3	146	Cga/Tga	2/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.318497170097495	2		509	657	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	61	603	0	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	1	2	FACETS	0.433	0.373	0.5	0.433	0.373	0.5	SUBCLONAL	1	TRUE	1	0.318497170097495	2		603	884	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980527	1980527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760185069	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	98	496	2	ENST00000382891.5:c.3989C>T	p.Ala1330Val	p.A1330V	ENST00000382891	NM_133335.3	1330	gCg/gTg	22/22	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.318497170097495	2		498	564	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402834	20402836	+	inframe_deletion	In_Frame_Del	DEL	GCG	GCG	-	rs746263274	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	16	54	0	ENST00000346618.3:c.385_387del	p.Gly129del	p.G129del	ENST00000346618	NM_001949.4	124	aGCGgc/agc	1/7	1	2	FACETS	1	0.82	1	1	0.82	1	CLONAL	1	TRUE	1	0.318497170097495	2		54	90	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262480	16262480	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	36	206	0	ENST00000375759.3:c.9745C>A	p.Pro3249Thr	p.P3249T	ENST00000375759	NM_015001.2	3249	Ccc/Acc	11/15	1	2	FACETS	0.887	0.733	1	0.887	0.733	1	CLONAL	1	TRUE	1	0.318497170097495	2		206	255	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024014	27024014	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	26	94	0	ENST00000324856.7:c.1120C>A	p.Leu374Ile	p.L374I	ENST00000324856	NM_006015.4	374	Ctc/Atc	1/20	1	2	FACETS	0.912	0.729	1	0.912	0.729	1	CLONAL	1	TRUE	1	0.318497170097495	2		94	179	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390781	118390781	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	67	268	0	ENST00000534358.1:c.11429+2T>C		p.X3810_splice	ENST00000534358	NM_005933.3	3810			1	2	FACETS	0.969	0.845	1	0.969	0.845	1	CLONAL	1	TRUE	1	0.318497170097495	2		268	434	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398022	4398022	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	86	438	0	ENST00000261254.3:c.586A>G	p.Met196Val	p.M196V	ENST00000261254	NM_001759.3	196	Atg/Gtg	4/5	NA	2	FACETS	0.725	0.641	0.815			1	INDETERMINATE	1	TRUE	NA	0.318497170097495	2		438	745	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493650	56493650	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	99	328	0	ENST00000267101.3:c.2966G>T	p.Gly989Val	p.G989V	ENST00000267101	NM_001982.3	989	gGg/gTg	25/28	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.318497170097495	2		328	502	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38064107	38064107	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	79	303	0	ENST00000250448.2:c.71A>G	p.Glu24Gly	p.E24G	ENST00000250448	NM_004496.3	24	gAg/gGg	1/2	1	2	FACETS	0.884	0.779	0.997	0.884	0.779	0.997	CLONAL	1	TRUE	1	0.318497170097495	2		303	561	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99452078	99452078	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763660010	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	60	338	1	ENST00000268035.6:c.1412G>A	p.Arg471His	p.R471H	ENST00000268035	NM_000875.3	471	cGc/cAc	6/21	1	2	FACETS	0.754	0.65	0.866	0.754	0.65	0.866	SUBCLONAL	1	TRUE	1	0.318497170097495	2		339	500	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820938	3820938	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	124	472	0	ENST00000262367.5:c.2513C>A	p.Pro838His	p.P838H	ENST00000262367	NM_004380.2	838	cCt/cAt	14/31	1	2	FACETS	0.992	0.898	1	0.992	0.898	1	CLONAL	1	TRUE	1	0.318497170097495	2		472	785	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119753	17119753	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1363880753	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	101	481	0	ENST00000285071.4:c.1241G>A	p.Arg414Gln	p.R414Q	ENST00000285071	NM_144997.5	414	cGg/cAg	11/14	1	2	FACETS	0.927	0.829	1	0.927	0.829	1	CLONAL	1	TRUE	1	0.318497170097495	2		481	684	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533376	29533376	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs147417054	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	78	211	0	ENST00000356175.3:c.1379T>C	p.Ile460Thr	p.I460T	ENST00000356175	NM_000267.3	460	aTa/aCa	12/57	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.318497170097495	2		211	411	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652995	29652996	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1135402867	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	121	343	0	ENST00000356175.3:c.4935dup	p.Pro1646SerfsTer15	p.P1646Sfs*15	ENST00000356175	NM_000267.3	1644	gtt/gTtt	36/57	1	2	FACETS	0.945	0.854	1	0.945	0.854	1	CLONAL	1	TRUE	1	0.318497170097495	2		343	804	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661858	29661858	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	91	351	0	ENST00000356175.3:c.5752A>G	p.Ile1918Val	p.I1918V	ENST00000356175	NM_000267.3	1918	Att/Gtt	39/57	1	2	FACETS	0.739	0.656	0.828	0.739	0.656	0.828	SUBCLONAL	1	TRUE	1	0.318497170097495	2		351	773	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320963	30320963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371166327	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	168	463	1	ENST00000322652.5:c.1373G>A	p.Arg458His	p.R458H	ENST00000322652	NM_015355.2	458	cGc/cAc	12/16	1	2	FACETS	0.995	0.914	1	0.995	0.914	1	CLONAL	1	TRUE	1	0.318497170097495	2		464	1060	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434885	56434885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1236934148	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	123	430	0	ENST00000407977.2:c.2252C>T	p.Thr751Ile	p.T751I	ENST00000407977		751	aCc/aTc	9/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.318497170097495	2		430	709	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740708	58740708	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	115	427	0	ENST00000305921.3:c.1613T>C	p.Leu538Ser	p.L538S	ENST00000305921	NM_003620.3	538	tTa/tCa	6/6	1	2	FACETS	0.915	0.825	1	0.915	0.825	1	CLONAL	1	TRUE	1	0.318497170097495	2		427	789	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226743	2226743	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	79	459	0	ENST00000398665.3:c.4223G>C	p.Gly1408Ala	p.G1408A	ENST00000398665	NM_032482.2	1408	gGc/gCc	27/28	1	2	FACETS	0.849	0.748	0.958	0.849	0.748	0.958	CLONAL	1	TRUE	1	0.318497170097495	2		459	584	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291061	10291061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377146699	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	104	405	0	ENST00000340748.4:c.410C>T	p.Thr137Met	p.T137M	ENST00000340748		137	aCg/aTg	4/40	1	2	FACETS	0.941	0.843	1	0.941	0.843	1	CLONAL	1	TRUE	1	0.318497170097495	2		405	694	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145606	11145606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61750054	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	77	449	0	ENST00000358026.2:c.3968G>A	p.Arg1323His	p.R1323H	ENST00000358026	NM_001128849.1	1323	cGc/cAc	29/36	1	2	FACETS	0.839	0.738	0.948	0.839	0.738	0.948	CLONAL	1	TRUE	1	0.318497170097495	2		449	576	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257424	19257424	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs745619777	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	136	579	0	ENST00000162023.5:c.709T>C	p.Ser237Pro	p.S237P	ENST00000162023		237	Tcc/Ccc	11/13	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.318497170097495	2		579	776	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753390	42753390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776319250	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	115	523	2	ENST00000222329.4:c.874G>A	p.Gly292Arg	p.G292R	ENST00000222329	NM_006494.2	292	Ggg/Agg	4/4	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.318497170097495	2		525	684	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025871	48025871	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587781275	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	93	292	0	ENST00000234420.5:c.749T>C	p.Val250Ala	p.V250A	ENST00000234420	NM_000179.2	250	gTc/gCc	4/10	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.318497170097495	2		292	569	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149939	99149939	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200860936	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	43	472	0	ENST00000074304.5:c.251C>T	p.Ala84Val	p.A84V	ENST00000074304	NM_001134224.1	84	gCa/gTa	5/26	1	2	FACETS	0.349	0.291	0.414	0.349	0.291	0.414	SUBCLONAL	1	TRUE	1	0.318497170097495	2		472	774	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151315	202151315	+	stop_lost	Nonstop_Mutation	SNP	T	T	C	rs761997594	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	107	399	0	ENST00000358485.4:c.1615T>C	p.Ter539ArgextTer88	p.*539Rext*88	ENST00000358485	NM_001080125.1	539	Tga/Cga	9/9	1	2	FACETS	0.83	0.744	0.921	0.83	0.744	0.921	CLONAL	1	TRUE	1	0.318497170097495	2		399	810	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215595197	215595197	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1350570988	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	134	401	2	ENST00000260947.4:c.1939C>T	p.Gln647Ter	p.Q647*	ENST00000260947	NM_000465.2	647	Cag/Tag	10/11	1	2	FACETS	0.966	0.878	1	0.966	0.878	1	CLONAL	1	TRUE	1	0.318497170097495	2		403	871	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37628917	37628917	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	149	576	0	ENST00000249071.6:c.149C>A	p.Pro50Gln	p.P50Q	ENST00000249071	NM_002872.4	50	cCa/cAa	3/7	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.318497170097495	2		576	846	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163727	47163727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1169288572	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	94	430	0	ENST00000409792.3:c.2399G>A	p.Ser800Asn	p.S800N	ENST00000409792	NM_014159.6	800	aGc/aAc	3/21	1	2	FACETS	0.784	0.697	0.876	0.784	0.697	0.876	SUBCLONAL	1	TRUE	1	0.318497170097495	2		430	753	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259641	89259641	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	65	281	0	ENST00000336596.2:c.785G>A	p.Gly262Asp	p.G262D	ENST00000336596	NM_005233.5	262	gGc/gAc	3/17	1	2	FACETS	0.926	0.805	1	0.926	0.805	1	CLONAL	1	TRUE	1	0.318497170097495	2		281	441	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146604	55146604	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs779246705	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	181	451	0	ENST00000257290.5:c.2278T>C	p.Ser760Pro	p.S760P	ENST00000257290	NM_006206.4	760	Tca/Cca	16/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.318497170097495	2		451	952	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356172	66356172	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	113	436	1	ENST00000273854.3:c.1325A>G	p.Glu442Gly	p.E442G	ENST00000273854	NM_004439.5	442	gAg/gGg	5/18	1	2	FACETS	0.951	0.856	1	0.951	0.856	1	CLONAL	1	TRUE	1	0.318497170097495	2		437	746	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249499	153249499	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	114	440	0	ENST00000281708.4:c.1279T>C	p.Ser427Pro	p.S427P	ENST00000281708	NM_033632.3	427	Tca/Cca	9/12	1	2	FACETS	0.858	0.772	0.949	0.858	0.772	0.949	CLONAL	1	TRUE	1	0.318497170097495	2		440	834	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557989	187557989	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	106	304	0	ENST00000441802.2:c.3722A>T	p.Asn1241Ile	p.N1241I	ENST00000441802	NM_005245.3	1241	aAc/aTc	5/27	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.318497170097495	2		304	634	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80037320	80037320	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs756837309	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	109	349	0	ENST00000265081.6:c.1606A>G	p.Thr536Ala	p.T536A	ENST00000265081	NM_002439.4	536	Aca/Gca	11/24	1	2	FACETS	0.884	0.794	0.98	0.884	0.794	0.98	CLONAL	1	TRUE	1	0.318497170097495	2		349	774	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738482	145738482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373187237	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	140	448	1	ENST00000428558.2:c.2503G>A	p.Asp835Asn	p.D835N	ENST00000428558	NM_004260.3	835	Gac/Aac	16/22	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.318497170097495	2		449	726	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126684	5126684	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	88	290	0	ENST00000381652.3:c.3292A>T	p.Ile1098Phe	p.I1098F	ENST00000381652	NM_004972.3	1098	Atc/Ttc	25/25	1	2	FACETS	0.982	0.871	1	0.982	0.871	1	CLONAL	1	TRUE	1	0.318497170097495	2		290	563	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434783	128434783	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1254700721	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	144	513	1	ENST00000265960.3:c.71C>T	p.Thr24Met	p.T24M	ENST00000265960	NM_001006617.1	24	aCg/aTg	2/12	1	2	FACETS	0.983	0.896	1	0.983	0.896	1	CLONAL	1	TRUE	1	0.318497170097495	2		514	920	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393677	139393677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	111	538	1	ENST00000277541.6:c.5969C>T	p.Ala1990Val	p.A1990V	ENST00000277541	NM_017617.3	1990	gCc/gTc	32/34	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.318497170097495	2		539	684	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854890	76854890	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	119	463	0	ENST00000373344.5:c.5946del	p.Lys1982AsnfsTer33	p.K1982Nfs*33	ENST00000373344	NM_000489.3	1982	aaA/aa	25/35	1	2	FACETS	0.843	0.761	0.931	0.843	0.761	0.931	CLONAL	1	TRUE	1	0.318497170097495	2		463	886	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29197675	29197675	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	121	440	1	ENST00000240100.2:c.519del	p.Ser174ValfsTer53	p.S174Vfs*53	ENST00000240100	NM_001394.6	173	ccC/cc	2/4	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.318497170097495	2		441	700	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003813	45003813	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	114	315	0	ENST00000558401.1:c.67+2T>C		p.X23_splice	ENST00000558401	NM_004048.2	23			0.268770055601743	2	FACETS	1	0.985	1	0.737	0.669	0.807	CLONAL	1	TRUE	0	0.399813145632892	2		315	387	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216189	36216189	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	123	497	0	ENST00000222270.7:c.3602del	p.Pro1201ArgfsTer154	p.P1201Rfs*154	ENST00000222270	NM_014727.1	1199	ggC/gg	11/37	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.399813145632892	2		497	572	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	206	565	5	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	1	2	FACETS	0.795	0.741	0.85	1	0.992	1	SUBCLONAL	2	TRUE	1	0.399813145632892	2		570	648	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	116	503	4	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.985	0.891	1	0.985	0.891	1	CLONAL	1	TRUE	1	0.399813145632892	2		507	589	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	86	357	2	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.832	0.738	0.932	0.832	0.738	0.932	CLONAL	1	TRUE	1	0.399813145632892	2		359	517	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671655	67671655	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1400980130	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	125	430	1	ENST00000264010.4:c.2070del	p.Glu691SerfsTer30	p.E691Sfs*30	ENST00000264010	NM_006565.3	688	gtA/gt	12/12	1	2	FACETS	0.895	0.811	0.983	0.895	0.811	0.983	CLONAL	1	TRUE	1	0.399813145632892	2		431	699	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100175	27100176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	65	365	0	ENST00000324856.7:c.3977dup	p.Gln1327AlafsTer11	p.Q1327Afs*11	ENST00000324856	NM_006015.4	1324	tac/taCc	16/20	1	2	FACETS	0.805	0.701	0.917	0.805	0.701	0.917	CLONAL	1	TRUE	1	0.399813145632892	2		365	404	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434005	49434005	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	126	611	1	ENST00000301067.7:c.7548del	p.Asn2517IlefsTer26	p.N2517Ifs*26	ENST00000301067	NM_003482.3	2516	ccC/cc	31/54	1	2	FACETS	0.866	0.785	0.951	0.866	0.785	0.951	CLONAL	1	TRUE	1	0.399813145632892	2		612	728	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027087	71027087	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	46	407	0	ENST00000318789.4:c.1240del	p.Leu414Ter	p.L414*	ENST00000318789	NM_032682.5	414	Ctg/tg	15/21	1	2	FACETS	0.385	0.323	0.453	0.385	0.323	0.453	SUBCLONAL	1	TRUE	1	0.399813145632892	2		407	598	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051053	180051053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755736057	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	53	452	0	ENST00000261937.6:c.1430G>A	p.Arg477Gln	p.R477Q	ENST00000261937	NM_182925.4	477	cGg/cAg	11/30	1	2	FACETS	0.428	0.364	0.497	0.428	0.364	0.497	SUBCLONAL	1	TRUE	1	0.399813145632892	2		452	620	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562850	21562850	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1418882962	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	49	635	2	ENST00000382592.4:c.1069G>A	p.Val357Met	p.V357M	ENST00000382592	NM_014572.2	357	Gtg/Atg	4/8	1	2	FACETS	0.312	0.263	0.366	0.312	0.263	0.366	SUBCLONAL	1	TRUE	1	0.399813145632892	2		637	785	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132438	11132438	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794284	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	133	542	1	ENST00000358026.2:c.2654G>A	p.Arg885His	p.R885H	ENST00000358026	NM_001128849.1	885	cGc/cAc	19/36	1	2	FACETS	0.932	0.848	1	0.932	0.848	1	CLONAL	1	TRUE	1	0.399813145632892	2		543	714	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968322	2968323	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762770988	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	78	480	2	ENST00000396946.4:c.1663dup	p.Arg555ProfsTer38	p.R555Pfs*38	ENST00000396946	NM_032415.4	555	cgg/cCgg	13/25	1	2	FACETS	0.588	0.516	0.664	0.588	0.516	0.664	SUBCLONAL	1	TRUE	1	0.399813145632892	2		482	664	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	32	455	1	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	0.329	0.266	0.399	0.329	0.266	0.399	SUBCLONAL	1	TRUE	1	0.399813145632892	2		456	487	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277275	41277275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	75	309	0	ENST00000349496.5:c.1744C>T	p.Arg582Trp	p.R582W	ENST00000349496	NM_001904.3	582	Cgg/Tgg	11/15	0.399813145632892	2	FACETS	0.761	0.669	0.86	0.381	0.334	0.43	SUBCLONAL	1	TRUE	0	0.399813145632892	2		309	493	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39644789	39644789	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	30	299	0	ENST00000262039.4:c.2522del	p.Lys841ArgfsTer8	p.K841Rfs*8	ENST00000262039	NM_002647.2	840	Aaa/aa	23/25	1	2	FACETS	0.341	0.274	0.417	0.341	0.274	0.417	SUBCLONAL	1	TRUE	1	0.399813145632892	2		299	440	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954272	32954273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359752	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	71	362	2	ENST00000380152.3:c.9253dup	p.Thr3085AsnfsTer26	p.T3085Nfs*26	ENST00000380152		3082	-/A	24/27	1	2	FACETS	0.826	0.724	0.935	0.826	0.724	0.935	CLONAL	1	TRUE	1	0.399813145632892	2		364	430	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81941311	81941311	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	99	536	0	ENST00000359376.3:c.1489G>A	p.Ala497Thr	p.A497T	ENST00000359376	NM_002661.3	497	Gcc/Acc	16/33	1	2	FACETS	0.744	0.664	0.828	0.744	0.664	0.828	SUBCLONAL	1	TRUE	1	0.399813145632892	2		536	666	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785963	135785964	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs118203506	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	98	516	0	ENST00000298552.3:c.1257dup	p.Arg420GlnfsTer22	p.R420Qfs*22	ENST00000298552	NM_001162426.1	419	-/C	12/23	0.341088986359695	3	FACETS	0.816	0.728	0.909	0.408	0.364	0.455	CLONAL	1	TRUE	1	0.399813145632892	3		516	721	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	98	293	2	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.399813145632892	2		295	399	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97873817	97873817	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	300	533	5	ENST00000289081.3:c.1257del	p.Thr420ArgfsTer27	p.T420Rfs*27	ENST00000289081	NM_000136.2	419	ccC/cc	13/15	0.341088986359695	3	FACETS	0.993	0.938	1	0.993	0.938	1	CLONAL	2	TRUE	1	0.399813145632892	3		538	907	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349689	70349689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs979229015	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	104	412	1	ENST00000374080.3:c.3851G>A	p.Arg1284His	p.R1284H	ENST00000374080		1284	cGc/cAc	27/45	1	2	FACETS	0.967	0.869	1	0.967	0.869	1	CLONAL	1	TRUE	1	0.399813145632892	2		413	538	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028225	48028225	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63749999	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	21	327	0	ENST00000234420.5:c.3103C>T	p.Arg1035Ter	p.R1035*	ENST00000234420	NM_000179.2	1035	Cga/Tga	4/10	1	2	FACETS	0.257	0.198	0.328	0.257	0.198	0.328	SUBCLONAL	1	TRUE	1	0.399813145632892	2		327	408	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401637	401637	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	89	441	0	ENST00000380956.4:c.963del	p.Asp322ThrfsTer62	p.D322Tfs*62	ENST00000380956	NM_001195286.1	320	gCc/gc	7/9	1	2	FACETS	0.834	0.741	0.932	0.834	0.741	0.932	CLONAL	1	TRUE	1	0.399813145632892	2		441	534	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120037	70120037	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	10	62	0	ENST00000245479.2:c.1039C>T	p.Gln347Ter	p.Q347*	ENST00000245479	NM_000346.3	347	Cag/Tag	3/3	0.399813145632892	2	FACETS	0.55	0.376	0.763	0.275	0.188	0.382	SUBCLONAL	1	TRUE	0	0.399813145632892	2		62	91	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119909	70119910	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	90	485	0	ENST00000245479.2:c.916dup	p.Val306GlyfsTer272	p.V306Gfs*272	ENST00000245479	NM_000346.3	304	ccg/ccGg	3/3	0.399813145632892	2	FACETS	0.753	0.669	0.842	0.376	0.334	0.421	SUBCLONAL	1	TRUE	0	0.399813145632892	2		485	598	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527808	157527808	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766931727	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	66	338	0	ENST00000346085.5:c.5533C>T	p.Arg1845Cys	p.R1845C	ENST00000346085	NM_020732.3	1845	Cgc/Tgc	20/20	1	2	FACETS	0.83	0.723	0.944	0.83	0.723	0.944	CLONAL	1	TRUE	1	0.399813145632892	2		338	398	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393401	139393401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544856644	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	351	609	0	ENST00000277541.6:c.6130G>A	p.Ala2044Thr	p.A2044T	ENST00000277541	NM_017617.3	2044	Gca/Aca	33/34	0.341088986359695	3	FACETS	0.979	0.928	1	0.979	0.928	1	CLONAL	2	TRUE	1	0.399813145632892	3		609	1076	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626865	14626865	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	142	514	0	ENST00000254322.2:c.910del	p.Leu304SerfsTer17	p.L304Sfs*17	ENST00000254322	NM_006145.1	304	Ctc/tc	3/3	1	2	FACETS	0.893	0.815	0.976	0.893	0.815	0.976	CLONAL	1	TRUE	1	0.399813145632892	2		514	795	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366987	40366987	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	96	573	0	ENST00000397332.2:c.210del	p.Thr71ArgfsTer69	p.T71Rfs*69	ENST00000397332	NM_001033082.2	70	ccC/cc	2/3	1	2	FACETS	0.722	0.644	0.805	0.722	0.644	0.805	SUBCLONAL	1	TRUE	1	0.399813145632892	2		573	665	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443617	49443617	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs727503987	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	126	547	0	ENST00000301067.7:c.3754C>T	p.Arg1252Ter	p.R1252*	ENST00000301067	NM_003482.3	1252	Cga/Tga	11/54	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.399813145632892	2		547	607	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021277	31021277	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	120	407	2	ENST00000375687.4:c.1281del	p.Lys427AsnfsTer35	p.K427Nfs*35	ENST00000375687	NM_015338.5	426	Aaa/aa	12/13	1	2	FACETS	0.968	0.877	1	0.968	0.877	1	CLONAL	1	TRUE	1	0.399813145632892	2		409	620	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816451	32816451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760636031	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	95	602	2	ENST00000354258.4:c.1724G>A	p.Arg575His	p.R575H	ENST00000354258	NM_000593.5	575	cGc/cAc	7/11	1	2	FACETS	0.517	0.459	0.579	0.517	0.459	0.579	SUBCLONAL	1	TRUE	1	0.399813145632892	2		604	919	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784996	9784996	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	21	350	0	ENST00000377346.4:c.2997+2T>C		p.X999_splice	ENST00000377346	NM_005026.3	999			1	2	FACETS	0.275	0.211	0.35	0.275	0.211	0.35	SUBCLONAL	1	TRUE	1	0.399813145632892	2		350	382	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797196	45797196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660539	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	38	598	0	ENST00000450313.1:c.1219G>A	p.Val407Met	p.V407M	ENST00000450313	NM_012222.2	407	Gtg/Atg	13/16	1	2	FACETS	0.305	0.251	0.365	0.305	0.251	0.365	SUBCLONAL	1	TRUE	1	0.399813145632892	2		598	624	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690383	117690383	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	126	431	0	ENST00000369458.3:c.746G>T	p.Ser249Ile	p.S249I	ENST00000369458	NM_024626.3	249	aGt/aTt	5/6	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.399813145632892	2		431	616	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112760224	112760224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	38	457	0	ENST00000369452.4:c.893C>T	p.Ala298Val	p.A298V	ENST00000369452	NM_007373.3	298	gCa/gTa	4/9	1	2	FACETS	0.28	0.23	0.335	0.28	0.23	0.335	SUBCLONAL	1	TRUE	1	0.399813145632892	2		457	680	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375506	118375507	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	20	247	0	ENST00000534358.1:c.8904dup	p.Ser2969IlefsTer6	p.S2969Ifs*6	ENST00000534358	NM_005933.3	2967	gaa/gAaa	27/36	1	2	FACETS	0.35	0.267	0.446	0.35	0.267	0.446	SUBCLONAL	1	TRUE	1	0.399813145632892	2		247	286	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972530	32972530	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	104	427	0	ENST00000380152.3:c.9880G>T	p.Ala3294Ser	p.A3294S	ENST00000380152		3294	Gca/Tca	27/27	1	2	FACETS	0.834	0.748	0.925	0.834	0.748	0.925	CLONAL	1	TRUE	1	0.399813145632892	2		427	624	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972852	32972852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55853199	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	85	303	0	ENST00000380152.3:c.10202C>T	p.Thr3401Met	p.T3401M	ENST00000380152		3401	aCg/aTg	27/27	1	2	FACETS	0.856	0.759	0.959	0.856	0.759	0.959	CLONAL	1	TRUE	1	0.399813145632892	2		303	497	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243026	105243026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773971502	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	162	626	1	ENST00000349310.3:c.257G>A	p.Arg86His	p.R86H	ENST00000349310	NM_001014432.1	86	cGc/cAc	5/15	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.399813145632892	2		627	797	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007777	45007778	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	25	371	0	ENST00000558401.1:c.227dup	p.Ser77GlnfsTer13	p.S77Qfs*13	ENST00000558401	NM_004048.2	75	tct/tcTt	2/4	0.268770055601743	2	FACETS	0.287	0.225	0.358	0.143	0.112	0.179	SUBCLONAL	1	TRUE	0	0.399813145632892	2		371	436	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094717	2094717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1200691336	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	112	605	2	ENST00000219066.1:c.463C>T	p.Arg155Trp	p.R155W	ENST00000219066	NM_002528.5	155	Cgg/Tgg	3/6	1	2	FACETS	0.703	0.632	0.778	0.703	0.632	0.778	SUBCLONAL	1	TRUE	1	0.399813145632892	2		607	797	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640073	3640073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766648339	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	49	696	0	ENST00000294008.3:c.3566G>A	p.Cys1189Tyr	p.C1189Y	ENST00000294008	NM_032444.2	1189	tGt/tAt	12/15	1	2	FACETS	0.263	0.222	0.309	0.263	0.222	0.309	SUBCLONAL	1	TRUE	1	0.399813145632892	2		696	931	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808031	3808031	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	63	318	0	ENST00000262367.5:c.3388A>G	p.Lys1130Glu	p.K1130E	ENST00000262367	NM_004380.2	1130	Aag/Gag	18/31	1	2	FACETS	0.747	0.648	0.853	0.747	0.648	0.853	SUBCLONAL	1	TRUE	1	0.399813145632892	2		318	422	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858038	40858038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748173627	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	159	437	0	ENST00000428826.2:c.1826G>A	p.Arg609His	p.R609H	ENST00000428826		609	cGt/cAt	16/21	0.399813145632892	2	FACETS	1	0.971	1	0.561	0.515	0.608	CLONAL	1	TRUE	0	0.399813145632892	2		437	709	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438222	56438223	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	195	491	0	ENST00000407977.2:c.770dup	p.Glu258Ter	p.E258*	ENST00000407977		257	ggt/ggGt	7/10	0.399813145632892	2	FACETS	0.825	0.768	0.883	0.825	0.768	0.883	CLONAL	2	TRUE	0	0.399813145632892	2		491	591	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63553975	63553976	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	249	409	0	ENST00000307078.5:c.763_764del	p.Leu255GlufsTer13	p.L255Efs*13	ENST00000307078	NM_004655.3	255	CTg/g	2/11	0.399813145632892	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.399813145632892	2		409	585	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250767	10250767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780156714	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	167	622	1	ENST00000340748.4:c.3713G>A	p.Arg1238His	p.R1238H	ENST00000340748		1238	cGc/cAc	32/40	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.399813145632892	2		623	805	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355347	15355347	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	20	369	0	ENST00000263377.2:c.2276del	p.Pro759ArgfsTer35	p.P759Rfs*35	ENST00000263377	NM_058243.2	759	cCg/cg	13/20	1	2	FACETS	0.276	0.21	0.352	0.276	0.21	0.352	SUBCLONAL	1	TRUE	1	0.399813145632892	2		369	363	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965716	18965716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	157	677	0	ENST00000262803.5:c.1294del	p.Val432TrpfsTer22	p.V432Wfs*22	ENST00000262803	NM_002911.3	432	Gtg/tg	10/24	1	2	FACETS	0.915	0.839	0.995	0.915	0.839	0.995	CLONAL	1	TRUE	1	0.399813145632892	2		677	858	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212545	36212545	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	69	658	1	ENST00000222270.7:c.2296C>A	p.Pro766Thr	p.P766T	ENST00000222270	NM_014727.1	766	Cca/Aca	3/37	1	2	FACETS	0.384	0.333	0.438	0.384	0.333	0.438	SUBCLONAL	1	TRUE	1	0.399813145632892	2		659	900	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082398	16082398	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	51	673	0	ENST00000281043.3:c.212G>A	p.Ser71Asn	p.S71N	ENST00000281043	NM_005378.4	71	aGc/aAc	2/3	1	2	FACETS	0.358	0.303	0.418	0.358	0.303	0.418	SUBCLONAL	1	TRUE	1	0.399813145632892	2		673	713	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028216	48028216	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	87	341	0	ENST00000234420.5:c.3094T>C	p.Cys1032Arg	p.C1032R	ENST00000234420	NM_000179.2	1032	Tgc/Cgc	4/10	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.399813145632892	2		341	407	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610467	215610468	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	90	353	0	ENST00000260947.4:c.1788dup	p.Tyr597IlefsTer3	p.Y597Ifs*3	ENST00000260947	NM_000465.2	596	-/A	8/11	1	2	FACETS	0.926	0.825	1	0.926	0.825	1	CLONAL	1	TRUE	1	0.399813145632892	2		353	486	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439860	220439860	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	42	599	0	ENST00000243786.2:c.713C>A	p.Ser238Tyr	p.S238Y	ENST00000243786	NM_002191.3	238	tCc/tAc	2/2	1	2	FACETS	0.336	0.279	0.398	0.336	0.279	0.398	SUBCLONAL	1	TRUE	1	0.399813145632892	2		599	626	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375211	31375211	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	127	592	0	ENST00000328111.2:c.608C>A	p.Pro203Gln	p.P203Q	ENST00000328111	NM_006892.3	203	cCg/cAg	6/23	1	2	FACETS	0.896	0.813	0.983	0.896	0.813	0.983	CLONAL	1	TRUE	1	0.399813145632892	2		592	709	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130433	29130433	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs786203458	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	150	531	0	ENST00000328354.6:c.277del	p.Trp93GlyfsTer17	p.W93Gfs*17	ENST00000328354	NM_007194.3	93	Tgg/gg	2/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.399813145632892	2		531	679	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069392	30069394	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	34	505	0	ENST00000338641.4:c.1264_1266del	p.Glu422del	p.E422del	ENST00000338641	NM_000268.3	419	acGGAg/acg	12/16	1	2	FACETS	0.26	0.212	0.315	0.26	0.212	0.315	SUBCLONAL	1	TRUE	1	0.399813145632892	2		505	654	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919194	178919194	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	29	224	0	ENST00000263967.3:c.685del	p.Thr229LeufsTer11	p.T229Lfs*11	ENST00000263967	NM_006218.2	227	Aaa/aa	4/21	1	2	FACETS	0.413	0.332	0.506	0.413	0.332	0.506	SUBCLONAL	1	TRUE	1	0.399813145632892	2		224	351	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509912	187509913	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	68	271	0	ENST00000441802.2:c.13600_13601del	p.Ser4534HisfsTer14	p.S4534Hfs*14	ENST00000441802	NM_005245.3	4534	AGc/c	27/27	1	2	FACETS	0.893	0.781	1	0.893	0.781	1	CLONAL	1	TRUE	1	0.399813145632892	2		271	381	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521375	187521375	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs772301580	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	29	364	0	ENST00000441802.2:c.11780T>C	p.Leu3927Pro	p.L3927P	ENST00000441802	NM_005245.3	3927	cTa/cCa	22/27	1	2	FACETS	0.286	0.229	0.351	0.286	0.229	0.351	SUBCLONAL	1	TRUE	1	0.399813145632892	2		364	507	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950066	38950066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1297105779	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	62	353	0	ENST00000357387.3:c.3884C>T	p.Thr1295Met	p.T1295M	ENST00000357387	NM_152756.3	1295	aCg/aTg	31/38	1	2	FACETS	0.764	0.662	0.873	0.764	0.662	0.873	SUBCLONAL	1	TRUE	1	0.399813145632892	2		353	406	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564441	86564441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	33	456	0	ENST00000274376.6:c.173C>T	p.Ala58Val	p.A58V	ENST00000274376	NM_002890.2	58	gCt/gTt	1/25	1	2	FACETS	0.314	0.255	0.381	0.314	0.255	0.381	SUBCLONAL	1	TRUE	1	0.399813145632892	2		456	525	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015875	112015875	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	110	398	0	ENST00000368678.4:c.1066G>T	p.Gly356Ter	p.G356*	ENST00000368678		356	Gga/Tga	10/13	1	2	FACETS	0.88	0.793	0.973	0.88	0.793	0.973	CLONAL	1	TRUE	1	0.399813145632892	2		398	625	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004679	150004679	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778912523	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	29	357	0	ENST00000253339.5:c.1546C>T	p.His516Tyr	p.H516Y	ENST00000253339		516	Cac/Tac	3/7	1	2	FACETS	0.252	0.201	0.31	0.252	0.201	0.31	SUBCLONAL	1	TRUE	1	0.399813145632892	2		357	576	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157470043	157470043	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	22	292	0	ENST00000346085.5:c.2837C>T	p.Ala946Val	p.A946V	ENST00000346085	NM_020732.3	946	gCc/gTc	9/20	1	2	FACETS	0.308	0.238	0.389	0.308	0.238	0.389	SUBCLONAL	1	TRUE	1	0.399813145632892	2		292	357	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371843	55371843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	53	234	0	ENST00000297316.4:c.533G>A	p.Gly178Asp	p.G178D	ENST00000297316	NM_022454.3	178	gGc/gAc	2/2	1	2	FACETS	0.986	0.848	1	0.986	0.848	1	CLONAL	1	TRUE	1	0.399813145632892	2		234	269	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737082	145737082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773088003	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	31	534	0	ENST00000428558.2:c.3484C>T	p.Arg1162Cys	p.R1162C	ENST00000428558	NM_004260.3	1162	Cgc/Tgc	21/22	1	2	FACETS	0.266	0.214	0.324	0.266	0.214	0.324	SUBCLONAL	1	TRUE	1	0.399813145632892	2		534	584	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402583	139402583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370696201	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	148	593	3	ENST00000277541.6:c.3334G>A	p.Val1112Ile	p.V1112I	ENST00000277541	NM_017617.3	1112	Gtt/Att	21/34	0.341088986359695	3	FACETS	1	0.95	1	0.529	0.483	0.577	CLONAL	1	TRUE	1	0.399813145632892	3		596	840	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139818432	139818432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1317680720	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	39	467	0	ENST00000247668.2:c.1267C>T	p.Arg423Trp	p.R423W	ENST00000247668	NM_021138.3	423	Cgg/Tgg	10/11	0.341088986359695	3	FACETS	0.327	0.27	0.391	0.164	0.135	0.196	SUBCLONAL	1	TRUE	1	0.399813145632892	3		467	715	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921999	39921999	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	106	442	0	ENST00000378444.4:c.4173G>T	p.Lys1391Asn	p.K1391N	ENST00000378444	NM_001123385.1	1391	aaG/aaT	9/15	1	2	FACETS	0.922	0.829	1	0.922	0.829	1	CLONAL	1	TRUE	1	0.399813145632892	2		442	575	SUCCESS
AR	367	MSKCC	GRCh37	X	66863148	66863148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	124	513	0	ENST00000374690.3:c.1667C>T	p.Pro556Leu	p.P556L	ENST00000374690	NM_000044.3	556	cCc/cTc	2/8	1	2	FACETS	0.981	0.89	1	0.981	0.89	1	CLONAL	1	TRUE	1	0.399813145632892	2		513	632	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161392	55161392	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767697835	NA	P-0027335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	97	417	0	ENST00000257290.5:c.3223G>A	p.Asp1075Asn	p.D1075N	ENST00000257290	NM_006206.4	1075	Gac/Aac	23/23	1	2	FACETS	0.916	0.819	1	0.916	0.819	1	CLONAL	1	TRUE	1	0.399813145632892	2		417	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0028433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	36	543	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.260344738718928	2	FACETS	1	0.92	1	0.602	0.499	0.715	CLONAL	1	TRUE	0	0.27684697787308	2		543	216	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749964	162749964	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	68	422	0	ENST00000367921.3:c.2496G>C	p.Trp832Cys	p.W832C	ENST00000367921	NM_006182.2	832	tgG/tgC	18/18	0.27684697787308	5	FACETS	1	0.952	1	0.301	0.262	0.344	CLONAL	1	TRUE	1	0.27684697787308	5		422	577	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252069	226252069	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	45	195	0	ENST00000366813.1:c.17A>C	p.Gln6Pro	p.Q6P	ENST00000366813		6	cAg/cCg	1/3	0.223315209130346	4	FACETS	1	0.896	1	0.361	0.304	0.424	CLONAL	1	TRUE	1	0.27684697787308	4		195	383	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118378311	118378311	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	59	473	0	ENST00000534358.1:c.10822G>C	p.Gly3608Arg	p.G3608R	ENST00000534358	NM_005933.3	3608	Ggg/Cgg	28/36	0.27684697787308	3	FACETS	1	0.925	1	0.555	0.479	0.638	CLONAL	1	TRUE	1	0.27684697787308	3		473	437	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640996	3640996	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	56	773	0	ENST00000294008.3:c.2643G>C	p.Glu881Asp	p.E881D	ENST00000294008	NM_032444.2	881	gaG/gaC	12/15	1	2	FACETS	0.804	0.69	0.929	0.804	0.69	0.929	CLONAL	1	TRUE	1	0.27684697787308	2		773	503	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029158	14029158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	31	322	0	ENST00000311895.7:c.1369G>A	p.Asp457Asn	p.D457N	ENST00000311895	NM_005236.2	457	Gac/Aac	8/11	1	2	FACETS	0.7	0.567	0.849	0.7	0.567	0.849	SUBCLONAL	1	TRUE	1	0.27684697787308	2		322	320	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946021	17946021	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs774135817	NA	P-0028433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	36	492	0	ENST00000458235.1:c.1918G>T	p.Asp640Tyr	p.D640Y	ENST00000458235	NM_000215.3	640	Gac/Tac	15/24	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.27684697787308	2		492	242	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99163158	99163158	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0028433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	23	386	0	ENST00000074304.5:c.1163+1G>C		p.X388_splice	ENST00000074304	NM_001134224.1	388			0.27684697787308	3	FACETS	0.612	0.477	0.768	0.306	0.238	0.384	SUBCLONAL	1	TRUE	1	0.27684697787308	3		386	309	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961480	54961480	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0028433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	73	393	0	ENST00000312783.6:c.152C>G	p.Ser51Ter	p.S51*	ENST00000312783	NM_198436.1	51	tCa/tGa	4/10	0.27684697787308	3	FACETS	1	0.968	1	0.67	0.588	0.758	CLONAL	1	TRUE	1	0.27684697787308	3		393	448	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671805	30671805	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	51	567	0	ENST00000376406.3:c.5155A>G	p.Ser1719Gly	p.S1719G	ENST00000376406	NM_014641.2	1719	Agt/Ggt	10/15	0.27684697787308	5	FACETS	1	0.953	1	0.328	0.28	0.382	CLONAL	1	TRUE	1	0.27684697787308	5		567	397	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484163	8484163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781290016	NA	P-0028433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	130	418	0	ENST00000356435.5:c.3369G>A	p.Met1123Ile	p.M1123I	ENST00000356435		1123	atG/atA	19/35	0.27684697787308	3	FACETS	1	0.979	1	0.825	0.754	0.898	CLONAL	2	TRUE	0	0.27684697787308	3		418	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0028912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	133	420	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.229107629432756	3	FACETS	0.773	0.702	0.848	0.773	0.702	0.848	SUBCLONAL	2	FALSE	1	0.229107629432756	3		420	837	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983080	111983081	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	141	168	0	ENST00000368678.4:c.1466_1467insT	p.Ile490HisfsTer5	p.I490Hfs*5	ENST00000368678		489	ccc/ccTc	13/13	0.229107629432756	3	FACETS	0.983	0.897	1	0.983	0.897	1	CLONAL	2	FALSE	1	0.229107629432756	3		168	698	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246994	53246994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	85	173	0	ENST00000375401.3:c.506C>T	p.Ser169Phe	p.S169F	ENST00000375401	NM_004187.3	169	tCt/tTt	4/26	0.229107629432756	3	FACETS	0.994	0.878	1	0.497	0.439	0.56	CLONAL	1	FALSE	1	0.229107629432756	3		173	832	SUCCESS
APC	324	MSKCC	GRCh37	5	112164646	112164646	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	79	312	0	ENST00000257430.4:c.1720G>T	p.Glu574Ter	p.E574*	ENST00000257430	NM_000038.5	574	Gaa/Taa	14/16	1	2	FACETS	0.781	0.689	0.879	0.781	0.689	0.879	SUBCLONAL	1	TRUE	1	0.443625141491518	2		312	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0029279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	170	636	2	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	0.415613294955745	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.443625141491518	1		638	587	SUCCESS
APC	324	MSKCC	GRCh37	5	112175174	112175174	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	87	260	0	ENST00000257430.4:c.3883G>T	p.Glu1295Ter	p.E1295*	ENST00000257430	NM_000038.5	1295	Gaa/Taa	16/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.443625141491518	2		260	278	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428488	78428488	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	101	459	1	ENST00000370768.2:c.1311C>G	p.Asp437Glu	p.D437E	ENST00000370768	NM_003902.3	437	gaC/gaG	14/20	1	2	FACETS	0.893	0.801	0.989	0.893	0.801	0.989	CLONAL	1	TRUE	1	0.443625141491518	2		460	510	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563204	21563204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769991034	NA	P-0029279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	337	814	4	ENST00000382592.4:c.715G>A	p.Val239Ile	p.V239I	ENST00000382592	NM_014572.2	239	Gta/Ata	4/8	0.332939043832662	4	FACETS	0.949	0.898	1			1	CLONAL	2	TRUE	NA	0.443625141491518	4		818	1155	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851574	134851574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747682274	NA	P-0030023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	56	412	0	ENST00000398015.3:c.980G>A	p.Arg327His	p.R327H	ENST00000398015	NM_004441.4	327	cGc/cAc	5/16	0.578648592662641	4	FACETS	1	0.963	1	0.667	0.579	0.76	CLONAL	1	TRUE	2	0.660820908286051	4		412	211	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	154	688	0	ENST00000269305.4:c.469del	p.Val157SerfsTer13	p.V157Sfs*13	ENST00000269305	NM_001126112.2	157	Gtc/tc	5/11	0.660820908286051	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.660820908286051	2		688	216	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2225386	2225386	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0030023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	86	496	0	ENST00000398665.3:c.3597-1G>C		p.X1199_splice	ENST00000398665	NM_032482.2	1199			0.660820908286051	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.660820908286051	1		496	119	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149982897	149982897	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	15	377	0	ENST00000253339.5:c.3361G>A	p.Glu1121Lys	p.E1121K	ENST00000253339		1121	Gag/Aag	7/7	0.595118672600625	3	FACETS	0.392	0.288	0.516	0.131	0.096	0.172	SUBCLONAL	1	TRUE	0	0.660820908286051	3		377	154	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667816	37667816	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	55	553	0	ENST00000447079.4:c.2701T>G	p.Tyr901Asp	p.Y901D	ENST00000447079	NM_015083.1	901	Tac/Gac	8/14	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.3	2		553	341	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650882	37650883	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0030162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	72	690	0	ENST00000447079.4:c.2356_2357del	p.Val786CysfsTer2	p.V786Cfs*2	ENST00000447079	NM_015083.1	785	aGT/a	5/14	1	2	FACETS	0.896	0.784	1	0.896	0.784	1	CLONAL	1	TRUE	1	0.3	2		690	536	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265202	46265202	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	32	390	1	ENST00000371998.3:c.2072A>G	p.Asn691Ser	p.N691S	ENST00000371998		691	aAt/aGt	12/23	1	2	FACETS	0.85	0.693	1	0.85	0.693	1	CLONAL	1	TRUE	1	0.3	2		391	251	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0030735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	200	555	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.205534660798034	3	FACETS	1	0.985	1	0.794	0.741	0.849	CLONAL	2	TRUE	0	0.338337416632643	3		557	580	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134881022	134881022	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	108	348	0	ENST00000398015.3:c.1585G>A	p.Asp529Asn	p.D529N	ENST00000398015	NM_004441.4	529	Gat/Aat	7/16	0.21816895661114	4	FACETS	0.812	0.732	0.897	0.812	0.732	0.897	CLONAL	2	TRUE	2	0.338337416632643	4		348	526	SUCCESS
APC	324	MSKCC	GRCh37	5	112175389	112175389	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	68	303	0	ENST00000257430.4:c.4098del	p.Gln1367ArgfsTer48	p.Q1367Rfs*48	ENST00000257430	NM_000038.5	1366	gcT/gc	16/16	0.21816895661114	4	FACETS	0.873	0.766	0.987	0.873	0.766	0.987	CLONAL	2	TRUE	2	0.338337416632643	4		303	308	SUCCESS
APC	324	MSKCC	GRCh37	5	112175493	112175493	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	89	361	0	ENST00000257430.4:c.4203del	p.Ile1401MetfsTer14	p.I1401Mfs*14	ENST00000257430	NM_000038.5	1401	aTt/at	16/16	0.21816895661114	4	FACETS	0.802	0.715	0.894	0.802	0.715	0.894	CLONAL	2	TRUE	2	0.338337416632643	4		361	439	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553000	106553000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	218	602	0	ENST00000369096.4:c.965C>T	p.Thr322Met	p.T322M	ENST00000369096	NM_001198.3	322	aCg/aTg	5/7	0.338337416632643	5	FACETS	0.945	0.879	1	0.63	0.586	0.676	CLONAL	2	TRUE	2	0.338337416632643	5		602	1028	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835903	151835903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1448088311	NA	P-0030735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	66	449	0	ENST00000262189.6:c.14621G>A	p.Arg4874Gln	p.R4874Q	ENST00000262189	NM_170606.2	4874	cGg/cAg	58/59	0.338337416632643	5	FACETS	0.955	0.829	1	0.239	0.207	0.273	CLONAL	1	TRUE	1	0.338337416632643	5		449	616	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0034227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	12	395	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.191	0.133	0.262	0.191	0.133	0.262	SUBCLONAL	1	TRUE	1	0.321653612114395	2		395	391	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0034227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	21	560	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.309495089835274	3	FACETS	0.18	0.138	0.23	0.09	0.069	0.115	SUBCLONAL	1	TRUE	1	0.321653612114395	3		561	841	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0034227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	280	798	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	NA	2	FACETS	0.931	0.876	0.987			1	INDETERMINATE	2	TRUE	NA	0.321653612114395	2		798	935	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181482	32181482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	86	679	0	ENST00000375023.3:c.2303C>T	p.Thr768Ile	p.T768I	ENST00000375023	NM_004557.3	768	aCt/aTt	14/30	0.312557358384543	3	FACETS	0.664	0.586	0.748	0.332	0.293	0.374	SUBCLONAL	1	TRUE	1	0.321653612114395	3		679	935	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440117	49440117	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	114	683	0	ENST00000301067.7:c.4509C>A	p.Ser1503Arg	p.S1503R	ENST00000301067	NM_003482.3	1503	agC/agA	16/54	0.309495089835274	3	FACETS	0.899	0.809	0.995	0.45	0.404	0.498	CLONAL	1	TRUE	1	0.321653612114395	3		683	915	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257824	198257824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	82	441	0	ENST00000335508.6:c.3628C>T	p.His1210Tyr	p.H1210Y	ENST00000335508	NM_012433.2	1210	Cac/Tac	24/25	0.309495089835274	3	FACETS	0.842	0.742	0.949	0.421	0.371	0.475	CLONAL	1	TRUE	1	0.321653612114395	3		441	703	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067168	37067168	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	67	427	0	ENST00000231790.2:c.1079T>C	p.Val360Ala	p.V360A	ENST00000231790	NM_000249.3	360	gTt/gCt	12/19	0.321653612114395	1	FACETS	0.84	0.733	0.955	0.84	0.733	0.955	CLONAL	1	TRUE	0	0.321653612114395	1		427	416	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0034710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	42	444	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.337486857066867	2	FACETS	0.326	0.272	0.388	0.163	0.136	0.194	SUBCLONAL	1	TRUE	0	0.3852034951916	2		444	668	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65349019	65349019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137855123	NA	P-0034710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	123	461	0	ENST00000342505.4:c.146G>A	p.Arg49Gln	p.R49Q	ENST00000342505	NM_002227.2	49	cGg/cAg	3/25	1	2	FACETS	0.95	0.861	1	0.95	0.861	1	CLONAL	1	TRUE	1	0.3852034951916	2		461	672	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679318	29679318	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	99	401	0	ENST00000356175.3:c.7438G>T	p.Glu2480Ter	p.E2480*	ENST00000356175	NM_000267.3	2480	Gaa/Taa	50/57	0.3852034951916	1	FACETS	0.876	0.785	0.971	0.876	0.785	0.971	CLONAL	1	TRUE	0	0.3852034951916	1		401	474	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890179	76890179	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	79	442	0	ENST00000373344.5:c.4715G>C	p.Trp1572Ser	p.W1572S	ENST00000373344	NM_000489.3	1572	tGg/tCg	17/35	0.249716105055464	0	FACETS	0.581	0.513	0.653			1	SUBCLONAL	1	TRUE	0	0.3852034951916	0		442	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0037072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	391	621	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.75061194567059	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.75061194567059	2		621	520	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121846	2121846	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1338802781	NA	P-0037072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	131	583	0	ENST00000219476.3:c.2008C>T	p.Pro670Ser	p.P670S	ENST00000219476	NM_000548.3	670	Cct/Tct	19/42	0.75061194567059	2	FACETS	0.835	0.765	0.908	0.418	0.382	0.454	CLONAL	1	TRUE	0	0.75061194567059	2		583	418	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971173	21971173	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	143	325	0	ENST00000304494.5:c.185T>C	p.Leu62Pro	p.L62P	ENST00000304494	NM_000077.4	62	cTg/cCg	2/3	1	2	FACETS	0.927	0.853	1	0.927	0.853	1	CLONAL	1	TRUE	1	0.705953082605026	2		325	437	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955465	48955467	+	inframe_deletion	In_Frame_Del	DEL	TTT	TTT	-	novel	NA	P-0038798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	153	341	0	ENST00000267163.4:c.1583_1585del	p.Phe528del	p.F528del	ENST00000267163	NM_000321.2	527	gaTTTt/gat	17/27	0.705953082605026	1	FACETS	0.954	0.891	1	0.954	0.891	1	CLONAL	1	TRUE	0	0.705953082605026	1		341	294	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3794922	3794922	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555475250	NA	P-0038798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	47	394	0	ENST00000262367.5:c.3955C>T	p.Arg1319Ter	p.R1319*	ENST00000262367	NM_004380.2	1319	Cga/Tga	23/31	1	2	FACETS	0.238	0.2	0.279	0.238	0.2	0.279	SUBCLONAL	1	TRUE	1	0.705953082605026	2		394	560	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378326	15378326	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	143	243	0	ENST00000263377.2:c.460G>C	p.Glu154Gln	p.E154Q	ENST00000263377	NM_058243.2	154	Gaa/Caa	4/20	1	2	FACETS	0.805	0.739	0.874	0.805	0.739	0.874	CLONAL	1	TRUE	1	0.705953082605026	2		243	503	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956999	2956999	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	198	509	0	ENST00000396946.4:c.2628A>C	p.Glu876Asp	p.E876D	ENST00000396946	NM_032415.4	876	gaA/gaC	20/25	0.687310040450583	3	FACETS	0.938	0.871	1	0.469	0.435	0.504	CLONAL	1	TRUE	1	0.705953082605026	3		509	809	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	119	668	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.266909237118709	2		673	860	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	234	470	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.927	0.865	0.99	1	0.994	1	CLONAL	2	TRUE	1	0.266909237118709	2		472	946	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	42	423	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.742	0.62	0.877	0.742	0.62	0.877	SUBCLONAL	1	TRUE	1	0.266909237118709	2		423	424	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	85	554	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.945	0.836	1	0.945	0.836	1	CLONAL	1	TRUE	1	0.266909237118709	2		555	674	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578215	28578216	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	162	604	0	ENST00000241453.7:c.2955_2956del	p.Pro986AlafsTer27	p.P986Afs*27	ENST00000241453	NM_004119.2	985	tcTCcg/tccg	24/24	0.198141649405379	4	FACETS	0.822	0.754	0.894	0.822	0.754	0.894	CLONAL	2	TRUE	2	0.266909237118709	4		604	935	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	45	522	3	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.521	0.437	0.615	0.521	0.437	0.615	SUBCLONAL	1	TRUE	1	0.266909237118709	2		525	647	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs1057519842	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	52	341	0	ENST00000274335.5:c.1727_1729del	p.Thr576del	p.T576del	ENST00000274335		575	aaGACg/aag	12/15	1	2	FACETS	0.926	0.79	1	0.926	0.79	1	CLONAL	1	TRUE	1	0.266909237118709	2		341	421	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281518	15281518	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1368023123	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	111	621	0	ENST00000263388.2:c.4855C>T	p.Arg1619Cys	p.R1619C	ENST00000263388	NM_000435.2	1619	Cgc/Tgc	26/33	1	2	FACETS	0.9	0.808	0.998	0.9	0.808	0.998	CLONAL	1	TRUE	1	0.266909237118709	2		621	924	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007688	45007688	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	62	386	0	ENST00000558401.1:c.135C>A	p.Cys45Ter	p.C45*	ENST00000558401	NM_004048.2	45	tgC/tgA	2/4	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.266909237118709	2		386	424	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139625	202139626	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	56	338	0	ENST00000358485.4:c.790dup	p.Val264GlyfsTer13	p.V264Gfs*13	ENST00000358485	NM_001080125.1	262	-/G	6/9	1	2	FACETS	0.941	0.808	1	0.941	0.808	1	CLONAL	1	TRUE	1	0.266909237118709	2		338	446	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193181198	193181198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	100	273	0	ENST00000367435.3:c.1034C>T	p.Ser345Phe	p.S345F	ENST00000367435	NM_024529.4	345	tCt/tTt	12/17	0.266909237118709	4	FACETS	0.947	0.855	1	0.947	0.855	1	CLONAL	3	TRUE	1	0.266909237118709	4		273	334	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211138	36211138	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1290	87	1020	0	ENST00000222270.7:c.889C>T	p.Arg297Ter	p.R297*	ENST00000222270	NM_014727.1	297	Cga/Tga	3/37	1	2	FACETS	0.473	0.417	0.534	0.473	0.417	0.534	SUBCLONAL	1	TRUE	1	0.266909237118709	2		1020	1377	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245924	16245924	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	53	305	0	ENST00000375759.3:c.1547C>A	p.Thr516Lys	p.T516K	ENST00000375759	NM_015001.2	516	aCa/aAa	8/15	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.266909237118709	2		305	396	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088727	27088727	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	102	648	0	ENST00000324856.7:c.2336G>A	p.Gly779Glu	p.G779E	ENST00000324856	NM_006015.4	779	gGa/gAa	7/20	1	2	FACETS	0.793	0.708	0.884	0.793	0.708	0.884	SUBCLONAL	1	TRUE	1	0.266909237118709	2		648	964	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163479	108163479	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780603110	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	62	587	0	ENST00000278616.4:c.4570C>T	p.Leu1524Phe	p.L1524F	ENST00000278616	NM_000051.3	1524	Ctt/Ttt	30/63	1	2	FACETS	0.787	0.68	0.904	0.787	0.68	0.904	CLONAL	1	TRUE	1	0.266909237118709	2		587	590	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355814	73355814	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	82	380	0	ENST00000377767.4:c.157C>T	p.Gln53Ter	p.Q53*	ENST00000377767	NM_014953.3	53	Cag/Tag	1/21	0.198141649405379	4	FACETS	1	0.954	1	0.583	0.514	0.657	CLONAL	1	TRUE	2	0.266909237118709	4		380	668	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90645570	90645570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1453618042	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	26	78	0	ENST00000330062.3:c.53G>A	p.Arg18Gln	p.R18Q	ENST00000330062	NM_002168.2	18	cGg/cAg	1/11	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.266909237118709	2		78	144	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652250	3652250	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	112	715	1	ENST00000294008.3:c.819G>T	p.Gln273His	p.Q273H	ENST00000294008	NM_032444.2	273	caG/caT	4/15	1	2	FACETS	0.859	0.771	0.952	0.859	0.771	0.952	CLONAL	1	TRUE	1	0.266909237118709	2		716	977	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351914	89351914	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1188	145	907	1	ENST00000301030.4:c.1036G>T	p.Glu346Ter	p.E346*	ENST00000301030	NM_001256183.1	346	Gag/Tag	9/13	1	2	FACETS	0.815	0.741	0.893	0.815	0.741	0.893	CLONAL	1	TRUE	1	0.266909237118709	2		908	1333	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118504	17118504	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	50	659	0	ENST00000285071.4:c.1427A>G	p.Asp476Gly	p.D476G	ENST00000285071	NM_144997.5	476	gAc/gGc	12/14	1	2	FACETS	0.417	0.352	0.488	0.417	0.352	0.488	SUBCLONAL	1	TRUE	1	0.266909237118709	2		659	899	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288827	15288827	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	24	126	0	ENST00000263388.2:c.3912C>G	p.Cys1304Trp	p.C1304W	ENST00000263388	NM_000435.2	1304	tgC/tgG	24/33	1	2	FACETS	0.947	0.747	1	0.947	0.747	1	CLONAL	1	TRUE	1	0.266909237118709	2		126	190	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375363	15375363	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	121	669	0	ENST00000263377.2:c.1064A>C	p.Lys355Thr	p.K355T	ENST00000263377	NM_058243.2	355	aAg/aCg	6/20	1	2	FACETS	0.95	0.858	1	0.95	0.858	1	CLONAL	1	TRUE	1	0.266909237118709	2		669	954	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303622	30303622	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	92	475	0	ENST00000262643.3:c.50A>C	p.Lys17Thr	p.K17T	ENST00000262643	NM_001238.2	17	aAg/aCg	3/12	1	2	FACETS	0.999	0.888	1	0.999	0.888	1	CLONAL	1	TRUE	1	0.266909237118709	2		475	690	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228643	36228643	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	129	694	0	ENST00000222270.7:c.7657A>G	p.Arg2553Gly	p.R2553G	ENST00000222270	NM_014727.1	2553	Aga/Gga	34/37	1	2	FACETS	0.903	0.818	0.994	0.903	0.818	0.994	CLONAL	1	TRUE	1	0.266909237118709	2		694	1070	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763519	41763519	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs773904444	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	62	458	0	ENST00000301178.4:c.2318A>G	p.Asp773Gly	p.D773G	ENST00000301178	NM_021913.4	773	gAc/gGc	19/20	1	2	FACETS	0.743	0.642	0.854	0.743	0.642	0.854	SUBCLONAL	1	TRUE	1	0.266909237118709	2		458	625	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728870	190728870	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	56	362	0	ENST00000441310.2:c.2258A>G	p.Glu753Gly	p.E753G	ENST00000441310	NM_000534.4	753	gAa/gGa	10/13	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.266909237118709	2		362	407	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285296	212285296	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	64	485	0	ENST00000342788.4:c.3005A>C	p.Lys1002Thr	p.K1002T	ENST00000342788	NM_005235.2	1002	aAg/aCg	25/28	1	2	FACETS	0.977	0.847	1	0.977	0.847	1	CLONAL	1	TRUE	1	0.266909237118709	2		485	491	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71050170	71050170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	53	346	0	ENST00000318789.4:c.1015G>A	p.Ala339Thr	p.A339T	ENST00000318789	NM_032682.5	339	Gcc/Acc	13/21	1	2	FACETS	0.959	0.82	1	0.959	0.82	1	CLONAL	1	TRUE	1	0.266909237118709	2		346	414	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067067	143067067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	63	505	0	ENST00000262992.4:c.1646G>A	p.Ser549Asn	p.S549N	ENST00000262992	NM_001101669.1	549	aGt/aAt	16/24	1	2	FACETS	0.939	0.813	1	0.939	0.813	1	CLONAL	1	TRUE	1	0.266909237118709	2		505	503	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628847	187628861	+	protein_altering_variant	In_Frame_Del	DEL	TGAGCATTGACAGAG	TGAGCATTGACAGAG	AAGCAC	novel	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	64	602	2	ENST00000441802.2:c.2121_2135delinsGTGCTT	p.His707_His712delinsGlnCysPhe	p.H707_H712delinsQCF	ENST00000441802	NM_005245.3	707	caCTCTGTCAATGCTCAc/caGTGCTTc	2/27	1	2	FACETS	0.667	0.577	0.765	0.667	0.577	0.765	SUBCLONAL	1	TRUE	1	0.266909237118709	2		604	719	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264529	1264529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446074617	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	74	663	0	ENST00000310581.5:c.2833G>A	p.Asp945Asn	p.D945N	ENST00000310581	NM_198253.2	945	Gac/Aac	11/16	1	2	FACETS	0.596	0.52	0.677	0.596	0.52	0.677	SUBCLONAL	1	TRUE	1	0.266909237118709	2		663	931	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680958	30680958	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	112	539	0	ENST00000376406.3:c.761C>T	p.Thr254Ile	p.T254I	ENST00000376406	NM_014641.2	254	aCt/aTt	5/15	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.266909237118709	2		539	830	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515235	106515235	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	103	323	1	ENST00000359195.3:c.2378C>G	p.Ala793Gly	p.A793G	ENST00000359195	NM_002649.2	793	gCa/gGa	5/11	0.266909237118709	3	FACETS	0.824	0.74	0.912	0.824	0.74	0.912	CLONAL	2	TRUE	1	0.266909237118709	3		324	531	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273533	38273533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1399523084	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	106	624	0	ENST00000425967.3:c.1802G>A	p.Arg601Gln	p.R601Q	ENST00000425967	NM_001174067.1	601	cGg/cAg	14/19	1	2	FACETS	0.895	0.802	0.995	0.895	0.802	0.995	CLONAL	1	TRUE	1	0.266909237118709	2		624	887	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409444	80409444	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	62	434	0	ENST00000286548.4:c.670A>G	p.Thr224Ala	p.T224A	ENST00000286548	NM_002072.3	224	Acc/Gcc	5/7	1	2	FACETS	0.96	0.831	1	0.96	0.831	1	CLONAL	1	TRUE	1	0.266909237118709	2		434	484	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	116	668	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.955	0.861	1	0.955	0.861	1	CLONAL	1	TRUE	1	0.331491369178414	2		673	733	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	210	470	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.193607657444295	2	FACETS	0.926	0.864	0.99	0.926	0.864	0.99	INDETERMINATE	2	TRUE	0	0.331491369178414	2		472	684	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120031	70120031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	23	55	0	ENST00000245479.2:c.1037del	p.Pro346ArgfsTer37	p.P346Rfs*37	ENST00000245479	NM_000346.3	345	Ccc/cc	3/3	0.193607657444295	2	FACETS	1	0.924	1	0.708	0.563	0.868	INDETERMINATE	1	TRUE	0	0.331491369178414	2		55	98	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	47	423	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.702	0.593	0.821	0.702	0.593	0.821	SUBCLONAL	1	TRUE	1	0.331491369178414	2		423	404	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	79	554	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.888	0.782	1	0.888	0.782	1	CLONAL	1	TRUE	1	0.331491369178414	2		555	537	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578215	28578216	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	218	604	0	ENST00000241453.7:c.2955_2956del	p.Pro986AlafsTer27	p.P986Afs*27	ENST00000241453	NM_004119.2	985	tcTCcg/tccg	24/24	0.275943417552005	4	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	2	0.331491369178414	4		604	854	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	38	522	3	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.352	0.29	0.421	0.352	0.29	0.421	SUBCLONAL	1	TRUE	1	0.331491369178414	2		525	652	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs1057519842	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	71	341	0	ENST00000274335.5:c.1727_1729del	p.Thr576del	p.T576del	ENST00000274335		575	aaGACg/aag	12/15	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.331491369178414	2		341	393	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281518	15281518	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1368023123	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	132	621	0	ENST00000263388.2:c.4855C>T	p.Arg1619Cys	p.R1619C	ENST00000263388	NM_000435.2	1619	Cgc/Tgc	26/33	1	2	FACETS	0.887	0.805	0.973	0.887	0.805	0.973	CLONAL	1	TRUE	1	0.331491369178414	2		621	898	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007688	45007688	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	64	386	0	ENST00000558401.1:c.135C>A	p.Cys45Ter	p.C45*	ENST00000558401	NM_004048.2	45	tgC/tgA	2/4	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.331491369178414	2		386	383	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139625	202139626	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	72	338	0	ENST00000358485.4:c.790dup	p.Val264GlyfsTer13	p.V264Gfs*13	ENST00000358485	NM_001080125.1	262	-/G	6/9	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.331491369178414	2		338	429	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs753143066	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	138	461	3	ENST00000295797.4:c.826dup	p.Thr276AsnfsTer16	p.T276Nfs*16	ENST00000295797	NM_002740.5	273	tta/ttAa	9/18	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.331491369178414	2		464	818	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193181198	193181198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	159	273	0	ENST00000367435.3:c.1034C>T	p.Ser345Phe	p.S345F	ENST00000367435	NM_024529.4	345	tCt/tTt	12/17	0.331491369178414	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	TRUE	1	0.331491369178414	4		273	393	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211138	36211138	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	64	1020	0	ENST00000222270.7:c.889C>T	p.Arg297Ter	p.R297*	ENST00000222270	NM_014727.1	297	Cga/Tga	3/37	1	2	FACETS	0.333	0.287	0.384	0.333	0.287	0.384	SUBCLONAL	1	TRUE	1	0.331491369178414	2		1020	1158	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117600	70117601	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	40	707	0	ENST00000245479.2:c.72dup	p.Thr25HisfsTer227	p.T25Hfs*227	ENST00000245479	NM_000346.3	23	agc/agCc	1/3	0.193607657444295	2	FACETS	0.329	0.273	0.393	0.165	0.136	0.197	INDETERMINATE	1	TRUE	0	0.331491369178414	2		707	733	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932065	39932065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1009877078	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	53	623	2	ENST00000378444.4:c.2534C>T	p.Ala845Val	p.A845V	ENST00000378444	NM_001123385.1	845	gCc/gTc	4/15	1	2	FACETS	0.41	0.349	0.478	0.41	0.349	0.478	SUBCLONAL	1	TRUE	1	0.331491369178414	2		625	779	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245924	16245924	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	63	305	0	ENST00000375759.3:c.1547C>A	p.Thr516Lys	p.T516K	ENST00000375759	NM_015001.2	516	aCa/aAa	8/15	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.331491369178414	2		305	371	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088727	27088727	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	125	648	0	ENST00000324856.7:c.2336G>A	p.Gly779Glu	p.G779E	ENST00000324856	NM_006015.4	779	gGa/gAa	7/20	1	2	FACETS	0.944	0.855	1	0.944	0.855	1	CLONAL	1	TRUE	1	0.331491369178414	2		648	799	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163479	108163479	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780603110	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	74	587	0	ENST00000278616.4:c.4570C>T	p.Leu1524Phe	p.L1524F	ENST00000278616	NM_000051.3	1524	Ctt/Ttt	30/63	1	2	FACETS	0.911	0.8	1	0.911	0.8	1	CLONAL	1	TRUE	1	0.331491369178414	2		587	490	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355814	73355814	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	105	380	0	ENST00000377767.4:c.157C>T	p.Gln53Ter	p.Q53*	ENST00000377767	NM_014953.3	53	Cag/Tag	1/21	0.275943417552005	4	FACETS	1	0.926	1	0.521	0.467	0.579	CLONAL	1	TRUE	2	0.331491369178414	4		380	809	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90645570	90645570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1453618042	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	11	78	0	ENST00000330062.3:c.53G>A	p.Arg18Gln	p.R18Q	ENST00000330062	NM_002168.2	18	cGg/cAg	1/11	1	2	FACETS	0.351	0.243	0.486	0.351	0.243	0.486	SUBCLONAL	1	TRUE	1	0.331491369178414	2		78	189	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652250	3652250	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	122	715	1	ENST00000294008.3:c.819G>T	p.Gln273His	p.Q273H	ENST00000294008	NM_032444.2	273	caG/caT	4/15	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.331491369178414	2		716	712	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351914	89351914	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	188	907	1	ENST00000301030.4:c.1036G>T	p.Glu346Ter	p.E346*	ENST00000301030	NM_001256183.1	346	Gag/Tag	9/13	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.331491369178414	2		908	1106	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118504	17118504	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	78	659	0	ENST00000285071.4:c.1427A>G	p.Asp476Gly	p.D476G	ENST00000285071	NM_144997.5	476	gAc/gGc	12/14	1	2	FACETS	0.704	0.619	0.796	0.704	0.619	0.796	SUBCLONAL	1	TRUE	1	0.331491369178414	2		659	668	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288827	15288827	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	43	126	0	ENST00000263388.2:c.3912C>G	p.Cys1304Trp	p.C1304W	ENST00000263388	NM_000435.2	1304	tgC/tgG	24/33	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.331491369178414	2		126	249	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375363	15375363	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	147	669	0	ENST00000263377.2:c.1064A>C	p.Lys355Thr	p.K355T	ENST00000263377	NM_058243.2	355	aAg/aCg	6/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.331491369178414	2		669	787	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303622	30303622	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	107	475	0	ENST00000262643.3:c.50A>C	p.Lys17Thr	p.K17T	ENST00000262643	NM_001238.2	17	aAg/aCg	3/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.331491369178414	2		475	549	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228643	36228643	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	162	694	0	ENST00000222270.7:c.7657A>G	p.Arg2553Gly	p.R2553G	ENST00000222270	NM_014727.1	2553	Aga/Gga	34/37	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.331491369178414	2		694	958	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763519	41763519	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs773904444	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	76	458	0	ENST00000301178.4:c.2318A>G	p.Asp773Gly	p.D773G	ENST00000301178	NM_021913.4	773	gAc/gGc	19/20	1	2	FACETS	0.984	0.866	1	0.984	0.866	1	CLONAL	1	TRUE	1	0.331491369178414	2		458	466	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728870	190728870	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	67	362	0	ENST00000441310.2:c.2258A>G	p.Glu753Gly	p.E753G	ENST00000441310	NM_000534.4	753	gAa/gGa	10/13	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.331491369178414	2		362	348	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285296	212285296	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	81	485	0	ENST00000342788.4:c.3005A>C	p.Lys1002Thr	p.K1002T	ENST00000342788	NM_005235.2	1002	aAg/aCg	25/28	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.331491369178414	2		485	450	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71050170	71050170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	70	346	0	ENST00000318789.4:c.1015G>A	p.Ala339Thr	p.A339T	ENST00000318789	NM_032682.5	339	Gcc/Acc	13/21	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.331491369178414	2		346	392	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067067	143067067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	92	505	0	ENST00000262992.4:c.1646G>A	p.Ser549Asn	p.S549N	ENST00000262992	NM_001101669.1	549	aGt/aAt	16/24	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.331491369178414	2		505	462	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628847	187628861	+	protein_altering_variant	In_Frame_Del	DEL	TGAGCATTGACAGAG	TGAGCATTGACAGAG	AAGCAC	novel	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	106	602	2	ENST00000441802.2:c.2121_2135delinsGTGCTT	p.His707_His712delinsGlnCysPhe	p.H707_H712delinsQCF	ENST00000441802	NM_005245.3	707	caCTCTGTCAATGCTCAc/caGTGCTTc	2/27	1	2	FACETS	0.968	0.869	1	0.968	0.869	1	CLONAL	1	TRUE	1	0.331491369178414	2		604	661	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264529	1264529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446074617	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	85	663	0	ENST00000310581.5:c.2833G>A	p.Asp945Asn	p.D945N	ENST00000310581	NM_198253.2	945	Gac/Aac	11/16	1	2	FACETS	0.718	0.635	0.808	0.718	0.635	0.808	SUBCLONAL	1	TRUE	1	0.331491369178414	2		663	714	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680958	30680958	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	115	539	0	ENST00000376406.3:c.761C>T	p.Thr254Ile	p.T254I	ENST00000376406	NM_014641.2	254	aCt/aTt	5/15	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.331491369178414	2		539	679	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515235	106515235	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	142	323	1	ENST00000359195.3:c.2378C>G	p.Ala793Gly	p.A793G	ENST00000359195	NM_002649.2	793	gCa/gGa	5/11	0.331491369178414	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	1	0.331491369178414	3		324	475	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273533	38273533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1399523084	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	111	624	0	ENST00000425967.3:c.1802G>A	p.Arg601Gln	p.R601Q	ENST00000425967	NM_001174067.1	601	cGg/cAg	14/19	0.331491369178414	3	FACETS	1	0.934	1	0.525	0.472	0.582	CLONAL	1	TRUE	1	0.331491369178414	3		624	743	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409444	80409444	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	92	434	0	ENST00000286548.4:c.670A>G	p.Thr224Ala	p.T224A	ENST00000286548	NM_002072.3	224	Acc/Gcc	5/7	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.331491369178414	2		434	452	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	126	599	5	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.587	0.533	0.643	0.587	0.533	0.643	SUBCLONAL	1	TRUE	1	0.752249892767874	2		604	571	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	251	903	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.752249892767874	2		906	597	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	190	872	8	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	0.752249892767874	3	FACETS	0.621	0.573	0.67	0.31	0.286	0.335	SUBCLONAL	1	TRUE	1	0.752249892767874	3		880	1120	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	153	490	7	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	0.4455576158505	2	FACETS	1	0.952	1	0.519	0.48	0.558	INDETERMINATE	1	TRUE	0	0.752249892767874	2		497	392	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	156	668	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.571	0.523	0.62	0.571	0.523	0.62	SUBCLONAL	1	TRUE	1	0.752249892767874	2		673	727	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	93	620	3	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	1	2	FACETS	0.427	0.38	0.477	0.427	0.38	0.477	SUBCLONAL	1	TRUE	1	0.752249892767874	2		623	579	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	333	682	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.752249892767874	2		683	828	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	60	283	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.469	0.406	0.537	0.469	0.406	0.537	SUBCLONAL	1	TRUE	1	0.752249892767874	2		283	340	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448408	49448408	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs797045661	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	121	707	1	ENST00000301067.7:c.303del	p.Ser102AlafsTer28	p.S102Afs*28	ENST00000301067	NM_003482.3	101	ggG/gg	3/54	1	2	FACETS	0.484	0.438	0.533	0.484	0.438	0.533	SUBCLONAL	1	TRUE	1	0.752249892767874	2		708	664	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670543	30670543	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	109	552	0	ENST00000376406.3:c.5977C>T	p.Arg1993Ter	p.R1993*	ENST00000376406	NM_014641.2	1993	Cga/Tga	13/15	1	2	FACETS	0.498	0.448	0.55	0.498	0.448	0.55	SUBCLONAL	1	TRUE	1	0.752249892767874	2		552	582	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	98	462	1	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	0.519	0.465	0.576	0.519	0.465	0.576	SUBCLONAL	1	TRUE	1	0.752249892767874	2		463	502	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	201	804	3	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.638	0.593	0.686	0.638	0.593	0.686	SUBCLONAL	1	TRUE	1	0.752249892767874	2		807	837	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955112	17955112	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755706305	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	183	812	2	ENST00000458235.1:c.115del	p.Gln39SerfsTer108	p.Q39Sfs*108	ENST00000458235	NM_000215.3	39	Cag/ag	2/24	1	2	FACETS	0.601	0.555	0.648	0.601	0.555	0.648	SUBCLONAL	1	TRUE	1	0.752249892767874	2		814	810	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097643	8097643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	41	305	0	ENST00000346208.3:c.25C>T	p.Arg9Cys	p.R9C	ENST00000346208		9	Cgc/Tgc	2/6	1	2	FACETS	0.454	0.381	0.534	0.454	0.381	0.534	SUBCLONAL	1	TRUE	1	0.752249892767874	2		305	240	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656951	47656951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63749849	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	80	373	1	ENST00000233146.2:c.1147C>T	p.Arg383Ter	p.R383*	ENST00000233146	NM_000251.2	383	Cga/Tga	7/16	1	2	FACETS	0.55	0.487	0.616	0.55	0.487	0.616	SUBCLONAL	1	TRUE	1	0.752249892767874	2		374	387	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1040397	1040397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35008685	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	117	610	0	ENST00000358495.3:c.175G>A	p.Gly59Arg	p.G59R	ENST00000358495	NM_134424.2	59	Gga/Aga	3/12	NA	2	FACETS	0.518	0.469	0.571			1	INDETERMINATE	1	TRUE	NA	0.752249892767874	2		610	600	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	114	581	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.431890818593264	1	FACETS	0.416	0.376	0.457	0.416	0.376	0.457	INDETERMINATE	1	TRUE	0	0.752249892767874	1		581	455	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168731	32168731	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1245029988	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	158	896	1	ENST00000375023.3:c.4192G>A	p.Ala1398Thr	p.A1398T	ENST00000375023	NM_004557.3	1398	Gca/Aca	23/30	1	2	FACETS	0.532	0.488	0.578	0.532	0.488	0.578	SUBCLONAL	1	TRUE	1	0.752249892767874	2		897	790	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752960	128752960	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	136	439	0	ENST00000377970.2:c.1121A>G	p.His374Arg	p.H374R	ENST00000377970	NM_002467.4	374	cAc/cGc	3/3	1	2	FACETS	0.536	0.488	0.586	0.536	0.488	0.586	SUBCLONAL	1	TRUE	1	0.752249892767874	2		439	675	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753910	133753910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149852028	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	115	563	1	ENST00000318560.5:c.1379G>A	p.Arg460His	p.R460H	ENST00000318560	NM_005157.4	460	cGc/cAc	8/11	1	2	FACETS	0.548	0.495	0.603	0.548	0.495	0.603	SUBCLONAL	1	TRUE	1	0.752249892767874	2		564	558	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612359	1612359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1341689226	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	191	907	0	ENST00000344749.5:c.1660C>T	p.Arg554Trp	p.R554W	ENST00000344749	NM_001136139.2	554	Cgg/Tgg	18/19	1	2	FACETS	0.542	0.501	0.584	0.542	0.501	0.584	SUBCLONAL	1	TRUE	1	0.752249892767874	2		907	937	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268793	98268793	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1554708751	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	104	526	1	ENST00000331920.6:c.290del	p.Asn97ThrfsTer20	p.N97Tfs*20	ENST00000331920	NM_000264.3	97	aAc/ac	2/24	1	2	FACETS	0.401	0.359	0.446	0.401	0.359	0.446	SUBCLONAL	1	TRUE	1	0.752249892767874	2		527	689	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718999	190718999	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147084726	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	44	235	0	ENST00000441310.2:c.1001C>T	p.Thr334Met	p.T334M	ENST00000441310	NM_000534.4	334	aCg/aTg	9/13	1	2	FACETS	0.515	0.436	0.601	0.515	0.436	0.601	SUBCLONAL	1	TRUE	1	0.752249892767874	2		235	227	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542110	187542110	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	50	384	1	ENST00000441802.2:c.5630del	p.Pro1877LeufsTer20	p.P1877Lfs*20	ENST00000441802	NM_005245.3	1877	cCt/ct	10/27	1	2	FACETS	0.465	0.397	0.538	0.465	0.397	0.538	SUBCLONAL	1	TRUE	1	0.752249892767874	2		385	286	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298120	15298120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376606994	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	171	880	1	ENST00000263388.2:c.1636G>A	p.Val546Met	p.V546M	ENST00000263388	NM_000435.2	546	Gtg/Atg	11/33	1	2	FACETS	0.561	0.517	0.608	0.561	0.517	0.608	SUBCLONAL	1	TRUE	1	0.752249892767874	2		881	810	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027087	71027087	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	139	407	0	ENST00000318789.4:c.1240del	p.Leu414Ter	p.L414*	ENST00000318789	NM_032682.5	414	Ctg/tg	15/21	1	2	FACETS	0.504	0.459	0.551	0.504	0.459	0.551	SUBCLONAL	1	TRUE	1	0.752249892767874	2		407	733	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858337	9858337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560057284	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	74	405	1	ENST00000330684.3:c.3064C>T	p.Arg1022Cys	p.R1022C	ENST00000330684	NM_001134407.1	1022	Cgc/Tgc	13/13	1	2	FACETS	0.562	0.495	0.633	0.562	0.495	0.633	SUBCLONAL	1	TRUE	1	0.752249892767874	2		406	350	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519008	66519008	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555813217	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	124	516	0	ENST00000358598.2:c.289C>T	p.Arg97Ter	p.R97*	ENST00000358598	NM_212471.2	97	Cga/Tga	3/11	1	2	FACETS	0.413	0.374	0.455	0.413	0.374	0.455	SUBCLONAL	1	TRUE	1	0.752249892767874	2		516	798	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932068	39932068	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140780988	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	188	724	0	ENST00000378444.4:c.2531C>T	p.Pro844Leu	p.P844L	ENST00000378444	NM_001123385.1	844	cCg/cTg	4/15	0.564462083187702	1	FACETS	0.504	0.468	0.541	0.504	0.468	0.541	SUBCLONAL	1	TRUE	0	0.752249892767874	1		724	619	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557762	21557762	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1172808550	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	165	713	1	ENST00000382592.4:c.2083G>A	p.Ala695Thr	p.A695T	ENST00000382592	NM_014572.2	695	Gcc/Acc	5/8	1	2	FACETS	0.524	0.481	0.569	0.524	0.481	0.569	SUBCLONAL	1	TRUE	1	0.752249892767874	2		714	837	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621158	1621158	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	123	873	0	ENST00000344749.5:c.988del	p.Asp330MetfsTer64	p.D330Mfs*64	ENST00000344749	NM_001136139.2	330	Gat/at	12/19	1	2	FACETS	0.492	0.446	0.541	0.492	0.446	0.541	SUBCLONAL	1	TRUE	1	0.752249892767874	2		873	664	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190666	11190666	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762176419	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	168	736	1	ENST00000361445.4:c.5533G>A	p.Glu1845Lys	p.E1845K	ENST00000361445	NM_004958.3	1845	Gag/Aag	39/58	0.149774925334042	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.752249892767874	0		737	788	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350270	15350270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760622695	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	187	871	1	ENST00000263377.2:c.3509C>T	p.Pro1170Leu	p.P1170L	ENST00000263377	NM_058243.2	1170	cCg/cTg	17/20	1	2	FACETS	0.687	0.636	0.739	0.687	0.636	0.739	SUBCLONAL	1	TRUE	1	0.752249892767874	2		872	724	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022303	26022304	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTG	rs750598660	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	90	604	0	ENST00000435504.4:c.351_353dup	p.Ser118dup	p.S118dup	ENST00000435504		118	agt/agCAGt	5/13	1	2	FACETS	0.358	0.318	0.401	0.358	0.318	0.401	SUBCLONAL	1	TRUE	1	0.752249892767874	2		604	668	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10264977	10264977	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1486893166	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	73	413	1	ENST00000340748.4:c.1963G>A	p.Val655Ile	p.V655I	ENST00000340748		655	Gtc/Atc	21/40	1	2	FACETS	0.576	0.507	0.649	0.576	0.507	0.649	SUBCLONAL	1	TRUE	1	0.752249892767874	2		414	337	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282719	1282719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776459827	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	106	630	0	ENST00000310581.5:c.1594G>A	p.Ala532Thr	p.A532T	ENST00000310581	NM_198253.2	532	Gca/Aca	3/16	1	2	FACETS	0.58	0.522	0.64	0.58	0.522	0.64	SUBCLONAL	1	TRUE	1	0.752249892767874	2		630	486	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629457	187629457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	166	668	2	ENST00000441802.2:c.1525C>T	p.Pro509Ser	p.P509S	ENST00000441802	NM_005245.3	509	Ccg/Tcg	2/27	1	2	FACETS	0.587	0.54	0.636	0.587	0.54	0.636	SUBCLONAL	1	TRUE	1	0.752249892767874	2		670	752	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467088	25467088	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs899717364	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	187	777	0	ENST00000264709.3:c.1787G>A	p.Arg596Gln	p.R596Q	ENST00000264709	NM_175629.2	596	cGg/cAg	15/23	1	2	FACETS	0.618	0.572	0.666	0.618	0.572	0.666	SUBCLONAL	1	TRUE	1	0.752249892767874	2		777	804	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258058	16258058	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766847660	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	117	434	1	ENST00000375759.3:c.5323G>A	p.Glu1775Lys	p.E1775K	ENST00000375759	NM_015001.2	1775	Gaa/Aaa	11/15	0.61969531851103	3	FACETS	0.865	0.784	0.949			1	CLONAL	1	TRUE	NA	0.752249892767874	3		435	495	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612056	43612056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554819146	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	120	891	1	ENST00000355710.3:c.2161C>T	p.Arg721Trp	p.R721W	ENST00000355710	NM_020975.4	721	Cgg/Tgg	12/20	1	2	FACETS	0.462	0.418	0.509	0.462	0.418	0.509	SUBCLONAL	1	TRUE	1	0.752249892767874	2		892	690	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445334	49445334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs893615522	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	231	965	1	ENST00000301067.7:c.2132C>T	p.Pro711Leu	p.P711L	ENST00000301067	NM_003482.3	711	cCg/cTg	10/54	1	2	FACETS	0.604	0.563	0.646	0.604	0.563	0.646	SUBCLONAL	1	TRUE	1	0.752249892767874	2		966	1017	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41020952	41020952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	119	612	2	ENST00000267868.3:c.574G>A	p.Ala192Thr	p.A192T	ENST00000267868	NM_002875.4	192	Gct/Act	7/10	1	2	FACETS	0.501	0.453	0.552	0.501	0.453	0.552	SUBCLONAL	1	TRUE	1	0.752249892767874	2		614	631	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15978994	15978994	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	110	446	0	ENST00000268712.3:c.3524C>A	p.Thr1175Asn	p.T1175N	ENST00000268712	NM_006311.3	1175	aCt/aAt	27/46	1	2	FACETS	0.571	0.515	0.63	0.571	0.515	0.63	SUBCLONAL	1	TRUE	1	0.752249892767874	2		446	512	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10305503	10305503	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	119	499	0	ENST00000340748.4:c.73C>A	p.Arg25Ser	p.R25S	ENST00000340748		25	Cgc/Agc	1/40	1	2	FACETS	0.534	0.484	0.588	0.534	0.484	0.588	SUBCLONAL	1	TRUE	1	0.752249892767874	2		499	592	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703577	47703631	+	frameshift_variant	Frame_Shift_Del	DEL	TGTTTTGTGCCATGTGAGTCAGCAGAAGTGTCCATTGTGGACTGCATCTTAGCCC	TGTTTTGTGCCATGTGAGTCAGCAGAAGTGTCCATTGTGGACTGCATCTTAGCCC	-	novel	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	81	628	0	ENST00000233146.2:c.2077_2131del	p.Cys693GlufsTer2	p.C693Efs*2	ENST00000233146	NM_000251.2	693	TGTTTTGTGCCATGTGAGTCAGCAGAAGTGTCCATTGTGGACTGCATCTTAGCCCga/ga	13/16	1	2	FACETS	0.369	0.326	0.416	0.369	0.326	0.416	SUBCLONAL	1	TRUE	1	0.752249892767874	2		628	583	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39709845	39709847	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	55	263	0	ENST00000361337.2:c.475_477del	p.Lys159del	p.K159del	ENST00000361337	NM_003286.2	158	AAG/-	7/21	1	2	FACETS	0.556	0.48	0.638	0.556	0.48	0.638	SUBCLONAL	1	TRUE	1	0.752249892767874	2		263	263	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655236	45655236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140894768	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	354	724	1	ENST00000407780.3:c.616G>A	p.Ala206Thr	p.A206T	ENST00000407780	NM_001283052.1	206	Gca/Aca	4/7	0.451560263064864	2	FACETS	1	0.995	1	0.663	0.633	0.693	CLONAL	1	TRUE	0	0.752249892767874	2		725	710	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127230	22127230	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	123	592	0	ENST00000215832.6:c.898A>G	p.Lys300Glu	p.K300E	ENST00000215832	NM_002745.4	300	Aag/Gag	7/9	1	2	FACETS	0.534	0.484	0.587	0.534	0.484	0.587	SUBCLONAL	1	TRUE	1	0.752249892767874	2		592	612	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933192	49933192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769560872	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	118	671	0	ENST00000296474.3:c.2918C>T	p.Ala973Val	p.A973V	ENST00000296474	NM_002447.2	973	gCg/gTg	12/20	1	2	FACETS	0.54	0.489	0.594	0.54	0.489	0.594	SUBCLONAL	1	TRUE	1	0.752249892767874	2		671	581	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613163	52613163	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	118	524	0	ENST00000394830.3:c.3365A>G	p.Tyr1122Cys	p.Y1122C	ENST00000394830	NM_018313.4	1122	tAc/tGc	22/30	1	2	FACETS	0.462	0.417	0.509	0.462	0.417	0.509	SUBCLONAL	1	TRUE	1	0.752249892767874	2		524	679	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014383	70014383	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780036017	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	144	553	0	ENST00000394351.3:c.1244C>T	p.Thr415Met	p.T415M	ENST00000394351	NM_000248.3	415	aCg/aTg	9/9	1	2	FACETS	0.542	0.495	0.59	0.542	0.495	0.59	SUBCLONAL	1	TRUE	1	0.752249892767874	2		553	707	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920289	1920289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146822227	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	163	735	0	ENST00000382891.5:c.1349G>A	p.Arg450Gln	p.R450Q	ENST00000382891	NM_133335.3	450	cGa/cAa	5/22	1	2	FACETS	0.597	0.549	0.647	0.597	0.549	0.647	SUBCLONAL	1	TRUE	1	0.752249892767874	2		735	726	SUCCESS
APC	324	MSKCC	GRCh37	5	112177653	112177653	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	43	343	0	ENST00000257430.4:c.6362C>G	p.Ala2121Gly	p.A2121G	ENST00000257430	NM_000038.5	2121	gCt/gGt	16/16	1	2	FACETS	0.416	0.35	0.488	0.416	0.35	0.488	SUBCLONAL	1	TRUE	1	0.752249892767874	2		343	275	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176718971	176718971	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758308969	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	40	229	0	ENST00000439151.2:c.6275C>T	p.Thr2092Met	p.T2092M	ENST00000439151	NM_022455.4	2092	aCg/aTg	22/23	1	2	FACETS	0.427	0.357	0.504	0.427	0.357	0.504	SUBCLONAL	1	TRUE	1	0.752249892767874	2		229	249	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820834	32820834	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	171	898	0	ENST00000354258.4:c.760G>A	p.Val254Met	p.V254M	ENST00000354258	NM_000593.5	254	Gtg/Atg	1/11	1	2	FACETS	0.505	0.465	0.547	0.505	0.465	0.547	SUBCLONAL	1	TRUE	1	0.752249892767874	2		898	900	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415036	109415036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	88	621	0	ENST00000436639.2:c.241G>A	p.Val81Met	p.V81M	ENST00000436639	NM_014454.2	81	Gtg/Atg	1/10	1	2	FACETS	0.43	0.382	0.482	0.43	0.382	0.482	SUBCLONAL	1	TRUE	1	0.752249892767874	2		621	544	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527935	157527935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs911169696	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	108	631	3	ENST00000346085.5:c.5660C>T	p.Ala1887Val	p.A1887V	ENST00000346085	NM_020732.3	1887	gCa/gTa	20/20	1	2	FACETS	0.444	0.399	0.491	0.444	0.399	0.491	SUBCLONAL	1	TRUE	1	0.752249892767874	2		634	647	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729847	41729847	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	89	448	0	ENST00000242208.4:c.682C>T	p.Gln228Ter	p.Q228*	ENST00000242208	NM_002192.2	228	Cag/Tag	3/3	1	2	FACETS	0.554	0.494	0.618	0.554	0.494	0.618	SUBCLONAL	1	TRUE	1	0.752249892767874	2		448	427	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534597	140534597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749247588	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	34	473	0	ENST00000288602.6:c.316G>A	p.Gly106Arg	p.G106R	ENST00000288602	NM_004333.4	106	Gga/Aga	3/18	1	2	FACETS	0.211	0.172	0.254	0.211	0.172	0.254	SUBCLONAL	1	TRUE	1	0.752249892767874	2		473	429	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93626849	93626869	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TTCTTACTTTTTTCTCTTTCA	TTCTTACTTTTTTCTCTTTCA	-	novel	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	36	330	0	ENST00000375746.1:c.718-22_718-2del		p.X240_splice	ENST00000375746	NM_001174167.1	240			1	2	FACETS	0.295	0.243	0.353	0.295	0.243	0.353	SUBCLONAL	1	TRUE	1	0.752249892767874	2		330	324	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133729508	133729508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371791060	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	144	608	0	ENST00000318560.5:c.137C>T	p.Ala46Val	p.A46V	ENST00000318560	NM_005157.4	46	gCt/gTt	2/11	1	2	FACETS	0.494	0.451	0.539	0.494	0.451	0.539	SUBCLONAL	1	TRUE	1	0.752249892767874	2		608	775	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321001	137321001	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343863109	NA	P-0040575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	182	885	2	ENST00000481739.1:c.958G>A	p.Val320Met	p.V320M	ENST00000481739	NM_002957.4	320	Gtg/Atg	7/10	1	2	FACETS	0.624	0.576	0.672	0.624	0.576	0.672	SUBCLONAL	1	TRUE	1	0.752249892767874	2		887	776	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0043780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	61	247	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	0.276574344557207	3	FACETS	0.926	0.801	1	0.463	0.4	0.531	CLONAL	1	TRUE	1	0.328429424051502	3		247	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0043780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	147	478	0	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.328429424051502	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.328429424051502	1		478	673	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	64	333	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.751	0.652	0.857	0.751	0.652	0.857	SUBCLONAL	1	TRUE	1	0.390262268162439	2		333	437	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0044075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	121	567	2	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.942	0.853	1	0.942	0.853	1	CLONAL	1	TRUE	1	0.390262268162439	2		569	658	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632303	215632303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782003	NA	P-0044075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	108	546	1	ENST00000260947.4:c.1471G>A	p.Gly491Arg	p.G491R	ENST00000260947	NM_000465.2	491	Ggg/Agg	6/11	1	2	FACETS	0.825	0.741	0.913	0.825	0.741	0.913	CLONAL	1	TRUE	1	0.390262268162439	2		547	671	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640629	3640629	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	181	779	0	ENST00000294008.3:c.3010C>T	p.Pro1004Ser	p.P1004S	ENST00000294008	NM_032444.2	1004	Ccc/Tcc	12/15	1	2	FACETS	0.996	0.919	1	0.996	0.919	1	CLONAL	1	TRUE	1	0.390262268162439	2		779	931	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032194	26032194	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	71	303	0	ENST00000244661.2:c.95C>G	p.Ala32Gly	p.A32G	ENST00000244661	NM_003537.3	32	gCt/gGt	1/1	1	2	FACETS	0.89	0.78	1	0.89	0.78	1	CLONAL	1	TRUE	1	0.390262268162439	2		303	409	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044075-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	88	333	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.821	0.73	0.918	0.821	0.73	0.918	CLONAL	1	FALSE	1	0.437258346497052	2		333	490	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0044075-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	138	567	2	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.916	0.835	1	0.916	0.835	1	CLONAL	1	FALSE	1	0.437258346497052	2		569	689	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632303	215632303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782003	NA	P-0044075-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	121	546	1	ENST00000260947.4:c.1471G>A	p.Gly491Arg	p.G491R	ENST00000260947	NM_000465.2	491	Ggg/Agg	6/11	NA	2	FACETS	1	0.909	1			1	INDETERMINATE	1	FALSE	NA	0.437258346497052	2		547	552	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640629	3640629	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044075-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	169	779	0	ENST00000294008.3:c.3010C>T	p.Pro1004Ser	p.P1004S	ENST00000294008	NM_032444.2	1004	Ccc/Tcc	12/15	NA	2	FACETS	0.818	0.752	0.887			1	INDETERMINATE	1	FALSE	NA	0.437258346497052	2		779	945	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733429	85733429	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044075-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	82	418	0	ENST00000370580.1:c.583C>T	p.Pro195Ser	p.P195S	ENST00000370580	NM_003921.4	195	Cct/Tct	3/3	NA	2	FACETS	0.8	0.708	0.898			1	INDETERMINATE	1	FALSE	NA	0.437258346497052	2		418	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0044075-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	297	533	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.461540901602095	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.461565707213201	2		533	622	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0044075-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	848	519	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.461565707213201	9	FACETS	0.988	0.963	1	0.988	0.963	1	CLONAL	7	TRUE	2	0.461565707213201	9		519	1389	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41199664	41199664	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044075-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	1275	556	0	ENST00000357654.3:c.5463C>A	p.Phe1821Leu	p.F1821L	ENST00000357654	NM_007294.3	1821	ttC/ttA	22/23	0.461565707213201	11	FACETS	0.976	0.956	0.995			1	CLONAL	9	TRUE	NA	0.461565707213201	11		556	1936	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027189	49027198	+	frameshift_variant	Frame_Shift_Del	DEL	CTTGAATCTG	CTTGAATCTG	-	rs587776784	NA	P-0044075-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	90	403	0	ENST00000267163.4:c.1760_1769del	p.Glu587ValfsTer21	p.E587Vfs*21	ENST00000267163	NM_000321.2	586	CTTGAATCTGct/ct	18/27	0.461540901602095	3	FACETS	0.734	0.652	0.822	0.367	0.326	0.411	SUBCLONAL	1	TRUE	1	0.461565707213201	3		403	654	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166266	118166266	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044075-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	422	792	0	ENST00000369448.3:c.776A>G	p.Asp259Gly	p.D259G	ENST00000369448	NM_017709.3	259	gAc/gGc	2/2	0.457451616990975	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.461565707213201	2		792	873	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948434	31948434	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752615678	NA	P-0044075-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	30	184	0	ENST00000375333.2:c.917G>A	p.Arg306His	p.R306H	ENST00000375333	NM_032454.1	306	cGc/cAc	7/8	0.461540901602095	3	FACETS	0.656	0.531	0.796	0.328	0.265	0.398	SUBCLONAL	1	TRUE	1	0.461565707213201	3		184	244	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009250	69009250	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0044075-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	45	393	0	ENST00000288368.4:c.2369-2A>C		p.X790_splice	ENST00000288368	NM_024870.2	790			0.461565707213201	7	FACETS	0.471	0.394	0.556	0.094	0.078	0.112	SUBCLONAL	1	TRUE	2	0.461565707213201	7		393	892	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	69	304	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.519749990206578	2		304	253	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	106	428	2	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.843	0.759	0.93	0.843	0.759	0.93	CLONAL	1	TRUE	1	0.519749990206578	2		430	484	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	72	490	7	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.88	0.775	0.99	0.88	0.775	0.99	CLONAL	1	TRUE	1	0.519749990206578	2		497	315	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	103	285	1	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	0.879	0.791	0.971	0.879	0.791	0.971	CLONAL	1	TRUE	1	0.519749990206578	2		286	451	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	180	513	0	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.917	0.848	0.989	0.917	0.848	0.989	CLONAL	1	TRUE	1	0.519749990206578	2		513	755	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	408	470	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.918	0.879	0.957	1	0.997	1	CLONAL	2	TRUE	1	0.519749990206578	2		472	855	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161324	55161324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514550	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	87	321	0	ENST00000257290.5:c.3155C>T	p.Thr1052Met	p.T1052M	ENST00000257290	NM_006206.4	1052	aCg/aTg	23/23	0.312066526664976	1	FACETS	0.663	0.591	0.738	0.663	0.591	0.738	SUBCLONAL	1	TRUE	0	0.519749990206578	1		321	374	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	73	230	6	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.805	0.709	0.907	0.805	0.709	0.907	CLONAL	1	TRUE	1	0.519749990206578	2		236	349	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347983	347983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760961378	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	86	590	4	ENST00000262320.3:c.1523del	p.Gly508ValfsTer197	p.G508Vfs*197	ENST00000262320	NM_003502.3	508	gGt/gt	6/11	1	2	FACETS	0.355	0.313	0.4	0.355	0.313	0.4	SUBCLONAL	1	TRUE	1	0.519749990206578	2		594	932	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212423	5212423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768007031	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	234	522	2	ENST00000357368.4:c.4694C>T	p.Thr1565Met	p.T1565M	ENST00000357368	NM_002850.3	1565	aCg/aTg	31/38	1	2	FACETS	0.992	0.926	1	0.992	0.926	1	CLONAL	1	TRUE	1	0.519749990206578	2		524	908	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687471	37687472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs760014508	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	182	220	0	ENST00000447079.4:c.4382dup	p.Thr1463AsnfsTer50	p.T1463Nfs*50	ENST00000447079	NM_015083.1	1459	tgg/tGgg	14/14	1	2	FACETS	0.79	0.737	0.844	1	0.992	1	SUBCLONAL	2	TRUE	1	0.519749990206578	2		220	443	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	35	172	1	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	0.312066526664976	1	FACETS	0.369	0.304	0.442	0.369	0.304	0.442	SUBCLONAL	1	TRUE	0	0.519749990206578	1		173	270	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982767	7982767	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	193	481	1	ENST00000319144.4:c.1018del	p.Leu340SerfsTer12	p.L340Sfs*12	ENST00000319144	NM_001139.2	340	Ctc/tc	8/15	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.519749990206578	2		482	737	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227851	36227851	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	192	590	0	ENST00000222270.7:c.7336C>T	p.Arg2446Ter	p.R2446*	ENST00000222270	NM_014727.1	2446	Cga/Tga	32/37	1	2	FACETS	0.846	0.783	0.911	0.846	0.783	0.911	CLONAL	1	TRUE	1	0.519749990206578	2		590	873	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs753143066	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	104	461	3	ENST00000295797.4:c.826dup	p.Thr276AsnfsTer16	p.T276Nfs*16	ENST00000295797	NM_002740.5	273	tta/ttAa	9/18	1	2	FACETS	0.848	0.763	0.937	0.848	0.763	0.937	CLONAL	1	TRUE	1	0.519749990206578	2		464	472	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	67	356	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.886	0.777	1	0.886	0.777	1	CLONAL	1	TRUE	1	0.519749990206578	2		356	291	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913253	39913253	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	118	405	2	ENST00000378444.4:c.4862del	p.Pro1621GlnfsTer53	p.P1621Qfs*53	ENST00000378444	NM_001123385.1	1621	cCa/ca	14/15	1	2	FACETS	0.974	0.885	1	0.974	0.885	1	CLONAL	1	TRUE	1	0.519749990206578	2		407	466	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921567	178921567	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553821144	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	34	212	0	ENST00000263967.3:c.1049A>G	p.Asp350Gly	p.D350G	ENST00000263967	NM_006218.2	350	gAc/gGc	5/21	1	2	FACETS	0.921	0.765	1	0.921	0.765	1	CLONAL	1	TRUE	1	0.519749990206578	2		212	142	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151290	202151290	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	85	295	0	ENST00000358485.4:c.1596del	p.Lys532AsnfsTer73	p.K532Nfs*73	ENST00000358485	NM_001080125.1	530	agA/ag	9/9	1	2	FACETS	0.798	0.709	0.891	0.798	0.709	0.891	SUBCLONAL	1	TRUE	1	0.519749990206578	2		295	410	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524468	187524469	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	127	446	0	ENST00000441802.2:c.11211_11212del	p.Cys3738ArgfsTer12	p.C3738Rfs*12	ENST00000441802	NM_005245.3	3737	ctCTgc/ctgc	19/27	1	2	FACETS	0.895	0.814	0.979	0.895	0.814	0.979	CLONAL	1	TRUE	1	0.519749990206578	2		446	546	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228172	53228172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	187	444	0	ENST00000375401.3:c.2230C>T	p.Arg744Trp	p.R744W	ENST00000375401	NM_004187.3	744	Cgg/Tgg	15/26	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.519749990206578	2		444	657	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928065	178928065	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	55	388	0	ENST00000263967.3:c.1343T>C	p.Val448Ala	p.V448A	ENST00000263967	NM_006218.2	448	gTa/gCa	8/21	1	2	FACETS	0.75	0.647	0.862	0.75	0.647	0.862	SUBCLONAL	1	TRUE	1	0.519749990206578	2		388	282	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106399	108106399	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs146382972	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	18	98	0	ENST00000278616.4:c.334G>A	p.Ala112Thr	p.A112T	ENST00000278616	NM_000051.3	112	Gca/Aca	5/63	1	2	FACETS	0.949	0.733	1	0.949	0.733	1	CLONAL	1	TRUE	1	0.519749990206578	2		98	73	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447773	49447773	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	29	455	0	ENST00000301067.7:c.661del	p.Ala221LeufsTer40	p.A221Lfs*40	ENST00000301067	NM_003482.3	221	Gct/ct	5/54	1	2	FACETS	0.198	0.158	0.243	0.198	0.158	0.243	SUBCLONAL	1	TRUE	1	0.519749990206578	2		455	564	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18958623	18958623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	77	491	0	ENST00000262803.5:c.442C>T	p.Arg148Cys	p.R148C	ENST00000262803	NM_002911.3	148	Cgt/Tgt	3/24	1	2	FACETS	0.622	0.548	0.702	0.622	0.548	0.702	SUBCLONAL	1	TRUE	1	0.519749990206578	2		491	476	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035163	6035163	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs878854059	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	81	296	0	ENST00000265849.7:c.903+2T>C		p.X301_splice	ENST00000265849	NM_000535.5	301			0.501829307749145	2	FACETS	0.986	0.877	1	0.493	0.438	0.551	CLONAL	1	TRUE	0	0.519749990206578	2		296	316	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884466	151884466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1435892915	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	60	286	0	ENST00000262189.6:c.4889C>T	p.Ser1630Leu	p.S1630L	ENST00000262189	NM_170606.2	1630	tCg/tTg	33/59	1	2	FACETS	0.831	0.722	0.946	0.831	0.722	0.946	CLONAL	1	TRUE	1	0.519749990206578	2		286	278	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435231	49435231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	186	485	0	ENST00000301067.7:c.6322C>T	p.Pro2108Ser	p.P2108S	ENST00000301067	NM_003482.3	2108	Ccg/Tcg	31/54	1	2	FACETS	0.901	0.834	0.971	0.901	0.834	0.971	CLONAL	1	TRUE	1	0.519749990206578	2		485	794	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393321	393321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	324	362	0	ENST00000380956.4:c.169G>A	p.Ala57Thr	p.A57T	ENST00000380956	NM_001195286.1	57	Gcg/Acg	2/9	0.506097091982149	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.519749990206578	2		362	581	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948745	17948745	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	201	539	0	ENST00000458235.1:c.1697T>C	p.Met566Thr	p.M566T	ENST00000458235	NM_000215.3	566	aTg/aCg	12/24	1	2	FACETS	0.992	0.921	1	0.992	0.921	1	CLONAL	1	TRUE	1	0.519749990206578	2		539	780	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485747	57485747	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	110	306	0	ENST00000371085.3:c.1048A>G	p.Thr350Ala	p.T350A	ENST00000371085	NM_000516.4	350	Act/Gct	13/13	1	2	FACETS	0.843	0.761	0.929	0.843	0.761	0.929	CLONAL	1	TRUE	1	0.519749990206578	2		306	502	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346092	152346092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144079294	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	73	399	0	ENST00000359321.1:c.478G>A	p.Val160Ile	p.V160I	ENST00000359321	NM_005431.1	160	Gtc/Atc	3/3	1	2	FACETS	0.849	0.748	0.955	0.849	0.748	0.955	CLONAL	1	TRUE	1	0.519749990206578	2		399	331	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987066	36987066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1325836054	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	182	443	0	ENST00000354822.5:c.623G>A	p.Arg208Gln	p.R208Q	ENST00000354822	NM_001079668.2	208	cGa/cAa	3/3	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.519749990206578	2		443	694	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910265	50910265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	200	491	0	ENST00000440232.2:c.1520G>A	p.Arg507His	p.R507H	ENST00000440232	NM_002691.3	507	cGc/cAc	13/27	1	2	FACETS	0.934	0.867	1	0.934	0.867	1	CLONAL	1	TRUE	1	0.519749990206578	2		491	824	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910710	29910710	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199474419	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	196	666	0	ENST00000376809.5:c.250T>C	p.Trp84Arg	p.W84R	ENST00000376809	NM_002116.7	84	Tgg/Cgg	2/8	0.506097091982149	2	FACETS	0.791	0.732	0.851	0.395	0.366	0.426	SUBCLONAL	1	TRUE	0	0.519749990206578	2		666	954	SUCCESS
AR	367	MSKCC	GRCh37	X	66765409	66765409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs865948546	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	173	525	2	ENST00000374690.3:c.421G>A	p.Ala141Thr	p.A141T	ENST00000374690	NM_000044.3	141	Gcc/Acc	1/8	0.312066526664976	1	FACETS	0.744	0.687	0.803	0.744	0.687	0.803	SUBCLONAL	1	TRUE	0	0.519749990206578	1		527	662	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11276216	11276216	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	60	342	0	ENST00000361445.4:c.3106A>G	p.Thr1036Ala	p.T1036A	ENST00000361445	NM_004958.3	1036	Acc/Gcc	20/58	1	2	FACETS	0.679	0.588	0.777	0.679	0.588	0.777	SUBCLONAL	1	TRUE	1	0.519749990206578	2		342	340	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259631	16259631	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs926461235	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	140	415	0	ENST00000375759.3:c.6896A>G	p.Lys2299Arg	p.K2299R	ENST00000375759	NM_015001.2	2299	aAg/aGg	11/15	1	2	FACETS	0.848	0.775	0.925	0.848	0.775	0.925	CLONAL	1	TRUE	1	0.519749990206578	2		415	635	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22413043	22413043	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	36	186	0	ENST00000344548.3:c.288+2T>C		p.X96_splice	ENST00000344548	NM_001039802.1	96			1	2	FACETS	0.882	0.736	1	0.882	0.736	1	CLONAL	1	TRUE	1	0.519749990206578	2		186	157	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276463	115276463	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs908936569	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	48	415	0	ENST00000438362.2:c.865A>G	p.Thr289Ala	p.T289A	ENST00000438362	NM_001242891.1	289	Aca/Gca	9/20	1	2	FACETS	0.604	0.513	0.702	0.604	0.513	0.702	SUBCLONAL	1	TRUE	1	0.519749990206578	2		415	306	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471638	120471638	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	97	345	0	ENST00000256646.2:c.3853A>G	p.Thr1285Ala	p.T1285A	ENST00000256646	NM_024408.3	1285	Acc/Gcc	23/34	1	2	FACETS	0.801	0.718	0.889	0.801	0.718	0.889	CLONAL	1	TRUE	1	0.519749990206578	2		345	466	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617442	43617442	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	83	360	0	ENST00000355710.3:c.2779A>G	p.Ile927Val	p.I927V	ENST00000355710	NM_020975.4	927	Atc/Gtc	16/20	1	2	FACETS	0.83	0.737	0.928	0.83	0.737	0.928	CLONAL	1	TRUE	1	0.519749990206578	2		360	385	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63817033	63817033	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	37	214	0	ENST00000279873.7:c.1004G>T	p.Arg335Met	p.R335M	ENST00000279873	NM_032199.2	335	aGg/aTg	6/10	1	2	FACETS	0.665	0.553	0.788	0.665	0.553	0.788	SUBCLONAL	1	TRUE	1	0.519749990206578	2		214	214	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219152	133219152	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775590365	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	200	535	0	ENST00000320574.5:c.4892G>A	p.Arg1631His	p.R1631H	ENST00000320574	NM_006231.2	1631	cGc/cAc	37/49	1	2	FACETS	0.88	0.816	0.945	0.88	0.816	0.945	CLONAL	1	TRUE	1	0.519749990206578	2		535	875	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237623	133237623	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	136	497	0	ENST00000320574.5:c.2992A>G	p.Thr998Ala	p.T998A	ENST00000320574	NM_006231.2	998	Acg/Gcg	25/49	1	2	FACETS	0.82	0.748	0.896	0.82	0.748	0.896	CLONAL	1	TRUE	1	0.519749990206578	2		497	638	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438006	110438006	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs778487451	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	74	202	0	ENST00000375856.3:c.395A>G	p.Gln132Arg	p.Q132R	ENST00000375856	NM_003749.2	132	cAg/cGg	1/2	1	2	FACETS	0.876	0.773	0.985	0.876	0.773	0.985	CLONAL	1	TRUE	1	0.519749990206578	2		202	325	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292700	91292700	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	69	373	1	ENST00000355112.3:c.202A>G	p.Thr68Ala	p.T68A	ENST00000355112	NM_000057.2	68	Acc/Gcc	3/22	1	2	FACETS	0.809	0.71	0.915	0.809	0.71	0.915	CLONAL	1	TRUE	1	0.519749990206578	2		374	328	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396244	396244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	170	506	0	ENST00000262320.3:c.782C>T	p.Ala261Val	p.A261V	ENST00000262320	NM_003502.3	261	gCt/gTt	2/11	1	2	FACETS	0.84	0.774	0.909	0.84	0.774	0.909	CLONAL	1	TRUE	1	0.519749990206578	2		506	779	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2115611	2115611	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	169	523	0	ENST00000219476.3:c.1691T>C	p.Val564Ala	p.V564A	ENST00000219476	NM_000548.3	564	gTc/gCc	16/42	1	2	FACETS	0.779	0.717	0.844	0.779	0.717	0.844	SUBCLONAL	1	TRUE	1	0.519749990206578	2		523	835	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858274	9858274	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	42	311	0	ENST00000330684.3:c.3127A>G	p.Thr1043Ala	p.T1043A	ENST00000330684	NM_001134407.1	1043	Acc/Gcc	13/13	1	2	FACETS	0.47	0.393	0.554	0.47	0.393	0.554	SUBCLONAL	1	TRUE	1	0.519749990206578	2		311	344	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983346	15983346	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	87	330	0	ENST00000268712.3:c.3433A>G	p.Thr1145Ala	p.T1145A	ENST00000268712	NM_006311.3	1145	Act/Gct	26/46	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.519749990206578	2		330	316	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688767	47688767	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1340081446	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	89	366	0	ENST00000347630.2:c.533T>C	p.Met178Thr	p.M178T	ENST00000347630	NM_001007230.1	178	aTg/aCg	7/11	1	2	FACETS	0.837	0.747	0.933	0.837	0.747	0.933	CLONAL	1	TRUE	1	0.519749990206578	2		366	409	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752465	55752465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1382332810	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	268	587	0	ENST00000284073.2:c.923C>T	p.Ser308Leu	p.S308L	ENST00000284073	NM_138962.2	308	tCg/tTg	12/14	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.519749990206578	2		587	965	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591898	48591898	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	69	377	0	ENST00000342988.3:c.1061T>C	p.Val354Ala	p.V354A	ENST00000342988	NM_005359.5	354	gTg/gCg	9/12	1	2	FACETS	0.797	0.699	0.902	0.797	0.699	0.902	CLONAL	1	TRUE	1	0.519749990206578	2		377	333	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604717	48604717	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	96	339	0	ENST00000342988.3:c.1541del	p.Pro514GlnfsTer23	p.P514Qfs*23	ENST00000342988	NM_005359.5	513	taC/ta	12/12	1	2	FACETS	0.996	0.895	1	0.996	0.895	1	CLONAL	1	TRUE	1	0.519749990206578	2		339	371	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244010	5244010	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	234	575	0	ENST00000357368.4:c.1472T>C	p.Leu491Pro	p.L491P	ENST00000357368	NM_002850.3	491	cTg/cCg	11/38	1	2	FACETS	0.979	0.914	1	0.979	0.914	1	CLONAL	1	TRUE	1	0.519749990206578	2		575	920	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244091	5244091	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	52	609	0	ENST00000357368.4:c.1391A>G	p.Tyr464Cys	p.Y464C	ENST00000357368	NM_002850.3	464	tAc/tGc	11/38	1	2	FACETS	0.214	0.181	0.25	0.214	0.181	0.25	SUBCLONAL	1	TRUE	1	0.519749990206578	2		609	934	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252754	10252754	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	155	489	0	ENST00000340748.4:c.3211T>C	p.Cys1071Arg	p.C1071R	ENST00000340748		1071	Tgc/Cgc	29/40	1	2	FACETS	0.719	0.658	0.782	0.719	0.658	0.782	SUBCLONAL	1	TRUE	1	0.519749990206578	2		489	830	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170549	11170549	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	199	518	0	ENST00000358026.2:c.4852T>C	p.Ser1618Pro	p.S1618P	ENST00000358026	NM_001128849.1	1618	Tcc/Ccc	34/36	1	2	FACETS	0.888	0.824	0.955	0.888	0.824	0.955	CLONAL	1	TRUE	1	0.519749990206578	2		518	862	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288814	15288814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	37	83	0	ENST00000263388.2:c.3925C>T	p.Arg1309Cys	p.R1309C	ENST00000263388	NM_000435.2	1309	Cgc/Tgc	24/33	1	2	FACETS	0.982	0.824	1	0.982	0.824	1	CLONAL	1	TRUE	1	0.519749990206578	2		83	145	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298023	15298023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745672629	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	231	594	0	ENST00000263388.2:c.1733G>A	p.Arg578His	p.R578H	ENST00000263388	NM_000435.2	578	cGc/cAc	11/33	1	2	FACETS	0.943	0.88	1	0.943	0.88	1	CLONAL	1	TRUE	1	0.519749990206578	2		594	943	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741956	40741956	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	189	629	0	ENST00000392038.2:c.1016T>C	p.Val339Ala	p.V339A	ENST00000392038	NM_001626.4	339	gTc/gCc	11/14	1	2	FACETS	0.83	0.768	0.895	0.83	0.768	0.895	CLONAL	1	TRUE	1	0.519749990206578	2		629	876	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905632	50905632	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	207	550	0	ENST00000440232.2:c.758+2T>C		p.X253_splice	ENST00000440232	NM_002691.3	253			1	2	FACETS	0.91	0.846	0.977	0.91	0.846	0.977	CLONAL	1	TRUE	1	0.519749990206578	2		550	875	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47596682	47596682	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs776646187	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	112	207	0	ENST00000263735.4:c.38T>C	p.Leu13Pro	p.L13P	ENST00000263735	NM_002354.2	13	cTt/cCt	1/9	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.519749990206578	2		207	399	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662187	227662187	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs141882284	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	215	624	0	ENST00000305123.5:c.1268G>T	p.Gly423Val	p.G423V	ENST00000305123	NM_005544.2	423	gGc/gTc	1/2	1	2	FACETS	0.984	0.916	1	0.984	0.916	1	CLONAL	1	TRUE	1	0.519749990206578	2		624	841	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524438	44524438	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	55	230	0	ENST00000291552.4:c.119C>T	p.Pro40Leu	p.P40L	ENST00000291552	NM_006758.2	40	cCg/cTg	2/8	1	2	FACETS	0.882	0.763	1	0.882	0.763	1	CLONAL	1	TRUE	1	0.519749990206578	2		230	240	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266904	41266904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	82	325	0	ENST00000349496.5:c.575C>A	p.Pro192His	p.P192H	ENST00000349496	NM_001904.3	192	cCt/cAt	5/15	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.519749990206578	2		325	302	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670327	134670328	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	26	356	0	ENST00000398015.3:c.244dup	p.Ala82GlyfsTer20	p.A82Gfs*20	ENST00000398015	NM_004441.4	80	cgg/cGgg	3/16	1	2	FACETS	0.199	0.157	0.247	0.199	0.157	0.247	SUBCLONAL	1	TRUE	1	0.519749990206578	2		356	504	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231159	142231159	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	116	377	0	ENST00000350721.4:c.4795C>G	p.Leu1599Val	p.L1599V	ENST00000350721	NM_001184.3	1599	Ctg/Gtg	27/47	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.519749990206578	2		377	443	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198036	185198036	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1374039394	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	56	268	0	ENST00000265026.3:c.2518A>G	p.Ser840Gly	p.S840G	ENST00000265026	NM_004721.4	840	Agc/Ggc	13/14	1	2	FACETS	0.826	0.714	0.945	0.826	0.714	0.945	CLONAL	1	TRUE	1	0.519749990206578	2		268	261	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467473	66467473	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	70	257	0	ENST00000273854.3:c.796T>A	p.Ser266Thr	p.S266T	ENST00000273854	NM_004439.5	266	Tct/Act	3/18	1	2	FACETS	0.804	0.706	0.908	0.804	0.706	0.908	CLONAL	1	TRUE	1	0.519749990206578	2		257	335	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157084	106157084	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	91	378	0	ENST00000380013.4:c.1985T>A	p.Phe662Tyr	p.F662Y	ENST00000380013	NM_001127208.2	662	tTc/tAc	3/11	1	2	FACETS	0.844	0.754	0.939	0.844	0.754	0.939	CLONAL	1	TRUE	1	0.519749990206578	2		378	415	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332775	153332777	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	91	421	0	ENST00000281708.4:c.179_181del	p.Val60del	p.V60del	ENST00000281708	NM_033632.3	60	gTTGga/gga	2/12	1	2	FACETS	0.907	0.811	1	0.907	0.811	1	CLONAL	1	TRUE	1	0.519749990206578	2		421	386	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515123	31515123	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	44	466	0	ENST00000344624.3:c.1262A>G	p.Tyr421Cys	p.Y421C	ENST00000344624		421	tAc/tGc	5/33	1	2	FACETS	0.338	0.283	0.399	0.338	0.283	0.399	SUBCLONAL	1	TRUE	1	0.519749990206578	2		466	501	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818747	170818747	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	14	265	0	ENST00000296930.5:c.296T>C	p.Val99Ala	p.V99A	ENST00000296930	NM_002520.6	99	gTc/gCc	4/11	1	2	FACETS	0.193	0.139	0.259	0.193	0.139	0.259	SUBCLONAL	1	TRUE	1	0.519749990206578	2		265	279	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910783	29910783	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs281864743	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	75	430	0	ENST00000376809.5:c.323A>G	p.Tyr108Cys	p.Y108C	ENST00000376809	NM_002116.7	108	tAc/tGc	2/8	0.506097091982149	2	FACETS	0.595	0.523	0.672	0.298	0.261	0.336	SUBCLONAL	1	TRUE	0	0.519749990206578	2		430	485	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323958	31323959	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	rs761596463	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	109	367	0	ENST00000412585.2:c.604_605del	p.Lys202AlafsTer5	p.K202Afs*5	ENST00000412585	NM_005514.6	202	AAg/g	3/8	0.506097091982149	2	FACETS	1	0.921	1	0.51	0.461	0.561	CLONAL	1	TRUE	0	0.519749990206578	2		367	411	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004499	150004499	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	116	504	0	ENST00000253339.5:c.1726A>T	p.Ile576Phe	p.I576F	ENST00000253339		576	Atc/Ttc	3/7	1	2	FACETS	0.806	0.729	0.886	0.806	0.729	0.886	CLONAL	1	TRUE	1	0.519749990206578	2		504	554	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420051	152420051	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	132	392	0	ENST00000206249.3:c.1738C>T	p.Gln580Ter	p.Q580*	ENST00000206249	NM_000125.3	580	Caa/Taa	8/8	1	2	FACETS	0.925	0.844	1	0.925	0.844	1	CLONAL	1	TRUE	1	0.519749990206578	2		392	549	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864373	162864373	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	108	355	0	ENST00000366898.1:c.140G>T	p.Gly47Val	p.G47V	ENST00000366898	NM_004562.2	47	gGg/gTg	2/12	1	2	FACETS	0.756	0.68	0.835	0.756	0.68	0.835	SUBCLONAL	1	TRUE	1	0.519749990206578	2		355	550	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873371	151873371	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	75	252	0	ENST00000262189.6:c.9167A>G	p.Gln3056Arg	p.Q3056R	ENST00000262189	NM_170606.2	3056	cAg/cGg	38/59	1	2	FACETS	0.968	0.857	1	0.968	0.857	1	CLONAL	1	TRUE	1	0.519749990206578	2		252	298	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209559	98209559	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs761753681	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	148	480	0	ENST00000331920.6:c.3979A>G	p.Thr1327Ala	p.T1327A	ENST00000331920	NM_000264.3	1327	Act/Gct	23/24	1	2	FACETS	0.78	0.714	0.849	0.78	0.714	0.849	SUBCLONAL	1	TRUE	1	0.519749990206578	2		480	730	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20150350	20150350	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	81	285	0	ENST00000379607.5:c.287A>G	p.Asn96Ser	p.N96S	ENST00000379607	NM_001412.3	96	aAt/aGt	5/7	1	2	FACETS	0.98	0.872	1	0.98	0.872	1	CLONAL	1	TRUE	1	0.519749990206578	2		285	318	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411314	63411314	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	152	544	1	ENST00000330258.3:c.1853C>T	p.Ala618Val	p.A618V	ENST00000330258	NM_152424.3	618	gCt/gTt	2/2	0.312066526664976	1	FACETS	0.606	0.556	0.659	0.606	0.556	0.659	SUBCLONAL	1	TRUE	0	0.519749990206578	1		545	714	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	66	267	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.995	0.87	1	0.995	0.87	1	CLONAL	1	TRUE	1	0.430875847721497	2		267	308	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	100	428	2	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.853	0.765	0.947	0.853	0.765	0.947	CLONAL	1	TRUE	1	0.430875847721497	2		430	544	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	62	668	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.637	0.551	0.729	0.637	0.551	0.729	SUBCLONAL	1	TRUE	1	0.430875847721497	2		673	452	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	68	470	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.387	0.336	0.443	0.387	0.336	0.443	SUBCLONAL	1	TRUE	1	0.430875847721497	2		472	815	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	130	334	1	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.901	0.819	0.987	0.901	0.819	0.987	CLONAL	1	TRUE	1	0.430875847721497	2		335	670	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	87	603	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.572	0.506	0.642	0.572	0.506	0.642	SUBCLONAL	1	TRUE	1	0.430875847721497	2		603	706	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	206	429	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.354925578861087	3	FACETS	0.873	0.813	0.933	0.873	0.813	0.933	CLONAL	2	TRUE	1	0.430875847721497	3		429	666	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	145	682	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	0.428181815387699	4	FACETS	0.775	0.706	0.849	0.258	0.235	0.283	SUBCLONAL	1	TRUE	1	0.430875847721497	4		683	1242	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	58	525	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	0.380057025590559	2	FACETS	0.343	0.294	0.397	0.172	0.147	0.199	SUBCLONAL	1	TRUE	0	0.430875847721497	2		527	784	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981832	63981832	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	41	621	3	ENST00000398590.3:c.2340del	p.Thr781ProfsTer11	p.T781Pfs*11	ENST00000398590	NM_001177387.1	778	ggC/gg	12/14	1	2	FACETS	0.249	0.207	0.297	0.249	0.207	0.297	SUBCLONAL	1	TRUE	1	0.430875847721497	2		624	764	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	135	399	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.405607956154164	3	FACETS	1	0.972	1	0.582	0.53	0.636	CLONAL	1	TRUE	1	0.430875847721497	3		399	654	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	107	462	1	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	0.818	0.736	0.906	0.818	0.736	0.906	CLONAL	1	TRUE	1	0.430875847721497	2		463	607	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	134	548	1	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	1	2	FACETS	0.782	0.711	0.857	0.782	0.711	0.857	SUBCLONAL	1	TRUE	1	0.430875847721497	2		549	795	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	185	581	0	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	0.97	0.897	1	0.97	0.897	1	CLONAL	1	TRUE	1	0.430875847721497	2		581	885	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	86	436	1	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.695	0.616	0.78	0.695	0.616	0.78	SUBCLONAL	1	TRUE	1	0.430875847721497	2		437	574	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	18	306	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.272	0.204	0.352	0.272	0.204	0.352	SUBCLONAL	1	TRUE	1	0.430875847721497	2		306	307	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431874	49431874	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	56	634	5	ENST00000301067.7:c.9265del	p.Val3089TrpfsTer30	p.V3089Wfs*30	ENST00000301067	NM_003482.3	3089	Gtg/tg	34/54	1	2	FACETS	0.341	0.291	0.395	0.341	0.291	0.395	SUBCLONAL	1	TRUE	1	0.430875847721497	2		639	763	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440757	56440757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774211426	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	174	531	0	ENST00000407977.2:c.461C>T	p.Pro154Leu	p.P154L	ENST00000407977		154	cCg/cTg	5/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.430875847721497	2		531	770	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447773	49447773	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	68	455	0	ENST00000301067.7:c.661del	p.Ala221LeufsTer40	p.A221Lfs*40	ENST00000301067	NM_003482.3	221	Gct/ct	5/54	1	2	FACETS	0.519	0.452	0.592	0.519	0.452	0.592	SUBCLONAL	1	TRUE	1	0.430875847721497	2		455	608	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186679	11186679	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	116	407	0	ENST00000361445.4:c.6526G>T	p.Gly2176Cys	p.G2176C	ENST00000361445	NM_004958.3	2176	Ggc/Tgc	46/58	1	2	FACETS	0.958	0.867	1	0.958	0.867	1	CLONAL	1	TRUE	1	0.430875847721497	2		407	562	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306942	65306942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776082057	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	112	470	0	ENST00000342505.4:c.2635C>T	p.Arg879Cys	p.R879C	ENST00000342505	NM_002227.2	879	Cgt/Tgt	19/25	1	2	FACETS	0.828	0.746	0.914	0.828	0.746	0.914	CLONAL	1	TRUE	1	0.430875847721497	2		470	628	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458380	120458380	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	115	769	0	ENST00000256646.2:c.6965C>A	p.Pro2322His	p.P2322H	ENST00000256646	NM_024408.3	2322	cCc/cAc	34/34	1	2	FACETS	0.615	0.553	0.68	0.615	0.553	0.68	SUBCLONAL	1	TRUE	1	0.430875847721497	2		769	868	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838439	156838439	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	57	604	0	ENST00000524377.1:c.717G>T	p.Met239Ile	p.M239I	ENST00000524377	NM_002529.3	239	atG/atT	6/17	0.243251520951227	3	FACETS	0.427	0.365	0.495	0.214	0.182	0.248	INDETERMINATE	1	TRUE	1	0.430875847721497	3		604	753	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957465	175957465	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	143	384	1	ENST00000367669.3:c.1931del	p.Asn644ThrfsTer3	p.N644Tfs*3	ENST00000367669	NM_022457.5	644	aAc/ac	17/20	0.243251520951227	3	FACETS	1	0.987	1	0.737	0.676	0.801	INDETERMINATE	1	TRUE	1	0.430875847721497	3		385	547	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942053	71942053	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	51	580	0	ENST00000298229.2:c.1322del	p.Asn441ThrfsTer2	p.N441Tfs*2	ENST00000298229	NM_001567.3	439	ccA/cc	12/28	1	2	FACETS	0.315	0.267	0.368	0.315	0.267	0.368	SUBCLONAL	1	TRUE	1	0.430875847721497	2		580	752	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948208	71948209	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs749079348	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	113	546	1	ENST00000298229.2:c.2927dup	p.Pro977ThrfsTer7	p.P977Tfs*7	ENST00000298229	NM_001567.3	974	gcc/gCcc	26/28	1	2	FACETS	0.817	0.737	0.902	0.817	0.737	0.902	CLONAL	1	TRUE	1	0.430875847721497	2		547	642	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94211915	94211915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773766504	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	52	378	0	ENST00000323929.3:c.530C>T	p.Ala177Val	p.A177V	ENST00000323929	NM_005591.3	177	gCg/gTg	6/20	1	2	FACETS	0.684	0.585	0.792	0.684	0.585	0.792	SUBCLONAL	1	TRUE	1	0.430875847721497	2		378	353	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448526	49448526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371342351	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	138	526	0	ENST00000301067.7:c.185C>T	p.Pro62Leu	p.P62L	ENST00000301067	NM_003482.3	62	cCg/cTg	3/54	1	2	FACETS	0.852	0.776	0.931	0.852	0.776	0.931	CLONAL	1	TRUE	1	0.430875847721497	2		526	752	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911443	32911443	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359365	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	67	460	0	ENST00000380152.3:c.2957del	p.Asn986IlefsTer5	p.N986Ifs*5	ENST00000380152		984	gAa/ga	11/27	1	2	FACETS	0.854	0.747	0.97	0.854	0.747	0.97	CLONAL	1	TRUE	1	0.430875847721497	2		460	364	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609934	81609934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369995834	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	178	662	0	ENST00000298171.2:c.1532C>T	p.Thr511Met	p.T511M	ENST00000298171	NM_000369.2	511	aCg/aTg	10/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.430875847721497	2		662	802	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213932	2213932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	144	493	1	ENST00000326181.6:c.11G>A	p.Gly4Asp	p.G4D	ENST00000326181	NM_032271.2	4	gGc/gAc	2/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.430875847721497	2		494	602	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943641	9943641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	49	461	0	ENST00000330684.3:c.1300G>A	p.Val434Met	p.V434M	ENST00000330684	NM_001134407.1	434	Gtg/Atg	5/13	1	2	FACETS	0.321	0.271	0.376	0.321	0.271	0.376	SUBCLONAL	1	TRUE	1	0.430875847721497	2		461	708	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991695	72991695	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1383503121	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	170	610	0	ENST00000268489.5:c.2350G>A	p.Ala784Thr	p.A784T	ENST00000268489	NM_006885.3	784	Gcc/Acc	2/10	1	2	FACETS	0.912	0.839	0.988	0.912	0.839	0.988	CLONAL	1	TRUE	1	0.430875847721497	2		610	865	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351041	89351042	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	122	537	0	ENST00000301030.4:c.1908_1909del	p.His636GlnfsTer26	p.H636Qfs*26	ENST00000301030	NM_001256183.1	636	caCAaa/caaa	9/13	1	2	FACETS	0.833	0.754	0.916	0.833	0.754	0.916	CLONAL	1	TRUE	1	0.430875847721497	2		537	680	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964780	15964780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1001018811	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	60	472	0	ENST00000268712.3:c.5816G>A	p.Arg1939Gln	p.R1939Q	ENST00000268712	NM_006311.3	1939	cGg/cAg	37/46	1	2	FACETS	0.45	0.387	0.518	0.45	0.387	0.518	SUBCLONAL	1	TRUE	1	0.430875847721497	2		472	619	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687514	37687514	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	49	505	0	ENST00000447079.4:c.4422del	p.Pro1475LeufsTer24	p.P1475Lfs*24	ENST00000447079	NM_015083.1	1473	cGg/cg	14/14	1	2	FACETS	0.337	0.285	0.395	0.337	0.285	0.395	SUBCLONAL	1	TRUE	1	0.430875847721497	2		505	675	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530163	63530163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145007501	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	111	418	0	ENST00000307078.5:c.2272G>A	p.Ala758Thr	p.A758T	ENST00000307078	NM_004655.3	758	Gcg/Acg	10/11	1	2	FACETS	0.882	0.795	0.974	0.882	0.795	0.974	CLONAL	1	TRUE	1	0.430875847721497	2		418	584	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584514	48584514	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	74	433	1	ENST00000342988.3:c.692del	p.Gly231AlafsTer10	p.G231Afs*10	ENST00000342988	NM_005359.5	229	ctG/ct	6/12	1	2	FACETS	0.574	0.503	0.651	0.574	0.503	0.651	SUBCLONAL	1	TRUE	1	0.430875847721497	2		434	598	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101031	4101031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375843855	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	120	364	0	ENST00000262948.5:c.691C>T	p.Arg231Cys	p.R231C	ENST00000262948	NM_030662.3	231	Cgc/Tgc	6/11	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.430875847721497	2		364	557	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223152	5223152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745426688	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	135	608	0	ENST00000357368.4:c.2651C>T	p.Pro884Leu	p.P884L	ENST00000357368	NM_002850.3	884	cCg/cTg	18/38	1	2	FACETS	0.951	0.866	1	0.951	0.866	1	CLONAL	1	TRUE	1	0.430875847721497	2		608	659	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	28	164	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.512	0.41	0.626	0.512	0.41	0.626	SUBCLONAL	1	TRUE	1	0.430875847721497	2		164	254	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240270	5240271	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1568455650	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	99	471	0	ENST00000357368.4:c.1643dup	p.Arg549AlafsTer78	p.R549Afs*78	ENST00000357368	NM_002850.3	548	ccg/ccCg	12/38	1	2	FACETS	0.738	0.659	0.82	0.738	0.659	0.82	SUBCLONAL	1	TRUE	1	0.430875847721497	2		471	623	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141426	11141426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	116	442	0	ENST00000358026.2:c.3403C>T	p.Arg1135Trp	p.R1135W	ENST00000358026	NM_001128849.1	1135	Cgg/Tgg	25/36	1	2	FACETS	0.836	0.755	0.921	0.836	0.755	0.921	CLONAL	1	TRUE	1	0.430875847721497	2		442	644	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141541	11141541	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	165	474	0	ENST00000358026.2:c.3522del	p.Phe1174LeufsTer42	p.F1174Lfs*42	ENST00000358026	NM_001128849.1	1173	aTt/at	25/36	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.430875847721497	2		474	699	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256769	19256769	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	127	618	3	ENST00000162023.5:c.944del	p.Pro315GlnfsTer?	p.P315Qfs*?	ENST00000162023		315	cCa/ca	13/13	1	2	FACETS	0.798	0.723	0.876	0.798	0.723	0.876	SUBCLONAL	1	TRUE	1	0.430875847721497	2		621	739	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216649	36216649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764567889	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	486	532	0	ENST00000222270.7:c.3815G>A	p.Arg1272His	p.R1272H	ENST00000222270	NM_014727.1	1272	cGc/cAc	13/37	0.428181815387699	4	FACETS	0.989	0.949	1	0.989	0.949	1	CLONAL	3	TRUE	1	0.430875847721497	4		532	1088	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223619	36223619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769427218	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	189	721	0	ENST00000222270.7:c.6169C>T	p.Arg2057Cys	p.R2057C	ENST00000222270	NM_014727.1	2057	Cgc/Tgc	28/37	0.428181815387699	4	FACETS	1	0.945	1	0.343	0.316	0.371	CLONAL	1	TRUE	1	0.430875847721497	4		721	1219	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046289	128046289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746827111	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	232	425	0	ENST00000285398.2:c.974G>A	p.Arg325Gln	p.R325Q	ENST00000285398	NM_000122.1	325	cGa/cAa	7/15	0.354925578861087	3	FACETS	0.831	0.777	0.886	0.831	0.777	0.886	CLONAL	2	TRUE	1	0.430875847721497	3		425	788	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29445543	29445543	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	134	599	0	ENST00000544604.2:c.1374G>T	p.Lys458Asn	p.K458N	ENST00000544604	NM_001206998.1	458	aaG/aaT	8/9	0.405607956154164	3	FACETS	0.997	0.907	1	0.499	0.453	0.546	CLONAL	1	TRUE	1	0.430875847721497	3		599	758	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446595	29446595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1236517906	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	83	524	1	ENST00000544604.2:c.2426C>T	p.Thr809Met	p.T809M	ENST00000544604	NM_001206998.1	809	aCg/aTg	8/9	0.405607956154164	3	FACETS	0.671	0.592	0.756	0.335	0.296	0.378	SUBCLONAL	1	TRUE	1	0.430875847721497	3		525	698	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981618	63981618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368917711	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	158	592	0	ENST00000398590.3:c.2120G>A	p.Arg707His	p.R707H	ENST00000398590	NM_001177387.1	707	cGc/cAc	12/14	1	2	FACETS	0.925	0.848	1	0.925	0.848	1	CLONAL	1	TRUE	1	0.430875847721497	2		592	793	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281841	142281842	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1172524685	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	58	378	0	ENST00000350721.4:c.402dup	p.Lys135Ter	p.K135*	ENST00000350721	NM_001184.3	134	-/T	4/47	0.405607956154164	3	FACETS	0.624	0.537	0.72	0.312	0.268	0.36	SUBCLONAL	1	TRUE	1	0.430875847721497	3		378	524	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683523	182683523	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	123	327	0	ENST00000292782.4:c.22C>T	p.Gln8Ter	p.Q8*	ENST00000292782	NM_020640.2	8	Cag/Tag	2/7	0.405607956154164	3	FACETS	0.883	0.806	0.962	0.883	0.806	0.962	CLONAL	2	TRUE	1	0.430875847721497	3		327	393	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447721	187447721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746850741	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	124	604	0	ENST00000232014.4:c.472C>T	p.Arg158Trp	p.R158W	ENST00000232014	NM_001130845.1	158	Cgg/Tgg	5/10	0.405607956154164	3	FACETS	0.788	0.712	0.868	0.394	0.356	0.434	SUBCLONAL	1	TRUE	1	0.430875847721497	3		604	888	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161690	56161690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	48	347	0	ENST00000399503.3:c.1187G>A	p.Arg396His	p.R396H	ENST00000399503	NM_005921.1	396	cGt/cAt	6/20	1	2	FACETS	0.553	0.468	0.646	0.553	0.468	0.646	SUBCLONAL	1	TRUE	1	0.430875847721497	2		347	403	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562321	176562321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	116	449	0	ENST00000439151.2:c.217C>T	p.Arg73Trp	p.R73W	ENST00000439151	NM_022455.4	73	Cgg/Tgg	2/23	1	2	FACETS	0.953	0.862	1	0.953	0.862	1	CLONAL	1	TRUE	1	0.430875847721497	2		449	565	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225647	26225647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746543899	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	203	724	0	ENST00000360408.1:c.265G>A	p.Ala89Thr	p.A89T	ENST00000360408	NM_003532.2	89	Gcg/Acg	1/1	1	2	FACETS	0.932	0.864	1	0.932	0.864	1	CLONAL	1	TRUE	1	0.430875847721497	2		724	1011	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519224	137519224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55924399	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	100	420	0	ENST00000367739.4:c.1414G>A	p.Gly472Ser	p.G472S	ENST00000367739	NM_000416.2	472	Ggt/Agt	7/7	1	2	FACETS	0.912	0.818	1	0.912	0.818	1	CLONAL	1	TRUE	1	0.430875847721497	2		420	509	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099718	157099718	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	64	299	0	ENST00000346085.5:c.659del	p.Gly220AlafsTer46	p.G220Afs*46	ENST00000346085	NM_020732.3	219	Ggg/gg	1/20	1	2	FACETS	0.887	0.773	1	0.887	0.773	1	CLONAL	1	TRUE	1	0.430875847721497	2		299	335	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528064	157528065	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	143	572	0	ENST00000346085.5:c.5791_5792del	p.Leu1931ValfsTer12	p.L1931Vfs*12	ENST00000346085	NM_020732.3	1930	cCT/c	20/20	1	2	FACETS	0.879	0.803	0.959	0.879	0.803	0.959	CLONAL	1	TRUE	1	0.430875847721497	2		572	755	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946171	13946171	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	104	419	0	ENST00000405192.2:c.925C>T	p.Arg309Ter	p.R309*	ENST00000405192	NM_001163147.1	309	Cga/Tga	10/12	1	2	FACETS	0.904	0.812	1	0.904	0.812	1	CLONAL	1	TRUE	1	0.430875847721497	2		419	534	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148513822	148513822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201135441	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	49	394	0	ENST00000320356.2:c.1459G>A	p.Ala487Thr	p.A487T	ENST00000320356	NM_004456.4	487	Gct/Act	12/20	1	2	FACETS	0.422	0.357	0.493	0.422	0.357	0.493	SUBCLONAL	1	TRUE	1	0.430875847721497	2		394	539	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848622	151848622	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376118166	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	101	418	0	ENST00000262189.6:c.12571G>A	p.Ala4191Thr	p.A4191T	ENST00000262189	NM_170606.2	4191	Gca/Aca	50/59	1	2	FACETS	0.936	0.84	1	0.936	0.84	1	CLONAL	1	TRUE	1	0.430875847721497	2		418	501	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	46	678	3	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	0.289	0.243	0.341	0.289	0.243	0.341	SUBCLONAL	1	TRUE	1	0.430875847721497	2		681	738	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982013	70982013	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1262764228	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	148	507	0	ENST00000276594.2:c.83C>T	p.Ala28Val	p.A28V	ENST00000276594	NM_024504.3	28	gCg/gTg	2/8	1	2	FACETS	0.997	0.913	1	0.997	0.913	1	CLONAL	1	TRUE	1	0.430875847721497	2		507	689	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753073	128753073	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	132	494	1	ENST00000377970.2:c.1239del	p.Ala414ProfsTer29	p.A414Pfs*29	ENST00000377970	NM_002467.4	412	Aaa/aa	3/3	1	2	FACETS	0.875	0.796	0.958	0.875	0.796	0.958	CLONAL	1	TRUE	1	0.430875847721497	2		495	700	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737320	145737320	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	74	583	0	ENST00000428558.2:c.3367C>T	p.Gln1123Ter	p.Q1123*	ENST00000428558	NM_004260.3	1123	Cag/Tag	20/22	1	2	FACETS	0.544	0.476	0.617	0.544	0.476	0.617	SUBCLONAL	1	TRUE	1	0.430875847721497	2		583	631	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2081995	2081995	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1554623112	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	65	393	0	ENST00000349721.2:c.2348C>T	p.Ser783Leu	p.S783L	ENST00000349721	NM_003070.3	783	tCg/tTg	15/34	1	2	FACETS	0.625	0.543	0.713	0.625	0.543	0.713	SUBCLONAL	1	TRUE	1	0.430875847721497	2		393	483	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	120	585	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	0.430875847721497	1	FACETS	0.78	0.707	0.857	0.78	0.707	0.857	SUBCLONAL	1	TRUE	0	0.430875847721497	1		585	560	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399420	139399420	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	141	541	1	ENST00000277541.6:c.4723G>C	p.Val1575Leu	p.V1575L	ENST00000277541	NM_017617.3	1575	Gtg/Ctg	26/34	1	2	FACETS	0.866	0.79	0.945	0.866	0.79	0.945	CLONAL	1	TRUE	1	0.430875847721497	2		542	756	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006896	47006896	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	121	445	0	ENST00000377604.3:c.16C>T	p.Arg6Cys	p.R6C	ENST00000377604	NM_001204468.1	6	Cgt/Tgt	2/24	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.430875847721497	2		445	539	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617582	100617582	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs782454588	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	103	441	0	ENST00000308731.7:c.487A>G	p.Met163Val	p.M163V	ENST00000308731	NM_000061.2	163	Atg/Gtg	6/19	1	2	FACETS	0.806	0.723	0.894	0.806	0.723	0.894	CLONAL	1	TRUE	1	0.430875847721497	2		441	593	SUCCESS
PHF6	84295	MSKCC	GRCh37	X	133549141	133549141	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	29	270	0	ENST00000332070.3:c.829del	p.Arg277GlufsTer2	p.R277Efs*2	ENST00000332070	NM_032458.2	275	ggA/gg	8/10	1	2	FACETS	0.526	0.424	0.641	0.526	0.424	0.641	SUBCLONAL	1	TRUE	1	0.430875847721497	2		270	256	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2039796	2039796	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs184126259	NA	P-0058060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	141	623	15	ENST00000349721.2:c.686A>C	p.Gln229Pro	p.Q229P	ENST00000349721	NM_003070.3	229	cAg/cCg	4/34	1	2	FACETS	0.785	0.715	0.858	0.785	0.715	0.858	SUBCLONAL	1	TRUE	1	0.430875847721497	2		638	834	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059170	42059170	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs756744691	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	223	792	1	ENST00000219905.7:c.8895del	p.Thr2966ProfsTer4	p.T2966Pfs*4	ENST00000219905	NM_001164273.1	2964	Ccc/cc	24/24	1	2	FACETS	0.832	0.777	0.889	0.832	0.777	0.889	CLONAL	1	TRUE	1	0.685269602929567	2		793	782	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217623	7217623	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	188	537	0	ENST00000380728.2:c.304C>T	p.Arg102Ter	p.R102*	ENST00000380728		102	Cga/Tga	4/11	0.628475936836578	1	FACETS	0.884	0.828	0.94	0.884	0.828	0.94	CLONAL	1	TRUE	0	0.685269602929567	1		537	408	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	289	817	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.628475936836578	1	FACETS	0.987	0.938	1	0.987	0.938	1	CLONAL	1	TRUE	0	0.685269602929567	1		817	562	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	86	503	4	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	0.280308477975498	2	FACETS	0.421	0.373	0.473	0.211	0.186	0.237	INDETERMINATE	1	TRUE	0	0.685269602929567	2		507	596	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114817	108114817	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786204543	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	94	351	0	ENST00000278616.4:c.640del	p.Ser214ProfsTer16	p.S214Pfs*16	ENST00000278616	NM_000051.3	212	Ttt/tt	6/63	1	2	FACETS	0.855	0.769	0.944	0.855	0.769	0.944	CLONAL	1	TRUE	1	0.685269602929567	2		351	321	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2493146	2493146	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs959689708	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	159	484	0	ENST00000355716.4:c.586A>G	p.Thr196Ala	p.T196A	ENST00000355716	NM_003820.2	196	Acc/Gcc	6/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.685269602929567	2		484	447	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199670	11199670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766533620	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	188	543	1	ENST00000361445.4:c.4918C>T	p.Arg1640Trp	p.R1640W	ENST00000361445	NM_004958.3	1640	Cgg/Tgg	35/58	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.685269602929567	2		544	534	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263839	16263839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs549789481	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	267	858	0	ENST00000375759.3:c.10208G>A	p.Arg3403His	p.R3403H	ENST00000375759	NM_015001.2	3403	cGc/cAc	12/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.685269602929567	2		858	705	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057937	27057937	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	61	804	1	ENST00000324856.7:c.1650del	p.Tyr551ThrfsTer68	p.Y551Tfs*68	ENST00000324856	NM_006015.4	549	Ccc/cc	3/20	1	2	FACETS	0.226	0.194	0.26	0.226	0.194	0.26	SUBCLONAL	1	TRUE	1	0.685269602929567	2		805	789	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106078	27106078	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	234	768	0	ENST00000324856.7:c.5693del	p.Pro1898HisfsTer25	p.P1898Hfs*25	ENST00000324856	NM_006015.4	1897	Ccc/cc	20/20	1	2	FACETS	0.883	0.827	0.941	0.883	0.827	0.941	CLONAL	1	TRUE	1	0.685269602929567	2		768	773	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726261	46726261	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	82	557	1	ENST00000371975.4:c.455T>G	p.Val152Gly	p.V152G	ENST00000371975	NM_003579.3	152	gTt/gGt	6/18	1	2	FACETS	0.434	0.383	0.489	0.434	0.383	0.489	SUBCLONAL	1	TRUE	1	0.685269602929567	2		558	551	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439843	51439843	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	80	575	0	ENST00000262662.1:c.412del	p.Asp138ThrfsTer18	p.D138Tfs*18	ENST00000262662		136	aaG/aa	4/4	1	2	FACETS	0.351	0.309	0.396	0.351	0.309	0.396	SUBCLONAL	1	TRUE	1	0.685269602929567	2		575	665	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104359285	104359285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746448939	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	70	499	0	ENST00000369902.3:c.1006G>A	p.Ala336Thr	p.A336T	ENST00000369902	NM_016169.3	336	Gcc/Acc	8/12	1	2	FACETS	0.36	0.314	0.409	0.36	0.314	0.409	SUBCLONAL	1	TRUE	1	0.685269602929567	2		499	568	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123246935	123246935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113014479	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	148	464	0	ENST00000358487.5:c.1990C>T	p.Arg664Trp	p.R664W	ENST00000358487	NM_000141.4	664	Cgg/Tgg	15/18	1	2	FACETS	0.896	0.825	0.97	0.896	0.825	0.97	CLONAL	1	TRUE	1	0.685269602929567	2		464	482	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098609	108098609	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	60	283	0	ENST00000278616.4:c.183del	p.Phe61LeufsTer15	p.F61Lfs*15	ENST00000278616	NM_000051.3	60	gTt/gt	3/63	1	2	FACETS	0.871	0.763	0.985	0.871	0.763	0.985	CLONAL	1	TRUE	1	0.685269602929567	2		283	201	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	164	745	4	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	1	2	FACETS	0.646	0.594	0.7	0.646	0.594	0.7	SUBCLONAL	1	TRUE	1	0.685269602929567	2		749	741	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1034620	1034620	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372461582	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	117	425	0	ENST00000358495.3:c.539G>A	p.Arg180His	p.R180H	ENST00000358495	NM_134424.2	180	cGc/cAc	7/12	1	2	FACETS	0.749	0.68	0.821	0.749	0.68	0.821	SUBCLONAL	1	TRUE	1	0.685269602929567	2		425	456	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562622	21562622	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	83	433	2	ENST00000382592.4:c.1297A>G	p.Thr433Ala	p.T433A	ENST00000382592	NM_014572.2	433	Acg/Gcg	4/8	0.470842562382418	1	FACETS	0.478	0.426	0.534	0.478	0.426	0.534	SUBCLONAL	1	TRUE	0	0.685269602929567	1		435	333	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880863	28880863	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	49	613	0	ENST00000282397.4:c.3767A>C	p.Lys1256Thr	p.K1256T	ENST00000282397	NM_002019.4	1256	aAg/aCg	29/30	0.470842562382418	1	FACETS	0.179	0.151	0.209	0.179	0.151	0.209	SUBCLONAL	1	TRUE	0	0.685269602929567	1		613	526	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435708	110435708	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	125	611	0	ENST00000375856.3:c.2693T>G	p.Leu898Arg	p.L898R	ENST00000375856	NM_003749.2	898	cTg/cGg	1/2	0.685269602929567	1	FACETS	0.908	0.839	0.978	0.908	0.839	0.978	CLONAL	1	TRUE	0	0.685269602929567	1		611	264	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574405	95574405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	119	334	0	ENST00000393063.1:c.2462G>A	p.Arg821His	p.R821H	ENST00000393063	NM_030621.3	821	cGc/cAc	17/28	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.685269602929567	2		334	347	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652269	3652269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752160984	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	211	615	1	ENST00000294008.3:c.800C>T	p.Ala267Val	p.A267V	ENST00000294008	NM_032444.2	267	gCg/gTg	4/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.685269602929567	2		616	591	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3827631	3827631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141098117	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	147	417	2	ENST00000262367.5:c.2141G>A	p.Arg714His	p.R714H	ENST00000262367	NM_004380.2	714	cGc/cAc	11/31	1	2	FACETS	0.879	0.808	0.952	0.879	0.808	0.952	CLONAL	1	TRUE	1	0.685269602929567	2		419	488	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	167	655	3	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	0.894	0.827	0.964	0.894	0.827	0.964	CLONAL	1	TRUE	1	0.685269602929567	2		658	545	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830135	72830135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	201	654	0	ENST00000268489.5:c.6446G>A	p.Arg2149His	p.R2149H	ENST00000268489	NM_006885.3	2149	cGc/cAc	9/10	1	2	FACETS	0.991	0.924	1	0.991	0.924	1	CLONAL	1	TRUE	1	0.685269602929567	2		654	592	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485767	40485767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567718244	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	167	512	0	ENST00000264657.5:c.973C>T	p.Arg325Trp	p.R325W	ENST00000264657	NM_139276.2	325	Cgg/Tgg	10/24	1	2	FACETS	0.904	0.836	0.974	0.904	0.836	0.974	CLONAL	1	TRUE	1	0.685269602929567	2		512	539	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244523	41244523	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	90	401	1	ENST00000357654.3:c.3025T>C	p.Ser1009Pro	p.S1009P	ENST00000357654	NM_007294.3	1009	Tca/Cca	10/23	1	2	FACETS	0.734	0.656	0.815	0.734	0.656	0.815	SUBCLONAL	1	TRUE	1	0.685269602929567	2		402	358	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229533	5229533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1259120475	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	154	502	0	ENST00000357368.4:c.2318G>A	p.Arg773His	p.R773H	ENST00000357368	NM_002850.3	773	cGc/cAc	15/38	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.685269602929567	2		502	416	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367924	15367924	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs201081104	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	225	561	0	ENST00000263377.2:c.1402G>C	p.Val468Leu	p.V468L	ENST00000263377	NM_058243.2	468	Gtg/Ctg	8/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.685269602929567	2		561	612	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	186	749	1	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.765	0.708	0.823	0.765	0.708	0.823	SUBCLONAL	1	TRUE	1	0.685269602929567	2		750	710	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229342	36229342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	212	680	1	ENST00000222270.7:c.8032C>T	p.Arg2678Cys	p.R2678C	ENST00000222270	NM_014727.1	2678	Cgc/Tgc	37/37	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.685269602929567	2		681	589	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796882	42796883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761345552	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	280	926	3	ENST00000575354.2:c.3347dup	p.Ser1117LysfsTer34	p.S1117Kfs*34	ENST00000575354	NM_015125.3	1114	gcc/gCcc	14/20	1	2	FACETS	0.903	0.85	0.957	0.903	0.85	0.957	CLONAL	1	TRUE	1	0.685269602929567	2		929	905	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028057	48028057	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1356451622	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	58	501	0	ENST00000234420.5:c.2935C>G	p.Leu979Val	p.L979V	ENST00000234420	NM_000179.2	979	Ctg/Gtg	4/10	1	2	FACETS	0.371	0.319	0.428	0.371	0.319	0.428	SUBCLONAL	1	TRUE	1	0.685269602929567	2		501	456	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368445	225368445	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	91	293	0	ENST00000264414.4:c.1301A>C	p.Gln434Pro	p.Q434P	ENST00000264414	NM_003590.4	434	cAa/cCa	9/16	1	2	FACETS	0.973	0.876	1	0.973	0.876	1	CLONAL	1	TRUE	1	0.685269602929567	2		293	273	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389135	31389135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1165118132	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	179	604	0	ENST00000328111.2:c.2048G>A	p.Arg683His	p.R683H	ENST00000328111	NM_006892.3	683	cGc/cAc	19/23	1	2	FACETS	0.859	0.796	0.924	0.859	0.796	0.924	CLONAL	1	TRUE	1	0.685269602929567	2		604	608	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743859	40743859	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369430281	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	153	476	2	ENST00000373198.4:c.3136C>T	p.Arg1046Cys	p.R1046C	ENST00000373198	NM_133170.3	1046	Cgc/Tgc	23/32	1	2	FACETS	0.95	0.876	1	0.95	0.876	1	CLONAL	1	TRUE	1	0.685269602929567	2		478	470	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72891538	72891538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs529764235	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	44	425	0	ENST00000325599.8:c.224G>A	p.Arg75His	p.R75H	ENST00000325599	NM_018130.2	75	cGc/cAc	3/11	1	2	FACETS	0.244	0.204	0.288	0.244	0.204	0.288	SUBCLONAL	1	TRUE	1	0.685269602929567	2		425	526	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138402522	138402522	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	62	208	0	ENST00000289153.2:c.2423A>G	p.Asp808Gly	p.D808G	ENST00000289153	NM_006219.2	808	gAt/gGt	16/22	1	2	FACETS	0.887	0.779	1	0.887	0.779	1	CLONAL	1	TRUE	1	0.685269602929567	2		208	204	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1959734	1959734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	80	532	0	ENST00000382891.5:c.2956C>T	p.Arg986Cys	p.R986C	ENST00000382891	NM_133335.3	986	Cgc/Tgc	16/22	0.64891374311848	3	FACETS	0.417	0.367	0.472	0.209	0.183	0.236	SUBCLONAL	1	TRUE	1	0.685269602929567	3		532	751	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133622	55133622	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1395338355	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	330	539	0	ENST00000257290.5:c.926T>C	p.Val309Ala	p.V309A	ENST00000257290	NM_006206.4	309	gTc/gCc	6/23	0.64891374311848	3	FACETS	0.992	0.946	1	0.992	0.946	1	CLONAL	2	TRUE	1	0.685269602929567	3		539	652	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976900	55976900	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	64	458	0	ENST00000263923.4:c.1012T>C	p.Ser338Pro	p.S338P	ENST00000263923	NM_002253.2	338	Tct/Cct	8/30	0.64891374311848	3	FACETS	0.409	0.354	0.469	0.205	0.177	0.235	SUBCLONAL	1	TRUE	1	0.685269602929567	3		458	613	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352365	143352368	+	frameshift_variant	Frame_Shift_Del	DEL	AAGA	AAGA	-	novel	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	157	377	0	ENST00000262992.4:c.45_48del	p.Pro17GlnfsTer42	p.P17Qfs*42	ENST00000262992	NM_001101669.1	15	ttTCTT/tt	2/24	0.64891374311848	3	FACETS	1	0.952	1	0.524	0.482	0.567	CLONAL	1	TRUE	1	0.685269602929567	3		377	587	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144354718	144354718	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	36	493	0	ENST00000262995.4:c.442T>C	p.Ser148Pro	p.S148P	ENST00000262995	NM_207123.2	148	Tcc/Ccc	3/11	0.64891374311848	3	FACETS	0.216	0.177	0.261	0.108	0.088	0.131	SUBCLONAL	1	TRUE	1	0.685269602929567	3		493	652	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	908163	908163	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs557262120	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	195	559	0	ENST00000166345.3:c.733G>A	p.Ala245Thr	p.A245T	ENST00000166345	NM_004237.3	245	Gcc/Acc	8/13	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.685269602929567	2		559	566	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593347	67593347	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	212	557	0	ENST00000274335.5:c.2093A>G	p.Tyr698Cys	p.Y698C	ENST00000274335		698	tAc/tGc	15/15	1	2	FACETS	0.923	0.862	0.986	0.923	0.862	0.986	CLONAL	1	TRUE	1	0.685269602929567	2		557	670	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287880	33287880	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	49	837	0	ENST00000374542.5:c.1373C>T	p.Ala458Val	p.A458V	ENST00000374542	NM_001141970.1	458	gCc/gTc	5/8	1	2	FACETS	0.173	0.146	0.203	0.173	0.146	0.203	SUBCLONAL	1	TRUE	1	0.685269602929567	2		837	826	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737346	145737346	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	195	723	1	ENST00000428558.2:c.3341A>G	p.Gln1114Arg	p.Q1114R	ENST00000428558	NM_004260.3	1114	cAg/cGg	20/22	1	2	FACETS	0.95	0.885	1	0.95	0.885	1	CLONAL	1	TRUE	1	0.685269602929567	2		724	599	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2039776	2039777	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAG	rs113070757	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	126	715	0	ENST00000349721.2:c.705_707dup	p.Gln238dup	p.Q238dup	ENST00000349721	NM_003070.3	238	-/CAG	4/34	0.470842562382418	1	FACETS	0.36	0.327	0.396	0.36	0.327	0.396	SUBCLONAL	1	TRUE	0	0.685269602929567	1		715	671	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971091	21971092	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	155	578	0	ENST00000304494.5:c.266dup	p.Phe90LeufsTer30	p.F90Lfs*30	ENST00000304494	NM_000077.4	89	ggc/ggGc	2/3	0.470842562382418	1	FACETS	0.67	0.619	0.722	0.67	0.619	0.722	SUBCLONAL	1	TRUE	0	0.685269602929567	1		578	444	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649611	48649611	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	108	598	0	ENST00000376670.3:c.95T>G	p.Val32Gly	p.V32G	ENST00000376670	NM_002049.3	32	gTt/gGt	2/6	1	2	FACETS	0.707	0.638	0.778	0.707	0.638	0.778	SUBCLONAL	1	TRUE	1	0.685269602929567	2		598	446	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920173	76920173	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	114	371	0	ENST00000373344.5:c.3904del	p.Arg1302GlufsTer44	p.R1302Efs*44	ENST00000373344	NM_000489.3	1302	Aga/ga	11/35	1	2	FACETS	0.855	0.777	0.936	0.855	0.777	0.936	CLONAL	1	TRUE	1	0.685269602929567	2		371	389	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	169	525	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.952	0.88	1	0.952	0.88	1	CLONAL	1	TRUE	1	0.613469396657969	2		527	579	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	110	230	6	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.71	0.641	0.783	0.71	0.641	0.783	SUBCLONAL	1	TRUE	1	0.613469396657969	2		236	505	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	70	265	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.885	0.781	0.994	0.885	0.781	0.994	CLONAL	1	TRUE	1	0.613469396657969	2		265	258	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	144	324	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.613469396657969	2		324	441	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480483	57480483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	163	260	0	ENST00000371085.3:c.478C>T	p.Arg160Cys	p.R160C	ENST00000371085	NM_000516.4	160	Cgt/Tgt	6/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.613469396657969	2		260	491	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007619	45007619	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs111482205	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	106	287	0	ENST00000558401.1:c.68-2A>G		p.X23_splice	ENST00000558401	NM_004048.2	23			1	2	FACETS	0.985	0.892	1	0.985	0.892	1	CLONAL	1	TRUE	1	0.613469396657969	2		287	351	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	20	101	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	0.621	0.483	0.777	0.621	0.483	0.777	SUBCLONAL	1	TRUE	1	0.613469396657969	2		101	105	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460516	149460516	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	163	311	0	ENST00000286301.3:c.121C>T	p.Arg41Ter	p.R41*	ENST00000286301	NM_005211.3	41	Cga/Tga	3/22	1	2	FACETS	0.971	0.897	1	0.971	0.897	1	CLONAL	1	TRUE	1	0.613469396657969	2		311	547	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265168	5265168	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	146	371	0	ENST00000357368.4:c.419G>A	p.Gly140Asp	p.G140D	ENST00000357368	NM_002850.3	140	gGc/gAc	5/38	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.613469396657969	2		371	466	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41554467	41554467	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1489896703	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	43	220	0	ENST00000263253.7:c.3553A>G	p.Ile1185Val	p.I1185V	ENST00000263253	NM_001429.3	1185	Ata/Gta	19/31	1	2	FACETS	0.273	0.228	0.323	0.273	0.228	0.323	SUBCLONAL	1	TRUE	1	0.613469396657969	2		220	513	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	56	227	2	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	1	2	FACETS	0.569	0.49	0.654	0.569	0.49	0.654	SUBCLONAL	1	TRUE	1	0.613469396657969	2		229	321	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	156	236	0	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.613469396657969	2		236	498	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661663	227661664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761880048	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	122	384	8	ENST00000305123.5:c.1791dup	p.His598AlafsTer13	p.H598Afs*13	ENST00000305123	NM_005544.2	597	-/G	1/2	1	2	FACETS	0.97	0.884	1	0.97	0.884	1	CLONAL	1	TRUE	1	0.613469396657969	2		392	410	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119780	70119781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	89	284	0	ENST00000245479.2:c.788dup	p.Arg264GlnfsTer32	p.R264Qfs*32	ENST00000245479	NM_000346.3	261	gag/gaGg	3/3	1	2	FACETS	0.846	0.757	0.939	0.846	0.757	0.939	CLONAL	1	TRUE	1	0.613469396657969	2		284	343	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411937	63411937	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	156	423	0	ENST00000330258.3:c.1230G>A	p.Trp410Ter	p.W410*	ENST00000330258	NM_152424.3	410	tgG/tgA	2/2	1	2	FACETS	0.902	0.83	0.976	0.902	0.83	0.976	CLONAL	1	TRUE	1	0.613469396657969	2		423	564	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729400	41729400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	39	335	0	ENST00000242208.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000242208	NM_002192.2	377	Cgc/Tgc	3/3	0.568922933282106	3	FACETS	0.28	0.231	0.335	0.14	0.115	0.168	SUBCLONAL	1	TRUE	1	0.613469396657969	3		335	593	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685289	89685289	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554897267	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	81	180	0	ENST00000371953.3:c.188del	p.Asn63ThrfsTer36	p.N63Tfs*36	ENST00000371953	NM_000314.4	62	Aaa/aa	3/9	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.613469396657969	2		180	253	SUCCESS
APC	324	MSKCC	GRCh37	5	112164565	112164566	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1554082091	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	104	232	0	ENST00000257430.4:c.1643dup	p.Leu548PhefsTer12	p.L548Ffs*12	ENST00000257430	NM_000038.5	547	gtt/gTtt	14/16	1	2	FACETS	0.997	0.903	1	0.997	0.903	1	CLONAL	1	TRUE	1	0.613469396657969	2		232	340	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273901	10273901	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	129	296	0	ENST00000330684.3:c.368C>A	p.Pro123His	p.P123H	ENST00000330684	NM_001134407.1	123	cCc/cAc	2/13	1	2	FACETS	0.978	0.894	1	0.978	0.894	1	CLONAL	1	TRUE	1	0.613469396657969	2		296	430	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879593	151879594	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	rs749417254	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	71	312	0	ENST00000262189.6:c.5349_5351dup	p.Gln1787dup	p.Q1787dup	ENST00000262189	NM_170606.2	1787	caa/caGCAa	36/59	0.568922933282106	3	FACETS	0.421	0.367	0.479	0.21	0.183	0.24	SUBCLONAL	1	TRUE	1	0.613469396657969	3		312	719	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	137	365	0	ENST00000257430.4:c.4665_4666dup	p.Thr1556LysfsTer10	p.T1556Kfs*10	ENST00000257430	NM_000038.5	1554	gaa/gAAaa	16/16	1	2	FACETS	0.888	0.813	0.966	0.888	0.813	0.966	CLONAL	1	TRUE	1	0.613469396657969	2		365	503	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109887	115109887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762342872	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	143	336	0	ENST00000257566.3:c.1991C>T	p.Ala664Val	p.A664V	ENST00000257566	NM_016569.3	664	gCg/gTg	8/8	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.613469396657969	2		336	426	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878764	151878764	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	103	371	0	ENST00000262189.6:c.6181T>C	p.Ser2061Pro	p.S2061P	ENST00000262189	NM_170606.2	2061	Tca/Cca	36/59	0.568922933282106	3	FACETS	0.667	0.597	0.74	0.333	0.298	0.37	SUBCLONAL	1	TRUE	1	0.613469396657969	3		371	658	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020562	69020562	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	40	235	0	ENST00000288368.4:c.2934G>T	p.Glu978Asp	p.E978D	ENST00000288368	NM_024870.2	978	gaG/gaT	24/40	1	2	FACETS	0.385	0.32	0.456	0.385	0.32	0.456	SUBCLONAL	1	TRUE	1	0.613469396657969	2		235	339	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519210	187519210	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	54	249	0	ENST00000441802.2:c.12173C>T	p.Ser4058Phe	p.S4058F	ENST00000441802	NM_005245.3	4058	tCc/tTc	23/27	1	2	FACETS	0.384	0.328	0.444	0.384	0.328	0.444	SUBCLONAL	1	TRUE	1	0.613469396657969	2		249	459	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225096	53225096	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	37	272	0	ENST00000375401.3:c.3120+2T>C		p.X1040_splice	ENST00000375401	NM_004187.3	1040			1	2	FACETS	0.265	0.218	0.317	0.265	0.218	0.317	SUBCLONAL	1	TRUE	1	0.613469396657969	2		272	456	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663908	29663908	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	64	236	0	ENST00000356175.3:c.6340A>G	p.Thr2114Ala	p.T2114A	ENST00000356175	NM_000267.3	2114	Act/Gct	41/57	1	2	FACETS	0.505	0.439	0.577	0.505	0.439	0.577	SUBCLONAL	1	TRUE	1	0.613469396657969	2		236	413	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576814	212576814	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs528780505	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	30	219	0	ENST00000342788.4:c.1085T>A	p.Ile362Asn	p.I362N	ENST00000342788	NM_005235.2	362	aTc/aAc	9/28	1	2	FACETS	0.439	0.355	0.532	0.439	0.355	0.532	SUBCLONAL	1	TRUE	1	0.613469396657969	2		219	223	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873389	136873389	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs757881953	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	143	296	0	ENST00000241393.3:c.109A>G	p.Asn37Asp	p.N37D	ENST00000241393	NM_003467.2	37	Aat/Gat	2/2	1	2	FACETS	0.953	0.875	1	0.953	0.875	1	CLONAL	1	TRUE	1	0.613469396657969	2		296	489	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504119	123504119	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	31	240	0	ENST00000371139.4:c.295C>T	p.Gln99Ter	p.Q99*	ENST00000371139	NM_001114937.2	99	Cag/Tag	3/4	1	2	FACETS	0.398	0.323	0.482	0.398	0.323	0.482	SUBCLONAL	1	TRUE	1	0.613469396657969	2		240	254	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880453	155880453	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	38	261	0	ENST00000368323.3:c.100A>G	p.Lys34Glu	p.K34E	ENST00000368323	NM_006912.5	34	Aag/Gag	2/6	1	2	FACETS	0.308	0.255	0.368	0.308	0.255	0.368	SUBCLONAL	1	TRUE	1	0.613469396657969	2		261	402	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843485	156843485	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	167	327	0	ENST00000524377.1:c.911C>A	p.Ser304Tyr	p.S304Y	ENST00000524377	NM_002529.3	304	tCt/tAt	8/17	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.613469396657969	2		327	502	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180654	56180654	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	20	226	0	ENST00000399503.3:c.3982+1G>T		p.X1328_splice	ENST00000399503	NM_005921.1	1328			1	2	FACETS	0.321	0.246	0.408	0.321	0.246	0.408	SUBCLONAL	1	TRUE	1	0.613469396657969	2		226	203	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77937994	77937994	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	183	312	0	ENST00000361507.4:c.724A>C	p.Ser242Arg	p.S242R	ENST00000361507	NM_080491.2	242	Agt/Cgt	4/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.613469396657969	2		312	559	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965819	90965819	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	74	267	0	ENST00000265433.3:c.1498T>A	p.Leu500Met	p.L500M	ENST00000265433	NM_002485.4	500	Ttg/Atg	11/16	1	2	FACETS	0.939	0.832	1	0.939	0.832	1	CLONAL	1	TRUE	1	0.613469396657969	2		267	257	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874147	151874148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	67	344	1	ENST00000262189.6:c.8389_8390dup	p.Glu2798ArgfsTer26	p.E2798Rfs*26	ENST00000262189	NM_170606.2	2797	aag/aaAAg	38/59	0.568922933282106	3	FACETS	0.531	0.461	0.605	0.265	0.23	0.303	SUBCLONAL	1	TRUE	1	0.613469396657969	3		345	538	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523075	25523075	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	146	289	0	ENST00000264709.3:c.110A>T	p.Glu37Val	p.E37V	ENST00000264709	NM_175629.2	37	gAg/gTg	3/23	1	2	FACETS	0.914	0.839	0.991	0.914	0.839	0.991	CLONAL	1	TRUE	1	0.613469396657969	2		289	521	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755782	39755782	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	46	292	0	ENST00000288319.7:c.983G>T	p.Ser328Ile	p.S328I	ENST00000288319	NM_182918.3	328	aGc/aTc	10/10	1	2	FACETS	0.348	0.293	0.408	0.348	0.293	0.408	SUBCLONAL	1	TRUE	1	0.613469396657969	2		292	431	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123245024	123245024	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	48	331	0	ENST00000358487.5:c.2080T>C	p.Trp694Arg	p.W694R	ENST00000358487	NM_000141.4	694	Tgg/Cgg	16/18	1	2	FACETS	0.316	0.267	0.37	0.316	0.267	0.37	SUBCLONAL	1	TRUE	1	0.613469396657969	2		331	495	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422558	47422558	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1421131228	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	48	309	0	ENST00000404338.3:c.626A>G	p.Tyr209Cys	p.Y209C	ENST00000404338	NM_004491.4	209	tAc/tGc	1/6	1	2	FACETS	0.3	0.254	0.352	0.3	0.254	0.352	SUBCLONAL	1	TRUE	1	0.613469396657969	2		309	521	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795088	45795088	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	53	288	0	ENST00000450313.1:c.1540T>C	p.Ser514Pro	p.S514P	ENST00000450313	NM_012222.2	514	Tcc/Ccc	16/16	1	2	FACETS	0.29	0.247	0.337	0.29	0.247	0.337	SUBCLONAL	1	TRUE	1	0.613469396657969	2		288	596	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259439	89259439	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	139	320	0	ENST00000336596.2:c.583G>T	p.Val195Leu	p.V195L	ENST00000336596	NM_005233.5	195	Gtg/Ttg	3/17	1	2	FACETS	0.936	0.858	1	0.936	0.858	1	CLONAL	1	TRUE	1	0.613469396657969	2		320	484	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630360	67630360	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	78	225	0	ENST00000272342.5:c.550del	p.Thr184HisfsTer9	p.T184Hfs*9	ENST00000272342	NM_019002.3	182	ttA/tt	5/6	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.613469396657969	2		225	248	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823903	3823903	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs147805823	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	32	317	1	ENST00000262367.5:c.2312A>G	p.Gln771Arg	p.Q771R	ENST00000262367	NM_004380.2	771	cAg/cGg	13/31	1	2	FACETS	0.223	0.181	0.272	0.223	0.181	0.272	SUBCLONAL	1	TRUE	1	0.613469396657969	2		318	467	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138657	37138657	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	109	318	0	ENST00000373509.5:c.189+2T>C		p.X63_splice	ENST00000373509	NM_002648.3	63			1	2	FACETS	0.971	0.88	1	0.971	0.88	1	CLONAL	1	TRUE	1	0.613469396657969	2		318	366	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860048	152860048	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	131	298	0	ENST00000406277.2:c.380T>C	p.Leu127Pro	p.L127P	ENST00000406277	NM_152274.4	127	cTg/cCg	5/7	1		FACETS		0.876	1				CLONAL	1	TRUE	1	0.613469396657969	2		298	446	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21351011	21351011	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs755260815	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	39	308	0	ENST00000215739.8:c.2246A>G	p.Tyr749Cys	p.Y749C	ENST00000215739	NM_006767.3	749	tAc/tGc	19/21	1	2	FACETS	0.274	0.227	0.327	0.274	0.227	0.327	SUBCLONAL	1	TRUE	1	0.613469396657969	2		308	464	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858110	152858110	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	181	327	0	ENST00000406277.2:c.505T>C	p.Trp169Arg	p.W169R	ENST00000406277	NM_152274.4	169	Tgg/Cgg	6/7	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.613469396657969	2		327	482	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748155	72748155	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	46	228	0	ENST00000357731.5:c.23A>G	p.Gln8Arg	p.Q8R	ENST00000357731	NM_173808.2	8	cAg/cGg	1/7	1	2	FACETS	0.422	0.357	0.494	0.422	0.357	0.494	SUBCLONAL	1	TRUE	1	0.613469396657969	2		228	355	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862797	9862797	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1012398659	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	51	367	0	ENST00000330684.3:c.2506A>C	p.Ile836Leu	p.I836L	ENST00000330684	NM_001134407.1	836	Atc/Ctc	12/13	1	2	FACETS	0.333	0.283	0.388	0.333	0.283	0.388	SUBCLONAL	1	TRUE	1	0.613469396657969	2		367	499	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77048446	77048446	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	30	268	0	ENST00000356341.3:c.1139T>C	p.Leu380Ser	p.L380S	ENST00000356341	NM_002576.4	380	tTg/tCg	12/15	1	2	FACETS	0.254	0.204	0.31	0.254	0.204	0.31	SUBCLONAL	1	TRUE	1	0.613469396657969	2		268	385	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873809	151873809	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	182	336	0	ENST00000262189.6:c.8729G>A	p.Gly2910Asp	p.G2910D	ENST00000262189	NM_170606.2	2910	gGc/gAc	38/59	0.568922933282106	3	FACETS	1	0.981	1	0.588	0.545	0.633	CLONAL	1	TRUE	1	0.613469396657969	3		336	659	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46543277	46543277	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	131	219	0	ENST00000262741.5:c.224T>C	p.Val75Ala	p.V75A	ENST00000262741	NM_003629.3	75	gTa/gCa	3/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.613469396657969	2		219	391	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814791	139814791	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	65	371	0	ENST00000247668.2:c.784A>G	p.Ser262Gly	p.S262G	ENST00000247668	NM_021138.3	262	Agc/Ggc	8/11	1	2	FACETS	0.363	0.315	0.416	0.363	0.315	0.416	SUBCLONAL	1	TRUE	1	0.613469396657969	2		371	583	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39763579	39763579	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	60	207	0	ENST00000288319.7:c.871+2T>C		p.X291_splice	ENST00000288319	NM_182918.3	291			1	2	FACETS	0.577	0.5	0.66	0.577	0.5	0.66	SUBCLONAL	1	TRUE	1	0.613469396657969	2		207	339	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941477	71941477	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	157	366	0	ENST00000298229.2:c.1162A>G	p.Thr388Ala	p.T388A	ENST00000298229	NM_001567.3	388	Act/Gct	10/28	1	2	FACETS	0.916	0.843	0.99	0.916	0.843	0.99	CLONAL	1	TRUE	1	0.613469396657969	2		366	559	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240392	98240392	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1564051512	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	173	303	1	ENST00000331920.6:c.1292T>C	p.Leu431Pro	p.L431P	ENST00000331920	NM_000264.3	431	cTg/cCg	9/24	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.613469396657969	2		304	500	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999131	100999131	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	30	361	0	ENST00000325455.5:c.671A>C	p.Glu224Ala	p.E224A	ENST00000325455	NM_001202474.3	224	gAg/gCg	1/8	1	2	FACETS	0.21	0.169	0.257	0.21	0.169	0.257	SUBCLONAL	1	TRUE	1	0.613469396657969	2		361	465	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736436	85736436	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	42	307	0	ENST00000370580.1:c.211T>C	p.Tyr71His	p.Y71H	ENST00000370580	NM_003921.4	71	Tac/Cac	2/3	1	2	FACETS	0.297	0.248	0.352	0.297	0.248	0.352	SUBCLONAL	1	TRUE	1	0.613469396657969	2		307	461	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245646	46245646	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	51	361	0	ENST00000334344.6:c.3740A>G	p.Glu1247Gly	p.E1247G	ENST00000334344	NM_152641.2	1247	gAg/gGg	15/21	1	2	FACETS	0.298	0.253	0.347	0.298	0.253	0.347	SUBCLONAL	1	TRUE	1	0.613469396657969	2		361	558	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812259	212812259	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	95	276	0	ENST00000342788.4:c.317G>C	p.Arg106Pro	p.R106P	ENST00000342788	NM_005235.2	106	cGt/cCt	3/28	1	2	FACETS	0.936	0.842	1	0.936	0.842	1	CLONAL	1	TRUE	1	0.613469396657969	2		276	331	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134855	41134855	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	46	322	0	ENST00000379561.5:c.773A>G	p.Asp258Gly	p.D258G	ENST00000379561	NM_002015.3	258	gAc/gGc	2/3	1	2	FACETS	0.275	0.231	0.323	0.275	0.231	0.323	SUBCLONAL	1	TRUE	1	0.613469396657969	2		322	546	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77931391	77931391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1448783711	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	46	344	0	ENST00000361507.4:c.1861C>T	p.Pro621Ser	p.P621S	ENST00000361507	NM_080491.2	621	Ccg/Tcg	9/10	1	2	FACETS	0.295	0.248	0.347	0.295	0.248	0.347	SUBCLONAL	1	TRUE	1	0.613469396657969	2		344	508	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143229	24143229	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	79	380	0	ENST00000263121.7:c.461A>T	p.Asn154Ile	p.N154I	ENST00000263121	NM_003073.3	154	aAc/aTc	4/9	1	2	FACETS	0.416	0.366	0.47	0.416	0.366	0.47	SUBCLONAL	1	TRUE	1	0.613469396657969	2		380	619	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40500506	40500506	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	126	221	0	ENST00000264657.5:c.29T>C	p.Leu10Pro	p.L10P	ENST00000264657	NM_139276.2	10	cTt/cCt	2/24	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.613469396657969	2		221	401	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741487	17741487	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	47	295	0	ENST00000250003.3:c.158T>C	p.Val53Ala	p.V53A	ENST00000250003	NM_002478.4	53	gTg/gCg	1/3	1	2	FACETS	0.376	0.317	0.44	0.376	0.317	0.44	SUBCLONAL	1	TRUE	1	0.613469396657969	2		295	408	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020768	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	CC	novel	NA	P-0066791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	25	288	0	ENST00000358127.4:c.77delinsGG	p.Val26GlyfsTer49	p.V26Gfs*49	ENST00000358127	NM_001280556.1	26	gTt/gGGt	2/10	1	2	FACETS	0.177	0.139	0.221	0.177	0.139	0.221	SUBCLONAL	1	TRUE	1	0.613469396657969	2		288	461	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0067516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	284	472	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	0.702883667173772	5	FACETS	0.971	0.923	1	0.971	0.923	1	CLONAL	3	TRUE	2	0.70254713424332	5		472	570	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752411	57752412	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0067516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	162	317	0	ENST00000274289.3:c.1161_1162del	p.Arg387SerfsTer3	p.R387Sfs*3	ENST00000274289	NM_006622.3	387	agAGtg/agtg	9/14	0.702883667173772	4	FACETS	0.962	0.905	1	0.962	0.905	1	CLONAL	3	TRUE	1	0.70254713424332	4		317	272	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853274	68853274	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	96	493	0	ENST00000261769.5:c.1657T>C	p.Phe553Leu	p.F553L	ENST00000261769	NM_004360.3	553	Ttt/Ctt	11/16	0.702883667173772	3	FACETS	1	0.958	1	0.561	0.505	0.62	CLONAL	1	TRUE	1	0.70254713424332	3		493	329	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385171	41385171	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	25	475	0	ENST00000373198.4:c.790A>C	p.Lys264Gln	p.K264Q	ENST00000373198	NM_133170.3	264	Aag/Cag	6/32	0.689409846293819	4	FACETS	0.293	0.231	0.366	0.147	0.115	0.183	SUBCLONAL	1	TRUE	2	0.70254713424332	4		475	413	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250778	26250778	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	99	592	1	ENST00000446824.2:c.56A>G	p.Lys19Arg	p.K19R	ENST00000446824	NM_021018.2	19	aAg/aGg	1/1	0.702883667173772	3	FACETS	0.902	0.811	0.999	0.451	0.405	0.5	CLONAL	1	TRUE	1	0.70254713424332	3		593	422	SUCCESS
ATR	545	MSKCC	GRCh37	3	142241684	142241684	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0067516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	54	300	0	ENST00000350721.4:c.4153-1G>A		p.X1385_splice	ENST00000350721	NM_001184.3	1385			0.70254713424332	6	FACETS	1	0.859	1	0.2	0.171	0.232	CLONAL	1	TRUE	1	0.70254713424332	6		300	369	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356401	70356402	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	A	novel	NA	P-0067516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	76	559	2	ENST00000374080.3:c.5296_5297delinsA	p.Pro1766ThrfsTer49	p.P1766Tfs*49	ENST00000374080		1766	CCc/Ac	37/45	0.702883667173772	3	FACETS	0.835	0.738	0.938	0.418	0.369	0.469	CLONAL	1	TRUE	1	0.70254713424332	3		561	350	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913381	NA	P-0004618-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	27	431	0	ENST00000304494.5:c.322G>T	p.Asp108Tyr	p.D108Y	ENST00000304494	NM_000077.4	108	Gat/Tat	2/3	1	2	FACETS	0.634	0.505	0.782	0.634	0.505	0.782	SUBCLONAL	1	TRUE	1	0.242486574185699	2		431	351	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849898	156849898	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004618-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	36	390	0	ENST00000524377.1:c.2154G>T	p.Trp718Cys	p.W718C	ENST00000524377	NM_002529.3	718	tgG/tgT	16/17	1	2	FACETS	0.508	0.416	0.61	0.508	0.416	0.61	SUBCLONAL	1	TRUE	1	0.242486574185699	2		390	585	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647473	117647473	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004618-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	63	506	0	ENST00000368508.3:c.5471G>T	p.Gly1824Val	p.G1824V	ENST00000368508	NM_002944.2	1824	gGa/gTa	33/43	0.204196068668086	3	FACETS	0.517	0.445	0.595	0.258	0.222	0.298	SUBCLONAL	1	TRUE	1	0.242486574185699	3		506	1128	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681010	117681010	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004618-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	56	357	0	ENST00000368508.3:c.3610C>G	p.Leu1204Val	p.L1204V	ENST00000368508	NM_002944.2	1204	Ctc/Gtc	23/43	0.204196068668086	3	FACETS	0.631	0.539	0.732	0.315	0.269	0.366	SUBCLONAL	1	TRUE	1	0.242486574185699	3		357	821	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683650	162683650	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004618-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	40	397	0	ENST00000366898.1:c.319C>T	p.Leu107Phe	p.L107F	ENST00000366898	NM_004562.2	107	Ctc/Ttc	3/12	0.123917409567201	4	FACETS	0.622	0.516	0.741	0.311	0.258	0.371	INDETERMINATE	1	TRUE	2	0.242486574185699	4		397	659	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374367	81374367	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004618-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	78	468	0	ENST00000222390.5:c.695G>T	p.Cys232Phe	p.C232F	ENST00000222390	NM_000601.4	232	tGt/tTt	6/18	1	2	FACETS	0.716	0.627	0.811	0.716	0.627	0.811	SUBCLONAL	1	TRUE	1	0.242486574185699	2		468	899	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577508	7577508	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060501201	NA	P-0004618-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	30	271	0	ENST00000269305.4:c.773A>G	p.Glu258Gly	p.E258G	ENST00000269305	NM_001126112.2	258	gAa/gGa	7/11	1	2	FACETS	0.68	0.548	0.829	0.68	0.548	0.829	SUBCLONAL	1	TRUE	1	0.242486574185699	2		271	364	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312689	30312689	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004618-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	50	400	0	ENST00000262643.3:c.670G>T	p.Asp224Tyr	p.D224Y	ENST00000262643	NM_001238.2	224	Gat/Tat	8/12	0.184391980712569	1	FACETS	0.613	0.52	0.716	0.613	0.52	0.716	SUBCLONAL	1	TRUE	0	0.242486574185699	1		400	591	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123189978	123189978	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004618-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	86	504	0	ENST00000218089.9:c.1197G>T	p.Gln399His	p.Q399H	ENST00000218089	NM_001042749.1	399	caG/caT	14/35	0.242486574185699	1	FACETS	0.78	0.689	0.877	0.78	0.689	0.877	SUBCLONAL	1	TRUE	0	0.242486574185699	1		504	799	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983299	149983300	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004618-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	52	315	0	ENST00000253339.5:c.2958dup	p.Lys987Ter	p.K987*	ENST00000253339		986	-/T	7/7	0.123917409567201	4	FACETS	0.831	0.707	0.968	0.416	0.353	0.484	INDETERMINATE	1	TRUE	2	0.242486574185699	4		315	641	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0034061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	192	418	35	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		453	345	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001281-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	93	387	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		387	283	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0001281-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5938	916	745	2	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		747	6854	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0001281-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4502	870	499	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		499	5372	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712017	89712017	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0001281-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	122	302	0	ENST00000371953.3:c.634+1G>A		p.X212_splice	ENST00000371953	NM_000314.4	212			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		302	258	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266500	55266500	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001281-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2650	2528	519	0	ENST00000275493.2:c.2792A>G	p.Glu931Gly	p.E931G	ENST00000275493	NM_005228.3	931	gAa/gGa	23/28	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		519	5178	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94908712	94908712	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001281-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	157	338	0	ENST00000536441.1:c.1342A>G	p.Thr448Ala	p.T448A	ENST00000536441	NM_144665.3	448	Aca/Gca	9/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		338	539	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934865	9934865	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0001281-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	28	437	0	ENST00000330684.3:c.1425C>G	p.Tyr475Ter	p.Y475*	ENST00000330684	NM_001134407.1	475	taC/taG	6/13	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		437	464	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10305545	10305545	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001281-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	115	556	0	ENST00000340748.4:c.31C>G	p.Pro11Ala	p.P11A	ENST00000340748		11	Ccc/Gcc	1/40	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		556	505	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872932	136872932	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001281-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	172	656	0	ENST00000241393.3:c.566T>A	p.Phe189Tyr	p.F189Y	ENST00000241393	NM_003467.2	189	tTc/tAc	2/2	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		656	595	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574695	41574695	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764378639	NA	P-0001281-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	190	751	0	ENST00000263253.7:c.6980C>G	p.Pro2327Arg	p.P2327R	ENST00000263253	NM_001429.3	2327	cCt/cGt	31/31	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		751	590	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30954260	30954260	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012861-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	147	385	0	ENST00000375687.4:c.131A>G	p.Lys44Arg	p.K44R	ENST00000375687	NM_015338.5	44	aAg/aGg	2/13	0.12628171664112	5	FACETS	0.823	0.755	0.894			1	INDETERMINATE	2	TRUE	NA	0.564473694344992	5		385	584	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104359209	104359209	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012861-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	54	335	0	ENST00000369902.3:c.930del	p.Thr311ProfsTer2	p.T311Pfs*2	ENST00000369902	NM_016169.3	310	gaG/ga	8/12	0.564473694344992	2	FACETS	0.374	0.319	0.433	0.187	0.159	0.217	SUBCLONAL	1	TRUE	0	0.564473694344992	2		335	512	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196953	108196953	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0012861-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	146	332	0	ENST00000278616.4:c.6975+1G>C		p.X2325_splice	ENST00000278616	NM_000051.3	2325			0.564473694344992	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.564473694344992	1		332	344	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49724647	49724647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012861-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	97	411	0	ENST00000449682.2:c.542C>T	p.Pro181Leu	p.P181L	ENST00000449682	NM_020998.3	181	cCt/cTt	5/18	1	2	FACETS	0.812	0.729	0.9	0.812	0.729	0.9	CLONAL	1	TRUE	1	0.564473694344992	2		411	423	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521302	8521302	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012861-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	62	407	0	ENST00000356435.5:c.936A>T	p.Glu312Asp	p.E312D	ENST00000356435		312	gaA/gaT	9/35	0.564473694344992	1	FACETS	0.44	0.382	0.503	0.44	0.382	0.503	SUBCLONAL	1	TRUE	0	0.564473694344992	1		407	358	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013712-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	38	387	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		387	126	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0013712-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	30	190	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		190	86	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0013712-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	64	586	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		586	207	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0013712-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	56	558	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		558	318	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983911	2983911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237589286	NA	P-0013712-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	40	321	0	ENST00000396946.4:c.619C>T	p.Arg207Cys	p.R207C	ENST00000396946	NM_032415.4	207	Cgc/Tgc	5/25	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		321	241	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092947	27092947	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013712-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	69	328	0	ENST00000324856.7:c.2879-1G>A		p.X960_splice	ENST00000324856	NM_006015.4	960			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		328	207	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935371	36935371	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1420858282	NA	P-0013712-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	45	309	0	ENST00000361632.4:c.1356del	p.Asn453IlefsTer8	p.N453Ifs*8	ENST00000361632		452	ccC/cc	10/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		309	225	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405138	70405138	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013712-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	23	368	0	ENST00000373644.4:c.2652G>C	p.Arg884Ser	p.R884S	ENST00000373644	NM_030625.2	884	agG/agC	4/12	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		368	136	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741912	17741912	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs997869046	NA	P-0013712-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	43	273	0	ENST00000250003.3:c.583G>T	p.Gly195Cys	p.G195C	ENST00000250003	NM_002478.4	195	Ggc/Tgc	1/3	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		273	108	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242647	46242647	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013712-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	26	274	0	ENST00000334344.6:c.1609G>C	p.Asp537His	p.D537H	ENST00000334344	NM_152641.2	537	Gat/Cat	13/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		274	101	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865236	57865236	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013712-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	28	326	0	ENST00000228682.2:c.2713C>T	p.Gln905Ter	p.Q905*	ENST00000228682	NM_005269.2	905	Caa/Taa	12/12	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		326	125	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130201	2130201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013712-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	43	378	0	ENST00000219476.3:c.3433C>T	p.Pro1145Ser	p.P1145S	ENST00000219476	NM_000548.3	1145	Ccg/Tcg	30/42	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		378	178	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832577	72832577	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013712-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	40	356	0	ENST00000268489.5:c.4004C>G	p.Ser1335Cys	p.S1335C	ENST00000268489	NM_006885.3	1335	tCc/tGc	9/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		356	175	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883998	37883998	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013712-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	62	369	0	ENST00000269571.5:c.3469C>G	p.Leu1157Val	p.L1157V	ENST00000269571		1157	Ctg/Gtg	27/27	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		369	336	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023070	31023070	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371542005	NA	P-0013712-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	28	386	0	ENST00000375687.4:c.2555C>T	p.Ser852Leu	p.S852L	ENST00000375687	NM_015338.5	852	tCa/tTa	13/13	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		386	209	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217475	142217475	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013712-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	30	304	0	ENST00000350721.4:c.5522G>C	p.Arg1841Thr	p.R1841T	ENST00000350721	NM_001184.3	1841	aGa/aCa	32/47	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		304	110	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190830	185190830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs961866050	NA	P-0013712-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	53	383	0	ENST00000265026.3:c.1711G>A	p.Gly571Arg	p.G571R	ENST00000265026	NM_004721.4	571	Gga/Aga	11/14	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		383	244	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228145	36228145	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013712-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	49	361	0	ENST00000222270.7:c.7531C>T	p.Arg2511Trp	p.R2511W	ENST00000222270	NM_014727.1	2511	Cgg/Tgg	33/37	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		361	268	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542172	141542172	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013712-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	64	262	0	ENST00000220592.5:c.2551G>A	p.Asp851Asn	p.D851N	ENST00000220592	NM_012154.3	851	Gac/Aac	19/19	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		262	337	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136182	11136182	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs267605281	NA	P-0013712-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	62	312	0	ENST00000358026.2:c.3166G>A	p.Glu1056Lys	p.E1056K	ENST00000358026	NM_001128849.1	1056	Gag/Aag	22/36	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		312	219	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542525	141542525	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013712-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	98	368	0	ENST00000220592.5:c.2461G>C	p.Glu821Gln	p.E821Q	ENST00000220592	NM_012154.3	821	Gaa/Caa	18/19	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		368	257	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542654	141542654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013712-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	47	338	0	ENST00000220592.5:c.2332G>A	p.Glu778Lys	p.E778K	ENST00000220592	NM_012154.3	778	Gag/Aag	18/19	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		338	226	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202932	27202932	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013712-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	26	362	0	ENST00000380036.4:c.2024A>T	p.Lys675Met	p.K675M	ENST00000380036	NM_000459.3	675	aAg/aTg	13/23	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		362	127	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017202-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	89	549	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.701134215779968	2	FACETS	1	0.947	1	0.538	0.485	0.592	CLONAL	1	TRUE	0	0.701134215779968	2		549	236	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658368	18658368	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017202-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	50	353	0	ENST00000266497.5:c.3173A>G	p.His1058Arg	p.H1058R	ENST00000266497		1058	cAt/cGt	22/31	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.701134215779968	2		353	140	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0020792-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	24	283	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		283	417	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610073	10610073	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020792-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	61	539	0	ENST00000171111.5:c.637G>T	p.Glu213Ter	p.E213*	ENST00000171111	NM_203500.1	213	Gag/Tag	2/6	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		539	684	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220382	1220382	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020792-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	45	630	0	ENST00000326873.7:c.475C>T	p.Gln159Ter	p.Q159*	ENST00000326873	NM_000455.4	159	Cag/Tag	4/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		630	637	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992804	68992804	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020792-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	53	456	0	ENST00000288368.4:c.1769T>C	p.Ile590Thr	p.I590T	ENST00000288368	NM_024870.2	590	aTa/aCa	16/40	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		456	587	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754874	29754874	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020792-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	46	594	0	ENST00000389048.3:c.1061A>G	p.His354Arg	p.H354R	ENST00000389048	NM_004304.4	354	cAc/cGc	4/29	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		594	678	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519663	176519663	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020792-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	61	680	0	ENST00000292408.4:c.935G>T	p.Ser312Ile	p.S312I	ENST00000292408	NM_213647.1	312	aGc/aTc	8/18	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		680	655	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0025127-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	24	266	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		266	61	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576889	7576890	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025127-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	10	435	0	ENST00000269305.4:c.956dup	p.Lys320GlufsTer17	p.K320Efs*17	ENST00000269305	NM_001126112.2	319	aag/aaAg	9/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		435	39	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647713	206647713	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1285749873	NA	P-0025127-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	10	369	0	ENST00000367120.3:c.127A>G	p.Thr43Ala	p.T43A	ENST00000367120	NM_014002.3	43	Acc/Gcc	4/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		369	65	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0026709-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	251	283	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		283	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0026709-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	165	320	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		320	481	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255205	16255205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115323964	NA	P-0026709-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	204	440	0	ENST00000375759.3:c.2470C>T	p.Arg824Cys	p.R824C	ENST00000375759	NM_015001.2	824	Cgc/Tgc	11/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		440	912	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664718	138664720	+	missense_variant	Missense_Mutation	TNP	CGG	CGG	TGA	novel	NA	P-0026709-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	126	235	0	ENST00000330315.3:c.845_847delinsTCA	p.Ala282_Ala283delinsValThr	p.A282_A283delinsVT	ENST00000330315	NM_023067.3	282	gCCGca/gTCAca	1/1	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		235	564	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486211	8486211	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs994861872	NA	P-0026709-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	304	423	0	ENST00000356435.5:c.2606C>A	p.Thr869Asn	p.T869N	ENST00000356435		869	aCt/aAt	17/35	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		423	623	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325550	87325550	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0026709-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	155	313	0	ENST00000277120.3:c.429-2A>G		p.X143_splice	ENST00000277120		143			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		313	529	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938173	76938173	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026709-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	152	447	0	ENST00000373344.5:c.2575G>T	p.Gly859Ter	p.G859*	ENST00000373344	NM_000489.3	859	Gga/Tga	9/35	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		447	988	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264380	16264380	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026709-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	150	418	0	ENST00000375759.3:c.10583C>G	p.Ser3528Cys	p.S3528C	ENST00000375759	NM_015001.2	3528	tCt/tGt	13/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		418	823	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939088	36939088	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026709-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	180	499	0	ENST00000361632.4:c.621T>A	p.Asn207Lys	p.N207K	ENST00000361632		207	aaT/aaA	5/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		499	1014	SUCCESS
FH	2271	MSKCC	GRCh37	1	241672066	241672066	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026709-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	205	298	0	ENST00000366560.3:c.575C>G	p.Pro192Arg	p.P192R	ENST00000366560	NM_000143.3	192	cCc/cGc	5/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		298	662	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573918	18573918	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026709-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	116	311	0	ENST00000266497.5:c.2236G>C	p.Asp746His	p.D746H	ENST00000266497		746	Gac/Cac	15/31	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		311	451	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893602	28893602	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs142586121	NA	P-0026709-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	157	316	0	ENST00000282397.4:c.3244G>T	p.Val1082Leu	p.V1082L	ENST00000282397	NM_002019.4	1082	Gtg/Ttg	24/30	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		316	538	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003458	42003458	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026709-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	385	397	0	ENST00000219905.7:c.2995G>T	p.Glu999Ter	p.E999*	ENST00000219905	NM_001164273.1	999	Gaa/Taa	8/24	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		397	716	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679775	33679775	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026709-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	218	483	0	ENST00000308377.4:c.2306G>T	p.Trp769Leu	p.W769L	ENST00000308377	NM_152270.3	769	tGg/tTg	5/5	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		483	1013	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215546	36215546	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026709-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	280	302	0	ENST00000222270.7:c.3343C>A	p.Leu1115Met	p.L1115M	ENST00000222270	NM_014727.1	1115	Ctg/Atg	9/37	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		302	518	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906371	50906371	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs538046428	NA	P-0026709-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	229	466	0	ENST00000440232.2:c.1032G>T	p.Trp344Cys	p.W344C	ENST00000440232	NM_002691.3	344	tgG/tgT	9/27	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		466	789	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641893	12641893	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026709-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	168	455	0	ENST00000251849.4:c.856G>T	p.Glu286Ter	p.E286*	ENST00000251849	NM_002880.3	286	Gaa/Taa	8/17	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		455	842	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934178	49934178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026709-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	390	477	0	ENST00000296474.3:c.2329C>T	p.Pro777Ser	p.P777S	ENST00000296474	NM_002447.2	777	Ccc/Tcc	8/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		477	890	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99806194	99806194	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026709-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	88	186	0	ENST00000280892.6:c.478G>A	p.Glu160Lys	p.E160K	ENST00000280892	NM_001130678.1	160	Gaa/Aaa	6/7	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		186	454	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278843	1278843	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026709-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	204	399	0	ENST00000310581.5:c.2199C>G	p.Ile733Met	p.I733M	ENST00000310581	NM_198253.2	733	atC/atG	6/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		399	1083	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915676	131915676	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026709-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	141	312	0	ENST00000265335.6:c.674A>C	p.Asp225Ala	p.D225A	ENST00000265335		225	gAt/gCt	5/25	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		312	609	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930377	39930377	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026709-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	202	386	0	ENST00000378444.4:c.3087A>C	p.Lys1029Asn	p.K1029N	ENST00000378444	NM_001123385.1	1029	aaA/aaC	6/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		386	855	SUCCESS
AR	367	MSKCC	GRCh37	X	66941707	66941707	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026709-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	314	355	0	ENST00000374690.3:c.2351A>C	p.Gln784Pro	p.Q784P	ENST00000374690	NM_000044.3	784	cAg/cCg	6/8	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		355	912	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0033313-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	891	310	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.965284888771037	6	FACETS	0.932	0.913	0.95	0.932	0.913	0.95	CLONAL	5	TRUE	1	0.965284888771037	6		310	1161	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0033313-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2	500	458	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.965284888771037	3	FACETS	1	0.998	1	1	0.998	1	CLONAL	3	TRUE	0	0.965284888771037	3		458	502	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976787	2976787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033313-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	145	418	0	ENST00000396946.4:c.1225G>A	p.Glu409Lys	p.E409K	ENST00000396946	NM_032415.4	409	Gag/Aag	9/25	0.965284888771037	8	FACETS	0.89	0.81	0.975			1	CLONAL	1	TRUE	NA	0.965284888771037	8		418	1315	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425106	49425106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034568-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	138	432	0	ENST00000301067.7:c.13382T>C	p.Leu4461Pro	p.L4461P	ENST00000301067	NM_003482.3	4461	cTg/cCg	39/54	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		432	462	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431721	49431722	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0034568-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	114	437	0	ENST00000301067.7:c.9417dup	p.Lys3140GlnfsTer36	p.K3140Qfs*36	ENST00000301067	NM_003482.3	3139	-/C	34/54	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		437	382	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433583	49433583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200913080	NA	P-0034568-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	80	464	0	ENST00000301067.7:c.7970C>T	p.Ala2657Val	p.A2657V	ENST00000301067	NM_003482.3	2657	gCg/gTg	31/54	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		464	448	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061483	38061483	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034568-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	113	365	0	ENST00000250448.2:c.506C>A	p.Ala169Asp	p.A169D	ENST00000250448	NM_004496.3	169	gCc/gAc	2/2	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		365	473	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81979830	81979830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772932697	NA	P-0034568-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	201	345	0	ENST00000359376.3:c.3532G>A	p.Ala1178Thr	p.A1178T	ENST00000359376	NM_002661.3	1178	Gct/Act	31/33	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		345	558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0034568-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	62	319	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		319	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203436	NA	P-0034568-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	333	468	0	ENST00000269305.4:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269305	NM_001126112.2	163	Tac/Cac	5/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		468	635	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761146	59761147	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs771654971	NA	P-0034568-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	160	362	0	ENST00000259008.2:c.3260dup	p.Asn1087LysfsTer4	p.N1087Kfs*4	ENST00000259008	NM_032043.2	1087	aat/aaAt	20/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		362	566	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803235	1803235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866735516	NA	P-0034568-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	107	461	0	ENST00000260795.2:c.587G>A	p.Arg196His	p.R196H	ENST00000260795		196	cGc/cAc	4/17	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		461	673	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104386997	104386997	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034568-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	71	305	0	ENST00000369902.3:c.1362G>T	p.Glu454Asp	p.E454D	ENST00000369902	NM_016169.3	454	gaG/gaT	11/12	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		305	472	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285857	46285857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034568-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	87	333	0	ENST00000334344.6:c.5125G>A	p.Gly1709Arg	p.G1709R	ENST00000334344	NM_152641.2	1709	Gga/Aga	18/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		333	476	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829229	72829229	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034568-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	78	382	0	ENST00000268489.5:c.7352A>G	p.Lys2451Arg	p.K2451R	ENST00000268489	NM_006885.3	2451	aAg/aGg	9/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		382	528	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281794	46281794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034568-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	69	398	1	ENST00000371998.3:c.4241G>A	p.Gly1414Asp	p.G1414D	ENST00000371998		1414	gGc/gAc	22/23	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		399	439	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197447	106197447	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034568-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	57	334	0	ENST00000380013.4:c.5780A>G	p.Glu1927Gly	p.E1927G	ENST00000380013	NM_001127208.2	1927	gAg/gGg	11/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		334	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0034696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	492	687	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.775258692630642	6	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	3	0.855768657504564	6		687	903	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989484	7989484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772959657	NA	P-0034696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	252	638	0	ENST00000319144.4:c.202C>T	p.Arg68Cys	p.R68C	ENST00000319144	NM_001139.2	68	Cgc/Tgc	2/15	0.775258692630642	6	FACETS	0.889	0.845	0.933	1	0.99	1	CLONAL	4	TRUE	3	0.855768657504564	6		638	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519988	NA	P-0034696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	340	643	0	ENST00000269305.4:c.808T>G	p.Phe270Val	p.F270V	ENST00000269305	NM_001126112.2	270	Ttt/Gtt	8/11	0.775258692630642	6	FACETS	0.878	0.835	0.922	0.878	0.835	0.922	CLONAL	3	TRUE	3	0.855768657504564	6		643	818	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0034696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	95	555	6	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	0.855768657504564	2	FACETS	0.91	0.855	0.96	0.91	0.855	0.96	CLONAL	2	TRUE	0	0.855768657504564	2		561	122	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410486	63410486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779325879	NA	P-0034696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	42	699	3	ENST00000330258.3:c.2681G>A	p.Arg894His	p.R894H	ENST00000330258	NM_152424.3	894	cGc/cAc	2/2	0.409625055993065	3	FACETS	1	0.957	1			1	INDETERMINATE	1	TRUE	NA	0.855768657504564	3		702	105	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228384	228384	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774160524	NA	P-0034696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	105	467	2	ENST00000264932.6:c.706G>A	p.Ala236Thr	p.A236T	ENST00000264932	NM_004168.2	236	Gca/Aca	6/15	0.257694385525383	3	FACETS	1	0.981	1	0.768	0.718	0.817	INDETERMINATE	2	TRUE	0	0.855768657504564	3		469	152	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215947	41215947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41293459	NA	P-0034696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	194	456	3	ENST00000357654.3:c.5096G>A	p.Arg1699Gln	p.R1699Q	ENST00000357654	NM_007294.3	1699	cGg/cAg	17/23	0.855768657504564	13	FACETS	0.98	0.914	1	0.7	0.653	0.748	CLONAL	5	TRUE	6	0.855768657504564	13		459	528	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120508105	120508105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	203	405	0	ENST00000256646.2:c.1652C>T	p.Pro551Leu	p.P551L	ENST00000256646	NM_024408.3	551	cCg/cTg	10/34	0.855768657504564	5	FACETS	1	0.994	1			1	CLONAL	5	TRUE	NA	0.855768657504564	5		405	209	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362641	118362641	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	77	418	2	ENST00000534358.1:c.5002C>T	p.Gln1668Ter	p.Q1668*	ENST00000534358	NM_005933.3	1668	Cag/Tag	15/36	0.855768657504564	4	FACETS	0.803	0.718	0.89	0.803	0.718	0.89	CLONAL	2	TRUE	2	0.855768657504564	4		420	208	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130378	2130378	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1555511663	NA	P-0034696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	251	561	1	ENST00000219476.3:c.3610G>A	p.Gly1204Arg	p.G1204R	ENST00000219476	NM_000548.3	1204	Ggg/Agg	30/42	0.855768657504564	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.855768657504564	3		562	266	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291914	15291914	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451498063	NA	P-0034696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	106	809	0	ENST00000263388.2:c.2852G>A	p.Arg951His	p.R951H	ENST00000263388	NM_000435.2	951	cGt/cAt	18/33	0.819955877073418	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.855768657504564	4		809	210	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227657	36227657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1261171231	NA	P-0034696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	134	588	0	ENST00000222270.7:c.7226G>A	p.Arg2409Gln	p.R2409Q	ENST00000222270	NM_014727.1	2409	cGg/cAg	31/37	0.855768657504564	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.855768657504564	2		588	148	SUCCESS
ATR	545	MSKCC	GRCh37	3	142241620	142241620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	94	520	0	ENST00000350721.4:c.4216G>A	p.Ala1406Thr	p.A1406T	ENST00000350721	NM_001184.3	1406	Gcg/Acg	23/47	0.320741291021952	5	FACETS	0.984	0.903	1	0.984	0.903	1	INDETERMINATE	3	TRUE	2	0.855768657504564	5		520	170	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160646	56160646	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343464548	NA	P-0034696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	55	335	0	ENST00000399503.3:c.920G>A	p.Arg307His	p.R307H	ENST00000399503	NM_005921.1	307	cGt/cAt	4/20	0.51718158465906	6	FACETS	1	0.945	1	0.83	0.738	0.921	CLONAL	3	TRUE	2	0.855768657504564	6		335	105	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938223	76938223	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	82	784	0	ENST00000373344.5:c.2525del	p.Pro842GlnfsTer27	p.P842Qfs*27	ENST00000373344	NM_000489.3	842	cCa/ca	9/35	0.855768657504564	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.855768657504564	1		784	93	SUCCESS
APC	324	MSKCC	GRCh37	5	112116509	112116509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1484797510	NA	P-0034696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	22	235	0	ENST00000257430.4:c.554C>T	p.Thr185Ile	p.T185I	ENST00000257430	NM_000038.5	185	aCc/aTc	6/16	0.446150276409191	3	FACETS	1	0.919	1	0.655	0.53	0.786	INDETERMINATE	1	TRUE	1	0.855768657504564	3		235	56	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345289	70345289	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	21	678	0	ENST00000374080.3:c.2315A>G	p.Lys772Arg	p.K772R	ENST00000374080		772	aAg/aGg	16/45	0.409625055993065	3	FACETS	0.49	0.381	0.614			1	INDETERMINATE	1	TRUE	NA	0.855768657504564	3		678	143	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137235	64137235	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	40	700	0	ENST00000334205.4:c.1667G>A	p.Arg556Gln	p.R556Q	ENST00000334205	NM_003942.2	556	cGg/cAg	14/17	0.855768657504564	4	FACETS	0.226	0.187	0.27	0.113	0.093	0.135	SUBCLONAL	1	TRUE	2	0.855768657504564	4		700	768	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0035444-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	39	288	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.85	0.703	1	0.85	0.703	1	CLONAL	1	TRUE	1	0.17	2		288	540	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876449	35876449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2229232	NA	P-0035444-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	74	578	0	ENST00000303115.3:c.1241C>T	p.Thr414Met	p.T414M	ENST00000303115	NM_002185.3	414	aCg/aTg	8/8	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.17	2		578	821	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241093	39241093	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035444-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	54	321	0	ENST00000402219.2:c.1978C>T	p.Arg660Cys	p.R660C	ENST00000402219	NM_005633.3	660	Cgc/Tgc	12/23	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.17	2		321	567	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25362797	25362798	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0035444-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	57	284	0	ENST00000311936.3:c.498_499del	p.His166GlnfsTer9	p.H166Qfs*9	ENST00000311936	NM_004985.3	166	caTAaa/caaa	5/5	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.17	2		284	605	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55269452	55269452	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142442994	NA	P-0035444-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	102	573	0	ENST00000275493.2:c.3139G>A	p.Val1047Met	p.V1047M	ENST00000275493	NM_005228.3	1047	Gtg/Atg	26/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.17	2		573	946	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039580-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	150	617	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		617	509	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118708	115118711	+	frameshift_variant	Frame_Shift_Del	DEL	GTTG	GTTG	-	novel	NA	P-0039580-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	124	593	0	ENST00000257566.3:c.630_633del	p.Asn211ThrfsTer31	p.N211Tfs*31	ENST00000257566	NM_016569.3	210	acCAAC/ac	2/8	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		593	474	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0041436-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	5	308	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.165	0.093	0.267	0.165	0.093	0.267	SUBCLONAL	1	TRUE	1	0.24	2		313	252	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0041436-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	6	0	0	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	0.092914493029863	3	FACETS	0.147	0.087	0.229	0.074	0.043	0.115	INDETERMINATE	1	TRUE	1	0.24	3		0	380	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38631981	38631981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1255149646	NA	P-0041436-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	2	0	0	ENST00000299084.4:c.471del	p.Gln158SerfsTer16	p.Q158Sfs*16	ENST00000299084	NM_152594.2	156	cTt/ct	5/7	1	2	FACETS	0.096	0.036	0.199	0.096	0.036	0.199	SUBCLONAL	1	TRUE	1	0.24	2		0	173	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47491255	47491255	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041436-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	23	498	0	ENST00000404338.3:c.3836C>G	p.Thr1279Arg	p.T1279R	ENST00000404338	NM_004491.4	1279	aCg/aGg	3/6	1	2	FACETS	0.54	0.421	0.678	0.54	0.421	0.678	SUBCLONAL	1	TRUE	1	0.24	2		498	355	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341238	8341238	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041436-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	15	606	0	ENST00000356435.5:c.4978A>G	p.Arg1660Gly	p.R1660G	ENST00000356435		1660	Agg/Ggg	30/35	1	2	FACETS	0.584	0.428	0.771	0.584	0.428	0.771	SUBCLONAL	1	TRUE	1	0.24	2		606	214	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0042526-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	56	283	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		283	370	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913315	NA	P-0042526-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	21	530	0	ENST00000326873.7:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000326873	NM_000455.4	194	Gac/Tac	4/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		530	448	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239948	98239948	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042526-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	55	444	0	ENST00000331920.6:c.1384T>G	p.Cys462Gly	p.C462G	ENST00000331920	NM_000264.3	462	Tgc/Ggc	10/24	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		444	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578386	7578386	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	199	591	0	ENST00000269305.4:c.544del	p.Cys182AlafsTer65	p.C182Afs*65	ENST00000269305	NM_001126112.2	182	Tgc/gc	5/11	0.290225847718278	2	FACETS	0.934	0.87	0.999	0.934	0.87	0.999	CLONAL	2	TRUE	0	0.347065170799567	2		591	614	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177010	56177013	+	frameshift_variant	Frame_Shift_Del	DEL	TATA	TATA	-	novel	NA	P-0042590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	43	308	0	ENST00000399503.3:c.2280_2283del	p.Arg763CysfsTer35	p.R763Cfs*35	ENST00000399503	NM_005921.1	760	ctTATA/ct	13/20	1	2	FACETS	0.86	0.724	1	0.86	0.724	1	CLONAL	1	TRUE	1	0.347065170799567	2		308	288	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0051920-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	55	310	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		310	612	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578494	7578497	+	frameshift_variant	Frame_Shift_Del	DEL	ACAG	ACAG	-	novel	NA	P-0051920-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1875	55	496	0	ENST00000269305.4:c.433_436del	p.Leu145GlyfsTer24	p.L145Gfs*24	ENST00000269305	NM_001126112.2	145	CTGTgg/gg	5/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		496	1930	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052108-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	179	387	0				ENST00000310581	NM_198253.2	-/1132			0.587892513641788	3	FACETS	1	0.964	1	0.531	0.493	0.57	CLONAL	1	TRUE	1	0.900461046948859	3		387	543	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0052108-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	262	538	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	0.928	0.876	0.98	0.928	0.876	0.98	CLONAL	1	TRUE	1	0.900461046948859	2		538	627	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101468	27101468	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052108-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	137	566	0	ENST00000324856.7:c.4750C>T	p.Gln1584Ter	p.Q1584*	ENST00000324856	NM_006015.4	1584	Cag/Tag	18/20	0.377413175668529	2	FACETS	0.478	0.436	0.522	0.239	0.218	0.261	INDETERMINATE	1	TRUE	0	0.900461046948859	2		566	636	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218538	5218538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767763908	NA	P-0052108-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	270	578	0	ENST00000357368.4:c.3941G>A	p.Arg1314His	p.R1314H	ENST00000357368	NM_002850.3	1314	cGc/cAc	25/38	0.39190561581928	1	FACETS	0.721	0.688	0.755	0.721	0.688	0.755	INDETERMINATE	1	TRUE	0	0.900461046948859	1		578	457	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856020	68856020	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052108-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	335	631	0	ENST00000261769.5:c.1828C>T	p.Gln610Ter	p.Q610*	ENST00000261769	NM_004360.3	610	Cag/Tag	12/16	0.900461046948859	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.900461046948859	1		631	382	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239915	53239915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052108-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	372	313	0	ENST00000375401.3:c.1526C>T	p.Ser509Leu	p.S509L	ENST00000375401	NM_004187.3	509	tCa/tTa	11/26	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.900461046948859	1		313	396	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023633	27023634	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCGGCTC	novel	NA	P-0052108-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	292	516	0	ENST00000324856.7:c.741_747dup	p.Lys250ArgfsTer152	p.K250Rfs*152	ENST00000324856	NM_006015.4	247	gcc/gCCGGCTCcc	1/20	0.377413175668529	2	FACETS	1	0.993	1	0.621	0.592	0.65	INDETERMINATE	1	TRUE	0	0.900461046948859	2		516	522	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858097	9858097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770546037	NA	P-0052108-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	319	623	0	ENST00000330684.3:c.3304G>A	p.Glu1102Lys	p.E1102K	ENST00000330684	NM_001134407.1	1102	Gag/Aag	13/13	0.683389974569542	3	FACETS	1	0.991	1	0.601	0.569	0.633	CLONAL	1	TRUE	1	0.900461046948859	3		623	855	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36024580	36024580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052108-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	301	594	0	ENST00000358208.4:c.569C>T	p.Ser190Leu	p.S190L	ENST00000358208		190	tCa/tTa	6/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.900461046948859	2		594	627	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420493	49420493	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs727503979	NA	P-0052108-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	168	650	0	ENST00000301067.7:c.15256C>T	p.Arg5086Ter	p.R5086*	ENST00000301067	NM_003482.3	5086	Cga/Tga	48/54	0.39190561581928	1	FACETS	0.344	0.317	0.371	0.344	0.317	0.371	INDETERMINATE	1	TRUE	0	0.900461046948859	1		650	597	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023064	27023079	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGCGAGGGCCCCGC	AAAGCGAGGGCCCCGC	-	novel	NA	P-0052108-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	101	418	0	ENST00000324856.7:c.170_185del	p.Glu57AlafsTer39	p.E57Afs*39	ENST00000324856	NM_006015.4	57	gAAAGCGAGGGCCCCGCc/gc	1/20	0.377413175668529	2	FACETS	0.564	0.507	0.622	0.282	0.253	0.311	INDETERMINATE	1	TRUE	0	0.900461046948859	2		418	398	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63810704	63810704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052108-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	343	554	1	ENST00000279873.7:c.791C>T	p.Ser264Leu	p.S264L	ENST00000279873	NM_032199.2	264	tCa/tTa	5/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.900461046948859	2		555	721	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69230490	69230528	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TACAGATTCATTTGAAGAAGATCCTGAAATTTCCTTAGC	TACAGATTCATTTGAAGAAGATCCTGAAATTTCCTTAGC	-	novel	NA	P-0052108-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	109	423	0	ENST00000462284.1:c.880_918del	p.Thr294_Ala306del	p.T294_A306del	ENST00000462284	NM_002392.5	293	gaTACAGATTCATTTGAAGAAGATCCTGAAATTTCCTTAGCt/gat	10/11	0.39190561581928	1	FACETS	0.337	0.305	0.37	0.337	0.305	0.37	INDETERMINATE	1	TRUE	0	0.900461046948859	1		423	395	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910542	32910542	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052108-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	271	535	0	ENST00000380152.3:c.2050C>T	p.Gln684Ter	p.Q684*	ENST00000380152		684	Cag/Tag	11/27	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.900461046948859	2		535	601	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060763	38060763	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1286708161	NA	P-0052108-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	205	711	0	ENST00000250448.2:c.1226C>T	p.Ser409Leu	p.S409L	ENST00000250448	NM_004496.3	409	tCg/tTg	2/2	0.327025020240314	1	FACETS	0.391	0.364	0.418	0.391	0.364	0.418	INDETERMINATE	1	TRUE	0	0.900461046948859	1		711	641	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647819	3647819	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052108-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	333	578	0	ENST00000294008.3:c.1345G>A	p.Glu449Lys	p.E449K	ENST00000294008	NM_032444.2	449	Gag/Aag	6/15	0.683389974569542	3	FACETS	1	0.992	1	0.621	0.59	0.654	CLONAL	1	TRUE	1	0.900461046948859	3		578	863	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349481	89349481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052108-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	369	569	0	ENST00000301030.4:c.3469G>A	p.Glu1157Lys	p.E1157K	ENST00000301030	NM_001256183.1	1157	Gag/Aag	9/13	0.900461046948859	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.900461046948859	1		569	418	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602479	10602479	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052108-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	162	643	0	ENST00000171111.5:c.1099G>T	p.Gly367Cys	p.G367C	ENST00000171111	NM_203500.1	367	Ggc/Tgc	3/6	0.39190561581928	1	FACETS	0.335	0.308	0.362	0.335	0.308	0.362	INDETERMINATE	1	TRUE	0	0.900461046948859	1		643	591	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024104	31024104	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052108-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	302	705	0	ENST00000375687.4:c.3589C>A	p.Pro1197Thr	p.P1197T	ENST00000375687	NM_015338.5	1197	Cct/Act	13/13	1	2	FACETS	0.974	0.924	1	0.974	0.924	1	CLONAL	1	TRUE	1	0.900461046948859	2		705	689	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641301	12641301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs551466727	NA	P-0052108-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	219	468	0	ENST00000251849.4:c.997C>T	p.Arg333Cys	p.R333C	ENST00000251849	NM_002880.3	333	Cgt/Tgt	10/17	1	2	FACETS	0.987	0.928	1	0.987	0.928	1	CLONAL	1	TRUE	1	0.900461046948859	2		468	493	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162539	47162539	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052108-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	277	476	0	ENST00000409792.3:c.3587C>G	p.Ser1196Cys	p.S1196C	ENST00000409792	NM_014159.6	1196	tCt/tGt	3/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.900461046948859	2		476	600	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723618	49723618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052108-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	120	226	0	ENST00000449682.2:c.1024C>T	p.Arg342Trp	p.R342W	ENST00000449682	NM_020998.3	342	Cgg/Tgg	9/18	1	2	FACETS	0.98	0.901	1	0.98	0.901	1	CLONAL	1	TRUE	1	0.900461046948859	2		226	272	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129926	55129926	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052108-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	325	613	0	ENST00000257290.5:c.460G>C	p.Asp154His	p.D154H	ENST00000257290	NM_006206.4	154	Gat/Cat	4/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.900461046948859	2		613	693	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31521270	31521270	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052108-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	402	498	0	ENST00000344624.3:c.907C>G	p.Leu303Val	p.L303V	ENST00000344624		303	Ctg/Gtg	3/33	0.587892513641788	3	FACETS	0.925	0.889	0.961	0.925	0.889	0.961	CLONAL	2	TRUE	1	0.900461046948859	3		498	700	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959969	38959969	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052108-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	353	534	0	ENST00000357387.3:c.1963C>G	p.Leu655Val	p.L655V	ENST00000357387	NM_152756.3	655	Ctt/Gtt	21/38	0.587892513641788	3	FACETS	0.88	0.842	0.918	0.88	0.842	0.918	CLONAL	2	TRUE	1	0.900461046948859	3		534	646	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562418	176562418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052108-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	324	624	1	ENST00000439151.2:c.314C>T	p.Ser105Leu	p.S105L	ENST00000439151	NM_022455.4	105	tCa/tTa	2/23	1	2	FACETS	0.937	0.89	0.984	0.937	0.89	0.984	CLONAL	1	TRUE	1	0.900461046948859	2		625	768	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940250	31940250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1358401217	NA	P-0052108-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	154	622	0	ENST00000375333.2:c.392G>A	p.Arg131Gln	p.R131Q	ENST00000375333	NM_032454.1	131	cGa/cAa	2/8	0.316404051285862	6	FACETS	0.865	0.791	0.944	0.216	0.197	0.236	INDETERMINATE	1	TRUE	2	0.900461046948859	6		622	1107	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869011	117869011	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0052108-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	120	386	0	ENST00000297338.2:c.689-1G>C		p.X230_splice	ENST00000297338	NM_006265.2	230			0.900461046948859	3	FACETS	0.514	0.464	0.566	0.257	0.232	0.283	SUBCLONAL	1	TRUE	1	0.900461046948859	3		386	752	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750755	128750755	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052108-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	285	636	0	ENST00000377970.2:c.292C>T	p.Arg98Trp	p.R98W	ENST00000377970	NM_002467.4	98	Cgg/Tgg	2/3	0.900461046948859	3	FACETS	1	0.965	1	0.516	0.486	0.547	CLONAL	1	TRUE	1	0.900461046948859	3		636	889	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916538	39916538	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052108-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	276	285	0	ENST00000378444.4:c.4465G>A	p.Asp1489Asn	p.D1489N	ENST00000378444	NM_001123385.1	1489	Gat/Aat	11/15	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.900461046948859	1		285	308	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024158	31024161	+	missense_variant	Missense_Mutation	ONP	CCAG	CCAG	TTAA	novel	NA	P-0052108-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	235	701	0	ENST00000375687.4:c.3643_3646delinsTTAA	p.Pro1215_Val1216delinsLeuMet	p.P1215_V1216delinsLM	ENST00000375687	NM_015338.5	1215	CCAGtg/TTAAtg	13/13	1	2	FACETS	0.854	0.803	0.907	0.854	0.803	0.907	CLONAL	1	TRUE	1	0.900461046948859	2		701	611	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754809	29754809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052108-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	132	601	0	ENST00000389048.3:c.1126C>T	p.Leu376Phe	p.L376F	ENST00000389048	NM_004304.4	376	Ctc/Ttc	4/29	0.482922030276134	1	FACETS	0.357	0.327	0.389	0.357	0.327	0.389	INDETERMINATE	1	TRUE	0	0.900461046948859	1		601	451	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246513	105246515	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0052108-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	124	563	0	ENST00000349310.3:c.85_87del	p.Leu29del	p.L29del	ENST00000349310	NM_001014432.1	29	CTC/-	4/15	0.327025020240314	1	FACETS	0.287	0.261	0.315	0.287	0.261	0.315	INDETERMINATE	1	TRUE	0	0.900461046948859	1		563	527	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	297	1304	1	ENST00000269305.4:c.430del	p.Gln144SerfsTer26	p.Q144Sfs*26	ENST00000269305	NM_001126112.2	144	Cag/ag	5/11	0.611351790302252	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.611351790302252	1		1305	634	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306758	41306758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	134	608	0	ENST00000373198.4:c.901G>A	p.Gly301Arg	p.G301R	ENST00000373198	NM_133170.3	301	Ggg/Agg	7/32	NA	2	FACETS	0.987	0.904	1			1	INDETERMINATE	1	TRUE	NA	0.611351790302252	2		608	444	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997874	149997874	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0054073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	135	459	0	ENST00000253339.5:c.2594-1G>A		p.X865_splice	ENST00000253339		865			0.611351790302252	1	FACETS	0.899	0.829	0.971	0.899	0.829	0.971	CLONAL	1	TRUE	0	0.611351790302252	1		459	341	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339853	116339853	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	135	499	0	ENST00000397752.3:c.715C>A	p.Pro239Thr	p.P239T	ENST00000397752	NM_000245.2	239	Cct/Act	2/21	0.611351790302252	2	FACETS	0.882	0.806	0.96	0.441	0.403	0.48	CLONAL	1	TRUE	0	0.611351790302252	2		499	501	SUCCESS
AR	367	MSKCC	GRCh37	X	66765163	66765163	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	32	389	0	ENST00000374690.3:c.175C>T	p.Gln59Ter	p.Q59*	ENST00000374690	NM_000044.3	59	Cag/Tag	1/8	0.611351790302252	1	FACETS	0.385	0.315	0.462	0.385	0.315	0.462	SUBCLONAL	1	TRUE	0	0.611351790302252	1		389	189	SUCCESS
AR	367	MSKCC	GRCh37	X	66765169	66765169	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	14	361	0	ENST00000374690.3:c.181C>T	p.Gln61Ter	p.Q61*	ENST00000374690	NM_000044.3	61	Cag/Tag	1/8	0.611351790302252	1	FACETS	0.178	0.128	0.237	0.178	0.128	0.237	SUBCLONAL	1	TRUE	0	0.611351790302252	1		361	179	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054073-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	162	1304	1	ENST00000269305.4:c.430del	p.Gln144SerfsTer26	p.Q144Sfs*26	ENST00000269305	NM_001126112.2	144	Cag/ag	5/11	0.625641501567164	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.625641501567164	1		1305	352	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306758	41306758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054073-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	148	608	0	ENST00000373198.4:c.901G>A	p.Gly301Arg	p.G301R	ENST00000373198	NM_133170.3	301	Ggg/Agg	7/32	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.625641501567164	2		608	446	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997874	149997874	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0054073-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	164	459	0	ENST00000253339.5:c.2594-1G>A		p.X865_splice	ENST00000253339		865			0.625641501567164	1	FACETS	0.938	0.873	1	0.938	0.873	1	CLONAL	1	TRUE	0	0.625641501567164	1		459	384	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339853	116339853	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054073-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	245	499	0	ENST00000397752.3:c.715C>A	p.Pro239Thr	p.P239T	ENST00000397752	NM_000245.2	239	Cct/Act	2/21	0.607764173909462	2	FACETS	1	0.963	1	0.518	0.486	0.551	CLONAL	1	TRUE	0	0.625641501567164	2		499	756	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631530	67631530	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054073-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	239	585	0	ENST00000272342.5:c.1716A>T	p.Lys572Asn	p.K572N	ENST00000272342	NM_019002.3	572	aaA/aaT	5/6	1	2	FACETS	0.876	0.82	0.934	0.876	0.82	0.934	CLONAL	1	TRUE	1	0.625641501567164	2		585	872	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111472	8111473	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0058429-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	134	529	0	ENST00000346208.3:c.959_960del	p.Cys320SerfsTer31	p.C320Sfs*31	ENST00000346208		320	TGt/t	5/6	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		529	574	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462802	69462803	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGGAGCGT	novel	NA	P-0058429-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	115	591	0	ENST00000227507.2:c.618_625dup	p.Val209GlyfsTer10	p.V209Gfs*10	ENST00000227507	NM_053056.2	205	-/GGGAGCGT	4/5	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		591	1050	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528441	29528441	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058429-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	90	329	0	ENST00000356175.3:c.1198C>T	p.Gln400Ter	p.Q400*	ENST00000356175	NM_000267.3	400	Cag/Tag	11/57	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		329	347	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0060088-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	19	311	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		311	62	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060088-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	36	387	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		387	79	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0060088-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	20	489	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		489	64	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934884	9934884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060088-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	22	399	0	ENST00000330684.3:c.1406G>A	p.Arg469Lys	p.R469K	ENST00000330684	NM_001134407.1	469	aGa/aAa	6/13	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		399	59	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139215	108139218	+	frameshift_variant	Frame_Shift_Del	DEL	TGTG	TGTG	-	rs786202695	NA	P-0060088-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	16	441	0	ENST00000278616.4:c.2720_2723del	p.Cys907Ter	p.C907*	ENST00000278616	NM_000051.3	906	tTGTGt/tt	18/63	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		441	59	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579485	7579485	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs869312782	NA	P-0060178-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	565	309	0	ENST00000269305.4:c.202G>T	p.Glu68Ter	p.E68*	ENST00000269305	NM_001126112.2	68	Gag/Tag	4/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		309	985	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881462	48881462	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060178-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	157	292	0	ENST00000267163.4:c.184C>T	p.Gln62Ter	p.Q62*	ENST00000267163	NM_000321.2	62	Cag/Tag	2/27	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		292	432	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564741	41564741	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060178-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	116	322	0	ENST00000263253.7:c.4042G>A	p.Glu1348Lys	p.E1348K	ENST00000263253	NM_001429.3	1348	Gag/Aag	25/31	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		322	648	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239788	41239788	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060178-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	102	294	0	ENST00000379561.5:c.562G>C	p.Glu188Gln	p.E188Q	ENST00000379561	NM_002015.3	188	Gag/Cag	1/3	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		294	971	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610421	10610421	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060178-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	394	245	0	ENST00000171111.5:c.289A>C	p.Lys97Gln	p.K97Q	ENST00000171111	NM_203500.1	97	Aag/Cag	2/6	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		245	815	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426780	121426780	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060178-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	240	291	0	ENST00000257555.6:c.471G>C	p.Gln157His	p.Q157H	ENST00000257555		157	caG/caC	2/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		291	772	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335833	73335833	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060178-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	195	358	0	ENST00000377767.4:c.2462A>C	p.His821Pro	p.H821P	ENST00000377767	NM_014953.3	821	cAc/cCc	18/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		358	464	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254450	10254450	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060178-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	315	177	0	ENST00000340748.4:c.3060G>C	p.Lys1020Asn	p.K1020N	ENST00000340748		1020	aaG/aaC	28/40	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		177	617	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748575	40748575	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060178-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	300	229	0	ENST00000392038.2:c.307A>G	p.Ile103Val	p.I103V	ENST00000392038	NM_001626.4	103	Atc/Gtc	5/14	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		229	618	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508554	106508554	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060178-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	71	275	0	ENST00000359195.3:c.548C>G	p.Pro183Arg	p.P183R	ENST00000359195	NM_002649.2	183	cCg/cGg	2/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		275	835	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397720	139397720	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060178-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	102	182	0	ENST00000277541.6:c.5081A>G	p.Gln1694Arg	p.Q1694R	ENST00000277541	NM_017617.3	1694	cAg/cGg	27/34	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		182	723	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100532	157100532	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060178-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	57	154	0	ENST00000346085.5:c.1469G>C	p.Trp490Ser	p.W490S	ENST00000346085	NM_020732.3	490	tGg/tCg	1/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		154	539	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925519	114925532	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCCGCCACCCGC	CCTCCGCCACCCGC	-	novel	NA	P-0060178-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	101	269	0	ENST00000543371.1:c.1602_1615del	p.Pro535AlafsTer3	p.P535Afs*3	ENST00000543371	NM_001198531.1	533	CCTCCGCCACCCGCc/c	14/14	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		269	634	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77051747	77051747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060178-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	134	376	0	ENST00000356341.3:c.1060G>A	p.Asp354Asn	p.D354N	ENST00000356341	NM_002576.4	354	Gat/Aat	11/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		376	899	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968289	15968289	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060178-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	99	353	0	ENST00000268712.3:c.4996C>A	p.His1666Asn	p.H1666N	ENST00000268712	NM_006311.3	1666	Cat/Aat	34/46	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		353	700	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996141	73996141	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060178-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	130	340	0	ENST00000318443.5:c.875A>T	p.Gln292Leu	p.Q292L	ENST00000318443	NM_001024736.1	292	cAg/cTg	5/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		340	715	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0061430-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	103	463	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		463	494	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023440	27023449	+	frameshift_variant	Frame_Shift_Del	DEL	AGCGCTGCAG	AGCGCTGCAG	-	novel	NA	P-0061430-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	60	371	0	ENST00000324856.7:c.550_559del	p.Leu184AlafsTer45	p.L184Afs*45	ENST00000324856	NM_006015.4	182	gcAGCGCTGCAG/gc	1/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		371	427	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101586	27101586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1420328983	NA	P-0061430-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	118	463	0	ENST00000324856.7:c.4868C>T	p.Ser1623Leu	p.S1623L	ENST00000324856	NM_006015.4	1623	tCg/tTg	18/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		463	539	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843721	156843721	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061430-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	206	525	0	ENST00000524377.1:c.1147T>A	p.Phe383Ile	p.F383I	ENST00000524377	NM_002529.3	383	Ttc/Atc	8/17	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		525	696	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983108	201983111	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	novel	NA	P-0061430-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	175	401	0	ENST00000359651.3:c.959_962del	p.Lys320ThrfsTer4	p.K320Tfs*4	ENST00000359651		319	aaAAAG/aa	7/8	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		401	470	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230486756	230486756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375905173	NA	P-0061430-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	103	387	0	ENST00000391860.1:c.497G>A	p.Arg166Gln	p.R166Q	ENST00000391860	NM_001258311.1	166	cGg/cAg	3/7	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		387	564	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710987	114710987	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061430-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	49	178	0	ENST00000543371.1:c.211C>T	p.Arg71Cys	p.R71C	ENST00000543371	NM_001198531.1	71	Cgc/Tgc	2/14	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		178	290	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115693	108115693	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061430-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	134	332	0	ENST00000278616.4:c.841G>A	p.Glu281Lys	p.E281K	ENST00000278616	NM_000051.3	281	Gaa/Aaa	7/63	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		332	257	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230568	46230568	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061430-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	116	379	0	ENST00000334344.6:c.817C>A	p.Pro273Thr	p.P273T	ENST00000334344	NM_152641.2	273	Cct/Act	8/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		379	801	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061305	38061316	+	inframe_deletion	In_Frame_Del	DEL	GAAGCAGTCATT	GAAGCAGTCATT	-	novel	NA	P-0061430-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	221	443	0	ENST00000250448.2:c.673_684del	p.Asn225_Phe228del	p.N225_F228del	ENST00000250448	NM_004496.3	225	AATGACTGCTTC/-	2/2	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		443	536	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934507	9934507	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061430-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	71	304	0	ENST00000330684.3:c.1648C>G	p.Leu550Val	p.L550V	ENST00000330684	NM_001134407.1	550	Cta/Gta	7/13	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		304	402	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819651	81819651	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061430-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	114	419	0	ENST00000359376.3:c.57G>C	p.Lys19Asn	p.K19N	ENST00000359376	NM_002661.3	19	aaG/aaC	2/33	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		419	599	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727894	78727894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778029024	NA	P-0061430-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	99	375	0	ENST00000306801.3:c.739G>A	p.Glu247Lys	p.E247K	ENST00000306801	NM_020761.2	247	Gag/Aag	6/34	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		375	596	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105651	11105651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061430-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	116	342	0	ENST00000358026.2:c.1567G>A	p.Glu523Lys	p.E523K	ENST00000358026	NM_001128849.1	523	Gag/Aag	9/36	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		342	550	SUCCESS
ALK	238	MSKCC	GRCh37	2	29450495	29450495	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061430-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	95	397	0	ENST00000389048.3:c.2859A>C	p.Glu953Asp	p.E953D	ENST00000389048	NM_004304.4	953	gaA/gaC	17/29	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		397	554	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39294764	39294771	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CATACCTC	CATACCTC	ATT	novel	NA	P-0061430-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	68	288	1	ENST00000402219.2:c.211_213+5delinsAAT		p.X71_splice	ENST00000402219	NM_005633.3	71		2/23	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		289	398	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131229	202131229	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061430-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	93	376	0	ENST00000358485.4:c.197T>G	p.Leu66Arg	p.L66R	ENST00000358485	NM_001080125.1	66	cTt/cGt	2/9	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		376	560	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165212	47165212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061430-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	72	392	0	ENST00000409792.3:c.914C>T	p.Thr305Ile	p.T305I	ENST00000409792	NM_014159.6	305	aCa/aTa	3/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		392	625	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165214	47165214	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1384724360	NA	P-0061430-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	74	389	0	ENST00000409792.3:c.912A>C	p.Lys304Asn	p.K304N	ENST00000409792	NM_014159.6	304	aaA/aaC	3/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		389	630	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141567225	141567225	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061430-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	76	371	0	ENST00000220592.5:c.989T>G	p.Val330Gly	p.V330G	ENST00000220592	NM_012154.3	330	gTc/gGc	8/19	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		371	737	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949977	44949978	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061430-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	129	272	0	ENST00000377967.4:c.3747dup	p.Lys1250Ter	p.K1250*	ENST00000377967	NM_021140.2	1249	tat/taTt	26/29	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		272	486	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966675	44966707	+	inframe_deletion	In_Frame_Del	DEL	TGAAGCAATGTCAGACATTGAGGGAAGCTCTCA	TGAAGCAATGTCAGACATTGAGGGAAGCTCTCA	-	novel	NA	P-0061430-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	209	343	0	ENST00000377967.4:c.3900_3932del	p.Lys1301_Ile1311del	p.K1301_I1311del	ENST00000377967	NM_021140.2	1300	cTGAAGCAATGTCAGACATTGAGGGAAGCTCTCAtt/ctt	27/29	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		343	519	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0061637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	113	182	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		182	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0061637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	458	754	2	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		756	650	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042509	42042509	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	165	355	0	ENST00000219905.7:c.6704G>A	p.Arg2235Lys	p.R2235K	ENST00000219905	NM_001164273.1	2235	aGa/aAa	17/24	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		355	454	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456514	29456514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	145	599	0	ENST00000389048.3:c.2404G>A	p.Glu802Lys	p.E802K	ENST00000389048	NM_004304.4	802	Gaa/Aaa	14/29	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		599	580	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550938	150550938	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1288	187	535	0	ENST00000369026.2:c.718G>A	p.Glu240Lys	p.E240K	ENST00000369026	NM_021960.4	240	Gaa/Aaa	2/3	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		535	1475	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550913	150550913	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1294528481	NA	P-0061637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1376	204	573	0	ENST00000369026.2:c.743G>T	p.Arg248Leu	p.R248L	ENST00000369026	NM_021960.4	248	cGa/cTa	2/3	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		573	1580	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640905	3640905	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	152	757	0	ENST00000294008.3:c.2734G>A	p.Gly912Arg	p.G912R	ENST00000294008	NM_032444.2	912	Gga/Aga	12/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		757	585	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923636	72923636	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	182	560	0	ENST00000268489.5:c.3442G>T	p.Asp1148Tyr	p.D1148Y	ENST00000268489	NM_006885.3	1148	Gac/Tac	4/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		560	462	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981568	55981570	+	missense_variant	Missense_Mutation	TNP	AGA	AGA	CTT	novel	NA	P-0061637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	56	170	0	ENST00000263923.4:c.367_369delinsAAG	p.Ser123Lys	p.S123K	ENST00000263923	NM_002253.2	123	TCT/AAG	4/30	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		170	177	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642480	117642480	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	154	551	0	ENST00000368508.3:c.5719G>T	p.Ala1907Ser	p.A1907S	ENST00000368508	NM_002944.2	1907	Gct/Tct	35/43	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		551	792	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157192748	157192749	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GA	GA	CT	novel	NA	P-0061637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	20	323	0	ENST00000346085.5:c.1738_1739delinsCT	p.Asp580Leu	p.D580L	ENST00000346085	NM_020732.3	580	GAc/CTc	3/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		323	289	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0062817-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	107	283	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.183807913534539	3	FACETS	0.753	0.685	0.821	0.753	0.685	0.821	INDETERMINATE	2	TRUE	1	0.670923193048918	3		283	283	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062817-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	60	387	0				ENST00000310581	NM_198253.2	-/1132			0.169572199305294	4	FACETS	0.977	0.862	1	0.977	0.862	1	INDETERMINATE	2	TRUE	2	0.670923193048918	4		387	153	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0062817-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	122	383	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.670923193048918	2		383	344	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109974	115109974	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062817-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	105	424	0	ENST00000257566.3:c.1904G>T	p.Arg635Leu	p.R635L	ENST00000257566	NM_016569.3	635	cGc/cTc	8/8	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.670923193048918	2		424	255	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477853	140477853	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs180177036	NA	P-0062817-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	137	303	0	ENST00000288602.6:c.1455G>C	p.Leu485Phe	p.L485F	ENST00000288602	NM_004333.4	485	ttG/ttC	12/18	0.670923193048918	3	FACETS	1	0.976	1	0.589	0.54	0.64	CLONAL	1	TRUE	1	0.670923193048918	3		303	463	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41489064	41489064	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0062817-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	64	307	0	ENST00000263253.7:c.56C>G	p.Ser19Ter	p.S19*	ENST00000263253	NM_001429.3	19	tCa/tGa	1/31	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.670923193048918	NA		307	185	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038828	47038828	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062817-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	81	209	0	ENST00000377604.3:c.835C>T	p.Gln279Ter	p.Q279*	ENST00000377604	NM_001204468.1	279	Cag/Tag	9/24	0.451408128505475	0	FACETS		NA	1			1	NA	2	TRUE	NA	0.670923193048918	0		209	102	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213589	27213589	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062817-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	80	255	0	ENST00000380036.4:c.2985G>C	p.Lys995Asn	p.K995N	ENST00000380036	NM_000459.3	995	aaG/aaC	18/23	0.670923193048918	2	FACETS	0.985	0.881	1	0.493	0.44	0.547	CLONAL	1	TRUE	0	0.670923193048918	2		255	242	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119822	108119822	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062817-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	227	228	0	ENST00000278616.4:c.1228G>C	p.Val410Leu	p.V410L	ENST00000278616	NM_000051.3	410	Gtg/Ctg	9/63	0.274121008966291	4	FACETS	1	0.977	1	1	0.977	1	INDETERMINATE	3	TRUE	1	0.670923193048918	4		228	361	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332721	153332721	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062817-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	131	401	0	ENST00000281708.4:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000281708	NM_033632.3	79	Gaa/Caa	2/12	1	2	FACETS	0.962	0.881	1	0.962	0.881	1	CLONAL	1	TRUE	1	0.670923193048918	2		401	406	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219355	1219356	+	missense_variant	Missense_Mutation	DNP	TG	TG	AT	novel	NA	P-0062817-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	85	416	0	ENST00000326873.7:c.407_408delinsAT	p.Met136Asn	p.M136N	ENST00000326873	NM_000455.4	136	aTG/aAT	3/10	0.670923193048918	2	FACETS	0.945	0.871	1	0.945	0.871	1	CLONAL	2	TRUE	0	0.670923193048918	2		416	134	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239324	105239324	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062817-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	247	480	0	ENST00000349310.3:c.1063G>C	p.Glu355Gln	p.E355Q	ENST00000349310	NM_001014432.1	355	Gag/Cag	12/15	0.670923193048918	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.670923193048918	3		480	452	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861799	57861799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062817-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	96	441	0	ENST00000228682.2:c.1100C>A	p.Pro367His	p.P367H	ENST00000228682	NM_005269.2	367	cCt/cAt	10/12	0.157468359315193	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.670923193048918	0		441	265	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732517	74732517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062817-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	74	440	0	ENST00000359995.5:c.392G>A	p.Arg131Gln	p.R131Q	ENST00000359995	NM_001195427.1	131	cGg/cAg	2/3	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.670923193048918	2		440	194	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39542597	39542597	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062817-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	147	359	0	ENST00000262039.4:c.401G>T	p.Gly134Val	p.G134V	ENST00000262039	NM_002647.2	134	gGc/gTc	3/25	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.670923193048918	2		359	371	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170431	11170431	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062817-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	65	350	0	ENST00000358026.2:c.4734C>G	p.Ile1578Met	p.I1578M	ENST00000358026	NM_001128849.1	1578	atC/atG	34/36	0.670923193048918	2	FACETS	0.964	0.85	1	0.482	0.425	0.542	CLONAL	1	TRUE	0	0.670923193048918	2		350	201	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46277781	46277781	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062817-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	108	357	0	ENST00000371998.3:c.3579G>C	p.Leu1193Phe	p.L1193F	ENST00000371998		1193	ttG/ttC	19/23	0.670923193048918	2	FACETS	1	0.969	1	0.571	0.52	0.623	CLONAL	1	TRUE	0	0.670923193048918	2		357	282	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067120	143067120	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062817-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	102	335	0	ENST00000262992.4:c.1593C>A	p.Ser531Arg	p.S531R	ENST00000262992	NM_001101669.1	531	agC/agA	16/24	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.670923193048918	2		335	303	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005302	150005302	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062817-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	136	503	0	ENST00000253339.5:c.923C>G	p.Ser308Cys	p.S308C	ENST00000253339		308	tCc/tGc	3/7	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.670923193048918	2		503	371	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335706	81335706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062817-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	130	323	0	ENST00000222390.5:c.1654G>A	p.Asp552Asn	p.D552N	ENST00000222390	NM_000601.4	552	Gat/Aat	15/18	0.670923193048918	3	FACETS	1	0.951	1	0.53	0.484	0.579	CLONAL	1	TRUE	1	0.670923193048918	3		323	488	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842278	151842278	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062817-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	139	426	0	ENST00000262189.6:c.14134G>C	p.Glu4712Gln	p.E4712Q	ENST00000262189	NM_170606.2	4712	Gaa/Caa	54/59	0.670923193048918	3	FACETS	1	0.969	1	0.56	0.513	0.609	CLONAL	1	TRUE	1	0.670923193048918	3		426	494	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884435	151884435	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062817-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	118	425	0	ENST00000262189.6:c.4920G>C	p.Glu1640Asp	p.E1640D	ENST00000262189	NM_170606.2	1640	gaG/gaC	33/59	0.670923193048918	3	FACETS	1	0.917	1	0.505	0.458	0.554	CLONAL	1	TRUE	1	0.670923193048918	3		425	465	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864525	56864525	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs868430124	NA	P-0062817-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	88	297	0	ENST00000519728.1:c.488G>A	p.Gly163Glu	p.G163E	ENST00000519728	NM_002350.3	163	gGa/gAa	7/13	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.670923193048918	2		297	242	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980596	70980596	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062817-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	168	475	0	ENST00000276594.2:c.781G>T	p.Gly261Cys	p.G261C	ENST00000276594	NM_024504.3	261	Ggt/Tgt	4/8	0.169572199305294	4	FACETS	0.864	0.801	0.929	0.864	0.801	0.929	INDETERMINATE	2	TRUE	2	0.670923193048918	4		475	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0063078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	504	697	0	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		697	745	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0063078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	219	319	0	ENST00000374690.3:c.2105T>A	p.Leu702His	p.L702H	ENST00000374690	NM_000044.3	702	cTc/cAc	4/8	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		319	502	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123120	5123120	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs772889316	NA	P-0063078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	104	289	0	ENST00000381652.3:c.3176C>T	p.Ala1059Val	p.A1059V	ENST00000381652	NM_004972.3	1059	gCg/gTg	23/25	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		289	448	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103749	47103749	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	333	487	0	ENST00000409792.3:c.6197A>G	p.Asp2066Gly	p.D2066G	ENST00000409792	NM_014159.6	2066	gAc/gGc	14/21	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		487	818	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641058	93641058	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	470	389	0	ENST00000375746.1:c.1404T>G	p.Asp468Glu	p.D468E	ENST00000375746	NM_001174167.1	468	gaT/gaG	11/14	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		389	819	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0063161-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	692	489	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		489	1147	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170840	11170840	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063161-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	245	665	0	ENST00000358026.2:c.4984G>A	p.Asp1662Asn	p.D1662N	ENST00000358026	NM_001128849.1	1662	Gac/Aac	35/36	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		665	737	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754698	41754698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063161-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	107	645	0	ENST00000301178.4:c.1684C>T	p.Leu562Phe	p.L562F	ENST00000301178	NM_021913.4	562	Ctc/Ttc	14/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		645	870	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053240	180053240	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777529468	NA	P-0063161-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	155	738	0	ENST00000261937.6:c.1129G>A	p.Gly377Arg	p.G377R	ENST00000261937	NM_182925.4	377	Ggg/Agg	9/30	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		738	679	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579415	7579415	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063596-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	246	569	0	ENST00000269305.4:c.272G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tGg/tAg	4/11	0.384428983895719	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.384428983895719	2		569	629	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001231	150001231	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063596-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	78	459	0	ENST00000253339.5:c.2373G>C	p.Met791Ile	p.M791I	ENST00000253339		791	atG/atC	4/7	1	2	FACETS	0.746	0.657	0.842	0.746	0.657	0.842	SUBCLONAL	1	TRUE	1	0.384428983895719	2		459	544	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622307	1623329	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTACCTGCCACGTAGAAGGGGGCGGGATAGGTGCTGCTGGGGGTCTTGGCGGACGGGTAGGCGGTGGCATCCCTGCCGTAGTCCTCACCTGAGCTGGGTGGGTACACCTGCGGGCGGGTGGGCGGTGGGGGGTGCAGTCAGGACGGAGGGACCACGATCAGCCCATGCACCTTGCCGGCCTCCTGTCCCCTCCTGGTAGCACATCTACCACCCCGTTTCCCTTCCCTGTAAAGCCACCCCCCTTTAGGTAAATCCCAGCCCCTGGCCAAGTTTGAGGTTCTTATGATGTCCTGGTCTCTCTCTCCTACTCCTTTTCCAGCCCCCACCTCCCGCCTCCCTGAACTTCTGACCTTTGTACTTGAGGACTTGGATCTGGCTCTGCCTACTAAACCTTTTTCCTCCTTAATCCAGAAAACTCCTATCGACCCATCAAAACCCCAGCTCCAACACCCCATCCCATCCTTCTCCCTTGTTCCCCAGCTGGAATCAATCTTCCAGTGCTGAGCTTCCCTTGGTCCCAGAGCAACATTCGTCCTTCACTAAAGTAACAGGAAGAGGGGTCTGTGAGTAGCGCCAGCTCTGACTGGTTGGCACTGCCTGGACTGTGGGGCTGGGGCCTGTTGGTAACGTCTGCTGCTGTGCTGGAGCGGGAAGTATGCTGGGTGGGCCTGATGTTGTAATAAACTGGGGGGCGGTTTCAGGGCAGAGAAAGTGCACCCTGGGGAAGGAGGGGAGTGAGTGATACTGTTGGGAGCAGAGCCTGACCACGCCTTTGGCCTGGGAAGTCAACCTGACTCTAACCCCGAACCCAGGCCTGTGGGGAGCTGGTCGGCTGGAGGGGTGAGGAGATGTATGCCCAGGGCTCTTGGGGCCAGCACAGGCACTGGGCAGAGGGTGGTTGGTGGCTACTGAGCCAGGGAATCGGCAAATTCCCTCTCCCTCCAGCGAGATGAGACCGCAGGAGTGTGGCACAGCAGCCTGGACCATCTGCGAGGCCTGGTAGGGAGGCAGGGATGCGGGGC	TGTACCTGCCACGTAGAAGGGGGCGGGATAGGTGCTGCTGGGGGTCTTGGCGGACGGGTAGGCGGTGGCATCCCTGCCGTAGTCCTCACCTGAGCTGGGTGGGTACACCTGCGGGCGGGTGGGCGGTGGGGGGTGCAGTCAGGACGGAGGGACCACGATCAGCCCATGCACCTTGCCGGCCTCCTGTCCCCTCCTGGTAGCACATCTACCACCCCGTTTCCCTTCCCTGTAAAGCCACCCCCCTTTAGGTAAATCCCAGCCCCTGGCCAAGTTTGAGGTTCTTATGATGTCCTGGTCTCTCTCTCCTACTCCTTTTCCAGCCCCCACCTCCCGCCTCCCTGAACTTCTGACCTTTGTACTTGAGGACTTGGATCTGGCTCTGCCTACTAAACCTTTTTCCTCCTTAATCCAGAAAACTCCTATCGACCCATCAAAACCCCAGCTCCAACACCCCATCCCATCCTTCTCCCTTGTTCCCCAGCTGGAATCAATCTTCCAGTGCTGAGCTTCCCTTGGTCCCAGAGCAACATTCGTCCTTCACTAAAGTAACAGGAAGAGGGGTCTGTGAGTAGCGCCAGCTCTGACTGGTTGGCACTGCCTGGACTGTGGGGCTGGGGCCTGTTGGTAACGTCTGCTGCTGTGCTGGAGCGGGAAGTATGCTGGGTGGGCCTGATGTTGTAATAAACTGGGGGGCGGTTTCAGGGCAGAGAAAGTGCACCCTGGGGAAGGAGGGGAGTGAGTGATACTGTTGGGAGCAGAGCCTGACCACGCCTTTGGCCTGGGAAGTCAACCTGACTCTAACCCCGAACCCAGGCCTGTGGGGAGCTGGTCGGCTGGAGGGGTGAGGAGATGTATGCCCAGGGCTCTTGGGGCCAGCACAGGCACTGGGCAGAGGGTGGTTGGTGGCTACTGAGCCAGGGAATCGGCAAATTCCCTCTCCCTCCAGCGAGATGAGACCGCAGGAGTGTGGCACAGCAGCCTGGACCATCTGCGAGGCCTGGTAGGGAGGCAGGGATGCGGGGC	-	novel	NA	P-0063596-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	71	602	0	ENST00000344749.5:c.549+621_652+5del		p.X183_splice	ENST00000344749	NM_001136139.2	183		9/19	0.384428983895719	1	FACETS	0.717	0.629	0.812	0.717	0.629	0.812	SUBCLONAL	1	TRUE	0	0.384428983895719	1		602	416	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170555	11170593	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCGAATGTGAGTCCCGGGGGGGTTCAGGACGCCGGGGT	TCCGAATGTGAGTCCCGGGGGGGTTCAGGACGCCGGGGT	-	novel	NA	P-0063596-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	36	603	0	ENST00000358026.2:c.4860_4864+34del		p.X1620_splice	ENST00000358026	NM_001128849.1	1620		34/36	0.334196695722509	3	FACETS	0.365	0.299	0.439	0.182	0.149	0.22	SUBCLONAL	1	TRUE	1	0.384428983895719	3		603	612	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	86	308	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		313	398	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	74	311	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		311	339	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045890	180045890	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868478447	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	41	683	0	ENST00000261937.6:c.2881C>T	p.Arg961Cys	p.R961C	ENST00000261937	NM_182925.4	961	Cgc/Tgc	21/30	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		683	497	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	200	657	5	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		662	714	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	140	470	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		470	507	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	188	831	1	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		832	395	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	158	811	4	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		815	607	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519505	137519506	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs780346130	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	166	512	5	ENST00000367739.4:c.1132_1133del	p.Ser378PhefsTer6	p.S378Ffs*6	ENST00000367739	NM_000416.2	378	AGt/t	7/7	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		517	639	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	180	677	1	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		678	621	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422384	47422384	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	44	195	0	ENST00000377045.4:c.23del	p.Pro8LeufsTer26	p.P8Lfs*26	ENST00000377045	NM_001654.4	6	ggC/gg	2/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		195	452	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	169	615	4	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		619	596	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	144	383	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		383	545	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	43	612	3	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		615	537	SUCCESS
MAD2L2	10459	MSKCC	GRCh37	1	11736105	11736105	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	107	465	0	ENST00000235310.3:c.425del	p.Pro142GlnfsTer45	p.P142Qfs*45	ENST00000235310		142	cCa/ca	8/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		465	458	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023909	27023923	+	inframe_deletion	In_Frame_Del	DEL	GCTGCGGCGGCGGCA	GCTGCGGCGGCGGCA	-	rs751352361	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	88	619	0	ENST00000324856.7:c.1029_1043del	p.Ala345_Ala349del	p.A345_A349del	ENST00000324856	NM_006015.4	339	GCTGCGGCGGCGGCA/-	1/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		619	416	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101611	27101612	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	173	573	0	ENST00000324856.7:c.4899dup	p.Met1634HisfsTer14	p.M1634Hfs*14	ENST00000324856	NM_006015.4	1631	-/C	18/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		573	701	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532705	46532705	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	76	400	0	ENST00000262741.5:c.373del	p.Ser125LeufsTer4	p.S125Lfs*4	ENST00000262741	NM_003629.3	125	Tct/ct	4/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		400	347	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740268	46740268	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs28363243	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	158	458	0	ENST00000371975.4:c.1748T>C	p.Ile583Thr	p.I583T	ENST00000371975	NM_003579.3	583	aTt/aCt	16/18	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		458	573	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	212	408	0	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		408	721	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115269698	115269698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	51	279	0	ENST00000438362.2:c.1508G>A	p.Gly503Asp	p.G503D	ENST00000438362	NM_001242891.1	503	gGc/gAc	13/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		279	277	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690387	117690387	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1289431844	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	133	398	0	ENST00000369458.3:c.742C>T	p.Arg248Trp	p.R248W	ENST00000369458	NM_024626.3	248	Cgg/Tgg	5/6	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		398	503	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414240	32414240	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	134	405	0	ENST00000332351.3:c.1311G>C	p.Gln437His	p.Q437H	ENST00000332351	NM_024426.4	437	caG/caC	8/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		405	483	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003943	57003943	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	145	599	0	ENST00000257254.3:c.536T>C	p.Val179Ala	p.V179A	ENST00000257254		179	gTg/gCg	1/2	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		599	562	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999024	100999024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	135	722	0	ENST00000325455.5:c.778del	p.Ala260ArgfsTer41	p.A260Rfs*41	ENST00000325455	NM_001202474.3	260	Gcg/cg	1/8	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		722	488	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420160	420160	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746956221	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	187	523	0	ENST00000399788.2:c.3107G>A	p.Arg1036His	p.R1036H	ENST00000399788	NM_001042603.1	1036	cGt/cAt	21/28	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		523	707	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445203	49445203	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	194	814	3	ENST00000301067.7:c.2263del	p.Arg755GlyfsTer175	p.R755Gfs*175	ENST00000301067	NM_003482.3	755	Cgg/gg	10/54	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		817	738	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495324	56495324	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	148	577	0	ENST00000267101.3:c.3514T>C	p.Ser1172Pro	p.S1172P	ENST00000267101	NM_001982.3	1172	Tcc/Ccc	28/28	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		577	615	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900419	32900419	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs80359790	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	70	296	0	ENST00000380152.3:c.516G>T	p.Lys172Asn	p.K172N	ENST00000380152		172	aaG/aaT	6/27	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		296	289	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32905069	32905070	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	59	199	0	ENST00000380152.3:c.700dup	p.Ser234PhefsTer4	p.S234Ffs*4	ENST00000380152		232	tat/taTt	9/27	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		199	240	SUCCESS
BLM	641	MSKCC	GRCh37	15	91326107	91326107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1596250378	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	80	301	0	ENST00000355112.3:c.2611C>T	p.Pro871Ser	p.P871S	ENST00000355112	NM_000057.2	871	Cct/Tct	13/22	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		301	342	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467906	99467906	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	38	431	0	ENST00000268035.6:c.2775G>T	p.Gln925His	p.Q925H	ENST00000268035	NM_000875.3	925	caG/caT	13/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		431	504	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222339	2222339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771191963	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	158	678	0	ENST00000326181.6:c.623G>A	p.Arg208Gln	p.R208Q	ENST00000326181	NM_032271.2	208	cGa/cAa	8/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		678	591	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976144	7976144	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	185	510	0	ENST00000319144.4:c.2051C>A	p.Pro684His	p.P684H	ENST00000319144	NM_001139.2	684	cCc/cAc	15/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		510	612	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440904	56440904	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1458799446	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	191	564	0	ENST00000407977.2:c.433C>T	p.Arg145Ter	p.R145*	ENST00000407977		145	Cga/Tga	4/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		564	589	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448297	56448298	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1567880599	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	174	622	1	ENST00000407977.2:c.349dup	p.Arg117ProfsTer8	p.R117Pfs*8	ENST00000407977		117	cgc/cCgc	3/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		623	730	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612350	1612355	+	inframe_deletion	In_Frame_Del	DEL	CCCGCT	CCCGCT	-	novel	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	145	656	0	ENST00000344749.5:c.1664_1669del	p.Glu555_Arg556del	p.E555_R556del	ENST00000344749	NM_001136139.2	555	gAGCGGGtg/gtg	18/19	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		656	566	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308382	15308383	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs749829137	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	109	563	0	ENST00000263388.2:c.125dup	p.Cys43LeufsTer32	p.C43Lfs*32	ENST00000263388	NM_000435.2	42	cct/ccCt	2/33	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		563	533	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946800	17946800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370419724	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	50	531	0	ENST00000458235.1:c.1847G>A	p.Gly616Asp	p.G616D	ENST00000458235	NM_000215.3	616	gGc/gAc	14/24	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		531	555	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312916	30312916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146040933	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	132	501	0	ENST00000262643.3:c.719G>A	p.Arg240His	p.R240H	ENST00000262643	NM_001238.2	240	cGt/cAt	9/12	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		501	526	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214143	36214143	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	34	545	0	ENST00000222270.7:c.2969T>C	p.Phe990Ser	p.F990S	ENST00000222270	NM_014727.1	990	tTt/tCt	6/37	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		545	599	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905175	50905175	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	158	722	0	ENST00000440232.2:c.461del	p.Pro154LeufsTer15	p.P154Lfs*15	ENST00000440232	NM_002691.3	153	Ccc/cc	4/27	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		722	636	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082313	16082314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs780080562	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	40	618	0	ENST00000281043.3:c.134dup	p.Glu47GlyfsTer8	p.E47Gfs*8	ENST00000281043	NM_005378.4	43	acc/aCcc	2/3	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		618	507	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607704	46607704	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	157	596	0	ENST00000263734.3:c.1893G>A	p.Met631Ile	p.M631I	ENST00000263734	NM_001430.4	631	atG/atA	12/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		596	518	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257170	198257170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	66	264	0	ENST00000335508.6:c.3772G>A	p.Ala1258Thr	p.A1258T	ENST00000335508	NM_012433.2	1258	Gcc/Acc	25/25	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		264	304	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151290	202151290	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	101	316	0	ENST00000358485.4:c.1596del	p.Lys532AsnfsTer73	p.K532Nfs*73	ENST00000358485	NM_001080125.1	530	agA/ag	9/9	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		316	439	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426814	212426814	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	93	354	0	ENST00000342788.4:c.2302-1G>T		p.X768_splice	ENST00000342788	NM_005235.2	768			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		354	436	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021476	31021476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141314105	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	187	630	0	ENST00000375687.4:c.1475C>T	p.Ala492Val	p.A492V	ENST00000375687	NM_015338.5	492	gCt/gTt	12/13	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		630	636	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45660687	45660687	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	117	518	0	ENST00000407780.3:c.14G>A	p.Ser5Asn	p.S5N	ENST00000407780	NM_001283052.1	5	aGt/aAt	1/7	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		518	414	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691872	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs79375991	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	219	450	7	ENST00000295754.5:c.383del	p.Lys128SerfsTer35	p.K128Sfs*35	ENST00000295754	NM_003242.5	125	gAa/ga	3/7	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		457	516	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053348	37053348	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63751653	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	101	368	0	ENST00000231790.2:c.588del	p.Lys196AsnfsTer6	p.K196Nfs*6	ENST00000231790	NM_000249.3	195	Aaa/aa	7/19	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		368	387	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665126	138665126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	122	522	0	ENST00000330315.3:c.439C>T	p.Arg147Cys	p.R147C	ENST00000330315	NM_023067.3	147	Cgc/Tgc	1/1	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		522	405	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170020899	170020899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	20	74	0	ENST00000295797.4:c.1775C>T	p.Ala592Val	p.A592V	ENST00000295797	NM_002740.5	592	gCa/gTa	18/18	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		74	80	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919194	178919194	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	69	262	1	ENST00000263967.3:c.685del	p.Thr229LeufsTer11	p.T229Lfs*11	ENST00000263967	NM_006218.2	227	Aaa/aa	4/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		263	318	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	132	699	4	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		703	603	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979551	55979551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375035755	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	104	395	0	ENST00000263923.4:c.896G>A	p.Arg299Gln	p.R299Q	ENST00000263923	NM_002253.2	299	cGg/cAg	7/30	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		395	493	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	127	490	5	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		495	589	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931451	131931452	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs397507178	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	126	374	8	ENST00000265335.6:c.2165dup	p.Glu723GlyfsTer5	p.E723Gfs*5	ENST00000265335		719	cta/ctAa	13/25	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		382	558	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509482	149509482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1562002990	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	59	620	0	ENST00000261799.4:c.1417G>A	p.Glu473Lys	p.E473K	ENST00000261799	NM_002609.3	473	Gag/Aag	10/23	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		620	627	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402605	20402605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775788562	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	37	643	1	ENST00000346618.3:c.142G>A	p.Ala48Thr	p.A48T	ENST00000346618	NM_001949.4	48	Gcc/Acc	1/7	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		644	536	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910344	29910344	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	376	730	0	ENST00000376809.5:c.14del	p.Ala5GlyfsTer15	p.A5Gfs*15	ENST00000376809	NM_002116.7	5	gCg/gg	1/8	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		730	681	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903731	41903731	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	171	656	0	ENST00000372991.4:c.826C>T	p.Gln276Ter	p.Q276*	ENST00000372991	NM_001760.3	276	Caa/Taa	5/5	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		656	633	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706847	117706847	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	128	371	0	ENST00000368508.3:c.2303T>G	p.Val768Gly	p.V768G	ENST00000368508	NM_002944.2	768	gTg/gGg	15/43	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		371	448	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005137	150005137	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1048146595	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	90	592	0	ENST00000253339.5:c.1088T>C	p.Val363Ala	p.V363A	ENST00000253339		363	gTc/gCc	3/7	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		592	683	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129133	152129133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	153	616	0	ENST00000206249.3:c.86C>T	p.Pro29Leu	p.P29L	ENST00000206249	NM_000125.3	29	cCg/cTg	1/8	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		616	507	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099982	157099990	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs587779747	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	101	814	0	ENST00000346085.5:c.936_944del	p.Gly317_Gly319del	p.G317_G319del	ENST00000346085	NM_020732.3	307	GGCGGCGGC/-	1/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		814	514	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962902	2962902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs186255478	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	77	468	0	ENST00000396946.4:c.2006C>T	p.Thr669Met	p.T669M	ENST00000396946	NM_032415.4	669	aCg/aTg	16/25	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		468	485	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402761	139402761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	166	665	0	ENST00000277541.6:c.3248G>A	p.Cys1083Tyr	p.C1083Y	ENST00000277541	NM_017617.3	1083	tGc/tAc	20/34	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		665	648	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409950	63409950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1205869591	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	323	325	0	ENST00000330258.3:c.3217C>T	p.Pro1073Ser	p.P1073S	ENST00000330258	NM_152424.3	1073	Cca/Tca	2/2	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		325	430	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177848	56177849	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAA	rs5868032	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	111	610	0	ENST00000399503.3:c.2845_2847dup	p.Thr949dup	p.T949dup	ENST00000399503	NM_005921.1	949	tca/tCAAca	14/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		610	670	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831357	72831358	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTG	rs34918837	NA	P-0063907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	89	569	2	ENST00000268489.5:c.5221_5223dup	p.Gln1741dup	p.Q1741dup	ENST00000268489	NM_006885.3	1741	-/CAA	9/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		571	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0063918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	280	571	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.888278951941595	1	FACETS	0.981	0.95	1	0.981	0.95	1	CLONAL	1	TRUE	0	0.911357931198305	1		571	341	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951144	48951144	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	71	282	0	ENST00000267163.4:c.1306C>T	p.Gln436Ter	p.Q436*	ENST00000267163	NM_000321.2	436	Cag/Tag	13/27	0.911357931198305	1	FACETS	0.998	0.937	1	0.998	0.937	1	CLONAL	1	TRUE	0	0.911357931198305	1		282	85	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377202	118377202	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	305	618	0	ENST00000534358.1:c.10595C>A	p.Ser3532Ter	p.S3532*	ENST00000534358	NM_005933.3	3532	tCa/tAa	27/36	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.911357931198305	2		618	648	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27228238	27228238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745861773	NA	P-0063918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	140	368	0	ENST00000380036.4:c.3235C>T	p.Pro1079Ser	p.P1079S	ENST00000380036	NM_000459.3	1079	Cct/Tct	22/23	1	2	FACETS	0.802	0.739	0.867	0.802	0.739	0.867	CLONAL	1	TRUE	1	0.911357931198305	2		368	383	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783704	50783707	+	frameshift_variant	Frame_Shift_Del	DEL	ACAA	ACAA	-	novel	NA	P-0063919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	148	400	1	ENST00000398568.2:c.102_105del	p.Gln34HisfsTer12	p.Q34Hfs*12	ENST00000398568	NM_001042412.1	32	gACAAa/ga	3/18	0.538530581663942	1	FACETS	0.845	0.778	0.914	0.845	0.778	0.914	CLONAL	1	TRUE	0	0.54134805047399	1		401	472	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124503540	124503540	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587777475	NA	P-0063919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	171	418	0	ENST00000357628.3:c.410G>A	p.Arg137His	p.R137H	ENST00000357628	NM_015450.2	137	cGt/cAt	8/19	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.54134805047399	2		418	588	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814734	139814734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	112	614	0	ENST00000247668.2:c.727C>T	p.His243Tyr	p.H243Y	ENST00000247668	NM_021138.3	243	Cac/Tac	8/11	0.281152493413368	1	FACETS	0.402	0.361	0.445	0.402	0.361	0.445	INDETERMINATE	1	TRUE	0	0.54134805047399	1		614	751	SUCCESS
BLM	641	MSKCC	GRCh37	15	91333888	91333888	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	49	346	0	ENST00000355112.3:c.2833G>A	p.Ala945Thr	p.A945T	ENST00000355112	NM_000057.2	945	Gct/Act	15/22	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		346	194	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396704	396704	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	146	547	0	ENST00000262320.3:c.322C>T	p.Gln108Ter	p.Q108*	ENST00000262320	NM_003502.3	108	Cag/Tag	2/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		547	438	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505201	25505351	+	splice_donor_variant,splice_donor_5th_base_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGCCACGACCCAGACCATCCTTCCTGGGACCTGCTGGAGAGCCAAGTCCCTGACTCTCAGGGTATGCTGGTGGGCCCAGAAGAGGCTGCCCCTGGTGCTGAGGACTCACCCGCTTCTGCAGGGGCTCCTCGGCCCTCCTTGGGGGTGCAGC	AGCCACGACCCAGACCATCCTTCCTGGGACCTGCTGGAGAGCCAAGTCCCTGACTCTCAGGGTATGCTGGTGGGCCCAGAAGAGGCTGCCCCTGGTGCTGAGGACTCACCCGCTTCTGCAGGGGCTCCTCGGCCCTCCTTGGGGGTGCAGC	-	novel	NA	P-0063920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	18	335	0	ENST00000264709.3:c.407_448+109del		p.X136_splice	ENST00000264709	NM_175629.2	136		4/23	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		335	256	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440320	52440320	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	143	545	0	ENST00000460680.1:c.732del	p.Arg244SerfsTer5	p.R244Sfs*5	ENST00000460680	NM_004656.3	244	agG/ag	9/17	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		545	332	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030293	180030293	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	115	608	0	ENST00000261937.6:c.3991G>C	p.Val1331Leu	p.V1331L	ENST00000261937	NM_182925.4	1331	Gtg/Ctg	30/30	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		608	453	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0063921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	122	311	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		311	397	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	138	387	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		387	489	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10773002	10773002	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	102	342	0	ENST00000361367.2:c.43G>A	p.Glu15Lys	p.E15K	ENST00000361367	NM_014633.3	15	Gag/Aag	1/25	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		342	350	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853256	68853256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	180	482	0	ENST00000261769.5:c.1639G>A	p.Glu547Lys	p.E547K	ENST00000261769	NM_004360.3	547	Gag/Aag	11/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		482	516	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576379	67576379	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	26	403	0	ENST00000274335.5:c.658A>G	p.Ile220Val	p.I220V	ENST00000274335		220	Att/Gtt	5/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		403	358	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151947033	151947033	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	85	355	0	ENST00000262189.6:c.1741C>G	p.Gln581Glu	p.Q581E	ENST00000262189	NM_170606.2	581	Caa/Gaa	13/59	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		355	281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577508	7577508	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060501201	NA	P-0063922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	17	494	0	ENST00000269305.4:c.773A>G	p.Glu258Gly	p.E258G	ENST00000269305	NM_001126112.2	258	gAa/gGa	7/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		494	713	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0063923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	304	662	1	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.646011533888724	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.646011533888724	1		663	575	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396746	139396746	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	234	499	0	ENST00000277541.6:c.5362G>A	p.Gly1788Ser	p.G1788S	ENST00000277541	NM_017617.3	1788	Ggc/Agc	28/34	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.646011533888724	2		499	584	SUCCESS
APC	324	MSKCC	GRCh37	5	112175749	112175750	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0063923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	113	587	0	ENST00000257430.4:c.4459dup	p.Thr1487AsnfsTer27	p.T1487Nfs*27	ENST00000257430	NM_000038.5	1486	-/A	16/16	0.41650977349191	1	FACETS	0.428	0.386	0.471	0.428	0.386	0.471	SUBCLONAL	1	TRUE	0	0.646011533888724	1		587	554	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445208	29445208	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0063923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	238	535	0	ENST00000389048.3:c.3515+2T>A		p.X1172_splice	ENST00000389048	NM_004304.4	1172			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.646011533888724	2		535	649	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457282	89457282	+	splice_donor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0063923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	31	368	0	ENST00000336596.2:c.1762+1del		p.X588_splice	ENST00000336596	NM_005233.5	588			1	2	FACETS	0.292	0.236	0.354	0.292	0.236	0.354	SUBCLONAL	1	TRUE	1	0.646011533888724	2		368	329	SUCCESS
APC	324	MSKCC	GRCh37	5	112162825	112162825	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	73	372	0	ENST00000257430.4:c.1429G>T	p.Glu477Ter	p.E477*	ENST00000257430	NM_000038.5	477	Gaa/Taa	12/16	0.41650977349191	1	FACETS	0.86	0.769	0.952	0.86	0.769	0.952	CLONAL	1	TRUE	0	0.646011533888724	1		372	178	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0063995-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	79	288	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		288	397	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974695	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691187	NA	P-0063995-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	121	581	0	ENST00000304494.5:c.132del	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	taC/ta	1/3	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		581	950	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063995-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	139	554	0	ENST00000269305.4:c.672G>C	p.Glu224Asp	p.E224D	ENST00000269305	NM_001126112.2	224	gaG/gaC	6/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		554	832	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467921	50467921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063995-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	64	583	0	ENST00000331340.3:c.1156C>T	p.Arg386Cys	p.R386C	ENST00000331340	NM_006060.4	386	Cgc/Tgc	8/8	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		583	933	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243397	46243397	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063995-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	46	439	0	ENST00000334344.6:c.1750G>C	p.Glu584Gln	p.E584Q	ENST00000334344	NM_152641.2	584	Gag/Cag	14/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		439	582	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0063996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	557	586	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		586	664	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	140	498	2	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		500	715	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139818373	139818373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754210099	NA	P-0063996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	334	417	3	ENST00000247668.2:c.1208G>A	p.Arg403Gln	p.R403Q	ENST00000247668	NM_021138.3	403	cGa/cAa	10/11	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		420	434	SUCCESS
APC	324	MSKCC	GRCh37	5	112164559	112164560	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0063996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	304	338	1	ENST00000257430.4:c.1634dup	p.Ser546GlufsTer14	p.S546Efs*14	ENST00000257430	NM_000038.5	545	gcg/gCcg	14/16	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		339	505	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0063997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	64	396	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		396	571	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637689	52637689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	45	362	0	ENST00000394830.3:c.2627G>A	p.Arg876His	p.R876H	ENST00000394830	NM_018313.4	876	cGt/cAt	18/30	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		362	247	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983126	201983127	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	138	507	0	ENST00000359651.3:c.976dup	p.Tyr326LeufsTer145	p.Y326Lfs*145	ENST00000359651		325	-/T	7/8	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		507	814	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994197	21994199	+	frameshift_variant	Frame_Shift_Del	DEL	AGG	AGG	TA	novel	NA	P-0063997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	59	471	0	ENST00000579755.1:c.132_134delinsTA	p.Leu45ThrfsTer3	p.L45Tfs*3	ENST00000579755		44	gcCCTc/gcTAc	1/3	NA				NA	NA				NA	NA	FALSE	NA	NA	NA		471	761	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0063998-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	66	379	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		379	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0063998-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	49	584	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		584	758	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs121913292	NA	P-0063998-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	26	321	0	ENST00000371953.3:c.389del	p.Arg130GlnfsTer4	p.R130Qfs*4	ENST00000371953	NM_000314.4	130	cGa/ca	5/9	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		321	357	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692794	89692794	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121909238	NA	P-0063998-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	13	206	0	ENST00000371953.3:c.278A>G	p.His93Arg	p.H93R	ENST00000371953	NM_000314.4	93	cAt/cGt	5/9	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		206	262	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210728	2210728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745700742	NA	P-0063999-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	40	661	0	ENST00000398665.3:c.1225C>T	p.Arg409Cys	p.R409C	ENST00000398665	NM_032482.2	409	Cgc/Tgc	14/28	1	2	FACETS	0.332	0.275	0.397	0.332	0.275	0.397	SUBCLONAL	1	TRUE	1	0.328321344964577	2		661	733	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574637	41574637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145312648	NA	P-0063999-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	80	640	0	ENST00000263253.7:c.6922C>T	p.Arg2308Cys	p.R2308C	ENST00000263253	NM_001429.3	2308	Cgc/Tgc	31/31	1	2	FACETS	0.706	0.622	0.797	0.706	0.622	0.797	SUBCLONAL	1	TRUE	1	0.328321344964577	2		640	690	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649669	48649669	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063999-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	30	309	0	ENST00000376670.3:c.153C>G	p.Ser51Arg	p.S51R	ENST00000376670	NM_002049.3	51	agC/agG	2/6	1	1	FACETS	0.52	0.42	0.632	0.52	0.42	0.632	SUBCLONAL	1	TRUE	0	0.328321344964577	1		309	294	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0064002-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	107	375	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.417780668228898	2		375	469	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519551	137519551	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064002-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	27	390	0	ENST00000367739.4:c.1087C>T	p.Pro363Ser	p.P363S	ENST00000367739	NM_000416.2	363	Cct/Tct	7/7	0.417780668228898	1	FACETS	0.209	0.166	0.259	0.209	0.166	0.259	SUBCLONAL	1	TRUE	0	0.417780668228898	1		390	489	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230665	46230665	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064002-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	37	396	0	ENST00000334344.6:c.914del	p.Leu305ProfsTer23	p.L305Pfs*23	ENST00000334344	NM_152641.2	305	cTc/cc	8/21	1	2	FACETS	0.437	0.361	0.523	0.437	0.361	0.523	SUBCLONAL	1	TRUE	1	0.417780668228898	2		396	405	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832497	72832497	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064002-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	262	440	0	ENST00000268489.5:c.4084T>A	p.Cys1362Ser	p.C1362S	ENST00000268489	NM_006885.3	1362	Tgc/Agc	9/10	0.417780668228898	3	FACETS	0.991	0.933	1	0.991	0.933	1	CLONAL	2	TRUE	1	0.417780668228898	3		440	765	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690355	33690355	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064002-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	119	431	0	ENST00000308377.4:c.472C>A	p.Pro158Thr	p.P158T	ENST00000308377	NM_152270.3	158	Cca/Aca	2/5	1	2	FACETS	0.931	0.842	1	0.931	0.842	1	CLONAL	1	TRUE	1	0.417780668228898	2		431	612	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952250	17952250	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1240876834	NA	P-0064002-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	124	378	0	ENST00000458235.1:c.1090G>T	p.Ala364Ser	p.A364S	ENST00000458235	NM_000215.3	364	Gca/Tca	8/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.417780668228898	2		378	522	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223033	36223033	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064002-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	174	696	0	ENST00000222270.7:c.5662C>T	p.Pro1888Ser	p.P1888S	ENST00000222270	NM_014727.1	1888	Cct/Tct	27/37	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.417780668228898	2		696	795	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076905	41076905	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064002-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	109	314	0	ENST00000373198.4:c.1515G>T	p.Gln505His	p.Q505H	ENST00000373198	NM_133170.3	505	caG/caT	9/32	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.417780668228898	2		314	438	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259276	36259276	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064002-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	111	465	0	ENST00000300305.3:c.215G>A	p.Arg72Lys	p.R72K	ENST00000300305		72	aGg/aAg	3/8	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.417780668228898	2		465	479	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020753	37020753	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064002-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	134	378	0	ENST00000358127.4:c.92G>A	p.Arg31Gln	p.R31Q	ENST00000358127	NM_001280556.1	31	cGg/cAg	2/10	0.417780668228898	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.417780668228898	1		378	470	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	111	385	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		385	438	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1686117	1686117	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	186	537	0	ENST00000378625.1:c.1144C>T	p.Arg382Trp	p.R382W	ENST00000378625	NM_001198994.1	382	Cgg/Tgg	10/14	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		537	648	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193205429	193205429	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	200	492	0	ENST00000367435.3:c.1360T>C	p.Phe454Leu	p.F454L	ENST00000367435	NM_024529.4	454	Ttc/Ctc	15/17	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		492	899	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653789	206653789	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1446375767	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	160	549	0	ENST00000367120.3:c.1341-1G>A		p.X447_splice	ENST00000367120	NM_014002.3	447			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		549	751	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597849	43597849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564490056	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	228	671	0	ENST00000355710.3:c.397C>T	p.Arg133Cys	p.R133C	ENST00000355710	NM_020975.4	133	Cgt/Tgt	3/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		671	807	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852746	63852746	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	179	558	0	ENST00000279873.7:c.3524C>T	p.Pro1175Leu	p.P1175L	ENST00000279873	NM_032199.2	1175	cCa/cTa	10/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		558	719	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405716	70405716	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	124	521	0	ENST00000373644.4:c.3230T>C	p.Val1077Ala	p.V1077A	ENST00000373644	NM_030625.2	1077	gTt/gCt	4/12	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		521	539	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141873	108141873	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs538105098	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	107	419	0	ENST00000278616.4:c.2921C>T	p.Ser974Phe	p.S974F	ENST00000278616	NM_000051.3	974	tCc/tTc	19/63	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		419	297	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148537	119148537	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs933954615	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	116	479	0	ENST00000264033.4:c.1078C>T	p.His360Tyr	p.H360Y	ENST00000264033	NM_005188.3	360	Cat/Tat	7/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		479	347	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944812	31944812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866971809	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	234	503	0	ENST00000340398.3:c.289G>A	p.Glu97Lys	p.E97K	ENST00000340398	NM_001013699.2	97	Gaa/Aaa	1/1	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		503	704	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811604	102811604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	180	614	0	ENST00000307046.8:c.580G>A	p.Gly194Arg	p.G194R	ENST00000307046	NM_001111285.1	194	Gga/Aga	4/4	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		614	675	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240679	133240679	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	146	598	0	ENST00000320574.5:c.2617C>T	p.Pro873Ser	p.P873S	ENST00000320574	NM_006231.2	873	Cca/Tca	23/49	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		598	597	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26971357	26971357	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1460879226	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	88	397	0	ENST00000381527.3:c.928C>T	p.His310Tyr	p.H310Y	ENST00000381527	NM_001260.1	310	Cac/Tac	9/13	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		397	347	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589298	28589298	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	105	372	0	ENST00000241453.7:c.2749G>A	p.Glu917Lys	p.E917K	ENST00000241453	NM_004119.2	917	Gaa/Aaa	22/24	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		372	452	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919595	28919595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs553261958	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	155	419	2	ENST00000282397.4:c.2342G>A	p.Arg781Gln	p.R781Q	ENST00000282397	NM_002019.4	781	cGa/cAa	16/30	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		421	523	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32921023	32921034	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	GTACCCTTTCGG	GTACCCTTTCGG	-	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	54	345	0	ENST00000380152.3:c.6997_7007+1del		p.X2333_splice	ENST00000380152		2333		13/27	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		345	343	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95592931	95592931	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	85	279	0	ENST00000393063.1:c.889T>G	p.Leu297Val	p.L297V	ENST00000393063	NM_030621.3	297	Tta/Gta	8/28	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		279	306	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38545401	38545408	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGACTT	GGCGACTT	-	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	103	425	0	ENST00000299084.4:c.15_22del	p.Ala6Ter	p.A6*	ENST00000299084	NM_152594.2	5	acGGCGACTTct/acct	1/7	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		425	492	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614499	38614499	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	124	318	0	ENST00000299084.4:c.265T>G	p.Phe89Val	p.F89V	ENST00000299084	NM_152594.2	89	Ttt/Gtt	3/7	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		318	387	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	164	571	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		571	702	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035319	42035319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	214	566	0	ENST00000219905.7:c.5161C>T	p.Pro1721Ser	p.P1721S	ENST00000219905	NM_001164273.1	1721	Cct/Tct	15/24	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		566	708	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50782541	50782541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	264	598	0	ENST00000307179.4:c.2053C>T	p.Pro685Ser	p.P685S	ENST00000307179		685	Cct/Tct	14/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		598	838	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727442	66727442	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	201	506	0	ENST00000307102.5:c.158T>A	p.Phe53Tyr	p.F53Y	ENST00000307102	NM_002755.3	53	tTt/tAt	2/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		506	704	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293124	91293124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1596218994	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	201	554	0	ENST00000355112.3:c.626C>T	p.Pro209Leu	p.P209L	ENST00000355112	NM_000057.2	209	cCt/cTt	3/22	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		554	723	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808875	3808875	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	168	445	0	ENST00000262367.5:c.3349C>T	p.Pro1117Ser	p.P1117S	ENST00000262367	NM_004380.2	1117	Ccc/Tcc	17/31	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		445	720	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858186	9858186	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377746289	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	217	630	0	ENST00000330684.3:c.3215G>A	p.Arg1072Lys	p.R1072K	ENST00000330684	NM_001134407.1	1072	aGg/aAg	13/13	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		630	802	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923465	9923465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771688818	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	170	544	0	ENST00000330684.3:c.1822C>T	p.Leu608Phe	p.L608F	ENST00000330684	NM_001134407.1	608	Ctt/Ttt	9/13	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		544	615	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9927982	9927982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768958947	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	173	438	0	ENST00000330684.3:c.1757G>A	p.Arg586Lys	p.R586K	ENST00000330684	NM_001134407.1	586	aGa/aAa	8/13	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		438	572	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831579	72831579	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	209	588	0	ENST00000268489.5:c.5002C>T	p.Pro1668Ser	p.P1668S	ENST00000268489	NM_006885.3	1668	Cca/Tca	9/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		588	784	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592318	29592318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	108	367	0	ENST00000356175.3:c.4733C>T	p.Ser1578Phe	p.S1578F	ENST00000356175	NM_000267.3	1578	tCc/tTc	35/57	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		367	297	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654784	29654784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769843989	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	205	582	0	ENST00000356175.3:c.5473C>T	p.Arg1825Trp	p.R1825W	ENST00000356175	NM_000267.3	1825	Cgg/Tgg	37/57	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		582	597	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533916	63533916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1399215718	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	185	585	0	ENST00000307078.5:c.1238C>T	p.Ser413Leu	p.S413L	ENST00000307078	NM_004655.3	413	tCg/tTg	6/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		585	709	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222744	5222744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	168	577	0	ENST00000357368.4:c.3059C>T	p.Pro1020Leu	p.P1020L	ENST00000357368	NM_002850.3	1020	cCc/cTc	18/38	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		577	550	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376325	15376326	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	170	645	0	ENST00000263377.2:c.688_689delinsTT	p.Pro230Leu	p.P230L	ENST00000263377	NM_058243.2	230	CCg/TTg	5/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		645	783	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946831	17946831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	178	572	0	ENST00000458235.1:c.1816G>A	p.Gly606Arg	p.G606R	ENST00000458235	NM_000215.3	606	Ggg/Agg	14/24	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		572	688	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974985	18974985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	145	472	0	ENST00000262803.5:c.2782C>G	p.Arg928Gly	p.R928G	ENST00000262803	NM_002911.3	928	Cgc/Ggc	20/24	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		472	562	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799258	42799258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs530430600	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	124	491	0	ENST00000575354.2:c.4742C>T	p.Ser1581Leu	p.S1581L	ENST00000575354	NM_015125.3	1581	tCg/tTg	20/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		491	456	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973144	25973145	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	212	607	0	ENST00000435504.4:c.1280_1281delinsTT	p.Ser427Phe	p.S427F	ENST00000435504		427	tCC/tTT	12/13	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		607	759	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872990	136872990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	200	650	0	ENST00000241393.3:c.508C>T	p.Pro170Ser	p.P170S	ENST00000241393	NM_003467.2	170	Ccc/Tcc	2/2	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		650	752	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281508	198281508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	208	540	0	ENST00000335508.6:c.623C>T	p.Pro208Leu	p.P208L	ENST00000335508	NM_012433.2	208	cCt/cTt	6/25	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		540	801	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547022	9547022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs58486349	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	160	638	0	ENST00000353224.5:c.1000G>A	p.Asp334Asn	p.D334N	ENST00000353224	NM_177990.2	334	Gat/Aat	5/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		638	759	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561201	9561201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	174	572	0	ENST00000353224.5:c.581G>A	p.Arg194Lys	p.R194K	ENST00000353224	NM_177990.2	194	aGa/aAa	4/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		572	789	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561496	9561496	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775097743	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	208	603	0	ENST00000353224.5:c.286C>T	p.Arg96Cys	p.R96C	ENST00000353224	NM_177990.2	96	Cgc/Tgc	4/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		603	916	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713470	40713470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318044562	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	210	635	1	ENST00000373198.4:c.4045C>T	p.Arg1349Cys	p.R1349C	ENST00000373198	NM_133170.3	1349	Cgt/Tgt	30/32	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		636	877	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790158	40790158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781621750	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	344	587	0	ENST00000373198.4:c.2573C>T	p.Ser858Phe	p.S858F	ENST00000373198	NM_133170.3	858	tCc/tTc	18/32	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		587	854	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306557	41306557	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	171	433	0	ENST00000373198.4:c.1102G>A	p.Gly368Arg	p.G368R	ENST00000373198	NM_133170.3	368	Ggg/Agg	7/32	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		433	713	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130450	29130464	+	inframe_deletion	In_Frame_Del	DEL	TCCTCAGGTTCTTGG	TCCTCAGGTTCTTGG	-	rs587780181	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	80	616	0	ENST00000328354.6:c.246_260del	p.Asp82_Glu86del	p.D82_E86del	ENST00000328354	NM_007194.3	82	gaCCAAGAACCTGAGGAg/gag	2/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		616	752	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266558	41266558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	201	530	0	ENST00000349496.5:c.355C>T	p.Pro119Ser	p.P119S	ENST00000349496	NM_001904.3	119	Ccc/Tcc	4/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		530	680	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521763	89521763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	197	437	0	ENST00000336596.2:c.2840C>T	p.Ser947Phe	p.S947F	ENST00000336596	NM_005233.5	947	tCc/tTc	16/17	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		437	656	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670400	134670400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	162	496	0	ENST00000398015.3:c.311G>A	p.Gly104Glu	p.G104E	ENST00000398015	NM_004441.4	104	gGa/gAa	3/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		496	592	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955073	55955073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	171	469	0	ENST00000263923.4:c.3472G>A	p.Glu1158Lys	p.E1158K	ENST00000263923	NM_002253.2	1158	Gaa/Aaa	26/30	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		469	650	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796418	57796418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	154	522	0	ENST00000309042.7:c.1394C>T	p.Ser465Phe	p.S465F	ENST00000309042	NM_005612.4	465	tCc/tTc	4/4	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		522	603	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293551	1293551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	187	564	0	ENST00000310581.5:c.1450G>A	p.Glu484Lys	p.E484K	ENST00000310581	NM_198253.2	484	Gaa/Aaa	2/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		564	612	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515273	149515273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	183	712	0	ENST00000261799.4:c.209C>T	p.Pro70Leu	p.P70L	ENST00000261799	NM_002609.3	70	cCa/cTa	3/23	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		712	818	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120269	94120269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	176	584	2	ENST00000369303.4:c.782G>A	p.Gly261Glu	p.G261E	ENST00000369303	NM_004440.3	261	gGa/gAa	3/17	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		586	720	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419897	152419897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	143	544	0	ENST00000206249.3:c.1584G>A	p.Met528Ile	p.M528I	ENST00000206249	NM_000125.3	528	atG/atA	8/8	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		544	602	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394449	162394449	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	124	394	0	ENST00000366898.1:c.619G>A	p.Glu207Lys	p.E207K	ENST00000366898	NM_004562.2	207	Gaa/Aaa	6/12	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		394	491	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979535	2979535	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	130	497	0	ENST00000396946.4:c.712A>G	p.Lys238Glu	p.K238E	ENST00000396946	NM_032415.4	238	Aag/Gag	6/25	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		497	673	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467675	50467675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759124417	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	136	526	0	ENST00000331340.3:c.910G>A	p.Glu304Lys	p.E304K	ENST00000331340	NM_006060.4	304	Gaa/Aaa	8/8	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		526	614	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331966	81331966	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	166	442	0	ENST00000222390.5:c.2118T>A	p.Phe706Leu	p.F706L	ENST00000222390	NM_000601.4	706	ttT/ttA	18/18	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		442	550	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509078	106509078	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs62001903	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	295	596	1	ENST00000359195.3:c.1072G>A	p.Asp358Asn	p.D358N	ENST00000359195	NM_002649.2	358	Gac/Aac	2/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		597	940	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339211	116339211	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	229	473	0	ENST00000397752.3:c.73G>A	p.Glu25Lys	p.E25K	ENST00000397752	NM_000245.2	25	Gag/Aag	2/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		473	881	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395478	116395478	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45602940	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	201	420	0	ENST00000397752.3:c.1771C>T	p.Arg591Trp	p.R591W	ENST00000397752	NM_000245.2	591	Cgg/Tgg	6/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		420	558	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481408	140481408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867748453	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	125	360	0	ENST00000288602.6:c.1400C>T	p.Ser467Leu	p.S467L	ENST00000288602	NM_004333.4	467	tCa/tTa	11/18	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		360	493	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949069	151949069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776295921	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	166	500	0	ENST00000262189.6:c.1576C>T	p.Arg526Cys	p.R526C	ENST00000262189	NM_170606.2	526	Cgt/Tgt	11/59	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		500	661	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29195912	29195912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	146	701	0	ENST00000240100.2:c.686C>T	p.Ser229Phe	p.S229F	ENST00000240100	NM_001394.6	229	tCc/tTc	3/4	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		701	722	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934334	68934334	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	136	311	0	ENST00000288368.4:c.400C>T	p.Leu134Phe	p.L134F	ENST00000288368	NM_024870.2	134	Ctt/Ttt	4/40	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		311	440	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058515	69058515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	100	403	0	ENST00000288368.4:c.4159C>T	p.His1387Tyr	p.H1387Y	ENST00000288368	NM_024870.2	1387	Cat/Tat	34/40	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		403	482	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5465549	5465549	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs2131229930	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	67	621	0	ENST00000381577.3:c.733G>C	p.Gly245Arg	p.G245R	ENST00000381577	NM_014143.3	245	Gga/Cga	5/7	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		621	577	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485307	8485307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	34	397	0	ENST00000356435.5:c.3073C>T	p.His1025Tyr	p.H1025Y	ENST00000356435		1025	Cat/Tat	18/35	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		397	368	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499732	8499732	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	160	565	0	ENST00000356435.5:c.2237G>A	p.Gly746Glu	p.G746E	ENST00000356435		746	gGa/gAa	14/35	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		565	560	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970988	21970988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34170727	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	212	770	0	ENST00000304494.5:c.370C>T	p.Arg124Cys	p.R124C	ENST00000304494	NM_000077.4	124	Cgc/Tgc	2/3	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		770	632	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915952	127915952	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs865855853	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	50	442	0	ENST00000373547.4:c.529C>T	p.Arg177Ter	p.R177*	ENST00000373547	NM_002721.4	177	Cga/Tga	6/7	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		442	467	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293685	137293685	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	171	670	0	ENST00000481739.1:c.236T>A	p.Val79Glu	p.V79E	ENST00000481739	NM_002957.4	79	gTg/gAg	2/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		670	504	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395209	139395209	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	53	641	1	ENST00000277541.6:c.5729T>C	p.Ile1910Thr	p.I1910T	ENST00000277541	NM_017617.3	1910	aTc/aCc	31/34	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		642	591	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191755	123191755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	131	201	0	ENST00000218089.9:c.1344G>A	p.Met448Ile	p.M448I	ENST00000218089	NM_001042749.1	448	atG/atA	15/35	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		201	246	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858109	152858109	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1557026076	NA	P-0064015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	193	315	0	ENST00000406277.2:c.506G>A	p.Trp169Ter	p.W169*	ENST00000406277	NM_152274.4	169	tGg/tAg	6/7	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		315	364	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0064016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	52	493	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.75	0.639	0.872	0.75	0.639	0.872	SUBCLONAL	1	TRUE	1	0.29	2		493	478	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	45	346	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		346	400	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106185	27106186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0064017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	109	537	0	ENST00000324856.7:c.5796_5797insT	p.Ile1933TyrfsTer12	p.I1933Yfs*12	ENST00000324856	NM_006015.4	1932	-/T	20/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		537	683	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245411	46245411	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	116	451	0	ENST00000334344.6:c.3505G>T	p.Gly1169Cys	p.G1169C	ENST00000334344	NM_152641.2	1169	Ggc/Tgc	15/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		451	695	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349065	11349065	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	83	432	0	ENST00000332029.2:c.271G>T	p.Glu91Ter	p.E91*	ENST00000332029	NM_003745.1	91	Gag/Tag	2/2	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		432	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0064020-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	190	475	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	NA	2	FACETS	1	0.95	1			1	INDETERMINATE	1	TRUE	NA	0.652495828869023	2		476	568	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422467	225422467	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1553535841	NA	P-0064020-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	136	357	0	ENST00000264414.4:c.173A>G	p.Tyr58Cys	p.Y58C	ENST00000264414	NM_003590.4	58	tAt/tGt	2/16	1	2	FACETS	0.908	0.832	0.987	0.908	0.832	0.987	CLONAL	1	TRUE	1	0.652495828869023	2		357	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578510	7578514	+	frameshift_variant	Frame_Shift_Del	DEL	GGTCT	GGTCT	-	novel	NA	P-0064020-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	241	551	0	ENST00000269305.4:c.416_420del	p.Lys139MetfsTer8	p.K139Mfs*8	ENST00000269305	NM_001126112.2	139	aAGACC/a	5/11	0.44706072224572	3	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.652495828869023	3		551	719	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603135	48603135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064020-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	20	365	0	ENST00000342988.3:c.1436C>T	p.Ala479Val	p.A479V	ENST00000342988	NM_005359.5	479	gCt/gTt	11/12	0.652495828869023	1	FACETS	0.12	0.091	0.154	0.12	0.091	0.154	SUBCLONAL	1	TRUE	0	0.652495828869023	1		365	344	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670448	134670448	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064020-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	183	460	1	ENST00000398015.3:c.359T>C	p.Val120Ala	p.V120A	ENST00000398015	NM_004441.4	120	gTc/gCc	3/16	0.636412651931876	3	FACETS	1	0.974	1	0.554	0.513	0.597	CLONAL	1	TRUE	1	0.652495828869023	3		461	671	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557332	187557333	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064020-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	170	474	0	ENST00000441802.2:c.4029dup	p.Glu1344Ter	p.E1344*	ENST00000441802	NM_005245.3	1343	-/T	6/27	1	2	FACETS	0.877	0.811	0.946	0.877	0.811	0.946	CLONAL	1	TRUE	1	0.652495828869023	2		474	594	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587781525	NA	P-0064022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	103	610	0	ENST00000269305.4:c.842A>T	p.Asp281Val	p.D281V	ENST00000269305	NM_001126112.2	281	gAc/gTc	8/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		610	263	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029453	16029454	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0064022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	70	406	0	ENST00000268712.3:c.1576_1577del	p.Glu526LysfsTer9	p.E526Kfs*9	ENST00000268712	NM_006311.3	526	GAa/a	15/46	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		406	172	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577091	7577091	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149633775	NA	P-0064022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	109	623	0	ENST00000269305.4:c.847C>G	p.Arg283Gly	p.R283G	ENST00000269305	NM_001126112.2	283	Cgc/Ggc	8/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		623	277	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966760	18966760	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	22	585	0	ENST00000262803.5:c.1571A>G	p.Asn524Ser	p.N524S	ENST00000262803	NM_002911.3	524	aAc/aGc	12/24	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		585	221	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288229	33288230	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0064022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	146	629	0	ENST00000374542.5:c.1178dup	p.Arg394GlufsTer24	p.R394Efs*24	ENST00000374542	NM_001141970.1	393	aag/aaAg	4/8	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		629	412	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411072	63411072	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1464385859	NA	P-0064025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	161	660	0	ENST00000330258.3:c.2095C>T	p.Arg699Cys	p.R699C	ENST00000330258	NM_152424.3	699	Cgt/Tgt	2/2	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		660	630	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138452278	138452278	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	83	266	0	ENST00000289153.2:c.975T>A	p.His325Gln	p.H325Q	ENST00000289153	NM_006219.2	325	caT/caA	6/22	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		266	384	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829756	76829757	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTTGA	novel	NA	P-0064025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	95	375	0	ENST00000373344.5:c.6280_6284dup	p.Arg2095SerfsTer16	p.R2095Sfs*16	ENST00000373344	NM_000489.3	2095	agg/agTCAAGg	28/35	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		375	340	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	243	387	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.904	0.851	0.957	0.904	0.851	0.957	CLONAL	1	TRUE	1	0.909863189849735	2		387	591	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0064126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	390	470	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.909863189849735	2	FACETS	0.997	0.977	1	0.997	0.977	1	CLONAL	2	TRUE	0	0.909863189849735	2		470	430	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6439806	6439806	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	363	305	0	ENST00000356142.4:c.332A>T	p.Asn111Ile	p.N111I	ENST00000356142	NM_018890.3	111	aAt/aTt	5/7	0.458218012319578	2	FACETS	0.779	0.752	0.805	0.779	0.752	0.805	INDETERMINATE	2	TRUE	0	0.909863189849735	2		305	512	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21630869	21630869	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	205	434	0	ENST00000421138.2:c.735C>A	p.Phe245Leu	p.F245L	ENST00000421138		245	ttC/ttA	8/16	1	2	FACETS	0.939	0.88	0.998	0.939	0.88	0.998	CLONAL	1	TRUE	1	0.909863189849735	2		434	480	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436882	110436883	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0064126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	320	655	0	ENST00000375856.3:c.1518_1519delinsTT	p.Pro507Ser	p.P507S	ENST00000375856	NM_003749.2	506	agCCca/agTTca	1/2	0.381085704503212	5	FACETS	1	0.993	1	0.34	0.32	0.36	INDETERMINATE	1	TRUE	1	0.909863189849735	5		655	1224	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81962188	81962188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779400707	NA	P-0064126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	198	351	0	ENST00000359376.3:c.2540C>T	p.Ser847Phe	p.S847F	ENST00000359376	NM_002661.3	847	tCt/tTt	24/33	1	2	FACETS	0.852	0.796	0.908	0.852	0.796	0.908	CLONAL	1	TRUE	1	0.909863189849735	2		351	511	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459743	149459743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	408	654	0	ENST00000286301.3:c.464C>T	p.Ser155Phe	p.S155F	ENST00000286301	NM_005211.3	155	tCc/tTc	4/22	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.909863189849735	2		654	859	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878029	151878029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369563648	NA	P-0064126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	164	574	0	ENST00000262189.6:c.6916C>T	p.Pro2306Ser	p.P2306S	ENST00000262189	NM_170606.2	2306	Cca/Tca	36/59	0.458218012319578	2	FACETS	0.514	0.472	0.556	0.257	0.236	0.278	INDETERMINATE	1	TRUE	0	0.909863189849735	2		574	702	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619258	37619258	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064127-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	46	703	0	ENST00000447079.4:c.934A>G	p.Ser312Gly	p.S312G	ENST00000447079	NM_015083.1	312	Agc/Ggc	1/14	1	2	FACETS	0.132	0.11	0.156	0.132	0.11	0.156	SUBCLONAL	1	TRUE	1	0.849816708586769	2		703	820	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980743	40980743	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064127-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	287	678	0	ENST00000373198.4:c.1743del	p.Ile582LeufsTer19	p.I582Lfs*19	ENST00000373198	NM_133170.3	581	cgG/cg	10/32	1	2	FACETS	0.951	0.9	1	0.951	0.9	1	CLONAL	1	TRUE	1	0.849816708586769	2		678	710	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065344-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	28	387	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		387	181	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0065344-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	72	558	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		558	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0065344-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	76	554	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		554	482	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247168	153247168	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1560758208	NA	P-0065344-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	68	444	0	ENST00000281708.4:c.1634A>G	p.Tyr545Cys	p.Y545C	ENST00000281708	NM_033632.3	545	tAt/tGt	10/12	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		444	409	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106300	27106300	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065344-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	67	607	0	ENST00000324856.7:c.5911C>G	p.Leu1971Val	p.L1971V	ENST00000324856	NM_006015.4	1971	Ctg/Gtg	20/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		607	538	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107195	27107195	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0065344-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	80	515	0	ENST00000324856.7:c.6806C>G	p.Ser2269Ter	p.S2269*	ENST00000324856	NM_006015.4	2269	tCa/tGa	20/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		515	529	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859702	151859702	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065344-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	89	613	0	ENST00000262189.6:c.10960C>T	p.Gln3654Ter	p.Q3654*	ENST00000262189	NM_170606.2	3654	Caa/Taa	43/59	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		613	577	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188545	32188545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752931284	NA	P-0065344-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	60	610	0	ENST00000375023.3:c.910G>A	p.Glu304Lys	p.E304K	ENST00000375023	NM_004557.3	304	Gaa/Aaa	5/30	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		610	443	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294550	1294550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065344-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	54	486	0	ENST00000310581.5:c.451C>T	p.His151Tyr	p.H151Y	ENST00000310581	NM_198253.2	151	Cac/Tac	2/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		486	390	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604286	189604286	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065344-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	54	510	0	ENST00000264731.3:c.1453C>T	p.Gln485Ter	p.Q485*	ENST00000264731	NM_003722.4	485	Cag/Tag	11/14	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		510	436	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965026	25965026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065344-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	82	504	0	ENST00000435504.4:c.4180G>A	p.Glu1394Lys	p.E1394K	ENST00000435504		1394	Gag/Aag	13/13	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		504	489	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718077	117718077	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1387248855	NA	P-0065344-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	23	393	0	ENST00000368508.3:c.779+1G>A		p.X260_splice	ENST00000368508	NM_002944.2	260			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		393	375	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039654	47039654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065344-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	74	529	0	ENST00000377604.3:c.1106C>T	p.Pro369Leu	p.P369L	ENST00000377604	NM_001204468.1	369	cCa/cTa	11/24	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		529	455	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718089	117718089	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065344-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	22	429	0	ENST00000368508.3:c.768T>A	p.Asn256Lys	p.N256K	ENST00000368508	NM_002944.2	256	aaT/aaA	7/43	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		429	396	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150027	202150027	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065344-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	93	588	0	ENST00000358485.4:c.1468G>C	p.Glu490Gln	p.E490Q	ENST00000358485	NM_001080125.1	490	Gag/Cag	8/9	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		588	472	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964994	25964994	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065344-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	101	552	0	ENST00000435504.4:c.4212G>C	p.Leu1404Phe	p.L1404F	ENST00000435504		1404	ttG/ttC	13/13	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		552	510	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965087	25965087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065344-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	89	518	0	ENST00000435504.4:c.4119G>A	p.Met1373Ile	p.M1373I	ENST00000435504		1373	atG/atA	13/13	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		518	524	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928977	49928977	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs549731289	NA	P-0065344-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	101	560	0	ENST00000296474.3:c.3389G>A	p.Arg1130Gln	p.R1130Q	ENST00000296474	NM_002447.2	1130	cGa/cAa	16/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		560	535	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107146	27107146	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065344-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	71	572	0	ENST00000324856.7:c.6757C>G	p.Leu2253Val	p.L2253V	ENST00000324856	NM_006015.4	2253	Ctg/Gtg	20/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		572	550	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0065687-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	65	586	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		586	446	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024381	31024381	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755522655	NA	P-0065687-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	25	517	0	ENST00000375687.4:c.3866G>A	p.Arg1289Gln	p.R1289Q	ENST00000375687	NM_015338.5	1289	cGg/cAg	13/13	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		517	464	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971209	21971209	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1554654224	NA	P-0065687-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	60	462	0	ENST00000304494.5:c.151-2A>G		p.X51_splice	ENST00000304494	NM_000077.4	51			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		462	359	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821269	72821269	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065687-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	26	407	2	ENST00000268489.5:c.10906T>A	p.Ser3636Thr	p.S3636T	ENST00000268489	NM_006885.3	3636	Tcc/Acc	10/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		409	363	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0065822-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	42	381	1	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		382	475	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0065822-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	65	464	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		464	492	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679366	29679366	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs866445127	NA	P-0065822-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	75	344	0	ENST00000356175.3:c.7486C>T	p.Arg2496Ter	p.R2496*	ENST00000356175	NM_000267.3	2496	Cga/Tga	50/57	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		344	562	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142865	30142865	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs199584443	NA	P-0065822-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	49	358	0	ENST00000389048.3:c.661G>C	p.Gly221Arg	p.G221R	ENST00000389048	NM_004304.4	221	Ggg/Cgg	1/29	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		358	498	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757461	40757461	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065822-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	67	376	0	ENST00000373198.4:c.2837C>A	p.Ser946Tyr	p.S946Y	ENST00000373198	NM_133170.3	946	tCc/tAc	20/32	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		376	599	SUCCESS
APC	324	MSKCC	GRCh37	5	112128164	112128164	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554074738	NA	P-0065822-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	20	237	1	ENST00000257430.4:c.667C>T	p.Gln223Ter	p.Q223*	ENST00000257430	NM_000038.5	223	Caa/Taa	7/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		238	372	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048839	180048839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773839174	NA	P-0065822-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	39	469	1	ENST00000261937.6:c.1723C>T	p.Leu575Phe	p.L575F	ENST00000261937	NM_182925.4	575	Ctc/Ttc	13/30	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		470	483	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	68	385	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.410900055263663	2		385	314	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317572	1317572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	33	187	0	ENST00000400841.2:c.493G>A	p.Glu165Lys	p.E165K	ENST00000400841		165	Gaa/Aaa	5/6	1	2	FACETS	0.795	0.653	0.952	0.795	0.653	0.952	CLONAL	1	TRUE	1	0.410900055263663	2		187	202	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073929	8073929	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	110	478	0	ENST00000377482.5:c.730C>T	p.Arg244Ter	p.R244*	ENST00000377482	NM_018948.3	244	Cga/Tga	4/4	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.410900055263663	2		478	504	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298651	11298651	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1235010967	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	97	469	0	ENST00000361445.4:c.1810C>T	p.Arg604Cys	p.R604C	ENST00000361445	NM_004958.3	604	Cgc/Tgc	12/58	1	2	FACETS	0.978	0.875	1	0.978	0.875	1	CLONAL	1	TRUE	1	0.410900055263663	2		469	483	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258745	16258745	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	133	619	0	ENST00000375759.3:c.6010C>T	p.Pro2004Ser	p.P2004S	ENST00000375759	NM_015001.2	2004	Ccg/Tcg	11/15	1	2	FACETS	0.972	0.885	1	0.972	0.885	1	CLONAL	1	TRUE	1	0.410900055263663	2		619	666	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259955	16259955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1482002539	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	129	546	0	ENST00000375759.3:c.7220C>T	p.Ser2407Phe	p.S2407F	ENST00000375759	NM_015001.2	2407	tCc/tTc	11/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.410900055263663	2		546	563	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120478170	120478170	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	107	509	0	ENST00000256646.2:c.3580C>T	p.Gln1194Ter	p.Q1194*	ENST00000256646	NM_024408.3	1194	Cag/Tag	22/34	1	2	FACETS	0.851	0.765	0.942	0.851	0.765	0.942	CLONAL	1	TRUE	1	0.410900055263663	2		509	612	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218892	193218892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1225502334	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	58	424	0	ENST00000367435.3:c.1450C>T	p.Arg484Cys	p.R484C	ENST00000367435	NM_024529.4	484	Cgt/Tgt	16/17	1	2	FACETS	0.92	0.796	1	0.92	0.796	1	CLONAL	1	TRUE	1	0.410900055263663	2		424	307	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230492738	230492739	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	90	568	0	ENST00000391860.1:c.315_316delinsTT	p.Arg106Cys	p.R106C	ENST00000391860	NM_001258311.1	105	ttCCgc/ttTTgc	2/7	1	2	FACETS	0.922	0.822	1	0.922	0.822	1	CLONAL	1	TRUE	1	0.410900055263663	2		568	475	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243778408	243778408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	61	378	0	ENST00000263826.5:c.617C>T	p.Pro206Leu	p.P206L	ENST00000263826	NM_005465.4	206	cCc/cTc	6/13	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.410900055263663	2		378	294	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852407	63852407	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	129	559	0	ENST00000279873.7:c.3185C>T	p.Ser1062Phe	p.S1062F	ENST00000279873	NM_032199.2	1062	tCc/tTc	10/10	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.410900055263663	2		559	596	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925406	114925407	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	121	470	0	ENST00000543371.1:c.1484_1485insT	p.Ser496LeufsTer17	p.S496Lfs*17	ENST00000543371	NM_001198531.1	495	ccc/ccTc	14/14	0.410900055263663	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.410900055263663	1		470	351	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909881	100909881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1565326353	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	70	442	0	ENST00000325455.5:c.2768G>A	p.Gly923Glu	p.G923E	ENST00000325455	NM_001202474.3	923	gGg/gAg	8/8	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.410900055263663	2		442	333	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201933	102201933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	88	465	0	ENST00000263464.3:c.1285G>A	p.Glu429Lys	p.E429K	ENST00000263464	NM_001165.4	429	Gaa/Aaa	6/9	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.410900055263663	2		465	417	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115732	108115732	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1218041868	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	52	409	0	ENST00000278616.4:c.880G>A	p.Gly294Arg	p.G294R	ENST00000278616	NM_000051.3	294	Gga/Aga	7/63	1	2	FACETS	0.786	0.673	0.909	0.786	0.673	0.909	CLONAL	1	TRUE	1	0.410900055263663	2		409	322	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156112	119156112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776999573	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	117	573	0	ENST00000264033.4:c.1777C>T	p.Arg593Trp	p.R593W	ENST00000264033	NM_005188.3	593	Cgg/Tgg	11/16	1	2	FACETS	0.951	0.86	1	0.951	0.86	1	CLONAL	1	TRUE	1	0.410900055263663	2		573	599	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170471	119170471	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	83	480	0	ENST00000264033.4:c.2701C>T	p.Pro901Ser	p.P901S	ENST00000264033	NM_005188.3	901	Cct/Tct	16/16	1	2	FACETS	0.873	0.773	0.978	0.873	0.773	0.978	CLONAL	1	TRUE	1	0.410900055263663	2		480	463	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	441056	441056	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766684341	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	111	541	0	ENST00000399788.2:c.1702C>T	p.Arg568Cys	p.R568C	ENST00000399788	NM_001042603.1	568	Cgt/Tgt	13/28	1	2	FACETS	0.963	0.869	1	0.963	0.869	1	CLONAL	1	TRUE	1	0.410900055263663	2		541	561	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524125	18524125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1391898033	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	72	385	0	ENST00000266497.5:c.1637C>T	p.Pro546Leu	p.P546L	ENST00000266497		546	cCc/cTc	11/31	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.410900055263663	2		385	306	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552603	18552603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	82	446	0	ENST00000266497.5:c.2014G>A	p.Glu672Lys	p.E672K	ENST00000266497		672	Gaa/Aaa	14/31	1	2	FACETS	0.973	0.863	1	0.973	0.863	1	CLONAL	1	TRUE	1	0.410900055263663	2		446	410	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18649067	18649067	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	47	493	0	ENST00000266497.5:c.2742A>T	p.Lys914Asn	p.K914N	ENST00000266497		914	aaA/aaT	19/31	1	2	FACETS	0.704	0.597	0.821	0.704	0.597	0.821	SUBCLONAL	1	TRUE	1	0.410900055263663	2		493	325	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658382	18658382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	94	402	0	ENST00000266497.5:c.3187G>A	p.Gly1063Arg	p.G1063R	ENST00000266497		1063	Gga/Aga	22/31	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.410900055263663	2		402	392	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691166	18691166	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	81	404	0	ENST00000266497.5:c.3277C>T	p.Gln1093Ter	p.Q1093*	ENST00000266497		1093	Caa/Taa	23/31	1	2	FACETS	0.952	0.843	1	0.952	0.843	1	CLONAL	1	TRUE	1	0.410900055263663	2		404	414	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699287	18699287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1370164516	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	83	476	0	ENST00000266497.5:c.3388G>A	p.Gly1130Arg	p.G1130R	ENST00000266497		1130	Gga/Aga	24/31	1	2	FACETS	0.92	0.816	1	0.92	0.816	1	CLONAL	1	TRUE	1	0.410900055263663	2		476	439	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46215212	46215212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	65	306	0	ENST00000334344.6:c.647C>T	p.Ser216Phe	p.S216F	ENST00000334344	NM_152641.2	216	tCc/tTc	6/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.410900055263663	2		306	253	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244227	46244227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	129	548	0	ENST00000334344.6:c.2321C>T	p.Pro774Leu	p.P774L	ENST00000334344	NM_152641.2	774	cCa/cTa	15/21	1	2	FACETS	0.951	0.864	1	0.951	0.864	1	CLONAL	1	TRUE	1	0.410900055263663	2		548	660	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285594	46285594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	102	461	0	ENST00000334344.6:c.4954C>T	p.His1652Tyr	p.H1652Y	ENST00000334344	NM_152641.2	1652	Cat/Tat	17/21	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.410900055263663	2		461	472	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434556	49434556	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370380369	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	128	613	0	ENST00000301067.7:c.6997C>T	p.Pro2333Ser	p.P2333S	ENST00000301067	NM_003482.3	2333	Cct/Tct	31/54	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.410900055263663	2		613	594	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114201	115114201	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	104	528	0	ENST00000257566.3:c.1016C>A	p.Ser339Tyr	p.S339Y	ENST00000257566	NM_016569.3	339	tCc/tAc	6/8	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.410900055263663	2		528	485	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800851	120800851	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	98	442	0	ENST00000257552.2:c.397G>A	p.Gly133Arg	p.G133R	ENST00000257552	NM_002442.3	133	Ggg/Agg	6/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.410900055263663	2		442	426	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202843	133202843	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369748519	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	119	578	0	ENST00000320574.5:c.6391C>T	p.Arg2131Cys	p.R2131C	ENST00000320574	NM_006231.2	2131	Cgc/Tgc	46/49	1	2	FACETS	0.973	0.881	1	0.973	0.881	1	CLONAL	1	TRUE	1	0.410900055263663	2		578	595	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608248	28608248	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	93	553	0	ENST00000241453.7:c.1808G>A	p.Trp603Ter	p.W603*	ENST00000241453	NM_004119.2	603	tGg/tAg	14/24	1	2	FACETS	0.857	0.765	0.956	0.857	0.765	0.956	CLONAL	1	TRUE	1	0.410900055263663	2		553	528	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964014	28964014	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	94	456	0	ENST00000282397.4:c.1888G>A	p.Asp630Asn	p.D630N	ENST00000282397	NM_002019.4	630	Gat/Aat	13/30	1	2	FACETS	0.862	0.769	0.96	0.862	0.769	0.96	CLONAL	1	TRUE	1	0.410900055263663	2		456	531	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001963	29001963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	89	440	0	ENST00000282397.4:c.1202G>A	p.Gly401Glu	p.G401E	ENST00000282397	NM_002019.4	401	gGg/gAg	9/30	1	2	FACETS	0.952	0.848	1	0.952	0.848	1	CLONAL	1	TRUE	1	0.410900055263663	2		440	455	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004205	29004205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	90	425	0	ENST00000282397.4:c.1088C>T	p.Pro363Leu	p.P363L	ENST00000282397	NM_002019.4	363	cCc/cTc	8/30	1	2	FACETS	0.924	0.823	1	0.924	0.823	1	CLONAL	1	TRUE	1	0.410900055263663	2		425	474	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041180	29041180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	96	469	0	ENST00000282397.4:c.248G>A	p.Arg83Lys	p.R83K	ENST00000282397	NM_002019.4	83	aGa/aAa	3/30	1	2	FACETS	0.818	0.731	0.911	0.818	0.731	0.911	CLONAL	1	TRUE	1	0.410900055263663	2		469	571	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919220	48919220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	49	317	0	ENST00000267163.4:c.385C>T	p.His129Tyr	p.H129Y	ENST00000267163	NM_000321.2	129	Cat/Tat	4/27	1	2	FACETS	0.849	0.724	0.984	0.849	0.724	0.984	CLONAL	1	TRUE	1	0.410900055263663	2		317	281	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514607	103514607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372636507	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	122	561	0	ENST00000355739.4:c.1108C>T	p.Arg370Cys	p.R370C	ENST00000355739	NM_000123.3	370	Cgt/Tgt	8/15	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.410900055263663	2		561	554	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034906	42034906	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	101	530	0	ENST00000219905.7:c.4748C>T	p.Ser1583Phe	p.S1583F	ENST00000219905	NM_001164273.1	1583	tCt/tTt	15/24	1	2	FACETS	0.853	0.765	0.947	0.853	0.765	0.947	CLONAL	1	TRUE	1	0.410900055263663	2		530	576	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51514645	51514645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772438452	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	128	507	0	ENST00000260433.2:c.529G>A	p.Glu177Lys	p.E177K	ENST00000260433		177	Gag/Aag	5/10	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.410900055263663	2		507	599	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66735663	66735663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	75	343	0	ENST00000307102.5:c.484C>T	p.Pro162Ser	p.P162S	ENST00000307102	NM_002755.3	162	Cct/Tct	4/11	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.410900055263663	2		343	324	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576115	88576115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	100	511	0	ENST00000360948.2:c.1558G>A	p.Gly520Arg	p.G520R	ENST00000360948	NM_001012338.2	520	Gga/Aga	13/19	1	2	FACETS	0.956	0.858	1	0.956	0.858	1	CLONAL	1	TRUE	1	0.410900055263663	2		511	509	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678602	88678602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243717189	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	64	519	0	ENST00000360948.2:c.934G>A	p.Glu312Lys	p.E312K	ENST00000360948	NM_001012338.2	312	Gag/Aag	9/19	1	2	FACETS	0.74	0.643	0.844	0.74	0.643	0.844	SUBCLONAL	1	TRUE	1	0.410900055263663	2		519	421	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726662	88726662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	56	393	0	ENST00000360948.2:c.382C>T	p.His128Tyr	p.H128Y	ENST00000360948	NM_001012338.2	128	Cat/Tat	4/19	1	2	FACETS	0.64	0.549	0.738	0.64	0.549	0.738	SUBCLONAL	1	TRUE	1	0.410900055263663	2		393	426	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820627	3820627	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776803900	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	116	607	0	ENST00000262367.5:c.2824C>T	p.Pro942Ser	p.P942S	ENST00000262367	NM_004380.2	942	Cct/Tct	14/31	1	2	FACETS	0.964	0.871	1	0.964	0.871	1	CLONAL	1	TRUE	1	0.410900055263663	2		607	586	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857163	9857163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	119	617	0	ENST00000330684.3:c.4238C>T	p.Ser1413Phe	p.S1413F	ENST00000330684	NM_001134407.1	1413	tCc/tTc	13/13	1	2	FACETS	0.977	0.884	1	0.977	0.884	1	CLONAL	1	TRUE	1	0.410900055263663	2		617	593	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934918	9934918	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	93	487	0	ENST00000330684.3:c.1372G>A	p.Gly458Arg	p.G458R	ENST00000330684	NM_001134407.1	458	Ggg/Agg	6/13	1	2	FACETS	0.82	0.731	0.915	0.82	0.731	0.915	CLONAL	1	TRUE	1	0.410900055263663	2		487	552	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50810116	50810116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	55	403	0	ENST00000398568.2:c.940C>T	p.Pro314Ser	p.P314S	ENST00000398568	NM_001042412.1	314	Ccc/Tcc	6/18	1	2	FACETS	0.78	0.671	0.899	0.78	0.671	0.899	SUBCLONAL	1	TRUE	1	0.410900055263663	2		403	343	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821275	72821275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750437411	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	94	465	0	ENST00000268489.5:c.10900C>T	p.Pro3634Ser	p.P3634S	ENST00000268489	NM_006885.3	3634	Cct/Tct	10/10	1	2	FACETS	0.969	0.866	1	0.969	0.866	1	CLONAL	1	TRUE	1	0.410900055263663	2		465	472	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822139	72822139	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	130	697	0	ENST00000268489.5:c.10036C>T	p.Pro3346Ser	p.P3346S	ENST00000268489	NM_006885.3	3346	Cct/Tct	10/10	1	2	FACETS	0.97	0.882	1	0.97	0.882	1	CLONAL	1	TRUE	1	0.410900055263663	2		697	652	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972440	81972440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs891516801	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	84	489	0	ENST00000359376.3:c.3233G>A	p.Arg1078Gln	p.R1078Q	ENST00000359376	NM_002661.3	1078	cGa/cAa	29/33	1	2	FACETS	0.785	0.695	0.88	0.785	0.695	0.88	SUBCLONAL	1	TRUE	1	0.410900055263663	2		489	521	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989484	7989484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772959657	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	75	638	0	ENST00000319144.4:c.202C>T	p.Arg68Cys	p.R68C	ENST00000319144	NM_001139.2	68	Cgc/Tgc	2/15	1	2	FACETS	0.833	0.733	0.94	0.833	0.733	0.94	CLONAL	1	TRUE	1	0.410900055263663	2		638	438	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960889	15960889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774844897	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	106	417	0	ENST00000268712.3:c.6331C>T	p.His2111Tyr	p.H2111Y	ENST00000268712	NM_006311.3	2111	Cat/Tat	40/46	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.410900055263663	2		417	491	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16001803	16001803	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771889820	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	74	370	0	ENST00000268712.3:c.2698C>T	p.Pro900Ser	p.P900S	ENST00000268712	NM_006311.3	900	Cct/Tct	21/46	1	2	FACETS	0.919	0.809	1	0.919	0.809	1	CLONAL	1	TRUE	1	0.410900055263663	2		370	392	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654712	29654712	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	119	505	1	ENST00000356175.3:c.5401C>T	p.Gln1801Ter	p.Q1801*	ENST00000356175	NM_000267.3	1801	Cag/Tag	37/57	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.410900055263663	2		506	578	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	61	404	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.964	0.838	1	0.964	0.838	1	CLONAL	1	TRUE	1	0.410900055263663	2		404	308	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679788	33679788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150521243	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	127	565	0	ENST00000308377.4:c.2293C>T	p.Pro765Ser	p.P765S	ENST00000308377	NM_152270.3	765	Cct/Tct	5/5	1	2	FACETS	0.98	0.89	1	0.98	0.89	1	CLONAL	1	TRUE	1	0.410900055263663	2		565	631	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690618	33690618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	105	265	0	ENST00000308377.4:c.209C>T	p.Pro70Leu	p.P70L	ENST00000308377	NM_152270.3	70	cCc/cTc	2/5	1	2	FACETS	0.858	0.779	0.938	1	0.987	1	CLONAL	2	TRUE	1	0.410900055263663	2		265	298	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811537	56811537	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	96	345	0	ENST00000337432.4:c.1085C>T	p.Ser362Phe	p.S362F	ENST00000337432	NM_058216.2	362	tCc/tTc	9/9	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.410900055263663	2		345	420	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593441	48593441	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	100	465	0	ENST00000342988.3:c.1192T>C	p.Trp398Arg	p.W398R	ENST00000342988	NM_005359.5	398	Tgg/Cgg	10/12	1	2	FACETS	0.94	0.842	1	0.94	0.842	1	CLONAL	1	TRUE	1	0.410900055263663	2		465	518	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61324638	61324638	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	70	353	0	ENST00000283752.5:c.478A>C	p.Lys160Gln	p.K160Q	ENST00000283752	NM_006919.2	160	Aaa/Caa	6/8	1	2	FACETS	0.965	0.847	1	0.965	0.847	1	CLONAL	1	TRUE	1	0.410900055263663	2		353	353	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615701	1615701	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	125	661	0	ENST00000344749.5:c.1570C>T	p.Pro524Ser	p.P524S	ENST00000344749	NM_001136139.2	524	Ccc/Tcc	17/19	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.410900055263663	2		661	564	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267524	7267524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	90	474	0	ENST00000302850.5:c.484C>T	p.Arg162Cys	p.R162C	ENST00000302850	NM_000208.2	162	Cgt/Tgt	2/22	1	2	FACETS	0.892	0.795	0.996	0.892	0.795	0.996	CLONAL	1	TRUE	1	0.410900055263663	2		474	491	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302346	15302346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1386908989	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	113	603	0	ENST00000263388.2:c.925G>A	p.Glu309Lys	p.E309K	ENST00000263388	NM_000435.2	309	Gag/Aag	6/33	1	2	FACETS	0.979	0.884	1	0.979	0.884	1	CLONAL	1	TRUE	1	0.410900055263663	2		603	562	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303260	15303260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555729604	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	112	613	0	ENST00000263388.2:c.268C>T	p.Arg90Cys	p.R90C	ENST00000263388	NM_000435.2	90	Cgt/Tgt	3/33	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.410900055263663	2		613	536	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950412	17950412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573731097	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	98	473	0	ENST00000458235.1:c.1315C>T	p.Leu439Phe	p.L439F	ENST00000458235	NM_000215.3	439	Ctt/Ttt	10/24	1	2	FACETS	0.996	0.893	1	0.996	0.893	1	CLONAL	1	TRUE	1	0.410900055263663	2		473	479	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257875	19257875	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	156	612	0	ENST00000162023.5:c.511C>T	p.Arg171Ter	p.R171*	ENST00000162023		171	Cga/Tga	9/13	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.410900055263663	2		612	705	SUCCESS
AXL	558	MSKCC	GRCh37	19	41725372	41725372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	79	405	0	ENST00000301178.4:c.75G>A	p.Met25Ile	p.M25I	ENST00000301178	NM_021913.4	25	atG/atA	1/20	1	2	FACETS	0.813	0.717	0.915	0.813	0.717	0.915	CLONAL	1	TRUE	1	0.410900055263663	2		405	473	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748841	41748841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	116	545	0	ENST00000301178.4:c.1366G>A	p.Gly456Arg	p.G456R	ENST00000301178	NM_021913.4	456	Gga/Aga	11/20	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.410900055263663	2		545	545	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867781	45867781	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	90	658	0	ENST00000391945.4:c.619T>C	p.Tyr207His	p.Y207H	ENST00000391945	NM_000400.3	207	Tat/Cat	8/23	1	2	FACETS	0.802	0.714	0.897	0.802	0.714	0.897	CLONAL	1	TRUE	1	0.410900055263663	2		658	546	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902220	50902220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	93	546	0	ENST00000440232.2:c.112C>A	p.Leu38Met	p.L38M	ENST00000440232	NM_002691.3	38	Ctg/Atg	2/27	1	2	FACETS	0.963	0.86	1	0.963	0.86	1	CLONAL	1	TRUE	1	0.410900055263663	2		546	470	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917119	50917119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057522945	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	87	603	0	ENST00000440232.2:c.2371C>T	p.Arg791Trp	p.R791W	ENST00000440232	NM_002691.3	791	Cgg/Tgg	19/27	1	2	FACETS	0.764	0.678	0.856	0.764	0.678	0.856	SUBCLONAL	1	TRUE	1	0.410900055263663	2		603	554	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085834	16085834	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	98	543	0	ENST00000281043.3:c.1010C>T	p.Pro337Leu	p.P337L	ENST00000281043	NM_005378.4	337	cCc/cTc	3/3	1	2	FACETS	0.958	0.858	1	0.958	0.858	1	CLONAL	1	TRUE	1	0.410900055263663	2		543	498	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462683	29462683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766541301	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	90	547	0	ENST00000389048.3:c.2218G>A	p.Gly740Arg	p.G740R	ENST00000389048	NM_004304.4	740	Gga/Aga	13/29	1	2	FACETS	0.938	0.836	1	0.938	0.836	1	CLONAL	1	TRUE	1	0.410900055263663	2		547	467	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47604194	47604194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772471530	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	66	362	0	ENST00000263735.4:c.533C>T	p.Pro178Leu	p.P178L	ENST00000263735	NM_002354.2	178	cCa/cTa	5/9	1	2	FACETS	0.875	0.764	0.995	0.875	0.764	0.995	CLONAL	1	TRUE	1	0.410900055263663	2		362	367	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61720185	61720185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	62	389	0	ENST00000401558.2:c.1249C>T	p.Arg417Cys	p.R417C	ENST00000401558	NM_003400.3	417	Cgt/Tgt	13/25	1	2	FACETS	0.72	0.624	0.824	0.72	0.624	0.824	SUBCLONAL	1	TRUE	1	0.410900055263663	2		389	419	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622630	158622630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	91	456	0	ENST00000263640.3:c.869C>T	p.Ser290Leu	p.S290L	ENST00000263640	NM_001105.4	290	tCg/tTg	8/11	1	2	FACETS	0.959	0.855	1	0.959	0.855	1	CLONAL	1	TRUE	1	0.410900055263663	2		456	462	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248372	212248372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	103	522	0	ENST00000342788.4:c.3895C>T	p.Pro1299Ser	p.P1299S	ENST00000342788	NM_005235.2	1299	Cca/Tca	28/28	1	2	FACETS	0.867	0.778	0.962	0.867	0.778	0.962	CLONAL	1	TRUE	1	0.410900055263663	2		522	578	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248631	212248631	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	104	554	0	ENST00000342788.4:c.3636T>A	p.Phe1212Leu	p.F1212L	ENST00000342788	NM_005235.2	1212	ttT/ttA	28/28	1	2	FACETS	0.874	0.785	0.969	0.874	0.785	0.969	CLONAL	1	TRUE	1	0.410900055263663	2		554	579	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251814	212251814	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	108	528	0	ENST00000342788.4:c.3245G>A	p.Arg1082Lys	p.R1082K	ENST00000342788	NM_005235.2	1082	aGa/aAa	27/28	1	2	FACETS	0.896	0.806	0.99	0.896	0.806	0.99	CLONAL	1	TRUE	1	0.410900055263663	2		528	587	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426668	212426668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	124	528	0	ENST00000342788.4:c.2447G>A	p.Gly816Glu	p.G816E	ENST00000342788	NM_005235.2	816	gGa/gAa	20/28	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.410900055263663	2		528	531	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578349	212578349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1484791833	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	62	363	0	ENST00000342788.4:c.908C>T	p.Ser303Phe	p.S303F	ENST00000342788	NM_005235.2	303	tCt/tTt	8/28	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.410900055263663	2		363	278	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440183	220440183	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	99	553	0	ENST00000243786.2:c.1036G>A	p.Gly346Arg	p.G346R	ENST00000243786	NM_002191.3	346	Gga/Aga	2/2	1	2	FACETS	0.927	0.83	1	0.927	0.83	1	CLONAL	1	TRUE	1	0.410900055263663	2		553	520	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793269	242793269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1381223113	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	102	513	0	ENST00000334409.5:c.808G>A	p.Gly270Ser	p.G270S	ENST00000334409	NM_005018.2	270	Ggc/Agc	5/5	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.410900055263663	2		513	452	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560902	9560902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756198440	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	89	534	0	ENST00000353224.5:c.880G>A	p.Glu294Lys	p.E294K	ENST00000353224	NM_177990.2	294	Gaa/Aaa	4/10	1	2	FACETS	0.791	0.703	0.884	0.791	0.703	0.884	SUBCLONAL	1	TRUE	1	0.410900055263663	2		534	548	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024357	31024357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	116	488	0	ENST00000375687.4:c.3842C>T	p.Ser1281Phe	p.S1281F	ENST00000375687	NM_015338.5	1281	tCc/tTc	13/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.410900055263663	2		488	498	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721201	39721201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	95	415	0	ENST00000361337.2:c.704C>T	p.Pro235Leu	p.P235L	ENST00000361337	NM_003286.2	235	cCa/cTa	9/21	1	2	FACETS	0.967	0.865	1	0.967	0.865	1	CLONAL	1	TRUE	1	0.410900055263663	2		415	478	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733229	40733229	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	101	479	0	ENST00000373198.4:c.3577C>A	p.Gln1193Lys	p.Q1193K	ENST00000373198	NM_133170.3	1193	Caa/Aaa	26/32	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.410900055263663	2		479	490	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770630	40770630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	75	499	0	ENST00000373198.4:c.2752G>A	p.Gly918Arg	p.G918R	ENST00000373198	NM_133170.3	918	Ggg/Agg	19/32	1	2	FACETS	0.754	0.663	0.852	0.754	0.663	0.852	SUBCLONAL	1	TRUE	1	0.410900055263663	2		499	484	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827984	40827984	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1174893851	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	107	514	0	ENST00000373198.4:c.2444G>A	p.Arg815Lys	p.R815K	ENST00000373198	NM_133170.3	815	aGg/aAg	17/32	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.410900055263663	2		514	515	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877334	40877334	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	68	461	0	ENST00000373198.4:c.2362A>T	p.Lys788Ter	p.K788*	ENST00000373198	NM_133170.3	788	Aaa/Taa	15/32	1	2	FACETS	0.761	0.664	0.865	0.761	0.664	0.865	SUBCLONAL	1	TRUE	1	0.410900055263663	2		461	435	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980798	40980798	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	108	468	0	ENST00000373198.4:c.1688C>T	p.Ser563Phe	p.S563F	ENST00000373198	NM_133170.3	563	tCc/tTc	10/32	1	2	FACETS	0.954	0.859	1	0.954	0.859	1	CLONAL	1	TRUE	1	0.410900055263663	2		468	551	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385182	41385182	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367872006	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	80	487	0	ENST00000373198.4:c.779G>A	p.Arg260Gln	p.R260Q	ENST00000373198	NM_133170.3	260	cGg/cAg	6/32	1	2	FACETS	0.918	0.812	1	0.918	0.812	1	CLONAL	1	TRUE	1	0.410900055263663	2		487	424	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514476	41514476	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	94	451	0	ENST00000373198.4:c.185A>T	p.Lys62Ile	p.K62I	ENST00000373198	NM_133170.3	62	aAa/aTa	2/32	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.410900055263663	2		451	421	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256669	46256669	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	81	379	0	ENST00000371998.3:c.725T>A	p.Leu242Ter	p.L242*	ENST00000371998		242	tTg/tAg	8/23	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.410900055263663	2		379	382	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21344699	21344699	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	96	505	0	ENST00000215739.8:c.676C>G	p.Pro226Ala	p.P226A	ENST00000215739	NM_006767.3	226	Cca/Gca	8/21	1	2	FACETS	0.935	0.836	1	0.935	0.836	1	CLONAL	1	TRUE	1	0.410900055263663	2		505	500	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095846	29095846	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs768973809	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	83	429	0	ENST00000328354.6:c.988C>T	p.Gln330Ter	p.Q330*	ENST00000328354	NM_007194.3	330	Cag/Tag	9/15	1	2	FACETS	0.94	0.833	1	0.94	0.833	1	CLONAL	1	TRUE	1	0.410900055263663	2		429	430	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29445395	29445396	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	101	696	0	ENST00000544604.2:c.1226_1227delinsTT	p.Ser409Phe	p.S409F	ENST00000544604	NM_001206998.1	409	tCC/tTT	8/9	1	2	FACETS	0.842	0.754	0.934	0.842	0.754	0.934	CLONAL	1	TRUE	1	0.410900055263663	2		696	584	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182309	38182309	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	98	503	0	ENST00000396334.3:c.745C>T	p.Gln249Ter	p.Q249*	ENST00000396334	NM_002468.4	249	Cag/Tag	4/5	1	2	FACETS	0.849	0.759	0.944	0.849	0.759	0.944	CLONAL	1	TRUE	1	0.410900055263663	2		503	562	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162639	47162639	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	104	454	0	ENST00000409792.3:c.3487C>A	p.Pro1163Thr	p.P1163T	ENST00000409792	NM_014159.6	1163	Cct/Act	3/21	1	2	FACETS	0.987	0.887	1	0.987	0.887	1	CLONAL	1	TRUE	1	0.410900055263663	2		454	513	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164268	47164268	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	86	428	0	ENST00000409792.3:c.1858C>T	p.Arg620Ter	p.R620*	ENST00000409792	NM_014159.6	620	Cga/Tga	3/21	1	2	FACETS	0.916	0.814	1	0.916	0.814	1	CLONAL	1	TRUE	1	0.410900055263663	2		428	457	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164832	47164832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1017636782	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	102	510	0	ENST00000409792.3:c.1294C>T	p.Arg432Cys	p.R432C	ENST00000409792	NM_014159.6	432	Cgt/Tgt	3/21	1	2	FACETS	0.898	0.805	0.995	0.898	0.805	0.995	CLONAL	1	TRUE	1	0.410900055263663	2		510	553	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164910	47164910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	98	469	0	ENST00000409792.3:c.1216C>T	p.His406Tyr	p.H406Y	ENST00000409792	NM_014159.6	406	Cac/Tac	3/21	1	2	FACETS	0.943	0.844	1	0.943	0.844	1	CLONAL	1	TRUE	1	0.410900055263663	2		469	506	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940163	49940163	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747692134	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	142	659	0	ENST00000296474.3:c.880C>T	p.Arg294Trp	p.R294W	ENST00000296474	NM_002447.2	294	Cgg/Tgg	1/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.410900055263663	2		659	647	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268332	142268332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	54	346	0	ENST00000350721.4:c.3160C>T	p.His1054Tyr	p.H1054Y	ENST00000350721	NM_001184.3	1054	Cat/Tat	15/47	1	2	FACETS	0.909	0.783	1	0.909	0.783	1	CLONAL	1	TRUE	1	0.410900055263663	2		346	289	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274730	142274730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	85	352	0	ENST00000350721.4:c.2330C>T	p.Pro777Leu	p.P777L	ENST00000350721	NM_001184.3	777	cCa/cTa	10/47	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.410900055263663	2		352	347	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281333	142281333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764261046	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	95	481	0	ENST00000350721.4:c.911C>T	p.Pro304Leu	p.P304L	ENST00000350721	NM_001184.3	304	cCc/cTc	4/47	1	2	FACETS	0.871	0.778	0.969	0.871	0.778	0.969	CLONAL	1	TRUE	1	0.410900055263663	2		481	531	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612217	189612217	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	93	513	0	ENST00000264731.3:c.1969G>T	p.Glu657Ter	p.E657*	ENST00000264731	NM_003722.4	657	Gag/Tag	14/14	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.410900055263663	2		513	451	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958873	55958873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	85	326	0	ENST00000263923.4:c.2980G>A	p.Asp994Asn	p.D994N	ENST00000263923	NM_002253.2	994	Gat/Aat	22/30	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.410900055263663	2		326	348	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961752	55961752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	55	375	0	ENST00000263923.4:c.2809C>T	p.Pro937Ser	p.P937S	ENST00000263923	NM_002253.2	937	Ccc/Tcc	20/30	1	2	FACETS	0.771	0.663	0.889	0.771	0.663	0.889	SUBCLONAL	1	TRUE	1	0.410900055263663	2		375	347	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979602	55979602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	77	434	0	ENST00000263923.4:c.845G>A	p.Gly282Glu	p.G282E	ENST00000263923	NM_002253.2	282	gGg/gAg	7/30	1	2	FACETS	0.854	0.753	0.962	0.854	0.753	0.962	CLONAL	1	TRUE	1	0.410900055263663	2		434	439	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270102	66270102	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	69	423	0	ENST00000273854.3:c.1780C>A	p.Leu594Ile	p.L594I	ENST00000273854	NM_004439.5	594	Ctc/Atc	8/18	1	2	FACETS	0.779	0.681	0.884	0.779	0.681	0.884	SUBCLONAL	1	TRUE	1	0.410900055263663	2		423	431	SUCCESS
ALB	213	MSKCC	GRCh37	4	74277741	74277741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1259433502	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	87	454	0	ENST00000295897.4:c.742C>T	p.Pro248Ser	p.P248S	ENST00000295897	NM_000477.5	248	Ccc/Tcc	7/15	1	2	FACETS	0.88	0.782	0.984	0.88	0.782	0.984	CLONAL	1	TRUE	1	0.410900055263663	2		454	481	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094807	143094807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	60	381	0	ENST00000262992.4:c.1337C>T	p.Ser446Phe	p.S446F	ENST00000262992	NM_001101669.1	446	tCt/tTt	14/24	1	2	FACETS	0.859	0.744	0.982	0.859	0.744	0.982	CLONAL	1	TRUE	1	0.410900055263663	2		381	340	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268084	153268084	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	92	395	0	ENST00000281708.4:c.724C>T	p.Gln242Ter	p.Q242*	ENST00000281708	NM_033632.3	242	Cag/Tag	4/12	1	2	FACETS	0.951	0.849	1	0.951	0.849	1	CLONAL	1	TRUE	1	0.410900055263663	2		395	471	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233750	233750	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs746165168	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	87	294	0	ENST00000264932.6:c.1054C>T	p.Arg352Ter	p.R352*	ENST00000264932	NM_004168.2	352	Cga/Tga	8/15	1	2	FACETS	0.784	0.704	0.868	1	0.982	1	SUBCLONAL	2	TRUE	1	0.410900055263663	2		294	270	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264594	1264594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387907251	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	83	626	2	ENST00000310581.5:c.2768C>T	p.Pro923Leu	p.P923L	ENST00000310581	NM_198253.2	923	cCg/cTg	11/16	1	2	FACETS	0.771	0.682	0.866	0.771	0.682	0.866	SUBCLONAL	1	TRUE	1	0.410900055263663	2		628	524	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295200	1295200	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	54	453	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.775	0.666	0.894	0.775	0.666	0.894	SUBCLONAL	1	TRUE	1	0.410900055263663	2		453	339	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295204	1295204	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs2735943	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	64	435	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.977	0.852	1	0.977	0.852	1	CLONAL	1	TRUE	1	0.410900055263663	2		435	319	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468103	31468104	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	84	496	1	ENST00000344624.3:c.2308_2309delinsTT	p.Pro770Leu	p.P770L	ENST00000344624		770	CCg/TTg	15/33	1	2	FACETS	0.859	0.761	0.963	0.859	0.761	0.963	CLONAL	1	TRUE	1	0.410900055263663	2		497	476	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515136	31515136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	96	501	0	ENST00000344624.3:c.1249C>T	p.His417Tyr	p.H417Y	ENST00000344624		417	Cat/Tat	5/33	1	2	FACETS	0.9	0.805	1	0.9	0.805	1	CLONAL	1	TRUE	1	0.410900055263663	2		501	519	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526697	31526697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs989590447	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	104	504	0	ENST00000344624.3:c.343C>T	p.Pro115Ser	p.P115S	ENST00000344624		115	Cct/Tct	2/33	1	2	FACETS	0.972	0.873	1	0.972	0.873	1	CLONAL	1	TRUE	1	0.410900055263663	2		504	521	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871297	35871297	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	78	380	0	ENST00000303115.3:c.519G>T	p.Lys173Asn	p.K173N	ENST00000303115	NM_002185.3	173	aaG/aaT	4/8	1	2	FACETS	0.877	0.774	0.986	0.877	0.774	0.986	CLONAL	1	TRUE	1	0.410900055263663	2		380	433	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876455	35876455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1419531227	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	96	574	0	ENST00000303115.3:c.1247C>T	p.Pro416Leu	p.P416L	ENST00000303115	NM_002185.3	416	cCc/cTc	8/8	1	2	FACETS	0.779	0.695	0.868	0.779	0.695	0.868	SUBCLONAL	1	TRUE	1	0.410900055263663	2		574	600	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876472	35876472	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	89	568	0	ENST00000303115.3:c.1264C>T	p.Gln422Ter	p.Q422*	ENST00000303115	NM_002185.3	422	Caa/Taa	8/8	1	2	FACETS	0.741	0.658	0.829	0.741	0.658	0.829	SUBCLONAL	1	TRUE	1	0.410900055263663	2		568	585	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755645	57755645	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	123	600	0	ENST00000274289.3:c.142C>T	p.Gln48Ter	p.Q48*	ENST00000274289	NM_006622.3	48	Cag/Tag	1/14	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.410900055263663	2		600	531	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149450111	149450111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	89	506	0	ENST00000286301.3:c.1106C>A	p.Pro369His	p.P369H	ENST00000286301	NM_005211.3	369	cCc/cAc	8/22	1	2	FACETS	0.831	0.739	0.929	0.831	0.739	0.929	CLONAL	1	TRUE	1	0.410900055263663	2		506	521	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495406	149495406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554107047	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	105	694	0	ENST00000261799.4:c.3241G>A	p.Glu1081Lys	p.E1081K	ENST00000261799	NM_002609.3	1081	Gag/Aag	23/23	NA	2	FACETS	0.892	0.801	0.987			1	INDETERMINATE	1	TRUE	NA	0.410900055263663	2		694	573	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497362	149497362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	82	442	0	ENST00000261799.4:c.2956C>T	p.Leu986Phe	p.L986F	ENST00000261799	NM_002609.3	986	Ctt/Ttt	22/23	NA	2	FACETS	0.922	0.817	1			1	INDETERMINATE	1	TRUE	NA	0.410900055263663	2		442	433	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504376	149504376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	64	457	0	ENST00000261799.4:c.1826G>A	p.Gly609Glu	p.G609E	ENST00000261799	NM_002609.3	609	gGg/gAg	13/23	NA	2	FACETS	0.797	0.693	0.908			1	INDETERMINATE	1	TRUE	NA	0.410900055263663	2		457	391	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517948	176517948	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	151	627	0	ENST00000292408.4:c.446G>A	p.Trp149Ter	p.W149*	ENST00000292408	NM_213647.1	149	tGg/tAg	5/18	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.410900055263663	2		627	634	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721985	176721986	+	missense_variant	Missense_Mutation	DNP	TT	TT	CA	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	93	615	0	ENST00000439151.2:c.7616_7617delinsCA	p.Leu2539Pro	p.L2539P	ENST00000439151	NM_022455.4	2539	cTT/cCA	23/23	1	2	FACETS	0.714	0.635	0.797	0.714	0.635	0.797	SUBCLONAL	1	TRUE	1	0.410900055263663	2		615	634	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047194	180047194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	98	526	0	ENST00000261937.6:c.2521C>T	p.Pro841Ser	p.P841S	ENST00000261937	NM_182925.4	841	Ccc/Tcc	17/30	1	2	FACETS	0.986	0.883	1	0.986	0.883	1	CLONAL	1	TRUE	1	0.410900055263663	2		526	484	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047693	180047693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	107	684	0	ENST00000261937.6:c.2322G>A	p.Met774Ile	p.M774I	ENST00000261937	NM_182925.4	774	atG/atA	16/30	1	2	FACETS	0.889	0.799	0.983	0.889	0.799	0.983	CLONAL	1	TRUE	1	0.410900055263663	2		684	586	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166764	32166764	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771787319	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	112	541	0	ENST00000375023.3:c.4474C>T	p.Arg1492Trp	p.R1492W	ENST00000375023	NM_004557.3	1492	Cgg/Tgg	24/30	1	2	FACETS	0.901	0.812	0.994	0.901	0.812	0.994	CLONAL	1	TRUE	1	0.410900055263663	2		541	605	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169002	32169002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	119	601	0	ENST00000375023.3:c.4031G>A	p.Gly1344Glu	p.G1344E	ENST00000375023	NM_004557.3	1344	gGg/gAg	22/30	1	2	FACETS	0.994	0.9	1	0.994	0.9	1	CLONAL	1	TRUE	1	0.410900055263663	2		601	583	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965572	93965572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	84	402	0	ENST00000369303.4:c.2356G>A	p.Asp786Asn	p.D786N	ENST00000369303	NM_004440.3	786	Gat/Aat	13/17	1	2	FACETS	0.864	0.766	0.969	0.864	0.766	0.969	CLONAL	1	TRUE	1	0.410900055263663	2		402	473	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967841	93967841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	102	391	0	ENST00000369303.4:c.2086C>T	p.His696Tyr	p.H696Y	ENST00000369303	NM_004440.3	696	Cat/Tat	11/17	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.410900055263663	2		391	496	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979257	93979257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	62	473	0	ENST00000369303.4:c.1571G>A	p.Gly524Glu	p.G524E	ENST00000369303	NM_004440.3	524	gGa/gAa	7/17	1	2	FACETS	0.747	0.648	0.854	0.747	0.648	0.854	SUBCLONAL	1	TRUE	1	0.410900055263663	2		473	404	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120257	94120257	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	116	532	0	ENST00000369303.4:c.794G>T	p.Cys265Phe	p.C265F	ENST00000369303	NM_004440.3	265	tGc/tTc	3/17	1	2	FACETS	0.848	0.765	0.935	0.848	0.765	0.935	CLONAL	1	TRUE	1	0.410900055263663	2		532	666	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120290	94120290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	141	548	0	ENST00000369303.4:c.761G>A	p.Gly254Glu	p.G254E	ENST00000369303	NM_004440.3	254	gGa/gAa	3/17	1	2	FACETS	0.982	0.896	1	0.982	0.896	1	CLONAL	1	TRUE	1	0.410900055263663	2		548	699	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622298	117622298	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	64	384	0	ENST00000368508.3:c.6572G>A	p.Trp2191Ter	p.W2191*	ENST00000368508	NM_002944.2	2191	tGg/tAg	42/43	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.410900055263663	2		384	311	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647515	117647515	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1256569613	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	111	554	0	ENST00000368508.3:c.5429C>T	p.Ser1810Phe	p.S1810F	ENST00000368508	NM_002944.2	1810	tCc/tTc	33/43	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.410900055263663	2		554	494	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678067	117678067	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs369009006	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	65	358	0	ENST00000368508.3:c.3866G>A	p.Trp1289Ter	p.W1289*	ENST00000368508	NM_002944.2	1289	tGg/tAg	25/43	1	2	FACETS	0.998	0.872	1	0.998	0.872	1	CLONAL	1	TRUE	1	0.410900055263663	2		358	317	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683824	117683824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754292558	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	66	447	0	ENST00000368508.3:c.3323C>T	p.Pro1108Leu	p.P1108L	ENST00000368508	NM_002944.2	1108	cCc/cTc	21/43	1	2	FACETS	0.747	0.651	0.851	0.747	0.651	0.851	SUBCLONAL	1	TRUE	1	0.410900055263663	2		447	430	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686270	117686270	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	70	463	0	ENST00000368508.3:c.3071G>A	p.Trp1024Ter	p.W1024*	ENST00000368508	NM_002944.2	1024	tGg/tAg	20/43	1	2	FACETS	0.8	0.7	0.907	0.8	0.7	0.907	CLONAL	1	TRUE	1	0.410900055263663	2		463	426	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708124	117708124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758924871	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	48	396	0	ENST00000368508.3:c.2053G>A	p.Gly685Arg	p.G685R	ENST00000368508	NM_002944.2	685	Ggg/Agg	14/43	1	2	FACETS	0.66	0.56	0.769	0.66	0.56	0.769	SUBCLONAL	1	TRUE	1	0.410900055263663	2		396	354	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710750	117710750	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	123	519	0	ENST00000368508.3:c.1522G>T	p.Asp508Tyr	p.D508Y	ENST00000368508	NM_002944.2	508	Gac/Tac	12/43	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.410900055263663	2		519	565	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519172	137519172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	72	436	0	ENST00000367739.4:c.1466C>T	p.Ser489Leu	p.S489L	ENST00000367739	NM_000416.2	489	tCa/tTa	7/7	1	2	FACETS	0.853	0.748	0.964	0.853	0.748	0.964	CLONAL	1	TRUE	1	0.410900055263663	2		436	411	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963907	2963907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	98	591	0	ENST00000396946.4:c.1900G>A	p.Glu634Lys	p.E634K	ENST00000396946	NM_032415.4	634	Gag/Aag	15/25	1	2	FACETS	0.919	0.823	1	0.919	0.823	1	CLONAL	1	TRUE	1	0.410900055263663	2		591	519	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979530	2979530	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868565027	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	80	460	1	ENST00000396946.4:c.717G>A	p.Met239Ile	p.M239I	ENST00000396946	NM_032415.4	239	atG/atA	6/25	1	2	FACETS	0.895	0.792	1	0.895	0.792	1	CLONAL	1	TRUE	1	0.410900055263663	2		461	435	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2998136	2998136	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	99	462	0	ENST00000396946.4:c.5C>T	p.Pro2Leu	p.P2L	ENST00000396946	NM_032415.4	2	cCa/cTa	2/25	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.410900055263663	2		462	419	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026966	6026966	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	30	147	0	ENST00000265849.7:c.1430C>T	p.Ser477Phe	p.S477F	ENST00000265849	NM_000535.5	477	tCc/tTc	11/15	0.10602690348929	4	FACETS	1	0.921	1	0.636	0.518	0.766	INDETERMINATE	1	TRUE	2	0.410900055263663	4		147	162	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729931	41729931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1379000367	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	103	552	0	ENST00000242208.4:c.598G>A	p.Glu200Lys	p.E200K	ENST00000242208	NM_002192.2	200	Gag/Aag	3/3	1	2	FACETS	0.92	0.826	1	0.92	0.826	1	CLONAL	1	TRUE	1	0.410900055263663	2		552	545	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355212	81355212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	85	405	0	ENST00000222390.5:c.1162G>A	p.Gly388Arg	p.G388R	ENST00000222390	NM_000601.4	388	Gga/Aga	9/18	1	2	FACETS	0.862	0.765	0.965	0.862	0.765	0.965	CLONAL	1	TRUE	1	0.410900055263663	2		405	480	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392036	81392036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	55	367	0	ENST00000222390.5:c.241C>T	p.Pro81Ser	p.P81S	ENST00000222390	NM_000601.4	81	Cca/Tca	2/18	1	2	FACETS	0.816	0.702	0.939	0.816	0.702	0.939	CLONAL	1	TRUE	1	0.410900055263663	2		367	328	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509637	106509637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766453335	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	101	574	0	ENST00000359195.3:c.1631G>A	p.Arg544Gln	p.R544Q	ENST00000359195	NM_002649.2	544	cGa/cAa	2/11	1	2	FACETS	0.883	0.791	0.979	0.883	0.791	0.979	CLONAL	1	TRUE	1	0.410900055263663	2		574	557	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526735	106526735	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	81	372	0	ENST00000359195.3:c.3028C>T	p.Gln1010Ter	p.Q1010*	ENST00000359195	NM_002649.2	1010	Cag/Tag	10/11	1	2	FACETS	0.971	0.86	1	0.971	0.86	1	CLONAL	1	TRUE	1	0.410900055263663	2		372	406	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845188	128845188	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs776727010	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	100	626	0	ENST00000249373.3:c.682C>T	p.Gln228Ter	p.Q228*	ENST00000249373	NM_005631.4	228	Cag/Tag	3/12	1	2	FACETS	0.954	0.856	1	0.954	0.856	1	CLONAL	1	TRUE	1	0.410900055263663	2		626	510	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524329	148524329	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	80	397	0	ENST00000320356.2:c.655C>T	p.Pro219Ser	p.P219S	ENST00000320356	NM_004456.4	219	Cct/Tct	7/20	1	2	FACETS	0.941	0.832	1	0.941	0.832	1	CLONAL	1	TRUE	1	0.410900055263663	2		397	414	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860476	151860476	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	117	526	0	ENST00000262189.6:c.10186C>T	p.Gln3396Ter	p.Q3396*	ENST00000262189	NM_170606.2	3396	Caa/Taa	43/59	1	2	FACETS	0.962	0.87	1	0.962	0.87	1	CLONAL	1	TRUE	1	0.410900055263663	2		526	592	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968135	68968135	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	66	399	0	ENST00000288368.4:c.1164G>A	p.Met388Ile	p.M388I	ENST00000288368	NM_024870.2	388	atG/atA	10/40	1	2	FACETS	0.809	0.705	0.92	0.809	0.705	0.92	CLONAL	1	TRUE	1	0.410900055263663	2		399	397	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028113	69028113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	82	475	0	ENST00000288368.4:c.3272G>A	p.Gly1091Glu	p.G1091E	ENST00000288368	NM_024870.2	1091	gGa/gAa	26/40	1	2	FACETS	0.864	0.765	0.969	0.864	0.765	0.969	CLONAL	1	TRUE	1	0.410900055263663	2		475	462	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033228	69033228	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	101	450	0	ENST00000288368.4:c.3668G>A	p.Trp1223Ter	p.W1223*	ENST00000288368	NM_024870.2	1223	tGg/tAg	30/40	1	2	FACETS	0.945	0.848	1	0.945	0.848	1	CLONAL	1	TRUE	1	0.410900055263663	2		450	520	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050711	69050711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	57	399	0	ENST00000288368.4:c.4046C>T	p.Ser1349Phe	p.S1349F	ENST00000288368	NM_024870.2	1349	tCc/tTc	33/40	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.410900055263663	2		399	275	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970886	70970886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	90	451	0	ENST00000276594.2:c.1375C>T	p.Arg459Trp	p.R459W	ENST00000276594	NM_024504.3	459	Cgg/Tgg	6/8	1	2	FACETS	0.905	0.806	1	0.905	0.806	1	CLONAL	1	TRUE	1	0.410900055263663	2		451	484	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566300	141566300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	100	541	0	ENST00000220592.5:c.1112C>T	p.Ser371Leu	p.S371L	ENST00000220592	NM_012154.3	371	tCg/tTg	9/19	1	2	FACETS	0.841	0.753	0.934	0.841	0.753	0.934	CLONAL	1	TRUE	1	0.410900055263663	2		541	579	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331706	8331706	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	142	478	0	ENST00000356435.5:c.5410C>T	p.Gln1804Ter	p.Q1804*	ENST00000356435		1804	Cag/Tag	33/35	0.339690475508096	2	FACETS	0.847	0.78	0.916	0.847	0.78	0.916	CLONAL	2	TRUE	0	0.410900055263663	2		478	408	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341914	8341914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	123	490	0	ENST00000356435.5:c.4726G>A	p.Glu1576Lys	p.E1576K	ENST00000356435		1576	Gaa/Aaa	29/35	0.339690475508096	2	FACETS	0.8	0.731	0.871	0.8	0.731	0.871	SUBCLONAL	2	TRUE	0	0.410900055263663	2		490	374	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449788	8449788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1267613597	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	136	427	0	ENST00000356435.5:c.3925G>A	p.Glu1309Lys	p.E1309K	ENST00000356435		1309	Gag/Aag	23/35	0.339690475508096	2	FACETS	0.811	0.745	0.879	0.811	0.745	0.879	CLONAL	2	TRUE	0	0.410900055263663	2		427	408	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8497265	8497265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1270795879	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	84	310	0	ENST00000356435.5:c.2326G>A	p.Glu776Lys	p.E776K	ENST00000356435		776	Gaa/Aaa	15/35	0.339690475508096	2	FACETS	0.877	0.788	0.969	0.877	0.788	0.969	CLONAL	2	TRUE	0	0.410900055263663	2		310	233	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636812	8636812	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	129	531	0	ENST00000356435.5:c.97C>T	p.Gln33Ter	p.Q33*	ENST00000356435		33	Cag/Tag	2/35	0.339690475508096	2	FACETS	1	0.986	1	0.714	0.652	0.777	CLONAL	1	TRUE	0	0.410900055263663	2		531	440	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412494	80412494	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	136	497	0	ENST00000286548.4:c.547C>T	p.Arg183Ter	p.R183*	ENST00000286548	NM_002072.3	183	Cga/Tga	4/7	0.170854027904377	3	FACETS	1	0.983	1	0.658	0.601	0.719	INDETERMINATE	1	TRUE	1	0.410900055263663	3		497	606	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342784	87342784	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	91	529	0	ENST00000277120.3:c.1069G>A	p.Gly357Arg	p.G357R	ENST00000277120		357	Ggg/Agg	9/19	0.170854027904377	3	FACETS	1	0.942	1	0.544	0.484	0.606	INDETERMINATE	1	TRUE	1	0.410900055263663	3		529	491	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624541	93624541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	111	535	1	ENST00000375746.1:c.632G>A	p.Gly211Glu	p.G211E	ENST00000375746	NM_001174167.1	211	gGg/gAg	4/14	0.170854027904377	3	FACETS	1	0.937	1	0.527	0.475	0.582	INDETERMINATE	1	TRUE	1	0.410900055263663	3		536	618	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624594	93624594	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	94	538	0	ENST00000375746.1:c.685C>A	p.Pro229Thr	p.P229T	ENST00000375746	NM_001174167.1	229	Ccc/Acc	4/14	0.170854027904377	3	FACETS	0.94	0.838	1	0.47	0.419	0.524	INDETERMINATE	1	TRUE	1	0.410900055263663	3		538	587	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797304	135797304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	140	550	0	ENST00000298552.3:c.565C>T	p.His189Tyr	p.H189Y	ENST00000298552	NM_001162426.1	189	Cat/Tat	7/23	0.170854027904377	3	FACETS	1	0.987	1	0.73	0.667	0.794	INDETERMINATE	1	TRUE	1	0.410900055263663	3		550	563	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396735	139396736	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	79	545	0	ENST00000277541.6:c.5372_5373delinsTT	p.Ser1791Phe	p.S1791F	ENST00000277541	NM_017617.3	1791	tCC/tTT	28/34	0.170854027904377	3	FACETS	1	0.914	1	0.521	0.46	0.586	INDETERMINATE	1	TRUE	1	0.410900055263663	3		545	445	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945112	44945112	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	58	411	0	ENST00000377967.4:c.3436C>T	p.His1146Tyr	p.H1146Y	ENST00000377967	NM_021140.2	1146	Cat/Tat	24/29	1	2	FACETS	0.885	0.765	1	0.885	0.765	1	CLONAL	1	TRUE	1	0.410900055263663	2		411	319	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430329	47430329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	105	594	0	ENST00000377045.4:c.1604C>T	p.Ser535Phe	p.S535F	ENST00000377045	NM_001654.4	535	tCc/tTc	15/16	1	2	FACETS	0.953	0.857	1	0.953	0.857	1	CLONAL	1	TRUE	1	0.410900055263663	2		594	536	SUCCESS
AR	367	MSKCC	GRCh37	X	66766427	66766427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	52	359	0	ENST00000374690.3:c.1439C>T	p.Pro480Leu	p.P480L	ENST00000374690	NM_000044.3	480	cCc/cTc	1/8	1	2	FACETS	0.873	0.748	1	0.873	0.748	1	CLONAL	1	TRUE	1	0.410900055263663	2		359	290	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339223	70339223	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	61	361	0	ENST00000374080.3:c.100G>T	p.Asp34Tyr	p.D34Y	ENST00000374080		34	Gat/Tat	2/45	1	2	FACETS	0.722	0.625	0.827	0.722	0.625	0.827	SUBCLONAL	1	TRUE	1	0.410900055263663	2		361	411	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349181	70349181	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	93	567	0	ENST00000374080.3:c.3593G>A	p.Gly1198Glu	p.G1198E	ENST00000374080		1198	gGa/gAa	26/45	1	2	FACETS	0.803	0.715	0.895	0.803	0.715	0.895	CLONAL	1	TRUE	1	0.410900055263663	2		567	564	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356239	70356239	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763233945	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	91	521	0	ENST00000374080.3:c.5134C>T	p.Arg1712Trp	p.R1712W	ENST00000374080		1712	Cgg/Tgg	37/45	1	2	FACETS	0.953	0.85	1	0.953	0.85	1	CLONAL	1	TRUE	1	0.410900055263663	2		521	465	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626628	100626628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	98	383	0	ENST00000308731.7:c.302C>T	p.Pro101Leu	p.P101L	ENST00000308731	NM_000061.2	101	cCc/cTc	4/19	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.410900055263663	2		383	417	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020236	123020236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	73	540	0	ENST00000355640.3:c.724G>A	p.Asp242Asn	p.D242N	ENST00000355640		242	Gat/Aat	2/7	1	2	FACETS	0.691	0.606	0.783	0.691	0.606	0.783	SUBCLONAL	1	TRUE	1	0.410900055263663	2		540	514	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210244	123210244	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	66	451	0	ENST00000218089.9:c.2596G>T	p.Ala866Ser	p.A866S	ENST00000218089	NM_001042749.1	866	Gca/Tca	26/35	1	2	FACETS	0.767	0.668	0.873	0.767	0.668	0.873	SUBCLONAL	1	TRUE	1	0.410900055263663	2		451	419	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961074	55961074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	56	440	0	ENST00000263923.4:c.2866C>T	p.Pro956Ser	p.P956S	ENST00000263923	NM_002253.2	956	Cct/Tct	21/30	1	2	FACETS	0.704	0.606	0.811	0.704	0.606	0.811	SUBCLONAL	1	TRUE	1	0.410900055263663	2		440	387	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243968	46243968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	98	519	0	ENST00000334344.6:c.2062C>T	p.Pro688Ser	p.P688S	ENST00000334344	NM_152641.2	688	Cct/Tct	15/21	1	2	FACETS	0.887	0.793	0.985	0.887	0.793	0.985	CLONAL	1	TRUE	1	0.410900055263663	2		519	538	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074345	8074345	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773932474	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	112	472	0	ENST00000377482.5:c.314C>T	p.Pro105Leu	p.P105L	ENST00000377482	NM_018948.3	105	cCa/cTa	4/4	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.410900055263663	2		472	539	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11308049	11308049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	105	512	0	ENST00000361445.4:c.943C>T	p.Pro315Ser	p.P315S	ENST00000361445	NM_004958.3	315	Ccc/Tcc	7/58	1	2	FACETS	0.938	0.843	1	0.938	0.843	1	CLONAL	1	TRUE	1	0.410900055263663	2		512	545	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255224	16255225	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	108	506	0	ENST00000375759.3:c.2489_2490delinsTT	p.Ser830Phe	p.S830F	ENST00000375759	NM_015001.2	830	tCC/tTT	11/15	1	2	FACETS	0.9	0.81	0.995	0.9	0.81	0.995	CLONAL	1	TRUE	1	0.410900055263663	2		506	584	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22413199	22413199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	49	250	0	ENST00000344548.3:c.326C>T	p.Pro109Leu	p.P109L	ENST00000344548	NM_001039802.1	109	cCt/cTt	6/7	1	2	FACETS	0.893	0.762	1	0.893	0.762	1	CLONAL	1	TRUE	1	0.410900055263663	2		250	267	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057941	27057941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	123	548	0	ENST00000324856.7:c.1649C>T	p.Pro550Leu	p.P550L	ENST00000324856	NM_006015.4	550	cCc/cTc	3/20	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.410900055263663	2		548	595	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28595715	28595715	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367784435	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	123	530	0	ENST00000253063.3:c.112C>T	p.Arg38Trp	p.R38W	ENST00000253063	NM_031459.4	38	Cgg/Tgg	2/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.410900055263663	2		530	565	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322640	39322640	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	85	514	0	ENST00000373001.3:c.352C>A	p.Pro118Thr	p.P118T	ENST00000373001	NM_022157.3	118	Cct/Act	2/7	1	2	FACETS	0.834	0.74	0.935	0.834	0.74	0.935	CLONAL	1	TRUE	1	0.410900055263663	2		514	496	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363394	40363394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	119	582	0	ENST00000397332.2:c.835G>A	p.Glu279Lys	p.E279K	ENST00000397332	NM_001033082.2	279	Gag/Aag	3/3	1	2	FACETS	0.969	0.877	1	0.969	0.877	1	CLONAL	1	TRUE	1	0.410900055263663	2		582	598	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344817	65344817	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	97	496	0	ENST00000342505.4:c.220T>A	p.Cys74Ser	p.C74S	ENST00000342505	NM_002227.2	74	Tgt/Agt	4/25	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.410900055263663	2		496	470	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458519	120458519	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	115	657	0	ENST00000256646.2:c.6826G>T	p.Glu2276Ter	p.E2276*	ENST00000256646	NM_024408.3	2276	Gag/Tag	34/34	1	2	FACETS	0.891	0.805	0.982	0.891	0.805	0.982	CLONAL	1	TRUE	1	0.410900055263663	2		657	628	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120478109	120478109	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	109	490	0	ENST00000256646.2:c.3641C>T	p.Pro1214Leu	p.P1214L	ENST00000256646	NM_024408.3	1214	cCa/cTa	22/34	1	2	FACETS	0.91	0.819	1	0.91	0.819	1	CLONAL	1	TRUE	1	0.410900055263663	2		490	583	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518800	204518800	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	82	465	0	ENST00000367182.3:c.1463T>A	p.Phe488Tyr	p.F488Y	ENST00000367182	NM_001278516.1	488	tTt/tAt	11/11	1	2	FACETS	0.851	0.753	0.955	0.851	0.753	0.955	CLONAL	1	TRUE	1	0.410900055263663	2		465	469	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647726	206647726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781921697	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	96	536	0	ENST00000367120.3:c.140G>A	p.Arg47Gln	p.R47Q	ENST00000367120	NM_014002.3	47	cGg/cAg	4/22	1	2	FACETS	0.916	0.819	1	0.916	0.819	1	CLONAL	1	TRUE	1	0.410900055263663	2		536	510	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666673	206666674	+	missense_variant	Missense_Mutation	DNP	TC	TC	CA	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	82	561	0	ENST00000367120.3:c.2007_2008delinsCA	p.Pro670Thr	p.P670T	ENST00000367120	NM_014002.3	669	gcTCct/gcCAct	20/22	1	2	FACETS	0.73	0.645	0.82	0.73	0.645	0.82	SUBCLONAL	1	TRUE	1	0.410900055263663	2		561	547	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612943	228612943	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	175	779	0	ENST00000366696.1:c.84G>T	p.Lys28Asn	p.K28N	ENST00000366696	NM_003493.2	28	aaG/aaT	1/1	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.410900055263663	2		779	763	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230468703	230468703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	110	642	0	ENST00000391860.1:c.815C>T	p.Pro272Leu	p.P272L	ENST00000391860	NM_001258311.1	272	cCc/cTc	5/7	1	2	FACETS	0.875	0.788	0.967	0.875	0.788	0.967	CLONAL	1	TRUE	1	0.410900055263663	2		642	612	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845517	63845517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	110	487	0	ENST00000279873.7:c.1256C>T	p.Pro419Leu	p.P419L	ENST00000279873	NM_032199.2	419	cCa/cTa	9/10	1	2	FACETS	0.958	0.863	1	0.958	0.863	1	CLONAL	1	TRUE	1	0.410900055263663	2		487	559	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333050	70333050	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	108	499	0	ENST00000373644.4:c.955G>A	p.Gly319Arg	p.G319R	ENST00000373644	NM_030625.2	319	Ggg/Agg	2/12	1	2	FACETS	0.979	0.882	1	0.979	0.882	1	CLONAL	1	TRUE	1	0.410900055263663	2		499	537	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446176	70446176	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	88	432	0	ENST00000373644.4:c.5116C>T	p.His1706Tyr	p.H1706Y	ENST00000373644	NM_030625.2	1706	Cat/Tat	11/12	1	2	FACETS	0.862	0.766	0.963	0.862	0.766	0.963	CLONAL	1	TRUE	1	0.410900055263663	2		432	497	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451095	70451095	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	104	574	0	ENST00000373644.4:c.5935C>T	p.Pro1979Ser	p.P1979S	ENST00000373644	NM_030625.2	1979	Ccc/Tcc	12/12	1	2	FACETS	0.944	0.849	1	0.944	0.849	1	CLONAL	1	TRUE	1	0.410900055263663	2		574	536	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003350	57003350	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	122	623	0	ENST00000257254.3:c.1129C>T	p.Leu377Phe	p.L377F	ENST00000257254		377	Ctt/Ttt	1/2	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.410900055263663	2		623	574	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003561	57003562	+	missense_variant,NMD_transcript_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	122	650	0	ENST00000257254.3:c.917_918delinsTT	p.Pro306Leu	p.P306L	ENST00000257254		306	cCC/cTT	1/2	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.410900055263663	2		650	564	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57004100	57004100	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	G	G	A	rs762740856	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	112	658	0	ENST00000257254.3:c.379C>T	p.Arg127Cys	p.R127C	ENST00000257254		127	Cgc/Tgc	1/2	1	2	FACETS	0.989	0.893	1	0.989	0.893	1	CLONAL	1	TRUE	1	0.410900055263663	2		658	551	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57004402	57004402	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	94	551	0	ENST00000257254.3:c.77C>T	p.Ser26Phe	p.S26F	ENST00000257254		26	tCc/tTc	1/2	1	2	FACETS	0.976	0.872	1	0.976	0.872	1	CLONAL	1	TRUE	1	0.410900055263663	2		551	469	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57004472	57004472	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	86	497	0	ENST00000257254.3:c.7G>A	p.Glu3Lys	p.E3K	ENST00000257254		3	Gaa/Aaa	1/2	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.410900055263663	2		497	414	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138945	64138945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	52	266	0	ENST00000334205.4:c.2312C>T	p.Pro771Leu	p.P771L	ENST00000334205	NM_003942.2	771	cCc/cTc	17/17	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.410900055263663	2		266	222	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939795	71939796	+	missense_variant	Missense_Mutation	DNP	TG	TG	AT	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	106	697	1	ENST00000298229.2:c.422_423delinsAT	p.Leu141His	p.L141H	ENST00000298229	NM_001567.3	141	cTG/cAT	4/28	1	2	FACETS	0.827	0.743	0.916	0.827	0.743	0.916	CLONAL	1	TRUE	1	0.410900055263663	2		698	624	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941014	71941014	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202155977	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	158	719	0	ENST00000298229.2:c.890C>T	p.Pro297Leu	p.P297L	ENST00000298229	NM_001567.3	297	cCg/cTg	8/28	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.410900055263663	2		719	663	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912798	100912798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	62	399	0	ENST00000325455.5:c.2524G>A	p.Glu842Lys	p.E842K	ENST00000325455	NM_001202474.3	842	Gag/Aag	7/8	1	2	FACETS	0.843	0.732	0.962	0.843	0.732	0.962	CLONAL	1	TRUE	1	0.410900055263663	2		399	358	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996834	100996834	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	102	457	0	ENST00000325455.5:c.1693A>T	p.Lys565Ter	p.K565*	ENST00000325455	NM_001202474.3	565	Aag/Tag	2/8	1	2	FACETS	0.985	0.885	1	0.985	0.885	1	CLONAL	1	TRUE	1	0.410900055263663	2		457	504	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998899	100998899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	90	634	0	ENST00000325455.5:c.903G>A	p.Met301Ile	p.M301I	ENST00000325455	NM_001202474.3	301	atG/atA	1/8	1	2	FACETS	0.89	0.793	0.994	0.89	0.793	0.994	CLONAL	1	TRUE	1	0.410900055263663	2		634	492	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102080285	102080285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	60	385	0	ENST00000282441.5:c.1022C>T	p.Pro341Leu	p.P341L	ENST00000282441	NM_001130145.2	341	cCa/cTa	6/9	1	2	FACETS	0.787	0.681	0.901	0.787	0.681	0.901	CLONAL	1	TRUE	1	0.410900055263663	2		385	371	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102094411	102094411	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	93	455	0	ENST00000282441.5:c.1091C>T	p.Pro364Leu	p.P364L	ENST00000282441	NM_001130145.2	364	cCa/cTa	7/9	1	2	FACETS	0.937	0.837	1	0.937	0.837	1	CLONAL	1	TRUE	1	0.410900055263663	2		455	483	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206699	102206699	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	89	373	0	ENST00000263464.3:c.1327G>A	p.Asp443Asn	p.D443N	ENST00000263464	NM_001165.4	443	Gat/Aat	7/9	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.410900055263663	2		373	405	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111959671	111959671	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	55	244	0	ENST00000375549.3:c.250T>A	p.Tyr84Asn	p.Y84N	ENST00000375549	NM_003002.3	84	Tat/Aat	3/4	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.410900055263663	2		244	264	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343847	118343848	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	112	569	0	ENST00000534358.1:c.1973_1974delinsTT	p.Pro658Leu	p.P658L	ENST00000534358	NM_005933.3	658	cCC/cTT	3/36	1	2	FACETS	0.861	0.776	0.951	0.861	0.776	0.951	CLONAL	1	TRUE	1	0.410900055263663	2		569	633	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363943	118363943	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	76	377	0	ENST00000534358.1:c.5176G>T	p.Val1726Leu	p.V1726L	ENST00000534358	NM_005933.3	1726	Gtg/Ttg	16/36	1	2	FACETS	0.992	0.875	1	0.992	0.875	1	CLONAL	1	TRUE	1	0.410900055263663	2		377	373	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148988	119148988	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	99	498	0	ENST00000264033.4:c.1208C>T	p.Ser403Phe	p.S403F	ENST00000264033	NM_005188.3	403	tCc/tTc	8/16	1	2	FACETS	0.994	0.891	1	0.994	0.891	1	CLONAL	1	TRUE	1	0.410900055263663	2		498	485	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149239	119149239	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	104	497	0	ENST00000264033.4:c.1247G>T	p.Cys416Phe	p.C416F	ENST00000264033	NM_005188.3	416	tGt/tTt	9/16	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.410900055263663	2		497	496	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435541	18435541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	73	475	0	ENST00000266497.5:c.526C>T	p.Pro176Ser	p.P176S	ENST00000266497		176	Cct/Tct	1/31	1	2	FACETS	0.838	0.736	0.947	0.838	0.736	0.947	CLONAL	1	TRUE	1	0.410900055263663	2		475	424	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18439790	18439790	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	51	373	0	ENST00000266497.5:c.688T>G	p.Cys230Gly	p.C230G	ENST00000266497		230	Tgt/Ggt	2/31	1	2	FACETS	0.819	0.701	0.948	0.819	0.701	0.948	CLONAL	1	TRUE	1	0.410900055263663	2		373	303	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552700	18552700	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	105	557	0	ENST00000266497.5:c.2111G>C	p.Arg704Thr	p.R704T	ENST00000266497		704	aGg/aCg	14/31	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.410900055263663	2		557	459	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644479	18644479	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	52	374	0	ENST00000266497.5:c.2657G>T	p.Gly886Val	p.G886V	ENST00000266497		886	gGg/gTg	18/31	1	2	FACETS	0.776	0.664	0.898	0.776	0.664	0.898	SUBCLONAL	1	TRUE	1	0.410900055263663	2		374	326	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18649061	18649061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1262695281	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	57	477	0	ENST00000266497.5:c.2736G>A	p.Met912Ile	p.M912I	ENST00000266497		912	atG/atA	19/31	1	2	FACETS	0.856	0.739	0.982	0.856	0.739	0.982	CLONAL	1	TRUE	1	0.410900055263663	2		477	324	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650625	18650625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	71	488	0	ENST00000266497.5:c.2836G>A	p.Glu946Lys	p.E946K	ENST00000266497		946	Gaa/Aaa	20/31	1	2	FACETS	0.937	0.822	1	0.937	0.822	1	CLONAL	1	TRUE	1	0.410900055263663	2		488	369	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18747479	18747479	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	68	374	0	ENST00000266497.5:c.3940G>T	p.Glu1314Ter	p.E1314*	ENST00000266497		1314	Gaa/Taa	28/31	1	2	FACETS	0.994	0.871	1	0.994	0.871	1	CLONAL	1	TRUE	1	0.410900055263663	2		374	333	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231304	46231304	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	86	417	0	ENST00000334344.6:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000334344	NM_152641.2	382	Tgc/Cgc	10/21	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.410900055263663	2		417	409	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46240672	46240672	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774328835	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	68	435	0	ENST00000334344.6:c.1532C>T	p.Pro511Leu	p.P511L	ENST00000334344	NM_152641.2	511	cCa/cTa	12/21	1	2	FACETS	0.965	0.845	1	0.965	0.845	1	CLONAL	1	TRUE	1	0.410900055263663	2		435	343	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243968	46243969	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	99	518	1	ENST00000334344.6:c.2062_2063delinsTT	p.Pro688Phe	p.P688F	ENST00000334344	NM_152641.2	688	CCt/TTt	15/21	1	2	FACETS	0.896	0.802	0.995	0.896	0.802	0.995	CLONAL	1	TRUE	1	0.410900055263663	2		519	538	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426288	49426288	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	103	664	0	ENST00000301067.7:c.12200C>T	p.Pro4067Leu	p.P4067L	ENST00000301067	NM_003482.3	4067	cCc/cTc	39/54	1	2	FACETS	0.802	0.719	0.89	0.802	0.719	0.89	CLONAL	1	TRUE	1	0.410900055263663	2		664	625	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431231	49431231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	139	769	0	ENST00000301067.7:c.9908C>T	p.Ser3303Phe	p.S3303F	ENST00000301067	NM_003482.3	3303	tCt/tTt	34/54	1	2	FACETS	0.978	0.892	1	0.978	0.892	1	CLONAL	1	TRUE	1	0.410900055263663	2		769	692	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434384	49434384	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	106	577	0	ENST00000301067.7:c.7169C>A	p.Pro2390Gln	p.P2390Q	ENST00000301067	NM_003482.3	2390	cCg/cAg	31/54	1	2	FACETS	0.992	0.893	1	0.992	0.893	1	CLONAL	1	TRUE	1	0.410900055263663	2		577	520	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445926	49445926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1488501817	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	121	630	0	ENST00000301067.7:c.1540C>T	p.Pro514Ser	p.P514S	ENST00000301067	NM_003482.3	514	Cca/Tca	10/54	1	2	FACETS	0.912	0.825	1	0.912	0.825	1	CLONAL	1	TRUE	1	0.410900055263663	2		630	646	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481859	56481859	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	132	548	0	ENST00000267101.3:c.787C>A	p.Leu263Ile	p.L263I	ENST00000267101	NM_001982.3	263	Ctt/Att	7/28	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.410900055263663	2		548	586	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856460	111856460	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	96	616	0	ENST00000341259.2:c.511G>T	p.Glu171Ter	p.E171*	ENST00000341259	NM_005475.2	171	Gag/Tag	2/8	1	2	FACETS	0.895	0.8	0.995	0.895	0.8	0.995	CLONAL	1	TRUE	1	0.410900055263663	2		616	522	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109705	115109705	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	100	564	0	ENST00000257566.3:c.2173C>T	p.Gln725Ter	p.Q725*	ENST00000257566	NM_016569.3	725	Cag/Tag	8/8	1	2	FACETS	0.951	0.852	1	0.951	0.852	1	CLONAL	1	TRUE	1	0.410900055263663	2		564	512	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117728	115117728	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	79	415	0	ENST00000257566.3:c.707T>A	p.Phe236Tyr	p.F236Y	ENST00000257566	NM_016569.3	236	tTt/tAt	3/8	1	2	FACETS	0.896	0.792	1	0.896	0.792	1	CLONAL	1	TRUE	1	0.410900055263663	2		415	429	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120785297	120785297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761676109	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	98	621	0	ENST00000257552.2:c.811G>A	p.Gly271Arg	p.G271R	ENST00000257552	NM_002442.3	271	Gga/Aga	12/15	1	2	FACETS	0.905	0.81	1	0.905	0.81	1	CLONAL	1	TRUE	1	0.410900055263663	2		621	527	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426810	121426811	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	95	551	0	ENST00000257555.6:c.501_502delinsTT	p.Arg168Cys	p.R168C	ENST00000257555		167	gtCCgc/gtTTgc	2/10	1	2	FACETS	0.889	0.794	0.99	0.889	0.794	0.99	CLONAL	1	TRUE	1	0.410900055263663	2		551	520	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434428	121434428	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	103	631	0	ENST00000257555.6:c.1192C>T	p.Gln398Ter	p.Q398*	ENST00000257555		398	Cag/Tag	6/10	1	2	FACETS	0.889	0.798	0.985	0.889	0.798	0.985	CLONAL	1	TRUE	1	0.410900055263663	2		631	564	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435465	121435465	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs921423540	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	131	668	0	ENST00000257555.6:c.1498C>A	p.His500Asn	p.H500N	ENST00000257555		500	Cac/Aac	7/10	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.410900055263663	2		668	617	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967647	26967647	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	66	409	0	ENST00000381527.3:c.790G>A	p.Asp264Asn	p.D264N	ENST00000381527	NM_001260.1	264	Gat/Aat	7/13	1	2	FACETS	0.9	0.786	1	0.9	0.786	1	CLONAL	1	TRUE	1	0.410900055263663	2		409	357	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589756	28589756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	96	427	0	ENST00000241453.7:c.2624G>A	p.Gly875Glu	p.G875E	ENST00000241453	NM_004119.2	875	gGa/gAa	21/24	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.410900055263663	2		427	435	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626768	28626768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	91	425	0	ENST00000241453.7:c.528G>A	p.Met176Ile	p.M176I	ENST00000241453	NM_004119.2	176	atG/atA	5/24	1	2	FACETS	0.925	0.824	1	0.925	0.824	1	CLONAL	1	TRUE	1	0.410900055263663	2		425	479	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28882983	28882983	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	78	448	0	ENST00000282397.4:c.3717T>G	p.Phe1239Leu	p.F1239L	ENST00000282397	NM_002019.4	1239	ttT/ttG	28/30	1	2	FACETS	0.891	0.787	1	0.891	0.787	1	CLONAL	1	TRUE	1	0.410900055263663	2		448	426	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28883040	28883040	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	76	445	0	ENST00000282397.4:c.3660G>T	p.Met1220Ile	p.M1220I	ENST00000282397	NM_002019.4	1220	atG/atT	28/30	1	2	FACETS	0.877	0.772	0.988	0.877	0.772	0.988	CLONAL	1	TRUE	1	0.410900055263663	2		445	422	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28979927	28979927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	77	383	0	ENST00000282397.4:c.1541G>A	p.Gly514Glu	p.G514E	ENST00000282397	NM_002019.4	514	gGa/gAa	11/30	1	2	FACETS	0.997	0.881	1	0.997	0.881	1	CLONAL	1	TRUE	1	0.410900055263663	2		383	376	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915075	32915075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	78	496	0	ENST00000380152.3:c.6583G>A	p.Gly2195Ser	p.G2195S	ENST00000380152		2195	Ggt/Agt	11/27	1	2	FACETS	0.9	0.794	1	0.9	0.794	1	CLONAL	1	TRUE	1	0.410900055263663	2		496	422	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749292	43749292	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	94	513	0	ENST00000382044.4:c.1514C>A	p.Ser505Tyr	p.S505Y	ENST00000382044	NM_001141980.1	505	tCc/tAc	12/28	1	2	FACETS	0.926	0.827	1	0.926	0.827	1	CLONAL	1	TRUE	1	0.410900055263663	2		513	494	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43772156	43772156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	122	432	0	ENST00000382044.4:c.559G>A	p.Glu187Lys	p.E187K	ENST00000382044	NM_001141980.1	187	Gag/Aag	6/28	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.410900055263663	2		432	550	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50782490	50782490	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	80	447	0	ENST00000307179.4:c.2002T>C	p.Tyr668His	p.Y668H	ENST00000307179		668	Tat/Cat	14/20	1	2	FACETS	0.83	0.733	0.933	0.83	0.733	0.933	CLONAL	1	TRUE	1	0.410900055263663	2		447	469	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51504627	51504627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	93	475	0	ENST00000260433.2:c.1153G>A	p.Gly385Ser	p.G385S	ENST00000260433		385	Ggc/Agc	9/10	1	2	FACETS	0.864	0.771	0.963	0.864	0.771	0.963	CLONAL	1	TRUE	1	0.410900055263663	2		475	524	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51507413	51507413	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	100	438	0	ENST00000260433.2:c.875C>A	p.Thr292Lys	p.T292K	ENST00000260433		292	aCa/aAa	8/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.410900055263663	2		438	424	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51520004	51520004	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	95	383	0	ENST00000260433.2:c.423G>A	p.Trp141Ter	p.W141*	ENST00000260433		141	tgG/tgA	4/10	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.410900055263663	2		383	437	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66737003	66737003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866411301	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	87	384	0	ENST00000307102.5:c.526G>A	p.Gly176Ser	p.G176S	ENST00000307102	NM_002755.3	176	Ggc/Agc	5/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.410900055263663	2		384	387	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457666	67457666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	100	594	0	ENST00000327367.4:c.476C>T	p.Ser159Phe	p.S159F	ENST00000327367	NM_005902.3	159	tCc/tTc	3/9	1	2	FACETS	0.851	0.762	0.945	0.851	0.762	0.945	CLONAL	1	TRUE	1	0.410900055263663	2		594	572	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678369	88678370	+	missense_variant	Missense_Mutation	DNP	CT	CT	TA	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	84	533	0	ENST00000360948.2:c.1166_1167delinsTA	p.Gln389Leu	p.Q389L	ENST00000360948	NM_001012338.2	389	cAG/cTA	9/19	1	2	FACETS	0.859	0.761	0.963	0.859	0.761	0.963	CLONAL	1	TRUE	1	0.410900055263663	2		533	476	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680716	88680716	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	83	455	0	ENST00000360948.2:c.541A>G	p.Lys181Glu	p.K181E	ENST00000360948	NM_001012338.2	181	Aag/Gag	6/19	1	2	FACETS	0.896	0.794	1	0.896	0.794	1	CLONAL	1	TRUE	1	0.410900055263663	2		455	451	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2115547	2115548	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	86	468	0	ENST00000219476.3:c.1627_1628delinsTT	p.Pro543Leu	p.P543L	ENST00000219476	NM_000548.3	543	CCg/TTg	16/42	1	2	FACETS	0.854	0.758	0.956	0.854	0.758	0.956	CLONAL	1	TRUE	1	0.410900055263663	2		468	490	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641141	3641141	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1314223448	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	103	579	0	ENST00000294008.3:c.2498T>C	p.Leu833Ser	p.L833S	ENST00000294008	NM_032444.2	833	tTg/tCg	12/15	1	2	FACETS	0.845	0.758	0.938	0.845	0.758	0.938	CLONAL	1	TRUE	1	0.410900055263663	2		579	593	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779719	3779719	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	143	603	0	ENST00000262367.5:c.5329C>A	p.Gln1777Lys	p.Q1777K	ENST00000262367	NM_004380.2	1777	Cag/Aag	31/31	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.410900055263663	2		603	622	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788642	3788642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	74	396	0	ENST00000262367.5:c.4312C>T	p.His1438Tyr	p.H1438Y	ENST00000262367	NM_004380.2	1438	Cat/Tat	26/31	1	2	FACETS	0.8	0.703	0.904	0.8	0.703	0.904	CLONAL	1	TRUE	1	0.410900055263663	2		396	450	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858487	9858487	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1555482811	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	118	490	1	ENST00000330684.3:c.2914A>T	p.Lys972Ter	p.K972*	ENST00000330684	NM_001134407.1	972	Aag/Tag	13/13	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.410900055263663	2		491	550	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024735	14024735	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	73	409	0	ENST00000311895.7:c.961G>T	p.Gly321Cys	p.G321C	ENST00000311895	NM_005236.2	321	Ggt/Tgt	5/11	1	2	FACETS	0.96	0.845	1	0.96	0.845	1	CLONAL	1	TRUE	1	0.410900055263663	2		409	370	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026079	14026079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	91	450	0	ENST00000311895.7:c.1039C>T	p.Pro347Ser	p.P347S	ENST00000311895	NM_005236.2	347	Cca/Tca	6/11	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.410900055263663	2		450	423	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038579	14038579	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	71	302	0	ENST00000311895.7:c.1906del		p.X636_splice	ENST00000311895	NM_005236.2	636			1	2	FACETS	0.993	0.873	1	0.993	0.873	1	CLONAL	1	TRUE	1	0.410900055263663	2		302	348	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038588	14038588	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	83	322	0	ENST00000311895.7:c.1913C>G	p.Ala638Gly	p.A638G	ENST00000311895	NM_005236.2	638	gCa/gGa	10/11	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.410900055263663	2		322	374	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041699	14041699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	121	582	0	ENST00000311895.7:c.2246C>T	p.Ser749Phe	p.S749F	ENST00000311895	NM_005236.2	749	tCc/tTc	11/11	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.410900055263663	2		582	575	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637587	23637588	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	69	420	0	ENST00000261584.4:c.2717_2718delinsAA	p.Trp906Ter	p.W906*	ENST00000261584	NM_024675.3	906	tGG/tAA	7/13	1	2	FACETS	0.767	0.67	0.871	0.767	0.67	0.871	SUBCLONAL	1	TRUE	1	0.410900055263663	2		420	438	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783760	50783760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	89	481	0	ENST00000398568.2:c.151C>T	p.Gln51Ter	p.Q51*	ENST00000398568	NM_001042412.1	51	Caa/Taa	3/18	1	2	FACETS	0.873	0.777	0.975	0.873	0.777	0.975	CLONAL	1	TRUE	1	0.410900055263663	2		481	496	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100663	67100663	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	85	446	0	ENST00000412916.2:c.361G>T	p.Gly121Cys	p.G121C	ENST00000412916		121	Ggt/Tgt	4/6	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.410900055263663	2		446	366	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990456	81990456	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1401906238	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	89	538	0	ENST00000359376.3:c.3727C>T	p.Gln1243Ter	p.Q1243*	ENST00000359376	NM_002661.3	1243	Cag/Tag	32/33	1	2	FACETS	0.863	0.768	0.964	0.863	0.768	0.964	CLONAL	1	TRUE	1	0.410900055263663	2		538	502	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544788	86544788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772320741	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	72	614	0	ENST00000262426.4:c.613G>A	p.Gly205Ser	p.G205S	ENST00000262426	NM_001451.2	205	Ggc/Agc	1/2	1	2	FACETS	0.892	0.783	1	0.892	0.783	1	CLONAL	1	TRUE	1	0.410900055263663	2		614	393	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89345491	89345491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	76	461	0	ENST00000301030.4:c.7459C>T	p.His2487Tyr	p.H2487Y	ENST00000301030	NM_001256183.1	2487	Cac/Tac	9/13	1	2	FACETS	0.937	0.826	1	0.937	0.826	1	CLONAL	1	TRUE	1	0.410900055263663	2		461	395	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965188	15965188	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	107	534	0	ENST00000268712.3:c.5408C>G	p.Pro1803Arg	p.P1803R	ENST00000268712	NM_006311.3	1803	cCt/cGt	37/46	1	2	FACETS	0.954	0.859	1	0.954	0.859	1	CLONAL	1	TRUE	1	0.410900055263663	2		534	546	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995368	15995368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778036596	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	90	422	0	ENST00000268712.3:c.2825C>T	p.Ser942Phe	p.S942F	ENST00000268712	NM_006311.3	942	tCc/tTc	22/46	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.410900055263663	2		422	428	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553490	29553490	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	111	499	0	ENST00000356175.3:c.2039G>T	p.Cys680Phe	p.C680F	ENST00000356175	NM_000267.3	680	tGc/tTc	18/57	1	2	FACETS	0.913	0.823	1	0.913	0.823	1	CLONAL	1	TRUE	1	0.410900055263663	2		499	592	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556269	29556269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	125	541	0	ENST00000356175.3:c.2636C>T	p.Ser879Leu	p.S879L	ENST00000356175	NM_000267.3	879	tCa/tTa	21/57	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.410900055263663	2		541	558	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667645	29667646	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	65	382	0	ENST00000356175.3:c.6981_6982delinsTA	p.Arg2328Ser	p.R2328S	ENST00000356175	NM_000267.3	2327	ctCCgt/ctTAgt	46/57	1	2	FACETS	0.809	0.705	0.921	0.809	0.705	0.921	CLONAL	1	TRUE	1	0.410900055263663	2		382	391	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33680055	33680055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	70	298	0	ENST00000308377.4:c.2026G>A	p.Glu676Lys	p.E676K	ENST00000308377	NM_152270.3	676	Gaa/Aaa	5/5	1	2	FACETS	0.979	0.859	1	0.979	0.859	1	CLONAL	1	TRUE	1	0.410900055263663	2		298	348	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33681039	33681039	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	113	244	0	ENST00000308377.4:c.1238G>A	p.Trp413Ter	p.W413*	ENST00000308377	NM_152270.3	413	tGg/tAg	4/5	1	2	FACETS	1	0.96	1	1	0.99	1	CLONAL	2	TRUE	1	0.410900055263663	2		244	255	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38792727	38792727	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	50	325	0	ENST00000348513.6:c.289G>T	p.Gly97Cys	p.G97C	ENST00000348513	NM_003079.4	97	Ggc/Tgc	6/11	1	2	FACETS	0.735	0.627	0.853	0.735	0.627	0.853	SUBCLONAL	1	TRUE	1	0.410900055263663	2		325	331	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223178	41223178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267604892	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	93	523	0	ENST00000357654.3:c.4753C>T	p.Pro1585Ser	p.P1585S	ENST00000357654	NM_007294.3	1585	Cca/Tca	15/23	1	2	FACETS	0.884	0.789	0.985	0.884	0.789	0.985	CLONAL	1	TRUE	1	0.410900055263663	2		523	512	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243826	41243826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	108	540	0	ENST00000357654.3:c.3722C>T	p.Ser1241Phe	p.S1241F	ENST00000357654	NM_007294.3	1241	tCt/tTt	10/23	1	2	FACETS	0.997	0.899	1	0.997	0.899	1	CLONAL	1	TRUE	1	0.410900055263663	2		540	527	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435033	56435033	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	130	639	0	ENST00000407977.2:c.2104G>T	p.Gly702Ter	p.G702*	ENST00000407977		702	Gga/Tga	9/10	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.410900055263663	2		639	617	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39647430	39647430	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	110	467	0	ENST00000262039.4:c.2602C>T	p.His868Tyr	p.H868Y	ENST00000262039	NM_002647.2	868	Cat/Tat	24/25	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.410900055263663	2		467	486	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45377678	45377678	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	31	253	0	ENST00000262160.6:c.751C>T	p.Pro251Ser	p.P251S	ENST00000262160	NM_005901.5	251	Cct/Tct	7/11	1	2	FACETS	0.677	0.551	0.817	0.677	0.551	0.817	SUBCLONAL	1	TRUE	1	0.410900055263663	2		253	223	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61323133	61323134	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	94	439	0	ENST00000283752.5:c.930_931delinsAA	p.Asp311Asn	p.D311N	ENST00000283752	NM_006919.2	310	ggGGat/ggAAat	8/8	1	2	FACETS	0.99	0.885	1	0.99	0.885	1	CLONAL	1	TRUE	1	0.410900055263663	2		439	462	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61325778	61325778	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193238900	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	14	55	0	ENST00000283752.5:c.438G>T	p.Lys146Asn	p.K146N	ENST00000283752	NM_006919.2	146	aaG/aaT	5/8	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.410900055263663	2		55	51	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4090662	4090662	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	100	439	0	ENST00000262948.5:c.1137T>A	p.Phe379Leu	p.F379L	ENST00000262948	NM_030662.3	379	ttT/ttA	11/11	1	2	FACETS	0.949	0.851	1	0.949	0.851	1	CLONAL	1	TRUE	1	0.410900055263663	2		439	513	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6227113	6227114	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	81	586	2	ENST00000252674.7:c.421-1_421delinsAA		p.X141_splice	ENST00000252674	NM_005934.3	141		5/12	1	2	FACETS	0.741	0.654	0.834	0.741	0.654	0.834	SUBCLONAL	1	TRUE	1	0.410900055263663	2		588	532	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170665	7170666	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	89	488	1	ENST00000302850.5:c.1365_1366delinsTT	p.His456Tyr	p.H456Y	ENST00000302850	NM_000208.2	455	ttCCac/ttTTac	6/22	1	2	FACETS	0.86	0.765	0.96	0.86	0.765	0.96	CLONAL	1	TRUE	1	0.410900055263663	2		489	504	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11019782	11019782	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	104	522	0	ENST00000327064.4:c.457T>A	p.Tyr153Asn	p.Y153N	ENST00000327064	NM_199141.1	153	Tat/Aat	4/16	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.410900055263663	2		522	477	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291899	15291899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1363008174	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	83	633	0	ENST00000263388.2:c.2867G>A	p.Gly956Glu	p.G956E	ENST00000263388	NM_000435.2	956	gGa/gAa	18/33	1	2	FACETS	0.833	0.738	0.934	0.833	0.738	0.934	CLONAL	1	TRUE	1	0.410900055263663	2		633	485	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295778	15295779	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	81	575	0	ENST00000263388.2:c.2348_2349delinsAA	p.Gly783Glu	p.G783E	ENST00000263388	NM_000435.2	783	gGG/gAA	15/33	1	2	FACETS	0.83	0.734	0.932	0.83	0.734	0.932	CLONAL	1	TRUE	1	0.410900055263663	2		575	475	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298754	15298754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1390903111	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	105	542	0	ENST00000263388.2:c.1544C>T	p.Pro515Leu	p.P515L	ENST00000263388	NM_000435.2	515	cCc/cTc	10/33	1	2	FACETS	0.957	0.861	1	0.957	0.861	1	CLONAL	1	TRUE	1	0.410900055263663	2		542	534	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355168	15355168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	82	564	0	ENST00000263377.2:c.2455C>T	p.Pro819Ser	p.P819S	ENST00000263377	NM_058243.2	819	Ccc/Tcc	13/20	1	2	FACETS	0.881	0.78	0.988	0.881	0.78	0.988	CLONAL	1	TRUE	1	0.410900055263663	2		564	453	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17940925	17940925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	99	568	0	ENST00000458235.1:c.3199C>T	p.Pro1067Ser	p.P1067S	ENST00000458235	NM_000215.3	1067	Cct/Tct	23/24	1	2	FACETS	0.966	0.866	1	0.966	0.866	1	CLONAL	1	TRUE	1	0.410900055263663	2		568	499	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945461	17945461	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	111	535	0	ENST00000458235.1:c.2269C>T	p.Gln757Ter	p.Q757*	ENST00000458235	NM_000215.3	757	Caa/Taa	17/24	1	2	FACETS	0.961	0.867	1	0.961	0.867	1	CLONAL	1	TRUE	1	0.410900055263663	2		535	562	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257135	19257136	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	63	364	0	ENST00000162023.5:c.827_828delinsTT	p.Ala276Val	p.A276V	ENST00000162023		276	gCC/gTT	12/13	1	2	FACETS	0.932	0.812	1	0.932	0.812	1	CLONAL	1	TRUE	1	0.410900055263663	2		364	329	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311668	30311669	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	70	365	1	ENST00000262643.3:c.522_523delinsTT	p.Arg175Trp	p.R175W	ENST00000262643	NM_001238.2	174	gaCCgg/gaTTgg	7/12	1	2	FACETS	0.883	0.774	0.999	0.883	0.774	0.999	CLONAL	1	TRUE	1	0.410900055263663	2		366	386	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792387	33792387	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	100	504	0	ENST00000498907.2:c.934C>G	p.Gln312Glu	p.Q312E	ENST00000498907	NM_004364.3	312	Cag/Gag	1/1	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.410900055263663	2		504	477	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211480	36211480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	97	411	0	ENST00000222270.7:c.1231C>T	p.Pro411Ser	p.P411S	ENST00000222270	NM_014727.1	411	Cct/Tct	3/37	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.410900055263663	2		411	419	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211538	36211538	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	45	271	0	ENST00000222270.7:c.1289C>T	p.Pro430Leu	p.P430L	ENST00000222270	NM_014727.1	430	cCt/cTt	3/37	1	2	FACETS	0.839	0.71	0.979	0.839	0.71	0.979	CLONAL	1	TRUE	1	0.410900055263663	2		271	261	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215973	36215974	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	87	578	1	ENST00000222270.7:c.3513_3514delinsTA	p.Arg1172Ser	p.R1172S	ENST00000222270	NM_014727.1	1171	gtCCgt/gtTAgt	10/37	1	2	FACETS	0.808	0.717	0.905	0.808	0.717	0.905	CLONAL	1	TRUE	1	0.410900055263663	2		579	524	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216515	36216515	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	113	594	0	ENST00000222270.7:c.3778C>A	p.Arg1260Ser	p.R1260S	ENST00000222270	NM_014727.1	1260	Cgt/Agt	12/37	1	2	FACETS	0.98	0.885	1	0.98	0.885	1	CLONAL	1	TRUE	1	0.410900055263663	2		594	561	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218832	36218833	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	117	686	0	ENST00000222270.7:c.4443_4444delinsAA	p.Gly1482Arg	p.G1482R	ENST00000222270	NM_014727.1	1481	gaGGga/gaAAga	18/37	1	2	FACETS	0.927	0.838	1	0.927	0.838	1	CLONAL	1	TRUE	1	0.410900055263663	2		686	614	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223122	36223122	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	109	705	0	ENST00000222270.7:c.5672C>T	p.Pro1891Leu	p.P1891L	ENST00000222270	NM_014727.1	1891	cCa/cTa	28/37	1	2	FACETS	0.895	0.805	0.989	0.895	0.805	0.989	CLONAL	1	TRUE	1	0.410900055263663	2		705	593	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753291	42753291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	112	675	0	ENST00000222329.4:c.973C>T	p.His325Tyr	p.H325Y	ENST00000222329	NM_006494.2	325	Cac/Tac	4/4	1	2	FACETS	0.853	0.769	0.942	0.853	0.769	0.942	CLONAL	1	TRUE	1	0.410900055263663	2		675	639	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422254	47422254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	108	519	0	ENST00000404338.3:c.322C>T	p.His108Tyr	p.H108Y	ENST00000404338	NM_004491.4	108	Cat/Tat	1/6	1	2	FACETS	0.973	0.877	1	0.973	0.877	1	CLONAL	1	TRUE	1	0.410900055263663	2		519	540	SUCCESS
ALK	238	MSKCC	GRCh37	2	29430065	29430065	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	79	390	0	ENST00000389048.3:c.3910G>A	p.Gly1304Arg	p.G1304R	ENST00000389048	NM_004304.4	1304	Gga/Aga	26/29	1	2	FACETS	0.901	0.796	1	0.901	0.796	1	CLONAL	1	TRUE	1	0.410900055263663	2		390	427	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498088	29498088	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	89	534	0	ENST00000389048.3:c.1918G>C	p.Gly640Arg	p.G640R	ENST00000389048	NM_004304.4	640	Gga/Cga	11/29	1	2	FACETS	0.856	0.762	0.956	0.856	0.762	0.956	CLONAL	1	TRUE	1	0.410900055263663	2		534	506	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213186	39213186	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	102	582	0	ENST00000402219.2:c.3781C>T	p.Pro1261Ser	p.P1261S	ENST00000402219	NM_005633.3	1261	Cct/Tct	23/23	1	2	FACETS	0.883	0.792	0.98	0.883	0.792	0.98	CLONAL	1	TRUE	1	0.410900055263663	2		582	562	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46587819	46587819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1267580705	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	96	493	0	ENST00000263734.3:c.497G>A	p.Arg166Gln	p.R166Q	ENST00000263734	NM_001430.4	166	cGg/cAg	5/16	1	2	FACETS	0.942	0.843	1	0.942	0.843	1	CLONAL	1	TRUE	1	0.410900055263663	2		493	496	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145412	61145412	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	93	369	0	ENST00000295025.8:c.622T>A	p.Cys208Ser	p.C208S	ENST00000295025	NM_002908.2	208	Tgt/Agt	6/11	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.410900055263663	2		369	450	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160374	99160374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	101	543	1	ENST00000074304.5:c.853C>A	p.Pro285Thr	p.P285T	ENST00000074304	NM_001134224.1	285	Cct/Act	11/26	1	2	FACETS	0.848	0.759	0.941	0.848	0.759	0.941	CLONAL	1	TRUE	1	0.410900055263663	2		544	580	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872491	136872491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	113	491	0	ENST00000241393.3:c.1007G>A	p.Gly336Glu	p.G336E	ENST00000241393	NM_003467.2	336	gGa/gAa	2/2	1	2	FACETS	0.906	0.817	0.999	0.906	0.817	0.999	CLONAL	1	TRUE	1	0.410900055263663	2		491	607	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872756	136872756	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	131	578	0	ENST00000241393.3:c.742T>A	p.Phe248Ile	p.F248I	ENST00000241393	NM_003467.2	248	Ttc/Atc	2/2	1	2	FACETS	0.976	0.888	1	0.976	0.888	1	CLONAL	1	TRUE	1	0.410900055263663	2		578	653	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488687	212488687	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	88	536	0	ENST00000342788.4:c.2162T>A	p.Val721Glu	p.V721E	ENST00000342788	NM_005235.2	721	gTa/gAa	18/28	1	2	FACETS	0.761	0.675	0.852	0.761	0.675	0.852	SUBCLONAL	1	TRUE	1	0.410900055263663	2		536	563	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537919	212537919	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	100	458	0	ENST00000342788.4:c.1686G>T	p.Met562Ile	p.M562I	ENST00000342788	NM_005235.2	562	atG/atT	14/28	1	2	FACETS	0.972	0.871	1	0.972	0.871	1	CLONAL	1	TRUE	1	0.410900055263663	2		458	501	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212615373	212615373	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	83	471	0	ENST00000342788.4:c.613T>A	p.Cys205Ser	p.C205S	ENST00000342788	NM_005235.2	205	Tgc/Agc	5/28	1	2	FACETS	0.786	0.695	0.882	0.786	0.695	0.882	SUBCLONAL	1	TRUE	1	0.410900055263663	2		471	514	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593531	215593531	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	110	538	0	ENST00000260947.4:c.2203C>G	p.Gln735Glu	p.Q735E	ENST00000260947	NM_000465.2	735	Cag/Gag	11/11	1	2	FACETS	0.926	0.835	1	0.926	0.835	1	CLONAL	1	TRUE	1	0.410900055263663	2		538	578	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645301	215645301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1574815914	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	83	459	0	ENST00000260947.4:c.1297C>T	p.His433Tyr	p.H433Y	ENST00000260947	NM_000465.2	433	Cat/Tat	4/11	1	2	FACETS	0.92	0.816	1	0.92	0.816	1	CLONAL	1	TRUE	1	0.410900055263663	2		459	439	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645759	215645759	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1574819068	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	100	522	0	ENST00000260947.4:c.839T>C	p.Leu280Ser	p.L280S	ENST00000260947	NM_000465.2	280	tTa/tCa	4/11	1	2	FACETS	0.936	0.839	1	0.936	0.839	1	CLONAL	1	TRUE	1	0.410900055263663	2		522	520	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662772	227662772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	94	589	0	ENST00000305123.5:c.683C>T	p.Ser228Phe	p.S228F	ENST00000305123	NM_005544.2	228	tCt/tTt	1/2	1	2	FACETS	0.87	0.776	0.969	0.87	0.776	0.969	CLONAL	1	TRUE	1	0.410900055263663	2		589	526	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560984	9560984	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs987695739	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	98	563	0	ENST00000353224.5:c.798G>T	p.Arg266Ser	p.R266S	ENST00000353224	NM_177990.2	266	agG/agT	4/10	1	2	FACETS	0.96	0.86	1	0.96	0.86	1	CLONAL	1	TRUE	1	0.410900055263663	2		563	497	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561313	9561314	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	77	460	0	ENST00000353224.5:c.468_469delinsAA	p.Asp157Asn	p.D157N	ENST00000353224	NM_177990.2	156	ctGGat/ctAAat	4/10	1	2	FACETS	0.826	0.727	0.93	0.826	0.727	0.93	CLONAL	1	TRUE	1	0.410900055263663	2		460	454	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023199	31023199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	105	560	1	ENST00000375687.4:c.2684C>T	p.Ser895Phe	p.S895F	ENST00000375687	NM_015338.5	895	tCt/tTt	13/13	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.410900055263663	2		561	507	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024981	31024981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	104	560	0	ENST00000375687.4:c.4466C>T	p.Ser1489Phe	p.S1489F	ENST00000375687	NM_015338.5	1489	tCc/tTc	13/13	1	2	FACETS	0.891	0.8	0.987	0.891	0.8	0.987	CLONAL	1	TRUE	1	0.410900055263663	2		560	568	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026237	36026237	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	76	525	0	ENST00000358208.4:c.839G>T	p.Cys280Phe	p.C280F	ENST00000358208		280	tGc/tTc	7/12	1	2	FACETS	0.787	0.693	0.888	0.787	0.693	0.888	SUBCLONAL	1	TRUE	1	0.410900055263663	2		525	470	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727063	40727063	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	105	578	0	ENST00000373198.4:c.3901C>T	p.Gln1301Ter	p.Q1301*	ENST00000373198	NM_133170.3	1301	Cag/Tag	28/32	1	2	FACETS	0.945	0.849	1	0.945	0.849	1	CLONAL	1	TRUE	1	0.410900055263663	2		578	541	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385261	41385262	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	84	489	0	ENST00000373198.4:c.699_700delinsAA	p.Asp234Asn	p.D234N	ENST00000373198	NM_133170.3	233	agGGac/agAAac	6/32	1	2	FACETS	0.923	0.819	1	0.923	0.819	1	CLONAL	1	TRUE	1	0.410900055263663	2		489	443	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420071	41420071	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	98	582	0	ENST00000373198.4:c.250T>G	p.Ser84Ala	p.S84A	ENST00000373198	NM_133170.3	84	Tct/Gct	3/32	1	2	FACETS	0.895	0.801	0.994	0.895	0.801	0.994	CLONAL	1	TRUE	1	0.410900055263663	2		582	533	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264785	46264785	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	104	482	0	ENST00000371998.3:c.1655C>A	p.Pro552His	p.P552H	ENST00000371998		552	cCc/cAc	12/23	1	2	FACETS	0.962	0.865	1	0.962	0.865	1	CLONAL	1	TRUE	1	0.410900055263663	2		482	526	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268356	46268356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	93	471	0	ENST00000371998.3:c.2743C>T	p.Pro915Ser	p.P915S	ENST00000371998		915	Cct/Tct	15/23	1	2	FACETS	0.916	0.818	1	0.916	0.818	1	CLONAL	1	TRUE	1	0.410900055263663	2		471	494	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164790	36164790	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1456340235	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	128	729	1	ENST00000300305.3:c.1085C>T	p.Ser362Leu	p.S362L	ENST00000300305		362	tCg/tTg	8/8	1	2	FACETS	0.933	0.847	1	0.933	0.847	1	CLONAL	1	TRUE	1	0.410900055263663	2		730	668	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817390	39817390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	86	568	0	ENST00000288319.7:c.173C>T	p.Ser58Phe	p.S58F	ENST00000288319	NM_182918.3	58	tCt/tTt	2/10	1	2	FACETS	0.731	0.647	0.819	0.731	0.647	0.819	SUBCLONAL	1	TRUE	1	0.410900055263663	2		568	573	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817513	39817513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778042834	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	107	514	0	ENST00000288319.7:c.50C>T	p.Ser17Leu	p.S17L	ENST00000288319	NM_182918.3	17	tCg/tTg	2/10	1	2	FACETS	0.914	0.822	1	0.914	0.822	1	CLONAL	1	TRUE	1	0.410900055263663	2		514	570	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121012	29121012	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs372168051	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	74	424	0	ENST00000328354.6:c.545C>A	p.Pro182His	p.P182H	ENST00000328354	NM_007194.3	182	cCt/cAt	4/15	1	2	FACETS	0.834	0.733	0.942	0.834	0.733	0.942	CLONAL	1	TRUE	1	0.410900055263663	2		424	432	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533686	41533686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	100	443	0	ENST00000263253.7:c.1652C>T	p.Pro551Leu	p.P551L	ENST00000263253	NM_001429.3	551	cCc/cTc	8/31	1	2	FACETS	0.997	0.895	1	0.997	0.895	1	CLONAL	1	TRUE	1	0.410900055263663	2		443	488	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37059080	37059080	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	116	468	0	ENST00000231790.2:c.874C>A	p.Leu292Met	p.L292M	ENST00000231790	NM_000249.3	292	Ctg/Atg	10/19	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.410900055263663	2		468	513	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41279549	41279549	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770804258	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	104	527	0	ENST00000349496.5:c.2119C>T	p.Leu707Phe	p.L707F	ENST00000349496	NM_001904.3	707	Ctt/Ttt	14/15	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.410900055263663	2		527	480	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924754	49924754	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	103	604	0	ENST00000296474.3:c.4189C>A	p.Pro1397Thr	p.P1397T	ENST00000296474	NM_002447.2	1397	Cct/Act	20/20	1	2	FACETS	0.823	0.738	0.913	0.823	0.738	0.913	CLONAL	1	TRUE	1	0.410900055263663	2		604	609	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940633	49940633	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs983418076	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	134	662	0	ENST00000296474.3:c.410C>T	p.Ser137Phe	p.S137F	ENST00000296474	NM_002447.2	137	tCc/tTc	1/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.410900055263663	2		662	631	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987003	69987003	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	100	451	0	ENST00000394351.3:c.64T>C	p.Tyr22His	p.Y22H	ENST00000394351	NM_000248.3	22	Tac/Cac	2/9	1	2	FACETS	0.97	0.87	1	0.97	0.87	1	CLONAL	1	TRUE	1	0.410900055263663	2		451	502	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247418	71247418	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	107	535	0	ENST00000318789.4:c.115G>C	p.Gly39Arg	p.G39R	ENST00000318789	NM_032682.5	39	Gga/Cga	6/21	1	2	FACETS	0.972	0.875	1	0.972	0.875	1	CLONAL	1	TRUE	1	0.410900055263663	2		535	536	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89444990	89444990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	96	508	0	ENST00000336596.2:c.1310C>T	p.Pro437Leu	p.P437L	ENST00000336596	NM_005233.5	437	cCa/cTa	6/17	1	2	FACETS	0.907	0.811	1	0.907	0.811	1	CLONAL	1	TRUE	1	0.410900055263663	2		508	515	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278217	142278218	+	missense_variant	Missense_Mutation	DNP	TG	TG	AT	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	69	418	0	ENST00000350721.4:c.1607_1608delinsAT	p.Ser536Tyr	p.S536Y	ENST00000350721	NM_001184.3	536	tCA/tAT	7/47	1	2	FACETS	0.87	0.762	0.986	0.87	0.762	0.986	CLONAL	1	TRUE	1	0.410900055263663	2		418	386	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198150	185198150	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	104	502	0	ENST00000265026.3:c.2632G>A	p.Glu878Lys	p.E878K	ENST00000265026	NM_004721.4	878	Gaa/Aaa	13/14	1	2	FACETS	0.932	0.838	1	0.932	0.838	1	CLONAL	1	TRUE	1	0.410900055263663	2		502	543	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185200185	185200185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747410744	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	101	499	0	ENST00000265026.3:c.2842G>A	p.Gly948Arg	p.G948R	ENST00000265026	NM_004721.4	948	Ggg/Agg	14/14	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.410900055263663	2		499	489	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455630	189455630	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	89	494	0	ENST00000264731.3:c.164T>A	p.Phe55Tyr	p.F55Y	ENST00000264731	NM_003722.4	55	tTc/tAc	2/14	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.410900055263663	2		494	387	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587117	189587117	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	88	396	0	ENST00000264731.3:c.1134T>A	p.Phe378Leu	p.F378L	ENST00000264731	NM_003722.4	378	ttT/ttA	9/14	1	2	FACETS	0.95	0.845	1	0.95	0.845	1	CLONAL	1	TRUE	1	0.410900055263663	2		396	451	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801480	1801480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751165912	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	82	553	0	ENST00000260795.2:c.386C>T	p.Pro129Leu	p.P129L	ENST00000260795		129	cCa/cTa	3/17	1	2	FACETS	0.905	0.802	1	0.905	0.802	1	CLONAL	1	TRUE	1	0.410900055263663	2		553	441	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806065	1806065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	110	480	0	ENST00000260795.2:c.1084G>A	p.Glu362Lys	p.E362K	ENST00000260795		362	Gag/Aag	8/17	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.410900055263663	2		480	471	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980430	1980430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035199365	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	84	526	0	ENST00000382891.5:c.3892C>T	p.Leu1298Phe	p.L1298F	ENST00000382891	NM_133335.3	1298	Ctc/Ttc	22/22	1	2	FACETS	0.76	0.673	0.853	0.76	0.673	0.853	SUBCLONAL	1	TRUE	1	0.410900055263663	2		526	538	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139852	55139852	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	102	518	0	ENST00000257290.5:c.1513A>G	p.Asn505Asp	p.N505D	ENST00000257290	NM_006206.4	505	Aat/Gat	10/23	1	2	FACETS	0.966	0.867	1	0.966	0.867	1	CLONAL	1	TRUE	1	0.410900055263663	2		518	514	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956184	55956184	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	98	425	0	ENST00000263923.4:c.3131T>G	p.Ile1044Ser	p.I1044S	ENST00000263923	NM_002253.2	1044	aTc/aGc	23/30	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.410900055263663	2		425	466	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961050	55961050	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	72	460	0	ENST00000263923.4:c.2890G>A	p.Asp964Asn	p.D964N	ENST00000263923	NM_002253.2	964	Gac/Aac	21/30	1	2	FACETS	0.851	0.746	0.962	0.851	0.746	0.962	CLONAL	1	TRUE	1	0.410900055263663	2		460	412	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961074	55961075	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	56	440	0	ENST00000263923.4:c.2865_2866delinsTT	p.Pro956Ser	p.P956S	ENST00000263923	NM_002253.2	955	atCCct/atTTct	21/30	1	2	FACETS	0.695	0.598	0.801	0.695	0.598	0.801	SUBCLONAL	1	TRUE	1	0.410900055263663	2		440	392	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971146	55971146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	79	368	0	ENST00000263923.4:c.1651C>T	p.Pro551Ser	p.P551S	ENST00000263923	NM_002253.2	551	Cct/Tct	13/30	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.410900055263663	2		368	380	SUCCESS
ALB	213	MSKCC	GRCh37	4	74272405	74272405	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1445650493	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	64	394	0	ENST00000295897.4:c.197T>C	p.Leu66Ser	p.L66S	ENST00000295897	NM_000477.5	66	tTa/tCa	3/15	1	2	FACETS	0.882	0.769	1	0.882	0.769	1	CLONAL	1	TRUE	1	0.410900055263663	2		394	353	SUCCESS
ALB	213	MSKCC	GRCh37	4	74275120	74275120	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	62	432	0	ENST00000295897.4:c.531A>C	p.Glu177Asp	p.E177D	ENST00000295897	NM_000477.5	177	gaA/gaC	5/15	1	2	FACETS	0.738	0.64	0.844	0.738	0.64	0.844	SUBCLONAL	1	TRUE	1	0.410900055263663	2		432	409	SUCCESS
ALB	213	MSKCC	GRCh37	4	74275124	74275124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	60	436	0	ENST00000295897.4:c.535C>T	p.Leu179Phe	p.L179F	ENST00000295897	NM_000477.5	179	Ctt/Ttt	5/15	1	2	FACETS	0.723	0.625	0.829	0.723	0.625	0.829	SUBCLONAL	1	TRUE	1	0.410900055263663	2		436	404	SUCCESS
ALB	213	MSKCC	GRCh37	4	74279218	74279218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	107	504	0	ENST00000295897.4:c.925G>A	p.Glu309Lys	p.E309K	ENST00000295897	NM_000477.5	309	Gaa/Aaa	8/15	1	2	FACETS	0.977	0.88	1	0.977	0.88	1	CLONAL	1	TRUE	1	0.410900055263663	2		504	533	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156807	106156807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779420187	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	109	581	0	ENST00000380013.4:c.1708C>T	p.Pro570Ser	p.P570S	ENST00000380013	NM_001127208.2	570	Cct/Tct	3/11	1	2	FACETS	0.87	0.783	0.961	0.87	0.783	0.961	CLONAL	1	TRUE	1	0.410900055263663	2		581	610	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518929	187518929	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	72	407	0	ENST00000441802.2:c.12275A>G	p.Tyr4092Cys	p.Y4092C	ENST00000441802	NM_005245.3	4092	tAc/tGc	24/27	1	2	FACETS	0.781	0.684	0.884	0.781	0.684	0.884	SUBCLONAL	1	TRUE	1	0.410900055263663	2		407	449	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521193	187521193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	107	537	0	ENST00000441802.2:c.11962C>T	p.Pro3988Ser	p.P3988S	ENST00000441802	NM_005245.3	3988	Cct/Tct	22/27	1	2	FACETS	0.938	0.844	1	0.938	0.844	1	CLONAL	1	TRUE	1	0.410900055263663	2		537	555	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235302	235302	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	69	366	0	ENST00000264932.6:c.1108C>T	p.His370Tyr	p.H370Y	ENST00000264932	NM_004168.2	370	Cac/Tac	9/15	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.410900055263663	2		366	314	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35860980	35860980	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	88	467	0	ENST00000303115.3:c.109G>T	p.Asp37Tyr	p.D37Y	ENST00000303115	NM_002185.3	37	Gac/Tac	2/8	1	2	FACETS	0.883	0.785	0.987	0.883	0.785	0.987	CLONAL	1	TRUE	1	0.410900055263663	2		467	485	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945105	38945105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	81	446	0	ENST00000357387.3:c.4699C>T	p.Pro1567Ser	p.P1567S	ENST00000357387	NM_152756.3	1567	Ccc/Tcc	35/38	1	2	FACETS	0.79	0.698	0.888	0.79	0.698	0.888	SUBCLONAL	1	TRUE	1	0.410900055263663	2		446	499	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457756	149457757	+	missense_variant	Missense_Mutation	DNP	TC	TC	CT	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	96	526	0	ENST00000286301.3:c.647_648delinsAG	p.Arg216Gln	p.R216Q	ENST00000286301	NM_005211.3	216	cGA/cAG	5/22	NA	2	FACETS	0.882	0.788	0.981			1	INDETERMINATE	1	TRUE	NA	0.410900055263663	2		526	530	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505089	149505089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	110	550	2	ENST00000261799.4:c.1726G>A	p.Gly576Ser	p.G576S	ENST00000261799	NM_002609.3	576	Ggc/Agc	12/23	NA	2	FACETS	1	0.921	1			1	INDETERMINATE	1	TRUE	NA	0.410900055263663	2		552	523	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517653	176517654	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	TG	TG	GT	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	91	585	1	ENST00000292408.4:c.354_355delinsGT	p.Asp119Tyr	p.D119Y	ENST00000292408	NM_213647.1	118	ggTGac/ggGTac	3/18	1	2	FACETS	0.758	0.675	0.848	0.758	0.675	0.848	SUBCLONAL	1	TRUE	1	0.410900055263663	2		586	584	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681090	30681091	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	93	456	1	ENST00000376406.3:c.628_629delinsTT	p.Pro210Leu	p.P210L	ENST00000376406	NM_014641.2	210	CCg/TTg	5/15	1	2	FACETS	0.864	0.771	0.963	0.864	0.771	0.963	CLONAL	1	TRUE	1	0.410900055263663	2		457	524	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967241	93967241	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	55	352	0	ENST00000369303.4:c.2111G>T	p.Gly704Val	p.G704V	ENST00000369303	NM_004440.3	704	gGg/gTg	12/17	1	2	FACETS	0.936	0.807	1	0.936	0.807	1	CLONAL	1	TRUE	1	0.410900055263663	2		352	286	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120543	94120543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	108	488	0	ENST00000369303.4:c.508G>A	p.Glu170Lys	p.E170K	ENST00000369303	NM_004440.3	170	Gag/Aag	3/17	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.410900055263663	2		488	492	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555236	106555236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746018999	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	102	467	0	ENST00000369096.4:c.2353C>T	p.Leu785Phe	p.L785F	ENST00000369096	NM_001198.3	785	Ctc/Ttc	7/7	1	2	FACETS	0.958	0.86	1	0.958	0.86	1	CLONAL	1	TRUE	1	0.410900055263663	2		467	518	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555257	106555257	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	100	469	0	ENST00000369096.4:c.2374T>A	p.Tyr792Asn	p.Y792N	ENST00000369096	NM_001198.3	792	Tat/Aat	7/7	1	2	FACETS	0.993	0.891	1	0.993	0.891	1	CLONAL	1	TRUE	1	0.410900055263663	2		469	490	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638350	117638350	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	116	489	0	ENST00000368508.3:c.6091G>T	p.Gly2031Ter	p.G2031*	ENST00000368508	NM_002944.2	2031	Gga/Tga	38/43	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.410900055263663	2		489	489	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714466	117714466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	78	381	0	ENST00000368508.3:c.1183G>A	p.Glu395Lys	p.E395K	ENST00000368508	NM_002944.2	395	Gag/Aag	11/43	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.410900055263663	2		381	335	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715859	117715859	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	68	385	0	ENST00000368508.3:c.899C>T	p.Ser300Phe	p.S300F	ENST00000368508	NM_002944.2	300	tCt/tTt	9/43	1	2	FACETS	0.873	0.764	0.99	0.873	0.764	0.99	CLONAL	1	TRUE	1	0.410900055263663	2		385	379	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005279	150005279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	104	560	1	ENST00000253339.5:c.946G>A	p.Gly316Arg	p.G316R	ENST00000253339		316	Gga/Aga	3/7	1	2	FACETS	0.922	0.828	1	0.922	0.828	1	CLONAL	1	TRUE	1	0.410900055263663	2		561	549	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265332	152265332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	89	458	0	ENST00000206249.3:c.785G>A	p.Gly262Glu	p.G262E	ENST00000206249	NM_000125.3	262	gGg/gAg	4/8	1	2	FACETS	0.976	0.869	1	0.976	0.869	1	CLONAL	1	TRUE	1	0.410900055263663	2		458	444	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505506	157505507	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	78	452	0	ENST00000346085.5:c.3487_3488delinsTT	p.Pro1163Leu	p.P1163L	ENST00000346085	NM_020732.3	1163	CCg/TTg	13/20	1	2	FACETS	0.723	0.637	0.816	0.723	0.637	0.816	SUBCLONAL	1	TRUE	1	0.410900055263663	2		452	525	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522092	157522092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	120	623	0	ENST00000346085.5:c.4364C>T	p.Ser1455Phe	p.S1455F	ENST00000346085	NM_020732.3	1455	tCc/tTc	18/20	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.410900055263663	2		623	568	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522100	157522100	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554235703	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	114	618	0	ENST00000346085.5:c.4372G>T	p.Glu1458Ter	p.E1458*	ENST00000346085	NM_020732.3	1458	Gag/Tag	18/20	1	2	FACETS	0.97	0.876	1	0.97	0.876	1	CLONAL	1	TRUE	1	0.410900055263663	2		618	572	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522238	157522238	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554235817	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	93	609	0	ENST00000346085.5:c.4510C>T	p.Gln1504Ter	p.Q1504*	ENST00000346085	NM_020732.3	1504	Cag/Tag	18/20	1	2	FACETS	0.845	0.753	0.941	0.845	0.753	0.941	CLONAL	1	TRUE	1	0.410900055263663	2		609	536	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522563	157522563	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	119	496	0	ENST00000346085.5:c.4835C>T	p.Ser1612Leu	p.S1612L	ENST00000346085	NM_020732.3	1612	tCa/tTa	18/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.410900055263663	2		496	536	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035201	6035201	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	132	542	0	ENST00000265849.7:c.867T>A	p.Phe289Leu	p.F289L	ENST00000265849	NM_000535.5	289	ttT/ttA	8/15	0.10602690348929	4	FACETS	0.797	0.726	0.87	0.797	0.726	0.87	INDETERMINATE	2	TRUE	2	0.410900055263663	4		542	569	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223558	55223558	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	111	511	1	ENST00000275493.2:c.925C>T	p.Arg309Ter	p.R309*	ENST00000275493	NM_005228.3	309	Cga/Tga	8/28	1	2	FACETS	0.995	0.898	1	0.995	0.898	1	CLONAL	1	TRUE	1	0.410900055263663	2		512	543	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227895	55227896	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	61	450	0	ENST00000275493.2:c.1362_1363delinsAA	p.Glu455Lys	p.E455K	ENST00000275493	NM_005228.3	454	aaGGag/aaAAag	12/28	1	2	FACETS	0.739	0.639	0.845	0.739	0.639	0.845	SUBCLONAL	1	TRUE	1	0.410900055263663	2		450	402	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240675	55240675	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	102	566	0	ENST00000275493.2:c.1920-1G>A		p.X640_splice	ENST00000275493	NM_005228.3	640			1	2	FACETS	0.882	0.791	0.978	0.882	0.791	0.978	CLONAL	1	TRUE	1	0.410900055263663	2		566	563	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372788	81372788	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	88	411	0	ENST00000222390.5:c.747-1G>A		p.X249_splice	ENST00000222390	NM_000601.4	249			1	2	FACETS	0.927	0.825	1	0.927	0.825	1	CLONAL	1	TRUE	1	0.410900055263663	2		411	462	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386590	81386590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	47	344	0	ENST00000222390.5:c.397G>A	p.Gly133Arg	p.G133R	ENST00000222390	NM_000601.4	133	Gga/Aga	4/18	1	2	FACETS	0.794	0.674	0.925	0.794	0.674	0.925	CLONAL	1	TRUE	1	0.410900055263663	2		344	288	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380997	116380997	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	128	443	0	ENST00000397752.3:c.1619G>A	p.Trp540Ter	p.W540*	ENST00000397752	NM_000245.2	540	tGg/tAg	5/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.410900055263663	2		443	574	SUCCESS
MET	4233	MSKCC	GRCh37	7	116399450	116399450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199808716	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	107	477	0	ENST00000397752.3:c.2270G>A	p.Gly757Glu	p.G757E	ENST00000397752	NM_000245.2	757	gGg/gAg	10/21	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.410900055263663	2		477	492	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482843	140482843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	111	565	0	ENST00000288602.6:c.1292C>T	p.Ser431Phe	p.S431F	ENST00000288602	NM_004333.4	431	tCc/tTc	10/18	1	2	FACETS	0.935	0.843	1	0.935	0.843	1	CLONAL	1	TRUE	1	0.410900055263663	2		565	578	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878776	151878776	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	115	622	0	ENST00000262189.6:c.6169T>A	p.Tyr2057Asn	p.Y2057N	ENST00000262189	NM_170606.2	2057	Tat/Aat	36/59	1	2	FACETS	0.965	0.872	1	0.965	0.872	1	CLONAL	1	TRUE	1	0.410900055263663	2		622	580	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879404	151879404	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	122	548	0	ENST00000262189.6:c.5541T>G	p.Phe1847Leu	p.F1847L	ENST00000262189	NM_170606.2	1847	ttT/ttG	36/59	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.410900055263663	2		548	550	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949064	151949064	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs760412796	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	77	439	0	ENST00000262189.6:c.1581A>T	p.Leu527Phe	p.L527F	ENST00000262189	NM_170606.2	527	ttA/ttT	11/59	1	2	FACETS	0.817	0.719	0.92	0.817	0.719	0.92	CLONAL	1	TRUE	1	0.410900055263663	2		439	459	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132817	152132817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	80	397	0	ENST00000262189.6:c.55C>T	p.Pro19Ser	p.P19S	ENST00000262189	NM_170606.2	19	Ccc/Tcc	1/59	1	2	FACETS	0.854	0.755	0.96	0.854	0.755	0.96	CLONAL	1	TRUE	1	0.410900055263663	2		397	456	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38153335	38153335	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	101	449	0	ENST00000317025.8:c.2894G>T	p.Trp965Leu	p.W965L	ENST00000317025	NM_023034.1	965	tGg/tTg	16/24	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.410900055263663	2		449	467	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968148	68968148	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	80	382	0	ENST00000288368.4:c.1177G>A	p.Gly393Arg	p.G393R	ENST00000288368	NM_024870.2	393	Gga/Aga	10/40	1	2	FACETS	0.973	0.862	1	0.973	0.862	1	CLONAL	1	TRUE	1	0.410900055263663	2		382	400	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020480	69020480	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	88	500	0	ENST00000288368.4:c.2852C>A	p.Ser951Ter	p.S951*	ENST00000288368	NM_024870.2	951	tCa/tAa	24/40	1	2	FACETS	0.837	0.743	0.935	0.837	0.743	0.935	CLONAL	1	TRUE	1	0.410900055263663	2		500	512	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021722	69021722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1455830470	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	65	464	0	ENST00000288368.4:c.3010G>A	p.Gly1004Arg	p.G1004R	ENST00000288368	NM_024870.2	1004	Gga/Aga	25/40	1	2	FACETS	0.695	0.604	0.793	0.695	0.604	0.793	SUBCLONAL	1	TRUE	1	0.410900055263663	2		464	455	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964347	70964347	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	49	361	0	ENST00000276594.2:c.1681T>G	p.Phe561Val	p.F561V	ENST00000276594	NM_024504.3	561	Ttc/Gtc	8/8	1	2	FACETS	0.769	0.655	0.893	0.769	0.655	0.893	SUBCLONAL	1	TRUE	1	0.410900055263663	2		361	310	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958433	90958433	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	36	407	0	ENST00000265433.3:c.2005T>A	p.Ser669Thr	p.S669T	ENST00000265433	NM_002485.4	669	Tcc/Acc	13/16	1	2	FACETS	0.661	0.546	0.788	0.661	0.546	0.788	SUBCLONAL	1	TRUE	1	0.410900055263663	2		407	265	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559323	141559323	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	101	562	0	ENST00000220592.5:c.1478A>G	p.Lys493Arg	p.K493R	ENST00000220592	NM_012154.3	493	aAa/aGa	12/19	1	2	FACETS	0.912	0.818	1	0.912	0.818	1	CLONAL	1	TRUE	1	0.410900055263663	2		562	539	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2088560	2088561	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	89	336	0	ENST00000349721.2:c.2830_2831delinsTT	p.Pro944Leu	p.P944L	ENST00000349721	NM_003070.3	944	CCa/TTa	19/34	0.339690475508096	2	FACETS	1	0.981	1	0.739	0.663	0.818	CLONAL	1	TRUE	0	0.410900055263663	2		336	293	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044413	5044413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	87	325	0	ENST00000381652.3:c.361C>T	p.Pro121Ser	p.P121S	ENST00000381652	NM_004972.3	121	Cct/Tct	5/25	0.339690475508096	2	FACETS	1	0.978	1	0.694	0.621	0.77	CLONAL	1	TRUE	0	0.410900055263663	2		325	305	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449742	8449742	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	130	403	0	ENST00000356435.5:c.3971T>C	p.Leu1324Pro	p.L1324P	ENST00000356435		1324	cTt/cCt	23/35	0.339690475508096	2	FACETS	0.807	0.739	0.877	0.807	0.739	0.877	CLONAL	2	TRUE	0	0.410900055263663	2		403	392	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499826	8499826	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867508268	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	135	462	0	ENST00000356435.5:c.2143C>T	p.Pro715Ser	p.P715S	ENST00000356435		715	Cct/Tct	14/35	0.339690475508096	2	FACETS	0.766	0.702	0.832	0.766	0.702	0.832	SUBCLONAL	2	TRUE	0	0.410900055263663	2		462	429	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518362	8518362	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	143	396	0	ENST00000356435.5:c.1029G>T	p.Trp343Cys	p.W343C	ENST00000356435		343	tgG/tgT	10/35	0.339690475508096	2	FACETS	0.835	0.768	0.902	0.835	0.768	0.902	CLONAL	2	TRUE	0	0.410900055263663	2		396	417	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8527354	8527354	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	53	215	0	ENST00000356435.5:c.542-1G>T		p.X181_splice	ENST00000356435		181			0.339690475508096	2	FACETS	1	0.966	1	0.705	0.611	0.804	CLONAL	1	TRUE	0	0.410900055263663	2		215	183	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639902	93639902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	109	537	0	ENST00000375746.1:c.1231C>T	p.Pro411Ser	p.P411S	ENST00000375746	NM_001174167.1	411	Ccc/Tcc	10/14	0.170854027904377	3	FACETS	1	0.955	1	0.553	0.498	0.611	INDETERMINATE	1	TRUE	1	0.410900055263663	3		537	578	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242295	98242295	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	86	494	0	ENST00000331920.6:c.1023G>T	p.Leu341Phe	p.L341F	ENST00000331920	NM_000264.3	341	ttG/ttT	7/24	0.170854027904377	3	FACETS	0.901	0.799	1	0.451	0.399	0.505	INDETERMINATE	1	TRUE	1	0.410900055263663	3		494	560	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434691	128434691	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	118	480	0	ENST00000265960.3:c.163C>A	p.Gln55Lys	p.Q55K	ENST00000265960	NM_001006617.1	55	Cag/Aag	2/12	0.170854027904377	3	FACETS	1	0.977	1	0.631	0.571	0.693	INDETERMINATE	1	TRUE	1	0.410900055263663	3		480	549	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133748382	133748382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	134	406	0	ENST00000318560.5:c.1043C>T	p.Ser348Leu	p.S348L	ENST00000318560	NM_005157.4	348	tCg/tTg	6/11	0.170854027904377	3	FACETS	0.844	0.772	0.918	0.844	0.772	0.918	INDETERMINATE	2	TRUE	1	0.410900055263663	3		406	466	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841196	15841196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	126	677	0	ENST00000307771.7:c.1280G>A	p.Arg427Lys	p.R427K	ENST00000307771	NM_005089.3	427	aGg/aAg	11/11	1	2	FACETS	0.922	0.837	1	0.922	0.837	1	CLONAL	1	TRUE	1	0.410900055263663	2		677	665	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923062	39923062	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	97	545	0	ENST00000378444.4:c.3646G>A	p.Glu1216Lys	p.E1216K	ENST00000378444	NM_001123385.1	1216	Gaa/Aaa	8/15	1	2	FACETS	0.815	0.729	0.907	0.815	0.729	0.907	CLONAL	1	TRUE	1	0.410900055263663	2		545	579	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932051	39932052	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	93	582	1	ENST00000378444.4:c.2547_2548delinsTT	p.Arg850Cys	p.R850C	ENST00000378444	NM_001123385.1	849	caCCgt/caTTgt	4/15	1	2	FACETS	0.84	0.749	0.936	0.84	0.749	0.936	CLONAL	1	TRUE	1	0.410900055263663	2		583	539	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934129	39934129	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	93	567	0	ENST00000378444.4:c.470A>G	p.Lys157Arg	p.K157R	ENST00000378444	NM_001123385.1	157	aAa/aGa	4/15	1	2	FACETS	0.834	0.743	0.929	0.834	0.743	0.929	CLONAL	1	TRUE	1	0.410900055263663	2		567	543	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929389	44929389	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	145	539	0	ENST00000377967.4:c.2489C>T	p.Pro830Leu	p.P830L	ENST00000377967	NM_021140.2	830	cCa/cTa	17/29	1	2	FACETS	0.988	0.904	1	0.988	0.904	1	CLONAL	1	TRUE	1	0.410900055263663	2		539	714	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424490	47424490	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	93	570	0	ENST00000377045.4:c.410C>A	p.Ser137Tyr	p.S137Y	ENST00000377045	NM_001654.4	137	tCc/tAc	5/16	1	2	FACETS	0.736	0.655	0.822	0.736	0.655	0.822	SUBCLONAL	1	TRUE	1	0.410900055263663	2		570	615	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411588	63411588	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs2147087915	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	123	646	0	ENST00000330258.3:c.1579G>T	p.Asp527Tyr	p.D527Y	ENST00000330258	NM_152424.3	527	Gac/Tac	2/2	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.410900055263663	2		646	550	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411852	63411852	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	85	581	0	ENST00000330258.3:c.1315C>T	p.Leu439Phe	p.L439F	ENST00000330258	NM_152424.3	439	Ctt/Ttt	2/2	1	2	FACETS	0.731	0.647	0.82	0.731	0.647	0.82	SUBCLONAL	1	TRUE	1	0.410900055263663	2		581	566	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412026	63412026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	92	661	0	ENST00000330258.3:c.1141G>A	p.Glu381Lys	p.E381K	ENST00000330258	NM_152424.3	381	Gag/Aag	2/2	1	2	FACETS	0.832	0.742	0.929	0.832	0.742	0.929	CLONAL	1	TRUE	1	0.410900055263663	2		661	538	SUCCESS
AR	367	MSKCC	GRCh37	X	66765022	66765022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1283306896	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	70	538	0	ENST00000374690.3:c.34C>T	p.Pro12Ser	p.P12S	ENST00000374690	NM_000044.3	12	Cct/Tct	1/8	1	2	FACETS	0.739	0.646	0.839	0.739	0.646	0.839	SUBCLONAL	1	TRUE	1	0.410900055263663	2		538	461	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346297	70346297	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	88	527	0	ENST00000374080.3:c.2648C>A	p.Ser883Ter	p.S883*	ENST00000374080		883	tCa/tAa	19/45	1	2	FACETS	0.835	0.742	0.934	0.835	0.742	0.934	CLONAL	1	TRUE	1	0.410900055263663	2		527	513	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776325	76776326	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	44	463	0	ENST00000373344.5:c.7140_7141delinsAA	p.Glu2381Lys	p.E2381K	ENST00000373344	NM_000489.3	2380	caGGag/caAAag	34/35	1	2	FACETS	0.628	0.528	0.737	0.628	0.528	0.737	SUBCLONAL	1	TRUE	1	0.410900055263663	2		463	341	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937439	76937439	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	54	483	0	ENST00000373344.5:c.3309G>C	p.Lys1103Asn	p.K1103N	ENST00000373344	NM_000489.3	1103	aaG/aaC	9/35	1	2	FACETS	0.757	0.65	0.874	0.757	0.65	0.874	SUBCLONAL	1	TRUE	1	0.410900055263663	2		483	347	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937534	76937534	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	75	497	0	ENST00000373344.5:c.3214G>T	p.Asp1072Tyr	p.D1072Y	ENST00000373344	NM_000489.3	1072	Gat/Tat	9/35	1	2	FACETS	0.904	0.796	1	0.904	0.796	1	CLONAL	1	TRUE	1	0.410900055263663	2		497	404	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938207	76938208	+	stop_gained	Nonsense_Mutation	DNP	AA	AA	TT	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	61	469	2	ENST00000373344.5:c.2540_2541inv	p.Phe847Ter	p.F847*	ENST00000373344	NM_000489.3	847	tTT/tAA	9/35	1	2	FACETS	0.715	0.619	0.819	0.715	0.619	0.819	SUBCLONAL	1	TRUE	1	0.410900055263663	2		471	415	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938223	76938223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	63	475	0	ENST00000373344.5:c.2525C>T	p.Pro842Leu	p.P842L	ENST00000373344	NM_000489.3	842	cCa/cTa	9/35	1	2	FACETS	0.748	0.649	0.854	0.748	0.649	0.854	SUBCLONAL	1	TRUE	1	0.410900055263663	2		475	410	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019753	123019754	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	82	505	0	ENST00000355640.3:c.241_242delinsAA	p.Gly81Lys	p.G81K	ENST00000355640		81	GGa/AAa	2/7	1	2	FACETS	0.76	0.672	0.854	0.76	0.672	0.854	SUBCLONAL	1	TRUE	1	0.410900055263663	2		505	525	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123022480	123022480	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	62	347	0	ENST00000355640.3:c.889A>G	p.Lys297Glu	p.K297E	ENST00000355640		297	Aaa/Gaa	3/7	1	2	FACETS	0.811	0.704	0.926	0.811	0.704	0.926	CLONAL	1	TRUE	1	0.410900055263663	2		347	372	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191763	123191763	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	72	398	0	ENST00000218089.9:c.1352G>A	p.Arg451Lys	p.R451K	ENST00000218089	NM_001042749.1	451	aGa/aAa	15/35	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.410900055263663	2		398	337	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197724	123197725	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	49	397	0	ENST00000218089.9:c.1848_1849delinsAT	p.Arg617Trp	p.R617W	ENST00000218089	NM_001042749.1	616	atCCgg/atATgg	20/35	1	2	FACETS	0.774	0.659	0.899	0.774	0.659	0.899	SUBCLONAL	1	TRUE	1	0.410900055263663	2		397	308	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197834	123197834	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	49	424	0	ENST00000218089.9:c.1958C>T	p.Ser653Leu	p.S653L	ENST00000218089	NM_001042749.1	653	tCa/tTa	20/35	1	2	FACETS	0.75	0.638	0.871	0.75	0.638	0.871	SUBCLONAL	1	TRUE	1	0.410900055263663	2		424	318	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215257	123215258	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	47	322	0	ENST00000218089.9:c.2803_2804delinsAA	p.Gly935Asn	p.G935N	ENST00000218089	NM_001042749.1	935	GGc/AAc	28/35	1	2	FACETS	0.8	0.679	0.931	0.8	0.679	0.931	CLONAL	1	TRUE	1	0.410900055263663	2		322	286	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861633	152861633	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	88	534	0	ENST00000406277.2:c.119G>A	p.Gly40Glu	p.G40E	ENST00000406277	NM_152274.4	40	gGg/gAg	4/7	1		FACETS		0.732	0.921				CLONAL	1	TRUE	1	0.410900055263663	2		534	520	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622630	158622630	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	91	456	0	ENST00000263640.3:c.869C>A	p.Ser290Ter	p.S290*	ENST00000263640	NM_001105.4	290	tCg/tAg	8/11	1	2	FACETS	0.959	0.855	1	0.959	0.855	1	CLONAL	1	TRUE	1	0.410900055263663	2		456	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587782289	NA	P-0066089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	214	311	0	ENST00000269305.4:c.706T>A	p.Tyr236Asn	p.Y236N	ENST00000269305	NM_001126112.2	236	Tac/Aac	7/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		311	344	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880963	134880963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773682419	NA	P-0066089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	540	402	0	ENST00000398015.3:c.1526G>A	p.Arg509His	p.R509H	ENST00000398015	NM_004441.4	509	cGc/cAc	7/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		402	941	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21348256	21348256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777180	NA	P-0066089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	292	479	0	ENST00000215739.8:c.1397G>A	p.Arg466Gln	p.R466Q	ENST00000215739	NM_006767.3	466	cGg/cAg	13/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		479	433	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422467	225422467	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1553535841	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	131	357	0	ENST00000264414.4:c.173A>G	p.Tyr58Cys	p.Y58C	ENST00000264414	NM_003590.4	58	tAt/tGt	2/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		357	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	141	452	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		452	461	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874261	155874261	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs483352822	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	234	439	0	ENST00000368323.3:c.270G>C	p.Met90Ile	p.M90I	ENST00000368323	NM_006912.5	90	atG/atC	5/6	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		439	790	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795338	39795338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	97	377	0	ENST00000288319.7:c.382C>T	p.Pro128Ser	p.P128S	ENST00000288319	NM_182918.3	128	Cca/Tca	3/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		377	424	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500304	99500304	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	37	439	0	ENST00000268035.6:c.3737G>T	p.Arg1246Leu	p.R1246L	ENST00000268035	NM_000875.3	1246	cGc/cTc	21/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		439	477	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466803	25466803	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	100	459	0	ENST00000264709.3:c.1900A>T	p.Ile634Phe	p.I634F	ENST00000264709	NM_175629.2	634	Atc/Ttc	16/23	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		459	527	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115111981	115111981	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	52	503	0	ENST00000257566.3:c.1759C>A	p.Leu587Met	p.L587M	ENST00000257566	NM_016569.3	587	Ctg/Atg	7/8	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		503	343	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136912	55136912	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	49	270	0	ENST00000257290.5:c.1234C>G	p.Gln412Glu	p.Q412E	ENST00000257290	NM_006206.4	412	Caa/Gaa	8/23	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		270	309	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105581	27105581	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	116	466	0	ENST00000324856.7:c.5192T>G	p.Leu1731Ter	p.L1731*	ENST00000324856	NM_006015.4	1731	tTa/tGa	20/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		466	502	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420326	88420326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370533197	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	114	423	0	ENST00000360948.2:c.2360G>A	p.Arg787His	p.R787H	ENST00000360948	NM_001012338.2	787	cGt/cAt	19/19	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		423	455	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141427	11141427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	46	422	0	ENST00000358026.2:c.3404G>A	p.Arg1135Gln	p.R1135Q	ENST00000358026	NM_001128849.1	1135	cGg/cAg	25/36	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		422	310	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538307	187538307	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	89	365	0	ENST00000441802.2:c.8927G>T	p.Trp2976Leu	p.W2976L	ENST00000441802	NM_005245.3	2976	tGg/tTg	11/27	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		365	382	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981403	70981403	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	47	410	0	ENST00000276594.2:c.693C>G	p.Asp231Glu	p.D231E	ENST00000276594	NM_024504.3	231	gaC/gaG	2/8	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		410	459	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120152	70120152	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	64	512	0	ENST00000245479.2:c.1154T>A	p.Leu385Gln	p.L385Q	ENST00000245479	NM_000346.3	385	cTg/cAg	3/3	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		512	414	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168725	32168725	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	121	434	0	ENST00000375023.3:c.4198C>G	p.Arg1400Gly	p.R1400G	ENST00000375023	NM_004557.3	1400	Cgc/Ggc	23/30	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		434	396	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211066	36211066	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	50	482	0	ENST00000222270.7:c.817G>T	p.Gly273Cys	p.G273C	ENST00000222270	NM_014727.1	273	Ggt/Tgt	3/37	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		482	639	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132816	152132816	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1043931017	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	78	379	0	ENST00000262189.6:c.56C>T	p.Pro19Leu	p.P19L	ENST00000262189	NM_170606.2	19	cCc/cTc	1/59	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		379	324	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577530	64577530	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	121	419	0	ENST00000312049.6:c.52G>T	p.Asp18Tyr	p.D18Y	ENST00000312049	NM_130799.2	18	Gac/Tac	2/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		419	443	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61306507	61306507	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	80	330	0	ENST00000341074.5:c.680T>A	p.Val227Glu	p.V227E	ENST00000341074	NM_002974.2	227	gTa/gAa	7/8	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		330	333	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946385	2946385	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	99	385	0	ENST00000396946.4:c.3352G>T	p.Ala1118Ser	p.A1118S	ENST00000396946	NM_032415.4	1118	Gcc/Tcc	25/25	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		385	415	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134051	41134051	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	92	500	0	ENST00000379561.5:c.1577G>T	p.Gly526Val	p.G526V	ENST00000379561	NM_002015.3	526	gGa/gTa	2/3	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		500	336	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102094386	102094386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	170	355	0	ENST00000282441.5:c.1066G>A	p.Glu356Lys	p.E356K	ENST00000282441	NM_001130145.2	356	Gag/Aag	7/9	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		355	519	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748080	72748080	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	58	412	1	ENST00000357731.5:c.98del	p.Pro33ArgfsTer16	p.P33Rfs*16	ENST00000357731	NM_173808.2	33	cCg/cg	1/7	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		413	399	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031834	10031834	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs367543120	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	65	435	0	ENST00000330684.3:c.989C>A	p.Pro330Gln	p.P330Q	ENST00000330684	NM_001134407.1	330	cCg/cAg	3/13	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		435	370	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371743	89371743	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	47	394	0	ENST00000301030.4:c.97A>G	p.Lys33Glu	p.K33E	ENST00000301030	NM_001256183.1	33	Aaa/Gaa	4/13	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		394	392	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771151	161771151	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	73	345	0	ENST00000366898.1:c.1378del	p.Asp460ThrfsTer181	p.D460Tfs*181	ENST00000366898	NM_004562.2	460	Gac/ac	12/12	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		345	309	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652314	36652314	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	76	379	0	ENST00000244741.5:c.436A>T	p.Ser146Cys	p.S146C	ENST00000244741	NM_000389.4	146	Agc/Tgc	2/3	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		379	427	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70005639	70005639	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs763119975	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	79	338	0	ENST00000394351.3:c.668G>T	p.Arg223Leu	p.R223L	ENST00000394351	NM_000248.3	223	cGc/cTc	7/9	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		338	366	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225567	225567	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	43	218	0	ENST00000264932.6:c.346G>T	p.Glu116Ter	p.E116*	ENST00000264932	NM_004168.2	116	Gag/Tag	4/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		218	329	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61324581	61324581	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	66	474	0	ENST00000283752.5:c.535G>T	p.Ala179Ser	p.A179S	ENST00000283752	NM_006919.2	179	Gca/Tca	6/8	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		474	451	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713223	43713223	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	56	425	0	ENST00000382044.4:c.4250G>T	p.Arg1417Ile	p.R1417I	ENST00000382044	NM_001141980.1	1417	aGa/aTa	20/28	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		425	418	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661844	227661844	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	60	448	0	ENST00000305123.5:c.1611G>T	p.Gln537His	p.Q537H	ENST00000305123	NM_005544.2	537	caG/caT	1/2	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		448	470	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392186	81392186	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	60	278	0	ENST00000222390.5:c.91G>T	p.Gly31Ter	p.G31*	ENST00000222390	NM_000601.4	31	Gga/Tga	2/18	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		278	299	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841427	156841427	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	54	460	0	ENST00000524377.1:c.730C>A	p.Leu244Met	p.L244M	ENST00000524377	NM_002529.3	244	Ctg/Atg	7/17	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		460	598	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261332	16261332	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	39	497	0	ENST00000375759.3:c.8597C>T	p.Pro2866Leu	p.P2866L	ENST00000375759	NM_015001.2	2866	cCt/cTt	11/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		497	579	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517997	8517997	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs751194677	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	57	424	0	ENST00000356435.5:c.1394A>G	p.Asn465Ser	p.N465S	ENST00000356435		465	aAc/aGc	10/35	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		424	309	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653216	206653216	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553386506	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	90	495	1	ENST00000367120.3:c.1187C>T	p.Ala396Val	p.A396V	ENST00000367120	NM_014002.3	396	gCt/gTt	11/22	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		496	535	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174927	56174927	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	49	404	0	ENST00000399503.3:c.2086A>T	p.Ser696Cys	p.S696C	ENST00000399503	NM_005921.1	696	Agc/Tgc	11/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		404	503	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790180	40790180	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	24	386	0	ENST00000373198.4:c.2551G>T	p.Asp851Tyr	p.D851Y	ENST00000373198	NM_133170.3	851	Gat/Tat	18/32	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		386	336	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431217	49431217	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	55	520	0	ENST00000301067.7:c.9922G>T	p.Gly3308Trp	p.G3308W	ENST00000301067	NM_003482.3	3308	Ggg/Tgg	34/54	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		520	448	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793266	242793266	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	33	452	0	ENST00000334409.5:c.811C>A	p.Pro271Thr	p.P271T	ENST00000334409	NM_005018.2	271	Cct/Act	5/5	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		452	404	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857025	9857025	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	58	330	0	ENST00000330684.3:c.4376G>C	p.Ser1459Thr	p.S1459T	ENST00000330684	NM_001134407.1	1459	aGt/aCt	13/13	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		330	344	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441818	49441818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	59	408	0	ENST00000301067.7:c.4166G>A	p.Gly1389Glu	p.G1389E	ENST00000301067	NM_003482.3	1389	gGg/gAg	14/54	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		408	409	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121792	2121792	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1555505954	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	36	437	0	ENST00000219476.3:c.1954G>T	p.Glu652Ter	p.E652*	ENST00000219476	NM_000548.3	652	Gag/Tag	19/42	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		437	282	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876621	59876621	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	123	333	0	ENST00000259008.2:c.1180G>T	p.Glu394Ter	p.E394*	ENST00000259008	NM_032043.2	394	Gaa/Taa	9/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		333	466	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508602	38508602	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	64	372	0	ENST00000254066.5:c.650G>C	p.Arg217Pro	p.R217P	ENST00000254066	NM_000964.3	217	cGt/cCt	6/9	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		372	428	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979288	93979288	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	70	425	0	ENST00000369303.4:c.1540C>A	p.Gln514Lys	p.Q514K	ENST00000369303	NM_004440.3	514	Cag/Aag	7/17	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		425	327	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170895	56170895	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	44	383	0	ENST00000399503.3:c.1723A>G	p.Arg575Gly	p.R575G	ENST00000399503	NM_005921.1	575	Aga/Gga	10/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		383	550	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021808	246021808	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	76	392	0	ENST00000388985.4:c.1066G>T	p.Glu356Ter	p.E356*	ENST00000388985		356	Gag/Tag	10/12	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		392	318	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527328	187527328	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	51	387	0	ENST00000441802.2:c.10246G>C	p.Gly3416Arg	p.G3416R	ENST00000441802	NM_005245.3	3416	Ggc/Cgc	17/27	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		387	425	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678017	117678017	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	55	385	0	ENST00000368508.3:c.3916A>T	p.Ser1306Cys	p.S1306C	ENST00000368508	NM_002944.2	1306	Agt/Tgt	25/43	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		385	359	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784012	120784012	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	61	491	0	ENST00000257552.2:c.973C>G	p.Gln325Glu	p.Q325E	ENST00000257552	NM_002442.3	325	Cag/Gag	13/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		491	397	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143468	108143468	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	147	366	0	ENST00000278616.4:c.3175del	p.Ala1059ProfsTer5	p.A1059Pfs*5	ENST00000278616	NM_000051.3	1058	tGg/tg	22/63	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		366	473	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126416	5126416	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	99	379	0	ENST00000381652.3:c.3261A>T	p.Arg1087Ser	p.R1087S	ENST00000381652	NM_004972.3	1087	agA/agT	24/25	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		379	320	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565516	41565516	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	46	306	0	ENST00000263253.7:c.4182C>A	p.Tyr1394Ter	p.Y1394*	ENST00000263253	NM_001429.3	1394	taC/taA	26/31	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		306	337	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540643	187540643	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	105	456	0	ENST00000441802.2:c.7097G>T	p.Gly2366Val	p.G2366V	ENST00000441802	NM_005245.3	2366	gGt/gTt	10/27	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		456	432	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118955	61118955	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	42	449	0	ENST00000295025.8:c.148A>C	p.Ile50Leu	p.I50L	ENST00000295025	NM_002908.2	50	Atc/Ctc	2/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		449	482	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741778	17741778	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	32	397	0	ENST00000250003.3:c.449T>C	p.Leu150Pro	p.L150P	ENST00000250003	NM_002478.4	150	cTg/cCg	1/3	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		397	306	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502233	157502233	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	97	484	0	ENST00000346085.5:c.3266G>C	p.Ser1089Thr	p.S1089T	ENST00000346085	NM_020732.3	1089	aGt/aCt	12/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		484	409	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058477	69058477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768578134	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	108	305	0	ENST00000288368.4:c.4121G>A	p.Arg1374Gln	p.R1374Q	ENST00000288368	NM_024870.2	1374	cGg/cAg	34/40	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		305	413	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39542596	39542596	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	49	346	0	ENST00000262039.4:c.400G>T	p.Gly134Cys	p.G134C	ENST00000262039	NM_002647.2	134	Ggc/Tgc	3/25	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		346	354	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679541	86679541	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	34	260	0	ENST00000274376.6:c.2702T>G	p.Phe901Cys	p.F901C	ENST00000274376	NM_002890.2	901	tTt/tGt	21/25	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		260	270	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161284199	161284199	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	41	323	0	ENST00000367975.2:c.4G>T	p.Ala2Ser	p.A2S	ENST00000367975	NM_003001.3	2	Gct/Tct	1/6	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		323	487	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390168	89390168	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	110	444	0	ENST00000336596.2:c.917G>C	p.Cys306Ser	p.C306S	ENST00000336596	NM_005233.5	306	tGt/tCt	4/17	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		444	488	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13949316	13949316	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	48	360	0	ENST00000405192.2:c.812T>A	p.Phe271Tyr	p.F271Y	ENST00000405192	NM_001163147.1	271	tTt/tAt	9/12	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		360	416	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2054676	2054676	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	94	400	0	ENST00000349721.2:c.1126G>T	p.Ala376Ser	p.A376S	ENST00000349721	NM_003070.3	376	Gca/Tca	6/34	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		400	369	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907636	76907636	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	58	446	0	ENST00000373344.5:c.4525G>A	p.Glu1509Lys	p.E1509K	ENST00000373344	NM_000489.3	1509	Gag/Aag	15/35	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		446	409	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518073	69518073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	54	382	0	ENST00000294312.3:c.292G>A	p.Val98Met	p.V98M	ENST00000294312	NM_005117.2	98	Gtg/Atg	2/3	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		382	434	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263177	115263177	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	52	350	0	ENST00000438362.2:c.2173G>T	p.Glu725Ter	p.E725*	ENST00000438362	NM_001242891.1	725	Gaa/Taa	17/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		350	364	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325095	123325095	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	60	494	0	ENST00000358487.5:c.233A>T	p.His78Leu	p.H78L	ENST00000358487	NM_000141.4	78	cAc/cTc	3/18	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		494	450	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751945	57751945	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	40	389	0	ENST00000274289.3:c.1292G>C	p.Gly431Ala	p.G431A	ENST00000274289	NM_006622.3	431	gGa/gCa	10/14	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		389	493	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006819	62006819	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	87	441	0	ENST00000392795.3:c.569G>T	p.Gly190Val	p.G190V	ENST00000392795	NM_001039933.1	190	gGc/gTc	5/6	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		441	444	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231470	46231470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1273463290	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	91	344	0	ENST00000334344.6:c.1310C>T	p.Ala437Val	p.A437V	ENST00000334344	NM_152641.2	437	gCa/gTa	10/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		344	342	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117378	115117378	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066212-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	47	446	0	ENST00000257566.3:c.796A>G	p.Ser266Gly	p.S266G	ENST00000257566	NM_016569.3	266	Agt/Ggt	4/8	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		446	441	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0066462-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	101	486	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		486	442	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350062	81350062	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs759145490	NA	P-0066462-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	125	289	0	ENST00000222390.5:c.1270C>T	p.Arg424Cys	p.R424C	ENST00000222390	NM_000601.4	424	Cgt/Tgt	10/18	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		289	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574005	7574005	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066462-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	178	492	0	ENST00000269305.4:c.1022T>G	p.Phe341Cys	p.F341C	ENST00000269305	NM_001126112.2	341	tTc/tGc	10/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		492	406	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662461	227662461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1172214075	NA	P-0066462-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	94	567	0	ENST00000305123.5:c.994G>A	p.Gly332Ser	p.G332S	ENST00000305123	NM_005544.2	332	Ggc/Agc	1/2	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		567	451	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242481	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAA	AATTAAGAGAAGCAA	TTC	rs727503016	NA	P-0066462-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	119	378	0	ENST00000275493.2:c.2237_2251delinsTTC	p.Glu746_Thr751delinsValPro	p.E746_T751delinsVP	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAAca/gTTCca	19/28	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		378	530	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181296	123181296	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066564-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	195	343	0	ENST00000218089.9:c.760A>G	p.Lys254Glu	p.K254E	ENST00000218089	NM_001042749.1	254	Aaa/Gaa	9/35	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		343	407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578555	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGTAC	AGTAC	TG	novel	NA	P-0066564-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	30	428	2	ENST00000269305.4:c.376-1_379delinsCA		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		430	538	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142967	47142967	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066631-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	130	325	0	ENST00000409792.3:c.4996T>C	p.Tyr1666His	p.Y1666H	ENST00000409792	NM_014159.6	1666	Tat/Cat	8/21	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		325	304	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593607	+	protein_altering_variant	In_Frame_Del	DEL	AGTGGAA	AGTGGAA	C	novel	NA	P-0066631-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	154	447	0	ENST00000288135.5:c.1667_1673delinsC	p.Gln556_Lys558delinsPro	p.Q556_K558delinsP	ENST00000288135	NM_000222.2	556	cAGTGGAAg/cCg	11/21	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		447	341	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0066883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	224	857	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		857	950	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0066883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	170	470	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		470	692	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207203	1207203	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs1131690950	NA	P-0066883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	241	544	0	ENST00000326873.7:c.290+1G>C		p.X97_splice	ENST00000326873	NM_000455.4	97			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		544	799	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610479	10610479	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	269	634	0	ENST00000171111.5:c.231T>G	p.Cys77Trp	p.C77W	ENST00000171111	NM_203500.1	77	tgT/tgG	2/6	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		634	909	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502688	149502688	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	199	763	0	ENST00000261799.4:c.2100C>A	p.Phe700Leu	p.F700L	ENST00000261799	NM_002609.3	700	ttC/ttA	15/23	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		763	831	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32438049	32438049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	68	540	0	ENST00000332351.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000332351	NM_024426.4	330	Gaa/Aaa	5/10	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		540	750	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066995-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	107	387	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		387	296	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587781525	NA	P-0066995-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	222	514	9	ENST00000269305.4:c.842A>G	p.Asp281Gly	p.D281G	ENST00000269305	NM_001126112.2	281	gAc/gGc	8/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		523	443	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976890	18976890	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066995-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	110	500	6	ENST00000262803.5:c.3275A>G	p.Asp1092Gly	p.D1092G	ENST00000262803	NM_002911.3	1092	gAc/gGc	23/24	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		506	437	SUCCESS
ALB	213	MSKCC	GRCh37	4	74276072	74276073	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0066995-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	177	390	2	ENST00000295897.4:c.662_663del	p.Arg221ThrfsTer30	p.R221Tfs*30	ENST00000295897	NM_000477.5	220	cAG/c	6/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		392	458	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211033	36211034	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0066995-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	200	506	12	ENST00000222270.7:c.785dup	p.Thr263AspfsTer71	p.T263Dfs*71	ENST00000222270	NM_014727.1	262	cag/cAag	3/37	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		518	623	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456434	89456434	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066995-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	94	408	7	ENST00000336596.2:c.1610G>A	p.Gly537Asp	p.G537D	ENST00000336596	NM_005233.5	537	gGt/gAt	8/17	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		415	219	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480420	89480420	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066995-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	176	417	10	ENST00000336596.2:c.2257T>A	p.Leu753Met	p.L753M	ENST00000336596	NM_005233.5	753	Ttg/Atg	13/17	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		427	299	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	229	478	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		478	516	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	51	387	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		387	139	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	160	504	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		504	319	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149251	119149251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267606708	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	8	510	0	ENST00000264033.4:c.1259G>A	p.Arg420Gln	p.R420Q	ENST00000264033	NM_005188.3	420	cGa/cAa	9/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		510	384	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100436	8100436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1220437638	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	255	600	0	ENST00000346208.3:c.410C>T	p.Ser137Leu	p.S137L	ENST00000346208		137	tCg/tTg	3/6	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		600	577	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797314	135797314	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	37	536	0	ENST00000298552.3:c.555C>G	p.Tyr185Ter	p.Y185*	ENST00000298552	NM_001162426.1	185	taC/taG	7/23	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		536	234	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440710	56440710	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	227	551	0	ENST00000407977.2:c.508G>T	p.Glu170Ter	p.E170*	ENST00000407977		170	Gag/Tag	5/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		551	453	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637232	176637232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1424984701	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	197	553	0	ENST00000439151.2:c.1832G>A	p.Arg611Gln	p.R611Q	ENST00000439151	NM_022455.4	611	cGa/cAa	5/23	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		553	441	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797300	135797300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs118203401	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	21	534	0	ENST00000298552.3:c.569del	p.Arg190ProfsTer20	p.R190Pfs*20	ENST00000298552	NM_001162426.1	190	cGc/cc	7/23	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		534	220	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883587	37883587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	202	584	0	ENST00000269571.5:c.3199G>A	p.Glu1067Lys	p.E1067K	ENST00000269571		1067	Gaa/Aaa	26/27	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		584	421	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213947	2213947	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	216	551	0	ENST00000326181.6:c.26A>G	p.Tyr9Cys	p.Y9C	ENST00000326181	NM_032271.2	9	tAc/tGc	2/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		551	387	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001099	150001099	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	122	452	0	ENST00000253339.5:c.2505G>C	p.Leu835Phe	p.L835F	ENST00000253339		835	ttG/ttC	4/7	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		452	268	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748923	43748923	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774605101	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	200	600	0	ENST00000382044.4:c.1883C>T	p.Ser628Leu	p.S628L	ENST00000382044	NM_001141980.1	628	tCg/tTg	12/28	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		600	409	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377246	118377246	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	192	559	2	ENST00000534358.1:c.10639C>T	p.Gln3547Ter	p.Q3547*	ENST00000534358	NM_005933.3	3547	Cag/Tag	27/36	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		561	421	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287199	33287199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs981409816	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	183	599	0	ENST00000374542.5:c.1898G>A	p.Arg633Gln	p.R633Q	ENST00000374542	NM_001141970.1	633	cGg/cAg	6/8	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		599	445	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994388	25994388	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	425	470	0	ENST00000435504.4:c.425C>G	p.Ser142Ter	p.S142*	ENST00000435504		142	tCa/tGa	6/13	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		470	450	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544224	86544224	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	149	509	0	ENST00000262426.4:c.49G>A	p.Gly17Ser	p.G17S	ENST00000262426	NM_001451.2	17	Ggc/Agc	1/2	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		509	279	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417760	138417760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	126	431	0	ENST00000289153.2:c.1759G>A	p.Asp587Asn	p.D587N	ENST00000289153	NM_006219.2	587	Gat/Aat	11/22	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		431	314	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109797	115109797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	227	554	0	ENST00000257566.3:c.2081G>A	p.Ser694Asn	p.S694N	ENST00000257566	NM_016569.3	694	aGc/aAc	8/8	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		554	487	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831525	72831525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	122	507	0	ENST00000268489.5:c.5056G>A	p.Glu1686Lys	p.E1686K	ENST00000268489	NM_006885.3	1686	Gag/Aag	9/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		507	279	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38153408	38153408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	158	428	2	ENST00000317025.8:c.2821G>A	p.Glu941Lys	p.E941K	ENST00000317025	NM_023034.1	941	Gaa/Aaa	16/24	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		430	342	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255150	16255150	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	245	645	0	ENST00000375759.3:c.2415G>C	p.Glu805Asp	p.E805D	ENST00000375759	NM_015001.2	805	gaG/gaC	11/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		645	506	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376944	118376944	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	197	581	0	ENST00000534358.1:c.10337C>A	p.Ser3446Tyr	p.S3446Y	ENST00000534358	NM_005933.3	3446	tCt/tAt	27/36	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		581	416	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376657	8376657	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	163	453	0	ENST00000356435.5:c.4456G>C	p.Asp1486His	p.D1486H	ENST00000356435		1486	Gat/Cat	27/35	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		453	189	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293953	1293953	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	161	544	0	ENST00000310581.5:c.1048C>G	p.Leu350Val	p.L350V	ENST00000310581	NM_198253.2	350	Ctg/Gtg	2/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		544	313	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679383	29679383	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	256	467	0	ENST00000356175.3:c.7503G>C	p.Met2501Ile	p.M2501I	ENST00000356175	NM_000267.3	2501	atG/atC	50/57	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		467	514	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305400	65305400	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	171	589	0	ENST00000342505.4:c.2728C>G	p.Leu910Val	p.L910V	ENST00000342505	NM_002227.2	910	Ctg/Gtg	20/25	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		589	356	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56859036	56859036	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	127	319	0	ENST00000519728.1:c.162G>C	p.Gln54His	p.Q54H	ENST00000519728	NM_002350.3	54	caG/caC	3/13	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		319	250	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859807	117859807	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1461696690	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	135	451	0	ENST00000297338.2:c.1828G>C	p.Glu610Gln	p.E610Q	ENST00000297338	NM_006265.2	610	Gag/Cag	14/14	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		451	278	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786102	3786102	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1555472931	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	150	479	0	ENST00000262367.5:c.4663G>T	p.Glu1555Ter	p.E1555*	ENST00000262367	NM_004380.2	1555	Gaa/Taa	28/31	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		479	319	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737904	145737904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35070885	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	179	572	0	ENST00000428558.2:c.2926G>A	p.Glu976Lys	p.E976K	ENST00000428558	NM_004260.3	976	Gag/Aag	18/22	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		572	374	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279744	46279744	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	168	486	0	ENST00000371998.3:c.3670C>G	p.Gln1224Glu	p.Q1224E	ENST00000371998		1224	Caa/Gaa	20/23	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		486	404	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797344	135797351	+	frameshift_variant	Frame_Shift_Del	DEL	GACTTCCG	GACTTCCG	-	novel	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	66	539	0	ENST00000298552.3:c.518_525del	p.Ala173ValfsTer42	p.A173Vfs*42	ENST00000298552	NM_001162426.1	173	gCGGAAGTC/g	7/23	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		539	213	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873413	151873413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	170	506	0	ENST00000262189.6:c.9125G>A	p.Arg3042Lys	p.R3042K	ENST00000262189	NM_170606.2	3042	aGa/aAa	38/59	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		506	368	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376953	118376953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	199	568	0	ENST00000534358.1:c.10346C>T	p.Ala3449Val	p.A3449V	ENST00000534358	NM_005933.3	3449	gCa/gTa	27/36	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		568	408	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31486597	31486597	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	169	452	0	ENST00000344624.3:c.1914+1G>A		p.X638_splice	ENST00000344624		638			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		452	320	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965432	15965432	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	149	504	0	ENST00000268712.3:c.5374C>G	p.Gln1792Glu	p.Q1792E	ENST00000268712	NM_006311.3	1792	Cag/Gag	36/46	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		504	298	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051622	30051622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	205	436	0	ENST00000338641.4:c.556G>A	p.Glu186Lys	p.E186K	ENST00000338641	NM_000268.3	186	Gag/Aag	6/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		436	411	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100081	11100081	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	210	501	0	ENST00000358026.2:c.1207G>T	p.Glu403Ter	p.E403*	ENST00000358026	NM_001128849.1	403	Gag/Tag	7/36	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		501	443	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260633	1260633	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	163	546	0	ENST00000310581.5:c.2926G>C	p.Gly976Arg	p.G976R	ENST00000310581	NM_198253.2	976	Ggg/Cgg	12/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		546	371	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	104	387	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		387	256	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0066997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	312	489	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		489	544	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0066997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	195	463	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		463	454	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788648	3788648	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	209	376	0	ENST00000262367.5:c.4306A>C	p.Ser1436Arg	p.S1436R	ENST00000262367	NM_004380.2	1436	Agt/Cgt	26/31	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		376	479	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923755	72923755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747650481	NA	P-0066997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	199	435	0	ENST00000268489.5:c.3323G>A	p.Arg1108His	p.R1108H	ENST00000268489	NM_006885.3	1108	cGc/cAc	4/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		435	478	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899258	78899258	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	488	495	0	ENST00000306801.3:c.2897A>G	p.Tyr966Cys	p.Y966C	ENST00000306801	NM_020761.2	966	tAt/tGt	24/34	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		495	794	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806094	1806094	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	193	459	0	ENST00000260795.2:c.1113T>A	p.Ser371Arg	p.S371R	ENST00000260795		371	agT/agA	8/17	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		459	462	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535448	66535448	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	110	354	0	ENST00000273854.3:c.13G>T	p.Gly5Trp	p.G5W	ENST00000273854	NM_004439.5	5	Ggg/Tgg	1/18	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		354	284	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47503880	47503880	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	201	400	0	ENST00000404338.3:c.4437del	p.Thr1480ProfsTer319	p.T1480Pfs*319	ENST00000404338	NM_004491.4	1479	Ccc/cc	6/6	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		400	470	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509800	106509800	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	167	505	0	ENST00000359195.3:c.1794G>A	p.Trp598Ter	p.W598*	ENST00000359195	NM_002649.2	598	tgG/tgA	2/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		505	402	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950056	44950058	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0066997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	92	396	0	ENST00000377967.4:c.3825_3827del	p.Trp1275_Asn1276delinsCys	p.W1275_N1276delinsC	ENST00000377967	NM_021140.2	1275	tgGAAt/tgt	26/29	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		396	151	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039440	47039440	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0066997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	168	433	0	ENST00000377604.3:c.1062+1G>A		p.X354_splice	ENST00000377604	NM_001204468.1	354			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		433	228	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211881	123211881	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	198	672	0	ENST00000218089.9:c.2748del	p.Lys917ArgfsTer14	p.K917Rfs*14	ENST00000218089	NM_001042749.1	916	gcT/gc	27/35	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		672	260	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0067000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1255	594	464	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		464	1849	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604572	43604572	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1848	267	468	0	ENST00000355710.3:c.1157C>A	p.Ala386Glu	p.A386E	ENST00000355710	NM_020975.4	386	gCg/gAg	6/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		468	2115	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913233	NA	P-0067000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2326	905	541	1	ENST00000451590.1:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000451590	NM_001130442.1	61	cAg/cTg	3/5	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		542	3231	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559168	29559168	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	171	223	0	ENST00000356175.3:c.3275G>C	p.Gly1092Ala	p.G1092A	ENST00000356175	NM_000267.3	1092	gGt/gCt	25/57	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		223	1257	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741238	40741238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1319165364	NA	P-0067000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	807	419	0	ENST00000392038.2:c.1195G>A	p.Asp399Asn	p.D399N	ENST00000392038	NM_001626.4	399	Gat/Aat	12/14	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		419	1868	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285863	39285863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1460	220	340	0	ENST00000402219.2:c.296G>A	p.Arg99Gln	p.R99Q	ENST00000402219	NM_005633.3	99	cGa/cAa	3/23	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		340	1680	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699379	117699379	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1772	598	425	0	ENST00000369458.3:c.262G>C	p.Asp88His	p.D88H	ENST00000369458	NM_024626.3	88	Gat/Cat	3/6	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		425	2370	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663338	67663338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	580	422	0	ENST00000264010.4:c.1739C>T	p.Pro580Leu	p.P580L	ENST00000264010	NM_006565.3	580	cCa/cTa	10/12	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		422	1726	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667854	37667854	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1843	269	378	0	ENST00000447079.4:c.2739C>A	p.Tyr913Ter	p.Y913*	ENST00000447079	NM_015083.1	913	taC/taA	8/14	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		378	2112	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641492	47641492	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1296650088	NA	P-0067000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1181	549	316	0	ENST00000233146.2:c.877A>G	p.Thr293Ala	p.T293A	ENST00000233146	NM_000251.2	293	Act/Gct	5/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		316	1730	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530198	212530199	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0067000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1595	662	429	0	ENST00000342788.4:c.1720_1721del	p.Pro574Ter	p.P574*	ENST00000342788	NM_005235.2	574	CCt/t	15/28	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		429	2257	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733222	40733222	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1474	539	438	0	ENST00000373198.4:c.3584A>G	p.Lys1195Arg	p.K1195R	ENST00000373198	NM_133170.3	1195	aAa/aGa	26/32	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		438	2013	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445050	89445052	+	missense_variant	Missense_Mutation	TNP	GGC	GGC	TGA	novel	NA	P-0067000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1612	279	468	0	ENST00000336596.2:c.1370_1372delinsTGA	p.Trp457_Gln458delinsLeuLys	p.W457_Q458delinsLK	ENST00000336596	NM_005233.5	457	tGGCaa/tTGAaa	6/17	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		468	1891	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445052	89445052	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1311	564	461	0	ENST00000336596.2:c.1372C>A	p.Gln458Lys	p.Q458K	ENST00000336596	NM_005233.5	458	Caa/Aaa	6/17	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		461	1875	SUCCESS
ALB	213	MSKCC	GRCh37	4	74274452	74274452	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs77238412	NA	P-0067000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1651	588	456	0	ENST00000295897.4:c.412C>T	p.Arg138Ter	p.R138*	ENST00000295897	NM_000477.5	138	Cga/Tga	4/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		456	2239	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332815	153332815	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1727	578	458	0	ENST00000281708.4:c.141A>T	p.Gln47His	p.Q47H	ENST00000281708	NM_033632.3	47	caA/caT	2/12	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		458	2305	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359919	87359919	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1711	305	378	0	ENST00000277120.3:c.1227C>G	p.Asp409Glu	p.D409E	ENST00000277120		409	gaC/gaG	11/19	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		378	2016	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424404	47424404	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1641	297	502	0	ENST00000377045.4:c.324C>G	p.Ser108Arg	p.S108R	ENST00000377045	NM_001654.4	108	agC/agG	5/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		502	1938	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341475	70341475	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1487	311	414	0	ENST00000374080.3:c.910A>G	p.Arg304Gly	p.R304G	ENST00000374080		304	Aga/Gga	7/45	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		414	1798	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939051	76939051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1445	266	395	1	ENST00000373344.5:c.1697C>T	p.Ser566Phe	p.S566F	ENST00000373344	NM_000489.3	566	tCt/tTt	9/35	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		396	1711	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224795	123224795	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1344	205	352	0	ENST00000218089.9:c.3559A>T	p.Thr1187Ser	p.T1187S	ENST00000218089	NM_001042749.1	1187	Act/Tct	32/35	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		352	1549	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579349	7579349	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1567555667	NA	P-0067001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	32	568	0	ENST00000269305.4:c.338T>G	p.Phe113Cys	p.F113C	ENST00000269305	NM_001126112.2	113	tTc/tGc	4/11	1	2	FACETS	0.592	0.479	0.721	0.592	0.479	0.721	SUBCLONAL	1	TRUE	1	0.15	2		568	721	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729094	66729099	+	inframe_deletion	In_Frame_Del	DEL	TGGAGA	TGGAGA	-	novel	NA	P-0067001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	39	550	0	ENST00000307102.5:c.303_308del	p.Glu102_Ile103del	p.E102_I103del	ENST00000307102	NM_002755.3	101	cTGGAGAtc/ctc	3/11	1	2	FACETS	0.807	0.668	0.964	0.807	0.668	0.964	CLONAL	1	TRUE	1	0.15	2		550	644	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878916	151878916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	40	617	0	ENST00000262189.6:c.6029C>T	p.Pro2010Leu	p.P2010L	ENST00000262189	NM_170606.2	2010	cCa/cTa	36/59	1	2	FACETS	0.727	0.602	0.866	0.727	0.602	0.866	SUBCLONAL	1	TRUE	1	0.15	2		617	734	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0067002-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	56	288	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		288	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572960	7572960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067002-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	61	445	0	ENST00000269305.4:c.1149del	p.Met384CysfsTer38	p.M384Cfs*38	ENST00000269305	NM_001126112.2	383	ctC/ct	11/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		445	309	SUCCESS
REST	5978	MSKCC	GRCh37	4	57797027	57797027	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067002-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	32	647	0	ENST00000309042.7:c.2003C>T	p.Pro668Leu	p.P668L	ENST00000309042	NM_005612.4	668	cCt/cTt	4/4	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		647	366	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974718	21974718	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067002-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	38	498	0	ENST00000304494.5:c.109del	p.Leu37CysfsTer16	p.L37Cfs*16	ENST00000304494	NM_000077.4	37	Ctg/tg	1/3	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		498	208	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0067003-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	31	500	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		500	385	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55962422	55962422	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067003-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	19	319	0	ENST00000263923.4:c.2702T>A	p.Leu901His	p.L901H	ENST00000263923	NM_002253.2	901	cTt/cAt	19/30	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		319	154	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991695	25991699	+	frameshift_variant	Frame_Shift_Del	DEL	TGCAT	TGCAT	-	novel	NA	P-0067003-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	15	392	0	ENST00000435504.4:c.543_547del	p.Cys182AlafsTer21	p.C182Afs*21	ENST00000435504		181	caATGCAgg/cagg	7/13	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		392	253	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0067005-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	118	586	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.257833416905547	2	FACETS	1	0.979	1	0.651	0.589	0.715	CLONAL	1	TRUE	0	0.330254239332418	2		586	549	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156935	106156936	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs763386429	NA	P-0067005-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	32	508	0	ENST00000380013.4:c.1842dup	p.Leu615AlafsTer23	p.L615Afs*23	ENST00000380013	NM_001127208.2	612	-/G	3/11	0.231368975701724	1	FACETS	0.311	0.252	0.378	0.311	0.252	0.378	SUBCLONAL	1	TRUE	0	0.330254239332418	1		508	520	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644818	67644818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773609766	NA	P-0067005-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	56	523	2	ENST00000264010.4:c.83G>A	p.Arg28His	p.R28H	ENST00000264010	NM_006565.3	28	cGc/cAc	3/12	0.197385068667939	3	FACETS	0.588	0.503	0.681	0.294	0.251	0.341	INDETERMINATE	1	TRUE	1	0.330254239332418	3		525	672	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022759	12022759	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067005-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	34	578	0	ENST00000396373.4:c.865C>A	p.Gln289Lys	p.Q289K	ENST00000396373	NM_001987.4	289	Cag/Aag	5/8	1	2	FACETS	0.331	0.27	0.401	0.331	0.27	0.401	SUBCLONAL	1	TRUE	1	0.330254239332418	2		578	622	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953221	81953221	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067005-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	48	408	0	ENST00000359376.3:c.2187G>C	p.Met729Ile	p.M729I	ENST00000359376	NM_002661.3	729	atG/atC	20/33	0.330254239332418	1	FACETS	0.567	0.48	0.663	0.567	0.48	0.663	SUBCLONAL	1	TRUE	0	0.330254239332418	1		408	428	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805917	32805917	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067005-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	38	499	1	ENST00000374899.4:c.94C>A	p.Pro32Thr	p.P32T	ENST00000374899	NM_018833.2	32	Cct/Act	2/12	1	2	FACETS	0.445	0.367	0.532	0.445	0.367	0.532	SUBCLONAL	1	TRUE	1	0.330254239332418	2		500	517	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416252	416252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1049074792	NA	P-0067005-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	34	421	0	ENST00000399788.2:c.3934C>T	p.His1312Tyr	p.H1312Y	ENST00000399788	NM_001042603.1	1312	Cac/Tac	24/28	1	2	FACETS	0.423	0.345	0.511	0.423	0.345	0.511	SUBCLONAL	1	TRUE	1	0.330254239332418	2		421	487	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069638	69069638	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067005-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	39	346	0	ENST00000288368.4:c.4313T>C	p.Leu1438Pro	p.L1438P	ENST00000288368	NM_024870.2	1438	cTg/cCg	35/40	0.264423285870049	3	FACETS	0.896	0.746	1	0.448	0.373	0.532	CLONAL	1	TRUE	1	0.330254239332418	3		346	307	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11172463	11172463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776222414	NA	P-0067005-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	34	375	0	ENST00000358026.2:c.5011C>T	p.Arg1671Cys	p.R1671C	ENST00000358026	NM_001128849.1	1671	Cgc/Tgc	36/36	0.132370937884019	3	FACETS	0.501	0.409	0.605	0.25	0.204	0.303	INDETERMINATE	1	TRUE	1	0.330254239332418	3		375	479	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524153	18524153	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067005-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	67	398	0	ENST00000266497.5:c.1665A>C	p.Glu555Asp	p.E555D	ENST00000266497		555	gaA/gaC	11/31	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.330254239332418	2		398	364	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0067040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	133	485	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		485	489	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268144	153268144	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs920052554	NA	P-0067040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	72	455	0	ENST00000281708.4:c.664C>T	p.Arg222Ter	p.R222*	ENST00000281708	NM_033632.3	222	Cga/Tga	4/12	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		455	498	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465453	99465453	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs70958396	NA	P-0067040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	69	409	1	ENST00000268035.6:c.2278G>A	p.Ala760Thr	p.A760T	ENST00000268035	NM_000875.3	760	Gca/Aca	11/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		410	539	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434555	140434555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	57	299	0	ENST00000288602.6:c.2143G>A	p.Glu715Lys	p.E715K	ENST00000288602	NM_004333.4	715	Gag/Aag	18/18	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		299	423	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937354	32937355	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs397507952	NA	P-0067040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	165	382	0	ENST00000380152.3:c.8021dup	p.Ile2675AspfsTer6	p.I2675Dfs*6	ENST00000380152		2672	ata/atAa	18/27	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		382	631	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958789	55958789	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	42	287	1	ENST00000263923.4:c.3064C>T	p.Arg1022Ter	p.R1022*	ENST00000263923	NM_002253.2	1022	Cga/Tga	22/30	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		288	399	SUCCESS
APC	324	MSKCC	GRCh37	5	112175761	112175762	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0067040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	49	435	0	ENST00000257430.4:c.4472_4473del	p.Phe1491CysfsTer22	p.F1491Cfs*22	ENST00000257430	NM_000038.5	1490	caTTtt/catt	16/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		435	569	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256572	115256572	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	38	313	0	ENST00000369535.4:c.139G>C	p.Asp47His	p.D47H	ENST00000369535	NM_002524.4	47	Gat/Cat	3/7	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		313	368	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912199	114912199	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0067040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	112	263	0	ENST00000543371.1:c.1269T>G	p.Tyr423Ter	p.Y423*	ENST00000543371	NM_001198531.1	423	taT/taG	11/14	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		263	430	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986727	36986727	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	53	452	0	ENST00000354822.5:c.962A>G	p.Gln321Arg	p.Q321R	ENST00000354822	NM_001079668.2	321	cAg/cGg	3/3	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		452	339	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190433	32190433	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	60	484	0	ENST00000375023.3:c.306G>C	p.Leu102Phe	p.L102F	ENST00000375023	NM_004557.3	102	ttG/ttC	3/30	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		484	586	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912812	100912812	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	23	402	0	ENST00000325455.5:c.2510G>T	p.Ser837Ile	p.S837I	ENST00000325455	NM_001202474.3	837	aGt/aTt	7/8	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		402	457	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142963	30142963	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770625956	NA	P-0067040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	67	473	1	ENST00000389048.3:c.563G>A	p.Arg188His	p.R188H	ENST00000389048	NM_004304.4	188	cGc/cAc	1/29	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		474	428	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0067041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	246	288	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		288	356	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142099	108142099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555085210	NA	P-0067077-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	231	350	0	ENST00000278616.4:c.3043C>T	p.Gln1015Ter	p.Q1015*	ENST00000278616	NM_000051.3	1015	Caa/Taa	20/63	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		350	446	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127808	64127808	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067077-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	80	277	0	ENST00000334205.4:c.301C>G	p.Leu101Val	p.L101V	ENST00000334205	NM_003942.2	101	Ctg/Gtg	3/17	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		277	380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	288	505	0	ENST00000269305.4:c.527G>C	p.Cys176Ser	p.C176S	ENST00000269305	NM_001126112.2	176	tGc/tCc	5/11	0.346637648563275	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	3	TRUE	0	0.445388881688439	3		505	522	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89478259	89478259	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	45	302	0	ENST00000336596.2:c.2078A>C	p.Lys693Thr	p.K693T	ENST00000336596	NM_005233.5	693	aAg/aCg	12/17	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.445388881688439	2		302	175	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922796	44922796	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1569534053	NA	P-0067079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	37	215	0	ENST00000377967.4:c.1657G>A	p.Val553Ile	p.V553I	ENST00000377967	NM_021140.2	553	Gtc/Atc	16/29	0.417428815346346	2	FACETS	0.538	0.445	0.641			1	SUBCLONAL	1	TRUE	NA	0.445388881688439	2		215	309	SUCCESS
APC	324	MSKCC	GRCh37	5	112175535	112175535	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	152	450	0	ENST00000257430.4:c.4244del	p.Ser1415MetfsTer4	p.S1415Mfs*4	ENST00000257430	NM_000038.5	1415	aGt/at	16/16	0.436032358426686	3	FACETS	0.853	0.786	0.922	0.853	0.786	0.922	CLONAL	2	TRUE	1	0.445388881688439	3		450	489	SUCCESS
APC	324	MSKCC	GRCh37	5	112174654	112174655	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	71	473	0	ENST00000257430.4:c.3365dup	p.Asn1122LysfsTer13	p.N1122Kfs*13	ENST00000257430	NM_000038.5	1121	-/A	16/16	0.436032358426686	3	FACETS	0.909	0.796	1	0.454	0.398	0.515	CLONAL	1	TRUE	1	0.445388881688439	3		473	429	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931700	39931700	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	185	171	0	ENST00000378444.4:c.2899G>T	p.Ala967Ser	p.A967S	ENST00000378444	NM_001123385.1	967	Gcc/Tcc	4/15	0.417428815346346	2	FACETS	0.911	0.861	0.96			1	CLONAL	3	TRUE	NA	0.445388881688439	2		171	304	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6222508	6222508	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772030204	NA	P-0067080-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1766	168	433	0	ENST00000252674.7:c.734C>T	p.Pro245Leu	p.P245L	ENST00000252674	NM_005934.3	245	cCa/cTa	6/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		433	1934	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038864	12038864	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067106-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	117	417	0	ENST00000396373.4:c.1157G>C	p.Arg386Thr	p.R386T	ENST00000396373	NM_001987.4	386	aGa/aCa	7/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		417	714	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0067106-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	132	421	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		421	575	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0067106-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	237	532	0	ENST00000397752.3:c.3028+1G>A		p.X1010_splice	ENST00000397752	NM_000245.2	1010			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		532	680	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231475590	231475590	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067106-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	74	321	0	ENST00000295050.7:c.297G>C	p.Leu99Phe	p.L99F	ENST00000295050	NM_032018.5	99	ttG/ttC	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		321	617	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589692	69589692	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067106-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	67	689	0	ENST00000168712.1:c.161C>G	p.Ser54Trp	p.S54W	ENST00000168712	NM_002007.2	54	tCg/tGg	1/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		689	746	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197365	94197365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781646	NA	P-0067106-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	41	352	0	ENST00000323929.3:c.1139G>A	p.Arg380His	p.R380H	ENST00000323929	NM_005591.3	380	cGc/cAc	11/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		352	460	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50784914	50784914	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0067106-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	41	326	0	ENST00000307179.4:c.2251A>T	p.Lys751Ter	p.K751*	ENST00000307179		751	Aaa/Taa	15/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		326	461	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857797	9857797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067106-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	66	536	0	ENST00000330684.3:c.3604G>A	p.Glu1202Lys	p.E1202K	ENST00000330684	NM_001134407.1	1202	Gag/Aag	13/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		536	672	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793436	242793436	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067106-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	61	459	0	ENST00000334409.5:c.641C>T	p.Ser214Leu	p.S214L	ENST00000334409	NM_005018.2	214	tCa/tTa	5/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		459	551	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161880	47161880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067106-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	86	465	0	ENST00000409792.3:c.4246G>A	p.Glu1416Lys	p.E1416K	ENST00000409792	NM_014159.6	1416	Gaa/Aaa	3/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		465	755	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30676066	30676066	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067106-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	60	404	0	ENST00000376406.3:c.2290G>C	p.Glu764Gln	p.E764Q	ENST00000376406	NM_014641.2	764	Gag/Cag	8/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		404	641	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	288	469	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		470	694	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	61	308	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		313	328	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	129	311	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		311	391	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790090	40790090	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	117	384	2	ENST00000373198.4:c.2641del	p.Arg881GlyfsTer20	p.R881Gfs*20	ENST00000373198	NM_133170.3	881	Cgg/gg	18/32	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		386	644	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	152	408	0	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		408	698	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259043	16259043	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	155	398	0	ENST00000375759.3:c.6313del	p.Ala2105LeufsTer33	p.A2105Lfs*33	ENST00000375759	NM_015001.2	2103	aGg/ag	11/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		398	716	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261245	16261246	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	132	371	0	ENST00000375759.3:c.8516dup	p.Ala2840GlyfsTer7	p.A2840Gfs*7	ENST00000375759	NM_015001.2	2837	atc/atCc	11/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		371	687	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092773	27092773	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	131	345	0	ENST00000324856.7:c.2794C>T	p.Gln932Ter	p.Q932*	ENST00000324856	NM_006015.4	932	Caa/Taa	9/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		345	524	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	169	443	1	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		444	671	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239441	123239442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	60	366	0	ENST00000358487.5:c.2395dup	p.Ser799PhefsTer22	p.S799Ffs*22	ENST00000358487	NM_000141.4	799	tct/tTct	18/18	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		366	592	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47594883	47594883	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs756343868	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	144	475	1	ENST00000430070.2:c.1204del	p.Glu402ArgfsTer27	p.E402Rfs*27	ENST00000430070	NM_018095.4	402	Gag/ag	4/4	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		476	659	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201718	67201718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199570304	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	162	511	0	ENST00000312629.5:c.1019G>A	p.Arg340His	p.R340H	ENST00000312629	NM_003952.2	340	cGt/cAt	12/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		511	691	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022634	12022634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144782370	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	175	391	0	ENST00000396373.4:c.740C>T	p.Ala247Val	p.A247V	ENST00000396373	NM_001987.4	247	gCg/gTg	5/8	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		391	798	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230604	46230604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	98	390	0	ENST00000334344.6:c.853C>T	p.Arg285Trp	p.R285W	ENST00000334344	NM_152641.2	285	Cgg/Tgg	8/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		390	546	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420204	49420204	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	126	384	2	ENST00000301067.7:c.15545del	p.Gly5182AlafsTer61	p.G5182Afs*61	ENST00000301067	NM_003482.3	5182	gGc/gc	48/54	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		386	713	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21565435	21565435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1217575272	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	29	437	0	ENST00000382592.4:c.451C>T	p.Arg151Trp	p.R151W	ENST00000382592	NM_014572.2	151	Cgg/Tgg	3/8	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		437	579	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913837	32913837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359507	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	32	352	0	ENST00000380152.3:c.5351del	p.Asn1784ThrfsTer7	p.N1784Tfs*7	ENST00000380152		1782	cAa/ca	11/27	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		352	191	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988308	36988309	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776709	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	107	337	0	ENST00000354822.5:c.344dup	p.Tyr116LeufsTer323	p.Y116Lfs*323	ENST00000354822	NM_001079668.2	115	ggc/ggGc	2/3	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		337	472	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061726	38061726	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	16	395	2	ENST00000250448.2:c.263del	p.Gly88AlafsTer6	p.G88Afs*6	ENST00000250448	NM_004496.3	88	gGc/gc	2/2	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		397	671	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223514	2223514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	175	431	0	ENST00000326181.6:c.1045G>A	p.Glu349Lys	p.E349K	ENST00000326181	NM_032271.2	349	Gag/Aag	11/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		431	743	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032163	10032163	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	26	364	0	ENST00000330684.3:c.660G>T	p.Lys220Asn	p.K220N	ENST00000330684	NM_001134407.1	220	aaG/aaT	3/13	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		364	509	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134383	30134383	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	96	305	0	ENST00000263025.4:c.148G>A	p.Glu50Lys	p.E50K	ENST00000263025	NM_002746.2	50	Gag/Aag	1/9	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		305	461	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821620	72821620	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751386892	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	113	369	0	ENST00000268489.5:c.10555G>A	p.Gly3519Ser	p.G3519S	ENST00000268489	NM_006885.3	3519	Ggt/Agt	10/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		369	595	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	144	731	5	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		736	618	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346424	89346424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1228696930	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	50	378	0	ENST00000301030.4:c.6526G>A	p.Gly2176Ser	p.G2176S	ENST00000301030	NM_001256183.1	2176	Ggt/Agt	9/13	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		378	616	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	147	491	9	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		500	660	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912835	50912835	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146530638	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	139	402	0	ENST00000440232.2:c.2066G>A	p.Arg689Gln	p.R689Q	ENST00000440232	NM_002691.3	689	cGg/cAg	17/27	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		402	582	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149894	99149894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368448330	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	110	336	0	ENST00000074304.5:c.206C>T	p.Ala69Val	p.A69V	ENST00000074304	NM_001134224.1	69	gCg/gTg	5/26	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		336	601	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046242	128046242	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	205	354	0	ENST00000285398.2:c.1021C>T	p.Pro341Ser	p.P341S	ENST00000285398	NM_000122.1	341	Ccc/Tcc	7/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		354	642	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660075	227660075	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462380251	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	260	438	0	ENST00000305123.5:c.3380del	p.Gly1127AlafsTer12	p.G1127Afs*12	ENST00000305123	NM_005544.2	1127	gGc/gc	1/2	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		438	803	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714369	40714369	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs775489787	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	227	377	0	ENST00000373198.4:c.4028G>A	p.Arg1343Gln	p.R1343Q	ENST00000373198	NM_133170.3	1343	cGg/cAg	29/32	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		377	641	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	120	354	2	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		356	539	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723029	49723029	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1225484117	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	86	219	0	ENST00000449682.2:c.1387G>A	p.Ala463Thr	p.A463T	ENST00000449682	NM_020998.3	463	Gct/Act	11/18	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		219	380	SUCCESS
ATR	545	MSKCC	GRCh37	3	142297540	142297540	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	70	290	0	ENST00000350721.4:c.7del	p.Glu3AsnfsTer9	p.E3Nfs*9	ENST00000350721	NM_001184.3	3	Gaa/aa	1/47	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		290	406	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31493321	31493322	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1330233722	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	26	346	2	ENST00000344624.3:c.1834dup	p.Leu612ProfsTer8	p.L612Pfs*8	ENST00000344624		612	ctg/cCtg	10/33	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		348	446	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950727	79950728	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGCCCC	rs60484572	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	38	296	0	ENST00000265081.6:c.195_203dup	p.Pro67_Pro69dup	p.P67_P69dup	ENST00000265081	NM_002439.4	67	gca/gCAGCGCCCCca	1/24	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		296	411	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	108	368	1	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		369	601	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323315	31323315	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	31	105	0	ENST00000412585.2:c.674T>C	p.Leu225Pro	p.L225P	ENST00000412585	NM_005514.6	225	cTg/cCg	4/8	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		105	184	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508253	106508253	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	274	386	0	ENST00000359195.3:c.247G>A	p.Val83Met	p.V83M	ENST00000359195	NM_002649.2	83	Gtg/Atg	2/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		386	742	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124532385	124532385	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	36	292	0	ENST00000357628.3:c.59G>A	p.Gly20Asp	p.G20D	ENST00000357628	NM_015450.2	20	gGt/gAt	6/19	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		292	241	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750686	128750686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	336	346	0	ENST00000377970.2:c.223C>T	p.Pro75Ser	p.P75S	ENST00000377970	NM_002467.4	75	Ccc/Tcc	2/3	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		346	921	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2104046	2104046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199759640	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	125	297	0	ENST00000349721.2:c.3169C>T	p.Arg1057Cys	p.R1057C	ENST00000349721	NM_003070.3	1057	Cgt/Tgt	23/34	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		297	538	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232209	98232209	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs960630296	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	81	310	0	ENST00000331920.6:c.1733C>T	p.Ala578Val	p.A578V	ENST00000331920	NM_000264.3	578	gCg/gTg	13/24	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		310	458	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300039	137300040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755912201	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	100	357	1	ENST00000481739.1:c.331dup	p.Leu111ProfsTer70	p.L111Pfs*70	ENST00000481739	NM_002957.4	108	-/C	3/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		358	514	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400022	139400023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	145	443	0	ENST00000277541.6:c.4325dup	p.Pro1443AlafsTer36	p.P1443Afs*36	ENST00000277541	NM_017617.3	1442	ccg/ccCg	25/34	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		443	732	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400248	139400248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758787267	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	140	399	0	ENST00000277541.6:c.4100C>T	p.Pro1367Leu	p.P1367L	ENST00000277541	NM_017617.3	1367	cCg/cTg	25/34	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		399	609	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	128	234	0	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		234	458	SUCCESS
AR	367	MSKCC	GRCh37	X	66942823	66942823	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	14	134	0	ENST00000374690.3:c.2604G>T	p.Gln868His	p.Q868H	ENST00000374690	NM_000044.3	868	caG/caT	7/8	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		134	198	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428582	78428582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	66	297	0	ENST00000370768.2:c.1217C>T	p.Ser406Phe	p.S406F	ENST00000370768	NM_003902.3	406	tCt/tTt	14/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		297	272	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104268968	104268968	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs141532626	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	113	357	0	ENST00000369902.3:c.225G>T	p.Arg75Ser	p.R75S	ENST00000369902	NM_016169.3	75	agG/agT	2/12	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		357	551	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998723	100998723	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs377716203	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	155	369	0	ENST00000325455.5:c.1079A>G	p.Asp360Gly	p.D360G	ENST00000325455	NM_001202474.3	360	gAc/gGc	1/8	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		369	617	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21630844	21630844	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs200538229	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	81	344	0	ENST00000421138.2:c.760A>G	p.Thr254Ala	p.T254A	ENST00000421138		254	Act/Gct	8/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		344	558	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426706	49426706	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	282	448	0	ENST00000301067.7:c.11782C>T	p.Gln3928Ter	p.Q3928*	ENST00000301067	NM_003482.3	3928	Cag/Tag	39/54	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		448	877	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562494	21562494	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	44	310	0	ENST00000382592.4:c.1425del	p.Ala476ProfsTer183	p.A476Pfs*183	ENST00000382592	NM_014572.2	475	ccC/cc	4/8	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		310	462	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73649849	73649849	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	110	313	0	ENST00000377687.4:c.1202del	p.Lys401SerfsTer20	p.K401Sfs*20	ENST00000377687	NM_001730.3	400	gAa/ga	4/4	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		313	470	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873812	35873812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	54	299	0	ENST00000216797.5:c.39G>A	p.Met13Ile	p.M13I	ENST00000216797	NM_020529.2	13	atG/atA	1/6	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		299	545	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989043	41989044	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	115	349	0	ENST00000219905.7:c.1840dup	p.Arg614LysfsTer11	p.R614Kfs*11	ENST00000219905	NM_001164273.1	612	gga/ggAa	3/24	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		349	489	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701221	43701221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	119	351	0	ENST00000382044.4:c.5474C>T	p.Ala1825Val	p.A1825V	ENST00000382044	NM_001141980.1	1825	gCc/gTc	26/28	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		351	592	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396954	396955	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	141	472	0	ENST00000262320.3:c.71dup	p.Val25SerfsTer4	p.V25Sfs*4	ENST00000262320	NM_003502.3	24	cca/ccCa	2/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		472	653	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647613	3647613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	59	395	0	ENST00000294008.3:c.1450G>A	p.Glu484Lys	p.E484K	ENST00000294008	NM_032444.2	484	Gag/Aag	7/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		395	614	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821600	72821601	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCGCCA	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	53	351	0	ENST00000268489.5:c.10574_10575insTGGCGG	p.Gly3526_Gly3527dup	p.G3526_G3527dup	ENST00000268489	NM_006885.3	3526	ggc/ggTGGCGGc	10/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		351	529	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350895	89350895	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	105	347	0	ENST00000301030.4:c.2055del	p.Val686CysfsTer2	p.V686Cfs*2	ENST00000301030	NM_001256183.1	685	aaA/aa	9/13	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		347	493	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690562	33690562	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	147	371	1	ENST00000308377.4:c.265G>T	p.Asp89Tyr	p.D89Y	ENST00000308377	NM_152270.3	89	Gat/Tat	2/5	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		372	601	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395760	45395760	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	127	338	0	ENST00000262160.6:c.374A>T	p.His125Leu	p.H125L	ENST00000262160	NM_005901.5	125	cAt/cTt	4/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		338	494	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56378167	56378167	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	54	272	0	ENST00000348428.3:c.940G>T	p.Ala314Ser	p.A314S	ENST00000348428	NM_006785.3	314	Gca/Tca	7/17	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		272	248	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184612	7184612	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	120	324	0	ENST00000302850.5:c.689C>A	p.Ala230Asp	p.A230D	ENST00000302850	NM_000208.2	230	gCc/gAc	3/22	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		324	510	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097084	11097084	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	56	341	0	ENST00000358026.2:c.579del	p.Gln194SerfsTer109	p.Q194Sfs*109	ENST00000358026	NM_001128849.1	192	aGg/ag	4/36	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		341	626	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278106	15278106	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	122	409	0	ENST00000263388.2:c.5316G>T	p.Gln1772His	p.Q1772H	ENST00000263388	NM_000435.2	1772	caG/caT	29/33	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		409	574	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085732	16085732	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	120	342	0	ENST00000281043.3:c.908C>A	p.Pro303His	p.P303H	ENST00000281043	NM_005378.4	303	cCc/cAc	3/3	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		342	602	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030970	36030970	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	223	424	0	ENST00000358208.4:c.1249A>C	p.Asn417His	p.N417H	ENST00000358208		417	Aat/Cat	10/12	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		424	667	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573065	41573065	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	181	419	0	ENST00000263253.7:c.5350C>T	p.Gln1784Ter	p.Q1784*	ENST00000263253	NM_001429.3	1784	Cag/Tag	31/31	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		419	691	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138431076	138431076	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	65	244	0	ENST00000289153.2:c.1373T>C	p.Ile458Thr	p.I458T	ENST00000289153	NM_006219.2	458	aTa/aCa	8/22	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		244	243	SUCCESS
REST	5978	MSKCC	GRCh37	4	57777675	57777675	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	75	283	0	ENST00000309042.7:c.871T>C	p.Tyr291His	p.Y291H	ENST00000309042	NM_005612.4	291	Tat/Cat	2/4	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		283	333	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230897	66230897	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	45	366	0	ENST00000273854.3:c.2074G>T	p.Gly692Ter	p.G692*	ENST00000273854	NM_004439.5	692	Gga/Tga	12/18	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		366	236	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193872	106193872	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	121	338	0	ENST00000380013.4:c.4334A>C	p.Gln1445Pro	p.Q1445P	ENST00000380013	NM_001127208.2	1445	cAg/cCg	10/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		338	501	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	917175	917175	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	136	401	0	ENST00000166345.3:c.1256A>G	p.Asp419Gly	p.D419G	ENST00000166345	NM_004237.3	419	gAc/gGc	13/13	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		401	623	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526915	31526915	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	115	330	0	ENST00000344624.3:c.125T>G	p.Leu42Arg	p.L42R	ENST00000344624		42	cTt/cGt	2/33	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		330	481	SUCCESS
APC	324	MSKCC	GRCh37	5	112175112	112175112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1470915050	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	99	370	0	ENST00000257430.4:c.3821G>A	p.Cys1274Tyr	p.C1274Y	ENST00000257430	NM_000038.5	1274	tGt/tAt	16/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		370	446	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675527	30675527	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	150	411	0	ENST00000376406.3:c.2829G>T	p.Glu943Asp	p.E943D	ENST00000376406	NM_014641.2	943	gaG/gaT	8/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		411	637	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31239110	31239110	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	120	305	0	ENST00000376228.5:c.359A>C	p.Gln120Pro	p.Q120P	ENST00000376228	NM_002117.5	120	cAg/cCg	3/8	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		305	475	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43739049	43739049	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	128	345	0	ENST00000523873.1:c.66G>T	p.Lys22Asn	p.K22N	ENST00000523873		22	aaG/aaT	1/8	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		345	528	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104723	69104723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200083700	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	254	344	1	ENST00000288368.4:c.4567G>A	p.Ala1523Thr	p.A1523T	ENST00000288368	NM_024870.2	1523	Gcc/Acc	37/40	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		345	795	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549089	87549089	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	78	304	0	ENST00000277120.3:c.1646T>A	p.Ile549Asn	p.I549N	ENST00000277120		549	aTc/aAc	15/19	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		304	448	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97869464	97869464	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	134	354	0	ENST00000289081.3:c.1417C>A	p.Gln473Lys	p.Q473K	ENST00000289081	NM_000136.2	473	Cag/Aag	14/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		354	572	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317419	1317419	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	95	244	0	ENST00000400841.2:c.646G>A	p.Asp216Asn	p.D216N	ENST00000400841		216	Gat/Aat	5/6	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		244	436	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349583	70349583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1422779785	NA	P-0067107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	142	204	0	ENST00000374080.3:c.3745C>T	p.Leu1249Phe	p.L1249F	ENST00000374080		1249	Ctt/Ttt	27/45	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		204	329	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0067108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	48	649	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		649	798	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648460	30648460	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	37	407	0	ENST00000295754.5:c.85C>T	p.Gln29Ter	p.Q29*	ENST00000295754	NM_003242.5	29	Cag/Tag	1/7	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		407	486	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	131	798	2	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		800	718	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	98	831	1	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		832	818	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	76	761	1	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		762	686	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	76	718	1	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		719	666	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	114	690	4	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		694	666	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	99	855	5	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		860	640	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845287	42845287	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	92	718	0	ENST00000398585.3:c.975del	p.Glu326SerfsTer4	p.E326Sfs*4	ENST00000398585	NM_001135099.1	325	ccC/cc	9/14	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		718	590	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38798715	38798715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	96	404	0	ENST00000348513.6:c.148C>T	p.Arg50Trp	p.R50W	ENST00000348513	NM_003079.4	50	Cgg/Tgg	4/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		404	477	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	171	731	5	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		736	668	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310541	65310541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	124	714	0	ENST00000342505.4:c.2147G>A	p.Cys716Tyr	p.C716Y	ENST00000342505	NM_002227.2	716	tGt/tAt	16/25	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		714	636	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589698	69589698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	137	1076	0	ENST00000168712.1:c.155C>T	p.Ala52Val	p.A52V	ENST00000168712	NM_002007.2	52	gCg/gTg	1/3	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		1076	772	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420661	49420661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555185875	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	122	743	0	ENST00000301067.7:c.15088C>T	p.Arg5030Cys	p.R5030C	ENST00000301067	NM_003482.3	5030	Cgt/Tgt	48/54	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		743	684	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431874	49431874	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	100	848	0	ENST00000301067.7:c.9265del	p.Val3089TrpfsTer30	p.V3089Wfs*30	ENST00000301067	NM_003482.3	3089	Gtg/tg	34/54	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		848	735	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	110	732	11	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		743	625	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993014	72993014	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	117	750	0	ENST00000268489.5:c.1031del	p.Asn344ThrfsTer8	p.N344Tfs*8	ENST00000268489	NM_006885.3	344	aAc/ac	2/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		750	641	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	98	611	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		611	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	90	805	0	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		805	747	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144113	11144113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	117	717	0	ENST00000358026.2:c.3694G>A	p.Gly1232Ser	p.G1232S	ENST00000358026	NM_001128849.1	1232	Ggc/Agc	26/36	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		717	621	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299079	15299079	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1284132838	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	92	603	1	ENST00000263388.2:c.1459C>T	p.Arg487Ter	p.R487*	ENST00000263388	NM_000435.2	487	Cga/Tga	9/33	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		604	550	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223649	36223649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533229757	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	117	852	3	ENST00000222270.7:c.6199G>A	p.Gly2067Ser	p.G2067S	ENST00000222270	NM_014727.1	2067	Ggc/Agc	28/37	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		855	731	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794440	42794441	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	85	717	0	ENST00000575354.2:c.1526dup	p.Leu510ThrfsTer4	p.L510Tfs*4	ENST00000575354	NM_015125.3	507	cgc/cgCc	10/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		717	670	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403206	213403206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	83	629	0	ENST00000342788.4:c.49G>A	p.Ala17Thr	p.A17T	ENST00000342788	NM_005235.2	17	Gcg/Acg	1/28	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		629	471	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231792	36231792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	123	761	0	ENST00000300305.3:c.592G>A	p.Asp198Asn	p.D198N	ENST00000300305		198	Gat/Aat	5/8	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		761	859	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566432	41566432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	96	531	0	ENST00000263253.7:c.4309G>A	p.Ala1437Thr	p.A1437T	ENST00000263253	NM_001429.3	1437	Gca/Aca	27/31	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		531	522	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434182	12434182	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776687	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	91	565	1	ENST00000287820.6:c.556del	p.Ser186ValfsTer47	p.S186Vfs*47	ENST00000287820	NM_015869.4	184	Aaa/aa	4/7	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		566	585	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534269	187534269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1401735284	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	76	577	0	ENST00000441802.2:c.9457G>A	p.Asp3153Asn	p.D3153N	ENST00000441802	NM_005245.3	3153	Gac/Aac	13/27	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		577	519	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052992	180052992	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	116	882	0	ENST00000261937.6:c.1298G>T	p.Ser433Ile	p.S433I	ENST00000261937	NM_182925.4	433	aGc/aTc	10/30	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		882	676	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748539	43748539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367571103	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	118	663	0	ENST00000523873.1:c.493G>A	p.Val165Met	p.V165M	ENST00000523873		165	Gtg/Atg	6/8	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		663	684	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273263	55273263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1379387764	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	107	669	0	ENST00000275493.2:c.3586G>A	p.Glu1196Lys	p.E1196K	ENST00000275493	NM_005228.3	1196	Gaa/Aaa	28/28	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		669	691	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945048	151945048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780852959	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	13	263	0	ENST00000262189.6:c.2471G>A	p.Gly824Asp	p.G824D	ENST00000262189	NM_170606.2	824	gGc/gAc	14/59	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		263	245	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372093	55372093	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	86	765	1	ENST00000297316.4:c.788del	p.Pro263ArgfsTer124	p.P263Rfs*124	ENST00000297316	NM_022454.3	261	ggC/gg	2/2	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		766	749	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372202	55372202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764648837	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	103	797	0	ENST00000297316.4:c.892G>A	p.Gly298Ser	p.G298S	ENST00000297316	NM_022454.3	298	Ggc/Agc	2/2	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		797	748	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331723	8331723	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367558329	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	88	548	0	ENST00000356435.5:c.5393G>A	p.Arg1798Gln	p.R1798Q	ENST00000356435		1798	cGa/cAa	33/35	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		548	587	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258365	16258365	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	93	796	0	ENST00000375759.3:c.5630G>T	p.Arg1877Met	p.R1877M	ENST00000375759	NM_015001.2	1877	aGg/aTg	11/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		796	727	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258371	16258371	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	87	797	0	ENST00000375759.3:c.5636C>T	p.Ala1879Val	p.A1879V	ENST00000375759	NM_015001.2	1879	gCt/gTt	11/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		797	738	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458755	120458755	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	111	781	0	ENST00000256646.2:c.6590A>G	p.His2197Arg	p.H2197R	ENST00000256646	NM_024408.3	2197	cAt/cGt	34/34	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		781	694	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015428	176015428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1373217036	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	46	418	2	ENST00000367669.3:c.1310C>T	p.Ala437Val	p.A437V	ENST00000367669	NM_022457.5	437	gCg/gTg	12/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		420	328	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230493045	230493045	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	118	702	0	ENST00000391860.1:c.9del	p.Ser4AlafsTer44	p.S4Afs*44	ENST00000391860	NM_001258311.1	3	ccC/cc	2/7	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		702	564	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128955	64128957	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs772657234	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	111	775	0	ENST00000334205.4:c.587_589del	p.Ser196del	p.S196del	ENST00000334205	NM_003942.2	195	ttCTCc/ttc	6/17	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		775	750	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373220	118373220	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	115	661	0	ENST00000534358.1:c.6616del	p.Gln2206SerfsTer7	p.Q2206Sfs*7	ENST00000534358	NM_005933.3	2205	Ccc/cc	27/36	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		661	694	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398283	25398284	+	missense_variant	Missense_Mutation	DNP	AC	AC	CA	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	107	386	0	ENST00000311936.3:c.35_36delinsTG	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGT/gTG	2/5	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		386	346	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421875	49421875	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	94	789	0	ENST00000301067.7:c.14432T>C	p.Ile4811Thr	p.I4811T	ENST00000301067	NM_003482.3	4811	aTc/aCc	46/54	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		789	700	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431294	49431294	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	117	760	0	ENST00000301067.7:c.9845A>G	p.Gln3282Arg	p.Q3282R	ENST00000301067	NM_003482.3	3282	cAg/cGg	34/54	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		760	722	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210942	133210942	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	87	671	0	ENST00000320574.5:c.5834del	p.Gly1945GlufsTer54	p.G1945Efs*54	ENST00000320574	NM_006231.2	1945	gGa/ga	43/49	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		671	660	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640516	3640516	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	107	864	0	ENST00000294008.3:c.3123G>T	p.Gln1041His	p.Q1041H	ENST00000294008	NM_032444.2	1041	caG/caT	12/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		864	731	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492882	56492883	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	GCCATCAGCAGCCAGGGCCAGAG	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	144	778	0	ENST00000407977.2:c.34_56dup	p.Thr20SerfsTer6	p.T20Sfs*6	ENST00000407977		19	gct/gcCTCTGGCCCTGGCTGCTGATGGCt	2/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		778	768	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770066	56770066	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	194	673	0	ENST00000337432.4:c.62C>A	p.Pro21Gln	p.P21Q	ENST00000337432	NM_058216.2	21	cCa/cAa	1/9	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		673	610	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61324180	61324180	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	119	746	1	ENST00000283752.5:c.653C>A	p.Ser218Tyr	p.S218Y	ENST00000283752	NM_006919.2	218	tCt/tAt	7/8	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		747	648	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918168	50918168	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	103	647	0	ENST00000440232.2:c.2485C>A	p.Leu829Met	p.L829M	ENST00000440232	NM_002691.3	829	Ctg/Atg	20/27	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		647	617	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162044	22162044	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	116	637	0	ENST00000215832.6:c.211G>T	p.Glu71Ter	p.E71*	ENST00000215832	NM_002745.4	71	Gag/Tag	2/9	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		637	670	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29280037	29280037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	77	843	0	ENST00000544604.2:c.283G>A	p.Glu95Lys	p.E95K	ENST00000544604	NM_001206998.1	95	Gag/Aag	1/9	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		843	616	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873058	134873058	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	95	641	0	ENST00000398015.3:c.1362G>C	p.Trp454Cys	p.W454C	ENST00000398015	NM_004441.4	454	tgG/tgC	6/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		641	549	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805422	1805422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	72	577	0	ENST00000260795.2:c.934G>A	p.Ala312Thr	p.A312T	ENST00000260795		312	Gcg/Acg	7/17	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		577	501	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535343	66535343	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	73	731	0	ENST00000273854.3:c.118del	p.Leu40SerfsTer22	p.L40Sfs*22	ENST00000273854	NM_004439.5	40	Ctc/tc	1/18	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		731	449	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383944	84383944	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	80	544	0	ENST00000321945.7:c.908del	p.Asn303IlefsTer17	p.N303Ifs*17	ENST00000321945	NM_139076.2	303	aAt/at	9/9	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		544	525	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630546	187630546	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	125	728	0	ENST00000441802.2:c.436A>T	p.Arg146Ter	p.R146*	ENST00000441802	NM_005245.3	146	Aga/Tga	2/27	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		728	648	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1296526	1296526	+	upstream_gene_variant	5'Flank	DEL	T	T	-	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	17	83	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		83	77	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324861	31324861	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	137	924	0	ENST00000412585.2:c.73+2T>C		p.X25_splice	ENST00000412585	NM_005514.6	25			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		924	825	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161970019	161970019	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	78	470	0	ENST00000366898.1:c.950A>T	p.Gln317Leu	p.Q317L	ENST00000366898	NM_004562.2	317	cAg/cTg	9/12	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		470	485	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2039712	2039712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750798867	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	109	768	0	ENST00000349721.2:c.602C>T	p.Thr201Met	p.T201M	ENST00000349721	NM_003070.3	201	aCg/aTg	4/34	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		768	684	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300081	137300081	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	69	619	0	ENST00000481739.1:c.369del	p.Ser124GlnfsTer44	p.S124Qfs*44	ENST00000481739	NM_002957.4	122	caC/ca	3/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		619	561	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390879	139390879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1163865960	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	104	797	0	ENST00000277541.6:c.7312C>T	p.Pro2438Ser	p.P2438S	ENST00000277541	NM_017617.3	2438	Ccg/Tcg	34/34	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		797	672	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933752	39933752	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367848648	NA	P-0067143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	112	434	0	ENST00000378444.4:c.847G>A	p.Ala283Thr	p.A283T	ENST00000378444	NM_001123385.1	283	Gca/Aca	4/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		434	328	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0067144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	68	288	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		288	449	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204686	128204686	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060500090	NA	P-0067144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	91	720	0	ENST00000341105.2:c.755A>G	p.Tyr252Cys	p.Y252C	ENST00000341105	NM_032638.4	252	tAt/tGt	3/6	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		720	613	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32409398	32410420	+	3_prime_UTR_variant	3'UTR	DEL	TGTAAGATCAACACCCAGTGATGCATCTAGTACTTATACAGTCCTAATTTTAGTTGTCAAAGAGCAAATCATTATCAGACATATATTTACACAGTAATTTCAAGCAACGGTAAATAATAAATTCCCTCCCTTAAAAAACAAAACACAACACAACACACACACACACACACACACACACACACACACGACCATCTTTAAACAATGGATTTCCTCACCCAGTAAGTCTCATTTTTTTCACATATACTTGTAGACCCAAAGGTCCTTAAGTTACTTAAAAACAGTCTTATCAGTGGAGATCCTGGACCATCCCCTATTTTCTTTTAAAGTCACTTTCATTTTTACAACTTGAAGCCATATACCAGCATGGTTTTTATACACTAAGGACACTCCCAGTGATGAAAATGAATTCCCCTCCATTTGTGCAAGGAGGTATGTACATCTATAAAGACACATATGATTACCACTCAAAAGAGTCAAAAACATACACAAAAAAATCTCAGATCTTCATAGTTTCTTAAGAGCAGTGTGCCAGTGTTCACATTGAATTAACTGAATGGTAAAATTCTTTTAGATTTCTATACAGAGGTACTGGTTAGTTCTGATTTTTTCTTCAGCTGCTTGAAATGCATGAGCTTTAAAAGTTGCCTGGCAGAACTACATCCTGCTTTCCAGGTTAGCAGCCTGGCTGACCTCGGGAATGTTAGACAAGATTCACCCCCGATGCCTTGCTCTCTGATTTATTTCTTGCTGTTGCTGTTAGTAAATGGAAACCATGACAAAGTTTACATTAGCAGACACATACACATGCCCTGGCCTATAAATATTCCATGATAGAAAATGGTACAATAATTCCATCCCCAGCGAAAACGAGCATAAAAAAAGAAGGGAAGGGTCAGGGGGACATGATCAGCTATGGCTCTTCTTACAGTAGAAAATCCACACCAAATGGCAATGGGCTTTTAACTAACCAGACATTGTTAGCTGCTTCTCCAGGGCCTGTGAGTCAACTAAAAGTAGGCAGGG	TGTAAGATCAACACCCAGTGATGCATCTAGTACTTATACAGTCCTAATTTTAGTTGTCAAAGAGCAAATCATTATCAGACATATATTTACACAGTAATTTCAAGCAACGGTAAATAATAAATTCCCTCCCTTAAAAAACAAAACACAACACAACACACACACACACACACACACACACACACACACGACCATCTTTAAACAATGGATTTCCTCACCCAGTAAGTCTCATTTTTTTCACATATACTTGTAGACCCAAAGGTCCTTAAGTTACTTAAAAACAGTCTTATCAGTGGAGATCCTGGACCATCCCCTATTTTCTTTTAAAGTCACTTTCATTTTTACAACTTGAAGCCATATACCAGCATGGTTTTTATACACTAAGGACACTCCCAGTGATGAAAATGAATTCCCCTCCATTTGTGCAAGGAGGTATGTACATCTATAAAGACACATATGATTACCACTCAAAAGAGTCAAAAACATACACAAAAAAATCTCAGATCTTCATAGTTTCTTAAGAGCAGTGTGCCAGTGTTCACATTGAATTAACTGAATGGTAAAATTCTTTTAGATTTCTATACAGAGGTACTGGTTAGTTCTGATTTTTTCTTCAGCTGCTTGAAATGCATGAGCTTTAAAAGTTGCCTGGCAGAACTACATCCTGCTTTCCAGGTTAGCAGCCTGGCTGACCTCGGGAATGTTAGACAAGATTCACCCCCGATGCCTTGCTCTCTGATTTATTTCTTGCTGTTGCTGTTAGTAAATGGAAACCATGACAAAGTTTACATTAGCAGACACATACACATGCCCTGGCCTATAAATATTCCATGATAGAAAATGGTACAATAATTCCATCCCCAGCGAAAACGAGCATAAAAAAAGAAGGGAAGGGTCAGGGGGACATGATCAGCTATGGCTCTTCTTACAGTAGAAAATCCACACCAAATGGCAATGGGCTTTTAACTAACCAGACATTGTTAGCTGCTTCTCCAGGGCCTGTGAGTCAACTAAAAGTAGGCAGGG	-	novel	NA	P-0067144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	0	22	2	0	ENST00000332351.3:c.*184_*1206del			ENST00000332351	NM_024426.4	-/517		10/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		2	22	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603056	48603071	+	frameshift_variant	Frame_Shift_Del	DEL	ACTGCACAAGCTGCAG	ACTGCACAAGCTGCAG	-	novel	NA	P-0067144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	64	504	0	ENST00000342988.3:c.1357_1372del	p.Thr453GlnfsTer18	p.T453Qfs*18	ENST00000342988	NM_005359.5	453	ACTGCACAAGCTGCAGca/ca	11/12	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		504	478	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589628	67589636	+	inframe_deletion	In_Frame_Del	DEL	ATAGATTAT	ATAGATTAT	-	novel	NA	P-0067144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	51	432	0	ENST00000274335.5:c.1393_1401del	p.Arg465_Tyr467del	p.R465_Y467del	ENST00000274335		464	gATAGATTATat/gat	10/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		432	361	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457286	67457288	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0067144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	53	849	0	ENST00000327367.4:c.260_262del	p.Ile87_Tyr88delinsAsn	p.I87_Y88delinsN	ENST00000327367	NM_005902.3	87	aTCTac/aac	2/9	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		849	1033	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165518	47165519	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0067145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	270	637	0	ENST00000409792.3:c.607_608del	p.Ser203IlefsTer33	p.S203Ifs*33	ENST00000409792	NM_014159.6	203	TCa/a	3/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		637	658	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949645	151949645	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0067145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	386	364	0	ENST00000262189.6:c.1455T>A	p.Cys485Ter	p.C485*	ENST00000262189	NM_170606.2	485	tgT/tgA	10/59	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		364	824	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0067146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	62	585	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		585	398	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586422	189586422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866267914	NA	P-0067146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	1977	574	0	ENST00000264731.3:c.1046G>A	p.Gly349Glu	p.G349E	ENST00000264731	NM_003722.4	349	gGa/gAa	8/14	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		574	2360	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682187	37682187	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	20	547	0	ENST00000447079.4:c.3378A>C	p.Gln1126His	p.Q1126H	ENST00000447079	NM_015083.1	1126	caA/caC	13/14	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		547	372	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564500	41564500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	59	519	0	ENST00000263253.7:c.3922G>A	p.Asp1308Asn	p.D1308N	ENST00000263253	NM_001429.3	1308	Gac/Aac	24/31	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		519	504	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484260	8484260	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	22	408	0	ENST00000356435.5:c.3272G>T	p.Ser1091Ile	p.S1091I	ENST00000356435		1091	aGt/aTt	19/35	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		408	430	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624496	140624498	+	missense_variant	Missense_Mutation	TNP	GCC	GCC	TTT	novel	NA	P-0067146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	33	523	1	ENST00000288602.6:c.6_8delinsAAA	p.Ala3Lys	p.A3K	ENST00000288602	NM_004333.4	2	gcGGCg/gcAAAg	1/18	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		524	265	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433019	49433019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	51	574	0	ENST00000301067.7:c.8352G>T	p.Met2784Ile	p.M2784I	ENST00000301067	NM_003482.3	2784	atG/atT	33/54	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		574	399	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131505	202131505	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	26	545	0	ENST00000358485.4:c.473del	p.Ser158LeufsTer14	p.S158Lfs*14	ENST00000358485	NM_001080125.1	158	tCt/tt	2/9	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		545	386	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27209139	27209139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	27	429	0	ENST00000380036.4:c.2596C>T	p.His866Tyr	p.H866Y	ENST00000380036	NM_000459.3	866	Cac/Tac	16/23	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		429	390	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918313	44918313	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	44	355	0	ENST00000377967.4:c.938A>T	p.Lys313Ile	p.K313I	ENST00000377967	NM_021140.2	313	aAa/aTa	11/29	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		355	267	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907812	76907812	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	39	470	0	ENST00000373344.5:c.4349A>C	p.Glu1450Ala	p.E1450A	ENST00000373344	NM_000489.3	1450	gAa/gCa	15/35	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		470	446	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966733	18966733	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0067146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	31	548	0	ENST00000262803.5:c.1545-1G>A		p.X515_splice	ENST00000262803	NM_002911.3	515			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		548	329	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0067147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	88	385	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		385	201	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0067147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	142	461	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		461	364	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32903612	32903612	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507873	NA	P-0067147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	79	282	0	ENST00000380152.3:c.664C>T	p.Pro222Ser	p.P222S	ENST00000380152		222	Cct/Tct	8/27	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		282	220	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117524	4117524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371852537	NA	P-0067147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	96	133	0	ENST00000262948.5:c.196G>A	p.Glu66Lys	p.E66K	ENST00000262948	NM_030662.3	66	Gaa/Aaa	2/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		133	174	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646423	23646423	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	167	486	0	ENST00000261584.4:c.1444C>A	p.Leu482Ile	p.L482I	ENST00000261584	NM_024675.3	482	Ctc/Atc	4/13	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		486	481	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49449064	49449065	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0067147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	93	330	2	ENST00000301067.7:c.43_44delinsTT	p.Pro15Leu	p.P15L	ENST00000301067	NM_003482.3	15	CCg/TTg	1/54	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		332	327	SUCCESS
AXL	558	MSKCC	GRCh37	19	41725365	41725365	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	89	384	0	ENST00000301178.4:c.68C>A	p.Ala23Glu	p.A23E	ENST00000301178	NM_021913.4	23	gCg/gAg	1/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		384	443	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38504602	38504602	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	140	455	0	ENST00000254066.5:c.213A>G	p.Ile71Met	p.I71M	ENST00000254066	NM_000964.3	71	atA/atG	3/9	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		455	363	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022580	36022580	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	124	504	0	ENST00000358208.4:c.453G>A	p.Trp151Ter	p.W151*	ENST00000358208		151	tgG/tgA	5/12	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		504	349	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741890	145741890	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	292	526	0	ENST00000428558.2:c.613C>T	p.Pro205Ser	p.P205S	ENST00000428558	NM_004260.3	205	Ccc/Tcc	5/22	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		526	623	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591085	67591085	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519839	NA	P-0067148-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	88	459	0	ENST00000274335.5:c.1678G>T	p.Asp560Tyr	p.D560Y	ENST00000274335		560	Gac/Tac	12/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		459	400	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0067148-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	326	653	1	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		654	791	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584607	48584607	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067148-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	138	529	0	ENST00000342988.3:c.781del	p.His261IlefsTer75	p.H261Ifs*75	ENST00000342988	NM_005359.5	260	taC/ta	6/12	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		529	559	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs770248150	NA	P-0067148-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	10	460	0	ENST00000311936.3:c.351A>C	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaC	4/5	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		460	246	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52693404	52693404	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067148-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	42	586	0	ENST00000322088.6:c.55G>T	p.Glu19Ter	p.E19*	ENST00000322088	NM_014225.5	19	Gaa/Taa	1/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		586	784	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265739	41266347	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAA	AAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAA	-	novel	NA	P-0067148-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	12	97	0	ENST00000349496.5:c.13+168_242-97del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		97	105	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0067149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	171	461	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.968	0.898	1	0.968	0.898	1	CLONAL	1	TRUE	1	0.712177617505953	2		461	496	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955550	48955550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913304	NA	P-0067149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	100	361	0	ENST00000267163.4:c.1666C>T	p.Arg556Ter	p.R556*	ENST00000267163	NM_000321.2	556	Cga/Tga	17/27	0.712177617505953	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.712177617505953	1		361	160	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244184	153244184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759610249	NA	P-0067149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	260	600	0	ENST00000281708.4:c.1973G>A	p.Arg658Gln	p.R658Q	ENST00000281708	NM_033632.3	658	cGa/cAa	12/12	0.712177617505953	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.712177617505953	1		600	449	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814713	139814713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753016580	NA	P-0067149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	253	600	0	ENST00000247668.2:c.706G>A	p.Glu236Lys	p.E236K	ENST00000247668	NM_021138.3	236	Gag/Aag	8/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.712177617505953	2		600	635	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578499	7578499	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs786203071	NA	P-0067149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	583	651	0	ENST00000269305.4:c.431A>C	p.Gln144Pro	p.Q144P	ENST00000269305	NM_001126112.2	144	cAg/cCg	5/11	0.712177617505953	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.712177617505953	2		651	766	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524401	187524401	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0067149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	40	530	0	ENST00000441802.2:c.11279C>G	p.Ser3760Ter	p.S3760*	ENST00000441802	NM_005245.3	3760	tCa/tGa	19/27	0.712177617505953	1	FACETS	0.186	0.155	0.221	0.186	0.155	0.221	SUBCLONAL	1	TRUE	0	0.712177617505953	1		530	388	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324875	31324875	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1231905919	NA	P-0067149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	325	533	0	ENST00000412585.2:c.61G>T	p.Glu21Ter	p.E21*	ENST00000412585	NM_005514.6	21	Gag/Tag	1/8	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.712177617505953	2		533	668	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445893	49445893	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	272	726	0	ENST00000301067.7:c.1573G>T	p.Glu525Ter	p.E525*	ENST00000301067	NM_003482.3	525	Gag/Tag	10/54	1	2	FACETS	0.996	0.939	1	0.996	0.939	1	CLONAL	1	TRUE	1	0.712177617505953	2		726	767	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106925	11106925	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	266	634	0	ENST00000358026.2:c.1630C>G	p.Gln544Glu	p.Q544E	ENST00000358026	NM_001128849.1	544	Cag/Gag	10/36	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.712177617505953	2		634	720	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334972	81334972	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	104	466	0	ENST00000222390.5:c.1855T>A	p.Tyr619Asn	p.Y619N	ENST00000222390	NM_000601.4	619	Tac/Aac	16/18	1	2	FACETS	0.983	0.893	1	0.983	0.893	1	CLONAL	1	TRUE	1	0.712177617505953	2		466	297	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892239	9892239	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1335	181	569	0	ENST00000330684.3:c.2251G>T	p.Gly751Trp	p.G751W	ENST00000330684	NM_001134407.1	751	Ggg/Tgg	11/13	1	2	FACETS	0.335	0.308	0.364	0.335	0.308	0.364	SUBCLONAL	1	TRUE	1	0.712177617505953	2		569	1516	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117824	108117824	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	106	384	0	ENST00000278616.4:c.1035G>C	p.Leu345Phe	p.L345F	ENST00000278616	NM_000051.3	345	ttG/ttC	8/63	0.712177617505953	3	FACETS	1	0.919	1	0.51	0.46	0.561	CLONAL	1	TRUE	1	0.712177617505953	3		384	396	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023699	31023699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776213974	NA	P-0067149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1848	191	551	0	ENST00000375687.4:c.3184C>T	p.Pro1062Ser	p.P1062S	ENST00000375687	NM_015338.5	1062	Cct/Tct	13/13	0.712177617505953	9	FACETS	0.919	0.846	0.996	0.115	0.105	0.125	CLONAL	1	TRUE	1	0.712177617505953	9		551	2039	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383367	4383367	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	220	516	0	ENST00000261254.3:c.161A>G	p.Tyr54Cys	p.Y54C	ENST00000261254	NM_001759.3	54	tAc/tGc	1/5	NA	2	FACETS	0.959	0.898	1			1	INDETERMINATE	1	TRUE	NA	0.712177617505953	2		516	644	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859850	151859850	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	203	623	0	ENST00000262189.6:c.10812G>C	p.Lys3604Asn	p.K3604N	ENST00000262189	NM_170606.2	3604	aaG/aaC	43/59	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.712177617505953	2		623	546	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565520	41565520	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	126	377	0	ENST00000263253.7:c.4186T>C	p.Ser1396Pro	p.S1396P	ENST00000263253	NM_001429.3	1396	Tct/Cct	26/31	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.712177617505953	2		377	351	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572246	64572246	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	272	809	0	ENST00000312049.6:c.1393G>T	p.Ala465Ser	p.A465S	ENST00000312049	NM_130799.2	465	Gcc/Tcc	10/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.712177617505953	2		809	733	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0067150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	27	346	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		346	479	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0067150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	38	658	2	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		660	758	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976476	25976476	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	41	380	0	ENST00000435504.4:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000435504		357	Cga/Tga	11/13	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		380	613	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466018	69466018	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	29	671	0	ENST00000227507.2:c.856A>G	p.Thr286Ala	p.T286A	ENST00000227507	NM_053056.2	286	Aca/Gca	5/5	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		671	874	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022345	26022346	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0067150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	50	473	0	ENST00000435504.4:c.311dup	p.Gln105SerfsTer8	p.Q105Sfs*8	ENST00000435504		104	ggt/ggGt	5/13	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		473	762	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088697	27088697	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	38	512	0	ENST00000324856.7:c.2306C>A	p.Ser769Ter	p.S769*	ENST00000324856	NM_006015.4	769	tCa/tAa	7/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		512	758	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196820	108196820	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1565520291	NA	P-0067150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	59	399	0	ENST00000278616.4:c.6843del	p.Tyr2281Ter	p.Y2281*	ENST00000278616	NM_000051.3	2281	taC/ta	47/63	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		399	585	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47502667	47503587	+	splice_acceptor_variant,splice_donor_variant,splice_donor_5th_base_variant,splice_polypyrimidine_tract_variant,intron_variant	Splice_Site	DEL	GTAAGTCGCAGGGCCTTCTGGTTGGTTTTTCCTCCTGAAAATTGACAGCCAGGGTCAGTGTGTCGCAGAACAAGGCTCTGTCCACAAGCCAGTAGAAGCCTCAGGCCCTGGCCTGGAAGGGGTGCTGGCTGGCCTCCCATGGTGCCCGCTGGTCTCGGTGCCCAGAGCCTCTGCCTCTCGCCCATCCTCAGGCCTCCCTCCTGCTCCTGTCTGAGGGCAGCCCACGTGGCCTCAAACCTGCCTAACACCAGATAGGGCACTTAGCTCCAGCGGGCATGGGGCCTCTTGTAGGCCTGTGTCCCAAAGCTGGCAGAGAGAGAAGATCTTCTGGTTGGTACTGATGCTCCAGAAATCTTCTCCTGAATCAAAAACACCTCAGAGTCCCTGAAAGTCCTCTCACAGCATTCACGTTCCCAGCTGGGGAGAACCGGGACACTGCACCTCGAGAGATGTGCTGCAGGAGACAGCCAGCCTCCGGCATGGAGCACAGCCGCAGGCGGGAGGCCGTATGGTTGTTCCCTGAAGTTCCATGTGTGTGGAGGAGATCTGCTGGCCGAGTGGCCTCTGATGGCGCTCTGGCTTAGGACACTCAGCCTCCCTCCCTCGTCACAGCCGGAGCACCGCCACTGCTTTGGCTGGCTGCAGAGTGAGTCCCTGAGGTGGTCCATCCACCCCCAGGGGTTTGCGGGGCTCCAGGCAGCCTTTCCGAGGTTGGCCATGTAGAGGCACTGGGCTGGAGGGGAGAGGACACTGAGGGCGCAGCCTCCCAGGCAGGGCAGGGTACAGAGAGCTGCGCATGGCCTTTTCTGCTCCACCTGAGGGAAGAAAGGTGGGCTCAGCCTGGGTGCTGAAGACCATGAGCGCCCAGGGCCAGGTGGGGCCCTGCACAGTTCTGACCATTGAGTTTGGTGTCGCCCGCAG	GTAAGTCGCAGGGCCTTCTGGTTGGTTTTTCCTCCTGAAAATTGACAGCCAGGGTCAGTGTGTCGCAGAACAAGGCTCTGTCCACAAGCCAGTAGAAGCCTCAGGCCCTGGCCTGGAAGGGGTGCTGGCTGGCCTCCCATGGTGCCCGCTGGTCTCGGTGCCCAGAGCCTCTGCCTCTCGCCCATCCTCAGGCCTCCCTCCTGCTCCTGTCTGAGGGCAGCCCACGTGGCCTCAAACCTGCCTAACACCAGATAGGGCACTTAGCTCCAGCGGGCATGGGGCCTCTTGTAGGCCTGTGTCCCAAAGCTGGCAGAGAGAGAAGATCTTCTGGTTGGTACTGATGCTCCAGAAATCTTCTCCTGAATCAAAAACACCTCAGAGTCCCTGAAAGTCCTCTCACAGCATTCACGTTCCCAGCTGGGGAGAACCGGGACACTGCACCTCGAGAGATGTGCTGCAGGAGACAGCCAGCCTCCGGCATGGAGCACAGCCGCAGGCGGGAGGCCGTATGGTTGTTCCCTGAAGTTCCATGTGTGTGGAGGAGATCTGCTGGCCGAGTGGCCTCTGATGGCGCTCTGGCTTAGGACACTCAGCCTCCCTCCCTCGTCACAGCCGGAGCACCGCCACTGCTTTGGCTGGCTGCAGAGTGAGTCCCTGAGGTGGTCCATCCACCCCCAGGGGTTTGCGGGGCTCCAGGCAGCCTTTCCGAGGTTGGCCATGTAGAGGCACTGGGCTGGAGGGGAGAGGACACTGAGGGCGCAGCCTCCCAGGCAGGGCAGGGTACAGAGAGCTGCGCATGGCCTTTTCTGCTCCACCTGAGGGAAGAAAGGTGGGCTCAGCCTGGGTGCTGAAGACCATGAGCGCCCAGGGCCAGGTGGGGCCCTGCACAGTTCTGACCATTGAGTTTGGTGTCGCCCGCAG	-	novel	NA	P-0067150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	41	348	0	ENST00000404338.3:c.4142+2_4143del		p.X1381_splice	ENST00000404338	NM_004491.4	1381			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		348	564	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0067151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	234	470	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		470	582	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485909	40485909	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	91	515	0	ENST00000264657.5:c.956G>A	p.Ser319Asn	p.S319N	ENST00000264657	NM_139276.2	319	aGt/aAt	9/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		515	629	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729871	39729871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	159	510	0	ENST00000361337.2:c.1186C>T	p.Pro396Ser	p.P396S	ENST00000361337	NM_003286.2	396	Cct/Tct	13/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		510	693	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462377	89462377	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374235660	NA	P-0067151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	98	447	0	ENST00000336596.2:c.1849G>A	p.Asp617Asn	p.D617N	ENST00000336596	NM_005233.5	617	Gat/Aat	10/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		447	530	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595549	55595550	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	49	452	0	ENST00000288135.5:c.2045dup	p.Leu682PhefsTer6	p.L682Ffs*6	ENST00000288135	NM_000222.2	680	aat/aaTt	14/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		452	404	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244148	153244148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	91	607	0	ENST00000281708.4:c.2009G>A	p.Gly670Glu	p.G670E	ENST00000281708	NM_033632.3	670	gGa/gAa	12/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		607	729	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609229	46609229	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0067151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	101	472	0	ENST00000263734.3:c.2287+1G>A		p.X763_splice	ENST00000263734	NM_001430.4	763			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		472	509	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339937	116339937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755954919	NA	P-0067151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	85	517	0	ENST00000397752.3:c.799G>A	p.Glu267Lys	p.E267K	ENST00000397752	NM_000245.2	267	Gaa/Aaa	2/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		517	614	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs967461896	NA	P-0006492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	114	382	0	ENST00000269305.4:c.526T>A	p.Cys176Ser	p.C176S	ENST00000269305	NM_001126112.2	176	Tgc/Agc	5/11	0.222081215892628	2	FACETS	0.86	0.778	0.945	0.86	0.778	0.945	CLONAL	2	TRUE	0	0.270061622852432	2		382	491	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087539	27087539	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	186	465	0	ENST00000324856.7:c.2113A>T	p.Ser705Cys	p.S705C	ENST00000324856	NM_006015.4	705	Agt/Tgt	5/20	0.270061622852432	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.270061622852432	3		465	695	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673221	30673221	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	58	594	2	ENST00000376406.3:c.3739G>A	p.Ala1247Thr	p.A1247T	ENST00000376406	NM_014641.2	1247	Gcc/Acc	10/15	0.206827334747536	4	FACETS	1	0.959	1	0.664	0.572	0.763	CLONAL	1	TRUE	2	0.270061622852432	4		596	411	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891287	101891287	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757374917	NA	P-0006492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	54	545	1	ENST00000374994.4:c.248C>T	p.Pro83Leu	p.P83L	ENST00000374994	NM_004612.2	83	cCg/cTg	2/9	0.270061622852432	1	FACETS	0.767	0.656	0.888	0.767	0.656	0.888	SUBCLONAL	1	TRUE	0	0.270061622852432	1		546	451	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884218	37884218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372043866	NA	P-0006492-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	56	482	1	ENST00000269571.5:c.3689G>A	p.Arg1230Gln	p.R1230Q	ENST00000269571		1230	cGg/cAg	27/27	0.222081215892628	2	FACETS	1	0.88	1	0.513	0.441	0.592	CLONAL	1	TRUE	0	0.270061622852432	2		483	404	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0008063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	29	364	1	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.788	0.632	0.966	0.788	0.632	0.966	CLONAL	1	TRUE	1	0.17	2		365	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0008063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	32	363	0	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	1	2	FACETS	0.86	0.697	1	0.86	0.697	1	CLONAL	1	TRUE	1	0.17	2		363	438	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393199	393199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	29	423	2	ENST00000380956.4:c.47C>T	p.Ala16Val	p.A16V	ENST00000380956	NM_001195286.1	16	gCg/gTg	2/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.17	NA		425	505	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717608	89717608	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0008063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	20	330	0	ENST00000371953.3:c.635-2A>C		p.X212_splice	ENST00000371953	NM_000314.4	212			1	2	FACETS	0.686	0.524	0.876	0.686	0.524	0.876	SUBCLONAL	1	TRUE	1	0.17	2		330	343	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398306	25398306	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs193929331	NA	P-0008063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	33	394	0	ENST00000311936.3:c.13A>G	p.Lys5Glu	p.K5E	ENST00000311936	NM_004985.3	5	Aaa/Gaa	2/5	1	2	FACETS	0.833	0.678	1	0.833	0.678	1	CLONAL	1	TRUE	1	0.17	2		394	466	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591910	48591910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	53	565	0	ENST00000342988.3:c.1073G>A	p.Gly358Glu	p.G358E	ENST00000342988	NM_005359.5	358	gGa/gAa	9/12	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.17	2		565	605	SUCCESS
APC	324	MSKCC	GRCh37	5	112175529	112175535	+	frameshift_variant	Frame_Shift_Del	DEL	TGGTAAG	TGGTAAG	-	novel	NA	P-0008063-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	47	361	0	ENST00000257430.4:c.4241_4247del	p.Val1414AlafsTer3	p.V1414Afs*3	ENST00000257430	NM_000038.5	1413	aTGGTAAGt/at	16/16	1	2	FACETS	0.982	0.828	1	0.982	0.828	1	CLONAL	1	TRUE	1	0.17	2		361	563	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611804	1611804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1343124101	NA	P-0010016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	47	741	0	ENST00000344749.5:c.1858G>A	p.Glu620Lys	p.E620K	ENST00000344749	NM_001136139.2	620	Gag/Aag	19/19	0.200452749056055	0	FACETS	0.539	0.454	0.634			1	SUBCLONAL	1	TRUE	0	0.200452749056055	0		741	695	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8497268	8497268	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	48	470	0	ENST00000356435.5:c.2323T>G	p.Trp775Gly	p.W775G	ENST00000356435		775	Tgg/Ggg	15/35	1	2	FACETS	0.577	0.486	0.678	0.577	0.486	0.678	SUBCLONAL	1	TRUE	1	0.200452749056055	2		470	830	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245425	41245425	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs80357182	NA	P-0010016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	62	709	0	ENST00000357654.3:c.2123C>G	p.Ser708Cys	p.S708C	ENST00000357654	NM_007294.3	708	tCt/tGt	10/23	1	2	FACETS	0.601	0.517	0.692	0.601	0.517	0.692	SUBCLONAL	1	TRUE	1	0.200452749056055	2		709	1030	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438274	49438274	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0121493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	195	346	2	ENST00000301067.7:c.4995A>T	p.Lys1665Asn	p.K1665N	ENST00000301067	NM_003482.3	1665	aaA/aaT	20/54	0.704691424011479	3	FACETS	0.85	0.787	0.914	0.425	0.393	0.457	CLONAL	1	NA	1	0.704691424011479	3		348	881	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495091	56495091	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	138	411	1	ENST00000267101.3:c.3448G>T	p.Gly1150Trp	p.G1150W	ENST00000267101	NM_001982.3	1150	Ggg/Tgg	27/28	0.704691424011479	3	FACETS	0.537	0.488	0.589	0.269	0.244	0.295	SUBCLONAL	1	NA	1	0.704691424011479	3		412	986	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293605	1293605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0121493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	57	356	3	ENST00000310581.5:c.1396C>T	p.Arg466Trp	p.R466W	ENST00000310581	NM_198253.2	466	Cgg/Tgg	2/16	1	2	FACETS	0.224	0.192	0.26	0.224	0.192	0.26	SUBCLONAL	1	NA	1	0.704691424011479	2		359	722	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	53	736	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.17	2		736	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0020183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	53	885	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.933	0.795	1	0.933	0.795	1	CLONAL	1	TRUE	1	0.17	2		885	668	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554492	63554493	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	47	844	0	ENST00000307078.5:c.246dup	p.His83ThrfsTer58	p.H83Tfs*58	ENST00000307078	NM_004655.3	82	-/A	2/11	1	2	FACETS	0.979	0.825	1	0.979	0.825	1	CLONAL	1	TRUE	1	0.17	2		844	565	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	38	587	0	ENST00000304494.5:c.143C>A	p.Pro48Gln	p.P48Q	ENST00000304494	NM_000077.4	48	cCg/cAg	1/3	1	2	FACETS	0.968	0.8	1	0.968	0.8	1	CLONAL	1	TRUE	1	0.17	2		587	462	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922806	44922807	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGGA	novel	NA	P-0020183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	41	593	0	ENST00000377967.4:c.1668_1671dup	p.Val558TrpfsTer24	p.V558Wfs*24	ENST00000377967	NM_021140.2	556	cct/ccTGGAt	16/29	1	2	FACETS	0.984	0.82	1	0.984	0.82	1	CLONAL	1	TRUE	1	0.17	2		593	490	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	292	736	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.385614330801614	7	FACETS	1	0.985	1	0.84	0.793	0.889	CLONAL	3	TRUE	3	0.385614330801614	7		736	885	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0026994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	93	327	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.391470617217201	4	FACETS	1	0.981	1	0.748	0.668	0.831	CLONAL	1	TRUE	2	0.385614330801614	4		327	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0026994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	122	673	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.378392134570627	4	FACETS	0.943	0.851	1			1	CLONAL	1	TRUE	NA	0.385614330801614	4		674	930	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0026994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	182	334	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.391470617217201	3	FACETS	0.931	0.871	0.992			1	CLONAL	3	TRUE	NA	0.385614330801614	3		334	403	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473722	67473722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs794727798	NA	P-0026994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	95	509	0	ENST00000327367.4:c.802C>T	p.Arg268Cys	p.R268C	ENST00000327367	NM_005902.3	268	Cgc/Tgc	6/9	0.391470617217201	4	FACETS	1	0.925	1	0.524	0.466	0.584	CLONAL	1	TRUE	2	0.385614330801614	4		509	652	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106926	11106928	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs876657378	NA	P-0026994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	109	700	0	ENST00000358026.2:c.1636_1638del	p.Lys546del	p.K546del	ENST00000358026	NM_001128849.1	544	cAGAag/cag	10/36	0.385614330801614	7	FACETS	0.889	0.796	0.988	0.222	0.199	0.247	CLONAL	1	TRUE	3	0.385614330801614	7		700	1249	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125634	47125634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1357325164	NA	P-0026994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	85	320	0	ENST00000409792.3:c.5636G>A	p.Arg1879His	p.R1879H	ENST00000409792	NM_014159.6	1879	cGc/cAc	12/21	0.385614330801614	6	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.385614330801614	6		320	577	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962929	2962929	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147006022	NA	P-0026994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	83	768	2	ENST00000396946.4:c.1979G>A	p.Arg660Gln	p.R660Q	ENST00000396946	NM_032415.4	660	cGg/cAg	16/25	NA	2	FACETS	0.825	0.73	0.926			1	INDETERMINATE	1	TRUE	NA	0.385614330801614	2		770	522	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267186	41267186	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553630452	NA	P-0026994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	119	335	0	ENST00000349496.5:c.770C>T	p.Thr257Ile	p.T257I	ENST00000349496	NM_001904.3	257	aCa/aTa	6/15	0.391470617217201	4	FACETS	0.758	0.687	0.833	0.758	0.687	0.833	SUBCLONAL	2	TRUE	2	0.385614330801614	4		335	564	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117878	70117888	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCAGGCGGC	GCGCAGGCGGC	-	novel	NA	P-0026994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	37	385	0	ENST00000245479.2:c.353_363del	p.Ala118GlufsTer130	p.A118Efs*130	ENST00000245479	NM_000346.3	116	GCGCAGGCGGCg/g	1/3	0.340327734934883	4	FACETS	0.787	0.65	0.939	0.393	0.325	0.47	CLONAL	1	TRUE	2	0.385614330801614	4		385	338	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465543	8465543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	283	482	0	ENST00000356435.5:c.3637G>A	p.Gly1213Arg	p.G1213R	ENST00000356435		1213	Gga/Aga	21/35	0.353492591625358	4	FACETS	0.974	0.921	1	0.974	0.921	1	CLONAL	3	TRUE	1	0.385614330801614	4		482	696	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457402	67457402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886038771	NA	P-0026994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	78	530	1	ENST00000327367.4:c.376C>T	p.His126Tyr	p.H126Y	ENST00000327367	NM_005902.3	126	Cac/Tac	2/9	0.391470617217201	4	FACETS	0.772	0.678	0.873	0.386	0.339	0.437	SUBCLONAL	1	TRUE	2	0.385614330801614	4		531	726	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477156	67477156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	128	507	1	ENST00000327367.4:c.964del	p.Gln322SerfsTer19	p.Q322Sfs*19	ENST00000327367	NM_005902.3	321	aaC/aa	7/9	0.391470617217201	4	FACETS	1	0.972	1	0.59	0.535	0.649	CLONAL	1	TRUE	2	0.385614330801614	4		508	779	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477178	67477187	+	frameshift_variant	Frame_Shift_Del	DEL	GCCACCGTCT	GCCACCGTCT	-	novel	NA	P-0026994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	65	443	0	ENST00000327367.4:c.987_996del	p.Thr330ArgfsTer8	p.T330Rfs*8	ENST00000327367	NM_005902.3	329	GCCACCGTCTgc/gc	7/9	0.391470617217201	4	FACETS	0.66	0.571	0.756	0.33	0.285	0.378	SUBCLONAL	1	TRUE	2	0.385614330801614	4		443	708	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790495	3790496	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	207	528	1	ENST00000262367.5:c.4037dup	p.Leu1346PhefsTer8	p.L1346Ffs*8	ENST00000262367	NM_004380.2	1346	ttg/ttTg	24/31	0.365637978575905	4	FACETS	0.986	0.918	1			1	CLONAL	2	TRUE	NA	0.385614330801614	4		529	754	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341299	89341299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	57	159	1	ENST00000301030.4:c.7636G>A	p.Ala2546Thr	p.A2546T	ENST00000301030	NM_001256183.1	2546	Gcc/Acc	11/13	0.385614330801614	5	FACETS	1	0.943	1	0.77	0.671	0.875	CLONAL	2	TRUE	2	0.385614330801614	5		160	202	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374932	45374932	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	288	510	0	ENST00000262160.6:c.911A>G	p.Asp304Gly	p.D304G	ENST00000262160	NM_005901.5	304	gAc/gGc	8/11	0.365637978575905	4	FACETS	0.984	0.932	1			1	CLONAL	3	TRUE	NA	0.385614330801614	4		510	701	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395643	45395643	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	94	444	0	ENST00000262160.6:c.491C>T	p.Pro164Leu	p.P164L	ENST00000262160	NM_005901.5	164	cCt/cTt	4/11	0.365637978575905	4	FACETS	0.92	0.819	1			1	CLONAL	1	TRUE	NA	0.385614330801614	4		444	734	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514459	41514459	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	88	401	0	ENST00000373198.4:c.202G>T	p.Ala68Ser	p.A68S	ENST00000373198	NM_133170.3	68	Gca/Tca	2/32	0.391470617217201	0	FACETS	1	0.952	1			1	CLONAL	1	TRUE	0	0.385614330801614	0		401	255	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096092	71096092	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0026994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	84	210	0	ENST00000318789.4:c.664+1G>A		p.X222_splice	ENST00000318789	NM_032682.5	222			0.341903104111131	5	FACETS	0.888	0.79	0.993			1	CLONAL	2	TRUE	NA	0.385614330801614	5		210	387	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508784	31508784	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0026994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	148	620	0	ENST00000344624.3:c.1531A>T	p.Lys511Ter	p.K511*	ENST00000344624		511	Aaa/Taa	7/33	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.385614330801614	2		620	622	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041022	112041022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376255649	NA	P-0026994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	80	360	0	ENST00000368678.4:c.233C>T	p.Thr78Met	p.T78M	ENST00000368678		78	aCg/aTg	3/13	0.385614330801614	6	FACETS	0.802	0.709	0.902			1	CLONAL	2	TRUE	NA	0.385614330801614	6		360	458	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0027859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	60	563	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		563	238	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881505	48881505	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0029591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	80	311	0	ENST00000267163.4:c.227T>G	p.Leu76Ter	p.L76*	ENST00000267163	NM_000321.2	76	tTa/tGa	2/27	0.255379520770042	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.255379520770042	1		311	457	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038617	14038617	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	88	426	1	ENST00000311895.7:c.1942G>T	p.Gly648Cys	p.G648C	ENST00000311895	NM_005236.2	648	Ggc/Tgc	10/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.255379520770042	2		427	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579393	+	frameshift_variant	Frame_Shift_Del	DEL	GGGAA	GGGAA	-	novel	NA	P-0029591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	100	637	0	ENST00000269305.4:c.294_298del	p.Ser99GlufsTer48	p.S99Efs*48	ENST00000269305	NM_001126112.2	98	ccTTCCCag/ccag	4/11	0.255379520770042	1	FACETS	0.933	0.834	1	0.933	0.834	1	CLONAL	1	TRUE	0	0.255379520770042	1		637	732	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860904	45860904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	99	655	0	ENST00000391945.4:c.1291C>T	p.Pro431Ser	p.P431S	ENST00000391945	NM_000400.3	431	Ccc/Tcc	13/23	0.255379520770042	1	FACETS	0.959	0.857	1	0.959	0.857	1	CLONAL	1	TRUE	0	0.255379520770042	1		655	705	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0036329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	449	605	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.603123904702527	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.603123904702527	1		605	894	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0036329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	243	281	0				ENST00000310581	NM_198253.2	-/1132			0.603123904702527	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.603123904702527	1		281	438	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0036329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	299	493	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.603123904702527	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.603123904702527	1		493	592	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265313	10265313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762421501	NA	P-0036329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	222	618	0	ENST00000340748.4:c.1733C>T	p.Thr578Ile	p.T578I	ENST00000340748		578	aCa/aTa	20/40	0.352915369523801	3	FACETS	0.917	0.853	0.983	0.458	0.426	0.492	INDETERMINATE	1	TRUE	1	0.603123904702527	3		618	1045	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100425	8100425	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	178	666	2	ENST00000346208.3:c.404del	p.Pro135ArgfsTer60	p.P135Rfs*60	ENST00000346208		133	taC/ta	3/6	0.603123904702527	1	FACETS	0.445	0.41	0.482	0.445	0.41	0.482	SUBCLONAL	1	TRUE	0	0.603123904702527	1		668	926	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0036329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	188	432	0	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	0.603123904702527	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.603123904702527	1		432	398	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865830	56865830	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145146218	NA	P-0036329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	67	285	1	ENST00000308159.5:c.1162C>T	p.Arg388Trp	p.R388W	ENST00000308159	NM_014669.4	388	Cgg/Tgg	11/22	0.603123904702527	1	FACETS	0.486	0.426	0.551	0.486	0.426	0.551	SUBCLONAL	1	TRUE	0	0.603123904702527	1		286	319	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248766	212248766	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs549128376	NA	P-0036329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	50	320	0	ENST00000342788.4:c.3501G>T	p.Glu1167Asp	p.E1167D	ENST00000342788	NM_005235.2	1167	gaG/gaT	28/28	0.585340449518492	2	FACETS	0.493	0.42	0.573	0.247	0.21	0.287	SUBCLONAL	1	TRUE	0	0.603123904702527	2		320	336	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560494	65560494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	540	564	0	ENST00000358664.4:c.103C>T	p.Arg35Cys	p.R35C	ENST00000358664	NM_002382.4	35	Cgt/Tgt	3/5	0.603123904702527	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.603123904702527	2		564	894	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395569	116395569	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs375951814	NA	P-0036329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	230	410	1	ENST00000397752.3:c.1862C>T	p.Thr621Ile	p.T621I	ENST00000397752	NM_000245.2	621	aCa/aTa	6/21	0.32290435297405	2	FACETS	0.772	0.728	0.816	0.772	0.728	0.816	INDETERMINATE	2	TRUE	0	0.603123904702527	2		411	494	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	495101	495101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201821956	NA	P-0036329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	151	446	0	ENST00000399788.2:c.205C>T	p.Arg69Cys	p.R69C	ENST00000399788	NM_001042603.1	69	Cgt/Tgt	2/28	0.603123904702527	1	FACETS	0.861	0.796	0.928	0.861	0.796	0.928	CLONAL	1	TRUE	0	0.603123904702527	1		446	406	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210784	5210784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762745270	NA	P-0036329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	155	712	0	ENST00000357368.4:c.5267C>T	p.Pro1756Leu	p.P1756L	ENST00000357368	NM_002850.3	1756	cCg/cTg	34/38	0.352915369523801	3	FACETS	0.557	0.508	0.607	0.278	0.254	0.304	INDETERMINATE	1	TRUE	1	0.603123904702527	3		712	1202	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224725	36224725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372416919	NA	P-0036329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1353	183	862	1	ENST00000222270.7:c.7111G>A	p.Asp2371Asn	p.D2371N	ENST00000222270	NM_014727.1	2371	Gat/Aat	30/37	0.352915369523801	3	FACETS	0.514	0.473	0.558	0.257	0.236	0.279	INDETERMINATE	1	TRUE	1	0.603123904702527	3		863	1536	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214574	5214574	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1205787412	NA	P-0036329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	106	630	0	ENST00000357368.4:c.4492C>T	p.Arg1498Trp	p.R1498W	ENST00000357368	NM_002850.3	1498	Cgg/Tgg	29/38	0.352915369523801	3	FACETS	0.452	0.404	0.503	0.226	0.202	0.252	INDETERMINATE	1	TRUE	1	0.603123904702527	3		630	1012	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368226	31368226	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773918660	NA	P-0036329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	104	584	0	ENST00000328111.2:c.97G>A	p.Asp33Asn	p.D33N	ENST00000328111	NM_006892.3	33	Gac/Aac	2/23	1	2	FACETS	0.431	0.385	0.479	0.431	0.385	0.479	SUBCLONAL	1	TRUE	1	0.603123904702527	2		584	801	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383182	42383182	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782657641	NA	P-0036329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	473	610	0	ENST00000221972.3:c.202C>T	p.Arg68Cys	p.R68C	ENST00000221972	NM_021601.3	68	Cgc/Tgc	2/5	0.352915369523801	3	FACETS	0.898	0.86	0.936	0.898	0.86	0.936	INDETERMINATE	2	TRUE	1	0.603123904702527	3		610	1137	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417475	139417475	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761616770	NA	P-0036329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	726	721	0	ENST00000277541.6:c.569G>A	p.Arg190His	p.R190H	ENST00000277541	NM_017617.3	190	cGc/cAc	4/34	0.592747970275827	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.603123904702527	1		721	1229	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942558	71942558	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	275	450	0	ENST00000298229.2:c.1514T>C	p.Leu505Pro	p.L505P	ENST00000298229	NM_001567.3	505	cTg/cCg	13/28	0.603123904702527	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.603123904702527	1		450	535	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643738	38643738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772476060	NA	P-0036329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	179	844	0	ENST00000299084.4:c.1208G>A	p.Arg403Gln	p.R403Q	ENST00000299084	NM_152594.2	403	cGa/cAa	7/7	0.603123904702527	1	FACETS	0.485	0.448	0.525	0.485	0.448	0.525	SUBCLONAL	1	TRUE	0	0.603123904702527	1		844	854	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133218	30133218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	289	574	1	ENST00000263025.4:c.280C>T	p.Arg94Cys	p.R94C	ENST00000263025	NM_002746.2	94	Cgc/Tgc	2/9	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.603123904702527	2		575	951	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822600	72822600	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	114	554	0	ENST00000268489.5:c.9575C>A	p.Pro3192His	p.P3192H	ENST00000268489	NM_006885.3	3192	cCt/cAt	10/10	0.603123904702527	1	FACETS	0.518	0.468	0.57	0.518	0.468	0.57	SUBCLONAL	1	TRUE	0	0.603123904702527	1		554	510	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170728	7170728	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	297	658	0	ENST00000302850.5:c.1303C>A	p.Leu435Ile	p.L435I	ENST00000302850	NM_000208.2	435	Cta/Ata	6/22	0.352915369523801	3	FACETS	1	0.973	1	0.528	0.497	0.561	INDETERMINATE	1	TRUE	1	0.603123904702527	3		658	1213	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096021	11096021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778890805	NA	P-0036329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	317	710	0	ENST00000358026.2:c.295C>T	p.Arg99Trp	p.R99W	ENST00000358026	NM_001128849.1	99	Cgg/Tgg	3/36	0.352915369523801	3	FACETS	1	0.981	1	0.546	0.514	0.578	INDETERMINATE	1	TRUE	1	0.603123904702527	3		710	1254	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288655	15288655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1484574156	NA	P-0036329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	17	4	0	ENST00000263388.2:c.4084G>A	p.Ala1362Thr	p.A1362T	ENST00000263388	NM_000435.2	1362	Gct/Act	24/33	0.352915369523801	3	FACETS	0.906	0.744	1	1	0.925	1	INDETERMINATE	3	TRUE	1	0.603123904702527	3		4	27	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753560	42753560	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs766060945	NA	P-0036329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	129	685	0	ENST00000222329.4:c.704A>G	p.Tyr235Cys	p.Y235C	ENST00000222329	NM_006494.2	235	tAt/tGt	4/4	0.352915369523801	3	FACETS	0.486	0.439	0.535	0.243	0.219	0.268	INDETERMINATE	1	TRUE	1	0.603123904702527	3		685	1146	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728547	190728547	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778382887	NA	P-0036329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	64	437	0	ENST00000441310.2:c.1935G>A	p.Met645Ile	p.M645I	ENST00000441310	NM_000534.4	645	atG/atA	10/13	0.585340449518492	2	FACETS	0.596	0.519	0.679	0.298	0.259	0.34	SUBCLONAL	1	TRUE	0	0.603123904702527	2		437	356	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089163	37089163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	114	420	0	ENST00000231790.2:c.1885G>A	p.Glu629Lys	p.E629K	ENST00000231790	NM_000249.3	629	Gaa/Aaa	16/19	0.603123904702527	1	FACETS	0.423	0.382	0.467	0.423	0.382	0.467	SUBCLONAL	1	TRUE	0	0.603123904702527	1		420	624	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125763	47125763	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144171734	NA	P-0036329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	240	409	0	ENST00000409792.3:c.5507C>T	p.Pro1836Leu	p.P1836L	ENST00000409792	NM_014159.6	1836	cCg/cTg	12/21	0.603123904702527	1	FACETS	0.962	0.906	1	0.962	0.906	1	CLONAL	1	TRUE	0	0.603123904702527	1		409	578	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442065	52442065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	451	517	0	ENST00000460680.1:c.284C>T	p.Ala95Val	p.A95V	ENST00000460680	NM_004656.3	95	gCc/gTc	5/17	0.603123904702527	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.603123904702527	1		517	760	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120446	94120446	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	22	348	0	ENST00000369303.4:c.605A>G	p.Tyr202Cys	p.Y202C	ENST00000369303	NM_004440.3	202	tAc/tGc	3/17	0.603123904702527	1	FACETS	0.129	0.099	0.163	0.129	0.099	0.163	SUBCLONAL	1	TRUE	0	0.603123904702527	1		348	396	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678004	117678004	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs772575534	NA	P-0036329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	103	486	0	ENST00000368508.3:c.3929A>G	p.His1310Arg	p.H1310R	ENST00000368508	NM_002944.2	1310	cAc/cGc	25/43	0.603123904702527	1	FACETS	0.389	0.348	0.431	0.389	0.348	0.431	SUBCLONAL	1	TRUE	0	0.603123904702527	1		486	614	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0041072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	399	882	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.701894514970054	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.701894514970054	1		883	726	SUCCESS
APC	324	MSKCC	GRCh37	5	112175162	112175162	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561588104	NA	P-0041072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	97	228	0	ENST00000257430.4:c.3871C>T	p.Gln1291Ter	p.Q1291*	ENST00000257430	NM_000038.5	1291	Cag/Tag	16/16	0.692239063082158	2	FACETS	0.966	0.899	1	0.966	0.899	1	CLONAL	2	TRUE	0	0.701894514970054	2		228	143	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799626	3799626	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0041072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	66	515	0	ENST00000262367.5:c.3836+2T>G		p.X1279_splice	ENST00000262367	NM_004380.2	1279			1	2	FACETS	0.729	0.64	0.823	0.729	0.64	0.823	SUBCLONAL	1	TRUE	1	0.701894514970054	2		515	258	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0041454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	70	477	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.149501806379262	3	FACETS	1	0.965	1	0.435	0.38	0.494	INDETERMINATE	1	TRUE	0	0.274080489970767	3		477	445	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835627	68835627	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	594	420	0	ENST00000261769.5:c.220del	p.Arg74AspfsTer9	p.R74Dfs*9	ENST00000261769	NM_004360.3	73	aCc/ac	3/16	0.821765112467897	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.821765112467897	2		420	719	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032818	30032818	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	163	357	0	ENST00000338641.4:c.193C>T	p.Gln65Ter	p.Q65*	ENST00000338641	NM_000268.3	65	Cag/Tag	2/16	0.695017761490772	1	FACETS	0.969	0.906	1	0.969	0.906	1	CLONAL	1	TRUE	0	0.695017761490772	1		357	316	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916766	48916766	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	191	236	0	ENST00000267163.4:c.296G>A	p.Trp99Ter	p.W99*	ENST00000267163	NM_000321.2	99	tGg/tAg	3/27	0.695017761490772	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.695017761490772	1		236	338	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549385	187549386	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAA	novel	NA	P-0052672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	265	497	0	ENST00000441802.2:c.4730_4732dup	p.Val1577dup	p.V1577dup	ENST00000441802	NM_005245.3	1577	ggc/gTTGgc	9/27	0.695017761490772	1	FACETS	0.893	0.846	0.941	0.893	0.846	0.941	CLONAL	1	TRUE	0	0.695017761490772	1		497	557	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879904	44879904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs912069418	NA	P-0052672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	215	377	1	ENST00000377967.4:c.493C>T	p.Arg165Ter	p.R165*	ENST00000377967	NM_021140.2	165	Cga/Tga	6/29	0.695017761490772	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.695017761490772	1		378	400	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0052672-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	10	600	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.78188774802656	1	FACETS	0.117	0.08	0.164	0.117	0.08	0.164	SUBCLONAL	1	TRUE	0	0.806450954193969	1		600	126	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032818	30032818	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052672-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	58	357	0	ENST00000338641.4:c.193C>T	p.Gln65Ter	p.Q65*	ENST00000338641	NM_000268.3	65	Cag/Tag	2/16	0.806450954193969	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.806450954193969	1		357	72	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600416	10600416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1021362446	NA	P-0052672-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	9	757	1	ENST00000171111.5:c.1439G>A	p.Gly480Glu	p.G480E	ENST00000171111	NM_203500.1	480	gGg/gAg	4/6	1	2	FACETS	0.065	0.043	0.094	0.065	0.043	0.094	SUBCLONAL	1	TRUE	1	0.806450954193969	2		758	342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0056860-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	1107	648	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.41073372655725	4	FACETS	1	0.994	1			1	INDETERMINATE	4	TRUE	NA	0.854766219465377	4		648	1194	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027127	49027127	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0056860-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	178	277	0	ENST00000267163.4:c.1696-2A>T		p.X566_splice	ENST00000267163	NM_000321.2	566			0.854766219465377	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.854766219465377	3		277	191	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602408	28602408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056860-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	524	457	0	ENST00000241453.7:c.1960G>A	p.Glu654Lys	p.E654K	ENST00000241453	NM_004119.2	654	Gaa/Aaa	16/24	0.854766219465377	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.854766219465377	3		457	583	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636196	28636196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056860-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	623	482	1	ENST00000241453.7:c.176C>T	p.Ser59Phe	p.S59F	ENST00000241453	NM_004119.2	59	tCc/tTc	3/24	0.854766219465377	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.854766219465377	3		483	675	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95573958	95573958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1256068472	NA	P-0056860-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	81	262	0	ENST00000393063.1:c.2791G>A	p.Val931Ile	p.V931I	ENST00000393063	NM_030621.3	931	Gtt/Att	18/28	0.854766219465377	4	FACETS	0.827	0.732	0.928	0.276	0.244	0.31	CLONAL	1	TRUE	1	0.854766219465377	4		262	425	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690810	89690810	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1488857080	NA	P-0056860-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	126	333	0	ENST00000371953.3:c.217G>T	p.Glu73Ter	p.E73*	ENST00000371953	NM_000314.4	73	Gaa/Taa	4/9	0.854766219465377	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.854766219465377	2		333	134	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15840928	15840928	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056860-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	107	182	0	ENST00000307771.7:c.1012G>C	p.Glu338Gln	p.E338Q	ENST00000307771	NM_005089.3	338	Gaa/Caa	11/11	0.592760201760212	2	FACETS	0.852	0.775	0.93			1	CLONAL	1	TRUE	NA	0.854766219465377	2		182	294	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841331	15841331	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056860-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	91	219	0	ENST00000307771.7:c.1415G>C	p.Arg472Thr	p.R472T	ENST00000307771	NM_005089.3	472	aGa/aCa	11/11	0.592760201760212	2	FACETS	0.563	0.504	0.626			1	SUBCLONAL	1	TRUE	NA	0.854766219465377	2		219	378	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058732	42058732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056860-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	95	261	0	ENST00000219905.7:c.8452G>A	p.Asp2818Asn	p.D2818N	ENST00000219905	NM_001164273.1	2818	Gat/Aat	24/24	0.854766219465377	2	FACETS	0.911	0.826	0.998	0.455	0.413	0.499	CLONAL	1	TRUE	0	0.854766219465377	2		261	244	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265578	152265578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064632-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	214	622	0	ENST00000206249.3:c.1031G>A	p.Gly344Asp	p.G344D	ENST00000206249	NM_000125.3	344	gGc/gAc	4/8	0.491021355411288	5	FACETS	0.967	0.907	1	0.58	0.544	0.617	CLONAL	3	TRUE	0	0.491021355411288	5		622	522	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716208	52716208	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064632-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	172	718	0	ENST00000322088.6:c.652G>A	p.Asp218Asn	p.D218N	ENST00000322088	NM_014225.5	218	Gac/Aac	6/15	0.328629480871792	3	FACETS	0.803	0.744	0.864			1	CLONAL	2	TRUE	NA	0.491021355411288	3		718	543	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657010	47657029	+	frameshift_variant	Frame_Shift_Del	DEL	AGATTGTTACCGACTCTATC	AGATTGTTACCGACTCTATC	-	novel	NA	P-0064632-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	47	346	0	ENST00000233146.2:c.1208_1227del	p.Asp403GlyfsTer7	p.D403Gfs*7	ENST00000233146	NM_000251.2	402	caAGATTGTTACCGACTCTATCag/caag	7/16	0.357313933394405	4	FACETS	0.892	0.767	1	0.892	0.767	1	CLONAL	2	TRUE	2	0.491021355411288	4		346	160	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681615	30681615	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751055479	NA	P-0064632-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	420	627	1	ENST00000376406.3:c.482G>A	p.Arg161Lys	p.R161K	ENST00000376406	NM_014641.2	161	aGg/aAg	3/15	0.491021355411288	8	FACETS	0.994	0.953	1			1	CLONAL	5	TRUE	NA	0.491021355411288	8		628	851	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325378	1325378	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066435-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	34	351	0	ENST00000400841.2:c.297C>G	p.Ile99Met	p.I99M	ENST00000400841		99	atC/atG	3/6	1	2	FACETS	0.643	0.525	0.776	0.643	0.525	0.776	SUBCLONAL	1	TRUE	1	0.229937625203686	2		351	460	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163023	47163023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	44	590	0	ENST00000409792.3:c.3103C>T	p.His1035Tyr	p.H1035Y	ENST00000409792	NM_014159.6	1035	Cat/Tat	3/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		590	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0067152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	117	605	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		605	508	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0067152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	105	240	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		240	649	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0067152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	89	745	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		745	603	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575645	55575645	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs757234342	NA	P-0067152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	83	376	0	ENST00000288135.5:c.1171A>G	p.Thr391Ala	p.T391A	ENST00000288135	NM_000222.2	391	Aca/Gca	7/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		376	477	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46738376	46738376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	66	680	0	ENST00000371975.4:c.1277G>A	p.Arg426Lys	p.R426K	ENST00000371975	NM_003579.3	426	aGg/aAg	12/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		680	671	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341328	89341328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	53	339	0	ENST00000301030.4:c.7607G>A	p.Arg2536Gln	p.R2536Q	ENST00000301030	NM_001256183.1	2536	cGg/cAg	11/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		339	272	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0067152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	76	332	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		332	370	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492805	56492806	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0067152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	106	736	0	ENST00000407977.2:c.132_133dup	p.Lys45ArgfsTer7	p.K45Rfs*7	ENST00000407977		45	aaa/aGAaa	2/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		736	594	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0067183-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	22	318	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		318	376	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249002	55249003	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGTGGA	rs397517109	NA	P-0067183-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	123	462	0	ENST00000275493.2:c.2303_2311dup	p.Ser768_Asp770dup	p.S768_D770dup	ENST00000275493	NM_005228.3	768	gcc/gcCAGCGTGGAc	20/28	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		462	490	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	27	332	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.9	0.725	1	0.9	0.725	1	CLONAL	1	TRUE	1	0.4	2		332	150	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	46	577	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.4	2		582	230	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466022	69466022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	50	505	0	ENST00000227507.2:c.860C>T	p.Pro287Leu	p.P287L	ENST00000227507	NM_053056.2	287	cCc/cTc	5/5	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.4	2		505	225	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	68	453	3	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.4	2		456	278	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	46	360	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.92	0.781	1	0.92	0.781	1	CLONAL	1	TRUE	1	0.4	2		360	250	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	46	495	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.819	0.694	0.954	0.819	0.694	0.954	CLONAL	1	TRUE	1	0.4	2		496	281	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	33	270	0	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	1	2	FACETS	0.821	0.674	0.983	0.821	0.674	0.983	CLONAL	1	TRUE	1	0.4	2		270	201	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591135	67591137	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	40	373	0	ENST00000274335.5:c.1728_1730del	p.Arg577del	p.R577del	ENST00000274335		576	acGAGa/aca	12/15	1	2	FACETS	0.926	0.777	1	0.926	0.777	1	CLONAL	1	TRUE	1	0.4	2		373	216	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543650	148543650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768812143	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	47	388	3	ENST00000320356.2:c.158C>T	p.Thr53Met	p.T53M	ENST00000320356	NM_004456.4	53	aCg/aTg	3/20	1	2	FACETS	0.81	0.688	0.944	0.81	0.688	0.944	CLONAL	1	TRUE	1	0.4	2		391	290	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	30	410	7	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.932	0.76	1	0.932	0.76	1	CLONAL	1	TRUE	1	0.4	2		417	161	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533939	63533940	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs771001164	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	30	440	0	ENST00000307078.5:c.1214_1215del	p.Glu405GlyfsTer56	p.E405Gfs*56	ENST00000307078	NM_004655.3	405	gAG/g	6/11	1	2	FACETS	0.777	0.632	0.939	0.777	0.632	0.939	CLONAL	1	TRUE	1	0.4	2		440	193	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	25	373	2	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	0.822	0.655	1	0.822	0.655	1	CLONAL	1	TRUE	1	0.4	2		375	152	SUCCESS
APC	324	MSKCC	GRCh37	5	112178033	112178033	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs773874693	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	29	415	2	ENST00000257430.4:c.6747del	p.Gly2250AlafsTer29	p.G2250Afs*29	ENST00000257430	NM_000038.5	2248	Aaa/aa	16/16	1	2	FACETS	0.704	0.569	0.855	0.704	0.569	0.855	SUBCLONAL	1	TRUE	1	0.4	2		417	206	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098816	178098816	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	43	427	0	ENST00000397062.3:c.229G>T	p.Asp77Tyr	p.D77Y	ENST00000397062	NM_006164.4	77	Gat/Tat	2/5	1	2	FACETS	0.991	0.838	1	0.991	0.838	1	CLONAL	1	TRUE	1	0.4	2		427	217	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653817	89653817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	32	289	0	ENST00000371953.3:c.115G>A	p.Ala39Thr	p.A39T	ENST00000371953	NM_000314.4	39	Gca/Aca	2/9	1	2	FACETS	0.988	0.812	1	0.988	0.812	1	CLONAL	1	TRUE	1	0.4	2		289	162	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	58	606	0	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.4	2		606	275	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322732	39322732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	38	372	0	ENST00000373001.3:c.260C>T	p.Pro87Leu	p.P87L	ENST00000373001	NM_022157.3	87	cCc/cTc	2/7	1	2	FACETS	0.927	0.774	1	0.927	0.774	1	CLONAL	1	TRUE	1	0.4	2		372	205	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376248	15376248	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	15	255	1	ENST00000263377.2:c.766del	p.Gln256SerfsTer27	p.Q256Sfs*27	ENST00000263377	NM_058243.2	256	Cag/ag	5/20	1	2	FACETS	0.714	0.529	0.931	0.714	0.529	0.931	CLONAL	1	TRUE	1	0.4	2		256	105	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3634827	3634827	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs543847606	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	59	432	0	ENST00000294008.3:c.4682C>T	p.Thr1561Met	p.T1561M	ENST00000294008	NM_032444.2	1561	aCg/aTg	13/15	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.4	2		432	293	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27098991	27098991	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs375417370	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	44	417	0	ENST00000324856.7:c.3407C>T	p.Ala1136Val	p.A1136V	ENST00000324856	NM_006015.4	1136	gCg/gTg	13/20	1	2	FACETS	0.978	0.828	1	0.978	0.828	1	CLONAL	1	TRUE	1	0.4	2		417	225	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351745	89351745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201526691	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	59	436	0	ENST00000301030.4:c.1205C>T	p.Ala402Val	p.A402V	ENST00000301030	NM_001256183.1	402	gCg/gTg	9/13	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.4	2		436	292	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805787	32805788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1174402903	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	38	481	0	ENST00000374899.4:c.223dup	p.Leu75ProfsTer92	p.L75Pfs*92	ENST00000374899	NM_018833.2	75	ctg/cCtg	2/12	1	2	FACETS	0.9	0.751	1	0.9	0.751	1	CLONAL	1	TRUE	1	0.4	2		481	211	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673717	176673717	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784117	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	54	359	0	ENST00000439151.2:c.4417C>T	p.Arg1473Ter	p.R1473*	ENST00000439151	NM_022455.4	1473	Cga/Tga	10/23	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.4	2		359	240	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211795	36211795	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	36	470	2	ENST00000222270.7:c.1549del	p.Ser517AlafsTer5	p.S517Afs*5	ENST00000222270	NM_014727.1	516	Aaa/aa	3/37	1	2	FACETS	0.779	0.645	0.927	0.779	0.645	0.927	CLONAL	1	TRUE	1	0.4	2		472	231	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140879	37140879	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	46	454	0	ENST00000373509.5:c.715G>T	p.Asp239Tyr	p.D239Y	ENST00000373509	NM_002648.3	239	Gat/Tat	5/6	1	2	FACETS	0.759	0.643	0.886	0.759	0.643	0.886	SUBCLONAL	1	TRUE	1	0.4	2		454	303	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754461	41754461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777326148	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	40	410	0	ENST00000301178.4:c.1580G>A	p.Arg527Gln	p.R527Q	ENST00000301178	NM_021913.4	527	cGg/cAg	13/20	1	2	FACETS	0.905	0.759	1	0.905	0.759	1	CLONAL	1	TRUE	1	0.4	2		410	221	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098425	11098425	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	32	374	1	ENST00000358026.2:c.947del	p.Pro316LeufsTer10	p.P316Lfs*10	ENST00000358026	NM_001128849.1	315	Ccc/cc	6/36	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.4	2		375	143	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534266	187534266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759492838	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	29	319	0	ENST00000441802.2:c.9460G>A	p.Ala3154Thr	p.A3154T	ENST00000441802	NM_005245.3	3154	Gca/Aca	13/27	1	2	FACETS	0.788	0.638	0.955	0.788	0.638	0.955	CLONAL	1	TRUE	1	0.4	2		319	184	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096058	11096059	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	42	501	0	ENST00000358026.2:c.336dup	p.Met113HisfsTer16	p.M113Hfs*16	ENST00000358026	NM_001128849.1	111	agc/agCc	3/36	1	2	FACETS	0.929	0.783	1	0.929	0.783	1	CLONAL	1	TRUE	1	0.4	2		501	226	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159040	24159040	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765514964	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	55	428	1	ENST00000263121.7:c.712G>A	p.Ala238Thr	p.A238T	ENST00000263121	NM_003073.3	238	Gcc/Acc	6/9	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.4	2		429	225	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57004384	57004384	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	27	467	1	ENST00000257254.3:c.95C>A	p.Pro32His	p.P32H	ENST00000257254		32	cCt/cAt	1/2	1	2	FACETS	0.726	0.582	0.887	0.726	0.582	0.887	SUBCLONAL	1	TRUE	1	0.4	2		468	186	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653817	89653818	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	36	287	2	ENST00000371953.3:c.115_116delinsAT	p.Ala39Ile	p.A39I	ENST00000371953	NM_000314.4	39	GCa/ATa	2/9	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.4	2		289	166	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653818	89653818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	36	286	0	ENST00000371953.3:c.116C>T	p.Ala39Val	p.A39V	ENST00000371953	NM_000314.4	39	gCa/gTa	2/9	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.4	2		286	166	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446771	29446772	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	44	417	0	ENST00000544604.2:c.2602_2603del	p.Arg868GlyfsTer17	p.R868Gfs*17	ENST00000544604	NM_001206998.1	868	AGg/g	8/9	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.4	2		417	169	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536650	120536650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	50	427	0	ENST00000229340.5:c.442G>A	p.Glu148Lys	p.E148K	ENST00000229340	NM_006861.6	148	Gag/Aag	5/6	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.4	2		427	240	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600417	10600417	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	15	347	0	ENST00000171111.5:c.1438G>T	p.Gly480Trp	p.G480W	ENST00000171111	NM_203500.1	480	Ggg/Tgg	4/6	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		347	742	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445170	49445170	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	89	536	0	ENST00000301067.7:c.2296G>T	p.Glu766Ter	p.E766*	ENST00000301067	NM_003482.3	766	Gag/Tag	10/54	1	2	FACETS	0.332	0.294	0.373	0.332	0.294	0.373	SUBCLONAL	1	TRUE	1	0.657230264693232	2		536	816	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330629	65330630	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	79	320	0	ENST00000342505.4:c.1016dup	p.Asn339LysfsTer2	p.N339Kfs*2	ENST00000342505	NM_002227.2	339	aat/aaAt	8/25	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		320	344	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309776	104309776	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	238	304	0	ENST00000369902.3:c.367C>A	p.Arg123Ser	p.R123S	ENST00000369902	NM_016169.3	123	Cgt/Agt	3/12	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		304	334	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003803	45004048	+	splice_donor_variant,splice_donor_5th_base_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTATCCAGCGTGAGTCTCTCCTACCCTCCCGCTCTGGTCCTTCCTCTCCCGCTCTGCACCCTCTGTGGCCCTCGCTGTGCTCTCTCGCTCCGTGACTTCCCTTCTCCAAGTTCTCCTTGGTGGCCCGCCGTGGGGCTAGTCCAGGGCTGGATCTCGGGGAAGCGGCGGGGTGGCCTGGGAGTGGGGAAGGGGGTGCGCACCCGGGACGCGCGCTACTTGCCCCTTTCGGCGGGGAGCAGGGGAGAC	CTATCCAGCGTGAGTCTCTCCTACCCTCCCGCTCTGGTCCTTCCTCTCCCGCTCTGCACCCTCTGTGGCCCTCGCTGTGCTCTCTCGCTCCGTGACTTCCCTTCTCCAAGTTCTCCTTGGTGGCCCGCCGTGGGGCTAGTCCAGGGCTGGATCTCGGGGAAGCGGCGGGGTGGCCTGGGAGTGGGGAAGGGGGTGCGCACCCGGGACGCGCGCTACTTGCCCCTTTCGGCGGGGAGCAGGGGAGAC	-	novel	NA	P-0067187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	20	340	0	ENST00000558401.1:c.61_67+239del		p.X21_splice	ENST00000558401	NM_004048.2	21		1/4	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		340	370	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68301879	68301879	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	242	283	0	ENST00000487270.1:c.281T>G	p.Leu94Arg	p.L94R	ENST00000487270	NM_133509.3	94	cTg/cGg	4/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		283	586	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0067188-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	108	882	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.209479524518294	2	FACETS	0.914	0.823	1	0.914	0.823	1	CLONAL	2	TRUE	0	0.209479524518294	2		883	564	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0067188-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	63	549	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.209479524518294	2		549	554	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346505	89346505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024078594	NA	P-0067188-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	125	526	0	ENST00000301030.4:c.6445G>A	p.Ala2149Thr	p.A2149T	ENST00000301030	NM_001256183.1	2149	Gca/Aca	9/13	0.189373457863748	5	FACETS	0.894	0.812	0.98	0.894	0.812	0.98	CLONAL	3	TRUE	2	0.209479524518294	5		526	585	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0067188-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	67	736	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.150028485445641	4	FACETS	1	0.914	1	1	0.977	1	CLONAL	3	TRUE	2	0.209479524518294	4		736	246	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589639	67589641	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0067188-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	36	323	0	ENST00000274335.5:c.1405_1407del	p.Glu469del	p.E469del	ENST00000274335		468	GAA/-	10/15	0.209479524518294	2	FACETS	0.999	0.832	1	0.999	0.832	1	CLONAL	2	TRUE	0	0.209479524518294	2		323	172	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711943	89711943	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067188-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	55	285	0	ENST00000371953.3:c.562del	p.Tyr188IlefsTer11	p.Y188Ifs*11	ENST00000371953	NM_000314.4	187	gaT/ga	6/9	0.20613431372625	4	FACETS	1	0.933	1	1	0.933	1	CLONAL	3	TRUE	1	0.209479524518294	4		285	189	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455564	189455565	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0067188-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	79	376	0	ENST00000264731.3:c.99_100del	p.Ser34LeufsTer14	p.S34Lfs*14	ENST00000264731	NM_003722.4	33	gAA/g	2/14	0.20613431372625	4	FACETS	1	0.936	1	1	0.936	1	CLONAL	3	TRUE	1	0.209479524518294	4		376	283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574026	7574026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	143	280	0	ENST00000269305.4:c.1001G>T	p.Gly334Val	p.G334V	ENST00000269305	NM_001126112.2	334	gGg/gTg	10/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.61784246332713	2		280	430	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061082	38061082	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	346	456	0	ENST00000250448.2:c.907C>A	p.Pro303Thr	p.P303T	ENST00000250448	NM_004496.3	303	Ccc/Acc	2/2	0.485504877950876	4	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.61784246332713	4		456	747	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577593	7577594	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0068269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	120	318	0	ENST00000269305.4:c.687dup	p.Thr230TyrfsTer10	p.T230Yfs*10	ENST00000269305	NM_001126112.2	229	-/T	7/11	1	2	FACETS	0.914	0.832	0.999	0.914	0.832	0.999	CLONAL	1	TRUE	1	0.61784246332713	2		318	425	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248297	59248297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1267587859	NA	P-0068269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	48	523	0	ENST00000371222.2:c.446C>T	p.Ser149Leu	p.S149L	ENST00000371222	NM_002228.3	149	tCg/tTg	1/1	1	2	FACETS	0.266	0.224	0.311	0.266	0.224	0.311	SUBCLONAL	1	TRUE	1	0.61784246332713	2		523	585	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923385	36923385	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006346-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	73	794	0	ENST00000358127.4:c.877G>T	p.Val293Leu	p.V293L	ENST00000358127	NM_001280556.1	293	Gtg/Ttg	7/10	1	2	FACETS	0.264	0.229	0.3	0.264	0.229	0.3	SUBCLONAL	1	TRUE	1	0.535285234931313	2		794	1035	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211464	46211464	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs146524163	NA	P-0018302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	43	208	0	ENST00000334344.6:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000334344	NM_152641.2	144	Caa/Taa	5/21	1	2	FACETS	0.92	0.783	1	0.92	0.783	1	CLONAL	1	FALSE	1	0.576862453565218	2		208	162	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660181	12660181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	218	526	1	ENST00000251849.4:c.40G>A	p.Gly14Ser	p.G14S	ENST00000251849	NM_002880.3	14	Ggt/Agt	2/17	0.156638090686156	3	FACETS	1	0.976	1	0.551	0.513	0.59	INDETERMINATE	1	FALSE	1	0.576862453565218	3		527	884	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268793	41268793	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	153	489	0	ENST00000349496.5:c.1031T>A	p.Leu344Gln	p.L344Q	ENST00000349496	NM_001904.3	344	cTg/cAg	7/15	0.156638090686156	3	FACETS	1	0.987	1	0.699	0.644	0.755	INDETERMINATE	1	FALSE	1	0.576862453565218	3		489	489	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061217	38061235	+	protein_altering_variant	In_Frame_Del	DEL	AGCCGTTCTCGAACATGTT	AGCCGTTCTCGAACATGTT	C	novel	NA	P-0018302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	117	471	0	ENST00000250448.2:c.754_772delinsG	p.Asn252_Cys258delinsGly	p.N252_C258delinsG	ENST00000250448	NM_004496.3	252	AACATGTTCGAGAACGGCTgc/Ggc	2/2	1	2	FACETS	0.726	0.657	0.798	0.726	0.657	0.798	SUBCLONAL	1	FALSE	1	0.576862453565218	2		471	559	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564372	86564372	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	65	466	1	ENST00000274376.6:c.104G>T	p.Arg35Leu	p.R35L	ENST00000274376	NM_002890.2	35	cGg/cTg	1/25	1	2	FACETS	0.957	0.831	1	0.957	0.831	1	CLONAL	1	TRUE	1	0.2778199158065	2		467	489	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729871	41729871	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	55	459	0	ENST00000242208.4:c.658G>T	p.Val220Phe	p.V220F	ENST00000242208	NM_002192.2	220	Gtc/Ttc	3/3	0.218333497469762	4	FACETS	0.891	0.762	1	0.297	0.254	0.344	CLONAL	1	TRUE	1	0.2778199158065	4		459	568	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28929495	NA	P-0027818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	102	684	0	ENST00000275493.2:c.2155G>T	p.Gly719Cys	p.G719C	ENST00000275493	NM_005228.3	719	Ggc/Tgc	18/28	0.218333497469762	4	FACETS	0.817	0.728	0.911	0.272	0.242	0.304	CLONAL	1	TRUE	1	0.2778199158065	4		684	1149	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0027818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	66	562	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.218333497469762	4	FACETS	0.769	0.666	0.88	0.256	0.222	0.294	SUBCLONAL	1	TRUE	1	0.2778199158065	4		562	790	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	45	363	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.823	0.691	0.969	0.823	0.691	0.969	CLONAL	1	TRUE	1	0.2	2		364	547	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	29	420	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.686	0.55	0.84	0.686	0.55	0.84	SUBCLONAL	1	TRUE	1	0.2	2		421	423	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190670397	190670397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576285843	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	58	289	0	ENST00000441310.2:c.335C>T	p.Thr112Met	p.T112M	ENST00000441310	NM_000534.4	112	aCg/aTg	4/13	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.2	2		289	465	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	84	280	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.782	0.692	0.878	1	0.979	1	SUBCLONAL	2	TRUE	1	0.2	2		283	537	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	46	784	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.833	0.701	0.979	0.833	0.701	0.979	CLONAL	1	TRUE	1	0.2	2		789	552	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979987	7979987	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746723399	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	37	393	0	ENST00000319144.4:c.1350del	p.Leu451SerfsTer16	p.L451Sfs*16	ENST00000319144	NM_001139.2	450	ggG/gg	10/15	1	2	FACETS	0.705	0.58	0.844	0.705	0.58	0.844	SUBCLONAL	1	TRUE	1	0.2	2		393	525	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	46	236	0	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.2	2		236	392	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213358	36213359	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	32	423	0	ENST00000222270.7:c.2561_2562del	p.Glu854AlafsTer34	p.E854Afs*34	ENST00000222270	NM_014727.1	852	aAG/a	4/37	1	2	FACETS	0.792	0.643	0.96	0.792	0.643	0.96	CLONAL	1	TRUE	1	0.2	2		423	404	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	51	366	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	0.973	0.827	1	0.973	0.827	1	CLONAL	1	TRUE	1	0.2	2		366	524	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	41	416	0	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.886	0.738	1	0.886	0.738	1	CLONAL	1	TRUE	1	0.2	2		416	463	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	36	368	0	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.624	0.512	0.75	0.624	0.512	0.75	SUBCLONAL	1	TRUE	1	0.2	2		368	577	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	20	326	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	1	2	FACETS	0.448	0.342	0.574	0.448	0.342	0.574	SUBCLONAL	1	TRUE	1	0.2	2		326	446	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	27	406	4	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.689	0.548	0.85	0.689	0.548	0.85	SUBCLONAL	1	TRUE	1	0.2	2		410	392	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821959	72821960	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762108866	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	24	450	4	ENST00000268489.5:c.10215dup	p.Gly3406ArgfsTer25	p.G3406Rfs*25	ENST00000268489	NM_006885.3	3405	-/C	10/10	1	2	FACETS	0.544	0.426	0.681	0.544	0.426	0.681	SUBCLONAL	1	TRUE	1	0.2	2		454	441	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882050	36882050	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs780753361	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	32	365	2	ENST00000358127.4:c.963del	p.Ala322LeufsTer11	p.A322Lfs*11	ENST00000358127	NM_001280556.1	321	ccC/cc	8/10	1	2	FACETS	0.777	0.63	0.942	0.777	0.63	0.942	CLONAL	1	TRUE	1	0.2	2		367	412	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78422373	78422373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766248444	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	41	340	0	ENST00000370768.2:c.1589C>T	p.Thr530Met	p.T530M	ENST00000370768	NM_003902.3	530	aCg/aTg	17/20	1	2	FACETS	0.802	0.668	0.952	0.802	0.668	0.952	CLONAL	1	TRUE	1	0.2	2		340	511	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492937	56492937	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	29	345	0	ENST00000407977.2:c.2T>C	p.Met1?	p.M1?	ENST00000407977		1	aTg/aCg	2/10	1	2	FACETS	0.927	0.745	1	0.927	0.745	1	CLONAL	1	TRUE	1	0.2	2		345	313	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442808	99442809	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	24	348	0	ENST00000268035.6:c.1211dup	p.Asn404LysfsTer66	p.N404Kfs*66	ENST00000268035	NM_000875.3	402	cta/ctAa	5/21	1	2	FACETS	0.567	0.444	0.71	0.567	0.444	0.71	SUBCLONAL	1	TRUE	1	0.2	2		348	423	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217557	142217557	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1268253442	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	34	259	0	ENST00000350721.4:c.5440del	p.Arg1814GlufsTer10	p.R1814Efs*10	ENST00000350721	NM_001184.3	1814	Aga/ga	32/47	1	2	FACETS	0.837	0.685	1	0.837	0.685	1	CLONAL	1	TRUE	1	0.2	2		259	406	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985583	60985583	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	38	458	0	ENST00000333681.4:c.317G>A	p.Arg106His	p.R106H	ENST00000333681		106	cGc/cAc	2/3	1	2	FACETS	0.898	0.743	1	0.898	0.743	1	CLONAL	1	TRUE	1	0.2	2		458	423	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942826	44942826	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	51	327	0	ENST00000377967.4:c.3406A>G	p.Met1136Val	p.M1136V	ENST00000377967	NM_021140.2	1136	Atg/Gtg	23/29	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.2	2		327	428	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005667	42005667	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	46	427	0	ENST00000219905.7:c.3407del	p.Lys1136ArgfsTer6	p.K1136Rfs*6	ENST00000219905	NM_001164273.1	1135	Aaa/aa	9/24	1	2	FACETS	0.931	0.784	1	0.931	0.784	1	CLONAL	1	TRUE	1	0.2	2		427	494	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440292	187440292	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750212558	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	44	314	0	ENST00000232014.4:c.2075G>A	p.Arg692His	p.R692H	ENST00000232014	NM_001130845.1	692	cGc/cAc	10/10	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.2	2		314	420	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223274	36223274	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	31	578	1	ENST00000222270.7:c.5828del	p.Pro1943LeufsTer44	p.P1943Lfs*44	ENST00000222270	NM_014727.1	1942	Ccc/cc	28/37	1	2	FACETS	0.607	0.49	0.739	0.607	0.49	0.739	SUBCLONAL	1	TRUE	1	0.2	2		579	511	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557846	187557848	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs764081811	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	41	367	0	ENST00000441802.2:c.3863_3865del	p.Ser1288del	p.S1288del	ENST00000441802	NM_005245.3	1288	tCCTac/tac	5/27	1	2	FACETS	0.755	0.628	0.896	0.755	0.628	0.896	SUBCLONAL	1	TRUE	1	0.2	2		367	543	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048772	180048772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758587669	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	37	470	0	ENST00000261937.6:c.1790C>T	p.Thr597Met	p.T597M	ENST00000261937	NM_182925.4	597	aCg/aTg	13/30	1	2	FACETS	0.71	0.585	0.851	0.71	0.585	0.851	SUBCLONAL	1	TRUE	1	0.2	2		470	521	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426771	49426772	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs944680171	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	31	480	0	ENST00000301067.7:c.11714_11716dup	p.Gln3905dup	p.Q3905dup	ENST00000301067	NM_003482.3	3905	ctg/cAGCtg	39/54	1	2	FACETS	0.518	0.417	0.632	0.518	0.417	0.632	SUBCLONAL	1	TRUE	1	0.2	2		480	599	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532568	63532568	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	41	520	0	ENST00000307078.5:c.2011del	p.Arg671AlafsTer18	p.R671Afs*18	ENST00000307078	NM_004655.3	671	Cgc/gc	8/11	1	2	FACETS	0.765	0.637	0.908	0.765	0.637	0.908	CLONAL	1	TRUE	1	0.2	2		520	536	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920582	127920582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140793926	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	54	273	0	ENST00000373547.4:c.317G>A	p.Arg106His	p.R106H	ENST00000373547	NM_002721.4	106	cGt/cAt	4/7	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.2	2		273	456	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089471	27089471	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	33	369	0	ENST00000324856.7:c.2430del	p.Arg811GlyfsTer22	p.R811Gfs*22	ENST00000324856	NM_006015.4	809	taC/ta	8/20	1	2	FACETS	0.743	0.605	0.899	0.743	0.605	0.899	SUBCLONAL	1	TRUE	1	0.2	2		369	444	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928639	49928639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1008363508	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	30	393	0	ENST00000296474.3:c.3635G>A	p.Arg1212Gln	p.R1212Q	ENST00000296474	NM_002447.2	1212	cGg/cAg	17/20	1	2	FACETS	0.654	0.526	0.799	0.654	0.526	0.799	SUBCLONAL	1	TRUE	1	0.2	2		393	459	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749376	41749376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	43	274	0	ENST00000226382.2:c.419C>T	p.Ala140Val	p.A140V	ENST00000226382	NM_003924.3	140	gCg/gTg	2/3	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.2	2		274	303	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424520	47424520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	49	436	0	ENST00000404338.3:c.2588G>A	p.Arg863His	p.R863H	ENST00000404338	NM_004491.4	863	cGt/cAt	1/6	1	2	FACETS	0.918	0.777	1	0.918	0.777	1	CLONAL	1	TRUE	1	0.2	2		436	534	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648391	30648391	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	28	351	0	ENST00000295754.5:c.16C>T	p.Leu6Phe	p.L6F	ENST00000295754	NM_003242.5	6	Ctc/Ttc	1/7	1	2	FACETS	0.831	0.665	1	0.831	0.665	1	CLONAL	1	TRUE	1	0.2	2		351	337	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347200	347201	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	21	341	0	ENST00000262320.3:c.1810dup	p.Arg604LysfsTer7	p.R604Kfs*7	ENST00000262320	NM_003502.3	604	aga/aAga	7/11	1	2	FACETS	0.572	0.44	0.727	0.572	0.44	0.727	SUBCLONAL	1	TRUE	1	0.2	2		341	367	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553555	106553555	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	38	433	0	ENST00000369096.4:c.1520A>G	p.Asp507Gly	p.D507G	ENST00000369096	NM_001198.3	507	gAc/gGc	5/7	1	2	FACETS	0.774	0.639	0.924	0.774	0.639	0.924	CLONAL	1	TRUE	1	0.2	2		433	491	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119513	193119513	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	56	269	0	ENST00000367435.3:c.907+1G>A		p.X303_splice	ENST00000367435	NM_024529.4	303			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.2	2		269	452	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683410	182683411	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	41	242	0	ENST00000292782.4:c.134dup	p.Gln46ProfsTer4	p.Q46Pfs*4	ENST00000292782	NM_020640.2	45	ttc/ttTc	2/7	1	2	FACETS	0.87	0.725	1	0.87	0.725	1	CLONAL	1	TRUE	1	0.2	2		242	471	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244386	46244386	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	43	417	0	ENST00000334344.6:c.2480A>G	p.Gln827Arg	p.Q827R	ENST00000334344	NM_152641.2	827	cAa/cGa	15/21	1	2	FACETS	0.793	0.663	0.938	0.793	0.663	0.938	CLONAL	1	TRUE	1	0.2	2		417	542	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50820775	50820776	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	32	292	0	ENST00000398568.2:c.1956_1957del	p.Ala653HisfsTer11	p.A653Hfs*11	ENST00000398568	NM_001042412.1	650	taTGtg/tatg	12/18	1	2	FACETS	0.773	0.627	0.937	0.773	0.627	0.937	CLONAL	1	TRUE	1	0.2	2		292	414	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831090	72831090	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	50	393	0	ENST00000268489.5:c.5491C>A	p.Leu1831Met	p.L1831M	ENST00000268489	NM_006885.3	1831	Ctg/Atg	9/10	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.2	2		393	432	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721129	61721129	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	41	331	0	ENST00000401558.2:c.1145G>T	p.Arg382Ile	p.R382I	ENST00000401558	NM_003400.3	382	aGa/aTa	12/25	1	2	FACETS	0.835	0.695	0.99	0.835	0.695	0.99	CLONAL	1	TRUE	1	0.2	2		331	491	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22408230	22408230	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	33	334	0	ENST00000344548.3:c.121G>A	p.Ala41Thr	p.A41T	ENST00000344548	NM_001039802.1	41	Gca/Aca	4/7	1	2	FACETS	0.725	0.59	0.878	0.725	0.59	0.878	SUBCLONAL	1	TRUE	1	0.2	2		334	455	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523136	176523136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	37	487	0	ENST00000292408.4:c.1900G>A	p.Ala634Thr	p.A634T	ENST00000292408	NM_213647.1	634	Gcc/Acc	14/18	1	2	FACETS	0.643	0.529	0.771	0.643	0.529	0.771	SUBCLONAL	1	TRUE	1	0.2	2		487	575	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73649861	73649861	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs374994842	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	29	324	0	ENST00000377687.4:c.1211A>G	p.Lys404Arg	p.K404R	ENST00000377687	NM_001730.3	404	aAg/aGg	4/4	1	2	FACETS	0.73	0.586	0.895	0.73	0.586	0.895	SUBCLONAL	1	TRUE	1	0.2	2		324	397	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057074	180057074	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	26	458	0	ENST00000261937.6:c.545A>G	p.Glu182Gly	p.E182G	ENST00000261937	NM_182925.4	182	gAg/gGg	5/30	1	2	FACETS	0.657	0.52	0.814	0.657	0.52	0.814	SUBCLONAL	1	TRUE	1	0.2	2		458	396	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462982	120462982	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	38	363	0	ENST00000256646.2:c.5349del	p.Ile1784LeufsTer36	p.I1784Lfs*36	ENST00000256646	NM_024408.3	1783	ccC/cc	30/34	1	2	FACETS	0.872	0.721	1	0.872	0.721	1	CLONAL	1	TRUE	1	0.2	2		363	436	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197152	106197152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	35	405	0	ENST00000380013.4:c.5485C>T	p.Pro1829Ser	p.P1829S	ENST00000380013	NM_001127208.2	1829	Cca/Tca	11/11	1	2	FACETS	0.778	0.637	0.936	0.778	0.637	0.936	CLONAL	1	TRUE	1	0.2	2		405	450	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347268	89347268	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	33	455	0	ENST00000301030.4:c.5682del	p.Arg1895GlufsTer68	p.R1895Efs*68	ENST00000301030	NM_001256183.1	1894	ccC/cc	9/13	1	2	FACETS	0.714	0.581	0.864	0.714	0.581	0.864	SUBCLONAL	1	TRUE	1	0.2	2		455	462	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52728987	52728987	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	37	365	0	ENST00000322088.6:c.1679T>C	p.Val560Ala	p.V560A	ENST00000322088	NM_014225.5	560	gTc/gCc	14/15	1	2	FACETS	0.794	0.654	0.95	0.794	0.654	0.95	CLONAL	1	TRUE	1	0.2	2		365	466	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650269	12650269	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	38	343	0	ENST00000251849.4:c.577C>T	p.Leu193Phe	p.L193F	ENST00000251849	NM_002880.3	193	Ctc/Ttc	5/17	1	2	FACETS	0.772	0.638	0.923	0.772	0.638	0.923	CLONAL	1	TRUE	1	0.2	2		343	492	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841536	156841536	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	49	504	0	ENST00000524377.1:c.839T>C	p.Val280Ala	p.V280A	ENST00000524377	NM_002529.3	280	gTc/gCc	7/17	1	2	FACETS	0.832	0.704	0.973	0.832	0.704	0.973	CLONAL	1	TRUE	1	0.2	2		504	589	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430377	181430377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	24	331	0	ENST00000325404.1:c.229G>A	p.Ala77Thr	p.A77T	ENST00000325404	NM_003106.3	77	Gcc/Acc	1/1	1	2	FACETS	0.63	0.493	0.788	0.63	0.493	0.788	SUBCLONAL	1	TRUE	1	0.2	2		331	381	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293175	212293175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1312174046	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	54	266	0	ENST00000342788.4:c.2677C>T	p.His893Tyr	p.H893Y	ENST00000342788	NM_005235.2	893	Cat/Tat	22/28	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.2	2		266	461	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557286	29557286	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753082620	NA	P-0036151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	32	289	0	ENST00000356175.3:c.2999G>A	p.Arg1000His	p.R1000H	ENST00000356175	NM_000267.3	1000	cGt/cAt	23/57	1	2	FACETS	0.882	0.716	1	0.882	0.716	1	CLONAL	1	TRUE	1	0.2	2		289	363	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	99	420	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.586414087832717	4	FACETS	0.987	0.896	1	0.987	0.896	1	CLONAL	2	FALSE	2	0.657230316964823	4		421	253	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	40	538	11	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	0.417466156082064	3	FACETS	0.785	0.659	0.922	0.393	0.329	0.461	CLONAL	1	FALSE	1	0.657230316964823	3		549	206	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	82	539	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.417466156082064	3	FACETS	0.666	0.589	0.748	0.333	0.294	0.374	SUBCLONAL	1	FALSE	1	0.657230316964823	3		539	498	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	29	503	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.657230316964823	3	FACETS	0.475	0.383	0.578	0.237	0.191	0.289	SUBCLONAL	1	FALSE	1	0.657230316964823	3		503	247	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	103	497	8	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	0.563923894961427	3	FACETS	1	0.967	1			1	CLONAL	1	FALSE	NA	0.657230316964823	3		505	357	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43733757	43733757	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	79	406	0	ENST00000382044.4:c.3065del	p.Asn1022MetfsTer20	p.N1022Mfs*20	ENST00000382044	NM_001141980.1	1022	aAt/at	15/28	0.417466156082064	3	FACETS	1	0.973	1	0.652	0.582	0.725	CLONAL	1	FALSE	1	0.657230316964823	3		406	245	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	221	784	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.336398874021195	3	FACETS	0.975	0.919	1	0.975	0.919	1	INDETERMINATE	2	FALSE	1	0.657230316964823	3		789	458	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	219	728	4	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	0.586414087832717	4	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	FALSE	2	0.657230316964823	4		732	542	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332273	70332273	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	60	429	1	ENST00000373644.4:c.184del	p.Thr62GlnfsTer13	p.T62Qfs*13	ENST00000373644	NM_030625.2	60	Aaa/aa	2/12	0.378220370952082	4	FACETS	0.796	0.698	0.899	0.796	0.698	0.899	INDETERMINATE	2	FALSE	2	0.657230316964823	4		430	190	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	174	892	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.657230316964823	4	FACETS	0.781	0.723	0.84	0.781	0.723	0.84	SUBCLONAL	2	FALSE	2	0.657230316964823	4		892	562	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578277	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs1555525902	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	111	647	1	ENST00000269305.4:c.572_574del	p.Pro191del	p.P191del	ENST00000269305	NM_001126112.2	191	cCTCag/cag	6/11	0.336398874021195	3	FACETS	1	0.985	1	0.722	0.657	0.787	INDETERMINATE	1	FALSE	1	0.657230316964823	3		648	311	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121791	2121792	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs137854144	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	125	794	0	ENST00000219476.3:c.1959_1960del	p.Gly654LeufsTer2	p.G654Lfs*2	ENST00000219476	NM_000548.3	651	ccAGag/ccag	19/42	0.472140033288084	2	FACETS	1	0.987	1	0.707	0.652	0.762	CLONAL	1	FALSE	0	0.657230316964823	2		794	269	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023246	1023246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs184776294	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	134	546	2	ENST00000358495.3:c.1009G>A	p.Asp337Asn	p.D337N	ENST00000358495	NM_134424.2	337	Gat/Aat	11/12	0.563923894961427	3	FACETS	1	0.976	1			1	CLONAL	1	FALSE	NA	0.657230316964823	3		548	459	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372022	55372022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	82	318	1	ENST00000297316.4:c.712G>A	p.Ala238Thr	p.A238T	ENST00000297316	NM_022454.3	238	Gcc/Acc	2/2	0.496643949302489	5	FACETS	0.985	0.871	1	0.328	0.29	0.369	CLONAL	1	FALSE	2	0.657230316964823	5		319	503	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956964	2956964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395288944	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	107	669	0	ENST00000396946.4:c.2663G>A	p.Arg888His	p.R888H	ENST00000396946	NM_032415.4	888	cGt/cAt	20/25	0.586414087832717	4	FACETS	0.837	0.752	0.926	0.418	0.376	0.463	CLONAL	1	FALSE	2	0.657230316964823	4		669	645	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	24	192	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	0.390688382414114	2	FACETS	0.589	0.469	0.723	0.294	0.234	0.362	INDETERMINATE	1	FALSE	0	0.657230316964823	2		192	124	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007825	45007825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	67	413	4	ENST00000558401.1:c.276del	p.Thr93LeufsTer10	p.T93Lfs*10	ENST00000558401	NM_004048.2	91	aCc/ac	2/4	0.417466156082064	3	FACETS	1	0.921	1	0.531	0.467	0.599	CLONAL	1	FALSE	1	0.657230316964823	3		417	255	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437288	220437288	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1190141661	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	70	908	1	ENST00000243786.2:c.197del	p.Gly66AlafsTer61	p.G66Afs*61	ENST00000243786	NM_002191.3	64	ctG/ct	1/2	0.378220370952082	4	FACETS	0.61	0.532	0.694	0.305	0.266	0.347	INDETERMINATE	1	FALSE	2	0.657230316964823	4		909	579	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2220125	2220125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542823835	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	145	729	1	ENST00000398665.3:c.2710G>A	p.Val904Met	p.V904M	ENST00000398665	NM_032482.2	904	Gtg/Atg	23/28	0.390688382414114	2	FACETS	1	0.986	1	0.659	0.61	0.708	INDETERMINATE	1	FALSE	0	0.657230316964823	2		730	335	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682810	190682810	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	54	393	1	ENST00000441310.2:c.492del	p.Lys164AsnfsTer6	p.K164Nfs*6	ENST00000441310	NM_000534.4	162	gcA/gc	5/13	0.378220370952082	4	FACETS	1	0.935	1	0.572	0.494	0.656	INDETERMINATE	1	FALSE	2	0.657230316964823	4		394	238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	98	778	1	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.336398874021195	3	FACETS	0.827	0.741	0.918	0.414	0.37	0.459	INDETERMINATE	1	FALSE	1	0.657230316964823	3		779	479	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187558038	187558039	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	26	270	0	ENST00000441802.2:c.3672dup	p.Lys1225GlnfsTer13	p.K1225Qfs*13	ENST00000441802	NM_005245.3	1224	-/C	5/27	0.657230316964823	3	FACETS	0.74	0.594	0.903	0.37	0.297	0.452	CLONAL	1	FALSE	1	0.657230316964823	3		270	142	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	72	571	1	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	0.308625475968134	5	FACETS	1	0.968	1	0.437	0.384	0.493	INDETERMINATE	1	FALSE	2	0.657230316964823	5		572	332	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998128	169998128	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs753143066	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	124	670	2	ENST00000295797.4:c.826del	p.Thr276GlnfsTer7	p.T276Qfs*7	ENST00000295797	NM_002740.5	273	ttA/tt	9/18	0.378220370952082	4	FACETS	1	0.986	1	0.737	0.673	0.805	INDETERMINATE	1	FALSE	2	0.657230316964823	4		672	424	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	65	675	1	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	0.27603361840348	4	FACETS	0.708	0.615	0.808	0.354	0.307	0.404	INDETERMINATE	1	FALSE	2	0.657230316964823	4		676	463	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606343	93606343	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200078199	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	88	804	1	ENST00000375746.1:c.163G>A	p.Val55Met	p.V55M	ENST00000375746	NM_001174167.1	55	Gtg/Atg	2/14	0.417466156082064	3	FACETS	0.901	0.803	1	0.45	0.401	0.502	CLONAL	1	FALSE	1	0.657230316964823	3		805	395	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444378	49444378	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	149	828	0	ENST00000301067.7:c.2993del	p.Pro998LeufsTer2	p.P998Lfs*2	ENST00000301067	NM_003482.3	998	cCt/ct	11/54	0.657230316964823	4	FACETS	1	0.986	1	0.687	0.631	0.745	CLONAL	1	FALSE	2	0.657230316964823	4		828	547	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251560	251560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1042170	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	34	647	0	ENST00000264932.6:c.1771G>A	p.Ala591Thr	p.A591T	ENST00000264932	NM_004168.2	591	Gcg/Acg	13/15	0.417466156082064	3	FACETS	0.253	0.206	0.306	0.127	0.103	0.153	SUBCLONAL	1	FALSE	1	0.657230316964823	3		647	543	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821889	72821890	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	56	418	0	ENST00000268489.5:c.10285dup	p.Arg3429ProfsTer2	p.R3429Pfs*2	ENST00000268489	NM_006885.3	3429	cgt/cCgt	10/10	0.417466156082064	3	FACETS	0.757	0.653	0.869	0.379	0.326	0.435	SUBCLONAL	1	FALSE	1	0.657230316964823	3		418	299	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829270	128829270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	80	630	0	ENST00000249373.3:c.278C>T	p.Ala93Val	p.A93V	ENST00000249373	NM_005631.4	93	gCc/gTc	1/12	0.586414087832717	4	FACETS	0.913	0.807	1	0.456	0.403	0.513	CLONAL	1	FALSE	2	0.657230316964823	4		630	442	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430206	181430208	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	22	284	0	ENST00000325404.1:c.67_69del	p.Gly23del	p.G23del	ENST00000325404	NM_003106.3	20	GGC/-	1/1	0.378220370952082	4	FACETS	0.337	0.261	0.426	0.169	0.13	0.213	INDETERMINATE	1	FALSE	2	0.657230316964823	4		284	329	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350154	81350154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745919057	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	77	307	0	ENST00000222390.5:c.1178G>A	p.Arg393His	p.R393H	ENST00000222390	NM_000601.4	393	cGt/cAt	10/18	0.586414087832717	4	FACETS	0.848	0.756	0.943	0.848	0.756	0.943	CLONAL	2	FALSE	2	0.657230316964823	4		307	229	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446875	18446875	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	22	297	0	ENST00000266497.5:c.964del	p.Cys322AlafsTer13	p.C322Afs*13	ENST00000266497		320	caT/ca	4/31	0.657230316964823	4	FACETS	0.44	0.342	0.554	0.22	0.171	0.277	SUBCLONAL	1	FALSE	2	0.657230316964823	4		297	252	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143010	47143010	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs759274882	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	70	581	0	ENST00000409792.3:c.4953del	p.Phe1651LeufsTer12	p.F1651Lfs*12	ENST00000409792	NM_014159.6	1651	ttT/tt	8/21	0.378220370952082	4	FACETS	1	0.946	1	0.569	0.5	0.642	INDETERMINATE	1	FALSE	2	0.657230316964823	4		581	310	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629493	187629493	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	24	666	0	ENST00000441802.2:c.1489T>C	p.Tyr497His	p.Y497H	ENST00000441802	NM_005245.3	497	Tac/Cac	2/27	0.657230316964823	3	FACETS	0.275	0.215	0.344	0.137	0.107	0.172	SUBCLONAL	1	FALSE	1	0.657230316964823	3		666	353	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434602	110434602	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	125	512	0	ENST00000375856.3:c.3799del	p.Gln1267SerfsTer64	p.Q1267Sfs*64	ENST00000375856	NM_003749.2	1267	Cag/ag	1/2	0.187135100235026	5	FACETS	0.874	0.798	0.954	0.583	0.532	0.636	INDETERMINATE	2	FALSE	2	0.657230316964823	5		512	432	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257918	16257918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143503694	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	64	621	1	ENST00000375759.3:c.5183C>T	p.Pro1728Leu	p.P1728L	ENST00000375759	NM_015001.2	1728	cCg/cTg	11/15	0.27603361840348	4	FACETS	0.832	0.724	0.948	0.416	0.362	0.474	INDETERMINATE	1	FALSE	2	0.657230316964823	4		622	388	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78422298	78422298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1297808957	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	43	399	0	ENST00000370768.2:c.1664C>T	p.Ala555Val	p.A555V	ENST00000370768	NM_003902.3	555	gCc/gTc	17/20	0.27603361840348	4	FACETS	0.606	0.508	0.713	0.303	0.254	0.357	INDETERMINATE	1	FALSE	2	0.657230316964823	4		399	358	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166248	118166248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779467652	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	53	394	0	ENST00000369448.3:c.758G>A	p.Arg253Gln	p.R253Q	ENST00000369448	NM_017709.3	253	cGg/cAg	2/2	0.27603361840348	4	FACETS	1	0.907	1	0.535	0.46	0.614	INDETERMINATE	1	FALSE	2	0.657230316964823	4		394	250	SUCCESS
H3C13	653604	MSKCC	GRCh37	1	149784855	149784855	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782462930	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	49	275	0	ENST00000331491.1:c.382G>A	p.Ala128Thr	p.A128T	ENST00000331491	NM_001123375.2	128	Gcc/Acc	1/1	0.27603361840348	4	FACETS	1	0.887	1	0.521	0.446	0.603	INDETERMINATE	1	FALSE	2	0.657230316964823	4		275	237	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596003	43596003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779915615	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	118	732	1	ENST00000355710.3:c.170G>A	p.Arg57Gln	p.R57Q	ENST00000355710	NM_020975.4	57	cGg/cAg	2/20	0.378220370952082	4	FACETS	1	0.979	1	0.643	0.583	0.704	INDETERMINATE	1	FALSE	2	0.657230316964823	4		733	463	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88651931	88651931	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	51	486	0	ENST00000372037.3:c.280del	p.Thr94ProfsTer3	p.T94Pfs*3	ENST00000372037	NM_004329.2	93	gAa/ga	5/13	0.378220370952082	4	FACETS	1	0.958	1	0.663	0.572	0.76	INDETERMINATE	1	FALSE	2	0.657230316964823	4		486	194	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659561	88659561	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	25	473	0	ENST00000372037.3:c.344A>G	p.Lys115Arg	p.K115R	ENST00000372037	NM_004329.2	115	aAa/aGa	6/13	0.378220370952082	4	FACETS	0.508	0.402	0.63	0.254	0.201	0.315	INDETERMINATE	1	FALSE	2	0.657230316964823	4		473	248	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659632	88659632	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1554888986	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	89	553	3	ENST00000372037.3:c.419del	p.Pro140LeufsTer4	p.P140Lfs*4	ENST00000372037	NM_004329.2	139	Ccc/cc	6/13	0.378220370952082	4	FACETS	0.763	0.685	0.845	0.763	0.685	0.845	INDETERMINATE	2	FALSE	2	0.657230316964823	4		556	294	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127963	64127963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	59	690	0	ENST00000334205.4:c.361G>A	p.Gly121Arg	p.G121R	ENST00000334205	NM_003942.2	121	Ggg/Agg	4/17	0.27603361840348	4	FACETS	0.775	0.669	0.889	0.387	0.334	0.445	INDETERMINATE	1	FALSE	2	0.657230316964823	4		690	384	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342634	118342634	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1565278132	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	29	300	0	ENST00000534358.1:c.766del	p.Ile256LeufsTer18	p.I256Lfs*18	ENST00000534358	NM_005933.3	254	Aaa/aa	3/36	0.27603361840348	4	FACETS	1	0.851	1	0.526	0.428	0.634	INDETERMINATE	1	FALSE	2	0.657230316964823	4		300	139	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417141	417142	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	65	316	0	ENST00000399788.2:c.3408dup	p.Glu1137ArgfsTer3	p.E1137Rfs*3	ENST00000399788	NM_001042603.1	1136	-/A	23/28	0.563923894961427	3	FACETS	1	0.96	1			1	CLONAL	1	FALSE	NA	0.657230316964823	3		316	215	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859040	57859040	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	149	690	0	ENST00000228682.2:c.534+2T>G		p.X178_splice	ENST00000228682	NM_005269.2	178			0.657230316964823	4	FACETS	0.822	0.757	0.889	0.822	0.757	0.889	CLONAL	2	FALSE	2	0.657230316964823	4		690	457	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877324	28877324	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs768011705	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	141	520	0	ENST00000282397.4:c.3997T>C	p.Tyr1333His	p.Y1333H	ENST00000282397	NM_002019.4	1333	Tac/Cac	30/30	0.187135100235026	5	FACETS	1	0.982	1	0.811	0.749	0.875	INDETERMINATE	2	FALSE	2	0.657230316964823	5		520	350	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937386	32937386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1184535660	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	55	453	0	ENST00000380152.3:c.8047G>A	p.Ala2683Thr	p.A2683T	ENST00000380152		2683	Gca/Aca	18/27	0.187135100235026	5	FACETS	0.875	0.76	0.995	0.583	0.507	0.664	INDETERMINATE	2	FALSE	2	0.657230316964823	5		453	190	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239867	41239868	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	66	397	0	ENST00000379561.5:c.482dup	p.Asn162GlnfsTer39	p.N162Qfs*39	ENST00000379561	NM_002015.3	161	ggc/ggGc	1/3	0.187135100235026	5	FACETS	1	0.961	1	0.421	0.368	0.477	INDETERMINATE	1	FALSE	2	0.657230316964823	5		397	316	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991898	72991898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	152	662	0	ENST00000268489.5:c.2147G>A	p.Gly716Asp	p.G716D	ENST00000268489	NM_006885.3	716	gGc/gAc	2/10	0.417466156082064	3	FACETS	1	0.986	1	0.671	0.619	0.724	CLONAL	1	FALSE	1	0.657230316964823	3		662	458	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559111	29559111	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	19	159	0	ENST00000356175.3:c.3218T>C	p.Met1073Thr	p.M1073T	ENST00000356175	NM_000267.3	1073	aTg/aCg	25/57	0.336398874021195	3	FACETS	0.569	0.436	0.722	0.285	0.218	0.361	INDETERMINATE	1	FALSE	1	0.657230316964823	3		159	135	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3113410	3113410	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	57	711	0	ENST00000078429.4:c.404T>C	p.Leu135Pro	p.L135P	ENST00000078429	NM_002067.2	135	cTg/cCg	3/7	0.390688382414114	2	FACETS	0.611	0.528	0.699	0.305	0.264	0.35	INDETERMINATE	1	FALSE	0	0.657230316964823	2		711	284	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216719	36216719	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs1568374482	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	105	507	0	ENST00000222270.7:c.3885G>A	p.Trp1295Ter	p.W1295*	ENST00000222270	NM_014727.1	1295	tgG/tgA	13/37	0.536985607226678	4	FACETS	1	0.981	1	0.693	0.626	0.763	CLONAL	1	FALSE	2	0.657230316964823	4		507	382	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228794	36228794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	166	863	2	ENST00000222270.7:c.7693C>T	p.Arg2565Cys	p.R2565C	ENST00000222270	NM_014727.1	2565	Cgt/Tgt	35/37	0.536985607226678	4	FACETS	0.816	0.755	0.879	0.816	0.755	0.879	CLONAL	2	FALSE	2	0.657230316964823	4		865	513	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753798	42753799	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	94	975	0	ENST00000222329.4:c.465dup	p.Thr156HisfsTer33	p.T156Hfs*33	ENST00000222329	NM_006494.2	155	-/C	4/4	0.536985607226678	4	FACETS	0.702	0.625	0.784	0.351	0.312	0.392	SUBCLONAL	1	FALSE	2	0.657230316964823	4		975	675	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867130	45867130	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1359840113	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	34	765	0	ENST00000391945.4:c.989T>C	p.Leu330Pro	p.L330P	ENST00000391945	NM_000400.3	330	cTg/cCg	11/23	0.536985607226678	4	FACETS	0.352	0.287	0.425	0.176	0.143	0.213	SUBCLONAL	1	FALSE	2	0.657230316964823	4		765	487	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965811	25965811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	95	725	0	ENST00000435504.4:c.3395G>A	p.Gly1132Asp	p.G1132D	ENST00000435504		1132	gGc/gAc	13/13	0.187135100235026	5	FACETS	0.753	0.676	0.835	0.502	0.45	0.557	INDETERMINATE	2	FALSE	2	0.657230316964823	5		725	381	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607816	46607816	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	159	851	0	ENST00000263734.3:c.2005C>G	p.Pro669Ala	p.P669A	ENST00000263734	NM_001430.4	669	Ccc/Gcc	12/16	0.187135100235026	5	FACETS	0.863	0.795	0.932	0.575	0.53	0.622	INDETERMINATE	2	FALSE	2	0.657230316964823	5		851	557	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99154373	99154373	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	84	629	0	ENST00000074304.5:c.515A>C	p.Gln172Pro	p.Q172P	ENST00000074304	NM_001134224.1	172	cAg/cCg	8/26	0.187135100235026	5	FACETS	1	0.974	1	0.448	0.398	0.5	INDETERMINATE	1	FALSE	2	0.657230316964823	5		629	378	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665419	138665419	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	32	621	1	ENST00000330315.3:c.146C>T	p.Pro49Leu	p.P49L	ENST00000330315	NM_023067.3	49	cCg/cTg	1/1	0.378220370952082	4	FACETS	0.339	0.275	0.412	0.17	0.137	0.206	INDETERMINATE	1	FALSE	2	0.657230316964823	4		622	476	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750447	41750447	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	85	587	0	ENST00000226382.2:c.181A>G	p.Thr61Ala	p.T61A	ENST00000226382	NM_003924.3	61	Acg/Gcg	1/3	0.657230316964823	3	FACETS	0.87	0.774	0.972	0.435	0.387	0.486	CLONAL	1	FALSE	1	0.657230316964823	3		587	395	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155920	106155920	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	96	385	0	ENST00000380013.4:c.821T>C	p.Ile274Thr	p.I274T	ENST00000380013	NM_001127208.2	274	aTc/aCc	3/11	0.657230316964823	3	FACETS	1	0.982	1	0.721	0.652	0.792	CLONAL	1	FALSE	1	0.657230316964823	3		385	269	SUCCESS
APC	324	MSKCC	GRCh37	5	112176797	112176797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766739164	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	40	380	0	ENST00000257430.4:c.5506G>A	p.Gly1836Arg	p.G1836R	ENST00000257430	NM_000038.5	1836	Gga/Aga	16/16	0.417466156082064	3	FACETS	1	0.911	1	0.558	0.472	0.649	CLONAL	1	FALSE	1	0.657230316964823	3		380	145	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056121	26056121	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	57	479	0	ENST00000343677.2:c.536T>C	p.Val179Ala	p.V179A	ENST00000343677	NM_005319.3	179	gTt/gCt	1/1	0.308625475968134	5	FACETS	0.848	0.73	0.976	0.283	0.243	0.326	INDETERMINATE	1	FALSE	2	0.657230316964823	5		479	406	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673628	30673628	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	155	752	0	ENST00000376406.3:c.3332A>G	p.Lys1111Arg	p.K1111R	ENST00000376406	NM_014641.2	1111	aAg/aGg	10/15	0.308625475968134	5	FACETS	1	0.969	1	0.728	0.673	0.784	INDETERMINATE	2	FALSE	2	0.657230316964823	5		752	429	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287857	33287880	+	inframe_deletion	In_Frame_Del	DEL	CCTCCTCCTCTTCAGAATCTGTGG	CCTCCTCCTCTTCAGAATCTGTGG	-	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	63	713	0	ENST00000374542.5:c.1373_1396del	p.Ala458_Glu465del	p.A458_E465del	ENST00000374542	NM_001141970.1	458	gCCACAGATTCTGAAGAGGAGGAGGat/gat	5/8	0.308625475968134	5	FACETS	0.734	0.635	0.84	0.245	0.211	0.28	INDETERMINATE	1	FALSE	2	0.657230316964823	5		713	519	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129185	152129185	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	203	779	0	ENST00000206249.3:c.138C>A	p.Ser46Arg	p.S46R	ENST00000206249	NM_000125.3	46	agC/agA	1/8	0.308625475968134	5	FACETS	1	0.987	1	0.807	0.755	0.859	INDETERMINATE	2	FALSE	2	0.657230316964823	5		779	507	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729797	41729797	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	98	399	0	ENST00000242208.4:c.732T>G	p.Cys244Trp	p.C244W	ENST00000242208	NM_002192.2	244	tgT/tgG	3/3	0.586414087832717	4	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	FALSE	2	0.657230316964823	4		399	231	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508042	106508043	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	rs771137585	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	26	236	0	ENST00000359195.3:c.41_42del	p.Glu14GlyfsTer147	p.E14Gfs*147	ENST00000359195	NM_002649.2	12	ctGAga/ctga	2/11	0.586414087832717	4	FACETS	0.701	0.56	0.861	0.351	0.28	0.431	SUBCLONAL	1	FALSE	2	0.657230316964823	4		236	187	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864678	68864678	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	133	311	0	ENST00000288368.4:c.49C>A	p.Leu17Met	p.L17M	ENST00000288368	NM_024870.2	17	Ctg/Atg	1/40	0.496643949302489	5	FACETS	1	0.954	1	0.705	0.647	0.764	CLONAL	2	FALSE	2	0.657230316964823	5		311	380	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396227	139396227	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	60	798	0	ENST00000277541.6:c.5611T>C	p.Cys1871Arg	p.C1871R	ENST00000277541	NM_017617.3	1871	Tgc/Cgc	30/34	0.417466156082064	3	FACETS	0.614	0.531	0.704	0.307	0.265	0.352	SUBCLONAL	1	FALSE	1	0.657230316964823	3		798	395	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399948	139399948	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	171	842	2	ENST00000277541.6:c.4400G>A	p.Cys1467Tyr	p.C1467Y	ENST00000277541	NM_017617.3	1467	tGc/tAc	25/34	0.417466156082064	3	FACETS	1	0.99	1	0.745	0.692	0.799	CLONAL	1	FALSE	1	0.657230316964823	3		844	464	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615725	100615725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	35	574	0	ENST00000308731.7:c.607C>T	p.Pro203Ser	p.P203S	ENST00000308731	NM_000061.2	203	Ccg/Tcg	8/19	0.414202767648343	1	FACETS	0.255	0.21	0.306	0.255	0.21	0.306	SUBCLONAL	1	FALSE	0	0.657230316964823	1		574	280	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981720	101981721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	12	247	1	ENST00000282441.5:c.147dup	p.Ala50ArgfsTer62	p.A50Rfs*62	ENST00000282441	NM_001130145.2	47	-/C	1/9	0.27603361840348	4	FACETS	0.297	0.208	0.405	0.148	0.104	0.203	INDETERMINATE	1	FALSE	2	0.657230316964823	4		248	204	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118872	61118872	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1558790056	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	16	338	0	ENST00000295025.8:c.65G>A	p.Arg22His	p.R22H	ENST00000295025	NM_002908.2	22	cGt/cAt	2/11	0.187135100235026	5	FACETS	0.342	0.252	0.449	0.114	0.084	0.15	INDETERMINATE	1	FALSE	2	0.657230316964823	5		338	283	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682771	190682818	+	frameshift_variant	Frame_Shift_Del	DEL	TAAGAATCTACCTGTAAGAAAGCAGTTTTACTCAACTGCAAAAAAATG	TAAGAATCTACCTGTAAGAAAGCAGTTTTACTCAACTGCAAAAAAATG	ATATCATATACCCAGAAACTTA	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	54	418	2	ENST00000441310.2:c.447_494delinsATATCATATACCCAGAAACTTA	p.Phe149LeufsTer9	p.F149Lfs*9	ENST00000441310	NM_000534.4	149	ttTAAGAATCTACCTGTAAGAAAGCAGTTTTACTCAACTGCAAAAAAATGt/ttATATCATATACCCAGAAACTTAt	5/13	0.378220370952082	4	FACETS	1	0.919	1	0.547	0.472	0.627	INDETERMINATE	1	FALSE	2	0.657230316964823	4		420	249	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433492	138433492	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1351648066	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	12	432	1	ENST00000289153.2:c.1120T>C	p.Ser374Pro	p.S374P	ENST00000289153	NM_006219.2	374	Tca/Cca	7/22	0.378220370952082	4	FACETS	0.258	0.181	0.352	0.129	0.09	0.176	INDETERMINATE	1	FALSE	2	0.657230316964823	4		433	235	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604272	189604272	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	26	569	0	ENST00000264731.3:c.1439A>G	p.Gln480Arg	p.Q480R	ENST00000264731	NM_003722.4	480	cAg/cGg	11/14	0.378220370952082	4	FACETS	0.266	0.21	0.33	0.133	0.105	0.165	INDETERMINATE	1	FALSE	2	0.657230316964823	4		569	493	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592130	67592130	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1389187507	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	13	276	1	ENST00000274335.5:c.1946G>A	p.Arg649Gln	p.R649Q	ENST00000274335		649	cGg/cAg	14/15	0.417466156082064	3	FACETS	0.256	0.183	0.346	0.128	0.091	0.173	SUBCLONAL	1	FALSE	1	0.657230316964823	3		277	205	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271348	26271348	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	23	573	0	ENST00000305910.3:c.265G>A	p.Ala89Thr	p.A89T	ENST00000305910	NM_003534.2	89	Gcg/Acg	1/1	0.308625475968134	5	FACETS	0.326	0.254	0.411	0.109	0.084	0.137	INDETERMINATE	1	FALSE	2	0.657230316964823	5		573	426	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89871737	89871737	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555571174	NA	P-0051302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	149	496	0	ENST00000389301.3:c.660G>C	p.Gln220His	p.Q220H	ENST00000389301	NM_000135.2	220	caG/caC	7/43	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.357482631096363	2		496	684	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458936	120458936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	160	571	0	ENST00000256646.2:c.6409G>A	p.Glu2137Lys	p.E2137K	ENST00000256646	NM_024408.3	2137	Gag/Aag	34/34	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.357482631096363	2		571	803	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910818	114910818	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	108	417	0	ENST00000543371.1:c.937G>C	p.Ala313Pro	p.A313P	ENST00000543371	NM_001198531.1	313	Gcc/Ccc	9/14	0.356229600316366	2	FACETS	0.924	0.83	1	0.462	0.415	0.512	CLONAL	1	TRUE	0	0.357482631096363	2		417	654	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914224	32914227	+	frameshift_variant	Frame_Shift_Del	DEL	ATGA	ATGA	-	novel	NA	P-0051302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	75	250	0	ENST00000380152.3:c.5735_5738del	p.Glu1912ValfsTer50	p.E1912Vfs*50	ENST00000380152		1911	gATGAa/ga	11/27	0.357482631096363	1	FACETS	0.96	0.847	1	0.96	0.847	1	CLONAL	1	TRUE	0	0.357482631096363	1		250	359	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553233	41553233	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	89	352	0	ENST00000263253.7:c.3322A>C	p.Thr1108Pro	p.T1108P	ENST00000263253	NM_001429.3	1108	Act/Cct	18/31	0.357482631096363	1	FACETS	0.874	0.778	0.975	0.874	0.778	0.975	CLONAL	1	TRUE	0	0.357482631096363	1		352	468	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31431681	31431681	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0051302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	83	259	0	ENST00000344624.3:c.3145+2T>C		p.X1049_splice	ENST00000344624		1049			1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.357482631096363	2		259	406	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346892	70346892	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	155	512	0	ENST00000374080.3:c.2759C>G	p.Thr920Ser	p.T920S	ENST00000374080		920	aCt/aGt	20/45	0.357482631096363	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.357482631096363	1		512	650	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202393	123202419	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTAATGTTAAATTTTTTCAAGGAGGAC	TTAATGTTAAATTTTTTCAAGGAGGAC	-	novel	NA	P-0051302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	26	123	0	ENST00000218089.9:c.2266-19_2273del		p.X756_splice	ENST00000218089	NM_001042749.1	756		24/35	0.357482631096363	1	FACETS	0.566	0.451	0.697	0.566	0.451	0.697	SUBCLONAL	1	TRUE	0	0.357482631096363	1		123	211	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89871737	89871737	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555571174	NA	P-0051302-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	244	496	0	ENST00000389301.3:c.660G>C	p.Gln220His	p.Q220H	ENST00000389301	NM_000135.2	220	caG/caC	7/43	0.587375305785674	3	FACETS	0.926	0.873	0.979	0.617	0.582	0.653	CLONAL	2	TRUE	0	0.608607263189824	3		496	565	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458936	120458936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051302-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	188	571	0	ENST00000256646.2:c.6409G>A	p.Glu2137Lys	p.E2137K	ENST00000256646	NM_024408.3	2137	Gag/Aag	34/34	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.608607263189824	2		571	603	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910818	114910818	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051302-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	181	417	0	ENST00000543371.1:c.937G>C	p.Ala313Pro	p.A313P	ENST00000543371	NM_001198531.1	313	Gcc/Ccc	9/14	0.58776303374694	2	FACETS	1	0.951	1	0.515	0.478	0.554	CLONAL	1	TRUE	0	0.608607263189824	2		417	577	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914224	32914227	+	frameshift_variant	Frame_Shift_Del	DEL	ATGA	ATGA	-	novel	NA	P-0051302-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	72	250	0	ENST00000380152.3:c.5735_5738del	p.Glu1912ValfsTer50	p.E1912Vfs*50	ENST00000380152		1911	gATGAa/ga	11/27	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.608607263189824	NA		250	269	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553233	41553233	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051302-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	169	352	0	ENST00000263253.7:c.3322A>C	p.Thr1108Pro	p.T1108P	ENST00000263253	NM_001429.3	1108	Act/Cct	18/31	0.608134139310893	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.608607263189824	1		352	384	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31431681	31431681	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0051302-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	97	259	0	ENST00000344624.3:c.3145+2T>C		p.X1049_splice	ENST00000344624		1049			1	2	FACETS	0.83	0.746	0.918	0.83	0.746	0.918	CLONAL	1	TRUE	1	0.608607263189824	2		259	384	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346892	70346892	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051302-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	153	512	0	ENST00000374080.3:c.2759C>G	p.Thr920Ser	p.T920S	ENST00000374080		920	aCt/aGt	20/45	0.608134139310893	1	FACETS	0.966	0.896	1	0.966	0.896	1	CLONAL	1	TRUE	0	0.608607263189824	1		512	362	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423661	47423661	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051302-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	198	502	0	ENST00000404338.3:c.1729C>G	p.Arg577Gly	p.R577G	ENST00000404338	NM_004491.4	577	Cgg/Ggg	1/6	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.608607263189824	2		502	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0055133-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	117	397	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	0.343889901849944	2	FACETS	1	0.985	1	0.718	0.653	0.784	CLONAL	1	TRUE	0	0.431228518725437	2		397	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0060169-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	160	704	7	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.343712686118246	2	FACETS	0.844	0.78	0.908	0.844	0.78	0.908	CLONAL	2	TRUE	0	0.408805561078005	2		711	464	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149974	202149974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301592633	NA	P-0060169-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	254	696	8	ENST00000358485.4:c.1415G>A	p.Arg472Gln	p.R472Q	ENST00000358485	NM_001080125.1	472	cGa/cAa	8/9	0.408805561078005	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.408805561078005	2		704	587	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390649	139390650	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs763016003	NA	P-0060169-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	184	828	2	ENST00000277541.6:c.7541_7542del	p.Pro2514ArgfsTer4	p.P2514Rfs*4	ENST00000277541	NM_017617.3	2514	cCT/c	34/34	0.343712686118246	2	FACETS	0.872	0.812	0.934	0.872	0.812	0.934	CLONAL	2	TRUE	0	0.408805561078005	2		830	516	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851883	134851883	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060169-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	63	647	0	ENST00000398015.3:c.1289A>G	p.Asn430Ser	p.N430S	ENST00000398015	NM_004441.4	430	aAc/aGc	5/16	0.201446121399457	4	FACETS	0.806	0.697	0.923	0.403	0.348	0.462	INDETERMINATE	1	TRUE	2	0.408805561078005	4		647	539	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146517	185146517	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060169-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	47	683	3	ENST00000265026.3:c.148G>C	p.Gly50Arg	p.G50R	ENST00000265026	NM_004721.4	50	Ggg/Cgg	2/14	0.201446121399457	4	FACETS	0.556	0.468	0.652	0.278	0.234	0.326	INDETERMINATE	1	TRUE	2	0.408805561078005	4		686	583	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947503	38947503	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	21	364	0	ENST00000357387.3:c.4177G>T	p.Asp1393Tyr	p.D1393Y	ENST00000357387	NM_152756.3	1393	Gat/Tat	32/38	1	2	FACETS	0.773	0.595	0.982	0.773	0.595	0.982	CLONAL	1	TRUE	1	0.14	2		364	388	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650071	93650071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1486347243	NA	P-0064327-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	79	239	0	ENST00000375746.1:c.1622C>T	p.Pro541Leu	p.P541L	ENST00000375746	NM_001174167.1	541	cCg/cTg	12/14	1	2	FACETS	0.853	0.76	0.95	0.853	0.76	0.95	CLONAL	1	TRUE	1	0.709687285828747	2		239	261	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426127	47426127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064327-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	11	306	0	ENST00000377045.4:c.647C>G	p.Pro216Arg	p.P216R	ENST00000377045	NM_001654.4	216	cCc/cGc	7/16	1	2	FACETS	0.126	0.086	0.174	0.126	0.086	0.174	SUBCLONAL	1	TRUE	1	0.709687285828747	2		306	247	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124499060	124499060	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064327-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	79	230	0	ENST00000357628.3:c.653T>G	p.Ile218Arg	p.I218R	ENST00000357628	NM_015450.2	218	aTa/aGa	9/19	0.709687285828747	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.709687285828747	1		230	141	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0064778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	427	536	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.761077779622722	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.761077779622722	3		536	507	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0064778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	134	268	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.72341939631708	5	FACETS	1	0.955	1	1	0.955	1	CLONAL	3	TRUE	2	0.761077779622722	5		268	243	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551682	150551682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	149	702	0	ENST00000369026.2:c.325G>A	p.Glu109Lys	p.E109K	ENST00000369026	NM_021960.4	109	Gag/Aag	1/3	0.589128906210628	5	FACETS	1	0.967	1	0.37	0.338	0.403	CLONAL	1	TRUE	2	0.761077779622722	5		702	755	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0064778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	122	539	3	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	0.72341939631708	5	FACETS	0.9	0.814	0.991	0.3	0.271	0.331	CLONAL	1	TRUE	2	0.761077779622722	5		542	763	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701248	43701248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773338141	NA	P-0064778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	322	623	0	ENST00000382044.4:c.5447G>A	p.Arg1816Gln	p.R1816Q	ENST00000382044	NM_001141980.1	1816	cGa/cAa	26/28	0.761077779622722	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.761077779622722	2		623	389	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55334132	55334132	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	146	442	0	ENST00000284073.2:c.29C>A	p.Ser10Ter	p.S10*	ENST00000284073	NM_138962.2	10	tCg/tAg	1/14	0.761077779622722	4	FACETS	1	0.985	1	0.337	0.309	0.366	CLONAL	1	TRUE	0	0.761077779622722	4		442	501	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749914	162749914	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	285	715	0	ENST00000367921.3:c.2446C>T	p.Gln816Ter	p.Q816*	ENST00000367921	NM_006182.2	816	Caa/Taa	18/18	0.589128906210628	5	FACETS	0.842	0.798	0.886	0.842	0.798	0.886	CLONAL	3	TRUE	2	0.761077779622722	5		715	635	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022263	31022263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763361634	NA	P-0064778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	118	651	0	ENST00000375687.4:c.1748G>A	p.Trp583Ter	p.W583*	ENST00000375687	NM_015338.5	583	tGg/tAg	13/13	0.761077779622722	3	FACETS	0.973	0.884	1	0.486	0.442	0.533	CLONAL	1	TRUE	1	0.761077779622722	3		651	440	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864854	117864854	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	117	485	0	ENST00000297338.2:c.1255G>C	p.Glu419Gln	p.E419Q	ENST00000297338	NM_006265.2	419	Gaa/Caa	10/14	0.761077779622722	8	FACETS	1	0.956	1	0.277	0.249	0.307	CLONAL	1	TRUE	4	0.761077779622722	8		485	910	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599875	28599875	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	171	587	0	ENST00000253063.3:c.757G>C	p.Glu253Gln	p.E253Q	ENST00000253063	NM_031459.4	253	Gag/Cag	6/10	0.443821520307982	2	FACETS	1	0.976	1	0.553	0.515	0.592	INDETERMINATE	1	TRUE	0	0.761077779622722	2		587	406	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380975	116380975	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	152	545	0	ENST00000397752.3:c.1597C>A	p.Pro533Thr	p.P533T	ENST00000397752	NM_000245.2	533	Cca/Aca	5/21	0.675018836731861	4	FACETS	0.974	0.893	1	0.487	0.446	0.53	CLONAL	1	TRUE	2	0.761077779622722	4		545	722	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0066825-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	42	430	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.676	0.566	0.797	0.676	0.566	0.797	SUBCLONAL	1	TRUE	1	0.368692345778633	2		430	337	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412958	49412958	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066825-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	87	495	0	ENST00000418115.1:c.65T>G	p.Leu22Arg	p.L22R	ENST00000418115	NM_001664.2	22	cTc/cGc	2/5	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.368692345778633	2		495	445	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070596	67070596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066825-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	72	477	0	ENST00000412916.2:c.220C>T	p.Gln74Ter	p.Q74*	ENST00000412916		74	Cag/Tag	3/6	0.368692345778633	1	FACETS	0.817	0.717	0.923	0.817	0.717	0.923	CLONAL	1	TRUE	0	0.368692345778633	1		477	390	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391695	139391695	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066825-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	52	655	0	ENST00000277541.6:c.6496C>A	p.Leu2166Met	p.L2166M	ENST00000277541	NM_017617.3	2166	Ctg/Atg	34/34	1	2	FACETS	0.7	0.597	0.812	0.7	0.597	0.812	SUBCLONAL	1	TRUE	1	0.368692345778633	2		655	403	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641629	23641629	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786201907	NA	P-0066825-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	23	467	0	ENST00000261584.4:c.1846G>C	p.Asp616His	p.D616H	ENST00000261584	NM_024675.3	616	Gat/Cat	5/13	1	2	FACETS	0.369	0.288	0.464	0.369	0.288	0.464	SUBCLONAL	1	TRUE	1	0.368692345778633	2		467	338	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849624	68849624	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066825-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	67	569	0	ENST00000261769.5:c.1527del	p.Ala510ProfsTer12	p.A510Pfs*12	ENST00000261769	NM_004360.3	509	acT/ac	10/16	0.368692345778633	1	FACETS	0.823	0.72	0.934	0.823	0.72	0.934	CLONAL	1	TRUE	0	0.368692345778633	1		569	360	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088787	27088788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	13	478	0	ENST00000324856.7:c.2402dup	p.Gln802SerfsTer15	p.Q802Sfs*15	ENST00000324856	NM_006015.4	799	cag/caGg	7/20	1	2	FACETS	0.259	0.184	0.35	0.259	0.184	0.35	SUBCLONAL	1	TRUE	1	0.414764092224814	2		478	242	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	42	350	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.414764092224814	2		350	176	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258735	16258735	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	49	597	0	ENST00000375759.3:c.6005del	p.Asn2002MetfsTer20	p.N2002Mfs*20	ENST00000375759	NM_015001.2	2000	ggA/gg	11/15	1	2	FACETS	0.556	0.472	0.648	0.556	0.472	0.648	SUBCLONAL	1	TRUE	1	0.414764092224814	2		597	425	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780023	9780023	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	27	495	0	ENST00000377346.4:c.1287G>T	p.Lys429Asn	p.K429N	ENST00000377346	NM_005026.3	429	aaG/aaT	10/24	1	2	FACETS	0.365	0.29	0.45	0.365	0.29	0.45	SUBCLONAL	1	TRUE	1	0.414764092224814	2		495	357	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256348	16256348	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	59	515	0	ENST00000375759.3:c.3613C>T	p.Arg1205Cys	p.R1205C	ENST00000375759	NM_015001.2	1205	Cgt/Tgt	11/15	1	2	FACETS	0.971	0.842	1	0.971	0.842	1	CLONAL	1	TRUE	1	0.414764092224814	2		515	293	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913077	32913077	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28897728	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	27	455	0	ENST00000380152.3:c.4585G>A	p.Gly1529Arg	p.G1529R	ENST00000380152		1529	Ggg/Agg	11/27	0.198655874172339	3	FACETS	0.819	0.656	1	0.409	0.328	0.501	INDETERMINATE	1	TRUE	1	0.414764092224814	3		455	192	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	10	602	0	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	0.126	0.085	0.178	0.126	0.085	0.178	SUBCLONAL	1	TRUE	1	0.414764092224814	2		602	383	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624300	89624300	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786204912	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	56	312	0	ENST00000371953.3:c.74T>C	p.Leu25Ser	p.L25S	ENST00000371953	NM_000314.4	25	tTg/tCg	1/9	0.198655874172339	3	FACETS	1	0.967	1	0.718	0.623	0.82	INDETERMINATE	1	TRUE	1	0.414764092224814	3		312	227	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223866	53223866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	43	565	0	ENST00000375401.3:c.3493C>T	p.Arg1165Cys	p.R1165C	ENST00000375401	NM_004187.3	1165	Cgt/Tgt	23/26	1	2	FACETS	0.658	0.553	0.774	0.658	0.553	0.774	SUBCLONAL	1	TRUE	1	0.414764092224814	2		565	315	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	37	383	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	0.198655874172339	3	FACETS	1	0.862	1	0.52	0.433	0.616	INDETERMINATE	1	TRUE	1	0.414764092224814	3		383	207	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440943	56440943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786205215	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	35	477	0	ENST00000407977.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000407977		132	Cga/Tga	4/10	1	2	FACETS	0.425	0.348	0.511	0.425	0.348	0.511	SUBCLONAL	1	TRUE	1	0.414764092224814	2		477	397	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341260	341260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374579262	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	71	369	0	ENST00000262320.3:c.2224G>A	p.Val742Ile	p.V742I	ENST00000262320	NM_003502.3	742	Gtc/Atc	9/11	1	2	FACETS	0.941	0.826	1	0.941	0.826	1	CLONAL	1	TRUE	1	0.414764092224814	2		369	364	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015042	71015042	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs772816590	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	40	343	0	ENST00000318789.4:c.1888G>A	p.Val630Met	p.V630M	ENST00000318789	NM_032682.5	630	Gtg/Atg	20/21	1	2	FACETS	0.853	0.715	1	0.853	0.715	1	CLONAL	1	TRUE	1	0.414764092224814	2		343	226	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333939	70333939	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	57	447	0	ENST00000373644.4:c.1844G>A	p.Ser615Asn	p.S615N	ENST00000373644	NM_030625.2	615	aGc/aAc	2/12	0.198655874172339	3	FACETS	1	0.963	1	0.675	0.585	0.77	INDETERMINATE	1	TRUE	1	0.414764092224814	3		447	246	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101086	41101086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776769442	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	28	536	1	ENST00000373198.4:c.1270G>A	p.Val424Met	p.V424M	ENST00000373198	NM_133170.3	424	Gtg/Atg	8/32	1	2	FACETS	0.381	0.305	0.469	0.381	0.305	0.469	SUBCLONAL	1	TRUE	1	0.414764092224814	2		537	354	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792732	33792737	+	inframe_deletion	In_Frame_Del	DEL	GCGGGT	GCGGGT	-	rs762459325	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	8	479	1	ENST00000498907.2:c.584_589del	p.His195_Pro196del	p.H195_P196del	ENST00000498907	NM_004364.3	195	cACCCGCcg/ccg	1/1	1	2	FACETS	0.125	0.08	0.184	0.125	0.08	0.184	SUBCLONAL	1	TRUE	1	0.414764092224814	2		480	308	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250272	39250272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397517147	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	126	488	0	ENST00000402219.2:c.1297G>A	p.Glu433Lys	p.E433K	ENST00000402219	NM_005633.3	433	Gag/Aag	10/23	0.38945351956803	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	3	TRUE	0	0.414764092224814	3		488	238	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	69	892	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.198655874172339	3	FACETS	0.997	0.872	1	0.498	0.436	0.565	INDETERMINATE	1	TRUE	1	0.414764092224814	3		892	403	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211355	36211357	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs201152143	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	69	577	0	ENST00000222270.7:c.1117_1119del	p.Glu373del	p.E373del	ENST00000222270	NM_014727.1	369	aAAGaa/aaa	3/37	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.414764092224814	2		577	329	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631422	117631422	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	32	345	0	ENST00000368508.3:c.6256C>A	p.Leu2086Ile	p.L2086I	ENST00000368508	NM_002944.2	2086	Ctt/Att	40/43	1	2	FACETS	0.867	0.711	1	0.867	0.711	1	CLONAL	1	TRUE	1	0.414764092224814	2		345	178	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683357	88683357	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201040	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	36	463	0	ENST00000372037.3:c.1480C>T	p.Arg494Ter	p.R494*	ENST00000372037	NM_004329.2	494	Cga/Tga	13/13	0.198655874172339	3	FACETS	1	0.912	1	0.579	0.481	0.685	INDETERMINATE	1	TRUE	1	0.414764092224814	3		463	181	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291170	10291170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369196079	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	63	709	1	ENST00000340748.4:c.301C>T	p.Arg101Trp	p.R101W	ENST00000340748		101	Cgg/Tgg	4/40	1	2	FACETS	0.878	0.764	1	0.878	0.764	1	CLONAL	1	TRUE	1	0.414764092224814	2		710	346	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526105	63526105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs527766429	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	72	476	0	ENST00000307078.5:c.2521C>T	p.Arg841Trp	p.R841W	ENST00000307078	NM_004655.3	841	Cgg/Tgg	11/11	1	2	FACETS	0.899	0.79	1	0.899	0.79	1	CLONAL	1	TRUE	1	0.414764092224814	2		476	386	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729744	162729744	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750450749	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	58	514	0	ENST00000367921.3:c.830G>A	p.Arg277His	p.R277H	ENST00000367921	NM_006182.2	277	cGc/cAc	8/18	0.380423387355551	3	FACETS	1	0.96	1	0.649	0.563	0.741	CLONAL	1	TRUE	1	0.414764092224814	3		514	260	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180343	38180343	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761769496	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	18	563	0	ENST00000396334.3:c.191C>T	p.Ala64Val	p.A64V	ENST00000396334	NM_002468.4	64	gCg/gTg	1/5	1	2	FACETS	0.249	0.187	0.323	0.249	0.187	0.323	SUBCLONAL	1	TRUE	1	0.414764092224814	2		563	348	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161690	56161690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	50	374	1	ENST00000399503.3:c.1187G>A	p.Arg396His	p.R396H	ENST00000399503	NM_005921.1	396	cGt/cAt	6/20	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.414764092224814	2		375	202	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245162	46245162	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	49	511	0	ENST00000334344.6:c.3260del	p.Pro1087LeufsTer69	p.P1087Lfs*69	ENST00000334344	NM_152641.2	1086	Ccc/cc	15/21	0.198655874172339	3	FACETS	1	0.912	1	0.549	0.468	0.635	INDETERMINATE	1	TRUE	1	0.414764092224814	3		511	260	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562247	21562247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143741195	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	55	542	0	ENST00000382592.4:c.1672C>T	p.Arg558Cys	p.R558C	ENST00000382592	NM_014572.2	558	Cgc/Tgc	4/8	1	2	FACETS	0.563	0.482	0.651	0.563	0.482	0.651	SUBCLONAL	1	TRUE	1	0.414764092224814	2		542	471	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714687	52714687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	75	508	0	ENST00000322088.6:c.445G>A	p.Gly149Ser	p.G149S	ENST00000322088	NM_014225.5	149	Ggc/Agc	4/15	1	2	FACETS	0.876	0.771	0.987	0.876	0.771	0.987	CLONAL	1	TRUE	1	0.414764092224814	2		508	413	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391076	139391076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373119531	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	109	545	0	ENST00000277541.6:c.7115G>A	p.Arg2372Gln	p.R2372Q	ENST00000277541	NM_017617.3	2372	cGg/cAg	34/34	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.414764092224814	2		545	390	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067867	30067867	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771675702	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	71	494	0	ENST00000338641.4:c.1052G>A	p.Arg351His	p.R351H	ENST00000338641	NM_000268.3	351	cGc/cAc	11/16	1	2	FACETS	0.796	0.698	0.902	0.796	0.698	0.902	CLONAL	1	TRUE	1	0.414764092224814	2		494	430	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929516	81929516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760949449	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	70	512	0	ENST00000359376.3:c.1177G>A	p.Ala393Thr	p.A393T	ENST00000359376	NM_002661.3	393	Gcc/Acc	13/33	1	2	FACETS	0.868	0.76	0.982	0.868	0.76	0.982	CLONAL	1	TRUE	1	0.414764092224814	2		512	389	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448579	89448579	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	23	472	0	ENST00000336596.2:c.1543G>A	p.Ala515Thr	p.A515T	ENST00000336596	NM_005233.5	515	Gct/Act	7/17	1	2	FACETS	0.462	0.361	0.578	0.462	0.361	0.578	SUBCLONAL	1	TRUE	1	0.414764092224814	2		472	240	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21347150	21347150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375451574	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	51	514	0	ENST00000215739.8:c.1217C>T	p.Thr406Met	p.T406M	ENST00000215739	NM_006767.3	406	aCg/aTg	11/21	1	2	FACETS	0.668	0.57	0.775	0.668	0.57	0.775	SUBCLONAL	1	TRUE	1	0.414764092224814	2		514	368	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665110	29665110	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658541	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	39	390	0	ENST00000356175.3:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000356175	NM_000267.3	2237	Cga/Tga	44/57	0.414764092224814	1	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	0	0.414764092224814	1		390	142	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51503148	51503148	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs72552260	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	48	493	0	ENST00000260433.2:c.1369C>T	p.Arg457Ter	p.R457*	ENST00000260433		457	Cga/Tga	10/10	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.414764092224814	2		493	202	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446943	187446943	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	33	606	1	ENST00000232014.4:c.1250C>A	p.Pro417His	p.P417H	ENST00000232014	NM_001130845.1	417	cCc/cAc	5/10	1	2	FACETS	0.354	0.288	0.429	0.354	0.288	0.429	SUBCLONAL	1	TRUE	1	0.414764092224814	2		607	449	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424759	47424759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	38	494	0	ENST00000404338.3:c.2827G>A	p.Glu943Lys	p.E943K	ENST00000404338	NM_004491.4	943	Gaa/Aaa	1/6	1	2	FACETS	0.751	0.625	0.889	0.751	0.625	0.889	SUBCLONAL	1	TRUE	1	0.414764092224814	2		494	244	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705439	47705439	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553369652	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	37	391	0	ENST00000233146.2:c.2239A>G	p.Ile747Val	p.I747V	ENST00000233146	NM_000251.2	747	Ata/Gta	14/16	0.38945351956803	3	FACETS	1	0.888	1	0.363	0.302	0.429	CLONAL	1	TRUE	0	0.414764092224814	3		391	198	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77961231	77961231	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	26	458	0	ENST00000361507.4:c.592T>C	p.Cys198Arg	p.C198R	ENST00000361507	NM_080491.2	198	Tgc/Cgc	3/10	1	2	FACETS	0.402	0.318	0.497	0.402	0.318	0.497	SUBCLONAL	1	TRUE	1	0.414764092224814	2		458	312	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940166	49940166	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	68	534	0	ENST00000296474.3:c.877T>C	p.Tyr293His	p.Y293H	ENST00000296474	NM_002447.2	293	Tat/Cat	1/20	1	2	FACETS	0.863	0.755	0.979	0.863	0.755	0.979	CLONAL	1	TRUE	1	0.414764092224814	2		534	380	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1268743	1268743	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	20	420	0	ENST00000310581.5:c.2474A>G	p.Tyr825Cys	p.Y825C	ENST00000310581	NM_198253.2	825	tAc/tGc	9/16	1	2	FACETS	0.353	0.27	0.45	0.353	0.27	0.45	SUBCLONAL	1	TRUE	1	0.414764092224814	2		420	273	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100279	157100279	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1256741858	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	41	328	0	ENST00000346085.5:c.1216G>A	p.Ala406Thr	p.A406T	ENST00000346085	NM_020732.3	406	Gcc/Acc	1/20	1	2	FACETS	0.941	0.792	1	0.941	0.792	1	CLONAL	1	TRUE	1	0.414764092224814	2		328	210	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992109	11992109	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	32	454	0	ENST00000396373.4:c.199G>A	p.Ala67Thr	p.A67T	ENST00000396373	NM_001987.4	67	Gcc/Acc	3/8	0.198655874172339	3	FACETS	0.529	0.43	0.641	0.265	0.215	0.321	INDETERMINATE	1	TRUE	1	0.414764092224814	3		454	352	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2039815	2039816	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAA	rs756562013	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	50	616	0	ENST00000349721.2:c.708_710dup	p.Gln238dup	p.Q238dup	ENST00000349721	NM_003070.3	238	-/CAA	4/34	1	2	FACETS	0.399	0.338	0.466	0.399	0.338	0.466	SUBCLONAL	1	TRUE	1	0.414764092224814	2		616	604	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878080	151878080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764025360	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	52	564	0	ENST00000262189.6:c.6865C>T	p.Arg2289Cys	p.R2289C	ENST00000262189	NM_170606.2	2289	Cgt/Tgt	36/59	1	2	FACETS	0.809	0.693	0.935	0.809	0.693	0.935	CLONAL	1	TRUE	1	0.414764092224814	2		564	310	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6213359	6213359	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	45	494	0	ENST00000252674.7:c.1540G>A	p.Val514Met	p.V514M	ENST00000252674	NM_005934.3	514	Gtg/Atg	11/12	1	2	FACETS	0.608	0.512	0.713	0.608	0.512	0.713	SUBCLONAL	1	TRUE	1	0.414764092224814	2		494	357	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115960	8115960	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	19	492	0	ENST00000346208.3:c.1306T>C	p.Ser436Pro	p.S436P	ENST00000346208		436	Tcc/Ccc	6/6	0.198655874172339	3	FACETS	0.302	0.229	0.389	0.151	0.114	0.195	INDETERMINATE	1	TRUE	1	0.414764092224814	3		492	366	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8111080	8111080	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	21	500	0	ENST00000585124.1:c.127A>G	p.Ser43Gly	p.S43G	ENST00000585124	NM_004217.3	43	Agc/Ggc	3/9	1	2	FACETS	0.268	0.206	0.341	0.268	0.206	0.341	SUBCLONAL	1	TRUE	1	0.414764092224814	2		500	378	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2047309	2047309	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	20	102	0	ENST00000349721.2:c.876del	p.Ala293GlnfsTer62	p.A293Qfs*62	ENST00000349721	NM_003070.3	291	Ccc/cc	5/34	1	2	FACETS	0.599	0.461	0.757	0.599	0.461	0.757	SUBCLONAL	1	TRUE	1	0.414764092224814	2		102	161	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522517	187522517	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	40	375	0	ENST00000441802.2:c.11546A>G	p.Asn3849Ser	p.N3849S	ENST00000441802	NM_005245.3	3849	aAc/aGc	21/27	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.414764092224814	2		375	179	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2191316	2191316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139124915	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	23	543	0	ENST00000349721.2:c.4645C>T	p.Arg1549Trp	p.R1549W	ENST00000349721	NM_003070.3	1549	Cgg/Tgg	33/34	1	2	FACETS	0.306	0.238	0.385	0.306	0.238	0.385	SUBCLONAL	1	TRUE	1	0.414764092224814	2		543	362	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414374	6414374	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	15	214	0	ENST00000356142.4:c.8C>T	p.Ala3Val	p.A3V	ENST00000356142	NM_018890.3	3	gCc/gTc	1/7	1	2	FACETS	0.473	0.347	0.621	0.473	0.347	0.621	SUBCLONAL	1	TRUE	1	0.414764092224814	2		214	153	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538319	9538319	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1461094602	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	15	507	0	ENST00000353224.5:c.1679A>G	p.His560Arg	p.H560R	ENST00000353224	NM_177990.2	560	cAt/cGt	7/10	1	2	FACETS	0.338	0.247	0.447	0.338	0.247	0.447	SUBCLONAL	1	TRUE	1	0.414764092224814	2		507	214	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273068	18273068	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	73	515	0	ENST00000222254.8:c.958G>T	p.Gly320Trp	p.G320W	ENST00000222254	NM_005027.3	320	Ggg/Tgg	8/16	1	2	FACETS	0.871	0.766	0.984	0.871	0.766	0.984	CLONAL	1	TRUE	1	0.414764092224814	2		515	404	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163297303	163297303	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	69	388	0	ENST00000271452.3:c.149T>C	p.Met50Thr	p.M50T	ENST00000271452	NM_145697.2	50	aTg/aCg	3/14	0.380423387355551	3	FACETS	0.934	0.827	1	0.934	0.827	1	CLONAL	2	TRUE	1	0.414764092224814	3		388	215	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664517	138664517	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	51	276	0	ENST00000330315.3:c.1048C>T	p.Gln350Ter	p.Q350*	ENST00000330315	NM_023067.3	350	Cag/Tag	1/1	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.414764092224814	2		276	245	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107960	30107960	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	57	466	0	ENST00000331968.5:c.847G>A	p.Val283Met	p.V283M	ENST00000331968	NM_002742.2	283	Gtg/Atg	5/18	1	2	FACETS	0.83	0.717	0.953	0.83	0.717	0.953	CLONAL	1	TRUE	1	0.414764092224814	2		466	331	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608321	100608321	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	19	434	0	ENST00000308731.7:c.1769T>A	p.Ile590Asn	p.I590N	ENST00000308731	NM_000061.2	590	aTt/aAt	18/19	1	2	FACETS	0.595	0.455	0.757	0.595	0.455	0.757	SUBCLONAL	1	TRUE	1	0.414764092224814	2		434	154	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31483675	31483675	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	26	434	0	ENST00000344624.3:c.2057T>C	p.Val686Ala	p.V686A	ENST00000344624		686	gTa/gCa	13/33	1	2	FACETS	0.793	0.635	0.971	0.793	0.635	0.971	CLONAL	1	TRUE	1	0.414764092224814	2		434	158	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527457	41527458	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	46	463	0	ENST00000263253.7:c.1353dup	p.Asn452GlnfsTer6	p.N452Qfs*6	ENST00000263253	NM_001429.3	450	gcc/gCcc	6/31	1	2	FACETS	0.902	0.766	1	0.902	0.766	1	CLONAL	1	TRUE	1	0.414764092224814	2		463	246	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073572	8073572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	71	485	0	ENST00000377482.5:c.1087G>A	p.Ala363Thr	p.A363T	ENST00000377482	NM_018948.3	363	Gca/Aca	4/4	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.414764092224814	2		485	342	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968290	134968290	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	26	509	0	ENST00000398015.3:c.2803G>A	p.Ala935Thr	p.A935T	ENST00000398015	NM_004441.4	935	Gct/Act	15/16	1	2	FACETS	0.459	0.364	0.567	0.459	0.364	0.567	SUBCLONAL	1	TRUE	1	0.414764092224814	2		509	273	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591859	48591859	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	27	539	0	ENST00000342988.3:c.1022T>C	p.Val341Ala	p.V341A	ENST00000342988	NM_005359.5	341	gTt/gCt	9/12	1	2	FACETS	0.589	0.471	0.722	0.589	0.471	0.722	SUBCLONAL	1	TRUE	1	0.414764092224814	2		539	221	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188853	32188853	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	75	578	0	ENST00000375023.3:c.701G>T	p.Arg234Leu	p.R234L	ENST00000375023	NM_004557.3	234	cGg/cTg	4/30	0.198655874172339	3	FACETS	1	0.97	1	0.664	0.586	0.746	INDETERMINATE	1	TRUE	1	0.414764092224814	3		578	329	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996078	73996078	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	58	571	0	ENST00000318443.5:c.816del	p.Glu273SerfsTer15	p.E273Sfs*15	ENST00000318443	NM_001024736.1	271	tCc/tc	5/10	1	2	FACETS	0.788	0.68	0.904	0.788	0.68	0.904	CLONAL	1	TRUE	1	0.414764092224814	2		571	355	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965715	90965715	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	37	469	0	ENST00000265433.3:c.1602T>A	p.Asn534Lys	p.N534K	ENST00000265433	NM_002485.4	534	aaT/aaA	11/16	1	2	FACETS	0.975	0.813	1	0.975	0.813	1	CLONAL	1	TRUE	1	0.414764092224814	2		469	183	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910437	32910437	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398122735	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	30	408	0	ENST00000380152.3:c.1945C>T	p.Gln649Ter	p.Q649*	ENST00000380152		649	Cag/Tag	11/27	0.198655874172339	3	FACETS	0.924	0.751	1	0.462	0.375	0.558	INDETERMINATE	1	TRUE	1	0.414764092224814	3		408	189	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562024	21562024	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1304367039	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	35	434	0	ENST00000382592.4:c.1895C>T	p.Ala632Val	p.A632V	ENST00000382592	NM_014572.2	632	gCc/gTc	4/8	1	2	FACETS	0.664	0.548	0.794	0.664	0.548	0.794	SUBCLONAL	1	TRUE	1	0.414764092224814	2		434	254	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944931	31944931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	42	237	0	ENST00000340398.3:c.170C>T	p.Ser57Leu	p.S57L	ENST00000340398	NM_001013699.2	57	tCg/tTg	1/1	0.198655874172339	3	FACETS	1	0.932	1	0.602	0.508	0.704	INDETERMINATE	1	TRUE	1	0.414764092224814	3		237	203	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902692	1902692	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	16	487	0	ENST00000382891.5:c.311A>G	p.Glu104Gly	p.E104G	ENST00000382891	NM_133335.3	104	gAa/gGa	2/22	0.198655874172339	3	FACETS	0.313	0.231	0.411	0.156	0.115	0.206	INDETERMINATE	1	TRUE	1	0.414764092224814	3		487	298	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915754	112915754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1373621596	NA	P-0067304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	50	450	0	ENST00000351677.2:c.1027C>T	p.Arg343Trp	p.R343W	ENST00000351677	NM_002834.3	343	Cgg/Tgg	9/16	0.198655874172339	3	FACETS	1	0.948	1	0.622	0.533	0.718	INDETERMINATE	1	TRUE	1	0.414764092224814	3		450	234	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	16	274	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.605	0.45	0.788	0.605	0.45	0.788	SUBCLONAL	1	TRUE	1	0.35	2		275	151	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	15	784	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.41	0.3	0.542	0.41	0.3	0.542	SUBCLONAL	1	TRUE	1	0.35	2		789	209	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	14	235	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	0.457	0.331	0.608	0.457	0.331	0.608	SUBCLONAL	1	TRUE	1	0.35	2		235	175	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309037	137309037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs537231520	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	15	194	0	ENST00000481739.1:c.644G>A	p.Arg215Gln	p.R215Q	ENST00000481739	NM_002957.4	215	cGg/cAg	5/10	1	2	FACETS	0.44	0.322	0.58	0.44	0.322	0.58	SUBCLONAL	1	TRUE	1	0.35	2		194	195	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108765	2108765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755631210	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	28	216	0	ENST00000219476.3:c.866C>T	p.Ala289Val	p.A289V	ENST00000219476	NM_000548.3	289	gCg/gTg	10/42	1	2	FACETS	0.766	0.616	0.934	0.766	0.616	0.934	CLONAL	1	TRUE	1	0.35	2		216	209	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763458	41763458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372169583	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	30	228	0	ENST00000301178.4:c.2257G>A	p.Val753Met	p.V753M	ENST00000301178	NM_021913.4	753	Gtg/Atg	19/20	1	2	FACETS	0.794	0.644	0.961	0.794	0.644	0.961	CLONAL	1	TRUE	1	0.35	2		228	216	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168682	32168682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs935064991	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	10	205	0	ENST00000375023.3:c.4241C>T	p.Ala1414Val	p.A1414V	ENST00000375023	NM_004557.3	1414	gCg/gTg	23/30	1	2	FACETS	0.289	0.195	0.406	0.289	0.195	0.406	SUBCLONAL	1	TRUE	1	0.35	2		205	198	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950397	15950397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs190623603	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	16	221	0	ENST00000268712.3:c.6547C>T	p.Arg2183Cys	p.R2183C	ENST00000268712	NM_006311.3	2183	Cgc/Tgc	42/46	1	2	FACETS	0.788	0.589	1	0.788	0.589	1	CLONAL	1	TRUE	1	0.35	2		221	116	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982386	25982386	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	23	183	0	ENST00000435504.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000435504		302	Cga/Tga	9/13	1	2	FACETS	0.76	0.597	0.945	0.76	0.597	0.945	CLONAL	1	TRUE	1	0.35	2		183	173	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798882	42798882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	24	265	0	ENST00000575354.2:c.4454C>T	p.Pro1485Leu	p.P1485L	ENST00000575354	NM_015125.3	1485	cCg/cTg	19/20	1	2	FACETS	0.696	0.549	0.863	0.696	0.549	0.863	SUBCLONAL	1	TRUE	1	0.35	2		265	197	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996194	73996194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759425133	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	10	212	0	ENST00000318443.5:c.928C>T	p.Arg310Cys	p.R310C	ENST00000318443	NM_001024736.1	310	Cgc/Tgc	5/10	1	2	FACETS	0.397	0.269	0.556	0.397	0.269	0.556	SUBCLONAL	1	TRUE	1	0.35	2		212	144	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622120	43622120	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	15	226	0	ENST00000355710.3:c.3142del	p.Leu1048SerfsTer61	p.L1048Sfs*61	ENST00000355710	NM_020975.4	1046	gCc/gc	19/20	1	2	FACETS	0.454	0.332	0.598	0.454	0.332	0.598	SUBCLONAL	1	TRUE	1	0.35	2		226	189	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673065	30673065	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1362687413	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	28	355	0	ENST00000376406.3:c.3895C>T	p.Arg1299Ter	p.R1299*	ENST00000376406	NM_014641.2	1299	Cga/Tga	10/15	1	2	FACETS	0.714	0.574	0.872	0.714	0.574	0.872	SUBCLONAL	1	TRUE	1	0.35	2		355	224	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738315	133738315	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	29	250	0	ENST00000318560.5:c.715C>T	p.Arg239Cys	p.R239C	ENST00000318560	NM_005157.4	239	Cgc/Tgc	4/11	1	2	FACETS	0.746	0.603	0.908	0.746	0.603	0.908	CLONAL	1	TRUE	1	0.35	2		250	222	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222595	157222595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199949701	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	26	248	2	ENST00000346085.5:c.1862C>T	p.Pro621Leu	p.P621L	ENST00000346085	NM_020732.3	621	cCg/cTg	4/20	1	2	FACETS	0.638	0.507	0.786	0.638	0.507	0.786	SUBCLONAL	1	TRUE	1	0.35	2		250	233	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532681	46532681	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201330473	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	17	197	0	ENST00000262741.5:c.397G>A	p.Val133Met	p.V133M	ENST00000262741	NM_003629.3	133	Gtg/Atg	4/10	1	2	FACETS	0.679	0.511	0.876	0.679	0.511	0.876	SUBCLONAL	1	TRUE	1	0.35	2		197	143	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401453	401453	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1407719860	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	16	260	0	ENST00000380956.4:c.775C>T	p.Arg259Trp	p.R259W	ENST00000380956	NM_001195286.1	259	Cgg/Tgg	7/9	1	2	FACETS	0.469	0.347	0.613	0.469	0.347	0.613	SUBCLONAL	1	TRUE	1	0.35	2		260	195	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632276	215632276	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779468443	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	14	222	0	ENST00000260947.4:c.1498G>A	p.Asp500Asn	p.D500N	ENST00000260947	NM_000465.2	500	Gat/Aat	6/11	1	2	FACETS	0.457	0.331	0.608	0.457	0.331	0.608	SUBCLONAL	1	TRUE	1	0.35	2		222	175	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447544	187447544	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376246678	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	36	258	0	ENST00000232014.4:c.649C>T	p.Arg217Trp	p.R217W	ENST00000232014	NM_001130845.1	217	Cgg/Tgg	5/10	1	2	FACETS	0.875	0.725	1	0.875	0.725	1	CLONAL	1	TRUE	1	0.35	2		258	235	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620666	52620666	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	12	220	0	ENST00000394830.3:c.3087G>T	p.Glu1029Asp	p.E1029D	ENST00000394830	NM_018313.4	1029	gaG/gaT	21/30	1	2	FACETS	0.448	0.316	0.609	0.448	0.316	0.609	SUBCLONAL	1	TRUE	1	0.35	2		220	153	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137313	64137313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	20	211	0	ENST00000334205.4:c.1745C>T	p.Ala582Val	p.A582V	ENST00000334205	NM_003942.2	582	gCg/gTg	14/17	1	2	FACETS	0.688	0.53	0.871	0.688	0.53	0.871	SUBCLONAL	1	TRUE	1	0.35	2		211	166	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145736897	145736897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376981214	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	18	238	0	ENST00000428558.2:c.3544C>T	p.Arg1182Cys	p.R1182C	ENST00000428558	NM_004260.3	1182	Cgc/Tgc	22/22	1	2	FACETS	0.627	0.475	0.804	0.627	0.475	0.804	SUBCLONAL	1	TRUE	1	0.35	2		238	164	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295376	1295376	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	11	245	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.587	0.409	0.805	0.587	0.409	0.805	SUBCLONAL	1	TRUE	1	0.35	2		245	107	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117105	7117105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	31	181	0	ENST00000302850.5:c.4111G>A	p.Gly1371Arg	p.G1371R	ENST00000302850	NM_000208.2	1371	Ggg/Agg	22/22	1	2	FACETS	0.881	0.719	1	0.881	0.719	1	CLONAL	1	TRUE	1	0.35	2		181	201	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508732	31508732	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	20	193	0	ENST00000344624.3:c.1583G>A	p.Gly528Asp	p.G528D	ENST00000344624		528	gGc/gAc	7/33	1	2	FACETS	0.621	0.478	0.787	0.621	0.478	0.787	SUBCLONAL	1	TRUE	1	0.35	2		193	184	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650416	48650416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	40	120	0	ENST00000376670.3:c.386G>A	p.Ser129Asn	p.S129N	ENST00000376670	NM_002049.3	129	aGc/aAc	3/6	1	1	FACETS	0.857	0.732	0.987	1	0.968	1	CLONAL	2	TRUE	0	0.35	1		120	110	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044465	5044465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777208458	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	10	171	0	ENST00000381652.3:c.413G>A	p.Arg138Gln	p.R138Q	ENST00000381652	NM_004972.3	138	cGa/cAa	5/25	1	2	FACETS	0.583	0.398	0.81	0.583	0.398	0.81	SUBCLONAL	1	TRUE	1	0.35	2		171	98	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287212	38287212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747842199	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	29	174	0	ENST00000425967.3:c.445G>A	p.Val149Ile	p.V149I	ENST00000425967	NM_001174067.1	149	Gtc/Atc	4/19	1	2	FACETS	0.778	0.629	0.945	0.778	0.629	0.945	CLONAL	1	TRUE	1	0.35	2		174	213	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435513	110435513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777793064	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	30	217	0	ENST00000375856.3:c.2888C>T	p.Pro963Leu	p.P963L	ENST00000375856	NM_003749.2	963	cCg/cTg	1/2	1	2	FACETS	1	0.826	1	1	0.826	1	CLONAL	1	TRUE	1	0.35	2		217	169	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559810	29559810	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868407539	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	31	262	0	ENST00000356175.3:c.3407G>A	p.Arg1136Gln	p.R1136Q	ENST00000356175	NM_000267.3	1136	cGg/cAg	26/57	1	2	FACETS	0.711	0.578	0.861	0.711	0.578	0.861	SUBCLONAL	1	TRUE	1	0.35	2		262	249	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825552	50825552	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	10	187	0	ENST00000398568.2:c.2183A>G	p.Gln728Arg	p.Q728R	ENST00000398568	NM_001042412.1	728	cAg/cGg	14/18	1	2	FACETS	0.649	0.445	0.9	0.649	0.445	0.9	SUBCLONAL	1	TRUE	1	0.35	2		187	88	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028259	48028259	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587779931	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	22	238	0	ENST00000234420.5:c.3137A>G	p.Asp1046Gly	p.D1046G	ENST00000234420	NM_000179.2	1046	gAc/gGc	4/10	0.3	1	FACETS	0.843	0.663	1	0.843	0.663	1	CLONAL	1	TRUE	0	0.35	1		238	123	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571971	64571974	+	frameshift_variant	Frame_Shift_Del	DEL	CTCA	CTCA	-	rs1114167510	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	17	228	0	ENST00000312049.6:c.1665_1668del	p.Ser555ArgfsTer3	p.S555Rfs*3	ENST00000312049	NM_130799.2	555	agTGAG/ag	10/10	1	2	FACETS	0.54	0.404	0.699	0.54	0.404	0.699	SUBCLONAL	1	TRUE	1	0.35	2		228	180	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295728	1295728	+	upstream_gene_variant	5'Flank	SNP	A	A	C	novel	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	24	209	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.758	0.598	0.938	0.758	0.598	0.938	CLONAL	1	TRUE	1	0.35	2		209	181	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225594	225594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780654623	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	10	129	0	ENST00000264932.6:c.373G>A	p.Asp125Asn	p.D125N	ENST00000264932	NM_004168.2	125	Gac/Aac	4/15	1	2	FACETS	0.794	0.546	1	0.794	0.546	1	CLONAL	1	TRUE	1	0.35	2		129	72	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705655	47705655	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	13	207	0	ENST00000233146.2:c.2457del	p.Gly820ValfsTer21	p.G820Vfs*21	ENST00000233146	NM_000251.2	819	Aaa/aa	14/16	0.3	1	FACETS	0.625	0.451	0.832	0.625	0.451	0.832	SUBCLONAL	1	TRUE	0	0.35	1		207	98	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968642	55968642	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	23	209	0	ENST00000263923.4:c.2021A>T	p.Glu674Val	p.E674V	ENST00000263923	NM_002253.2	674	gAg/gTg	14/30	1	2	FACETS	0.738	0.58	0.919	0.738	0.58	0.919	CLONAL	1	TRUE	1	0.35	2		209	178	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870273	155870273	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749213571	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	13	231	0	ENST00000368323.3:c.566C>T	p.Ala189Val	p.A189V	ENST00000368323	NM_006912.5	189	gCa/gTa	6/6	1	2	FACETS	0.59	0.423	0.789	0.59	0.423	0.789	SUBCLONAL	1	TRUE	1	0.35	2		231	126	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466033	69466033	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1292246537	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	32	246	0	ENST00000227507.2:c.871C>T	p.Arg291Trp	p.R291W	ENST00000227507	NM_053056.2	291	Cgg/Tgg	5/5	1	2	FACETS	0.919	0.752	1	0.919	0.752	1	CLONAL	1	TRUE	1	0.35	2		246	199	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514232	69514232	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	12	259	0	ENST00000294312.3:c.449A>T	p.Gln150Leu	p.Q150L	ENST00000294312	NM_005117.2	150	cAg/cTg	3/3	1	2	FACETS	0.367	0.258	0.5	0.367	0.258	0.5	SUBCLONAL	1	TRUE	1	0.35	2		259	187	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41558757	41558757	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	19	286	0	ENST00000263253.7:c.3707del	p.Asn1236MetfsTer41	p.N1236Mfs*41	ENST00000263253	NM_001429.3	1234	agA/ag	21/31	0.451402791346422	2	FACETS	0.273	0.207	0.351	0.137	0.103	0.176	SUBCLONAL	1	TRUE	0	0.451402791346422	2		286	308	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550956	150550956	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1181707820	NA	P-0067898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	54	426	0	ENST00000369026.2:c.700A>C	p.Lys234Gln	p.K234Q	ENST00000369026	NM_021960.4	234	Aaa/Caa	2/3	0.425653565521206	3	FACETS	0.5	0.427	0.581	0.167	0.142	0.194	SUBCLONAL	1	TRUE	0	0.451402791346422	3		426	586	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0068242-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	17	704	7	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.428	0.318	0.56	0.428	0.318	0.56	SUBCLONAL	1	TRUE	1	0.14	2		711	567	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0068242-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	30	391	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	0.120678678658567	3	FACETS	0.74	0.594	0.906	0.37	0.297	0.453	CLONAL	1	TRUE	1	0.14	3		391	620	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912770	32912771	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs80359439	NA	P-0068242-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	24	367	0	ENST00000380152.3:c.4284dup	p.Gln1429SerfsTer9	p.Q1429Sfs*9	ENST00000380152		1426	-/T	11/27	1	2	FACETS	0.736	0.576	0.921	0.736	0.576	0.921	CLONAL	1	TRUE	1	0.14	2		367	466	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0068242-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	13	413	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	0.325	0.231	0.442	0.325	0.231	0.442	SUBCLONAL	1	TRUE	1	0.14	2		413	571	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542109	187542110	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1560943587	NA	P-0068242-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	32	456	0	ENST00000441802.2:c.5630dup	p.Val1878CysfsTer8	p.V1878Cfs*8	ENST00000441802	NM_005245.3	1877	cct/ccCt	10/27	1	2	FACETS	0.818	0.662	0.994	0.818	0.662	0.994	CLONAL	1	TRUE	1	0.14	2		456	559	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191488	10191488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs5030818	NA	P-0068242-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	11	327	1	ENST00000256474.2:c.481C>T	p.Arg161Ter	p.R161*	ENST00000256474	NM_000551.3	161	Cga/Tga	3/3	1	2	FACETS	0.323	0.222	0.45	0.323	0.222	0.45	SUBCLONAL	1	TRUE	1	0.14	2		328	487	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163309259	163309260	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0068242-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	17	286	0	ENST00000271452.3:c.604dup	p.Thr202AsnfsTer24	p.T202Nfs*24	ENST00000271452	NM_145697.2	200	caa/cAaa	8/14	1	2	FACETS	0.812	0.606	1	0.812	0.606	1	CLONAL	1	TRUE	1	0.14	2		286	299	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287212	33287213	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1268651006	NA	P-0068242-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	44	466	0	ENST00000374542.5:c.1884dup	p.Cys629LeufsTer29	p.C629Lfs*29	ENST00000374542	NM_001141970.1	628	-/C	6/8	0.120678678658567	3	FACETS	0.978	0.818	1	0.489	0.409	0.578	CLONAL	1	TRUE	1	0.14	3		466	688	SUCCESS
APC	324	MSKCC	GRCh37	5	112174516	112174516	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0068242-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	30	418	0	ENST00000257430.4:c.3225T>A	p.Tyr1075Ter	p.Y1075*	ENST00000257430	NM_000038.5	1075	taT/taA	16/16	1	2	FACETS	0.753	0.605	0.922	0.753	0.605	0.922	CLONAL	1	TRUE	1	0.14	2		418	569	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984454	72984454	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs533692914	NA	P-0068242-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	27	384	0	ENST00000268489.5:c.3130G>A	p.Ala1044Thr	p.A1044T	ENST00000268489	NM_006885.3	1044	Gcc/Acc	3/10	1	2	FACETS	0.742	0.589	0.917	0.742	0.589	0.917	CLONAL	1	TRUE	1	0.14	2		384	520	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360685	70360685	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068242-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	36	467	0	ENST00000374080.3:c.6245A>G	p.Gln2082Arg	p.Q2082R	ENST00000374080		2082	cAg/cGg	42/45	0.120678678658567	0	FACETS	0.759	0.622	0.912			1	CLONAL	1	TRUE	0	0.14	0		467	583	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946367	2946367	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs576383569	NA	P-0068242-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	32	399	0	ENST00000396946.4:c.3370A>G	p.Met1124Val	p.M1124V	ENST00000396946	NM_032415.4	1124	Atg/Gtg	25/25	1	2	FACETS	0.896	0.726	1	0.896	0.726	1	CLONAL	1	TRUE	1	0.14	2		399	510	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438198	110438198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068242-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	30	308	0	ENST00000375856.3:c.203C>T	p.Pro68Leu	p.P68L	ENST00000375856	NM_003749.2	68	cCg/cTg	1/2	1	2	FACETS	0.9	0.725	1	0.9	0.725	1	CLONAL	1	TRUE	1	0.14	2		308	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068301-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	93	369	0	ENST00000269305.4:c.659del	p.Tyr220LeufsTer27	p.Y220Lfs*27	ENST00000269305	NM_001126112.2	220	tAt/tt	6/11	0.241910279312925	2	FACETS	0.776	0.695	0.861	0.776	0.695	0.861	SUBCLONAL	2	FALSE	0	0.308732976322026	2		369	388	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057056	180057056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142274156	NA	P-0068301-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	15	312	0	ENST00000261937.6:c.563G>A	p.Arg188Gln	p.R188Q	ENST00000261937	NM_182925.4	188	cGg/cAg	5/30	1	2	FACETS	0.424	0.31	0.561	0.424	0.31	0.561	SUBCLONAL	1	FALSE	1	0.308732976322026	2		312	229	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90633755	90633755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068301-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	23	349	0	ENST00000330062.3:c.329C>T	p.Ala110Val	p.A110V	ENST00000330062	NM_002168.2	110	gCt/gTt	3/11	0.174327705654672	1	FACETS	0.345	0.269	0.434	0.345	0.269	0.434	INDETERMINATE	1	FALSE	0	0.308732976322026	1		349	365	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72861909	72861909	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068301-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	24	356	0	ENST00000325599.8:c.973G>C	p.Gly325Arg	p.G325R	ENST00000325599	NM_018130.2	325	Gga/Cga	9/11	0.244413977647855	2	FACETS	0.762	0.601	0.946	0.381	0.3	0.473	CLONAL	1	FALSE	0	0.308732976322026	2		356	204	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902454	1902454	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068301-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	28	334	0	ENST00000382891.5:c.73C>G	p.Pro25Ala	p.P25A	ENST00000382891	NM_133335.3	25	Cca/Gca	2/22	0.244413977647855	2	FACETS	0.55	0.44	0.675	0.275	0.22	0.338	SUBCLONAL	1	FALSE	0	0.308732976322026	2		334	330	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279249	1279539	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCACCCTAGGTGCCAGGTGTGTCCTCAACAGTGACAGGGTCACCTGCACTCCCTGCGGCCCACCCAGGAGTACCTCCTCCACCCAACATGAGGTGCCAATCAGGCAGCCACTCCCAAGGTCCAGCAGGGCTGCTCACGGGGGTCCCCGGCACCCACCTTGACAAAGTACAGCTCAGGCGGCGGGTCCTGGGCCCGCACACGCAGCACGAAGGTGCGCCAGGCCCTGTGGATATCGTCCAGGCCCAGCACAGAGGCGCCCAGGAGGCCGGGGCGCCGCGCCCGCTCGTAGT	TCCACCCTAGGTGCCAGGTGTGTCCTCAACAGTGACAGGGTCACCTGCACTCCCTGCGGCCCACCCAGGAGTACCTCCTCCACCCAACATGAGGTGCCAATCAGGCAGCCACTCCCAAGGTCCAGCAGGGCTGCTCACGGGGGTCCCCGGCACCCACCTTGACAAAGTACAGCTCAGGCGGCGGGTCCTGGGCCCGCACACGCAGCACGAAGGTGCGCCAGGCCCTGTGGATATCGTCCAGGCCCAGCACAGAGGCGCCCAGGAGGCCGGGGCGCCGCGCCCGCTCGTAGT	-	novel	NA	P-0068301-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	25	94	0	ENST00000310581.5:c.1997_2130+157del		p.X666_splice	ENST00000310581	NM_198253.2	666		5/16	0.232805159350158	3	FACETS	1	0.869	1	1	0.96	1	CLONAL	5	FALSE	0	0.308732976322026	3		94	37	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835718	68835718	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068447-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	124	352	0	ENST00000261769.5:c.309G>A	p.Trp103Ter	p.W103*	ENST00000261769	NM_004360.3	103	tgG/tgA	3/16	0.285964835888668	1	FACETS	0.967	0.875	1	0.967	0.875	1	CLONAL	1	TRUE	0	0.285964835888668	1		352	769	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068447-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	20	323	0	ENST00000263967.3:c.331A>C	p.Lys111Gln	p.K111Q	ENST00000263967	NM_006218.2	111	Aag/Cag	2/21	1	2	FACETS	0.237	0.18	0.304	0.237	0.18	0.304	SUBCLONAL	1	TRUE	1	0.285964835888668	2		323	591	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112745421	112745421	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068447-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	72	282	0	ENST00000369452.4:c.739C>T	p.His247Tyr	p.H247Y	ENST00000369452	NM_007373.3	247	Cac/Tac	3/9	1	2	FACETS	0.939	0.822	1	0.939	0.822	1	CLONAL	1	TRUE	1	0.285964835888668	2		282	536	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961381	54961381	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs45533839	NA	P-0068447-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	73	206	0	ENST00000312783.6:c.251T>C	p.Val84Ala	p.V84A	ENST00000312783	NM_198436.1	84	gTa/gCa	4/10	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.285964835888668	2		206	465	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133179	30133179	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068447-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	127	319	0	ENST00000263025.4:c.319C>G	p.Leu107Val	p.L107V	ENST00000263025	NM_002746.2	107	Ctg/Gtg	2/9	0.274979670965047	3	FACETS	1	0.967	1	0.574	0.519	0.631	CLONAL	1	TRUE	1	0.285964835888668	3		319	885	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398843	398843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068447-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	115	280	0	ENST00000380956.4:c.653G>A	p.Gly218Glu	p.G218E	ENST00000380956	NM_001195286.1	218	gGa/gAa	6/9	1	2	FACETS	0.975	0.878	1	0.975	0.878	1	CLONAL	1	TRUE	1	0.285964835888668	2		280	825	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952151	178952154	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	INS	GAAA	GAAA	TTTTC	novel	NA	P-0068447-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	90	313	0	ENST00000263967.3:c.3206_*2delinsTTTTC		p.*1069*	ENST00000263967	NM_006218.2	1069		21/21	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.285964835888668	2		313	619	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0068469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	58	268	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.520105411688992	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.520105411688992	2		268	95	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0068469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	49	172	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	0.520105411688992	3	FACETS	0.833	0.71	0.966	0.417	0.355	0.483	CLONAL	1	TRUE	1	0.520105411688992	3		172	285	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs1202793339	NA	P-0068469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	122	218	0	ENST00000269305.4:c.560-1G>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.520105411688992	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.520105411688992	2		218	222	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522423	176522423	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	62	195	0	ENST00000292408.4:c.1612G>C	p.Gly538Arg	p.G538R	ENST00000292408	NM_213647.1	538	Ggt/Cgt	12/18	0.520105411688992	3	FACETS	1	0.929	1	0.55	0.48	0.625	CLONAL	1	TRUE	1	0.520105411688992	3		195	273	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131895039	131895039	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	63	102	0	ENST00000265335.6:c.193A>C	p.Thr65Pro	p.T65P	ENST00000265335		65	Aca/Cca	2/25	0.520105411688992	3	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	1	0.520105411688992	3		102	143	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0068518-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	92	492	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	1	2	FACETS	0.755	0.67	0.846	0.755	0.67	0.846	SUBCLONAL	1	TRUE	1	0.31	2		492	786	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0068518-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	182	464	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.240231573566285	2	FACETS	0.76	0.702	0.819	0.76	0.702	0.819	SUBCLONAL	2	TRUE	0	0.31	2		464	773	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974769	21974770	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCCGT	rs1563892769	NA	P-0068518-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	70	483	0	ENST00000304494.5:c.52_57dup	p.Thr18_Ala19dup	p.T18_A19dup	ENST00000304494	NM_000077.4	18	-/ACGGCC	1/3	1	2	FACETS	0.639	0.556	0.728	0.639	0.556	0.728	SUBCLONAL	1	TRUE	1	0.31	2		483	707	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099312	157099312	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068518-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	154	451	0	ENST00000346085.5:c.249G>C	p.Gln83His	p.Q83H	ENST00000346085	NM_020732.3	83	caG/caC	1/20	0.23272881468023	3	FACETS	1	0.983	1	0.653	0.597	0.711	CLONAL	1	TRUE	1	0.31	3		451	879	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522569	106522569	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746783339	NA	P-0068518-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	56	236	0	ENST00000359195.3:c.2546G>A	p.Arg849Gln	p.R849Q	ENST00000359195	NM_002649.2	849	cGa/cAa	7/11	0.232463979768106	4	FACETS	0.914	0.783	1	0.457	0.391	0.528	CLONAL	1	TRUE	2	0.31	4		236	518	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598223	52598223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1389353528	NA	P-0068518-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	38	358	0	ENST00000394830.3:c.3643G>A	p.Asp1215Asn	p.D1215N	ENST00000394830	NM_018313.4	1215	Gac/Aac	24/30	0.302139714583847	3	FACETS	0.392	0.323	0.469	0.196	0.161	0.235	SUBCLONAL	1	TRUE	1	0.31	3		358	723	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937711	36937711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752325760	NA	P-0068518-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	108	462	0	ENST00000361632.4:c.1027C>T	p.Arg343Trp	p.R343W	ENST00000361632		343	Cgg/Tgg	8/16	0.23272881468023	3	FACETS	0.967	0.868	1	0.484	0.434	0.537	CLONAL	1	TRUE	1	0.31	3		462	832	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421355	12421355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777334819	NA	P-0068518-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	274	407	0	ENST00000287820.6:c.235G>A	p.Glu79Lys	p.E79K	ENST00000287820	NM_015869.4	79	Gaa/Aaa	2/7	0.231351972027391	3	FACETS	1	0.99	1	0.824	0.776	0.873	CLONAL	2	TRUE	0	0.31	3		407	826	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93657811	93657811	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068518-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	85	400	0	ENST00000375746.1:c.1837G>A	p.Val613Met	p.V613M	ENST00000375746	NM_001174167.1	613	Gtg/Atg	14/14	0.23272881468023	3	FACETS	0.849	0.75	0.955	0.425	0.375	0.478	CLONAL	1	TRUE	1	0.31	3		400	746	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70000979	70000980	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0068518-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	97	267	0	ENST00000394351.3:c.578_579del	p.Glu193ValfsTer2	p.E193Vfs*2	ENST00000394351	NM_000248.3	192	acAGag/acag	6/9	0.142622766272462	2	FACETS	1	0.972	1	0.632	0.566	0.702	INDETERMINATE	1	TRUE	0	0.31	2		267	495	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634345	23634345	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068572-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	141	409	0	ENST00000261584.4:c.2941del	p.Ser981ValfsTer9	p.S981Vfs*9	ENST00000261584	NM_024675.3	981	Agt/gt	9/13	1	2	FACETS	0.989	0.908	1	0.989	0.908	1	CLONAL	1	TRUE	1	0.622873768856709	2		409	458	SUCCESS
RET	5979	MSKCC	GRCh37	10	43598010	43598010	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068572-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	163	446	0	ENST00000355710.3:c.558C>G	p.His186Gln	p.H186Q	ENST00000355710	NM_020975.4	186	caC/caG	3/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.622873768856709	2		446	462	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782744	135782810	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCATTCTCTCTTCCTGAAAAGATAAGTATCATTTATATCACAAGACGAAAAATGTTGCACATGTTC	TCCATTCTCTCTTCCTGAAAAGATAAGTATCATTTATATCACAAGACGAAAAATGTTGCACATGTTC	-	novel	NA	P-0068572-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	47	386	0	ENST00000298552.3:c.1264-53_1277del		p.X422_splice	ENST00000298552	NM_001162426.1	422		13/23	0.622873768856709	1	FACETS	0.442	0.376	0.513	0.442	0.376	0.513	SUBCLONAL	1	TRUE	0	0.622873768856709	1		386	235	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647512	23647512	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068572-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	132	353	0	ENST00000261584.4:c.355C>T	p.Gln119Ter	p.Q119*	ENST00000261584	NM_024675.3	119	Caa/Taa	4/13	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.622873768856709	2		353	381	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62293281	62293281	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769163032	NA	P-0068572-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	250	374	0	ENST00000360203.5:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000360203	NM_001283009.1	127	cGg/cAg	4/35	0.622873768856709	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.622873768856709	3		374	511	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829622	72829622	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068572-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	138	450	0	ENST00000268489.5:c.6959A>T	p.Tyr2320Phe	p.Y2320F	ENST00000268489	NM_006885.3	2320	tAc/tTc	9/10	1	2	FACETS	0.897	0.822	0.975	0.897	0.822	0.975	CLONAL	1	TRUE	1	0.622873768856709	2		450	494	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0068683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	84	362	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.354530543568451	2		362	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934576	NA	P-0068683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	117	617	0	ENST00000269305.4:c.818G>C	p.Arg273Pro	p.R273P	ENST00000269305	NM_001126112.2	273	cGt/cCt	8/11	0.354530543568451	1	FACETS	0.925	0.837	1	0.925	0.837	1	CLONAL	1	TRUE	0	0.354530543568451	1		617	587	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544957	86544957	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	74	586	0	ENST00000262426.4:c.782C>A	p.Ala261Asp	p.A261D	ENST00000262426	NM_001451.2	261	gCc/gAc	1/2	1	2	FACETS	0.89	0.782	1	0.89	0.782	1	CLONAL	1	TRUE	1	0.354530543568451	2		586	469	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120478168	120478168	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	124	620	0	ENST00000256646.2:c.3582G>C	p.Gln1194His	p.Q1194H	ENST00000256646	NM_024408.3	1194	caG/caC	22/34	1	2	FACETS	0.958	0.868	1	0.958	0.868	1	CLONAL	1	TRUE	1	0.354530543568451	2		620	730	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0068740-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	239	485	0	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	0.717918901746543	1	FACETS	0.959	0.909	1	0.959	0.909	1	CLONAL	1	TRUE	0	0.717918901746543	1		485	445	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551393	150551394	+	missense_variant	Missense_Mutation	DNP	GT	GT	AA	novel	NA	P-0068740-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	270	431	0	ENST00000369026.2:c.613_614delinsTT	p.Thr205Phe	p.T205F	ENST00000369026	NM_021960.4	205	ACc/TTc	1/3	0.279777951777733	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.717918901746543	0		431	535	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138550	11138550	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068740-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	224	448	0	ENST00000358026.2:c.3306C>A	p.Phe1102Leu	p.F1102L	ENST00000358026	NM_001128849.1	1102	ttC/ttA	24/36	1	2	FACETS	0.866	0.809	0.923	0.866	0.809	0.923	CLONAL	1	TRUE	1	0.717918901746543	2		448	721	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626973	14626973	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068740-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	318	506	0	ENST00000254322.2:c.802G>T	p.Gly268Cys	p.G268C	ENST00000254322	NM_006145.1	268	Ggc/Tgc	3/3	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.717918901746543	2		506	876	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134955	2134955	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068740-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	285	432	0	ENST00000219476.3:c.4497C>A	p.Phe1499Leu	p.F1499L	ENST00000219476	NM_000548.3	1499	ttC/ttA	35/42	0.717918901746543	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.717918901746543	1		432	486	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289501	33289501	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068740-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	233	361	0	ENST00000374542.5:c.202G>T	p.Glu68Ter	p.E68*	ENST00000374542	NM_001141970.1	68	Gaa/Taa	2/8	0.717918901746543	1	FACETS	0.988	0.937	1	0.988	0.937	1	CLONAL	1	TRUE	0	0.717918901746543	1		361	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0068743-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	328	418	0	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.510155982836951	3	FACETS	0.983	0.95	1			1	CLONAL	3	TRUE	NA	0.685080036768611	3		418	436	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952115	76952115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782431661	NA	P-0068743-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	294	265	0	ENST00000373344.5:c.320C>T	p.Ala107Val	p.A107V	ENST00000373344	NM_000489.3	107	gCg/gTg	5/35	0.384817495451551	3	FACETS	0.955	0.908	1	0.955	0.908	1	INDETERMINATE	2	TRUE	1	0.685080036768611	3		265	603	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627927	37627928	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0068769-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	216	500	0	ENST00000447079.4:c.1843_1844del	p.Val615AsnfsTer25	p.V615Nfs*25	ENST00000447079	NM_015083.1	614	tcTGta/tcta	2/14	0.292874669732105	6	FACETS	0.981	0.918	1			1	CLONAL	4	TRUE	NA	0.292874669732105	6		500	596	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650819	37650831	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAGGGCTTCCC	AAGAGGGCTTCCC	-	novel	NA	P-0068769-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	50	414	0	ENST00000447079.4:c.2293_2305del	p.Glu765SerfsTer13	p.E765Sfs*13	ENST00000447079	NM_015083.1	764	aAAGAGGGCTTCCCa/aa	5/14	0.292874669732105	6	FACETS	1	0.878	1			1	CLONAL	1	TRUE	NA	0.292874669732105	6		414	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	161	410	0	ENST00000269305.4:c.853G>T	p.Glu285Ter	p.E285*	ENST00000269305	NM_001126112.2	285	Gag/Tag	8/11	0.376705685990133	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.390462663848359	2		410	353	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806089	1806089	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913479	NA	P-0068784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	124	369	0	ENST00000260795.2:c.1108G>T	p.Gly370Cys	p.G370C	ENST00000260795		370	Ggc/Tgc	8/17	0.205706387496836	3	FACETS	1	0.915	1	0.668	0.61	0.727	INDETERMINATE	2	TRUE	0	0.390462663848359	3		369	379	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570416	95570416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	52	282	0	ENST00000393063.1:c.3317C>T	p.Ser1106Phe	p.S1106F	ENST00000393063	NM_030621.3	1106	tCt/tTt	22/28	0.394685172387438	3	FACETS	0.983	0.841	1	0.491	0.42	0.568	CLONAL	1	TRUE	1	0.390462663848359	3		282	324	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069037	5069037	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	22	229	0	ENST00000381652.3:c.1342G>T	p.Glu448Ter	p.E448*	ENST00000381652	NM_004972.3	448	Gaa/Taa	11/25	0.394685172387438	1	FACETS	0.714	0.561	0.887	0.714	0.561	0.887	SUBCLONAL	1	TRUE	0	0.390462663848359	1		229	127	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436015	49436015	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754420100	NA	P-0068784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	53	352	0	ENST00000301067.7:c.5966C>T	p.Thr1989Met	p.T1989M	ENST00000301067	NM_003482.3	1989	aCg/aTg	28/54	0.256900502284159	3	FACETS	0.836	0.715	0.968	0.418	0.357	0.484	CLONAL	1	TRUE	1	0.390462663848359	3		352	388	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44970627	44970628	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0068784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	46	100	0	ENST00000377967.4:c.4178dup	p.Pro1394SerfsTer16	p.P1394Sfs*16	ENST00000377967	NM_021140.2	1393	gct/gCct	29/29	1	1	FACETS	0.977	0.855	1	1	0.977	1	CLONAL	2	TRUE	0	0.390462663848359	1		100	97	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431635	431635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	55	243	0	ENST00000399788.2:c.2374G>A	p.Glu792Lys	p.E792K	ENST00000399788	NM_001042603.1	792	Gag/Aag	17/28	0.11731320411156	5	FACETS	1	0.958	1			1	INDETERMINATE	1	TRUE	NA	0.390462663848359	5		243	338	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430404	181430404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	130	356	0	ENST00000325404.1:c.256G>A	p.Glu86Lys	p.E86K	ENST00000325404	NM_003106.3	86	Gag/Aag	1/1	0.171233097660921	3	FACETS	1	0.956	1			1	INDETERMINATE	2	TRUE	NA	0.390462663848359	3		356	374	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582329	119582329	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	88	309	0	ENST00000316626.5:c.1072G>T	p.Asp358Tyr	p.D358Y	ENST00000316626		358	Gac/Tac	10/12	0.155533828912915	2	FACETS	1	0.959	1	0.578	0.515	0.644	INDETERMINATE	1	TRUE	0	0.390462663848359	2		309	390	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056500	26056500	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs372319415	NA	P-0068784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	145	356	0	ENST00000343677.2:c.157G>C	p.Glu53Gln	p.E53Q	ENST00000343677	NM_005319.3	53	Gag/Cag	1/1	0.358834796186045	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.390462663848359	3		356	390	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431641	431641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	53	244	0	ENST00000399788.2:c.2368G>A	p.Glu790Lys	p.E790K	ENST00000399788	NM_001042603.1	790	Gaa/Aaa	17/28	0.11731320411156	5	FACETS	1	0.96	1			1	INDETERMINATE	1	TRUE	NA	0.390462663848359	5		244	315	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132618	11132618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	158	342	0	ENST00000358026.2:c.2834C>T	p.Ala945Val	p.A945V	ENST00000358026	NM_001128849.1	945	gCa/gTa	19/36	0.259144225533533	5	FACETS	0.856	0.79	0.923	0.856	0.79	0.923	CLONAL	3	TRUE	2	0.390462663848359	5		342	500	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412995	49413003	+	inframe_deletion	In_Frame_Del	DEL	TCACCAGTT	TCACCAGTT	-	novel	NA	P-0068784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	48	297	0	ENST00000418115.1:c.20_28del	p.Lys7_Val9del	p.K7_V9del	ENST00000418115	NM_001664.2	7	aAACTGGTGAtt/att	2/5	NA	2	FACETS	0.811	0.69	0.944			1	INDETERMINATE	1	TRUE	NA	0.390462663848359	2		297	303	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105530	30105530	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	80	314	0	ENST00000331968.5:c.1156G>C	p.Asp386His	p.D386H	ENST00000331968	NM_002742.2	386	Gac/Cac	7/18	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.390462663848359	2		314	298	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949338	71949358	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGTGCAGGACCCGGCTCAC	GGGGTGCAGGACCCGGCTCAC	A	novel	NA	P-0068784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	66	367	0	ENST00000298229.2:c.3718_3738delinsA	p.Gly1240LysfsTer138	p.G1240Kfs*138	ENST00000298229	NM_001567.3	1240	GGGGTGCAGGACCCGGCTCAC/A	28/28	0.259144225533533	5	FACETS	1	0.91	1	0.353	0.307	0.403	CLONAL	1	TRUE	2	0.390462663848359	5		367	506	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639789	3639789	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373107728	NA	P-0068824-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	19	567	0	ENST00000294008.3:c.3850G>A	p.Val1284Met	p.V1284M	ENST00000294008	NM_032444.2	1284	Gtg/Atg	12/15	1	2	FACETS	0.63	0.477	0.81	0.63	0.477	0.81	SUBCLONAL	1	TRUE	1	0.16	2		567	377	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	97	420	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.959	1	1	0.988	1	CLONAL	2	FALSE	1	0.251330592315229	2		421	343	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	96	418	4	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.872	0.781	0.967	1	0.985	1	CLONAL	2	FALSE	1	0.251330592315229	2		422	438	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	153	539	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.842	0.776	0.91	1	0.993	1	CLONAL	3	FALSE	1	0.251330592315229	2		539	482	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	156	280	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.956	1	1	0.994	1	CLONAL	3	FALSE	1	0.251330592315229	2		283	396	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	145	383	2	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.971	0.896	1	1	0.993	1	CLONAL	3	FALSE	1	0.251330592315229	2		385	396	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	168	497	8	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	1	0.973	1	1	0.993	1	CLONAL	2	FALSE	1	0.251330592315229	2		505	600	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	321	784	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.976	1	1	0.997	1	CLONAL	4	FALSE	1	0.251330592315229	2		789	616	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	137	454	1	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	1	2	FACETS	0.977	0.893	1	1	0.991	1	CLONAL	2	FALSE	1	0.251330592315229	2		455	558	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	167	553	1	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	1	2	FACETS	1	0.963	1	1	0.993	1	CLONAL	2	FALSE	1	0.251330592315229	2		554	620	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	38	133	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	1	0.904	1	1	0.971	1	CLONAL	2	FALSE	1	0.251330592315229	2		133	137	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	42	425	1	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	0.599	0.499	0.71	0.599	0.499	0.71	SUBCLONAL	1	FALSE	1	0.251330592315229	2		426	558	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403254	213403254	+	frameshift_variant,start_lost,start_retained_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	113	428	0	ENST00000342788.4:c.1del	p.Met1?	p.M1?	ENST00000342788	NM_005235.2	1	Atg/tg	1/28	1	2	FACETS	1	0.907	1	1	0.989	1	CLONAL	2	FALSE	1	0.251330592315229	2		428	449	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	103	458	0	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.949	0.854	1	1	0.987	1	CLONAL	2	FALSE	1	0.251330592315229	2		458	432	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	34	236	0	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	0.822	0.674	0.989	0.822	0.674	0.989	CLONAL	1	FALSE	1	0.251330592315229	2		236	329	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	69	381	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.251330592315229	2		381	384	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	167	485	10	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	1	0.984	1	1	0.993	1	CLONAL	2	FALSE	1	0.251330592315229	2		495	538	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780023	9780023	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	201	495	0	ENST00000377346.4:c.1287G>T	p.Lys429Asn	p.K429N	ENST00000377346	NM_005026.3	429	aaG/aaT	10/24	1	2	FACETS	0.978	0.914	1	1	0.995	1	CLONAL	3	FALSE	1	0.251330592315229	2		495	545	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023641	27023642	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	117	441	0	ENST00000324856.7:c.749dup	p.Pro251AlafsTer149	p.P251Afs*149	ENST00000324856	NM_006015.4	249	-/A	1/20	1	2	FACETS	0.887	0.809	0.967	1	0.991	1	CLONAL	3	FALSE	1	0.251330592315229	2		441	350	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932232	36932232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1382959301	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	157	560	0	ENST00000361632.4:c.2237C>T	p.Thr746Ile	p.T746I	ENST00000361632		746	aCc/aTc	16/16	1	2	FACETS	1	0.982	1	1	0.993	1	CLONAL	2	FALSE	1	0.251330592315229	2		560	513	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851391	156851391	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	136	512	0	ENST00000524377.1:c.2348C>T	p.Ala783Val	p.A783V	ENST00000524377	NM_002529.3	783	gCc/gTc	17/17	1	2	FACETS	1	0.971	1	1	0.992	1	CLONAL	2	FALSE	1	0.251330592315229	2		512	477	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332273	70332273	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	167	429	1	ENST00000373644.4:c.184del	p.Thr62GlnfsTer13	p.T62Qfs*13	ENST00000373644	NM_030625.2	60	Aaa/aa	2/12	1	2	FACETS	1	0.972	1	1	0.993	1	CLONAL	2	FALSE	1	0.251330592315229	2		430	598	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720712	89720712	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	26	95	0	ENST00000371953.3:c.867del	p.Val290Ter	p.V290*	ENST00000371953	NM_000314.4	288	gAa/ga	8/9	1	2	FACETS	1	0.887	1	1	0.959	1	CLONAL	2	FALSE	1	0.251330592315229	2		95	91	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	132	474	3	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	1	0.969	1	1	0.991	1	CLONAL	2	FALSE	1	0.251330592315229	2		477	466	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240066	41240066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	65	225	0	ENST00000379561.5:c.284C>T	p.Ala95Val	p.A95V	ENST00000379561	NM_002015.3	95	gCg/gTg	1/3	1	2	FACETS	0.974	0.862	1	1	0.985	1	CLONAL	3	FALSE	1	0.251330592315229	2		225	177	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609672	81609672	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778742	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	185	575	0	ENST00000298171.2:c.1270G>A	p.Val424Ile	p.V424I	ENST00000298171	NM_000369.2	424	Gtt/Att	10/10	1	2	FACETS	1	0.984	1	1	0.994	1	CLONAL	2	FALSE	1	0.251330592315229	2		575	604	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50789365	50789365	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752820652	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	46	413	1	ENST00000307179.4:c.2975G>A	p.Arg992Gln	p.R992Q	ENST00000307179		992	cGg/cAg	18/20	1	2	FACETS	0.855	0.721	1	0.855	0.721	1	CLONAL	1	FALSE	1	0.251330592315229	2		414	428	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396233	396234	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769619638	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	134	460	0	ENST00000262320.3:c.792dup	p.Gly265ArgfsTer20	p.G265Rfs*20	ENST00000262320	NM_003502.3	264	-/C	2/11	1	2	FACETS	0.911	0.831	0.995	1	0.99	1	CLONAL	2	FALSE	1	0.251330592315229	2		460	585	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274123	10274123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774442834	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	137	497	0	ENST00000330684.3:c.146G>A	p.Arg49His	p.R49H	ENST00000330684	NM_001134407.1	49	cGc/cAc	2/13	1	2	FACETS	1	0.97	1	1	0.992	1	CLONAL	2	FALSE	1	0.251330592315229	2		497	483	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827511	72827511	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	142	457	0	ENST00000268489.5:c.9070del	p.Thr3024GlnfsTer52	p.T3024Qfs*52	ENST00000268489	NM_006885.3	3024	Aca/ca	9/10	1	2	FACETS	1	0.968	1	1	0.992	1	CLONAL	2	FALSE	1	0.251330592315229	2		457	508	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15938195	15938195	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	147	407	1	ENST00000268712.3:c.7019C>A	p.Pro2340His	p.P2340H	ENST00000268712	NM_006311.3	2340	cCt/cAt	45/46	1	2	FACETS	1	0.982	1	1	0.993	1	CLONAL	2	FALSE	1	0.251330592315229	2		408	472	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510611	38510611	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	141	429	0	ENST00000254066.5:c.865G>T	p.Gly289Trp	p.G289W	ENST00000254066	NM_000964.3	289	Ggg/Tgg	7/9	1	2	FACETS	1	0.932	1	1	0.991	1	CLONAL	2	FALSE	1	0.251330592315229	2		429	550	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511656	38511656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775118101	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	142	450	0	ENST00000254066.5:c.1154G>A	p.Arg385Gln	p.R385Q	ENST00000254066	NM_000964.3	385	cGa/cAa	8/9	1	2	FACETS	1	0.98	1	1	0.992	1	CLONAL	2	FALSE	1	0.251330592315229	2		450	466	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	23	418	0	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	0.432	0.336	0.543	0.432	0.336	0.543	SUBCLONAL	1	FALSE	1	0.251330592315229	2		418	424	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926602	59926603	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs587781416	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	90	349	0	ENST00000259008.2:c.394dup	p.Thr132AsnfsTer10	p.T132Nfs*10	ENST00000259008	NM_032043.2	132	acc/aAcc	5/20	1	2	FACETS	1	0.952	1	1	0.987	1	CLONAL	2	FALSE	1	0.251330592315229	2		349	323	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117173	7117173	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764041031	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	186	480	0	ENST00000302850.5:c.4043C>T	p.Ser1348Leu	p.S1348L	ENST00000302850	NM_000208.2	1348	tCg/tTg	22/22	0.125699162033782	3	FACETS	0.978	0.909	1	1	0.991	1	INDETERMINATE	3	FALSE	1	0.251330592315229	3		480	568	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184544	7184544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	148	390	0	ENST00000302850.5:c.757G>A	p.Val253Met	p.V253M	ENST00000302850	NM_000208.2	253	Gtg/Atg	3/22	0.125699162033782	3	FACETS	1	0.98	1	1	0.98	1	INDETERMINATE	2	FALSE	1	0.251330592315229	3		390	543	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937659	17937659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144968714	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	169	483	0	ENST00000458235.1:c.3268G>A	p.Ala1090Thr	p.A1090T	ENST00000458235	NM_000215.3	1090	Gcc/Acc	24/24	0.125699162033782	3	FACETS	1	0.983	1	1	0.983	1	INDETERMINATE	2	FALSE	1	0.251330592315229	3		483	613	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211082	36211082	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	151	520	0	ENST00000222270.7:c.837del	p.Arg280GlyfsTer25	p.R280Gfs*25	ENST00000222270	NM_014727.1	278	aCc/ac	3/37	0.125699162033782	3	FACETS	1	0.974	1	1	0.974	1	INDETERMINATE	2	FALSE	1	0.251330592315229	3		520	589	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216189	36216189	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	37	474	6	ENST00000222270.7:c.3602del	p.Pro1201ArgfsTer154	p.P1201Rfs*154	ENST00000222270	NM_014727.1	1199	ggC/gg	11/37	0.125699162033782	3	FACETS	0.577	0.475	0.692	0.289	0.237	0.346	INDETERMINATE	1	FALSE	1	0.251330592315229	3		480	574	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918125	50918127	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs763850764	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	129	485	0	ENST00000440232.2:c.2446_2448del	p.Ser816del	p.S816del	ENST00000440232	NM_002691.3	814	ttCTCc/ttc	20/27	0.125699162033782	3	FACETS	0.869	0.794	0.947	1	0.982	1	INDETERMINATE	3	FALSE	1	0.251330592315229	3		485	443	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457281	25457281	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	128	439	0	ENST00000264709.3:c.2606G>T	p.Gly869Val	p.G869V	ENST00000264709	NM_175629.2	869	gGt/gTt	23/23	1	2	FACETS	1	0.965	1	1	0.991	1	CLONAL	2	FALSE	1	0.251330592315229	2		439	458	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222520	39222520	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	116	350	0	ENST00000402219.2:c.3090del	p.Lys1030AsnfsTer6	p.K1030Nfs*6	ENST00000402219	NM_005633.3	1030	aaA/aa	20/23	1	2	FACETS	1	0.91	1	1	0.989	1	CLONAL	2	FALSE	1	0.251330592315229	2		350	460	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136346	202136346	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1244888701	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	69	339	0	ENST00000358485.4:c.588+2T>C		p.X196_splice	ENST00000358485	NM_001080125.1	196			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.251330592315229	2		339	440	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139625	202139626	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	79	412	0	ENST00000358485.4:c.790dup	p.Val264GlyfsTer13	p.V264Gfs*13	ENST00000358485	NM_001080125.1	262	-/G	6/9	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.251330592315229	2		412	533	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31372633	31372633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149520896	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	62	418	0	ENST00000328111.2:c.274C>T	p.Arg92Trp	p.R92W	ENST00000328111	NM_006892.3	92	Cgg/Tgg	4/23	1	2	FACETS	0.9	0.778	1	0.9	0.778	1	CLONAL	1	FALSE	1	0.251330592315229	2		418	548	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100975	41100975	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	126	494	0	ENST00000373198.4:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000373198	NM_133170.3	461	Cga/Tga	8/32	1	2	FACETS	1	0.96	1	1	0.991	1	CLONAL	2	FALSE	1	0.251330592315229	2		494	459	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755427	39755427	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	62	543	1	ENST00000288319.7:c.1338del	p.Phe446LeufsTer59	p.F446Lfs*59	ENST00000288319	NM_182918.3	446	ttT/tt	10/10	1	2	FACETS	0.895	0.774	1	0.895	0.774	1	CLONAL	1	FALSE	1	0.251330592315229	2		544	551	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524474	44524474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	130	348	0	ENST00000291552.4:c.83G>A	p.Arg28His	p.R28H	ENST00000291552	NM_006758.2	28	cGt/cAt	2/8	1	2	FACETS	1	0.97	1	1	0.991	1	CLONAL	2	FALSE	1	0.251330592315229	2		348	454	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655413	45655413	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	43	500	0	ENST00000407780.3:c.439del	p.His147ThrfsTer15	p.H147Tfs*15	ENST00000407780	NM_001283052.1	147	Cac/ac	4/7	1	2	FACETS	0.492	0.411	0.583	0.492	0.411	0.583	SUBCLONAL	1	FALSE	1	0.251330592315229	2		500	695	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21348979	21348979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	67	532	0	ENST00000215739.8:c.1748G>A	p.Cys583Tyr	p.C583Y	ENST00000215739	NM_006767.3	583	tGc/tAc	15/21	1	2	FACETS	0.916	0.797	1	0.916	0.797	1	CLONAL	1	FALSE	1	0.251330592315229	2		532	582	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574678	41574679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs754418509	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	76	604	0	ENST00000263253.7:c.6970dup	p.His2324ProfsTer55	p.H2324Pfs*55	ENST00000263253	NM_001429.3	2321	-/C	31/31	1	2	FACETS	0.892	0.782	1	0.892	0.782	1	CLONAL	1	FALSE	1	0.251330592315229	2		604	678	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940111	49940112	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760002850	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	168	510	1	ENST00000296474.3:c.931dup	p.Ala311GlyfsTer26	p.A311Gfs*26	ENST00000296474	NM_002447.2	311	gcc/gGcc	1/20	1	2	FACETS	1	0.977	1	1	0.993	1	CLONAL	2	FALSE	1	0.251330592315229	2		511	582	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438571	52438571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374620220	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	166	439	0	ENST00000460680.1:c.1148G>A	p.Arg383His	p.R383H	ENST00000460680	NM_004656.3	383	cGc/cAc	12/17	1	2	FACETS	1	0.98	1	1	0.993	1	CLONAL	2	FALSE	1	0.251330592315229	2		439	562	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748119	41748121	+	inframe_deletion	In_Frame_Del	DEL	CCG	CCG	-	rs760638643	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	126	360	9	ENST00000226382.2:c.648_650del	p.Gly217del	p.G217del	ENST00000226382	NM_003924.3	216	ggCGGg/ggg	3/3	1	2	FACETS	1	0.976	1	1	0.991	1	CLONAL	2	FALSE	1	0.251330592315229	2		369	420	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796900	57796900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs2228991	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	147	629	0	ENST00000309042.7:c.1876G>A	p.Val626Ile	p.V626I	ENST00000309042	NM_005612.4	626	Gtt/Att	4/4	1	2	FACETS	1	0.926	1	1	0.991	1	CLONAL	2	FALSE	1	0.251330592315229	2		629	579	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467589	66467589	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772693559	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	101	467	1	ENST00000273854.3:c.680G>A	p.Arg227His	p.R227H	ENST00000273854	NM_004439.5	227	cGt/cAt	3/18	1	2	FACETS	0.975	0.878	1	1	0.987	1	CLONAL	2	FALSE	1	0.251330592315229	2		468	412	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509954	187509954	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs993828603	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	55	500	0	ENST00000441802.2:c.13559C>T	p.Pro4520Leu	p.P4520L	ENST00000441802	NM_005245.3	4520	cCg/cTg	27/27	1	2	FACETS	0.808	0.691	0.935	0.808	0.691	0.935	CLONAL	1	FALSE	1	0.251330592315229	2		500	542	SUCCESS
APC	324	MSKCC	GRCh37	5	112175069	112175069	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	100	420	0	ENST00000257430.4:c.3778C>T	p.Gln1260Ter	p.Q1260*	ENST00000257430	NM_000038.5	1260	Cag/Tag	16/16	1	2	FACETS	0.93	0.836	1	1	0.987	1	CLONAL	2	FALSE	1	0.251330592315229	2		420	428	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043381	180043381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760077499	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	184	488	1	ENST00000261937.6:c.3205G>A	p.Val1069Ile	p.V1069I	ENST00000261937	NM_182925.4	1069	Gtc/Atc	23/30	1	2	FACETS	1	0.977	1	1	0.994	1	CLONAL	2	FALSE	1	0.251330592315229	2		489	649	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672067	30672067	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	228	649	0	ENST00000376406.3:c.4893del	p.Lys1632SerfsTer44	p.K1632Sfs*44	ENST00000376406	NM_014641.2	1631	ccC/cc	10/15	1	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	2	FALSE	1	0.251330592315229	2		649	770	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948457	31948457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355123936	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	43	206	0	ENST00000375333.2:c.940C>T	p.Arg314Trp	p.R314W	ENST00000375333	NM_032454.1	314	Cgg/Tgg	7/8	1	2	FACETS	1	0.85	1	1	0.972	1	CLONAL	2	FALSE	1	0.251330592315229	2		206	171	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821048	32821048	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	36	598	3	ENST00000354258.4:c.546del	p.Ser184ProfsTer54	p.S184Pfs*54	ENST00000354258	NM_000593.5	182	ccC/cc	1/11	1	2	FACETS	0.598	0.491	0.718	0.598	0.491	0.718	SUBCLONAL	1	FALSE	1	0.251330592315229	2		601	479	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468150	50468150	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	55	459	0	ENST00000331340.3:c.1385A>G	p.Tyr462Cys	p.Y462C	ENST00000331340	NM_006060.4	462	tAc/tGc	8/8	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	FALSE	1	0.251330592315229	2		459	429	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748399150	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	127	414	4	ENST00000220592.5:c.1806del	p.Ala603ProfsTer92	p.A603Pfs*92	ENST00000220592	NM_012154.3	602	ccC/cc	14/19	1	2	FACETS	0.922	0.839	1	1	0.989	1	CLONAL	2	FALSE	1	0.251330592315229	2		418	548	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045494	47045494	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	97	509	0	ENST00000377604.3:c.2461C>T	p.Arg821Cys	p.R821C	ENST00000377604	NM_001204468.1	821	Cgc/Tgc	22/24	0.251330592315229	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	0	0.251330592315229	1		509	492	SUCCESS
AR	367	MSKCC	GRCh37	X	66765403	66765403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1264061748	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	72	523	0	ENST00000374690.3:c.415G>A	p.Val139Met	p.V139M	ENST00000374690	NM_000044.3	139	Gtg/Atg	1/8	0.251330592315229	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	0	0.251330592315229	1		523	385	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427265	49427266	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	rs398123707	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	79	629	0	ENST00000301067.7:c.11220_11222dup	p.Gln3745dup	p.Q3745dup	ENST00000301067	NM_003482.3	3745	caa/caGCAa	39/54	1	2	FACETS	0.95	0.835	1	0.95	0.835	1	CLONAL	1	FALSE	1	0.251330592315229	2		629	662	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438317	110438322	+	inframe_deletion	In_Frame_Del	DEL	GTTGTT	GTTGTT	-	rs532810290	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	62	406	0	ENST00000375856.3:c.79_84del	p.Asn27_Asn28del	p.N27_N28del	ENST00000375856	NM_003749.2	27	AACAAC/-	1/2	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.251330592315229	2		406	370	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1688546	1688546	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	124	417	0	ENST00000378625.1:c.779del	p.Pro260ArgfsTer9	p.P260Rfs*9	ENST00000378625	NM_001198994.1	260	cCg/cg	6/14	1	2	FACETS	0.985	0.896	1	1	0.99	1	CLONAL	2	FALSE	1	0.251330592315229	2		417	501	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262193	16262193	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	113	595	0	ENST00000375759.3:c.9458A>G	p.Gln3153Arg	p.Q3153R	ENST00000375759	NM_015001.2	3153	cAg/cGg	11/15	1	2	FACETS	0.927	0.839	1	1	0.988	1	CLONAL	2	FALSE	1	0.251330592315229	2		595	485	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933524	36933524	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	42	619	0	ENST00000361632.4:c.1763A>G	p.His588Arg	p.H588R	ENST00000361632		588	cAt/cGt	13/16	1	2	FACETS	0.6	0.5	0.711	0.6	0.5	0.711	SUBCLONAL	1	FALSE	1	0.251330592315229	2		619	557	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46738142	46738142	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	192	393	0	ENST00000371975.4:c.1174C>A	p.Leu392Met	p.L392M	ENST00000371975	NM_003579.3	392	Ctg/Atg	11/18	1	2	FACETS	0.928	0.864	0.992	1	0.995	1	CLONAL	3	FALSE	1	0.251330592315229	2		393	549	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058635	72058635	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	43	348	0	ENST00000357731.5:c.805C>T	p.Gln269Ter	p.Q269*	ENST00000357731	NM_173808.2	269	Caa/Taa	6/7	1	2	FACETS	0.9	0.755	1	0.9	0.755	1	CLONAL	1	FALSE	1	0.251330592315229	2		348	380	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248574	8248574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747347634	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	58	478	0	ENST00000335790.3:c.313C>T	p.Arg105Trp	p.R105W	ENST00000335790	NM_002315.2	105	Cgg/Tgg	3/4	1	2	FACETS	0.796	0.684	0.918	0.796	0.684	0.918	CLONAL	1	FALSE	1	0.251330592315229	2		478	580	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589653	69589653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	144	810	0	ENST00000168712.1:c.200C>T	p.Ala67Val	p.A67V	ENST00000168712	NM_002007.2	67	gCg/gTg	1/3	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.251330592315229	2		810	766	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941448	71941448	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1279925582	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	167	540	0	ENST00000298229.2:c.1133G>A	p.Gly378Asp	p.G378D	ENST00000298229	NM_001567.3	378	gGt/gAt	10/28	1	2	FACETS	1	0.962	1	1	0.993	1	CLONAL	2	FALSE	1	0.251330592315229	2		540	621	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77054913	77054913	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	121	421	0	ENST00000356341.3:c.949C>A	p.Leu317Met	p.L317M	ENST00000356341	NM_002576.4	317	Ctg/Atg	10/15	1	2	FACETS	1	0.971	1	1	0.991	1	CLONAL	2	FALSE	1	0.251330592315229	2		421	417	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94910881	94910881	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	23	328	0	ENST00000536441.1:c.1247+2T>C		p.X416_splice	ENST00000536441	NM_144665.3	416			1	2	FACETS	0.598	0.467	0.75	0.598	0.467	0.75	SUBCLONAL	1	FALSE	1	0.251330592315229	2		328	306	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164079	108164079	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	127	337	0	ENST00000278616.4:c.4651G>T	p.Asp1551Tyr	p.D1551Y	ENST00000278616	NM_000051.3	1551	Gat/Tat	31/63	1	2	FACETS	1	0.926	1	1	0.992	1	CLONAL	3	FALSE	1	0.251330592315229	2		337	334	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503072	125503072	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	74	380	0	ENST00000428830.2:c.439T>C	p.Ser147Pro	p.S147P	ENST00000428830	NM_001114121.2	147	Tca/Cca	6/14	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.251330592315229	2		380	404	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495714	56495714	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	145	421	0	ENST00000267101.3:c.3904G>C	p.Ala1302Pro	p.A1302P	ENST00000267101	NM_001982.3	1302	Gcc/Ccc	28/28	1	2	FACETS	1	0.977	1	1	0.992	1	CLONAL	2	FALSE	1	0.251330592315229	2		421	490	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856017	111856017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760472328	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	113	509	0	ENST00000341259.2:c.68C>T	p.Pro23Leu	p.P23L	ENST00000341259	NM_005475.2	23	cCg/cTg	2/8	1	2	FACETS	1	0.907	1	1	0.989	1	CLONAL	2	FALSE	1	0.251330592315229	2		509	449	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51507971	51507971	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	124	389	1	ENST00000260433.2:c.787del	p.Arg263AspfsTer20	p.R263Dfs*20	ENST00000260433		263	Aga/ga	7/10	1	2	FACETS	0.891	0.815	0.97	1	0.992	1	CLONAL	3	FALSE	1	0.251330592315229	2		390	369	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857274	9857274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544975518	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	101	468	0	ENST00000330684.3:c.4127G>A	p.Arg1376His	p.R1376H	ENST00000330684	NM_001134407.1	1376	cGc/cAc	13/13	1	2	FACETS	0.755	0.677	0.838	1	0.982	1	SUBCLONAL	2	FALSE	1	0.251330592315229	2		468	532	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346058	89346058	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	16	61	0	ENST00000301030.4:c.6892C>T	p.Arg2298Cys	p.R2298C	ENST00000301030	NM_001256183.1	2298	Cgt/Tgt	9/13	1	2	FACETS	0.987	0.765	1	1	0.944	1	CLONAL	3	FALSE	1	0.251330592315229	2		61	43	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961246	15961246	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	161	456	0	ENST00000268712.3:c.6143T>C	p.Leu2048Pro	p.L2048P	ENST00000268712	NM_006311.3	2048	cTg/cCg	39/46	1	2	FACETS	1	0.978	1	1	0.993	1	CLONAL	2	FALSE	1	0.251330592315229	2		456	552	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657414	29657414	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	135	364	0	ENST00000356175.3:c.5647A>G	p.Asn1883Asp	p.N1883D	ENST00000356175	NM_000267.3	1883	Aac/Gac	38/57	1	2	FACETS	0.897	0.824	0.973	1	0.992	1	CLONAL	3	FALSE	1	0.251330592315229	2		364	399	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33434066	33434066	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	148	468	0	ENST00000345365.6:c.421C>A	p.Leu141Met	p.L141M	ENST00000345365	NM_002878.3	141	Ctg/Atg	5/10	1	2	FACETS	1	0.966	1	1	0.992	1	CLONAL	2	FALSE	1	0.251330592315229	2		468	538	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618824	37618824	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1452240517	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	187	523	0	ENST00000447079.4:c.500C>T	p.Ala167Val	p.A167V	ENST00000447079	NM_015083.1	167	gCc/gTc	1/14	1	2	FACETS	1	0.981	1	1	0.994	1	CLONAL	2	FALSE	1	0.251330592315229	2		523	638	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78599564	78599564	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765839062	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	167	436	0	ENST00000306801.3:c.236C>T	p.Thr79Met	p.T79M	ENST00000306801	NM_020761.2	79	aCg/aTg	2/34	1	2	FACETS	0.874	0.809	0.94	1	0.994	1	CLONAL	3	FALSE	1	0.251330592315229	2		436	507	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11019827	11019827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	186	541	0	ENST00000327064.4:c.502C>T	p.Arg168Trp	p.R168W	ENST00000327064	NM_199141.1	168	Cgg/Tgg	4/16	0.125699162033782	3	FACETS	1	0.983	1	1	0.983	1	INDETERMINATE	2	FALSE	1	0.251330592315229	3		541	698	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129671	11129671	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	212	456	0	ENST00000358026.2:c.2481del	p.Ser828ProfsTer3	p.S828Pfs*3	ENST00000358026	NM_001128849.1	826	gCc/gc	17/36	0.125699162033782	3	FACETS	0.932	0.87	0.996	1	0.991	1	INDETERMINATE	3	FALSE	1	0.251330592315229	3		456	679	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132630	11132630	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	148	484	0	ENST00000358026.2:c.2846T>C	p.Met949Thr	p.M949T	ENST00000358026	NM_001128849.1	949	aTg/aCg	19/36	0.125699162033782	3	FACETS	1	0.98	1	1	0.98	1	INDETERMINATE	2	FALSE	1	0.251330592315229	3		484	548	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272417	15272417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1425436352	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	197	496	0	ENST00000263388.2:c.6022C>T	p.Pro2008Ser	p.P2008S	ENST00000263388	NM_000435.2	2008	Ccg/Tcg	33/33	0.125699162033782	3	FACETS	0.99	0.923	1	1	0.991	1	INDETERMINATE	3	FALSE	1	0.251330592315229	3		496	594	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353979	15353979	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	48	149	0	ENST00000263377.2:c.2901G>T	p.Gln967His	p.Q967H	ENST00000263377	NM_058243.2	967	caG/caT	14/20	0.125699162033782	3	FACETS	1	0.942	1	1	0.942	1	INDETERMINATE	2	FALSE	1	0.251330592315229	3		149	179	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223570	36223571	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	194	659	0	ENST00000222270.7:c.6122_6123del	p.Val2041GlyfsTer18	p.V2041Gfs*18	ENST00000222270	NM_014727.1	2040	acTGtg/actg	28/37	0.125699162033782	3	FACETS	0.886	0.823	0.95	1	0.989	1	INDETERMINATE	3	FALSE	1	0.251330592315229	3		659	654	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731467	47731468	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	98	461	0	ENST00000449228.1:c.324dup	p.Phe109ValfsTer141	p.F109Vfs*141	ENST00000449228	NM_001127240.2	108	-/G	2/4	0.125699162033782	3	FACETS	1	0.943	1	1	0.943	1	INDETERMINATE	2	FALSE	1	0.251330592315229	3		461	409	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082854	16082854	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1251913339	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	98	311	0	ENST00000281043.3:c.668C>T	p.Ala223Val	p.A223V	ENST00000281043	NM_005378.4	223	gCg/gTg	2/3	1	2	FACETS	0.847	0.765	0.932	1	0.989	1	CLONAL	3	FALSE	1	0.251330592315229	2		311	307	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241068	39241068	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1227177181	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	52	326	0	ENST00000402219.2:c.2003A>G	p.Gln668Arg	p.Q668R	ENST00000402219	NM_005633.3	668	cAa/cGa	12/23	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	1	0.251330592315229	2		326	328	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010520	48010520	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs374597395	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	90	451	0	ENST00000234420.5:c.148T>C	p.Trp50Arg	p.W50R	ENST00000234420	NM_000179.2	50	Tgg/Cgg	1/10	1	2	FACETS	1	0.916	1	1	0.987	1	CLONAL	2	FALSE	1	0.251330592315229	2		451	349	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661398	227661398	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	147	549	1	ENST00000305123.5:c.2057G>A	p.Ser686Asn	p.S686N	ENST00000305123	NM_005544.2	686	aGc/aAc	1/2	1	2	FACETS	1	0.974	1	1	0.992	1	CLONAL	2	FALSE	1	0.251330592315229	2		550	511	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400186	41400186	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	79	338	0	ENST00000373198.4:c.573del	p.Ala192HisfsTer12	p.A192Hfs*12	ENST00000373198	NM_133170.3	191	aaA/aa	5/32	1	2	FACETS	0.798	0.706	0.896	1	0.979	1	SUBCLONAL	2	FALSE	1	0.251330592315229	2		338	394	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41818294	41818294	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253049408	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	212	732	0	ENST00000373198.4:c.80G>A	p.Ser27Asn	p.S27N	ENST00000373198	NM_133170.3	27	aGc/aAc	1/32	1	2	FACETS	0.843	0.787	0.901	1	0.995	1	CLONAL	3	FALSE	1	0.251330592315229	2		732	667	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321654	62321654	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745535053	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	36	527	0	ENST00000360203.5:c.2273C>T	p.Ala758Val	p.A758V	ENST00000360203	NM_001283009.1	758	gCg/gTg	26/35	1	2	FACETS	0.565	0.464	0.679	0.565	0.464	0.679	SUBCLONAL	1	FALSE	1	0.251330592315229	2		527	507	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326211	62326211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781481182	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	151	440	0	ENST00000360203.5:c.3227G>A	p.Cys1076Tyr	p.C1076Y	ENST00000360203	NM_001283009.1	1076	tGt/tAt	32/35	1	2	FACETS	1	0.978	1	1	0.993	1	CLONAL	2	FALSE	1	0.251330592315229	2		440	510	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22161992	22161992	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	132	420	0	ENST00000215832.6:c.263A>T	p.Asp88Val	p.D88V	ENST00000215832	NM_002745.4	88	gAc/gTc	2/9	1	2	FACETS	1	0.942	1	1	0.991	1	CLONAL	2	FALSE	1	0.251330592315229	2		420	505	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29445647	29445647	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	127	504	0	ENST00000544604.2:c.1481del	p.Gly494AlafsTer76	p.G494Afs*76	ENST00000544604	NM_001206998.1	493	cGg/cg	8/9	1	2	FACETS	1	0.936	1	1	0.99	1	CLONAL	2	FALSE	1	0.251330592315229	2		504	489	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189349353	189349353	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	133	399	0	ENST00000264731.3:c.49C>A	p.Pro17Thr	p.P17T	ENST00000264731	NM_003722.4	17	Cct/Act	1/14	1	2	FACETS	0.85	0.779	0.923	1	0.992	1	CLONAL	3	FALSE	1	0.251330592315229	2		399	415	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160673	56160674	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	124	480	0	ENST00000399503.3:c.948_949del	p.Tyr317LeufsTer8	p.Y317Lfs*8	ENST00000399503	NM_005921.1	316	cTG/c	4/20	1	2	FACETS	1	0.911	1	1	0.99	1	CLONAL	2	FALSE	1	0.251330592315229	2		480	493	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672504	30672504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	58	696	0	ENST00000376406.3:c.4456C>T	p.Pro1486Ser	p.P1486S	ENST00000376406	NM_014641.2	1486	Cct/Tct	10/15	1	2	FACETS	0.55	0.471	0.636	0.55	0.471	0.636	SUBCLONAL	1	FALSE	1	0.251330592315229	2		696	839	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818739	32818741	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	53	398	0	ENST00000354258.4:c.1210_1212del	p.Lys404del	p.K404del	ENST00000354258	NM_000593.5	404	AAG/-	4/11	1	2	FACETS	0.802	0.684	0.931	0.802	0.684	0.931	CLONAL	1	FALSE	1	0.251330592315229	2		398	526	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781122	161781122	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	126	389	1	ENST00000366898.1:c.1283del	p.Asn428MetfsTer7	p.N428Mfs*7	ENST00000366898	NM_004562.2	428	aAt/at	11/12	1	2	FACETS	1	0.961	1	1	0.991	1	CLONAL	2	FALSE	1	0.251330592315229	2		390	457	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468125	50468125	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	47	501	0	ENST00000331340.3:c.1360A>G	p.Thr454Ala	p.T454A	ENST00000331340	NM_006060.4	454	Acc/Gcc	8/8	1	2	FACETS	0.862	0.728	1	0.862	0.728	1	CLONAL	1	FALSE	1	0.251330592315229	2		501	434	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878668	151878668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	57	469	0	ENST00000262189.6:c.6277C>T	p.Pro2093Ser	p.P2093S	ENST00000262189	NM_170606.2	2093	Cca/Tca	36/59	1	2	FACETS	0.951	0.817	1	0.951	0.817	1	CLONAL	1	FALSE	1	0.251330592315229	2		469	477	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205082	38205082	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs748986383	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	83	369	0	ENST00000317025.8:c.608A>G	p.His203Arg	p.H203R	ENST00000317025	NM_023034.1	203	cAt/cGt	2/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.251330592315229	2		369	442	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981890	70981890	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	150	499	0	ENST00000276594.2:c.206T>C	p.Phe69Ser	p.F69S	ENST00000276594	NM_024504.3	69	tTc/tCc	2/8	1	2	FACETS	1	0.973	1	1	0.992	1	CLONAL	2	FALSE	1	0.251330592315229	2		499	528	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878886	117878886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	96	362	0	ENST00000297338.2:c.83C>T	p.Thr28Ile	p.T28I	ENST00000297338	NM_006265.2	28	aCc/aTc	2/14	1	2	FACETS	1	0.928	1	1	0.987	1	CLONAL	2	FALSE	1	0.251330592315229	2		362	367	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5077566	5077566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757690445	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	25	298	0	ENST00000381652.3:c.1978G>A	p.Ala660Thr	p.A660T	ENST00000381652	NM_004972.3	660	Gcc/Acc	15/25	1	2	FACETS	0.698	0.551	0.866	0.698	0.551	0.866	SUBCLONAL	1	FALSE	1	0.251330592315229	2		298	285	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128322074	128322074	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	24	374	1	ENST00000265960.3:c.686C>A	p.Ala229Asp	p.A229D	ENST00000265960	NM_001006617.1	229	gCc/gAc	6/12	1	2	FACETS	0.475	0.372	0.594	0.475	0.372	0.594	SUBCLONAL	1	FALSE	1	0.251330592315229	2		375	402	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760543	133760543	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	39	517	0	ENST00000318560.5:c.2870del	p.Lys957SerfsTer112	p.K957Sfs*112	ENST00000318560	NM_005157.4	956	Aaa/aa	11/11	1	2	FACETS	0.555	0.459	0.662	0.555	0.459	0.662	SUBCLONAL	1	FALSE	1	0.251330592315229	2		517	559	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413916	139413916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1468729123	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	147	432	0	ENST00000277541.6:c.844C>T	p.Arg282Cys	p.R282C	ENST00000277541	NM_017617.3	282	Cgc/Tgc	5/34	1	2	FACETS	1	0.976	1	1	0.992	1	CLONAL	2	FALSE	1	0.251330592315229	2		432	504	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412089	63412089	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760684276	NA	P-0068825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	74	532	0	ENST00000330258.3:c.1078T>C	p.Ser360Pro	p.S360P	ENST00000330258	NM_152424.3	360	Tcc/Ccc	2/2	0.251330592315229	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	FALSE	0	0.251330592315229	1		532	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579366	7579366	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs770776262	NA	P-0068902-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	420	515	2	ENST00000269305.4:c.321C>A	p.Tyr107Ter	p.Y107*	ENST00000269305	NM_001126112.2	107	taC/taA	4/11	0.451406213289219	1	FACETS	0.928	0.903	0.951	1	0.998	1	CLONAL	3	TRUE	0	0.448480804796372	1		517	522	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156734	20156734	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068902-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	90	287	0	ENST00000379607.5:c.23G>C	p.Gly8Ala	p.G8A	ENST00000379607	NM_001412.3	8	gGa/gCa	2/7	0.40123331965134	2	FACETS	0.817	0.728	0.912	0.409	0.364	0.456	CLONAL	1	TRUE	0	0.448480804796372	2		287	491	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349230	11349230	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068902-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	414	468	1	ENST00000332029.2:c.106C>A	p.Pro36Thr	p.P36T	ENST00000332029	NM_003745.1	36	Ccc/Acc	2/2	0.451406213289219	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.448480804796372	3		469	1118	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0068963-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	193	324	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.496406207759662	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.496406207759662	1		324	472	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0068963-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	102	291	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.496406207759662	2		291	377	SUCCESS
APC	324	MSKCC	GRCh37	5	112175772	112175772	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068963-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	69	344	0	ENST00000257430.4:c.4483del	p.Ser1495ValfsTer12	p.S1495Vfs*12	ENST00000257430	NM_000038.5	1494	gAa/ga	16/16	1	2	FACETS	0.972	0.855	1	0.972	0.855	1	CLONAL	1	TRUE	1	0.496406207759662	2		344	286	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184471	7184472	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0068963-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	98	284	0	ENST00000302850.5:c.829_830delinsTT	p.Asp277Phe	p.D277F	ENST00000302850	NM_000208.2	277	GAc/TTc	3/22	0.154621090333766	3	FACETS	1	0.896	1	0.5	0.448	0.555	INDETERMINATE	1	TRUE	1	0.496406207759662	3		284	493	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	122	498	0	ENST00000397752.3:c.3028G>T	p.Asp1010Tyr	p.D1010Y	ENST00000397752	NM_000245.2	1010	Gat/Tat	14/21	NA	2	FACETS	0.764	0.691	0.842			1	INDETERMINATE	2	TRUE	NA	0.19	2		498	840	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578266	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs942158624	NA	P-0069041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	100	570	0	ENST00000269305.4:c.583A>T	p.Ile195Phe	p.I195F	ENST00000269305	NM_001126112.2	195	Atc/Ttc	6/11	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.19	2		570	986	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462324	89462324	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	35	392	0	ENST00000336596.2:c.1796C>A	p.Pro599Gln	p.P599Q	ENST00000336596	NM_005233.5	599	cCa/cAa	10/17	1	2	FACETS	0.623	0.51	0.752	0.623	0.51	0.752	SUBCLONAL	1	TRUE	1	0.19	2		392	591	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410807	63410807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	199	492	0	ENST00000330258.3:c.2360C>A	p.Ser787Tyr	p.S787Y	ENST00000330258	NM_152424.3	787	tCc/tAc	2/2	0.277012794382264	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.19	3		492	919	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462330	89462330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751984150	NA	P-0069041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	35	390	0	ENST00000336596.2:c.1802C>T	p.Thr601Ile	p.T601I	ENST00000336596	NM_005233.5	601	aCa/aTa	10/17	1	2	FACETS	0.609	0.498	0.734	0.609	0.498	0.734	SUBCLONAL	1	TRUE	1	0.19	2		390	605	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609724	81609724	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	94	599	0	ENST00000298171.2:c.1322C>A	p.Thr441Asn	p.T441N	ENST00000298171	NM_000369.2	441	aCc/aAc	10/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.19	2		599	868	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13949293	13949295	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	novel	NA	P-0069041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	37	382	0	ENST00000405192.2:c.833_835del	p.Phe278del	p.F278del	ENST00000405192	NM_001163147.1	278	tTTTat/tat	9/12	0.151240505875879	3	FACETS	0.619	0.509	0.743	0.309	0.254	0.372	SUBCLONAL	1	TRUE	1	0.19	3		382	689	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022317	36022317	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	94	537	0	ENST00000358208.4:c.370G>T	p.Ala124Ser	p.A124S	ENST00000358208		124	Gcc/Tcc	4/12	0.151240505875879	3	FACETS	1	0.971	1	0.645	0.573	0.722	CLONAL	1	TRUE	1	0.19	3		537	840	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405140	70405140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	36	458	0	ENST00000373644.4:c.2654G>A	p.Arg885Lys	p.R885K	ENST00000373644	NM_030625.2	885	aGa/aAa	4/12	1	2	FACETS	0.569	0.466	0.685	0.569	0.466	0.685	SUBCLONAL	1	TRUE	1	0.19	2		458	666	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223487	53223487	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	197	462	0	ENST00000375401.3:c.3872G>C	p.Arg1291Pro	p.R1291P	ENST00000375401	NM_004187.3	1291	cGc/cCc	23/26	0.277012794382264	3	FACETS	0.872	0.808	0.938	1	0.987	1	CLONAL	3	TRUE	1	0.19	3		462	868	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033879	49033879	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	35	402	0	ENST00000267163.4:c.2016G>C	p.Glu672Asp	p.E672D	ENST00000267163	NM_000321.2	672	gaG/gaC	20/27	1	2	FACETS	0.548	0.448	0.661	0.548	0.448	0.661	SUBCLONAL	1	TRUE	1	0.19	2		402	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0069043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	22	394	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.661	0.511	0.836	0.661	0.511	0.836	SUBCLONAL	1	TRUE	1	0.16	2		395	416	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0069043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	17	311	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.975	0.729	1	0.975	0.729	1	CLONAL	1	TRUE	1	0.16	2		311	218	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249440	153249440	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	27	383	0	ENST00000281708.4:c.1338G>T	p.Trp446Cys	p.W446C	ENST00000281708	NM_033632.3	446	tgG/tgT	9/12	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.16	2		383	259	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928067	178928067	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	20	333	0	ENST00000263967.3:c.1345C>A	p.Pro449Thr	p.P449T	ENST00000263967	NM_006218.2	449	Cct/Act	8/21	1	2	FACETS	0.871	0.667	1	0.871	0.667	1	CLONAL	1	TRUE	1	0.16	2		333	287	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913527	NA	P-0069043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	23	333	0	ENST00000311936.3:c.436G>C	p.Ala146Pro	p.A146P	ENST00000311936	NM_004985.3	146	Gca/Cca	4/5	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.16	2		333	242	SUCCESS
APC	324	MSKCC	GRCh37	5	112175568	112175568	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	23	506	0	ENST00000257430.4:c.4277del	p.Ser1426ThrfsTer47	p.S1426Tfs*47	ENST00000257430	NM_000038.5	1426	aGc/ac	16/16	1	2	FACETS	0.799	0.622	1	0.799	0.622	1	CLONAL	1	TRUE	1	0.16	2		506	360	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110091	115110091	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	69	298	0	ENST00000257566.3:c.1787C>T	p.Pro596Leu	p.P596L	ENST00000257566	NM_016569.3	596	cCt/cTt	8/8	0.520129166507696	4	FACETS	0.925	0.809	1	0.308	0.269	0.35	CLONAL	1	TRUE	1	0.520129166507696	4		298	436	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112328	115112328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1438073122	NA	P-0069260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	57	388	1	ENST00000257566.3:c.1412G>A	p.Arg471His	p.R471H	ENST00000257566	NM_016569.3	471	cGc/cAc	7/8	0.520129166507696	4	FACETS	0.992	0.856	1	0.331	0.285	0.38	CLONAL	1	TRUE	1	0.520129166507696	4		389	336	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419061	419061	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	188	313	0	ENST00000399788.2:c.3286C>G	p.Leu1096Val	p.L1096V	ENST00000399788	NM_001042603.1	1096	Cta/Gta	22/28	0.520129166507696	4	FACETS	0.949	0.882	1	0.633	0.588	0.678	CLONAL	2	TRUE	1	0.520129166507696	4		313	579	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578453	7578457	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGC	GGCGC	-	novel	NA	P-0069260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	228	431	1	ENST00000269305.4:c.473_477del	p.Arg158HisfsTer21	p.R158Hfs*21	ENST00000269305	NM_001126112.2	158	cGCGCC/c	5/11	0.517026678670757	2	FACETS	0.972	0.918	1	0.972	0.918	1	CLONAL	2	TRUE	0	0.520129166507696	2		432	451	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056943	180056943	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	94	438	0	ENST00000261937.6:c.676G>T	p.Gly226Cys	p.G226C	ENST00000261937	NM_182925.4	226	Ggc/Tgc	5/30	1	2	FACETS	0.913	0.818	1	0.913	0.818	1	CLONAL	1	TRUE	1	0.520129166507696	2		438	396	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281273	49281273	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	156	362	0	ENST00000282018.3:c.320G>T	p.Gly107Val	p.G107V	ENST00000282018	NM_020377.2	107	gGa/gTa	1/1	0.520129166507696	3	FACETS	0.922	0.854	0.991	0.615	0.569	0.661	CLONAL	2	TRUE	0	0.520129166507696	3		362	410	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911561	39911561	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	112	361	0	ENST00000378444.4:c.5069T>C	p.Val1690Ala	p.V1690A	ENST00000378444	NM_001123385.1	1690	gTc/gCc	15/15	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.520129166507696	2		361	410	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590741	95590741	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	378	261	0	ENST00000393063.1:c.1168T>A	p.Tyr390Asn	p.Y390N	ENST00000393063	NM_030621.3	390	Tat/Aat	9/28	0.501013171643056	4	FACETS	0.957	0.922	0.991	0.957	0.922	0.991	CLONAL	4	TRUE	0	0.520129166507696	4		261	577	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133047	30133047	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs765126230	NA	P-0069260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	91	246	0	ENST00000331968.5:c.554A>G	p.His185Arg	p.H185R	ENST00000331968	NM_002742.2	185	cAt/cGt	4/18	0.294620445424777	5	FACETS	1	0.94	1	0.362	0.322	0.405	INDETERMINATE	1	TRUE	2	0.520129166507696	5		246	573	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752677	128752677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1195526437	NA	P-0069260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	111	295	0	ENST00000377970.2:c.838G>C	p.Val280Leu	p.V280L	ENST00000377970	NM_002467.4	280	Gtt/Ctt	3/3	0.294620445424777	5	FACETS	1	0.974	1	0.415	0.373	0.458	INDETERMINATE	1	TRUE	2	0.520129166507696	5		295	611	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445476	49445476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs558509938	NA	P-0069260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	76	403	0	ENST00000301067.7:c.1990C>T	p.Pro664Ser	p.P664S	ENST00000301067	NM_003482.3	664	Cca/Tca	10/54	0.520129166507696	2	FACETS	0.786	0.693	0.883	0.393	0.346	0.442	SUBCLONAL	1	TRUE	0	0.520129166507696	2		403	372	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231695	66231695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	93	282	0	ENST00000273854.3:c.2005G>A	p.Glu669Lys	p.E669K	ENST00000273854	NM_004439.5	669	Gag/Aag	11/18	0.400759673528327	4	FACETS	0.786	0.705	0.87	0.786	0.705	0.87	SUBCLONAL	2	TRUE	2	0.520129166507696	4		282	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0069267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	64	433	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.192933159525783	2		433	545	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103844	209103844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	28	269	0	ENST00000345146.2:c.1105G>A	p.Ala369Thr	p.A369T	ENST00000345146	NM_005896.2	369	Gct/Act	9/10	1	2	FACETS	0.776	0.62	0.954	0.776	0.62	0.954	CLONAL	1	TRUE	1	0.192933159525783	2		269	374	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690805	89690805	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	20	158	0	ENST00000371953.3:c.212G>C	p.Cys71Ser	p.C71S	ENST00000371953	NM_000314.4	71	tGt/tCt	4/9	1	2	FACETS	0.875	0.671	1	0.875	0.671	1	CLONAL	1	TRUE	1	0.192933159525783	2		158	237	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938397	44938398	+	missense_variant	Missense_Mutation	DNP	GA	GA	CT	novel	NA	P-0069267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	17	185	0	ENST00000377967.4:c.2945_2946delinsCT	p.Gly982Ala	p.G982A	ENST00000377967	NM_021140.2	982	gGA/gCT	20/29	1	2	FACETS	0.565	0.421	0.736	0.565	0.421	0.736	SUBCLONAL	1	TRUE	1	0.192933159525783	2		185	312	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718677	190718677	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	29	205	0	ENST00000441310.2:c.835C>T	p.His279Tyr	p.H279Y	ENST00000441310	NM_000534.4	279	Cat/Tat	8/13	1	2	FACETS	0.884	0.71	1	0.884	0.71	1	CLONAL	1	TRUE	1	0.192933159525783	2		205	340	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271169	38271169	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	32	227	0	ENST00000425967.3:c.2539A>G	p.Asn847Asp	p.N847D	ENST00000425967	NM_001174067.1	847	Aat/Gat	19/19	1	2	FACETS	0.984	0.8	1	0.984	0.8	1	CLONAL	1	TRUE	1	0.192933159525783	2		227	337	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796612	42796612	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	53	343	0	ENST00000575354.2:c.3169C>G	p.Leu1057Val	p.L1057V	ENST00000575354	NM_015125.3	1057	Ctc/Gtc	13/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.192933159525783	2		343	443	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032794	30032822	+	frameshift_variant	Frame_Shift_Del	DEL	CGAGAAACCTGGTTCTTTGGACTGCAGTA	CGAGAAACCTGGTTCTTTGGACTGCAGTA	-	novel	NA	P-0069293-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	77	425	0	ENST00000338641.4:c.170_198del	p.Arg57HisfsTer19	p.R57Hfs*19	ENST00000338641	NM_000268.3	57	CGAGAAACCTGGTTCTTTGGACTGCAGTAc/c	2/16	0.0976654258971877	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		425	501	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067938	30067938	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1569304774	NA	P-0069293-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	54	422	0	ENST00000338641.4:c.1122+1G>A		p.X374_splice	ENST00000338641	NM_000268.3	374			0.0976654258971877	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		422	361	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0069352-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	95	394	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.823	0.737	0.914	0.823	0.737	0.914	CLONAL	1	FALSE	1	0.539291587568839	2		394	428	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221319	1221319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913322	NA	P-0069352-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	10	503	0	ENST00000326873.7:c.842C>T	p.Pro281Leu	p.P281L	ENST00000326873	NM_000455.4	281	cCg/cTg	6/10	1	2	FACETS	0.111	0.074	0.157	0.111	0.074	0.157	SUBCLONAL	1	FALSE	1	0.539291587568839	2		503	335	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913283	NA	P-0069352-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	47	372	0	ENST00000263967.3:c.3129G>T	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atT	21/21	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	FALSE	1	0.539291587568839	2		372	164	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373689	118373689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782524513	NA	P-0069352-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	10	418	0	ENST00000534358.1:c.7082C>T	p.Ser2361Leu	p.S2361L	ENST00000534358	NM_005933.3	2361	tCg/tTg	27/36	1	2	FACETS	0.204	0.138	0.286	0.204	0.138	0.286	SUBCLONAL	1	FALSE	1	0.539291587568839	2		418	182	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132611	67132611	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0069352-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	91	303	0	ENST00000412916.2:c.496-2A>G		p.X166_splice	ENST00000412916		166			0.507535898078707	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	FALSE	0	0.539291587568839	2		303	135	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661945	29661945	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854552	NA	P-0069367-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	191	311	0	ENST00000356175.3:c.5839C>T	p.Arg1947Ter	p.R1947*	ENST00000356175	NM_000267.3	1947	Cga/Tga	39/57	0.863351827630756	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.863351827630756	2		311	220	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200240	67200240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069367-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	83	419	0	ENST00000312629.5:c.548G>A	p.Gly183Asp	p.G183D	ENST00000312629	NM_003952.2	183	gGc/gAc	7/15	NA	2	FACETS	0.503	0.447	0.563			1	INDETERMINATE	1	TRUE	NA	0.863351827630756	2		419	382	SUCCESS
APC	324	MSKCC	GRCh37	5	112178938	112178939	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0069367-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	112	377	0	ENST00000257430.4:c.7648dup	p.Glu2550GlyfsTer33	p.E2550Gfs*33	ENST00000257430	NM_000038.5	2549	-/G	16/16	0.856907345477767	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.863351827630756	1		377	144	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045942	26045942	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069367-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	209	454	0	ENST00000540144.1:c.304G>C	p.Val102Leu	p.V102L	ENST00000540144	NM_003531.2	102	Gtg/Ctg	1/1	0.734840443428598	3	FACETS	1	0.98	1	0.564	0.526	0.602	CLONAL	1	TRUE	1	0.863351827630756	3		454	615	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397714	116397852	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGCCGAAATACGGTCCTATGGCTGGTGGCACTTTACTTACTTTAACTGGAAATTACCTAAACAGTGGGAATTCTAGACACATTTCAATTGGTGGAAAAACATGTACTTTAAAAAGGTGTTGTAAATTTATTTTTTGTTG	CGCCGAAATACGGTCCTATGGCTGGTGGCACTTTACTTACTTTAACTGGAAATTACCTAAACAGTGGGAATTCTAGACACATTTCAATTGGTGGAAAAACATGTACTTTAAAAAGGTGTTGTAAATTTATTTTTTGTTG	-	novel	NA	P-0069367-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	143	319	2	ENST00000397752.3:c.1989_2102+25del		p.X663_splice	ENST00000397752	NM_000245.2	663		8/21	0.863351827630756	3	FACETS	0.841	0.782	0.899			1	CLONAL	2	TRUE	NA	0.863351827630756	3		321	282	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857671	78857678	+	frameshift_variant	Frame_Shift_Del	DEL	CTCGGCAG	CTCGGCAG	A	novel	NA	P-0069367-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	111	395	1	ENST00000306801.3:c.1741_1748delinsA	p.Leu581ArgfsTer14	p.L581Rfs*14	ENST00000306801	NM_020761.2	581	CTCGGCAGg/Ag	16/34	0.863351827630756	2	FACETS	0.887	0.809	0.966	0.443	0.404	0.483	CLONAL	1	TRUE	0	0.863351827630756	2		396	290	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0069379-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	148	249	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.42168239708196	3	FACETS	0.916	0.843	0.991	0.916	0.843	0.991	CLONAL	2	TRUE	1	0.42168239708196	3		249	464	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261155	16261155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1032279699	NA	P-0069379-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	114	467	0	ENST00000375759.3:c.8420G>A	p.Arg2807His	p.R2807H	ENST00000375759	NM_015001.2	2807	cGt/cAt	11/15	0.330651520637118	1	FACETS	0.896	0.812	0.985	0.896	0.812	0.985	CLONAL	1	TRUE	0	0.42168239708196	1		467	476	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132542	11132542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069379-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	115	445	0	ENST00000358026.2:c.2758G>A	p.Glu920Lys	p.E920K	ENST00000358026	NM_001128849.1	920	Gag/Aag	19/36	0.42168239708196	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.42168239708196	1		445	423	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178712	108178712	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs869312756	NA	P-0069379-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	77	246	0	ENST00000278616.4:c.5762+1G>T		p.X1921_splice	ENST00000278616	NM_000051.3	1921			1	2	FACETS	0.932	0.823	1	0.932	0.823	1	CLONAL	1	TRUE	1	0.42168239708196	2		246	392	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048788	180048788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375315719	NA	P-0069405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	39	470	0	ENST00000261937.6:c.1774C>T	p.Arg592Cys	p.R592C	ENST00000261937	NM_182925.4	592	Cgc/Tgc	13/30	1	2	FACETS	0.694	0.575	0.826	0.694	0.575	0.826	SUBCLONAL	1	TRUE	1	0.25271186340476	2		470	445	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216584	108216584	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	29	302	0	ENST00000278616.4:c.8533T>C	p.Trp2845Arg	p.W2845R	ENST00000278616	NM_000051.3	2845	Tgg/Cgg	58/63	0.25271186340476	1	FACETS	0.675	0.543	0.824	0.675	0.543	0.824	SUBCLONAL	1	TRUE	0	0.25271186340476	1		302	297	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849939	156849939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	53	351	0	ENST00000524377.1:c.2195C>T	p.Ser732Phe	p.S732F	ENST00000524377	NM_002529.3	732	tCc/tTc	16/17	0.25271186340476	3	FACETS	0.98	0.837	1	0.49	0.418	0.569	CLONAL	1	TRUE	1	0.25271186340476	3		351	482	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212588	133212588	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	65	377	1	ENST00000320574.5:c.5701C>T	p.His1901Tyr	p.H1901Y	ENST00000320574	NM_006231.2	1901	Cat/Tat	42/49	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.25271186340476	2		378	441	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0069450-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	127	362	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.700283219856745	2		362	356	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0069450-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	99	199	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.700283219856745	2		199	263	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0069450-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	164	315	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.630847013475196	1	FACETS	0.909	0.849	0.969	0.909	0.849	0.969	CLONAL	1	TRUE	0	0.700283219856745	1		315	335	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280804	41280804	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069450-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	189	327	0	ENST00000349496.5:c.2317C>T	p.Gln773Ter	p.Q773*	ENST00000349496	NM_001904.3	773	Cag/Tag	15/15	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.700283219856745	2		327	538	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193892	106193892	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1049545383	NA	P-0069450-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	191	269	2	ENST00000380013.4:c.4354C>T	p.Arg1452Ter	p.R1452*	ENST00000380013	NM_001127208.2	1452	Cga/Tga	10/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.700283219856745	2		271	523	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604668	48604668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069450-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	171	330	0	ENST00000342988.3:c.1490G>A	p.Arg497His	p.R497H	ENST00000342988	NM_005359.5	497	cGc/cAc	12/12	0.700283219856745	1	FACETS	0.917	0.858	0.976	0.917	0.858	0.976	CLONAL	1	TRUE	0	0.700283219856745	1		330	346	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919596	28919596	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1244106213	NA	P-0069450-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	168	272	0	ENST00000282397.4:c.2341C>T	p.Arg781Ter	p.R781*	ENST00000282397	NM_002019.4	781	Cga/Tga	16/30	0.664825865251058	3	FACETS	1	0.973	1	0.557	0.515	0.601	CLONAL	1	TRUE	1	0.700283219856745	3		272	581	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398220	25398220	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069450-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	133	216	0	ENST00000311936.3:c.99T>A	p.Asp33Glu	p.D33E	ENST00000311936	NM_004985.3	33	gaT/gaA	2/5	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.700283219856745	2		216	372	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0069551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	56	704	7	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.335	0.287	0.388	0.335	0.287	0.388	SUBCLONAL	1	TRUE	1	0.54	2		711	619	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0069551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	326	230	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.3	7	FACETS	0.985	0.937	1	0.657	0.625	0.689	INDETERMINATE	4	TRUE	1	0.54	7		230	720	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974720	21974720	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs200382984	NA	P-0069551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	37	363	0	ENST00000304494.5:c.107C>G	p.Ala36Gly	p.A36G	ENST00000304494	NM_000077.4	36	gCg/gGg	1/3	1	2	FACETS	0.29	0.238	0.347	0.29	0.238	0.347	SUBCLONAL	1	TRUE	1	0.54	2		363	473	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974715	21974719	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGC	GCAGC	-	novel	NA	P-0069551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	36	358	0	ENST00000304494.5:c.108_112del	p.Leu37GlnfsTer5	p.L37Qfs*5	ENST00000304494	NM_000077.4	36	gcGCTGCcc/gccc	1/3	1	2	FACETS	0.281	0.23	0.337	0.281	0.23	0.337	SUBCLONAL	1	TRUE	1	0.54	2		358	475	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0069592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	307	354	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		354	619	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	467	314	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		314	904	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913338	NA	P-0069592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	172	245	0	ENST00000288602.6:c.1781A>C	p.Asp594Ala	p.D594A	ENST00000288602	NM_004333.4	594	gAt/gCt	15/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		245	438	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670690	134670690	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	103	332	0	ENST00000398015.3:c.601C>A	p.Gln201Lys	p.Q201K	ENST00000398015	NM_004441.4	201	Caa/Aaa	3/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		332	696	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851378	63851378	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	122	353	0	ENST00000279873.7:c.2156A>G	p.Lys719Arg	p.K719R	ENST00000279873	NM_032199.2	719	aAa/aGa	10/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		353	492	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416750	121416750	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	253	392	0	ENST00000257555.6:c.179T>C	p.Leu60Pro	p.L60P	ENST00000257555		60	cTg/cCg	1/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		392	651	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630900	187630900	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	271	368	0	ENST00000441802.2:c.82G>T	p.Glu28Ter	p.E28*	ENST00000441802	NM_005245.3	28	Gaa/Taa	2/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		368	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0069665-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	80	274	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.345361518933523	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.345361518933523	1		274	366	SUCCESS
APC	324	MSKCC	GRCh37	5	112174670	112174670	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069665-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	46	373	0	ENST00000257430.4:c.3379C>T	p.Gln1127Ter	p.Q1127*	ENST00000257430	NM_000038.5	1127	Cag/Tag	16/16	0.313022200990873	1	FACETS	0.492	0.414	0.577	0.492	0.414	0.577	SUBCLONAL	1	TRUE	0	0.345361518933523	1		373	448	SUCCESS
APC	324	MSKCC	GRCh37	5	112175302	112175303	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	AT	novel	NA	P-0069665-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	61	358	1	ENST00000257430.4:c.4011_4012delinsAT	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1337	ctGCag/ctATag	16/16	0.313022200990873	1	FACETS	0.626	0.541	0.718	0.626	0.541	0.718	SUBCLONAL	1	TRUE	0	0.345361518933523	1		359	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574035	7574035	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0069724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	119	307	0	ENST00000269305.4:c.994-2A>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			NA	2	FACETS	0.796	0.727	0.867			1	INDETERMINATE	2	TRUE	NA	0.436968286502857	2		307	342	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129699	47129699	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	69	372	0	ENST00000409792.3:c.5181G>T	p.Glu1727Asp	p.E1727D	ENST00000409792	NM_014159.6	1727	gaG/gaT	10/21	0.39958250702202	1	FACETS	0.59	0.516	0.67	0.59	0.516	0.67	SUBCLONAL	1	TRUE	0	0.436968286502857	1		372	418	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223573	55223573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs552062864	NA	P-0069724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	47	442	0	ENST00000275493.2:c.940G>A	p.Asp314Asn	p.D314N	ENST00000275493	NM_005228.3	314	Gac/Aac	8/28	0.319734431463072	1	FACETS	0.368	0.31	0.431	0.368	0.31	0.431	SUBCLONAL	1	TRUE	0	0.436968286502857	1		442	457	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0069729-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	111	314	0	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	1	1	FACETS	0.82	0.744	0.898	1	0.987	1	CLONAL	2	TRUE	0	0.31	1		314	369	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0069760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	86	339	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.255066528722361	2		339	528	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420094	152420094	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138891155	NA	P-0069760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	42	253	0	ENST00000206249.3:c.1781C>T	p.Thr594Met	p.T594M	ENST00000206249	NM_000125.3	594	aCg/aTg	8/8	0.255066528722361	11	FACETS	0.86	0.716	1			1	CLONAL	1	TRUE	NA	0.255066528722361	11		253	822	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845409	76845409	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	23	259	0	ENST00000373344.5:c.6112C>T	p.Leu2038Phe	p.L2038F	ENST00000373344	NM_000489.3	2038	Ctt/Ttt	27/35	0.205927878936971	2	FACETS	0.422	0.328	0.531	0.211	0.164	0.266	SUBCLONAL	1	TRUE	0	0.255066528722361	2		259	427	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851484	151851484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	93	334	0	ENST00000262189.6:c.12007C>T	p.Pro4003Ser	p.P4003S	ENST00000262189	NM_170606.2	4003	Ccc/Tcc	47/59	0.313431831149387	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.313804416459407	1		334	478	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098803	178098803	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	88	323	0	ENST00000397062.3:c.242G>C	p.Gly81Ala	p.G81A	ENST00000397062	NM_006164.4	81	gGt/gCt	2/5	0.313804416459407	3	FACETS	0.951	0.843	1	0.476	0.421	0.534	CLONAL	1	TRUE	1	0.313804416459407	3		323	682	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50821763	50821763	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	40	210	0	ENST00000398568.2:c.2099+1del		p.R700fs	ENST00000398568	NM_001042412.1	700	aGa/aa	13/18	0.270407428288519	4	FACETS	0.846	0.704	1			1	CLONAL	1	TRUE	NA	0.313804416459407	4		210	396	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138376576	138376576	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	66	228	0	ENST00000289153.2:c.2898T>A	p.His966Gln	p.H966Q	ENST00000289153	NM_006219.2	966	caT/caA	20/22	1	2	FACETS	0.967	0.842	1	0.967	0.842	1	CLONAL	1	TRUE	1	0.313804416459407	2		228	435	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185616	27185618	+	missense_variant	Missense_Mutation	TNP	TTT	TTT	ATC	novel	NA	P-0069763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	74	302	0	ENST00000380036.4:c.1316_1318delinsATC	p.Ile439_Ser440delinsAsnPro	p.I439_S440delinsNP	ENST00000380036	NM_000459.3	439	aTTTct/aATCct	9/23	1	2	FACETS	0.83	0.728	0.941	0.83	0.728	0.941	CLONAL	1	TRUE	1	0.313804416459407	2		302	568	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	49	358	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.24	2		358	367	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325158	123325158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56226109	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	47	505	1	ENST00000358487.5:c.170C>T	p.Ser57Leu	p.S57L	ENST00000358487	NM_000141.4	57	tCg/tTg	3/18	1	2	FACETS	0.724	0.611	0.849	0.724	0.611	0.849	SUBCLONAL	1	TRUE	1	0.24	2		506	541	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838396	156838396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	229	698	0	ENST00000524377.1:c.674C>T	p.Ala225Val	p.A225V	ENST00000524377	NM_002529.3	225	gCc/gTc	6/17	1	2	FACETS	1	0.936	1	1	0.994	1	CLONAL	2	TRUE	1	0.24	2		698	951	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422937	49422937	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	92	664	0	ENST00000301067.7:c.14158C>T	p.Pro4720Ser	p.P4720S	ENST00000301067	NM_003482.3	4720	Cct/Tct	44/54	1	2	FACETS	0.935	0.83	1	0.935	0.83	1	CLONAL	1	TRUE	1	0.24	2		664	820	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261338	115261338	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs558231202	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	76	338	0	ENST00000438362.2:c.2383C>T	p.Arg795Ter	p.R795*	ENST00000438362	NM_001242891.1	795	Cga/Tga	19/20	1	2	FACETS	0.767	0.676	0.864	1	0.977	1	SUBCLONAL	2	TRUE	1	0.24	2		338	413	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760927	133760927	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	82	695	0	ENST00000318560.5:c.3250C>T	p.Arg1084Ter	p.R1084*	ENST00000318560	NM_005157.4	1084	Cga/Tga	11/11	1	2	FACETS	0.765	0.673	0.864	0.765	0.673	0.864	SUBCLONAL	1	TRUE	1	0.24	2		695	893	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574292	95574292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144649926	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	39	238	0	ENST00000393063.1:c.2575C>T	p.Arg859Trp	p.R859W	ENST00000393063	NM_030621.3	859	Cgg/Tgg	17/28	1	2	FACETS	0.898	0.746	1	0.898	0.746	1	CLONAL	1	TRUE	1	0.24	2		238	362	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658349	117658349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	52	610	0	ENST00000368508.3:c.5234G>A	p.Ser1745Asn	p.S1745N	ENST00000368508	NM_002944.2	1745	aGc/aAc	31/43	1	2	FACETS	0.672	0.571	0.783	0.672	0.571	0.783	SUBCLONAL	1	TRUE	1	0.24	2		610	645	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326482	62326482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150686112	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	89	895	1	ENST00000360203.5:c.3407C>T	p.Thr1136Ile	p.T1136I	ENST00000360203	NM_001283009.1	1136	aCc/aTc	33/35	1	2	FACETS	0.712	0.629	0.8	0.712	0.629	0.8	SUBCLONAL	1	TRUE	1	0.24	2		896	1042	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670477	246670477	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	141	437	0	ENST00000388985.4:c.43G>A	p.Gly15Arg	p.G15R	ENST00000388985		15	Gga/Aga	1/12	1	2	FACETS	0.869	0.794	0.948	1	0.989	1	CLONAL	2	TRUE	1	0.24	2		437	676	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999015	100999015	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	50	441	0	ENST00000325455.5:c.787G>A	p.Gly263Arg	p.G263R	ENST00000325455	NM_001202474.3	263	Gga/Aga	1/8	1	2	FACETS	0.863	0.732	1	0.863	0.732	1	CLONAL	1	TRUE	1	0.24	2		441	483	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427116	49427116	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	62	644	0	ENST00000301067.7:c.11372C>T	p.Ser3791Phe	p.S3791F	ENST00000301067	NM_003482.3	3791	tCc/tTc	39/54	1	2	FACETS	0.763	0.659	0.877	0.763	0.659	0.877	SUBCLONAL	1	TRUE	1	0.24	2		644	677	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434610	49434611	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	110	842	0	ENST00000301067.7:c.6942_6943delinsTT	p.His2315Tyr	p.H2315Y	ENST00000301067	NM_003482.3	2314	acCCac/acTTac	31/54	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.24	2		842	883	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488225	56488225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	75	485	0	ENST00000267101.3:c.1744G>A	p.Gly582Arg	p.G582R	ENST00000267101	NM_001982.3	582	Ggg/Agg	15/28	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.24	2		485	622	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210804	133210804	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	73	518	0	ENST00000320574.5:c.5972C>T	p.Ser1991Phe	p.S1991F	ENST00000320574	NM_006231.2	1991	tCc/tTc	43/49	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.24	2		518	563	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679255	88679255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	72	514	0	ENST00000360948.2:c.782C>T	p.Thr261Ile	p.T261I	ENST00000360948	NM_001012338.2	261	aCc/aTc	8/19	1	2	FACETS	0.896	0.782	1	0.896	0.782	1	CLONAL	1	TRUE	1	0.24	2		514	670	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778810	3778810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	124	762	1	ENST00000262367.5:c.6238C>T	p.Pro2080Ser	p.P2080S	ENST00000262367	NM_004380.2	2080	Cct/Tct	31/31	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.24	2		763	913	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66524020	66524020	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	12	178	0	ENST00000358598.2:c.748C>A	p.Leu250Ile	p.L250I	ENST00000358598	NM_212471.2	250	Ctt/Att	8/11	1	2	FACETS	0.424	0.297	0.579	0.424	0.297	0.579	SUBCLONAL	1	TRUE	1	0.24	2		178	236	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097662	11097662	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	98	746	0	ENST00000358026.2:c.842C>T	p.Pro281Leu	p.P281L	ENST00000358026	NM_001128849.1	281	cCc/cTc	5/36	1	2	FACETS	0.905	0.807	1	0.905	0.807	1	CLONAL	1	TRUE	1	0.24	2		746	902	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136980	11136981	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	76	594	3	ENST00000358026.2:c.3173_3174delinsTT	p.Ser1058Phe	p.S1058F	ENST00000358026	NM_001128849.1	1058	tCC/tTT	23/36	1	2	FACETS	0.762	0.667	0.865	0.762	0.667	0.865	SUBCLONAL	1	TRUE	1	0.24	2		597	831	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224698	36224699	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	108	841	1	ENST00000222270.7:c.7084_7085delinsTT	p.Pro2362Leu	p.P2362L	ENST00000222270	NM_014727.1	2362	CCg/TTg	30/37	1	2	FACETS	0.824	0.738	0.916	0.824	0.738	0.916	CLONAL	1	TRUE	1	0.24	2		842	1092	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182211	99182211	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	58	515	0	ENST00000074304.5:c.2276C>T	p.Pro759Leu	p.P759L	ENST00000074304	NM_001134224.1	759	cCc/cTc	21/26	1	2	FACETS	0.694	0.596	0.802	0.694	0.596	0.802	SUBCLONAL	1	TRUE	1	0.24	2		515	696	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279942	46279942	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	88	718	0	ENST00000371998.3:c.3868C>T	p.Pro1290Ser	p.P1290S	ENST00000371998		1290	Ccc/Tcc	20/23	1	2	FACETS	0.741	0.655	0.833	0.741	0.655	0.833	SUBCLONAL	1	TRUE	1	0.24	2		718	990	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961537	54961537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	58	400	0	ENST00000312783.6:c.95C>T	p.Pro32Leu	p.P32L	ENST00000312783	NM_198436.1	32	cCt/cTt	4/10	1	2	FACETS	0.935	0.804	1	0.935	0.804	1	CLONAL	1	TRUE	1	0.24	2		400	517	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442854	187442855	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	84	334	0	ENST00000232014.4:c.1851_1852delinsTT	p.Arg618Cys	p.R618C	ENST00000232014	NM_001130845.1	617	ctCCgt/ctTTgt	9/10	1	2	FACETS	0.827	0.735	0.926	1	0.982	1	CLONAL	2	TRUE	1	0.24	2		334	423	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447553	187447553	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs189037992	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	76	617	0	ENST00000232014.4:c.640C>T	p.Arg214Trp	p.R214W	ENST00000232014	NM_001130845.1	214	Cgg/Tgg	5/10	1	2	FACETS	0.93	0.816	1	0.93	0.816	1	CLONAL	1	TRUE	1	0.24	2		617	681	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157386	106157386	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	18	262	0	ENST00000380013.4:c.2287C>T	p.Pro763Ser	p.P763S	ENST00000380013	NM_001127208.2	763	Ccc/Tcc	3/11	1	2	FACETS	0.473	0.356	0.612	0.473	0.356	0.612	SUBCLONAL	1	TRUE	1	0.24	2		262	317	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630191	187630191	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	36	449	0	ENST00000441802.2:c.791C>T	p.Pro264Leu	p.P264L	ENST00000441802	NM_005245.3	264	cCa/cTa	2/27	1	2	FACETS	0.549	0.451	0.66	0.549	0.451	0.66	SUBCLONAL	1	TRUE	1	0.24	2		449	546	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066600	94066600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355103404	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	47	417	0	ENST00000369303.4:c.1159G>A	p.Gly387Arg	p.G387R	ENST00000369303	NM_004440.3	387	Gga/Aga	5/17	1	2	FACETS	0.763	0.644	0.895	0.763	0.644	0.895	SUBCLONAL	1	TRUE	1	0.24	2		417	513	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687398	117687398	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	37	283	0	ENST00000368508.3:c.2653C>T	p.Gln885Ter	p.Q885*	ENST00000368508	NM_002944.2	885	Cag/Tag	18/43	1	2	FACETS	0.979	0.81	1	0.979	0.81	1	CLONAL	1	TRUE	1	0.24	2		283	315	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771151	161771151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	66	617	1	ENST00000366898.1:c.1378G>A	p.Asp460Asn	p.D460N	ENST00000366898	NM_004562.2	460	Gac/Aac	12/12	1	2	FACETS	0.683	0.592	0.783	0.683	0.592	0.783	SUBCLONAL	1	TRUE	1	0.24	2		618	805	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418855	116418856	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	35	253	1	ENST00000397752.3:c.3366_3367delinsTT	p.Gln1123Ter	p.Q1123*	ENST00000397752	NM_000245.2	1122	tcCCaa/tcTTaa	17/21	1	2	FACETS	0.822	0.675	0.986	0.822	0.675	0.986	CLONAL	1	TRUE	1	0.24	2		254	355	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069672	69069672	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1229920429	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	41	313	0	ENST00000288368.4:c.4346+1G>A		p.X1449_splice	ENST00000288368	NM_024870.2	1449			1	2	FACETS	0.909	0.759	1	0.909	0.759	1	CLONAL	1	TRUE	1	0.24	2		313	376	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650317	48650317	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	79	669	1	ENST00000376670.3:c.287G>A	p.Trp96Ter	p.W96*	ENST00000376670	NM_002049.3	96	tGg/tAg	3/6	1	2	FACETS	0.821	0.721	0.928	0.821	0.721	0.928	CLONAL	1	TRUE	1	0.24	2		670	802	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410207	63410207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	81	621	0	ENST00000330258.3:c.2960C>T	p.Ser987Phe	p.S987F	ENST00000330258	NM_152424.3	987	tCt/tTt	2/2	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.24	2		621	611	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410807	63410807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747564770	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	61	573	0	ENST00000330258.3:c.2360C>T	p.Ser787Phe	p.S787F	ENST00000330258	NM_152424.3	787	tCc/tTc	2/2	1	2	FACETS	0.792	0.683	0.911	0.792	0.683	0.911	CLONAL	1	TRUE	1	0.24	2		573	642	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912049	76912049	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0038070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	47	298	0	ENST00000373344.5:c.4214+1G>A		p.X1405_splice	ENST00000373344	NM_000489.3	1405			1	2	FACETS	0.965	0.816	1	0.965	0.816	1	CLONAL	1	TRUE	1	0.24	2		298	406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0057840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	169	323	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.52599910190522	2	FACETS	0.918	0.858	0.978	0.918	0.858	0.978	CLONAL	2	TRUE	0	0.52599910190522	2		323	350	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101285	27101285	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	164	379	0	ENST00000324856.7:c.4567T>G	p.Tyr1523Asp	p.Y1523D	ENST00000324856	NM_006015.4	1523	Tat/Gat	18/20	NA	2	FACETS	1	0.949	1			1	INDETERMINATE	2	TRUE	NA	0.52599910190522	2		379	307	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111191	193111192	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0057840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	35	177	1	ENST00000367435.3:c.724_725delinsTT	p.Gly242Leu	p.G242L	ENST00000367435	NM_024529.4	242	GGa/TTa	7/17	0.52599910190522	3	FACETS	0.778	0.643	0.927	0.389	0.321	0.464	CLONAL	1	TRUE	1	0.52599910190522	3		178	216	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933176	100933176	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0057840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	60	197	0	ENST00000325455.5:c.2212+2T>C		p.X738_splice	ENST00000325455	NM_001202474.3	738			1	2	FACETS	0.827	0.719	0.942	0.827	0.719	0.942	CLONAL	1	TRUE	1	0.52599910190522	2		197	276	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391205	89391205	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	117	193	0	ENST00000336596.2:c.1271A>T	p.Gln424Leu	p.Q424L	ENST00000336596	NM_005233.5	424	cAg/cTg	5/17	0.52599910190522	2	FACETS	1	0.978	1	0.616	0.561	0.673	CLONAL	1	TRUE	0	0.52599910190522	2		193	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782664	NA	P-0060233-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	149	430	0	ENST00000269305.4:c.711G>C	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atC	7/11	0.366089884498435	1	FACETS	0.837	0.769	0.907	0.837	0.769	0.907	CLONAL	1	TRUE	0	0.495964247031341	1		430	540	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267384	198267384	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060233-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	380	495	0	ENST00000335508.6:c.1973G>T	p.Trp658Leu	p.W658L	ENST00000335508	NM_012433.2	658	tGg/tTg	14/25	0.482931893122601	4	FACETS	0.949	0.901	0.997	0.949	0.901	0.997	CLONAL	2	TRUE	2	0.495964247031341	4		495	1208	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399291	139399302	+	inframe_deletion	In_Frame_Del	DEL	GGAAGATCATCT	GGAAGATCATCT	-	novel	NA	P-0060233-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	688	604	0	ENST00000277541.6:c.4841_4852del	p.Gln1614_Phe1617del	p.Q1614_F1617del	ENST00000277541	NM_017617.3	1614	cAGATGATCTTCCcc/ccc	26/34	0.497095199801386	4	FACETS	0.98	0.949	1	0.98	0.949	1	CLONAL	3	TRUE	1	0.495964247031341	4		604	1411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782664	NA	P-0060233-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	209	430	0	ENST00000269305.4:c.711G>C	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atC	7/11	0.687615428885292	1	FACETS		NA	1	1	0.996	1	NA	2	TRUE	0	0.754205956473045	1		430	223	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267384	198267384	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060233-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	611	495	0	ENST00000335508.6:c.1973G>T	p.Trp658Leu	p.W658L	ENST00000335508	NM_012433.2	658	tGg/tTg	14/25	0.754205956473045	6	FACETS	0.955	0.92	0.99			1	CLONAL	3	TRUE	NA	0.754205956473045	6		495	1419	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399291	139399302	+	inframe_deletion	In_Frame_Del	DEL	GGAAGATCATCT	GGAAGATCATCT	-	novel	NA	P-0060233-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	938	604	0	ENST00000277541.6:c.4841_4852del	p.Gln1614_Phe1617del	p.Q1614_F1617del	ENST00000277541	NM_017617.3	1614	cAGATGATCTTCCcc/ccc	26/34	0.754205956473045	9	FACETS	1	0.996	1			1	CLONAL	7	TRUE	NA	0.754205956473045	9		604	1223	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521088	187521088	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	228	489	0	ENST00000441802.2:c.12067C>T	p.Gln4023Ter	p.Q4023*	ENST00000441802	NM_005245.3	4023	Cag/Tag	22/27	0.768557544824387	1	FACETS	0.964	0.916	1	0.964	0.916	1	CLONAL	1	TRUE	0	0.768557544824387	1		489	379	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9927978	9927978	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	20	363	0	ENST00000330684.3:c.1761C>A	p.Asn587Lys	p.N587K	ENST00000330684	NM_001134407.1	587	aaC/aaA	8/13	1	2	FACETS	0.142	0.108	0.182	0.142	0.108	0.182	SUBCLONAL	1	TRUE	1	0.768557544824387	2		363	367	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942034	81942034	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	175	399	0	ENST00000359376.3:c.1571C>A	p.Thr524Lys	p.T524K	ENST00000359376	NM_002661.3	524	aCa/aAa	17/33	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.768557544824387	2		399	423	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101078	26101078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	191	375	0	ENST00000435504.4:c.14G>A	p.Gly5Glu	p.G5E	ENST00000435504		5	gGa/gAa	1/13	1	2	FACETS	0.824	0.766	0.884	0.824	0.766	0.884	CLONAL	1	TRUE	1	0.768557544824387	2		375	603	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226910	142226910	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	126	381	0	ENST00000350721.4:c.4894T>A	p.Phe1632Ile	p.F1632I	ENST00000350721	NM_001184.3	1632	Ttt/Att	28/47	0.55236854472699	4	FACETS	1	0.983	1	0.448	0.409	0.489	CLONAL	1	TRUE	1	0.768557544824387	4		381	431	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998971	169998971	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	77	281	0	ENST00000295797.4:c.900G>C	p.Gln300His	p.Q300H	ENST00000295797	NM_002740.5	300	caG/caC	10/18	0.55236854472699	4	FACETS	1	0.962	1	0.4	0.355	0.448	CLONAL	1	TRUE	1	0.768557544824387	4		281	295	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146485	185146485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	366	456	0	ENST00000265026.3:c.116C>T	p.Ser39Phe	p.S39F	ENST00000265026	NM_004721.4	39	tCt/tTt	2/14	0.55236854472699	4	FACETS	1	0.993	1	0.801	0.766	0.835	CLONAL	2	TRUE	1	0.768557544824387	4		456	701	SUCCESS
REST	5978	MSKCC	GRCh37	4	57798017	57798017	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	236	443	0	ENST00000309042.7:c.2993C>G	p.Ala998Gly	p.A998G	ENST00000309042	NM_005612.4	998	gCa/gGa	4/4	0.387336809316175	3	FACETS	0.796	0.75	0.842	0.796	0.75	0.842	INDETERMINATE	2	TRUE	1	0.768557544824387	3		443	534	SUCCESS
APC	324	MSKCC	GRCh37	5	112176022	112176037	+	frameshift_variant	Frame_Shift_Del	DEL	ATGTATTATTTCTGCC	ATGTATTATTTCTGCC	-	novel	NA	P-0065381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	165	495	0	ENST00000257430.4:c.4734_4749del	p.Ile1579GlnfsTer66	p.I1579Qfs*66	ENST00000257430	NM_000038.5	1577	gaATGTATTATTTCTGCC/ga	16/16	0.768557544824387	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.768557544824387	1		495	250	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579386	7579388	+	frameshift_variant	Frame_Shift_Del	DEL	TCT	TCT	G	novel	NA	P-0065381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	298	537	0	ENST00000269305.4:c.299_301delinsC	p.Gln100ProfsTer48	p.Q100Pfs*48	ENST00000269305	NM_001126112.2	100	cAGAaa/cCaa	4/11	0.768557544824387	1	FACETS	0.982	0.94	1	0.982	0.94	1	CLONAL	1	TRUE	0	0.768557544824387	1		537	486	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0068538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	59	322	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.430762479355257	2		322	272	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	159	414	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.430762479355257	2		414	653	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0068538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	167	567	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.430762479355257	1	FACETS	0.951	0.877	1	0.951	0.877	1	CLONAL	1	TRUE	0	0.430762479355257	1		567	640	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820602	3820602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749011678	NA	P-0068538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	164	465	0	ENST00000262367.5:c.2849C>T	p.Thr950Met	p.T950M	ENST00000262367	NM_004380.2	950	aCg/aTg	14/31	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.430762479355257	2		465	704	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856097	111856097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1013978345	NA	P-0068538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	139	470	0	ENST00000341259.2:c.148C>T	p.Arg50Trp	p.R50W	ENST00000341259	NM_005475.2	50	Cgg/Tgg	2/8	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.430762479355257	2		470	613	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864639	68864639	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	88	323	0	ENST00000288368.4:c.10G>A	p.Asp4Asn	p.D4N	ENST00000288368	NM_024870.2	4	Gac/Aac	1/40	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.430762479355257	2		323	388	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826570	50826570	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	60	306	0	ENST00000398568.2:c.2295A>C	p.Lys765Asn	p.K765N	ENST00000398568	NM_001042412.1	765	aaA/aaC	15/18	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.430762479355257	2		306	270	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879439	56879439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	141	446	0	ENST00000519728.1:c.956C>T	p.Thr319Ile	p.T319I	ENST00000519728	NM_002350.3	319	aCc/aTc	9/13	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.430762479355257	2		446	646	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351226	89351226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	149	524	1	ENST00000301030.4:c.1724G>A	p.Ser575Asn	p.S575N	ENST00000301030	NM_001256183.1	575	aGc/aAc	9/13	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.430762479355257	2		525	651	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324534	31324535	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0068538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	29	372	0	ENST00000412585.2:c.273dup	p.Lys92GlnfsTer7	p.K92Qfs*7	ENST00000412585	NM_005514.6	91	-/C	2/8	0.430762479355257	1	FACETS	0.313	0.252	0.384	0.313	0.252	0.384	SUBCLONAL	1	TRUE	0	0.430762479355257	1		372	337	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492698	56492698	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0068538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	109	461	0	ENST00000407977.2:c.241A>T	p.Lys81Ter	p.K81*	ENST00000407977		81	Aaa/Taa	2/10	0.430762479355257	1	FACETS	0.959	0.868	1	0.959	0.868	1	CLONAL	1	TRUE	0	0.430762479355257	1		461	414	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229207	55229207	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	74	431	0	ENST00000275493.2:c.1514T>A	p.Val505Asp	p.V505D	ENST00000275493	NM_005228.3	505	gTc/gAc	13/28	1	2	FACETS	0.54	0.473	0.613	0.54	0.473	0.613	SUBCLONAL	1	TRUE	1	0.430762479355257	2		431	636	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247364	153247364	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	109	404	0	ENST00000281708.4:c.1438G>T	p.Asp480Tyr	p.D480Y	ENST00000281708	NM_033632.3	480	Gat/Tat	10/12	1	2	FACETS	0.848	0.763	0.937	0.848	0.763	0.937	CLONAL	1	TRUE	1	0.430762479355257	2		404	597	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021817	71021817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs797045586	NA	P-0068644-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	65	325	0	ENST00000318789.4:c.1541G>A	p.Arg514His	p.R514H	ENST00000318789	NM_032682.5	514	cGt/cAt	18/21	0.386566602294239	4	FACETS	0.859	0.745	0.982	0.429	0.372	0.491	CLONAL	1	TRUE	2	0.386566602294239	4		325	543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0068649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	309	323	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	0.784	0.741	0.827			1	INDETERMINATE	2	TRUE	NA	0.45168443753782	2		323	873	SUCCESS
APC	324	MSKCC	GRCh37	5	112175411	112175411	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	87	646	0	ENST00000257430.4:c.4120G>T	p.Glu1374Ter	p.E1374*	ENST00000257430	NM_000038.5	1374	Gaa/Taa	16/16	0.353927656176496	1	FACETS	0.448	0.397	0.503	0.448	0.397	0.503	SUBCLONAL	1	TRUE	0	0.45168443753782	1		646	665	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551307	29551307	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	90	763	0	ENST00000389048.3:c.1323C>A	p.Phe441Leu	p.F441L	ENST00000389048	NM_004304.4	441	ttC/ttA	6/29	0.333506316207736	1	FACETS	0.402	0.356	0.451	0.402	0.356	0.451	SUBCLONAL	1	TRUE	0	0.45168443753782	1		763	767	SUCCESS
APC	324	MSKCC	GRCh37	5	112157658	112157658	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	141	420	0	ENST00000257430.4:c.1378G>T	p.Glu460Ter	p.E460*	ENST00000257430	NM_000038.5	460	Gaa/Taa	11/16	0.353927656176496	1	FACETS	0.91	0.834	0.989	0.91	0.834	0.989	CLONAL	1	TRUE	0	0.45168443753782	1		420	531	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46275987	46275987	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1236	70	702	2	ENST00000371998.3:c.3423G>T	p.Gln1141His	p.Q1141H	ENST00000371998		1141	caG/caT	18/23	0.360778583705704	6	FACETS	0.452	0.392	0.517	0.113	0.098	0.13	SUBCLONAL	1	TRUE	2	0.45168443753782	6		704	1306	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504553	103504553	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	111	576	0	ENST00000355739.4:c.174G>T	p.Leu58Phe	p.L58F	ENST00000355739	NM_000123.3	58	ttG/ttT	2/15	0.153825320988413	5	FACETS	1	0.954	1	0.369	0.331	0.408	INDETERMINATE	1	TRUE	2	0.45168443753782	5		576	745	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307586	118307586	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	93	653	0	ENST00000534358.1:c.359C>A	p.Ala120Asp	p.A120D	ENST00000534358	NM_005933.3	120	gCc/gAc	1/36	0.153825320988413	5	FACETS	0.757	0.672	0.848	0.252	0.224	0.283	INDETERMINATE	1	TRUE	2	0.45168443753782	5		653	913	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0068666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	208	484	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.81	2		484	422	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664581	138664585	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTG	GGCTG	-	novel	NA	P-0068666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	78	305	0	ENST00000330315.3:c.980_984del	p.Pro327HisfsTer205	p.P327Hfs*205	ENST00000330315	NM_023067.3	327	cCAGCC/c	1/1	1	2	FACETS	0.793	0.707	0.882	0.793	0.707	0.882	SUBCLONAL	1	TRUE	1	0.81	2		305	243	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	64	441	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.17	2		441	735	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	58	477	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.814	0.698	0.942	0.814	0.698	0.942	CLONAL	1	TRUE	1	0.17	2		478	838	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953730	48953730	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs3092891	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	17	248	0	ENST00000267163.4:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000267163	NM_000321.2	445	Cga/Tga	14/27	1	2	FACETS	0.581	0.433	0.758	0.581	0.433	0.758	SUBCLONAL	1	TRUE	1	0.17	2		248	344	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	73	523	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.220265890732451	3	FACETS	1	0.954	1	0.604	0.527	0.686	CLONAL	1	TRUE	1	0.17	3		523	772	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	85	577	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.17	2		577	785	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131301	202131301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748087575	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	61	507	0	ENST00000358485.4:c.269C>T	p.Pro90Leu	p.P90L	ENST00000358485	NM_001080125.1	90	cCg/cTg	2/9	0.3	2	FACETS	0.934	0.805	1			1	CLONAL	1	TRUE	NA	0.17	2		507	768	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776541	9776541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779226622	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	58	474	1	ENST00000377346.4:c.644C>T	p.Ala215Val	p.A215V	ENST00000377346	NM_005026.3	215	gCg/gTg	6/24	1	2	FACETS	0.99	0.85	1	0.99	0.85	1	CLONAL	1	TRUE	1	0.17	2		475	689	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255164	16255164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150519231	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	66	521	0	ENST00000375759.3:c.2429G>A	p.Arg810Gln	p.R810Q	ENST00000375759	NM_015001.2	810	cGg/cAg	11/15	1	2	FACETS	0.854	0.74	0.979	0.854	0.74	0.979	CLONAL	1	TRUE	1	0.17	2		521	909	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023327	27023327	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	38	329	0	ENST00000324856.7:c.437del	p.Pro146GlnfsTer86	p.P146Qfs*86	ENST00000324856	NM_006015.4	145	Ccc/cc	1/20	1	2	FACETS	0.929	0.768	1	0.929	0.768	1	CLONAL	1	TRUE	1	0.17	2		329	481	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	45	453	0	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	1	2	FACETS	0.787	0.66	0.928	0.787	0.66	0.928	CLONAL	1	TRUE	1	0.17	2		453	673	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653224	206653224	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782392890	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	53	537	0	ENST00000367120.3:c.1195G>A	p.Val399Ile	p.V399I	ENST00000367120	NM_014002.3	399	Gtc/Atc	11/22	1	2	FACETS	0.697	0.592	0.812	0.697	0.592	0.812	SUBCLONAL	1	TRUE	1	0.17	2		537	895	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710595	114710597	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs754968616	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	62	477	0	ENST00000543371.1:c.85_87del	p.Glu29del	p.E29del	ENST00000543371	NM_001198531.1	27	cAGGag/cag	1/14	1	2	FACETS	0.995	0.858	1	0.995	0.858	1	CLONAL	1	TRUE	1	0.17	2		477	733	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562678	21562678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754388230	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	61	478	0	ENST00000382592.4:c.1241C>T	p.Pro414Leu	p.P414L	ENST00000382592	NM_014572.2	414	cCg/cTg	4/8	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.17	2		478	688	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240069	41240069	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1482440466	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	15	209	0	ENST00000379561.5:c.281T>C	p.Val94Ala	p.V94A	ENST00000379561	NM_002015.3	94	gTg/gCg	1/3	1	2	FACETS	0.7	0.512	0.926	0.7	0.512	0.926	SUBCLONAL	1	TRUE	1	0.17	2		209	252	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827708	72827708	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	68	478	0	ENST00000268489.5:c.8873T>C	p.Leu2958Pro	p.L2958P	ENST00000268489	NM_006885.3	2958	cTg/cCg	9/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.17	2		478	691	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268332	46268332	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs763186106	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	51	447	0	ENST00000371998.3:c.2719C>T	p.Arg907Ter	p.R907*	ENST00000371998		907	Cga/Tga	15/23	1	2	FACETS	0.849	0.72	0.991	0.849	0.72	0.991	CLONAL	1	TRUE	1	0.17	2		447	707	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21344765	21344765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869320686	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	38	468	0	ENST00000215739.8:c.742G>A	p.Gly248Arg	p.G248R	ENST00000215739	NM_006767.3	248	Gga/Aga	8/21	1	2	FACETS	0.651	0.536	0.779	0.651	0.536	0.779	SUBCLONAL	1	TRUE	1	0.17	2		468	687	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573977	41573977	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201569846	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	61	535	1	ENST00000263253.7:c.6262C>T	p.Arg2088Trp	p.R2088W	ENST00000263253	NM_001429.3	2088	Cgg/Tgg	31/31	1	2	FACETS	0.943	0.812	1	0.943	0.812	1	CLONAL	1	TRUE	1	0.17	2		536	761	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574679	41574679	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	68	610	1	ENST00000263253.7:c.6970del	p.His2324ThrfsTer29	p.H2324Tfs*29	ENST00000263253	NM_001429.3	2322	Ccc/cc	31/31	1	2	FACETS	0.91	0.79	1	0.91	0.79	1	CLONAL	1	TRUE	1	0.17	2		611	879	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261554	142261555	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1043355995	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	35	372	0	ENST00000350721.4:c.3402dup	p.Asn1135Ter	p.N1135*	ENST00000350721	NM_001184.3	1134	-/T	17/47	1	2	FACETS	0.631	0.515	0.761	0.631	0.515	0.761	SUBCLONAL	1	TRUE	1	0.17	2		372	653	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190891	185190891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777869754	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	67	512	1	ENST00000265026.3:c.1772G>A	p.Arg591His	p.R591H	ENST00000265026	NM_004721.4	591	cGc/cAc	11/14	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.17	2		513	772	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598153	55598153	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1309976246	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	44	440	0	ENST00000288135.5:c.2350G>A	p.Ala784Thr	p.A784T	ENST00000288135	NM_000222.2	784	Gcc/Acc	16/21	1	2	FACETS	0.731	0.612	0.864	0.731	0.612	0.864	SUBCLONAL	1	TRUE	1	0.17	2		440	708	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436092	116436092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45578433	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	42	456	1	ENST00000397752.3:c.4087G>A	p.Ala1363Thr	p.A1363T	ENST00000397752	NM_000245.2	1363	Gct/Act	21/21	1	2	FACETS	0.672	0.56	0.798	0.672	0.56	0.798	SUBCLONAL	1	TRUE	1	0.17	2		457	735	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319952	8319952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1460608894	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	38	424	0	ENST00000356435.5:c.5549G>A	p.Arg1850Lys	p.R1850K	ENST00000356435		1850	aGa/aAa	34/35	1	2	FACETS	0.715	0.59	0.856	0.715	0.59	0.856	SUBCLONAL	1	TRUE	1	0.17	2		424	625	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	76	559	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.17	2		559	677	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045495	47045495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	61	282	0	ENST00000377604.3:c.2462G>A	p.Arg821His	p.R821H	ENST00000377604	NM_001204468.1	821	cGc/cAc	22/24	1	1	FACETS	0.922	0.8	1	1	0.977	1	CLONAL	2	TRUE	0	0.17	1		282	356	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1736002	1736002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	62	391	0	ENST00000378609.4:c.286C>T	p.Arg96Cys	p.R96C	ENST00000378609	NM_002074.3	96	Cgc/Tgc	7/12	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.17	2		391	630	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983121	201983121	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	52	543	0	ENST00000359651.3:c.970A>G	p.Met324Val	p.M324V	ENST00000359651		324	Atg/Gtg	7/8	1	2	FACETS	0.809	0.687	0.943	0.809	0.687	0.943	CLONAL	1	TRUE	1	0.17	2		543	756	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10794128	10794130	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	59	433	0	ENST00000361367.2:c.2511_2513del	p.Glu838del	p.E838del	ENST00000361367	NM_014633.3	836	GAA/-	20/25	1	2	FACETS	0.953	0.819	1	0.953	0.819	1	CLONAL	1	TRUE	1	0.17	2		433	728	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33680045	33680045	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	42	344	0	ENST00000308377.4:c.2036A>G	p.Asp679Gly	p.D679G	ENST00000308377	NM_152270.3	679	gAc/gGc	5/5	0.220265890732451	3	FACETS	0.939	0.783	1	0.469	0.391	0.556	CLONAL	1	TRUE	1	0.17	3		344	571	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210421	2210421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	31	437	0	ENST00000398665.3:c.1028G>A	p.Arg343His	p.R343H	ENST00000398665	NM_032482.2	343	cGc/cAc	13/28	1	2	FACETS	0.638	0.514	0.778	0.638	0.514	0.778	SUBCLONAL	1	TRUE	1	0.17	2		437	572	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227033	2227033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764534851	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	50	480	0	ENST00000398665.3:c.4513G>A	p.Ala1505Thr	p.A1505T	ENST00000398665	NM_032482.2	1505	Gca/Aca	27/28	1	2	FACETS	0.871	0.738	1	0.871	0.738	1	CLONAL	1	TRUE	1	0.17	2		480	675	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383233	42383233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781949432	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	50	517	0	ENST00000221972.3:c.253G>A	p.Glu85Lys	p.E85K	ENST00000221972	NM_021601.3	85	Gag/Aag	2/5	1	2	FACETS	0.837	0.709	0.978	0.837	0.709	0.978	CLONAL	1	TRUE	1	0.17	2		517	703	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662601	227662601	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs765204298	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	71	550	0	ENST00000305123.5:c.854G>T	p.Arg285Leu	p.R285L	ENST00000305123	NM_005544.2	285	cGc/cTc	1/2	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.17	2		550	788	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446862	29446862	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	43	415	0	ENST00000544604.2:c.2693G>A	p.Gly898Asp	p.G898D	ENST00000544604	NM_001206998.1	898	gGt/gAt	8/9	1	2	FACETS	0.927	0.775	1	0.927	0.775	1	CLONAL	1	TRUE	1	0.17	2		415	546	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225633	26225633	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767947981	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	79	644	0	ENST00000360408.1:c.251G>A	p.Arg84His	p.R84H	ENST00000360408	NM_003532.2	84	cGc/cAc	1/1	1	2	FACETS	0.869	0.762	0.985	0.869	0.762	0.985	CLONAL	1	TRUE	1	0.17	2		644	1069	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873303	151873303	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	48	461	0	ENST00000262189.6:c.9235C>T	p.Arg3079Ter	p.R3079*	ENST00000262189	NM_170606.2	3079	Cga/Tga	38/59	1	2	FACETS	0.766	0.646	0.899	0.766	0.646	0.899	SUBCLONAL	1	TRUE	1	0.17	2		461	737	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	61	287	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.79	0.681	0.908	0.79	0.681	0.908	CLONAL	1	TRUE	1	0.241740550567811	2		287	639	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	89	427	3	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.241740550567811	2		430	561	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	73	396	1	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.241740550567811	2		397	486	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	78	472	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.241740550567811	2		474	496	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	61	424	0	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	0.895	0.772	1	0.895	0.772	1	CLONAL	1	TRUE	1	0.241740550567811	2		424	564	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517762	187517762	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	32	348	0	ENST00000441802.2:c.12932del	p.Pro4311HisfsTer38	p.P4311Hfs*38	ENST00000441802	NM_005245.3	4311	cCa/ca	25/27	1	2	FACETS	0.437	0.353	0.532	0.437	0.353	0.532	SUBCLONAL	1	TRUE	1	0.241740550567811	2		348	606	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627361	37627361	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	110	343	0	ENST00000447079.4:c.1280del	p.Leu427CysfsTer9	p.L427Cfs*9	ENST00000447079	NM_015083.1	426	Ttt/tt	2/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.241740550567811	2		343	661	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	70	302	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.241740550567811	2		302	553	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510606	38510606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	72	338	0	ENST00000254066.5:c.860C>T	p.Ser287Leu	p.S287L	ENST00000254066	NM_000964.3	287	tCg/tTg	7/9	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.241740550567811	2		338	583	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445211	29445211	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	70	350	0	ENST00000389048.3:c.3514A>G	p.Ser1172Gly	p.S1172G	ENST00000389048	NM_004304.4	1172	Agc/Ggc	22/29	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.241740550567811	2		350	534	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77069989	77069990	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAT	rs149665907	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	64	350	0	ENST00000356341.3:c.548_550dup	p.Asp183dup	p.D183dup	ENST00000356341	NM_002576.4	183	gct/gATGct	6/15	1	2	FACETS	0.84	0.728	0.963	0.84	0.728	0.963	CLONAL	1	TRUE	1	0.241740550567811	2		350	630	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939260	71939260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	99	390	1	ENST00000298229.2:c.209G>A	p.Arg70His	p.R70H	ENST00000298229	NM_001567.3	70	cGc/cAc	2/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.241740550567811	2		391	619	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	87	471	0	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.241740550567811	2		471	648	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119016	3119016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	81	401	0	ENST00000078429.4:c.700G>A	p.Glu234Lys	p.E234K	ENST00000078429	NM_002067.2	234	Gaa/Aaa	5/7	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.241740550567811	2		401	582	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748660	43748661	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	82	378	0	ENST00000382044.4:c.2145dup	p.Glu716ArgfsTer9	p.E716Rfs*9	ENST00000382044	NM_001141980.1	715	-/A	12/28	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.241740550567811	2		378	637	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42851110	42851110	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	74	244	0	ENST00000398585.3:c.783del	p.Lys261AsnfsTer19	p.K261Nfs*19	ENST00000398585	NM_001135099.1	261	aaA/aa	7/14	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.241740550567811	2		244	588	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214714	36214714	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	62	380	0	ENST00000222270.7:c.3145del	p.Ala1049ArgfsTer133	p.A1049Rfs*133	ENST00000222270	NM_014727.1	1047	cGg/cg	8/37	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.241740550567811	2		380	452	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73047240	73047240	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	67	248	0	ENST00000356692.5:c.51del	p.Lys19ArgfsTer14	p.K19Rfs*14	ENST00000356692		16	aGg/ag	2/9	0.241740550567811	1	FACETS	0.907	0.79	1	0.907	0.79	1	CLONAL	1	TRUE	0	0.241740550567811	1		248	537	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829819	76829819	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	50	247	0	ENST00000373344.5:c.6222G>T	p.Glu2074Asp	p.E2074D	ENST00000373344	NM_000489.3	2074	gaG/gaT	28/35	1	2	FACETS	0.917	0.779	1	0.917	0.779	1	CLONAL	1	TRUE	1	0.241740550567811	2		247	451	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	71	456	0	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	1	2	FACETS	0.963	0.841	1	0.963	0.841	1	CLONAL	1	TRUE	1	0.241740550567811	2		456	610	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107184	11107186	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs1484395538	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	92	320	0	ENST00000358026.2:c.1778_1780del	p.Glu593del	p.E593del	ENST00000358026	NM_001128849.1	592	gcAGAa/gca	11/36	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.241740550567811	2		320	596	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225607	26225607	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	118	491	0	ENST00000360408.1:c.225A>G	p.Ile75Met	p.I75M	ENST00000360408	NM_003532.2	75	atA/atG	1/1	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.241740550567811	2		491	809	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150921733	150921733	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	89	415	0	ENST00000271640.5:c.1408del	p.Gln470LysfsTer18	p.Q470Kfs*18	ENST00000271640	NM_001145415.1	468	tCc/tc	11/22	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.241740550567811	2		415	727	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557235	187557235	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	78	349	0	ENST00000441802.2:c.4127T>C	p.Met1376Thr	p.M1376T	ENST00000441802	NM_005245.3	1376	aTg/aCg	6/27	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.241740550567811	2		349	623	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435323	56435323	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	89	468	0	ENST00000407977.2:c.1814C>T	p.Ala605Val	p.A605V	ENST00000407977		605	gCc/gTc	9/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.241740550567811	2		468	645	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164047	108164047	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	58	217	0	ENST00000278616.4:c.4619A>G	p.Asp1540Gly	p.D1540G	ENST00000278616	NM_000051.3	1540	gAc/gGc	31/63	1	2	FACETS	0.941	0.809	1	0.941	0.809	1	CLONAL	1	TRUE	1	0.241740550567811	2		217	510	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423509	116423509	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	65	273	0	ENST00000397752.3:c.3784A>G	p.Thr1262Ala	p.T1262A	ENST00000397752	NM_000245.2	1262	Acc/Gcc	19/21	1	2	FACETS	0.896	0.777	1	0.896	0.777	1	CLONAL	1	TRUE	1	0.241740550567811	2		273	600	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177637	56177638	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	61	382	0	ENST00000399503.3:c.2612dup	p.Leu871PhefsTer33	p.L871Ffs*33	ENST00000399503	NM_005921.1	870	-/T	14/20	1	2	FACETS	0.86	0.742	0.988	0.86	0.742	0.988	CLONAL	1	TRUE	1	0.241740550567811	2		382	587	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845768	151845768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	61	372	0	ENST00000262189.6:c.13244G>A	p.Gly4415Glu	p.G4415E	ENST00000262189	NM_170606.2	4415	gGa/gAa	52/59	1	2	FACETS	0.809	0.697	0.93	0.809	0.697	0.93	CLONAL	1	TRUE	1	0.241740550567811	2		372	624	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128246812	128246812	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	87	296	0	ENST00000265960.3:c.1117A>G	p.Thr373Ala	p.T373A	ENST00000265960	NM_001006617.1	373	Aca/Gca	9/12	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.241740550567811	2		296	625	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430300	181430300	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	33	215	0	ENST00000325404.1:c.152G>A	p.Trp51Ter	p.W51*	ENST00000325404	NM_003106.3	51	tGg/tAg	1/1	1	2	FACETS	0.986	0.806	1	0.986	0.806	1	CLONAL	1	TRUE	1	0.241740550567811	2		215	277	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260531	16260531	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753076589	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	122	397	0	ENST00000375759.3:c.7796C>T	p.Ser2599Leu	p.S2599L	ENST00000375759	NM_015001.2	2599	tCg/tTg	11/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.241740550567811	2		397	740	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645457	67645457	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	91	336	0	ENST00000264010.4:c.722A>G	p.Asn241Ser	p.N241S	ENST00000264010	NM_006565.3	241	aAt/aGt	3/12	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.241740550567811	2		336	731	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936092	71936092	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	41	346	0	ENST00000298229.2:c.64T>C	p.Tyr22His	p.Y22H	ENST00000298229	NM_001567.3	22	Tac/Cac	1/28	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.241740550567811	2		346	331	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433452	138433452	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	97	275	0	ENST00000289153.2:c.1160T>C	p.Phe387Ser	p.F387S	ENST00000289153	NM_006219.2	387	tTt/tCt	7/22	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.241740550567811	2		275	584	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179024	123179024	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	63	233	0	ENST00000218089.9:c.473A>T	p.Asp158Val	p.D158V	ENST00000218089	NM_001042749.1	158	gAt/gTt	8/35	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.241740550567811	2		233	431	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426733	121426733	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	63	470	0	ENST00000257555.6:c.424T>C	p.Ser142Pro	p.S142P	ENST00000257555		142	Tcc/Ccc	2/10	1	2	FACETS	0.889	0.769	1	0.889	0.769	1	CLONAL	1	TRUE	1	0.241740550567811	2		470	586	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815643	139815643	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	76	358	1	ENST00000247668.2:c.1114C>A	p.Arg372Ser	p.R372S	ENST00000247668	NM_021138.3	372	Cgc/Agc	9/11	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.241740550567811	2		359	586	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468148	31468148	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	75	285	0	ENST00000344624.3:c.2264A>T	p.Asp755Val	p.D755V	ENST00000344624		755	gAt/gTt	15/33	1	2	FACETS	0.946	0.829	1	0.946	0.829	1	CLONAL	1	TRUE	1	0.241740550567811	2		285	656	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720212	43720212	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	62	289	0	ENST00000382044.4:c.3828+2T>C		p.X1276_splice	ENST00000382044	NM_001141980.1	1276			1	2	FACETS	0.835	0.721	0.959	0.835	0.721	0.959	CLONAL	1	TRUE	1	0.241740550567811	2		289	614	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220266	55220266	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	55	291	0	ENST00000275493.2:c.656G>A	p.Cys219Tyr	p.C219Y	ENST00000275493	NM_005228.3	219	tGc/tAc	6/28	1	2	FACETS	0.942	0.807	1	0.942	0.807	1	CLONAL	1	TRUE	1	0.241740550567811	2		291	483	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512364	149512364	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	110	446	0	ENST00000261799.4:c.1076A>G	p.Asp359Gly	p.D359G	ENST00000261799	NM_002609.3	359	gAc/gGc	7/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.241740550567811	2		446	707	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158470	26158470	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	89	384	0	ENST00000289316.2:c.73A>G	p.Lys25Glu	p.K25E	ENST00000289316	NM_138720.2	25	Aag/Gag	1/2	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.241740550567811	2		384	633	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304192	65304192	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	95	305	0	ENST00000342505.4:c.2923A>G	p.Ile975Val	p.I975V	ENST00000342505	NM_002227.2	975	Ata/Gta	21/25	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.241740550567811	2		305	698	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514493	103514493	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	87	351	0	ENST00000355739.4:c.994G>T	p.Glu332Ter	p.E332*	ENST00000355739	NM_000123.3	332	Gag/Tag	8/15	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.241740550567811	2		351	634	SUCCESS
APC	324	MSKCC	GRCh37	5	112175198	112175198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068901-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	39	506	0	ENST00000257430.4:c.3907C>T	p.Gln1303Ter	p.Q1303*	ENST00000257430	NM_000038.5	1303	Caa/Taa	16/16	1	2	FACETS	0.642	0.531	0.767	0.642	0.531	0.767	SUBCLONAL	1	TRUE	1	0.19	2		506	639	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481417	140481417	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913348	NA	P-0068901-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	31	345	0	ENST00000288602.6:c.1391G>T	p.Gly464Val	p.G464V	ENST00000288602	NM_004333.4	464	gGa/gTa	11/18	1	2	FACETS	0.678	0.548	0.827	0.678	0.548	0.827	SUBCLONAL	1	TRUE	1	0.19	2		345	481	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717684	89717690	+	protein_altering_variant	In_Frame_Del	DEL	AAGTTCA	AAGTTCA	G	novel	NA	P-0068901-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	30	352	0	ENST00000371953.3:c.709_715delinsG	p.Lys237_Met239delinsVal	p.K237_M239delinsV	ENST00000371953	NM_000314.4	237	AAGTTCAtg/Gtg	7/9	1	2	FACETS	0.654	0.526	0.799	0.654	0.526	0.799	SUBCLONAL	1	TRUE	1	0.19	2		352	483	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123875203	123875203	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068901-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	39	207	0	ENST00000330479.4:c.159G>C	p.Lys53Asn	p.K53N	ENST00000330479	NM_020382.3	53	aaG/aaC	3/9	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.19	2		207	351	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56792460	56792460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068901-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	40	397	0	ENST00000308159.5:c.190C>T	p.Leu64Phe	p.L64F	ENST00000308159	NM_014669.4	64	Ctc/Ttc	3/22	1	2	FACETS	0.629	0.522	0.75	0.629	0.522	0.75	SUBCLONAL	1	TRUE	1	0.19	2		397	669	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628895	187628895	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068901-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	116	512	0	ENST00000441802.2:c.2087A>T	p.Gln696Leu	p.Q696L	ENST00000441802	NM_005245.3	696	cAg/cTg	2/27	1	2	FACETS	0.899	0.812	0.991	1	0.987	1	CLONAL	2	TRUE	1	0.19	2		512	679	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961802	41961802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068901-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	39	500	1	ENST00000219905.7:c.710C>T	p.Thr237Ile	p.T237I	ENST00000219905	NM_001164273.1	237	aCa/aTa	2/24	1	2	FACETS	0.575	0.475	0.687	0.575	0.475	0.687	SUBCLONAL	1	TRUE	1	0.19	2		501	714	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450741	70450741	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	170	431	0	ENST00000373644.4:c.5581C>T	p.Pro1861Ser	p.P1861S	ENST00000373644	NM_030625.2	1861	Cca/Tca	12/12	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.34280680009631	2		431	802	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394757	45394757	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	87	202	0	ENST00000262160.6:c.592C>G	p.His198Asp	p.H198D	ENST00000262160	NM_005901.5	198	Cac/Gac	5/11	0.339961942214795	4	FACETS	1	0.979	1	0.722	0.645	0.802	INDETERMINATE	1	TRUE	2	0.607395421859821	4		202	319	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285059	15285059	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs367543285	NA	P-0069055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	579	294	0	ENST00000263388.2:c.4556T>C	p.Leu1519Pro	p.L1519P	ENST00000263388	NM_000435.2	1519	cTg/cCg	25/33	0.607395421859821	16	FACETS	1	0.984	1			1	CLONAL	13	TRUE	NA	0.607395421859821	16		294	761	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14021913	14021913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	101	282	0	ENST00000311895.7:c.613G>A	p.Glu205Lys	p.E205K	ENST00000311895	NM_005236.2	205	Gaa/Aaa	4/11	0.599552410454414	4	FACETS	0.759	0.685	0.836	0.506	0.457	0.558	SUBCLONAL	2	TRUE	1	0.607395421859821	4		282	352	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884044	37884045	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0069055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	53	363	0	ENST00000269571.5:c.3520_3521del	p.Ser1174ProfsTer102	p.S1174Pfs*102	ENST00000269571		1172	aCT/a	27/27	0.611833578033579	3	FACETS	0.944	0.813	1	0.315	0.271	0.362	CLONAL	1	TRUE	0	0.607395421859821	3		363	241	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244287	5244287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	81	336	0	ENST00000357368.4:c.1195G>A	p.Glu399Lys	p.E399K	ENST00000357368	NM_002850.3	399	Gag/Aag	11/38	0.611833578033579	3	FACETS	1	0.979	1	0.724	0.648	0.803	CLONAL	1	TRUE	1	0.607395421859821	3		336	240	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111767	56111767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1189576862	NA	P-0069055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	37	183	0	ENST00000399503.3:c.367C>T	p.His123Tyr	p.H123Y	ENST00000399503	NM_005921.1	123	Cac/Tac	1/20	0.175266175652981	3	FACETS	0.913	0.803	1	1	0.964	1	INDETERMINATE	3	TRUE	1	0.607395421859821	3		183	58	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459233	99459237	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTT	CTCTT	-	novel	NA	P-0069055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	119	252	0	ENST00000268035.6:c.1872_1876del	p.Ser625ValfsTer55	p.S625Vfs*55	ENST00000268035	NM_000875.3	623	tcCTCTTct/tcct	9/21	0.144830399774295	5	FACETS	0.967	0.891	1	0.726	0.668	0.784	INDETERMINATE	3	TRUE	1	0.607395421859821	5		252	258	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0069117-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	86	460	0	ENST00000349496.5:c.101G>A	p.Gly34Glu	p.G34E	ENST00000349496	NM_001904.3	34	gGa/gAa	3/15	0.899378364563202	3	FACETS	1	0.943	1	0.537	0.482	0.594	CLONAL	1	TRUE	1	0.899378364563202	3		460	258	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699292	18699292	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0069117-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	76	425	0	ENST00000266497.5:c.3393T>G	p.Ile1131Met	p.I1131M	ENST00000266497		1131	atT/atG	24/31	0.899378364563202	3	FACETS	1	0.959	1	0.578	0.516	0.642	CLONAL	1	TRUE	1	0.899378364563202	3		425	212	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89815162	89815162	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	237	381	0	ENST00000389301.3:c.3253C>G	p.Leu1085Val	p.L1085V	ENST00000389301	NM_000135.2	1085	Ctg/Gtg	33/43	0.919103385710622	2	FACETS	0.999	0.976	1	0.999	0.976	1	CLONAL	2	TRUE	0	0.919103385710622	2		381	258	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191470	10191470	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs5030817	NA	P-0069315-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	69	319	0	ENST00000256474.2:c.464-1G>T		p.X155_splice	ENST00000256474	NM_000551.3	155			0.343824267130226	1	FACETS	0.896	0.785	1	0.896	0.785	1	CLONAL	1	TRUE	0	0.343824267130226	1		319	371	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62293944	62293944	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0069315-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	109	431	0	ENST00000360203.5:c.441T>G	p.His147Gln	p.H147Q	ENST00000360203	NM_001283009.1	147	caT/caG	5/35	1	2	FACETS	0.98	0.881	1	0.98	0.881	1	CLONAL	1	TRUE	1	0.343824267130226	2		431	647	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793433	242793433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs2227982	NA	P-0069353-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	26	423	0	ENST00000334409.5:c.644C>T	p.Ala215Val	p.A215V	ENST00000334409	NM_005018.2	215	gCc/gTc	5/5	0.27930503162999	1	FACETS	0.769	0.613	0.945	0.769	0.613	0.945	CLONAL	1	TRUE	0	0.286856172979627	1		423	202	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0069556-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	335	323	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.480319692785321	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.480319692785321	2		323	666	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0069556-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	95	244	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.480319692785321	3	FACETS	1	0.973	1	0.631	0.565	0.699	CLONAL	1	TRUE	1	0.480319692785321	3		244	389	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TT	rs730881673	NA	P-0069556-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	133	415	0	ENST00000304494.5:c.131_132insAA	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAAc	1/3	0.480319692785321	1	FACETS	0.946	0.866	1	0.946	0.866	1	CLONAL	1	TRUE	0	0.480319692785321	1		415	445	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441978	52441978	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069556-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	181	334	0	ENST00000460680.1:c.371del	p.Pro124LeufsTer63	p.P124Lfs*63	ENST00000460680	NM_004656.3	124	cCt/ct	5/17	0.480319692785321	2	FACETS	0.862	0.804	0.921	0.862	0.804	0.921	CLONAL	2	TRUE	0	0.480319692785321	2		334	437	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0069558-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	12	358	0				ENST00000310581	NM_198253.2	-/1132			0.539330796586267	1	FACETS	0.973	0.719	1	0.973	0.719	1	CLONAL	1	TRUE	0	0.521129688577715	1		358	35	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274589	198274589	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1193846732	NA	P-0069558-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	40	415	0	ENST00000335508.6:c.809G>A	p.Arg270Gln	p.R270Q	ENST00000335508	NM_012433.2	270	cGa/cAa	7/25	0.228401116670748	4	FACETS	0.773	0.654	0.901	0.773	0.654	0.901	INDETERMINATE	2	TRUE	2	0.521129688577715	4		415	151	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0069559-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	141	322	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.290572896177604	5	FACETS	0.86	0.792	0.93	0.86	0.792	0.93	CLONAL	3	TRUE	2	0.457128783146691	5		322	403	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0069559-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	71	286	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.457128783146691	3	FACETS	0.935	0.82	1	0.468	0.41	0.53	CLONAL	1	TRUE	1	0.457128783146691	3		286	408	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0069559-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	186	314	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.457128783146691	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	0	0.457128783146691	2		314	404	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450100	32450100	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069559-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	348	439	0	ENST00000332351.3:c.712C>A	p.Gln238Lys	p.Q238K	ENST00000332351	NM_024426.4	238	Cag/Aag	2/10	0.457128783146691	5	FACETS	0.925	0.879	0.972			1	CLONAL	3	TRUE	NA	0.457128783146691	5		439	925	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733470	85733470	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069559-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	48	357	0	ENST00000370580.1:c.542G>A	p.Arg181Lys	p.R181K	ENST00000370580	NM_003921.4	181	aGa/aAa	3/3	0.322177170454165	5	FACETS	0.531	0.448	0.623			1	SUBCLONAL	1	TRUE	NA	0.457128783146691	5		357	667	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456457	99456457	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069559-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	53	396	0	ENST00000268035.6:c.1774G>C	p.Asp592His	p.D592H	ENST00000268035	NM_000875.3	592	Gac/Cac	8/21	0.230936999180511	3	FACETS	0.469	0.399	0.545	0.156	0.133	0.182	INDETERMINATE	1	TRUE	0	0.457128783146691	3		396	608	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966738	18966738	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069559-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	193	461	0	ENST00000262803.5:c.1549G>T	p.Val517Leu	p.V517L	ENST00000262803	NM_002911.3	517	Gtg/Ttg	12/24	0.214062874552559	5	FACETS	1	0.973	1	0.728	0.676	0.781	INDETERMINATE	2	TRUE	2	0.457128783146691	5		461	652	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724162	112724162	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069559-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	85	169	0	ENST00000369452.4:c.46C>G	p.Pro16Ala	p.P16A	ENST00000369452	NM_007373.3	16	Ccc/Gcc	2/9	0.236953643935935	3	FACETS	0.921	0.827	1	0.614	0.551	0.679	INDETERMINATE	2	TRUE	0	0.457128783146691	3		169	248	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210723	2210723	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1200812026	NA	P-0069559-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	111	524	0	ENST00000398665.3:c.1220C>T	p.Ala407Val	p.A407V	ENST00000398665	NM_032482.2	407	gCt/gTt	14/28	0.214062874552559	5	FACETS	1	0.957	1	0.372	0.335	0.412	INDETERMINATE	1	TRUE	2	0.457128783146691	5		524	733	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611878	100611878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069559-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	96	312	0	ENST00000308731.7:c.1243G>A	p.Val415Ile	p.V415I	ENST00000308731	NM_000061.2	415	Gta/Ata	14/19	0.457128783146691	3	FACETS	0.965	0.862	1	0.482	0.431	0.537	CLONAL	1	TRUE	1	0.457128783146691	3		312	535	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888709	76888709	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782142791	NA	P-0069559-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	168	270	0	ENST00000373344.5:c.5120C>T	p.Ala1707Val	p.A1707V	ENST00000373344	NM_000489.3	1707	gCt/gTt	19/35	0.457128783146691	4	FACETS	1	0.984	1			1	CLONAL	2	TRUE	NA	0.457128783146691	4		270	439	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61328320	61328320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069559-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	65	278	0	ENST00000283752.5:c.131G>T	p.Gly44Val	p.G44V	ENST00000283752	NM_006919.2	44	gGa/gTa	2/8	0.457128783146691	1	FACETS	0.91	0.799	1	0.91	0.799	1	CLONAL	1	TRUE	0	0.457128783146691	1		278	241	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197840	123197840	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069559-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	62	293	0	ENST00000218089.9:c.1964G>C	p.Ser655Thr	p.S655T	ENST00000218089	NM_001042749.1	655	aGt/aCt	20/35	0.457128783146691	3	FACETS	0.861	0.747	0.984	0.431	0.373	0.492	CLONAL	1	TRUE	1	0.457128783146691	3		293	387	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115279428	115279428	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069559-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	57	283	0	ENST00000438362.2:c.589C>G	p.Gln197Glu	p.Q197E	ENST00000438362	NM_001242891.1	197	Cag/Gag	6/20	0.290572896177604	5	FACETS	0.887	0.762	1	0.296	0.254	0.341	CLONAL	1	TRUE	2	0.457128783146691	5		283	474	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371847	116371847	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069559-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	72	291	0	ENST00000397752.3:c.1326A>G	p.Ile442Met	p.I442M	ENST00000397752	NM_000245.2	442	atA/atG	3/21	0.457128783146691	5	FACETS	0.823	0.719	0.936	0.274	0.239	0.312	CLONAL	1	TRUE	2	0.457128783146691	5		291	645	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197766	66197766	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	41	342	0	ENST00000273854.3:c.2933A>G	p.Lys978Arg	p.K978R	ENST00000273854	NM_004439.5	978	aAg/aGg	17/18	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.222942771150858	2		342	343	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085972	16085972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs998174759	NA	P-0069560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	72	393	0	ENST00000281043.3:c.1148G>A	p.Arg383His	p.R383H	ENST00000281043	NM_005378.4	383	cGc/cAc	3/3	0.222824287602331	3	FACETS	1	0.898	1	1	0.898	1	CLONAL	2	TRUE	1	0.222942771150858	3		393	351	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453387	40453387	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761867798	NA	P-0069560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	35	431	0	ENST00000345506.4:c.1084G>A	p.Val362Met	p.V362M	ENST00000345506	NM_003152.3	362	Gtg/Atg	10/20	0.208691712307732	3	FACETS	0.772	0.633	0.929	0.386	0.316	0.465	CLONAL	1	TRUE	1	0.222942771150858	3		431	452	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052635	42052635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	62	383	0	ENST00000219905.7:c.7306C>T	p.Arg2436Cys	p.R2436C	ENST00000219905	NM_001164273.1	2436	Cgt/Tgt	20/24	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.222942771150858	2		383	481	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577080	7577080	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0069560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	111	423	0	ENST00000269305.4:c.858del	p.Glu287ArgfsTer58	p.E287Rfs*58	ENST00000269305	NM_001126112.2	286	gaA/ga	8/11	0.151250050475082	2	FACETS	0.914	0.83	1	1	0.982	1	CLONAL	3	TRUE	0	0.222942771150858	2		423	363	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958798	55958798	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	34	271	0	ENST00000263923.4:c.3055T>A	p.Leu1019Met	p.L1019M	ENST00000263923	NM_002253.2	1019	Ttg/Atg	22/30	1	2	FACETS	0.913	0.748	1	0.913	0.748	1	CLONAL	1	TRUE	1	0.222942771150858	2		271	334	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395909	395909	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	86	440	0	ENST00000380956.4:c.466A>G	p.Thr156Ala	p.T156A	ENST00000380956	NM_001195286.1	156	Acg/Gcg	4/9	0.222942771150858	2	FACETS	0.984	0.876	1	0.984	0.876	1	CLONAL	2	TRUE	0	0.222942771150858	2		440	392	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0069561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	8	249	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.443	0.284	0.65	0.443	0.284	0.65	SUBCLONAL	1	TRUE	1	0.12	2		249	301	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645067	86645067	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	26	298	0	ENST00000274376.6:c.1139A>G	p.Asp380Gly	p.D380G	ENST00000274376	NM_002890.2	380	gAt/gGt	8/25	1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	1	0.12	2		298	392	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0069561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	24	352	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	1	2	FACETS	1	0.797	1	1	0.797	1	CLONAL	1	TRUE	1	0.12	2		352	393	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933451	100933452	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0069561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	26	295	0	ENST00000325455.5:c.1938_1939del	p.Arg646SerfsTer19	p.R646Sfs*19	ENST00000325455	NM_001202474.3	646	agAGtt/agtt	4/8	1	2	FACETS	0.93	0.735	1	0.93	0.735	1	CLONAL	1	TRUE	1	0.12	2		295	466	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589597	67589605	+	inframe_deletion	In_Frame_Del	DEL	ACTCAGTTT	ACTCAGTTT	-	novel	NA	P-0069561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	10	250	0	ENST00000274335.5:c.1360_1368del	p.Thr454_Phe456del	p.T454_F456del	ENST00000274335		454	ACTCAGTTT/-	10/15	1	2	FACETS	0.487	0.329	0.688	0.487	0.329	0.688	SUBCLONAL	1	TRUE	1	0.12	2		250	342	SUCCESS
APC	324	MSKCC	GRCh37	5	112173560	112173561	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0069562-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	123	270	0	ENST00000257430.4:c.2274dup	p.Ala759SerfsTer16	p.A759Sfs*16	ENST00000257430	NM_000038.5	757	caa/cAaa	16/16	0.275845496132446	2	FACETS	1	0.984	1	0.714	0.649	0.781	CLONAL	1	TRUE	0	0.36589149191291	2		270	471	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0069563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	37	322	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.16	2		322	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750600586	NA	P-0069563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	43	374	0	ENST00000269305.4:c.413C>T	p.Ala138Val	p.A138V	ENST00000269305	NM_001126112.2	138	gCc/gTc	5/11	1	2	FACETS	0.619	0.516	0.734	0.619	0.516	0.734	SUBCLONAL	1	TRUE	1	0.16	2		374	868	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216087	7216087	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	58	370	0	ENST00000380728.2:c.972C>A	p.Phe324Leu	p.F324L	ENST00000380728		324	ttC/ttA	11/11	1	2	FACETS	0.906	0.777	1	0.906	0.777	1	CLONAL	1	TRUE	1	0.16	2		370	800	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589866	212589866	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561236916	NA	P-0069563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	37	378	0	ENST00000342788.4:c.676G>A	p.Val226Ile	p.V226I	ENST00000342788	NM_005235.2	226	Gtc/Atc	6/28	1	2	FACETS	0.668	0.549	0.802	0.668	0.549	0.802	SUBCLONAL	1	TRUE	1	0.16	2		378	692	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0069564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	239	439	0	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	0.111670840772179	5	FACETS	1	0.966	1	0.694	0.652	0.737	INDETERMINATE	2	TRUE	2	0.706819394905336	5		439	669	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641775	12641775	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755977690	NA	P-0069564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	283	421	0	ENST00000251849.4:c.866C>T	p.Ser289Leu	p.S289L	ENST00000251849	NM_002880.3	289	tCa/tTa	9/17	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.706819394905336	2		421	790	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0069564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	224	378	1	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	0.706819394905336	3	FACETS	1	0.939	1	0.503	0.469	0.538	CLONAL	1	TRUE	1	0.706819394905336	3		379	852	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094386	27094386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	353	451	0	ENST00000324856.7:c.3094G>A	p.Glu1032Lys	p.E1032K	ENST00000324856	NM_006015.4	1032	Gag/Aag	11/20	0.158053741444748	3	FACETS	0.755	0.718	0.793	0.755	0.718	0.793	INDETERMINATE	2	TRUE	1	0.706819394905336	3		451	895	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647089	23647089	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555461627	NA	P-0069564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	237	479	0	ENST00000261584.4:c.778C>T	p.Gln260Ter	p.Q260*	ENST00000261584	NM_024675.3	260	Cag/Tag	4/13	0.635175692048837	4	FACETS	1	0.989	1	0.431	0.403	0.46	CLONAL	1	TRUE	1	0.706819394905336	4		479	885	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628329	187628329	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	728	521	0	ENST00000441802.2:c.2653C>T	p.Arg885Ter	p.R885*	ENST00000441802	NM_005245.3	885	Cga/Tga	2/27	0.706819394905336	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.706819394905336	2		521	881	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884438	151884438	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	221	395	0	ENST00000262189.6:c.4917G>A	p.Trp1639Ter	p.W1639*	ENST00000262189	NM_170606.2	1639	tgG/tgA	33/59	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.706819394905336	2		395	607	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441780	49441780	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555195442	NA	P-0069564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	621	361	0	ENST00000301067.7:c.4204C>T	p.Gln1402Ter	p.Q1402*	ENST00000301067	NM_003482.3	1402	Cag/Tag	14/54	0.635175692048837	4	FACETS	0.862	0.834	0.89	0.862	0.834	0.89	CLONAL	3	TRUE	1	0.706819394905336	4		361	1160	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430992	181430992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1403	443	570	0	ENST00000325404.1:c.844G>A	p.Glu282Lys	p.E282K	ENST00000325404	NM_003106.3	282	Gag/Aag	1/1	0.569948394922606	6	FACETS	0.819	0.779	0.86	0.546	0.519	0.574	CLONAL	2	TRUE	3	0.706819394905336	6		570	1846	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643503	38643503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057518683	NA	P-0069564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	152	401	0	ENST00000299084.4:c.973C>T	p.Arg325Ter	p.R325*	ENST00000299084	NM_152594.2	325	Cga/Tga	7/7	0.111670840772179	5	FACETS	1	0.973	1	0.74	0.685	0.797	INDETERMINATE	2	TRUE	2	0.706819394905336	5		401	399	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428450	49428450	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0069564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	344	505	0	ENST00000301067.7:c.10356-1G>A		p.X3452_splice	ENST00000301067	NM_003482.3	3452			0.635175692048837	4	FACETS	1	0.994	1	0.458	0.434	0.484	CLONAL	1	TRUE	1	0.706819394905336	4		505	1208	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220587	123220587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1443844104	NA	P-0069564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	121	384	0	ENST00000218089.9:c.3244C>T	p.Arg1082Trp	p.R1082W	ENST00000218089	NM_001042749.1	1082	Cgg/Tgg	30/35	0.281829478144233	3	FACETS	0.727	0.659	0.8	0.242	0.219	0.267	INDETERMINATE	1	TRUE	0	0.706819394905336	3		384	637	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101160	41101160	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866048434	NA	P-0069564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	190	466	0	ENST00000373198.4:c.1196G>A	p.Arg399Lys	p.R399K	ENST00000373198	NM_133170.3	399	aGa/aAa	8/32	NA	2	FACETS	0.792	0.735	0.85			1	INDETERMINATE	1	TRUE	NA	0.706819394905336	2		466	679	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537129	80537129	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	163	368	0	ENST00000286548.4:c.269T>C	p.Met90Thr	p.M90T	ENST00000286548	NM_002072.3	90	aTg/aCg	2/7	0.706819394905336	3	FACETS	0.949	0.874	1	0.474	0.437	0.513	CLONAL	1	TRUE	1	0.706819394905336	3		368	658	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161316	185161316	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	232	416	0	ENST00000265026.3:c.743G>A	p.Gly248Asp	p.G248D	ENST00000265026	NM_004721.4	248	gGc/gAc	4/14	0.569948394922606	6	FACETS	1	0.991	1	0.479	0.446	0.513	CLONAL	1	TRUE	3	0.706819394905336	6		416	1103	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169108	32169108	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	357	471	0	ENST00000375023.3:c.3925G>A	p.Asp1309Asn	p.D1309N	ENST00000375023	NM_004557.3	1309	Gac/Aac	22/30	0.620471189980305	3	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.706819394905336	3		471	1289	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991913	72991913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	235	496	0	ENST00000268489.5:c.2132C>T	p.Pro711Leu	p.P711L	ENST00000268489	NM_006885.3	711	cCc/cTc	2/10	0.706819394905336	3	FACETS	0.969	0.905	1	0.484	0.452	0.517	CLONAL	1	TRUE	1	0.706819394905336	3		496	929	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031891	26031891	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1316	486	484	0	ENST00000244661.2:c.398G>C	p.Gly133Ala	p.G133A	ENST00000244661	NM_003537.3	133	gGa/gCa	1/1	0.706819394905336	6	FACETS	0.921	0.879	0.964			1	CLONAL	2	TRUE	NA	0.706819394905336	6		484	1802	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1685744	1685744	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0069564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	410	534	0	ENST00000378625.1:c.1357A>C	p.Ile453Leu	p.I453L	ENST00000378625	NM_001198994.1	453	Atc/Ctc	11/14	0.706819394905336	3	FACETS	1	0.99	1	0.574	0.546	0.603	CLONAL	1	TRUE	1	0.706819394905336	3		534	1368	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422855	47422855	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	316	368	0	ENST00000404338.3:c.923A>G	p.Tyr308Cys	p.Y308C	ENST00000404338	NM_004491.4	308	tAt/tGt	1/6	0.706819394905336	3	FACETS	1	0.981	1	0.543	0.512	0.574	CLONAL	1	TRUE	1	0.706819394905336	3		368	1115	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050364	176050364	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	59	289	0	ENST00000367669.3:c.1201C>G	p.Arg401Gly	p.R401G	ENST00000367669	NM_022457.5	401	Cga/Gga	11/20	0.706819394905336	3	FACETS	0.949	0.827	1	0.475	0.413	0.54	CLONAL	1	TRUE	1	0.706819394905336	3		289	238	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107267	193107267	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	105	368	0	ENST00000367435.3:c.476G>C	p.Gly159Ala	p.G159A	ENST00000367435	NM_024529.4	159	gGt/gCt	6/17	0.706819394905336	3	FACETS	0.96	0.866	1	0.48	0.433	0.529	CLONAL	1	TRUE	1	0.706819394905336	3		368	419	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164127	108164127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659069	NA	P-0069564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	117	265	0	ENST00000278616.4:c.4699G>A	p.Asp1567Asn	p.D1567N	ENST00000278616	NM_000051.3	1567	Gac/Aac	31/63	0.158053741444748	3	FACETS	1	0.986	1	0.744	0.681	0.809	INDETERMINATE	1	TRUE	1	0.706819394905336	3		265	301	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0069566-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	175	431	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.215683076955775	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.215683076955775	2		431	713	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236085	108236085	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069566-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	129	397	0	ENST00000278616.4:c.9021A>T	p.Glu3007Asp	p.E3007D	ENST00000278616	NM_000051.3	3007	gaA/gaT	63/63	0.212441966715722	4	FACETS	0.893	0.81	0.981	0.893	0.81	0.981	CLONAL	2	TRUE	2	0.215683076955775	4		397	814	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391266	139391266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752136178	NA	P-0069566-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	93	549	0	ENST00000277541.6:c.6925G>A	p.Glu2309Lys	p.E2309K	ENST00000277541	NM_017617.3	2309	Gag/Aag	34/34	0.215683076955775	3	FACETS	1	0.936	1	0.54	0.479	0.605	CLONAL	1	TRUE	1	0.215683076955775	3		549	885	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0069566-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	342	304	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	0.215683076955775	12	FACETS	1	0.949	1	0.858	0.813	0.905	CLONAL	6	TRUE	5	0.215683076955775	12		304	1097	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393570	139393570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069566-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	95	471	0	ENST00000277541.6:c.6076G>A	p.Asp2026Asn	p.D2026N	ENST00000277541	NM_017617.3	2026	Gac/Aac	32/34	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.215683076955775	NA		471	816	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391319	139391319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069566-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	93	542	0	ENST00000277541.6:c.6872G>A	p.Gly2291Glu	p.G2291E	ENST00000277541	NM_017617.3	2291	gGa/gAa	34/34	0.215683076955775	3	FACETS	1	0.958	1	0.581	0.516	0.651	CLONAL	1	TRUE	1	0.215683076955775	3		542	822	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039278	47039278	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0069566-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	73	488	0	ENST00000377604.3:c.902-1G>T		p.X301_splice	ENST00000377604	NM_001204468.1	301			1	2	FACETS	0.973	0.85	1	0.973	0.85	1	CLONAL	1	TRUE	1	0.215683076955775	2		488	696	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259641	11259641	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069566-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	145	448	0	ENST00000361445.4:c.4064A>T	p.Gln1355Leu	p.Q1355L	ENST00000361445	NM_004958.3	1355	cAg/cTg	27/58	0.215683076955775	3	FACETS	0.977	0.893	1	0.977	0.893	1	CLONAL	2	TRUE	1	0.215683076955775	3		448	762	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157488254	157488254	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs780818465	NA	P-0069566-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	161	410	0	ENST00000346085.5:c.2960C>G	p.Ser987Cys	p.S987C	ENST00000346085	NM_020732.3	987	tCt/tGt	10/20	0.212441966715722	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	2	0.215683076955775	4		410	845	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082379	16082379	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069566-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	150	466	0	ENST00000281043.3:c.193C>G	p.Arg65Gly	p.R65G	ENST00000281043	NM_005378.4	65	Cgt/Ggt	2/3	0.215683076955775	3	FACETS	0.97	0.888	1	0.97	0.888	1	CLONAL	2	TRUE	1	0.215683076955775	3		466	794	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923733	39923734	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0069566-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	128	444	0	ENST00000378444.4:c.3357_3358delinsTT	p.Gln1119_Val1120delinsHisLeu	p.Q1119_V1120delinsHL	ENST00000378444	NM_001123385.1	1119	caGGtg/caTTtg	7/15	1	2	FACETS	0.839	0.762	0.921	1	0.988	1	CLONAL	2	TRUE	1	0.215683076955775	2		444	707	SUCCESS
BTK	695	MSKCC	GRCh37	X	100604933	100604933	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069566-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	93	217	0	ENST00000308731.7:c.1920G>C	p.Glu640Asp	p.E640D	ENST00000308731	NM_000061.2	640	gaG/gaC	19/19	0.215683076955775	1	FACETS	0.991	0.888	1	1	0.986	1	CLONAL	2	TRUE	0	0.215683076955775	1		217	388	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248179	110248179	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069566-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	145	282	0	ENST00000374672.4:c.1293C>G	p.Asp431Glu	p.D431E	ENST00000374672	NM_004235.4	431	gaC/gaG	5/5	0.215683076955775	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.215683076955775	2		282	620	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390648	139390648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069566-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	98	470	0	ENST00000277541.6:c.7543G>A	p.Glu2515Lys	p.E2515K	ENST00000277541	NM_017617.3	2515	Gag/Aag	34/34	0.215683076955775	3	FACETS	1	0.958	1	0.575	0.512	0.642	CLONAL	1	TRUE	1	0.215683076955775	3		470	875	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942861	68942861	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069566-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	53	376	0	ENST00000288368.4:c.673G>T	p.Glu225Ter	p.E225*	ENST00000288368	NM_024870.2	225	Gag/Tag	6/40	0.215683076955775	4	FACETS	0.838	0.713	0.975	0.279	0.237	0.325	CLONAL	1	TRUE	1	0.215683076955775	4		376	713	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121444	108121444	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069566-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	90	302	0	ENST00000278616.4:c.1252C>T	p.Gln418Ter	p.Q418*	ENST00000278616	NM_000051.3	418	Caa/Taa	10/63	0.212441966715722	4	FACETS	0.861	0.765	0.963	0.861	0.765	0.963	CLONAL	2	TRUE	2	0.215683076955775	4		302	589	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375051	31375051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069566-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	171	473	0	ENST00000328111.2:c.448G>A	p.Ala150Thr	p.A150T	ENST00000328111	NM_006892.3	150	Gca/Aca	6/23	0.215683076955775	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.215683076955775	3		473	822	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0069567-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	42	285	3	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.294364623339861	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	2	TRUE	0	0.381176060397519	2		288	100	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069567-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	60	475	0	ENST00000269305.4:c.569del	p.Pro190LeufsTer57	p.P190Lfs*57	ENST00000269305	NM_001126112.2	190	cCt/ct	6/11	0.221997708782995	3	FACETS	0.966	0.847	1	0.644	0.564	0.728	INDETERMINATE	2	TRUE	0	0.381176060397519	3		475	194	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222932	36222932	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374674556	NA	P-0069567-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	53	517	0	ENST00000222270.7:c.5561C>T	p.Pro1854Leu	p.P1854L	ENST00000222270	NM_014727.1	1854	cCt/cTt	27/37	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.381176060397519	2		517	256	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69000032	69000032	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069567-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	20	284	0	ENST00000288368.4:c.2101G>A	p.Ala701Thr	p.A701T	ENST00000288368	NM_024870.2	701	Gct/Act	19/40	0.381176060397519	1	FACETS	0.779	0.605	0.976	0.779	0.605	0.976	CLONAL	1	TRUE	0	0.381176060397519	1		284	109	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374987	45374987	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069567-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	28	337	0	ENST00000262160.6:c.856G>T	p.Val286Phe	p.V286F	ENST00000262160	NM_005901.5	286	Gtt/Ttt	8/11	0.308021187009597	2	FACETS	0.807	0.663	0.962	0.807	0.663	0.962	CLONAL	2	TRUE	0	0.381176060397519	2		337	91	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038524	47038524	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069583-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	280	177	0	ENST00000377604.3:c.686G>T	p.Arg229Leu	p.R229L	ENST00000377604	NM_001204468.1	229	cGc/cTc	8/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		177	308	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0069585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	30	253	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		253	223	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937678	76937678	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	69	304	0	ENST00000373344.5:c.3070G>T	p.Glu1024Ter	p.E1024*	ENST00000373344	NM_000489.3	1024	Gaa/Taa	9/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		304	484	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324464	31324464	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1168937188	NA	P-0069585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	56	236	0	ENST00000412585.2:c.343+1G>A		p.X115_splice	ENST00000412585	NM_005514.6	115			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		236	484	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910793	29910793	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs41555312	NA	P-0069585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	106	264	0	ENST00000376809.5:c.333G>C	p.Gln111His	p.Q111H	ENST00000376809	NM_002116.7	111	caG/caC	2/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		264	508	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910667	29910667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	112	402	0	ENST00000376809.5:c.207G>A	p.Met69Ile	p.M69I	ENST00000376809	NM_002116.7	69	atG/atA	2/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		402	686	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138384007	138384007	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs150848927	NA	P-0069585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	98	200	0	ENST00000289153.2:c.2543C>G	p.Ser848Cys	p.S848C	ENST00000289153	NM_006219.2	848	tCt/tGt	18/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		200	590	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0069586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	19	208	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		208	207	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577569	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGAACTGTTACA	CAGGAACTGTTACA	-	novel	NA	P-0069586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	69	310	0	ENST00000269305.4:c.712_725del	p.Cys238HisfsTer21	p.C238Hfs*21	ENST00000269305	NM_001126112.2	238	TGTAACAGTTCCTGc/c	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		310	448	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76931793	76931793	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	17	238	0	ENST00000373344.5:c.3737G>A	p.Gly1246Glu	p.G1246E	ENST00000373344	NM_000489.3	1246	gGa/gAa	10/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		238	270	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971200	21971226	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCATGACCTGCCAGAGAGAACAGAAT	ATCATGACCTGCCAGAGAGAACAGAAT	-	novel	NA	P-0069586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	59	367	0	ENST00000304494.5:c.151-19_158del		p.X51_splice	ENST00000304494	NM_000077.4	51		2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		367	445	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0069587-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	113	441	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		441	560	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591925	48591925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660556	NA	P-0069587-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	79	317	0	ENST00000342988.3:c.1088G>A	p.Cys363Tyr	p.C363Y	ENST00000342988	NM_005359.5	363	tGt/tAt	9/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		317	524	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503835	186503835	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069587-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	42	240	0	ENST00000323963.5:c.512A>G	p.Tyr171Cys	p.Y171C	ENST00000323963		171	tAc/tGc	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		240	594	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844182	68844184	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0069587-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	47	304	0	ENST00000261769.5:c.774_776del	p.Asn258del	p.N258del	ENST00000261769	NM_004360.3	257	gACAac/gac	6/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		304	485	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591825	48591825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767342	NA	P-0069588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	35	341	0	ENST00000342988.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000342988	NM_005359.5	330	Gaa/Aaa	9/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		341	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs967461896	NA	P-0069588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	227	488	0	ENST00000269305.4:c.526T>C	p.Cys176Arg	p.C176R	ENST00000269305	NM_001126112.2	176	Tgc/Cgc	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		488	701	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247328	153247328	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	275	341	0	ENST00000281708.4:c.1474C>T	p.Gln492Ter	p.Q492*	ENST00000281708	NM_033632.3	492	Cag/Tag	10/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		341	645	SUCCESS
APC	324	MSKCC	GRCh37	5	112175707	112175707	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0069588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	299	425	0	ENST00000257430.4:c.4418del	p.Asn1473MetfsTer34	p.N1473Mfs*34	ENST00000257430	NM_000038.5	1472	gtA/gt	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		425	655	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593520	48593520	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	95	254	0	ENST00000342988.3:c.1271A>T	p.Asp424Val	p.D424V	ENST00000342988	NM_005359.5	424	gAt/gTt	10/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		254	372	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067107	143067107	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	102	268	0	ENST00000262992.4:c.1606A>T	p.Ile536Phe	p.I536F	ENST00000262992	NM_001101669.1	536	Att/Ttt	16/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		268	541	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130309	11130309	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	108	374	0	ENST00000358026.2:c.2548A>G	p.Ser850Gly	p.S850G	ENST00000358026	NM_001128849.1	850	Agt/Ggt	18/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		374	668	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118901	70118901	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	201	477	0	ENST00000245479.2:c.473C>A	p.Ala158Glu	p.A158E	ENST00000245479	NM_000346.3	158	gCg/gAg	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		477	753	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78935264	78935264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	192	404	0	ENST00000306801.3:c.3676C>T	p.His1226Tyr	p.H1226Y	ENST00000306801	NM_020761.2	1226	Cac/Tac	31/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		404	665	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358631	67358631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	35	408	0	ENST00000327367.4:c.139C>T	p.Gln47Ter	p.Q47*	ENST00000327367	NM_005902.3	47	Cag/Tag	1/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		408	576	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739699	41739699	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	79	375	0	ENST00000242208.4:c.274G>C	p.Val92Leu	p.V92L	ENST00000242208	NM_002192.2	92	Gtg/Ctg	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		375	717	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121912580	NA	P-0069589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	97	273	0	ENST00000342988.3:c.1157G>T	p.Gly386Val	p.G386V	ENST00000342988	NM_005359.5	386	gGt/gTt	10/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		273	414	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540003	187540003	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	104	340	0	ENST00000441802.2:c.7737C>G	p.Phe2579Leu	p.F2579L	ENST00000441802	NM_005245.3	2579	ttC/ttG	10/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		340	523	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89842203	89842203	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs533599861	NA	P-0069589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	102	312	0	ENST00000389301.3:c.1847C>G	p.Ser616Cys	p.S616C	ENST00000389301	NM_000135.2	616	tCt/tGt	21/43	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		312	439	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829756	76829756	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0069589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	68	242	0	ENST00000373344.5:c.6285del	p.Lys2096ArgfsTer13	p.K2096Rfs*13	ENST00000373344	NM_000489.3	2095	agG/ag	28/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		242	357	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190771	106190771	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0069591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	83	239	0	ENST00000380013.4:c.4050del	p.Glu1350AspfsTer13	p.E1350Dfs*13	ENST00000380013	NM_001127208.2	1350	gAa/ga	9/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		239	395	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38785083	38785083	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	131	304	0	ENST00000348513.6:c.1190A>T	p.Glu397Val	p.E397V	ENST00000348513	NM_003079.4	397	gAg/gTg	11/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		304	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0069593-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	551	409	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.744662722358964	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.743173709969254	2		409	650	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738654	145738654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753536598	NA	P-0069593-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	212	413	0	ENST00000428558.2:c.2410C>T	p.Arg804Trp	p.R804W	ENST00000428558	NM_004260.3	804	Cgg/Tgg	15/22	0.545552182131237	4	FACETS	0.821	0.761	0.882	0.274	0.253	0.295	CLONAL	1	TRUE	1	0.743173709969254	4		413	1212	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427309	427309	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069593-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	154	284	0	ENST00000399788.2:c.2860C>T	p.Arg954Ter	p.R954*	ENST00000399788	NM_001042603.1	954	Cga/Tga	19/28	0.744662722358964	2	FACETS	0.765	0.704	0.827	0.382	0.352	0.414	SUBCLONAL	1	TRUE	0	0.743173709969254	2		284	542	SUCCESS
AR	367	MSKCC	GRCh37	X	66905891	66905891	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069593-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	114	169	0	ENST00000374690.3:c.1808C>G	p.Thr603Ser	p.T603S	ENST00000374690	NM_000044.3	603	aCt/aGt	3/8	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.743173709969254	1		169	165	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220665	1220665	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1339614614	NA	P-0069593-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	283	403	2	ENST00000326873.7:c.683T>C	p.Leu228Pro	p.L228P	ENST00000326873	NM_000455.4	228	cTg/cCg	5/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.743173709969254	2		405	683	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592273	29592274	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0069593-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	248	210	0	ENST00000356175.3:c.4688_4689insGG	p.Phe1563LeufsTer5	p.F1563Lfs*5	ENST00000356175	NM_000267.3	1563	ttc/ttGGc	35/57	0.744662722358964	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.743173709969254	2		210	286	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645445	215645445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782436	NA	P-0069593-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	213	334	0	ENST00000260947.4:c.1153G>A	p.Asp385Asn	p.D385N	ENST00000260947	NM_000465.2	385	Gat/Aat	4/11	0.744662722358964	3	FACETS	1	0.979	1	0.558	0.521	0.597	CLONAL	1	TRUE	1	0.743173709969254	3		334	704	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151919136	151919136	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069593-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	365	230	1	ENST00000262189.6:c.3449G>C	p.Cys1150Ser	p.C1150S	ENST00000262189	NM_170606.2	1150	tGc/tCc	22/59	0.744662722358964	4	FACETS	0.934	0.897	0.971	1	0.996	1	CLONAL	3	TRUE	2	0.743173709969254	4		231	611	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980373	7980373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069593-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	62	359	0	ENST00000319144.4:c.1210C>T	p.Leu404Phe	p.L404F	ENST00000319144	NM_001139.2	404	Ctc/Ttc	9/15	0.744662722358964	2	FACETS	0.254	0.219	0.292	0.127	0.109	0.146	SUBCLONAL	1	TRUE	0	0.743173709969254	2		359	657	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0069595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	187	300	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.237274547746607	10	FACETS	0.972	0.911	1	1	0.98	1	CLONAL	8	FALSE	3	0.237274547746607	10		300	395	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685287	89685287	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	68	248	0	ENST00000371953.3:c.182A>C	p.His61Pro	p.H61P	ENST00000371953	NM_000314.4	61	cAt/cCt	3/9	0.237274547746607	3	FACETS	0.902	0.795	1	0.902	0.795	1	CLONAL	3	FALSE	0	0.237274547746607	3		248	237	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946370	2946370	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201877328	NA	P-0069595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	129	350	0	ENST00000396946.4:c.3367G>A	p.Asp1123Asn	p.D1123N	ENST00000396946	NM_032415.4	1123	Gac/Aac	25/25	0.237274547746607	10	FACETS	1	0.932	1	0.587	0.535	0.641	CLONAL	4	FALSE	3	0.237274547746607	10		350	516	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427735	72427735	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	86	358	0	ENST00000477973.2:c.755T>C	p.Val252Ala	p.V252A	ENST00000477973	NM_012234.5	252	gTg/gCg	4/4	0.237274547746607	2	FACETS	0.888	0.79	0.992	0.888	0.79	0.992	CLONAL	2	FALSE	0	0.237274547746607	2		358	408	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106519993	106519993	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	44	241	0	ENST00000359195.3:c.2421G>C	p.Lys807Asn	p.K807N	ENST00000359195	NM_002649.2	807	aaG/aaC	6/11	0.237274547746607	10	FACETS	1	0.899	1	0.312	0.262	0.366	CLONAL	2	FALSE	3	0.237274547746607	10		241	331	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652321	36652321	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	105	311	0	ENST00000244741.5:c.443C>T	p.Thr148Ile	p.T148I	ENST00000244741	NM_000389.4	148	aCa/aTa	2/3	0.237274547746607	5	FACETS	0.98	0.885	1	0.735	0.664	0.81	CLONAL	3	FALSE	1	0.237274547746607	5		311	408	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129063	30129063	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	60	336	0	ENST00000263025.4:c.703C>G	p.Leu235Val	p.L235V	ENST00000263025	NM_002746.2	235	Ctg/Gtg	5/9	0.237274547746607	6	FACETS	1	0.966	1	0.356	0.307	0.41	CLONAL	1	FALSE	2	0.237274547746607	6		336	523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0069596-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	63	312	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.159561591580072	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.159561591580072	1		312	618	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0069596-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	43	276	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.159561591580072	1	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	0	0.159561591580072	1		276	468	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798990	45798990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069596-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	64	400	0	ENST00000450313.1:c.355G>A	p.Asp119Asn	p.D119N	ENST00000450313	NM_012222.2	119	Gat/Aat	4/16	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.159561591580072	2		400	790	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332731	65332731	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069596-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	66	386	0	ENST00000342505.4:c.808T>G	p.Tyr270Asp	p.Y270D	ENST00000342505	NM_002227.2	270	Tac/Gac	7/25	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.159561591580072	2		386	769	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175747	176175747	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069596-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	55	389	0	ENST00000367669.3:c.368T>A	p.Leu123His	p.L123H	ENST00000367669	NM_022457.5	123	cTc/cAc	1/20	1	2	FACETS	0.981	0.838	1	0.981	0.838	1	CLONAL	1	TRUE	1	0.159561591580072	2		389	703	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871247	12871247	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069596-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	39	285	0	ENST00000228872.4:c.474C>A	p.Asp158Glu	p.D158E	ENST00000228872	NM_004064.3	158	gaC/gaA	1/3	0.159561591580072	1	FACETS	0.862	0.714	1	0.862	0.714	1	CLONAL	1	TRUE	0	0.159561591580072	1		285	522	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369210	40369210	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069596-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	70	360	0	ENST00000293328.3:c.1348G>A	p.Val450Ile	p.V450I	ENST00000293328	NM_012448.3	450	Gtt/Att	11/19	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.159561591580072	2		360	719	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591843	48591843	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069596-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	53	367	0	ENST00000342988.3:c.1006G>T	p.Gly336Ter	p.G336*	ENST00000342988	NM_005359.5	336	Gga/Tga	9/12	0.159561591580072	1	FACETS	0.886	0.754	1	0.886	0.754	1	CLONAL	1	TRUE	0	0.159561591580072	1		367	690	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219959	5219959	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069596-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	44	277	0	ENST00000357368.4:c.3756G>C	p.Lys1252Asn	p.K1252N	ENST00000357368	NM_002850.3	1252	aaG/aaC	22/38	0.159561591580072	1	FACETS	0.958	0.803	1	0.958	0.803	1	CLONAL	1	TRUE	0	0.159561591580072	1		277	530	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971654	18971654	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069596-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	46	282	0	ENST00000262803.5:c.2320G>T	p.Glu774Ter	p.E774*	ENST00000262803	NM_002911.3	774	Gag/Tag	17/24	1	2	FACETS	0.941	0.791	1	0.941	0.791	1	CLONAL	1	TRUE	1	0.159561591580072	2		282	613	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5029800	5029800	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069596-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	36	281	0	ENST00000381652.3:c.244C>T	p.His82Tyr	p.H82Y	ENST00000381652	NM_004972.3	82	Cat/Tat	4/25	1	2	FACETS	0.864	0.71	1	0.864	0.71	1	CLONAL	1	TRUE	1	0.159561591580072	2		281	522	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0069597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	198	329	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.326200843948145	2	FACETS	0.964	0.899	1	0.964	0.899	1	CLONAL	2	TRUE	0	0.36616194832613	2		329	561	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972428	81972428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1341635199	NA	P-0069597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	71	271	0	ENST00000359376.3:c.3221C>T	p.Pro1074Leu	p.P1074L	ENST00000359376	NM_002661.3	1074	cCc/cTc	29/33	0.289206612195993	3	FACETS	0.794	0.693	0.902	0.397	0.346	0.451	CLONAL	1	TRUE	1	0.36616194832613	3		271	578	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285566	46285566	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	66	223	0	ENST00000334344.6:c.4926G>A	p.Trp1642Ter	p.W1642*	ENST00000334344	NM_152641.2	1642	tgG/tgA	17/21	0.270818653186784	1	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	0	0.36616194832613	1		223	286	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561474	141561474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772070879	NA	P-0069597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	170	417	1	ENST00000220592.5:c.1331C>T	p.Thr444Met	p.T444M	ENST00000220592	NM_012154.3	444	aCg/aTg	11/19	0.273290543960342	4	FACETS	0.958	0.884	1	0.958	0.884	1	CLONAL	2	TRUE	2	0.36616194832613	4		418	662	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5207979	5207979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs115470613	NA	P-0069597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	141	389	2	ENST00000357368.4:c.5732C>T	p.Thr1911Met	p.T1911M	ENST00000357368	NM_002850.3	1911	aCg/aTg	37/38	0.357531634355045	2	FACETS	0.752	0.689	0.817	0.752	0.689	0.817	SUBCLONAL	2	TRUE	0	0.36616194832613	2		391	512	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106433	27106434	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0069597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	281	382	1	ENST00000324856.7:c.6046dup	p.Leu2016ProfsTer17	p.L2016Pfs*17	ENST00000324856	NM_006015.4	2015	atc/atCc	20/20	0.309748796048152	3	FACETS	0.877	0.83	0.925	0.877	0.83	0.925	CLONAL	3	TRUE	0	0.36616194832613	3		383	690	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0069598-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	113	331	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.144485962067212	3	FACETS	1	0.976	1	0.629	0.568	0.692	INDETERMINATE	1	TRUE	1	0.43	3		331	508	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041662	47041662	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0069598-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	79	324	0	ENST00000377604.3:c.1887del	p.Ala631HisfsTer73	p.A631Hfs*73	ENST00000377604	NM_001204468.1	629	acA/ac	17/24	1	2	FACETS	0.78	0.688	0.878	0.78	0.688	0.878	SUBCLONAL	1	TRUE	1	0.43	2		324	471	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0069599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	53	112	0				ENST00000310581	NM_198253.2	-/1132			0.131141475095448	0	FACETS	0.585	0.5	0.677			1	INDETERMINATE	1	TRUE	0	0.322300711145234	0		112	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0069599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	63	457	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	NA	2	FACETS	0.473	0.408	0.544			1	INDETERMINATE	1	TRUE	NA	0.322300711145234	2		457	826	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717704	89717704	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0069599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	76	263	0	ENST00000371953.3:c.731del	p.Pro244LeufsTer12	p.P244Lfs*12	ENST00000371953	NM_000314.4	243	ttC/tt	7/9	0.322300711145234	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.322300711145234	1		263	313	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624268	89624268	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	67	158	0	ENST00000371953.3:c.42G>C	p.Arg14Ser	p.R14S	ENST00000371953	NM_000314.4	14	agG/agC	1/9	0.322300711145234	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.322300711145234	1		158	275	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860139	152860139	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0069599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	20	153	0	ENST00000406277.2:c.291-2A>G		p.X97_splice	ENST00000406277	NM_152274.4	97			1		FACETS		0.267	0.446				SUBCLONAL	1	TRUE	0	0.322300711145234	1		153	298	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133236095	133236095	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	64	328	1	ENST00000320574.5:c.3061G>A	p.Ala1021Thr	p.A1021T	ENST00000320574	NM_006231.2	1021	Gca/Aca	26/49	1	2	FACETS	0.759	0.658	0.869	0.759	0.658	0.869	SUBCLONAL	1	TRUE	1	0.322300711145234	2		329	523	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120783395	120783395	+	stop_lost	Nonstop_Mutation	SNP	C	C	A	novel	NA	P-0069599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	89	330	0	ENST00000257552.2:c.1088G>T	p.Ter363LeuextTer19	p.*363Lext*19	ENST00000257552	NM_002442.3	363	tGa/tTa	14/15	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.322300711145234	2		330	529	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0069603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	81	274	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.28	2		274	399	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061191	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069604-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	101	374	0	ENST00000250448.2:c.798C>G	p.Phe266Leu	p.F266L	ENST00000250448	NM_004496.3	266	ttC/ttG	2/2	0.125799176009068	3	FACETS	0.836	0.749	0.928	0.836	0.749	0.928	INDETERMINATE	2	TRUE	1	0.231636832618112	3		374	582	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0069604-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	32	312	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	0.618	0.501	0.75	0.618	0.501	0.75	SUBCLONAL	1	TRUE	1	0.231636832618112	2		312	447	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719758	190719758	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069604-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	41	306	0	ENST00000441310.2:c.1760C>G	p.Pro587Arg	p.P587R	ENST00000441310	NM_000534.4	587	cCt/cGt	9/13	1	2	FACETS	0.908	0.757	1	0.908	0.757	1	CLONAL	1	TRUE	1	0.231636832618112	2		306	390	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519020	103519591	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCCATGGAAGCAGAGGCGCAGTGCGCCATCCTGGACCTGACTGATCAGACTTCCGGAACCATCACTGATGACAGTGATATCTGGCTGTTTGGAGCGCGGCATGTCTATAGAAACTTTTTTAATAAAAACAAGTTTGTAGAATATTATCAATATGTGGACTTTCACAATCAATTGGGTAAGACTTCAGAGTCTTTTTGATTACTTTCTGACATTTACCTTCAGAGTTTGTCCTAGGAAGTTTTCTTTCCAAGGAACTAGTTTGATGCATTGATGGAAATTGCAGGTCTATGCAAATTTTTATATGAGTGATCTTTGGCTTATATAGAGGAATAGGATTTTAAACATTTGAATTAAGGAATTAAAGTCCTAGTATGTTTAGGTAGTTAATCAACTGACTTAGTTAAACTTTGACTAGTTACCCGAGATCTCCACAGTGAACAAAAGGTGGTGGAGAGGGGAAGCAGGCCGCGCCTGGGCCTGTATTCGGGTTTCTGGCACTGATCTTCTTCTGTTCATCCAGCAAATATATGTTTGGTGACTCCTATATGCCAGTTGTTCTTAACAAGAGGGA	TCCCATGGAAGCAGAGGCGCAGTGCGCCATCCTGGACCTGACTGATCAGACTTCCGGAACCATCACTGATGACAGTGATATCTGGCTGTTTGGAGCGCGGCATGTCTATAGAAACTTTTTTAATAAAAACAAGTTTGTAGAATATTATCAATATGTGGACTTTCACAATCAATTGGGTAAGACTTCAGAGTCTTTTTGATTACTTTCTGACATTTACCTTCAGAGTTTGTCCTAGGAAGTTTTCTTTCCAAGGAACTAGTTTGATGCATTGATGGAAATTGCAGGTCTATGCAAATTTTTATATGAGTGATCTTTGGCTTATATAGAGGAATAGGATTTTAAACATTTGAATTAAGGAATTAAAGTCCTAGTATGTTTAGGTAGTTAATCAACTGACTTAGTTAAACTTTGACTAGTTACCCGAGATCTCCACAGTGAACAAAAGGTGGTGGAGAGGGGAAGCAGGCCGCGCCTGGGCCTGTATTCGGGTTTCTGGCACTGATCTTCTTCTGTTCATCCAGCAAATATATGTTTGGTGACTCCTATATGCCAGTTGTTCTTAACAAGAGGGA	-	novel	NA	P-0069604-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	26	315	0	ENST00000355739.4:c.2358_2533+396del		p.X786_splice	ENST00000355739	NM_000123.3	786		11/15	1	2	FACETS	0.514	0.406	0.637	0.514	0.406	0.637	SUBCLONAL	1	TRUE	1	0.231636832618112	2		315	437	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367109	40367110	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0069604-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	31	450	0	ENST00000397332.2:c.87_88del	p.Asp30HisfsTer14	p.D30Hfs*14	ENST00000397332	NM_001033082.2	29	gcGGac/gcac	2/3	1	2	FACETS	0.488	0.394	0.596	0.488	0.394	0.596	SUBCLONAL	1	TRUE	1	0.231636832618112	2		450	548	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438532	49438532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069604-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	52	257	0	ENST00000301067.7:c.4958G>A	p.Gly1653Asp	p.G1653D	ENST00000301067	NM_003482.3	1653	gGt/gAt	19/54	0.208867672536249	3	FACETS	0.994	0.847	1	0.497	0.423	0.578	CLONAL	1	TRUE	1	0.231636832618112	3		257	504	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020471	14020471	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1436917947	NA	P-0069604-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	54	276	0	ENST00000311895.7:c.442A>C	p.Ile148Leu	p.I148L	ENST00000311895	NM_005236.2	148	Atc/Ctc	3/11	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.231636832618112	2		276	453	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	126	287	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.290540916716267	2		287	602	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	36	514	2	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.404	0.331	0.486	0.404	0.331	0.486	SUBCLONAL	1	TRUE	1	0.290540916716267	2		516	613	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907421	32907421	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359306	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	102	325	2	ENST00000380152.3:c.1813del	p.Ile605TyrfsTer9	p.I605Yfs*9	ENST00000380152		602	ggA/gg	10/27	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.290540916716267	2		327	648	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	131	475	2	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.290540916716267	2		477	708	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	85	246	2	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.290540916716267	2		248	460	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	129	243	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.290540916716267	2		246	617	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913286	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	46	168	0	ENST00000263967.3:c.1636C>G	p.Gln546Glu	p.Q546E	ENST00000263967	NM_006218.2	546	Cag/Gag	10/21	1	2	FACETS	0.993	0.84	1	0.993	0.84	1	CLONAL	1	TRUE	1	0.290540916716267	2		168	319	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	182	319	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.822	0.76	0.886	1	0.991	1	CLONAL	2	TRUE	1	0.290540916716267	2		319	762	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	92	393	2	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.952	0.847	1	0.952	0.847	1	CLONAL	1	TRUE	1	0.290540916716267	2		395	665	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968322	2968323	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762770988	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	59	308	0	ENST00000396946.4:c.1663dup	p.Arg555ProfsTer38	p.R555Pfs*38	ENST00000396946	NM_032415.4	555	cgg/cCgg	13/25	1	2	FACETS	0.846	0.729	0.973	0.846	0.729	0.973	CLONAL	1	TRUE	1	0.290540916716267	2		308	480	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671655	67671655	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1400980130	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	38	342	1	ENST00000264010.4:c.2070del	p.Glu691SerfsTer30	p.E691Sfs*30	ENST00000264010	NM_006565.3	688	gtA/gt	12/12	0.290540916716267	1	FACETS	0.358	0.295	0.428	0.358	0.295	0.428	SUBCLONAL	1	TRUE	0	0.290540916716267	1		343	625	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692981	89692982	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	35	314	0	ENST00000371953.3:c.469dup	p.Glu157GlyfsTer23	p.E157Gfs*23	ENST00000371953	NM_000314.4	155	-/G	5/9	1	2	FACETS	0.445	0.364	0.537	0.445	0.364	0.537	SUBCLONAL	1	TRUE	1	0.290540916716267	2		314	541	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	203	434	0	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	0.182506891678974	3	FACETS	0.963	0.894	1	0.963	0.894	1	CLONAL	2	TRUE	1	0.290540916716267	3		434	831	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	72	282	6	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	1	2	FACETS	0.961	0.841	1	0.961	0.841	1	CLONAL	1	TRUE	1	0.290540916716267	2		288	516	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	123	327	0	ENST00000281708.4:c.1393C>A	p.Arg465Ser	p.R465S	ENST00000281708	NM_033632.3	465	Cgt/Agt	9/12	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.290540916716267	2		327	601	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100727	8100728	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs771019738	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	134	355	2	ENST00000346208.3:c.708dup	p.Ser237GlnfsTer66	p.S237Qfs*66	ENST00000346208		234	ttc/ttCc	3/6	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.290540916716267	2		357	647	SUCCESS
APC	324	MSKCC	GRCh37	5	112175101	112175101	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs587783033	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	113	293	0	ENST00000257430.4:c.3814del	p.Ser1272GlnfsTer16	p.S1272Qfs*16	ENST00000257430	NM_000038.5	1270	tgT/tg	16/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.290540916716267	2		293	582	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801727	3801727	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs777015995	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	145	308	0	ENST00000262367.5:c.3779C>T	p.Thr1260Met	p.T1260M	ENST00000262367	NM_004380.2	1260	aCg/aTg	20/31	1	2	FACETS	0.874	0.801	0.95	1	0.99	1	CLONAL	2	TRUE	1	0.290540916716267	2		308	571	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524567	103524568	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs759551120	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	87	275	0	ENST00000355739.4:c.2705dup	p.Asn902LysfsTer7	p.N902Kfs*7	ENST00000355739	NM_000123.3	900	caa/cAaa	13/15	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.290540916716267	2		275	597	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416952	416953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs771545848	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	105	382	7	ENST00000399788.2:c.3597dup	p.Gly1200ArgfsTer7	p.G1200Rfs*7	ENST00000399788	NM_001042603.1	1199	-/A	23/28	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.290540916716267	2		389	670	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	108	457	0	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	0.933	0.837	1	0.933	0.837	1	CLONAL	1	TRUE	1	0.290540916716267	2		457	797	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498316	29498316	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	90	330	0	ENST00000389048.3:c.1864A>G	p.Ile622Val	p.I622V	ENST00000389048	NM_004304.4	622	Atc/Gtc	10/29	1	2	FACETS	0.991	0.881	1	0.991	0.881	1	CLONAL	1	TRUE	1	0.290540916716267	2		330	625	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137522041	137522041	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	41	243	0	ENST00000367739.4:c.838del	p.Ser280AlafsTer2	p.S280Afs*2	ENST00000367739	NM_000416.2	280	Agc/gc	6/7	1	2	FACETS	0.462	0.384	0.549	0.462	0.384	0.549	SUBCLONAL	1	TRUE	1	0.290540916716267	2		243	611	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717719	89717720	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs780264945	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	48	236	0	ENST00000371953.3:c.750_751del	p.Cys250TrpfsTer2	p.C250Wfs*2	ENST00000371953	NM_000314.4	248	ccTGtg/cctg	7/9	1	2	FACETS	0.653	0.552	0.764	0.653	0.552	0.764	SUBCLONAL	1	TRUE	1	0.290540916716267	2		236	506	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300039	137300040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755912201	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	48	279	0	ENST00000481739.1:c.331dup	p.Leu111ProfsTer70	p.L111Pfs*70	ENST00000481739	NM_002957.4	108	-/C	3/10	1	2	FACETS	0.634	0.536	0.742	0.634	0.536	0.742	SUBCLONAL	1	TRUE	1	0.290540916716267	2		279	521	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367969	15367969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759001252	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	98	306	0	ENST00000263377.2:c.1357C>T	p.Arg453Cys	p.R453C	ENST00000263377	NM_058243.2	453	Cgc/Tgc	8/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.290540916716267	2		306	537	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025765	48025765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145959653	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	53	267	0	ENST00000234420.5:c.643G>A	p.Val215Ile	p.V215I	ENST00000234420	NM_000179.2	215	Gta/Ata	4/10	1	2	FACETS	0.593	0.505	0.69	0.593	0.505	0.69	SUBCLONAL	1	TRUE	1	0.290540916716267	2		267	615	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662441	117662441	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs761904834	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	163	357	0	ENST00000368508.3:c.4936A>G	p.Thr1646Ala	p.T1646A	ENST00000368508	NM_002944.2	1646	Aca/Gca	30/43	1	2	FACETS	0.83	0.764	0.898	1	0.99	1	CLONAL	2	TRUE	1	0.290540916716267	2		357	676	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191026	185191026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	130	414	0	ENST00000265026.3:c.1907C>A	p.Ser636Tyr	p.S636Y	ENST00000265026	NM_004721.4	636	tCt/tAt	11/14	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.290540916716267	2		414	805	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736457	85736457	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	60	354	0	ENST00000370580.1:c.190A>G	p.Arg64Gly	p.R64G	ENST00000370580	NM_003921.4	64	Agg/Ggg	2/3	1	2	FACETS	0.589	0.507	0.679	0.589	0.507	0.679	SUBCLONAL	1	TRUE	1	0.290540916716267	2		354	701	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479831	67479831	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	97	329	0	ENST00000327367.4:c.1138T>C	p.Trp380Arg	p.W380R	ENST00000327367	NM_005902.3	380	Tgg/Cgg	8/9	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.290540916716267	2		329	600	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913527	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	129	255	0	ENST00000311936.3:c.436G>C	p.Ala146Pro	p.A146P	ENST00000311936	NM_004985.3	146	Gca/Cca	4/5	1	2	FACETS	0.867	0.791	0.947	1	0.989	1	CLONAL	2	TRUE	1	0.290540916716267	2		255	512	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231488893	231488894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs567805129	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	104	329	0	ENST00000295050.7:c.1263dup	p.Ile422TyrfsTer11	p.I422Yfs*11	ENST00000295050	NM_032018.5	419	aat/aaTt	5/5	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.290540916716267	2		329	617	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10794726	10794726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1397467879	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	170	300	0	ENST00000361367.2:c.2633G>A	p.Arg878Gln	p.R878Q	ENST00000361367	NM_014633.3	878	cGg/cAg	21/25	1	2	FACETS	0.875	0.807	0.944	1	0.991	1	CLONAL	2	TRUE	1	0.290540916716267	2		300	669	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852224	63852224	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	37	387	0	ENST00000279873.7:c.3002T>C	p.Met1001Thr	p.M1001T	ENST00000279873	NM_032199.2	1001	aTg/aCg	10/10	1	2	FACETS	0.366	0.301	0.439	0.366	0.301	0.439	SUBCLONAL	1	TRUE	1	0.290540916716267	2		387	696	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40871160	40871160	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	106	173	0	ENST00000428826.2:c.730T>C	p.Phe244Leu	p.F244L	ENST00000428826		244	Ttc/Ctc	8/21	1	2	FACETS	0.852	0.769	0.939	1	0.986	1	CLONAL	2	TRUE	1	0.290540916716267	2		173	428	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650746	12650746	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	75	285	0	ENST00000251849.4:c.409A>G	p.Thr137Ala	p.T137A	ENST00000251849	NM_002880.3	137	Aca/Gca	4/17	1	2	FACETS	0.995	0.874	1	0.995	0.874	1	CLONAL	1	TRUE	1	0.290540916716267	2		285	519	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265365	152265365	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	89	353	0	ENST00000206249.3:c.818A>G	p.Asp273Gly	p.D273G	ENST00000206249	NM_000125.3	273	gAt/gGt	4/8	1	2	FACETS	0.987	0.876	1	0.987	0.876	1	CLONAL	1	TRUE	1	0.290540916716267	2		353	621	SUCCESS
ATR	545	MSKCC	GRCh37	3	142172071	142172071	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	97	216	0	ENST00000350721.4:c.7660T>G	p.Leu2554Val	p.L2554V	ENST00000350721	NM_001184.3	2554	Tta/Gta	46/47	1	2	FACETS	0.804	0.722	0.891	1	0.984	1	CLONAL	2	TRUE	1	0.290540916716267	2		216	415	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948462	54948462	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	113	240	0	ENST00000312783.6:c.854+2T>C		p.X285_splice	ENST00000312783	NM_198436.1	285			1	2	FACETS	0.794	0.718	0.873	1	0.986	1	SUBCLONAL	2	TRUE	1	0.290540916716267	2		240	490	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	223685	223685	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	26	163	0	ENST00000264932.6:c.150+2T>C		p.X50_splice	ENST00000264932	NM_004168.2	50			1	2	FACETS	0.534	0.423	0.661	0.534	0.423	0.661	SUBCLONAL	1	TRUE	1	0.290540916716267	2		163	335	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11168253	11168253	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs111575164	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	88	249	0	ENST00000361445.4:c.7619A>G	p.Gln2540Arg	p.Q2540R	ENST00000361445	NM_004958.3	2540	cAg/cGg	57/58	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.290540916716267	2		249	527	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41023304	41023305	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	143	279	0	ENST00000267868.3:c.951_952del	p.Pro318LeufsTer4	p.P318Lfs*4	ENST00000267868	NM_002875.4	316	gaCTct/gact	10/10	1	2	FACETS	0.767	0.701	0.835	1	0.988	1	SUBCLONAL	2	TRUE	1	0.290540916716267	2		279	642	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10792033	10792033	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	42	275	0	ENST00000361367.2:c.2227-1G>T		p.X743_splice	ENST00000361367	NM_014633.3	743			1	2	FACETS	0.456	0.38	0.541	0.456	0.38	0.541	SUBCLONAL	1	TRUE	1	0.290540916716267	2		275	634	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797270	32797270	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	109	375	0	ENST00000374899.4:c.1839A>T	p.Gln613His	p.Q613H	ENST00000374899	NM_018833.2	613	caA/caT	11/12	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.290540916716267	2		375	659	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51504683	51504683	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	98	316	0	ENST00000260433.2:c.1097A>G	p.Tyr366Cys	p.Y366C	ENST00000260433		366	tAc/tGc	9/10	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.290540916716267	2		316	639	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606958	47606959	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	90	327	0	ENST00000263735.4:c.712dup	p.Glu238GlyfsTer16	p.E238Gfs*16	ENST00000263735	NM_002354.2	236	-/G	7/9	1	2	FACETS	0.967	0.858	1	0.967	0.858	1	CLONAL	1	TRUE	1	0.290540916716267	2		327	641	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197333	26197333	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	207	560	0	ENST00000356476.2:c.146T>G	p.Leu49Arg	p.L49R	ENST00000356476		49	cTg/cGg	1/1	1	2	FACETS	0.79	0.734	0.848	1	0.992	1	SUBCLONAL	2	TRUE	1	0.290540916716267	2		560	902	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257402	19257402	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	111	390	0	ENST00000162023.5:c.731del	p.Pro244HisfsTer?	p.P244Hfs*?	ENST00000162023		244	cCa/ca	11/13	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.290540916716267	2		390	665	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800402	32800402	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	96	383	0	ENST00000374899.4:c.1143+2T>C		p.X381_splice	ENST00000374899	NM_018833.2	381			1	2	FACETS	0.991	0.884	1	0.991	0.884	1	CLONAL	1	TRUE	1	0.290540916716267	2		383	667	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818170	32818170	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	80	340	0	ENST00000354258.4:c.1355A>G	p.Glu452Gly	p.E452G	ENST00000354258	NM_000593.5	452	gAa/gGa	5/11	1	2	FACETS	0.845	0.744	0.953	0.845	0.744	0.953	CLONAL	1	TRUE	1	0.290540916716267	2		340	652	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220386	98220386	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs763031827	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	108	371	0	ENST00000331920.6:c.3077A>G	p.His1026Arg	p.H1026R	ENST00000331920	NM_000264.3	1026	cAc/cGc	18/24	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.290540916716267	2		371	603	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541834	187541834	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	98	345	0	ENST00000441802.2:c.5906T>C	p.Val1969Ala	p.V1969A	ENST00000441802	NM_005245.3	1969	gTg/gCg	10/27	1	2	FACETS	0.907	0.809	1	0.907	0.809	1	CLONAL	1	TRUE	1	0.290540916716267	2		345	744	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039847	47039847	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	127	152	0	ENST00000377604.3:c.1190T>C	p.Ile397Thr	p.I397T	ENST00000377604	NM_001204468.1	397	aTc/aCc	12/24	1	1	FACETS	0.94	0.869	1	1	0.993	1	CLONAL	3	TRUE	0	0.290540916716267	1		152	265	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762391	41762391	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	80	329	0	ENST00000301178.4:c.2071T>C	p.Phe691Leu	p.F691L	ENST00000301178	NM_021913.4	691	Ttc/Ctc	18/20	1	2	FACETS	0.922	0.813	1	0.922	0.813	1	CLONAL	1	TRUE	1	0.290540916716267	2		329	597	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038358	180038358	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	123	390	0	ENST00000261937.6:c.3659G>A	p.Ser1220Asn	p.S1220N	ENST00000261937	NM_182925.4	1220	aGc/aAc	27/30	1	2	FACETS	0.755	0.685	0.827	1	0.986	1	SUBCLONAL	2	TRUE	1	0.290540916716267	2		390	561	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224467	55224467	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	31	371	0	ENST00000275493.2:c.1149T>G	p.His383Gln	p.H383Q	ENST00000275493	NM_005228.3	383	caT/caG	10/28	1	2	FACETS	0.348	0.28	0.424	0.348	0.28	0.424	SUBCLONAL	1	TRUE	1	0.290540916716267	2		371	614	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136919	64136919	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	66	275	0	ENST00000334205.4:c.1430T>C	p.Leu477Pro	p.L477P	ENST00000334205	NM_003942.2	477	cTg/cCg	13/17	1	2	FACETS	0.971	0.845	1	0.971	0.845	1	CLONAL	1	TRUE	1	0.290540916716267	2		275	468	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879243	151879244	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	157	377	0	ENST00000262189.6:c.5701dup	p.Met1901AsnfsTer13	p.M1901Nfs*13	ENST00000262189	NM_170606.2	1901	atg/aAtg	36/59	1	2	FACETS	0.766	0.704	0.832	1	0.989	1	SUBCLONAL	2	TRUE	1	0.290540916716267	2		377	705	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205738	128205738	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	89	403	0	ENST00000341105.2:c.137A>G	p.Asp46Gly	p.D46G	ENST00000341105	NM_032638.4	46	gAc/gGc	2/6	1	2	FACETS	0.971	0.862	1	0.971	0.862	1	CLONAL	1	TRUE	1	0.290540916716267	2		403	631	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245419	46245419	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	107	375	0	ENST00000334344.6:c.3513G>T	p.Gln1171His	p.Q1171H	ENST00000334344	NM_152641.2	1171	caG/caT	15/21	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.290540916716267	2		375	717	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992977	72992977	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	56	390	0	ENST00000268489.5:c.1068C>G	p.Asn356Lys	p.N356K	ENST00000268489	NM_006885.3	356	aaC/aaG	2/10	0.290540916716267	1	FACETS	0.564	0.483	0.653	0.564	0.483	0.653	SUBCLONAL	1	TRUE	0	0.290540916716267	1		390	584	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350574	89350576	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	14	266	0	ENST00000301030.4:c.2374_2376del	p.Glu792del	p.E792del	ENST00000301030	NM_001256183.1	792	GAG/-	9/13	1	2	FACETS	0.184	0.132	0.247	0.184	0.132	0.247	SUBCLONAL	1	TRUE	1	0.290540916716267	2		266	524	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231487255	231487256	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs752960031	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	61	375	0	ENST00000295050.7:c.663dup	p.Gly222ArgfsTer18	p.G222Rfs*18	ENST00000295050	NM_032018.5	219	tca/tcAa	4/5	1	2	FACETS	0.621	0.535	0.715	0.621	0.535	0.715	SUBCLONAL	1	TRUE	1	0.290540916716267	2		375	676	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67462909	67462909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	118	296	0	ENST00000327367.4:c.625C>T	p.Pro209Ser	p.P209S	ENST00000327367	NM_005902.3	209	Ccg/Tcg	5/9	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.290540916716267	2		296	571	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467622	66467622	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	70	340	0	ENST00000273854.3:c.647A>G	p.Asp216Gly	p.D216G	ENST00000273854	NM_004439.5	216	gAt/gGt	3/18	1	2	FACETS	0.867	0.756	0.985	0.867	0.756	0.985	CLONAL	1	TRUE	1	0.290540916716267	2		340	556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0069606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	52	413	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	1	2	FACETS	0.57	0.484	0.665	0.57	0.484	0.665	SUBCLONAL	1	FALSE	1	0.251990609823219	2		413	724	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475063	40475063	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	70	323	0	ENST00000264657.5:c.1847A>G	p.Glu616Gly	p.E616G	ENST00000264657	NM_139276.2	616	gAa/gGa	20/24	1	2	FACETS	0.788	0.686	0.898	0.788	0.686	0.898	SUBCLONAL	1	FALSE	1	0.251990609823219	2		323	705	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619277	37619278	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0069606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	69	355	0	ENST00000447079.4:c.955dup	p.Tyr319LeufsTer32	p.Y319Lfs*32	ENST00000447079	NM_015083.1	318	tct/tcTt	1/14	1	2	FACETS	0.804	0.7	0.917	0.804	0.7	0.917	CLONAL	1	FALSE	1	0.251990609823219	2		355	681	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242478	+	protein_altering_variant	In_Frame_Del	DEL	ATTAAGAGAAG	ATTAAGAGAAG	GC	rs121913435	NA	P-0069606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	59	282	0	ENST00000275493.2:c.2238_2248delinsGC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGca/gaGCca	19/28	0.175830447383337	3	FACETS	1	0.91	1	0.537	0.462	0.618	CLONAL	1	FALSE	1	0.251990609823219	3		282	491	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0069607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	50	358	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.470843194479345	2		358	208	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0069607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	92	308	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.769	0.695	0.846	1	0.983	1	SUBCLONAL	2	TRUE	1	0.470843194479345	2		308	254	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946261	81946261	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	54	330	0	ENST00000359376.3:c.1994G>A	p.Arg665Gln	p.R665Q	ENST00000359376	NM_002661.3	665	cGg/cAg	19/33	0.470843194479345	1	FACETS	0.517	0.444	0.597	0.517	0.444	0.597	SUBCLONAL	1	TRUE	0	0.470843194479345	1		330	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0069608-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	99	294	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.160021178622057	2	FACETS	0.778	0.699	0.86	0.778	0.699	0.86	INDETERMINATE	2	TRUE	0	0.318254709235352	2		294	400	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971137	21971137	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069608-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	131	379	0	ENST00000304494.5:c.221A>G	p.Asp74Gly	p.D74G	ENST00000304494	NM_000077.4	74	gAc/gGc	2/3	0.222117287754969	2	FACETS	0.837	0.764	0.912	0.837	0.764	0.912	CLONAL	2	TRUE	0	0.318254709235352	2		379	492	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011154	12011155	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0069608-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	40	269	0	ENST00000353533.5:c.565dup	p.Tyr189LeufsTer6	p.Y189Lfs*6	ENST00000353533	NM_003010.3	187	-/T	5/11	0.160021178622057	2	FACETS	1	0.919	1	0.582	0.488	0.684	INDETERMINATE	1	TRUE	0	0.318254709235352	2		269	216	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224440	53224440	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069608-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	24	182	0	ENST00000375401.3:c.3273G>T	p.Lys1091Asn	p.K1091N	ENST00000375401	NM_004187.3	1091	aaG/aaT	21/26	1	1	FACETS	0.518	0.407	0.644	0.518	0.407	0.644	SUBCLONAL	1	TRUE	0	0.318254709235352	1		182	245	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654691	29654691	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069608-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	137	376	0	ENST00000356175.3:c.5380C>T	p.Gln1794Ter	p.Q1794*	ENST00000356175	NM_000267.3	1794	Cag/Tag	37/57	0.246078775889855	4	FACETS	0.864	0.788	0.943	0.864	0.788	0.943	CLONAL	2	TRUE	2	0.318254709235352	4		376	657	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502207	157502207	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069608-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	97	336	0	ENST00000346085.5:c.3241del	p.Glu1081LysfsTer49	p.E1081Kfs*49	ENST00000346085	NM_020732.3	1080	atG/at	12/20	0.222117287754969	2	FACETS	1	0.98	1	0.719	0.645	0.797	CLONAL	1	TRUE	0	0.318254709235352	2		336	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0069608-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	216	294	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.434937455722539	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.434937455722539	2		294	463	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971137	21971137	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069608-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	261	379	0	ENST00000304494.5:c.221A>G	p.Asp74Gly	p.D74G	ENST00000304494	NM_000077.4	74	gAc/gGc	2/3	0.434937455722539	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.434937455722539	2		379	498	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011154	12011155	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0069608-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	105	269	0	ENST00000353533.5:c.565dup	p.Tyr189LeufsTer6	p.Y189Lfs*6	ENST00000353533	NM_003010.3	187	-/T	5/11	0.434937455722539	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	2	TRUE	0	0.434937455722539	2		269	241	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654691	29654691	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069608-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	262	376	0	ENST00000356175.3:c.5380C>T	p.Gln1794Ter	p.Q1794*	ENST00000356175	NM_000267.3	1794	Cag/Tag	37/57	0.434937455722539	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.434937455722539	4		376	790	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502207	157502207	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069608-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	228	336	0	ENST00000346085.5:c.3241del	p.Glu1081LysfsTer49	p.E1081Kfs*49	ENST00000346085	NM_020732.3	1080	atG/at	12/20	0.434937455722539	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.434937455722539	2		336	512	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0069610-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	105	276	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.257041776578123	4	FACETS	1	0.977	1	0.321	0.29	0.355	INDETERMINATE	1	TRUE	0	0.643820267955124	4		276	417	SUCCESS
APC	324	MSKCC	GRCh37	5	112175513	112175513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069610-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	135	295	0	ENST00000257430.4:c.4222G>T	p.Glu1408Ter	p.E1408*	ENST00000257430	NM_000038.5	1408	Gaa/Taa	16/16	0.20941455945641	3	FACETS	1	0.979	1	0.613	0.562	0.667	INDETERMINATE	1	TRUE	1	0.643820267955124	3		295	452	SUCCESS
APC	324	MSKCC	GRCh37	5	112173578	112173578	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069610-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	196	315	0	ENST00000257430.4:c.2287G>T	p.Glu763Ter	p.E763*	ENST00000257430	NM_000038.5	763	Gaa/Taa	16/16	0.20941455945641	3	FACETS	0.815	0.761	0.869	0.815	0.761	0.869	INDETERMINATE	2	TRUE	1	0.643820267955124	3		315	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs760043106	NA	P-0069610-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	298	383	0	ENST00000269305.4:c.584T>G	p.Ile195Ser	p.I195S	ENST00000269305	NM_001126112.2	195	aTc/aGc	6/11	0.613373137049028	2	FACETS	0.948	0.907	0.989	0.948	0.907	0.989	CLONAL	2	TRUE	0	0.643820267955124	2		383	488	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132718	152132718	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1202370478	NA	P-0069610-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	65	89	1	ENST00000262189.6:c.154A>G	p.Arg52Gly	p.R52G	ENST00000262189	NM_170606.2	52	Aga/Gga	1/59	0.643820267955124	4	FACETS	1	0.972	1	0.477	0.419	0.538	CLONAL	1	TRUE	1	0.643820267955124	4		90	232	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003267	143003333	+	frameshift_variant	Frame_Shift_Del	DEL	CACTGACATCGATGTCCTGTCTTTGGCACTTTTACAACAGGTGAAACGAATACCATTCAGTTTGCGG	CACTGACATCGATGTCCTGTCTTTGGCACTTTTACAACAGGTGAAACGAATACCATTCAGTTTGCGG	-	novel	NA	P-0069610-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	71	213	0	ENST00000262992.4:c.2493_2559del	p.Cys831Ter	p.C831*	ENST00000262992	NM_001101669.1	831	tgCCGCAAACTGAATGGTATTCGTTTCACCTGTTGTAAAAGTGCCAAAGACAGGACATCGATGTCAGTG/tg	23/24	0.643820267955124	2	FACETS	0.817	0.721	0.918	0.408	0.36	0.459	CLONAL	1	TRUE	0	0.643820267955124	2		213	270	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0069611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	39	281	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	1	2	FACETS	0.73	0.605	0.871	0.73	0.605	0.871	SUBCLONAL	1	TRUE	1	0.19	2		281	562	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715721	30715721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893816	NA	P-0069611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	34	317	0	ENST00000295754.5:c.1379G>A	p.Arg460His	p.R460H	ENST00000295754	NM_003242.5	460	cGc/cAc	5/7	1	2	FACETS	0.584	0.476	0.706	0.584	0.476	0.706	SUBCLONAL	1	TRUE	1	0.19	2		317	613	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016606	12016606	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	29	307	0	ENST00000353533.5:c.742T>A	p.Phe248Ile	p.F248I	ENST00000353533	NM_003010.3	248	Ttc/Atc	7/11	1	2	FACETS	0.669	0.537	0.821	0.669	0.537	0.821	SUBCLONAL	1	TRUE	1	0.19	2		307	456	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913355	NA	P-0069616-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	17	385	0	ENST00000288602.6:c.1406G>T	p.Gly469Val	p.G469V	ENST00000288602	NM_004333.4	469	gGa/gTa	11/18	1	2	FACETS	0.895	0.674	1	0.895	0.674	1	CLONAL	1	TRUE	1	0.290109251592608	2		385	131	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730919	40730919	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1478583387	NA	P-0069616-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	33	550	0	ENST00000373198.4:c.3616C>A	p.Pro1206Thr	p.P1206T	ENST00000373198	NM_133170.3	1206	Ccc/Acc	27/32	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.290109251592608	2		550	207	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111965527	111965527	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0069616-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	18	364	0	ENST00000375549.3:c.315-2A>G		p.X105_splice	ENST00000375549	NM_003002.3	105			1	2	FACETS	0.734	0.556	0.942	0.734	0.556	0.942	CLONAL	1	TRUE	1	0.290109251592608	2		364	169	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451824	29451828	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCA	CCCCA	TTTT	novel	NA	P-0069616-T01-IM7	NA	A	A	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	15	243	0	ENST00000389048.3:c.2737_2741delinsAAAA	p.Trp913LysfsTer26	p.W913Kfs*26	ENST00000389048	NM_004304.4	913	TGGGGg/AAAAg	16/29	1	2	FACETS	0.869	0.642	1	0.869	0.642	1	CLONAL	1	TRUE	1	0.290109251592608	2		243	119	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039658	47039659	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0069616-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	41	257	0	ENST00000377604.3:c.1111dup	p.Thr371AsnfsTer10	p.T371Nfs*10	ENST00000377604	NM_001204468.1	370	-/A	11/24	1	1	FACETS	0.902	0.767	1	1	0.969	1	CLONAL	2	TRUE	0	0.290109251592608	1		257	134	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128017002	128017002	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs201806429	NA	P-0069616-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	33	442	0	ENST00000285398.2:c.2087T>C	p.Met696Thr	p.M696T	ENST00000285398	NM_000122.1	696	aTg/aCg	14/15	1	2	FACETS	0.968	0.793	1	0.968	0.793	1	CLONAL	1	TRUE	1	0.290109251592608	2		442	235	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409198	31409199	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0069616-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	29	476	0	ENST00000344624.3:c.3818_3819delinsTT	p.Arg1273Ile	p.R1273I	ENST00000344624		1273	aGG/aTT	30/33	1	2	FACETS	1	0.836	1	1	0.836	1	CLONAL	1	TRUE	1	0.290109251592608	2		476	193	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352976	70352976	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	71	409	0	ENST00000374080.3:c.4531G>A	p.Val1511Met	p.V1511M	ENST00000374080		1511	Gtg/Atg	33/45	0.327249412355513	4	FACETS	0.955	0.834	1	0.318	0.278	0.362	CLONAL	1	TRUE	1	0.327249412355513	4		409	603	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0069621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	61	244	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.997	0.864	1	0.997	0.864	1	CLONAL	1	TRUE	1	0.34	2		244	360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0069621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	127	409	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.301622370959951	1	FACETS	0.938	0.852	1	0.938	0.852	1	CLONAL	1	TRUE	0	0.34	1		409	661	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106710	27106710	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0069621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	133	444	0	ENST00000324856.7:c.6324del	p.Asn2109MetfsTer26	p.N2109Mfs*26	ENST00000324856	NM_006015.4	2107	ggC/gg	20/20	0.301622370959951	1	FACETS	0.933	0.849	1	0.933	0.849	1	CLONAL	1	TRUE	0	0.34	1		444	696	SUCCESS
APC	324	MSKCC	GRCh37	5	112102976	112102976	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs74953290	NA	P-0069621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	46	326	0	ENST00000257430.4:c.311C>A	p.Ser104Ter	p.S104*	ENST00000257430	NM_000038.5	104	tCa/tAa	4/16	0.301622370959951	1	FACETS	0.447	0.377	0.526	0.447	0.377	0.526	SUBCLONAL	1	TRUE	0	0.34	1		326	502	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165777	108165777	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	34	313	0	ENST00000278616.4:c.4900G>C	p.Ala1634Pro	p.A1634P	ENST00000278616	NM_000051.3	1634	Gct/Cct	32/63	1	2	FACETS	0.557	0.456	0.671	0.557	0.456	0.671	SUBCLONAL	1	TRUE	1	0.34	2		313	359	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0069622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	9	253	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.179	0.118	0.257	0.179	0.118	0.257	SUBCLONAL	1	TRUE	1	0.4544450643358	2		253	221	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925183	81925183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	143	358	0	ENST00000359376.3:c.974C>T	p.Ser325Leu	p.S325L	ENST00000359376	NM_002661.3	325	tCg/tTg	11/33	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.4544450643358	2		358	532	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743865	40743865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758531464	NA	P-0069622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	135	298	0	ENST00000373198.4:c.3130G>A	p.Val1044Ile	p.V1044I	ENST00000373198	NM_133170.3	1044	Gtc/Atc	23/32	NA	2	FACETS	1	0.947	1			1	INDETERMINATE	1	TRUE	NA	0.4544450643358	2		298	565	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191158	185191158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1267105230	NA	P-0069622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	142	403	0	ENST00000265026.3:c.2039G>A	p.Arg680Gln	p.R680Q	ENST00000265026	NM_004721.4	680	cGg/cAg	11/14	1	2	FACETS	0.881	0.805	0.962	0.881	0.805	0.962	CLONAL	1	TRUE	1	0.4544450643358	2		403	709	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920217	1920217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200784805	NA	P-0069622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	149	401	1	ENST00000382891.5:c.1277C>T	p.Thr426Met	p.T426M	ENST00000382891	NM_133335.3	426	aCg/aTg	5/22	0.446150914986991	2	FACETS	0.847	0.775	0.923	0.424	0.387	0.462	CLONAL	1	TRUE	0	0.4544450643358	2		402	774	SUCCESS
APC	324	MSKCC	GRCh37	5	112175136	112175136	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	312	405	0	ENST00000257430.4:c.3845C>A	p.Ser1282Ter	p.S1282*	ENST00000257430	NM_000038.5	1282	tCa/tAa	16/16	0.451464524967574	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.4544450643358	2		405	662	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7590693	7590693	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0069622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	138	341	0	ENST00000269305.4:c.-29+2T>C		p.X10_splice	ENST00000269305	NM_001126112.2	10			0.4544450643358	1	FACETS	0.874	0.799	0.951	0.874	0.799	0.951	CLONAL	1	TRUE	0	0.4544450643358	1		341	537	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229687	5229687	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1374310303	NA	P-0069622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	96	241	0	ENST00000357368.4:c.2164G>A	p.Ala722Thr	p.A722T	ENST00000357368	NM_002850.3	722	Gcg/Acg	15/38	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.4544450643358	2		241	371	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945996	17945997	+	inframe_insertion	In_Frame_Ins	INS	-	-	CATTGC	novel	NA	P-0069622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	210	458	0	ENST00000458235.1:c.1937_1942dup	p.Gly646_Asn647dup	p.G646_N647dup	ENST00000458235	NM_000215.3	646	gtc/gGCAATGtc	15/24	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.4544450643358	2		458	910	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40709562	40709562	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	122	320	0	ENST00000373198.4:c.4340A>T	p.Lys1447Ile	p.K1447I	ENST00000373198	NM_133170.3	1447	aAa/aTa	32/32	NA	2	FACETS	0.615	0.555	0.678			1	INDETERMINATE	1	TRUE	NA	0.4544450643358	2		320	873	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866643	117866643	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	91	325	0	ENST00000297338.2:c.1002C>A	p.Ser334Arg	p.S334R	ENST00000297338	NM_006265.2	334	agC/agA	9/14	0.4544450643358	4	FACETS	0.756	0.671	0.848	0.252	0.223	0.283	SUBCLONAL	1	TRUE	1	0.4544450643358	4		325	770	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0069623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	94	358	0				ENST00000310581	NM_198253.2	-/1132			0.10324588712834	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.96	0		358	188	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0069623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	157	253	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.10324588712834	3	FACETS	1	0.984	1	0.617	0.572	0.663	INDETERMINATE	1	TRUE	1	0.96	3		253	392	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0069623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	212	485	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.962	0.905	1	0.962	0.905	1	CLONAL	1	TRUE	1	0.96	2		485	459	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432310	49432310	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	254	568	0	ENST00000301067.7:c.8829del	p.Asn2943LysfsTer61	p.N2943Kfs*61	ENST00000301067	NM_003482.3	2943	aaC/aa	34/54	0.10324588712834	3	FACETS	1	0.99	1	0.624	0.588	0.66	INDETERMINATE	1	TRUE	1	0.96	3		568	628	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	246	425	0	ENST00000263967.3:c.3012G>C	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atC	21/21	0.10324588712834	3	FACETS	1	0.99	1	0.624	0.587	0.661	INDETERMINATE	1	TRUE	1	0.96	3		425	608	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281805	39281805	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs889231089	NA	P-0069623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	280	314	0	ENST00000402219.2:c.670A>G	p.Lys224Glu	p.K224E	ENST00000402219	NM_005633.3	224	Aaa/Gaa	5/23	1	2	FACETS	0.938	0.889	0.987	0.938	0.889	0.987	CLONAL	1	TRUE	1	0.96	2		314	622	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214492	5214492	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0069623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	185	455	0	ENST00000357368.4:c.4495-1G>A		p.X1499_splice	ENST00000357368	NM_002850.3	1499			0.10324588712834	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.96	0		455	420	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143324151	143324151	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	279	295	0	ENST00000262992.4:c.312C>G	p.Ile104Met	p.I104M	ENST00000262992	NM_001101669.1	104	atC/atG	5/24	0.10324588712834	3	FACETS	1	0.991	1	0.614	0.58	0.648	INDETERMINATE	1	TRUE	1	0.96	3		295	701	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448455	49448456	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0069623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	245	435	0	ENST00000301067.7:c.255dup	p.Glu86Ter	p.E86*	ENST00000301067	NM_003482.3	85	-/T	3/54	0.10324588712834	3	FACETS	1	0.992	1	0.663	0.625	0.701	INDETERMINATE	1	TRUE	1	0.96	3		435	570	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215269	123215272	+	frameshift_variant	Frame_Shift_Del	DEL	GATA	GATA	-	novel	NA	P-0069623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	245	283	0	ENST00000218089.9:c.2818_2821del	p.Arg940HisfsTer8	p.R940Hfs*8	ENST00000218089	NM_001042749.1	939	GATAga/ga	28/35	1	2	FACETS	0.945	0.892	0.998	0.945	0.892	0.998	CLONAL	1	TRUE	1	0.96	2		283	540	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386401	31386401	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1227641097	NA	P-0069623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	251	456	0	ENST00000328111.2:c.1626G>C	p.Trp542Cys	p.W542C	ENST00000328111	NM_006892.3	542	tgG/tgC	15/23	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.96	2		456	523	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056599	26056599	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1484542952	NA	P-0069624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	123	388	0	ENST00000343677.2:c.58G>A	p.Val20Ile	p.V20I	ENST00000343677	NM_005319.3	20	Gta/Ata	1/1	0.499184446383417	6	FACETS	0.775	0.703	0.852	0.388	0.351	0.426	SUBCLONAL	2	TRUE	2	0.499184446383417	6		388	635	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976914	55976914	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762779214	NA	P-0069624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	104	305	0	ENST00000263923.4:c.998G>A	p.Gly333Glu	p.G333E	ENST00000263923	NM_002253.2	333	gGa/gAa	8/30	0.253986046645864	5	FACETS	0.785	0.707	0.867	0.523	0.471	0.578	INDETERMINATE	2	TRUE	2	0.499184446383417	5		305	464	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559854	29559873	+	frameshift_variant	Frame_Shift_Del	DEL	AACTTACTCAATGCCAACGT	AACTTACTCAATGCCAACGT	-	novel	NA	P-0069624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	143	359	0	ENST00000356175.3:c.3452_3471del	p.Asn1151ArgfsTer37	p.N1151Rfs*37	ENST00000356175	NM_000267.3	1151	AACTTACTCAATGCCAACGTa/a	26/57	0.355009554176969	3	FACETS	0.962	0.888	1	0.642	0.592	0.692	CLONAL	2	TRUE	0	0.499184446383417	3		359	372	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63537655	63537655	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	397	308	0	ENST00000307078.5:c.977G>C	p.Arg326Pro	p.R326P	ENST00000307078	NM_004655.3	326	cGt/cCt	4/11	0.499184446383417	6	FACETS	1	0.982	1	1	0.982	1	CLONAL	6	TRUE	0	0.499184446383417	6		308	521	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981113	55981113	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	99	384	0	ENST00000263923.4:c.586G>T	p.Gly196Cys	p.G196C	ENST00000263923	NM_002253.2	196	Ggc/Tgc	5/30	0.253986046645864	5	FACETS	1	0.922	1	0.684	0.617	0.754	INDETERMINATE	2	TRUE	2	0.499184446383417	5		384	338	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0069626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	108	358	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		358	413	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441217	52441217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	227	499	0	ENST00000460680.1:c.553G>A	p.Gly185Arg	p.G185R	ENST00000460680	NM_004656.3	185	Ggg/Agg	7/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		499	716	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440356	52440356	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0069626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	235	500	0	ENST00000460680.1:c.696del	p.Val233TrpfsTer16	p.V233Wfs*16	ENST00000460680	NM_004656.3	232	gcA/gc	9/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		500	721	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137540445	137540445	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0069626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	166	348	0	ENST00000367739.4:c.20del	p.Leu7HisfsTer8	p.L7Hfs*8	ENST00000367739	NM_000416.2	7	cTa/ca	1/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		348	601	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	129	343	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.995	0.913	1	0.995	0.913	1	CLONAL	1	TRUE	1	0.712523821581289	2		343	364	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	132	491	0	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	0.712523821581289	3	FACETS	0.447	0.405	0.492	0.224	0.202	0.246	SUBCLONAL	1	TRUE	1	0.712523821581289	3		491	1124	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	72	459	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.363	0.318	0.413	0.363	0.318	0.413	SUBCLONAL	1	TRUE	1	0.712523821581289	2		459	556	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	193	523	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.712523821581289	3	FACETS	0.894	0.828	0.962	0.447	0.414	0.481	CLONAL	1	TRUE	1	0.712523821581289	3		523	822	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	91	598	3	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.414	0.368	0.463	0.414	0.368	0.463	SUBCLONAL	1	TRUE	1	0.712523821581289	2		601	617	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	70	472	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.321	0.279	0.365	0.321	0.279	0.365	SUBCLONAL	1	TRUE	1	0.712523821581289	2		474	613	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	55	465	2	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.197	0.167	0.229	0.197	0.167	0.229	SUBCLONAL	1	TRUE	1	0.712523821581289	2		467	785	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	157	422	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.712523821581289	2		422	421	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099424	157099426	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	rs754060642	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	45	590	1	ENST00000346085.5:c.363_365del	p.Gln131del	p.Q131del	ENST00000346085	NM_020732.3	121	CAA/-	1/20	1	2	FACETS	0.159	0.133	0.188	0.159	0.133	0.188	SUBCLONAL	1	TRUE	1	0.712523821581289	2		591	793	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	245	351	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.712523821581289	2		351	588	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103346	2103346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777459404	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	44	393	0	ENST00000219476.3:c.229G>A	p.Ala77Thr	p.A77T	ENST00000219476	NM_000548.3	77	Gca/Aca	4/42	1	2	FACETS	0.155	0.129	0.183	0.155	0.129	0.183	SUBCLONAL	1	TRUE	1	0.712523821581289	2		393	799	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	20	451	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	0.084	0.063	0.108	0.084	0.063	0.108	SUBCLONAL	1	TRUE	1	0.712523821581289	2		451	671	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466022	69466022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	222	461	0	ENST00000227507.2:c.860C>T	p.Pro287Leu	p.P287L	ENST00000227507	NM_053056.2	287	cCc/cTc	5/5	1	2	FACETS	0.903	0.845	0.963	0.903	0.845	0.963	CLONAL	1	TRUE	1	0.712523821581289	2		461	690	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560514	65560514	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	199	334	0	ENST00000358664.4:c.83A>G	p.His28Arg	p.H28R	ENST00000358664	NM_002382.4	28	cAt/cGt	3/5	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.712523821581289	2		334	526	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429977	78429978	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1200882279	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	71	303	1	ENST00000370768.2:c.901dup	p.Ile301AsnfsTer4	p.I301Nfs*4	ENST00000370768	NM_003902.3	301	ata/aAta	11/20	1	2	FACETS	0.615	0.541	0.694	0.615	0.541	0.694	SUBCLONAL	1	TRUE	1	0.712523821581289	2		304	324	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	106	442	1	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.501	0.45	0.555	0.501	0.45	0.555	SUBCLONAL	1	TRUE	1	0.712523821581289	2		443	594	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121909229	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	89	260	0	ENST00000371953.3:c.389G>T	p.Arg130Leu	p.R130L	ENST00000371953	NM_000314.4	130	cGa/cTa	5/9	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.712523821581289	2		260	231	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905055	50905055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	58	315	2	ENST00000440232.2:c.342del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	113	Ggg/gg	4/27	1	2	FACETS	0.28	0.24	0.324	0.28	0.24	0.324	SUBCLONAL	1	TRUE	1	0.712523821581289	2		317	581	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830450	72830450	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	33	242	1	ENST00000268489.5:c.6131del	p.Pro2044LeufsTer57	p.P2044Lfs*57	ENST00000268489	NM_006885.3	2044	cCt/ct	9/10	1	2	FACETS	0.26	0.212	0.314	0.26	0.212	0.314	SUBCLONAL	1	TRUE	1	0.712523821581289	2		243	356	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939177	36939177	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs186379741	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	103	479	0	ENST00000361632.4:c.532G>A	p.Val178Met	p.V178M	ENST00000361632		178	Gtg/Atg	5/16	1	2	FACETS	0.476	0.427	0.529	0.476	0.427	0.529	SUBCLONAL	1	TRUE	1	0.712523821581289	2		479	607	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357060	89357060	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	140	441	0	ENST00000301030.4:c.574del	p.Ala192GlnfsTer36	p.A192Qfs*36	ENST00000301030	NM_001256183.1	192	Gca/ca	6/13	1	2	FACETS	0.452	0.412	0.495	0.452	0.412	0.495	SUBCLONAL	1	TRUE	1	0.712523821581289	2		441	869	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265285	46265285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1447875218	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	49	448	0	ENST00000371998.3:c.2155G>A	p.Gly719Arg	p.G719R	ENST00000371998		719	Gga/Aga	12/23	1	2	FACETS	0.342	0.29	0.399	0.342	0.29	0.399	SUBCLONAL	1	TRUE	1	0.712523821581289	2		448	402	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591101	67591101	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	89	331	1	ENST00000274335.5:c.1694G>T	p.Ser565Ile	p.S565I	ENST00000274335		565	aGc/aTc	12/15	1	2	FACETS	0.853	0.765	0.944	0.853	0.765	0.944	CLONAL	1	TRUE	1	0.712523821581289	2		332	293	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944177	71944178	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs1226924888	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	113	505	0	ENST00000298229.2:c.2012_2013del	p.Tyr671CysfsTer19	p.Y671Cfs*19	ENST00000298229	NM_001567.3	670	acATat/acat	17/28	1	2	FACETS	0.458	0.412	0.506	0.458	0.412	0.506	SUBCLONAL	1	TRUE	1	0.712523821581289	2		505	693	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803738	1803738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774047997	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	114	433	0	ENST00000260795.2:c.916G>A	p.Val306Ile	p.V306I	ENST00000260795		306	Gtt/Att	6/17	1	2	FACETS	0.472	0.425	0.521	0.472	0.425	0.521	SUBCLONAL	1	TRUE	1	0.712523821581289	2		433	678	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10789396	10789396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	63	360	0	ENST00000361367.2:c.1730C>T	p.Ala577Val	p.A577V	ENST00000361367	NM_014633.3	577	gCa/gTa	14/25	1	2	FACETS	0.49	0.426	0.559	0.49	0.426	0.559	SUBCLONAL	1	TRUE	1	0.712523821581289	2		360	361	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949742	151949742	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	17	369	0	ENST00000262189.6:c.1358G>T	p.Cys453Phe	p.C453F	ENST00000262189	NM_170606.2	453	tGc/tTc	10/59	1	2	FACETS	0.168	0.125	0.219	0.168	0.125	0.219	SUBCLONAL	1	TRUE	1	0.712523821581289	2		369	284	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24129384	24129384	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	70	329	0	ENST00000263121.7:c.28T>G	p.Phe10Val	p.F10V	ENST00000263121	NM_003073.3	10	Ttc/Gtc	1/9	1	2	FACETS	0.335	0.292	0.382	0.335	0.292	0.382	SUBCLONAL	1	TRUE	1	0.712523821581289	2		329	586	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134183	41134183	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	189	460	0	ENST00000379561.5:c.1445del	p.Pro482LeufsTer3	p.P482Lfs*3	ENST00000379561	NM_002015.3	482	cCt/ct	2/3	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.712523821581289	2		460	522	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042223	42042223	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	21	406	0	ENST00000219905.7:c.6420del	p.Phe2140LeufsTer39	p.F2140Lfs*39	ENST00000219905	NM_001164273.1	2140	Ttt/tt	17/24	1	2	FACETS	0.162	0.125	0.207	0.162	0.125	0.207	SUBCLONAL	1	TRUE	1	0.712523821581289	2		406	363	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624278	89624278	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554890385	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	74	195	0	ENST00000371953.3:c.52G>T	p.Glu18Ter	p.E18*	ENST00000371953	NM_000314.4	18	Gag/Tag	1/9	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.712523821581289	2		195	204	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59820427	59820427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	24	347	0	ENST00000259008.2:c.2326G>A	p.Ala776Thr	p.A776T	ENST00000259008	NM_032043.2	776	Gcc/Acc	16/20	0.712523821581289	3	FACETS	0.211	0.165	0.264	0.106	0.082	0.132	SUBCLONAL	1	TRUE	1	0.712523821581289	3		347	433	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944186	71944186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	109	517	0	ENST00000298229.2:c.2019G>A	p.Trp673Ter	p.W673*	ENST00000298229	NM_001567.3	673	tgG/tgA	17/28	1	2	FACETS	0.419	0.376	0.464	0.419	0.376	0.464	SUBCLONAL	1	TRUE	1	0.712523821581289	2		517	731	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2029054	2029054	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	97	465	0	ENST00000349721.2:c.32C>A	p.Pro11His	p.P11H	ENST00000349721	NM_003070.3	11	cCc/cAc	2/34	1	2	FACETS	0.47	0.42	0.524	0.47	0.42	0.524	SUBCLONAL	1	TRUE	1	0.712523821581289	2		465	579	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483305	120483305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	156	417	0	ENST00000256646.2:c.3056G>A	p.Gly1019Glu	p.G1019E	ENST00000256646	NM_024408.3	1019	gGa/gAa	19/34	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.712523821581289	2		417	404	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409797	63409797	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	97	404	0	ENST00000330258.3:c.3370T>A	p.Tyr1124Asn	p.Y1124N	ENST00000330258	NM_152424.3	1124	Tac/Aac	2/2	1	2	FACETS	0.597	0.535	0.663	0.597	0.535	0.663	SUBCLONAL	1	TRUE	1	0.712523821581289	2		404	456	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191018	2191018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	100	367	0	ENST00000398665.3:c.272G>A	p.Gly91Asp	p.G91D	ENST00000398665	NM_032482.2	91	gGc/gAc	5/28	1	2	FACETS	0.423	0.378	0.471	0.423	0.378	0.471	SUBCLONAL	1	TRUE	1	0.712523821581289	2		367	663	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1685545	1685545	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	89	506	0	ENST00000378625.1:c.1481G>A	p.Cys494Tyr	p.C494Y	ENST00000378625	NM_001198994.1	494	tGc/tAc	12/14	1	2	FACETS	0.333	0.295	0.374	0.333	0.295	0.374	SUBCLONAL	1	TRUE	1	0.712523821581289	2		506	750	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458349	12458349	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	53	436	0	ENST00000287820.6:c.966G>T	p.Gln322His	p.Q322H	ENST00000287820	NM_015869.4	322	caG/caT	6/7	1	2	FACETS	0.275	0.234	0.32	0.275	0.234	0.32	SUBCLONAL	1	TRUE	1	0.712523821581289	2		436	541	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178368	56178368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	49	337	0	ENST00000399503.3:c.3344del	p.Pro1115GlnfsTer2	p.P1115Qfs*2	ENST00000399503	NM_005921.1	1114	aCc/ac	14/20	1	2	FACETS	0.539	0.461	0.624	0.539	0.461	0.624	SUBCLONAL	1	TRUE	1	0.712523821581289	2		337	255	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119893	70119893	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	153	456	3	ENST00000245479.2:c.895C>T	p.Pro299Ser	p.P299S	ENST00000245479	NM_000346.3	299	Ccg/Tcg	3/3	0.712523821581289	3	FACETS	0.611	0.559	0.666	0.306	0.279	0.333	SUBCLONAL	1	TRUE	1	0.712523821581289	3		459	953	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0069648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	68	316	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.298144518237931	1	FACETS	0.783	0.682	0.892	0.783	0.682	0.892	SUBCLONAL	1	TRUE	0	0.29	1		316	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0069648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	61	224	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.298144518237931	1	FACETS	0.879	0.761	1	0.879	0.761	1	CLONAL	1	TRUE	0	0.29	1		224	409	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652879	29652879	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	70	241	0	ENST00000356175.3:c.4814A>T	p.His1605Leu	p.H1605L	ENST00000356175	NM_000267.3	1605	cAt/cTt	36/57	1	2	FACETS	0.758	0.661	0.863	0.758	0.661	0.863	SUBCLONAL	1	TRUE	1	0.29	2		241	637	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900983	114900984	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0069648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	61	298	0	ENST00000543371.1:c.598dup	p.Leu200ProfsTer10	p.L200Pfs*10	ENST00000543371	NM_001198531.1	198	cac/caCc	6/14	0.185101285581918	1	FACETS	0.583	0.503	0.67	0.583	0.503	0.67	SUBCLONAL	1	TRUE	0	0.29	1		298	617	SUCCESS
CALR	811	MSKCC	GRCh37	19	13049545	13049545	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	86	260	0	ENST00000316448.5:c.52G>T	p.Glu18Ter	p.E18*	ENST00000316448	NM_004343.3	18	Gag/Tag	1/9	0.117942747234421	3	FACETS	1	0.893	1			1	INDETERMINATE	1	TRUE	NA	0.29	3		260	673	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378278	225378278	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	69	244	0	ENST00000264414.4:c.617A>G	p.Glu206Gly	p.E206G	ENST00000264414	NM_003590.4	206	gAg/gGg	5/16	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.29	2		244	420	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0069651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	137	358	0				ENST00000310581	NM_198253.2	-/1132			0.1167011178136	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.745330417447817	0		358	486	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0069651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	19	282	1	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.147	0.111	0.189	0.147	0.111	0.189	SUBCLONAL	1	TRUE	1	0.745330417447817	2		283	347	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653834	89653834	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0069651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	139	329	0	ENST00000371953.3:c.132del	p.Val45TyrfsTer9	p.V45Yfs*9	ENST00000371953	NM_000314.4	44	ggC/gg	2/9	1	2	FACETS	0.743	0.681	0.808	0.743	0.681	0.808	SUBCLONAL	1	TRUE	1	0.745330417447817	2		329	502	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717630	89717630	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554825168	NA	P-0069651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	145	399	0	ENST00000371953.3:c.655C>T	p.Gln219Ter	p.Q219*	ENST00000371953	NM_000314.4	219	Cag/Tag	7/9	1	2	FACETS	0.672	0.616	0.73	0.672	0.616	0.73	SUBCLONAL	1	TRUE	1	0.745330417447817	2		399	579	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0069652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	548	112	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		112	679	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602354	28602354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1367367961	NA	P-0069652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	195	311	0	ENST00000241453.7:c.2014G>A	p.Glu672Lys	p.E672K	ENST00000241453	NM_004119.2	672	Gag/Aag	16/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		311	408	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401080	139401080	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775602958	NA	P-0069652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	40	428	0	ENST00000277541.6:c.3913G>A	p.Glu1305Lys	p.E1305K	ENST00000277541	NM_017617.3	1305	Gag/Aag	24/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		428	382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574035	7574035	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs867389695	NA	P-0069652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	165	285	0	ENST00000269305.4:c.994-2A>G		p.X332_splice	ENST00000269305	NM_001126112.2	332			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		285	201	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469919	157469919	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	38	440	1	ENST00000346085.5:c.2713C>T	p.Gln905Ter	p.Q905*	ENST00000346085	NM_020732.3	905	Cag/Tag	9/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		441	356	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968244	2968244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161484391	NA	P-0069652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	272	362	0	ENST00000396946.4:c.1742C>T	p.Ala581Val	p.A581V	ENST00000396946	NM_032415.4	581	gCg/gTg	13/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		362	480	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602426	28602426	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0069652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	169	243	0	ENST00000241453.7:c.1943-1G>A		p.X648_splice	ENST00000241453	NM_004119.2	648			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		243	334	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755928	133755928	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	27	380	0	ENST00000318560.5:c.1555G>C	p.Val519Leu	p.V519L	ENST00000318560	NM_005157.4	519	Gtg/Ctg	10/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		380	398	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137294	64137294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	17	405	0	ENST00000334205.4:c.1726G>A	p.Ala576Thr	p.A576T	ENST00000334205	NM_003942.2	576	Gct/Act	14/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		405	305	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731479	47731479	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	168	353	0	ENST00000449228.1:c.313del	p.Arg105AlafsTer124	p.R105Afs*124	ENST00000449228	NM_001127240.2	105	Cgc/gc	2/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		353	356	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948790	55948790	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	13	237	0	ENST00000263923.4:c.3675G>C	p.Gln1225His	p.Q1225H	ENST00000263923	NM_002253.2	1225	caG/caC	28/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		237	178	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76777853	76777853	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	25	362	0	ENST00000373344.5:c.6863G>T	p.Arg2288Leu	p.R2288L	ENST00000373344	NM_000489.3	2288	cGt/cTt	32/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		362	402	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61306554	61306554	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	23	380	0	ENST00000341074.5:c.633G>C	p.Gln211His	p.Q211H	ENST00000341074	NM_002974.2	211	caG/caC	7/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		380	336	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980418	201980418	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	235	389	1	ENST00000359651.3:c.154G>T	p.Glu52Ter	p.E52*	ENST00000359651		52	Gag/Tag	1/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		390	690	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955522	48955522	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	20	313	0	ENST00000267163.4:c.1638G>C	p.Met546Ile	p.M546I	ENST00000267163	NM_000321.2	546	atG/atC	17/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		313	169	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039417	49039418	+	frameshift_variant	Frame_Shift_Ins	INS	GA	GA	CAG	novel	NA	P-0069652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	218	393	0	ENST00000267163.4:c.2402_2403delinsCAG	p.Gly801AlafsTer14	p.G801Afs*14	ENST00000267163	NM_000321.2	801	gGA/gCAG	23/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		393	259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0069653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	233	329	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.801663540481263	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.801663540481263	1		329	303	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794756	120794756	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	162	292	0	ENST00000257552.2:c.601C>G	p.Arg201Gly	p.R201G	ENST00000257552	NM_002442.3	201	Cga/Gga	9/15	0.160453333522351	2	FACETS	0.894	0.828	0.962	0.447	0.414	0.481	INDETERMINATE	1	TRUE	0	0.801663540481263	2		292	452	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123666	46123666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	223	397	0	ENST00000334344.6:c.47G>A	p.Gly16Glu	p.G16E	ENST00000334344	NM_152641.2	16	gGa/gAa	1/21	0.160453333522351	2	FACETS	1	0.988	1	0.596	0.561	0.63	INDETERMINATE	1	TRUE	0	0.801663540481263	2		397	467	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592121	67592121	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	362	258	0	ENST00000274335.5:c.1937T>C	p.Phe646Ser	p.F646S	ENST00000274335		646	tTt/tCt	14/15	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.801663540481263	2		258	438	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	82	294	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.145547400887131	3	FACETS	0.778	0.703	0.855	0.778	0.703	0.855	INDETERMINATE	2	TRUE	1	0.790676764206502	3		294	186	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61324085	61324085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	24	239	0	ENST00000283752.5:c.748G>A	p.Glu250Lys	p.E250K	ENST00000283752	NM_006919.2	250	Gaa/Aaa	7/8	0.175661589983675	1	FACETS	0.437	0.352	0.53	0.437	0.352	0.53	INDETERMINATE	1	TRUE	0	0.790676764206502	1		239	84	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488718	212488718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267599191	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	113	369	0	ENST00000342788.4:c.2131C>T	p.Arg711Cys	p.R711C	ENST00000342788	NM_005235.2	711	Cgt/Tgt	18/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.790676764206502	2		369	242	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	42	273	0				ENST00000310581	NM_198253.2	-/1132			0.241494627981617	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.790676764206502	0		273	83	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557782	187557782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200252550	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	98	331	0	ENST00000441802.2:c.3929C>T	p.Ser1310Leu	p.S1310L	ENST00000441802	NM_005245.3	1310	tCg/tTg	5/27	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.790676764206502	2		331	221	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	84	293	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.790676764206502	2		293	188	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520274	176520274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1562071377	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	61	315	0	ENST00000292408.4:c.1193G>A	p.Arg398Gln	p.R398Q	ENST00000292408	NM_213647.1	398	cGg/cAg	9/18	0.175661589983675	1	FACETS	0.618	0.547	0.691	0.618	0.547	0.691	INDETERMINATE	1	TRUE	0	0.790676764206502	1		315	151	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93973599	93973599	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750462795	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	57	223	0	ENST00000369303.4:c.1777G>A	p.Asp593Asn	p.D593N	ENST00000369303	NM_004440.3	593	Gat/Aat	9/17	0.175661589983675	1	FACETS	0.589	0.518	0.663	0.589	0.518	0.663	INDETERMINATE	1	TRUE	0	0.790676764206502	1		223	148	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511630	46511630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773472193	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	98	244	0	ENST00000262741.5:c.1147C>T	p.Arg383Cys	p.R383C	ENST00000262741	NM_003629.3	383	Cgt/Tgt	9/10	0.145547400887131	3	FACETS	1	0.984	1	0.727	0.661	0.794	INDETERMINATE	1	TRUE	1	0.790676764206502	3		244	238	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420092	41420092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	48	312	0	ENST00000373198.4:c.229G>A	p.Val77Met	p.V77M	ENST00000373198	NM_133170.3	77	Gtg/Atg	3/32	0.793115983389536	1	FACETS	0.583	0.506	0.662	0.583	0.506	0.662	SUBCLONAL	1	TRUE	0	0.790676764206502	1		312	126	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8497265	8497265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1270795879	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	52	212	0	ENST00000356435.5:c.2326G>A	p.Glu776Lys	p.E776K	ENST00000356435		776	Gaa/Aaa	15/35	0.410649929961109	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.790676764206502	0		212	129	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168751	32168751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377716761	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	84	387	0	ENST00000375023.3:c.4172G>A	p.Arg1391His	p.R1391H	ENST00000375023	NM_004557.3	1391	cGc/cAc	23/30	0.565699510445542	4	FACETS	1	0.976	1	0.455	0.406	0.505	CLONAL	1	TRUE	1	0.790676764206502	4		387	279	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050656	69050656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752015034	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	91	222	0	ENST00000288368.4:c.3991G>A	p.Glu1331Lys	p.E1331K	ENST00000288368	NM_024870.2	1331	Gaa/Aaa	33/40	0.540991901528585	1	FACETS	0.854	0.783	0.924	0.854	0.783	0.924	CLONAL	1	TRUE	0	0.790676764206502	1		222	163	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841231	15841242	+	inframe_deletion	In_Frame_Del	DEL	AGCCGGAGCCGG	AGCCGGAGCCGG	-	rs752736259	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	81	223	0	ENST00000307771.7:c.1332_1343del	p.Ser445_Arg448del	p.S445_R448del	ENST00000307771	NM_005089.3	439	AGCCGGAGCCGG/-	11/11	0.549157606282773	2	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.790676764206502	2		223	147	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285570	46285570	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs78222561	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	83	274	0	ENST00000334344.6:c.4930C>T	p.Gln1644Ter	p.Q1644*	ENST00000334344	NM_152641.2	1644	Cag/Tag	17/21	0.188243065181144	4	FACETS	1	0.936	1	1	0.936	1	INDETERMINATE	2	TRUE	2	0.790676764206502	4		274	180	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799258	42799258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs530430600	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	83	292	0	ENST00000575354.2:c.4742C>T	p.Ser1581Leu	p.S1581L	ENST00000575354	NM_015125.3	1581	tCg/tTg	20/20	0.188243065181144	4	FACETS	0.899	0.81	0.991	0.899	0.81	0.991	INDETERMINATE	2	TRUE	2	0.790676764206502	4		292	209	SUCCESS
YES1	7525	MSKCC	GRCh37	18	732954	732954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	101	292	0	ENST00000314574.4:c.1303C>T	p.Pro435Ser	p.P435S	ENST00000314574	NM_005433.3	435	Cca/Tca	11/12	0.793115983389536	3	FACETS	1	0.965	1	0.571	0.517	0.628	CLONAL	1	TRUE	1	0.790676764206502	3		292	312	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020422	69020422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	32	328	0	ENST00000288368.4:c.2794G>A	p.Asp932Asn	p.D932N	ENST00000288368	NM_024870.2	932	Gat/Aat	24/40	0.540991901528585	1	FACETS	0.302	0.248	0.361	0.302	0.248	0.361	SUBCLONAL	1	TRUE	0	0.790676764206502	1		328	162	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710638	40710638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	41	322	0	ENST00000373198.4:c.4213G>A	p.Gly1405Arg	p.G1405R	ENST00000373198	NM_133170.3	1405	Gga/Aga	31/32	0.793115983389536	1	FACETS	0.494	0.421	0.571	0.494	0.421	0.571	SUBCLONAL	1	TRUE	0	0.790676764206502	1		322	127	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873410	136873410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	79	348	0	ENST00000241393.3:c.88C>T	p.Arg30Cys	p.R30C	ENST00000241393	NM_003467.2	30	Cgt/Tgt	2/2	1	2	FACETS	0.994	0.892	1	0.994	0.892	1	CLONAL	1	TRUE	1	0.790676764206502	2		348	201	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935517	13935517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	158	363	0	ENST00000405192.2:c.1339C>T	p.Pro447Ser	p.P447S	ENST00000405192	NM_001163147.1	447	Ccc/Tcc	12/12	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.790676764206502	2		363	357	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35860977	35860977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1177711424	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	84	317	0	ENST00000303115.3:c.106G>A	p.Asp36Asn	p.D36N	ENST00000303115	NM_002185.3	36	Gat/Aat	2/8	1	2	FACETS	0.966	0.869	1	0.966	0.869	1	CLONAL	1	TRUE	1	0.790676764206502	2		317	220	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231302	46231302	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	80	302	0	ENST00000334344.6:c.1142T>G	p.Leu381Arg	p.L381R	ENST00000334344	NM_152641.2	381	cTt/cGt	10/21	0.188243065181144	4	FACETS	0.839	0.752	0.928	0.839	0.752	0.928	INDETERMINATE	2	TRUE	2	0.790676764206502	4		302	216	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439262	52439262	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	121	359	0	ENST00000460680.1:c.980G>A	p.Ser327Asn	p.S327N	ENST00000460680	NM_004656.3	327	aGc/aAc	11/17	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.790676764206502	2		359	287	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914380	32914380	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659836	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	64	369	0	ENST00000380152.3:c.5888G>A	p.Gly1963Glu	p.G1963E	ENST00000380152		1963	gGg/gAg	11/27	1	2	FACETS	0.794	0.699	0.893	0.794	0.699	0.893	SUBCLONAL	1	TRUE	1	0.790676764206502	2		369	204	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843490	156843490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	75	388	0	ENST00000524377.1:c.916G>A	p.Asp306Asn	p.D306N	ENST00000524377	NM_002529.3	306	Gat/Aat	8/17	0.793115983389536	3	FACETS	0.935	0.829	1	0.468	0.414	0.524	CLONAL	1	TRUE	1	0.790676764206502	3		388	283	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805767	43805767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28928908	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	73	355	0	ENST00000372470.3:c.823C>T	p.Pro275Ser	p.P275S	ENST00000372470	NM_005373.2	275	Cct/Tct	5/12	0.145547400887131	3	FACETS	1	0.972	1	0.657	0.586	0.73	INDETERMINATE	1	TRUE	1	0.790676764206502	3		355	196	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209106754	209106754	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	101	330	0	ENST00000345146.2:c.814T>A	p.Tyr272Asn	p.Y272N	ENST00000345146	NM_005896.2	272	Tat/Aat	7/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.790676764206502	2		330	221	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488657	212488657	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	119	335	0	ENST00000342788.4:c.2192C>G	p.Thr731Arg	p.T731R	ENST00000342788	NM_005235.2	731	aCg/aGg	18/28	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.790676764206502	2		335	274	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717740	89717741	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs869312780	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	19	218	0	ENST00000371953.3:c.767_768del	p.Glu256ValfsTer41	p.E256Vfs*41	ENST00000371953	NM_000314.4	255	gtAGag/gtag	7/9	1	2	FACETS	0.21	0.159	0.269	0.21	0.159	0.269	SUBCLONAL	1	TRUE	1	0.790676764206502	2		218	229	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319063	62319063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	159	386	0	ENST00000360203.5:c.1421C>T	p.Ser474Phe	p.S474F	ENST00000360203	NM_001283009.1	474	tCc/tTc	17/35	0.145547400887131	3	FACETS	0.782	0.727	0.837	0.782	0.727	0.837	INDETERMINATE	2	TRUE	1	0.790676764206502	3		386	359	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444217	49444217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	113	474	0	ENST00000301067.7:c.3154C>T	p.Pro1052Ser	p.P1052S	ENST00000301067	NM_003482.3	1052	Ccc/Tcc	11/54	0.188243065181144	4	FACETS	0.812	0.741	0.886	0.812	0.741	0.886	INDETERMINATE	2	TRUE	2	0.790676764206502	4		474	315	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162735817	162735817	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1433620058	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	28	320	0	ENST00000367921.3:c.1126G>A	p.Ala376Thr	p.A376T	ENST00000367921	NM_006182.2	376	Gcc/Acc	10/18	0.793115983389536	3	FACETS	0.253	0.202	0.311	0.126	0.101	0.156	SUBCLONAL	1	TRUE	1	0.790676764206502	3		320	391	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128018859	128018859	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	79	305	0	ENST00000285398.2:c.2009T>C	p.Met670Thr	p.M670T	ENST00000285398	NM_000122.1	670	aTg/aCg	13/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.790676764206502	2		305	179	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205136	128205136	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	84	357	0	ENST00000341105.2:c.305A>C	p.Lys102Thr	p.K102T	ENST00000341105	NM_032638.4	102	aAa/aCa	3/6	1	2	FACETS	0.975	0.877	1	0.975	0.877	1	CLONAL	1	TRUE	1	0.790676764206502	2		357	218	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223121	36223121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243979676	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	112	390	0	ENST00000222270.7:c.5671C>T	p.Pro1891Ser	p.P1891S	ENST00000222270	NM_014727.1	1891	Cca/Tca	28/37	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.790676764206502	2		390	266	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515163	149515163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	96	385	0	ENST00000261799.4:c.319G>A	p.Gly107Arg	p.G107R	ENST00000261799	NM_002609.3	107	Gga/Aga	3/23	0.790676764206502	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.790676764206502	1		385	139	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032116	10032116	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	31	314	0	ENST00000330684.3:c.707C>T	p.Ala236Val	p.A236V	ENST00000330684	NM_001134407.1	236	gCt/gTt	3/13	NA	2	FACETS	0.852	0.71	1			1	INDETERMINATE	1	TRUE	NA	0.790676764206502	2		314	92	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79974881	79974881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	89	263	0	ENST00000265081.6:c.1309G>A	p.Glu437Lys	p.E437K	ENST00000265081	NM_002439.4	437	Gag/Aag	8/24	1	2	FACETS	0.938	0.846	1	0.938	0.846	1	CLONAL	1	TRUE	1	0.790676764206502	2		263	240	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056280	26056280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1561927269	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	169	411	0	ENST00000343677.2:c.377C>T	p.Thr126Ile	p.T126I	ENST00000343677	NM_005319.3	126	aCc/aTc	1/1	0.565699510445542	4	FACETS	1	0.984	1	0.418	0.386	0.452	CLONAL	1	TRUE	1	0.790676764206502	4		411	610	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190742140	190742140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	68	236	0	ENST00000441310.2:c.2777C>T	p.Thr926Ile	p.T926I	ENST00000441310	NM_000534.4	926	aCc/aTc	13/13	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.790676764206502	2		236	170	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260156	16260156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	88	409	0	ENST00000375759.3:c.7421C>T	p.Ser2474Phe	p.S2474F	ENST00000375759	NM_015001.2	2474	tCt/tTt	11/15	0.145547400887131	3	FACETS	1	0.973	1	0.626	0.564	0.691	INDETERMINATE	1	TRUE	1	0.790676764206502	3		409	248	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99162431	99162432	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	55	268	0	ENST00000074304.5:c.950-1_950delinsAA		p.X317_splice	ENST00000074304	NM_001134224.1	317		12/26	1	2	FACETS	0.795	0.693	0.902	0.795	0.693	0.902	CLONAL	1	TRUE	1	0.790676764206502	2		268	175	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431346	121431346	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	69	327	0	ENST00000257555.6:c.550G>A	p.Gly184Arg	p.G184R	ENST00000257555		184	Ggg/Agg	3/10	0.175661589983675	1	FACETS	0.555	0.493	0.62	0.555	0.493	0.62	INDETERMINATE	1	TRUE	0	0.790676764206502	1		327	190	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619278	23619278	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	85	287	0	ENST00000261584.4:c.3257G>C	p.Arg1086Pro	p.R1086P	ENST00000261584	NM_024675.3	1086	cGa/cCa	12/13	1	2	FACETS	0.982	0.885	1	0.982	0.885	1	CLONAL	1	TRUE	1	0.790676764206502	2		287	219	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146410	185146410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	46	273	0	ENST00000265026.3:c.41C>T	p.Pro14Leu	p.P14L	ENST00000265026	NM_004721.4	14	cCa/cTa	2/14	1	2	FACETS	0.881	0.76	1	0.881	0.76	1	CLONAL	1	TRUE	1	0.790676764206502	2		273	132	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967783	90967783	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1057519588	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	163	258	0	ENST00000265433.3:c.1125G>A	p.Trp375Ter	p.W375*	ENST00000265433	NM_002485.4	375	tgG/tgA	10/16	0.793115983389536	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.790676764206502	3		258	261	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31239796	31239796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	38	287	0	ENST00000376228.5:c.53C>T	p.Ala18Val	p.A18V	ENST00000376228	NM_002117.5	18	gCc/gTc	1/8	0.565699510445542	4	FACETS	0.533	0.442	0.634	0.178	0.147	0.212	SUBCLONAL	1	TRUE	1	0.790676764206502	4		287	323	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350810	15350810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	72	293	0	ENST00000263377.2:c.3193C>T	p.Pro1065Ser	p.P1065S	ENST00000263377	NM_058243.2	1065	Ccg/Tcg	15/20	1	2	FACETS	0.855	0.76	0.954	0.855	0.76	0.954	CLONAL	1	TRUE	1	0.790676764206502	2		293	213	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099954	27099955	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	90	395	0	ENST00000324856.7:c.3833_3834delinsTT	p.His1278Leu	p.H1278L	ENST00000324856	NM_006015.4	1278	cAC/cTT	15/20	0.145547400887131	3	FACETS	1	0.965	1	0.584	0.525	0.645	INDETERMINATE	1	TRUE	1	0.790676764206502	3		395	272	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123260439	123260440	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	54	323	0	ENST00000358487.5:c.1461_1462delinsAA	p.Gly488Arg	p.G488R	ENST00000358487	NM_000141.4	487	ctGGga/ctAAga	11/18	1	2	FACETS	0.781	0.679	0.887	0.781	0.679	0.887	SUBCLONAL	1	TRUE	1	0.790676764206502	2		323	175	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1687953	1687953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	105	390	0	ENST00000378625.1:c.923C>T	p.Thr308Ile	p.T308I	ENST00000378625	NM_001198994.1	308	aCc/aTc	7/14	0.145547400887131	3	FACETS	1	0.984	1	0.707	0.645	0.771	INDETERMINATE	1	TRUE	1	0.790676764206502	3		390	262	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152357804	152357804	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	84	232	0	ENST00000359321.1:c.103G>A	p.Glu35Lys	p.E35K	ENST00000359321	NM_005431.1	35	Gaa/Aaa	2/3	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.790676764206502	2		232	192	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022353	31022353	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1287753337	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	93	370	0	ENST00000375687.4:c.1838C>T	p.Thr613Ile	p.T613I	ENST00000375687	NM_015338.5	613	aCc/aTc	13/13	1	2	FACETS	0.976	0.883	1	0.976	0.883	1	CLONAL	1	TRUE	1	0.790676764206502	2		370	241	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125513727	125513727	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	93	313	0	ENST00000428830.2:c.855G>T	p.Glu285Asp	p.E285D	ENST00000428830	NM_001114121.2	285	gaG/gaT	9/14	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.790676764206502	2		313	206	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843329	128843362	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTGCCAGGCCACCCGAGGCCCCTGTGCCATCG	CTCTGCCAGGCCACCCGAGGCCCCTGTGCCATCG	TC	novel	NA	P-0069654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	52	334	1	ENST00000249373.3:c.436_469delinsTC	p.Leu146SerfsTer9	p.L146Sfs*9	ENST00000249373	NM_005631.4	146	CTCTGCCAGGCCACCCGAGGCCCCTGTGCCATCGtg/TCtg	2/12	1	2	FACETS	0.838	0.728	0.952	0.838	0.728	0.952	CLONAL	1	TRUE	1	0.790676764206502	2		335	157	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765633	41765633	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs146164767	NA	P-0069655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	129	405	0	ENST00000301178.4:c.2509G>T	p.Ala837Ser	p.A837S	ENST00000301178	NM_021913.4	837	Gca/Tca	20/20	1	2	FACETS	0.708	0.644	0.776	0.708	0.644	0.776	SUBCLONAL	1	TRUE	1	0.564616605500675	2		405	645	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0069656-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	79	308	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.316070736648472	2		308	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0069656-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	87	308	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.316070736648472	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.316070736648472	1		308	450	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069656-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	61	414	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.82	0.708	0.94	0.82	0.708	0.94	CLONAL	1	TRUE	1	0.316070736648472	2		414	471	SUCCESS
RET	5979	MSKCC	GRCh37	10	43613892	43613892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1400642102	NA	P-0069656-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	60	236	0	ENST00000355710.3:c.2356C>T	p.His786Tyr	p.H786Y	ENST00000355710	NM_020975.4	786	Cat/Tat	13/20	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.316070736648472	2		236	379	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942662	48942662	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0069656-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	34	207	0	ENST00000267163.4:c.1050-1G>C		p.X350_splice	ENST00000267163	NM_000321.2	350			0.309980522318604	3	FACETS	0.593	0.485	0.715	0.297	0.242	0.358	SUBCLONAL	1	TRUE	1	0.316070736648472	3		207	420	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980408	55980408	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069657-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	73	360	0	ENST00000263923.4:c.683T>A	p.Leu228Gln	p.L228Q	ENST00000263923	NM_002253.2	228	cTg/cAg	6/30	1	2	FACETS	0.894	0.787	1	0.894	0.787	1	CLONAL	1	TRUE	1	0.461465789092887	2		360	354	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0069658-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	22	244	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.748	0.579	0.943	0.748	0.579	0.943	CLONAL	1	TRUE	1	0.18	2		244	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0069658-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	24	409	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.635	0.497	0.794	0.635	0.497	0.794	SUBCLONAL	1	TRUE	1	0.18	2		409	420	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867545	101867588	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCGGCGGCGGCGGCGGCGGCGCTGCTCCCGGGGGCGACGGGTGA	GCGGCGGCGGCGGCGGCGGCGCTGCTCCCGGGGGCGACGGGTGA	-	novel	NA	P-0069658-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	16	174	0	ENST00000374994.4:c.67_97+13del		p.X23_splice	ENST00000374994	NM_004612.2	23		1/9	1	2	FACETS	1	0.827	1	1	0.827	1	CLONAL	1	TRUE	1	0.18	2		174	154	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0069661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	152	285	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	0.171735827642577	4	FACETS	1	0.982	1			1	INDETERMINATE	2	TRUE	NA	0.327494721001551	4		285	502	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354038	15354038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201742792	NA	P-0069661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	31	175	0	ENST00000263377.2:c.2842G>A	p.Val948Met	p.V948M	ENST00000263377	NM_058243.2	948	Gtg/Atg	14/20	1	2	FACETS	0.838	0.682	1	0.838	0.682	1	CLONAL	1	TRUE	1	0.327494721001551	2		175	226	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566827	212566827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202247795	NA	P-0069661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	79	337	0	ENST00000342788.4:c.1354G>A	p.Glu452Lys	p.E452K	ENST00000342788	NM_005235.2	452	Gaa/Aaa	12/28	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.327494721001551	2		337	451	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612176	189612176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	57	306	0	ENST00000264731.3:c.1928G>A	p.Arg643Gln	p.R643Q	ENST00000264731	NM_003722.4	643	cGa/cAa	14/14	1	2	FACETS	0.893	0.769	1	0.893	0.769	1	CLONAL	1	TRUE	1	0.327494721001551	2		306	390	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895604	28895604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	51	266	0	ENST00000282397.4:c.3170G>A	p.Gly1057Glu	p.G1057E	ENST00000282397	NM_002019.4	1057	gGa/gAa	23/30	1	2	FACETS	0.74	0.63	0.86	0.74	0.63	0.86	SUBCLONAL	1	TRUE	1	0.327494721001551	2		266	421	SUCCESS
BTK	695	MSKCC	GRCh37	X	100609658	100609658	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782740486	NA	P-0069661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	72	116	0	ENST00000308731.7:c.1591G>A	p.Asp531Asn	p.D531N	ENST00000308731	NM_000061.2	531	Gat/Aat	16/19	1	1	FACETS	0.796	0.706	0.89	1	0.979	1	SUBCLONAL	2	TRUE	0	0.327494721001551	1		116	231	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992729	68992729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779079528	NA	P-0069661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	65	280	0	ENST00000288368.4:c.1694C>T	p.Ser565Leu	p.S565L	ENST00000288368	NM_024870.2	565	tCg/tTg	16/40	0.27110852042035	3	FACETS	1	0.938	1	0.566	0.493	0.645	CLONAL	1	TRUE	1	0.327494721001551	3		280	408	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716366	18716366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs935135637	NA	P-0069661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	71	281	0	ENST00000266497.5:c.3713C>T	p.Ser1238Leu	p.S1238L	ENST00000266497		1238	tCa/tTa	26/31	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.327494721001551	2		281	395	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804342	46804342	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770172581	NA	P-0069661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	66	274	0	ENST00000290295.7:c.665C>T	p.Pro222Leu	p.P222L	ENST00000290295	NM_006361.5	222	cCg/cTg	2/2	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.327494721001551	2		274	360	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271193	153271193	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0069661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	41	186	0	ENST00000281708.4:c.584+1G>A		p.X195_splice	ENST00000281708	NM_033632.3	195			1	2	FACETS	0.91	0.763	1	0.91	0.763	1	CLONAL	1	TRUE	1	0.327494721001551	2		186	275	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524651	176524651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	59	354	0	ENST00000292408.4:c.2383C>T	p.Pro795Ser	p.P795S	ENST00000292408	NM_213647.1	795	Ccc/Tcc	18/18	1	2	FACETS	0.875	0.755	1	0.875	0.755	1	CLONAL	1	TRUE	1	0.327494721001551	2		354	412	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332595	153332595	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	85	403	0	ENST00000281708.4:c.361G>T	p.Glu121Ter	p.E121*	ENST00000281708	NM_033632.3	121	Gag/Tag	2/12	1	2	FACETS	0.944	0.836	1	0.944	0.836	1	CLONAL	1	TRUE	1	0.327494721001551	2		403	550	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999521	100999521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780296630	NA	P-0069661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	67	365	0	ENST00000325455.5:c.281G>A	p.Arg94Lys	p.R94K	ENST00000325455	NM_001202474.3	94	aGg/aAg	1/8	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.327494721001551	2		365	404	SUCCESS
APC	324	MSKCC	GRCh37	5	112177805	112177805	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	79	340	0	ENST00000257430.4:c.6514G>T	p.Glu2172Ter	p.E2172*	ENST00000257430	NM_000038.5	2172	Gag/Tag	16/16	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.327494721001551	2		340	471	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955431	48955431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	56	226	0	ENST00000267163.4:c.1547G>A	p.Trp516Ter	p.W516*	ENST00000267163	NM_000321.2	516	tGg/tAg	17/27	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.327494721001551	2		226	334	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149238612	149238612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239352404	NA	P-0069661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	96	275	0	ENST00000360632.3:c.1183C>T	p.Pro395Ser	p.P395S	ENST00000360632	NM_015472.4	395	Ccc/Tcc	7/7	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.327494721001551	2		275	442	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553452	29553452	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1555613743	NA	P-0069661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	77	290	0	ENST00000356175.3:c.2002-1G>A		p.X668_splice	ENST00000356175	NM_000267.3	668			1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.327494721001551	2		290	425	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954378	48954378	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1131690909	NA	P-0069661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	63	172	0	ENST00000267163.4:c.1498+1G>A		p.X500_splice	ENST00000267163	NM_000321.2	500			1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.327494721001551	2		172	363	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226084	2226084	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	64	357	0	ENST00000326181.6:c.1781C>T	p.Thr594Ile	p.T594I	ENST00000326181	NM_032271.2	594	aCc/aTc	19/21	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.327494721001551	2		357	380	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17124889	17124890	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0069661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	59	369	0	ENST00000285071.4:c.832_833delinsTT	p.Pro278Leu	p.P278L	ENST00000285071	NM_144997.5	278	CCg/TTg	8/14	1	2	FACETS	0.877	0.757	1	0.877	0.757	1	CLONAL	1	TRUE	1	0.327494721001551	2		369	411	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851567	134851567	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	58	231	0	ENST00000398015.3:c.973G>A	p.Gly325Ser	p.G325S	ENST00000398015	NM_004441.4	325	Ggt/Agt	5/16	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.327494721001551	2		231	334	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257513	16257513	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0069661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	80	393	0	ENST00000375759.3:c.4778T>G	p.Met1593Arg	p.M1593R	ENST00000375759	NM_015001.2	1593	aTg/aGg	11/15	1	2	FACETS	0.987	0.871	1	0.987	0.871	1	CLONAL	1	TRUE	1	0.327494721001551	2		393	495	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587378	29587388	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTTGAAGGT	TTTTTGAAGGT	-	novel	NA	P-0069661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	67	220	0	ENST00000356175.3:c.4368-5_4373del		p.X1456_splice	ENST00000356175	NM_000267.3	1456		33/57	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.327494721001551	2		220	339	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138561	55138561	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	71	207	0	ENST00000257290.5:c.1238T>C	p.Val413Ala	p.V413A	ENST00000257290	NM_006206.4	413	gTt/gCt	9/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.327494721001551	2		207	355	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536159	106536159	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs770298280	NA	P-0069661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	56	292	0	ENST00000369096.4:c.126G>T	p.Glu42Asp	p.E42D	ENST00000369096	NM_001198.3	42	gaG/gaT	2/7	1	2	FACETS	0.844	0.726	0.973	0.844	0.726	0.973	CLONAL	1	TRUE	1	0.327494721001551	2		292	405	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027023	71027023	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	75	372	0	ENST00000318789.4:c.1304T>C	p.Ile435Thr	p.I435T	ENST00000318789	NM_032682.5	435	aTc/aCc	15/21	1	2	FACETS	0.9	0.79	1	0.9	0.79	1	CLONAL	1	TRUE	1	0.327494721001551	2		372	509	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998101	169998101	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0069661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	61	254	0	ENST00000295797.4:c.792T>G	p.Ser264Arg	p.S264R	ENST00000295797	NM_002740.5	264	agT/agG	9/18	1	2	FACETS	0.893	0.773	1	0.893	0.773	1	CLONAL	1	TRUE	1	0.327494721001551	2		254	417	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197588	106197588	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	65	348	0	ENST00000380013.4:c.5922del	p.Thr1975ProfsTer4	p.T1975Pfs*4	ENST00000380013	NM_001127208.2	1974	aGg/ag	11/11	1	2	FACETS	0.968	0.843	1	0.968	0.843	1	CLONAL	1	TRUE	1	0.327494721001551	2		348	410	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0069662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	159	112	0				ENST00000310581	NM_198253.2	-/1132			0.30601503152049	4	FACETS	1	0.976	1	1	0.991	1	CLONAL	4	TRUE	1	0.30601503152049	4		112	309	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0069662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	258	167	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	0.30601503152049	4	FACETS	0.964	0.912	1	1	0.992	1	CLONAL	4	TRUE	1	0.30601503152049	4		167	571	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983125	201983126	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAT	novel	NA	P-0069662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	82	130	0	ENST00000359651.3:c.975_976insATC	p.Thr325_Tyr326insIle	p.T325_Y326insI	ENST00000359651		325	acc/acCATc	7/8	0.246864187688774	4	FACETS	0.814	0.721	0.912	0.543	0.481	0.608	CLONAL	2	TRUE	1	0.30601503152049	4		130	430	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961819	41961819	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	40	168	0	ENST00000219905.7:c.727C>G	p.Gln243Glu	p.Q243E	ENST00000219905	NM_001164273.1	243	Cag/Gag	2/24	0.30601503152049	3	FACETS	1	0.936	1	0.628	0.526	0.74	CLONAL	1	TRUE	1	0.30601503152049	3		168	240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0069663-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	119	299	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.458842192829782	3	FACETS	1	0.938	1	0.687	0.629	0.746	CLONAL	2	TRUE	0	0.452627771694186	3		299	313	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729888	41729888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1043609570	NA	P-0069663-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	48	327	0	ENST00000242208.4:c.641G>A	p.Arg214Gln	p.R214Q	ENST00000242208	NM_002192.2	214	cGg/cAg	3/3	0.264482484394699	4	FACETS	0.844	0.716	0.984	0.422	0.358	0.492	INDETERMINATE	1	TRUE	2	0.452627771694186	4		327	365	SUCCESS
AR	367	MSKCC	GRCh37	X	66931262	66931262	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069663-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	95	175	0	ENST00000374690.3:c.1904T>C	p.Leu635Pro	p.L635P	ENST00000374690	NM_000044.3	635	cTt/cCt	4/8	0.458842192829782	2	FACETS	1	0.959	1			1	CLONAL	2	TRUE	NA	0.452627771694186	2		175	193	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995501	68995501	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1326956245	NA	P-0069663-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	56	286	0	ENST00000288368.4:c.1905G>T	p.Lys635Asn	p.K635N	ENST00000288368	NM_024870.2	635	aaG/aaT	18/40	0.443260471481703	4	FACETS	0.875	0.751	1	0.437	0.375	0.504	CLONAL	1	TRUE	2	0.452627771694186	4		286	411	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044840	47044840	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0069663-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	53	256	0	ENST00000377604.3:c.2167-1G>A		p.X723_splice	ENST00000377604	NM_001204468.1	723			0.458842192829782	2	FACETS	0.929	0.8	1			1	CLONAL	1	TRUE	NA	0.452627771694186	2		256	252	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858299	9858299	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069663-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	46	424	1	ENST00000330684.3:c.3102G>T	p.Arg1034Ser	p.R1034S	ENST00000330684	NM_001134407.1	1034	agG/agT	13/13	1	2	FACETS	0.718	0.609	0.838	0.718	0.609	0.838	SUBCLONAL	1	TRUE	1	0.452627771694186	2		425	283	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805562	32805562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751087452	NA	P-0069663-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	141	377	0	ENST00000374899.4:c.449C>T	p.Pro150Leu	p.P150L	ENST00000374899	NM_018833.2	150	cCt/cTt	2/12	0.222137519348796	5	FACETS	1	0.923	1	0.672	0.616	0.73	INDETERMINATE	2	TRUE	2	0.452627771694186	5		377	519	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467838	66467838	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069663-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	40	370	0	ENST00000273854.3:c.431T>A	p.Leu144Gln	p.L144Q	ENST00000273854	NM_004439.5	144	cTg/cAg	3/18	1	2	FACETS	0.572	0.477	0.677	0.572	0.477	0.677	SUBCLONAL	1	TRUE	1	0.452627771694186	2		370	309	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526613	106526613	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0069663-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	85	248	0	ENST00000359195.3:c.2906T>G	p.Leu969Arg	p.L969R	ENST00000359195	NM_002649.2	969	cTt/cGt	10/11	0.458842192829782	3	FACETS	1	0.971	1	0.64	0.57	0.713	CLONAL	1	TRUE	1	0.452627771694186	3		248	360	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0069664-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	62	244	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.778	0.675	0.889	1	0.972	1	SUBCLONAL	2	TRUE	1	0.206941231075443	2		244	385	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686258	30686259	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0069664-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	47	406	0	ENST00000295754.5:c.115_116del	p.Thr39Ter	p.T39*	ENST00000295754	NM_003242.5	38	gtCAct/gtct	2/7	0.206941231075443	1	FACETS	0.861	0.727	1	0.861	0.727	1	CLONAL	1	TRUE	0	0.206941231075443	1		406	473	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0069666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	27	322	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.696	0.562	0.846	0.696	0.562	0.846	SUBCLONAL	1	TRUE	1	0.553971897076222	2		322	140	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0069666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	46	202	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.553971897076222	1	FACETS	0.846	0.728	0.969	0.846	0.728	0.969	CLONAL	1	TRUE	0	0.553971897076222	1		202	142	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272498	15272498	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200541224	NA	P-0069666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	55	273	0	ENST00000263388.2:c.5941C>T	p.Arg1981Cys	p.R1981C	ENST00000263388	NM_000435.2	1981	Cgc/Tgc	33/33	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.553971897076222	2		273	170	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945198	44945198	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	33	231	0	ENST00000377967.4:c.3522G>A	p.Trp1174Ter	p.W1174*	ENST00000377967	NM_021140.2	1174	tgG/tgA	24/29	0.553971897076222	1	FACETS	0.907	0.76	1	0.907	0.76	1	CLONAL	1	TRUE	0	0.553971897076222	1		231	95	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424840	47424841	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1365296949	NA	P-0069667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	135	397	0	ENST00000404338.3:c.2914dup	p.Arg972ProfsTer40	p.R972Pfs*40	ENST00000404338	NM_004491.4	970	tcc/tCcc	1/6	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.632135049745206	2		397	423	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745507	162745507	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	73	337	0	ENST00000367921.3:c.1922T>C	p.Leu641Ser	p.L641S	ENST00000367921	NM_006182.2	641	tTa/tCa	15/18	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.632135049745206	2		337	210	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189585674	189585674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057520664	NA	P-0069667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	66	339	0	ENST00000264731.3:c.935G>A	p.Cys312Tyr	p.C312Y	ENST00000264731	NM_003722.4	312	tGt/tAt	7/14	0.632135049745206	3	FACETS	0.84	0.735	0.953	0.42	0.367	0.477	CLONAL	1	TRUE	1	0.632135049745206	3		339	327	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927401	178927402	+	missense_variant	Missense_Mutation	DNP	TT	TT	CA	novel	NA	P-0069667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	26	221	0	ENST00000263967.3:c.1164_1165delinsCA	p.Tyr389Asn	p.Y389N	ENST00000263967	NM_006218.2	388	aaTTat/aaCAat	7/21	0.632135049745206	3	FACETS	0.698	0.559	0.854	0.349	0.279	0.427	SUBCLONAL	1	TRUE	1	0.632135049745206	3		221	155	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261272	16261272	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	100	418	0	ENST00000375759.3:c.8537A>T	p.Glu2846Val	p.E2846V	ENST00000375759	NM_015001.2	2846	gAa/gTa	11/15	1	2	FACETS	0.853	0.768	0.941	0.853	0.768	0.941	CLONAL	1	TRUE	1	0.632135049745206	2		418	371	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0069669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	247	294	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.133256067373082	6	FACETS	0.883	0.836	0.93			1	INDETERMINATE	4	TRUE	NA	0.658422930758308	6		294	492	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031882	26031882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756571457	NA	P-0069669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	135	330	1	ENST00000244661.2:c.407C>T	p.Ala136Val	p.A136V	ENST00000244661	NM_003537.3	136	gCg/gTg	1/1	0.658422930758308	3	FACETS	0.907	0.827	0.99	0.453	0.413	0.495	CLONAL	1	TRUE	1	0.658422930758308	3		331	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0069669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	223	266	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.658422930758308	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.658422930758308	2		266	313	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878862	151878862	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778364715	NA	P-0069669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	272	353	0	ENST00000262189.6:c.6083G>A	p.Arg2028Gln	p.R2028Q	ENST00000262189	NM_170606.2	2028	cGa/cAa	36/59	0.298702636989869	6	FACETS	0.962	0.909	1	0.962	0.909	1	INDETERMINATE	3	TRUE	3	0.658422930758308	6		353	663	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155562	106155562	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	123	289	0	ENST00000380013.4:c.463G>T	p.Ala155Ser	p.A155S	ENST00000380013	NM_001127208.2	155	Gcc/Tcc	3/11	1	2	FACETS	0.851	0.775	0.93	0.851	0.775	0.93	CLONAL	1	TRUE	1	0.658422930758308	2		289	439	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941908	44942072	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTAGTATTTCTTTTTAAAAGGCATGTTTCTAATACTGTGTCTCTTTTTTAAGTTCTGGGAGGAGGAGGAAAGGACCCTTTAAAACCATAAAGTTTGGGACCAATATTGACCTATCTGATGACAAAAAGTAAGTCCTTGTAGTAATATTTCTGTGAACTGATGCAA	TTAGTATTTCTTTTTAAAAGGCATGTTTCTAATACTGTGTCTCTTTTTTAAGTTCTGGGAGGAGGAGGAAAGGACCCTTTAAAACCATAAAGTTTGGGACCAATATTGACCTATCTGATGACAAAAAGTAAGTCCTTGTAGTAATATTTCTGTGAACTGATGCAA	-	novel	NA	P-0069669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	83	237	0	ENST00000377967.4:c.3209+23_3284+38del		p.X1070_splice	ENST00000377967	NM_021140.2	1070		22/29	0.386004784919645	1	FACETS	0.566	0.504	0.63	0.566	0.504	0.63	INDETERMINATE	1	TRUE	0	0.658422930758308	1		237	299	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444583	187444583	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	230	322	0	ENST00000232014.4:c.1644T>G	p.Cys548Trp	p.C548W	ENST00000232014	NM_001130845.1	548	tgT/tgG	7/10	0.55099424169301	4	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	2	0.658422930758308	4		322	571	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584530	48584530	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	34	304	0	ENST00000342988.3:c.703G>T	p.Glu235Ter	p.E235*	ENST00000342988	NM_005359.5	235	Gaa/Taa	6/12	0.658422930758308	1	FACETS	0.27	0.221	0.323	0.27	0.221	0.323	SUBCLONAL	1	TRUE	0	0.658422930758308	1		304	257	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341197	8341197	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	97	270	0	ENST00000356435.5:c.5019T>G	p.Asn1673Lys	p.N1673K	ENST00000356435		1673	aaT/aaG	30/35	0.612293691713927	3	FACETS	0.913	0.819	1	0.456	0.409	0.506	CLONAL	1	TRUE	1	0.658422930758308	3		270	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0069671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	270	478	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.523878251254593	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.582705108806565	2		478	458	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498518	89498518	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	70	309	0	ENST00000336596.2:c.2490T>A	p.Asn830Lys	p.N830K	ENST00000336596	NM_005233.5	830	aaT/aaA	14/17	0.582705108806565	3	FACETS	0.744	0.651	0.843	0.372	0.325	0.422	SUBCLONAL	1	TRUE	1	0.582705108806565	3		309	417	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557554	21557554	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	209	493	0	ENST00000382592.4:c.2291C>A	p.Pro764His	p.P764H	ENST00000382592	NM_014572.2	764	cCt/cAt	5/8	0.160053446112506	6	FACETS	0.843	0.788	0.9	0.843	0.788	0.9	INDETERMINATE	3	TRUE	3	0.582705108806565	6		493	614	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982595	10982595	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	18	583	0	ENST00000327064.4:c.217A>C	p.Ser73Arg	p.S73R	ENST00000327064	NM_199141.1	73	Agc/Cgc	1/16	0.275355145327394	1	FACETS	0.22	0.165	0.286	0.22	0.165	0.286	SUBCLONAL	1	TRUE	0	0.386441296761424	1		583	341	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0069674-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	80	288	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.282061601134949	2		288	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0069674-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	122	296	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.276929250054927	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	FALSE	0	0.282061601134949	2		296	380	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0069674-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	91	288	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.351742004943577	3	FACETS	0.975	0.875	1	0.975	0.875	1	CLONAL	2	TRUE	1	0.351742004943577	3		288	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0069674-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	165	296	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.310986702994126	4	FACETS	1	0.981	1	0.862	0.803	0.921	CLONAL	3	TRUE	0	0.351742004943577	4		296	368	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054948	176054948	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069674-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	16	229	0	ENST00000367669.3:c.1105C>T	p.Gln369Ter	p.Q369*	ENST00000367669	NM_022457.5	369	Cag/Tag	10/20	0.20069490108025	5	FACETS	1	0.855	1	0.41	0.306	0.531	INDETERMINATE	1	TRUE	2	0.351742004943577	5		229	113	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0069675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	29	308	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.559	0.447	0.687	0.559	0.447	0.687	SUBCLONAL	1	TRUE	1	0.17	2		308	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	86	432	0	ENST00000269305.4:c.542G>C	p.Arg181Pro	p.R181P	ENST00000269305	NM_001126112.2	181	cGc/cCc	5/11	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.17	2		432	1009	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211586	46211586	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0069675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	55	280	0	ENST00000334344.6:c.554del	p.Asn185MetfsTer30	p.N185Mfs*30	ENST00000334344	NM_152641.2	184	tcA/tc	5/21	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.17	2		280	639	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0069676-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	18	175	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.754	1	1	0.754	1	CLONAL	1	TRUE	1	0.14	2		175	257	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466362	120466363	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0069676-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	31	398	0	ENST00000256646.2:c.4756dup	p.Glu1586GlyfsTer10	p.E1586Gfs*10	ENST00000256646	NM_024408.3	1586	gaa/gGaa	26/34	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.14	2		398	366	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453149	140453149	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913361	NA	P-0069676-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	12	283	0	ENST00000288602.6:c.1786G>C	p.Gly596Arg	p.G596R	ENST00000288602	NM_004333.4	596	Ggt/Cgt	15/18	1	2	FACETS	0.41	0.287	0.563	0.41	0.287	0.563	SUBCLONAL	1	TRUE	1	0.14	2		283	418	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494891	56494891	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069676-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	24	370	0	ENST00000267101.3:c.3248C>G	p.Ser1083Cys	p.S1083C	ENST00000267101	NM_001982.3	1083	tCt/tGt	27/28	1	2	FACETS	0.912	0.715	1	0.912	0.715	1	CLONAL	1	TRUE	1	0.14	2		370	376	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404395	139404395	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0069676-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	35	462	0	ENST00000277541.6:c.2759del	p.Gly920AlafsTer259	p.G920Afs*259	ENST00000277541	NM_017617.3	920	gGc/gc	18/34	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.14	2		462	375	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968201	134968201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201702941	NA	P-0069676-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	17	437	0	ENST00000398015.3:c.2714G>A	p.Arg905His	p.R905H	ENST00000398015	NM_004441.4	905	cGc/cAc	15/16	1	2	FACETS	0.769	0.573	1	0.769	0.573	1	CLONAL	1	TRUE	1	0.14	2		437	316	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984963	55984967	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GTCCC	GTCCC	-	novel	NA	P-0069676-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	16	287	0	ENST00000263923.4:c.162_166del	p.Gly55GlufsTer10	p.G55Efs*10	ENST00000263923	NM_002253.2	54	agGGGACag/agag	3/30	1	2	FACETS	0.735	0.543	0.965	0.735	0.543	0.965	CLONAL	1	TRUE	1	0.14	2		287	311	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494858	56494858	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760520385	NA	P-0069676-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	20	360	0	ENST00000267101.3:c.3215C>T	p.Ser1072Phe	p.S1072F	ENST00000267101	NM_001982.3	1072	tCt/tTt	27/28	1	2	FACETS	0.75	0.573	0.958	0.75	0.573	0.958	CLONAL	1	TRUE	1	0.14	2		360	381	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996131	73996136	+	frameshift_variant	Frame_Shift_Del	DEL	GACACC	GACACC	CACAA	novel	NA	P-0069676-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	29	611	0	ENST00000318443.5:c.865_870delinsCACAA	p.Asp289HisfsTer37	p.D289Hfs*37	ENST00000318443	NM_001024736.1	289	GACACC/CACAA	5/10	1	2	FACETS	0.984	0.789	1	0.984	0.789	1	CLONAL	1	TRUE	1	0.14	2		611	421	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0069677-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	187	358	0				ENST00000310581	NM_198253.2	-/1132			0.419125582556634	4	FACETS	0.962	0.899	1	0.962	0.899	1	CLONAL	3	TRUE	1	0.419125582556634	4		358	439	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421234	12421234	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069677-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	146	362	0	ENST00000287820.6:c.114C>G	p.Phe38Leu	p.F38L	ENST00000287820	NM_015869.4	38	ttC/ttG	2/7	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.419125582556634	2		362	641	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092809	27092809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069677-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	125	334	0	ENST00000324856.7:c.2830C>T	p.Gln944Ter	p.Q944*	ENST00000324856	NM_006015.4	944	Cag/Tag	9/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.419125582556634	2		334	478	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117515	4117515	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1427916025	NA	P-0069677-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	28	126	0	ENST00000262948.5:c.205G>C	p.Asp69His	p.D69H	ENST00000262948	NM_030662.3	69	Gac/Cac	2/11	1	2	FACETS	0.941	0.763	1	0.941	0.763	1	CLONAL	1	TRUE	1	0.419125582556634	2		126	142	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73649902	73649902	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069677-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	100	349	0	ENST00000377687.4:c.1252G>A	p.Asp418Asn	p.D418N	ENST00000377687	NM_001730.3	418	Gat/Aat	4/4	1	2	FACETS	0.936	0.839	1	0.936	0.839	1	CLONAL	1	TRUE	1	0.419125582556634	2		349	510	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307484	118307484	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069677-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	72	318	0	ENST00000534358.1:c.257C>A	p.Ser86Ter	p.S86*	ENST00000534358	NM_005933.3	86	tCg/tAg	1/36	1	2	FACETS	0.85	0.747	0.961	0.85	0.747	0.961	CLONAL	1	TRUE	1	0.419125582556634	2		318	404	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246210	46246210	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0069677-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	109	421	0	ENST00000334344.6:c.4304C>G	p.Ser1435Ter	p.S1435*	ENST00000334344	NM_152641.2	1435	tCa/tGa	15/21	1	2	FACETS	0.965	0.87	1	0.965	0.87	1	CLONAL	1	TRUE	1	0.419125582556634	2		421	539	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280772	41280773	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0069677-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	114	371	0	ENST00000349496.5:c.2286_2287dup	p.Met763ThrfsTer26	p.M763Tfs*26	ENST00000349496	NM_001904.3	762	ctc/ctCAc	15/15	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.419125582556634	2		371	535	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648417	30648417	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069677-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	84	329	0	ENST00000295754.5:c.42C>G	p.Ile14Met	p.I14M	ENST00000295754	NM_003242.5	14	atC/atG	1/7	1	2	FACETS	0.948	0.841	1	0.948	0.841	1	CLONAL	1	TRUE	1	0.419125582556634	2		329	423	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817523	39817523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069677-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	113	358	0	ENST00000288319.7:c.40G>A	p.Glu14Lys	p.E14K	ENST00000288319	NM_182918.3	14	Gag/Aag	2/10	0.419125582556634	1	FACETS	0.667	0.601	0.736	0.667	0.601	0.736	SUBCLONAL	1	TRUE	0	0.419125582556634	1		358	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0068695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	60	428	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.225350607341644	2		428	466	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0068695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	129	411	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.225350607341644	5	FACETS	1	0.916	1			1	CLONAL	2	TRUE	NA	0.225350607341644	5		411	758	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379685	17379685	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371905545	NA	P-0068695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	40	458	0	ENST00000359435.4:c.70C>T	p.Arg24Trp	p.R24W	ENST00000359435	NM_001033549.1	24	Cgg/Tgg	2/9	0.106228325288701	3	FACETS	0.685	0.568	0.815	0.342	0.284	0.408	INDETERMINATE	1	TRUE	1	0.225350607341644	3		458	577	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163437	47163437	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	44	407	0	ENST00000409792.3:c.2689C>G	p.Leu897Val	p.L897V	ENST00000409792	NM_014159.6	897	Ctc/Gtc	3/21	1	2	FACETS	0.967	0.812	1	0.967	0.812	1	CLONAL	1	TRUE	1	0.225350607341644	2		407	404	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38135882	38135882	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	45	374	0	ENST00000317025.8:c.3809G>C	p.Arg1270Thr	p.R1270T	ENST00000317025	NM_023034.1	1270	aGa/aCa	22/24	1	2	FACETS	0.8	0.673	0.942	0.8	0.673	0.942	CLONAL	1	TRUE	1	0.225350607341644	2		374	499	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288992	33288992	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	76	439	0	ENST00000374542.5:c.560A>G	p.Gln187Arg	p.Q187R	ENST00000374542	NM_001141970.1	187	cAg/cGg	3/8	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.225350607341644	2		439	588	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62323128	62323128	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	33	380	0	ENST00000360203.5:c.2590G>C	p.Glu864Gln	p.E864Q	ENST00000360203	NM_001283009.1	864	Gag/Cag	28/35	1	2	FACETS	0.672	0.547	0.813	0.672	0.547	0.813	SUBCLONAL	1	TRUE	1	0.225350607341644	2		380	436	SUCCESS
REST	5978	MSKCC	GRCh37	4	57797419	57797419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	57	628	0	ENST00000309042.7:c.2395C>T	p.Pro799Ser	p.P799S	ENST00000309042	NM_005612.4	799	Cct/Tct	4/4	0.225350607341644	1	FACETS	0.914	0.785	1	0.914	0.785	1	CLONAL	1	TRUE	0	0.225350607341644	1		628	491	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845681	68845703	+	frameshift_variant	Frame_Shift_Del	DEL	TGAGCTCCCTGACAAAAATATGT	TGAGCTCCCTGACAAAAATATGT	-	novel	NA	P-0068695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	59	394	0	ENST00000261769.5:c.928_950del	p.Glu310HisfsTer3	p.E310Hfs*3	ENST00000261769	NM_004360.3	309	ccTGAGCTCCCTGACAAAAATATGTtc/cctc	7/16	0.225350607341644	1	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	0	0.225350607341644	1		394	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0068696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	272	319	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.98	0.928	1	0.98	0.928	1	CLONAL	1	TRUE	1	0.944315372048107	2		320	588	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039374	49039374	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853293	NA	P-0068696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	185	398	0	ENST00000267163.4:c.2359C>T	p.Arg787Ter	p.R787*	ENST00000267163	NM_000321.2	787	Cga/Tga	23/27	1	2	FACETS	0.958	0.896	1	0.958	0.896	1	CLONAL	1	TRUE	1	0.944315372048107	2		398	409	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592216	55592216	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	128	234	0	ENST00000288135.5:c.1540G>A	p.Glu514Lys	p.E514K	ENST00000288135	NM_000222.2	514	Gag/Aag	9/21	0.424045704895947	1	FACETS	0.561	0.519	0.603	0.561	0.519	0.603	INDETERMINATE	1	TRUE	0	0.944315372048107	1		234	255	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022616	31022616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	310	436	0	ENST00000375687.4:c.2101C>T	p.Pro701Ser	p.P701S	ENST00000375687	NM_015338.5	701	Cct/Tct	13/13	1	2	FACETS	0.95	0.903	0.998	0.95	0.903	0.998	CLONAL	1	TRUE	1	0.944315372048107	2		436	691	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570878	226570878	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1383847803	NA	P-0068696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	176	292	0	ENST00000366794.5:c.1018C>T	p.Arg340Ter	p.R340*	ENST00000366794	NM_001618.3	340	Cga/Tga	8/23	1	2	FACETS	0.834	0.776	0.892	0.834	0.776	0.892	CLONAL	1	TRUE	1	0.944315372048107	2		292	447	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651277	45651277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	350	385	0	ENST00000407780.3:c.748G>A	p.Gly250Ser	p.G250S	ENST00000407780	NM_001283052.1	250	Ggc/Agc	5/7	0.487494478507066	1	FACETS	0.711	0.684	0.739	0.711	0.684	0.739	INDETERMINATE	1	TRUE	0	0.944315372048107	1		385	550	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350155	81350155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758567520	NA	P-0068696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	139	214	0	ENST00000222390.5:c.1177C>T	p.Arg393Cys	p.R393C	ENST00000222390	NM_000601.4	393	Cgt/Tgt	10/18	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.944315372048107	2		214	263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs878854073	NA	P-0068696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	284	337	0	ENST00000269305.4:c.673-1G>A		p.X225_splice	ENST00000269305	NM_001126112.2	225			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.944315372048107	2		337	581	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970964	70970964	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868518861	NA	P-0068696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	241	365	0	ENST00000276594.2:c.1297C>T	p.Pro433Ser	p.P433S	ENST00000276594	NM_024504.3	433	Ccc/Tcc	6/8	0.314175993071786	3	FACETS	1	0.989	1	0.609	0.573	0.646	INDETERMINATE	1	TRUE	1	0.944315372048107	3		365	617	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068238	30068238	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	116	268	0	ENST00000331968.5:c.2161C>T	p.Pro721Ser	p.P721S	ENST00000331968	NM_002742.2	721	Cct/Tct	15/18	1	2	FACETS	0.92	0.845	0.997	0.92	0.845	0.997	CLONAL	1	TRUE	1	0.944315372048107	2		268	267	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5239059	5239059	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768636218	NA	P-0068696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	302	396	0	ENST00000357368.4:c.1720G>A	p.Asp574Asn	p.D574N	ENST00000357368	NM_002850.3	574	Gac/Aac	13/38	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.944315372048107	NA		396	687	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040659	16040659	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	90	272	0	ENST00000268712.3:c.1475G>A	p.Arg492Lys	p.R492K	ENST00000268712	NM_006311.3	492	aGa/aAa	14/46	1	2	FACETS	0.899	0.815	0.985	0.899	0.815	0.985	CLONAL	1	TRUE	1	0.944315372048107	2		272	212	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733359	40733359	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0068696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	281	313	0	ENST00000373198.4:c.3448-1G>A		p.X1150_splice	ENST00000373198	NM_133170.3	1150			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.944315372048107	2		313	562	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143261	24143261	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	363	474	0	ENST00000263121.7:c.493C>T	p.Pro165Ser	p.P165S	ENST00000263121	NM_003073.3	165	Ccc/Tcc	4/9	0.924167635964167	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.944315372048107	1		474	392	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799745	72799745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	299	416	0	ENST00000325599.8:c.1424C>T	p.Ser475Leu	p.S475L	ENST00000325599	NM_018130.2	475	tCa/tTa	11/11	0.944315372048107	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.944315372048107	1		416	311	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29279806	29279806	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	152	112	0	ENST00000544604.2:c.52C>T	p.Arg18Cys	p.R18C	ENST00000544604	NM_001206998.1	18	Cgc/Tgc	1/9	0.924167635964167	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.944315372048107	1		112	160	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938234	36938234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	356	420	0	ENST00000361632.4:c.727C>T	p.Pro243Ser	p.P243S	ENST00000361632		243	Cct/Tct	6/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.944315372048107	2		420	739	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525054	157525054	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	255	383	0	ENST00000346085.5:c.4949A>G	p.Glu1650Gly	p.E1650G	ENST00000346085	NM_020732.3	1650	gAg/gGg	19/20	NA	2	FACETS	0.987	0.934	1			1	INDETERMINATE	1	TRUE	NA	0.944315372048107	2		383	547	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911176	32911176	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	108	325	0	ENST00000380152.3:c.2684C>T	p.Ala895Val	p.A895V	ENST00000380152		895	gCt/gTt	11/27	1	2	FACETS	0.901	0.823	0.979	0.901	0.823	0.979	CLONAL	1	TRUE	1	0.944315372048107	2		325	254	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639375	3639375	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	299	400	0	ENST00000294008.3:c.4264C>T	p.Pro1422Ser	p.P1422S	ENST00000294008	NM_032444.2	1422	Cca/Tca	12/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.944315372048107	2		400	584	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304090	91304090	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	252	449	0	ENST00000355112.3:c.1487T>C	p.Leu496Ser	p.L496S	ENST00000355112	NM_000057.2	496	tTa/tCa	7/22	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.944315372048107	2		449	507	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2170438	2170439	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0068696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	158	285	0	ENST00000349721.2:c.4219_4220delinsTT	p.Pro1407Phe	p.P1407F	ENST00000349721	NM_003070.3	1407	CCc/TTc	29/34	NA	2	FACETS	0.834	0.774	0.896			1	INDETERMINATE	1	TRUE	NA	0.944315372048107	2		285	401	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180247	38180247	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759720432	NA	P-0068696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	389	476	0	ENST00000396334.3:c.95C>T	p.Ser32Phe	p.S32F	ENST00000396334	NM_002468.4	32	tCc/tTc	1/5	0.944315372048107	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.944315372048107	1		476	421	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042533	42042533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	230	426	0	ENST00000219905.7:c.6728C>T	p.Ser2243Phe	p.S2243F	ENST00000219905	NM_001164273.1	2243	tCt/tTt	17/24	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.944315372048107	2		426	481	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149436948	149436948	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0068696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	233	399	0	ENST00000286301.3:c.2222-1G>A		p.X741_splice	ENST00000286301	NM_005211.3	741			0.187143055290781	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.944315372048107	0		399	505	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690627	33690627	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	269	451	0	ENST00000308377.4:c.200T>C	p.Val67Ala	p.V67A	ENST00000308377	NM_152270.3	67	gTt/gCt	2/5	1	2	FACETS	0.993	0.94	1	0.993	0.94	1	CLONAL	1	TRUE	1	0.944315372048107	2		451	574	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10789890	10789890	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	188	338	0	ENST00000361367.2:c.1961G>A	p.Gly654Glu	p.G654E	ENST00000361367	NM_014633.3	654	gGa/gAa	16/25	1	2	FACETS	0.974	0.912	1	0.974	0.912	1	CLONAL	1	TRUE	1	0.944315372048107	2		338	409	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112307	115112307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs557929464	NA	P-0068696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	213	441	0	ENST00000257566.3:c.1433C>T	p.Ala478Val	p.A478V	ENST00000257566	NM_016569.3	478	gCc/gTc	7/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.944315372048107	2		441	420	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89791034	89791034	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	261	307	0	ENST00000336032.3:c.421C>T	p.Pro141Ser	p.P141S	ENST00000336032	NM_006813.2	141	Ccg/Tcg	1/2	1	2	FACETS	0.973	0.921	1	0.973	0.921	1	CLONAL	1	TRUE	1	0.944315372048107	2		307	568	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210937	36210937	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	399	449	0	ENST00000222270.7:c.688C>T	p.Pro230Ser	p.P230S	ENST00000222270	NM_014727.1	230	Ccc/Tcc	3/37	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.944315372048107	2		449	822	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589302	67589302	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	106	324	0	ENST00000274335.5:c.1290A>C	p.Lys430Asn	p.K430N	ENST00000274335		430	aaA/aaC	9/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.944315372048107	2		324	209	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476413	88476414	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0068696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	200	286	0	ENST00000360948.2:c.1718_1719delinsTT	p.Ala573Val	p.A573V	ENST00000360948	NM_001012338.2	573	gCC/gTT	15/19	1	2	FACETS	0.919	0.861	0.977	0.919	0.861	0.977	CLONAL	1	TRUE	1	0.944315372048107	2		286	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0068697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	368	470	15	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.842064360655926	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.842064360655926	2		485	427	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654646	67654646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	226	468	6	ENST00000264010.4:c.1133C>T	p.Pro378Leu	p.P378L	ENST00000264010	NM_006565.3	378	cCg/cTg	6/12	0.839775735405591	3	FACETS	1	0.979	1	0.552	0.516	0.588	CLONAL	1	TRUE	1	0.842064360655926	3		474	691	SUCCESS
REST	5978	MSKCC	GRCh37	4	57797265	57797265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs144031960	NA	P-0068697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	10	498	6	ENST00000309042.7:c.2241A>G	p.Ile747Met	p.I747M	ENST00000309042	NM_005612.4	747	atA/atG	4/4	0.842064360655926	2	FACETS	0.183	0.124	0.256	0.091	0.062	0.128	SUBCLONAL	1	TRUE	0	0.842064360655926	2		504	130	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947630	48947630	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0068697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	319	280	3	ENST00000267163.4:c.1215+2T>C		p.X405_splice	ENST00000267163	NM_000321.2	405			0.842064360655926	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.842064360655926	2		283	362	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409984	139409984	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	227	704	3	ENST00000277541.6:c.1854C>A	p.Cys618Ter	p.C618*	ENST00000277541	NM_017617.3	618	tgC/tgA	11/34	0.783981906676813	3	FACETS	1	0.944	1	0.505	0.472	0.539	CLONAL	1	TRUE	1	0.842064360655926	3		707	758	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8338972	8338972	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	235	491	10	ENST00000356435.5:c.5329T>G	p.Tyr1777Asp	p.Y1777D	ENST00000356435		1777	Tac/Gac	32/35	0.839775735405591	3	FACETS	1	0.971	1	0.532	0.498	0.566	CLONAL	1	TRUE	1	0.842064360655926	3		501	746	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763467	59763467	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	178	479	0	ENST00000259008.2:c.2635G>T	p.Glu879Ter	p.E879*	ENST00000259008	NM_032043.2	879	Gaa/Taa	19/20	0.842064360655926	2	FACETS	0.905	0.843	0.969	0.453	0.421	0.485	CLONAL	1	TRUE	0	0.842064360655926	2		479	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0068698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	189	294	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.517999552437447	2	FACETS	0.982	0.923	1	0.982	0.923	1	CLONAL	2	TRUE	0	0.520216112123778	2		294	370	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0068698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	103	557	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.520216112123778	2		557	373	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197716	123197716	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	43	390	0	ENST00000218089.9:c.1840C>T	p.Arg614Ter	p.R614*	ENST00000218089	NM_001042749.1	614	Cga/Tga	20/35	0.505986393462048	3	FACETS	0.706	0.594	0.829	0.353	0.297	0.415	SUBCLONAL	1	TRUE	1	0.520216112123778	3		390	295	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967323	38967323	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	85	458	0	ENST00000357387.3:c.1158C>A	p.Asp386Glu	p.D386E	ENST00000357387	NM_152756.3	386	gaC/gaA	14/38	0.494391206448268	4	FACETS	0.836	0.74	0.939	0.209	0.185	0.235	CLONAL	1	TRUE	0	0.520216112123778	4		458	594	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0068699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	97	356	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.28	2		356	682	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685300	89685300	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs878853936	NA	P-0068699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	35	300	0	ENST00000371953.3:c.195C>G	p.Tyr65Ter	p.Y65*	ENST00000371953	NM_000314.4	65	taC/taG	3/9	1	2	FACETS	0.977	0.805	1	0.977	0.805	1	CLONAL	1	TRUE	1	0.28	2		300	256	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338671	70338671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	58	356	0	ENST00000374080.3:c.67G>T	p.Asp23Tyr	p.D23Y	ENST00000374080		23	Gat/Tat	1/45	1	2	FACETS	0.977	0.842	1	0.977	0.842	1	CLONAL	1	TRUE	1	0.28	2		356	424	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951955	178951955	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	38	390	0	ENST00000263967.3:c.3010A>G	p.Met1004Val	p.M1004V	ENST00000263967	NM_006218.2	1004	Atg/Gtg	21/21	1	2	FACETS	0.823	0.682	0.978	0.823	0.682	0.978	CLONAL	1	TRUE	1	0.28	2		390	330	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488249	56488249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	65	442	2	ENST00000267101.3:c.1768C>T	p.Pro590Ser	p.P590S	ENST00000267101	NM_001982.3	590	Ccc/Tcc	15/28	1	2	FACETS	0.815	0.707	0.931	0.815	0.707	0.931	CLONAL	1	TRUE	1	0.28	2		444	570	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059207	27059207	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	48	338	0	ENST00000324856.7:c.1848del	p.Ser617GlnfsTer2	p.S617Qfs*2	ENST00000324856	NM_006015.4	615	gCc/gc	4/20	1	2	FACETS	0.762	0.645	0.891	0.762	0.645	0.891	SUBCLONAL	1	TRUE	1	0.28	2		338	450	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094413	27094413	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	69	476	0	ENST00000324856.7:c.3121del	p.Leu1041CysfsTer18	p.L1041Cfs*18	ENST00000324856	NM_006015.4	1041	Ctg/tg	11/20	1	2	FACETS	0.817	0.712	0.931	0.817	0.712	0.931	CLONAL	1	TRUE	1	0.28	2		476	603	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692903	89692906	+	frameshift_variant	Frame_Shift_Del	DEL	ACGA	ACGA	-	novel	NA	P-0068699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	31	335	0	ENST00000371953.3:c.389_392del	p.Arg130LeufsTer3	p.R130Lfs*3	ENST00000371953	NM_000314.4	129	ggACGA/gg	5/9	1	2	FACETS	0.788	0.64	0.955	0.788	0.64	0.955	CLONAL	1	TRUE	1	0.28	2		335	281	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624227	89624227	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1554890324	NA	P-0068699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	25	116	0	ENST00000371953.3:c.1A>G	p.Met1?	p.M1?	ENST00000371953	NM_000314.4	1	Atg/Gtg	1/9	1	2	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	TRUE	1	0.28	2		116	166	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591137	67591152	+	protein_altering_variant,splice_region_variant	In_Frame_Del	DEL	GAGACCAATACTTGAT	GAGACCAATACTTGAT	A	novel	NA	P-0068699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	43	398	0	ENST00000274335.5:c.1730_1745delinsA	p.Arg577_Met582delinsLys	p.R577_M582delinsK	ENST00000274335		577	aGAGACCAATACTTGATg/aAg	12/15	1	2	FACETS	0.922	0.775	1	0.922	0.775	1	CLONAL	1	TRUE	1	0.28	2		398	333	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101008	41101008	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	137	321	1	ENST00000373198.4:c.1348C>T	p.Arg450Ter	p.R450*	ENST00000373198	NM_133170.3	450	Cga/Tga	8/32	0.604976947749789	4	FACETS	1	0.94	1	0.519	0.474	0.567	CLONAL	1	TRUE	2	0.674114030905296	4		322	655	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111497	8111498	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGGAGGAATGCC	novel	NA	P-0068700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	110	312	0	ENST00000346208.3:c.984_996dup	p.Asn333GlufsTer23	p.N333Efs*23	ENST00000346208		328	tgg/tgGAGGAGGAATGCCg	5/6	0.674326356311257	3	FACETS	0.725	0.653	0.801	0.362	0.326	0.401	SUBCLONAL	1	TRUE	1	0.674114030905296	3		312	602	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059278	27059278	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	129	228	0	ENST00000324856.7:c.1915T>G	p.Leu639Val	p.L639V	ENST00000324856	NM_006015.4	639	Ttg/Gtg	4/20	0.674326356311257	3	FACETS	1	0.968	1	0.562	0.513	0.613	CLONAL	1	TRUE	1	0.674114030905296	3		228	455	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0068701-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	56	257	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.461201133420266	4	FACETS	0.988	0.85	1	0.494	0.425	0.569	CLONAL	1	FALSE	2	0.457641818574399	4		257	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0068702-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	954	474	0	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.792338791535372	3	FACETS	0.999	0.983	1	0.999	0.983	1	CLONAL	3	TRUE	0	0.792338791535372	3		474	1122	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552152	29552152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199474738	NA	P-0068702-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	143	315	0	ENST00000356175.3:c.1885G>A	p.Gly629Arg	p.G629R	ENST00000356175	NM_000267.3	629	Ggg/Agg	17/57	0.792338791535372	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.792338791535372	1		315	208	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645679	215645679	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068702-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	31	456	0	ENST00000260947.4:c.919T>G	p.Tyr307Asp	p.Y307D	ENST00000260947	NM_000465.2	307	Tat/Gat	4/11	1	2	FACETS	0.153	0.123	0.187	0.153	0.123	0.187	SUBCLONAL	1	TRUE	1	0.792338791535372	2		456	510	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801039	135801088	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGTCTTATGACATGACCCAGTAACGAGAGGATGGATAAACGAGTGGCG	GCAGTCTTATGACATGACCCAGTAACGAGAGGATGGATAAACGAGTGGCG	-	novel	NA	P-0068702-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	210	409	0	ENST00000298552.3:c.249_298del	p.Thr85IlefsTer5	p.T85Ifs*5	ENST00000298552	NM_001162426.1	83	gcCGCCACTCGTTTATCCATCCTCTCGTTACTGGGTCATGTCATAAGACTGCag/gcag	5/23	0.792338791535372	1	FACETS	0.964	0.916	1	0.964	0.916	1	CLONAL	1	TRUE	0	0.792338791535372	1		409	332	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076653	102076653	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068702-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	244	436	0	ENST00000282441.5:c.832C>A	p.Pro278Thr	p.P278T	ENST00000282441	NM_001130145.2	278	Cca/Aca	5/9	0.781641758500787	3	FACETS	0.718	0.67	0.768	0.359	0.335	0.384	SUBCLONAL	1	TRUE	1	0.792338791535372	3		436	1197	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007651	45007994	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCCAGCAGAGAATGGAAAGTCAAATTTCCTGAATTGCTATGTGTCTGGGTTTCATCCATCCGACATTGAAGTTGACTTACTGAAGAATGGAGAGAGAATTGAAAAAGTGGAGCATTCAGACTTGTCTTTCAGCAAGGACTGGTCTTTCTATCTCTTGTACTACACTGAATTCACCCCCACTGAAAAAGATGAGTATGCCTGCCGTGTGAACCATGTGACTTTGTCACAGCCCAAGATAGTTAAGTGGGGTAAGTCTTACATTCTTTTGTAAGCTGCTGAAAGTTGTGTATGAGTAGTCATATCATAAAGCTGCTTTGATATAAAAAAGGTCTATGGCCATACT	ATCCAGCAGAGAATGGAAAGTCAAATTTCCTGAATTGCTATGTGTCTGGGTTTCATCCATCCGACATTGAAGTTGACTTACTGAAGAATGGAGAGAGAATTGAAAAAGTGGAGCATTCAGACTTGTCTTTCAGCAAGGACTGGTCTTTCTATCTCTTGTACTACACTGAATTCACCCCCACTGAAAAAGATGAGTATGCCTGCCGTGTGAACCATGTGACTTTGTCACAGCCCAAGATAGTTAAGTGGGGTAAGTCTTACATTCTTTTGTAAGCTGCTGAAAGTTGTGTATGAGTAGTCATATCATAAAGCTGCTTTGATATAAAAAAGGTCTATGGCCATACT	-	novel	NA	P-0068702-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	99	461	0	ENST00000558401.1:c.99_346+96del		p.X33_splice	ENST00000558401	NM_004048.2	33		2/4	0.792338791535372	1	FACETS	0.567	0.514	0.622	0.567	0.514	0.622	SUBCLONAL	1	TRUE	0	0.792338791535372	1		461	266	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710591	117710591	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068702-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	310	449	0	ENST00000368508.3:c.1681C>G	p.Pro561Ala	p.P561A	ENST00000368508	NM_002944.2	561	Ccg/Gcg	12/43	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.792338791535372	2		449	727	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0068703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	74	349	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		349	186	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0068704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	6446	319	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		319	6799	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0068704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	169	411	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		411	820	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0068704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	7204	452	2	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		454	7637	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332882	153332882	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0068704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	52	401	0	ENST00000281708.4:c.74C>G	p.Ser25Ter	p.S25*	ENST00000281708	NM_033632.3	25	tCa/tGa	2/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		401	629	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101910003	101910003	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	25	374	0	ENST00000374994.4:c.1323G>C	p.Met441Ile	p.M441I	ENST00000374994	NM_004612.2	441	atG/atC	8/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		374	360	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229363	36229363	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	77	520	0	ENST00000222270.7:c.8053G>T	p.Glu2685Ter	p.E2685*	ENST00000222270	NM_014727.1	2685	Gag/Tag	37/37	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		520	1118	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103767	47103767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745410359	NA	P-0068704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	72	421	0	ENST00000409792.3:c.6179C>T	p.Ser2060Leu	p.S2060L	ENST00000409792	NM_014159.6	2060	tCa/tTa	14/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		421	579	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266538	55266538	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	6469	314	3	ENST00000275493.2:c.2830T>G	p.Tyr944Asp	p.Y944D	ENST00000275493	NM_005228.3	944	Tac/Gac	23/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		317	6923	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472535	88472535	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	54	481	0	ENST00000360948.2:c.2020C>A	p.His674Asn	p.H674N	ENST00000360948	NM_001012338.2	674	Cac/Aac	16/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		481	474	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225142	53225142	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	70	454	0	ENST00000375401.3:c.3076C>G	p.Leu1026Val	p.L1026V	ENST00000375401	NM_004187.3	1026	Ctt/Gtt	20/26	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		454	582	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771199	161771199	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs772592654	NA	P-0068704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	41	322	0	ENST00000366898.1:c.1330G>C	p.Glu444Gln	p.E444Q	ENST00000366898	NM_004562.2	444	Gag/Cag	12/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		322	456	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815609	139815609	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	69	434	0	ENST00000247668.2:c.1080C>A	p.Asp360Glu	p.D360E	ENST00000247668	NM_021138.3	360	gaC/gaA	9/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		434	657	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89865588	89865588	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs767288683	NA	P-0068704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	85	449	0	ENST00000389301.3:c.879G>C	p.Lys293Asn	p.K293N	ENST00000389301	NM_000135.2	293	aaG/aaC	10/43	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		449	689	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946450	2946450	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	54	421	0	ENST00000396946.4:c.3287A>G	p.Glu1096Gly	p.E1096G	ENST00000396946	NM_032415.4	1096	gAg/gGg	25/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		421	579	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309764	104309764	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	64	345	0	ENST00000369902.3:c.355G>C	p.Glu119Gln	p.E119Q	ENST00000369902	NM_016169.3	119	Gag/Cag	3/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		345	446	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606984	47606984	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	46	405	0	ENST00000263735.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000263735	NM_002354.2	245	gGt/gTt	7/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		405	502	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344414	118344414	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	116	410	0	ENST00000534358.1:c.2540G>A	p.Arg847Lys	p.R847K	ENST00000534358	NM_005933.3	847	aGa/aAa	3/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		410	659	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224491	108224491	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0068704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	81	295	0	ENST00000278616.4:c.8672-2A>C		p.X2891_splice	ENST00000278616	NM_000051.3	2891			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		295	446	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0068705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	220	312	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.446917004122999	2	FACETS	0.978	0.919	1	0.978	0.919	1	CLONAL	2	TRUE	0	0.45187496495073	2		312	498	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218415	1218415	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs112675807	NA	P-0068705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	225	341	0	ENST00000326873.7:c.291-1G>T		p.X97_splice	ENST00000326873	NM_000455.4	97			0.288793452342152	3	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.45187496495073	3		341	505	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819954	170819968	+	inframe_deletion	In_Frame_Del	DEL	GATGATGATGAAGAG	GATGATGATGAAGAG	-	rs764077801	NA	P-0068705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	182	309	0	ENST00000296930.5:c.511_524+1del		p.DDDEEdel	ENST00000296930	NM_002520.6	166	GATGATGATGAAGAG/-	6/11	0.45187496495073	4	FACETS	1	0.962	1	0.702	0.652	0.754	CLONAL	2	TRUE	1	0.45187496495073	4		309	555	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843501	3843501	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	217	434	0	ENST00000262367.5:c.1102C>T	p.Gln368Ter	p.Q368*	ENST00000262367	NM_004380.2	368	Cag/Tag	4/31	0.392475505853004	4	FACETS	0.995	0.929	1	0.995	0.929	1	CLONAL	2	TRUE	2	0.45187496495073	4		434	701	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098380	11098380	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	221	434	0	ENST00000358026.2:c.898C>T	p.Gln300Ter	p.Q300*	ENST00000358026	NM_001128849.1	300	Cag/Tag	6/36	0.45187496495073	2	FACETS	0.939	0.882	0.996	0.939	0.882	0.996	CLONAL	2	TRUE	0	0.45187496495073	2		434	521	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097266	11097266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1210836682	NA	P-0068705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	209	416	0	ENST00000358026.2:c.757C>T	p.His253Tyr	p.H253Y	ENST00000358026	NM_001128849.1	253	Cat/Tat	4/36	0.45187496495073	2	FACETS	0.95	0.891	1	0.95	0.891	1	CLONAL	2	TRUE	0	0.45187496495073	2		416	487	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101917	11101917	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	251	524	0	ENST00000358026.2:c.1337C>G	p.Ser446Cys	p.S446C	ENST00000358026	NM_001128849.1	446	tCc/tGc	8/36	0.45187496495073	2	FACETS	0.961	0.907	1	0.961	0.907	1	CLONAL	2	TRUE	0	0.45187496495073	2		524	578	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679450	30679450	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	35	329	0	ENST00000376406.3:c.2122C>G	p.Leu708Val	p.L708V	ENST00000376406	NM_014641.2	708	Ctg/Gtg	6/15	0.45187496495073	3	FACETS	0.399	0.327	0.48	0.199	0.163	0.24	SUBCLONAL	1	TRUE	1	0.45187496495073	3		329	476	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610488	10610504	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGCTGAGCCGCAGCT	CTGGCTGAGCCGCAGCT	-	novel	NA	P-0068705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	267	415	0	ENST00000171111.5:c.206_222del	p.Glu69AlafsTer4	p.E69Afs*4	ENST00000171111	NM_203500.1	69	gAGCTGCGGCTCAGCCAG/g	2/6	0.45187496495073	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.45187496495073	2		415	558	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144447	11144447	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	142	290	0	ENST00000358026.2:c.3779G>C	p.Arg1260Thr	p.R1260T	ENST00000358026	NM_001128849.1	1260	aGa/aCa	27/36	0.45187496495073	2	FACETS	0.888	0.82	0.957	0.888	0.82	0.957	CLONAL	2	TRUE	0	0.45187496495073	2		290	354	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097186	11097186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	256	484	0	ENST00000358026.2:c.677C>T	p.Ser226Phe	p.S226F	ENST00000358026	NM_001128849.1	226	tCc/tTc	4/36	0.45187496495073	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.45187496495073	2		484	561	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10785313	10785313	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	107	389	0	ENST00000361367.2:c.1081T>G	p.Ser361Ala	p.S361A	ENST00000361367	NM_014633.3	361	Tct/Gct	9/25	0.45187496495073	3	FACETS	0.982	0.883	1			1	CLONAL	1	TRUE	NA	0.45187496495073	3		389	591	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11114057	11114057	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502104	NA	P-0068705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	188	297	0	ENST00000358026.2:c.1985C>T	p.Ser662Leu	p.S662L	ENST00000358026	NM_001128849.1	662	tCa/tTa	13/36	0.45187496495073	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.45187496495073	2		297	405	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511586	66511586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886041228	NA	P-0068705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	202	346	0	ENST00000358598.2:c.46C>T	p.Arg16Ter	p.R16*	ENST00000358598	NM_212471.2	16	Cga/Tga	2/11	0.445886611800741	4	FACETS	0.884	0.822	0.948	0.884	0.822	0.948	CLONAL	2	TRUE	2	0.45187496495073	4		346	734	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10785008	10785276	+	splice_donor_variant,splice_acceptor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	CATGCATTCCATAATACAGAAGTGGAAGCTATGCAAGCAGAGAGCTGCTATCAGCTAGCTAGATCATTCCATGTTCAGGTAATTTTATAACTTCTCTAAATGTCTAATCTTTTTACTTATAGTGTTTTAAGTCTTTCCAATACTTTTGTACATATTGGTCTTTTTTAATTTTCATTCTTTAGGAAGATTATGACCAAGCTTTTCAGTACTATTATCAAGCCACACAGTTTGCCTCATCCTCTTTTGTGCTCCCATTTTTTGGTTTGGGA	CATGCATTCCATAATACAGAAGTGGAAGCTATGCAAGCAGAGAGCTGCTATCAGCTAGCTAGATCATTCCATGTTCAGGTAATTTTATAACTTCTCTAAATGTCTAATCTTTTTACTTATAGTGTTTTAAGTCTTTCCAATACTTTTGTACATATTGGTCTTTTTTAATTTTCATTCTTTAGGAAGATTATGACCAAGCTTTTCAGTACTATTATCAAGCCACACAGTTTGCCTCATCCTCTTTTGTGCTCCCATTTTTTGGTTTGGGA	-	novel	NA	P-0068705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	88	365	0	ENST00000361367.2:c.882_1046del		p.X294_splice	ENST00000361367	NM_014633.3	294	CATGCATTCCATAATACAGAAGTGGAAGCTATGCAAGCAGAGAGCTGCTATCAGCTAGCTAGATCATTCCATGTTCAGGTAATTTTATAACTTCTCTAAATGTCTAATCTTTTTACTTATAGTGTTTTAAGTCTTTCCAATACTTTTGTACATATTGGTCTTTTTTAATTTTCATTCTTTAGGAAGATTATGACCAAGCTTTTCAGTACTATTATCAAGCCACACAGTTTGCCTCATCCTCTTTTGTGCTCCCATTTTTTGGTTTGGGA/-	8-9/25	0.45187496495073	3	FACETS	0.899	0.799	1			1	CLONAL	1	TRUE	NA	0.45187496495073	3		365	531	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097617	11097617	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	247	426	0	ENST00000358026.2:c.797C>G	p.Ser266Trp	p.S266W	ENST00000358026	NM_001128849.1	266	tCg/tGg	5/36	0.45187496495073	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.45187496495073	2		426	509	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096933	11096934	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0068705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	234	469	0	ENST00000358026.2:c.424_425delinsTT	p.Gly142Leu	p.G142L	ENST00000358026	NM_001128849.1	142	GGg/TTg	4/36	0.45187496495073	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.45187496495073	2		469	513	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742928	17742928	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	101	410	0	ENST00000250003.3:c.836C>A	p.Pro279His	p.P279H	ENST00000250003	NM_002478.4	279	cCt/cAt	3/3	0.372504299106645	3	FACETS	0.986	0.884	1	0.493	0.442	0.547	CLONAL	1	TRUE	1	0.45187496495073	3		410	556	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661904	29661904	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	212	343	0	ENST00000356175.3:c.5798C>A	p.Ser1933Ter	p.S1933*	ENST00000356175	NM_000267.3	1933	tCa/tAa	39/57	0.45187496495073	2	FACETS	0.918	0.861	0.976	0.918	0.861	0.976	CLONAL	2	TRUE	0	0.45187496495073	2		343	511	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001414	29001414	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	158	413	1	ENST00000282397.4:c.1318G>T	p.Asp440Tyr	p.D440Y	ENST00000282397	NM_002019.4	440	Gac/Tac	10/30	0.196352945696471	5	FACETS	0.924	0.85	1	0.616	0.566	0.667	INDETERMINATE	2	TRUE	2	0.45187496495073	5		414	635	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096933	11096933	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	234	467	0	ENST00000358026.2:c.424G>T	p.Gly142Trp	p.G142W	ENST00000358026	NM_001128849.1	142	Ggg/Tgg	4/36	0.45187496495073	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.45187496495073	2		467	513	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988534	36988534	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	181	404	0	ENST00000354822.5:c.119C>T	p.Pro40Leu	p.P40L	ENST00000354822	NM_001079668.2	40	cCg/cTg	2/3	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.771697438103555	2		404	461	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144359458	144359458	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	209	339	0	ENST00000262995.4:c.900G>A	p.Met300Ile	p.M300I	ENST00000262995	NM_207123.2	300	atG/atA	4/11	0.663030967223548	4	FACETS	1	0.947	1			1	CLONAL	1	TRUE	NA	0.771697438103555	4		339	938	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0068707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	113	536	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.826056631031783	2		536	239	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	52	406	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.777	0.675	0.884	0.777	0.675	0.884	SUBCLONAL	1	TRUE	1	0.826056631031783	2		406	162	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0068707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	148	278	0	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	1	2	FACETS	0.921	0.851	0.992	0.921	0.851	0.992	CLONAL	1	TRUE	1	0.826056631031783	2		278	389	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743902	46743902	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	279	302	0	ENST00000371975.4:c.2192T>A	p.Ile731Asn	p.I731N	ENST00000371975	NM_003579.3	731	aTc/aAc	18/18	0.764854368057184	3	FACETS	0.887	0.843	0.931	0.887	0.843	0.931	CLONAL	2	TRUE	1	0.826056631031783	3		302	538	SUCCESS
APC	324	MSKCC	GRCh37	5	112154960	112154960	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	182	260	0	ENST00000257430.4:c.1231G>A	p.Glu411Lys	p.E411K	ENST00000257430	NM_000038.5	411	Gaa/Aaa	10/16	0.679792614834803	3	FACETS	1	0.963	1	0.529	0.491	0.569	CLONAL	1	TRUE	1	0.826056631031783	3		260	588	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555234	226555234	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs769670480	NA	P-0068707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	194	361	0	ENST00000366794.5:c.2353A>G	p.Ser785Gly	p.S785G	ENST00000366794	NM_001618.3	785	Agc/Ggc	17/23	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.826056631031783	2		361	437	SUCCESS
ATR	545	MSKCC	GRCh37	3	142184050	142184050	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	78	176	0	ENST00000350721.4:c.6930G>T	p.Lys2310Asn	p.K2310N	ENST00000350721	NM_001184.3	2310	aaG/aaT	41/47	0.826056631031783	4	FACETS	0.789	0.696	0.888	0.263	0.232	0.296	SUBCLONAL	1	TRUE	1	0.826056631031783	4		176	437	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0068708-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	76	289	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.439	0.387	0.494	0.439	0.387	0.494	SUBCLONAL	1	TRUE	1	0.877010431082374	2		289	395	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835933	151835946	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTCAAAAGTCAC	CTCTCAAAAGTCAC	-	novel	NA	P-0068708-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	230	303	0	ENST00000262189.6:c.14578_14591del	p.Val4860ArgfsTer21	p.V4860Rfs*21	ENST00000262189	NM_170606.2	4860	GTGACTTTTGAGAGa/a	58/59	0.832077555352137	3	FACETS	0.9	0.853	0.948	0.9	0.853	0.948	CLONAL	2	TRUE	1	0.877010431082374	3		303	419	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68993068	68993069	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0068708-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	46	235	0	ENST00000288368.4:c.1873_1874delinsAT	p.Ala625Ile	p.A625I	ENST00000288368	NM_024870.2	625	GCt/ATt	17/40	0.81115483969146	1	FACETS	0.483	0.418	0.55	0.483	0.418	0.55	SUBCLONAL	1	TRUE	0	0.877010431082374	1		235	122	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211765	36211765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068708-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	166	400	0	ENST00000222270.7:c.1516C>T	p.Pro506Ser	p.P506S	ENST00000222270	NM_014727.1	506	Cct/Tct	3/37	1	2	FACETS	0.756	0.699	0.813	0.756	0.699	0.813	SUBCLONAL	1	TRUE	1	0.877010431082374	2		400	501	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68993014	68993014	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068708-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	54	252	0	ENST00000288368.4:c.1819T>A	p.Leu607Ile	p.L607I	ENST00000288368	NM_024870.2	607	Tta/Ata	17/40	0.81115483969146	1	FACETS	0.586	0.517	0.656	0.586	0.517	0.656	SUBCLONAL	1	TRUE	0	0.877010431082374	1		252	118	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349181	89349181	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068708-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	157	366	0	ENST00000301030.4:c.3769A>G	p.Lys1257Glu	p.K1257E	ENST00000301030	NM_001256183.1	1257	Aaa/Gaa	9/13	0.832077555352137	3	FACETS	0.966	0.891	1	0.483	0.445	0.522	CLONAL	1	TRUE	1	0.877010431082374	3		366	533	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	20	406	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		406	111	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	24	369	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		369	139	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	35	419	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		419	142	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406520	70406520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150543016	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	33	415	0	ENST00000373644.4:c.4034C>T	p.Pro1345Leu	p.P1345L	ENST00000373644	NM_030625.2	1345	cCc/cTc	4/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		415	119	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446313	187446313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137878288	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	44	365	0	ENST00000232014.4:c.1375C>T	p.Arg459Cys	p.R459C	ENST00000232014	NM_001130845.1	459	Cgc/Tgc	6/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		365	254	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956220	55956220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190050670	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	16	305	0	ENST00000263923.4:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000263923	NM_002253.2	1032	cGa/cAa	23/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		305	88	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584549	189584549	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	27	388	0	ENST00000264731.3:c.845G>A	p.Gly282Glu	p.G282E	ENST00000264731	NM_003722.4	282	gGa/gAa	6/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		388	128	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857784	9857784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145861983	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	19	495	0	ENST00000330684.3:c.3617G>A	p.Arg1206Gln	p.R1206Q	ENST00000330684	NM_001134407.1	1206	cGa/cAa	13/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		495	295	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968197	134968197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780597750	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	49	432	0	ENST00000398015.3:c.2710G>A	p.Asp904Asn	p.D904N	ENST00000398015	NM_004441.4	904	Gac/Aac	15/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		432	276	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088663	27088663	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	29	423	0	ENST00000324856.7:c.2272C>T	p.Gln758Ter	p.Q758*	ENST00000324856	NM_006015.4	758	Cag/Tag	7/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		423	222	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857127	9857127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs976259560	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	32	399	0	ENST00000330684.3:c.4274C>T	p.Ser1425Leu	p.S1425L	ENST00000330684	NM_001134407.1	1425	tCg/tTg	13/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		399	105	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101092	41101092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs724159837	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	23	491	0	ENST00000373198.4:c.1264C>T	p.Leu422Phe	p.L422F	ENST00000373198	NM_133170.3	422	Ctc/Ttc	8/32	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		491	225	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341914	8341914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	10	404	0	ENST00000356435.5:c.4726G>A	p.Glu1576Lys	p.E1576K	ENST00000356435		1576	Gaa/Aaa	29/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		404	94	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546922	9546922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	50	428	0	ENST00000353224.5:c.1100C>T	p.Ser367Phe	p.S367F	ENST00000353224	NM_177990.2	367	tCc/tTc	5/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		428	203	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658340	18658340	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	14	311	0	ENST00000266497.5:c.3145C>T	p.His1049Tyr	p.H1049Y	ENST00000266497		1049	Cat/Tat	22/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		311	51	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106862	27106862	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142069738	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	8	528	0	ENST00000324856.7:c.6473G>A	p.Arg2158Gln	p.R2158Q	ENST00000324856	NM_006015.4	2158	cGa/cAa	20/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		528	319	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739911	41739911	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	66	423	0	ENST00000242208.4:c.62C>T	p.Ser21Phe	p.S21F	ENST00000242208	NM_002192.2	21	tCc/tTc	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		423	280	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032197	10032197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774932381	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	25	377	0	ENST00000330684.3:c.626C>T	p.Ser209Phe	p.S209F	ENST00000330684	NM_001134407.1	209	tCc/tTc	3/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		377	99	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189349321	189349321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	32	377	0	ENST00000264731.3:c.17C>T	p.Ser6Leu	p.S6L	ENST00000264731	NM_003722.4	6	tCa/tTa	1/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		377	123	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076761	72076761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	40	481	0	ENST00000357731.5:c.736G>A	p.Glu246Lys	p.E246K	ENST00000357731	NM_173808.2	246	Gaa/Aaa	5/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		481	314	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504333	8504333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754609275	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	26	326	0	ENST00000356435.5:c.1750C>T	p.Arg584Cys	p.R584C	ENST00000356435		584	Cgt/Tgt	12/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		326	124	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844184	156844184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199646180	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	61	706	1	ENST00000524377.1:c.1187C>T	p.Ser396Leu	p.S396L	ENST00000524377	NM_002529.3	396	tCg/tTg	9/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		707	435	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444346	50444346	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	45	460	0	ENST00000331340.3:c.276G>A	p.Met92Ile	p.M92I	ENST00000331340	NM_006060.4	92	atG/atA	4/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		460	254	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41522037	41522037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756328815	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	17	317	0	ENST00000263253.7:c.899C>T	p.Pro300Leu	p.P300L	ENST00000263253	NM_001429.3	300	cCc/cTc	3/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		317	85	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744378	41744378	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	34	384	0	ENST00000301178.4:c.998C>T	p.Pro333Leu	p.P333L	ENST00000301178	NM_021913.4	333	cCc/cTc	8/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		384	139	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912693	100912693	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	14	322	0	ENST00000325455.5:c.2629C>T	p.Leu877Phe	p.L877F	ENST00000325455	NM_001202474.3	877	Ctt/Ttt	7/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		322	78	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447561	12447561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	13	431	0	ENST00000287820.6:c.800G>A	p.Gly267Glu	p.G267E	ENST00000287820	NM_015869.4	267	gGa/gAa	5/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		431	183	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612250	189612250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749906547	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	13	403	0	ENST00000264731.3:c.2002C>T	p.Arg668Cys	p.R668C	ENST00000264731	NM_003722.4	668	Cgc/Tgc	14/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		403	189	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372512	118372512	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	30	442	0	ENST00000534358.1:c.6445C>T	p.Arg2149Ter	p.R2149*	ENST00000534358	NM_005933.3	2149	Cga/Tga	26/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		442	163	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553668	106553668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1261004652	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	53	482	0	ENST00000369096.4:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000369096	NM_001198.3	545	Gaa/Aaa	5/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		482	226	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127340	55127340	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	23	466	0	ENST00000257290.5:c.128C>T	p.Ser43Leu	p.S43L	ENST00000257290	NM_006206.4	43	tCa/tTa	3/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		466	139	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636826	8636826	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1353675904	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	22	398	0	ENST00000356435.5:c.83G>A	p.Arg28Gln	p.R28Q	ENST00000356435		28	cGa/cAa	2/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		398	154	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351548	89351548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555075240	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	35	487	0	ENST00000301030.4:c.1402C>T	p.Arg468Cys	p.R468C	ENST00000301030	NM_001256183.1	468	Cgc/Tgc	9/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		487	331	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858024	9858024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	37	437	0	ENST00000330684.3:c.3377C>T	p.Pro1126Leu	p.P1126L	ENST00000330684	NM_001134407.1	1126	cCt/cTt	13/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		437	143	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245389	153245389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	10	360	0	ENST00000281708.4:c.1802C>T	p.Ser601Phe	p.S601F	ENST00000281708	NM_033632.3	601	tCt/tTt	11/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		360	96	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742782	39742782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	12	350	0	ENST00000361337.2:c.1625C>T	p.Pro542Leu	p.P542L	ENST00000361337	NM_003286.2	542	cCt/cTt	15/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		350	132	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097694	27097694	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	46	453	0	ENST00000324856.7:c.3283C>T	p.Gln1095Ter	p.Q1095*	ENST00000324856	NM_006015.4	1095	Cag/Tag	12/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		453	215	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775595	39775595	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	41	431	0	ENST00000288319.7:c.425G>A	p.Trp142Ter	p.W142*	ENST00000288319	NM_182918.3	142	tGg/tAg	4/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		431	229	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108203	8108203	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs267605101	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	67	393	0	ENST00000585124.1:c.1021C>T	p.Gln341Ter	p.Q341*	ENST00000585124	NM_004217.3	341	Caa/Taa	9/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		393	221	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169036	32169036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745902446	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	30	474	0	ENST00000375023.3:c.3997C>T	p.Arg1333Cys	p.R1333C	ENST00000375023	NM_004557.3	1333	Cgt/Tgt	22/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		474	202	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923309	9923309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	15	362	0	ENST00000330684.3:c.1978G>A	p.Asp660Asn	p.D660N	ENST00000330684	NM_001134407.1	660	Gac/Aac	9/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		362	90	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153598	55153598	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	12	354	0	ENST00000257290.5:c.2564C>T	p.Thr855Ile	p.T855I	ENST00000257290	NM_006206.4	855	aCc/aTc	19/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		354	90	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435978	116435978	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778444	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	27	476	0	ENST00000397752.3:c.3973G>A	p.Glu1325Lys	p.E1325K	ENST00000397752	NM_000245.2	1325	Gaa/Aaa	21/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		476	161	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106592	27106592	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	74	481	0	ENST00000324856.7:c.6203C>T	p.Ser2068Leu	p.S2068L	ENST00000324856	NM_006015.4	2068	tCg/tTg	20/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		481	285	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373178	118373178	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200497972	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	33	368	0	ENST00000534358.1:c.6571C>T	p.Arg2191Ter	p.R2191*	ENST00000534358	NM_005933.3	2191	Cga/Tga	27/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		368	177	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510154	149510154	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1013933182	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	24	375	0	ENST00000261799.4:c.1315C>T	p.Arg439Trp	p.R439W	ENST00000261799	NM_002609.3	439	Cgg/Tgg	9/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		375	219	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189349	99189349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777754514	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	117	415	0	ENST00000074304.5:c.2605C>T	p.Arg869Trp	p.R869W	ENST00000074304	NM_001134224.1	869	Cgg/Tgg	24/26	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		415	364	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695991	117695991	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	17	359	0	ENST00000369458.3:c.446C>T	p.Ala149Val	p.A149V	ENST00000369458	NM_024626.3	149	gCc/gTc	4/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		359	166	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909500	50909500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	50	456	0	ENST00000440232.2:c.1304C>T	p.Ser435Leu	p.S435L	ENST00000440232	NM_002691.3	435	tCa/tTa	11/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		456	265	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431625	49431625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756129096	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	49	492	0	ENST00000301067.7:c.9514C>T	p.Pro3172Ser	p.P3172S	ENST00000301067	NM_003482.3	3172	Cca/Tca	34/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		492	204	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61323000	61323000	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	15	471	0	ENST00000283752.5:c.1064C>T	p.Ser355Leu	p.S355L	ENST00000283752	NM_006919.2	355	tCa/tTa	8/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		471	133	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727481	88727481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	40	434	0	ENST00000360948.2:c.298G>A	p.Glu100Lys	p.E100K	ENST00000360948	NM_001012338.2	100	Gag/Aag	3/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		434	248	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560404	95560404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	113	352	0	ENST00000393063.1:c.5185C>T	p.Pro1729Ser	p.P1729S	ENST00000393063	NM_030621.3	1729	Ccg/Tcg	25/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		352	311	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981185	55981185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370917098	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	14	348	0	ENST00000263923.4:c.514C>T	p.Pro172Ser	p.P172S	ENST00000263923	NM_002253.2	172	Cct/Tct	5/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		348	82	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17940925	17940925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	46	419	0	ENST00000458235.1:c.3199C>T	p.Pro1067Ser	p.P1067S	ENST00000458235	NM_000215.3	1067	Cct/Tct	23/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		419	299	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446070	29446070	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199892375	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	45	348	0	ENST00000544604.2:c.1901C>T	p.Pro634Leu	p.P634L	ENST00000544604	NM_001206998.1	634	cCg/cTg	8/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		348	224	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029240	14029240	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	35	475	0	ENST00000311895.7:c.1451C>T	p.Thr484Ile	p.T484I	ENST00000311895	NM_005236.2	484	aCc/aTc	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		475	185	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31435967	31435967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	13	312	1	ENST00000344624.3:c.2947C>T	p.His983Tyr	p.H983Y	ENST00000344624		983	Cat/Tat	22/33	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		313	61	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534359	63534359	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	118	594	0	ENST00000307078.5:c.1162C>G	p.Arg388Gly	p.R388G	ENST00000307078	NM_004655.3	388	Cgc/Ggc	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		594	356	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015065	71015065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	17	383	0	ENST00000318789.4:c.1865C>T	p.Pro622Leu	p.P622L	ENST00000318789	NM_032682.5	622	cCa/cTa	20/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		383	189	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28607309	28607309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	101	489	0	ENST00000253063.3:c.1439C>T	p.Thr480Ile	p.T480I	ENST00000253063	NM_031459.4	480	aCc/aTc	10/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		489	344	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246498722	246498722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201729065	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	45	325	0	ENST00000388985.4:c.283C>T	p.Pro95Ser	p.P95S	ENST00000388985		95	Ccc/Tcc	3/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		325	190	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933221	100933221	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	26	397	0	ENST00000325455.5:c.2169G>C	p.Glu723Asp	p.E723D	ENST00000325455	NM_001202474.3	723	gaG/gaC	4/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		397	129	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526263	189526263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	84	567	0	ENST00000264731.3:c.527G>A	p.Ser176Asn	p.S176N	ENST00000264731	NM_003722.4	176	aGt/aAt	4/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		567	410	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50741621	50741621	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	15	254	0	ENST00000307179.4:c.274C>T	p.Pro92Ser	p.P92S	ENST00000307179		92	Cct/Tct	4/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		254	94	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372141	45372141	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	25	368	0	ENST00000262160.6:c.1028G>C	p.Gly343Ala	p.G343A	ENST00000262160	NM_005901.5	343	gGg/gCg	9/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		368	115	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228059	53228059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	45	242	0	ENST00000375401.3:c.2255C>T	p.Thr752Ile	p.T752I	ENST00000375401	NM_004187.3	752	aCc/aTc	16/26	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		242	94	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430819	47430819	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	90	236	0	ENST00000377045.4:c.1784C>T	p.Pro595Leu	p.P595L	ENST00000377045	NM_001654.4	595	cCt/cTt	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		236	253	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431966	121431966	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1463923467	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	68	422	0	ENST00000257555.6:c.714-1G>A		p.X238_splice	ENST00000257555		238			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		422	199	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104359252	104359253	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	41	361	0	ENST00000369902.3:c.973_974delinsTT	p.Pro325Leu	p.P325L	ENST00000369902	NM_016169.3	325	CCa/TTa	8/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		361	209	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879180	151879180	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	53	449	0	ENST00000262189.6:c.5765C>T	p.Pro1922Leu	p.P1922L	ENST00000262189	NM_170606.2	1922	cCa/cTa	36/59	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		449	172	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245596	46245596	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	38	488	0	ENST00000334344.6:c.3690T>A	p.Cys1230Ter	p.C1230*	ENST00000334344	NM_152641.2	1230	tgT/tgA	15/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		488	109	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944319	81944319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	18	352	0	ENST00000359376.3:c.1928C>T	p.Ser643Phe	p.S643F	ENST00000359376	NM_002661.3	643	tCc/tTc	18/33	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		352	198	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244353	46244353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	31	488	0	ENST00000334344.6:c.2447C>T	p.Ser816Leu	p.S816L	ENST00000334344	NM_152641.2	816	tCa/tTa	15/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		488	124	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198260927	198260927	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	14	356	0	ENST00000335508.6:c.3392C>T	p.Ala1131Val	p.A1131V	ENST00000335508	NM_012433.2	1131	gCc/gTc	23/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		356	104	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034756	42034756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	24	441	0	ENST00000219905.7:c.4598C>T	p.Ser1533Phe	p.S1533F	ENST00000219905	NM_001164273.1	1533	tCt/tTt	15/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		441	183	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487888	56487888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	38	383	0	ENST00000267101.3:c.1619C>T	p.Pro540Leu	p.P540L	ENST00000267101	NM_001982.3	540	cCt/cTt	14/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		383	186	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498328	29498328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	30	408	0	ENST00000389048.3:c.1852G>A	p.Gly618Arg	p.G618R	ENST00000389048	NM_004304.4	618	Gga/Aga	10/29	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		408	147	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120802536	120802537	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	32	334	0	ENST00000257552.2:c.289_290delinsTT	p.Pro97Phe	p.P97F	ENST00000257552	NM_002442.3	97	CCt/TTt	5/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		334	142	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934199	49934199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	14	435	0	ENST00000296474.3:c.2308C>T	p.Pro770Ser	p.P770S	ENST00000296474	NM_002447.2	770	Cct/Tct	8/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		435	169	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800520	32800520	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759115387	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	99	516	0	ENST00000374899.4:c.1027C>T	p.Arg343Cys	p.R343C	ENST00000374899	NM_018833.2	343	Cgc/Tgc	6/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		516	442	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27203117	27203117	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	11	389	0	ENST00000380036.4:c.2209G>A	p.Ala737Thr	p.A737T	ENST00000380036	NM_000459.3	737	Gca/Aca	13/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		389	91	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468039	120468039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	38	513	0	ENST00000256646.2:c.4400C>T	p.Ser1467Phe	p.S1467F	ENST00000256646	NM_024408.3	1467	tCc/tTc	25/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		513	178	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912055	56912055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	21	327	0	ENST00000519728.1:c.1283C>T	p.Ser428Phe	p.S428F	ENST00000519728	NM_002350.3	428	tCc/tTc	12/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		327	107	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864307	57864307	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	41	544	0	ENST00000228682.2:c.1784C>T	p.Ser595Leu	p.S595L	ENST00000228682	NM_005269.2	595	tCa/tTa	12/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		544	211	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876508	35876508	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1365126170	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	14	480	0	ENST00000303115.3:c.1300G>A	p.Gly434Ser	p.G434S	ENST00000303115	NM_002185.3	434	Ggt/Agt	8/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		480	143	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256149	123256149	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	14	366	0	ENST00000358487.5:c.1760C>T	p.Ser587Phe	p.S587F	ENST00000358487	NM_000141.4	587	tCc/tTc	13/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		366	142	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257133	19257133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	13	295	0	ENST00000162023.5:c.830C>T	p.Pro277Leu	p.P277L	ENST00000162023		277	cCc/cTc	12/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		295	121	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519210	187519210	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	20	377	0	ENST00000441802.2:c.12173C>T	p.Ser4058Phe	p.S4058F	ENST00000441802	NM_005245.3	4058	tCc/tTc	23/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		377	118	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544951	86544951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	59	350	0	ENST00000262426.4:c.776C>T	p.Pro259Leu	p.P259L	ENST00000262426	NM_001451.2	259	cCg/cTg	1/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		350	181	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128848627	128848627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	58	319	0	ENST00000249373.3:c.1292G>A	p.Ser431Asn	p.S431N	ENST00000249373	NM_005631.4	431	aGc/aAc	7/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		319	228	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262103	10262103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	56	422	0	ENST00000340748.4:c.2188C>T	p.Arg730Cys	p.R730C	ENST00000340748		730	Cgc/Tgc	23/40	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		422	251	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867409	35867409	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	15	321	0	ENST00000303115.3:c.223G>A	p.Gly75Arg	p.G75R	ENST00000303115	NM_002185.3	75	Ggg/Agg	3/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		321	140	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679159	117679159	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777430404	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	22	302	0	ENST00000368508.3:c.3662C>T	p.Ser1221Leu	p.S1221L	ENST00000368508	NM_002944.2	1221	tCa/tTa	24/43	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		302	91	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149452939	149452939	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	43	432	0	ENST00000286301.3:c.1007G>A	p.Trp336Ter	p.W336*	ENST00000286301	NM_005211.3	336	tGg/tAg	7/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		432	173	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546748	9546748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	98	455	0	ENST00000353224.5:c.1274C>T	p.Ser425Phe	p.S425F	ENST00000353224	NM_177990.2	425	tCc/tTc	5/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		455	385	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27109613	27109613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745710118	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	26	303	0	ENST00000380036.4:c.25C>T	p.Leu9Phe	p.L9F	ENST00000380036	NM_000459.3	9	Ctc/Ttc	1/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		303	95	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796810	57796810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749346190	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	13	478	0	ENST00000309042.7:c.1786C>T	p.Pro596Ser	p.P596S	ENST00000309042	NM_005612.4	596	Cct/Tct	4/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		478	139	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118368745	118368745	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	24	476	0	ENST00000534358.1:c.5759C>T	p.Ser1920Leu	p.S1920L	ENST00000534358	NM_005933.3	1920	tCa/tTa	21/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		476	170	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727408	66727408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516789	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	46	338	0	ENST00000307102.5:c.124C>T	p.Leu42Phe	p.L42F	ENST00000307102	NM_002755.3	42	Ctt/Ttt	2/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		338	258	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516863	187516863	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	10	363	0	ENST00000441802.2:c.13118C>T	p.Ser4373Phe	p.S4373F	ENST00000441802	NM_005245.3	4373	tCc/tTc	26/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		363	146	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691908	30691908	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	37	378	0	ENST00000295754.5:c.410C>T	p.Ser137Phe	p.S137F	ENST00000295754	NM_003242.5	137	tCc/tTc	3/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		378	118	SUCCESS
CBL	867	MSKCC	GRCh37	11	119158650	119158650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	21	304	0	ENST00000264033.4:c.2030C>T	p.Ala677Val	p.A677V	ENST00000264033	NM_005188.3	677	gCt/gTt	12/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		304	139	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5563197	5563197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766028047	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	28	322	0	ENST00000397747.3:c.802G>A	p.Glu268Lys	p.E268K	ENST00000397747	NM_025239.3	268	Gaa/Aaa	6/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		322	157	SUCCESS
ALB	213	MSKCC	GRCh37	4	74277723	74277723	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754953092	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	20	336	0	ENST00000295897.4:c.724C>T	p.Arg242Cys	p.R242C	ENST00000295897	NM_000477.5	242	Cgc/Tgc	7/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		336	101	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227813	36227813	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs917137399	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	21	491	0	ENST00000222270.7:c.7298G>A	p.Gly2433Glu	p.G2433E	ENST00000222270	NM_014727.1	2433	gGg/gAg	32/37	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		491	269	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381570	81381570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	31	283	0	ENST00000222390.5:c.491C>T	p.Pro164Leu	p.P164L	ENST00000222390	NM_000601.4	164	cCt/cTt	5/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		283	136	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679835	33679835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2141921665	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	38	435	0	ENST00000308377.4:c.2246G>A	p.Arg749Lys	p.R749K	ENST00000308377	NM_152270.3	749	aGa/aAa	5/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		435	97	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499385	89499385	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	49	438	0	ENST00000336596.2:c.2555C>T	p.Ala852Val	p.A852V	ENST00000336596	NM_005233.5	852	gCc/gTc	15/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		438	194	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332312	70332312	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138684329	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	10	390	0	ENST00000373644.4:c.217C>T	p.Leu73Phe	p.L73F	ENST00000373644	NM_030625.2	73	Ctt/Ttt	2/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		390	129	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008261	29008261	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	21	359	0	ENST00000282397.4:c.610C>T	p.Leu204Phe	p.L204F	ENST00000282397	NM_002019.4	204	Ctt/Ttt	5/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		359	100	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662301	67662301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	18	420	0	ENST00000264010.4:c.1547C>T	p.Thr516Ile	p.T516I	ENST00000264010	NM_006565.3	516	aCc/aTc	9/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		420	275	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933493	49933494	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	18	556	0	ENST00000296474.3:c.2696_2697delinsTT	p.Thr899Ile	p.T899I	ENST00000296474	NM_002447.2	899	aCC/aTT	11/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		556	247	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978698	70978698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886137633	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	23	397	0	ENST00000276594.2:c.955G>A	p.Gly319Arg	p.G319R	ENST00000276594	NM_024504.3	319	Gga/Aga	5/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		397	124	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47503913	47503913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	62	354	0	ENST00000404338.3:c.4468C>T	p.Pro1490Ser	p.P1490S	ENST00000404338	NM_004491.4	1490	Ccc/Tcc	6/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		354	220	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434767	110434767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	30	450	0	ENST00000375856.3:c.3634C>T	p.Pro1212Ser	p.P1212S	ENST00000375856	NM_003749.2	1212	Cct/Tct	1/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		450	242	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056779	180056779	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	30	449	0	ENST00000261937.6:c.733G>A	p.Gly245Arg	p.G245R	ENST00000261937	NM_182925.4	245	Ggg/Agg	6/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		449	164	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139563085	139563085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1332331433	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	37	434	0	ENST00000308874.7:c.157C>T	p.Leu53Phe	p.L53F	ENST00000308874		53	Ctc/Ttc	4/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		434	238	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285830	87285830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	41	444	0	ENST00000277120.3:c.167C>T	p.Pro56Leu	p.P56L	ENST00000277120		56	cCg/cTg	2/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		444	148	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272075	15272075	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs570331972	NA	P-0068709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	57	471	0	ENST00000263388.2:c.6364C>T	p.Pro2122Ser	p.P2122S	ENST00000263388	NM_000435.2	2122	Ccc/Tcc	33/33	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		471	215	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0068710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	42	315	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.993	0.858	1	0.993	0.858	1	CLONAL	1	TRUE	1	0.863338237682119	2		315	98	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379793	17379793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	52	443	0	ENST00000359435.4:c.178G>A	p.Asp60Asn	p.D60N	ENST00000359435	NM_001033549.1	60	Gat/Aat	2/9	1	2	FACETS	0.92	0.804	1	0.92	0.804	1	CLONAL	1	TRUE	1	0.863338237682119	2		443	131	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15938139	15938139	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	62	336	0	ENST00000268712.3:c.7075del	p.Glu2359LysfsTer30	p.E2359Kfs*30	ENST00000268712	NM_006311.3	2359	Gaa/aa	45/46	1	2	FACETS	0.933	0.826	1	0.933	0.826	1	CLONAL	1	TRUE	1	0.863338237682119	2		336	154	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852656	63852656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	46	431	0	ENST00000279873.7:c.3434C>T	p.Ala1145Val	p.A1145V	ENST00000279873	NM_032199.2	1145	gCt/gTt	10/10	1	2	FACETS	0.888	0.769	1	0.888	0.769	1	CLONAL	1	TRUE	1	0.863338237682119	2		431	120	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128432166	128432167	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0068710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	43	273	0	ENST00000265960.3:c.279_280delinsTT	p.Arg94Ter	p.R94*	ENST00000265960	NM_001006617.1	93	ctCCga/ctTTga	3/12	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.863338237682119	2		273	93	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0068711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	30	332	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	NA	2	FACETS	0.897	0.725	1			1	INDETERMINATE	1	TRUE	NA	0.226036044923848	2		332	296	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0068712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	38	206	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.506	0.422	0.596	0.506	0.422	0.596	SUBCLONAL	1	TRUE	1	0.778925799389078	2		206	193	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871003	12871003	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	285	324	0	ENST00000228872.4:c.230A>C	p.Gln77Pro	p.Q77P	ENST00000228872	NM_004064.3	77	cAa/cCa	1/3	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.778925799389078	2		324	582	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639953	3639953	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	99	384	0	ENST00000294008.3:c.3686T>C	p.Leu1229Ser	p.L1229S	ENST00000294008	NM_032444.2	1229	tTg/tCg	12/15	1	2	FACETS	0.491	0.439	0.545	0.491	0.439	0.545	SUBCLONAL	1	TRUE	1	0.778925799389078	2		384	518	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0068713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	18	269	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.18	0.135	0.232	0.18	0.135	0.232	SUBCLONAL	1	TRUE	1	0.932327296871467	2		269	215	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357598	70357599	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0068713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	87	378	0	ENST00000374080.3:c.5849_5850del	p.His1950ArgfsTer100	p.H1950Rfs*100	ENST00000374080		1950	cAT/c	41/45	1	2	FACETS	0.569	0.508	0.632	0.569	0.508	0.632	SUBCLONAL	1	TRUE	1	0.932327296871467	2		378	328	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81340829	81340829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	24	131	0	ENST00000222390.5:c.1412G>A	p.Gly471Asp	p.G471D	ENST00000222390	NM_000601.4	471	gGt/gAt	12/18	1	2	FACETS	0.358	0.283	0.441	0.358	0.283	0.441	SUBCLONAL	1	TRUE	1	0.932327296871467	2		131	144	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0068726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	62	257	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.923	1	1	0.985	1	CLONAL	3	TRUE	1	0.199594067259961	2		257	194	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130707	29130707	+	start_lost	Translation_Start_Site	SNP	C	C	T	rs786203977	NA	P-0068726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	151	240	0	ENST00000328354.6:c.3G>A	p.Met1?	p.M1?	ENST00000328354	NM_007194.3	1	atG/atA	2/15	1	2	FACETS	1	0.947	1	1	0.994	1	CLONAL	4	TRUE	1	0.199594067259961	2		240	368	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0068726-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	126	257	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.65	2		257	378	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130707	29130707	+	start_lost	Translation_Start_Site	SNP	C	C	T	rs786203977	NA	P-0068726-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	188	240	0	ENST00000328354.6:c.3G>A	p.Met1?	p.M1?	ENST00000328354	NM_007194.3	1	atG/atA	2/15	1	2	FACETS	0.989	0.919	1	0.989	0.919	1	CLONAL	1	TRUE	1	0.65	2		240	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912664	NA	P-0068727-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	155	236	0	ENST00000269305.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000269305	NM_001126112.2	337	cGc/cAc	10/11	0.350801851857922	3	FACETS	0.856	0.808	0.902	0.856	0.808	0.902	INDETERMINATE	3	TRUE	0	0.699463904935959	3		236	233	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0068728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	105	439	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.188026756011703	2	FACETS	1	0.978	1	0.684	0.613	0.76	CLONAL	1	FALSE	0	0.199906419669645	2		440	768	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0068728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	173	538	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.199906419669645	1	FACETS	1	0.972	1	1	0.994	1	CLONAL	3	FALSE	0	0.199906419669645	1		538	476	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252066	226252066	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	87	106	0	ENST00000366813.1:c.14A>T	p.Lys5Met	p.K5M	ENST00000366813		5	aAg/aTg	1/3	1	2	FACETS	0.834	0.744	0.928	1	0.988	1	CLONAL	3	FALSE	1	0.199906419669645	2		106	348	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482607	56482607	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	19	308	0	ENST00000267101.3:c.1064C>A	p.Thr355Asn	p.T355N	ENST00000267101	NM_001982.3	355	aCc/aAc	9/28	0.152360579766016	4	FACETS	0.312	0.236	0.404	0.156	0.118	0.202	SUBCLONAL	1	FALSE	2	0.199906419669645	4		308	730	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577569	7577569	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519981	NA	P-0068728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	16	291	0	ENST00000269305.4:c.712T>A	p.Cys238Ser	p.C238S	ENST00000269305	NM_001126112.2	238	Tgt/Agt	7/11	0.188026756011703	2	FACETS	0.27	0.199	0.357	0.135	0.099	0.179	SUBCLONAL	1	FALSE	0	0.199906419669645	2		291	592	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713470	40713470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318044562	NA	P-0068728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	141	367	1	ENST00000373198.4:c.4045C>T	p.Arg1349Cys	p.R1349C	ENST00000373198	NM_133170.3	1349	Cgt/Tgt	30/32	0.199906419669645	0	FACETS	1	0.94	1			1	CLONAL	2	FALSE	0	0.199906419669645	0		368	546	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602733	55602733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555650901	NA	P-0068728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	58	265	0	ENST00000288135.5:c.2554G>A	p.Val852Ile	p.V852I	ENST00000288135	NM_000222.2	852	Gtc/Atc	18/21	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	1	0.199906419669645	2		265	495	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453153	140453153	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913337	NA	P-0068728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	9	267	0	ENST00000288602.6:c.1782T>A	p.Asp594Glu	p.D594E	ENST00000288602	NM_004333.4	594	gaT/gaA	15/18	1	2	FACETS	0.227	0.149	0.327	0.227	0.149	0.327	SUBCLONAL	1	FALSE	1	0.199906419669645	2		267	397	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14021985	14022020	+	inframe_deletion	In_Frame_Del	DEL	ATACTGGACATTTTAAATGCATGTCTAAAGGAACTA	ATACTGGACATTTTAAATGCATGTCTAAAGGAACTA	-	novel	NA	P-0068728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	38	341	0	ENST00000311895.7:c.686_721del	p.Ile229_Leu240del	p.I229_L240del	ENST00000311895	NM_005236.2	229	ATACTGGACATTTTAAATGCATGTCTAAAGGAACTA/-	4/11	0.17205147982186	3	FACETS	0.929	0.768	1	0.465	0.384	0.555	CLONAL	1	FALSE	1	0.199906419669645	3		341	450	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197475	26197475	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	183	364	0	ENST00000356476.2:c.4G>T	p.Ala2Ser	p.A2S	ENST00000356476		2	Gct/Tct	1/1	0.199906419669645	4	FACETS	0.951	0.88	1			1	CLONAL	3	FALSE	NA	0.199906419669645	4		364	770	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933930	39933931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0068728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	24	213	0	ENST00000378444.4:c.668dup	p.Gln224SerfsTer77	p.Q224Sfs*77	ENST00000378444	NM_001123385.1	223	cct/ccCt	4/15	0.199906419669645	2	FACETS	0.654	0.513	0.818			1	SUBCLONAL	1	FALSE	NA	0.199906419669645	2		213	367	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950082	44950082	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	24	138	0	ENST00000377967.4:c.3851C>A	p.Ser1284Ter	p.S1284*	ENST00000377967	NM_021140.2	1284	tCa/tAa	26/29	0.199906419669645	2	FACETS	1	0.917	1			1	CLONAL	1	FALSE	NA	0.199906419669645	2		138	175	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555526101	NA	P-0068729-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	167	455	0	ENST00000269305.4:c.497C>G	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tGa	5/11	0.256093272132926	2	FACETS	0.85	0.786	0.917	0.85	0.786	0.917	CLONAL	2	TRUE	0	0.344014974661517	2		455	571	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628313	86628328	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTTCAAATAGGATTA	TGTTCAAATAGGATTA	-	novel	NA	P-0068729-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	62	256	0	ENST00000274376.6:c.693-10_698del		p.X231_splice	ENST00000274376	NM_002890.2	231		3/25	0.344014974661517	1	FACETS	0.939	0.816	1	0.939	0.816	1	CLONAL	1	TRUE	0	0.344014974661517	1		256	318	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667664	29667664	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0068729-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	95	243	0	ENST00000356175.3:c.6999+1G>T		p.X2333_splice	ENST00000356175	NM_000267.3	2333			0.256093272132926	2	FACETS	1	0.982	1	0.748	0.672	0.828	CLONAL	1	TRUE	0	0.344014974661517	2		243	369	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129650	47129651	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0068730-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	98	291	0	ENST00000409792.3:c.5229dup	p.Arg1744Ter	p.R1744*	ENST00000409792	NM_014159.6	1743	-/T	10/21	0.2358757711624	3	FACETS	0.869	0.782	0.961	0.579	0.521	0.641	CLONAL	2	TRUE	0	0.345178532641067	3		291	383	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374844	149374844	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068730-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	61	262	0	ENST00000360632.3:c.250C>A	p.His84Asn	p.H84N	ENST00000360632	NM_015472.4	84	Cat/Aat	2/7	0.345178532641067	4	FACETS	1	0.925	1	0.552	0.477	0.632	CLONAL	1	TRUE	2	0.345178532641067	4		262	431	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183870	10183884	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTACGGGCCCGGC	AGGTACGGGCCCGGC	-	novel	NA	P-0068730-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	78	261	0	ENST00000256474.2:c.339_340+13del		p.X113_splice	ENST00000256474	NM_000551.3	113		1/3	0.2358757711624	3	FACETS	0.866	0.768	0.968	0.577	0.512	0.646	CLONAL	2	TRUE	0	0.345178532641067	3		261	306	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643864	52643864	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068730-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	67	282	0	ENST00000394830.3:c.2032C>G	p.Arg678Gly	p.R678G	ENST00000394830	NM_018313.4	678	Cgc/Ggc	17/30	0.289866658998734	3	FACETS	0.849	0.746	0.958	0.566	0.497	0.639	CLONAL	2	TRUE	0	0.345178532641067	3		282	268	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226969	53226969	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068730-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	77	123	0	ENST00000375401.3:c.2606del	p.Gln869ArgfsTer66	p.Q869Rfs*66	ENST00000375401	NM_004187.3	869	cAg/cg	18/26	0.345178532641067	2	FACETS	0.896	0.808	0.985			1	CLONAL	3	TRUE	NA	0.345178532641067	2		123	166	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0068731-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	193	365	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.451060341692734	3	FACETS	0.975	0.929	1	1	0.993	1	CLONAL	4	TRUE	0	0.451060341692734	3		365	269	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0068731-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	117	379	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.341969283388849	0	FACETS	1	0.945	1			1	CLONAL	1	TRUE	0	0.451060341692734	0		379	274	SUCCESS
APC	324	MSKCC	GRCh37	5	112175621	112175621	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068731-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	232	335	0	ENST00000257430.4:c.4330C>T	p.Gln1444Ter	p.Q1444*	ENST00000257430	NM_000038.5	1444	Caa/Taa	16/16	1	2	FACETS	0.776	0.727	0.825	1	0.993	1	SUBCLONAL	2	TRUE	1	0.451060341692734	2		335	663	SUCCESS
APC	324	MSKCC	GRCh37	5	112173995	112173995	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068731-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	173	319	0	ENST00000257430.4:c.2704G>T	p.Glu902Ter	p.E902*	ENST00000257430	NM_000038.5	902	Gaa/Taa	16/16	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.451060341692734	2		319	545	SUCCESS
AR	367	MSKCC	GRCh37	X	66766357	66766392	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	-	rs746853821	NA	P-0068731-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	101	75	1	ENST00000374690.3:c.1385_1420del	p.Gly462_Gly473del	p.G462_G473del	ENST00000374690	NM_000044.3	457	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC/-	1/8	0.277212130264152	4	FACETS	0.863	0.785	0.942	1	0.98	1	CLONAL	3	TRUE	2	0.451060341692734	4		76	251	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298703	15298703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749628786	NA	P-0068731-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	142	310	0	ENST00000263388.2:c.1595G>A	p.Arg532His	p.R532H	ENST00000263388	NM_000435.2	532	cGc/cAc	10/33	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.451060341692734	2		310	433	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	183	437	2	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.987	0.912	1	0.987	0.912	1	CLONAL	1	TRUE	1	0.434139011475993	2		439	854	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	305	394	2	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.434139011475993	2		396	628	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	141	257	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.434139011475993	2		257	519	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	211	569	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.434139011475993	2		571	864	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	147	338	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.434139011475993	2		338	599	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	123	343	2	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.434139011475993	2		345	552	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	47	124	0	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.434139011475993	1		124	130	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	139	379	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.434139011475993	2		379	623	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	47	134	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.434139011475993	2		134	209	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332272	70332273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1446158817	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	143	376	0	ENST00000373644.4:c.184dup	p.Thr62AsnfsTer4	p.T62Nfs*4	ENST00000373644	NM_030625.2	59	-/A	2/12	1	2	FACETS	0.88	0.803	0.96	0.88	0.803	0.96	CLONAL	1	TRUE	1	0.434139011475993	2		376	749	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775990	9775990	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138463758	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	183	423	0	ENST00000377346.4:c.454G>A	p.Ala152Thr	p.A152T	ENST00000377346	NM_005026.3	152	Gcc/Acc	5/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.434139011475993	2		423	767	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101612	27101612	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	170	470	0	ENST00000324856.7:c.4899del	p.Met1634Ter	p.M1634*	ENST00000324856	NM_006015.4	1632	Ccc/cc	18/20	1	2	FACETS	0.979	0.902	1	0.979	0.902	1	CLONAL	1	TRUE	1	0.434139011475993	2		470	800	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115269008	115269008	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	125	291	0	ENST00000438362.2:c.1603-1G>T		p.X535_splice	ENST00000438362	NM_001242891.1	535			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.434139011475993	2		291	521	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480570	120480570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	41	383	0	ENST00000256646.2:c.3247G>A	p.Ala1083Thr	p.A1083T	ENST00000256646	NM_024408.3	1083	Gca/Aca	20/34	1	2	FACETS	0.247	0.204	0.294	0.247	0.204	0.294	SUBCLONAL	1	TRUE	1	0.434139011475993	2		383	766	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112764487	112764487	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	145	329	0	ENST00000369452.4:c.1096C>T	p.Arg366Ter	p.R366*	ENST00000369452	NM_007373.3	366	Cga/Tga	5/9	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.434139011475993	2		329	552	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154242	2154242	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755455183	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	158	469	1	ENST00000434045.2:c.686del	p.Pro229GlnfsTer27	p.P229Qfs*27	ENST00000434045	NM_001127598.1	229	cCa/ca	5/5	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.434139011475993	2		470	709	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47594882	47594883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs756343868	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	176	478	0	ENST00000430070.2:c.1204dup	p.Glu402GlyfsTer4	p.E402Gfs*4	ENST00000430070	NM_018095.4	402	gag/gGag	4/4	1	2	FACETS	0.951	0.876	1	0.951	0.876	1	CLONAL	1	TRUE	1	0.434139011475993	2		478	853	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160516	108160516	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs34640941	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	158	366	0	ENST00000278616.4:c.4424A>G	p.Tyr1475Cys	p.Y1475C	ENST00000278616	NM_000051.3	1475	tAt/tGt	29/63	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.434139011475993	2		366	606	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420203	49420204	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	198	434	0	ENST00000301067.7:c.15545dup	p.Leu5183ProfsTer16	p.L5183Pfs*16	ENST00000301067	NM_003482.3	5182	ggc/ggGc	48/54	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.434139011475993	2		434	856	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431874	49431874	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	175	453	0	ENST00000301067.7:c.9265del	p.Val3089TrpfsTer30	p.V3089Wfs*30	ENST00000301067	NM_003482.3	3089	Gtg/tg	34/54	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.434139011475993	2		453	804	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536740	120536740	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	200	475	0	ENST00000229340.5:c.353-1G>A		p.X118_splice	ENST00000229340	NM_006861.6	118			1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.434139011475993	2		475	919	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001410	29001410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771714708	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	144	363	0	ENST00000282397.4:c.1322C>T	p.Pro441Leu	p.P441L	ENST00000282397	NM_002019.4	441	cCg/cTg	10/30	1	2	FACETS	0.971	0.888	1	0.971	0.888	1	CLONAL	1	TRUE	1	0.434139011475993	2		363	683	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034837	42034837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	108	425	0	ENST00000219905.7:c.4681del	p.Thr1561ProfsTer15	p.T1561Pfs*15	ENST00000219905	NM_001164273.1	1560	cAa/ca	15/24	1	2	FACETS	0.565	0.506	0.627	0.565	0.506	0.627	SUBCLONAL	1	TRUE	1	0.434139011475993	2		425	881	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576177	88576177	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	138	407	0	ENST00000360948.2:c.1496A>G	p.Asp499Gly	p.D499G	ENST00000360948	NM_001012338.2	499	gAc/gGc	13/19	1	2	FACETS	0.903	0.823	0.987	0.903	0.823	0.987	CLONAL	1	TRUE	1	0.434139011475993	2		407	704	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347983	347983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760961378	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	186	513	4	ENST00000262320.3:c.1523del	p.Gly508ValfsTer197	p.G508Vfs*197	ENST00000262320	NM_003502.3	508	gGt/gt	6/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.434139011475993	2		517	819	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348211	348211	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1458136153	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	149	452	1	ENST00000262320.3:c.1295del	p.Pro432GlnfsTer48	p.P432Qfs*48	ENST00000262320	NM_003502.3	432	cCa/ca	6/11	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.434139011475993	2		453	673	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274013	10274013	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758742694	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	170	437	0	ENST00000330684.3:c.256G>A	p.Val86Met	p.V86M	ENST00000330684	NM_001134407.1	86	Gtg/Atg	2/13	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.434139011475993	2		437	707	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	153	428	2	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.949	0.869	1	0.949	0.869	1	CLONAL	1	TRUE	1	0.434139011475993	2		430	743	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362446	40362447	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1202978138	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	111	353	0	ENST00000293328.3:c.1749dup	p.His584ThrfsTer8	p.H584Tfs*8	ENST00000293328	NM_012448.3	583	-/A	14/19	1	2	FACETS	0.702	0.632	0.777	0.702	0.632	0.777	SUBCLONAL	1	TRUE	1	0.434139011475993	2		353	728	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11015633	11015634	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	142	348	0	ENST00000327064.4:c.235_236dup	p.Phe80SerfsTer46	p.F80Sfs*46	ENST00000327064	NM_199141.1	76	gat/gaTGt	2/16	1	2	FACETS	0.988	0.903	1	0.988	0.903	1	CLONAL	1	TRUE	1	0.434139011475993	2		348	662	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353819	15353819	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	67	203	0	ENST00000263377.2:c.3061del	p.His1021IlefsTer47	p.H1021Ifs*47	ENST00000263377	NM_058243.2	1021	Cat/at	14/20	1	2	FACETS	0.919	0.804	1	0.919	0.804	1	CLONAL	1	TRUE	1	0.434139011475993	2		203	336	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354151	15354152	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	52	300	0	ENST00000263377.2:c.2728dup	p.Gln910ProfsTer7	p.Q910Pfs*7	ENST00000263377	NM_058243.2	910	caa/cCaa	14/20	1	2	FACETS	0.514	0.438	0.597	0.514	0.438	0.597	SUBCLONAL	1	TRUE	1	0.434139011475993	2		300	466	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950344	17950344	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	183	409	0	ENST00000458235.1:c.1383del	p.Leu462CysfsTer3	p.L462Cfs*3	ENST00000458235	NM_000215.3	461	ggG/gg	10/24	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.434139011475993	2		409	786	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210893	36210893	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	102	432	0	ENST00000222270.7:c.649del	p.Arg217GlyfsTer22	p.R217Gfs*22	ENST00000222270	NM_014727.1	215	aCc/ac	3/37	1	2	FACETS	0.569	0.508	0.633	0.569	0.508	0.633	SUBCLONAL	1	TRUE	1	0.434139011475993	2		432	826	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	185	480	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.434139011475993	2		481	839	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	196	464	0	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.434139011475993	2		464	823	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797806	42797807	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	165	478	0	ENST00000575354.2:c.3862dup	p.Glu1288GlyfsTer56	p.E1288Gfs*56	ENST00000575354	NM_015125.3	1286	-/G	16/20	1	2	FACETS	0.936	0.861	1	0.936	0.861	1	CLONAL	1	TRUE	1	0.434139011475993	2		478	812	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630430	47630430	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793541	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	48	339	0	ENST00000233146.2:c.100G>A	p.Val34Met	p.V34M	ENST00000233146	NM_000251.2	34	Gtg/Atg	1/16	0.431902923953303	3	FACETS	0.283	0.238	0.333	0.141	0.119	0.167	SUBCLONAL	1	TRUE	1	0.434139011475993	3		339	951	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266477	198266477	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	119	341	0	ENST00000335508.6:c.2359del	p.Ile787LeufsTer3	p.I787Lfs*3	ENST00000335508	NM_012433.2	787	Att/tt	16/25	0.431902923953303	3	FACETS	0.95	0.859	1	0.475	0.429	0.524	CLONAL	1	TRUE	1	0.434139011475993	3		341	702	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151253	202151254	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	311	366	0	ENST00000358485.4:c.1557dup	p.Lys520GlufsTer19	p.K520Efs*19	ENST00000358485	NM_001080125.1	518	atg/atGg	9/9	0.431902923953303	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.434139011475993	3		366	821	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795103	242795104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768249210	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	241	449	1	ENST00000334409.5:c.105dup	p.Thr36HisfsTer70	p.T36Hfs*70	ENST00000334409	NM_005018.2	35	-/C	2/5	0.431902923953303	3	FACETS	1	0.992	1	0.738	0.691	0.788	CLONAL	1	TRUE	1	0.434139011475993	3		450	915	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980814	40980814	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	169	383	0	ENST00000373198.4:c.1672C>A	p.Pro558Thr	p.P558T	ENST00000373198	NM_133170.3	558	Cca/Aca	10/32	NA	2	FACETS	1	0.961	1			1	INDETERMINATE	1	TRUE	NA	0.434139011475993	2		383	728	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	335	440	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.959	0.911	1	1	0.996	1	CLONAL	2	TRUE	1	0.434139011475993	2		440	805	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103754	47103755	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	rs749901643	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	171	432	0	ENST00000409792.3:c.6190_6191dup	p.Asp2064GlufsTer84	p.D2064Efs*84	ENST00000409792	NM_014159.6	2064	gac/gaGAc	14/21	1	2	FACETS	0.908	0.835	0.983	0.908	0.835	0.983	CLONAL	1	TRUE	1	0.434139011475993	2		432	868	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937423	178937423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	36	93	0	ENST00000263967.3:c.1811G>A	p.Cys604Tyr	p.C604Y	ENST00000263967	NM_006218.2	604	tGt/tAt	12/21	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.434139011475993	2		93	127	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509085	66509085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	78	308	1	ENST00000273854.3:c.242del	p.Asn81MetfsTer24	p.N81Mfs*24	ENST00000273854	NM_004439.5	81	aAt/at	2/18	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.434139011475993	2		309	339	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31464435	31464435	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1471632102	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	120	361	1	ENST00000344624.3:c.2482del	p.Ile828TyrfsTer7	p.I828Yfs*7	ENST00000344624		828	Ata/ta	17/33	1	2	FACETS	0.914	0.827	1	0.914	0.827	1	CLONAL	1	TRUE	1	0.434139011475993	2		362	605	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672638	30672638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	242	546	0	ENST00000376406.3:c.4322C>T	p.Ser1441Phe	p.S1441F	ENST00000376406	NM_014641.2	1441	tCt/tTt	10/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.434139011475993	2		546	1043	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846357	128846357	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760560948	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	183	416	1	ENST00000249373.3:c.1193G>A	p.Arg398Gln	p.R398Q	ENST00000249373	NM_005631.4	398	cGa/cAa	6/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.434139011475993	2		417	775	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965666	90965666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	148	507	0	ENST00000265433.3:c.1651del	p.Arg551GlyfsTer8	p.R551Gfs*8	ENST00000265433	NM_002485.4	551	Agg/gg	11/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.434139011475993	2		507	586	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268792	98268793	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	152	388	1	ENST00000331920.6:c.290dup	p.Asn97LysfsTer43	p.N97Kfs*43	ENST00000331920	NM_000264.3	97	aac/aaAc	2/24	1	2	FACETS	0.97	0.889	1	0.97	0.889	1	CLONAL	1	TRUE	1	0.434139011475993	2		389	722	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	109	292	3	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	1	2	FACETS	0.998	0.901	1	0.998	0.901	1	CLONAL	1	TRUE	1	0.434139011475993	2		295	503	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324886	31324887	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760037174	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	42	290	0	ENST00000412585.2:c.49_50insG	p.Leu17ArgfsTer82	p.L17Rfs*82	ENST00000412585	NM_005514.6	17	ctg/cGtg	1/8	1	2	FACETS	0.295	0.245	0.35	0.295	0.245	0.35	SUBCLONAL	1	TRUE	1	0.434139011475993	2		290	656	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260566	16260566	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	190	418	0	ENST00000375759.3:c.7831G>T	p.Ala2611Ser	p.A2611S	ENST00000375759	NM_015001.2	2611	Gct/Tct	11/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.434139011475993	2		418	825	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598222	28598223	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	169	378	0	ENST00000253063.3:c.198dup	p.Leu67AlafsTer22	p.L67Afs*22	ENST00000253063	NM_031459.4	65	ctg/ctGg	3/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.434139011475993	2		378	696	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226589983	226589983	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	191	438	0	ENST00000366794.5:c.218G>T	p.Gly73Val	p.G73V	ENST00000366794	NM_001618.3	73	gGg/gTg	2/23	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.434139011475993	2		438	832	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021944	246021944	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	125	353	0	ENST00000388985.4:c.930G>T	p.Gln310His	p.Q310H	ENST00000388985		310	caG/caT	10/12	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.434139011475993	2		353	561	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57004456	57004456	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	166	394	0	ENST00000257254.3:c.23A>G	p.Asp8Gly	p.D8G	ENST00000257254		8	gAc/gGc	1/2	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.434139011475993	2		394	609	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158359	108158359	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	121	317	0	ENST00000278616.4:c.4026G>T	p.Glu1342Asp	p.E1342D	ENST00000278616	NM_000051.3	1342	gaG/gaT	27/63	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.434139011475993	2		317	508	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236108	108236108	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1565609065	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	167	403	0	ENST00000278616.4:c.9044A>G	p.Glu3015Gly	p.E3015G	ENST00000278616	NM_000051.3	3015	gAg/gGg	63/63	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.434139011475993	2		403	764	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240589	133240589	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	33	345	0	ENST00000320574.5:c.2706+1G>A		p.X902_splice	ENST00000320574	NM_006231.2	902			1	2	FACETS	0.247	0.2	0.3	0.247	0.2	0.3	SUBCLONAL	1	TRUE	1	0.434139011475993	2		345	616	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061769	38061770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	224	472	0	ENST00000250448.2:c.219_220insT	p.Gly74TrpfsTer153	p.G74Wfs*153	ENST00000250448	NM_004496.3	73	-/T	2/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.434139011475993	2		472	901	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609513	81609513	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	174	473	4	ENST00000298171.2:c.1115del	p.Asn372ThrfsTer40	p.N372Tfs*40	ENST00000298171	NM_000369.2	371	Aaa/aa	10/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.434139011475993	2		477	749	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95593052	95593052	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	140	326	0	ENST00000393063.1:c.768T>A	p.Asp256Glu	p.D256E	ENST00000393063	NM_030621.3	256	gaT/gaA	8/28	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.434139011475993	2		326	581	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799514	88799514	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1233002788	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	20	88	0	ENST00000360948.2:c.-16+1G>A		p.X6_splice	ENST00000360948	NM_001012338.2	6			1	2	FACETS	0.815	0.633	1	0.815	0.633	1	CLONAL	1	TRUE	1	0.434139011475993	2		88	113	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467147	99467147	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	150	341	0	ENST00000268035.6:c.2528G>T	p.Arg843Met	p.R843M	ENST00000268035	NM_000875.3	843	aGg/aTg	12/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.434139011475993	2		341	601	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348989	89348989	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	194	460	0	ENST00000301030.4:c.3961C>A	p.Leu1321Met	p.L1321M	ENST00000301030	NM_001256183.1	1321	Ctg/Atg	9/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.434139011475993	2		460	805	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8113541	8113541	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1226752309	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	126	308	0	ENST00000585124.1:c.2T>C	p.Met1?	p.M1?	ENST00000585124	NM_004217.3	1	aTg/aCg	2/9	1	2	FACETS	0.972	0.883	1	0.972	0.883	1	CLONAL	1	TRUE	1	0.434139011475993	2		308	597	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496973	29496973	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	53	214	0	ENST00000356175.3:c.544T>C	p.Tyr182His	p.Y182H	ENST00000356175	NM_000267.3	182	Tat/Cat	5/57	1	2	FACETS	0.676	0.579	0.782	0.676	0.579	0.782	SUBCLONAL	1	TRUE	1	0.434139011475993	2		214	361	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40478186	40478186	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	99	215	0	ENST00000264657.5:c.1313T>C	p.Leu438Pro	p.L438P	ENST00000264657	NM_139276.2	438	cTg/cCg	15/24	1	2	FACETS	0.889	0.797	0.987	0.889	0.797	0.987	CLONAL	1	TRUE	1	0.434139011475993	2		215	513	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438176	56438177	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	150	420	0	ENST00000407977.2:c.816_817del	p.Ala273HisfsTer8	p.A273Hfs*8	ENST00000407977		272	tgTGcc/tgcc	7/10	1	2	FACETS	0.977	0.895	1	0.977	0.895	1	CLONAL	1	TRUE	1	0.434139011475993	2		420	707	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971726	18971726	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	169	365	0	ENST00000262803.5:c.2392G>T	p.Gly798Cys	p.G798C	ENST00000262803	NM_002911.3	798	Ggc/Tgc	17/24	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.434139011475993	2		365	737	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222817	36222817	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	157	366	0	ENST00000222270.7:c.5446G>T	p.Gly1816Cys	p.G1816C	ENST00000222270	NM_014727.1	1816	Ggt/Tgt	27/37	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.434139011475993	2		366	681	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440090	220440090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	324	361	1	ENST00000243786.2:c.943G>A	p.Ala315Thr	p.A315T	ENST00000243786	NM_002191.3	315	Gcc/Acc	2/2	0.431902923953303	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.434139011475993	3		362	827	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292821	62292822	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs769909059	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	126	382	0	ENST00000360203.5:c.287_289dup	p.Ala96dup	p.A96dup	ENST00000360203	NM_001283009.1	96	-/GCT	3/35	1	2	FACETS	0.781	0.708	0.858	0.781	0.708	0.858	SUBCLONAL	1	TRUE	1	0.434139011475993	2		382	743	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755808	39755808	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	154	356	0	ENST00000288319.7:c.957G>T	p.Glu319Asp	p.E319D	ENST00000288319	NM_182918.3	319	gaG/gaT	10/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.434139011475993	2		356	613	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067907	30067907	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	182	380	0	ENST00000338641.4:c.1092A>C	p.Lys364Asn	p.K364N	ENST00000338641	NM_000268.3	364	aaA/aaC	11/16	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.434139011475993	2		380	744	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12632312	12632312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555781462	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	142	378	0	ENST00000251849.4:c.1355C>T	p.Thr452Met	p.T452M	ENST00000251849	NM_002880.3	452	aCg/aTg	12/17	1	2	FACETS	0.88	0.803	0.961	0.88	0.803	0.961	CLONAL	1	TRUE	1	0.434139011475993	2		378	743	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651278	52651278	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	182	358	0	ENST00000394830.3:c.1818G>T	p.Gln606His	p.Q606H	ENST00000394830	NM_018313.4	606	caG/caT	15/30	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.434139011475993	2		358	679	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361220	66361220	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	139	428	0	ENST00000273854.3:c.952A>G	p.Ser318Gly	p.S318G	ENST00000273854	NM_004439.5	318	Agc/Ggc	4/18	1	2	FACETS	0.907	0.827	0.99	0.907	0.827	0.99	CLONAL	1	TRUE	1	0.434139011475993	2		428	706	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629927	187629927	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	118	480	0	ENST00000441802.2:c.1055T>C	p.Val352Ala	p.V352A	ENST00000441802	NM_005245.3	352	gTc/gCc	2/27	1	2	FACETS	0.65	0.586	0.718	0.65	0.586	0.718	SUBCLONAL	1	TRUE	1	0.434139011475993	2		480	836	SUCCESS
APC	324	MSKCC	GRCh37	5	112179188	112179188	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	145	393	0	ENST00000257430.4:c.7897G>T	p.Gly2633Cys	p.G2633C	ENST00000257430	NM_000038.5	2633	Ggt/Tgt	16/16	1	2	FACETS	0.982	0.898	1	0.982	0.898	1	CLONAL	1	TRUE	1	0.434139011475993	2		393	680	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456895	149456895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	218	478	1	ENST00000286301.3:c.833G>A	p.Cys278Tyr	p.C278Y	ENST00000286301	NM_005211.3	278	tGc/tAc	6/22	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.434139011475993	2		479	878	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911081	29911082	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	114	404	0	ENST00000376809.5:c.384dup	p.Ser129ValfsTer48	p.S129Vfs*48	ENST00000376809	NM_002116.7	127	gtg/gtGg	3/8	1	2	FACETS	0.715	0.644	0.789	0.715	0.644	0.789	SUBCLONAL	1	TRUE	1	0.434139011475993	2		404	735	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485264	8485264	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	134	327	0	ENST00000356435.5:c.3116A>G	p.Glu1039Gly	p.E1039G	ENST00000356435		1039	gAg/gGg	18/35	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.434139011475993	2		327	498	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220420	98220421	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	122	409	0	ENST00000331920.6:c.3042dup	p.Phe1015LeufsTer130	p.F1015Lfs*130	ENST00000331920	NM_000264.3	1014	-/C	18/24	1	2	FACETS	0.809	0.732	0.889	0.809	0.732	0.889	CLONAL	1	TRUE	1	0.434139011475993	2		409	695	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399317	139399317	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	43	406	0	ENST00000277541.6:c.4826A>G	p.Asp1609Gly	p.D1609G	ENST00000277541	NM_017617.3	1609	gAc/gGc	26/34	1	2	FACETS	0.282	0.235	0.334	0.282	0.235	0.334	SUBCLONAL	1	TRUE	1	0.434139011475993	2		406	703	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566462	139566462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs2119163180	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	146	332	0	ENST00000308874.7:c.721G>A	p.Val241Met	p.V241M	ENST00000308874		241	Gtg/Atg	9/10	1	2	FACETS	0.993	0.909	1	0.993	0.909	1	CLONAL	1	TRUE	1	0.434139011475993	2		332	677	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321407	1321407	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1426083675	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	144	326	0	ENST00000400841.2:c.350-2A>G		p.X117_splice	ENST00000400841		117			1	1	FACETS	0.86	0.787	0.935	0.86	0.787	0.935	CLONAL	1	TRUE	0	0.434139011475993	1		326	604	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410479	63410480	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	161	219	0	ENST00000330258.3:c.2687_2688del	p.Leu896ArgfsTer23	p.L896Rfs*23	ENST00000330258	NM_152424.3	896	cTC/c	2/2	1	1	FACETS	0.754	0.701	0.808	1	0.99	1	SUBCLONAL	2	TRUE	0	0.434139011475993	1		219	385	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410619	63410619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	42	206	0	ENST00000330258.3:c.2548G>A	p.Ala850Thr	p.A850T	ENST00000330258	NM_152424.3	850	Gcc/Acc	2/2	1	1	FACETS	0.382	0.319	0.451	0.382	0.319	0.451	SUBCLONAL	1	TRUE	0	0.434139011475993	1		206	397	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0068733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	27	269	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.464	0.37	0.569	0.464	0.37	0.569	SUBCLONAL	1	TRUE	1	0.485427843117533	2		269	240	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0068733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	44	224	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.485427843117533	2		224	157	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717715	89717716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587782341	NA	P-0068733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	66	232	0	ENST00000371953.3:c.741dup	p.Pro248ThrfsTer5	p.P248Tfs*5	ENST00000371953	NM_000314.4	247	tta/ttAa	7/9	0.427658030784217	3	FACETS	1	0.9	1	0.517	0.452	0.586	CLONAL	1	TRUE	1	0.485427843117533	3		232	327	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	59	297	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	1	2	FACETS	0.617	0.533	0.708	0.617	0.533	0.708	SUBCLONAL	1	TRUE	1	0.485427843117533	2		297	394	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189412	56189412	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	79	280	0	ENST00000399503.3:c.4444C>T	p.Arg1482Ter	p.R1482*	ENST00000399503	NM_005921.1	1482	Cga/Tga	20/20	1	2	FACETS	0.664	0.586	0.748	0.664	0.586	0.748	SUBCLONAL	1	TRUE	1	0.485427843117533	2		280	490	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0068733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	124	314	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.87	0.79	0.954	0.87	0.79	0.954	CLONAL	1	TRUE	1	0.485427843117533	2		314	587	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511611	38511611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs899025600	NA	P-0068733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	61	277	0	ENST00000254066.5:c.1109G>A	p.Arg370His	p.R370H	ENST00000254066	NM_000964.3	370	cGc/cAc	8/9	1	2	FACETS	0.578	0.5	0.662	0.578	0.5	0.662	SUBCLONAL	1	TRUE	1	0.485427843117533	2		277	435	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717695	89717695	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs190070312	NA	P-0068733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	107	228	0	ENST00000371953.3:c.720C>G	p.Tyr240Ter	p.Y240*	ENST00000371953	NM_000314.4	240	taC/taG	7/9	0.427658030784217	3	FACETS	0.753	0.681	0.826	0.753	0.681	0.826	SUBCLONAL	2	TRUE	1	0.485427843117533	3		228	364	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023715	27023716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0068733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	19	517	0	ENST00000324856.7:c.827dup	p.Gly277ArgfsTer123	p.G277Rfs*123	ENST00000324856	NM_006015.4	274	atg/atGg	1/20	1	2	FACETS	0.3	0.228	0.385	0.3	0.228	0.385	SUBCLONAL	1	TRUE	1	0.485427843117533	2		517	261	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645181	67645181	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	109	346	0	ENST00000264010.4:c.448del	p.Ser150ValfsTer4	p.S150Vfs*4	ENST00000264010	NM_006565.3	149	gAa/ga	3/12	1	2	FACETS	0.947	0.855	1	0.947	0.855	1	CLONAL	1	TRUE	1	0.485427843117533	2		346	474	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390168	89390168	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	106	248	0	ENST00000336596.2:c.917G>T	p.Cys306Phe	p.C306F	ENST00000336596	NM_005233.5	306	tGt/tTt	4/17	1	2	FACETS	0.846	0.762	0.935	0.846	0.762	0.935	CLONAL	1	TRUE	1	0.485427843117533	2		248	516	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0068736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	107	349	0				ENST00000310581	NM_198253.2	-/1132			0.198631421019522	3	FACETS	0.859	0.784	0.936	0.859	0.784	0.936	INDETERMINATE	3	TRUE	0	0.37	3		349	266	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0068736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	118	349	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.26705028683419	2	FACETS	0.822	0.748	0.898	0.822	0.748	0.898	CLONAL	2	TRUE	0	0.37	2		349	388	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755601	57755609	+	inframe_deletion	In_Frame_Del	DEL	ATGGTGGTG	ATGGTGGTG	-	rs1561217633	NA	P-0068736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	26	483	0	ENST00000274289.3:c.178_186del	p.His60_His62del	p.H60_H62del	ENST00000274289	NM_006622.3	60	CACCACCAT/-	1/14	0.3	1	FACETS	0.291	0.23	0.361	0.291	0.23	0.361	SUBCLONAL	1	TRUE	0	0.37	1		483	394	SUCCESS
BLM	641	MSKCC	GRCh37	15	91352385	91352385	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372134818	NA	P-0068736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	37	317	0	ENST00000355112.3:c.3770C>T	p.Pro1257Leu	p.P1257L	ENST00000355112	NM_000057.2	1257	cCt/cTt	20/22	1	2	FACETS	0.477	0.394	0.571	0.477	0.394	0.571	SUBCLONAL	1	TRUE	1	0.37	2		317	419	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210842	36210846	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGG	GGCGG	-	novel	NA	P-0068736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	210	515	0	ENST00000222270.7:c.594_598del	p.Arg199ProfsTer12	p.R199Pfs*12	ENST00000222270	NM_014727.1	198	cGGCGG/c	3/37	0.199174814193673	4	FACETS	1	0.957	1	0.77	0.722	0.818	INDETERMINATE	3	TRUE	0	0.37	4		515	505	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209085	36209086	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCGGGCGGAGCCGAGC	novel	NA	P-0068736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	30	374	0	ENST00000222270.7:c.171_186dup	p.Glu63ArgfsTer58	p.E63Rfs*58	ENST00000222270	NM_014727.1	55	-/CCGGGCGGAGCCGAGC	1/37	0.199174814193673	4	FACETS	0.523	0.421	0.638	0.131	0.105	0.16	INDETERMINATE	1	TRUE	0	0.37	4		374	425	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375014	118375014	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	55	462	0	ENST00000534358.1:c.8407C>T	p.Gln2803Ter	p.Q2803*	ENST00000534358	NM_005933.3	2803	Cag/Tag	27/36	1	2	FACETS	0.619	0.53	0.716	0.619	0.53	0.716	SUBCLONAL	1	TRUE	1	0.37	2		462	480	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073756	8073756	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	63	469	0	ENST00000377482.5:c.903G>A	p.Trp301Ter	p.W301*	ENST00000377482	NM_018948.3	301	tgG/tgA	4/4	NA	2	FACETS	0.691	0.598	0.791			1	INDETERMINATE	1	TRUE	NA	0.37	2		469	493	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068737-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	127	340	1	ENST00000347630.2:c.397T>C	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	Ttc/Ctc	6/11	1	2	FACETS	0.97	0.883	1	0.97	0.883	1	CLONAL	1	TRUE	1	0.511451408408884	2		341	512	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061208	38061208	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1292426539	NA	P-0068737-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	119	426	0	ENST00000250448.2:c.781C>G	p.Arg261Gly	p.R261G	ENST00000250448	NM_004496.3	261	Cgc/Ggc	2/2	1	2	FACETS	0.904	0.819	0.991	0.904	0.819	0.991	CLONAL	1	TRUE	1	0.511451408408884	2		426	515	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863677	68863677	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068737-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	139	306	0	ENST00000261769.5:c.2416G>T	p.Glu806Ter	p.E806*	ENST00000261769	NM_004360.3	806	Gaa/Taa	15/16	0.511451408408884	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.511451408408884	1		306	345	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115733	8115733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068737-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	103	418	0	ENST00000346208.3:c.1079G>A	p.Gly360Asp	p.G360D	ENST00000346208		360	gGc/gAc	6/6	1	2	FACETS	0.709	0.636	0.786	0.709	0.636	0.786	SUBCLONAL	1	TRUE	1	0.511451408408884	2		418	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0068738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	75	428	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.17	2		428	674	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929095	32929095	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	37	352	0	ENST00000380152.3:c.7105G>T	p.Glu2369Ter	p.E2369*	ENST00000380152		2369	Gaa/Taa	14/27	1	2	FACETS	0.888	0.732	1	0.888	0.732	1	CLONAL	1	TRUE	1	0.17	2		352	490	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363559	40363565	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCTCG	CTGCTCG	-	novel	NA	P-0068738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	36	435	0	ENST00000397332.2:c.664_670del	p.Arg222ThrfsTer7	p.R222Tfs*7	ENST00000397332	NM_001033082.2	222	CGAGCAGac/ac	3/3	1	2	FACETS	0.631	0.517	0.759	0.631	0.517	0.759	SUBCLONAL	1	TRUE	1	0.17	2		435	671	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1691304	1691330	+	inframe_deletion	In_Frame_Del	DEL	AAGGCAGCAGCTGAGATGCGAGTGACA	AAGGCAGCAGCTGAGATGCGAGTGACA	-	novel	NA	P-0068738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	50	449	0	ENST00000378625.1:c.275_301del	p.Leu92_Pro100del	p.L92_P100del	ENST00000378625	NM_001198994.1	92	tTGTCACTCGCATCTCAGCTGCTGCCTTca/tca	4/14	1	2	FACETS	0.947	0.803	1	0.947	0.803	1	CLONAL	1	TRUE	1	0.17	2		449	621	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946226	71946226	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1565395002	NA	P-0068738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	56	422	0	ENST00000298229.2:c.2482A>G	p.Met828Val	p.M828V	ENST00000298229	NM_001567.3	828	Atg/Gtg	22/28	0.169199672729366	3	FACETS	0.816	0.697	0.947	0.408	0.348	0.474	CLONAL	1	TRUE	1	0.17	3		422	876	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051642	30051642	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	128	381	0	ENST00000338641.4:c.576C>A	p.Tyr192Ter	p.Y192*	ENST00000338641	NM_000268.3	192	taC/taA	6/16	0.719088468935351	1	FACETS	0.931	0.863	0.998	0.931	0.863	0.998	CLONAL	1	TRUE	0	0.719088468935351	1		381	245	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0068741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	177	269	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.540098529468518	2	FACETS	0.958	0.899	1	0.958	0.899	1	CLONAL	2	TRUE	0	0.540098529468518	2		269	342	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0068741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	135	511	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.540098529468518	3	FACETS	0.81	0.737	0.887	0.405	0.368	0.444	CLONAL	1	TRUE	1	0.540098529468518	3		511	784	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925316	114925317	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs745872748	NA	P-0068741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	232	346	6	ENST00000543371.1:c.1403dup	p.Cys469ValfsTer8	p.C469Vfs*8	ENST00000543371	NM_001198531.1	465	aga/agAa	14/14	0.52496759452512	2	FACETS	0.834	0.786	0.883	0.834	0.786	0.883	CLONAL	2	TRUE	0	0.540098529468518	2		352	515	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915951	127915951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	333	461	0	ENST00000373547.4:c.530G>A	p.Arg177Gln	p.R177Q	ENST00000373547	NM_002721.4	177	cGa/cAa	6/7	0.540098529468518	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.540098529468518	3		461	726	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281888	49281888	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	165	445	0	ENST00000282018.3:c.935T>A	p.Phe312Tyr	p.F312Y	ENST00000282018	NM_020377.2	312	tTt/tAt	1/1	0.540098529468518	3	FACETS	1	0.959	1	0.533	0.49	0.577	CLONAL	1	TRUE	1	0.540098529468518	3		445	728	SUCCESS
APC	324	MSKCC	GRCh37	5	112175773	112175775	+	frameshift_variant	Frame_Shift_Del	DEL	AAG	AAG	TA	novel	NA	P-0068741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	313	504	0	ENST00000257430.4:c.4482_4484delinsTA	p.Glu1494AspfsTer13	p.E1494Dfs*13	ENST00000257430	NM_000038.5	1494	gaAAGt/gaTAt	16/16	0.540098529468518	3	FACETS	0.921	0.873	0.97	0.921	0.873	0.97	CLONAL	2	TRUE	1	0.540098529468518	3		504	799	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0068742-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	90	436	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.271484676939179	2		436	561	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0068770-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	83	206	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.328824661047127	3	FACETS	0.945	0.843	1	0.945	0.843	1	CLONAL	2	TRUE	1	0.328824661047127	3		206	311	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741690	17741690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068770-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	51	441	0	ENST00000250003.3:c.361C>T	p.Arg121Cys	p.R121C	ENST00000250003	NM_002478.4	121	Cgc/Tgc	1/3	0.145446234459369	0	FACETS	1	0.862	1			1	INDETERMINATE	1	TRUE	0	0.328824661047127	0		441	208	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981819	201981819	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068770-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	79	433	0	ENST00000359651.3:c.530G>T	p.Ser177Ile	p.S177I	ENST00000359651		177	aGc/aTc	4/8	0.328824661047127	4	FACETS	1	0.958	1	0.399	0.352	0.45	CLONAL	1	TRUE	1	0.328824661047127	4		433	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0068789-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	122	419	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		419	538	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0068789-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	123	368	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		368	491	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426722	212426722	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068789-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	113	479	0	ENST00000342788.4:c.2393T>G	p.Leu798Arg	p.L798R	ENST00000342788	NM_005235.2	798	cTt/cGt	20/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		479	572	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696597	47696597	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068789-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	86	393	0	ENST00000347630.2:c.351G>T	p.Met117Ile	p.M117I	ENST00000347630	NM_001007230.1	117	atG/atT	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		393	429	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925314	114925314	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068789-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	84	315	0	ENST00000543371.1:c.1392G>C	p.Arg464Ser	p.R464S	ENST00000543371	NM_001198531.1	464	agG/agC	14/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		315	427	SUCCESS
BTK	695	MSKCC	GRCh37	X	100609665	100609668	+	frameshift_variant	Frame_Shift_Del	DEL	CAAA	CAAA	-	rs1555977592	NA	P-0068789-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	25	334	0	ENST00000308731.7:c.1581_1584del	p.Cys527TrpfsTer2	p.C527Wfs*2	ENST00000308731	NM_000061.2	527	tgTTTG/tg	16/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		334	414	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602679	10602680	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	AGTC	novel	NA	P-0068789-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	117	523	0	ENST00000171111.5:c.895_898dup	p.Tyr300Ter	p.Y300*	ENST00000171111	NM_203500.1	300	tac/tGACTac	3/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		523	570	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665150	29665150	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068789-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	34	291	0	ENST00000356175.3:c.6749T>A	p.Leu2250His	p.L2250H	ENST00000356175	NM_000267.3	2250	cTt/cAt	44/57	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		291	295	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741669	145741671	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0068789-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	81	573	0	ENST00000428558.2:c.832_834del	p.Glu278del	p.E278del	ENST00000428558	NM_004260.3	278	GAG/-	5/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		573	555	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151868391	151868391	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068789-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	40	357	0	ENST00000262189.6:c.9411G>C	p.Gln3137His	p.Q3137H	ENST00000262189	NM_170606.2	3137	caG/caC	40/59	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		357	375	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987106	36987107	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0068789-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	82	449	0	ENST00000354822.5:c.581_582dup	p.Arg195AlafsTer34	p.R195Afs*34	ENST00000354822	NM_001079668.2	194	-/GC	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		449	384	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0068790-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	25	536	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		536	198	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0068790-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	14	276	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		276	229	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913396	NA	P-0068790-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	38	310	0	ENST00000349496.5:c.95A>T	p.Asp32Val	p.D32V	ENST00000349496	NM_001904.3	32	gAc/gTc	3/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		310	311	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236203	108236203	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434219	NA	P-0068790-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	50	293	0	ENST00000278616.4:c.9139C>T	p.Arg3047Ter	p.R3047*	ENST00000278616	NM_000051.3	3047	Cga/Tga	63/63	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		293	283	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246315	46246315	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068790-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	59	345	0	ENST00000334344.6:c.4409C>A	p.Ser1470Ter	p.S1470*	ENST00000334344	NM_152641.2	1470	tCa/tAa	15/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		345	354	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927364	49927364	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068790-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	42	353	0	ENST00000296474.3:c.3940G>T	p.Asp1314Tyr	p.D1314Y	ENST00000296474	NM_002447.2	1314	Gat/Tat	19/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		353	345	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189006	32189006	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068790-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	83	357	0	ENST00000375023.3:c.548C>A	p.Pro183Gln	p.P183Q	ENST00000375023	NM_004557.3	183	cCa/cAa	4/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		357	450	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001901	29001901	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068790-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	16	229	0	ENST00000282397.4:c.1264C>A	p.Leu422Ile	p.L422I	ENST00000282397	NM_002019.4	422	Cta/Ata	9/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		229	207	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56376703	56376703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068790-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	23	249	0	ENST00000348428.3:c.743G>A	p.Cys248Tyr	p.C248Y	ENST00000348428	NM_006785.3	248	tGt/tAt	5/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		249	243	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0068791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	382	290	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.656677008800487	5	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	2	0.656677008800487	5		290	732	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0068791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	133	421	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.656677008800487	2		421	383	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446900	18446900	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	441	306	0	ENST00000266497.5:c.985C>A	p.Pro329Thr	p.P329T	ENST00000266497		329	Ccc/Acc	4/31	0.656677008800487	5	FACETS	0.98	0.94	1	0.98	0.94	1	CLONAL	3	TRUE	2	0.656677008800487	5		306	907	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912660	NA	P-0068791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	359	526	0	ENST00000269305.4:c.839G>T	p.Arg280Ile	p.R280I	ENST00000269305	NM_001126112.2	280	aGa/aTa	8/11	0.656677008800487	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.656677008800487	2		526	530	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860764	45860764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	201	612	1	ENST00000391945.4:c.1345G>A	p.Glu449Lys	p.E449K	ENST00000391945	NM_000400.3	449	Gag/Aag	14/23	0.654113957679693	3	FACETS	1	0.959	1	0.523	0.486	0.562	CLONAL	1	TRUE	1	0.656677008800487	3		613	777	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961451	1961451	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1162500705	NA	P-0068791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	154	476	0	ENST00000382891.5:c.3239A>G	p.Lys1080Arg	p.K1080R	ENST00000382891	NM_133335.3	1080	aAg/aGg	17/22	0.654113957679693	3	FACETS	0.912	0.837	0.99	0.456	0.418	0.495	CLONAL	1	TRUE	1	0.656677008800487	3		476	683	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411645	116411645	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	193	534	1	ENST00000397752.3:c.2824T>C	p.Ser942Pro	p.S942P	ENST00000397752	NM_000245.2	942	Tca/Cca	13/21	0.656324918991539	4	FACETS	0.905	0.836	0.976	0.302	0.278	0.326	CLONAL	1	TRUE	1	0.656677008800487	4		535	1076	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971153	21971153	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913383	NA	P-0068791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	420	626	0	ENST00000304494.5:c.205G>T	p.Glu69Ter	p.E69*	ENST00000304494	NM_000077.4	69	Gag/Tag	2/3	0.656677008800487	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.656677008800487	2		626	630	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44896898	44896898	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0068791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	104	284	0	ENST00000377967.4:c.620-2A>T		p.X207_splice	ENST00000377967	NM_021140.2	207			1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.656677008800487	2		284	310	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412763	63412763	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	147	580	0	ENST00000330258.3:c.404G>T	p.Gly135Val	p.G135V	ENST00000330258	NM_152424.3	135	gGg/gTg	2/2	1	2	FACETS	0.927	0.853	1	0.927	0.853	1	CLONAL	1	TRUE	1	0.656677008800487	2		580	483	SUCCESS
AR	367	MSKCC	GRCh37	X	66941737	66941737	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	127	444	0	ENST00000374690.3:c.2381A>G	p.Glu794Gly	p.E794G	ENST00000374690	NM_000044.3	794	gAg/gGg	6/8	1	2	FACETS	0.879	0.803	0.958	0.879	0.803	0.958	CLONAL	1	TRUE	1	0.656677008800487	2		444	440	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699264	117699264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	190	423	0	ENST00000369458.3:c.377G>A	p.Gly126Asp	p.G126D	ENST00000369458	NM_024626.3	126	gGc/gAc	3/6	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.656677008800487	2		423	493	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150915155	150915155	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	638	483	0	ENST00000271640.5:c.664C>T	p.Gln222Ter	p.Q222*	ENST00000271640	NM_001145415.1	222	Cag/Tag	6/22	0.655618288210714	4	FACETS	0.983	0.96	1	0.983	0.96	1	CLONAL	4	TRUE	0	0.656677008800487	4		483	819	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552839	226552839	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	174	504	0	ENST00000366794.5:c.2522G>T	p.Arg841Leu	p.R841L	ENST00000366794	NM_001618.3	841	cGt/cTt	19/23	0.655618288210714	4	FACETS	1	0.932	1	0.253	0.233	0.274	CLONAL	1	TRUE	0	0.656677008800487	4		504	867	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759859	63759859	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	179	452	0	ENST00000279873.7:c.512A>T	p.Glu171Val	p.E171V	ENST00000279873	NM_032199.2	171	gAg/gTg	4/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.656677008800487	2		452	500	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415882	49415882	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	224	503	0	ENST00000301067.7:c.16465G>T	p.Asp5489Tyr	p.D5489Y	ENST00000301067	NM_003482.3	5489	Gac/Tac	53/54	0.656677008800487	5	FACETS	1	0.985	1	0.404	0.376	0.434	CLONAL	1	TRUE	2	0.656677008800487	5		503	1117	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437528	110437528	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	271	465	0	ENST00000375856.3:c.873G>T	p.Met291Ile	p.M291I	ENST00000375856	NM_003749.2	291	atG/atT	1/2	NA	2	FACETS	0.951	0.908	0.993			1	INDETERMINATE	2	TRUE	NA	0.656677008800487	2		465	434	SUCCESS
BLM	641	MSKCC	GRCh37	15	91290677	91290677	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0068791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	219	412	0	ENST00000355112.3:c.55A>T	p.Arg19Ter	p.R19*	ENST00000355112	NM_000057.2	19	Aga/Tga	2/22	0.607989006630927	4	FACETS	0.933	0.874	0.993	0.933	0.874	0.993	CLONAL	2	TRUE	2	0.656677008800487	4		412	592	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3634842	3634842	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs993431348	NA	P-0068791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	323	487	0	ENST00000294008.3:c.4667C>T	p.Pro1556Leu	p.P1556L	ENST00000294008	NM_032444.2	1556	cCc/cTc	13/15	0.656677008800487	3	FACETS	0.948	0.903	0.994	0.632	0.602	0.663	CLONAL	2	TRUE	0	0.656677008800487	3		487	689	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6222227	6222227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	187	645	0	ENST00000252674.7:c.1015G>A	p.Glu339Lys	p.E339K	ENST00000252674	NM_005934.3	339	Gag/Aag	6/12	0.654664702609405	3	FACETS	1	0.958	1	0.35	0.324	0.377	CLONAL	1	TRUE	0	0.656677008800487	3		645	721	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097257	11097257	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	118	491	0	ENST00000358026.2:c.748A>T	p.Ser250Cys	p.S250C	ENST00000358026	NM_001128849.1	250	Agc/Tgc	4/36	0.656677008800487	2	FACETS	0.91	0.828	0.994	0.455	0.414	0.497	CLONAL	1	TRUE	0	0.656677008800487	2		491	395	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143994	11143994	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	317	520	0	ENST00000358026.2:c.3575G>T	p.Arg1192Leu	p.R1192L	ENST00000358026	NM_001128849.1	1192	cGc/cTc	26/36	0.656677008800487	2	FACETS	0.965	0.926	1	0.965	0.926	1	CLONAL	2	TRUE	0	0.656677008800487	2		520	500	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42385032	42385032	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	135	471	0	ENST00000221972.3:c.666G>C	p.Gln222His	p.Q222H	ENST00000221972	NM_021601.3	222	caG/caC	5/5	0.654113957679693	3	FACETS	0.918	0.837	1	0.459	0.418	0.501	CLONAL	1	TRUE	1	0.656677008800487	3		471	595	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965259	25965259	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	125	428	0	ENST00000435504.4:c.3947del	p.Leu1316CysfsTer8	p.L1316Cfs*8	ENST00000435504		1316	tTg/tg	13/13	0.654113957679693	3	FACETS	0.94	0.855	1	0.47	0.427	0.515	CLONAL	1	TRUE	1	0.656677008800487	3		428	538	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41818332	41818332	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	210	758	1	ENST00000373198.4:c.42G>C	p.Arg14Ser	p.R14S	ENST00000373198	NM_133170.3	14	agG/agC	1/32	0.656677008800487	3	FACETS	1	0.98	1	0.567	0.528	0.607	CLONAL	1	TRUE	1	0.656677008800487	3		759	749	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720993	176720993	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0068791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	385	602	0	ENST00000439151.2:c.6624T>A	p.Cys2208Ter	p.C2208*	ENST00000439151	NM_022455.4	2208	tgT/tgA	23/23	0.656677008800487	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.656677008800487	2		602	550	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047941	180047941	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	187	679	0	ENST00000261937.6:c.2234G>T	p.Arg745Leu	p.R745L	ENST00000261937	NM_182925.4	745	cGc/cTc	15/30	0.656677008800487	2	FACETS	0.989	0.919	1	0.494	0.459	0.53	CLONAL	1	TRUE	0	0.656677008800487	2		679	576	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680278	30680278	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	542	532	0	ENST00000376406.3:c.1441del	p.Val481LeufsTer58	p.V481Lfs*58	ENST00000376406	NM_014641.2	481	Gtt/tt	5/15	0.656677008800487	5	FACETS	0.938	0.903	0.974	0.938	0.903	0.974	CLONAL	3	TRUE	2	0.656677008800487	5		532	1164	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341139	8341139	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	807	440	0	ENST00000356435.5:c.5077G>T	p.Gly1693Ter	p.G1693*	ENST00000356435		1693	Gga/Tga	30/35	0.656677008800487	5	FACETS	1	0.995	1	1	0.995	1	CLONAL	5	TRUE	0	0.656677008800487	5		440	948	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426468	47426468	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	177	649	0	ENST00000377045.4:c.811C>A	p.His271Asn	p.H271N	ENST00000377045	NM_001654.4	271	Cat/Aat	9/16	1	2	FACETS	0.973	0.902	1	0.973	0.902	1	CLONAL	1	TRUE	1	0.656677008800487	2		649	554	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608205	100608205	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555977326	NA	P-0068791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	273	402	0	ENST00000308731.7:c.1885A>G	p.Ile629Val	p.I629V	ENST00000308731	NM_000061.2	629	Atc/Gtc	18/19	0.656677008800487	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.656677008800487	3		402	542	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0068797-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	118	640	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.722661206828595	1	FACETS	0.702	0.643	0.762	0.702	0.643	0.762	SUBCLONAL	1	TRUE	0	0.722661206828595	1		640	297	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56871568	56871568	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750817566	NA	P-0068797-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	166	491	0	ENST00000308159.5:c.1948G>A	p.Val650Ile	p.V650I	ENST00000308159	NM_014669.4	650	Gtc/Atc	18/22	0.555458445571216	1	FACETS	0.813	0.758	0.868	0.813	0.758	0.868	CLONAL	1	TRUE	0	0.722661206828595	1		491	361	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202123044	202123044	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068797-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	126	541	0	ENST00000358485.4:c.90C>G	p.His30Gln	p.H30Q	ENST00000358485	NM_001080125.1	30	caC/caG	1/9	1	2	FACETS	0.502	0.455	0.552	0.502	0.455	0.552	SUBCLONAL	1	TRUE	1	0.722661206828595	2		541	694	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47594951	47594951	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068797-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	54	647	0	ENST00000430070.2:c.1136A>G	p.Gln379Arg	p.Q379R	ENST00000430070	NM_018095.4	379	cAg/cGg	4/4	0.523918423749419	1	FACETS	0.198	0.169	0.229	0.198	0.169	0.229	SUBCLONAL	1	TRUE	0	0.722661206828595	1		647	483	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911451	39911451	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068797-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	11	273	0	ENST00000378444.4:c.5179del	p.Val1727TrpfsTer15	p.V1727Wfs*15	ENST00000378444	NM_001123385.1	1727	Gtg/tg	15/15	0.722661206828595	0	FACETS		NA	1			1	NA	1	TRUE	NA	0.722661206828595	0		273	182	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528432	29528432	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068797-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	201	421	0	ENST00000356175.3:c.1189T>C	p.Cys397Arg	p.C397R	ENST00000356175	NM_000267.3	397	Tgc/Cgc	11/57	0.67403732761479	2	FACETS	0.943	0.897	0.987	0.943	0.897	0.987	CLONAL	2	TRUE	0	0.722661206828595	2		421	295	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280094	142280094	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068797-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	196	313	0	ENST00000350721.4:c.1340A>T	p.Gln447Leu	p.Q447L	ENST00000350721	NM_001184.3	447	cAg/cTg	5/47	0.680774052313565	2	FACETS	0.938	0.892	0.983	0.938	0.892	0.983	CLONAL	2	TRUE	0	0.722661206828595	2		313	289	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0068803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	82	536	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.842	0.747	0.943	0.842	0.747	0.943	CLONAL	1	TRUE	1	0.500612014949851	2		536	389	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0068803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	22	435	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.193	0.149	0.245	0.193	0.149	0.245	SUBCLONAL	1	TRUE	1	0.500612014949851	2		435	455	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0068803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	84	405	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	1	2	FACETS	0.831	0.738	0.929	0.831	0.738	0.929	CLONAL	1	TRUE	1	0.500612014949851	2		405	404	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604789	48604789	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	141	371	0	ENST00000342988.3:c.1611C>G	p.Asp537Glu	p.D537E	ENST00000342988	NM_005359.5	537	gaC/gaG	12/12	0.500612014949851	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.500612014949851	1		371	389	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5535014	5535014	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200938803	NA	P-0068803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	112	340	0	ENST00000397747.3:c.325G>A	p.Ala109Thr	p.A109T	ENST00000397747	NM_025239.3	109	Gcc/Acc	3/7	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.500612014949851	2		340	435	SUCCESS
APC	324	MSKCC	GRCh37	5	112174745	112174745	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064795228	NA	P-0068803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	119	429	0	ENST00000257430.4:c.3454C>T	p.Gln1152Ter	p.Q1152*	ENST00000257430	NM_000038.5	1152	Cag/Tag	16/16	1	2	FACETS	0.94	0.852	1	0.94	0.852	1	CLONAL	1	TRUE	1	0.500612014949851	2		429	506	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119926	70119942	+	frameshift_variant	Frame_Shift_Del	DEL	CACGGCCAGGTCACCTA	CACGGCCAGGTCACCTA	-	novel	NA	P-0068803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	123	390	0	ENST00000245479.2:c.933_949del	p.Val313LeufsTer259	p.V313Lfs*259	ENST00000245479	NM_000346.3	310	CACGGCCAGGTCACCTAc/c	3/3	1	2	FACETS	0.947	0.86	1	0.947	0.86	1	CLONAL	1	TRUE	1	0.500612014949851	2		390	519	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729577	41729577	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	144	448	0	ENST00000242208.4:c.952G>C	p.Val318Leu	p.V318L	ENST00000242208	NM_002192.2	318	Gtc/Ctc	3/3	0.481949055909696	3	FACETS	1	0.941	1	0.518	0.473	0.565	CLONAL	1	TRUE	1	0.500612014949851	3		448	694	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911540	114911540	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	135	379	0	ENST00000543371.1:c.1058C>G	p.Pro353Arg	p.P353R	ENST00000543371	NM_001198531.1	353	cCt/cGt	10/14	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.500612014949851	2		379	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0068804-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	263	310	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.24896142344764	3	FACETS	0.954	0.916	0.99			1	INDETERMINATE	3	TRUE	NA	0.66592106446614	3		310	368	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419906	41419906	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068804-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	115	388	0	ENST00000373198.4:c.415T>C	p.Ser139Pro	p.S139P	ENST00000373198	NM_133170.3	139	Tcc/Ccc	3/32	0.242250173089152	6	FACETS	1	0.967	1	0.388	0.35	0.428	INDETERMINATE	1	TRUE	3	0.66592106446614	6		388	692	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907771	76907771	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068804-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	181	301	0	ENST00000373344.5:c.4390G>T	p.Glu1464Ter	p.E1464*	ENST00000373344	NM_000489.3	1464	Gaa/Taa	15/35	0.66592106446614	3	FACETS	0.831	0.775	0.887	0.831	0.775	0.887	CLONAL	2	TRUE	1	0.66592106446614	3		301	436	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738254	190738254	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068804-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	84	269	0	ENST00000441310.2:c.2506G>C	p.Glu836Gln	p.E836Q	ENST00000441310	NM_000534.4	836	Gaa/Caa	12/13	0.550521397180722	3	FACETS	1	0.953	1			1	CLONAL	1	TRUE	NA	0.66592106446614	3		269	299	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946402	2946402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	19	358	0	ENST00000396946.4:c.3335C>T	p.Ala1112Val	p.A1112V	ENST00000396946	NM_032415.4	1112	gCc/gTc	25/25	0.335255679509277	3	FACETS	0.417	0.316	0.536	0.209	0.158	0.268	SUBCLONAL	1	TRUE	1	0.335332528100758	3		358	317	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0068806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	52	295	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.330760019743777	1	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	FALSE	0	0.330760019743777	1		295	259	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0068806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	81	264	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.330760019743777	2		264	365	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441464	52441464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	65	427	0	ENST00000460680.1:c.388G>A	p.Ala130Thr	p.A130T	ENST00000460680	NM_004656.3	130	Gcg/Acg	6/17	0.330760019743777	1	FACETS	0.884	0.771	1	0.884	0.771	1	CLONAL	1	FALSE	0	0.330760019743777	1		427	371	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443611	52443616	+	inframe_deletion	In_Frame_Del	DEL	CACCCC	CACCCC	-	novel	NA	P-0068806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	57	394	0	ENST00000460680.1:c.76_81del	p.Gly26_Val27del	p.G26_V27del	ENST00000460680	NM_004656.3	26	GGGGTG/-	3/17	0.330760019743777	1	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	FALSE	0	0.330760019743777	1		394	274	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279328	38279328	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	110	386	0	ENST00000425967.3:c.1161G>C	p.Leu387Phe	p.L387F	ENST00000425967	NM_001174067.1	387	ttG/ttC	9/19	0.122489447850773	3	FACETS	0.964	0.873	1	0.643	0.582	0.706	INDETERMINATE	2	FALSE	0	0.330760019743777	3		386	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578234	7578234	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0068807-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	123	478	0	ENST00000269305.4:c.615T>G	p.Tyr205Ter	p.Y205*	ENST00000269305	NM_001126112.2	205	taT/taG	6/11	0.388562301720243	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.388562301720243	1		478	493	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862205	68862205	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs876658575	NA	P-0068808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	15	256	0	ENST00000261769.5:c.2293C>T	p.Gln765Ter	p.Q765*	ENST00000261769	NM_004360.3	765	Cag/Tag	14/16	0.283232218890781	1	FACETS	0.71	0.524	0.93	0.71	0.524	0.93	CLONAL	1	TRUE	0	0.283232218890781	1		256	128	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063311	67063311	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0068808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	16	218	0	ENST00000412916.2:c.1A>G	p.Met1?	p.M1?	ENST00000412916		1	Atg/Gtg	1/6	0.283232218890781	1	FACETS	0.66	0.491	0.858	0.66	0.491	0.858	SUBCLONAL	1	TRUE	0	0.283232218890781	1		218	147	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111549	8111549	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	35	288	0	ENST00000346208.3:c.1035C>A	p.Tyr345Ter	p.Y345*	ENST00000346208		345	taC/taA	5/6	0.225919771581995	4	FACETS	0.857	0.71	1	0.571	0.473	0.679	CLONAL	2	TRUE	1	0.283232218890781	4		288	185	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685269	89685269	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs786203847	NA	P-0068808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	18	190	0	ENST00000371953.3:c.165-1G>C		p.X55_splice	ENST00000371953	NM_000314.4	55			0.269986719692442	2	FACETS	0.836	0.645	1	0.836	0.645	1	CLONAL	2	TRUE	0	0.283232218890781	2		190	76	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094365	27094368	+	frameshift_variant	Frame_Shift_Del	DEL	GACC	GACC	-	novel	NA	P-0068808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	24	341	0	ENST00000324856.7:c.3074_3077del	p.Asp1025ValfsTer13	p.D1025Vfs*13	ENST00000324856	NM_006015.4	1025	GACCgt/gt	11/20	0.283232218890781	1	FACETS	0.921	0.729	1	0.921	0.729	1	CLONAL	1	TRUE	0	0.283232218890781	1		341	158	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0068813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	131	326	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		326	158	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0068813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	240	428	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		428	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0068813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	183	371	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		371	438	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037865	49037865	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0068813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	41	263	0	ENST00000267163.4:c.2107-2A>G		p.X703_splice	ENST00000267163	NM_000321.2	703			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		263	53	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602473	10602473	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	210	565	0	ENST00000171111.5:c.1105G>T	p.Val369Leu	p.V369L	ENST00000171111	NM_203500.1	369	Gtg/Ttg	3/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		565	276	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196968	123196968	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	34	295	0	ENST00000218089.9:c.1734C>A	p.Tyr578Ter	p.Y578*	ENST00000218089	NM_001042749.1	578	taC/taA	19/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		295	69	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012582	36012582	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	164	386	0	ENST00000358208.4:c.26A>G	p.Lys9Arg	p.K9R	ENST00000358208		9	aAg/aGg	2/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		386	414	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490644	20490644	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	162	364	0	ENST00000346618.3:c.1381G>T	p.Asp461Tyr	p.D461Y	ENST00000346618	NM_001949.4	461	Gac/Tac	7/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		364	352	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981173	55981173	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	47	338	0	ENST00000263923.4:c.526A>G	p.Arg176Gly	p.R176G	ENST00000263923	NM_002253.2	176	Aga/Gga	5/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		338	126	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222503	1223032	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCGAGCCCCGAGGCCACCCACTGAGACCGGCTCTGGGAGTGGGAGTGTCCGGACCCCTGAGGCGCTGGTGCTGATTGTGCCTTGGGGGTCTCTGCACAGCTCGGGTCATCTGGGCGCCTGGCGGGGACTGGGGCTGCCCCCCGATAGCCTCCTGGGCTGGGATGTGCTCAGGGCCCCCCAGACCCCCTTCTGGCCTTTGCTGGCTTTGCAGCCAGCATCCATCTGGTGGGTGCTGGCTTCTGAGTGCCACCTGGGACACAGGCCTCAGGGTGGAGGGGACATCTGTCAGGCTTGGAGTCAGGTCAGCCTGCCTGCTCCTAGAGGACATGGCTGAGCTTCTGTGGTCACAGCCACCCCTTGCACGGCCTGGTCCCAGCTCCTGAGTGTGTGGCAGGTACCCTGGGCCCAGAGGAGCTGGGTCGGAAAACTGGACCGCCCTGGTGCCAGCCTGACAGGCGCCACTGCTTCTGGGCGTTTGCAGCTGGTTCCGGAAGAAACATCCTCCGGCTGAAGCACCAGTGCCCATCCCA	CCGAGCCCCGAGGCCACCCACTGAGACCGGCTCTGGGAGTGGGAGTGTCCGGACCCCTGAGGCGCTGGTGCTGATTGTGCCTTGGGGGTCTCTGCACAGCTCGGGTCATCTGGGCGCCTGGCGGGGACTGGGGCTGCCCCCCGATAGCCTCCTGGGCTGGGATGTGCTCAGGGCCCCCCAGACCCCCTTCTGGCCTTTGCTGGCTTTGCAGCCAGCATCCATCTGGTGGGTGCTGGCTTCTGAGTGCCACCTGGGACACAGGCCTCAGGGTGGAGGGGACATCTGTCAGGCTTGGAGTCAGGTCAGCCTGCCTGCTCCTAGAGGACATGGCTGAGCTTCTGTGGTCACAGCCACCCCTTGCACGGCCTGGTCCCAGCTCCTGAGTGTGTGGCAGGTACCCTGGGCCCAGAGGAGCTGGGTCGGAAAACTGGACCGCCCTGGTGCCAGCCTGACAGGCGCCACTGCTTCTGGGCGTTTGCAGCTGGTTCCGGAAGAAACATCCTCCGGCTGAAGCACCAGTGCCCATCCCA	-	novel	NA	P-0068813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	133	3	0	ENST00000326873.7:c.921-473_977del		p.X307_splice	ENST00000326873	NM_000455.4	307		8/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		3	138	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781377	3781377	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	222	432	1	ENST00000262367.5:c.4988G>T	p.Gly1663Val	p.G1663V	ENST00000262367	NM_004380.2	1663	gGg/gTg	30/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		433	555	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450280	50450280	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	224	390	0	ENST00000331340.3:c.466del	p.Gln156ArgfsTer37	p.Q156Rfs*37	ENST00000331340	NM_006060.4	155	aCc/ac	5/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		390	505	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664849	138664849	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	114	334	0	ENST00000330315.3:c.716C>G	p.Pro239Arg	p.P239R	ENST00000330315	NM_023067.3	239	cCt/cGt	1/1	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		334	271	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410403	63410403	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	195	469	0	ENST00000330258.3:c.2764C>T	p.Gln922Ter	p.Q922*	ENST00000330258	NM_152424.3	922	Cag/Tag	2/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		469	471	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965866	25965866	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	220	392	0	ENST00000435504.4:c.3340A>G	p.Arg1114Gly	p.R1114G	ENST00000435504		1114	Agg/Ggg	13/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		392	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0068818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	279	294	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.865665156738072	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.865665156738072	2		294	313	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667616	29667616	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1060500359	NA	P-0068818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	108	297	0	ENST00000356175.3:c.6952G>T	p.Glu2318Ter	p.E2318*	ENST00000356175	NM_000267.3	2318	Gaa/Taa	46/57	0.865665156738072	1	FACETS	0.963	0.904	1	0.963	0.904	1	CLONAL	1	TRUE	0	0.865665156738072	1		297	147	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106519962	106519962	+	splice_acceptor_variant	Splice_Site	DEL	A	A	-	novel	NA	P-0068818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	70	250	0	ENST00000359195.3:c.2392-2del		p.X798_splice	ENST00000359195	NM_002649.2	798			1	2	FACETS	0.817	0.726	0.911	0.817	0.726	0.911	CLONAL	1	TRUE	1	0.865665156738072	2		250	198	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068823-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	79	406	0				ENST00000310581	NM_198253.2	-/1132			0.386080083684454	3	FACETS	0.822	0.731	0.918	0.822	0.731	0.918	CLONAL	2	TRUE	1	0.386080083684454	3		406	297	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404185	139404186	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0068823-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	141	466	0	ENST00000277541.6:c.2968_2969del	p.Ser990LeufsTer34	p.S990Lfs*34	ENST00000277541	NM_017617.3	990	AGc/c	18/34	0.283110143988791	3	FACETS	0.853	0.782	0.926	0.568	0.521	0.618	CLONAL	2	TRUE	0	0.386080083684454	3		466	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1131691023	NA	P-0068823-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	62	620	0	ENST00000269305.4:c.470T>C	p.Val157Ala	p.V157A	ENST00000269305	NM_001126112.2	157	gTc/gCc	5/11	1	2	FACETS	0.707	0.613	0.81	0.707	0.613	0.81	SUBCLONAL	1	TRUE	1	0.386080083684454	2		620	454	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0068826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	74	326	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.136915280281171	5	FACETS	0.871	0.764	0.985			1	INDETERMINATE	2	FALSE	NA	0.237035477910032	5		326	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0068826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	63	557	0	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.237035477910032	2		557	366	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205672	128205672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	20	416	0	ENST00000341105.2:c.203C>T	p.Ala68Val	p.A68V	ENST00000341105	NM_032638.4	68	gCg/gTg	2/6	0.208493504166409	0	FACETS	0.644	0.494	0.817			1	SUBCLONAL	1	FALSE	0	0.237035477910032	0		416	200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0068827-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	139	366	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.429834985642955	1	FACETS	0.911	0.835	0.99	0.911	0.835	0.99	CLONAL	1	TRUE	0	0.475534666943153	1		366	489	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917107	50917107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068827-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	147	517	0	ENST00000440232.2:c.2359C>T	p.Pro787Ser	p.P787S	ENST00000440232	NM_002691.3	787	Ccg/Tcg	19/27	1	2	FACETS	0.959	0.878	1	0.959	0.878	1	CLONAL	1	TRUE	1	0.475534666943153	2		517	645	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119780	70119781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0068827-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	124	440	0	ENST00000245479.2:c.788dup	p.Arg264GlnfsTer32	p.R264Qfs*32	ENST00000245479	NM_000346.3	261	gag/gaGg	3/3	0.118408635432041	4	FACETS	1	0.983	1	0.685	0.622	0.75	INDETERMINATE	1	TRUE	2	0.475534666943153	4		440	562	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100095	157100116	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCGGCGGCAGCAGCAGGA	GGCGGCGGCGGCAGCAGCAGGA	-	novel	NA	P-0068827-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	104	648	0	ENST00000346085.5:c.1044_1065del	p.Gly351MetfsTer11	p.G351Mfs*11	ENST00000346085	NM_020732.3	344	gcGGCGGCGGCGGCAGCAGCAGGA/gc	1/20	1	2	FACETS	0.446	0.398	0.497	0.446	0.398	0.497	SUBCLONAL	1	TRUE	1	0.475534666943153	2		648	981	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517800	176517800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199792541	NA	P-0068827-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	143	583	0	ENST00000292408.4:c.410C>T	p.Ser137Leu	p.S137L	ENST00000292408	NM_213647.1	137	tCg/tTg	4/18	1	2	FACETS	0.924	0.845	1	0.924	0.845	1	CLONAL	1	TRUE	1	0.475534666943153	2		583	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0068828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	21	548	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	1	2	FACETS	0.635	0.487	0.809	0.635	0.487	0.809	SUBCLONAL	1	TRUE	1	0.12	2		548	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0068828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	23	569	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.677	0.526	0.853	0.677	0.526	0.853	SUBCLONAL	1	TRUE	1	0.12	2		569	566	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31381344	31381351	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GTTAATAA	GTTAATAA	-	novel	NA	P-0068830-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	26	346	0	ENST00000328111.2:c.1071_1078del	p.Asn358GlufsTer8	p.N358Efs*8	ENST00000328111	NM_006892.3	357	GTTAATAAg/g	10/23	1	2	FACETS	0.463	0.367	0.574	0.463	0.367	0.574	SUBCLONAL	1	FALSE	1	0.3	2		346	374	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917677	151917677	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1160567943	NA	P-0068830-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	15	207	0	ENST00000262189.6:c.3643G>T	p.Ala1215Ser	p.A1215S	ENST00000262189	NM_170606.2	1215	Gcc/Tcc	23/59	0.262401334150232	4	FACETS	0.586	0.429	0.774	0.195	0.143	0.258	SUBCLONAL	1	FALSE	1	0.3	4		207	222	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347974	347974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140190126	NA	P-0068831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	234	729	0	ENST00000262320.3:c.1532C>T	p.Ser511Leu	p.S511L	ENST00000262320	NM_003502.3	511	tCg/tTg	6/11	0.610306718249536	2	FACETS	1	0.965	1	0.522	0.488	0.556	CLONAL	1	TRUE	0	0.610306718249536	2		729	735	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027160	49027160	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0068831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	290	424	0	ENST00000267163.4:c.1727C>G	p.Ser576Ter	p.S576*	ENST00000267163	NM_000321.2	576	tCa/tGa	18/27	0.610306718249536	3	FACETS	0.931	0.892	0.969	0.931	0.892	0.969	CLONAL	3	TRUE	0	0.610306718249536	3		424	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0068831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	345	474	0	ENST00000269305.4:c.782+1G>C		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.610306718249536	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.610306718249536	2		474	523	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171442	123171442	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	108	208	0	ENST00000218089.9:c.354C>G	p.Ile118Met	p.I118M	ENST00000218089	NM_001042749.1	118	atC/atG	6/35	0.521506815043308	2	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.610306718249536	2		208	270	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435610	49436017	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTGGGGAGCGGAAAGAACTGAGGTAAATTACCCAAAGATCCCTCCCTCCCTCTCAGTTCCCACGCTAATCCATGCTCCTTTCTGCCTCACCAGGTAGGGGGCTTTGTCAGCTGCTGGAACCTTTCTCCAGAGCTTCATGATTTGTTTGCAACGGCTTGACCAGTCTGGAGGGCAGAGAGAGTGAGTCAGAGAAGACTTGGCAGGCGACTCCTCCACCTGCCATGTTGCCAGGCTGTCTCCCTTGCCCTCATCCCACAGGTACCTGGGTAGTCTTGCTTGAGATTAGGAAAATTAATGTTGGCATAGAGCACAGGTGAGATGGTGGACAGCTGGCCCAACTCCTCATCCTTCTCCCAGCGCTGAAGACTCCGCTGGTTATAGGAGAGTCCGTCGCCCTCACCCTCCGTG	GTGGGGAGCGGAAAGAACTGAGGTAAATTACCCAAAGATCCCTCCCTCCCTCTCAGTTCCCACGCTAATCCATGCTCCTTTCTGCCTCACCAGGTAGGGGGCTTTGTCAGCTGCTGGAACCTTTCTCCAGAGCTTCATGATTTGTTTGCAACGGCTTGACCAGTCTGGAGGGCAGAGAGAGTGAGTCAGAGAAGACTTGGCAGGCGACTCCTCCACCTGCCATGTTGCCAGGCTGTCTCCCTTGCCCTCATCCCACAGGTACCTGGGTAGTCTTGCTTGAGATTAGGAAAATTAATGTTGGCATAGAGCACAGGTGAGATGGTGGACAGCTGGCCCAACTCCTCATCCTTCTCCCAGCGCTGAAGACTCCGCTGGTTATAGGAGAGTCCGTCGCCCTCACCCTCCGTG	-	novel	NA	P-0068831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	131	413	0	ENST00000301067.7:c.5964_6183+90del		p.X1988_splice	ENST00000301067	NM_003482.3	1988		28-29/54	0.610306718249536	2	FACETS	0.996	0.911	1	0.498	0.455	0.542	CLONAL	1	TRUE	0	0.610306718249536	2		413	431	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10283828	10283828	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	345	459	0	ENST00000340748.4:c.658G>C	p.Glu220Gln	p.E220Q	ENST00000340748		220	Gaa/Caa	8/40	0.610306718249536	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.610306718249536	2		459	535	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80109412	80109412	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	286	491	0	ENST00000265081.6:c.2665G>A	p.Glu889Lys	p.E889K	ENST00000265081	NM_002439.4	889	Gag/Aag	20/24	0.606352885270411	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.610306718249536	2		491	423	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366947	40366947	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068834-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	83	465	0	ENST00000397332.2:c.250C>G	p.Pro84Ala	p.P84A	ENST00000397332	NM_001033082.2	84	Ccg/Gcg	2/3	0.17165888560402	4	FACETS	1	0.954	1	0.585	0.515	0.659	CLONAL	1	TRUE	2	0.231608416366106	4		465	755	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271482	26271482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068834-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	72	595	0	ENST00000305910.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000305910	NM_003534.2	44	cCc/cTc	1/1	0.234267684338137	5	FACETS	0.909	0.792	1	0.303	0.264	0.345	CLONAL	1	TRUE	2	0.231608416366106	5		595	922	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112029181	112029181	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068834-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	37	296	0	ENST00000368678.4:c.387G>C	p.Glu129Asp	p.E129D	ENST00000368678		129	gaG/gaC	5/13	0.194637386420184	3	FACETS	0.841	0.693	1	0.28	0.231	0.335	CLONAL	1	TRUE	0	0.231608416366106	3		296	424	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845366	151845366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068834-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	32	441	0	ENST00000262189.6:c.13646G>A	p.Arg4549His	p.R4549H	ENST00000262189	NM_170606.2	4549	cGc/cAc	52/59	0.447431970467432	3	FACETS	0.701	0.572	0.845	0.351	0.286	0.423	SUBCLONAL	1	FALSE	1	0.455689657630776	3		441	246	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772262	68772262	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0068834-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	117	381	0	ENST00000261769.5:c.111C>G	p.Tyr37Ter	p.Y37*	ENST00000261769	NM_004360.3	37	taC/taG	2/16	0.432961538432787	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	FALSE	0	0.455689657630776	2		381	212	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118862	115118863	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0068834-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	255	427	0	ENST00000257566.3:c.478dup	p.Asp160GlyfsTer5	p.D160Gfs*5	ENST00000257566	NM_016569.3	160	gac/gGac	2/8	0.175347591271888	3	FACETS	1	0.983	1	1	0.983	1	INDETERMINATE	2	FALSE	1	0.455689657630776	3		427	620	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0068837-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	147	435	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.271544211100905	3	FACETS	0.767	0.711	0.825	0.767	0.711	0.825	INDETERMINATE	2	TRUE	1	0.762796465256624	3		435	347	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0068837-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	406	289	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.762796465256624	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	0	0.762796465256624	3		289	481	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068837-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	226	439	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.762796465256624	2		439	501	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0068837-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	201	405	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	0.271544211100905	3	FACETS	1	0.99	1	0.669	0.625	0.714	INDETERMINATE	1	TRUE	1	0.762796465256624	3		405	544	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098912	47098912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068837-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	307	462	0	ENST00000409792.3:c.6362G>A	p.Arg2121His	p.R2121H	ENST00000409792	NM_014159.6	2121	cGc/cAc	15/21	0.271544211100905	3	FACETS	0.931	0.887	0.975	0.931	0.887	0.975	INDETERMINATE	2	TRUE	1	0.762796465256624	3		462	597	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129044	2129044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137854410	NA	P-0068837-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	171	383	2	ENST00000219476.3:c.2978C>T	p.Thr993Met	p.T993M	ENST00000219476	NM_000548.3	993	aCg/aTg	27/42	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.762796465256624	2		385	432	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120811	115120811	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068837-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	120	477	0	ENST00000257566.3:c.195G>T	p.Met65Ile	p.M65I	ENST00000257566	NM_016569.3	65	atG/atT	1/8	1	2	FACETS	0.881	0.805	0.96	0.881	0.805	0.96	CLONAL	1	TRUE	1	0.762796465256624	2		477	357	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748487	162748487	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068837-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	165	412	0	ENST00000367921.3:c.2401A>G	p.Thr801Ala	p.T801A	ENST00000367921	NM_006182.2	801	Act/Gct	17/18	0.762796465256624	4	FACETS	0.922	0.848	1	0.307	0.282	0.334	CLONAL	1	TRUE	1	0.762796465256624	4		412	827	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572570	64572570	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757803925	NA	P-0068837-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	235	594	0	ENST00000312049.6:c.1286C>T	p.Thr429Met	p.T429M	ENST00000312049	NM_130799.2	429	aCg/aTg	9/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.762796465256624	2		594	589	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920756	100920767	+	inframe_deletion	In_Frame_Del	DEL	ATAATGAATAGA	ATAATGAATAGA	-	novel	NA	P-0068837-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	87	366	0	ENST00000325455.5:c.2381_2392del	p.Phe794_Leu797del	p.F794_L797del	ENST00000325455	NM_001202474.3	794	tTCTATTCATTATgc/tgc	6/8	0.762796465256624	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.762796465256624	1		366	115	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102129	27102130	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0068837-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	175	452	0	ENST00000324856.7:c.5055_5056del	p.Trp1686GlyfsTer11	p.W1686Gfs*11	ENST00000324856	NM_006015.4	1685	acATgg/acgg	19/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.762796465256624	2		452	401	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061028	38061031	+	frameshift_variant	Frame_Shift_Del	DEL	CTAG	CTAG	-	novel	NA	P-0068842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	188	577	0	ENST00000250448.2:c.958_961del	p.Leu320ArgfsTer29	p.L320Rfs*29	ENST00000250448	NM_004496.3	320	CTAGag/ag	2/2	0.459330909329535	16	FACETS	0.917	0.852	0.984			1	CLONAL	6	FALSE	NA	0.459330909329535	16		577	627	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912030	127912030	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	64	423	0	ENST00000373547.4:c.840A>T	p.Arg280Ser	p.R280S	ENST00000373547	NM_002721.4	280	agA/agT	7/7	0.110931128638891	4	FACETS	1	0.956	1	1	0.956	1	INDETERMINATE	2	FALSE	2	0.459330909329535	4		423	173	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49449064	49449067	+	frameshift_variant	Frame_Shift_Del	DEL	GGTT	GGTT	-	novel	NA	P-0068842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	81	344	0	ENST00000301067.7:c.41_44del	p.Glu14GlyfsTer115	p.E14Gfs*115	ENST00000301067	NM_003482.3	14	gAACCg/gg	1/54	0.468978710693861	4	FACETS	0.858	0.772	0.946	1	0.974	1	CLONAL	3	FALSE	2	0.459330909329535	4		344	200	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31421465	31421465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	300	309	0	ENST00000344624.3:c.3439G>A	p.Glu1147Lys	p.E1147K	ENST00000344624		1147	Gaa/Aaa	27/33	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.950133442723087	2		309	630	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37882058	37882058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769262054	NA	P-0068852-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	84	419	0	ENST00000269571.5:c.2824C>T	p.Pro942Ser	p.P942S	ENST00000269571		942	Ccc/Tcc	23/27	1	2	FACETS	0.884	0.781	0.993	0.884	0.781	0.993	CLONAL	1	TRUE	1	0.309114461765295	2		419	615	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912333	32912333	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068852-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	49	363	0	ENST00000380152.3:c.3844del	p.Thr1282LeufsTer2	p.T1282Lfs*2	ENST00000380152		1281	Aaa/aa	11/27	0.309114461765295	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.309114461765295	1		363	219	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90627556	90627568	+	frameshift_variant	Frame_Shift_Del	DEL	GTGTTCAGGAAGT	GTGTTCAGGAAGT	-	novel	NA	P-0068852-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	99	485	0	ENST00000330062.3:c.1289_1301del	p.His430ProfsTer34	p.H430Pfs*34	ENST00000330062	NM_002168.2	430	cACTTCCTGAACACc/cc	11/11	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.309114461765295	2		485	586	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436357	52436357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068852-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	93	534	0	ENST00000460680.1:c.2137C>T	p.Arg713Trp	p.R713W	ENST00000460680	NM_004656.3	713	Cgg/Tgg	17/17	1	2	FACETS	0.982	0.874	1	0.982	0.874	1	CLONAL	1	TRUE	1	0.309114461765295	2		534	613	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061221	38061222	+	protein_altering_variant	In_Frame_Ins	INS	-	-	AAC	novel	NA	P-0068852-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	153	561	0	ENST00000250448.2:c.767_768insGTT	p.Asn256delinsLysPhe	p.N256delinsKF	ENST00000250448	NM_004496.3	256	aac/aaGTTc	2/2	1	2	FACETS	0.826	0.759	0.896	1	0.99	1	CLONAL	2	TRUE	1	0.309114461765295	2		561	599	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443613	29443613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519783	NA	P-0068865-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	97	521	1	ENST00000389048.3:c.3604G>A	p.Gly1202Arg	p.G1202R	ENST00000389048	NM_004304.4	1202	Gga/Aga	23/29	1	2	FACETS	0.959	0.856	1	0.959	0.856	1	CLONAL	1	TRUE	1	0.286029044643449	2		522	707	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445447	29445447	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068865-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	88	509	0	ENST00000389048.3:c.3386A>T	p.Glu1129Val	p.E1129V	ENST00000389048	NM_004304.4	1129	gAg/gTg	21/29	1	2	FACETS	0.89	0.789	0.999	0.89	0.789	0.999	CLONAL	1	TRUE	1	0.286029044643449	2		509	691	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061414	38061414	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs926601303	NA	P-0068866-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	214	352	0	ENST00000250448.2:c.575C>T	p.Thr192Met	p.T192M	ENST00000250448	NM_004496.3	192	aCg/aTg	2/2	0.100370274663508	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.862793305168878	0		352	466	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235838	108235838	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068866-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	181	326	0	ENST00000278616.4:c.8880G>C	p.Trp2960Cys	p.W2960C	ENST00000278616	NM_000051.3	2960	tgG/tgC	62/63	0.313565675236267	1	FACETS	0.672	0.63	0.714	0.672	0.63	0.714	INDETERMINATE	1	FALSE	0	0.862793305168878	1		326	355	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	61	406	0				ENST00000310581	NM_198253.2	-/1132			0.18300869629157	5	FACETS	0.983	0.864	1	0.655	0.576	0.738	INDETERMINATE	2	TRUE	2	0.682998515863878	5		406	184	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	323	284	0	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	0.384193247496562	3	FACETS	1	0.989	1	1	0.989	1	INDETERMINATE	3	TRUE	0	0.682998515863878	3		284	405	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106094	8106094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	84	406	0	ENST00000346208.3:c.914G>A	p.Arg305Gln	p.R305Q	ENST00000346208		305	cGa/cAa	4/6	0.18300869629157	5	FACETS	0.904	0.8	1	0.301	0.266	0.339	INDETERMINATE	1	TRUE	2	0.682998515863878	5		406	551	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201833	66201833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778795902	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	73	390	0	ENST00000273854.3:c.2669C>T	p.Ala890Val	p.A890V	ENST00000273854	NM_004439.5	890	gCg/gTg	16/18	0.393924063761118	1	FACETS	0.434	0.383	0.489	0.434	0.383	0.489	INDETERMINATE	1	TRUE	0	0.682998515863878	1		390	324	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30323856	30323856	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	54	313	0	ENST00000322652.5:c.1834G>A	p.Glu612Lys	p.E612K	ENST00000322652	NM_015355.2	612	Gaa/Aaa	15/16	0.506951392250279	3	FACETS	0.403	0.344	0.468	0.202	0.172	0.234	SUBCLONAL	1	TRUE	1	0.682998515863878	3		313	526	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183559	10183559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519261	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	207	412	0	ENST00000256474.2:c.28G>A	p.Glu10Lys	p.E10K	ENST00000256474	NM_000551.3	10	Gag/Aag	1/3	0.242897709834165	6	FACETS	1	0.962	1	0.516	0.484	0.548	INDETERMINATE	3	TRUE	0	0.682998515863878	6		412	463	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998756	100998756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749674024	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	103	422	0	ENST00000325455.5:c.1046C>T	p.Ser349Leu	p.S349L	ENST00000325455	NM_001202474.3	349	tCg/tTg	1/8	0.49738306930954	4	FACETS	0.843	0.765	0.924	0.562	0.51	0.616	CLONAL	2	TRUE	1	0.682998515863878	4		422	301	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211623	46211623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	92	315	0	ENST00000334344.6:c.589C>T	p.Pro197Ser	p.P197S	ENST00000334344	NM_152641.2	197	Cct/Tct	5/21	0.49738306930954	4	FACETS	0.884	0.788	0.985	0.295	0.262	0.329	CLONAL	1	TRUE	1	0.682998515863878	4		315	513	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980478	70980478	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	90	420	0	ENST00000276594.2:c.899C>T	p.Ser300Phe	p.S300F	ENST00000276594	NM_024504.3	300	tCt/tTt	4/8	0.222540385752133	2	FACETS	0.652	0.582	0.726	0.326	0.291	0.363	INDETERMINATE	1	TRUE	0	0.682998515863878	2		420	404	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794581	42794581	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	76	503	0	ENST00000575354.2:c.1661C>G	p.Ser554Ter	p.S554*	ENST00000575354	NM_015125.3	554	tCa/tGa	10/20	0.623350688506954	3	FACETS	0.648	0.57	0.731	0.324	0.285	0.366	SUBCLONAL	1	TRUE	1	0.682998515863878	3		503	461	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104681	69104681	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	81	382	0	ENST00000288368.4:c.4525G>A	p.Gly1509Arg	p.G1509R	ENST00000288368	NM_024870.2	1509	Gga/Aga	37/40	0.222540385752133	2	FACETS	0.634	0.562	0.71	0.317	0.281	0.355	INDETERMINATE	1	TRUE	0	0.682998515863878	2		382	374	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213502	36213502	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1568370990	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	58	551	0	ENST00000222270.7:c.2604C>G	p.Ile868Met	p.I868M	ENST00000222270	NM_014727.1	868	atC/atG	5/37	0.623350688506954	3	FACETS	0.484	0.416	0.557	0.242	0.208	0.279	SUBCLONAL	1	TRUE	1	0.682998515863878	3		551	471	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110031	115110031	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	67	391	0	ENST00000257566.3:c.1847C>T	p.Ser616Phe	p.S616F	ENST00000257566	NM_016569.3	616	tCt/tTt	8/8	0.49738306930954	4	FACETS	0.935	0.818	1	0.312	0.272	0.354	CLONAL	1	TRUE	1	0.682998515863878	4		391	353	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047507	49047507	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1131690906	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	176	285	0	ENST00000267163.4:c.2501C>A	p.Ser834Ter	p.S834*	ENST00000267163	NM_000321.2	834	tCa/tAa	24/27	0.682998515863878	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.682998515863878	1		285	287	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216232	36216232	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	81	442	0	ENST00000222270.7:c.3640G>A	p.Glu1214Lys	p.E1214K	ENST00000222270	NM_014727.1	1214	Gag/Aag	11/37	0.623350688506954	3	FACETS	0.639	0.564	0.718	0.319	0.282	0.359	SUBCLONAL	1	TRUE	1	0.682998515863878	3		442	498	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641001	23641001	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs146218439	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	99	406	0	ENST00000261584.4:c.2474G>C	p.Arg825Thr	p.R825T	ENST00000261584	NM_024675.3	825	aGa/aCa	5/13	0.266168265917373	2	FACETS	0.692	0.622	0.766	0.346	0.311	0.383	INDETERMINATE	1	TRUE	0	0.682998515863878	2		406	419	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858308	59858308	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	101	382	0	ENST00000259008.2:c.1687G>C	p.Asp563His	p.D563H	ENST00000259008	NM_032043.2	563	Gat/Cat	12/20	0.506951392250279	3	FACETS	0.622	0.556	0.691	0.311	0.278	0.346	SUBCLONAL	1	TRUE	1	0.682998515863878	3		382	638	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466588	120466588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	83	378	0	ENST00000256646.2:c.4531G>A	p.Asp1511Asn	p.D1511N	ENST00000256646	NM_024408.3	1511	Gac/Aac	26/34	0.393924063761118	1	FACETS	0.433	0.384	0.484	0.433	0.384	0.484	INDETERMINATE	1	TRUE	0	0.682998515863878	1		378	370	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100919	27100919	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	96	374	0	ENST00000324856.7:c.4201C>T	p.Gln1401Ter	p.Q1401*	ENST00000324856	NM_006015.4	1401	Cag/Tag	18/20	0.222366009164158	4	FACETS	1	0.958	1	0.567	0.508	0.629	INDETERMINATE	1	TRUE	2	0.682998515863878	4		374	417	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753158	42753158	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	78	556	0	ENST00000222329.4:c.1106C>G	p.Ser369Cys	p.S369C	ENST00000222329	NM_006494.2	369	tCt/tGt	4/4	0.623350688506954	3	FACETS	0.503	0.442	0.568	0.252	0.221	0.284	SUBCLONAL	1	TRUE	1	0.682998515863878	3		556	609	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113101	209113101	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	138	370	0	ENST00000345146.2:c.406G>T	p.Gly136Trp	p.G136W	ENST00000345146	NM_005896.2	136	Ggg/Tgg	4/10	0.242338666226624	2	FACETS	0.89	0.816	0.966	0.445	0.408	0.483	INDETERMINATE	1	TRUE	0	0.682998515863878	2		370	454	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433962	149433962	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	71	334	0	ENST00000286301.3:c.2686G>C	p.Glu896Gln	p.E896Q	ENST00000286301	NM_005211.3	896	Gag/Cag	21/22	0.682998515863878	2	FACETS	0.684	0.602	0.77	0.342	0.301	0.385	SUBCLONAL	1	TRUE	0	0.682998515863878	2		334	304	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032220	10032220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	105	448	0	ENST00000330684.3:c.603G>T	p.Gln201His	p.Q201H	ENST00000330684	NM_001134407.1	201	caG/caT	3/13	0.266168265917373	2	FACETS	0.732	0.66	0.807	0.366	0.33	0.404	INDETERMINATE	1	TRUE	0	0.682998515863878	2		448	420	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421029	49421029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs189256695	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	98	429	0	ENST00000301067.7:c.14720C>T	p.Ser4907Leu	p.S4907L	ENST00000301067	NM_003482.3	4907	tCg/tTg	48/54	0.49738306930954	4	FACETS	1	0.95	1	0.366	0.328	0.406	CLONAL	1	TRUE	1	0.682998515863878	4		429	440	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792453	33792453	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	68	313	0	ENST00000498907.2:c.868G>C	p.Glu290Gln	p.E290Q	ENST00000498907	NM_004364.3	290	Gag/Cag	1/1	0.623350688506954	3	FACETS	0.666	0.582	0.756	0.333	0.291	0.378	SUBCLONAL	1	TRUE	1	0.682998515863878	3		313	401	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160630	56160630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	132	426	0	ENST00000399503.3:c.904G>A	p.Glu302Lys	p.E302K	ENST00000399503	NM_005921.1	302	Gag/Aag	4/20	0.682998515863878	2	FACETS	0.733	0.669	0.8	0.367	0.334	0.4	SUBCLONAL	1	TRUE	0	0.682998515863878	2		426	527	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231235	98231235	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	185	535	0	ENST00000331920.6:c.2048C>T	p.Ser683Phe	p.S683F	ENST00000331920	NM_000264.3	683	tCc/tTc	14/24	0.171080830505949	5	FACETS	1	0.946	1	0.68	0.632	0.728	INDETERMINATE	2	TRUE	2	0.682998515863878	5		535	538	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434595	49434595	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	74	460	0	ENST00000301067.7:c.6958G>C	p.Glu2320Gln	p.E2320Q	ENST00000301067	NM_003482.3	2320	Gag/Cag	31/54	0.49738306930954	4	FACETS	0.889	0.782	1	0.296	0.26	0.335	CLONAL	1	TRUE	1	0.682998515863878	4		460	410	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097180	11097180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1368858108	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	64	453	0	ENST00000358026.2:c.671C>T	p.Ser224Leu	p.S224L	ENST00000358026	NM_001128849.1	224	tCg/tTg	4/36	0.273238240044398	3	FACETS	0.663	0.577	0.756	0.221	0.192	0.252	INDETERMINATE	1	TRUE	0	0.682998515863878	3		453	379	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424267	47424267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	101	418	0	ENST00000404338.3:c.2335G>A	p.Asp779Asn	p.D779N	ENST00000404338	NM_004491.4	779	Gat/Aat	1/6	0.623350688506954	3	FACETS	0.537	0.48	0.598	0.268	0.24	0.299	SUBCLONAL	1	TRUE	1	0.682998515863878	3		418	739	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158626	26158626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772836222	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	57	212	0	ENST00000289316.2:c.229G>A	p.Glu77Lys	p.E77K	ENST00000289316	NM_138720.2	77	Gag/Aag	1/2	0.481349401654869	3	FACETS	0.868	0.752	0.992	0.289	0.25	0.331	CLONAL	1	TRUE	0	0.682998515863878	3		212	258	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759433	133759433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	188	427	0	ENST00000318560.5:c.1756G>A	p.Glu586Lys	p.E586K	ENST00000318560	NM_005157.4	586	Gaa/Aaa	11/11	0.671390001795322	3	FACETS	1	0.988	1	0.655	0.609	0.702	CLONAL	1	TRUE	1	0.682998515863878	3		427	564	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18958627	18958627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	84	331	0	ENST00000262803.5:c.446G>A	p.Gly149Glu	p.G149E	ENST00000262803	NM_002911.3	149	gGa/gAa	3/24	0.273238240044398	3	FACETS	0.788	0.699	0.881	0.263	0.233	0.294	INDETERMINATE	1	TRUE	0	0.682998515863878	3		331	419	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661986	29661986	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	87	435	0	ENST00000356175.3:c.5880G>A	p.Met1960Ile	p.M1960I	ENST00000356175	NM_000267.3	1960	atG/atA	39/57	0.506951392250279	3	FACETS	0.519	0.46	0.583	0.26	0.23	0.292	SUBCLONAL	1	TRUE	1	0.682998515863878	3		435	658	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778163	135778163	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	217	385	0	ENST00000298552.3:c.2220G>C	p.Leu740Phe	p.L740F	ENST00000298552	NM_001162426.1	740	ttG/ttC	18/23	0.671390001795322	3	FACETS	1	0.992	1	0.727	0.681	0.774	CLONAL	1	TRUE	1	0.682998515863878	3		385	586	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112436	115112436	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	62	435	0	ENST00000257566.3:c.1304C>G	p.Ser435Ter	p.S435*	ENST00000257566	NM_016569.3	435	tCa/tGa	7/8	0.49738306930954	4	FACETS	0.802	0.696	0.916	0.267	0.232	0.306	CLONAL	1	TRUE	1	0.682998515863878	4		435	381	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489811	40489811	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	84	516	0	ENST00000264657.5:c.615G>C	p.Gln205His	p.Q205H	ENST00000264657	NM_139276.2	205	caG/caC	7/24	0.506951392250279	3	FACETS	0.564	0.499	0.634	0.282	0.249	0.317	SUBCLONAL	1	TRUE	1	0.682998515863878	3		516	585	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21553880	21553880	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	159	325	0	ENST00000382592.4:c.2722G>C	p.Val908Leu	p.V908L	ENST00000382592	NM_014572.2	908	Gtg/Ctg	7/8	0.18300869629157	5	FACETS	1	0.983	1	0.806	0.748	0.864	INDETERMINATE	2	TRUE	2	0.682998515863878	5		325	390	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38788601	38788601	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	86	307	0	ENST00000348513.6:c.560C>G	p.Ser187Ter	p.S187*	ENST00000348513	NM_003079.4	187	tCa/tGa	8/11	0.506951392250279	3	FACETS	0.619	0.548	0.694	0.309	0.274	0.347	SUBCLONAL	1	TRUE	1	0.682998515863878	3		307	546	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40478146	40478146	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	75	283	0	ENST00000264657.5:c.1353G>C	p.Lys451Asn	p.K451N	ENST00000264657	NM_139276.2	451	aaG/aaC	15/24	0.506951392250279	3	FACETS	0.648	0.569	0.731	0.324	0.284	0.366	SUBCLONAL	1	TRUE	1	0.682998515863878	3		283	455	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197763	66197763	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	105	389	0	ENST00000273854.3:c.2936T>C	p.Met979Thr	p.M979T	ENST00000273854	NM_004439.5	979	aTg/aCg	17/18	0.393924063761118	1	FACETS	0.537	0.485	0.591	0.537	0.485	0.591	INDETERMINATE	1	TRUE	0	0.682998515863878	1		389	377	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592260	29592260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	99	292	0	ENST00000356175.3:c.4675G>A	p.Glu1559Lys	p.E1559K	ENST00000356175	NM_000267.3	1559	Gaa/Aaa	35/57	0.506951392250279	3	FACETS	0.804	0.72	0.891	0.402	0.36	0.446	CLONAL	1	TRUE	1	0.682998515863878	3		292	484	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724556	162724556	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	103	513	0	ENST00000367921.3:c.328C>G	p.His110Asp	p.H110D	ENST00000367921	NM_006182.2	110	Cat/Gat	5/18	1	2	FACETS	0.646	0.581	0.714	0.646	0.581	0.714	SUBCLONAL	1	TRUE	1	0.682998515863878	2		513	467	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794703	42794703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778472492	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	82	422	0	ENST00000575354.2:c.1783C>T	p.Pro595Ser	p.P595S	ENST00000575354	NM_015125.3	595	Cct/Tct	10/20	0.623350688506954	3	FACETS	0.703	0.623	0.789	0.352	0.311	0.395	SUBCLONAL	1	TRUE	1	0.682998515863878	3		422	458	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424306	47424306	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	94	432	0	ENST00000404338.3:c.2374G>C	p.Asp792His	p.D792H	ENST00000404338	NM_004491.4	792	Gat/Cat	1/6	0.623350688506954	3	FACETS	0.509	0.453	0.569	0.255	0.226	0.285	SUBCLONAL	1	TRUE	1	0.682998515863878	3		432	725	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271447	26271447	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1453083205	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	143	559	0	ENST00000305910.3:c.166C>T	p.Gln56Ter	p.Q56*	ENST00000305910	NM_003534.2	56	Cag/Tag	1/1	0.481349401654869	3	FACETS	0.648	0.591	0.708	0.216	0.197	0.236	SUBCLONAL	1	TRUE	0	0.682998515863878	3		559	867	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18972819	18972819	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	55	315	0	ENST00000262803.5:c.2458G>A	p.Glu820Lys	p.E820K	ENST00000262803	NM_002911.3	820	Gag/Aag	18/24	0.273238240044398	3	FACETS	0.706	0.608	0.812	0.235	0.202	0.271	INDETERMINATE	1	TRUE	0	0.682998515863878	3		315	306	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447286	187447286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777942698	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	37	493	0	ENST00000232014.4:c.907G>A	p.Glu303Lys	p.E303K	ENST00000232014	NM_001130845.1	303	Gaa/Aaa	5/10	0.247597462003455	2	FACETS	0.236	0.194	0.283	0.118	0.097	0.142	INDETERMINATE	1	TRUE	0	0.682998515863878	2		493	459	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425010	47425010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	101	492	0	ENST00000404338.3:c.3078G>A	p.Met1026Ile	p.M1026I	ENST00000404338	NM_004491.4	1026	atG/atA	1/6	0.623350688506954	3	FACETS	0.564	0.504	0.627	0.282	0.252	0.314	SUBCLONAL	1	TRUE	1	0.682998515863878	3		492	704	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104353414	104353414	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	72	353	0	ENST00000369902.3:c.619G>C	p.Glu207Gln	p.E207Q	ENST00000369902	NM_016169.3	207	Gag/Cag	5/12	0.682998515863878	1	FACETS	0.593	0.526	0.664	0.593	0.526	0.664	SUBCLONAL	1	TRUE	0	0.682998515863878	1		353	234	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424753	47424758	+	frameshift_variant	Frame_Shift_Del	DEL	GTGGTG	GTGGTG	ATGGT	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	87	528	1	ENST00000404338.3:c.2821_2826delinsATGGT	p.Val941MetfsTer7	p.V941Mfs*7	ENST00000404338	NM_004491.4	941	GTGGTG/ATGGT	1/6	0.623350688506954	3	FACETS	0.513	0.454	0.576	0.257	0.227	0.288	SUBCLONAL	1	TRUE	1	0.682998515863878	3		529	666	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95577782	95577782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	78	335	0	ENST00000393063.1:c.2128G>A	p.Asp710Asn	p.D710N	ENST00000393063	NM_030621.3	710	Gac/Aac	15/28	0.18300869629157	5	FACETS	0.963	0.849	1	0.321	0.283	0.362	INDETERMINATE	1	TRUE	2	0.682998515863878	5		335	480	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40457631	40457631	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	64	361	0	ENST00000345506.4:c.1384C>G	p.Leu462Val	p.L462V	ENST00000345506	NM_003152.3	462	Ctg/Gtg	13/20	0.506951392250279	3	FACETS	0.556	0.483	0.635	0.278	0.241	0.318	SUBCLONAL	1	TRUE	1	0.682998515863878	3		361	452	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732971	74732971	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	82	370	0	ENST00000359995.5:c.272G>C	p.Arg91Pro	p.R91P	ENST00000359995	NM_001195427.1	91	cGc/cCc	1/3	0.506951392250279	3	FACETS	0.765	0.678	0.857	0.383	0.339	0.429	SUBCLONAL	1	TRUE	1	0.682998515863878	3		370	421	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514795	44514795	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	117	466	0	ENST00000291552.4:c.452G>C	p.Arg151Thr	p.R151T	ENST00000291552	NM_006758.2	151	aGa/aCa	6/8	0.658621868886246	4	FACETS	0.676	0.609	0.747	0.338	0.304	0.374	SUBCLONAL	1	TRUE	2	0.682998515863878	4		466	853	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423777	47423777	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	110	455	0	ENST00000404338.3:c.1845G>T	p.Glu615Asp	p.E615D	ENST00000404338	NM_004491.4	615	gaG/gaT	1/6	0.623350688506954	3	FACETS	0.635	0.571	0.702	0.317	0.285	0.351	SUBCLONAL	1	TRUE	1	0.682998515863878	3		455	681	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155243	55155243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	88	414	0	ENST00000257290.5:c.2842G>A	p.Glu948Lys	p.E948K	ENST00000257290	NM_006206.4	948	Gag/Aag	21/23	0.242338666226624	2	FACETS	0.63	0.561	0.702	0.315	0.28	0.351	INDETERMINATE	1	TRUE	0	0.682998515863878	2		414	409	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167469	24167469	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	134	411	0	ENST00000263121.7:c.853G>C	p.Glu285Gln	p.E285Q	ENST00000263121	NM_003073.3	285	Gag/Cag	7/9	0.258273550669297	3	FACETS	1	0.986	1	0.461	0.423	0.499	INDETERMINATE	1	TRUE	0	0.682998515863878	3		411	381	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033934	49033934	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	108	404	0	ENST00000267163.4:c.2071G>C	p.Glu691Gln	p.E691Q	ENST00000267163	NM_000321.2	691	Gag/Cag	20/27	0.682998515863878	1	FACETS	0.56	0.507	0.615	0.56	0.507	0.615	SUBCLONAL	1	TRUE	0	0.682998515863878	1		404	372	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51507303	51507303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	103	387	0	ENST00000260433.2:c.985G>A	p.Glu329Lys	p.E329K	ENST00000260433		329	Gaa/Aaa	8/10	0.681732440198951	2	FACETS	0.804	0.726	0.886	0.402	0.363	0.443	CLONAL	1	TRUE	0	0.682998515863878	2		387	375	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817823	3817823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	89	427	0	ENST00000262367.5:c.3148G>A	p.Glu1050Lys	p.E1050K	ENST00000262367	NM_004380.2	1050	Gaa/Aaa	16/31	0.266168265917373	2	FACETS	0.543	0.483	0.606	0.271	0.241	0.303	INDETERMINATE	1	TRUE	0	0.682998515863878	2		427	480	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62320407	62320407	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	38	316	0	ENST00000360203.5:c.1801-1G>C		p.X601_splice	ENST00000360203	NM_001283009.1	601			0.258273550669297	3	FACETS	0.551	0.458	0.654	0.184	0.152	0.218	INDETERMINATE	1	TRUE	0	0.682998515863878	3		316	271	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673740	176673740	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	83	366	0	ENST00000439151.2:c.4440G>C	p.Lys1480Asn	p.K1480N	ENST00000439151	NM_022455.4	1480	aaG/aaC	10/23	0.682998515863878	2	FACETS	0.614	0.545	0.687	0.307	0.272	0.344	SUBCLONAL	1	TRUE	0	0.682998515863878	2		366	396	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322755	30322755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	88	366	0	ENST00000322652.5:c.1768G>A	p.Glu590Lys	p.E590K	ENST00000322652	NM_015355.2	590	Gaa/Aaa	14/16	0.506951392250279	3	FACETS	0.566	0.502	0.634	0.283	0.251	0.317	SUBCLONAL	1	TRUE	1	0.682998515863878	3		366	611	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424138	47424138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	122	447	0	ENST00000404338.3:c.2206G>A	p.Ala736Thr	p.A736T	ENST00000404338	NM_004491.4	736	Gct/Act	1/6	0.623350688506954	3	FACETS	0.69	0.624	0.758	0.345	0.312	0.379	SUBCLONAL	1	TRUE	1	0.682998515863878	3		447	695	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425080	47425080	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	123	506	0	ENST00000404338.3:c.3148G>C	p.Glu1050Gln	p.E1050Q	ENST00000404338	NM_004491.4	1050	Gaa/Caa	1/6	0.623350688506954	3	FACETS	0.679	0.614	0.746	0.339	0.307	0.373	SUBCLONAL	1	TRUE	1	0.682998515863878	3		506	712	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280103	18280103	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	68	326	0	ENST00000222254.8:c.2186G>C	p.Ter729SerextTer102	p.*729Sext*102	ENST00000222254	NM_005027.3	729	tGa/tCa	16/16	0.273238240044398	3	FACETS	0.87	0.763	0.983	0.29	0.254	0.328	INDETERMINATE	1	TRUE	0	0.682998515863878	3		326	307	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282701	1282701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	111	467	0	ENST00000310581.5:c.1612G>A	p.Glu538Lys	p.E538K	ENST00000310581	NM_198253.2	538	Gag/Aag	3/16	0.18300869629157	5	FACETS	1	0.983	1	0.477	0.431	0.525	INDETERMINATE	1	TRUE	2	0.682998515863878	5		467	460	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213373	36213373	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs370754915	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	65	481	0	ENST00000222270.7:c.2570C>T	p.Ser857Leu	p.S857L	ENST00000222270	NM_014727.1	857	tCa/tTa	4/37	0.623350688506954	3	FACETS	0.52	0.452	0.594	0.26	0.226	0.297	SUBCLONAL	1	TRUE	1	0.682998515863878	3		481	491	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524309	176524309	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	55	436	0	ENST00000292408.4:c.2170G>T	p.Glu724Ter	p.E724*	ENST00000292408	NM_213647.1	724	Gag/Tag	17/18	0.682998515863878	2	FACETS	0.569	0.49	0.654	0.285	0.245	0.327	SUBCLONAL	1	TRUE	0	0.682998515863878	2		436	283	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255583	16255583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	169	449	0	ENST00000375759.3:c.2848G>A	p.Glu950Lys	p.E950K	ENST00000375759	NM_015001.2	950	Gaa/Aaa	11/15	0.222366009164158	4	FACETS	1	0.989	1	0.732	0.677	0.789	INDETERMINATE	1	TRUE	2	0.682998515863878	4		449	569	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271460	26271460	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	237	563	0	ENST00000305910.3:c.153G>C	p.Glu51Asp	p.E51D	ENST00000305910	NM_003534.2	51	gaG/gaC	1/1	0.481349401654869	3	FACETS	1	0.978	1	0.368	0.344	0.392	CLONAL	1	TRUE	0	0.682998515863878	3		563	844	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958600	38958600	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	95	384	0	ENST00000357387.3:c.2365C>G	p.Gln789Glu	p.Q789E	ENST00000357387	NM_152756.3	789	Cag/Gag	24/38	0.623350688506954	3	FACETS	0.624	0.557	0.696	0.312	0.278	0.348	SUBCLONAL	1	TRUE	1	0.682998515863878	3		384	598	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971374	15971374	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	97	417	0	ENST00000268712.3:c.4575G>C	p.Gln1525His	p.Q1525H	ENST00000268712	NM_006311.3	1525	caG/caC	32/46	0.506951392250279	3	FACETS	0.62	0.553	0.69	0.31	0.276	0.345	SUBCLONAL	1	TRUE	1	0.682998515863878	3		417	615	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425020	47425020	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	95	487	0	ENST00000404338.3:c.3088G>C	p.Glu1030Gln	p.E1030Q	ENST00000404338	NM_004491.4	1030	Gag/Cag	1/6	0.623350688506954	3	FACETS	0.54	0.481	0.603	0.27	0.24	0.302	SUBCLONAL	1	TRUE	1	0.682998515863878	3		487	691	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473727	67473727	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	64	388	0	ENST00000327367.4:c.807C>G	p.Phe269Leu	p.F269L	ENST00000327367	NM_005902.3	269	ttC/ttG	6/9	0.682998515863878	1	FACETS	0.42	0.366	0.477	0.42	0.366	0.477	SUBCLONAL	1	TRUE	0	0.682998515863878	1		388	294	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3634853	3634853	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	87	396	0	ENST00000294008.3:c.4656G>T	p.Lys1552Asn	p.K1552N	ENST00000294008	NM_032444.2	1552	aaG/aaT	13/15	0.266168265917373	2	FACETS	0.53	0.47	0.592	0.265	0.235	0.296	INDETERMINATE	1	TRUE	0	0.682998515863878	2		396	481	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397721	49397721	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	47	416	0	ENST00000418115.1:c.503G>A	p.Arg168Lys	p.R168K	ENST00000418115	NM_001664.2	168	aGa/aAa	5/5	0.682998515863878	1	FACETS	0.225	0.19	0.263	0.225	0.19	0.263	SUBCLONAL	1	TRUE	0	0.682998515863878	1		416	403	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10777316	10777316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	84	334	0	ENST00000361367.2:c.476C>T	p.Ser159Phe	p.S159F	ENST00000361367	NM_014633.3	159	tCt/tTt	4/25	0.445534807649931	2	FACETS	0.587	0.521	0.657	0.294	0.26	0.329	SUBCLONAL	1	TRUE	0	0.682998515863878	2		334	419	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423643	47423643	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	123	469	0	ENST00000404338.3:c.1711G>C	p.Glu571Gln	p.E571Q	ENST00000404338	NM_004491.4	571	Gag/Cag	1/6	0.623350688506954	3	FACETS	0.695	0.629	0.764	0.348	0.314	0.382	SUBCLONAL	1	TRUE	1	0.682998515863878	3		469	695	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18943021	18943021	+	start_lost	Translation_Start_Site	SNP	G	G	C	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	108	418	0	ENST00000262803.5:c.3G>C	p.Met1?	p.M1?	ENST00000262803	NM_002911.3	1	atG/atC	1/24	0.273238240044398	3	FACETS	0.907	0.818	0.999	0.302	0.272	0.333	INDETERMINATE	1	TRUE	0	0.682998515863878	3		418	468	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449857	149449857	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	79	478	0	ENST00000286301.3:c.1207G>C	p.Glu403Gln	p.E403Q	ENST00000286301	NM_005211.3	403	Gag/Cag	9/22	0.682998515863878	2	FACETS	0.686	0.609	0.769	0.343	0.304	0.385	SUBCLONAL	1	TRUE	0	0.682998515863878	2		478	337	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219323	5219323	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	60	460	0	ENST00000357368.4:c.3921G>C	p.Lys1307Asn	p.K1307N	ENST00000357368	NM_002850.3	1307	aaG/aaC	23/38	0.273238240044398	3	FACETS	0.612	0.529	0.701	0.204	0.176	0.234	INDETERMINATE	1	TRUE	0	0.682998515863878	3		460	385	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423278	47423278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	90	450	0	ENST00000404338.3:c.1346G>A	p.Gly449Glu	p.G449E	ENST00000404338	NM_004491.4	449	gGa/gAa	1/6	0.623350688506954	3	FACETS	0.555	0.493	0.621	0.278	0.246	0.311	SUBCLONAL	1	TRUE	1	0.682998515863878	3		450	637	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654780	29654780	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	85	409	0	ENST00000356175.3:c.5469G>T	p.Lys1823Asn	p.K1823N	ENST00000356175	NM_000267.3	1823	aaG/aaT	37/57	0.506951392250279	3	FACETS	0.507	0.448	0.57	0.253	0.224	0.285	SUBCLONAL	1	TRUE	1	0.682998515863878	3		409	659	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321677	30321677	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	79	375	0	ENST00000322652.5:c.1532G>T	p.Gly511Val	p.G511V	ENST00000322652	NM_015355.2	511	gGa/gTa	13/16	0.506951392250279	3	FACETS	0.527	0.464	0.595	0.263	0.232	0.298	SUBCLONAL	1	TRUE	1	0.682998515863878	3		375	589	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423748	47423748	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	111	478	0	ENST00000404338.3:c.1816G>C	p.Asp606His	p.D606H	ENST00000404338	NM_004491.4	606	Gac/Cac	1/6	0.623350688506954	3	FACETS	0.632	0.569	0.699	0.316	0.284	0.35	SUBCLONAL	1	TRUE	1	0.682998515863878	3		478	690	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509871	187509871	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	31	471	0	ENST00000441802.2:c.13642G>C	p.Asp4548His	p.D4548H	ENST00000441802	NM_005245.3	4548	Gac/Cac	27/27	0.363480557466788	3	FACETS	0.272	0.219	0.331	0.136	0.109	0.166	INDETERMINATE	1	TRUE	1	0.682998515863878	3		471	448	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983764	15983764	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	122	376	0	ENST00000268712.3:c.3358G>C	p.Glu1120Gln	p.E1120Q	ENST00000268712	NM_006311.3	1120	Gag/Cag	25/46	0.506951392250279	3	FACETS	0.816	0.74	0.896	0.408	0.37	0.448	CLONAL	1	TRUE	1	0.682998515863878	3		376	587	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588859	29588859	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	81	350	0	ENST00000356175.3:c.4645G>C	p.Glu1549Gln	p.E1549Q	ENST00000356175	NM_000267.3	1549	Gag/Cag	34/57	0.506951392250279	3	FACETS	0.698	0.617	0.784	0.349	0.308	0.392	SUBCLONAL	1	TRUE	1	0.682998515863878	3		350	456	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636810	8636810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs770685926	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	102	438	0	ENST00000356435.5:c.99G>C	p.Gln33His	p.Q33H	ENST00000356435		33	caG/caC	2/35	0.671390001795322	3	FACETS	0.591	0.529	0.657	0.295	0.264	0.329	SUBCLONAL	1	TRUE	1	0.682998515863878	3		438	678	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610273	10610273	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	93	471	0	ENST00000171111.5:c.437C>G	p.Ser146Cys	p.S146C	ENST00000171111	NM_203500.1	146	tCc/tGc	2/6	0.273238240044398	3	FACETS	0.753	0.672	0.839	0.251	0.224	0.28	INDETERMINATE	1	TRUE	0	0.682998515863878	3		471	485	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420322	49420322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	85	470	0	ENST00000301067.7:c.15427G>A	p.Glu5143Lys	p.E5143K	ENST00000301067	NM_003482.3	5143	Gag/Aag	48/54	0.49738306930954	4	FACETS	0.834	0.74	0.935	0.278	0.246	0.312	CLONAL	1	TRUE	1	0.682998515863878	4		470	502	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181341	185181341	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	70	306	0	ENST00000265026.3:c.1282G>T	p.Glu428Ter	p.E428*	ENST00000265026	NM_004721.4	428	Gaa/Taa	8/14	0.247597462003455	2	FACETS	0.55	0.482	0.622	0.275	0.241	0.311	INDETERMINATE	1	TRUE	0	0.682998515863878	2		306	373	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38964961	38964961	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	96	359	0	ENST00000357387.3:c.1333C>G	p.His445Asp	p.H445D	ENST00000357387	NM_152756.3	445	Cat/Gat	16/38	0.623350688506954	3	FACETS	0.555	0.495	0.62	0.278	0.247	0.31	SUBCLONAL	1	TRUE	1	0.682998515863878	3		359	679	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856316	111856316	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	58	368	0	ENST00000341259.2:c.367G>A	p.Glu123Lys	p.E123K	ENST00000341259	NM_005475.2	123	Gag/Aag	2/8	0.49738306930954	4	FACETS	1	0.901	1	0.349	0.302	0.399	CLONAL	1	TRUE	1	0.682998515863878	4		368	273	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5081837	5081837	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	99	380	0	ENST00000381652.3:c.2547G>C	p.Leu849Phe	p.L849F	ENST00000381652	NM_004972.3	849	ttG/ttC	19/25	0.671390001795322	3	FACETS	0.556	0.497	0.62	0.278	0.248	0.31	SUBCLONAL	1	TRUE	1	0.682998515863878	3		380	699	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533791	63533791	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs779863826	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	69	470	0	ENST00000307078.5:c.1363C>G	p.Pro455Ala	p.P455A	ENST00000307078	NM_004655.3	455	Cca/Gca	6/11	0.506951392250279	3	FACETS	0.546	0.477	0.621	0.273	0.238	0.311	SUBCLONAL	1	TRUE	1	0.682998515863878	3		470	496	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930380	39930380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	104	229	0	ENST00000378444.4:c.3084G>A	p.Met1028Ile	p.M1028I	ENST00000378444	NM_001123385.1	1028	atG/atA	6/15	1	1	FACETS	0.735	0.668	0.803	0.735	0.668	0.803	SUBCLONAL	1	TRUE	0	0.682998515863878	1		229	273	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484369	8484369	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	75	376	0	ENST00000356435.5:c.3163G>C	p.Asp1055His	p.D1055H	ENST00000356435		1055	Gat/Cat	19/35	0.671390001795322	3	FACETS	0.521	0.457	0.59	0.261	0.228	0.295	SUBCLONAL	1	TRUE	1	0.682998515863878	3		376	565	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679994	33679994	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs769253715	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	77	420	0	ENST00000308377.4:c.2087G>C	p.Gly696Ala	p.G696A	ENST00000308377	NM_152270.3	696	gGa/gCa	5/5	0.506951392250279	3	FACETS	0.564	0.496	0.637	0.282	0.248	0.319	SUBCLONAL	1	TRUE	1	0.682998515863878	3		420	536	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006587	62006591	+	stop_lost	Nonstop_Mutation	ONP	CACTC	CACTC	GACTG	novel	NA	P-0068893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	80	361	0	ENST00000392795.3:c.688_692delinsCAGTC	p.Glu230_Ter231delinsGlnSer	p.E230_*231delinsQS	ENST00000392795	NM_001039933.1	230	GAGTGa/CAGTCa	6/6	0.506951392250279	3	FACETS	0.81	0.717	0.908	0.405	0.358	0.454	CLONAL	1	TRUE	1	0.682998515863878	3		361	388	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16235812	16235856	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCAGCAGTGATTCCAGCAGTAGTTCAAGTGATGATTCTCCAGCTC	GCAGCAGTGATTCCAGCAGTAGTTCAAGTGATGATTCTCCAGCTC	-	novel	NA	P-0068897-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	102	409	0	ENST00000375759.3:c.882-3_923del		p.X294_splice	ENST00000375759	NM_015001.2	294		4/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		409	686	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	217	269	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.498004842537114	3	FACETS	0.828	0.774	0.883	0.828	0.774	0.883	CLONAL	2	TRUE	1	0.508839380865309	3		269	646	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	174	567	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.713	0.656	0.772	0.713	0.656	0.772	SUBCLONAL	1	TRUE	1	0.508839380865309	2		569	959	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023831	27023831	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1415214478	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	182	583	1	ENST00000324856.7:c.941del	p.Gly314AlafsTer49	p.G314Afs*49	ENST00000324856	NM_006015.4	313	Ggg/gg	1/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.508839380865309	2		584	682	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097751	27097751	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	77	572	0	ENST00000324856.7:c.3344del	p.Pro1115GlnfsTer46	p.P1115Qfs*46	ENST00000324856	NM_006015.4	1114	Ccc/cc	12/20	1	2	FACETS	0.385	0.337	0.436	0.385	0.337	0.436	SUBCLONAL	1	TRUE	1	0.508839380865309	2		572	786	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551849	150551849	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	168	570	0	ENST00000369026.2:c.158C>T	p.Ala53Val	p.A53V	ENST00000369026	NM_021960.4	53	gCc/gTc	1/3	1	2	FACETS	0.996	0.919	1	0.996	0.919	1	CLONAL	1	TRUE	1	0.508839380865309	2		570	663	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446284	70446284	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	204	540	0	ENST00000373644.4:c.5230del	p.Arg1744GlufsTer18	p.R1744Efs*18	ENST00000373644	NM_030625.2	1742	Aaa/aa	11/12	1	2	FACETS	0.948	0.88	1	0.948	0.88	1	CLONAL	1	TRUE	1	0.508839380865309	2		540	846	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945397	71945397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374511786	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	182	550	0	ENST00000298229.2:c.2285G>A	p.Arg762His	p.R762H	ENST00000298229	NM_001567.3	762	cGc/cAc	20/28	1	2	FACETS	0.931	0.861	1	0.931	0.861	1	CLONAL	1	TRUE	1	0.508839380865309	2		550	768	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18576910	18576910	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	150	423	0	ENST00000266497.5:c.2318C>A	p.Pro773His	p.P773H	ENST00000266497		773	cCt/cAt	16/31	0.498004842537114	3	FACETS	0.935	0.855	1	0.467	0.427	0.509	CLONAL	1	TRUE	1	0.508839380865309	3		423	791	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244763	46244763	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	374	603	0	ENST00000334344.6:c.2857G>A	p.Ala953Thr	p.A953T	ENST00000334344	NM_152641.2	953	Gct/Act	15/21	0.498004842537114	3	FACETS	0.947	0.901	0.993	0.947	0.901	0.993	CLONAL	2	TRUE	1	0.508839380865309	3		603	974	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432329	49432329	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	254	678	0	ENST00000301067.7:c.8810del	p.Pro2937HisfsTer6	p.P2937Hfs*6	ENST00000301067	NM_003482.3	2937	cCa/ca	34/54	0.498004842537114	3	FACETS	1	0.983	1	0.57	0.533	0.608	CLONAL	1	TRUE	1	0.508839380865309	3		678	1099	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448408	49448408	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs797045661	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	56	625	0	ENST00000301067.7:c.303del	p.Ser102AlafsTer28	p.S102Afs*28	ENST00000301067	NM_003482.3	101	ggG/gg	3/54	0.498004842537114	3	FACETS	0.289	0.247	0.336	0.145	0.123	0.168	SUBCLONAL	1	TRUE	1	0.508839380865309	3		625	954	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133208986	133208986	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	60	568	0	ENST00000320574.5:c.6245A>G	p.Glu2082Gly	p.E2082G	ENST00000320574	NM_006231.2	2082	gAg/gGg	45/49	0.498004842537114	3	FACETS	0.325	0.279	0.375	0.162	0.139	0.188	SUBCLONAL	1	TRUE	1	0.508839380865309	3		568	911	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252771	133252771	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	162	462	0	ENST00000320574.5:c.929G>T	p.Arg310Met	p.R310M	ENST00000320574	NM_006231.2	310	aGg/aTg	10/49	0.498004842537114	3	FACETS	0.953	0.875	1	0.477	0.437	0.517	CLONAL	1	TRUE	1	0.508839380865309	3		462	838	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041061	29041061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	52	401	0	ENST00000282397.4:c.367G>A	p.Ala123Thr	p.A123T	ENST00000282397	NM_002019.4	123	Gca/Aca	3/30	1	2	FACETS	0.333	0.283	0.388	0.333	0.283	0.388	SUBCLONAL	1	TRUE	1	0.508839380865309	2		401	613	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913837	32913837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359507	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	177	384	0	ENST00000380152.3:c.5351del	p.Asn1784ThrfsTer7	p.N1784Tfs*7	ENST00000380152		1782	cAa/ca	11/27	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.508839380865309	2		384	627	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434944	110434946	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	182	644	0	ENST00000375856.3:c.3455_3457del	p.Phe1152del	p.F1152del	ENST00000375856	NM_003749.2	1152	tTCTcc/tcc	1/2	1	2	FACETS	0.912	0.843	0.984	0.912	0.843	0.984	CLONAL	1	TRUE	1	0.508839380865309	2		644	784	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986656	36986656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	147	549	1	ENST00000354822.5:c.1033G>A	p.Ala345Thr	p.A345T	ENST00000354822	NM_001079668.2	345	Gca/Aca	3/3	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.508839380865309	2		550	544	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120571	2120571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45469298	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	175	548	0	ENST00000219476.3:c.1831C>T	p.Arg611Trp	p.R611W	ENST00000219476	NM_000548.3	611	Cgg/Tgg	17/42	1	2	FACETS	0.922	0.851	0.996	0.922	0.851	0.996	CLONAL	1	TRUE	1	0.508839380865309	2		548	746	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779724	3779724	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	199	618	1	ENST00000262367.5:c.5324G>A	p.Cys1775Tyr	p.C1775Y	ENST00000262367	NM_004380.2	1775	tGc/tAc	31/31	1	2	FACETS	0.979	0.909	1	0.979	0.909	1	CLONAL	1	TRUE	1	0.508839380865309	2		619	799	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274124	10274124	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	172	567	0	ENST00000330684.3:c.145C>T	p.Arg49Cys	p.R49C	ENST00000330684	NM_001134407.1	49	Cgc/Tgc	2/13	1	2	FACETS	0.956	0.882	1	0.956	0.882	1	CLONAL	1	TRUE	1	0.508839380865309	2		567	707	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038650	14038650	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	152	389	0	ENST00000311895.7:c.1975G>T	p.Gly659Cys	p.G659C	ENST00000311895	NM_005236.2	659	Ggc/Tgc	10/11	1	2	FACETS	0.973	0.893	1	0.973	0.893	1	CLONAL	1	TRUE	1	0.508839380865309	2		389	614	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646981	23646981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	64	516	0	ENST00000261584.4:c.886del	p.Met296Ter	p.M296*	ENST00000261584	NM_024675.3	296	Atg/tg	4/13	1	2	FACETS	0.313	0.27	0.359	0.313	0.27	0.359	SUBCLONAL	1	TRUE	1	0.508839380865309	2		516	804	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81914559	81914559	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	115	393	0	ENST00000359376.3:c.692+1G>A		p.X231_splice	ENST00000359376	NM_002661.3	231			1	2	FACETS	0.79	0.714	0.87	0.79	0.714	0.87	SUBCLONAL	1	TRUE	1	0.508839380865309	2		393	572	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544956	86544956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769749299	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	136	551	0	ENST00000262426.4:c.781G>A	p.Ala261Thr	p.A261T	ENST00000262426	NM_001451.2	261	Gcc/Acc	1/2	1	2	FACETS	0.953	0.87	1	0.953	0.87	1	CLONAL	1	TRUE	1	0.508839380865309	2		551	561	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110608	4110608	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749389113	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	212	618	0	ENST00000262948.5:c.349C>T	p.Arg117Cys	p.R117C	ENST00000262948	NM_030662.3	117	Cgc/Tgc	3/11	1	2	FACETS	0.946	0.88	1	0.946	0.88	1	CLONAL	1	TRUE	1	0.508839380865309	2		618	881	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229048	36229048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866415691	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	433	633	0	ENST00000222270.7:c.7828C>T	p.Arg2610Cys	p.R2610C	ENST00000222270	NM_014727.1	2610	Cgc/Tgc	36/37	0.508839380865309	2	FACETS	0.935	0.896	0.974	0.935	0.896	0.974	CLONAL	2	TRUE	0	0.508839380865309	2		633	910	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794048	42794048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762143212	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	344	548	0	ENST00000575354.2:c.1409G>A	p.Arg470Gln	p.R470Q	ENST00000575354	NM_015125.3	470	cGg/cAg	9/20	0.508839380865309	2	FACETS	0.927	0.884	0.971	0.927	0.884	0.971	CLONAL	2	TRUE	0	0.508839380865309	2		548	729	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966442	25966442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757928113	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	217	599	0	ENST00000435504.4:c.2764G>A	p.Ala922Thr	p.A922T	ENST00000435504		922	Gca/Aca	13/13	1	2	FACETS	0.871	0.81	0.934	0.871	0.81	0.934	CLONAL	1	TRUE	1	0.508839380865309	2		599	979	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46587791	46587791	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	155	474	0	ENST00000263734.3:c.475del	p.Ser159AlafsTer12	p.S159Afs*12	ENST00000263734	NM_001430.4	157	Aaa/aa	5/16	1	2	FACETS	0.929	0.853	1	0.929	0.853	1	CLONAL	1	TRUE	1	0.508839380865309	2		474	656	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61722744	61722744	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	161	322	0	ENST00000401558.2:c.893T>C	p.Leu298Pro	p.L298P	ENST00000401558	NM_003400.3	298	cTt/cCt	11/25	1	2	FACETS	0.972	0.895	1	0.972	0.895	1	CLONAL	1	TRUE	1	0.508839380865309	2		322	651	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485739	57485739	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	208	500	0	ENST00000371085.3:c.1040G>T	p.Arg347Met	p.R347M	ENST00000371085	NM_000516.4	347	aGg/aTg	13/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.508839380865309	2		500	774	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513282	44513287	+	inframe_deletion	In_Frame_Del	DEL	CCACCG	CCACCG	-	rs745888281	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	138	421	1	ENST00000291552.4:c.648_653del	p.Gly222_Gly223del	p.G222_G223del	ENST00000291552	NM_006758.2	216	ggCGGTGGt/ggt	8/8	1	2	FACETS	0.711	0.647	0.777	0.711	0.647	0.777	SUBCLONAL	1	TRUE	1	0.508839380865309	2		422	763	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	56	359	0	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	0.287	0.245	0.333	0.287	0.245	0.333	SUBCLONAL	1	TRUE	1	0.508839380865309	2		359	768	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604640	55604640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146374006	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	157	435	0	ENST00000288135.5:c.2848G>A	p.Val950Met	p.V950M	ENST00000288135	NM_000222.2	950	Gtg/Atg	21/21	1	2	FACETS	0.828	0.76	0.899	0.828	0.76	0.899	CLONAL	1	TRUE	1	0.508839380865309	2		435	745	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268089	153268090	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	150	465	0	ENST00000281708.4:c.718dup	p.Met240AsnfsTer16	p.M240Nfs*16	ENST00000281708	NM_033632.3	240	atg/aAtg	4/12	1	2	FACETS	0.77	0.704	0.838	0.77	0.704	0.838	SUBCLONAL	1	TRUE	1	0.508839380865309	2		465	766	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542785	187542785	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	214	475	0	ENST00000441802.2:c.4955C>A	p.Ser1652Tyr	p.S1652Y	ENST00000441802	NM_005245.3	1652	tCt/tAt	10/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.508839380865309	2		475	744	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707623	176707623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	222	452	0	ENST00000439151.2:c.5680C>T	p.Arg1894Cys	p.R1894C	ENST00000439151	NM_022455.4	1894	Cgt/Tgt	18/23	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.508839380865309	2		452	799	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324503	31324503	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1487068101	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	186	361	0	ENST00000412585.2:c.305T>C	p.Leu102Pro	p.L102P	ENST00000412585	NM_005514.6	102	cTg/cCg	2/8	0.508839380865309	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.508839380865309	1		361	508	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797867	32797867	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	155	544	0	ENST00000374899.4:c.1636-1G>T		p.X546_splice	ENST00000374899	NM_018833.2	546			0.508839380865309	1	FACETS	0.835	0.769	0.903	0.835	0.769	0.903	CLONAL	1	TRUE	0	0.508839380865309	1		544	544	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983103	111983103	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	197	586	0	ENST00000368678.4:c.1444A>G	p.Met482Val	p.M482V	ENST00000368678		482	Atg/Gtg	13/13	1	2	FACETS	0.974	0.904	1	0.974	0.904	1	CLONAL	1	TRUE	1	0.508839380865309	2		586	795	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	388	492	14	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	1	2	FACETS	0.932	0.891	0.973	1	0.997	1	CLONAL	2	TRUE	1	0.508839380865309	2		506	818	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992683	68992684	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1347814436	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	109	451	1	ENST00000288368.4:c.1654dup	p.Ser552LysfsTer6	p.S552Kfs*6	ENST00000288368	NM_024870.2	550	gaa/gAaa	16/40	1	2	FACETS	0.766	0.69	0.846	0.766	0.69	0.846	SUBCLONAL	1	TRUE	1	0.508839380865309	2		452	559	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68993073	68993073	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	46	321	0	ENST00000288368.4:c.1878G>T	p.Glu626Asp	p.E626D	ENST00000288368	NM_024870.2	626	gaG/gaT	17/40	1	2	FACETS	0.377	0.317	0.442	0.377	0.317	0.442	SUBCLONAL	1	TRUE	1	0.508839380865309	2		321	480	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069121	5069121	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	76	427	0	ENST00000381652.3:c.1426G>T	p.Asp476Tyr	p.D476Y	ENST00000381652	NM_004972.3	476	Gat/Tat	11/25	1	2	FACETS	0.451	0.396	0.511	0.451	0.396	0.511	SUBCLONAL	1	TRUE	1	0.508839380865309	2		427	662	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933593	39933594	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	192	680	0	ENST00000378444.4:c.1005dup	p.Ser336LeufsTer45	p.S336Lfs*45	ENST00000378444	NM_001123385.1	335	-/C	4/15	1	2	FACETS	0.839	0.777	0.904	0.839	0.777	0.904	CLONAL	1	TRUE	1	0.508839380865309	2		680	899	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410604	63410604	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	185	632	0	ENST00000330258.3:c.2563C>G	p.His855Asp	p.H855D	ENST00000330258	NM_152424.3	855	Cat/Gat	2/2	1	2	FACETS	0.948	0.877	1	0.948	0.877	1	CLONAL	1	TRUE	1	0.508839380865309	2		632	767	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31239453	31239454	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs755090232	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	62	641	0	ENST00000376228.5:c.265_266del	p.Gln89GlufsTer9	p.Q89Efs*9	ENST00000376228	NM_002117.5	89	CAg/g	2/8	0.508839380865309	1	FACETS	0.29	0.25	0.333	0.29	0.25	0.333	SUBCLONAL	1	TRUE	0	0.508839380865309	1		641	627	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794556	42794556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	42	602	2	ENST00000575354.2:c.1636G>A	p.Ala546Thr	p.A546T	ENST00000575354	NM_015125.3	546	Gca/Aca	10/20	0.508839380865309	2	FACETS	0.219	0.182	0.261	0.11	0.091	0.131	SUBCLONAL	1	TRUE	0	0.508839380865309	2		604	753	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0068899-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	236	269	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.301906876263885	5	FACETS	1	0.959	1			1	CLONAL	4	TRUE	NA	0.32331138929385	5		269	531	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938442	44938450	+	inframe_deletion	In_Frame_Del	DEL	TGGTAGAAG	TGGTAGAAG	-	novel	NA	P-0068899-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	56	134	0	ENST00000377967.4:c.2992_3000del	p.Val998_Val1000del	p.V998_V1000del	ENST00000377967	NM_021140.2	997	aTGGTAGAAGtg/atg	20/29	1	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.32331138929385	1		134	245	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578270	7578271	+	missense_variant	Missense_Mutation	DNP	AT	AT	GC	novel	NA	P-0068899-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	134	500	0	ENST00000269305.4:c.578_579delinsGC	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAT/cGC	6/11	0.32331138929385	1	FACETS	0.918	0.835	1	0.918	0.835	1	CLONAL	1	TRUE	0	0.32331138929385	1		500	757	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332608	65332608	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs904336241	NA	P-0068899-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	63	412	0	ENST00000342505.4:c.931C>T	p.Leu311Phe	p.L311F	ENST00000342505	NM_002227.2	311	Ctc/Ttc	7/25	1	2	FACETS	0.575	0.497	0.66	0.575	0.497	0.66	SUBCLONAL	1	TRUE	1	0.32331138929385	2		412	678	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437677	49437677	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068899-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	73	515	0	ENST00000301067.7:c.5293G>A	p.Glu1765Lys	p.E1765K	ENST00000301067	NM_003482.3	1765	Gag/Aag	22/54	0.318886424443757	3	FACETS	0.481	0.419	0.548	0.241	0.209	0.274	SUBCLONAL	1	TRUE	1	0.32331138929385	3		515	1090	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	133	406	0				ENST00000310581	NM_198253.2	-/1132			0.693708790661888	3	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	1	0.693708790661888	3		406	256	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0068916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	159	257	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.677744118957196	4	FACETS	0.945	0.876	1	0.945	0.876	1	CLONAL	2	TRUE	2	0.693708790661888	4		257	411	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690847	89690847	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776667	NA	P-0068916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	158	266	0	ENST00000371953.3:c.253+1G>A		p.X85_splice	ENST00000371953	NM_000314.4	85			0.693708790661888	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.693708790661888	2		266	197	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015094	37015094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	150	527	0	ENST00000358127.4:c.310C>T	p.Arg104Cys	p.R104C	ENST00000358127	NM_001280556.1	104	Cgc/Tgc	3/10	0.593755585764441	4	FACETS	0.969	0.887	1	0.484	0.443	0.528	CLONAL	1	TRUE	2	0.693708790661888	4		527	756	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200205	123200205	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs12389430	NA	P-0068916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	96	348	0	ENST00000218089.9:c.2185-1G>A		p.X729_splice	ENST00000218089	NM_001042749.1	729			0.617525047449113	3	FACETS	1	0.974	1	0.621	0.56	0.684	CLONAL	1	TRUE	1	0.693708790661888	3		348	300	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0068917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	97	536	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.266914186970565	3	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.646964248749554	3		536	268	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0068917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	288	295	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.646964248749554	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.646964248749554	1		295	568	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917661	94917661	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1405101705	NA	P-0068917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	83	410	1	ENST00000536441.1:c.860G>A	p.Ser287Asn	p.S287N	ENST00000536441	NM_144665.3	287	aGc/aAc	6/10	1	2	FACETS	0.768	0.684	0.857	0.768	0.684	0.857	SUBCLONAL	1	TRUE	1	0.646964248749554	2		411	334	SUCCESS
APC	324	MSKCC	GRCh37	5	112175193	112175194	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0068917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	131	424	3	ENST00000257430.4:c.3903_3904del	p.Leu1302AlafsTer12	p.L1302Afs*12	ENST00000257430	NM_000038.5	1301	aCC/a	16/16	0.646964248749554	1	FACETS	0.848	0.781	0.916	0.848	0.781	0.916	CLONAL	1	TRUE	0	0.646964248749554	1		427	323	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741996	162741996	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	177	584	0	ENST00000367921.3:c.1687C>A	p.Leu563Ile	p.L563I	ENST00000367921	NM_006182.2	563	Cta/Ata	13/18	0.60388905392253	4	FACETS	1	0.922	1	0.333	0.307	0.361	CLONAL	1	TRUE	1	0.60388905392253	4		584	940	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0068920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	255	481	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	0.505697991980649	2	FACETS	0.999	0.946	1	0.999	0.946	1	CLONAL	2	TRUE	0	0.505697991980649	2		481	505	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928060	178928086	+	inframe_deletion	In_Frame_Del	DEL	GCCAGTACCTCATGGATTAGAAGATTT	GCCAGTACCTCATGGATTAGAAGATTT	-	novel	NA	P-0068920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	212	426	0	ENST00000263967.3:c.1340_1366del	p.Pro447_Leu455del	p.P447_L455del	ENST00000263967	NM_006218.2	446	tgGCCAGTACCTCATGGATTAGAAGATTTg/tgg	8/21	0.393278066978019	3	FACETS	0.869	0.82	0.918	0.869	0.82	0.918	CLONAL	3	TRUE	0	0.505697991980649	3		426	403	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533676	63533676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367697282	NA	P-0068920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	118	611	0	ENST00000307078.5:c.1478C>T	p.Ser493Leu	p.S493L	ENST00000307078	NM_004655.3	493	tCg/tTg	6/11	0.445967365512986	4	FACETS	0.956	0.863	1	0.478	0.431	0.527	CLONAL	1	TRUE	2	0.505697991980649	4		611	735	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749443	41749443	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	45	341	0	ENST00000226382.2:c.352G>A	p.Ala118Thr	p.A118T	ENST00000226382	NM_003924.3	118	Gcg/Acg	2/3	0.505697991980649	2	FACETS	0.527	0.444	0.617	0.263	0.222	0.309	SUBCLONAL	1	TRUE	0	0.505697991980649	2		341	338	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099442	27099442	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs875989849	NA	P-0068920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	198	503	0	ENST00000324856.7:c.3679G>T	p.Glu1227Ter	p.E1227*	ENST00000324856	NM_006015.4	1227	Gag/Tag	14/20	0.505697991980649	3	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	1	0.505697991980649	3		503	486	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112508	115112508	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755311630	NA	P-0068920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	290	517	0	ENST00000257566.3:c.1232C>T	p.Ala411Val	p.A411V	ENST00000257566	NM_016569.3	411	gCg/gTg	7/8	0.505697991980649	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.505697991980649	3		517	628	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151847995	151847995	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0068920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	78	325	0	ENST00000262189.6:c.12764C>G	p.Ser4255Ter	p.S4255*	ENST00000262189	NM_170606.2	4255	tCa/tGa	51/59	0.505697991980649	3	FACETS	0.88	0.777	0.991	0.44	0.388	0.496	CLONAL	1	TRUE	1	0.505697991980649	3		325	439	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761105	59761105	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	96	487	0	ENST00000259008.2:c.3302C>A	p.Pro1101Gln	p.P1101Q	ENST00000259008	NM_032043.2	1101	cCa/cAa	20/20	0.445967365512986	4	FACETS	0.969	0.865	1	0.484	0.432	0.54	CLONAL	1	TRUE	2	0.505697991980649	4		487	590	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471113	25471113	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	120	469	0	ENST00000264709.3:c.648G>T	p.Lys216Asn	p.K216N	ENST00000264709	NM_175629.2	216	aaG/aaT	7/23	0.505697991980649	3	FACETS	1	0.95	1	0.537	0.486	0.589	CLONAL	1	TRUE	1	0.505697991980649	3		469	554	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056337	27056338	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0068920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	140	472	0	ENST00000324856.7:c.1337_1338del	p.Ser446LeufsTer176	p.S446Lfs*176	ENST00000324856	NM_006015.4	445	CTc/c	2/20	0.505697991980649	3	FACETS	1	0.926	1	0.508	0.463	0.554	CLONAL	1	TRUE	1	0.505697991980649	3		472	683	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845300	151845300	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	110	563	0	ENST00000262189.6:c.13712C>G	p.Ser4571Cys	p.S4571C	ENST00000262189	NM_170606.2	4571	tCt/tGt	52/59	0.505697991980649	3	FACETS	0.953	0.859	1	0.476	0.429	0.526	CLONAL	1	TRUE	1	0.505697991980649	3		563	572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0068921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	604	319	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.742671099954028	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.742671099954028	3		320	690	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683824	117683824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754292558	NA	P-0068921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	109	458	0	ENST00000368508.3:c.3323C>T	p.Pro1108Leu	p.P1108L	ENST00000368508	NM_002944.2	1108	cCc/cTc	21/43	0.662834702375064	5	FACETS	0.662	0.594	0.735	0.221	0.198	0.245	SUBCLONAL	1	TRUE	2	0.742671099954028	5		458	937	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0068922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	126	359	0	ENST00000397752.3:c.3028+1G>A		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.188387664732433	2	FACETS	0.773	0.702	0.848	0.773	0.702	0.848	SUBCLONAL	2	TRUE	0	0.254262918943016	2		359	641	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218589	98218589	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	47	313	0	ENST00000331920.6:c.3275T>C	p.Ile1092Thr	p.I1092T	ENST00000331920	NM_000264.3	1092	aTa/aCa	19/24	1	2	FACETS	0.5	0.42	0.587	0.5	0.42	0.587	SUBCLONAL	1	TRUE	1	0.254262918943016	2		313	740	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0068964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	114	319	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.489901351698069	2		319	462	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244908	46244908	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	88	449	0	ENST00000334344.6:c.3002C>T	p.Pro1001Leu	p.P1001L	ENST00000334344	NM_152641.2	1001	cCt/cTt	15/21	0.277302657840105	1	FACETS	0.458	0.406	0.513	0.458	0.406	0.513	INDETERMINATE	1	TRUE	0	0.489901351698069	1		449	592	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045113	47045113	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0068964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	153	423	0	ENST00000377604.3:c.2356-2A>T		p.X786_splice	ENST00000377604	NM_001204468.1	786			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.489901351698069	2		423	523	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441848	49441849	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs398123744	NA	P-0068965-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	22	284	0	ENST00000301067.7:c.4135_4136del	p.Met1379ValfsTer52	p.M1379Vfs*52	ENST00000301067	NM_003482.3	1379	ATg/g	14/54	0.127250465750351	3	FACETS	0.247	0.191	0.313	0.124	0.095	0.157	INDETERMINATE	1	TRUE	1	0.55490086950675	3		284	410	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001230	150001249	+	frameshift_variant	Frame_Shift_Del	DEL	TCATCATATCACCCCCAGGA	TCATCATATCACCCCCAGGA	-	novel	NA	P-0068965-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	97	324	0	ENST00000253339.5:c.2355_2374del	p.Ile785MetfsTer5	p.I785Mfs*5	ENST00000253339		785	atTCCTGGGGGTGATATGATGAgc/atgc	4/7	0.129790966958723	4	FACETS	1	0.98	1	0.704	0.633	0.779	INDETERMINATE	1	TRUE	2	0.55490086950675	4		324	386	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0068966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	240	257	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		257	424	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285819	87285819	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	40	372	0	ENST00000277120.3:c.156C>G	p.Ile52Met	p.I52M	ENST00000277120		52	atC/atG	2/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		372	441	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28631523	28631523	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	71	175	0	ENST00000241453.7:c.445G>T	p.Ala149Ser	p.A149S	ENST00000241453	NM_004119.2	149	Gct/Tct	4/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		175	282	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0068967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	112	248	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	1	2	FACETS	0.973	0.885	1	0.973	0.885	1	CLONAL	1	TRUE	1	0.66734708772531	2		248	345	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857816	57857816	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs780874033	NA	P-0068967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	122	260	0	ENST00000228682.2:c.135C>A	p.Asn45Lys	p.N45K	ENST00000228682	NM_005269.2	45	aaC/aaA	3/12	1	2	FACETS	0.776	0.706	0.849	0.776	0.706	0.849	SUBCLONAL	1	TRUE	1	0.66734708772531	2		260	471	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0068968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	132	244	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	0.944	0.868	1	0.944	0.868	1	CLONAL	1	TRUE	1	0.785418711907648	2		244	356	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63898533	63898533	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	142	312	0	ENST00000398590.3:c.260del	p.Pro87LeufsTer3	p.P87Lfs*3	ENST00000398590	NM_001177387.1	87	Cct/ct	3/14	1	2	FACETS	0.886	0.816	0.958	0.886	0.816	0.958	CLONAL	1	TRUE	1	0.785418711907648	2		312	408	SUCCESS
ATR	545	MSKCC	GRCh37	3	142180872	142180872	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	128	216	0	ENST00000350721.4:c.7102A>T	p.Ile2368Phe	p.I2368F	ENST00000350721	NM_001184.3	2368	Att/Ttt	42/47	0.67889781231279	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.785418711907648	1		216	182	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0068969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	76	366	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.218625355364165	3	FACETS	0.959	0.846	1	0.959	0.846	1	CLONAL	2	TRUE	1	0.218625355364165	3		366	402	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0068969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	52	229	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.218625355364165	3	FACETS	0.907	0.783	1	1	0.962	1	CLONAL	3	TRUE	1	0.218625355364165	3		229	194	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716326	52716326	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	84	432	0	ENST00000322088.6:c.770G>T	p.Trp257Leu	p.W257L	ENST00000322088	NM_014225.5	257	tGg/tTg	6/15	0.136742820146484	4	FACETS	0.95	0.842	1	0.95	0.842	1	CLONAL	2	TRUE	2	0.218625355364165	4		432	493	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742142	145742142	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	31	410	0	ENST00000428558.2:c.361C>A	p.Pro121Thr	p.P121T	ENST00000428558	NM_004260.3	121	Cca/Aca	5/22	0.218625355364165	5	FACETS	0.886	0.716	1			1	CLONAL	1	TRUE	NA	0.218625355364165	5		410	425	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598082	52598082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	62	257	0	ENST00000394830.3:c.3784G>A	p.Glu1262Lys	p.E1262K	ENST00000394830	NM_018313.4	1262	Gaa/Aaa	24/30	1	2	FACETS	0.906	0.788	1	0.906	0.788	1	CLONAL	1	TRUE	1	0.41613181749882	2		257	329	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589663	67589663	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587777709	NA	P-0068970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	56	207	0	ENST00000274335.5:c.1425+1G>A		p.X475_splice	ENST00000274335		475			0.289363035518778	1	FACETS	0.751	0.66	0.844	1	0.973	1	SUBCLONAL	2	TRUE	0	0.41613181749882	1		207	142	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690801	89690801	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0068970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	43	192	0	ENST00000371953.3:c.210-2A>C		p.X70_splice	ENST00000371953	NM_000314.4	70			0.425837876472783	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.41613181749882	1		192	129	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884286	37884286	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs36085723	NA	P-0068970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	240	253	1	ENST00000269571.5:c.3757G>A	p.Val1253Met	p.V1253M	ENST00000269571		1253	Gtg/Atg	27/27	NA	2	FACETS	0.84	0.795	0.884			1	INDETERMINATE	3	TRUE	NA	0.41613181749882	2		254	458	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856347	45856347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	67	318	2	ENST00000391945.4:c.1825G>A	p.Asp609Asn	p.D609N	ENST00000391945	NM_000400.3	609	Gac/Aac	19/23	NA	2	FACETS	0.681	0.593	0.775			1	INDETERMINATE	1	TRUE	NA	0.41613181749882	2		320	473	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245520	46245520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	71	337	0	ENST00000334344.6:c.3614G>A	p.Gly1205Glu	p.G1205E	ENST00000334344	NM_152641.2	1205	gGa/gAa	15/21	0.183140199728709	3	FACETS	0.846	0.741	0.96	0.423	0.37	0.48	INDETERMINATE	1	TRUE	1	0.41613181749882	3		337	487	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37038177	37038177	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs63751428	NA	P-0068970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	79	255	0	ENST00000231790.2:c.184C>A	p.Gln62Lys	p.Q62K	ENST00000231790	NM_000249.3	62	Caa/Aaa	2/19	0.183140199728709	3	FACETS	0.962	0.849	1	0.481	0.424	0.541	INDETERMINATE	1	TRUE	1	0.41613181749882	3		255	477	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465379	120465379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	83	318	0	ENST00000256646.2:c.4882G>A	p.Asp1628Asn	p.D1628N	ENST00000256646	NM_024408.3	1628	Gac/Aac	27/34	0.289363035518778	1	FACETS	0.75	0.666	0.84	0.75	0.666	0.84	SUBCLONAL	1	TRUE	0	0.41613181749882	1		318	421	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366396	15366396	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	99	304	0	ENST00000263377.2:c.1759G>T	p.Glu587Ter	p.E587*	ENST00000263377	NM_058243.2	587	Gag/Tag	10/20	0.425837876472783	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.41613181749882	1		304	332	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98241332	98241332	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	48	268	0	ENST00000331920.6:c.1165G>A	p.Glu389Lys	p.E389K	ENST00000331920	NM_000264.3	389	Gag/Aag	8/24	0.28836581732475	2	FACETS	0.56	0.474	0.654	0.28	0.237	0.327	SUBCLONAL	1	TRUE	0	0.41613181749882	2		268	412	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068972-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	197	406	0				ENST00000310581	NM_198253.2	-/1132			0.255020176464169	5	FACETS	1	0.984	1	0.787	0.734	0.84	INDETERMINATE	2	FALSE	2	0.590508142965128	5		406	533	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467539	66467539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068972-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	286	371	0	ENST00000273854.3:c.730C>A	p.Pro244Thr	p.P244T	ENST00000273854	NM_004439.5	244	Cct/Act	3/18	0.305917390216707	5	FACETS	0.971	0.914	1	0.647	0.609	0.686	INDETERMINATE	2	FALSE	2	0.590508142965128	5		371	941	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332026	81332026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068972-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	337	315	0	ENST00000222390.5:c.2058G>T	p.Met686Ile	p.M686I	ENST00000222390	NM_000601.4	686	atG/atT	18/18	0.590508142965128	6	FACETS	1	0.989	1			1	CLONAL	4	FALSE	NA	0.590508142965128	6		315	567	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909734	50909734	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068972-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	342	381	0	ENST00000440232.2:c.1454A>C	p.Gln485Pro	p.Q485P	ENST00000440232	NM_002691.3	485	cAg/cCg	12/27	0.394490772729279	4	FACETS	1	0.959	1			1	CLONAL	2	FALSE	NA	0.590508142965128	4		381	911	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900953	3900953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068972-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	207	304	0	ENST00000262367.5:c.143G>A	p.Gly48Glu	p.G48E	ENST00000262367	NM_004380.2	48	gGa/gAa	2/31	0.394490772729279	4	FACETS	0.899	0.839	0.96			1	CLONAL	2	FALSE	NA	0.590508142965128	4		304	620	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0068982-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	17	269	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.644	0.48	0.84	0.644	0.48	0.84	SUBCLONAL	1	TRUE	1	0.15	2		269	352	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0068982-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	37	396	0	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	1	2	FACETS	0.91	0.749	1	0.91	0.749	1	CLONAL	1	TRUE	1	0.15	2		396	542	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0068982-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	32	505	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.801	0.649	0.973	0.801	0.649	0.973	CLONAL	1	TRUE	1	0.15	2		505	533	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456872	32456872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068982-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	23	391	0	ENST00000332351.3:c.20C>T	p.Thr7Met	p.T7M	ENST00000332351	NM_024426.4	7	aCg/aTg	1/10	1	2	FACETS	0.854	0.666	1	0.854	0.666	1	CLONAL	1	TRUE	1	0.15	2		391	359	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120258	70120259	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0068982-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	31	521	0	ENST00000245479.2:c.1261dup	p.Ser421LysfsTer157	p.S421Kfs*157	ENST00000245479	NM_000346.3	420	-/A	3/3	1	2	FACETS	0.835	0.674	1	0.835	0.674	1	CLONAL	1	TRUE	1	0.15	2		521	495	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581243	48581243	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068982-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	30	423	0	ENST00000342988.3:c.547C>T	p.Gln183Ter	p.Q183*	ENST00000342988	NM_005359.5	183	Cag/Tag	5/12	1	2	FACETS	0.717	0.576	0.877	0.717	0.576	0.877	SUBCLONAL	1	TRUE	1	0.15	2		423	558	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288819	15288819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1392500489	NA	P-0068982-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	25	416	0	ENST00000263388.2:c.3920C>T	p.Thr1307Met	p.T1307M	ENST00000263388	NM_000435.2	1307	aCg/aTg	24/33	1	2	FACETS	1	0.803	1	1	0.803	1	CLONAL	1	TRUE	1	0.15	2		416	327	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171607	36171607	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1569008655	NA	P-0068982-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	32	409	0	ENST00000300305.3:c.958C>T	p.Arg320Ter	p.R320*	ENST00000300305		320	Cga/Tga	7/8	1	2	FACETS	0.749	0.606	0.91	0.749	0.606	0.91	CLONAL	1	TRUE	1	0.15	2		409	570	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144679	55144679	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367722824	NA	P-0068982-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	28	344	0	ENST00000257290.5:c.2153G>A	p.Arg718Gln	p.R718Q	ENST00000257290	NM_006206.4	718	cGg/cAg	15/23	1	2	FACETS	0.822	0.656	1	0.822	0.656	1	CLONAL	1	TRUE	1	0.15	2		344	454	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050689	5050689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765494796	NA	P-0068982-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	19	295	0	ENST00000381652.3:c.472C>T	p.Arg158Trp	p.R158W	ENST00000381652	NM_004972.3	158	Cgg/Tgg	6/25	1	2	FACETS	0.685	0.519	0.88	0.685	0.519	0.88	SUBCLONAL	1	TRUE	1	0.15	2		295	370	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8733794	8733794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs949202374	NA	P-0068982-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	25	430	1	ENST00000356435.5:c.50G>A	p.Arg17His	p.R17H	ENST00000356435		17	cGc/cAc	1/35	1	2	FACETS	0.687	0.54	0.857	0.687	0.54	0.857	SUBCLONAL	1	TRUE	1	0.15	2		431	485	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423941	47423941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068982-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	34	513	0	ENST00000404338.3:c.2009C>T	p.Ser670Leu	p.S670L	ENST00000404338	NM_004491.4	670	tCg/tTg	1/6	1	2	FACETS	0.776	0.633	0.938	0.776	0.633	0.938	CLONAL	1	TRUE	1	0.15	2		513	584	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288332	33288332	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772837276	NA	P-0068982-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	41	488	0	ENST00000374542.5:c.1076G>A	p.Arg359Gln	p.R359Q	ENST00000374542	NM_001141970.1	359	cGg/cAg	4/8	1	2	FACETS	0.919	0.764	1	0.919	0.764	1	CLONAL	1	TRUE	1	0.15	2		488	595	SUCCESS
AR	367	MSKCC	GRCh37	X	66931527	66931527	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068982-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	21	199	0	ENST00000374690.3:c.2169G>T	p.Leu723Phe	p.L723F	ENST00000374690	NM_000044.3	723	ttG/ttT	4/8	1	1	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	0	0.15	1		199	202	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448600	89448600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759973751	NA	P-0068983-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	109	493	0	ENST00000336596.2:c.1564C>T	p.Arg522Cys	p.R522C	ENST00000336596	NM_005233.5	522	Cgc/Tgc	7/17	0.46659730037635	3	FACETS	0.537	0.483	0.594	0.269	0.241	0.298	INDETERMINATE	1	TRUE	1	0.887926844896912	3		493	660	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645714	12645714	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1457670031	NA	P-0068983-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	235	446	1	ENST00000251849.4:c.755C>T	p.Ser252Phe	p.S252F	ENST00000251849	NM_002880.3	252	tCc/tTc	7/17	0.46659730037635	3	FACETS	1	0.983	1	0.564	0.529	0.599	INDETERMINATE	1	TRUE	1	0.887926844896912	3		447	678	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0068991-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	217	290	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		290	552	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218423	1218423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068991-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	122	287	0	ENST00000326873.7:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000326873	NM_000455.4	100	Caa/Taa	2/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		287	462	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2193777	2193777	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068991-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	147	270	0	ENST00000398665.3:c.583G>C	p.Ala195Pro	p.A195P	ENST00000398665	NM_032482.2	195	Gcg/Ccg	6/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		270	561	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105575	11105575	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068991-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	152	280	0	ENST00000358026.2:c.1492del	p.Gln498ArgfsTer3	p.Q498Rfs*3	ENST00000358026	NM_001128849.1	497	atC/at	9/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		280	645	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355111	15355111	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068991-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	136	302	1	ENST00000263377.2:c.2512C>G	p.His838Asp	p.H838D	ENST00000263377	NM_058243.2	838	Cac/Gac	13/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		303	619	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140500238	140500238	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068991-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	156	265	0	ENST00000288602.6:c.904C>G	p.Gln302Glu	p.Q302E	ENST00000288602	NM_004333.4	302	Cag/Gag	7/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		265	680	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350849	89350849	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068991-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	33	236	1	ENST00000301030.4:c.2101A>G	p.Ser701Gly	p.S701G	ENST00000301030	NM_001256183.1	701	Agc/Ggc	9/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		237	461	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0068993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	58	153	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		153	342	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388059	81388059	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	20	290	0	ENST00000222390.5:c.316A>G	p.Ser106Gly	p.S106G	ENST00000222390	NM_000601.4	106	Agt/Ggt	3/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		290	208	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0068995-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	144	290	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.325745474161702	3	FACETS	0.848	0.782	0.916	0.848	0.782	0.916	CLONAL	3	FALSE	0	0.325745474161702	3		290	404	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0068995-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	64	224	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.325745474161702	4	FACETS	0.822	0.717	0.934	0.822	0.717	0.934	CLONAL	2	FALSE	2	0.325745474161702	4		224	317	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007719	45007719	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068995-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	97	512	0	ENST00000558401.1:c.166G>T	p.Glu56Ter	p.E56*	ENST00000558401	NM_004048.2	56	Gaa/Taa	2/4	0.220474567257703	2	FACETS	1	0.971	1	0.619	0.554	0.687	CLONAL	1	FALSE	0	0.325745474161702	2		512	481	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs11575997	NA	P-0068995-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	93	415	0	ENST00000269305.4:c.993+1G>T		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.2410503681056	2	FACETS	1	0.981	1	0.745	0.668	0.827	CLONAL	1	FALSE	0	0.325745474161702	2		415	383	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446255	29446256	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0068995-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	42	545	0	ENST00000389048.3:c.3311_3312delinsAA	p.Ser1104Ter	p.S1104*	ENST00000389048	NM_004304.4	1104	tCC/tAA	20/29	0.325745474161702	3	FACETS	0.73	0.61	0.862	0.365	0.305	0.431	SUBCLONAL	1	FALSE	1	0.325745474161702	3		545	411	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12393098	12393098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068995-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	126	397	0	ENST00000287820.6:c.7G>A	p.Glu3Lys	p.E3K	ENST00000287820	NM_015869.4	3	Gaa/Aaa	1/7	0.220474567257703	2	FACETS	0.904	0.825	0.985	0.904	0.825	0.985	CLONAL	2	FALSE	0	0.325745474161702	2		397	428	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139789	55139789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149031291	NA	P-0068995-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	57	473	0	ENST00000257290.5:c.1450G>A	p.Val484Met	p.V484M	ENST00000257290	NM_006206.4	484	Gtg/Atg	10/23	0.325745474161702	3	FACETS	0.933	0.803	1	0.467	0.401	0.538	CLONAL	1	FALSE	1	0.325745474161702	3		473	436	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372699	81372699	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068995-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	32	413	0	ENST00000222390.5:c.835C>A	p.Arg279Ser	p.R279S	ENST00000222390	NM_000601.4	279	Cgc/Agc	7/18	0.273212149483036	3	FACETS	0.544	0.441	0.66	0.272	0.22	0.33	SUBCLONAL	1	FALSE	1	0.325745474161702	3		413	420	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755923	133755923	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068995-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	35	465	0	ENST00000318560.5:c.1550G>T	p.Gly517Val	p.G517V	ENST00000318560	NM_005157.4	517	gGg/gTg	10/11	1	2	FACETS	0.587	0.482	0.705	0.587	0.482	0.705	SUBCLONAL	1	FALSE	1	0.325745474161702	2		465	366	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154783	2154783	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068995-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	52	611	0	ENST00000434045.2:c.438del	p.Glu147ArgfsTer68	p.E147Rfs*68	ENST00000434045	NM_001127598.1	146	tcC/tc	4/5	0.173802032049549	4	FACETS	1	0.947	1	0.621	0.531	0.718	INDETERMINATE	1	FALSE	2	0.325745474161702	4		611	341	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936036	71936036	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068995-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	24	362	0	ENST00000298229.2:c.8C>A	p.Ser3Ter	p.S3*	ENST00000298229	NM_001567.3	3	tCg/tAg	1/28	0.173802032049549	4	FACETS	0.962	0.759	1	0.481	0.379	0.597	INDETERMINATE	1	FALSE	2	0.325745474161702	4		362	203	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988029	85988029	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068995-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	80	404	0	ENST00000263360.6:c.974A>G	p.Glu325Gly	p.E325G	ENST00000263360	NM_003797.3	325	gAa/gGa	10/12	0.173802032049549	4	FACETS	1	0.976	1	0.727	0.642	0.817	INDETERMINATE	1	FALSE	2	0.325745474161702	4		404	448	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50827483	50827483	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068995-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	83	373	0	ENST00000398568.2:c.2368G>T	p.Gly790Trp	p.G790W	ENST00000398568	NM_001042412.1	790	Ggg/Tgg	16/18	0.273212149483036	3	FACETS	1	0.941	1	0.551	0.487	0.619	CLONAL	1	FALSE	1	0.325745474161702	3		373	538	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259363	36259363	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068995-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	47	548	0	ENST00000300305.3:c.128C>G	p.Pro43Arg	p.P43R	ENST00000300305		43	cCt/cGt	3/8	1	2	FACETS	0.75	0.634	0.876	0.75	0.634	0.876	SUBCLONAL	1	FALSE	1	0.325745474161702	2		548	385	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521118	187521118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1320492053	NA	P-0068995-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	94	507	0	ENST00000441802.2:c.12037G>T	p.Ala4013Ser	p.A4013S	ENST00000441802	NM_005245.3	4013	Gcc/Tcc	22/27	0.325745474161702	3	FACETS	0.953	0.856	1	0.953	0.856	1	CLONAL	2	FALSE	1	0.325745474161702	3		507	352	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874566	35874566	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068995-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	82	417	0	ENST00000303115.3:c.722T>C	p.Ile241Thr	p.I241T	ENST00000303115	NM_002185.3	241	aTc/aCc	6/8	0.325745474161702	5	FACETS	1	0.934	1	0.272	0.24	0.307	CLONAL	1	FALSE	1	0.325745474161702	5		417	688	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839994	27839994	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068995-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	71	693	0	ENST00000328488.2:c.100G>A	p.Gly34Ser	p.G34S	ENST00000328488	NM_003533.2	34	Ggt/Agt	1/1	0.286799837354924	4	FACETS	0.955	0.834	1	0.318	0.278	0.362	CLONAL	1	FALSE	1	0.325745474161702	4		693	605	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739914	41739914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068995-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	87	464	0	ENST00000242208.4:c.59G>A	p.Ser20Asn	p.S20N	ENST00000242208	NM_002192.2	20	aGt/aAt	2/3	0.273212149483036	3	FACETS	1	0.974	1	0.669	0.595	0.748	CLONAL	1	FALSE	1	0.325745474161702	3		464	464	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20153874	20153874	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068995-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	30	218	0	ENST00000379607.5:c.186A>T	p.Arg62Ser	p.R62S	ENST00000379607	NM_001412.3	62	agA/agT	3/7	1	2	FACETS	0.774	0.627	0.939	0.774	0.627	0.939	CLONAL	1	FALSE	1	0.325745474161702	2		218	238	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429291	47429291	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0068995-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	29	510	0	ENST00000377045.4:c.1420-1G>T		p.X474_splice	ENST00000377045	NM_001654.4	474			1	2	FACETS	0.512	0.411	0.626	0.512	0.411	0.626	SUBCLONAL	1	FALSE	1	0.325745474161702	2		510	348	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411179	63411179	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068995-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	25	586	0	ENST00000330258.3:c.1988T>A	p.Val663Glu	p.V663E	ENST00000330258	NM_152424.3	663	gTg/gAg	2/2	1	2	FACETS	0.634	0.502	0.785	0.634	0.502	0.785	SUBCLONAL	1	FALSE	1	0.325745474161702	2		586	242	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346228	70346228	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068995-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	19	572	0	ENST00000374080.3:c.2579C>A	p.Ala860Asp	p.A860D	ENST00000374080		860	gCc/gAc	19/45	1	2	FACETS	0.328	0.248	0.421	0.328	0.248	0.421	SUBCLONAL	1	FALSE	1	0.325745474161702	2		572	356	SUCCESS
BTK	695	MSKCC	GRCh37	X	100609643	100609643	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0068995-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	121	403	0	ENST00000308731.7:c.1606A>T	p.Lys536Ter	p.K536*	ENST00000308731	NM_000061.2	536	Aaa/Taa	16/19	0.325745474161702	3	FACETS	0.898	0.816	0.983	0.898	0.816	0.983	CLONAL	2	FALSE	1	0.325745474161702	3		403	481	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0068998-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	178	353	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.285578819209193	3	FACETS	1	0.982	1	0.794	0.736	0.854	CLONAL	2	TRUE	0	0.285447848831316	3		353	598	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0068998-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	146	529	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.159302009802306	3	FACETS	1	0.941	1	1	0.941	1	INDETERMINATE	2	TRUE	1	0.285447848831316	3		529	566	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0068998-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	83	538	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.285447848831316	2		538	482	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272207	15272207	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1051094199	NA	P-0068998-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	30	330	1	ENST00000263388.2:c.6232C>T	p.Arg2078Trp	p.R2078W	ENST00000263388	NM_000435.2	2078	Cgg/Tgg	33/33	0.144828328134235	4	FACETS	0.585	0.471	0.715	0.292	0.235	0.358	INDETERMINATE	1	TRUE	2	0.285447848831316	4		331	462	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030433	47030433	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068998-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	23	116	0	ENST00000377604.3:c.208T>C	p.Tyr70His	p.Y70H	ENST00000377604	NM_001204468.1	70	Tac/Cac	4/24	0.285447848831316	2	FACETS	0.655	0.512	0.819			1	SUBCLONAL	1	TRUE	NA	0.285447848831316	2		116	246	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881114	37881114	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368094521	NA	P-0068998-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	45	340	0	ENST00000269571.5:c.2443G>A	p.Gly815Arg	p.G815R	ENST00000269571		815	Gga/Aga	20/27	0.285578819209193	4	FACETS	0.6	0.503	0.707	0.2	0.167	0.236	SUBCLONAL	1	TRUE	1	0.285447848831316	4		340	676	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604776	48604776	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs377767382	NA	P-0068998-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	78	255	0	ENST00000342988.3:c.1598T>C	p.Leu533Pro	p.L533P	ENST00000342988	NM_005359.5	533	cTc/cCc	12/12	0.285578819209193	3	FACETS	1	0.952	1	0.388	0.342	0.438	CLONAL	1	TRUE	0	0.285447848831316	3		255	536	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562118	21562118	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068998-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	85	322	0	ENST00000382592.4:c.1801G>A	p.Ala601Thr	p.A601T	ENST00000382592	NM_014572.2	601	Gcc/Acc	4/8	0.285447848831316	6	FACETS	1	0.911	1	0.26	0.229	0.293	CLONAL	1	TRUE	2	0.285447848831316	6		322	901	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218802	5218802	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370343222	NA	P-0068998-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	55	227	0	ENST00000357368.4:c.3931G>A	p.Asp1311Asn	p.D1311N	ENST00000357368	NM_002850.3	1311	Gac/Aac	24/38	0.144828328134235	4	FACETS	1	0.929	1	0.569	0.488	0.658	INDETERMINATE	1	TRUE	2	0.285447848831316	4		227	435	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589887	212589887	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068998-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	81	239	0	ENST00000342788.4:c.655G>T	p.Gly219Cys	p.G219C	ENST00000342788	NM_005235.2	219	Ggc/Tgc	6/28	0.285447848831316	5	FACETS	1	0.976	1	0.484	0.427	0.545	CLONAL	1	TRUE	2	0.285447848831316	5		239	558	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591841	48591852	+	inframe_deletion	In_Frame_Del	DEL	TAGGAGAGACAT	TAGGAGAGACAT	-	novel	NA	P-0068998-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	111	290	0	ENST00000342988.3:c.1005_1016del	p.Gly336_Phe339del	p.G336_F339del	ENST00000342988	NM_005359.5	335	gTAGGAGAGACATtt/gtt	9/12	0.285578819209193	3	FACETS	0.93	0.84	1	0.62	0.56	0.682	CLONAL	2	TRUE	0	0.285447848831316	3		290	478	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808881	3808881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068998-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	34	225	0	ENST00000262367.5:c.3343G>A	p.Val1115Ile	p.V1115I	ENST00000262367	NM_004380.2	1115	Gta/Ata	17/31	0.285578819209193	3	FACETS	0.623	0.509	0.751	0.311	0.254	0.376	SUBCLONAL	1	TRUE	1	0.285447848831316	3		225	437	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409101	139409101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764112977	NA	P-0068998-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	78	300	0	ENST00000277541.6:c.2068G>A	p.Gly690Arg	p.G690R	ENST00000277541	NM_017617.3	690	Ggg/Agg	13/34	0.285578819209193	4	FACETS	1	0.945	1	0.566	0.497	0.639	CLONAL	1	TRUE	2	0.285447848831316	4		300	621	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459260	99459260	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068998-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	119	235	0	ENST00000268035.6:c.1896C>G	p.Asn632Lys	p.N632K	ENST00000268035	NM_000875.3	632	aaC/aaG	9/21	0.228012278578332	3	FACETS	0.92	0.834	1			1	CLONAL	2	TRUE	NA	0.285447848831316	3		235	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577155	7577172	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTACTCAGGATAGGAAA	ACTACTCAGGATAGGAAA	-	novel	NA	P-0068998-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	75	240	0	ENST00000269305.4:c.783-17_783del		p.X261_splice	ENST00000269305	NM_001126112.2	261		8/11	0.159302009802306	3	FACETS	1	0.975	1	0.727	0.64	0.82	INDETERMINATE	1	TRUE	1	0.285447848831316	3		240	413	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964361	70964361	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0068998-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	56	211	0	ENST00000276594.2:c.1667C>G	p.Ser556Ter	p.S556*	ENST00000276594	NM_024504.3	556	tCa/tGa	8/8	0.247660898463299	4	FACETS	1	0.947	1	0.612	0.526	0.706	CLONAL	1	TRUE	2	0.285447848831316	4		211	412	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0069002-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	31	206	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.819	1	1	0.819	1	CLONAL	1	TRUE	1	0.310255388306915	2		206	199	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0069002-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	89	290	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.277394411249049	2	FACETS	0.894	0.8	0.991	0.894	0.8	0.991	CLONAL	2	TRUE	0	0.310255388306915	2		290	321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0069002-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	120	422	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.233182405790277	2	FACETS	0.839	0.763	0.919	0.839	0.763	0.919	CLONAL	2	TRUE	0	0.310255388306915	2		422	461	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456384	32456384	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069002-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	32	304	0	ENST00000332351.3:c.508G>T	p.Gly170Cys	p.G170C	ENST00000332351	NM_024426.4	170	Ggc/Tgc	1/10	1	2	FACETS	0.607	0.493	0.734	0.607	0.493	0.734	SUBCLONAL	1	TRUE	1	0.310255388306915	2		304	340	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619258	23619258	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069002-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	79	282	0	ENST00000261584.4:c.3277A>G	p.Ile1093Val	p.I1093V	ENST00000261584	NM_024675.3	1093	Att/Gtt	12/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.310255388306915	2		282	409	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2115841	2115841	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs281875187	NA	P-0069002-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	74	300	0	ENST00000349721.2:c.3476G>A	p.Arg1159Gln	p.R1159Q	ENST00000349721	NM_003070.3	1159	cGa/cAa	25/34	0.219193005249859	1	FACETS	0.886	0.778	1	0.886	0.778	1	CLONAL	1	TRUE	0	0.310255388306915	1		300	455	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039843	47039843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069002-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	60	237	0	ENST00000377604.3:c.1186C>T	p.Arg396Cys	p.R396C	ENST00000377604	NM_001204468.1	396	Cgc/Tgc	12/24	0.310255388306915	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.310255388306915	1		237	306	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281769	142281769	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069002-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	61	260	0	ENST00000350721.4:c.475C>G	p.Leu159Val	p.L159V	ENST00000350721	NM_001184.3	159	Ctc/Gtc	4/47	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.310255388306915	2		260	315	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942083	81942083	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069002-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	48	303	0	ENST00000359376.3:c.1620G>T	p.Arg540Ser	p.R540S	ENST00000359376	NM_002661.3	540	agG/agT	17/33	1	2	FACETS	0.797	0.676	0.931	0.797	0.676	0.931	CLONAL	1	TRUE	1	0.310255388306915	2		303	388	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040743	47040743	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069002-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	46	312	0	ENST00000377604.3:c.1378C>A	p.Leu460Ile	p.L460I	ENST00000377604	NM_001204468.1	460	Ctc/Atc	13/24	0.310255388306915	1	FACETS	0.827	0.7	0.965	0.827	0.7	0.965	CLONAL	1	TRUE	0	0.310255388306915	1		312	303	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138550	11138550	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069002-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	72	332	0	ENST00000358026.2:c.3306C>G	p.Phe1102Leu	p.F1102L	ENST00000358026	NM_001128849.1	1102	ttC/ttG	24/36	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.310255388306915	2		332	453	SUCCESS
EED	8726	MSKCC	GRCh37	11	85961489	85961489	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069002-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	43	163	0	ENST00000263360.6:c.266A>T	p.Lys89Met	p.K89M	ENST00000263360	NM_003797.3	89	aAg/aTg	2/12	1	2	FACETS	0.912	0.767	1	0.912	0.767	1	CLONAL	1	TRUE	1	0.310255388306915	2		163	304	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976405	25976405	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069002-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	31	140	0	ENST00000435504.4:c.1140G>T	p.Gln380His	p.Q380H	ENST00000435504		380	caG/caT	11/13	1	2	FACETS	0.806	0.655	0.975	0.806	0.655	0.975	CLONAL	1	TRUE	1	0.310255388306915	2		140	248	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81891879	81891879	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069002-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	58	302	0	ENST00000359376.3:c.349G>C	p.Glu117Gln	p.E117Q	ENST00000359376	NM_002661.3	117	Gag/Cag	4/33	1	2	FACETS	0.897	0.773	1	0.897	0.773	1	CLONAL	1	TRUE	1	0.310255388306915	2		302	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579536	7579536	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567556930	NA	P-0069003-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	301	437	0	ENST00000269305.4:c.151G>T	p.Glu51Ter	p.E51*	ENST00000269305	NM_001126112.2	51	Gaa/Taa	4/11	0.338842796268098	3	FACETS	1	0.991	1	0.807	0.766	0.849	CLONAL	2	TRUE	0	0.441900093320897	3		437	687	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0069003-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	1992	283	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.441900093320897	24	FACETS	0.988	0.976	0.999			1	CLONAL	22	TRUE	NA	0.441900093320897	24		283	2432	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29099518	29099518	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1345979642	NA	P-0069003-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	108	288	0	ENST00000328354.6:c.883G>C	p.Glu295Gln	p.E295Q	ENST00000328354	NM_007194.3	295	Gaa/Caa	8/15	0.443814129982433	2	FACETS	1	0.968	1	0.585	0.528	0.643	CLONAL	1	TRUE	0	0.441900093320897	2		288	418	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40458461	40458461	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069003-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	114	324	0	ENST00000345506.4:c.1676A>G	p.Asn559Ser	p.N559S	ENST00000345506	NM_003152.3	559	aAc/aGc	14/20	0.443814129982433	4	FACETS	1	0.933	1	0.522	0.471	0.577	CLONAL	1	TRUE	2	0.441900093320897	4		324	712	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172386	7172386	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069003-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	127	289	0	ENST00000302850.5:c.1183C>G	p.Leu395Val	p.L395V	ENST00000302850	NM_000208.2	395	Cta/Gta	5/22	0.443814129982433	2	FACETS	0.969	0.881	1	0.485	0.44	0.531	CLONAL	1	TRUE	0	0.441900093320897	2		289	593	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201775	102201775	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0069003-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	154	297	0	ENST00000263464.3:c.1127T>G	p.Met376Arg	p.M376R	ENST00000263464	NM_001165.4	376	aTg/aGg	6/9	0.42987545843487	4	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	2	0.441900093320897	4		297	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0069007-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	107	419	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.858	0.77	0.951	1	0.986	1	CLONAL	2	FALSE	1	0.169423979624076	2		419	736	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0069007-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	67	312	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.169423979624076	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	0	0.169423979624076	1		312	599	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0069007-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	108	348	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.169423979624076	5	FACETS	1	0.97	1	0.809	0.727	0.895	CLONAL	2	FALSE	2	0.169423979624076	5		348	659	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912756	32912756	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069007-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	58	430	0	ENST00000380152.3:c.4264G>C	p.Glu1422Gln	p.E1422Q	ENST00000380152		1422	Gag/Cag	11/27	0.157268383272879	3	FACETS	1	0.871	1	0.508	0.436	0.587	CLONAL	1	FALSE	1	0.169423979624076	3		430	731	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106747	27106747	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069007-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	61	588	0	ENST00000324856.7:c.6358G>T	p.Glu2120Ter	p.E2120*	ENST00000324856	NM_006015.4	2120	Gaa/Taa	20/20	0.0946140029007454	4	FACETS	0.941	0.81	1	0.47	0.405	0.542	INDETERMINATE	1	FALSE	2	0.169423979624076	4		588	895	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549445	5549445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141466336	NA	P-0069007-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	49	487	0	ENST00000397747.3:c.472G>A	p.Val158Ile	p.V158I	ENST00000397747	NM_025239.3	158	Gtc/Atc	4/7	0.169423979624076	1	FACETS	0.831	0.703	0.973	0.831	0.703	0.973	CLONAL	1	FALSE	0	0.169423979624076	1		487	637	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299914	15299914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069007-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	60	559	0	ENST00000263388.2:c.1264G>A	p.Gly422Ser	p.G422S	ENST00000263388	NM_000435.2	422	Ggc/Agc	8/33	0.152430419547354	4	FACETS	0.984	0.846	1	0.492	0.423	0.568	CLONAL	1	FALSE	2	0.169423979624076	4		559	842	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0069009-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	54	518	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.3	3	FACETS	0.959	0.823	1	0.959	0.823	1	CLONAL	2	TRUE	1	0.18	3		518	341	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0069009-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	25	316	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	0.225462442089999	1	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	0	0.18	1		316	226	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525041	157525041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069009-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	19	434	0	ENST00000346085.5:c.4936G>A	p.Gly1646Ser	p.G1646S	ENST00000346085	NM_020732.3	1646	Ggt/Agt	19/20	1	2	FACETS	0.614	0.465	0.789	0.614	0.465	0.789	SUBCLONAL	1	TRUE	1	0.18	2		434	344	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974706	21974707	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	A	novel	NA	P-0069009-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	35	386	0	ENST00000304494.5:c.120_121delinsT	p.Pro41ArgfsTer12	p.P41Rfs*12	ENST00000304494	NM_000077.4	40	gcACcg/gcTcg	1/3	1	2	FACETS	0.824	0.68	0.983	1	0.956	1	CLONAL	2	TRUE	1	0.18	2		386	236	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0069010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	9	206	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		206	199	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444346	50444346	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	60	460	0	ENST00000331340.3:c.276G>A	p.Met92Ile	p.M92I	ENST00000331340	NM_006060.4	92	atG/atA	4/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		460	958	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878127	48878127	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1276653645	NA	P-0069010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	105	429	0	ENST00000267163.4:c.83del	p.Pro28LeufsTer37	p.P28Lfs*37	ENST00000267163	NM_000321.2	27	Ccc/cc	1/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		429	721	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0069010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	139	431	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		431	698	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589776	69589776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747109892	NA	P-0069010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	57	659	0	ENST00000168712.1:c.77G>A	p.Arg26Gln	p.R26Q	ENST00000168712	NM_002007.2	26	cGa/cAa	1/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		659	806	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469071	25469071	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	53	422	0	ENST00000264709.3:c.1387G>C	p.Glu463Gln	p.E463Q	ENST00000264709	NM_175629.2	463	Gag/Cag	11/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		422	626	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431759	49431759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1359665754	NA	P-0069010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	58	474	1	ENST00000301067.7:c.9380G>A	p.Arg3127His	p.R3127H	ENST00000301067	NM_003482.3	3127	cGc/cAc	34/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		475	682	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960850	15960850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1403202191	NA	P-0069010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	57	317	0	ENST00000268712.3:c.6370C>T	p.Leu2124Phe	p.L2124F	ENST00000268712	NM_006311.3	2124	Ctt/Ttt	40/46	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		317	450	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412030	116412049	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TACTTTTCCAGAAGGTATAT	TACTTTTCCAGAAGGTATAT	-	novel	NA	P-0069010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	84	484	0	ENST00000397752.3:c.3016_3028+7del		p.X1006_splice	ENST00000397752	NM_000245.2	1006		14/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		484	548	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143293	108143293	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659877	NA	P-0069010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	44	252	0	ENST00000278616.4:c.3112G>C	p.Val1038Leu	p.V1038L	ENST00000278616	NM_000051.3	1038	Gta/Cta	21/63	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		252	440	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113380	209113380	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	50	337	0	ENST00000345146.2:c.127G>C	p.Asp43His	p.D43H	ENST00000345146	NM_005896.2	43	Gat/Cat	4/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		337	486	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441068	149441068	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	40	256	0	ENST00000286301.3:c.1844T>G	p.Val615Gly	p.V615G	ENST00000286301	NM_005211.3	615	gTg/gGg	13/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		256	394	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76777752	76777752	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	38	317	0	ENST00000373344.5:c.6964C>G	p.Gln2322Glu	p.Q2322E	ENST00000373344	NM_000489.3	2322	Caa/Gaa	32/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		317	572	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437149	49437149	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	47	402	0	ENST00000301067.7:c.5530C>A	p.Pro1844Thr	p.P1844T	ENST00000301067	NM_003482.3	1844	Cca/Aca	24/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		402	669	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89818553	89818553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	30	335	1	ENST00000389301.3:c.3059G>A	p.Arg1020Lys	p.R1020K	ENST00000389301	NM_000135.2	1020	aGa/aAa	31/43	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		336	577	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272382	21272382	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	75	506	0	ENST00000354336.3:c.160G>C	p.Glu54Gln	p.E54Q	ENST00000354336	NM_005207.3	54	Gag/Cag	1/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		506	883	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819244	3819244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	44	358	0	ENST00000262367.5:c.2991G>A	p.Met997Ile	p.M997I	ENST00000262367	NM_004380.2	997	atG/atA	15/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		358	729	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819216	3819216	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	48	391	0	ENST00000262367.5:c.3019G>T	p.Glu1007Ter	p.E1007*	ENST00000262367	NM_004380.2	1007	Gag/Tag	15/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		391	716	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731085	162731085	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	46	418	0	ENST00000367921.3:c.940G>T	p.Glu314Ter	p.E314*	ENST00000367921	NM_006182.2	314	Gaa/Taa	9/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		418	715	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143519	30143519	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	36	310	0	ENST00000389048.3:c.7G>C	p.Ala3Pro	p.A3P	ENST00000389048	NM_004304.4	3	Gcc/Ccc	1/29	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		310	439	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285544	38285544	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	60	398	0	ENST00000425967.3:c.609G>C	p.Lys203Asn	p.K203N	ENST00000425967	NM_001174067.1	203	aaG/aaC	6/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		398	603	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933444	100933444	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	32	276	0	ENST00000325455.5:c.1946G>C	p.Arg649Thr	p.R649T	ENST00000325455	NM_001202474.3	649	aGa/aCa	4/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		276	427	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778253	27778253	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	86	450	0	ENST00000369163.2:c.402G>C	p.Glu134Asp	p.E134D	ENST00000369163	NM_003536.2	134	gaG/gaC	1/1	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		450	760	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50782681	50782681	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	49	376	0	ENST00000307179.4:c.2193G>C	p.Lys731Asn	p.K731N	ENST00000307179		731	aaG/aaC	14/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		376	643	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1718796	1718796	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	48	319	0	ENST00000378609.4:c.997G>C	p.Asp333His	p.D333H	ENST00000378609	NM_002074.3	333	Gat/Cat	11/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		319	563	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539056	23539056	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	52	419	0	ENST00000380871.4:c.383G>C	p.Arg128Pro	p.R128P	ENST00000380871	NM_006167.3	128	cGa/cCa	2/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		419	653	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598194	28598194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	67	359	0	ENST00000253063.3:c.166G>A	p.Glu56Lys	p.E56K	ENST00000253063	NM_031459.4	56	Gag/Aag	3/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		359	609	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0069021-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	29	349	0				ENST00000310581	NM_198253.2	-/1132			0.103610306240454	0	FACETS	0.515	0.413	0.631			1	INDETERMINATE	1	FALSE	0	0.210289572107938	0		349	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069021-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	69	471	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	FALSE	1	0.210289572107938	2		471	583	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587777893	NA	P-0069021-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	48	478	0	ENST00000361445.4:c.5930C>A	p.Thr1977Lys	p.T1977K	ENST00000361445	NM_004958.3	1977	aCa/aAa	43/58	1	2	FACETS	0.871	0.736	1	0.871	0.736	1	CLONAL	1	FALSE	1	0.210289572107938	2		478	524	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295215	1295215	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0069021-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	23	432	0				ENST00000310581	NM_198253.2	-/1132			0.103610306240454	0	FACETS	0.438	0.341	0.551			1	INDETERMINATE	1	FALSE	0	0.210289572107938	0		432	394	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042458	16042458	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1393424638	NA	P-0069021-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	51	257	0	ENST00000268712.3:c.1216A>G	p.Met406Val	p.M406V	ENST00000268712	NM_006311.3	406	Atg/Gtg	12/46	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.210289572107938	2		257	378	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216688	36216688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069021-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	41	506	0	ENST00000222270.7:c.3854C>T	p.Pro1285Leu	p.P1285L	ENST00000222270	NM_014727.1	1285	cCa/cTa	13/37	1	2	FACETS	0.654	0.544	0.777	0.654	0.544	0.777	SUBCLONAL	1	FALSE	1	0.210289572107938	2		506	596	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942749	15942749	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069021-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	53	404	0	ENST00000268712.3:c.6953C>T	p.Ser2318Leu	p.S2318L	ENST00000268712	NM_006311.3	2318	tCa/tTa	44/46	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	FALSE	1	0.210289572107938	2		404	459	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661158	227661158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069021-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	75	576	0	ENST00000305123.5:c.2297C>T	p.Ser766Leu	p.S766L	ENST00000305123	NM_005544.2	766	tCa/tTa	1/2	0.204451263187432	3	FACETS	1	0.894	1	0.512	0.448	0.581	CLONAL	1	FALSE	1	0.210289572107938	3		576	770	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446387	49446388	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0069021-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	59	585	0	ENST00000301067.7:c.1217_1218del	p.Pro406GlnfsTer9	p.P406Qfs*9	ENST00000301067	NM_003482.3	406	cCC/c	9/54	1	2	FACETS	0.881	0.757	1	0.881	0.757	1	CLONAL	1	FALSE	1	0.210289572107938	2		585	637	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602620	10602620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	29	413	0	ENST00000171111.5:c.958C>T	p.Arg320Trp	p.R320W	ENST00000171111	NM_203500.1	320	Cgg/Tgg	3/6	1	2	FACETS	0.559	0.447	0.687	0.559	0.447	0.687	SUBCLONAL	1	TRUE	1	0.17	2		413	610	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948483	71948484	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0069022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	28	453	0	ENST00000298229.2:c.3201dup	p.Ser1068GlnfsTer17	p.S1068Qfs*17	ENST00000298229	NM_001567.3	1065	-/C	26/28	1	2	FACETS	0.671	0.535	0.826	0.671	0.535	0.826	SUBCLONAL	1	TRUE	1	0.17	2		453	491	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0069022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	36	443	2	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	1	2	FACETS	0.822	0.675	0.988	0.822	0.675	0.988	CLONAL	1	TRUE	1	0.17	2		445	515	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448743	49448744	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0069022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	40	369	0	ENST00000301067.7:c.115_116del	p.Gly39ArgfsTer6	p.G39Rfs*6	ENST00000301067	NM_003482.3	39	GGa/a	2/54	1	2	FACETS	0.796	0.661	0.948	0.796	0.661	0.948	CLONAL	1	TRUE	1	0.17	2		369	591	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067478	37067479	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0069022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	29	335	0	ENST00000231790.2:c.1390_1391dup	p.Thr465LeufsTer27	p.T465Lfs*27	ENST00000231790	NM_000249.3	463	-/CC	12/19	1	2	FACETS	0.702	0.562	0.861	0.702	0.562	0.861	SUBCLONAL	1	TRUE	1	0.17	2		335	486	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346674	81346674	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	30	234	0	ENST00000222390.5:c.1279T>A	p.Phe427Ile	p.F427I	ENST00000222390	NM_000601.4	427	Ttc/Atc	11/18	1	2	FACETS	0.891	0.718	1	0.891	0.718	1	CLONAL	1	TRUE	1	0.17	2		234	396	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0069023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	66	356	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	NA	2	FACETS	0.156	0.134	0.179			1	INDETERMINATE	1	TRUE	NA	0.806752025769856	2		356	1050	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0069023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	58	298	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.806752025769856	3	FACETS	0.897	0.78	1	0.448	0.39	0.51	CLONAL	1	TRUE	1	0.806752025769856	3		298	225	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828915	72828915	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0069023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	255	330	0	ENST00000268489.5:c.7666del	p.Ala2556ArgfsTer56	p.A2556Rfs*56	ENST00000268489	NM_006885.3	2556	Gcg/cg	9/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.806752025769856	2		330	597	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279605	123279605	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	539	371	0	ENST00000358487.5:c.827T>G	p.Phe276Cys	p.F276C	ENST00000358487	NM_000141.4	276	tTt/tGt	7/18	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	1	TRUE	NA	0.806752025769856	2		371	1001	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094474	27094474	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0069023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	220	297	0	ENST00000324856.7:c.3183del	p.Ile1061MetfsTer4	p.I1061Mfs*4	ENST00000324856	NM_006015.4	1061	aTt/at	11/20	1	2	FACETS	0.976	0.915	1	0.976	0.915	1	CLONAL	1	TRUE	1	0.806752025769856	2		297	559	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984378	201984378	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	680	364	0	ENST00000359651.3:c.1043G>T	p.Arg348Leu	p.R348L	ENST00000359651		348	cGg/cTg	8/8	0.757891374762038	4	FACETS	0.949	0.922	0.975	0.949	0.922	0.975	CLONAL	3	TRUE	1	0.806752025769856	4		364	1070	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685243	86685244	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	AA	novel	NA	P-0069023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	140	309	0	ENST00000274376.6:c.2959_2960insAA	p.Ser987Ter	p.S987*	ENST00000274376	NM_002890.2	987	tct/tAAct	24/25	1	2	FACETS	0.838	0.771	0.908	0.838	0.771	0.908	CLONAL	1	TRUE	1	0.806752025769856	2		309	414	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589212	67589217	+	inframe_deletion	In_Frame_Del	DEL	TGTGGT	TGTGGT	-	novel	NA	P-0069023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	28	306	0	ENST00000274335.5:c.1202_1207del	p.Val401_Val402del	p.V401_V402del	ENST00000274335		400	tcTGTGGTt/tct	9/15	1	2	FACETS	0.574	0.467	0.691	0.574	0.467	0.691	SUBCLONAL	1	TRUE	1	0.806752025769856	2		306	121	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0069025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	129	319	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.107838131367862	4	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.362221021346403	4		319	666	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0069025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	164	523	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.362221021346403	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.362221021346403	1		523	602	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200113	123200113	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0069025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	48	386	0	ENST00000218089.9:c.2184+1G>T		p.X728_splice	ENST00000218089	NM_001042749.1	728			0.210251758007333	3	FACETS	0.649	0.549	0.76	0.325	0.274	0.38	INDETERMINATE	1	TRUE	1	0.362221021346403	3		386	482	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0069031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	159	448	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.290512133727316	1	FACETS	0.673	0.622	0.725	0.673	0.622	0.725	INDETERMINATE	1	TRUE	0	0.685585842707824	1		448	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0069031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	514	618	2	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.685585842707824	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.685585842707824	2		620	665	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939950	76939950	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0069031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	158	481	0	ENST00000373344.5:c.798C>G	p.Tyr266Ter	p.Y266*	ENST00000373344	NM_000489.3	266	taC/taG	9/35	1	2	FACETS	0.989	0.914	1	0.989	0.914	1	CLONAL	1	TRUE	1	0.685585842707824	2		481	466	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717772	89717778	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	AAAAGGT	AAAAGGT	-	novel	NA	P-0069031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	198	318	0	ENST00000371953.3:c.797_801+2del		p.X266_splice	ENST00000371953	NM_000314.4	266		7/9	0.685585842707824	2	FACETS	0.999	0.951	1	0.999	0.951	1	CLONAL	2	TRUE	0	0.685585842707824	2		318	289	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577069	7577069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55819519	NA	P-0069040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	12	456	0	ENST00000269305.4:c.869G>A	p.Arg290His	p.R290H	ENST00000269305	NM_001126112.2	290	cGc/cAc	8/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		456	496	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0069042-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	10	290	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.36	0.243	0.507	0.36	0.243	0.507	SUBCLONAL	1	TRUE	1	0.2	2		290	278	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0069047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	52	468	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	0.869	0.742	1	0.869	0.742	1	CLONAL	1	TRUE	1	0.31	2		468	386	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0069047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	15	406	0				ENST00000310581	NM_198253.2	-/1132			0.298281563089978	0	FACETS	0.805	0.599	1			1	CLONAL	1	TRUE	0	0.31	0		406	83	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0069047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	38	312	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	1	0.836	1	1	0.836	1	CLONAL	1	TRUE	1	0.31	2		312	244	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481627	56481627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1429784531	NA	P-0069047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	49	513	1	ENST00000267101.3:c.662C>T	p.Pro221Leu	p.P221L	ENST00000267101	NM_001982.3	221	cCc/cTc	6/28	0.189708519450485	4	FACETS	1	0.907	1	0.548	0.465	0.638	CLONAL	1	TRUE	2	0.31	4		514	378	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021428	42021428	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	10	389	0	ENST00000219905.7:c.3724C>T	p.Arg1242Ter	p.R1242*	ENST00000219905	NM_001164273.1	1242	Cga/Tga	11/24	1	2	FACETS	0.175	0.118	0.247	0.175	0.118	0.247	SUBCLONAL	1	TRUE	1	0.31	2		389	369	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481403	140481403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913357	NA	P-0069047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	30	268	0	ENST00000288602.6:c.1405G>A	p.Gly469Arg	p.G469R	ENST00000288602	NM_004333.4	469	Gga/Aga	11/18	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.31	2		268	176	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727429	66727429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	47	353	0	ENST00000307102.5:c.145C>T	p.Arg49Cys	p.R49C	ENST00000307102	NM_002755.3	49	Cgc/Tgc	2/11	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.31	2		353	299	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37863341	37863341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	50	432	0	ENST00000269571.5:c.172G>A	p.Gly58Arg	p.G58R	ENST00000269571		58	Gga/Aga	2/27	1	2	FACETS	0.972	0.828	1	0.972	0.828	1	CLONAL	1	TRUE	1	0.31	2		432	332	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88676897	88676897	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782682	NA	P-0069047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	19	230	0	ENST00000372037.3:c.682C>T	p.Arg228Ter	p.R228*	ENST00000372037	NM_004329.2	228	Cga/Tga	9/13	1	2	FACETS	0.598	0.455	0.764	0.598	0.455	0.764	SUBCLONAL	1	TRUE	1	0.31	2		230	205	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352601	118352602	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0069047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	36	472	0	ENST00000534358.1:c.3808_3809del	p.Lys1270GlufsTer2	p.K1270Efs*2	ENST00000534358	NM_005933.3	1269	gAA/g	7/36	1	2	FACETS	0.651	0.536	0.779	0.651	0.536	0.779	SUBCLONAL	1	TRUE	1	0.31	2		472	357	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686347	30686354	+	frameshift_variant	Frame_Shift_Del	DEL	TGAGCAAC	TGAGCAAC	-	novel	NA	P-0069047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	50	489	0	ENST00000295754.5:c.205_212del	p.Ser69GlnfsTer7	p.S69Qfs*7	ENST00000295754	NM_003242.5	68	aTGAGCAAC/a	2/7	1	2	FACETS	0.421	0.356	0.493	0.421	0.356	0.493	SUBCLONAL	1	TRUE	1	0.31	2		489	766	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0069048-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	43	365	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.176119542287319	4	FACETS	0.971	0.818	1	0.648	0.545	0.759	CLONAL	2	FALSE	1	0.200559467195335	4		365	265	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0069048-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	106	425	1	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	0.128415511790994	4	FACETS	1	0.961	1	0.758	0.682	0.839	CLONAL	2	FALSE	1	0.200559467195335	4		426	558	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780675	9780675	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069048-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	90	481	0	ENST00000377346.4:c.1477G>T	p.Glu493Ter	p.E493*	ENST00000377346	NM_005026.3	493	Gag/Tag	12/24	0.193972604711806	3	FACETS	0.925	0.823	1	0.925	0.823	1	CLONAL	2	FALSE	1	0.200559467195335	3		481	534	SUCCESS
APC	324	MSKCC	GRCh37	5	112173567	112173567	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0069048-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	56	500	0	ENST00000257430.4:c.2278del	p.Leu760Ter	p.L760*	ENST00000257430	NM_000038.5	759	gCc/gc	16/16	0.200559467195335	3	FACETS	1	0.958	1	0.668	0.573	0.771	CLONAL	1	FALSE	1	0.200559467195335	3		500	460	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163479	108163479	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs780603110	NA	P-0069048-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	61	383	0	ENST00000278616.4:c.4570C>G	p.Leu1524Val	p.L1524V	ENST00000278616	NM_000051.3	1524	Ctt/Gtt	30/63	0.200559467195335	3	FACETS	1	0.877	1	1	0.877	1	CLONAL	2	FALSE	1	0.200559467195335	3		383	331	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0069049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	55	269	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.897	0.772	1	0.897	0.772	1	CLONAL	1	TRUE	1	0.383432712896284	2		269	320	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0069049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	202	505	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.381504597292329	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.383432712896284	2		505	504	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230468760	230468760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs889200747	NA	P-0069049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	77	548	0	ENST00000391860.1:c.758C>T	p.Ala253Val	p.A253V	ENST00000391860	NM_001258311.1	253	gCg/gTg	5/7	1	2	FACETS	0.963	0.85	1	0.963	0.85	1	CLONAL	1	TRUE	1	0.383432712896284	2		548	417	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729394	41729394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	128	487	0	ENST00000242208.4:c.1135C>T	p.Arg379Trp	p.R379W	ENST00000242208	NM_002192.2	379	Cgg/Tgg	3/3	0.172068996167557	3	FACETS	0.786	0.716	0.859	0.786	0.716	0.859	INDETERMINATE	2	TRUE	1	0.383432712896284	3		487	506	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120479	70120480	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0069049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	87	536	0	ENST00000245479.2:c.1486dup	p.Gln496ProfsTer82	p.Q496Pfs*82	ENST00000245479	NM_000346.3	494	agc/agCc	3/3	1	2	FACETS	0.791	0.701	0.886	0.791	0.701	0.886	SUBCLONAL	1	TRUE	1	0.383432712896284	2		536	574	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939260	71939260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	85	546	0	ENST00000298229.2:c.209G>A	p.Arg70His	p.R70H	ENST00000298229	NM_001567.3	70	cGc/cAc	2/28	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.383432712896284	2		546	428	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348536	70348536	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387907360	NA	P-0069049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	111	255	0	ENST00000374080.3:c.3443G>A	p.Arg1148His	p.R1148H	ENST00000374080		1148	cGc/cAc	24/45	1	1	FACETS	1	0.927	1	1	0.99	1	CLONAL	2	TRUE	0	0.383432712896284	1		255	232	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946495	71946495	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs747360226	NA	P-0069049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	75	487	0	ENST00000298229.2:c.2659G>A	p.Glu887Lys	p.E887K	ENST00000298229	NM_001567.3	887	Gag/Aag	23/28	1	2	FACETS	0.947	0.834	1	0.947	0.834	1	CLONAL	1	TRUE	1	0.383432712896284	2		487	413	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298024	15298024	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769773673	NA	P-0069049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	65	605	1	ENST00000263388.2:c.1732C>T	p.Arg578Cys	p.R578C	ENST00000263388	NM_000435.2	578	Cgc/Tgc	11/33	1	2	FACETS	0.843	0.734	0.961	0.843	0.734	0.961	CLONAL	1	TRUE	1	0.383432712896284	2		606	402	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250992	10250992	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764541314	NA	P-0069049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	99	464	0	ENST00000340748.4:c.3488C>T	p.Thr1163Met	p.T1163M	ENST00000340748		1163	aCg/aTg	32/40	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.383432712896284	2		464	398	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534371	63534371	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	105	628	0	ENST00000307078.5:c.1150G>T	p.Glu384Ter	p.E384*	ENST00000307078	NM_004655.3	384	Gag/Tag	5/11	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.383432712896284	2		628	524	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033161	69033161	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	86	364	0	ENST00000288368.4:c.3601C>A	p.Gln1201Lys	p.Q1201K	ENST00000288368	NM_024870.2	1201	Caa/Aaa	30/40	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.383432712896284	2		364	408	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532511	63532512	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	GGTCA	novel	NA	P-0069049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	83	527	0	ENST00000307078.5:c.2063_2067dup	p.Pro690Ter	p.P690*	ENST00000307078	NM_004655.3	689	-/TGACC	8/11	1	2	FACETS	0.884	0.782	0.991	0.884	0.782	0.991	CLONAL	1	TRUE	1	0.383432712896284	2		527	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	84	496	0	ENST00000269305.4:c.470T>G	p.Val157Gly	p.V157G	ENST00000269305	NM_001126112.2	157	gTc/gGc	5/11	0.277397752226029	2	FACETS	1	0.96	1	0.592	0.526	0.663	CLONAL	1	TRUE	0	0.33932733743963	2		496	418	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0069052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	16	269	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.916	0.678	1	0.916	0.678	1	CLONAL	1	TRUE	1	0.15	2		269	233	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0069052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	21	306	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.645	0.496	0.82	0.645	0.496	0.82	SUBCLONAL	1	TRUE	1	0.15	2		306	434	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589623	67589634	+	inframe_deletion	In_Frame_Del	DEL	ATATGATAGATT	ATATGATAGATT	-	novel	NA	P-0069052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	8	200	0	ENST00000274335.5:c.1392_1403del	p.Asp464_Tyr467del	p.D464_Y467del	ENST00000274335		462	gaATATGATAGATTa/gaa	10/15	1	2	FACETS	0.332	0.213	0.488	0.332	0.213	0.488	SUBCLONAL	1	TRUE	1	0.15	2		200	321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0069053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	161	294	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.498529607826577	2	FACETS	0.888	0.827	0.949	0.888	0.827	0.949	CLONAL	2	TRUE	0	0.519679814129206	2		294	349	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348954	11348954	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	92	325	0	ENST00000332029.2:c.382G>C	p.Val128Leu	p.V128L	ENST00000332029	NM_003745.1	128	Gtg/Ctg	2/2	0.140801434597931	6	FACETS	1	0.912	1	0.68	0.609	0.754	INDETERMINATE	2	TRUE	3	0.519679814129206	6		325	354	SUCCESS
APC	324	MSKCC	GRCh37	5	112173965	112173966	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0069053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	127	257	0	ENST00000257430.4:c.2676dup	p.Glu893ArgfsTer19	p.E893Rfs*19	ENST00000257430	NM_000038.5	892	gaa/gAaa	16/16	0.482623006597226	3	FACETS	0.804	0.736	0.874	0.804	0.736	0.874	CLONAL	2	TRUE	1	0.519679814129206	3		257	383	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015128	71015128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	67	254	0	ENST00000318789.4:c.1802C>T	p.Ala601Val	p.A601V	ENST00000318789	NM_032682.5	601	gCa/gTa	20/21	0.482623006597226	3	FACETS	0.8	0.698	0.909	0.4	0.349	0.455	CLONAL	1	TRUE	1	0.519679814129206	3		254	406	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0069079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	53	406	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.749	0.648	0.856	0.749	0.648	0.856	SUBCLONAL	1	TRUE	1	0.718143939642731	2		406	197	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0069079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	170	440	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.718143939642731	2		440	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0069079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	185	439	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.718143939642731	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.718143939642731	1		440	304	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50143288	50143288	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1245401713	NA	P-0069079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	59	306	1	ENST00000246792.3:c.68A>G	p.Asp23Gly	p.D23G	ENST00000246792	NM_006270.3	23	gAc/gGc	1/6	1	2	FACETS	0.809	0.707	0.917	0.809	0.707	0.917	CLONAL	1	TRUE	1	0.718143939642731	2		307	203	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266053	41266217	+	inframe_deletion	In_Frame_Del	DEL	ACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTC	ACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTC	-	novel	NA	P-0069079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	230	362	0	ENST00000349496.5:c.51_215del	p.Asp17_Gln72delinsGlu	p.D17_Q72delinsE	ENST00000349496	NM_001904.3	17	gACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCag/gag	3/15	0.718143939642731	2	FACETS	0.866	0.823	0.907	0.866	0.823	0.907	CLONAL	2	TRUE	0	0.718143939642731	2		362	370	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146628	55146628	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs778762046	NA	P-0069079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	91	307	0	ENST00000257290.5:c.2302T>C	p.Tyr768His	p.Y768H	ENST00000257290	NM_006206.4	768	Tat/Cat	16/23	1	2	FACETS	0.975	0.879	1	0.975	0.879	1	CLONAL	1	TRUE	1	0.718143939642731	2		307	260	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124503486	124503486	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	133	337	0	ENST00000357628.3:c.464A>T	p.Asp155Val	p.D155V	ENST00000357628	NM_015450.2	155	gAt/gTt	8/19	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.718143939642731	2		337	359	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876659675	NA	P-0069080-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	100	305	0	ENST00000269305.4:c.764T>G	p.Ile255Ser	p.I255S	ENST00000269305	NM_001126112.2	255	aTc/aGc	7/11	0.3	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.35	1		305	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519988	NA	P-0069080-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	36	367	0	ENST00000269305.4:c.808T>C	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	Ttt/Ctt	8/11	0.3	1	FACETS	0.434	0.357	0.52	0.434	0.357	0.52	SUBCLONAL	1	TRUE	0	0.35	1		367	391	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435927	56435927	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767761157	NA	P-0069080-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	64	495	1	ENST00000407977.2:c.1210C>T	p.Arg404Cys	p.R404C	ENST00000407977		404	Cgc/Tgc	9/10	1	2	FACETS	0.599	0.518	0.686	0.599	0.518	0.686	SUBCLONAL	1	TRUE	1	0.35	2		496	611	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433053	49433053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069080-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	94	369	0	ENST00000301067.7:c.8318C>T	p.Ser2773Phe	p.S2773F	ENST00000301067	NM_003482.3	2773	tCc/tTc	33/54	NA	3	FACETS	1	0.967	1	0.607	0.542	0.676	INDETERMINATE	1	TRUE	1	0.35	3		369	520	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829935	72829940	+	frameshift_variant	Frame_Shift_Del	DEL	TAGGAG	TAGGAG	C	novel	NA	P-0069080-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	73	391	0	ENST00000268489.5:c.6641_6646delinsG	p.Pro2214ArgfsTer10	p.P2214Rfs*10	ENST00000268489	NM_006885.3	2214	cCTCCTAtc/cGtc	9/10	0.3	1	FACETS	0.761	0.668	0.861	0.761	0.668	0.861	SUBCLONAL	1	TRUE	0	0.35	1		391	452	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439933	56439942	+	frameshift_variant	Frame_Shift_Del	DEL	ATGCGCAGCA	ATGCGCAGCA	TGCTG	novel	NA	P-0069080-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	180	358	0	ENST00000407977.2:c.650_659delinsCAGCA	p.Val217AlafsTer40	p.V217Afs*40	ENST00000407977		217	gTGCTGCGCATc/gCAGCAc	6/10	1	2	FACETS	0.859	0.796	0.923	1	0.992	1	CLONAL	2	TRUE	1	0.35	2		358	599	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0069081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	246	213	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.528262129744437	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.535567884106532	2		213	425	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644703	134644703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536029159	NA	P-0069081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	73	423	0	ENST00000398015.3:c.104C>T	p.Thr35Met	p.T35M	ENST00000398015	NM_004441.4	35	aCg/aTg	2/16	NA	2	FACETS	0.508	0.444	0.575			1	INDETERMINATE	1	TRUE	NA	0.535567884106532	2		423	537	SUCCESS
APC	324	MSKCC	GRCh37	5	112175301	112175302	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0069081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	300	593	0	ENST00000257430.4:c.4010_4011del	p.Leu1337ProfsTer4	p.L1337Pfs*4	ENST00000257430	NM_000038.5	1337	cTG/c	16/16	0.523275409773949	2	FACETS	0.956	0.91	1	0.956	0.91	1	CLONAL	2	TRUE	0	0.535567884106532	2		593	586	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912198	114912198	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	122	270	0	ENST00000543371.1:c.1268A>G	p.Tyr423Cys	p.Y423C	ENST00000543371	NM_001198531.1	423	tAt/tGt	11/14	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.535567884106532	2		270	410	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952547	17952547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	228	576	0	ENST00000458235.1:c.886C>T	p.Pro296Ser	p.P296S	ENST00000458235	NM_000215.3	296	Cca/Tca	7/24	0.247123950614239	3	FACETS	0.91	0.854	0.967	0.91	0.854	0.967	INDETERMINATE	2	TRUE	1	0.535567884106532	3		576	593	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119717	17119717	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0069081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	116	552	0	ENST00000285071.4:c.1277del	p.Ile426ThrfsTer42	p.I426Tfs*42	ENST00000285071	NM_144997.5	426	aTc/ac	11/14	0.523001130056941	1	FACETS	0.947	0.864	1	0.947	0.864	1	CLONAL	1	TRUE	0	0.535567884106532	1		552	335	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0069082-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	20	233	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	0.11351109579064	4	FACETS	0.301	0.229	0.386	0.151	0.114	0.193	INDETERMINATE	1	TRUE	2	0.29	4		233	591	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252176	226252177	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0069082-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	165	222	0	ENST00000366813.1:c.125dup	p.Tyr42Ter	p.Y42*	ENST00000366813		42	tac/tAac	1/3	0.153279374246146	4	FACETS	1	0.969	1	1	0.991	1	INDETERMINATE	3	TRUE	2	0.29	4		222	452	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250882	153250892	+	frameshift_variant	Frame_Shift_Del	DEL	CGGTTACCACA	CGGTTACCACA	-	novel	NA	P-0069082-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	214	235	0	ENST00000281708.4:c.1168_1178del	p.Cys390AsnfsTer3	p.C390Nfs*3	ENST00000281708	NM_033632.3	390	TGTGGTAACCGa/a	8/12	0.153279374246146	4	FACETS	1	0.972	1	1	0.993	1	INDETERMINATE	3	TRUE	2	0.29	4		235	594	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478221	99478235	+	inframe_deletion	In_Frame_Del	DEL	GTGAGAGGATTGAGT	GTGAGAGGATTGAGT	-	novel	NA	P-0069082-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	146	340	0	ENST00000268035.6:c.3125_3139del	p.Arg1042_Phe1047delinsLeu	p.R1042_F1047delinsL	ENST00000268035	NM_000875.3	1042	cGTGAGAGGATTGAGTtt/ctt	16/21	0.115787853062931	3	FACETS	1	0.974	1	1	0.974	1	INDETERMINATE	2	TRUE	1	0.29	3		340	505	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860001	151860001	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069082-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	29	360	0	ENST00000262189.6:c.10661del	p.Thr3554AsnfsTer10	p.T3554Nfs*10	ENST00000262189	NM_170606.2	3554	aCa/aa	43/59	1	2	FACETS	0.426	0.341	0.522	0.426	0.341	0.522	SUBCLONAL	1	TRUE	1	0.29	2		360	470	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0069083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	78	392	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.166941027893925	3	FACETS	1	0.98	1	0.75	0.67	0.832	INDETERMINATE	1	TRUE	1	0.605162920953892	3		392	224	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0069083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	27	183	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.255355152358659	1	FACETS	0.75	0.615	0.894	0.75	0.615	0.894	INDETERMINATE	1	TRUE	0	0.605162920953892	1		183	83	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578266	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs942158624	NA	P-0069083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	103	462	0	ENST00000269305.4:c.583A>T	p.Ile195Phe	p.I195F	ENST00000269305	NM_001126112.2	195	Atc/Ttc	6/11	0.605162920953892	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.605162920953892	1		462	188	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427168	49427168	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	73	489	0	ENST00000301067.7:c.11320C>T	p.Gln3774Ter	p.Q3774*	ENST00000301067	NM_003482.3	3774	Cag/Tag	39/54	0.166941027893925	3	FACETS	1	0.973	1	0.674	0.599	0.753	INDETERMINATE	1	TRUE	1	0.605162920953892	3		489	233	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178941917	178941917	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	73	336	0	ENST00000263967.3:c.2236G>T	p.Asp746Tyr	p.D746Y	ENST00000263967	NM_006218.2	746	Gat/Tat	15/21	0.255355152358659	1	FACETS	0.863	0.77	0.959	0.863	0.77	0.959	INDETERMINATE	1	TRUE	0	0.605162920953892	1		336	195	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47503893	47503893	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0069083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	291	320	0	ENST00000404338.3:c.4451del	p.Pro1484GlnfsTer315	p.P1484Qfs*315	ENST00000404338	NM_004491.4	1483	tCc/tc	6/6	0.488278840176019	6	FACETS	0.93	0.897	0.961	0.93	0.897	0.961	CLONAL	6	TRUE	0	0.605162920953892	6		320	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0069084-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	102	294	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.503429307520049	1	FACETS	0.871	0.787	0.959	0.871	0.787	0.959	CLONAL	1	TRUE	0	0.503429307520049	1		294	348	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0069084-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	158	381	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.503429307520049	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.503429307520049	1		381	378	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268138	153268138	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1406877044	NA	P-0069084-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	79	363	0	ENST00000281708.4:c.670C>T	p.Arg224Ter	p.R224*	ENST00000281708	NM_033632.3	224	Cga/Tga	4/12	0.371655057743401	1	FACETS	0.484	0.427	0.545	0.484	0.427	0.545	SUBCLONAL	1	TRUE	0	0.503429307520049	1		363	485	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244214	153244214	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069084-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	124	390	0	ENST00000281708.4:c.1943T>G	p.Leu648Arg	p.L648R	ENST00000281708	NM_033632.3	648	cTa/cGa	12/12	0.371655057743401	1	FACETS	0.853	0.778	0.931	0.853	0.778	0.931	CLONAL	1	TRUE	0	0.503429307520049	1		390	432	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048797	180048797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069084-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	69	450	0	ENST00000261937.6:c.1765C>T	p.Arg589Cys	p.R589C	ENST00000261937	NM_182925.4	589	Cgc/Tgc	13/30	0.503429307520049	1	FACETS	0.517	0.452	0.586	0.517	0.452	0.586	SUBCLONAL	1	TRUE	0	0.503429307520049	1		450	397	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098557	11098557	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1213473194	NA	P-0069084-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	126	424	0	ENST00000358026.2:c.1075C>T	p.Arg359Trp	p.R359W	ENST00000358026	NM_001128849.1	359	Cgg/Tgg	6/36	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.503429307520049	2		424	458	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952088	178952088	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553826184	NA	P-0069085-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	23	352	0	ENST00000263967.3:c.3143A>G	p.His1048Arg	p.H1048R	ENST00000263967	NM_006218.2	1048	cAt/cGt	21/21	1	2	FACETS	0.368	0.287	0.463	0.368	0.287	0.463	SUBCLONAL	1	TRUE	1	0.35986255450458	2		352	347	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922973	44922973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069085-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	93	362	0	ENST00000377967.4:c.1834C>T	p.Arg612Ter	p.R612*	ENST00000377967	NM_021140.2	612	Cga/Tga	16/29	1	2	FACETS	0.843	0.751	0.941	0.843	0.751	0.941	CLONAL	1	TRUE	1	0.35986255450458	2		362	613	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943788	71943788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771815535	NA	P-0069085-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	34	486	0	ENST00000298229.2:c.1831C>T	p.Arg611Cys	p.R611C	ENST00000298229	NM_001567.3	611	Cgc/Tgc	15/28	1	2	FACETS	0.375	0.306	0.453	0.375	0.306	0.453	SUBCLONAL	1	TRUE	1	0.35986255450458	2		486	504	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720858	89720858	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1564568660	NA	P-0069085-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	72	113	0	ENST00000371953.3:c.1012del	p.Ser338LeufsTer6	p.S338Lfs*6	ENST00000371953	NM_000314.4	337	Ttt/tt	8/9	0.349618358501398	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.35986255450458	2		113	183	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952076	178952076	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1064793838	NA	P-0069085-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	39	359	0	ENST00000263967.3:c.3131A>G	p.Asn1044Ser	p.N1044S	ENST00000263967	NM_006218.2	1044	aAt/aGt	21/21	1	2	FACETS	0.625	0.519	0.742	0.625	0.519	0.742	SUBCLONAL	1	TRUE	1	0.35986255450458	2		359	347	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022645	31022645	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0069085-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	67	433	0	ENST00000375687.4:c.2131del	p.Thr711LeufsTer14	p.T711Lfs*14	ENST00000375687	NM_015338.5	710	ggA/gg	13/13	1	2	FACETS	0.732	0.637	0.834	0.732	0.637	0.834	SUBCLONAL	1	TRUE	1	0.35986255450458	2		433	509	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936076	178936076	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069085-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	33	164	0	ENST00000263967.3:c.1618C>G	p.Leu540Val	p.L540V	ENST00000263967	NM_006218.2	540	Ctc/Gtc	10/21	1	2	FACETS	1	0.838	1	1	0.838	1	CLONAL	1	TRUE	1	0.35986255450458	2		164	180	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591075	67591083	+	inframe_deletion	In_Frame_Del	DEL	TCGAGAAAT	TCGAGAAAT	-	novel	NA	P-0069085-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	41	352	0	ENST00000274335.5:c.1669_1677del	p.Arg557_Ile559del	p.R557_I559del	ENST00000274335		556	taTCGAGAAATt/tat	12/15	1	2	FACETS	0.557	0.464	0.66	0.557	0.464	0.66	SUBCLONAL	1	TRUE	1	0.35986255450458	2		352	409	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33680016	33680016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775406951	NA	P-0069085-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	51	353	0	ENST00000308377.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000308377	NM_152270.3	689	Cgg/Tgg	5/5	1	2	FACETS	0.595	0.506	0.693	0.595	0.506	0.693	SUBCLONAL	1	TRUE	1	0.35986255450458	2		353	476	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023842	27023842	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069085-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	41	341	0	ENST00000324856.7:c.948C>A	p.Tyr316Ter	p.Y316*	ENST00000324856	NM_006015.4	316	taC/taA	1/20	1	2	FACETS	0.788	0.66	0.93	0.788	0.66	0.93	CLONAL	1	TRUE	1	0.35986255450458	2		341	289	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829971	72829972	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0069085-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	73	344	0	ENST00000268489.5:c.6609dup	p.Asn2204Ter	p.N2204*	ENST00000268489	NM_006885.3	2203	-/T	9/10	1	2	FACETS	0.816	0.716	0.924	0.816	0.716	0.924	CLONAL	1	TRUE	1	0.35986255450458	2		344	497	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0069086-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	62	257	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.180076932270926	2		257	509	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956220	55956220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190050670	NA	P-0069086-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	46	305	0	ENST00000263923.4:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000263923	NM_002253.2	1032	cGa/cAa	23/30	1	2	FACETS	0.898	0.755	1	0.898	0.755	1	CLONAL	1	FALSE	1	0.180076932270926	2		305	569	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971016	21971017	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0069086-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	156	395	0	ENST00000304494.5:c.341_342delinsTT	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCC/cTT	2/3	0.180076932270926	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	FALSE	0	0.180076932270926	2		395	763	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523561	106523561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069086-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	30	322	0	ENST00000359195.3:c.2713G>A	p.Glu905Lys	p.E905K	ENST00000359195	NM_002649.2	905	Gaa/Aaa	8/11	1	2	FACETS	0.571	0.458	0.698	0.571	0.458	0.698	SUBCLONAL	1	FALSE	1	0.180076932270926	2		322	584	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295253	+	upstream_gene_variant	5'Flank	ONP	GAGG	GAGG	AAGA	novel	NA	P-0069086-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	136	330	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.973	1	1	0.991	1	CLONAL	2	FALSE	1	0.180076932270926	2		330	644	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224158	39224158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069086-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	65	256	0	ENST00000402219.2:c.2986C>T	p.Pro996Ser	p.P996S	ENST00000402219	NM_005633.3	996	Ccg/Tcg	19/23	1	2	FACETS	0.839	0.73	0.957	1	0.976	1	CLONAL	2	FALSE	1	0.180076932270926	2		256	430	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47502617	47502617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1458450841	NA	P-0069086-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	41	328	0	ENST00000404338.3:c.4093C>T	p.Pro1365Ser	p.P1365S	ENST00000404338	NM_004491.4	1365	Cca/Tca	5/6	1	2	FACETS	0.882	0.735	1	0.882	0.735	1	CLONAL	1	FALSE	1	0.180076932270926	2		328	516	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290286	15290286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069086-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	43	440	0	ENST00000263388.2:c.3349G>A	p.Asp1117Asn	p.D1117N	ENST00000263388	NM_000435.2	1117	Gat/Aat	21/33	1	2	FACETS	0.615	0.513	0.729	0.615	0.513	0.729	SUBCLONAL	1	FALSE	1	0.180076932270926	2		440	776	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157516	106157516	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0069086-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	63	338	0	ENST00000380013.4:c.2417T>G	p.Leu806Arg	p.L806R	ENST00000380013	NM_001127208.2	806	cTg/cGg	3/11	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	FALSE	1	0.180076932270926	2		338	630	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561353	9561354	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0069086-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	67	416	1	ENST00000353224.5:c.428_429delinsAT	p.Thr143Asn	p.T143N	ENST00000353224	NM_177990.2	143	aCC/aAT	4/10	0.129712441760409	3	FACETS	0.974	0.845	1			1	CLONAL	1	FALSE	NA	0.180076932270926	3		417	833	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114143	73114143	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069086-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	70	349	0	ENST00000356692.5:c.779C>T	p.Ala260Val	p.A260V	ENST00000356692		260	gCc/gTc	8/9	0.180076932270926	3	FACETS	1	0.933	1	0.558	0.485	0.636	CLONAL	1	FALSE	1	0.180076932270926	3		349	760	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0069111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	40	206	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.189638328235045	12	FACETS	1	0.857	1	0.206	0.171	0.245	CLONAL	2	TRUE	2	0.189638328235045	12		206	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0069111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	79	234	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	NA	2	FACETS	0.942	0.832	1			1	INDETERMINATE	2	TRUE	NA	0.189638328235045	2		234	442	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0069111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	461	301	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.189638328235045	12	FACETS	1	0.966	1	1	0.966	1	CLONAL	10	TRUE	2	0.189638328235045	12		301	941	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131951767	131951767	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	40	201	0	ENST00000265335.6:c.3109G>C	p.Glu1037Gln	p.E1037Q	ENST00000265335		1037	Gaa/Caa	20/25	0.138723613185552	4	FACETS	0.865	0.718	1	0.433	0.359	0.515	CLONAL	1	TRUE	2	0.189638328235045	4		201	580	SUCCESS
AR	367	MSKCC	GRCh37	X	66905906	66905906	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137852573	NA	P-0069111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	32	226	0	ENST00000374690.3:c.1823G>A	p.Arg608Gln	p.R608Q	ENST00000374690	NM_000044.3	608	cGa/cAa	3/8	0.189638328235045	3	FACETS	0.735	0.595	0.892	0.367	0.297	0.446	SUBCLONAL	1	TRUE	1	0.189638328235045	3		226	503	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156087	106156087	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	112	347	0	ENST00000380013.4:c.988G>C	p.Glu330Gln	p.E330Q	ENST00000380013	NM_001127208.2	330	Gag/Cag	3/11	0.138723613185552	4	FACETS	1	0.911	1	1	0.911	1	CLONAL	2	TRUE	2	0.189638328235045	4		347	694	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39212966	39212966	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0069111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	104	268	0	ENST00000402219.2:c.4001G>C	p.Ter1334SerextTer31	p.*1334Sext*31	ENST00000402219	NM_005633.3	1334	tGa/tCa	23/23	0.138723613185552	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	2	0.189638328235045	4		268	582	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573855	41573855	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	64	367	0	ENST00000263253.7:c.6140C>G	p.Ser2047Cys	p.S2047C	ENST00000263253	NM_001429.3	2047	tCt/tGt	31/31	0.189638328235045	4	FACETS	1	0.904	1	0.528	0.457	0.606	CLONAL	1	TRUE	2	0.189638328235045	4		367	760	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865087	57865087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	79	292	0	ENST00000228682.2:c.2564C>T	p.Ser855Phe	p.S855F	ENST00000228682	NM_005269.2	855	tCt/tTt	12/12	0.174251489635601	4	FACETS	0.792	0.697	0.894	0.396	0.348	0.447	SUBCLONAL	2	TRUE	0	0.189638328235045	4		292	626	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319369	62319369	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774688252	NA	P-0069111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	131	324	0	ENST00000360203.5:c.1561G>A	p.Asp521Asn	p.D521N	ENST00000360203	NM_001283009.1	521	Gat/Aat	18/35	0.189638328235045	8	FACETS	1	0.963	1	0.375	0.339	0.412	CLONAL	2	TRUE	2	0.189638328235045	8		324	964	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038443	180038443	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1581616817	NA	P-0069111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	103	299	0	ENST00000261937.6:c.3574C>T	p.Gln1192Ter	p.Q1192*	ENST00000261937	NM_182925.4	1192	Cag/Tag	27/30	0.138723613185552	4	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	2	0.189638328235045	4		299	606	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352401	143352402	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0069111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	50	166	0	ENST00000262992.4:c.11_12del	p.Lys4ArgfsTer19	p.K4Rfs*19	ENST00000262992	NM_001101669.1	4	aAA/a	2/24	0.138723613185552	4	FACETS	0.765	0.651	0.89	0.765	0.651	0.89	SUBCLONAL	2	TRUE	2	0.189638328235045	4		166	410	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367093	40367093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1225122779	NA	P-0069111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	91	384	0	ENST00000397332.2:c.104C>T	p.Ser35Leu	p.S35L	ENST00000397332	NM_001033082.2	35	tCg/tTg	2/3	0.189638328235045	2	FACETS	0.854	0.76	0.954	0.854	0.76	0.954	CLONAL	2	TRUE	0	0.189638328235045	2		384	562	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218368	69218369	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0069111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	56	215	0	ENST00000462284.1:c.461dup	p.Ser155IlefsTer7	p.S155Ifs*7	ENST00000462284	NM_002392.5	154	tca/tCca	7/11	0.189638328235045	12	FACETS	1	0.957	1	0.168	0.143	0.195	CLONAL	1	TRUE	4	0.189638328235045	12		215	857	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124499073	124499073	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	16	166	0	ENST00000357628.3:c.640C>T	p.Gln214Ter	p.Q214*	ENST00000357628	NM_015450.2	214	Caa/Taa	9/19	0.189638328235045	2	FACETS	0.537	0.397	0.706	0.269	0.198	0.353	SUBCLONAL	1	TRUE	0	0.189638328235045	2		166	314	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0069114-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	54	269	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.958	0.825	1	0.958	0.825	1	CLONAL	1	TRUE	1	0.39	2		269	289	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0069114-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	176	538	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.296557442433405	2	FACETS	0.99	0.921	1	0.99	0.921	1	CLONAL	2	TRUE	0	0.39	2		538	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0069115-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	31	472	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	1	2	FACETS	0.465	0.375	0.568	0.465	0.375	0.568	SUBCLONAL	1	TRUE	1	0.2	2		472	666	SUCCESS
APC	324	MSKCC	GRCh37	5	112175504	112175510	+	frameshift_variant	Frame_Shift_Del	DEL	GTTCAGA	GTTCAGA	-	novel	NA	P-0069115-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	16	422	0	ENST00000257430.4:c.4215_4221del	p.Gln1406AsnfsTer7	p.Q1406Nfs*7	ENST00000257430	NM_000038.5	1405	GTTCAGAgt/gt	16/16	1	2	FACETS	0.516	0.381	0.678	0.516	0.381	0.678	SUBCLONAL	1	TRUE	1	0.2	2		422	310	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878068	48878069	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0069116-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	81	280	0	ENST00000267163.4:c.25dup	p.Thr9AsnfsTer22	p.T9Nfs*22	ENST00000267163	NM_000321.2	7	cga/cgAa	1/27	1	2	FACETS	0.837	0.738	0.944	0.837	0.738	0.944	CLONAL	1	TRUE	1	0.31	2		280	624	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418400	139418400	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069116-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	56	311	0	ENST00000277541.6:c.172C>T	p.Gln58Ter	p.Q58*	ENST00000277541	NM_017617.3	58	Cag/Tag	3/34	0.301941537505844	1	FACETS	0.569	0.487	0.657	0.569	0.487	0.657	SUBCLONAL	1	TRUE	0	0.31	1		311	537	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40856670	40856670	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069116-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	80	218	0	ENST00000428826.2:c.1967G>T	p.Gly656Val	p.G656V	ENST00000428826		656	gGa/gTa	18/21	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.31	2		218	491	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793411	18793411	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069116-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	60	237	0	ENST00000266497.5:c.4108T>A	p.Leu1370Ile	p.L1370I	ENST00000266497		1370	Tta/Ata	30/31	0.273665214798458	1	FACETS	0.693	0.598	0.796	0.693	0.598	0.796	SUBCLONAL	1	TRUE	0	0.31	1		237	472	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088715	27088715	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069116-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	80	321	0	ENST00000324856.7:c.2324A>T	p.Gln775Leu	p.Q775L	ENST00000324856	NM_006015.4	775	cAg/cTg	7/20	1	2	FACETS	0.751	0.661	0.848	0.751	0.661	0.848	SUBCLONAL	1	TRUE	1	0.31	2		321	687	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980813	40980813	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069116-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	85	283	0	ENST00000373198.4:c.1673C>A	p.Pro558Gln	p.P558Q	ENST00000373198	NM_133170.3	558	cCa/cAa	10/32	0.301941537505844	1	FACETS	0.74	0.655	0.832	0.74	0.655	0.832	SUBCLONAL	1	TRUE	0	0.31	1		283	626	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579503	+	frameshift_variant	Frame_Shift_Del	DEL	CGGGGGGAGCAGCCTCTGGCATTCTGGGAGCTTC	CGGGGGGAGCAGCCTCTGGCATTCTGGGAGCTTC	-	novel	NA	P-0069116-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	108	422	0	ENST00000269305.4:c.184_217del	p.Glu62TrpfsTer50	p.E62Wfs*50	ENST00000269305	NM_001126112.2	62	GAAGCTCCCAGAATGCCAGAGGCTGCTCCCCCCGtg/tg	4/11	1	2	FACETS	0.949	0.852	1	0.949	0.852	1	CLONAL	1	TRUE	1	0.31	2		422	734	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667596	29667596	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0069116-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	91	285	0	ENST00000356175.3:c.6932C>G	p.Ser2311Ter	p.S2311*	ENST00000356175	NM_000267.3	2311	tCa/tGa	46/57	1	2	FACETS	0.987	0.878	1	0.987	0.878	1	CLONAL	1	TRUE	1	0.31	2		285	595	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	219	536	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.787643167715454	2		536	546	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	145	329	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.987	0.912	1	0.987	0.912	1	CLONAL	1	TRUE	1	0.787643167715454	2		329	373	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175874	24175874	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	97	309	0	ENST00000263121.7:c.1102C>T	p.Gln368Ter	p.Q368*	ENST00000263121	NM_003073.3	368	Cag/Tag	8/9	1	2	FACETS	0.36	0.32	0.401	0.36	0.32	0.401	SUBCLONAL	1	TRUE	1	0.787643167715454	2		309	685	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227959	123227959	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	76	346	0	ENST00000218089.9:c.3670G>A	p.Glu1224Lys	p.E1224K	ENST00000218089	NM_001042749.1	1224	Gag/Aag	33/35	1	2	FACETS	0.321	0.281	0.363	0.321	0.281	0.363	SUBCLONAL	1	TRUE	1	0.787643167715454	2		346	602	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	92	397	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	0.354	0.314	0.396	0.354	0.314	0.396	SUBCLONAL	1	TRUE	1	0.787643167715454	2		397	660	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814797	139814797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144427288	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	337	462	0	ENST00000247668.2:c.790G>A	p.Ala264Thr	p.A264T	ENST00000247668	NM_021138.3	264	Gcg/Acg	8/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.787643167715454	2		462	827	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1555525367	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	153	355	0	ENST00000269305.4:c.783-1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	0.633	0.581	0.686	0.633	0.581	0.686	SUBCLONAL	1	TRUE	1	0.787643167715454	2		355	614	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021637	31021637	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1264792645	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	104	433	0	ENST00000375687.4:c.1636C>T	p.Gln546Ter	p.Q546*	ENST00000375687	NM_015338.5	546	Cag/Tag	12/13	1	2	FACETS	0.338	0.302	0.376	0.338	0.302	0.376	SUBCLONAL	1	TRUE	1	0.787643167715454	2		433	782	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031876	10031876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1452471642	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	103	390	0	ENST00000330684.3:c.947C>T	p.Ala316Val	p.A316V	ENST00000330684	NM_001134407.1	316	gCc/gTc	3/13	1	2	FACETS	0.375	0.335	0.417	0.375	0.335	0.417	SUBCLONAL	1	TRUE	1	0.787643167715454	2		390	698	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845749	68845749	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	119	433	0	ENST00000261769.5:c.995G>A	p.Gly332Glu	p.G332E	ENST00000261769	NM_004360.3	332	gGg/gAg	7/16	1	2	FACETS	0.454	0.41	0.5	0.454	0.41	0.5	SUBCLONAL	1	TRUE	1	0.787643167715454	2		433	666	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202413	123202413	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	98	233	0	ENST00000218089.9:c.2266-1G>A		p.X756_splice	ENST00000218089	NM_001042749.1	756			1	2	FACETS	0.671	0.603	0.741	0.671	0.603	0.741	SUBCLONAL	1	TRUE	1	0.787643167715454	2		233	371	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445140	49445140	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	316	533	0	ENST00000301067.7:c.2326G>T	p.Glu776Ter	p.E776*	ENST00000301067	NM_003482.3	776	Gag/Tag	10/54	1	2	FACETS	0.974	0.923	1	0.974	0.923	1	CLONAL	1	TRUE	1	0.787643167715454	2		533	824	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636787	176636787	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	127	497	0	ENST00000439151.2:c.1387G>T	p.Asp463Tyr	p.D463Y	ENST00000439151	NM_022455.4	463	Gat/Tat	5/23	1	2	FACETS	0.391	0.354	0.43	0.391	0.354	0.43	SUBCLONAL	1	TRUE	1	0.787643167715454	2		497	824	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79968094	79968094	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1228477054	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	99	408	0	ENST00000265081.6:c.824A>G	p.His275Arg	p.H275R	ENST00000265081	NM_002439.4	275	cAt/cGt	5/24	1	2	FACETS	0.346	0.308	0.385	0.346	0.308	0.385	SUBCLONAL	1	TRUE	1	0.787643167715454	2		408	727	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134277	11134277	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	36	388	0	ENST00000358026.2:c.2943G>T	p.Lys981Asn	p.K981N	ENST00000358026	NM_001128849.1	981	aaG/aaT	20/36	1	2	FACETS	0.139	0.113	0.168	0.139	0.113	0.168	SUBCLONAL	1	TRUE	1	0.787643167715454	2		388	658	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662401	117662401	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	124	466	0	ENST00000368508.3:c.4976C>A	p.Pro1659Gln	p.P1659Q	ENST00000368508	NM_002944.2	1659	cCa/cAa	30/43	1	2	FACETS	0.373	0.337	0.41	0.373	0.337	0.41	SUBCLONAL	1	TRUE	1	0.787643167715454	2		466	845	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451797	29451797	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	64	203	0	ENST00000389048.3:c.2768G>T	p.Gly923Val	p.G923V	ENST00000389048	NM_004304.4	923	gGg/gTg	16/29	1	2	FACETS	0.511	0.446	0.581	0.511	0.446	0.581	SUBCLONAL	1	TRUE	1	0.787643167715454	2		203	318	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458568	12458568	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	61	519	0	ENST00000287820.6:c.1185G>C	p.Lys395Asn	p.K395N	ENST00000287820	NM_015869.4	395	aaG/aaC	6/7	0.787643167715454	2	FACETS	0.176	0.151	0.203	0.088	0.075	0.102	SUBCLONAL	1	TRUE	0	0.787643167715454	2		519	880	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422182	47422182	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	216	471	0	ENST00000404338.3:c.250G>T	p.Glu84Ter	p.E84*	ENST00000404338	NM_004491.4	84	Gag/Tag	1/6	1	2	FACETS	0.714	0.666	0.764	0.714	0.666	0.764	SUBCLONAL	1	TRUE	1	0.787643167715454	2		471	768	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159001	24159001	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768379745	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	38	419	0	ENST00000263121.7:c.673G>T	p.Asp225Tyr	p.D225Y	ENST00000263121	NM_003073.3	225	Gat/Tat	6/9	1	2	FACETS	0.133	0.109	0.159	0.133	0.109	0.159	SUBCLONAL	1	TRUE	1	0.787643167715454	2		419	727	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095965	11095965	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	55	391	0	ENST00000358026.2:c.239A>G	p.His80Arg	p.H80R	ENST00000358026	NM_001128849.1	80	cAt/cGt	3/36	1	2	FACETS	0.193	0.164	0.224	0.193	0.164	0.224	SUBCLONAL	1	TRUE	1	0.787643167715454	2		391	724	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022446	31022446	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	79	427	0	ENST00000375687.4:c.1931G>T	p.Gly644Val	p.G644V	ENST00000375687	NM_015338.5	644	gGg/gTg	13/13	1	2	FACETS	0.273	0.24	0.309	0.273	0.24	0.309	SUBCLONAL	1	TRUE	1	0.787643167715454	2		427	735	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2056823	2056823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752101801	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	106	401	0	ENST00000349721.2:c.1325G>A	p.Arg442Lys	p.R442K	ENST00000349721	NM_003070.3	442	aGg/aAg	7/34	1	2	FACETS	0.346	0.31	0.385	0.346	0.31	0.385	SUBCLONAL	1	TRUE	1	0.787643167715454	2		401	777	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132531	11132531	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	80	464	0	ENST00000358026.2:c.2747A>T	p.Asn916Ile	p.N916I	ENST00000358026	NM_001128849.1	916	aAc/aTc	19/36	1	2	FACETS	0.253	0.222	0.286	0.253	0.222	0.286	SUBCLONAL	1	TRUE	1	0.787643167715454	2		464	804	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124492004	124492004	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	62	271	0	ENST00000357628.3:c.871G>T	p.Asp291Tyr	p.D291Y	ENST00000357628	NM_015450.2	291	Gat/Tat	11/19	1	2	FACETS	0.373	0.323	0.427	0.373	0.323	0.427	SUBCLONAL	1	TRUE	1	0.787643167715454	2		271	422	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425051	49425052	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	303	515	0	ENST00000301067.7:c.13436_13437del	p.Gly4479ValfsTer7	p.G4479Vfs*7	ENST00000301067	NM_003482.3	4479	gGG/g	39/54	1	2	FACETS	0.951	0.9	1	0.951	0.9	1	CLONAL	1	TRUE	1	0.787643167715454	2		515	809	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42026792	42026792	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	179	340	0	ENST00000219905.7:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000219905	NM_001164273.1	1306	Gaa/Taa	12/24	1	2	FACETS	0.709	0.656	0.763	0.709	0.656	0.763	SUBCLONAL	1	TRUE	1	0.787643167715454	2		340	641	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994785	73994785	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	267	433	0	ENST00000318443.5:c.269C>A	p.Ala90Asp	p.A90D	ENST00000318443	NM_001024736.1	90	gCc/gAc	3/10	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.787643167715454	2		433	669	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660502	67660502	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	90	310	0	ENST00000264010.4:c.1402A>T	p.Lys468Ter	p.K468*	ENST00000264010	NM_006565.3	468	Aaa/Taa	8/12	1	2	FACETS	0.359	0.318	0.402	0.359	0.318	0.402	SUBCLONAL	1	TRUE	1	0.787643167715454	2		310	637	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223949	2223949	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	107	442	0	ENST00000326181.6:c.1163G>A	p.Cys388Tyr	p.C388Y	ENST00000326181	NM_032271.2	388	tGc/tAc	13/21	1	2	FACETS	0.351	0.315	0.39	0.351	0.315	0.39	SUBCLONAL	1	TRUE	1	0.787643167715454	2		442	774	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104572	193104572	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	300	426	0	ENST00000367435.3:c.359G>T	p.Arg120Leu	p.R120L	ENST00000367435	NM_024529.4	120	cGa/cTa	4/17	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.787643167715454	2		426	734	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76953071	76953071	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	63	246	0	ENST00000373344.5:c.242G>T	p.Arg81Met	p.R81M	ENST00000373344	NM_000489.3	81	aGg/aTg	4/35	1	2	FACETS	0.388	0.337	0.444	0.388	0.337	0.444	SUBCLONAL	1	TRUE	1	0.787643167715454	2		246	412	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024066	31024066	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	311	522	0	ENST00000375687.4:c.3551C>G	p.Thr1184Arg	p.T1184R	ENST00000375687	NM_015338.5	1184	aCa/aGa	13/13	1	2	FACETS	0.976	0.925	1	0.976	0.925	1	CLONAL	1	TRUE	1	0.787643167715454	2		522	809	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478151	99478151	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	152	434	0	ENST00000268035.6:c.3055A>T	p.Lys1019Ter	p.K1019*	ENST00000268035	NM_000875.3	1019	Aag/Tag	16/21	1	2	FACETS	0.47	0.429	0.511	0.47	0.429	0.511	SUBCLONAL	1	TRUE	1	0.787643167715454	2		434	822	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819753	170819753	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	30	178	0	ENST00000296930.5:c.392A>T	p.Glu131Val	p.E131V	ENST00000296930	NM_002520.6	131	gAg/gTg	5/11	1	2	FACETS	0.253	0.204	0.308	0.253	0.204	0.308	SUBCLONAL	1	TRUE	1	0.787643167715454	2		178	301	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957857	1957858	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	103	411	1	ENST00000382891.5:c.2823_2824delinsTT	p.Glu941_Gly942delinsAspTrp	p.E941_G942delinsDW	ENST00000382891	NM_133335.3	941	gaGGgg/gaTTgg	15/22	1	2	FACETS	0.367	0.328	0.408	0.367	0.328	0.408	SUBCLONAL	1	TRUE	1	0.787643167715454	2		412	713	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350041	89350041	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	108	517	0	ENST00000301030.4:c.2909A>T	p.Glu970Val	p.E970V	ENST00000301030	NM_001256183.1	970	gAg/gTg	9/13	1	2	FACETS	0.329	0.295	0.366	0.329	0.295	0.366	SUBCLONAL	1	TRUE	1	0.787643167715454	2		517	833	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247159	153247159	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	98	341	0	ENST00000281708.4:c.1643A>C	p.Gln548Pro	p.Q548P	ENST00000281708	NM_033632.3	548	cAg/cCg	10/12	1	2	FACETS	0.398	0.355	0.443	0.398	0.355	0.443	SUBCLONAL	1	TRUE	1	0.787643167715454	2		341	626	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526544	66526544	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	217	403	0	ENST00000358598.2:c.1100A>T	p.Lys367Ile	p.K367I	ENST00000358598	NM_212471.2	367	aAa/aTa	11/11	1	2	FACETS	0.644	0.599	0.689	0.644	0.599	0.689	SUBCLONAL	1	TRUE	1	0.787643167715454	2		403	856	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52709215	52709215	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	75	330	0	ENST00000322088.6:c.170-1G>T		p.X57_splice	ENST00000322088	NM_014225.5	57			1	2	FACETS	0.323	0.283	0.366	0.323	0.283	0.366	SUBCLONAL	1	TRUE	1	0.787643167715454	2		330	590	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132904	30132904	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	104	355	0	ENST00000331968.5:c.696+1G>T		p.X232_splice	ENST00000331968	NM_002742.2	232			1	2	FACETS	0.364	0.326	0.404	0.364	0.326	0.404	SUBCLONAL	1	TRUE	1	0.787643167715454	2		355	726	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259503	89259503	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	126	427	0	ENST00000336596.2:c.647T>C	p.Val216Ala	p.V216A	ENST00000336596	NM_005233.5	216	gTa/gCa	3/17	1	2	FACETS	0.421	0.381	0.463	0.421	0.381	0.463	SUBCLONAL	1	TRUE	1	0.787643167715454	2		427	760	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934606	9934606	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	51	418	0	ENST00000330684.3:c.1549G>C	p.Glu517Gln	p.E517Q	ENST00000330684	NM_001134407.1	517	Gaa/Caa	7/13	1	2	FACETS	0.183	0.155	0.214	0.183	0.155	0.214	SUBCLONAL	1	TRUE	1	0.787643167715454	2		418	708	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397734	49397734	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	652	388	0	ENST00000418115.1:c.490A>G	p.Lys164Glu	p.K164E	ENST00000418115	NM_001664.2	164	Aaa/Gaa	5/5	0.787643167715454	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.787643167715454	2		388	810	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72834011	72834016	+	frameshift_variant	Frame_Shift_Del	DEL	CATCTC	CATCTC	A	novel	NA	P-0069118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	111	369	0	ENST00000268489.5:c.3877_3882delinsT	p.Glu1293CysfsTer29	p.E1293Cfs*29	ENST00000268489	NM_006885.3	1293	GAGATG/T	8/10	1	2	FACETS	0.41	0.368	0.453	0.41	0.368	0.453	SUBCLONAL	1	TRUE	1	0.787643167715454	2		369	688	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0069119-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	46	298	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		298	378	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250883	153250883	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069119-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	14	351	0	ENST00000281708.4:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000281708	NM_033632.3	393	Cga/Tga	8/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		351	364	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0069119-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	26	452	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		452	494	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435692	110435700	+	inframe_deletion	In_Frame_Del	DEL	GCTGGGCAG	GCTGGGCAG	-	rs752700578	NA	P-0069119-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	22	454	0	ENST00000375856.3:c.2701_2709del	p.Leu901_Ser903del	p.L901_S903del	ENST00000375856	NM_003749.2	901	CTGCCCAGC/-	1/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		454	398	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165864	47165864	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069119-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	29	516	0	ENST00000409792.3:c.262T>G	p.Phe88Val	p.F88V	ENST00000409792	NM_014159.6	88	Ttt/Gtt	3/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		516	440	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253766	153253766	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069119-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	27	306	0	ENST00000281708.4:c.967G>T	p.Glu323Ter	p.E323*	ENST00000281708	NM_033632.3	323	Gag/Tag	6/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		306	355	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593362	48593385	+	splice_region_variant,intron_variant	Splice_Region	DEL	AAATGTAATTTCTTTTTTCTTCCT	AAATGTAATTTCTTTTTTCTTCCT	-	novel	NA	P-0069119-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	15	283	0	ENST00000342988.3:c.1140-25_1140-2del		p.X380_splice	ENST00000342988	NM_005359.5	380			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		283	299	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0069138-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	441	403	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.260250335340821	3	FACETS	0.921	0.886	0.956			1	INDETERMINATE	3	TRUE	NA	0.500174423185675	3		404	798	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0069138-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	209	312	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.500174423185675	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.500174423185675	1		312	551	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0069138-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	194	330	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.500174423185675	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.500174423185675	1		330	519	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910883	114910883	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1477809102	NA	P-0069138-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	236	296	0	ENST00000543371.1:c.1001+1G>A		p.X334_splice	ENST00000543371	NM_001198531.1	334			1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.500174423185675	2		296	677	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020758	26020758	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069138-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	45	313	0	ENST00000357647.3:c.41G>C	p.Gly14Ala	p.G14A	ENST00000357647	NM_003529.2	14	gGc/gCc	1/1	0.159657637497419	2	FACETS	0.239	0.2	0.282	0.119	0.1	0.141	INDETERMINATE	1	TRUE	0	0.500174423185675	2		313	754	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90970996	90970996	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1563538728	NA	P-0069138-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	98	280	0	ENST00000265433.3:c.1081A>G	p.Thr361Ala	p.T361A	ENST00000265433	NM_002485.4	361	Aca/Gca	9/16	0.159657637497419	2	FACETS	0.714	0.639	0.793	0.357	0.319	0.397	INDETERMINATE	1	TRUE	0	0.500174423185675	2		280	549	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12632469	12632469	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0069138-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	93	327	0	ENST00000251849.4:c.1198A>C	p.Thr400Pro	p.T400P	ENST00000251849	NM_002880.3	400	Aca/Cca	12/17	0.159657637497419	2	FACETS	0.542	0.482	0.606	0.271	0.241	0.303	INDETERMINATE	1	TRUE	0	0.500174423185675	2		327	686	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0069150-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	19	269	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.738	0.56	0.947	0.738	0.56	0.947	CLONAL	1	TRUE	1	0.18	2		269	286	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0069150-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	31	505	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.505	0.407	0.617	0.505	0.407	0.617	SUBCLONAL	1	TRUE	1	0.18	2		505	682	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573443	41573443	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069150-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	56	695	0	ENST00000263253.7:c.5728C>T	p.Pro1910Ser	p.P1910S	ENST00000263253	NM_001429.3	1910	Cct/Tct	31/31	1	2	FACETS	0.669	0.571	0.776	0.669	0.571	0.776	SUBCLONAL	1	TRUE	1	0.18	2		695	930	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0069153-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	72	295	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.325559151652575	2	FACETS	0.802	0.71	0.897	0.802	0.71	0.897	CLONAL	2	TRUE	0	0.374164628324022	2		295	240	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552705	226552705	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs776746526	NA	P-0069153-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	82	412	0	ENST00000366794.5:c.2656G>A	p.Val886Met	p.V886M	ENST00000366794	NM_001618.3	886	Gtg/Atg	19/23	0.248726943968252	4	FACETS	0.907	0.807	1	0.907	0.807	1	CLONAL	2	TRUE	2	0.374164628324022	4		412	332	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337261	89337261	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069153-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	46	263	0	ENST00000301030.4:c.7770G>T	p.Trp2590Cys	p.W2590C	ENST00000301030	NM_001256183.1	2590	tgG/tgT	12/13	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.374164628324022	2		263	193	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0069153-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	132	295	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.308631068928523	1	FACETS	0.731	0.665	0.8	0.731	0.665	0.8	SUBCLONAL	1	TRUE	0	0.42552630761424	1		295	668	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552705	226552705	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs776746526	NA	P-0069153-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	161	412	0	ENST00000366794.5:c.2656G>A	p.Val886Met	p.V886M	ENST00000366794	NM_001618.3	886	Gtg/Atg	19/23	0.272356281670619	1	FACETS	0.726	0.667	0.789	0.726	0.667	0.789	SUBCLONAL	1	TRUE	0	0.42552630761424	1		412	820	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337261	89337261	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069153-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	83	263	0	ENST00000301030.4:c.7770G>T	p.Trp2590Cys	p.W2590C	ENST00000301030	NM_001256183.1	2590	tgG/tgT	12/13	1	2	FACETS	0.793	0.702	0.89	0.793	0.702	0.89	SUBCLONAL	1	TRUE	1	0.42552630761424	2		263	492	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157488298	157488298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs527731946	NA	P-0069153-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	56	371	0	ENST00000346085.5:c.3004G>A	p.Ala1002Thr	p.A1002T	ENST00000346085	NM_020732.3	1002	Gcc/Acc	10/20	1	2	FACETS	0.38	0.325	0.441	0.38	0.325	0.441	SUBCLONAL	1	TRUE	1	0.42552630761424	2		371	692	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249680	110249680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747664688	NA	P-0069153-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	58	478	0	ENST00000374672.4:c.995C>T	p.Pro332Leu	p.P332L	ENST00000374672	NM_004235.4	332	cCt/cTt	3/5	1	2	FACETS	0.266	0.227	0.308	0.266	0.227	0.308	SUBCLONAL	1	TRUE	1	0.42552630761424	2		478	1025	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032002	10032002	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs539907710	NA	P-0069153-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	35	420	0	ENST00000330684.3:c.821C>A	p.Ser274Ter	p.S274*	ENST00000330684	NM_001134407.1	274	tCg/tAg	3/13	0.42552630761424	1	FACETS	0.243	0.199	0.293	0.243	0.199	0.293	SUBCLONAL	1	TRUE	0	0.42552630761424	1		420	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0069156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	148	343	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.288350979561811	2	FACETS	0.925	0.849	1	0.925	0.849	1	CLONAL	2	TRUE	0	0.288350979561811	2		343	555	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12647733	12647733	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761703202	NA	P-0069156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	33	288	0	ENST00000251849.4:c.647G>A	p.Arg216His	p.R216H	ENST00000251849	NM_002880.3	216	cGt/cAt	6/17	0.27555223254672	3	FACETS	0.499	0.405	0.604	0.249	0.202	0.302	SUBCLONAL	1	TRUE	1	0.288350979561811	3		288	525	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134277	11134277	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	70	336	0	ENST00000358026.2:c.2943G>C	p.Lys981Asn	p.K981N	ENST00000358026	NM_001128849.1	981	aaG/aaC	20/36	0.288350979561811	2	FACETS	1	0.906	1	0.522	0.456	0.593	CLONAL	1	TRUE	0	0.288350979561811	2		336	465	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227073	2227073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	85	429	0	ENST00000398665.3:c.4553C>T	p.Thr1518Ile	p.T1518I	ENST00000398665	NM_032482.2	1518	aCc/aTc	27/28	0.288350979561811	2	FACETS	1	0.948	1	0.561	0.497	0.63	CLONAL	1	TRUE	0	0.288350979561811	2		429	525	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176488	142176488	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	56	272	0	ENST00000350721.4:c.7613T>C	p.Val2538Ala	p.V2538A	ENST00000350721	NM_001184.3	2538	gTt/gCt	45/47	0.262360737390986	4	FACETS	0.923	0.791	1	0.462	0.395	0.534	CLONAL	1	TRUE	2	0.288350979561811	4		272	542	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210994	36210994	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	107	447	0	ENST00000222270.7:c.745A>C	p.Lys249Gln	p.K249Q	ENST00000222270	NM_014727.1	249	Aaa/Caa	3/37	0.27555223254672	3	FACETS	1	0.951	1	0.55	0.493	0.61	CLONAL	1	TRUE	1	0.288350979561811	3		447	772	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43817973	43817973	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs971379181	NA	P-0069156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	146	430	0	ENST00000372470.3:c.1652C>T	p.Pro551Leu	p.P551L	ENST00000372470	NM_005373.2	551	cCg/cTg	11/12	0.27555223254672	3	FACETS	0.847	0.775	0.922	0.847	0.775	0.922	CLONAL	2	TRUE	1	0.288350979561811	3		430	684	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538260	187538260	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	64	334	0	ENST00000441802.2:c.8974T>C	p.Tyr2992His	p.Y2992H	ENST00000441802	NM_005245.3	2992	Tac/Cac	11/27	0.262360737390986	4	FACETS	0.973	0.843	1	0.486	0.421	0.557	CLONAL	1	TRUE	2	0.288350979561811	4		334	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576926	7576941	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTAGGAAAGAGGCAA	GCTAGGAAAGAGGCAA	-	novel	NA	P-0069157-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	61	311	0	ENST00000269305.4:c.920-15_920del		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	0.397337613990047	6	FACETS	0.995	0.867	1	0.497	0.433	0.565	CLONAL	2	FALSE	2	0.446603077570126	6		311	260	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89874772	89874772	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069157-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	36	216	0	ENST00000389301.3:c.526T>A	p.Ser176Thr	p.S176T	ENST00000389301	NM_000135.2	176	Tct/Act	6/43	0.274767539820162	5	FACETS	1	0.945	1	0.463	0.384	0.549	CLONAL	1	FALSE	2	0.446603077570126	5		216	194	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0069161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	39	550	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.726043641789294	1	FACETS	0.358	0.3	0.421	0.358	0.3	0.421	SUBCLONAL	1	TRUE	0	0.726043641789294	1		550	191	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971133	21971133	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	18	587	0	ENST00000304494.5:c.225del	p.Ala76ProfsTer70	p.A76Pfs*70	ENST00000304494	NM_000077.4	75	ccC/cc	2/3	0.726043641789294	1	FACETS	0.16	0.121	0.207	0.16	0.121	0.207	SUBCLONAL	1	TRUE	0	0.726043641789294	1		587	197	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692908	89692908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514560	NA	P-0069161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	157	349	0	ENST00000371953.3:c.392C>T	p.Thr131Ile	p.T131I	ENST00000371953	NM_000314.4	131	aCt/aTt	5/9	0.726043641789294	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.726043641789294	1		349	271	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974678	21974678	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	rs587778189	NA	P-0069161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	23	545	0	ENST00000304494.5:c.149A>T	p.Gln50Leu	p.Q50L	ENST00000304494	NM_000077.4	50	cAg/cTg	1/3	0.726043641789294	1	FACETS	0.191	0.149	0.239	0.191	0.149	0.239	SUBCLONAL	1	TRUE	0	0.726043641789294	1		545	211	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495683	72495683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	171	418	0	ENST00000477973.2:c.389G>A	p.Cys130Tyr	p.C130Y	ENST00000477973	NM_012234.5	130	tGc/tAc	1/4	0.726043641789294	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.726043641789294	1		418	287	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39774523	39774530	+	protein_altering_variant	In_Frame_Del	DEL	TTATCAAC	TTATCAAC	GT	novel	NA	P-0069161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	66	433	1	ENST00000288319.7:c.622_629delinsAC	p.Val208_Lys210delinsThr	p.V208_K210delinsT	ENST00000288319	NM_182918.3	208	GTTGATAAa/ACa	5/10	0.34100349035124	1	FACETS	0.372	0.326	0.422	0.372	0.326	0.422	INDETERMINATE	1	TRUE	0	0.726043641789294	1		434	311	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0069162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	224	395	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.5	2		396	857	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0069162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	375	500	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.96	1	1	0.997	1	CLONAL	2	TRUE	1	0.5	2		501	747	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0069162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	69	286	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.8	0.701	0.905	0.8	0.701	0.905	CLONAL	1	TRUE	1	0.5	2		286	345	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0069162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	97	236	0	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	1	2	FACETS	0.985	0.885	1	0.985	0.885	1	CLONAL	1	TRUE	1	0.5	2		236	394	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717608	89717608	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1564566706	NA	P-0069162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	109	241	0	ENST00000371953.3:c.635-2A>G		p.X212_splice	ENST00000371953	NM_000314.4	212			1	2	FACETS	0.971	0.877	1	0.971	0.877	1	CLONAL	1	TRUE	1	0.5	2		241	449	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796883	42796883	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0069162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	183	572	1	ENST00000575354.2:c.3347del	p.Pro1116GlnfsTer45	p.P1116Qfs*45	ENST00000575354	NM_015125.3	1114	gCc/gc	14/20	1	2	FACETS	0.822	0.759	0.888	0.822	0.759	0.888	CLONAL	1	TRUE	1	0.5	2		573	890	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713427	40713427	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752787425	NA	P-0069162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	203	473	0	ENST00000373198.4:c.4088G>A	p.Arg1363Gln	p.R1363Q	ENST00000373198	NM_133170.3	1363	cGg/cAg	30/32	0.3	1	FACETS	0.757	0.704	0.813	0.757	0.704	0.813	SUBCLONAL	1	TRUE	0	0.5	1		473	804	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0069162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	43	518	3	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	0.238	0.198	0.282	0.238	0.198	0.282	SUBCLONAL	1	TRUE	1	0.5	2		521	722	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261555	142261555	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0069162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	102	226	1	ENST00000350721.4:c.3402del	p.Phe1134LeufsTer6	p.F1134Lfs*6	ENST00000350721	NM_001184.3	1134	ttT/tt	17/47	1	2	FACETS	0.995	0.896	1	0.995	0.896	1	CLONAL	1	TRUE	1	0.5	2		227	410	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332853	153332853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751626529	NA	P-0069162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	234	400	1	ENST00000281708.4:c.103C>T	p.Arg35Cys	p.R35C	ENST00000281708	NM_033632.3	35	Cgt/Tgt	2/12	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.5	2		401	896	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274851	38274851	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519898	NA	P-0069162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	194	318	0	ENST00000425967.3:c.1729A>G	p.Asn577Asp	p.N577D	ENST00000425967	NM_001174067.1	577	Aac/Gac	13/19	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.5	2		318	669	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655272	45655272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764295138	NA	P-0069162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	169	417	0	ENST00000407780.3:c.580C>T	p.Arg194Trp	p.R194W	ENST00000407780	NM_001283052.1	194	Cgg/Tgg	4/7	1	2	FACETS	0.828	0.762	0.897	0.828	0.762	0.897	CLONAL	1	TRUE	1	0.5	2		417	816	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919025	50919025	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	160	448	0	ENST00000440232.2:c.2762G>A	p.Arg921His	p.R921H	ENST00000440232	NM_002691.3	921	cGc/cAc	22/27	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.5	2		448	635	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420606	49420606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886041404	NA	P-0069162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	217	533	0	ENST00000301067.7:c.15143G>A	p.Arg5048His	p.R5048H	ENST00000301067	NM_003482.3	5048	cGt/cAt	48/54	1	2	FACETS	0.955	0.889	1	0.955	0.889	1	CLONAL	1	TRUE	1	0.5	2		533	909	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908277	41908277	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	172	389	0	ENST00000372991.4:c.245T>C	p.Met82Thr	p.M82T	ENST00000372991	NM_001760.3	82	aTg/aCg	2/5	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.5	2		389	659	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023171	27023171	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	125	431	0	ENST00000324856.7:c.279del	p.Gly95AlafsTer6	p.G95Afs*6	ENST00000324856	NM_006015.4	93	Ggg/gg	1/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.5	2		431	463	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21350124	21350124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780217270	NA	P-0069162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	179	491	0	ENST00000215739.8:c.2032C>T	p.Arg678Trp	p.R678W	ENST00000215739	NM_006767.3	678	Cgg/Tgg	17/21	1	2	FACETS	0.969	0.895	1	0.969	0.895	1	CLONAL	1	TRUE	1	0.5	2		491	739	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106298	27106313	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTGGACTGGCAGGA	TTCTGGACTGGCAGGA	-	novel	NA	P-0069162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	180	455	0	ENST00000324856.7:c.5913_5928del	p.Asp1972LeufsTer38	p.D1972Lfs*38	ENST00000324856	NM_006015.4	1970	cTTCTGGACTGGCAGGAt/ct	20/20	1	2	FACETS	0.952	0.88	1	0.952	0.88	1	CLONAL	1	TRUE	1	0.5	2		455	756	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72893518	72893518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	62	234	0	ENST00000325599.8:c.200C>T	p.Ala67Val	p.A67V	ENST00000325599	NM_018130.2	67	gCa/gTa	2/11	1	2	FACETS	0.695	0.603	0.793	0.695	0.603	0.793	SUBCLONAL	1	TRUE	1	0.5	2		234	357	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255093	16255093	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0069162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	217	458	0	ENST00000375759.3:c.2363del	p.Asn788MetfsTer21	p.N788Mfs*21	ENST00000375759	NM_015001.2	786	acA/ac	11/15	1	2	FACETS	0.969	0.902	1	0.969	0.902	1	CLONAL	1	TRUE	1	0.5	2		458	896	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513019	106513019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	108	360	0	ENST00000359195.3:c.2033C>T	p.Ala678Val	p.A678V	ENST00000359195	NM_002649.2	678	gCc/gTc	3/11	1	2	FACETS	0.852	0.768	0.94	0.852	0.768	0.94	CLONAL	1	TRUE	1	0.5	2		360	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0069163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	375	294	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.667198980744525	2	FACETS	0.942	0.907	0.975	0.942	0.907	0.975	CLONAL	2	TRUE	0	0.701173016212666	2		294	568	SUCCESS
EED	8726	MSKCC	GRCh37	11	85956364	85956365	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0069163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	275	494	0	ENST00000263360.6:c.94_95del	p.Asp32ProfsTer7	p.D32Pfs*7	ENST00000263360	NM_003797.3	31	ccAGac/ccac	1/12	0.701173016212666	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.701173016212666	1		494	453	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0069164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	166	206	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.829	0.766	0.893	0.829	0.766	0.893	CLONAL	1	TRUE	1	0.74885296107089	2		206	535	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0069164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	12	183	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.085	0.059	0.117	0.085	0.059	0.117	SUBCLONAL	1	TRUE	1	0.74885296107089	2		183	378	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115955	8115956	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0069164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	365	457	0	ENST00000346208.3:c.1305dup	p.Ser436LeufsTer71	p.S436Lfs*71	ENST00000346208		434	cac/caCc	6/6	1	2	FACETS	0.991	0.942	1	0.991	0.942	1	CLONAL	1	TRUE	1	0.74885296107089	2		457	984	SUCCESS
AR	367	MSKCC	GRCh37	X	66765025	66765025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1335991486	NA	P-0069164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	249	452	0	ENST00000374690.3:c.37C>T	p.Arg13Trp	p.R13W	ENST00000374690	NM_000044.3	13	Cgg/Tgg	1/8	0.74885296107089	1	FACETS	0.912	0.866	0.958	0.912	0.866	0.958	CLONAL	1	TRUE	0	0.74885296107089	1		452	456	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164773	36164773	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	299	646	0	ENST00000300305.3:c.1102A>T	p.Met368Leu	p.M368L	ENST00000300305		368	Atg/Ttg	8/8	1	2	FACETS	0.952	0.9	1	0.952	0.9	1	CLONAL	1	TRUE	1	0.74885296107089	2		646	839	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51503066	51503066	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	259	403	0	ENST00000260433.2:c.1451C>G	p.Thr484Ser	p.T484S	ENST00000260433		484	aCt/aGt	10/10	1	2	FACETS	0.925	0.87	0.98	0.925	0.87	0.98	CLONAL	1	TRUE	1	0.74885296107089	2		403	748	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0069169-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	294	435	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.366196510897199	3	FACETS	1	0.993	1	0.8	0.766	0.834	INDETERMINATE	2	TRUE	0	0.704742010103618	3		435	470	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649869	88649869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781556	NA	P-0069169-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	60	232	0	ENST00000372037.3:c.118G>A	p.Asp40Asn	p.D40N	ENST00000372037	NM_004329.2	40	Gac/Aac	4/13	0.452719632622511	1	FACETS	0.811	0.719	0.904	0.811	0.719	0.904	CLONAL	1	TRUE	0	0.704742010103618	1		232	136	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069170-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	33	364	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	0.143436664997806	4	FACETS	0.229	0.186	0.279	0.115	0.093	0.14	INDETERMINATE	1	TRUE	2	0.81	4		364	643	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444286	49444286	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069170-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	343	530	0	ENST00000301067.7:c.3085C>T	p.Gln1029Ter	p.Q1029*	ENST00000301067	NM_003482.3	1029	Cag/Tag	11/54	0.131995260765962	3	FACETS	1	0.995	1	0.725	0.689	0.76	INDETERMINATE	1	TRUE	1	0.81	3		530	821	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754871	57754872	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0069170-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	280	289	0	ENST00000274289.3:c.318dup	p.Val107SerfsTer14	p.V107Sfs*14	ENST00000274289	NM_006622.3	106	-/A	2/14	0.143436664997806	4	FACETS	0.884	0.835	0.933	0.884	0.835	0.933	INDETERMINATE	2	TRUE	2	0.81	4		289	708	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0069171-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	34	406	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.842	0.701	0.994	1	0.97	1	CLONAL	3	TRUE	1	0.202463761660052	2		406	133	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110624	4110642	+	protein_altering_variant	In_Frame_Del	DEL	GATGGCCGGCTTGATCTCA	GATGGCCGGCTTGATCTCA	AAATCTGGTTCCG	novel	NA	P-0069171-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	72	396	2	ENST00000262948.5:c.315_333delinsCGGAACCAGATTT	p.Glu106_Ile111delinsGlyThrArgPhe	p.E106_I111delinsGTRF	ENST00000262948	NM_030662.3	105	ctTGAGATCAAGCCGGCCATC/ctCGGAACCAGATTT	3/11	0.202463761660052	1	FACETS	1	0.936	1	1	0.984	1	CLONAL	2	TRUE	0	0.202463761660052	1		398	292	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0069172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	58	435	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.26	2		435	375	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266112	41266112	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913228	NA	P-0069172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	93	325	0	ENST00000349496.5:c.109T>G	p.Ser37Ala	p.S37A	ENST00000349496	NM_001904.3	37	Tct/Gct	3/15	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.26	2		325	660	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445397	29445397	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	87	356	0	ENST00000389048.3:c.3436C>A	p.Gln1146Lys	p.Q1146K	ENST00000389048	NM_004304.4	1146	Caa/Aaa	21/29	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.26	2		356	654	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850704	63850705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0069172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	62	370	0	ENST00000279873.7:c.1489dup	p.Ile497AsnfsTer31	p.I497Nfs*31	ENST00000279873	NM_032199.2	494	-/A	10/10	1	2	FACETS	0.741	0.639	0.851	0.741	0.639	0.851	SUBCLONAL	1	TRUE	1	0.26	2		370	644	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653842	89653842	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057518425	NA	P-0069172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	25	197	0	ENST00000371953.3:c.140G>A	p.Arg47Lys	p.R47K	ENST00000371953	NM_000314.4	47	aGg/aAg	2/9	1	2	FACETS	0.723	0.571	0.896	0.723	0.571	0.896	SUBCLONAL	1	TRUE	1	0.26	2		197	266	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692847	89692847	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	16	100	0	ENST00000371953.3:c.331T>A	p.Trp111Arg	p.W111R	ENST00000371953	NM_000314.4	111	Tgg/Agg	5/9	1	2	FACETS	1	0.753	1	1	0.753	1	CLONAL	1	TRUE	1	0.26	2		100	122	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670664	67670664	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	107	286	0	ENST00000264010.4:c.1909G>T	p.Glu637Ter	p.E637*	ENST00000264010	NM_006565.3	637	Gag/Tag	11/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.26	2		286	681	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266850	18266850	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0069172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	58	399	0	ENST00000222254.8:c.161T>G	p.Val54Gly	p.V54G	ENST00000222254	NM_005027.3	54	gTg/gGg	2/16	1	2	FACETS	0.894	0.769	1	0.894	0.769	1	CLONAL	1	TRUE	1	0.26	2		399	499	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117717359	117717359	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	41	333	0	ENST00000368508.3:c.848C>G	p.Ser283Cys	p.S283C	ENST00000368508	NM_002944.2	283	tCt/tGt	8/43	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		333	446	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	31	328	0	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		328	409	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564620	139564620	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs755108877	NA	P-0069173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	30	417	0	ENST00000308874.7:c.410-1G>C		p.X137_splice	ENST00000308874		137			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		417	313	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14022087	14022087	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	27	333	0	ENST00000311895.7:c.787G>C	p.Asp263His	p.D263H	ENST00000311895	NM_005236.2	263	Gac/Cac	4/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		333	399	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139013	50139013	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	55	482	0	ENST00000246792.3:c.550G>C	p.Glu184Gln	p.E184Q	ENST00000246792	NM_006270.3	184	Gag/Cag	5/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		482	452	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072612	5072613	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0069173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	63	355	0	ENST00000381652.3:c.1763_1764del	p.Arg588LysfsTer8	p.R588Kfs*8	ENST00000381652	NM_004972.3	588	AGa/a	13/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		355	359	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989112	41989112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	112	390	0	ENST00000219905.7:c.1904C>T	p.Ser635Phe	p.S635F	ENST00000219905	NM_001164273.1	635	tCt/tTt	3/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		390	452	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911391	32911391	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs80358539	NA	P-0069173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	64	415	0	ENST00000380152.3:c.2899C>G	p.Leu967Val	p.L967V	ENST00000380152		967	Cta/Gta	11/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		415	367	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223742	53223742	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0069173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	49	248	0	ENST00000375401.3:c.3617A>C	p.Gln1206Pro	p.Q1206P	ENST00000375401	NM_004187.3	1206	cAg/cCg	23/26	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		248	269	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945340	151945341	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0069173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	19	83	0	ENST00000262189.6:c.2178_2179del	p.Lys727ArgfsTer4	p.K727Rfs*4	ENST00000262189	NM_170606.2	726	caGAaa/caaa	14/59	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		83	77	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118370607	118370607	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	32	341	0	ENST00000534358.1:c.6137A>C	p.Lys2046Thr	p.K2046T	ENST00000534358	NM_005933.3	2046	aAg/aCg	24/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		341	404	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643588	52643588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1329110900	NA	P-0069173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	44	403	0	ENST00000394830.3:c.2308C>T	p.His770Tyr	p.H770Y	ENST00000394830	NM_018313.4	770	Cat/Tat	17/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		403	463	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720710	89720711	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0069173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	17	73	0	ENST00000371953.3:c.862_863del	p.Glu288LysfsTer9	p.E288Kfs*9	ENST00000371953	NM_000314.4	287	tcAGaa/tcaa	8/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		73	104	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502885	186502885	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	50	367	0	ENST00000323963.5:c.343C>T	p.Gln115Ter	p.Q115*	ENST00000323963		115	Caa/Taa	4/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		367	540	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962622	38962622	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	25	300	0	ENST00000357387.3:c.1633G>C	p.Glu545Gln	p.E545Q	ENST00000357387	NM_152756.3	545	Gaa/Caa	18/38	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		300	342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578507	7578512	+	inframe_deletion	In_Frame_Del	DEL	GCAGGT	GCAGGT	-	novel	NA	P-0069173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	124	501	0	ENST00000269305.4:c.418_423del	p.Thr140_Cys141del	p.T140_C141del	ENST00000269305	NM_001126112.2	140	ACCTGC/-	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		501	561	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410671	32410671	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0069173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	28	435	0	ENST00000332351.3:c.1487C>G	p.Ser496Ter	p.S496*	ENST00000332351	NM_024426.4	496	tCa/tGa	10/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		435	509	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964942	15964942	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	132	441	2	ENST00000268712.3:c.5654C>A	p.Ser1885Ter	p.S1885*	ENST00000268712	NM_006311.3	1885	tCa/tAa	37/46	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		443	479	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119545660	119545660	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	62	378	0	ENST00000316626.5:c.1277C>T	p.Ser426Phe	p.S426F	ENST00000316626		426	tCt/tTt	12/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		378	578	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72873674	72873674	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	62	339	0	ENST00000325599.8:c.628G>C	p.Glu210Gln	p.E210Q	ENST00000325599	NM_018130.2	210	Gaa/Caa	6/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		339	446	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145376	58145376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	55	501	0	ENST00000257904.6:c.125G>A	p.Gly42Glu	p.G42E	ENST00000257904	NM_000075.3	42	gGa/gAa	2/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		501	662	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509534	29509534	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	61	337	0	ENST00000356175.3:c.739G>T	p.Glu247Ter	p.E247*	ENST00000356175	NM_000267.3	247	Gaa/Taa	8/57	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		337	323	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550804	150550804	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	105	490	0	ENST00000369026.2:c.852A>T	p.Glu284Asp	p.E284D	ENST00000369026	NM_021960.4	284	gaA/gaT	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		490	660	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158564	26158564	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	69	418	0	ENST00000289316.2:c.167C>G	p.Ser56Cys	p.S56C	ENST00000289316	NM_138720.2	56	tCt/tGt	1/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		418	539	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604760	48604760	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	70	428	0	ENST00000342988.3:c.1582C>G	p.His528Asp	p.H528D	ENST00000342988	NM_005359.5	528	Cac/Gac	12/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		428	543	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438208	56438208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	97	427	0	ENST00000407977.2:c.785C>T	p.Ser262Leu	p.S262L	ENST00000407977		262	tCa/tTa	7/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		427	413	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050933	49050934	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0069173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	39	355	0	ENST00000267163.4:c.2621_2622del	p.Lys874ThrfsTer4	p.K874Tfs*4	ENST00000267163	NM_000321.2	873	AAa/a	25/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		355	335	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325888	65325888	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	61	435	0	ENST00000342505.4:c.1234T>A	p.Tyr412Asn	p.Y412N	ENST00000342505	NM_002227.2	412	Tac/Aac	9/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		435	565	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952039	178952039	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	48	365	0	ENST00000263967.3:c.3094G>C	p.Glu1032Gln	p.E1032Q	ENST00000263967	NM_006218.2	1032	Gag/Cag	21/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		365	416	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544158	18544158	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0069173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	70	330	0	ENST00000266497.5:c.1975A>T	p.Arg659Ter	p.R659*	ENST00000266497		659	Aga/Tga	13/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		330	386	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90995081	90995081	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs745439506	NA	P-0069173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	36	267	0	ENST00000265433.3:c.40G>A	p.Glu14Lys	p.E14K	ENST00000265433	NM_002485.4	14	Gaa/Aaa	2/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		267	380	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662992	227662992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	33	484	0	ENST00000305123.5:c.463C>T	p.Pro155Ser	p.P155S	ENST00000305123	NM_005544.2	155	Ccc/Tcc	1/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		484	392	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18963858	18963858	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	31	353	0	ENST00000262803.5:c.1035C>A	p.Phe345Leu	p.F345L	ENST00000262803	NM_002911.3	345	ttC/ttA	7/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		353	451	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0069175-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	73	372	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.29	2		372	448	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913351	NA	P-0069175-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	57	278	0	ENST00000288602.6:c.1397G>A	p.Gly466Glu	p.G466E	ENST00000288602	NM_004333.4	466	gGa/gAa	11/18	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.29	2		278	360	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0069179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	5	206	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.524	0.298	0.831	0.524	0.298	0.831	SUBCLONAL	1	FALSE	1	0.28083450761122	2		206	68	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0069179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	38	297	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	0.882	0.732	1	0.882	0.732	1	CLONAL	1	FALSE	1	0.28083450761122	2		297	307	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992630	72992630	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1189486286	NA	P-0069179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	46	403	2	ENST00000268489.5:c.1415C>A	p.Ala472Glu	p.A472E	ENST00000268489	NM_006885.3	472	gCg/gAg	2/10	1	2	FACETS	0.48	0.403	0.566	0.48	0.403	0.566	SUBCLONAL	1	FALSE	1	0.28083450761122	2		405	682	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	69061276	69061276	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	14	130	0	ENST00000487270.1:c.1111C>T	p.Gln371Ter	p.Q371*	ENST00000487270	NM_133509.3	371	Cag/Tag	11/11	1	2	FACETS	0.739	0.537	0.978	0.739	0.537	0.978	CLONAL	1	FALSE	1	0.28083450761122	2		130	135	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343506	343506	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141807086	NA	P-0069179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	49	291	2	ENST00000262320.3:c.2168G>A	p.Arg723Gln	p.R723Q	ENST00000262320	NM_003502.3	723	cGa/cAa	8/11	1	2	FACETS	0.708	0.6	0.827	0.708	0.6	0.827	SUBCLONAL	1	FALSE	1	0.28083450761122	2		293	493	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281630	49281630	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	17	411	1	ENST00000282018.3:c.677G>T	p.Arg226Leu	p.R226L	ENST00000282018	NM_020377.2	226	cGg/cTg	1/1	1	2	FACETS	0.599	0.449	0.777	0.599	0.449	0.777	SUBCLONAL	1	FALSE	1	0.28083450761122	2		412	202	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259190	16259191	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGTGT	novel	NA	P-0069179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	26	419	0	ENST00000375759.3:c.6457_6461dup	p.Ala2155CysfsTer13	p.A2155Cfs*13	ENST00000375759	NM_015001.2	2152	gac/gaCGTGTc	11/15	0.28083450761122	1	FACETS	0.596	0.473	0.736	0.596	0.473	0.736	SUBCLONAL	1	FALSE	0	0.28083450761122	1		419	267	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61717812	61717812	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	10	286	0	ENST00000401558.2:c.1987C>A	p.Gln663Lys	p.Q663K	ENST00000401558	NM_003400.3	663	Caa/Aaa	17/25	1	2	FACETS	0.698	0.477	0.971	0.698	0.477	0.971	SUBCLONAL	1	FALSE	1	0.28083450761122	2		286	102	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0069185-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	264	536	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.564270972775013	3	FACETS	0.985	0.942	1	0.985	0.942	1	CLONAL	3	TRUE	0	0.564270972775013	3		536	406	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306734	41306734	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069185-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	231	439	0	ENST00000373198.4:c.925C>A	p.Pro309Thr	p.P309T	ENST00000373198	NM_133170.3	309	Cca/Aca	7/32	0.564270972775013	3	FACETS	0.994	0.927	1	0.497	0.463	0.532	CLONAL	1	TRUE	1	0.564270972775013	3		439	1056	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521298	187521299	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0069185-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	183	512	0	ENST00000441802.2:c.11856dup	p.Gly3953TrpfsTer19	p.G3953Wfs*19	ENST00000441802	NM_005245.3	3952	-/T	22/27	0.492780775792745	3	FACETS	0.908	0.838	0.98	0.303	0.279	0.327	CLONAL	1	TRUE	0	0.564270972775013	3		512	916	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578471	7578471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069185-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	359	602	0	ENST00000269305.4:c.459del	p.Gly154AlafsTer16	p.G154Afs*16	ENST00000269305	NM_001126112.2	153	ccC/cc	5/11	0.564270972775013	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.564270972775013	1		602	782	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971098	21971098	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069185-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	285	501	0	ENST00000304494.5:c.260G>T	p.Arg87Leu	p.R87L	ENST00000304494	NM_000077.4	87	cGg/cTg	2/3	0.530148463058888	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.564270972775013	1		501	723	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336065	73336065	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069185-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	277	434	1	ENST00000377767.4:c.2338A>G	p.Arg780Gly	p.R780G	ENST00000377767	NM_014953.3	780	Aga/Gga	17/21	0.52060623321761	4	FACETS	0.87	0.819	0.922	0.87	0.819	0.922	CLONAL	2	TRUE	2	0.564270972775013	4		435	883	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733233	74733233	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069185-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	299	458	0	ENST00000359995.5:c.10G>T	p.Gly4Cys	p.G4C	ENST00000359995	NM_001195427.1	4	Ggc/Tgc	1/3	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.564270972775013	2		458	1033	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861486	152861486	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069185-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	362	427	0	ENST00000406277.2:c.266G>T	p.Arg89Leu	p.R89L	ENST00000406277	NM_152274.4	89	cGt/cTt	4/7	0.420345791268136		FACETS		0.95	1				CLONAL	2	TRUE	NA	0.564270972775013	3		427	825	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166207	32166207	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069185-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	356	430	0	ENST00000375023.3:c.4747C>A	p.Arg1583Ser	p.R1583S	ENST00000375023	NM_004557.3	1583	Cgt/Agt	26/30	0.498778673630208	2	FACETS	0.925	0.885	0.965	0.925	0.885	0.965	CLONAL	2	TRUE	0	0.564270972775013	2		430	682	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372752	81372753	+	missense_variant	Missense_Mutation	DNP	CG	CG	AT	novel	NA	P-0069185-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	373	367	0	ENST00000222390.5:c.781_782delinsAT	p.Arg261Ile	p.R261I	ENST00000222390	NM_000601.4	261	CGc/ATc	7/18	0.52060623321761	4	FACETS	0.905	0.859	0.951	0.905	0.859	0.951	CLONAL	2	TRUE	2	0.564270972775013	4		367	1143	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216988	2216988	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs927931566	NA	P-0069185-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	185	523	0	ENST00000398665.3:c.2443C>G	p.Gln815Glu	p.Q815E	ENST00000398665	NM_032482.2	815	Cag/Gag	21/28	0.564270972775013	2	FACETS	0.798	0.738	0.86	0.399	0.369	0.43	SUBCLONAL	1	TRUE	0	0.564270972775013	2		523	822	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55219016	55219016	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069185-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	450	436	0	ENST00000275493.2:c.589G>T	p.Gly197Trp	p.G197W	ENST00000275493	NM_005228.3	197	Ggg/Tgg	5/28	0.52060623321761	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.564270972775013	4		436	1202	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775610	39775610	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069185-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	188	455	0	ENST00000288319.7:c.410A>T	p.Asp137Val	p.D137V	ENST00000288319	NM_182918.3	137	gAc/gTc	4/10	0.564270972775013	3	FACETS	0.749	0.691	0.81	0.375	0.345	0.405	SUBCLONAL	1	TRUE	1	0.564270972775013	3		455	1140	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467774	50467774	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069185-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	430	519	0	ENST00000331340.3:c.1009G>T	p.Gly337Cys	p.G337C	ENST00000331340	NM_006060.4	337	Ggt/Tgt	8/8	0.52060623321761	4	FACETS	0.878	0.837	0.921	0.878	0.837	0.921	CLONAL	2	TRUE	2	0.564270972775013	4		519	1357	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690509	33690509	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069185-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	266	468	0	ENST00000308377.4:c.318T>A	p.Phe106Leu	p.F106L	ENST00000308377	NM_152270.3	106	ttT/ttA	2/5	0.564270972775013	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.564270972775013	1		468	641	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0069188-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	122	334	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.375392508345126	2		334	608	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0069188-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	124	318	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	1	2	FACETS	0.785	0.716	0.856	1	0.987	1	SUBCLONAL	2	TRUE	1	0.375392508345126	2		318	421	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061463	38061463	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069188-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	123	412	0	ENST00000250448.2:c.526A>G	p.Ile176Val	p.I176V	ENST00000250448	NM_004496.3	176	Atc/Gtc	2/2	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.375392508345126	2		412	559	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835629	68835630	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0069188-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	109	424	0	ENST00000261769.5:c.220_221insA	p.Arg74GlnfsTer20	p.R74Qfs*20	ENST00000261769	NM_004360.3	74	cga/cAga	3/16	0.375392508345126	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.375392508345126	1		424	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0069189-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	99	295	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.275429696479206	3	FACETS	0.822	0.739	0.91			1	CLONAL	2	TRUE	NA	0.329955213020478	3		295	425	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0069189-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	135	347	3	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	0.229865687317694	4	FACETS	0.824	0.751	0.901	0.824	0.751	0.901	CLONAL	2	TRUE	2	0.329955213020478	4		350	660	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641214	3641214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs546657275	NA	P-0069189-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	132	384	0	ENST00000294008.3:c.2425G>A	p.Glu809Lys	p.E809K	ENST00000294008	NM_032444.2	809	Gaa/Aaa	12/15	0.237048580629517	3	FACETS	1	0.986	1	0.746	0.679	0.816	CLONAL	1	TRUE	1	0.329955213020478	3		384	625	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846036	68846036	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0069189-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	170	313	0	ENST00000261769.5:c.1009-2A>G		p.X337_splice	ENST00000261769	NM_004360.3	337			0.217051239297692	3	FACETS	1	0.979	1			1	CLONAL	2	TRUE	NA	0.329955213020478	3		313	519	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249510	153249510	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1157879635	NA	P-0069189-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	57	331	0	ENST00000281708.4:c.1268G>T	p.Gly423Val	p.G423V	ENST00000281708	NM_033632.3	423	gGa/gTa	9/12	1	2	FACETS	0.823	0.708	0.947	0.823	0.708	0.947	CLONAL	1	TRUE	1	0.329955213020478	2		331	420	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443844	49443844	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069189-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	73	440	0	ENST00000301067.7:c.3527C>A	p.Ala1176Glu	p.A1176E	ENST00000301067	NM_003482.3	1176	gCa/gAa	11/54	0.237048580629517	3	FACETS	0.751	0.657	0.854	0.376	0.328	0.427	SUBCLONAL	1	TRUE	1	0.329955213020478	3		440	686	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73635949	73636076	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGAGATGGTGAATCAGGTGGATTATGCATTTTATATCTCTTCTTTTTTAGACAAGATGTGAAATGGAGAAGTATCTGACACCTCAGCTTCCTCCAGTTCCTATAATTCCAGAGCATAAAAAGTATAGA	CGAGATGGTGAATCAGGTGGATTATGCATTTTATATCTCTTCTTTTTTAGACAAGATGTGAAATGGAGAAGTATCTGACACCTCAGCTTCCTCCAGTTCCTATAATTCCAGAGCATAAAAAGTATAGA	-	novel	NA	P-0069189-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	32	221	0	ENST00000377687.4:c.262-45_344del		p.X88_splice	ENST00000377687	NM_001730.3	88		2/4	0.238057864725306	2	FACETS	0.622	0.506	0.752	0.311	0.253	0.376	SUBCLONAL	1	TRUE	0	0.329955213020478	2		221	312	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218456	36218456	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069189-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	63	368	0	ENST00000222270.7:c.4235G>A	p.Gly1412Asp	p.G1412D	ENST00000222270	NM_014727.1	1412	gGc/gAc	16/37	0.229865687317694	4	FACETS	0.851	0.736	0.975	0.425	0.368	0.488	CLONAL	1	TRUE	2	0.329955213020478	4		368	597	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0069193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	98	349	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.348090592316642	2		349	402	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0069193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	191	315	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.305714209977613	5	FACETS	0.947	0.881	1	0.947	0.881	1	CLONAL	3	TRUE	2	0.348090592316642	5		315	588	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	194	377	0	ENST00000304494.5:c.143C>T	p.Pro48Leu	p.P48L	ENST00000304494	NM_000077.4	48	cCg/cTg	1/3	0.354251550010131	1	FACETS	0.869	0.81	0.928	1	0.993	1	CLONAL	2	TRUE	0	0.348090592316642	1		377	530	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857172	9857172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555481986	NA	P-0069193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	105	394	0	ENST00000330684.3:c.4229C>T	p.Ser1410Leu	p.S1410L	ENST00000330684	NM_001134407.1	1410	tCg/tTg	13/13	0.262308527161782	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.348090592316642	1		394	473	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351844	89351844	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1041612791	NA	P-0069193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	15	363	0	ENST00000301030.4:c.1106A>G	p.Lys369Arg	p.K369R	ENST00000301030	NM_001256183.1	369	aAg/aGg	9/13	0.277026428897204	4	FACETS	0.177	0.128	0.236			1	SUBCLONAL	1	TRUE	NA	0.348090592316642	4		363	656	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366302	15366302	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	126	317	0	ENST00000263377.2:c.1853T>C	p.Leu618Pro	p.L618P	ENST00000263377	NM_058243.2	618	cTc/cCc	10/20	0.217259702759349	4	FACETS	0.771	0.7	0.845	0.771	0.7	0.845	SUBCLONAL	2	TRUE	2	0.348090592316642	4		317	633	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639383	3639383	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	135	409	0	ENST00000294008.3:c.4256C>T	p.Pro1419Leu	p.P1419L	ENST00000294008	NM_032444.2	1419	cCc/cTc	12/15	0.217259702759349	4	FACETS	0.803	0.732	0.878	0.803	0.732	0.878	CLONAL	2	TRUE	2	0.348090592316642	4		409	651	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0069194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	93	269	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.198985472061856	4	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.253861363731853	4		269	622	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912655	NA	P-0069194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	79	424	0	ENST00000269305.4:c.725G>C	p.Cys242Ser	p.C242S	ENST00000269305	NM_001126112.2	242	tGc/tCc	7/11	0.103575981229971	3	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.253861363731853	3		424	521	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100980	41100980	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868706902	NA	P-0069194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	33	383	2	ENST00000373198.4:c.1376G>A	p.Arg459Gln	p.R459Q	ENST00000373198	NM_133170.3	459	cGg/cAg	8/32	0.251242086878426	0	FACETS	0.386	0.313	0.467			1	SUBCLONAL	1	TRUE	0	0.253861363731853	0		385	503	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673811	30673811	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	44	357	0	ENST00000376406.3:c.3149A>G	p.Gln1050Arg	p.Q1050R	ENST00000376406	NM_014641.2	1050	cAa/cGa	10/15	1	2	FACETS	0.68	0.57	0.801	0.68	0.57	0.801	SUBCLONAL	1	TRUE	1	0.253861363731853	2		357	510	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226180	2226180	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	87	435	0	ENST00000326181.6:c.1877G>A	p.Arg626Lys	p.R626K	ENST00000326181	NM_032271.2	626	aGg/aAg	19/21	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.253861363731853	2		435	615	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0069195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	83	437	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.264773146440341	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.264773146440341	1		437	501	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	195	381	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	0.221722798544312	3	FACETS	0.939	0.875	1	0.939	0.875	1	CLONAL	3	TRUE	0	0.264773146440341	3		381	592	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15938198	15938202	+	frameshift_variant	Frame_Shift_Del	DEL	ATAGG	ATAGG	-	novel	NA	P-0069195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	35	327	0	ENST00000268712.3:c.7012_7016del	p.Pro2338ThrfsTer25	p.P2338Tfs*25	ENST00000268712	NM_006311.3	2338	CCTATa/a	45/46	0.264773146440341	1	FACETS	0.632	0.519	0.759	0.632	0.519	0.759	SUBCLONAL	1	TRUE	0	0.264773146440341	1		327	363	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0069196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	73	536	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.176884913964059	3	FACETS	0.769	0.677	0.867	0.769	0.677	0.867	INDETERMINATE	2	FALSE	1	0.3	3		536	364	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432137	49432137	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0069196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	71	443	0	ENST00000301067.7:c.9002del	p.Lys3001ArgfsTer3	p.K3001Rfs*3	ENST00000301067	NM_003482.3	3001	aAg/ag	34/54	0.176884913964059	3	FACETS	1	0.962	1	0.633	0.554	0.717	INDETERMINATE	1	FALSE	1	0.3	3		443	430	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0069197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	16	290	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.193025475584833	4	FACETS	0.618	0.456	0.811	0.309	0.228	0.406	SUBCLONAL	1	FALSE	2	0.217562968281351	4		290	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0069197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	376	439	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.217562968281351	2	FACETS	1	0.986	1	1	0.997	1	CLONAL	5	FALSE	0	0.217562968281351	2		440	653	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0069197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	231	289	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.217562968281351	2	FACETS	1	0.979	1	1	0.996	1	CLONAL	5	FALSE	0	0.217562968281351	2		289	400	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681100	30681100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765107298	NA	P-0069197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	54	327	0	ENST00000376406.3:c.619G>A	p.Gly207Ser	p.G207S	ENST00000376406	NM_014641.2	207	Ggc/Agc	5/15	0.217562968281351	5	FACETS	0.99	0.845	1	0.33	0.281	0.384	CLONAL	1	FALSE	2	0.217562968281351	5		327	665	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665354	138665354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	44	379	0	ENST00000330315.3:c.211G>A	p.Ala71Thr	p.A71T	ENST00000330315	NM_023067.3	71	Gcg/Acg	1/1	0.217562968281351	1	FACETS	0.884	0.742	1	0.884	0.742	1	CLONAL	1	FALSE	0	0.217562968281351	1		379	408	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11018769	11018769	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769201815	NA	P-0069197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	83	382	0	ENST00000327064.4:c.401G>A	p.Arg134Gln	p.R134Q	ENST00000327064	NM_199141.1	134	cGg/cAg	3/16	0.217562968281351	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	0	0.217562968281351	1		382	508	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526279	31526279	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	144	353	0	ENST00000344624.3:c.761G>T	p.Arg254Leu	p.R254L	ENST00000344624		254	cGc/cTc	2/33	0.217562968281351	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	FALSE	1	0.217562968281351	3		353	644	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250761	26250761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1174747724	NA	P-0069197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	79	452	0	ENST00000446824.2:c.73G>A	p.Ala25Thr	p.A25T	ENST00000446824	NM_021018.2	25	Gcg/Acg	1/1	0.217562968281351	5	FACETS	1	0.892	1	0.339	0.298	0.385	CLONAL	1	FALSE	2	0.217562968281351	5		452	946	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69032461	69032461	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	80	268	0	ENST00000288368.4:c.3535C>A	p.Gln1179Lys	p.Q1179K	ENST00000288368	NM_024870.2	1179	Cag/Aag	29/40	0.217562968281351	4	FACETS	1	0.921	1	0.702	0.621	0.789	CLONAL	2	FALSE	1	0.217562968281351	4		268	425	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740539	145740539	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1245043798	NA	P-0069197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	102	467	0	ENST00000428558.2:c.1478T>C	p.Leu493Pro	p.L493P	ENST00000428558	NM_004260.3	493	cTg/cCg	8/22	0.217562968281351	7	FACETS	0.752	0.672	0.839	0.251	0.224	0.28	SUBCLONAL	2	FALSE	1	0.217562968281351	7		467	962	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798984	45798985	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0069197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	91	397	0	ENST00000450313.1:c.360_361del	p.Glu120AspfsTer132	p.E120Dfs*132	ENST00000450313	NM_012222.2	120	gaGAtg/gatg	4/16	0.217562968281351	7	FACETS	1	0.978	1			1	CLONAL	1	FALSE	NA	0.217562968281351	7		397	887	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877444	40877444	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	33	355	0	ENST00000373198.4:c.2252C>A	p.Ser751Tyr	p.S751Y	ENST00000373198	NM_133170.3	751	tCt/tAt	15/32	NA	2	FACETS	0.55	0.447	0.666			1	INDETERMINATE	1	FALSE	NA	0.217562968281351	2		355	552	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878968	151878968	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	43	353	0	ENST00000262189.6:c.5977C>T	p.Gln1993Ter	p.Q1993*	ENST00000262189	NM_170606.2	1993	Caa/Taa	36/59	0.217562968281351	3	FACETS	0.835	0.698	0.986	0.417	0.349	0.493	CLONAL	1	FALSE	1	0.217562968281351	3		353	525	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0069198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	85	406	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.861	0.772	0.954	0.861	0.772	0.954	CLONAL	1	TRUE	1	0.742089440397897	2		406	266	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180050958	180050958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781305649	NA	P-0069198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	154	354	0	ENST00000261937.6:c.1525G>A	p.Glu509Lys	p.E509K	ENST00000261937	NM_182925.4	509	Gag/Aag	11/30	1	2	FACETS	0.856	0.789	0.924	0.856	0.789	0.924	CLONAL	1	TRUE	1	0.742089440397897	2		354	485	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813324	102813324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377124814	NA	P-0069198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	213	355	0	ENST00000307046.8:c.365G>A	p.Arg122His	p.R122H	ENST00000307046	NM_001111285.1	122	cGt/cAt	3/4	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.742089440397897	2		355	504	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658343	18658343	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	127	250	0	ENST00000266497.5:c.3148A>G	p.Ile1050Val	p.I1050V	ENST00000266497		1050	Att/Gtt	22/31	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.742089440397897	2		250	320	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0069199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	79	257	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.95	0.842	1	0.95	0.842	1	CLONAL	1	TRUE	1	0.483339158001759	2		257	344	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0069199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	14	131	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.483339158001759	1	FACETS	0.472	0.346	0.62	0.472	0.346	0.62	SUBCLONAL	1	TRUE	0	0.483339158001759	1		131	93	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727441	66727441	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519728	NA	P-0069199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	118	316	0	ENST00000307102.5:c.157T>C	p.Phe53Leu	p.F53L	ENST00000307102	NM_002755.3	53	Ttt/Ctt	2/11	0.483339158001759	3	FACETS	1	0.947	1	0.534	0.483	0.587	CLONAL	1	TRUE	1	0.483339158001759	3		316	568	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123040864	123040864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1489246570	NA	P-0069199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	73	173	0	ENST00000355640.3:c.1327C>T	p.Arg443Cys	p.R443C	ENST00000355640		443	Cgc/Tgc	7/7	1	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.483339158001759	1		173	164	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295230	+	upstream_gene_variant	5'Flank	TNP	GGG	GGG	AGA	novel	NA	P-0069199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	45	360	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.766	0.649	0.893	0.766	0.649	0.893	SUBCLONAL	1	TRUE	1	0.483339158001759	2		360	243	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975717	26975717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	136	389	0	ENST00000381527.3:c.1225C>T	p.Pro409Ser	p.P409S	ENST00000381527	NM_001260.1	409	Cct/Tct	12/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.483339158001759	2		389	486	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165171	47165171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	104	337	0	ENST00000409792.3:c.955C>T	p.Leu319Phe	p.L319F	ENST00000409792	NM_014159.6	319	Ctt/Ttt	3/21	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.483339158001759	2		337	423	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61322946	61322946	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	44	242	0	ENST00000283752.5:c.1118T>G	p.Ile373Arg	p.I373R	ENST00000283752	NM_006919.2	373	aTa/aGa	8/8	1	2	FACETS	0.824	0.698	0.96	0.824	0.698	0.96	CLONAL	1	TRUE	1	0.483339158001759	2		242	221	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289967	15289967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	130	592	0	ENST00000263388.2:c.3587G>A	p.Gly1196Glu	p.G1196E	ENST00000263388	NM_000435.2	1196	gGa/gAa	22/33	0.483339158001759	2	FACETS	1	0.965	1	0.555	0.506	0.605	CLONAL	1	TRUE	0	0.483339158001759	2		592	485	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741493	145741493	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	121	504	0	ENST00000428558.2:c.1010C>T	p.Ala337Val	p.A337V	ENST00000428558	NM_004260.3	337	gCc/gTc	5/22	1	2	FACETS	0.988	0.897	1	0.988	0.897	1	CLONAL	1	TRUE	1	0.483339158001759	2		504	507	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38949892	38949892	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	82	391	0	ENST00000357387.3:c.4058C>A	p.Ser1353Tyr	p.S1353Y	ENST00000357387	NM_152756.3	1353	tCt/tAt	31/38	1	2	FACETS	0.85	0.754	0.952	0.85	0.754	0.952	CLONAL	1	TRUE	1	0.483339158001759	2		391	399	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222074	2222074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	205	530	0	ENST00000398665.3:c.2906C>T	p.Ser969Phe	p.S969F	ENST00000398665	NM_032482.2	969	tCc/tTc	24/28	0.483339158001759	2	FACETS	0.991	0.932	1	0.991	0.932	1	CLONAL	2	TRUE	0	0.483339158001759	2		530	428	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0069200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	124	289	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.327863312696976	3	FACETS	0.902	0.821	0.987	0.902	0.821	0.987	CLONAL	2	FALSE	1	0.320843279641475	3		289	497	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589623	67589634	+	inframe_deletion	In_Frame_Del	DEL	ATATGATAGATT	ATATGATAGATT	-	novel	NA	P-0069200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	56	200	0	ENST00000274335.5:c.1392_1403del	p.Asp464_Tyr467del	p.D464_Y467del	ENST00000274335		462	gaATATGATAGATTa/gaa	10/15	0.327863312696976	4	FACETS	0.72	0.617	0.834			1	SUBCLONAL	1	FALSE	NA	0.320843279641475	4		200	640	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572535	64572535	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	209	481	0	ENST00000312049.6:c.1321G>T	p.Val441Leu	p.V441L	ENST00000312049	NM_130799.2	441	Gtg/Ttg	9/10	0.318924684943031	3	FACETS	0.938	0.873	1			1	CLONAL	2	FALSE	NA	0.320843279641475	3		481	806	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211815	2211815	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	45	252	0	ENST00000398665.3:c.1531C>G	p.Leu511Val	p.L511V	ENST00000398665	NM_032482.2	511	Ctg/Gtg	16/28	0.199994602513569	0	FACETS	0.482	0.406	0.566			1	SUBCLONAL	1	FALSE	0	0.320843279641475	0		252	395	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589556	67589579	+	inframe_deletion	In_Frame_Del	DEL	ATAATATTGAAGCTGTAGGGAAAA	ATAATATTGAAGCTGTAGGGAAAA	-	novel	NA	P-0069200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	70	182	0	ENST00000274335.5:c.1320_1343del	p.Asp440_Lys448delinsGlu	p.D440_K448delinsE	ENST00000274335		440	gATAATATTGAAGCTGTAGGGAAAAaa/gaa	10/15	0.327863312696976	4	FACETS	0.95	0.828	1			1	CLONAL	1	FALSE	NA	0.320843279641475	4		182	607	SUCCESS
APC	324	MSKCC	GRCh37	5	112175935	112175935	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0069200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	80	305	0	ENST00000257430.4:c.4645del	p.Gln1549LysfsTer16	p.Q1549Kfs*16	ENST00000257430	NM_000038.5	1548	aaC/aa	16/16	0.327863312696976	1	FACETS	0.992	0.878	1	0.992	0.878	1	CLONAL	1	FALSE	0	0.320843279641475	1		305	422	SUCCESS
APC	324	MSKCC	GRCh37	5	112175982	112175982	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0069200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	87	312	0	ENST00000257430.4:c.4691T>G	p.Leu1564Ter	p.L1564*	ENST00000257430	NM_000038.5	1564	tTa/tGa	16/16	0.327863312696976	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	0	0.320843279641475	1		312	405	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517998	8518005	+	frameshift_variant	Frame_Shift_Del	DEL	TGTTGACA	TGTTGACA	-	novel	NA	P-0069200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	62	283	0	ENST00000356435.5:c.1386_1393del	p.His462GlnfsTer9	p.H462Qfs*9	ENST00000356435		462	caTGTCAACAac/caac	10/35	0.327863312696976	1	FACETS	0.791	0.686	0.905	0.791	0.686	0.905	CLONAL	1	FALSE	0	0.320843279641475	1		283	410	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455627	189455637	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	TTTTCCAGCAT	TTTTCCAGCAT	ACTGAAA	novel	NA	P-0069200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	35	276	1	ENST00000264731.3:c.161_171delinsACTGAAA	p.Val54AspfsTer2	p.V54Dfs*2	ENST00000264731	NM_003722.4	54	gTTTTCCAGCAT/gACTGAAA	2/14	1	2	FACETS	0.366	0.299	0.442	0.366	0.299	0.442	SUBCLONAL	1	FALSE	1	0.320843279641475	2		277	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0069201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	11	407	0	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		407	437	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0069202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	57	269	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.182486738994049	5	FACETS	1	0.968	1	0.491	0.424	0.564	INDETERMINATE	1	TRUE	2	0.363264916562449	5		269	329	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184589	11184589	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	46	296	0	ENST00000361445.4:c.6628G>C	p.Ala2210Pro	p.A2210P	ENST00000361445	NM_004958.3	2210	Gcc/Ccc	47/58	0.363264916562449	1	FACETS	0.754	0.639	0.878	0.754	0.639	0.878	SUBCLONAL	1	TRUE	0	0.363264916562449	1		296	275	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942168	71942168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	67	443	0	ENST00000298229.2:c.1432G>A	p.Asp478Asn	p.D478N	ENST00000298229	NM_001567.3	478	Gac/Aac	12/28	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.363264916562449	2		443	361	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001366	29001366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779189056	NA	P-0069202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	79	352	0	ENST00000282397.4:c.1366G>A	p.Ala456Thr	p.A456T	ENST00000282397	NM_002019.4	456	Gca/Aca	10/30	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.363264916562449	2		352	406	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919021	50919021	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501811	NA	P-0069202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	50	412	0	ENST00000440232.2:c.2758G>A	p.Asp920Asn	p.D920N	ENST00000440232	NM_002691.3	920	Gac/Aac	22/27	0.363264916562449	1	FACETS	0.959	0.822	1	0.959	0.822	1	CLONAL	1	TRUE	0	0.363264916562449	1		412	235	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0069202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	69	373	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.363264916562449	2		373	380	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0069202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	167	353	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.354378404919384	2	FACETS	0.954	0.884	1	0.954	0.884	1	CLONAL	2	TRUE	0	0.363264916562449	2		353	482	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468397	89468398	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1467832547	NA	P-0069202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	41	252	0	ENST00000336596.2:c.1938dup	p.Glu647ArgfsTer7	p.E647Rfs*7	ENST00000336596	NM_005233.5	644	tca/tcAa	11/17	1	2	FACETS	0.57	0.475	0.675	0.57	0.475	0.675	SUBCLONAL	1	TRUE	1	0.363264916562449	2		252	396	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587133	189587133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	91	261	0	ENST00000264731.3:c.1150G>A	p.Gly384Ser	p.G384S	ENST00000264731	NM_003722.4	384	Ggt/Agt	9/14	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.363264916562449	2		261	423	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467590	66467590	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746706656	NA	P-0069202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	61	342	0	ENST00000273854.3:c.679C>T	p.Arg227Cys	p.R227C	ENST00000273854	NM_004439.5	227	Cgt/Tgt	3/18	1	2	FACETS	0.84	0.727	0.961	0.84	0.727	0.961	CLONAL	1	TRUE	1	0.363264916562449	2		342	400	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983862	2983862	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1399673665	NA	P-0069202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	70	310	0	ENST00000396946.4:c.668G>A	p.Arg223Gln	p.R223Q	ENST00000396946	NM_032415.4	223	cGa/cAa	5/25	0.363264916562449	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.363264916562449	1		310	283	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231428	98231428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502266	NA	P-0069202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	77	402	0	ENST00000331920.6:c.1855G>A	p.Val619Ile	p.V619I	ENST00000331920	NM_000264.3	619	Gtc/Atc	14/24	0.357537126183196	3	FACETS	1	0.969	1	0.656	0.579	0.737	CLONAL	1	TRUE	1	0.363264916562449	3		402	382	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0069203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	36	306	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.535	0.439	0.642	0.535	0.439	0.642	SUBCLONAL	1	TRUE	1	0.28	2		306	481	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633847	86633847	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069214-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	43	292	0	ENST00000274376.6:c.956G>A	p.Trp319Ter	p.W319*	ENST00000274376	NM_002890.2	319	tGg/tAg	5/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		292	420	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241722	55241722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1051753269	NA	P-0069214-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	342	286	1	ENST00000275493.2:c.2170G>A	p.Gly724Ser	p.G724S	ENST00000275493	NM_005228.3	724	Ggc/Agc	18/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		287	979	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242485	+	protein_altering_variant	In_Frame_Del	DEL	GGAATTAAGAGAAGCAACATC	GGAATTAAGAGAAGCAACATC	AAT	novel	NA	P-0069214-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	376	255	0	ENST00000275493.2:c.2235_2255delinsAAT	p.Glu746_Ser752delinsIle	p.E746_S752delinsI	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCAACATCt/aaAATt	19/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		255	861	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098539	11098539	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069214-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	82	396	0	ENST00000358026.2:c.1057A>T	p.Thr353Ser	p.T353S	ENST00000358026	NM_001128849.1	353	Acc/Tcc	6/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		396	782	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729854	41729854	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069214-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	52	342	0	ENST00000242208.4:c.675C>A	p.Ser225Arg	p.S225R	ENST00000242208	NM_002192.2	225	agC/agA	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		342	766	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0069255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	135	536	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.59506952798313	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.595235111166508	4		536	303	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782177	NA	P-0069255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	228	341	3	ENST00000269305.4:c.644G>T	p.Ser215Ile	p.S215I	ENST00000269305	NM_001126112.2	215	aGt/aTt	6/11	0.520817511751672	3	FACETS	0.933	0.889	0.977	0.933	0.889	0.977	CLONAL	3	TRUE	0	0.595235111166508	3		344	355	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517201	NA	P-0069255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	74	172	0	ENST00000263967.3:c.1637A>C	p.Gln546Pro	p.Q546P	ENST00000263967	NM_006218.2	546	cAg/cCg	10/21	0.59506952798313	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	2	0.595235111166508	4		172	167	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991703	72991703	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201821212	NA	P-0069255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	198	302	0	ENST00000268489.5:c.2342C>T	p.Ala781Val	p.A781V	ENST00000268489	NM_006885.3	781	gCg/gTg	2/10	0.59506952798313	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.595235111166508	3		302	400	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38991089	38991089	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	82	217	1	ENST00000357387.3:c.545G>C	p.Arg182Thr	p.R182T	ENST00000357387	NM_152756.3	182	aGa/aCa	7/38	0.512487013590715	4	FACETS	0.923	0.827	1			1	CLONAL	2	TRUE	NA	0.595235111166508	4		218	238	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718214	117718214	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	110	281	0	ENST00000368508.3:c.643T>G	p.Trp215Gly	p.W215G	ENST00000368508	NM_002944.2	215	Tgg/Ggg	7/43	0.218775614324609	2	FACETS	1	0.959	1	0.548	0.498	0.6	INDETERMINATE	1	TRUE	0	0.595235111166508	2		281	337	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453565	138453565	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	128	282	4	ENST00000289153.2:c.883C>G	p.Gln295Glu	p.Q295E	ENST00000289153	NM_006219.2	295	Caa/Gaa	5/22	0.59506952798313	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	2	0.595235111166508	4		286	320	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150934631	150934631	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0069255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	22	94	0	ENST00000271640.5:c.3155C>G	p.Ser1052Ter	p.S1052*	ENST00000271640	NM_001145415.1	1052	tCa/tGa	17/22	0.595235111166508	6	FACETS	0.57	0.442	0.718			1	SUBCLONAL	1	TRUE	NA	0.595235111166508	6		94	284	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997830	149997830	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	84	291	1	ENST00000253339.5:c.2637G>C	p.Trp879Cys	p.W879C	ENST00000253339		879	tgG/tgC	5/7	0.553054919651801	4	FACETS	0.968	0.859	1	0.323	0.286	0.362	CLONAL	1	TRUE	1	0.595235111166508	4		292	465	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0069258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	91	536	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		536	323	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	359972	359972	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0069258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	57	907	1	ENST00000262320.3:c.1116+1G>A		p.X372_splice	ENST00000262320	NM_003502.3	372			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		908	212	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0069258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	65	843	1	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		844	217	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453990	140453990	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	49	588	0	ENST00000288602.6:c.1738A>G	p.Asn580Asp	p.N580D	ENST00000288602	NM_004333.4	580	Aat/Gat	14/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		588	245	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2115822	2115822	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	84	1115	0	ENST00000349721.2:c.3457G>T	p.Asp1153Tyr	p.D1153Y	ENST00000349721	NM_003070.3	1153	Gat/Tat	25/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1115	293	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0069259-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	15	226	0	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	0.209021514817913	1	FACETS	0.585	0.428	0.772	0.585	0.428	0.772	SUBCLONAL	1	FALSE	0	0.213227458261239	1		226	215	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069259-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	39	305	1	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.71	0.588	0.847	0.71	0.588	0.847	SUBCLONAL	1	FALSE	1	0.213227458261239	2		306	515	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828733	3828733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069259-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	30	308	0	ENST00000262367.5:c.1909G>A	p.Glu637Lys	p.E637K	ENST00000262367	NM_004380.2	637	Gaa/Aaa	9/31	1	2	FACETS	0.625	0.503	0.764	0.625	0.503	0.764	SUBCLONAL	1	FALSE	1	0.213227458261239	2		308	450	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0069259-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	65	454	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.141169165681597	3	FACETS	0.985	0.853	1	0.492	0.426	0.564	CLONAL	1	FALSE	1	0.213227458261239	3		454	685	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102198822	102198822	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0069259-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	16	216	0	ENST00000263464.3:c.994del	p.Arg332ValfsTer45	p.R332Vfs*45	ENST00000263464	NM_001165.4	331	atC/at	4/9	1	2	FACETS	0.67	0.496	0.877	0.67	0.496	0.877	SUBCLONAL	1	FALSE	1	0.213227458261239	2		216	224	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779545	3779545	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069259-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	44	504	1	ENST00000262367.5:c.5503G>A	p.Glu1835Lys	p.E1835K	ENST00000262367	NM_004380.2	1835	Gaa/Aaa	31/31	1	2	FACETS	0.635	0.531	0.75	0.635	0.531	0.75	SUBCLONAL	1	FALSE	1	0.213227458261239	2		505	650	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781918	3781918	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069259-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	45	374	0	ENST00000262367.5:c.4749G>C	p.Lys1583Asn	p.K1583N	ENST00000262367	NM_004380.2	1583	aaG/aaC	29/31	1	2	FACETS	0.82	0.689	0.964	0.82	0.689	0.964	CLONAL	1	FALSE	1	0.213227458261239	2		374	515	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929311	44929312	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0069259-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	39	206	0	ENST00000377967.4:c.2414dup	p.Ala806SerfsTer7	p.A806Sfs*7	ENST00000377967	NM_021140.2	804	cac/caCc	17/29	1	1	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	FALSE	0	0.213227458261239	1		206	312	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441214	52441232	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCATCCAGCTCAAAGAG	GCCCATCCAGCTCAAAGAG	-	novel	NA	P-0069259-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	41	395	0	ENST00000460680.1:c.538_556del	p.Leu180Ter	p.L180*	ENST00000460680	NM_004656.3	180	CTCTTTGAGCTGGATGGGCtg/tg	7/17	1	2	FACETS	0.69	0.574	0.82	0.69	0.574	0.82	SUBCLONAL	1	FALSE	1	0.213227458261239	2		395	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0069261-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	190	441	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	0.184938976219781	2	FACETS	0.917	0.85	0.986	0.917	0.85	0.986	CLONAL	2	TRUE	0	0.278838557939477	2		441	743	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435894	149435894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs690016548	NA	P-0069261-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	54	328	0	ENST00000286301.3:c.2330G>A	p.Arg777Gln	p.R777Q	ENST00000286301	NM_005211.3	777	cGg/cAg	18/22	1	2	FACETS	0.721	0.616	0.836	0.721	0.616	0.836	SUBCLONAL	1	TRUE	1	0.278838557939477	2		328	537	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023530	27023530	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0069261-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	269	380	0	ENST00000324856.7:c.636C>G	p.Tyr212Ter	p.Y212*	ENST00000324856	NM_006015.4	212	taC/taG	1/20	0.236939706177064	4	FACETS	1	0.98	1	0.816	0.769	0.864	CLONAL	3	TRUE	0	0.278838557939477	4		380	756	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437186	52437186	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069261-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	63	372	0	ENST00000460680.1:c.1858G>T	p.Glu620Ter	p.E620*	ENST00000460680	NM_004656.3	620	Gag/Tag	14/17	1	2	FACETS	0.726	0.628	0.833	0.726	0.628	0.833	SUBCLONAL	1	TRUE	1	0.278838557939477	2		372	622	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0069262-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	44	153	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.24	2		153	268	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0069262-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	39	252	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	0.869	0.722	1	0.869	0.722	1	CLONAL	1	TRUE	1	0.24	2		252	374	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981169	201981170	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0069262-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	35	303	0	ENST00000359651.3:c.249dup	p.Lys84GlnfsTer8	p.K84Qfs*8	ENST00000359651		83	aac/aaCc	2/8	1	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	TRUE	1	0.24	2		303	285	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022452	12022453	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0069262-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	67	345	0	ENST00000396373.4:c.559dup	p.Thr187AsnfsTer9	p.T187Nfs*9	ENST00000396373	NM_001987.4	186	-/A	5/8	0.162403285925846	2	FACETS	1	0.963	1	0.652	0.569	0.742	CLONAL	1	TRUE	0	0.24	2		345	428	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0069263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	166	232	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	NA	2	FACETS	0.757	0.698	0.817			1	INDETERMINATE	2	TRUE	NA	0.363273466623397	2		232	604	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414399	6414399	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	55	152	0	ENST00000356142.4:c.33C>A	p.Asp11Glu	p.D11E	ENST00000356142	NM_018890.3	11	gaC/gaA	1/7	1	2	FACETS	0.707	0.607	0.817	0.707	0.607	0.817	SUBCLONAL	1	TRUE	1	0.363273466623397	2		152	428	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923762	72923762	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	96	288	0	ENST00000268489.5:c.3316C>T	p.His1106Tyr	p.H1106Y	ENST00000268489	NM_006885.3	1106	Cat/Tat	4/10	1	2	FACETS	0.891	0.796	0.993	0.891	0.796	0.993	CLONAL	1	TRUE	1	0.363273466623397	2		288	593	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923774	72923774	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	100	282	0	ENST00000268489.5:c.3304A>T	p.Asn1102Tyr	p.N1102Y	ENST00000268489	NM_006885.3	1102	Aac/Tac	4/10	1	2	FACETS	0.933	0.835	1	0.933	0.835	1	CLONAL	1	TRUE	1	0.363273466623397	2		282	590	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790827	89790827	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	114	336	0	ENST00000336032.3:c.214C>A	p.Pro72Thr	p.P72T	ENST00000336032	NM_006813.2	72	Cct/Act	1/2	0.299483842598492	1	FACETS	0.725	0.654	0.801	0.725	0.654	0.801	SUBCLONAL	1	TRUE	0	0.363273466623397	1		336	708	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508721	38508721	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	50	230	0	ENST00000254066.5:c.769C>T	p.Gln257Ter	p.Q257*	ENST00000254066	NM_000964.3	257	Cag/Tag	6/9	1	2	FACETS	0.411	0.348	0.481	0.411	0.348	0.481	SUBCLONAL	1	TRUE	1	0.363273466623397	2		230	669	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090099	37090099	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs63751682	NA	P-0069263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	80	159	0	ENST00000231790.2:c.1988A>C	p.Glu663Ala	p.E663A	ENST00000231790	NM_000249.3	663	gAg/gCg	17/19	0.363273466623397	1	FACETS	0.873	0.772	0.979	0.873	0.772	0.979	CLONAL	1	TRUE	0	0.363273466623397	1		159	413	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36824367	36824367	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	97	226	0	ENST00000373129.3:c.169G>T	p.Asp57Tyr	p.D57Y	ENST00000373129	NM_032017.1	57	Gat/Tat	4/12	0.299483842598492	1	FACETS	0.697	0.622	0.776	0.697	0.622	0.776	SUBCLONAL	1	TRUE	0	0.363273466623397	1		226	627	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416105	29416105	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	105	255	0	ENST00000389048.3:c.4848C>A	p.Asn1616Lys	p.N1616K	ENST00000389048	NM_004304.4	1616	aaC/aaA	29/29	1	2	FACETS	0.918	0.824	1	0.918	0.824	1	CLONAL	1	TRUE	1	0.363273466623397	2		255	630	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669302	241669303	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0069263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	31	162	0	ENST00000366560.3:c.904_904+1delinsTT		p.X302_splice	ENST00000366560	NM_000143.3	302		6/10	0.299483842598492	1	FACETS	0.477	0.386	0.578	0.477	0.386	0.578	SUBCLONAL	1	TRUE	0	0.363273466623397	1		162	293	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445126	49445126	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	75	304	2	ENST00000301067.7:c.2340C>A	p.Cys780Ter	p.C780*	ENST00000301067	NM_003482.3	780	tgC/tgA	10/54	1	2	FACETS	0.579	0.507	0.657	0.579	0.507	0.657	SUBCLONAL	1	TRUE	1	0.363273466623397	2		306	713	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0069264-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	140	476	0	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	1	2	FACETS	0.91	0.833	0.989	1	0.99	1	CLONAL	2	TRUE	1	0.289820607065965	2		476	531	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221975	1221975	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069264-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	130	352	0	ENST00000326873.7:c.890G>C	p.Arg297Thr	p.R297T	ENST00000326873	NM_000455.4	297	aGg/aCg	7/10	0.289820607065965	1	FACETS	0.757	0.69	0.826	1	0.987	1	SUBCLONAL	2	TRUE	0	0.289820607065965	1		352	507	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864724	68864724	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069264-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	74	311	0	ENST00000288368.4:c.95A>T	p.Gln32Leu	p.Q32L	ENST00000288368	NM_024870.2	32	cAg/cTg	1/40	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.289820607065965	2		311	424	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148996	119149018	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACATCCTGGCAGGTACGGATCTA	ACATCCTGGCAGGTACGGATCTA	-	novel	NA	P-0069264-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	61	380	0	ENST00000264033.4:c.1217_1227+12del		p.X406_splice	ENST00000264033	NM_005188.3	406		8/16	1	2	FACETS	0.959	0.83	1	0.959	0.83	1	CLONAL	1	TRUE	1	0.289820607065965	2		380	439	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946272	55946272	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069264-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	100	452	0	ENST00000263923.4:c.3907A>T	p.Ser1303Cys	p.S1303C	ENST00000263923	NM_002253.2	1303	Agc/Tgc	30/30	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.289820607065965	2		452	548	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874052	151874052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069264-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	79	485	0	ENST00000262189.6:c.8486C>T	p.Pro2829Leu	p.P2829L	ENST00000262189	NM_170606.2	2829	cCa/cTa	38/59	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.289820607065965	2		485	510	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878061	48878062	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1131690852	NA	P-0069268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	54	364	0	ENST00000267163.4:c.19dup	p.Arg7ProfsTer24	p.R7Pfs*24	ENST00000267163	NM_000321.2	5	acc/aCcc	1/27	0.209468417425037	3	FACETS	0.469	0.4	0.545	0.156	0.133	0.182	INDETERMINATE	1	TRUE	0	0.478670104898581	3		364	596	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878068	48878068	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564059250	NA	P-0069268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	71	341	0	ENST00000267163.4:c.20G>A	p.Arg7Gln	p.R7Q	ENST00000267163	NM_000321.2	7	cGa/cAa	1/27	0.209468417425037	3	FACETS	0.672	0.587	0.763	0.224	0.195	0.255	INDETERMINATE	1	TRUE	0	0.478670104898581	3		341	547	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947540	48947540	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0069268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	154	201	0	ENST00000267163.4:c.1128-1G>C		p.X376_splice	ENST00000267163	NM_000321.2	376			0.209468417425037	3	FACETS	1	0.973	1	0.732	0.679	0.786	INDETERMINATE	2	TRUE	0	0.478670104898581	3		201	363	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035154	30035154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	144	265	0	ENST00000338641.4:c.316G>A	p.Glu106Lys	p.E106K	ENST00000338641	NM_000268.3	106	Gaa/Aaa	3/16	0.469807227234048	2	FACETS	0.898	0.831	0.965	0.898	0.831	0.965	CLONAL	2	TRUE	0	0.478670104898581	2		265	335	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870630	40870630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777571053	NA	P-0069268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	206	282	0	ENST00000428826.2:c.773G>A	p.Arg258Gln	p.R258Q	ENST00000428826		258	cGa/cAa	9/21	0.478670104898581	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.478670104898581	2		282	405	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157987	27157987	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	142	362	0	ENST00000380036.4:c.211C>T	p.Pro71Ser	p.P71S	ENST00000380036	NM_000459.3	71	Ccg/Tcg	2/23	0.337771213519719	3	FACETS	1	0.973	1	0.578	0.528	0.63	CLONAL	1	TRUE	1	0.478670104898581	3		362	636	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118913	70118913	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	334	427	0	ENST00000245479.2:c.485G>C	p.Arg162Pro	p.R162P	ENST00000245479	NM_000346.3	162	cGc/cCc	2/3	0.478670104898581	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.478670104898581	2		427	628	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035157	30035157	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	147	257	0	ENST00000338641.4:c.319G>T	p.Glu107Ter	p.E107*	ENST00000338641	NM_000268.3	107	Gag/Tag	3/16	0.469807227234048	2	FACETS	0.895	0.83	0.962	0.895	0.83	0.962	CLONAL	2	TRUE	0	0.478670104898581	2		257	343	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047145	77047145	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	123	298	0	ENST00000356341.3:c.1399G>A	p.Glu467Lys	p.E467K	ENST00000356341	NM_002576.4	467	Gaa/Aaa	13/15	0.478670104898581	3	FACETS	1	0.968	1	0.575	0.522	0.63	CLONAL	1	TRUE	1	0.478670104898581	3		298	554	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1296380	1296380	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1014589501	NA	P-0069268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	115	211	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.478670104898581	NA		211	421	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219381	1219381	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	130	385	0	ENST00000326873.7:c.433G>T	p.Glu145Ter	p.E145*	ENST00000326873	NM_000455.4	145	Gag/Tag	3/10	0.399469826907254	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	0	0.399469826907254	2		385	324	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430947	181430947	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	136	488	0	ENST00000325404.1:c.799G>T	p.Ala267Ser	p.A267S	ENST00000325404	NM_003106.3	267	Gcc/Tcc	1/1	0.398928504523406	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	0	0.399469826907254	2		488	332	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426131	47426131	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	118	243	0	ENST00000377045.4:c.651C>G	p.Asn217Lys	p.N217K	ENST00000377045	NM_001654.4	217	aaC/aaG	7/16	0.384764779570267	2	FACETS	0.853	0.787	0.917			1	CLONAL	3	TRUE	NA	0.399469826907254	2		243	231	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578233	226578233	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1368616500	NA	P-0069269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	135	384	0	ENST00000366794.5:c.495G>C	p.Lys165Asn	p.K165N	ENST00000366794	NM_001618.3	165	aaG/aaC	4/23	0.293787583202493	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.399469826907254	4		384	439	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216158	36216158	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	60	439	0	ENST00000222270.7:c.3566G>T	p.Gly1189Val	p.G1189V	ENST00000222270	NM_014727.1	1189	gGc/gTc	11/37	0.341444492777534	4	FACETS	0.994	0.859	1	0.497	0.429	0.57	CLONAL	1	TRUE	2	0.399469826907254	4		439	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782177	NA	P-0069271-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	104	437	0	ENST00000269305.4:c.644G>C	p.Ser215Thr	p.S215T	ENST00000269305	NM_001126112.2	215	aGt/aCt	6/11	0.640071463646368	1	FACETS	0.891	0.813	0.97	0.891	0.813	0.97	CLONAL	1	TRUE	0	0.640071463646368	1		437	248	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865611	57865611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1027428919	NA	P-0069271-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	80	506	0	ENST00000228682.2:c.3088G>A	p.Glu1030Lys	p.E1030K	ENST00000228682	NM_005269.2	1030	Gaa/Aaa	12/12	1	2	FACETS	0.729	0.647	0.815	0.729	0.647	0.815	SUBCLONAL	1	TRUE	1	0.640071463646368	2		506	343	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627325	14627328	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0069271-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	56	467	0	ENST00000254322.2:c.742_745del	p.Lys248GlufsTer23	p.K248Efs*23	ENST00000254322	NM_006145.1	248	AAGAga/ga	2/3	1	2	FACETS	0.446	0.384	0.514	0.446	0.384	0.514	SUBCLONAL	1	TRUE	1	0.640071463646368	2		467	392	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209156	36209156	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1020958708	NA	P-0069271-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	44	434	0	ENST00000222270.7:c.236G>T	p.Arg79Leu	p.R79L	ENST00000222270	NM_014727.1	79	cGg/cTg	1/37	1	2	FACETS	0.396	0.333	0.465	0.396	0.333	0.465	SUBCLONAL	1	TRUE	1	0.640071463646368	2		434	347	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692993	89693012	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACCAGAGACAAAAAGGTAA	GACCAGAGACAAAAAGGTAA	-	novel	NA	P-0069271-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	25	325	0	ENST00000371953.3:c.478_492+5del		p.X160_splice	ENST00000371953	NM_000314.4	160		5/9	1	2	FACETS	0.27	0.213	0.336	0.27	0.213	0.336	SUBCLONAL	1	TRUE	1	0.640071463646368	2		325	289	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	83	269	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.556637754969804	3	FACETS	1	0.978	1	0.711	0.636	0.79	CLONAL	1	TRUE	1	0.556637754969804	3		269	268	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	131	500	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.999	0.913	1	0.999	0.913	1	CLONAL	1	TRUE	1	0.556637754969804	2		501	471	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	107	394	2	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.94	0.85	1	0.94	0.85	1	CLONAL	1	TRUE	1	0.556637754969804	2		396	409	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	339	569	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.972	1	1	0.997	1	CLONAL	2	TRUE	1	0.556637754969804	2		571	597	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743932	41743933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs778012871	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	126	484	1	ENST00000301178.4:c.874dup	p.His292ProfsTer47	p.H292Pfs*47	ENST00000301178	NM_021913.4	289	-/C	7/20	1	2	FACETS	0.928	0.845	1	0.928	0.845	1	CLONAL	1	TRUE	1	0.556637754969804	2		485	488	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	142	457	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.556637754969804	3	FACETS	0.925	0.845	1	0.463	0.422	0.505	CLONAL	1	TRUE	1	0.556637754969804	3		457	705	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760024	133760024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	119	378	0	ENST00000318560.5:c.2352del	p.Arg785GlyfsTer3	p.R785Gfs*3	ENST00000318560	NM_005157.4	783	Ccc/cc	11/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.556637754969804	2		378	390	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759832	133759832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145494071	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	89	399	0	ENST00000318560.5:c.2155G>A	p.Ala719Thr	p.A719T	ENST00000318560	NM_005157.4	719	Gcc/Acc	11/11	1	2	FACETS	0.919	0.822	1	0.919	0.822	1	CLONAL	1	TRUE	1	0.556637754969804	2		399	348	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367926	15367926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs929177624	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	37	364	0	ENST00000263377.2:c.1400C>T	p.Ala467Val	p.A467V	ENST00000263377	NM_058243.2	467	gCc/gTc	8/20	1	2	FACETS	0.287	0.236	0.344	0.287	0.236	0.344	SUBCLONAL	1	TRUE	1	0.556637754969804	2		364	463	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	124	366	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.984	0.896	1	0.984	0.896	1	CLONAL	1	TRUE	1	0.556637754969804	2		366	453	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631878	90631878	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1319035463	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	285	457	0	ENST00000330062.3:c.475C>T	p.Arg159Cys	p.R159C	ENST00000330062	NM_002168.2	159	Cgc/Tgc	4/11	0.366411501924684	2	FACETS	0.869	0.825	0.913	0.869	0.825	0.913	CLONAL	2	TRUE	0	0.556637754969804	2		457	589	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	157	432	7	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	0.94	0.865	1	0.94	0.865	1	CLONAL	1	TRUE	1	0.556637754969804	2		439	600	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134823	41134823	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	139	377	0	ENST00000379561.5:c.805C>T	p.Arg269Ter	p.R269*	ENST00000379561	NM_002015.3	269	Cga/Tga	2/3	1	2	FACETS	0.97	0.888	1	0.97	0.888	1	CLONAL	1	TRUE	1	0.556637754969804	2		377	515	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	145	535	8	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	0.556637754969804	3	FACETS	1	0.946	1	0.523	0.478	0.569	CLONAL	1	TRUE	1	0.556637754969804	3		543	637	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	101	399	4	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.894	0.805	0.987	0.894	0.805	0.987	CLONAL	1	TRUE	1	0.556637754969804	2		403	406	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390736	139390736	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	170	500	0	ENST00000277541.6:c.7455del	p.Ser2486ArgfsTer103	p.S2486Rfs*103	ENST00000277541	NM_017617.3	2485	ccC/cc	34/34	1	2	FACETS	0.976	0.901	1	0.976	0.901	1	CLONAL	1	TRUE	1	0.556637754969804	2		500	626	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639588	47639588	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63749897	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	69	220	0	ENST00000233146.2:c.687del	p.Ala230LeufsTer16	p.A230Lfs*16	ENST00000233146	NM_000251.2	227	agA/ag	4/16	1	2	FACETS	0.867	0.762	0.977	0.867	0.762	0.977	CLONAL	1	TRUE	1	0.556637754969804	2		220	286	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008201	29008201	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	92	397	0	ENST00000282397.4:c.670C>T	p.Arg224Ter	p.R224*	ENST00000282397	NM_002019.4	224	Cga/Tga	5/30	1	2	FACETS	0.865	0.775	0.961	0.865	0.775	0.961	CLONAL	1	TRUE	1	0.556637754969804	2		397	382	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059170	42059170	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs756744691	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	70	548	1	ENST00000219905.7:c.8895del	p.Thr2966ProfsTer4	p.T2966Pfs*4	ENST00000219905	NM_001164273.1	2964	Ccc/cc	24/24	0.366411501924684	2	FACETS	0.41	0.358	0.467	0.205	0.179	0.234	SUBCLONAL	1	TRUE	0	0.556637754969804	2		549	613	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821614	72821614	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1462530890	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	79	267	0	ENST00000268489.5:c.10561G>A	p.Gly3521Ser	p.G3521S	ENST00000268489	NM_006885.3	3521	Ggc/Agc	10/10	1	2	FACETS	0.928	0.824	1	0.928	0.824	1	CLONAL	1	TRUE	1	0.556637754969804	2		267	306	SUCCESS
APC	324	MSKCC	GRCh37	5	112164664	112164664	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1060503259	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	67	296	0	ENST00000257430.4:c.1742del	p.Lys581ArgfsTer9	p.K581Rfs*9	ENST00000257430	NM_000038.5	580	Aaa/aa	14/16	1	2	FACETS	0.678	0.593	0.769	0.678	0.593	0.769	SUBCLONAL	1	TRUE	1	0.556637754969804	2		296	355	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934864	9934864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766162952	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	162	396	0	ENST00000330684.3:c.1426G>A	p.Asp476Asn	p.D476N	ENST00000330684	NM_001134407.1	476	Gac/Aac	6/13	0.547571785438248	2	FACETS	0.877	0.818	0.935	0.877	0.818	0.935	CLONAL	2	TRUE	0	0.556637754969804	2		396	332	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265386	10265386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1003447106	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	155	462	0	ENST00000340748.4:c.1660G>A	p.Ala554Thr	p.A554T	ENST00000340748		554	Gcg/Acg	20/40	1	2	FACETS	0.942	0.867	1	0.942	0.867	1	CLONAL	1	TRUE	1	0.556637754969804	2		462	591	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401700	401700	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200311468	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	161	521	0	ENST00000380956.4:c.1022C>T	p.Ala341Val	p.A341V	ENST00000380956	NM_001195286.1	341	gCg/gTg	7/9	1	2	FACETS	0.944	0.869	1	0.944	0.869	1	CLONAL	1	TRUE	1	0.556637754969804	2		521	613	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs753143066	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	88	317	2	ENST00000295797.4:c.826dup	p.Thr276AsnfsTer16	p.T276Nfs*16	ENST00000295797	NM_002740.5	273	tta/ttAa	9/18	1	2	FACETS	0.773	0.689	0.862	0.773	0.689	0.862	SUBCLONAL	1	TRUE	1	0.556637754969804	2		319	409	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108338	8108338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1454860641	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	132	406	0	ENST00000585124.1:c.886G>A	p.Val296Met	p.V296M	ENST00000585124	NM_004217.3	296	Gtg/Atg	9/9	1	2	FACETS	0.988	0.903	1	0.988	0.903	1	CLONAL	1	TRUE	1	0.556637754969804	2		406	480	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855831	45855831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747646421	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	149	465	0	ENST00000391945.4:c.1979C>T	p.Ala660Val	p.A660V	ENST00000391945	NM_000400.3	660	gCg/gTg	21/23	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.556637754969804	2		465	511	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324862	31324862	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	113	538	0	ENST00000412585.2:c.73+1G>A		p.X25_splice	ENST00000412585	NM_005514.6	25			1	2	FACETS	0.809	0.731	0.89	0.809	0.731	0.89	CLONAL	1	TRUE	1	0.556637754969804	2		538	502	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098012	178098012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	58	322	1	ENST00000397062.3:c.368del	p.Leu123TrpfsTer8	p.L123Wfs*8	ENST00000397062	NM_006164.4	123	tTg/tg	3/5	1	2	FACETS	0.674	0.583	0.772	0.674	0.583	0.772	SUBCLONAL	1	TRUE	1	0.556637754969804	2		323	309	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	226	408	2	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	0.556637754969804	3	FACETS	0.782	0.732	0.832	0.782	0.732	0.832	SUBCLONAL	2	TRUE	1	0.556637754969804	3		410	664	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972512	81972512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263457484	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	110	327	0	ENST00000359376.3:c.3305C>T	p.Thr1102Met	p.T1102M	ENST00000359376	NM_002661.3	1102	aCg/aTg	29/33	1	2	FACETS	0.88	0.796	0.968	0.88	0.796	0.968	CLONAL	1	TRUE	1	0.556637754969804	2		327	449	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020732	112020732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	177	334	0	ENST00000368678.4:c.839C>T	p.Ala280Val	p.A280V	ENST00000368678		280	gCt/gTt	8/13	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.556637754969804	2		334	636	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43733757	43733757	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	31	251	0	ENST00000382044.4:c.3065del	p.Asn1022MetfsTer20	p.N1022Mfs*20	ENST00000382044	NM_001141980.1	1022	aAt/at	15/28	0.366411501924684	2	FACETS	0.323	0.261	0.392	0.161	0.13	0.196	SUBCLONAL	1	TRUE	0	0.556637754969804	2		251	345	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939413	71939413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148394356	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	149	446	0	ENST00000298229.2:c.268C>T	p.Arg90Cys	p.R90C	ENST00000298229	NM_001567.3	90	Cgc/Tgc	3/28	1	2	FACETS	0.986	0.906	1	0.986	0.906	1	CLONAL	1	TRUE	1	0.556637754969804	2		446	543	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564829	226564829	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1558236428	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	91	335	0	ENST00000366794.5:c.1921del	p.Leu641TrpfsTer12	p.L641Wfs*12	ENST00000366794	NM_001618.3	641	Ctg/tg	13/23	1	2	FACETS	0.766	0.684	0.852	0.766	0.684	0.852	SUBCLONAL	1	TRUE	1	0.556637754969804	2		335	427	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030338	11030340	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	119	414	0	ENST00000327064.4:c.1091_1093del	p.Glu364del	p.E364del	ENST00000327064	NM_199141.1	363	aAAGaa/aaa	9/16	1	2	FACETS	0.885	0.804	0.97	0.885	0.804	0.97	CLONAL	1	TRUE	1	0.556637754969804	2		414	483	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778596	3778596	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs749783719	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	241	458	0	ENST00000262367.5:c.6452G>T	p.Arg2151Leu	p.R2151L	ENST00000262367	NM_004380.2	2151	cGg/cTg	31/31	0.547571785438248	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.556637754969804	2		458	426	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846107	151846107	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	127	459	0	ENST00000262189.6:c.12905del	p.Pro4302LeufsTer24	p.P4302Lfs*24	ENST00000262189	NM_170606.2	4302	cCt/ct	52/59	1	2	FACETS	0.732	0.665	0.803	0.732	0.665	0.803	SUBCLONAL	1	TRUE	1	0.556637754969804	2		459	623	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213861	2213861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1204733528	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	95	486	2	ENST00000398665.3:c.1673C>T	p.Ala558Val	p.A558V	ENST00000398665	NM_032482.2	558	gCg/gTg	18/28	1	2	FACETS	0.608	0.543	0.678	0.608	0.543	0.678	SUBCLONAL	1	TRUE	1	0.556637754969804	2		488	561	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244197	5244197	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754224013	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	146	490	0	ENST00000357368.4:c.1285G>A	p.Ala429Thr	p.A429T	ENST00000357368	NM_002850.3	429	Gcg/Acg	11/38	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.556637754969804	2		490	451	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285524	38285524	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	158	431	0	ENST00000425967.3:c.629C>A	p.Pro210His	p.P210H	ENST00000425967	NM_001174067.1	210	cCt/cAt	6/19	1	2	FACETS	0.931	0.856	1	0.931	0.856	1	CLONAL	1	TRUE	1	0.556637754969804	2		431	610	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864882	117864882	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	79	287	0	ENST00000297338.2:c.1227G>T	p.Glu409Asp	p.E409D	ENST00000297338	NM_006265.2	409	gaG/gaT	10/14	1	2	FACETS	0.749	0.663	0.84	0.749	0.663	0.84	SUBCLONAL	1	TRUE	1	0.556637754969804	2		287	379	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188187	32188187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754712190	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	118	471	1	ENST00000375023.3:c.1154G>A	p.Arg385His	p.R385H	ENST00000375023	NM_004557.3	385	cGc/cAc	6/30	1	2	FACETS	0.918	0.833	1	0.918	0.833	1	CLONAL	1	TRUE	1	0.556637754969804	2		472	462	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576452	67576453	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	60	319	0	ENST00000274335.5:c.735dup	p.His246ThrfsTer21	p.H246Tfs*21	ENST00000274335		244	tta/ttAa	5/15	1	2	FACETS	0.731	0.635	0.834	0.731	0.635	0.834	SUBCLONAL	1	TRUE	1	0.556637754969804	2		319	295	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322882	31322882	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1476457470	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	112	330	0	ENST00000412585.2:c.1012+2T>C		p.X338_splice	ENST00000412585	NM_005514.6	338			1	2	FACETS	0.904	0.819	0.994	0.904	0.819	0.994	CLONAL	1	TRUE	1	0.556637754969804	2		330	445	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489543	40489543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	158	419	0	ENST00000264657.5:c.707C>T	p.Thr236Met	p.T236M	ENST00000264657	NM_139276.2	236	aCg/aTg	8/24	1	2	FACETS	0.991	0.913	1	0.991	0.913	1	CLONAL	1	TRUE	1	0.556637754969804	2		419	573	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191555	10191555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs5030823	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	137	372	0	ENST00000256474.2:c.548C>T	p.Ser183Leu	p.S183L	ENST00000256474	NM_000551.3	183	tCg/tTg	3/3	1	2	FACETS	0.908	0.83	0.989	0.908	0.83	0.989	CLONAL	1	TRUE	1	0.556637754969804	2		372	542	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925622	114925622	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1189031682	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	134	392	0	ENST00000543371.1:c.1704del	p.Ser569ProfsTer33	p.S569Pfs*33	ENST00000543371	NM_001198531.1	567	gCc/gc	14/14	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.556637754969804	2		392	408	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445512	49445512	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301516107	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	112	366	0	ENST00000301067.7:c.1954C>T	p.Arg652Cys	p.R652C	ENST00000301067	NM_003482.3	652	Cgc/Tgc	10/54	0.556637754969804	3	FACETS	0.828	0.747	0.914	0.414	0.373	0.457	CLONAL	1	TRUE	1	0.556637754969804	3		366	621	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46736432	46736432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764014400	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	150	359	0	ENST00000371975.4:c.1144C>T	p.Arg382Trp	p.R382W	ENST00000371975	NM_003579.3	382	Cgg/Tgg	10/18	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.556637754969804	2		359	513	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430390	78430390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367853057	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	91	413	0	ENST00000370768.2:c.778G>A	p.Gly260Ser	p.G260S	ENST00000370768	NM_003902.3	260	Ggt/Agt	10/20	1	2	FACETS	0.94	0.842	1	0.94	0.842	1	CLONAL	1	TRUE	1	0.556637754969804	2		413	348	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625177	69625177	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs281860305	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	116	467	0	ENST00000334134.2:c.616del	p.Val206SerfsTer?	p.V206Sfs*?	ENST00000334134	NM_005247.2	206	Gtc/tc	3/3	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.556637754969804	2		467	398	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	256470	256470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3211483	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	123	257	0	ENST00000264932.6:c.1930G>A	p.Val644Met	p.V644M	ENST00000264932	NM_004168.2	644	Gtg/Atg	15/15	1	2	FACETS	0.993	0.905	1	0.993	0.905	1	CLONAL	1	TRUE	1	0.556637754969804	2		257	445	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137183	64137183	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	122	450	2	ENST00000334205.4:c.1615G>A	p.Ala539Thr	p.A539T	ENST00000334205	NM_003942.2	539	Gcc/Acc	14/17	1	2	FACETS	0.987	0.899	1	0.987	0.899	1	CLONAL	1	TRUE	1	0.556637754969804	2		452	444	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803738	1803738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774047997	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	87	387	0	ENST00000260795.2:c.916G>A	p.Val306Ile	p.V306I	ENST00000260795		306	Gtt/Att	6/17	1	2	FACETS	0.891	0.795	0.991	0.891	0.795	0.991	CLONAL	1	TRUE	1	0.556637754969804	2		387	351	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030883	36030883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1252138081	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	127	378	0	ENST00000358208.4:c.1162C>T	p.Arg388Trp	p.R388W	ENST00000358208		388	Cgg/Tgg	10/12	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.556637754969804	2		378	447	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108696	8108696	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	118	320	0	ENST00000585124.1:c.699G>A	p.Met233Ile	p.M233I	ENST00000585124	NM_004217.3	233	atG/atA	8/9	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.556637754969804	2		320	395	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657081	47657081	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs267607950	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	92	248	0	ENST00000233146.2:c.1276+1G>T		p.X426_splice	ENST00000233146	NM_000251.2	426			1	2	FACETS	0.918	0.823	1	0.918	0.823	1	CLONAL	1	TRUE	1	0.556637754969804	2		248	360	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316113	11316113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs968103570	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	142	386	0	ENST00000361445.4:c.641G>A	p.Arg214His	p.R214H	ENST00000361445	NM_004958.3	214	cGt/cAt	5/58	1	2	FACETS	0.916	0.839	0.996	0.916	0.839	0.996	CLONAL	1	TRUE	1	0.556637754969804	2		386	557	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	160	389	0	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	0.556637754969804	3	FACETS	0.855	0.792	0.919	0.855	0.792	0.919	CLONAL	2	TRUE	1	0.556637754969804	3		389	430	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428256	49428256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201127814	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	133	448	0	ENST00000301067.7:c.10444C>T	p.Arg3482Trp	p.R3482W	ENST00000301067	NM_003482.3	3482	Cgg/Tgg	37/54	0.556637754969804	3	FACETS	0.893	0.813	0.977	0.447	0.406	0.489	CLONAL	1	TRUE	1	0.556637754969804	3		448	684	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691872	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs79375991	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	197	367	6	ENST00000295754.5:c.383del	p.Lys128SerfsTer35	p.K128Sfs*35	ENST00000295754	NM_003242.5	125	gAa/ga	3/7	1	2	FACETS	0.792	0.742	0.842	1	0.993	1	SUBCLONAL	2	TRUE	1	0.556637754969804	2		373	447	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552243	29552243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151138158	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	63	260	0	ENST00000356175.3:c.1976G>A	p.Arg659Gln	p.R659Q	ENST00000356175	NM_000267.3	659	cGg/cAg	17/57	1	2	FACETS	0.861	0.752	0.976	0.861	0.752	0.976	CLONAL	1	TRUE	1	0.556637754969804	2		260	263	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57004007	57004007	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	C	C	T	rs761618705	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	137	442	1	ENST00000257254.3:c.472G>A	p.Ala158Thr	p.A158T	ENST00000257254		158	Gcc/Acc	1/2	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.556637754969804	2		443	455	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137522070	137522070	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	49	316	0	ENST00000367739.4:c.809T>A	p.Ile270Asn	p.I270N	ENST00000367739	NM_000416.2	270	aTt/aAt	6/7	1	2	FACETS	0.581	0.495	0.675	0.581	0.495	0.675	SUBCLONAL	1	TRUE	1	0.556637754969804	2		316	303	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755447	39755447	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1363790097	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	130	411	0	ENST00000288319.7:c.1318G>A	p.Val440Met	p.V440M	ENST00000288319	NM_182918.3	440	Gtg/Atg	10/10	1	2	FACETS	0.938	0.856	1	0.938	0.856	1	CLONAL	1	TRUE	1	0.556637754969804	2		411	498	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456496	32456497	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	74	349	0	ENST00000332351.3:c.395dup	p.Pro133AlafsTer66	p.P133Afs*66	ENST00000332351	NM_024426.4	132	ccg/ccCg	1/10	1	2	FACETS	0.911	0.805	1	0.911	0.805	1	CLONAL	1	TRUE	1	0.556637754969804	2		349	292	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448345	56448345	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	167	430	0	ENST00000407977.2:c.302C>A	p.Pro101His	p.P101H	ENST00000407977		101	cCt/cAt	3/10	1	2	FACETS	0.993	0.917	1	0.993	0.917	1	CLONAL	1	TRUE	1	0.556637754969804	2		430	604	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573588	41573588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776916559	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	133	523	0	ENST00000263253.7:c.5873C>T	p.Pro1958Leu	p.P1958L	ENST00000263253	NM_001429.3	1958	cCg/cTg	31/31	1	2	FACETS	0.937	0.856	1	0.937	0.856	1	CLONAL	1	TRUE	1	0.556637754969804	2		523	510	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1953898	1953898	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760749890	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	126	454	0	ENST00000382891.5:c.2077G>A	p.Ala693Thr	p.A693T	ENST00000382891	NM_133335.3	693	Gcc/Acc	11/22	1	2	FACETS	0.969	0.884	1	0.969	0.884	1	CLONAL	1	TRUE	1	0.556637754969804	2		454	467	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135058	11135058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777562578	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	130	301	0	ENST00000358026.2:c.3025C>T	p.Arg1009Cys	p.R1009C	ENST00000358026	NM_001128849.1	1009	Cgc/Tgc	21/36	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.556637754969804	2		301	453	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	917132	917132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753736754	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	125	361	0	ENST00000166345.3:c.1213G>A	p.Val405Ile	p.V405I	ENST00000166345	NM_004237.3	405	Gtc/Atc	13/13	1	2	FACETS	0.983	0.896	1	0.983	0.896	1	CLONAL	1	TRUE	1	0.556637754969804	2		361	457	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1627407	1627407	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	169	381	0	ENST00000344749.5:c.317del	p.Gly106AlafsTer15	p.G106Afs*15	ENST00000344749	NM_001136139.2	106	gGc/gc	6/19	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.556637754969804	2		381	542	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122850	2122851	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	210	367	0	ENST00000219476.3:c.2224dup	p.Ser742PhefsTer20	p.S742Ffs*20	ENST00000219476	NM_000548.3	741	ctt/cTtt	21/42	0.547571785438248	2	FACETS	0.879	0.828	0.931	0.879	0.828	0.931	CLONAL	2	TRUE	0	0.556637754969804	2		367	429	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602757	55602757	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	70	314	0	ENST00000288135.5:c.2578T>A	p.Trp860Arg	p.W860R	ENST00000288135	NM_000222.2	860	Tgg/Agg	18/21	1	2	FACETS	0.827	0.728	0.933	0.827	0.728	0.933	CLONAL	1	TRUE	1	0.556637754969804	2		314	304	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446437	49446437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748251797	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	307	444	0	ENST00000301067.7:c.1168G>A	p.Val390Ile	p.V390I	ENST00000301067	NM_003482.3	390	Gtt/Att	9/54	0.556637754969804	3	FACETS	0.993	0.942	1	0.993	0.942	1	CLONAL	2	TRUE	1	0.556637754969804	3		444	710	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112035549	112035549	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	64	261	0	ENST00000368678.4:c.344+1G>A		p.X115_splice	ENST00000368678		115			1	2	FACETS	0.73	0.637	0.829	0.73	0.637	0.829	SUBCLONAL	1	TRUE	1	0.556637754969804	2		261	315	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301168	65301168	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	101	308	0	ENST00000342505.4:c.3280C>A	p.Pro1094Thr	p.P1094T	ENST00000342505	NM_002227.2	1094	Cca/Aca	24/25	1	2	FACETS	0.881	0.793	0.973	0.881	0.793	0.973	CLONAL	1	TRUE	1	0.556637754969804	2		308	412	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098405	11098405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770322996	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	105	471	0	ENST00000358026.2:c.923C>T	p.Thr308Met	p.T308M	ENST00000358026	NM_001128849.1	308	aCg/aTg	6/36	1	2	FACETS	0.799	0.72	0.883	0.799	0.72	0.883	SUBCLONAL	1	TRUE	1	0.556637754969804	2		471	472	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873659	151873659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142287778	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	161	431	0	ENST00000262189.6:c.8879C>T	p.Pro2960Leu	p.P2960L	ENST00000262189	NM_170606.2	2960	cCg/cTg	38/59	1	2	FACETS	0.982	0.905	1	0.982	0.905	1	CLONAL	1	TRUE	1	0.556637754969804	2		431	589	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1696697	1696697	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	161	370	0	ENST00000378625.1:c.149C>T	p.Ser50Leu	p.S50L	ENST00000378625	NM_001198994.1	50	tCg/tTg	2/14	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.556637754969804	2		370	557	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030478	47030478	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782600932	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	112	190	0	ENST00000377604.3:c.253C>T	p.Arg85Trp	p.R85W	ENST00000377604	NM_001204468.1	85	Cgg/Tgg	4/24	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.556637754969804	1		190	217	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915895	127915895	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	103	362	0	ENST00000373547.4:c.586T>C	p.Trp196Arg	p.W196R	ENST00000373547	NM_002721.4	196	Tgg/Cgg	6/7	1	2	FACETS	0.964	0.87	1	0.964	0.87	1	CLONAL	1	TRUE	1	0.556637754969804	2		362	384	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169011	11169011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555795063	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	140	322	0	ENST00000358026.2:c.4601G>A	p.Arg1534His	p.R1534H	ENST00000358026	NM_001128849.1	1534	cGc/cAc	32/36	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.556637754969804	2		322	465	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661704	227661704	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	88	436	0	ENST00000305123.5:c.1751A>G	p.Glu584Gly	p.E584G	ENST00000305123	NM_005544.2	584	gAg/gGg	1/2	1	2	FACETS	0.792	0.707	0.883	0.792	0.707	0.883	SUBCLONAL	1	TRUE	1	0.556637754969804	2		436	399	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31237157	31237157	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1166235395	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	39	404	0	ENST00000376228.5:c.1054A>G	p.Asn352Asp	p.N352D	ENST00000376228	NM_002117.5	352	Aac/Gac	7/8	1	2	FACETS	0.369	0.306	0.439	0.369	0.306	0.439	SUBCLONAL	1	TRUE	1	0.556637754969804	2		404	380	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045802	26045802	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	137	538	0	ENST00000540144.1:c.164A>G	p.Tyr55Cys	p.Y55C	ENST00000540144	NM_003531.2	55	tAc/tGc	1/1	1	2	FACETS	0.829	0.757	0.904	0.829	0.757	0.904	CLONAL	1	TRUE	1	0.556637754969804	2		538	594	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248064	110248064	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	149	326	0	ENST00000374672.4:c.1408C>A	p.His470Asn	p.H470N	ENST00000374672	NM_004235.4	470	Cac/Aac	5/5	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.556637754969804	2		326	520	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49449106	49449106	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1057520167	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	115	277	0	ENST00000301067.7:c.2T>C	p.Met1?	p.M1?	ENST00000301067	NM_003482.3	1	aTg/aCg	1/54	0.556637754969804	3	FACETS	1	0.93	1	0.517	0.468	0.568	CLONAL	1	TRUE	1	0.556637754969804	3		277	511	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39774496	39774496	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	99	317	0	ENST00000288319.7:c.656T>A	p.Met219Lys	p.M219K	ENST00000288319	NM_182918.3	219	aTg/aAg	5/10	1	2	FACETS	0.676	0.606	0.751	0.676	0.606	0.751	SUBCLONAL	1	TRUE	1	0.556637754969804	2		317	526	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707859	47707859	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	77	275	0	ENST00000233146.2:c.2484del	p.His829MetfsTer12	p.H829Mfs*12	ENST00000233146	NM_000251.2	828	aTt/at	15/16	1	2	FACETS	0.935	0.829	1	0.935	0.829	1	CLONAL	1	TRUE	1	0.556637754969804	2		275	296	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223354	36223355	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	105	565	0	ENST00000222270.7:c.5909dup	p.Glu1971Ter	p.E1971*	ENST00000222270	NM_014727.1	1968	-/C	28/37	1	2	FACETS	0.804	0.724	0.888	0.804	0.724	0.888	CLONAL	1	TRUE	1	0.556637754969804	2		565	469	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152864501	152864501	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1557027814	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	26	100	0	ENST00000406277.2:c.27del	p.Pro10LeufsTer30	p.P10Lfs*30	ENST00000406277	NM_152274.4	9	ggG/gg	2/7	1		FACETS		0.92	1				CLONAL	1	TRUE	0	0.556637754969804	1		100	56	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324515	31324515	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs41552212	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	149	523	0	ENST00000412585.2:c.293A>G	p.Asp98Gly	p.D98G	ENST00000412585	NM_005514.6	98	gAc/gGc	2/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.556637754969804	2		523	490	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638316	117638316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369340872	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	80	301	0	ENST00000368508.3:c.6125G>A	p.Arg2042Gln	p.R2042Q	ENST00000368508	NM_002944.2	2042	cGg/cAg	38/43	1	2	FACETS	0.831	0.737	0.93	0.831	0.737	0.93	CLONAL	1	TRUE	1	0.556637754969804	2		301	346	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150933117	150933117	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	145	414	0	ENST00000271640.5:c.2579T>A	p.Ile860Asn	p.I860N	ENST00000271640	NM_001145415.1	860	aTc/aAc	16/22	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.556637754969804	2		414	510	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066694	5066694	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	60	254	0	ENST00000381652.3:c.1231A>C	p.Ser411Arg	p.S411R	ENST00000381652	NM_004972.3	411	Agt/Cgt	10/25	1	2	FACETS	0.946	0.825	1	0.946	0.825	1	CLONAL	1	TRUE	1	0.556637754969804	2		254	228	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0069273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	83	248	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.152958896416671	2	FACETS	0.768	0.679	0.862	0.768	0.679	0.862	SUBCLONAL	2	TRUE	0	0.20948555512504	2		248	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0069273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	76	294	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.20948555512504	2		294	568	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625218	69625218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168737490	NA	P-0069273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	67	293	0	ENST00000334134.2:c.575G>A	p.Arg192Gln	p.R192Q	ENST00000334134	NM_005247.2	192	cGg/cAg	3/3	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.20948555512504	2		293	584	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212230	5212230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367918810	NA	P-0069273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	42	331	0	ENST00000357368.4:c.4801G>A	p.Val1601Ile	p.V1601I	ENST00000357368	NM_002850.3	1601	Gtc/Atc	32/38	1	2	FACETS	0.627	0.522	0.743	0.627	0.522	0.743	SUBCLONAL	1	TRUE	1	0.20948555512504	2		331	640	SUCCESS
APC	324	MSKCC	GRCh37	5	112175038	112175038	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	60	292	0	ENST00000257430.4:c.3747C>A	p.Cys1249Ter	p.C1249*	ENST00000257430	NM_000038.5	1249	tgC/tgA	16/16	1	2	FACETS	0.872	0.751	1	0.872	0.751	1	CLONAL	1	TRUE	1	0.20948555512504	2		292	657	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0069274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	86	287	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.394179042003495	1	FACETS	0.734	0.652	0.822	0.734	0.652	0.822	SUBCLONAL	1	TRUE	0	0.394179042003495	1		287	477	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225613	133225613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138443282	NA	P-0069274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	95	456	0	ENST00000320574.5:c.4051G>A	p.Val1351Ile	p.V1351I	ENST00000320574	NM_006231.2	1351	Gtt/Att	32/49	1	2	FACETS	0.803	0.717	0.896	0.803	0.717	0.896	CLONAL	1	TRUE	1	0.394179042003495	2		456	600	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373385	118373385	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	46	438	0	ENST00000534358.1:c.6778G>C	p.Gly2260Arg	p.G2260R	ENST00000534358	NM_005933.3	2260	Ggg/Cgg	27/36	1	2	FACETS	0.368	0.309	0.433	0.368	0.309	0.433	SUBCLONAL	1	TRUE	1	0.394179042003495	2		438	635	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0069275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	70	213	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.258932681745998	0	FACETS	0.403	0.355	0.453			1	INDETERMINATE	1	TRUE	0	0.566291876938873	0		213	266	SUCCESS
APC	324	MSKCC	GRCh37	5	112175246	112175246	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1057517558	NA	P-0069275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	185	452	0	ENST00000257430.4:c.3956del	p.Pro1319LeufsTer2	p.P1319Lfs*2	ENST00000257430	NM_000038.5	1319	Cct/ct	16/16	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.566291876938873	2		452	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0069275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	205	303	0	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.564226260964906	1	FACETS	0.965	0.902	1	0.965	0.902	1	CLONAL	1	TRUE	0	0.566291876938873	1		303	538	SUCCESS
APC	324	MSKCC	GRCh37	5	112174476	112174477	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs1060503362	NA	P-0069275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	134	382	0	ENST00000257430.4:c.3186_3187del	p.Ser1063Ter	p.S1063*	ENST00000257430	NM_000038.5	1062	cAA/c	16/16	1	2	FACETS	0.992	0.908	1	0.992	0.908	1	CLONAL	1	TRUE	1	0.566291876938873	2		382	477	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6227020	6227020	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	216	404	0	ENST00000252674.7:c.514C>T	p.Pro172Ser	p.P172S	ENST00000252674	NM_005934.3	172	Ccc/Tcc	5/12	1	2	FACETS	0.982	0.915	1	0.982	0.915	1	CLONAL	1	TRUE	1	0.566291876938873	2		404	777	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554423	63554423	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	252	453	0	ENST00000307078.5:c.316G>C	p.Asp106His	p.D106H	ENST00000307078	NM_004655.3	106	Gat/Cat	2/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.566291876938873	2		453	865	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0069276-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	66	403	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.169379136777207	2	FACETS	0.888	0.774	1	0.888	0.774	1	CLONAL	2	FALSE	0	0.181279189830003	2		404	410	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519893	NA	P-0069276-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	99	349	0	ENST00000267101.3:c.310G>T	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ttg	3/28	0.181279189830003	3	FACETS	1	0.906	1	1	0.906	1	CLONAL	3	FALSE	0	0.181279189830003	3		349	394	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265989	41266253	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTA	TAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTA	-	novel	NA	P-0069276-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	22	249	0	ENST00000349496.5:c.14-27_241+10del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.181279189830003	3	FACETS	1	0.867	1	0.39	0.303	0.491	CLONAL	1	FALSE	0	0.181279189830003	3		249	226	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645775	215645775	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs776157713	NA	P-0069276-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	22	349	0	ENST00000260947.4:c.823T>A	p.Leu275Ile	p.L275I	ENST00000260947	NM_000465.2	275	Tta/Ata	4/11	0.177694716660977	3	FACETS	0.984	0.764	1	0.492	0.382	0.62	CLONAL	1	FALSE	1	0.181279189830003	3		349	269	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521511	8521511	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1193937945	NA	P-0069276-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	40	331	0	ENST00000356435.5:c.727A>G	p.Thr243Ala	p.T243A	ENST00000356435		243	Act/Gct	9/35	0.177694716660977	3	FACETS	1	0.938	1	0.649	0.54	0.769	CLONAL	1	FALSE	1	0.181279189830003	3		331	371	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259503	89259503	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0069276-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	25	398	0	ENST00000336596.2:c.647T>G	p.Val216Gly	p.V216G	ENST00000336596	NM_005233.5	216	gTa/gGa	3/17	0.177694716660977	3	FACETS	0.796	0.627	0.99	0.398	0.313	0.495	CLONAL	1	FALSE	1	0.181279189830003	3		398	378	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398278	25398279	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGC	novel	NA	P-0069276-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	43	253	0	ENST00000311936.3:c.38_40dup	p.Gly13dup	p.G13dup	ENST00000311936	NM_004985.3	13	gta/gGCGta	2/5	0.181279189830003	3	FACETS	0.898	0.761	1	0.898	0.761	1	CLONAL	3	FALSE	0	0.181279189830003	3		253	192	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0069277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	80	290	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.342497148301127	2		290	421	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672975	30672975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446862496	NA	P-0069277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	110	465	0	ENST00000376406.3:c.3985G>A	p.Ala1329Thr	p.A1329T	ENST00000376406	NM_014641.2	1329	Gcc/Acc	10/15	1	2	FACETS	0.734	0.659	0.814	0.734	0.659	0.814	SUBCLONAL	1	TRUE	1	0.342497148301127	2		465	875	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602848	10602848	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	36	409	0	ENST00000171111.5:c.730G>A	p.Glu244Lys	p.E244K	ENST00000171111	NM_203500.1	244	Gag/Aag	3/6	0.342497148301127	1	FACETS	0.258	0.211	0.311	0.258	0.211	0.311	SUBCLONAL	1	TRUE	0	0.342497148301127	1		409	675	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715792	18715792	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	83	249	0	ENST00000266497.5:c.3623C>A	p.Ala1208Glu	p.A1208E	ENST00000266497		1208	gCa/gAa	25/31	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.342497148301127	2		249	362	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207136	1207142	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCCGT	GGGCCGT	-	novel	NA	P-0069277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	199	353	0	ENST00000326873.7:c.224_230del	p.Arg75ThrfsTer19	p.R75Tfs*19	ENST00000326873	NM_000455.4	75	aGGGCCGTc/ac	1/10	0.342497148301127	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.342497148301127	1		353	821	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190067	123190067	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	24	223	1	ENST00000218089.9:c.1286G>A	p.Gly429Glu	p.G429E	ENST00000218089	NM_001042749.1	429	gGa/gAa	14/35	0.342497148301127	1	FACETS	0.351	0.275	0.438	0.351	0.275	0.438	SUBCLONAL	1	TRUE	0	0.342497148301127	1		224	331	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573068	41573068	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	14	354	0	ENST00000263253.7:c.5353C>T	p.Leu1785Phe	p.L1785F	ENST00000263253	NM_001429.3	1785	Ctc/Ttc	31/31	0.430951019104121	3	FACETS	0.243	0.175	0.325	0.121	0.087	0.163	SUBCLONAL	1	TRUE	1	0.569535159927706	3		354	260	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941678	48941707	+	inframe_deletion	In_Frame_Del	DEL	GATCTAGATGCAAGATTATTTTTGGATCAT	GATCTAGATGCAAGATTATTTTTGGATCAT	-	novel	NA	P-0069278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	50	164	0	ENST00000267163.4:c.991_1020del	p.Leu331_Asp340del	p.L331_D340del	ENST00000267163	NM_000321.2	330	GATCTAGATGCAAGATTATTTTTGGATCAT/-	10/27	0.569535159927706	2	FACETS	0.887	0.783	0.991	0.887	0.783	0.991	CLONAL	2	TRUE	0	0.569535159927706	2		164	99	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660088	227660088	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777666532	NA	P-0069278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	71	429	0	ENST00000305123.5:c.3367G>A	p.Ala1123Thr	p.A1123T	ENST00000305123	NM_005544.2	1123	Gca/Aca	1/2	0.569535159927706	2	FACETS	0.897	0.791	1	0.448	0.395	0.504	CLONAL	1	TRUE	0	0.569535159927706	2		429	278	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579555	7579555	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0069278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	119	342	0	ENST00000269305.4:c.132del	p.Met44IlefsTer79	p.M44Ifs*79	ENST00000269305	NM_001126112.2	44	atG/at	4/11	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	2	TRUE	NA	0.569535159927706	2		342	192	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889188	76889194	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAACT	GAAAACT	-	novel	NA	P-0069278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	82	241	0	ENST00000373344.5:c.4816_4822del	p.Ser1606PhefsTer16	p.S1606Ffs*16	ENST00000373344	NM_000489.3	1606	AGTTTTCtt/tt	18/35	0.430951019104121	3	FACETS	0.925	0.833	1	0.925	0.833	1	CLONAL	2	TRUE	1	0.569535159927706	3		241	200	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0069289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	118	269	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.268215998015246	5	FACETS	0.842	0.77	0.915	0.842	0.77	0.915	INDETERMINATE	3	TRUE	2	0.550344494996833	5		269	310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0069289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	259	529	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.550344494996833	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.550344494996833	2		529	469	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0069289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	85	345	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.550344494996833	3	FACETS	0.968	0.861	1	0.484	0.43	0.541	CLONAL	1	TRUE	1	0.550344494996833	3		345	407	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30102151	30102151	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1439477100	NA	P-0069289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	45	227	0	ENST00000331968.5:c.1316G>A	p.Arg439Gln	p.R439Q	ENST00000331968	NM_002742.2	439	cGg/cAg	9/18	1	2	FACETS	0.839	0.714	0.973	0.839	0.714	0.973	CLONAL	1	TRUE	1	0.550344494996833	2		227	195	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137320998	137320998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771637845	NA	P-0069289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	100	421	0	ENST00000481739.1:c.955G>A	p.Ala319Thr	p.A319T	ENST00000481739	NM_002957.4	319	Gcc/Acc	7/10	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.550344494996833	2		421	336	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572204	64572204	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	122	495	0	ENST00000312049.6:c.1435C>T	p.Arg479Trp	p.R479W	ENST00000312049	NM_130799.2	479	Cgg/Tgg	10/10	0.550344494996833	3	FACETS	1	0.954	1	0.54	0.491	0.593	CLONAL	1	TRUE	1	0.550344494996833	3		495	523	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119808	70119809	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGCGA	novel	NA	P-0069289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	157	407	0	ENST00000245479.2:c.813_817dup	p.Val273AlafsTer8	p.V273Afs*8	ENST00000245479	NM_000346.3	270	-/CGCGA	3/3	0.550344494996833	3	FACETS	0.844	0.781	0.908	0.844	0.781	0.908	CLONAL	2	TRUE	1	0.550344494996833	3		407	431	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993030	90993030	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1563578967	NA	P-0069289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	154	278	0	ENST00000265433.3:c.412T>C	p.Phe138Leu	p.F138L	ENST00000265433	NM_002485.4	138	Ttt/Ctt	4/16	0.489909141325687	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.550344494996833	3		278	313	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843247	128843247	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	182	416	0	ENST00000249373.3:c.354C>A	p.Cys118Ter	p.C118*	ENST00000249373	NM_005631.4	118	tgC/tgA	2/12	0.354221901207085	4	FACETS	0.955	0.887	1	0.955	0.887	1	CLONAL	2	TRUE	2	0.550344494996833	4		416	537	SUCCESS
APC	324	MSKCC	GRCh37	5	112170854	112170862	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GGACCACAG	GGACCACAG	-	novel	NA	P-0069289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	88	273	0	ENST00000257430.4:c.1951_1958+1del		p.EDHRdel	ENST00000257430	NM_000038.5	650	gaGGACCACAGg/gag	15/16	0.550344494996833	3	FACETS	0.914	0.826	1	0.914	0.826	1	CLONAL	2	TRUE	1	0.550344494996833	3		273	223	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0069292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	40	206	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.491	0.409	0.581	0.491	0.409	0.581	SUBCLONAL	1	TRUE	1	0.501741002672994	2		206	325	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0069292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	221	286	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.501741002672994	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.501741002672994	2		286	400	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0069292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	96	383	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	0.575	0.513	0.642	0.575	0.513	0.642	SUBCLONAL	1	TRUE	1	0.501741002672994	2		383	665	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591105	67591106	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0069292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	116	320	0	ENST00000274335.5:c.1701dup	p.Pro568ThrfsTer34	p.P568Tfs*34	ENST00000274335		566	-/A	12/15	0.185994387215771	2	FACETS	0.72	0.65	0.794	0.36	0.325	0.397	INDETERMINATE	1	TRUE	0	0.501741002672994	2		320	642	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445028	49445028	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs75226229	NA	P-0069292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	76	468	0	ENST00000301067.7:c.2438C>T	p.Pro813Leu	p.P813L	ENST00000301067	NM_003482.3	813	cCg/cTg	10/54	1	2	FACETS	0.463	0.406	0.525	0.463	0.406	0.525	SUBCLONAL	1	TRUE	1	0.501741002672994	2		468	654	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288886	11288886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	84	437	0	ENST00000361445.4:c.2869C>T	p.Arg957Trp	p.R957W	ENST00000361445	NM_004958.3	957	Cgg/Tgg	19/58	1	2	FACETS	0.557	0.492	0.626	0.557	0.492	0.626	SUBCLONAL	1	TRUE	1	0.501741002672994	2		437	601	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562188	95562188	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	92	403	0	ENST00000393063.1:c.5069C>T	p.Ala1690Val	p.A1690V	ENST00000393063	NM_030621.3	1690	gCc/gTc	24/28	1	2	FACETS	0.569	0.506	0.637	0.569	0.506	0.637	SUBCLONAL	1	TRUE	1	0.501741002672994	2		403	644	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645405	67645406	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0069292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	153	454	0	ENST00000264010.4:c.671_672del	p.Ser224CysfsTer5	p.S224Cfs*5	ENST00000264010	NM_006565.3	224	TCt/t	3/12	1	2	FACETS	0.998	0.917	1	0.998	0.917	1	CLONAL	1	TRUE	1	0.501741002672994	2		454	611	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578491	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGTGGAATCAAC	GGTGTGGAATCAAC	-	novel	NA	P-0069292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	156	475	0	ENST00000269305.4:c.439_452del	p.Val147ProfsTer29	p.V147Pfs*29	ENST00000269305	NM_001126112.2	147	GTTGATTCCACACCc/c	5/11	0.291920506550876	1	FACETS	0.869	0.801	0.94	0.869	0.801	0.94	INDETERMINATE	1	TRUE	0	0.501741002672994	1		475	536	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657491	29657491	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs786202591	NA	P-0069292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	68	331	0	ENST00000356175.3:c.5724G>C	p.Glu1908Asp	p.E1908D	ENST00000356175	NM_000267.3	1908	gaG/gaC	38/57	0.291920506550876	1	FACETS	0.514	0.449	0.584	0.514	0.449	0.584	INDETERMINATE	1	TRUE	0	0.501741002672994	1		331	395	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262117	10262119	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0069294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	159	483	2	ENST00000340748.4:c.2172_2174del	p.Lys725del	p.K725del	ENST00000340748		724	aaGAAa/aaa	23/40	0.408170382943258	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.408170382943258	1		485	527	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003799	45003799	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	145	436	0	ENST00000558401.1:c.55G>T	p.Glu19Ter	p.E19*	ENST00000558401	NM_004048.2	19	Gag/Tag	1/4	0.408170382943258	1	FACETS	0.889	0.814	0.968	0.889	0.814	0.968	CLONAL	1	TRUE	0	0.408170382943258	1		436	636	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259353	11259353	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	139	476	0	ENST00000361445.4:c.4215G>C	p.Gln1405His	p.Q1405H	ENST00000361445	NM_004958.3	1405	caG/caC	28/58	1	2	FACETS	0.951	0.867	1	0.951	0.867	1	CLONAL	1	TRUE	1	0.408170382943258	2		476	716	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772068	135772068	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554812930	NA	P-0069294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	144	442	0	ENST00000298552.3:c.3049G>A	p.Glu1017Lys	p.E1017K	ENST00000298552	NM_001162426.1	1017	Gag/Aag	23/23	0.208360659447292	1	FACETS	0.887	0.812	0.966	0.887	0.812	0.966	INDETERMINATE	1	TRUE	0	0.408170382943258	1		442	633	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216586	2216586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	186	582	0	ENST00000398665.3:c.2230G>A	p.Asp744Asn	p.D744N	ENST00000398665	NM_032482.2	744	Gac/Aac	20/28	0.408170382943258	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.408170382943258	1		582	644	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632354	3632354	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	128	398	0	ENST00000294008.3:c.5494G>C	p.Glu1832Gln	p.E1832Q	ENST00000294008	NM_032444.2	1832	Gag/Cag	15/15	0.133919389377706	0	FACETS	0.681	0.62	0.745			1	INDETERMINATE	1	TRUE	0	0.408170382943258	0		398	545	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221961	1221961	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0069294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	138	326	0	ENST00000326873.7:c.876C>G	p.Tyr292Ter	p.Y292*	ENST00000326873	NM_000455.4	292	taC/taG	7/10	0.408170382943258	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.408170382943258	1		326	503	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0069294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	205	274	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.408170382943258	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.408170382943258	3		274	558	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021212	31021212	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	86	436	0	ENST00000375687.4:c.1211G>C	p.Arg404Pro	p.R404P	ENST00000375687	NM_015338.5	404	cGa/cCa	12/13	0.208360659447292	1	FACETS	0.515	0.456	0.579	0.515	0.456	0.579	INDETERMINATE	1	TRUE	0	0.408170382943258	1		436	651	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149450082	149450082	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	131	462	0	ENST00000286301.3:c.1135T>A	p.Tyr379Asn	p.Y379N	ENST00000286301	NM_005211.3	379	Tac/Aac	8/22	0.208360659447292	1	FACETS	0.893	0.814	0.976	0.893	0.814	0.976	INDETERMINATE	1	TRUE	0	0.408170382943258	1		462	572	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956165	175956165	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	98	303	0	ENST00000367669.3:c.2047G>T	p.Val683Phe	p.V683F	ENST00000367669	NM_022457.5	683	Gtc/Ttc	18/20	0.208360659447292	1	FACETS	0.842	0.755	0.933	0.842	0.755	0.933	INDETERMINATE	1	TRUE	0	0.408170382943258	1		303	454	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864373	57864373	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	180	566	0	ENST00000228682.2:c.1850T>A	p.Met617Lys	p.M617K	ENST00000228682	NM_005269.2	617	aTg/aAg	12/12	0.408170382943258	3	FACETS	1	0.961	1	0.534	0.492	0.578	CLONAL	1	TRUE	1	0.408170382943258	3		566	994	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608199	100608199	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	114	162	0	ENST00000308731.7:c.1891T>A	p.Tyr631Asn	p.Y631N	ENST00000308731	NM_000061.2	631	Tac/Aac	18/19	1	1	FACETS	0.833	0.763	0.903	1	0.988	1	CLONAL	2	TRUE	0	0.408170382943258	1		162	267	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485049	57485049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	159	441	0	ENST00000371085.3:c.883G>A	p.Asp295Asn	p.D295N	ENST00000371085	NM_000516.4	295	Gat/Aat	11/13	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.408170382943258	2		441	739	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632444	3632444	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	149	477	0	ENST00000294008.3:c.5404G>C	p.Asp1802His	p.D1802H	ENST00000294008	NM_032444.2	1802	Gac/Cac	15/15	0.133919389377706	0	FACETS	0.714	0.655	0.776			1	INDETERMINATE	1	TRUE	0	0.408170382943258	0		477	605	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632400	3632400	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	133	451	0	ENST00000294008.3:c.5448G>C	p.Glu1816Asp	p.E1816D	ENST00000294008	NM_032444.2	1816	gaG/gaC	15/15	0.133919389377706	0	FACETS	0.672	0.613	0.734			1	INDETERMINATE	1	TRUE	0	0.408170382943258	0		451	574	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207089	1207089	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0069294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	189	432	0	ENST00000326873.7:c.178del	p.Tyr60ThrfsTer4	p.Y60Tfs*4	ENST00000326873	NM_000455.4	59	tcT/tc	1/10	0.408170382943258	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.408170382943258	1		432	638	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33680980	33680980	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	129	383	0	ENST00000308377.4:c.1297C>G	p.Pro433Ala	p.P433A	ENST00000308377	NM_152270.3	433	Cct/Gct	4/5	1	2	FACETS	0.949	0.862	1	0.949	0.862	1	CLONAL	1	TRUE	1	0.408170382943258	2		383	666	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170348	119170348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	153	407	0	ENST00000264033.4:c.2578G>A	p.Glu860Lys	p.E860K	ENST00000264033	NM_005188.3	860	Gag/Aag	16/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.408170382943258	2		407	615	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0069296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	223	290	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.534880752178299	3	FACETS	0.982	0.923	1	0.982	0.923	1	CLONAL	2	TRUE	1	0.534880752178299	3		290	538	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138835	64138857	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGCGGAGCGCCACCGCCTCCC	GCTGCGGAGCGCCACCGCCTCCC	-	novel	NA	P-0069296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	156	318	0	ENST00000334205.4:c.2204_2226del	p.Leu735ProfsTer61	p.L735Pfs*61	ENST00000334205	NM_003942.2	734	aaGCTGCGGAGCGCCACCGCCTCCCgc/aagc	17/17	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.534880752178299	2		318	541	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138863	64138863	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	166	340	0	ENST00000334205.4:c.2230G>T	p.Gly744Cys	p.G744C	ENST00000334205	NM_003942.2	744	Ggc/Tgc	17/17	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.534880752178299	2		340	552	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940992	71941008	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTCCACAGCACCCCC	AGCTCCACAGCACCCCC	-	novel	NA	P-0069296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	183	511	0	ENST00000298229.2:c.874_890del	p.Thr292AlafsTer6	p.T292Afs*6	ENST00000298229	NM_001567.3	290	AGCTCCACAGCACCCCCa/a	8/28	0.534880752178299	3	FACETS	0.856	0.79	0.925	0.428	0.395	0.463	CLONAL	1	TRUE	1	0.534880752178299	3		511	1013	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343384	118343384	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	149	366	0	ENST00000534358.1:c.1510A>C	p.Ser504Arg	p.S504R	ENST00000534358	NM_005933.3	504	Agc/Cgc	3/36	0.534880752178299	3	FACETS	0.87	0.795	0.948	0.435	0.397	0.474	CLONAL	1	TRUE	1	0.534880752178299	3		366	812	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907316	32907317	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs886040383	NA	P-0069296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	176	423	0	ENST00000380152.3:c.1705_1706del	p.Gln569GlufsTer20	p.Q569Efs*20	ENST00000380152		567	acCAca/acca	10/27	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.534880752178299	2		423	637	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849455	68849455	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	151	350	0	ENST00000261769.5:c.1358A>G	p.His453Arg	p.H453R	ENST00000261769	NM_004360.3	453	cAc/cGc	10/16	1	2	FACETS	0.921	0.845	1	0.921	0.845	1	CLONAL	1	TRUE	1	0.534880752178299	2		350	613	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4102432	4102432	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	322	381	0	ENST00000262948.5:c.470A>G	p.Gln157Arg	p.Q157R	ENST00000262948	NM_030662.3	157	cAg/cGg	4/11	0.519252078916767	3	FACETS	1	0.977	1			1	CLONAL	2	TRUE	NA	0.534880752178299	3		381	730	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095554	178095554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	158	356	0	ENST00000397062.3:c.1777C>T	p.Leu593Phe	p.L593F	ENST00000397062	NM_006164.4	593	Ctt/Ttt	5/5	0.519252078916767	3	FACETS	0.997	0.915	1			1	CLONAL	1	TRUE	NA	0.534880752178299	3		356	751	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156958	89156959	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0069296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	101	286	0	ENST00000336596.2:c.60_61delinsTT	p.Glu21Ter	p.E21*	ENST00000336596	NM_005233.5	20	ggGGaa/ggTTaa	1/17	1	2	FACETS	0.743	0.667	0.824	0.743	0.667	0.824	SUBCLONAL	1	TRUE	1	0.534880752178299	2		286	508	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502870	186502870	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	159	341	0	ENST00000323963.5:c.328A>C	p.Thr110Pro	p.T110P	ENST00000323963		110	Acc/Ccc	4/11	1	2	FACETS	0.941	0.866	1	0.941	0.866	1	CLONAL	1	TRUE	1	0.534880752178299	2		341	632	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876188	35876188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536561203	NA	P-0069296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	366	349	0	ENST00000303115.3:c.980C>T	p.Thr327Met	p.T327M	ENST00000303115	NM_002185.3	327	aCg/aTg	8/8	0.534880752178299	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	1	0.534880752178299	3		349	861	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350065	81350065	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	197	242	0	ENST00000222390.5:c.1267C>A	p.His423Asn	p.H423N	ENST00000222390	NM_000601.4	423	Cat/Aat	10/18	0.22441161347607	5	FACETS	0.964	0.903	1			1	INDETERMINATE	3	TRUE	NA	0.534880752178299	5		242	459	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045006	47045006	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	227	509	0	ENST00000377604.3:c.2332C>T	p.Gln778Ter	p.Q778*	ENST00000377604	NM_001204468.1	778	Cag/Tag	20/24	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.534880752178299	2		509	772	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748222	43748222	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069297-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	33	494	0	ENST00000382044.4:c.2584G>T	p.Glu862Ter	p.E862*	ENST00000382044	NM_001141980.1	862	Gag/Tag	12/28	1	2	FACETS	0.238	0.194	0.288	0.238	0.194	0.288	SUBCLONAL	1	TRUE	1	0.761528040157371	2		494	364	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0069309-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	227	437	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.365971914903282	2	FACETS	1	0.993	1	0.746	0.699	0.793	CLONAL	1	TRUE	0	0.49987401695306	2		437	609	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066718	5066718	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069309-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	57	236	0	ENST00000381652.3:c.1255C>G	p.Gln419Glu	p.Q419E	ENST00000381652	NM_004972.3	419	Cag/Gag	10/25	0.299554754646791	2	FACETS	0.748	0.646	0.857	0.374	0.323	0.429	INDETERMINATE	1	TRUE	0	0.49987401695306	2		236	305	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797351	42797351	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069309-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	115	492	0	ENST00000575354.2:c.3713C>A	p.Thr1238Asn	p.T1238N	ENST00000575354	NM_015125.3	1238	aCc/aAc	15/20	0.365971914903282	2	FACETS	0.809	0.731	0.89	0.404	0.365	0.445	CLONAL	1	TRUE	0	0.49987401695306	2		492	569	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258293	16258293	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069309-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	97	432	0	ENST00000375759.3:c.5558A>G	p.Lys1853Arg	p.K1853R	ENST00000375759	NM_015001.2	1853	aAg/aGg	11/15	0.442862751266196	2	FACETS	0.715	0.639	0.795	0.357	0.319	0.398	SUBCLONAL	1	TRUE	0	0.49987401695306	2		432	543	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245261	46245261	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069309-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	111	382	0	ENST00000334344.6:c.3355C>G	p.Gln1119Glu	p.Q1119E	ENST00000334344	NM_152641.2	1119	Cag/Gag	15/21	0.247193987906777	4	FACETS	1	0.959	1	0.56	0.504	0.618	INDETERMINATE	1	TRUE	2	0.49987401695306	4		382	595	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468053	31468053	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069309-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	73	270	0	ENST00000344624.3:c.2359G>C	p.Asp787His	p.D787H	ENST00000344624		787	Gac/Cac	15/33	0.49987401695306	3	FACETS	0.754	0.661	0.854	0.377	0.33	0.427	SUBCLONAL	1	TRUE	1	0.49987401695306	3		270	484	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864199	117864199	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069309-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	89	306	0	ENST00000297338.2:c.1458G>C	p.Glu486Asp	p.E486D	ENST00000297338	NM_006265.2	486	gaG/gaC	11/14	0.49987401695306	4	FACETS	0.8	0.709	0.896	0.2	0.177	0.224	SUBCLONAL	1	TRUE	0	0.49987401695306	4		306	668	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857355	9857355	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069309-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	77	371	0	ENST00000330684.3:c.4046A>T	p.Glu1349Val	p.E1349V	ENST00000330684	NM_001134407.1	1349	gAg/gTg	13/13	1	2	FACETS	0.697	0.614	0.785	0.697	0.614	0.785	SUBCLONAL	1	TRUE	1	0.49987401695306	2		371	442	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962636	38962636	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0069309-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	80	249	0	ENST00000357387.3:c.1619A>C	p.His540Pro	p.H540P	ENST00000357387	NM_152756.3	540	cAt/cCt	18/38	0.49987401695306	3	FACETS	0.998	0.883	1	0.499	0.441	0.56	CLONAL	1	TRUE	1	0.49987401695306	3		249	401	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914629	32914630	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0069309-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	112	372	0	ENST00000380152.3:c.6141_6142dup	p.Asn2048IlefsTer4	p.N2048Ifs*4	ENST00000380152		2046	tca/tcATa	11/27	0.454245606594693	2	FACETS	1	0.979	1	0.64	0.582	0.7	CLONAL	1	TRUE	0	0.49987401695306	2		372	350	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633355	8633370	+	frameshift_variant	Frame_Shift_Del	DEL	CCCACATTATTTGAGG	CCCACATTATTTGAGG	-	novel	NA	P-0069309-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	60	271	0	ENST00000356435.5:c.299_314del	p.Ala100GlufsTer3	p.A100Efs*3	ENST00000356435		100	gCCTCAAATAATGTGGGa/ga	3/35	0.299554754646791	2	FACETS	0.63	0.545	0.722	0.315	0.272	0.361	INDETERMINATE	1	TRUE	0	0.49987401695306	2		271	381	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0069314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	83	406	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.89	0.793	0.991	1	0.988	1	CLONAL	3	TRUE	1	0.199996653145655	2		406	311	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0069314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	197	301	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	1	2	FACETS	1	0.976	1	1	0.995	1	CLONAL	3	TRUE	1	0.199996653145655	2		301	595	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31424571	31424571	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	141	280	0	ENST00000344624.3:c.3224G>C	p.Arg1075Pro	p.R1075P	ENST00000344624		1075	cGc/cCc	25/33	1	2	FACETS	1	0.959	1	1	0.993	1	CLONAL	3	TRUE	1	0.199996653145655	2		280	439	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218656	36218656	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	137	424	0	ENST00000222270.7:c.4360C>T	p.Gln1454Ter	p.Q1454*	ENST00000222270	NM_014727.1	1454	Cag/Tag	17/37	1	2	FACETS	1	0.943	1	1	0.991	1	CLONAL	2	TRUE	1	0.199996653145655	2		424	656	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699369	47699369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069316-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	236	339	0	ENST00000347630.2:c.139G>A	p.Glu47Lys	p.E47K	ENST00000347630	NM_001007230.1	47	Gaa/Aaa	4/11	0.770362712316495	3	FACETS	0.991	0.94	1	0.991	0.94	1	CLONAL	2	TRUE	1	0.770362712316495	3		339	428	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577112	7577112	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1131691029	NA	P-0069316-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	358	416	0	ENST00000269305.4:c.826G>C	p.Ala276Pro	p.A276P	ENST00000269305	NM_001126112.2	276	Gcc/Ccc	8/11	0.770362712316495	2	FACETS	0.995	0.964	1	0.995	0.964	1	CLONAL	2	TRUE	0	0.770362712316495	2		416	467	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790029	40790029	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0069316-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	135	435	0	ENST00000373198.4:c.2702A>C	p.Lys901Thr	p.K901T	ENST00000373198	NM_133170.3	901	aAg/aCg	18/32	0.570589285736356	4	FACETS	0.91	0.829	0.995	0.455	0.414	0.498	CLONAL	1	TRUE	2	0.770362712316495	4		435	682	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0069317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	19	397	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	1	2	FACETS	0.508	0.384	0.654	0.508	0.384	0.654	SUBCLONAL	1	TRUE	1	0.17	2		397	440	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487277	56487277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035001455	NA	P-0069317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	22	294	0	ENST00000267101.3:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000267101	NM_001982.3	475	Cgg/Tgg	12/28	1	2	FACETS	0.606	0.469	0.766	0.606	0.469	0.766	SUBCLONAL	1	TRUE	1	0.17	2		294	427	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119881	70119881	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	30	358	0	ENST00000245479.2:c.883G>C	p.Asp295His	p.D295H	ENST00000245479	NM_000346.3	295	Gac/Cac	3/3	1	2	FACETS	0.887	0.715	1	0.887	0.715	1	CLONAL	1	TRUE	1	0.17	2		358	398	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665213	138665213	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	8	345	0	ENST00000330315.3:c.352G>T	p.Glu118Ter	p.E118*	ENST00000330315	NM_023067.3	118	Gag/Tag	1/1	1	2	FACETS	0.339	0.217	0.497	0.339	0.217	0.497	SUBCLONAL	1	TRUE	1	0.17	2		345	278	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0069318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	25	213	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.354	0.278	0.441	0.354	0.278	0.441	SUBCLONAL	1	TRUE	1	0.328313590709537	2		213	430	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0069318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	62	529	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.602	0.52	0.692	0.602	0.52	0.692	SUBCLONAL	1	TRUE	1	0.328313590709537	2		529	627	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489842	40489842	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	76	462	0	ENST00000264657.5:c.584T>C	p.Val195Ala	p.V195A	ENST00000264657	NM_139276.2	195	gTg/gCg	7/24	1	2	FACETS	0.591	0.517	0.67	0.591	0.517	0.67	SUBCLONAL	1	TRUE	1	0.328313590709537	2		462	784	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814285	76814285	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069319-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	146	140	0	ENST00000373344.5:c.6359G>T	p.Gly2120Val	p.G2120V	ENST00000373344	NM_000489.3	2120	gGa/gTa	29/35	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.903091233949346	1		140	158	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577274	64577275	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTC	novel	NA	P-0069319-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	327	355	0	ENST00000312049.6:c.307_308insGACA	p.Leu103ArgfsTer15	p.L103Rfs*15	ENST00000312049	NM_130799.2	103	ctg/cGACAtg	2/10	0.903091233949346	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.903091233949346	1		355	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0069320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	100	366	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	NA	2	FACETS	0.894	0.812	0.978			1	INDETERMINATE	2	TRUE	NA	0.4252709844265	2		366	263	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0069320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	66	248	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.419119234882887	2	FACETS	0.913	0.811	1	0.913	0.811	1	CLONAL	2	TRUE	0	0.4252709844265	2		248	170	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0069320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	79	298	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.25071219818757	3	FACETS	1	0.904	1	0.673	0.602	0.747	INDETERMINATE	2	TRUE	0	0.4252709844265	3		298	223	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519896	NA	P-0069320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	8	380	0	ENST00000281708.4:c.1514G>A	p.Arg505His	p.R505H	ENST00000281708	NM_033632.3	505	cGc/cAc	10/12	0.25071219818757	3	FACETS	0.134	0.086	0.197	0.045	0.028	0.066	INDETERMINATE	1	TRUE	0	0.4252709844265	3		380	340	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063717	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs924551538	NA	P-0069320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	21	392	1	ENST00000412916.2:c.165+1G>A		p.X55_splice	ENST00000412916		55			1	2	FACETS	0.304	0.234	0.386	0.304	0.234	0.386	SUBCLONAL	1	TRUE	1	0.4252709844265	2		393	325	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199953	108199953	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	32	271	0	ENST00000278616.4:c.7295T>C	p.Ile2432Thr	p.I2432T	ENST00000278616	NM_000051.3	2432	aTt/aCt	49/63	1	2	FACETS	0.772	0.632	0.926	0.772	0.632	0.926	CLONAL	1	TRUE	1	0.4252709844265	2		271	195	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251555	212251660	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTTTCTGAATAATCAGTTCATACCTTGTTTGGGTTTGTCTCGCATAGGAGTCATGTAACCTTCCTCATCCAGCTCTCCTCGTGGGCTCCGTTCTGGGGCAAACACG	GTTTCTGAATAATCAGTTCATACCTTGTTTGGGTTTGTCTCGCATAGGAGTCATGTAACCTTCCTCATCCAGCTCTCCTCGTGGGCTCCGTTCTGGGGCAAACACG	-	novel	NA	P-0069320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	19	304	0	ENST00000342788.4:c.3399_3481+23del		p.X1133_splice	ENST00000342788	NM_005235.2	1133		27/28	1	2	FACETS	0.38	0.289	0.487	0.38	0.289	0.487	SUBCLONAL	1	TRUE	1	0.4252709844265	2		304	235	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37680953	37680953	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	22	414	0	ENST00000447079.4:c.3122A>C	p.Glu1041Ala	p.E1041A	ENST00000447079	NM_015083.1	1041	gAg/gCg	12/14	0.258803596018332	1	FACETS	0.268	0.207	0.338	0.268	0.207	0.338	SUBCLONAL	1	TRUE	0	0.4252709844265	1		414	304	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73649974	73649974	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	47	398	0	ENST00000377687.4:c.1324T>C	p.Phe442Leu	p.F442L	ENST00000377687	NM_001730.3	442	Ttc/Ctc	4/4	0.4252709844265	4	FACETS	0.44	0.37	0.517	0.11	0.092	0.13	SUBCLONAL	1	TRUE	0	0.4252709844265	4		398	716	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570369	87570369	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	35	468	0	ENST00000277120.3:c.2109C>G	p.Asn703Lys	p.N703K	ENST00000277120		703	aaC/aaG	17/19	0.258803596018332	1	FACETS	0.461	0.379	0.552	0.461	0.379	0.552	SUBCLONAL	1	TRUE	0	0.4252709844265	1		468	281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0069345-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	42	393	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	1	2	FACETS	0.916	0.766	1	0.916	0.766	1	CLONAL	1	TRUE	1	0.230465695065758	2		393	398	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845391	151845391	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069345-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	50	379	0	ENST00000262189.6:c.13621C>T	p.Arg4541Ter	p.R4541*	ENST00000262189	NM_170606.2	4541	Cga/Tga	52/59	1	2	FACETS	0.995	0.846	1	0.995	0.846	1	CLONAL	1	TRUE	1	0.230465695065758	2		379	436	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78435608	78435608	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0069345-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	15	210	0	ENST00000370768.2:c.211+1G>C		p.X71_splice	ENST00000370768	NM_003902.3	71			1	2	FACETS	0.454	0.331	0.601	0.454	0.331	0.601	SUBCLONAL	1	TRUE	1	0.230465695065758	2		210	287	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939033	48939033	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069345-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	40	151	0	ENST00000267163.4:c.865A>G	p.Lys289Glu	p.K289E	ENST00000267163	NM_000321.2	289	Aaa/Gaa	9/27	0.230465695065758	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.230465695065758	1		151	220	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31495410	31495410	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069345-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	35	273	0	ENST00000344624.3:c.1738C>A	p.Pro580Thr	p.P580T	ENST00000344624		580	Ccg/Acg	9/33	1	2	FACETS	1	0.835	1	1	0.835	1	CLONAL	1	TRUE	1	0.230465695065758	2		273	299	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0069345-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	35	304	0	ENST00000274335.5:c.1042del	p.Arg348GlufsTer25	p.R348Efs*25	ENST00000274335		348	Cga/ga	8/15	1	2	FACETS	0.825	0.677	0.991	0.825	0.677	0.991	CLONAL	1	TRUE	1	0.230465695065758	2		304	368	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514341	148514342	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0069345-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	19	236	0	ENST00000320356.2:c.1382_1383del	p.Arg461IlefsTer8	p.R461Ifs*8	ENST00000320356	NM_004456.4	461	aGG/a	11/20	1	2	FACETS	0.474	0.359	0.609	0.474	0.359	0.609	SUBCLONAL	1	TRUE	1	0.230465695065758	2		236	348	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340368	8340368	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069345-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	31	293	0	ENST00000356435.5:c.5228T>G	p.Leu1743Arg	p.L1743R	ENST00000356435		1743	cTc/cGc	31/35	1	2	FACETS	0.579	0.467	0.705	0.579	0.467	0.705	SUBCLONAL	1	TRUE	1	0.230465695065758	2		293	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0069346-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	233	394	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.682056669206609	2	FACETS	0.964	0.919	1	0.964	0.919	1	CLONAL	2	TRUE	0	0.676877729857287	2		394	357	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349730	15349730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750347317	NA	P-0069346-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	96	610	0	ENST00000263377.2:c.3844C>T	p.Arg1282Cys	p.R1282C	ENST00000263377	NM_058243.2	1282	Cgc/Tgc	19/20	0.682056669206609	2	FACETS	0.66	0.591	0.732	0.33	0.295	0.366	SUBCLONAL	1	TRUE	0	0.676877729857287	2		610	430	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125583	47125583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750289124	NA	P-0069346-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	169	416	0	ENST00000409792.3:c.5687C>T	p.Ala1896Val	p.A1896V	ENST00000409792	NM_014159.6	1896	gCa/gTa	12/21	0.286748621955742	1	FACETS	0.949	0.887	1	0.949	0.887	1	INDETERMINATE	1	TRUE	0	0.676877729857287	1		416	348	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356197	66356197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161959870	NA	P-0069346-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	196	527	0	ENST00000273854.3:c.1300C>T	p.His434Tyr	p.H434Y	ENST00000273854	NM_004439.5	434	Cac/Tac	5/18	0.682056669206609	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.676877729857287	1		527	319	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554325	141554325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069346-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	79	460	0	ENST00000220592.5:c.1826C>T	p.Pro609Leu	p.P609L	ENST00000220592	NM_012154.3	609	cCc/cTc	14/19	0.682056669206609	2	FACETS	0.669	0.593	0.749	0.334	0.296	0.375	SUBCLONAL	1	TRUE	0	0.676877729857287	2		460	349	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964477	93964477	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069346-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	42	363	0	ENST00000369303.4:c.2420C>A	p.Ala807Asp	p.A807D	ENST00000369303	NM_004440.3	807	gCc/gAc	14/17	NA	2	FACETS	0.361	0.302	0.426			1	INDETERMINATE	1	TRUE	NA	0.676877729857287	2		363	344	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857229	78857229	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771456961	NA	P-0069346-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	72	429	0	ENST00000306801.3:c.1595G>A	p.Arg532Gln	p.R532Q	ENST00000306801	NM_020761.2	532	cGg/cAg	15/34	0.355380741505758	2	FACETS	0.514	0.451	0.581	0.257	0.225	0.291	INDETERMINATE	1	TRUE	0	0.676877729857287	2		429	414	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89176391	89176391	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069346-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	31	306	0	ENST00000336596.2:c.121G>T	p.Glu41Ter	p.E41*	ENST00000336596	NM_005233.5	41	Gag/Tag	2/17	0.482582260172275	1	FACETS	0.449	0.369	0.536	0.449	0.369	0.536	SUBCLONAL	1	TRUE	0	0.676877729857287	1		306	135	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs28934577	NA	P-0069347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	60	373	0	ENST00000269305.4:c.770T>G	p.Leu257Arg	p.L257R	ENST00000269305	NM_001126112.2	257	cTg/cGg	7/11	1	2	FACETS	0.845	0.731	0.967	0.845	0.731	0.967	CLONAL	1	TRUE	1	0.37	2		373	384	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448615	89448615	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	26	372	0	ENST00000336596.2:c.1579G>A	p.Glu527Lys	p.E527K	ENST00000336596	NM_005233.5	527	Gaa/Aaa	7/17	1	2	FACETS	0.317	0.25	0.393	0.317	0.25	0.393	SUBCLONAL	1	TRUE	1	0.37	2		372	444	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562483	21562488	+	inframe_deletion	In_Frame_Del	DEL	GGGGCG	GGGGCG	-	rs550642106	NA	P-0069347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	8	443	1	ENST00000382592.4:c.1431_1436del	p.Pro479_Ala480del	p.P479_A480del	ENST00000382592	NM_014572.2	477	ccCGCCCCg/ccg	4/8	1	2	FACETS	0.124	0.079	0.182	0.124	0.079	0.182	SUBCLONAL	1	TRUE	1	0.37	2		444	350	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353767	40353767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760771231	NA	P-0069347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	82	410	0	ENST00000293328.3:c.2353G>A	p.Ala785Thr	p.A785T	ENST00000293328	NM_012448.3	785	Gca/Aca	19/19	1	2	FACETS	0.841	0.743	0.945	0.841	0.743	0.945	CLONAL	1	TRUE	1	0.37	2		410	527	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042452	37042452	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553640187	NA	P-0069347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	25	217	0	ENST00000231790.2:c.214G>A	p.Asp72Asn	p.D72N	ENST00000231790	NM_000249.3	72	Gat/Aat	3/19	1	2	FACETS	0.516	0.407	0.639	0.516	0.407	0.639	SUBCLONAL	1	TRUE	1	0.37	2		217	262	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216615	108216615	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	23	287	0	ENST00000278616.4:c.8564G>A	p.Ser2855Asn	p.S2855N	ENST00000278616	NM_000051.3	2855	aGt/aAt	58/63	1	2	FACETS	0.491	0.384	0.615	0.491	0.384	0.615	SUBCLONAL	1	TRUE	1	0.37	2		287	253	SUCCESS
SCG5	6447	MSKCC	GRCh37	15	32936000	32936000	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	22	369	0	ENST00000300175.4:c.209del	p.Gly70AlafsTer29	p.G70Afs*29	ENST00000300175	NM_001144757.1	69	gtG/gt	2/6	1	2	FACETS	0.307	0.238	0.388	0.307	0.238	0.388	SUBCLONAL	1	TRUE	1	0.37	2		369	387	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829609	72829609	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	24	377	0	ENST00000268489.5:c.6972C>A	p.Ser2324Arg	p.S2324R	ENST00000268489	NM_006885.3	2324	agC/agA	9/10	1	2	FACETS	0.366	0.287	0.458	0.366	0.287	0.458	SUBCLONAL	1	TRUE	1	0.37	2		377	354	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550828	150551003	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTAGCCACAAAGGCACCAAAAGAAATGAGAGTCACAATCCTGCCCCAGTTTGTTACGCCGTCGCTGAAAACATGGATCATCACTCGAGACAACGATTTCACATCGTCTTCGTTTTTGATGTCCAGTTTCCGAAGCATGCCTGAGAAAGAAAAGCATGCAGGTCCTCACGGCCTCC	TTTAGCCACAAAGGCACCAAAAGAAATGAGAGTCACAATCCTGCCCCAGTTTGTTACGCCGTCGCTGAAAACATGGATCATCACTCGAGACAACGATTTCACATCGTCTTCGTTTTTGATGTCCAGTTTCCGAAGCATGCCTGAGAAAGAAAAGCATGCAGGTCCTCACGGCCTCC	-	novel	NA	P-0069347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	29	428	0	ENST00000369026.2:c.689-36_828del		p.X230_splice	ENST00000369026	NM_021960.4	230		2/3	1	2	FACETS	0.299	0.239	0.367	0.299	0.239	0.367	SUBCLONAL	1	TRUE	1	0.37	2		428	524	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0069348-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	121	290	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		290	329	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0069348-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	112	334	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		334	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0069348-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	146	523	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		523	420	SUCCESS
APC	324	MSKCC	GRCh37	5	112137048	112137048	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1326410920	NA	P-0069348-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	55	270	0	ENST00000257430.4:c.802G>T	p.Glu268Ter	p.E268*	ENST00000257430	NM_000038.5	268	Gaa/Taa	8/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		270	329	SUCCESS
APC	324	MSKCC	GRCh37	5	112175171	112175171	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085373	NA	P-0069348-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	224	407	0	ENST00000257430.4:c.3880C>T	p.Gln1294Ter	p.Q1294*	ENST00000257430	NM_000038.5	1294	Cag/Tag	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		407	434	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210691	5210691	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069348-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	70	477	0	ENST00000357368.4:c.5360G>A	p.Arg1787Gln	p.R1787Q	ENST00000357368	NM_002850.3	1787	cGg/cAg	34/38	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		477	367	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460351	149460351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1318254419	NA	P-0069348-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	68	345	0	ENST00000286301.3:c.286G>A	p.Ala96Thr	p.A96T	ENST00000286301	NM_005211.3	96	Gcc/Acc	3/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		345	318	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120291	70120292	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0069348-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	255	422	0	ENST00000245479.2:c.1294dup	p.Tyr432LeufsTer146	p.Y432Lfs*146	ENST00000245479	NM_000346.3	431	-/T	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		422	525	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001505	150001576	+	inframe_deletion	In_Frame_Del	DEL	ATTTTAGCCCTTTTAAGACGGATGTAATTAGATTCTTTTTGGCAAAGCATCTTTCTCATTTGATCCTGGGCA	ATTTTAGCCCTTTTAAGACGGATGTAATTAGATTCTTTTTGGCAAAGCATCTTTCTCATTTGATCCTGGGCA	-	novel	NA	P-0069348-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	37	339	0	ENST00000253339.5:c.2028_2099del	p.Asp676_Met700delinsGlu	p.D676_M700delinsE	ENST00000253339		676	gaTGCCCAGGATCAAATGAGAAAGATGCTTTGCCAAAAAGAATCTAATTACATCCGTCTTAAAAGGGCTAAAATg/gag	4/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		339	261	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712526	52712526	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069348-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	184	299	0	ENST00000394830.3:c.226C>A	p.Pro76Thr	p.P76T	ENST00000394830	NM_018313.4	76	Cca/Aca	3/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		299	423	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436979	110436979	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069348-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	108	468	0	ENST00000375856.3:c.1422C>G	p.His474Gln	p.H474Q	ENST00000375856	NM_003749.2	474	caC/caG	1/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		468	592	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509403	46509403	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069348-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	92	385	0	ENST00000262741.5:c.1328C>A	p.Ser443Tyr	p.S443Y	ENST00000262741	NM_003629.3	443	tCc/tAc	10/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		385	355	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0069349-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	149	319	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.26269613114812	3	FACETS	0.796	0.731	0.863	0.796	0.731	0.863	SUBCLONAL	2	TRUE	1	0.414775698643445	3		319	545	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259521	55259521	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069349-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	155	309	0	ENST00000275493.2:c.2579A>T	p.Lys860Ile	p.K860I	ENST00000275493	NM_005228.3	860	aAa/aTa	21/28	0.26269613114812	3	FACETS	0.809	0.744	0.875	0.809	0.744	0.875	CLONAL	2	TRUE	1	0.414775698643445	3		309	558	SUCCESS
APC	324	MSKCC	GRCh37	5	112174291	112174291	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1580629755	NA	P-0069349-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	36	371	0	ENST00000257430.4:c.3000C>A	p.Tyr1000Ter	p.Y1000*	ENST00000257430	NM_000038.5	1000	taC/taA	16/16	0.414775698643445	1	FACETS	0.335	0.275	0.402	0.335	0.275	0.402	SUBCLONAL	1	TRUE	0	0.414775698643445	1		371	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0069350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	25	394	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.307947906551024	1	FACETS	0.348	0.277	0.427	0.348	0.277	0.427	INDETERMINATE	1	TRUE	0	0.639214042067786	1		394	153	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0069350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	29	406	0				ENST00000310581	NM_198253.2	-/1132			0.186129503261109	1	FACETS	0.556	0.456	0.665	0.556	0.456	0.665	INDETERMINATE	1	TRUE	0	0.639214042067786	1		406	111	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0069350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	93	529	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.307947906551024	1	FACETS	0.861	0.78	0.943	0.861	0.78	0.943	INDETERMINATE	1	TRUE	0	0.639214042067786	1		529	230	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0069350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	121	538	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.624833922830235	2	FACETS	0.971	0.905	1	0.971	0.905	1	CLONAL	2	TRUE	0	0.639214042067786	2		538	195	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007635	45007635	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	37	423	0	ENST00000558401.1:c.82C>T	p.Gln28Ter	p.Q28*	ENST00000558401	NM_004048.2	28	Cag/Tag	2/4	0.307947906551024	1	FACETS	0.382	0.318	0.453	0.382	0.318	0.453	INDETERMINATE	1	TRUE	0	0.639214042067786	1		423	206	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402563	139402564	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0069350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	59	533	0	ENST00000277541.6:c.3353dup	p.His1118GlnfsTer26	p.H1118Qfs*26	ENST00000277541	NM_017617.3	1118	cat/caAt	21/34	1	2	FACETS	0.918	0.803	1	0.918	0.803	1	CLONAL	1	TRUE	1	0.639214042067786	2		533	201	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007624	45007624	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	38	410	0	ENST00000558401.1:c.71C>G	p.Thr24Ser	p.T24S	ENST00000558401	NM_004048.2	24	aCt/aGt	2/4	0.307947906551024	1	FACETS	0.387	0.323	0.457	0.387	0.323	0.457	INDETERMINATE	1	TRUE	0	0.639214042067786	1		410	209	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539495	187539495	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	196	459	0	ENST00000441802.2:c.8245G>T	p.Glu2749Ter	p.E2749*	ENST00000441802	NM_005245.3	2749	Gag/Tag	10/27	1	2	FACETS	1	0.98	1	1	0.995	1	CLONAL	2	TRUE	1	0.639214042067786	2		459	289	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713854	30713854	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	74	516	0	ENST00000295754.5:c.1179C>G	p.Cys393Trp	p.C393W	ENST00000295754	NM_003242.5	393	tgC/tgG	4/7	0.625456998616096	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.639214042067786	1		516	154	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158225	47158225	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	56	212	0	ENST00000409792.3:c.4474C>T	p.Arg1492Ter	p.R1492*	ENST00000409792	NM_014159.6	1492	Cga/Tga	4/21	1	2	FACETS	0.931	0.805	1	1	0.976	1	CLONAL	2	TRUE	1	0.223605705082457	2		212	269	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403477	139403478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAACGAGTTGATGC	novel	NA	P-0069351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	23	502	0	ENST00000277541.6:c.3002_3015dup	p.Thr1006AlafsTer178	p.T1006Afs*178	ENST00000277541	NM_017617.3	1005	-/GCATCAACTCGTTC	19/34	1	2	FACETS	0.454	0.353	0.572	0.454	0.353	0.572	SUBCLONAL	1	TRUE	1	0.223605705082457	2		502	453	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390881	139390882	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CTCCACTCAGGAAG	novel	NA	P-0069351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	26	494	0	ENST00000277541.6:c.7296_7309dup	p.Glu2437AlafsTer3	p.E2437Afs*3	ENST00000277541	NM_017617.3	2437	gag/gCTTCCTGAGTGGAGag	34/34	1	2	FACETS	0.483	0.382	0.6	0.483	0.382	0.6	SUBCLONAL	1	TRUE	1	0.223605705082457	2		494	481	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	113	394	2	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.798	0.724	0.874	1	0.986	1	SUBCLONAL	2	TRUE	1	0.354186272650248	2		396	400	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	55	257	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.965	0.83	1	0.965	0.83	1	CLONAL	1	TRUE	1	0.354186272650248	2		257	322	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	63	440	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.901	0.782	1	0.901	0.782	1	CLONAL	1	TRUE	1	0.354186272650248	2		440	395	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513282	44513287	+	inframe_deletion	In_Frame_Del	DEL	CCACCG	CCACCG	-	rs745888281	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	17	421	1	ENST00000291552.4:c.648_653del	p.Gly222_Gly223del	p.G222_G223del	ENST00000291552	NM_006758.2	216	ggCGGTGGt/ggt	8/8	1	2	FACETS	0.209	0.155	0.274	0.209	0.155	0.274	SUBCLONAL	1	TRUE	1	0.354186272650248	2		422	459	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	34	359	0	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	0.436	0.356	0.526	0.436	0.356	0.526	SUBCLONAL	1	TRUE	1	0.354186272650248	2		359	440	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564516	55564516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1174814949	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	75	392	0	ENST00000288135.5:c.404G>A	p.Arg135His	p.R135H	ENST00000288135	NM_000222.2	135	cGc/cAc	3/21	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.354186272650248	2		392	376	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779211	3779211	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783507	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	14	372	0	ENST00000262367.5:c.5837del	p.Pro1946HisfsTer30	p.P1946Hfs*30	ENST00000262367	NM_004380.2	1946	cCa/ca	31/31	1	2	FACETS	0.348	0.252	0.465	0.348	0.252	0.465	SUBCLONAL	1	TRUE	1	0.354186272650248	2		372	227	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	98	590	0	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.354186272650248	2		590	476	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	47	538	0	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.788	0.667	0.919	0.788	0.667	0.919	CLONAL	1	TRUE	1	0.354186272650248	2		538	337	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226568861	226568861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150379323	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	50	405	1	ENST00000366794.5:c.1208G>A	p.Arg403Gln	p.R403Q	ENST00000366794	NM_001618.3	403	cGg/cAg	9/23	1	2	FACETS	0.786	0.67	0.914	0.786	0.67	0.914	CLONAL	1	TRUE	1	0.354186272650248	2		406	359	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790494	3790494	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867855180	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	44	383	1	ENST00000262367.5:c.4039C>T	p.Arg1347Trp	p.R1347W	ENST00000262367	NM_004380.2	1347	Cgg/Tgg	24/31	1	2	FACETS	0.605	0.508	0.711	0.605	0.508	0.711	SUBCLONAL	1	TRUE	1	0.354186272650248	2		384	411	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	73	517	6	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.918	0.806	1	0.918	0.806	1	CLONAL	1	TRUE	1	0.354186272650248	2		523	449	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346158	89346158	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs878855327	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	67	561	2	ENST00000301030.4:c.6792del	p.Ala2265ProfsTer72	p.A2265Pfs*72	ENST00000301030	NM_001256183.1	2264	ccC/cc	9/13	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.354186272650248	2		563	330	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022999	27022999	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1436957504	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	33	417	0	ENST00000324856.7:c.110del	p.Gly37AlafsTer14	p.G37Afs*14	ENST00000324856	NM_006015.4	35	gcG/gc	1/20	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.354186272650248	2		417	160	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027196	48027196	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs267608083	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	27	419	0	ENST00000234420.5:c.2079del	p.Lys693AsnfsTer43	p.K693Nfs*43	ENST00000234420	NM_000179.2	692	Aaa/aa	4/10	1	2	FACETS	0.411	0.327	0.507	0.411	0.327	0.507	SUBCLONAL	1	TRUE	1	0.354186272650248	2		419	371	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252961	36252961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	36	404	0	ENST00000300305.3:c.401C>T	p.Ala134Val	p.A134V	ENST00000300305		134	gCt/gTt	4/8	1	2	FACETS	0.452	0.371	0.542	0.452	0.371	0.542	SUBCLONAL	1	TRUE	1	0.354186272650248	2		404	450	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151290	202151290	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	36	333	0	ENST00000358485.4:c.1596del	p.Lys532AsnfsTer73	p.K532Nfs*73	ENST00000358485	NM_001080125.1	530	agA/ag	9/9	1	2	FACETS	0.508	0.418	0.609	0.508	0.418	0.609	SUBCLONAL	1	TRUE	1	0.354186272650248	2		333	400	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671654	67671655	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	94	444	4	ENST00000264010.4:c.2070dup	p.Glu691ArgfsTer5	p.E691Rfs*5	ENST00000264010	NM_006565.3	688	gta/gtAa	12/12	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.354186272650248	2		448	444	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358979	81358979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754502188	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	60	353	0	ENST00000222390.5:c.982C>T	p.Arg328Cys	p.R328C	ENST00000222390	NM_000601.4	328	Cgt/Tgt	8/18	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.354186272650248	2		353	338	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157998	106157998	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1560547088	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	99	488	0	ENST00000380013.4:c.2899C>T	p.Gln967Ter	p.Q967*	ENST00000380013	NM_001127208.2	967	Caa/Taa	3/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.354186272650248	2		488	445	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251108	99251109	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs746570875	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	65	469	0	ENST00000268035.6:c.418dup	p.Ala140GlyfsTer5	p.A140Gfs*5	ENST00000268035	NM_000875.3	138	cgg/cGgg	2/21	1	2	FACETS	0.976	0.851	1	0.976	0.851	1	CLONAL	1	TRUE	1	0.354186272650248	2		469	376	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428410	49428411	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1284500089	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	23	497	0	ENST00000301067.7:c.10394dup	p.Pro3466ThrfsTer2	p.P3466Tfs*2	ENST00000301067	NM_003482.3	3465	gga/ggGa	36/54	1	2	FACETS	0.326	0.253	0.409	0.326	0.253	0.409	SUBCLONAL	1	TRUE	1	0.354186272650248	2		497	399	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602449	10602449	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	77	596	1	ENST00000171111.5:c.1129G>A	p.Val377Met	p.V377M	ENST00000171111	NM_203500.1	377	Gtg/Atg	3/6	1	2	FACETS	0.906	0.798	1	0.906	0.798	1	CLONAL	1	TRUE	1	0.354186272650248	2		597	480	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213485	36213485	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	63	539	0	ENST00000222270.7:c.2587G>A	p.Val863Met	p.V863M	ENST00000222270	NM_014727.1	863	Gtg/Atg	5/37	1	2	FACETS	0.87	0.755	0.993	0.87	0.755	0.993	CLONAL	1	TRUE	1	0.354186272650248	2		539	409	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994829	73994829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751833994	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	20	226	0	ENST00000318443.5:c.313G>A	p.Ala105Thr	p.A105T	ENST00000318443	NM_001024736.1	105	Gca/Aca	3/10	1	2	FACETS	0.743	0.573	0.938	0.743	0.573	0.938	CLONAL	1	TRUE	1	0.354186272650248	2		226	152	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281248	15281248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754875491	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	73	613	0	ENST00000263388.2:c.5008G>A	p.Glu1670Lys	p.E1670K	ENST00000263388	NM_000435.2	1670	Gag/Aag	27/33	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.354186272650248	2		613	377	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445019	89445019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780126700	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	73	406	0	ENST00000336596.2:c.1339C>T	p.Arg447Trp	p.R447W	ENST00000336596	NM_005233.5	447	Cgg/Tgg	6/17	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.354186272650248	2		406	388	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407932	139407934	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs587778559	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	35	436	0	ENST00000277541.6:c.2263_2265del	p.Asn755del	p.N755del	ENST00000277541	NM_017617.3	755	AAT/-	14/34	1	2	FACETS	0.417	0.341	0.502	0.417	0.341	0.502	SUBCLONAL	1	TRUE	1	0.354186272650248	2		436	474	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880194	37880195	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	22	458	0	ENST00000269571.5:c.2242dup	p.Ile748AsnfsTer126	p.I748Nfs*126	ENST00000269571		746	-/A	19/27	1	2	FACETS	0.349	0.27	0.441	0.349	0.27	0.441	SUBCLONAL	1	TRUE	1	0.354186272650248	2		458	356	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435668	56435669	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	132	526	0	ENST00000407977.2:c.1468dup	p.Val490GlyfsTer15	p.V490Gfs*15	ENST00000407977		490	gtc/gGtc	9/10	0.354186272650248	2	FACETS	0.963	0.884	1	0.963	0.884	1	CLONAL	2	TRUE	0	0.354186272650248	2		526	387	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981767	63981767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760471271	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	78	535	0	ENST00000398590.3:c.2269G>A	p.Gly757Ser	p.G757S	ENST00000398590	NM_001177387.1	757	Ggc/Agc	12/14	1	2	FACETS	0.923	0.814	1	0.923	0.814	1	CLONAL	1	TRUE	1	0.354186272650248	2		535	477	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543379	65543379	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	48	442	0	ENST00000358664.4:c.298C>A	p.Arg100Ser	p.R100S	ENST00000358664	NM_002382.4	100	Cgt/Agt	5/5	1	2	FACETS	0.741	0.628	0.864	0.741	0.628	0.864	SUBCLONAL	1	TRUE	1	0.354186272650248	2		442	366	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100886	27100886	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1434951491	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	24	446	0	ENST00000324856.7:c.4168A>G	p.Ser1390Gly	p.S1390G	ENST00000324856	NM_006015.4	1390	Agc/Ggc	18/20	1	2	FACETS	0.338	0.264	0.423	0.338	0.264	0.423	SUBCLONAL	1	TRUE	1	0.354186272650248	2		446	401	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261454	16261454	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	69	510	0	ENST00000375759.3:c.8719C>T	p.Pro2907Ser	p.P2907S	ENST00000375759	NM_015001.2	2907	Cca/Tca	11/15	1	2	FACETS	0.884	0.772	1	0.884	0.772	1	CLONAL	1	TRUE	1	0.354186272650248	2		510	441	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149450114	149450115	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	19	421	0	ENST00000286301.3:c.1102_1103del	p.Leu368AlafsTer7	p.L368Afs*7	ENST00000286301	NM_005211.3	368	CTg/g	8/22	1	2	FACETS	0.313	0.237	0.402	0.313	0.237	0.402	SUBCLONAL	1	TRUE	1	0.354186272650248	2		421	343	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46733179	46733179	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1167366835	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	96	411	0	ENST00000371975.4:c.940A>G	p.Ser314Gly	p.S314G	ENST00000371975	NM_003579.3	314	Agc/Ggc	9/18	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.354186272650248	2		411	432	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743347	162743347	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	76	438	0	ENST00000367921.3:c.1817C>A	p.Ala606Asp	p.A606D	ENST00000367921	NM_006182.2	606	gCt/gAt	14/18	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.354186272650248	2		438	420	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625188	69625188	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	22	502	0	ENST00000334134.2:c.605del	p.Pro202LeufsTer?	p.P202Lfs*?	ENST00000334134	NM_005247.2	202	cCt/ct	3/3	1	2	FACETS	0.364	0.282	0.46	0.364	0.282	0.46	SUBCLONAL	1	TRUE	1	0.354186272650248	2		502	341	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035066	37035066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1193754562	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	72	451	0	ENST00000231790.2:c.28C>T	p.Arg10Trp	p.R10W	ENST00000231790	NM_000249.3	10	Cgg/Tgg	1/19	1	2	FACETS	0.878	0.77	0.994	0.878	0.77	0.994	CLONAL	1	TRUE	1	0.354186272650248	2		451	463	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968074	55968075	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	45	286	0	ENST00000263923.4:c.2255dup	p.Ile753HisfsTer38	p.I753Hfs*38	ENST00000263923	NM_002253.2	752	ttc/ttTc	15/30	1	2	FACETS	0.97	0.821	1	0.97	0.821	1	CLONAL	1	TRUE	1	0.354186272650248	2		286	262	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124467253	124467274	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCTCTGATACTTACAGAATCC	ACCTCTGATACTTACAGAATCC	-	novel	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	38	248	0	ENST00000357628.3:c.1680_1686+15del		p.X560_splice	ENST00000357628	NM_015450.2	560		17/19	1	2	FACETS	0.967	0.806	1	0.967	0.806	1	CLONAL	1	TRUE	1	0.354186272650248	2		248	222	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058512	72058512	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	77	411	0	ENST00000357731.5:c.928C>G	p.Leu310Val	p.L310V	ENST00000357731	NM_173808.2	310	Ctg/Gtg	6/7	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.354186272650248	2		411	396	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256949	16256950	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	27	467	0	ENST00000375759.3:c.4220dup	p.Leu1407PhefsTer11	p.L1407Ffs*11	ENST00000375759	NM_015001.2	1405	tct/tcTt	11/15	1	2	FACETS	0.318	0.253	0.394	0.318	0.253	0.394	SUBCLONAL	1	TRUE	1	0.354186272650248	2		467	479	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980374	201980374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762316328	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	30	520	0	ENST00000359651.3:c.110C>T	p.Ala37Val	p.A37V	ENST00000359651		37	gCc/gTc	1/8	1	2	FACETS	0.357	0.287	0.436	0.357	0.287	0.436	SUBCLONAL	1	TRUE	1	0.354186272650248	2		520	475	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129833	55129833	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1465072853	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	25	352	0	ENST00000257290.5:c.368-1G>A		p.X123_splice	ENST00000257290	NM_006206.4	123			1	2	FACETS	0.408	0.321	0.508	0.408	0.321	0.508	SUBCLONAL	1	TRUE	1	0.354186272650248	2		352	346	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196646	67196646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	52	466	0	ENST00000312629.5:c.175C>T	p.Pro59Ser	p.P59S	ENST00000312629	NM_003952.2	59	Cca/Tca	3/15	1	2	FACETS	0.796	0.68	0.922	0.796	0.68	0.922	CLONAL	1	TRUE	1	0.354186272650248	2		466	369	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0069363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	351	257	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.52070338202847	5	FACETS	0.964	0.918	1	0.964	0.918	1	CLONAL	3	TRUE	2	0.52070338202847	5		257	830	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs11575997	NA	P-0069363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	274	415	0	ENST00000269305.4:c.993+1G>T		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.52070338202847	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.52070338202847	2		415	464	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003184	42003184	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	43	376	0	ENST00000219905.7:c.2721C>G	p.Phe907Leu	p.F907L	ENST00000219905	NM_001164273.1	907	ttC/ttG	8/24	1	2	FACETS	0.298	0.248	0.352	0.298	0.248	0.352	SUBCLONAL	1	TRUE	1	0.52070338202847	2		376	555	SUCCESS
APC	324	MSKCC	GRCh37	5	112178130	112178130	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	256	402	0	ENST00000257430.4:c.6839C>T	p.Ser2280Leu	p.S2280L	ENST00000257430	NM_000038.5	2280	tCa/tTa	16/16	0.410299287373125	4	FACETS	0.929	0.872	0.986	0.929	0.872	0.986	CLONAL	2	TRUE	2	0.52070338202847	4		402	805	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007064	152007064	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0069363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	127	249	0	ENST00000262189.6:c.836C>G	p.Ser279Ter	p.S279*	ENST00000262189	NM_170606.2	279	tCa/tGa	6/59	0.52070338202847	5	FACETS	1	0.944	1	0.353	0.319	0.388	CLONAL	1	TRUE	2	0.52070338202847	5		249	821	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391404	139391404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770022692	NA	P-0069363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	133	396	0	ENST00000277541.6:c.6787C>T	p.Arg2263Trp	p.R2263W	ENST00000277541	NM_017617.3	2263	Cgg/Tgg	34/34	0.52070338202847	2	FACETS	1	0.964	1	0.55	0.503	0.599	CLONAL	1	TRUE	0	0.52070338202847	2		396	464	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984361	201984361	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	322	321	0	ENST00000359651.3:c.1027del	p.Glu343AsnfsTer104	p.E343Nfs*104	ENST00000359651		342	ctG/ct	8/8	0.52070338202847	5	FACETS	1	0.988	1	0.574	0.543	0.605	CLONAL	2	TRUE	1	0.52070338202847	5		321	960	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007580	62007580	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	214	399	0	ENST00000392795.3:c.287G>C	p.Arg96Pro	p.R96P	ENST00000392795	NM_001039933.1	96	cGc/cCc	3/6	0.489616048200751	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.52070338202847	4		399	605	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400098	41400098	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	59	271	0	ENST00000373198.4:c.661C>T	p.Gln221Ter	p.Q221*	ENST00000373198	NM_133170.3	221	Cag/Tag	5/32	1	2	FACETS	0.621	0.537	0.712	0.621	0.537	0.712	SUBCLONAL	1	TRUE	1	0.52070338202847	2		271	365	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170002313	170002313	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	58	139	0	ENST00000295797.4:c.1132G>C	p.Asp378His	p.D378H	ENST00000295797	NM_002740.5	378	Gat/Cat	12/18	0.489616048200751	4	FACETS	0.923	0.797	1	0.462	0.398	0.53	CLONAL	1	TRUE	2	0.52070338202847	4		139	367	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293914	1293914	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	103	447	0	ENST00000310581.5:c.1087A>T	p.Thr363Ser	p.T363S	ENST00000310581	NM_198253.2	363	Acc/Tcc	2/16	0.52070338202847	7	FACETS	0.91	0.812	1	0.182	0.162	0.203	CLONAL	1	TRUE	2	0.52070338202847	7		447	1001	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052980	180052980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	104	657	0	ENST00000261937.6:c.1310G>A	p.Arg437His	p.R437H	ENST00000261937	NM_182925.4	437	cGt/cAt	10/30	1	2	FACETS	0.997	0.896	1	0.997	0.896	1	CLONAL	1	TRUE	1	0.397253512111871	2		657	525	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	54	394	2	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.706	0.605	0.816	0.706	0.605	0.816	SUBCLONAL	1	TRUE	1	0.397253512111871	2		396	385	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	67	257	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.878	0.767	0.998	0.878	0.767	0.998	CLONAL	1	TRUE	1	0.397253512111871	2		257	384	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	79	435	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.397253512111871	2		435	371	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974721	21974721	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	82	560	1	ENST00000304494.5:c.106del	p.Ala36ArgfsTer17	p.A36Rfs*17	ENST00000304494	NM_000077.4	36	Gcg/cg	1/3	1	2	FACETS	0.882	0.781	0.99	0.882	0.781	0.99	CLONAL	1	TRUE	1	0.397253512111871	2		561	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514495	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	146	605	0	ENST00000269305.4:c.542G>A	p.Arg181His	p.R181H	ENST00000269305	NM_001126112.2	181	cGc/cAc	5/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.397253512111871	2		605	682	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	96	518	3	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	0.935	0.836	1	0.935	0.836	1	CLONAL	1	TRUE	1	0.397253512111871	2		521	517	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	101	535	8	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	0.875	0.784	0.971	0.875	0.784	0.971	CLONAL	1	TRUE	1	0.397253512111871	2		543	581	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366162	15366162	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1005077274	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	107	487	0	ENST00000263377.2:c.1993C>T	p.Arg665Cys	p.R665C	ENST00000263377	NM_058243.2	665	Cgt/Tgt	10/20	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.397253512111871	2		487	516	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533703	63533703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	119	630	0	ENST00000307078.5:c.1451G>A	p.Gly484Asp	p.G484D	ENST00000307078	NM_004655.3	484	gGt/gAt	6/11	0.397253512111871	2	FACETS	1	0.935	1	0.52	0.471	0.572	CLONAL	1	TRUE	0	0.397253512111871	2		630	576	SUCCESS
AR	367	MSKCC	GRCh37	X	66765149	66765151	+	inframe_deletion	In_Frame_Del	DEL	TGC	TGC	-	rs752055010	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	14	166	2	ENST00000374690.3:c.170_172del	p.Leu57del	p.L57del	ENST00000374690	NM_000044.3	54	tTGCtg/ttg	1/8	1	1	FACETS	0.428	0.311	0.567	0.428	0.311	0.567	SUBCLONAL	1	TRUE	0	0.397253512111871	1		168	132	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	98	507	6	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.922	0.825	1	0.922	0.825	1	CLONAL	1	TRUE	1	0.397253512111871	2		513	535	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733513	85733513	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs387906350	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	85	538	1	ENST00000370580.1:c.499del	p.Ser167LeufsTer6	p.S167Lfs*6	ENST00000370580	NM_003921.4	167	Tct/ct	3/3	1	2	FACETS	0.905	0.803	1	0.905	0.803	1	CLONAL	1	TRUE	1	0.397253512111871	2		539	473	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511172	148511172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554486390	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	145	484	1	ENST00000320356.2:c.1730C>T	p.Pro577Leu	p.P577L	ENST00000320356	NM_004456.4	577	cCg/cTg	15/20	1	2	FACETS	0.995	0.909	1	0.995	0.909	1	CLONAL	1	TRUE	1	0.397253512111871	2		485	734	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619838	21619838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746455173	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	92	409	1	ENST00000382592.4:c.328G>A	p.Ala110Thr	p.A110T	ENST00000382592	NM_014572.2	110	Gca/Aca	2/8	1	2	FACETS	0.93	0.829	1	0.93	0.829	1	CLONAL	1	TRUE	1	0.397253512111871	2		410	498	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955112	17955112	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755706305	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	93	514	1	ENST00000458235.1:c.115del	p.Gln39SerfsTer108	p.Q39Sfs*108	ENST00000458235	NM_000215.3	39	Cag/ag	2/24	1	2	FACETS	0.906	0.808	1	0.906	0.808	1	CLONAL	1	TRUE	1	0.397253512111871	2		515	517	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655413	45655413	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	124	551	0	ENST00000407780.3:c.439del	p.His147ThrfsTer15	p.H147Tfs*15	ENST00000407780	NM_001283052.1	147	Cac/ac	4/7	1	2	FACETS	0.98	0.889	1	0.98	0.889	1	CLONAL	1	TRUE	1	0.397253512111871	2		551	637	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612344	1612344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1320707074	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	97	536	0	ENST00000344749.5:c.1675G>A	p.Val559Met	p.V559M	ENST00000344749	NM_001136139.2	559	Gtg/Atg	18/19	1	2	FACETS	0.851	0.76	0.947	0.851	0.76	0.947	CLONAL	1	TRUE	1	0.397253512111871	2		536	574	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592079	55592079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200518498	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	98	404	0	ENST00000288135.5:c.1403C>T	p.Pro468Leu	p.P468L	ENST00000288135	NM_000222.2	468	cCg/cTg	9/21	1	2	FACETS	0.902	0.807	1	0.902	0.807	1	CLONAL	1	TRUE	1	0.397253512111871	2		404	547	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474420	40474420	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs747639500	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	87	517	0	ENST00000264657.5:c.1981G>T	p.Asp661Tyr	p.D661Y	ENST00000264657	NM_139276.2	661	Gat/Tat	21/24	1	2	FACETS	0.942	0.837	1	0.942	0.837	1	CLONAL	1	TRUE	1	0.397253512111871	2		517	465	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870595	40870595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	144	522	0	ENST00000428826.2:c.808C>T	p.Pro270Ser	p.P270S	ENST00000428826		270	Ccc/Tcc	9/21	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.397253512111871	2		522	657	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865628	57865628	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	87	613	0	ENST00000228682.2:c.3109del	p.Leu1037TrpfsTer23	p.L1037Wfs*23	ENST00000228682	NM_005269.2	1035	aaC/aa	12/12	1	2	FACETS	0.825	0.732	0.923	0.825	0.732	0.923	CLONAL	1	TRUE	1	0.397253512111871	2		613	531	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918754	50918754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754832710	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	116	536	0	ENST00000440232.2:c.2624G>A	p.Arg875His	p.R875H	ENST00000440232	NM_002691.3	875	cGc/cAc	21/27	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.397253512111871	2		536	477	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001595	150001595	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	54	361	0	ENST00000253339.5:c.2011-2A>G		p.X671_splice	ENST00000253339		671			1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.397253512111871	2		361	257	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139532	47139532	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	114	440	1	ENST00000409792.3:c.5055C>A	p.Cys1685Ter	p.C1685*	ENST00000409792	NM_014159.6	1685	tgC/tgA	9/21	1	2	FACETS	0.941	0.849	1	0.941	0.849	1	CLONAL	1	TRUE	1	0.397253512111871	2		441	610	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512474	38512474	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	97	542	0	ENST00000254066.5:c.1385C>A	p.Pro462Gln	p.P462Q	ENST00000254066	NM_000964.3	462	cCg/cAg	9/9	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.397253512111871	2		542	468	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039600	180039600	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	85	428	0	ENST00000261937.6:c.3443T>C	p.Met1148Thr	p.M1148T	ENST00000261937	NM_182925.4	1148	aTg/aCg	26/30	1	2	FACETS	0.993	0.882	1	0.993	0.882	1	CLONAL	1	TRUE	1	0.397253512111871	2		428	431	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222265	2222265	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369350082	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	107	627	0	ENST00000398665.3:c.3097G>A	p.Gly1033Ser	p.G1033S	ENST00000398665	NM_032482.2	1033	Ggc/Agc	24/28	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.397253512111871	2		627	510	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096639	178096639	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs779897588	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	148	410	0	ENST00000397062.3:c.692C>G	p.Ser231Cys	p.S231C	ENST00000397062	NM_006164.4	231	tCt/tGt	5/5	0.370451642301155	3	FACETS	1	0.925	1	1	0.925	1	CLONAL	2	TRUE	1	0.397253512111871	3		410	445	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29445998	29445999	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	81	513	2	ENST00000544604.2:c.1835dup	p.Ser613LeufsTer68	p.S613Lfs*68	ENST00000544604	NM_001206998.1	610	gcg/gcGg	8/9	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.397253512111871	2		515	395	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29279873	29279873	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs978074103	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	35	272	0	ENST00000544604.2:c.119T>C	p.Leu40Pro	p.L40P	ENST00000544604	NM_001206998.1	40	cTg/cCg	1/9	1	2	FACETS	0.787	0.65	0.938	0.787	0.65	0.938	CLONAL	1	TRUE	1	0.397253512111871	2		272	224	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992996	72992996	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs983979744	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	106	573	0	ENST00000268489.5:c.1049C>T	p.Pro350Leu	p.P350L	ENST00000268489	NM_006885.3	350	cCt/cTt	2/10	1	2	FACETS	0.933	0.839	1	0.933	0.839	1	CLONAL	1	TRUE	1	0.397253512111871	2		573	572	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096048	11096048	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	107	559	0	ENST00000358026.2:c.326del	p.Pro109ArgfsTer194	p.P109Rfs*194	ENST00000358026	NM_001128849.1	108	Ccc/cc	3/36	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.397253512111871	2		559	519	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111886013	111886013	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	129	651	0	ENST00000341259.2:c.1635G>T	p.Glu545Asp	p.E545D	ENST00000341259	NM_005475.2	545	gaG/gaT	8/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.397253512111871	2		651	591	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38785191	38785191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766200637	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	126	431	0	ENST00000348513.6:c.1082C>T	p.Thr361Met	p.T361M	ENST00000348513	NM_003079.4	361	aCg/aTg	11/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.397253512111871	2		431	585	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178623	56178623	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	113	482	0	ENST00000399503.3:c.3596A>G	p.Gln1199Arg	p.Q1199R	ENST00000399503	NM_005921.1	1199	cAg/cGg	14/20	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.397253512111871	2		482	530	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212522516	212522516	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	78	491	0	ENST00000342788.4:c.1909C>T	p.Pro637Ser	p.P637S	ENST00000342788	NM_005235.2	637	Cca/Tca	16/28	0.370451642301155	3	FACETS	0.85	0.748	0.959	0.425	0.374	0.48	CLONAL	1	TRUE	1	0.397253512111871	3		491	554	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982090	201982090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41270965	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	124	510	0	ENST00000359651.3:c.614G>A	p.Arg205Gln	p.R205Q	ENST00000359651		205	cGg/cAg	5/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.397253512111871	2		510	496	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221331	1221331	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555738724	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	243	629	0	ENST00000326873.7:c.854T>C	p.Leu285Pro	p.L285P	ENST00000326873	NM_000455.4	285	cTg/cCg	6/10	1	2	FACETS	1	0.96	1	1	0.995	1	CLONAL	2	TRUE	1	0.397253512111871	2		629	597	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441304	149441304	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	113	540	0	ENST00000286301.3:c.1735del	p.Arg579GlyfsTer33	p.R579Gfs*33	ENST00000286301	NM_005211.3	579	Cgg/gg	12/22	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.397253512111871	2		540	569	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311610	15311610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1311684711	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	87	793	0	ENST00000263388.2:c.107C>T	p.Pro36Leu	p.P36L	ENST00000263388	NM_000435.2	36	cCg/cTg	1/33	1	2	FACETS	0.828	0.735	0.927	0.828	0.735	0.927	CLONAL	1	TRUE	1	0.397253512111871	2		793	529	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843570	3843570	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	108	545	0	ENST00000262367.5:c.1033A>G	p.Thr345Ala	p.T345A	ENST00000262367	NM_004380.2	345	Act/Gct	4/31	1	2	FACETS	0.863	0.776	0.955	0.863	0.776	0.955	CLONAL	1	TRUE	1	0.397253512111871	2		545	630	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858065	40858065	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	108	465	0	ENST00000428826.2:c.1799T>C	p.Val600Ala	p.V600A	ENST00000428826		600	gTt/gCt	16/21	1	2	FACETS	0.998	0.899	1	0.998	0.899	1	CLONAL	1	TRUE	1	0.397253512111871	2		465	545	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572378	41572378	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	130	584	0	ENST00000263253.7:c.4907A>G	p.Asp1636Gly	p.D1636G	ENST00000263253	NM_001429.3	1636	gAc/gGc	30/31	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.397253512111871	2		584	617	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019417	42019417	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	61	467	2	ENST00000219905.7:c.3470A>G	p.Tyr1157Cys	p.Y1157C	ENST00000219905	NM_001164273.1	1157	tAc/tGc	10/24	1	2	FACETS	0.839	0.727	0.959	0.839	0.727	0.959	CLONAL	1	TRUE	1	0.397253512111871	2		469	366	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740360	145740360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766354337	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	105	537	0	ENST00000428558.2:c.1580C>T	p.Thr527Met	p.T527M	ENST00000428558	NM_004260.3	527	aCg/aTg	9/22	0.397253512111871	3	FACETS	1	0.952	1	0.55	0.494	0.609	CLONAL	1	TRUE	1	0.397253512111871	3		537	576	SUCCESS
APC	324	MSKCC	GRCh37	5	112179143	112179143	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs863224551	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	84	474	0	ENST00000257430.4:c.7852A>G	p.Asn2618Asp	p.N2618D	ENST00000257430	NM_000038.5	2618	Aat/Gat	16/16	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.397253512111871	2		474	408	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440761	56440761	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	275	583	0	ENST00000407977.2:c.457C>T	p.Gln153Ter	p.Q153*	ENST00000407977		153	Cag/Tag	5/10	0.397253512111871	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.397253512111871	2		583	638	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353883	40353883	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	96	459	1	ENST00000293328.3:c.2238-1G>T		p.X746_splice	ENST00000293328	NM_012448.3	746			1	2	FACETS	0.971	0.868	1	0.971	0.868	1	CLONAL	1	TRUE	1	0.397253512111871	2		460	498	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104668	69104668	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	132	479	0	ENST00000288368.4:c.4512T>A	p.Ser1504Arg	p.S1504R	ENST00000288368	NM_024870.2	1504	agT/agA	37/40	1	2	FACETS	0.918	0.834	1	0.918	0.834	1	CLONAL	1	TRUE	1	0.397253512111871	2		479	724	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100015	11100015	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs972341316	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	112	456	0	ENST00000358026.2:c.1141C>T	p.Arg381Ter	p.R381*	ENST00000358026	NM_001128849.1	381	Cga/Tga	7/36	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.397253512111871	2		456	533	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755644	39755644	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	107	530	0	ENST00000288319.7:c.1121A>T	p.Asp374Val	p.D374V	ENST00000288319	NM_182918.3	374	gAc/gTc	10/10	1	2	FACETS	0.948	0.853	1	0.948	0.853	1	CLONAL	1	TRUE	1	0.397253512111871	2		530	568	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396223	139396223	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	94	548	0	ENST00000277541.6:c.5615T>A	p.Met1872Lys	p.M1872K	ENST00000277541	NM_017617.3	1872	aTg/aAg	30/34	1	2	FACETS	0.956	0.854	1	0.956	0.854	1	CLONAL	1	TRUE	1	0.397253512111871	2		548	495	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120493356	120493356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	121	502	2	ENST00000256646.2:c.2470C>T	p.Pro824Ser	p.P824S	ENST00000256646	NM_024408.3	824	Cca/Tca	15/34	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.397253512111871	2		504	602	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796314	57796315	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	82	502	0	ENST00000309042.7:c.1296dup	p.Arg433ThrfsTer4	p.R433Tfs*4	ENST00000309042	NM_005612.4	430	-/A	4/4	1	2	FACETS	0.873	0.772	0.98	0.873	0.772	0.98	CLONAL	1	TRUE	1	0.397253512111871	2		502	473	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996795	73996795	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	77	398	0	ENST00000318443.5:c.1351G>T	p.Gly451Cys	p.G451C	ENST00000318443	NM_001024736.1	451	Ggc/Tgc	6/10	1	2	FACETS	0.952	0.841	1	0.952	0.841	1	CLONAL	1	TRUE	1	0.397253512111871	2		398	407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0069368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	52	419	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.2	2		419	438	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0069368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	12	294	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	0.408	0.286	0.559	0.408	0.286	0.559	SUBCLONAL	1	TRUE	1	0.2	2		294	294	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630085	67630085	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	12	269	0	ENST00000272342.5:c.521G>C	p.Arg174Thr	p.R174T	ENST00000272342	NM_019002.3	174	aGa/aCa	4/6	1	2	FACETS	0.511	0.358	0.698	0.511	0.358	0.698	SUBCLONAL	1	TRUE	1	0.2	2		269	235	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272171	18272190	+	frameshift_variant	Frame_Shift_Del	DEL	GCACCTGGGCCGCGTGGCCA	GCACCTGGGCCGCGTGGCCA	C	novel	NA	P-0069368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	55	501	0	ENST00000222254.8:c.681_700delinsC	p.Gln227HisfsTer108	p.Q227Hfs*108	ENST00000222254	NM_005027.3	227	caGCACCTGGGCCGCGTGGCCAgc/caCgc	6/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.2	2		501	376	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0069369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	97	269	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.814529363700862	2		269	173	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	155	471	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.790730567757566	1	FACETS	0.94	0.886	0.992	0.94	0.886	0.992	CLONAL	1	TRUE	0	0.814529363700862	1		471	240	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581229	48581229	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs377767331	NA	P-0069369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	15	369	0	ENST00000342988.3:c.533C>G	p.Ser178Ter	p.S178*	ENST00000342988	NM_005359.5	178	tCa/tGa	5/12	0.814529363700862	1	FACETS	0.1	0.073	0.132	0.1	0.073	0.132	SUBCLONAL	1	TRUE	0	0.814529363700862	1		369	219	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557570	21557570	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756702960	NA	P-0069369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	167	449	0	ENST00000382592.4:c.2275C>T	p.Arg759Trp	p.R759W	ENST00000382592	NM_014572.2	759	Cgg/Tgg	5/8	1	2	FACETS	0.979	0.91	1	0.979	0.91	1	CLONAL	1	TRUE	1	0.814529363700862	2		449	419	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94910925	94910925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749067368	NA	P-0069369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	112	292	0	ENST00000536441.1:c.1205G>A	p.Arg402His	p.R402H	ENST00000536441	NM_144665.3	402	cGc/cAc	8/10	0.814529363700862	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.814529363700862	1		292	153	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435856	56435860	+	frameshift_variant	Frame_Shift_Del	DEL	GTGCT	GTGCT	-	novel	NA	P-0069369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	78	581	0	ENST00000407977.2:c.1277_1281del	p.Gln426ProfsTer15	p.Q426Pfs*15	ENST00000407977		426	cAGCAC/c	9/10	0.814529363700862	1	FACETS	0.477	0.425	0.531	0.477	0.425	0.531	SUBCLONAL	1	TRUE	0	0.814529363700862	1		581	238	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46270986	46270986	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	60	314	0	ENST00000371998.3:c.3110T>C	p.Leu1037Pro	p.L1037P	ENST00000371998		1037	cTt/cCt	17/23	0.710730494575496	3	FACETS	0.423	0.365	0.486			1	SUBCLONAL	1	TRUE	NA	0.814529363700862	3		314	490	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670040	29670040	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	15	245	0	ENST00000356175.3:c.7013T>C	p.Val2338Ala	p.V2338A	ENST00000356175	NM_000267.3	2338	gTa/gCa	47/57	1	2	FACETS	0.146	0.106	0.193	0.146	0.106	0.193	SUBCLONAL	1	TRUE	1	0.814529363700862	2		245	253	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679841	30679841	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	84	444	0	ENST00000376406.3:c.1878G>C	p.Gln626His	p.Q626H	ENST00000376406	NM_014641.2	626	caG/caC	5/15	1	2	FACETS	0.476	0.423	0.533	0.476	0.423	0.533	SUBCLONAL	1	TRUE	1	0.814529363700862	2		444	433	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573389	48573428	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	TTTGATTTAAAAGGAAAAACTTGAACAAATGGACAATATG	TTTGATTTAAAAGGAAAAACTTGAACAAATGGACAATATG	-	novel	NA	P-0069369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	44	284	0	ENST00000342988.3:c.-27_13del		p.*9*	ENST00000342988	NM_005359.5	?-4/552		2/12	0.814529363700862	1	FACETS	0.421	0.36	0.487	0.421	0.36	0.487	SUBCLONAL	1	TRUE	0	0.814529363700862	1		284	152	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0069370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	40	206	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.509204322784087	3	FACETS	0.832	0.697	0.98	0.416	0.348	0.49	CLONAL	1	TRUE	1	0.509204322784087	3		206	237	SUCCESS
APC	324	MSKCC	GRCh37	5	112103041	112103041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	101	318	0	ENST00000257430.4:c.376G>A	p.Gly126Arg	p.G126R	ENST00000257430	NM_000038.5	126	Gga/Aga	4/16	1	2	FACETS	0.947	0.852	1	0.947	0.852	1	CLONAL	1	TRUE	1	0.509204322784087	2		318	419	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831241	3831241	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0069370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	96	340	0	ENST00000262367.5:c.1640C>G	p.Ser547Ter	p.S547*	ENST00000262367	NM_004380.2	547	tCa/tGa	7/31	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.509204322784087	2		340	361	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127460	55127460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779332376	NA	P-0069370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	110	409	0	ENST00000257290.5:c.248C>T	p.Thr83Met	p.T83M	ENST00000257290	NM_006206.4	83	aCg/aTg	3/23	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.509204322784087	2		409	407	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151164264	151164264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	41	191	0	ENST00000262187.5:c.496G>A	p.Glu166Lys	p.E166K	ENST00000262187	NM_005614.3	166	Gag/Aag	8/8	1	2	FACETS	0.87	0.734	1	0.87	0.734	1	CLONAL	1	TRUE	1	0.509204322784087	2		191	185	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123691	11123691	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	84	399	0	ENST00000358026.2:c.2341A>G	p.Met781Val	p.M781V	ENST00000358026	NM_001128849.1	781	Atg/Gtg	16/36	1	2	FACETS	0.815	0.724	0.911	0.815	0.724	0.911	CLONAL	1	TRUE	1	0.509204322784087	2		399	405	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033262	69033262	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	68	334	0	ENST00000288368.4:c.3702G>C	p.Gln1234His	p.Q1234H	ENST00000288368	NM_024870.2	1234	caG/caC	30/40	0.150556780855941	0	FACETS	0.497	0.437	0.56			1	INDETERMINATE	1	TRUE	0	0.509204322784087	0		334	264	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326442	62326442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479921630	NA	P-0069370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	101	467	0	ENST00000360203.5:c.3367C>T	p.His1123Tyr	p.H1123Y	ENST00000360203	NM_001283009.1	1123	Cac/Tac	33/35	1	2	FACETS	0.786	0.705	0.87	0.786	0.705	0.87	SUBCLONAL	1	TRUE	1	0.509204322784087	2		467	505	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832796	3832796	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	109	440	0	ENST00000262367.5:c.1462C>G	p.Leu488Val	p.L488V	ENST00000262367	NM_004380.2	488	Ctc/Gtc	6/31	1	2	FACETS	0.892	0.805	0.983	0.892	0.805	0.983	CLONAL	1	TRUE	1	0.509204322784087	2		440	480	SUCCESS
EED	8726	MSKCC	GRCh37	11	85963211	85963211	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	50	234	0	ENST00000263360.6:c.289T>C	p.Phe97Leu	p.F97L	ENST00000263360	NM_003797.3	97	Ttt/Ctt	3/12	1	2	FACETS	0.815	0.698	0.94	0.815	0.698	0.94	CLONAL	1	TRUE	1	0.509204322784087	2		234	241	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295152	91295152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	77	278	0	ENST00000355112.3:c.935C>T	p.Ser312Phe	p.S312F	ENST00000355112	NM_000057.2	312	tCt/tTt	4/22	NA	2	FACETS	0.933	0.827	1			1	INDETERMINATE	1	TRUE	NA	0.509204322784087	2		278	324	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985358	60985358	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	146	460	0	ENST00000333681.4:c.542T>A	p.Leu181Gln	p.L181Q	ENST00000333681		181	cTg/cAg	2/3	0.55413025008789	4	FACETS	0.9	0.822	0.982	0.45	0.411	0.491	CLONAL	1	TRUE	2	0.696410326121451	4		460	790	SUCCESS
EED	8726	MSKCC	GRCh37	11	85979509	85979509	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	59	297	0	ENST00000263360.6:c.872C>T	p.Ser291Phe	p.S291F	ENST00000263360	NM_003797.3	291	tCt/tTt	9/12	0.410223364014748	5	FACETS	0.476	0.409	0.549			1	INDETERMINATE	1	TRUE	NA	0.696410326121451	5		297	728	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244672	41244672	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	36	389	0	ENST00000357654.3:c.2876G>C	p.Arg959Thr	p.R959T	ENST00000357654	NM_007294.3	959	aGa/aCa	10/23	0.766127237557199	1	FACETS	0.226	0.187	0.27	0.226	0.187	0.27	SUBCLONAL	1	TRUE	0	0.766127237557199	1		389	256	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351966	89351983	+	inframe_deletion	In_Frame_Del	DEL	CTTGAGGCCTTTTTCGAA	CTTGAGGCCTTTTTCGAA	-	novel	NA	P-0069374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	162	380	0	ENST00000301030.4:c.967_984del	p.Phe323_Lys328del	p.F323_K328del	ENST00000301030	NM_001256183.1	323	TTCGAAAAAGGCCTCAAG/-	9/13	1	2	FACETS	0.795	0.734	0.858	0.795	0.734	0.858	SUBCLONAL	1	TRUE	1	0.766127237557199	2		380	532	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874206	155874206	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	206	334	0	ENST00000368323.3:c.325del	p.His109MetfsTer33	p.H109Mfs*33	ENST00000368323	NM_006912.5	109	Cat/at	5/6	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.766127237557199	2		334	512	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923777	39923780	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	novel	NA	P-0069374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	216	357	0	ENST00000378444.4:c.3311_3314del	p.Lys1104ThrfsTer8	p.K1104Tfs*8	ENST00000378444	NM_001123385.1	1104	aAGTAc/ac	7/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.766127237557199	2		357	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587781525	NA	P-0069375-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	148	454	1	ENST00000269305.4:c.842A>G	p.Asp281Gly	p.D281G	ENST00000269305	NM_001126112.2	281	gAc/gGc	8/11	0.418270909993839	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.418270909993839	1		455	524	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0069376-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	25	131	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.495757944796869	1	FACETS	0.998	0.812	1	0.998	0.812	1	CLONAL	1	TRUE	0	0.495757944796869	1		131	76	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0069376-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	99	451	1	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.495757944796869	2		452	342	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938230	76938230	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0069376-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	105	172	0	ENST00000373344.5:c.2518del	p.Arg840GlufsTer29	p.R840Efs*29	ENST00000373344	NM_000489.3	840	Aga/ga	9/35	1	1	FACETS	0.813	0.748	0.877	1	0.988	1	CLONAL	2	TRUE	0	0.495757944796869	1		172	196	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104356980	104356981	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1477199832	NA	P-0069376-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	69	284	0	ENST00000369902.3:c.846dup	p.Glu283ArgfsTer3	p.E283Rfs*3	ENST00000369902	NM_016169.3	280	-/C	7/12	0.495757944796869	1	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	0	0.495757944796869	1		284	205	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21350104	21350105	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0069376-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	39	394	0	ENST00000215739.8:c.2013_2014del	p.Leu672AlafsTer2	p.L672Afs*2	ENST00000215739	NM_006767.3	671	cTG/c	17/21	1	2	FACETS	0.393	0.326	0.468	0.393	0.326	0.468	SUBCLONAL	1	TRUE	1	0.495757944796869	2		394	400	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760884	59760884	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs372799558	NA	P-0069376-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	55	339	0	ENST00000259008.2:c.3523A>G	p.Thr1175Ala	p.T1175A	ENST00000259008	NM_032043.2	1175	Act/Gct	20/20	0.281309856258942	2	FACETS	0.589	0.505	0.679	0.294	0.252	0.34	INDETERMINATE	1	TRUE	0	0.495757944796869	2		339	377	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182586	99182586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758889570	NA	P-0069376-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	49	346	0	ENST00000074304.5:c.2389G>A	p.Val797Ile	p.V797I	ENST00000074304	NM_001134224.1	797	Gtc/Atc	22/26	1	2	FACETS	0.536	0.455	0.624	0.536	0.455	0.624	SUBCLONAL	1	TRUE	1	0.495757944796869	2		346	369	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8252051	8252051	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069376-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	89	374	0	ENST00000335790.3:c.26G>A	p.Gly9Asp	p.G9D	ENST00000335790	NM_002315.2	9	gGc/gAc	2/4	0.380985035647943	1	FACETS	0.912	0.819	1	0.912	0.819	1	CLONAL	1	TRUE	0	0.495757944796869	1		374	296	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508119	106508119	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069376-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	54	354	0	ENST00000359195.3:c.113T>C	p.Ile38Thr	p.I38T	ENST00000359195	NM_002649.2	38	aTc/aCc	2/11	1	2	FACETS	0.561	0.481	0.649	0.561	0.481	0.649	SUBCLONAL	1	TRUE	1	0.495757944796869	2		354	388	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754561	42754561	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069376-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	137	384	0	ENST00000222329.4:c.179C>A	p.Pro60His	p.P60H	ENST00000222329	NM_006494.2	60	cCt/cAt	2/4	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.495757944796869	2		384	413	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068946	30068946	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0069376-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	72	280	0	ENST00000331968.5:c.1983del	p.Lys661AsnfsTer9	p.K661Nfs*9	ENST00000331968	NM_002742.2	661	aaA/aa	14/18	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.495757944796869	2		280	288	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0069378-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	468	305	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	0.36503786834048	7	FACETS	1	0.989	1			1	CLONAL	5	TRUE	NA	0.36503786834048	7		305	913	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719271	61719271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069378-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	40	322	0	ENST00000401558.2:c.1786C>T	p.Arg596Cys	p.R596C	ENST00000401558	NM_003400.3	596	Cgc/Tgc	16/25	0.346047068622807	3	FACETS	0.422	0.35	0.503	0.211	0.175	0.252	SUBCLONAL	1	TRUE	1	0.36503786834048	3		322	614	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058874	42058874	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069378-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	133	396	0	ENST00000219905.7:c.8594G>A	p.Ser2865Asn	p.S2865N	ENST00000219905	NM_001164273.1	2865	aGt/aAt	24/24	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.36503786834048	2		396	678	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619007	37619008	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0069378-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	137	461	0	ENST00000447079.4:c.683_684insG	p.Asp229Ter	p.D229*	ENST00000447079	NM_015083.1	228	tct/tcGt	1/14	0.350137130257096	4	FACETS	0.989	0.898	1			1	CLONAL	1	TRUE	NA	0.36503786834048	4		461	1036	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0069380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	118	269	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.642266446141428	2		269	359	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057976	27057976	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	218	600	0	ENST00000324856.7:c.1684C>T	p.Gln562Ter	p.Q562*	ENST00000324856	NM_006015.4	562	Cag/Tag	3/20	1	2	FACETS	0.943	0.88	1	0.943	0.88	1	CLONAL	1	TRUE	1	0.642266446141428	2		600	720	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935319	36935319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748675453	NA	P-0069380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	200	468	0	ENST00000361632.4:c.1408G>A	p.Ala470Thr	p.A470T	ENST00000361632		470	Gcg/Acg	10/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.642266446141428	2		468	589	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474041	29474041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs78723472	NA	P-0069380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	138	503	0	ENST00000389048.3:c.2134G>A	p.Val712Met	p.V712M	ENST00000389048	NM_004304.4	712	Gtg/Atg	12/29	1	2	FACETS	0.812	0.743	0.884	0.812	0.743	0.884	CLONAL	1	TRUE	1	0.642266446141428	2		503	529	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730831	40730831	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372700928	NA	P-0069380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	108	524	0	ENST00000373198.4:c.3704G>A	p.Arg1235His	p.R1235H	ENST00000373198	NM_133170.3	1235	cGc/cAc	27/32	0.642266446141428	3	FACETS	0.587	0.527	0.651	0.293	0.263	0.326	SUBCLONAL	1	TRUE	1	0.642266446141428	3		524	757	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390995	89390995	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144727411	NA	P-0069380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	146	415	0	ENST00000336596.2:c.1061G>A	p.Arg354Gln	p.R354Q	ENST00000336596	NM_005233.5	354	cGg/cAg	5/17	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.642266446141428	2		415	447	SUCCESS
APC	324	MSKCC	GRCh37	5	112174559	112174559	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	170	474	0	ENST00000257430.4:c.3268C>T	p.Gln1090Ter	p.Q1090*	ENST00000257430	NM_000038.5	1090	Caa/Taa	16/16	1	2	FACETS	0.932	0.862	1	0.932	0.862	1	CLONAL	1	TRUE	1	0.642266446141428	2		474	568	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673724	30673724	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61733207	NA	P-0069380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	242	550	1	ENST00000376406.3:c.3236G>A	p.Arg1079His	p.R1079H	ENST00000376406	NM_014641.2	1079	cGt/cAt	10/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.642266446141428	2		551	660	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099982	157099993	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGCGGC	GGCGGCGGCGGC	-	rs587779747	NA	P-0069380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	166	606	0	ENST00000346085.5:c.933_944del	p.Gly316_Gly319del	p.G316_G319del	ENST00000346085	NM_020732.3	307	GGCGGCGGCGGC/-	1/20	1	2	FACETS	0.664	0.61	0.719	0.664	0.61	0.719	SUBCLONAL	1	TRUE	1	0.642266446141428	2		606	779	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63810683	63810690	+	frameshift_variant	Frame_Shift_Del	DEL	CATGCCCA	CATGCCCA	-	novel	NA	P-0069380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	206	364	0	ENST00000279873.7:c.772_779del	p.Cys258LysfsTer9	p.C258Kfs*9	ENST00000279873	NM_032199.2	257	cCATGCCCA/c	5/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.642266446141428	2		364	576	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562749	29562759	+	frameshift_variant	Frame_Shift_Del	DEL	GGCAACAGCTT	GGCAACAGCTT	-	novel	NA	P-0069380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	174	358	0	ENST00000356175.3:c.3832_3842del	p.Asn1278GlnfsTer2	p.N1278Qfs*2	ENST00000356175	NM_000267.3	1277	GGCAACAGCTTg/g	28/57	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.642266446141428	2		358	484	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856343	45856343	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	46	348	0	ENST00000391945.4:c.1829T>A	p.Phe610Tyr	p.F610Y	ENST00000391945	NM_000400.3	610	tTt/tAt	19/23	1	2	FACETS	0.763	0.644	0.893	1	0.961	1	SUBCLONAL	2	FALSE	1	0.15869830441432	2		348	380	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0069382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	83	257	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.939	0.838	1	0.939	0.838	1	CLONAL	1	TRUE	1	0.581293574908936	2		257	304	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0069382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	112	236	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.581293574908936	2		236	334	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561352	9561352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773981325	NA	P-0069382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	136	334	0	ENST00000353224.5:c.430G>A	p.Glu144Lys	p.E144K	ENST00000353224	NM_177990.2	144	Gaa/Aaa	4/10	0.581293574908936	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.581293574908936	1		334	291	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178199	142178199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746049210	NA	P-0069382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	84	218	0	ENST00000350721.4:c.7219C>T	p.Arg2407Cys	p.R2407C	ENST00000350721	NM_001184.3	2407	Cgc/Tgc	43/47	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.581293574908936	2		218	278	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012420	29012420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	109	307	0	ENST00000282397.4:c.451G>A	p.Gly151Arg	p.G151R	ENST00000282397	NM_002019.4	151	Gga/Aga	4/30	0.136479882565706	3	FACETS	1	0.982	1	0.691	0.627	0.758	INDETERMINATE	1	TRUE	1	0.581293574908936	3		307	350	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979995	7979995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	135	366	0	ENST00000319144.4:c.1342G>A	p.Glu448Lys	p.E448K	ENST00000319144	NM_001139.2	448	Gag/Aag	10/15	0.581293574908936	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.581293574908936	1		366	308	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549265	21549265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	141	366	0	ENST00000382592.4:c.3011C>T	p.Pro1004Leu	p.P1004L	ENST00000382592	NM_014572.2	1004	cCc/cTc	8/8	0.136479882565706	3	FACETS	1	0.983	1	0.643	0.59	0.698	INDETERMINATE	1	TRUE	1	0.581293574908936	3		366	487	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309887	65309887	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	13	295	0	ENST00000342505.4:c.2263C>G	p.Arg755Gly	p.R755G	ENST00000342505	NM_002227.2	755	Cga/Gga	17/25	0.581293574908936	1	FACETS	0.138	0.098	0.187	0.138	0.098	0.187	SUBCLONAL	1	TRUE	0	0.581293574908936	1		295	230	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428260	72428260	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	120	269	0	ENST00000477973.2:c.632C>A	p.Pro211His	p.P211H	ENST00000477973	NM_012234.5	211	cCt/cAt	3/4	1	2	FACETS	0.791	0.718	0.868	0.791	0.718	0.868	SUBCLONAL	1	TRUE	1	0.581293574908936	2		269	522	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56882338	56882338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	115	315	0	ENST00000519728.1:c.1036G>A	p.Asp346Asn	p.D346N	ENST00000519728	NM_002350.3	346	Gac/Aac	10/13	0.581293574908936	3	FACETS	0.885	0.8	0.975	0.443	0.4	0.488	CLONAL	1	TRUE	1	0.581293574908936	3		315	577	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50763942	50763942	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	117	279	0	ENST00000307179.4:c.799G>C	p.Asp267His	p.D267H	ENST00000307179		267	Gat/Cat	8/20	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.581293574908936	2		279	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578266	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs942158624	NA	P-0069383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	105	462	0	ENST00000269305.4:c.583A>T	p.Ile195Phe	p.I195F	ENST00000269305	NM_001126112.2	195	Atc/Ttc	6/11	0.25511984948416	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.25511984948416	2		462	376	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806564	1806564	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	85	520	0	ENST00000260795.2:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000260795		427	tCc/tTc	9/17	0.179171228359409	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.25511984948416	4		520	353	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465561	8465561	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0069383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	53	399	0	ENST00000356435.5:c.3619del	p.Asp1207MetfsTer24	p.D1207Mfs*24	ENST00000356435		1207	Gat/at	21/35	0.25511984948416	2	FACETS	1	0.953	1	0.641	0.55	0.74	CLONAL	1	TRUE	0	0.25511984948416	2		399	324	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43746222	43746222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	92	416	0	ENST00000523873.1:c.341G>A	p.Gly114Asp	p.G114D	ENST00000523873		114	gGc/gAc	4/8	0.25511984948416	5	FACETS	1	0.918	1	0.69	0.615	0.768	CLONAL	2	TRUE	2	0.25511984948416	5		416	482	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288589	15288589	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	24	293	0	ENST00000263388.2:c.4150G>T	p.Glu1384Ter	p.E1384*	ENST00000263388	NM_000435.2	1384	Gag/Tag	24/33	1	2	FACETS	0.759	0.604	0.931	1	0.932	1	CLONAL	2	TRUE	1	0.25511984948416	2		293	124	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800860	120800860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	51	350	0	ENST00000257552.2:c.388G>A	p.Glu130Lys	p.E130K	ENST00000257552	NM_002442.3	130	Gag/Aag	6/15	0.251866875164674	3	FACETS	1	0.935	1	0.592	0.504	0.687	CLONAL	1	TRUE	1	0.25511984948416	3		350	381	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664724	138664724	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	55	334	0	ENST00000330315.3:c.841C>A	p.Pro281Thr	p.P281T	ENST00000330315	NM_023067.3	281	Ccg/Acg	1/1	0.25511984948416	5	FACETS	1	0.911	1	0.717	0.619	0.823	CLONAL	2	TRUE	2	0.25511984948416	5		334	277	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226301	133226301	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0069383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	46	435	0	ENST00000320574.5:c.3757del	p.Glu1253LysfsTer108	p.E1253Kfs*108	ENST00000320574	NM_006231.2	1253	Gaa/aa	30/49	0.251866875164674	3	FACETS	1	0.918	1	0.569	0.481	0.666	CLONAL	1	TRUE	1	0.25511984948416	3		435	357	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455042	50455042	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0069383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	32	351	0	ENST00000331340.3:c.590-1G>T		p.X197_splice	ENST00000331340	NM_006060.4	197			0.179171228359409	4	FACETS	0.753	0.611	0.914	0.377	0.305	0.457	CLONAL	1	TRUE	2	0.25511984948416	4		351	418	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801034	1801034	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	39	489	0	ENST00000260795.2:c.163G>T	p.Asp55Tyr	p.D55Y	ENST00000260795		55	Gat/Tat	2/17	0.179171228359409	4	FACETS	1	0.921	1	0.598	0.497	0.709	CLONAL	1	TRUE	2	0.25511984948416	4		489	321	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804392	46804392	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs766169510	NA	P-0069383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	89	471	0	ENST00000290295.7:c.615G>T	p.Gln205His	p.Q205H	ENST00000290295	NM_006361.5	205	caG/caT	2/2	0.217634517674602	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	2	0.25511984948416	4		471	384	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355095	73355095	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1246775389	NA	P-0069383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	108	317	0	ENST00000377767.4:c.275A>G	p.Gln92Arg	p.Q92R	ENST00000377767	NM_014953.3	92	cAa/cGa	2/21	0.25511984948416	4	FACETS	1	0.973	1	0.811	0.732	0.892	CLONAL	2	TRUE	1	0.25511984948416	4		317	437	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846234	156846234	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	70	430	0	ENST00000524377.1:c.1675C>A	p.Arg559Ser	p.R559S	ENST00000524377	NM_002529.3	559	Cgt/Agt	14/17	0.251866875164674	3	FACETS	1	0.886	1	1	0.886	1	CLONAL	2	TRUE	1	0.25511984948416	3		430	307	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268800	98268800	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	47	391	0	ENST00000331920.6:c.283C>A	p.Gln95Lys	p.Q95K	ENST00000331920	NM_000264.3	95	Caa/Aaa	2/24	0.25511984948416	2	FACETS	1	0.896	1	0.537	0.455	0.627	CLONAL	1	TRUE	0	0.25511984948416	2		391	343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	104	284	0	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	0.197468631491341	4	FACETS	1	0.965	1	0.569	0.515	0.626	INDETERMINATE	2	TRUE	0	0.370151018577326	4		284	338	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278172	15278172	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	69	408	0	ENST00000263388.2:c.5250G>A	p.Trp1750Ter	p.W1750*	ENST00000263388	NM_000435.2	1750	tgG/tgA	29/33	0.213407453261206	4	FACETS	1	0.951	1	0.593	0.518	0.673	INDETERMINATE	1	TRUE	2	0.370151018577326	4		408	431	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840002	27840002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767622437	NA	P-0069384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	116	510	0	ENST00000328488.2:c.92C>T	p.Pro31Leu	p.P31L	ENST00000328488	NM_003533.2	31	cCg/cTg	1/1	0.370151018577326	4	FACETS	1	0.971	1	0.4	0.36	0.441	CLONAL	1	TRUE	1	0.370151018577326	4		510	716	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938916	76938916	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	72	342	0	ENST00000373344.5:c.1832A>G	p.Asp611Gly	p.D611G	ENST00000373344	NM_000489.3	611	gAt/gGt	9/35	0.283278449278371	2	FACETS	1	0.919	1	0.53	0.466	0.598	CLONAL	1	TRUE	0	0.370151018577326	2		342	367	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44919312	44919312	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0069384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	21	126	0	ENST00000377967.4:c.1240A>T	p.Lys414Ter	p.K414*	ENST00000377967	NM_021140.2	414	Aaa/Taa	13/29	0.283278449278371	2	FACETS	0.772	0.6	0.968	0.386	0.3	0.484	CLONAL	1	TRUE	0	0.370151018577326	2		126	147	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802635	135802635	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	88	340	0	ENST00000298552.3:c.163C>G	p.Gln55Glu	p.Q55E	ENST00000298552	NM_001162426.1	55	Cag/Gag	4/23	0.370151018577326	4	FACETS	1	0.977	1	0.473	0.421	0.529	CLONAL	1	TRUE	1	0.370151018577326	4		340	459	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175874	24175874	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	52	309	0	ENST00000263121.7:c.1102C>T	p.Gln368Ter	p.Q368*	ENST00000263121	NM_003073.3	368	Cag/Tag	8/9	0.232342459207714	2	FACETS	0.895	0.776	1	1	0.961	1	CLONAL	3	TRUE	0	0.22	2		309	176	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732433	74732456	+	inframe_deletion	In_Frame_Del	DEL	GACCGAGATCGAGAACGAGTGCGG	GACCGAGATCGAGAACGAGTGCGG	-	rs760875189	NA	P-0069385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	88	378	0	ENST00000359995.5:c.453_476del	p.Arg152_Ser159del	p.R152_S159del	ENST00000359995	NM_001195427.1	151	tcCCGCACTCGTTCTCGATCTCGGTCg/tcg	2/3	0.285010399293922	4	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	2	0.22	4		378	458	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862858	9862858	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs754929310	NA	P-0069385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	25	339	0	ENST00000330684.3:c.2445C>A	p.Asp815Glu	p.D815E	ENST00000330684	NM_001134407.1	815	gaC/gaA	12/13	0.3	3	FACETS	1	0.798	1	0.505	0.399	0.625	CLONAL	1	TRUE	1	0.22	3		339	250	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439940	51439940	+	stop_lost	Nonstop_Mutation	SNP	T	T	A	novel	NA	P-0069385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	14	239	0	ENST00000262662.1:c.505T>A	p.Ter169LysextTer16	p.*169Kext*16	ENST00000262662		169	Taa/Aaa	4/4	0.133761992434184	5	FACETS	0.81	0.586	1	0.202	0.146	0.27	CLONAL	1	TRUE	1	0.22	5		239	209	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807595	1807595	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	23	464	0	ENST00000260795.2:c.1764G>T	p.Gln588His	p.Q588H	ENST00000260795		588	caG/caT	12/17	NA	2	FACETS	0.826	0.646	1			1	INDETERMINATE	1	TRUE	NA	0.22	2		464	253	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750600586	NA	P-0069386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	275	360	0	ENST00000269305.4:c.413C>T	p.Ala138Val	p.A138V	ENST00000269305	NM_001126112.2	138	gCc/gTc	5/11	0.720336271575141	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.720336271575141	2		360	372	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21343151	21343151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758338373	NA	P-0069386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	238	380	0	ENST00000215739.8:c.583G>A	p.Gly195Ser	p.G195S	ENST00000215739	NM_006767.3	195	Ggc/Agc	6/21	0.282166753272044	3	FACETS	0.992	0.939	1	0.661	0.626	0.697	INDETERMINATE	2	TRUE	0	0.720336271575141	3		380	453	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966946	25966946	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	104	399	0	ENST00000435504.4:c.2260T>C	p.Ser754Pro	p.S754P	ENST00000435504		754	Tct/Cct	13/13	0.458841426560592	5	FACETS	0.92	0.825	1	0.307	0.275	0.341	CLONAL	1	TRUE	2	0.720336271575141	5		399	653	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0069678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	44	244	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	0.771	0.646	0.911	0.771	0.646	0.911	CLONAL	1	TRUE	1	0.18	2		244	634	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060711	38060711	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0069678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	53	519	0	ENST00000250448.2:c.1278C>G	p.Tyr426Ter	p.Y426*	ENST00000250448	NM_004496.3	426	taC/taG	2/2	1	2	FACETS	0.759	0.646	0.884	0.759	0.646	0.884	SUBCLONAL	1	TRUE	1	0.18	2		519	776	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121912666	NA	P-0069686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	239	515	0	ENST00000269305.4:c.659A>C	p.Tyr220Ser	p.Y220S	ENST00000269305	NM_001126112.2	220	tAt/tCt	6/11	NA	2	FACETS	0.77	0.721	0.819			1	INDETERMINATE	2	TRUE	NA	0.407450676423948	2		515	762	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066540	94066540	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	92	390	0	ENST00000369303.4:c.1219G>T	p.Ala407Ser	p.A407S	ENST00000369303	NM_004440.3	407	Gcc/Tcc	5/17	0.238062831767591	3	FACETS	0.807	0.717	0.902	0.403	0.358	0.451	INDETERMINATE	1	TRUE	1	0.407450676423948	3		390	674	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274201	10274201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs969233060	NA	P-0069686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5493	292	351	0	ENST00000330684.3:c.68C>T	p.Pro23Leu	p.P23L	ENST00000330684	NM_001134407.1	23	cCg/cTg	2/13	0.407450676423948	24	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.407450676423948	24		351	5785	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186507028	186507029	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATGCCCA	novel	NA	P-0069686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	45	287	0	ENST00000323963.5:c.1195_1201dup	p.Met401AsnfsTer7	p.M401Nfs*7	ENST00000323963		398	-/ATGCCCA	11/11	0.278796291317832	3	FACETS	0.357	0.299	0.421	0.178	0.149	0.211	SUBCLONAL	1	TRUE	1	0.407450676423948	3		287	745	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089558	27089558	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0069686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	178	523	0	ENST00000324856.7:c.2514del	p.Gly839ValfsTer20	p.G839Vfs*20	ENST00000324856	NM_006015.4	838	ggA/gg	8/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.407450676423948	2		523	732	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039680	47039681	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0069686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	102	227	0	ENST00000377604.3:c.1132_1133del	p.Asn378CysfsTer2	p.N378Cfs*2	ENST00000377604	NM_001204468.1	378	AAt/t	11/24	1	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.407450676423948	1		227	334	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976970	18976970	+	stop_lost	Nonstop_Mutation	SNP	T	T	C	novel	NA	P-0069686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	183	447	0	ENST00000262803.5:c.3355T>C	p.Ter1119GlnextTer12	p.*1119Qext*12	ENST00000262803	NM_002911.3	1119	Taa/Caa	23/24	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.407450676423948	2		447	800	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641650	12641651	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0069686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	97	375	0	ENST00000251849.4:c.990dup	p.Arg331Ter	p.R331*	ENST00000251849	NM_002880.3	330	-/T		1	2	FACETS	0.703	0.627	0.784	0.703	0.627	0.784	SUBCLONAL	1	TRUE	1	0.407450676423948	2		375	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0069707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	481	450	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.395803464315053	3	FACETS	0.923	0.89	0.957	0.923	0.89	0.957	CLONAL	3	TRUE	0	0.514128986551809	3		450	849	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259516	+	missense_variant	Missense_Mutation	DNP	TG	TG	GT	rs1057519848	NA	P-0069707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	269	314	0	ENST00000275493.2:c.2573_2574delinsGT	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTG/cGT	21/28	0.201728326935996	3	FACETS	0.916	0.864	0.969	0.611	0.576	0.646	INDETERMINATE	2	TRUE	0	0.514128986551809	3		314	718	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803464	32803464	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1409379915	NA	P-0069707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	54	329	0	ENST00000374899.4:c.695C>T	p.Ser232Phe	p.S232F	ENST00000374899	NM_018833.2	232	tCc/tTc	4/12	0.158459102755673	5	FACETS	0.472	0.402	0.549	0.157	0.134	0.183	INDETERMINATE	1	TRUE	2	0.514128986551809	5		329	788	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880096	151880096	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	40	246	0	ENST00000262189.6:c.5228G>C	p.Arg1743Thr	p.R1743T	ENST00000262189	NM_170606.2	1743	aGa/aCa	35/59	0.398037123929366	3	FACETS	0.456	0.379	0.542	0.228	0.189	0.271	SUBCLONAL	1	TRUE	1	0.514128986551809	3		246	429	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215276	142215276	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	77	226	0	ENST00000350721.4:c.5825A>G	p.Asn1942Ser	p.N1942S	ENST00000350721	NM_001184.3	1942	aAt/aGt	34/47	0.50115535272589	2	FACETS	0.673	0.593	0.758	0.337	0.296	0.379	SUBCLONAL	1	TRUE	0	0.514128986551809	2		226	445	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148513857	148513858	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0069707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	73	279	0	ENST00000320356.2:c.1423_1424insT	p.Arg475MetfsTer6	p.R475Mfs*6	ENST00000320356	NM_004456.4	475	aga/aTga	12/20	0.398037123929366	3	FACETS	0.594	0.52	0.674	0.297	0.26	0.337	SUBCLONAL	1	TRUE	1	0.514128986551809	3		279	601	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148513878	148514900	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGGCACAGTCACAGAGCCATGAGGACAGTCTTATTTAGGCAAACCATTCTTATACTCATGCATACCAGAAAAATGTCTTTGTCTCTTCTGTGACACTGCTAGATGCTGGGGATATAACACACATCGCTGTCCCTACCCTCACATTAGGGGTAGCTGTAATTATATTCTGGTCAAGAACTGTGATGCTAAATTTCAATTCTTACTAGCTTTTAAAAGCTACTGCTATCTAACCTTAAAAGTCTACATTGGGGAAATTCTGTAACATACCTGGAGAATAATTTTCATTCAATTCCCTCTTGGGAAGAAAAAAAAATTATTTTTAGGAGATGAATAGGAGCTTAGTAATAACCAAGAATTTTCTTTGTTTGGACAACGAGTACAGTTTTATCTCTATGTTTGAAGCTCTTTTAACAACATTTTTATCGGATATCTTACCTGTCTACATGTTTTGGTCCCAATTAACCTAGCAATGGCACAGAAATTGTCATAGTAAGTGCCAATGAGGACTCTAAACATTGAGGCTTCAGCACCACTCCACTCCACATTCTCAGGAGGTTCAATATTTGGCTTCATCTTTATTGGTGTTTGACACCGAGAATTTGCTTCTACAAAACCAAATGTAAGCACTGGTCAAGAAATGATTGGAAATAATATTAAGAAGTACAATTCAGGGTGTGCTTAAGAAAAAAGCGAAAAGATGAGGACAACTCAAATCCAATCGGCAAAACACTAACCCATCGTAGTTCACATTTTCCAACAAAACTACTCACAGAACGTCAAGAATATTAAACCAAATGATCCAAATTTCATTATTCCCTACCTGAGAAAGATCGAAAAAAGAAAATGGCACAAAGAATGAGAATAAAGTGCATCATCAGCTTTCAAACAACCAAGCAGGGCAAACACCACAAGCTAGGGTACGGGTGCAGGCAGGAAACAGAAACAACACAGCTACACATTCTTGAGATAACTCTGGTCTTTATACTGAAACTAACCAACTAAGAAAATTATTCAATGCATTA	GAGGCACAGTCACAGAGCCATGAGGACAGTCTTATTTAGGCAAACCATTCTTATACTCATGCATACCAGAAAAATGTCTTTGTCTCTTCTGTGACACTGCTAGATGCTGGGGATATAACACACATCGCTGTCCCTACCCTCACATTAGGGGTAGCTGTAATTATATTCTGGTCAAGAACTGTGATGCTAAATTTCAATTCTTACTAGCTTTTAAAAGCTACTGCTATCTAACCTTAAAAGTCTACATTGGGGAAATTCTGTAACATACCTGGAGAATAATTTTCATTCAATTCCCTCTTGGGAAGAAAAAAAAATTATTTTTAGGAGATGAATAGGAGCTTAGTAATAACCAAGAATTTTCTTTGTTTGGACAACGAGTACAGTTTTATCTCTATGTTTGAAGCTCTTTTAACAACATTTTTATCGGATATCTTACCTGTCTACATGTTTTGGTCCCAATTAACCTAGCAATGGCACAGAAATTGTCATAGTAAGTGCCAATGAGGACTCTAAACATTGAGGCTTCAGCACCACTCCACTCCACATTCTCAGGAGGTTCAATATTTGGCTTCATCTTTATTGGTGTTTGACACCGAGAATTTGCTTCTACAAAACCAAATGTAAGCACTGGTCAAGAAATGATTGGAAATAATATTAAGAAGTACAATTCAGGGTGTGCTTAAGAAAAAAGCGAAAAGATGAGGACAACTCAAATCCAATCGGCAAAACACTAACCCATCGTAGTTCACATTTTCCAACAAAACTACTCACAGAACGTCAAGAATATTAAACCAAATGATCCAAATTTCATTATTCCCTACCTGAGAAAGATCGAAAAAAGAAAATGGCACAAAGAATGAGAATAAAGTGCATCATCAGCTTTCAAACAACCAAGCAGGGCAAACACCACAAGCTAGGGTACGGGTGCAGGCAGGAAACAGAAACAACACAGCTACACATTCTTGAGATAACTCTGGTCTTTATACTGAAACTAACCAACTAAGAAAATTATTCAATGCATTA	-	novel	NA	P-0069707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	67	266	0	ENST00000320356.2:c.1240+70_1411-7del		p.X414_splice	ENST00000320356	NM_004456.4	414		11/20	0.398037123929366	3	FACETS	0.581	0.505	0.663	0.29	0.252	0.332	SUBCLONAL	1	TRUE	1	0.514128986551809	3		266	564	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977584	2977584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746318779	NA	P-0069708-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	43	218	0	ENST00000396946.4:c.1100C>T	p.Thr367Met	p.T367M	ENST00000396946	NM_032415.4	367	aCg/aTg	8/25	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.25	2		218	295	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600009	10600009	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069708-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	45	358	0	ENST00000171111.5:c.1567G>T	p.Gly523Trp	p.G523W	ENST00000171111	NM_203500.1	523	Ggg/Tgg	5/6	0.208720910939881	1	FACETS	0.766	0.645	0.9	0.766	0.645	0.9	SUBCLONAL	1	TRUE	0	0.25	1		358	411	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0069708-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	44	290	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.176820666673147	1	FACETS	0.895	0.753	1	0.895	0.753	1	CLONAL	1	TRUE	0	0.25	1		290	344	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748605	40748605	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069708-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	22	221	0	ENST00000373198.4:c.2911C>A	p.His971Asn	p.H971N	ENST00000373198	NM_133170.3	971	Cat/Aat	21/32	1	2	FACETS	0.613	0.476	0.773	0.613	0.476	0.773	SUBCLONAL	1	TRUE	1	0.25	2		221	287	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240343	41240343	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069708-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	14	235	0	ENST00000379561.5:c.7G>T	p.Glu3Ter	p.E3*	ENST00000379561	NM_002015.3	3	Gag/Tag	1/3	1	2	FACETS	0.401	0.29	0.537	0.401	0.29	0.537	SUBCLONAL	1	TRUE	1	0.25	2		235	279	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450292	50450292	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069708-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	32	316	0	ENST00000331340.3:c.476A>C	p.Asn159Thr	p.N159T	ENST00000331340	NM_006060.4	159	aAc/aCc	5/8	1	2	FACETS	0.684	0.556	0.829	0.684	0.556	0.829	SUBCLONAL	1	TRUE	1	0.25	2		316	374	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288759	15288759	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0069708-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	27	295	0	ENST00000263388.2:c.3980del	p.Phe1327SerfsTer93	p.F1327Sfs*93	ENST00000263388	NM_000435.2	1327	tTc/tc	24/33	0.208720910939881	1	FACETS	0.815	0.651	0.999	0.815	0.651	0.999	CLONAL	1	TRUE	0	0.25	1		295	232	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619240	23619240	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069708-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	37	255	0	ENST00000261584.4:c.3295A>G	p.Thr1099Ala	p.T1099A	ENST00000261584	NM_024675.3	1099	Acg/Gcg	12/13	1	2	FACETS	0.759	0.626	0.907	0.759	0.626	0.907	CLONAL	1	TRUE	1	0.25	2		255	390	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317881	8317881	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069708-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	22	224	0	ENST00000356435.5:c.5732C>G	p.Ala1911Gly	p.A1911G	ENST00000356435		1911	gCa/gGa	35/35	0.176820666673147	1	FACETS	0.386	0.298	0.488	0.386	0.298	0.488	SUBCLONAL	1	TRUE	0	0.25	1		224	399	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022739	12022739	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069708-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	55	419	0	ENST00000396373.4:c.845G>C	p.Arg282Pro	p.R282P	ENST00000396373	NM_001987.4	282	cGg/cCg	5/8	0.176820666673147	1	FACETS	0.816	0.699	0.943	0.816	0.699	0.943	CLONAL	1	TRUE	0	0.25	1		419	472	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0069709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	64	206	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.859	0.748	0.978	0.859	0.748	0.978	CLONAL	1	TRUE	1	0.415083965471417	2		206	359	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851843	134851843	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1305200941	NA	P-0069709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	74	467	0	ENST00000398015.3:c.1249C>T	p.Pro417Ser	p.P417S	ENST00000398015	NM_004441.4	417	Ccc/Tcc	5/16	0.311965885022289	0	FACETS	0.5	0.44	0.565			1	SUBCLONAL	1	TRUE	0	0.415083965471417	0		467	417	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155721	56155722	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0069709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	97	375	0	ENST00000399503.3:c.816_817del	p.Arg273SerfsTer27	p.R273Sfs*27	ENST00000399503	NM_005921.1	271	agAAaa/agaa	3/20	1	2	FACETS	0.809	0.723	0.9	0.809	0.723	0.9	CLONAL	1	TRUE	1	0.415083965471417	2		375	578	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189387	56189387	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0069709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	139	363	0	ENST00000399503.3:c.4421del	p.Pro1474LeufsTer16	p.P1474Lfs*16	ENST00000399503	NM_005921.1	1473	atC/at	20/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.415083965471417	2		363	605	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0069709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	84	269	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.933	0.828	1	0.933	0.828	1	CLONAL	1	TRUE	1	0.415083965471417	2		269	434	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155621	56155622	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0069709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	142	292	0	ENST00000399503.3:c.715dup	p.Ser239LysfsTer62	p.S239Kfs*62	ENST00000399503	NM_005921.1	238	gca/gcAa	3/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.415083965471417	2		292	637	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0069710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	85	536	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.324465549631427	3	FACETS	1	0.915	1	0.52	0.461	0.584	CLONAL	1	TRUE	1	0.324465549631427	3		536	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882019	NA	P-0069710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	157	425	0	ENST00000269305.4:c.455dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	ccg/ccCg	5/11	0.324465549631427	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.324465549631427	1		425	697	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201759	66201759	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	129	320	0	ENST00000273854.3:c.2743T>A	p.Trp915Arg	p.W915R	ENST00000273854	NM_004439.5	915	Tgg/Agg	16/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		320	506	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846175	151846175	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	25	394	0	ENST00000262189.6:c.12837G>C	p.Gln4279His	p.Q4279H	ENST00000262189	NM_170606.2	4279	caG/caC	52/59	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		394	429	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061248	38061248	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069715-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	266	380	0	ENST00000250448.2:c.741C>G	p.His247Gln	p.H247Q	ENST00000250448	NM_004496.3	247	caC/caG	2/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.548217521647003	2		380	872	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0069715-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	237	443	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.548217521647003	1	FACETS	0.961	0.903	1	0.961	0.903	1	CLONAL	1	TRUE	0	0.548217521647003	1		443	653	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119820	17119822	+	splice_region_variant,intron_variant	Splice_Region	DEL	GAG	GAG	-	rs767671406	NA	P-0069718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	104	358	0	ENST00000285071.4:c.1177-5_1177-3del		p.X393_splice	ENST00000285071	NM_144997.5	393			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		358	329	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0069719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	49	476	0	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.167719157636031	1	FACETS	0.949	0.804	1	0.949	0.804	1	CLONAL	1	TRUE	0	0.19	1		476	492	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221720	55221720	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372202099	NA	P-0069719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	40	480	0	ENST00000275493.2:c.764G>A	p.Arg255Gln	p.R255Q	ENST00000275493	NM_005228.3	255	cGa/cAa	7/28	1	2	FACETS	0.722	0.599	0.86	0.722	0.599	0.86	SUBCLONAL	1	TRUE	1	0.19	2		480	583	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066912	30066912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752897300	NA	P-0069719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	64	273	0	ENST00000331968.5:c.2219G>A	p.Arg740Gln	p.R740Q	ENST00000331968	NM_002742.2	740	cGg/cAg	16/18	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.19	2		273	590	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0069719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	45	287	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	1	2	FACETS	0.788	0.661	0.929	0.788	0.661	0.929	CLONAL	1	TRUE	1	0.19	2		287	601	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410075	63410075	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	29	535	0	ENST00000330258.3:c.3092G>T	p.Gly1031Val	p.G1031V	ENST00000330258	NM_152424.3	1031	gGc/gTc	2/2	1	2	FACETS	0.603	0.483	0.74	0.603	0.483	0.74	SUBCLONAL	1	TRUE	1	0.19	2		535	506	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439930	56439930	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	47	351	0	ENST00000407977.2:c.662G>T	p.Arg221Leu	p.R221L	ENST00000407977		221	cGg/cTg	6/10	1	2	FACETS	0.888	0.749	1	0.888	0.749	1	CLONAL	1	TRUE	1	0.19	2		351	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578400	7578400	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs751477326	NA	P-0069721-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	232	363	0	ENST00000269305.4:c.530C>G	p.Pro177Arg	p.P177R	ENST00000269305	NM_001126112.2	177	cCc/cGc	5/11	0.45212363159946	2	FACETS	0.93	0.875	0.985	0.93	0.875	0.985	CLONAL	2	TRUE	0	0.45212363159946	2		363	552	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696404	47696404	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069721-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	103	275	0	ENST00000347630.2:c.419A>G	p.Asp140Gly	p.D140G	ENST00000347630	NM_001007230.1	140	gAt/gGt	6/11	0.266003247552954	5	FACETS	1	0.973	1	0.42	0.376	0.466	INDETERMINATE	1	TRUE	2	0.45212363159946	5		275	607	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462809	69462809	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1011426441	NA	P-0069721-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	120	332	0	ENST00000227507.2:c.622G>A	p.Val208Met	p.V208M	ENST00000227507	NM_053056.2	208	Gtg/Atg	4/5	0.42534667455357	4	FACETS	1	0.95	1	0.54	0.488	0.595	CLONAL	1	TRUE	2	0.45212363159946	4		332	714	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989633	15989633	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069721-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	238	267	0	ENST00000268712.3:c.3140A>G	p.Glu1047Gly	p.E1047G	ENST00000268712	NM_006311.3	1047	gAa/gGa	23/46	0.45212363159946	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.45212363159946	2		267	513	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881619	37881619	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069721-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	146	261	0	ENST00000269571.5:c.2689C>G	p.Arg897Gly	p.R897G	ENST00000269571		897	Cgg/Ggg	22/27	0.255738466298881	3	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.45212363159946	3		261	603	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0069722-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	192	406	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.923	0.859	0.988	0.923	0.859	0.988	CLONAL	1	TRUE	1	0.713671940051232	2		406	583	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0069722-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11758	2836	615	1	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.713671940051232	57	FACETS	1	0.991	1	0.201	0.196	0.205	CLONAL	11	TRUE	1	0.713671940051232	57		616	14594	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813023	89813023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142833057	NA	P-0069722-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	123	433	0	ENST00000389301.3:c.3482C>T	p.Thr1161Met	p.T1161M	ENST00000389301	NM_000135.2	1161	aCg/aTg	35/43	1	2	FACETS	0.833	0.759	0.908	0.833	0.759	0.908	CLONAL	1	TRUE	1	0.713671940051232	2		433	414	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387412	17387414	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs755646838	NA	P-0069722-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	211	557	0	ENST00000359435.4:c.680_682del	p.Ser227del	p.S227del	ENST00000359435	NM_001033549.1	226	ttCTCc/ttc	7/9	0.713671940051232	3	FACETS	0.963	0.896	1	0.482	0.448	0.516	CLONAL	1	TRUE	1	0.713671940051232	3		557	833	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120795666	120795666	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1270520592	NA	P-0069722-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	78	281	0	ENST00000257552.2:c.487G>A	p.Val163Met	p.V163M	ENST00000257552	NM_002442.3	163	Gtg/Atg	8/15	1	2	FACETS	0.976	0.872	1	0.976	0.872	1	CLONAL	1	TRUE	1	0.713671940051232	2		281	224	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873483	136873483	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0069722-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	27	383	0	ENST00000241393.3:c.16-1G>T		p.X6_splice	ENST00000241393	NM_003467.2	6			1	2	FACETS	0.814	0.664	0.975	0.814	0.664	0.975	CLONAL	1	TRUE	1	0.713671940051232	2		383	93	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0069723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	30	224	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.240054394544175	1	FACETS	0.984	0.813	1	0.984	0.813	1	INDETERMINATE	1	TRUE	0	0.467153464798621	1		224	100	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052980	180052980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	228	657	0	ENST00000261937.6:c.1310G>A	p.Arg437His	p.R437H	ENST00000261937	NM_182925.4	437	cGt/cAt	10/30	0.467153464798621	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.467153464798621	1		657	643	SUCCESS
APC	324	MSKCC	GRCh37	5	112155026	112155026	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs863225309	NA	P-0069723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	83	333	0	ENST00000257430.4:c.1297C>T	p.Gln433Ter	p.Q433*	ENST00000257430	NM_000038.5	433	Cag/Tag	10/16	0.467153464798621	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.467153464798621	1		333	263	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0069723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	56	365	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.305657084689824	2	FACETS	1	0.972	1	0.749	0.656	0.846	CLONAL	1	TRUE	0	0.467153464798621	2		365	160	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577152	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGTAGATTA	CCAGTAGATTA	-	novel	NA	P-0069723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	156	336	0	ENST00000269305.4:c.786_796del	p.Asn263ThrfsTer5	p.N263Tfs*5	ENST00000269305	NM_001126112.2	262	ggTAATCTACTGGga/ggga	8/11	0.467153464798621	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.467153464798621	1		336	426	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023290	27023290	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	33	367	0	ENST00000324856.7:c.400del	p.Ala134ArgfsTer98	p.A134Rfs*98	ENST00000324856	NM_006015.4	132	gtG/gt	1/20	1	2	FACETS	0.315	0.257	0.38	0.315	0.257	0.38	SUBCLONAL	1	TRUE	1	0.697690153659283	2		367	300	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101552	27101552	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	36	520	0	ENST00000324856.7:c.4837del	p.Met1613CysfsTer13	p.M1613Cfs*13	ENST00000324856	NM_006015.4	1612	Aaa/aa	18/20	1	2	FACETS	0.193	0.158	0.232	0.193	0.158	0.232	SUBCLONAL	1	TRUE	1	0.697690153659283	2		520	535	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	31	437	2	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.172	0.138	0.209	0.172	0.138	0.209	SUBCLONAL	1	TRUE	1	0.697690153659283	2		439	518	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106196	27106196	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	200	499	0	ENST00000324856.7:c.5807del	p.Ser1936ThrfsTer20	p.S1936Tfs*20	ENST00000324856	NM_006015.4	1936	aGc/ac	20/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.697690153659283	2		499	550	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809480	36809480	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	65	361	0	ENST00000373129.3:c.985A>G	p.Ser329Gly	p.S329G	ENST00000373129	NM_032017.1	329	Agt/Ggt	10/12	1	2	FACETS	0.433	0.377	0.494	0.433	0.377	0.494	SUBCLONAL	1	TRUE	1	0.697690153659283	2		361	430	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	194	395	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.967	0.901	1	0.967	0.901	1	CLONAL	1	TRUE	1	0.697690153659283	2		396	575	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	188	699	4	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.697690153659283	2		703	534	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870382	155870382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	190	418	0	ENST00000368323.3:c.457G>A	p.Ala153Thr	p.A153T	ENST00000368323	NM_006912.5	153	Gcc/Acc	6/6	0.635041380801004	4	FACETS	1	0.929	1	0.503	0.465	0.542	CLONAL	1	TRUE	2	0.697690153659283	4		418	920	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849842	156849842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	178	402	1	ENST00000524377.1:c.2098C>A	p.Leu700Met	p.L700M	ENST00000524377	NM_002529.3	700	Ctg/Atg	16/17	0.635041380801004	4	FACETS	1	0.974	1	0.563	0.519	0.607	CLONAL	1	TRUE	2	0.697690153659283	4		403	770	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851291	156851291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1009726086	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	151	468	0	ENST00000524377.1:c.2248C>T	p.Arg750Cys	p.R750C	ENST00000524377	NM_002529.3	750	Cgt/Tgt	17/17	0.635041380801004	4	FACETS	0.993	0.909	1	0.497	0.454	0.54	CLONAL	1	TRUE	2	0.697690153659283	4		468	740	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	80	182	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.697690153659283	2	FACETS	0.775	0.705	0.844	0.775	0.705	0.844	SUBCLONAL	2	TRUE	0	0.697690153659283	2		182	148	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256095	123256095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	169	379	0	ENST00000358487.5:c.1814C>T	p.Ser605Leu	p.S605L	ENST00000358487	NM_000141.4	605	tCa/tTa	13/18	0.697690153659283	2	FACETS	0.987	0.915	1	0.493	0.457	0.53	CLONAL	1	TRUE	0	0.697690153659283	2		379	491	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	188	356	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.697690153659283	2	FACETS	0.936	0.87	1	0.468	0.435	0.502	CLONAL	1	TRUE	0	0.697690153659283	2		356	576	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943380	71943380	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1394942069	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	182	439	0	ENST00000298229.2:c.1712G>A	p.Arg571Gln	p.R571Q	ENST00000298229	NM_001567.3	571	cGg/cAg	14/28	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.697690153659283	2		439	514	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	170	518	1	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.963	0.893	1	0.963	0.893	1	CLONAL	1	TRUE	1	0.697690153659283	2		519	506	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	141	500	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.844	0.774	0.916	0.844	0.774	0.916	CLONAL	1	TRUE	1	0.697690153659283	2		501	479	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	70	541	4	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.27	0.235	0.308	0.27	0.235	0.308	SUBCLONAL	1	TRUE	1	0.697690153659283	2		545	743	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372531	118372531	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs900114876	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	236	454	0	ENST00000534358.1:c.6464C>T	p.Pro2155Leu	p.P2155L	ENST00000534358	NM_005933.3	2155	cCa/cTa	26/36	1	2	FACETS	0.993	0.932	1	0.993	0.932	1	CLONAL	1	TRUE	1	0.697690153659283	2		454	681	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	172	477	1	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.697690153659283	2		478	492	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856504	111856504	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	124	481	0	ENST00000341259.2:c.555G>T	p.Trp185Cys	p.W185C	ENST00000341259	NM_005475.2	185	tgG/tgT	2/8	1	2	FACETS	0.935	0.855	1	0.935	0.855	1	CLONAL	1	TRUE	1	0.697690153659283	2		481	380	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714177	43714177	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	204	515	0	ENST00000382044.4:c.3976C>T	p.Leu1326Phe	p.L1326F	ENST00000382044	NM_001141980.1	1326	Ctc/Ttc	19/28	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.697690153659283	2		515	573	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778412	3778413	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGT	rs1555470928	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	55	533	0	ENST00000262367.5:c.6633_6635dup	p.Gln2216dup	p.Q2216dup	ENST00000262367	NM_004380.2	2216	cag/caACAg	31/31	1	2	FACETS	0.274	0.234	0.318	0.274	0.234	0.318	SUBCLONAL	1	TRUE	1	0.697690153659283	2		533	575	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820920	3820920	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	157	395	0	ENST00000262367.5:c.2531C>A	p.Pro844His	p.P844H	ENST00000262367	NM_004380.2	844	cCt/cAt	14/31	1	2	FACETS	0.922	0.851	0.995	0.922	0.851	0.995	CLONAL	1	TRUE	1	0.697690153659283	2		395	488	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	220	519	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.919	0.859	0.981	0.919	0.859	0.981	CLONAL	1	TRUE	1	0.697690153659283	2		519	686	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346588	89346588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747992186	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	170	522	0	ENST00000301030.4:c.6362C>T	p.Ala2121Val	p.A2121V	ENST00000301030	NM_001256183.1	2121	gCg/gTg	9/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.697690153659283	2		522	452	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553478	29553478	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781807	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	178	395	0	ENST00000356175.3:c.2033del	p.Pro678ArgfsTer10	p.P678Rfs*10	ENST00000356175	NM_000267.3	676	aCc/ac	18/57	1	2	FACETS	0.859	0.796	0.924	0.859	0.796	0.924	CLONAL	1	TRUE	1	0.697690153659283	2		395	594	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588751	29588751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760703505	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	165	281	0	ENST00000356175.3:c.4537C>T	p.Arg1513Ter	p.R1513*	ENST00000356175	NM_000267.3	1513	Cga/Tga	34/57	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.697690153659283	2		281	418	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687472	37687472	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	187	514	0	ENST00000447079.4:c.4382del	p.Gly1461AlafsTer38	p.G1461Afs*38	ENST00000447079	NM_015083.1	1459	tGg/tg	14/14	1	2	FACETS	0.984	0.915	1	0.984	0.915	1	CLONAL	1	TRUE	1	0.697690153659283	2		514	545	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435426	56435426	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408875424	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	358	469	1	ENST00000407977.2:c.1711C>T	p.Pro571Ser	p.P571S	ENST00000407977		571	Cca/Tca	9/10	0.697690153659283	2	FACETS	0.961	0.926	0.995	0.961	0.926	0.995	CLONAL	2	TRUE	0	0.697690153659283	2		470	534	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760902	59760902	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782029	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	355	391	0	ENST00000259008.2:c.3505G>T	p.Asp1169Tyr	p.D1169Y	ENST00000259008	NM_032043.2	1169	Gac/Tac	20/20	0.697690153659283	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.697690153659283	2		391	479	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733223	74733223	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	43	415	0	ENST00000359995.5:c.20del	p.Pro7LeufsTer7	p.P7Lfs*7	ENST00000359995	NM_001195427.1	7	cCt/ct	1/3	0.697690153659283	2	FACETS	0.347	0.291	0.409	0.174	0.145	0.205	SUBCLONAL	1	TRUE	0	0.697690153659283	2		415	355	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625592	1625592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1280061503	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	150	428	0	ENST00000344749.5:c.482C>T	p.Ala161Val	p.A161V	ENST00000344749	NM_001136139.2	161	gCg/gTg	7/19	1	2	FACETS	0.929	0.856	1	0.929	0.856	1	CLONAL	1	TRUE	1	0.697690153659283	2		428	463	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5207964	5207964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	142	546	0	ENST00000357368.4:c.5747G>A	p.Arg1916Gln	p.R1916Q	ENST00000357368	NM_002850.3	1916	cGa/cAa	37/38	1	2	FACETS	0.848	0.778	0.92	0.848	0.778	0.92	CLONAL	1	TRUE	1	0.697690153659283	2		546	480	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6213976	6213976	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs772076449	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	117	407	2	ENST00000252674.7:c.1381del	p.Gln461ArgfsTer46	p.Q461Rfs*46	ENST00000252674	NM_005934.3	461	Cag/ag	9/12	1	2	FACETS	0.953	0.869	1	0.953	0.869	1	CLONAL	1	TRUE	1	0.697690153659283	2		409	352	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610253	10610253	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	184	485	0	ENST00000171111.5:c.457C>A	p.Leu153Ile	p.L153I	ENST00000171111	NM_203500.1	153	Ctc/Atc	2/6	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.697690153659283	2		485	519	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216405	36216413	+	inframe_deletion	In_Frame_Del	DEL	ACCCATTCC	ACCCATTCC	-	novel	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	152	480	0	ENST00000222270.7:c.3676_3684del	p.His1226_Phe1228del	p.H1226_F1228del	ENST00000222270	NM_014727.1	1223	gACCCATTCCac/gac	12/37	1	2	FACETS	0.877	0.808	0.948	0.877	0.808	0.948	CLONAL	1	TRUE	1	0.697690153659283	2		480	497	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281898	39281898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	110	299	0	ENST00000402219.2:c.577C>T	p.Pro193Ser	p.P193S	ENST00000402219	NM_005633.3	193	Cct/Tct	5/23	0.697690153659283	3	FACETS	0.852	0.769	0.939	0.426	0.384	0.47	CLONAL	1	TRUE	1	0.697690153659283	3		299	499	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033472	48033472	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	167	422	0	ENST00000234420.5:c.3776A>G	p.Asn1259Ser	p.N1259S	ENST00000234420	NM_000179.2	1259	aAt/aGt	8/10	0.697690153659283	3	FACETS	0.911	0.839	0.985	0.455	0.419	0.493	CLONAL	1	TRUE	1	0.697690153659283	3		422	709	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99162497	99162497	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	151	407	0	ENST00000074304.5:c.1015C>A	p.His339Asn	p.H339N	ENST00000074304	NM_001134224.1	339	Cac/Aac	12/26	0.697690153659283	3	FACETS	0.879	0.806	0.955	0.44	0.403	0.478	CLONAL	1	TRUE	1	0.697690153659283	3		407	664	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098024	178098024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217896899	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	172	364	0	ENST00000397062.3:c.356G>A	p.Cys119Tyr	p.C119Y	ENST00000397062	NM_006164.4	119	tGc/tAc	3/5	0.697690153659283	3	FACETS	0.987	0.911	1	0.493	0.455	0.533	CLONAL	1	TRUE	1	0.697690153659283	3		364	674	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645975	215645975	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs587780033	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	168	445	0	ENST00000260947.4:c.623del	p.Lys208ArgfsTer4	p.K208Rfs*4	ENST00000260947	NM_000465.2	208	aAg/ag	4/11	0.697690153659283	3	FACETS	0.883	0.813	0.955	0.441	0.406	0.478	CLONAL	1	TRUE	1	0.697690153659283	3		445	736	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29439342	29439342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	53	378	0	ENST00000544604.2:c.557C>T	p.Ala186Val	p.A186V	ENST00000544604	NM_001206998.1	186	gCa/gTa	4/9	1	2	FACETS	0.308	0.263	0.358	0.308	0.263	0.358	SUBCLONAL	1	TRUE	1	0.697690153659283	2		378	493	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042468	37042468	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750437	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	133	304	0	ENST00000231790.2:c.230G>A	p.Cys77Tyr	p.C77Y	ENST00000231790	NM_000249.3	77	tGt/tAt	3/19	1	2	FACETS	0.968	0.888	1	0.968	0.888	1	CLONAL	1	TRUE	1	0.697690153659283	2		304	394	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259601	89259601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773846066	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	67	457	0	ENST00000336596.2:c.745G>A	p.Glu249Lys	p.E249K	ENST00000336596	NM_005233.5	249	Gaa/Aaa	3/17	1	2	FACETS	0.393	0.342	0.448	0.393	0.342	0.448	SUBCLONAL	1	TRUE	1	0.697690153659283	2		457	489	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628551	187628551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765982067	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	165	524	0	ENST00000441802.2:c.2431G>A	p.Val811Met	p.V811M	ENST00000441802	NM_005245.3	811	Gtg/Atg	2/27	1	2	FACETS	0.854	0.789	0.921	0.854	0.789	0.921	CLONAL	1	TRUE	1	0.697690153659283	2		524	554	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591246	67591246	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	227	424	0	ENST00000274335.5:c.1746-2A>G		p.X582_splice	ENST00000274335		582			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.697690153659283	2		424	594	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	248	394	2	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.697690153659283	2		396	493	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638726	176638726	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	83	432	0	ENST00000439151.2:c.3326A>G	p.His1109Arg	p.H1109R	ENST00000439151	NM_022455.4	1109	cAt/cGt	5/23	1	2	FACETS	0.417	0.368	0.469	0.417	0.368	0.469	SUBCLONAL	1	TRUE	1	0.697690153659283	2		432	571	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323288	31323288	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	98	449	0	ENST00000412585.2:c.701C>A	p.Pro234His	p.P234H	ENST00000412585	NM_005514.6	234	cCt/cAt	4/8	1	2	FACETS	0.634	0.569	0.703	0.634	0.569	0.703	SUBCLONAL	1	TRUE	1	0.697690153659283	2		449	443	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32814922	32814922	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs375324960	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	153	403	0	ENST00000354258.4:c.2143C>T	p.Arg715Ter	p.R715*	ENST00000354258	NM_000593.5	715	Cga/Tga	10/11	1	2	FACETS	0.908	0.837	0.981	0.908	0.837	0.981	CLONAL	1	TRUE	1	0.697690153659283	2		403	483	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522454	157522454	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	221	490	1	ENST00000346085.5:c.4726C>T	p.Pro1576Ser	p.P1576S	ENST00000346085	NM_020732.3	1576	Ccg/Tcg	18/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.697690153659283	2		491	572	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224488	55224488	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	150	364	0	ENST00000275493.2:c.1170G>T	p.Gln390His	p.Q390H	ENST00000275493	NM_005228.3	390	caG/caT	10/28	1	2	FACETS	0.915	0.843	0.989	0.915	0.843	0.989	CLONAL	1	TRUE	1	0.697690153659283	2		364	470	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241652	55241652	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	236	540	0	ENST00000275493.2:c.2100C>G	p.Asn700Lys	p.N700K	ENST00000275493	NM_005228.3	700	aaC/aaG	18/28	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.697690153659283	2		540	594	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759406	133759406	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1371645607	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	55	408	0	ENST00000318560.5:c.1729C>T	p.Arg577Ter	p.R577*	ENST00000318560	NM_005157.4	577	Cga/Tga	11/11	1	2	FACETS	0.368	0.315	0.425	0.368	0.315	0.425	SUBCLONAL	1	TRUE	1	0.697690153659283	2		408	429	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923004	44923004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	229	497	0	ENST00000377967.4:c.1865C>T	p.Thr622Ile	p.T622I	ENST00000377967	NM_021140.2	622	aCa/aTa	16/29	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.697690153659283	2		497	655	SUCCESS
AR	367	MSKCC	GRCh37	X	66765149	66765154	+	inframe_deletion	In_Frame_Del	DEL	TGCTGC	TGCTGC	-	rs752055010	NA	P-0069725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	18	317	0	ENST00000374690.3:c.167_172del	p.Leu56_Leu57del	p.L56_L57del	ENST00000374690	NM_000044.3	54	tTGCTGCtg/ttg	1/8	1	2	FACETS	0.181	0.136	0.234	0.181	0.136	0.234	SUBCLONAL	1	TRUE	1	0.697690153659283	2		317	285	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681160	117681160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	20	342	0	ENST00000368508.3:c.3460C>T	p.Pro1154Ser	p.P1154S	ENST00000368508	NM_002944.2	1154	Cct/Tct	23/43	0.26182200163484	1	FACETS	0.935	0.722	1	0.935	0.722	1	CLONAL	1	TRUE	0	0.26182200163484	1		342	142	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716006	52716006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	17	552	0	ENST00000322088.6:c.571G>A	p.Glu191Lys	p.E191K	ENST00000322088	NM_014225.5	191	Gag/Aag	5/15	1	2	FACETS	0.934	0.703	1	0.934	0.703	1	CLONAL	1	TRUE	1	0.26182200163484	2		552	139	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220070	133220070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	28	561	0	ENST00000320574.5:c.4367C>T	p.Ser1456Leu	p.S1456L	ENST00000320574	NM_006231.2	1456	tCa/tTa	34/49	1	2	FACETS	0.938	0.765	1	1	0.955	1	CLONAL	2	TRUE	1	0.26182200163484	2		561	114	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28644650	28644650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1394449672	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	12	363	0	ENST00000241453.7:c.143G>A	p.Gly48Glu	p.G48E	ENST00000241453	NM_004119.2	48	gGg/gAg	2/24	0.26182200163484	1	FACETS	0.789	0.56	1	0.789	0.56	1	CLONAL	1	TRUE	0	0.26182200163484	1		363	101	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623858	28623858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	25	481	0	ENST00000241453.7:c.796G>A	p.Glu266Lys	p.E266K	ENST00000241453	NM_004119.2	266	Gaa/Aaa	7/24	0.26182200163484	1	FACETS	0.943	0.749	1	0.943	0.749	1	CLONAL	1	TRUE	0	0.26182200163484	1		481	176	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149260	119149260	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs868103494	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	64	472	0	ENST00000264033.4:c.1268T>A	p.Ile423Asn	p.I423N	ENST00000264033	NM_005188.3	423	aTt/aAt	9/16	0.250698632283397	3	FACETS	1	0.961	1	0.83	0.729	0.936	CLONAL	2	TRUE	0	0.26182200163484	3		472	222	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223461	2223461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	17	468	0	ENST00000398665.3:c.3572C>T	p.Ser1191Phe	p.S1191F	ENST00000398665	NM_032482.2	1191	tCt/tTt	25/28	0.26182200163484	1	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	0	0.26182200163484	1		468	94	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2189768	2189768	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479024523	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	17	474	0	ENST00000398665.3:c.238C>T	p.Arg80Cys	p.R80C	ENST00000398665	NM_032482.2	80	Cgt/Tgt	4/28	0.26182200163484	1	FACETS	1	0.836	1	1	0.836	1	CLONAL	1	TRUE	0	0.26182200163484	1		474	99	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710585	117710585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	21	511	0	ENST00000368508.3:c.1687G>A	p.Glu563Lys	p.E563K	ENST00000368508	NM_002944.2	563	Gag/Aag	12/43	0.26182200163484	1	FACETS	0.83	0.644	1	0.83	0.644	1	CLONAL	1	TRUE	0	0.26182200163484	1		511	168	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405915	49405915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866298036	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	27	451	0	ENST00000418115.1:c.223C>T	p.Pro75Ser	p.P75S	ENST00000418115	NM_001664.2	75	Cca/Tca	3/5	0.26182200163484	3	FACETS	1	0.917	1	0.652	0.523	0.796	CLONAL	1	TRUE	1	0.26182200163484	3		451	179	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675068	40675068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	46	446	0	ENST00000249776.8:c.32G>A	p.Arg11Lys	p.R11K	ENST00000249776	NM_033286.3	11	aGa/aAa	1/9	1	2	FACETS	0.935	0.798	1	1	0.972	1	CLONAL	2	TRUE	1	0.26182200163484	2		446	188	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730858	40730858	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200227405	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	23	559	0	ENST00000373198.4:c.3677G>A	p.Arg1226Gln	p.R1226Q	ENST00000373198	NM_133170.3	1226	cGa/cAa	27/32	0.26182200163484	1	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	0	0.26182200163484	1		559	132	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25990556	25990556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1293915045	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	18	456	0	ENST00000435504.4:c.671G>A	p.Ser224Asn	p.S224N	ENST00000435504		224	aGc/aAc	8/13	0.116385638540028	4	FACETS	0.859	0.649	1	0.429	0.324	0.553	INDETERMINATE	1	TRUE	2	0.26182200163484	4		456	202	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730107	41730107	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	33	457	0	ENST00000242208.4:c.422C>T	p.Ser141Phe	p.S141F	ENST00000242208	NM_002192.2	141	tCc/tTc	3/3	0.21339914496218	5	FACETS	0.944	0.777	1	0.629	0.518	0.752	CLONAL	2	TRUE	2	0.26182200163484	5		457	186	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006381	12006381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765265003	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	45	486	0	ENST00000396373.4:c.349C>T	p.Leu117Phe	p.L117F	ENST00000396373	NM_001987.4	117	Ctt/Ttt	4/8	0.26182200163484	3	FACETS	0.962	0.819	1	0.962	0.819	1	CLONAL	2	TRUE	1	0.26182200163484	3		486	202	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738311	133738311	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	32	508	0	ENST00000318560.5:c.711G>A	p.Met237Ile	p.M237I	ENST00000318560	NM_005157.4	237	atG/atA	4/11	0.26182200163484	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.26182200163484	1		508	174	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752363	55752363	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745388891	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	10	433	0	ENST00000284073.2:c.821C>T	p.Pro274Leu	p.P274L	ENST00000284073	NM_138962.2	274	cCg/cTg	12/14	0.26182200163484	3	FACETS	0.568	0.386	0.796	0.284	0.193	0.398	SUBCLONAL	1	TRUE	1	0.26182200163484	3		433	152	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27209227	27209227	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs765053701	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	11	314	0	ENST00000380036.4:c.2684G>A	p.Arg895Gln	p.R895Q	ENST00000380036	NM_000459.3	895	cGa/cAa	16/23	0.26182200163484	1	FACETS	0.753	0.525	1	0.753	0.525	1	CLONAL	1	TRUE	0	0.26182200163484	1		314	97	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377289	118377290	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	61	613	1	ENST00000534358.1:c.10682_10683delinsTT	p.Ser3561Phe	p.S3561F	ENST00000534358	NM_005933.3	3561	tCC/tTT	27/36	0.250698632283397	3	FACETS	1	0.958	1	0.825	0.722	0.933	CLONAL	2	TRUE	0	0.26182200163484	3		614	213	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031850	10031850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	26	478	0	ENST00000330684.3:c.973G>A	p.Glu325Lys	p.E325K	ENST00000330684	NM_001134407.1	325	Gag/Aag	3/13	1	2	FACETS	1	0.83	1	1	0.83	1	CLONAL	1	TRUE	1	0.26182200163484	2		478	190	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639858	3639858	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141860134	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	16	503	0	ENST00000294008.3:c.3781C>T	p.Pro1261Ser	p.P1261S	ENST00000294008	NM_032444.2	1261	Ccg/Tcg	12/15	1	2	FACETS	1	0.783	1	1	0.783	1	CLONAL	1	TRUE	1	0.26182200163484	2		503	116	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120461	94120461	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	27	465	0	ENST00000369303.4:c.590C>T	p.Ser197Phe	p.S197F	ENST00000369303	NM_004440.3	197	tCt/tTt	3/17	0.26182200163484	3	FACETS	0.804	0.648	0.978	0.804	0.648	0.978	CLONAL	2	TRUE	1	0.26182200163484	3		465	145	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245219	46245219	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	38	498	0	ENST00000334344.6:c.3313C>T	p.Gln1105Ter	p.Q1105*	ENST00000334344	NM_152641.2	1105	Caa/Taa	15/21	0.26182200163484	3	FACETS	0.805	0.672	0.95	0.805	0.672	0.95	CLONAL	2	TRUE	1	0.26182200163484	3		498	204	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101510	27101510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781689378	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	22	600	0	ENST00000324856.7:c.4792C>T	p.Arg1598Cys	p.R1598C	ENST00000324856	NM_006015.4	1598	Cgc/Tgc	18/20	0.26182200163484	3	FACETS	0.985	0.768	1	0.492	0.384	0.617	CLONAL	1	TRUE	1	0.26182200163484	3		600	193	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59820399	59820399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	22	365	0	ENST00000259008.2:c.2354C>T	p.Pro785Leu	p.P785L	ENST00000259008	NM_032043.2	785	cCt/cTt	16/20	0.26182200163484	3	FACETS	0.955	0.744	1	0.478	0.372	0.599	CLONAL	1	TRUE	1	0.26182200163484	3		365	199	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318775	163318775	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	20	373	0	ENST00000271452.3:c.1165G>A	p.Glu389Lys	p.E389K	ENST00000271452	NM_145697.2	389	Gaa/Aaa	13/14	0.26182200163484	3	FACETS	1	0.822	1	0.54	0.416	0.683	CLONAL	1	TRUE	1	0.26182200163484	3		373	160	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258586	16258586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	39	629	0	ENST00000375759.3:c.5851G>A	p.Gly1951Arg	p.G1951R	ENST00000375759	NM_015001.2	1951	Gga/Aga	11/15	0.26182200163484	3	FACETS	0.826	0.691	0.972	0.826	0.691	0.972	CLONAL	2	TRUE	1	0.26182200163484	3		629	204	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95583017	95583017	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886037672	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	35	392	0	ENST00000393063.1:c.1525C>T	p.Arg509Ter	p.R509*	ENST00000393063	NM_030621.3	509	Cga/Tga	11/28	0.26182200163484	3	FACETS	0.869	0.721	1	0.869	0.721	1	CLONAL	2	TRUE	1	0.26182200163484	3		392	174	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46276064	46276065	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	22	521	0	ENST00000371998.3:c.3500_3501delinsTT	p.Pro1167Leu	p.P1167L	ENST00000371998		1167	cCC/cTT	18/23	0.26182200163484	3	FACETS	0.809	0.629	1	0.404	0.314	0.508	CLONAL	1	TRUE	1	0.26182200163484	3		521	235	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781210	9781210	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	37	465	0	ENST00000377346.4:c.1715C>A	p.Pro572Gln	p.P572Q	ENST00000377346	NM_005026.3	572	cCg/cAg	14/24	0.26182200163484	3	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	1	0.26182200163484	3		465	130	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715622	30715622	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893818	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	26	419	0	ENST00000295754.5:c.1280C>T	p.Pro427Leu	p.P427L	ENST00000295754	NM_003242.5	427	cCa/cTa	5/7	0.26182200163484	3	FACETS	1	0.846	1	0.537	0.428	0.661	CLONAL	1	TRUE	1	0.26182200163484	3		419	209	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188178	108188179	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	33	318	0	ENST00000278616.4:c.6277_6278delinsTT	p.Pro2093Phe	p.P2093F	ENST00000278616	NM_000051.3	2093	CCt/TTt	43/63	0.250698632283397	3	FACETS	1	0.918	1	0.792	0.659	0.935	CLONAL	2	TRUE	0	0.26182200163484	3		318	120	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295782	212295782	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	26	436	0	ENST00000342788.4:c.2531T>C	p.Leu844Ser	p.L844S	ENST00000342788	NM_005235.2	844	tTg/tCg	21/28	0.26182200163484	0	FACETS	0.984	0.789	1			1	CLONAL	1	TRUE	0	0.26182200163484	0		436	149	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422940	12422940	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1346246354	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	17	425	0	ENST00000287820.6:c.430G>A	p.Asp144Asn	p.D144N	ENST00000287820	NM_015869.4	144	Gat/Aat	3/7	0.26182200163484	3	FACETS	0.854	0.641	1	0.427	0.32	0.552	CLONAL	1	TRUE	1	0.26182200163484	3		425	172	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31435921	31435921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	18	395	0	ENST00000344624.3:c.2993C>T	p.Thr998Ile	p.T998I	ENST00000344624		998	aCc/aTc	22/33	0.116385638540028	4	FACETS	1	0.889	1	0.672	0.511	0.858	INDETERMINATE	1	TRUE	2	0.26182200163484	4		395	129	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251833	212251833	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs981589205	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	26	478	0	ENST00000342788.4:c.3226G>A	p.Gly1076Arg	p.G1076R	ENST00000342788	NM_005235.2	1076	Gga/Aga	27/28	0.116385638540028	4	FACETS	1	0.892	1	0.6	0.478	0.737	INDETERMINATE	1	TRUE	2	0.26182200163484	4		478	209	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405904	157405904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	50	490	0	ENST00000346085.5:c.2146G>A	p.Ala716Thr	p.A716T	ENST00000346085	NM_020732.3	716	Gcg/Acg	6/20	0.217509651323212	3	FACETS	0.821	0.702	0.949	0.547	0.468	0.633	CLONAL	2	TRUE	0	0.26182200163484	3		490	263	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858379	9858379	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	29	545	0	ENST00000330684.3:c.3022T>C	p.Ser1008Pro	p.S1008P	ENST00000330684	NM_001134407.1	1008	Tct/Cct	13/13	1	2	FACETS	0.769	0.626	0.927	1	0.944	1	CLONAL	2	TRUE	1	0.26182200163484	2		545	144	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647217	2647217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263044277	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	20	455	0	ENST00000342085.4:c.1495C>T	p.Pro499Ser	p.P499S	ENST00000342085	NM_002613.4	499	Cct/Tct	13/14	1	2	FACETS	0.986	0.76	1	0.986	0.76	1	CLONAL	1	TRUE	1	0.26182200163484	2		455	155	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527558	29527558	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	26	341	0	ENST00000356175.3:c.1007G>A	p.Trp336Ter	p.W336*	ENST00000356175	NM_000267.3	336	tGg/tAg	9/57	0.26182200163484	3	FACETS	0.769	0.617	0.939	0.769	0.617	0.939	CLONAL	2	TRUE	1	0.26182200163484	3		341	146	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50481239	50481239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	24	473	0	ENST00000394963.4:c.625C>T	p.Leu209Phe	p.L209F	ENST00000394963	NM_003076.4	209	Ctt/Ttt	5/13	0.26182200163484	3	FACETS	0.785	0.617	0.978	0.393	0.308	0.489	CLONAL	1	TRUE	1	0.26182200163484	3		473	264	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8109892	8109892	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	19	523	0	ENST00000585124.1:c.603A>G	p.Ile201Met	p.I201M	ENST00000585124	NM_004217.3	201	atA/atG	7/9	0.26182200163484	3	FACETS	0.846	0.645	1	0.423	0.322	0.54	CLONAL	1	TRUE	1	0.26182200163484	3		523	194	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1685016	1685016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	21	397	0	ENST00000378625.1:c.1609C>T	p.His537Tyr	p.H537Y	ENST00000378625	NM_001198994.1	537	Cat/Tat	13/14	0.26182200163484	3	FACETS	0.81	0.633	1	0.81	0.633	1	CLONAL	2	TRUE	1	0.26182200163484	3		397	112	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982703	90982703	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	28	431	0	ENST00000265433.3:c.785T>G	p.Phe262Cys	p.F262C	ENST00000265433	NM_002485.4	262	tTc/tGc	7/16	0.26182200163484	3	FACETS	1	0.897	1	0.596	0.479	0.726	CLONAL	1	TRUE	1	0.26182200163484	3		431	203	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273143	198273143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1159430616	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	26	429	0	ENST00000335508.6:c.1067G>A	p.Gly356Glu	p.G356E	ENST00000335508	NM_012433.2	356	gGa/gAa	8/25	0.116385638540028	4	FACETS	1	0.919	1	0.674	0.538	0.827	INDETERMINATE	1	TRUE	2	0.26182200163484	4		429	186	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624623	93624623	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	15	379	0	ENST00000375746.1:c.714G>T	p.Trp238Cys	p.W238C	ENST00000375746	NM_001174167.1	238	tgG/tgT	4/14	0.26182200163484	1	FACETS	1	0.768	1	1	0.768	1	CLONAL	1	TRUE	0	0.26182200163484	1		379	96	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445481	49445481	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	33	561	1	ENST00000301067.7:c.1985T>G	p.Leu662Arg	p.L662R	ENST00000301067	NM_003482.3	662	cTg/cGg	10/54	0.26182200163484	3	FACETS	0.801	0.659	0.956	0.801	0.659	0.956	CLONAL	2	TRUE	1	0.26182200163484	3		562	178	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928864	49928864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	20	578	0	ENST00000296474.3:c.3502G>A	p.Asp1168Asn	p.D1168N	ENST00000296474	NM_002447.2	1168	Gac/Aac	16/20	0.26182200163484	3	FACETS	0.831	0.646	1	0.831	0.646	1	CLONAL	2	TRUE	1	0.26182200163484	3		578	104	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783226	9783226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	19	446	0	ENST00000377346.4:c.2470C>T	p.Leu824Phe	p.L824F	ENST00000377346	NM_005026.3	824	Ctc/Ttc	20/24	0.26182200163484	3	FACETS	0.966	0.738	1	0.483	0.369	0.615	CLONAL	1	TRUE	1	0.26182200163484	3		446	170	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690571	33690571	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	26	483	0	ENST00000308377.4:c.256C>T	p.Gln86Ter	p.Q86*	ENST00000308377	NM_152270.3	86	Cag/Tag	2/5	0.26182200163484	3	FACETS	0.936	0.744	1	0.468	0.372	0.577	CLONAL	1	TRUE	1	0.26182200163484	3		483	240	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193477	99193477	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	25	538	0	ENST00000074304.5:c.2672G>T	p.Arg891Leu	p.R891L	ENST00000074304	NM_001134224.1	891	cGg/cTg	25/26	0.116385638540028	4	FACETS	1	0.817	1	1	0.817	1	INDETERMINATE	2	TRUE	2	0.26182200163484	4		538	118	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650554	18650555	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CT	CT	GG	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	19	337	0	ENST00000266497.5:c.2765_2766delinsGG	p.Ala922Gly	p.A922G	ENST00000266497		922	gCT/gGG	20/31	0.26182200163484	1	FACETS	0.956	0.733	1	0.956	0.733	1	CLONAL	1	TRUE	0	0.26182200163484	1		337	132	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299157	15299157	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	11	390	0	ENST00000263388.2:c.1381T>G	p.Phe461Val	p.F461V	ENST00000263388	NM_000435.2	461	Ttc/Gtc	9/33	1	2	FACETS	0.744	0.517	1	0.744	0.517	1	CLONAL	1	TRUE	1	0.26182200163484	2		390	113	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902184	50902184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	15	454	0	ENST00000440232.2:c.76G>A	p.Asp26Asn	p.D26N	ENST00000440232	NM_002691.3	26	Gat/Aat	2/27	1	2	FACETS	0.996	0.736	1	0.996	0.736	1	CLONAL	1	TRUE	1	0.26182200163484	2		454	115	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857385	9857385	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	18	486	0	ENST00000330684.3:c.4016A>T	p.Lys1339Ile	p.K1339I	ENST00000330684	NM_001134407.1	1339	aAa/aTa	13/13	1	2	FACETS	1	0.822	1	1	0.822	1	CLONAL	1	TRUE	1	0.26182200163484	2		486	125	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302454	15302454	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	13	576	0	ENST00000263388.2:c.817G>A	p.Glu273Lys	p.E273K	ENST00000263388	NM_000435.2	273	Gag/Aag	6/33	1	2	FACETS	0.842	0.605	1	0.842	0.605	1	CLONAL	1	TRUE	1	0.26182200163484	2		576	118	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661314	227661314	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	19	652	0	ENST00000305123.5:c.2141C>T	p.Pro714Leu	p.P714L	ENST00000305123	NM_005544.2	714	cCc/cTc	1/2	0.116385638540028	4	FACETS	1	0.86	1	0.595	0.455	0.756	INDETERMINATE	1	TRUE	2	0.26182200163484	4		652	154	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259451	55259451	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	29	392	0	ENST00000275493.2:c.2509G>C	p.Asp837His	p.D837H	ENST00000275493	NM_005228.3	837	Gac/Cac	21/28	1	2	FACETS	0.791	0.644	0.953	1	0.947	1	CLONAL	2	TRUE	1	0.26182200163484	2		392	140	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912804	50912804	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	11	477	0	ENST00000440232.2:c.2035G>A	p.Asp679Asn	p.D679N	ENST00000440232	NM_002691.3	679	Gac/Aac	17/27	1	2	FACETS	0.808	0.563	1	0.808	0.563	1	CLONAL	1	TRUE	1	0.26182200163484	2		477	104	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28979969	28979969	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	14	352	0	ENST00000282397.4:c.1499A>T	p.Asn500Ile	p.N500I	ENST00000282397	NM_002019.4	500	aAc/aTc	11/30	0.26182200163484	1	FACETS	0.611	0.444	0.812	0.611	0.444	0.812	SUBCLONAL	1	TRUE	0	0.26182200163484	1		352	152	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247523	71247523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	15	297	0	ENST00000318789.4:c.10G>A	p.Glu4Lys	p.E4K	ENST00000318789	NM_032682.5	4	Gaa/Aaa	6/21	0.26182200163484	3	FACETS	1	0.835	1	0.594	0.44	0.776	CLONAL	1	TRUE	1	0.26182200163484	3		297	109	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1686110	1686110	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	18	482	0	ENST00000378625.1:c.1151G>C	p.Arg384Pro	p.R384P	ENST00000378625	NM_001198994.1	384	cGg/cCg	10/14	0.26182200163484	3	FACETS	1	0.86	1	0.603	0.458	0.769	CLONAL	1	TRUE	1	0.26182200163484	3		482	129	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933804	49933805	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	13	552	0	ENST00000296474.3:c.2472_2473delinsTT	p.Arg825Cys	p.R825C	ENST00000296474	NM_002447.2	824	tgCCgc/tgTTgc	10/20	0.26182200163484	3	FACETS	0.985	0.709	1	0.493	0.354	0.658	CLONAL	1	TRUE	1	0.26182200163484	3		552	114	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481613	40481613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	39	543	0	ENST00000264657.5:c.1192G>A	p.Glu398Lys	p.E398K	ENST00000264657	NM_139276.2	398	Gaa/Aaa	13/24	0.26182200163484	3	FACETS	1	0.954	1	0.739	0.617	0.872	CLONAL	1	TRUE	1	0.26182200163484	3		543	228	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96931019	96931019	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1451389209	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	22	476	0	ENST00000258439.3:c.101C>T	p.Ala34Val	p.A34V	ENST00000258439	NM_001193304.2	34	gCc/gTc	2/4	0.116385638540028	4	FACETS	0.78	0.611	0.97	0.78	0.611	0.97	INDETERMINATE	2	TRUE	2	0.26182200163484	4		476	136	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625307	69625308	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	28	558	2	ENST00000334134.2:c.485_486delinsAA	p.Arg162Gln	p.R162Q	ENST00000334134	NM_005247.2	162	cGG/cAA	3/3	0.26182200163484	0	FACETS	0.887	0.729	1			1	CLONAL	2	TRUE	0	0.26182200163484	0		560	89	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251219	99251220	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	38	496	1	ENST00000268035.6:c.523_524delinsTT	p.Pro175Leu	p.P175L	ENST00000268035	NM_000875.3	175	CCa/TTa	2/21	1	2	FACETS	0.825	0.691	0.97	1	0.961	1	CLONAL	2	TRUE	1	0.26182200163484	2		497	176	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354441	40354442	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	14	573	0	ENST00000293328.3:c.2153_2154delinsTT	p.Ala718Val	p.A718V	ENST00000293328	NM_012448.3	718	gCC/gTT	18/19	0.26182200163484	3	FACETS	0.602	0.436	0.802	0.301	0.218	0.401	SUBCLONAL	1	TRUE	1	0.26182200163484	3		573	201	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759978	63759979	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	44	480	0	ENST00000279873.7:c.631_632delinsAA	p.Gly211Lys	p.G211K	ENST00000279873	NM_032199.2	211	GGg/AAg	4/10	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.26182200163484	2		480	261	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618413	37618413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1021399334	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	28	559	0	ENST00000447079.4:c.89C>T	p.Ser30Phe	p.S30F	ENST00000447079	NM_015083.1	30	tCt/tTt	1/14	0.26182200163484	3	FACETS	0.991	0.796	1	0.496	0.398	0.606	CLONAL	1	TRUE	1	0.26182200163484	3		559	244	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156612	2156612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1018841144	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	15	501	0	ENST00000434045.2:c.310C>T	p.Arg104Cys	p.R104C	ENST00000434045	NM_001127598.1	104	Cgc/Tgc	3/5	1	2	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	1	0.26182200163484	2		501	92	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912812	50912813	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	11	507	0	ENST00000440232.2:c.2043_2044delinsTT	p.Arg682Trp	p.R682W	ENST00000440232	NM_002691.3	681	ctCCgg/ctTTgg	17/27	1	2	FACETS	0.894	0.624	1	0.894	0.624	1	CLONAL	1	TRUE	1	0.26182200163484	2		507	94	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349619	89349619	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	30	555	0	ENST00000301030.4:c.3331A>T	p.Lys1111Ter	p.K1111*	ENST00000301030	NM_001256183.1	1111	Aaa/Taa	9/13	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.26182200163484	2		555	170	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348713	89348713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140373729	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	19	489	0	ENST00000301030.4:c.4237G>A	p.Glu1413Lys	p.E1413K	ENST00000301030	NM_001256183.1	1413	Gaa/Aaa	9/13	1	2	FACETS	1	0.815	1	1	0.815	1	CLONAL	1	TRUE	1	0.26182200163484	2		489	135	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170376	32170376	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	17	413	0	ENST00000375023.3:c.3232G>A	p.Gly1078Ser	p.G1078S	ENST00000375023	NM_004557.3	1078	Ggt/Agt	21/30	1	2	FACETS	0.807	0.606	1	0.807	0.606	1	CLONAL	1	TRUE	1	0.26182200163484	2		413	161	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183256	56183256	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	38	398	0	ENST00000399503.3:c.4166T>C	p.Phe1389Ser	p.F1389S	ENST00000399503	NM_005921.1	1389	tTt/tCt	18/20	0.116385638540028	4	FACETS	0.84	0.701	0.993	0.84	0.701	0.993	INDETERMINATE	2	TRUE	2	0.26182200163484	4		398	218	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231825	36231825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1429953108	NA	P-0069727-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	182	501	0	ENST00000300305.3:c.559G>A	p.Ala187Thr	p.A187T	ENST00000300305		187	Gcc/Acc	5/8	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.29	2		501	1218	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949768	151949768	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0069727-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	190	350	0	ENST00000262189.6:c.1332del	p.Ser445LeufsTer10	p.S445Lfs*10	ENST00000262189	NM_170606.2	444	cgG/cg	10/59	0.19727963968878	3	FACETS	0.825	0.763	0.89	0.825	0.763	0.89	CLONAL	2	TRUE	1	0.29	3		350	909	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0069730-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	65	206	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.217435100799453	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		206	344	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0069730-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	20	490	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		490	750	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0069730-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	26	482	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		482	752	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27217702	27217702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773518368	NA	P-0069731-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	119	378	0	ENST00000380036.4:c.3008G>A	p.Arg1003His	p.R1003H	ENST00000380036	NM_000459.3	1003	cGc/cAc	19/23	0.449929475356955	3	FACETS	1	0.952	1	0.542	0.49	0.596	CLONAL	1	TRUE	1	0.449929475356955	3		378	598	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222288	39222288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199856844	NA	P-0069731-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	75	416	0	ENST00000402219.2:c.3322G>A	p.Asp1108Asn	p.D1108N	ENST00000402219	NM_005633.3	1108	Gat/Aat	20/23	0.164784378638854	5	FACETS	0.855	0.749	0.969	0.285	0.249	0.323	INDETERMINATE	1	TRUE	2	0.449929475356955	5		416	653	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43806108	43806108	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069731-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	82	532	0	ENST00000372470.3:c.904C>T	p.Gln302Ter	p.Q302*	ENST00000372470	NM_005373.2	302	Caa/Taa	6/12	1	2	FACETS	0.596	0.525	0.671	0.596	0.525	0.671	SUBCLONAL	1	TRUE	1	0.449929475356955	2		532	612	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587431	29587431	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069731-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	30	394	0	ENST00000356175.3:c.4412T>C	p.Val1471Ala	p.V1471A	ENST00000356175	NM_000267.3	1471	gTa/gCa	33/57	1	2	FACETS	0.301	0.242	0.368	0.301	0.242	0.368	SUBCLONAL	1	TRUE	1	0.449929475356955	2		394	443	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214382	5214382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs977538185	NA	P-0069757-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	81	255	0	ENST00000357368.4:c.4604C>T	p.Ser1535Phe	p.S1535F	ENST00000357368	NM_002850.3	1535	tCt/tTt	30/38	0.251354215675418	4	FACETS	1	0.969	1	0.655	0.577	0.738	CLONAL	1	TRUE	2	0.251354215675418	4		255	616	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366309	15366309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069757-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	78	322	0	ENST00000263377.2:c.1846C>T	p.Arg616Trp	p.R616W	ENST00000263377	NM_058243.2	616	Cgg/Tgg	10/20	0.251354215675418	4	FACETS	1	0.956	1	0.596	0.523	0.673	CLONAL	1	TRUE	2	0.251354215675418	4		322	652	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163435	32163435	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs758742555	NA	P-0069757-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	55	306	0	ENST00000375023.3:c.5791C>T	p.Arg1931Ter	p.R1931*	ENST00000375023	NM_004557.3	1931	Cga/Tga	30/30	1	2	FACETS	0.867	0.742	1	0.867	0.742	1	CLONAL	1	TRUE	1	0.251354215675418	2		306	505	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937629	76937630	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0069757-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	71	253	0	ENST00000373344.5:c.3118dup	p.Thr1040AsnfsTer2	p.T1040Nfs*2	ENST00000373344	NM_000489.3	1040	act/aAct	9/35	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.251354215675418	2		253	443	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0069758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	32	206	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.837	0.693	0.993	0.837	0.693	0.993	CLONAL	1	TRUE	1	0.61647870924954	2		206	124	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0069758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	55	406	0				ENST00000310581	NM_198253.2	-/1132			0.221047332701848	0	FACETS	0.374	0.325	0.425			1	INDETERMINATE	1	TRUE	0	0.61647870924954	0		406	183	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0069758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	69	257	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.973	0.86	1	0.973	0.86	1	CLONAL	1	TRUE	1	0.61647870924954	2		257	230	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740432	58740432	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs775750934	NA	P-0069758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	88	303	0	ENST00000305921.3:c.1337C>G	p.Ser446Ter	p.S446*	ENST00000305921	NM_003620.3	446	tCa/tGa	6/6	0.61483306770874	3	FACETS	1	0.945	1	0.546	0.488	0.607	CLONAL	1	TRUE	1	0.61647870924954	3		303	342	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37637643	37637643	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	132	327	0	ENST00000249071.6:c.91G>C	p.Glu31Gln	p.E31Q	ENST00000249071	NM_002872.4	31	Gag/Cag	2/7	1	2	FACETS	0.962	0.881	1	0.962	0.881	1	CLONAL	1	TRUE	1	0.61647870924954	2		327	445	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442074	52442074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	123	377	0	ENST00000460680.1:c.275C>T	p.Ala92Val	p.A92V	ENST00000460680	NM_004656.3	92	gCa/gTa	5/17	0.250364335606947	2	FACETS	1	0.985	1	0.742	0.673	0.814	CLONAL	1	TRUE	0	0.284424149573223	2		377	583	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129627	47129628	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0069764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	164	295	0	ENST00000409792.3:c.5252_5253insCT	p.Lys1751AsnfsTer18	p.K1751Nfs*18	ENST00000409792	NM_014159.6	1751	aaa/aaCTa	10/21	0.250364335606947	2	FACETS	0.933	0.86	1	0.933	0.86	1	CLONAL	2	TRUE	0	0.284424149573223	2		295	618	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1686905	1686905	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	72	309	0	ENST00000378625.1:c.1031C>T	p.Pro344Leu	p.P344L	ENST00000378625	NM_001198994.1	344	cCt/cTt	9/14	1	2	FACETS	0.924	0.808	1	0.924	0.808	1	CLONAL	1	TRUE	1	0.284424149573223	2		309	548	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105641	30105641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	92	338	0	ENST00000331968.5:c.1045G>A	p.Asp349Asn	p.D349N	ENST00000331968	NM_002742.2	349	Gat/Aat	7/18	1	2	FACETS	0.829	0.737	0.927	0.829	0.737	0.927	CLONAL	1	TRUE	1	0.336916544564284	2		338	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	114	284	0	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	0.294288963944302	1	FACETS	0.889	0.802	0.981	0.889	0.802	0.981	CLONAL	1	TRUE	0	0.336916544564284	1		284	633	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289895	15289895	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	181	528	0	ENST00000263388.2:c.3659G>T	p.Arg1220Leu	p.R1220L	ENST00000263388	NM_000435.2	1220	cGg/cTg	22/33	1	2	FACETS	0.981	0.904	1	0.981	0.904	1	CLONAL	1	TRUE	1	0.336916544564284	2		528	1095	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519920	NA	P-0069767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	98	318	0	ENST00000397062.3:c.85G>C	p.Asp29His	p.D29H	ENST00000397062	NM_006164.4	29	Gat/Cat	2/5	1	2	FACETS	0.935	0.836	1	0.935	0.836	1	CLONAL	1	TRUE	1	0.336916544564284	2		318	622	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916929	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519931	NA	P-0069767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	141	280	0	ENST00000263967.3:c.316G>C	p.Gly106Arg	p.G106R	ENST00000263967	NM_006218.2	106	Ggc/Cgc	2/21	0.336916544564284	3	FACETS	0.984	0.902	1	0.984	0.902	1	CLONAL	2	TRUE	1	0.336916544564284	3		280	497	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0069767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	248	422	1	ENST00000304494.5:c.151-1G>A		p.X51_splice	ENST00000304494	NM_000077.4	51			0.289530036554768	2	FACETS	0.895	0.84	0.953	0.895	0.84	0.953	CLONAL	2	TRUE	0	0.336916544564284	2		423	822	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441469	40441469	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	122	329	0	ENST00000345506.4:c.40G>T	p.Ala14Ser	p.A14S	ENST00000345506	NM_003152.3	14	Gcg/Tcg	3/20	1	2	FACETS	0.878	0.793	0.967	0.878	0.793	0.967	CLONAL	1	TRUE	1	0.336916544564284	2		329	825	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291606	15291606	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	177	440	0	ENST00000263388.2:c.3028C>T	p.Gln1010Ter	p.Q1010*	ENST00000263388	NM_000435.2	1010	Caa/Taa	19/33	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.336916544564284	2		440	1004	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557861	187557862	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0069767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	141	388	0	ENST00000441802.2:c.3849dup	p.Asn1284GlnfsTer13	p.N1284Qfs*13	ENST00000441802	NM_005245.3	1283	-/C	5/27	0.336916544564284	1	FACETS	0.963	0.878	1	0.963	0.878	1	CLONAL	1	TRUE	0	0.336916544564284	1		388	723	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874090	151874090	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	95	359	0	ENST00000262189.6:c.8448del	p.Thr2817LeufsTer6	p.T2817Lfs*6	ENST00000262189	NM_170606.2	2816	tcC/tc	38/59	0.246244782471448	1	FACETS	0.834	0.745	0.929	0.834	0.745	0.929	CLONAL	1	TRUE	0	0.336916544564284	1		359	562	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0069768-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	37	372	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.672	0.552	0.807	0.672	0.552	0.807	SUBCLONAL	1	TRUE	1	0.14	2		372	787	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913255	NA	P-0069768-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	39	309	0	ENST00000369535.4:c.183A>T	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caT	3/7	1	2	FACETS	0.697	0.576	0.834	0.697	0.576	0.834	SUBCLONAL	1	TRUE	1	0.14	2		309	799	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915952	127915952	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs865855853	NA	P-0069768-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	43	304	0	ENST00000373547.4:c.529C>T	p.Arg177Ter	p.R177*	ENST00000373547	NM_002721.4	177	Cga/Tga	6/7	1	2	FACETS	0.83	0.693	0.983	0.83	0.693	0.983	CLONAL	1	TRUE	1	0.14	2		304	740	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161717	47161717	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069768-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	41	314	0	ENST00000409792.3:c.4409C>T	p.Pro1470Leu	p.P1470L	ENST00000409792	NM_014159.6	1470	cCa/cTa	3/21	1	2	FACETS	0.79	0.657	0.94	0.79	0.657	0.94	CLONAL	1	TRUE	1	0.14	2		314	741	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0069768-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	35	349	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.838	0.685	1	0.838	0.685	1	CLONAL	1	TRUE	1	0.14	2		349	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0069769-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	253	307	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.278543447723859	4	FACETS	0.878	0.827	0.93	0.878	0.827	0.93	CLONAL	4	TRUE	0	0.278543447723859	4		307	661	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197875	123197875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776905490	NA	P-0069769-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	40	190	0	ENST00000218089.9:c.1999C>T	p.Arg667Trp	p.R667W	ENST00000218089	NM_001042749.1	667	Cgg/Tgg	20/35	0.206781006046903	4	FACETS	1	0.9	1	0.729	0.614	0.852	CLONAL	2	TRUE	1	0.278543447723859	4		190	168	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913398	28913398	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069769-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	32	216	0	ENST00000282397.4:c.2395A>G	p.Met799Val	p.M799V	ENST00000282397	NM_002019.4	799	Atg/Gtg	17/30	0.262943482673486	4	FACETS	0.677	0.549	0.821	0.226	0.183	0.274	SUBCLONAL	1	TRUE	1	0.278543447723859	4		216	434	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857678	59857678	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069769-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	40	194	0	ENST00000259008.2:c.1879C>T	p.Leu627Phe	p.L627F	ENST00000259008	NM_032043.2	627	Ctt/Ttt	13/20	0.235394051861032	4	FACETS	1	0.842	1	0.506	0.421	0.6	CLONAL	1	TRUE	2	0.278543447723859	4		194	363	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915291	32915291	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069769-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	38	271	0	ENST00000380152.3:c.6799T>A	p.Ser2267Thr	p.S2267T	ENST00000380152		2267	Tca/Aca	11/27	0.262943482673486	4	FACETS	1	0.907	1	0.383	0.317	0.455	CLONAL	1	TRUE	1	0.278543447723859	4		271	304	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961235	41961235	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069769-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	52	256	0	ENST00000219905.7:c.143G>A	p.Cys48Tyr	p.C48Y	ENST00000219905	NM_001164273.1	48	tGt/tAt	2/24	0.278543447723859	3	FACETS	0.726	0.618	0.845	0.242	0.206	0.282	SUBCLONAL	1	TRUE	0	0.278543447723859	3		256	586	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045844	26045844	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069769-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	299	419	0	ENST00000540144.1:c.206A>T	p.Gln69Leu	p.Q69L	ENST00000540144	NM_003531.2	69	cAg/cTg	1/1	0.278543447723859	6	FACETS	1	0.989	1	0.483	0.454	0.513	CLONAL	2	TRUE	1	0.278543447723859	6		419	1385	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44733198	44733198	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	27	118	0	ENST00000377967.4:c.190G>T	p.Glu64Ter	p.E64*	ENST00000377967	NM_021140.2	64	Gaa/Taa	2/29	1	1	FACETS	0.212	0.168	0.261	0.212	0.168	0.261	SUBCLONAL	1	TRUE	0	0.525367335559625	1		118	358	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907465	32907465	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs397507278	NA	P-0069770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	134	240	0	ENST00000380152.3:c.1850C>A	p.Ser617Ter	p.S617*	ENST00000380152		617	tCa/tAa	10/27	0.525367335559625	1	FACETS	0.811	0.742	0.882	0.811	0.742	0.882	CLONAL	1	TRUE	0	0.525367335559625	1		240	464	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101201	41101201	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069772-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	91	195	0	ENST00000373198.4:c.1155T>A	p.Asp385Glu	p.D385E	ENST00000373198	NM_133170.3	385	gaT/gaA	8/32	0.229226888195142	3	FACETS	0.739	0.658	0.826	0.246	0.219	0.276	INDETERMINATE	1	TRUE	0	0.572453225693853	3		195	553	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135310	2135310	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0069772-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	208	254	0	ENST00000219476.3:c.4649T>G	p.Val1550Gly	p.V1550G	ENST00000219476	NM_000548.3	1550	gTt/gGt	36/42	0.570457336366816	2	FACETS	0.867	0.816	0.918	0.867	0.816	0.918	CLONAL	2	TRUE	0	0.572453225693853	2		254	419	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14028657	14028657	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069772-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	142	183	0	ENST00000405192.2:c.21G>T	p.Gln7His	p.Q7H	ENST00000405192	NM_001163147.1	7	caG/caT	2/12	0.46579387009856	4	FACETS	0.788	0.723	0.855	0.788	0.723	0.855	SUBCLONAL	2	TRUE	2	0.572453225693853	4		183	495	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874383	76874407	+	frameshift_variant	Frame_Shift_Del	DEL	AATCTATTCCTGAACTCCTTAATGG	AATCTATTCCTGAACTCCTTAATGG	TAA	novel	NA	P-0069772-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	88	76	0	ENST00000373344.5:c.5315_5339delinsTTA	p.Ser1772PhefsTer3	p.S1772Ffs*3	ENST00000373344	NM_000489.3	1772	tCCATTAAGGAGTTCAGGAATAGATTt/tTTAt	21/35	0.550961201398124	2	FACETS	1	0.969	1			1	CLONAL	2	TRUE	NA	0.572453225693853	2		76	139	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061191	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs879499034	NA	P-0069773-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	77	443	0	ENST00000250448.2:c.798C>A	p.Phe266Leu	p.F266L	ENST00000250448	NM_004496.3	266	ttC/ttA	2/2	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.241680582092823	2		443	633	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15975503	15975504	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0069773-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	31	257	0	ENST00000268712.3:c.3850dup	p.Ser1284PhefsTer2	p.S1284Ffs*2	ENST00000268712	NM_006311.3	1284	tct/tTct	29/46	1	2	FACETS	0.659	0.533	0.802	0.659	0.533	0.802	SUBCLONAL	1	TRUE	1	0.241680582092823	2		257	389	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820605	44820605	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069773-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	31	144	0	ENST00000377967.4:c.302A>C	p.His101Pro	p.H101P	ENST00000377967	NM_021140.2	101	cAc/cCc	3/29	1	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.241680582092823	1		144	185	SUCCESS
EED	8726	MSKCC	GRCh37	11	85956297	85956297	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs751356706	NA	P-0069773-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	45	281	0	ENST00000263360.6:c.26C>A	p.Ala9Glu	p.A9E	ENST00000263360	NM_003797.3	9	gCg/gAg	1/12	1	2	FACETS	0.687	0.577	0.809	0.687	0.577	0.809	SUBCLONAL	1	TRUE	1	0.241680582092823	2		281	542	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0069775-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	232	269	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		269	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578530	7578530	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069775-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	272	1292	0	ENST00000269305.4:c.400T>G	p.Phe134Val	p.F134V	ENST00000269305	NM_001126112.2	134	Ttt/Gtt	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1292	505	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541243	187541244	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTTTT	novel	NA	P-0069775-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	74	888	0	ENST00000441802.2:c.6496_6497insAAAAG	p.Ala2166GlufsTer12	p.A2166Efs*12	ENST00000441802	NM_005245.3	2166	gcg/gAAAAGcg	10/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		888	356	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242486	+	inframe_deletion	In_Frame_Del	DEL	TTAAGAGAAGCAACATCT	TTAAGAGAAGCAACATCT	-	rs121913440	NA	P-0069776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	74	173	0	ENST00000275493.2:c.2239_2256del	p.Leu747_Ser752del	p.L747_S752del	ENST00000275493	NM_005228.3	747	TTAAGAGAAGCAACATCT/-	19/28	1	2	FACETS	0.896	0.788	1	0.896	0.788	1	CLONAL	1	TRUE	1	0.404878851326988	2		173	408	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357660	70357660	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	97	171	0	ENST00000374080.3:c.5911C>T	p.Gln1971Ter	p.Q1971*	ENST00000374080		1971	Cag/Tag	41/45	1	1	FACETS	0.79	0.717	0.864	1	0.985	1	SUBCLONAL	2	TRUE	0	0.404878851326988	1		171	242	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828893	72828905	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTGGATGAACT	GGGTGGATGAACT	-	novel	NA	P-0069777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	182	342	0	ENST00000268489.5:c.7676_7688del	p.Gln2559ProfsTer49	p.Q2559Pfs*49	ENST00000268489	NM_006885.3	2559	cAGTTCATCCACCCc/cc	9/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		342	710	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221313	1221314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs121913321	NA	P-0069784-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	259	460	0	ENST00000326873.7:c.842dup	p.Leu282AlafsTer3	p.L282Afs*3	ENST00000326873	NM_000455.4	279	ggc/ggCc	6/10	0.21104034012782	2	FACETS	0.863	0.809	0.918	1	0.99	1	CLONAL	3	TRUE	0	0.21104034012782	2		460	948	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0069784-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	155	326	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.147392602846601	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.21104034012782	2		326	689	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713428	40713428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200056702	NA	P-0069784-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	177	449	2	ENST00000373198.4:c.4087C>T	p.Arg1363Trp	p.R1363W	ENST00000373198	NM_133170.3	1363	Cgg/Tgg	30/32	0.133232299371252	4	FACETS	0.96	0.884	1	0.96	0.884	1	CLONAL	2	TRUE	2	0.21104034012782	4		451	1058	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032069	26032069	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069784-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	101	551	0	ENST00000244661.2:c.220G>T	p.Glu74Ter	p.E74*	ENST00000244661	NM_003537.3	74	Gaa/Taa	1/1	0.0784452644244258	4	FACETS	1	0.933	1	0.532	0.474	0.594	INDETERMINATE	1	TRUE	2	0.21104034012782	4		551	1090	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61322901	61322901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069784-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	49	191	0	ENST00000283752.5:c.1163C>T	p.Ser388Leu	p.S388L	ENST00000283752	NM_006919.2	388	tCa/tTa	8/8	0.21104034012782	3	FACETS	1	0.922	1	0.572	0.485	0.667	CLONAL	1	TRUE	1	0.21104034012782	3		191	449	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690630	88690630	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069784-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	53	279	0	ENST00000360948.2:c.400C>G	p.Leu134Val	p.L134V	ENST00000360948	NM_001012338.2	134	Ctg/Gtg	5/19	0.133232299371252	4	FACETS	0.969	0.825	1	0.484	0.412	0.563	CLONAL	1	TRUE	2	0.21104034012782	4		279	628	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443729	52443729	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0069784-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	202	489	0	ENST00000460680.1:c.67+1del		p.X23_splice	ENST00000460680	NM_004656.3	23			0.21104034012782	2	FACETS	0.994	0.922	1	0.994	0.922	1	CLONAL	2	TRUE	0	0.21104034012782	2		489	963	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038349	180038349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373742042	NA	P-0001876-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	14	0	0	ENST00000261937.6:c.3668G>A	p.Arg1223His	p.R1223H	ENST00000261937	NM_182925.4	1223	cGc/cAc	27/30	1	2	FACETS	0.58	0.418	0.777	0.58	0.418	0.777	SUBCLONAL	1	TRUE	1	0.14	2		0	345	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134611	2134611	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001876-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	5	0	0	ENST00000219476.3:c.4388T>A	p.Ile1463Asn	p.I1463N	ENST00000219476	NM_000548.3	1463	aTc/aAc	34/42	1	2	FACETS	0.178	0.1	0.288	0.178	0.1	0.288	SUBCLONAL	1	TRUE	1	0.14	2		0	401	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231127	46231131	+	frameshift_variant	Frame_Shift_Del	DEL	CAAAA	CAAAA	-	novel	NA	P-0002768-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	155	212	0	ENST00000334344.6:c.1048_1052del	p.Lys350TyrfsTer17	p.K350Yfs*17	ENST00000334344	NM_152641.2	349	ttCAAAAct/ttct	9/21	0.424086706136313	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.428026852473177	4		212	455	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953735	48953735	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0002768-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	93	119	0	ENST00000267163.4:c.1338C>G	p.Tyr446Ter	p.Y446*	ENST00000267163	NM_000321.2	446	taC/taG	14/27	0.428026852473177	2	FACETS	0.857	0.786	0.927	1	0.981	1	CLONAL	3	TRUE	0	0.428026852473177	2		119	169	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0002768-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	179	226	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.428026852473177	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.428026852473177	2		226	358	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374244	138374244	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002768-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	87	52	0	ENST00000289153.2:c.3200A>T	p.Asp1067Val	p.D1067V	ENST00000289153	NM_006219.2	1067	gAc/gTc	22/22	0.428026852473177	4	FACETS	1	0.974	1	0.449	0.399	0.501	CLONAL	1	TRUE	1	0.428026852473177	4		52	431	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0002768-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	109	274	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.424086706136313	4	FACETS	0.916	0.829	1	0.916	0.829	1	CLONAL	2	TRUE	2	0.428026852473177	4		274	397	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0002768-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	147	336	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.424086706136313	4	FACETS	0.975	0.896	1	0.975	0.896	1	CLONAL	2	TRUE	2	0.428026852473177	4		336	503	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180407	94180407	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002768-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	65	224	0	ENST00000323929.3:c.1761A>T	p.Arg587Ser	p.R587S	ENST00000323929	NM_005591.3	587	agA/agT	15/20	0.413479915416318	3	FACETS	1	0.914	1	0.531	0.463	0.604	CLONAL	1	TRUE	1	0.428026852473177	3		224	347	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63973820	63973820	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002768-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	81	253	0	ENST00000398590.3:c.1181G>T	p.Arg394Met	p.R394M	ENST00000398590	NM_001177387.1	394	aGg/aTg	9/14	0.428026852473177	2	FACETS	1	0.918	1	0.521	0.462	0.584	CLONAL	1	TRUE	0	0.428026852473177	2		253	363	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226806	142226813	+	frameshift_variant	Frame_Shift_Del	DEL	CTTCTTTT	CTTCTTTT	-	novel	NA	P-0002768-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	63	172	0	ENST00000350721.4:c.4991_4998del	p.Glu1664AlafsTer19	p.E1664Afs*19	ENST00000350721	NM_001184.3	1664	gAAAAGAAG/g	28/47	0.428026852473177	4	FACETS	0.98	0.85	1	0.327	0.283	0.374	CLONAL	1	TRUE	1	0.428026852473177	4		172	429	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978328	2978329	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0002768-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	69	221	0	ENST00000396946.4:c.1001_1002del	p.Glu334GlyfsTer25	p.E334Gfs*25	ENST00000396946	NM_032415.4	334	gAG/g	7/25	0.428026852473177	6	FACETS	0.894	0.779	1	0.224	0.194	0.255	CLONAL	1	TRUE	2	0.428026852473177	6		221	669	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335678	81335678	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002768-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	64	192	0	ENST00000222390.5:c.1682G>C	p.Cys561Ser	p.C561S	ENST00000222390	NM_000601.4	561	tGc/tCc	15/18	0.428026852473177	3	FACETS	1	0.903	1	0.522	0.454	0.594	CLONAL	1	TRUE	1	0.428026852473177	3		192	348	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981370	68981370	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002768-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	51	152	0	ENST00000288368.4:c.1442A>C	p.Lys481Thr	p.K481T	ENST00000288368	NM_024870.2	481	aAg/aCg	12/40	0.424086706136313	4	FACETS	1	0.896	1	0.53	0.453	0.614	CLONAL	1	TRUE	2	0.428026852473177	4		152	321	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465559	8465559	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002768-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	146	254	0	ENST00000356435.5:c.3621T>G	p.Asp1207Glu	p.D1207E	ENST00000356435		1207	gaT/gaG	21/35	0.413479915416318	3	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	1	0.428026852473177	3		254	401	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870877	12870877	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375297371	NA	P-0002838-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	50	362	0	ENST00000228872.4:c.104C>T	p.Pro35Leu	p.P35L	ENST00000228872	NM_004064.3	35	cCg/cTg	1/3	1	2	FACETS	0.581	0.491	0.679	0.581	0.491	0.679	SUBCLONAL	1	TRUE	1	0.234284135639772	2		362	735	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577157	7577157	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0002838-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	63	299	0	ENST00000269305.4:c.783-2A>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.234284135639772	2		299	517	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894916	101894916	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060502040	NA	P-0002838-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	54	346	0	ENST00000374994.4:c.469C>T	p.Arg157Ter	p.R157*	ENST00000374994	NM_004612.2	157	Cga/Tga	3/9	0.234284135639772	1	FACETS	0.703	0.6	0.816	0.703	0.6	0.816	SUBCLONAL	1	TRUE	0	0.234284135639772	1		346	579	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434061	49434061	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002838-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	99	319	0	ENST00000301067.7:c.7492C>G	p.Leu2498Val	p.L2498V	ENST00000301067	NM_003482.3	2498	Ctg/Gtg	31/54	0.175707018454602	3	FACETS	1	0.98	1	0.719	0.642	0.8	CLONAL	1	TRUE	1	0.234284135639772	3		319	657	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219271	133219271	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002838-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	68	357	0	ENST00000320574.5:c.4773G>A	p.Trp1591Ter	p.W1591*	ENST00000320574	NM_006231.2	1591	tgG/tgA	37/49	1	2	FACETS	0.908	0.79	1	0.908	0.79	1	CLONAL	1	TRUE	1	0.234284135639772	2		357	639	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489840	40489840	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002838-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	88	419	0	ENST00000264657.5:c.586A>G	p.Thr196Ala	p.T196A	ENST00000264657	NM_139276.2	196	Acc/Gcc	7/24	1	2	FACETS	0.877	0.776	0.985	0.877	0.776	0.985	CLONAL	1	TRUE	1	0.234284135639772	2		419	857	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260048	19260048	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1211742770	NA	P-0002838-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	77	344	0	ENST00000162023.5:c.245C>G	p.Thr82Ser	p.T82S	ENST00000162023		82	aCt/aGt	7/13	1	2	FACETS	0.987	0.867	1	0.987	0.867	1	CLONAL	1	TRUE	1	0.234284135639772	2		344	666	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971008	55971008	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002838-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	70	345	0	ENST00000263923.4:c.1789G>T	p.Glu597Ter	p.E597*	ENST00000263923	NM_002253.2	597	Gag/Tag	13/30	0.214619226669627	1	FACETS	0.905	0.79	1	0.905	0.79	1	CLONAL	1	TRUE	0	0.234284135639772	1		345	583	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133311	38133311	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002838-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	2038	319	0	ENST00000317025.8:c.4162G>C	p.Asp1388His	p.D1388H	ENST00000317025	NM_023034.1	1388	Gat/Cat	24/24	0.234284135639772	5	FACETS	1	0.985	1			1	CLONAL	8	TRUE	NA	0.234284135639772	5		319	2940	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407880	139407880	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002838-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	79	390	0	ENST00000277541.6:c.2317del	p.Ser773ValfsTer29	p.S773Vfs*29	ENST00000277541	NM_017617.3	773	Agt/gt	14/34	1	2	FACETS	0.983	0.865	1	0.983	0.865	1	CLONAL	1	TRUE	1	0.234284135639772	2		390	686	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349263	70349263	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002838-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	81	147	0	ENST00000374080.3:c.3675G>C	p.Lys1225Asn	p.K1225N	ENST00000374080		1225	aaG/aaC	26/45	0.0697382516343188	2	FACETS	0.864	0.766	0.969			1	INDETERMINATE	2	TRUE	NA	0.234284135639772	2		147	400	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003785-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	28	317	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.889	0.713	1	0.889	0.713	1	CLONAL	1	TRUE	1	0.238718793273915	2		317	264	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466578	120466578	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs893877808	NA	P-0003785-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	29	608	2	ENST00000256646.2:c.4541A>G	p.Lys1514Arg	p.K1514R	ENST00000256646	NM_024408.3	1514	aAa/aGa	26/34	0.238718793273915	1	FACETS	0.856	0.69	1	0.856	0.69	1	CLONAL	1	TRUE	0	0.238718793273915	1		610	250	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244517	46244517	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003785-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	47	597	0	ENST00000334344.6:c.2611C>T	p.Gln871Ter	p.Q871*	ENST00000334344	NM_152641.2	871	Cag/Tag	15/21	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.238718793273915	2		597	330	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872475	35872475	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003785-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	46	776	0	ENST00000216797.5:c.428G>C	p.Arg143Pro	p.R143P	ENST00000216797	NM_020529.2	143	cGa/cCa	3/6	0.238718793273915	3	FACETS	1	0.931	1	0.596	0.503	0.697	CLONAL	1	TRUE	1	0.238718793273915	3		776	362	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789600	3789600	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003785-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	95	585	0	ENST00000262367.5:c.4259A>C	p.Asp1420Ala	p.D1420A	ENST00000262367	NM_004380.2	1420	gAt/gCt	25/31	0.157013954610894	3	FACETS	0.9	0.81	0.994	0.9	0.81	0.994	CLONAL	3	TRUE	0	0.238718793273915	3		585	330	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16097838	16097838	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003785-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	31	316	0	ENST00000268712.3:c.46G>T	p.Glu16Ter	p.E16*	ENST00000268712	NM_006311.3	16	Gaa/Taa	2/46	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.238718793273915	2		316	197	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541485	29541485	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs746149047	NA	P-0003785-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	37	96	0	ENST00000356175.3:c.1413del	p.Val472Ter	p.V472*	ENST00000356175	NM_000267.3	470	gAa/ga	13/57	1	2	FACETS	0.994	0.832	1	1	0.967	1	CLONAL	2	TRUE	1	0.238718793273915	2		96	156	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715660	30715668	+	inframe_deletion	In_Frame_Del	DEL	GAGTCCTTC	GAGTCCTTC	-	novel	NA	P-0003785-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	85	534	0	ENST00000295754.5:c.1318_1326del	p.Glu440_Phe442del	p.E440_F442del	ENST00000295754	NM_003242.5	440	GAGTCCTTC/-	5/7	0.22531859742917	3	FACETS	0.886	0.792	0.984	0.886	0.792	0.984	CLONAL	3	TRUE	0	0.238718793273915	3		534	300	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924919	49924919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003785-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	30	788	0	ENST00000296474.3:c.4024G>A	p.Glu1342Lys	p.E1342K	ENST00000296474	NM_002447.2	1342	Gag/Aag	20/20	1	2	FACETS	0.978	0.792	1	0.978	0.792	1	CLONAL	1	TRUE	1	0.238718793273915	2		788	257	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582380	119582380	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs753950587	NA	P-0003785-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	62	587	0	ENST00000316626.5:c.1021C>T	p.Arg341Ter	p.R341*	ENST00000316626		341	Cga/Tga	10/12	1	2	FACETS	0.814	0.708	0.928	1	0.975	1	CLONAL	2	TRUE	1	0.238718793273915	2		587	319	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587119	189587119	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003785-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	8	369	0	ENST00000264731.3:c.1136G>T	p.Arg379Leu	p.R379L	ENST00000264731	NM_003722.4	379	cGt/cTt	9/14	0.238718793273915	1	FACETS	0.226	0.145	0.332	0.226	0.145	0.332	SUBCLONAL	1	TRUE	0	0.238718793273915	1		369	261	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217294	66217294	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003785-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	44	437	0	ENST00000273854.3:c.2321T>A	p.Val774Glu	p.V774E	ENST00000273854	NM_004439.5	774	gTg/gAg	14/18	0.146482127642396	0	FACETS	1	0.925	1			1	CLONAL	1	TRUE	0	0.238718793273915	0		437	241	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591099	67591099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs773686816	NA	P-0003785-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	10	341	0	ENST00000274335.5:c.1692C>A	p.Asn564Lys	p.N564K	ENST00000274335		564	aaC/aaA	12/15	1	2	FACETS	0.259	0.175	0.366	0.259	0.175	0.366	SUBCLONAL	1	TRUE	1	0.238718793273915	2		341	323	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0003785-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	35	285	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.238718793273915	2		285	228	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224206	98224206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750373573	NA	P-0003785-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	38	585	0	ENST00000331920.6:c.2635G>A	p.Asp879Asn	p.D879N	ENST00000331920	NM_000264.3	879	Gat/Aat	16/24	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.238718793273915	2		585	269	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932412	39932412	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003785-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	83	741	0	ENST00000378444.4:c.2187G>T	p.Leu729Phe	p.L729F	ENST00000378444	NM_001123385.1	729	ttG/ttT	4/15	0.238718793273915	5	FACETS	1	0.946	1	0.823	0.735	0.915	CLONAL	3	TRUE	1	0.238718793273915	5		741	287	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424454	47424454	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003785-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	83	815	0	ENST00000377045.4:c.374G>C	p.Cys125Ser	p.C125S	ENST00000377045	NM_001654.4	125	tGc/tCc	5/16	NA	2	FACETS	1	0.91	1			1	INDETERMINATE	2	TRUE	NA	0.238718793273915	2		815	339	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087504	27087504	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003785-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	8	819	0	ENST00000324856.7:c.2078G>T	p.Arg693Leu	p.R693L	ENST00000324856	NM_006015.4	693	cGa/cTa	5/20	1	2	FACETS	0.203	0.13	0.299	0.203	0.13	0.299	SUBCLONAL	1	TRUE	1	0.238718793273915	2		819	330	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115751	8115751	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003785-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	8	528	0	ENST00000346208.3:c.1097G>T	p.Arg366Leu	p.R366L	ENST00000346208		366	cGa/cTa	6/6	1	2	FACETS	0.194	0.124	0.285	0.194	0.124	0.285	SUBCLONAL	1	TRUE	1	0.238718793273915	2		528	346	SUCCESS
EED	8726	MSKCC	GRCh37	11	85956274	85956274	+	start_lost	Translation_Start_Site	SNP	G	G	T	novel	NA	P-0003785-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	11	548	0	ENST00000263360.6:c.3G>T	p.Met1?	p.M1?	ENST00000263360	NM_003797.3	1	atG/atT	1/12	0.238718793273915	3	FACETS	0.469	0.324	0.65	0.234	0.162	0.325	SUBCLONAL	1	TRUE	1	0.238718793273915	3		548	220	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577087	7577087	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003785-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	8	650	0	ENST00000269305.4:c.851C>A	p.Thr284Lys	p.T284K	ENST00000269305	NM_001126112.2	284	aCa/aAa	8/11	1	2	FACETS	0.231	0.148	0.339	0.231	0.148	0.339	SUBCLONAL	1	TRUE	1	0.238718793273915	2		650	290	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272378	15272378	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003785-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	10	866	0	ENST00000263388.2:c.6061G>T	p.Val2021Leu	p.V2021L	ENST00000263388	NM_000435.2	2021	Gtg/Ttg	33/33	1	2	FACETS	0.436	0.295	0.613	0.436	0.295	0.613	SUBCLONAL	1	TRUE	1	0.238718793273915	2		866	192	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311664	15311664	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003785-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	11	1312	1	ENST00000263388.2:c.53C>T	p.Pro18Leu	p.P18L	ENST00000263388	NM_000435.2	18	cCa/cTa	1/33	1	2	FACETS	0.512	0.354	0.708	0.512	0.354	0.708	SUBCLONAL	1	TRUE	1	0.238718793273915	2		1313	180	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867259	45867259	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1799793	NA	P-0003785-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	9	875	0	ENST00000391945.4:c.934G>T	p.Asp312Tyr	p.D312Y	ENST00000391945	NM_000400.3	312	Gac/Tac	10/23	1	2	FACETS	0.359	0.237	0.515	0.359	0.237	0.515	SUBCLONAL	1	TRUE	1	0.238718793273915	2		875	210	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033352	48033352	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs63750949	NA	P-0003785-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	8	333	0	ENST00000234420.5:c.3656C>A	p.Thr1219Asn	p.T1219N	ENST00000234420	NM_000179.2	1219	aCt/aAt	8/10	1	2	FACETS	0.213	0.136	0.313	0.213	0.136	0.313	SUBCLONAL	1	TRUE	1	0.238718793273915	2		333	315	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525060	157525060	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003785-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	13	515	0	ENST00000346085.5:c.4955C>A	p.Thr1652Lys	p.T1652K	ENST00000346085	NM_020732.3	1652	aCg/aAg	19/20	1	2	FACETS	0.345	0.245	0.467	0.345	0.245	0.467	SUBCLONAL	1	TRUE	1	0.238718793273915	2		515	316	SUCCESS
AR	367	MSKCC	GRCh37	X	66765216	66765216	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003785-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	12	669	0	ENST00000374690.3:c.228G>T	p.Gln76His	p.Q76H	ENST00000374690	NM_000044.3	76	caG/caT	1/8	0.238718793273915	1	FACETS	0.41	0.288	0.56	0.41	0.288	0.56	SUBCLONAL	1	TRUE	0	0.238718793273915	1		669	216	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466578	120466578	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs893877808	NA	P-0003785-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	89	608	2	ENST00000256646.2:c.4541A>G	p.Lys1514Arg	p.K1514R	ENST00000256646	NM_024408.3	1514	aAa/aGa	26/34	1	2	FACETS	0.484	0.428	0.545	0.484	0.428	0.545	SUBCLONAL	1	TRUE	1	0.36	2		610	1021	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789600	3789600	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003785-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	226	585	0	ENST00000262367.5:c.4259A>C	p.Asp1420Ala	p.D1420A	ENST00000262367	NM_004380.2	1420	gAt/gCt	25/31	0.213939184334268	3	FACETS	1	0.978	1	0.563	0.523	0.605	INDETERMINATE	1	TRUE	1	0.36	3		585	1315	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541485	29541485	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs746149047	NA	P-0003785-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	10	96	0	ENST00000356175.3:c.1413del	p.Val472Ter	p.V472*	ENST00000356175	NM_000267.3	470	gAa/ga	13/57	1	2	FACETS	0.631	0.432	0.875	0.631	0.432	0.875	SUBCLONAL	1	TRUE	1	0.36	2		96	88	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715660	30715668	+	inframe_deletion	In_Frame_Del	DEL	GAGTCCTTC	GAGTCCTTC	-	novel	NA	P-0003785-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	75	534	0	ENST00000295754.5:c.1318_1326del	p.Glu440_Phe442del	p.E440_F442del	ENST00000295754	NM_003242.5	440	GAGTCCTTC/-	5/7	1	2	FACETS	0.501	0.438	0.569	0.501	0.438	0.569	SUBCLONAL	1	TRUE	1	0.36	2		534	831	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582380	119582380	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs753950587	NA	P-0003785-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	94	587	0	ENST00000316626.5:c.1021C>T	p.Arg341Ter	p.R341*	ENST00000316626		341	Cga/Tga	10/12	1	2	FACETS	0.466	0.413	0.523	0.466	0.413	0.523	SUBCLONAL	1	TRUE	1	0.36	2		587	1120	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217294	66217294	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003785-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	51	437	0	ENST00000273854.3:c.2321T>A	p.Val774Glu	p.V774E	ENST00000273854	NM_004439.5	774	gTg/gAg	14/18	1	2	FACETS	0.535	0.454	0.623	0.535	0.454	0.623	SUBCLONAL	1	TRUE	1	0.36	2		437	530	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0003785-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	27	285	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	0.485	0.387	0.598	0.485	0.387	0.598	SUBCLONAL	1	TRUE	1	0.36	2		285	309	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932412	39932412	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003785-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	493	741	0	ENST00000378444.4:c.2187G>T	p.Leu729Phe	p.L729F	ENST00000378444	NM_001123385.1	729	ttG/ttT	4/15	0.29083602198785	4	FACETS	0.835	0.799	0.872	0.835	0.799	0.872	CLONAL	3	TRUE	1	0.36	4		741	1487	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424454	47424454	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003785-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	458	815	0	ENST00000377045.4:c.374G>C	p.Cys125Ser	p.C125S	ENST00000377045	NM_001654.4	125	tGc/tCc	5/16	0.29083602198785	4	FACETS	1	0.993	1	0.791	0.754	0.827	CLONAL	2	TRUE	1	0.36	4		815	1459	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573335	41573335	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003785-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1657	154	1005	0	ENST00000263253.7:c.5620C>G	p.Gln1874Glu	p.Q1874E	ENST00000263253	NM_001429.3	1874	Cag/Gag	31/31	1	2	FACETS	0.472	0.43	0.517	0.472	0.43	0.517	SUBCLONAL	1	TRUE	1	0.36	2		1005	1811	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38981983	38981983	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003785-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	22	269	0	ENST00000357387.3:c.739G>C	p.Asp247His	p.D247H	ENST00000357387	NM_152756.3	247	Gat/Cat	8/38	1	2	FACETS	0.389	0.302	0.491	0.389	0.302	0.491	SUBCLONAL	1	TRUE	1	0.36	2		269	314	SUCCESS
APC	324	MSKCC	GRCh37	5	112177841	112177841	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794107	NA	P-0003785-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	34	354	0	ENST00000257430.4:c.6550G>A	p.Glu2184Lys	p.E2184K	ENST00000257430	NM_000038.5	2184	Gaa/Aaa	16/16	1	2	FACETS	0.376	0.307	0.455	0.376	0.307	0.455	SUBCLONAL	1	TRUE	1	0.36	2		354	502	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2105439	2105439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773662047	NA	P-0003785-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	98	595	1	ENST00000219476.3:c.518C>T	p.Ser173Phe	p.S173F	ENST00000219476	NM_000548.3	173	tCc/tTc	6/42	0.213939184334268	3	FACETS	0.587	0.522	0.656	0.293	0.261	0.328	INDETERMINATE	1	TRUE	1	0.36	3		596	1095	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73649905	73649905	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003785-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	79	266	0	ENST00000377687.4:c.1255G>A	p.Glu419Lys	p.E419K	ENST00000377687	NM_001730.3	419	Gag/Aag	4/4	1	2	FACETS	0.385	0.338	0.437	0.385	0.338	0.437	SUBCLONAL	1	TRUE	1	0.36	2		266	1139	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514149	69514149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003785-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1431	118	761	0	ENST00000294312.3:c.532G>A	p.Asp178Asn	p.D178N	ENST00000294312	NM_005117.2	178	Gac/Aac	3/3	0.213939184334268	3	FACETS	0.499	0.449	0.554	0.25	0.224	0.277	INDETERMINATE	1	TRUE	1	0.36	3		761	1549	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90627517	90627517	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003785-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	133	721	0	ENST00000330062.3:c.1340G>T	p.Arg447Ile	p.R447I	ENST00000330062	NM_002168.2	447	aGa/aTa	11/11	1	2	FACETS	0.579	0.524	0.637	0.579	0.524	0.637	SUBCLONAL	1	TRUE	1	0.36	2		721	1277	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639004	176639004	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1365157854	NA	P-0003785-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	186	576	0	ENST00000439151.2:c.3604G>A	p.Glu1202Lys	p.E1202K	ENST00000439151	NM_022455.4	1202	Gag/Aag	5/23	1	2	FACETS	0.957	0.883	1	0.957	0.883	1	CLONAL	1	TRUE	1	0.36	2		576	1080	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726549	46726549	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003785-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	154	742	0	ENST00000371975.4:c.628G>A	p.Glu210Lys	p.E210K	ENST00000371975	NM_003579.3	210	Gaa/Aaa	7/18	1	2	FACETS	0.674	0.615	0.736	0.674	0.615	0.736	SUBCLONAL	1	TRUE	1	0.36	2		742	1270	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955017	93955017	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003785-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	13	209	0	ENST00000369303.4:c.2881G>C	p.Glu961Gln	p.E961Q	ENST00000369303	NM_004440.3	961	Gag/Cag	16/17	1	2	FACETS	0.347	0.248	0.468	0.347	0.248	0.468	SUBCLONAL	1	TRUE	1	0.36	2		209	208	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76764089	76764089	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1557034957	NA	P-0004233-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	192	307	0	ENST00000373344.5:c.7219C>T	p.Arg2407Ter	p.R2407*	ENST00000373344	NM_000489.3	2407	Cga/Tga	35/35	1	2	FACETS	0.912	0.851	0.973	0.912	0.851	0.973	CLONAL	1	TRUE	1	0.854452913150001	2		307	493	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0004233-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	136	385	0				ENST00000310581	NM_198253.2	-/1132			0.16790367212266	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.854452913150001	0		385	312	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970971	21970971	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0004233-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	280	429	0	ENST00000304494.5:c.387C>G	p.Tyr129Ter	p.Y129*	ENST00000304494	NM_000077.4	129	taC/taG	2/3	0.718308254677175	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.854452913150001	1		429	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0004701-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	27	474	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.647	0.514	0.8	0.647	0.514	0.8	SUBCLONAL	1	TRUE	1	0.19	2		474	439	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004701-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	18	264	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.877	0.662	1	0.877	0.662	1	CLONAL	1	TRUE	1	0.19	2		264	216	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923422	36923422	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004701-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	23	528	0	ENST00000358127.4:c.840T>A	p.Asn280Lys	p.N280K	ENST00000358127	NM_001280556.1	280	aaT/aaA	7/10	1	2	FACETS	0.789	0.615	0.989	0.789	0.615	0.989	CLONAL	1	TRUE	1	0.19	2		528	307	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0004994-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	253	405	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.261503873608119	8	FACETS	1	0.975	1	0.54	0.505	0.576	CLONAL	3	FALSE	2	0.261503873608119	8		405	1066	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061636	38061636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004994-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	355	407	0	ENST00000250448.2:c.353C>T	p.Ala118Val	p.A118V	ENST00000250448	NM_004496.3	118	gCg/gTg	2/2	1	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	3	FALSE	1	0.261503873608119	2		407	808	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130136	143130136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004994-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	18	312	0	ENST00000262992.4:c.880G>A	p.Asp294Asn	p.D294N	ENST00000262992	NM_001101669.1	294	Gac/Aac	11/24	0.167121844920974	0	FACETS	0.299	0.225	0.387			1	SUBCLONAL	1	FALSE	0	0.261503873608119	0		312	340	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123691	11123691	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004994-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	191	342	0	ENST00000358026.2:c.2341A>G	p.Met781Val	p.M781V	ENST00000358026	NM_001128849.1	781	Atg/Gtg	16/36	1	2	FACETS	1	0.986	1	1	0.994	1	CLONAL	2	FALSE	1	0.261503873608119	2		342	585	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0005713-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	224	240	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.601808165521304	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	FALSE	0	0.600331502869671	2		240	368	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871182	12871182	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1328655695	NA	P-0005713-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	229	314	1	ENST00000228872.4:c.410del	p.Pro137ArgfsTer8	p.P137Rfs*8	ENST00000228872	NM_004064.3	137	Ccg/cg	1/3	0.142208592362272	4	FACETS	0.881	0.825	0.938	0.881	0.825	0.938	INDETERMINATE	2	FALSE	2	0.600331502869671	4		315	693	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155241	185155241	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005713-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	268	299	0	ENST00000265026.3:c.482G>C	p.Trp161Ser	p.W161S	ENST00000265026	NM_004721.4	161	tGg/tCg	3/14	0.601808165521304	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	FALSE	1	0.600331502869671	3		299	544	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506669	103506669	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs188898060	NA	P-0005713-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	70	294	0	ENST00000355739.4:c.412C>T	p.Arg138Ter	p.R138*	ENST00000355739	NM_000123.3	138	Cga/Tga	4/15	1	2	FACETS	0.821	0.723	0.925	0.821	0.723	0.925	CLONAL	1	FALSE	1	0.600331502869671	2		294	284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0007292-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	16	652	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	0.492	0.362	0.649	0.492	0.362	0.649	SUBCLONAL	1	TRUE	1	0.12	2		652	542	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233037	55233037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1477025000	NA	P-0007292-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	24	574	0	ENST00000275493.2:c.1787C>T	p.Pro596Leu	p.P596L	ENST00000275493	NM_005228.3	596	cCg/cTg	15/28	1	2	FACETS	0.765	0.598	0.958	0.765	0.598	0.958	CLONAL	1	TRUE	1	0.12	2		574	523	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44920576	44920576	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007292-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	22	181	0	ENST00000377967.4:c.1337del	p.Ser446LeufsTer24	p.S446Lfs*24	ENST00000377967	NM_021140.2	446	tCt/tt	14/29	1	1	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	0	0.12	1		181	272	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652366	48652366	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007292-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	32	374	0	ENST00000376670.3:c.1037G>T	p.Cys346Phe	p.C346F	ENST00000376670	NM_002049.3	346	tGt/tTt	6/6	1	1	FACETS	0.847	0.69	1	1	0.953	1	CLONAL	2	TRUE	0	0.12	1		374	296	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007565-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	8	264	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.114	0.073	0.167	0.114	0.073	0.167	SUBCLONAL	1	TRUE	1	0.42	2		264	335	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0007565-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	38	960	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.275	0.226	0.329	0.275	0.226	0.329	SUBCLONAL	1	TRUE	1	0.42	2		963	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0007565-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	31	464	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.168629999017104	4	FACETS	0.319	0.257	0.389	0.159	0.128	0.195	INDETERMINATE	1	TRUE	2	0.42	4		464	658	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588798	52588798	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1559827261	NA	P-0007565-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	26	403	0	ENST00000394830.3:c.4230del	p.Pro1411LeufsTer21	p.P1411Lfs*21	ENST00000394830	NM_018313.4	1410	ggG/gg	27/30	1	2	FACETS	0.245	0.193	0.305	0.245	0.193	0.305	SUBCLONAL	1	TRUE	1	0.42	2		403	505	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007565-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	46	551	0	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	0.155910745222537	3	FACETS	0.342	0.287	0.403	0.171	0.143	0.202	INDETERMINATE	1	TRUE	1	0.42	3		551	775	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221211	1221211	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0007565-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	41	418	0	ENST00000326873.7:c.735-1G>T		p.X245_splice	ENST00000326873	NM_000455.4	245			0.155910745222537	3	FACETS	0.36	0.299	0.428	0.18	0.149	0.214	INDETERMINATE	1	TRUE	1	0.42	3		418	656	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793517	42793517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560617801	NA	P-0007565-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	50	439	0	ENST00000575354.2:c.1319G>A	p.Arg440His	p.R440H	ENST00000575354	NM_015125.3	440	cGc/cAc	8/20	0.155910745222537	3	FACETS	0.479	0.405	0.559	0.239	0.202	0.28	INDETERMINATE	1	TRUE	1	0.42	3		439	602	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739852	41739852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs984438766	NA	P-0007565-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	24	463	0	ENST00000242208.4:c.121G>A	p.Ala41Thr	p.A41T	ENST00000242208	NM_002192.2	41	Gcc/Acc	2/3	1	2	FACETS	0.241	0.188	0.302	0.241	0.188	0.302	SUBCLONAL	1	TRUE	1	0.42	2		463	474	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430392	47430392	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007565-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	42	482	0	ENST00000377045.4:c.1667A>G	p.Glu556Gly	p.E556G	ENST00000377045	NM_001654.4	556	gAg/gGg	15/16	1	2	FACETS	0.295	0.245	0.35	0.295	0.245	0.35	SUBCLONAL	1	TRUE	1	0.42	2		482	679	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446745	29446745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200918833	NA	P-0007565-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	24	385	0	ENST00000544604.2:c.2576G>A	p.Arg859Gln	p.R859Q	ENST00000544604	NM_001206998.1	859	cGa/cAa	8/9	1	2	FACETS	0.255	0.199	0.32	0.255	0.199	0.32	SUBCLONAL	1	TRUE	1	0.42	2		385	448	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0007816-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	95	329	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.363354858807018	4	FACETS	0.961	0.863	1	0.961	0.863	1	CLONAL	2	TRUE	2	0.363354858807018	4		329	371	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755527	57755527	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007816-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	150	364	1	ENST00000274289.3:c.260T>A	p.Val87Glu	p.V87E	ENST00000274289	NM_006622.3	87	gTg/gAg	1/14	0.363354858807018	3	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	1	0.363354858807018	3		365	480	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198852	67198852	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007816-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	147	313	0	ENST00000312629.5:c.323G>C	p.Arg108Pro	p.R108P	ENST00000312629	NM_003952.2	108	cGc/cCc	5/15	0.363354858807018	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	2	0.363354858807018	4		313	493	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226618	1226618	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs730881992	NA	P-0007816-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	139	414	1	ENST00000326873.7:c.1274G>C	p.Arg425Pro	p.R425P	ENST00000326873	NM_000455.4	425	cGc/cCc	9/10	0.363354858807018	3	FACETS	0.757	0.692	0.825	0.757	0.692	0.825	SUBCLONAL	2	TRUE	1	0.363354858807018	3		415	597	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028898	47028898	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0007816-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	116	375	0	ENST00000377604.3:c.201+1G>T		p.X67_splice	ENST00000377604	NM_001204468.1	67			0.363354858807018	4	FACETS	0.918	0.832	1	0.918	0.832	1	CLONAL	2	TRUE	2	0.363354858807018	4		375	474	SUCCESS
PHF6	84295	MSKCC	GRCh37	X	133551256	133551256	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007816-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	123	246	0	ENST00000332070.3:c.892G>T	p.Val298Phe	p.V298F	ENST00000332070	NM_032458.2	298	Gtt/Ttt	9/10	0.363354858807018	4	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	2	0.363354858807018	4		246	445	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590599	95590599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007816-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	64	256	0	ENST00000393063.1:c.1310C>T	p.Pro437Leu	p.P437L	ENST00000393063	NM_030621.3	437	cCt/cTt	9/28	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.363354858807018	2		256	341	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479288	50479288	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	32	308	0	ENST00000394963.4:c.136C>G	p.Gln46Glu	p.Q46E	ENST00000394963	NM_003076.4	46	Caa/Gaa	1/13	1	2	FACETS	0.338	0.274	0.41	0.338	0.274	0.41	SUBCLONAL	1	TRUE	1	0.485232385572516	2		308	390	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120527	70120527	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	180	394	0	ENST00000245479.2:c.1529G>C	p.Ter510SerextTer49	p.*510Sext*49	ENST00000245479	NM_000346.3	510	tGa/tCa	3/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.485232385572516	2		394	595	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845757	68845757	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587780784	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	185	310	0	ENST00000261769.5:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000261769	NM_004360.3	335	Cga/Tga	7/16	0.45075236339225	2	FACETS	0.934	0.874	0.995	0.934	0.874	0.995	CLONAL	2	TRUE	0	0.485232385572516	2		310	408	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827998	40827998	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs200127403	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	92	351	0	ENST00000373198.4:c.2430G>C	p.Gln810His	p.Q810H	ENST00000373198	NM_133170.3	810	caG/caC	17/32	1	2	FACETS	0.848	0.758	0.944	0.848	0.758	0.944	CLONAL	1	TRUE	1	0.485232385572516	2		351	447	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040686	47040686	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	103	324	0	ENST00000377604.3:c.1321G>A	p.Asp441Asn	p.D441N	ENST00000377604	NM_001204468.1	441	Gat/Aat	13/24	0.139448436588087	1	FACETS	0.715	0.643	0.79	0.715	0.643	0.79	INDETERMINATE	1	TRUE	0	0.485232385572516	1		324	450	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259368	89259368	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	103	395	0	ENST00000336596.2:c.512T>C	p.Val171Ala	p.V171A	ENST00000336596	NM_005233.5	171	gTa/gCa	3/17	1	2	FACETS	0.95	0.855	1	0.95	0.855	1	CLONAL	1	TRUE	1	0.485232385572516	2		395	447	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856313	111856313	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	93	350	0	ENST00000341259.2:c.364G>T	p.Glu122Ter	p.E122*	ENST00000341259	NM_005475.2	122	Gag/Tag	2/8	1	2	FACETS	0.879	0.786	0.977	0.879	0.786	0.977	CLONAL	1	TRUE	1	0.485232385572516	2		350	436	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866689	37866689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149210045	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	145	456	0	ENST00000269571.5:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269571		286	Gag/Aag	7/27	1	2	FACETS	0.952	0.871	1	0.952	0.871	1	CLONAL	1	TRUE	1	0.485232385572516	2		456	628	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403604	138403604	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	75	252	0	ENST00000289153.2:c.2178C>G	p.Ile726Met	p.I726M	ENST00000289153	NM_006219.2	726	atC/atG	15/22	1	2	FACETS	0.765	0.674	0.862	0.765	0.674	0.862	SUBCLONAL	1	TRUE	1	0.485232385572516	2		252	404	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223186	5223186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	110	448	0	ENST00000357368.4:c.2617G>A	p.Glu873Lys	p.E873K	ENST00000357368	NM_002850.3	873	Gag/Aag	18/38	1	2	FACETS	0.951	0.859	1	0.951	0.859	1	CLONAL	1	TRUE	1	0.485232385572516	2		448	477	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164717	47164717	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	124	353	0	ENST00000409792.3:c.1409C>G	p.Ser470Ter	p.S470*	ENST00000409792	NM_014159.6	470	tCa/tGa	3/21	1	2	FACETS	0.934	0.849	1	0.934	0.849	1	CLONAL	1	TRUE	1	0.485232385572516	2		353	547	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873518	151873518	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	123	409	0	ENST00000262189.6:c.9020del	p.Gly3007GlufsTer25	p.G3007Efs*25	ENST00000262189	NM_170606.2	3007	gGa/ga	38/59	1	2	FACETS	0.867	0.786	0.951	0.867	0.786	0.951	CLONAL	1	TRUE	1	0.485232385572516	2		409	585	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884510	151884510	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	119	309	0	ENST00000262189.6:c.4845G>A	p.Trp1615Ter	p.W1615*	ENST00000262189	NM_170606.2	1615	tgG/tgA	33/59	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.485232385572516	2		309	479	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780677	56780677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502588	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	101	316	0	ENST00000337432.4:c.692C>T	p.Ser231Leu	p.S231L	ENST00000337432	NM_058216.2	231	tCa/tTa	4/9	1	2	FACETS	0.925	0.832	1	0.925	0.832	1	CLONAL	1	TRUE	1	0.485232385572516	2		316	450	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415628	49415628	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	111	322	0	ENST00000301067.7:c.16549G>C	p.Glu5517Gln	p.E5517Q	ENST00000301067	NM_003482.3	5517	Gag/Cag	54/54	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.485232385572516	2		322	452	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740453	58740453	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765346414	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	101	327	0	ENST00000305921.3:c.1358C>T	p.Ser453Leu	p.S453L	ENST00000305921	NM_003620.3	453	tCa/tTa	6/6	1	2	FACETS	0.844	0.758	0.935	0.844	0.758	0.935	CLONAL	1	TRUE	1	0.485232385572516	2		327	493	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056210	26056210	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	171	406	0	ENST00000343677.2:c.447G>C	p.Lys149Asn	p.K149N	ENST00000343677	NM_005319.3	149	aaG/aaC	1/1	0.485232385572516	3	FACETS	0.958	0.882	1	0.479	0.441	0.519	CLONAL	1	TRUE	1	0.485232385572516	3		406	914	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796105	57796105	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	103	338	0	ENST00000309042.7:c.1081C>G	p.Leu361Val	p.L361V	ENST00000309042	NM_005612.4	361	Ctt/Gtt	4/4	0.139448436588087	1	FACETS	0.671	0.604	0.742	0.671	0.604	0.742	INDETERMINATE	1	TRUE	0	0.485232385572516	1		338	479	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449514	31449514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	84	334	0	ENST00000344624.3:c.2695C>T	p.His899Tyr	p.H899Y	ENST00000344624		899	Cat/Tat	19/33	1	2	FACETS	0.832	0.739	0.931	0.832	0.739	0.931	CLONAL	1	TRUE	1	0.485232385572516	2		334	416	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920210	1920210	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	135	417	0	ENST00000382891.5:c.1270C>G	p.Gln424Glu	p.Q424E	ENST00000382891	NM_133335.3	424	Caa/Gaa	5/22	0.139448436588087	1	FACETS	0.761	0.695	0.83	0.761	0.695	0.83	INDETERMINATE	1	TRUE	0	0.485232385572516	1		417	554	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378270	15378270	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	103	314	0	ENST00000263377.2:c.516G>C	p.Met172Ile	p.M172I	ENST00000263377	NM_058243.2	172	atG/atC	4/20	1	2	FACETS	0.95	0.855	1	0.95	0.855	1	CLONAL	1	TRUE	1	0.485232385572516	2		314	447	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30323850	30323850	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	85	242	0	ENST00000322652.5:c.1828G>A	p.Glu610Lys	p.E610K	ENST00000322652	NM_015355.2	610	Gag/Aag	15/16	1	2	FACETS	0.915	0.814	1	0.915	0.814	1	CLONAL	1	TRUE	1	0.485232385572516	2		242	383	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679761	33679761	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs150899761	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	128	408	0	ENST00000308377.4:c.2320C>T	p.Gln774Ter	p.Q774*	ENST00000308377	NM_152270.3	774	Cag/Tag	5/5	1	2	FACETS	0.884	0.804	0.968	0.884	0.804	0.968	CLONAL	1	TRUE	1	0.485232385572516	2		408	597	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542759	187542759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1325785710	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	107	425	0	ENST00000441802.2:c.4981G>A	p.Asp1661Asn	p.D1661N	ENST00000441802	NM_005245.3	1661	Gac/Aac	10/27	0.139448436588087	1	FACETS	0.687	0.619	0.759	0.687	0.619	0.759	INDETERMINATE	1	TRUE	0	0.485232385572516	1		425	486	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519483	176519483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372605354	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	116	461	1	ENST00000292408.4:c.889G>A	p.Asp297Asn	p.D297N	ENST00000292408	NM_213647.1	297	Gac/Aac	7/18	1	2	FACETS	0.852	0.771	0.938	0.852	0.771	0.938	CLONAL	1	TRUE	1	0.485232385572516	2		462	561	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119720	108119720	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	111	309	0	ENST00000278616.4:c.1126G>C	p.Glu376Gln	p.E376Q	ENST00000278616	NM_000051.3	376	Gaa/Caa	9/63	0.485232385572516	1	FACETS	0.96	0.872	1	0.96	0.872	1	CLONAL	1	TRUE	0	0.485232385572516	1		309	361	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175713	176175713	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	103	338	0	ENST00000367669.3:c.402C>A	p.Phe134Leu	p.F134L	ENST00000367669	NM_022457.5	134	ttC/ttA	1/20	0.478566285137368	4	FACETS	0.909	0.814	1	0.454	0.407	0.505	CLONAL	1	TRUE	2	0.485232385572516	4		338	694	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029305	14029305	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	251	419	0	ENST00000311895.7:c.1516G>A	p.Glu506Lys	p.E506K	ENST00000311895	NM_005236.2	506	Gag/Aag	8/11	0.398197284150891	3	FACETS	0.869	0.816	0.922	0.869	0.816	0.922	CLONAL	2	TRUE	1	0.485232385572516	3		419	740	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431826	49431826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	119	404	0	ENST00000301067.7:c.9313G>A	p.Asp3105Asn	p.D3105N	ENST00000301067	NM_003482.3	3105	Gat/Aat	34/54	1	2	FACETS	0.907	0.822	0.995	0.907	0.822	0.995	CLONAL	1	TRUE	1	0.485232385572516	2		404	541	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96930935	96930935	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	144	359	0	ENST00000258439.3:c.185C>G	p.Ser62Trp	p.S62W	ENST00000258439	NM_001193304.2	62	tCg/tGg	2/4	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.485232385572516	2		359	561	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557891	21557891	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	110	378	0	ENST00000382592.4:c.1954G>C	p.Glu652Gln	p.E652Q	ENST00000382592	NM_014572.2	652	Gag/Cag	5/8	0.485232385572516	1	FACETS	0.814	0.736	0.894	0.814	0.736	0.894	CLONAL	1	TRUE	0	0.485232385572516	1		378	422	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538206	187538206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1327390871	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	94	359	0	ENST00000441802.2:c.9028G>A	p.Glu3010Lys	p.E3010K	ENST00000441802	NM_005245.3	3010	Gaa/Aaa	11/27	0.139448436588087	1	FACETS	0.725	0.649	0.804	0.725	0.649	0.804	INDETERMINATE	1	TRUE	0	0.485232385572516	1		359	405	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346689	225346689	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	77	257	0	ENST00000264414.4:c.1949C>G	p.Ser650Ter	p.S650*	ENST00000264414	NM_003590.4	650	tCa/tGa	14/16	1	2	FACETS	0.902	0.797	1	0.902	0.797	1	CLONAL	1	TRUE	1	0.485232385572516	2		257	352	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554488	63554488	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs878854729	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	115	394	0	ENST00000307078.5:c.251C>G	p.Ser84Cys	p.S84C	ENST00000307078	NM_004655.3	84	tCc/tGc	2/11	1	2	FACETS	0.789	0.712	0.869	0.789	0.712	0.869	SUBCLONAL	1	TRUE	1	0.485232385572516	2		394	601	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845075	128845075	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	82	361	0	ENST00000249373.3:c.569C>T	p.Ser190Leu	p.S190L	ENST00000249373	NM_005631.4	190	tCa/tTa	3/12	1	2	FACETS	0.793	0.703	0.889	0.793	0.703	0.889	SUBCLONAL	1	TRUE	1	0.485232385572516	2		361	426	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794983	42794983	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	118	386	0	ENST00000575354.2:c.2063C>G	p.Ser688Cys	p.S688C	ENST00000575354	NM_015125.3	688	tCt/tGt	10/20	1	2	FACETS	0.833	0.754	0.916	0.833	0.754	0.916	CLONAL	1	TRUE	1	0.485232385572516	2		386	584	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310155	91310155	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	111	253	0	ENST00000355112.3:c.2209C>G	p.Leu737Val	p.L737V	ENST00000355112	NM_000057.2	737	Ctg/Gtg	10/22	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.485232385572516	2		253	390	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	443461	443461	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	114	331	0	ENST00000399788.2:c.1436C>G	p.Ser479Cys	p.S479C	ENST00000399788	NM_001042603.1	479	tCt/tGt	11/28	1	2	FACETS	0.902	0.816	0.992	0.902	0.816	0.992	CLONAL	1	TRUE	1	0.485232385572516	2		331	521	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63898535	63898537	+	frameshift_variant	Frame_Shift_Del	DEL	TGA	TGA	C	novel	NA	P-0008398-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	90	347	0	ENST00000398590.3:c.261_263delinsC	p.Glu88SerfsTer12	p.E88Sfs*12	ENST00000398590	NM_001177387.1	87	ccTGAa/ccCa	3/14	1	2	FACETS	0.733	0.653	0.818	0.733	0.653	0.818	SUBCLONAL	1	TRUE	1	0.485232385572516	2		347	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0008422-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	266	418	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.620764253508222	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.61932333180385	2		418	413	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216631	2216631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769937964	NA	P-0008422-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	110	546	0	ENST00000398665.3:c.2275C>T	p.Arg759Cys	p.R759C	ENST00000398665	NM_032482.2	759	Cgc/Tgc	20/28	0.453543527542185	3	FACETS	0.638	0.574	0.707	0.213	0.191	0.236	SUBCLONAL	1	TRUE	0	0.61932333180385	3		546	729	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917845	29917845	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008422-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	192	386	0	ENST00000389048.3:c.823G>T	p.Glu275Ter	p.E275*	ENST00000389048	NM_004304.4	275	Gag/Tag	3/29	0.620764253508222	5	FACETS	0.807	0.748	0.867	0.538	0.499	0.578	CLONAL	2	TRUE	2	0.61932333180385	5		386	741	SUCCESS
ATR	545	MSKCC	GRCh37	3	142184044	142184044	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008422-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	109	210	0	ENST00000350721.4:c.6936T>G	p.Ile2312Met	p.I2312M	ENST00000350721	NM_001184.3	2312	atT/atG	41/47	0.61932333180385	8	FACETS	1	0.982	1	0.209	0.187	0.231	CLONAL	1	TRUE	1	0.61932333180385	8		210	689	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000307	42000307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008422-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	67	256	0	ENST00000219905.7:c.2326G>A	p.Gly776Arg	p.G776R	ENST00000219905	NM_001164273.1	776	Gga/Aga	7/24	0.548417396210848	3	FACETS	0.728	0.636	0.828	0.364	0.318	0.414	SUBCLONAL	1	TRUE	1	0.61932333180385	3		256	389	SUCCESS
REST	5978	MSKCC	GRCh37	4	57797426	57797426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008422-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	78	525	0	ENST00000309042.7:c.2402G>A	p.Arg801Lys	p.R801K	ENST00000309042	NM_005612.4	801	aGa/aAa	4/4	0.61932333180385	6	FACETS	0.438	0.383	0.498	0.11	0.095	0.125	SUBCLONAL	1	TRUE	2	0.61932333180385	6		525	1287	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76919028	76919029	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010496-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	166	259	0	ENST00000373344.5:c.3962dup	p.Asn1321LysfsTer3	p.N1321Kfs*3	ENST00000373344	NM_000489.3	1321	aat/aaAt	12/35	0.575678928961912	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.710670647533174	1		259	205	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286530	33286530	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011479-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	231	265	0	ENST00000374542.5:c.2213A>T	p.Asp738Val	p.D738V	ENST00000374542	NM_001141970.1	738	gAc/gTc	8/8	0.487517524138311	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.496937426299841	2		265	456	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142982	30142982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1229550831	NA	P-0012039-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	74	535	0	ENST00000389048.3:c.544G>A	p.Glu182Lys	p.E182K	ENST00000389048	NM_004304.4	182	Gaa/Aaa	1/29	1	2	FACETS	0.492	0.431	0.559	0.492	0.431	0.559	SUBCLONAL	1	TRUE	1	0.441995579911769	2		535	680	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830184	72830184	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012039-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	123	581	0	ENST00000268489.5:c.6397C>T	p.Gln2133Ter	p.Q2133*	ENST00000268489	NM_006885.3	2133	Cag/Tag	9/10	0.441995579911769	1	FACETS	0.9	0.818	0.984	0.9	0.818	0.984	CLONAL	1	TRUE	0	0.441995579911769	1		581	482	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367954	15367954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012039-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	176	409	0	ENST00000263377.2:c.1372C>T	p.Pro458Ser	p.P458S	ENST00000263377	NM_058243.2	458	Ccg/Tcg	8/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.441995579911769	2		409	552	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202798	16202798	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012039-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	111	456	0	ENST00000375759.3:c.506A>G	p.Tyr169Cys	p.Y169C	ENST00000375759	NM_015001.2	169	tAc/tGc	3/15	0.382082183551392	1	FACETS	0.616	0.555	0.681	0.616	0.555	0.681	SUBCLONAL	1	TRUE	0	0.441995579911769	1		456	635	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891591	151891591	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587777073	NA	P-0012039-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	122	406	3	ENST00000262189.6:c.4441C>T	p.Arg1481Ter	p.R1481*	ENST00000262189	NM_170606.2	1481	Cga/Tga	29/59	1	2	FACETS	0.761	0.689	0.838	0.761	0.689	0.838	SUBCLONAL	1	TRUE	1	0.441995579911769	2		409	725	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579536	7579536	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012089-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	247	633	0	ENST00000269305.4:c.151del	p.Glu51AsnfsTer72	p.E51Nfs*72	ENST00000269305	NM_001126112.2	51	Gaa/aa	4/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		633	336	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30668406	30668406	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012089-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	63	460	0	ENST00000376406.3:c.6106C>G	p.Gln2036Glu	p.Q2036E	ENST00000376406	NM_014641.2	2036	Cag/Gag	15/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		460	387	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0012089-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	605	348	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		348	723	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849417	68849417	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0012836-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	81	356	0	ENST00000261769.5:c.1321-1G>A		p.X441_splice	ENST00000261769	NM_004360.3	441			0.786632960763183	2	FACETS	0.933	0.867	0.994	0.933	0.867	0.994	CLONAL	2	TRUE	0	0.78220237475616	2		356	111	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024145	31024145	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012836-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	49	466	0	ENST00000375687.4:c.3630T>A	p.Phe1210Leu	p.F1210L	ENST00000375687	NM_015338.5	1210	ttT/ttA	13/13	0.593703577887051	4	FACETS	0.797	0.68	0.925			1	CLONAL	1	TRUE	NA	0.78220237475616	4		466	280	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575679	55575679	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012836-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	77	276	0	ENST00000288135.5:c.1205C>G	p.Ala402Gly	p.A402G	ENST00000288135	NM_000222.2	402	gCc/gGc	7/21	0.755484669980225	4	FACETS	1	0.939	1	0.547	0.484	0.613	CLONAL	1	TRUE	2	0.78220237475616	4		276	321	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013183-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	131	300	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.310898623704193	3	FACETS	0.998	0.911	1	0.998	0.911	1	CLONAL	2	TRUE	1	0.310898623704193	3		300	488	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0013183-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	71	410	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.310898623704193	1	FACETS	0.83	0.726	0.94	0.83	0.726	0.94	CLONAL	1	TRUE	0	0.310898623704193	1		410	465	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913385	NA	P-0013183-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	75	414	0	ENST00000304494.5:c.247C>G	p.His83Asp	p.H83D	ENST00000304494	NM_000077.4	83	Cac/Gac	2/3	0.310898623704193	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.310898623704193	1		414	357	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845600	72845600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772299356	NA	P-0013183-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	91	427	0	ENST00000268489.5:c.3740C>T	p.Ser1247Leu	p.S1247L	ENST00000268489	NM_006885.3	1247	tCg/tTg	7/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.310898623704193	2		427	520	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686282	30686293	+	inframe_deletion	In_Frame_Del	DEL	GTTTCCACAACT	GTTTCCACAACT	-	novel	NA	P-0013183-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	66	349	0	ENST00000295754.5:c.140_151del	p.Phe47_Leu50del	p.F47_L50del	ENST00000295754	NM_003242.5	46	aaGTTTCCACAACTg/aag	2/7	0.310898623704193	1	FACETS	0.808	0.703	0.92	0.808	0.703	0.92	CLONAL	1	TRUE	0	0.310898623704193	1		349	444	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0013909-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	213	385	0				ENST00000310581	NM_198253.2	-/1132			0.470309043306344	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.51046113208178	4		385	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0013909-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	294	452	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.51046113208178	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.51046113208178	2		452	539	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919244	48919244	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913296	NA	P-0013909-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	194	274	0	ENST00000267163.4:c.409G>T	p.Glu137Ter	p.E137*	ENST00000267163	NM_000321.2	137	Gaa/Taa	4/27	0.51046113208178	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.51046113208178	2		274	374	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589629	67589630	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGATTA	novel	NA	P-0013909-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	165	303	0	ENST00000274335.5:c.1393_1398dup	p.Arg465_Leu466dup	p.R465_L466dup	ENST00000274335		465	-/AGATTA	10/15	0.51046113208178	2	FACETS	0.794	0.738	0.851	0.794	0.738	0.851	SUBCLONAL	2	TRUE	0	0.51046113208178	2		303	407	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841532	156841532	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs368040165	NA	P-0013909-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	166	624	0	ENST00000524377.1:c.835C>T	p.Gln279Ter	p.Q279*	ENST00000524377	NM_002529.3	279	Cag/Tag	7/17	0.51046113208178	4	FACETS	1	0.973	1	0.569	0.522	0.617	CLONAL	1	TRUE	2	0.51046113208178	4		624	864	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474022	29474022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013909-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	130	471	0	ENST00000389048.3:c.2153G>A	p.Gly718Asp	p.G718D	ENST00000389048	NM_004304.4	718	gGc/gAc	12/29	0.51046113208178	2	FACETS	1	0.962	1	0.548	0.5	0.597	CLONAL	1	TRUE	0	0.51046113208178	2		471	465	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003868	57003868	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	G	G	A	rs202019294	NA	P-0013909-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	126	579	0	ENST00000257254.3:c.611C>T	p.Ser204Leu	p.S204L	ENST00000257254		204	tCg/tTg	1/2	NA	2	FACETS	0.85	0.772	0.931			1	INDETERMINATE	1	TRUE	NA	0.51046113208178	2		579	581	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631129	69631129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs281860303	NA	P-0014385-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	115	595	0	ENST00000334134.2:c.283C>T	p.Arg95Trp	p.R95W	ENST00000334134	NM_005247.2	95	Cgg/Tgg	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		595	517	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443631	29443631	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519784	NA	P-0014385-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	161	351	0	ENST00000389048.3:c.3586C>A	p.Leu1196Met	p.L1196M	ENST00000389048	NM_004304.4	1196	Ctg/Atg	23/29	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		351	534	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015218	128015218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372094432	NA	P-0014385-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	50	504	1	ENST00000285398.2:c.2303C>T	p.Ala768Val	p.A768V	ENST00000285398	NM_000122.1	768	gCg/gTg	15/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		505	473	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457737	149457737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759467764	NA	P-0014385-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	42	435	0	ENST00000286301.3:c.667G>A	p.Val223Met	p.V223M	ENST00000286301	NM_005211.3	223	Gtg/Atg	5/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		435	580	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115904	8115904	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014995-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	271	617	0	ENST00000346208.3:c.1251del	p.Thr418ArgfsTer57	p.T418Rfs*57	ENST00000346208		417	aCc/ac	6/6	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.656739424053398	2		617	576	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014995-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	268	501	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.08975181967801	3	FACETS	1	0.954	1			1	INDETERMINATE	3	FALSE	NA	0.375412949071714	3		501	561	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115904	8115904	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014995-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	227	617	0	ENST00000346208.3:c.1251del	p.Thr418ArgfsTer57	p.T418Rfs*57	ENST00000346208		417	aCc/ac	6/6	1	2	FACETS	1	0.977	1	1	0.995	1	CLONAL	2	FALSE	1	0.375412949071714	2		617	561	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630454	47630455	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCTATA	novel	NA	P-0014995-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	138	490	0	ENST00000233146.2:c.125_130dup	p.Tyr43_Thr44insIleTyr	p.Y43_T44insIY	ENST00000233146	NM_000251.2	42	ttc/tTCTATAtc	1/16	1	2	FACETS	1	0.967	1	1	0.992	1	CLONAL	2	FALSE	1	0.375412949071714	2		490	338	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0016869-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	42	344	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.18	2		344	416	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0016869-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	24	199	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	1	0.836	1	1	0.836	1	CLONAL	1	TRUE	1	0.18	2		200	248	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0016869-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	24	371	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.61	0.478	0.764	0.61	0.478	0.764	SUBCLONAL	1	TRUE	1	0.18	2		371	437	SUCCESS
AR	367	MSKCC	GRCh37	X	66931342	66931342	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016869-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	31	203	0	ENST00000374690.3:c.1984G>T	p.Val662Leu	p.V662L	ENST00000374690	NM_000044.3	662	Gtg/Ttg	4/8	0.228694019210097	2	FACETS	1	0.909	1			1	CLONAL	1	TRUE	NA	0.18	2		203	283	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485794	8485794	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016869-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	71	256	0	ENST00000356435.5:c.3023G>T	p.Ser1008Ile	p.S1008I	ENST00000356435		1008	aGt/aTt	17/35	1	2	FACETS	0.994	0.871	1	1	0.982	1	CLONAL	2	TRUE	1	0.18	2		256	397	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562994	21562994	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749559845	NA	P-0016869-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	137	489	1	ENST00000382592.4:c.925G>A	p.Ala309Thr	p.A309T	ENST00000382592	NM_014572.2	309	Gcc/Acc	4/8	0.191711509967007	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.18	3		490	712	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636669	73636669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016869-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	107	418	0	ENST00000377687.4:c.932G>A	p.Ser311Asn	p.S311N	ENST00000377687	NM_001730.3	311	aGt/aAt	2/4	0.191711509967007	3	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	1	0.18	3		418	624	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202123053	202123053	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016869-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	34	340	0	ENST00000358485.4:c.99A>C	p.Leu33Phe	p.L33F	ENST00000358485	NM_001080125.1	33	ttA/ttC	1/9	1	2	FACETS	0.614	0.501	0.743	0.614	0.501	0.743	SUBCLONAL	1	TRUE	1	0.18	2		340	615	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628266	187628266	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017420-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	17	560	0	ENST00000441802.2:c.2716C>T	p.Gln906Ter	p.Q906*	ENST00000441802	NM_005245.3	906	Cag/Tag	2/27	0.581990361277627	0	FACETS		NA	1			1	NA	1	TRUE	0	0.683298997697486	0		560	289	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0019364-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	276	547	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.607841019850703	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.607841019850703	3		547	555	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019364-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	170	322	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.607841019850703	3	FACETS	1	0.978	1	0.58	0.535	0.626	CLONAL	1	TRUE	1	0.607841019850703	3		322	629	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259744	16259744	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019364-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	347	450	0	ENST00000375759.3:c.7009C>T	p.Arg2337Ter	p.R2337*	ENST00000375759	NM_015001.2	2337	Cga/Tga	11/15	0.607841019850703	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.607841019850703	2		450	546	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115710	8115711	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019364-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	472	299	0	ENST00000346208.3:c.1060dup	p.Leu354ProfsTer17	p.L354Pfs*17	ENST00000346208		352	-/C	6/6	0.607841019850703	6	FACETS	1	0.988	1	0.805	0.772	0.839	CLONAL	3	TRUE	2	0.607841019850703	6		299	1068	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239525	123239526	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0019364-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6594	478	496	0	ENST00000358487.5:c.2311_2312del	p.Asp771ProfsTer11	p.D771Pfs*11	ENST00000358487	NM_000141.4	771	GAc/c	18/18	0.607841019850703	27	FACETS	0.956	0.907	1			1	CLONAL	2	TRUE	NA	0.607841019850703	27		496	7072	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2206746	2206746	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019364-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	156	309	0	ENST00000398665.3:c.806C>G	p.Ser269Trp	p.S269W	ENST00000398665	NM_032482.2	269	tCg/tGg	10/28	0.607841019850703	3	FACETS	0.997	0.916	1	0.499	0.458	0.541	CLONAL	1	TRUE	1	0.607841019850703	3		309	671	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252962	36252962	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs74315451	NA	P-0019364-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	297	310	0	ENST00000300305.3:c.400G>C	p.Ala134Pro	p.A134P	ENST00000300305		134	Gct/Cct	4/8	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	2	TRUE	NA	0.607841019850703	2		310	484	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821610	72821618	+	inframe_deletion	In_Frame_Del	DEL	CCGCCGCCA	CCGCCGCCA	-	rs760306096	NA	P-0019364-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	67	357	0	ENST00000268489.5:c.10557_10565del	p.Gly3525_Gly3527del	p.G3525_G3527del	ENST00000268489	NM_006885.3	3519	ggTGGCGGCGGc/ggc	10/10	0.607841019850703	3	FACETS	0.659	0.575	0.75	0.33	0.287	0.375	SUBCLONAL	1	TRUE	1	0.607841019850703	3		357	436	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0020838-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	219	235	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.735892225626854	3	FACETS	0.903	0.851	0.955	0.903	0.851	0.955	CLONAL	2	TRUE	1	0.735892225626854	3		235	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578537	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs879254214	NA	P-0020838-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	327	340	0	ENST00000269305.4:c.393_395del	p.Asn131del	p.N131del	ENST00000269305	NM_001126112.2	131	aaCAAg/aag	5/11	0.735892225626854	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.735892225626854	2		340	420	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217614	142217614	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020838-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	69	263	0	ENST00000350721.4:c.5383G>T	p.Gly1795Ter	p.G1795*	ENST00000350721	NM_001184.3	1795	Gga/Tga	32/47	0.635624526570414	3	FACETS	0.852	0.749	0.962	0.426	0.374	0.481	CLONAL	1	TRUE	1	0.735892225626854	3		263	301	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189585691	189585691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1205536026	NA	P-0020838-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	204	284	0	ENST00000264731.3:c.952C>T	p.Arg318Cys	p.R318C	ENST00000264731	NM_003722.4	318	Cgc/Tgc	7/14	0.661911032567922	4	FACETS	0.837	0.782	0.893	0.837	0.782	0.893	CLONAL	2	TRUE	2	0.735892225626854	4		284	575	SUCCESS
ALB	213	MSKCC	GRCh37	4	74279203	74279204	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020838-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	126	335	0	ENST00000295897.4:c.915dup	p.Pro306ThrfsTer15	p.P306Tfs*15	ENST00000295897	NM_000477.5	304	gaa/gAaa	8/15	0.735892225626854	2	FACETS	1	0.937	1	0.513	0.47	0.556	CLONAL	1	TRUE	0	0.735892225626854	2		335	334	SUCCESS
APC	324	MSKCC	GRCh37	5	112173345	112173345	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020838-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	136	347	0	ENST00000257430.4:c.2054G>A	p.Trp685Ter	p.W685*	ENST00000257430	NM_000038.5	685	tGg/tAg	16/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.735892225626854	2		347	335	SUCCESS
APC	324	MSKCC	GRCh37	5	112175358	112175358	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1554085480	NA	P-0020838-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	122	367	0	ENST00000257430.4:c.4067C>G	p.Ser1356Ter	p.S1356*	ENST00000257430	NM_000038.5	1356	tCa/tGa	16/16	1	2	FACETS	0.947	0.866	1	0.947	0.866	1	CLONAL	1	TRUE	1	0.735892225626854	2		367	350	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	92	264	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.426254397478605	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.426254397478605	3		264	236	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0022181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	177	508	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.426254397478605	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.426254397478605	2		508	402	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	62	474	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	0.426254397478605	3	FACETS	0.983	0.854	1	0.492	0.427	0.561	CLONAL	1	TRUE	1	0.426254397478605	3		474	359	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001278	150001278	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	85	225	0	ENST00000253339.5:c.2326G>T	p.Asp776Tyr	p.D776Y	ENST00000253339		776	Gac/Tac	4/7	0.426254397478605	2	FACETS	0.923	0.832	1	0.923	0.832	1	CLONAL	2	TRUE	0	0.426254397478605	2		225	216	SUCCESS
APC	324	MSKCC	GRCh37	5	112175482	112175482	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	293	206	0	ENST00000257430.4:c.4191del	p.Ser1398ValfsTer17	p.S1398Vfs*17	ENST00000257430	NM_000038.5	1397	gaG/ga	16/16	0.426254397478605	4	FACETS	0.921	0.878	0.964	0.921	0.878	0.964	CLONAL	4	TRUE	0	0.426254397478605	4		206	532	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022387-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	5	382	0				ENST00000310581	NM_198253.2	-/1132			0.12923980543059	0	FACETS	0.337	0.191	0.538			1	INDETERMINATE	1	TRUE	0	0.24	0		382	94	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692775	89692775	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554898053	NA	P-0022387-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	26	73	0	ENST00000371953.3:c.259C>T	p.Gln87Ter	p.Q87*	ENST00000371953	NM_000314.4	87	Caa/Taa	5/9	1	2	FACETS	0.52	0.411	0.644	0.52	0.411	0.644	SUBCLONAL	1	TRUE	1	0.24	2		73	417	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942124	81942124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781434235	NA	P-0022387-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	14	91	0	ENST00000359376.3:c.1661C>T	p.Thr554Met	p.T554M	ENST00000359376	NM_002661.3	554	aCg/aTg	17/33	0.12923980543059	0	FACETS	0.355	0.256	0.474			1	INDETERMINATE	1	TRUE	0	0.24	0		91	250	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970993	70970993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022387-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	37	93	0	ENST00000276594.2:c.1268C>T	p.Pro423Leu	p.P423L	ENST00000276594	NM_024504.3	423	cCc/cTc	6/8	1	2	FACETS	0.801	0.661	0.957	0.801	0.661	0.957	CLONAL	1	TRUE	1	0.24	2		93	385	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121856	2121856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745897413	NA	P-0022387-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	2	0	0	ENST00000219476.3:c.2018C>T	p.Ala673Val	p.A673V	ENST00000219476	NM_000548.3	673	gCg/gTg	19/42	0.3	0	FACETS	0.087	0.033	0.181			1	SUBCLONAL	1	TRUE	0	0.24	0		0	145	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50490675	50490675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1473235153	NA	P-0022387-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	16	89	0	ENST00000394963.4:c.1312C>T	p.Arg438Trp	p.R438W	ENST00000394963	NM_003076.4	438	Cgg/Tgg	11/13	1	2	FACETS	0.538	0.397	0.705	0.538	0.397	0.705	SUBCLONAL	1	TRUE	1	0.24	2		89	248	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63662157	63662157	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022387-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	50	99	0	ENST00000279873.7:c.261T>G	p.Asn87Lys	p.N87K	ENST00000279873	NM_032199.2	87	aaT/aaG	2/10	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.24	2		99	413	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675192	176675192	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022387-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	39	78	0	ENST00000439151.2:c.4508T>C	p.Met1503Thr	p.M1503T	ENST00000439151	NM_022455.4	1503	aTg/aCg	11/23	0.12923980543059	0	FACETS	0.642	0.532	0.763			1	INDETERMINATE	1	TRUE	0	0.24	0		78	385	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690457	33690457	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140675117	NA	P-0022387-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	45	95	0	ENST00000308377.4:c.370C>T	p.Arg124Cys	p.R124C	ENST00000308377	NM_152270.3	124	Cgc/Tgc	2/5	1	2	FACETS	0.808	0.68	0.95	0.808	0.68	0.95	CLONAL	1	TRUE	1	0.24	2		95	464	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970897	70970897	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022387-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	31	94	0	ENST00000276594.2:c.1364A>G	p.His455Arg	p.H455R	ENST00000276594	NM_024504.3	455	cAt/cGt	6/8	1	2	FACETS	0.783	0.634	0.95	0.783	0.634	0.95	CLONAL	1	TRUE	1	0.24	2		94	330	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586058	29586058	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022387-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	35	66	0	ENST00000356175.3:c.4278G>T	p.Gln1426His	p.Q1426H	ENST00000356175	NM_000267.3	1426	caG/caT	32/57	1	2	FACETS	0.766	0.628	0.919	0.766	0.628	0.919	CLONAL	1	TRUE	1	0.24	2		66	381	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443631	29443631	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519784	NA	P-0022509-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1617	381	351	0	ENST00000389048.3:c.3586C>A	p.Leu1196Met	p.L1196M	ENST00000389048	NM_004304.4	1196	Ctg/Atg	23/29	0.656766833281037	11	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.656766833281037	11		351	1998	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914562	32914562	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022509-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	132	394	0	ENST00000380152.3:c.6070C>A	p.Gln2024Lys	p.Q2024K	ENST00000380152		2024	Cag/Aag	11/27	0.219910635340541	1	FACETS	1	0.983	1	1	0.983	1	INDETERMINATE	1	TRUE	0	0.656766833281037	1		394	227	SUCCESS
REST	5978	MSKCC	GRCh37	4	57777430	57777430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022509-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	175	405	0	ENST00000309042.7:c.626G>A	p.Gly209Glu	p.G209E	ENST00000309042	NM_005612.4	209	gGa/gAa	2/4	0.656766833281037	6	FACETS	0.993	0.913	1	0.248	0.228	0.27	CLONAL	1	TRUE	2	0.656766833281037	6		405	1241	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950421	68950421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022509-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	53	255	0	ENST00000288368.4:c.733G>A	p.Glu245Lys	p.E245K	ENST00000288368	NM_024870.2	245	Gaa/Aaa	7/40	0.410973948342719	1	FACETS	0.484	0.417	0.555	0.484	0.417	0.555	SUBCLONAL	1	TRUE	0	0.656766833281037	1		255	224	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446377	70446377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022509-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	154	432	0	ENST00000373644.4:c.5317G>A	p.Val1773Met	p.V1773M	ENST00000373644	NM_030625.2	1773	Gtg/Atg	11/12	0.656766833281037	2	FACETS	1	0.942	1	0.512	0.472	0.553	CLONAL	1	TRUE	0	0.656766833281037	2		432	458	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205236	38205236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022509-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	106	351	0	ENST00000317025.8:c.454G>A	p.Glu152Lys	p.E152K	ENST00000317025	NM_023034.1	152	Gaa/Aaa	2/24	0.656766833281037	1	FACETS	0.9	0.823	0.977	0.9	0.823	0.977	CLONAL	1	TRUE	0	0.656766833281037	1		351	241	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133006	30133006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022509-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	194	291	0	ENST00000331968.5:c.595G>A	p.Val199Met	p.V199M	ENST00000331968	NM_002742.2	199	Gtg/Atg	4/18	0.381157411838713	3	FACETS	0.923	0.865	0.981	0.923	0.865	0.981	INDETERMINATE	2	TRUE	1	0.656766833281037	3		291	425	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0023357-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	319	237	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.884778079374932	3	FACETS	0.979	0.938	1	0.979	0.938	1	CLONAL	2	TRUE	1	0.884778079374932	3		237	531	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0023357-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	321	237	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	0.884778079374932	3	FACETS	0.978	0.937	1	0.978	0.937	1	CLONAL	2	TRUE	1	0.884778079374932	3		237	535	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226174	2226174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023357-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	439	441	1	ENST00000326181.6:c.1871C>T	p.Ser624Phe	p.S624F	ENST00000326181	NM_032271.2	624	tCc/tTc	19/21	0.884778079374932	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.884778079374932	4		442	885	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252880	36252880	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023357-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	432	283	0	ENST00000300305.3:c.482T>A	p.Leu161His	p.L161H	ENST00000300305		161	cTc/cAc	4/8	0.884778079374932	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.884778079374932	3		283	659	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827262	72827262	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023357-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	507	365	0	ENST00000268489.5:c.9319C>T	p.Gln3107Ter	p.Q3107*	ENST00000268489	NM_006885.3	3107	Cag/Tag	9/10	0.884778079374932	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.884778079374932	2		365	565	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217458	7217458	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023357-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	455	412	0	ENST00000380728.2:c.338C>A	p.Ser113Ter	p.S113*	ENST00000380728		113	tCa/tAa	5/11	0.884778079374932	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.884778079374932	2		412	505	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100041	157100055	+	inframe_deletion	In_Frame_Del	DEL	AGGAGGAGCAGGAGC	AGGAGGAGCAGGAGC	-	rs773423003	NA	P-0023357-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	41	423	0	ENST00000346085.5:c.993_1007del	p.Gly333_Gly337del	p.G333_G337del	ENST00000346085	NM_020732.3	326	ggAGGAGGAGCAGGAGCa/gga	1/20	0.884778079374932	3	FACETS	0.562	0.471	0.66	0.281	0.235	0.33	SUBCLONAL	1	TRUE	1	0.884778079374932	3		423	238	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849652	68849652	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023357-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	494	335	0	ENST00000261769.5:c.1555C>T	p.Gln519Ter	p.Q519*	ENST00000261769	NM_004360.3	519	Cag/Tag	10/16	0.884778079374932	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.884778079374932	2		335	542	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016559	12016559	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023357-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	367	280	0	ENST00000353533.5:c.695C>T	p.Pro232Leu	p.P232L	ENST00000353533	NM_003010.3	232	cCt/cTt	7/11	0.884778079374932	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.884778079374932	2		280	412	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118339493	118339493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782605513	NA	P-0023357-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	177	318	0	ENST00000534358.1:c.436G>A	p.Glu146Lys	p.E146K	ENST00000534358	NM_005933.3	146	Gag/Aag	2/36	0.884778079374932	3	FACETS	0.992	0.919	1	0.496	0.459	0.533	CLONAL	1	TRUE	1	0.884778079374932	3		318	582	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911982	32911982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023357-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	297	399	0	ENST00000380152.3:c.3490C>T	p.Leu1164Phe	p.L1164F	ENST00000380152		1164	Ctt/Ttt	11/27	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.884778079374932	2		399	606	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978815	13978815	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023357-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	531	323	0	ENST00000405192.2:c.292G>C	p.Glu98Gln	p.E98Q	ENST00000405192	NM_001163147.1	98	Gaa/Caa	6/12	0.884778079374932	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.884778079374932	4		323	1076	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44733219	44733219	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023357-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	289	259	0	ENST00000377967.4:c.211G>C	p.Ala71Pro	p.A71P	ENST00000377967	NM_021140.2	71	Gcc/Ccc	2/29	0.725545236592922	5	FACETS	1	0.964	1	1	0.964	1	CLONAL	3	TRUE	2	0.884778079374932	5		259	501	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223070	41223070	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023357-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	400	452	0	ENST00000357654.3:c.4861G>A	p.Asp1621Asn	p.D1621N	ENST00000357654	NM_007294.3	1621	Gat/Aat	15/23	0.884778079374932	2	FACETS	1	0.99	1	0.557	0.534	0.581	CLONAL	1	TRUE	0	0.884778079374932	2		452	811	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247304	153247304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023357-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	203	369	0	ENST00000281708.4:c.1498C>T	p.His500Tyr	p.H500Y	ENST00000281708	NM_033632.3	500	Cat/Tat	10/12	0.857393283492208	3	FACETS	1	0.966	1	0.529	0.493	0.565	CLONAL	1	TRUE	1	0.884778079374932	3		369	626	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279976	46279978	+	missense_variant	Missense_Mutation	TNP	TGC	TGC	CGA	novel	NA	P-0023357-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	104	427	0	ENST00000371998.3:c.3902_3904delinsCGA	p.Met1301_Pro1302delinsThrThr	p.M1301_P1302delinsTT	ENST00000371998		1301	aTGCca/aCGAca	20/23	0.418812180609402	5	FACETS	0.64	0.572	0.712	0.213	0.19	0.238	INDETERMINATE	1	TRUE	2	0.884778079374932	5		427	855	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0024657-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	46	323	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	0.248238704254682	3	FACETS	0.392	0.33	0.461	0.131	0.11	0.154	INDETERMINATE	1	TRUE	0	0.508005121980016	3		323	579	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0024657-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	124	332	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.508005121980016	2		332	481	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319836	8319836	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024657-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	99	309	0	ENST00000356435.5:c.5665A>G	p.Thr1889Ala	p.T1889A	ENST00000356435		1889	Aca/Gca	34/35	1	2	FACETS	0.902	0.81	0.999	0.902	0.81	0.999	CLONAL	1	TRUE	1	0.508005121980016	2		309	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0024726-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	321	292	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.780459827434115	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	FALSE	0	0.778475123911712	2		292	361	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274248	5274282	+	frameshift_variant	Frame_Shift_Del	DEL	TCCAGGTCACTCGTGGCTTGGGGTCACCCGTGGCC	TCCAGGTCACTCGTGGCTTGGGGTCACCCGTGGCC	-	novel	NA	P-0024726-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	362	254	0	ENST00000357368.4:c.165_199del	p.Ala56GlnfsTer12	p.A56Qfs*12	ENST00000357368	NM_002850.3	55	caGGCCACGGGTGACCCCAAGCCACGAGTGACCTGGAac/caac	3/38	0.710747890089346	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	FALSE	2	0.778475123911712	4		254	741	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252793	10252793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024726-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	334	346	0	ENST00000340748.4:c.3172G>A	p.Gly1058Ser	p.G1058S	ENST00000340748		1058	Ggc/Agc	29/40	0.710747890089346	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	FALSE	2	0.778475123911712	4		346	729	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121438988	121438988	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024726-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	68	304	0	ENST00000257555.6:c.1889C>A	p.Ser630Tyr	p.S630Y	ENST00000257555		630	tCc/tAc	10/10	0.780459827434115	4	FACETS	0.48	0.417	0.548	0.12	0.104	0.137	SUBCLONAL	1	FALSE	0	0.778475123911712	4		304	647	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508932	106508932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025097-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	42	528	1	ENST00000359195.3:c.926C>T	p.Thr309Met	p.T309M	ENST00000359195	NM_002649.2	309	aCg/aTg	2/11	0.198048944118424	4	FACETS	0.799	0.672	0.938	0.799	0.672	0.938	CLONAL	2	TRUE	2	0.250983865345639	4		529	262	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21565432	21565432	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025097-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	40	518	0	ENST00000382592.4:c.454G>A	p.Val152Ile	p.V152I	ENST00000382592	NM_014572.2	152	Gtc/Atc	3/8	0.250983865345639	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.250983865345639	1		518	248	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813918	50813918	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025097-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	37	464	0	ENST00000398568.2:c.1472C>G	p.Pro491Arg	p.P491R	ENST00000398568	NM_001042412.1	491	cCa/cGa	8/18	0.16928825715372	2	FACETS	1	0.878	1	0.538	0.446	0.64	CLONAL	1	TRUE	0	0.250983865345639	2		464	274	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024662	11024662	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025097-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	31	509	0	ENST00000327064.4:c.779G>C	p.Gly260Ala	p.G260A	ENST00000327064	NM_199141.1	260	gGc/gCc	6/16	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.250983865345639	2		509	211	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495713	72495713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778318924	NA	P-0025097-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	39	412	0	ENST00000477973.2:c.359C>T	p.Thr120Ile	p.T120I	ENST00000477973	NM_012234.5	120	aCc/aTc	1/4	1	2	FACETS	0.896	0.744	1	0.896	0.744	1	CLONAL	1	TRUE	1	0.250983865345639	2		412	347	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025203-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	275	382	0				ENST00000310581	NM_198253.2	-/1132			0.531241668314038	4	FACETS	0.89	0.85	0.929	0.89	0.85	0.929	CLONAL	4	TRUE	0	0.539176871604716	4		382	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0025203-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	247	452	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.539176871604716	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.539176871604716	1		452	594	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385183	41385183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1423243089	NA	P-0025203-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	33	407	0	ENST00000373198.4:c.778C>T	p.Arg260Trp	p.R260W	ENST00000373198	NM_133170.3	260	Cgg/Tgg	6/32	NA	2	FACETS	0.21	0.17	0.254			1	INDETERMINATE	1	TRUE	NA	0.539176871604716	2		407	584	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653780	89653781	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	rs1554893747	NA	P-0025203-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	158	299	0	ENST00000371953.3:c.80-1_80del		p.X27_splice	ENST00000371953	NM_000314.4	27			0.539176871604716	1	FACETS	0.969	0.896	1	0.969	0.896	1	CLONAL	1	TRUE	0	0.539176871604716	1		299	442	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693815	47693816	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0025203-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	238	406	0	ENST00000233146.2:c.1530_1531del	p.Gln510HisfsTer2	p.Q510Hfs*2	ENST00000233146	NM_000251.2	510	cAG/c	10/16	0.188042265682276	2	FACETS	1	0.991	1	0.677	0.636	0.719	INDETERMINATE	1	TRUE	0	0.539176871604716	2		406	652	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77937713	77937714	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025203-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	33	417	0	ENST00000361507.4:c.1004dup	p.Asn335LysfsTer43	p.N335Kfs*43	ENST00000361507	NM_080491.2	335	aac/aaAc	4/10	0.202674987674888	2	FACETS	0.186	0.151	0.226	0.093	0.075	0.113	INDETERMINATE	1	TRUE	0	0.539176871604716	2		417	657	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803577	1803577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025203-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	33	505	1	ENST00000260795.2:c.755G>A	p.Arg252Gln	p.R252Q	ENST00000260795		252	cGg/cAg	6/17	0.539176871604716	1	FACETS	0.19	0.154	0.231	0.19	0.154	0.231	SUBCLONAL	1	TRUE	0	0.539176871604716	1		506	470	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589614	67589616	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0025203-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	67	318	0	ENST00000274335.5:c.1377_1379del	p.Lys459_Ser460delinsAsn	p.K459_S460delinsN	ENST00000274335		459	aaAAGt/aat	10/15	0.539176871604716	1	FACETS	0.327	0.284	0.373	0.327	0.284	0.373	SUBCLONAL	1	TRUE	0	0.539176871604716	1		318	555	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879781	123879796	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCATCAAGGGCAAA	GCCCATCAAGGGCAAA	AAAGCCATCGC	novel	NA	P-0025203-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	27	210	0	ENST00000330479.4:c.477_492delinsAAAGCCATCGC	p.Pro160LysfsTer40	p.P160Kfs*40	ENST00000330479	NM_020382.3	159	aaGCCCATCAAGGGCAAA/aaAAAGCCATCGC	4/9	0.369677414542491	1	FACETS	0.221	0.176	0.273	0.221	0.176	0.273	SUBCLONAL	1	TRUE	0	0.539176871604716	1		210	331	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0025546-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	187	329	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.384689433412735	4	FACETS	0.91	0.854	0.966	0.91	0.854	0.966	CLONAL	4	TRUE	0	0.380194824617381	4		329	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0025546-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	308	652	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.384689433412735	3	FACETS	0.967	0.919	1	0.967	0.919	1	CLONAL	3	TRUE	0	0.380194824617381	3		652	665	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732484	74732519	+	inframe_deletion	In_Frame_Del	DEL	GATCGGCTGCGAGACCTGGAACGACTCCGACTCCGG	GATCGGCTGCGAGACCTGGAACGACTCCGACTCCGG	-	rs1270919613	NA	P-0025546-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	54	0	0	ENST00000359995.5:c.390_425del	p.Ser132_Arg143del	p.S132_R143del	ENST00000359995	NM_001195427.1	130	tcCCGGAGTCGGAGTCGTTCCAGGTCTCGCAGCCGATCt/tct	2/3	0.237576651889505	5	FACETS	0.412	0.351	0.48	0.137	0.117	0.16	SUBCLONAL	1	TRUE	2	0.380194824617381	5		0	1082	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941668	48941669	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025546-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	44	159	0	ENST00000267163.4:c.983dup	p.Asn328LysfsTer2	p.N328Kfs*2	ENST00000267163	NM_000321.2	326	-/A	10/27	0.384689433412735	3	FACETS	1	0.912	1	0.723	0.621	0.829	CLONAL	2	TRUE	0	0.380194824617381	3		159	127	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902604	1902604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025546-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	69	373	0	ENST00000382891.5:c.223C>T	p.Pro75Ser	p.P75S	ENST00000382891	NM_133335.3	75	Cca/Tca	2/22	0.340785721008274	2	FACETS	0.491	0.427	0.561	0.246	0.213	0.281	SUBCLONAL	1	TRUE	0	0.380194824617381	2		373	739	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444666	78444666	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025546-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	152	349	0	ENST00000370768.2:c.23del	p.Pro8LeufsTer46	p.P8Lfs*46	ENST00000370768	NM_003902.3	8	cCt/ct	1/20	0.384689433412735	5	FACETS	1	0.977	1	0.399	0.364	0.436	CLONAL	1	TRUE	2	0.380194824617381	5		349	1048	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720717	89720717	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025546-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	29	49	0	ENST00000371953.3:c.868del	p.Val290Ter	p.V290*	ENST00000371953	NM_000314.4	290	Gta/ta	8/9	0.340785721008274	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	2	TRUE	0	0.380194824617381	2		49	67	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426578	49426592	+	inframe_deletion	In_Frame_Del	DEL	CTGCTGCTGTTGAAA	CTGCTGCTGTTGAAA	-	rs1195849154	NA	P-0025546-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	295	448	0	ENST00000301067.7:c.11896_11910del	p.Phe3966_Gln3970del	p.F3966_Q3970del	ENST00000301067	NM_003482.3	3966	TTTCAACAGCAGCAG/-	39/54	0.384689433412735	4	FACETS	1	0.986	1	0.761	0.718	0.805	CLONAL	2	TRUE	1	0.380194824617381	4		448	938	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865120	57865120	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025546-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	263	347	0	ENST00000228682.2:c.2597C>A	p.Thr866Asn	p.T866N	ENST00000228682	NM_005269.2	866	aCc/aAc	12/12	0.384689433412735	4	FACETS	0.931	0.877	0.984	0.931	0.877	0.984	CLONAL	3	TRUE	1	0.380194824617381	4		347	684	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631604	119631604	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025546-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	43	215	0	ENST00000316626.5:c.662A>T	p.Tyr221Phe	p.Y221F	ENST00000316626		221	tAc/tTc	6/12	0.384689433412735	5	FACETS	0.836	0.7	0.986	0.209	0.175	0.247	CLONAL	1	TRUE	1	0.380194824617381	5		215	425	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176940	56176940	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025546-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	57	257	0	ENST00000399503.3:c.2210T>A	p.Val737Asp	p.V737D	ENST00000399503	NM_005921.1	737	gTc/gAc	13/20	0.355806283942429	4	FACETS	1	0.96	1	0.661	0.571	0.758	CLONAL	1	TRUE	2	0.380194824617381	4		257	313	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465563	8465563	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025546-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	64	261	0	ENST00000356435.5:c.3617G>T	p.Gly1206Val	p.G1206V	ENST00000356435		1206	gGg/gTg	21/35	0.375668587132458	3	FACETS	0.938	0.815	1	0.469	0.407	0.536	CLONAL	1	TRUE	1	0.380194824617381	3		261	427	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197720	123197720	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025546-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	77	248	0	ENST00000218089.9:c.1844A>G	p.Gln615Arg	p.Q615R	ENST00000218089	NM_001042749.1	615	cAg/cGg	20/35	0.192351861542802	5	FACETS	1	0.945	1	0.739	0.656	0.826	INDETERMINATE	2	TRUE	2	0.380194824617381	5		248	287	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271162	38271162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437821654	NA	P-0025546-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	36	240	0	ENST00000425967.3:c.2546G>A	p.Gly849Glu	p.G849E	ENST00000425967	NM_001174067.1	849	gGa/gAa	19/19	0.375668587132458	3	FACETS	0.482	0.395	0.578	0.241	0.197	0.289	SUBCLONAL	1	TRUE	1	0.380194824617381	3		240	468	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50785023	50785023	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025546-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	32	151	0	ENST00000307179.4:c.2360A>T	p.Tyr787Phe	p.Y787F	ENST00000307179		787	tAt/tTt	15/20	0.15202484450917	3	FACETS	0.959	0.784	1	0.479	0.392	0.576	INDETERMINATE	1	TRUE	1	0.380194824617381	3		151	209	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38798805	38798805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025546-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	134	190	0	ENST00000348513.6:c.58C>T	p.Pro20Ser	p.P20S	ENST00000348513	NM_003079.4	20	Ccc/Tcc	4/11	0.380194824617381	5	FACETS	1	0.948	1	0.701	0.641	0.765	CLONAL	2	TRUE	2	0.380194824617381	5		190	526	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2119461	2119461	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025546-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	128	209	0	ENST00000349721.2:c.3688G>T	p.Glu1230Ter	p.E1230*	ENST00000349721	NM_003070.3	1230	Gaa/Taa	26/34	0.375668587132458	3	FACETS	0.947	0.866	1	0.947	0.866	1	CLONAL	2	TRUE	1	0.380194824617381	3		209	423	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519966	NA	P-0026202-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	105	348	0	ENST00000347630.2:c.397T>A	p.Phe133Ile	p.F133I	ENST00000347630	NM_001007230.1	133	Ttc/Atc	6/11	1	2	FACETS	0.869	0.78	0.963	0.869	0.78	0.963	CLONAL	1	TRUE	1	0.388495318715417	2		348	622	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11022869	11022869	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026202-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	114	326	0	ENST00000327064.4:c.568G>T	p.Asp190Tyr	p.D190Y	ENST00000327064	NM_199141.1	190	Gat/Tat	5/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.388495318715417	2		326	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	155	464	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.665750769665602	2		464	383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	135	508	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.665750769665602	2		508	384	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120457954	120457954	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	89	439	0	ENST00000256646.2:c.7391A>G	p.His2464Arg	p.H2464R	ENST00000256646	NM_024408.3	2464	cAc/cGc	34/34	0.332434335256113	1	FACETS	0.526	0.471	0.584	0.526	0.471	0.584	INDETERMINATE	1	TRUE	0	0.665750769665602	1		439	339	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451288	70451288	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771754741	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	128	474	0	ENST00000373644.4:c.6128G>A	p.Arg2043His	p.R2043H	ENST00000373644	NM_030625.2	2043	cGc/cAc	12/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.665750769665602	2		474	361	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	96	248	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.665750769665602	2		251	276	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925621	114925621	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763934346	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	65	373	0	ENST00000543371.1:c.1699G>A	p.Ala567Thr	p.A567T	ENST00000543371	NM_001198531.1	567	Gcc/Acc	14/14	1	2	FACETS	0.669	0.585	0.758	0.669	0.585	0.758	SUBCLONAL	1	TRUE	1	0.665750769665602	2		373	292	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274653	123274653	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	24	346	0	ENST00000358487.5:c.1265T>C	p.Ile422Thr	p.I422T	ENST00000358487	NM_000141.4	422	aTc/aCc	9/18	1	2	FACETS	0.225	0.176	0.282	0.225	0.176	0.282	SUBCLONAL	1	TRUE	1	0.665750769665602	2		346	320	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625281	69625281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35983315	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	79	534	0	ENST00000334134.2:c.512G>A	p.Arg171His	p.R171H	ENST00000334134	NM_005247.2	171	cGc/cAc	3/3	1	2	FACETS	0.726	0.644	0.812	0.726	0.644	0.812	SUBCLONAL	1	TRUE	1	0.665750769665602	2		534	327	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	136	364	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.665750769665602	2		364	400	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865315	57865316	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs747342182	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	115	365	0	ENST00000228682.2:c.2798dup	p.Ser934PhefsTer4	p.S934Ffs*4	ENST00000228682	NM_005269.2	931	ctg/ctGg	12/12	1	2	FACETS	0.902	0.82	0.987	0.902	0.82	0.987	CLONAL	1	TRUE	1	0.665750769665602	2		365	383	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041262	29041262	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	40	321	0	ENST00000282397.4:c.166del	p.Glu56LysfsTer12	p.E56Kfs*12	ENST00000282397	NM_002019.4	56	Gaa/aa	3/30	0.475969552004584	2	FACETS	0.356	0.296	0.421	0.178	0.148	0.211	SUBCLONAL	1	TRUE	0	0.665750769665602	2		321	338	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103498626	103498626	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	23	312	0	ENST00000355739.4:c.10C>T	p.Gln4Ter	p.Q4*	ENST00000355739	NM_000123.3	4	Cag/Tag	1/15	0.475969552004584	2	FACETS	0.252	0.197	0.316	0.126	0.098	0.158	SUBCLONAL	1	TRUE	0	0.665750769665602	2		312	274	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434972	110434973	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	17	407	1	ENST00000375856.3:c.3428dup	p.Arg1144ProfsTer181	p.R1144Pfs*181	ENST00000375856	NM_003749.2	1143	ggc/ggGc	1/2	0.475969552004584	2	FACETS	0.157	0.116	0.205	0.078	0.058	0.103	SUBCLONAL	1	TRUE	0	0.665750769665602	2		408	326	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748660	43748661	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	167	488	0	ENST00000382044.4:c.2145dup	p.Glu716ArgfsTer9	p.E716Rfs*9	ENST00000382044	NM_001141980.1	715	-/A	12/28	0.235872906207322	3	FACETS	0.882	0.822	0.943	0.588	0.548	0.629	INDETERMINATE	2	TRUE	0	0.665750769665602	3		488	379	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007824	45007825	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	176	382	0	ENST00000558401.1:c.276dup	p.Thr93HisfsTer2	p.T93Hfs*2	ENST00000558401	NM_004048.2	91	acc/aCcc	2/4	0.235872906207322	3	FACETS	0.935	0.874	0.996	0.623	0.582	0.664	INDETERMINATE	2	TRUE	0	0.665750769665602	3		382	377	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50733661	50733661	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1567603601	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	56	258	0	ENST00000307179.4:c.226del	p.Arg76AspfsTer36	p.R76Dfs*36	ENST00000307179		74	Aaa/aa	3/20	0.235872906207322	3	FACETS	0.723	0.624	0.831	0.241	0.208	0.277	INDETERMINATE	1	TRUE	0	0.665750769665602	3		258	310	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782948	66782948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200442489	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	64	258	0	ENST00000307102.5:c.1177G>A	p.Val393Ile	p.V393I	ENST00000307102	NM_002755.3	393	Gtc/Atc	11/11	0.235872906207322	3	FACETS	1	0.877	1	0.334	0.292	0.378	INDETERMINATE	1	TRUE	0	0.665750769665602	3		258	256	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	165	407	6	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	0.235872906207322	3	FACETS	0.89	0.829	0.952	0.594	0.553	0.635	INDETERMINATE	2	TRUE	0	0.665750769665602	3		413	371	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029333	14029333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766111215	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	131	416	0	ENST00000311895.7:c.1544G>A	p.Arg515His	p.R515H	ENST00000311895	NM_005236.2	515	cGt/cAt	8/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.665750769665602	2		416	368	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821382	72821382	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs774585182	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	39	260	1	ENST00000268489.5:c.10793del	p.Pro3598LeufsTer96	p.P3598Lfs*96	ENST00000268489	NM_006885.3	3598	cCt/ct	10/10	1	2	FACETS	0.574	0.481	0.676	0.574	0.481	0.676	SUBCLONAL	1	TRUE	1	0.665750769665602	2		261	204	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822585	72822586	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs764626362	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	74	436	0	ENST00000268489.5:c.9589dup	p.Gln3197ProfsTer42	p.Q3197Pfs*42	ENST00000268489	NM_006885.3	3197	cag/cCag	10/10	1	2	FACETS	0.619	0.546	0.697	0.619	0.546	0.697	SUBCLONAL	1	TRUE	1	0.665750769665602	2		436	359	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346436	89346436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369545274	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	100	418	0	ENST00000301030.4:c.6514G>A	p.Gly2172Arg	p.G2172R	ENST00000301030	NM_001256183.1	2172	Ggg/Agg	9/13	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.665750769665602	2		418	283	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347108	89347108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs907255990	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	114	469	0	ENST00000301030.4:c.5842G>A	p.Val1948Ile	p.V1948I	ENST00000301030	NM_001256183.1	1948	Gtt/Att	9/13	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.665750769665602	2		469	327	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687471	37687472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs760014508	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	21	383	0	ENST00000447079.4:c.4382dup	p.Thr1463AsnfsTer50	p.T1463Nfs*50	ENST00000447079	NM_015083.1	1459	tgg/tGgg	14/14	1	2	FACETS	0.171	0.131	0.217	0.171	0.131	0.217	SUBCLONAL	1	TRUE	1	0.665750769665602	2		383	370	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214058	36214058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1385766471	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	144	374	1	ENST00000222270.7:c.2884C>T	p.Arg962Cys	p.R962C	ENST00000222270	NM_014727.1	962	Cgc/Tgc	6/37	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.665750769665602	2		375	381	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416364	29416364	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs141242925	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	27	422	0	ENST00000389048.3:c.4589G>T	p.Arg1530Met	p.R1530M	ENST00000389048	NM_004304.4	1530	aGg/aTg	29/29	1	2	FACETS	0.247	0.196	0.304	0.247	0.196	0.304	SUBCLONAL	1	TRUE	1	0.665750769665602	2		422	329	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	89	415	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.679	0.606	0.755	0.679	0.606	0.755	SUBCLONAL	1	TRUE	1	0.665750769665602	2		417	394	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030648	48030648	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	25	379	0	ENST00000234420.5:c.3263del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1088	Ttc/tc	5/10	1	2	FACETS	0.205	0.161	0.255	0.205	0.161	0.255	SUBCLONAL	1	TRUE	1	0.665750769665602	2		379	367	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660807	227660808	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs747646240	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	74	471	1	ENST00000305123.5:c.2645_2647dup	p.Gln882dup	p.Q882dup	ENST00000305123	NM_005544.2	882	ccc/cAGCcc	1/2	1	2	FACETS	0.616	0.542	0.694	0.616	0.542	0.694	SUBCLONAL	1	TRUE	1	0.665750769665602	2		472	361	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	128	454	12	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	0.665750769665602	3	FACETS	1	0.975	1	0.589	0.538	0.642	CLONAL	1	TRUE	1	0.665750769665602	3		466	435	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741497	39741497	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	39	339	0	ENST00000361337.2:c.1384C>T	p.Arg462Ter	p.R462*	ENST00000361337	NM_003286.2	462	Cga/Tga	14/21	0.665750769665602	3	FACETS	0.288	0.238	0.343	0.144	0.119	0.172	SUBCLONAL	1	TRUE	1	0.665750769665602	3		339	543	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478633	57478633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1131691999	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	96	414	0	ENST00000371085.3:c.305C>T	p.Ala102Val	p.A102V	ENST00000371085	NM_000516.4	102	gCg/gTg	4/13	0.665750769665602	3	FACETS	0.699	0.624	0.778	0.349	0.312	0.389	SUBCLONAL	1	TRUE	1	0.665750769665602	3		414	550	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527551	41527551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs533244094	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	118	376	0	ENST00000263253.7:c.1442C>T	p.Pro481Leu	p.P481L	ENST00000263253	NM_001429.3	481	cCg/cTg	6/31	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.665750769665602	2		376	338	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	219	428	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	0.665750769665602	2	FACETS	0.937	0.891	0.983	0.937	0.891	0.983	CLONAL	2	TRUE	0	0.665750769665602	2		428	351	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200118	128200118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553770434	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	156	438	0	ENST00000341105.2:c.1187G>A	p.Arg396Gln	p.R396Q	ENST00000341105	NM_032638.4	396	cGg/cAg	6/6	0.665750769665602	2	FACETS	1	0.982	1	0.596	0.552	0.641	CLONAL	1	TRUE	0	0.665750769665602	2		438	393	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157231	106157231	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	142	383	0	ENST00000380013.4:c.2132A>G	p.Glu711Gly	p.E711G	ENST00000380013	NM_001127208.2	711	gAg/gGg	3/11	0.332434335256113	1	FACETS	0.765	0.706	0.825	0.765	0.706	0.825	INDETERMINATE	1	TRUE	0	0.665750769665602	1		383	372	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	144	360	2	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	0.332434335256113	1	FACETS	0.763	0.705	0.823	0.763	0.705	0.823	INDETERMINATE	1	TRUE	0	0.665750769665602	1		362	378	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294613	1294613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1389956132	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	86	479	0	ENST00000310581.5:c.388G>A	p.Ala130Thr	p.A130T	ENST00000310581	NM_198253.2	130	Gca/Aca	2/16	1	2	FACETS	0.785	0.701	0.873	0.785	0.701	0.873	SUBCLONAL	1	TRUE	1	0.665750769665602	2		479	329	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	61	313	1	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	1	2	FACETS	0.764	0.667	0.866	0.764	0.667	0.866	SUBCLONAL	1	TRUE	1	0.665750769665602	2		314	240	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	95	294	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.945	0.852	1	0.945	0.852	1	CLONAL	1	TRUE	1	0.665750769665602	2		298	302	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	177	331	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.665750769665602	2		331	245	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931452	131931452	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507178	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	108	335	9	ENST00000265335.6:c.2165del	p.Lys722ArgfsTer14	p.K722Rfs*14	ENST00000265335		719	ctA/ct	13/25	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.665750769665602	2		344	318	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323353	31323354	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	149	250	0	ENST00000412585.2:c.635_636del	p.His212ArgfsTer8	p.H212Rfs*8	ENST00000412585	NM_005514.6	212	cAC/c	4/8	0.665750769665602	3	FACETS	0.975	0.907	1	0.975	0.907	1	CLONAL	2	TRUE	1	0.665750769665602	3		250	306	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	75	353	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	0.665750769665602	3	FACETS	0.873	0.771	0.981	0.436	0.385	0.491	CLONAL	1	TRUE	1	0.665750769665602	3		353	344	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32191695	32191695	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	40	360	0	ENST00000375023.3:c.11del	p.Pro4LeufsTer39	p.P4Lfs*39	ENST00000375023	NM_004557.3	4	cCt/ct	1/30	0.665750769665602	3	FACETS	0.377	0.313	0.448	0.188	0.156	0.224	SUBCLONAL	1	TRUE	1	0.665750769665602	3		360	425	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288569	33288569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266548613	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	150	371	0	ENST00000374542.5:c.983G>A	p.Arg328His	p.R328H	ENST00000374542	NM_001141970.1	328	cGt/cAt	3/8	0.665750769665602	3	FACETS	0.776	0.718	0.835	0.776	0.718	0.835	SUBCLONAL	2	TRUE	1	0.665750769665602	3		371	387	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959079	2959079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542412710	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	250	369	0	ENST00000396946.4:c.2437G>A	p.Glu813Lys	p.E813K	ENST00000396946	NM_032415.4	813	Gag/Aag	18/25	0.585366810155015	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.665750769665602	3		369	479	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141565995	141565995	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	266	330	0	ENST00000220592.5:c.1269G>T	p.Arg423Ser	p.R423S	ENST00000220592	NM_012154.3	423	agG/agT	10/19	0.644267849995443	4	FACETS	0.975	0.929	1	0.975	0.929	1	CLONAL	3	TRUE	1	0.665750769665602	4		330	455	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636203	87636203	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	88	337	0	ENST00000277120.3:c.2368C>T	p.Arg790Ter	p.R790*	ENST00000277120		790	Cga/Tga	19/19	0.665750769665602	3	FACETS	0.908	0.81	1	0.454	0.405	0.506	CLONAL	1	TRUE	1	0.665750769665602	3		337	388	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279836	46279837	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAG	rs3830809	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	47	391	2	ENST00000371998.3:c.3789_3791dup	p.Gln1276dup	p.Q1276dup	ENST00000371998		1276	-/CAG	20/23	0.665750769665602	3	FACETS	0.382	0.322	0.448	0.191	0.161	0.224	SUBCLONAL	1	TRUE	1	0.665750769665602	3		393	493	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105640	27105640	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	21	436	0	ENST00000324856.7:c.5251A>C	p.Ser1751Arg	p.S1751R	ENST00000324856	NM_006015.4	1751	Agc/Cgc	20/20	0.332434335256113	1	FACETS	0.12	0.092	0.153	0.12	0.092	0.153	INDETERMINATE	1	TRUE	0	0.665750769665602	1		436	351	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606806	43606806	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	115	498	0	ENST00000355710.3:c.1415C>T	p.Ala472Val	p.A472V	ENST00000355710	NM_020975.4	472	gCc/gTc	7/20	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.665750769665602	2		498	345	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112764360	112764361	+	splice_region_variant,intron_variant	Splice_Region	DEL	AC	AC	-	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	18	262	0	ENST00000369452.4:c.973-3_973-2del		p.X325_splice	ENST00000369452	NM_007373.3	325			1	2	FACETS	0.25	0.189	0.323	0.25	0.189	0.323	SUBCLONAL	1	TRUE	1	0.665750769665602	2		262	216	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247506	123247506	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	70	268	1	ENST00000358487.5:c.1985A>T	p.Asn662Ile	p.N662I	ENST00000358487	NM_000141.4	662	aAt/aTt	14/18	1	2	FACETS	0.862	0.761	0.967	0.862	0.761	0.967	CLONAL	1	TRUE	1	0.665750769665602	2		269	244	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10774218	10774218	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	58	226	0	ENST00000361367.2:c.46-1G>T		p.X16_splice	ENST00000361367	NM_014633.3	16			1	2	FACETS	0.675	0.586	0.771	0.675	0.586	0.771	SUBCLONAL	1	TRUE	1	0.665750769665602	2		226	258	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424422	49424422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1255523264	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	132	359	0	ENST00000301067.7:c.13801C>T	p.Pro4601Ser	p.P4601S	ENST00000301067	NM_003482.3	4601	Ccc/Tcc	41/54	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.665750769665602	2		359	312	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442944	49442944	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368209841	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	114	335	0	ENST00000301067.7:c.3964C>T	p.Arg1322Cys	p.R1322C	ENST00000301067	NM_003482.3	1322	Cgt/Tgt	12/54	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.665750769665602	2		335	342	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869474	102869474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	151	305	0	ENST00000307046.8:c.167C>T	p.Ala56Val	p.A56V	ENST00000307046	NM_001111285.1	56	gCt/gTt	2/4	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.665750769665602	2		305	304	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623799	28623799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	34	409	0	ENST00000241453.7:c.855G>T	p.Trp285Cys	p.W285C	ENST00000241453	NM_004119.2	285	tgG/tgT	7/24	0.475969552004584	2	FACETS	0.352	0.289	0.423	0.176	0.144	0.212	SUBCLONAL	1	TRUE	0	0.665750769665602	2		409	290	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103510686	103510686	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	15	307	0	ENST00000355739.4:c.590C>A	p.Pro197His	p.P197H	ENST00000355739	NM_000123.3	197	cCc/cAc	6/15	0.475969552004584	2	FACETS	0.187	0.136	0.248	0.093	0.068	0.124	SUBCLONAL	1	TRUE	0	0.665750769665602	2		307	241	SUCCESS
SCG5	6447	MSKCC	GRCh37	15	32983960	32983960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757352985	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	19	337	0	ENST00000300175.4:c.539G>A	p.Arg180Gln	p.R180Q	ENST00000300175	NM_001144757.1	180	cGg/cAg	5/6	0.235872906207322	3	FACETS	0.202	0.153	0.261	0.067	0.051	0.087	INDETERMINATE	1	TRUE	0	0.665750769665602	3		337	376	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122321	2122321	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	69	421	0	ENST00000219476.3:c.2180del	p.Pro727LeufsTer44	p.P727Lfs*44	ENST00000219476	NM_000548.3	726	tCc/tc	20/42	1	2	FACETS	0.686	0.603	0.775	0.686	0.603	0.775	SUBCLONAL	1	TRUE	1	0.665750769665602	2		421	302	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646226	3646226	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	71	403	0	ENST00000294008.3:c.1852C>A	p.Leu618Met	p.L618M	ENST00000294008	NM_032444.2	618	Ctg/Atg	8/15	1	2	FACETS	0.927	0.822	1	0.927	0.822	1	CLONAL	1	TRUE	1	0.665750769665602	2		403	230	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779839	3779839	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	45	419	0	ENST00000262367.5:c.5209A>G	p.Ser1737Gly	p.S1737G	ENST00000262367	NM_004380.2	1737	Agc/Ggc	31/31	1	2	FACETS	0.416	0.351	0.487	0.416	0.351	0.487	SUBCLONAL	1	TRUE	1	0.665750769665602	2		419	325	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346552	89346552	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	114	471	0	ENST00000301030.4:c.6398T>C	p.Leu2133Pro	p.L2133P	ENST00000301030	NM_001256183.1	2133	cTg/cCg	9/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.665750769665602	2		471	291	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37863330	37863330	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	140	454	0	ENST00000269571.5:c.161A>G	p.Gln54Arg	p.Q54R	ENST00000269571		54	cAg/cGg	2/27	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.665750769665602	2		454	350	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40451797	40451797	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	111	297	0	ENST00000345506.4:c.583del	p.Gln195ArgfsTer4	p.Q195Rfs*4	ENST00000345506	NM_003152.3	193	agC/ag	7/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.665750769665602	2		297	263	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245820	41245820	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	14	287	0	ENST00000357654.3:c.1728del	p.Glu577AsnfsTer11	p.E577Nfs*11	ENST00000357654	NM_007294.3	576	aaA/aa	10/23	1	2	FACETS	0.177	0.128	0.237	0.177	0.128	0.237	SUBCLONAL	1	TRUE	1	0.665750769665602	2		287	237	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210495	2210495	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560836480	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	89	444	0	ENST00000398665.3:c.1102G>A	p.Ala368Thr	p.A368T	ENST00000398665	NM_032482.2	368	Gcc/Acc	13/28	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.665750769665602	2		444	231	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6216449	6216449	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	106	427	0	ENST00000252674.7:c.1274C>A	p.Ala425Asp	p.A425D	ENST00000252674	NM_005934.3	425	gCt/gAt	8/12	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.665750769665602	2		427	316	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030612	11030612	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	143	446	0	ENST00000327064.4:c.1166T>C	p.Phe389Ser	p.F389S	ENST00000327064	NM_199141.1	389	tTc/tCc	10/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.665750769665602	2		446	368	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107058	11107058	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	156	416	0	ENST00000358026.2:c.1761+2T>C		p.X587_splice	ENST00000358026	NM_001128849.1	587			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.665750769665602	2		416	430	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945427	17945427	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	25	351	1	ENST00000458235.1:c.2303C>A	p.Pro768His	p.P768H	ENST00000458235	NM_000215.3	768	cCc/cAc	17/24	1	2	FACETS	0.273	0.215	0.339	0.273	0.215	0.339	SUBCLONAL	1	TRUE	1	0.665750769665602	2		352	275	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422516	47422516	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1053684230	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	142	425	0	ENST00000404338.3:c.584T>C	p.Ile195Thr	p.I195T	ENST00000404338	NM_004491.4	195	aTa/aCa	1/6	1	2	FACETS	0.999	0.919	1	0.999	0.919	1	CLONAL	1	TRUE	1	0.665750769665602	2		425	427	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912140	50912140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	84	393	0	ENST00000440232.2:c.1874G>A	p.Gly625Glu	p.G625E	ENST00000440232	NM_002691.3	625	gGg/gAg	15/27	1	2	FACETS	0.719	0.64	0.802	0.719	0.64	0.802	SUBCLONAL	1	TRUE	1	0.665750769665602	2		393	351	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719051	52719051	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	129	375	0	ENST00000322088.6:c.827C>T	p.Pro276Leu	p.P276L	ENST00000322088	NM_014225.5	276	cCt/cTt	7/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.665750769665602	2		375	333	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026142	36026142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	42	447	0	ENST00000358208.4:c.744C>A	p.Cys248Ter	p.C248*	ENST00000358208		248	tgC/tgA	7/12	0.665750769665602	3	FACETS	0.352	0.293	0.417	0.176	0.146	0.209	SUBCLONAL	1	TRUE	1	0.665750769665602	3		447	478	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62312025	62312025	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	19	355	0	ENST00000360203.5:c.1144G>A	p.Val382Met	p.V382M	ENST00000360203	NM_001283009.1	382	Gtg/Atg	14/35	0.665750769665602	3	FACETS	0.245	0.186	0.315	0.123	0.093	0.158	SUBCLONAL	1	TRUE	1	0.665750769665602	3		355	310	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092887	29092887	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	73	306	0	ENST00000328354.6:c.1095+2T>C		p.X365_splice	ENST00000328354	NM_007194.3	365			1	2	FACETS	0.906	0.804	1	0.906	0.804	1	CLONAL	1	TRUE	1	0.665750769665602	2		306	242	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565619	41565619	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	80	250	0	ENST00000263253.7:c.4285G>T	p.Gly1429Cys	p.G1429C	ENST00000263253	NM_001429.3	1429	Ggt/Tgt	26/31	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.665750769665602	2		250	239	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713883	30713883	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143095746	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	253	460	0	ENST00000295754.5:c.1208G>A	p.Arg403His	p.R403H	ENST00000295754	NM_003242.5	403	cGt/cAt	4/7	0.665750769665602	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.665750769665602	2		460	356	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948054	178948055	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	86	344	0	ENST00000263967.3:c.2832dup	p.Phe945IlefsTer4	p.F945Ifs*4	ENST00000263967	NM_006218.2	942	-/A	20/21	0.665750769665602	2	FACETS	0.876	0.784	0.972	0.438	0.392	0.486	CLONAL	1	TRUE	0	0.665750769665602	2		344	295	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156712	55156712	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	65	363	0	ENST00000257290.5:c.3113A>G	p.Asn1038Ser	p.N1038S	ENST00000257290	NM_006206.4	1038	aAc/aGc	22/23	0.414411921282178	1	FACETS	0.509	0.446	0.575	0.509	0.446	0.575	SUBCLONAL	1	TRUE	0	0.665750769665602	1		363	256	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981095	55981095	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1435582465	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	50	275	0	ENST00000263923.4:c.604G>A	p.Ala202Thr	p.A202T	ENST00000263923	NM_002253.2	202	Gca/Aca	5/30	0.414411921282178	1	FACETS	0.482	0.414	0.554	0.482	0.414	0.554	SUBCLONAL	1	TRUE	0	0.665750769665602	1		275	208	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796904	57796904	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1181615706	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	21	477	1	ENST00000309042.7:c.1880A>G	p.Gln627Arg	p.Q627R	ENST00000309042	NM_005612.4	627	cAg/cGg	4/4	0.414411921282178	1	FACETS	0.122	0.093	0.155	0.122	0.093	0.155	SUBCLONAL	1	TRUE	0	0.665750769665602	1		478	345	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947364	38947364	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	36	279	0	ENST00000357387.3:c.4314+2T>C		p.X1438_splice	ENST00000357387	NM_152756.3	1438			1	2	FACETS	0.494	0.409	0.587	0.494	0.409	0.587	SUBCLONAL	1	TRUE	1	0.665750769665602	2		279	219	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967479	38967479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	107	386	0	ENST00000357387.3:c.1111G>A	p.Ala371Thr	p.A371T	ENST00000357387	NM_152756.3	371	Gct/Act	13/38	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.665750769665602	2		386	277	SUCCESS
APC	324	MSKCC	GRCh37	5	112177808	112177808	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	117	397	0	ENST00000257430.4:c.6520del	p.Ser2174ValfsTer8	p.S2174Vfs*8	ENST00000257430	NM_000038.5	2173	Aaa/aa	16/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.665750769665602	2		397	319	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056577	26056577	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	118	390	1	ENST00000343677.2:c.80del	p.Lys27ArgfsTer36	p.K27Rfs*36	ENST00000343677	NM_005319.3	27	aAg/ag	1/1	0.665750769665602	3	FACETS	1	0.958	1	0.547	0.497	0.599	CLONAL	1	TRUE	1	0.665750769665602	3		391	432	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250760	26250760	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	149	514	0	ENST00000446824.2:c.74C>T	p.Ala25Val	p.A25V	ENST00000446824	NM_021018.2	25	gCg/gTg	1/1	0.665750769665602	3	FACETS	1	0.958	1	0.534	0.49	0.579	CLONAL	1	TRUE	1	0.665750769665602	3		514	559	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675511	30675512	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	98	486	0	ENST00000376406.3:c.2844_2845del	p.Glu950AlafsTer65	p.E950Afs*65	ENST00000376406	NM_014641.2	948	agAGgg/aggg	8/15	0.665750769665602	3	FACETS	0.861	0.772	0.954	0.43	0.386	0.477	CLONAL	1	TRUE	1	0.665750769665602	3		486	456	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940140	31940140	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	231	527	0	ENST00000375333.2:c.282C>A	p.Phe94Leu	p.F94L	ENST00000375333	NM_032454.1	94	ttC/ttA	2/8	0.665750769665602	3	FACETS	0.995	0.939	1	0.995	0.939	1	CLONAL	2	TRUE	1	0.665750769665602	3		527	465	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150022931	150022931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	128	282	0	ENST00000253339.5:c.332C>T	p.Ala111Val	p.A111V	ENST00000253339		111	gCt/gTt	1/7	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.665750769665602	2		282	264	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559309	141559309	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	304	457	0	ENST00000220592.5:c.1492del	p.Ala498ArgfsTer11	p.A498Rfs*11	ENST00000220592	NM_012154.3	498	Gcg/cg	12/19	0.644267849995443	4	FACETS	0.968	0.925	1	0.968	0.925	1	CLONAL	3	TRUE	1	0.665750769665602	4		457	524	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2115918	2115918	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	21	348	0	ENST00000349721.2:c.3553C>A	p.Leu1185Ile	p.L1185I	ENST00000349721	NM_003070.3	1185	Ctc/Atc	25/34	0.665750769665602	2	FACETS	0.191	0.146	0.242	0.095	0.073	0.121	SUBCLONAL	1	TRUE	0	0.665750769665602	2		348	331	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27229229	27229229	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	26	273	0	ENST00000380036.4:c.3374A>G	p.Ter1125TrpextTer31	p.*1125Wext*31	ENST00000380036	NM_000459.3	1125	tAg/tGg	23/23	0.665750769665602	2	FACETS	0.321	0.255	0.397	0.161	0.127	0.199	SUBCLONAL	1	TRUE	0	0.665750769665602	2		273	243	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211515	98211515	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1564008713	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	29	389	0	ENST00000331920.6:c.3640A>G	p.Thr1214Ala	p.T1214A	ENST00000331920	NM_000264.3	1214	Acg/Gcg	22/24	0.665750769665602	3	FACETS	0.268	0.215	0.329	0.134	0.107	0.165	SUBCLONAL	1	TRUE	1	0.665750769665602	3		389	433	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402782	139402782	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	23	469	0	ENST00000277541.6:c.3227A>C	p.Gln1076Pro	p.Q1076P	ENST00000277541	NM_017617.3	1076	cAg/cCg	20/34	0.665750769665602	3	FACETS	0.204	0.159	0.257	0.102	0.079	0.129	SUBCLONAL	1	TRUE	1	0.665750769665602	3		469	451	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933302	39933302	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	17	250	0	ENST00000378444.4:c.1297A>G	p.Thr433Ala	p.T433A	ENST00000378444	NM_001123385.1	433	Acc/Gcc	4/15	1	1	FACETS	0.17	0.127	0.22	0.17	0.127	0.22	SUBCLONAL	1	TRUE	0	0.665750769665602	1		250	201	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2	229	237	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.956405025820083	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.956405025820083	1		237	231	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	246	135	1	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.956405025820083	2	FACETS	0.919	0.893	0.942	0.919	0.893	0.942	CLONAL	2	TRUE	0	0.956405025820083	2		136	280	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699369	47699369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	95	361	0	ENST00000347630.2:c.139G>A	p.Glu47Lys	p.E47K	ENST00000347630	NM_001007230.1	47	Gaa/Aaa	4/11	0.492125934745397	1	FACETS	0.229	0.205	0.255	0.229	0.205	0.255	INDETERMINATE	1	TRUE	0	0.956405025820083	1		361	452	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844241	68844241	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	237	384	0	ENST00000261769.5:c.830del	p.Pro277GlnfsTer5	p.P277Qfs*5	ENST00000261769	NM_004360.3	277	Cca/ca	6/16	0.956405025820083	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.956405025820083	1		384	248	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41489079	41489079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373061594	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	35	349	0	ENST00000263253.7:c.71C>T	p.Ser24Leu	p.S24L	ENST00000263253	NM_001429.3	24	tCg/tTg	1/31	0.956405025820083	1	FACETS	0.123	0.101	0.148	0.123	0.101	0.148	SUBCLONAL	1	TRUE	0	0.956405025820083	1		349	310	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465606	99465606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	23	458	0	ENST00000268035.6:c.2431G>A	p.Glu811Lys	p.E811K	ENST00000268035	NM_000875.3	811	Gag/Aag	11/21	0.956405025820083	1	FACETS	0.074	0.057	0.093	0.074	0.057	0.093	SUBCLONAL	1	TRUE	0	0.956405025820083	1		458	341	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254863	16254863	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	145	506	0	ENST00000375759.3:c.2128G>C	p.Glu710Gln	p.E710Q	ENST00000375759	NM_015001.2	710	Gag/Cag	11/15	0.956405025820083	1	FACETS	0.42	0.387	0.453	0.42	0.387	0.453	SUBCLONAL	1	TRUE	0	0.956405025820083	1		506	377	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787747	135787747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1467020958	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	162	385	0	ENST00000298552.3:c.835C>T	p.His279Tyr	p.H279Y	ENST00000298552	NM_001162426.1	279	Cac/Tac	9/23	0.492125934745397	1	FACETS	0.316	0.291	0.341	0.316	0.291	0.341	INDETERMINATE	1	TRUE	0	0.956405025820083	1		385	560	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961471	54961471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	83	321	0	ENST00000312783.6:c.161C>T	p.Ser54Phe	p.S54F	ENST00000312783	NM_198436.1	54	tCc/tTc	4/10	0.7014382591891	4	FACETS	0.48	0.423	0.54			1	SUBCLONAL	1	TRUE	NA	0.956405025820083	4		321	708	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972664	76972664	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	59	338	0	ENST00000373344.5:c.77C>T	p.Ser26Leu	p.S26L	ENST00000373344	NM_000489.3	26	tCa/tTa	2/35	0.476857931994974	1	FACETS	0.276	0.24	0.314	0.276	0.24	0.314	INDETERMINATE	1	TRUE	0	0.956405025820083	1		338	233	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427369	49427369	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1565779294	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	142	542	2	ENST00000301067.7:c.11119C>T	p.Arg3707Ter	p.R3707*	ENST00000301067	NM_003482.3	3707	Cga/Tga	39/54	1	2	FACETS	0.526	0.481	0.572	0.526	0.481	0.572	SUBCLONAL	1	TRUE	1	0.956405025820083	2		544	565	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257995	16257995	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1176124993	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	112	565	1	ENST00000375759.3:c.5260G>A	p.Asp1754Asn	p.D1754N	ENST00000375759	NM_015001.2	1754	Gac/Aac	11/15	0.956405025820083	1	FACETS	0.398	0.363	0.434	0.398	0.363	0.434	SUBCLONAL	1	TRUE	0	0.956405025820083	1		566	307	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058045	27058045	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	123	477	1	ENST00000324856.7:c.1753C>T	p.Gln585Ter	p.Q585*	ENST00000324856	NM_006015.4	585	Cag/Tag	3/20	0.956405025820083	1	FACETS	0.526	0.486	0.567	0.526	0.486	0.567	SUBCLONAL	1	TRUE	0	0.956405025820083	1		478	255	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185125	99185125	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	17	353	0	ENST00000074304.5:c.2527G>C	p.Glu843Gln	p.E843Q	ENST00000074304	NM_001134224.1	843	Gag/Cag	23/26	0.492125934745397	1	FACETS	0.057	0.042	0.075	0.057	0.042	0.075	INDETERMINATE	1	TRUE	0	0.956405025820083	1		353	323	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433784	49433784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760007799	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	110	531	0	ENST00000301067.7:c.7769C>T	p.Ser2590Leu	p.S2590L	ENST00000301067	NM_003482.3	2590	tCg/tTg	31/54	1	2	FACETS	0.405	0.365	0.447	0.405	0.365	0.447	SUBCLONAL	1	TRUE	1	0.956405025820083	2		531	568	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482861	67482861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	32	452	0	ENST00000327367.4:c.1265C>T	p.Ser422Phe	p.S422F	ENST00000327367	NM_005902.3	422	tCc/tTc	9/9	0.956405025820083	1	FACETS	0.105	0.085	0.128	0.105	0.085	0.128	SUBCLONAL	1	TRUE	0	0.956405025820083	1		452	331	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257344	16257344	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	130	467	0	ENST00000375759.3:c.4609G>C	p.Glu1537Gln	p.E1537Q	ENST00000375759	NM_015001.2	1537	Gaa/Caa	11/15	0.956405025820083	1	FACETS	0.411	0.378	0.446	0.411	0.378	0.446	SUBCLONAL	1	TRUE	0	0.956405025820083	1		467	345	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258310	16258310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542606165	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	27	509	0	ENST00000375759.3:c.5575C>T	p.Arg1859Trp	p.R1859W	ENST00000375759	NM_015001.2	1859	Cgg/Tgg	11/15	0.956405025820083	1	FACETS	0.08	0.063	0.099	0.08	0.063	0.099	SUBCLONAL	1	TRUE	0	0.956405025820083	1		509	368	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40879737	40879737	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	122	312	0	ENST00000428826.2:c.162G>T	p.Gln54His	p.Q54H	ENST00000428826		54	caG/caT	4/21	0.492125934745397	1	FACETS	0.357	0.326	0.389	0.357	0.326	0.389	INDETERMINATE	1	TRUE	0	0.956405025820083	1		312	373	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039363	47039363	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	225	498	2	ENST00000377604.3:c.986C>A	p.Ser329Tyr	p.S329Y	ENST00000377604	NM_001204468.1	329	tCc/tAc	10/24	0.476857931994974	1	FACETS	0.633	0.6	0.665	0.633	0.6	0.665	INDETERMINATE	1	TRUE	0	0.956405025820083	1		500	388	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972667	76972667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	62	344	0	ENST00000373344.5:c.74C>T	p.Ser25Leu	p.S25L	ENST00000373344	NM_000489.3	25	tCa/tTa	2/35	0.476857931994974	1	FACETS	0.288	0.252	0.326	0.288	0.252	0.326	INDETERMINATE	1	TRUE	0	0.956405025820083	1		344	235	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258619	16258619	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	163	593	0	ENST00000375759.3:c.5884G>A	p.Glu1962Lys	p.E1962K	ENST00000375759	NM_015001.2	1962	Gaa/Aaa	11/15	0.956405025820083	1	FACETS	0.428	0.397	0.459	0.428	0.397	0.459	SUBCLONAL	1	TRUE	0	0.956405025820083	1		593	416	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259055	153259055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	152	361	0	ENST00000281708.4:c.760G>A	p.Asp254Asn	p.D254N	ENST00000281708	NM_033632.3	254	Gat/Aat	5/12	0.492125934745397	1	FACETS	0.393	0.363	0.424	0.393	0.363	0.424	INDETERMINATE	1	TRUE	0	0.956405025820083	1		361	422	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623229	52623229	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141067977	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	20	433	0	ENST00000394830.3:c.2822C>T	p.Ser941Leu	p.S941L	ENST00000394830	NM_018313.4	941	tCa/tTa	19/30	0.956405025820083	1	FACETS	0.066	0.05	0.084	0.066	0.05	0.084	SUBCLONAL	1	TRUE	0	0.956405025820083	1		433	332	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050770	5050770	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	23	382	0	ENST00000381652.3:c.553G>C	p.Asp185His	p.D185H	ENST00000381652	NM_004972.3	185	Gat/Cat	6/25	0.492125934745397	1	FACETS	0.076	0.059	0.096	0.076	0.059	0.096	INDETERMINATE	1	TRUE	0	0.956405025820083	1		382	331	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28601408	28601408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	25	584	0	ENST00000253063.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000253063	NM_031459.4	365	Gag/Aag	8/10	0.956405025820083	1	FACETS	0.068	0.053	0.085	0.068	0.053	0.085	SUBCLONAL	1	TRUE	0	0.956405025820083	1		584	404	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103510708	103510708	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	25	413	0	ENST00000355739.4:c.612C>G	p.Ile204Met	p.I204M	ENST00000355739	NM_000123.3	204	atC/atG	6/15	0.360040467346998	1	FACETS	0.061	0.048	0.077	0.061	0.048	0.077	INDETERMINATE	1	TRUE	0	0.956405025820083	1		413	444	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165737	47165737	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	25	490	0	ENST00000409792.3:c.389C>G	p.Ser130Cys	p.S130C	ENST00000409792	NM_014159.6	130	tCt/tGt	3/21	0.956405025820083	1	FACETS	0.101	0.08	0.126	0.101	0.08	0.126	SUBCLONAL	1	TRUE	0	0.956405025820083	1		490	269	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79965953	79965953	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1408201880	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	29	407	0	ENST00000265081.6:c.617C>T	p.Ser206Leu	p.S206L	ENST00000265081	NM_002439.4	206	tCa/tTa	4/24	0.492125934745397	1	FACETS	0.077	0.061	0.094	0.077	0.061	0.094	INDETERMINATE	1	TRUE	0	0.956405025820083	1		407	413	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651981	36651981	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	35	522	0	ENST00000244741.5:c.103G>T	p.Asp35Tyr	p.D35Y	ENST00000244741	NM_000389.4	35	Gat/Tat	2/3	1	2	FACETS	0.117	0.095	0.142	0.117	0.095	0.142	SUBCLONAL	1	TRUE	1	0.956405025820083	2		522	625	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151167665	151167665	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	31	291	0	ENST00000262187.5:c.454G>T	p.Glu152Ter	p.E152*	ENST00000262187	NM_005614.3	152	Gaa/Taa	7/8	1	2	FACETS	0.141	0.114	0.172	0.141	0.114	0.172	SUBCLONAL	1	TRUE	1	0.956405025820083	2		291	459	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400009	139400009	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	42	584	0	ENST00000277541.6:c.4339G>C	p.Glu1447Gln	p.E1447Q	ENST00000277541	NM_017617.3	1447	Gag/Cag	25/34	0.492125934745397	1	FACETS	0.069	0.057	0.082	0.069	0.057	0.082	INDETERMINATE	1	TRUE	0	0.956405025820083	1		584	664	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271294	26271294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1577	280	629	0	ENST00000305910.3:c.319G>A	p.Asp107Asn	p.D107N	ENST00000305910	NM_003534.2	107	Gat/Aat	1/1	0.750912518849917	4	FACETS	0.617	0.577	0.658	0.206	0.192	0.22	SUBCLONAL	1	TRUE	1	0.956405025820083	4		629	1857	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258277	16258277	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	134	531	0	ENST00000375759.3:c.5542G>C	p.Asp1848His	p.D1848H	ENST00000375759	NM_015001.2	1848	Gac/Cac	11/15	0.956405025820083	1	FACETS	0.438	0.403	0.473	0.438	0.403	0.473	SUBCLONAL	1	TRUE	0	0.956405025820083	1		531	334	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258628	16258628	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	164	601	0	ENST00000375759.3:c.5893G>T	p.Glu1965Ter	p.E1965*	ENST00000375759	NM_015001.2	1965	Gag/Tag	11/15	0.956405025820083	1	FACETS	0.446	0.414	0.479	0.446	0.414	0.479	SUBCLONAL	1	TRUE	0	0.956405025820083	1		601	401	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258670	16258670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	165	617	0	ENST00000375759.3:c.5935G>A	p.Glu1979Lys	p.E1979K	ENST00000375759	NM_015001.2	1979	Gag/Aag	11/15	0.956405025820083	1	FACETS	0.445	0.413	0.477	0.445	0.413	0.477	SUBCLONAL	1	TRUE	0	0.956405025820083	1		617	405	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749990	162749990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	143	452	0	ENST00000367921.3:c.2522C>T	p.Ser841Leu	p.S841L	ENST00000367921	NM_006182.2	841	tCa/tTa	18/18	0.910786493938892	4	FACETS	0.598	0.545	0.654	0.199	0.181	0.218	SUBCLONAL	1	TRUE	1	0.956405025820083	4		452	978	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163309214	163309214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	128	333	0	ENST00000271452.3:c.553G>A	p.Asp185Asn	p.D185N	ENST00000271452	NM_145697.2	185	Gat/Aat	8/14	0.910786493938892	4	FACETS	0.423	0.382	0.467	0.141	0.127	0.156	SUBCLONAL	1	TRUE	1	0.956405025820083	4		333	1237	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807344	3807344	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	115	333	0	ENST00000262367.5:c.3643G>A	p.Gly1215Arg	p.G1215R	ENST00000262367	NM_004380.2	1215	Ggg/Agg	19/31	1	2	FACETS	0.438	0.396	0.482	0.438	0.396	0.482	SUBCLONAL	1	TRUE	1	0.956405025820083	2		333	549	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679981	33679981	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	172	429	0	ENST00000308377.4:c.2100C>G	p.Ile700Met	p.I700M	ENST00000308377	NM_152270.3	700	atC/atG	5/5	0.492125934745397	1	FACETS	0.289	0.266	0.312	0.289	0.266	0.312	INDETERMINATE	1	TRUE	0	0.956405025820083	1		429	650	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696704	47696704	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	99	403	0	ENST00000347630.2:c.244G>C	p.Asp82His	p.D82H	ENST00000347630	NM_001007230.1	82	Gat/Cat	5/11	0.492125934745397	1	FACETS	0.284	0.256	0.314	0.284	0.256	0.314	INDETERMINATE	1	TRUE	0	0.956405025820083	1		403	380	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226889	142226889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	152	423	0	ENST00000350721.4:c.4915G>A	p.Asp1639Asn	p.D1639N	ENST00000350721	NM_001184.3	1639	Gat/Aat	28/47	0.956405025820083	1	FACETS	0.459	0.426	0.494	0.459	0.426	0.494	SUBCLONAL	1	TRUE	0	0.956405025820083	1		423	361	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155204	106155204	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	138	459	0	ENST00000380013.4:c.105G>C	p.Gln35His	p.Q35H	ENST00000380013	NM_001127208.2	35	caG/caC	3/11	0.492125934745397	1	FACETS	0.247	0.225	0.27	0.247	0.225	0.27	INDETERMINATE	1	TRUE	0	0.956405025820083	1		459	610	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696652	176696652	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1384505425	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	193	463	0	ENST00000439151.2:c.5353G>C	p.Asp1785His	p.D1785H	ENST00000439151	NM_022455.4	1785	Gat/Cat	16/23	0.492125934745397	1	FACETS	0.327	0.303	0.35	0.327	0.303	0.35	INDETERMINATE	1	TRUE	0	0.956405025820083	1		463	645	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176700699	176700699	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	135	375	0	ENST00000439151.2:c.5536G>T	p.Glu1846Ter	p.E1846*	ENST00000439151	NM_022455.4	1846	Gag/Tag	17/23	0.492125934745397	1	FACETS	0.317	0.29	0.345	0.317	0.29	0.345	INDETERMINATE	1	TRUE	0	0.956405025820083	1		375	465	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424483	47424483	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029064-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	126	512	0	ENST00000377045.4:c.403C>A	p.His135Asn	p.H135N	ENST00000377045	NM_001654.4	135	Cat/Aat	5/16	0.476857931994974	1	FACETS	0.278	0.253	0.304	0.278	0.253	0.304	INDETERMINATE	1	TRUE	0	0.956405025820083	1		512	495	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0029787-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	497	336	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.621021172876422	7	FACETS	0.891	0.852	0.931	0.382	0.365	0.399	CLONAL	3	TRUE	0	0.621021172876422	7		336	1528	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0029787-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	834	348	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.621021172876422	7	FACETS	0.949	0.931	0.966	0.949	0.931	0.966	CLONAL	7	TRUE	0	0.621021172876422	7		348	1032	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170435	119170435	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029787-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	25	279	0	ENST00000264033.4:c.2665A>G	p.Lys889Glu	p.K889E	ENST00000264033	NM_005188.3	889	Aaa/Gaa	16/16	0.21389555237257	2	FACETS	0.164	0.129	0.205	0.082	0.064	0.103	INDETERMINATE	1	TRUE	0	0.621021172876422	2		279	490	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190345	32190345	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1304701623	NA	P-0029787-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	153	370	0	ENST00000375023.3:c.394C>T	p.Arg132Cys	p.R132C	ENST00000375023	NM_004557.3	132	Cgc/Tgc	3/30	0.491763850720018	3	FACETS	0.906	0.83	0.984	0.453	0.415	0.492	CLONAL	1	TRUE	1	0.621021172876422	3		370	713	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249091	55249091	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029787-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	466	326	0	ENST00000275493.2:c.2389T>G	p.Cys797Gly	p.C797G	ENST00000275493	NM_005228.3	797	Tgc/Ggc	20/28	0.621021172876422	7	FACETS	0.86	0.821	0.9	0.369	0.352	0.386	CLONAL	3	TRUE	0	0.621021172876422	7		326	1485	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445088	89445088	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029787-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	72	293	0	ENST00000336596.2:c.1408T>G	p.Tyr470Asp	p.Y470D	ENST00000336596	NM_005233.5	470	Tac/Gac	6/17	0.237158266177192	1	FACETS	0.332	0.291	0.377	0.332	0.291	0.377	INDETERMINATE	1	TRUE	0	0.621021172876422	1		293	481	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858447	9858447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030430-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	23	376	0	ENST00000330684.3:c.2954C>T	p.Pro985Leu	p.P985L	ENST00000330684	NM_001134407.1	985	cCt/cTt	13/13	1	2	FACETS	0.867	0.675	1	0.867	0.675	1	CLONAL	1	TRUE	1	0.12	2		376	442	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398286	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0030430-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	49	208	0	ENST00000311936.3:c.33_34delinsCT	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	11	gcTGgt/gcCTgt	2/5	1	2	FACETS	1	0.86	1	1	0.974	1	CLONAL	2	TRUE	1	0.12	2		208	403	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044861	47044861	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030430-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	17	231	0	ENST00000377604.3:c.2188del	p.Ala730GlnfsTer72	p.A730Qfs*72	ENST00000377604	NM_001204468.1	729	gtG/gt	20/24	1	1	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	0	0.12	1		231	214	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10776584	10776584	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030430-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	29	351	0	ENST00000361367.2:c.224A>G	p.Tyr75Cys	p.Y75C	ENST00000361367	NM_014633.3	75	tAt/tGt	3/25	1	2	FACETS	0.882	0.706	1	0.882	0.706	1	CLONAL	1	TRUE	1	0.12	2		351	548	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132020	176132020	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030430-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	22	283	0	ENST00000367669.3:c.747G>T	p.Lys249Asn	p.K249N	ENST00000367669	NM_022457.5	249	aaG/aaT	5/20	1	2	FACETS	0.94	0.728	1	0.94	0.728	1	CLONAL	1	TRUE	1	0.12	2		283	390	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56872914	56872914	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs777069106	NA	P-0030430-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	26	371	0	ENST00000308159.5:c.2069A>G	p.Tyr690Cys	p.Y690C	ENST00000308159	NM_014669.4	690	tAt/tGt	19/22	1	2	FACETS	0.928	0.734	1	0.928	0.734	1	CLONAL	1	TRUE	1	0.12	2		371	467	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0030729-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	771	501	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.681045863373143	7	FACETS	1	0.983	1	1	0.983	1	CLONAL	6	TRUE	1	0.681045863373143	7		501	1014	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061208	38061208	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1292426539	NA	P-0030729-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	197	551	0	ENST00000250448.2:c.781C>G	p.Arg261Gly	p.R261G	ENST00000250448	NM_004496.3	261	Cgc/Ggc	2/2	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.681045863373143	2		551	483	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139873	55139873	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs866988382	NA	P-0030729-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	102	443	0	ENST00000257290.5:c.1534C>T	p.Arg512Ter	p.R512*	ENST00000257290	NM_006206.4	512	Cga/Tga	10/23	0.268814631592717	1	FACETS	0.602	0.545	0.662	0.602	0.545	0.662	INDETERMINATE	1	TRUE	0	0.681045863373143	1		443	328	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853186	68853186	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0030729-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	122	406	0	ENST00000261769.5:c.1569T>G	p.Tyr523Ter	p.Y523*	ENST00000261769	NM_004360.3	523	taT/taG	11/16	0.681045863373143	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.681045863373143	1		406	212	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120227	70120236	+	frameshift_variant	Frame_Shift_Del	DEL	AGCAGCAGCA	AGCAGCAGCA	-	novel	NA	P-0030729-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	212	636	0	ENST00000245479.2:c.1229_1238del	p.Gln410ProfsTer57	p.Q410Pfs*57	ENST00000245479	NM_000346.3	410	cAGCAGCAGCAc/cc	3/3	0.628523592634069	3	FACETS	1	0.977	1	0.555	0.517	0.594	CLONAL	1	TRUE	1	0.681045863373143	3		636	752	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936984	48936984	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030729-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	9	330	0	ENST00000267163.4:c.752G>T	p.Arg251Leu	p.R251L	ENST00000267163	NM_000321.2	251	cGa/cTa	8/27	1	2	FACETS	0.065	0.042	0.093	0.065	0.042	0.093	SUBCLONAL	1	TRUE	1	0.681045863373143	2		330	409	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176105675	176105675	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030729-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	161	297	0	ENST00000367669.3:c.840A>C	p.Glu280Asp	p.E280D	ENST00000367669	NM_022457.5	280	gaA/gaC	7/20	0.649846876921795	4	FACETS	1	0.977	1	0.39	0.358	0.422	CLONAL	1	TRUE	1	0.681045863373143	4		297	680	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677834	47677834	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0030729-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	114	477	0	ENST00000347630.2:c.1031C>G	p.Ser344Ter	p.S344*	ENST00000347630	NM_001007230.1	344	tCa/tGa	11/11	0.628523592634069	3	FACETS	0.807	0.729	0.889	0.404	0.364	0.445	CLONAL	1	TRUE	1	0.681045863373143	3		477	556	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920137	76920137	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030948-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	26	181	0	ENST00000373344.5:c.3940G>T	p.Glu1314Ter	p.E1314*	ENST00000373344	NM_000489.3	1314	Gag/Tag	11/35	0.199433869054416	2	FACETS	0.765	0.607	0.947			1	CLONAL	1	TRUE	NA	0.209092434741895	2		181	325	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964831	15964831	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030948-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	68	411	0	ENST00000268712.3:c.5765G>C	p.Arg1922Thr	p.R1922T	ENST00000268712	NM_006311.3	1922	aGa/aCa	37/46	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.209092434741895	2		411	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0031709-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	123	304	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.445421934994503	1	FACETS	0.804	0.741	0.869	1	0.989	1	CLONAL	2	TRUE	0	0.436298254040908	1		304	274	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350825	89350825	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs761634605	NA	P-0031709-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	56	327	0	ENST00000301030.4:c.2125G>C	p.Glu709Gln	p.E709Q	ENST00000301030	NM_001256183.1	709	Gaa/Caa	9/13	1	2	FACETS	0.715	0.615	0.823	0.715	0.615	0.823	SUBCLONAL	1	TRUE	1	0.436298254040908	2		327	359	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372157	55372157	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031709-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	56	426	0	ENST00000297316.4:c.847A>T	p.Ile283Phe	p.I283F	ENST00000297316	NM_022454.3	283	Att/Ttt	2/2	0.436298254040908	6	FACETS	0.735	0.629	0.851			1	SUBCLONAL	1	TRUE	NA	0.436298254040908	6		426	654	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160165	22160165	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031709-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	63	422	0	ENST00000215832.6:c.466C>G	p.Leu156Val	p.L156V	ENST00000215832	NM_002745.4	156	Ctg/Gtg	3/9	0.445421934994503	4	FACETS	0.67	0.579	0.769	0.223	0.193	0.257	SUBCLONAL	1	TRUE	1	0.436298254040908	4		422	619	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912154	32912154	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031709-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	60	325	0	ENST00000380152.3:c.3662C>G	p.Ser1221Cys	p.S1221C	ENST00000380152		1221	tCt/tGt	11/27	0.150794013863732	4	FACETS	0.689	0.594	0.793	0.345	0.297	0.397	INDETERMINATE	1	TRUE	2	0.436298254040908	4		325	573	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624395	140624395	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031709-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	55	254	0	ENST00000288602.6:c.109T>C	p.Ser37Pro	p.S37P	ENST00000288602	NM_004333.4	37	Tcg/Ccg	1/18	0.325658367236602	4	FACETS	0.894	0.767	1	0.447	0.383	0.516	CLONAL	1	TRUE	2	0.436298254040908	4		254	405	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61323118	61323118	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031709-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	81	396	0	ENST00000283752.5:c.946G>A	p.Gly316Ser	p.G316S	ENST00000283752	NM_006919.2	316	Ggc/Agc	8/8	1	2	FACETS	0.874	0.773	0.98	0.874	0.773	0.98	CLONAL	1	TRUE	1	0.436298254040908	2		396	425	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0032070-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	29	307	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.484396219658129	2		307	106	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0032070-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	130	464	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.439530800796812	2	FACETS	0.976	0.903	1	0.976	0.903	1	CLONAL	2	TRUE	0	0.484396219658129	2		464	275	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0032070-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	150	337	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.484396219658129	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.484396219658129	3		337	221	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711962	89711962	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032070-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	28	220	0	ENST00000371953.3:c.580T>G	p.Leu194Val	p.L194V	ENST00000371953	NM_000314.4	194	Ttg/Gtg	6/9	0.484396219658129	2	FACETS	0.856	0.695	1	0.428	0.347	0.517	CLONAL	1	TRUE	0	0.484396219658129	2		220	135	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699293	18699293	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032070-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	36	302	0	ENST00000266497.5:c.3394C>A	p.Gln1132Lys	p.Q1132K	ENST00000266497		1132	Caa/Aaa	24/31	0.11660083826844	0	FACETS	0.54	0.451	0.635			1	INDETERMINATE	1	TRUE	0	0.484396219658129	0		302	142	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218339	69218339	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032070-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	43	281	0	ENST00000462284.1:c.431T>A	p.Leu144His	p.L144H	ENST00000462284	NM_002392.5	144	cTt/cAt	7/11	1	2	FACETS	0.845	0.715	0.986	0.845	0.715	0.986	CLONAL	1	TRUE	1	0.484396219658129	2		281	210	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026150	48026150	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032070-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	88	369	0	ENST00000234420.5:c.1028C>A	p.Pro343His	p.P343H	ENST00000234420	NM_000179.2	343	cCt/cAt	4/10	0.242936940842649	4	FACETS	0.817	0.731	0.907	0.817	0.731	0.907	INDETERMINATE	2	TRUE	2	0.484396219658129	4		369	330	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726737	41726737	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs760376383	NA	P-0032070-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	108	281	0	ENST00000301178.4:c.282T>A	p.Asp94Glu	p.D94E	ENST00000301178	NM_021913.4	94	gaT/gaA	2/20	0.458945658812279	3	FACETS	0.952	0.867	1	0.952	0.867	1	CLONAL	2	TRUE	1	0.484396219658129	3		281	291	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412442	63412442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032070-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	40	391	0	ENST00000330258.3:c.725C>T	p.Thr242Ile	p.T242I	ENST00000330258	NM_152424.3	242	aCa/aTa	2/2	NA	2	FACETS	0.628	0.525	0.741			1	INDETERMINATE	1	TRUE	NA	0.484396219658129	2		391	263	SUCCESS
ALB	213	MSKCC	GRCh37	4	74277781	74277781	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032070-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	54	287	0	ENST00000295897.4:c.782A>G	p.Asp261Gly	p.D261G	ENST00000295897	NM_000477.5	261	gAt/gGt	7/15	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.484396219658129	2		287	206	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0032316-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	168	869	1	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.182270750670457	3	FACETS	1	0.98	1	0.787	0.727	0.848	CLONAL	2	TRUE	0	0.280369641207228	3		870	579	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390587	139390587	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032316-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	60	950	1	ENST00000277541.6:c.7604G>T	p.Gly2535Val	p.G2535V	ENST00000277541	NM_017617.3	2535	gGc/gTc	34/34	0.170010720236534	3	FACETS	0.792	0.682	0.912	0.396	0.341	0.456	CLONAL	1	TRUE	1	0.280369641207228	3		951	616	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0032811-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	77	440	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.825	0.728	0.927	0.825	0.728	0.927	CLONAL	1	TRUE	1	0.49672696962221	2		440	376	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636204	87636204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs532184896	NA	P-0032811-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	101	452	0	ENST00000277120.3:c.2369G>A	p.Arg790Gln	p.R790Q	ENST00000277120		790	cGa/cAa	19/19	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.49672696962221	2		452	353	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898765	134898765	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032811-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	57	409	0	ENST00000398015.3:c.1823G>T	p.Arg608Leu	p.R608L	ENST00000398015	NM_004441.4	608	cGg/cTg	10/16	0.469350889357142	0	FACETS	0.494	0.428	0.563			1	SUBCLONAL	1	TRUE	0	0.49672696962221	0		409	234	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842683	68842684	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032811-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	86	510	0	ENST00000261769.5:c.621dup	p.Glu208Ter	p.E208*	ENST00000261769	NM_004360.3	207	att/aTtt	5/16	0.49672696962221	1	FACETS	0.87	0.779	0.966	0.87	0.779	0.966	CLONAL	1	TRUE	0	0.49672696962221	1		510	299	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0033313-T11-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	524	348	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.658943218425997	8	FACETS	0.944	0.914	0.974	0.944	0.914	0.974	CLONAL	6	TRUE	2	0.658943218425997	8		348	836	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0033313-T11-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	408	652	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.658943218425997	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.658943218425997	3		652	516	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976787	2976787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033313-T11-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	92	468	0	ENST00000396946.4:c.1225G>A	p.Glu409Lys	p.E409K	ENST00000396946	NM_032415.4	409	Gag/Aag	9/25	0.658943218425997	9	FACETS	0.861	0.763	0.966	0.123	0.109	0.138	CLONAL	1	TRUE	2	0.658943218425997	9		468	1072	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851515	63851515	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033453-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	71	329	0	ENST00000279873.7:c.2293G>A	p.Glu765Lys	p.E765K	ENST00000279873	NM_032199.2	765	Gag/Aag	10/10	0.390910933290304	2	FACETS	0.966	0.848	1	0.483	0.424	0.546	CLONAL	1	TRUE	0	0.390910933290304	2		329	376	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943664	9943664	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033453-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	61	265	0	ENST00000330684.3:c.1277C>A	p.Thr426Asn	p.T426N	ENST00000330684	NM_001134407.1	426	aCc/aAc	5/13	0.286360427195173	4	FACETS	0.918	0.793	1	0.459	0.396	0.526	CLONAL	1	TRUE	2	0.390910933290304	4		265	473	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418370	139418371	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0033453-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	117	307	0	ENST00000277541.6:c.201dup	p.Cys68LeufsTer75	p.C68Lfs*75	ENST00000277541	NM_017617.3	67	-/C	3/34	0.390910933290304	4	FACETS	0.911	0.827	0.999	0.607	0.551	0.666	CLONAL	2	TRUE	1	0.390910933290304	4		307	457	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214746	36214746	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781441766	NA	P-0033453-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	36	255	0	ENST00000222270.7:c.3172G>A	p.Val1058Met	p.V1058M	ENST00000222270	NM_014727.1	1058	Gtg/Atg	8/37	0.343821634160723	5	FACETS	0.862	0.71	1	0.287	0.236	0.344	CLONAL	1	TRUE	2	0.390910933290304	5		255	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0033884-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	70	322	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.7513358402572	4	FACETS	1	0.957	1	0.398	0.351	0.448	CLONAL	1	TRUE	1	0.751645479340029	4		322	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578188	7578188	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201592	NA	P-0033884-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	165	382	0	ENST00000269305.4:c.661G>T	p.Glu221Ter	p.E221*	ENST00000269305	NM_001126112.2	221	Gag/Tag	6/11	0.7513358402572	4	FACETS	0.994	0.938	1	0.994	0.938	1	CLONAL	3	TRUE	1	0.751645479340029	4		382	258	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243484	46243484	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033884-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	80	345	0	ENST00000334344.6:c.1837C>T	p.Gln613Ter	p.Q613*	ENST00000334344	NM_152641.2	613	Cag/Tag	14/21	0.7513358402572	5	FACETS	1	0.916	1	0.209	0.184	0.235	CLONAL	1	TRUE	0	0.751645479340029	5		345	434	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602284	10602302	+	frameshift_variant	Frame_Shift_Del	DEL	GGGAGCCGCCGACGGCATA	GGGAGCCGCCGACGGCATA	-	novel	NA	P-0033884-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	169	415	0	ENST00000171111.5:c.1276_1294del	p.Tyr426ThrfsTer26	p.Y426Tfs*26	ENST00000171111	NM_203500.1	426	TATGCCGTCGGCGGCTCCCac/ac	3/6	0.7513358402572	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.751645479340029	3		415	189	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868196	45868196	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033884-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	143	361	0	ENST00000391945.4:c.494G>T	p.Gly165Val	p.G165V	ENST00000391945	NM_000400.3	165	gGg/gTg	7/23	0.7513358402572	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	3	TRUE	0	0.751645479340029	3		361	173	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456429	89456429	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1257548456	NA	P-0033884-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	395	290	0	ENST00000336596.2:c.1605C>G	p.Ile535Met	p.I535M	ENST00000336596	NM_005233.5	535	atC/atG	8/17	0.571288425535883	6	FACETS	0.999	0.979	1			1	CLONAL	6	TRUE	NA	0.751645479340029	6		290	439	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424216	47424216	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033884-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	47	359	0	ENST00000377045.4:c.221G>T	p.Trp74Leu	p.W74L	ENST00000377045	NM_001654.4	74	tGg/tTg	4/16	0.7513358402572	3	FACETS	0.812	0.693	0.939	0.406	0.346	0.47	CLONAL	1	TRUE	1	0.751645479340029	3		359	212	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179176	123179176	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033884-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	58	279	0	ENST00000218089.9:c.625G>T	p.Asp209Tyr	p.D209Y	ENST00000218089	NM_001042749.1	209	Gac/Tac	8/35	0.7513358402572	3	FACETS	0.829	0.72	0.946	0.415	0.36	0.473	CLONAL	1	TRUE	1	0.751645479340029	3		279	256	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375906	118375906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033884-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	86	456	0	ENST00000534358.1:c.9299G>A	p.Gly3100Glu	p.G3100E	ENST00000534358	NM_005933.3	3100	gGa/gAa	27/36	0.7513358402572	4	FACETS	1	0.89	1	0.25	0.222	0.279	CLONAL	1	TRUE	0	0.751645479340029	4		456	401	SUCCESS
REST	5978	MSKCC	GRCh37	4	57777678	57777678	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033884-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	76	276	0	ENST00000309042.7:c.874G>A	p.Val292Ile	p.V292I	ENST00000309042	NM_005612.4	292	Gtt/Att	2/4	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.751645479340029	2		276	199	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393240	393240	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033884-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	20	372	0	ENST00000380956.4:c.88G>C	p.Asp30His	p.D30H	ENST00000380956	NM_001195286.1	30	Gac/Cac	2/9	0.727750124084502	5	FACETS	0.453	0.347	0.577	0.151	0.115	0.193	SUBCLONAL	1	TRUE	2	0.751645479340029	5		372	250	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50811808	50811808	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0033884-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	81	259	0	ENST00000398568.2:c.1085C>G	p.Ser362Ter	p.S362*	ENST00000398568	NM_001042412.1	362	tCa/tGa	7/18	0.7513358402572	3	FACETS	1	0.963	1	0.591	0.528	0.656	CLONAL	1	TRUE	1	0.751645479340029	3		259	251	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256922	16256922	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs747781851	NA	P-0033884-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	15	384	0	ENST00000375759.3:c.4187C>G	p.Ser1396Cys	p.S1396C	ENST00000375759	NM_015001.2	1396	tCt/tGt	11/15	0.7513358402572	3	FACETS	0.185	0.135	0.245	0.092	0.067	0.123	SUBCLONAL	1	TRUE	1	0.751645479340029	3		384	297	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409076	4409077	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0033884-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	33	363	0	ENST00000261254.3:c.771_772delinsAA	p.Ser257_Leu258delinsArgMet	p.S257_L258delinsRM	ENST00000261254	NM_001759.3	257	agCCtg/agAAtg	5/5	0.7513358402572	4	FACETS	0.511	0.417	0.616	0.128	0.104	0.154	SUBCLONAL	1	TRUE	0	0.751645479340029	4		363	301	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243308	123243308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033884-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	38	447	0	ENST00000358487.5:c.2205G>A	p.Met735Ile	p.M735I	ENST00000358487	NM_000141.4	735	atG/atA	17/18	0.751645479340029	7	FACETS	0.387	0.319	0.464			1	SUBCLONAL	1	TRUE	NA	0.751645479340029	7		447	752	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658666	3658666	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033884-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	21	421	2	ENST00000294008.3:c.300del	p.Thr102ProfsTer24	p.T102Pfs*24	ENST00000294008	NM_032444.2	100	acC/ac	2/15	0.7513358402572	3	FACETS	0.254	0.195	0.322	0.127	0.097	0.161	SUBCLONAL	1	TRUE	1	0.751645479340029	3		423	303	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40744858	40744865	+	frameshift_variant	Frame_Shift_Del	DEL	GTCTGGAA	GTCTGGAA	CTCT	novel	NA	P-0033884-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	133	285	1	ENST00000392038.2:c.655_662delinsAGAG	p.Phe219ArgfsTer9	p.F219Rfs*9	ENST00000392038	NM_001626.4	219	TTCCAGACc/AGAGc	8/14	0.7513358402572	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	0	0.751645479340029	3		286	159	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034194-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	38	317	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.554422319545353	5	FACETS	0.997	0.83	1	0.249	0.207	0.296	CLONAL	1	TRUE	1	0.592100848951456	5		317	243	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0034194-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	300	348	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.592100848951456	6	FACETS	1	0.97	1	1	0.97	1	CLONAL	4	TRUE	2	0.592100848951456	6		348	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1064795203	NA	P-0034194-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	488	431	0	ENST00000269305.4:c.532C>G	p.His178Asp	p.H178D	ENST00000269305	NM_001126112.2	178	Cac/Gac	5/11	0.592100848951456	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	4	TRUE	0	0.592100848951456	4		431	631	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961567	41961567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034194-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	81	317	0	ENST00000219905.7:c.475C>T	p.His159Tyr	p.H159Y	ENST00000219905	NM_001164273.1	159	Cat/Tat	2/24	0.592100848951456	3	FACETS	0.985	0.874	1	0.328	0.291	0.368	CLONAL	1	TRUE	0	0.592100848951456	3		317	360	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830178	72830178	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034194-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	97	346	0	ENST00000268489.5:c.6403C>A	p.Gln2135Lys	p.Q2135K	ENST00000268489	NM_006885.3	2135	Cag/Aag	9/10	0.580586626804901	2	FACETS	0.996	0.897	1	0.498	0.448	0.549	CLONAL	1	TRUE	0	0.592100848951456	2		346	329	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954379	48954379	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0034194-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	124	216	0	ENST00000267163.4:c.1498+2T>A		p.X500_splice	ENST00000267163	NM_000321.2	500			0.592100848951456	2	FACETS	0.911	0.845	0.976	0.911	0.845	0.976	CLONAL	2	TRUE	0	0.592100848951456	2		216	230	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034268-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	98	322	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.86	0.77	0.954	0.86	0.77	0.954	CLONAL	1	TRUE	1	0.459592568909177	2		322	496	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0034268-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	261	440	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.459592568909177	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	1	0.459592568909177	4		440	516	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50782639	50782641	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs672601306	NA	P-0034268-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	51	352	0	ENST00000307179.4:c.2155_2157del	p.Ser719del	p.S719del	ENST00000307179		717	taCTCc/tac	14/20	0.342406234945393	1	FACETS	0.45	0.383	0.522	0.45	0.383	0.522	SUBCLONAL	1	TRUE	0	0.459592568909177	1		352	380	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0034514-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	64	298	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.384024532469867	3	FACETS	0.574	0.497	0.658	0.191	0.165	0.22	SUBCLONAL	1	TRUE	0	0.448769088589071	3		298	608	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913273	NA	P-0034514-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	27	135	0	ENST00000263967.3:c.1624G>C	p.Glu542Gln	p.E542Q	ENST00000263967	NM_006218.2	542	Gaa/Caa	10/21	1	2	FACETS	0.68	0.546	0.83	0.68	0.546	0.83	SUBCLONAL	1	TRUE	1	0.448769088589071	2		135	177	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526311	189526311	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034514-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	42	369	0	ENST00000264731.3:c.575G>A	p.Trp192Ter	p.W192*	ENST00000264731	NM_003722.4	192	tGg/tAg	4/14	1	2	FACETS	0.283	0.235	0.336	0.283	0.235	0.336	SUBCLONAL	1	TRUE	1	0.448769088589071	2		369	662	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549137	21549137	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034514-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	125	337	0	ENST00000382592.4:c.3139G>C	p.Asp1047His	p.D1047H	ENST00000382592	NM_014572.2	1047	Gat/Cat	8/8	0.448769088589071	1	FACETS	0.993	0.906	1	0.993	0.906	1	CLONAL	1	TRUE	0	0.448769088589071	1		337	435	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865356	57865356	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1439280977	NA	P-0034514-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	285	293	0	ENST00000228682.2:c.2833G>A	p.Val945Met	p.V945M	ENST00000228682	NM_005269.2	945	Gtg/Atg	12/12	0.33338762900079	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.448769088589071	4		293	813	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42381403	42381403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555843091	NA	P-0034514-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	154	353	0	ENST00000221972.3:c.29C>T	p.Ala10Val	p.A10V	ENST00000221972	NM_021601.3	10	gCt/gTt	1/5	1	2	FACETS	0.986	0.905	1	0.986	0.905	1	CLONAL	1	TRUE	1	0.448769088589071	2		353	696	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914564	32914689	+	inframe_deletion	In_Frame_Del	DEL	GCTCACAAGAGAAGAAAATACTGCTATACGTACTCCAGAACATTTAATATCCCAAAAAGGCTTTTCATATAATGTGGTAAATTCATCTGCTTTCTCTGGATTTAGTACAGCAAGTGGAAAGCAAGT	GCTCACAAGAGAAGAAAATACTGCTATACGTACTCCAGAACATTTAATATCCCAAAAAGGCTTTTCATATAATGTGGTAAATTCATCTGCTTTCTCTGGATTTAGTACAGCAAGTGGAAAGCAAGT	-	novel	NA	P-0034514-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	73	372	0	ENST00000380152.3:c.6072_6197del	p.Gln2024_Val2066delinsHis	p.Q2024_V2066delinsH	ENST00000380152		2024	caGCTCACAAGAGAAGAAAATACTGCTATACGTACTCCAGAACATTTAATATCCCAAAAAGGCTTTTCATATAATGTGGTAAATTCATCTGCTTTCTCTGGATTTAGTACAGCAAGTGGAAAGCAAGTt/cat	11/27	0.416594327957197	1	FACETS	0.841	0.743	0.945	0.841	0.743	0.945	CLONAL	1	TRUE	0	0.448769088589071	1		372	300	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32931954	32931954	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764761862	NA	P-0034514-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	97	288	0	ENST00000380152.3:c.7693G>A	p.Glu2565Lys	p.E2565K	ENST00000380152		2565	Gaa/Aaa	16/27	0.416594327957197	1	FACETS	0.95	0.855	1	0.95	0.855	1	CLONAL	1	TRUE	0	0.448769088589071	1		288	353	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32899293	32899293	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs571823764	NA	P-0034514-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	84	220	0	ENST00000380152.3:c.397C>A	p.Pro133Thr	p.P133T	ENST00000380152		133	Cca/Aca	4/27	0.416594327957197	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.448769088589071	1		220	281	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910621	32910621	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034514-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	88	336	0	ENST00000380152.3:c.2129C>T	p.Ser710Leu	p.S710L	ENST00000380152		710	tCa/tTa	11/27	0.416594327957197	1	FACETS	0.805	0.718	0.896	0.805	0.718	0.896	CLONAL	1	TRUE	0	0.448769088589071	1		336	378	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549254	21549254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034514-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	130	372	0	ENST00000382592.4:c.3022G>A	p.Glu1008Lys	p.E1008K	ENST00000382592	NM_014572.2	1008	Gaa/Aaa	8/8	0.448769088589071	1	FACETS	0.826	0.753	0.902	0.826	0.753	0.902	CLONAL	1	TRUE	0	0.448769088589071	1		372	544	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549257	21549257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034514-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	125	381	0	ENST00000382592.4:c.3019G>T	p.Glu1007Ter	p.E1007*	ENST00000382592	NM_014572.2	1007	Gaa/Taa	8/8	0.448769088589071	1	FACETS	0.799	0.726	0.874	0.799	0.726	0.874	SUBCLONAL	1	TRUE	0	0.448769088589071	1		381	541	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0034524-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	121	393	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.448302522323936	2		393	494	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040911	47040911	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs782684857	NA	P-0034524-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	86	187	0	ENST00000377604.3:c.1441G>T	p.Glu481Ter	p.E481*	ENST00000377604	NM_001204468.1	481	Gag/Tag	14/24	1	1	FACETS	0.865	0.787	0.943	1	0.986	1	CLONAL	2	FALSE	0	0.448302522323936	1		187	172	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915315	32915315	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034524-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	107	344	0	ENST00000380152.3:c.6823G>T	p.Glu2275Ter	p.E2275*	ENST00000380152		2275	Gag/Tag	11/27	1	2	FACETS	0.955	0.86	1	0.955	0.86	1	CLONAL	1	FALSE	1	0.448302522323936	2		344	500	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741436	39741436	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034524-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	108	336	0	ENST00000361337.2:c.1323G>A	p.Trp441Ter	p.W441*	ENST00000361337	NM_003286.2	441	tgG/tgA	14/21	1	2	FACETS	0.941	0.848	1	0.941	0.848	1	CLONAL	1	FALSE	1	0.448302522323936	2		336	512	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425805	49425805	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034524-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	78	422	0	ENST00000301067.7:c.12683A>T	p.Gln4228Leu	p.Q4228L	ENST00000301067	NM_003482.3	4228	cAg/cTg	39/54	1	2	FACETS	0.969	0.858	1	0.969	0.858	1	CLONAL	1	FALSE	1	0.448302522323936	2		422	359	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344695	70344695	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0034524-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	61	157	0	ENST00000374080.3:c.2055+1G>T		p.X685_splice	ENST00000374080		685			1	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	0	0.448302522323936	1		157	162	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193205420	193205420	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034524-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	124	343	0	ENST00000367435.3:c.1351G>T	p.Ala451Ser	p.A451S	ENST00000367435	NM_024529.4	451	Gca/Tca	15/17	1	2	FACETS	0.99	0.899	1	0.99	0.899	1	CLONAL	1	FALSE	1	0.448302522323936	2		343	559	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436148	56436148	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034524-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	92	368	0	ENST00000407977.2:c.989G>T	p.Arg330Leu	p.R330L	ENST00000407977		330	cGa/cTa	9/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.448302522323936	2		368	350	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246518397	246518397	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0034524-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	110	296	0	ENST00000388985.4:c.165-1G>T		p.X55_splice	ENST00000388985		55			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.448302522323936	2		296	441	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77069987	77069987	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034524-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	117	396	0	ENST00000356341.3:c.553A>T	p.Thr185Ser	p.T185S	ENST00000356341	NM_002576.4	185	Acc/Tcc	6/15	NA	2	FACETS	1	0.953	1			1	INDETERMINATE	1	FALSE	NA	0.448302522323936	2		396	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0034638-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	117	371	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	0.462137429805971	2	FACETS	1	0.986	1	0.709	0.651	0.768	CLONAL	1	TRUE	0	0.609139569785687	2		371	271	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0034638-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	176	362	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.319653476031213	5	FACETS	0.919	0.858	0.981	0.919	0.858	0.981	INDETERMINATE	3	TRUE	2	0.609139569785687	5		362	401	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0034638-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	179	386	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.319653476031213	5	FACETS	1	0.979	1	0.756	0.703	0.81	INDETERMINATE	2	TRUE	2	0.609139569785687	5		386	496	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857428	68857428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034638-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	121	386	0	ENST00000261769.5:c.2063G>A	p.Cys688Tyr	p.C688Y	ENST00000261769	NM_004360.3	688	tGt/tAt	13/16	0.422880156603403	4	FACETS	1	0.986	1	0.743	0.677	0.812	CLONAL	1	TRUE	2	0.609139569785687	4		386	430	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333323	70333324	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0034638-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	72	422	1	ENST00000373644.4:c.1228_1229delinsTT	p.Gly410Phe	p.G410F	ENST00000373644	NM_030625.2	410	GGt/TTt	2/12	0.455346155665892	3	FACETS	0.854	0.751	0.964	0.427	0.375	0.482	CLONAL	1	TRUE	1	0.609139569785687	3		423	361	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337681	73337681	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034638-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	94	342	0	ENST00000377767.4:c.2035C>T	p.His679Tyr	p.H679Y	ENST00000377767	NM_014953.3	679	Cat/Tat	16/21	0.210957071192509	5	FACETS	0.994	0.896	1	0.663	0.597	0.731	INDETERMINATE	2	TRUE	2	0.609139569785687	5		342	297	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218453	36218453	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034638-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	99	407	0	ENST00000222270.7:c.4232G>T	p.Gly1411Val	p.G1411V	ENST00000222270	NM_014727.1	1411	gGg/gTg	16/37	0.210957071192509	5	FACETS	0.852	0.767	0.94	0.568	0.511	0.627	INDETERMINATE	2	TRUE	2	0.609139569785687	5		407	365	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416469	29416469	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034638-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	184	505	0	ENST00000389048.3:c.4484C>A	p.Ser1495Tyr	p.S1495Y	ENST00000389048	NM_004304.4	1495	tCc/tAc	29/29	0.455346155665892	3	FACETS	0.886	0.827	0.945	0.886	0.827	0.945	CLONAL	2	TRUE	1	0.609139569785687	3		505	445	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023704	31023704	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034638-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	146	396	0	ENST00000375687.4:c.3189G>T	p.Gln1063His	p.Q1063H	ENST00000375687	NM_015338.5	1063	caG/caT	13/13	0.484659090068228	3	FACETS	0.834	0.77	0.898	0.834	0.77	0.898	CLONAL	2	TRUE	1	0.609139569785687	3		396	375	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827952	40827952	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034638-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	87	490	0	ENST00000373198.4:c.2476C>A	p.Pro826Thr	p.P826T	ENST00000373198	NM_133170.3	826	Ccc/Acc	17/32	0.484659090068228	3	FACETS	0.894	0.796	0.997	0.447	0.398	0.499	CLONAL	1	TRUE	1	0.609139569785687	3		490	417	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521616	89521616	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034638-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	101	322	0	ENST00000336596.2:c.2693C>T	p.Pro898Leu	p.P898L	ENST00000336596	NM_005233.5	898	cCa/cTa	16/17	0.394990877391217	2	FACETS	1	0.981	1	0.666	0.606	0.727	CLONAL	1	TRUE	0	0.609139569785687	2		322	249	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151919153	151919153	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	rs1470642402	NA	P-0034638-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	101	315	0	ENST00000262189.6:c.3434-2A>T		p.X1145_splice	ENST00000262189	NM_170606.2	1145			0.399229244242172	5	FACETS	0.853	0.776	0.931	0.853	0.776	0.931	CLONAL	3	TRUE	2	0.609139569785687	5		315	248	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499759	8499759	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1297546114	NA	P-0034638-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	157	403	0	ENST00000356435.5:c.2210C>T	p.Pro737Leu	p.P737L	ENST00000356435		737	cCc/cTc	14/35	0.45442638733857	2	FACETS	1	0.99	1	0.72	0.669	0.771	CLONAL	1	TRUE	0	0.609139569785687	2		403	358	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343005	70343005	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034638-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	105	404	0	ENST00000374080.3:c.1546C>G	p.Arg516Gly	p.R516G	ENST00000374080		516	Cgt/Ggt	11/45	0.210957071192509	5	FACETS	0.784	0.707	0.864	0.522	0.471	0.576	INDETERMINATE	2	TRUE	2	0.609139569785687	5		404	421	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349640	70349640	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034638-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	117	511	0	ENST00000374080.3:c.3802A>T	p.Ile1268Phe	p.I1268F	ENST00000374080		1268	Atc/Ttc	27/45	0.210957071192509	5	FACETS	1	0.98	1	0.446	0.403	0.49	INDETERMINATE	1	TRUE	2	0.609139569785687	5		511	550	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544788	86544788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772320741	NA	P-0034638-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	114	452	0	ENST00000262426.4:c.613G>A	p.Gly205Ser	p.G205S	ENST00000262426	NM_001451.2	205	Ggc/Agc	1/2	0.422880156603403	4	FACETS	1	0.984	1	0.731	0.663	0.801	CLONAL	1	TRUE	2	0.609139569785687	4		452	412	SUCCESS
APC	324	MSKCC	GRCh37	5	112174491	112174495	+	frameshift_variant	Frame_Shift_Del	DEL	AATCA	AATCA	-	novel	NA	P-0034638-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	106	412	0	ENST00000257430.4:c.3201_3205del	p.Ser1068GlufsTer11	p.S1068Efs*11	ENST00000257430	NM_000038.5	1067	cAATCA/c	16/16	0.492634320973812	2	FACETS	0.757	0.693	0.821	0.757	0.693	0.821	SUBCLONAL	2	TRUE	0	0.609139569785687	2		412	230	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435833	56435833	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs778332855	NA	P-0034638-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	86	516	0	ENST00000407977.2:c.1304T>G	p.Leu435Arg	p.L435R	ENST00000407977		435	cTa/cGa	9/10	0.422880156603403	4	FACETS	0.806	0.714	0.903	0.403	0.357	0.452	CLONAL	1	TRUE	2	0.609139569785687	4		516	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0034913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	140	338	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.122264229540301	3	FACETS	1	0.983	1	0.449	0.409	0.491	INDETERMINATE	1	TRUE	0	0.322875762482314	3		338	748	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92355058	92355058	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	233	296	0	ENST00000265734.4:c.419G>T	p.Arg140Leu	p.R140L	ENST00000265734	NM_001259.6	140	cGa/cTa	4/8	0.322875762482314	5	FACETS	1	0.987	1	0.815	0.762	0.87	CLONAL	2	TRUE	2	0.322875762482314	5		296	876	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90645617	90645633	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	GGCCATCCCAAGCTGGA	GGCCATCCCAAGCTGGA	-	novel	NA	P-0034913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	36	195	0	ENST00000330062.3:c.-11_6del		p.*4*	ENST00000330062	NM_002168.2	?-2/452		1/11	0.080031841942064	4	FACETS	0.615	0.505	0.738	0.307	0.252	0.369	INDETERMINATE	1	TRUE	2	0.322875762482314	4		195	480	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229253	36229254	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0034913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	159	340	0	ENST00000222270.7:c.7944_7945del	p.Arg2649LeufsTer7	p.R2649Lfs*7	ENST00000222270	NM_014727.1	2648	gCC/g	37/37	0.322875762482314	5	FACETS	1	0.973	1	0.386	0.352	0.421	CLONAL	1	TRUE	2	0.322875762482314	5		340	1264	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246659	41246659	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	74	267	0	ENST00000357654.3:c.889A>T	p.Met297Leu	p.M297L	ENST00000357654	NM_007294.3	297	Atg/Ttg	10/23	0.122264229540301	3	FACETS	1	0.969	1	0.444	0.39	0.501	INDETERMINATE	1	TRUE	0	0.322875762482314	3		267	400	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129933	69129933	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	145	245	0	ENST00000288368.4:c.4687A>G	p.Thr1563Ala	p.T1563A	ENST00000288368	NM_024870.2	1563	Aca/Gca	38/40	0.224156117591807	3	FACETS	1	0.963	1	0.369	0.336	0.403	CLONAL	1	TRUE	0	0.322875762482314	3		245	943	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0036263-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	129	281	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		281	275	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0036263-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	382	479	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		479	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577138	7577138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780075	NA	P-0036263-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	183	431	0	ENST00000269305.4:c.800G>A	p.Arg267Gln	p.R267Q	ENST00000269305	NM_001126112.2	267	cGg/cAg	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		431	243	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519896	NA	P-0036263-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	240	411	0	ENST00000281708.4:c.1514G>T	p.Arg505Leu	p.R505L	ENST00000281708	NM_033632.3	505	cGc/cTc	10/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		411	520	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631271	117631271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036263-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	141	375	0	ENST00000368508.3:c.6407G>A	p.Gly2136Glu	p.G2136E	ENST00000368508	NM_002944.2	2136	gGa/gAa	40/43	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		375	314	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334828	81334828	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs769585774	NA	P-0036263-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	126	415	0	ENST00000222390.5:c.1888C>T	p.Arg630Ter	p.R630*	ENST00000222390	NM_000601.4	630	Cga/Tga	17/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		415	301	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226345	2226345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036263-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	150	546	0	ENST00000326181.6:c.1958G>A	p.Arg653Gln	p.R653Q	ENST00000326181	NM_032271.2	653	cGg/cAg	20/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		546	420	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131295	17131295	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036263-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	201	518	0	ENST00000285071.4:c.157C>T	p.Gln53Ter	p.Q53*	ENST00000285071	NM_144997.5	53	Cag/Tag	4/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		518	254	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38787089	38787089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036263-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	77	423	0	ENST00000348513.6:c.904G>A	p.Glu302Lys	p.E302K	ENST00000348513	NM_003079.4	302	Gaa/Aaa	10/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		423	614	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392116	118392116	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036263-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	191	436	0	ENST00000534358.1:c.11627A>C	p.Lys3876Thr	p.K3876T	ENST00000534358	NM_005933.3	3876	aAg/aCg	35/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		436	250	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036946-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	134	264	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.863	0.785	0.944	1	0.992	1	CLONAL	3	FALSE	1	0.150753600232842	2		264	687	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026078	48026078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs188252826	NA	P-0036946-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	86	224	1	ENST00000234420.5:c.956C>T	p.Thr319Met	p.T319M	ENST00000234420	NM_000179.2	319	aCg/aTg	4/10	1	2	FACETS	1	0.963	1	1	0.987	1	CLONAL	2	FALSE	1	0.150753600232842	2		225	473	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849152	156849152	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs768180688	NA	P-0036946-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1218	212	543	0	ENST00000524377.1:c.2044C>T	p.Arg682Cys	p.R682C	ENST00000524377	NM_002529.3	682	Cgt/Tgt	15/17	1	2	FACETS	0.983	0.911	1	1	0.993	1	CLONAL	2	FALSE	1	0.150753600232842	2		543	1430	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036946-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	140	444	0	ENST00000269305.4:c.569del	p.Pro190LeufsTer57	p.P190Lfs*57	ENST00000269305	NM_001126112.2	190	cCt/ct	6/11	0.152708701359156	1	FACETS	1	0.943	1	1	0.991	1	CLONAL	2	FALSE	0	0.150753600232842	1		444	820	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0036946-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1475	244	0	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.150753600232842	5	FACETS	1	0.982	1	0.77	0.716	0.825	CLONAL	2	FALSE	2	0.150753600232842	5		0	1719	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420213	49420213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267607237	NA	P-0036946-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	161	511	0	ENST00000301067.7:c.15536G>A	p.Arg5179His	p.R5179H	ENST00000301067	NM_003482.3	5179	cGt/cAt	48/54	1	2	FACETS	0.948	0.868	1	1	0.991	1	CLONAL	2	FALSE	1	0.150753600232842	2		511	1127	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106561	27106561	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036946-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	139	496	1	ENST00000324856.7:c.6172G>T	p.Glu2058Ter	p.E2058*	ENST00000324856	NM_006015.4	2058	Gaa/Taa	20/20	0.152708701359156	1	FACETS	0.877	0.798	0.961	1	0.989	1	CLONAL	2	FALSE	0	0.150753600232842	1		497	972	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630125	187630125	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs201488687	NA	P-0036946-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	159	467	0	ENST00000441802.2:c.857A>G	p.Asn286Ser	p.N286S	ENST00000441802	NM_005245.3	286	aAt/aGt	2/27	0.150753600232842	5	FACETS	1	0.979	1			1	CLONAL	2	FALSE	NA	0.150753600232842	5		467	1071	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945478	151945478	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036946-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	186	724	0	ENST00000262189.6:c.2041G>T	p.Glu681Ter	p.E681*	ENST00000262189	NM_170606.2	681	Gaa/Taa	14/59	0.150753600232842	1	FACETS	1	0.928	1	1	0.993	1	CLONAL	2	FALSE	0	0.150753600232842	1		724	1133	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036946-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	155	264	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.28	2		264	968	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026078	48026078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs188252826	NA	P-0036946-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	78	224	1	ENST00000234420.5:c.956C>T	p.Thr319Met	p.T319M	ENST00000234420	NM_000179.2	319	aCg/aTg	4/10	1	2	FACETS	0.997	0.877	1	0.997	0.877	1	CLONAL	1	TRUE	1	0.28	2		225	559	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849152	156849152	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs768180688	NA	P-0036946-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1247	195	543	0	ENST00000524377.1:c.2044C>T	p.Arg682Cys	p.R682C	ENST00000524377	NM_002529.3	682	Cgt/Tgt	15/17	1	2	FACETS	0.966	0.891	1	0.966	0.891	1	CLONAL	1	TRUE	1	0.28	2		543	1442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036946-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	158	444	0	ENST00000269305.4:c.569del	p.Pro190LeufsTer57	p.P190Lfs*57	ENST00000269305	NM_001126112.2	190	cCt/ct	6/11	0.3	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.28	1		444	852	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0036946-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1282	165	0	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	0.814	0.745	0.887	0.814	0.745	0.887	CLONAL	1	TRUE	1	0.28	2		0	1447	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420213	49420213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267607237	NA	P-0036946-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	185	511	0	ENST00000301067.7:c.15536G>A	p.Arg5179His	p.R5179H	ENST00000301067	NM_003482.3	5179	cGt/cAt	48/54	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.28	2		511	1304	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106561	27106561	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036946-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	165	496	1	ENST00000324856.7:c.6172G>T	p.Glu2058Ter	p.E2058*	ENST00000324856	NM_006015.4	2058	Gaa/Taa	20/20	0.3	1	FACETS	0.871	0.798	0.947	0.871	0.798	0.947	CLONAL	1	TRUE	0	0.28	1		497	1164	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630125	187630125	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs201488687	NA	P-0036946-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1325	260	467	0	ENST00000441802.2:c.857A>G	p.Asn286Ser	p.N286S	ENST00000441802	NM_005245.3	286	aAt/aGt	2/27	0.3	3	FACETS	1	0.99	1			1	CLONAL	1	TRUE	NA	0.28	3		467	1585	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945478	151945478	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036946-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1311	241	724	0	ENST00000262189.6:c.2041G>T	p.Glu681Ter	p.E681*	ENST00000262189	NM_170606.2	681	Gaa/Taa	14/59	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.28	2		724	1552	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783216	9783216	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121480-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	95	529	1	ENST00000377346.4:c.2460C>A	p.Asp820Glu	p.D820E	ENST00000377346	NM_005026.3	820	gaC/gaA	20/24	0.864751431232451	3	FACETS	1	0.921	1	0.513	0.462	0.565	CLONAL	1	NA	1	0.864751431232451	3		530	307	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417167	417167	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121480-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	147	507	0	ENST00000399788.2:c.3383C>A	p.Ala1128Glu	p.A1128E	ENST00000399788	NM_001042603.1	1128	gCa/gAa	23/28	0.864751431232451	4	FACETS	0.919	0.841	1	0.459	0.42	0.5	CLONAL	1	NA	2	0.864751431232451	4		507	690	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871133	12871134	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0121480-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	145	571	0	ENST00000228872.4:c.361_362dup	p.Pro122LeufsTer24	p.P122Lfs*24	ENST00000228872	NM_004064.3	120	-/GC	1/3	0.864751431232451	4	FACETS	1	0.953	1	0.529	0.485	0.575	CLONAL	1	NA	2	0.864751431232451	4		571	591	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432516	49432516	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121480-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	126	600	0	ENST00000301067.7:c.8623G>T	p.Ala2875Ser	p.A2875S	ENST00000301067	NM_003482.3	2875	Gcc/Tcc	34/54	0.764316069063718	6	FACETS	1	0.974	1			1	CLONAL	1	NA	NA	0.864751431232451	6		600	660	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435156	49435156	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121480-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	78	436	0	ENST00000301067.7:c.6397G>T	p.Ala2133Ser	p.A2133S	ENST00000301067	NM_003482.3	2133	Gcc/Tcc	31/54	0.764316069063718	6	FACETS	1	0.976	1			1	CLONAL	1	NA	NA	0.864751431232451	6		436	341	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029430	16029430	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121480-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	146	336	0	ENST00000268712.3:c.1600G>T	p.Asp534Tyr	p.D534Y	ENST00000268712	NM_006311.3	534	Gat/Tat	15/46	0.864751431232451	3	FACETS	0.79	0.724	0.859	0.395	0.362	0.43	SUBCLONAL	1	NA	1	0.864751431232451	3		336	612	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772478	56772478	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0121480-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	144	496	0	ENST00000337432.4:c.332T>C	p.Leu111Pro	p.L111P	ENST00000337432	NM_058216.2	111	cTt/cCt	2/9	0.864751431232451	5	FACETS	0.964	0.879	1	0.321	0.293	0.351	CLONAL	1	NA	2	0.864751431232451	5		496	794	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58725318	58725318	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121480-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	172	377	0	ENST00000305921.3:c.892G>T	p.Val298Phe	p.V298F	ENST00000305921	NM_003620.3	298	Gtc/Ttc	4/6	0.864751431232451	5	FACETS	1	0.981	1	0.399	0.368	0.432	CLONAL	1	NA	2	0.864751431232451	5		377	763	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796972	78796973	+	missense_variant	Missense_Mutation	DNP	GC	GC	CT	novel	NA	P-0121480-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	84	511	0	ENST00000306801.3:c.1085_1086delinsCT	p.Cys362Ser	p.C362S	ENST00000306801	NM_020761.2	362	tGC/tCT	9/34	0.864751431232451	5	FACETS	0.643	0.568	0.724	0.214	0.189	0.242	SUBCLONAL	1	NA	2	0.864751431232451	5		511	694	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636934	158636934	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121480-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	151	545	0	ENST00000263640.3:c.246G>T	p.Lys82Asn	p.K82N	ENST00000263640	NM_001105.4	82	aaG/aaT	4/11	0.864751431232451	3	FACETS	1	0.978	1	0.582	0.537	0.628	CLONAL	1	NA	1	0.864751431232451	3		545	430	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117717425	117717425	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0121480-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	120	456	0	ENST00000368508.3:c.782T>A	p.Phe261Tyr	p.F261Y	ENST00000368508	NM_002944.2	261	tTt/tAt	8/43	0.864751431232451	3	FACETS	0.92	0.837	1	0.46	0.418	0.503	CLONAL	1	NA	1	0.864751431232451	3		456	432	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468213	50468213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0121480-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	193	590	1	ENST00000331340.3:c.1448G>A	p.Cys483Tyr	p.C483Y	ENST00000331340	NM_006060.4	483	tGc/tAc	8/8	0.654965375693738	3	FACETS	0.975	0.921	1	0.975	0.921	1	CLONAL	2	NA	1	0.864751431232451	3		591	328	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103525695	103525695	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0121480-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	105	266	0	ENST00000355739.4:c.2964+2T>G		p.X988_splice	ENST00000355739	NM_000123.3	988			1	2	FACETS	0.903	0.822	0.985	0.903	0.822	0.985	CLONAL	1	NA	1	0.864751431232451	2		266	269	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50786469	50786469	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121480-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	122	362	0	ENST00000307179.4:c.2650C>A	p.Leu884Ile	p.L884I	ENST00000307179		884	Cta/Ata	16/20	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	NA	1	0.864751431232451	2		362	277	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244426	41244426	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs397509035	NA	P-0121480-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	163	411	0	ENST00000357654.3:c.3122C>G	p.Ser1041Ter	p.S1041*	ENST00000357654	NM_007294.3	1041	tCa/tGa	10/23	0.864751431232451	5	FACETS	0.9	0.826	0.978	0.3	0.275	0.326	CLONAL	1	NA	2	0.864751431232451	5		411	962	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326263	62326263	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121480-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	100	545	0	ENST00000360203.5:c.3279C>A	p.Asp1093Glu	p.D1093E	ENST00000360203	NM_001283009.1	1093	gaC/gaA	32/35	0.864751431232451	4	FACETS	0.914	0.82	1	0.305	0.273	0.338	CLONAL	1	NA	1	0.864751431232451	4		545	472	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564454	41564454	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121480-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	142	325	0	ENST00000263253.7:c.3876G>T	p.Arg1292Ser	p.R1292S	ENST00000263253	NM_001429.3	1292	agG/agT	24/31	0.864751431232451	3	FACETS	0.954	0.876	1	0.318	0.292	0.346	CLONAL	1	NA	0	0.864751431232451	3		325	493	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783216	9783216	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121480-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	188	529	1	ENST00000377346.4:c.2460C>A	p.Asp820Glu	p.D820E	ENST00000377346	NM_005026.3	820	gaC/gaA	20/24	0.587366576128095	3	FACETS	1	0.94	1	0.509	0.471	0.548	CLONAL	1	NA	1	0.646110780334167	3		530	757	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417167	417167	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121480-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	126	507	0	ENST00000399788.2:c.3383C>A	p.Ala1128Glu	p.A1128E	ENST00000399788	NM_001042603.1	1128	gCa/gAa	23/28	0.505414966736607	4	FACETS	0.881	0.798	0.967	0.294	0.266	0.323	CLONAL	1	NA	1	0.646110780334167	4		507	729	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871133	12871134	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0121480-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	140	571	0	ENST00000228872.4:c.361_362dup	p.Pro122LeufsTer24	p.P122Lfs*24	ENST00000228872	NM_004064.3	120	-/GC	1/3	0.505414966736607	4	FACETS	0.853	0.777	0.933	0.284	0.259	0.311	CLONAL	1	NA	1	0.646110780334167	4		571	836	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432516	49432516	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121480-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	140	600	0	ENST00000301067.7:c.8623G>T	p.Ala2875Ser	p.A2875S	ENST00000301067	NM_003482.3	2875	Gcc/Tcc	34/54	0.505414966736607	4	FACETS	0.821	0.747	0.898	0.274	0.249	0.3	CLONAL	1	NA	1	0.646110780334167	4		600	869	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435156	49435156	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121480-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	98	436	0	ENST00000301067.7:c.6397G>T	p.Ala2133Ser	p.A2133S	ENST00000301067	NM_003482.3	2133	Gcc/Tcc	31/54	0.505414966736607	4	FACETS	0.841	0.751	0.935	0.28	0.25	0.312	CLONAL	1	NA	1	0.646110780334167	4		436	594	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772478	56772478	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0121480-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	173	496	0	ENST00000337432.4:c.332T>C	p.Leu111Pro	p.L111P	ENST00000337432	NM_058216.2	111	cTt/cCt	2/9	0.593850778108571	5	FACETS	0.895	0.822	0.971	0.298	0.274	0.324	CLONAL	1	NA	2	0.646110780334167	5		496	1178	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796972	78796973	+	missense_variant	Missense_Mutation	DNP	GC	GC	CT	novel	NA	P-0121480-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	123	511	0	ENST00000306801.3:c.1085_1086delinsCT	p.Cys362Ser	p.C362S	ENST00000306801	NM_020761.2	362	tGC/tCT	9/34	0.524221357901866	4	FACETS	0.853	0.772	0.938	0.284	0.257	0.313	CLONAL	1	NA	1	0.646110780334167	4		511	735	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636934	158636934	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121480-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	179	545	0	ENST00000263640.3:c.246G>T	p.Lys82Asn	p.K82N	ENST00000263640	NM_001105.4	82	aaG/aaT	4/11	0.646110780334167	3	FACETS	0.915	0.845	0.988	0.458	0.422	0.494	CLONAL	1	NA	1	0.646110780334167	3		545	801	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117717425	117717425	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0121480-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	117	456	0	ENST00000368508.3:c.782T>A	p.Phe261Tyr	p.F261Y	ENST00000368508	NM_002944.2	261	tTt/tAt	8/43	0.646110780334167	3	FACETS	0.886	0.802	0.973	0.443	0.401	0.487	CLONAL	1	NA	1	0.646110780334167	3		456	541	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468213	50468213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0121480-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	244	590	1	ENST00000331340.3:c.1448G>A	p.Cys483Tyr	p.C483Y	ENST00000331340	NM_006060.4	483	tGc/tAc	8/8	0.320362831192102	5	FACETS	1	0.984	1	0.753	0.708	0.799	INDETERMINATE	2	NA	2	0.646110780334167	5		591	658	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50786469	50786469	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121480-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	102	362	0	ENST00000307179.4:c.2650C>A	p.Leu884Ile	p.L884I	ENST00000307179		884	Cta/Ata	16/20	1	2	FACETS	0.918	0.829	1	0.918	0.829	1	CLONAL	1	NA	1	0.646110780334167	2		362	344	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326263	62326263	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121480-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	94	545	0	ENST00000360203.5:c.3279C>A	p.Asp1093Glu	p.D1093E	ENST00000360203	NM_001283009.1	1093	gaC/gaA	32/35	0.646110780334167	4	FACETS	0.843	0.752	0.94	0.281	0.25	0.314	CLONAL	1	NA	1	0.646110780334167	4		545	568	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562324	176562324	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1046092949	NA	P-0121480-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	100	585	0	ENST00000439151.2:c.220A>G	p.Arg74Gly	p.R74G	ENST00000439151	NM_022455.4	74	Aga/Gga	2/23	0.646110780334167	3	FACETS	0.662	0.592	0.735	0.331	0.296	0.368	SUBCLONAL	1	NA	1	0.646110780334167	3		585	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0038287-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	212	464	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.972	0.912	1	0.972	0.912	1	CLONAL	1	TRUE	1	0.860161697680819	2		464	507	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0038287-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	189	284	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.860161697680819	2		284	436	SUCCESS
APC	324	MSKCC	GRCh37	5	112175198	112175198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038287-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	213	376	0	ENST00000257430.4:c.3907C>T	p.Gln1303Ter	p.Q1303*	ENST00000257430	NM_000038.5	1303	Caa/Taa	16/16	1	2	FACETS	0.864	0.809	0.921	0.864	0.809	0.921	CLONAL	1	TRUE	1	0.860161697680819	2		376	573	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591125	67591125	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038287-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	214	346	0	ENST00000274335.5:c.1718T>C	p.Leu573Pro	p.L573P	ENST00000274335		573	cTg/cCg	12/15	1	2	FACETS	0.983	0.923	1	0.983	0.923	1	CLONAL	1	TRUE	1	0.860161697680819	2		346	506	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961688	41961688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038287-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	149	468	1	ENST00000219905.7:c.596G>A	p.Arg199His	p.R199H	ENST00000219905	NM_001164273.1	199	cGt/cAt	2/24	0.434331812039108	1	FACETS	0.385	0.354	0.417	0.385	0.354	0.417	INDETERMINATE	1	TRUE	0	0.860161697680819	1		469	513	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26956950	26956950	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0038287-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	217	216	0	ENST00000381527.3:c.457-1G>T		p.X153_splice	ENST00000381527	NM_001260.1	153			0.860165257850408	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.860161697680819	1		216	275	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332763	153332763	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0038287-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	524	488	0	ENST00000281708.4:c.193A>T	p.Arg65Ter	p.R65*	ENST00000281708	NM_033632.3	65	Aga/Tga	2/12	0.860165257850408	2	FACETS	0.976	0.955	0.996	0.976	0.955	0.996	CLONAL	2	TRUE	0	0.860161697680819	2		488	624	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633858	86633858	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038287-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	197	297	0	ENST00000274376.6:c.967T>G	p.Leu323Val	p.L323V	ENST00000274376	NM_002890.2	323	Tta/Gta	5/25	1	2	FACETS	0.861	0.804	0.919	0.861	0.804	0.919	CLONAL	1	TRUE	1	0.860161697680819	2		297	532	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075445	8075554	+	splice_acceptor_variant,splice_donor_variant,intron_variant	Splice_Site	DEL	CTGAAAGGAGAGGAAGCTACTTTGGTCATAAGCGAAGAGCAATCACAGCCTCTCCCATTTTAGTGTCACATATTTATCCAGATTACAGCAGCATTACATCCTCTACTTAC	CTGAAAGGAGAGGAAGCTACTTTGGTCATAAGCGAAGAGCAATCACAGCCTCTCCCATTTTAGTGTCACATATTTATCCAGATTACAGCAGCATTACATCCTCTACTTAC	-	novel	NA	P-0038287-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	121	377	0	ENST00000377482.5:c.125+1_126-1del		p.X42_splice	ENST00000377482	NM_018948.3	42			0.503789726187256	1	FACETS	0.268	0.242	0.294	0.268	0.242	0.294	INDETERMINATE	1	TRUE	0	0.860161697680819	1		377	599	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0038287-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	401	260	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.859691111992283	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.860161697680819	2		260	452	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074456	8075366	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTGGAATGAACGAGAGATATTAATAAAAGATCAACAATCCTCTCTCCACCTGTGTGAGGGAGAGAGCACCCCAGCTACCTATGCTTCCACAGCTTTCTTCCTGAGTGAAACACTTGACTGCTGTCACCCCGAGAACACCCATGCAACCACCACAGGTGTAATTAGAGAGCAGAAGATTCTTAACGCACATGGTGTGGTTCAAAGAACAAACTATCTCCTCTATCTCCCTTGGACATGTGCACAGCGCACACCCACACATCACAGGCAAGTTTTGTGACGTGTGTAAAATTCGCGGAAGATGAATAGCATATAATTTACATGAATACCATACTGTACCAGCCTTGCCATTTAAGACATGCGACCATACTAGGCACGTAGGGTACCAATGAGATAAGACAAAGTCCTTATTGCTGGCACATCATAATATTGTGAGTGAATGGACTTGCCTGCAATGTGTTCAGTTCACACACAGCTCTTGACAAAGATCCAAGGAACAGAATATTCACATTAAAAATACTATTTTTTAAGTTTTGAGGAACATTTATACTATTTTCATCTATTACTGTCAAACATGCATTCGATACTAGTAAGAAAGGTGGGAAATCTCGCCTAAGGTTTCATGAAGTAAAGTATGCATCAGAGCTGGAATGAGAACTAATTCTTGATTTTAGAAGATCCCACGTCCATGAACAGTCCTACTTAGCAATCAGTGACTCAGAATGAAGGCAGTCGAGTACAATAGCTTGAGAAAAACACAGTTATCTTCTGAATCTGTTGCCACTAGGGGTCAGGCTGTTGTTGGAAATAGTTCAGGTTTCCTCATTTAAAAAATAATGCTGGAGGACAAGCTAACCCGAATCCAGACTGTTCTTCTCAAATGCTTACTGTGATCAGATTTTCAGAATACATA	CCTGGAATGAACGAGAGATATTAATAAAAGATCAACAATCCTCTCTCCACCTGTGTGAGGGAGAGAGCACCCCAGCTACCTATGCTTCCACAGCTTTCTTCCTGAGTGAAACACTTGACTGCTGTCACCCCGAGAACACCCATGCAACCACCACAGGTGTAATTAGAGAGCAGAAGATTCTTAACGCACATGGTGTGGTTCAAAGAACAAACTATCTCCTCTATCTCCCTTGGACATGTGCACAGCGCACACCCACACATCACAGGCAAGTTTTGTGACGTGTGTAAAATTCGCGGAAGATGAATAGCATATAATTTACATGAATACCATACTGTACCAGCCTTGCCATTTAAGACATGCGACCATACTAGGCACGTAGGGTACCAATGAGATAAGACAAAGTCCTTATTGCTGGCACATCATAATATTGTGAGTGAATGGACTTGCCTGCAATGTGTTCAGTTCACACACAGCTCTTGACAAAGATCCAAGGAACAGAATATTCACATTAAAAATACTATTTTTTAAGTTTTGAGGAACATTTATACTATTTTCATCTATTACTGTCAAACATGCATTCGATACTAGTAAGAAAGGTGGGAAATCTCGCCTAAGGTTTCATGAAGTAAAGTATGCATCAGAGCTGGAATGAGAACTAATTCTTGATTTTAGAAGATCCCACGTCCATGAACAGTCCTACTTAGCAATCAGTGACTCAGAATGAAGGCAGTCGAGTACAATAGCTTGAGAAAAACACAGTTATCTTCTGAATCTGTTGCCACTAGGGGTCAGGCTGTTGTTGGAAATAGTTCAGGTTTCCTCATTTAAAAAATAATGCTGGAGGACAAGCTAACCCGAATCCAGACTGTTCTTCTCAAATGCTTACTGTGATCAGATTTTCAGAATACATA	-	novel	NA	P-0038287-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	129	331	0	ENST00000377482.5:c.202+2_203del		p.X68_splice	ENST00000377482	NM_018948.3	68		4/4	0.503789726187256	1	FACETS	0.331	0.302	0.362	0.331	0.302	0.362	INDETERMINATE	1	TRUE	0	0.860161697680819	1		331	516	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104353792	104353792	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038287-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	150	366	0	ENST00000369902.3:c.726G>T	p.Glu242Asp	p.E242D	ENST00000369902	NM_016169.3	242	gaG/gaT	6/12	0.297270775396532	1	FACETS	0.478	0.441	0.515	0.478	0.441	0.515	INDETERMINATE	1	TRUE	0	0.860161697680819	1		366	416	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139818433	139818433	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038287-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	197	355	0	ENST00000247668.2:c.1268G>T	p.Arg423Leu	p.R423L	ENST00000247668	NM_021138.3	423	cGg/cTg	10/11	0.503789726187256	1	FACETS	0.709	0.668	0.75	0.709	0.668	0.75	INDETERMINATE	1	TRUE	0	0.860161697680819	1		355	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039940-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	184	361	0	ENST00000269305.4:c.859G>T	p.Glu287Ter	p.E287*	ENST00000269305	NM_001126112.2	287	Gag/Tag	8/11	0.827265715702708	1	FACETS	0.669	0.627	0.711	0.669	0.627	0.711	SUBCLONAL	1	TRUE	0	0.843377312322175	1		361	377	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0039940-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	317	433	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.843377312322175	2		433	708	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958127	2958127	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs769192567	NA	P-0039940-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	64	321	0	ENST00000396946.4:c.2605C>T	p.Arg869Trp	p.R869W	ENST00000396946	NM_032415.4	869	Cgg/Tgg	19/25	NA	2	FACETS	0.347	0.301	0.397			1	INDETERMINATE	1	TRUE	NA	0.843377312322175	2		321	437	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947590	48947590	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039940-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	56	195	0	ENST00000267163.4:c.1177A>T	p.Ser393Cys	p.S393C	ENST00000267163	NM_000321.2	393	Agt/Tgt	12/27	0.843377312322175	1	FACETS	0.668	0.592	0.743	0.668	0.592	0.743	SUBCLONAL	1	TRUE	0	0.843377312322175	1		195	115	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128420031	128420031	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039940-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	78	287	0	ENST00000265960.3:c.397C>G	p.Pro133Ala	p.P133A	ENST00000265960	NM_001006617.1	133	Cct/Gct	4/12	1	2	FACETS	0.462	0.408	0.52	0.462	0.408	0.52	SUBCLONAL	1	TRUE	1	0.843377312322175	2		287	400	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965503	18965503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043001-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	22	364	2	ENST00000262803.5:c.1250C>T	p.Ser417Leu	p.S417L	ENST00000262803	NM_002911.3	417	tCg/tTg	9/24	1	2	FACETS	0.927	0.718	1	0.927	0.718	1	CLONAL	1	TRUE	1	0.13	2		366	365	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713818	30713818	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043001-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	20	473	0	ENST00000295754.5:c.1143G>T	p.Lys381Asn	p.K381N	ENST00000295754	NM_003242.5	381	aaG/aaT	4/7	1	2	FACETS	0.793	0.605	1	0.793	0.605	1	CLONAL	1	TRUE	1	0.13	2		473	388	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0043051-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	92	209	0				ENST00000310581	NM_198253.2	-/1132			0.522483702437477	6	FACETS	0.919	0.834	1	0.919	0.834	1	CLONAL	3	TRUE	3	0.78893650689034	6		209	218	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249853	133249853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854842	NA	P-0043051-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	208	227	0	ENST00000320574.5:c.1370C>T	p.Thr457Met	p.T457M	ENST00000320574	NM_006231.2	457	aCg/aTg	14/49	0.22739322953461	3	FACETS	0.996	0.942	1	0.996	0.942	1	INDETERMINATE	2	TRUE	1	0.78893650689034	3		227	369	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112491	115112495	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGG	AAAGG	-	novel	NA	P-0043051-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	113	336	0	ENST00000257566.3:c.1245_1249del	p.Leu416ArgfsTer3	p.L416Rfs*3	ENST00000257566	NM_016569.3	415	caCCTTTtc/catc	7/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.78893650689034	2		336	269	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310891	123310891	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043051-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	22	250	0	ENST00000358487.5:c.537C>A	p.Cys179Ter	p.C179*	ENST00000358487	NM_000141.4	179	tgC/tgA	5/18	1	2	FACETS	0.153	0.118	0.194	0.153	0.118	0.194	SUBCLONAL	1	TRUE	1	0.78893650689034	2		250	364	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0043184-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	225	334	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.434054310979161	4	FACETS	0.877	0.829	0.924	0.877	0.829	0.924	CLONAL	4	TRUE	0	0.433808103022229	4		334	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0043184-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	156	508	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.338012676591909	2	FACETS	0.929	0.862	0.998	0.929	0.862	0.998	CLONAL	2	TRUE	0	0.433808103022229	2		508	387	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111562	8111562	+	splice_donor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0043184-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	110	285	0	ENST00000346208.3:c.1047+1del		p.X349_splice	ENST00000346208		349			0.135751745516708	6	FACETS	0.976	0.882	1	0.651	0.588	0.717	INDETERMINATE	2	TRUE	3	0.433808103022229	6		285	485	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574494	41574494	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043184-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	139	359	0	ENST00000263253.7:c.6779A>G	p.Tyr2260Cys	p.Y2260C	ENST00000263253	NM_001429.3	2260	tAt/tGt	31/31	0.433808103022229	2	FACETS	0.895	0.825	0.966	0.895	0.825	0.966	CLONAL	2	TRUE	0	0.433808103022229	2		359	358	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933512	49933512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771786833	NA	P-0043184-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	115	387	0	ENST00000296474.3:c.2678G>A	p.Cys893Tyr	p.C893Y	ENST00000296474	NM_002447.2	893	tGt/tAt	11/20	0.338012676591909	2	FACETS	1	0.985	1	0.747	0.68	0.816	CLONAL	1	TRUE	0	0.433808103022229	2		387	355	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868897	117868897	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043184-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	80	213	0	ENST00000297338.2:c.802G>A	p.Asp268Asn	p.D268N	ENST00000297338	NM_006265.2	268	Gat/Aat	7/14	0.433808103022229	5	FACETS	1	0.972	1	0.448	0.396	0.504	CLONAL	1	TRUE	2	0.433808103022229	5		213	453	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638700	176638701	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GATG	novel	NA	P-0043184-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	26	318	0	ENST00000439151.2:c.3302_3305dup	p.Asp1103TrpfsTer2	p.D1103Wfs*2	ENST00000439151	NM_022455.4	1100	-/GATG	5/23	0.155101572117933	5	FACETS	0.483	0.382	0.598	0.161	0.127	0.2	INDETERMINATE	1	TRUE	2	0.433808103022229	5		318	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0043778-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	158	361	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.253764407065454	2	FACETS	0.786	0.722	0.852	0.786	0.722	0.852	SUBCLONAL	2	FALSE	0	0.3	2		361	670	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041262	29041262	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	64	321	0	ENST00000282397.4:c.166del	p.Glu56LysfsTer12	p.E56Kfs*12	ENST00000282397	NM_002019.4	56	Gaa/aa	3/30	0.32637048816861	4	FACETS	0.673	0.582	0.771	0.336	0.291	0.386	SUBCLONAL	1	TRUE	2	0.406787624222816	4		321	658	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094361	27094361	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	89	345	0	ENST00000324856.7:c.3069G>A	p.Trp1023Ter	p.W1023*	ENST00000324856	NM_006015.4	1023	tgG/tgA	11/20	0.392206550589826	2	FACETS	0.734	0.652	0.822	0.367	0.326	0.411	SUBCLONAL	1	TRUE	0	0.406787624222816	2		345	596	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843748	156843748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537263008	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	62	536	0	ENST00000524377.1:c.1174C>T	p.Pro392Ser	p.P392S	ENST00000524377	NM_002529.3	392	Cct/Tct	8/17	0.406425121513011	3	FACETS	0.441	0.38	0.508	0.147	0.126	0.17	SUBCLONAL	1	TRUE	0	0.406787624222816	3		536	831	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944139	71944139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	99	375	1	ENST00000298229.2:c.1972C>T	p.Pro658Ser	p.P658S	ENST00000298229	NM_001567.3	658	Cca/Tca	17/28	0.40150661491214	2	FACETS	0.865	0.774	0.961	0.432	0.387	0.481	CLONAL	1	TRUE	0	0.406787624222816	2		376	563	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933421	100933421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	63	282	0	ENST00000325455.5:c.1969C>T	p.Pro657Ser	p.P657S	ENST00000325455	NM_001202474.3	657	Cca/Tca	4/8	0.40150661491214	2	FACETS	0.885	0.77	1	0.442	0.385	0.504	CLONAL	1	TRUE	0	0.406787624222816	2		282	350	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433781	49433781	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	118	425	0	ENST00000301067.7:c.7772G>A	p.Gly2591Asp	p.G2591D	ENST00000301067	NM_003482.3	2591	gGc/gAc	31/54	0.406787624222816	4	FACETS	1	0.908	1	0.503	0.454	0.555	CLONAL	1	TRUE	2	0.406787624222816	4		425	811	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001970	29001970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	42	292	0	ENST00000282397.4:c.1195G>A	p.Asp399Asn	p.D399N	ENST00000282397	NM_002019.4	399	Gat/Aat	9/30	0.32637048816861	4	FACETS	0.598	0.499	0.707	0.299	0.249	0.354	SUBCLONAL	1	TRUE	2	0.406787624222816	4		292	486	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915319	32915319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748541466	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	58	299	0	ENST00000380152.3:c.6827C>T	p.Pro2276Leu	p.P2276L	ENST00000380152		2276	cCc/cTc	11/27	0.32637048816861	4	FACETS	0.87	0.749	1	0.435	0.374	0.501	CLONAL	1	TRUE	2	0.406787624222816	4		299	461	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434634	99434634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775630539	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	90	429	0	ENST00000268035.6:c.721G>A	p.Ala241Thr	p.A241T	ENST00000268035	NM_000875.3	241	Gcg/Acg	3/21	0.391088573840367	2	FACETS	0.764	0.679	0.855	0.382	0.339	0.428	SUBCLONAL	1	TRUE	0	0.406787624222816	2		429	579	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396473	396473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	82	423	0	ENST00000262320.3:c.553G>A	p.Ala185Thr	p.A185T	ENST00000262320	NM_003502.3	185	Gcc/Acc	2/11	0.40150661491214	2	FACETS	0.729	0.644	0.82	0.365	0.322	0.41	SUBCLONAL	1	TRUE	0	0.406787624222816	2		423	553	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820710	3820710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756935046	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	155	445	1	ENST00000262367.5:c.2741G>A	p.Ser914Asn	p.S914N	ENST00000262367	NM_004380.2	914	aGc/aAc	14/31	0.40150661491214	2	FACETS	0.966	0.885	1	0.483	0.442	0.525	CLONAL	1	TRUE	0	0.406787624222816	2		446	789	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826578	50826578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	56	187	0	ENST00000398568.2:c.2303C>T	p.Pro768Leu	p.P768L	ENST00000398568	NM_001042412.1	768	cCt/cTt	15/18	0.392206550589826	2	FACETS	1	0.931	1	0.562	0.486	0.642	CLONAL	1	TRUE	0	0.406787624222816	2		187	245	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	116	369	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	0.392206550589826	2	FACETS	0.868	0.784	0.957	0.434	0.392	0.479	CLONAL	1	TRUE	0	0.406787624222816	2		369	657	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942876	15942876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	90	316	0	ENST00000268712.3:c.6826G>A	p.Asp2276Asn	p.D2276N	ENST00000268712	NM_006311.3	2276	Gat/Aat	44/46	0.406787624222816	4	FACETS	0.885	0.786	0.992	0.443	0.393	0.496	CLONAL	1	TRUE	2	0.406787624222816	4		316	703	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627841	37627841	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1462649581	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	94	376	0	ENST00000447079.4:c.1756C>T	p.Pro586Ser	p.P586S	ENST00000447079	NM_015083.1	586	Cct/Tct	2/14	0.406787624222816	4	FACETS	0.802	0.713	0.897	0.401	0.356	0.449	CLONAL	1	TRUE	2	0.406787624222816	4		376	811	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740536	58740536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	96	361	0	ENST00000305921.3:c.1441G>A	p.Ala481Thr	p.A481T	ENST00000305921	NM_003620.3	481	Gcc/Acc	6/6	0.406787624222816	4	FACETS	1	0.945	1	0.546	0.487	0.609	CLONAL	1	TRUE	2	0.406787624222816	4		361	608	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007607	62007607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	76	444	0	ENST00000392795.3:c.260C>T	p.Pro87Leu	p.P87L	ENST00000392795	NM_001039933.1	87	cCc/cTc	3/6	0.406787624222816	4	FACETS	0.674	0.59	0.764	0.337	0.295	0.382	SUBCLONAL	1	TRUE	2	0.406787624222816	4		444	780	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272347	15272347	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779314594	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	88	482	0	ENST00000263388.2:c.6092G>A	p.Arg2031His	p.R2031H	ENST00000263388	NM_000435.2	2031	cGc/cAc	33/33	0.406787624222816	3	FACETS	0.687	0.608	0.771	0.229	0.202	0.257	SUBCLONAL	1	TRUE	0	0.406787624222816	3		482	758	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302310	15302310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1374454805	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	98	381	0	ENST00000263388.2:c.961G>A	p.Ala321Thr	p.A321T	ENST00000263388	NM_000435.2	321	Gcc/Acc	6/33	0.406787624222816	3	FACETS	0.835	0.746	0.931	0.278	0.248	0.311	CLONAL	1	TRUE	0	0.406787624222816	3		381	694	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745120	41745120	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1177926109	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	94	349	0	ENST00000301178.4:c.1186G>A	p.Asp396Asn	p.D396N	ENST00000301178	NM_021913.4	396	Gac/Aac	9/20	0.32637048816861	4	FACETS	0.832	0.74	0.931	0.416	0.37	0.466	CLONAL	1	TRUE	2	0.406787624222816	4		349	781	SUCCESS
ALK	238	MSKCC	GRCh37	2	29430109	29430109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173246434	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	31	278	0	ENST00000389048.3:c.3866C>T	p.Ala1289Val	p.A1289V	ENST00000389048	NM_004304.4	1289	gCc/gTc	26/29	0.391088573840367	2	FACETS	0.359	0.29	0.438	0.18	0.145	0.219	SUBCLONAL	1	TRUE	0	0.406787624222816	2		278	424	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660483	227660483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745750129	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	32	455	0	ENST00000305123.5:c.2972C>T	p.Thr991Ile	p.T991I	ENST00000305123	NM_005544.2	991	aCc/aTc	1/2	0.391088573840367	2	FACETS	0.271	0.219	0.33	0.136	0.109	0.165	SUBCLONAL	1	TRUE	0	0.406787624222816	2		455	580	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546949	9546949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs921511471	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	111	379	0	ENST00000353224.5:c.1073C>T	p.Pro358Leu	p.P358L	ENST00000353224	NM_177990.2	358	cCt/cTt	5/10	0.394630256648673	4	FACETS	0.988	0.888	1	0.494	0.444	0.547	CLONAL	1	TRUE	2	0.406787624222816	4		379	777	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165300	47165300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	77	327	0	ENST00000409792.3:c.826G>A	p.Asp276Asn	p.D276N	ENST00000409792	NM_014159.6	276	Gat/Aat	3/21	0.392206550589826	2	FACETS	0.839	0.74	0.946	0.42	0.37	0.473	CLONAL	1	TRUE	0	0.406787624222816	2		327	451	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114283	73114285	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs1559572227	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	33	288	0	ENST00000356692.5:c.926_928del	p.Glu310del	p.E310del	ENST00000356692		307	GAA/-	8/9	0.392206550589826	2	FACETS	0.361	0.294	0.437	0.181	0.147	0.219	SUBCLONAL	1	TRUE	0	0.406787624222816	2		288	449	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182681805	182681805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	65	247	0	ENST00000292782.4:c.253G>A	p.Gly85Ser	p.G85S	ENST00000292782	NM_020640.2	85	Ggc/Agc	3/7	0.40150661491214	2	FACETS	0.845	0.737	0.962	0.423	0.368	0.481	CLONAL	1	TRUE	0	0.406787624222816	2		247	378	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524450	187524450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	42	338	1	ENST00000441802.2:c.11230C>T	p.Pro3744Ser	p.P3744S	ENST00000441802	NM_005245.3	3744	Ccc/Tcc	19/27	0.32637048816861	4	FACETS	0.499	0.416	0.592	0.25	0.208	0.296	SUBCLONAL	1	TRUE	2	0.406787624222816	4		339	582	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630804	187630804	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	87	402	0	ENST00000441802.2:c.178G>A	p.Gly60Ser	p.G60S	ENST00000441802	NM_005245.3	60	Ggt/Agt	2/27	0.32637048816861	4	FACETS	0.933	0.827	1	0.466	0.413	0.524	CLONAL	1	TRUE	2	0.406787624222816	4		402	645	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167761	56167761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	74	300	0	ENST00000399503.3:c.1326G>A	p.Met442Ile	p.M442I	ENST00000399503	NM_005921.1	442	atG/atA	7/20	0.394630256648673	4	FACETS	0.836	0.732	0.948	0.418	0.366	0.474	CLONAL	1	TRUE	2	0.406787624222816	4		300	612	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457745	149457745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752816265	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	42	393	0	ENST00000286301.3:c.659C>T	p.Ala220Val	p.A220V	ENST00000286301	NM_005211.3	220	gCc/gTc	5/22	0.394630256648673	4	FACETS	0.371	0.308	0.44	0.185	0.154	0.22	SUBCLONAL	1	TRUE	2	0.406787624222816	4		393	784	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964450	93964450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145700620	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	45	329	0	ENST00000369303.4:c.2447C>T	p.Ala816Val	p.A816V	ENST00000369303	NM_004440.3	816	gCc/gTc	14/17	0.406787624222816	2	FACETS	0.832	0.704	0.971	0.416	0.352	0.486	CLONAL	1	TRUE	0	0.406787624222816	2		329	266	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346571	81346571	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	78	298	0	ENST00000222390.5:c.1382G>A	p.Trp461Ter	p.W461*	ENST00000222390	NM_000601.4	461	tGg/tAg	11/18	0.406787624222816	4	FACETS	0.799	0.702	0.904	0.4	0.351	0.452	CLONAL	1	TRUE	2	0.406787624222816	4		298	675	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273575	38273575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243758431	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	42	351	0	ENST00000425967.3:c.1760C>T	p.Pro587Leu	p.P587L	ENST00000425967	NM_001174067.1	587	cCc/cTc	14/19	0.219416967064551	5	FACETS	0.43	0.358	0.511	0.143	0.119	0.171	INDETERMINATE	1	TRUE	2	0.406787624222816	5		351	773	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507344	8507344	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573381420	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	29	363	0	ENST00000356435.5:c.1634C>T	p.Ala545Val	p.A545V	ENST00000356435		545	gCc/gTc	11/35	0.406787624222816	2	FACETS	0.379	0.304	0.464	0.19	0.152	0.232	SUBCLONAL	1	TRUE	0	0.406787624222816	2		363	376	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849000	156849000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	236	415	0	ENST00000524377.1:c.1892C>T	p.Ala631Val	p.A631V	ENST00000524377	NM_002529.3	631	gCt/gTt	15/17	0.406425121513011	3	FACETS	1	0.941	1	0.669	0.627	0.711	CLONAL	2	TRUE	0	0.406787624222816	3		415	696	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230472992	230472992	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	97	322	0	ENST00000391860.1:c.592G>A	p.Asp198Asn	p.D198N	ENST00000391860	NM_001258311.1	198	Gat/Aat	4/7	0.40150661491214	2	FACETS	0.921	0.824	1	0.46	0.412	0.512	CLONAL	1	TRUE	0	0.406787624222816	2		322	518	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47594885	47594885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	131	433	0	ENST00000430070.2:c.1202G>A	p.Gly401Glu	p.G401E	ENST00000430070	NM_018095.4	401	gGg/gAg	4/4	0.30059054974984	3	FACETS	1	0.957	1			1	CLONAL	1	TRUE	NA	0.406787624222816	3		433	712	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003550	57003550	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	95	456	0	ENST00000257254.3:c.929C>T	p.Ala310Val	p.A310V	ENST00000257254		310	gCc/gTc	1/2	0.392206550589826	2	FACETS	0.724	0.645	0.808	0.362	0.322	0.404	SUBCLONAL	1	TRUE	0	0.406787624222816	2		456	645	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577257	64577257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	266	395	0	ENST00000312049.6:c.325G>T	p.Glu109Ter	p.E109*	ENST00000312049	NM_130799.2	109	Gaa/Taa	2/10	0.392206550589826	2	FACETS	0.976	0.921	1	0.976	0.921	1	CLONAL	2	TRUE	0	0.406787624222816	2		395	670	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94225952	94225952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501784	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	76	265	0	ENST00000323929.3:c.16G>A	p.Ala6Thr	p.A6T	ENST00000323929	NM_005591.3	6	Gca/Aca	2/20	0.40150661491214	2	FACETS	0.989	0.872	1	0.494	0.436	0.556	CLONAL	1	TRUE	0	0.406787624222816	2		265	378	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196104	108196104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1433554922	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	51	265	0	ENST00000278616.4:c.6640G>A	p.Asp2214Asn	p.D2214N	ENST00000278616	NM_000051.3	2214	Gac/Aac	46/63	0.40150661491214	2	FACETS	0.856	0.732	0.989	0.428	0.366	0.495	CLONAL	1	TRUE	0	0.406787624222816	2		265	293	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307367	118307367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	60	214	0	ENST00000534358.1:c.140G>A	p.Gly47Asp	p.G47D	ENST00000534358	NM_005933.3	47	gGc/gAc	1/36	0.392206550589826	2	FACETS	0.961	0.834	1	0.48	0.417	0.549	CLONAL	1	TRUE	0	0.406787624222816	2		214	307	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373146	118373146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	72	314	0	ENST00000534358.1:c.6539C>T	p.Thr2180Ile	p.T2180I	ENST00000534358	NM_005933.3	2180	aCa/aTa	27/36	0.392206550589826	2	FACETS	0.755	0.661	0.855	0.377	0.33	0.428	SUBCLONAL	1	TRUE	0	0.406787624222816	2		314	469	SUCCESS
CBL	867	MSKCC	GRCh37	11	119167641	119167641	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778154	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	68	296	0	ENST00000264033.4:c.2050C>T	p.Pro684Ser	p.P684S	ENST00000264033	NM_005188.3	684	Cca/Tca	13/16	0.392206550589826	2	FACETS	0.724	0.631	0.823	0.362	0.315	0.412	SUBCLONAL	1	TRUE	0	0.406787624222816	2		296	462	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427606	427606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	66	298	0	ENST00000399788.2:c.2563G>A	p.Glu855Lys	p.E855K	ENST00000399788	NM_001042603.1	855	Gag/Aag	19/28	0.406787624222816	4	FACETS	0.78	0.678	0.892	0.39	0.339	0.446	SUBCLONAL	1	TRUE	2	0.406787624222816	4		298	585	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871206	12871206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	115	321	0	ENST00000228872.4:c.433G>A	p.Ala145Thr	p.A145T	ENST00000228872	NM_004064.3	145	Gcg/Acg	1/3	0.406787624222816	5	FACETS	1	0.918	1			1	CLONAL	1	TRUE	NA	0.406787624222816	5		321	891	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499676	18499676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	77	398	0	ENST00000266497.5:c.1531C>T	p.Pro511Ser	p.P511S	ENST00000266497		511	Cct/Tct	10/31	0.168297947954921	5	FACETS	1	0.918	1	0.352	0.309	0.398	INDETERMINATE	1	TRUE	2	0.406787624222816	5		398	577	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641425	18641425	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1375260257	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	60	307	0	ENST00000266497.5:c.2424G>A	p.Trp808Ter	p.W808*	ENST00000266497		808	tgG/tgA	17/31	0.168297947954921	5	FACETS	1	0.932	1	0.377	0.326	0.433	INDETERMINATE	1	TRUE	2	0.406787624222816	5		307	420	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21626574	21626574	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	52	254	0	ENST00000421138.2:c.1358G>A	p.Cys453Tyr	p.C453Y	ENST00000421138		453	tGt/tAt	13/16	0.406787624222816	4	FACETS	0.942	0.804	1	0.471	0.402	0.546	CLONAL	1	TRUE	2	0.406787624222816	4		254	382	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434756	49434756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	55	462	0	ENST00000301067.7:c.6797G>A	p.Gly2266Asp	p.G2266D	ENST00000301067	NM_003482.3	2266	gGc/gAc	31/54	0.406787624222816	4	FACETS	0.38	0.324	0.442	0.19	0.162	0.221	SUBCLONAL	1	TRUE	2	0.406787624222816	4		462	1000	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26978124	26978124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	71	312	0	ENST00000381527.3:c.1301C>T	p.Pro434Leu	p.P434L	ENST00000381527	NM_001260.1	434	cCt/cTt	13/13	0.32637048816861	4	FACETS	0.844	0.737	0.959	0.422	0.368	0.48	CLONAL	1	TRUE	2	0.406787624222816	4		312	582	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912760	32912760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	59	303	0	ENST00000380152.3:c.4268C>T	p.Thr1423Ile	p.T1423I	ENST00000380152		1423	aCt/aTt	11/27	0.32637048816861	4	FACETS	0.936	0.807	1	0.468	0.403	0.538	CLONAL	1	TRUE	2	0.406787624222816	4		303	436	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133041	30133041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	51	252	0	ENST00000331968.5:c.560G>A	p.Arg187Lys	p.R187K	ENST00000331968	NM_002742.2	187	aGa/aAa	4/18	0.406787624222816	5	FACETS	0.733	0.623	0.854			1	SUBCLONAL	1	TRUE	NA	0.406787624222816	5		252	551	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748576	43748576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	105	376	0	ENST00000382044.4:c.2230G>A	p.Glu744Lys	p.E744K	ENST00000382044	NM_001141980.1	744	Gaa/Aaa	12/28	0.392206550589826	2	FACETS	1	0.968	1	0.589	0.531	0.65	CLONAL	1	TRUE	0	0.406787624222816	2		376	438	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678358	88678358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257351492	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	25	373	0	ENST00000360948.2:c.1178G>A	p.Gly393Asp	p.G393D	ENST00000360948	NM_001012338.2	393	gGc/gAc	9/19	0.406787624222816	1	FACETS	0.241	0.19	0.301	0.241	0.19	0.301	SUBCLONAL	1	TRUE	0	0.406787624222816	1		373	406	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785629	50785629	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	86	296	0	ENST00000398568.2:c.619G>A	p.Asp207Asn	p.D207N	ENST00000398568	NM_001042412.1	207	Gat/Aat	4/18	0.392206550589826	2	FACETS	0.866	0.769	0.97	0.433	0.384	0.485	CLONAL	1	TRUE	0	0.406787624222816	2		296	488	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785665	50785665	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	64	295	0	ENST00000398568.2:c.655C>T	p.Pro219Ser	p.P219S	ENST00000398568	NM_001042412.1	219	Cct/Tct	4/18	0.392206550589826	2	FACETS	0.675	0.586	0.772	0.338	0.293	0.386	SUBCLONAL	1	TRUE	0	0.406787624222816	2		295	466	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821892	72821892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375049833	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	111	391	0	ENST00000268489.5:c.10283C>T	p.Pro3428Leu	p.P3428L	ENST00000268489	NM_006885.3	3428	cCc/cTc	10/10	0.40150661491214	2	FACETS	0.963	0.868	1	0.481	0.434	0.531	CLONAL	1	TRUE	0	0.406787624222816	2		391	567	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347962	89347962	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	121	405	0	ENST00000301030.4:c.4988C>T	p.Ala1663Val	p.A1663V	ENST00000301030	NM_001256183.1	1663	gCc/gTc	9/13	0.40150661491214	2	FACETS	1	0.949	1	0.534	0.484	0.586	CLONAL	1	TRUE	0	0.406787624222816	2		405	557	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042463	16042463	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	39	250	0	ENST00000268712.3:c.1211C>T	p.Pro404Leu	p.P404L	ENST00000268712	NM_006311.3	404	cCa/cTa	12/46	0.406787624222816	4	FACETS	0.817	0.68	0.97	0.409	0.34	0.485	CLONAL	1	TRUE	2	0.406787624222816	4		250	330	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40876345	40876345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	101	354	0	ENST00000428826.2:c.344C>T	p.Ser115Phe	p.S115F	ENST00000428826		115	tCc/tTc	5/21	0.406787624222816	4	FACETS	1	0.932	1	0.528	0.472	0.587	CLONAL	1	TRUE	2	0.406787624222816	4		354	662	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55704595	55704595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	84	262	0	ENST00000284073.2:c.658C>T	p.Pro220Ser	p.P220S	ENST00000284073	NM_138962.2	220	Ccc/Tcc	10/14	0.406787624222816	4	FACETS	1	0.894	1	0.505	0.447	0.568	CLONAL	1	TRUE	2	0.406787624222816	4		262	575	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007435	62007435	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs747265164	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	125	388	0	ENST00000392795.3:c.432G>A	p.Met144Ile	p.M144I	ENST00000392795	NM_001039933.1	144	atG/atA	3/6	0.406787624222816	4	FACETS	1	0.948	1	0.535	0.484	0.589	CLONAL	1	TRUE	2	0.406787624222816	4		388	808	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2220126	2220126	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	116	348	0	ENST00000398665.3:c.2711T>C	p.Val904Ala	p.V904A	ENST00000398665	NM_032482.2	904	gTg/gCg	23/28	0.406787624222816	3	FACETS	0.93	0.839	1	0.31	0.279	0.342	CLONAL	1	TRUE	0	0.406787624222816	3		348	738	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218523	5218523	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762505033	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	73	368	0	ENST00000357368.4:c.3956C>T	p.Pro1319Leu	p.P1319L	ENST00000357368	NM_002850.3	1319	cCc/cTc	25/38	0.406787624222816	3	FACETS	0.675	0.59	0.766	0.225	0.196	0.256	SUBCLONAL	1	TRUE	0	0.406787624222816	3		368	640	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10257097	10257097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	78	343	0	ENST00000340748.4:c.2776G>A	p.Ala926Thr	p.A926T	ENST00000340748		926	Gcc/Acc	27/40	0.406787624222816	3	FACETS	0.681	0.598	0.77	0.227	0.199	0.257	SUBCLONAL	1	TRUE	0	0.406787624222816	3		343	678	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281148	15281148	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257083112	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	80	407	0	ENST00000263388.2:c.5108G>A	p.Gly1703Asp	p.G1703D	ENST00000263388	NM_000435.2	1703	gGc/gAc	27/33	0.406787624222816	3	FACETS	0.587	0.516	0.664	0.196	0.172	0.222	SUBCLONAL	1	TRUE	0	0.406787624222816	3		407	806	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290306	15290306	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	114	397	0	ENST00000263388.2:c.3329G>A	p.Cys1110Tyr	p.C1110Y	ENST00000263388	NM_000435.2	1110	tGt/tAt	21/33	0.406787624222816	3	FACETS	0.852	0.767	0.941	0.284	0.255	0.314	CLONAL	1	TRUE	0	0.406787624222816	3		397	792	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376184	15376184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	94	266	1	ENST00000263377.2:c.830C>T	p.Ala277Val	p.A277V	ENST00000263377	NM_058243.2	277	gCc/gTc	5/20	0.406787624222816	3	FACETS	0.866	0.772	0.967	0.289	0.257	0.323	CLONAL	1	TRUE	0	0.406787624222816	3		267	642	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272109	18272109	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	55	521	0	ENST00000222254.8:c.619C>T	p.Pro207Ser	p.P207S	ENST00000222254	NM_005027.3	207	Ccg/Tcg	6/16	0.406787624222816	3	FACETS	0.307	0.261	0.357	0.102	0.087	0.119	SUBCLONAL	1	TRUE	0	0.406787624222816	3		521	1061	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314662	30314662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	97	357	0	ENST00000262643.3:c.1211G>A	p.Ser404Asn	p.S404N	ENST00000262643	NM_001238.2	404	aGc/aAc	12/12	0.32637048816861	4	FACETS	0.871	0.777	0.972	0.436	0.388	0.486	CLONAL	1	TRUE	2	0.406787624222816	4		357	770	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40742274	40742274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1473345359	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	71	317	0	ENST00000392038.2:c.850G>A	p.Asp284Asn	p.D284N	ENST00000392038	NM_001626.4	284	Gac/Aac	10/14	0.32637048816861	4	FACETS	0.79	0.689	0.898	0.395	0.344	0.449	SUBCLONAL	1	TRUE	2	0.406787624222816	4		317	622	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762884	40762884	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	89	348	0	ENST00000392038.2:c.124C>T	p.Pro42Ser	p.P42S	ENST00000392038	NM_001626.4	42	Ccc/Tcc	3/14	0.32637048816861	4	FACETS	0.787	0.697	0.883	0.394	0.348	0.442	SUBCLONAL	1	TRUE	2	0.406787624222816	4		348	782	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383613	42383613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782159652	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	101	359	0	ENST00000221972.3:c.388C>T	p.Pro130Ser	p.P130S	ENST00000221972	NM_021601.3	130	Ccc/Tcc	3/5	0.32637048816861	4	FACETS	0.919	0.822	1	0.46	0.411	0.512	CLONAL	1	TRUE	2	0.406787624222816	4		359	760	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753524	42753524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	122	514	0	ENST00000222329.4:c.740C>T	p.Pro247Leu	p.P247L	ENST00000222329	NM_006494.2	247	cCc/cTc	4/4	0.32637048816861	4	FACETS	0.815	0.736	0.9	0.408	0.368	0.45	CLONAL	1	TRUE	2	0.406787624222816	4		514	1035	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792026	42792026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	84	407	0	ENST00000575354.2:c.830C>T	p.Ser277Phe	p.S277F	ENST00000575354	NM_015125.3	277	tCc/tTc	6/20	0.32637048816861	4	FACETS	0.696	0.614	0.784	0.348	0.307	0.392	SUBCLONAL	1	TRUE	2	0.406787624222816	4		407	835	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425012	47425012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1221753325	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	83	344	0	ENST00000404338.3:c.3080G>A	p.Ser1027Asn	p.S1027N	ENST00000404338	NM_004491.4	1027	aGc/aAc	1/6	0.406787624222816	4	FACETS	0.771	0.68	0.868			1	SUBCLONAL	1	TRUE	NA	0.406787624222816	4		344	745	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731454	47731454	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	80	414	0	ENST00000449228.1:c.338G>A	p.Trp113Ter	p.W113*	ENST00000449228	NM_001127240.2	113	tGg/tAg	2/4	0.406787624222816	4	FACETS	0.656	0.577	0.742			1	SUBCLONAL	1	TRUE	NA	0.406787624222816	4		414	843	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630346	47630346	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	266	440	0	ENST00000233146.2:c.17del	p.Lys6ArgfsTer58	p.K6Rfs*58	ENST00000233146	NM_000251.2	6	Aag/ag	1/16	0.391088573840367	2	FACETS	0.886	0.835	0.938	0.886	0.835	0.938	CLONAL	2	TRUE	0	0.406787624222816	2		440	738	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635561	47635561	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs892915951	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	61	247	0	ENST00000233146.2:c.233T>C	p.Val78Ala	p.V78A	ENST00000233146	NM_000251.2	78	gTt/gCt	2/16	0.391088573840367	2	FACETS	0.885	0.768	1	0.442	0.384	0.505	CLONAL	1	TRUE	0	0.406787624222816	2		247	339	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426747	212426747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	98	362	0	ENST00000342788.4:c.2368C>T	p.Pro790Ser	p.P790S	ENST00000342788	NM_005235.2	790	Cca/Tca	20/28	0.406787624222816	1	FACETS	0.827	0.742	0.917	0.827	0.742	0.917	CLONAL	1	TRUE	0	0.406787624222816	1		362	464	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371651	225371651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	60	298	0	ENST00000264414.4:c.953G>A	p.Ser318Asn	p.S318N	ENST00000264414	NM_003590.4	318	aGt/aAt	7/16	0.391088573840367	2	FACETS	1	0.902	1	0.523	0.454	0.596	CLONAL	1	TRUE	0	0.406787624222816	2		298	282	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936056	49936056	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	95	425	0	ENST00000296474.3:c.1614G>T	p.Arg538Ser	p.R538S	ENST00000296474	NM_002447.2	538	agG/agT	4/20	0.392206550589826	2	FACETS	0.741	0.661	0.827	0.371	0.33	0.414	SUBCLONAL	1	TRUE	0	0.406787624222816	2		425	630	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584545	52584545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	50	372	0	ENST00000394830.3:c.4468C>T	p.Pro1490Ser	p.P1490S	ENST00000394830	NM_018313.4	1490	Ccc/Tcc	29/30	0.392206550589826	2	FACETS	0.385	0.326	0.45	0.193	0.163	0.225	SUBCLONAL	1	TRUE	0	0.406787624222816	2		372	638	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63973940	63973940	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	110	321	0	ENST00000398590.3:c.1301C>T	p.Pro434Leu	p.P434L	ENST00000398590	NM_001177387.1	434	cCt/cTt	9/14	0.392206550589826	2	FACETS	0.901	0.812	0.996	0.451	0.406	0.498	CLONAL	1	TRUE	0	0.406787624222816	2		321	600	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928035	178928035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	54	259	0	ENST00000263967.3:c.1313C>T	p.Ser438Phe	p.S438F	ENST00000263967	NM_006218.2	438	tCt/tTt	8/21	0.40150661491214	2	FACETS	0.865	0.743	0.996	0.432	0.371	0.498	CLONAL	1	TRUE	0	0.406787624222816	2		259	307	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535416	187535416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756123882	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	67	315	0	ENST00000441802.2:c.9158G>A	p.Arg3053His	p.R3053H	ENST00000441802	NM_005245.3	3053	cGc/cAc	12/27	0.32637048816861	4	FACETS	0.986	0.859	1	0.493	0.429	0.562	CLONAL	1	TRUE	2	0.406787624222816	4		315	470	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628394	187628394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	91	382	0	ENST00000441802.2:c.2588C>T	p.Thr863Ile	p.T863I	ENST00000441802	NM_005245.3	863	aCa/aTa	2/27	0.32637048816861	4	FACETS	0.828	0.735	0.928	0.414	0.367	0.464	CLONAL	1	TRUE	2	0.406787624222816	4		382	760	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233607	233607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	44	135	0	ENST00000264932.6:c.911G>A	p.Gly304Asp	p.G304D	ENST00000264932	NM_004168.2	304	gGt/gAt	8/15	0.168297947954921	5	FACETS	1	0.935	1	0.406	0.342	0.476	INDETERMINATE	1	TRUE	2	0.406787624222816	5		135	286	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39021188	39021188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	47	233	0	ENST00000357387.3:c.148G>A	p.Gly50Arg	p.G50R	ENST00000357387	NM_152756.3	50	Gga/Aga	3/38	0.394630256648673	4	FACETS	0.813	0.687	0.95	0.406	0.343	0.475	CLONAL	1	TRUE	2	0.406787624222816	4		233	400	SUCCESS
APC	324	MSKCC	GRCh37	5	112175879	112175879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1580649974	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	99	375	0	ENST00000257430.4:c.4588G>A	p.Glu1530Lys	p.E1530K	ENST00000257430	NM_000038.5	1530	Gaa/Aaa	16/16	0.394630256648673	4	FACETS	1	0.933	1	0.53	0.474	0.59	CLONAL	1	TRUE	2	0.406787624222816	4		375	646	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131893137	131893137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554096658	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	96	347	0	ENST00000265335.6:c.121G>A	p.Gly41Arg	p.G41R	ENST00000265335		41	Gga/Aga	1/25	0.394630256648673	4	FACETS	1	0.915	1	0.515	0.459	0.574	CLONAL	1	TRUE	2	0.406787624222816	4		347	645	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513467	149513467	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	122	448	0	ENST00000261799.4:c.736G>A	p.Glu246Lys	p.E246K	ENST00000261799	NM_002609.3	246	Gag/Aag	5/23	0.394630256648673	4	FACETS	0.961	0.868	1	0.481	0.434	0.53	CLONAL	1	TRUE	2	0.406787624222816	4		448	878	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047645	180047645	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	80	395	0	ENST00000261937.6:c.2370G>A	p.Trp790Ter	p.W790*	ENST00000261937	NM_182925.4	790	tgG/tgA	16/30	0.270038731007204	3	FACETS	0.748	0.658	0.843	0.374	0.329	0.422	SUBCLONAL	1	TRUE	1	0.406787624222816	3		395	633	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048832	180048832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	85	413	0	ENST00000261937.6:c.1730G>A	p.Ser577Asn	p.S577N	ENST00000261937	NM_182925.4	577	aGc/aAc	13/30	0.270038731007204	3	FACETS	0.679	0.599	0.764	0.339	0.299	0.382	SUBCLONAL	1	TRUE	1	0.406787624222816	3		413	741	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225765	26225765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749997198	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	52	491	0	ENST00000360408.1:c.383C>T	p.Ala128Val	p.A128V	ENST00000360408	NM_003532.2	128	gCc/gTc	1/1	0.406787624222816	4	FACETS	0.471	0.4	0.55	0.157	0.133	0.184	SUBCLONAL	1	TRUE	1	0.406787624222816	4		491	763	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672618	30672618	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751090753	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	49	543	0	ENST00000376406.3:c.4342G>A	p.Val1448Ile	p.V1448I	ENST00000376406	NM_014641.2	1448	Gtt/Att	10/15	0.278245665780656	3	FACETS	0.337	0.285	0.396	0.113	0.095	0.132	SUBCLONAL	1	TRUE	0	0.406787624222816	3		543	859	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171605	32171605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs968431928	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	85	341	0	ENST00000375023.3:c.3173G>A	p.Gly1058Glu	p.G1058E	ENST00000375023	NM_004557.3	1058	gGa/gAa	20/30	0.278245665780656	3	FACETS	0.956	0.847	1	0.319	0.282	0.358	CLONAL	1	TRUE	0	0.406787624222816	3		341	526	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163889	152163889	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	79	308	0	ENST00000206249.3:c.610G>A	p.Gly204Ser	p.G204S	ENST00000206249	NM_000125.3	204	Ggc/Agc	2/8	0.391088573840367	2	FACETS	0.895	0.791	1	0.447	0.395	0.503	CLONAL	1	TRUE	0	0.406787624222816	2		308	434	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979433	2979433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	89	303	0	ENST00000396946.4:c.814G>A	p.Glu272Lys	p.E272K	ENST00000396946	NM_032415.4	272	Gag/Aag	6/25	0.394630256648673	4	FACETS	0.913	0.81	1	0.457	0.405	0.512	CLONAL	1	TRUE	2	0.406787624222816	4		303	674	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026730	6026730	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	42	176	0	ENST00000265849.7:c.1666G>A	p.Glu556Lys	p.E556K	ENST00000265849	NM_000535.5	556	Gaa/Aaa	11/15	0.394630256648673	4	FACETS	0.962	0.807	1	0.481	0.403	0.566	CLONAL	1	TRUE	2	0.406787624222816	4		176	302	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468087	50468087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	94	427	0	ENST00000331340.3:c.1322C>T	p.Ala441Val	p.A441V	ENST00000331340	NM_006060.4	441	gCc/gTc	8/8	0.168297947954921	5	FACETS	1	0.931	1	0.354	0.315	0.396	INDETERMINATE	1	TRUE	2	0.406787624222816	5		427	700	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412010	116412010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	124	363	0	ENST00000397752.3:c.2995G>A	p.Glu999Lys	p.E999K	ENST00000397752	NM_000245.2	999	Gaa/Aaa	14/21	0.394630256648673	4	FACETS	1	0.973	1	0.6	0.543	0.659	CLONAL	1	TRUE	2	0.406787624222816	4		363	715	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624386	140624386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1161707003	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	69	301	0	ENST00000288602.6:c.118G>A	p.Asp40Asn	p.D40N	ENST00000288602	NM_004333.4	40	Gac/Aac	1/18	0.394630256648673	4	FACETS	0.756	0.659	0.862	0.378	0.329	0.431	SUBCLONAL	1	TRUE	2	0.406787624222816	4		301	631	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875069	151875069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1021421694	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	23	213	0	ENST00000262189.6:c.7469G>A	p.Gly2490Asp	p.G2490D	ENST00000262189	NM_170606.2	2490	gGt/gAt	38/59	0.394630256648673	4	FACETS	0.395	0.307	0.496	0.197	0.153	0.248	SUBCLONAL	1	TRUE	2	0.406787624222816	4		213	403	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880109	151880109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267601429	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	67	257	0	ENST00000262189.6:c.5215C>T	p.Pro1739Ser	p.P1739S	ENST00000262189	NM_170606.2	1739	Cct/Tct	35/59	0.394630256648673	4	FACETS	1	0.939	1	0.565	0.493	0.643	CLONAL	1	TRUE	2	0.406787624222816	4		257	410	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38178622	38178622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	58	232	0	ENST00000317025.8:c.1777G>A	p.Val593Ile	p.V593I	ENST00000317025	NM_023034.1	593	Gtt/Att	8/24	0.406787624222816	5	FACETS	1	0.921	1			1	CLONAL	1	TRUE	NA	0.406787624222816	5		232	417	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187038	38187038	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	36	321	1	ENST00000317025.8:c.1439C>T	p.Pro480Leu	p.P480L	ENST00000317025	NM_023034.1	480	cCa/cTa	6/24	0.406787624222816	5	FACETS	0.42	0.344	0.505			1	SUBCLONAL	1	TRUE	NA	0.406787624222816	5		322	679	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020545	69020545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1162684255	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	55	271	0	ENST00000288368.4:c.2917G>A	p.Glu973Lys	p.E973K	ENST00000288368	NM_024870.2	973	Gaa/Aaa	24/40	0.219416967064551	5	FACETS	0.992	0.85	1	0.331	0.283	0.382	INDETERMINATE	1	TRUE	2	0.406787624222816	5		271	439	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021777	69021777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146544818	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	76	346	0	ENST00000288368.4:c.3065C>T	p.Thr1022Ile	p.T1022I	ENST00000288368	NM_024870.2	1022	aCc/aTc	25/40	0.219416967064551	5	FACETS	1	0.943	1	0.375	0.329	0.424	INDETERMINATE	1	TRUE	2	0.406787624222816	5		346	535	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981896	70981896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	112	450	0	ENST00000276594.2:c.200C>T	p.Pro67Leu	p.P67L	ENST00000276594	NM_024504.3	67	cCc/cTc	2/8	0.219416967064551	5	FACETS	1	0.962	1	0.38	0.342	0.421	INDETERMINATE	1	TRUE	2	0.406787624222816	5		450	777	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90994975	90994975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1450189149	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	48	220	0	ENST00000265433.3:c.146C>T	p.Thr49Ile	p.T49I	ENST00000265433	NM_002485.4	49	aCt/aTt	2/16	0.219416967064551	5	FACETS	0.907	0.768	1	0.302	0.256	0.353	INDETERMINATE	1	TRUE	2	0.406787624222816	5		220	419	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2181609	2181609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	28	234	0	ENST00000349721.2:c.4292C>T	p.Pro1431Leu	p.P1431L	ENST00000349721	NM_003070.3	1431	cCt/cTt	30/34	0.406787624222816	2	FACETS	0.398	0.318	0.489	0.199	0.159	0.245	SUBCLONAL	1	TRUE	0	0.406787624222816	2		234	346	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158140	27158140	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	75	347	0	ENST00000380036.4:c.364G>A	p.Ala122Thr	p.A122T	ENST00000380036	NM_000459.3	122	Gct/Act	2/23	0.219416967064551	5	FACETS	0.941	0.825	1	0.314	0.275	0.356	INDETERMINATE	1	TRUE	2	0.406787624222816	5		347	631	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27220097	27220097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	99	308	0	ENST00000380036.4:c.3154C>T	p.Pro1052Ser	p.P1052S	ENST00000380036	NM_000459.3	1052	Ccc/Tcc	21/23	0.219416967064551	5	FACETS	1	0.974	1	0.432	0.386	0.48	INDETERMINATE	1	TRUE	2	0.406787624222816	5		308	605	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787785	135787785	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554817662	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	79	283	0	ENST00000298552.3:c.797C>T	p.Pro266Leu	p.P266L	ENST00000298552	NM_001162426.1	266	cCc/cTc	9/23	0.394630256648673	4	FACETS	1	0.893	1	0.507	0.446	0.571	CLONAL	1	TRUE	2	0.406787624222816	4		283	539	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802643	135802643	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	85	312	0	ENST00000298552.3:c.155C>T	p.Thr52Ile	p.T52I	ENST00000298552	NM_001162426.1	52	aCc/aTc	4/23	0.394630256648673	4	FACETS	0.852	0.753	0.958	0.426	0.376	0.479	CLONAL	1	TRUE	2	0.406787624222816	4		312	690	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407969	139407969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	87	324	0	ENST00000277541.6:c.2228C>T	p.Pro743Leu	p.P743L	ENST00000277541	NM_017617.3	743	cCt/cTt	14/34	0.394630256648673	4	FACETS	0.818	0.724	0.918	0.409	0.362	0.459	CLONAL	1	TRUE	2	0.406787624222816	4		324	736	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921454	39921454	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	102	147	0	ENST00000378444.4:c.4366C>T	p.Leu1456Phe	p.L1456F	ENST00000378444	NM_001123385.1	1456	Ctt/Ttt	10/15	0.406787624222816	2	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.406787624222816	2		147	404	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006898	47006898	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	34	154	0	ENST00000377604.3:c.17+1G>A		p.X6_splice	ENST00000377604	NM_001204468.1	6			0.406787624222816	2	FACETS	0.433	0.354	0.522			1	SUBCLONAL	1	TRUE	NA	0.406787624222816	2		154	386	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413121	63413121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1279998398	NA	P-0043903-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	72	177	0	ENST00000330258.3:c.46G>A	p.Ala16Thr	p.A16T	ENST00000330258	NM_152424.3	16	Gcc/Acc	2/2	0.305301223216677	2	FACETS	1	0.952	1			1	CLONAL	1	TRUE	NA	0.406787624222816	2		177	305	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044639-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	52	300	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	1	0.948	1			1	INDETERMINATE	1	TRUE	NA	0.210239648012675	2		300	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578399	7578403	+	protein_altering_variant	In_Frame_Del	DEL	GGGGC	GGGGC	AG	novel	NA	P-0044639-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	54	319	1	ENST00000269305.4:c.527_531delinsCT	p.Cys176_Pro177delinsSer	p.C176_P177delinsS	ENST00000269305	NM_001126112.2	176	tGCCCC/tCT	5/11	0.116653503002128	3	FACETS	0.855	0.729	0.993			1	INDETERMINATE	1	TRUE	NA	0.210239648012675	3		320	664	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0044796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4	293	491	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.934616690089587	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.932154982720502	2		491	297	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42384800	42384800	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	96	326	0	ENST00000221972.3:c.562T>G	p.Tyr188Asp	p.Y188D	ENST00000221972	NM_021601.3	188	Tat/Gat	4/5	0.932154982720502	6	FACETS	0.786	0.7	0.877	0.262	0.233	0.293	SUBCLONAL	1	TRUE	3	0.932154982720502	6		326	751	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562181	21562181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	290	532	1	ENST00000382592.4:c.1738G>A	p.Val580Ile	p.V580I	ENST00000382592	NM_014572.2	580	Gtc/Atc	4/8	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.932154982720502	2		533	304	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050809	49050910	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTAAAGTAAAGAATTCTGTAATTTGTAGACTTCTGAGAAGTTCCAGAAAATAAATCAGATGGTATGTAACAGCGACCGTGTGCTCAAAAGAAGTGCTGAAGG	TTAAAGTAAAGAATTCTGTAATTTGTAGACTTCTGAGAAGTTCCAGAAAATAAATCAGATGGTATGTAACAGCGACCGTGTGCTCAAAAGAAGTGCTGAAGG	-	novel	NA	P-0044796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	88	218	0	ENST00000267163.4:c.2521-28_2594del		p.X841_splice	ENST00000267163	NM_000321.2	841		25/27	0.934616690089587	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.932154982720502	1		218	94	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650662	67650662	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0044796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	85	336	0	ENST00000264010.4:c.967A>T	p.Lys323Ter	p.K323*	ENST00000264010	NM_006565.3	323	Aag/Tag	5/12	0.934616690089587	3	FACETS	0.99	0.887	1	0.495	0.443	0.549	CLONAL	1	TRUE	1	0.932154982720502	3		336	270	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243868	41243868	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1295353818	NA	P-0044796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	365	410	0	ENST00000357654.3:c.3680A>G	p.Gln1227Arg	p.Q1227R	ENST00000357654	NM_007294.3	1227	cAa/cGa	10/23	0.934616690089587	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.932154982720502	2		410	379	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499710	8499710	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	218	340	0	ENST00000356435.5:c.2259G>T	p.Arg753Ser	p.R753S	ENST00000356435		753	agG/agT	14/35	0.934616690089587	4	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	2	0.932154982720502	4		340	450	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914413	32914445	+	inframe_deletion	In_Frame_Del	DEL	CTTGTGGGATTTTTAGCACAGCAAGTGGAAAAT	CTTGTGGGATTTTTAGCACAGCAAGTGGAAAAT	-	novel	NA	P-0044796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	126	348	0	ENST00000380152.3:c.5923_5955del	p.Cys1975_Ser1985del	p.C1975_S1985del	ENST00000380152		1974	aCTTGTGGGATTTTTAGCACAGCAAGTGGAAAATct/act	11/27	0.934616690089587	1	FACETS	0.897	0.85	0.939	0.897	0.85	0.939	CLONAL	1	TRUE	0	0.932154982720502	1		348	161	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593680	55593696	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGTTTCCCAGAAACA	GGAGTTTCCCAGAAACA	-	novel	NA	P-0044796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	166	304	0	ENST00000288135.5:c.1748_1764del	p.Glu583AlafsTer17	p.E583Afs*17	ENST00000288135	NM_000222.2	582	tgGGAGTTTCCCAGAAACAgg/tggg	11/21	0.934616690089587	4	FACETS	0.964	0.888	1	0.241	0.222	0.261	CLONAL	1	TRUE	0	0.932154982720502	4		304	714	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626809	28626815	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TATCTAA	TATCTAA	-	novel	NA	P-0044796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	67	277	0	ENST00000241453.7:c.485-4_487del		p.X162_splice	ENST00000241453	NM_004119.2	162		5/24	0.934616690089587	4	FACETS	0.852	0.746	0.965	0.213	0.186	0.242	CLONAL	1	TRUE	0	0.932154982720502	4		277	326	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156093	106156093	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	138	423	0	ENST00000380013.4:c.994T>C	p.Cys332Arg	p.C332R	ENST00000380013	NM_001127208.2	332	Tgc/Cgc	3/11	0.934616690089587	4	FACETS	0.986	0.901	1	0.247	0.225	0.269	CLONAL	1	TRUE	0	0.932154982720502	4		423	580	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260833	16260833	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045507-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	69	632	0	ENST00000375759.3:c.8098C>G	p.Leu2700Val	p.L2700V	ENST00000375759	NM_015001.2	2700	Ctt/Gtt	11/15	0.113491525415372	4	FACETS	1	0.929	1	0.548	0.479	0.623	INDETERMINATE	1	FALSE	2	0.348392809982086	4		632	487	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261044	16261044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746961330	NA	P-0045507-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	75	510	0	ENST00000375759.3:c.8309C>T	p.Ser2770Leu	p.S2770L	ENST00000375759	NM_015001.2	2770	tCa/tTa	11/15	0.113491525415372	4	FACETS	1	0.968	1	0.658	0.579	0.743	INDETERMINATE	1	FALSE	2	0.348392809982086	4		510	441	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56415066	56415066	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045507-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	71	277	0	ENST00000348428.3:c.2467G>C	p.Glu823Gln	p.E823Q	ENST00000348428	NM_006785.3	823	Gaa/Caa	17/17	0.107319150455927	4	FACETS	1	0.969	1	0.682	0.598	0.772	INDETERMINATE	1	FALSE	2	0.348392809982086	4		277	403	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797265	135797266	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0045507-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	21	409	0	ENST00000298552.3:c.603dup	p.Phe202LeufsTer16	p.F202Lfs*16	ENST00000298552	NM_001162426.1	201	-/C	7/23	0.321147255650082	0	FACETS	0.239	0.183	0.303			1	SUBCLONAL	1	FALSE	0	0.348392809982086	0		409	329	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105645	11105645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045507-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	42	385	0	ENST00000358026.2:c.1561C>T	p.Arg521Trp	p.R521W	ENST00000358026	NM_001128849.1	521	Cgg/Tgg	9/36	1	2	FACETS	0.817	0.686	0.962	0.817	0.686	0.962	CLONAL	1	FALSE	1	0.348392809982086	2		385	295	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713171	30713171	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045507-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	74	370	0	ENST00000295754.5:c.496C>T	p.Gln166Ter	p.Q166*	ENST00000295754	NM_003242.5	166	Caa/Taa	4/7	0.262671891913412	4	FACETS	1	0.905	1	0.519	0.455	0.588	CLONAL	1	FALSE	2	0.348392809982086	4		370	552	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101423	27101423	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046110-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	280	240	0	ENST00000324856.7:c.4706del	p.Pro1569HisfsTer43	p.P1569Hfs*43	ENST00000324856	NM_006015.4	1569	Cca/ca	18/20	0.58870154953257	3	FACETS	1	0.989	1	0.745	0.71	0.78	CLONAL	2	TRUE	0	0.688358519655934	3		240	489	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041753	42041753	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0046110-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	291	391	0	ENST00000219905.7:c.5948C>G	p.Ser1983Ter	p.S1983*	ENST00000219905	NM_001164273.1	1983	tCa/tGa	17/24	0.303751432385977	2	FACETS	1	0.993	1	0.65	0.617	0.684	INDETERMINATE	1	TRUE	0	0.688358519655934	2		391	650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579317	7579317	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046110-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	584	367	0	ENST00000269305.4:c.370T>C	p.Cys124Arg	p.C124R	ENST00000269305	NM_001126112.2	124	Tgc/Cgc	4/11	0.612493026667642	3	FACETS	0.917	0.892	0.942	0.917	0.892	0.942	CLONAL	3	TRUE	0	0.688358519655934	3		367	829	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302276	15302276	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs774985086	NA	P-0046110-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	283	409	0	ENST00000263388.2:c.995G>T	p.Arg332Leu	p.R332L	ENST00000263388	NM_000435.2	332	cGc/cTc	6/33	0.554053440686278	2	FACETS	0.777	0.74	0.815	0.777	0.74	0.815	SUBCLONAL	2	TRUE	0	0.688358519655934	2		409	529	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467828	50467828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1040607869	NA	P-0046110-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	364	424	1	ENST00000331340.3:c.1063G>A	p.Ala355Thr	p.A355T	ENST00000331340	NM_006060.4	355	Gcg/Acg	8/8	0.624809511852778	2	FACETS	0.902	0.867	0.937	0.902	0.867	0.937	CLONAL	2	TRUE	0	0.688358519655934	2		425	586	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022490	12022510	+	inframe_deletion	In_Frame_Del	DEL	GGCCCCTCCGGTCCCCCCTGG	GGCCCCTCCGGTCCCCCCTGG	-	novel	NA	P-0046110-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	119	522	0	ENST00000396373.4:c.596_616del	p.Arg199_Asp206delinsHis	p.R199_D206delinsH	ENST00000396373	NM_001987.4	199	cGGCCCCTCCGGTCCCCCCTGGac/cac	5/8	0.554053440686278	2	FACETS	0.54	0.488	0.595	0.27	0.244	0.298	SUBCLONAL	1	TRUE	0	0.688358519655934	2		522	640	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644558	21644558	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046110-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	235	336	1	ENST00000421138.2:c.109C>T	p.Gln37Ter	p.Q37*	ENST00000421138		37	Cag/Tag	4/16	0.554053440686278	2	FACETS	0.774	0.733	0.815	0.774	0.733	0.815	SUBCLONAL	2	TRUE	0	0.688358519655934	2		337	441	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425325	49425332	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTGGGT	TTCTGGGT	-	novel	NA	P-0046110-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	231	435	0	ENST00000301067.7:c.13156_13163del	p.Thr4386AlafsTer21	p.T4386Afs*21	ENST00000301067	NM_003482.3	4386	ACCCAGAAg/g	39/54	0.581712545634531	3	FACETS	1	0.968	1	0.353	0.329	0.377	CLONAL	1	TRUE	0	0.688358519655934	3		435	852	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434547	110434547	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046110-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	210	455	0	ENST00000375856.3:c.3854del	p.Gly1285AlafsTer46	p.G1285Afs*46	ENST00000375856	NM_003749.2	1285	gGc/gc	1/2	0.648265118752509	2	FACETS	0.836	0.779	0.894	0.418	0.389	0.447	CLONAL	1	TRUE	0	0.688358519655934	2		455	730	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610159	10610159	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046110-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	321	461	0	ENST00000171111.5:c.551C>G	p.Ala184Gly	p.A184G	ENST00000171111	NM_203500.1	184	gCc/gGc	2/6	0.554053440686278	2	FACETS	0.803	0.767	0.838	0.803	0.767	0.838	CLONAL	2	TRUE	0	0.688358519655934	2		461	581	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664931	138664931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750300712	NA	P-0046110-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	142	305	0	ENST00000330315.3:c.634C>T	p.Pro212Ser	p.P212S	ENST00000330315	NM_023067.3	212	Ccc/Tcc	1/1	0.688358519655934	3	FACETS	0.793	0.724	0.865	0.264	0.241	0.289	SUBCLONAL	1	TRUE	0	0.688358519655934	3		305	699	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803481	32803482	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0046110-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	75	426	0	ENST00000374899.4:c.677_678delinsTA	p.Arg226Leu	p.R226L	ENST00000374899	NM_018833.2	226	cGG/cTA	4/12	0.203175068067671	5	FACETS	0.555	0.485	0.63	0.185	0.161	0.21	INDETERMINATE	1	TRUE	2	0.688358519655934	5		426	798	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0046836-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	74	165	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	0.14255635969015	3	FACETS	1	0.975	1	0.727	0.64	0.819	INDETERMINATE	1	TRUE	1	0.319226007128014	3		165	370	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573133	64573133	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046836-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	155	212	0	ENST00000312049.6:c.1159G>T	p.Glu387Ter	p.E387*	ENST00000312049	NM_130799.2	387	Gag/Tag	8/10	0.319226007128014	5	FACETS	0.798	0.73	0.869	0.532	0.487	0.579	SUBCLONAL	2	TRUE	2	0.319226007128014	5		212	900	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575555	64575570	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GCTGTCCAATTTGGTG	GCTGTCCAATTTGGTG	-	novel	NA	P-0046836-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	155	260	0	ENST00000312049.6:c.447_462del	p.Thr150ProfsTer30	p.T150Pfs*30	ENST00000312049	NM_130799.2	149	ggCACCAAATTGGACAGC/gg	3/10	0.319226007128014	5	FACETS	0.767	0.702	0.835	0.511	0.468	0.557	SUBCLONAL	2	TRUE	2	0.319226007128014	5		260	936	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924622	94924622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046836-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	60	215	0	ENST00000536441.1:c.288G>A	p.Met96Ile	p.M96I	ENST00000536441	NM_144665.3	96	atG/atA	3/10	0.242573441932702	5	FACETS	0.977	0.842	1	0.326	0.28	0.375	CLONAL	1	TRUE	2	0.319226007128014	5		215	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	G	rs1131691003	NA	P-0046836-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	128	166	0	ENST00000269305.4:c.96+1G>C		p.X32_splice	ENST00000269305	NM_001126112.2	32			0.216049730765579	4	FACETS	1	0.966	1	0.559	0.51	0.61	CLONAL	2	TRUE	0	0.319226007128014	4		166	473	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164884	106164884	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1339287432	NA	P-0046836-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	92	185	0	ENST00000380013.4:c.3752C>T	p.Thr1251Met	p.T1251M	ENST00000380013	NM_001127208.2	1251	aCg/aTg	6/11	0.14255635969015	3	FACETS	1	0.97	1	0.629	0.561	0.702	INDETERMINATE	1	TRUE	1	0.319226007128014	3		185	531	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629127	86629127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046836-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	39	175	0	ENST00000274376.6:c.872C>G	p.Thr291Arg	p.T291R	ENST00000274376	NM_002890.2	291	aCa/aGa	4/25	0.14255635969015	3	FACETS	1	0.878	1	0.533	0.444	0.63	INDETERMINATE	1	TRUE	1	0.319226007128014	3		175	266	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0047567-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	172	264	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.79723454394567	2		264	386	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220687	1220687	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047567-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	138	413	0	ENST00000326873.7:c.706del	p.Val236TrpfsTer51	p.V236Wfs*51	ENST00000326873	NM_000455.4	235	aaG/aa	5/10	0.794844227553524	1	FACETS	0.942	0.883	1	0.942	0.883	1	CLONAL	1	TRUE	0	0.79723454394567	1		413	221	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206618	108206618	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047567-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	167	318	0	ENST00000278616.4:c.8198A>C	p.Gln2733Pro	p.Q2733P	ENST00000278616	NM_000051.3	2733	cAg/cCg	56/63	0.79723454394567	1	FACETS	0.937	0.883	0.989	0.937	0.883	0.989	CLONAL	1	TRUE	0	0.79723454394567	1		318	269	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807549	36807549	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs768567087	NA	P-0047567-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	182	352	0	ENST00000373129.3:c.1115A>G	p.Gln372Arg	p.Q372R	ENST00000373129	NM_032017.1	372	cAg/cGg	12/12	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.79723454394567	2		352	454	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0047741-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	162	329	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.247797603665742	4	FACETS	0.958	0.881	1	1	0.988	1	CLONAL	3	TRUE	2	0.19	4		329	706	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517911	8517911	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047741-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	52	325	0	ENST00000356435.5:c.1480G>T	p.Ala494Ser	p.A494S	ENST00000356435		494	Gct/Tct	10/35	1	2	FACETS	0.967	0.823	1	0.967	0.823	1	CLONAL	1	TRUE	1	0.19	2		325	566	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220502	1220502	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	rs121913317	NA	P-0047741-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	50	474	0	ENST00000326873.7:c.595G>T	p.Glu199Ter	p.E199*	ENST00000326873	NM_000455.4	199	Gag/Tag	4/10	0.298139807502846	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.19	1		474	342	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498313	29498313	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047741-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	46	380	0	ENST00000389048.3:c.1867G>C	p.Val623Leu	p.V623L	ENST00000389048	NM_004304.4	623	Gtg/Ctg	10/29	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.19	2		380	418	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55987293	55987293	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047741-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	29	252	0	ENST00000263923.4:c.132G>T	p.Lys44Asn	p.K44N	ENST00000263923	NM_002253.2	44	aaG/aaT	2/30	1	2	FACETS	0.683	0.547	0.837	0.683	0.547	0.837	SUBCLONAL	1	TRUE	1	0.19	2		252	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0048231-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	414	480	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.385985686498041	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	4	TRUE	0	0.425739307135396	4		480	665	SUCCESS
ATR	545	MSKCC	GRCh37	3	142180912	142180924	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTGCATCTTTT	CTCTGCATCTTTT	-	novel	NA	P-0048231-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	29	201	0	ENST00000350721.4:c.7050_7062del	p.Arg2350SerfsTer17	p.R2350Sfs*17	ENST00000350721	NM_001184.3	2350	agAAAAGATGCAGAG/ag	42/47	0.239608276458942	4	FACETS	1	0.864	1	0.362	0.293	0.438	INDETERMINATE	1	TRUE	1	0.425739307135396	4		201	179	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748092	43748093	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CT	CT	AA	novel	NA	P-0048231-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	40	278	0	ENST00000382044.4:c.2713_2714delinsTT	p.Ser905Phe	p.S905F	ENST00000382044	NM_001141980.1	905	AGt/TTt	12/28	0.148289914723146	3	FACETS	0.789	0.658	0.932	0.263	0.219	0.311	INDETERMINATE	1	TRUE	0	0.425739307135396	3		278	289	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0048461-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	8	406	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	0.36134825444784	3	FACETS	0.129	0.083	0.19	0.065	0.041	0.095	SUBCLONAL	1	TRUE	1	0.417514246084045	3		406	358	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578393	7578393	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876660821	NA	P-0048461-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	128	541	0	ENST00000269305.4:c.537T>A	p.His179Gln	p.H179Q	ENST00000269305	NM_001126112.2	179	caT/caA	5/11	0.347673091363068	2	FACETS	0.907	0.833	0.983	0.907	0.833	0.983	CLONAL	2	TRUE	0	0.417514246084045	2		541	338	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937873	76937873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048461-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	45	254	0	ENST00000373344.5:c.2875G>A	p.Asp959Asn	p.D959N	ENST00000373344	NM_000489.3	959	Gat/Aat	9/35	0.417514246084045	3	FACETS	0.67	0.564	0.786			1	SUBCLONAL	1	TRUE	NA	0.417514246084045	3		254	389	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715683	18715683	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048461-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	41	458	0	ENST00000266497.5:c.3514T>A	p.Leu1172Met	p.L1172M	ENST00000266497		1172	Ttg/Atg	25/31	0.417514246084045	0	FACETS	0.241	0.2	0.286			1	SUBCLONAL	1	TRUE	0	0.417514246084045	0		458	475	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0048783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	107	300	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.996	0.905	1	0.996	0.905	1	CLONAL	1	TRUE	1	0.690966733194448	2		300	311	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219357	1219357	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730881970	NA	P-0048783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	199	336	0	ENST00000326873.7:c.409C>T	p.Gln137Ter	p.Q137*	ENST00000326873	NM_000455.4	137	Cag/Tag	3/10	0.690966733194448	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.690966733194448	1		336	349	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628857	187628858	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	170	390	0	ENST00000441802.2:c.2124dup	p.Val709CysfsTer9	p.V709Cfs*9	ENST00000441802	NM_005245.3	708	-/T	2/27	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.690966733194448	2		390	482	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171377	123171377	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	139	224	0	ENST00000218089.9:c.289T>A	p.Ser97Thr	p.S97T	ENST00000218089	NM_001042749.1	97	Tcg/Acg	6/35	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.690966733194448	2		224	371	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098586	108098591	+	frameshift_variant	Frame_Shift_Del	DEL	AAAATA	AAAATA	T	novel	NA	P-0048783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	128	259	0	ENST00000278616.4:c.156_161delinsT	p.Lys53PhefsTer8	p.K53Ffs*8	ENST00000278616	NM_000051.3	52	ggAAAATAt/ggTt	3/63	1	2	FACETS	0.955	0.874	1	0.955	0.874	1	CLONAL	1	TRUE	1	0.690966733194448	2		259	388	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683774	162683774	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	22	283	0	ENST00000366898.1:c.195C>A	p.Ser65Arg	p.S65R	ENST00000366898	NM_004562.2	65	agC/agA	3/12	0.690966733194448	1	FACETS	0.135	0.104	0.17	0.135	0.104	0.17	SUBCLONAL	1	TRUE	0	0.690966733194448	1		283	309	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99181120	99181120	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	43	327	0	ENST00000074304.5:c.2061C>G	p.Cys687Trp	p.C687W	ENST00000074304	NM_001134224.1	687	tgC/tgG	20/26	1	2	FACETS	0.248	0.207	0.293	0.248	0.207	0.293	SUBCLONAL	1	TRUE	1	0.690966733194448	2		327	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0049188-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	146	403	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	1	2	FACETS	0.829	0.76	0.901	0.829	0.76	0.901	CLONAL	1	TRUE	1	0.605107153084708	2		403	582	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061389	38061389	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049188-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	165	358	0	ENST00000250448.2:c.600C>G	p.Ile200Met	p.I200M	ENST00000250448	NM_004496.3	200	atC/atG	2/2	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.605107153084708	2		358	513	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0049752-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	95	399	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.591515633316143	7	FACETS	0.99	0.895	1	0.743	0.671	0.816	CLONAL	3	TRUE	3	0.591515633316143	7		399	268	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251752	212251752	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1237135640	NA	P-0049752-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	50	585	0	ENST00000342788.4:c.3307G>T	p.Asp1103Tyr	p.D1103Y	ENST00000342788	NM_005235.2	1103	Gat/Tat	27/28	0.570444623572161	3	FACETS	0.794	0.69	0.901	0.794	0.69	0.901	CLONAL	2	TRUE	1	0.591515633316143	3		585	138	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0050019-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	525	411	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.867891529280058	2	FACETS	0.955	0.936	0.972	0.955	0.936	0.972	CLONAL	2	TRUE	0	0.913218479097162	2		412	602	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0050019-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	67	135	1	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.913218479097162	1	FACETS	0.725	0.658	0.789	0.725	0.658	0.789	SUBCLONAL	1	TRUE	0	0.913218479097162	1		136	110	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108544	8108544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866443565	NA	P-0050019-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	231	340	0	ENST00000585124.1:c.851G>A	p.Arg284His	p.R284H	ENST00000585124	NM_004217.3	284	cGc/cAc	8/9	0.867891529280058	2	FACETS	0.894	0.84	0.948	0.447	0.42	0.474	CLONAL	1	TRUE	0	0.913218479097162	2		340	566	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0050019-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	64	370	0	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	0.862230984110039	2	FACETS	0.202	0.175	0.232	0.101	0.087	0.116	SUBCLONAL	1	TRUE	0	0.913218479097162	2		370	693	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0050019-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	629	461	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.867891529280058	2	FACETS	0.896	0.877	0.914	0.896	0.877	0.914	CLONAL	2	TRUE	0	0.913218479097162	2		461	769	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0050019-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	219	297	1	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	0.867891529280058	2	FACETS	0.671	0.626	0.716	0.335	0.313	0.358	SUBCLONAL	1	TRUE	0	0.913218479097162	2		298	715	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0050019-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	328	234	0	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			0.865483528101634	2	FACETS	0.94	0.916	0.963	0.94	0.916	0.963	CLONAL	2	TRUE	0	0.913218479097162	2		234	382	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0050019-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	576	438	0	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	0.867891529280058	2	FACETS	0.953	0.935	0.97	0.953	0.935	0.97	CLONAL	2	TRUE	0	0.913218479097162	2		438	662	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226899	2226899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762029066	NA	P-0050019-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	613	547	0	ENST00000398665.3:c.4379C>T	p.Thr1460Met	p.T1460M	ENST00000398665	NM_032482.2	1460	aCg/aTg	27/28	0.862230984110039	2	FACETS	0.945	0.928	0.962	0.945	0.928	0.962	CLONAL	2	TRUE	0	0.913218479097162	2		547	710	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246557	46246557	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161560614	NA	P-0050019-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	333	406	0	ENST00000334344.6:c.4651G>A	p.Ala1551Thr	p.A1551T	ENST00000334344	NM_152641.2	1551	Gca/Aca	15/21	0.873600550795842	2	FACETS	0.992	0.945	1	0.496	0.472	0.52	CLONAL	1	TRUE	0	0.913218479097162	2		406	735	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050019-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	591	545	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.873600550795842	2	FACETS	0.901	0.882	0.92	0.901	0.882	0.92	CLONAL	2	TRUE	0	0.913218479097162	2		545	718	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508460	106508460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050019-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	259	367	0	ENST00000359195.3:c.454C>T	p.Arg152Trp	p.R152W	ENST00000359195	NM_002649.2	152	Cgg/Tgg	2/11	0.833267283461578	4	FACETS	1	0.939	1	0.501	0.469	0.534	CLONAL	1	TRUE	2	0.913218479097162	4		367	1083	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445068	49445068	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050019-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	619	441	0	ENST00000301067.7:c.2398C>T	p.Gln800Ter	p.Q800*	ENST00000301067	NM_003482.3	800	Cag/Tag	10/54	0.873600550795842	2	FACETS	0.972	0.956	0.988	0.972	0.956	0.988	CLONAL	2	TRUE	0	0.913218479097162	2		441	697	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905567	50905567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760077781	NA	P-0050019-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	572	615	0	ENST00000440232.2:c.695G>A	p.Arg232His	p.R232H	ENST00000440232	NM_002691.3	232	cGt/cAt	6/27	0.862230984110039	2	FACETS	0.924	0.905	0.942	0.924	0.905	0.942	CLONAL	2	TRUE	0	0.913218479097162	2		615	678	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027541	48027541	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050019-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	500	395	0	ENST00000234420.5:c.2419del	p.Glu807LysfsTer3	p.E807Kfs*3	ENST00000234420	NM_000179.2	807	Gaa/aa	4/10	0.865483528101634	2	FACETS	0.925	0.905	0.944	0.925	0.905	0.944	CLONAL	2	TRUE	0	0.913218479097162	2		395	592	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218568	98218568	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050019-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	226	453	0	ENST00000331920.6:c.3296A>G	p.His1099Arg	p.H1099R	ENST00000331920	NM_000264.3	1099	cAc/cGc	19/24	0.867891529280058	2	FACETS	0.776	0.727	0.826	0.388	0.363	0.413	SUBCLONAL	1	TRUE	0	0.913218479097162	2		453	638	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532652	63532652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050019-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	307	410	0	ENST00000307078.5:c.1927G>A	p.Ala643Thr	p.A643T	ENST00000307078	NM_004655.3	643	Gcc/Acc	8/11	0.867891529280058	2	FACETS	0.954	0.905	1	0.477	0.452	0.501	CLONAL	1	TRUE	0	0.913218479097162	2		410	705	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27203090	27203090	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050019-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	275	426	0	ENST00000380036.4:c.2182G>C	p.Glu728Gln	p.E728Q	ENST00000380036	NM_000459.3	728	Gaa/Caa	13/23	0.867891529280058	2	FACETS	0.906	0.856	0.956	0.453	0.428	0.478	CLONAL	1	TRUE	0	0.913218479097162	2		426	665	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2060967	2060967	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1219804499	NA	P-0050019-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	354	478	0	ENST00000349721.2:c.1673A>G	p.Lys558Arg	p.K558R	ENST00000349721	NM_003070.3	558	aAg/aGg	9/34	0.867891529280058	2	FACETS	0.859	0.816	0.901	0.429	0.408	0.451	CLONAL	1	TRUE	0	0.913218479097162	2		478	903	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119693	17119693	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0050019-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	504	417	0	ENST00000285071.4:c.1300+1G>T		p.X434_splice	ENST00000285071	NM_144997.5	434			0.867891529280058	2	FACETS	0.95	0.931	0.968	0.95	0.931	0.968	CLONAL	2	TRUE	0	0.913218479097162	2		417	581	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176176077	176176077	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050019-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	478	461	0	ENST00000367669.3:c.38G>T	p.Gly13Val	p.G13V	ENST00000367669	NM_022457.5	13	gGg/gTg	1/20	0.867891529280058	2	FACETS	0.94	0.92	0.959	0.94	0.92	0.959	CLONAL	2	TRUE	0	0.913218479097162	2		461	557	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62318996	62318996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050019-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	234	505	0	ENST00000360203.5:c.1354G>A	p.Val452Met	p.V452M	ENST00000360203	NM_001283009.1	452	Gtg/Atg	17/35	0.862230984110039	2	FACETS	0.815	0.765	0.865	0.407	0.382	0.433	CLONAL	1	TRUE	0	0.913218479097162	2		505	629	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922993	39922993	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050019-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	340	444	0	ENST00000378444.4:c.3715C>G	p.Gln1239Glu	p.Q1239E	ENST00000378444	NM_001123385.1	1239	Cag/Gag	8/15	0.863252957227301	1	FACETS	0.961	0.933	0.988	0.961	0.933	0.988	CLONAL	1	TRUE	0	0.913218479097162	1		444	421	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61213457	61213457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1565130851	NA	P-0050019-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	256	398	0	ENST00000301761.2:c.415C>A	p.Leu139Met	p.L139M	ENST00000301761	NM_017841.2	139	Ctg/Atg	4/4	0.857881802354154	2	FACETS	0.864	0.814	0.914	0.432	0.407	0.457	CLONAL	1	TRUE	0	0.913218479097162	2		398	649	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29422388	29422419	+	splice_donor_variant,intron_variant	Splice_Site	DEL	GTAACCGGCCCGTGGCGGGCGGGAGGTGGGAG	GTAACCGGCCCGTGGCGGGCGGGAGGTGGGAG	CTAA	novel	NA	P-0050019-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	266	242	3	ENST00000356175.3:c.60+1_60+32delinsCTAA		p.X20_splice	ENST00000356175	NM_000267.3	20			0.867891529280058	2	FACETS	0.913	0.885	0.939	0.913	0.885	0.939	CLONAL	2	TRUE	0	0.913218479097162	2		245	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0050430-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	314	383	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.878469324500736	2	FACETS	0.987	0.963	1	0.987	0.963	1	CLONAL	2	TRUE	0	0.888525675366212	2		383	358	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100419	2100419	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050430-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	37	287	0	ENST00000219476.3:c.158del	p.Gly53AlafsTer8	p.G53Afs*8	ENST00000219476	NM_000548.3	53	Ggc/gc	3/42	0.877099687453696	2	FACETS	0.216	0.178	0.258	0.108	0.089	0.129	SUBCLONAL	1	TRUE	0	0.888525675366212	2		287	386	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2104156	2104162	+	frameshift_variant	Frame_Shift_Del	DEL	CCTACGC	CCTACGC	-	novel	NA	P-0050430-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	308	314	0	ENST00000349721.2:c.3280_3286del	p.Arg1095MetfsTer13	p.R1095Mfs*13	ENST00000349721	NM_003070.3	1093	taCCTACGC/ta	23/34	0.879358137983514	2	FACETS	0.95	0.923	0.974	0.95	0.923	0.974	CLONAL	2	TRUE	0	0.888525675366212	2		314	365	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	T	rs1023835002	NA	P-0050544-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	137	290	0	ENST00000558401.1:c.1A>T	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Ttg	1/4	0.573768782678177	3	FACETS	0.911	0.856	0.965	0.911	0.856	0.965	CLONAL	3	TRUE	0	0.62679825327464	3		290	210	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156541	55156541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368266633	NA	P-0050544-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	34	323	0	ENST00000257290.5:c.2942G>A	p.Arg981His	p.R981H	ENST00000257290	NM_006206.4	981	cGt/cAt	22/23	0.378310268045721	3	FACETS	0.651	0.536	0.778	0.325	0.268	0.389	SUBCLONAL	1	TRUE	1	0.62679825327464	3		323	219	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774119	56774119	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1555594699	NA	P-0050544-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	191	275	0	ENST00000337432.4:c.470T>G	p.Phe157Cys	p.F157C	ENST00000337432	NM_058216.2	157	tTt/tGt	3/9	0.575667351579401	4	FACETS	0.984	0.941	1	0.984	0.941	1	CLONAL	4	TRUE	0	0.62679825327464	4		275	252	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974695	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050544-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	123	389	0	ENST00000304494.5:c.132C>A	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	taC/taA	1/3	0.590547820429186	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.62679825327464	2		389	169	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164165	47164165	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050544-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	36	272	0	ENST00000409792.3:c.1961C>G	p.Ser654Cys	p.S654C	ENST00000409792	NM_014159.6	654	tCt/tGt	3/21	0.623194524480659	3	FACETS	0.712	0.59	0.845	0.356	0.295	0.423	SUBCLONAL	1	TRUE	1	0.62679825327464	3		272	212	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870285	155870285	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050544-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	29	301	0	ENST00000368323.3:c.554A>G	p.Lys185Arg	p.K185R	ENST00000368323	NM_006912.5	185	aAa/aGa	6/6	0.520516811388857	4	FACETS	0.586	0.472	0.714	0.293	0.236	0.357	SUBCLONAL	1	TRUE	2	0.62679825327464	4		301	257	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0050677-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	105	252	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.315028735009432	5	FACETS	0.98	0.882	1	0.653	0.588	0.722	CLONAL	2	TRUE	2	0.315028735009432	5		252	501	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984672	11984672	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0050677-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	28	207	0	ENST00000353533.5:c.219-1G>C		p.X73_splice	ENST00000353533	NM_003010.3	73			0.258679786073948	1	FACETS	0.619	0.497	0.757	0.619	0.497	0.757	SUBCLONAL	1	TRUE	0	0.315028735009432	1		207	242	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923272	26923272	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050677-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	49	245	0	ENST00000381527.3:c.268G>A	p.Asp90Asn	p.D90N	ENST00000381527	NM_001260.1	90	Gat/Aat	3/13	0.26563017200882	4	FACETS	0.74	0.626	0.865	0.37	0.313	0.433	SUBCLONAL	1	TRUE	2	0.315028735009432	4		245	553	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176678824	176678825	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0050677-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	49	308	0	ENST00000439151.2:c.4735_4736delinsAA	p.Gly1579Lys	p.G1579K	ENST00000439151	NM_022455.4	1579	GGa/AAa	12/23	0.315028735009432	5	FACETS	0.78	0.66	0.913	0.26	0.22	0.305	CLONAL	1	TRUE	2	0.315028735009432	5		308	587	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400335	225400362	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGAATTTAGTACATCTTCTCGCACCTAG	TGAATTTAGTACATCTTCTCGCACCTAG	-	novel	NA	P-0050677-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	43	198	0	ENST00000264414.4:c.265-4_288del		p.X89_splice	ENST00000264414	NM_003590.4	89		3/16	0.26563017200882	4	FACETS	0.827	0.693	0.976	0.414	0.346	0.488	CLONAL	1	TRUE	2	0.315028735009432	4		198	434	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050985-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	167	264	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.351410203814872	5	FACETS	1	0.939	1	1	0.939	1	CLONAL	3	TRUE	2	0.404431938909968	5		264	437	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221264	1221267	+	frameshift_variant	Frame_Shift_Del	DEL	TTGT	TTGT	-	rs121913320	NA	P-0050985-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	94	402	0	ENST00000326873.7:c.790_793del	p.Phe264ArgfsTer22	p.F264Rfs*22	ENST00000326873	NM_000455.4	263	TTGTtt/tt	6/10	0.385849953638537	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	0	0.404431938909968	2		402	222	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41209069	41209072	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CTTT	CTTT	-	novel	NA	P-0050985-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	85	402	0	ENST00000357654.3:c.5274_5277del	p.Lys1759SerfsTer5	p.K1759Sfs*5	ENST00000357654	NM_007294.3	1758	agAAAG/ag	19/23	0.404431938909968	3	FACETS	0.899	0.805	0.997	0.599	0.536	0.665	CLONAL	2	TRUE	0	0.404431938909968	3		402	281	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69456265	69456265	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050985-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	87	409	0	ENST00000227507.2:c.184A>T	p.Thr62Ser	p.T62S	ENST00000227507	NM_053056.2	62	Acc/Tcc	1/5	0.404431938909968	8	FACETS	0.887	0.787	0.993	0.296	0.262	0.331	CLONAL	2	TRUE	2	0.404431938909968	8		409	537	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67626745	67626745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050985-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	82	316	0	ENST00000272342.5:c.416G>A	p.Arg139His	p.R139H	ENST00000272342	NM_019002.3	139	cGt/cAt	3/6	0.404431938909968	3	FACETS	1	0.942	1	0.551	0.488	0.619	CLONAL	1	TRUE	1	0.404431938909968	3		316	442	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484167	8484170	+	frameshift_variant	Frame_Shift_Del	DEL	CCAT	CCAT	-	novel	NA	P-0050985-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	30	399	0	ENST00000356435.5:c.3362_3365del	p.Asp1121AlafsTer2	p.D1121Afs*2	ENST00000356435		1121	gATGGc/gc	19/35	1	2	FACETS	0.757	0.615	0.915	0.757	0.615	0.915	CLONAL	1	TRUE	1	0.404431938909968	2		399	196	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	92	382	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.989	0.895	1	0.989	0.895	1	CLONAL	1	TRUE	1	0.788000990758395	2		382	236	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625281	69625281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35983315	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	26	534	0	ENST00000334134.2:c.512G>A	p.Arg171His	p.R171H	ENST00000334134	NM_005247.2	171	cGc/cAc	3/3	1	2	FACETS	0.156	0.123	0.194	0.156	0.123	0.194	SUBCLONAL	1	TRUE	1	0.788000990758395	2		534	422	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199670	11199670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766533620	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	49	429	1	ENST00000361445.4:c.4918C>T	p.Arg1640Trp	p.R1640W	ENST00000361445	NM_004958.3	1640	Cgg/Tgg	35/58	0.788000990758395	1	FACETS	0.383	0.328	0.441	0.383	0.328	0.441	SUBCLONAL	1	TRUE	0	0.788000990758395	1		430	197	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439698	51439698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	203	525	0	ENST00000262662.1:c.263C>T	p.Thr88Ile	p.T88I	ENST00000262662		88	aCt/aTt	4/4	0.788000990758395	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.788000990758395	1		525	311	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163298661	163298661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1172182551	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	134	346	0	ENST00000271452.3:c.301G>A	p.Val101Met	p.V101M	ENST00000271452	NM_145697.2	101	Gtg/Atg	5/14	1	2	FACETS	0.958	0.882	1	0.958	0.882	1	CLONAL	1	TRUE	1	0.788000990758395	2		346	355	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567722	226567722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879911445	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	154	461	0	ENST00000366794.5:c.1444G>A	p.Gly482Arg	p.G482R	ENST00000366794	NM_001618.3	482	Ggg/Agg	10/23	1	2	FACETS	0.876	0.809	0.945	0.876	0.809	0.945	CLONAL	1	TRUE	1	0.788000990758395	2		461	446	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669369	241669369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	153	295	0	ENST00000366560.3:c.838G>A	p.Gly280Ser	p.G280S	ENST00000366560	NM_000143.3	280	Ggt/Agt	6/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.788000990758395	2		295	368	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100678	8100678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	171	545	0	ENST00000346208.3:c.652C>T	p.Pro218Ser	p.P218S	ENST00000346208		218	Ccc/Tcc	3/6	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.788000990758395	2		545	429	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601969	43601969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377767433	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	145	510	0	ENST00000355710.3:c.1013C>T	p.Thr338Ile	p.T338I	ENST00000355710	NM_020975.4	338	aCc/aTc	5/20	1	2	FACETS	0.878	0.809	0.949	0.878	0.809	0.949	CLONAL	1	TRUE	1	0.788000990758395	2		510	419	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649921	88649921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	103	237	0	ENST00000372037.3:c.170C>T	p.Pro57Leu	p.P57L	ENST00000372037	NM_004329.2	57	cCt/cTt	4/13	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.788000990758395	2		237	251	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690847	89690847	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776667	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	15	234	0	ENST00000371953.3:c.253+1G>A		p.X85_splice	ENST00000371953	NM_000314.4	85			1	2	FACETS	0.121	0.088	0.161	0.121	0.088	0.161	SUBCLONAL	1	TRUE	1	0.788000990758395	2		234	314	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692802	89692802	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123320	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	85	227	0	ENST00000371953.3:c.286C>T	p.Pro96Ser	p.P96S	ENST00000371953	NM_000314.4	96	Cca/Tca	5/9	1	2	FACETS	0.873	0.784	0.966	0.873	0.784	0.966	CLONAL	1	TRUE	1	0.788000990758395	2		227	247	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717609	89717609	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs876661024	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	15	311	0	ENST00000371953.3:c.635-1G>A		p.X212_splice	ENST00000371953	NM_000314.4	212			1	2	FACETS	0.101	0.073	0.134	0.101	0.073	0.134	SUBCLONAL	1	TRUE	1	0.788000990758395	2		311	377	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207523	102207523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	146	315	0	ENST00000263464.3:c.1612G>A	p.Asp538Asn	p.D538N	ENST00000263464	NM_001165.4	538	Gat/Aat	8/9	1	2	FACETS	0.929	0.857	1	0.929	0.857	1	CLONAL	1	TRUE	1	0.788000990758395	2		315	399	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207736	102207736	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	161	374	0	ENST00000263464.3:c.1718G>A	p.Gly573Asp	p.G573D	ENST00000263464	NM_001165.4	573	gGt/gAt	9/9	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.788000990758395	2		374	385	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376035	118376035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	149	536	0	ENST00000534358.1:c.9428C>T	p.Pro3143Leu	p.P3143L	ENST00000534358	NM_005933.3	3143	cCa/cTa	27/36	1	2	FACETS	0.927	0.856	0.999	0.927	0.856	0.999	CLONAL	1	TRUE	1	0.788000990758395	2		536	408	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380704	118380704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	151	398	0	ENST00000534358.1:c.10942C>T	p.Pro3648Ser	p.P3648S	ENST00000534358	NM_005933.3	3648	Cca/Tca	30/36	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.788000990758395	2		398	376	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	493265	493265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	125	347	0	ENST00000399788.2:c.298C>T	p.Leu100Phe	p.L100F	ENST00000399788	NM_001042603.1	100	Ctt/Ttt	3/28	NA	2	FACETS	0.839	0.768	0.913			1	INDETERMINATE	1	TRUE	NA	0.788000990758395	2		347	378	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418630	49418630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	137	537	0	ENST00000301067.7:c.15884G>A	p.Gly5295Glu	p.G5295E	ENST00000301067	NM_003482.3	5295	gGg/gAg	49/54	1	2	FACETS	0.906	0.833	0.98	0.906	0.833	0.98	CLONAL	1	TRUE	1	0.788000990758395	2		537	384	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426993	49426993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	133	527	0	ENST00000301067.7:c.11495C>T	p.Ser3832Phe	p.S3832F	ENST00000301067	NM_003482.3	3832	tCc/tTc	39/54	1	2	FACETS	0.922	0.848	0.999	0.922	0.848	0.999	CLONAL	1	TRUE	1	0.788000990758395	2		527	366	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856250	111856250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1246649893	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	127	431	0	ENST00000341259.2:c.301G>A	p.Glu101Lys	p.E101K	ENST00000341259	NM_005475.2	101	Gag/Aag	2/8	1	2	FACETS	0.968	0.889	1	0.968	0.889	1	CLONAL	1	TRUE	1	0.788000990758395	2		431	333	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120785294	120785294	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767743668	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	97	517	0	ENST00000257552.2:c.814C>T	p.Pro272Ser	p.P272S	ENST00000257552	NM_002442.3	272	Cca/Tca	12/15	1	2	FACETS	0.571	0.512	0.633	0.571	0.512	0.633	SUBCLONAL	1	TRUE	1	0.788000990758395	2		517	431	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562384	21562384	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	142	455	0	ENST00000382592.4:c.1535G>A	p.Arg512Lys	p.R512K	ENST00000382592	NM_014572.2	512	aGg/aAg	4/8	1	2	FACETS	0.964	0.889	1	0.964	0.889	1	CLONAL	1	TRUE	1	0.788000990758395	2		455	374	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26927898	26927898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	178	336	0	ENST00000381527.3:c.337G>A	p.Ala113Thr	p.A113T	ENST00000381527	NM_001260.1	113	Gct/Act	4/13	0.253868417131133	1	FACETS	0.607	0.565	0.65	0.607	0.565	0.65	INDETERMINATE	1	TRUE	0	0.788000990758395	1		336	451	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623565	28623565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752394054	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	153	375	0	ENST00000241453.7:c.992C>T	p.Ser331Phe	p.S331F	ENST00000241453	NM_004119.2	331	tCc/tTc	8/24	0.253868417131133	1	FACETS	0.552	0.51	0.595	0.552	0.51	0.595	INDETERMINATE	1	TRUE	0	0.788000990758395	1		375	426	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911308	32911308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	180	421	0	ENST00000380152.3:c.2816C>T	p.Thr939Ile	p.T939I	ENST00000380152		939	aCc/aTc	11/27	1	2	FACETS	0.991	0.923	1	0.991	0.923	1	CLONAL	1	TRUE	1	0.788000990758395	2		421	461	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050972	49050972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1460190600	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	141	349	0	ENST00000267163.4:c.2656G>A	p.Asp886Asn	p.D886N	ENST00000267163	NM_000321.2	886	Gat/Aat	25/27	1	2	FACETS	0.937	0.863	1	0.937	0.863	1	CLONAL	1	TRUE	1	0.788000990758395	2		349	382	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003236	42003236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	164	445	0	ENST00000219905.7:c.2773C>T	p.Pro925Ser	p.P925S	ENST00000219905	NM_001164273.1	925	Cca/Tca	8/24	1	2	FACETS	0.993	0.922	1	0.993	0.922	1	CLONAL	1	TRUE	1	0.788000990758395	2		445	419	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712548	43712548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	199	520	0	ENST00000382044.4:c.4636G>A	p.Asp1546Asn	p.D1546N	ENST00000382044	NM_001141980.1	1546	Gac/Aac	21/28	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.788000990758395	2		520	481	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720356	43720358	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs755965497	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	141	395	0	ENST00000382044.4:c.3684_3686del	p.Glu1229del	p.E1229del	ENST00000382044	NM_001141980.1	1228	gaAGAg/gag	18/28	1	2	FACETS	0.92	0.848	0.994	0.92	0.848	0.994	CLONAL	1	TRUE	1	0.788000990758395	2		395	389	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729231	66729231	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	132	415	0	ENST00000307102.5:c.438+1G>A		p.X146_splice	ENST00000307102	NM_002755.3	146			1	2	FACETS	0.875	0.803	0.949	0.875	0.803	0.949	CLONAL	1	TRUE	1	0.788000990758395	2		415	383	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134271	2134271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	158	526	0	ENST00000219476.3:c.4048G>A	p.Glu1350Lys	p.E1350K	ENST00000219476	NM_000548.3	1350	Gag/Aag	34/42	1	2	FACETS	0.976	0.904	1	0.976	0.904	1	CLONAL	1	TRUE	1	0.788000990758395	2		526	411	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656481	3656481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	133	439	1	ENST00000294008.3:c.754G>A	p.Gly252Arg	p.G252R	ENST00000294008	NM_032444.2	252	Ggg/Agg	3/15	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.788000990758395	2		440	329	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777883	3777883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	157	522	0	ENST00000262367.5:c.7165G>A	p.Val2389Ile	p.V2389I	ENST00000262367	NM_004380.2	2389	Gtc/Atc	31/31	1	2	FACETS	0.864	0.799	0.932	0.864	0.799	0.932	CLONAL	1	TRUE	1	0.788000990758395	2		522	461	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934639	9934639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368188808	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	135	340	0	ENST00000330684.3:c.1516G>A	p.Val506Ile	p.V506I	ENST00000330684	NM_001134407.1	506	Gtc/Atc	7/13	1	2	FACETS	0.993	0.915	1	0.993	0.915	1	CLONAL	1	TRUE	1	0.788000990758395	2		340	345	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014128	14014128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	127	410	0	ENST00000311895.7:c.106G>A	p.Ala36Thr	p.A36T	ENST00000311895	NM_005236.2	36	Gcc/Acc	1/11	1	2	FACETS	0.86	0.787	0.934	0.86	0.787	0.934	CLONAL	1	TRUE	1	0.788000990758395	2		410	375	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132631	67132631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	133	380	0	ENST00000412916.2:c.514C>T	p.Pro172Ser	p.P172S	ENST00000412916		172	Cct/Tct	6/6	1	2	FACETS	0.893	0.82	0.968	0.893	0.82	0.968	CLONAL	1	TRUE	1	0.788000990758395	2		380	378	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662414	67662414	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	166	465	0	ENST00000264010.4:c.1660G>A	p.Ala554Thr	p.A554T	ENST00000264010	NM_006565.3	554	Gct/Act	9/12	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.788000990758395	2		465	391	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831954	72831954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	188	440	0	ENST00000268489.5:c.4627C>T	p.Arg1543Cys	p.R1543C	ENST00000268489	NM_006885.3	1543	Cgc/Tgc	9/10	1	2	FACETS	0.984	0.918	1	0.984	0.918	1	CLONAL	1	TRUE	1	0.788000990758395	2		440	485	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991953	72991953	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375392183	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	178	504	0	ENST00000268489.5:c.2092G>A	p.Gly698Arg	p.G698R	ENST00000268489	NM_006885.3	698	Ggg/Agg	2/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.788000990758395	2		504	414	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341586	89341586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	128	378	0	ENST00000301030.4:c.7484C>T	p.Pro2495Leu	p.P2495L	ENST00000301030	NM_001256183.1	2495	cCc/cTc	10/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.788000990758395	2		378	289	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349770	89349770	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	141	385	0	ENST00000301030.4:c.3180del	p.Asp1061IlefsTer257	p.D1061Ifs*257	ENST00000301030	NM_001256183.1	1060	aaA/aa	9/13	1	2	FACETS	0.908	0.837	0.982	0.908	0.837	0.982	CLONAL	1	TRUE	1	0.788000990758395	2		385	394	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349940	89349940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	229	603	0	ENST00000301030.4:c.3010C>T	p.His1004Tyr	p.H1004Y	ENST00000301030	NM_001256183.1	1004	Cac/Tac	9/13	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.788000990758395	2		603	552	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836386	89836386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746098172	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	25	547	0	ENST00000389301.3:c.2363C>T	p.Ala788Val	p.A788V	ENST00000389301	NM_000135.2	788	gCc/gTc	26/43	1	2	FACETS	0.151	0.119	0.189	0.151	0.119	0.189	SUBCLONAL	1	TRUE	1	0.788000990758395	2		547	420	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845385	89845385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	155	443	0	ENST00000389301.3:c.1742C>T	p.Ser581Phe	p.S581F	ENST00000389301	NM_000135.2	581	tCc/tTc	19/43	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.788000990758395	2		443	375	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108696	8108696	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	130	400	0	ENST00000585124.1:c.699G>A	p.Met233Ile	p.M233I	ENST00000585124	NM_004217.3	233	atG/atA	8/9	1	2	FACETS	0.929	0.853	1	0.929	0.853	1	CLONAL	1	TRUE	1	0.788000990758395	2		400	355	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011158	12011158	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	132	311	0	ENST00000353533.5:c.565T>C	p.Tyr189His	p.Y189H	ENST00000353533	NM_003010.3	189	Tac/Cac	5/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.788000990758395	2		311	329	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16046997	16046997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	140	310	0	ENST00000268712.3:c.1096G>A	p.Gly366Arg	p.G366R	ENST00000268712	NM_006311.3	366	Gga/Aga	11/46	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.788000990758395	2		310	346	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17124922	17124922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	143	488	0	ENST00000285071.4:c.800G>A	p.Ser267Asn	p.S267N	ENST00000285071	NM_144997.5	267	aGc/aAc	8/14	1	2	FACETS	0.968	0.893	1	0.968	0.893	1	CLONAL	1	TRUE	1	0.788000990758395	2		488	375	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37865703	37865703	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	179	459	0	ENST00000269571.5:c.572C>T	p.Ala191Val	p.A191V	ENST00000269571		191	gCc/gTc	4/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.788000990758395	2		459	405	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40879700	40879700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	122	337	0	ENST00000428826.2:c.199C>T	p.Pro67Ser	p.P67S	ENST00000428826		67	Cct/Tct	4/21	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.788000990758395	2		337	307	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40880884	40880884	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	131	382	0	ENST00000428826.2:c.76C>T	p.Leu26Phe	p.L26F	ENST00000428826		26	Ctt/Ttt	3/21	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.788000990758395	2		382	321	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243967	41243967	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357290	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	174	522	0	ENST00000357654.3:c.3581C>T	p.Thr1194Ile	p.T1194I	ENST00000357654	NM_007294.3	1194	aCc/aTc	10/23	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.788000990758395	2		522	436	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804402	46804402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	129	465	0	ENST00000290295.7:c.605C>T	p.Ser202Phe	p.S202F	ENST00000290295	NM_006361.5	202	tCc/tTc	2/2	1	2	FACETS	0.972	0.893	1	0.972	0.893	1	CLONAL	1	TRUE	1	0.788000990758395	2		465	337	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47679312	47679312	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371674237	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	161	388	0	ENST00000347630.2:c.895G>A	p.Val299Met	p.V299M	ENST00000347630	NM_001007230.1	299	Gtg/Atg	10/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.788000990758395	2		388	379	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534422	63534422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	188	550	1	ENST00000307078.5:c.1099C>T	p.Pro367Ser	p.P367S	ENST00000307078	NM_004655.3	367	Ccc/Tcc	5/11	1	2	FACETS	0.899	0.837	0.962	0.899	0.837	0.962	CLONAL	1	TRUE	1	0.788000990758395	2		551	531	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554720	63554720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878854723	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	164	477	0	ENST00000307078.5:c.19G>A	p.Val7Met	p.V7M	ENST00000307078	NM_004655.3	7	Gtg/Atg	2/11	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.788000990758395	2		477	416	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66521968	66521968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	172	342	1	ENST00000358598.2:c.623G>A	p.Gly208Glu	p.G208E	ENST00000358598	NM_212471.2	208	gGa/gAa	7/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.788000990758395	2		343	409	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60795956	60795956	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	168	482	0	ENST00000333681.4:c.622C>T	p.Pro208Ser	p.P208S	ENST00000333681		208	Cct/Tct	3/3	1	2	FACETS	0.95	0.882	1	0.95	0.882	1	CLONAL	1	TRUE	1	0.788000990758395	2		482	449	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612236	1612236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	124	441	0	ENST00000344749.5:c.1783G>A	p.Val595Ile	p.V595I	ENST00000344749	NM_001136139.2	595	Gtc/Atc	18/19	0.253868417131133	1	FACETS	0.587	0.538	0.637	0.587	0.538	0.637	INDETERMINATE	1	TRUE	0	0.788000990758395	1		441	325	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244370	5244370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	141	513	0	ENST00000357368.4:c.1112G>A	p.Ser371Asn	p.S371N	ENST00000357368	NM_002850.3	371	aGc/aAc	11/38	0.253868417131133	1	FACETS	0.55	0.507	0.595	0.55	0.507	0.595	INDETERMINATE	1	TRUE	0	0.788000990758395	1		513	394	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353726	15353726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	127	406	0	ENST00000263377.2:c.3154G>A	p.Asp1052Asn	p.D1052N	ENST00000263377	NM_058243.2	1052	Gac/Aac	14/20	0.253868417131133	1	FACETS	0.531	0.486	0.577	0.531	0.486	0.577	INDETERMINATE	1	TRUE	0	0.788000990758395	1		406	368	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15365022	15365022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	131	397	0	ENST00000263377.2:c.2099C>T	p.Ser700Phe	p.S700F	ENST00000263377	NM_058243.2	700	tCc/tTc	11/20	0.253868417131133	1	FACETS	0.6	0.551	0.649	0.6	0.551	0.649	INDETERMINATE	1	TRUE	0	0.788000990758395	1		397	336	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216627	36216627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	123	544	0	ENST00000222270.7:c.3793C>T	p.Leu1265Phe	p.L1265F	ENST00000222270	NM_014727.1	1265	Ctc/Ttc	13/37	0.788000990758395	1	FACETS	0.955	0.892	1	0.955	0.892	1	CLONAL	1	TRUE	0	0.788000990758395	1		544	198	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224211	36224211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764595621	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	148	338	0	ENST00000222270.7:c.6761C>T	p.Pro2254Leu	p.P2254L	ENST00000222270	NM_014727.1	2254	cCc/cTc	28/37	0.788000990758395	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.788000990758395	1		338	212	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795243	42795243	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	134	488	0	ENST00000575354.2:c.2327del	p.Pro776LeufsTer148	p.P776Lfs*148	ENST00000575354	NM_015125.3	775	Ccc/cc	10/20	0.788000990758395	1	FACETS	0.996	0.934	1	0.996	0.934	1	CLONAL	1	TRUE	0	0.788000990758395	1		488	207	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241937	39241937	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	153	318	0	ENST00000402219.2:c.1909C>T	p.Pro637Ser	p.P637S	ENST00000402219	NM_005633.3	637	Cct/Tct	11/23	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.788000990758395	2		318	381	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635695	47635695	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs267607924	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	146	279	0	ENST00000233146.2:c.366+1G>A		p.X122_splice	ENST00000233146	NM_000251.2	122			1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.788000990758395	2		279	354	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095902	178095902	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	203	463	0	ENST00000397062.3:c.1429C>T	p.Pro477Ser	p.P477S	ENST00000397062	NM_006164.4	477	Cct/Tct	5/5	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.788000990758395	2		463	505	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267335	198267337	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	181	420	0	ENST00000335508.6:c.2020_2022del	p.Leu674del	p.L674del	ENST00000335508	NM_012433.2	674	CTT/-	14/25	1	2	FACETS	0.892	0.829	0.956	0.892	0.829	0.956	CLONAL	1	TRUE	1	0.788000990758395	2		420	515	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202123063	202123063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	188	451	0	ENST00000358485.4:c.109G>A	p.Gly37Arg	p.G37R	ENST00000358485	NM_001080125.1	37	Ggg/Agg	1/9	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.788000990758395	2		451	454	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	199	343	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.788000990758395	2		343	485	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212252681	212252681	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	112	387	0	ENST00000342788.4:c.3172C>T	p.Pro1058Ser	p.P1058S	ENST00000342788	NM_005235.2	1058	Ccc/Tcc	26/28	1	2	FACETS	0.648	0.586	0.711	0.648	0.586	0.711	SUBCLONAL	1	TRUE	1	0.788000990758395	2		387	439	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587207	212587207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	210	417	0	ENST00000342788.4:c.794C>T	p.Thr265Ile	p.T265I	ENST00000342788	NM_005235.2	265	aCc/aTc	7/28	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.788000990758395	2		417	531	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741500	39741500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	169	446	0	ENST00000361337.2:c.1387G>A	p.Glu463Lys	p.E463K	ENST00000361337	NM_003286.2	463	Gaa/Aaa	14/21	1	2	FACETS	0.949	0.881	1	0.949	0.881	1	CLONAL	1	TRUE	1	0.788000990758395	2		446	452	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231783	36231783	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057519748	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	191	510	0	ENST00000300305.3:c.601C>T	p.Arg201Ter	p.R201*	ENST00000300305		201	Cga/Tga	5/8	1	2	FACETS	0.936	0.873	1	0.936	0.873	1	CLONAL	1	TRUE	1	0.788000990758395	2		510	518	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764361	39764361	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368736293	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	28	379	0	ENST00000288319.7:c.751C>T	p.Pro251Ser	p.P251S	ENST00000288319	NM_182918.3	251	Cca/Tca	7/10	1	2	FACETS	0.168	0.134	0.207	0.168	0.134	0.207	SUBCLONAL	1	TRUE	1	0.788000990758395	2		379	423	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39772499	39772499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	25	417	0	ENST00000288319.7:c.742C>T	p.Pro248Ser	p.P248S	ENST00000288319	NM_182918.3	248	Cca/Tca	6/10	1	2	FACETS	0.167	0.131	0.208	0.167	0.131	0.208	SUBCLONAL	1	TRUE	1	0.788000990758395	2		417	380	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817445	39817445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769957252	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	173	486	0	ENST00000288319.7:c.118G>A	p.Asp40Asn	p.D40N	ENST00000288319	NM_182918.3	40	Gac/Aac	2/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.788000990758395	2		486	410	SUCCESS
NF2	4771	MSKCC	GRCh37	22	29999991	29999991	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	110	310	0	ENST00000338641.4:c.4G>A	p.Ala2Thr	p.A2T	ENST00000338641	NM_000268.3	2	Gcc/Acc	1/16	0.253868417131133	1	FACETS	0.62	0.566	0.674	0.62	0.566	0.674	INDETERMINATE	1	TRUE	0	0.788000990758395	1		310	273	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421214	12421214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1010142067	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	140	394	0	ENST00000287820.6:c.94G>A	p.Val32Ile	p.V32I	ENST00000287820	NM_015869.4	32	Gtt/Att	2/7	1	2	FACETS	0.86	0.791	0.931	0.86	0.791	0.931	CLONAL	1	TRUE	1	0.788000990758395	2		394	413	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650412	12650412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762448032	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	148	391	0	ENST00000251849.4:c.434C>T	p.Thr145Met	p.T145M	ENST00000251849	NM_002880.3	145	aCg/aTg	5/17	1	2	FACETS	0.894	0.825	0.965	0.894	0.825	0.965	CLONAL	1	TRUE	1	0.788000990758395	2		391	420	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098809	47098810	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	156	518	0	ENST00000409792.3:c.6464_6465del	p.Leu2155ArgfsTer3	p.L2155Rfs*3	ENST00000409792	NM_014159.6	2155	cTT/c	15/21	1	2	FACETS	0.876	0.809	0.944	0.876	0.809	0.944	CLONAL	1	TRUE	1	0.788000990758395	2		518	452	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125401	47125401	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	151	467	0	ENST00000409792.3:c.5869del	p.Asp1957ThrfsTer4	p.D1957Tfs*4	ENST00000409792	NM_014159.6	1957	Gac/ac	12/21	1	2	FACETS	0.906	0.837	0.977	0.906	0.837	0.977	CLONAL	1	TRUE	1	0.788000990758395	2		467	423	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165642	47165642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1375690681	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	201	553	0	ENST00000409792.3:c.484G>A	p.Ala162Thr	p.A162T	ENST00000409792	NM_014159.6	162	Gca/Aca	3/21	1	2	FACETS	0.979	0.916	1	0.979	0.916	1	CLONAL	1	TRUE	1	0.788000990758395	2		553	521	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149243908	149243908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	128	242	0	ENST00000360632.3:c.910C>T	p.Pro304Ser	p.P304S	ENST00000360632	NM_015472.4	304	Cca/Tca	6/7	1	2	FACETS	0.883	0.809	0.958	0.883	0.809	0.958	CLONAL	1	TRUE	1	0.788000990758395	2		242	368	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927995	178927995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	21	304	0	ENST00000263967.3:c.1273G>A	p.Gly425Arg	p.G425R	ENST00000263967	NM_006218.2	425	Gga/Aga	8/21	1	2	FACETS	0.14	0.107	0.179	0.14	0.107	0.179	SUBCLONAL	1	TRUE	1	0.788000990758395	2		304	380	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447294	187447294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	199	517	0	ENST00000232014.4:c.899G>A	p.Ser300Asn	p.S300N	ENST00000232014	NM_001130845.1	300	aGc/aAc	5/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.788000990758395	2		517	425	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604263	189604263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	216	471	0	ENST00000264731.3:c.1430C>T	p.Ser477Phe	p.S477F	ENST00000264731	NM_003722.4	477	tCt/tTt	11/14	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.788000990758395	2		471	513	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920106	1920106	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	157	477	0	ENST00000382891.5:c.1166C>T	p.Ser389Phe	p.S389F	ENST00000382891	NM_133335.3	389	tCt/tTt	5/22	1	2	FACETS	0.979	0.907	1	0.979	0.907	1	CLONAL	1	TRUE	1	0.788000990758395	2		477	407	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956221	55956221	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs767542615	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	128	341	0	ENST00000263923.4:c.3094C>T	p.Arg1032Ter	p.R1032*	ENST00000263923	NM_002253.2	1032	Cga/Tga	23/30	1	2	FACETS	0.897	0.823	0.974	0.897	0.823	0.974	CLONAL	1	TRUE	1	0.788000990758395	2		341	362	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516863	187516863	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	24	365	0	ENST00000441802.2:c.13118C>T	p.Ser4373Phe	p.S4373F	ENST00000441802	NM_005245.3	4373	tCc/tTc	26/27	1	2	FACETS	0.17	0.133	0.213	0.17	0.133	0.213	SUBCLONAL	1	TRUE	1	0.788000990758395	2		365	358	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522556	187522556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	161	352	0	ENST00000441802.2:c.11507G>A	p.Gly3836Glu	p.G3836E	ENST00000441802	NM_005245.3	3836	gGa/gAa	21/27	1	2	FACETS	0.994	0.922	1	0.994	0.922	1	CLONAL	1	TRUE	1	0.788000990758395	2		352	411	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233630	233630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	52	88	0	ENST00000264932.6:c.934C>T	p.Arg312Cys	p.R312C	ENST00000264932	NM_004168.2	312	Cgt/Tgt	8/15	1	2	FACETS	0.963	0.841	1	0.963	0.841	1	CLONAL	1	TRUE	1	0.788000990758395	2		88	137	SUCCESS
APC	324	MSKCC	GRCh37	5	112177554	112177554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	181	442	0	ENST00000257430.4:c.6263C>T	p.Ser2088Leu	p.S2088L	ENST00000257430	NM_000038.5	2088	tCa/tTa	16/16	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.788000990758395	2		442	451	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495406	149495406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554107047	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	186	546	0	ENST00000261799.4:c.3241G>A	p.Glu1081Lys	p.E1081K	ENST00000261799	NM_002609.3	1081	Gag/Aag	23/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.788000990758395	2		546	455	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815325	32815325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	165	421	0	ENST00000354258.4:c.2048G>A	p.Ser683Asn	p.S683N	ENST00000354258	NM_000593.5	683	aGt/aAt	9/11	1	2	FACETS	0.961	0.891	1	0.961	0.891	1	CLONAL	1	TRUE	1	0.788000990758395	2		421	436	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117717368	117717368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	178	364	0	ENST00000368508.3:c.839C>T	p.Thr280Ile	p.T280I	ENST00000368508	NM_002944.2	280	aCc/aTc	8/43	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.788000990758395	2		364	451	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265613	152265613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	177	458	0	ENST00000206249.3:c.1066C>T	p.His356Tyr	p.H356Y	ENST00000206249	NM_000125.3	356	Cac/Tac	4/8	1	2	FACETS	0.942	0.876	1	0.942	0.876	1	CLONAL	1	TRUE	1	0.788000990758395	2		458	477	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55231503	55231503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	148	392	0	ENST00000275493.2:c.1709C>T	p.Thr570Ile	p.T570I	ENST00000275493	NM_005228.3	570	aCc/aTc	14/28	0.788000990758395	3	FACETS	1	0.957	1	0.531	0.488	0.575	CLONAL	1	TRUE	1	0.788000990758395	3		392	493	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843264	128843264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1389568034	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	140	497	0	ENST00000249373.3:c.371C>T	p.Pro124Leu	p.P124L	ENST00000249373	NM_005631.4	124	cCc/cTc	2/12	0.788000990758395	3	FACETS	0.942	0.862	1	0.471	0.431	0.512	CLONAL	1	TRUE	1	0.788000990758395	3		497	526	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852027	128852027	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	143	514	0	ENST00000249373.3:c.2099C>T	p.Thr700Ile	p.T700I	ENST00000249373	NM_005631.4	700	aCc/aTc	12/12	0.788000990758395	3	FACETS	0.984	0.903	1	0.492	0.451	0.535	CLONAL	1	TRUE	1	0.788000990758395	3		514	514	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434495	140434495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	63	364	0	ENST00000288602.6:c.2203C>T	p.Arg735Trp	p.R735W	ENST00000288602	NM_004333.4	735	Cgg/Tgg	18/18	0.788000990758395	3	FACETS	0.491	0.426	0.562	0.245	0.212	0.281	SUBCLONAL	1	TRUE	1	0.788000990758395	3		364	454	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874226	151874226	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	159	396	0	ENST00000262189.6:c.8312del	p.Ser2771ThrfsTer7	p.S2771Tfs*7	ENST00000262189	NM_170606.2	2771	aGc/ac	38/59	0.573974597499809	3	FACETS	0.98	0.903	1			1	CLONAL	1	TRUE	NA	0.788000990758395	3		396	574	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738520	145738520	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	100	423	0	ENST00000428558.2:c.2465G>A	p.Gly822Asp	p.G822D	ENST00000428558	NM_004260.3	822	gGc/gAc	16/22	1	2	FACETS	0.843	0.763	0.926	0.843	0.763	0.926	CLONAL	1	TRUE	1	0.788000990758395	2		423	301	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340431	8340431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	164	413	0	ENST00000356435.5:c.5165C>T	p.Ala1722Val	p.A1722V	ENST00000356435		1722	gCa/gTa	31/35	1	2	FACETS	0.989	0.918	1	0.989	0.918	1	CLONAL	1	TRUE	1	0.788000990758395	2		413	421	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971169	21971169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1309566180	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	42	549	0	ENST00000579755.1:c.232G>A	p.Ala78Thr	p.A78T	ENST00000579755		78	Gct/Act	2/3	1	2	FACETS	0.22	0.183	0.26	0.22	0.183	0.26	SUBCLONAL	1	TRUE	1	0.788000990758395	2		549	485	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636213	87636213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs988042143	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	189	475	0	ENST00000277120.3:c.2378C>T	p.Thr793Met	p.T793M	ENST00000277120		793	aCg/aTg	19/19	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.788000990758395	2		475	439	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231217	98231217	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766812549	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	167	516	0	ENST00000331920.6:c.2066C>T	p.Pro689Leu	p.P689L	ENST00000331920	NM_000264.3	689	cCc/cTc	14/24	1	2	FACETS	0.87	0.806	0.936	0.87	0.806	0.936	CLONAL	1	TRUE	1	0.788000990758395	2		516	487	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98241300	98241300	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	147	362	0	ENST00000331920.6:c.1197G>A	p.Trp399Ter	p.W399*	ENST00000331920	NM_000264.3	399	tgG/tgA	8/24	1	2	FACETS	0.995	0.92	1	0.995	0.92	1	CLONAL	1	TRUE	1	0.788000990758395	2		362	375	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270447	98270447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1025299062	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	138	361	0	ENST00000331920.6:c.197C>T	p.Ser66Phe	p.S66F	ENST00000331920	NM_000264.3	66	tCc/tTc	1/24	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.788000990758395	2		361	336	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779816	135779816	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768189353	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	93	223	0	ENST00000298552.3:c.2023G>A	p.Asp675Asn	p.D675N	ENST00000298552	NM_001162426.1	675	Gac/Aac	16/23	1	2	FACETS	0.992	0.898	1	0.992	0.898	1	CLONAL	1	TRUE	1	0.788000990758395	2		223	238	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390926	139390926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	192	663	1	ENST00000277541.6:c.7265G>A	p.Ser2422Asn	p.S2422N	ENST00000277541	NM_017617.3	2422	aGc/aAc	34/34	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.788000990758395	2		664	485	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923844	39923845	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	TA	TA	-	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	151	191	0	ENST00000378444.4:c.3246_3247del	p.Tyr1082Ter	p.Y1082*	ENST00000378444	NM_001123385.1	1082	taTAgt/tagt	7/15	1	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.788000990758395	1		191	217	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1696715	1696715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	154	478	0	ENST00000378625.1:c.131C>T	p.Ser44Phe	p.S44F	ENST00000378625	NM_001198994.1	44	tCt/tTt	2/14	0.788000990758395	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.788000990758395	1		478	234	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202906	16202906	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	46	495	0	ENST00000375759.3:c.614C>T	p.Ala205Val	p.A205V	ENST00000375759	NM_015001.2	205	gCt/gTt	3/15	0.788000990758395	1	FACETS	0.28	0.237	0.326	0.28	0.237	0.326	SUBCLONAL	1	TRUE	0	0.788000990758395	1		495	253	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932089	36932089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	113	544	0	ENST00000361632.4:c.2380G>A	p.Ala794Thr	p.A794T	ENST00000361632		794	Gcc/Acc	16/16	0.788000990758395	1	FACETS	0.715	0.657	0.774	0.715	0.657	0.774	SUBCLONAL	1	TRUE	0	0.788000990758395	1		544	243	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247973	59247973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1250010402	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	58	566	0	ENST00000371222.2:c.770G>A	p.Arg257Lys	p.R257K	ENST00000371222	NM_002228.3	257	aGg/aAg	1/1	0.788000990758395	1	FACETS	0.252	0.217	0.289	0.252	0.217	0.289	SUBCLONAL	1	TRUE	0	0.788000990758395	1		566	354	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150900392	150900392	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	24	482	0	ENST00000271640.5:c.202G>A	p.Val68Ile	p.V68I	ENST00000271640	NM_001145415.1	68	Gta/Ata	2/22	1	2	FACETS	0.14	0.109	0.176	0.14	0.109	0.176	SUBCLONAL	1	TRUE	1	0.788000990758395	2		482	434	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012946	176012946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	95	276	0	ENST00000367669.3:c.1430G>A	p.Ser477Asn	p.S477N	ENST00000367669	NM_022457.5	477	aGt/aAt	13/20	1	2	FACETS	0.728	0.655	0.805	0.728	0.655	0.805	SUBCLONAL	1	TRUE	1	0.788000990758395	2		276	331	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094313	193094313	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	45	410	0	ENST00000367435.3:c.203A>G	p.His68Arg	p.H68R	ENST00000367435	NM_024529.4	68	cAc/cGc	2/17	NA	2	FACETS	0.288	0.242	0.338			1	INDETERMINATE	1	TRUE	NA	0.788000990758395	2		410	397	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651682	206651682	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs782786838	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	146	454	0	ENST00000367120.3:c.992C>T	p.Thr331Met	p.T331M	ENST00000367120	NM_014002.3	331	aCg/aTg	9/22	1	2	FACETS	0.991	0.916	1	0.991	0.916	1	CLONAL	1	TRUE	1	0.788000990758395	2		454	374	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231487275	231487275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142741946	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	34	508	0	ENST00000295050.7:c.676G>A	p.Ala226Thr	p.A226T	ENST00000295050	NM_032018.5	226	Gca/Aca	4/5	1	2	FACETS	0.172	0.14	0.208	0.172	0.14	0.208	SUBCLONAL	1	TRUE	1	0.788000990758395	2		508	503	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604622	43604622	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1449633271	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	34	474	2	ENST00000355710.3:c.1207C>T	p.His403Tyr	p.H403Y	ENST00000355710	NM_020975.4	403	Cac/Tac	6/20	1	2	FACETS	0.228	0.186	0.275	0.228	0.186	0.275	SUBCLONAL	1	TRUE	1	0.788000990758395	2		476	378	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332607	70332607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	28	354	0	ENST00000373644.4:c.512C>T	p.Thr171Ile	p.T171I	ENST00000373644	NM_030625.2	171	aCt/aTt	2/12	1	2	FACETS	0.234	0.187	0.287	0.234	0.187	0.287	SUBCLONAL	1	TRUE	1	0.788000990758395	2		354	304	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10777224	10777224	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	132	298	0	ENST00000361367.2:c.385-1G>A		p.X129_splice	ENST00000361367	NM_014633.3	129			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.788000990758395	2		298	296	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10792118	10792118	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	202	438	0	ENST00000361367.2:c.2311G>A	p.Asp771Asn	p.D771N	ENST00000361367	NM_014633.3	771	Gat/Aat	18/25	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.788000990758395	2		438	465	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402336	402336	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	35	330	0	ENST00000399788.2:c.4456-1G>A		p.X1486_splice	ENST00000399788	NM_001042603.1	1486			NA	2	FACETS	0.239	0.196	0.288			1	INDETERMINATE	1	TRUE	NA	0.788000990758395	2		330	371	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438255	49438255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	31	467	0	ENST00000301067.7:c.5014C>T	p.Pro1672Ser	p.P1672S	ENST00000301067	NM_003482.3	1672	Cct/Tct	20/54	1	2	FACETS	0.184	0.148	0.224	0.184	0.148	0.224	SUBCLONAL	1	TRUE	1	0.788000990758395	2		467	428	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445421	49445421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	35	641	0	ENST00000301067.7:c.2045C>T	p.Pro682Leu	p.P682L	ENST00000301067	NM_003482.3	682	cCt/cTt	10/54	1	2	FACETS	0.168	0.137	0.203	0.168	0.137	0.203	SUBCLONAL	1	TRUE	1	0.788000990758395	2		641	528	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620038	21620038	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	30	487	0	ENST00000382592.4:c.128G>A	p.Ser43Asn	p.S43N	ENST00000382592	NM_014572.2	43	aGt/aAt	2/8	1	2	FACETS	0.185	0.148	0.226	0.185	0.148	0.226	SUBCLONAL	1	TRUE	1	0.788000990758395	2		487	412	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913305	28913305	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	29	349	0	ENST00000282397.4:c.2488G>A	p.Gly830Ser	p.G830S	ENST00000282397	NM_002019.4	830	Ggc/Agc	17/30	0.253868417131133	1	FACETS	0.112	0.089	0.137	0.112	0.089	0.137	INDETERMINATE	1	TRUE	0	0.788000990758395	1		349	399	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636459	73636459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	43	479	1	ENST00000377687.4:c.722G>A	p.Ser241Asn	p.S241N	ENST00000377687	NM_001730.3	241	aGt/aAt	2/4	1	2	FACETS	0.202	0.169	0.24	0.202	0.169	0.24	SUBCLONAL	1	TRUE	1	0.788000990758395	2		480	539	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434773	110434773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768270538	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	50	494	0	ENST00000375856.3:c.3628G>A	p.Ala1210Thr	p.A1210T	ENST00000375856	NM_003749.2	1210	Gcg/Acg	1/2	1	2	FACETS	0.316	0.269	0.368	0.316	0.269	0.368	SUBCLONAL	1	TRUE	1	0.788000990758395	2		494	401	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872430	35872430	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1199743715	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	164	500	1	ENST00000216797.5:c.473C>T	p.Ala158Val	p.A158V	ENST00000216797	NM_020529.2	158	gCc/gTc	3/6	1	2	FACETS	0.778	0.719	0.839	0.778	0.719	0.839	SUBCLONAL	1	TRUE	1	0.788000990758395	2		501	535	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560371	95560371	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	52	402	0	ENST00000393063.1:c.5218G>A	p.Val1740Ile	p.V1740I	ENST00000393063	NM_030621.3	1740	Gtc/Atc	25/28	1	2	FACETS	0.273	0.233	0.318	0.273	0.233	0.318	SUBCLONAL	1	TRUE	1	0.788000990758395	2		402	483	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582881	95582881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	198	392	0	ENST00000393063.1:c.1661G>A	p.Arg554Lys	p.R554K	ENST00000393063	NM_030621.3	554	aGg/aAg	11/28	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.788000990758395	2		392	462	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714072	43714072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	37	474	0	ENST00000382044.4:c.4081G>A	p.Gly1361Arg	p.G1361R	ENST00000382044	NM_001141980.1	1361	Gga/Aga	19/28	1	2	FACETS	0.204	0.168	0.245	0.204	0.168	0.245	SUBCLONAL	1	TRUE	1	0.788000990758395	2		474	460	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396307	396307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	32	502	0	ENST00000262320.3:c.719C>T	p.Thr240Ile	p.T240I	ENST00000262320	NM_003502.3	240	aCc/aTc	2/11	1	2	FACETS	0.233	0.189	0.283	0.233	0.189	0.283	SUBCLONAL	1	TRUE	1	0.788000990758395	2		502	348	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647388	3647388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1174853638	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	19	511	0	ENST00000294008.3:c.1675C>T	p.Pro559Ser	p.P559S	ENST00000294008	NM_032444.2	559	Cct/Tct	7/15	1	2	FACETS	0.136	0.103	0.175	0.136	0.103	0.175	SUBCLONAL	1	TRUE	1	0.788000990758395	2		511	354	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858069	9858069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	29	450	0	ENST00000330684.3:c.3332G>A	p.Ser1111Asn	p.S1111N	ENST00000330684	NM_001134407.1	1111	aGc/aAc	13/13	1	2	FACETS	0.177	0.141	0.217	0.177	0.141	0.217	SUBCLONAL	1	TRUE	1	0.788000990758395	2		450	417	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992129	72992129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	29	574	0	ENST00000268489.5:c.1916G>A	p.Gly639Asp	p.G639D	ENST00000268489	NM_006885.3	639	gGc/gAc	2/10	1	2	FACETS	0.165	0.132	0.203	0.165	0.132	0.203	SUBCLONAL	1	TRUE	1	0.788000990758395	2		574	445	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548913	29548913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	68	211	0	ENST00000356175.3:c.1687C>T	p.Pro563Ser	p.P563S	ENST00000356175	NM_000267.3	563	Cct/Tct	15/57	1	2	FACETS	0.904	0.802	1	0.904	0.802	1	CLONAL	1	TRUE	1	0.788000990758395	2		211	191	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246776	41246776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	25	452	0	ENST00000357654.3:c.772C>T	p.Pro258Ser	p.P258S	ENST00000357654	NM_007294.3	258	Cca/Tca	10/23	1	2	FACETS	0.161	0.126	0.2	0.161	0.126	0.2	SUBCLONAL	1	TRUE	1	0.788000990758395	2		452	395	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696737	47696737	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	28	370	0	ENST00000347630.2:c.211G>A	p.Val71Ile	p.V71I	ENST00000347630	NM_001007230.1	71	Gta/Ata	5/11	1	2	FACETS	0.181	0.144	0.223	0.181	0.144	0.223	SUBCLONAL	1	TRUE	1	0.788000990758395	2		370	393	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621854	1621854	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	46	559	0	ENST00000344749.5:c.938G>A	p.Gly313Glu	p.G313E	ENST00000344749	NM_001136139.2	313	gGg/gAg	11/19	0.253868417131133	1	FACETS	0.191	0.161	0.224	0.191	0.161	0.224	INDETERMINATE	1	TRUE	0	0.788000990758395	1		559	370	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219952	5219952	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	90	442	0	ENST00000357368.4:c.3763C>T	p.Pro1255Ser	p.P1255S	ENST00000357368	NM_002850.3	1255	Cct/Tct	22/38	0.253868417131133	1	FACETS	0.406	0.363	0.451	0.406	0.363	0.451	INDETERMINATE	1	TRUE	0	0.788000990758395	1		442	341	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221032	5221032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866466115	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	19	494	0	ENST00000357368.4:c.3434G>A	p.Gly1145Asp	p.G1145D	ENST00000357368	NM_002850.3	1145	gGc/gAc	20/38	0.253868417131133	1	FACETS	0.083	0.063	0.107	0.083	0.063	0.107	INDETERMINATE	1	TRUE	0	0.788000990758395	1		494	351	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6230637	6230637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	21	505	0	ENST00000252674.7:c.364C>T	p.Leu122Phe	p.L122F	ENST00000252674	NM_005934.3	122	Ctc/Ttc	4/12	0.253868417131133	1	FACETS	0.082	0.063	0.105	0.082	0.063	0.105	INDETERMINATE	1	TRUE	0	0.788000990758395	1		505	394	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094856	11094856	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	27	400	0	ENST00000358026.2:c.29G>A	p.Gly10Glu	p.G10E	ENST00000358026	NM_001128849.1	10	gGa/gAa	2/36	0.253868417131133	1	FACETS	0.124	0.099	0.154	0.124	0.099	0.154	INDETERMINATE	1	TRUE	0	0.788000990758395	1		400	334	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303925	30303925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	17	419	0	ENST00000262643.3:c.161G>A	p.Arg54Lys	p.R54K	ENST00000262643	NM_001238.2	54	aGg/aAg	4/12	0.788000990758395	1	FACETS	0.102	0.076	0.133	0.102	0.076	0.133	SUBCLONAL	1	TRUE	0	0.788000990758395	1		419	256	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209062	36209062	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	24	448	0	ENST00000222270.7:c.142C>T	p.Arg48Trp	p.R48W	ENST00000222270	NM_014727.1	48	Cgg/Tgg	1/37	0.788000990758395	1	FACETS	0.183	0.144	0.227	0.183	0.144	0.227	SUBCLONAL	1	TRUE	0	0.788000990758395	1		448	202	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50138850	50138850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770517668	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	24	479	0	ENST00000246792.3:c.640C>T	p.Pro214Ser	p.P214S	ENST00000246792	NM_006270.3	214	Ccc/Tcc	6/6	0.788000990758395	1	FACETS	0.166	0.13	0.206	0.166	0.13	0.206	SUBCLONAL	1	TRUE	0	0.788000990758395	1		479	223	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99136587	99136587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	36	395	0	ENST00000074304.5:c.76G>A	p.Ala26Thr	p.A26T	ENST00000074304	NM_001134224.1	26	Gcg/Acg	3/26	1	2	FACETS	0.23	0.189	0.276	0.23	0.189	0.276	SUBCLONAL	1	TRUE	1	0.788000990758395	2		395	397	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281470	198281470	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	32	367	0	ENST00000335508.6:c.661G>A	p.Ala221Thr	p.A221T	ENST00000335508	NM_012433.2	221	Gca/Aca	6/25	1	2	FACETS	0.202	0.164	0.245	0.202	0.164	0.245	SUBCLONAL	1	TRUE	1	0.788000990758395	2		367	402	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439833	220439833	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	36	514	0	ENST00000243786.2:c.686G>A	p.Arg229Lys	p.R229K	ENST00000243786	NM_002191.3	229	aGa/aAa	2/2	1	2	FACETS	0.237	0.195	0.285	0.237	0.195	0.285	SUBCLONAL	1	TRUE	1	0.788000990758395	2		514	385	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661171	227661171	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	42	565	0	ENST00000305123.5:c.2284C>A	p.Leu762Ile	p.L762I	ENST00000305123	NM_005544.2	762	Ctc/Atc	1/2	1	2	FACETS	0.197	0.164	0.233	0.197	0.164	0.233	SUBCLONAL	1	TRUE	1	0.788000990758395	2		565	542	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795113	242795113	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	107	535	0	ENST00000334409.5:c.96G>A	p.Trp32Ter	p.W32*	ENST00000334409	NM_005018.2	32	tgG/tgA	2/5	1	2	FACETS	0.667	0.603	0.734	0.667	0.603	0.734	SUBCLONAL	1	TRUE	1	0.788000990758395	2		535	407	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21351184	21351184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	37	544	0	ENST00000215739.8:c.2335G>A	p.Ala779Thr	p.A779T	ENST00000215739	NM_006767.3	779	Gca/Aca	20/21	0.253868417131133	1	FACETS	0.137	0.113	0.165	0.137	0.113	0.165	INDETERMINATE	1	TRUE	0	0.788000990758395	1		544	414	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47079250	47079250	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	22	432	0	ENST00000409792.3:c.7256C>T	p.Pro2419Leu	p.P2419L	ENST00000409792	NM_014159.6	2419	cCt/cTt	18/21	1	2	FACETS	0.159	0.122	0.201	0.159	0.122	0.201	SUBCLONAL	1	TRUE	1	0.788000990758395	2		432	352	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163409	47163409	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	108	410	0	ENST00000409792.3:c.2717C>T	p.Pro906Leu	p.P906L	ENST00000409792	NM_014159.6	906	cCa/cTa	3/21	1	2	FACETS	0.71	0.643	0.78	0.71	0.643	0.78	SUBCLONAL	1	TRUE	1	0.788000990758395	2		410	386	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72861821	72861821	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs752415535	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	34	368	0	ENST00000325599.8:c.1060+1G>A		p.X354_splice	ENST00000325599	NM_018130.2	354			1	2	FACETS	0.212	0.173	0.255	0.212	0.173	0.255	SUBCLONAL	1	TRUE	1	0.788000990758395	2		368	408	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72891484	72891484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	42	409	0	ENST00000325599.8:c.278C>T	p.Ala93Val	p.A93V	ENST00000325599	NM_018130.2	93	gCt/gTt	3/11	1	2	FACETS	0.21	0.175	0.249	0.21	0.175	0.249	SUBCLONAL	1	TRUE	1	0.788000990758395	2		409	508	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200684	128200684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1559985057	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	21	404	0	ENST00000341105.2:c.1121G>A	p.Gly374Asp	p.G374D	ENST00000341105	NM_032638.4	374	gGc/gAc	5/6	1	2	FACETS	0.163	0.125	0.207	0.163	0.125	0.207	SUBCLONAL	1	TRUE	1	0.788000990758395	2		404	327	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191085	185191085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	45	509	0	ENST00000265026.3:c.1966C>T	p.Leu656Phe	p.L656F	ENST00000265026	NM_004721.4	656	Ctc/Ttc	11/14	1	2	FACETS	0.236	0.198	0.278	0.236	0.198	0.278	SUBCLONAL	1	TRUE	1	0.788000990758395	2		509	484	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447502	187447502	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1270887193	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	109	593	0	ENST00000232014.4:c.691C>T	p.Pro231Ser	p.P231S	ENST00000232014	NM_001130845.1	231	Cca/Tca	5/10	1	2	FACETS	0.526	0.474	0.581	0.526	0.474	0.581	SUBCLONAL	1	TRUE	1	0.788000990758395	2		593	526	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955049	55955049	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1312704512	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	45	332	0	ENST00000263923.4:c.3496G>A	p.Ala1166Thr	p.A1166T	ENST00000263923	NM_002253.2	1166	Gct/Act	26/30	1	2	FACETS	0.299	0.252	0.351	0.299	0.252	0.351	SUBCLONAL	1	TRUE	1	0.788000990758395	2		332	382	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55987358	55987358	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	30	271	1	ENST00000263923.4:c.68-1G>A		p.X23_splice	ENST00000263923	NM_002253.2	23			1	2	FACETS	0.256	0.206	0.311	0.256	0.206	0.311	SUBCLONAL	1	TRUE	1	0.788000990758395	2		272	298	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193902	106193902	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	32	414	0	ENST00000380013.4:c.4364G>A	p.Arg1455Lys	p.R1455K	ENST00000380013	NM_001127208.2	1455	aGg/aAg	10/11	1	2	FACETS	0.17	0.138	0.207	0.17	0.138	0.207	SUBCLONAL	1	TRUE	1	0.788000990758395	2		414	477	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144378901	144378901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	72	315	0	ENST00000262995.4:c.1654G>A	p.Asp552Asn	p.D552N	ENST00000262995	NM_207123.2	552	Gac/Aac	7/11	1	2	FACETS	0.566	0.498	0.637	0.566	0.498	0.637	SUBCLONAL	1	TRUE	1	0.788000990758395	2		315	323	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522348	176522348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1159015556	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	24	369	0	ENST00000292408.4:c.1537G>A	p.Asp513Asn	p.D513N	ENST00000292408	NM_213647.1	513	Gac/Aac	12/18	1	2	FACETS	0.179	0.14	0.223	0.179	0.14	0.223	SUBCLONAL	1	TRUE	1	0.788000990758395	2		369	341	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288000	33288000	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1433988747	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	29	446	0	ENST00000374542.5:c.1253G>A	p.Gly418Asp	p.G418D	ENST00000374542	NM_001141970.1	418	gGc/gAc	5/8	1	2	FACETS	0.17	0.136	0.209	0.17	0.136	0.209	SUBCLONAL	1	TRUE	1	0.788000990758395	2		446	432	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528561	157528561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	48	451	0	ENST00000346085.5:c.6286G>A	p.Val2096Met	p.V2096M	ENST00000346085	NM_020732.3	2096	Gtg/Atg	20/20	1	2	FACETS	0.253	0.213	0.296	0.253	0.213	0.296	SUBCLONAL	1	TRUE	1	0.788000990758395	2		451	482	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739695	41739695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	56	394	1	ENST00000242208.4:c.278G>A	p.Gly93Asp	p.G93D	ENST00000242208	NM_002192.2	93	gGc/gAc	2/3	0.788000990758395	3	FACETS	0.382	0.327	0.441	0.191	0.163	0.221	SUBCLONAL	1	TRUE	1	0.788000990758395	3		395	519	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852041	128852041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	50	539	0	ENST00000249373.3:c.2113C>T	p.Pro705Ser	p.P705S	ENST00000249373	NM_005631.4	705	Cct/Tct	12/12	0.788000990758395	3	FACETS	0.316	0.268	0.37	0.158	0.134	0.185	SUBCLONAL	1	TRUE	1	0.788000990758395	3		539	559	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859890	151859890	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	99	508	0	ENST00000262189.6:c.10772A>G	p.Gln3591Arg	p.Q3591R	ENST00000262189	NM_170606.2	3591	cAg/cGg	43/59	0.573974597499809	3	FACETS	0.509	0.455	0.567			1	SUBCLONAL	1	TRUE	NA	0.788000990758395	3		508	688	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980467	70980467	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1356259445	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	21	404	0	ENST00000276594.2:c.910G>A	p.Glu304Lys	p.E304K	ENST00000276594	NM_024504.3	304	Gag/Aag	4/8	1	2	FACETS	0.136	0.104	0.173	0.136	0.104	0.173	SUBCLONAL	1	TRUE	1	0.788000990758395	2		404	393	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976695	90976695	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660584	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	61	304	0	ENST00000265433.3:c.937G>A	p.Ala313Thr	p.A313T	ENST00000265433	NM_002485.4	313	Gcg/Acg	8/16	1	2	FACETS	0.409	0.354	0.467	0.409	0.354	0.467	SUBCLONAL	1	TRUE	1	0.788000990758395	2		304	379	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145736860	145736860	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	31	447	0	ENST00000428558.2:c.3581C>T	p.Ala1194Val	p.A1194V	ENST00000428558	NM_004260.3	1194	gCc/gTc	22/22	1	2	FACETS	0.214	0.173	0.26	0.214	0.173	0.26	SUBCLONAL	1	TRUE	1	0.788000990758395	2		447	368	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534889	5534889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1820550340	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	49	481	0	ENST00000397747.3:c.200C>T	p.Ser67Phe	p.S67F	ENST00000397747	NM_025239.3	67	tCc/tTc	3/7	1	2	FACETS	0.283	0.239	0.33	0.283	0.239	0.33	SUBCLONAL	1	TRUE	1	0.788000990758395	2		481	440	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465581	8465581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	45	421	0	ENST00000356435.5:c.3599C>T	p.Pro1200Leu	p.P1200L	ENST00000356435		1200	cCc/cTc	21/35	1	2	FACETS	0.232	0.194	0.273	0.232	0.194	0.273	SUBCLONAL	1	TRUE	1	0.788000990758395	2		421	493	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87356807	87356807	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs551310223	NA	P-0051040-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	23	293	0	ENST00000277120.3:c.1160G>A	p.Gly387Asp	p.G387D	ENST00000277120		387	gGt/gAt	10/19	1	2	FACETS	0.199	0.155	0.249	0.199	0.155	0.249	SUBCLONAL	1	TRUE	1	0.788000990758395	2		293	294	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0051054-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	168	405	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.406422906298212	8	FACETS	1	0.942	1	0.343	0.315	0.372	CLONAL	2	TRUE	2	0.406422906298212	8		405	891	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0051054-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	155	383	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.400834224076642	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.406422906298212	3		383	438	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039368	47039369	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0051054-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	121	218	0	ENST00000377604.3:c.992dup	p.Arg332AlafsTer49	p.R332Afs*49	ENST00000377604	NM_001204468.1	331	gtg/gTtg	10/24	1	1	FACETS	0.988	0.913	1	1	0.991	1	CLONAL	2	TRUE	0	0.406422906298212	1		218	240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1064795203	NA	P-0051054-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	95	508	0	ENST00000269305.4:c.532C>A	p.His178Asn	p.H178N	ENST00000269305	NM_001126112.2	178	Cac/Aac	5/11	0.400834224076642	3	FACETS	0.955	0.852	1	0.477	0.426	0.532	CLONAL	1	TRUE	1	0.406422906298212	3		508	589	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831455	89831455	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051054-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	74	416	0	ENST00000389301.3:c.2621G>C	p.Arg874Thr	p.R874T	ENST00000389301	NM_000135.2	874	aGa/aCa	28/43	0.360687170126678	4	FACETS	0.972	0.852	1	0.324	0.284	0.367	CLONAL	1	TRUE	1	0.406422906298212	4		416	527	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265109	46265109	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051054-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	96	455	0	ENST00000371998.3:c.1979C>G	p.Ser660Cys	p.S660C	ENST00000371998		660	tCc/tGc	12/23	0.406422906298212	5	FACETS	0.998	0.889	1	0.333	0.296	0.372	CLONAL	1	TRUE	2	0.406422906298212	5		455	762	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575366	64575366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051054-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	110	491	0	ENST00000312049.6:c.651G>T	p.Glu217Asp	p.E217D	ENST00000312049	NM_130799.2	217	gaG/gaT	3/10	0.406422906298212	3	FACETS	1	0.959	1	0.561	0.506	0.62	CLONAL	1	TRUE	1	0.406422906298212	3		491	580	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202600	67202600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779262747	NA	P-0051054-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	102	493	0	ENST00000312629.5:c.1409C>T	p.Thr470Ile	p.T470I	ENST00000312629	NM_003952.2	470	aCc/aTc	15/15	0.406422906298212	3	FACETS	0.997	0.893	1	0.498	0.446	0.553	CLONAL	1	TRUE	1	0.406422906298212	3		493	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0052005-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	207	374	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.591898356031584	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.599686351255149	2		374	324	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219388	1219389	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052005-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	145	311	0	ENST00000326873.7:c.443dup	p.Val150SerfsTer13	p.V150Sfs*13	ENST00000326873	NM_000455.4	147	cgt/cgTt	3/10	0.599686351255149	2	FACETS	0.876	0.816	0.935	0.876	0.816	0.935	CLONAL	2	TRUE	0	0.599686351255149	2		311	276	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724121	61724121	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052005-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	53	242	0	ENST00000401558.2:c.781C>G	p.Arg261Gly	p.R261G	ENST00000401558	NM_003400.3	261	Cga/Gga	10/25	0.599686351255149	3	FACETS	0.682	0.584	0.788	0.341	0.292	0.394	SUBCLONAL	1	TRUE	1	0.599686351255149	3		242	337	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111719	56111719	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052005-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	13	264	0	ENST00000399503.3:c.319C>G	p.Pro107Ala	p.P107A	ENST00000399503	NM_005921.1	107	Cct/Gct	1/20	0.599686351255149	3	FACETS	0.223	0.158	0.301	0.111	0.079	0.151	SUBCLONAL	1	TRUE	1	0.599686351255149	3		264	253	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980862	40980862	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052008-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	120	398	0	ENST00000373198.4:c.1624G>T	p.Val542Leu	p.V542L	ENST00000373198	NM_133170.3	542	Gtg/Ttg	10/32	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.786760585557436	2		398	276	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574931	41574931	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052008-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	227	377	0	ENST00000263253.7:c.7216C>G	p.Leu2406Val	p.L2406V	ENST00000263253	NM_001429.3	2406	Ctc/Gtc	31/31	0.786760585557436	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.786760585557436	2		377	264	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259268	89259268	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052008-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	101	413	0	ENST00000336596.2:c.412C>A	p.His138Asn	p.H138N	ENST00000336596	NM_005233.5	138	Cat/Aat	3/17	0.352391583758893	3	FACETS	1	0.972	1	0.598	0.542	0.657	INDETERMINATE	1	TRUE	1	0.786760585557436	3		413	299	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0052008-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	156	258	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.786760585557436	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.786760585557436	3		258	252	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0052289-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	41	317	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.212228688488408	3	FACETS	0.976	0.821	1	0.976	0.821	1	CLONAL	2	TRUE	1	0.212228688488408	3		317	219	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0052289-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	31	397	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	0.212228688488408	5	FACETS	0.603	0.486	0.736			1	SUBCLONAL	1	TRUE	NA	0.212228688488408	5		397	639	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678007	58678025	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCTCCCGGACGCCGGGG	CCTCTCCCGGACGCCGGGG	-	novel	NA	P-0052289-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	28	402	0	ENST00000305921.3:c.236_254del	p.Leu79ArgfsTer80	p.L79Rfs*80	ENST00000305921	NM_003620.3	78	CCTCTCCCGGACGCCGGGGcc/cc	1/6	1	2	FACETS	0.521	0.416	0.642	0.521	0.416	0.642	SUBCLONAL	1	TRUE	1	0.212228688488408	2		402	506	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407476	407476	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052289-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	25	309	0	ENST00000380956.4:c.1234C>G	p.Gln412Glu	p.Q412E	ENST00000380956	NM_001195286.1	412	Caa/Gaa	9/9	1	2	FACETS	0.589	0.464	0.733	0.589	0.464	0.733	SUBCLONAL	1	TRUE	1	0.212228688488408	2		309	400	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021819	69021819	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052289-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	287	358	0	ENST00000288368.4:c.3107C>A	p.Ala1036Glu	p.A1036E	ENST00000288368	NM_024870.2	1036	gCa/gAa	25/40	0.212228688488408	8	FACETS	0.994	0.943	1	0.994	0.943	1	CLONAL	7	TRUE	1	0.212228688488408	8		358	636	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040962	47040965	+	frameshift_variant	Frame_Shift_Del	DEL	CGCG	CGCG	-	novel	NA	P-0052289-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	33	426	0	ENST00000377604.3:c.1493_1496del	p.Arg498ProfsTer205	p.R498Pfs*205	ENST00000377604	NM_001204468.1	498	CGCGcc/cc	14/24	1	2	FACETS	0.643	0.523	0.778	0.643	0.523	0.778	SUBCLONAL	1	TRUE	1	0.212228688488408	2		426	484	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1296014	1296014	+	upstream_gene_variant	5'Flank	SNP	C	C	G	novel	NA	P-0052289-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	36	472	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.576	0.472	0.693	0.576	0.472	0.693	SUBCLONAL	1	TRUE	1	0.212228688488408	2		472	589	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578281	7578281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052569-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	255	586	0	ENST00000269305.4:c.568C>T	p.Pro190Ser	p.P190S	ENST00000269305	NM_001126112.2	190	Cct/Tct	6/11	0.838213072508017	1	FACETS	0.951	0.911	0.99	0.951	0.911	0.99	CLONAL	1	FALSE	0	0.841684254043185	1		586	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0052797-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	228	464	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.81750736859501	2	FACETS	0.996	0.961	1	0.996	0.961	1	CLONAL	2	TRUE	0	0.81750736859501	2		464	280	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0052797-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	339	493	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.798665390647964	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.81750736859501	3		493	386	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938577	44938577	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0052797-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	178	335	0	ENST00000377967.4:c.3125C>G	p.Ser1042Ter	p.S1042*	ENST00000377967	NM_021140.2	1042	tCa/tGa	20/29	0.81750736859501	2	FACETS	0.943	0.901	0.982	0.943	0.901	0.982	CLONAL	2	TRUE	0	0.81750736859501	2		335	231	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20486949	20486949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188266138	NA	P-0052797-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	67	258	0	ENST00000346618.3:c.914G>A	p.Arg305Gln	p.R305Q	ENST00000346618	NM_001949.4	305	cGa/cAa	5/7	0.74368999017792	4	FACETS	0.837	0.732	0.949	0.418	0.366	0.475	CLONAL	1	TRUE	2	0.81750736859501	4		258	356	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416398	49416399	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0052797-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	244	327	0	ENST00000301067.7:c.16312dup	p.Arg5438ProfsTer21	p.R5438Pfs*21	ENST00000301067	NM_003482.3	5438	cgg/cCgg	51/54	0.802803796813297	4	FACETS	0.977	0.922	1	0.977	0.922	1	CLONAL	2	TRUE	2	0.81750736859501	4		327	555	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052975-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	203	501	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.690807267818679	2	FACETS	1	0.95	1	0.511	0.476	0.545	CLONAL	1	TRUE	0	0.687934077112469	2		501	578	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070557	67070557	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052975-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	771	417	0	ENST00000412916.2:c.181G>C	p.Gly61Arg	p.G61R	ENST00000412916		61	Gga/Cga	3/6	0.690807267818679	4	FACETS	0.994	0.974	1			1	CLONAL	4	TRUE	NA	0.687934077112469	4		417	952	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554308	29554308	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052975-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	443	415	0	ENST00000356175.3:c.2324A>T	p.Glu775Val	p.E775V	ENST00000356175	NM_000267.3	775	gAg/gTg	19/57	0.690699506110436	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	0	0.687934077112469	3		415	574	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0053157-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	193	540	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.615086050913793	1	FACETS	0.985	0.923	1	0.985	0.923	1	CLONAL	1	TRUE	0	0.634098896630825	1		540	422	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0053923-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	26	300	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.679	0.537	0.842	0.679	0.537	0.842	SUBCLONAL	1	TRUE	1	0.190469205398215	2		300	402	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0053923-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	46	311	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.831	0.699	0.977	0.831	0.699	0.977	CLONAL	1	TRUE	1	0.190469205398215	2		311	581	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044850	47044850	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053923-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	42	420	0	ENST00000377604.3:c.2176C>T	p.Arg726Ter	p.R726*	ENST00000377604	NM_001204468.1	726	Cga/Tga	20/24	1	2	FACETS	0.959	0.801	1	0.959	0.801	1	CLONAL	1	TRUE	1	0.190469205398215	2		420	460	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2185874	2185874	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1378442482	NA	P-0053923-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	53	295	0	ENST00000398665.3:c.146C>T	p.Pro49Leu	p.P49L	ENST00000398665	NM_032482.2	49	cCg/cTg	3/28	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.190469205398215	2		295	522	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941064	71941064	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0053923-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	41	415	0	ENST00000298229.2:c.939+1G>A		p.X313_splice	ENST00000298229	NM_001567.3	313			1	2	FACETS	0.759	0.632	0.902	0.759	0.632	0.902	CLONAL	1	TRUE	1	0.190469205398215	2		415	567	SUCCESS
APC	324	MSKCC	GRCh37	5	112179035	112179036	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053923-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	46	304	0	ENST00000257430.4:c.7749dup	p.Ala2584SerfsTer4	p.A2584Sfs*4	ENST00000257430	NM_000038.5	2582	gaa/gAaa	16/16	1	2	FACETS	0.962	0.81	1	0.962	0.81	1	CLONAL	1	TRUE	1	0.190469205398215	2		304	502	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877198	151877198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053923-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	77	306	0	ENST00000262189.6:c.7163G>A	p.Arg2388His	p.R2388H	ENST00000262189	NM_170606.2	2388	cGt/cAt	37/59	0.190469205398215	3	FACETS	0.834	0.733	0.941	0.834	0.733	0.941	CLONAL	2	TRUE	1	0.190469205398215	3		306	531	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38139000	38139000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053923-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	50	219	0	ENST00000317025.8:c.3603G>A	p.Met1201Ile	p.M1201I	ENST00000317025	NM_023034.1	1201	atG/atA	20/24	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.190469205398215	2		219	496	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713856	30713856	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553630289	NA	P-0053923-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	107	371	0	ENST00000295754.5:c.1181G>A	p.Cys394Tyr	p.C394Y	ENST00000295754	NM_003242.5	394	tGc/tAc	4/7	0.190469205398215	2	FACETS	0.949	0.853	1	0.949	0.853	1	CLONAL	2	TRUE	0	0.190469205398215	2		371	592	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775012	73775012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053923-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	27	181	0	ENST00000254810.4:c.161G>A	p.Arg54His	p.R54H	ENST00000254810	NM_005324.3	54	cGt/cAt	3/4	1	2	FACETS	0.961	0.766	1	0.961	0.766	1	CLONAL	1	TRUE	1	0.190469205398215	2		181	295	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0054137-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	66	682	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.408931107177634	1	FACETS	0.863	0.757	0.976	0.863	0.757	0.976	CLONAL	1	TRUE	0	0.432642521030663	1		682	277	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644668	134644668	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054137-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	47	505	0	ENST00000398015.3:c.69G>T	p.Met23Ile	p.M23I	ENST00000398015	NM_004441.4	23	atG/atT	2/16	0.354629683745811	0	FACETS	0.652	0.558	0.753			1	SUBCLONAL	1	TRUE	0	0.432642521030663	0		505	189	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs730881677	NA	P-0054137-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	175	562	0	ENST00000304494.5:c.151-1G>T		p.X51_splice	ENST00000304494	NM_000077.4	51			0.432642521030663	3	FACETS	0.904	0.845	0.962	0.904	0.845	0.962	CLONAL	3	TRUE	0	0.432642521030663	3		562	363	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469889	157469889	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054137-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	56	636	0	ENST00000346085.5:c.2686del	p.Leu896TrpfsTer18	p.L896Wfs*18	ENST00000346085	NM_020732.3	895	Ccc/cc	9/20	1	2	FACETS	0.852	0.735	0.977	0.852	0.735	0.977	CLONAL	1	TRUE	1	0.432642521030663	2		636	304	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444960	49444960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054137-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	68	685	1	ENST00000301067.7:c.2506del	p.Gln836SerfsTer94	p.Q836Sfs*94	ENST00000301067	NM_003482.3	836	Cag/ag	10/54	1	2	FACETS	0.903	0.791	1	0.903	0.791	1	CLONAL	1	TRUE	1	0.432642521030663	2		686	348	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420554	49420554	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587783696	NA	P-0054137-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	79	650	0	ENST00000301067.7:c.15195G>A	p.Trp5065Ter	p.W5065*	ENST00000301067	NM_003482.3	5065	tgG/tgA	48/54	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.432642521030663	2		650	318	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671874	30671874	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054137-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	78	675	0	ENST00000376406.3:c.5086A>G	p.Thr1696Ala	p.T1696A	ENST00000376406	NM_014641.2	1696	Acc/Gcc	10/15	0.140303898103587	4	FACETS	0.751	0.665	0.842	0.751	0.665	0.842	INDETERMINATE	2	TRUE	2	0.432642521030663	4		675	344	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437109	110437109	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054137-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	37	464	0	ENST00000375856.3:c.1292T>A	p.Met431Lys	p.M431K	ENST00000375856	NM_003749.2	431	aTg/aAg	1/2	0.432642521030663	1	FACETS	0.894	0.749	1	0.894	0.749	1	CLONAL	1	TRUE	0	0.432642521030663	1		464	150	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636079	28636079	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054137-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	53	515	0	ENST00000241453.7:c.293C>G	p.Pro98Arg	p.P98R	ENST00000241453	NM_004119.2	98	cCa/cGa	3/24	0.317853458173979	0	FACETS	0.76	0.659	0.866			1	SUBCLONAL	1	TRUE	0	0.432642521030663	0		515	183	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272520	15272520	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054137-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	72	580	0	ENST00000263388.2:c.5919G>C	p.Glu1973Asp	p.E1973D	ENST00000263388	NM_000435.2	1973	gaG/gaC	33/33	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.432642521030663	2		580	241	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149915	202149915	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054137-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	47	647	0	ENST00000358485.4:c.1358del	p.Pro453ArgfsTer13	p.P453Rfs*13	ENST00000358485	NM_001080125.1	452	atC/at	8/9	1	2	FACETS	0.796	0.676	0.926	0.796	0.676	0.926	CLONAL	1	TRUE	1	0.432642521030663	2		647	273	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158655948	158655948	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054137-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	29	502	0	ENST00000263640.3:c.58A>G	p.Ser20Gly	p.S20G	ENST00000263640	NM_001105.4	20	Agt/Ggt	3/11	1	2	FACETS	0.766	0.621	0.927	0.766	0.621	0.927	CLONAL	1	TRUE	1	0.432642521030663	2		502	175	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652516	48652516	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054137-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	41	614	0	ENST00000376670.3:c.1187C>A	p.Thr396Lys	p.T396K	ENST00000376670	NM_002049.3	396	aCa/aAa	6/6	1	2	FACETS	0.699	0.586	0.824	0.699	0.586	0.824	SUBCLONAL	1	TRUE	1	0.432642521030663	2		614	271	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441416	52441436	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TGGCATGGCTATTATGGGCCT	TGGCATGGCTATTATGGGCCT	-	novel	NA	P-0054137-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	71	826	0	ENST00000460680.1:c.416_436del	p.Lys139_Ala145del	p.K139_A145del	ENST00000460680	NM_004656.3	139	aAGGCCCATAATAGCCATGCCAgg/agg	6/17	0.408931107177634	1	FACETS	0.799	0.703	0.901	0.799	0.703	0.901	CLONAL	1	TRUE	0	0.432642521030663	1		826	322	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735312	204735312	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054137-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	44	533	0	ENST00000302823.3:c.113T>A	p.Met38Lys	p.M38K	ENST00000302823	NM_005214.4	38	aTg/aAg	2/4	1	2	FACETS	0.732	0.617	0.856	0.732	0.617	0.856	SUBCLONAL	1	TRUE	1	0.432642521030663	2		533	278	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	461415	461415	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs537935217	NA	P-0054137-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	39	410	0	ENST00000399788.2:c.1105A>G	p.Met369Val	p.M369V	ENST00000399788	NM_001042603.1	369	Atg/Gtg	9/28	0.140303898103587	4	FACETS	1	0.947	1	0.68	0.57	0.799	INDETERMINATE	1	TRUE	2	0.432642521030663	4		410	190	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771415	112771415	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054137-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	56	492	0	ENST00000369452.4:c.1588C>A	p.Leu530Met	p.L530M	ENST00000369452	NM_007373.3	530	Ctg/Atg	9/9	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.432642521030663	2		492	209	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530153	212530153	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054137-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	36	581	0	ENST00000342788.4:c.1766G>T	p.Cys589Phe	p.C589F	ENST00000342788	NM_005235.2	589	tGt/tTt	15/28	0.354629683745811	0	FACETS	0.647	0.54	0.761			1	SUBCLONAL	1	TRUE	0	0.432642521030663	0		581	146	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541602	29541602	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054137-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	12	249	0	ENST00000356175.3:c.1526G>T	p.Cys509Phe	p.C509F	ENST00000356175	NM_000267.3	509	tGt/tTt	13/57	1	2	FACETS	1	0.728	1	1	0.728	1	CLONAL	1	TRUE	1	0.432642521030663	2		249	55	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411194	63411194	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773774270	NA	P-0054137-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	33	628	0	ENST00000330258.3:c.1973C>T	p.Pro658Leu	p.P658L	ENST00000330258	NM_152424.3	658	cCc/cTc	2/2	0.197268769164499	0	FACETS	0.422	0.347	0.506			1	INDETERMINATE	1	TRUE	0	0.432642521030663	0		628	205	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631668	67631668	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054137-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	30	570	0	ENST00000272342.5:c.1854A>C	p.Glu618Asp	p.E618D	ENST00000272342	NM_019002.3	618	gaA/gaC	5/6	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.432642521030663	2		570	129	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170628	7170628	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054137-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	46	548	0	ENST00000302850.5:c.1403A>G	p.Lys468Arg	p.K468R	ENST00000302850	NM_000208.2	468	aAg/aGg	6/22	1	2	FACETS	0.762	0.646	0.889	0.762	0.646	0.889	SUBCLONAL	1	TRUE	1	0.432642521030663	2		548	279	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341517	70341517	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054137-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	53	601	0	ENST00000374080.3:c.952C>A	p.His318Asn	p.H318N	ENST00000374080		318	Cat/Aat	7/45	0.197268769164499	0	FACETS	0.417	0.358	0.482			1	INDETERMINATE	1	TRUE	0	0.432642521030663	0		601	333	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0054325-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	196	440	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.51736530595448	6	FACETS	1	0.98	1	0.573	0.532	0.614	CLONAL	2	TRUE	2	0.51736530595448	6		440	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs786201838	NA	P-0054325-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	168	441	0	ENST00000269305.4:c.578A>C	p.His193Pro	p.H193P	ENST00000269305	NM_001126112.2	193	cAt/cCt	6/11	0.521995781877695	1	FACETS	0.797	0.748	0.846	1	0.992	1	SUBCLONAL	2	TRUE	0	0.51736530595448	1		441	302	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817493	39817493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755303168	NA	P-0054325-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	386	327	0	ENST00000288319.7:c.70G>A	p.Gly24Arg	p.G24R	ENST00000288319	NM_182918.3	24	Gga/Aga	2/10	0.51736530595448	5	FACETS	0.992	0.953	1	0.992	0.953	1	CLONAL	4	TRUE	1	0.51736530595448	5		327	668	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134614	2134614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054325-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	178	479	0	ENST00000219476.3:c.4391C>T	p.Ser1464Phe	p.S1464F	ENST00000219476	NM_000548.3	1464	tCc/tTc	34/42	0.0714643934255796	4	FACETS	0.851	0.794	0.908			1	INDETERMINATE	3	TRUE	NA	0.51736530595448	4		479	409	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134918	41134918	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054325-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	188	346	2	ENST00000379561.5:c.710G>A	p.Trp237Ter	p.W237*	ENST00000379561	NM_002015.3	237	tGg/tAg	2/3	0.521995781877695	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.51736530595448	3		348	418	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56854546	56854546	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054325-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	81	290	0	ENST00000519728.1:c.128G>T	p.Arg43Met	p.R43M	ENST00000519728	NM_002350.3	43	aGg/aTg	2/13	NA	2	FACETS	1	0.954	1			1	INDETERMINATE	1	TRUE	NA	0.51736530595448	2		290	277	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0054600-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	98	381	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.242963611223505	4	FACETS	1	0.973	1	0.634	0.567	0.704	INDETERMINATE	1	TRUE	2	0.438859948328331	4		381	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0054600-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	171	386	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.242963611223505	4	FACETS	1	0.956	1	1	0.956	1	INDETERMINATE	2	TRUE	2	0.438859948328331	4		386	537	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218500	1218500	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1131690951	NA	P-0054600-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	146	269	0	ENST00000326873.7:c.374+1A>G		p.X125_splice	ENST00000326873	NM_000455.4	125			0.438859948328331	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.438859948328331	2		269	287	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94153299	94153299	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1554996680	NA	P-0054600-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	85	156	0	ENST00000323929.3:c.2119A>G	p.Arg707Gly	p.R707G	ENST00000323929	NM_005591.3	707	Aga/Gga	20/20	0.273700895932745	5	FACETS	1	0.964	1	0.784	0.702	0.869	CLONAL	2	TRUE	2	0.438859948328331	5		156	273	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94209559	94209559	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054600-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	111	223	0	ENST00000323929.3:c.555del	p.Asp186MetfsTer13	p.D186Mfs*13	ENST00000323929	NM_005591.3	185	ccA/cc	7/20	0.273700895932745	5	FACETS	0.85	0.773	0.929	0.85	0.773	0.929	CLONAL	3	TRUE	2	0.438859948328331	5		223	329	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497720	125497720	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054600-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	106	228	0	ENST00000428830.2:c.284G>T	p.Arg95Ile	p.R95I	ENST00000428830	NM_001114121.2	95	aGa/aTa	3/14	0.28641576474221	3	FACETS	1	0.977	1			1	CLONAL	2	TRUE	NA	0.438859948328331	3		228	244	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242734	46242735	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0054600-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	79	236	0	ENST00000334344.6:c.1696_1697delinsTT	p.Gly566Leu	p.G566L	ENST00000334344	NM_152641.2	566	GGa/TTa	13/21	0.225097543091134	6	FACETS	1	0.967	1	0.822	0.732	0.917	INDETERMINATE	2	TRUE	3	0.438859948328331	6		236	274	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643645	38643671	+	inframe_deletion	In_Frame_Del	DEL	CAGAGAGCATGTTGTATCATTGTATGT	CAGAGAGCATGTTGTATCATTGTATGT	-	novel	NA	P-0054600-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	115	293	0	ENST00000299084.4:c.1119_1145del	p.Glu373_Ser381del	p.E373_S381del	ENST00000299084	NM_152594.2	372	gCAGAGAGCATGTTGTATCATTGTATGTca/gca	7/7	0.336909741722845	4	FACETS	0.887	0.805	0.972	0.887	0.805	0.972	CLONAL	2	TRUE	2	0.438859948328331	4		293	425	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610312	10610312	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054600-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	196	430	0	ENST00000171111.5:c.398T>C	p.Met133Thr	p.M133T	ENST00000171111	NM_203500.1	133	aTg/aCg	2/6	0.438859948328331	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.438859948328331	2		430	408	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145656	11145656	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054600-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	157	364	0	ENST00000358026.2:c.4018G>T	p.Glu1340Ter	p.E1340*	ENST00000358026	NM_001128849.1	1340	Gag/Tag	29/36	0.438859948328331	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.438859948328331	2		364	318	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213860	66213860	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054600-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	48	307	0	ENST00000273854.3:c.2570C>A	p.Ser857Tyr	p.S857Y	ENST00000273854	NM_004439.5	857	tCt/tAt	15/18	0.208568257157529	4	FACETS	0.974	0.828	1	0.325	0.276	0.378	INDETERMINATE	1	TRUE	1	0.438859948328331	4		307	323	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927727	131927727	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0054600-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	74	161	0	ENST00000265335.6:c.1793+1G>T		p.X598_splice	ENST00000265335		598			0.192628366929693	3	FACETS	0.857	0.761	0.957	0.857	0.761	0.957	INDETERMINATE	2	TRUE	1	0.438859948328331	3		161	240	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120490	94120490	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054600-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	111	327	1	ENST00000369303.4:c.561G>T	p.Gln187His	p.Q187H	ENST00000369303	NM_004440.3	187	caG/caT	3/17	0.114551224127321	4	FACETS	1	0.922	1	1	0.922	1	INDETERMINATE	2	TRUE	2	0.438859948328331	4		328	358	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0054615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	286	411	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.598757872956306	2	FACETS	0.995	0.95	1	0.995	0.95	1	CLONAL	2	TRUE	0	0.598757872956306	2		412	480	SUCCESS
APC	324	MSKCC	GRCh37	5	112173801	112173801	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs79512956	NA	P-0054615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	141	480	0	ENST00000257430.4:c.2510C>A	p.Ser837Ter	p.S837*	ENST00000257430	NM_000038.5	837	tCa/tAa	16/16	0.598757872956306	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.598757872956306	1		480	305	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434924	49434924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201190869	NA	P-0054615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	164	498	0	ENST00000301067.7:c.6629C>T	p.Pro2210Leu	p.P2210L	ENST00000301067	NM_003482.3	2210	cCg/cTg	31/54	0.598757872956306	3	FACETS	0.975	0.897	1	0.488	0.448	0.528	CLONAL	1	TRUE	1	0.598757872956306	3		498	730	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395213	139395213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751228412	NA	P-0054615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	90	507	0	ENST00000277541.6:c.5725G>A	p.Val1909Ile	p.V1909I	ENST00000277541	NM_017617.3	1909	Gtc/Atc	31/34	0.321245358050731	3	FACETS	0.673	0.599	0.753	0.224	0.199	0.251	INDETERMINATE	1	TRUE	0	0.598757872956306	3		507	580	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016570	12016570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	177	369	0	ENST00000353533.5:c.706C>T	p.Leu236Phe	p.L236F	ENST00000353533	NM_003010.3	236	Ctt/Ttt	7/11	0.598757872956306	2	FACETS	0.957	0.901	1	0.957	0.901	1	CLONAL	2	TRUE	0	0.598757872956306	2		369	309	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793470	89793471	+	splice_acceptor_variant	Splice_Site	DNP	AG	AG	TT	novel	NA	P-0054615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	65	338	0	ENST00000336032.3:c.541-2_541-1delinsTT		p.X181_splice	ENST00000336032	NM_006813.2	181			0.598757872956306	3	FACETS	0.788	0.687	0.896	0.394	0.343	0.448	SUBCLONAL	1	TRUE	1	0.598757872956306	3		338	358	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054658-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	186	457	0	ENST00000347630.2:c.305T>C	p.Phe102Ser	p.F102S	ENST00000347630	NM_001007230.1	102	tTc/tCc	5/11	1	2	FACETS	0.869	0.81	0.929	0.869	0.81	0.929	CLONAL	1	TRUE	1	0.882944645358736	2		457	485	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138762	64138762	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054658-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	193	334	0	ENST00000334205.4:c.2129A>C	p.Asn710Thr	p.N710T	ENST00000334205	NM_003942.2	710	aAc/aCc	17/17	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.882944645358736	2		334	413	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262545	16263442	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CACAGTTACCCCCAGTAACCAACTCCAGGGGCTGCCTCTGACCCCTCCTGTGGTGGTGACCCATGGGGTGCAGATTGTGCACTCCAGCGGGGAGCTGTTTCAAGAGTACCGGTACGGCGACATCCGCACCTACCACCCCCCGGCCCAGCTCACACACACTCAGTTTCCCGCCGCTTCCTCTGTTGGCCTGCCTTCCCGGACCAAGACAGCTGCTCAGGTGAGCCAGCCAGGTATCTCCCCACTGTCTGTTGGGCATGTGCTTGTGGGGCTCAGCAGGCTTTTAAGCCAAGATGTGTGAAAGAAATCAGGGGCCAGGTGTGGTGGCTTATGCCTGTAATCCCAGCACTGTGGGAGGCCCAGATGGGAGGACTGCTTAAGCCCGGGAGTTCGAGACCAGCCTGGGCAACATGGCAAAACCCCATCTCGTACAAAAAAAAAAAATTACAAAAATTAGCCAGGTGTGGTGGCACACACCTGTGGTTTCAGCTACCTGGGAGGCTGAGGTGGGAAAATTGCTTGAGCCCTGGAGGCAGAGGTTGCATTGAACCAAGGTCGTGCCACTAGGCTCCAGTGACAGAGCGAGACCCAGTCTCAAAAAAAAAAAAAGCCGGGCATAGTGGCTCACGCCTGTAATCCCAACACTTTGGGAGGCCAGGGCTGGCAGATCACTTGAGGTCAGGAGTTCAAGACCAGCTTGGCCAACATGGTGAAACTCTGTCCCTACTTAAAGAAAAAGAAATCCGCCTTTTGGTAAAGATAGTGGTTGAGTACAAGTGAACTGGTCAGCTAGTCCCTAAAGATGTTGATCTTTTCATGAGTTTAAAGAGCTTTCTTAGTTCTGAGATGAAAGTATTAGATCACATCATGGGGAGTTCTGCATATGGGGAGGGAGCTCTTG	CACAGTTACCCCCAGTAACCAACTCCAGGGGCTGCCTCTGACCCCTCCTGTGGTGGTGACCCATGGGGTGCAGATTGTGCACTCCAGCGGGGAGCTGTTTCAAGAGTACCGGTACGGCGACATCCGCACCTACCACCCCCCGGCCCAGCTCACACACACTCAGTTTCCCGCCGCTTCCTCTGTTGGCCTGCCTTCCCGGACCAAGACAGCTGCTCAGGTGAGCCAGCCAGGTATCTCCCCACTGTCTGTTGGGCATGTGCTTGTGGGGCTCAGCAGGCTTTTAAGCCAAGATGTGTGAAAGAAATCAGGGGCCAGGTGTGGTGGCTTATGCCTGTAATCCCAGCACTGTGGGAGGCCCAGATGGGAGGACTGCTTAAGCCCGGGAGTTCGAGACCAGCCTGGGCAACATGGCAAAACCCCATCTCGTACAAAAAAAAAAAATTACAAAAATTAGCCAGGTGTGGTGGCACACACCTGTGGTTTCAGCTACCTGGGAGGCTGAGGTGGGAAAATTGCTTGAGCCCTGGAGGCAGAGGTTGCATTGAACCAAGGTCGTGCCACTAGGCTCCAGTGACAGAGCGAGACCCAGTCTCAAAAAAAAAAAAAGCCGGGCATAGTGGCTCACGCCTGTAATCCCAACACTTTGGGAGGCCAGGGCTGGCAGATCACTTGAGGTCAGGAGTTCAAGACCAGCTTGGCCAACATGGTGAAACTCTGTCCCTACTTAAAGAAAAAGAAATCCGCCTTTTGGTAAAGATAGTGGTTGAGTACAAGTGAACTGGTCAGCTAGTCCCTAAAGATGTTGATCTTTTCATGAGTTTAAAGAGCTTTCTTAGTTCTGAGATGAAAGTATTAGATCACATCATGGGGAGTTCTGCATATGGGGAGGGAGCTCTTG	-	novel	NA	P-0054658-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	152	448	0	ENST00000375759.3:c.9811_10027-215del		p.X3271_splice	ENST00000375759	NM_015001.2	3271		11/15	1	2	FACETS	0.861	0.796	0.927	0.861	0.796	0.927	CLONAL	1	TRUE	1	0.882944645358736	2		448	400	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055046-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	25	382	0				ENST00000310581	NM_198253.2	-/1132			0.259958347898351	0	FACETS	1	0.891	1			1	CLONAL	1	TRUE	0	0.25720799415808	0		382	122	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622086	43622086	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055046-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	28	290	0	ENST00000355710.3:c.3103G>C	p.Glu1035Gln	p.E1035Q	ENST00000355710	NM_020975.4	1035	Gag/Cag	19/20	0.259958347898351	1	FACETS	0.556	0.445	0.683	0.556	0.445	0.683	SUBCLONAL	1	TRUE	0	0.25720799415808	1		290	341	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828878	26828878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055046-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	56	351	0	ENST00000381527.3:c.100C>T	p.His34Tyr	p.H34Y	ENST00000381527	NM_001260.1	34	Cac/Tac	1/13	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.25720799415808	2		351	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572932	7572932	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055046-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	239	345	0	ENST00000269305.4:c.1177G>C	p.Asp393His	p.D393H	ENST00000269305	NM_001126112.2	393	Gac/Cac	11/11	0.25720799415808	7	FACETS	0.939	0.885	0.993	0.939	0.885	0.993	CLONAL	6	TRUE	1	0.25720799415808	7		345	542	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587782272	NA	P-0055046-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	193	389	0	ENST00000269305.4:c.994-1G>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.25720799415808	7	FACETS	1	0.972	1	0.893	0.836	0.952	CLONAL	5	TRUE	1	0.25720799415808	7		389	460	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285182	212285182	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055046-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	76	291	0	ENST00000342788.4:c.3119G>A	p.Arg1040Lys	p.R1040K	ENST00000342788	NM_005235.2	1040	aGa/aAa	25/28	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.25720799415808	2		291	395	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657051	215657051	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs758972589	NA	P-0055046-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	58	277	0	ENST00000260947.4:c.334C>T	p.Arg112Ter	p.R112*	ENST00000260947	NM_000465.2	112	Cga/Tga	3/11	0.15901476693656	5	FACETS	1	0.963	1	0.462	0.398	0.532	CLONAL	1	TRUE	2	0.25720799415808	5		277	451	SUCCESS
APC	324	MSKCC	GRCh37	5	112154831	112154831	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055046-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	47	331	0	ENST00000257430.4:c.1102G>C	p.Val368Leu	p.V368L	ENST00000257430	NM_000038.5	368	Gta/Cta	10/16	0.246987864906055	4	FACETS	1	0.851	1	0.504	0.425	0.59	CLONAL	1	TRUE	2	0.25720799415808	4		331	456	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176671248	176671248	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055046-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	53	265	0	ENST00000439151.2:c.4355C>G	p.Ser1452Cys	p.S1452C	ENST00000439151	NM_022455.4	1452	tCt/tGt	9/23	0.187245720180119	3	FACETS	0.921	0.786	1	0.461	0.393	0.535	CLONAL	1	TRUE	1	0.25720799415808	3		265	505	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394913	394913	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055046-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	26	322	0	ENST00000380956.4:c.309G>C	p.Lys103Asn	p.K103N	ENST00000380956	NM_001195286.1	103	aaG/aaC	3/9	NA	2	FACETS	0.472	0.373	0.586			1	INDETERMINATE	1	TRUE	NA	0.25720799415808	2		322	428	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435985	116435985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1443741792	NA	P-0055046-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	77	375	0	ENST00000397752.3:c.3980G>A	p.Arg1327His	p.R1327H	ENST00000397752	NM_000245.2	1327	cGc/cAc	21/21	0.25720799415808	8	FACETS	1	0.967	1			1	CLONAL	1	TRUE	NA	0.25720799415808	8		375	803	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874091	151874091	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055046-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	163	378	0	ENST00000262189.6:c.8447C>G	p.Ser2816Cys	p.S2816C	ENST00000262189	NM_170606.2	2816	tCc/tGc	38/59	0.189851039587869	4	FACETS	1	0.977	1	0.778	0.716	0.842	CLONAL	2	TRUE	1	0.25720799415808	4		378	683	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224251	98224251	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055046-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	45	329	0	ENST00000331920.6:c.2590G>A	p.Glu864Lys	p.E864K	ENST00000331920	NM_000264.3	864	Gaa/Aaa	16/24	0.259958347898351	2	FACETS	1	0.898	1	0.543	0.458	0.636	CLONAL	1	TRUE	0	0.25720799415808	2		329	322	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176105634	176105634	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055046-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	55	244	0	ENST00000367669.3:c.881A>T	p.Lys294Met	p.K294M	ENST00000367669	NM_022457.5	294	aAg/aTg	7/20	0.245699875343755	3	FACETS	1	0.935	1	0.582	0.499	0.672	CLONAL	1	TRUE	1	0.25720799415808	3		244	415	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345970	73345970	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0055046-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	55	261	0	ENST00000377767.4:c.1568C>G	p.Ser523Ter	p.S523*	ENST00000377767	NM_014953.3	523	tCa/tGa	11/21	0.25720799415808	6	FACETS	0.983	0.84	1	0.328	0.28	0.38	CLONAL	1	TRUE	3	0.25720799415808	6		261	659	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961635	18961635	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055046-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	35	288	0	ENST00000262803.5:c.768G>C	p.Gln256His	p.Q256H	ENST00000262803	NM_002911.3	256	caG/caC	5/24	0.155526820240259	4	FACETS	0.922	0.757	1			1	CLONAL	1	TRUE	NA	0.25720799415808	4		288	371	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681142	117681142	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055046-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	40	293	0	ENST00000368508.3:c.3478C>G	p.Leu1160Val	p.L1160V	ENST00000368508	NM_002944.2	1160	Ctt/Gtt	23/43	0.259958347898351	2	FACETS	0.676	0.562	0.803	0.338	0.281	0.402	SUBCLONAL	1	TRUE	0	0.25720799415808	2		293	460	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467761	50467761	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055046-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	71	342	0	ENST00000331340.3:c.996G>T	p.Gln332His	p.Q332H	ENST00000331340	NM_006060.4	332	caG/caT	8/8	0.189851039587869	4	FACETS	0.994	0.874	1	0.663	0.582	0.749	CLONAL	2	TRUE	1	0.25720799415808	4		342	349	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233140	66233140	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs769393148	NA	P-0055086-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	31	211	0	ENST00000273854.3:c.1859G>A	p.Arg620Gln	p.R620Q	ENST00000273854	NM_004439.5	620	cGg/cAg	10/18	1	2	FACETS	0.554	0.448	0.674	0.554	0.448	0.674	SUBCLONAL	1	TRUE	1	0.267153583346841	2		211	419	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328368	137328368	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055086-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	40	290	0	ENST00000481739.1:c.1297C>G	p.Leu433Val	p.L433V	ENST00000481739	NM_002957.4	433	Ctg/Gtg	10/10	1	2	FACETS	0.46	0.381	0.548	0.46	0.381	0.548	SUBCLONAL	1	TRUE	1	0.267153583346841	2		290	651	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0055175-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	548	440	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.619156369618299	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.621682023225266	2		440	867	SUCCESS
ATM	472	MSKCC	GRCh37	11	108099973	108099973	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0055175-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	290	336	0	ENST00000278616.4:c.254C>G	p.Ser85Ter	p.S85*	ENST00000278616	NM_000051.3	85	tCa/tGa	4/63	0.621682023225266	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.621682023225266	1		336	598	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597327	10597354	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	CTCAACAGGTACAGTTCTGCTGGTCAAT	CTCAACAGGTACAGTTCTGCTGGTCAAT	-	novel	NA	P-0055175-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	232	374	0	ENST00000171111.5:c.1849_*1del		p.*617*	ENST00000171111	NM_203500.1	617		6/6	0.621682023225266	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.621682023225266	1		374	503	SUCCESS
APC	324	MSKCC	GRCh37	5	112174404	112174404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1375326078	NA	P-0055175-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	259	384	0	ENST00000257430.4:c.3113C>T	p.Ser1038Phe	p.S1038F	ENST00000257430	NM_000038.5	1038	tCt/tTt	16/16	0.621682023225266	1	FACETS	0.929	0.877	0.982	0.929	0.877	0.982	CLONAL	1	TRUE	0	0.621682023225266	1		384	618	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0055502-T10-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	54	405	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.212077030555678	1	FACETS	0.831	0.71	0.963	0.831	0.71	0.963	CLONAL	1	TRUE	0	0.212077030555678	1		405	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0055502-T10-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	63	383	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.154439329777535	4	FACETS	1	0.941	1	0.584	0.504	0.669	CLONAL	1	TRUE	2	0.212077030555678	4		383	617	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259439	55259439	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs397517126	NA	P-0055502-T10-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	41	368	0	ENST00000275493.2:c.2497T>G	p.Leu833Val	p.L833V	ENST00000275493	NM_005228.3	833	Ttg/Gtg	21/28	0.212077030555678	1	FACETS	0.745	0.621	0.883	0.745	0.621	0.883	SUBCLONAL	1	TRUE	0	0.212077030555678	1		368	464	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046749	180046749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121909657	NA	P-0055502-T10-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	84	522	0	ENST00000261937.6:c.2563G>A	p.Ala855Thr	p.A855T	ENST00000261937	NM_182925.4	855	Gcc/Acc	18/30	0.197085791030067	0	FACETS	1	0.945	1			1	CLONAL	1	TRUE	0	0.212077030555678	0		522	559	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003238	42003238	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055502-T10-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	62	449	0	ENST00000219905.7:c.2777del	p.Lys926SerfsTer7	p.K926Sfs*7	ENST00000219905	NM_001164273.1	925	ccA/cc	8/24	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.212077030555678	2		449	512	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0055799-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	68	348	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.30709100243991	3	FACETS	0.758	0.664	0.858	0.758	0.664	0.858	SUBCLONAL	2	TRUE	1	0.30709100243991	3		348	337	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473723	67473723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223740	NA	P-0055799-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	30	596	0	ENST00000327367.4:c.803G>A	p.Arg268His	p.R268H	ENST00000327367	NM_005902.3	268	cGc/cAc	6/9	1	2	FACETS	0.737	0.596	0.896	0.737	0.596	0.896	SUBCLONAL	1	TRUE	1	0.30709100243991	2		596	265	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518070	176518070	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055799-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	180	449	0	ENST00000292408.4:c.568G>T	p.Ala190Ser	p.A190S	ENST00000292408	NM_213647.1	190	Gcc/Tcc	5/18	0.30709100243991	5	FACETS	1	0.981	1	0.865	0.804	0.926	CLONAL	3	TRUE	1	0.30709100243991	5		449	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750600586	NA	P-0057013-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	153	361	0	ENST00000269305.4:c.413C>T	p.Ala138Val	p.A138V	ENST00000269305	NM_001126112.2	138	gCc/gTc	5/11	0.674617238323613	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.674617238323613	3		361	175	SUCCESS
AR	367	MSKCC	GRCh37	X	66766228	66766228	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057013-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	22	156	0	ENST00000374690.3:c.1240C>A	p.Leu414Met	p.L414M	ENST00000374690	NM_000044.3	414	Ctg/Atg	1/8	1	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.674617238323613	1		156	31	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961056	55961056	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1312670638	NA	P-0057013-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	3	294	0	ENST00000263923.4:c.2884C>T	p.Arg962Cys	p.R962C	ENST00000263923	NM_002253.2	962	Cgc/Tgc	21/30	0.674617238323613	2	FACETS	0.075	0.034	0.137	0.037	0.017	0.069	SUBCLONAL	1	TRUE	0	0.674617238323613	2		294	119	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631824	90631824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057013-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	42	351	0	ENST00000330062.3:c.529G>A	p.Asp177Asn	p.D177N	ENST00000330062	NM_002168.2	177	Gac/Aac	4/11	0.587000060419115	4	FACETS	1	0.952	1	0.448	0.381	0.521	CLONAL	1	TRUE	1	0.674617238323613	4		351	155	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559231	141559231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057013-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	123	291	0	ENST00000220592.5:c.1570G>A	p.Gly524Ser	p.G524S	ENST00000220592	NM_012154.3	524	Ggc/Agc	12/19	0.674617238323613	3	FACETS		NA	1	1	0.991	1	NA	4	TRUE	0	0.674617238323613	3		291	136	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316389	14316389	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057013-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	1316	265	1	ENST00000256196.4:c.216A>C	p.Gln72His	p.Q72H	ENST00000256196		72	caA/caC	3/6	0.674617238323613	21	FACETS	1	0.991	1			1	CLONAL	20	TRUE	NA	0.674617238323613	21		266	1443	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760132	133760132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373527910	NA	P-0057013-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	51	301	0	ENST00000318560.5:c.2455C>T	p.Arg819Trp	p.R819W	ENST00000318560	NM_005157.4	819	Cgg/Tgg	11/11	0.674617238323613	3	FACETS	1	0.967	1	0.712	0.62	0.808	CLONAL	1	TRUE	1	0.674617238323613	3		301	142	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393213	393213	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057013-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	29	284	0	ENST00000380956.4:c.61A>T	p.Asn21Tyr	p.N21Y	ENST00000380956	NM_001195286.1	21	Aac/Tac	2/9	0.674617238323613	8	FACETS	0.769	0.624	0.931	0.308	0.249	0.373	CLONAL	2	TRUE	3	0.674617238323613	8		284	169	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260749	16260749	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057013-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	6	0	0	ENST00000375759.3:c.8014G>T	p.Val2672Leu	p.V2672L	ENST00000375759	NM_015001.2	2672	Gtg/Ttg	11/15	0.674617238323613	2	FACETS	0.103	0.061	0.16	0.052	0.03	0.08	SUBCLONAL	1	TRUE	0	0.674617238323613	2		0	172	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642722	3642722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057013-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4	100	286	0	ENST00000294008.3:c.2305G>A	p.Glu769Lys	p.E769K	ENST00000294008	NM_032444.2	769	Gag/Aag	11/15	0.674617238323613	2	FACETS		NA	1	1	0.992	1	NA	3	TRUE	0	0.674617238323613	2		286	104	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213285	36213285	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057013-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	83	279	0	ENST00000222270.7:c.2482G>T	p.Glu828Ter	p.E828*	ENST00000222270	NM_014727.1	828	Gag/Tag	4/37	0.664979056714033	5	FACETS	1	0.929	1	1	0.929	1	CLONAL	3	TRUE	2	0.674617238323613	5		279	161	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004789	150004789	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057013-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	47	364	0	ENST00000253339.5:c.1436C>G	p.Ser479Cys	p.S479C	ENST00000253339		479	tCt/tGt	3/7	0.674617238323613	3	FACETS	1	0.883	1	0.518	0.443	0.597	CLONAL	1	TRUE	1	0.674617238323613	3		364	180	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258990	153258995	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGGG	CTGGGG	A	novel	NA	P-0057013-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	73	297	0	ENST00000281708.4:c.820_825delinsT	p.Pro274PhefsTer11	p.P274Ffs*11	ENST00000281708	NM_033632.3	274	CCCCAG/T	5/12	0.674617238323613	3	FACETS	1	0.933	1	1	0.933	1	CLONAL	3	TRUE	0	0.674617238323613	3		297	96	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259319	89259319	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057013-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	65	294	0	ENST00000336596.2:c.463A>G	p.Met155Val	p.M155V	ENST00000336596	NM_005233.5	155	Atg/Gtg	3/17	0.674617238323613	5	FACETS	0.766	0.665	0.875	0.255	0.221	0.292	SUBCLONAL	1	TRUE	2	0.674617238323613	5		294	506	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762210	43762210	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057013-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	50	269	0	ENST00000382044.4:c.1235A>T	p.Lys412Met	p.K412M	ENST00000382044	NM_001141980.1	412	aAg/aTg	11/28	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.674617238323613	2		269	129	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394352	162394352	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057013-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	20	272	0	ENST00000366898.1:c.716T>A	p.Ile239Asn	p.I239N	ENST00000366898	NM_004562.2	239	aTt/aAt	6/12	0.674617238323613	3	FACETS	0.499	0.384	0.63	0.249	0.192	0.315	SUBCLONAL	1	TRUE	1	0.674617238323613	3		272	159	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057512-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	42	382	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.719514055538696	2		382	110	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590491	67590494	+	frameshift_variant	Frame_Shift_Del	DEL	AGAA	AGAA	-	novel	NA	P-0057512-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	79	294	0	ENST00000274335.5:c.1558_1561del	p.Glu520TyrfsTer11	p.E520Yfs*11	ENST00000274335		518	gAGAAa/ga	11/15	1	2	FACETS	0.796	0.708	0.887	0.796	0.708	0.887	SUBCLONAL	1	TRUE	1	0.719514055538696	2		294	276	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865509	57865509	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057512-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	59	436	0	ENST00000228682.2:c.2986C>T	p.Pro996Ser	p.P996S	ENST00000228682	NM_005269.2	996	Ccc/Tcc	12/12	1	2	FACETS	0.548	0.475	0.627	0.548	0.475	0.627	SUBCLONAL	1	TRUE	1	0.719514055538696	2		436	299	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439692	51439692	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0057512-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	131	403	0	ENST00000262662.1:c.257T>G	p.Leu86Ter	p.L86*	ENST00000262662		86	tTa/tGa	4/4	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.719514055538696	2		403	345	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509827	187509827	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057512-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	94	413	0	ENST00000441802.2:c.13686T>A	p.Ser4562Arg	p.S4562R	ENST00000441802	NM_005245.3	4562	agT/agA	27/27	1	2	FACETS	0.927	0.836	1	0.927	0.836	1	CLONAL	1	TRUE	1	0.719514055538696	2		413	282	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865245	57865245	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057512-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	51	371	0	ENST00000228682.2:c.2722C>G	p.Leu908Val	p.L908V	ENST00000228682	NM_005269.2	908	Cta/Gta	12/12	1	2	FACETS	0.65	0.559	0.748	0.65	0.559	0.748	SUBCLONAL	1	TRUE	1	0.719514055538696	2		371	218	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0057588-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	86	300	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.20920035891772	4	FACETS	0.751	0.664	0.843	0.751	0.664	0.843	SUBCLONAL	2	TRUE	2	0.20920035891772	4		300	662	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220691	1220691	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs878853247	NA	P-0057588-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	108	380	0	ENST00000326873.7:c.709G>T	p.Asp237Tyr	p.D237Y	ENST00000326873	NM_000455.4	237	Gac/Tac	5/10	0.20920035891772	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.20920035891772	1		380	741	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098815	178098815	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057588-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	174	310	0	ENST00000397062.3:c.230A>G	p.Asp77Gly	p.D77G	ENST00000397062	NM_006164.4	77	gAt/gGt	2/5	0.113349825846498	5	FACETS	1	0.967	1	0.548	0.504	0.594	INDETERMINATE	2	TRUE	1	0.20920035891772	5		310	997	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556657	41556657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057588-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	68	369	0	ENST00000263253.7:c.3602G>A	p.Cys1201Tyr	p.C1201Y	ENST00000263253	NM_001429.3	1201	tGt/tAt	20/31	1	2	FACETS	0.766	0.665	0.875	0.766	0.665	0.875	SUBCLONAL	1	TRUE	1	0.20920035891772	2		369	849	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681594	30681594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762846533	NA	P-0057588-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	77	373	0	ENST00000376406.3:c.503C>T	p.Ser168Leu	p.S168L	ENST00000376406	NM_014641.2	168	tCg/tTg	3/15	1	2	FACETS	0.722	0.632	0.82	0.722	0.632	0.82	SUBCLONAL	1	TRUE	1	0.20920035891772	2		373	1019	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40874900	40874900	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057588-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	66	283	0	ENST00000428826.2:c.400T>C	p.Tyr134His	p.Y134H	ENST00000428826		134	Tac/Cac	6/21	1	2	FACETS	0.799	0.692	0.915	0.799	0.692	0.915	CLONAL	1	TRUE	1	0.20920035891772	2		283	790	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970984	21970984	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1408195053	NA	P-0057588-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	53	441	0	ENST00000304494.5:c.374A>G	p.Asp125Gly	p.D125G	ENST00000304494	NM_000077.4	125	gAt/gGt	2/3	0.18526257184111	1	FACETS	0.54	0.459	0.629	0.54	0.459	0.629	SUBCLONAL	1	TRUE	0	0.20920035891772	1		441	840	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953229	81953229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	20	389	0	ENST00000359376.3:c.2195G>A	p.Arg732His	p.R732H	ENST00000359376	NM_002661.3	732	cGc/cAc	20/33	1	2	FACETS	0.308	0.235	0.393	0.308	0.235	0.393	SUBCLONAL	1	TRUE	1	0.370374918069293	2		389	351	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317136	87317136	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	55	361	0	ENST00000277120.3:c.275G>T	p.Gly92Val	p.G92V	ENST00000277120		92	gGa/gTa	3/19	1	2	FACETS	0.874	0.751	1	0.874	0.751	1	CLONAL	1	TRUE	1	0.370374918069293	2		361	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579526	7579526	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	89	474	0	ENST00000269305.4:c.161del	p.Phe54SerfsTer69	p.F54Sfs*69	ENST00000269305	NM_001126112.2	54	tTc/tc	4/11	0.370374918069293	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.370374918069293	1		474	297	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058109-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	32	382	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.603	0.49	0.731	0.603	0.49	0.731	SUBCLONAL	1	TRUE	1	0.27	2		382	393	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0058109-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	39	380	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.18900476497784	3	FACETS	0.48	0.397	0.574	0.24	0.198	0.287	SUBCLONAL	1	TRUE	1	0.27	3		380	683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0058109-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	122	386	0	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	0.268329636974559	2	FACETS	0.816	0.74	0.895	0.816	0.74	0.895	CLONAL	2	TRUE	0	0.27	2		386	554	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075194	16075194	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058109-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	118	348	0	ENST00000268712.3:c.358C>T	p.Gln120Ter	p.Q120*	ENST00000268712	NM_006311.3	120	Cag/Tag	4/46	0.268329636974559	2	FACETS	1	0.984	1	0.725	0.656	0.797	CLONAL	1	TRUE	0	0.27	2		348	603	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600468	43600468	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058109-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	73	473	0	ENST00000355710.3:c.694G>A	p.Glu232Lys	p.E232K	ENST00000355710	NM_020975.4	232	Gag/Aag	4/20	1	2	FACETS	0.795	0.695	0.903	0.795	0.695	0.903	CLONAL	1	TRUE	1	0.27	2		473	680	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022374	31022374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750708574	NA	P-0058109-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	67	439	0	ENST00000375687.4:c.1859G>A	p.Arg620His	p.R620H	ENST00000375687	NM_015338.5	620	cGt/cAt	13/13	0.205294712652621	3	FACETS	0.675	0.585	0.772	0.225	0.195	0.258	SUBCLONAL	1	TRUE	0	0.27	3		439	835	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023050	27023051	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0058109-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	94	394	0	ENST00000324856.7:c.157dup	p.Ala53GlyfsTer58	p.A53Gfs*58	ENST00000324856	NM_006015.4	52	-/G	1/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.27	2		394	600	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105744	27105744	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1557619847	NA	P-0058109-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	94	480	0	ENST00000324856.7:c.5355T>A	p.Asp1785Glu	p.D1785E	ENST00000324856	NM_006015.4	1785	gaT/gaA	20/20	1	2	FACETS	0.881	0.784	0.986	0.881	0.784	0.986	CLONAL	1	TRUE	1	0.27	2		480	790	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315366	30315366	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058109-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	49	315	0	ENST00000322652.5:c.1051C>G	p.Gln351Glu	p.Q351E	ENST00000322652	NM_015355.2	351	Cag/Gag	10/16	0.302279687834602	4	FACETS	0.643	0.543	0.753			1	SUBCLONAL	1	TRUE	NA	0.27	4		315	717	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315421	30315421	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1298450451	NA	P-0058109-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	52	345	0	ENST00000322652.5:c.1106C>A	p.Ser369Tyr	p.S369Y	ENST00000322652	NM_015355.2	369	tCt/tAt	10/16	0.302279687834602	4	FACETS	0.652	0.554	0.76			1	SUBCLONAL	1	TRUE	NA	0.27	4		345	750	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411583	116411583	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058109-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	134	335	0	ENST00000397752.3:c.2762G>C	p.Gly921Ala	p.G921A	ENST00000397752	NM_000245.2	921	gGa/gCa	13/21	1	2	FACETS	0.816	0.744	0.892	1	0.988	1	CLONAL	2	TRUE	1	0.27	2		335	608	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843359	128843359	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs749414966	NA	P-0058109-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	130	455	0	ENST00000249373.3:c.466A>G	p.Ile156Val	p.I156V	ENST00000249373	NM_005631.4	156	Atc/Gtc	2/12	1	2	FACETS	0.805	0.733	0.881	1	0.988	1	CLONAL	2	TRUE	1	0.27	2		455	598	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0058127-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	76	307	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.613393688874376	2		307	220	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0058127-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	72	383	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.827	0.73	0.929	0.827	0.73	0.929	CLONAL	1	TRUE	1	0.613393688874376	2		383	284	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0058127-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	144	516	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.613393688874376	1	FACETS	0.978	0.905	1	0.978	0.905	1	CLONAL	1	TRUE	0	0.613393688874376	1		516	333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691039	NA	P-0058127-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	328	522	2	ENST00000269305.4:c.919+1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.613393688874376	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.613393688874376	1		524	662	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913322	28913322	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765475765	NA	P-0058127-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	121	406	0	ENST00000282397.4:c.2471G>A	p.Arg824Gln	p.R824Q	ENST00000282397	NM_002019.4	824	cGg/cAg	17/30	0.490703946791808	3	FACETS	0.515	0.464	0.569	0.172	0.154	0.19	SUBCLONAL	1	TRUE	0	0.613393688874376	3		406	1001	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058127-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	199	471	3	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	0.613393688874376	1	FACETS	0.974	0.912	1	0.974	0.912	1	CLONAL	1	TRUE	0	0.613393688874376	1		474	462	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200940	108200940	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0058127-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	75	293	0	ENST00000278616.4:c.7308-1G>A		p.X2436_splice	ENST00000278616	NM_000051.3	2436			1	2	FACETS	0.771	0.682	0.866	0.771	0.682	0.866	SUBCLONAL	1	TRUE	1	0.613393688874376	2		293	317	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467877	66467877	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058127-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	32	333	0	ENST00000273854.3:c.392A>C	p.Lys131Thr	p.K131T	ENST00000273854	NM_004439.5	131	aAa/aCa	3/18	1	2	FACETS	0.284	0.23	0.344	0.284	0.23	0.344	SUBCLONAL	1	TRUE	1	0.613393688874376	2		333	368	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998079	169998080	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCGGGTAATAGGAAGAGGAAGTTATGCCAAAGTA	novel	NA	P-0058127-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	22	343	0	ENST00000295797.4:c.772_805dup	p.Leu269ProfsTer34	p.L269Pfs*34	ENST00000295797	NM_002740.5	257	ctc/ctCCGGGTAATAGGAAGAGGAAGTTATGCCAAAGTAc	9/18	1	2	FACETS	0.191	0.147	0.241	0.191	0.147	0.241	SUBCLONAL	1	TRUE	1	0.613393688874376	2		343	376	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998890	11998890	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0058127-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	76	271	0	ENST00000353533.5:c.394-2A>C		p.X132_splice	ENST00000353533	NM_003010.3	132			0.613393688874376	1	FACETS	0.954	0.857	1	0.954	0.857	1	CLONAL	1	TRUE	0	0.613393688874376	1		271	180	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	69061220	69061220	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058127-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	155	202	0	ENST00000487270.1:c.1055T>C	p.Val352Ala	p.V352A	ENST00000487270	NM_133509.3	352	gTc/gCc	11/11	0.613393688874376	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.613393688874376	1		202	315	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081544	143081544	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058127-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	189	378	0	ENST00000262992.4:c.1530A>G	p.Ile510Met	p.I510M	ENST00000262992	NM_001101669.1	510	atA/atG	15/24	1	2	FACETS	0.977	0.907	1	0.977	0.907	1	CLONAL	1	TRUE	1	0.613393688874376	2		378	631	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437914	110437914	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058127-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	123	235	0	ENST00000375856.3:c.487T>G	p.Cys163Gly	p.C163G	ENST00000375856	NM_003749.2	163	Tgc/Ggc	1/2	0.613393688874376	4	FACETS	0.942	0.873	1	0.942	0.873	1	CLONAL	3	TRUE	1	0.613393688874376	4		235	229	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123693	11123693	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058127-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	53	425	0	ENST00000358026.2:c.2343G>A	p.Met781Ile	p.M781I	ENST00000358026	NM_001128849.1	781	atG/atA	16/36	0.508069649677167	1	FACETS	0.217	0.185	0.253	0.217	0.185	0.253	SUBCLONAL	1	TRUE	0	0.613393688874376	1		425	551	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841839	151841839	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058127-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	37	392	0	ENST00000262189.6:c.14302G>C	p.Glu4768Gln	p.E4768Q	ENST00000262189	NM_170606.2	4768	Gaa/Caa	55/59	1	2	FACETS	0.169	0.138	0.203	0.169	0.138	0.203	SUBCLONAL	1	TRUE	1	0.613393688874376	2		392	715	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0058606-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	89	440	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.373622796074141	2		440	411	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0058606-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	72	285	1	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.373622796074141	2		286	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0058721-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	457	553	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.955119916418534	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.955119916418534	2		553	477	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880219	37880229	+	protein_altering_variant	In_Frame_Del	DEL	TTGAGGGAAAA	TTGAGGGAAAA	GCCAAAGC	novel	NA	P-0058721-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	438	403	0	ENST00000269571.5:c.2263_2273delinsGCCAAAGC	p.Leu755_Asn758delinsAlaLysAla	p.L755_N758delinsAKA	ENST00000269571		755	TTGAGGGAAAAc/GCCAAAGCc	19/27	0.683699694339687	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.955119916418534	1		403	449	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281473	198281473	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058721-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	46	319	0	ENST00000335508.6:c.658C>G	p.Gln220Glu	p.Q220E	ENST00000335508	NM_012433.2	220	Cag/Gag	6/25	0.955119916418534	2	FACETS	0.422	0.359	0.491	0.211	0.179	0.246	SUBCLONAL	1	TRUE	0	0.955119916418534	2		319	228	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0058899-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	161	547	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	0.536859380595114	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.536859380595114	1		547	411	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929073	44929073	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058899-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	129	474	0	ENST00000377967.4:c.2174del	p.Leu725Ter	p.L725*	ENST00000377967	NM_021140.2	725	Ttg/tg	17/29	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.536859380595114	2		474	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578195	7578197	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0059163-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	190	498	0	ENST00000269305.4:c.652_654del	p.Val218del	p.V218del	ENST00000269305	NM_001126112.2	218	GTG/-	6/11	0.872539960760582	2	FACETS	0.848	0.809	0.884	0.848	0.809	0.884	CLONAL	2	TRUE	0	0.872177137265039	2		498	257	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857044	9857044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201707833	NA	P-0059163-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	176	361	1	ENST00000330684.3:c.4357G>A	p.Val1453Met	p.V1453M	ENST00000330684	NM_001134407.1	1453	Gtg/Atg	13/13	0.876334326238047	4	FACETS	1	0.979	1	0.387	0.358	0.417	CLONAL	1	TRUE	1	0.872177137265039	4		362	651	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380577	31380577	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0059163-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	116	398	0	ENST00000328111.2:c.1066+1G>A		p.X356_splice	ENST00000328111	NM_006892.3	356			0.876334326238047	3	FACETS	0.979	0.891	1	0.49	0.445	0.536	CLONAL	1	TRUE	1	0.872177137265039	3		398	390	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604181	189604181	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0059163-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	358	347	0	ENST00000264731.3:c.1350-2A>T		p.X450_splice	ENST00000264731	NM_003722.4	450			0.876334326238047	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.872177137265039	2		347	378	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517945	8517946	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0059163-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	168	373	0	ENST00000356435.5:c.1445dup	p.Leu482PhefsTer25	p.L482Ffs*25	ENST00000356435		482	tta/ttTa	10/35	0.690515965085466	6	FACETS	0.979	0.899	1	0.326	0.299	0.355	CLONAL	1	TRUE	3	0.872177137265039	6		373	1080	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0059209-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	160	383	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.51257396661312	2		383	583	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55231508	55231508	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059209-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	147	376	0	ENST00000275493.2:c.1714A>G	p.Thr572Ala	p.T572A	ENST00000275493	NM_005228.3	572	Aca/Gca	14/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.51257396661312	2		376	475	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221230	1221255	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGTACCCCTTCGAAGGGGACAACA	TCTGTACCCCTTCGAAGGGGACAACA	-	novel	NA	P-0059209-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	145	513	0	ENST00000326873.7:c.756_781del	p.Tyr253GlnfsTer4	p.Y253Qfs*4	ENST00000326873	NM_000455.4	251	ggTCTGTACCCCTTCGAAGGGGACAACAtc/ggtc	6/10	0.51257396661312	1	FACETS	0.878	0.807	0.952	0.878	0.807	0.952	CLONAL	1	TRUE	0	0.51257396661312	1		513	479	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291545	15291545	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059209-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	159	485	0	ENST00000263388.2:c.3089G>C	p.Gly1030Ala	p.G1030A	ENST00000263388	NM_000435.2	1030	gGa/gCa	19/33	1	2	FACETS	0.965	0.888	1	0.965	0.888	1	CLONAL	1	TRUE	1	0.51257396661312	2		485	643	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056557	26056557	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0059209-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	149	486	0	ENST00000343677.2:c.100A>T	p.Lys34Ter	p.K34*	ENST00000343677	NM_005319.3	34	Aag/Tag	1/1	0.278325774126525	1	FACETS	0.739	0.678	0.802	0.739	0.678	0.802	INDETERMINATE	1	TRUE	0	0.51257396661312	1		486	585	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139677	202139703	+	splice_donor_variant,intron_variant	Splice_Site	DEL	GTAGACGGAAACCTCCAAATCCTTTTT	GTAGACGGAAACCTCCAAATCCTTTTT	ATTCTAGTTA	novel	NA	P-0059209-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	95	474	3	ENST00000358485.4:c.837+1_837+27delinsATTCTAGTTA		p.X279_splice	ENST00000358485	NM_001080125.1	279			0.51257396661312	1	FACETS	0.751	0.674	0.831	0.751	0.674	0.831	SUBCLONAL	1	TRUE	0	0.51257396661312	1		477	367	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154793	2154793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059209-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	46	566	0	ENST00000434045.2:c.428C>T	p.Pro143Leu	p.P143L	ENST00000434045	NM_001127598.1	143	cCc/cTc	4/5	0.278325774126525	1	FACETS	0.234	0.196	0.275	0.234	0.196	0.275	INDETERMINATE	1	TRUE	0	0.51257396661312	1		566	571	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0059222-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	57	385	0				ENST00000310581	NM_198253.2	-/1132			0.596687182034802	1	FACETS	0.363	0.316	0.413	0.363	0.316	0.413	SUBCLONAL	1	TRUE	0	0.89427049735992	1		385	194	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0059222-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	283	361	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	0.956	0.905	1	0.956	0.905	1	CLONAL	1	TRUE	1	0.89427049735992	2		361	662	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0059222-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	237	322	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.89427049735992	2		322	501	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274192	10274192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765986049	NA	P-0059222-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	164	375	0	ENST00000330684.3:c.77C>T	p.Ala26Val	p.A26V	ENST00000330684	NM_001134407.1	26	gCg/gTg	2/13	0.582058048468935	1	FACETS	0.687	0.645	0.73	0.687	0.645	0.73	SUBCLONAL	1	TRUE	0	0.89427049735992	1		375	295	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624263	89624267	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	novel	NA	P-0059222-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	130	154	0	ENST00000371953.3:c.37_41del	p.Lys13GlufsTer29	p.K13Efs*29	ENST00000371953	NM_000314.4	13	AAAAGg/g	1/9	0.89427049735992	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.89427049735992	1		154	150	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218807	36218807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059222-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	147	450	0	ENST00000222270.7:c.4418G>A	p.Gly1473Asp	p.G1473D	ENST00000222270	NM_014727.1	1473	gGc/gAc	18/37	0.596687182034802	1	FACETS	0.432	0.398	0.466	0.432	0.398	0.466	SUBCLONAL	1	TRUE	0	0.89427049735992	1		450	421	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144361431	144361431	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059222-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	100	400	0	ENST00000262995.4:c.1481A>G	p.His494Arg	p.H494R	ENST00000262995	NM_207123.2	494	cAt/cGt	6/11	1	2	FACETS	0.398	0.356	0.442	0.398	0.356	0.442	SUBCLONAL	1	TRUE	1	0.89427049735992	2		400	562	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196198	108196198	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555119214	NA	P-0059222-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	100	281	0	ENST00000278616.4:c.6734A>G	p.Glu2245Gly	p.E2245G	ENST00000278616	NM_000051.3	2245	gAa/gGa	46/63	1	2	FACETS	0.461	0.414	0.511	0.461	0.414	0.511	SUBCLONAL	1	TRUE	1	0.89427049735992	2		281	485	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059597-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	101	382	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.385123867785339	2		382	518	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0059597-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	8	393	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.385123867785339	1	FACETS	0.067	0.043	0.1	0.067	0.043	0.1	SUBCLONAL	1	TRUE	0	0.385123867785339	1		393	497	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907047	101907047	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0059597-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	228	390	0	ENST00000374994.4:c.1007C>G	p.Ser336Ter	p.S336*	ENST00000374994	NM_004612.2	336	tCa/tGa	6/9	0.385123867785339	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.385123867785339	2		390	547	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200943	108200943	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1555122944	NA	P-0059597-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	118	447	0	ENST00000278616.4:c.7310A>G	p.Tyr2437Cys	p.Y2437C	ENST00000278616	NM_000051.3	2437	tAc/tGc	50/63	0.385123867785339	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.385123867785339	1		447	412	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059630-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	1432	382	0				ENST00000310581	NM_198253.2	-/1132			0.432775346750014	5	FACETS	0.928	0.912	0.944	0.742	0.729	0.755	INDETERMINATE	4	TRUE	0	0.879160236324318	5		382	2035	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040642	16040642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059630-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	12	176	0	ENST00000268712.3:c.1492C>T	p.Arg498Cys	p.R498C	ENST00000268712	NM_006311.3	498	Cgc/Tgc	14/46	0.879160236324318	1	FACETS	0.51	0.381	0.647	0.51	0.381	0.647	SUBCLONAL	1	TRUE	0	0.879160236324318	1		176	30	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477806	140477806	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs180177039	NA	P-0059630-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	19	190	0	ENST00000288602.6:c.1502A>T	p.Glu501Val	p.E501V	ENST00000288602	NM_004333.4	501	gAa/gTa	12/18	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.879160236324318	2		190	42	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913233	NA	P-0059630-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	506	217	0	ENST00000451590.1:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000451590	NM_001130442.1	61	cAg/cTg	3/5	0.879160236324318	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.879160236324318	1		217	641	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176328	24176328	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059630-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	165	114	0	ENST00000263121.7:c.1119G>T	p.Arg373Ser	p.R373S	ENST00000263121	NM_003073.3	373	agG/agT	9/9	0.48395933290892	1	FACETS	0.226	0.207	0.245	0.226	0.207	0.245	INDETERMINATE	1	TRUE	0	0.879160236324318	1		114	932	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519938	NA	P-0060756-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	40	275	0	ENST00000263967.3:c.1034A>T	p.Asn345Ile	p.N345I	ENST00000263967	NM_006218.2	345	aAt/aTt	5/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		275	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578369	7578369	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0060756-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	47	578	0	ENST00000269305.4:c.559+2T>G		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.142728405403107	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		578	692	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0061438-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	147	243	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	0.798736016101753	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.798736016101753	1		243	199	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156719	20156719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061438-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	192	365	0	ENST00000379607.5:c.38G>A	p.Arg13His	p.R13H	ENST00000379607	NM_001412.3	13	cGc/cAc	2/7	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.798736016101753	2		365	412	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790864	89790864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061438-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	275	613	0	ENST00000336032.3:c.251C>T	p.Ala84Val	p.A84V	ENST00000336032	NM_006813.2	84	gCc/gTc	1/2	NA	2	FACETS	1	0.953	1			1	INDETERMINATE	1	TRUE	NA	0.798736016101753	2		613	682	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772813	135772813	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061438-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	316	508	0	ENST00000298552.3:c.2810C>T	p.Ala937Val	p.A937V	ENST00000298552	NM_001162426.1	937	gCa/gTa	21/23	0.798736016101753	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.798736016101753	1		508	436	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876523	35876523	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061438-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	212	537	0	ENST00000303115.3:c.1315A>C	p.Thr439Pro	p.T439P	ENST00000303115	NM_002185.3	439	Act/Cct	8/8	1	2	FACETS	0.903	0.844	0.962	0.903	0.844	0.962	CLONAL	1	TRUE	1	0.798736016101753	2		537	588	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719250	61719250	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061438-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	215	487	0	ENST00000401558.2:c.1807C>G	p.Gln603Glu	p.Q603E	ENST00000401558	NM_003400.3	603	Cag/Gag	16/25	0.165964007547192	4	FACETS	0.912	0.855	0.969	0.912	0.855	0.969	INDETERMINATE	2	TRUE	2	0.798736016101753	4		487	531	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287497	46287497	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061438-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	162	397	0	ENST00000334344.6:c.5356G>C	p.Gly1786Arg	p.G1786R	ENST00000334344	NM_152641.2	1786	Ggt/Cgt	20/21	1	2	FACETS	0.964	0.894	1	0.964	0.894	1	CLONAL	1	TRUE	1	0.798736016101753	2		397	421	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790735	89790740	+	missense_variant	Missense_Mutation	ONP	CTTTAC	CTTTAC	TTTTAT	novel	NA	P-0061438-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	298	636	0	ENST00000336032.3:c.122_127delinsTTTTAT	p.Pro41_Pro43delinsLeuLeuSer	p.P41_P43delinsLLS	ENST00000336032	NM_006813.2	41	cCTTTACcc/cTTTTATcc	1/2	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.798736016101753	2		636	730	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121110	11121110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749349816	NA	P-0061562-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	93	389	0	ENST00000358026.2:c.2177G>A	p.Arg726His	p.R726H	ENST00000358026	NM_001128849.1	726	cGt/cAt	15/36	0.330083603653971	3	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	1	0.329434034052942	3		389	314	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965481	68965481	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs753425478	NA	P-0061562-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	29	341	0	ENST00000288368.4:c.1093G>T	p.Gly365Cys	p.G365C	ENST00000288368	NM_024870.2	365	Ggt/Tgt	9/40	0.329434034052942	5	FACETS	0.778	0.631	0.942	0.389	0.315	0.471	CLONAL	2	TRUE	1	0.329434034052942	5		341	169	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061665-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	35	382	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.441	0.363	0.528	0.441	0.363	0.528	SUBCLONAL	1	TRUE	1	0.560497566618914	2		382	283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0061665-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	29	411	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.216	0.172	0.265	0.216	0.172	0.265	SUBCLONAL	1	TRUE	1	0.560497566618914	2		412	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0061665-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	48	424	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	1	2	FACETS	0.339	0.286	0.397	0.339	0.286	0.397	SUBCLONAL	1	TRUE	1	0.560497566618914	2		424	505	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941653	48941653	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0061665-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	29	227	0	ENST00000267163.4:c.963C>G	p.Tyr321Ter	p.Y321*	ENST00000267163	NM_000321.2	321	taC/taG	10/27	1	2	FACETS	0.438	0.354	0.534	0.438	0.354	0.534	SUBCLONAL	1	TRUE	1	0.560497566618914	2		227	236	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056214	27056214	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061665-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	45	528	0	ENST00000324856.7:c.1210C>T	p.Gln404Ter	p.Q404*	ENST00000324856	NM_006015.4	404	Caa/Taa	2/20	1	2	FACETS	0.294	0.246	0.346	0.294	0.246	0.346	SUBCLONAL	1	TRUE	1	0.560497566618914	2		528	547	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920786	100920786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752995251	NA	P-0061665-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	21	380	0	ENST00000325455.5:c.2362C>T	p.Arg788Trp	p.R788W	ENST00000325455	NM_001202474.3	788	Cgg/Tgg	6/8	1	2	FACETS	0.255	0.196	0.323	0.255	0.196	0.323	SUBCLONAL	1	TRUE	1	0.560497566618914	2		380	294	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719568	61719568	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs758975202	NA	P-0061665-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	50	446	0	ENST00000401558.2:c.1615A>G	p.Ile539Val	p.I539V	ENST00000401558	NM_003400.3	539	Att/Gtt	15/25	1	2	FACETS	0.436	0.371	0.508	0.436	0.371	0.508	SUBCLONAL	1	TRUE	1	0.560497566618914	2		446	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0061799-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	50	472	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.264728547206772	3	FACETS	1	0.96	1	0.701	0.598	0.813	CLONAL	1	TRUE	1	0.264728547206772	3		472	305	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0062493-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	112	440	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.165526029488722	3	FACETS	1	0.973	1	1	0.973	1	INDETERMINATE	3	FALSE	0	0.28858028147969	3		440	256	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576870	7576870	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062493-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	96	385	0	ENST00000269305.4:c.976del	p.Glu326AsnfsTer19	p.E326Nfs*19	ENST00000269305	NM_001126112.2	326	Gaa/aa	9/11	0.28895372162685	1	FACETS	0.982	0.886	1	1	0.987	1	CLONAL	2	FALSE	0	0.28858028147969	1		385	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0062518-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	70	427	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	0.334116089880593	1	FACETS	0.801	0.701	0.907	0.801	0.701	0.907	CLONAL	1	TRUE	0	0.348058003944121	1		427	415	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061131	38061210	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTGGCGGCGCA	GCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTGGCGGCGCA	-	novel	NA	P-0062518-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	21	401	0	ENST00000250448.2:c.779_858del	p.Leu260CysfsTer6	p.L260Cfs*6	ENST00000250448	NM_004496.3	260	tTGCGCCGCCAGAAGCGCTTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGGC/t	2/2	1	2	FACETS	0.286	0.219	0.364	0.286	0.219	0.364	SUBCLONAL	1	TRUE	1	0.348058003944121	2		401	422	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492862	56492862	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062518-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	57	453	0	ENST00000407977.2:c.77G>C	p.Gly26Ala	p.G26A	ENST00000407977		26	gGa/gCa	2/10	1	2	FACETS	0.577	0.495	0.666	0.577	0.495	0.666	SUBCLONAL	1	TRUE	1	0.348058003944121	2		453	568	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267481	198267481	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs769888451	NA	P-0062950-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	116	487	0	ENST00000335508.6:c.1876A>G	p.Asn626Asp	p.N626D	ENST00000335508	NM_012433.2	626	Aac/Gac	14/25	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.651717411339399	2		487	355	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626786	28626786	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062950-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	125	372	0	ENST00000241453.7:c.510A>C	p.Arg170Ser	p.R170S	ENST00000241453	NM_004119.2	170	agA/agC	5/24	1	2	FACETS	0.905	0.826	0.987	0.905	0.826	0.987	CLONAL	1	TRUE	1	0.651717411339399	2		372	424	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063532-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	60	478	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	0.367186311332961	3	FACETS	0.951	0.826	1	1	0.968	1	CLONAL	3	TRUE	1	0.164392493375348	3		478	277	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144723	119144723	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs376182596	NA	P-0063532-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	29	489	0	ENST00000264033.4:c.736C>T	p.Arg246Ter	p.R246*	ENST00000264033	NM_005188.3	246	Cga/Tga	4/16	0.164392493375348	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	2	TRUE	0	0.164392493375348	2		489	151	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653814	89653814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780004	NA	P-0063532-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	18	330	0	ENST00000371953.3:c.112C>T	p.Pro38Ser	p.P38S	ENST00000371953	NM_000314.4	38	Cct/Tct	2/9	0.164392493375348	2	FACETS	1	0.807	1	1	0.94	1	CLONAL	4	TRUE	0	0.164392493375348	2		330	53	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0063532-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	39	386	11	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	0.164392493375348	2	FACETS	0.824	0.686	0.976	0.824	0.686	0.976	CLONAL	2	TRUE	0	0.164392493375348	2		397	288	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431665	431665	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs754467075	NA	P-0063532-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	25	420	0	ENST00000399788.2:c.2344C>T	p.Arg782Ter	p.R782*	ENST00000399788	NM_001042603.1	782	Cga/Tga	17/28	0.164392493375348	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	2	TRUE	0	0.164392493375348	2		420	135	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988382	41988382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774833703	NA	P-0063532-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	22	484	0	ENST00000219905.7:c.1174G>A	p.Glu392Lys	p.E392K	ENST00000219905	NM_001164273.1	392	Gaa/Aaa	3/24	0.164392493375348	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	2	TRUE	0	0.164392493375348	2		484	123	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798218	42798218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568528562	NA	P-0063532-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	67	649	0	ENST00000575354.2:c.4172G>A	p.Arg1391His	p.R1391H	ENST00000575354	NM_015125.3	1391	cGc/cAc	17/20	0.367186311332961	3	FACETS	1	0.894	1	1	0.894	1	CLONAL	2	TRUE	1	0.164392493375348	3		649	429	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303751	65303751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063532-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	40	418	2	ENST00000342505.4:c.3004C>T	p.Arg1002Trp	p.R1002W	ENST00000342505	NM_002227.2	1002	Cgg/Tgg	22/25	0.367186311332961	3	FACETS	0.84	0.705	0.987	1	0.938	1	CLONAL	3	TRUE	1	0.164392493375348	3		420	209	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1696718	1696718	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063532-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	43	556	0	ENST00000378625.1:c.128A>G	p.Lys43Arg	p.K43R	ENST00000378625	NM_001198994.1	43	aAg/aGg	2/14	0.367186311332961	3	FACETS	1	0.928	1	0.602	0.504	0.711	CLONAL	1	TRUE	1	0.164392493375348	3		556	470	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050355	176050355	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063532-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	13	431	1	ENST00000367669.3:c.1210T>C	p.Ser404Pro	p.S404P	ENST00000367669	NM_022457.5	404	Tca/Cca	11/20	0.367186311332961	3	FACETS	0.951	0.688	1	0.951	0.688	1	CLONAL	2	TRUE	1	0.164392493375348	3		432	90	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665764	241665764	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063532-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	35	395	0	ENST00000366560.3:c.1215G>T	p.Leu405Phe	p.L405F	ENST00000366560	NM_000143.3	405	ttG/ttT	8/10	0.367186311332961	3	FACETS	1	0.879	1	1	0.879	1	CLONAL	2	TRUE	1	0.164392493375348	3		395	213	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439846	49439846	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0063532-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	55	557	0	ENST00000301067.7:c.4693+2T>C		p.X1565_splice	ENST00000301067	NM_003482.3	1565			0.164392493375348	2	FACETS	0.843	0.723	0.972	0.843	0.723	0.972	CLONAL	2	TRUE	0	0.164392493375348	2		557	397	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123889615	123889615	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063532-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	55	325	0	ENST00000330479.4:c.842C>A	p.Thr281Asn	p.T281N	ENST00000330479	NM_020382.3	281	aCc/aAc	7/9	0.164392493375348	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.164392493375348	2		325	272	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919213	48919214	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TA	TA	-	novel	NA	P-0063532-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	14	298	0	ENST00000267163.4:c.381-3_381-2del		p.X127_splice	ENST00000267163	NM_000321.2	127			0.164392493375348	2	FACETS	1	0.842	1	1	0.842	1	CLONAL	2	TRUE	0	0.164392493375348	2		298	70	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543201	65543201	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063532-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	78	434	0	ENST00000358664.4:c.476C>G	p.Ala159Gly	p.A159G	ENST00000358664	NM_002382.4	159	gCc/gGc	5/5	0.367186311332961	3	FACETS	0.94	0.832	1	1	0.975	1	CLONAL	3	TRUE	1	0.164392493375348	3		434	364	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119757	17119757	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063532-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	107	520	0	ENST00000285071.4:c.1237T>C	p.Tyr413His	p.Y413H	ENST00000285071	NM_144997.5	413	Tat/Cat	11/14	0.367186311332961	3	FACETS	1	0.965	1	1	0.987	1	CLONAL	3	TRUE	1	0.164392493375348	3		520	410	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78797007	78797007	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063532-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	142	455	0	ENST00000306801.3:c.1120T>C	p.Tyr374His	p.Y374H	ENST00000306801	NM_020761.2	374	Tac/Cac	9/34	0.367186311332961	3	FACETS	1	0.949	1	1	0.992	1	CLONAL	4	TRUE	1	0.164392493375348	3		455	448	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026324	48026324	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063532-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	43	560	0	ENST00000234420.5:c.1202A>T	p.Asp401Val	p.D401V	ENST00000234420	NM_000179.2	401	gAt/gTt	4/10	0.164392493375348	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	2	TRUE	0	0.164392493375348	2		560	256	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21304060	21304060	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063532-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	59	412	0	ENST00000354336.3:c.839A>G	p.Asn280Ser	p.N280S	ENST00000354336	NM_005207.3	280	aAc/aGc	3/3	0.164392493375348	2	FACETS	0.899	0.777	1	0.899	0.777	1	CLONAL	2	TRUE	0	0.164392493375348	2		412	399	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960081	134960081	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063532-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	64	530	0	ENST00000398015.3:c.2438T>C	p.Val813Ala	p.V813A	ENST00000398015	NM_004441.4	813	gTc/gCc	13/16	0.367186311332961	3	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	1	0.164392493375348	3		530	366	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515435	149515435	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063532-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	37	497	0	ENST00000261799.4:c.47T>C	p.Leu16Pro	p.L16P	ENST00000261799	NM_002609.3	16	cTg/cCg	3/23	0.146215100967119	2	FACETS	0.758	0.627	0.903	0.758	0.627	0.903	CLONAL	2	TRUE	0	0.164392493375348	2		497	297	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566297	141566297	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063532-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	62	545	0	ENST00000220592.5:c.1115C>T	p.Ala372Val	p.A372V	ENST00000220592	NM_012154.3	372	gCg/gTg	9/19	0.164392493375348	5	FACETS	0.958	0.829	1	0.958	0.829	1	CLONAL	2	TRUE	3	0.164392493375348	5		545	491	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248123	110248123	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063532-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	67	466	0	ENST00000374672.4:c.1349A>G	p.His450Arg	p.H450R	ENST00000374672	NM_004235.4	450	cAc/cGc	5/5	0.164392493375348	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	2	TRUE	0	0.164392493375348	2		466	396	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84393410	84393410	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063532-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	12	322	0	ENST00000321945.7:c.247C>T	p.Gln83Ter	p.Q83*	ENST00000321945	NM_139076.2	83	Caa/Taa	4/9	0.367186311332961	3	FACETS	1	0.862	1	0.731	0.519	0.988	CLONAL	1	TRUE	1	0.164392493375348	3		322	108	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928018	49928018	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063532-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	21	573	0	ENST00000296474.3:c.3710A>T	p.Glu1237Val	p.E1237V	ENST00000296474	NM_002447.2	1237	gAg/gTg	18/20	0.367186311332961	3	FACETS	0.7	0.538	0.889	0.35	0.269	0.445	SUBCLONAL	1	TRUE	1	0.164392493375348	3		573	395	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880989	134880989	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063532-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	28	474	0	ENST00000398015.3:c.1552A>G	p.Ser518Gly	p.S518G	ENST00000398015	NM_004441.4	518	Agt/Ggt	7/16	0.367186311332961	3	FACETS	0.948	0.757	1	0.474	0.378	0.583	CLONAL	1	TRUE	1	0.164392493375348	3		474	389	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0063541-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	58	405	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.265	0.228	0.305	0.265	0.228	0.305	SUBCLONAL	1	TRUE	1	1	2		405	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576857	7576857	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063541-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	36	768	0	ENST00000269305.4:c.989T>G	p.Leu330Arg	p.L330R	ENST00000269305	NM_001126112.2	330	cTt/cGt	9/11	1	2	FACETS	0.134	0.11	0.161	0.134	0.11	0.161	SUBCLONAL	1	TRUE	1	1	2		768	537	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699342	117699342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201673499	NA	P-0063839-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	171	440	0	ENST00000369458.3:c.299G>A	p.Arg100Gln	p.R100Q	ENST00000369458	NM_024626.3	100	cGg/cAg	3/6	1	2	FACETS	0.871	0.805	0.939	0.871	0.805	0.939	CLONAL	1	TRUE	1	0.6523108208898	2		440	602	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61305338	61305338	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148653112	NA	P-0063839-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	18	7	0	ENST00000341074.5:c.788C>T	p.Ala263Val	p.A263V	ENST00000341074	NM_002974.2	263	gCt/gTt	8/8	1	2	FACETS	0.862	0.702	1	1	0.941	1	CLONAL	2	TRUE	1	0.6523108208898	2		7	32	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913444	NA	P-0063839-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	31	347	0	ENST00000275493.2:c.2582T>C	p.Leu861Pro	p.L861P	ENST00000275493	NM_005228.3	861	cTg/cCg	21/28	1	2	FACETS	0.162	0.13	0.198	0.162	0.13	0.198	SUBCLONAL	1	TRUE	1	0.6523108208898	2		347	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063927-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	32	560	0	ENST00000269305.4:c.398T>A	p.Met133Lys	p.M133K	ENST00000269305	NM_001126112.2	133	aTg/aAg	5/11	0.148155742193467	2	FACETS	1	0.923	1	0.642	0.523	0.776	CLONAL	1	FALSE	0	0.170152504095958	2		560	293	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905118	50905118	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063927-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	24	647	0	ENST00000440232.2:c.400G>A	p.Gly134Arg	p.G134R	ENST00000440232	NM_002691.3	134	Ggg/Agg	4/27	0.132377986620421	3	FACETS	0.933	0.732	1	0.467	0.366	0.583	CLONAL	1	FALSE	1	0.170152504095958	3		647	328	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063955-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	215	382	0				ENST00000310581	NM_198253.2	-/1132			0.454358147689308	6	FACETS	1	0.956	1			1	CLONAL	5	TRUE	NA	0.454358147689308	6		382	358	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070841	30070841	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063955-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	61	311	0	ENST00000338641.4:c.1357C>T	p.Gln453Ter	p.Q453*	ENST00000338641	NM_000268.3	453	Cag/Tag	13/16	0.454358147689308	1	FACETS	0.786	0.685	0.894	0.786	0.685	0.894	SUBCLONAL	1	TRUE	0	0.454358147689308	1		311	264	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098703	47098703	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063955-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	85	468	0	ENST00000409792.3:c.6571A>G	p.Thr2191Ala	p.T2191A	ENST00000409792	NM_014159.6	2191	Aca/Gca	15/21	0.454358147689308	1	FACETS	0.763	0.679	0.851	0.763	0.679	0.851	SUBCLONAL	1	TRUE	0	0.454358147689308	1		468	379	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136371	2136381	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ATCATGCAAGG	ATCATGCAAGG	-	novel	NA	P-0063955-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	54	361	0	ENST00000219476.3:c.4840_4849+1del		p.X1614_splice	ENST00000219476	NM_000548.3	1614		37/42	0.357124638358977	0	FACETS	0.54	0.466	0.62			1	SUBCLONAL	1	TRUE	0	0.454358147689308	0		361	240	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0064036-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	81	348	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	1	0.956	1	1	0.986	1	CLONAL	2	TRUE	1	0.147667043305755	2		348	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0064036-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	59	533	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.147667043305755	2		533	609	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138567	55138567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064036-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	42	469	0	ENST00000257290.5:c.1244C>T	p.Ser415Leu	p.S415L	ENST00000257290	NM_006206.4	415	tCa/tTa	9/23	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.147667043305755	2		469	489	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195490	102195490	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064036-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	60	619	0	ENST00000263464.3:c.250G>C	p.Glu84Gln	p.E84Q	ENST00000263464	NM_001165.4	84	Gaa/Caa	2/9	0.147667043305755	3	FACETS	1	0.944	1	0.6	0.516	0.692	CLONAL	1	TRUE	1	0.147667043305755	3		619	727	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	893120	893120	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064036-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	44	509	0	ENST00000166345.3:c.7G>T	p.Glu3Ter	p.E3*	ENST00000166345	NM_004237.3	3	Gag/Tag	1/13	0.147667043305755	5	FACETS	1	0.855	1	0.256	0.214	0.303	CLONAL	1	TRUE	1	0.147667043305755	5		509	711	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140146	50140146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064036-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	48	612	0	ENST00000246792.3:c.279G>A	p.Met93Ile	p.M93I	ENST00000246792	NM_006270.3	93	atG/atA	3/6	1	2	FACETS	0.846	0.714	0.993	0.846	0.714	0.993	CLONAL	1	TRUE	1	0.147667043305755	2		612	768	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0064042-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	97	317	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		317	165	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061463	38061463	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064042-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	222	310	1	ENST00000250448.2:c.526A>G	p.Ile176Val	p.I176V	ENST00000250448	NM_004496.3	176	Atc/Gtc	2/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		311	490	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90634835	90634835	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064042-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	141	309	0	ENST00000330062.3:c.157A>G	p.Met53Val	p.M53V	ENST00000330062	NM_002168.2	53	Atg/Gtg	2/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		309	517	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560349	95560349	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064042-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	128	312	0	ENST00000393063.1:c.5240C>T	p.Ser1747Leu	p.S1747L	ENST00000393063	NM_030621.3	1747	tCg/tTg	25/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		312	633	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578230	7578231	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAAATACTCCACACGCAAATT	novel	NA	P-0064042-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	226	341	0	ENST00000269305.4:c.598_618dup	p.Asn200_Leu206dup	p.N200_L206dup	ENST00000269305	NM_001126112.2	200	-/AATTTGCGTGTGGAGTATTTG	6/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		341	469	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217900	2217900	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1304751376	NA	P-0064042-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	139	321	0	ENST00000398665.3:c.2674A>G	p.Ser892Gly	p.S892G	ENST00000398665	NM_032482.2	892	Agc/Ggc	22/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		321	317	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0064192-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	34	300	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.20848969132611	3	FACETS	0.753	0.616	0.909	0.377	0.308	0.455	CLONAL	1	TRUE	1	0.233270273371965	3		300	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0064192-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	131	474	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.228622512134924	2	FACETS	0.906	0.824	0.991	0.906	0.824	0.991	CLONAL	2	TRUE	0	0.233270273371965	2		474	620	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0064192-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	144	404	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	1	2	FACETS	0.988	0.904	1	1	0.991	1	CLONAL	2	TRUE	1	0.233270273371965	2		404	625	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509619	106509619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142822484	NA	P-0064192-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	71	430	0	ENST00000359195.3:c.1613C>T	p.Pro538Leu	p.P538L	ENST00000359195	NM_002649.2	538	cCg/cTg	2/11	0.211065536544079	4	FACETS	0.901	0.785	1	0.451	0.392	0.514	CLONAL	1	TRUE	2	0.233270273371965	4		430	833	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211580	98211580	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762040036	NA	P-0064192-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	57	381	0	ENST00000331920.6:c.3575G>T	p.Arg1192Leu	p.R1192L	ENST00000331920	NM_000264.3	1192	cGc/cTc	22/24	0.20848969132611	3	FACETS	0.944	0.81	1	0.472	0.405	0.546	CLONAL	1	TRUE	1	0.233270273371965	3		381	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs760043106	NA	P-0064600-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	636	481	0	ENST00000269305.4:c.584T>A	p.Ile195Asn	p.I195N	ENST00000269305	NM_001126112.2	195	aTc/aAc	6/11	0.753479922168961	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.745909289186621	3		481	718	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0064600-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	180	331	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	0.753479922168961	3	FACETS	1	0.967	1	0.537	0.497	0.578	CLONAL	1	TRUE	1	0.745909289186621	3		331	617	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409161	4409161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064600-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1338	73	356	1	ENST00000261254.3:c.856G>A	p.Asp286Asn	p.D286N	ENST00000261254	NM_001759.3	286	Gat/Aat	5/5	0.745909289186621	8	FACETS	0.449	0.391	0.512	0.112	0.097	0.128	SUBCLONAL	1	TRUE	4	0.745909289186621	8		357	1411	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380350	14380350	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064600-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	557	381	0	ENST00000256196.4:c.67G>T	p.Gly23Cys	p.G23C	ENST00000256196		23	Ggc/Tgc	1/6	0.753479922168961	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.745909289186621	3		381	609	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671293	30671293	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs746504351	NA	P-0064600-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	440	428	0	ENST00000376406.3:c.5584G>C	p.Gly1862Arg	p.G1862R	ENST00000376406	NM_014641.2	1862	Ggc/Cgc	11/15	0.753479922168961	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.745909289186621	2		428	504	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884485	151884485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064600-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	155	298	0	ENST00000262189.6:c.4870G>A	p.Gly1624Arg	p.G1624R	ENST00000262189	NM_170606.2	1624	Gga/Aga	33/59	0.753479922168961	3	FACETS	1	0.967	1	0.546	0.502	0.59	CLONAL	1	TRUE	1	0.745909289186621	3		298	523	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939788	71939788	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064600-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	64	499	0	ENST00000298229.2:c.415C>T	p.Pro139Ser	p.P139S	ENST00000298229	NM_001567.3	139	Ccc/Tcc	4/28	0.753479922168961	3	FACETS	0.276	0.238	0.317	0.138	0.119	0.159	SUBCLONAL	1	TRUE	1	0.745909289186621	3		499	853	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437695	110437695	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064600-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	45	375	0	ENST00000375856.3:c.706C>A	p.Pro236Thr	p.P236T	ENST00000375856	NM_003749.2	236	Ccg/Acg	1/2	0.753479922168961	2	FACETS	0.287	0.241	0.337	0.143	0.12	0.169	SUBCLONAL	1	TRUE	0	0.745909289186621	2		375	421	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724294	52724294	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064600-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	132	401	0	ENST00000322088.6:c.1426G>T	p.Glu476Ter	p.E476*	ENST00000322088	NM_014225.5	476	Gag/Tag	12/15	0.753479922168961	2	FACETS	0.851	0.779	0.924	0.425	0.389	0.462	CLONAL	1	TRUE	0	0.745909289186621	2		401	416	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374079	118374079	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064600-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	33	362	0	ENST00000534358.1:c.7472G>T	p.Gly2491Val	p.G2491V	ENST00000534358	NM_005933.3	2491	gGt/gTt	27/36	0.753479922168961	3	FACETS	0.228	0.185	0.277	0.114	0.092	0.139	SUBCLONAL	1	TRUE	1	0.745909289186621	3		362	532	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028699	42028699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064600-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	145	426	0	ENST00000219905.7:c.4237G>A	p.Gly1413Arg	p.G1413R	ENST00000219905	NM_001164273.1	1413	Gga/Aga	13/24	0.753479922168961	3	FACETS	0.919	0.842	0.998	0.459	0.421	0.499	CLONAL	1	TRUE	1	0.745909289186621	3		426	581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0064672-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	41	473	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	1	2	FACETS	0.709	0.589	0.842	0.709	0.589	0.842	SUBCLONAL	1	FALSE	1	0.195805794894734	2		473	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0064841-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	228	502	0	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	0.34764581434097	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.35022117819011	2		502	639	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064841-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	88	431	0	ENST00000263967.3:c.3132T>G	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaG	21/21	0.30199514840641	5	FACETS	0.913	0.807	1	0.304	0.269	0.342	CLONAL	1	TRUE	2	0.35022117819011	5		431	840	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73633589	73633589	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064841-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	67	293	0	ENST00000377687.4:c.124G>C	p.Asp42His	p.D42H	ENST00000377687	NM_001730.3	42	Gac/Cac	1/4	0.313663443333181	3	FACETS	1	0.921	1	0.539	0.47	0.613	CLONAL	1	TRUE	1	0.35022117819011	3		293	417	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023183	33023183	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064841-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	105	538	0	ENST00000300177.4:c.292C>G	p.Pro98Ala	p.P98A	ENST00000300177	NM_001191322.1	98	Ccg/Gcg	2/2	NA	2	FACETS	0.952	0.854	1			1	INDETERMINATE	1	TRUE	NA	0.35022117819011	2		538	630	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531079	187531079	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064841-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	59	454	0	ENST00000441802.2:c.9944T>A	p.Leu3315Gln	p.L3315Q	ENST00000441802	NM_005245.3	3315	cTg/cAg	15/27	0.354912422314345	1	FACETS	0.515	0.443	0.593	0.515	0.443	0.593	SUBCLONAL	1	TRUE	0	0.35022117819011	1		454	540	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202085	67202085	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064841-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	107	537	1	ENST00000312629.5:c.1188C>A	p.Asp396Glu	p.D396E	ENST00000312629	NM_003952.2	396	gaC/gaA	14/15	0.34764581434097	2	FACETS	0.88	0.79	0.976	0.44	0.395	0.488	CLONAL	1	TRUE	0	0.35022117819011	2		538	694	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95597934	95597934	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0064841-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	181	394	0	ENST00000393063.1:c.350C>G	p.Ser117Ter	p.S117*	ENST00000393063	NM_030621.3	117	tCa/tGa	5/28	0.303317975916978	4	FACETS	1	0.946	1	0.684	0.633	0.737	CLONAL	2	TRUE	1	0.35022117819011	4		394	680	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971114	21971115	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGGTCGGGTGAGAGTGGCG	novel	NA	P-0064953-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	30	371	0	ENST00000304494.5:c.225_243dup	p.Val82ArgfsTer44	p.V82Rfs*44	ENST00000304494	NM_000077.4	81	-/CGCCACTCTCACCCGACCC	2/3	0.279394426124999	1	FACETS	0.508	0.409	0.619	0.508	0.409	0.619	SUBCLONAL	1	FALSE	0	0.279394426124999	1		371	364	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424109	47424109	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	62	286	0	ENST00000404338.3:c.2177G>C	p.Ser726Thr	p.S726T	ENST00000404338	NM_004491.4	726	aGc/aCc	1/6	1	2	FACETS	0.236	0.203	0.272	0.236	0.203	0.272	SUBCLONAL	1	TRUE	1	0.782528625938773	2		286	671	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342848	118342848	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	230	276	0	ENST00000534358.1:c.974A>G	p.Glu325Gly	p.E325G	ENST00000534358	NM_005933.3	325	gAa/gGa	3/36	1	2	FACETS	0.956	0.897	1	0.956	0.897	1	CLONAL	1	TRUE	1	0.782528625938773	2		276	615	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0065030-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	21	300	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.67	0.515	0.851	0.67	0.515	0.851	SUBCLONAL	1	TRUE	1	0.16	2		300	392	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425853	49425853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772665565	NA	P-0065030-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	36	525	0	ENST00000301067.7:c.12635G>A	p.Arg4212Gln	p.R4212Q	ENST00000301067	NM_003482.3	4212	cGg/cAg	39/54	1	2	FACETS	0.769	0.631	0.925	0.769	0.631	0.925	CLONAL	1	TRUE	1	0.16	2		525	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577060	7577069	+	frameshift_variant	Frame_Shift_Del	DEL	CCTTTCTTGC	CCTTTCTTGC	GCAAGAAA	novel	NA	P-0065030-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	45	538	0	ENST00000269305.4:c.869_878delinsTTTCTTGC	p.Arg290LeufsTer15	p.R290Lfs*15	ENST00000269305	NM_001126112.2	290	cGCAAGAAAGGg/cTTTCTTGCg	8/11	1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	1	0.16	2		538	556	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524444	44524444	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065030-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	34	348	0	ENST00000291552.4:c.113A>T	p.Asn38Ile	p.N38I	ENST00000291552	NM_006758.2	38	aAt/aTt	2/8	1	2	FACETS	0.899	0.734	1	0.899	0.734	1	CLONAL	1	TRUE	1	0.16	2		348	473	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121512	193121512	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065030-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	31	296	0	ENST00000367435.3:c.910A>G	p.Thr304Ala	p.T304A	ENST00000367435	NM_024529.4	304	Acg/Gcg	10/17	1	2	FACETS	1	0.828	1	1	0.828	1	CLONAL	1	TRUE	1	0.16	2		296	378	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045718	47045718	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065077-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	31	440	0	ENST00000377604.3:c.2599C>T	p.Gln867Ter	p.Q867*	ENST00000377604	NM_001204468.1	867	Cag/Tag	23/24	1	2	FACETS	0.28	0.226	0.34	0.28	0.226	0.34	SUBCLONAL	1	TRUE	1	0.65	2		440	341	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412038	116412047	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGAAGGTAT	CAGAAGGTAT	-	novel	NA	P-0065077-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	29	391	0	ENST00000397752.3:c.3023_3028+4del		p.X1008_splice	ENST00000397752	NM_000245.2	1008		14/21	1	2	FACETS	0.337	0.271	0.411	0.337	0.271	0.411	SUBCLONAL	1	TRUE	1	0.65	2		391	265	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221135	5221135	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065077-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	28	402	0	ENST00000357368.4:c.3331C>T	p.Gln1111Ter	p.Q1111*	ENST00000357368	NM_002850.3	1111	Cag/Tag	20/38	1	2	FACETS	0.221	0.176	0.272	0.221	0.176	0.272	SUBCLONAL	1	TRUE	1	0.65	2		402	390	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194826	30194826	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065147-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	108	473	0	ENST00000331968.5:c.319G>T	p.Asp107Tyr	p.D107Y	ENST00000331968	NM_002742.2	107	Gac/Tac	2/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		473	404	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245832	46245832	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0065147-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	153	493	0	ENST00000334344.6:c.3926C>G	p.Ser1309Ter	p.S1309*	ENST00000334344	NM_152641.2	1309	tCa/tGa	15/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		493	522	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231349	46231349	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065147-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	116	397	0	ENST00000334344.6:c.1189C>T	p.Gln397Ter	p.Q397*	ENST00000334344	NM_152641.2	397	Cag/Tag	10/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		397	400	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390779	139390779	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771318379	NA	P-0065147-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	148	595	0	ENST00000277541.6:c.7412C>T	p.Ser2471Leu	p.S2471L	ENST00000277541	NM_017617.3	2471	tCg/tTg	34/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		595	484	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039278	47039278	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0065147-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	155	512	0	ENST00000377604.3:c.902-1G>A		p.X301_splice	ENST00000377604	NM_001204468.1	301			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		512	414	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223671	36223671	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368981212	NA	P-0065147-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	173	582	1	ENST00000222270.7:c.6221C>T	p.Ala2074Val	p.A2074V	ENST00000222270	NM_014727.1	2074	gCg/gTg	28/37	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		583	883	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742970	17742970	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065147-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	113	413	0	ENST00000250003.3:c.878G>T	p.Ser293Ile	p.S293I	ENST00000250003	NM_002478.4	293	aGc/aTc	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		413	344	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127829	64127829	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065147-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	111	487	0	ENST00000334205.4:c.322G>T	p.Asp108Tyr	p.D108Y	ENST00000334205	NM_003942.2	108	Gat/Tat	3/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		487	412	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415843	49415843	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065147-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	138	521	0	ENST00000301067.7:c.16504A>G	p.Ile5502Val	p.I5502V	ENST00000301067	NM_003482.3	5502	Atc/Gtc	53/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		521	473	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352596	68352596	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065147-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	111	402	0	ENST00000487270.1:c.463A>T	p.Ile155Leu	p.I155L	ENST00000487270	NM_133509.3	155	Ata/Tta	6/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		402	348	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51503086	51503086	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065147-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	127	438	0	ENST00000260433.2:c.1431G>T	p.Leu477Phe	p.L477F	ENST00000260433		477	ttG/ttT	10/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		438	399	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396605	396606	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0065147-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	122	526	0	ENST00000262320.3:c.420_421delinsTT	p.Ala141Ser	p.A141S	ENST00000262320	NM_003502.3	140	ctGGcg/ctTTcg	2/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		526	501	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61306924	61306924	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065147-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	171	496	0	ENST00000341074.5:c.556T>A	p.Trp186Arg	p.W186R	ENST00000341074	NM_002974.2	186	Tgg/Agg	6/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		496	455	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220378	1220378	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065147-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	254	501	0	ENST00000326873.7:c.471del	p.Cys158ValfsTer3	p.C158Vfs*3	ENST00000326873	NM_000455.4	157	ttC/tt	4/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		501	441	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974277	18974277	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065147-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	121	500	0	ENST00000262803.5:c.2631G>C	p.Lys877Asn	p.K877N	ENST00000262803	NM_002911.3	877	aaG/aaC	19/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		500	418	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743908	40743908	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065147-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	87	446	0	ENST00000373198.4:c.3087C>A	p.Asp1029Glu	p.D1029E	ENST00000373198	NM_133170.3	1029	gaC/gaA	23/32	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		446	326	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522680	176522680	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065147-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	140	504	0	ENST00000292408.4:c.1777G>T	p.Ala593Ser	p.A593S	ENST00000292408	NM_213647.1	593	Gcc/Tcc	13/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		504	481	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120785	94120785	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065147-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	134	468	0	ENST00000369303.4:c.266G>A	p.Trp89Ter	p.W89*	ENST00000369303	NM_004440.3	89	tGg/tAg	3/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		468	300	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410197	63410197	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778708592	NA	P-0065147-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	93	550	0	ENST00000330258.3:c.2970G>T	p.Arg990Ser	p.R990S	ENST00000330258	NM_152424.3	990	agG/agT	2/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		550	412	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972093	55972093	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065225-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	98	274	0	ENST00000263923.4:c.1551del	p.Val518LeufsTer25	p.V518Lfs*25	ENST00000263923	NM_002253.2	517	ctT/ct	12/30	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.57868962826856	2		274	337	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986550	36986555	+	inframe_deletion	In_Frame_Del	DEL	AGGTGG	AGGTGG	-	novel	NA	P-0065225-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	82	365	0	ENST00000354822.5:c.1134_1139del	p.His379_Leu380del	p.H379_L380del	ENST00000354822	NM_001079668.2	378	tcCCACCTg/tcg	3/3	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.57868962826856	2		365	238	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191514	10191518	+	frameshift_variant	Frame_Shift_Del	DEL	AGTCA	AGTCA	-	novel	NA	P-0065225-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	131	269	0	ENST00000256474.2:c.509_513del	p.Val170AlafsTer2	p.V170Afs*2	ENST00000256474	NM_000551.3	169	ctAGTCAag/ctag	3/3	0.57868962826856	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.57868962826856	1		269	305	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193882	106193882	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065225-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	128	294	0	ENST00000380013.4:c.4345del	p.Ser1449LeufsTer9	p.S1449Lfs*9	ENST00000380013	NM_001127208.2	1448	agT/ag	10/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.57868962826856	2		294	420	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505385	125505385	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065225-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	82	281	0	ENST00000428830.2:c.675A>C	p.Lys225Asn	p.K225N	ENST00000428830	NM_001114121.2	225	aaA/aaC	7/14	1	2	FACETS	0.88	0.783	0.982	0.88	0.783	0.982	CLONAL	1	TRUE	1	0.57868962826856	2		281	322	SUCCESS
ALK	238	MSKCC	GRCh37	2	29419707	29419708	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065225-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	84	281	0	ENST00000389048.3:c.4092_4093insA	p.Cys1365MetfsTer7	p.C1365Mfs*7	ENST00000389048	NM_004304.4	1364	-/A	28/29	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.57868962826856	2		281	286	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527452	29527453	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	T	novel	NA	P-0065225-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	81	250	0	ENST00000356175.3:c.901_902delinsT	p.Asp301SerfsTer16	p.D301Sfs*16	ENST00000356175	NM_000267.3	301	GAc/Tc	9/57	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.57868962826856	2		250	267	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065331-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	137	482	0	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.387057530563353	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.387057530563353	1		482	450	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867291	45867291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199863965	NA	P-0065331-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	42	583	0	ENST00000391945.4:c.902C>T	p.Thr301Met	p.T301M	ENST00000391945	NM_000400.3	301	aCg/aTg	10/23	0.268488406598109	4	FACETS	0.45	0.375	0.534	0.15	0.125	0.178	SUBCLONAL	1	TRUE	1	0.387057530563353	4		583	669	SUCCESS
APC	324	MSKCC	GRCh37	5	112174437	112174437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs876658667	NA	P-0065331-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	109	415	0	ENST00000257430.4:c.3146G>A	p.Trp1049Ter	p.W1049*	ENST00000257430	NM_000038.5	1049	tGg/tAg	16/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.387057530563353	2		415	458	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811554	56811554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780253	NA	P-0065331-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	57	289	0	ENST00000337432.4:c.1102C>T	p.Arg368Trp	p.R368W	ENST00000337432	NM_058216.2	368	Cgg/Tgg	9/9	1	2	FACETS	0.687	0.59	0.791	0.687	0.59	0.791	SUBCLONAL	1	TRUE	1	0.387057530563353	2		289	429	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202314	133202314	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065331-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	57	505	0	ENST00000320574.5:c.6574G>T	p.Ala2192Ser	p.A2192S	ENST00000320574	NM_006231.2	2192	Gcg/Tcg	47/49	1	2	FACETS	0.666	0.573	0.768	0.666	0.573	0.768	SUBCLONAL	1	TRUE	1	0.387057530563353	2		505	442	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032282	26032282	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065331-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	37	451	0	ENST00000244661.2:c.7C>G	p.Arg3Gly	p.R3G	ENST00000244661	NM_003537.3	3	Cgt/Ggt	1/1	1	2	FACETS	0.412	0.339	0.493	0.412	0.339	0.493	SUBCLONAL	1	TRUE	1	0.387057530563353	2		451	464	SUCCESS
APC	324	MSKCC	GRCh37	5	112162927	112162927	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065331-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	29	285	0	ENST00000257430.4:c.1532del	p.Gly511GlufsTer3	p.G511Efs*3	ENST00000257430	NM_000038.5	511	Gga/ga	12/16	1	2	FACETS	0.405	0.325	0.496	0.405	0.325	0.496	SUBCLONAL	1	TRUE	1	0.387057530563353	2		285	370	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522509	187522509	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065331-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	87	341	0	ENST00000441802.2:c.11554G>C	p.Glu3852Gln	p.E3852Q	ENST00000441802	NM_005245.3	3852	Gag/Cag	21/27	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.387057530563353	2		341	410	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172034	99172034	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065331-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	141	453	0	ENST00000074304.5:c.1600G>A	p.Val534Met	p.V534M	ENST00000074304	NM_001134224.1	534	Gtg/Atg	17/26	0.274141594980508	3	FACETS	0.841	0.771	0.914	0.841	0.771	0.914	CLONAL	2	TRUE	1	0.387057530563353	3		453	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0065517-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	370	639	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.822420855199653	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.822420855199653	1		639	492	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842344	151842344	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs749571160	NA	P-0065517-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	41	549	0	ENST00000262189.6:c.14068C>T	p.Arg4690Ter	p.R4690*	ENST00000262189	NM_170606.2	4690	Cga/Tga	54/59	1	2	FACETS	0.141	0.117	0.168	0.141	0.117	0.168	SUBCLONAL	1	TRUE	1	0.822420855199653	2		549	708	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932769	39932781	+	frameshift_variant	Frame_Shift_Del	DEL	GCTACTGTGCTTG	GCTACTGTGCTTG	-	novel	NA	P-0065517-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	368	683	0	ENST00000378444.4:c.1818_1830del	p.Lys607AlafsTer58	p.K607Afs*58	ENST00000378444	NM_001123385.1	606	gcCAAGCACAGTAGC/gc	4/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.822420855199653	2		683	862	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933199	49933199	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065517-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	332	715	0	ENST00000296474.3:c.2911G>C	p.Ala971Pro	p.A971P	ENST00000296474	NM_002447.2	971	Gca/Cca	12/20	1	2	FACETS	0.98	0.931	1	0.98	0.931	1	CLONAL	1	TRUE	1	0.822420855199653	2		715	824	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174395	11174395	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	73	327	0	ENST00000361445.4:c.7280T>G	p.Leu2427Arg	p.L2427R	ENST00000361445	NM_004958.3	2427	cTg/cGg	53/58	1	2	FACETS	0.978	0.857	1	0.978	0.857	1	CLONAL	1	TRUE	1	0.28	2		327	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0065980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	70	292	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.294026976614076	1	FACETS	0.998	0.874	1	0.998	0.874	1	CLONAL	1	TRUE	0	0.294026976614076	1		292	407	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168950	32168950	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	82	650	0	ENST00000375023.3:c.4083G>C	p.Glu1361Asp	p.E1361D	ENST00000375023	NM_004557.3	1361	gaG/gaC	22/30	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.294026976614076	2		650	549	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134885835	134885835	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	91	636	0	ENST00000398015.3:c.1746C>A	p.Tyr582Ter	p.Y582*	ENST00000398015	NM_004441.4	582	taC/taA	9/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.294026976614076	2		636	442	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12043155	12043155	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0065980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	54	337	0	ENST00000353533.5:c.1041-1G>A		p.X347_splice	ENST00000353533	NM_003010.3	347			0.294026976614076	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.294026976614076	1		337	255	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589622	67589623	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATATGATAGATT	novel	NA	P-0065980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	28	376	0	ENST00000274335.5:c.1392_1403dup	p.Asp464_Tyr467dup	p.D464_Y467dup	ENST00000274335		464	gaa/gaATATGATAGATTa	10/15	1	2	FACETS	0.635	0.508	0.778	0.635	0.508	0.778	SUBCLONAL	1	TRUE	1	0.294026976614076	2		376	300	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46715699	46715699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1421471663	NA	P-0065980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	67	487	0	ENST00000371975.4:c.118G>A	p.Glu40Lys	p.E40K	ENST00000371975	NM_003579.3	40	Gag/Aag	3/18	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.294026976614076	2		487	421	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989609	15989609	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	57	441	0	ENST00000268712.3:c.3164del	p.Gly1055AlafsTer12	p.G1055Afs*12	ENST00000268712	NM_006311.3	1055	gGc/gc	23/46	0.294026976614076	1	FACETS	0.873	0.752	1	0.873	0.752	1	CLONAL	1	TRUE	0	0.294026976614076	1		441	379	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217762	7217810	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCAAACGAAGAAATCAAAGCTGGGAAAGTTCAAGGGACTGCTTACTTGT	TCAAACGAAGAAATCAAAGCTGGGAAAGTTCAAGGGACTGCTTACTTGT	-	novel	NA	P-0065980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	71	600	0	ENST00000380728.2:c.201_205-40del		p.X67_splice	ENST00000380728		67		3/11	0.294026976614076	1	FACETS	0.771	0.674	0.876	0.771	0.674	0.876	SUBCLONAL	1	TRUE	0	0.294026976614076	1		600	534	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415025	116415025	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	46	570	0	ENST00000397752.3:c.3119C>T	p.Ser1040Phe	p.S1040F	ENST00000397752	NM_000245.2	1040	tCt/tTt	15/21	1	2	FACETS	0.702	0.591	0.823	0.702	0.591	0.823	SUBCLONAL	1	TRUE	1	0.294026976614076	2		570	446	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965821	90965821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772411713	NA	P-0065980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	33	479	0	ENST00000265433.3:c.1496C>T	p.Ser499Leu	p.S499L	ENST00000265433	NM_002485.4	499	tCa/tTa	11/16	1	2	FACETS	0.653	0.532	0.788	0.653	0.532	0.788	SUBCLONAL	1	TRUE	1	0.294026976614076	2		479	344	SUCCESS
REL	5966	MSKCC	GRCh37	2	61121563	61121563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1190862054	NA	P-0065980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	54	482	0	ENST00000295025.8:c.185G>A	p.Arg62Lys	p.R62K	ENST00000295025	NM_002908.2	62	aGa/aAa	3/11	1	2	FACETS	0.99	0.849	1	0.99	0.849	1	CLONAL	1	TRUE	1	0.294026976614076	2		482	371	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129715	108129715	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	25	374	0	ENST00000278616.4:c.2379G>C	p.Lys793Asn	p.K793N	ENST00000278616	NM_000051.3	793	aaG/aaC	16/63	1	2	FACETS	0.413	0.325	0.514	0.413	0.325	0.514	SUBCLONAL	1	TRUE	1	0.294026976614076	2		374	412	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344186	70344186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	29	464	0	ENST00000374080.3:c.1922C>T	p.Ala641Val	p.A641V	ENST00000374080		641	gCc/gTc	13/45	1	2	FACETS	0.494	0.397	0.606	0.494	0.397	0.606	SUBCLONAL	1	TRUE	1	0.294026976614076	2		464	399	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27229223	27229223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369356295	NA	P-0066121-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	34	316	0	ENST00000380036.4:c.3368C>T	p.Ala1123Val	p.A1123V	ENST00000380036	NM_000459.3	1123	gCg/gTg	23/23	0.231566606193936	1	FACETS	0.835	0.684	1	0.835	0.684	1	CLONAL	1	TRUE	0	0.231566606193936	1		316	311	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0066121-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	121	0	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.858	0.782	0.937	1	0.991	1	CLONAL	3	TRUE	1	0.231566606193936	2		0	406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0066121-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	55	456	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.231566606193936	1	FACETS	0.957	0.82	1	0.957	0.82	1	CLONAL	1	TRUE	0	0.231566606193936	1		456	439	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459795	149459795	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755093010	NA	P-0066121-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	47	482	0	ENST00000286301.3:c.412G>A	p.Val138Ile	p.V138I	ENST00000286301	NM_005211.3	138	Gtc/Atc	4/22	1	2	FACETS	0.908	0.767	1	0.908	0.767	1	CLONAL	1	TRUE	1	0.231566606193936	2		482	447	SUCCESS
APC	324	MSKCC	GRCh37	5	112175533	112175533	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066121-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	116	397	0	ENST00000257430.4:c.4243del	p.Ser1415ValfsTer4	p.S1415Vfs*4	ENST00000257430	NM_000038.5	1414	gtA/gt	16/16	1	2	FACETS	1	0.969	1	1	0.99	1	CLONAL	2	TRUE	1	0.231566606193936	2		397	432	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679016	117679016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066121-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	21	327	0	ENST00000368508.3:c.3805C>T	p.His1269Tyr	p.H1269Y	ENST00000368508	NM_002944.2	1269	Cac/Tac	24/43	1	2	FACETS	0.578	0.445	0.733	0.578	0.445	0.733	SUBCLONAL	1	TRUE	1	0.231566606193936	2		327	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0066333-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	276	361	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.538831038211548	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.538831038211548	2		361	506	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522436	187522436	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753570968	NA	P-0066333-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	81	257	0	ENST00000441802.2:c.11627A>G	p.Tyr3876Cys	p.Y3876C	ENST00000441802	NM_005245.3	3876	tAt/tGt	21/27	0.538831038211548	3	FACETS	1	0.92	1	0.349	0.309	0.39	CLONAL	1	TRUE	0	0.538831038211548	3		257	365	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066593-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	139	382	0				ENST00000310581	NM_198253.2	-/1132			0.539228268740412	6	FACETS	1	0.917	1	0.501	0.458	0.545	CLONAL	2	TRUE	2	0.539228268740412	6		382	535	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0066593-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	81	133	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.509311477304126	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.539228268740412	4		133	201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066593-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	170	383	0	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	0.250643533790798	5	FACETS	1	0.974	1	0.743	0.688	0.798	INDETERMINATE	2	TRUE	2	0.539228268740412	5		383	512	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048241	180048241	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066593-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	194	423	0	ENST00000261937.6:c.2032C>T	p.Pro678Ser	p.P678S	ENST00000261937	NM_182925.4	678	Cct/Tct	14/30	0.539228268740412	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.539228268740412	2		423	343	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006898	47006898	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1556762493	NA	P-0066593-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	176	190	0	ENST00000377604.3:c.17+1G>T		p.X6_splice	ENST00000377604	NM_001204468.1	6			0.475552626291316	2	FACETS	0.881	0.838	0.922			1	CLONAL	3	TRUE	NA	0.539228268740412	2		190	247	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332384	70332384	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066593-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	18	387	0	ENST00000373644.4:c.289T>G	p.Leu97Val	p.L97V	ENST00000373644	NM_030625.2	97	Tta/Gta	2/12	0.539228268740412	2	FACETS	0.185	0.139	0.24	0.093	0.069	0.12	SUBCLONAL	1	TRUE	0	0.539228268740412	2		387	360	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118370550	118370550	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1057519403	NA	P-0066593-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	168	330	0	ENST00000534358.1:c.6080G>A	p.Gly2027Glu	p.G2027E	ENST00000534358	NM_005933.3	2027	gGg/gAg	24/36	0.253713399957246	4	FACETS	1	0.972	1	1	0.972	1	INDETERMINATE	2	TRUE	2	0.539228268740412	4		330	440	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17386609	17386609	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0066593-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	122	348	0	ENST00000359435.4:c.545-1G>C		p.X182_splice	ENST00000359435	NM_001033549.1	182			0.184809068791561	3	FACETS	0.997	0.917	1	0.665	0.611	0.72	INDETERMINATE	2	TRUE	0	0.539228268740412	3		348	288	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453552	138453552	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066593-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	39	373	0	ENST00000289153.2:c.896C>A	p.Ala299Asp	p.A299D	ENST00000289153	NM_006219.2	299	gCc/gAc	5/22	0.509311477304126	4	FACETS	0.434	0.359	0.518	0.217	0.179	0.259	SUBCLONAL	1	TRUE	2	0.539228268740412	4		373	513	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143326457	143326457	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs927648635	NA	P-0066593-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	179	331	0	ENST00000262992.4:c.157C>T	p.Pro53Ser	p.P53S	ENST00000262992	NM_001101669.1	53	Cct/Tct	4/24	0.539228268740412	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.539228268740412	2		331	310	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965878	90965878	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066593-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	124	345	0	ENST00000265433.3:c.1439C>A	p.Ser480Ter	p.S480*	ENST00000265433	NM_002485.4	480	tCa/tAa	11/16	0.253713399957246	4	FACETS	1	0.96	1	1	0.96	1	INDETERMINATE	2	TRUE	2	0.539228268740412	4		345	328	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0066688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	51	133	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.241921506777501	5	FACETS	0.856	0.737	0.982	0.57	0.491	0.655	INDETERMINATE	2	FALSE	2	0.534185456470195	5		133	201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0066688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	170	464	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.495399148614893	2	FACETS	0.942	0.881	1	0.942	0.881	1	CLONAL	2	FALSE	0	0.534185456470195	2		464	338	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508932	106508932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	120	528	1	ENST00000359195.3:c.926C>T	p.Thr309Met	p.T309M	ENST00000359195	NM_002649.2	309	aCg/aTg	2/11	0.333918819782583	2	FACETS	1	0.983	1	0.669	0.611	0.727	CLONAL	1	FALSE	0	0.534185456470195	2		529	336	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981767	201981767	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0066688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	496	565	0	ENST00000359651.3:c.479-1G>A		p.X160_splice	ENST00000359651		160			0.452404336431941	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	4	FALSE	0	0.534185456470195	4		565	655	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99452036	99452036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	127	507	0	ENST00000268035.6:c.1370C>T	p.Ser457Phe	p.S457F	ENST00000268035	NM_000875.3	457	tCc/tTc	6/21	0.483426627075509	2	FACETS	0.762	0.701	0.824	0.762	0.701	0.824	SUBCLONAL	2	FALSE	0	0.534185456470195	2		507	312	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	226	480	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.450826936144681	6	FACETS	0.927	0.874	0.98	0.927	0.874	0.98	CLONAL	4	FALSE	2	0.534185456470195	6		480	472	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136252	202136252	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	61	363	0	ENST00000358485.4:c.496C>T	p.Gln166Ter	p.Q166*	ENST00000358485	NM_001080125.1	166	Cag/Tag	3/9	1	2	FACETS	0.627	0.544	0.717	0.627	0.544	0.717	SUBCLONAL	1	FALSE	1	0.534185456470195	2		363	364	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972013	55972013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	91	390	0	ENST00000263923.4:c.1631C>T	p.Ser544Phe	p.S544F	ENST00000263923	NM_002253.2	544	tCc/tTc	12/30	0.316445774507637	3	FACETS	1	0.973	1	0.633	0.567	0.702	INDETERMINATE	1	FALSE	1	0.534185456470195	3		390	341	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519895	NA	P-0066688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	68	385	0	ENST00000281708.4:c.1394G>C	p.Arg465Pro	p.R465P	ENST00000281708	NM_033632.3	465	cGt/cCt	9/12	0.316445774507637	3	FACETS	1	0.931	1	0.545	0.478	0.616	INDETERMINATE	1	FALSE	1	0.534185456470195	3		385	296	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927377	245927377	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866883139	NA	P-0066688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	43	401	0	ENST00000388985.4:c.1151G>A	p.Gly384Asp	p.G384D	ENST00000388985		384	gGc/gAc	11/12	0.452404336431941	4	FACETS	0.624	0.523	0.735	0.156	0.13	0.184	SUBCLONAL	1	FALSE	0	0.534185456470195	4		401	396	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137759	64137817	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCCGAGATCATGTGCAAAATCCGCGAGGGGCGCTTCTCCCTTGACGGGGAGGCCT	GGCGGCCGAGATCATGTGCAAAATCCGCGAGGGGCGCTTCTCCCTTGACGGGGAGGCCT	-	novel	NA	P-0066688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	48	491	0	ENST00000334205.4:c.1863_1921del	p.Ala622GlyfsTer162	p.A622Gfs*162	ENST00000334205	NM_003942.2	620	caGGCGGCCGAGATCATGTGCAAAATCCGCGAGGGGCGCTTCTCCCTTGACGGGGAGGCCTgg/cagg	15/17	0.333918819782583	2	FACETS	0.686	0.584	0.796	0.343	0.292	0.398	SUBCLONAL	1	FALSE	0	0.534185456470195	2		491	262	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738621	43738621	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	94	411	0	ENST00000382044.4:c.3004G>C	p.Glu1002Gln	p.E1002Q	ENST00000382044	NM_001141980.1	1002	Gag/Cag	14/28	0.483426627075509	2	FACETS	1	0.977	1	0.649	0.586	0.714	CLONAL	1	FALSE	0	0.534185456470195	2		411	271	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18943139	18943139	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1429628130	NA	P-0066688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	126	381	0	ENST00000262803.5:c.121C>T	p.Pro41Ser	p.P41S	ENST00000262803	NM_002911.3	41	Cct/Tct	1/24	0.450826936144681	6	FACETS	0.951	0.872	1	0.713	0.654	0.774	CLONAL	3	FALSE	2	0.534185456470195	6		381	342	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131287	202131287	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	115	513	0	ENST00000358485.4:c.255C>A	p.Ser85Arg	p.S85R	ENST00000358485	NM_001080125.1	85	agC/agA	2/9	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.534185456470195	2		513	381	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267153	41267153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	140	538	0	ENST00000349496.5:c.737C>T	p.Ser246Leu	p.S246L	ENST00000349496	NM_001904.3	246	tCa/tTa	6/15	0.49129881411115	4	FACETS	0.784	0.718	0.852	0.784	0.718	0.852	SUBCLONAL	2	FALSE	2	0.534185456470195	4		538	513	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588145	67588148	+	frameshift_variant	Frame_Shift_Del	DEL	TATG	TATG	-	novel	NA	P-0066688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	42	272	0	ENST00000274335.5:c.976_979del	p.Met326ProfsTer17	p.M326Pfs*17	ENST00000274335		325	aaTATG/aa	7/15	1	2	FACETS	0.629	0.529	0.738	0.629	0.529	0.738	SUBCLONAL	1	FALSE	1	0.534185456470195	2		272	250	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031939	26031939	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	108	664	0	ENST00000244661.2:c.350G>T	p.Arg117Leu	p.R117L	ENST00000244661	NM_003537.3	117	cGa/cTa	1/1	0.189336654725343	5	FACETS	1	0.983	1	0.487	0.438	0.537	INDETERMINATE	1	FALSE	2	0.534185456470195	5		664	499	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056594	26056594	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	66	449	2	ENST00000343677.2:c.63G>T	p.Lys21Asn	p.K21N	ENST00000343677	NM_005319.3	21	aaG/aaT	1/1	0.189336654725343	5	FACETS	1	0.962	1	0.426	0.372	0.484	INDETERMINATE	1	FALSE	2	0.534185456470195	5		451	348	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0066822-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	28	300	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.813	1	1	0.813	1	CLONAL	1	TRUE	1	0.15	2		300	367	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039906	47039906	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0066822-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	15	209	0	ENST00000377604.3:c.1248+1G>T		p.X416_splice	ENST00000377604	NM_001204468.1	416			1	1	FACETS	0.959	0.703	1	0.959	0.703	1	CLONAL	1	TRUE	0	0.15	1		209	193	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59878784	59878784	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066822-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	31	546	0	ENST00000259008.2:c.970A>T	p.Thr324Ser	p.T324S	ENST00000259008	NM_032043.2	324	Aca/Tca	8/20	1	2	FACETS	0.861	0.696	1	0.861	0.696	1	CLONAL	1	TRUE	1	0.15	2		546	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579403	7579413	+	frameshift_variant	Frame_Shift_Del	DEL	GATGACAGGGG	GATGACAGGGG	-	novel	NA	P-0066822-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	32	736	0	ENST00000269305.4:c.274_284del	p.Pro92PhefsTer53	p.P92Ffs*53	ENST00000269305	NM_001126112.2	92	CCCCTGTCATCt/t	4/11	1	2	FACETS	0.716	0.58	0.871	0.716	0.58	0.871	SUBCLONAL	1	TRUE	1	0.15	2		736	596	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464578	25464578	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0066895-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	251	440	0	ENST00000264709.3:c.1937-2A>T		p.X646_splice	ENST00000264709	NM_175629.2	646			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.82	2		440	608	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922889	39922890	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0066895-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	320	247	0	ENST00000378444.4:c.3818_3819del	p.Glu1273ValfsTer3	p.E1273Vfs*3	ENST00000378444	NM_001123385.1	1273	gAG/g	8/15	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.82	1		247	380	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356728	70356728	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0066895-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	257	233	0	ENST00000374080.3:c.5401del		p.X1801_splice	ENST00000374080		1801			1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.82	1		233	339	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057310	180057310	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066922-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	135	422	0	ENST00000261937.6:c.428C>G	p.Pro143Arg	p.P143R	ENST00000261937	NM_182925.4	143	cCt/cGt	4/30	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.420598936920658	2		422	452	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651590	48651590	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066922-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	55	415	0	ENST00000376670.3:c.756A>T	p.Lys252Asn	p.K252N	ENST00000376670	NM_002049.3	252	aaA/aaT	5/6	1	2	FACETS	0.575	0.492	0.664	0.575	0.492	0.664	SUBCLONAL	1	TRUE	1	0.420598936920658	2		415	455	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663891	241663891	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	47	186	1	ENST00000366560.3:c.1237-1G>T		p.X413_splice	ENST00000366560	NM_000143.3	413			1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.44	2		187	179	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	91	506	0	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	1	2	FACETS	0.925	0.826	1	0.925	0.826	1	CLONAL	1	TRUE	1	0.44	2		506	447	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942686	48942686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767011440	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	81	306	0	ENST00000267163.4:c.1073G>A	p.Arg358Gln	p.R358Q	ENST00000267163	NM_000321.2	358	cGa/cAa	11/27	1	2	FACETS	0.984	0.873	1	0.984	0.873	1	CLONAL	1	TRUE	1	0.44	2		306	374	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509723	106509723	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	117	578	1	ENST00000359195.3:c.1717G>T	p.Glu573Ter	p.E573*	ENST00000359195	NM_002649.2	573	Gaa/Taa	2/11	1	2	FACETS	0.979	0.887	1	0.979	0.887	1	CLONAL	1	TRUE	1	0.44	2		579	543	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	52	260	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.721	0.617	0.833	0.721	0.617	0.833	SUBCLONAL	1	TRUE	1	0.44	2		260	328	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473723	67473723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223740	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	110	596	0	ENST00000327367.4:c.803G>A	p.Arg268His	p.R268H	ENST00000327367	NM_005902.3	268	cGc/cAc	6/9	1	2	FACETS	0.933	0.841	1	0.933	0.841	1	CLONAL	1	TRUE	1	0.44	2		596	536	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074259	8074259	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	132	661	0	ENST00000377482.5:c.400A>C	p.Lys134Gln	p.K134Q	ENST00000377482	NM_018948.3	134	Aaa/Caa	4/4	1	2	FACETS	0.917	0.835	1	0.917	0.835	1	CLONAL	1	TRUE	1	0.44	2		661	654	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074308	8074308	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	129	649	0	ENST00000377482.5:c.351A>C	p.Lys117Asn	p.K117N	ENST00000377482	NM_018948.3	117	aaA/aaC	4/4	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.44	2		649	552	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307976	11307976	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	120	619	0	ENST00000361445.4:c.1016A>G	p.His339Arg	p.H339R	ENST00000361445	NM_004958.3	339	cAc/cGc	7/58	1	2	FACETS	0.985	0.893	1	0.985	0.893	1	CLONAL	1	TRUE	1	0.44	2		619	554	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257144	16257144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775010663	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	108	607	0	ENST00000375759.3:c.4409G>A	p.Arg1470Gln	p.R1470Q	ENST00000375759	NM_015001.2	1470	cGa/cAa	11/15	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.44	2		607	468	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059192	27059192	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	96	386	0	ENST00000324856.7:c.1829C>T	p.Ser610Phe	p.S610F	ENST00000324856	NM_006015.4	610	tCt/tTt	4/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.44	2		386	386	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363236	40363236	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	157	665	0	ENST00000397332.2:c.993C>A	p.Phe331Leu	p.F331L	ENST00000397332	NM_001033082.2	331	ttC/ttA	3/3	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.44	2		665	680	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805714	43805714	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs993195285	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	97	577	1	ENST00000372470.3:c.770G>A	p.Arg257His	p.R257H	ENST00000372470	NM_005373.2	257	cGc/cAc	5/12	1	2	FACETS	0.885	0.793	0.983	0.885	0.793	0.983	CLONAL	1	TRUE	1	0.44	2		578	498	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739328	46739328	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1020176839	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	115	550	0	ENST00000371975.4:c.1519G>A	p.Val507Met	p.V507M	ENST00000371975	NM_003579.3	507	Gtg/Atg	14/18	1	2	FACETS	0.894	0.807	0.984	0.894	0.807	0.984	CLONAL	1	TRUE	1	0.44	2		550	585	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241873	72241873	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1252345844	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	84	457	0	ENST00000357731.5:c.517C>T	p.Arg173Ter	p.R173*	ENST00000357731	NM_173808.2	173	Cga/Tga	3/7	1	2	FACETS	0.734	0.65	0.824	0.734	0.65	0.824	SUBCLONAL	1	TRUE	1	0.44	2		457	520	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733503	85733503	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	135	615	0	ENST00000370580.1:c.509C>A	p.Ser170Tyr	p.S170Y	ENST00000370580	NM_003921.4	170	tCt/tAt	3/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.44	2		615	533	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150913815	150913815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	79	366	0	ENST00000271640.5:c.458C>T	p.Ala153Val	p.A153V	ENST00000271640	NM_001145415.1	153	gCt/gTt	5/22	1	2	FACETS	0.909	0.804	1	0.909	0.804	1	CLONAL	1	TRUE	1	0.44	2		366	395	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162688912	162688912	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	69	426	0	ENST00000367921.3:c.59C>A	p.Ser20Tyr	p.S20Y	ENST00000367921	NM_006182.2	20	tCt/tAt	3/18	1	2	FACETS	0.817	0.715	0.926	0.817	0.715	0.926	CLONAL	1	TRUE	1	0.44	2		426	384	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746018	162746018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	115	577	0	ENST00000367921.3:c.2141G>A	p.Arg714Gln	p.R714Q	ENST00000367921	NM_006182.2	714	cGa/cAa	16/18	1	2	FACETS	0.975	0.882	1	0.975	0.882	1	CLONAL	1	TRUE	1	0.44	2		577	536	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176104197	176104197	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs2149730404	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	75	434	0	ENST00000367669.3:c.917T>C	p.Val306Ala	p.V306A	ENST00000367669	NM_022457.5	306	gTc/gCc	8/20	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.44	2		434	339	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552729	226552729	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746139482	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	150	648	0	ENST00000366794.5:c.2632C>T	p.Arg878Trp	p.R878W	ENST00000366794	NM_001618.3	878	Cgg/Tgg	19/23	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.44	2		648	668	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63700053	63700053	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	121	526	0	ENST00000279873.7:c.388A>C	p.Lys130Gln	p.K130Q	ENST00000279873	NM_032199.2	130	Aaa/Caa	3/10	1	2	FACETS	0.995	0.902	1	0.995	0.902	1	CLONAL	1	TRUE	1	0.44	2		526	553	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405608	70405608	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	99	493	0	ENST00000373644.4:c.3122G>T	p.Arg1041Ile	p.R1041I	ENST00000373644	NM_030625.2	1041	aGa/aTa	4/12	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.44	2		493	401	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88677032	88677032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782400	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	23	154	0	ENST00000372037.3:c.817C>T	p.Arg273Ter	p.R273*	ENST00000372037	NM_004329.2	273	Cga/Tga	9/13	1	2	FACETS	0.731	0.576	0.906	0.731	0.576	0.906	CLONAL	1	TRUE	1	0.44	2		154	143	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685272	89685272	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs748031178	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	88	364	0	ENST00000371953.3:c.167T>G	p.Phe56Cys	p.F56C	ENST00000371953	NM_000314.4	56	tTt/tGt	3/9	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.44	2		364	354	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	73	391	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.954	0.84	1	0.954	0.84	1	CLONAL	1	TRUE	1	0.44	2		391	348	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717778	89717778	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	52	357	0	ENST00000371953.3:c.801+2T>C		p.X267_splice	ENST00000371953	NM_000314.4	267			1	2	FACETS	0.799	0.684	0.922	0.799	0.684	0.922	CLONAL	1	TRUE	1	0.44	2		357	296	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414232	32414232	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	113	488	0	ENST00000332351.3:c.1319G>T	p.Arg440Ile	p.R440I	ENST00000332351	NM_024426.4	440	aGa/aTa	8/10	1	2	FACETS	0.964	0.871	1	0.964	0.871	1	CLONAL	1	TRUE	1	0.44	2		488	533	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449551	32449551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	88	524	2	ENST00000332351.3:c.823G>A	p.Asp275Asn	p.D275N	ENST00000332351	NM_024426.4	275	Gac/Aac	3/10	1	2	FACETS	0.873	0.777	0.975	0.873	0.777	0.975	CLONAL	1	TRUE	1	0.44	2		526	458	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132927	64132927	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145356210	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	111	624	0	ENST00000334205.4:c.1061G>A	p.Arg354Gln	p.R354Q	ENST00000334205	NM_003942.2	354	cGa/cAa	9/17	1	2	FACETS	0.961	0.868	1	0.961	0.868	1	CLONAL	1	TRUE	1	0.44	2		624	525	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94170371	94170371	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745614941	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	70	325	0	ENST00000323929.3:c.1898G>A	p.Arg633Gln	p.R633Q	ENST00000323929	NM_005591.3	633	cGa/cAa	17/20	1	2	FACETS	0.867	0.76	0.981	0.867	0.76	0.981	CLONAL	1	TRUE	1	0.44	2		325	367	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194110	94194110	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773469981	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	81	351	0	ENST00000323929.3:c.1318G>A	p.Ala440Thr	p.A440T	ENST00000323929	NM_005591.3	440	Gca/Aca	12/20	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.44	2		351	342	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212851	94212851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368403414	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	104	456	0	ENST00000323929.3:c.391G>A	p.Asp131Asn	p.D131N	ENST00000323929	NM_005591.3	131	Gat/Aat	5/20	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.44	2		456	453	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924618	94924618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1400088899	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	112	531	1	ENST00000536441.1:c.292C>T	p.Arg98Cys	p.R98C	ENST00000536441	NM_144665.3	98	Cgc/Tgc	3/10	1	2	FACETS	0.957	0.864	1	0.957	0.864	1	CLONAL	1	TRUE	1	0.44	2		532	532	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155078	108155078	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	59	455	0	ENST00000278616.4:c.3871C>A	p.Leu1291Ile	p.L1291I	ENST00000278616	NM_000051.3	1291	Ctt/Att	26/63	1	2	FACETS	0.739	0.639	0.847	0.739	0.639	0.847	SUBCLONAL	1	TRUE	1	0.44	2		455	363	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205756	108205756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531980488	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	48	500	0	ENST00000278616.4:c.8071C>T	p.Arg2691Cys	p.R2691C	ENST00000278616	NM_000051.3	2691	Cgc/Tgc	55/63	1	2	FACETS	0.671	0.57	0.782	0.671	0.57	0.782	SUBCLONAL	1	TRUE	1	0.44	2		500	325	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376311	118376311	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	128	705	0	ENST00000534358.1:c.9704A>C	p.Lys3235Thr	p.K3235T	ENST00000534358	NM_005933.3	3235	aAa/aCa	27/36	1	2	FACETS	0.971	0.883	1	0.971	0.883	1	CLONAL	1	TRUE	1	0.44	2		705	599	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125513761	125513761	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	77	513	0	ENST00000428830.2:c.889A>T	p.Asn297Tyr	p.N297Y	ENST00000428830	NM_001114121.2	297	Aat/Tat	9/14	1	2	FACETS	0.864	0.763	0.972	0.864	0.763	0.972	CLONAL	1	TRUE	1	0.44	2		513	405	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552613	18552613	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1371859788	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	82	519	0	ENST00000266497.5:c.2024G>T	p.Arg675Ile	p.R675I	ENST00000266497		675	aGa/aTa	14/31	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.44	2		519	369	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552625	18552625	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	63	562	0	ENST00000266497.5:c.2036T>G	p.Phe679Cys	p.F679C	ENST00000266497		679	tTt/tGt	14/31	1	2	FACETS	0.762	0.662	0.869	0.762	0.662	0.869	SUBCLONAL	1	TRUE	1	0.44	2		562	376	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205293	46205293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	45	469	0	ENST00000334344.6:c.377C>T	p.Ala126Val	p.A126V	ENST00000334344	NM_152641.2	126	gCa/gTa	4/21	1	2	FACETS	0.607	0.512	0.711	0.607	0.512	0.711	SUBCLONAL	1	TRUE	1	0.44	2		469	337	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231331	46231331	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	71	471	0	ENST00000334344.6:c.1171A>G	p.Ile391Val	p.I391V	ENST00000334344	NM_152641.2	391	Att/Gtt	10/21	1	2	FACETS	0.889	0.781	1	0.889	0.781	1	CLONAL	1	TRUE	1	0.44	2		471	363	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249857	133249857	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1565972665	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	103	492	0	ENST00000320574.5:c.1366G>C	p.Ala456Pro	p.A456P	ENST00000320574	NM_006231.2	456	Gcc/Ccc	14/49	1	2	FACETS	0.992	0.892	1	0.992	0.892	1	CLONAL	1	TRUE	1	0.44	2		492	472	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557791	21557791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	115	573	0	ENST00000382592.4:c.2054C>T	p.Ala685Val	p.A685V	ENST00000382592	NM_014572.2	685	gCt/gTt	5/8	1	2	FACETS	0.873	0.788	0.961	0.873	0.788	0.961	CLONAL	1	TRUE	1	0.44	2		573	599	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28644727	28644727	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	70	405	0	ENST00000241453.7:c.66del	p.Phe22LeufsTer11	p.F22Lfs*11	ENST00000241453	NM_004119.2	22	ttT/tt	2/24	1	2	FACETS	0.758	0.663	0.859	0.758	0.663	0.859	SUBCLONAL	1	TRUE	1	0.44	2		405	420	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906931	32906931	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	92	583	0	ENST00000380152.3:c.1316T>G	p.Phe439Cys	p.F439C	ENST00000380152		439	tTt/tGt	10/27	1	2	FACETS	0.862	0.769	0.961	0.862	0.769	0.961	CLONAL	1	TRUE	1	0.44	2		583	485	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950818	32950818	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	92	432	0	ENST00000380152.3:c.8644A>C	p.Lys2882Gln	p.K2882Q	ENST00000380152		2882	Aaa/Caa	21/27	1	2	FACETS	0.826	0.737	0.921	0.826	0.737	0.921	CLONAL	1	TRUE	1	0.44	2		432	506	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939073	48939073	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1208736713	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	61	310	0	ENST00000267163.4:c.905C>A	p.Ser302Tyr	p.S302Y	ENST00000267163	NM_000321.2	302	tCt/tAt	9/27	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.44	2		310	274	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506181	103506181	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	100	441	0	ENST00000355739.4:c.339T>G	p.Phe113Leu	p.F113L	ENST00000355739	NM_000123.3	113	ttT/ttG	3/15	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.44	2		441	440	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506670	103506670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1372959301	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	112	472	0	ENST00000355739.4:c.413G>A	p.Arg138Gln	p.R138Q	ENST00000355739	NM_000123.3	138	cGa/cAa	4/15	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.44	2		472	476	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574747	95574747	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1131691210	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	72	490	0	ENST00000393063.1:c.2350G>T	p.Glu784Ter	p.E784*	ENST00000393063	NM_030621.3	784	Gaa/Taa	16/28	1	2	FACETS	0.885	0.777	0.999	0.885	0.777	0.999	CLONAL	1	TRUE	1	0.44	2		490	370	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023435	33023435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	133	588	0	ENST00000300177.4:c.544G>A	p.Asp182Asn	p.D182N	ENST00000300177	NM_001191322.1	182	Gat/Aat	2/2	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.44	2		588	586	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042423	42042423	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	115	641	0	ENST00000219905.7:c.6618G>T	p.Lys2206Asn	p.K2206N	ENST00000219905	NM_001164273.1	2206	aaG/aaT	17/24	1	2	FACETS	0.909	0.822	1	0.909	0.822	1	CLONAL	1	TRUE	1	0.44	2		641	575	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748744	43748744	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs753789253	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	113	595	0	ENST00000382044.4:c.2062A>C	p.Asn688His	p.N688H	ENST00000382044	NM_001141980.1	688	Aat/Cat	12/28	1	2	FACETS	0.973	0.879	1	0.973	0.879	1	CLONAL	1	TRUE	1	0.44	2		595	528	SUCCESS
B2M	567	MSKCC	GRCh37	15	45008529	45008529	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	66	369	0	ENST00000558401.1:c.349C>T	p.Arg117Ter	p.R117*	ENST00000558401	NM_004048.2	117	Cga/Tga	3/4	1	2	FACETS	0.685	0.596	0.78	0.685	0.596	0.78	SUBCLONAL	1	TRUE	1	0.44	2		369	438	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50757355	50757355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	18	73	0	ENST00000307179.4:c.653C>T	p.Ser218Phe	p.S218F	ENST00000307179		218	tCt/tTt	7/20	1	2	FACETS	0.758	0.593	0.935	1	0.92	1	CLONAL	2	TRUE	1	0.44	2		73	54	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457330	67457330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	170	719	0	ENST00000327367.4:c.304G>A	p.Glu102Lys	p.E102K	ENST00000327367	NM_005902.3	102	Gag/Aag	2/9	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.44	2		719	728	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346808	91346808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771776126	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	78	493	0	ENST00000355112.3:c.3416G>A	p.Arg1139Gln	p.R1139Q	ENST00000355112	NM_000057.2	1139	cGa/cAa	18/22	1	2	FACETS	0.933	0.825	1	0.933	0.825	1	CLONAL	1	TRUE	1	0.44	2		493	380	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3794921	3794921	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1252438256	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	83	438	0	ENST00000262367.5:c.3956G>A	p.Arg1319Gln	p.R1319Q	ENST00000262367	NM_004380.2	1319	cGa/cAa	23/31	0.128291962846545	3	FACETS	0.945	0.837	1	0.473	0.418	0.53	INDETERMINATE	1	TRUE	1	0.44	3		438	487	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782308	56782308	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34670294	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	108	446	1	ENST00000308159.5:c.149G>A	p.Arg50His	p.R50H	ENST00000308159	NM_014669.4	50	cGc/cAc	2/22	0.128291962846545	3	FACETS	1	0.95	1	0.544	0.49	0.602	INDETERMINATE	1	TRUE	1	0.44	3		447	550	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865869	56865869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761782738	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	94	449	2	ENST00000308159.5:c.1201G>A	p.Asp401Asn	p.D401N	ENST00000308159	NM_014669.4	401	Gac/Aac	11/22	0.128291962846545	3	FACETS	0.939	0.838	1	0.47	0.419	0.524	INDETERMINATE	1	TRUE	1	0.44	3		451	555	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857314	68857314	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747235838	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	109	423	0	ENST00000261769.5:c.1949T>C	p.Ile650Thr	p.I650T	ENST00000261769	NM_004360.3	650	aTc/aCc	13/16	0.128291962846545	3	FACETS	1	0.967	1	0.586	0.528	0.646	INDETERMINATE	1	TRUE	1	0.44	3		423	516	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828383	72828383	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1277890729	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	153	687	0	ENST00000268489.5:c.8198G>A	p.Arg2733His	p.R2733H	ENST00000268489	NM_006885.3	2733	cGt/cAt	9/10	0.128291962846545	3	FACETS	1	0.981	1	0.618	0.567	0.672	INDETERMINATE	1	TRUE	1	0.44	3		687	686	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829497	72829497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761486040	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	91	523	0	ENST00000268489.5:c.7084G>A	p.Asp2362Asn	p.D2362N	ENST00000268489	NM_006885.3	2362	Gac/Aac	9/10	0.128291962846545	3	FACETS	1	0.95	1	0.557	0.497	0.621	INDETERMINATE	1	TRUE	1	0.44	3		523	453	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929510	81929510	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	131	568	1	ENST00000359376.3:c.1171G>T	p.Asp391Tyr	p.D391Y	ENST00000359376	NM_002661.3	391	Gac/Tac	13/33	0.128291962846545	3	FACETS	1	0.976	1	0.604	0.55	0.661	INDETERMINATE	1	TRUE	1	0.44	3		569	601	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813006	89813006	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	131	469	0	ENST00000389301.3:c.3499T>G	p.Leu1167Val	p.L1167V	ENST00000389301	NM_000135.2	1167	Ttg/Gtg	35/43	0.128291962846545	3	FACETS	1	0.984	1	0.684	0.624	0.747	INDETERMINATE	1	TRUE	1	0.44	3		469	531	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679514	33679514	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs939685161	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	67	390	0	ENST00000308377.4:c.2567G>T	p.Arg856Leu	p.R856L	ENST00000308377	NM_152270.3	856	cGa/cTa	5/5	1	2	FACETS	0.814	0.711	0.924	0.814	0.711	0.924	CLONAL	1	TRUE	1	0.44	2		390	374	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40864329	40864329	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	95	552	0	ENST00000428826.2:c.1379T>C	p.Leu460Pro	p.L460P	ENST00000428826		460	cTg/cCg	12/21	1	2	FACETS	0.83	0.742	0.924	0.83	0.742	0.924	CLONAL	1	TRUE	1	0.44	2		552	520	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245425	41245425	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs80357182	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	118	584	0	ENST00000357654.3:c.2123C>A	p.Ser708Tyr	p.S708Y	ENST00000357654	NM_007294.3	708	tCt/tAt	10/23	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.44	2		584	491	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246815	41246815	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs147519994	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	44	521	0	ENST00000357654.3:c.733G>T	p.Asp245Tyr	p.D245Y	ENST00000357654	NM_007294.3	245	Gat/Tat	10/23	1	2	FACETS	0.398	0.333	0.469	0.398	0.333	0.469	SUBCLONAL	1	TRUE	1	0.44	2		521	503	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438156	56438156	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs141997049	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	132	565	0	ENST00000407977.2:c.837C>A	p.Phe279Leu	p.F279L	ENST00000407977		279	ttC/ttA	7/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.44	2		565	502	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006834	62006834	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	106	592	0	ENST00000392795.3:c.554A>G	p.Asp185Gly	p.D185G	ENST00000392795	NM_001039933.1	185	gAt/gGt	5/6	1	2	FACETS	0.977	0.88	1	0.977	0.88	1	CLONAL	1	TRUE	1	0.44	2		592	493	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584329	39584329	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	73	412	0	ENST00000262039.4:c.994A>C	p.Lys332Gln	p.K332Q	ENST00000262039	NM_002647.2	332	Aaa/Caa	10/25	1	2	FACETS	0.862	0.758	0.973	0.862	0.758	0.973	CLONAL	1	TRUE	1	0.44	2		412	385	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372045	45372045	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	70	455	0	ENST00000262160.6:c.1124A>C	p.Lys375Thr	p.K375T	ENST00000262160	NM_005901.5	375	aAa/aCa	9/11	1	2	FACETS	0.914	0.803	1	0.914	0.803	1	CLONAL	1	TRUE	1	0.44	2		455	348	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375002	45375002	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	105	471	0	ENST00000262160.6:c.841G>T	p.Glu281Ter	p.E281*	ENST00000262160	NM_005901.5	281	Gaa/Taa	8/11	1	2	FACETS	0.978	0.88	1	0.978	0.88	1	CLONAL	1	TRUE	1	0.44	2		471	488	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210815	2210815	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200004531	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	137	644	0	ENST00000398665.3:c.1312G>A	p.Ala438Thr	p.A438T	ENST00000398665	NM_032482.2	438	Gct/Act	14/28	0.128291962846545	3	FACETS	1	0.986	1	0.717	0.655	0.78	INDETERMINATE	1	TRUE	1	0.44	3		644	530	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210733	5210733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779302415	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	123	657	0	ENST00000357368.4:c.5318C>T	p.Ser1773Leu	p.S1773L	ENST00000357368	NM_002850.3	1773	tCg/tTg	34/38	0.128291962846545	3	FACETS	1	0.964	1	0.564	0.511	0.619	INDETERMINATE	1	TRUE	1	0.44	3		657	605	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15379822	15379822	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	121	503	0	ENST00000263377.2:c.317A>G	p.Asp106Gly	p.D106G	ENST00000263377	NM_058243.2	106	gAt/gGt	3/20	0.128291962846545	3	FACETS	1	0.984	1	0.717	0.652	0.785	INDETERMINATE	1	TRUE	1	0.44	3		503	468	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425290	47425290	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178800275	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	134	625	0	ENST00000404338.3:c.3358C>T	p.Arg1120Trp	p.R1120W	ENST00000404338	NM_004491.4	1120	Cgg/Tgg	1/6	0.128291962846545	3	FACETS	1	0.978	1	0.615	0.561	0.672	INDETERMINATE	1	TRUE	1	0.44	3		625	604	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068357	26068357	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	120	325	1	ENST00000435504.4:c.133G>T	p.Glu45Ter	p.E45*	ENST00000435504		45	Gaa/Taa	2/13	1	2	FACETS	0.957	0.879	1	1	0.99	1	CLONAL	2	TRUE	1	0.44	2		326	285	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068393	26068393	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	17	347	0	ENST00000435504.4:c.97G>T	p.Glu33Ter	p.E33*	ENST00000435504		33	Gaa/Taa	2/13	1	2	FACETS	0.262	0.195	0.341	0.262	0.195	0.341	SUBCLONAL	1	TRUE	1	0.44	2		347	295	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462559	29462559	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	104	563	0	ENST00000389048.3:c.2342A>G	p.Asp781Gly	p.D781G	ENST00000389048	NM_004304.4	781	gAc/gGc	13/29	1	2	FACETS	0.961	0.864	1	0.961	0.864	1	CLONAL	1	TRUE	1	0.44	2		563	492	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606678	29606678	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs188859061	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	125	531	0	ENST00000389048.3:c.1202G>A	p.Arg401Gln	p.R401Q	ENST00000389048	NM_004304.4	401	cGa/cAa	5/29	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.44	2		531	560	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61712937	61712937	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	71	512	0	ENST00000401558.2:c.2474C>T	p.Ala825Val	p.A825V	ENST00000401558	NM_003400.3	825	gCt/gTt	20/25	1	2	FACETS	0.776	0.68	0.878	0.776	0.68	0.878	SUBCLONAL	1	TRUE	1	0.44	2		512	416	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	74	429	0	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	0.843	0.742	0.951	0.843	0.742	0.951	CLONAL	1	TRUE	1	0.44	2		429	399	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715794	61715794	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	96	554	0	ENST00000401558.2:c.2135G>T	p.Arg712Ile	p.R712I	ENST00000401558	NM_003400.3	712	aGa/aTa	18/25	1	2	FACETS	0.907	0.812	1	0.907	0.812	1	CLONAL	1	TRUE	1	0.44	2		554	481	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724120	61724120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781425578	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	80	525	0	ENST00000401558.2:c.782G>A	p.Arg261Gln	p.R261Q	ENST00000401558	NM_003400.3	261	cGa/cAa	10/25	1	2	FACETS	0.821	0.726	0.922	0.821	0.726	0.922	CLONAL	1	TRUE	1	0.44	2		525	443	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630589	67630589	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1345206133	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	75	582	0	ENST00000272342.5:c.775A>G	p.Thr259Ala	p.T259A	ENST00000272342	NM_019002.3	259	Acc/Gcc	5/6	1	2	FACETS	0.773	0.68	0.872	0.773	0.68	0.872	SUBCLONAL	1	TRUE	1	0.44	2		582	441	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921750	111921750	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs185078669	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	101	493	0	ENST00000393256.3:c.539G>A	p.Arg180Gln	p.R180Q	ENST00000393256	NM_006538.4	180	cGa/cAa	4/4	1	2	FACETS	0.885	0.794	0.98	0.885	0.794	0.98	CLONAL	1	TRUE	1	0.44	2		493	519	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038133	128038133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369244363	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	142	450	0	ENST00000285398.2:c.1417G>A	p.Glu473Lys	p.E473K	ENST00000285398	NM_000122.1	473	Gaa/Aaa	9/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.44	2		450	595	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131192	202131192	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	93	459	2	ENST00000358485.4:c.160C>A	p.Leu54Ile	p.L54I	ENST00000358485	NM_001080125.1	54	Ctc/Atc	2/9	1	2	FACETS	0.923	0.825	1	0.923	0.825	1	CLONAL	1	TRUE	1	0.44	2		461	458	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136279	202136279	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	93	512	0	ENST00000358485.4:c.523G>T	p.Glu175Ter	p.E175*	ENST00000358485	NM_001080125.1	175	Gaa/Taa	3/9	1	2	FACETS	0.837	0.747	0.932	0.837	0.747	0.932	CLONAL	1	TRUE	1	0.44	2		512	505	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736148	204736148	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	136	514	1	ENST00000302823.3:c.505G>A	p.Ala169Thr	p.A169T	ENST00000302823	NM_005214.4	169	Gca/Aca	3/4	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.44	2		515	563	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483964	212483964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	67	441	0	ENST00000342788.4:c.2239C>T	p.Pro747Ser	p.P747S	ENST00000342788	NM_005235.2	747	Cct/Tct	19/28	1	2	FACETS	0.86	0.752	0.976	0.86	0.752	0.976	CLONAL	1	TRUE	1	0.44	2		441	354	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543625	9543625	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	113	500	0	ENST00000353224.5:c.1529A>G	p.Tyr510Cys	p.Y510C	ENST00000353224	NM_177990.2	510	tAc/tGc	6/10	1	2	FACETS	0.911	0.822	1	0.911	0.822	1	CLONAL	1	TRUE	1	0.44	2		500	564	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31020738	31020738	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	78	469	0	ENST00000375687.4:c.1035G>T	p.Lys345Asn	p.K345N	ENST00000375687	NM_015338.5	345	aaG/aaT	11/13	1	2	FACETS	0.921	0.814	1	0.921	0.814	1	CLONAL	1	TRUE	1	0.44	2		469	385	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39704921	39704921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778237366	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	121	531	0	ENST00000361337.2:c.266G>A	p.Arg89Gln	p.R89Q	ENST00000361337	NM_003286.2	89	cGa/cAa	4/21	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.44	2		531	548	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39709875	39709875	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	85	396	0	ENST00000361337.2:c.502G>A	p.Glu168Lys	p.E168K	ENST00000361337	NM_003286.2	168	Gaa/Aaa	7/21	1	2	FACETS	0.882	0.783	0.987	0.882	0.783	0.987	CLONAL	1	TRUE	1	0.44	2		396	438	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775575	39775575	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	141	571	0	ENST00000288319.7:c.445G>T	p.Glu149Ter	p.E149*	ENST00000288319	NM_182918.3	149	Gaa/Taa	4/10	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.44	2		571	621	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288152	21288152	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	128	550	0	ENST00000354336.3:c.397G>T	p.Asp133Tyr	p.D133Y	ENST00000354336	NM_005207.3	133	Gat/Tat	2/3	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.44	2		550	564	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513431	41513431	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752713674	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	114	595	0	ENST00000263253.7:c.335G>A	p.Ser112Asn	p.S112N	ENST00000263253	NM_001429.3	112	aGt/aAt	2/31	1	2	FACETS	0.946	0.855	1	0.946	0.855	1	CLONAL	1	TRUE	1	0.44	2		595	548	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275192	41275192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	178	650	0	ENST00000349496.5:c.1358G>A	p.Arg453Gln	p.R453Q	ENST00000349496	NM_001904.3	453	cGg/cAg	9/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.44	2		650	654	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164118	47164118	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	88	512	0	ENST00000409792.3:c.2008G>T	p.Glu670Ter	p.E670*	ENST00000409792	NM_014159.6	670	Gaa/Taa	3/21	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.44	2		512	398	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643390	52643390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1438592568	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	88	523	0	ENST00000394830.3:c.2506C>T	p.Arg836Trp	p.R836W	ENST00000394830	NM_018313.4	836	Cgg/Tgg	17/30	1	2	FACETS	0.93	0.829	1	0.93	0.829	1	CLONAL	1	TRUE	1	0.44	2		523	430	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	65	532	0	ENST00000394830.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000394830	NM_018313.4	710	Cga/Tga	17/30	1	2	FACETS	0.814	0.71	0.926	0.814	0.71	0.926	CLONAL	1	TRUE	1	0.44	2		532	363	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696238	52696238	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	135	536	0	ENST00000394830.3:c.439A>G	p.Thr147Ala	p.T147A	ENST00000394830	NM_018313.4	147	Aca/Gca	5/30	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.44	2		536	578	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008431	70008431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	117	432	0	ENST00000394351.3:c.718C>T	p.Arg240Cys	p.R240C	ENST00000394351	NM_000248.3	240	Cgc/Tgc	8/9	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.44	2		432	496	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799436	72799436	+	stop_lost	Nonstop_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	138	447	0	ENST00000325599.8:c.1733G>T	p.Ter578LeuextTer9	p.*578Lext*9	ENST00000325599	NM_018130.2	578	tGa/tTa	11/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.44	2		447	522	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259557	89259557	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	89	551	0	ENST00000336596.2:c.701C>A	p.Ser234Tyr	p.S234Y	ENST00000336596	NM_005233.5	234	tCt/tAt	3/17	1	2	FACETS	0.928	0.827	1	0.928	0.827	1	CLONAL	1	TRUE	1	0.44	2		551	436	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260151	149260151	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1307297959	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	71	503	0	ENST00000360632.3:c.742C>T	p.Arg248Ter	p.R248*	ENST00000360632	NM_015472.4	248	Cga/Tga	4/7	1	2	FACETS	0.805	0.706	0.911	0.805	0.706	0.911	CLONAL	1	TRUE	1	0.44	2		503	401	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916948	178916948	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	56	437	0	ENST00000263967.3:c.335T>C	p.Ile112Thr	p.I112T	ENST00000263967	NM_006218.2	112	aTc/aCc	2/21	1	2	FACETS	0.758	0.652	0.871	0.758	0.652	0.871	SUBCLONAL	1	TRUE	1	0.44	2		437	336	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	63	502	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	0.78	0.678	0.89	0.78	0.678	0.89	SUBCLONAL	1	TRUE	1	0.44	2		502	367	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502222	186502222	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	104	446	0	ENST00000323963.5:c.31G>T	p.Glu11Ter	p.E11*	ENST00000323963		11	Gaa/Taa	2/11	1	2	FACETS	0.934	0.84	1	0.934	0.84	1	CLONAL	1	TRUE	1	0.44	2		446	506	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455609	189455609	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	109	549	0	ENST00000264731.3:c.143A>C	p.Glu48Ala	p.E48A	ENST00000264731	NM_003722.4	48	gAa/gCa	2/14	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.44	2		549	487	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749415	41749415	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	74	388	0	ENST00000226382.2:c.380C>A	p.Thr127Asn	p.T127N	ENST00000226382	NM_003924.3	127	aCt/aAt	2/3	1	2	FACETS	0.972	0.857	1	0.972	0.857	1	CLONAL	1	TRUE	1	0.44	2		388	346	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129932	55129934	+	missense_variant	Missense_Mutation	TNP	GAG	GAG	AAT	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	104	610	0	ENST00000257290.5:c.466_468delinsAAT	p.Glu156Asn	p.E156N	ENST00000257290	NM_006206.4	156	GAG/AAT	4/23	1	2	FACETS	0.867	0.779	0.96	0.867	0.779	0.96	CLONAL	1	TRUE	1	0.44	2		610	545	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133597	55133597	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	121	544	0	ENST00000257290.5:c.901G>T	p.Glu301Ter	p.E301*	ENST00000257290	NM_006206.4	301	Gaa/Taa	6/23	1	2	FACETS	0.998	0.905	1	0.998	0.905	1	CLONAL	1	TRUE	1	0.44	2		544	551	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592115	55592115	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	99	451	0	ENST00000288135.5:c.1439C>A	p.Ser480Tyr	p.S480Y	ENST00000288135	NM_000222.2	480	tCt/tAt	9/21	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.44	2		451	405	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604643	55604643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745651409	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	130	550	0	ENST00000288135.5:c.2851G>A	p.Val951Ile	p.V951I	ENST00000288135	NM_000222.2	951	Gta/Ata	21/21	1	2	FACETS	0.977	0.889	1	0.977	0.889	1	CLONAL	1	TRUE	1	0.44	2		550	605	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964394	55964394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	98	499	0	ENST00000263923.4:c.2419G>A	p.Asp807Asn	p.D807N	ENST00000263923	NM_002253.2	807	Gat/Aat	17/30	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.44	2		499	425	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976642	55976642	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	86	578	0	ENST00000263923.4:c.1183A>C	p.Asn395His	p.N395H	ENST00000263923	NM_002253.2	395	Aat/Cat	9/30	1	2	FACETS	0.995	0.886	1	0.995	0.886	1	CLONAL	1	TRUE	1	0.44	2		578	393	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796501	57796501	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs749881609	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	119	601	0	ENST00000309042.7:c.1477C>T	p.Arg493Ter	p.R493*	ENST00000309042	NM_005612.4	493	Cga/Tga	4/4	1	2	FACETS	0.966	0.875	1	0.966	0.875	1	CLONAL	1	TRUE	1	0.44	2		601	560	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230870	66230870	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	99	521	0	ENST00000273854.3:c.2101G>T	p.Glu701Ter	p.E701*	ENST00000273854	NM_004439.5	701	Gaa/Taa	12/18	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.44	2		521	449	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231757	66231757	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	54	393	0	ENST00000273854.3:c.1943G>T	p.Arg648Ile	p.R648I	ENST00000273854	NM_004439.5	648	aGa/aTa	11/18	1	2	FACETS	0.772	0.663	0.889	0.772	0.663	0.889	SUBCLONAL	1	TRUE	1	0.44	2		393	318	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144390320	144390320	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757720830	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	130	519	0	ENST00000262995.4:c.2153C>T	p.Thr718Met	p.T718M	ENST00000262995	NM_207123.2	718	aCg/aTg	11/11	1	2	FACETS	0.953	0.867	1	0.953	0.867	1	CLONAL	1	TRUE	1	0.44	2		519	620	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244184	153244184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759610249	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	200	631	0	ENST00000281708.4:c.1973G>A	p.Arg658Gln	p.R658Q	ENST00000281708	NM_033632.3	658	cGa/cAa	12/12	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.44	2		631	765	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251990	153251990	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	96	394	0	ENST00000281708.4:c.1016G>T	p.Arg339Ile	p.R339I	ENST00000281708	NM_033632.3	339	aGa/aTa	7/12	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.44	2		394	384	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332762	153332762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	110	596	0	ENST00000281708.4:c.194G>A	p.Arg65Lys	p.R65K	ENST00000281708	NM_033632.3	65	aGa/aAa	2/12	1	2	FACETS	0.935	0.843	1	0.935	0.843	1	CLONAL	1	TRUE	1	0.44	2		596	535	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584515	187584515	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	93	603	0	ENST00000441802.2:c.3518A>C	p.Lys1173Thr	p.K1173T	ENST00000441802	NM_005245.3	1173	aAg/aCg	3/27	1	2	FACETS	0.896	0.8	0.997	0.896	0.8	0.997	CLONAL	1	TRUE	1	0.44	2		603	472	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584530	187584530	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200633985	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	92	618	0	ENST00000441802.2:c.3503C>T	p.Ser1168Leu	p.S1168L	ENST00000441802	NM_005245.3	1168	tCg/tTg	3/27	1	2	FACETS	0.89	0.794	0.991	0.89	0.794	0.991	CLONAL	1	TRUE	1	0.44	2		618	470	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295845	1295845	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	119	750	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.833	0.754	0.917	0.833	0.754	0.917	CLONAL	1	TRUE	1	0.44	2		750	649	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409261	31409261	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	90	582	0	ENST00000344624.3:c.3756C>A	p.Phe1252Leu	p.F1252L	ENST00000344624		1252	ttC/ttA	30/33	1	2	FACETS	0.934	0.833	1	0.934	0.833	1	CLONAL	1	TRUE	1	0.44	2		582	438	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861079	35861079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769426499	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	91	466	0	ENST00000303115.3:c.208G>A	p.Glu70Lys	p.E70K	ENST00000303115	NM_002185.3	70	Gaa/Aaa	2/8	1	2	FACETS	0.913	0.815	1	0.913	0.815	1	CLONAL	1	TRUE	1	0.44	2		466	453	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947466	38947466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	72	516	0	ENST00000357387.3:c.4214G>A	p.Arg1405Gln	p.R1405Q	ENST00000357387	NM_152756.3	1405	cGa/cAa	32/38	1	2	FACETS	0.768	0.674	0.869	0.768	0.674	0.869	SUBCLONAL	1	TRUE	1	0.44	2		516	426	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670084	86670084	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	82	424	0	ENST00000274376.6:c.1881A>C	p.Lys627Asn	p.K627N	ENST00000274376	NM_002890.2	627	aaA/aaC	14/25	1	2	FACETS	0.966	0.857	1	0.966	0.857	1	CLONAL	1	TRUE	1	0.44	2		424	386	SUCCESS
APC	324	MSKCC	GRCh37	5	112103015	112103015	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1064793535	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	80	512	0	ENST00000257430.4:c.350C>A	p.Ser117Ter	p.S117*	ENST00000257430	NM_000038.5	117	tCa/tAa	4/16	1	2	FACETS	0.9	0.797	1	0.9	0.797	1	CLONAL	1	TRUE	1	0.44	2		512	404	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	94	456	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	0.841	0.751	0.936	0.841	0.751	0.936	CLONAL	1	TRUE	1	0.44	2		456	508	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	156	612	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.44	2		612	702	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818360	170818360	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	39	215	0	ENST00000296930.5:c.190G>A	p.Ala64Thr	p.A64T	ENST00000296930	NM_002520.6	64	Gca/Aca	3/11	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.44	2		215	175	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058713	180058713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777334601	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	95	568	0	ENST00000261937.6:c.124G>A	p.Asp42Asn	p.D42N	ENST00000261937	NM_182925.4	42	Gac/Aac	2/30	1	2	FACETS	0.915	0.818	1	0.915	0.818	1	CLONAL	1	TRUE	1	0.44	2		568	472	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323184	31323184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2308488	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	194	797	1	ENST00000412585.2:c.805G>A	p.Ala269Thr	p.A269T	ENST00000412585	NM_005514.6	269	Gca/Aca	4/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.44	2		798	740	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555167	106555167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747743863	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	134	592	0	ENST00000369096.4:c.2284G>A	p.Val762Met	p.V762M	ENST00000369096	NM_001198.3	762	Gtg/Atg	7/7	1	2	FACETS	0.91	0.829	0.996	0.91	0.829	0.996	CLONAL	1	TRUE	1	0.44	2		592	669	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109315802	109315802	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	79	395	0	ENST00000436639.2:c.983C>A	p.Ser328Tyr	p.S328Y	ENST00000436639	NM_014454.2	328	tCt/tAt	6/10	1	2	FACETS	0.851	0.752	0.956	0.851	0.752	0.956	CLONAL	1	TRUE	1	0.44	2		395	422	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662727	117662727	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	79	516	0	ENST00000368508.3:c.4738G>T	p.Glu1580Ter	p.E1580*	ENST00000368508	NM_002944.2	1580	Gaa/Taa	29/43	1	2	FACETS	0.762	0.673	0.858	0.762	0.673	0.858	SUBCLONAL	1	TRUE	1	0.44	2		516	471	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663635	117663635	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs755903627	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	61	409	0	ENST00000368508.3:c.4597A>C	p.Lys1533Gln	p.K1533Q	ENST00000368508	NM_002944.2	1533	Aaa/Caa	28/43	1	2	FACETS	0.825	0.716	0.942	0.825	0.716	0.942	CLONAL	1	TRUE	1	0.44	2		409	336	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199594	138199594	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	96	538	0	ENST00000237289.4:c.1012G>T	p.Glu338Ter	p.E338*	ENST00000237289	NM_001270507.1	338	Gaa/Taa	7/9	1	2	FACETS	0.873	0.781	0.97	0.873	0.781	0.97	CLONAL	1	TRUE	1	0.44	2		538	500	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005679	150005679	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	148	562	0	ENST00000253339.5:c.546A>C	p.Lys182Asn	p.K182N	ENST00000253339		182	aaA/aaC	3/7	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.44	2		562	592	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150022982	150022982	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	82	491	0	ENST00000253339.5:c.281C>A	p.Ser94Tyr	p.S94Y	ENST00000253339		94	tCt/tAt	1/7	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.44	2		491	350	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265335	152265335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	49	482	0	ENST00000206249.3:c.788G>A	p.Arg263Lys	p.R263K	ENST00000206249	NM_000125.3	263	aGa/aAa	4/8	1	2	FACETS	0.52	0.441	0.607	0.52	0.441	0.607	SUBCLONAL	1	TRUE	1	0.44	2		482	428	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026397	6026397	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	63	244	0	ENST00000265849.7:c.1999G>T	p.Glu667Ter	p.E667*	ENST00000265849	NM_000535.5	667	Gag/Tag	11/15	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.44	2		244	277	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509539	106509539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	111	647	0	ENST00000359195.3:c.1533G>T	p.Glu511Asp	p.E511D	ENST00000359195	NM_002649.2	511	gaG/gaT	2/11	1	2	FACETS	0.906	0.817	0.999	0.906	0.817	0.999	CLONAL	1	TRUE	1	0.44	2		647	557	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124503691	124503691	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	87	337	1	ENST00000357628.3:c.259C>A	p.Gln87Lys	p.Q87K	ENST00000357628	NM_015450.2	87	Caa/Aaa	8/19	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.44	2		338	351	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140500260	140500260	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	119	520	0	ENST00000288602.6:c.882C>A	p.Phe294Leu	p.F294L	ENST00000288602	NM_004333.4	294	ttC/ttA	7/18	1	2	FACETS	0.918	0.831	1	0.918	0.831	1	CLONAL	1	TRUE	1	0.44	2		520	589	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523708	148523708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520183	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	82	495	0	ENST00000320356.2:c.745G>A	p.Glu249Lys	p.E249K	ENST00000320356	NM_004456.4	249	Gaa/Aaa	8/20	1	2	FACETS	0.843	0.747	0.946	0.843	0.747	0.946	CLONAL	1	TRUE	1	0.44	2		495	442	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148544359	148544359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1400051032	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	95	495	0	ENST00000320356.2:c.32G>A	p.Gly11Glu	p.G11E	ENST00000320356	NM_004456.4	11	gGa/gAa	2/20	1	2	FACETS	0.986	0.883	1	0.986	0.883	1	CLONAL	1	TRUE	1	0.44	2		495	438	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879084	151879084	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	103	655	0	ENST00000262189.6:c.5861C>A	p.Ser1954Tyr	p.S1954Y	ENST00000262189	NM_170606.2	1954	tCt/tAt	36/59	1	2	FACETS	0.853	0.766	0.945	0.853	0.766	0.945	CLONAL	1	TRUE	1	0.44	2		655	549	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902278	151902278	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554526666	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	17	122	0	ENST00000262189.6:c.3874C>T	p.Arg1292Ter	p.R1292*	ENST00000262189	NM_170606.2	1292	Cga/Tga	25/59	1	2	FACETS	0.92	0.7	1	0.92	0.7	1	CLONAL	1	TRUE	1	0.44	2		122	84	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187135	38187135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356401338	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	118	620	0	ENST00000317025.8:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000317025	NM_023034.1	448	Cgg/Tgg	6/24	1	2	FACETS	0.891	0.806	0.98	0.891	0.806	0.98	CLONAL	1	TRUE	1	0.44	2		620	602	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69012038	69012038	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	85	449	1	ENST00000288368.4:c.2675G>T	p.Arg892Ile	p.R892I	ENST00000288368	NM_024870.2	892	aGa/aTa	23/40	1	2	FACETS	0.94	0.836	1	0.94	0.836	1	CLONAL	1	TRUE	1	0.44	2		450	411	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964514	70964514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762086448	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	141	659	0	ENST00000276594.2:c.1514G>A	p.Arg505His	p.R505H	ENST00000276594	NM_024504.3	505	cGc/cAc	8/8	1	2	FACETS	0.903	0.824	0.985	0.903	0.824	0.985	CLONAL	1	TRUE	1	0.44	2		659	710	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978540	70978540	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	125	564	0	ENST00000276594.2:c.1113G>T	p.Glu371Asp	p.E371D	ENST00000276594	NM_024504.3	371	gaG/gaT	5/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.44	2		564	488	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141569503	141569503	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	108	504	0	ENST00000220592.5:c.781G>T	p.Glu261Ter	p.E261*	ENST00000220592	NM_012154.3	261	Gaa/Taa	6/19	1	2	FACETS	0.918	0.827	1	0.918	0.827	1	CLONAL	1	TRUE	1	0.44	2		504	535	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2182150	2182150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217286722	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	84	400	0	ENST00000349721.2:c.4369C>T	p.Arg1457Cys	p.R1457C	ENST00000349721	NM_003070.3	1457	Cgt/Tgt	31/34	1	2	FACETS	0.927	0.823	1	0.927	0.823	1	CLONAL	1	TRUE	1	0.44	2		400	412	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054649	5054649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373174105	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	76	500	1	ENST00000381652.3:c.701G>A	p.Arg234His	p.R234H	ENST00000381652	NM_004972.3	234	cGc/cAc	7/25	1	2	FACETS	0.89	0.785	1	0.89	0.785	1	CLONAL	1	TRUE	1	0.44	2		501	388	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404588	8404588	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	62	462	0	ENST00000356435.5:c.4159G>C	p.Ala1387Pro	p.A1387P	ENST00000356435		1387	Gcg/Ccg	25/35	1	2	FACETS	0.867	0.754	0.988	0.867	0.754	0.988	CLONAL	1	TRUE	1	0.44	2		462	325	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636738	8636738	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	119	519	0	ENST00000356435.5:c.171G>A	p.Trp57Ter	p.W57*	ENST00000356435		57	tgG/tgA	2/35	1	2	FACETS	0.872	0.789	0.96	0.872	0.789	0.96	CLONAL	1	TRUE	1	0.44	2		519	620	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239843	98239843	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1398130707	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	73	429	0	ENST00000331920.6:c.1489G>A	p.Ala497Thr	p.A497T	ENST00000331920	NM_000264.3	497	Gct/Act	10/24	1	2	FACETS	0.683	0.599	0.773	0.683	0.599	0.773	SUBCLONAL	1	TRUE	1	0.44	2		429	486	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128432165	128432165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1371596131	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	93	353	0	ENST00000265960.3:c.281G>A	p.Arg94Gln	p.R94Q	ENST00000265960	NM_001006617.1	94	cGa/cAa	3/12	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.44	2		353	396	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20150371	20150371	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	79	160	0	ENST00000379607.5:c.266C>T	p.Ala89Val	p.A89V	ENST00000379607	NM_001412.3	89	gCt/gTt	5/7	0.3	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.44	2		160	149	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916574	39916574	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	95	241	0	ENST00000378444.4:c.4429G>T	p.Glu1477Ter	p.E1477*	ENST00000378444	NM_001123385.1	1477	Gaa/Taa	11/15	0.3	2	FACETS	0.951	0.864	1	0.951	0.864	1	CLONAL	2	TRUE	0	0.44	2		241	227	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344180	70344180	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	116	277	0	ENST00000374080.3:c.1916A>C	p.Asp639Ala	p.D639A	ENST00000374080		639	gAt/gCt	13/45	0.3	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.44	2		277	253	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875930	76875930	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	77	210	0	ENST00000373344.5:c.5205G>T	p.Met1735Ile	p.M1735I	ENST00000373344	NM_000489.3	1735	atG/atT	20/35	0.3	2	FACETS	0.926	0.831	1	0.926	0.831	1	CLONAL	2	TRUE	0	0.44	2		210	189	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220477	123220477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1372684971	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	91	268	0	ENST00000218089.9:c.3134G>A	p.Arg1045Gln	p.R1045Q	ENST00000218089	NM_001042749.1	1045	cGa/cAa	30/35	0.3	2	FACETS	0.907	0.821	0.995	0.907	0.821	0.995	CLONAL	2	TRUE	0	0.44	2		268	228	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968167	68968167	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	72	406	0	ENST00000288368.4:c.1196G>T	p.Arg399Leu	p.R399L	ENST00000288368	NM_024870.2	399	cGa/cTa	10/40	1	2	FACETS	0.777	0.682	0.879	0.777	0.682	0.879	SUBCLONAL	1	TRUE	1	0.44	2		406	421	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9770540	9770540	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	44	547	0	ENST00000377346.4:c.27G>A	p.Met9Ile	p.M9I	ENST00000377346	NM_005026.3	9	atG/atA	3/24	1	2	FACETS	0.376	0.315	0.444	0.376	0.315	0.444	SUBCLONAL	1	TRUE	1	0.44	2		547	532	SUCCESS
MAD2L2	10459	MSKCC	GRCh37	1	11740520	11740520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373974519	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	88	601	0	ENST00000235310.3:c.49G>A	p.Asp17Asn	p.D17N	ENST00000235310		17	Gat/Aat	5/11	1	2	FACETS	0.777	0.69	0.869	0.777	0.69	0.869	SUBCLONAL	1	TRUE	1	0.44	2		601	515	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165933	118165933	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	62	636	0	ENST00000369448.3:c.443A>G	p.Asp148Gly	p.D148G	ENST00000369448	NM_017709.3	148	gAc/gGc	2/2	1	2	FACETS	0.418	0.36	0.48	0.418	0.36	0.48	SUBCLONAL	1	TRUE	1	0.44	2		636	675	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506323	120506323	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	108	550	0	ENST00000256646.2:c.1789C>A	p.Pro597Thr	p.P597T	ENST00000256646	NM_024408.3	597	Ccc/Acc	11/34	1	2	FACETS	0.877	0.789	0.969	0.877	0.789	0.969	CLONAL	1	TRUE	1	0.44	2		550	560	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150934607	150934607	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	42	261	0	ENST00000271640.5:c.3131A>C	p.Asp1044Ala	p.D1044A	ENST00000271640	NM_001145415.1	1044	gAc/gCc	17/22	1	2	FACETS	0.718	0.603	0.843	0.718	0.603	0.843	SUBCLONAL	1	TRUE	1	0.44	2		261	266	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104352477	104352477	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	81	478	0	ENST00000369902.3:c.593T>C	p.Leu198Pro	p.L198P	ENST00000369902	NM_016169.3	198	cTc/cCc	4/12	1	2	FACETS	0.788	0.697	0.886	0.788	0.697	0.886	SUBCLONAL	1	TRUE	1	0.44	2		478	467	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933393	100933393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	96	484	0	ENST00000325455.5:c.1997G>A	p.Ser666Asn	p.S666N	ENST00000325455	NM_001202474.3	666	aGc/aAc	4/8	1	2	FACETS	0.844	0.755	0.939	0.844	0.755	0.939	CLONAL	1	TRUE	1	0.44	2		484	517	SUCCESS
CBL	867	MSKCC	GRCh37	11	119146807	119146807	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	35	523	0	ENST00000264033.4:c.970C>A	p.Leu324Ile	p.L324I	ENST00000264033	NM_005188.3	324	Ctc/Atc	6/16	1	2	FACETS	0.349	0.286	0.42	0.349	0.286	0.42	SUBCLONAL	1	TRUE	1	0.44	2		523	456	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864937	57864937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376640247	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	111	660	0	ENST00000228682.2:c.2414G>A	p.Arg805Gln	p.R805Q	ENST00000228682	NM_005269.2	805	cGa/cAa	12/12	1	2	FACETS	0.87	0.784	0.96	0.87	0.784	0.96	CLONAL	1	TRUE	1	0.44	2		660	580	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123892115	123892115	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	14	104	0	ENST00000330479.4:c.924A>C	p.Lys308Asn	p.K308N	ENST00000330479	NM_020382.3	308	aaA/aaC	8/9	1	2	FACETS	0.786	0.578	1	0.786	0.578	1	CLONAL	1	TRUE	1	0.44	2		104	81	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28885789	28885789	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	73	468	0	ENST00000282397.4:c.3573G>T	p.Glu1191Asp	p.E1191D	ENST00000282397	NM_002019.4	1191	gaG/gaT	27/30	1	2	FACETS	0.846	0.744	0.955	0.846	0.744	0.955	CLONAL	1	TRUE	1	0.44	2		468	392	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964146	28964146	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	85	507	0	ENST00000282397.4:c.1756G>T	p.Asp586Tyr	p.D586Y	ENST00000282397	NM_002019.4	586	Gac/Tac	13/30	1	2	FACETS	0.936	0.832	1	0.936	0.832	1	CLONAL	1	TRUE	1	0.44	2		507	413	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28979923	28979923	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	49	317	0	ENST00000282397.4:c.1545G>T	p.Lys515Asn	p.K515N	ENST00000282397	NM_002019.4	515	aaG/aaT	11/30	1	2	FACETS	0.725	0.618	0.842	0.725	0.618	0.842	SUBCLONAL	1	TRUE	1	0.44	2		317	307	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911316	32911316	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	27	578	0	ENST00000380152.3:c.2824T>C	p.Ser942Pro	p.S942P	ENST00000380152		942	Tca/Cca	11/27	1	2	FACETS	0.254	0.201	0.314	0.254	0.201	0.314	SUBCLONAL	1	TRUE	1	0.44	2		578	483	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103513878	103513878	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	54	441	0	ENST00000355739.4:c.694T>C	p.Tyr232His	p.Y232H	ENST00000355739	NM_000123.3	232	Tac/Cac	7/15	1	2	FACETS	0.641	0.549	0.74	0.641	0.549	0.74	SUBCLONAL	1	TRUE	1	0.44	2		441	383	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43699658	43699658	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	74	645	0	ENST00000382044.4:c.5857A>C	p.Ile1953Leu	p.I1953L	ENST00000382044	NM_001141980.1	1953	Atc/Ctc	28/28	1	2	FACETS	0.439	0.383	0.498	0.439	0.383	0.498	SUBCLONAL	1	TRUE	1	0.44	2		645	767	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396728	396728	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	54	621	0	ENST00000262320.3:c.298A>C	p.Ser100Arg	p.S100R	ENST00000262320	NM_003502.3	100	Agc/Cgc	2/11	0.128291962846545	3	FACETS	0.519	0.443	0.602	0.259	0.221	0.301	INDETERMINATE	1	TRUE	1	0.44	3		621	577	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220615	2220615	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	95	552	0	ENST00000326181.6:c.232C>A	p.Pro78Thr	p.P78T	ENST00000326181	NM_032271.2	78	Ccc/Acc	5/21	0.128291962846545	3	FACETS	1	0.963	1	0.585	0.524	0.65	INDETERMINATE	1	TRUE	1	0.44	3		552	450	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779345	3779345	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	88	637	0	ENST00000262367.5:c.5703G>T	p.Gln1901His	p.Q1901H	ENST00000262367	NM_004380.2	1901	caG/caT	31/31	0.128291962846545	3	FACETS	0.988	0.878	1	0.494	0.439	0.552	INDETERMINATE	1	TRUE	1	0.44	3		637	494	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029246	14029246	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	91	568	0	ENST00000311895.7:c.1457A>C	p.Lys486Thr	p.K486T	ENST00000311895	NM_005236.2	486	aAa/aCa	8/11	0.128291962846545	3	FACETS	0.748	0.664	0.837	0.374	0.332	0.419	INDETERMINATE	1	TRUE	1	0.44	3		568	675	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644861	67644861	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	152	626	0	ENST00000264010.4:c.126G>T	p.Gln42His	p.Q42H	ENST00000264010	NM_006565.3	42	caG/caT	3/12	0.128291962846545	3	FACETS	1	0.976	1	0.586	0.537	0.637	INDETERMINATE	1	TRUE	1	0.44	3		626	719	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40457662	40457662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	92	445	0	ENST00000345506.4:c.1415G>T	p.Gly472Val	p.G472V	ENST00000345506	NM_003152.3	472	gGc/gTc	13/20	1	2	FACETS	0.859	0.766	0.957	0.859	0.766	0.957	CLONAL	1	TRUE	1	0.44	2		445	487	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573489	48573489	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	76	617	0	ENST00000342988.3:c.73T>C	p.Cys25Arg	p.C25R	ENST00000342988	NM_005359.5	25	Tgc/Cgc	2/12	1	2	FACETS	0.721	0.634	0.814	0.721	0.634	0.814	SUBCLONAL	1	TRUE	1	0.44	2		617	479	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273524	5273524	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	117	559	0	ENST00000357368.4:c.308A>G	p.Asn103Ser	p.N103S	ENST00000357368	NM_002850.3	103	aAc/aGc	4/38	0.128291962846545	3	FACETS	1	0.922	1	0.512	0.462	0.564	INDETERMINATE	1	TRUE	1	0.44	3		559	634	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170551	7170551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	89	487	0	ENST00000302850.5:c.1480T>C	p.Ser494Pro	p.S494P	ENST00000302850	NM_000208.2	494	Tcc/Ccc	6/22	0.128291962846545	3	FACETS	1	0.896	1	0.504	0.448	0.563	INDETERMINATE	1	TRUE	1	0.44	3		487	490	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416322	29416322	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	133	672	0	ENST00000389048.3:c.4631A>G	p.Asn1544Ser	p.N1544S	ENST00000389048	NM_004304.4	1544	aAc/aGc	29/29	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.44	2		672	600	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705627	47705627	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	83	478	0	ENST00000233146.2:c.2427G>T	p.Glu809Asp	p.E809D	ENST00000233146	NM_000251.2	809	gaG/gaT	14/16	1	2	FACETS	0.938	0.833	1	0.938	0.833	1	CLONAL	1	TRUE	1	0.44	2		478	402	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719218	61719218	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	87	485	0	ENST00000401558.2:c.1839A>C	p.Glu613Asp	p.E613D	ENST00000401558	NM_003400.3	613	gaA/gaC	16/25	1	2	FACETS	0.901	0.801	1	0.901	0.801	1	CLONAL	1	TRUE	1	0.44	2		485	439	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67632122	67632122	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1558581846	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	45	536	0	ENST00000272342.5:c.2308C>A	p.Leu770Ile	p.L770I	ENST00000272342	NM_019002.3	770	Ctt/Att	5/6	1	2	FACETS	0.673	0.568	0.787	0.673	0.568	0.787	SUBCLONAL	1	TRUE	1	0.44	2		536	304	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368508	225368508	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199469656	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	76	455	0	ENST00000264414.4:c.1238A>G	p.Asp413Gly	p.D413G	ENST00000264414	NM_003590.4	413	gAt/gGt	9/16	1	2	FACETS	0.897	0.792	1	0.897	0.792	1	CLONAL	1	TRUE	1	0.44	2		455	385	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661066	227661066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs980309168	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	90	674	0	ENST00000305123.5:c.2389C>T	p.Arg797Cys	p.R797C	ENST00000305123	NM_005544.2	797	Cgc/Tgc	1/2	1	2	FACETS	0.865	0.771	0.965	0.865	0.771	0.965	CLONAL	1	TRUE	1	0.44	2		674	473	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41818342	41818342	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	78	708	0	ENST00000373198.4:c.32T>C	p.Leu11Pro	p.L11P	ENST00000373198	NM_133170.3	11	cTg/cCg	1/32	1	2	FACETS	0.884	0.781	0.994	0.884	0.781	0.994	CLONAL	1	TRUE	1	0.44	2		708	401	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155492	47155492	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	79	441	0	ENST00000409792.3:c.4589C>A	p.Ser1530Tyr	p.S1530Y	ENST00000409792	NM_014159.6	1530	tCt/tAt	5/21	1	2	FACETS	0.833	0.736	0.936	0.833	0.736	0.936	CLONAL	1	TRUE	1	0.44	2		441	431	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259312	89259312	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	38	583	0	ENST00000336596.2:c.456C>A	p.Phe152Leu	p.F152L	ENST00000336596	NM_005233.5	152	ttC/ttA	3/17	1	2	FACETS	0.352	0.29	0.42	0.352	0.29	0.42	SUBCLONAL	1	TRUE	1	0.44	2		583	491	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170016853	170016853	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	59	365	0	ENST00000295797.4:c.1658A>C	p.Asp553Ala	p.D553A	ENST00000295797	NM_002740.5	553	gAt/gCt	17/18	1	2	FACETS	0.733	0.633	0.84	0.733	0.633	0.84	SUBCLONAL	1	TRUE	1	0.44	2		365	366	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1919892	1919892	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	81	478	0	ENST00000382891.5:c.952T>G	p.Leu318Val	p.L318V	ENST00000382891	NM_133335.3	318	Ttg/Gtg	5/22	1	2	FACETS	0.809	0.716	0.909	0.809	0.716	0.909	CLONAL	1	TRUE	1	0.44	2		478	455	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920318	1920318	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	99	519	0	ENST00000382891.5:c.1378T>C	p.Phe460Leu	p.F460L	ENST00000382891	NM_133335.3	460	Ttt/Ctt	5/22	1	2	FACETS	0.833	0.746	0.925	0.833	0.746	0.925	CLONAL	1	TRUE	1	0.44	2		519	540	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968115	55968115	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	88	420	0	ENST00000263923.4:c.2215G>T	p.Ala739Ser	p.A739S	ENST00000263923	NM_002253.2	739	Gca/Tca	15/30	1	2	FACETS	0.871	0.775	0.973	0.871	0.775	0.973	CLONAL	1	TRUE	1	0.44	2		420	459	SUCCESS
ALB	213	MSKCC	GRCh37	4	74270072	74270072	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	80	426	0	ENST00000295897.4:c.28C>A	p.Leu10Ile	p.L10I	ENST00000295897	NM_000477.5	10	Ctt/Att	1/15	1	2	FACETS	0.787	0.695	0.885	0.787	0.695	0.885	SUBCLONAL	1	TRUE	1	0.44	2		426	462	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518861	187518861	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1192074001	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	53	515	0	ENST00000441802.2:c.12343T>C	p.Cys4115Arg	p.C4115R	ENST00000441802	NM_005245.3	4115	Tgt/Cgt	24/27	1	2	FACETS	0.457	0.39	0.531	0.457	0.39	0.531	SUBCLONAL	1	TRUE	1	0.44	2		515	527	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524449	187524449	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	34	559	0	ENST00000441802.2:c.11231C>A	p.Pro3744His	p.P3744H	ENST00000441802	NM_005245.3	3744	cCc/cAc	19/27	1	2	FACETS	0.238	0.194	0.289	0.238	0.194	0.289	SUBCLONAL	1	TRUE	1	0.44	2		559	648	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557388	187557388	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	90	521	0	ENST00000441802.2:c.3974T>C	p.Ile1325Thr	p.I1325T	ENST00000441802	NM_005245.3	1325	aTt/aCt	6/27	1	2	FACETS	0.865	0.771	0.965	0.865	0.771	0.965	CLONAL	1	TRUE	1	0.44	2		521	473	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627960	187627960	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	116	561	0	ENST00000441802.2:c.3022A>G	p.Lys1008Glu	p.K1008E	ENST00000441802	NM_005245.3	1008	Aag/Gag	2/27	1	2	FACETS	0.855	0.772	0.941	0.855	0.772	0.941	CLONAL	1	TRUE	1	0.44	2		561	617	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064665	80064665	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	73	489	0	ENST00000265081.6:c.2096A>C	p.Lys699Thr	p.K699T	ENST00000265081	NM_002439.4	699	aAa/aCa	15/24	1	2	FACETS	0.882	0.776	0.996	0.882	0.776	0.996	CLONAL	1	TRUE	1	0.44	2		489	376	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158768	26158768	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	63	459	0	ENST00000289316.2:c.371G>T	p.Ser124Ile	p.S124I	ENST00000289316	NM_138720.2	124	aGt/aTt	1/2	1	2	FACETS	0.654	0.567	0.747	0.654	0.567	0.747	SUBCLONAL	1	TRUE	1	0.44	2		459	438	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797743	32797743	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	50	603	0	ENST00000374899.4:c.1759G>T	p.Asp587Tyr	p.D587Y	ENST00000374899	NM_018833.2	587	Gac/Tac	10/12	1	2	FACETS	0.356	0.302	0.416	0.356	0.302	0.416	SUBCLONAL	1	TRUE	1	0.44	2		603	638	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117650542	117650542	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	107	708	1	ENST00000368508.3:c.5316G>T	p.Glu1772Asp	p.E1772D	ENST00000368508	NM_002944.2	1772	gaG/gaT	32/43	1	2	FACETS	0.85	0.765	0.94	0.85	0.765	0.94	CLONAL	1	TRUE	1	0.44	2		709	572	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538871	23538871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	98	485	0	ENST00000380871.4:c.568G>A	p.Asp190Asn	p.D190N	ENST00000380871	NM_006167.3	190	Gac/Aac	2/2	1	2	FACETS	0.875	0.784	0.972	0.875	0.784	0.972	CLONAL	1	TRUE	1	0.44	2		485	509	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540392	23540392	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	51	471	0	ENST00000380871.4:c.11T>C	p.Val4Ala	p.V4A	ENST00000380871	NM_006167.3	4	gTt/gCt	1/2	1	2	FACETS	0.768	0.656	0.888	0.768	0.656	0.888	SUBCLONAL	1	TRUE	1	0.44	2		471	302	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028011	69028011	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	72	490	0	ENST00000288368.4:c.3170C>A	p.Ser1057Tyr	p.S1057Y	ENST00000288368	NM_024870.2	1057	tCt/tAt	26/40	1	2	FACETS	0.946	0.832	1	0.946	0.832	1	CLONAL	1	TRUE	1	0.44	2		490	346	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70971046	70971046	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	92	496	0	ENST00000276594.2:c.1215T>G	p.Cys405Trp	p.C405W	ENST00000276594	NM_024504.3	405	tgT/tgG	6/8	1	2	FACETS	0.859	0.766	0.957	0.859	0.766	0.957	CLONAL	1	TRUE	1	0.44	2		496	487	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072575	5072575	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	78	459	0	ENST00000381652.3:c.1725A>C	p.Glu575Asp	p.E575D	ENST00000381652	NM_004972.3	575	gaA/gaC	13/25	1	2	FACETS	0.813	0.718	0.915	0.813	0.718	0.915	CLONAL	1	TRUE	1	0.44	2		459	436	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537142	80537142	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	29	399	0	ENST00000286548.4:c.256G>T	p.Ala86Ser	p.A86S	ENST00000286548	NM_002072.3	86	Gcc/Tcc	2/7	1	2	FACETS	0.379	0.304	0.464	0.379	0.304	0.464	SUBCLONAL	1	TRUE	1	0.44	2		399	348	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248093	98248093	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	112	507	0	ENST00000331920.6:c.458T>G	p.Phe153Cys	p.F153C	ENST00000331920	NM_000264.3	153	tTt/tGt	3/24	1	2	FACETS	0.952	0.859	1	0.952	0.859	1	CLONAL	1	TRUE	1	0.44	2		507	535	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325338	1325338	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	70	506	0	ENST00000400841.2:c.337A>G	p.Met113Val	p.M113V	ENST00000400841		113	Atg/Gtg	3/6	0.3	2	FACETS	0.678	0.593	0.77	0.339	0.296	0.385	SUBCLONAL	1	TRUE	0	0.44	2		506	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0067001-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	15	381	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	0.256	0.186	0.341	0.256	0.186	0.341	SUBCLONAL	1	TRUE	1	0.16	2		381	733	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579349	7579349	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1567555667	NA	P-0067001-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	27	534	0	ENST00000269305.4:c.338T>G	p.Phe113Cys	p.F113C	ENST00000269305	NM_001126112.2	113	tTc/tGc	4/11	1	2	FACETS	0.427	0.338	0.53	0.427	0.338	0.53	SUBCLONAL	1	TRUE	1	0.16	2		534	790	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729094	66729099	+	inframe_deletion	In_Frame_Del	DEL	TGGAGA	TGGAGA	-	novel	NA	P-0067001-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	71	495	0	ENST00000307102.5:c.303_308del	p.Glu102_Ile103del	p.E102_I103del	ENST00000307102	NM_002755.3	101	cTGGAGAtc/ctc	3/11	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.16	2		495	797	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878916	151878916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067001-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	43	505	0	ENST00000262189.6:c.6029C>T	p.Pro2010Leu	p.P2010L	ENST00000262189	NM_170606.2	2010	cCa/cTa	36/59	1	2	FACETS	0.673	0.561	0.797	0.673	0.561	0.797	SUBCLONAL	1	TRUE	1	0.16	2		505	799	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546107	29546108	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067001-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	63	459	0	ENST00000356175.3:c.1613dup	p.Met538IlefsTer20	p.M538Ifs*20	ENST00000356175	NM_000267.3	538	atg/aTtg	14/57	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.16	2		459	741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0067009-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	27	433	10	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.638207038103411	1	FACETS	0.797	0.698	0.885	1	0.963	1	SUBCLONAL	2	TRUE	0	0.62780175232012	1		443	37	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827951	40827951	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067009-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	16	512	7	ENST00000373198.4:c.2477C>G	p.Pro826Arg	p.P826R	ENST00000373198	NM_133170.3	826	cCc/cGc	17/32	0.358225446086782	1	FACETS	0.564	0.429	0.715	0.564	0.429	0.715	INDETERMINATE	1	TRUE	0	0.62780175232012	1		519	62	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878233	151878233	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067009-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	11	523	5	ENST00000262189.6:c.6712A>C	p.Met2238Leu	p.M2238L	ENST00000262189	NM_170606.2	2238	Atg/Ctg	36/59	0.638207038103411	0	FACETS	0.466	0.342	0.598			1	SUBCLONAL	1	TRUE	0	0.62780175232012	0		528	28	SUCCESS
ALB	213	MSKCC	GRCh37	4	74274486	74274486	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067009-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	13	397	6	ENST00000295897.4:c.446C>A	p.Thr149Asn	p.T149N	ENST00000295897	NM_000477.5	149	aCt/aAt	4/15	0.222988797784784	2	FACETS	0.781	0.574	1	0.391	0.287	0.508	INDETERMINATE	1	TRUE	0	0.62780175232012	2		403	53	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	12	474	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	0.274349470928286	3	FACETS	0.148	0.103	0.204	0.074	0.051	0.102	SUBCLONAL	1	TRUE	1	0.338253809607338	3		474	559	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0067075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	158	444	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.274349470928286	3	FACETS	0.96	0.884	1	0.96	0.884	1	CLONAL	2	TRUE	1	0.338253809607338	3		444	569	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709505	176709505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	32	393	0	ENST00000439151.2:c.5932G>A	p.Glu1978Lys	p.E1978K	ENST00000439151	NM_022455.4	1978	Gaa/Aaa	19/23	1	2	FACETS	0.394	0.319	0.479	0.394	0.319	0.479	SUBCLONAL	1	TRUE	1	0.338253809607338	2		393	480	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	68	488	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.338253809607338	1	FACETS	0.741	0.646	0.842	0.741	0.646	0.842	SUBCLONAL	1	TRUE	0	0.338253809607338	1		488	451	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879331	151879331	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1563292120	NA	P-0067075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	75	580	0	ENST00000262189.6:c.5614C>T	p.Gln1872Ter	p.Q1872*	ENST00000262189	NM_170606.2	1872	Cag/Tag	36/59	1	2	FACETS	0.555	0.485	0.63	0.555	0.485	0.63	SUBCLONAL	1	TRUE	1	0.338253809607338	2		580	799	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273033	115273033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1230709037	NA	P-0067075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	59	510	0	ENST00000438362.2:c.1340C>T	p.Ser447Phe	p.S447F	ENST00000438362	NM_001242891.1	447	tCt/tTt	12/20	1	2	FACETS	0.645	0.555	0.743	0.645	0.555	0.743	SUBCLONAL	1	TRUE	1	0.338253809607338	2		510	541	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207729	29207729	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	73	589	0	ENST00000240100.2:c.67G>C	p.Glu23Gln	p.E23Q	ENST00000240100	NM_001394.6	23	Gag/Cag	1/4	1	2	FACETS	0.582	0.508	0.661	0.582	0.508	0.661	SUBCLONAL	1	TRUE	1	0.338253809607338	2		589	742	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293529	137293529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	81	644	0	ENST00000481739.1:c.80C>T	p.Ser27Phe	p.S27F	ENST00000481739	NM_002957.4	27	tCc/tTc	2/10	1	2	FACETS	0.614	0.54	0.693	0.614	0.54	0.693	SUBCLONAL	1	TRUE	1	0.338253809607338	2		644	780	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884822	151884822	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	28	464	0	ENST00000262189.6:c.4771C>T	p.Gln1591Ter	p.Q1591*	ENST00000262189	NM_170606.2	1591	Caa/Taa	32/59	1	2	FACETS	0.313	0.249	0.386	0.313	0.249	0.386	SUBCLONAL	1	TRUE	1	0.338253809607338	2		464	529	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872841	37872841	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	105	593	0	ENST00000269571.5:c.1720G>T	p.Val574Leu	p.V574L	ENST00000269571		574	Gtg/Ttg	14/27	1	2	FACETS	0.855	0.766	0.949	0.855	0.766	0.949	CLONAL	1	TRUE	1	0.338253809607338	2		593	726	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973266	25973266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	55	530	0	ENST00000435504.4:c.1159G>A	p.Glu387Lys	p.E387K	ENST00000435504		387	Gaa/Aaa	12/13	1	2	FACETS	0.575	0.491	0.666	0.575	0.491	0.666	SUBCLONAL	1	TRUE	1	0.338253809607338	2		530	566	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913315	NA	P-0067125-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	103	483	0	ENST00000326873.7:c.580G>A	p.Asp194Asn	p.D194N	ENST00000326873	NM_000455.4	194	Gac/Aac	4/10	0.255382278172845	1	FACETS	0.977	0.875	1	0.977	0.875	1	CLONAL	1	TRUE	0	0.255382278172845	1		483	720	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819648	81819648	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067125-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	95	391	0	ENST00000359376.3:c.54C>G	p.Ile18Met	p.I18M	ENST00000359376	NM_002661.3	18	atC/atG	2/33	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.255382278172845	2		391	741	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288339	21288339	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067125-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	123	419	0	ENST00000354336.3:c.584C>T	p.Ser195Phe	p.S195F	ENST00000354336	NM_005207.3	195	tCc/tTc	2/3	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.255382278172845	2		419	855	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0067331-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	40	331	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		331	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578440	7578440	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0067331-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	33	397	0	ENST00000269305.4:c.490A>T	p.Lys164Ter	p.K164*	ENST00000269305	NM_001126112.2	164	Aag/Tag	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		397	468	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354292	15354292	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067331-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	20	248	0	ENST00000263377.2:c.2588A>G	p.His863Arg	p.H863R	ENST00000263377	NM_058243.2	863	cAc/cGc	14/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		248	297	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220426	1220427	+	missense_variant	Missense_Mutation	DNP	GC	GC	TG	novel	NA	P-0067331-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	28	407	0	ENST00000326873.7:c.519_520delinsTG	p.His174Asp	p.H174D	ENST00000326873	NM_000455.4	173	gtGCac/gtTGac	4/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		407	382	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459981	99459981	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067331-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	23	273	0	ENST00000268035.6:c.2077G>T	p.Gly693Cys	p.G693C	ENST00000268035	NM_000875.3	693	Ggt/Tgt	10/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		273	418	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0067362-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	42	321	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	0.67	0.559	0.793	0.67	0.559	0.793	SUBCLONAL	1	TRUE	1	0.248201489560012	2		321	505	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100436	8100436	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067362-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	62	531	0	ENST00000346208.3:c.410C>G	p.Ser137Trp	p.S137W	ENST00000346208		137	tCg/tGg	3/6	1	2	FACETS	0.759	0.655	0.872	0.759	0.655	0.872	SUBCLONAL	1	TRUE	1	0.248201489560012	2		531	658	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372699	81372699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756224070	NA	P-0067510-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	104	258	0	ENST00000222390.5:c.835C>T	p.Arg279Cys	p.R279C	ENST00000222390	NM_000601.4	279	Cgc/Tgc	7/18	0.74709002746963	4	FACETS	1	0.951	1	0.545	0.491	0.602	CLONAL	1	TRUE	2	0.74709002746963	4		258	446	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098806	178098806	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067510-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	85	322	0	ENST00000397062.3:c.239C>T	p.Thr80Ile	p.T80I	ENST00000397062	NM_006164.4	80	aCa/aTa	2/5	1	2	FACETS	0.952	0.856	1	0.952	0.856	1	CLONAL	1	TRUE	1	0.74709002746963	2		322	239	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349989	89349989	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067510-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	159	502	0	ENST00000301030.4:c.2961C>G	p.Asp987Glu	p.D987E	ENST00000301030	NM_001256183.1	987	gaC/gaG	9/13	1	2	FACETS	0.967	0.896	1	0.967	0.896	1	CLONAL	1	TRUE	1	0.74709002746963	2		502	440	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132583	11132583	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067510-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	145	393	0	ENST00000358026.2:c.2799C>G	p.Phe933Leu	p.F933L	ENST00000358026	NM_001128849.1	933	ttC/ttG	19/36	0.106847425413157	4	FACETS	0.989	0.915	1	0.989	0.915	1	INDETERMINATE	2	TRUE	2	0.74709002746963	4		393	343	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74858968	74858968	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	40	164	0	ENST00000284811.8:c.236A>G	p.Tyr79Cys	p.Y79C	ENST00000284811		79	tAc/tGc	4/4	0.489163991992324	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		164	119	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906457	50906457	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	62	449	0	ENST00000440232.2:c.1118A>T	p.Lys373Met	p.K373M	ENST00000440232	NM_002691.3	373	aAg/aTg	9/27	0.115152199659727	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		449	219	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0067654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	174	381	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.718871356877524	1	FACETS	0.917	0.86	0.975	0.917	0.86	0.975	CLONAL	1	TRUE	0	0.718871356877524	1		381	338	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575219	48575219	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	81	192	0	ENST00000342988.3:c.413C>A	p.Ser138Ter	p.S138*	ENST00000342988	NM_005359.5	138	tCa/tAa	3/12	0.718871356877524	1	FACETS	0.864	0.783	0.946	0.864	0.783	0.946	CLONAL	1	TRUE	0	0.718871356877524	1		192	167	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271304	26271329	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCACCAAGTAGGCCTCGCAGGCCT	CCCCACCAAGTAGGCCTCGCAGGCCT	-	novel	NA	P-0067654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	246	439	0	ENST00000305910.3:c.284_309del	p.Glu95AlafsTer3	p.E95Afs*3	ENST00000305910	NM_003534.2	95	gAGGCCTGCGAGGCCTACTTGGTGGGG/g	1/1	0.706425063688964	2	FACETS	0.901	0.845	0.957	0.45	0.422	0.479	CLONAL	1	TRUE	0	0.718871356877524	2		439	760	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936149	71936149	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	178	213	0	ENST00000298229.2:c.121G>A	p.Asp41Asn	p.D41N	ENST00000298229	NM_001567.3	41	Gat/Aat	1/28	0.718871356877524	3	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.718871356877524	3		213	599	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730361	133730361	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	362	320	0	ENST00000318560.5:c.427A>T	p.Ser143Cys	p.S143C	ENST00000318560	NM_005157.4	143	Agc/Tgc	3/11	0.718871356877524	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.718871356877524	3		320	681	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058454	42058454	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	179	336	0	ENST00000219905.7:c.8174C>G	p.Ser2725Cys	p.S2725C	ENST00000219905	NM_001164273.1	2725	tCt/tGt	24/24	1	2	FACETS	0.988	0.919	1	0.988	0.919	1	CLONAL	1	TRUE	1	0.718871356877524	2		336	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573976	7573976	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0067776-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	183	304	0	ENST00000269305.4:c.1051A>T	p.Lys351Ter	p.K351*	ENST00000269305	NM_001126112.2	351	Aag/Tag	10/11	0.52207458640731	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.52207458640731	2		304	346	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71064758	71064758	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067776-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	196	308	0	ENST00000318789.4:c.916G>T	p.Gly306Cys	p.G306C	ENST00000318789	NM_032682.5	306	Ggt/Tgt	12/21	0.499868075702246	2	FACETS	0.97	0.912	1	0.97	0.912	1	CLONAL	2	TRUE	0	0.52207458640731	2		308	387	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120509094	120509094	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067776-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	65	312	0	ENST00000256646.2:c.1472G>T	p.Cys491Phe	p.C491F	ENST00000256646	NM_024408.3	491	tGt/tTt	9/34	0.455573471681946	3	FACETS	0.789	0.687	0.899	0.394	0.343	0.45	SUBCLONAL	1	TRUE	1	0.52207458640731	3		312	398	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38991105	38991105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777554944	NA	P-0067776-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	54	267	0	ENST00000357387.3:c.529C>T	p.Leu177Phe	p.L177F	ENST00000357387	NM_152756.3	177	Ctt/Ttt	7/38	0.52207458640731	5	FACETS	0.665	0.568	0.771	0.222	0.189	0.257	SUBCLONAL	1	TRUE	2	0.52207458640731	5		267	555	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281736	142281736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067776-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	86	321	0	ENST00000350721.4:c.508G>A	p.Glu170Lys	p.E170K	ENST00000350721	NM_001184.3	170	Gaa/Aaa	4/47	0.402893607283831	5	FACETS	1	0.934	1	0.359	0.318	0.402	CLONAL	1	TRUE	2	0.52207458640731	5		321	546	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210791	36210791	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067776-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	102	489	0	ENST00000222270.7:c.545del	p.Gly182ValfsTer12	p.G182Vfs*12	ENST00000222270	NM_014727.1	181	cGg/cg	3/37	0.47060413050783	4	FACETS	0.842	0.754	0.936	0.281	0.251	0.312	CLONAL	1	TRUE	1	0.52207458640731	4		489	706	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410015	139410015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067776-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	398	461	0	ENST00000277541.6:c.1823C>T	p.Ser608Phe	p.S608F	ENST00000277541	NM_017617.3	608	tCc/tTc	11/34	0.45851955882685	5	FACETS	1	0.993	1	0.89	0.858	0.921	CLONAL	4	TRUE	0	0.52207458640731	5		461	611	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860134	57860134	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067776-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	95	354	0	ENST00000228682.2:c.874A>T	p.Met292Leu	p.M292L	ENST00000228682	NM_005269.2	292	Atg/Ttg	8/12	0.445762930894144	3	FACETS	1	0.916	1	0.513	0.459	0.57	CLONAL	1	TRUE	1	0.52207458640731	3		354	447	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187188	38187188	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067776-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1317	106	371	0	ENST00000317025.8:c.1289C>T	p.Pro430Leu	p.P430L	ENST00000317025	NM_023034.1	430	cCa/cTa	6/24	0.52207458640731	12	FACETS	1	0.916	1			1	CLONAL	1	TRUE	NA	0.52207458640731	12		371	1423	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1940226	1940226	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067776-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	41	201	0	ENST00000382891.5:c.1723A>G	p.Met575Val	p.M575V	ENST00000382891	NM_133335.3	575	Atg/Gtg	8/22	0.502488507934866	2	FACETS	0.614	0.514	0.722	0.307	0.257	0.361	SUBCLONAL	1	TRUE	0	0.52207458640731	2		201	256	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	13	382	0				ENST00000310581	NM_198253.2	-/1132			0.157482502661352	0	FACETS	0.4	0.288	0.534			1	INDETERMINATE	1	TRUE	0	0.379906683380574	0		382	106	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	82	292	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.379906683380574	2		292	343	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	57	335	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.379906683380574	2		335	243	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	148	251	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.379906683380574	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	1	0.379906683380574	3		251	444	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971116	21971116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552823	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	61	361	0	ENST00000304494.5:c.242C>T	p.Pro81Leu	p.P81L	ENST00000304494	NM_000077.4	81	cCc/cTc	2/3	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.379906683380574	2		361	258	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	14	284	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	1	2	FACETS	0.221	0.159	0.296	0.221	0.159	0.296	SUBCLONAL	1	TRUE	1	0.379906683380574	2		284	334	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259388	89259388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	78	411	0	ENST00000336596.2:c.532G>A	p.Gly178Arg	p.G178R	ENST00000336596	NM_005233.5	178	Gga/Aga	3/17	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.379906683380574	2		411	299	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579395	7579395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	87	448	0	ENST00000269305.4:c.292C>T	p.Pro98Ser	p.P98S	ENST00000269305	NM_001126112.2	98	Cct/Tct	4/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.379906683380574	2		448	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781371	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	89	433	0	ENST00000269305.4:c.328C>T	p.Arg110Cys	p.R110C	ENST00000269305	NM_001126112.2	110	Cgt/Tgt	4/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.379906683380574	2		433	345	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430562	80430562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	42	156	0	ENST00000286548.4:c.446G>A	p.Arg149Gln	p.R149Q	ENST00000286548	NM_002072.3	149	cGa/cAa	3/7	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.379906683380574	2		156	170	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814824	139814824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755691522	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	60	417	0	ENST00000247668.2:c.817G>A	p.Glu273Lys	p.E273K	ENST00000247668	NM_021138.3	273	Gag/Aag	8/11	1	2	FACETS	0.921	0.798	1	0.921	0.798	1	CLONAL	1	TRUE	1	0.379906683380574	2		417	343	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335633	81335633	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	69	372	0	ENST00000222390.5:c.1727G>A	p.Gly576Glu	p.G576E	ENST00000222390	NM_000601.4	576	gGa/gAa	15/18	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.379906683380574	2		372	311	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381466	81381466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	66	271	0	ENST00000222390.5:c.595G>A	p.Glu199Lys	p.E199K	ENST00000222390	NM_000601.4	199	Gaa/Aaa	5/18	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.379906683380574	2		271	347	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412381	139412381	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	42	350	0	ENST00000277541.6:c.1264C>T	p.Pro422Ser	p.P422S	ENST00000277541	NM_017617.3	422	Ccc/Tcc	8/34	1	2	FACETS	0.867	0.729	1	0.867	0.729	1	CLONAL	1	TRUE	1	0.379906683380574	2		350	255	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101129	41101130	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	28	364	0	ENST00000373198.4:c.1226_1227delinsTT	p.Pro409Leu	p.P409L	ENST00000373198	NM_133170.3	409	cCC/cTT	8/32	0.371202961054126	0	FACETS	0.376	0.302	0.46			1	SUBCLONAL	1	TRUE	0	0.379906683380574	0		364	243	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416111	29416111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	66	306	0	ENST00000389048.3:c.4842C>A	p.Ser1614Arg	p.S1614R	ENST00000389048	NM_004304.4	1614	agC/agA	29/29	1	2	FACETS	0.955	0.833	1	0.955	0.833	1	CLONAL	1	TRUE	1	0.379906683380574	2		306	364	SUCCESS
APC	324	MSKCC	GRCh37	5	112174307	112174307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253876	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	65	404	0	ENST00000257430.4:c.3016C>T	p.His1006Tyr	p.H1006Y	ENST00000257430	NM_000038.5	1006	Cat/Tat	16/16	0.212515226794797	3	FACETS	1	0.962	1	0.642	0.561	0.729	INDETERMINATE	1	TRUE	1	0.379906683380574	3		404	317	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700229	117700229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	38	291	0	ENST00000368508.3:c.2590G>A	p.Gly864Arg	p.G864R	ENST00000368508	NM_002944.2	864	Gga/Aga	17/43	0.228197551477358	0	FACETS	0.551	0.459	0.652			1	SUBCLONAL	1	TRUE	0	0.379906683380574	0		291	225	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911166	40911166	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	33	159	0	ENST00000373198.4:c.2140-1G>A		p.X714_splice	ENST00000373198	NM_133170.3	714			0.371202961054126	0	FACETS	0.589	0.484	0.704			1	SUBCLONAL	1	TRUE	0	0.379906683380574	0		159	183	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983048	111983048	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	76	380	0	ENST00000368678.4:c.1499G>A	p.Trp500Ter	p.W500*	ENST00000368678		500	tGg/tAg	13/13	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.379906683380574	2		380	363	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295230	1295230	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs796516131	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	11	297	0				ENST00000310581	NM_198253.2	-/1132			0.157482502661352	0	FACETS	0.332	0.231	0.456			1	INDETERMINATE	1	TRUE	0	0.379906683380574	0		297	108	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356361	66356361	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772108237	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	71	410	0	ENST00000273854.3:c.1136C>T	p.Pro379Leu	p.P379L	ENST00000273854	NM_004439.5	379	cCg/cTg	5/18	0.259180117812021	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.379906683380574	1		410	281	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659851	227659851	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	37	147	0	ENST00000305123.5:c.3604C>T	p.Pro1202Ser	p.P1202S	ENST00000305123	NM_005544.2	1202	Ccc/Tcc	1/2	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.379906683380574	2		147	131	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964400	93964400	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1051471746	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	39	317	0	ENST00000369303.4:c.2497G>A	p.Gly833Arg	p.G833R	ENST00000369303	NM_004440.3	833	Gga/Aga	14/17	1	2	FACETS	0.863	0.72	1	0.863	0.72	1	CLONAL	1	TRUE	1	0.379906683380574	2		317	238	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367248	50367248	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	46	322	0	ENST00000331340.3:c.55C>T	p.Pro19Ser	p.P19S	ENST00000331340	NM_006060.4	19	Cct/Tct	3/8	1	2	FACETS	0.738	0.624	0.863	0.738	0.624	0.863	SUBCLONAL	1	TRUE	1	0.379906683380574	2		322	328	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082895	16082895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1412185126	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	22	198	0	ENST00000281043.3:c.709C>T	p.Pro237Ser	p.P237S	ENST00000281043	NM_005378.4	237	Ccg/Tcg	2/3	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.379906683380574	2		198	103	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851570	134851570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	53	292	0	ENST00000398015.3:c.976C>T	p.Pro326Ser	p.P326S	ENST00000398015	NM_004441.4	326	Ccc/Tcc	5/16	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.379906683380574	2		292	246	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640578	3640578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138344471	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	64	428	0	ENST00000294008.3:c.3061C>T	p.Arg1021Cys	p.R1021C	ENST00000294008	NM_032444.2	1021	Cgc/Tgc	12/15	0.201243466169984	1	FACETS	0.886	0.773	1	0.886	0.773	1	INDETERMINATE	1	TRUE	0	0.379906683380574	1		428	308	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675118	40675118	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	72	370	0	ENST00000249776.8:c.82C>T	p.Pro28Ser	p.P28S	ENST00000249776	NM_033286.3	28	Ccg/Tcg	1/9	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.379906683380574	2		370	372	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638533	176638533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377148087	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	81	419	0	ENST00000439151.2:c.3133C>T	p.Arg1045Cys	p.R1045C	ENST00000439151	NM_022455.4	1045	Cgt/Tgt	5/23	0.212515226794797	3	FACETS	1	0.929	1	0.535	0.473	0.601	INDETERMINATE	1	TRUE	1	0.379906683380574	3		419	474	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800945	18800945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	49	254	0	ENST00000266497.5:c.4321G>A	p.Gly1441Arg	p.G1441R	ENST00000266497		1441	Gga/Aga	31/31	1	2	FACETS	0.985	0.841	1	0.985	0.841	1	CLONAL	1	TRUE	1	0.379906683380574	2		254	262	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486089	8486089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	43	403	0	ENST00000356435.5:c.2728G>A	p.Glu910Lys	p.E910K	ENST00000356435		910	Gag/Aag	17/35	0.340650714219038	0	FACETS	0.53	0.446	0.621			1	SUBCLONAL	1	TRUE	0	0.379906683380574	0		403	265	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932242	36932242	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	57	406	0	ENST00000361632.4:c.2227C>T	p.Gln743Ter	p.Q743*	ENST00000361632		743	Cag/Tag	16/16	1	2	FACETS	0.971	0.839	1	0.971	0.839	1	CLONAL	1	TRUE	1	0.379906683380574	2		406	309	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74003508	74003508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	56	297	0	ENST00000318443.5:c.1579G>A	p.Glu527Lys	p.E527K	ENST00000318443	NM_001024736.1	527	Gaa/Aaa	9/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.379906683380574	2		297	213	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136205	64136205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	15	344	0	ENST00000334205.4:c.1364C>T	p.Ala455Val	p.A455V	ENST00000334205	NM_003942.2	455	gCt/gTt	12/17	1	2	FACETS	0.311	0.227	0.412	0.311	0.227	0.412	SUBCLONAL	1	TRUE	1	0.379906683380574	2		344	254	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250997	99250997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	65	398	0	ENST00000268035.6:c.301C>T	p.Pro101Ser	p.P101S	ENST00000268035	NM_000875.3	101	Ccc/Tcc	2/21	1	2	FACETS	0.94	0.82	1	0.94	0.82	1	CLONAL	1	TRUE	1	0.379906683380574	2		398	364	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646443	23646443	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039479	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	42	319	0	ENST00000261584.4:c.1424C>T	p.Ser475Leu	p.S475L	ENST00000261584	NM_024675.3	475	tCa/tTa	4/13	0.201243466169984	1	FACETS	0.548	0.459	0.646	0.548	0.459	0.646	INDETERMINATE	1	TRUE	0	0.379906683380574	1		319	327	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549515	187549515	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs577375480	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	84	328	1	ENST00000441802.2:c.4603C>T	p.Arg1535Ter	p.R1535*	ENST00000441802	NM_005245.3	1535	Cga/Tga	9/27	0.379906683380574	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.379906683380574	1		329	258	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791471	42791471	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	20	455	0	ENST00000575354.2:c.453-1G>A		p.X151_splice	ENST00000575354	NM_015125.3	151			1	2	FACETS	0.26	0.198	0.333	0.26	0.198	0.333	SUBCLONAL	1	TRUE	1	0.379906683380574	2		455	405	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997874	149997874	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	90	350	0	ENST00000253339.5:c.2594-1G>A		p.X865_splice	ENST00000253339		865			1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.379906683380574	2		350	409	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333641	70333641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	57	352	0	ENST00000373644.4:c.1546C>T	p.Pro516Ser	p.P516S	ENST00000373644	NM_030625.2	516	Cca/Tca	2/12	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.379906683380574	2		352	293	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575376	64575376	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	70	386	0	ENST00000312049.6:c.641G>T	p.Gly214Val	p.G214V	ENST00000312049	NM_130799.2	214	gGt/gTt	3/10	1	2	FACETS	0.828	0.724	0.939	0.828	0.724	0.939	CLONAL	1	TRUE	1	0.379906683380574	2		386	445	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811604	102811604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	49	430	0	ENST00000307046.8:c.580G>A	p.Gly194Arg	p.G194R	ENST00000307046	NM_001111285.1	194	Gga/Aga	4/4	1	2	FACETS	0.801	0.682	0.931	0.801	0.682	0.931	CLONAL	1	TRUE	1	0.379906683380574	2		430	322	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807552	36807552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	78	371	0	ENST00000373129.3:c.1112C>T	p.Ser371Phe	p.S371F	ENST00000373129	NM_032017.1	371	tCc/tTc	12/12	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.379906683380574	2		371	376	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12647761	12647761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	71	309	0	ENST00000251849.4:c.619C>T	p.Pro207Ser	p.P207S	ENST00000251849	NM_002880.3	207	Cca/Tca	6/17	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.379906683380574	2		309	351	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598213	52598213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	103	297	0	ENST00000394830.3:c.3653C>T	p.Ser1218Phe	p.S1218F	ENST00000394830	NM_018313.4	1218	tCc/tTc	24/30	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.379906683380574	2		297	390	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289241	33289242	+	missense_variant	Missense_Mutation	DNP	TC	TC	CT	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	93	348	0	ENST00000374542.5:c.310_311delinsAG	p.Glu104Arg	p.E104R	ENST00000374542	NM_001141970.1	104	GAg/AGg	3/8	1	2	FACETS	0.913	0.815	1	0.913	0.815	1	CLONAL	1	TRUE	1	0.379906683380574	2		348	536	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843668	156843668	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	50	423	0	ENST00000524377.1:c.1094A>G	p.Asn365Ser	p.N365S	ENST00000524377	NM_002529.3	365	aAc/aGc	8/17	1	2	FACETS	0.671	0.571	0.781	0.671	0.571	0.781	SUBCLONAL	1	TRUE	1	0.379906683380574	2		423	392	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374316	81374316	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	54	253	0	ENST00000222390.5:c.746G>A	p.Arg249Lys	p.R249K	ENST00000222390	NM_000601.4	249	aGa/aAa	6/18	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.379906683380574	2		253	247	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523009	25523009	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	44	313	0	ENST00000264709.3:c.176C>A	p.Pro59Gln	p.P59Q	ENST00000264709	NM_175629.2	59	cCg/cAg	3/23	1	2	FACETS	0.827	0.698	0.968	0.827	0.698	0.968	CLONAL	1	TRUE	1	0.379906683380574	2		313	280	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400938	72400938	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	85	352	0	ENST00000357731.5:c.233T>A	p.Ile78Asn	p.I78N	ENST00000357731	NM_173808.2	78	aTt/aAt	2/7	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.379906683380574	2		352	387	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332310	70332310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	95	342	0	ENST00000373644.4:c.215G>A	p.Ser72Asn	p.S72N	ENST00000373644	NM_030625.2	72	aGc/aAc	2/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.379906683380574	2		342	358	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271408	26271408	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs200234697	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	108	530	0	ENST00000305910.3:c.205C>T	p.Gln69Ter	p.Q69*	ENST00000305910	NM_003534.2	69	Caa/Taa	1/1	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.379906683380574	2		530	531	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032540	12032540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	42	226	0	ENST00000353533.5:c.976C>T	p.Pro326Ser	p.P326S	ENST00000353533	NM_003010.3	326	Ccg/Tcg	9/11	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.379906683380574	2		226	197	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980328	201980328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	108	370	0	ENST00000359651.3:c.64G>A	p.Glu22Lys	p.E22K	ENST00000359651		22	Gag/Aag	1/8	0.212515226794797	3	FACETS	0.945	0.857	1	0.945	0.857	1	INDETERMINATE	2	TRUE	1	0.379906683380574	3		370	358	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038826	47038826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	56	159	0	ENST00000377604.3:c.833C>T	p.Ala278Val	p.A278V	ENST00000377604	NM_001204468.1	278	gCc/gTc	9/24	1	1	FACETS	0.995	0.881	1	1	0.981	1	CLONAL	2	TRUE	0	0.379906683380574	1		159	120	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344191	118344192	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	82	438	1	ENST00000534358.1:c.2317_2318delinsTT	p.Pro773Leu	p.P773L	ENST00000534358	NM_005933.3	773	CCg/TTg	3/36	1	2	FACETS	0.943	0.834	1	0.943	0.834	1	CLONAL	1	TRUE	1	0.379906683380574	2		439	458	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979295	40979295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	55	349	0	ENST00000373198.4:c.1838C>T	p.Pro613Leu	p.P613L	ENST00000373198	NM_133170.3	613	cCc/cTc	11/32	0.371202961054126	0	FACETS	0.663	0.572	0.76			1	SUBCLONAL	1	TRUE	0	0.379906683380574	0		349	271	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022636	31022637	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	36	419	0	ENST00000375687.4:c.2121_2122delinsTT	p.Gln708Ter	p.Q708*	ENST00000375687	NM_015338.5	707	acCCag/acTTag	13/13	1	2	FACETS	0.718	0.593	0.856	0.718	0.593	0.856	SUBCLONAL	1	TRUE	1	0.379906683380574	2		419	264	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426023	49426024	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	62	415	0	ENST00000301067.7:c.12464_12465delinsTT	p.Pro4155Leu	p.P4155L	ENST00000301067	NM_003482.3	4155	cCC/cTT	39/54	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.379906683380574	2		415	285	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162475203	162475203	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	31	309	0	ENST00000366898.1:c.538C>T	p.Pro180Ser	p.P180S	ENST00000366898	NM_004562.2	180	Cca/Tca	5/12	1	2	FACETS	0.729	0.593	0.88	0.729	0.593	0.88	SUBCLONAL	1	TRUE	1	0.379906683380574	2		309	224	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631249	176631249	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1430670372	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	94	382	0	ENST00000439151.2:c.1192C>T	p.Leu398Phe	p.L398F	ENST00000439151	NM_022455.4	398	Ctt/Ttt	4/23	0.212515226794797	3	FACETS	1	0.977	1	0.677	0.606	0.752	INDETERMINATE	1	TRUE	1	0.379906683380574	3		382	435	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	359988	359989	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	22	303	0	ENST00000262320.3:c.1100_1101delinsTT	p.Pro367Leu	p.P367L	ENST00000262320	NM_003502.3	367	cCC/cTT	4/11	0.201243466169984	1	FACETS	0.411	0.32	0.517	0.411	0.32	0.517	INDETERMINATE	1	TRUE	0	0.379906683380574	1		303	228	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099866	157099866	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	53	254	0	ENST00000346085.5:c.803C>T	p.Ser268Phe	p.S268F	ENST00000346085	NM_020732.3	268	tCc/tTc	1/20	1	2	FACETS	0.962	0.826	1	0.962	0.826	1	CLONAL	1	TRUE	1	0.379906683380574	2		254	290	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974330	93974330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	38	254	0	ENST00000369303.4:c.1724G>A	p.Gly575Asp	p.G575D	ENST00000369303	NM_004440.3	575	gGc/gAc	8/17	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.379906683380574	2		254	187	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679306	29679306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1336098547	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	75	341	0	ENST00000356175.3:c.7426C>T	p.Pro2476Ser	p.P2476S	ENST00000356175	NM_000267.3	2476	Ccc/Tcc	50/57	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.379906683380574	2		341	364	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300083	15300083	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	41	364	0	ENST00000263388.2:c.1192+1G>A		p.X398_splice	ENST00000263388	NM_000435.2	398			1	2	FACETS	0.959	0.806	1	0.959	0.806	1	CLONAL	1	TRUE	1	0.379906683380574	2		364	225	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624522	21624522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	68	399	0	ENST00000421138.2:c.1507G>A	p.Ala503Thr	p.A503T	ENST00000421138		503	Gca/Aca	14/16	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.379906683380574	2		399	340	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526137	189526137	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1381645678	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	81	430	0	ENST00000264731.3:c.401A>G	p.Tyr134Cys	p.Y134C	ENST00000264731	NM_003722.4	134	tAt/tGt	4/14	1	2	FACETS	0.844	0.746	0.949	0.844	0.746	0.949	CLONAL	1	TRUE	1	0.379906683380574	2		430	505	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631248	176631249	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	94	386	0	ENST00000439151.2:c.1191_1192delinsTT	p.Leu398Phe	p.L398F	ENST00000439151	NM_022455.4	397	gtCCtt/gtTTtt	4/23	0.212515226794797	3	FACETS	1	0.976	1	0.669	0.599	0.744	INDETERMINATE	1	TRUE	1	0.379906683380574	3		386	440	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121060	29121060	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	71	305	0	ENST00000328354.6:c.497A>C	p.Asn166Thr	p.N166T	ENST00000328354	NM_007194.3	166	aAt/aCt	4/15	0.201243466169984	1	FACETS	1	0.937	1	1	0.937	1	INDETERMINATE	1	TRUE	0	0.379906683380574	1		305	276	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395029	139395029	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	42	256	1	ENST00000277541.6:c.5909C>T	p.Ser1970Phe	p.S1970F	ENST00000277541	NM_017617.3	1970	tCt/tTt	31/34	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.379906683380574	2		257	189	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544145	18544145	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	48	297	0	ENST00000266497.5:c.1965del	p.Lys655AsnfsTer39	p.K655Nfs*39	ENST00000266497		654	atA/at	13/31	1	2	FACETS	0.916	0.779	1	0.916	0.779	1	CLONAL	1	TRUE	1	0.379906683380574	2		297	276	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90960112	90960112	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	64	222	0	ENST00000265433.3:c.1854T>G	p.Asn618Lys	p.N618K	ENST00000265433	NM_002485.4	618	aaT/aaG	12/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.379906683380574	2		222	273	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879441	151879441	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239127912	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	58	458	0	ENST00000262189.6:c.5504C>T	p.Pro1835Leu	p.P1835L	ENST00000262189	NM_170606.2	1835	cCc/cTc	36/59	1	2	FACETS	0.812	0.701	0.932	0.812	0.701	0.932	CLONAL	1	TRUE	1	0.379906683380574	2		458	376	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624790	9624790	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	54	319	0	ENST00000353224.5:c.187C>T	p.Gln63Ter	p.Q63*	ENST00000353224	NM_177990.2	63	Cag/Tag	3/10	1	2	FACETS	0.967	0.832	1	0.967	0.832	1	CLONAL	1	TRUE	1	0.379906683380574	2		319	294	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523013	25523013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	47	316	0	ENST00000264709.3:c.172C>T	p.Pro58Ser	p.P58S	ENST00000264709	NM_175629.2	58	Ccc/Tcc	3/23	1	2	FACETS	0.85	0.722	0.99	0.85	0.722	0.99	CLONAL	1	TRUE	1	0.379906683380574	2		316	291	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561309	9561309	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs760330867	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	64	368	0	ENST00000353224.5:c.473C>A	p.Pro158Gln	p.P158Q	ENST00000353224	NM_177990.2	158	cCg/cAg	4/10	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.379906683380574	2		368	310	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166203	32166203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	80	315	0	ENST00000375023.3:c.4751G>A	p.Gly1584Glu	p.G1584E	ENST00000375023	NM_004557.3	1584	gGa/gAa	26/30	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.379906683380574	2		315	413	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670698	67670698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	64	367	0	ENST00000264010.4:c.1943C>T	p.Ala648Val	p.A648V	ENST00000264010	NM_006565.3	648	gCc/gTc	11/12	0.201243466169984	1	FACETS	0.798	0.695	0.908	0.798	0.695	0.908	INDETERMINATE	1	TRUE	0	0.379906683380574	1		367	342	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449601	149449601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	59	339	0	ENST00000286301.3:c.1345G>A	p.Val449Ile	p.V449I	ENST00000286301	NM_005211.3	449	Gtc/Atc	10/22	0.212515226794797	3	FACETS	1	0.885	1	0.513	0.444	0.588	INDETERMINATE	1	TRUE	1	0.379906683380574	3		339	360	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791382	42791382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	65	399	0	ENST00000575354.2:c.442C>T	p.His148Tyr	p.H148Y	ENST00000575354	NM_015125.3	148	Cat/Tat	3/20	1	2	FACETS	0.935	0.815	1	0.935	0.815	1	CLONAL	1	TRUE	1	0.379906683380574	2		399	366	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662646	117662646	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753442951	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	44	400	0	ENST00000368508.3:c.4819C>T	p.Pro1607Ser	p.P1607S	ENST00000368508	NM_002944.2	1607	Cct/Tct	29/43	0.228197551477358	0	FACETS	0.526	0.444	0.616			1	SUBCLONAL	1	TRUE	0	0.379906683380574	0		400	273	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243948	5243948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	51	338	0	ENST00000357368.4:c.1534C>T	p.Leu512Phe	p.L512F	ENST00000357368	NM_002850.3	512	Ctc/Ttc	11/38	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.379906683380574	2		338	248	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741821	145741821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1316434470	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	48	414	0	ENST00000428558.2:c.682C>T	p.Leu228Phe	p.L228F	ENST00000428558	NM_004260.3	228	Ctt/Ttt	5/22	1	2	FACETS	0.8	0.679	0.931	0.8	0.679	0.931	CLONAL	1	TRUE	1	0.379906683380574	2		414	316	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534476	187534476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	65	330	0	ENST00000441802.2:c.9250C>T	p.Pro3084Ser	p.P3084S	ENST00000441802	NM_005245.3	3084	Ccc/Tcc	13/27	0.379906683380574	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.379906683380574	1		330	251	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448415	49448415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765815816	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	40	361	0	ENST00000301067.7:c.296C>T	p.Pro99Leu	p.P99L	ENST00000301067	NM_003482.3	99	cCt/cTt	3/54	1	2	FACETS	0.65	0.542	0.769	0.65	0.542	0.769	SUBCLONAL	1	TRUE	1	0.379906683380574	2		361	324	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40447769	40447769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	88	443	0	ENST00000345506.4:c.508G>A	p.Glu170Lys	p.E170K	ENST00000345506	NM_003152.3	170	Gag/Aag	6/20	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.379906683380574	2		443	429	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022680	36022680	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	61	259	0	ENST00000358208.4:c.553G>A	p.Gly185Ser	p.G185S	ENST00000358208		185	Ggt/Agt	5/12	1	2	FACETS	0.988	0.858	1	0.988	0.858	1	CLONAL	1	TRUE	1	0.379906683380574	2		259	325	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137522022	137522022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746134574	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	53	237	0	ENST00000367739.4:c.857C>T	p.Ser286Phe	p.S286F	ENST00000367739	NM_000416.2	286	tCc/tTc	6/7	0.241740770452171	4	FACETS	1	0.935	1	0.583	0.5	0.674	CLONAL	1	TRUE	2	0.379906683380574	4		237	330	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180397	94180397	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1215450873	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	105	298	0	ENST00000323929.3:c.1771C>T	p.Gln591Ter	p.Q591*	ENST00000323929	NM_005591.3	591	Caa/Taa	15/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.379906683380574	2		298	418	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55143591	55143591	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1560482703	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	101	345	0	ENST00000257290.5:c.1823T>C	p.Val608Ala	p.V608A	ENST00000257290	NM_006206.4	608	gTt/gCt	13/23	0.259180117812021	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.379906683380574	1		345	363	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638532	176638533	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	83	419	0	ENST00000439151.2:c.3132_3133delinsTT	p.Arg1045Cys	p.R1045C	ENST00000439151	NM_022455.4	1044	aaCCgt/aaTTgt	5/23	0.212515226794797	3	FACETS	1	0.938	1	0.545	0.483	0.611	INDETERMINATE	1	TRUE	1	0.379906683380574	3		419	477	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799121	42799122	+	missense_variant	Missense_Mutation	DNP	CC	CC	GT	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	44	360	0	ENST00000575354.2:c.4605_4606delinsGT	p.Pro1536Ser	p.P1536S	ENST00000575354	NM_015125.3	1535	ctCCct/ctGTct	20/20	1	2	FACETS	0.871	0.735	1	0.871	0.735	1	CLONAL	1	TRUE	1	0.379906683380574	2		360	266	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793194	33793194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	21	286	0	ENST00000498907.2:c.127C>T	p.Pro43Ser	p.P43S	ENST00000498907	NM_004364.3	43	Ccc/Tcc	1/1	1	2	FACETS	0.67	0.52	0.842	0.67	0.52	0.842	SUBCLONAL	1	TRUE	1	0.379906683380574	2		286	165	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572253	64572254	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	56	404	0	ENST00000312049.6:c.1385_1386delinsTT	p.Ala462Val	p.A462V	ENST00000312049	NM_130799.2	462	gCC/gTT	10/10	1	2	FACETS	0.96	0.828	1	0.96	0.828	1	CLONAL	1	TRUE	1	0.379906683380574	2		404	307	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652206	36652206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	40	325	0	ENST00000244741.5:c.328C>T	p.His110Tyr	p.H110Y	ENST00000244741	NM_000389.4	110	Cat/Tat	2/3	1	2	FACETS	0.729	0.608	0.861	0.729	0.608	0.861	SUBCLONAL	1	TRUE	1	0.379906683380574	2		325	289	SUCCESS
MTAP	4507	MSKCC	GRCh37	9	21859322	21859322	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	71	288	0	ENST00000380172.4:c.711A>T	p.Leu237Phe	p.L237F	ENST00000380172	NM_002451.3	237	ttA/ttT	7/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.379906683380574	2		288	287	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500798	8500798	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	62	368	0	ENST00000356435.5:c.2084C>T	p.Pro695Leu	p.P695L	ENST00000356435		695	cCt/cTt	13/35	0.340650714219038	0	FACETS	0.627	0.545	0.714			1	SUBCLONAL	1	TRUE	0	0.379906683380574	0		368	323	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873732	35873732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	78	310	0	ENST00000303115.3:c.688G>A	p.Glu230Lys	p.E230K	ENST00000303115	NM_002185.3	230	Gag/Aag	5/8	0.212515226794797	3	FACETS	0.756	0.67	0.847	0.756	0.67	0.847	INDETERMINATE	2	TRUE	1	0.379906683380574	3		310	323	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237641	16237641	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	78	350	0	ENST00000375759.3:c.1088G>T	p.Gly363Val	p.G363V	ENST00000375759	NM_015001.2	363	gGa/gTa	5/15	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.379906683380574	2		350	359	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771828	135771828	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	40	402	0	ENST00000298552.3:c.3289del	p.Arg1097ValfsTer13	p.R1097Vfs*13	ENST00000298552	NM_001162426.1	1097	Cgt/gt	23/23	1	2	FACETS	0.636	0.53	0.753	0.636	0.53	0.753	SUBCLONAL	1	TRUE	1	0.379906683380574	2		402	331	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533757	63533757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793954	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	61	439	0	ENST00000307078.5:c.1397C>T	p.Ser466Phe	p.S466F	ENST00000307078	NM_004655.3	466	tCc/tTc	6/11	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.379906683380574	2		439	298	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146667	185146668	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	73	358	0	ENST00000265026.3:c.298_299delinsAA	p.Gly100Lys	p.G100K	ENST00000265026	NM_004721.4	100	GGg/AAg	2/14	1	2	FACETS	0.961	0.844	1	0.961	0.844	1	CLONAL	1	TRUE	1	0.379906683380574	2		358	400	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797272	42797272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751126298	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	56	374	0	ENST00000575354.2:c.3634C>T	p.Pro1212Ser	p.P1212S	ENST00000575354	NM_015125.3	1212	Cca/Tca	15/20	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.379906683380574	2		374	269	SUCCESS
APC	324	MSKCC	GRCh37	5	112176848	112176848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561601033	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	67	385	0	ENST00000257430.4:c.5557C>T	p.Pro1853Ser	p.P1853S	ENST00000257430	NM_000038.5	1853	Cct/Tct	16/16	0.212515226794797	3	FACETS	1	0.95	1	0.588	0.514	0.667	INDETERMINATE	1	TRUE	1	0.379906683380574	3		385	357	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682650	86682653	+	frameshift_variant	Frame_Shift_Del	DEL	ACAT	ACAT	CTA	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	80	352	0	ENST00000274376.6:c.2855_2858delinsCTA	p.Tyr952SerfsTer16	p.Y952Sfs*16	ENST00000274376	NM_002890.2	952	tACATg/tCTAg	23/25	0.212515226794797	3	FACETS	1	0.975	1	0.706	0.626	0.79	INDETERMINATE	1	TRUE	1	0.379906683380574	3		352	355	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133769	55133769	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs772538462	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	72	364	0	ENST00000257290.5:c.982A>G	p.Asn328Asp	p.N328D	ENST00000257290	NM_006206.4	328	Aac/Gac	7/23	0.259180117812021	1	FACETS	0.997	0.879	1	0.997	0.879	1	CLONAL	1	TRUE	0	0.379906683380574	1		364	308	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796102	57796102	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	99	344	0	ENST00000309042.7:c.1078C>A	p.Pro360Thr	p.P360T	ENST00000309042	NM_005612.4	360	Cct/Act	4/4	0.259180117812021	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.379906683380574	1		344	349	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641186	117641186	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	74	420	0	ENST00000368508.3:c.5785C>A	p.Pro1929Thr	p.P1929T	ENST00000368508	NM_002944.2	1929	Cca/Aca	36/43	0.228197551477358	0	FACETS	0.767	0.677	0.862			1	SUBCLONAL	1	TRUE	0	0.379906683380574	0		420	315	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484176	8484176	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	45	330	0	ENST00000356435.5:c.3356A>G	p.Asn1119Ser	p.N1119S	ENST00000356435		1119	aAc/aGc	19/35	0.340650714219038	0	FACETS	0.528	0.447	0.617			1	SUBCLONAL	1	TRUE	0	0.379906683380574	0		330	278	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573446	41573446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761000930	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	72	492	0	ENST00000263253.7:c.5731C>T	p.Pro1911Ser	p.P1911S	ENST00000263253	NM_001429.3	1911	Cct/Tct	31/31	0.201243466169984	1	FACETS	0.895	0.788	1	0.895	0.788	1	INDETERMINATE	1	TRUE	0	0.379906683380574	1		492	343	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2084126	2084126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1004796796	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	75	323	0	ENST00000349721.2:c.2456G>A	p.Arg819Gln	p.R819Q	ENST00000349721	NM_003070.3	819	cGg/cAg	17/34	1	2	FACETS	0.977	0.861	1	0.977	0.861	1	CLONAL	1	TRUE	1	0.379906683380574	2		323	404	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544149	18544149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	51	290	0	ENST00000266497.5:c.1966C>T	p.His656Tyr	p.H656Y	ENST00000266497		656	Cat/Tat	13/31	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.379906683380574	2		290	260	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376235	15376235	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	41	254	0	ENST00000263377.2:c.779C>T	p.Pro260Leu	p.P260L	ENST00000263377	NM_058243.2	260	cCa/cTa	5/20	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.379906683380574	2		254	196	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508625	106508625	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	49	296	0	ENST00000359195.3:c.619C>T	p.Leu207Phe	p.L207F	ENST00000359195	NM_002649.2	207	Ctc/Ttc	2/11	1	2	FACETS	0.89	0.758	1	0.89	0.758	1	CLONAL	1	TRUE	1	0.379906683380574	2		296	290	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226890	2226891	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	36	384	0	ENST00000398665.3:c.4370_4371delinsAT	p.Ser1457Tyr	p.S1457Y	ENST00000398665	NM_032482.2	1457	tCC/tAT	27/28	1	2	FACETS	0.707	0.584	0.843	0.707	0.584	0.843	SUBCLONAL	1	TRUE	1	0.379906683380574	2		384	268	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759653	133759653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	56	331	0	ENST00000318560.5:c.1976C>T	p.Ser659Phe	p.S659F	ENST00000318560	NM_005157.4	659	tCc/tTc	11/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.379906683380574	2		331	238	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412632	139412632	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	45	392	0	ENST00000277541.6:c.1212C>A	p.Tyr404Ter	p.Y404*	ENST00000277541	NM_017617.3	404	taC/taA	7/34	1	2	FACETS	0.722	0.609	0.846	0.722	0.609	0.846	SUBCLONAL	1	TRUE	1	0.379906683380574	2		392	328	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0067858-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	121	287	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	1	2	FACETS	0.9	0.828	0.974	1	0.99	1	CLONAL	2	TRUE	1	0.48	2		287	280	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911564	134911564	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	42	368	0	ENST00000398015.3:c.2029C>T	p.His677Tyr	p.H677Y	ENST00000398015	NM_004441.4	677	Cat/Tat	11/16	1	2	FACETS	0.676	0.564	0.801	0.676	0.564	0.801	SUBCLONAL	1	TRUE	1	0.23	2		368	540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0067935-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	48	544	0	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	1	2	FACETS	0.803	0.677	0.942	0.803	0.677	0.942	CLONAL	1	TRUE	1	0.167901288654143	2		544	712	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0067935-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	28	352	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.813	1	1	0.813	1	CLONAL	1	TRUE	1	0.167901288654143	2		352	328	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0067935-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	37	367	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.167901288654143	2		367	370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0067969-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	234	508	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.861627907137503	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.851554624872071	1		508	278	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0068013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	67	317	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		317	204	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	101	382	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		382	455	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449514	31449514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	111	334	0	ENST00000344624.3:c.2695C>T	p.His899Tyr	p.H899Y	ENST00000344624		899	Cat/Tat	19/33	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		334	441	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0068013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	144	493	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		493	665	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0068013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	70	187	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		187	221	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710670	114710670	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0068013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	151	464	0	ENST00000543371.1:c.155C>G	p.Ser52Ter	p.S52*	ENST00000543371	NM_001198531.1	52	tCa/tGa	1/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		464	639	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610265	10610265	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	420	534	1	ENST00000171111.5:c.445G>A	p.Glu149Lys	p.E149K	ENST00000171111	NM_203500.1	149	Gag/Aag	2/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		535	777	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503994	186503994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	150	349	0	ENST00000323963.5:c.559G>A	p.Glu187Lys	p.E187K	ENST00000323963		187	Gaa/Aaa	6/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		349	635	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355551	15355551	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	153	448	0	ENST00000263377.2:c.2181G>C	p.Lys727Asn	p.K727N	ENST00000263377	NM_058243.2	727	aaG/aaC	12/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		448	656	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532539	187532539	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0068013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	105	382	0	ENST00000441802.2:c.9853+1G>A		p.X3285_splice	ENST00000441802	NM_005245.3	3285			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		382	471	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415856	49415858	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	rs587783704	NA	P-0068013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	130	480	0	ENST00000301067.7:c.16489_16491del	p.Ile5497del	p.I5497del	ENST00000301067	NM_003482.3	5497	ATC/-	53/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		480	654	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508940	106508940	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	148	529	0	ENST00000359195.3:c.934G>T	p.Asp312Tyr	p.D312Y	ENST00000359195	NM_002649.2	312	Gac/Tac	2/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		529	676	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518134	187518136	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	rs750605265	NA	P-0068013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	135	478	1	ENST00000441802.2:c.12558_12560del	p.Val4187del	p.V4187del	ENST00000441802	NM_005245.3	4186	gtTGTg/gtg	25/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		479	674	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432094	121432094	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	194	488	0	ENST00000257555.6:c.841C>G	p.Leu281Val	p.L281V	ENST00000257555		281	Ctg/Gtg	4/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		488	649	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444974	49444974	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0068013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	186	561	0	ENST00000301067.7:c.2492C>G	p.Ser831Ter	p.S831*	ENST00000301067	NM_003482.3	831	tCa/tGa	10/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		561	798	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630484	67630484	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	149	330	0	ENST00000272342.5:c.670G>C	p.Glu224Gln	p.E224Q	ENST00000272342	NM_019002.3	224	Gaa/Caa	5/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		330	465	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149669	202149669	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	209	501	0	ENST00000358485.4:c.1110C>G	p.Ile370Met	p.I370M	ENST00000358485	NM_001080125.1	370	atC/atG	8/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		501	779	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654672	29654673	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0068013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	192	511	0	ENST00000356175.3:c.5363dup	p.Leu1789AlafsTer9	p.L1789Afs*9	ENST00000356175	NM_000267.3	1787	-/C	37/57	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		511	719	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522225	157522225	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1391970327	NA	P-0068013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	196	555	0	ENST00000346085.5:c.4497G>C	p.Met1499Ile	p.M1499I	ENST00000346085	NM_020732.3	1499	atG/atC	18/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		555	739	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412356	139412369	+	frameshift_variant	Frame_Shift_Del	DEL	ATGCACTTGCCCGC	ATGCACTTGCCCGC	-	novel	NA	P-0068013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	180	459	0	ENST00000277541.6:c.1276_1289del	p.Ala426GlnfsTer81	p.A426Qfs*81	ENST00000277541	NM_017617.3	426	GCGGGCAAGTGCATc/c	8/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		459	708	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874550	151874550	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0068013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	191	501	0	ENST00000262189.6:c.7988C>G	p.Ser2663Ter	p.S2663*	ENST00000262189	NM_170606.2	2663	tCa/tGa	38/59	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		501	685	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27190653	27190653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	138	432	0	ENST00000380036.4:c.1454C>T	p.Pro485Leu	p.P485L	ENST00000380036	NM_000459.3	485	cCc/cTc	10/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		432	535	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70362028	70362028	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	128	203	0	ENST00000374080.3:c.6494C>T	p.Thr2165Ile	p.T2165I	ENST00000374080		2165	aCc/aTc	45/45	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		203	286	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503718	186503718	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	134	377	0	ENST00000323963.5:c.395G>C	p.Cys132Ser	p.C132S	ENST00000323963		132	tGt/tCt	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		377	536	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733053	74733053	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	190	422	0	ENST00000359995.5:c.190G>A	p.Asp64Asn	p.D64N	ENST00000359995	NM_001195427.1	64	Gac/Aac	1/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		422	637	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941095	36941095	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	187	537	1	ENST00000361632.4:c.244A>T	p.Thr82Ser	p.T82S	ENST00000361632		82	Acc/Tcc	3/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		538	743	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522540	67522540	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	116	363	0	ENST00000274335.5:c.37G>C	p.Asp13His	p.D13H	ENST00000274335		13	Gat/Cat	1/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		363	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0068023-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	260	508	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.281572713819512	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.281572713819512	2		508	814	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21968242	21968242	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0068023-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	95	293	0	ENST00000304494.5:c.458-1G>A		p.X153_splice	ENST00000304494	NM_000077.4	153			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.281572713819512	2		293	560	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434521	140434521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777533608	NA	P-0068023-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	38	191	0	ENST00000288602.6:c.2177G>A	p.Arg726His	p.R726H	ENST00000288602	NM_004333.4	726	cGc/cAc	18/18	1	2	FACETS	0.619	0.512	0.739	0.619	0.512	0.739	SUBCLONAL	1	TRUE	1	0.281572713819512	2		191	436	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213841	66213841	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068023-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	43	226	0	ENST00000273854.3:c.2589T>G	p.Ser863Arg	p.S863R	ENST00000273854	NM_004439.5	863	agT/agG	15/18	1	2	FACETS	0.771	0.647	0.909	0.771	0.647	0.909	CLONAL	1	TRUE	1	0.281572713819512	2		226	396	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241895	72241895	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068023-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	60	266	0	ENST00000357731.5:c.495A>C	p.Lys165Asn	p.K165N	ENST00000357731	NM_173808.2	165	aaA/aaC	3/7	1	2	FACETS	0.901	0.778	1	0.901	0.778	1	CLONAL	1	TRUE	1	0.281572713819512	2		266	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0068081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	336	610	2	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.569102421081984	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	TRUE	0	0.569102421081984	3		612	501	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750587	128750589	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs776242757	NA	P-0068081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	46	470	0	ENST00000377970.2:c.130_132del	p.Glu44del	p.E44del	ENST00000377970	NM_002467.4	42	GAG/-	2/3	0.520787263007971	4	FACETS	0.39	0.328	0.459	0.195	0.164	0.23	SUBCLONAL	1	TRUE	2	0.569102421081984	4		470	650	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099090	27099091	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0068081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	267	545	1	ENST00000324856.7:c.3510_3511del	p.His1170GlnfsTer22	p.H1170Qfs*22	ENST00000324856	NM_006015.4	1169	cCA/c	13/20	0.559270589403407	2	FACETS	0.942	0.895	0.989	0.942	0.895	0.989	CLONAL	2	TRUE	0	0.569102421081984	2		546	498	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12393144	12393144	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	51	463	0	ENST00000287820.6:c.53C>G	p.Thr18Ser	p.T18S	ENST00000287820	NM_015869.4	18	aCt/aGt	1/7	0.504506794493025	2	FACETS	0.929	0.801	1	0.464	0.4	0.532	CLONAL	1	TRUE	0	0.569102421081984	2		463	193	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201759	102201762	+	frameshift_variant	Frame_Shift_Del	DEL	TCAG	TCAG	-	novel	NA	P-0068081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	49	374	0	ENST00000263464.3:c.1111_1114del	p.Ser371LysfsTer5	p.S371Kfs*5	ENST00000263464	NM_001165.4	371	TCAGaa/aa	6/9	0.567623438523974	2	FACETS	1	0.947	1	0.602	0.521	0.686	CLONAL	1	TRUE	0	0.569102421081984	2		374	143	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435564	56435564	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	403	532	0	ENST00000407977.2:c.1573A>C	p.Ser525Arg	p.S525R	ENST00000407977		525	Agt/Cgt	9/10	0.569102421081984	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.569102421081984	3		532	551	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786773	3786775	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs1555473122	NA	P-0068081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	204	372	0	ENST00000262367.5:c.4436_4438del	p.Gly1479del	p.G1479del	ENST00000262367	NM_004380.2	1479	gGAGat/gat	27/31	0.559270589403407	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.569102421081984	2		372	354	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151868358	151868358	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	39	417	0	ENST00000262189.6:c.9444del	p.Ile3149PhefsTer7	p.I3149Ffs*7	ENST00000262189	NM_170606.2	3148	gcC/gc	40/59	0.560251346808842	3	FACETS	0.513	0.426	0.61	0.257	0.213	0.305	SUBCLONAL	1	TRUE	1	0.569102421081984	3		417	343	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833950	44833952	+	inframe_deletion	In_Frame_Del	DEL	ACT	ACT	-	novel	NA	P-0068081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	32	134	0	ENST00000377967.4:c.377_379del	p.Tyr126del	p.Y126del	ENST00000377967	NM_021140.2	125	gACTac/gac	4/29	0.530740327979863	2	FACETS	1	0.937	1			1	CLONAL	1	TRUE	NA	0.569102421081984	2		134	88	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36028556	36028556	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	126	402	0	ENST00000358208.4:c.898C>G	p.Leu300Val	p.L300V	ENST00000358208		300	Ctg/Gtg	8/12	0.310566077711631	6	FACETS	1	0.976	1	0.311	0.281	0.342	INDETERMINATE	1	TRUE	2	0.569102421081984	6		402	762	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880984	37880985	+	inframe_insertion	In_Frame_Ins	INS	-	-	TACGTGATGGCT	rs397516977	NA	P-0068134-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	1219	170	0	ENST00000269571.5:c.2314_2325dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/TACGTGATGGCT	20/27	0.794745478486783	10	FACETS	1	0.991	1	0.768	0.751	0.785	CLONAL	6	TRUE	2	0.794745478486783	10		170	2086	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944142	81944180	+	frameshift_variant	Frame_Shift_Del	DEL	AGCACTGCCGGATCCGCTCCACCATGGAGGGCGGGACCC	AGCACTGCCGGATCCGCTCCACCATGGAGGGCGGGACCC	CAGGACCG	novel	NA	P-0068134-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	232	245	1	ENST00000359376.3:c.1751_1789delinsCAGGACCG	p.Gln584ProfsTer4	p.Q584Pfs*4	ENST00000359376	NM_002661.3	584	cAGCACTGCCGGATCCGCTCCACCATGGAGGGCGGGACCCtg/cCAGGACCGtg	18/33	0.794745478486783	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.794745478486783	1		246	349	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268778	98268820	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAACTTGCCGCAGTTTTTTTGAATGTAACAACCCAGTTTAA	AAGAACTTGCCGCAGTTTTTTTGAATGTAACAACCCAGTTTAA	-	novel	NA	P-0068135-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	302	508	0	ENST00000331920.6:c.263_305del	p.Phe88TrpfsTer15	p.F88Wfs*15	ENST00000331920	NM_000264.3	88	tTTAAACTGGGTTGTTACATTCAAAAAAACTGCGGCAAGTTCTTg/tg	2/24	0.938423732086015	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.938423732086015	1		508	341	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0068158-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	64	264	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		264	182	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs864622237	NA	P-0068158-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	71	362	0	ENST00000269305.4:c.700T>A	p.Tyr234Asn	p.Y234N	ENST00000269305	NM_001126112.2	234	Tac/Aac	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		362	530	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819239	3819239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772991403	NA	P-0068158-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	84	446	0	ENST00000262367.5:c.2996C>T	p.Thr999Met	p.T999M	ENST00000262367	NM_004380.2	999	aCg/aTg	15/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		446	695	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403162	116403162	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068158-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	27	390	0	ENST00000397752.3:c.2423A>C	p.Gln808Pro	p.Q808P	ENST00000397752	NM_000245.2	808	cAg/cCg	11/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		390	178	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928951	49928951	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068158-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	47	528	0	ENST00000296474.3:c.3415A>T	p.Asn1139Tyr	p.N1139Y	ENST00000296474	NM_002447.2	1139	Aac/Tac	16/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		528	708	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165632	47165632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068158-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	69	571	0	ENST00000409792.3:c.494C>T	p.Ser165Phe	p.S165F	ENST00000409792	NM_014159.6	165	tCt/tTt	3/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		571	641	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796502	57796502	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755693790	NA	P-0068158-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	36	429	0	ENST00000309042.7:c.1478G>A	p.Arg493Gln	p.R493Q	ENST00000309042	NM_005612.4	493	cGa/cAa	4/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		429	259	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	51	382	0				ENST00000310581	NM_198253.2	-/1132			0.335487347810528	0	FACETS	0.57	0.49	0.656			1	SUBCLONAL	1	TRUE	0	0.445167232922093	0		382	223	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559859	29559862	+	frameshift_variant	Frame_Shift_Del	DEL	ACTC	ACTC	-	rs1321848637	NA	P-0068163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	217	396	0	ENST00000356175.3:c.3457_3460del	p.Leu1153MetfsTer4	p.L1153Mfs*4	ENST00000356175	NM_000267.3	1152	ttACTC/tt	26/57	0.453127669621828	4	FACETS	0.901	0.84	0.963	0.901	0.84	0.963	CLONAL	2	TRUE	2	0.445167232922093	4		396	782	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971330	13971330	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	340	337	0	ENST00000405192.2:c.599T>C	p.Leu200Ser	p.L200S	ENST00000405192	NM_001163147.1	200	tTg/tCg	8/12	0.453127669621828	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.445167232922093	3		337	779	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068163-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	28	382	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.992	0.799	1	0.992	0.799	1	CLONAL	1	TRUE	1	0.27	2		382	209	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559859	29559862	+	frameshift_variant	Frame_Shift_Del	DEL	ACTC	ACTC	-	rs1321848637	NA	P-0068163-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	28	396	0	ENST00000356175.3:c.3457_3460del	p.Leu1153MetfsTer4	p.L1153Mfs*4	ENST00000356175	NM_000267.3	1152	ttACTC/tt	26/57	1	2	FACETS	0.914	0.734	1	0.914	0.734	1	CLONAL	1	TRUE	1	0.27	2		396	227	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971330	13971330	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068163-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	42	337	0	ENST00000405192.2:c.599T>C	p.Leu200Ser	p.L200S	ENST00000405192	NM_001163147.1	200	tTg/tCg	8/12	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.27	2		337	251	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0068180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	64	481	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.468100957019255	1	FACETS	0.416	0.361	0.476	0.416	0.361	0.476	SUBCLONAL	1	TRUE	0	0.474722602522591	1		481	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0068180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	31	361	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.468100957019255	1	FACETS	0.184	0.148	0.225	0.184	0.148	0.225	SUBCLONAL	1	TRUE	0	0.474722602522591	1		361	541	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266711	198266711	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	104	417	0	ENST00000335508.6:c.2221A>G	p.Lys741Glu	p.K741E	ENST00000335508	NM_012433.2	741	Aag/Gag	15/25	1	2	FACETS	0.924	0.832	1	0.924	0.832	1	CLONAL	1	TRUE	1	0.474722602522591	2		417	474	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044541	47044541	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	151	416	0	ENST00000377604.3:c.2038C>T	p.Arg680Ter	p.R680*	ENST00000377604	NM_001204468.1	680	Cga/Tga	18/24	1	2	FACETS	0.789	0.73	0.85	1	0.99	1	SUBCLONAL	2	TRUE	1	0.474722602522591	2		416	403	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044525	47044525	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	149	396	0	ENST00000377604.3:c.2022G>T	p.Gln674His	p.Q674H	ENST00000377604	NM_001204468.1	674	caG/caT	18/24	1	2	FACETS	0.783	0.723	0.844	1	0.99	1	SUBCLONAL	2	TRUE	1	0.474722602522591	2		396	401	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780711	9780711	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	74	316	0	ENST00000377346.4:c.1513G>T	p.Glu505Ter	p.E505*	ENST00000377346	NM_005026.3	505	Gag/Tag	12/24	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.474722602522591	2		316	297	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483074	29483074	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs753189381	NA	P-0068180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	115	352	0	ENST00000356175.3:c.134A>G	p.Asn45Ser	p.N45S	ENST00000356175	NM_000267.3	45	aAt/aGt	2/57	0.468100957019255	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.474722602522591	1		352	281	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29686003	29686003	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	GG	novel	NA	P-0068180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	70	302	0	ENST00000356175.3:c.8067delinsGG	p.Leu2690ValfsTer19	p.L2690Vfs*19	ENST00000356175	NM_000267.3	2689	ggC/ggGG	55/57	0.468100957019255	1	FACETS	0.929	0.821	1	0.929	0.821	1	CLONAL	1	TRUE	0	0.474722602522591	1		302	242	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0068193-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	68	292	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.195285338569847	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	2	TRUE	0	0.2	2		292	320	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597402	10597402	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068193-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	63	315	0	ENST00000171111.5:c.1801C>G	p.Arg601Gly	p.R601G	ENST00000171111	NM_203500.1	601	Cgg/Ggg	6/6	0.195285338569847	2	FACETS	0.897	0.781	1	0.897	0.781	1	CLONAL	2	TRUE	0	0.2	2		315	351	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615775	1615775	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068193-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	52	297	0	ENST00000344749.5:c.1496G>C	p.Arg499Pro	p.R499P	ENST00000344749	NM_001136139.2	499	cGg/cCg	17/19	0.195285338569847	2	FACETS	0.754	0.644	0.872	0.754	0.644	0.872	SUBCLONAL	2	TRUE	0	0.2	2		297	345	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486017	8486017	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068227-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	154	417	0	ENST00000356435.5:c.2800T>G	p.Ser934Ala	p.S934A	ENST00000356435		934	Tcc/Gcc	17/35	1	2	FACETS	0.779	0.72	0.839	0.779	0.72	0.839	SUBCLONAL	1	TRUE	1	0.909115163349406	2		417	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0068239-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	662	527	0	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	0.698924679063965	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	4	TRUE	0	0.692384796655973	4		527	785	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026449	6026449	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068239-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	52	43	0	ENST00000265849.7:c.1947G>T	p.Arg649Ser	p.R649S	ENST00000265849	NM_000535.5	649	agG/agT	11/15	0.698924679063965	4	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	2	0.692384796655973	4		43	111	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55339528	55339528	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068239-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	186	378	0	ENST00000284073.2:c.287C>A	p.Ala96Glu	p.A96E	ENST00000284073	NM_138962.2	96	gCa/gAa	5/14	0.698924679063965	2	FACETS	1	0.97	1	0.537	0.5	0.575	CLONAL	1	TRUE	0	0.692384796655973	2		378	500	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0068288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	83	467	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	1	2	FACETS	0.608	0.538	0.681	0.608	0.538	0.681	SUBCLONAL	1	TRUE	1	0.597829103152291	2		467	457	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070880	30070880	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315504	NA	P-0068288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	33	294	1	ENST00000338641.4:c.1396C>T	p.Arg466Ter	p.R466*	ENST00000338641	NM_000268.3	466	Cga/Tga	13/16	0.479350332466892	0	FACETS	0.243	0.199	0.29			1	SUBCLONAL	1	TRUE	0	0.597829103152291	0		295	183	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149353	119149355	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	novel	NA	P-0068292-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	14	465	0	ENST00000264033.4:c.1363_1365del	p.Tyr455del	p.Y455del	ENST00000264033	NM_005188.3	454	aATTat/aat	9/16	0.71544175655832	2	FACETS	0.149	0.107	0.199	0.074	0.053	0.1	SUBCLONAL	1	TRUE	0	0.71544175655832	2		465	263	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149355	119149355	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068292-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	186	477	0	ENST00000264033.4:c.1363T>G	p.Tyr455Asp	p.Y455D	ENST00000264033	NM_005188.3	455	Tat/Gat	9/16	0.71544175655832	2	FACETS	0.942	0.894	0.988	0.942	0.894	0.988	CLONAL	2	TRUE	0	0.71544175655832	2		477	276	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0068314-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	37	288	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		288	184	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584772	48584773	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0068314-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	94	364	0	ENST00000342988.3:c.854dup	p.Asn285LysfsTer23	p.N285Kfs*23	ENST00000342988	NM_005359.5	284	caa/cAaa	7/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		364	479	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971165	21971187	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGCAGCAGCTCCGCCACTCGG	GCAGCAGCAGCTCCGCCACTCGG	-	novel	NA	P-0068314-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	186	462	0	ENST00000304494.5:c.171_193del	p.Arg58ProfsTer54	p.R58Pfs*54	ENST00000304494	NM_000077.4	57	gcCCGAGTGGCGGAGCTGCTGCTGCtc/gctc	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		462	567	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440943	56440943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786205215	NA	P-0068343-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	268	317	0	ENST00000407977.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000407977		132	Cga/Tga	4/10	0.601645491043583	2	FACETS	0.981	0.937	1	0.981	0.937	1	CLONAL	2	TRUE	0	0.639796177278703	2		317	427	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930634	32930634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56070345	NA	P-0068343-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	131	274	0	ENST00000380152.3:c.7505G>A	p.Arg2502His	p.R2502H	ENST00000380152		2502	cGc/cAc	15/27	0.601645491043583	2	FACETS	0.939	0.859	1	0.47	0.429	0.511	CLONAL	1	TRUE	0	0.639796177278703	2		274	436	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876427	35876427	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068343-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	183	315	0	ENST00000303115.3:c.1219A>T	p.Ser407Cys	p.S407C	ENST00000303115	NM_002185.3	407	Agc/Tgc	8/8	0.307662585511915	3	FACETS	1	0.986	1	0.624	0.579	0.67	INDETERMINATE	1	TRUE	1	0.639796177278703	3		315	605	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525874	148525874	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068343-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	40	237	0	ENST00000320356.2:c.583G>A	p.Glu195Lys	p.E195K	ENST00000320356	NM_004456.4	195	Gaa/Aaa	6/20	0.601645491043583	2	FACETS	0.436	0.364	0.515	0.218	0.182	0.258	SUBCLONAL	1	TRUE	0	0.639796177278703	2		237	287	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50490732	50490732	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068343-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	81	227	0	ENST00000394963.4:c.1369C>A	p.Gln457Lys	p.Q457K	ENST00000394963	NM_003076.4	457	Cag/Aag	11/13	0.307662585511915	3	FACETS	0.809	0.717	0.907	0.405	0.358	0.454	INDETERMINATE	1	TRUE	1	0.639796177278703	3		227	413	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148526879	148526879	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068343-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	26	221	0	ENST00000320356.2:c.425A>T	p.Asp142Val	p.D142V	ENST00000320356	NM_004456.4	142	gAt/gTt	5/20	0.601645491043583	2	FACETS	0.332	0.263	0.409	0.166	0.131	0.205	SUBCLONAL	1	TRUE	0	0.639796177278703	2		221	245	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420229	88420229	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068343-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	57	269	0	ENST00000360948.2:c.2457G>C	p.Glu819Asp	p.E819D	ENST00000360948	NM_001012338.2	819	gaG/gaC	19/19	0.362877758918143	3	FACETS	0.495	0.425	0.571	0.248	0.212	0.286	INDETERMINATE	1	TRUE	1	0.639796177278703	3		269	475	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337744	73337744	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068343-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	38	215	0	ENST00000377767.4:c.1972G>A	p.Glu658Lys	p.E658K	ENST00000377767	NM_014953.3	658	Gaa/Aaa	16/21	0.601645491043583	2	FACETS	0.459	0.381	0.544	0.229	0.19	0.272	SUBCLONAL	1	TRUE	0	0.639796177278703	2		215	259	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873172	71873172	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068343-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	53	268	0	ENST00000357731.5:c.1022C>A	p.Ser341Tyr	p.S341Y	ENST00000357731	NM_173808.2	341	tCt/tAt	7/7	0.362877758918143	3	FACETS	0.509	0.434	0.589	0.254	0.217	0.295	INDETERMINATE	1	TRUE	1	0.639796177278703	3		268	430	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62322235	62322235	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068343-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	90	277	0	ENST00000360203.5:c.2491C>T	p.Pro831Ser	p.P831S	ENST00000360203	NM_001283009.1	831	Ccc/Tcc	27/35	0.458715404369199	4	FACETS	0.85	0.756	0.949	0.425	0.378	0.475	CLONAL	1	TRUE	2	0.639796177278703	4		277	543	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056985	180056985	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068343-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	179	352	0	ENST00000261937.6:c.634G>A	p.Asp212Asn	p.D212N	ENST00000261937	NM_182925.4	212	Gac/Aac	5/30	0.639796177278703	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.639796177278703	1		352	374	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554729	63554729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1175877868	NA	P-0068353-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	283	428	0	ENST00000307078.5:c.10G>A	p.Ala4Thr	p.A4T	ENST00000307078	NM_004655.3	4	Gct/Act	2/11	0.684651919654258	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.679533643487878	4		428	645	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0068366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	51	560	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.110400890518752	3	FACETS	0.823	0.699	0.96	0.549	0.466	0.64	CLONAL	2	TRUE	0	0.110400890518752	3		560	592	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950412	17950412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573731097	NA	P-0068366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	34	426	0	ENST00000458235.1:c.1315C>T	p.Leu439Phe	p.L439F	ENST00000458235	NM_000215.3	439	Ctt/Ttt	10/24	0.090436580505417	3	FACETS	1	0.933	1	0.673	0.549	0.812	CLONAL	1	TRUE	1	0.110400890518752	3		426	483	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443584	29443606	+	frameshift_variant	Frame_Shift_Del	DEL	GGTCTCTCGGAGGAAGGACTTGA	GGTCTCTCGGAGGAAGGACTTGA	-	novel	NA	P-0068366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	48	480	0	ENST00000389048.3:c.3611_3633del	p.Leu1204ProfsTer73	p.L1204Pfs*73	ENST00000389048	NM_004304.4	1204	cTCAAGTCCTTCCTCCGAGAGACC/c	23/29	0.0949999585958969	3	FACETS	0.79	0.667	0.925	0.526	0.444	0.617	CLONAL	2	TRUE	0	0.110400890518752	3		480	581	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941638	48941638	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	73	251	0	ENST00000267163.4:c.948del	p.Leu317PhefsTer15	p.L317Ffs*15	ENST00000267163	NM_000321.2	316	aaT/aa	10/27	0.110400890518752	3	FACETS	1	0.927	1	1	0.927	1	CLONAL	3	TRUE	0	0.110400890518752	3		251	431	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0068377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	203	334	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.856518287491411	2		334	457	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069640	69069640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	281	209	2	ENST00000288368.4:c.4315G>A	p.Glu1439Lys	p.E1439K	ENST00000288368	NM_024870.2	1439	Gaa/Aaa	35/40	0.856518287491411	6	FACETS	1	0.99	1	0.481	0.454	0.508	CLONAL	2	TRUE	1	0.856518287491411	6		211	740	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573993	7573994	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCAGCTCTCGGAACATCTCGAA	novel	NA	P-0068377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	138	219	0	ENST00000269305.4:c.1012_1033dup	p.Asn345IlefsTer9	p.N345Ifs*9	ENST00000269305	NM_001126112.2	345	aat/aTTCGAGATGTTCCGAGAGCTGAat	10/11	0.83170678578562	1	FACETS	0.62	0.575	0.666	0.62	0.575	0.666	SUBCLONAL	1	TRUE	0	0.856518287491411	1		219	297	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069621	69069621	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	254	204	1	ENST00000288368.4:c.4296G>C	p.Gln1432His	p.Q1432H	ENST00000288368	NM_024870.2	1432	caG/caC	35/40	0.856518287491411	6	FACETS	1	0.985	1	0.455	0.427	0.482	CLONAL	2	TRUE	1	0.856518287491411	6		205	708	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477826	140477840	+	inframe_deletion	In_Frame_Del	DEL	CTGCTGAGGTGTAGG	CTGCTGAGGTGTAGG	-	novel	NA	P-0068377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	128	190	0	ENST00000288602.6:c.1468_1482del	p.Pro490_Gln494del	p.P490_Q494del	ENST00000288602	NM_004333.4	490	CCTACACCTCAGCAG/-	12/18	1	2	FACETS	0.847	0.777	0.918	0.847	0.777	0.918	CLONAL	1	TRUE	1	0.856518287491411	2		190	353	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69068893	69069607	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AATCTGAAAGAGGTAGCTTTGAACTTAGGCTTAAATATAACCATTTTCTACTGAGAAGAAGGGTCTAGGGAAGGCCCAGTTATGGGGAGGTGACCAGGAAAGCACCATAAAAAAAAGGGTAAGATTTGTTGTGCAGATAAAACTATCTGTGATCATCTTCCTTCTCTTCCTAGTACAGAGGGGGAGACACTGTTACAAGTAGAGGTTTCCTTTATGGATGTAAATTTTCCTTATCAAAGGGAAACTTCTACTCGGTTTTCAGAGTTTCTCCTGTGTCTGCGTGCAGTTTCTCAAAATAACCAGATCAAAATAATCCTTATGCCAATGAGGCATATTTTGGGGTGATATATTCTGGTCTCCTACAGTTATATTTTGGAGCGGCATATTTTGGGCTCCCACAACATATACAAAATGTTTTAAAAATAGAGGACAGTTAAACCAGAAATTTTCTTTGCCCATTGGACAGAAAAATCACCAAATGTTTGATATTTATTTTGAGAGCAGAACAGTTTTCATTCATTTTTGGACCTAACATAGTTTTTTTGCATATATGTTGATAATTGGTCCTATTTGCTAAATTTACTAATAATCAATAAAATTATACTACACGTGGAGAAATTGAGTTATAAAGTTGCTTGTAAAATATGTTTACTTGTTTACACAGCACTAGAGAGCATGGAAGGATATTATTACAGAGACAATGTTTCTGTGGAAG	AATCTGAAAGAGGTAGCTTTGAACTTAGGCTTAAATATAACCATTTTCTACTGAGAAGAAGGGTCTAGGGAAGGCCCAGTTATGGGGAGGTGACCAGGAAAGCACCATAAAAAAAAGGGTAAGATTTGTTGTGCAGATAAAACTATCTGTGATCATCTTCCTTCTCTTCCTAGTACAGAGGGGGAGACACTGTTACAAGTAGAGGTTTCCTTTATGGATGTAAATTTTCCTTATCAAAGGGAAACTTCTACTCGGTTTTCAGAGTTTCTCCTGTGTCTGCGTGCAGTTTCTCAAAATAACCAGATCAAAATAATCCTTATGCCAATGAGGCATATTTTGGGGTGATATATTCTGGTCTCCTACAGTTATATTTTGGAGCGGCATATTTTGGGCTCCCACAACATATACAAAATGTTTTAAAAATAGAGGACAGTTAAACCAGAAATTTTCTTTGCCCATTGGACAGAAAAATCACCAAATGTTTGATATTTATTTTGAGAGCAGAACAGTTTTCATTCATTTTTGGACCTAACATAGTTTTTTTGCATATATGTTGATAATTGGTCCTATTTGCTAAATTTACTAATAATCAATAAAATTATACTACACGTGGAGAAATTGAGTTATAAAGTTGCTTGTAAAATATGTTTACTTGTTTACACAGCACTAGAGAGCATGGAAGGATATTATTACAGAGACAATGTTTCTGTGGAAG	-	novel	NA	P-0068377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3	221	0	0	ENST00000288368.4:c.4232-661_4285del		p.X1411_splice	ENST00000288368	NM_024870.2	1411		35/40	0.856518287491411	6	FACETS	1	0.995	1	1	0.996	1	CLONAL	6	TRUE	1	0.856518287491411	6		0	224	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444806	49444810	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGG	CCAGG	T	novel	NA	P-0068377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	237	364	0	ENST00000301067.7:c.2656_2660delinsA	p.Pro886ArgfsTer43	p.P886Rfs*43	ENST00000301067	NM_003482.3	886	CCTGGg/Ag	10/54	1	2	FACETS	0.986	0.929	1	0.986	0.929	1	CLONAL	1	TRUE	1	0.856518287491411	2		364	561	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0068397-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	117	300	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.211664252262832	2	FACETS	1	0.984	1	0.742	0.671	0.817	CLONAL	1	TRUE	0	0.257284631234795	2		300	613	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0068397-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	38	320	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.411	0.339	0.493	0.411	0.339	0.493	SUBCLONAL	1	TRUE	1	0.257284631234795	2		320	718	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134885835	134885835	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068397-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	99	636	0	ENST00000398015.3:c.1746C>A	p.Tyr582Ter	p.Y582*	ENST00000398015	NM_004441.4	582	taC/taA	9/16	1	2	FACETS	0.86	0.767	0.959	0.86	0.767	0.959	CLONAL	1	TRUE	1	0.257284631234795	2		636	895	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579582	7579583	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0068397-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	119	706	0	ENST00000269305.4:c.104dup	p.Leu35PhefsTer8	p.L35Ffs*8	ENST00000269305	NM_001126112.2	35	ttg/ttTg	4/11	0.257284631234795	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.257284631234795	1		706	775	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183655	10183655	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068397-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	65	790	0	ENST00000256474.2:c.124G>C	p.Glu42Gln	p.E42Q	ENST00000256474	NM_000551.3	42	Gag/Cag	1/3	1	2	FACETS	0.607	0.525	0.696	0.607	0.525	0.696	SUBCLONAL	1	TRUE	1	0.257284631234795	2		790	833	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751391	57751391	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068397-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	56	683	1	ENST00000274289.3:c.1600C>T	p.His534Tyr	p.H534Y	ENST00000274289	NM_006622.3	534	Cac/Tac	11/14	1	2	FACETS	0.478	0.408	0.555	0.478	0.408	0.555	SUBCLONAL	1	TRUE	1	0.257284631234795	2		684	910	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603078	48603078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068397-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	99	496	0	ENST00000342988.3:c.1379C>T	p.Ala460Val	p.A460V	ENST00000342988	NM_005359.5	460	gCc/gTc	11/12	0.257284631234795	1	FACETS	0.993	0.888	1	0.993	0.888	1	CLONAL	1	TRUE	0	0.257284631234795	1		496	675	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779489	3779489	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068397-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	70	836	0	ENST00000262367.5:c.5559G>T	p.Gln1853His	p.Q1853H	ENST00000262367	NM_004380.2	1853	caG/caT	31/31	1	2	FACETS	0.523	0.454	0.597	0.523	0.454	0.597	SUBCLONAL	1	TRUE	1	0.257284631234795	2		836	1041	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124464126	124464126	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068397-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	66	388	0	ENST00000357628.3:c.1795G>C	p.Ala599Pro	p.A599P	ENST00000357628	NM_015450.2	599	Gca/Cca	19/19	0.126116696066088	3	FACETS	0.845	0.733	0.967	0.423	0.366	0.484	INDETERMINATE	1	TRUE	1	0.257284631234795	3		388	685	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177642	56177642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068397-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	55	674	0	ENST00000399503.3:c.2615G>A	p.Gly872Asp	p.G872D	ENST00000399503	NM_005921.1	872	gGc/gAc	14/20	1	2	FACETS	0.47	0.401	0.547	0.47	0.401	0.547	SUBCLONAL	1	TRUE	1	0.257284631234795	2		674	909	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212720	27212720	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068397-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	41	629	0	ENST00000380036.4:c.2702C>A	p.Ala901Asp	p.A901D	ENST00000380036	NM_000459.3	901	gCc/gAc	17/23	1	2	FACETS	0.407	0.338	0.485	0.407	0.338	0.485	SUBCLONAL	1	TRUE	1	0.257284631234795	2		629	783	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228158	53228158	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0068397-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	119	770	0	ENST00000375401.3:c.2243+1G>T		p.X748_splice	ENST00000375401	NM_004187.3	748			0.257284631234795	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.257284631234795	1		770	770	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944707	31944707	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068397-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	15	44	0	ENST00000340398.3:c.394G>T	p.Gly132Ter	p.G132*	ENST00000340398	NM_001013699.2	132	Gga/Tga	1/1	0.211664252262832	2	FACETS	1	0.891	1	0.729	0.543	0.942	CLONAL	1	TRUE	0	0.257284631234795	2		44	80	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40681810	40681810	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068397-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	47	465	0	ENST00000249776.8:c.589C>T	p.Gln197Ter	p.Q197*	ENST00000249776	NM_033286.3	197	Cag/Tag	5/9	1	2	FACETS	0.642	0.541	0.753	0.642	0.541	0.753	SUBCLONAL	1	TRUE	1	0.257284631234795	2		465	569	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212886	94212886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068397-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	55	426	0	ENST00000323929.3:c.356C>T	p.Ser119Leu	p.S119L	ENST00000323929	NM_005591.3	119	tCa/tTa	5/20	0.257284631234795	3	FACETS	0.585	0.499	0.679	0.292	0.249	0.34	SUBCLONAL	1	TRUE	1	0.257284631234795	3		426	825	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456444	189456444	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1330936376	NA	P-0068397-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	94	568	0	ENST00000264731.3:c.205G>C	p.Val69Leu	p.V69L	ENST00000264731	NM_003722.4	69	Gtt/Ctt	3/14	1	2	FACETS	0.956	0.851	1	0.956	0.851	1	CLONAL	1	TRUE	1	0.257284631234795	2		568	764	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375368	118375368	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068397-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	53	718	0	ENST00000534358.1:c.8761G>C	p.Glu2921Gln	p.E2921Q	ENST00000534358	NM_005933.3	2921	Gag/Cag	27/36	0.257284631234795	3	FACETS	0.496	0.422	0.579	0.248	0.211	0.29	SUBCLONAL	1	TRUE	1	0.257284631234795	3		718	937	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0068401-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	11	301	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.715	0.495	0.987	0.715	0.495	0.987	CLONAL	1	TRUE	1	0.18	2		302	171	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	223682	223682	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs369321221	NA	P-0068401-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	18	217	0	ENST00000264932.6:c.149C>T	p.Ser50Phe	p.S50F	ENST00000264932	NM_004168.2	50	tCc/tTc	2/15	1	2	FACETS	1	0.836	1	1	0.836	1	CLONAL	1	TRUE	1	0.18	2		217	175	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827922	40827922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068401-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	28	399	0	ENST00000373198.4:c.2506G>A	p.Asp836Asn	p.D836N	ENST00000373198	NM_133170.3	836	Gat/Aat	17/32	1	2	FACETS	0.71	0.567	0.874	0.71	0.567	0.874	SUBCLONAL	1	TRUE	1	0.18	2		399	438	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956676	93956676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465960814	NA	P-0068401-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	22	330	0	ENST00000369303.4:c.2560C>T	p.Arg854Cys	p.R854C	ENST00000369303	NM_004440.3	854	Cgt/Tgt	15/17	1	2	FACETS	0.82	0.636	1	0.82	0.636	1	CLONAL	1	TRUE	1	0.18	2		330	298	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702657	52702657	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068401-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	22	256	0	ENST00000394830.3:c.241C>T	p.Gln81Ter	p.Q81*	ENST00000394830	NM_018313.4	81	Caa/Taa	4/30	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.18	2		256	191	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729097	66729102	+	inframe_deletion	In_Frame_Del	DEL	AGATCA	AGATCA	-	novel	NA	P-0068401-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	22	397	0	ENST00000307102.5:c.306_311del	p.Ile103_Lys104del	p.I103_K104del	ENST00000307102	NM_002755.3	102	gAGATCAaa/gaa	3/11	1	2	FACETS	0.642	0.497	0.81	0.642	0.497	0.81	SUBCLONAL	1	TRUE	1	0.18	2		397	381	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932705	39932705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762605753	NA	P-0068401-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	30	243	0	ENST00000378444.4:c.1894G>A	p.Gly632Ser	p.G632S	ENST00000378444	NM_001123385.1	632	Ggc/Agc	4/15	0.0181818608226458	2	FACETS	0.765	0.62	0.926			1	INDETERMINATE	2	TRUE	NA	0.18	2		243	218	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851653	134851653	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068401-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	28	346	0	ENST00000398015.3:c.1059T>A	p.Asp353Glu	p.D353E	ENST00000398015	NM_004441.4	353	gaT/gaA	5/16	1	2	FACETS	0.894	0.715	1	0.894	0.715	1	CLONAL	1	TRUE	1	0.18	2		346	348	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933789	36933789	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068401-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	26	432	0	ENST00000361632.4:c.1610A>C	p.His537Pro	p.H537P	ENST00000361632		537	cAc/cCc	12/16	1	2	FACETS	0.703	0.556	0.871	0.703	0.556	0.871	SUBCLONAL	1	TRUE	1	0.18	2		432	411	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680878	30680878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068401-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	35	517	0	ENST00000376406.3:c.841G>A	p.Gly281Arg	p.G281R	ENST00000376406	NM_014641.2	281	Ggg/Agg	5/15	0.110873057096596	3	FACETS	0.836	0.684	1	0.418	0.342	0.504	CLONAL	1	TRUE	1	0.18	3		517	507	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400155	41400155	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068401-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	26	359	0	ENST00000373198.4:c.604G>A	p.Glu202Lys	p.E202K	ENST00000373198	NM_133170.3	202	Gag/Aag	5/32	1	2	FACETS	0.772	0.612	0.957	0.772	0.612	0.957	CLONAL	1	TRUE	1	0.18	2		359	374	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376021	8376021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068401-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	20	329	0	ENST00000356435.5:c.4576G>A	p.Glu1526Lys	p.E1526K	ENST00000356435		1526	Gaa/Aaa	28/35	1	2	FACETS	0.656	0.501	0.837	0.656	0.501	0.837	SUBCLONAL	1	TRUE	1	0.18	2		329	339	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634642	158634642	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0068401-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	26	360	0	ENST00000263640.3:c.543+1G>A		p.X181_splice	ENST00000263640	NM_001105.4	181			1	2	FACETS	0.791	0.627	0.98	0.791	0.627	0.98	CLONAL	1	TRUE	1	0.18	2		360	365	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888845	76888845	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068401-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	21	182	0	ENST00000373344.5:c.4984C>T	p.Pro1662Ser	p.P1662S	ENST00000373344	NM_000489.3	1662	Cct/Tct	19/35	0.0181818608226458	2	FACETS	0.827	0.644	1			1	INDETERMINATE	2	TRUE	NA	0.18	2		182	141	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447468	12447469	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0068401-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	25	436	0	ENST00000287820.6:c.707_708delinsTT	p.Ser236Phe	p.S236F	ENST00000287820	NM_015869.4	236	tCC/tTT	5/7	1	2	FACETS	0.642	0.505	0.799	0.642	0.505	0.799	SUBCLONAL	1	TRUE	1	0.18	2		436	433	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230459227	230459227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068401-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	29	372	0	ENST00000391860.1:c.1174G>A	p.Gly392Arg	p.G392R	ENST00000391860	NM_001258311.1	392	Gga/Aga	7/7	1	2	FACETS	0.885	0.711	1	0.885	0.711	1	CLONAL	1	TRUE	1	0.18	2		372	364	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206677	27206677	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068401-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	16	363	0	ENST00000380036.4:c.2462G>A	p.Trp821Ter	p.W821*	ENST00000380036	NM_000459.3	821	tGg/tAg	15/23	1	2	FACETS	0.568	0.419	0.746	0.568	0.419	0.746	SUBCLONAL	1	TRUE	1	0.18	2		363	313	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81968137	81968137	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0068401-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	27	314	0	ENST00000359376.3:c.2842+1G>C		p.X948_splice	ENST00000359376	NM_002661.3	948			1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	1	0.18	2		314	279	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375255	31375255	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068401-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	29	408	0	ENST00000328111.2:c.652C>T	p.Gln218Ter	p.Q218*	ENST00000328111	NM_006892.3	218	Cag/Tag	6/23	1	2	FACETS	0.839	0.674	1	0.839	0.674	1	CLONAL	1	TRUE	1	0.18	2		408	384	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068416-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	30	382	0				ENST00000310581	NM_198253.2	-/1132			0.26729722121426	1	FACETS	0.513	0.414	0.624	0.513	0.414	0.624	SUBCLONAL	1	TRUE	0	0.341501974079073	1		382	284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578213	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs864309495	NA	P-0068416-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	360	547	0	ENST00000269305.4:c.636del	p.Arg213AspfsTer34	p.R213Dfs*34	ENST00000269305	NM_001126112.2	212	ttT/tt	6/11	0.258150568717247	4	FACETS	1	0.991	1	0.87	0.829	0.911	CLONAL	3	TRUE	0	0.341501974079073	4		547	813	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978895	25978895	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068416-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	99	294	0	ENST00000435504.4:c.1028T>G	p.Leu343Arg	p.L343R	ENST00000435504		343	cTc/cGc	10/13	0.15470441749064	3	FACETS	1	0.903	1			1	INDETERMINATE	2	TRUE	NA	0.341501974079073	3		294	339	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172211	99172211	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068416-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	54	618	0	ENST00000074304.5:c.1777C>T	p.Pro593Ser	p.P593S	ENST00000074304	NM_001134224.1	593	Ccc/Tcc	17/26	0.203605015831584	2	FACETS	0.432	0.368	0.502	0.216	0.184	0.251	INDETERMINATE	1	TRUE	0	0.341501974079073	2		618	732	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862885	117862885	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1281760771	NA	P-0068416-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	31	267	0	ENST00000297338.2:c.1592A>G	p.Lys531Arg	p.K531R	ENST00000297338	NM_006265.2	531	aAg/aGg	12/14	0.276233142043611	3	FACETS	0.555	0.449	0.675	0.185	0.149	0.225	SUBCLONAL	1	TRUE	0	0.341501974079073	3		267	383	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973820	15973820	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068416-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	342	428	0	ENST00000268712.3:c.4172A>G	p.Asp1391Gly	p.D1391G	ENST00000268712	NM_006311.3	1391	gAc/gGc	31/46	0.258150568717247	4	FACETS	0.896	0.853	0.938	0.896	0.853	0.938	CLONAL	4	TRUE	0	0.341501974079073	4		428	750	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821389	32821389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781627254	NA	P-0068416-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	121	508	0	ENST00000354258.4:c.205C>T	p.Pro69Ser	p.P69S	ENST00000354258	NM_000593.5	69	Ccc/Tcc	1/11	0.159451941650634	3	FACETS	1	0.984	1	0.725	0.657	0.796	INDETERMINATE	1	TRUE	1	0.341501974079073	3		508	572	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436619	8436619	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068416-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	22	303	0	ENST00000356435.5:c.4059C>A	p.Asp1353Glu	p.D1353E	ENST00000356435		1353	gaC/gaA	24/35	NA	2	FACETS	0.447	0.347	0.564			1	INDETERMINATE	1	TRUE	NA	0.341501974079073	2		303	288	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775950	9775950	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068416-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	40	466	0	ENST00000377346.4:c.414C>G	p.Asp138Glu	p.D138E	ENST00000377346	NM_005026.3	138	gaC/gaG	5/24	0.317585839071764	2	FACETS	0.424	0.351	0.504	0.212	0.175	0.252	SUBCLONAL	1	TRUE	0	0.341501974079073	2		466	553	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193721	106193721	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068416-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	46	378	0	ENST00000380013.4:c.4183G>C	p.Val1395Leu	p.V1395L	ENST00000380013	NM_001127208.2	1395	Gta/Cta	10/11	0.341501974079073	1	FACETS	0.517	0.436	0.607	0.517	0.436	0.607	SUBCLONAL	1	TRUE	0	0.341501974079073	1		378	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0068435-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	434	425	0	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.333237929703204	4	FACETS	1	0.99	1	0.825	0.791	0.86	CLONAL	3	TRUE	0	0.408110608263795	4		425	907	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721882	176721882	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068435-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	137	356	0	ENST00000439151.2:c.7513G>C	p.Glu2505Gln	p.E2505Q	ENST00000439151	NM_022455.4	2505	Gag/Cag	23/23	0.408110608263795	5	FACETS	0.981	0.891	1	0.245	0.222	0.27	CLONAL	1	TRUE	1	0.408110608263795	5		356	1103	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332040	81332040	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068435-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	26	255	0	ENST00000222390.5:c.2044C>T	p.His682Tyr	p.H682Y	ENST00000222390	NM_000601.4	682	Cat/Tat	18/18	0.116185592525624	1	FACETS	0.351	0.278	0.434	0.351	0.278	0.434	INDETERMINATE	1	TRUE	0	0.408110608263795	1		255	289	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150913814	150913814	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068435-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	74	190	0	ENST00000271640.5:c.457G>T	p.Ala153Ser	p.A153S	ENST00000271640	NM_001145415.1	153	Gct/Tct	5/22	0.409943397757333	4	FACETS	0.848	0.743	0.961	0.212	0.185	0.241	CLONAL	1	TRUE	0	0.408110608263795	4		190	602	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821773	72821773	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068435-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	110	326	0	ENST00000268489.5:c.10402C>G	p.Arg3468Gly	p.R3468G	ENST00000268489	NM_006885.3	3468	Cgc/Ggc	10/10	0.152516250925559	5	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.408110608263795	5		326	770	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22153406	22153487	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAGTCACAGATCTAAGAGAGAAAAAAAACAGGATAACTTCTTAGAAATTCTAACCTTTCATATCAAAACATCACAAAAATA	AAAGTCACAGATCTAAGAGAGAAAAAAAACAGGATAACTTCTTAGAAATTCTAACCTTTCATATCAAAACATCACAAAAATA	-	novel	NA	P-0068435-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	53	306	0	ENST00000215832.6:c.493-70_504del		p.X165_splice	ENST00000215832	NM_002745.4	165		4/9	0.409943397757333	4	FACETS	0.553	0.471	0.644	0.277	0.235	0.322	SUBCLONAL	1	TRUE	2	0.408110608263795	4		306	661	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931663	39931663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068435-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	99	244	0	ENST00000378444.4:c.2936G>A	p.Cys979Tyr	p.C979Y	ENST00000378444	NM_001123385.1	979	tGt/tAt	4/15	0.152516250925559	5	FACETS	1	0.967	1			1	INDETERMINATE	1	TRUE	NA	0.408110608263795	5		244	648	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0068443-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	22	300	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.337	0.26	0.426	0.337	0.26	0.426	SUBCLONAL	1	TRUE	1	0.325895798183354	2		300	401	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713723	30713724	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0068443-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	28	501	0	ENST00000295754.5:c.1048_1049del	p.Leu350GlyfsTer14	p.L350Gfs*14	ENST00000295754	NM_003242.5	350	CTg/g	4/7	1	2	FACETS	0.321	0.256	0.396	0.321	0.256	0.396	SUBCLONAL	1	TRUE	1	0.325895798183354	2		501	535	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647027	23647028	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0068466-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	92	490	0	ENST00000261584.4:c.839dup	p.Asn280LysfsTer3	p.N280Kfs*3	ENST00000261584	NM_024675.3	280	aac/aaAc	4/13	0.737095813747215	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.733024774495428	1		490	142	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579558	7579558	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs754332870	NA	P-0068466-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	329	563	0	ENST00000269305.4:c.129G>C	p.Leu43Phe	p.L43F	ENST00000269305	NM_001126112.2	43	ttG/ttC	4/11	0.737095813747215	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.733024774495428	1		563	467	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485757	57485757	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068466-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	142	446	0	ENST00000371085.3:c.1058G>C	p.Gly353Ala	p.G353A	ENST00000371085	NM_000516.4	353	gGa/gCa	13/13	0.432741952917978	2	FACETS	0.658	0.602	0.716	0.329	0.301	0.358	INDETERMINATE	1	TRUE	0	0.733024774495428	2		446	589	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022898	27022898	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068466-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	289	458	0	ENST00000324856.7:c.4G>T	p.Ala2Ser	p.A2S	ENST00000324856	NM_006015.4	2	Gcc/Tcc	1/20	0.414756298674469	1	FACETS	0.864	0.821	0.907	0.864	0.821	0.907	INDETERMINATE	1	TRUE	0	0.733024774495428	1		458	578	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32903543	32903604	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGATAATATACAATACACATAAATTTTTATCTTACAGTCAGAAATGAAGAAGCATCTGAAAC	TGATAATATACAATACACATAAATTTTTATCTTACAGTCAGAAATGAAGAAGCATCTGAAAC	-	novel	NA	P-0068466-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	23	206	0	ENST00000380152.3:c.632-35_658del		p.X211_splice	ENST00000380152		211		8/27	0.737095813747215	1	FACETS	0.828	0.683	0.975	0.828	0.683	0.975	CLONAL	1	TRUE	0	0.733024774495428	1		206	48	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068466-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	281	484	1	ENST00000269305.4:c.836G>C	p.Gly279Ala	p.G279A	ENST00000269305	NM_001126112.2	279	gGg/gCg	8/11	0.737095813747215	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.733024774495428	1		485	446	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12043156	12043156	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068466-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	56	265	0	ENST00000353533.5:c.1041C>A	p.Cys347Ter	p.C347*	ENST00000353533	NM_003010.3	347	tgC/tgA	10/11	0.737095813747215	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.733024774495428	1		265	79	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120015	70120083	+	inframe_deletion	In_Frame_Del	DEL	GCAGGCGCCGCCGCCACCCCCGCAGCAGCCCCCACAGGCCCCGCCGGCCCCGCAGGCGCCCCCGCAGCC	GCAGGCGCCGCCGCCACCCCCGCAGCAGCCCCCACAGGCCCCGCCGGCCCCGCAGGCGCCCCCGCAGCC	-	novel	NA	P-0068466-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	484	541	0	ENST00000245479.2:c.1024_1092del	p.Pro342_Ala364del	p.P342_A364del	ENST00000245479	NM_000346.3	339	caGCAGGCGCCGCCGCCACCCCCGCAGCAGCCCCCACAGGCCCCGCCGGCCCCGCAGGCGCCCCCGCAGCCg/cag	3/3	0.670917738114688	3	FACETS	0.999	0.962	1	0.999	0.962	1	CLONAL	2	TRUE	1	0.733024774495428	3		541	903	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374696	118374696	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068466-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	124	512	0	ENST00000534358.1:c.8089G>C	p.Glu2697Gln	p.E2697Q	ENST00000534358	NM_005933.3	2697	Gag/Cag	27/36	1	2	FACETS	0.646	0.587	0.707	0.646	0.587	0.707	SUBCLONAL	1	TRUE	1	0.733024774495428	2		512	524	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057593	27057647	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCCTCATGCAGGAGAGTCAGTGCTAAAAGTATATTTTCCTTTCCTACAGATTCC	TTCCTCATGCAGGAGAGTCAGTGCTAAAAGTATATTTTCCTTTCCTACAGATTCC	ACAGAT	novel	NA	P-0068466-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	227	483	2	ENST00000324856.7:c.1351-50_1355delinsACAGAT		p.X451_splice	ENST00000324856	NM_006015.4	451		3/20	0.414756298674469	1	FACETS	0.762	0.717	0.807	0.762	0.717	0.807	INDETERMINATE	1	TRUE	0	0.733024774495428	1		485	515	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246582	46246582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068466-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	229	484	0	ENST00000334344.6:c.4676G>A	p.Gly1559Glu	p.G1559E	ENST00000334344	NM_152641.2	1559	gGa/gAa	15/21	0.737095813747215	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.733024774495428	1		484	322	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64286796	64286796	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068466-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	62	344	0	ENST00000370651.3:c.11T>C	p.Met4Thr	p.M4T	ENST00000370651	NM_003463.4	4	aTg/aCg	2/6	0.330440659761149	1	FACETS	0.411	0.358	0.466	0.411	0.358	0.466	INDETERMINATE	1	TRUE	0	0.733024774495428	1		344	261	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15952260	15952276	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCGAAGAGACGTGAC	CTCCGAAGAGACGTGAC	A	novel	NA	P-0068466-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	275	435	2	ENST00000268712.3:c.6419_6435delinsT	p.Ser2140IlefsTer44	p.S2140Ifs*44	ENST00000268712	NM_006311.3	2140	aGTCACGTCTCTTCGGAG/aT	41/46	0.737095813747215	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.733024774495428	1		437	404	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0068467-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	91	547	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.172453388249349	4	FACETS	0.935	0.833	1	0.468	0.416	0.522	INDETERMINATE	1	TRUE	2	0.601781089636748	4		547	518	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880451	155880451	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068467-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	76	321	0	ENST00000368323.3:c.102G>C	p.Lys34Asn	p.K34N	ENST00000368323	NM_006912.5	34	aaG/aaC	2/6	0.172453388249349	4	FACETS	0.812	0.714	0.917	0.406	0.357	0.459	INDETERMINATE	1	TRUE	2	0.601781089636748	4		321	498	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068467-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	143	441	0	ENST00000269305.4:c.548C>A	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tAa	5/11	0.601781089636748	1	FACETS	0.684	0.628	0.742	0.684	0.628	0.742	SUBCLONAL	1	TRUE	0	0.601781089636748	1		441	486	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202468	67202482	+	inframe_deletion	In_Frame_Del	DEL	AGTTCTCCCCTTTTG	AGTTCTCCCCTTTTG	-	novel	NA	P-0068467-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	151	362	0	ENST00000312629.5:c.1279_1293del	p.Phe427_Glu431del	p.F427_E431del	ENST00000312629	NM_003952.2	426	aAGTTCTCCCCTTTTGag/aag	15/15	0.212805377798678	4	FACETS	0.88	0.805	0.96	0.44	0.402	0.48	INDETERMINATE	1	TRUE	2	0.601781089636748	4		362	913	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409408	80409408	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068467-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	80	213	0	ENST00000286548.4:c.706G>C	p.Asp236His	p.D236H	ENST00000286548	NM_002072.3	236	Gat/Cat	5/7	0.472718962465257	1	FACETS	0.645	0.574	0.72	0.645	0.574	0.72	SUBCLONAL	1	TRUE	0	0.601781089636748	1		213	288	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407981	139407981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068467-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	102	318	0	ENST00000277541.6:c.2216G>A	p.Cys739Tyr	p.C739Y	ENST00000277541	NM_017617.3	739	tGc/tAc	14/34	0.428960569775452	1	FACETS	0.491	0.441	0.543	0.491	0.441	0.543	SUBCLONAL	1	TRUE	0	0.601781089636748	1		318	483	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820190	32820190	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs757711839	NA	P-0068467-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	73	365	0	ENST00000354258.4:c.868C>G	p.Leu290Val	p.L290V	ENST00000354258	NM_000593.5	290	Ctc/Gtc	2/11	0.239984705348751	2	FACETS	0.491	0.43	0.556	0.246	0.215	0.278	INDETERMINATE	1	TRUE	0	0.601781089636748	2		365	494	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	58	382	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.851798628407095	2		382	135	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0068471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	129	184	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.851798628407095	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.851798628407095	1		184	158	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730877	40730877	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1479203418	NA	P-0068471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	263	185	0	ENST00000373198.4:c.3658C>T	p.Arg1220Trp	p.R1220W	ENST00000373198	NM_133170.3	1220	Cgg/Tgg	27/32	0.851798628407095	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.851798628407095	3		185	412	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528596	8528596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	72	136	0	ENST00000356435.5:c.536G>A	p.Arg179Gln	p.R179Q	ENST00000356435		179	cGa/cAa	4/35	1	2	FACETS	0.939	0.839	1	0.939	0.839	1	CLONAL	1	TRUE	1	0.851798628407095	2		136	180	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443757	52443757	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1208026193	NA	P-0068471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	130	217	0	ENST00000460680.1:c.40C>T	p.Leu14Phe	p.L14F	ENST00000460680	NM_004656.3	14	Ctc/Ttc	2/17	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.851798628407095	2		217	274	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914527	32914527	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	98	177	0	ENST00000380152.3:c.6035C>T	p.Ser2012Phe	p.S2012F	ENST00000380152		2012	tCc/tTc	11/27	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.851798628407095	2		177	226	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630083	117630083	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	74	108	0	ENST00000368508.3:c.6443G>A	p.Gly2148Glu	p.G2148E	ENST00000368508	NM_002944.2	2148	gGa/gAa	41/43	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.851798628407095	2		108	167	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906781	32906781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507263	NA	P-0068471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	91	180	0	ENST00000380152.3:c.1166C>T	p.Pro389Leu	p.P389L	ENST00000380152		389	cCg/cTg	10/27	1	2	FACETS	0.925	0.837	1	0.925	0.837	1	CLONAL	1	TRUE	1	0.851798628407095	2		180	231	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874311	151874311	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs952132535	NA	P-0068471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	67	160	0	ENST00000262189.6:c.8227C>T	p.Pro2743Ser	p.P2743S	ENST00000262189	NM_170606.2	2743	Ccc/Tcc	38/59	1	2	FACETS	0.936	0.833	1	0.936	0.833	1	CLONAL	1	TRUE	1	0.851798628407095	2		160	168	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095537	178095540	+	frameshift_variant	Frame_Shift_Del	DEL	CTTA	CTTA	-	rs748937667	NA	P-0068471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	14	124	0	ENST00000397062.3:c.1791_1794del	p.Ser597ArgfsTer14	p.S597Rfs*14	ENST00000397062	NM_006164.4	597	agTAAG/ag	5/5	1	2	FACETS	0.186	0.134	0.247	0.186	0.134	0.247	SUBCLONAL	1	TRUE	1	0.851798628407095	2		124	177	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166250	118166250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1462556539	NA	P-0068471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	158	174	0	ENST00000369448.3:c.760G>A	p.Asp254Asn	p.D254N	ENST00000369448	NM_017709.3	254	Gac/Aac	2/2	0.851798628407095	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.851798628407095	1		174	191	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262246	46262246	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	83	130	0	ENST00000371998.3:c.830T>C	p.Val277Ala	p.V277A	ENST00000371998		277	gTt/gCt	9/23	0.851798628407095	3	FACETS	1	0.954	1	0.56	0.502	0.621	CLONAL	1	TRUE	1	0.851798628407095	3		130	248	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098933	178098933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	103	160	0	ENST00000397062.3:c.112G>A	p.Asp38Asn	p.D38N	ENST00000397062	NM_006164.4	38	Gac/Aac	2/5	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.851798628407095	2		160	237	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679723	88679733	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGTGACTAT	CCAGTGACTAT	-	novel	NA	P-0068471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	237	125	0	ENST00000360948.2:c.730_740del	p.Ile244AlafsTer29	p.I244Afs*29	ENST00000360948	NM_001012338.2	244	ATAGTCACTGGg/g	7/19	0.598301859960623	4	FACETS	1	0.989	1	0.818	0.785	0.849	CLONAL	3	TRUE	0	0.851798628407095	4		125	315	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754602	57754602	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	70	141	0	ENST00000274289.3:c.445T>C	p.Phe149Leu	p.F149L	ENST00000274289	NM_006622.3	149	Ttc/Ctc	3/14	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.851798628407095	2		141	163	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0068477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	56	264	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.162423954131228	2		264	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0068477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	76	508	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.162423954131228	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	0	0.162423954131228	1		508	692	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70353052	70353052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	39	342	1	ENST00000374080.3:c.4607G>A	p.Arg1536Gln	p.R1536Q	ENST00000374080		1536	cGg/cAg	33/45	1	2	FACETS	0.872	0.721	1	0.872	0.721	1	CLONAL	1	FALSE	1	0.162423954131228	2		343	551	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023241	27023242	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0068477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	60	386	0	ENST00000324856.7:c.347_348insAT	p.Asn116LysfsTer117	p.N116Kfs*117	ENST00000324856	NM_006015.4	116	aac/aaATc	1/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.162423954131228	2		386	572	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726726	41726727	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0068477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	62	431	0	ENST00000301178.4:c.271_272delinsAT	p.Asp91Ile	p.D91I	ENST00000301178	NM_021913.4	91	GAt/ATt	2/20	0.162423954131228	3	FACETS	1	0.944	1	0.593	0.511	0.682	CLONAL	1	FALSE	1	0.162423954131228	3		431	696	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0068478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	64	385	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.464515733443479	2		385	244	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575080	48575080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	24	439	0	ENST00000342988.3:c.274C>T	p.His92Tyr	p.H92Y	ENST00000342988	NM_005359.5	92	Cat/Tat	3/12	1	2	FACETS	0.268	0.209	0.335	0.268	0.209	0.335	SUBCLONAL	1	TRUE	1	0.464515733443479	2		439	386	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639376	3639376	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	82	531	0	ENST00000294008.3:c.4263T>G	p.Ile1421Met	p.I1421M	ENST00000294008	NM_032444.2	1421	atT/atG	12/15	1	2	FACETS	0.924	0.82	1	0.924	0.82	1	CLONAL	1	TRUE	1	0.464515733443479	2		531	382	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188244	10188245	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0068478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	94	350	0	ENST00000256474.2:c.387_388del	p.Val130Ter	p.V130*	ENST00000256474	NM_000551.3	129	ctGGtt/cttt	2/3	0.464515733443479	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.464515733443479	1		350	280	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643761	52643761	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	82	468	0	ENST00000394830.3:c.2135del	p.His712ProfsTer2	p.H712Pfs*2	ENST00000394830	NM_018313.4	712	cAc/cc	17/30	0.464515733443479	1	FACETS	0.85	0.756	0.948	0.85	0.756	0.948	CLONAL	1	TRUE	0	0.464515733443479	1		468	319	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0068479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	99	317	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		317	269	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402833	20402834	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCG	rs746263274	NA	P-0068479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	29	477	0	ENST00000346618.3:c.385_387dup	p.Gly129dup	p.G129dup	ENST00000346618	NM_001949.4	129	agc/aGCGgc	1/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		477	285	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374250	15374255	+	inframe_deletion	In_Frame_Del	DEL	GCCACC	GCCACC	-	novel	NA	P-0068479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	65	489	0	ENST00000263377.2:c.1317_1322del	p.Val440_Ala441del	p.V440_A441del	ENST00000263377	NM_058243.2	439	gtGGTGGCc/gtc	7/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		489	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	732	639	0	ENST00000269305.4:c.517G>C	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ctg	5/11	0.71407815763338	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	4	TRUE	0	0.709501858218626	4		639	864	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226846	142226846	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	334	404	0	ENST00000350721.4:c.4958G>A	p.Arg1653Gln	p.R1653Q	ENST00000350721	NM_001184.3	1653	cGa/cAa	28/47	0.709501858218626	6	FACETS	1	0.969	1			1	CLONAL	2	TRUE	NA	0.709501858218626	6		404	1101	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034529	123034529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	76	222	0	ENST00000355640.3:c.1286C>T	p.Thr429Ile	p.T429I	ENST00000355640		429	aCt/aTt	6/7	NA	2	FACETS	0.793	0.704	0.887			1	INDETERMINATE	1	TRUE	NA	0.709501858218626	2		222	270	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884820	134884820	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	109	379	0	ENST00000398015.3:c.1596G>C	p.Lys532Asn	p.K532N	ENST00000398015	NM_004441.4	532	aaG/aaC	8/16	0.71407815763338	3	FACETS	0.499	0.447	0.553			1	SUBCLONAL	1	TRUE	NA	0.709501858218626	3		379	835	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518378	8518378	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1518	355	431	0	ENST00000356435.5:c.1013G>T	p.Ser338Ile	p.S338I	ENST00000356435		338	aGc/aTc	10/35	0.709501858218626	9	FACETS	0.931	0.878	0.984	0.233	0.219	0.246	CLONAL	2	TRUE	1	0.709501858218626	9		431	1873	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845305	76845305	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	109	339	0	ENST00000373344.5:c.6216A>C	p.Lys2072Asn	p.K2072N	ENST00000373344	NM_000489.3	2072	aaA/aaC	27/35	0.298364182039837	2	FACETS	0.695	0.628	0.765	0.348	0.314	0.383	INDETERMINATE	1	TRUE	0	0.709501858218626	2		339	442	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753362	42753362	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	194	650	0	ENST00000222329.4:c.902C>G	p.Ser301Cys	p.S301C	ENST00000222329	NM_006494.2	301	tCc/tGc	4/4	0.71407815763338	3	FACETS	0.93	0.862	1	0.465	0.431	0.5	CLONAL	1	TRUE	1	0.709501858218626	3		650	797	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256571	16256571	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	216	556	0	ENST00000375759.3:c.3836C>G	p.Pro1279Arg	p.P1279R	ENST00000375759	NM_015001.2	1279	cCt/cGt	11/15	0.681136383507506	3	FACETS	0.976	0.909	1			1	CLONAL	1	TRUE	NA	0.709501858218626	3		556	845	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs985033810	NA	P-0068482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	182	278	0	ENST00000269305.4:c.731G>T	p.Gly244Val	p.G244V	ENST00000269305	NM_001126112.2	244	gGc/gTc	7/11	0.407869537309107	4	FACETS	0.991	0.931	1	0.743	0.698	0.788	CLONAL	3	FALSE	0	0.552309954473549	4		278	344	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0068483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	111	527	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	1	2	FACETS	0.708	0.638	0.781	0.708	0.638	0.781	SUBCLONAL	1	TRUE	1	0.516013087752647	2		527	608	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265573	198265573	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	107	395	0	ENST00000335508.6:c.2584G>A	p.Glu862Lys	p.E862K	ENST00000335508	NM_012433.2	862	Gaa/Aaa	18/25	1	2	FACETS	0.894	0.806	0.986	0.894	0.806	0.986	CLONAL	1	TRUE	1	0.516013087752647	2		395	464	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040723	47040723	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	154	465	0	ENST00000377604.3:c.1360del	p.Leu454SerfsTer31	p.L454Sfs*31	ENST00000377604	NM_001204468.1	453	tCc/tc	13/24	1	2	FACETS	0.978	0.899	1	0.978	0.899	1	CLONAL	1	TRUE	1	0.516013087752647	2		465	610	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356338	70356338	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	154	499	0	ENST00000374080.3:c.5237del	p.Pro1746GlnfsTer12	p.P1746Qfs*12	ENST00000374080		1745	Ccc/cc	37/45	1	2	FACETS	0.886	0.813	0.961	0.886	0.813	0.961	CLONAL	1	TRUE	1	0.516013087752647	2		499	674	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105891	27105892	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	TT	novel	NA	P-0068483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	173	513	0	ENST00000324856.7:c.5502_5503delinsTT	p.Gln1835Ter	p.Q1835*	ENST00000324856	NM_006015.4	1834	gtGCag/gtTTag	20/20	1	2	FACETS	0.973	0.899	1	0.973	0.899	1	CLONAL	1	TRUE	1	0.516013087752647	2		513	689	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878141	48878141	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	131	491	0	ENST00000267163.4:c.93G>C	p.Glu31Asp	p.E31D	ENST00000267163	NM_000321.2	31	gaG/gaC	1/27	1	2	FACETS	0.832	0.758	0.91	0.832	0.758	0.91	CLONAL	1	TRUE	1	0.516013087752647	2		491	610	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0068484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	140	300	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.468273600421113	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.468273600421113	2		300	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0068484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	126	474	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.468279418103423	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.468273600421113	1		474	342	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0068484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	65	331	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.817	0.712	0.928	0.817	0.712	0.928	CLONAL	1	TRUE	1	0.468273600421113	2		331	340	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0068484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	255	467	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.469954002275059	4	FACETS	0.952	0.9	1	0.952	0.9	1	CLONAL	3	TRUE	1	0.468273600421113	4		467	560	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0068484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	83	474	5	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	0.468279418103423	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.468273600421113	1		479	261	SUCCESS
APC	324	MSKCC	GRCh37	5	112176015	112176015	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	100	447	0	ENST00000257430.4:c.4724del	p.Leu1575GlnfsTer75	p.L1575Qfs*75	ENST00000257430	NM_000038.5	1575	cTa/ca	16/16	1	2	FACETS	0.958	0.86	1	0.958	0.86	1	CLONAL	1	TRUE	1	0.468273600421113	2		447	446	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845366	151845366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	101	444	0	ENST00000262189.6:c.13646G>A	p.Arg4549His	p.R4549H	ENST00000262189	NM_170606.2	4549	cGc/cAc	52/59	0.222870726023182	3	FACETS	1	0.966	1	0.589	0.529	0.652	INDETERMINATE	1	TRUE	1	0.468273600421113	3		444	452	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262290	46262290	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	69	442	0	ENST00000371998.3:c.874G>A	p.Gly292Ser	p.G292S	ENST00000371998		292	Ggc/Agc	9/23	0.468273600421113	5	FACETS	0.768	0.669	0.876	0.192	0.167	0.219	SUBCLONAL	1	TRUE	1	0.468273600421113	5		442	653	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857434	68857434	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	103	453	0	ENST00000261769.5:c.2069G>T	p.Gly690Val	p.G690V	ENST00000261769	NM_004360.3	690	gGg/gTg	13/16	1	2	FACETS	0.963	0.866	1	0.963	0.866	1	CLONAL	1	TRUE	1	0.468273600421113	2		453	457	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976966	18976966	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	74	478	0	ENST00000262803.5:c.3351G>C	p.Gln1117His	p.Q1117H	ENST00000262803	NM_002911.3	1117	caG/caC	23/24	0.42172650526525	3	FACETS	0.726	0.637	0.822	0.363	0.318	0.411	SUBCLONAL	1	TRUE	1	0.468273600421113	3		478	537	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0068487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	24	335	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.574	0.449	0.72	0.574	0.449	0.72	SUBCLONAL	1	TRUE	1	0.14	2		335	597	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225896	2225896	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	32	411	0	ENST00000326181.6:c.1688A>G	p.Tyr563Cys	p.Y563C	ENST00000326181	NM_032271.2	563	tAc/tGc	18/21	1	2	FACETS	0.827	0.67	1	0.827	0.67	1	CLONAL	1	TRUE	1	0.14	2		411	553	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0068488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	155	506	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.283392165821354	4	FACETS	1	0.98	1	0.799	0.736	0.865	CLONAL	2	TRUE	1	0.320126162174347	4		506	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0068488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	90	560	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.304355842844576	1	FACETS	0.952	0.848	1	0.952	0.848	1	CLONAL	1	TRUE	0	0.320126162174347	1		560	496	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0068488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	61	408	1				ENST00000310581	NM_198253.2	-/1132			0.319659705495669	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.320126162174347	1		409	304	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586422	189586422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866267914	NA	P-0068488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	45	498	0	ENST00000264731.3:c.1046G>A	p.Gly349Glu	p.G349E	ENST00000264731	NM_003722.4	349	gGa/gAa	8/14	1	2	FACETS	0.599	0.504	0.705	0.599	0.504	0.705	SUBCLONAL	1	TRUE	1	0.320126162174347	2		498	469	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852527	42852527	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs748560513	NA	P-0068488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	62	461	0	ENST00000398585.3:c.559C>T	p.Arg187Cys	p.R187C	ENST00000398585	NM_001135099.1	187	Cgc/Tgc	6/14	1	2	FACETS	0.844	0.731	0.966	0.844	0.731	0.966	CLONAL	1	TRUE	1	0.320126162174347	2		461	459	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164397	47164397	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	64	436	1	ENST00000409792.3:c.1729G>T	p.Glu577Ter	p.E577*	ENST00000409792	NM_014159.6	577	Gaa/Taa	3/21	1	2	FACETS	0.992	0.863	1	0.992	0.863	1	CLONAL	1	TRUE	1	0.320126162174347	2		437	403	SUCCESS
AR	367	MSKCC	GRCh37	X	66931438	66931438	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	69	549	0	ENST00000374690.3:c.2080C>T	p.Gln694Ter	p.Q694*	ENST00000374690	NM_000044.3	694	Cag/Tag	4/8	0.304355842844576	1	FACETS	0.784	0.684	0.89	0.784	0.684	0.89	SUBCLONAL	1	TRUE	0	0.320126162174347	1		549	462	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998934	11998934	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	76	405	0	ENST00000353533.5:c.436C>A	p.Leu146Ile	p.L146I	ENST00000353533	NM_003010.3	146	Ctt/Att	4/11	0.304355842844576	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.320126162174347	1		405	297	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264784	46264784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377652350	NA	P-0068488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	77	511	0	ENST00000371998.3:c.1654C>T	p.Pro552Ser	p.P552S	ENST00000371998		552	Ccc/Tcc	12/23	1	2	FACETS	0.994	0.875	1	0.994	0.875	1	CLONAL	1	TRUE	1	0.320126162174347	2		511	484	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36846874	36846874	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	62	521	0	ENST00000358127.4:c.1065C>G	p.Asn355Lys	p.N355K	ENST00000358127	NM_001280556.1	355	aaC/aaG	9/10	0.304355842844576	1	FACETS	0.745	0.645	0.852	0.745	0.645	0.852	SUBCLONAL	1	TRUE	0	0.320126162174347	1		521	437	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641461	23641461	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	82	499	0	ENST00000261584.4:c.2014G>T	p.Glu672Ter	p.E672*	ENST00000261584	NM_024675.3	672	Gaa/Taa	5/13	0.234164159809257	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.320126162174347	1		499	395	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120482	94120482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	101	524	0	ENST00000369303.4:c.569G>A	p.Gly190Glu	p.G190E	ENST00000369303	NM_004440.3	190	gGg/gAg	3/17	0.319659705495669	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.320126162174347	1		524	438	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404924	404924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772244111	NA	P-0068488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	72	417	0	ENST00000399788.2:c.4270C>T	p.Pro1424Ser	p.P1424S	ENST00000399788	NM_001042603.1	1424	Cct/Tct	26/28	NA	2	FACETS	0.995	0.872	1			1	INDETERMINATE	1	TRUE	NA	0.320126162174347	2		417	452	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2033060	2033060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	65	479	0	ENST00000349721.2:c.334C>T	p.Pro112Ser	p.P112S	ENST00000349721	NM_003070.3	112	Cca/Tca	3/34	0.304355842844576	1	FACETS	0.838	0.729	0.955	0.838	0.729	0.955	CLONAL	1	TRUE	0	0.320126162174347	1		479	407	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151947956	151947956	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	78	331	0	ENST00000262189.6:c.1717C>T	p.Pro573Ser	p.P573S	ENST00000262189	NM_170606.2	573	Cct/Tct	12/59	0.270864263253293	3	FACETS	0.77	0.681	0.864	0.77	0.681	0.864	SUBCLONAL	2	TRUE	1	0.320126162174347	3		331	367	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670313	134670313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	60	471	0	ENST00000398015.3:c.224C>T	p.Thr75Ile	p.T75I	ENST00000398015	NM_004441.4	75	aCc/aTc	3/16	1	2	FACETS	0.791	0.683	0.908	0.791	0.683	0.908	CLONAL	1	TRUE	1	0.320126162174347	2		471	474	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348028	348028	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750117207	NA	P-0068489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	198	678	0	ENST00000262320.3:c.1478C>T	p.Ser493Phe	p.S493F	ENST00000262320	NM_003502.3	493	tCc/tTc	6/11	0.234887058351904	4	FACETS		NA	1			1	NA	NA	FALSE	2	NA	4		678	1223	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225958	53225958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1292051601	NA	P-0068489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	73	621	0	ENST00000375401.3:c.2891C>T	p.Pro964Leu	p.P964L	ENST00000375401	NM_004187.3	964	cCt/cTt	19/26	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		621	773	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936969	48937098	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTAATGGTTCACCTCGAACACCCAGGCGAGGTCAGAACAGGAGTGCACGGATAGCAAAACAACTAGAAAATGATACAAGAATTATTGAAGTTCTCTGTAAAGAACATGAATGTAATATAGATGAGGTAAT	TTAATGGTTCACCTCGAACACCCAGGCGAGGTCAGAACAGGAGTGCACGGATAGCAAAACAACTAGAAAATGATACAAGAATTATTGAAGTTCTCTGTAAAGAACATGAATGTAATATAGATGAGGTAAT	-	novel	NA	P-0068490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	148	339	0	ENST00000267163.4:c.741_861+9del		p.X247_splice	ENST00000267163	NM_000321.2	247		8/27	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		339	255	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	70	382	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.93	0.821	1	0.93	0.821	1	CLONAL	1	TRUE	1	0.602243688784288	2		382	250	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690802	89690802	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs1114167621	NA	P-0068498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	140	315	0	ENST00000371953.3:c.210-1G>C		p.X70_splice	ENST00000371953	NM_000314.4	70			0.602243688784288	1	FACETS	0.947	0.875	1	0.947	0.875	1	CLONAL	1	TRUE	0	0.602243688784288	1		315	343	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665752	29665755	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1555535032	NA	P-0068498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	189	369	0	ENST00000356175.3:c.6789_6792del	p.Tyr2264ThrfsTer5	p.Y2264Tfs*5	ENST00000356175	NM_000267.3	2263	ACTTac/ac	45/57	0.602243688784288	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.602243688784288	1		369	403	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196846	123196846	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0068498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	148	181	0	ENST00000218089.9:c.1731+2T>G		p.X577_splice	ENST00000218089	NM_001042749.1	577			1	1	FACETS	0.76	0.716	0.803	1	0.992	1	SUBCLONAL	2	TRUE	0	0.602243688784288	1		181	226	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678479	88678479	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	154	512	0	ENST00000360948.2:c.1057T>C	p.Tyr353His	p.Y353H	ENST00000360948	NM_001012338.2	353	Tac/Cac	9/19	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.602243688784288	2		512	499	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212307	36212308	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0068520-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	70	372	0	ENST00000222270.7:c.2061_2062del	p.Pro688SerfsTer2	p.P688Sfs*2	ENST00000222270	NM_014727.1	686	gaCTct/gact	3/37	0.305208738902994	1	FACETS	0.772	0.682	0.867	0.772	0.682	0.867	INDETERMINATE	1	TRUE	0	0.54009982779184	1		372	245	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0068525-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	91	405	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.167101203659276	4	FACETS	0.839	0.748	0.935	0.839	0.748	0.935	INDETERMINATE	2	TRUE	2	0.308505861001703	4		405	460	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044967	47044967	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068525-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	110	284	0	ENST00000377604.3:c.2293C>T	p.Arg765Ter	p.R765*	ENST00000377604	NM_001204468.1	765	Cga/Tga	20/24	1	1	FACETS	0.963	0.877	1	1	0.989	1	CLONAL	2	TRUE	0	0.308505861001703	1		284	313	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216667	2216668	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0068525-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	33	634	0	ENST00000398665.3:c.2314_2315dup	p.Arg773LeufsTer10	p.R773Lfs*10	ENST00000398665	NM_032482.2	771	tac/tACac	20/28	1	2	FACETS	0.35	0.284	0.424	0.35	0.284	0.424	SUBCLONAL	1	TRUE	1	0.308505861001703	2		634	612	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476370	88476370	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068525-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	38	444	0	ENST00000360948.2:c.1762G>T	p.Glu588Ter	p.E588*	ENST00000360948	NM_001012338.2	588	Gag/Tag	15/19	0.136959586467855	0	FACETS	0.419	0.346	0.499			1	INDETERMINATE	1	TRUE	0	0.308505861001703	0		444	407	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005931	69005931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068525-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	26	380	0	ENST00000288368.4:c.2342G>A	p.Gly781Glu	p.G781E	ENST00000288368	NM_024870.2	781	gGg/gAg	21/40	1	2	FACETS	0.375	0.297	0.466	0.375	0.297	0.466	SUBCLONAL	1	TRUE	1	0.308505861001703	2		380	449	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0068537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	44	317	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.274461862325537	2		317	267	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0068537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	42	329	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.741	0.619	0.876	0.741	0.619	0.876	SUBCLONAL	1	TRUE	1	0.274461862325537	2		329	413	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433847	78433848	+	splice_donor_variant	Splice_Site	DEL	AC	AC	-	rs1477051807	NA	P-0068537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	32	302	0	ENST00000370768.2:c.250+1_250+2del		p.X84_splice	ENST00000370768	NM_003902.3	84			1	2	FACETS	0.682	0.554	0.825	0.682	0.554	0.825	SUBCLONAL	1	TRUE	1	0.274461862325537	2		302	342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0068537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	105	560	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.274461862325537	2		560	693	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0068537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	25	456	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.366	0.287	0.456	0.366	0.287	0.456	SUBCLONAL	1	TRUE	1	0.274461862325537	2		457	498	SUCCESS
APC	324	MSKCC	GRCh37	5	112175651	112175651	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	78	538	1	ENST00000257430.4:c.4364del	p.Asn1455IlefsTer18	p.N1455Ifs*18	ENST00000257430	NM_000038.5	1454	Aaa/aa	16/16	1	2	FACETS	0.848	0.745	0.959	0.848	0.745	0.959	CLONAL	1	TRUE	1	0.274461862325537	2		539	670	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030585	47030585	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs377667483	NA	P-0068537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	25	453	2	ENST00000377604.3:c.360T>G	p.Asp120Glu	p.D120E	ENST00000377604	NM_001204468.1	120	gaT/gaG	4/24	1	2	FACETS	0.4	0.315	0.499	0.4	0.315	0.499	SUBCLONAL	1	TRUE	1	0.274461862325537	2		455	455	SUCCESS
APC	324	MSKCC	GRCh37	5	112174094	112174095	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs863225332	NA	P-0068537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	66	501	0	ENST00000257430.4:c.2804dup	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	tac/tAac	16/16	1	2	FACETS	0.763	0.662	0.873	0.763	0.662	0.873	SUBCLONAL	1	TRUE	1	0.274461862325537	2		501	630	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589558	67589558	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	61	362	0	ENST00000274335.5:c.1321A>C	p.Asn441His	p.N441H	ENST00000274335		441	Aat/Cat	10/15	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.274461862325537	2		362	389	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254731	46254731	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0068537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	59	304	0	ENST00000334344.6:c.4921A>T	p.Lys1641Ter	p.K1641*	ENST00000334344	NM_152641.2	1641	Aag/Tag	16/21	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.274461862325537	2		304	413	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657081	215657081	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs140254589	NA	P-0068537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	70	415	0	ENST00000260947.4:c.304G>C	p.Asp102His	p.D102H	ENST00000260947	NM_000465.2	102	Gac/Cac	3/11	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.274461862325537	2		415	481	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591885	48591886	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTGATGGATACGTGGACCCTTCTGGAGGAGATCGCTTTTGTTTGGGTCAACTCTCCA	novel	NA	P-0068537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	36	451	0	ENST00000342988.3:c.1049_1105dup	p.Ser368_Asn369insIleAspGlyTyrValAspProSerGlyGlyAspArgPheCysLeuGlyGlnLeuSer	p.S368_N369insIDGYVDPSGGDRFCLGQLS	ENST00000342988	NM_005359.5	350	gtt/gTTGATGGATACGTGGACCCTTCTGGAGGAGATCGCTTTTGTTTGGGTCAACTCTCCAtt	9/12	0.274461862325537	1	FACETS	0.349	0.286	0.42	0.349	0.286	0.42	SUBCLONAL	1	TRUE	0	0.274461862325537	1		451	649	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247243	153247243	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	21	475	0	ENST00000281708.4:c.1559A>G	p.Asp520Gly	p.D520G	ENST00000281708	NM_033632.3	520	gAt/gGt	10/12	1	2	FACETS	0.234	0.179	0.299	0.234	0.179	0.299	SUBCLONAL	1	TRUE	1	0.274461862325537	2		475	654	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0068537-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	98	317	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.52453918245649	3	FACETS	1	0.913	1	1	0.913	1	CLONAL	2	TRUE	1	0.52453918245649	3		317	235	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0068537-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	168	329	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.515563386247913	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.52453918245649	3		329	351	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433847	78433848	+	splice_donor_variant	Splice_Site	DEL	AC	AC	-	rs1477051807	NA	P-0068537-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	74	302	0	ENST00000370768.2:c.250+1_250+2del		p.X84_splice	ENST00000370768	NM_003902.3	84			0.52453918245649	3	FACETS	1	0.928	1	0.536	0.473	0.603	CLONAL	1	TRUE	1	0.52453918245649	3		302	332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0068537-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	277	560	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.515757661583388	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.52453918245649	2		560	512	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0068537-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	99	456	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.515563386247913	3	FACETS	0.942	0.844	1	0.471	0.422	0.523	CLONAL	1	TRUE	1	0.52453918245649	3		457	506	SUCCESS
APC	324	MSKCC	GRCh37	5	112175651	112175651	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068537-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	240	538	1	ENST00000257430.4:c.4364del	p.Asn1455IlefsTer18	p.N1455Ifs*18	ENST00000257430	NM_000038.5	1454	Aaa/aa	16/16	0.507585368231836	4	FACETS	0.904	0.847	0.962	0.904	0.847	0.962	CLONAL	2	TRUE	2	0.52453918245649	4		539	772	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030585	47030585	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs377667483	NA	P-0068537-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	68	453	2	ENST00000377604.3:c.360T>G	p.Asp120Glu	p.D120E	ENST00000377604	NM_001204468.1	120	gaT/gaG	4/24	0.52453918245649	3	FACETS	0.852	0.745	0.967	0.426	0.372	0.484	CLONAL	1	TRUE	1	0.52453918245649	3		455	384	SUCCESS
APC	324	MSKCC	GRCh37	5	112174094	112174095	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs863225332	NA	P-0068537-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	212	501	0	ENST00000257430.4:c.2804dup	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	tac/tAac	16/16	0.507585368231836	4	FACETS	0.969	0.905	1	0.969	0.905	1	CLONAL	2	TRUE	2	0.52453918245649	4		501	636	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589558	67589558	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068537-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	163	362	0	ENST00000274335.5:c.1321A>C	p.Asn441His	p.N441H	ENST00000274335		441	Aat/Cat	10/15	0.507585368231836	4	FACETS	0.981	0.908	1	0.981	0.908	1	CLONAL	2	TRUE	2	0.52453918245649	4		362	483	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254731	46254731	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0068537-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	185	304	0	ENST00000334344.6:c.4921A>T	p.Lys1641Ter	p.K1641*	ENST00000334344	NM_152641.2	1641	Aag/Tag	16/21	0.515563386247913	3	FACETS	0.987	0.921	1	0.987	0.921	1	CLONAL	2	TRUE	1	0.52453918245649	3		304	451	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657081	215657081	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs140254589	NA	P-0068537-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	196	415	0	ENST00000260947.4:c.304G>C	p.Asp102His	p.D102H	ENST00000260947	NM_000465.2	102	Gac/Cac	3/11	0.52453918245649	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.52453918245649	3		415	452	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591885	48591886	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTGATGGATACGTGGACCCTTCTGGAGGAGATCGCTTTTGTTTGGGTCAACTCTCCA	novel	NA	P-0068537-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	104	451	0	ENST00000342988.3:c.1049_1105dup	p.Ser368_Asn369insIleAspGlyTyrValAspProSerGlyGlyAspArgPheCysLeuGlyGlnLeuSer	p.S368_N369insIDGYVDPSGGDRFCLGQLS	ENST00000342988	NM_005359.5	350	gtt/gTTGATGGATACGTGGACCCTTCTGGAGGAGATCGCTTTTGTTTGGGTCAACTCTCCAtt	9/12	0.515757661583388	2	FACETS	0.643	0.576	0.713	0.321	0.288	0.357	SUBCLONAL	1	TRUE	0	0.52453918245649	2		451	617	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77051769	77051772	+	frameshift_variant	Frame_Shift_Del	DEL	GTAT	GTAT	AA	novel	NA	P-0068537-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	64	334	0	ENST00000356341.3:c.1035_1038delinsTT	p.Glu345AspfsTer18	p.E345Dfs*18	ENST00000356341	NM_002576.4	345	gaATAC/gaTT	11/15	0.461554428508239	4	FACETS	0.507	0.438	0.582	0.253	0.219	0.291	SUBCLONAL	1	TRUE	2	0.52453918245649	4		334	734	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778870	9778870	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs866028543	NA	P-0068539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	51	503	0	ENST00000377346.4:c.1139A>G	p.Asn380Ser	p.N380S	ENST00000377346	NM_005026.3	380	aAc/aGc	9/24	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.24	2		503	409	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447815	49447832	+	inframe_deletion	In_Frame_Del	DEL	TGGATAGGAAGGAACCGC	TGGATAGGAAGGAACCGC	-	novel	NA	P-0068539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	40	452	0	ENST00000301067.7:c.602_619del	p.Ser201_Ser206del	p.S201_S206del	ENST00000301067	NM_003482.3	201	aGCGGTTCCTTCCTATCCAtg/atg	5/54	1	2	FACETS	0.835	0.695	0.991	0.835	0.695	0.991	CLONAL	1	TRUE	1	0.24	2		452	399	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999098	100999098	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750042441	NA	P-0068539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	29	615	0	ENST00000325455.5:c.704C>T	p.Pro235Leu	p.P235L	ENST00000325455	NM_001202474.3	235	cCg/cTg	1/8	1	2	FACETS	0.634	0.509	0.777	0.634	0.509	0.777	SUBCLONAL	1	TRUE	1	0.24	2		615	381	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7978942	7978942	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068540-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	22	483	0	ENST00000319144.4:c.1625A>C	p.Lys542Thr	p.K542T	ENST00000319144	NM_001139.2	542	aAa/aCa	12/15	1	2	FACETS	0.428	0.331	0.541	0.428	0.331	0.541	SUBCLONAL	1	FALSE	1	0.258292065256359	2		483	398	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630594	67630594	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068540-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	16	506	0	ENST00000272342.5:c.780G>T	p.Lys260Asn	p.K260N	ENST00000272342	NM_019002.3	260	aaG/aaT	5/6	1	2	FACETS	0.475	0.351	0.623	0.475	0.351	0.623	SUBCLONAL	1	FALSE	1	0.258292065256359	2		506	261	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0068548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	194	329	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		329	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0068548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	198	433	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		433	673	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857788	9857788	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs918332999	NA	P-0068548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	159	431	0	ENST00000330684.3:c.3613G>T	p.Glu1205Ter	p.E1205*	ENST00000330684	NM_001134407.1	1205	Gag/Tag	13/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		431	990	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40745987	40745987	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748177849	NA	P-0068548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	134	337	0	ENST00000392038.2:c.604C>T	p.Arg202Trp	p.R202W	ENST00000392038	NM_001626.4	202	Cgg/Tgg	7/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		337	574	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100258	157100258	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	45	216	0	ENST00000346085.5:c.1195G>T	p.Ala399Ser	p.A399S	ENST00000346085	NM_020732.3	399	Gcg/Tcg	1/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		216	298	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596038	43596038	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	115	355	0	ENST00000355710.3:c.205G>T	p.Gly69Cys	p.G69C	ENST00000355710	NM_020975.4	69	Ggc/Tgc	2/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		355	546	SUCCESS
ALB	213	MSKCC	GRCh37	4	74283373	74283373	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	69	255	0	ENST00000295897.4:c.1415G>T	p.Cys472Phe	p.C472F	ENST00000295897	NM_000477.5	472	tGt/tTt	11/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		255	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579350	7579350	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068549-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	38	364	0	ENST00000269305.4:c.337T>A	p.Phe113Ile	p.F113I	ENST00000269305	NM_001126112.2	113	Ttc/Atc	4/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		364	281	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426550	49426550	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068549-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	21	459	0	ENST00000301067.7:c.11938C>T	p.Gln3980Ter	p.Q3980*	ENST00000301067	NM_003482.3	3980	Cag/Tag	39/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		459	362	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428571	72428571	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068549-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	25	290	0	ENST00000477973.2:c.433C>G	p.Arg145Gly	p.R145G	ENST00000477973	NM_012234.5	145	Cgg/Ggg	2/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		290	296	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0068550-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	66	264	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		264	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0068550-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	89	468	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		468	405	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	72	393	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		393	302	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748660	43748661	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	140	488	0	ENST00000382044.4:c.2145dup	p.Glu716ArgfsTer9	p.E716Rfs*9	ENST00000382044	NM_001141980.1	715	-/A	12/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		488	497	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	259	428	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		428	542	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	94	294	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		298	316	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	149	461	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		461	564	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	139	516	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		516	537	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259759	16259759	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	196	541	0	ENST00000375759.3:c.7024C>T	p.Arg2342Ter	p.R2342*	ENST00000375759	NM_015001.2	2342	Cga/Tga	11/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		541	789	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101611	27101612	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	88	489	0	ENST00000324856.7:c.4899dup	p.Met1634HisfsTer14	p.M1634Hfs*14	ENST00000324856	NM_006015.4	1631	-/C	18/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		489	636	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231483640	231483640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766305995	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	98	376	1	ENST00000295050.7:c.419G>A	p.Arg140His	p.R140H	ENST00000295050	NM_032018.5	140	cGc/cAc	3/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		377	383	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371743	118371743	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782768278	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	145	356	0	ENST00000534358.1:c.6200G>A	p.Arg2067His	p.R2067H	ENST00000534358	NM_005933.3	2067	cGc/cAc	25/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		356	526	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	81	464	1	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		465	536	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1023835002	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	125	433	0	ENST00000558401.1:c.1A>G	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Gtg	1/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		433	539	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442774	99442774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771834417	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	138	420	0	ENST00000268035.6:c.1171C>T	p.Arg391Cys	p.R391C	ENST00000268035	NM_000875.3	391	Cgc/Tgc	5/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		420	567	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779211	3779211	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783507	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	29	353	2	ENST00000262367.5:c.5837del	p.Pro1946HisfsTer30	p.P1946Hfs*30	ENST00000262367	NM_004380.2	1946	cCa/ca	31/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		355	332	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923375	9923375	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	125	417	0	ENST00000330684.3:c.1912G>A	p.Ala638Thr	p.A638T	ENST00000330684	NM_001134407.1	638	Gct/Act	9/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		417	508	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	35	395	1	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		396	360	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33680061	33680061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201406101	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	55	276	0	ENST00000308377.4:c.2020C>T	p.Arg674Cys	p.R674C	ENST00000308377	NM_152270.3	674	Cgt/Tgt	5/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		276	336	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120447	70120448	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	151	467	1	ENST00000245479.2:c.1451_1452del	p.Ser484TrpfsTer93	p.S484Wfs*93	ENST00000245479	NM_000346.3	483	acCTct/acct	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		468	687	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289953	15289953	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772172068	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	37	502	0	ENST00000263388.2:c.3601C>T	p.Arg1201Cys	p.R1201C	ENST00000263388	NM_000435.2	1201	Cgc/Tgc	22/33	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		502	660	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18276988	18276988	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	70	438	0	ENST00000222254.8:c.1435A>G	p.Thr479Ala	p.T479A	ENST00000222254	NM_005027.3	479	Act/Gct	12/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		438	557	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314638	30314638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	163	425	0	ENST00000262643.3:c.1187C>T	p.Pro396Leu	p.P396L	ENST00000262643	NM_001238.2	396	cCg/cTg	12/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		425	596	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213242	39213243	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1558454973	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	144	517	0	ENST00000402219.2:c.3724dup	p.Ser1242LysfsTer2	p.S1242Kfs*2	ENST00000402219	NM_005633.3	1242	agt/aAgt	23/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		517	676	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171593	36171596	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CTTA	CTTA	-	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	91	359	0	ENST00000300305.3:c.967+2_967+5del		p.X323_splice	ENST00000300305		323			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		359	547	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755554	39755554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs919467999	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	188	497	0	ENST00000288319.7:c.1211C>T	p.Pro404Leu	p.P404L	ENST00000288319	NM_182918.3	404	cCg/cTg	10/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		497	721	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183848	10183848	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1446876735	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	112	331	0	ENST00000256474.2:c.317G>A	p.Gly106Asp	p.G106D	ENST00000256474	NM_000551.3	106	gGc/gAc	1/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		331	403	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584510	52584511	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	168	441	0	ENST00000394830.3:c.4502_4503del	p.Glu1501GlyfsTer7	p.E1501Gfs*7	ENST00000394830	NM_018313.4	1501	gAG/g	29/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		441	623	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294576	1294576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	141	432	0	ENST00000310581.5:c.425G>A	p.Arg142His	p.R142H	ENST00000310581	NM_198253.2	142	cGc/cAc	2/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		432	471	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	58	324	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		324	229	SUCCESS
APC	324	MSKCC	GRCh37	5	112175022	112175022	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	42	414	0	ENST00000257430.4:c.3734del	p.Lys1245ArgfsTer20	p.K1245Rfs*20	ENST00000257430	NM_000038.5	1244	cAa/ca	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		414	426	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675170	30675172	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1472156046	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	71	473	0	ENST00000376406.3:c.3073_3075del	p.Lys1025del	p.K1025del	ENST00000376406	NM_014641.2	1025	AAG/-	9/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		473	645	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129329	152129329	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	139	359	1	ENST00000206249.3:c.287del	p.Gly96ValfsTer13	p.G96Vfs*13	ENST00000206249	NM_000125.3	94	ctG/ct	1/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		360	479	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959063	2959063	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41497250	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	128	428	0	ENST00000396946.4:c.2453G>A	p.Arg818Gln	p.R818Q	ENST00000396946	NM_032415.4	818	cGg/cAg	18/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		428	530	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	142	406	2	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		408	581	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187222	38187222	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	84	404	0	ENST00000317025.8:c.1255del	p.Thr419ProfsTer8	p.T419Pfs*8	ENST00000317025	NM_023034.1	419	Acc/cc	6/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		404	645	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209504	98209504	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766315655	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	25	424	0	ENST00000331920.6:c.4034G>A	p.Arg1345His	p.R1345H	ENST00000331920	NM_000264.3	1345	cGt/cAt	23/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		424	490	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409816	139409816	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	64	392	1	ENST00000277541.6:c.1940G>A	p.Ser647Asn	p.S647N	ENST00000277541	NM_017617.3	647	aGc/aAc	12/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		393	482	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923087	39923087	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	215	387	1	ENST00000378444.4:c.3621del	p.Lys1207AsnfsTer31	p.K1207Nfs*31	ENST00000378444	NM_001123385.1	1207	aaA/aa	8/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		388	653	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426420	47426420	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	63	595	0	ENST00000377045.4:c.763C>G	p.Arg255Gly	p.R255G	ENST00000377045	NM_001654.4	255	Cgg/Ggg	9/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		595	692	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411281	63411281	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs766863778	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	61	492	0	ENST00000330258.3:c.1886A>G	p.Gln629Arg	p.Q629R	ENST00000330258	NM_152424.3	629	cAg/cGg	2/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		492	741	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300414	11300414	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760445750	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	56	403	0	ENST00000361445.4:c.1732G>A	p.Asp578Asn	p.D578N	ENST00000361445	NM_004958.3	578	Gat/Aat	11/58	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		403	543	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259514	16259514	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	91	442	0	ENST00000375759.3:c.6779A>C	p.Glu2260Ala	p.E2260A	ENST00000375759	NM_015001.2	2260	gAg/gCg	11/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		442	651	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056256	27056256	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	64	468	0	ENST00000324856.7:c.1252C>A	p.Pro418Thr	p.P418T	ENST00000324856	NM_006015.4	418	Cca/Aca	2/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		468	676	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087898	27087898	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	74	398	0	ENST00000324856.7:c.2187del	p.Ser730ValfsTer12	p.S730Vfs*12	ENST00000324856	NM_006015.4	729	Ccc/cc	6/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		398	545	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932893	36932893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	146	430	1	ENST00000361632.4:c.1978C>T	p.Pro660Ser	p.P660S	ENST00000361632		660	Cca/Tca	15/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		431	552	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78435653	78435653	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	39	284	0	ENST00000370768.2:c.167A>C	p.Asn56Thr	p.N56T	ENST00000370768	NM_003902.3	56	aAt/aCt	2/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		284	258	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218982	193218982	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	13	353	0	ENST00000367435.3:c.1543del	p.Trp515GlyfsTer9	p.W515Gfs*9	ENST00000367435	NM_024529.4	514	Ttt/tt	16/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		353	220	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597861	43597861	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	70	502	0	ENST00000355710.3:c.409T>C	p.Cys137Arg	p.C137R	ENST00000355710	NM_020975.4	137	Tgc/Cgc	3/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		502	573	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451302	70451302	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	89	494	0	ENST00000373644.4:c.6142T>C	p.Phe2048Leu	p.F2048L	ENST00000373644	NM_030625.2	2048	Ttt/Ctt	12/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		494	648	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495487	56495487	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	107	530	0	ENST00000267101.3:c.3677A>G	p.Asp1226Gly	p.D1226G	ENST00000267101	NM_001982.3	1226	gAt/gGt	28/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		530	701	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145103	58145103	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	90	446	1	ENST00000257904.6:c.241T>C	p.Ser81Pro	p.S81P	ENST00000257904	NM_000075.3	81	Tcc/Ccc	3/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		447	754	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233091	69233091	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	63	410	0	ENST00000462284.1:c.956C>A	p.Pro319His	p.P319H	ENST00000462284	NM_002392.5	319	cCc/cAc	11/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		410	447	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037928	49037928	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	42	258	0	ENST00000267163.4:c.2168T>C	p.Ile723Thr	p.I723T	ENST00000267163	NM_000321.2	723	aTc/aCc	21/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		258	188	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987085	36987085	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	108	353	0	ENST00000354822.5:c.604C>T	p.Gln202Ter	p.Q202*	ENST00000354822	NM_001079668.2	202	Cag/Tag	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		353	386	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50754496	50754496	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	27	245	0	ENST00000307179.4:c.522del	p.Lys174AsnfsTer18	p.K174Nfs*18	ENST00000307179		173	gAa/ga	6/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		245	217	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633255	3633255	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	153	470	1	ENST00000294008.3:c.4996del	p.Arg1666AspfsTer49	p.R1666Dfs*49	ENST00000294008	NM_032444.2	1666	Cga/ga	14/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		471	618	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786709	3786709	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	101	383	0	ENST00000262367.5:c.4502A>G	p.Glu1501Gly	p.E1501G	ENST00000262367	NM_004380.2	1501	gAg/gGg	27/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		383	698	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819310	3819310	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	74	424	0	ENST00000262367.5:c.2925del	p.Ser976ProfsTer22	p.S976Pfs*22	ENST00000262367	NM_004380.2	975	ccC/cc	15/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		424	664	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50818299	50818299	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	34	402	0	ENST00000398568.2:c.1877A>T	p.Asp626Val	p.D626V	ENST00000398568	NM_001042412.1	626	gAt/gTt	11/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		402	297	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924258	11924258	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	35	492	0	ENST00000353533.5:c.55G>A	p.Gly19Ser	p.G19S	ENST00000353533	NM_003010.3	19	Ggc/Agc	1/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		492	516	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701046	29701046	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555538515	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	81	386	0	ENST00000356175.3:c.8330A>G	p.Asn2777Ser	p.N2777S	ENST00000356175	NM_000267.3	2777	aAc/aGc	57/57	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		386	619	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220321	5220321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	68	385	0	ENST00000357368.4:c.3499G>A	p.Gly1167Ser	p.G1167S	ENST00000357368	NM_002850.3	1167	Ggc/Agc	21/38	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		385	478	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097200	11097205	+	inframe_deletion	In_Frame_Del	DEL	GGCCCT	GGCCCT	-	rs372601826	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	58	396	0	ENST00000358026.2:c.708_713del	p.Gly243_Pro244del	p.G243_P244del	ENST00000358026	NM_001128849.1	231	GGCCCT/-	4/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		396	504	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297945	15297945	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	86	452	0	ENST00000263388.2:c.1811A>G	p.Tyr604Cys	p.Y604C	ENST00000263388	NM_000435.2	604	tAc/tGc	11/33	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		452	572	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919018	50919018	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	112	358	0	ENST00000440232.2:c.2755G>T	p.Gly919Cys	p.G919C	ENST00000440232	NM_002691.3	919	Ggc/Tgc	22/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		358	474	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446362	29446362	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	69	495	0	ENST00000389048.3:c.3205A>G	p.Met1069Val	p.M1069V	ENST00000389048	NM_004304.4	1069	Atg/Gtg	20/29	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		495	641	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61725890	61725890	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	36	371	0	ENST00000401558.2:c.677T>C	p.Leu226Ser	p.L226S	ENST00000401558	NM_003400.3	226	tTg/tCg	9/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		371	327	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137500	202137500	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	145	497	0	ENST00000358485.4:c.727+1G>A		p.X243_splice	ENST00000358485	NM_001080125.1	243			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		497	585	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346674	225346674	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	89	341	0	ENST00000264414.4:c.1964A>G	p.Asn655Ser	p.N655S	ENST00000264414	NM_003590.4	655	aAt/aGt	14/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		341	309	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319662	62319662	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408202470	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	128	452	0	ENST00000360203.5:c.1645G>A	p.Ala549Thr	p.A549T	ENST00000360203	NM_001283009.1	549	Gcc/Acc	20/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		452	574	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437717	52437717	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	36	426	0	ENST00000460680.1:c.1444T>A	p.Ser482Thr	p.S482T	ENST00000460680	NM_004656.3	482	Tcg/Acg	13/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		426	596	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443728	52443728	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	96	460	0	ENST00000460680.1:c.67+2T>C		p.X23_splice	ENST00000460680	NM_004656.3	23			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		460	640	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391210	89391210	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	49	383	0	ENST00000336596.2:c.1276G>A	p.Ala426Thr	p.A426T	ENST00000336596	NM_005233.5	426	Gct/Act	5/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		383	489	SUCCESS
ATR	545	MSKCC	GRCh37	3	142285080	142285080	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	55	369	0	ENST00000350721.4:c.175A>G	p.Thr59Ala	p.T59A	ENST00000350721	NM_001184.3	59	Act/Gct	3/47	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		369	401	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430716	181430716	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	212	519	0	ENST00000325404.1:c.568G>A	p.Gly190Ser	p.G190S	ENST00000325404	NM_003106.3	190	Ggc/Agc	1/1	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		519	653	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801502	1801503	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	119	398	0	ENST00000260795.2:c.412dup	p.Glu138GlyfsTer5	p.E138Gfs*5	ENST00000260795		136	-/G	3/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		398	490	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957494	1957494	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1281027436	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	142	369	0	ENST00000382891.5:c.2593G>A	p.Gly865Ser	p.G865S	ENST00000382891	NM_133335.3	865	Ggc/Agc	14/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		369	528	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749393	41749393	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	18	289	0	ENST00000226382.2:c.402G>T	p.Lys134Asn	p.K134N	ENST00000226382	NM_003924.3	134	aaG/aaT	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		289	315	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968565	55968565	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	27	341	0	ENST00000263923.4:c.2098T>C	p.Trp700Arg	p.W700R	ENST00000263923	NM_002253.2	700	Tgg/Cgg	14/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		341	490	SUCCESS
REST	5978	MSKCC	GRCh37	4	57777042	57777042	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1342633562	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	57	409	0	ENST00000309042.7:c.238G>A	p.Gly80Arg	p.G80R	ENST00000309042	NM_005612.4	80	Ggg/Agg	2/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		409	599	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541745	187541745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1341239896	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	160	468	0	ENST00000441802.2:c.5995G>A	p.Ala1999Thr	p.A1999T	ENST00000441802	NM_005245.3	1999	Gct/Act	10/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		468	621	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630179	187630179	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	81	475	0	ENST00000441802.2:c.803A>G	p.Asp268Gly	p.D268G	ENST00000441802	NM_005245.3	268	gAc/gGc	2/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		475	659	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509371	149509371	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	74	443	0	ENST00000261799.4:c.1528C>A	p.Leu510Met	p.L510M	ENST00000261799	NM_002609.3	510	Ctg/Atg	10/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		443	596	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680892	30680892	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	98	530	0	ENST00000376406.3:c.827G>T	p.Arg276Met	p.R276M	ENST00000376406	NM_014641.2	276	aGg/aTg	5/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		530	659	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790615	89790615	+	start_lost	Translation_Start_Site	SNP	T	T	C	rs1274242000	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	104	313	0	ENST00000336032.3:c.2T>C	p.Met1?	p.M1?	ENST00000336032	NM_006813.2	1	aTg/aCg	1/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		313	458	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553264	106553265	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	61	494	0	ENST00000369096.4:c.1233dup	p.Lys412GlnfsTer12	p.K412Qfs*12	ENST00000369096	NM_001198.3	410	tac/taCc	5/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		494	654	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021707	69021707	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	84	398	0	ENST00000288368.4:c.2995T>C	p.Ser999Pro	p.S999P	ENST00000288368	NM_024870.2	999	Tca/Cca	25/40	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		398	542	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002714	37002714	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	31	398	0	ENST00000358127.4:c.535T>C	p.Tyr179His	p.Y179H	ENST00000358127	NM_001280556.1	179	Tac/Cac	5/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		398	529	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212205	98212205	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	139	353	1	ENST00000331920.6:c.3467T>C	p.Leu1156Pro	p.L1156P	ENST00000331920	NM_000264.3	1156	cTg/cCg	21/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		354	513	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135780983	135780983	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	95	371	0	ENST00000298552.3:c.1982G>T	p.Ser661Ile	p.S661I	ENST00000298552	NM_001162426.1	661	aGc/aTc	15/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		371	600	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390727	139390727	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	95	508	0	ENST00000277541.6:c.7464del	p.His2488GlnfsTer101	p.H2488Qfs*101	ENST00000277541	NM_017617.3	2488	caC/ca	34/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		508	646	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200239	123200239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1311707382	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	14	332	0	ENST00000218089.9:c.2218G>A	p.Val740Ile	p.V740I	ENST00000218089	NM_001042749.1	740	Gta/Ata	23/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		332	218	SUCCESS
PHF6	84295	MSKCC	GRCh37	X	133512056	133512056	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	20	247	0	ENST00000332070.3:c.160T>A	p.Ser54Thr	p.S54T	ENST00000332070	NM_032458.2	54	Tca/Aca	3/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		247	237	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0068552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	37	385	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		385	395	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0068552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	41	393	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		393	439	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375132	104375132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	37	454	0	ENST00000369902.3:c.1130C>T	p.Ser377Phe	p.S377F	ENST00000369902	NM_016169.3	377	tCc/tTc	9/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		454	441	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514089	69514089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	49	521	0	ENST00000294312.3:c.592G>A	p.Asp198Asn	p.D198N	ENST00000294312	NM_005117.2	198	Gac/Aac	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		521	549	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245204	46245204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	116	499	0	ENST00000334344.6:c.3298C>T	p.Gln1100Ter	p.Q1100*	ENST00000334344	NM_152641.2	1100	Cag/Tag	15/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		499	616	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884070	37884070	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776754071	NA	P-0068552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	64	587	1	ENST00000269571.5:c.3541G>A	p.Val1181Ile	p.V1181I	ENST00000269571		1181	Gtc/Atc	27/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		588	658	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792764	33792764	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1367523224	NA	P-0068552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	31	354	0	ENST00000498907.2:c.557C>T	p.Pro186Leu	p.P186L	ENST00000498907	NM_004364.3	186	cCg/cTg	1/1	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		354	362	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421260	12421260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772234905	NA	P-0068552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	40	521	0	ENST00000287820.6:c.140C>T	p.Ser47Phe	p.S47F	ENST00000287820	NM_015869.4	47	tCc/tTc	2/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		521	560	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164805	47164805	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	51	501	0	ENST00000409792.3:c.1321C>T	p.Arg441Ter	p.R441*	ENST00000409792	NM_014159.6	441	Cga/Tga	3/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		501	582	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462359	89462359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	62	407	0	ENST00000336596.2:c.1831G>A	p.Glu611Lys	p.E611K	ENST00000336596	NM_005233.5	611	Gag/Aag	10/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		407	472	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193841	106193841	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	50	448	0	ENST00000380013.4:c.4303C>T	p.Gln1435Ter	p.Q1435*	ENST00000380013	NM_001127208.2	1435	Cag/Tag	10/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		448	518	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169586	27169586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	54	482	0	ENST00000380036.4:c.587G>A	p.Gly196Glu	p.G196E	ENST00000380036	NM_000459.3	196	gGa/gAa	4/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		482	487	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78914298	78914299	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0068552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	33	368	0	ENST00000306801.3:c.2922_2923delinsTT	p.Pro975Ser	p.P975S	ENST00000306801	NM_020761.2	974	atCCca/atTTca	25/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		368	431	SUCCESS
REST	5978	MSKCC	GRCh37	4	57797822	57797822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777335033	NA	P-0068552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	46	488	0	ENST00000309042.7:c.2798C>T	p.Thr933Ile	p.T933I	ENST00000309042	NM_005612.4	933	aCt/aTt	4/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		488	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0068553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	85	492	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		492	603	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714670	52714670	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112759633	NA	P-0068553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	75	525	0	ENST00000322088.6:c.428C>T	p.Ser143Phe	p.S143F	ENST00000322088	NM_014225.5	143	tCc/tTc	4/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		525	507	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044907	47044907	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	29	269	0	ENST00000377604.3:c.2237del	p.Gly746AlafsTer56	p.G746Afs*56	ENST00000377604	NM_001204468.1	745	Ggg/gg	20/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		269	230	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411667	116411667	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	37	530	0	ENST00000397752.3:c.2846T>G	p.Leu949Arg	p.L949R	ENST00000397752	NM_000245.2	949	cTt/cGt	13/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		530	529	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157039	106157039	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs763505294	NA	P-0068553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	87	548	0	ENST00000380013.4:c.1940T>C	p.Val647Ala	p.V647A	ENST00000380013	NM_001127208.2	647	gTg/gCg	3/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		548	557	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987031	36987031	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	62	308	0	ENST00000354822.5:c.658G>T	p.Glu220Ter	p.E220*	ENST00000354822	NM_001079668.2	220	Gag/Tag	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		308	264	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753135	42753135	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	33	549	0	ENST00000222329.4:c.1129T>G	p.Phe377Val	p.F377V	ENST00000222329	NM_006494.2	377	Ttt/Gtt	4/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		549	561	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670567	134670567	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	85	504	0	ENST00000398015.3:c.478A>G	p.Thr160Ala	p.T160A	ENST00000398015	NM_004441.4	160	Aca/Gca	3/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		504	503	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366373	15366373	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	38	367	0	ENST00000263377.2:c.1782G>T	p.Lys594Asn	p.K594N	ENST00000263377	NM_058243.2	594	aaG/aaT	10/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		367	494	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553533	106553533	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	22	437	0	ENST00000369096.4:c.1498G>T	p.Gly500Trp	p.G500W	ENST00000369096	NM_001198.3	500	Ggg/Tgg	5/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		437	407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0068554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	98	494	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		494	600	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603080	48603081	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0068554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	50	396	0	ENST00000342988.3:c.1381_1382del	p.Gln461GlyfsTer32	p.Q461Gfs*32	ENST00000342988	NM_005359.5	461	CAg/g	11/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		396	476	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944167	71944167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	133	560	0	ENST00000298229.2:c.2000C>T	p.Ser667Phe	p.S667F	ENST00000298229	NM_001567.3	667	tCc/tTc	17/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		560	742	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411884	116411905	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTTTCTCTCTGTTTTAAGATC	TCTTTCTCTCTGTTTTAAGATC	-	novel	NA	P-0068554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	113	555	0	ENST00000397752.3:c.2888-18_2891del		p.X963_splice	ENST00000397752	NM_000245.2	963		14/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		555	644	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922258	39922258	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	39	414	0	ENST00000378444.4:c.3914A>C	p.Lys1305Thr	p.K1305T	ENST00000378444	NM_001123385.1	1305	aAg/aCg	9/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		414	516	SUCCESS
ATR	545	MSKCC	GRCh37	3	142234344	142234344	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	65	364	0	ENST00000350721.4:c.4396C>G	p.Gln1466Glu	p.Q1466E	ENST00000350721	NM_001184.3	1466	Cag/Gag	25/47	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		364	376	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215954	142215954	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148475359	NA	P-0068554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	88	344	0	ENST00000350721.4:c.5639C>T	p.Ser1880Phe	p.S1880F	ENST00000350721	NM_001184.3	1880	tCt/tTt	33/47	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		344	535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0068561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	9	420	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.306593989803525	1	FACETS	0.129	0.085	0.187	0.129	0.085	0.187	SUBCLONAL	1	TRUE	0	0.306593989803525	1		420	384	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412282	139412282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	8	426	0	ENST00000277541.6:c.1363G>A	p.Glu455Lys	p.E455K	ENST00000277541	NM_017617.3	455	Gag/Aag	8/34	0.207056780582881	2	FACETS	0.181	0.116	0.265	0.09	0.058	0.133	SUBCLONAL	1	TRUE	0	0.306593989803525	2		426	289	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156654	2156654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	35	483	0	ENST00000434045.2:c.268G>A	p.Gly90Ser	p.G90S	ENST00000434045	NM_001127598.1	90	Ggc/Agc	3/5	1	2	FACETS	0.672	0.551	0.806	0.672	0.551	0.806	SUBCLONAL	1	TRUE	1	0.306593989803525	2		483	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574009	7574019	+	frameshift_variant	Frame_Shift_Del	DEL	TCTCGAAGCGC	TCTCGAAGCGC	-	novel	NA	P-0068561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	64	355	0	ENST00000269305.4:c.1008_1018del	p.Glu336AspfsTer7	p.E336Dfs*7	ENST00000269305	NM_001126112.2	336	gaGCGCTTCGAGAtg/gatg	10/11	0.306593989803525	1	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	0	0.306593989803525	1		355	342	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397786	116397786	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	45	340	0	ENST00000397752.3:c.2060C>G	p.Ser687Cys	p.S687C	ENST00000397752	NM_000245.2	687	tCt/tGt	8/21	0.20057366021264	3	FACETS	1	0.866	1	0.676	0.577	0.781	CLONAL	2	TRUE	0	0.306593989803525	3		340	167	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0068567-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	130	300	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.440981174774176	2		300	496	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024001	27024002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0068567-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	35	192	0	ENST00000324856.7:c.1113dup	p.Gln372AlafsTer28	p.Q372Afs*28	ENST00000324856	NM_006015.4	369	-/G	1/20	0.221746972037601	1	FACETS	0.393	0.323	0.471	0.393	0.323	0.471	INDETERMINATE	1	FALSE	0	0.440981174774176	1		192	315	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711311	114711311	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068567-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	98	298	0	ENST00000543371.1:c.326C>T	p.Pro109Leu	p.P109L	ENST00000543371	NM_001198531.1	109	cCc/cTc	3/14	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	FALSE	1	0.440981174774176	2		298	423	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299946	15299946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555729077	NA	P-0068567-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	149	364	0	ENST00000263388.2:c.1232C>T	p.Thr411Met	p.T411M	ENST00000263388	NM_000435.2	411	aCg/aTg	8/33	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.440981174774176	2		364	457	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0068567-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	79	403	0	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	0.299137324070265	1	FACETS	0.486	0.428	0.548	0.486	0.428	0.548	SUBCLONAL	1	FALSE	0	0.440981174774176	1		403	575	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028895	47028895	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068567-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	106	333	0	ENST00000377604.3:c.199G>T	p.Glu67Ter	p.E67*	ENST00000377604	NM_001204468.1	67	Gag/Tag	3/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.440981174774176	2		333	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577560	7577563	+	frameshift_variant	Frame_Shift_Del	DEL	AACT	AACT	-	novel	NA	P-0068567-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	138	306	0	ENST00000269305.4:c.718_721del	p.Ser240ProfsTer6	p.S240Pfs*6	ENST00000269305	NM_001126112.2	240	AGTTcc/cc	7/11	0.440981174774176	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	0	0.440981174774176	1		306	400	SUCCESS
APC	324	MSKCC	GRCh37	5	112173882	112173883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0068567-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	142	408	0	ENST00000257430.4:c.2592_2593dup	p.Pro865LeufsTer52	p.P865Lfs*52	ENST00000257430	NM_000038.5	864	cat/caTCt	16/16	0.299137324070265	1	FACETS	0.938	0.86	1	0.938	0.86	1	CLONAL	1	FALSE	0	0.440981174774176	1		408	535	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151927400	151927400	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs759892421	NA	P-0068567-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	17	34	0	ENST00000262189.6:c.2776A>C	p.Thr926Pro	p.T926P	ENST00000262189	NM_170606.2	926	Act/Cct	17/59	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	FALSE	1	0.440981174774176	2		34	54	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426893	6426893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519948	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	117	279	0	ENST00000356142.4:c.86C>T	p.Pro29Leu	p.P29L	ENST00000356142	NM_018890.3	29	cCt/cTt	2/7	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.41	2		279	434	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956220	55956220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190050670	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	84	264	0	ENST00000263923.4:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000263923	NM_002253.2	1032	cGa/cAa	23/30	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.41	2		264	340	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	114	385	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.912	0.833	0.993	1	0.989	1	CLONAL	2	TRUE	1	0.41	2		385	305	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214058	36214058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1385766471	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	171	374	1	ENST00000222270.7:c.2884C>T	p.Arg962Cys	p.R962C	ENST00000222270	NM_014727.1	962	Cgc/Tgc	6/37	1	2	FACETS	0.848	0.786	0.911	1	0.992	1	CLONAL	2	TRUE	1	0.41	2		375	492	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743893	46743893	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	159	391	0	ENST00000371975.4:c.2183C>T	p.Ser728Phe	p.S728F	ENST00000371975	NM_003579.3	728	tCc/tTc	18/18	1	2	FACETS	0.787	0.727	0.848	1	0.99	1	SUBCLONAL	2	TRUE	1	0.41	2		391	493	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163811	72163811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	101	362	0	ENST00000357731.5:c.547G>A	p.Glu183Lys	p.E183K	ENST00000357731	NM_173808.2	183	Gaa/Aaa	4/7	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.41	2		362	338	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849818	156849818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761967383	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	104	295	0	ENST00000524377.1:c.2074C>T	p.Arg692Cys	p.R692C	ENST00000524377	NM_002529.3	692	Cgc/Tgc	16/17	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.41	2		295	419	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948448	71948448	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	161	409	0	ENST00000298229.2:c.3160C>T	p.Pro1054Ser	p.P1054S	ENST00000298229	NM_001567.3	1054	Cca/Tca	26/28	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.41	2		409	536	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800819	18800819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868545833	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	89	258	0	ENST00000266497.5:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000266497		1399	Gat/Aat	31/31	0.148275093036126	0	FACETS	0.931	0.837	1			1	INDETERMINATE	1	TRUE	0	0.41	0		258	275	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244853	46244853	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	196	492	0	ENST00000334344.6:c.2947C>T	p.Gln983Ter	p.Q983*	ENST00000334344	NM_152641.2	983	Caa/Taa	15/21	1	2	FACETS	0.772	0.719	0.827	1	0.992	1	SUBCLONAL	2	TRUE	1	0.41	2		492	619	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988387	36988387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1488542462	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	112	269	0	ENST00000354822.5:c.266G>A	p.Gly89Glu	p.G89E	ENST00000354822	NM_001079668.2	89	gGg/gAg	2/3	1	2	FACETS	0.89	0.811	0.97	1	0.988	1	CLONAL	2	TRUE	1	0.41	2		269	307	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023105	33023105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	147	386	0	ENST00000300177.4:c.214G>A	p.Glu72Lys	p.E72K	ENST00000300177	NM_001191322.1	72	Gag/Aag	2/2	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.41	2		386	487	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892238	9892238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	119	409	0	ENST00000330684.3:c.2252G>A	p.Gly751Glu	p.G751E	ENST00000330684	NM_001134407.1	751	gGg/gAg	11/13	0.3	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.41	1		409	439	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56871587	56871587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758034157	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	139	349	0	ENST00000308159.5:c.1967C>T	p.Pro656Leu	p.P656L	ENST00000308159	NM_014669.4	656	cCg/cTg	18/22	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.41	2		349	462	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645919	67645919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	154	355	0	ENST00000264010.4:c.847C>T	p.Arg283Cys	p.R283C	ENST00000264010	NM_006565.3	283	Cgt/Tgt	4/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.41	2		355	524	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30293176	30293176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764786746	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	90	181	0	ENST00000322652.5:c.466C>T	p.His156Tyr	p.H156Y	ENST00000322652	NM_015355.2	156	Cat/Tat	5/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.41	2		181	314	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250948	10250948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1255153711	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	117	281	0	ENST00000340748.4:c.3532C>T	p.Arg1178Trp	p.R1178W	ENST00000340748		1178	Cgg/Tgg	32/40	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.41	2		281	439	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730858	40730858	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200227405	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	132	422	0	ENST00000373198.4:c.3677G>A	p.Arg1226Gln	p.R1226Q	ENST00000373198	NM_133170.3	1226	cGa/cAa	27/32	0.3	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.41	1		422	453	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730876	40730876	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372862828	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	128	417	0	ENST00000373198.4:c.3659G>A	p.Arg1220Gln	p.R1220Q	ENST00000373198	NM_133170.3	1220	cGg/cAg	27/32	0.3	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.41	1		417	458	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400179	41400179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	119	333	0	ENST00000373198.4:c.580C>T	p.His194Tyr	p.H194Y	ENST00000373198	NM_133170.3	194	Cat/Tat	5/32	0.3	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.41	1		333	408	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183868	10183868	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs5030810	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	110	275	0	ENST00000256474.2:c.337C>T	p.Arg113Ter	p.R113*	ENST00000256474	NM_000551.3	113	Cga/Tga	1/3	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.41	2		275	438	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142949	47142949	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	85	237	0	ENST00000409792.3:c.5014G>A	p.Gly1672Arg	p.G1672R	ENST00000409792	NM_014159.6	1672	Gga/Aga	8/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.41	2		237	300	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119666195	119666195	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1163587458	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	119	296	0	ENST00000316626.5:c.286C>T	p.Arg96Ter	p.R96*	ENST00000316626		96	Cga/Tga	3/12	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.41	2		296	417	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670351	134670351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	120	356	0	ENST00000398015.3:c.262G>A	p.Glu88Lys	p.E88K	ENST00000398015	NM_004441.4	88	Gag/Aag	3/16	0.3	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.41	1		356	396	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526115	189526115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375508394	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	152	423	0	ENST00000264731.3:c.379G>A	p.Gly127Ser	p.G127S	ENST00000264731	NM_003722.4	127	Ggc/Agc	4/14	1	2	FACETS	0.76	0.7	0.821	1	0.989	1	SUBCLONAL	2	TRUE	1	0.41	2		423	488	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056291	180056291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199942873	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	119	363	0	ENST00000261937.6:c.953G>A	p.Arg318Gln	p.R318Q	ENST00000261937	NM_182925.4	318	cGa/cAa	7/30	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.41	2		363	427	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672218	30672218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	217	570	0	ENST00000376406.3:c.4742C>T	p.Ser1581Phe	p.S1581F	ENST00000376406	NM_014641.2	1581	tCc/tTc	10/15	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.41	2		570	736	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169019	32169019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	153	393	0	ENST00000375023.3:c.4014G>A	p.Met1338Ile	p.M1338I	ENST00000375023	NM_004557.3	1338	atG/atA	22/30	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.41	2		393	564	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967960	93967960	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	114	337	0	ENST00000369303.4:c.1967G>A	p.Gly656Glu	p.G656E	ENST00000369303	NM_004440.3	656	gGg/gAg	11/17	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.41	2		337	394	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374353	81374353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	118	247	0	ENST00000222390.5:c.709C>T	p.His237Tyr	p.H237Y	ENST00000222390	NM_000601.4	237	Cat/Tat	6/18	1	2	FACETS	0.791	0.721	0.863	1	0.987	1	SUBCLONAL	2	TRUE	1	0.41	2		247	364	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	722	313	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.3	12	FACETS	1	0.993	1	0.949	0.926	0.972	CLONAL	10	TRUE	1	0.41	12		313	1029	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864636	68864636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371341697	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	66	196	0	ENST00000288368.4:c.7G>A	p.Glu3Lys	p.E3K	ENST00000288368	NM_024870.2	3	Gag/Aag	1/40	0.3	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.41	1		196	205	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534771	5534771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	143	352	0	ENST00000397747.3:c.82G>A	p.Glu28Lys	p.E28K	ENST00000397747	NM_025239.3	28	Gaa/Aaa	3/7	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.41	2		352	497	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624541	93624541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	143	360	0	ENST00000375746.1:c.632G>A	p.Gly211Glu	p.G211E	ENST00000375746	NM_001174167.1	211	gGg/gAg	4/14	1	2	FACETS	0.76	0.698	0.823	1	0.988	1	SUBCLONAL	2	TRUE	1	0.41	2		360	459	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624594	93624594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	124	345	0	ENST00000375746.1:c.685C>T	p.Pro229Ser	p.P229S	ENST00000375746	NM_001174167.1	229	Ccc/Tcc	4/14	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.41	2		345	438	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176104162	176104162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	95	373	0	ENST00000367669.3:c.952C>T	p.Pro318Ser	p.P318S	ENST00000367669	NM_022457.5	318	Cct/Tct	8/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.41	2		373	371	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118379876	118379876	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	118	369	0	ENST00000534358.1:c.10861C>T	p.Gln3621Ter	p.Q3621*	ENST00000534358	NM_005933.3	3621	Cag/Tag	29/36	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.41	2		369	429	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142580	119142593	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TTTTGGGGAAAAGT	TTTTGGGGAAAAGT	-	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	132	317	0	ENST00000264033.4:c.579_590+2del		p.X193_splice	ENST00000264033	NM_005188.3	193		3/16	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.41	2		317	458	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466954	18466954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1476973395	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	104	301	0	ENST00000266497.5:c.1093C>T	p.His365Tyr	p.H365Y	ENST00000266497		365	Cac/Tac	5/31	0.148275093036126	0	FACETS	0.825	0.745	0.907			1	INDETERMINATE	1	TRUE	0	0.41	0		301	363	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719906	18719906	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	116	299	0	ENST00000266497.5:c.3803C>T	p.Pro1268Leu	p.P1268L	ENST00000266497		1268	cCt/cTt	27/31	0.148275093036126	0	FACETS	1	0.942	1			1	INDETERMINATE	1	TRUE	0	0.41	0		299	321	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244981	133244981	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749194160	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	125	391	0	ENST00000320574.5:c.2134C>T	p.Arg712Cys	p.R712C	ENST00000320574	NM_006231.2	712	Cgc/Tgc	19/49	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.41	2		391	516	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592681	28592681	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148480385	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	126	443	0	ENST00000241453.7:c.2464G>A	p.Gly822Arg	p.G822R	ENST00000241453	NM_004119.2	822	Ggg/Agg	20/24	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.41	2		443	424	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50773849	50773849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771430115	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	177	402	0	ENST00000307179.4:c.1390C>T	p.Arg464Cys	p.R464C	ENST00000307179		464	Cgt/Tgt	11/20	1	2	FACETS	0.782	0.725	0.84	1	0.991	1	SUBCLONAL	2	TRUE	1	0.41	2		402	552	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858375	9858375	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	147	408	0	ENST00000330684.3:c.3026G>A	p.Arg1009Lys	p.R1009K	ENST00000330684	NM_001134407.1	1009	aGa/aAa	13/13	0.3	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.41	1		408	446	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934956	9934956	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	117	362	0	ENST00000330684.3:c.1334C>T	p.Ser445Leu	p.S445L	ENST00000330684	NM_001134407.1	445	tCa/tTa	6/13	0.3	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.41	1		362	385	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351667	89351668	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	GTCTCAGCTTCTCTCCT	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	105	453	0	ENST00000301030.4:c.1266_1282dup	p.Leu428GlnfsTer5	p.L428Qfs*5	ENST00000301030	NM_001256183.1	428	ctc/cAGGAGAGAAGCTGAGACtc	9/13	1	2	FACETS	0.945	0.85	1	0.945	0.85	1	CLONAL	1	TRUE	1	0.41	2		453	542	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973670	15973670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	165	359	0	ENST00000268712.3:c.4322G>A	p.Gly1441Asp	p.G1441D	ENST00000268712	NM_006311.3	1441	gGc/gAc	31/46	1	2	FACETS	0.767	0.709	0.826	1	0.99	1	SUBCLONAL	2	TRUE	1	0.41	2		359	525	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560133	29560133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199474732	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	137	391	0	ENST00000356175.3:c.3610C>T	p.Arg1204Trp	p.R1204W	ENST00000356175	NM_000267.3	1204	Cgg/Tgg	27/57	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.41	2		391	516	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123784	11123784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	135	373	0	ENST00000358026.2:c.2434C>T	p.Leu812Phe	p.L812F	ENST00000358026	NM_001128849.1	812	Ctc/Ttc	16/36	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.41	2		373	469	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228110	36228130	+	frameshift_variant	Frame_Shift_Del	DEL	AGGAGGAGCCGCCCCTGAATC	AGGAGGAGCCGCCCCTGAATC	GAAT	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	141	407	2	ENST00000222270.7:c.7496_7516delinsGAAT	p.Gln2499ArgfsTer18	p.Q2499Rfs*18	ENST00000222270	NM_014727.1	2499	cAGGAGGAGCCGCCCCTGAATCcc/cGAATcc	33/37	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.41	2		409	509	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693949	47693949	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1553366680	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	122	321	0	ENST00000233146.2:c.1661+2T>C		p.X554_splice	ENST00000233146	NM_000251.2	554			1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.41	2		321	406	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483978	212483978	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	80	336	0	ENST00000342788.4:c.2225A>T	p.Glu742Val	p.E742V	ENST00000342788	NM_005235.2	742	gAa/gTa	19/28	0.3	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.41	1		336	277	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661846	227661846	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	140	386	0	ENST00000305123.5:c.1609C>T	p.Gln537Ter	p.Q537*	ENST00000305123	NM_005544.2	537	Cag/Tag	1/2	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.41	2		386	482	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545969	41545969	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	169	418	0	ENST00000263253.7:c.2584C>A	p.Pro862Thr	p.P862T	ENST00000263253	NM_001429.3	862	Cct/Act	14/31	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.41	2		418	588	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37048481	37048481	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs267607744	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	115	302	0	ENST00000231790.2:c.381-1G>A		p.X127_splice	ENST00000231790	NM_000249.3	127			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.41	2		302	460	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428261	72428261	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	145	305	0	ENST00000477973.2:c.631C>T	p.Pro211Ser	p.P211S	ENST00000477973	NM_012234.5	211	Cct/Tct	3/4	1	2	FACETS	0.786	0.723	0.851	1	0.989	1	SUBCLONAL	2	TRUE	1	0.41	2		305	450	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170006	32170006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	124	364	0	ENST00000375023.3:c.3602G>A	p.Gly1201Glu	p.G1201E	ENST00000375023	NM_004557.3	1201	gGg/gAg	21/30	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.41	2		364	467	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70971015	70971015	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	137	415	0	ENST00000276594.2:c.1246G>A	p.Asp416Asn	p.D416N	ENST00000276594	NM_024504.3	416	Gat/Aat	6/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.41	2		415	467	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595350	141595350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	166	452	0	ENST00000220592.5:c.83G>A	p.Arg28Lys	p.R28K	ENST00000220592	NM_012154.3	28	aGa/aAa	2/19	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.41	2		452	572	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27172613	27172613	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1463342917	NA	P-0068568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	135	315	0	ENST00000380036.4:c.629-1G>A		p.X210_splice	ENST00000380036	NM_000459.3	210			1	2	FACETS	0.778	0.714	0.845	1	0.988	1	SUBCLONAL	2	TRUE	1	0.41	2		315	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577539	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0068569-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	22	335	0	ENST00000269305.4:c.742dup	p.Arg248ProfsTer16	p.R248Pfs*16	ENST00000269305	NM_001126112.2	248	cgg/cCgg	7/11	1	2	FACETS	0.46	0.355	0.583	0.46	0.355	0.583	SUBCLONAL	1	TRUE	1	0.16	2		335	598	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0068571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	56	410	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.923	0.791	1	0.923	0.791	1	CLONAL	1	TRUE	1	0.218329819141268	2		410	556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0068571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	18	292	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.377	0.283	0.489	0.377	0.283	0.489	SUBCLONAL	1	TRUE	1	0.218329819141268	2		292	437	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265569	152265569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	25	333	0	ENST00000206249.3:c.1022C>T	p.Ser341Leu	p.S341L	ENST00000206249	NM_000125.3	341	tCg/tTg	4/8	1	2	FACETS	0.596	0.47	0.742	0.596	0.47	0.742	SUBCLONAL	1	TRUE	1	0.218329819141268	2		333	384	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245471	46245471	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	31	355	0	ENST00000334344.6:c.3565C>T	p.Gln1189Ter	p.Q1189*	ENST00000334344	NM_152641.2	1189	Cag/Tag	15/21	0.190047638166191	1	FACETS	0.544	0.439	0.663	0.544	0.439	0.663	SUBCLONAL	1	TRUE	0	0.218329819141268	1		355	465	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600558	43600558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775772444	NA	P-0068571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	24	307	0	ENST00000355710.3:c.784G>A	p.Val262Met	p.V262M	ENST00000355710	NM_020975.4	262	Gtg/Atg	4/20	1	2	FACETS	0.527	0.413	0.66	0.527	0.413	0.66	SUBCLONAL	1	TRUE	1	0.218329819141268	2		307	417	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729262	41729262	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	23	288	0	ENST00000242208.4:c.1267T>C	p.Cys423Arg	p.C423R	ENST00000242208	NM_002192.2	423	Tgt/Cgt	3/3	1	2	FACETS	0.566	0.441	0.712	0.566	0.441	0.712	SUBCLONAL	1	TRUE	1	0.218329819141268	2		288	372	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50754520	50754521	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0068571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	31	213	0	ENST00000307179.4:c.541+2dup		p.X181_splice	ENST00000307179		181			1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	1	0.218329819141268	2		213	270	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591924	48591924	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	13	342	0	ENST00000342988.3:c.1087T>A	p.Cys363Ser	p.C363S	ENST00000342988	NM_005359.5	363	Tgt/Agt	9/12	1	2	FACETS	0.274	0.195	0.372	0.274	0.195	0.372	SUBCLONAL	1	TRUE	1	0.218329819141268	2		342	434	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884368	151884369	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0068571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	20	343	0	ENST00000262189.6:c.4986dup	p.Asn1663GlnfsTer8	p.N1663Qfs*8	ENST00000262189	NM_170606.2	1662	-/C	33/59	1	2	FACETS	0.544	0.415	0.694	0.544	0.415	0.694	SUBCLONAL	1	TRUE	1	0.218329819141268	2		343	337	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821637	72821639	+	inframe_deletion	In_Frame_Del	DEL	CTG	CTG	-	rs1429156408	NA	P-0068573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	28	405	0	ENST00000268489.5:c.10536_10538del	p.Ser3513del	p.S3513del	ENST00000268489	NM_006885.3	3512	ggCAGt/ggt	10/10	0.655917991119569	1	FACETS	0.197	0.158	0.242	0.197	0.158	0.242	SUBCLONAL	1	TRUE	0	0.655917991119569	1		405	291	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564854	41564854	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	191	403	0	ENST00000263253.7:c.4155C>A	p.Cys1385Ter	p.C1385*	ENST00000263253	NM_001429.3	1385	tgC/tgA	25/31	0.655917991119569	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.655917991119569	1		403	340	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348949	89348949	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs765151001	NA	P-0068573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	43	434	0	ENST00000301030.4:c.4001C>G	p.Pro1334Arg	p.P1334R	ENST00000301030	NM_001256183.1	1334	cCg/cGg	9/13	0.655917991119569	1	FACETS	0.23	0.193	0.271	0.23	0.193	0.271	SUBCLONAL	1	TRUE	0	0.655917991119569	1		434	383	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821619	72821639	+	inframe_deletion	In_Frame_Del	DEL	CCGCCGCCGCCGCCGCCACTG	CCGCCGCCGCCGCCGCCACTG	-	novel	NA	P-0068573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	105	416	0	ENST00000268489.5:c.10536_10556del	p.Ser3513_Gly3519del	p.S3513_G3519del	ENST00000268489	NM_006885.3	3512	ggCAGTGGCGGCGGCGGCGGCGGt/ggt	10/10	0.655917991119569	1	FACETS	0.708	0.643	0.775	0.708	0.643	0.775	SUBCLONAL	1	TRUE	0	0.655917991119569	1		416	304	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267764	46267764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	142	400	0	ENST00000371998.3:c.2525C>T	p.Ser842Leu	p.S842L	ENST00000371998		842	tCa/tTa	14/23	1	2	FACETS	0.954	0.876	1	0.954	0.876	1	CLONAL	1	TRUE	1	0.655917991119569	2		400	454	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433337	78433337	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	190	313	0	ENST00000370768.2:c.264del	p.Gln88HisfsTer13	p.Q88Hfs*13	ENST00000370768	NM_003902.3	88	caG/ca	4/20	1	2	FACETS	0.917	0.866	0.966	1	0.994	1	CLONAL	2	TRUE	1	0.655917991119569	2		313	316	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673700	37673700	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	381	361	0	ENST00000447079.4:c.2854T>G	p.Cys952Gly	p.C952G	ENST00000447079	NM_015083.1	952	Tgt/Ggt	10/14	0.655917991119569	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.655917991119569	2		361	529	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857044	9857044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201707833	NA	P-0068574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	68	361	1	ENST00000330684.3:c.4357G>A	p.Val1453Met	p.V1453M	ENST00000330684	NM_001134407.1	1453	Gtg/Atg	13/13	0.382394702178698	3	FACETS	0.755	0.658	0.861	0.378	0.329	0.431	SUBCLONAL	1	TRUE	1	0.382394702178698	3		362	561	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0068574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	126	291	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	0.364878503260471	3	FACETS	0.795	0.724	0.868	0.795	0.724	0.868	SUBCLONAL	2	TRUE	1	0.382394702178698	3		291	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579316	7579317	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0068574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	194	325	0	ENST00000269305.4:c.370dup	p.Cys124LeufsTer25	p.C124Lfs*25	ENST00000269305	NM_001126112.2	124	tgc/tTgc	4/11	NA	2	FACETS	0.938	0.874	1			1	INDETERMINATE	2	TRUE	NA	0.382394702178698	2		325	541	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412243	139412243	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	115	352	0	ENST00000277541.6:c.1402C>A	p.Leu468Met	p.L468M	ENST00000277541	NM_017617.3	468	Ctg/Atg	8/34	0.382394702178698	5	FACETS	1	0.962	1	0.285	0.256	0.315	CLONAL	1	TRUE	1	0.382394702178698	5		352	831	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911644	114911644	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0068574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	103	273	0	ENST00000543371.1:c.1161+1G>A		p.X387_splice	ENST00000543371	NM_001198531.1	387			0.364878503260471	3	FACETS	1	0.961	1	0.574	0.515	0.636	CLONAL	1	TRUE	1	0.382394702178698	3		273	559	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117861	70117861	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	97	370	0	ENST00000245479.2:c.329A>C	p.Asn110Thr	p.N110T	ENST00000245479	NM_000346.3	110	aAc/aCc	1/3	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.382394702178698	2		370	479	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016181	31016181	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1179121574	NA	P-0068574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	375	331	2	ENST00000375687.4:c.427C>T	p.Arg143Ter	p.R143*	ENST00000375687	NM_015338.5	143	Cga/Tga	6/13	0.382394702178698	5	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	2	0.382394702178698	5		333	969	SUCCESS
BLM	641	MSKCC	GRCh37	15	91333877	91333880	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGGT	AGGT	-	novel	NA	P-0068574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	85	295	0	ENST00000355112.3:c.2824-2_2825del		p.X942_splice	ENST00000355112	NM_000057.2	942		15/22	1	2	FACETS	0.932	0.827	1	0.932	0.827	1	CLONAL	1	TRUE	1	0.382394702178698	2		295	477	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858491	27858491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	27	475	0	ENST00000359303.2:c.80G>A	p.Arg27His	p.R27H	ENST00000359303	NM_003535.2	27	cGc/cAc	1/1	1	2	FACETS	0.23	0.182	0.285	0.23	0.182	0.285	SUBCLONAL	1	TRUE	1	0.454563638855722	2		475	517	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061245	38061246	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0068575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	75	395	0	ENST00000250448.2:c.743dup	p.Asp249GlyfsTer44	p.D249Gfs*44	ENST00000250448	NM_004496.3	248	ccg/ccCg	2/2	1	2	FACETS	0.917	0.809	1	0.917	0.809	1	CLONAL	1	TRUE	1	0.454563638855722	2		395	360	SUCCESS
ALB	213	MSKCC	GRCh37	4	74282003	74282003	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs898245331	NA	P-0068575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	15	284	0	ENST00000295897.4:c.1222C>T	p.Pro408Ser	p.P408S	ENST00000295897	NM_000477.5	408	Cct/Tct	10/15	1	2	FACETS	0.277	0.203	0.367	0.277	0.203	0.367	SUBCLONAL	1	TRUE	1	0.454563638855722	2		284	238	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0068577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	152	440	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.269738782890418	3	FACETS	0.891	0.827	0.955	0.891	0.827	0.955	INDETERMINATE	2	TRUE	1	0.659495299484199	3		440	344	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728847	190728847	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1200062574	NA	P-0068577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	109	334	0	ENST00000441310.2:c.2235G>T	p.Met745Ile	p.M745I	ENST00000441310	NM_000534.4	745	atG/atT	10/13	0.650113475385963	3	FACETS	1	0.973	1	0.599	0.543	0.657	CLONAL	1	TRUE	1	0.659495299484199	3		334	367	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223172	36223172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	118	543	0	ENST00000222270.7:c.5722G>A	p.Ala1908Thr	p.A1908T	ENST00000222270	NM_014727.1	1908	Gct/Act	28/37	0.650113475385963	3	FACETS	0.688	0.621	0.758	0.344	0.31	0.379	SUBCLONAL	1	TRUE	1	0.659495299484199	3		543	692	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36208922	36208923	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCGGC	rs898578503	NA	P-0068577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	123	224	0	ENST00000222270.7:c.11_16dup	p.Ala4_Ala5dup	p.A4_A5dup	ENST00000222270	NM_014727.1	4	atg/atGGCGGCg	1/37	0.650113475385963	3	FACETS	0.756	0.693	0.821	0.756	0.693	0.821	SUBCLONAL	2	TRUE	1	0.659495299484199	3		224	328	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222808	36222808	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0068577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	70	394	0	ENST00000222270.7:c.5438-1G>C		p.X1813_splice	ENST00000222270	NM_014727.1	1813			0.650113475385963	3	FACETS	0.542	0.473	0.616	0.271	0.236	0.308	SUBCLONAL	1	TRUE	1	0.659495299484199	3		394	521	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032455	12032455	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0068577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	179	371	0	ENST00000353533.5:c.892-1G>T		p.X298_splice	ENST00000353533	NM_003010.3	298			0.619369422480781	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.659495299484199	2		371	266	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222913	36222913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	84	505	0	ENST00000222270.7:c.5542G>A	p.Asp1848Asn	p.D1848N	ENST00000222270	NM_014727.1	1848	Gat/Aat	27/37	0.650113475385963	3	FACETS	0.576	0.509	0.647	0.288	0.254	0.324	SUBCLONAL	1	TRUE	1	0.659495299484199	3		505	588	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872934	35872934	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	94	323	0	ENST00000216797.5:c.298G>T	p.Asp100Tyr	p.D100Y	ENST00000216797	NM_020529.2	100	Gac/Tac	2/6	0.659495299484199	3	FACETS	0.812	0.726	0.903	0.406	0.363	0.452	CLONAL	1	TRUE	1	0.659495299484199	3		323	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0068605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	369	639	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.802379298664465	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.802379298664465	2		639	454	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170020841	170020841	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	196	220	0	ENST00000295797.4:c.1717A>G	p.Lys573Glu	p.K573E	ENST00000295797	NM_002740.5	573	Aag/Gag	18/18	0.802379298664465	6	FACETS	0.925	0.86	0.992	0.462	0.43	0.496	CLONAL	2	TRUE	2	0.802379298664465	6		220	688	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1684414	1684414	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	209	416	0	ENST00000378625.1:c.1705T>G	p.Cys569Gly	p.C569G	ENST00000378625	NM_001198994.1	569	Tgc/Ggc	14/14	0.802379298664465	3	FACETS	1	0.969	1	0.533	0.497	0.57	CLONAL	1	TRUE	1	0.802379298664465	3		416	685	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098816	178098816	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	374	363	0	ENST00000397062.3:c.229G>A	p.Asp77Asn	p.D77N	ENST00000397062	NM_006164.4	77	Gat/Aat	2/5	0.802379298664465	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.802379298664465	2		363	440	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49724648	49724648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	319	246	0	ENST00000449682.2:c.541C>T	p.Pro181Ser	p.P181S	ENST00000449682	NM_020998.3	181	Cct/Tct	5/18	0.802379298664465	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.802379298664465	2		246	362	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247185	153247185	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	460	310	0	ENST00000281708.4:c.1617del	p.His540IlefsTer16	p.H540Ifs*16	ENST00000281708	NM_033632.3	539	ggG/gg	10/12	0.802379298664465	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	0	0.802379298664465	3		310	534	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0068606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	13	371	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	0.429242289468799	2	FACETS	0.122	0.086	0.166	0.061	0.043	0.083	SUBCLONAL	1	TRUE	0	0.441954829503681	2		371	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0068606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	284	474	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.429242289468799	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.441954829503681	2		474	569	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946259	55946259	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	78	490	0	ENST00000263923.4:c.3920C>G	p.Ser1307Cys	p.S1307C	ENST00000263923	NM_002253.2	1307	tCc/tGc	30/30	0.241835863972748	4	FACETS	0.837	0.736	0.945	0.419	0.368	0.473	INDETERMINATE	1	TRUE	2	0.441954829503681	4		490	608	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230561490	230561491	+	upstream_gene_variant	5'Flank	DEL	TC	TC	-	novel	NA	P-0068606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	293	627	1				ENST00000391860	NM_001258311.1	-/409			0.441954829503681	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.441954829503681	3		628	725	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0068607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	82	560	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.224975539257571	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.224975539257571	1		560	609	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0068607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	53	513	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.766	0.653	0.891	0.766	0.653	0.891	SUBCLONAL	1	TRUE	1	0.224975539257571	2		513	615	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	123	455	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	0.20755906202591	3	FACETS	0.93	0.843	1	0.93	0.843	1	CLONAL	2	TRUE	1	0.224975539257571	3		455	654	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928074	178928074	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	72	406	0	ENST00000263967.3:c.1352G>T	p.Gly451Val	p.G451V	ENST00000263967	NM_006218.2	451	gGa/gTa	8/21	0.20755906202591	3	FACETS	0.899	0.789	1	0.899	0.789	1	CLONAL	2	TRUE	1	0.224975539257571	3		406	396	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371723	116371723	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	67	242	1	ENST00000397752.3:c.1202C>A	p.Thr401Lys	p.T401K	ENST00000397752	NM_000245.2	401	aCa/aAa	3/21	1	2	FACETS	0.889	0.778	1	1	0.979	1	CLONAL	2	TRUE	1	0.224975539257571	2		243	335	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0068608-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	70	371	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	1	2	FACETS	0.95	0.829	1	1	0.98	1	CLONAL	2	TRUE	1	0.123421448091408	2		371	597	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198269885	198269885	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068608-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	46	329	0	ENST00000335508.6:c.1454C>A	p.Ser485Ter	p.S485*	ENST00000335508	NM_012433.2	485	tCa/tAa	11/25	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.123421448091408	2		329	634	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51514711	51514711	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068608-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	56	396	0	ENST00000260433.2:c.463C>A	p.Pro155Thr	p.P155T	ENST00000260433		155	Ccc/Acc	5/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.123421448091408	2		396	620	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488286	56488286	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068608-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	64	411	0	ENST00000267101.3:c.1805A>C	p.Lys602Thr	p.K602T	ENST00000267101	NM_001982.3	602	aAg/aCg	15/28	1	2	FACETS	0.911	0.79	1	1	0.978	1	CLONAL	2	TRUE	1	0.123421448091408	2		411	569	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994169	21994173	+	frameshift_variant	Frame_Shift_Del	DEL	ACGCT	ACGCT	-	novel	NA	P-0068608-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	56	360	0	ENST00000579755.1:c.158_162del	p.Gln53ProfsTer8	p.Q53Pfs*8	ENST00000579755		53	cAGCGT/c	1/3	0.123421448091408				0.839	1				CLONAL	2	TRUE	0	0.123421448091408	1		360	436	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59938814	59938814	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769585673	NA	P-0068610-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	140	313	0	ENST00000259008.2:c.87G>T	p.Met29Ile	p.M29I	ENST00000259008	NM_032043.2	29	atG/atT	2/20	1	2	FACETS	0.918	0.843	0.995	0.918	0.843	0.995	CLONAL	1	TRUE	1	0.682673270655171	2		313	447	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603134	48603154	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTCCAGCTATCAGTAAGTAT	GCTCCAGCTATCAGTAAGTAT	-	novel	NA	P-0068610-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	140	294	0	ENST00000342988.3:c.1438_1447+11del		p.X480_splice	ENST00000342988	NM_005359.5	480		11/12	0.682673270655171	1	FACETS	0.928	0.862	0.995	0.928	0.862	0.995	CLONAL	1	TRUE	0	0.682673270655171	1		294	291	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575550	64575550	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs794728648	NA	P-0068610-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	236	428	0	ENST00000312049.6:c.467G>T	p.Gly156Val	p.G156V	ENST00000312049	NM_130799.2	156	gGt/gTt	3/10	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.682673270655171	2		428	686	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51520054	51520054	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068610-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	174	291	0	ENST00000260433.2:c.373A>T	p.Ile125Phe	p.I125F	ENST00000260433		125	Atc/Ttc	4/10	0.66177782720633	1	FACETS	0.903	0.844	0.962	0.903	0.844	0.962	CLONAL	1	TRUE	0	0.682673270655171	1		291	372	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221293	1221304	+	inframe_deletion	In_Frame_Del	DEL	CGCCATCCCGGG	CGCCATCCCGGG	-	novel	NA	P-0068610-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	254	478	0	ENST00000326873.7:c.818_829del	p.Ala273_Gly276del	p.A273_G276del	ENST00000326873	NM_000455.4	272	taCGCCATCCCGGGc/tac	6/10	0.682673270655171	1	FACETS	0.971	0.92	1	0.971	0.92	1	CLONAL	1	TRUE	0	0.682673270655171	1		478	505	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006864	47006864	+	5_prime_UTR_variant	5'UTR	SNP	G	G	A	novel	NA	P-0068611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	174	405	0	ENST00000377604.3:c.-17G>A		p.*6*	ENST00000377604	NM_001204468.1	-/852		2/24	0.835328245962486	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.835328245962486	1		405	227	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0068611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	484	440	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.835328245962486	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.835328245962486	2		440	545	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281905	39281905	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs55980502	NA	P-0068611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	174	278	0	ENST00000402219.2:c.570C>G	p.Asp190Glu	p.D190E	ENST00000402219	NM_005633.3	190	gaC/gaG	5/23	0.835328245962486	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.835328245962486	3		278	284	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131183	202131183	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0068611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	131	316	0	ENST00000358485.4:c.152-1G>A		p.X51_splice	ENST00000358485	NM_001080125.1	51			0.835328245962486	3	FACETS	0.975	0.891	1	0.488	0.445	0.531	CLONAL	1	TRUE	1	0.835328245962486	3		316	456	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518381	8518381	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	23	350	0	ENST00000356435.5:c.1010C>G	p.Thr337Arg	p.T337R	ENST00000356435		337	aCa/aGa	10/35	0.835328245962486	1	FACETS	0.139	0.109	0.175	0.139	0.109	0.175	SUBCLONAL	1	TRUE	0	0.835328245962486	1		350	230	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0068612-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	4134	405	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.432962486195094	56	FACETS	0.992	0.986	0.997	0.992	0.986	0.997	CLONAL	54	TRUE	2	0.432962486195094	56		405	4525	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934234	48934234	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068612-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	114	299	0	ENST00000267163.4:c.689C>A	p.Ser230Ter	p.S230*	ENST00000267163	NM_000321.2	230	tCa/tAa	7/27	0.334882558587108	2	FACETS	0.841	0.768	0.917	0.841	0.768	0.917	CLONAL	2	TRUE	0	0.432962486195094	2		299	313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0068612-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	94	329	0	ENST00000269305.4:c.673-2del		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.334882558587108	2	FACETS	0.754	0.68	0.831	0.754	0.68	0.831	SUBCLONAL	2	TRUE	0	0.432962486195094	2		329	288	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391833	139391833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375969725	NA	P-0068612-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	88	431	1	ENST00000277541.6:c.6358C>T	p.Arg2120Cys	p.R2120C	ENST00000277541	NM_017617.3	2120	Cgc/Tgc	34/34	0.289667043751256	3	FACETS	0.933	0.829	1	0.467	0.414	0.522	CLONAL	1	TRUE	1	0.432962486195094	3		432	530	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38064147	38064147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068612-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	61	513	0	ENST00000250448.2:c.31G>A	p.Glu11Lys	p.E11K	ENST00000250448	NM_004496.3	11	Gaa/Aaa	1/2	0.432962486195094	5	FACETS	0.597	0.514	0.688	0.199	0.171	0.23	SUBCLONAL	1	TRUE	2	0.432962486195094	5		513	778	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255148	16255148	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068612-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	139	404	0	ENST00000375759.3:c.2413G>C	p.Glu805Gln	p.E805Q	ENST00000375759	NM_015001.2	805	Gag/Cag	11/15	0.404759263078257	4	FACETS	1	0.986	1	0.71	0.648	0.775	CLONAL	1	TRUE	2	0.432962486195094	4		404	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0068613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	156	383	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.290535674619555	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.290535674619555	2		383	501	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0068613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	51	284	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.290535674619555	2		284	291	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956226	55956226	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	53	407	0	ENST00000263923.4:c.3089C>T	p.Ala1030Val	p.A1030V	ENST00000263923	NM_002253.2	1030	gCg/gTg	23/30	1	2	FACETS	0.814	0.696	0.944	0.814	0.696	0.944	CLONAL	1	TRUE	1	0.290535674619555	2		407	448	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710662	114710663	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0068613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	38	397	0	ENST00000543371.1:c.149dup	p.Asn50LysfsTer2	p.N50Kfs*2	ENST00000543371	NM_001198531.1	49	-/A	1/14	0.166354033371656	3	FACETS	0.532	0.439	0.636	0.177	0.146	0.212	INDETERMINATE	1	TRUE	0	0.290535674619555	3		397	563	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712754	43712754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	184	499	0	ENST00000382044.4:c.4430G>A	p.Gly1477Asp	p.G1477D	ENST00000382044	NM_001141980.1	1477	gGc/gAc	21/28	0.288300949849507	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.290535674619555	3		499	635	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144359555	144359555	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	48	503	0	ENST00000262995.4:c.997A>C	p.Lys333Gln	p.K333Q	ENST00000262995	NM_207123.2	333	Aag/Cag	4/11	1	2	FACETS	0.553	0.466	0.648	0.553	0.466	0.648	SUBCLONAL	1	TRUE	1	0.290535674619555	2		503	598	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982995	201982998	+	missense_variant	Missense_Mutation	ONP	ATCC	ATCC	GACA	novel	NA	P-0068613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	72	497	0	ENST00000359651.3:c.844_847delinsGACA	p.Ile282_Leu283delinsAspIle	p.I282_L283delinsDI	ENST00000359651		282	ATCCtc/GACAtc	7/8	0.288300949849507	3	FACETS	0.841	0.734	0.956	0.42	0.367	0.478	CLONAL	1	TRUE	1	0.290535674619555	3		497	675	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579315	7579315	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1555526478	NA	P-0068615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	223	530	0	ENST00000269305.4:c.372C>A	p.Cys124Ter	p.C124*	ENST00000269305	NM_001126112.2	124	tgC/tgA	4/11	0.390754920358214	3	FACETS	0.953	0.896	1	0.635	0.597	0.674	CLONAL	2	TRUE	0	0.583455296324726	3		530	518	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612164	43612164	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	92	563	1	ENST00000355710.3:c.2269G>A	p.Val757Met	p.V757M	ENST00000355710	NM_020975.4	757	Gtg/Atg	12/20	0.428799727743366	3	FACETS	0.645	0.573	0.72	0.322	0.286	0.36	SUBCLONAL	1	TRUE	1	0.583455296324726	3		564	632	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143993	11143993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568509370	NA	P-0068615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	273	497	0	ENST00000358026.2:c.3574C>T	p.Arg1192Cys	p.R1192C	ENST00000358026	NM_001128849.1	1192	Cgc/Tgc	26/36	0.454294162560386	2	FACETS	0.807	0.765	0.849	0.807	0.765	0.849	CLONAL	2	TRUE	0	0.583455296324726	2		497	580	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068627-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	48	382	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		382	155	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0068627-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	10	547	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		547	376	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503838	149503838	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs864309711	NA	P-0068627-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	111	756	0	ENST00000261799.4:c.1998C>G	p.Asn666Lys	p.N666K	ENST00000261799	NM_002609.3	666	aaC/aaG	14/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		756	326	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73650012	73650012	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068627-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	153	713	0	ENST00000377687.4:c.1362G>T	p.Arg454Ser	p.R454S	ENST00000377687	NM_001730.3	454	agG/agT	4/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		713	393	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591080	67591081	+	inframe_insertion	In_Frame_Ins	INS	-	-	AATTGACAAACGTATGAACAGCATTAAACCAGACCTTATCCAGCTGAGAAAGACGAG	novel	NA	P-0068627-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	31	686	0	ENST00000274335.5:c.1675_1731dup	p.Ile559_Arg577dup	p.I559_R577dup	ENST00000274335		559	gaa/gaAATTGACAAACGTATGAACAGCATTAAACCAGACCTTATCCAGCTGAGAAAGACGAGa	12/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		686	495	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871770	37871770	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367606199	NA	P-0068627-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	139	724	0	ENST00000269571.5:c.1294C>T	p.Arg432Trp	p.R432W	ENST00000269571		432	Cgg/Tgg	11/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		724	340	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576477	67576480	+	frameshift_variant	Frame_Shift_Del	DEL	AACC	AACC	GGT	novel	NA	P-0068627-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	111	562	2	ENST00000274335.5:c.756_759delinsGGT	p.Thr253ValfsTer7	p.T253Vfs*7	ENST00000274335		252	caAACC/caGGT	5/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		564	364	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0068629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	445	334	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.43636861947497	4	FACETS	1	0.994	1	0.875	0.842	0.907	CLONAL	3	TRUE	0	0.480383197745386	4		334	784	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214065	108214074	+	frameshift_variant	Frame_Shift_Del	DEL	TTTCAGTGCC	TTTCAGTGCC	-	rs786202800	NA	P-0068629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	75	410	0	ENST00000278616.4:c.8395_8404del	p.Phe2799LysfsTer4	p.F2799Kfs*4	ENST00000278616	NM_000051.3	2795	gaTTTCAGTGCC/ga	57/63	0.384926539203555	2	FACETS	1	0.974	1	0.676	0.601	0.753	CLONAL	1	TRUE	0	0.480383197745386	2		410	231	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115796	8115796	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0068629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	76	547	0	ENST00000346208.3:c.1142C>G	p.Ser381Ter	p.S381*	ENST00000346208		381	tCa/tGa	6/6	0.459786725184813	4	FACETS	0.542	0.474	0.615	0.271	0.237	0.308	SUBCLONAL	1	TRUE	2	0.480383197745386	4		547	864	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0068630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	133	356	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.126205825048268	4	FACETS	0.86	0.792	0.93			1	INDETERMINATE	3	TRUE	NA	0.431508226412102	4		356	342	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032303	10032303	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	19	364	0	ENST00000330684.3:c.520A>G	p.Thr174Ala	p.T174A	ENST00000330684	NM_001134407.1	174	Acc/Gcc	3/13	0.124330328459857	3	FACETS	0.413	0.314	0.53	0.207	0.157	0.265	INDETERMINATE	1	TRUE	1	0.431508226412102	3		364	259	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612774	228612793	+	frameshift_variant	Frame_Shift_Del	DEL	AGCGCAGGTCGGTCTTAAAG	AGCGCAGGTCGGTCTTAAAG	-	novel	NA	P-0068630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	92	542	0	ENST00000366696.1:c.234_253del	p.Phe79ProfsTer21	p.F79Pfs*21	ENST00000366696	NM_003493.2	78	gaCTTTAAGACCGACCTGCGCTtc/gatc	1/1	0.279648658037258	5	FACETS	1	0.952	1	0.376	0.334	0.42	CLONAL	1	TRUE	2	0.431508226412102	5		542	623	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670702	134670702	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs764596237	NA	P-0068630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	37	406	0	ENST00000398015.3:c.613G>C	p.Val205Leu	p.V205L	ENST00000398015	NM_004441.4	205	Gtg/Ctg	3/16	0.351913581309621	6	FACETS	0.878	0.725	1	0.219	0.181	0.262	CLONAL	1	TRUE	2	0.431508226412102	6		406	364	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864862	117864862	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	25	324	0	ENST00000297338.2:c.1247T>C	p.Phe416Ser	p.F416S	ENST00000297338	NM_006265.2	416	tTc/tCc	10/14	0.384116095789876	3	FACETS	0.615	0.487	0.761	0.308	0.243	0.381	SUBCLONAL	1	TRUE	1	0.431508226412102	3		324	229	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022913	27022938	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGCCGCCGCCAGCAGCCTGGGCAA	CCCGCCGCCGCCAGCAGCCTGGGCAA	-	rs797045262	NA	P-0068631-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	155	351	0	ENST00000324856.7:c.31_56del	p.Ser11AlafsTer91	p.S11Afs*91	ENST00000324856	NM_006015.4	7	CCCGCCGCCGCCAGCAGCCTGGGCAAc/c	1/20	1	2	FACETS	0.681	0.626	0.737	0.681	0.626	0.737	SUBCLONAL	1	FALSE	1	0.812022594867855	2		351	561	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645066	67645066	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068631-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	38	389	0	ENST00000264010.4:c.332del	p.Gly111GlufsTer12	p.G111Efs*12	ENST00000264010	NM_006565.3	111	Gga/ga	3/12	1	2	FACETS	0.178	0.147	0.213	0.178	0.147	0.213	SUBCLONAL	1	FALSE	1	0.812022594867855	2		389	526	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097645	27097646	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0068631-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	227	390	0	ENST00000324856.7:c.3236dup	p.Asn1079LysfsTer26	p.N1079Kfs*26	ENST00000324856	NM_006015.4	1078	-/A	12/20	1	2	FACETS	0.88	0.825	0.937	0.88	0.825	0.937	CLONAL	1	FALSE	1	0.812022594867855	2		390	635	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399396	139399397	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGG	novel	NA	P-0068631-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	178	421	0	ENST00000277541.6:c.4744_4746dup	p.Pro1582dup	p.P1582dup	ENST00000277541	NM_017617.3	1582	-/CCG	26/34	0.812022594867855	3	FACETS	0.715	0.659	0.773			1	SUBCLONAL	1	FALSE	NA	0.812022594867855	3		421	862	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925711	114925711	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068631-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	174	360	0	ENST00000543371.1:c.1789G>T	p.Val597Phe	p.V597F	ENST00000543371	NM_001198531.1	597	Gtc/Ttc	14/14	1	2	FACETS	0.772	0.715	0.831	0.772	0.715	0.831	SUBCLONAL	1	FALSE	1	0.812022594867855	2		360	555	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945544	151945544	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068631-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	139	121	0	ENST00000262189.6:c.1975C>T	p.Gln659Ter	p.Q659*	ENST00000262189	NM_170606.2	659	Cag/Tag	14/59	1	2	FACETS	1	0.986	1	1	0.994	1	CLONAL	2	FALSE	1	0.812022594867855	2		121	160	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390862	139390863	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0068631-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	570	394	0	ENST00000277541.6:c.7328_7329insCT	p.Gln2444CysfsTer34	p.Q2444Cfs*34	ENST00000277541	NM_017617.3	2443	gtg/gtCTg	34/34	0.812022594867855	3	FACETS	0.958	0.926	0.99			1	CLONAL	2	FALSE	NA	0.812022594867855	3		394	1030	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752745	128752745	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs139697494	NA	P-0068632-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	80	333	0	ENST00000377970.2:c.906C>A	p.His302Gln	p.H302Q	ENST00000377970	NM_002467.4	302	caC/caA	3/3	1	2	FACETS	0.692	0.61	0.78	0.692	0.61	0.78	SUBCLONAL	1	TRUE	1	0.41	2		333	564	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830353	72830353	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068632-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	64	378	0	ENST00000268489.5:c.6228del	p.Ile2076MetfsTer25	p.I2076Mfs*25	ENST00000268489	NM_006885.3	2076	atT/at	9/10	1	2	FACETS	0.676	0.586	0.772	0.676	0.586	0.772	SUBCLONAL	1	TRUE	1	0.41	2		378	462	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061221	38061232	+	inframe_deletion	In_Frame_Del	DEL	GTTCTCGAACAT	GTTCTCGAACAT	-	novel	NA	P-0068633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	120	456	0	ENST00000250448.2:c.757_768del	p.Met253_Asn256del	p.M253_N256del	ENST00000250448	NM_004496.3	253	ATGTTCGAGAAC/-	2/2	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.425942368395619	2		456	439	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632332	1632332	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs928663365	NA	P-0068633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	62	375	1	ENST00000344749.5:c.218G>A	p.Arg73Gln	p.R73Q	ENST00000344749	NM_001136139.2	73	cGg/cAg	4/19	1	2	FACETS	0.43	0.371	0.494	0.43	0.371	0.494	SUBCLONAL	1	TRUE	1	0.425942368395619	2		376	677	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45854976	45854976	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	86	304	0	ENST00000391945.4:c.2194del	p.Asp732IlefsTer13	p.D732Ifs*13	ENST00000391945	NM_000400.3	732	Gat/at	23/23	1	2	FACETS	0.852	0.757	0.953	0.852	0.757	0.953	CLONAL	1	TRUE	1	0.425942368395619	2		304	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576920	7576936	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCAGTGCTAGGAAAGA	GGCAGTGCTAGGAAAGA	-	novel	NA	P-0068634-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	147	448	0	ENST00000269305.4:c.920-10_926del		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	0.71484263367851	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.71484263367851	1		448	250	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914137	32914137	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs80358785	NA	P-0068634-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	74	278	0	ENST00000380152.3:c.5645C>A	p.Ser1882Ter	p.S1882*	ENST00000380152		1882	tCa/tAa	11/27	0.71484263367851	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.71484263367851	1		278	131	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868259	56868284	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGAGTTGTTTATTTCCCTTACAGGGA	TGAGTTGTTTATTTCCCTTACAGGGA	-	novel	NA	P-0068634-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	31	332	0	ENST00000308159.5:c.1665-19_1671del		p.X555_splice	ENST00000308159	NM_014669.4	555		15/22	1	2	FACETS	0.278	0.225	0.338	0.278	0.225	0.338	SUBCLONAL	1	TRUE	1	0.71484263367851	2		332	312	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061206	38061229	+	inframe_deletion	In_Frame_Del	DEL	GCGCAAGTAGCAGCCGTTCTCGAA	GCGCAAGTAGCAGCCGTTCTCGAA	-	novel	NA	P-0068634-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	121	368	0	ENST00000250448.2:c.760_783del	p.Phe254_Arg261del	p.F254_R261del	ENST00000250448	NM_004496.3	254	TTCGAGAACGGCTGCTACTTGCGC/-	2/2	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.71484263367851	2		368	307	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627439	14627439	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068634-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	117	301	0	ENST00000254322.2:c.631G>T	p.Gly211Trp	p.G211W	ENST00000254322	NM_006145.1	211	Ggg/Tgg	2/3	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.71484263367851	2		301	290	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84388692	84388711	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTGTAAAAAATTACCATTTC	CTGTAAAAAATTACCATTTC	-	novel	NA	P-0068634-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	11	93	0	ENST00000321945.7:c.597-20_597-1del		p.X199_splice	ENST00000321945	NM_139076.2	199			1	2	FACETS	0.244	0.169	0.336	0.244	0.169	0.336	SUBCLONAL	1	TRUE	1	0.71484263367851	2		93	126	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61760993	61760993	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769916613	NA	P-0068634-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	74	216	0	ENST00000401558.2:c.40C>T	p.Arg14Cys	p.R14C	ENST00000401558	NM_003400.3	14	Cgt/Tgt	2/25	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.71484263367851	2		216	202	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456581	32456581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068634-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	13	232	0	ENST00000332351.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000332351	NM_024426.4	104	cCg/cTg	1/10	1	2	FACETS	0.192	0.137	0.26	0.192	0.137	0.26	SUBCLONAL	1	TRUE	1	0.71484263367851	2		232	189	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922936	44922939	+	frameshift_variant	Frame_Shift_Del	DEL	AGGA	AGGA	-	novel	NA	P-0068634-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	141	173	0	ENST00000377967.4:c.1799_1802del	p.Gly600ValfsTer24	p.G600Vfs*24	ENST00000377967	NM_021140.2	599	acAGGA/ac	16/29	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.71484263367851	1		173	195	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	29	382	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.771	0.625	0.932	1	0.943	1	CLONAL	2	FALSE	1	0.221381772045397	2		382	170	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666657	206666657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782804652	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	61	451	0	ENST00000367120.3:c.1991C>T	p.Ser664Leu	p.S664L	ENST00000367120	NM_014002.3	664	tCg/tTg	20/22	1	2	FACETS	0.759	0.658	0.868	1	0.971	1	SUBCLONAL	2	FALSE	1	0.221381772045397	2		451	363	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	99	425	0	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	0.221381772045397	1	FACETS	0.898	0.806	0.994	1	0.986	1	CLONAL	2	FALSE	0	0.221381772045397	1		425	443	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs121913468	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	217	356	0	ENST00000269571.5:c.2305G>C	p.Asp769His	p.D769H	ENST00000269571		769	Gac/Cac	19/27	0.221381772045397	11	FACETS	0.932	0.872	0.992	0.652	0.61	0.695	CLONAL	7	FALSE	1	0.221381772045397	11		356	600	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119789	70119789	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	25	310	0	ENST00000245479.2:c.791G>C	p.Arg264Thr	p.R264T	ENST00000245479	NM_000346.3	264	aGa/aCa	3/3	0.0940725290381579	3	FACETS	0.833	0.658	1	0.417	0.329	0.518	INDETERMINATE	1	FALSE	1	0.221381772045397	3		310	301	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682422	52682422	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	50	310	0	ENST00000394830.3:c.751G>C	p.Asp251His	p.D251H	ENST00000394830	NM_018313.4	251	Gat/Cat	8/30	1	2	FACETS	0.75	0.64	0.869	1	0.964	1	SUBCLONAL	2	FALSE	1	0.221381772045397	2		310	301	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229601	98229601	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	58	368	0	ENST00000331920.6:c.2357G>C	p.Arg786Thr	p.R786T	ENST00000331920	NM_000264.3	786	aGa/aCa	15/24	0.221381772045397	1	FACETS	0.754	0.652	0.863	1	0.97	1	SUBCLONAL	2	FALSE	0	0.221381772045397	1		368	309	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495496	56495496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217262342	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	28	455	0	ENST00000267101.3:c.3686C>T	p.Ser1229Leu	p.S1229L	ENST00000267101	NM_001982.3	1229	tCa/tTa	28/28	0.0940725290381579	3	FACETS	0.697	0.557	0.857	0.349	0.278	0.429	INDETERMINATE	1	FALSE	1	0.221381772045397	3		455	403	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426787	49426787	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	72	475	0	ENST00000301067.7:c.11701C>T	p.Gln3901Ter	p.Q3901*	ENST00000301067	NM_003482.3	3901	Cag/Tag	39/54	0.0940725290381579	3	FACETS	0.864	0.758	0.977	0.864	0.758	0.977	INDETERMINATE	2	FALSE	1	0.221381772045397	3		475	418	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10259681	10259681	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	40	219	0	ENST00000340748.4:c.2551C>T	p.Pro851Ser	p.P851S	ENST00000340748		851	Ccc/Tcc	26/40	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.221381772045397	2		219	256	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412969	49412969	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	56	331	0	ENST00000418115.1:c.54G>C	p.Lys18Asn	p.K18N	ENST00000418115	NM_001664.2	18	aaG/aaC	2/5	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.221381772045397	2		331	375	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972384	32972384	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	32	382	0	ENST00000380152.3:c.9734C>T	p.Ser3245Leu	p.S3245L	ENST00000380152		3245	tCa/tTa	27/27	1	2	FACETS	0.801	0.651	0.97	0.801	0.651	0.97	CLONAL	1	FALSE	1	0.221381772045397	2		382	361	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626928	158626928	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	39	343	0	ENST00000263640.3:c.742G>C	p.Glu248Gln	p.E248Q	ENST00000263640	NM_001105.4	248	Gaa/Caa	7/11	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	FALSE	1	0.221381772045397	2		343	324	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466576	120466576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	18	383	0	ENST00000256646.2:c.4543G>A	p.Asp1515Asn	p.D1515N	ENST00000256646	NM_024408.3	1515	Gac/Aac	26/34	1	2	FACETS	0.475	0.357	0.615	0.475	0.357	0.615	SUBCLONAL	1	FALSE	1	0.221381772045397	2		383	342	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512600	148512600	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	9	297	0	ENST00000320356.2:c.1544A>G	p.Lys515Arg	p.K515R	ENST00000320356	NM_004456.4	515	aAg/aGg	13/20	0.217632876106664	3	FACETS	0.302	0.199	0.434	0.101	0.066	0.145	SUBCLONAL	1	FALSE	0	0.221381772045397	3		297	299	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223256	41223256	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs80358008	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	21	352	0	ENST00000357654.3:c.4676-1G>A		p.X1559_splice	ENST00000357654	NM_007294.3	1559			0.221381772045397	1	FACETS	0.785	0.607	0.991	0.785	0.607	0.991	CLONAL	1	FALSE	0	0.221381772045397	1		352	215	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097180	11097180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1368858108	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	22	385	0	ENST00000358026.2:c.671C>T	p.Ser224Leu	p.S224L	ENST00000358026	NM_001128849.1	224	tCg/tTg	4/36	1	2	FACETS	0.549	0.425	0.693	0.549	0.425	0.693	SUBCLONAL	1	FALSE	1	0.221381772045397	2		385	362	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29422382	29422382	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs786203307	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	55	287	0	ENST00000356175.3:c.55G>T	p.Glu19Ter	p.E19*	ENST00000356175	NM_000267.3	19	Gag/Tag	1/57	0.221381772045397	1	FACETS	0.909	0.786	1	1	0.976	1	CLONAL	2	FALSE	0	0.221381772045397	1		287	243	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983168	149983168	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	21	359	0	ENST00000253339.5:c.3090C>G	p.Ile1030Met	p.I1030M	ENST00000253339		1030	atC/atG	7/7	1	2	FACETS	0.523	0.402	0.664	0.523	0.402	0.664	SUBCLONAL	1	FALSE	1	0.221381772045397	2		359	363	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201307	133201307	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	20	369	0	ENST00000320574.5:c.6837G>C	p.Gln2279His	p.Q2279H	ENST00000320574	NM_006231.2	2279	caG/caC	49/49	0.0940725290381579	3	FACETS	0.641	0.49	0.818	0.321	0.245	0.409	INDETERMINATE	1	FALSE	1	0.221381772045397	3		369	313	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867239	68867239	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	32	383	0	ENST00000261769.5:c.2486C>G	p.Ser829Cys	p.S829C	ENST00000261769	NM_004360.3	829	tCt/tGt	16/16	1	2	FACETS	0.721	0.585	0.874	0.721	0.585	0.874	SUBCLONAL	1	FALSE	1	0.221381772045397	2		383	401	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291485	11291485	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	20	346	0	ENST00000361445.4:c.2521C>A	p.Leu841Met	p.L841M	ENST00000361445	NM_004958.3	841	Ctg/Atg	17/58	1	2	FACETS	0.51	0.39	0.652	0.51	0.39	0.652	SUBCLONAL	1	FALSE	1	0.221381772045397	2		346	354	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761466	59761466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	20	290	0	ENST00000259008.2:c.2941G>A	p.Glu981Lys	p.E981K	ENST00000259008	NM_032043.2	981	Gaa/Aaa	20/20	0.0940725290381579	3	FACETS	0.61	0.466	0.779	0.305	0.233	0.39	INDETERMINATE	1	FALSE	1	0.221381772045397	3		290	329	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191034	2191034	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	34	383	0	ENST00000398665.3:c.288G>T	p.Met96Ile	p.M96I	ENST00000398665	NM_032482.2	96	atG/atT	5/28	1	2	FACETS	0.79	0.646	0.951	0.79	0.646	0.951	CLONAL	1	FALSE	1	0.221381772045397	2		383	389	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47599570	47599570	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	63	363	0	ENST00000430070.2:c.30G>C	p.Gln10His	p.Q10H	ENST00000430070	NM_018095.4	10	caG/caC	2/4	1	2	FACETS	0.763	0.663	0.87	1	0.972	1	SUBCLONAL	2	FALSE	1	0.221381772045397	2		363	373	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958538	175958538	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	43	343	0	ENST00000367669.3:c.1807T>A	p.Ser603Thr	p.S603T	ENST00000367669	NM_022457.5	603	Tct/Act	16/20	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	FALSE	1	0.221381772045397	2		343	326	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466310	120466310	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	34	377	0	ENST00000256646.2:c.4809G>C	p.Gln1603His	p.Q1603H	ENST00000256646	NM_024408.3	1603	caG/caC	26/34	1	2	FACETS	0.837	0.685	1	0.837	0.685	1	CLONAL	1	FALSE	1	0.221381772045397	2		377	367	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421341	12421341	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	43	361	0	ENST00000287820.6:c.221C>G	p.Ser74Cys	p.S74C	ENST00000287820	NM_015869.4	74	tCt/tGt	2/7	1	2	FACETS	1	0.84	1	1	0.84	1	CLONAL	1	FALSE	1	0.221381772045397	2		361	388	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497662	125497662	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	73	312	0	ENST00000428830.2:c.226G>C	p.Glu76Gln	p.E76Q	ENST00000428830	NM_001114121.2	76	Gaa/Caa	3/14	1	2	FACETS	1	0.884	1	1	0.983	1	CLONAL	2	FALSE	1	0.221381772045397	2		312	329	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880188	37880188	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	249	373	0	ENST00000269571.5:c.2232G>C	p.Glu744Asp	p.E744D	ENST00000269571		744	gaG/gaC	19/27	0.221381772045397	11	FACETS	0.955	0.898	1	0.668	0.629	0.709	CLONAL	7	FALSE	1	0.221381772045397	11		373	672	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046978	128046978	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	48	404	0	ENST00000285398.2:c.757G>C	p.Glu253Gln	p.E253Q	ENST00000285398	NM_000122.1	253	Gag/Cag	6/15	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.221381772045397	2		404	327	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040874	42040874	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	36	344	0	ENST00000219905.7:c.5252C>G	p.Ser1751Cys	p.S1751C	ENST00000219905	NM_001164273.1	1751	tCt/tGt	16/24	1	2	FACETS	0.84	0.692	1	0.84	0.692	1	CLONAL	1	FALSE	1	0.221381772045397	2		344	387	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523641	148523641	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	35	370	0	ENST00000320356.2:c.812C>G	p.Ser271Cys	p.S271C	ENST00000320356	NM_004456.4	271	tCt/tGt	8/20	0.217632876106664	3	FACETS	1	0.876	1	0.361	0.297	0.433	CLONAL	1	FALSE	0	0.221381772045397	3		370	324	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502774	186502774	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	30	319	0	ENST00000323963.5:c.232C>T	p.Gln78Ter	p.Q78*	ENST00000323963		78	Cag/Tag	4/11	1	2	FACETS	0.795	0.641	0.969	0.795	0.641	0.969	CLONAL	1	FALSE	1	0.221381772045397	2		319	341	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866537	117866537	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	14	323	0	ENST00000297338.2:c.1108G>A	p.Glu370Lys	p.E370K	ENST00000297338	NM_006265.2	370	Gaa/Aaa	9/14	NA	2	FACETS	0.485	0.35	0.648			1	INDETERMINATE	1	FALSE	NA	0.221381772045397	2		323	261	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622165	162622165	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	34	382	0	ENST00000366898.1:c.532C>T	p.Gln178Ter	p.Q178*	ENST00000366898	NM_004562.2	178	Cag/Tag	4/12	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	FALSE	1	0.221381772045397	2		382	270	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281462	49281462	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	26	449	0	ENST00000282018.3:c.509C>G	p.Ser170Ter	p.S170*	ENST00000282018	NM_020377.2	170	tCa/tGa	1/1	1	2	FACETS	0.818	0.65	1	0.818	0.65	1	CLONAL	1	FALSE	1	0.221381772045397	2		449	287	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864593	37864593	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	60	397	0	ENST00000269571.5:c.245G>T	p.Gly82Val	p.G82V	ENST00000269571		82	gGc/gTc	3/27	0.221381772045397	11	FACETS	0.78	0.671	0.898	0.156	0.134	0.18	SUBCLONAL	2	FALSE	1	0.221381772045397	11		397	694	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040850	42040850	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	34	344	1	ENST00000219905.7:c.5228T>A	p.Ile1743Asn	p.I1743N	ENST00000219905	NM_001164273.1	1743	aTt/aAt	16/24	1	2	FACETS	0.885	0.725	1	0.885	0.725	1	CLONAL	1	FALSE	1	0.221381772045397	2		345	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0068636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	54	508	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.495	0.422	0.575	0.495	0.422	0.575	SUBCLONAL	1	FALSE	1	0.291350999860708	2		508	749	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339230	70339230	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	55	272	0	ENST00000374080.3:c.107T>C	p.Leu36Pro	p.L36P	ENST00000374080		36	cTg/cCg	2/45	1	2	FACETS	0.758	0.649	0.877	0.758	0.649	0.877	SUBCLONAL	1	FALSE	1	0.291350999860708	2		272	498	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844172	68844172	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1555515445	NA	P-0068636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	105	347	0	ENST00000261769.5:c.760G>T	p.Asp254Tyr	p.D254Y	ENST00000261769	NM_004360.3	254	Gat/Tat	6/16	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.291350999860708	2		347	657	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405860	49405861	+	stop_gained,frameshift_variant,splice_region_variant	Nonsense_Mutation	INS	-	-	CTAAA	novel	NA	P-0068636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	40	301	0	ENST00000418115.1:c.273_277dup	p.Glu93ValfsTer2	p.E93Vfs*2	ENST00000418115	NM_001664.2	93	gaa/gTTTAGaa		1	2	FACETS	0.483	0.401	0.575	0.483	0.401	0.575	SUBCLONAL	1	FALSE	1	0.291350999860708	2		301	568	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	230999	230999	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	35	310	0	ENST00000264932.6:c.779G>T	p.Gly260Val	p.G260V	ENST00000264932	NM_004168.2	260	gGg/gTg	7/15	1	2	FACETS	0.409	0.335	0.494	0.409	0.335	0.494	SUBCLONAL	1	FALSE	1	0.291350999860708	2		310	587	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589289	67589289	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	12	205	0	ENST00000274335.5:c.1277A>C	p.Tyr426Ser	p.Y426S	ENST00000274335		426	tAt/tCt	9/15	1	2	FACETS	0.351	0.246	0.479	0.351	0.246	0.479	SUBCLONAL	1	FALSE	1	0.291350999860708	2		205	235	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	148	464	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.464431100238408	2		464	514	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	139	410	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.464431100238408	2		410	560	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	186	360	2	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.464431100238408	2		362	723	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	91	294	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.933	0.833	1	0.933	0.833	1	CLONAL	1	TRUE	1	0.464431100238408	2		298	420	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149243908	149243908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	91	242	0	ENST00000360632.3:c.910C>T	p.Pro304Ser	p.P304S	ENST00000360632	NM_015472.4	304	Cca/Tca	6/7	1	2	FACETS	0.951	0.85	1	0.951	0.85	1	CLONAL	1	TRUE	1	0.464431100238408	2		242	412	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	165	386	11	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.464431100238408	2		397	662	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	122	407	0	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.986	0.895	1	0.986	0.895	1	CLONAL	1	TRUE	1	0.464431100238408	2		407	533	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2492097	2492097	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs772088410	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	114	374	0	ENST00000355716.4:c.500del	p.Pro167ArgfsTer23	p.P167Rfs*23	ENST00000355716	NM_003820.2	165	tgC/tg	5/8	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.464431100238408	2		374	491	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260214	16260214	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	157	457	0	ENST00000375759.3:c.7484del	p.Pro2495LeufsTer4	p.P2495Lfs*4	ENST00000375759	NM_015001.2	2493	agC/ag	11/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.464431100238408	2		457	620	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335141	65335141	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	117	325	0	ENST00000342505.4:c.500T>C	p.Val167Ala	p.V167A	ENST00000342505	NM_002227.2	167	gTg/gCg	6/25	1	2	FACETS	0.87	0.787	0.957	0.87	0.787	0.957	CLONAL	1	TRUE	1	0.464431100238408	2		325	579	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266569	115266569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	88	283	0	ENST00000438362.2:c.1946G>A	p.Arg649His	p.R649H	ENST00000438362	NM_001242891.1	649	cGc/cAc	16/20	1	2	FACETS	0.746	0.663	0.834	0.746	0.663	0.834	SUBCLONAL	1	TRUE	1	0.464431100238408	2		283	508	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	32	90	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	0.464431100238408	1	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	0	0.464431100238408	1		90	103	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900984	114900984	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778855667	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	144	392	0	ENST00000543371.1:c.598del	p.Leu200SerfsTer25	p.L200Sfs*25	ENST00000543371	NM_001198531.1	198	caC/ca	6/14	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.464431100238408	2		392	614	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258036	123258036	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	122	284	0	ENST00000358487.5:c.1645A>G	p.Asn549Asp	p.N549D	ENST00000358487	NM_000141.4	549	Aat/Gat	12/18	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.464431100238408	2		284	447	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948755	71948755	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1565399032	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	117	470	1	ENST00000298229.2:c.3470del	p.Gly1157AspfsTer45	p.G1157Dfs*45	ENST00000298229	NM_001567.3	1156	cGg/cg	26/28	1	2	FACETS	0.965	0.874	1	0.965	0.874	1	CLONAL	1	TRUE	1	0.464431100238408	2		471	522	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420661	49420661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555185875	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	171	426	1	ENST00000301067.7:c.15088C>T	p.Arg5030Cys	p.R5030C	ENST00000301067	NM_003482.3	5030	Cgt/Tgt	48/54	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.464431100238408	2		427	576	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913436	32913436	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	92	315	0	ENST00000380152.3:c.4948del	p.Ser1650ValfsTer20	p.S1650Vfs*20	ENST00000380152		1648	gcA/gc	11/27	1	2	FACETS	0.875	0.781	0.973	0.875	0.781	0.973	CLONAL	1	TRUE	1	0.464431100238408	2		315	453	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	69061320	69061320	+	stop_lost	Nonstop_Mutation	SNP	A	A	T	rs892904253	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	30	89	1	ENST00000487270.1:c.1155A>T	p.Ter385TyrextTer64	p.*385Yext*64	ENST00000487270	NM_133509.3	385	taA/taT	11/11	1	2	FACETS	0.979	0.802	1	0.979	0.802	1	CLONAL	1	TRUE	1	0.464431100238408	2		90	132	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132677	67132677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200416354	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	93	279	0	ENST00000412916.2:c.560G>A	p.Arg187His	p.R187H	ENST00000412916		187	cGt/cAt	6/6	1	2	FACETS	0.972	0.87	1	0.972	0.87	1	CLONAL	1	TRUE	1	0.464431100238408	2		279	412	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835781	68835781	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060501215	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	159	360	0	ENST00000261769.5:c.377del	p.Pro126ArgfsTer89	p.P126Rfs*89	ENST00000261769	NM_004360.3	124	cgC/cg	3/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.464431100238408	2		360	629	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974830	15974830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	124	342	0	ENST00000268712.3:c.4045C>T	p.Arg1349Cys	p.R1349C	ENST00000268712	NM_006311.3	1349	Cgt/Tgt	30/46	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.464431100238408	2		342	512	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439919	56439919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	158	341	0	ENST00000407977.2:c.673del	p.Arg225AlafsTer194	p.R225Afs*194	ENST00000407977		225	Cgc/gc	6/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.464431100238408	2		341	623	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1620992	1620992	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	176	497	0	ENST00000344749.5:c.1068del	p.Val357TrpfsTer37	p.V357Wfs*37	ENST00000344749	NM_001136139.2	356	ccC/cc	13/19	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.464431100238408	2		497	674	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231610	5231611	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	49	129	1	ENST00000357368.4:c.1865dup	p.Gln623SerfsTer4	p.Q623Sfs*4	ENST00000357368	NM_002850.3	622	cct/ccCt	14/38	1	2	FACETS	0.865	0.739	1	0.865	0.739	1	CLONAL	1	TRUE	1	0.464431100238408	2		130	244	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244098	5244098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs73545312	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	112	406	0	ENST00000357368.4:c.1384G>A	p.Val462Ile	p.V462I	ENST00000357368	NM_002850.3	462	Gtc/Atc	11/38	1	2	FACETS	0.959	0.867	1	0.959	0.867	1	CLONAL	1	TRUE	1	0.464431100238408	2		406	503	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211082	36211082	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	150	410	0	ENST00000222270.7:c.837del	p.Arg280GlyfsTer25	p.R280Gfs*25	ENST00000222270	NM_014727.1	278	aCc/ac	3/37	0.432520258572145	3	FACETS	1	0.965	1	0.55	0.503	0.598	CLONAL	1	TRUE	1	0.464431100238408	3		410	724	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219029	36219029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748191051	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	113	417	0	ENST00000222270.7:c.4528G>A	p.Ala1510Thr	p.A1510T	ENST00000222270	NM_014727.1	1510	Gcc/Acc	19/37	0.432520258572145	3	FACETS	0.874	0.788	0.965	0.437	0.394	0.483	CLONAL	1	TRUE	1	0.464431100238408	3		417	686	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223858	36223858	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	243	431	6	ENST00000222270.7:c.6413del	p.Pro2138ArgfsTer15	p.P2138Rfs*15	ENST00000222270	NM_014727.1	2136	ctC/ct	28/37	0.432520258572145	3	FACETS	0.964	0.906	1	0.964	0.906	1	CLONAL	2	TRUE	1	0.464431100238408	3		437	669	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792125	42792125	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	81	338	0	ENST00000575354.2:c.929G>T	p.Gly310Val	p.G310V	ENST00000575354	NM_015125.3	310	gGg/gTg	6/20	0.432520258572145	3	FACETS	0.886	0.783	0.996	0.443	0.391	0.498	CLONAL	1	TRUE	1	0.464431100238408	3		338	485	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796882	42796883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761345552	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	156	445	3	ENST00000575354.2:c.3347dup	p.Ser1117LysfsTer34	p.S1117Kfs*34	ENST00000575354	NM_015125.3	1114	gcc/gCcc	14/20	0.432520258572145	3	FACETS	1	0.97	1	0.559	0.513	0.608	CLONAL	1	TRUE	1	0.464431100238408	3		448	740	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	104	440	1	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			0.432520258572145	3	FACETS	1	0.925	1	0.518	0.465	0.573	CLONAL	1	TRUE	1	0.464431100238408	3		441	533	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149542	202149542	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	107	387	0	ENST00000358485.4:c.983C>G	p.Ala328Gly	p.A328G	ENST00000358485	NM_001080125.1	328	gCt/gGt	8/9	1	2	FACETS	0.816	0.734	0.902	0.816	0.734	0.902	CLONAL	1	TRUE	1	0.464431100238408	2		387	565	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113103	209113103	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	121	306	0	ENST00000345146.2:c.404A>G	p.Tyr135Cys	p.Y135C	ENST00000345146	NM_005896.2	135	tAt/tGt	4/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.464431100238408	2		306	461	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661664	227661664	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs761880048	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	172	403	7	ENST00000305123.5:c.1791del	p.His598ThrfsTer38	p.H598Tfs*38	ENST00000305123	NM_005544.2	597	ggG/gg	1/2	1	2	FACETS	0.821	0.763	0.88	1	0.992	1	CLONAL	2	TRUE	1	0.464431100238408	2		410	451	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	87	400	0	ENST00000375687.4:c.1933_1934dup	p.Gly646ValfsTer58	p.G646Vfs*58	ENST00000375687	NM_015338.5	642	-/GG	13/13	1	2	FACETS	0.732	0.65	0.819	0.732	0.65	0.819	SUBCLONAL	1	TRUE	1	0.464431100238408	2		400	512	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	260	345	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.464431100238408	2	FACETS	0.965	0.913	1	0.965	0.913	1	CLONAL	2	TRUE	0	0.464431100238408	2		345	580	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940112	49940112	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760002850	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	85	382	0	ENST00000296474.3:c.931del	p.Ala311ProfsTer27	p.A311Pfs*27	ENST00000296474	NM_002447.2	311	Gcc/cc	1/20	0.464431100238408	2	FACETS	0.799	0.709	0.895	0.4	0.354	0.448	SUBCLONAL	1	TRUE	0	0.464431100238408	2		382	458	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628340	187628340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536104649	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	53	407	0	ENST00000441802.2:c.2642G>A	p.Arg881His	p.R881H	ENST00000441802	NM_005245.3	881	cGc/cAc	2/27	1	2	FACETS	0.331	0.282	0.386	0.331	0.282	0.386	SUBCLONAL	1	TRUE	1	0.464431100238408	2		407	689	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	99	374	1	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.692	0.619	0.77	0.692	0.619	0.77	SUBCLONAL	1	TRUE	1	0.464431100238408	2		375	616	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	104	277	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	0.976	0.879	1	0.976	0.879	1	CLONAL	1	TRUE	1	0.464431100238408	2		277	459	SUCCESS
APC	324	MSKCC	GRCh37	5	112178033	112178033	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs773874693	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	136	358	1	ENST00000257430.4:c.6747del	p.Gly2250AlafsTer29	p.G2250Afs*29	ENST00000257430	NM_000038.5	2248	Aaa/aa	16/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.464431100238408	2		359	526	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931451	131931452	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs397507178	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	121	284	3	ENST00000265335.6:c.2165dup	p.Glu723GlyfsTer5	p.E723Gfs*5	ENST00000265335		719	cta/ctAa	13/25	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.464431100238408	2		287	481	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165126	32165126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1213449936	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	78	372	0	ENST00000375023.3:c.5002C>T	p.Arg1668Cys	p.R1668C	ENST00000375023	NM_004557.3	1668	Cgc/Tgc	27/30	1	2	FACETS	0.661	0.582	0.745	0.661	0.582	0.745	SUBCLONAL	1	TRUE	1	0.464431100238408	2		372	508	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805363	32805363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	110	339	0	ENST00000374899.4:c.559del	p.His187MetfsTer63	p.H187Mfs*63	ENST00000374899	NM_018833.2	187	Cat/at	3/12	1	2	FACETS	0.895	0.808	0.988	0.895	0.808	0.988	CLONAL	1	TRUE	1	0.464431100238408	2		339	529	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805787	32805788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1174402903	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	127	451	0	ENST00000374899.4:c.223dup	p.Leu75ProfsTer92	p.L75Pfs*92	ENST00000374899	NM_018833.2	75	ctg/cCtg	2/12	1	2	FACETS	0.93	0.846	1	0.93	0.846	1	CLONAL	1	TRUE	1	0.464431100238408	2		451	588	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6442009	6442009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	56	102	0	ENST00000356142.4:c.568G>A	p.Glu190Lys	p.E190K	ENST00000356142	NM_018890.3	190	Gaa/Aaa	7/7	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.464431100238408	2		102	206	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332070	81332070	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	100	284	0	ENST00000222390.5:c.2014del	p.Asp672IlefsTer13	p.D672Ifs*13	ENST00000222390	NM_000601.4	672	Gat/at	18/18	1	2	FACETS	0.999	0.898	1	0.999	0.898	1	CLONAL	1	TRUE	1	0.464431100238408	2		284	431	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851177	151851177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141966811	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	122	372	0	ENST00000262189.6:c.12194C>T	p.Ala4065Val	p.A4065V	ENST00000262189	NM_170606.2	4065	gCg/gTg	48/59	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.464431100238408	2		372	504	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	141	342	0	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.464431100238408	2		342	546	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771987	135771988	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs2234980	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	99	355	2	ENST00000298552.3:c.3127_3129dup	p.Ser1043dup	p.S1043dup	ENST00000298552	NM_001162426.1	1043	-/AGC	23/23	1	2	FACETS	0.664	0.593	0.739	0.664	0.593	0.739	SUBCLONAL	1	TRUE	1	0.464431100238408	2		357	642	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650448	48650448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781904528	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	132	226	0	ENST00000376670.3:c.418C>T	p.Arg140Trp	p.R140W	ENST00000376670	NM_002049.3	140	Cgg/Tgg	3/6	1	1	FACETS	0.755	0.698	0.813	1	0.989	1	SUBCLONAL	2	TRUE	0	0.464431100238408	1		226	289	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275329	115275329	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	86	345	0	ENST00000438362.2:c.1084G>C	p.Val362Leu	p.V362L	ENST00000438362	NM_001242891.1	362	Gtt/Ctt	10/20	1	2	FACETS	0.836	0.743	0.934	0.836	0.743	0.934	CLONAL	1	TRUE	1	0.464431100238408	2		345	443	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731036	162731036	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	130	349	0	ENST00000367921.3:c.891G>T	p.Lys297Asn	p.K297N	ENST00000367921	NM_006182.2	297	aaG/aaT	9/18	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.464431100238408	2		349	535	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343232	118343232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555035935	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	130	358	0	ENST00000534358.1:c.1358C>T	p.Ala453Val	p.A453V	ENST00000534358	NM_005933.3	453	gCc/gTc	3/36	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.464431100238408	2		358	543	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443881	49443881	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	142	432	0	ENST00000301067.7:c.3490A>T	p.Thr1164Ser	p.T1164S	ENST00000301067	NM_003482.3	1164	Acc/Tcc	11/54	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.464431100238408	2		432	591	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445146	49445146	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	94	486	0	ENST00000301067.7:c.2320C>G	p.Pro774Ala	p.P774A	ENST00000301067	NM_003482.3	774	Cct/Gct	10/54	1	2	FACETS	0.74	0.66	0.825	0.74	0.66	0.825	SUBCLONAL	1	TRUE	1	0.464431100238408	2		486	547	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494877	56494877	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	46	332	0	ENST00000267101.3:c.3238del	p.Arg1080ValfsTer22	p.R1080Vfs*22	ENST00000267101	NM_001982.3	1078	tgC/tg	27/28	1	2	FACETS	0.382	0.322	0.449	0.382	0.322	0.449	SUBCLONAL	1	TRUE	1	0.464431100238408	2		332	518	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437151	110437151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1405112911	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	53	235	0	ENST00000375856.3:c.1250C>T	p.Ala417Val	p.A417V	ENST00000375856	NM_003749.2	417	gCg/gTg	1/2	1	2	FACETS	0.947	0.816	1	0.947	0.816	1	CLONAL	1	TRUE	1	0.464431100238408	2		235	241	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107966	30107966	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	157	361	0	ENST00000331968.5:c.841C>T	p.Pro281Ser	p.P281S	ENST00000331968	NM_002742.2	281	Ccc/Tcc	5/18	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.464431100238408	2		361	567	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986826	36986826	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	99	369	0	ENST00000354822.5:c.863T>C	p.Val288Ala	p.V288A	ENST00000354822	NM_001079668.2	288	gTg/gCg	3/3	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.464431100238408	2		369	405	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95598951	95598951	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	75	309	0	ENST00000393063.1:c.208A>G	p.Lys70Glu	p.K70E	ENST00000393063	NM_030621.3	70	Aag/Gag	4/28	1	2	FACETS	0.792	0.697	0.892	0.792	0.697	0.892	SUBCLONAL	1	TRUE	1	0.464431100238408	2		309	408	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99439996	99439996	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs778294422	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	106	284	0	ENST00000268035.6:c.964A>G	p.Ile322Val	p.I322V	ENST00000268035	NM_000875.3	322	Atc/Gtc	4/21	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.464431100238408	2		284	449	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038666	14038666	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	100	261	0	ENST00000311895.7:c.1991A>G	p.Asp664Gly	p.D664G	ENST00000311895	NM_005236.2	664	gAt/gGt	10/11	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.464431100238408	2		261	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573999	7573999	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	105	264	2	ENST00000269305.4:c.1028A>G	p.Glu343Gly	p.E343G	ENST00000269305	NM_001126112.2	343	gAg/gGg	10/11	1	2	FACETS	0.936	0.843	1	0.936	0.843	1	CLONAL	1	TRUE	1	0.464431100238408	2		266	483	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040663	16040663	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778056591	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	86	239	0	ENST00000268712.3:c.1471G>A	p.Val491Ile	p.V491I	ENST00000268712	NM_006311.3	491	Gtc/Atc	14/46	1	2	FACETS	0.993	0.885	1	0.993	0.885	1	CLONAL	1	TRUE	1	0.464431100238408	2		239	373	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29497017	29497017	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1135402791	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	81	197	0	ENST00000356175.3:c.586+2T>C		p.X196_splice	ENST00000356175	NM_000267.3	196			0.464431100238408	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.464431100238408	1		197	248	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55334111	55334111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	69	195	0	ENST00000284073.2:c.8C>T	p.Ala3Val	p.A3V	ENST00000284073	NM_138962.2	3	gCa/gTa	1/14	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.464431100238408	2		195	290	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526582	66526582	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	119	291	0	ENST00000358598.2:c.1138T>C	p.Ser380Pro	p.S380P	ENST00000358598	NM_212471.2	380	Tct/Cct	11/11	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.464431100238408	2		291	498	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223515	36223515	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	120	430	0	ENST00000222270.7:c.6065A>G	p.Asp2022Gly	p.D2022G	ENST00000222270	NM_014727.1	2022	gAc/gGc	28/37	0.432520258572145	3	FACETS	0.955	0.864	1	0.477	0.432	0.525	CLONAL	1	TRUE	1	0.464431100238408	3		430	667	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752628	42752628	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764412749	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	119	348	0	ENST00000222329.4:c.1636C>T	p.Arg546Ter	p.R546*	ENST00000222329	NM_006494.2	546	Cga/Tga	4/4	0.432520258572145	3	FACETS	1	0.935	1	0.521	0.471	0.573	CLONAL	1	TRUE	1	0.464431100238408	3		348	606	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867056	45867056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	215	573	0	ENST00000391945.4:c.1063C>T	p.Pro355Ser	p.P355S	ENST00000391945	NM_000400.3	355	Ccc/Tcc	11/23	0.432520258572145	3	FACETS	0.757	0.705	0.809	0.757	0.705	0.809	SUBCLONAL	2	TRUE	1	0.464431100238408	3		573	754	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868331	45868331	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	56	572	0	ENST00000391945.4:c.446A>C	p.Asp149Ala	p.D149A	ENST00000391945	NM_000400.3	149	gAc/gCc	6/23	0.432520258572145	3	FACETS	0.325	0.277	0.378	0.163	0.138	0.189	SUBCLONAL	1	TRUE	1	0.464431100238408	3		572	914	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940470	29940470	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	93	297	0	ENST00000389048.3:c.761C>A	p.Pro254His	p.P254H	ENST00000389048	NM_004304.4	254	cCt/cAt	2/29	1	2	FACETS	0.999	0.894	1	0.999	0.894	1	CLONAL	1	TRUE	1	0.464431100238408	2		297	401	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264377	46264377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	111	422	0	ENST00000371998.3:c.1424C>T	p.Pro475Leu	p.P475L	ENST00000371998		475	cCa/cTa	11/23	1	2	FACETS	0.83	0.748	0.916	0.83	0.748	0.916	CLONAL	1	TRUE	1	0.464431100238408	2		422	576	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288305	21288305	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	68	366	0	ENST00000354336.3:c.550T>G	p.Ser184Ala	p.S184A	ENST00000354336	NM_005207.3	184	Tcc/Gcc	2/3	1	2	FACETS	0.484	0.421	0.552	0.484	0.421	0.552	SUBCLONAL	1	TRUE	1	0.464431100238408	2		366	605	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29120963	29120963	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	70	213	0	ENST00000328354.6:c.592+2T>C		p.X198_splice	ENST00000328354	NM_007194.3	198			1	2	FACETS	0.833	0.73	0.942	0.833	0.73	0.942	CLONAL	1	TRUE	1	0.464431100238408	2		213	362	SUCCESS
ALB	213	MSKCC	GRCh37	4	74282071	74282071	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs779988470	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	88	231	0	ENST00000295897.4:c.1289+1G>A		p.X430_splice	ENST00000295897	NM_000477.5	430			1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.464431100238408	2		231	344	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99809066	99809066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	88	233	0	ENST00000280892.6:c.319C>T	p.Pro107Ser	p.P107S	ENST00000280892	NM_001130678.1	107	Cct/Tct	4/7	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.464431100238408	2		233	331	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31521249	31521250	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1222049728	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	100	317	1	ENST00000344624.3:c.927dup	p.Glu310ArgfsTer3	p.E310Rfs*3	ENST00000344624		309	-/A	3/33	1	2	FACETS	0.938	0.843	1	0.938	0.843	1	CLONAL	1	TRUE	1	0.464431100238408	2		318	459	SUCCESS
APC	324	MSKCC	GRCh37	5	112173857	112173857	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566005215	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	110	349	0	ENST00000257430.4:c.2566C>T	p.Arg856Cys	p.R856C	ENST00000257430	NM_000038.5	856	Cgc/Tgc	16/16	1	2	FACETS	0.951	0.859	1	0.951	0.859	1	CLONAL	1	TRUE	1	0.464431100238408	2		349	498	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045907	26045907	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	198	498	0	ENST00000540144.1:c.269T>C	p.Val90Ala	p.V90A	ENST00000540144	NM_003531.2	90	gTg/gCg	1/1	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.464431100238408	2		498	725	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056292	26056292	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	107	391	0	ENST00000343677.2:c.365del	p.Lys122ArgfsTer45	p.K122Rfs*45	ENST00000343677	NM_005319.3	122	aAg/ag	1/1	1	2	FACETS	0.824	0.742	0.911	0.824	0.742	0.911	CLONAL	1	TRUE	1	0.464431100238408	2		391	559	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803479	32803479	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	130	345	0	ENST00000374899.4:c.680A>C	p.Glu227Ala	p.E227A	ENST00000374899	NM_018833.2	227	gAg/gCg	4/12	1	2	FACETS	0.909	0.827	0.994	0.909	0.827	0.994	CLONAL	1	TRUE	1	0.464431100238408	2		345	616	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967931	93967931	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	77	277	0	ENST00000369303.4:c.1996del	p.Thr666ProfsTer2	p.T666Pfs*2	ENST00000369303	NM_004440.3	666	Acc/cc	11/17	1	2	FACETS	0.817	0.721	0.919	0.817	0.721	0.919	CLONAL	1	TRUE	1	0.464431100238408	2		277	406	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200022	138200022	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	129	380	0	ENST00000237289.4:c.1443del	p.Gly482AlafsTer6	p.G482Afs*6	ENST00000237289	NM_001270507.1	480	agC/ag	7/9	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.464431100238408	2		380	553	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508923	106508923	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs144045366	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	119	369	0	ENST00000359195.3:c.917T>C	p.Val306Ala	p.V306A	ENST00000359195	NM_002649.2	306	gTa/gCa	2/11	1	2	FACETS	0.937	0.849	1	0.937	0.849	1	CLONAL	1	TRUE	1	0.464431100238408	2		369	547	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931829	68931829	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	83	252	0	ENST00000288368.4:c.259T>C	p.Phe87Leu	p.F87L	ENST00000288368	NM_024870.2	87	Ttc/Ctc	3/40	1	2	FACETS	0.889	0.789	0.995	0.889	0.789	0.995	CLONAL	1	TRUE	1	0.464431100238408	2		252	402	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396481	139396481	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs752013175	NA	P-0068637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	134	458	0	ENST00000277541.6:c.5444A>G	p.Asp1815Gly	p.D1815G	ENST00000277541	NM_017617.3	1815	gAc/gGc	29/34	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.464431100238408	2		458	524	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15827443	15827443	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0068638-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	41	125	0	ENST00000307771.7:c.557+2T>G		p.X186_splice	ENST00000307771	NM_005089.3	186			1	1	FACETS	0.714	0.602	0.835	0.714	0.602	0.835	SUBCLONAL	1	TRUE	0	0.47	1		125	187	SUCCESS
ATR	545	MSKCC	GRCh37	3	142257365	142257365	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068638-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	113	305	0	ENST00000350721.4:c.3684A>T	p.Lys1228Asn	p.K1228N	ENST00000350721	NM_001184.3	1228	aaA/aaT	19/47	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.47	2		305	471	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200961	108200961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782310	NA	P-0068639-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	22	337	0	ENST00000278616.4:c.7328G>A	p.Arg2443Gln	p.R2443Q	ENST00000278616	NM_000051.3	2443	cGa/cAa	50/63	0.265741318261487	0	FACETS	0.307	0.238	0.388			1	SUBCLONAL	1	TRUE	0	0.33041138371345	0		337	290	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439898	52439898	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068639-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	80	375	0	ENST00000460680.1:c.814C>T	p.Gln272Ter	p.Q272*	ENST00000460680	NM_004656.3	272	Cag/Tag	10/17	0.33041138371345	1	FACETS	0.962	0.851	1	0.962	0.851	1	CLONAL	1	TRUE	0	0.33041138371345	1		375	420	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143326469	143326469	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068639-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	30	293	0	ENST00000262992.4:c.145G>A	p.Asp49Asn	p.D49N	ENST00000262992	NM_001101669.1	49	Gat/Aat	4/24	0.33041138371345	1	FACETS	0.414	0.334	0.505	0.414	0.334	0.505	SUBCLONAL	1	TRUE	0	0.33041138371345	1		293	366	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651356	52651356	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0068639-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	86	465	0	ENST00000394830.3:c.1740T>G	p.Tyr580Ter	p.Y580*	ENST00000394830	NM_018313.4	580	taT/taG	15/30	0.33041138371345	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.33041138371345	1		465	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0068640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	145	361	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.588922696941283	1	FACETS	0.815	0.751	0.881	0.815	0.751	0.881	CLONAL	1	TRUE	0	0.59614005624363	1		361	419	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436360	52436360	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	160	528	0	ENST00000460680.1:c.2134C>T	p.Gln712Ter	p.Q712*	ENST00000460680	NM_004656.3	712	Cag/Tag	17/17	0.588922696941283	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.59614005624363	1		528	357	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929414	81929414	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	129	462	2	ENST00000359376.3:c.1075G>A	p.Asp359Asn	p.D359N	ENST00000359376	NM_002661.3	359	Gac/Aac	13/33	1	2	FACETS	0.975	0.891	1	0.975	0.891	1	CLONAL	1	TRUE	1	0.59614005624363	2		464	444	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0068641-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	55	333	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		333	380	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0068658-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	150	491	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	1	2	FACETS	1	0.959	1	1	0.994	1	CLONAL	5	FALSE	1	0.155134821526006	2		491	367	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0068661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	21	440	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.199	0.153	0.254	0.199	0.153	0.254	SUBCLONAL	1	TRUE	1	0.46	2		440	458	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857430	68857430	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068665-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	100	392	0	ENST00000261769.5:c.2065G>T	p.Glu689Ter	p.E689*	ENST00000261769	NM_004360.3	689	Gaa/Taa	13/16	0.326984506926677	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.326984506926677	1		392	458	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550728	150550731	+	frameshift_variant	Frame_Shift_Del	DEL	TTTG	TTTG	-	novel	NA	P-0068665-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	110	462	0	ENST00000369026.2:c.925_928del	p.Gln309GlufsTer12	p.Q309Efs*12	ENST00000369026	NM_021960.4	309	CAAAga/ga	2/3	0.326984506926677	3	FACETS	1	0.949	1	0.544	0.489	0.603	CLONAL	1	TRUE	1	0.326984506926677	3		462	719	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0068667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	16	307	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.127	0.093	0.167	0.127	0.093	0.167	SUBCLONAL	1	TRUE	1	0.81	2		307	312	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0068667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	10	320	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.055	0.037	0.079	0.055	0.037	0.079	SUBCLONAL	1	TRUE	1	0.81	2		320	446	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0068669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	350	383	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.84311419691255	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.84311419691255	1		383	410	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827886	40827886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201911869	NA	P-0068669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	237	630	0	ENST00000373198.4:c.2542G>A	p.Gly848Arg	p.G848R	ENST00000373198	NM_133170.3	848	Gga/Aga	17/32	NA	2	FACETS	0.587	0.549	0.628			1	INDETERMINATE	1	TRUE	NA	0.84311419691255	2		630	957	SUCCESS
APC	324	MSKCC	GRCh37	5	112137078	112137078	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1554076217	NA	P-0068669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	74	387	0	ENST00000257430.4:c.832C>T	p.Gln278Ter	p.Q278*	ENST00000257430	NM_000038.5	278	Cag/Tag	8/16	0.535845016732011	1	FACETS	0.317	0.28	0.357	0.317	0.28	0.357	SUBCLONAL	1	TRUE	0	0.84311419691255	1		387	320	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0068669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	232	576	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.535845016732011	1	FACETS	0.688	0.65	0.726	0.688	0.65	0.726	SUBCLONAL	1	TRUE	0	0.84311419691255	1		576	463	SUCCESS
AR	367	MSKCC	GRCh37	X	66765382	66765382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770661499	NA	P-0068669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	225	721	0	ENST00000374690.3:c.394G>A	p.Val132Ile	p.V132I	ENST00000374690	NM_000044.3	132	Gtc/Atc	1/8	0.84311419691255	1	FACETS	0.744	0.704	0.784	0.744	0.704	0.784	SUBCLONAL	1	TRUE	0	0.84311419691255	1		721	415	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245071	133245071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878854848	NA	P-0068669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	249	737	0	ENST00000320574.5:c.2044G>A	p.Glu682Lys	p.E682K	ENST00000320574	NM_006231.2	682	Gaa/Aaa	19/49	1	2	FACETS	0.95	0.895	1	0.95	0.895	1	CLONAL	1	TRUE	1	0.84311419691255	2		737	622	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020474	14020474	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	151	606	0	ENST00000311895.7:c.445T>G	p.Leu149Val	p.L149V	ENST00000311895	NM_005236.2	149	Ttg/Gtg	3/11	0.441402529828644	2	FACETS	0.574	0.527	0.623	0.287	0.263	0.312	INDETERMINATE	1	TRUE	0	0.84311419691255	2		606	624	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86546675	86546675	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	90	548	0	ENST00000262426.4:c.1124A>G	p.Lys375Arg	p.K375R	ENST00000262426	NM_001451.2	375	aAg/aGg	2/2	0.433835653958144	2	FACETS	0.502	0.448	0.56	0.251	0.224	0.28	INDETERMINATE	1	TRUE	0	0.84311419691255	2		548	425	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348782	89348782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201207422	NA	P-0068669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	31	779	2	ENST00000301030.4:c.4168G>A	p.Gly1390Ser	p.G1390S	ENST00000301030	NM_001256183.1	1390	Ggc/Agc	9/13	0.433835653958144	2	FACETS	0.12	0.096	0.147	0.06	0.048	0.074	INDETERMINATE	1	TRUE	0	0.84311419691255	2		781	613	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719291	52719291	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	345	694	0	ENST00000322088.6:c.957G>C	p.Glu319Asp	p.E319D	ENST00000322088	NM_014225.5	319	gaG/gaC	8/15	0.433835653958144	2	FACETS	0.769	0.739	0.798	0.769	0.739	0.798	INDETERMINATE	2	TRUE	0	0.84311419691255	2		694	532	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119721071	119721071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	127	482	0	ENST00000316626.5:c.104G>A	p.Ser35Asn	p.S35N	ENST00000316626		35	aGc/aAc	2/12	0.435493984250868	3	FACETS	0.575	0.521	0.631	0.287	0.26	0.316	INDETERMINATE	1	TRUE	1	0.84311419691255	3		482	745	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117650498	117650498	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	162	629	0	ENST00000368508.3:c.5360A>G	p.Glu1787Gly	p.E1787G	ENST00000368508	NM_002944.2	1787	gAg/gGg	32/43	1	2	FACETS	0.6	0.552	0.649	0.6	0.552	0.649	SUBCLONAL	1	TRUE	1	0.84311419691255	2		629	641	SUCCESS
MET	4233	MSKCC	GRCh37	7	116381046	116381046	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	161	640	0	ENST00000397752.3:c.1668G>T	p.Trp556Cys	p.W556C	ENST00000397752	NM_000245.2	556	tgG/tgT	5/21	0.359786335604	3	FACETS	0.593	0.544	0.645	0.297	0.272	0.323	INDETERMINATE	1	TRUE	1	0.84311419691255	3		640	915	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606545	93606545	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	105	623	0	ENST00000375746.1:c.365A>G	p.Asp122Gly	p.D122G	ENST00000375746	NM_001174167.1	122	gAt/gGt	2/14	1	2	FACETS	0.492	0.443	0.544	0.492	0.443	0.544	SUBCLONAL	1	TRUE	1	0.84311419691255	2		623	506	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939622	76939623	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	AA	novel	NA	P-0068670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	105	504	0	ENST00000373344.5:c.1125_1126delinsTT	p.Lys375_Gln376delinsAsnTer	p.K375_Q376delinsN*	ENST00000373344	NM_000489.3	375	aaGCag/aaTTag	9/35	0.261792172393678	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.25718478547669	1		504	523	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0068671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	27	133	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.902	0.72	1	0.902	0.72	1	CLONAL	1	TRUE	1	0.22	2		133	272	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0068671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	54	390	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	1	2	FACETS	0.675	0.576	0.785	0.675	0.576	0.785	SUBCLONAL	1	TRUE	1	0.22	2		390	727	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0068671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	37	329	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.907	0.749	1	0.907	0.749	1	CLONAL	1	TRUE	1	0.22	2		329	371	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73649905	73649905	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	66	266	0	ENST00000377687.4:c.1255G>A	p.Glu419Lys	p.E419K	ENST00000377687	NM_001730.3	419	Gag/Aag	4/4	1	2	FACETS	0.808	0.7	0.924	0.808	0.7	0.924	CLONAL	1	TRUE	1	0.22	2		266	743	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541715	120541715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1261521534	NA	P-0068671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	68	289	0	ENST00000229340.5:c.142C>T	p.Arg48Trp	p.R48W	ENST00000229340	NM_006861.6	48	Cgg/Tgg	3/6	1	2	FACETS	0.738	0.64	0.843	0.738	0.64	0.843	SUBCLONAL	1	TRUE	1	0.22	2		289	838	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929432	81929432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775728338	NA	P-0068671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	51	230	0	ENST00000359376.3:c.1093G>A	p.Asp365Asn	p.D365N	ENST00000359376	NM_002661.3	365	Gat/Aat	13/33	1	2	FACETS	0.593	0.503	0.693	0.593	0.503	0.693	SUBCLONAL	1	TRUE	1	0.22	2		230	782	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938278	76938278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	59	221	0	ENST00000373344.5:c.2470G>A	p.Glu824Lys	p.E824K	ENST00000373344	NM_000489.3	824	Gag/Aag	9/35	1	2	FACETS	0.912	0.785	1	0.912	0.785	1	CLONAL	1	TRUE	1	0.22	2		221	588	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853293	151853293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	59	244	0	ENST00000262189.6:c.11809G>A	p.Glu3937Lys	p.E3937K	ENST00000262189	NM_170606.2	3937	Gaa/Aaa	45/59	1	2	FACETS	0.789	0.678	0.91	0.789	0.678	0.91	CLONAL	1	TRUE	1	0.22	2		244	680	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191216	185191216	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	69	247	0	ENST00000265026.3:c.2097C>G	p.Ile699Met	p.I699M	ENST00000265026	NM_004721.4	699	atC/atG	11/14	1	2	FACETS	0.808	0.703	0.923	0.808	0.703	0.923	CLONAL	1	TRUE	1	0.22	2		247	776	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548886	29548886	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs953440640	NA	P-0068671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	25	247	0	ENST00000356175.3:c.1660C>T	p.Gln554Ter	p.Q554*	ENST00000356175	NM_000267.3	554	Cag/Tag	15/57	1	2	FACETS	0.578	0.455	0.72	0.578	0.455	0.72	SUBCLONAL	1	TRUE	1	0.22	2		247	393	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30293171	30293171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1265298635	NA	P-0068671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	26	82	0	ENST00000322652.5:c.461C>T	p.Ser154Leu	p.S154L	ENST00000322652	NM_015355.2	154	tCa/tTa	5/16	1	2	FACETS	0.758	0.601	0.937	0.758	0.601	0.937	CLONAL	1	TRUE	1	0.22	2		82	312	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759433	133759433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	53	295	0	ENST00000318560.5:c.1756G>A	p.Glu586Lys	p.E586K	ENST00000318560	NM_005157.4	586	Gaa/Aaa	11/11	1	2	FACETS	0.642	0.546	0.747	0.642	0.546	0.747	SUBCLONAL	1	TRUE	1	0.22	2		295	751	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357037	70357037	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	62	286	0	ENST00000374080.3:c.5552G>T	p.Gly1851Val	p.G1851V	ENST00000374080		1851	gGt/gTt	39/45	1	2	FACETS	0.605	0.521	0.697	0.605	0.521	0.697	SUBCLONAL	1	TRUE	1	0.22	2		286	932	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244049	41244049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	70	260	0	ENST00000357654.3:c.3499G>A	p.Glu1167Lys	p.E1167K	ENST00000357654	NM_007294.3	1167	Gaa/Aaa	10/23	1	2	FACETS	0.928	0.808	1	0.928	0.808	1	CLONAL	1	TRUE	1	0.22	2		260	686	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191146	2191146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	77	318	0	ENST00000398665.3:c.400G>A	p.Glu134Lys	p.E134K	ENST00000398665	NM_032482.2	134	Gag/Aag	5/28	1	2	FACETS	0.684	0.598	0.776	0.684	0.598	0.776	SUBCLONAL	1	TRUE	1	0.22	2		318	1024	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370856	55370856	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1586329068	NA	P-0068671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	51	281	0	ENST00000297316.4:c.158G>A	p.Gly53Glu	p.G53E	ENST00000297316	NM_022454.3	53	gGa/gAa	1/2	1	2	FACETS	0.654	0.555	0.763	0.654	0.555	0.763	SUBCLONAL	1	TRUE	1	0.22	2		281	709	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964505	70964505	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	63	282	0	ENST00000276594.2:c.1523T>C	p.Ile508Thr	p.I508T	ENST00000276594	NM_024504.3	508	aTc/aCc	8/8	1	2	FACETS	0.684	0.59	0.787	0.684	0.59	0.787	SUBCLONAL	1	TRUE	1	0.22	2		282	837	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587781845	NA	P-0068679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	620	670	0	ENST00000269305.4:c.511G>T	p.Glu171Ter	p.E171*	ENST00000269305	NM_001126112.2	171	Gag/Tag	5/11	0.609591127920868	3	FACETS	0.987	0.961	1	0.987	0.961	1	CLONAL	3	TRUE	0	0.628392149914446	3		670	876	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291638	15291638	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs768565833	NA	P-0068679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	641	656	0	ENST00000263388.2:c.2996C>T	p.Thr999Met	p.T999M	ENST00000263388	NM_000435.2	999	aCg/aTg	19/33	0.593906089047011	4	FACETS	0.926	0.896	0.956	0.926	0.896	0.956	CLONAL	3	TRUE	1	0.628392149914446	4		656	1196	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098969	178098969	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	340	433	0	ENST00000397062.3:c.76C>G	p.Gln26Glu	p.Q26E	ENST00000397062	NM_006164.4	26	Caa/Gaa	2/5	0.628392149914446	3	FACETS	0.893	0.85	0.937	0.893	0.85	0.937	CLONAL	2	TRUE	1	0.628392149914446	3		433	796	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178082	142178082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	123	452	0	ENST00000350721.4:c.7336G>A	p.Asp2446Asn	p.D2446N	ENST00000350721	NM_001184.3	2446	Gat/Aat	43/47	0.628392149914446	4	FACETS	0.721	0.652	0.795	0.24	0.217	0.265	SUBCLONAL	1	TRUE	1	0.628392149914446	4		452	884	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0068680-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	345	304	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.457630255075762	3	FACETS	0.985	0.943	1	0.985	0.943	1	CLONAL	3	TRUE	0	0.461020229341559	3		304	623	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098957	178098957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	43	482	0	ENST00000397062.3:c.88C>T	p.Leu30Phe	p.L30F	ENST00000397062	NM_006164.4	30	Ctt/Ttt	2/5	1	2	FACETS	0.547	0.457	0.647	0.547	0.457	0.647	SUBCLONAL	1	TRUE	1	0.29	2		482	542	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0068681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	34	346	0	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	1	2	FACETS	0.666	0.545	0.802	0.666	0.545	0.802	SUBCLONAL	1	TRUE	1	0.29	2		346	352	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937422	178937422	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	8	113	0	ENST00000263967.3:c.1810T>C	p.Cys604Arg	p.C604R	ENST00000263967	NM_006218.2	604	Tgt/Cgt	12/21	1	2	FACETS	0.606	0.393	0.876	0.606	0.393	0.876	SUBCLONAL	1	TRUE	1	0.29	2		113	91	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781644	9781644	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs765392990	NA	P-0068681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	43	497	0	ENST00000377346.4:c.1954C>T	p.Arg652Cys	p.R652C	ENST00000377346	NM_005026.3	652	Cgc/Tgc	15/24	1	2	FACETS	0.515	0.43	0.609	0.515	0.43	0.609	SUBCLONAL	1	TRUE	1	0.29	2		497	576	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998898	100998898	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	33	688	0	ENST00000325455.5:c.904G>T	p.Asp302Tyr	p.D302Y	ENST00000325455	NM_001202474.3	302	Gat/Tat	1/8	1	2	FACETS	0.387	0.314	0.469	0.387	0.314	0.469	SUBCLONAL	1	TRUE	1	0.29	2		688	588	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092844	27092859	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CAACAATTCTGCAGGT	CAACAATTCTGCAGGT	-	novel	NA	P-0068681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	49	575	0	ENST00000324856.7:c.2865_2878+2del		p.X955_splice	ENST00000324856	NM_006015.4	955		9/20	1	2	FACETS	0.475	0.401	0.557	0.475	0.401	0.557	SUBCLONAL	1	TRUE	1	0.29	2		575	711	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0068684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	187	474	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.526478851990599	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.526478851990599	1		474	501	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0068684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	308	281	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.396872499357495	3	FACETS	0.852	0.813	0.892	0.852	0.813	0.892	CLONAL	3	TRUE	0	0.526478851990599	3		281	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0068684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	15	440	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.526478851990599	1	FACETS	0.06	0.043	0.08	0.06	0.043	0.08	SUBCLONAL	1	TRUE	0	0.526478851990599	1		440	700	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0068684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	353	467	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	0.52523475423011	2	FACETS	0.879	0.838	0.92	0.879	0.838	0.92	CLONAL	2	TRUE	0	0.526478851990599	2		467	763	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909232	41909232	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	127	444	0	ENST00000372991.4:c.156C>G	p.Ile52Met	p.I52M	ENST00000372991	NM_001760.3	52	atC/atG	1/5	0.230680728129181	3	FACETS	0.688	0.623	0.757	0.344	0.311	0.379	INDETERMINATE	1	TRUE	1	0.526478851990599	3		444	886	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108286	8108286	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144169786	NA	P-0068684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	35	439	0	ENST00000585124.1:c.938C>T	p.Ser313Leu	p.S313L	ENST00000585124	NM_004217.3	313	tCg/tTg	9/9	0.526478851990599	1	FACETS	0.172	0.14	0.207	0.172	0.14	0.207	SUBCLONAL	1	TRUE	0	0.526478851990599	1		439	570	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2193712	2193712	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	139	453	0	ENST00000398665.3:c.518T>C	p.Val173Ala	p.V173A	ENST00000398665	NM_032482.2	173	gTt/gCt	6/28	0.526478851990599	1	FACETS	0.817	0.749	0.888	0.817	0.749	0.888	CLONAL	1	TRUE	0	0.526478851990599	1		453	476	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680528	241680528	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	38	289	0	ENST00000366560.3:c.221G>T	p.Arg74Ile	p.R74I	ENST00000366560	NM_000143.3	74	aGa/aTa	2/10	1	2	FACETS	0.259	0.214	0.31	0.259	0.214	0.31	SUBCLONAL	1	TRUE	1	0.526478851990599	2		289	557	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678441	88678441	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	369	449	0	ENST00000360948.2:c.1095C>A	p.Phe365Leu	p.F365L	ENST00000360948	NM_001012338.2	365	ttC/ttA	9/19	0.526478851990599	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.526478851990599	2		449	660	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244417	41244417	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	75	409	1	ENST00000357654.3:c.3131T>A	p.Ile1044Asn	p.I1044N	ENST00000357654	NM_007294.3	1044	aTt/aAt	10/23	1	2	FACETS	0.399	0.349	0.453	0.399	0.349	0.453	SUBCLONAL	1	TRUE	1	0.526478851990599	2		410	714	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	244	960	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.188051430505618	3	FACETS	0.967	0.916	1	1	0.996	1	CLONAL	5	FALSE	1	0.241158610204996	3		963	469	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	65	393	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.911	0.796	1	1	0.979	1	CLONAL	2	FALSE	1	0.241158610204996	2		393	296	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	233	294	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.986	1	1	0.996	1	CLONAL	4	FALSE	1	0.241158610204996	2		298	433	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124258	2124258	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768683470	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	102	709	0	ENST00000219476.3:c.2413G>A	p.Val805Ile	p.V805I	ENST00000219476	NM_000548.3	805	Gtc/Atc	22/42	0.188051430505618	3	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	FALSE	1	0.241158610204996	3		709	447	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	75	771	7	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.978	0.865	1	1	0.983	1	CLONAL	2	FALSE	1	0.241158610204996	2		778	318	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	145	752	10	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	0.241158610204996	4	FACETS	0.884	0.815	0.956	1	0.979	1	CLONAL	4	FALSE	1	0.241158610204996	4		762	422	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260544	10260544	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1201583942	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	82	572	0	ENST00000340748.4:c.2318C>T	p.Pro773Leu	p.P773L	ENST00000340748		773	cCg/cTg	24/40	0.188051430505618	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	FALSE	1	0.241158610204996	3		572	328	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397230	397230	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	93	781	0	ENST00000380956.4:c.615G>A	p.Trp205Ter	p.W205*	ENST00000380956	NM_001195286.1	205	tgG/tgA	5/9	1	2	FACETS	0.872	0.78	0.97	1	0.984	1	CLONAL	2	FALSE	1	0.241158610204996	2		781	442	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504513	103504513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140917545	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	74	483	0	ENST00000355739.4:c.134G>A	p.Arg45His	p.R45H	ENST00000355739	NM_000123.3	45	cGc/cAc	2/15	1	2	FACETS	1	0.922	1	1	0.984	1	CLONAL	2	FALSE	1	0.241158610204996	2		483	291	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114817	108114817	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786204543	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	104	473	1	ENST00000278616.4:c.640del	p.Ser214ProfsTer16	p.S214Pfs*16	ENST00000278616	NM_000051.3	212	Ttt/tt	6/63	1	2	FACETS	1	0.932	1	1	0.988	1	CLONAL	2	FALSE	1	0.241158610204996	2		474	414	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	122	765	0	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	0.188051430505618	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	FALSE	1	0.241158610204996	3		765	490	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341245	341245	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1189783498	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	77	515	0	ENST00000262320.3:c.2239G>A	p.Ala747Thr	p.A747T	ENST00000262320	NM_003502.3	747	Gcg/Acg	9/11	0.188051430505618	3	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	FALSE	1	0.241158610204996	3		515	338	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053023	180053023	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	25	848	3	ENST00000261937.6:c.1267del	p.Gln423ArgfsTer70	p.Q423Rfs*70	ENST00000261937	NM_182925.4	423	Cag/ag	10/30	1	2	FACETS	0.613	0.484	0.763	0.613	0.484	0.763	SUBCLONAL	1	FALSE	1	0.241158610204996	2		851	338	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610439	10610439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202181679	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	116	719	0	ENST00000171111.5:c.271G>A	p.Ala91Thr	p.A91T	ENST00000171111	NM_203500.1	91	Gcc/Acc	2/6	0.188051430505618	3	FACETS	0.879	0.798	0.962	1	0.981	1	CLONAL	3	FALSE	1	0.241158610204996	3		719	409	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874637	35874637	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	77	525	2	ENST00000303115.3:c.799del	p.Arg267GlyfsTer28	p.R267Gfs*28	ENST00000303115	NM_002185.3	265	Aaa/aa	6/8	1	2	FACETS	0.979	0.867	1	1	0.984	1	CLONAL	2	FALSE	1	0.241158610204996	2		527	326	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048788	180048788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375315719	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	103	818	0	ENST00000261937.6:c.1774C>T	p.Arg592Cys	p.R592C	ENST00000261937	NM_182925.4	592	Cgc/Tgc	13/30	1	2	FACETS	1	0.937	1	1	0.988	1	CLONAL	2	FALSE	1	0.241158610204996	2		818	406	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	106	623	2	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	1	0.972	1	1	0.99	1	CLONAL	2	FALSE	1	0.241158610204996	2		625	366	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1255443	1255443	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763381198	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	86	715	0	ENST00000310581.5:c.3116C>T	p.Thr1039Met	p.T1039M	ENST00000310581	NM_198253.2	1039	aCg/aTg	14/16	1	2	FACETS	0.921	0.821	1	1	0.984	1	CLONAL	2	FALSE	1	0.241158610204996	2		715	387	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875722	56875722	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768650810	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	107	657	1	ENST00000308159.5:c.2326C>T	p.Arg776Ter	p.R776*	ENST00000308159	NM_014669.4	776	Cga/Tga	21/22	0.188051430505618	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	FALSE	1	0.241158610204996	3		658	445	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807902	3807902	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	91	631	0	ENST00000262367.5:c.3517C>T	p.Arg1173Ter	p.R1173*	ENST00000262367	NM_004380.2	1173	Cga/Tga	18/31	0.188051430505618	3	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	FALSE	1	0.241158610204996	3		631	396	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259480	16259480	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	100	802	0	ENST00000375759.3:c.6750del	p.Ala2251GlnfsTer102	p.A2251Qfs*102	ENST00000375759	NM_015001.2	2249	Ccc/cc	11/15	1	2	FACETS	0.987	0.888	1	1	0.987	1	CLONAL	2	FALSE	1	0.241158610204996	2		802	420	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945961	17945961	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	72	756	0	ENST00000458235.1:c.1978del	p.Ala660LeufsTer10	p.A660Lfs*10	ENST00000458235	NM_000215.3	660	Gct/ct	15/24	0.188051430505618	3	FACETS	0.899	0.79	1	0.899	0.79	1	CLONAL	2	FALSE	1	0.241158610204996	3		756	372	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460538	8460538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772029273	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	68	568	0	ENST00000356435.5:c.3748G>A	p.Val1250Met	p.V1250M	ENST00000356435		1250	Gtg/Atg	22/35	1	2	FACETS	1	0.952	1	1	0.984	1	CLONAL	2	FALSE	1	0.241158610204996	2		568	243	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403254	213403254	+	frameshift_variant,start_lost,start_retained_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	81	596	0	ENST00000342788.4:c.1del	p.Met1?	p.M1?	ENST00000342788	NM_005235.2	1	Atg/tg	1/28	1	2	FACETS	0.928	0.823	1	1	0.983	1	CLONAL	2	FALSE	1	0.241158610204996	2		596	362	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907420	32907421	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359306	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	102	629	1	ENST00000380152.3:c.1813dup	p.Ile605AsnfsTer11	p.I605Nfs*11	ENST00000380152		602	gga/ggAa	10/27	1	2	FACETS	1	0.957	1	1	0.989	1	CLONAL	2	FALSE	1	0.241158610204996	2		630	380	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825519	50825519	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	68	495	1	ENST00000398568.2:c.2156del	p.Asn719MetfsTer13	p.N719Mfs*13	ENST00000398568	NM_001042412.1	717	gAa/ga	14/18	0.188051430505618	3	FACETS	1	0.913	1	1	0.913	1	CLONAL	2	FALSE	1	0.241158610204996	3		496	301	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864658	68864658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1418006656	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	72	424	0	ENST00000288368.4:c.29G>A	p.Arg10His	p.R10H	ENST00000288368	NM_024870.2	10	cGc/cAc	1/40	1	2	FACETS	1	0.965	1	1	0.985	1	CLONAL	2	FALSE	1	0.241158610204996	2		424	240	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384726	17384726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368554117	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	133	652	0	ENST00000359435.4:c.358G>A	p.Ala120Thr	p.A120T	ENST00000359435	NM_001033549.1	120	Gcc/Acc	4/9	0.188051430505618	3	FACETS	0.853	0.78	0.929	1	0.981	1	CLONAL	3	FALSE	1	0.241158610204996	3		652	483	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601944	43601944	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1172318035	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	90	742	0	ENST00000355710.3:c.988C>T	p.Arg330Trp	p.R330W	ENST00000355710	NM_020975.4	330	Cgg/Tgg	5/20	1	2	FACETS	0.982	0.878	1	1	0.986	1	CLONAL	2	FALSE	1	0.241158610204996	2		742	380	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44520605	44520605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	117	557	0	ENST00000291552.4:c.157C>T	p.Arg53Cys	p.R53C	ENST00000291552	NM_006758.2	53	Cgt/Tgt	3/8	0.188051430505618	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	FALSE	1	0.241158610204996	3		557	435	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245133	53245133	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1569278313	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	66	785	0	ENST00000375401.3:c.807del	p.Thr270GlnfsTer2	p.T270Qfs*2	ENST00000375401	NM_004187.3	269	ccC/cc	7/26	1	2	FACETS	0.81	0.707	0.919	1	0.976	1	CLONAL	2	FALSE	1	0.241158610204996	2		785	338	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753452	42753452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	152	846	0	ENST00000222329.4:c.812C>T	p.Thr271Met	p.T271M	ENST00000222329	NM_006494.2	271	aCg/aTg	4/4	0.188051430505618	3	FACETS	0.897	0.825	0.971	1	0.986	1	CLONAL	3	FALSE	1	0.241158610204996	3		846	525	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412634	63412634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753930754	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	51	667	0	ENST00000330258.3:c.533G>A	p.Arg178His	p.R178H	ENST00000330258	NM_152424.3	178	cGt/cAt	2/2	1	2	FACETS	0.908	0.78	1	1	0.974	1	CLONAL	2	FALSE	1	0.241158610204996	2		667	233	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332760	70332760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749194238	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	33	572	0	ENST00000373644.4:c.665G>A	p.Arg222His	p.R222H	ENST00000373644	NM_030625.2	222	cGc/cAc	2/12	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	FALSE	1	0.241158610204996	2		572	225	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131976422	131976422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	75	687	0	ENST00000265335.6:c.3677G>A	p.Gly1226Asp	p.G1226D	ENST00000265335		1226	gGc/gAc	24/25	1	2	FACETS	0.812	0.716	0.914	1	0.979	1	CLONAL	2	FALSE	1	0.241158610204996	2		687	383	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919865	50919866	+	splice_acceptor_variant	Splice_Site	INS	-	-	G	rs756872503	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	106	695	3	ENST00000440232.2:c.2959dup		p.X987_splice	ENST00000440232	NM_002691.3	987			0.188051430505618	3	FACETS	0.857	0.775	0.943	1	0.977	1	CLONAL	3	FALSE	1	0.241158610204996	3		698	383	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431115	49431115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371869550	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	54	892	0	ENST00000301067.7:c.10024C>T	p.Arg3342Cys	p.R3342C	ENST00000301067	NM_003482.3	3342	Cgc/Tgc	34/54	0.241158610204996	4	FACETS	1	0.896	1	0.354	0.302	0.41	CLONAL	1	FALSE	1	0.241158610204996	4		892	524	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294087	1294087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750129321	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	124	857	0	ENST00000310581.5:c.914C>T	p.Ala305Val	p.A305V	ENST00000310581	NM_198253.2	305	gCg/gTg	2/16	1	2	FACETS	1	0.97	1	1	0.991	1	CLONAL	2	FALSE	1	0.241158610204996	2		857	447	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64290026	64290026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	84	519	1	ENST00000370651.3:c.469C>T	p.Arg157Trp	p.R157W	ENST00000370651	NM_003463.4	157	Cgg/Tgg	6/6	1	2	FACETS	1	0.966	1	1	0.987	1	CLONAL	2	FALSE	1	0.241158610204996	2		520	289	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149309	61149309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	75	638	0	ENST00000295025.8:c.1499C>T	p.Thr500Ile	p.T500I	ENST00000295025	NM_002908.2	500	aCa/aTa	11/11	1	2	FACETS	1	0.922	1	1	0.984	1	CLONAL	2	FALSE	1	0.241158610204996	2		638	295	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527913	157527913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs551038862	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	38	706	0	ENST00000346085.5:c.5638G>A	p.Val1880Ile	p.V1880I	ENST00000346085	NM_020732.3	1880	Gtc/Atc	20/20	1	2	FACETS	0.731	0.605	0.872	0.731	0.605	0.872	SUBCLONAL	1	FALSE	1	0.241158610204996	2		706	431	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61197623	61197623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867394650	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	94	489	0	ENST00000301761.2:c.5C>T	p.Ala2Val	p.A2V	ENST00000301761	NM_017841.2	2	gCg/gTg	1/4	1	2	FACETS	1	0.903	1	1	0.987	1	CLONAL	2	FALSE	1	0.241158610204996	2		489	387	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144359460	144359460	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	79	687	0	ENST00000262995.4:c.902G>T	p.Arg301Met	p.R301M	ENST00000262995	NM_207123.2	301	aGg/aTg	4/11	1	2	FACETS	1	0.926	1	1	0.985	1	CLONAL	2	FALSE	1	0.241158610204996	2		687	310	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117730747	117730747	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	75	476	0	ENST00000368508.3:c.287T>C	p.Leu96Pro	p.L96P	ENST00000368508	NM_002944.2	96	cTg/cCg	4/43	1	2	FACETS	1	0.924	1	1	0.984	1	CLONAL	2	FALSE	1	0.241158610204996	2		476	294	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39542468	39542468	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	48	470	0	ENST00000262039.4:c.272T>C	p.Leu91Pro	p.L91P	ENST00000262039	NM_002647.2	91	cTg/cCg	3/25	0.165755316140049	1	FACETS	0.936	0.803	1	1	0.973	1	CLONAL	2	FALSE	0	0.241158610204996	1		470	187	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438013	49438013	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	121	826	0	ENST00000301067.7:c.5158G>T	p.Val1720Leu	p.V1720L	ENST00000301067	NM_003482.3	1720	Gtg/Ttg	21/54	0.241158610204996	4	FACETS	0.939	0.85	1	0.626	0.567	0.689	CLONAL	2	FALSE	1	0.241158610204996	4		826	663	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193181552	193181552	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1314797741	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	72	545	0	ENST00000367435.3:c.1099G>A	p.Ala367Thr	p.A367T	ENST00000367435	NM_024529.4	367	Gct/Act	13/17	1	2	FACETS	0.827	0.727	0.933	1	0.979	1	CLONAL	2	FALSE	1	0.241158610204996	2		545	361	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292403	15292403	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	21	653	0	ENST00000263388.2:c.2776C>T	p.Pro926Ser	p.P926S	ENST00000263388	NM_000435.2	926	Ccc/Tcc	17/33	0.188051430505618	3	FACETS	0.571	0.439	0.724	0.285	0.219	0.362	SUBCLONAL	1	FALSE	1	0.241158610204996	3		653	342	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644468	21644468	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754016839	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	205	626	0	ENST00000421138.2:c.199G>A	p.Ala67Thr	p.A67T	ENST00000421138		67	Gct/Act	4/16	0.241158610204996	4	FACETS	1	0.975	1	1	0.992	1	CLONAL	4	FALSE	1	0.241158610204996	4		626	489	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480183	20480184	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	60	507	0	ENST00000346618.3:c.505dup	p.Thr169AsnfsTer12	p.T169Nfs*12	ENST00000346618	NM_001949.4	167	cca/ccAa	2/7	1	2	FACETS	0.835	0.725	0.953	1	0.975	1	CLONAL	2	FALSE	1	0.241158610204996	2		507	298	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202123	67202123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569000234	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	98	669	0	ENST00000312629.5:c.1226G>A	p.Arg409His	p.R409H	ENST00000312629	NM_003952.2	409	cGc/cAc	14/15	1	2	FACETS	1	0.917	1	1	0.987	1	CLONAL	2	FALSE	1	0.241158610204996	2		669	397	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251739	212251739	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	79	701	1	ENST00000342788.4:c.3320G>A	p.Cys1107Tyr	p.C1107Y	ENST00000342788	NM_005235.2	1107	tGt/tAt	27/28	1	2	FACETS	1	0.958	1	1	0.986	1	CLONAL	2	FALSE	1	0.241158610204996	2		702	281	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285167	212285167	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	45	531	0	ENST00000342788.4:c.3134G>T	p.Arg1045Met	p.R1045M	ENST00000342788	NM_005235.2	1045	aGg/aTg	25/28	1	2	FACETS	1	0.936	1	1	0.976	1	CLONAL	2	FALSE	1	0.241158610204996	2		531	158	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224555	39224555	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	79	470	0	ENST00000402219.2:c.2803A>G	p.Thr935Ala	p.T935A	ENST00000402219	NM_005633.3	935	Act/Gct	18/23	1	2	FACETS	1	0.967	1	1	0.987	1	CLONAL	2	FALSE	1	0.241158610204996	2		470	266	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120789165	120789166	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	252	592	0	ENST00000257552.2:c.771dup	p.Val258SerfsTer121	p.V258Sfs*121	ENST00000257552	NM_002442.3	257	-/A	11/15	0.241158610204996	4	FACETS	0.962	0.91	1	1	0.994	1	CLONAL	5	FALSE	1	0.241158610204996	4		592	539	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230492718	230492718	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	93	732	0	ENST00000391860.1:c.336del	p.His112GlnfsTer33	p.H112Qfs*33	ENST00000391860	NM_001258311.1	112	caC/ca	2/7	1	2	FACETS	1	0.95	1	1	0.988	1	CLONAL	2	FALSE	1	0.241158610204996	2		732	351	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78425908	78425908	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	78	746	0	ENST00000370768.2:c.1537G>A	p.Ala513Thr	p.A513T	ENST00000370768	NM_003902.3	513	Gca/Aca	16/20	1	2	FACETS	0.949	0.84	1	1	0.983	1	CLONAL	2	FALSE	1	0.241158610204996	2		746	341	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679402	29679402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555536370	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	100	486	0	ENST00000356175.3:c.7522C>T	p.Pro2508Ser	p.P2508S	ENST00000356175	NM_000267.3	2508	Cct/Tct	50/57	0.188051430505618	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	FALSE	1	0.241158610204996	3		486	414	SUCCESS
ALB	213	MSKCC	GRCh37	4	74276126	74276126	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1359715511	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	73	467	0	ENST00000295897.4:c.713G>T	p.Trp238Leu	p.W238L	ENST00000295897	NM_000477.5	238	tGg/tTg	6/15	1	2	FACETS	1	0.96	1	1	0.985	1	CLONAL	2	FALSE	1	0.241158610204996	2		467	254	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740448	58740448	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	74	600	0	ENST00000305921.3:c.1353G>T	p.Glu451Asp	p.E451D	ENST00000305921	NM_003620.3	451	gaG/gaT	6/6	0.188051430505618	3	FACETS	0.843	0.746	0.944	1	0.967	1	CLONAL	3	FALSE	1	0.241158610204996	3		600	272	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398621	116398621	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	70	541	0	ENST00000397752.3:c.2211T>A	p.Ser737Arg	p.S737R	ENST00000397752	NM_000245.2	737	agT/agA	9/21	1	2	FACETS	0.869	0.763	0.982	1	0.979	1	CLONAL	2	FALSE	1	0.241158610204996	2		541	334	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223704	36223704	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	159	897	0	ENST00000222270.7:c.6254C>A	p.Pro2085His	p.P2085H	ENST00000222270	NM_014727.1	2085	cCt/cAt	28/37	0.188051430505618	3	FACETS	0.987	0.912	1	1	0.989	1	CLONAL	3	FALSE	1	0.241158610204996	3		897	499	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143042	58143042	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	93	733	0	ENST00000257904.6:c.742G>A	p.Ala248Thr	p.A248T	ENST00000257904	NM_000075.3	248	Gcc/Acc	7/8	0.241158610204996	4	FACETS	0.815	0.726	0.91	0.544	0.484	0.607	CLONAL	2	FALSE	1	0.241158610204996	4		733	587	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78426109	78426111	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	59	680	0	ENST00000370768.2:c.1414_1416del	p.Pro472del	p.P472del	ENST00000370768	NM_003902.3	472	CCT/-	15/20	1	2	FACETS	0.861	0.747	0.983	1	0.976	1	CLONAL	2	FALSE	1	0.241158610204996	2		680	284	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229686	98229687	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	88	532	0	ENST00000331920.6:c.2271dup	p.Leu758SerfsTer32	p.L758Sfs*32	ENST00000331920	NM_000264.3	757	-/T	15/24	1	2	FACETS	1	0.928	1	1	0.986	1	CLONAL	2	FALSE	1	0.241158610204996	2		532	348	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718810	190718810	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0068685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	49	438	0	ENST00000441310.2:c.966+2T>C		p.X322_splice	ENST00000441310	NM_000534.4	322			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.241158610204996	2		438	311	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139519	47139519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	217	509	0	ENST00000409792.3:c.5068G>A	p.Gly1690Arg	p.G1690R	ENST00000409792	NM_014159.6	1690	Gga/Aga	9/21	0.581182779008165	1	FACETS	0.99	0.929	1	0.99	0.929	1	CLONAL	1	TRUE	0	0.581182779008165	1		509	535	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763238	59763238	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	44	492	0	ENST00000259008.2:c.2864del	p.Asn955IlefsTer30	p.N955Ifs*30	ENST00000259008	NM_032043.2	955	aAt/at	19/20	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.581182779008165	2		492	151	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191606	10191633	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTGACACAGGAGCGCATTGCACATCA	GGCTGACACAGGAGCGCATTGCACATCA	TGTGT	novel	NA	P-0068686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	169	475	1	ENST00000256474.2:c.599_626delinsTGTGT	p.Arg200LeufsTer48	p.R200Lfs*48	ENST00000256474	NM_000551.3	200	cGGCTGACACAGGAGCGCATTGCACATCAa/cTGTGTa	3/3	0.581182779008165	1	FACETS	0.683	0.631	0.737	0.683	0.631	0.737	SUBCLONAL	1	TRUE	0	0.581182779008165	1		476	604	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626361	12626361	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068687-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	202	498	0	ENST00000251849.4:c.1788G>T	p.Arg596Ser	p.R596S	ENST00000251849	NM_002880.3	596	agG/agT	16/17	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.503151053088657	2		498	775	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602493	10602493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068693-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	471	421	0	ENST00000171111.5:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000171111	NM_203500.1	362	cGg/cAg	3/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		421	617	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576881	7576881	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068693-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	340	405	0	ENST00000269305.4:c.965del	p.Pro322HisfsTer23	p.P322Hfs*23	ENST00000269305	NM_001126112.2	322	cCa/ca	9/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		405	439	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481403	140481403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913357	NA	P-0068693-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	27	217	0	ENST00000288602.6:c.1405G>A	p.Gly469Arg	p.G469R	ENST00000288602	NM_004333.4	469	Gga/Aga	11/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		217	320	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517326	157517326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371538726	NA	P-0068693-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	121	193	0	ENST00000346085.5:c.3890C>T	p.Thr1297Met	p.T1297M	ENST00000346085	NM_020732.3	1297	aCg/aTg	16/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		193	499	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332882	70332882	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068693-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	121	334	0	ENST00000373644.4:c.787C>G	p.Gln263Glu	p.Q263E	ENST00000373644	NM_030625.2	263	Caa/Gaa	2/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		334	480	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433336	138433336	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068693-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	59	244	0	ENST00000289153.2:c.1276C>G	p.Gln426Glu	p.Q426E	ENST00000289153	NM_006219.2	426	Cag/Gag	7/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		244	312	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124467288	124467288	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1584747742	NA	P-0068693-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	18	201	0	ENST00000357628.3:c.1666G>C	p.Glu556Gln	p.E556Q	ENST00000357628	NM_015450.2	556	Gaa/Caa	17/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		201	309	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949154	151949201	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTCACACTCTAGGTGAACCCACCTGCAGTGATAAGTATACTTAAATAA	GTCACACTCTAGGTGAACCCACCTGCAGTGATAAGTATACTTAAATAA	-	novel	NA	P-0068693-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	93	204	0	ENST00000262189.6:c.1470-26_1491del		p.X490_splice	ENST00000262189	NM_170606.2	490		11/59	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		204	300	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435814	56435815	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0068693-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	169	460	0	ENST00000407977.2:c.1321_1322dup	p.Asp442LeufsTer61	p.D442Lfs*61	ENST00000407977		441	cct/ccCCt	9/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		460	1052	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953783	131953783	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068693-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	74	210	0	ENST00000265335.6:c.3186G>C	p.Glu1062Asp	p.E1062D	ENST00000265335		1062	gaG/gaC	21/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		210	187	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745986	745986	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068693-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	72	285	0	ENST00000314574.4:c.536G>C	p.Arg179Pro	p.R179P	ENST00000314574	NM_005433.3	179	cGa/cCa	5/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		285	254	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0068694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	109	289	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		289	529	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610330	10610330	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	243	615	0	ENST00000171111.5:c.380G>T	p.Gly127Val	p.G127V	ENST00000171111	NM_203500.1	127	gGt/gTt	2/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		615	463	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0068694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	337	360	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		360	469	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0068701-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	55	393	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.498	0.428	0.574	0.498	0.428	0.574	SUBCLONAL	1	FALSE	1	0.642202273372849	2		393	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576888	7576888	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0068714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	217	493	0	ENST00000269305.4:c.958A>T	p.Lys320Ter	p.K320*	ENST00000269305	NM_001126112.2	320	Aag/Tag	9/11	0.35079727981174	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.36546940369412	2		493	587	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856020	68856020	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	281	367	0	ENST00000261769.5:c.1828C>T	p.Gln610Ter	p.Q610*	ENST00000261769	NM_004360.3	610	Cag/Tag	12/16	0.309681978102739	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.36546940369412	3		367	560	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881426	37881426	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	117	468	0	ENST00000269571.5:c.2618A>G	p.Asp873Gly	p.D873G	ENST00000269571		873	gAc/gGc	21/27	0.36546940369412	3	FACETS	1	0.966	1	0.577	0.521	0.636	CLONAL	1	TRUE	1	0.36546940369412	3		468	656	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649173	23649173	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	524	324	0	ENST00000261584.4:c.209C>T	p.Ser70Leu	p.S70L	ENST00000261584	NM_024675.3	70	tCa/tTa	3/13	0.36546940369412	3	FACETS	0.897	0.866	0.928			1	CLONAL	4	TRUE	NA	0.36546940369412	3		324	945	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432348	49432348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	80	486	0	ENST00000301067.7:c.8791C>T	p.Pro2931Ser	p.P2931S	ENST00000301067	NM_003482.3	2931	Cca/Tca	34/54	0.36546940369412	4	FACETS	0.78	0.686	0.882	0.39	0.343	0.441	SUBCLONAL	1	TRUE	2	0.36546940369412	4		486	766	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058778	42058778	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs867346365	NA	P-0068714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	43	406	0	ENST00000219905.7:c.8498T>G	p.Leu2833Arg	p.L2833R	ENST00000219905	NM_001164273.1	2833	cTt/cGt	24/24	0.36546940369412	3	FACETS	0.451	0.377	0.534	0.226	0.188	0.267	SUBCLONAL	1	TRUE	1	0.36546940369412	3		406	617	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070623	67070623	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	210	401	0	ENST00000412916.2:c.247C>T	p.Arg83Ter	p.R83*	ENST00000412916		83	Cga/Tga	3/6	0.309681978102739	3	FACETS	1	0.987	1	0.815	0.763	0.868	CLONAL	2	TRUE	0	0.36546940369412	3		401	556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0068715-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	252	295	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.317984657195316	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.317984657195316	3		295	552	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278074	18278074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1131691683	NA	P-0068715-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	49	251	0	ENST00000222254.8:c.1694C>G	p.Pro565Arg	p.P565R	ENST00000222254	NM_005027.3	565	cCg/cGg	13/16	0.235731863764978	2	FACETS	0.782	0.664	0.911	0.391	0.332	0.456	CLONAL	1	TRUE	0	0.317984657195316	2		251	394	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	908102	908102	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs1131692330	NA	P-0068715-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	30	241	0	ENST00000166345.3:c.673-1G>C		p.X225_splice	ENST00000166345	NM_004237.3	225			0.317984657195316	6	FACETS	0.514	0.413	0.63	0.129	0.103	0.158	SUBCLONAL	1	TRUE	2	0.317984657195316	6		241	600	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432273	49432273	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs777346353	NA	P-0068715-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	42	358	0	ENST00000301067.7:c.8866A>G	p.Thr2956Ala	p.T2956A	ENST00000301067	NM_003482.3	2956	Acc/Gcc	34/54	1	2	FACETS	0.533	0.444	0.631	0.533	0.444	0.631	SUBCLONAL	1	TRUE	1	0.317984657195316	2		358	496	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416152	416152	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs759860948	NA	P-0068715-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	51	283	0	ENST00000399788.2:c.4034C>G	p.Ser1345Cys	p.S1345C	ENST00000399788	NM_001042603.1	1345	tCt/tGt	24/28	0.317984657195316	5	FACETS	0.762	0.647	0.888	0.254	0.215	0.296	SUBCLONAL	1	TRUE	2	0.317984657195316	5		283	622	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919337	48919337	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0068715-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	49	167	0	ENST00000267163.4:c.500+2T>C		p.X167_splice	ENST00000267163	NM_000321.2	167			0.317984657195316	2	FACETS	1	0.955	1	0.664	0.568	0.767	CLONAL	1	TRUE	0	0.317984657195316	2		167	232	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861885	57861885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374429707	NA	P-0068716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	129	400	0	ENST00000228682.2:c.1186C>T	p.Arg396Trp	p.R396W	ENST00000228682	NM_005269.2	396	Cgg/Tgg	10/12	0.670141132613679	4	FACETS	0.988	0.898	1	0.329	0.299	0.361	CLONAL	1	TRUE	1	0.673330193926629	4		400	649	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132841	152132841	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	137	213	0	ENST00000262189.6:c.31C>T	p.Gln11Ter	p.Q11*	ENST00000262189	NM_170606.2	11	Cag/Tag	1/59	NA	2	FACETS	0.933	0.875	0.99			1	INDETERMINATE	2	TRUE	NA	0.673330193926629	2		213	218	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604528	43604536	+	inframe_deletion	In_Frame_Del	DEL	GCTGGCGGT	GCTGGCGGT	-	novel	NA	P-0068716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	203	350	0	ENST00000355710.3:c.1118_1126del	p.Ala373_Leu375del	p.A373_L375del	ENST00000355710	NM_020975.4	371	caGCTGGCGGTg/cag	6/20	0.661186092683139	4	FACETS	0.907	0.848	0.968	0.907	0.848	0.968	CLONAL	2	TRUE	2	0.673330193926629	4		350	556	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246535	46246535	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	302	360	0	ENST00000334344.6:c.4632del	p.Asn1545ThrfsTer21	p.N1545Tfs*21	ENST00000334344	NM_152641.2	1543	gaC/ga	15/21	0.670141132613679	4	FACETS	0.898	0.857	0.94	0.898	0.857	0.94	CLONAL	3	TRUE	1	0.673330193926629	4		360	557	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432062	49432062	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	132	395	0	ENST00000301067.7:c.9077G>T	p.Gly3026Val	p.G3026V	ENST00000301067	NM_003482.3	3026	gGc/gTc	34/54	0.670141132613679	4	FACETS	1	0.957	1	0.361	0.329	0.395	CLONAL	1	TRUE	1	0.673330193926629	4		395	605	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590737	95590738	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0068716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	102	381	0	ENST00000393063.1:c.1171_1172delinsTT	p.Glu391Leu	p.E391L	ENST00000393063	NM_030621.3	391	GAg/TTg	9/28	0.420733942080216	3	FACETS	0.973	0.877	1	0.487	0.438	0.538	CLONAL	1	TRUE	1	0.673330193926629	3		381	416	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348805	11349649	+	splice_acceptor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	CAGCTCCTGCAGCGGCCGCACGCGGCGCTGGCGCAGCGGGGCCCCCAGCATGCGGCGCGGCGCCGCCACGTAGTGCTCCAGCAGCTCGAAGAGGCAGTCGAAGCTCTCGCGGCTGCCATCCAGGTGAAAGCGGCCGGCCTGAAAGTGCACGCGGATGCTCGTGGGTCCCGAGGCCATCTTCACGCTAAGGGCGAAAAAGCAGTTCCGCTGGCGGCTGTCGCGCACCAGGAAGGTGCCCACGGGCTCGGCGCGCAGCCGCTCGTGCGCCCCGTGCACGCTCAGGGGCCCCCAGTAGAATCCGCAGGCGTCCAGGAGCGCGCTGGCGCGCGTGATGCGCCGGTAATCGGCGTGCGAACGGAATGTGCGGAAGTGCGTGTCGCCGGGGGCCGGGGCCGGGACCGCGGGGCACGGCCGCGGGCGCGCGGGGGCCGCGGGCGAGGAGGAGGAAGAGGAGGAAGGTTCTGGCCGCCGTCGGGGCTCTGCTGCTGTGGAGACTGCATTGTCGGCTGCCACCTGGTTGTGTGCTACCATCCTACAGAAGGGGCCAGCCGGAGGGGTGGGCCATAGCGTCCGGGGGTGCGCTGCGGGAGAGACAAAGAGGTGAGCTGGGGCGCTGCGGGGCCGGGCAGGTGTGCGCCGGCCGGACAACTCCGGAGGGCGGCGCTCCCGGCGGACCCGGCCCTAGGGGGCGAGCACGGAGCACCAAGTCCGCGCGGATCCGTTCAGCCTCAGTGGACACAGCTAGAAAATGGGCTCTGTACTCCGCGGAGCTCTTCCCGGCGGGTGGGGGCTCGGTGGAGGCGGAGTCCGGCCTCCGGGCAGCACCGAGAGGGGGGCGTGGAGAG	CAGCTCCTGCAGCGGCCGCACGCGGCGCTGGCGCAGCGGGGCCCCCAGCATGCGGCGCGGCGCCGCCACGTAGTGCTCCAGCAGCTCGAAGAGGCAGTCGAAGCTCTCGCGGCTGCCATCCAGGTGAAAGCGGCCGGCCTGAAAGTGCACGCGGATGCTCGTGGGTCCCGAGGCCATCTTCACGCTAAGGGCGAAAAAGCAGTTCCGCTGGCGGCTGTCGCGCACCAGGAAGGTGCCCACGGGCTCGGCGCGCAGCCGCTCGTGCGCCCCGTGCACGCTCAGGGGCCCCCAGTAGAATCCGCAGGCGTCCAGGAGCGCGCTGGCGCGCGTGATGCGCCGGTAATCGGCGTGCGAACGGAATGTGCGGAAGTGCGTGTCGCCGGGGGCCGGGGCCGGGACCGCGGGGCACGGCCGCGGGCGCGCGGGGGCCGCGGGCGAGGAGGAGGAAGAGGAGGAAGGTTCTGGCCGCCGTCGGGGCTCTGCTGCTGTGGAGACTGCATTGTCGGCTGCCACCTGGTTGTGTGCTACCATCCTACAGAAGGGGCCAGCCGGAGGGGTGGGCCATAGCGTCCGGGGGTGCGCTGCGGGAGAGACAAAGAGGTGAGCTGGGGCGCTGCGGGGCCGGGCAGGTGTGCGCCGGCCGGACAACTCCGGAGGGCGGCGCTCCCGGCGGACCCGGCCCTAGGGGGCGAGCACGGAGCACCAAGTCCGCGCGGATCCGTTCAGCCTCAGTGGACACAGCTAGAAAATGGGCTCTGTACTCCGCGGAGCTCTTCCCGGCGGGTGGGGGCTCGGTGGAGGCGGAGTCCGGCCTCCGGGCAGCACCGAGAGGGGGGCGTGGAGAG	-	novel	NA	P-0068716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	107	273	0	ENST00000332029.2:c.-50-264_531del		p.X17_splice	ENST00000332029	NM_003745.1	17		2/2	0.673330193926629	3	FACETS	0.811	0.74	0.883	0.811	0.74	0.883	CLONAL	2	TRUE	1	0.673330193926629	3		273	262	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133212	30133212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	102	345	0	ENST00000263025.4:c.286C>T	p.Arg96Cys	p.R96C	ENST00000263025	NM_002746.2	96	Cgc/Tgc	2/9	0.673330193926629	3	FACETS	0.853	0.766	0.943	0.426	0.383	0.472	CLONAL	1	TRUE	1	0.673330193926629	3		345	475	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578511	+	inframe_deletion	In_Frame_Del	DEL	CAGGGCAGG	CAGGGCAGG	-	novel	NA	P-0068716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	380	407	0	ENST00000269305.4:c.419_427del	p.Thr140_Val143delinsMet	p.T140_V143delinsM	ENST00000269305	NM_001126112.2	140	aCCTGCCCTGtg/atg	5/11	0.673330193926629	3	FACETS	0.984	0.953	1	0.984	0.953	1	CLONAL	3	TRUE	0	0.673330193926629	3		407	511	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016566	12016566	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	307	270	0	ENST00000353533.5:c.702del	p.Asn234LysfsTer42	p.N234Kfs*42	ENST00000353533	NM_003010.3	234	aaT/aa	7/11	0.673330193926629	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.673330193926629	3		270	395	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288804	15288804	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	136	207	0	ENST00000263388.2:c.3935G>A	p.Arg1312His	p.R1312H	ENST00000263388	NM_000435.2	1312	cGc/cAc	24/33	0.673330193926629	2	FACETS	0.995	0.936	1	0.995	0.936	1	CLONAL	2	TRUE	0	0.673330193926629	2		207	203	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38173023	38173023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	103	310	0	ENST00000317025.8:c.2026G>A	p.Ala676Thr	p.A676T	ENST00000317025	NM_023034.1	676	Gca/Aca	11/24	0.670141132613679	4	FACETS	0.95	0.853	1	0.317	0.284	0.351	CLONAL	1	TRUE	1	0.673330193926629	4		310	539	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245104	53245104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	233	383	0	ENST00000375401.3:c.836G>A	p.Gly279Glu	p.G279E	ENST00000375401	NM_004187.3	279	gGg/gAg	7/26	0.673330193926629	2	FACETS	0.98	0.935	1	0.98	0.935	1	CLONAL	2	TRUE	0	0.673330193926629	2		383	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934575	NA	P-0068717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	452	180	0	ENST00000269305.4:c.733G>C	p.Gly245Arg	p.G245R	ENST00000269305	NM_001126112.2	245	Ggc/Cgc	7/11	0.76943838358612	7	FACETS	0.981	0.963	0.998			1	CLONAL	7	FALSE	NA	0.76943838358612	7		180	500	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353797	40353797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1490632558	NA	P-0068717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	125	257	0	ENST00000293328.3:c.2323C>T	p.Arg775Trp	p.R775W	ENST00000293328	NM_012448.3	775	Cgg/Tgg	19/19	0.779758254178112	4	FACETS	1	0.975	1	0.598	0.544	0.653	CLONAL	1	FALSE	2	0.76943838358612	4		257	481	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982122	93982122	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	96	254	0	ENST00000369303.4:c.1343G>T	p.Gly448Val	p.G448V	ENST00000369303	NM_004440.3	448	gGa/gTa	6/17	NA	2	FACETS	0.546	0.489	0.606			1	INDETERMINATE	1	FALSE	NA	0.76943838358612	2		254	457	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0068718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	81	300	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.447869591566922	2		300	308	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0068718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	75	352	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.132412047263543	3	FACETS	1	0.967	1	0.64	0.566	0.719	INDETERMINATE	1	TRUE	1	0.447869591566922	3		352	320	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930087	68930087	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	14	232	0	ENST00000288368.4:c.148T>G	p.Leu50Val	p.L50V	ENST00000288368	NM_024870.2	50	Tta/Gta	2/40	1	2	FACETS	0.165	0.118	0.221	0.165	0.118	0.221	SUBCLONAL	1	TRUE	1	0.447869591566922	2		232	380	SUCCESS
APC	324	MSKCC	GRCh37	5	112163677	112163677	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0068718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	78	267	0	ENST00000257430.4:c.1600A>T	p.Lys534Ter	p.K534*	ENST00000257430	NM_000038.5	534	Aaa/Taa	13/16	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.447869591566922	2		267	341	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268138	153268138	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1406877044	NA	P-0068718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	127	299	0	ENST00000281708.4:c.670C>T	p.Arg224Ter	p.R224*	ENST00000281708	NM_033632.3	224	Cga/Tga	4/12	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.447869591566922	2		299	536	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591902	48591902	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519740	NA	P-0068718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	136	350	0	ENST00000342988.3:c.1065C>A	p.Asp355Glu	p.D355E	ENST00000342988	NM_005359.5	355	gaC/gaA	9/12	0.447869591566922	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.447869591566922	1		350	404	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879583	37879583	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	143	324	2	ENST00000269571.5:c.1958C>T	p.Ser653Phe	p.S653F	ENST00000269571		653	tCc/tTc	17/27	0.132412047263543	3	FACETS	1	0.984	1	0.666	0.609	0.724	INDETERMINATE	1	TRUE	1	0.447869591566922	3		326	587	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912276	29912276	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1380293193	NA	P-0068718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	109	387	0	ENST00000376809.5:c.896-1G>T		p.X299_splice	ENST00000376809	NM_002116.7	299			0.132412047263543	3	FACETS	1	0.964	1	0.573	0.516	0.632	INDETERMINATE	1	TRUE	1	0.447869591566922	3		387	520	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332747	153332747	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	112	336	1	ENST00000281708.4:c.209del	p.Asn70MetfsTer18	p.N70Mfs*18	ENST00000281708	NM_033632.3	70	aAt/at	2/12	1	2	FACETS	0.945	0.854	1	0.945	0.854	1	CLONAL	1	TRUE	1	0.447869591566922	2		337	529	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194846	30194846	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	20	266	0	ENST00000331968.5:c.299A>C	p.Lys100Thr	p.K100T	ENST00000331968	NM_002742.2	100	aAg/aCg	2/18	0.447869591566922	1	FACETS	0.217	0.166	0.278	0.217	0.166	0.278	SUBCLONAL	1	TRUE	0	0.447869591566922	1		266	319	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524205	18524205	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	17	269	0	ENST00000266497.5:c.1717A>C	p.Asn573His	p.N573H	ENST00000266497		573	Aat/Cat	11/31	1	2	FACETS	0.225	0.168	0.294	0.225	0.168	0.294	SUBCLONAL	1	TRUE	1	0.447869591566922	2		269	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578175	7578176	+	splice_donor_variant	Splice_Site	INS	-	-	CCTC	novel	NA	P-0068718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	131	352	0	ENST00000269305.4:c.670_672+1dup		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.447869591566922	1	FACETS	0.989	0.904	1	0.989	0.904	1	CLONAL	1	TRUE	0	0.447869591566922	1		352	459	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007838	45007842	+	frameshift_variant	Frame_Shift_Del	DEL	AGATG	AGATG	-	novel	NA	P-0068718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	96	322	0	ENST00000558401.1:c.287_291del	p.Asp96ValfsTer17	p.D96Vfs*17	ENST00000558401	NM_004048.2	95	aaAGATGag/aaag	2/4	0.447869591566922	1	FACETS	0.696	0.623	0.773	0.696	0.623	0.773	SUBCLONAL	1	TRUE	0	0.447869591566922	1		322	478	SUCCESS
APC	324	MSKCC	GRCh37	5	112175759	112175760	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAAT	novel	NA	P-0068718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	127	363	0	ENST00000257430.4:c.4469_4470insAATA	p.His1490GlnfsTer25	p.H1490Qfs*25	ENST00000257430	NM_000038.5	1490	cat/cAAATat	16/16	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.447869591566922	2		363	556	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730020	41730020	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs777791358	NA	P-0068718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	58	326	0	ENST00000242208.4:c.509A>C	p.Lys170Thr	p.K170T	ENST00000242208	NM_002192.2	170	aAa/aCa	3/3	1	2	FACETS	0.499	0.429	0.575	0.499	0.429	0.575	SUBCLONAL	1	TRUE	1	0.447869591566922	2		326	519	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530147	212530147	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	70	354	0	ENST00000342788.4:c.1772A>C	p.Glu591Ala	p.E591A	ENST00000342788	NM_005235.2	591	gAa/gCa	15/28	1	2	FACETS	0.681	0.595	0.773	0.681	0.595	0.773	SUBCLONAL	1	TRUE	1	0.447869591566922	2		354	459	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0068719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	113	440	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.967	0.875	1	0.967	0.875	1	CLONAL	1	TRUE	1	0.48	2		440	487	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061208	38061208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	89	342	0	ENST00000250448.2:c.781C>T	p.Arg261Cys	p.R261C	ENST00000250448	NM_004496.3	261	Cgc/Tgc	2/2	1	2	FACETS	0.849	0.756	0.946	0.849	0.756	0.946	CLONAL	1	TRUE	1	0.48	2		342	437	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061178	38061178	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	110	347	0	ENST00000250448.2:c.811C>T	p.Gln271Ter	p.Q271*	ENST00000250448	NM_004496.3	271	Cag/Tag	2/2	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.48	2		347	429	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285577	38285577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	53	371	2	ENST00000425967.3:c.576G>A	p.Met192Ile	p.M192I	ENST00000425967	NM_001174067.1	192	atG/atA	6/19	1	2	FACETS	0.361	0.307	0.42	0.361	0.307	0.42	SUBCLONAL	1	TRUE	1	0.48	2		373	612	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759620	133759620	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	100	368	0	ENST00000318560.5:c.1943T>C	p.Phe648Ser	p.F648S	ENST00000318560	NM_005157.4	648	tTc/tCc	11/11	1	2	FACETS	0.924	0.83	1	0.924	0.83	1	CLONAL	1	TRUE	1	0.48	2		368	451	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404981	70404981	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs74925160	NA	P-0068721-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	58	456	0	ENST00000373644.4:c.2495G>A	p.Cys832Tyr	p.C832Y	ENST00000373644	NM_030625.2	832	tGc/tAc	4/12	0.437451289600504	3	FACETS	0.885	0.764	1	0.443	0.382	0.508	CLONAL	1	TRUE	1	0.437451289600504	3		456	365	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879283	151879284	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0068721-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	184	454	0	ENST00000262189.6:c.5661dup	p.Asn1888Ter	p.N1888*	ENST00000262189	NM_170606.2	1887	-/T	36/59	0.437451289600504	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	1	0.437451289600504	3		454	500	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066482	94066482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542602078	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	103	400	0	ENST00000369303.4:c.1277G>A	p.Arg426Gln	p.R426Q	ENST00000369303	NM_004440.3	426	cGa/cAa	5/17	0.419492053688624	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.419492053688624	1		400	357	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	256	390	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.301109198195806	3	FACETS	1	0.99	1	0.812	0.767	0.858	CLONAL	2	TRUE	0	0.419492053688624	3		390	606	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	143	335	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.419492053688624	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.419492053688624	1		335	392	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498004	29498004	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1208550472	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	134	390	0	ENST00000389048.3:c.2002G>A	p.Glu668Lys	p.E668K	ENST00000389048	NM_004304.4	668	Gaa/Aaa	11/29	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.419492053688624	2		390	592	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781467	135781467	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203537	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	72	474	0	ENST00000298552.3:c.1498C>T	p.Arg500Ter	p.R500*	ENST00000298552	NM_001162426.1	500	Cga/Tga	15/23	1	2	FACETS	0.786	0.689	0.889	0.786	0.689	0.889	SUBCLONAL	1	TRUE	1	0.419492053688624	2		474	437	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123245021	123245021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	76	440	0	ENST00000358487.5:c.2083G>A	p.Glu695Lys	p.E695K	ENST00000358487	NM_000141.4	695	Gag/Aag	16/18	1	2	FACETS	0.811	0.714	0.914	0.811	0.714	0.914	CLONAL	1	TRUE	1	0.419492053688624	2		440	447	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922258	100922258	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	88	309	0	ENST00000325455.5:c.2254C>T	p.Gln752Ter	p.Q752*	ENST00000325455	NM_001202474.3	752	Cag/Tag	5/8	0.419492053688624	6	FACETS	1	0.97	1	0.258	0.229	0.289	CLONAL	1	TRUE	1	0.419492053688624	6		309	598	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760421	133760421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368347512	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	119	472	0	ENST00000318560.5:c.2744C>T	p.Ser915Leu	p.S915L	ENST00000318560	NM_005157.4	915	tCg/tTg	11/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.419492053688624	2		472	471	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861972	57861972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	87	467	0	ENST00000228682.2:c.1273G>A	p.Glu425Lys	p.E425K	ENST00000228682	NM_005269.2	425	Gag/Aag	10/12	1	2	FACETS	0.9	0.8	1	0.9	0.8	1	CLONAL	1	TRUE	1	0.419492053688624	2		467	461	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456474	189456474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1484040098	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	90	367	0	ENST00000264731.3:c.235G>A	p.Glu79Lys	p.E79K	ENST00000264731	NM_003722.4	79	Gaa/Aaa	3/14	0.378390076294103	1	FACETS	0.627	0.557	0.7	0.627	0.557	0.7	SUBCLONAL	1	TRUE	0	0.419492053688624	1		367	541	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519886	29519886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	85	404	0	ENST00000389048.3:c.1685G>A	p.Gly562Glu	p.G562E	ENST00000389048	NM_004304.4	562	gGa/gAa	9/29	1	2	FACETS	0.889	0.789	0.995	0.889	0.789	0.995	CLONAL	1	TRUE	1	0.419492053688624	2		404	456	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528636	89528636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	93	342	0	ENST00000336596.2:c.2936G>A	p.Gly979Asp	p.G979D	ENST00000336596	NM_005233.5	979	gGc/gAc	17/17	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.419492053688624	2		342	442	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523654	176523654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	77	554	0	ENST00000292408.4:c.2065C>T	p.Pro689Ser	p.P689S	ENST00000292408	NM_213647.1	689	Ccg/Tcg	16/18	1	2	FACETS	0.681	0.599	0.769	0.681	0.599	0.769	SUBCLONAL	1	TRUE	1	0.419492053688624	2		554	539	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945120	38945120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	75	299	0	ENST00000357387.3:c.4684C>T	p.Pro1562Ser	p.P1562S	ENST00000357387	NM_152756.3	1562	Cct/Tct	35/38	1	2	FACETS	0.956	0.843	1	0.956	0.843	1	CLONAL	1	TRUE	1	0.419492053688624	2		299	374	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282656	1282656	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749051614	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	69	478	0	ENST00000310581.5:c.1657G>A	p.Val553Ile	p.V553I	ENST00000310581	NM_198253.2	553	Gtc/Atc	3/16	1	2	FACETS	0.638	0.556	0.725	0.638	0.556	0.725	SUBCLONAL	1	TRUE	1	0.419492053688624	2		478	516	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070324	37070324	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63749795	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	120	417	0	ENST00000231790.2:c.1459C>T	p.Arg487Ter	p.R487*	ENST00000231790	NM_000249.3	487	Cga/Tga	13/19	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.419492053688624	2		417	534	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912075	56912075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	72	320	0	ENST00000519728.1:c.1303G>A	p.Glu435Lys	p.E435K	ENST00000519728	NM_002350.3	435	Gaa/Aaa	12/13	1	2	FACETS	0.808	0.709	0.914	0.808	0.709	0.914	CLONAL	1	TRUE	1	0.419492053688624	2		320	425	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046410	69046410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868582467	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	90	448	0	ENST00000288368.4:c.3883G>A	p.Glu1295Lys	p.E1295K	ENST00000288368	NM_024870.2	1295	Gaa/Aaa	32/40	1	2	FACETS	0.819	0.729	0.915	0.819	0.729	0.915	CLONAL	1	TRUE	1	0.419492053688624	2		448	524	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615568	100615568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	93	203	0	ENST00000308731.7:c.764G>A	p.Arg255Gln	p.R255Q	ENST00000308731	NM_000061.2	255	cGa/cAa	8/19	1	1	FACETS	0.793	0.719	0.867	1	0.985	1	SUBCLONAL	2	TRUE	0	0.419492053688624	1		203	221	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259934	16259934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs988832507	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	141	451	0	ENST00000375759.3:c.7199C>T	p.Ser2400Phe	p.S2400F	ENST00000375759	NM_015001.2	2400	tCt/tTt	11/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.419492053688624	2		451	620	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432034	121432034	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	128	460	0	ENST00000257555.6:c.781G>A	p.Glu261Lys	p.E261K	ENST00000257555		261	Gag/Aag	4/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.419492053688624	2		460	546	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41521995	41521995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764980716	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	66	287	0	ENST00000263253.7:c.857C>T	p.Pro286Leu	p.P286L	ENST00000263253	NM_001429.3	286	cCa/cTa	3/31	0.255560580898927	3	FACETS	0.898	0.782	1	0.449	0.391	0.511	CLONAL	1	TRUE	1	0.419492053688624	3		287	424	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755552	39755552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	99	453	0	ENST00000288319.7:c.1213G>A	p.Glu405Lys	p.E405K	ENST00000288319	NM_182918.3	405	Gag/Aag	10/10	1	2	FACETS	0.959	0.86	1	0.959	0.86	1	CLONAL	1	TRUE	1	0.419492053688624	2		453	492	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611935	100611935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	69	164	0	ENST00000308731.7:c.1186G>A	p.Glu396Lys	p.E396K	ENST00000308731	NM_000061.2	396	Gaa/Aaa	14/19	1	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.419492053688624	1		164	210	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49929262	49929262	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	79	380	0	ENST00000296474.3:c.3281G>A	p.Gly1094Glu	p.G1094E	ENST00000296474	NM_002447.2	1094	gGa/gAa	15/20	1	2	FACETS	0.833	0.736	0.937	0.833	0.736	0.937	CLONAL	1	TRUE	1	0.419492053688624	2		380	452	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226569	2226569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777538090	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	159	558	0	ENST00000398665.3:c.4049C>T	p.Pro1350Leu	p.P1350L	ENST00000398665	NM_032482.2	1350	cCg/cTg	27/28	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.419492053688624	2		558	563	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606980	47606980	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755757555	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	132	360	0	ENST00000263735.4:c.730C>T	p.Pro244Ser	p.P244S	ENST00000263735	NM_002354.2	244	Cct/Tct	7/9	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.419492053688624	2		360	569	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434469	49434469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1449737126	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	86	478	0	ENST00000301067.7:c.7084C>T	p.Pro2362Ser	p.P2362S	ENST00000301067	NM_003482.3	2362	Cct/Tct	31/54	1	2	FACETS	0.822	0.729	0.92	0.822	0.729	0.92	CLONAL	1	TRUE	1	0.419492053688624	2		478	499	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562641	29562641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854562	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	101	333	0	ENST00000356175.3:c.3721C>T	p.Arg1241Ter	p.R1241*	ENST00000356175	NM_000267.3	1241	Cga/Tga	28/57	0.301109198195806	3	FACETS	1	0.981	1	0.477	0.429	0.527	CLONAL	1	TRUE	0	0.419492053688624	3		333	407	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050247	128050247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	143	437	0	ENST00000285398.2:c.410C>T	p.Thr137Ile	p.T137I	ENST00000285398	NM_000122.1	137	aCc/aTc	3/15	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.419492053688624	2		437	582	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680247	30680248	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	170	407	0	ENST00000376406.3:c.1471_1472delinsTT	p.Pro491Phe	p.P491F	ENST00000376406	NM_014641.2	491	CCt/TTt	5/15	0.152745554007425	2	FACETS	1	0.989	1	0.702	0.649	0.757	INDETERMINATE	1	TRUE	0	0.419492053688624	2		407	577	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420059	41420059	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760479842	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	77	400	0	ENST00000373198.4:c.262G>A	p.Ala88Thr	p.A88T	ENST00000373198	NM_133170.3	88	Gcc/Acc	3/32	0.419492053688624	1	FACETS	0.699	0.617	0.787	0.699	0.617	0.787	SUBCLONAL	1	TRUE	0	0.419492053688624	1		400	415	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231725	66231725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	156	335	0	ENST00000273854.3:c.1975C>T	p.Pro659Ser	p.P659S	ENST00000273854	NM_004439.5	659	Ccc/Tcc	11/18	0.0951747671821458	6	FACETS	1	0.964	1			1	INDETERMINATE	3	TRUE	NA	0.419492053688624	6		335	426	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257228	133257228	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	85	357	0	ENST00000320574.5:c.250T>G	p.Tyr84Asp	p.Y84D	ENST00000320574	NM_006231.2	84	Tac/Gac	3/49	1	2	FACETS	0.809	0.717	0.906	0.809	0.717	0.906	CLONAL	1	TRUE	1	0.419492053688624	2		357	501	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615703	1615703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	120	534	1	ENST00000344749.5:c.1568C>T	p.Ala523Val	p.A523V	ENST00000344749	NM_001136139.2	523	gCc/gTc	17/19	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.419492053688624	2		535	450	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266479	55266479	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1421825015	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	94	392	0	ENST00000275493.2:c.2771C>T	p.Ser924Phe	p.S924F	ENST00000275493	NM_005228.3	924	tCc/tTc	23/28	0.255560580898927	3	FACETS	1	0.939	1	0.538	0.48	0.599	CLONAL	1	TRUE	1	0.419492053688624	3		392	504	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355334	81355334	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	112	331	0	ENST00000222390.5:c.1041-1G>A		p.X347_splice	ENST00000222390	NM_000601.4	347			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.419492053688624	2		331	389	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350150	89350150	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752116186	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	137	480	0	ENST00000301030.4:c.2800C>T	p.Leu934Phe	p.L934F	ENST00000301030	NM_001256183.1	934	Ctt/Ttt	9/13	0.419492053688624	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.419492053688624	1		480	492	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205163	38205163	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	98	299	0	ENST00000317025.8:c.527T>A	p.Leu176His	p.L176H	ENST00000317025	NM_023034.1	176	cTt/cAt	2/24	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.419492053688624	2		299	396	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222811	5222811	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1379393228	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	94	430	0	ENST00000357368.4:c.2992C>T	p.Gln998Ter	p.Q998*	ENST00000357368	NM_002850.3	998	Cag/Tag	18/38	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.419492053688624	2		430	444	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56409114	56409114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	50	264	0	ENST00000348428.3:c.1621C>T	p.Leu541Phe	p.L541F	ENST00000348428	NM_006785.3	541	Ctt/Ttt	14/17	1	2	FACETS	0.828	0.707	0.958	0.828	0.707	0.958	CLONAL	1	TRUE	1	0.419492053688624	2		264	288	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486536	56486536	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	115	360	0	ENST00000267101.3:c.1115C>T	p.Pro372Leu	p.P372L	ENST00000267101	NM_001982.3	372	cCc/cTc	10/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.419492053688624	2		360	468	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398882	398883	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	68	407	0	ENST00000380956.4:c.692_693delinsTT	p.Pro231Leu	p.P231L	ENST00000380956	NM_001195286.1	231	cCC/cTT	6/9	0.152745554007425	2	FACETS	0.677	0.59	0.77	0.338	0.295	0.385	INDETERMINATE	1	TRUE	0	0.419492053688624	2		407	479	SUCCESS
ATM	472	MSKCC	GRCh37	11	108128280	108128280	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	169	287	0	ENST00000278616.4:c.2323T>G	p.Ser775Ala	p.S775A	ENST00000278616	NM_000051.3	775	Tcc/Gcc	15/63	0.419492053688624	6	FACETS	1	0.954	1	0.419	0.386	0.453	CLONAL	2	TRUE	1	0.419492053688624	6		287	707	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350515	15350515	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1186050912	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	91	338	0	ENST00000263377.2:c.3400C>T	p.Pro1134Ser	p.P1134S	ENST00000263377	NM_058243.2	1134	Ccc/Tcc	16/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.419492053688624	2		338	329	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383637	42383637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758922246	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	98	371	0	ENST00000221972.3:c.412G>A	p.Glu138Lys	p.E138K	ENST00000221972	NM_021601.3	138	Gag/Aag	3/5	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.419492053688624	2		371	448	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667613	29667613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	142	329	0	ENST00000356175.3:c.6949C>T	p.Leu2317Phe	p.L2317F	ENST00000356175	NM_000267.3	2317	Ctt/Ttt	46/57	0.301109198195806	3	FACETS	0.91	0.836	0.986	0.607	0.557	0.657	CLONAL	2	TRUE	0	0.419492053688624	3		329	450	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343644	343644	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	127	453	0	ENST00000262320.3:c.2030C>G	p.Pro677Arg	p.P677R	ENST00000262320	NM_003502.3	677	cCt/cGt	8/11	0.419492053688624	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.419492053688624	1		453	367	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466482	120466482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	121	494	0	ENST00000256646.2:c.4637C>T	p.Thr1546Ile	p.T1546I	ENST00000256646	NM_024408.3	1546	aCc/aTc	26/34	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.419492053688624	2		494	543	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325132	123325132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148514974	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	90	417	0	ENST00000358487.5:c.196G>A	p.Asp66Asn	p.D66N	ENST00000358487	NM_000141.4	66	Gat/Aat	3/18	1	2	FACETS	0.937	0.835	1	0.937	0.835	1	CLONAL	1	TRUE	1	0.419492053688624	2		417	458	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741842	40741842	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758765375	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	149	458	0	ENST00000392038.2:c.1130C>T	p.Ala377Val	p.A377V	ENST00000392038	NM_001626.4	377	gCc/gTc	11/14	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.419492053688624	2		458	589	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798445	32798445	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	72	469	0	ENST00000374899.4:c.1411C>G	p.Gln471Glu	p.Q471E	ENST00000374899	NM_018833.2	471	Caa/Gaa	8/12	0.152745554007425	2	FACETS	0.643	0.562	0.729	0.321	0.281	0.365	INDETERMINATE	1	TRUE	0	0.419492053688624	2		469	534	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560175	29560175	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	118	354	0	ENST00000356175.3:c.3652C>T	p.Gln1218Ter	p.Q1218*	ENST00000356175	NM_000267.3	1218	Caa/Taa	27/57	0.301109198195806	3	FACETS	1	0.984	1	0.48	0.435	0.526	CLONAL	1	TRUE	0	0.419492053688624	3		354	473	SUCCESS
APC	324	MSKCC	GRCh37	5	112170832	112170832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060503291	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	112	317	0	ENST00000257430.4:c.1928C>T	p.Ser643Phe	p.S643F	ENST00000257430	NM_000038.5	643	tCc/tTc	15/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.419492053688624	2		317	426	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562822	21562822	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318715498	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	102	502	0	ENST00000382592.4:c.1097C>T	p.Ser366Phe	p.S366F	ENST00000382592	NM_014572.2	366	tCc/tTc	4/8	0.419492053688624	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.419492053688624	1		502	369	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917650	94917650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	129	371	0	ENST00000536441.1:c.871G>A	p.Glu291Lys	p.E291K	ENST00000536441	NM_144665.3	291	Gaa/Aaa	6/10	0.419492053688624	6	FACETS	1	0.978	1	0.254	0.229	0.279	CLONAL	1	TRUE	1	0.419492053688624	6		371	892	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982001	70982001	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	111	427	0	ENST00000276594.2:c.95C>G	p.Pro32Arg	p.P32R	ENST00000276594	NM_024504.3	32	cCt/cGt	2/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.419492053688624	2		427	426	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988313	36988313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	77	355	0	ENST00000354822.5:c.340G>A	p.Gly114Arg	p.G114R	ENST00000354822	NM_001079668.2	114	Ggg/Agg	2/3	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.419492053688624	2		355	338	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590875	95590875	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	92	371	0	ENST00000393063.1:c.1034T>C	p.Leu345Ser	p.L345S	ENST00000393063	NM_030621.3	345	tTa/tCa	9/28	1	2	FACETS	0.92	0.821	1	0.92	0.821	1	CLONAL	1	TRUE	1	0.419492053688624	2		371	477	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855287	76855291	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	ONP	ACCCT	ACCCT	GCCCA	novel	NA	P-0068744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	49	117	0	ENST00000373344.5:c.5698-2_5700delinsTGGGC		p.X1900_splice	ENST00000373344	NM_000489.3	1900		24/35	1	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.419492053688624	1		117	135	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0068745-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	200	393	1	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.411646655035806	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.411595670678902	2		394	458	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795353	39795353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs187337793	NA	P-0068745-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	68	415	0	ENST00000288319.7:c.367C>T	p.Arg123Cys	p.R123C	ENST00000288319	NM_182918.3	123	Cgc/Tgc	3/10	0.222150834135549	3	FACETS	1	0.916	1	0.354	0.309	0.402	INDETERMINATE	1	TRUE	0	0.411595670678902	3		415	375	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494908	56494908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs551223118	NA	P-0068745-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	37	389	0	ENST00000267101.3:c.3265C>T	p.Arg1089Trp	p.R1089W	ENST00000267101	NM_001982.3	1089	Cgg/Tgg	27/28	1	2	FACETS	0.393	0.324	0.471	0.393	0.324	0.471	SUBCLONAL	1	TRUE	1	0.411595670678902	2		389	457	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561756	55561756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376469897	NA	P-0068745-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	33	344	0	ENST00000288135.5:c.146G>A	p.Arg49His	p.R49H	ENST00000288135	NM_000222.2	49	cGc/cAc	2/21	0.38858256458013	2	FACETS	0.473	0.386	0.571	0.237	0.193	0.286	SUBCLONAL	1	TRUE	0	0.411595670678902	2		344	339	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603038	48603039	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCAGCAGCAGGCGGCTACTGCACAAGC	rs876660720	NA	P-0068745-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	25	295	0	ENST00000342988.3:c.1349_1376dup	p.Ala460GlyfsTer43	p.A460Gfs*43	ENST00000342988	NM_005359.5	447	atg/aTGCAGCAGCAGGCGGCTACTGCACAAGCtg	11/12	0.26009805018922	1	FACETS	0.307	0.242	0.382	0.307	0.242	0.382	SUBCLONAL	1	TRUE	0	0.411595670678902	1		295	314	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21967974	21968257	+	splice_acceptor_variant,coding_sequence_variant,3_prime_UTR_variant,intron_variant	Splice_Site	DEL	GAAAAGGCAGAAGCGGTGTTTTTCTTTTTTACATTTTTATAAGAATATATAAAAAATGATATAAATGGACATTTACGGTAGTGGGGGAAGGCATATATCTACGTTAAAAGGCAGGACATTTTTAAAAGCTCTATTTTCTAAATGAAAACTACGAAAGCGGGGTGGGTTGTGGCGGGGGCAGTTGTGGCCCTGTAGGACCTTCGGTGACTGATGATCTAAGTTTCCCGAGGTTTCTCAGAGCCTCTCTGGTTCTTTCAATCGGGGATGTCTGCAGAGGGCAGAAA	GAAAAGGCAGAAGCGGTGTTTTTCTTTTTTACATTTTTATAAGAATATATAAAAAATGATATAAATGGACATTTACGGTAGTGGGGGAAGGCATATATCTACGTTAAAAGGCAGGACATTTTTAAAAGCTCTATTTTCTAAATGAAAACTACGAAAGCGGGGTGGGTTGTGGCGGGGGCAGTTGTGGCCCTGTAGGACCTTCGGTGACTGATGATCTAAGTTTCCCGAGGTTTCTCAGAGCCTCTCTGGTTCTTTCAATCGGGGATGTCTGCAGAGGGCAGAAA	-	novel	NA	P-0068745-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	100	21	0	ENST00000304494.5:c.458-16_*254del		p.X153_splice	ENST00000304494	NM_000077.4	153		3/3	0.399744412453287	2	FACETS	1	0.985	1	1	0.992	1	CLONAL	4	TRUE	0	0.411595670678902	2		21	112	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626896	14626896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068745-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	35	458	0	ENST00000254322.2:c.879G>A	p.Met293Ile	p.M293I	ENST00000254322	NM_006145.1	293	atG/atA	3/3	NA	2	FACETS	0.419	0.343	0.504			1	INDETERMINATE	1	TRUE	NA	0.411595670678902	2		458	406	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965322	25965322	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068745-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	58	442	0	ENST00000435504.4:c.3884C>T	p.Pro1295Leu	p.P1295L	ENST00000435504		1295	cCt/cTt	13/13	0.200723492898961	5	FACETS	0.769	0.66	0.887	0.256	0.22	0.296	INDETERMINATE	1	TRUE	2	0.411595670678902	5		442	593	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112745410	112745410	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068745-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	60	281	0	ENST00000369452.4:c.728T>G	p.Leu243Arg	p.L243R	ENST00000369452	NM_007373.3	243	cTg/cGg	3/9	0.38956669688403	3	FACETS	1	0.9	1	0.523	0.453	0.598	CLONAL	1	TRUE	1	0.411595670678902	3		281	336	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0068746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	158	530	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.932	0.862	1	0.932	0.862	1	CLONAL	1	TRUE	1	0.718040428415315	2		530	472	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0068746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	481	463	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	0.706591087457872	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.718040428415315	3		463	600	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239508	123239508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374993905	NA	P-0068746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	190	506	0	ENST00000358487.5:c.2329G>A	p.Glu777Lys	p.E777K	ENST00000358487	NM_000141.4	777	Gaa/Aaa	18/18	0.706591087457872	3	FACETS	1	0.979	1	0.378	0.351	0.406	CLONAL	1	TRUE	0	0.718040428415315	3		506	634	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720666	89720666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	115	160	0	ENST00000371953.3:c.820del	p.Trp274GlyfsTer2	p.W274Gfs*2	ENST00000371953	NM_000314.4	273	Ttt/tt	8/9	0.706591087457872	3	FACETS	0.834	0.779	0.887	0.834	0.779	0.887	CLONAL	3	TRUE	0	0.718040428415315	3		160	174	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109852	115109852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1013102657	NA	P-0068746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	127	473	1	ENST00000257566.3:c.2026G>A	p.Ala676Thr	p.A676T	ENST00000257566	NM_016569.3	676	Gcc/Acc	8/8	1	2	FACETS	0.946	0.866	1	0.946	0.866	1	CLONAL	1	TRUE	1	0.718040428415315	2		474	374	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023922	27023940	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCTGCGGCGGCGGCCGC	CAGCTGCGGCGGCGGCCGC	-	novel	NA	P-0068746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	95	477	0	ENST00000324856.7:c.1029_1047del	p.Ala344ArgfsTer13	p.A344Rfs*13	ENST00000324856	NM_006015.4	343	gCAGCTGCGGCGGCGGCCGCc/gc	1/20	1	2	FACETS	0.865	0.779	0.953	0.865	0.779	0.953	CLONAL	1	TRUE	1	0.718040428415315	2		477	306	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056223	27056223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1002145958	NA	P-0068746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	193	547	0	ENST00000324856.7:c.1219C>T	p.Pro407Ser	p.P407S	ENST00000324856	NM_006015.4	407	Cct/Tct	2/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.718040428415315	2		547	488	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591099	67591110	+	inframe_deletion	In_Frame_Del	DEL	CAGCATTAAACC	CAGCATTAAACC	-	novel	NA	P-0068746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	106	402	0	ENST00000274335.5:c.1692_1703del	p.Asn564_Pro568delinsLys	p.N564_P568delinsK	ENST00000274335		564	aaCAGCATTAAACCa/aaa	12/15	1	2	FACETS	0.987	0.898	1	0.987	0.898	1	CLONAL	1	TRUE	1	0.718040428415315	2		402	299	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431357	49431357	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	162	521	0	ENST00000301067.7:c.9782del	p.Gln3261ArgfsTer69	p.Q3261Rfs*69	ENST00000301067	NM_003482.3	3261	cAg/cg	34/54	1	2	FACETS	0.975	0.902	1	0.975	0.902	1	CLONAL	1	TRUE	1	0.718040428415315	2		521	463	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107100	27107100	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	172	580	0	ENST00000324856.7:c.6711del	p.Leu2238CysfsTer29	p.L2238Cfs*29	ENST00000324856	NM_006015.4	2237	gcG/gc	20/20	1	2	FACETS	0.899	0.833	0.967	0.899	0.833	0.967	CLONAL	1	TRUE	1	0.718040428415315	2		580	533	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50773691	50773691	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068747-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3756	547	304	0	ENST00000307179.4:c.1232A>C	p.Lys411Thr	p.K411T	ENST00000307179		411	aAa/aCa	11/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		304	4303	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50773844	50773844	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068747-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4792	816	434	0	ENST00000307179.4:c.1385A>G	p.Lys462Arg	p.K462R	ENST00000307179		462	aAg/aGg	11/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		434	5608	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068748-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	38	382	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.711	0.598	0.832	0.711	0.598	0.832	SUBCLONAL	1	TRUE	1	0.732462609971817	2		382	146	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0068748-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	35	393	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.364935694666339	5	FACETS	0.364	0.298	0.439	0.121	0.099	0.147	INDETERMINATE	1	TRUE	2	0.732462609971817	5		393	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0068748-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	83	292	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.621	0.552	0.694	0.621	0.552	0.694	SUBCLONAL	1	TRUE	1	0.732462609971817	2		292	365	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220274	55220274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068748-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	3342	310	0	ENST00000275493.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000275493	NM_005228.3	222	Cgc/Tgc	6/28	0.732462609971817	29	FACETS	1	0.996	1	1	0.996	1	CLONAL	27	TRUE	2	0.732462609971817	29		310	3662	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692977	89692977	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068748-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	123	311	0	ENST00000371953.3:c.461T>G	p.Phe154Cys	p.F154C	ENST00000371953	NM_000314.4	154	tTc/tGc	5/9	0.732462609971817	1	FACETS	0.954	0.886	1	0.954	0.886	1	CLONAL	1	TRUE	0	0.732462609971817	1		311	223	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0068749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	128	317	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.461620922157909	3	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	1	0.510472615706462	3		317	306	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998898	11998898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	94	326	0	ENST00000353533.5:c.400C>T	p.Arg134Trp	p.R134W	ENST00000353533	NM_003010.3	134	Cgg/Tgg	4/11	0.510472615706462	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.510472615706462	1		326	260	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115711	8115711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	74	372	0	ENST00000346208.3:c.1057C>T	p.Pro353Ser	p.P353S	ENST00000346208		353	Ccc/Tcc	6/6	1	2	FACETS	0.61	0.536	0.69	0.61	0.536	0.69	SUBCLONAL	1	TRUE	1	0.510472615706462	2		372	475	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355239	81355239	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	94	310	0	ENST00000222390.5:c.1135C>T	p.Gln379Ter	p.Q379*	ENST00000222390	NM_000601.4	379	Caa/Taa	9/18	1	2	FACETS	0.817	0.73	0.908	0.817	0.73	0.908	CLONAL	1	TRUE	1	0.510472615706462	2		310	451	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945589	151945602	+	frameshift_variant	Frame_Shift_Del	DEL	CAATTTGATCTTCG	CAATTTGATCTTCG	A	novel	NA	P-0068749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	53	109	0	ENST00000262189.6:c.1917_1930delinsT	p.Glu640LysfsTer6	p.E640Kfs*6	ENST00000262189	NM_170606.2	639	ggCGAAGATCAAATTGaa/ggTaa	14/59	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.510472615706462	2		109	162	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341229	70341229	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068750-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	57	228	0	ENST00000374080.3:c.788A>T	p.Glu263Val	p.E263V	ENST00000374080		263	gAg/gTg	6/45	0.212962383046214	2	FACETS	0.896	0.773	1			1	INDETERMINATE	1	TRUE	NA	0.38	2		228	335	SUCCESS
AR	367	MSKCC	GRCh37	X	66943544	66943552	+	missense_variant	Missense_Mutation	ONP	ATCAGTTCA	ATCAGTTCA	TAATCAAGT	novel	NA	P-0068750-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	20	199	0	ENST00000374690.3:c.2624_2632delinsTAATCAAGT	p.His875_Thr878delinsLeuIleLysSer	p.H875_T878delinsLIKS	ENST00000374690	NM_000044.3	875	cATCAGTTCAct/cTAATCAAGTct	8/8	0.212962383046214	2	FACETS	0.405	0.31	0.516			1	INDETERMINATE	1	TRUE	NA	0.38	2		199	260	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	43	353	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.18549952905961	2		353	420	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	65	434	4	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.876	0.763	0.998	1	0.978	1	CLONAL	2	TRUE	1	0.18549952905961	2		438	400	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945696	17945696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3213409	NA	P-0068752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	53	379	0	ENST00000458235.1:c.2164G>A	p.Val722Ile	p.V722I	ENST00000458235	NM_000215.3	722	Gtc/Atc	16/24	0.150356437767043	3	FACETS	0.779	0.666	0.901	0.779	0.666	0.901	CLONAL	2	TRUE	1	0.18549952905961	3		379	401	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624242	89624243	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs121913290	NA	P-0068752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	14	122	0	ENST00000371953.3:c.17_18del	p.Lys6ArgfsTer4	p.K6Rfs*4	ENST00000371953	NM_000314.4	6	AAa/a	1/9	1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	TRUE	1	0.18549952905961	2		122	120	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913253	39913253	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	54	196	2	ENST00000378444.4:c.4862del	p.Pro1621GlnfsTer53	p.P1621Qfs*53	ENST00000378444	NM_001123385.1	1621	cCa/ca	14/15	1	1	FACETS	0.933	0.803	1	1	0.975	1	CLONAL	2	TRUE	0	0.18549952905961	1		198	283	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074255	8074255	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	36	426	0	ENST00000377482.5:c.404del	p.Asn135ThrfsTer40	p.N135Tfs*40	ENST00000377482	NM_018948.3	135	aAc/ac	4/4	1	2	FACETS	0.944	0.777	1	0.944	0.777	1	CLONAL	1	TRUE	1	0.18549952905961	2		426	411	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217557	142217557	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1268253442	NA	P-0068752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	27	304	0	ENST00000350721.4:c.5440del	p.Arg1814GlufsTer10	p.R1814Efs*10	ENST00000350721	NM_001184.3	1814	Aga/ga	32/47	0.160823435116991	3	FACETS	0.743	0.591	0.918	0.248	0.197	0.306	CLONAL	1	TRUE	0	0.18549952905961	3		304	428	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119910	70119910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1297203260	NA	P-0068752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	29	415	1	ENST00000245479.2:c.916del	p.Val306CysfsTer77	p.V306Cfs*77	ENST00000245479	NM_000346.3	304	ccG/cc	3/3	1	2	FACETS	0.901	0.724	1	0.901	0.724	1	CLONAL	1	TRUE	1	0.18549952905961	2		416	347	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981721	101981721	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555075353	NA	P-0068752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	25	344	0	ENST00000282441.5:c.147del	p.Ala50ProfsTer24	p.A50Pfs*24	ENST00000282441	NM_001130145.2	48	Ccc/cc	1/9	1	2	FACETS	0.908	0.716	1	0.908	0.716	1	CLONAL	1	TRUE	1	0.18549952905961	2		344	297	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	33	407	0	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.977	0.797	1	0.977	0.797	1	CLONAL	1	TRUE	1	0.18549952905961	2		407	364	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0068752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	22	446	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.621	0.481	0.784	0.621	0.481	0.784	SUBCLONAL	1	TRUE	1	0.18549952905961	2		448	382	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089123	37089125	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs63751247	NA	P-0068752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	24	375	0	ENST00000231790.2:c.1852_1854del	p.Lys618del	p.K618del	ENST00000231790	NM_000249.3	615	ctGAAg/ctg	16/19	0.18549952905961	1	FACETS	0.593	0.464	0.742	0.593	0.464	0.742	SUBCLONAL	1	TRUE	0	0.18549952905961	1		375	396	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214728	36214728	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	44	323	1	ENST00000222270.7:c.3159del	p.Arg1055GlyfsTer127	p.R1055Gfs*127	ENST00000222270	NM_014727.1	1052	Ggg/gg	8/37	0.150356437767043	3	FACETS	1	0.958	1	0.738	0.621	0.867	CLONAL	1	TRUE	1	0.18549952905961	3		324	351	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896548	78896548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242627252	NA	P-0068752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	22	342	1	ENST00000306801.3:c.2545C>T	p.Arg849Cys	p.R849C	ENST00000306801	NM_020761.2	849	Cgc/Tgc	22/34	1	2	FACETS	0.682	0.528	0.86	0.682	0.528	0.86	SUBCLONAL	1	TRUE	1	0.18549952905961	2		343	348	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142066	108142066	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	45	350	0	ENST00000278616.4:c.3010A>C	p.Ser1004Arg	p.S1004R	ENST00000278616	NM_000051.3	1004	Agc/Cgc	20/63	1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.18549952905961	2		350	484	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6270665	6270665	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1216051684	NA	P-0068752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	65	485	2	ENST00000252674.7:c.118G>A	p.Glu40Lys	p.E40K	ENST00000252674	NM_005934.3	40	Gag/Aag	2/12	0.150356437767043	3	FACETS	0.893	0.776	1	0.893	0.776	1	CLONAL	2	TRUE	1	0.18549952905961	3		487	429	SUCCESS
CALR	811	MSKCC	GRCh37	19	13049510	13049510	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	28	382	0	ENST00000316448.5:c.17C>A	p.Pro6Gln	p.P6Q	ENST00000316448	NM_004343.3	6	cCg/cAg	1/9	0.150356437767043	3	FACETS	0.797	0.636	0.98	0.398	0.318	0.49	CLONAL	1	TRUE	1	0.18549952905961	3		382	414	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737689	145737689	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	48	552	0	ENST00000428558.2:c.3074G>T	p.Gly1025Val	p.G1025V	ENST00000428558	NM_004260.3	1025	gGg/gTg	19/22	1	2	FACETS	0.941	0.795	1	0.941	0.795	1	CLONAL	1	TRUE	1	0.18549952905961	2		552	550	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336323	80336324	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0068752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	33	371	0	ENST00000286548.4:c.995_996del	p.Thr332ArgfsTer44	p.T332Rfs*44	ENST00000286548	NM_002072.3	332	aCA/a	7/7	1	2	FACETS	0.859	0.7	1	0.859	0.7	1	CLONAL	1	TRUE	1	0.18549952905961	2		371	414	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044688	47044722	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCTCCACCCCAGGGAGCACTAGCCGAGAGACAGC	CCCTCCACCCCAGGGAGCACTAGCCGAGAGACAGC	-	novel	NA	P-0068752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	29	272	0	ENST00000377604.3:c.2101-13_2122del		p.X701_splice	ENST00000377604	NM_001204468.1	701		19/24	1	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	0	0.18549952905961	1		272	228	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325638	87325638	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	27	300	0	ENST00000277120.3:c.515A>G	p.Gln172Arg	p.Q172R	ENST00000277120		172	cAg/cGg	6/19	1	2	FACETS	0.735	0.585	0.907	0.735	0.585	0.907	CLONAL	1	TRUE	1	0.18549952905961	2		300	396	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383208	42383209	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0068752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	37	448	0	ENST00000221972.3:c.233dup	p.Glu79Ter	p.E79*	ENST00000221972	NM_021601.3	76	-/C	2/5	0.150356437767043	3	FACETS	0.838	0.69	1	0.419	0.345	0.502	CLONAL	1	TRUE	1	0.18549952905961	3		448	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0068753-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	113	420	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.41	2		420	487	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154846	2154848	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0068753-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	57	431	0	ENST00000434045.2:c.373_375del	p.Glu125del	p.E125del	ENST00000434045	NM_001127598.1	125	GAG/-	4/5	1	2	FACETS	0.745	0.642	0.857	0.745	0.642	0.857	SUBCLONAL	1	TRUE	1	0.41	2		431	373	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143999	11143999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1171822727	NA	P-0068753-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	87	363	0	ENST00000358026.2:c.3580G>A	p.Gly1194Arg	p.G1194R	ENST00000358026	NM_001128849.1	1194	Ggg/Agg	26/36	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.41	2		363	404	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0068754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	165	367	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.558367255740111	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.579064199022433	2		367	276	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012660	36012660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	119	388	0	ENST00000358208.4:c.104C>T	p.Ser35Leu	p.S35L	ENST00000358208		35	tCg/tTg	2/12	0.579064199022433	5	FACETS	0.986	0.89	1	0.329	0.296	0.363	CLONAL	1	TRUE	2	0.579064199022433	5		388	779	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248633	59248634	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0068754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	143	418	0	ENST00000371222.2:c.109_110del	p.Ser37HisfsTer69	p.S37Hfs*69	ENST00000371222	NM_002228.3	37	AGc/c	1/1	0.579064199022433	3	FACETS	1	0.925	1	0.506	0.463	0.551	CLONAL	1	TRUE	1	0.579064199022433	3		418	629	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579321	7579322	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs587780067	NA	P-0068754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	239	424	0	ENST00000269305.4:c.365_366del	p.Val122AspfsTer26	p.V122Dfs*26	ENST00000269305	NM_001126112.2	122	gTG/g	4/11	0.558367255740111	2	FACETS	0.964	0.915	1	0.964	0.915	1	CLONAL	2	TRUE	0	0.579064199022433	2		424	428	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944267	81944267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	113	379	0	ENST00000359376.3:c.1876G>A	p.Glu626Lys	p.E626K	ENST00000359376	NM_002661.3	626	Gag/Aag	18/33	0.579064199022433	3	FACETS	1	0.952	1	0.541	0.49	0.595	CLONAL	1	TRUE	1	0.579064199022433	3		379	465	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640115	3640115	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	83	398	0	ENST00000294008.3:c.3524C>T	p.Pro1175Leu	p.P1175L	ENST00000294008	NM_032444.2	1175	cCt/cTt	12/15	0.579064199022433	3	FACETS	0.772	0.683	0.866	0.386	0.341	0.433	SUBCLONAL	1	TRUE	1	0.579064199022433	3		398	479	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63531762	63531762	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	118	325	0	ENST00000307078.5:c.2219C>T	p.Pro740Leu	p.P740L	ENST00000307078	NM_004655.3	740	cCa/cTa	9/11	0.500106191088923	4	FACETS	1	0.963	1	0.564	0.51	0.62	CLONAL	1	TRUE	2	0.579064199022433	4		325	571	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819778	81819778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	109	367	2	ENST00000359376.3:c.184G>A	p.Glu62Lys	p.E62K	ENST00000359376	NM_002661.3	62	Gag/Aag	2/33	1	2	FACETS	0.973	0.878	1	0.973	0.878	1	CLONAL	1	TRUE	1	0.448145112646367	2		369	500	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291915	15291915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775964142	NA	P-0068767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	80	447	2	ENST00000263388.2:c.2851C>T	p.Arg951Cys	p.R951C	ENST00000263388	NM_000435.2	951	Cgt/Tgt	18/33	1	2	FACETS	0.801	0.708	0.899	0.801	0.708	0.899	CLONAL	1	TRUE	1	0.448145112646367	2		449	446	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28600670	28600670	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0068767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	114	365	0	ENST00000253063.3:c.1020+1G>A		p.X340_splice	ENST00000253063	NM_031459.4	340			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.448145112646367	2		365	474	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643846	38643846	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	132	329	0	ENST00000299084.4:c.1316A>C	p.Lys439Thr	p.K439T	ENST00000299084	NM_152594.2	439	aAa/aCa	7/7	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.448145112646367	2		329	545	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225365108	225365108	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	114	384	0	ENST00000264414.4:c.1582C>A	p.Pro528Thr	p.P528T	ENST00000264414	NM_003590.4	528	Cca/Aca	11/16	1	2	FACETS	0.889	0.803	0.98	0.889	0.803	0.98	CLONAL	1	TRUE	1	0.448145112646367	2		384	572	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183851	10183852	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAAA	novel	NA	P-0068767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	117	384	0	ENST00000256474.2:c.321_322insAAAC	p.Arg108LysfsTer25	p.R108Kfs*25	ENST00000256474	NM_000551.3	107	cgc/cgCAAAc	1/3	0.448145112646367	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.448145112646367	1		384	369	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713662	52713662	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	127	404	2	ENST00000394830.3:c.66del	p.His23ThrfsTer22	p.H23Tfs*22	ENST00000394830	NM_018313.4	22	ggG/gg	2/30	0.448145112646367	1	FACETS	0.997	0.91	1	0.997	0.91	1	CLONAL	1	TRUE	0	0.448145112646367	1		406	441	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231054	53231054	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	70	197	0	ENST00000375401.3:c.1848C>A	p.Asn616Lys	p.N616K	ENST00000375401	NM_004187.3	616	aaC/aaA	13/26	1	1	FACETS	0.762	0.67	0.86	0.762	0.67	0.86	SUBCLONAL	1	TRUE	0	0.448145112646367	1		197	318	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245320	53245337	+	frameshift_variant	Frame_Shift_Del	DEL	ATAGATCTGTAGCTTTTT	ATAGATCTGTAGCTTTTT	G	novel	NA	P-0068767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	74	188	0	ENST00000375401.3:c.700_717delinsC	p.Lys234ArgfsTer23	p.K234Rfs*23	ENST00000375401	NM_004187.3	234	AAAAAGCTACAGATCTAT/C	6/26	1	1	FACETS	0.932	0.825	1	0.932	0.825	1	CLONAL	1	TRUE	0	0.448145112646367	1		188	275	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0068768-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	197	334	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.571097180735832	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.571097180735832	2		334	340	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70442602	70442602	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068768-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	34	397	0	ENST00000373644.4:c.4924G>C	p.Glu1642Gln	p.E1642Q	ENST00000373644	NM_030625.2	1642	Gaa/Caa	10/12	1	2	FACETS	0.309	0.253	0.373	0.309	0.253	0.373	SUBCLONAL	1	TRUE	1	0.571097180735832	2		397	385	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623777	28623777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs530568732	NA	P-0068768-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	37	462	0	ENST00000241453.7:c.877G>A	p.Glu293Lys	p.E293K	ENST00000241453	NM_004119.2	293	Gag/Aag	7/24	1	2	FACETS	0.378	0.312	0.451	0.378	0.312	0.451	SUBCLONAL	1	TRUE	1	0.571097180735832	2		462	343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578412	7578414	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0068768-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	173	535	0	ENST00000269305.4:c.516_518del	p.Val173del	p.V173del	ENST00000269305	NM_001126112.2	172	gtTGTg/gtg	5/11	0.571097180735832	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.571097180735832	1		535	350	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729929	39729929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068768-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	60	373	0	ENST00000361337.2:c.1244C>T	p.Ser415Phe	p.S415F	ENST00000361337	NM_003286.2	415	tCc/tTc	13/21	1	2	FACETS	0.58	0.502	0.664	0.58	0.502	0.664	SUBCLONAL	1	TRUE	1	0.571097180735832	2		373	362	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428494	72428496	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0068768-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	127	415	0	ENST00000477973.2:c.506_508del	p.Lys170del	p.K170del	ENST00000477973	NM_012234.5	170	AAG/-	2/4	0.395953441025881	1	FACETS	0.83	0.759	0.902	0.83	0.759	0.902	CLONAL	1	TRUE	0	0.571097180735832	1		415	383	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602916	55602916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372795544	NA	P-0068768-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	36	344	0	ENST00000288135.5:c.2626G>A	p.Asp876Asn	p.D876N	ENST00000288135	NM_000222.2	876	Gat/Aat	19/21	0.430330105238384	1	FACETS	0.349	0.288	0.416	0.349	0.288	0.416	SUBCLONAL	1	TRUE	0	0.571097180735832	1		344	258	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528306	157528306	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554237841	NA	P-0068768-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	30	504	0	ENST00000346085.5:c.6031G>T	p.Glu2011Ter	p.E2011*	ENST00000346085	NM_020732.3	2011	Gag/Tag	20/20	1	2	FACETS	0.238	0.191	0.291	0.238	0.191	0.291	SUBCLONAL	1	TRUE	1	0.571097180735832	2		504	441	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474345	40474345	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068768-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	68	426	0	ENST00000264657.5:c.2056T>G	p.Tyr686Asp	p.Y686D	ENST00000264657	NM_139276.2	686	Tat/Gat	21/24	0.344615228892081	0	FACETS	0.309	0.27	0.35			1	SUBCLONAL	1	TRUE	0	0.571097180735832	0		426	331	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67637070	67637070	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068768-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	30	329	0	ENST00000272342.5:c.2681C>T	p.Ser894Phe	p.S894F	ENST00000272342	NM_019002.3	894	tCt/tTt	6/6	1	2	FACETS	0.331	0.267	0.404	0.331	0.267	0.404	SUBCLONAL	1	TRUE	1	0.571097180735832	2		329	317	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0068770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	81	317	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.416435143780428	3	FACETS	0.911	0.814	1	0.911	0.814	1	CLONAL	2	TRUE	1	0.426280199708908	3		317	253	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436089	51436089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141609461	NA	P-0068770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	53	415	0	ENST00000262662.1:c.49G>A	p.Asp17Asn	p.D17N	ENST00000262662		17	Gac/Aac	3/4	1	2	FACETS	0.325	0.277	0.379	0.325	0.277	0.379	SUBCLONAL	1	TRUE	1	0.426280199708908	2		415	764	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0068771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	219	508	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.307668166992568	4	FACETS	0.912	0.852	0.973	0.912	0.852	0.973	CLONAL	3	FALSE	1	0.302183036696298	4		508	690	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102904	71102904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	63	306	0	ENST00000318789.4:c.303G>A	p.Met101Ile	p.M101I	ENST00000318789	NM_032682.5	101	atG/atA	8/21	0.267765373334298	4	FACETS	0.948	0.82	1	0.316	0.273	0.362	CLONAL	1	FALSE	1	0.302183036696298	4		306	573	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077510	30077510	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	44	398	0	ENST00000338641.4:c.1657G>T	p.Glu553Ter	p.E553*	ENST00000338641	NM_000268.3	553	Gag/Tag	15/16	0.202085758217375	4	FACETS	0.795	0.667	0.937	0.397	0.333	0.469	CLONAL	1	FALSE	2	0.302183036696298	4		398	477	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427225	49427225	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783681	NA	P-0068771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	68	437	0	ENST00000301067.7:c.11263C>T	p.Gln3755Ter	p.Q3755*	ENST00000301067	NM_003482.3	3755	Cag/Tag	39/54	0.302183036696298	5	FACETS	0.797	0.692	0.911	0.398	0.346	0.456	CLONAL	1	FALSE	3	0.302183036696298	5		437	821	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857332	9857332	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs763809945	NA	P-0068771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	39	386	0	ENST00000330684.3:c.4069C>G	p.Leu1357Val	p.L1357V	ENST00000330684	NM_001134407.1	1357	Ctc/Gtc	13/13	NA	2	FACETS	0.696	0.578	0.827			1	INDETERMINATE	1	FALSE	NA	0.302183036696298	2		386	371	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252865	36252868	+	frameshift_variant	Frame_Shift_Del	DEL	CGAC	CGAC	-	novel	NA	P-0068771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	120	316	0	ENST00000300305.3:c.494_497del	p.Gly165GlufsTer10	p.G165Efs*10	ENST00000300305		165	gGTCGa/ga	4/8	0.267765373334298	4	FACETS	0.937	0.849	1	0.625	0.566	0.686	CLONAL	2	FALSE	1	0.302183036696298	4		316	552	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449559	32449559	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	55	359	0	ENST00000332351.3:c.815C>G	p.Thr272Ser	p.T272S	ENST00000332351	NM_024426.4	272	aCc/aGc	3/10	0.215837994434478	2	FACETS	0.901	0.773	1	0.451	0.386	0.52	CLONAL	1	FALSE	0	0.302183036696298	2		359	404	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680908	30680908	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	53	368	0	ENST00000376406.3:c.811G>A	p.Asp271Asn	p.D271N	ENST00000376406	NM_014641.2	271	Gat/Aat	5/15	0.302183036696298	7	FACETS	0.745	0.633	0.867	0.186	0.158	0.217	SUBCLONAL	1	FALSE	3	0.302183036696298	7		368	827	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799011	42799011	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	78	415	0	ENST00000575354.2:c.4495G>A	p.Asp1499Asn	p.D1499N	ENST00000575354	NM_015125.3	1499	Gac/Aac	20/20	0.202085758217375	4	FACETS	1	0.927	1	0.539	0.473	0.609	CLONAL	1	FALSE	2	0.302183036696298	4		415	624	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796292	57796292	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0068771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	37	348	0	ENST00000309042.7:c.1268C>G	p.Ser423Ter	p.S423*	ENST00000309042	NM_005612.4	423	tCa/tGa	4/4	0.285012396803919	3	FACETS	0.586	0.483	0.702	0.293	0.241	0.351	SUBCLONAL	1	FALSE	1	0.302183036696298	3		348	481	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874388	151874388	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	96	355	0	ENST00000262189.6:c.8150T>C	p.Leu2717Pro	p.L2717P	ENST00000262189	NM_170606.2	2717	cTt/cCt	38/59	0.302183036696298	5	FACETS	1	0.933	1			1	CLONAL	2	FALSE	NA	0.302183036696298	5		355	438	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814517	43814517	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	27	308	0	ENST00000372470.3:c.1312C>G	p.Leu438Val	p.L438V	ENST00000372470	NM_005373.2	438	Ctg/Gtg	9/12	0.202175339290615	4	FACETS	0.463	0.367	0.572	0.231	0.183	0.286	SUBCLONAL	1	FALSE	2	0.302183036696298	4		308	503	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615574	100615574	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	58	356	0	ENST00000308731.7:c.758G>C	p.Arg253Thr	p.R253T	ENST00000308731	NM_000061.2	253	aGa/aCa	8/19	0.215837994434478	2	FACETS	0.844	0.726	0.971	0.422	0.363	0.486	CLONAL	1	FALSE	0	0.302183036696298	2		356	455	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946179	55946179	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	129	362	0	ENST00000263923.4:c.4000G>C	p.Val1334Leu	p.V1334L	ENST00000263923	NM_002253.2	1334	Gtg/Ctg	30/30	0.285012396803919	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	FALSE	1	0.302183036696298	3		362	457	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273284	198273284	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	54	296	0	ENST00000335508.6:c.926G>C	p.Gly309Ala	p.G309A	ENST00000335508	NM_012433.2	309	gGa/gCa	8/25	0.302183036696298	5	FACETS	0.924	0.789	1	0.308	0.263	0.358	CLONAL	1	FALSE	2	0.302183036696298	5		296	562	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091186	29091186	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555913484	NA	P-0068771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	10	114	0	ENST00000328354.6:c.1304C>T	p.Ser435Leu	p.S435L	ENST00000328354	NM_007194.3	435	tCa/tTa	12/15	0.28090420979231	5	FACETS	0.654	0.444	0.916	0.218	0.148	0.306	SUBCLONAL	1	FALSE	2	0.302183036696298	5		114	147	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170011231	170011231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	53	292	0	ENST00000295797.4:c.1352C>T	p.Ser451Phe	p.S451F	ENST00000295797	NM_002740.5	451	tCt/tTt	14/18	0.302183036696298	5	FACETS	0.951	0.811	1	0.317	0.27	0.368	CLONAL	1	FALSE	2	0.302183036696298	5		292	536	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201096	108201096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774281788	NA	P-0068772-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	75	432	0	ENST00000278616.4:c.7463G>A	p.Cys2488Tyr	p.C2488Y	ENST00000278616	NM_000051.3	2488	tGt/tAt	50/63	0.365759401950317	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.365759401950317	1		432	265	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609976	81609977	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGCCATGCGCCTGGAC	novel	NA	P-0068772-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	33	644	0	ENST00000298171.2:c.1577_1592dup	p.Lys532AlafsTer36	p.K532Afs*36	ENST00000298171	NM_000369.2	525	ttc/ttCGCCATGCGCCTGGACc	10/10	0.268582055317689	4	FACETS	0.405	0.329	0.491	0.202	0.164	0.246	SUBCLONAL	1	TRUE	2	0.365759401950317	4		644	609	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0068773-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	28	464	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.558	0.445	0.687	0.558	0.445	0.687	SUBCLONAL	1	TRUE	1	0.21	2		464	478	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0068773-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	48	479	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	1	2	FACETS	0.816	0.695	0.948	1	0.967	1	CLONAL	2	TRUE	1	0.21	2		479	280	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0068774-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	53	329	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.316742568855096	2		329	226	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068774-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	49	424	0	ENST00000358664.4:c.179G>T	p.Arg60Leu	p.R60L	ENST00000358664	NM_002382.4	60	cGg/cTg	4/5	0.316742568855096	1	FACETS	0.787	0.669	0.914	0.787	0.669	0.914	CLONAL	1	TRUE	0	0.316742568855096	1		424	331	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317577	163317577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068774-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	54	361	0	ENST00000271452.3:c.973G>A	p.Glu325Lys	p.E325K	ENST00000271452	NM_145697.2	325	Gag/Aag	12/14	1	2	FACETS	0.912	0.782	1	0.912	0.782	1	CLONAL	1	TRUE	1	0.316742568855096	2		361	374	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149452863	149452863	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0068774-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	77	428	0	ENST00000286301.3:c.1082+1G>T		p.X361_splice	ENST00000286301	NM_005211.3	361			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.316742568855096	2		428	380	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878083	48878120	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCCGCCGCTGCCGCCGCGGAACCCCCGGCACCGCCG	CCGCCGCCGCTGCCGCCGCGGAACCCCCGGCACCGCCG	-	novel	NA	P-0068775-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	309	453	2	ENST00000267163.4:c.43_80del	p.Ala15ProfsTer3	p.A15Pfs*3	ENST00000267163	NM_000321.2	12	aCCGCCGCCGCTGCCGCCGCGGAACCCCCGGCACCGCCG/a	1/27	0.703628010742786	4	FACETS	0.86	0.813	0.907	0.86	0.813	0.907	CLONAL	2	FALSE	2	0.69191305225222	4		455	879	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0068775-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	375	440	0	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	0.179125929538738	3	FACETS	0.946	0.915	0.976			1	INDETERMINATE	3	FALSE	NA	0.69191305225222	3		440	514	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10792092	10792092	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068775-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	232	408	0	ENST00000361367.2:c.2285A>G	p.Gln762Arg	p.Q762R	ENST00000361367	NM_014633.3	762	cAa/cGa	18/25	0.703628010742786	4	FACETS	0.95	0.893	1	0.95	0.893	1	CLONAL	2	FALSE	2	0.69191305225222	4		408	597	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445202	49445203	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	A	novel	NA	P-0068775-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	360	465	1	ENST00000301067.7:c.2263_2264delinsT	p.Arg755CysfsTer175	p.R755Cfs*175	ENST00000301067	NM_003482.3	755	CGg/Tg	10/54	0.46373531986189	4	FACETS	0.857	0.82	0.894	0.857	0.82	0.894	CLONAL	3	FALSE	1	0.69191305225222	4		466	685	SUCCESS
APC	324	MSKCC	GRCh37	5	112178112	112178113	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGCT	novel	NA	P-0068775-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	237	414	0	ENST00000257430.4:c.6822_6823insGCTC	p.Lys2275AlafsTer24	p.K2275Afs*24	ENST00000257430	NM_000038.5	2274	gcc/gcCGCTc	16/16	0.703628010742786	3	FACETS	0.937	0.885	0.989	0.937	0.885	0.989	CLONAL	2	FALSE	1	0.69191305225222	3		414	492	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188815	32188815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068775-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	286	512	0	ENST00000375023.3:c.739G>A	p.Gly247Ser	p.G247S	ENST00000375023	NM_004557.3	247	Ggc/Agc	4/30	0.703628010742786	3	FACETS	0.932	0.885	0.979			1	CLONAL	2	FALSE	NA	0.69191305225222	3		512	597	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681005	117681005	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068775-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	97	364	2	ENST00000368508.3:c.3615T>A	p.Phe1205Leu	p.F1205L	ENST00000368508	NM_002944.2	1205	ttT/ttA	23/43	0.468837373011671	1	FACETS	0.997	0.914	1	0.997	0.914	1	CLONAL	1	FALSE	0	0.69191305225222	1		366	184	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843411	128843411	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068775-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	118	410	2	ENST00000249373.3:c.518G>T	p.Arg173Leu	p.R173L	ENST00000249373	NM_005631.4	173	cGc/cTc	2/12	0.703628010742786	3	FACETS	1	0.935	1	0.518	0.471	0.568	CLONAL	1	FALSE	1	0.69191305225222	3		412	443	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	54	382	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.809	0.707	0.916	0.809	0.707	0.916	CLONAL	1	TRUE	1	0.866581342576345	2		382	154	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0068776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	32	192	1	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	2	FACETS	0.377	0.308	0.453	0.377	0.308	0.453	SUBCLONAL	1	TRUE	1	0.866581342576345	2		193	196	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0068776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	174	343	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.866581342576345	2		343	376	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791372	42791373	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0068776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	137	382	0	ENST00000575354.2:c.436_437del	p.Ser146Ter	p.S146*	ENST00000575354	NM_015125.3	144	acAGag/acag	3/20	0.866581342576345	1	FACETS	0.753	0.703	0.802	0.753	0.703	0.802	SUBCLONAL	1	TRUE	0	0.866581342576345	1		382	238	SUCCESS
AR	367	MSKCC	GRCh37	X	66765148	66765149	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	rs752055010	NA	P-0068776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	21	212	0	ENST00000374690.3:c.170_172dup	p.Leu57dup	p.L57dup	ENST00000374690	NM_000044.3	57	ttg/tTGCtg	1/8	1	2	FACETS	0.216	0.167	0.274	0.216	0.167	0.274	SUBCLONAL	1	TRUE	1	0.866581342576345	2		212	224	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794066	42794067	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0068776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	28	319	0	ENST00000575354.2:c.1428_1429del	p.Ser476ArgfsTer37	p.S476Rfs*37	ENST00000575354	NM_015125.3	476	aGT/a	9/20	0.866581342576345	1	FACETS	0.197	0.158	0.24	0.197	0.158	0.24	SUBCLONAL	1	TRUE	0	0.866581342576345	1		319	186	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413129	139413131	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0068776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	80	366	0	ENST00000277541.6:c.1011_1013del	p.Asp338del	p.D338del	ENST00000277541	NM_017617.3	337	gaTGAc/gac	6/34	0.18306833761892	2	FACETS	0.398	0.351	0.448	0.199	0.175	0.224	INDETERMINATE	1	TRUE	0	0.866581342576345	2		366	464	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433346	78433368	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAAGCTATCAAAAAATTAAATA	AAAAGCTATCAAAAAATTAAATA	-	novel	NA	P-0068776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	130	236	0	ENST00000370768.2:c.251-18_255del		p.X84_splice	ENST00000370768	NM_003902.3	84		4/20	0.866581342576345	1	FACETS	0.934	0.881	0.985	0.934	0.881	0.985	CLONAL	1	TRUE	0	0.866581342576345	1		236	182	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412327	139412327	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	11	390	0	ENST00000277541.6:c.1318T>C	p.Cys440Arg	p.C440R	ENST00000277541	NM_017617.3	440	Tgt/Cgt	8/34	0.18306833761892	2	FACETS	0.057	0.038	0.079	0.028	0.019	0.04	INDETERMINATE	1	TRUE	0	0.866581342576345	2		390	449	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0068777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	98	393	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.919	0.823	1	1	0.986	1	CLONAL	2	TRUE	1	0.2154966640165	2		393	495	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629996	187629997	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0068777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	138	406	0	ENST00000441802.2:c.985_986delinsTT	p.Pro329Phe	p.P329F	ENST00000441802	NM_005245.3	329	CCt/TTt	2/27	1	2	FACETS	1	0.964	1	1	0.991	1	CLONAL	2	TRUE	1	0.2154966640165	2		406	580	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504009	186504010	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0068777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	49	325	0	ENST00000323963.5:c.574_575delinsAA	p.Gly192Asn	p.G192N	ENST00000323963		192	GGt/AAt	6/11	1	2	FACETS	0.803	0.68	0.939	0.803	0.68	0.939	CLONAL	1	TRUE	1	0.2154966640165	2		325	566	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588124	69588125	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0068777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	78	378	1	ENST00000168712.1:c.573_574delinsTT	p.Arg192Ter	p.R192*	ENST00000168712	NM_002007.2	191	aaCCga/aaTTga	3/3	1	2	FACETS	0.881	0.778	0.99	1	0.982	1	CLONAL	2	TRUE	1	0.2154966640165	2		379	411	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225752	26225752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368380591	NA	P-0068777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	164	487	0	ENST00000360408.1:c.370G>A	p.Asp124Asn	p.D124N	ENST00000360408	NM_003532.2	124	Gac/Aac	1/1	1	2	FACETS	1	0.962	1	1	0.992	1	CLONAL	2	TRUE	1	0.2154966640165	2		487	709	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	105	382	0				ENST00000310581	NM_198253.2	-/1132			0.678929655158859	5	FACETS	0.761	0.687	0.839	0.508	0.458	0.559	SUBCLONAL	2	TRUE	2	0.678929655158859	5		382	410	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623229	52623229	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0068778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	88	382	0	ENST00000394830.3:c.2822C>G	p.Ser941Ter	p.S941*	ENST00000394830	NM_018313.4	941	tCa/tGa	19/30	0.607425760346323	1	FACETS	0.719	0.648	0.793	0.719	0.648	0.793	SUBCLONAL	1	TRUE	0	0.678929655158859	1		382	238	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982134	201982135	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0068778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	200	484	0	ENST00000359651.3:c.659dup	p.Asp220GlufsTer4	p.D220Efs*4	ENST00000359651		220	gat/gAat	5/8	0.608035512641913	3	FACETS	0.918	0.861	0.974	0.918	0.861	0.974	CLONAL	2	TRUE	1	0.678929655158859	3		484	430	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231786	36231786	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	563	498	0	ENST00000300305.3:c.598C>G	p.Pro200Ala	p.P200A	ENST00000300305		200	Ccc/Gcc	5/8	0.479120796586146	5	FACETS	1	0.995	1	0.875	0.852	0.898	CLONAL	4	TRUE	0	0.678929655158859	5		498	765	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158637047	158637054	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CATTACCG	CATTACCG	-	novel	NA	P-0068778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	194	425	0	ENST00000263640.3:c.126_133del	p.Cys42Ter	p.C42*	ENST00000263640	NM_001105.4	42	tgCGGTAATGag/tgag	4/11	0.521382994060947	2	FACETS	1	0.992	1	0.731	0.687	0.775	CLONAL	1	TRUE	0	0.678929655158859	2		425	391	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0068779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	91	264	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.468166884738563	3	FACETS	1	0.975	1	0.639	0.576	0.705	CLONAL	1	TRUE	1	0.726708268256896	3		264	267	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0068779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	121	240	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.879	0.802	0.958	0.879	0.802	0.958	CLONAL	1	TRUE	1	0.726708268256896	2		240	379	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473616	67473616	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	178	262	0	ENST00000327367.4:c.696G>T	p.Trp232Cys	p.W232C	ENST00000327367	NM_005902.3	232	tgG/tgT	6/9	0.694884233546219	2	FACETS	0.921	0.873	0.967	0.921	0.873	0.967	CLONAL	2	TRUE	0	0.726708268256896	2		262	266	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579563	7579566	+	frameshift_variant	Frame_Shift_Del	DEL	CATC	CATC	-	novel	NA	P-0068779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	101	235	0	ENST00000269305.4:c.121_124del	p.Asp41IlefsTer2	p.D41Ifs*2	ENST00000269305	NM_001126112.2	41	GATGat/at	4/11	0.723553125751554	1	FACETS	0.839	0.768	0.91	0.839	0.768	0.91	CLONAL	1	TRUE	0	0.726708268256896	1		235	211	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959066	2959066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772566311	NA	P-0068779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	203	235	0	ENST00000396946.4:c.2450C>T	p.Ala817Val	p.A817V	ENST00000396946	NM_032415.4	817	gCg/gTg	18/25	0.64558694103596	4	FACETS	0.907	0.848	0.967	0.604	0.565	0.645	CLONAL	2	TRUE	1	0.726708268256896	4		235	532	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279904	18279904	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768641921	NA	P-0068779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	216	231	0	ENST00000222254.8:c.1987G>A	p.Gly663Ser	p.G663S	ENST00000222254	NM_005027.3	663	Ggc/Agc	16/16	0.468166884738563	3	FACETS	0.984	0.929	1	0.984	0.929	1	CLONAL	2	TRUE	1	0.726708268256896	3		231	412	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245427	153245427	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	55	191	0	ENST00000281708.4:c.1764del	p.Glu588AspfsTer40	p.E588Dfs*40	ENST00000281708	NM_033632.3	588	gaA/ga	11/12	0.390146854014388	1	FACETS	0.421	0.364	0.481	0.421	0.364	0.481	INDETERMINATE	1	TRUE	0	0.726708268256896	1		191	229	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450287	50450287	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	108	245	0	ENST00000331340.3:c.471G>T	p.Lys157Asn	p.K157N	ENST00000331340	NM_006060.4	157	aaG/aaT	5/8	0.64558694103596	4	FACETS	1	0.95	1	0.362	0.326	0.399	CLONAL	1	TRUE	1	0.726708268256896	4		245	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0068780-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	379	474	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.378727920031451	6	FACETS	0.962	0.934	0.988			1	CLONAL	6	FALSE	NA	0.604656235484562	6		474	480	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0068780-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	176	513	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.511898607432439	4	FACETS	0.998	0.928	1	0.998	0.928	1	CLONAL	2	FALSE	2	0.604656235484562	4		513	468	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597404	10597404	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068780-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	659	352	0	ENST00000171111.5:c.1799G>C	p.Gly600Ala	p.G600A	ENST00000171111	NM_203500.1	600	gGc/gCc	6/6	0.604656235484562	8	FACETS	1	0.993	1			1	CLONAL	6	FALSE	NA	0.604656235484562	8		352	964	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0068781-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	31	289	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.363	0.293	0.441	0.363	0.293	0.441	SUBCLONAL	1	TRUE	1	0.457073615158527	2		289	374	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0068781-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	47	217	0	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.457073615158527	2		217	187	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027156	49027159	+	frameshift_variant	Frame_Shift_Del	DEL	CAAT	CAAT	-	novel	NA	P-0068781-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	30	205	0	ENST00000267163.4:c.1726_1729del	p.Ser576ArgfsTer34	p.S576Rfs*34	ENST00000267163	NM_000321.2	575	CAATca/ca	18/27	1	2	FACETS	0.71	0.577	0.857	0.71	0.577	0.857	SUBCLONAL	1	TRUE	1	0.457073615158527	2		205	185	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589539	67589562	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TCAAGTTGTCAAAGAAGATAATAT	TCAAGTTGTCAAAGAAGATAATAT	-	novel	NA	P-0068781-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	39	205	0	ENST00000274335.5:c.1303_1326del	p.Gln435_Ile442del	p.Q435_I442del	ENST00000274335		434	gaTCAAGTTGTCAAAGAAGATAATATt/gat	10/15	1	2	FACETS	0.871	0.73	1	0.871	0.73	1	CLONAL	1	TRUE	1	0.457073615158527	2		205	196	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711942	89711943	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0068781-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	66	243	0	ENST00000371953.3:c.562dup	p.Tyr188LeufsTer2	p.Y188Lfs*2	ENST00000371953	NM_000314.4	187	gat/gaTt	6/9	0.32869178425218	2	FACETS	0.816	0.723	0.911	0.816	0.723	0.911	CLONAL	2	TRUE	0	0.457073615158527	2		243	177	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163929	47163980	+	frameshift_variant	Frame_Shift_Del	DEL	CCAAGTCTTTTTCTTTGCACCTACTAATATTCTGAAATCCATTTGATGAAAG	CCAAGTCTTTTTCTTTGCACCTACTAATATTCTGAAATCCATTTGATGAAAG	-	novel	NA	P-0068781-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	54	323	0	ENST00000409792.3:c.2146_2197del	p.Leu716MetfsTer34	p.L716Mfs*34	ENST00000409792	NM_014159.6	716	CTTTCATCAAATGGATTTCAGAATATTAGTAGGTGCAAAGAAAAAGACTTGGat/at	3/21	1	2	FACETS	0.78	0.67	0.898	0.78	0.67	0.898	SUBCLONAL	1	TRUE	1	0.457073615158527	2		323	303	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911045	94911045	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068781-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	58	273	0	ENST00000536441.1:c.1085C>T	p.Ser362Phe	p.S362F	ENST00000536441	NM_144665.3	362	tCc/tTc	8/10	1	2	FACETS	0.972	0.844	1	0.972	0.844	1	CLONAL	1	TRUE	1	0.457073615158527	2		273	261	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637276	176637276	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068781-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	72	329	0	ENST00000439151.2:c.1876G>C	p.Ala626Pro	p.A626P	ENST00000439151	NM_022455.4	626	Gca/Cca	5/23	1	2	FACETS	0.786	0.69	0.888	0.786	0.69	0.888	SUBCLONAL	1	TRUE	1	0.457073615158527	2		329	401	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855262	76855262	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	155	266	0	ENST00000373344.5:c.5725G>T	p.Glu1909Ter	p.E1909*	ENST00000373344	NM_000489.3	1909	Gaa/Taa	24/35	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.652247501624706	2		266	405	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121434595	NA	P-0068782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	145	259	1	ENST00000369535.4:c.37G>T	p.Gly13Cys	p.G13C	ENST00000369535	NM_002524.4	13	Ggt/Tgt	2/7	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.652247501624706	2		260	420	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964510	93964510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1435219791	NA	P-0068782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	119	270	0	ENST00000369303.4:c.2387G>A	p.Gly796Glu	p.G796E	ENST00000369303	NM_004440.3	796	gGa/gAa	14/17	NA	2	FACETS	0.919	0.837	1			1	INDETERMINATE	1	TRUE	NA	0.652247501624706	2		270	397	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88671957	88671957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs574695821	NA	P-0068782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	94	253	0	ENST00000360948.2:c.1213G>A	p.Asp405Asn	p.D405N	ENST00000360948	NM_001012338.2	405	Gat/Aat	10/19	1	2	FACETS	0.876	0.788	0.968	0.876	0.788	0.968	CLONAL	1	TRUE	1	0.652247501624706	2		253	329	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858247	9858247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	182	390	0	ENST00000330684.3:c.3154C>T	p.Leu1052Phe	p.L1052F	ENST00000330684	NM_001134407.1	1052	Ctt/Ttt	13/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.652247501624706	2		390	523	SUCCESS
APC	324	MSKCC	GRCh37	5	112178117	112178118	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0068782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	147	403	1	ENST00000257430.4:c.6826_6827delinsTT	p.Pro2276Leu	p.P2276L	ENST00000257430	NM_000038.5	2276	CCa/TTa	16/16	1	2	FACETS	0.811	0.744	0.88	0.811	0.744	0.88	CLONAL	1	TRUE	1	0.652247501624706	2		404	556	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673188	30673188	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	337	371	0	ENST00000376406.3:c.3772C>T	p.Gln1258Ter	p.Q1258*	ENST00000376406	NM_014641.2	1258	Cag/Tag	10/15	0.652247501624706	3	FACETS	0.98	0.935	1	0.98	0.935	1	CLONAL	2	TRUE	1	0.652247501624706	3		371	699	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69229634	69229634	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	145	292	0	ENST00000462284.1:c.710A>C	p.His237Pro	p.H237P	ENST00000462284	NM_002392.5	237	cAt/cCt	9/11	1	2	FACETS	0.938	0.862	1	0.938	0.862	1	CLONAL	1	TRUE	1	0.652247501624706	2		292	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578369	7578389	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ACCATCGCTATCTGAGCAGCG	ACCATCGCTATCTGAGCAGCG	-	novel	NA	P-0068782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	226	458	0	ENST00000269305.4:c.541_559+2del		p.X181_splice	ENST00000269305	NM_001126112.2	181		5/11	0.652247501624706	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.652247501624706	1		458	433	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162475142	162475142	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	150	303	0	ENST00000366898.1:c.599A>C	p.His200Pro	p.H200P	ENST00000366898	NM_004562.2	200	cAc/cCc	5/12	1	2	FACETS	0.728	0.667	0.791	0.728	0.667	0.791	SUBCLONAL	1	TRUE	1	0.652247501624706	2		303	632	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123025137	123025137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	236	449	0	ENST00000355640.3:c.1027C>T	p.His343Tyr	p.H343Y	ENST00000355640		343	Cat/Tat	4/7	1	2	FACETS	0.989	0.926	1	0.989	0.926	1	CLONAL	1	TRUE	1	0.652247501624706	2		449	732	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548868	29548868	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	133	220	0	ENST00000356175.3:c.1642G>C	p.Ala548Pro	p.A548P	ENST00000356175	NM_000267.3	548	Gct/Cct	15/57	0.652247501624706	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.652247501624706	1		220	256	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916257	9916257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	145	375	0	ENST00000330684.3:c.2032C>T	p.Pro678Ser	p.P678S	ENST00000330684	NM_001134407.1	678	Cca/Tca	10/13	1	2	FACETS	0.879	0.807	0.953	0.879	0.807	0.953	CLONAL	1	TRUE	1	0.652247501624706	2		375	506	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609638	28609638	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	162	306	0	ENST00000241453.7:c.1591T>C	p.Ser531Pro	p.S531P	ENST00000241453	NM_004119.2	531	Tct/Cct	12/24	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.652247501624706	2		306	489	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030429	47030429	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	118	296	0	ENST00000377604.3:c.204T>G	p.Asp68Glu	p.D68E	ENST00000377604	NM_001204468.1	68	gaT/gaG	4/24	1	2	FACETS	0.916	0.834	1	0.916	0.834	1	CLONAL	1	TRUE	1	0.652247501624706	2		296	395	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020868	26020868	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	238	619	0	ENST00000357647.3:c.151G>A	p.Glu51Lys	p.E51K	ENST00000357647	NM_003529.2	51	Gag/Aag	1/1	0.652247501624706	3	FACETS	0.991	0.925	1	0.495	0.462	0.529	CLONAL	1	TRUE	1	0.652247501624706	3		619	977	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636733	8636733	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	178	280	0	ENST00000356435.5:c.176A>T	p.Lys59Ile	p.K59I	ENST00000356435		59	aAa/aTa	2/35	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.652247501624706	2		280	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068783-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	200	301	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.61501262447075	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.612819589769074	2		301	289	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446203	187446203	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068783-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	177	338	0	ENST00000232014.4:c.1485del	p.Thr496ArgfsTer94	p.T496Rfs*94	ENST00000232014	NM_001130845.1	495	ccC/cc	6/10	0.612819589769074	7	FACETS	0.87	0.802	0.94	0.348	0.321	0.376	CLONAL	2	TRUE	2	0.612819589769074	7		338	841	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27168586	27168586	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068783-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	124	233	1	ENST00000380036.4:c.458C>T	p.Ala153Val	p.A153V	ENST00000380036	NM_000459.3	153	gCa/gTa	3/23	0.61501262447075	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.612819589769074	2		234	176	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597477	28597499	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGAGCATACCGACTTAAATTCC	AGGAGCATACCGACTTAAATTCC	-	novel	NA	P-0068783-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	104	279	0	ENST00000241453.7:c.2406_2418+10del		p.X802_splice	ENST00000241453	NM_004119.2	802		19/24	0.61501262447075	2	FACETS	0.908	0.837	0.977	0.908	0.837	0.977	CLONAL	2	TRUE	0	0.612819589769074	2		279	187	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636599	73636631	+	inframe_deletion	In_Frame_Del	DEL	ATGCCAAGTCAGTTTCTTCCACAACAGGCCACT	ATGCCAAGTCAGTTTCTTCCACAACAGGCCACT	-	novel	NA	P-0068783-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	197	389	0	ENST00000377687.4:c.862_894del	p.Met288_Thr298del	p.M288_T298del	ENST00000377687	NM_001730.3	288	ATGCCAAGTCAGTTTCTTCCACAACAGGCCACT/-	2/4	0.612819589769074	6	FACETS	0.91	0.845	0.978	0.455	0.422	0.489	CLONAL	2	TRUE	2	0.612819589769074	6		389	786	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28903769	28903769	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068783-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	16	279	0	ENST00000282397.4:c.2690C>A	p.Ala897Asp	p.A897D	ENST00000282397	NM_002019.4	897	gCc/gAc	19/30	0.61501262447075	2	FACETS	0.249	0.184	0.326	0.124	0.092	0.163	SUBCLONAL	1	TRUE	0	0.612819589769074	2		279	210	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023536	27023732	+	frameshift_variant	Frame_Shift_Del	DEL	CTACTACCCCAACCGCAGCGCCTACCCCCCGCCCGCCCCGGCCTACGCGCTGAGCTCCCCGAGAGGTGGCACTCCGGGCTCCGGCGCGGCGGCGGCTGCCGGCTCCAAGCCGCCTCCCTCCTCCAGCGCCTCCGCCTCCTCGTCGTCTTCGTCCTTCGCTCAGCAGCGCTTCGGGGCCATGGGGGGAGGCGGCCCCT	CTACTACCCCAACCGCAGCGCCTACCCCCCGCCCGCCCCGGCCTACGCGCTGAGCTCCCCGAGAGGTGGCACTCCGGGCTCCGGCGCGGCGGCGGCTGCCGGCTCCAAGCCGCCTCCCTCCTCCAGCGCCTCCGCCTCCTCGTCGTCTTCGTCCTTCGCTCAGCAGCGCTTCGGGGCCATGGGGGGAGGCGGCCCCT	-	novel	NA	P-0068783-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	129	359	0	ENST00000324856.7:c.643_839del	p.Tyr215ArgfsTer119	p.Y215Rfs*119	ENST00000324856	NM_006015.4	214	tcCTACTACCCCAACCGCAGCGCCTACCCCCCGCCCGCCCCGGCCTACGCGCTGAGCTCCCCGAGAGGTGGCACTCCGGGCTCCGGCGCGGCGGCGGCTGCCGGCTCCAAGCCGCCTCCCTCCTCCAGCGCCTCCGCCTCCTCGTCGTCTTCGTCCTTCGCTCAGCAGCGCTTCGGGGCCATGGGGGGAGGCGGCCCCTcc/tccc	1/20	0.61501262447075	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.612819589769074	2		359	202	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0068785-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	14	334	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.218	0.157	0.294	0.218	0.157	0.294	SUBCLONAL	1	TRUE	1	0.263687902905916	2		334	486	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0068785-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	68	258	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.263687902905916	2		258	400	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0068785-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	119	394	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	0.803	0.727	0.882	1	0.986	1	CLONAL	2	TRUE	1	0.263687902905916	2		394	562	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577526	7577526	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121912653	NA	P-0068785-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	54	288	0	ENST00000269305.4:c.755T>C	p.Leu252Pro	p.L252P	ENST00000269305	NM_001126112.2	252	cTc/cCc	7/11	1	2	FACETS	0.846	0.724	0.98	0.846	0.724	0.98	CLONAL	1	TRUE	1	0.263687902905916	2		288	484	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962530	100962530	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752817186	NA	P-0068785-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	39	298	0	ENST00000325455.5:c.1867C>T	p.Arg623Cys	p.R623C	ENST00000325455	NM_001202474.3	623	Cgc/Tgc	3/8	1	2	FACETS	0.602	0.499	0.718	0.602	0.499	0.718	SUBCLONAL	1	TRUE	1	0.263687902905916	2		298	491	SUCCESS
APC	324	MSKCC	GRCh37	5	112174117	112174117	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068785-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	92	343	0	ENST00000257430.4:c.2827del	p.Ser943GlnfsTer12	p.S943Qfs*12	ENST00000257430	NM_000038.5	942	aaT/aa	16/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.263687902905916	2		343	498	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236228	108236228	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068786-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	244	337	0	ENST00000278616.4:c.9164G>C	p.Trp3055Ser	p.W3055S	ENST00000278616	NM_000051.3	3055	tGg/tCg	63/63	0.52580810587812	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.52580810587812	1		337	537	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440947	56440948	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCG	novel	NA	P-0068786-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	314	421	0	ENST00000407977.2:c.386_389dup	p.Glu131GlyfsTer2	p.E131Gfs*2	ENST00000407977		130	ggt/ggCGGGt	4/10	0.52580810587812	2	FACETS	0.973	0.927	1	0.973	0.927	1	CLONAL	2	TRUE	0	0.52580810587812	2		421	614	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0068787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	92	260	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.260236298658532	3	FACETS	0.919	0.821	1	0.919	0.821	1	CLONAL	2	TRUE	1	0.24	3		260	467	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0068787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	66	479	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.24	2		479	497	SUCCESS
APC	324	MSKCC	GRCh37	5	112137048	112137048	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1326410920	NA	P-0068787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	37	249	0	ENST00000257430.4:c.802G>T	p.Glu268Ter	p.E268*	ENST00000257430	NM_000038.5	268	Gaa/Taa	8/16	1	2	FACETS	0.82	0.677	0.979	0.82	0.677	0.979	CLONAL	1	TRUE	1	0.24	2		249	376	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374905	45374905	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	72	348	0	ENST00000262160.6:c.938T>C	p.Leu313Ser	p.L313S	ENST00000262160	NM_005901.5	313	tTa/tCa	8/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.24	2		348	506	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117614	70117614	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	71	414	0	ENST00000245479.2:c.82G>T	p.Glu28Ter	p.E28*	ENST00000245479	NM_000346.3	28	Gag/Tag	1/3	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.24	2		414	572	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119692	70119692	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	62	345	1	ENST00000245479.2:c.694C>T	p.Gln232Ter	p.Q232*	ENST00000245479	NM_000346.3	232	Cag/Tag	3/3	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.24	2		346	466	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368268	45368268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	61	329	0	ENST00000262160.6:c.1334C>T	p.Pro445Leu	p.P445L	ENST00000262160	NM_005901.5	445	cCt/cTt	11/11	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.24	2		329	505	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280815	41280815	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	29	336	0	ENST00000349496.5:c.2328G>A	p.Trp776Ter	p.W776*	ENST00000349496	NM_001904.3	776	tgG/tgA	15/15	0.260236298658532	3	FACETS	0.483	0.387	0.594	0.242	0.193	0.297	SUBCLONAL	1	TRUE	1	0.24	3		336	560	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727128	40727128	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	60	312	0	ENST00000373198.4:c.3836T>A	p.Phe1279Tyr	p.F1279Y	ENST00000373198	NM_133170.3	1279	tTc/tAc	28/32	0.185537827794529	1	FACETS	0.717	0.617	0.825	0.717	0.617	0.825	SUBCLONAL	1	TRUE	0	0.24	1		312	614	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0068788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	57	264	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.283701144572599	2		264	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579378	7579378	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	81	479	0	ENST00000269305.4:c.309C>A	p.Tyr103Ter	p.Y103*	ENST00000269305	NM_001126112.2	103	taC/taA	4/11	0.265058472465829	1	FACETS	0.889	0.785	1	0.889	0.785	1	CLONAL	1	TRUE	0	0.283701144572599	1		479	551	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485837	57485837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	73	443	0	ENST00000371085.3:c.1138C>T	p.Arg380Cys	p.R380C	ENST00000371085	NM_000516.4	380	Cgt/Tgt	13/13	0.272267523490088	3	FACETS	0.942	0.824	1	0.471	0.412	0.535	CLONAL	1	TRUE	1	0.283701144572599	3		443	624	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334836	81334836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770723689	NA	P-0068788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	61	346	0	ENST00000222390.5:c.1880G>A	p.Gly627Asp	p.G627D	ENST00000222390	NM_000601.4	627	gGc/gAc	17/18	1	2	FACETS	0.998	0.863	1	0.998	0.863	1	CLONAL	1	TRUE	1	0.283701144572599	2		346	431	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161332160	161332160	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0068788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	42	161	0	ENST00000367975.2:c.447C>G	p.Tyr149Ter	p.Y149*	ENST00000367975	NM_003001.3	149	taC/taG	6/6	0.263918370787129	4	FACETS	1	0.934	1	0.413	0.346	0.486	CLONAL	1	TRUE	1	0.283701144572599	4		161	307	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729914	30729915	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0068788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	150	335	0	ENST00000295754.5:c.1438dup	p.Glu480GlyfsTer36	p.E480Gfs*36	ENST00000295754	NM_003242.5	479	cgg/cGgg	6/7	0.13767298910845	3	FACETS	1	0.974	1			1	INDETERMINATE	2	TRUE	NA	0.283701144572599	3		335	530	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	78	382	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.451926874630647	2		382	314	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467539	66467539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	108	419	0	ENST00000273854.3:c.730C>A	p.Pro244Thr	p.P244T	ENST00000273854	NM_004439.5	244	Cct/Act	3/18	1	2	FACETS	0.791	0.712	0.875	0.791	0.712	0.875	SUBCLONAL	1	TRUE	1	0.451926874630647	2		419	604	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900953	3900953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	103	330	0	ENST00000262367.5:c.143G>A	p.Gly48Glu	p.G48E	ENST00000262367	NM_004380.2	48	gGa/gAa	2/31	NA	2	FACETS	1	0.909	1			1	INDETERMINATE	1	TRUE	NA	0.451926874630647	2		330	451	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909734	50909734	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	191	438	1	ENST00000440232.2:c.1454A>C	p.Gln485Pro	p.Q485P	ENST00000440232	NM_002691.3	485	cAg/cCg	12/27	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.451926874630647	2		439	623	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976587	55976587	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	86	270	0	ENST00000263923.4:c.1238T>A	p.Val413Asp	p.V413D	ENST00000263923	NM_002253.2	413	gTc/gAc	9/30	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.451926874630647	2		270	349	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332026	81332026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	101	319	1	ENST00000222390.5:c.2058G>T	p.Met686Ile	p.M686I	ENST00000222390	NM_000601.4	686	atG/atT	18/18	0.442758492026104	3	FACETS	0.815	0.737	0.897			1	CLONAL	2	TRUE	NA	0.451926874630647	3		320	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0068981-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	372	652	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	NA	2	FACETS	0.97	0.929	1			1	INDETERMINATE	2	TRUE	NA	0.545424541713621	2		652	703	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549383	21549383	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749117314	NA	P-0068981-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	81	540	0	ENST00000382592.4:c.2893G>A	p.Asp965Asn	p.D965N	ENST00000382592	NM_014572.2	965	Gat/Aat	8/8	0.545424541713621	1	FACETS	0.399	0.352	0.449	0.399	0.352	0.449	SUBCLONAL	1	TRUE	0	0.545424541713621	1		540	542	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004879	150004879	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs769204431	NA	P-0068981-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	237	554	0	ENST00000253339.5:c.1346A>G	p.His449Arg	p.H449R	ENST00000253339		449	cAt/cGt	3/7	0.545424541713621	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.545424541713621	1		554	599	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005463	42005463	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068981-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	338	551	0	ENST00000219905.7:c.3199C>T	p.Gln1067Ter	p.Q1067*	ENST00000219905	NM_001164273.1	1067	Caa/Taa	9/24	0.504598813082736	2	FACETS	0.91	0.868	0.952	0.91	0.868	0.952	CLONAL	2	TRUE	0	0.545424541713621	2		551	681	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206785	36206785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068981-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	253	560	0	ENST00000300305.3:c.727C>T	p.Pro243Ser	p.P243S	ENST00000300305		243	Cca/Tca	6/8	0.545424541713621	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.545424541713621	1		560	644	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968197	134968197	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs780597750	NA	P-0068981-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	190	485	0	ENST00000398015.3:c.2710G>T	p.Asp904Tyr	p.D904Y	ENST00000398015	NM_004441.4	904	Gac/Tac	15/16	0.448517322482008	1	FACETS	0.744	0.69	0.799	0.744	0.69	0.799	SUBCLONAL	1	TRUE	0	0.545424541713621	1		485	681	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241925	72241925	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068981-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	73	472	0	ENST00000357731.5:c.465C>A	p.Asn155Lys	p.N155K	ENST00000357731	NM_173808.2	155	aaC/aaA	3/7	0.322257981438657	1	FACETS	0.356	0.311	0.404	0.356	0.311	0.404	INDETERMINATE	1	TRUE	0	0.545424541713621	1		472	547	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46738376	46738376	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068981-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	127	494	0	ENST00000371975.4:c.1277G>C	p.Arg426Thr	p.R426T	ENST00000371975	NM_003579.3	426	aGg/aCg	12/18	0.322257981438657	1	FACETS	0.517	0.469	0.567	0.517	0.469	0.567	INDETERMINATE	1	TRUE	0	0.545424541713621	1		494	655	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599103	28599103	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068981-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	36	557	0	ENST00000253063.3:c.549G>C	p.Lys183Asn	p.K183N	ENST00000253063	NM_031459.4	183	aaG/aaC	5/10	0.322257981438657	1	FACETS	0.146	0.12	0.176	0.146	0.12	0.176	INDETERMINATE	1	TRUE	0	0.545424541713621	1		557	656	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs80338963	NA	P-0069033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	37	523	2	ENST00000342988.3:c.1081C>A	p.Arg361Ser	p.R361S	ENST00000342988	NM_005359.5	361	Cgc/Agc	9/12	0.238753849164965	1	FACETS	0.502	0.413	0.601	0.502	0.413	0.601	SUBCLONAL	1	TRUE	0	0.238753849164965	1		525	544	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867145	45867145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530045760	NA	P-0069033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	46	552	0	ENST00000391945.4:c.974C>T	p.Thr325Met	p.T325M	ENST00000391945	NM_000400.3	325	aCg/aTg	11/23	0.132271423260449	3	FACETS	0.592	0.498	0.698	0.296	0.249	0.349	INDETERMINATE	1	TRUE	1	0.238753849164965	3		552	728	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0069033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	132	362	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.178963782688422	3	FACETS	1	0.953	1	0.713	0.649	0.779	CLONAL	2	TRUE	0	0.238753849164965	3		362	579	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201692	66201692	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753118521	NA	P-0069033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	55	440	0	ENST00000273854.3:c.2810G>A	p.Arg937His	p.R937H	ENST00000273854	NM_004439.5	937	cGt/cAt	16/18	0.0898194570687165	3	FACETS	0.847	0.724	0.981	0.423	0.362	0.491	INDETERMINATE	1	TRUE	1	0.238753849164965	3		440	609	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57004279	57004279	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	A	A	G	rs753248942	NA	P-0069033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	54	568	0	ENST00000257254.3:c.200T>C	p.Phe67Ser	p.F67S	ENST00000257254		67	tTc/tCc	1/2	0.132271423260449	3	FACETS	0.65	0.554	0.756	0.325	0.277	0.378	INDETERMINATE	1	TRUE	1	0.238753849164965	3		568	779	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748303	41748303	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	89	444	0	ENST00000226382.2:c.466C>A	p.Gln156Lys	p.Q156K	ENST00000226382	NM_003924.3	156	Cag/Aag	3/3	0.0898194570687165	3	FACETS	1	0.977	1	0.719	0.639	0.805	INDETERMINATE	1	TRUE	1	0.238753849164965	3		444	580	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577599	7577600	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1567550002	NA	P-0069035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	54	346	0	ENST00000269305.4:c.681dup	p.Asp228Ter	p.D228*	ENST00000269305	NM_001126112.2	227	-/T	7/11	0.244123566543185	3	FACETS	0.84	0.718	0.973	0.42	0.359	0.487	CLONAL	1	TRUE	1	0.291858487117146	3		346	505	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624290	89624290	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660420	NA	P-0069035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	36	224	0	ENST00000371953.3:c.64G>T	p.Asp22Tyr	p.D22Y	ENST00000371953	NM_000314.4	22	Gac/Tac	1/9	0.26622620246614	1	FACETS	0.539	0.443	0.646	0.539	0.443	0.646	SUBCLONAL	1	TRUE	0	0.291858487117146	1		224	391	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962983	38962983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1292288715	NA	P-0069035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	52	302	1	ENST00000357387.3:c.1561C>T	p.Leu521Phe	p.L521F	ENST00000357387	NM_152756.3	521	Ctt/Ttt	17/38	0.244123566543185	3	FACETS	1	0.949	1	0.628	0.538	0.726	CLONAL	1	TRUE	1	0.291858487117146	3		303	325	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653838	89653838	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	38	263	0	ENST00000371953.3:c.136T>C	p.Tyr46His	p.Y46H	ENST00000371953	NM_000314.4	46	Tac/Cac	2/9	0.26622620246614	1	FACETS	0.603	0.499	0.718	0.603	0.499	0.718	SUBCLONAL	1	TRUE	0	0.291858487117146	1		263	369	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425853	49425853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772665565	NA	P-0069035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	73	525	0	ENST00000301067.7:c.12635G>A	p.Arg4212Gln	p.R4212Q	ENST00000301067	NM_003482.3	4212	cGg/cAg	39/54	0.162221089753713	4	FACETS	1	0.88	1	0.503	0.44	0.572	INDETERMINATE	1	TRUE	2	0.291858487117146	4		525	642	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27173298	27173298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753348341	NA	P-0069035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	59	395	0	ENST00000380036.4:c.839G>A	p.Cys280Tyr	p.C280Y	ENST00000380036	NM_000459.3	280	tGt/tAt	6/23	0.291858487117146	1	FACETS	0.921	0.796	1	0.921	0.796	1	CLONAL	1	TRUE	0	0.291858487117146	1		395	375	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172945	38172945	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	112	302	0	ENST00000317025.8:c.2104A>T	p.Thr702Ser	p.T702S	ENST00000317025	NM_023034.1	702	Act/Tct	11/24	0.177044469627671	4	FACETS	0.946	0.855	1			1	CLONAL	2	TRUE	NA	0.291858487117146	4		302	524	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239324	105239324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	93	563	0	ENST00000349310.3:c.1063G>A	p.Glu355Lys	p.E355K	ENST00000349310	NM_001014432.1	355	Gag/Aag	12/15	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.291858487117146	2		563	637	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498270	29498270	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	46	398	0	ENST00000389048.3:c.1910C>G	p.Thr637Ser	p.T637S	ENST00000389048	NM_004304.4	637	aCc/aGc	10/29	0.26622620246614	1	FACETS	0.537	0.452	0.631	0.537	0.452	0.631	SUBCLONAL	1	TRUE	0	0.291858487117146	1		398	501	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753028	128753028	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	146	407	0	ENST00000377970.2:c.1189C>G	p.Pro397Ala	p.P397A	ENST00000377970	NM_002467.4	397	Ccg/Gcg	3/3	0.162221089753713	4	FACETS	0.763	0.696	0.833	0.763	0.696	0.833	INDETERMINATE	2	TRUE	2	0.291858487117146	4		407	847	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570424	39570424	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	16	220	0	ENST00000262039.4:c.620G>A	p.Ser207Asn	p.S207N	ENST00000262039	NM_002647.2	207	aGt/aAt	6/25	0.26622620246614	1	FACETS	0.424	0.313	0.555	0.424	0.313	0.555	SUBCLONAL	1	TRUE	0	0.291858487117146	1		220	221	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434880	49434880	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	92	512	0	ENST00000301067.7:c.6673G>T	p.Glu2225Ter	p.E2225*	ENST00000301067	NM_003482.3	2225	Gaa/Taa	31/54	0.162221089753713	4	FACETS	1	0.925	1	0.527	0.468	0.59	INDETERMINATE	1	TRUE	2	0.291858487117146	4		512	773	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1253908	1253908	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1579541689	NA	P-0069035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	32	400	0	ENST00000310581.5:c.3334C>A	p.Leu1112Met	p.L1112M	ENST00000310581	NM_198253.2	1112	Ctg/Atg	16/16	1	2	FACETS	0.422	0.341	0.513	0.422	0.341	0.513	SUBCLONAL	1	TRUE	1	0.291858487117146	2		400	520	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124483003	124483003	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs767757297	NA	P-0069035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	16	278	0	ENST00000357628.3:c.1021C>A	p.Gln341Lys	p.Q341K	ENST00000357628	NM_015450.2	341	Cag/Aag	13/19	1	2	FACETS	0.414	0.306	0.543	0.414	0.306	0.543	SUBCLONAL	1	TRUE	1	0.291858487117146	2		278	265	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752944	128752944	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	157	384	0	ENST00000377970.2:c.1105G>T	p.Val369Phe	p.V369F	ENST00000377970	NM_002467.4	369	Gtc/Ttc	3/3	0.162221089753713	4	FACETS	0.794	0.728	0.864	0.794	0.728	0.864	INDETERMINATE	2	TRUE	2	0.291858487117146	4		384	875	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609034	43609034	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1249950304	NA	P-0069035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	69	532	0	ENST00000355710.3:c.1790G>A	p.Gly597Glu	p.G597E	ENST00000355710	NM_020975.4	597	gGg/gAg	10/20	0.26622620246614	1	FACETS	0.628	0.547	0.716	0.628	0.547	0.716	SUBCLONAL	1	TRUE	0	0.291858487117146	1		532	643	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752927	128752927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	153	371	0	ENST00000377970.2:c.1088C>T	p.Ser363Leu	p.S363L	ENST00000377970	NM_002467.4	363	tCg/tTg	3/3	0.162221089753713	4	FACETS	0.814	0.745	0.886	0.814	0.745	0.886	INDETERMINATE	2	TRUE	2	0.291858487117146	4		371	832	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0069389-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	38	317	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.239057583776994	3	FACETS	1	0.838	1	0.506	0.419	0.602	CLONAL	1	TRUE	1	0.239057583776994	3		317	352	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670325	134670325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069389-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	40	0	0	ENST00000398015.3:c.236G>A	p.Arg79Gln	p.R79Q	ENST00000398015	NM_004441.4	79	cGg/cAg	3/16	1	2	FACETS	0.48	0.398	0.572	0.48	0.398	0.572	SUBCLONAL	1	TRUE	1	0.239057583776994	2		0	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578499	7578499	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs786203071	NA	P-0069389-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	105	556	0	ENST00000269305.4:c.431A>C	p.Gln144Pro	p.Q144P	ENST00000269305	NM_001126112.2	144	cAg/cCg	5/11	0.181805857954519	3	FACETS	1	0.979	1	0.687	0.616	0.762	CLONAL	1	TRUE	1	0.239057583776994	3		556	716	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106730	27106730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773818181	NA	P-0069389-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	159	594	1	ENST00000324856.7:c.6341C>T	p.Pro2114Leu	p.P2114L	ENST00000324856	NM_006015.4	2114	cCg/cTg	20/20	0.180576607313963	2	FACETS	0.883	0.811	0.958	0.883	0.811	0.958	CLONAL	2	TRUE	0	0.239057583776994	2		595	753	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970981	21970981	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs104894098	NA	P-0069389-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	144	587	0	ENST00000304494.5:c.377T>A	p.Val126Asp	p.V126D	ENST00000304494	NM_000077.4	126	gTc/gAc	2/3	0.188050272485337	2	FACETS	0.845	0.772	0.921	0.845	0.772	0.921	CLONAL	2	TRUE	0	0.239057583776994	2		587	713	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0069389-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	100	421	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	0.239057583776994	3	FACETS	0.765	0.685	0.85	0.765	0.685	0.85	SUBCLONAL	2	TRUE	1	0.239057583776994	3		421	612	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250323	110250323	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069389-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	117	511	0	ENST00000374672.4:c.352G>T	p.Glu118Ter	p.E118*	ENST00000374672	NM_004235.4	118	Gag/Tag	3/5	0.188050272485337	2	FACETS	0.766	0.692	0.844	0.766	0.692	0.844	SUBCLONAL	2	TRUE	0	0.239057583776994	2		511	639	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041678	47041678	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069389-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	99	0	0	ENST00000377604.3:c.1903G>T	p.Glu635Ter	p.E635*	ENST00000377604	NM_001204468.1	635	Gag/Tag	17/24	0.239057583776994	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.239057583776994	1		0	685	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471070	25471070	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069396-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	91	343	0	ENST00000264709.3:c.691C>T	p.Gln231Ter	p.Q231*	ENST00000264709	NM_175629.2	231	Cag/Tag	7/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		343	516	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0069397-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	12	310	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	0.721	0.505	0.988	0.721	0.505	0.988	CLONAL	1	TRUE	1	0.1	2		310	333	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0069397-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	27	530	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.812	0.644	1	0.812	0.644	1	CLONAL	1	TRUE	1	0.1	2		530	665	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913396	NA	P-0069397-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	18	318	0	ENST00000349496.5:c.95A>G	p.Asp32Gly	p.D32G	ENST00000349496	NM_001904.3	32	gAc/gGc	3/15	1	2	FACETS	0.69	0.517	0.895	0.69	0.517	0.895	SUBCLONAL	1	TRUE	1	0.1	2		318	522	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685307	89685307	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123317	NA	P-0069398-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	97	251	0	ENST00000371953.3:c.202T>C	p.Tyr68His	p.Y68H	ENST00000371953	NM_000314.4	68	Tac/Cac	3/9	0.233608476861244	2	FACETS	1	0.976	1	0.65	0.583	0.719	CLONAL	1	TRUE	0	0.38	2		251	393	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0069398-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	128	300	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.110910291477732	3	FACETS	0.893	0.815	0.973	0.893	0.815	0.973	INDETERMINATE	2	TRUE	1	0.38	3		300	449	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176594	56176594	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069398-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	90	349	0	ENST00000399503.3:c.2144G>C	p.Gly715Ala	p.G715A	ENST00000399503	NM_005921.1	715	gGa/gCa	12/20	1	2	FACETS	0.88	0.783	0.984	0.88	0.783	0.984	CLONAL	1	TRUE	1	0.38	2		349	538	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426893	6426893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519948	NA	P-0069399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	16	279	0	ENST00000356142.4:c.86C>T	p.Pro29Leu	p.P29L	ENST00000356142	NM_018890.3	29	cCt/cTt	2/7	0.3	4	FACETS	0.454	0.333	0.599			1	SUBCLONAL	1	TRUE	NA	0.11	4		279	712	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363547	40363547	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1317819335	NA	P-0069399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	42	400	0	ENST00000397332.2:c.682C>T	p.Pro228Ser	p.P228S	ENST00000397332	NM_001033082.2	228	Ccc/Tcc	3/3	0.109816401290066	3	FACETS	1	0.876	1	0.531	0.442	0.631	CLONAL	1	TRUE	1	0.11	3		400	758	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944944	31944944	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144139961	NA	P-0069399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	23	223	0	ENST00000340398.3:c.157C>T	p.Arg53Cys	p.R53C	ENST00000340398	NM_001013699.2	53	Cgt/Tgt	1/1	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.11	2		223	391	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649519	48649519	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0069399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	13	340	0	ENST00000376670.3:c.3G>A	p.Met1?	p.M1?	ENST00000376670	NM_002049.3	1	atG/atA	2/6	1	2	FACETS	0.411	0.291	0.558	0.411	0.291	0.558	SUBCLONAL	1	TRUE	1	0.11	2		340	575	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136836	69136836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	27	301	0	ENST00000288368.4:c.4750G>A	p.Asp1584Asn	p.D1584N	ENST00000288368	NM_024870.2	1584	Gac/Aac	39/40	1	2	FACETS	0.953	0.757	1	0.953	0.757	1	CLONAL	1	TRUE	1	0.11	2		301	515	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0069400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	98	382	0				ENST00000310581	NM_198253.2	-/1132			0.202901173660132	5	FACETS	1	0.973	1	0.818	0.739	0.9	INDETERMINATE	2	TRUE	2	0.440594428084455	5		382	301	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0069400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	158	527	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	0.440594428084455	4	FACETS	0.909	0.844	0.975	0.909	0.844	0.975	CLONAL	3	TRUE	1	0.440594428084455	4		527	379	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293050	91293050	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	30	482	0	ENST00000355112.3:c.552G>C	p.Gln184His	p.Q184H	ENST00000355112	NM_000057.2	184	caG/caC	3/22	0.141228942843376	4	FACETS	0.49	0.395	0.599	0.245	0.197	0.3	INDETERMINATE	1	TRUE	2	0.440594428084455	4		482	400	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50488224	50488224	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	111	363	0	ENST00000394963.4:c.1138G>C	p.Asp380His	p.D380H	ENST00000394963	NM_003076.4	380	Gac/Cac	10/13	0.202901173660132	5	FACETS	1	0.958	1	0.732	0.664	0.803	INDETERMINATE	2	TRUE	2	0.440594428084455	5		363	381	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61729133	61729133	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	32	294	0	ENST00000401558.2:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000401558	NM_003400.3	136	Cag/Tag	6/25	0.440594428084455	6	FACETS	0.641	0.52	0.778	0.214	0.173	0.26	SUBCLONAL	1	TRUE	3	0.440594428084455	6		294	426	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965437	25965437	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	80	450	0	ENST00000435504.4:c.3769G>C	p.Asp1257His	p.D1257H	ENST00000435504		1257	Gat/Cat	13/13	0.392305727814241	5	FACETS	0.925	0.815	1	0.308	0.271	0.348	CLONAL	1	TRUE	2	0.440594428084455	5		450	652	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431634	6431634	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	102	209	0	ENST00000356142.4:c.187G>A	p.Asp63Asn	p.D63N	ENST00000356142	NM_018890.3	63	Gat/Aat	3/7	0.440594428084455	5	FACETS	0.956	0.869	1	0.956	0.869	1	CLONAL	3	TRUE	2	0.440594428084455	5		209	268	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483267	120483267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	70	463	0	ENST00000256646.2:c.3094C>T	p.His1032Tyr	p.H1032Y	ENST00000256646	NM_024408.3	1032	Cat/Tat	19/34	0.330405445539718	5	FACETS	0.902	0.787	1	0.301	0.262	0.342	CLONAL	1	TRUE	2	0.440594428084455	5		463	585	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929235	44929235	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	173	199	1	ENST00000377967.4:c.2335C>T	p.Gln779Ter	p.Q779*	ENST00000377967	NM_021140.2	779	Cag/Tag	17/29	0.416919052560558	2	FACETS	1	0.981	1			1	CLONAL	3	TRUE	NA	0.440594428084455	2		200	245	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576911	7576912	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0069400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	306	505	0	ENST00000269305.4:c.934_935del	p.Thr312GlnfsTer24	p.T312Qfs*24	ENST00000269305	NM_001126112.2	312	ACc/c	9/11	0.433684396686924	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	4	TRUE	0	0.440594428084455	4		505	483	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950665	79950665	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	41	427	0	ENST00000265081.6:c.119C>T	p.Ser40Phe	p.S40F	ENST00000265081	NM_002439.4	40	tCc/tTc	1/24	0.294739336332027	3	FACETS	0.695	0.581	0.82	0.347	0.29	0.41	SUBCLONAL	1	TRUE	1	0.440594428084455	3		427	327	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293231	91293231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772711706	NA	P-0069400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	34	480	0	ENST00000355112.3:c.733G>A	p.Glu245Lys	p.E245K	ENST00000355112	NM_000057.2	245	Gaa/Aaa	3/22	0.141228942843376	4	FACETS	0.633	0.518	0.762	0.317	0.259	0.381	INDETERMINATE	1	TRUE	2	0.440594428084455	4		480	351	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495772	56495772	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	101	428	0	ENST00000267101.3:c.3962C>G	p.Ser1321Cys	p.S1321C	ENST00000267101	NM_001982.3	1321	tCt/tGt	28/28	0.202901173660132	5	FACETS	0.966	0.87	1	0.644	0.58	0.711	INDETERMINATE	2	TRUE	2	0.440594428084455	5		428	394	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195692	123195692	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	30	145	0	ENST00000218089.9:c.1606C>T	p.His536Tyr	p.H536Y	ENST00000218089	NM_001042749.1	536	Cat/Tat	17/35	0.440594428084455	2	FACETS	0.946	0.773	1			1	CLONAL	1	TRUE	NA	0.440594428084455	2		145	144	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913085	44913085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	42	174	0	ENST00000377967.4:c.760C>T	p.His254Tyr	p.H254Y	ENST00000377967	NM_021140.2	254	Cac/Tac	10/29	0.416919052560558	2	FACETS	0.978	0.826	1			1	CLONAL	1	TRUE	NA	0.440594428084455	2		174	195	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875058	151875058	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0069400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	45	293	0	ENST00000262189.6:c.7480del	p.Ser2494ValfsTer21	p.S2494Vfs*21	ENST00000262189	NM_170606.2	2494	Agt/gt	38/59	0.202901173660132	5	FACETS	0.9	0.758	1	0.3	0.252	0.352	INDETERMINATE	1	TRUE	2	0.440594428084455	5		293	377	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374292	15374292	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	48	428	0	ENST00000263377.2:c.1280C>G	p.Ser427Cys	p.S427C	ENST00000263377	NM_058243.2	427	tCc/tGc	7/20	0.440594428084455	3	FACETS	0.649	0.549	0.757	0.324	0.274	0.379	SUBCLONAL	1	TRUE	1	0.440594428084455	3		428	410	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464875	120464875	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	29	419	0	ENST00000256646.2:c.5197G>C	p.Asp1733His	p.D1733H	ENST00000256646	NM_024408.3	1733	Gat/Cat	28/34	0.330405445539718	5	FACETS	0.463	0.371	0.568	0.154	0.123	0.19	SUBCLONAL	1	TRUE	2	0.440594428084455	5		419	472	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647087	23647087	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	35	461	0	ENST00000261584.4:c.780G>C	p.Gln260His	p.Q260H	ENST00000261584	NM_024675.3	260	caG/caC	4/13	0.180772423670155	5	FACETS	0.54	0.442	0.65	0.18	0.147	0.217	INDETERMINATE	1	TRUE	2	0.440594428084455	5		461	489	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858394	9858394	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	56	442	0	ENST00000330684.3:c.3007G>C	p.Glu1003Gln	p.E1003Q	ENST00000330684	NM_001134407.1	1003	Gaa/Caa	13/13	0.180772423670155	5	FACETS	0.955	0.82	1	0.318	0.273	0.368	INDETERMINATE	1	TRUE	2	0.440594428084455	5		442	442	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740776	145740776	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	51	506	0	ENST00000428558.2:c.1324G>C	p.Glu442Gln	p.E442Q	ENST00000428558	NM_004260.3	442	Gag/Cag	7/22	0.440594428084455	6	FACETS	0.578	0.49	0.675	0.116	0.098	0.135	SUBCLONAL	1	TRUE	1	0.440594428084455	6		506	754	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495837	56496346	+	stop_retained_variant,3_prime_UTR_variant	Silent	DEL	TAACTCCTGCTCCCTGTGGCACTCAGGGAGCATTTAATGGCAGCTAGTGCCTTTAGAGGGTACCGTCTTCTCCCTATTCCCTCTCTCTCCCAGGTCCCAGCCCCTTTTCCCCAGTCCCAGACAATTCCATTCAATCTTTGGAGGCTTTTAAACATTTTGACACAAAATTCTTATGGTATGTAGCCAGCTGTGCACTTTCTTCTCTTTCCCAACCCCAGGAAAGGTTTTCCTTATTTTGTGTGCTTTCCCAGTCCCATTCCTCAGCTTCTTCACAGGCACTCCTGGAGATATGAAGGATTACTCTCCATATCCCTTCCTCTCAGGCTCTTGACTACTTGGAACTAGGCTCTTATGTGTGCCTTTGTTTCCCATCAGACTGTCAAGAAGAGGAAAGGGAGGAAACCTAGCAGAGGAAAGTGTAATTTTGGTTTATGACTCTTAACCCCCTAGAAAGACAGAAGCTTAAAATCTGTGAAGAAAGAGGTTAGGAGTAGATATTGATTACTATCA	TAACTCCTGCTCCCTGTGGCACTCAGGGAGCATTTAATGGCAGCTAGTGCCTTTAGAGGGTACCGTCTTCTCCCTATTCCCTCTCTCTCCCAGGTCCCAGCCCCTTTTCCCCAGTCCCAGACAATTCCATTCAATCTTTGGAGGCTTTTAAACATTTTGACACAAAATTCTTATGGTATGTAGCCAGCTGTGCACTTTCTTCTCTTTCCCAACCCCAGGAAAGGTTTTCCTTATTTTGTGTGCTTTCCCAGTCCCATTCCTCAGCTTCTTCACAGGCACTCCTGGAGATATGAAGGATTACTCTCCATATCCCTTCCTCTCAGGCTCTTGACTACTTGGAACTAGGCTCTTATGTGTGCCTTTGTTTCCCATCAGACTGTCAAGAAGAGGAAAGGGAGGAAACCTAGCAGAGGAAAGTGTAATTTTGGTTTATGACTCTTAACCCCCTAGAAAGACAGAAGCTTAAAATCTGTGAAGAAAGAGGTTAGGAGTAGATATTGATTACTATCA	-	novel	NA	P-0069400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	78	342	0	ENST00000267101.3:c.*1_*510del			ENST00000267101	NM_001982.3	1343		28/28	0.202901173660132	5	FACETS	0.98	0.87	1	0.653	0.58	0.731	INDETERMINATE	2	TRUE	2	0.440594428084455	5		342	300	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097233	11097233	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555753773	NA	P-0069400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	110	475	0	ENST00000358026.2:c.724C>T	p.Pro242Ser	p.P242S	ENST00000358026	NM_001128849.1	242	Ccc/Tcc	4/36	0.440594428084455	3	FACETS	0.783	0.71	0.86	0.783	0.71	0.86	SUBCLONAL	2	TRUE	1	0.440594428084455	3		475	389	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952045	178952045	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	171	380	0	ENST00000263967.3:c.3100G>C	p.Glu1034Gln	p.E1034Q	ENST00000263967	NM_006218.2	1034	Gag/Cag	21/21	0.440594428084455	4	FACETS	0.976	0.91	1	0.976	0.91	1	CLONAL	3	TRUE	1	0.440594428084455	4		380	382	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495576	56495576	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	119	543	0	ENST00000267101.3:c.3766C>G	p.Pro1256Ala	p.P1256A	ENST00000267101	NM_001982.3	1256	Cca/Gca	28/28	0.202901173660132	5	FACETS	0.819	0.742	0.899	0.546	0.494	0.6	INDETERMINATE	2	TRUE	2	0.440594428084455	5		543	548	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914935	32914935	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	102	421	0	ENST00000380152.3:c.6443C>G	p.Ser2148Cys	p.S2148C	ENST00000380152		2148	tCt/tGt	11/27	0.383481011596944	3	FACETS	0.971	0.881	1	0.971	0.881	1	CLONAL	2	TRUE	1	0.440594428084455	3		421	291	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224604	108224604	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	80	341	0	ENST00000278616.4:c.8783G>C	p.Arg2928Thr	p.R2928T	ENST00000278616	NM_000051.3	2928	aGa/aCa	60/63	0.362306375084992	4	FACETS	1	0.967	1	0.423	0.374	0.475	CLONAL	1	TRUE	1	0.440594428084455	4		341	412	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221325	1221325	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	50	556	0	ENST00000326873.7:c.848C>G	p.Ser283Cys	p.S283C	ENST00000326873	NM_000455.4	283	tCt/tGt	6/10	0.294739336332027	3	FACETS	0.653	0.555	0.76	0.327	0.277	0.38	SUBCLONAL	1	TRUE	1	0.440594428084455	3		556	424	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279744	46279744	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763852130	NA	P-0069400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	51	419	0	ENST00000371998.3:c.3670C>A	p.Gln1224Lys	p.Q1224K	ENST00000371998		1224	Caa/Aaa	20/23	0.392305727814241	5	FACETS	0.706	0.599	0.822	0.235	0.199	0.274	SUBCLONAL	1	TRUE	2	0.440594428084455	5		419	545	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288818	11288818	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	62	475	0	ENST00000361445.4:c.2937C>G	p.Phe979Leu	p.F979L	ENST00000361445	NM_004958.3	979	ttC/ttG	19/58	0.440594428084455	3	FACETS	0.753	0.652	0.862	0.377	0.326	0.431	SUBCLONAL	1	TRUE	1	0.440594428084455	3		475	456	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162107	38162107	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	107	369	0	ENST00000317025.8:c.2609G>A	p.Arg870Lys	p.R870K	ENST00000317025	NM_023034.1	870	aGa/aAa	14/24	0.141228942843376	4	FACETS	0.946	0.856	1	0.946	0.856	1	INDETERMINATE	2	TRUE	2	0.440594428084455	4		369	370	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339981	70339981	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	84	180	0	ENST00000374080.3:c.514G>C	p.Glu172Gln	p.E172Q	ENST00000374080		172	Gag/Cag	4/45	0.440594428084455	2	FACETS	0.875	0.787	0.964			1	CLONAL	2	TRUE	NA	0.440594428084455	2		180	218	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099296	157099296	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752961325	NA	P-0069400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	147	479	0	ENST00000346085.5:c.233C>T	p.Ala78Val	p.A78V	ENST00000346085	NM_020732.3	78	gCg/gTg	1/20	0.249212878030975	2	FACETS	0.828	0.764	0.893	0.828	0.764	0.893	INDETERMINATE	2	TRUE	0	0.440594428084455	2		479	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0069401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	467	458	0	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.664719557372823	2	FACETS	0.941	0.91	0.971	0.941	0.91	0.971	CLONAL	2	TRUE	0	0.69146117014585	2		458	718	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480514	123480514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	213	314	0	ENST00000371139.4:c.22C>T	p.His8Tyr	p.H8Y	ENST00000371139	NM_001114937.2	8	Cat/Tat	1/4	0.338998238448697	4	FACETS	0.762	0.711	0.814	0.762	0.711	0.814	INDETERMINATE	2	TRUE	2	0.69146117014585	4		314	684	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026740	48026740	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs201996928	NA	P-0069401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	180	383	0	ENST00000234420.5:c.1618C>G	p.Leu540Val	p.L540V	ENST00000234420	NM_000179.2	540	Ctt/Gtt	4/10	0.578970452294203	4	FACETS	0.779	0.723	0.837	0.779	0.723	0.837	SUBCLONAL	2	TRUE	2	0.69146117014585	4		383	565	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593411	215593411	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	65	328	0	ENST00000260947.4:c.2323C>G	p.Leu775Val	p.L775V	ENST00000260947	NM_000465.2	775	Ctt/Gtt	11/11	0.578970452294203	4	FACETS	0.649	0.564	0.741	0.324	0.282	0.371	SUBCLONAL	1	TRUE	2	0.69146117014585	4		328	490	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877996	151877996	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	55	435	0	ENST00000262189.6:c.6949C>G	p.Gln2317Glu	p.Q2317E	ENST00000262189	NM_170606.2	2317	Caa/Gaa	36/59	0.338998238448697	4	FACETS	0.35	0.298	0.406	0.175	0.149	0.203	INDETERMINATE	1	TRUE	2	0.69146117014585	4		435	769	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11204740	11204740	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1349787033	NA	P-0069401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	268	348	0	ENST00000361445.4:c.4837G>A	p.Glu1613Lys	p.E1613K	ENST00000361445	NM_004958.3	1613	Gag/Aag	34/58	0.69146117014585	3	FACETS	1	0.988	1	0.398	0.374	0.423	CLONAL	1	TRUE	0	0.69146117014585	3		348	873	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346846	91346846	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	25	298	0	ENST00000355112.3:c.3454G>C	p.Asp1152His	p.D1152H	ENST00000355112	NM_000057.2	1152	Gac/Cac	18/22	0.612309300576149	6	FACETS	0.404	0.317	0.503	0.101	0.079	0.126	SUBCLONAL	1	TRUE	2	0.69146117014585	6		298	427	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317043	11317043	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	91	461	0	ENST00000361445.4:c.451C>T	p.Arg151Ter	p.R151*	ENST00000361445	NM_004958.3	151	Cga/Tga	4/58	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.322184812829091	2		461	440	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256435	16256435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199763346	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	74	531	0	ENST00000375759.3:c.3700G>A	p.Asp1234Asn	p.D1234N	ENST00000375759	NM_015001.2	1234	Gat/Aat	11/15	1	2	FACETS	0.855	0.75	0.968	0.855	0.75	0.968	CLONAL	1	TRUE	1	0.322184812829091	2		531	537	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258605	16258605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779248361	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	72	529	0	ENST00000375759.3:c.5870G>A	p.Arg1957His	p.R1957H	ENST00000375759	NM_015001.2	1957	cGc/cAc	11/15	1	2	FACETS	0.925	0.811	1	0.925	0.811	1	CLONAL	1	TRUE	1	0.322184812829091	2		529	483	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932352	36932352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776535279	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	98	522	0	ENST00000361632.4:c.2117C>T	p.Pro706Leu	p.P706L	ENST00000361632		706	cCg/cTg	16/16	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.322184812829091	2		522	519	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36940987	36940987	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs928090621	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	63	407	0	ENST00000361632.4:c.352C>T	p.Arg118Cys	p.R118C	ENST00000361632		118	Cgc/Tgc	3/16	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.322184812829091	2		407	372	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531852	46531852	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	65	311	0	ENST00000262741.5:c.496-1G>T		p.X166_splice	ENST00000262741	NM_003629.3	166			1	2	FACETS	0.797	0.692	0.911	0.797	0.692	0.911	CLONAL	1	TRUE	1	0.322184812829091	2		311	506	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310506	65310506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	73	494	0	ENST00000342505.4:c.2182G>A	p.Asp728Asn	p.D728N	ENST00000342505	NM_002227.2	728	Gac/Aac	16/25	1	2	FACETS	0.958	0.84	1	0.958	0.84	1	CLONAL	1	TRUE	1	0.322184812829091	2		494	473	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120496243	120496243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782306821	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	57	447	0	ENST00000256646.2:c.2288C>T	p.Ser763Leu	p.S763L	ENST00000256646	NM_024408.3	763	tCg/tTg	14/34	1	2	FACETS	0.618	0.53	0.713	0.618	0.53	0.713	SUBCLONAL	1	TRUE	1	0.322184812829091	2		447	573	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161298226	161298226	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs978019587	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	55	293	0	ENST00000367975.2:c.118C>T	p.Arg40Trp	p.R40W	ENST00000367975	NM_003001.3	40	Cgg/Tgg	3/6	0.322184812829091	2	FACETS	0.785	0.673	0.907	0.392	0.336	0.454	CLONAL	1	TRUE	0	0.322184812829091	2		293	435	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725039	162725039	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778072557	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	77	477	2	ENST00000367921.3:c.511G>A	p.Asp171Asn	p.D171N	ENST00000367921	NM_006182.2	171	Gac/Aac	6/18	0.322184812829091	2	FACETS	1	0.923	1	0.531	0.468	0.599	CLONAL	1	TRUE	0	0.322184812829091	2		479	450	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740216	162740216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775098890	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	99	475	0	ENST00000367921.3:c.1418G>A	p.Arg473His	p.R473H	ENST00000367921	NM_006182.2	473	cGc/cAc	12/18	0.322184812829091	2	FACETS	1	0.956	1	0.563	0.504	0.625	CLONAL	1	TRUE	0	0.322184812829091	2		475	546	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163297332	163297332	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1292835761	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	38	298	0	ENST00000271452.3:c.178C>T	p.Arg60Ter	p.R60*	ENST00000271452	NM_145697.2	60	Cga/Tga	3/14	0.322184812829091	2	FACETS	0.545	0.45	0.65	0.272	0.225	0.325	SUBCLONAL	1	TRUE	0	0.322184812829091	2		298	433	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091356	193091356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	132	440	0	ENST00000367435.3:c.26G>A	p.Arg9Gln	p.R9Q	ENST00000367435	NM_024529.4	9	cGa/cAa	1/17	0.322184812829091	2	FACETS	1	0.986	1	0.74	0.674	0.808	CLONAL	1	TRUE	0	0.322184812829091	2		440	554	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099338	193099338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	57	349	0	ENST00000367435.3:c.272G>A	p.Arg91Gln	p.R91Q	ENST00000367435	NM_024529.4	91	cGa/cAa	3/17	0.322184812829091	2	FACETS	0.783	0.673	0.902	0.391	0.336	0.451	CLONAL	1	TRUE	0	0.322184812829091	2		349	452	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567661	226567661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs183533639	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	65	454	0	ENST00000366794.5:c.1505C>T	p.Ala502Val	p.A502V	ENST00000366794	NM_001618.3	502	gCg/gTg	10/23	0.322184812829091	2	FACETS	0.984	0.857	1	0.492	0.428	0.561	CLONAL	1	TRUE	0	0.322184812829091	2		454	410	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663891	241663891	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	26	186	1	ENST00000366560.3:c.1237-1G>T		p.X413_splice	ENST00000366560	NM_000143.3	413			0.322184812829091	2	FACETS	0.711	0.566	0.876	0.356	0.283	0.438	SUBCLONAL	1	TRUE	0	0.322184812829091	2		187	227	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800978	243800978	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	45	382	0	ENST00000263826.5:c.496C>T	p.Arg166Ter	p.R166*	ENST00000263826	NM_005465.4	166	Cga/Tga	5/13	0.322184812829091	2	FACETS	0.558	0.468	0.656	0.279	0.234	0.328	SUBCLONAL	1	TRUE	0	0.322184812829091	2		382	501	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246518359	246518359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746219350	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	38	352	0	ENST00000388985.4:c.202G>A	p.Ala68Thr	p.A68T	ENST00000388985		68	Gcc/Acc	2/12	NA	2	FACETS	0.581	0.481	0.693			1	INDETERMINATE	1	TRUE	NA	0.322184812829091	2		352	406	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111532	8111532	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	81	376	0	ENST00000346208.3:c.1018G>A	p.Ala340Thr	p.A340T	ENST00000346208		340	Gcc/Acc	5/6	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.322184812829091	2		376	397	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622039	43622039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1371891301	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	51	419	0	ENST00000355710.3:c.3056C>T	p.Ala1019Val	p.A1019V	ENST00000355710	NM_020975.4	1019	gCg/gTg	19/20	1	2	FACETS	0.846	0.722	0.982	0.846	0.722	0.982	CLONAL	1	TRUE	1	0.322184812829091	2		419	374	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333858	70333858	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	71	493	0	ENST00000373644.4:c.1763G>T	p.Arg588Ile	p.R588I	ENST00000373644	NM_030625.2	588	aGa/aTa	2/12	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.322184812829091	2		493	405	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681434	88681434	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782496	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	44	246	0	ENST00000372037.3:c.1324C>T	p.Arg442Cys	p.R442C	ENST00000372037	NM_004329.2	442	Cgt/Tgt	11/13	1	2	FACETS	0.955	0.806	1	0.955	0.806	1	CLONAL	1	TRUE	1	0.322184812829091	2		246	286	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	64	506	0	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.322184812829091	2		506	393	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127996	64127996	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	93	479	0	ENST00000334205.4:c.394T>C	p.Tyr132His	p.Y132H	ENST00000334205	NM_003942.2	132	Tac/Cac	4/17	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.322184812829091	2		479	431	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989562	85989562	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs767548896	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	50	277	0	ENST00000263360.6:c.1321C>T	p.Arg441Ter	p.R441*	ENST00000263360	NM_003797.3	441	Cga/Tga	12/12	1	2	FACETS	0.828	0.705	0.962	0.828	0.705	0.962	CLONAL	1	TRUE	1	0.322184812829091	2		277	375	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917635	94917635	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	49	397	0	ENST00000536441.1:c.886G>T	p.Glu296Ter	p.E296*	ENST00000536441	NM_144665.3	296	Gaa/Taa	6/10	1	2	FACETS	0.591	0.5	0.69	0.591	0.5	0.69	SUBCLONAL	1	TRUE	1	0.322184812829091	2		397	515	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984923	101984923	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587777249	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	70	327	0	ENST00000282441.5:c.370C>T	p.Arg124Ter	p.R124*	ENST00000282441	NM_001130145.2	124	Cga/Tga	2/9	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.322184812829091	2		327	351	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435524	18435524	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1009436030	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	58	435	0	ENST00000266497.5:c.509G>A	p.Gly170Glu	p.G170E	ENST00000266497		170	gGa/gAa	1/31	0.244905330782248	1	FACETS	0.604	0.519	0.696	0.604	0.519	0.696	SUBCLONAL	1	TRUE	0	0.322184812829091	1		435	500	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443863	18443863	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774001673	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	49	357	0	ENST00000266497.5:c.836C>T	p.Pro279Leu	p.P279L	ENST00000266497		279	cCg/cTg	3/31	0.244905330782248	1	FACETS	0.622	0.528	0.726	0.622	0.528	0.726	SUBCLONAL	1	TRUE	0	0.322184812829091	1		357	410	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699296	18699296	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	31	354	0	ENST00000266497.5:c.3397G>T	p.Asp1133Tyr	p.D1133Y	ENST00000266497		1133	Gac/Tac	24/31	0.244905330782248	1	FACETS	0.416	0.336	0.506	0.416	0.336	0.506	SUBCLONAL	1	TRUE	0	0.322184812829091	1		354	388	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438192	49438192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	64	401	0	ENST00000301067.7:c.5077C>T	p.Arg1693Trp	p.R1693W	ENST00000301067	NM_003482.3	1693	Cgg/Tgg	20/54	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.322184812829091	2		401	362	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445934	49445934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	101	593	0	ENST00000301067.7:c.1532C>T	p.Pro511Leu	p.P511L	ENST00000301067	NM_003482.3	511	cCt/cTt	10/54	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.322184812829091	2		593	594	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490366	56490366	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	54	458	0	ENST00000267101.3:c.2135T>G	p.Leu712Arg	p.L712R	ENST00000267101	NM_001982.3	712	cTt/cGt	18/28	1	2	FACETS	0.769	0.658	0.89	0.769	0.658	0.89	SUBCLONAL	1	TRUE	1	0.322184812829091	2		458	436	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864148	57864148	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766159479	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	68	537	1	ENST00000228682.2:c.1625G>A	p.Arg542His	p.R542H	ENST00000228682	NM_005269.2	542	cGc/cAc	12/12	1	2	FACETS	0.879	0.767	1	0.879	0.767	1	CLONAL	1	TRUE	1	0.322184812829091	2		538	480	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891035	112891035	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs755619262	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	103	312	0	ENST00000351677.2:c.369G>T	p.Glu123Asp	p.E123D	ENST00000351677	NM_002834.3	123	gaG/gaT	4/16	1	2	FACETS	0.805	0.726	0.888	1	0.985	1	CLONAL	2	TRUE	1	0.322184812829091	2		312	397	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112569	115112569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180836314	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	100	460	1	ENST00000257566.3:c.1171G>A	p.Asp391Asn	p.D391N	ENST00000257566	NM_016569.3	391	Gac/Aac	7/8	1	2	FACETS	0.766	0.689	0.847	1	0.983	1	SUBCLONAL	2	TRUE	1	0.322184812829091	2		461	405	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800928	120800928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1337094477	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	67	422	0	ENST00000257552.2:c.320G>A	p.Arg107Gln	p.R107Q	ENST00000257552	NM_002442.3	107	cGa/cAa	6/15	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.322184812829091	2		422	375	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218928	133218928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500823	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	84	498	0	ENST00000320574.5:c.5008G>A	p.Asp1670Asn	p.D1670N	ENST00000320574	NM_006231.2	1670	Gac/Aac	38/49	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.322184812829091	2		498	414	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245468	133245468	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377657524	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	76	507	0	ENST00000320574.5:c.1852G>A	p.Glu618Lys	p.E618K	ENST00000320574	NM_006231.2	618	Gag/Aag	17/49	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.322184812829091	2		507	406	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	51	476	0	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	1	2	FACETS	0.897	0.765	1	0.897	0.765	1	CLONAL	1	TRUE	1	0.322184812829091	2		476	353	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555725	21555725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778450722	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	52	475	0	ENST00000382592.4:c.2545C>T	p.Arg849Trp	p.R849W	ENST00000382592	NM_014572.2	849	Cgg/Tgg	6/8	1	2	FACETS	0.767	0.654	0.89	0.767	0.654	0.89	SUBCLONAL	1	TRUE	1	0.322184812829091	2		475	421	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959351	26959351	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	70	305	0	ENST00000381527.3:c.518A>G	p.Asp173Gly	p.D173G	ENST00000381527	NM_001260.1	173	gAc/gGc	6/13	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.322184812829091	2		305	393	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005419	29005419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55687105	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	86	395	0	ENST00000282397.4:c.842G>A	p.Arg281Gln	p.R281Q	ENST00000282397	NM_002019.4	281	cGa/cAa	7/30	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.322184812829091	NA		395	476	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941649	48941649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760787104	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	45	236	0	ENST00000267163.4:c.959G>A	p.Arg320Gln	p.R320Q	ENST00000267163	NM_000321.2	320	cGa/cAa	10/27	1	2	FACETS	0.735	0.619	0.862	0.735	0.619	0.862	SUBCLONAL	1	TRUE	1	0.322184812829091	2		236	380	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942686	48942686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767011440	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	41	306	0	ENST00000267163.4:c.1073G>A	p.Arg358Gln	p.R358Q	ENST00000267163	NM_000321.2	358	cGa/cAa	11/27	1	2	FACETS	0.603	0.503	0.714	0.603	0.503	0.714	SUBCLONAL	1	TRUE	1	0.322184812829091	2		306	422	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347916	73347916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139907646	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	127	340	0	ENST00000377767.4:c.1145G>A	p.Arg382Gln	p.R382Q	ENST00000377767	NM_014953.3	382	cGa/cAa	8/21	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.322184812829091	2		340	534	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514595	103514595	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs966111552	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	70	469	0	ENST00000355739.4:c.1096C>T	p.Arg366Ter	p.R366*	ENST00000355739	NM_000123.3	366	Cga/Tga	8/15	1	2	FACETS	0.887	0.775	1	0.887	0.775	1	CLONAL	1	TRUE	1	0.322184812829091	2		469	490	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515433	103515433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs189280373	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	56	320	0	ENST00000355739.4:c.1934C>T	p.Ser645Leu	p.S645L	ENST00000355739	NM_000123.3	645	tCg/tTg	8/15	1	2	FACETS	0.976	0.841	1	0.976	0.841	1	CLONAL	1	TRUE	1	0.322184812829091	2		320	356	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518106	103518106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759972289	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	22	401	0	ENST00000355739.4:c.2044G>A	p.Glu682Lys	p.E682K	ENST00000355739	NM_000123.3	682	Gaa/Aaa	9/15	1	2	FACETS	0.324	0.25	0.409	0.324	0.25	0.409	SUBCLONAL	1	TRUE	1	0.322184812829091	2		401	422	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107713	30107713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1160777726	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	65	459	0	ENST00000331968.5:c.967G>A	p.Glu323Lys	p.E323K	ENST00000331968	NM_002742.2	323	Gaa/Aaa	6/18	1	2	FACETS	0.928	0.807	1	0.928	0.807	1	CLONAL	1	TRUE	1	0.322184812829091	2		459	435	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544702	65544702	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	86	504	0	ENST00000358664.4:c.224G>A	p.Arg75Gln	p.R75Q	ENST00000358664	NM_002382.4	75	cGa/cAa	4/5	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.322184812829091	2		504	472	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352661	68352661	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	64	342	0	ENST00000487270.1:c.528A>C	p.Lys176Asn	p.K176N	ENST00000487270	NM_133509.3	176	aaA/aaC	6/11	1	2	FACETS	0.763	0.661	0.872	0.763	0.661	0.872	SUBCLONAL	1	TRUE	1	0.322184812829091	2		342	521	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81574778	81574778	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1186709643	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	46	447	0	ENST00000298171.2:c.674A>G	p.Tyr225Cys	p.Y225C	ENST00000298171	NM_000369.2	225	tAc/tGc	8/10	1	2	FACETS	0.588	0.495	0.69	0.588	0.495	0.69	SUBCLONAL	1	TRUE	1	0.322184812829091	2		447	486	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95592973	95592973	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	52	336	0	ENST00000393063.1:c.847G>T	p.Asp283Tyr	p.D283Y	ENST00000393063	NM_030621.3	283	Gat/Tat	8/28	1	2	FACETS	0.754	0.643	0.875	0.754	0.643	0.875	SUBCLONAL	1	TRUE	1	0.322184812829091	2		336	428	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95595941	95595941	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749484792	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	50	329	0	ENST00000393063.1:c.602G>A	p.Arg201His	p.R201H	ENST00000393063	NM_030621.3	201	cGc/cAc	7/28	1	2	FACETS	0.652	0.554	0.76	0.652	0.554	0.76	SUBCLONAL	1	TRUE	1	0.322184812829091	2		329	476	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643719	38643719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	70	426	0	ENST00000299084.4:c.1189G>A	p.Asp397Asn	p.D397N	ENST00000299084	NM_152594.2	397	Gac/Aac	7/7	1	2	FACETS	0.828	0.723	0.941	0.828	0.723	0.941	CLONAL	1	TRUE	1	0.322184812829091	2		426	525	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040852	42040852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	80	439	0	ENST00000219905.7:c.5230C>T	p.Pro1744Ser	p.P1744S	ENST00000219905	NM_001164273.1	1744	Cca/Tca	16/24	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.322184812829091	2		439	472	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041074	42041074	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	85	491	0	ENST00000219905.7:c.5452C>T	p.Arg1818Ter	p.R1818*	ENST00000219905	NM_001164273.1	1818	Cga/Tga	16/24	1	2	FACETS	0.979	0.867	1	0.979	0.867	1	CLONAL	1	TRUE	1	0.322184812829091	2		491	539	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052629	42052629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	114	410	0	ENST00000219905.7:c.7300C>T	p.Arg2434Trp	p.R2434W	ENST00000219905	NM_001164273.1	2434	Cgg/Tgg	20/24	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.322184812829091	2		410	601	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701149	43701149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756730049	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	81	446	0	ENST00000382044.4:c.5546G>A	p.Arg1849His	p.R1849H	ENST00000382044	NM_001141980.1	1849	cGt/cAt	26/28	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.322184812829091	2		446	468	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43739581	43739581	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	50	325	0	ENST00000382044.4:c.2819G>T	p.Arg940Ile	p.R940I	ENST00000382044	NM_001141980.1	940	aGa/aTa	13/28	1	2	FACETS	0.607	0.515	0.708	0.607	0.515	0.708	SUBCLONAL	1	TRUE	1	0.322184812829091	2		325	511	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748837	43748837	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	72	453	0	ENST00000382044.4:c.1969G>T	p.Glu657Ter	p.E657*	ENST00000382044	NM_001141980.1	657	Gaa/Taa	12/28	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.322184812829091	2		453	421	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670452	88670452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143617169	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	61	398	0	ENST00000360948.2:c.1234G>A	p.Glu412Lys	p.E412K	ENST00000360948	NM_001012338.2	412	Gaa/Aaa	11/19	0.322184812829091	1	FACETS	0.875	0.759	1	0.875	0.759	1	CLONAL	1	TRUE	0	0.322184812829091	1		398	363	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442819	99442819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1365982598	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	50	419	0	ENST00000268035.6:c.1216C>T	p.Arg406Cys	p.R406C	ENST00000268035	NM_000875.3	406	Cgc/Tgc	5/21	1	2	FACETS	0.786	0.668	0.914	0.786	0.668	0.914	CLONAL	1	TRUE	1	0.322184812829091	2		419	395	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098638	2098638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	116	436	0	ENST00000219476.3:c.22G>A	p.Asp8Asn	p.D8N	ENST00000219476	NM_000548.3	8	Gat/Aat	2/42	1	2	FACETS	0.788	0.715	0.864	1	0.986	1	SUBCLONAL	2	TRUE	1	0.322184812829091	2		436	457	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858517	9858517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765370528	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	68	477	0	ENST00000330684.3:c.2884G>A	p.Glu962Lys	p.E962K	ENST00000330684	NM_001134407.1	962	Gaa/Aaa	13/13	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.322184812829091	2		477	361	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031893	10031893	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	57	450	0	ENST00000330684.3:c.930C>A	p.Phe310Leu	p.F310L	ENST00000330684	NM_001134407.1	310	ttC/ttA	3/13	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.322184812829091	2		450	354	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032120	10032120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	69	437	0	ENST00000330684.3:c.703G>A	p.Glu235Lys	p.E235K	ENST00000330684	NM_001134407.1	235	Gag/Aag	3/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.322184812829091	2		437	324	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274114	10274114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	68	555	0	ENST00000330684.3:c.155G>A	p.Arg52Gln	p.R52Q	ENST00000330684	NM_001134407.1	52	cGa/cAa	2/13	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.322184812829091	2		555	358	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070635	67070635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753519175	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	30	375	0	ENST00000412916.2:c.259G>A	p.Asp87Asn	p.D87N	ENST00000412916		87	Gac/Aac	3/6	1	2	FACETS	0.317	0.255	0.389	0.317	0.255	0.389	SUBCLONAL	1	TRUE	1	0.322184812829091	2		375	587	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830958	72830958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393698686	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	79	561	0	ENST00000268489.5:c.5623G>A	p.Glu1875Lys	p.E1875K	ENST00000268489	NM_006885.3	1875	Gaa/Aaa	9/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.322184812829091	2		561	397	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888069	81888069	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	53	292	0	ENST00000359376.3:c.214G>T	p.Glu72Ter	p.E72*	ENST00000359376	NM_002661.3	72	Gaa/Taa	3/33	1	2	FACETS	0.864	0.739	0.999	0.864	0.739	0.999	CLONAL	1	TRUE	1	0.322184812829091	2		292	381	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942036	81942036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	47	405	0	ENST00000359376.3:c.1573G>A	p.Glu525Lys	p.E525K	ENST00000359376	NM_002661.3	525	Gaa/Aaa	17/33	1	2	FACETS	0.834	0.706	0.973	0.834	0.706	0.973	CLONAL	1	TRUE	1	0.322184812829091	2		405	350	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957133	81957133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1476399695	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	67	422	0	ENST00000359376.3:c.2351G>A	p.Arg784Gln	p.R784Q	ENST00000359376	NM_002661.3	784	cGa/cAa	22/33	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.322184812829091	2		422	363	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972509	81972509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755617580	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	66	354	0	ENST00000359376.3:c.3302C>T	p.Thr1101Met	p.T1101M	ENST00000359376	NM_002661.3	1101	aCg/aTg	29/33	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.322184812829091	2		354	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	89	.	.	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	NA	2	FACETS	1	0.949	1			1	INDETERMINATE	1	TRUE	NA	0.322184812829091	2		0	495	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979514	7979514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141010860	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	64	390	0	ENST00000319144.4:c.1511C>T	p.Ala504Val	p.A504V	ENST00000319144	NM_001139.2	504	gCg/gTg	11/15	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.322184812829091	2		390	376	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998898	11998898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	46	326	0	ENST00000353533.5:c.400C>T	p.Arg134Trp	p.R134W	ENST00000353533	NM_003010.3	134	Cgg/Tgg	4/11	1	2	FACETS	0.661	0.557	0.775	0.661	0.557	0.775	SUBCLONAL	1	TRUE	1	0.322184812829091	2		326	432	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998919	11998919	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	51	351	0	ENST00000353533.5:c.421G>T	p.Glu141Ter	p.E141*	ENST00000353533	NM_003010.3	141	Gaa/Taa	4/11	1	2	FACETS	0.693	0.589	0.806	0.693	0.589	0.806	SUBCLONAL	1	TRUE	1	0.322184812829091	2		351	457	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961036	15961036	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	55	357	0	ENST00000268712.3:c.6184G>T	p.Asp2062Tyr	p.D2062Y	ENST00000268712	NM_006311.3	2062	Gat/Tat	40/46	1	2	FACETS	0.943	0.81	1	0.943	0.81	1	CLONAL	1	TRUE	1	0.322184812829091	2		357	362	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	63	350	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.77	0.667	0.881	0.77	0.667	0.881	SUBCLONAL	1	TRUE	1	0.322184812829091	2		350	508	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315354	30315354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1480541649	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	62	349	0	ENST00000322652.5:c.1039G>A	p.Glu347Lys	p.E347K	ENST00000322652	NM_015355.2	347	Gaa/Aaa	10/16	1	2	FACETS	0.891	0.772	1	0.891	0.772	1	CLONAL	1	TRUE	1	0.322184812829091	2		349	432	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448280	56448280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	113	505	0	ENST00000407977.2:c.367G>A	p.Ala123Thr	p.A123T	ENST00000407977		123	Gct/Act	3/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.322184812829091	2		505	528	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007156	62007156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148032848	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	67	504	0	ENST00000392795.3:c.526G>A	p.Val176Met	p.V176M	ENST00000392795	NM_001039933.1	176	Gtg/Atg	4/6	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.322184812829091	2		504	361	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724435	724435	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	50	378	0	ENST00000314574.4:c.1621G>T	p.Glu541Ter	p.E541*	ENST00000314574	NM_005433.3	541	Gaa/Taa	12/12	1	2	FACETS	0.748	0.636	0.87	0.748	0.636	0.87	SUBCLONAL	1	TRUE	1	0.322184812829091	2		378	415	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570433	39570433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747825815	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	82	264	0	ENST00000262039.4:c.629G>A	p.Arg210Gln	p.R210Q	ENST00000262039	NM_002647.2	210	cGa/cAa	6/25	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.322184812829091	2		264	409	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609382	39609382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463795009	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	67	303	0	ENST00000262039.4:c.1684G>A	p.Glu562Lys	p.E562K	ENST00000262039	NM_002647.2	562	Gaa/Aaa	15/25	1	2	FACETS	0.852	0.742	0.971	0.852	0.742	0.971	CLONAL	1	TRUE	1	0.322184812829091	2		303	488	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222221	5222221	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	53	363	1	ENST00000357368.4:c.3114G>T	p.Lys1038Asn	p.K1038N	ENST00000357368	NM_002850.3	1038	aaG/aaT	19/38	0.322184812829091	1	FACETS	0.945	0.812	1	0.945	0.812	1	CLONAL	1	TRUE	0	0.322184812829091	1		364	292	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221489	36221489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1331677016	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	84	520	0	ENST00000222270.7:c.5248G>A	p.Glu1750Lys	p.E1750K	ENST00000222270	NM_014727.1	1750	Gag/Aag	25/37	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.322184812829091	2		520	462	SUCCESS
ALK	238	MSKCC	GRCh37	2	29420510	29420510	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	75	363	0	ENST00000389048.3:c.3971C>A	p.Ser1324Tyr	p.S1324Y	ENST00000389048	NM_004304.4	1324	tCt/tAt	27/29	0.322184812829091	1	FACETS	0.937	0.825	1	0.937	0.825	1	CLONAL	1	TRUE	0	0.322184812829091	1		363	417	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142901	30142901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1365924896	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	62	527	0	ENST00000389048.3:c.625C>T	p.Arg209Cys	p.R209C	ENST00000389048	NM_004304.4	209	Cgc/Tgc	1/29	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.322184812829091	2		527	345	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67632300	67632300	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	79	346	0	ENST00000272342.5:c.2486C>A	p.Ser829Tyr	p.S829Y	ENST00000272342	NM_019002.3	829	tCt/tAt	5/6	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.322184812829091	2		346	463	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151189	202151189	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	41	352	0	ENST00000358485.4:c.1489G>T	p.Asp497Tyr	p.D497Y	ENST00000358485	NM_001080125.1	497	Gat/Tat	9/9	1	2	FACETS	0.656	0.547	0.776	0.656	0.547	0.776	SUBCLONAL	1	TRUE	1	0.322184812829091	2		352	388	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251749	212251749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	87	482	0	ENST00000342788.4:c.3310G>A	p.Asp1104Asn	p.D1104N	ENST00000342788	NM_005235.2	1104	Gac/Aac	27/28	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.322184812829091	2		482	489	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215617226	215617226	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777937955	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	57	313	0	ENST00000260947.4:c.1622C>T	p.Ser541Leu	p.S541L	ENST00000260947	NM_000465.2	541	tCg/tTg	7/11	1	2	FACETS	0.797	0.685	0.918	0.797	0.685	0.918	CLONAL	1	TRUE	1	0.322184812829091	2		313	444	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388078	31388078	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1477651398	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	66	410	0	ENST00000328111.2:c.1879G>A	p.Asp627Asn	p.D627N	ENST00000328111	NM_006892.3	627	Gac/Aac	17/23	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.322184812829091	2		410	408	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770575	40770575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1294592345	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	45	405	0	ENST00000373198.4:c.2807G>A	p.Arg936Gln	p.R936Q	ENST00000373198	NM_133170.3	936	cGa/cAa	19/32	0.322184812829091	0	FACETS	0.572	0.483	0.67			1	SUBCLONAL	1	TRUE	0	0.322184812829091	0		405	331	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877444	40877444	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	46	419	0	ENST00000373198.4:c.2252C>A	p.Ser751Tyr	p.S751Y	ENST00000373198	NM_133170.3	751	tCt/tAt	15/32	0.322184812829091	0	FACETS	0.515	0.434	0.603			1	SUBCLONAL	1	TRUE	0	0.322184812829091	0		419	376	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944562	40944562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868189942	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	25	457	0	ENST00000373198.4:c.1940C>T	p.Ser647Leu	p.S647L	ENST00000373198	NM_133170.3	647	tCg/tTg	12/32	0.322184812829091	0	FACETS	0.27	0.213	0.337			1	SUBCLONAL	1	TRUE	0	0.322184812829091	0		457	389	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256699	46256699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749607074	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	63	321	0	ENST00000371998.3:c.755G>A	p.Arg252His	p.R252H	ENST00000371998		252	cGc/cAc	8/23	1	2	FACETS	0.983	0.853	1	0.983	0.853	1	CLONAL	1	TRUE	1	0.322184812829091	2		321	398	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54959339	54959339	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	43	211	0	ENST00000312783.6:c.361G>T	p.Glu121Ter	p.E121*	ENST00000312783	NM_198436.1	121	Gaa/Taa	5/10	1	2	FACETS	0.676	0.566	0.796	0.676	0.566	0.796	SUBCLONAL	1	TRUE	1	0.322184812829091	2		211	395	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755594	39755594	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780042015	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	83	553	0	ENST00000288319.7:c.1171G>A	p.Asp391Asn	p.D391N	ENST00000288319	NM_182918.3	391	Gac/Aac	10/10	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.322184812829091	2		553	485	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817460	39817460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774083516	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	56	428	0	ENST00000288319.7:c.103G>A	p.Ala35Thr	p.A35T	ENST00000288319	NM_182918.3	35	Gcg/Acg	2/10	1	2	FACETS	0.83	0.713	0.957	0.83	0.713	0.957	CLONAL	1	TRUE	1	0.322184812829091	2		428	419	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29090026	29090026	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	15	103	0	ENST00000328354.6:c.1455G>A	p.Trp485Ter	p.W485*	ENST00000328354	NM_007194.3	485	tgG/tgA	13/15	1	2	FACETS	0.789	0.583	1	0.789	0.583	1	CLONAL	1	TRUE	1	0.322184812829091	2		103	118	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627979	37627979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780585104	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	53	410	0	ENST00000249071.6:c.281G>A	p.Arg94His	p.R94H	ENST00000249071	NM_002872.4	94	cGc/cAc	4/7	1	2	FACETS	0.837	0.716	0.969	0.837	0.716	0.969	CLONAL	1	TRUE	1	0.322184812829091	2		410	393	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12393114	12393114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	31	349	0	ENST00000287820.6:c.23C>T	p.Ser8Phe	p.S8F	ENST00000287820	NM_015869.4	8	tCt/tTt	1/7	1	2	FACETS	0.361	0.291	0.44	0.361	0.291	0.44	SUBCLONAL	1	TRUE	1	0.322184812829091	2		349	533	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641905	12641905	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs755926381	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	68	454	0	ENST00000251849.4:c.844C>T	p.Arg282Ter	p.R282*	ENST00000251849	NM_002880.3	282	Cga/Tga	8/17	1	2	FACETS	0.998	0.872	1	0.998	0.872	1	CLONAL	1	TRUE	1	0.322184812829091	2		454	423	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158162	47158162	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	53	327	0	ENST00000409792.3:c.4537G>T	p.Glu1513Ter	p.E1513*	ENST00000409792	NM_014159.6	1513	Gaa/Taa	4/21	1	2	FACETS	0.723	0.618	0.838	0.723	0.618	0.838	SUBCLONAL	1	TRUE	1	0.322184812829091	2		327	455	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164268	47164268	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	61	408	0	ENST00000409792.3:c.1858C>T	p.Arg620Ter	p.R620*	ENST00000409792	NM_014159.6	620	Cga/Tga	3/21	1	2	FACETS	0.747	0.645	0.857	0.747	0.645	0.857	SUBCLONAL	1	TRUE	1	0.322184812829091	2		408	507	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725022	49725022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs575861028	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	98	475	0	ENST00000449682.2:c.322C>T	p.Arg108Cys	p.R108C	ENST00000449682	NM_020998.3	108	Cgt/Tgt	3/18	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.322184812829091	2		475	468	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453531	138453531	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372119491	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	59	349	0	ENST00000289153.2:c.917G>A	p.Arg306Gln	p.R306Q	ENST00000289153	NM_006219.2	306	cGa/cAa	5/22	1	2	FACETS	0.778	0.67	0.894	0.778	0.67	0.894	SUBCLONAL	1	TRUE	1	0.322184812829091	2		349	471	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461576	138461576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	41	318	0	ENST00000289153.2:c.445C>T	p.Arg149Ter	p.R149*	ENST00000289153	NM_006219.2	149	Cga/Tga	3/22	1	2	FACETS	0.597	0.498	0.708	0.597	0.498	0.708	SUBCLONAL	1	TRUE	1	0.322184812829091	2		318	426	SUCCESS
ATR	545	MSKCC	GRCh37	3	142243011	142243011	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	49	354	0	ENST00000350721.4:c.3976G>T	p.Glu1326Ter	p.E1326*	ENST00000350721	NM_001184.3	1326	Gaa/Taa	22/47	1	2	FACETS	0.619	0.525	0.724	0.619	0.525	0.724	SUBCLONAL	1	TRUE	1	0.322184812829091	2		354	491	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917544	178917544	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1382877640	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	62	390	0	ENST00000263967.3:c.419G>A	p.Arg140Gln	p.R140Q	ENST00000263967	NM_006218.2	140	cGa/cAa	3/21	1	2	FACETS	0.807	0.698	0.924	0.807	0.698	0.924	CLONAL	1	TRUE	1	0.322184812829091	2		390	477	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922301	178922301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	31	229	0	ENST00000263967.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000263967	NM_006218.2	357	cGa/cAa	6/21	1	2	FACETS	0.623	0.505	0.756	0.623	0.505	0.756	SUBCLONAL	1	TRUE	1	0.322184812829091	2		229	309	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	30	230	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	1	2	FACETS	0.633	0.512	0.771	0.633	0.512	0.771	SUBCLONAL	1	TRUE	1	0.322184812829091	2		230	294	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748035	41748035	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	35	236	0	ENST00000226382.2:c.734C>T	p.Ala245Val	p.A245V	ENST00000226382	NM_003924.3	245	gCg/gTg	3/3	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.322184812829091	2		236	152	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133561	55133561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs958381664	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	57	393	1	ENST00000257290.5:c.865G>A	p.Glu289Lys	p.E289K	ENST00000257290	NM_006206.4	289	Gaa/Aaa	6/23	0.322184812829091	1	FACETS	0.719	0.618	0.827	0.719	0.618	0.827	SUBCLONAL	1	TRUE	0	0.322184812829091	1		394	413	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140786	55140786	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs747156883	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	64	345	0	ENST00000257290.5:c.1647G>A	p.Trp549Ter	p.W549*	ENST00000257290	NM_006206.4	549	tgG/tgA	11/23	0.322184812829091	1	FACETS	0.955	0.832	1	0.955	0.832	1	CLONAL	1	TRUE	0	0.322184812829091	1		345	349	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955615	55955615	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	37	334	0	ENST00000263923.4:c.3330G>T	p.Lys1110Asn	p.K1110N	ENST00000263923	NM_002253.2	1110	aaG/aaT	25/30	0.322184812829091	1	FACETS	0.622	0.514	0.741	0.622	0.514	0.741	SUBCLONAL	1	TRUE	0	0.322184812829091	1		334	310	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956220	55956220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190050670	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	54	264	0	ENST00000263923.4:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000263923	NM_002253.2	1032	cGa/cAa	23/30	0.322184812829091	1	FACETS	0.76	0.652	0.878	0.76	0.652	0.878	SUBCLONAL	1	TRUE	0	0.322184812829091	1		264	370	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143226689	143226689	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs149208667	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	63	282	0	ENST00000262992.4:c.425G>A	p.Arg142Gln	p.R142Q	ENST00000262992	NM_001101669.1	142	cGa/cAa	7/24	1	2	FACETS	0.869	0.754	0.994	0.869	0.754	0.994	CLONAL	1	TRUE	1	0.322184812829091	2		282	450	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	111	446	0	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.322184812829091	2		446	606	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268137	153268137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752114536	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	66	401	0	ENST00000281708.4:c.671G>A	p.Arg224Gln	p.R224Q	ENST00000281708	NM_033632.3	224	cGa/cAa	4/12	1	2	FACETS	0.704	0.611	0.804	0.704	0.611	0.804	SUBCLONAL	1	TRUE	1	0.322184812829091	2		401	582	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332918	153332918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471232420	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	57	424	0	ENST00000281708.4:c.38G>A	p.Arg13Gln	p.R13Q	ENST00000281708	NM_033632.3	13	cGa/cAa	2/12	1	2	FACETS	0.781	0.671	0.9	0.781	0.671	0.9	SUBCLONAL	1	TRUE	1	0.322184812829091	2		424	453	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542870	187542870	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	57	375	0	ENST00000441802.2:c.4870G>T	p.Glu1624Ter	p.E1624*	ENST00000441802	NM_005245.3	1624	Gaa/Taa	10/27	1	2	FACETS	0.786	0.676	0.906	0.786	0.676	0.906	CLONAL	1	TRUE	1	0.322184812829091	2		375	450	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279431	1279431	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754809046	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	53	380	0	ENST00000310581.5:c.2105C>T	p.Pro702Leu	p.P702L	ENST00000310581	NM_198253.2	702	cCg/cTg	5/16	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.322184812829091	2		380	258	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294420	1294420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	91	571	0	ENST00000310581.5:c.581G>A	p.Arg194Gln	p.R194Q	ENST00000310581	NM_198253.2	194	cGa/cAa	2/16	1	2	FACETS	0.755	0.676	0.839	1	0.981	1	SUBCLONAL	2	TRUE	1	0.322184812829091	2		571	374	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38978751	38978751	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1432686344	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	35	246	0	ENST00000357387.3:c.755G>T	p.Arg252Ile	p.R252I	ENST00000357387	NM_152756.3	252	aGa/aTa	9/38	1	2	FACETS	0.652	0.536	0.783	0.652	0.536	0.783	SUBCLONAL	1	TRUE	1	0.322184812829091	2		246	333	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982057	38982057	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	64	374	0	ENST00000357387.3:c.665G>A	p.Arg222Gln	p.R222Q	ENST00000357387	NM_152756.3	222	cGa/cAa	8/38	1	2	FACETS	0.799	0.693	0.914	0.799	0.693	0.914	CLONAL	1	TRUE	1	0.322184812829091	2		374	497	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161689	56161689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1490957244	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	57	321	0	ENST00000399503.3:c.1186C>T	p.Arg396Cys	p.R396C	ENST00000399503	NM_005921.1	396	Cgt/Tgt	6/20	1	2	FACETS	0.74	0.636	0.854	0.74	0.636	0.854	SUBCLONAL	1	TRUE	1	0.322184812829091	2		321	478	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752845	57752845	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	85	397	0	ENST00000274289.3:c.1083G>T	p.Lys361Asn	p.K361N	ENST00000274289	NM_006622.3	361	aaG/aaT	8/14	1	2	FACETS	0.97	0.859	1	0.97	0.859	1	CLONAL	1	TRUE	1	0.322184812829091	2		397	544	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	48	165	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	0.635	0.537	0.743	0.635	0.537	0.743	SUBCLONAL	1	TRUE	1	0.322184812829091	2		165	469	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961018	79961018	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	58	413	0	ENST00000265081.6:c.415G>T	p.Glu139Ter	p.E139*	ENST00000265081	NM_002439.4	139	Gaa/Taa	3/24	1	2	FACETS	0.797	0.686	0.917	0.797	0.686	0.917	CLONAL	1	TRUE	1	0.322184812829091	2		413	452	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649005	86649005	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	39	283	0	ENST00000274376.6:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000274376	NM_002890.2	429	Gaa/Taa	9/25	1	2	FACETS	0.484	0.401	0.577	0.484	0.401	0.577	SUBCLONAL	1	TRUE	1	0.322184812829091	2		283	500	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685312	86685312	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	63	318	0	ENST00000274376.6:c.3028C>T	p.Arg1010Ter	p.R1010*	ENST00000274376	NM_002890.2	1010	Cga/Tga	24/25	1	2	FACETS	0.798	0.691	0.913	0.798	0.691	0.913	CLONAL	1	TRUE	1	0.322184812829091	2		318	490	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	51	422	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	1	2	FACETS	0.681	0.579	0.792	0.681	0.579	0.792	SUBCLONAL	1	TRUE	1	0.322184812829091	2		422	465	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915579	131915579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28903087	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	54	254	0	ENST00000265335.6:c.577C>T	p.Arg193Trp	p.R193W	ENST00000265335		193	Cgg/Tgg	5/25	1	2	FACETS	0.88	0.754	1	0.88	0.754	1	CLONAL	1	TRUE	1	0.322184812829091	2		254	381	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977992	131977992	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	29	307	0	ENST00000265335.6:c.3875A>G	p.Asn1292Ser	p.N1292S	ENST00000265335		1292	aAc/aGc	25/25	1	2	FACETS	0.507	0.407	0.621	0.507	0.407	0.621	SUBCLONAL	1	TRUE	1	0.322184812829091	2		307	355	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518782	176518782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752817668	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	69	525	0	ENST00000292408.4:c.700C>T	p.Arg234Cys	p.R234C	ENST00000292408	NM_213647.1	234	Cgc/Tgc	6/18	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.322184812829091	2		525	378	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166773	32166773	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1231739465	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	81	466	0	ENST00000375023.3:c.4465C>T	p.Arg1489Ter	p.R1489*	ENST00000375023	NM_004557.3	1489	Cga/Tga	24/30	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.322184812829091	2		466	478	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169237	32169237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139941835	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	61	463	0	ENST00000375023.3:c.3796G>A	p.Gly1266Arg	p.G1266R	ENST00000375023	NM_004557.3	1266	Ggg/Agg	22/30	1	2	FACETS	0.915	0.792	1	0.915	0.792	1	CLONAL	1	TRUE	1	0.322184812829091	2		463	414	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955086	93955086	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	31	315	0	ENST00000369303.4:c.2812G>T	p.Glu938Ter	p.E938*	ENST00000369303	NM_004440.3	938	Gaa/Taa	16/17	1	2	FACETS	0.541	0.437	0.657	0.541	0.437	0.657	SUBCLONAL	1	TRUE	1	0.322184812829091	2		315	356	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967820	93967820	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	48	335	1	ENST00000369303.4:c.2107A>G	p.Arg703Gly	p.R703G	ENST00000369303	NM_004440.3	703	Aga/Gga	11/17	1	2	FACETS	0.642	0.543	0.751	0.642	0.543	0.751	SUBCLONAL	1	TRUE	1	0.322184812829091	2		336	464	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979344	93979344	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	39	371	0	ENST00000369303.4:c.1484C>A	p.Thr495Asn	p.T495N	ENST00000369303	NM_004440.3	495	aCc/aAc	7/17	1	2	FACETS	0.506	0.419	0.604	0.506	0.419	0.604	SUBCLONAL	1	TRUE	1	0.322184812829091	2		371	478	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066482	94066482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542602078	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	79	400	0	ENST00000369303.4:c.1277G>A	p.Arg426Gln	p.R426Q	ENST00000369303	NM_004440.3	426	cGa/cAa	5/17	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.322184812829091	2		400	488	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555110	106555110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141223053	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	90	550	0	ENST00000369096.4:c.2227G>A	p.Glu743Lys	p.E743K	ENST00000369096	NM_001198.3	743	Gag/Aag	7/7	0.322184812829091	3	FACETS	1	0.94	1			1	CLONAL	1	TRUE	NA	0.322184812829091	3		550	596	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109321750	109321750	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1032022376	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	56	366	0	ENST00000436639.2:c.673G>T	p.Glu225Ter	p.E225*	ENST00000436639	NM_014454.2	225	Gaa/Taa	4/10	0.322184812829091	3	FACETS	0.784	0.672	0.906			1	CLONAL	1	TRUE	NA	0.322184812829091	3		366	515	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024169	112024169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465963577	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	45	351	0	ENST00000368678.4:c.616C>T	p.Arg206Cys	p.R206C	ENST00000368678		206	Cgc/Tgc	7/13	1	2	FACETS	0.653	0.549	0.767	0.653	0.549	0.767	SUBCLONAL	1	TRUE	1	0.322184812829091	2		351	428	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117680985	117680985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771443531	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	58	326	0	ENST00000368508.3:c.3635G>A	p.Arg1212His	p.R1212H	ENST00000368508	NM_002944.2	1212	cGc/cAc	23/43	1	2	FACETS	0.841	0.725	0.967	0.841	0.725	0.967	CLONAL	1	TRUE	1	0.322184812829091	2		326	428	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706936	117706936	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	69	358	0	ENST00000368508.3:c.2214G>T	p.Glu738Asp	p.E738D	ENST00000368508	NM_002944.2	738	gaG/gaT	15/43	1	2	FACETS	0.939	0.821	1	0.939	0.821	1	CLONAL	1	TRUE	1	0.322184812829091	2		358	456	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001523	150001523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264217871	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	46	402	0	ENST00000253339.5:c.2081G>A	p.Arg694His	p.R694H	ENST00000253339		694	cGt/cAt	4/7	1	2	FACETS	0.595	0.501	0.698	0.595	0.501	0.698	SUBCLONAL	1	TRUE	1	0.322184812829091	2		402	480	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099840	157099840	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	70	404	0	ENST00000346085.5:c.777A>C	p.Gln259His	p.Q259H	ENST00000346085	NM_020732.3	259	caA/caC	1/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.322184812829091	2		404	378	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157488293	157488293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750810656	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	79	379	0	ENST00000346085.5:c.2999C>T	p.Ala1000Val	p.A1000V	ENST00000346085	NM_020732.3	1000	gCg/gTg	10/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.322184812829091	2		379	402	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13949266	13949266	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	50	341	0	ENST00000405192.2:c.862A>C	p.Lys288Gln	p.K288Q	ENST00000405192	NM_001163147.1	288	Aaa/Caa	9/12	1	2	FACETS	0.679	0.577	0.791	0.679	0.577	0.791	SUBCLONAL	1	TRUE	1	0.322184812829091	2		341	457	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971370	13971370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748346103	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	79	415	0	ENST00000405192.2:c.559C>T	p.Arg187Cys	p.R187C	ENST00000405192	NM_001163147.1	187	Cgc/Tgc	8/12	1	2	FACETS	0.963	0.85	1	0.963	0.85	1	CLONAL	1	TRUE	1	0.322184812829091	2		415	509	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739796	41739796	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	88	399	0	ENST00000242208.4:c.177G>T	p.Lys59Asn	p.K59N	ENST00000242208	NM_002192.2	59	aaG/aaT	2/3	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.322184812829091	2		399	453	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468285	50468285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	63	452	0	ENST00000331340.3:c.1520C>T	p.Ser507Leu	p.S507L	ENST00000331340	NM_006060.4	507	tCg/tTg	8/8	1	2	FACETS	0.843	0.731	0.964	0.843	0.731	0.964	CLONAL	1	TRUE	1	0.322184812829091	2		452	464	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259533	55259533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	63	408	0	ENST00000275493.2:c.2591C>T	p.Ala864Val	p.A864V	ENST00000275493	NM_005228.3	864	gCg/gTg	21/28	0.241023104154342	0	FACETS	0.722	0.628	0.824			1	SUBCLONAL	1	TRUE	0	0.322184812829091	0		408	367	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509723	106509723	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	57	578	1	ENST00000359195.3:c.1717G>T	p.Glu573Ter	p.E573*	ENST00000359195	NM_002649.2	573	Gaa/Taa	2/11	1	2	FACETS	0.698	0.599	0.805	0.698	0.599	0.805	SUBCLONAL	1	TRUE	1	0.322184812829091	2		579	507	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520111	106520111	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	43	269	0	ENST00000359195.3:c.2538+1G>A		p.X846_splice	ENST00000359195	NM_002649.2	846			1	2	FACETS	0.686	0.575	0.809	0.686	0.575	0.809	SUBCLONAL	1	TRUE	1	0.322184812829091	2		269	389	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339184	116339184	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	76	365	0	ENST00000397752.3:c.46T>C	p.Phe16Leu	p.F16L	ENST00000397752	NM_000245.2	16	Ttt/Ctt	2/21	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.322184812829091	2		365	433	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845086	128845086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761395599	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	21	450	0	ENST00000249373.3:c.580G>A	p.Glu194Lys	p.E194K	ENST00000249373	NM_005631.4	194	Gaa/Aaa	3/12	1	2	FACETS	0.355	0.273	0.451	0.355	0.273	0.451	SUBCLONAL	1	TRUE	1	0.322184812829091	2		450	367	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850885	128850885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61740964	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	83	382	0	ENST00000249373.3:c.1732G>A	p.Glu578Lys	p.E578K	ENST00000249373	NM_005631.4	578	Gag/Aag	10/12	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.322184812829091	2		382	397	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860866	151860866	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs924381304	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	74	394	1	ENST00000262189.6:c.9796C>T	p.Arg3266Trp	p.R3266W	ENST00000262189	NM_170606.2	3266	Cgg/Tgg	43/59	1	2	FACETS	0.99	0.87	1	0.99	0.87	1	CLONAL	1	TRUE	1	0.322184812829091	2		395	464	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874713	151874713	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	102	469	1	ENST00000262189.6:c.7825C>T	p.Arg2609Ter	p.R2609*	ENST00000262189	NM_170606.2	2609	Cga/Tga	38/59	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.322184812829091	2		470	584	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2161812	2161812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	79	443	0	ENST00000349721.2:c.4108C>T	p.Arg1370Cys	p.R1370C	ENST00000349721	NM_003070.3	1370	Cgc/Tgc	28/34	1	2	FACETS	0.846	0.745	0.954	0.846	0.745	0.954	CLONAL	1	TRUE	1	0.322184812829091	2		443	580	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069023	5069023	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs753648225	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	53	363	0	ENST00000381652.3:c.1328G>A	p.Arg443Gln	p.R443Q	ENST00000381652	NM_004972.3	443	cGa/cAa	11/25	1	2	FACETS	0.751	0.642	0.87	0.751	0.642	0.87	SUBCLONAL	1	TRUE	1	0.322184812829091	2		363	438	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212762	27212762	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906745	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	78	441	0	ENST00000380036.4:c.2744G>A	p.Arg915His	p.R915H	ENST00000380036	NM_000459.3	915	cGc/cAc	17/23	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.322184812829091	2		441	399	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27229223	27229223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369356295	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	46	316	0	ENST00000380036.4:c.3368C>T	p.Ala1123Val	p.A1123V	ENST00000380036	NM_000459.3	1123	gCg/gTg	23/23	1	2	FACETS	0.879	0.743	1	0.879	0.743	1	CLONAL	1	TRUE	1	0.322184812829091	2		316	325	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020640	37020640	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	63	343	0	ENST00000358127.4:c.205C>A	p.Leu69Ile	p.L69I	ENST00000358127	NM_001280556.1	69	Ctt/Att	2/10	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.322184812829091	2		343	385	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020670	37020670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	67	384	0	ENST00000358127.4:c.175C>T	p.Arg59Trp	p.R59W	ENST00000358127	NM_001280556.1	59	Cgg/Tgg	2/10	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.322184812829091	2		384	413	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285748	87285748	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1440777069	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	100	504	0	ENST00000277120.3:c.85G>A	p.Ala29Thr	p.A29T	ENST00000277120		29	Gct/Act	2/19	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.322184812829091	2		504	426	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891367	101891367	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	53	370	0	ENST00000374994.4:c.328G>T	p.Glu110Ter	p.E110*	ENST00000374994	NM_004612.2	110	Gaa/Taa	2/9	1	2	FACETS	0.741	0.633	0.859	0.741	0.633	0.859	SUBCLONAL	1	TRUE	1	0.322184812829091	2		370	444	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006864	47006864	+	5_prime_UTR_variant	5'UTR	SNP	G	G	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	85	405	0	ENST00000377604.3:c.-17G>A		p.*6*	ENST00000377604	NM_001204468.1	-/852		2/24	1	1	FACETS	0.95	0.854	1	1	0.986	1	CLONAL	2	TRUE	0	0.322184812829091	1		405	233	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250079	53250079	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	61	207	0	ENST00000375401.3:c.170C>T	p.Ala57Val	p.A57V	ENST00000375401	NM_004187.3	57	gCt/gTt	2/26	0.244905330782248	0	FACETS	0.658	0.577	0.743			1	SUBCLONAL	2	TRUE	NA	0.322184812829091	0		207	195	SUCCESS
AR	367	MSKCC	GRCh37	X	66765409	66765409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs865948546	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	77	261	0	ENST00000374690.3:c.421G>A	p.Ala141Thr	p.A141T	ENST00000374690	NM_000044.3	141	Gcc/Acc	1/8	0.244905330782248	0	FACETS	0.844	0.757	0.933			1	CLONAL	2	TRUE	NA	0.322184812829091	0		261	192	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348270	70348270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	71	237	0	ENST00000374080.3:c.3334G>A	p.Asp1112Asn	p.D1112N	ENST00000374080		1112	Gat/Aat	23/45	1	1	FACETS	0.8	0.709	0.896	1	0.979	1	SUBCLONAL	2	TRUE	0	0.322184812829091	1		237	231	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76764089	76764089	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1557034957	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	56	307	0	ENST00000373344.5:c.7219C>T	p.Arg2407Ter	p.R2407*	ENST00000373344	NM_000489.3	2407	Cga/Tga	35/35	1	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.322184812829091	1		307	205	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938406	76938406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	59	193	0	ENST00000373344.5:c.2342G>A	p.Arg781Gln	p.R781Q	ENST00000373344	NM_000489.3	781	cGa/cAa	9/35	1	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.322184812829091	1		193	269	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179197	123179197	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	54	145	0	ENST00000218089.9:c.646C>T	p.Arg216Ter	p.R216*	ENST00000218089	NM_001042749.1	216	Cga/Tga	8/35	1	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.322184812829091	1		145	218	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255119	16255119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194601008	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	75	485	0	ENST00000375759.3:c.2384G>A	p.Arg795Gln	p.R795Q	ENST00000375759	NM_015001.2	795	cGa/cAa	11/15	1	2	FACETS	0.818	0.718	0.926	0.818	0.718	0.926	CLONAL	1	TRUE	1	0.322184812829091	2		485	569	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938140	36938140	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559297734	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	76	509	0	ENST00000361632.4:c.821G>A	p.Arg274His	p.R274H	ENST00000361632		274	cGt/cAt	6/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.322184812829091	2		509	338	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322629	39322629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1267098530	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	65	436	0	ENST00000373001.3:c.363G>A	p.Met121Ile	p.M121I	ENST00000373001	NM_022157.3	121	atG/atA	2/7	1	2	FACETS	0.758	0.658	0.867	0.758	0.658	0.867	SUBCLONAL	1	TRUE	1	0.322184812829091	2		436	532	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304199	65304199	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	60	396	0	ENST00000342505.4:c.2916G>T	p.Lys972Asn	p.K972N	ENST00000342505	NM_002227.2	972	aaG/aaT	21/25	1	2	FACETS	0.815	0.704	0.936	0.815	0.704	0.936	CLONAL	1	TRUE	1	0.322184812829091	2		396	457	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117712755	117712755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	65	364	0	ENST00000369458.3:c.71C>T	p.Ala24Val	p.A24V	ENST00000369458	NM_024626.3	24	gCa/gTa	2/6	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.322184812829091	2		364	403	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150923562	150923562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269300889	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	68	451	0	ENST00000271640.5:c.2209G>A	p.Asp737Asn	p.D737N	ENST00000271640	NM_001145415.1	737	Gac/Aac	13/22	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.322184812829091	2		451	396	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845350	156845350	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	81	684	0	ENST00000524377.1:c.1393T>C	p.Ser465Pro	p.S465P	ENST00000524377	NM_002529.3	465	Tcc/Ccc	12/17	0.322184812829091	2	FACETS	1	0.903	1	0.512	0.452	0.576	CLONAL	1	TRUE	0	0.322184812829091	2		684	491	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176105647	176105647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	42	236	0	ENST00000367669.3:c.868G>A	p.Glu290Lys	p.E290K	ENST00000367669	NM_022457.5	290	Gaa/Aaa	7/20	0.322184812829091	2	FACETS	0.762	0.638	0.899	0.381	0.319	0.45	SUBCLONAL	1	TRUE	0	0.322184812829091	2		236	342	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132987	176132987	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	42	275	0	ENST00000367669.3:c.606A>C	p.Glu202Asp	p.E202D	ENST00000367669	NM_022457.5	202	gaA/gaC	4/20	0.322184812829091	2	FACETS	0.642	0.537	0.759	0.321	0.268	0.38	SUBCLONAL	1	TRUE	0	0.322184812829091	2		275	406	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230492737	230492737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773389998	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	73	438	0	ENST00000391860.1:c.317G>A	p.Arg106His	p.R106H	ENST00000391860	NM_001258311.1	106	cGc/cAc	2/7	0.322184812829091	2	FACETS	1	0.964	1	0.633	0.557	0.714	CLONAL	1	TRUE	0	0.322184812829091	2		438	358	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243708870	243708871	+	missense_variant	Missense_Mutation	DNP	TC	TC	GA	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	38	252	0	ENST00000263826.5:c.1192_1193inv	p.Glu398Ser	p.E398S	ENST00000263826	NM_005465.4	398	GAa/TCa	11/13	0.322184812829091	2	FACETS	0.551	0.456	0.658	0.276	0.228	0.329	SUBCLONAL	1	TRUE	0	0.322184812829091	2		252	428	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333995	70333995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	46	404	0	ENST00000373644.4:c.1900G>A	p.Val634Ile	p.V634I	ENST00000373644	NM_030625.2	634	Gtt/Att	2/12	1	2	FACETS	0.847	0.716	0.991	0.847	0.716	0.991	CLONAL	1	TRUE	1	0.322184812829091	2		404	337	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404827	70404827	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	54	363	0	ENST00000373644.4:c.2341G>T	p.Glu781Ter	p.E781*	ENST00000373644	NM_030625.2	781	Gaa/Taa	4/12	1	2	FACETS	0.715	0.611	0.828	0.715	0.611	0.828	SUBCLONAL	1	TRUE	1	0.322184812829091	2		363	469	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406337	70406337	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	69	432	0	ENST00000373644.4:c.3851C>A	p.Ser1284Tyr	p.S1284Y	ENST00000373644	NM_030625.2	1284	tCt/tAt	4/12	1	2	FACETS	0.971	0.849	1	0.971	0.849	1	CLONAL	1	TRUE	1	0.322184812829091	2		432	441	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104377082	104377082	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	57	369	0	ENST00000369902.3:c.1193A>C	p.Lys398Thr	p.K398T	ENST00000369902	NM_016169.3	398	aAa/aCa	10/12	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.322184812829091	2		369	307	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925567	114925567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1414332733	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	87	485	2	ENST00000543371.1:c.1645G>A	p.Ala549Thr	p.A549T	ENST00000543371	NM_001198531.1	549	Gcc/Acc	14/14	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.322184812829091	2		487	411	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10789683	10789683	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	75	380	0	ENST00000361367.2:c.1935G>T	p.Lys645Asn	p.K645N	ENST00000361367	NM_014633.3	645	aaG/aaT	15/25	1	2	FACETS	0.933	0.82	1	0.933	0.82	1	CLONAL	1	TRUE	1	0.322184812829091	2		380	499	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180592	94180592	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	56	364	0	ENST00000323929.3:c.1576G>A	p.Ala526Thr	p.A526T	ENST00000323929	NM_005591.3	526	Gcc/Acc	15/20	1	2	FACETS	0.86	0.739	0.992	0.86	0.739	0.992	CLONAL	1	TRUE	1	0.322184812829091	2		364	404	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998399	100998399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	44	413	0	ENST00000325455.5:c.1403C>T	p.Ala468Val	p.A468V	ENST00000325455	NM_001202474.3	468	gCg/gTg	1/8	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.322184812829091	2		413	241	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098365	108098365	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	56	310	0	ENST00000278616.4:c.14T>G	p.Leu5Arg	p.L5R	ENST00000278616	NM_000051.3	5	cTt/cGt	2/63	1	2	FACETS	0.607	0.52	0.702	0.607	0.52	0.702	SUBCLONAL	1	TRUE	1	0.322184812829091	2		310	573	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158377	108158377	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	60	348	0	ENST00000278616.4:c.4044G>T	p.Leu1348Phe	p.L1348F	ENST00000278616	NM_000051.3	1348	ttG/ttT	27/63	1	2	FACETS	0.817	0.705	0.938	0.817	0.705	0.938	CLONAL	1	TRUE	1	0.322184812829091	2		348	456	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180938	108180938	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	40	325	0	ENST00000278616.4:c.5814T>G	p.Tyr1938Ter	p.Y1938*	ENST00000278616	NM_000051.3	1938	taT/taG	39/63	1	2	FACETS	0.576	0.479	0.684	0.576	0.479	0.684	SUBCLONAL	1	TRUE	1	0.322184812829091	2		325	431	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344547	118344547	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	63	507	0	ENST00000534358.1:c.2673G>T	p.Glu891Asp	p.E891D	ENST00000534358	NM_005933.3	891	gaG/gaT	3/36	1	2	FACETS	0.768	0.665	0.88	0.768	0.665	0.88	SUBCLONAL	1	TRUE	1	0.322184812829091	2		507	509	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118370096	118370096	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	45	376	0	ENST00000534358.1:c.6040C>A	p.Leu2014Ile	p.L2014I	ENST00000534358	NM_005933.3	2014	Ctc/Atc	23/36	1	2	FACETS	0.678	0.571	0.796	0.678	0.571	0.796	SUBCLONAL	1	TRUE	1	0.322184812829091	2		376	412	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392874	118392874	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	64	444	0	ENST00000534358.1:c.11906A>C	p.Lys3969Thr	p.K3969T	ENST00000534358	NM_005933.3	3969	aAg/aCg	36/36	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.322184812829091	2		444	394	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	461447	461447	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	43	311	0	ENST00000399788.2:c.1073T>C	p.Val358Ala	p.V358A	ENST00000399788	NM_001042603.1	358	gTa/gCa	9/28	1	2	FACETS	0.686	0.575	0.809	0.686	0.575	0.809	SUBCLONAL	1	TRUE	1	0.322184812829091	2		311	389	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534733	18534733	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	56	346	0	ENST00000266497.5:c.1791G>T	p.Met597Ile	p.M597I	ENST00000266497		597	atG/atT	12/31	0.244905330782248	1	FACETS	0.667	0.573	0.77	0.667	0.573	0.77	SUBCLONAL	1	TRUE	0	0.322184812829091	1		346	437	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944947	31944947	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868835690	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	54	280	0	ENST00000340398.3:c.154C>T	p.Arg52Cys	p.R52C	ENST00000340398	NM_001013699.2	52	Cgt/Tgt	1/1	1	2	FACETS	0.969	0.831	1	0.969	0.831	1	CLONAL	1	TRUE	1	0.322184812829091	2		280	346	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244748	46244748	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	85	471	0	ENST00000334344.6:c.2842C>T	p.Leu948Phe	p.L948F	ENST00000334344	NM_152641.2	948	Ctt/Ttt	15/21	1	2	FACETS	0.951	0.842	1	0.951	0.842	1	CLONAL	1	TRUE	1	0.322184812829091	2		471	555	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418718	49418718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760369709	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	78	394	0	ENST00000301067.7:c.15796C>T	p.Arg5266Cys	p.R5266C	ENST00000301067	NM_003482.3	5266	Cgc/Tgc	49/54	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.322184812829091	2		394	422	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427080	49427080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	57	573	0	ENST00000301067.7:c.11408G>A	p.Gly3803Asp	p.G3803D	ENST00000301067	NM_003482.3	3803	gGc/gAc	39/54	1	2	FACETS	0.994	0.857	1	0.994	0.857	1	CLONAL	1	TRUE	1	0.322184812829091	2		573	356	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220025	133220025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113809231	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	59	523	0	ENST00000320574.5:c.4412G>A	p.Arg1471His	p.R1471H	ENST00000320574	NM_006231.2	1471	cGc/cAc	34/49	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.322184812829091	2		523	341	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241025	133241025	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	53	454	0	ENST00000320574.5:c.2492T>C	p.Met831Thr	p.M831T	ENST00000320574	NM_006231.2	831	aTg/aCg	22/49	1	2	FACETS	0.979	0.839	1	0.979	0.839	1	CLONAL	1	TRUE	1	0.322184812829091	2		454	336	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931787	28931787	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	66	416	0	ENST00000282397.4:c.2152A>T	p.Ile718Phe	p.I718F	ENST00000282397	NM_002019.4	718	Att/Ttt	15/30	1	2	FACETS	0.895	0.779	1	0.895	0.779	1	CLONAL	1	TRUE	1	0.322184812829091	2		416	458	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001990	29001990	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	54	351	0	ENST00000282397.4:c.1175T>G	p.Ile392Ser	p.I392S	ENST00000282397	NM_002019.4	392	aTc/aGc	9/30	1	2	FACETS	0.722	0.618	0.836	0.722	0.618	0.836	SUBCLONAL	1	TRUE	1	0.322184812829091	2		351	464	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906634	32906634	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	46	440	0	ENST00000380152.3:c.1019A>C	p.Glu340Ala	p.E340A	ENST00000380152		340	gAa/gCa	10/27	1	2	FACETS	0.569	0.479	0.668	0.569	0.479	0.668	SUBCLONAL	1	TRUE	1	0.322184812829091	2		440	502	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133660	41133660	+	stop_lost	Nonstop_Mutation	SNP	T	T	C	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	67	457	0	ENST00000379561.5:c.1968A>G	p.Ter656TrpextTer15	p.*656Wext*15	ENST00000379561	NM_002015.3	656	tgA/tgG	2/3	1	2	FACETS	0.854	0.744	0.973	0.854	0.744	0.973	CLONAL	1	TRUE	1	0.322184812829091	2		457	487	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941678	48941678	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	42	240	0	ENST00000267163.4:c.988G>T	p.Asp330Tyr	p.D330Y	ENST00000267163	NM_000321.2	330	Gat/Tat	10/27	1	2	FACETS	0.645	0.54	0.762	0.645	0.54	0.762	SUBCLONAL	1	TRUE	1	0.322184812829091	2		240	404	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955517	48955517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	43	367	0	ENST00000267163.4:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000267163	NM_000321.2	545	Gaa/Aaa	17/27	1	2	FACETS	0.636	0.532	0.75	0.636	0.532	0.75	SUBCLONAL	1	TRUE	1	0.322184812829091	2		367	420	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562165	95562165	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	65	410	0	ENST00000393063.1:c.5092A>C	p.Thr1698Pro	p.T1698P	ENST00000393063	NM_030621.3	1698	Act/Cct	24/28	1	2	FACETS	0.883	0.768	1	0.883	0.768	1	CLONAL	1	TRUE	1	0.322184812829091	2		410	457	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95577791	95577791	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1555371642	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	73	296	0	ENST00000393063.1:c.2119G>A	p.Glu707Lys	p.E707K	ENST00000393063	NM_030621.3	707	Gaa/Aaa	15/28	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.322184812829091	2		296	439	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95597863	95597863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	46	321	1	ENST00000393063.1:c.421G>A	p.Glu141Lys	p.E141K	ENST00000393063	NM_030621.3	141	Gag/Aag	5/28	1	2	FACETS	0.606	0.511	0.712	0.606	0.511	0.712	SUBCLONAL	1	TRUE	1	0.322184812829091	2		322	471	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988430	41988430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	64	428	0	ENST00000219905.7:c.1222G>A	p.Asp408Asn	p.D408N	ENST00000219905	NM_001164273.1	408	Gat/Aat	3/24	1	2	FACETS	0.86	0.746	0.982	0.86	0.746	0.982	CLONAL	1	TRUE	1	0.322184812829091	2		428	462	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058211	42058211	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	37	343	0	ENST00000219905.7:c.7931A>C	p.Asp2644Ala	p.D2644A	ENST00000219905	NM_001164273.1	2644	gAc/gCc	24/24	1	2	FACETS	0.54	0.446	0.646	0.54	0.446	0.646	SUBCLONAL	1	TRUE	1	0.322184812829091	2		343	425	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50769120	50769120	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	84	386	0	ENST00000307179.4:c.924T>G	p.Tyr308Ter	p.Y308*	ENST00000307179		308	taT/taG	9/20	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.322184812829091	2		386	480	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50776551	50776551	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	56	365	0	ENST00000307179.4:c.1883G>T	p.Arg628Ile	p.R628I	ENST00000307179		628	aGa/aTa	12/20	1	2	FACETS	0.773	0.663	0.891	0.773	0.663	0.891	SUBCLONAL	1	TRUE	1	0.322184812829091	2		365	450	SUCCESS
BLM	641	MSKCC	GRCh37	15	91341486	91341486	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	55	292	0	ENST00000355112.3:c.3277T>G	p.Ser1093Ala	p.S1093A	ENST00000355112	NM_000057.2	1093	Tca/Gca	17/22	1	2	FACETS	0.733	0.628	0.847	0.733	0.628	0.847	SUBCLONAL	1	TRUE	1	0.322184812829091	2		292	466	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347521	91347521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	51	349	0	ENST00000355112.3:c.3683C>T	p.Ser1228Phe	p.S1228F	ENST00000355112	NM_000057.2	1228	tCt/tTt	19/22	1	2	FACETS	0.704	0.599	0.818	0.704	0.599	0.818	SUBCLONAL	1	TRUE	1	0.322184812829091	2		349	450	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658776	3658776	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	83	416	0	ENST00000294008.3:c.190A>C	p.Lys64Gln	p.K64Q	ENST00000294008	NM_032444.2	64	Aaa/Caa	2/15	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.322184812829091	2		416	488	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943804	9943804	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	60	419	0	ENST00000330684.3:c.1137G>T	p.Glu379Asp	p.E379D	ENST00000330684	NM_001134407.1	379	gaG/gaT	5/13	1	2	FACETS	0.927	0.801	1	0.927	0.801	1	CLONAL	1	TRUE	1	0.322184812829091	2		419	402	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647224	23647224	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1555461693	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	58	433	0	ENST00000261584.4:c.643G>T	p.Glu215Ter	p.E215*	ENST00000261584	NM_024675.3	215	Gaa/Taa	4/13	1	2	FACETS	0.79	0.68	0.909	0.79	0.68	0.909	CLONAL	1	TRUE	1	0.322184812829091	2		433	456	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647280	23647280	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881904	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	57	381	0	ENST00000261584.4:c.587G>A	p.Arg196Lys	p.R196K	ENST00000261584	NM_024675.3	196	aGa/aAa	4/13	1	2	FACETS	0.799	0.687	0.92	0.799	0.687	0.92	CLONAL	1	TRUE	1	0.322184812829091	2		381	443	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828966	72828966	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	84	527	0	ENST00000268489.5:c.7615T>G	p.Phe2539Val	p.F2539V	ENST00000268489	NM_006885.3	2539	Ttt/Gtt	9/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.322184812829091	2		527	431	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830823	72830823	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	77	503	0	ENST00000268489.5:c.5758G>T	p.Glu1920Ter	p.E1920*	ENST00000268489	NM_006885.3	1920	Gag/Tag	9/10	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.322184812829091	2		503	408	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990715	7990715	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	68	298	0	ENST00000319144.4:c.46T>C	p.Ser16Pro	p.S16P	ENST00000319144	NM_001139.2	16	Tcg/Ccg	1/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.322184812829091	2		298	298	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013717	12013717	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	44	286	0	ENST00000353533.5:c.659A>C	p.Lys220Thr	p.K220T	ENST00000353533	NM_003010.3	220	aAa/aCa	6/11	1	2	FACETS	0.683	0.574	0.803	0.683	0.574	0.803	SUBCLONAL	1	TRUE	1	0.322184812829091	2		286	400	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550523	29550523	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	60	291	0	ENST00000356175.3:c.1783G>T	p.Glu595Ter	p.E595*	ENST00000356175	NM_000267.3	595	Gaa/Taa	16/57	1	2	FACETS	0.841	0.726	0.965	0.841	0.726	0.965	CLONAL	1	TRUE	1	0.322184812829091	2		291	443	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550524	29550524	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	41	302	0	ENST00000356175.3:c.1784A>C	p.Glu595Ala	p.E595A	ENST00000356175	NM_000267.3	595	gAa/gCa	16/57	1	2	FACETS	0.563	0.469	0.667	0.563	0.469	0.667	SUBCLONAL	1	TRUE	1	0.322184812829091	2		302	452	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33445578	33445578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763439048	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	101	415	0	ENST00000345365.6:c.205G>A	p.Ala69Thr	p.A69T	ENST00000345365	NM_002878.3	69	Gct/Act	3/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.322184812829091	2		415	420	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690588	33690588	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	68	502	0	ENST00000308377.4:c.239C>A	p.Ser80Tyr	p.S80Y	ENST00000308377	NM_152270.3	80	tCt/tAt	2/5	1	2	FACETS	0.829	0.723	0.944	0.829	0.723	0.944	CLONAL	1	TRUE	1	0.322184812829091	2		502	509	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245987	41245987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80357122	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	53	407	0	ENST00000357654.3:c.1561G>A	p.Ala521Thr	p.A521T	ENST00000357654	NM_007294.3	521	Gca/Aca	10/23	1	2	FACETS	0.857	0.733	0.991	0.857	0.733	0.991	CLONAL	1	TRUE	1	0.322184812829091	2		407	384	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246598	41246598	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	62	436	0	ENST00000357654.3:c.950A>C	p.Gln317Pro	p.Q317P	ENST00000357654	NM_007294.3	317	cAa/cCa	10/23	1	2	FACETS	0.787	0.681	0.902	0.787	0.681	0.902	CLONAL	1	TRUE	1	0.322184812829091	2		436	489	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772402	56772402	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	71	447	0	ENST00000337432.4:c.256A>G	p.Thr86Ala	p.T86A	ENST00000337432	NM_058216.2	86	Aca/Gca	2/9	1	2	FACETS	0.916	0.802	1	0.916	0.802	1	CLONAL	1	TRUE	1	0.322184812829091	2		447	481	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78765262	78765262	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	48	293	0	ENST00000306801.3:c.843G>T	p.Gln281His	p.Q281H	ENST00000306801	NM_020761.2	281	caG/caT	7/34	1	2	FACETS	0.816	0.692	0.952	0.816	0.692	0.952	CLONAL	1	TRUE	1	0.322184812829091	2		293	365	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422998	45422998	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	105	420	0	ENST00000262160.6:c.130G>T	p.Ala44Ser	p.A44S	ENST00000262160	NM_005901.5	44	Gca/Tca	2/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.322184812829091	2		420	591	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61323003	61323003	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	99	483	0	ENST00000283752.5:c.1061C>A	p.Ser354Ter	p.S354*	ENST00000283752	NM_006919.2	354	tCa/tAa	8/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.322184812829091	2		483	498	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5206816	5206816	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	63	426	0	ENST00000357368.4:c.5816A>G	p.Tyr1939Cys	p.Y1939C	ENST00000357368	NM_002850.3	1939	tAc/tGc	38/38	0.322184812829091	1	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	0	0.322184812829091	1		426	319	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245856	5245856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	77	487	0	ENST00000357368.4:c.919G>A	p.Ala307Thr	p.A307T	ENST00000357368	NM_002850.3	307	Gcc/Acc	10/38	0.322184812829091	1	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	0	0.322184812829091	1		487	394	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7168033	7168033	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	94	400	0	ENST00000302850.5:c.1556A>G	p.Tyr519Cys	p.Y519C	ENST00000302850	NM_000208.2	519	tAc/tGc	7/22	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.322184812829091	2		400	415	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311670	15311670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	24	611	0	ENST00000263388.2:c.47C>T	p.Ser16Leu	p.S16L	ENST00000263388	NM_000435.2	16	tCg/tTg	1/33	1	2	FACETS	0.379	0.297	0.474	0.379	0.297	0.474	SUBCLONAL	1	TRUE	1	0.322184812829091	2		611	393	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18958569	18958569	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753936939	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	48	304	0	ENST00000262803.5:c.388G>A	p.Asp130Asn	p.D130N	ENST00000262803	NM_002911.3	130	Gat/Aat	3/24	1	2	FACETS	0.801	0.679	0.934	0.801	0.679	0.934	CLONAL	1	TRUE	1	0.322184812829091	2		304	372	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40742240	40742240	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	66	475	0	ENST00000392038.2:c.884G>A	p.Gly295Asp	p.G295D	ENST00000392038	NM_001626.4	295	gGc/gAc	10/14	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.322184812829091	2		475	326	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745620	41745620	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	64	353	0	ENST00000301178.4:c.1307A>C	p.Gln436Pro	p.Q436P	ENST00000301178	NM_021913.4	436	cAg/cCg	10/20	1	2	FACETS	0.93	0.808	1	0.93	0.808	1	CLONAL	1	TRUE	1	0.322184812829091	2		353	427	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763472	41763472	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	75	438	0	ENST00000301178.4:c.2271G>T	p.Glu757Asp	p.E757D	ENST00000301178	NM_021913.4	757	gaG/gaT	19/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.322184812829091	2		438	419	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723008	52723008	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910814626	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	70	502	0	ENST00000322088.6:c.1193G>A	p.Arg398Gln	p.R398Q	ENST00000322088	NM_014225.5	398	cGg/cAg	10/15	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.322184812829091	2		502	425	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262580	39262580	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	46	379	0	ENST00000402219.2:c.926A>G	p.Asp309Gly	p.D309G	ENST00000402219	NM_005633.3	309	gAt/gGt	7/23	1	2	FACETS	0.59	0.497	0.693	0.59	0.497	0.693	SUBCLONAL	1	TRUE	1	0.322184812829091	2		379	484	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033720	48033720	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749522534	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	54	395	0	ENST00000234420.5:c.3931G>A	p.Glu1311Lys	p.E1311K	ENST00000234420	NM_000179.2	1311	Gaa/Aaa	9/10	1	2	FACETS	0.67	0.573	0.777	0.67	0.573	0.777	SUBCLONAL	1	TRUE	1	0.322184812829091	2		395	500	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61709574	61709574	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	67	325	0	ENST00000401558.2:c.2913A>C	p.Gln971His	p.Q971H	ENST00000401558	NM_003400.3	971	caA/caC	23/25	1	2	FACETS	0.883	0.769	1	0.883	0.769	1	CLONAL	1	TRUE	1	0.322184812829091	2		325	471	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719556	61719556	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	65	406	0	ENST00000401558.2:c.1627A>G	p.Asn543Asp	p.N543D	ENST00000401558	NM_003400.3	543	Aat/Gat	15/25	1	2	FACETS	0.754	0.655	0.862	0.754	0.655	0.862	SUBCLONAL	1	TRUE	1	0.322184812829091	2		406	535	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99137161	99137161	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	47	270	0	ENST00000074304.5:c.118G>T	p.Asp40Tyr	p.D40Y	ENST00000074304	NM_001134224.1	40	Gac/Tac	4/26	1	2	FACETS	0.75	0.634	0.877	0.75	0.634	0.877	SUBCLONAL	1	TRUE	1	0.322184812829091	2		270	389	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99203969	99203969	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	68	404	0	ENST00000074304.5:c.2832G>T	p.Lys944Asn	p.K944N	ENST00000074304	NM_001134224.1	944	aaG/aaT	26/26	1	2	FACETS	0.863	0.753	0.982	0.863	0.753	0.982	CLONAL	1	TRUE	1	0.322184812829091	2		404	489	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881473	111881473	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	86	442	0	ENST00000393256.3:c.151G>T	p.Glu51Ter	p.E51*	ENST00000393256	NM_006538.4	51	Gaa/Taa	2/4	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.322184812829091	2		442	483	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047336	128047336	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	86	468	0	ENST00000285398.2:c.586G>T	p.Glu196Ter	p.E196*	ENST00000285398	NM_000122.1	196	Gaa/Taa	5/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.322184812829091	2		468	440	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273261	198273261	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	64	369	0	ENST00000335508.6:c.949G>A	p.Asp317Asn	p.D317N	ENST00000335508	NM_012433.2	317	Gat/Aat	8/25	1	2	FACETS	0.885	0.768	1	0.885	0.768	1	CLONAL	1	TRUE	1	0.322184812829091	2		369	449	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295693	212295693	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	40	386	0	ENST00000342788.4:c.2620G>T	p.Glu874Ter	p.E874*	ENST00000342788	NM_005235.2	874	Gag/Tag	21/28	1	2	FACETS	0.554	0.461	0.658	0.554	0.461	0.658	SUBCLONAL	1	TRUE	1	0.322184812829091	2		386	448	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400280	225400280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	47	317	0	ENST00000264414.4:c.343G>A	p.Ala115Thr	p.A115T	ENST00000264414	NM_003590.4	115	Gct/Act	3/16	1	2	FACETS	0.693	0.586	0.811	0.693	0.586	0.811	SUBCLONAL	1	TRUE	1	0.322184812829091	2		317	421	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742631	39742631	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	82	353	0	ENST00000361337.2:c.1474G>T	p.Glu492Ter	p.E492*	ENST00000361337	NM_003286.2	492	Gaa/Taa	15/21	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.322184812829091	2		353	463	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944442	40944442	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	74	447	0	ENST00000373198.4:c.2060A>G	p.Tyr687Cys	p.Y687C	ENST00000373198	NM_133170.3	687	tAc/tGc	12/32	0.322184812829091	0	FACETS	0.809	0.712	0.912			1	CLONAL	1	TRUE	0	0.322184812829091	0		447	385	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385275	41385275	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	55	421	0	ENST00000373198.4:c.686A>G	p.Gln229Arg	p.Q229R	ENST00000373198	NM_133170.3	229	cAa/cGa	6/32	0.322184812829091	0	FACETS	0.689	0.592	0.793			1	SUBCLONAL	1	TRUE	0	0.322184812829091	0		421	336	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62325782	62325782	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	88	373	0	ENST00000360203.5:c.3050A>G	p.Asp1017Gly	p.D1017G	ENST00000360203	NM_001283009.1	1017	gAc/gGc	31/35	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.322184812829091	2		373	378	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553290	41553290	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	83	382	0	ENST00000263253.7:c.3379A>C	p.Asn1127His	p.N1127H	ENST00000263253	NM_001429.3	1127	Aat/Cat	18/31	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.322184812829091	2		382	438	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573584	41573584	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1301322622	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	77	549	2	ENST00000263253.7:c.5869C>T	p.Pro1957Ser	p.P1957S	ENST00000263253	NM_001429.3	1957	Ccc/Tcc	31/31	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.322184812829091	2		551	404	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266945	41266945	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	72	495	0	ENST00000349496.5:c.616A>C	p.Asn206His	p.N206H	ENST00000349496	NM_001904.3	206	Aat/Cat	5/15	1	2	FACETS	0.866	0.758	0.982	0.866	0.758	0.982	CLONAL	1	TRUE	1	0.322184812829091	2		495	516	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139492	47139492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	67	398	0	ENST00000409792.3:c.5095G>A	p.Ala1699Thr	p.A1699T	ENST00000409792	NM_014159.6	1699	Gca/Aca	9/21	1	2	FACETS	0.811	0.706	0.924	0.811	0.706	0.924	CLONAL	1	TRUE	1	0.322184812829091	2		398	513	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584593	52584593	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	71	446	0	ENST00000394830.3:c.4420G>T	p.Ala1474Ser	p.A1474S	ENST00000394830	NM_018313.4	1474	Gct/Tct	29/30	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.322184812829091	2		446	439	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981194	63981194	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	61	392	0	ENST00000398590.3:c.1696G>T	p.Val566Leu	p.V566L	ENST00000398590	NM_001177387.1	566	Gtg/Ttg	12/14	1	2	FACETS	0.872	0.755	1	0.872	0.755	1	CLONAL	1	TRUE	1	0.322184812829091	2		392	434	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453578	138453578	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	58	353	0	ENST00000289153.2:c.870G>T	p.Lys290Asn	p.K290N	ENST00000289153	NM_006219.2	290	aaG/aaT	5/22	1	2	FACETS	0.776	0.668	0.893	0.776	0.668	0.893	SUBCLONAL	1	TRUE	1	0.322184812829091	2		353	464	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665049	182665049	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	55	319	0	ENST00000292782.4:c.677A>G	p.Asp226Gly	p.D226G	ENST00000292782	NM_020640.2	226	gAc/gGc	6/7	1	2	FACETS	0.681	0.583	0.788	0.681	0.583	0.788	SUBCLONAL	1	TRUE	1	0.322184812829091	2		319	501	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182679086	182679086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	50	293	0	ENST00000292782.4:c.448G>A	p.Glu150Lys	p.E150K	ENST00000292782	NM_020640.2	150	Gaa/Aaa	4/7	1	2	FACETS	0.623	0.529	0.727	0.623	0.529	0.727	SUBCLONAL	1	TRUE	1	0.322184812829091	2		293	498	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902392	1902392	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753120179	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	58	403	0	ENST00000382891.5:c.11G>A	p.Ser4Asn	p.S4N	ENST00000382891	NM_133335.3	4	aGc/aAc	2/22	1	2	FACETS	0.889	0.766	1	0.889	0.766	1	CLONAL	1	TRUE	1	0.322184812829091	2		403	405	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55124951	55124951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	54	324	0	ENST00000257290.5:c.16C>T	p.Pro6Ser	p.P6S	ENST00000257290	NM_006206.4	6	Ccg/Tcg	2/23	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.322184812829091	NA		324	433	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946305	55946305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	68	466	0	ENST00000263923.4:c.3874G>A	p.Glu1292Lys	p.E1292K	ENST00000263923	NM_002253.2	1292	Gag/Aag	30/30	0.322184812829091	1	FACETS	0.798	0.696	0.907	0.798	0.696	0.907	CLONAL	1	TRUE	0	0.322184812829091	1		466	444	SUCCESS
ALB	213	MSKCC	GRCh37	4	74281983	74281983	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	43	364	0	ENST00000295897.4:c.1202T>G	p.Phe401Cys	p.F401C	ENST00000295897	NM_000477.5	401	tTt/tGt	10/15	1	2	FACETS	0.674	0.565	0.794	0.674	0.565	0.794	SUBCLONAL	1	TRUE	1	0.322184812829091	2		364	396	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383974	84383974	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	65	363	0	ENST00000321945.7:c.878T>G	p.Phe293Cys	p.F293C	ENST00000321945	NM_139076.2	293	tTt/tGt	9/9	1	2	FACETS	0.753	0.653	0.86	0.753	0.653	0.86	SUBCLONAL	1	TRUE	1	0.322184812829091	2		363	536	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156706	106156706	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	75	438	0	ENST00000380013.4:c.1607A>C	p.Lys536Thr	p.K536T	ENST00000380013	NM_001127208.2	536	aAa/aCa	3/11	1	2	FACETS	0.976	0.858	1	0.976	0.858	1	CLONAL	1	TRUE	1	0.322184812829091	2		438	477	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144336784	144336784	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	46	375	0	ENST00000262995.4:c.227A>C	p.Lys76Thr	p.K76T	ENST00000262995	NM_207123.2	76	aAa/aCa	2/11	1	2	FACETS	0.617	0.52	0.724	0.617	0.52	0.724	SUBCLONAL	1	TRUE	1	0.322184812829091	2		375	463	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530984	187530984	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	22	395	0	ENST00000441802.2:c.10039G>T	p.Asp3347Tyr	p.D3347Y	ENST00000441802	NM_005245.3	3347	Gat/Tat	15/27	1	2	FACETS	0.311	0.24	0.394	0.311	0.24	0.394	SUBCLONAL	1	TRUE	1	0.322184812829091	2		395	439	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950754	38950754	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	49	432	0	ENST00000357387.3:c.3196G>T	p.Glu1066Ter	p.E1066*	ENST00000357387	NM_152756.3	1066	Gaa/Taa	31/38	1	2	FACETS	0.613	0.519	0.716	0.613	0.519	0.716	SUBCLONAL	1	TRUE	1	0.322184812829091	2		432	496	SUCCESS
APC	324	MSKCC	GRCh37	5	112173285	112173285	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	60	331	0	ENST00000257430.4:c.1994T>G	p.Leu665Ter	p.L665*	ENST00000257430	NM_000038.5	665	tTa/tGa	16/16	1	2	FACETS	0.817	0.705	0.938	0.817	0.705	0.938	CLONAL	1	TRUE	1	0.322184812829091	2		331	456	SUCCESS
APC	324	MSKCC	GRCh37	5	112174590	112174590	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	53	470	0	ENST00000257430.4:c.3299C>A	p.Ser1100Tyr	p.S1100Y	ENST00000257430	NM_000038.5	1100	tCt/tAt	16/16	1	2	FACETS	0.678	0.579	0.787	0.678	0.579	0.787	SUBCLONAL	1	TRUE	1	0.322184812829091	2		470	485	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911529	131911529	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	36	352	0	ENST00000265335.6:c.274G>T	p.Glu92Ter	p.E92*	ENST00000265335		92	Gaa/Taa	3/25	1	2	FACETS	0.522	0.429	0.626	0.522	0.429	0.626	SUBCLONAL	1	TRUE	1	0.322184812829091	2		352	428	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170832312	170832312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458436735	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	28	156	0	ENST00000296930.5:c.676G>A	p.Glu226Lys	p.E226K	ENST00000296930	NM_002520.6	226	Gaa/Aaa	9/11	1	2	FACETS	0.776	0.624	0.947	0.776	0.624	0.947	CLONAL	1	TRUE	1	0.322184812829091	2		156	224	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562489	176562489	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	78	499	0	ENST00000439151.2:c.385G>A	p.Glu129Lys	p.E129K	ENST00000439151	NM_022455.4	129	Gaa/Aaa	2/23	1	2	FACETS	0.86	0.757	0.971	0.86	0.757	0.971	CLONAL	1	TRUE	1	0.322184812829091	2		499	563	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637137	176637137	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	59	468	0	ENST00000439151.2:c.1737G>T	p.Lys579Asn	p.K579N	ENST00000439151	NM_022455.4	579	aaG/aaT	5/23	1	2	FACETS	0.807	0.696	0.927	0.807	0.696	0.927	CLONAL	1	TRUE	1	0.322184812829091	2		468	454	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839941	27839941	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	143	591	0	ENST00000328488.2:c.153G>C	p.Glu51Asp	p.E51D	ENST00000328488	NM_003533.2	51	gaG/gaC	1/1	0.322184812829091	5	FACETS	0.875	0.799	0.955	0.875	0.799	0.955	CLONAL	2	TRUE	3	0.322184812829091	5		591	752	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670915	30670915	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	65	482	0	ENST00000376406.3:c.5831G>A	p.Gly1944Glu	p.G1944E	ENST00000376406	NM_014641.2	1944	gGa/gAa	12/15	1	2	FACETS	0.901	0.783	1	0.901	0.783	1	CLONAL	1	TRUE	1	0.322184812829091	2		482	448	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187498	32187498	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	70	543	0	ENST00000375023.3:c.1381T>G	p.Cys461Gly	p.C461G	ENST00000375023	NM_004557.3	461	Tgc/Ggc	8/30	1	2	FACETS	0.974	0.852	1	0.974	0.852	1	CLONAL	1	TRUE	1	0.322184812829091	2		543	446	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192498	138192498	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1422470027	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	84	425	0	ENST00000237289.4:c.134G>A	p.Arg45Gln	p.R45Q	ENST00000237289	NM_001270507.1	45	cGa/cAa	2/9	0.322184812829091	3	FACETS	0.906	0.801	1			1	CLONAL	1	TRUE	NA	0.322184812829091	3		425	668	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196933	138196933	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	59	434	0	ENST00000237289.4:c.595C>A	p.Leu199Ile	p.L199I	ENST00000237289	NM_001270507.1	199	Ctt/Att	4/9	0.322184812829091	3	FACETS	0.758	0.652	0.873			1	SUBCLONAL	1	TRUE	NA	0.322184812829091	3		434	561	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138197171	138197171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751503246	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	77	460	0	ENST00000237289.4:c.673G>A	p.Ala225Thr	p.A225T	ENST00000237289	NM_001270507.1	225	Gcc/Acc	5/9	0.322184812829091	3	FACETS	0.91	0.799	1			1	CLONAL	1	TRUE	NA	0.322184812829091	3		460	610	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510859	157510859	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	57	495	0	ENST00000346085.5:c.3634C>T	p.Pro1212Ser	p.P1212S	ENST00000346085	NM_020732.3	1212	Cca/Tca	14/20	1	2	FACETS	0.801	0.688	0.922	0.801	0.688	0.922	CLONAL	1	TRUE	1	0.322184812829091	2		495	442	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974257	2974257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868593694	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	49	314	0	ENST00000396946.4:c.1348C>T	p.Pro450Ser	p.P450S	ENST00000396946	NM_032415.4	450	Ccc/Tcc	10/25	1	2	FACETS	0.933	0.794	1	0.933	0.794	1	CLONAL	1	TRUE	1	0.322184812829091	2		314	326	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512616	148512616	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	41	378	0	ENST00000320356.2:c.1528A>G	p.Lys510Glu	p.K510E	ENST00000320356	NM_004456.4	510	Aag/Gag	13/20	1	2	FACETS	0.625	0.521	0.74	0.625	0.521	0.74	SUBCLONAL	1	TRUE	1	0.322184812829091	2		378	407	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864389	151864389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	54	354	0	ENST00000262189.6:c.9592C>T	p.Leu3198Phe	p.L3198F	ENST00000262189	NM_170606.2	3198	Ctt/Ttt	42/59	1	2	FACETS	0.721	0.617	0.835	0.721	0.617	0.835	SUBCLONAL	1	TRUE	1	0.322184812829091	2		354	465	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38156991	38156991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766760275	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	71	404	0	ENST00000317025.8:c.2729C>T	p.Ser910Leu	p.S910L	ENST00000317025	NM_023034.1	910	tCg/tTg	15/24	1	2	FACETS	0.896	0.784	1	0.896	0.784	1	CLONAL	1	TRUE	1	0.322184812829091	2		404	492	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38157028	38157028	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	35	423	0	ENST00000317025.8:c.2692C>T	p.Arg898Cys	p.R898C	ENST00000317025	NM_023034.1	898	Cgt/Tgt	15/24	1	2	FACETS	0.445	0.364	0.536	0.445	0.364	0.536	SUBCLONAL	1	TRUE	1	0.322184812829091	2		423	488	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38318615	38318615	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	62	342	0	ENST00000425967.3:c.10A>T	p.Arg4Trp	p.R4W	ENST00000425967	NM_001174067.1	4	Agg/Tgg	2/19	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.322184812829091	2		342	321	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965375	68965375	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	47	360	0	ENST00000288368.4:c.987G>T	p.Lys329Asn	p.K329N	ENST00000288368	NM_024870.2	329	aaG/aaT	9/40	0.322184812829091	1	FACETS	0.58	0.49	0.679	0.58	0.49	0.679	SUBCLONAL	1	TRUE	0	0.322184812829091	1		360	422	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046416	69046416	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	71	426	0	ENST00000288368.4:c.3889G>T	p.Glu1297Ter	p.E1297*	ENST00000288368	NM_024870.2	1297	Gag/Tag	32/40	0.322184812829091	1	FACETS	0.876	0.768	0.992	0.876	0.768	0.992	CLONAL	1	TRUE	0	0.322184812829091	1		426	422	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136801	69136801	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	49	325	0	ENST00000288368.4:c.4715G>T	p.Arg1572Ile	p.R1572I	ENST00000288368	NM_024870.2	1572	aGa/aTa	39/40	0.322184812829091	1	FACETS	0.629	0.533	0.733	0.629	0.533	0.733	SUBCLONAL	1	TRUE	0	0.322184812829091	1		325	406	SUCCESS
MTAP	4507	MSKCC	GRCh37	9	21802752	21802752	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	82	292	0	ENST00000380172.4:c.5C>T	p.Ala2Val	p.A2V	ENST00000380172	NM_002451.3	2	gCc/gTc	1/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.322184812829091	2		292	387	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409446	80409446	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	27	207	0	ENST00000286548.4:c.668T>C	p.Val223Ala	p.V223A	ENST00000286548	NM_002072.3	223	gTc/gCc	5/7	1	2	FACETS	0.748	0.599	0.917	0.748	0.599	0.917	CLONAL	1	TRUE	1	0.322184812829091	2		207	224	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912214	97912214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1166491683	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	59	358	0	ENST00000289081.3:c.677C>T	p.Ala226Val	p.A226V	ENST00000289081	NM_000136.2	226	gCc/gTc	7/15	1	2	FACETS	0.92	0.795	1	0.92	0.795	1	CLONAL	1	TRUE	1	0.322184812829091	2		358	398	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242839	98242839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765174527	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	30	388	0	ENST00000331920.6:c.778G>A	p.Asp260Asn	p.D260N	ENST00000331920	NM_000264.3	260	Gac/Aac	6/24	1	2	FACETS	0.453	0.365	0.553	0.453	0.365	0.553	SUBCLONAL	1	TRUE	1	0.322184812829091	2		388	411	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891169	101891169	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	47	376	0	ENST00000374994.4:c.130G>T	p.Asp44Tyr	p.D44Y	ENST00000374994	NM_004612.2	44	Gac/Tac	2/9	1	2	FACETS	0.663	0.56	0.776	0.663	0.56	0.776	SUBCLONAL	1	TRUE	1	0.322184812829091	2		376	440	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139565450	139565450	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1845821536	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	40	285	0	ENST00000308874.7:c.620T>C	p.Val207Ala	p.V207A	ENST00000308874		207	gTg/gCg	8/10	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.322184812829091	2		285	230	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430812	47430812	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	75	245	0	ENST00000377045.4:c.1777G>T	p.Glu593Ter	p.E593*	ENST00000377045	NM_001654.4	593	Gag/Tag	16/16	1	1	FACETS	0.896	0.799	0.997	1	0.983	1	CLONAL	2	TRUE	0	0.322184812829091	1		245	218	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938430	76938430	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	51	188	0	ENST00000373344.5:c.2318A>C	p.Lys773Thr	p.K773T	ENST00000373344	NM_000489.3	773	aAa/aCa	9/35	1	1	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	0	0.322184812829091	1		188	264	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034395	123034395	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	58	156	0	ENST00000355640.3:c.1152C>A	p.Phe384Leu	p.F384L	ENST00000355640		384	ttC/ttA	6/7	1	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.322184812829091	1		156	214	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0069404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	8	308	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	0.48	0.308	0.704	0.48	0.308	0.704	SUBCLONAL	1	TRUE	1	0.14	2		308	238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0069410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	513	474	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.641780357253387	3	FACETS	0.898	0.88	0.915	1	0.997	1	CLONAL	4	FALSE	0	0.634113874297819	3		474	593	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440943	56440943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786205215	NA	P-0069410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	81	317	0	ENST00000407977.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000407977		132	Cga/Tga	4/10	0.240708652344124	3	FACETS	0.725	0.641	0.814	0.363	0.32	0.408	INDETERMINATE	1	FALSE	1	0.634113874297819	3		317	464	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643326	38643327	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs864622410	NA	P-0069410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	262	511	0	ENST00000299084.4:c.796_797del	p.Met266ValfsTer4	p.M266Vfs*4	ENST00000299084	NM_152594.2	266	ATg/g	7/7	0.170295127590644	3	FACETS	1	0.977	1	0.703	0.667	0.739	INDETERMINATE	2	FALSE	0	0.634113874297819	3		511	516	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0069412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	47	317	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.41003453056192	3	FACETS	0.888	0.753	1	0.444	0.376	0.518	CLONAL	1	FALSE	1	0.41003453056192	3		317	311	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653815	206653815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782278442	NA	P-0069412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	100	533	0	ENST00000367120.3:c.1366C>T	p.Arg456Trp	p.R456W	ENST00000367120	NM_014002.3	456	Cgg/Tgg	13/22	0.41003453056192	3	FACETS	0.921	0.824	1	0.461	0.412	0.512	CLONAL	1	FALSE	1	0.41003453056192	3		533	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0069412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	264	420	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.124619759199794	4	FACETS	1	0.96	1			1	INDETERMINATE	3	FALSE	NA	0.41003453056192	4		420	594	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272113	15272113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243104564	NA	P-0069412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	103	627	0	ENST00000263388.2:c.6326G>A	p.Arg2109Gln	p.R2109Q	ENST00000263388	NM_000435.2	2109	cGg/cAg	33/33	0.41003453056192	3	FACETS	1	0.92	1	0.515	0.462	0.571	CLONAL	1	FALSE	1	0.41003453056192	3		627	588	SUCCESS
APC	324	MSKCC	GRCh37	5	112175366	112175366	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs863225352	NA	P-0069412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	296	494	0	ENST00000257430.4:c.4075A>T	p.Lys1359Ter	p.K1359*	ENST00000257430	NM_000038.5	1359	Aaa/Taa	16/16	0.41003453056192	3	FACETS	0.967	0.919	1	0.967	0.919	1	CLONAL	3	FALSE	0	0.41003453056192	3		494	600	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253862	153253863	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0069412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	143	281	0	ENST00000281708.4:c.870_871del	p.Tyr291CysfsTer25	p.Y291Cfs*25	ENST00000281708	NM_033632.3	290	ctCTat/ctat	6/12	0.41003453056192	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	FALSE	0	0.41003453056192	2		281	323	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0069446-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	243	339	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.548108819727662	3	FACETS	0.949	0.894	1	0.949	0.894	1	CLONAL	2	TRUE	1	0.548108819727662	3		339	595	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041757	42041758	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0069446-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	256	422	0	ENST00000219905.7:c.5955_5956del	p.Glu1987AlafsTer17	p.E1987Afs*17	ENST00000219905	NM_001164273.1	1984	atAAaa/ataa	17/24	0.544744922230608	2	FACETS	0.903	0.856	0.951	0.903	0.856	0.951	CLONAL	2	TRUE	0	0.548108819727662	2		422	517	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0069447-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	115	334	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.925	0.837	1	1	0.988	1	CLONAL	2	FALSE	1	0.235462961068783	2		334	528	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0069447-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	20	547	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.338	0.257	0.433	0.338	0.257	0.433	SUBCLONAL	1	FALSE	1	0.235462961068783	2		547	503	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0069447-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	54	133	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.84	0.723	0.965	1	0.972	1	CLONAL	2	FALSE	1	0.235462961068783	2		133	273	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069447-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	99	362	0	ENST00000263967.3:c.3073A>T	p.Thr1025Ser	p.T1025S	ENST00000263967	NM_006218.2	1025	Acc/Tcc	21/21	1	2	FACETS	0.767	0.687	0.852	1	0.982	1	SUBCLONAL	2	FALSE	1	0.235462961068783	2		362	548	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331643	8331643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770713312	NA	P-0069447-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	48	372	1	ENST00000356435.5:c.5473G>A	p.Gly1825Ser	p.G1825S	ENST00000356435		1825	Ggc/Agc	33/35	1	2	FACETS	0.853	0.722	0.997	0.853	0.722	0.997	CLONAL	1	FALSE	1	0.235462961068783	2		373	478	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56171089	56171095	+	frameshift_variant	Frame_Shift_Del	DEL	GTCAATG	GTCAATG	-	novel	NA	P-0069447-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	87	360	0	ENST00000399503.3:c.1920_1926del	p.Met641ValfsTer13	p.M641Vfs*13	ENST00000399503	NM_005921.1	639	ctGTCAATG/ct	10/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.235462961068783	2		360	493	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178590	56178591	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0069447-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	49	376	0	ENST00000399503.3:c.3566dup	p.Leu1189PhefsTer23	p.L1189Ffs*23	ENST00000399503	NM_005921.1	1188	gct/gcTt	14/20	1	2	FACETS	0.71	0.601	0.831	0.71	0.601	0.831	SUBCLONAL	1	FALSE	1	0.235462961068783	2		376	586	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0069448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	44	382	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.664	0.565	0.77	0.664	0.565	0.77	SUBCLONAL	1	TRUE	1	0.732451036547457	2		382	181	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	119	250	0	ENST00000263967.3:c.1034A>G	p.Asn345Ser	p.N345S	ENST00000263967	NM_006218.2	345	aAt/aGt	5/21	1	2	FACETS	0.92	0.84	1	0.92	0.84	1	CLONAL	1	TRUE	1	0.732451036547457	2		250	353	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16041478	16041478	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	106	175	0	ENST00000268712.3:c.1401G>C	p.Glu467Asp	p.E467D	ENST00000268712	NM_006311.3	467	gaG/gaC	13/46	1	2	FACETS	0.922	0.837	1	0.922	0.837	1	CLONAL	1	TRUE	1	0.732451036547457	2		175	314	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245843	46245843	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	240	415	0	ENST00000334344.6:c.3937C>T	p.Gln1313Ter	p.Q1313*	ENST00000334344	NM_152641.2	1313	Caa/Taa	15/21	1	2	FACETS	0.995	0.94	1	0.995	0.94	1	CLONAL	1	TRUE	1	0.94754181776663	2		415	509	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485442	57485442	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	513	273	0	ENST00000371085.3:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000371085	NM_000516.4	342	Cga/Tga	12/13	0.632978257861592	4	FACETS	0.963	0.935	0.99	0.963	0.935	0.99	CLONAL	3	TRUE	1	0.94754181776663	4		273	730	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256531	+	missense_variant	Missense_Mutation	DNP	GT	GT	TG	novel	NA	P-0069449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	729	313	0	ENST00000369535.4:c.180_181delinsCA	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	60	ggACaa/ggCAaa	3/7	0.862083628442125	5	FACETS	0.965	0.944	0.986			1	CLONAL	4	TRUE	NA	0.94754181776663	5		313	965	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420093	41420093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	426	350	0	ENST00000373198.4:c.228G>A	p.Met76Ile	p.M76I	ENST00000373198	NM_133170.3	76	atG/atA	3/32	0.632978257861592	4	FACETS	0.912	0.881	0.942	0.912	0.881	0.942	CLONAL	3	TRUE	1	0.94754181776663	4		350	640	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759696	133759697	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0069449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	147	353	0	ENST00000318560.5:c.2019_2020delinsTT	p.Arg674Trp	p.R674W	ENST00000318560	NM_005157.4	673	ctCCgg/ctTTgg	11/11	0.944570020382996	2	FACETS	1	0.956	1	0.519	0.483	0.555	CLONAL	1	TRUE	0	0.94754181776663	2		353	299	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239851	98239851	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	156	283	0	ENST00000331920.6:c.1481C>T	p.Ser494Phe	p.S494F	ENST00000331920	NM_000264.3	494	tCc/tTc	10/24	0.94754181776663	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.94754181776663	1		283	173	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528078	103528078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368829739	NA	P-0069449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	220	327	0	ENST00000355739.4:c.3386C>T	p.Ser1129Leu	p.S1129L	ENST00000355739	NM_000123.3	1129	tCg/tTg	15/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.94754181776663	2		327	441	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169999008	169999008	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	298	233	0	ENST00000295797.4:c.937C>T	p.Pro313Ser	p.P313S	ENST00000295797	NM_002740.5	313	Cct/Tct	10/18	0.803983492010418	3	FACETS	0.97	0.928	1	0.97	0.928	1	CLONAL	2	TRUE	1	0.94754181776663	3		233	478	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350155	81350155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758567520	NA	P-0069449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	311	211	0	ENST00000222390.5:c.1177C>T	p.Arg393Cys	p.R393C	ENST00000222390	NM_000601.4	393	Cgt/Tgt	10/18	0.474122561826583	6	FACETS	0.896	0.851	0.941	0.896	0.851	0.941	INDETERMINATE	3	TRUE	3	0.94754181776663	6		211	707	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133968	41133968	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767908809	NA	P-0069449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	227	422	0	ENST00000379561.5:c.1660C>T	p.Arg554Cys	p.R554C	ENST00000379561	NM_002015.3	554	Cgc/Tgc	2/3	1	2	FACETS	0.879	0.826	0.932	0.879	0.826	0.932	CLONAL	1	TRUE	1	0.94754181776663	2		422	545	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0069449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	98	385	0				ENST00000310581	NM_198253.2	-/1132			0.93242807515998	3	FACETS	1	0.942	1	0.529	0.478	0.582	CLONAL	1	TRUE	1	0.94754181776663	3		385	288	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956955	2956955	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	343	324	0	ENST00000396946.4:c.2672G>A	p.Arg891Gln	p.R891Q	ENST00000396946	NM_032415.4	891	cGa/cAa	20/25	0.829059542956105	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.94754181776663	4		324	642	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248422	212248422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	266	382	0	ENST00000342788.4:c.3845C>T	p.Pro1282Leu	p.P1282L	ENST00000342788	NM_005235.2	1282	cCt/cTt	28/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.94754181776663	2		382	516	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760719	59760719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	235	312	0	ENST00000259008.2:c.3688G>A	p.Glu1230Lys	p.E1230K	ENST00000259008	NM_032043.2	1230	Gaa/Aaa	20/20	0.94754181776663	4	FACETS	1	0.958	1	0.344	0.321	0.368	CLONAL	1	TRUE	1	0.94754181776663	4		312	935	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560491	95560491	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	183	326	0	ENST00000393063.1:c.5098T>C	p.Cys1700Arg	p.C1700R	ENST00000393063	NM_030621.3	1700	Tgt/Cgt	25/28	1	2	FACETS	0.971	0.908	1	0.971	0.908	1	CLONAL	1	TRUE	1	0.94754181776663	2		326	398	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78426129	78426129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	213	348	0	ENST00000370768.2:c.1396C>T	p.Pro466Ser	p.P466S	ENST00000370768	NM_003902.3	466	Cca/Tca	15/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.94754181776663	2		348	428	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845732	151845732	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	199	372	0	ENST00000262189.6:c.13280G>A	p.Trp4427Ter	p.W4427*	ENST00000262189	NM_170606.2	4427	tGg/tAg	52/59	0.474122561826583	6	FACETS	1	0.988	1	0.439	0.406	0.472	INDETERMINATE	1	TRUE	3	0.94754181776663	6		372	924	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108254	8108254	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	160	370	0	ENST00000585124.1:c.970C>T	p.His324Tyr	p.H324Y	ENST00000585124	NM_004217.3	324	Cac/Tac	9/9	1	2	FACETS	0.886	0.824	0.95	0.886	0.824	0.95	CLONAL	1	TRUE	1	0.94754181776663	2		370	381	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099437	27099437	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	220	357	0	ENST00000324856.7:c.3674C>T	p.Ser1225Phe	p.S1225F	ENST00000324856	NM_006015.4	1225	tCc/tTc	14/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.94754181776663	2		357	439	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41249303	41249303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854961	NA	P-0069449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	170	208	0	ENST00000357654.3:c.551C>T	p.Ser184Phe	p.S184F	ENST00000357654	NM_007294.3	184	tCt/tTt	8/23	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.94754181776663	2		208	349	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110609	8110609	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	182	322	0	ENST00000585124.1:c.283C>T	p.Arg95Trp	p.R95W	ENST00000585124	NM_004217.3	95	Cgg/Tgg	5/9	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.94754181776663	2		322	372	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61324136	61324136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	186	278	0	ENST00000283752.5:c.697G>A	p.Glu233Lys	p.E233K	ENST00000283752	NM_006919.2	233	Gaa/Aaa	7/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.94754181776663	2		278	376	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032374	10032374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	194	290	0	ENST00000330684.3:c.449C>T	p.Ser150Phe	p.S150F	ENST00000330684	NM_001134407.1	150	tCc/tTc	3/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.94754181776663	2		290	386	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245590	46245599	+	frameshift_variant	Frame_Shift_Del	DEL	ATCATGTACT	ATCATGTACT	-	novel	NA	P-0069449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	234	361	0	ENST00000334344.6:c.3685_3694del	p.Ser1229LeufsTer11	p.S1229Lfs*11	ENST00000334344	NM_152641.2	1228	tcATCATGTACT/tc	15/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.94754181776663	2		361	460	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606275	93606275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	152	414	0	ENST00000375746.1:c.95G>A	p.Gly32Glu	p.G32E	ENST00000375746	NM_001174167.1	32	gGg/gAg	2/14	0.94754181776663	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.94754181776663	1		414	163	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222990	1222990	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	221	349	0	ENST00000326873.7:c.927C>A	p.Phe309Leu	p.F309L	ENST00000326873	NM_000455.4	309	ttC/ttA	8/10	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.94754181776663	2		349	418	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265192	5265192	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	109	351	0	ENST00000357368.4:c.395C>G	p.Ser132Cys	p.S132C	ENST00000357368	NM_002850.3	132	tCt/tGt	5/38	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.333316801123709	2		351	646	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279352	18279352	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	116	398	0	ENST00000222254.8:c.1804G>A	p.Glu602Lys	p.E602K	ENST00000222254	NM_005027.3	602	Gag/Aag	14/16	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.333316801123709	2		398	674	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198269871	198269871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	128	316	0	ENST00000335508.6:c.1468G>A	p.Glu490Lys	p.E490K	ENST00000335508	NM_012433.2	490	Gaa/Aaa	11/25	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.333316801123709	2		316	646	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42002918	42002918	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	94	283	0	ENST00000219905.7:c.2455C>A	p.Arg819Ser	p.R819S	ENST00000219905	NM_001164273.1	819	Cgt/Agt	8/24	1	2	FACETS	0.92	0.82	1	0.92	0.82	1	CLONAL	1	TRUE	1	0.333316801123709	2		283	613	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867239	68867239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	98	395	0	ENST00000261769.5:c.2486C>T	p.Ser829Phe	p.S829F	ENST00000261769	NM_004360.3	829	tCt/tTt	16/16	1	2	FACETS	0.895	0.799	0.997	0.895	0.799	0.997	CLONAL	1	TRUE	1	0.333316801123709	2		395	657	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955581	90955581	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	79	261	0	ENST00000265433.3:c.2084G>C	p.Gly695Ala	p.G695A	ENST00000265433	NM_002485.4	695	gGa/gCa	14/16	0.333316801123709	7	FACETS	0.929	0.816	1	0.155	0.136	0.176	CLONAL	1	TRUE	1	0.333316801123709	7		261	935	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793847	89793847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	119	393	0	ENST00000336032.3:c.916G>A	p.Glu306Lys	p.E306K	ENST00000336032	NM_006813.2	306	Gaa/Aaa	2/2	0.333316801123709	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.333316801123709	1		393	590	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931931	39931931	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	154	412	0	ENST00000378444.4:c.2668G>C	p.Glu890Gln	p.E890Q	ENST00000378444	NM_001123385.1	890	Gag/Cag	4/15	0.333316801123709	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.333316801123709	1		412	557	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176500	142176500	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	116	261	0	ENST00000350721.4:c.7601G>C	p.Arg2534Thr	p.R2534T	ENST00000350721	NM_001184.3	2534	aGa/aCa	45/47	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.333316801123709	2		261	566	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518165	187518165	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	91	398	0	ENST00000441802.2:c.12529A>T	p.Ile4177Phe	p.I4177F	ENST00000441802	NM_005245.3	4177	Att/Ttt	25/27	1	2	FACETS	0.869	0.773	0.972	0.869	0.773	0.972	CLONAL	1	TRUE	1	0.333316801123709	2		398	628	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374368	138374368	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	105	304	0	ENST00000289153.2:c.3076G>A	p.Asp1026Asn	p.D1026N	ENST00000289153	NM_006219.2	1026	Gac/Aac	22/22	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.333316801123709	2		304	609	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056998	180056998	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	120	450	0	ENST00000261937.6:c.621G>C	p.Glu207Asp	p.E207D	ENST00000261937	NM_182925.4	207	gaG/gaC	5/30	0.107593357464051	0	FACETS	0.754	0.682	0.829			1	INDETERMINATE	1	TRUE	0	0.333316801123709	0		450	637	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112052	115112052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	119	451	0	ENST00000257566.3:c.1688C>T	p.Ser563Phe	p.S563F	ENST00000257566	NM_016569.3	563	tCt/tTt	7/8	0.304821368055758	3	FACETS	1	0.941	1	0.529	0.478	0.584	CLONAL	1	TRUE	1	0.333316801123709	3		451	787	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888312	112888312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507518	NA	P-0069451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	95	310	0	ENST00000351677.2:c.328G>A	p.Glu110Lys	p.E110K	ENST00000351677	NM_002834.3	110	Gaa/Aaa	3/16	0.304821368055758	3	FACETS	0.942	0.839	1	0.471	0.419	0.526	CLONAL	1	TRUE	1	0.333316801123709	3		310	706	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257426	16257426	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	106	382	0	ENST00000375759.3:c.4691A>C	p.Gln1564Pro	p.Q1564P	ENST00000375759	NM_015001.2	1564	cAg/cCg	11/15	1	2	FACETS	0.831	0.745	0.923	0.831	0.745	0.923	CLONAL	1	TRUE	1	0.333316801123709	2		382	765	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213936	2213936	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs748444237	NA	P-0069451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	140	437	0	ENST00000326181.6:c.15G>C	p.Lys5Asn	p.K5N	ENST00000326181	NM_032271.2	5	aaG/aaC	2/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.333316801123709	2		437	675	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636729	2636729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	126	410	0	ENST00000342085.4:c.1178C>T	p.Ser393Phe	p.S393F	ENST00000342085	NM_002613.4	393	tCc/tTc	11/14	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.333316801123709	2		410	728	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544947	86544947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	59	286	0	ENST00000262426.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000262426	NM_001451.2	258	Gag/Aag	1/2	1	2	FACETS	0.799	0.689	0.918	0.799	0.689	0.918	CLONAL	1	TRUE	1	0.333316801123709	2		286	443	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574715	41574715	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	134	468	0	ENST00000263253.7:c.7000C>T	p.Gln2334Ter	p.Q2334*	ENST00000263253	NM_001429.3	2334	Cag/Tag	31/31	1	2	FACETS	0.993	0.902	1	0.993	0.902	1	CLONAL	1	TRUE	1	0.333316801123709	2		468	810	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350629	89350629	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0069451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	115	324	0	ENST00000301030.4:c.2321C>G	p.Ser774Ter	p.S774*	ENST00000301030	NM_001256183.1	774	tCa/tGa	9/13	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.333316801123709	2		324	684	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0069454-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	25	317	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.323014995961502	2	FACETS	1	0.867	1	0.558	0.446	0.684	CLONAL	1	TRUE	0	0.326776914105964	2		317	137	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0069454-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	115	374	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.326776914105964	2	FACETS	0.844	0.773	0.916	1	0.981	1	CLONAL	3	TRUE	0	0.326776914105964	2		374	278	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243984	5243984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173811578	NA	P-0069454-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	106	252	1	ENST00000357368.4:c.1498C>T	p.Arg500Trp	p.R500W	ENST00000357368	NM_002850.3	500	Cgg/Tgg	11/38	0.326776914105964	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.326776914105964	2		253	307	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755704	39755704	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1404777513	NA	P-0069454-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	73	238	0	ENST00000288319.7:c.1061G>A	p.Arg354Gln	p.R354Q	ENST00000288319	NM_182918.3	354	cGg/cAg	10/10	0.189589236116978	3	FACETS	0.822	0.725	0.925	0.822	0.725	0.925	INDETERMINATE	2	TRUE	1	0.326776914105964	3		238	316	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845572	128845572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775852783	NA	P-0069454-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	33	230	0	ENST00000249373.3:c.869G>A	p.Arg290His	p.R290H	ENST00000249373	NM_005631.4	290	cGc/cAc	4/12	0.317097154305089	4	FACETS	0.698	0.569	0.843	0.233	0.189	0.281	SUBCLONAL	1	TRUE	1	0.326776914105964	4		230	384	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980416	201980417	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGAG	novel	NA	P-0069454-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	237	239	0	ENST00000359651.3:c.155_158dup	p.Thr54GlyfsTer39	p.T54Gfs*39	ENST00000359651		51	ttg/ttGGAGg	1/8	0.317097154305089	4	FACETS	0.923	0.871	0.976	1	0.99	1	CLONAL	4	TRUE	1	0.326776914105964	4		239	521	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819210	3819210	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141734994	NA	P-0069454-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	86	272	0	ENST00000262367.5:c.3025G>A	p.Asp1009Asn	p.D1009N	ENST00000262367	NM_004380.2	1009	Gat/Aat	15/31	0.21177920051037	5	FACETS	1	0.92	1	0.694	0.618	0.773	CLONAL	2	TRUE	2	0.326776914105964	5		272	377	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0069455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	88	382	0				ENST00000310581	NM_198253.2	-/1132			0.262664843680458	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.392888334476017	1		382	240	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447085	49447086	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0069455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	172	335	0	ENST00000301067.7:c.858dup	p.Lys287Ter	p.K287*	ENST00000301067	NM_003482.3	286	-/T	7/54	1	2	FACETS	0.831	0.77	0.893	1	0.991	1	CLONAL	2	TRUE	1	0.392888334476017	2		335	527	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0069455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	152	266	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	0.889	0.821	0.959	1	0.991	1	CLONAL	2	TRUE	1	0.392888334476017	2		266	435	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0069455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	20	383	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.195	0.148	0.25	0.195	0.148	0.25	SUBCLONAL	1	TRUE	1	0.392888334476017	2		383	522	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859782	151859782	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0069455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	213	365	0	ENST00000262189.6:c.10880C>G	p.Ser3627Ter	p.S3627*	ENST00000262189	NM_170606.2	3627	tCa/tGa	43/59	1	2	FACETS	0.833	0.778	0.889	1	0.993	1	CLONAL	2	TRUE	1	0.392888334476017	2		365	651	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0069455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	314	333	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.392888334476017	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	3	TRUE	0	0.392888334476017	2		333	492	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49423183	49423183	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1057516039	NA	P-0069455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	152	288	0	ENST00000301067.7:c.14075+1G>A		p.X4692_splice	ENST00000301067	NM_003482.3	4692			1	2	FACETS	0.783	0.721	0.847	1	0.989	1	SUBCLONAL	2	TRUE	1	0.392888334476017	2		288	494	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061349	38061394	+	frameshift_variant	Frame_Shift_Del	DEL	AGCGCTGCTGGTTCTGCCGGTAATAGGGGAAGAGGTCCATGATCCA	AGCGCTGCTGGTTCTGCCGGTAATAGGGGAAGAGGTCCATGATCCA	-	novel	NA	P-0069455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	11	334	0	ENST00000250448.2:c.595_640del	p.Trp199GlyfsTer107	p.W199Gfs*107	ENST00000250448	NM_004496.3	199	TGGATCATGGACCTCTTCCCCTATTACCGGCAGAACCAGCAGCGCTgg/gg	2/2	0.392888334476017	1	FACETS	0.117	0.08	0.163	0.117	0.08	0.163	SUBCLONAL	1	TRUE	0	0.392888334476017	1		334	385	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781790	3781791	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0069455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	142	309	0	ENST00000262367.5:c.4876dup	p.Glu1626GlyfsTer34	p.E1626Gfs*34	ENST00000262367	NM_004380.2	1626	gag/gGag	29/31	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.392888334476017	2		309	521	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46252719	46252719	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	128	211	0	ENST00000371998.3:c.148G>C	p.Glu50Gln	p.E50Q	ENST00000371998		50	Gag/Cag	4/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.392888334476017	2		211	446	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253863	153253865	+	frameshift_variant	Frame_Shift_Del	DEL	GAG	GAG	AA	novel	NA	P-0069455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	19	178	0	ENST00000281708.4:c.868_870delinsTT	p.Leu290PhefsTer52	p.L290Ffs*52	ENST00000281708	NM_033632.3	290	CTC/TT	6/12	1	2	FACETS	0.286	0.217	0.368	0.286	0.217	0.368	SUBCLONAL	1	TRUE	1	0.392888334476017	2		178	338	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220539	123220540	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0069455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	154	156	0	ENST00000218089.9:c.3201dup	p.Ser1068ValfsTer6	p.S1068Vfs*6	ENST00000218089	NM_001042749.1	1066	cgg/cGgg	30/35	1	1	FACETS	0.875	0.824	0.924	1	0.994	1	CLONAL	3	TRUE	0	0.392888334476017	1		156	240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0069456-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	256	639	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.711104711722316	2	FACETS	0.833	0.796	0.87	0.833	0.796	0.87	CLONAL	2	TRUE	0	0.773947196557308	2		639	397	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048629	6048629	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	rs772406975	NA	P-0069457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	72	397	0	ENST00000265849.7:c.22A>T	p.Ser8Cys	p.S8C	ENST00000265849	NM_000535.5	8	Agt/Tgt	1/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.18	2		397	601	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509101	106509101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1209717028	NA	P-0069457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	41	283	0	ENST00000359195.3:c.1095C>G	p.Ile365Met	p.I365M	ENST00000359195	NM_002649.2	365	atC/atG	2/11	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.18	2		283	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0069458-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	214	390	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		390	314	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624974	9624974	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0069458-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	84	247	0	ENST00000353224.5:c.3G>A	p.Met1?	p.M1?	ENST00000353224	NM_177990.2	1	atG/atA	3/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		247	423	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465587	8465587	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069458-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	93	268	0	ENST00000356435.5:c.3593T>C	p.Val1198Ala	p.V1198A	ENST00000356435		1198	gTc/gCc	21/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		268	384	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396739	139396763	+	frameshift_variant	Frame_Shift_Del	DEL	TCCTCGCCGAGGGGCTCCCGCCGCT	TCCTCGCCGAGGGGCTCCCGCCGCT	-	novel	NA	P-0069458-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	286	263	0	ENST00000277541.6:c.5345_5369del	p.Lys1782ThrfsTer8	p.K1782Tfs*8	ENST00000277541	NM_017617.3	1782	aAGCGGCGGGAGCCCCTCGGCGAGGAc/ac	28/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		263	436	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877870	151877870	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069458-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	233	339	0	ENST00000262189.6:c.7075G>C	p.Val2359Leu	p.V2359L	ENST00000262189	NM_170606.2	2359	Gtg/Ctg	36/59	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		339	324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0069461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	111	420	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.32144569567693	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.32144569567693	2		420	295	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0069461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	66	395	4	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.32144569567693	2		399	302	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81927367	81927367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781016626	NA	P-0069461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	38	274	0	ENST00000359376.3:c.1040G>A	p.Arg347His	p.R347H	ENST00000359376	NM_002661.3	347	cGc/cAc	12/33	1	2	FACETS	0.909	0.756	1	0.909	0.756	1	CLONAL	1	TRUE	1	0.32144569567693	2		274	260	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604707	48604707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	48	432	3	ENST00000342988.3:c.1529G>A	p.Gly510Glu	p.G510E	ENST00000342988	NM_005359.5	510	gGa/gAa	12/12	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.32144569567693	2		435	294	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467750	50467750	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	62	412	5	ENST00000331340.3:c.985C>T	p.Pro329Ser	p.P329S	ENST00000331340	NM_006060.4	329	Ccg/Tcg	8/8	0.32144569567693	5	FACETS	0.956	0.833	1	0.956	0.833	1	CLONAL	2	TRUE	3	0.32144569567693	5		417	299	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238957	5238957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760549393	NA	P-0069461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	24	354	7	ENST00000357368.4:c.1822G>A	p.Val608Met	p.V608M	ENST00000357368	NM_002850.3	608	Gtg/Atg	13/38	0.215906158492234	1	FACETS	0.586	0.461	0.727	0.586	0.461	0.727	SUBCLONAL	1	TRUE	0	0.32144569567693	1		361	214	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600594	43600594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	13	417	0	ENST00000355710.3:c.820G>A	p.Ala274Thr	p.A274T	ENST00000355710	NM_020975.4	274	Gcg/Acg	4/20	0.215768012197596	3	FACETS	0.383	0.273	0.518	0.192	0.136	0.259	SUBCLONAL	1	TRUE	1	0.32144569567693	3		417	245	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330643	65330651	+	inframe_deletion	In_Frame_Del	DEL	CAACAGAAA	CAACAGAAA	-	novel	NA	P-0069461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	17	377	0	ENST00000342505.4:c.995_1003del	p.Val332_Val334del	p.V332_V334del	ENST00000342505	NM_002227.2	332	gTTTCTGTTGaa/gaa	8/25	0.32144569567693	3	FACETS	0.378	0.281	0.493	0.189	0.14	0.247	SUBCLONAL	1	TRUE	1	0.32144569567693	3		377	325	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118862	70118862	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0069461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	108	433	7	ENST00000245479.2:c.435del	p.Leu146Ter	p.L146*	ENST00000245479	NM_000346.3	145	cTt/ct	2/3	0.32144569567693	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.32144569567693	2		440	273	SUCCESS
REST	5978	MSKCC	GRCh37	4	57797199	57797200	+	missense_variant	Missense_Mutation	DNP	GA	GA	TC	novel	NA	P-0069461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	26	509	0	ENST00000309042.7:c.2175_2176inv	p.Gln725_Lys726delinsHisGln	p.Q725_K726delinsHQ	ENST00000309042	NM_005612.4	725	caGAag/caTCag	4/4	0.32144569567693	1	FACETS	0.465	0.369	0.575	0.465	0.369	0.575	SUBCLONAL	1	TRUE	0	0.32144569567693	1		509	292	SUCCESS
AR	367	MSKCC	GRCh37	X	66766096	66766096	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1326711596	NA	P-0069461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	12	460	0	ENST00000374690.3:c.1108G>T	p.Ala370Ser	p.A370S	ENST00000374690	NM_000044.3	370	Gct/Tct	1/8	0.121846073186309	0	FACETS	0.228	0.16	0.312			1	INDETERMINATE	1	TRUE	0	0.32144569567693	0		460	222	SUCCESS
APC	324	MSKCC	GRCh37	5	112175128	112175128	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0069461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	49	399	1	ENST00000257430.4:c.3839del	p.Leu1280CysfsTer8	p.L1280Cfs*8	ENST00000257430	NM_000038.5	1279	tcT/tc	16/16	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.32144569567693	2		400	305	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057916	27057916	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1268688430	NA	P-0069461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	17	434	0	ENST00000324856.7:c.1624C>G	p.Gln542Glu	p.Q542E	ENST00000324856	NM_006015.4	542	Cag/Gag	3/20	NA	2	FACETS	0.312	0.232	0.407			1	INDETERMINATE	1	TRUE	NA	0.32144569567693	2		434	339	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110689	2110689	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	15	315	0	ENST00000219476.3:c.994G>C	p.Glu332Gln	p.E332Q	ENST00000219476	NM_000548.3	332	Gag/Cag	11/42	1	2	FACETS	0.332	0.242	0.44	0.332	0.242	0.44	SUBCLONAL	1	TRUE	1	0.32144569567693	2		315	281	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932930	39932961	+	frameshift_variant	Frame_Shift_Del	DEL	CGTTAGTGATGACAGCATCGGTGCCGCCCATG	CGTTAGTGATGACAGCATCGGTGCCGCCCATG	-	novel	NA	P-0069461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	18	489	0	ENST00000378444.4:c.1638_1669del	p.Met547PhefsTer53	p.M547Ffs*53	ENST00000378444	NM_001123385.1	546	cgCATGGGCGGCACCGATGCTGTCATCACTAACGtt/cgtt	4/15	0.32144569567693	3	FACETS	0.371	0.279	0.481	0.186	0.139	0.241	SUBCLONAL	1	TRUE	1	0.32144569567693	3		489	350	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818800	32818800	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	98	400	2	ENST00000354258.4:c.1151C>T	p.Ser384Leu	p.S384L	ENST00000354258	NM_000593.5	384	tCa/tTa	4/11	0.188878590110798	5	FACETS	1	0.971	1	0.812	0.731	0.897	INDETERMINATE	2	TRUE	2	0.32144569567693	5		402	371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587781702	NA	P-0069485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	264	339	0	ENST00000269305.4:c.920-1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.357111505008342	4	FACETS	0.855	0.805	0.907	0.855	0.805	0.907	CLONAL	3	TRUE	1	0.354602124633977	4		339	786	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225367728	225367728	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0069485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	78	221	0	ENST00000264414.4:c.1439C>G	p.Ser480Ter	p.S480*	ENST00000264414	NM_003590.4	480	tCa/tGa	10/16	0.348923147150475	2	FACETS	1	0.938	1	0.549	0.484	0.617	CLONAL	1	TRUE	0	0.354602124633977	2		221	401	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396362	139396362	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	197	366	0	ENST00000277541.6:c.5476G>T	p.Glu1826Ter	p.E1826*	ENST00000277541	NM_017617.3	1826	Gag/Tag	30/34	0.247831089267915	3	FACETS	1	0.976	1	0.735	0.685	0.787	CLONAL	2	TRUE	0	0.354602124633977	3		366	593	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045670	26045670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	106	381	0	ENST00000540144.1:c.32C>T	p.Ser11Phe	p.S11F	ENST00000540144	NM_003531.2	11	tCt/tTt	1/1	0.354602124633977	5	FACETS	1	0.901	1			1	CLONAL	1	TRUE	NA	0.354602124633977	5		381	910	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264900	46264900	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	108	350	0	ENST00000371998.3:c.1770A>T	p.Arg590Ser	p.R590S	ENST00000371998		590	agA/agT	12/23	0.247831089267915	3	FACETS	1	0.969	1	0.4	0.359	0.442	CLONAL	1	TRUE	0	0.354602124633977	3		350	598	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550857	150550857	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	156	364	0	ENST00000369026.2:c.799C>G	p.Leu267Val	p.L267V	ENST00000369026	NM_021960.4	267	Ctc/Gtc	2/3	0.345215520642705	4	FACETS	1	0.925	1	0.338	0.308	0.368	CLONAL	1	TRUE	1	0.354602124633977	4		364	1177	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288698	198288702	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTAT	TCTAT	-	novel	NA	P-0069485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	85	210	0	ENST00000335508.6:c.29-4_29del		p.X10_splice	ENST00000335508	NM_012433.2	10		2/25	0.354602124633977	5	FACETS	1	0.952	1			1	CLONAL	1	TRUE	NA	0.354602124633977	5		210	641	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778116	27778117	+	missense_variant	Missense_Mutation	DNP	GC	GC	CT	novel	NA	P-0069485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	149	496	0	ENST00000369163.2:c.265_266delinsCT	p.Ala89Leu	p.A89L	ENST00000369163	NM_003536.2	89	GCg/CTg	1/1	0.354602124633977	5	FACETS	1	0.962	1			1	CLONAL	1	TRUE	NA	0.354602124633977	5		496	1172	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0069486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	125	381	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.216841697795126	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.216841697795126	2		381	534	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254594	1254594	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35719940	NA	P-0069486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	44	276	0	ENST00000310581.5:c.3184G>A	p.Ala1062Thr	p.A1062T	ENST00000310581	NM_198253.2	1062	Gcc/Acc	15/16	0.216841697795126	3	FACETS	1	0.936	1	0.62	0.521	0.728	CLONAL	1	TRUE	1	0.216841697795126	3		276	363	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0069487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	131	405	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.162263425231125	4	FACETS	0.843	0.767	0.922	0.843	0.767	0.922	INDETERMINATE	2	TRUE	2	0.339043267143551	4		405	614	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401555	401555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	49	379	0	ENST00000380956.4:c.877C>T	p.Pro293Ser	p.P293S	ENST00000380956	NM_001195286.1	293	Ccc/Tcc	7/9	1	2	FACETS	0.567	0.48	0.662	0.567	0.48	0.662	SUBCLONAL	1	TRUE	1	0.339043267143551	2		379	510	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574032	7574032	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0069487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	74	243	0	ENST00000269305.4:c.995T>A	p.Ile332Asn	p.I332N	ENST00000269305	NM_001126112.2	332	aTc/aAc	10/11	0.282248194026634	1	FACETS	0.957	0.842	1	0.957	0.842	1	CLONAL	1	TRUE	0	0.339043267143551	1		243	379	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039905	47039905	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	65	214	0	ENST00000377604.3:c.1248G>T	p.Gln416His	p.Q416H	ENST00000377604	NM_001204468.1	416	caG/caT	12/24	0.253388667332717	1	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	0	0.339043267143551	1		214	311	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0069515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	152	371	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.548558593614245	2		371	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0069515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	305	420	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.489276403489705	2	FACETS	0.89	0.846	0.933	0.89	0.846	0.933	CLONAL	2	TRUE	0	0.548558593614245	2		420	625	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2969661	2969661	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112690795	NA	P-0069515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	135	271	0	ENST00000396946.4:c.1618G>A	p.Gly540Arg	p.G540R	ENST00000396946	NM_032415.4	540	Gga/Aga	12/25	1	2	FACETS	0.954	0.872	1	0.954	0.872	1	CLONAL	1	TRUE	1	0.548558593614245	2		271	516	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123697	46123697	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0069515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	140	321	0	ENST00000334344.6:c.79del	p.His27ThrfsTer31	p.H27Tfs*31	ENST00000334344	NM_152641.2	26	ttC/tt	1/21	1	2	FACETS	0.983	0.901	1	0.983	0.901	1	CLONAL	1	TRUE	1	0.548558593614245	2		321	519	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132982	30132982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750421913	NA	P-0069515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	107	317	0	ENST00000331968.5:c.619G>A	p.Val207Ile	p.V207I	ENST00000331968	NM_002742.2	207	Gtt/Att	4/18	1	2	FACETS	0.762	0.686	0.841	0.762	0.686	0.841	SUBCLONAL	1	TRUE	1	0.548558593614245	2		317	512	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652803	212652803	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200302763	NA	P-0069515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	82	230	0	ENST00000342788.4:c.503G>A	p.Arg168Gln	p.R168Q	ENST00000342788	NM_005235.2	168	cGg/cAg	4/28	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.548558593614245	2		230	292	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285565	46285565	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	103	204	0	ENST00000334344.6:c.4925G>A	p.Trp1642Ter	p.W1642*	ENST00000334344	NM_152641.2	1642	tGg/tAg	17/21	1	2	FACETS	0.92	0.83	1	0.92	0.83	1	CLONAL	1	TRUE	1	0.548558593614245	2		204	408	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524957	8524957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776042694	NA	P-0069515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	136	195	0	ENST00000356435.5:c.647G>A	p.Arg216His	p.R216H	ENST00000356435		216	cGc/cAc	7/35	0.548558593614245	1	FACETS	0.981	0.902	1	0.981	0.902	1	CLONAL	1	TRUE	0	0.548558593614245	1		195	367	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124491933	124491933	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	66	195	0	ENST00000357628.3:c.942C>A	p.Ser314Arg	p.S314R	ENST00000357628	NM_015450.2	314	agC/agA	11/19	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.548558593614245	2		195	237	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969346	44969346	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	88	252	0	ENST00000377967.4:c.4028T>A	p.Phe1343Tyr	p.F1343Y	ENST00000377967	NM_021140.2	1343	tTt/tAt	28/29	1	2	FACETS	0.849	0.757	0.945	0.849	0.757	0.945	CLONAL	1	TRUE	1	0.548558593614245	2		252	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0069516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	230	420	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.37299435233514	2	FACETS	0.949	0.89	1	0.949	0.89	1	CLONAL	2	TRUE	0	0.37299435233514	2		420	650	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0069516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	45	192	1	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	0.339271719222225	2	FACETS	1	0.933	1			1	CLONAL	1	TRUE	NA	0.37299435233514	2		193	204	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519499	176519499	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	230	424	0	ENST00000292408.4:c.905T>A	p.Val302Glu	p.V302E	ENST00000292408	NM_213647.1	302	gTg/gAg	7/18	0.370925181567087	4	FACETS	0.978	0.913	1	0.489	0.456	0.522	CLONAL	2	TRUE	0	0.37299435233514	4		424	866	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101063	26101063	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775926681	NA	P-0069516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	172	267	0	ENST00000435504.4:c.29G>A	p.Gly10Asp	p.G10D	ENST00000435504		10	gGc/gAc	1/13	0.354592095753252	3	FACETS	0.935	0.865	1	0.935	0.865	1	CLONAL	2	TRUE	1	0.37299435233514	3		267	585	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29279857	29279857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	49	112	0	ENST00000544604.2:c.103C>T	p.Pro35Ser	p.P35S	ENST00000544604	NM_001206998.1	35	Ccg/Tcg	1/9	0.363280798050268	2	FACETS	1	0.91	1	0.545	0.466	0.63	CLONAL	1	TRUE	0	0.37299435233514	2		112	241	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522644	106522644	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	110	191	0	ENST00000359195.3:c.2621A>G	p.Asp874Gly	p.D874G	ENST00000359195	NM_002649.2	874	gAc/gGc	7/11	0.232021832207832	5	FACETS	1	0.977	1	0.833	0.756	0.913	CLONAL	2	TRUE	2	0.37299435233514	5		191	368	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63973852	63973852	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	97	358	0	ENST00000398590.3:c.1213C>A	p.Gln405Lys	p.Q405K	ENST00000398590	NM_001177387.1	405	Cag/Aag	9/14	0.37299435233514	3	FACETS	0.813	0.725	0.907	0.407	0.362	0.454	CLONAL	1	TRUE	1	0.37299435233514	3		358	759	SUCCESS
APC	324	MSKCC	GRCh37	5	112175769	112175771	+	frameshift_variant	Frame_Shift_Del	DEL	CGG	CGG	A	novel	NA	P-0069516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	94	346	0	ENST00000257430.4:c.4478_4480delinsA	p.Thr1493LysfsTer20	p.T1493Kfs*20	ENST00000257430	NM_000038.5	1493	aCGGaa/aAaa	16/16	0.37299435233514	1	FACETS	0.871	0.778	0.968	0.871	0.778	0.968	CLONAL	1	TRUE	0	0.37299435233514	1		346	471	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0069533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	46	334	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.154763038638251	2		334	466	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519922	NA	P-0069533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	59	402	0	ENST00000397062.3:c.235G>A	p.Glu79Lys	p.E79K	ENST00000397062	NM_006164.4	79	Gag/Aag	2/5	0.154763038638251	3	FACETS	1	0.887	1	0.346	0.297	0.4	CLONAL	1	TRUE	0	0.154763038638251	3		402	791	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0069533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	50	364	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.154763038638251	2		364	631	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589619	67589630	+	inframe_deletion	In_Frame_Del	DEL	GAGAATATGATA	GAGAATATGATA	-	novel	NA	P-0069533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	26	247	0	ENST00000274335.5:c.1384_1395del	p.Glu462_Arg465del	p.E462_R465del	ENST00000274335		461	cGAGAATATGATAga/cga	10/15	1	2	FACETS	0.71	0.562	0.882	0.71	0.562	0.882	SUBCLONAL	1	TRUE	1	0.154763038638251	2		247	473	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057937	27057937	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0069533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	52	563	0	ENST00000324856.7:c.1650del	p.Tyr551ThrfsTer68	p.Y551Tfs*68	ENST00000324856	NM_006015.4	549	Ccc/cc	3/20	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.154763038638251	2		563	636	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521504	46521504	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	48	281	0	ENST00000262741.5:c.904C>G	p.Leu302Val	p.L302V	ENST00000262741	NM_003629.3	302	Ctg/Gtg	7/10	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.154763038638251	2		281	573	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92300846	92300846	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766767871	NA	P-0069533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	31	292	0	ENST00000265734.4:c.541G>A	p.Val181Ile	p.V181I	ENST00000265734	NM_001259.6	181	Gtc/Atc	5/8	0.154763038638251	3	FACETS	0.804	0.649	0.98	0.402	0.324	0.49	CLONAL	1	TRUE	1	0.154763038638251	3		292	537	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458252	120458252	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	67	711	0	ENST00000256646.2:c.7093G>T	p.Val2365Leu	p.V2365L	ENST00000256646	NM_024408.3	2365	Gta/Tta	34/34	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.154763038638251	2		711	715	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032069	26032069	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	65	607	0	ENST00000244661.2:c.220G>C	p.Glu74Gln	p.E74Q	ENST00000244661	NM_003537.3	74	Gaa/Caa	1/1	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.154763038638251	2		607	749	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437713	49437720	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTCTTC	TCTTCTTC	-	novel	NA	P-0069533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	59	550	0	ENST00000301067.7:c.5250_5257del	p.Lys1751AlafsTer34	p.K1751Afs*34	ENST00000301067	NM_003482.3	1750	gaGAAGAAGAag/gaag	22/54	0.154763038638251	3	FACETS	1	0.889	1	0.347	0.298	0.401	CLONAL	1	TRUE	0	0.154763038638251	3		550	789	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115277067	115277067	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1457149485	NA	P-0069533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	38	262	0	ENST00000438362.2:c.716T>C	p.Met239Thr	p.M239T	ENST00000438362	NM_001242891.1	239	aTg/aCg	7/20	1	2	FACETS	0.998	0.825	1	0.998	0.825	1	CLONAL	1	TRUE	1	0.154763038638251	2		262	492	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588181	67588182	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0069533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	41	233	0	ENST00000274335.5:c.1011_1012insG	p.Ile338AspfsTer8	p.I338Dfs*8	ENST00000274335		337	-/G	7/15	1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	TRUE	1	0.154763038638251	2		233	522	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057778	27057778	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0069533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	57	578	0	ENST00000324856.7:c.1486del	p.Ala496ProfsTer123	p.A496Pfs*123	ENST00000324856	NM_006015.4	496	Gcc/cc	3/20	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.154763038638251	2		578	709	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101053	26101053	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069535-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	139	445	0	ENST00000435504.4:c.39G>A	p.Trp13Ter	p.W13*	ENST00000435504		13	tgG/tgA	1/13	0.691749991745763	1	FACETS	0.959	0.892	1	0.959	0.892	1	CLONAL	1	TRUE	0	0.691749991745763	1		445	274	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0069536-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	13	382	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.672	0.479	0.906	0.672	0.479	0.906	SUBCLONAL	1	TRUE	1	0.18	2		382	215	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220717	1220717	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587782018	NA	P-0069536-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	31	453	0	ENST00000326873.7:c.734+1G>T		p.X245_splice	ENST00000326873	NM_000455.4	245			1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.18	2		453	338	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602763	10602763	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs774469695	NA	P-0069536-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	41	602	0	ENST00000171111.5:c.815G>C	p.Arg272Pro	p.R272P	ENST00000171111	NM_203500.1	272	cGc/cCc	3/6	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.18	2		602	439	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0069536-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	12	329	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.601	0.422	0.82	0.601	0.422	0.82	SUBCLONAL	1	TRUE	1	0.18	2		329	222	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609940	81609940	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069536-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	38	601	0	ENST00000298171.2:c.1538C>A	p.Thr513Lys	p.T513K	ENST00000298171	NM_000369.2	513	aCg/aAg	10/10	1	2	FACETS	0.797	0.658	0.952	0.797	0.658	0.952	CLONAL	1	TRUE	1	0.18	2		601	530	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633454	3633454	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069536-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	40	497	0	ENST00000294008.3:c.4797C>A	p.Phe1599Leu	p.F1599L	ENST00000294008	NM_032444.2	1599	ttC/ttA	14/15	1	2	FACETS	0.999	0.83	1	0.999	0.83	1	CLONAL	1	TRUE	1	0.18	2		497	445	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459508	50459508	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069536-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	29	402	0	ENST00000331340.3:c.797G>T	p.Arg266Ile	p.R266I	ENST00000331340	NM_006060.4	266	aGa/aTa	7/8	1	2	FACETS	0.792	0.635	0.97	0.792	0.635	0.97	CLONAL	1	TRUE	1	0.18	2		402	407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578412	7578412	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519747	NA	P-0069541-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	16	383	0	ENST00000269305.4:c.518T>C	p.Val173Ala	p.V173A	ENST00000269305	NM_001126112.2	173	gTg/gCg	5/11	1	2	FACETS	0.753	0.556	0.989	0.753	0.556	0.989	CLONAL	1	TRUE	1	0.13	2		383	327	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206817	36206817	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069541-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	27	324	0	ENST00000300305.3:c.695G>T	p.Arg232Leu	p.R232L	ENST00000300305		232	cGg/cTg	6/8	0.241932609313629	3	FACETS	1	0.876	1			1	CLONAL	1	TRUE	NA	0.13	3		324	385	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433650	49433650	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs794727549	NA	P-0069541-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	33	391	0	ENST00000301067.7:c.7903C>T	p.Arg2635Ter	p.R2635*	ENST00000301067	NM_003482.3	2635	Cga/Tga	31/54	0.117655267629833	3	FACETS	0.898	0.734	1	0.898	0.734	1	CLONAL	2	TRUE	1	0.13	3		391	301	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176458	123176458	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069541-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	12	99	0	ENST00000218089.9:c.425C>G	p.Ser142Cys	p.S142C	ENST00000218089	NM_001042749.1	142	tCt/tGt	7/35	0.154855388942635	2	FACETS	1	0.729	1			1	CLONAL	1	TRUE	NA	0.13	2		99	178	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0069542-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	8	203	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.345	0.221	0.507	0.345	0.221	0.507	SUBCLONAL	1	TRUE	1	0.14	2		203	331	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0069542-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	16	192	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.497	0.366	0.655	0.497	0.366	0.655	SUBCLONAL	1	TRUE	1	0.14	2		192	460	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0069542-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	22	274	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.669	0.517	0.846	0.669	0.517	0.846	SUBCLONAL	1	TRUE	1	0.14	2		274	470	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069542-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	45	310	0	ENST00000397062.3:c.246A>T	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaT	2/5	1	2	FACETS	0.986	0.827	1	0.986	0.827	1	CLONAL	1	TRUE	1	0.14	2		310	652	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0069542-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	13	220	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.339	0.24	0.46	0.339	0.24	0.46	SUBCLONAL	1	TRUE	1	0.14	2		220	548	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624265	89624275	+	frameshift_variant	Frame_Shift_Del	DEL	AAGGAGATATC	AAGGAGATATC	-	novel	NA	P-0069542-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	23	134	0	ENST00000371953.3:c.42_52del	p.Arg15GlyfsTer25	p.R15Gfs*25	ENST00000371953	NM_000314.4	13	aaAAGGAGATATCaa/aaaa	1/9	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.14	2		134	274	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579439	7579440	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs867725248	NA	P-0069543-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	335	408	0	ENST00000269305.4:c.247dup	p.Ala83GlyfsTer66	p.A83Gfs*66	ENST00000269305	NM_001126112.2	83	gcg/gGcg	4/11	0.46959408228881	3	FACETS	0.945	0.903	0.987	0.945	0.903	0.987	CLONAL	3	TRUE	0	0.469817732117581	3		408	621	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107189	27107189	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069543-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	94	291	0	ENST00000324856.7:c.6800T>C	p.Met2267Thr	p.M2267T	ENST00000324856	NM_006015.4	2267	aTg/aCg	20/20	0.422979129959287	3	FACETS	0.907	0.809	1	0.453	0.404	0.505	CLONAL	1	TRUE	1	0.469817732117581	3		291	545	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813626	50813626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149427272	NA	P-0069544-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	75	255	0	ENST00000398568.2:c.1180C>T	p.Arg394Cys	p.R394C	ENST00000398568	NM_001042412.1	394	Cgt/Tgt	8/18	1	2	FACETS	0.744	0.658	0.835	0.744	0.658	0.835	SUBCLONAL	1	TRUE	1	0.650559092940146	2		255	310	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497813	120497813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258121114	NA	P-0069544-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	105	330	0	ENST00000256646.2:c.2069C>T	p.Pro690Leu	p.P690L	ENST00000256646	NM_024408.3	690	cCc/cTc	13/34	1	2	FACETS	0.944	0.855	1	0.944	0.855	1	CLONAL	1	TRUE	1	0.650559092940146	2		330	342	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374292	15374292	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069544-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	82	284	0	ENST00000263377.2:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000263377	NM_058243.2	427	tCc/tTc	7/20	0.565345714632822	4	FACETS	0.968	0.857	1	0.323	0.285	0.362	CLONAL	1	TRUE	1	0.650559092940146	4		284	430	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	80	382	0				ENST00000310581	NM_198253.2	-/1132			0.223402818808744	4	FACETS	0.965	0.856	1	0.965	0.856	1	CLONAL	2	TRUE	2	0.323779543178483	4		382	339	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	691	301	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.323779543178483	15	FACETS	0.986	0.96	1			1	CLONAL	13	TRUE	NA	0.323779543178483	15		301	1034	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129346	64129346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780738455	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	159	357	0	ENST00000334205.4:c.778C>T	p.Pro260Ser	p.P260S	ENST00000334205	NM_003942.2	260	Ccc/Tcc	8/17	0.323779543178483	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.323779543178483	3		357	508	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944121	71944121	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	142	329	0	ENST00000298229.2:c.1954G>A	p.Glu652Lys	p.E652K	ENST00000298229	NM_001567.3	652	Gag/Aag	17/28	0.323779543178483	3	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	TRUE	1	0.323779543178483	3		329	506	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909867	100909867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	51	233	0	ENST00000325455.5:c.2782C>T	p.Leu928Phe	p.L928F	ENST00000325455	NM_001202474.3	928	Ctt/Ttt	8/8	0.323779543178483	3	FACETS	1	0.91	1	0.546	0.466	0.633	CLONAL	1	TRUE	1	0.323779543178483	3		233	335	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962554	100962554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	35	222	0	ENST00000325455.5:c.1843C>T	p.Arg615Cys	p.R615C	ENST00000325455	NM_001202474.3	615	Cgc/Tgc	3/8	0.323779543178483	3	FACETS	0.688	0.565	0.826	0.344	0.282	0.413	SUBCLONAL	1	TRUE	1	0.323779543178483	3		222	365	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433899	49433899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	136	380	0	ENST00000301067.7:c.7654C>T	p.Pro2552Ser	p.P2552S	ENST00000301067	NM_003482.3	2552	Cct/Tct	31/54	0.323779543178483	4	FACETS	0.895	0.817	0.977	0.895	0.817	0.977	CLONAL	2	TRUE	2	0.323779543178483	4		380	621	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856002	111856002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	138	301	0	ENST00000341259.2:c.53C>T	p.Ser18Phe	p.S18F	ENST00000341259	NM_005475.2	18	tCc/tTc	2/8	0.323779543178483	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	2	0.323779543178483	4		301	528	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828039	3828039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	68	272	0	ENST00000262367.5:c.2086C>T	p.Pro696Ser	p.P696S	ENST00000262367	NM_004380.2	696	Cca/Tca	10/31	0.323779543178483	3	FACETS	1	0.939	1	0.565	0.493	0.642	CLONAL	1	TRUE	1	0.323779543178483	3		272	432	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934623	9934623	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267604688	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	64	239	0	ENST00000330684.3:c.1532C>T	p.Ser511Leu	p.S511L	ENST00000330684	NM_001134407.1	511	tCg/tTg	7/13	0.323779543178483	3	FACETS	1	0.946	1	0.587	0.511	0.67	CLONAL	1	TRUE	1	0.323779543178483	3		239	391	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546050	29546050	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	124	280	0	ENST00000356175.3:c.1555C>T	p.Gln519Ter	p.Q519*	ENST00000356175	NM_000267.3	519	Caa/Taa	14/57	0.323779543178483	4	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	2	0.323779543178483	4		280	476	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657313	29657313	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	128	232	0	ENST00000356175.3:c.5547-1G>A		p.X1849_splice	ENST00000356175	NM_000267.3	1849			0.323779543178483	4	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	2	0.323779543178483	4		232	493	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682543	37682543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758668404	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	128	279	0	ENST00000447079.4:c.3734C>T	p.Pro1245Leu	p.P1245L	ENST00000447079	NM_015083.1	1245	cCc/cTc	13/14	0.323779543178483	4	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	2	0.323779543178483	4		279	499	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440643	56440643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139557480	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	159	328	0	ENST00000407977.2:c.575C>T	p.Pro192Leu	p.P192L	ENST00000407977		192	cCg/cTg	5/10	0.323779543178483	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.323779543178483	4		328	543	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110515	4110515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	151	348	0	ENST00000262948.5:c.442G>A	p.Glu148Lys	p.E148K	ENST00000262948	NM_030662.3	148	Gaa/Aaa	3/11	0.323779543178483	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	2	0.323779543178483	4		348	550	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308384	15308385	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	60	346	0	ENST00000263388.2:c.123_124delinsTT	p.Pro42Ser	p.P42S	ENST00000263388	NM_000435.2	41	ccCCct/ccTTct	2/33	0.323779543178483	4	FACETS	0.997	0.861	1	0.499	0.43	0.573	CLONAL	1	TRUE	2	0.323779543178483	4		346	492	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758775	41758775	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374737642	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	120	300	0	ENST00000301178.4:c.1829G>A	p.Arg610Gln	p.R610Q	ENST00000301178	NM_021913.4	610	cGa/cAa	16/20	0.323779543178483	4	FACETS	0.999	0.907	1	0.999	0.907	1	CLONAL	2	TRUE	2	0.323779543178483	4		300	491	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867698	45867698	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	156	377	0	ENST00000391945.4:c.702C>G	p.Asp234Glu	p.D234E	ENST00000391945	NM_000400.3	234	gaC/gaG	8/23	0.323779543178483	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	2	0.323779543178483	4		377	597	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285224	198285224	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757758244	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	58	285	0	ENST00000335508.6:c.343C>T	p.Arg115Trp	p.R115W	ENST00000335508	NM_012433.2	115	Cgg/Tgg	4/25	0.323779543178483	3	FACETS	0.982	0.846	1	0.491	0.423	0.565	CLONAL	1	TRUE	1	0.323779543178483	3		285	424	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980868	40980868	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	134	326	0	ENST00000373198.4:c.1618G>A	p.Gly540Arg	p.G540R	ENST00000373198	NM_133170.3	540	Ggg/Agg	10/32	0.323779543178483	4	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	2	0.323779543178483	4		326	525	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076936	41076936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1031395862	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	43	258	0	ENST00000373198.4:c.1484G>A	p.Gly495Glu	p.G495E	ENST00000373198	NM_133170.3	495	gGg/gAg	9/32	0.323779543178483	4	FACETS	0.993	0.834	1	0.497	0.417	0.585	CLONAL	1	TRUE	2	0.323779543178483	4		258	354	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521711	89521711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	111	271	0	ENST00000336596.2:c.2788G>A	p.Glu930Lys	p.E930K	ENST00000336596	NM_005233.5	930	Gaa/Aaa	16/17	0.323779543178483	3	FACETS	0.96	0.869	1	0.96	0.869	1	CLONAL	2	TRUE	1	0.323779543178483	3		271	415	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967321	134967321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	51	292	0	ENST00000398015.3:c.2660G>A	p.Ser887Asn	p.S887N	ENST00000398015	NM_004441.4	887	aGt/aAt	14/16	0.323779543178483	3	FACETS	0.806	0.686	0.938	0.403	0.343	0.469	CLONAL	1	TRUE	1	0.323779543178483	3		292	454	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272144	142272144	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	34	242	0	ENST00000350721.4:c.2730A>T	p.Glu910Asp	p.E910D	ENST00000350721	NM_001184.3	910	gaA/gaT	13/47	0.323779543178483	3	FACETS	0.709	0.581	0.854	0.355	0.29	0.427	SUBCLONAL	1	TRUE	1	0.323779543178483	3		242	344	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	51	321	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	0.323779543178483	3	FACETS	1	0.858	1	0.503	0.429	0.583	CLONAL	1	TRUE	1	0.323779543178483	3		321	364	SUCCESS
ALB	213	MSKCC	GRCh37	4	74283258	74283258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs78575701	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	72	238	0	ENST00000295897.4:c.1300C>T	p.Arg434Cys	p.R434C	ENST00000295897	NM_000477.5	434	Cgt/Tgt	11/15	0.323779543178483	3	FACETS	1	0.963	1	0.632	0.554	0.714	CLONAL	1	TRUE	1	0.323779543178483	3		238	409	SUCCESS
ALB	213	MSKCC	GRCh37	4	74283322	74283322	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	111	268	0	ENST00000295897.4:c.1364G>A	p.Gly455Glu	p.G455E	ENST00000295897	NM_000477.5	455	gGa/gAa	11/15	0.323779543178483	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	1	0.323779543178483	3		268	374	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164913	106164913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs898441677	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	84	229	0	ENST00000380013.4:c.3781C>T	p.Arg1261Cys	p.R1261C	ENST00000380013	NM_001127208.2	1261	Cgc/Tgc	6/11	0.323779543178483	3	FACETS	0.922	0.822	1	0.922	0.822	1	CLONAL	2	TRUE	1	0.323779543178483	3		229	327	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294150	1294150	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1279190294	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	145	372	0	ENST00000310581.5:c.851C>T	p.Ser284Phe	p.S284F	ENST00000310581	NM_198253.2	284	tCt/tTt	2/16	0.223402818808744	4	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	2	0.323779543178483	4		372	578	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180050958	180050958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781305649	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	219	330	0	ENST00000261937.6:c.1525G>A	p.Glu509Lys	p.E509K	ENST00000261937	NM_182925.4	509	Gag/Aag	11/30	0.323779543178483	4	FACETS	1	0.948	1			1	CLONAL	3	TRUE	NA	0.323779543178483	4		330	589	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188847	32188847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	90	378	0	ENST00000375023.3:c.707G>A	p.Gly236Glu	p.G236E	ENST00000375023	NM_004557.3	236	gGa/gAa	4/30	0.323779543178483	4	FACETS	1	0.962	1	0.596	0.53	0.667	CLONAL	1	TRUE	2	0.323779543178483	4		378	617	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967209	93967209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	82	226	0	ENST00000369303.4:c.2143G>A	p.Glu715Lys	p.E715K	ENST00000369303	NM_004440.3	715	Gaa/Aaa	12/17	0.323779543178483	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	0	0.323779543178483	2		226	243	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956771	68956771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774302685	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	46	218	0	ENST00000288368.4:c.889C>T	p.Arg297Cys	p.R297C	ENST00000288368	NM_024870.2	297	Cgt/Tgt	8/40	0.323779543178483	7	FACETS	0.991	0.834	1	0.165	0.139	0.194	CLONAL	1	TRUE	1	0.323779543178483	7		218	519	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005903	69005903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	46	233	0	ENST00000288368.4:c.2314C>T	p.His772Tyr	p.H772Y	ENST00000288368	NM_024870.2	772	Cac/Tac	21/40	0.323779543178483	7	FACETS	0.945	0.796	1	0.158	0.132	0.186	CLONAL	1	TRUE	1	0.323779543178483	7		233	544	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779106	135779106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	123	272	0	ENST00000298552.3:c.2140C>T	p.Leu714Phe	p.L714F	ENST00000298552	NM_001162426.1	714	Ctc/Ttc	17/23	0.323779543178483	3	FACETS	0.974	0.887	1	0.974	0.887	1	CLONAL	2	TRUE	1	0.323779543178483	3		272	453	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298662	11298662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	230	280	0	ENST00000361445.4:c.1799C>T	p.Thr600Ile	p.T600I	ENST00000361445	NM_004958.3	600	aCc/aTc	12/58	0.323779543178483	5	FACETS	0.99	0.932	1	0.99	0.932	1	CLONAL	4	TRUE	1	0.323779543178483	5		280	533	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65311291	65311291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	60	306	0	ENST00000342505.4:c.2020C>T	p.Pro674Ser	p.P674S	ENST00000342505	NM_002227.2	674	Cct/Tct	15/25	0.323779543178483	3	FACETS	1	0.888	1	0.515	0.445	0.591	CLONAL	1	TRUE	1	0.323779543178483	3		306	418	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731215	162731215	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	139	330	0	ENST00000367921.3:c.1070T>G	p.Met357Arg	p.M357R	ENST00000367921	NM_006182.2	357	aTg/aGg	9/18	0.323779543178483	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	2	0.323779543178483	4		330	524	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534222	534222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	109	272	0	ENST00000451590.1:c.101C>T	p.Pro34Leu	p.P34L	ENST00000451590	NM_001130442.1	34	cCc/cTc	2/5	0.323779543178483	3	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	1	0.323779543178483	3		272	380	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390342	118390342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	56	283	0	ENST00000534358.1:c.11156G>A	p.Gly3719Asp	p.G3719D	ENST00000534358	NM_005933.3	3719	gGt/gAt	32/36	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.323779543178483	2		283	345	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74005292	74005292	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	41	195	0	ENST00000318443.5:c.1600G>C	p.Ala534Pro	p.A534P	ENST00000318443	NM_001024736.1	534	Gcc/Ccc	10/10	0.323779543178483	3	FACETS	0.962	0.805	1	0.481	0.402	0.568	CLONAL	1	TRUE	1	0.323779543178483	3		195	306	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2113020	2113020	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	114	297	0	ENST00000219476.3:c.1409C>T	p.Ser470Phe	p.S470F	ENST00000219476	NM_000548.3	470	tCc/tTc	14/42	0.323779543178483	3	FACETS	0.995	0.903	1	0.995	0.903	1	CLONAL	2	TRUE	1	0.323779543178483	3		297	411	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972433	81972433	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1272977976	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	54	255	0	ENST00000359376.3:c.3226C>G	p.Leu1076Val	p.L1076V	ENST00000359376	NM_002661.3	1076	Ctt/Gtt	29/33	1	2	FACETS	0.948	0.813	1	0.948	0.813	1	CLONAL	1	TRUE	1	0.323779543178483	2		255	352	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108310	8108310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	122	309	0	ENST00000585124.1:c.914C>T	p.Ser305Phe	p.S305F	ENST00000585124	NM_004217.3	305	tCc/tTc	9/9	0.323779543178483	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	2	0.323779543178483	4		309	462	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8109903	8109903	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	56	301	0	ENST00000585124.1:c.592C>T	p.His198Tyr	p.H198Y	ENST00000585124	NM_004217.3	198	Cac/Tac	7/9	0.323779543178483	4	FACETS	0.929	0.797	1	0.464	0.398	0.537	CLONAL	1	TRUE	2	0.323779543178483	4		301	493	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690244	33690244	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	65	369	0	ENST00000308377.4:c.583C>T	p.Gln195Ter	p.Q195*	ENST00000308377	NM_152270.3	195	Caa/Taa	2/5	0.323779543178483	4	FACETS	1	0.924	1	0.547	0.475	0.624	CLONAL	1	TRUE	2	0.323779543178483	4		369	486	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690506	33690506	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	126	328	0	ENST00000308377.4:c.321del	p.Lys108AsnfsTer45	p.K108Nfs*45	ENST00000308377	NM_152270.3	107	gtT/gt	2/5	0.323779543178483	4	FACETS	0.967	0.879	1	0.967	0.879	1	CLONAL	2	TRUE	2	0.323779543178483	4		328	533	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690745	33690745	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	116	324	0	ENST00000308377.4:c.82G>A	p.Glu28Lys	p.E28K	ENST00000308377	NM_152270.3	28	Gaa/Aaa	2/5	0.323779543178483	4	FACETS	0.954	0.865	1	0.954	0.865	1	CLONAL	2	TRUE	2	0.323779543178483	4		324	497	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295803	212295803	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1366287589	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	40	224	0	ENST00000342788.4:c.2510G>A	p.Arg837Lys	p.R837K	ENST00000342788	NM_005235.2	837	aGa/aAa	21/28	0.323779543178483	4	FACETS	0.708	0.588	0.841	0.236	0.196	0.281	SUBCLONAL	1	TRUE	1	0.323779543178483	4		224	462	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422569	225422569	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	46	192	0	ENST00000264414.4:c.71C>T	p.Thr24Ile	p.T24I	ENST00000264414	NM_003590.4	24	aCc/aTc	2/16	0.323779543178483	4	FACETS	1	0.932	1	0.398	0.337	0.465	CLONAL	1	TRUE	1	0.323779543178483	4		192	315	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755381	39755381	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	62	403	0	ENST00000288319.7:c.1384C>T	p.Pro462Ser	p.P462S	ENST00000288319	NM_182918.3	462	Ccc/Tcc	10/10	1	2	FACETS	0.921	0.798	1	0.921	0.798	1	CLONAL	1	TRUE	1	0.323779543178483	2		403	416	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817351	39817351	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	62	286	0	ENST00000288319.7:c.212A>G	p.Asn71Ser	p.N71S	ENST00000288319	NM_182918.3	71	aAc/aGc	2/10	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.323779543178483	2		286	365	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21345966	21345966	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395990299	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	131	409	0	ENST00000215739.8:c.841C>T	p.Pro281Ser	p.P281S	ENST00000215739	NM_006767.3	281	Ccg/Tcg	9/21	0.323779543178483	4	FACETS	0.95	0.865	1	0.95	0.865	1	CLONAL	2	TRUE	2	0.323779543178483	4		409	564	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651330	52651332	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	144	278	0	ENST00000394830.3:c.1764_1766del	p.Glu588del	p.E588del	ENST00000394830	NM_018313.4	588	gaAGAc/gac	15/30	0.323779543178483	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.323779543178483	3		278	463	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920253	1920253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs533653843	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	112	309	0	ENST00000382891.5:c.1313C>T	p.Pro438Leu	p.P438L	ENST00000382891	NM_133335.3	438	cCt/cTt	5/22	0.323779543178483	3	FACETS	0.878	0.794	0.965	0.878	0.794	0.965	CLONAL	2	TRUE	1	0.323779543178483	3		309	458	SUCCESS
REST	5978	MSKCC	GRCh37	4	57797717	57797717	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	78	345	0	ENST00000309042.7:c.2693G>A	p.Gly898Glu	p.G898E	ENST00000309042	NM_005612.4	898	gGa/gAa	4/4	0.323779543178483	3	FACETS	1	0.939	1	0.552	0.486	0.623	CLONAL	1	TRUE	1	0.323779543178483	3		345	507	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155922	106155922	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	70	355	0	ENST00000380013.4:c.823A>G	p.Asn275Asp	p.N275D	ENST00000380013	NM_001127208.2	275	Aat/Gat	3/11	0.323779543178483	3	FACETS	1	0.935	1	0.556	0.486	0.631	CLONAL	1	TRUE	1	0.323779543178483	3		355	452	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526403	31526403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1263164551	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	127	331	0	ENST00000344624.3:c.637C>T	p.Pro213Ser	p.P213S	ENST00000344624		213	Cca/Tca	2/33	0.323779543178483	4	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	2	0.323779543178483	4		331	511	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526765	31526765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746810149	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	67	238	0	ENST00000344624.3:c.275C>T	p.Pro92Leu	p.P92L	ENST00000344624		92	cCt/cTt	2/33	0.323779543178483	4	FACETS	0.794	0.694	0.9	0.794	0.694	0.9	SUBCLONAL	2	TRUE	2	0.323779543178483	4		238	345	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871301	35871301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1561423358	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	111	239	0	ENST00000303115.3:c.523G>A	p.Glu175Lys	p.E175K	ENST00000303115	NM_002185.3	175	Gaa/Aaa	4/8	0.323779543178483	4	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	2	0.323779543178483	4		239	432	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508728	148508729	+	missense_variant	Missense_Mutation	DNP	AT	AT	TC	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	83	220	0	ENST00000320356.2:c.1935_1936delinsGA	p.Tyr646Asn	p.Y646N	ENST00000320356	NM_004456.4	645	gaATac/gaGAac	16/20	0.323779543178483	4	FACETS	0.751	0.665	0.842	0.751	0.665	0.842	SUBCLONAL	2	TRUE	2	0.323779543178483	4		220	452	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371764	55371764	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	373	343	0	ENST00000297316.4:c.454G>A	p.Glu152Lys	p.E152K	ENST00000297316	NM_022454.3	152	Gag/Aag	2/2	0.323779543178483	7	FACETS	1	0.987	1	1	0.987	1	CLONAL	6	TRUE	1	0.323779543178483	7		343	652	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031745	69031745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	56	246	0	ENST00000288368.4:c.3500G>A	p.Ser1167Asn	p.S1167N	ENST00000288368	NM_024870.2	1167	aGc/aAc	28/40	0.323779543178483	7	FACETS	1	0.873	1	0.17	0.145	0.197	CLONAL	1	TRUE	1	0.323779543178483	7		246	613	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759512	133759512	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	91	444	0	ENST00000318560.5:c.1835C>G	p.Pro612Arg	p.P612R	ENST00000318560	NM_005157.4	612	cCa/cGa	11/11	0.323779543178483	3	FACETS	1	0.949	1	0.558	0.496	0.624	CLONAL	1	TRUE	1	0.323779543178483	3		444	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	273	276	0	ENST00000269305.4:c.403del	p.Cys135AlafsTer35	p.C135Afs*35	ENST00000269305	NM_001126112.2	135	Tgc/gc	5/11	0.214661440241863	3	FACETS	1	0.988	1	0.785	0.739	0.833	CLONAL	2	TRUE	0	0.305704291279969	3		276	874	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098973	178098973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	72	255	0	ENST00000397062.3:c.72G>C	p.Trp24Cys	p.W24C	ENST00000397062	NM_006164.4	24	tgG/tgC	2/5	0.308831879730228	3	FACETS	0.733	0.64	0.834	0.366	0.32	0.417	SUBCLONAL	1	TRUE	1	0.305704291279969	3		255	741	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041590	42041590	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	93	319	0	ENST00000219905.7:c.5785C>T	p.Gln1929Ter	p.Q1929*	ENST00000219905	NM_001164273.1	1929	Cag/Tag	17/24	1	2	FACETS	0.838	0.745	0.937	0.838	0.745	0.937	CLONAL	1	TRUE	1	0.305704291279969	2		319	726	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923819	39923819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	100	130	0	ENST00000378444.4:c.3272C>T	p.Pro1091Leu	p.P1091L	ENST00000378444	NM_001123385.1	1091	cCc/cTc	7/15	0.308831879730228	2	FACETS	0.901	0.812	0.994			1	CLONAL	2	TRUE	NA	0.305704291279969	2		130	363	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991805	72991805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	94	305	0	ENST00000268489.5:c.2240C>T	p.Ser747Phe	p.S747F	ENST00000268489	NM_006885.3	747	tCt/tTt	2/10	0.308831879730228	2	FACETS	0.942	0.839	1	0.471	0.419	0.526	CLONAL	1	TRUE	0	0.305704291279969	2		305	653	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317267	87317267	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1052977316	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	84	298	0	ENST00000277120.3:c.292A>G	p.Ile98Val	p.I98V	ENST00000277120		98	Att/Gtt	4/19	0.298109773831019	3	FACETS	1	0.889	1	0.503	0.444	0.565	CLONAL	1	TRUE	1	0.305704291279969	3		298	630	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825537	50825537	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	66	201	0	ENST00000398568.2:c.2168G>T	p.Gly723Val	p.G723V	ENST00000398568	NM_001042412.1	723	gGc/gTc	14/18	0.308831879730228	2	FACETS	1	0.934	1	0.556	0.485	0.633	CLONAL	1	TRUE	0	0.305704291279969	2		201	388	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021710	69021710	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	71	225	0	ENST00000288368.4:c.2998G>T	p.Gly1000Cys	p.G1000C	ENST00000288368	NM_024870.2	1000	Ggt/Tgt	25/40	0.293984381493085	3	FACETS	0.842	0.735	0.958	0.421	0.367	0.479	CLONAL	1	TRUE	1	0.305704291279969	3		225	636	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647572	117647572	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	81	304	0	ENST00000368508.3:c.5372G>T	p.Ser1791Ile	p.S1791I	ENST00000368508	NM_002944.2	1791	aGc/aTc	33/43	0.308831879730228	0	FACETS	0.956	0.847	1			1	CLONAL	1	TRUE	0	0.305704291279969	0		304	385	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420308	88420308	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	82	279	0	ENST00000360948.2:c.2378G>T	p.Arg793Leu	p.R793L	ENST00000360948	NM_001012338.2	793	cGa/cTa	19/19	0.308831879730228	1	FACETS	0.795	0.702	0.894	0.795	0.702	0.894	SUBCLONAL	1	TRUE	0	0.305704291279969	1		279	572	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88428931	88428931	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	28	170	0	ENST00000360948.2:c.2169G>T	p.Trp723Cys	p.W723C	ENST00000360948	NM_001012338.2	723	tgG/tgT	17/19	0.308831879730228	1	FACETS	0.69	0.554	0.842	0.69	0.554	0.842	SUBCLONAL	1	TRUE	0	0.305704291279969	1		170	225	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570117	212570117	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	51	209	0	ENST00000342788.4:c.1125-1G>T		p.X375_splice	ENST00000342788	NM_005235.2	375			0.308831879730228	3	FACETS	0.899	0.765	1	0.449	0.382	0.522	CLONAL	1	TRUE	1	0.305704291279969	3		209	428	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438048	438048	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	198	239	0	ENST00000399788.2:c.1921C>G	p.Leu641Val	p.L641V	ENST00000399788	NM_001042603.1	641	Ctc/Gtc	14/28	0.267797656553256	4	FACETS	1	0.967	1			1	CLONAL	2	TRUE	NA	0.305704291279969	4		239	790	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082602	16082602	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs906249646	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	57	130	0	ENST00000281043.3:c.416G>T	p.Gly139Val	p.G139V	ENST00000281043	NM_005378.4	139	gGg/gTg	2/3	1	2	FACETS	0.875	0.753	1	0.875	0.753	1	CLONAL	1	TRUE	1	0.305704291279969	2		130	426	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843243	128843243	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	193	243	0	ENST00000249373.3:c.350G>T	p.Arg117Leu	p.R117L	ENST00000249373	NM_005631.4	117	cGc/cTc	2/12	0.195044256140492	5	FACETS	1	0.983	1	0.8	0.742	0.86	CLONAL	2	TRUE	2	0.305704291279969	5		243	767	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293141	212293141	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	68	206	0	ENST00000342788.4:c.2711G>T	p.Trp904Leu	p.W904L	ENST00000342788	NM_005235.2	904	tGg/tTg	22/28	0.308831879730228	3	FACETS	1	0.948	1	0.585	0.511	0.666	CLONAL	1	TRUE	1	0.305704291279969	3		206	438	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204507379	204507379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1257063291	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	78	255	0	ENST00000367182.3:c.454G>A	p.Glu152Lys	p.E152K	ENST00000367182	NM_001278516.1	152	Gaa/Aaa	7/11	0.195044256140492	5	FACETS	0.948	0.832	1	0.316	0.277	0.358	CLONAL	1	TRUE	2	0.305704291279969	5		255	785	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965608	93965608	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	72	277	0	ENST00000369303.4:c.2320G>T	p.Val774Leu	p.V774L	ENST00000369303	NM_004440.3	774	Gtg/Ttg	13/17	0.254540279310335	0	FACETS	0.926	0.815	1			1	CLONAL	1	TRUE	0	0.305704291279969	0		277	353	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533741	63533741	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1213025395	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	233	325	0	ENST00000307078.5:c.1413C>G	p.His471Gln	p.H471Q	ENST00000307078	NM_004655.3	471	caC/caG	6/11	0.308831879730228	3	FACETS	0.904	0.844	0.966	0.904	0.844	0.966	CLONAL	2	TRUE	1	0.305704291279969	3		325	972	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112612	115112612	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	168	233	0	ENST00000257566.3:c.1128C>G	p.Asp376Glu	p.D376E	ENST00000257566	NM_016569.3	376	gaC/gaG	7/8	0.308831879730228	2	FACETS	0.857	0.791	0.926	0.857	0.791	0.926	CLONAL	2	TRUE	0	0.305704291279969	2		233	641	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150931712	150931712	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	99	306	0	ENST00000271640.5:c.2389G>T	p.Val797Leu	p.V797L	ENST00000271640	NM_001145415.1	797	Gtg/Ttg	15/22	0.305704291279969	5	FACETS	0.959	0.855	1	0.32	0.285	0.357	CLONAL	1	TRUE	2	0.305704291279969	5		306	985	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47607076	47607076	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	246	276	0	ENST00000263735.4:c.826G>T	p.Val276Leu	p.V276L	ENST00000263735	NM_002354.2	276	Gtg/Ttg	7/9	0.293984381493085	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.305704291279969	3		276	791	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72994032	72994032	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1381862487	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	169	259	0	ENST00000268489.5:c.13G>T	p.Asp5Tyr	p.D5Y	ENST00000268489	NM_006885.3	5	Gac/Tac	2/10	0.308831879730228	2	FACETS	0.928	0.857	1	0.928	0.857	1	CLONAL	2	TRUE	0	0.305704291279969	2		259	596	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658243	18658243	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	86	273	0	ENST00000266497.5:c.3048C>G	p.Phe1016Leu	p.F1016L	ENST00000266497		1016	ttC/ttG	22/31	0.308831879730228	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.305704291279969	1		273	410	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027816	152027816	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	93	249	0	ENST00000262189.6:c.259G>C	p.Glu87Gln	p.E87Q	ENST00000262189	NM_170606.2	87	Gaa/Caa	3/59	0.195044256140492	5	FACETS	1	0.95	1	0.374	0.332	0.419	CLONAL	1	TRUE	2	0.305704291279969	5		249	790	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519909	29519909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	158	235	0	ENST00000389048.3:c.1662G>T	p.Trp554Cys	p.W554C	ENST00000389048	NM_004304.4	554	tgG/tgT	9/29	0.293984381493085	3	FACETS	0.995	0.916	1	0.995	0.916	1	CLONAL	2	TRUE	1	0.305704291279969	3		235	599	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166636	118166636	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	97	228	0	ENST00000369448.3:c.1146G>T	p.Gln382His	p.Q382H	ENST00000369448	NM_017709.3	382	caG/caT	2/2	0.293984381493085	3	FACETS	1	0.959	1	0.575	0.513	0.641	CLONAL	1	TRUE	1	0.305704291279969	3		228	636	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045954	26045954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	131	313	0	ENST00000540144.1:c.316G>A	p.Glu106Lys	p.E106K	ENST00000540144	NM_003531.2	106	Gaa/Aaa	1/1	0.218985546379058	4	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.305704291279969	4		313	895	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420194	88420194	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	59	224	0	ENST00000360948.2:c.2492C>A	p.Thr831Asn	p.T831N	ENST00000360948	NM_001012338.2	831	aCc/aAc	19/19	0.308831879730228	1	FACETS	0.599	0.515	0.69	0.599	0.515	0.69	SUBCLONAL	1	TRUE	0	0.305704291279969	1		224	546	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17949130	17949130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	115	260	0	ENST00000458235.1:c.1511C>A	p.Ser504Tyr	p.S504Y	ENST00000458235	NM_000215.3	504	tCc/tAc	11/24	0.245901588917917	2	FACETS	0.987	0.89	1	0.494	0.445	0.545	CLONAL	1	TRUE	0	0.305704291279969	2		260	762	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489231	2489231	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	75	249	0	ENST00000355716.4:c.136G>T	p.Glu46Ter	p.E46*	ENST00000355716	NM_003820.2	46	Gag/Tag	2/8	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.305704291279969	NA		249	751	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019383	42019384	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	65	221	0	ENST00000219905.7:c.3438_3439del	p.Cys1146Ter	p.C1146*	ENST00000219905	NM_001164273.1	1146	TGt/t	10/24	1	2	FACETS	0.839	0.728	0.958	0.839	0.728	0.958	CLONAL	1	TRUE	1	0.305704291279969	2		221	507	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499762	18499762	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs758340301	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	181	268	0	ENST00000266497.5:c.1617G>C	p.Trp539Cys	p.W539C	ENST00000266497		539	tgG/tgC	10/31	0.308831879730228	1	FACETS	1	0.957	1	1	0.993	1	CLONAL	2	TRUE	0	0.305704291279969	1		268	483	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143326451	143326451	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776542387	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	173	248	0	ENST00000262992.4:c.163C>T	p.Arg55Cys	p.R55C	ENST00000262992	NM_001101669.1	55	Cgt/Tgt	4/24	0.308831879730228	2	FACETS	0.922	0.852	0.993	0.922	0.852	0.993	CLONAL	2	TRUE	0	0.305704291279969	2		248	614	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21343913	21343913	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	74	225	0	ENST00000215739.8:c.594-1G>T		p.X198_splice	ENST00000215739	NM_006767.3	198			1	2	FACETS	0.857	0.751	0.971	0.857	0.751	0.971	CLONAL	1	TRUE	1	0.305704291279969	2		225	565	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570376	87570376	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	84	313	0	ENST00000277120.3:c.2116G>T	p.Val706Leu	p.V706L	ENST00000277120		706	Gtg/Ttg	17/19	0.298109773831019	3	FACETS	0.821	0.724	0.924	0.41	0.362	0.462	CLONAL	1	TRUE	1	0.305704291279969	3		313	772	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6270692	6270692	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	94	288	0	ENST00000252674.7:c.91G>A	p.Asp31Asn	p.D31N	ENST00000252674	NM_005934.3	31	Gac/Aac	2/12	0.245901588917917	2	FACETS	0.757	0.673	0.847	0.379	0.336	0.424	SUBCLONAL	1	TRUE	0	0.305704291279969	2		288	812	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375238	15375238	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	105	182	0	ENST00000263377.2:c.1189C>T	p.Pro397Ser	p.P397S	ENST00000263377	NM_058243.2	397	Ccc/Tcc	6/20	0.245901588917917	2	FACETS	1	0.927	1	0.52	0.467	0.577	CLONAL	1	TRUE	0	0.305704291279969	2		182	660	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924433	112924433	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	76	220	0	ENST00000351677.2:c.1379G>C	p.Ser460Thr	p.S460T	ENST00000351677	NM_002834.3	460	aGt/aCt	11/16	0.308831879730228	2	FACETS	0.965	0.849	1	0.483	0.424	0.545	CLONAL	1	TRUE	0	0.305704291279969	2		220	515	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439826	51439826	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	232	299	0	ENST00000262662.1:c.391G>T	p.Gly131Trp	p.G131W	ENST00000262662		131	Ggg/Tgg	4/4	0.293984381493085	3	FACETS	0.946	0.883	1	0.946	0.883	1	CLONAL	2	TRUE	1	0.305704291279969	3		299	925	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003745	57003745	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	79	304	0	ENST00000257254.3:c.734G>T	p.Arg245Leu	p.R245L	ENST00000257254		245	cGg/cTg	1/2	0.308831879730228	1	FACETS	0.792	0.697	0.893	0.792	0.697	0.893	SUBCLONAL	1	TRUE	0	0.305704291279969	1		304	553	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860145	57860145	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	159	243	0	ENST00000228682.2:c.885C>A	p.His295Gln	p.H295Q	ENST00000228682	NM_005269.2	295	caC/caA	8/12	0.214661440241863	3	FACETS	0.924	0.85	1	0.616	0.566	0.667	CLONAL	2	TRUE	0	0.305704291279969	3		243	649	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800136	32800136	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	191	239	0	ENST00000374899.4:c.1246C>T	p.Gln416Ter	p.Q416*	ENST00000374899	NM_018833.2	416	Cag/Tag	7/12	0.214661440241863	3	FACETS	1	0.968	1	0.716	0.664	0.768	CLONAL	2	TRUE	0	0.305704291279969	3		239	671	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287331	38287331	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	101	242	0	ENST00000425967.3:c.326G>T	p.Ser109Ile	p.S109I	ENST00000425967	NM_001174067.1	109	aGc/aTc	4/19	0.308831879730228	2	FACETS	0.903	0.807	1	0.451	0.403	0.502	CLONAL	1	TRUE	0	0.305704291279969	2		242	732	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508605	106508605	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	141	197	0	ENST00000359195.3:c.599C>A	p.Pro200Gln	p.P200Q	ENST00000359195	NM_002649.2	200	cCg/cAg	2/11	0.195044256140492	5	FACETS	0.904	0.825	0.987	0.603	0.55	0.658	CLONAL	2	TRUE	2	0.305704291279969	5		197	744	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544780	86544780	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	127	217	0	ENST00000262426.4:c.605A>C	p.Asn202Thr	p.N202T	ENST00000262426	NM_001451.2	202	aAc/aCc	1/2	0.308831879730228	2	FACETS	0.761	0.692	0.832	0.761	0.692	0.832	SUBCLONAL	2	TRUE	0	0.305704291279969	2		217	546	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298149	15298149	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	143	210	0	ENST00000263388.2:c.1607G>T	p.Gly536Val	p.G536V	ENST00000263388	NM_000435.2	536	gGc/gTc	11/33	0.245901588917917	2	FACETS	0.896	0.822	0.973	0.896	0.822	0.973	CLONAL	2	TRUE	0	0.305704291279969	2		210	522	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902229	151902229	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1588184096	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	37	132	0	ENST00000262189.6:c.3923C>T	p.Ser1308Leu	p.S1308L	ENST00000262189	NM_170606.2	1308	tCa/tTa	25/59	0.195044256140492	5	FACETS	0.986	0.815	1	0.329	0.271	0.393	CLONAL	1	TRUE	2	0.305704291279969	5		132	358	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539894	187539894	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	102	285	0	ENST00000441802.2:c.7846G>T	p.Val2616Phe	p.V2616F	ENST00000441802	NM_005245.3	2616	Gtt/Ttt	10/27	0.308831879730228	2	FACETS	0.992	0.888	1	0.496	0.444	0.551	CLONAL	1	TRUE	0	0.305704291279969	2		285	673	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434527	121434527	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	78	318	0	ENST00000257555.6:c.1291G>T	p.Ala431Ser	p.A431S	ENST00000257555		431	Gcc/Tcc	6/10	0.308831879730228	2	FACETS	0.859	0.756	0.97	0.43	0.378	0.485	CLONAL	1	TRUE	0	0.305704291279969	2		318	594	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038097	128038097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	69	231	0	ENST00000285398.2:c.1453G>A	p.Gly485Arg	p.G485R	ENST00000285398	NM_000122.1	485	Ggg/Agg	9/15	0.293984381493085	3	FACETS	0.682	0.593	0.779	0.341	0.296	0.39	SUBCLONAL	1	TRUE	1	0.305704291279969	3		231	763	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0069548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	82	353	9	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	0.331945565598671	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.331945565598671	1		362	309	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947603	48947603	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0069548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	39	178	0	ENST00000267163.4:c.1190C>A	p.Ser397Ter	p.S397*	ENST00000267163	NM_000321.2	397	tCa/tAa	12/27	0.331945565598671	1	FACETS	0.82	0.685	0.968	0.82	0.685	0.968	CLONAL	1	TRUE	0	0.331945565598671	1		178	239	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453138	140453139	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTA	rs727502902	NA	P-0069548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	47	241	0	ENST00000288602.6:c.1794_1796dup	p.Thr599dup	p.T599dup	ENST00000288602	NM_004333.4	599	aca/acTACa	15/18	1	2	FACETS	0.882	0.748	1	0.882	0.748	1	CLONAL	1	TRUE	1	0.331945565598671	2		241	321	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604673	48604673	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060500738	NA	P-0069548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	65	320	1	ENST00000342988.3:c.1495T>C	p.Cys499Arg	p.C499R	ENST00000342988	NM_005359.5	499	Tgc/Cgc	12/12	0.331945565598671	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.331945565598671	1		321	275	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243047	105243048	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCAGGCAGCGGATGATGAAGGTGTTGGGCCGGGGCC	novel	NA	P-0069548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	38	313	5	ENST00000349310.3:c.200_235dup	p.Arg67_Leu78dup	p.R67_L78dup	ENST00000349310	NM_001014432.1	67	cag/cGGCCCCGGCCCAACACCTTCATCATCCGCTGCCTGCag	5/15	0.28020940089027	3	FACETS	0.706	0.585	0.841	0.353	0.292	0.421	SUBCLONAL	1	TRUE	1	0.331945565598671	3		318	378	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38788534	38788534	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	48	222	0	ENST00000348513.6:c.627G>C	p.Glu209Asp	p.E209D	ENST00000348513	NM_003079.4	209	gaG/gaC	8/11	0.331945565598671	1	FACETS	0.84	0.715	0.977	0.84	0.715	0.977	CLONAL	1	TRUE	0	0.331945565598671	1		222	287	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0069549-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	184	405	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.377032471160347	4	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	2	0.38601296235771	4		405	654	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0069549-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	105	494	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.38601296235771	2	FACETS	1	0.939	1	0.53	0.477	0.586	CLONAL	1	TRUE	0	0.38601296235771	2		494	513	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352697	NA	P-0069549-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	260	342	0	ENST00000269305.4:c.587G>A	p.Arg196Gln	p.R196Q	ENST00000269305	NM_001126112.2	196	cGa/cAa	6/11	0.38601296235771	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.38601296235771	2		342	619	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039708	47039708	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0069549-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	115	329	2	ENST00000377604.3:c.1160G>T	p.Arg387Met	p.R387M	ENST00000377604	NM_001204468.1	387	aGg/aTg	11/24	0.38601296235771	3	FACETS	1	0.969	1	0.59	0.533	0.651	CLONAL	1	TRUE	1	0.38601296235771	3		331	602	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1941450	1941450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0069549-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	107	274	0	ENST00000382891.5:c.1826C>T	p.Ser609Leu	p.S609L	ENST00000382891	NM_133335.3	609	tCa/tTa	9/22	0.38601296235771	5	FACETS	1	0.968	1	0.4	0.359	0.444	CLONAL	1	TRUE	2	0.38601296235771	5		274	729	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012392	176012392	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069549-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	147	223	0	ENST00000367669.3:c.1542G>C	p.Lys514Asn	p.K514N	ENST00000367669	NM_022457.5	514	aaG/aaC	14/20	NA	2	FACETS	1	0.933	1			1	INDETERMINATE	2	TRUE	NA	0.38601296235771	2		223	377	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608974	100608975	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	TA	TA	AT	novel	NA	P-0069549-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	41	198	0	ENST00000308731.7:c.1633_1634delinsAT	p.Tyr545Ile	p.Y545I	ENST00000308731	NM_000061.2	545	TAt/ATt	17/19	0.38601296235771	3	FACETS	0.632	0.527	0.748	0.316	0.263	0.374	SUBCLONAL	1	TRUE	1	0.38601296235771	3		198	401	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587504	29587504	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1567863000	NA	P-0069549-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	72	225	0	ENST00000356175.3:c.4485G>C	p.Glu1495Asp	p.E1495D	ENST00000356175	NM_000267.3	1495	gaG/gaC	33/57	0.38601296235771	5	FACETS	0.995	0.87	1	0.332	0.29	0.377	CLONAL	1	TRUE	2	0.38601296235771	5		225	592	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984530	72984530	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069549-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	122	351	0	ENST00000268489.5:c.3054C>G	p.Ile1018Met	p.I1018M	ENST00000268489	NM_006885.3	1018	atC/atG	3/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.38601296235771	2		351	539	SUCCESS
AR	367	MSKCC	GRCh37	X	66766450	66766450	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069549-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	50	272	0	ENST00000374690.3:c.1462C>A	p.Gln488Lys	p.Q488K	ENST00000374690	NM_000044.3	488	Cag/Aag	1/8	0.38601296235771	3	FACETS	0.707	0.601	0.824	0.354	0.3	0.412	SUBCLONAL	1	TRUE	1	0.38601296235771	3		272	437	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020769	26020769	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0069549-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	145	329	0	ENST00000357647.3:c.52C>G	p.Arg18Gly	p.R18G	ENST00000357647	NM_003529.2	18	Cgc/Ggc	1/1	0.38601296235771	3	FACETS	1	0.979	1	0.616	0.562	0.671	CLONAL	1	TRUE	1	0.38601296235771	3		329	728	SUCCESS
ATM	472	MSKCC	GRCh37	11	108168106	108168106	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs747317946	NA	P-0069549-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	66	175	0	ENST00000278616.4:c.5002C>G	p.Leu1668Val	p.L1668V	ENST00000278616	NM_000051.3	1668	Cta/Gta	33/63	0.38601296235771	2	FACETS	0.922	0.804	1	0.461	0.402	0.524	CLONAL	1	TRUE	0	0.38601296235771	2		175	371	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0069550-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	166	387	1	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	1	2	FACETS	0.825	0.758	0.895	1	0.99	1	CLONAL	2	TRUE	1	0.232332050705326	2		388	866	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150936539	150936539	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069550-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	68	319	0	ENST00000271640.5:c.3738G>C	p.Trp1246Cys	p.W1246C	ENST00000271640	NM_001145415.1	1246	tgG/tgC	21/22	1	2	FACETS	0.766	0.666	0.875	0.766	0.666	0.875	SUBCLONAL	1	TRUE	1	0.232332050705326	2		319	764	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934839	49934839	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0069550-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	57	376	0	ENST00000296474.3:c.2057T>C	p.Leu686Pro	p.L686P	ENST00000296474	NM_002447.2	686	cTg/cCg	7/20	1	2	FACETS	0.657	0.562	0.76	0.657	0.562	0.76	SUBCLONAL	1	TRUE	1	0.232332050705326	2		376	747	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557639	95557639	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0069554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	376	364	0	ENST00000393063.1:c.5428G>T	p.Asp1810Tyr	p.D1810Y	ENST00000393063	NM_030621.3	1810	Gat/Tat	26/28	0.862140336515754	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.876663820518099	2		364	426	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124469365	124469365	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069555-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	125	329	0	ENST00000357628.3:c.1537C>G	p.Gln513Glu	p.Q513E	ENST00000357628	NM_015450.2	513	Caa/Gaa	16/19	1	2	FACETS	0.919	0.846	0.993	0.919	0.846	0.993	CLONAL	1	TRUE	1	0.944514199509591	2		329	288	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490349	56490349	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0069555-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	319	399	0	ENST00000267101.3:c.2118G>C	p.Glu706Asp	p.E706D	ENST00000267101	NM_001982.3	706	gaG/gaC	18/28	0.944514199509591	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.944514199509591	1		399	326	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256180	123256180	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0069555-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	322	387	0	ENST00000358487.5:c.1729C>T	p.Arg577Ter	p.R577*	ENST00000358487	NM_000141.4	577	Cga/Tga	13/18	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.944514199509591	2		387	651	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003524-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	142	350	0				ENST00000310581	NM_198253.2	-/1132			0.654987359832288	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	2	0.707539893607788	4		350	328	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226859	2226879	+	inframe_deletion	In_Frame_Del	DEL	GCGGCGTCCTCCGCAGGCGGC	GCGGCGTCCTCCGCAGGCGGC	-	rs748637415	NA	P-0003524-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	169	585	0	ENST00000398665.3:c.4353_4373del	p.Gly1452_Ala1458del	p.G1452_A1458del	ENST00000398665	NM_032482.2	1447	GCGGCGTCCTCCGCAGGCGGC/-	27/28	0.654987359832288	4	FACETS	1	0.99	1	0.746	0.69	0.803	CLONAL	1	TRUE	2	0.707539893607788	4		585	547	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579851	7579851	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003524-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	200	468	0	ENST00000269305.4:c.62del	p.Asp21AlafsTer23	p.D21Afs*23	ENST00000269305	NM_001126112.2	21	gAc/gc	2/11	0.707539893607788	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.707539893607788	2		468	272	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31939810	31939810	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003524-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	373	551	1	ENST00000375333.2:c.37A>C	p.Ile13Leu	p.I13L	ENST00000375333	NM_032454.1	13	Att/Ctt	1/8	0.707539893607788	5	FACETS	0.991	0.948	1	0.991	0.948	1	CLONAL	3	TRUE	2	0.707539893607788	5		552	731	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77937750	77937750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003524-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	294	477	0	ENST00000361507.4:c.968C>T	p.Ala323Val	p.A323V	ENST00000361507	NM_080491.2	323	gCc/gTc	4/10	0.654987359832288	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.707539893607788	4		477	638	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874611	151874611	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003524-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	270	607	0	ENST00000262189.6:c.7927T>G	p.Ser2643Ala	p.S2643A	ENST00000262189	NM_170606.2	2643	Tct/Gct	38/59	0.575939686879638	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.707539893607788	4		607	620	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466543	120466543	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003524-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	304	536	1	ENST00000256646.2:c.4576G>T	p.Glu1526Ter	p.E1526*	ENST00000256646	NM_024408.3	1526	Gag/Tag	26/34	0.707539893607788	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.707539893607788	4		537	665	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457242	25457242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147001633	NA	P-0005467-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	189	1167	6	ENST00000264709.3:c.2645G>A	p.Arg882His	p.R882H	ENST00000264709	NM_175629.2	882	cGc/cAc	23/23	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.65	2		1173	550	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202607	108202607	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555124459	NA	P-0005467-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	142	518	0	ENST00000278616.4:c.7631T>C	p.Leu2544Pro	p.L2544P	ENST00000278616	NM_000051.3	2544	cTa/cCa	52/63	1	2	FACETS	0.995	0.915	1	0.995	0.915	1	CLONAL	1	TRUE	1	0.65	2		518	439	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0006105-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	393	401	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		401	619	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0006105-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	379	479	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		479	782	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266112	41266112	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913228	NA	P-0006105-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	150	503	0	ENST00000349496.5:c.109T>G	p.Ser37Ala	p.S37A	ENST00000349496	NM_001904.3	37	Tct/Gct	3/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		503	497	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720850	89720850	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1206321984	NA	P-0006105-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	32	151	0	ENST00000371953.3:c.1001A>G	p.Asn334Ser	p.N334S	ENST00000371953	NM_000314.4	334	aAc/aGc	8/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		151	140	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249091	55249091	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006105-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	351	473	0	ENST00000275493.2:c.2389T>G	p.Cys797Gly	p.C797G	ENST00000275493	NM_005228.3	797	Tgc/Ggc	20/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		473	736	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057800	180057800	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0006105-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	115	486	0	ENST00000261937.6:c.156-1G>A		p.X52_splice	ENST00000261937	NM_182925.4	52			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		486	475	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118635	11118635	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs751565055	NA	P-0006105-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	131	487	0	ENST00000358026.2:c.2059A>G	p.Lys687Glu	p.K687E	ENST00000358026	NM_001128849.1	687	Aag/Gag	14/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		487	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0006948-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	128	373	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.52451474642904	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.523997417730157	2		373	202	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467946	66467946	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs767139493	NA	P-0006948-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	39	369	0	ENST00000273854.3:c.323A>T	p.Asn108Ile	p.N108I	ENST00000273854	NM_004439.5	108	aAt/aTt	3/18	0.360873401181763	2	FACETS	0.846	0.71	0.992	0.423	0.355	0.496	CLONAL	1	TRUE	0	0.523997417730157	2		369	176	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876498	59876498	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501758	NA	P-0006948-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	37	369	0	ENST00000259008.2:c.1303C>T	p.His435Tyr	p.H435Y	ENST00000259008	NM_032043.2	435	Cat/Tat	9/20	0.527294993988157	2	FACETS	0.785	0.655	0.926	0.392	0.327	0.463	CLONAL	1	TRUE	0	0.523997417730157	2		369	180	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467676	50467676	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006948-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	62	417	0	ENST00000331340.3:c.911A>C	p.Glu304Ala	p.E304A	ENST00000331340	NM_006060.4	304	gAa/gCa	8/8	0.523997417730157	7	FACETS	0.696	0.6	0.801	0.116	0.1	0.134	SUBCLONAL	1	TRUE	1	0.523997417730157	7		417	785	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229426	36229426	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006948-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	174	446	0	ENST00000222270.7:c.8116G>T	p.Gly2706Cys	p.G2706C	ENST00000222270	NM_014727.1	2706	Ggc/Tgc	37/37	0.212300689312852	5	FACETS	1	0.974	1	0.739	0.685	0.794	INDETERMINATE	2	TRUE	2	0.523997417730157	5		446	535	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244822	41244830	+	inframe_deletion	In_Frame_Del	DEL	TTTTCTTCC	TTTTCTTCC	-	novel	NA	P-0006948-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	22	432	0	ENST00000357654.3:c.2718_2726del	p.Lys906_Glu908del	p.K906_E908del	ENST00000357654	NM_007294.3	906	aaGGAAGAAAAt/aat	10/23	0.527294993988157	2	FACETS	0.677	0.532	0.841	0.339	0.266	0.421	SUBCLONAL	1	TRUE	0	0.523997417730157	2		432	124	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434767	110434767	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006948-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	58	476	0	ENST00000375856.3:c.3634C>G	p.Pro1212Ala	p.P1212A	ENST00000375856	NM_003749.2	1212	Cct/Gct	1/2	0.527294993988157	3	FACETS	0.72	0.621	0.827	0.36	0.31	0.414	SUBCLONAL	1	TRUE	1	0.523997417730157	3		476	388	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500373	99500373	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006948-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	72	579	0	ENST00000268035.6:c.3806A>C	p.Glu1269Ala	p.E1269A	ENST00000268035	NM_000875.3	1269	gAg/gCg	21/21	0.527294993988157	1	FACETS	0.835	0.739	0.934	0.835	0.739	0.934	CLONAL	1	TRUE	0	0.523997417730157	1		579	243	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0006948-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	63	373	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.280774843400392	2	FACETS	0.854	0.758	0.951	0.854	0.758	0.951	INDETERMINATE	2	TRUE	0	0.495189937292698	2		373	149	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467946	66467946	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs767139493	NA	P-0006948-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	36	369	0	ENST00000273854.3:c.323A>T	p.Asn108Ile	p.N108I	ENST00000273854	NM_004439.5	108	aAt/aTt	3/18	0.264359220702388	5	FACETS	1	0.927	1	0.412	0.342	0.489	INDETERMINATE	1	TRUE	2	0.495189937292698	5		369	205	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762910	40762910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006948-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	10	468	0	ENST00000392038.2:c.98G>A	p.Gly33Asp	p.G33D	ENST00000392038	NM_001626.4	33	gGc/gAc	3/14	0.184337852752193	3	FACETS	0.334	0.226	0.468	0.167	0.113	0.234	INDETERMINATE	1	TRUE	1	0.495189937292698	3		468	151	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0007356-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	81	483	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.298515779510162	3	FACETS	0.997	0.896	1	1	0.986	1	CLONAL	4	TRUE	1	0.22	3		483	205	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258035	123258035	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs763017169	NA	P-0007356-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	4	0	0	ENST00000358487.5:c.1646A>G	p.Asn549Ser	p.N549S	ENST00000358487	NM_000141.4	549	aAt/aGt	12/18	0.220520835663142	2	FACETS	0.186	0.097	0.315	0.093	0.048	0.158	SUBCLONAL	1	TRUE	0	0.22	2		0	196	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287449	46287449	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007356-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	32	278	0	ENST00000334344.6:c.5308C>G	p.Leu1770Val	p.L1770V	ENST00000334344	NM_152641.2	1770	Cta/Gta	20/21	0.277851256388385	3	FACETS	1	0.887	1			1	CLONAL	1	TRUE	NA	0.22	3		278	286	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855268	76855268	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007356-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	41	150	0	ENST00000373344.5:c.5719A>G	p.Met1907Val	p.M1907V	ENST00000373344	NM_000489.3	1907	Atg/Gtg	24/35	1	1	FACETS	0.953	0.815	1	1	0.977	1	CLONAL	3	TRUE	0	0.22	1		150	116	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211849	123211849	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0007356-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	92	241	0	ENST00000218089.9:c.2716A>T	p.Lys906Ter	p.K906*	ENST00000218089	NM_001042749.1	906	Aaa/Taa	27/35	0.29749391804392	2	FACETS	0.955	0.866	1			1	CLONAL	4	TRUE	NA	0.22	2		241	219	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579314	7579342	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TGCAAGTCACAGACTTGGCTGTCCCAGAA	TGCAAGTCACAGACTTGGCTGTCCCAGAA	-	novel	NA	P-0007356-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	39	355	0	ENST00000269305.4:c.345_373del	p.Ser116ValfsTer23	p.S116Vfs*23	ENST00000269305	NM_001126112.2	115	caTTCTGGGACAGCCAAGTCTGTGACTTGCAcg/cacg	4/11	0.29749391804392	6	FACETS	1	0.92	1			1	CLONAL	2	TRUE	NA	0.22	6		355	217	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923008	44923008	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007356-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	84	192	0	ENST00000377967.4:c.1870del	p.Leu624Ter	p.L624*	ENST00000377967	NM_021140.2	623	aaC/aa	16/29	0.29749391804392	2	FACETS	0.95	0.857	1			1	CLONAL	4	TRUE	NA	0.22	2		192	201	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90990454	90990454	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1586101162	NA	P-0007356-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	20	214	0	ENST00000265433.3:c.578T>C	p.Ile193Thr	p.I193T	ENST00000265433	NM_002485.4	193	aTt/aCt	5/16	0.29749391804392	5	FACETS	0.693	0.529	0.885	0.346	0.264	0.443	SUBCLONAL	1	TRUE	3	0.22	5		214	349	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33689794	33689794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs541053267	NA	P-0007356-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	14	341	0	ENST00000308377.4:c.1033G>A	p.Glu345Lys	p.E345K	ENST00000308377	NM_152270.3	345	Gag/Aag	2/5	0.277851256388385	3	FACETS	0.529	0.382	0.707			1	SUBCLONAL	1	TRUE	NA	0.22	3		341	267	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843618	3843618	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007356-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	53	306	0	ENST00000262367.5:c.985C>T	p.Gln329Ter	p.Q329*	ENST00000262367	NM_004380.2	329	Caa/Taa	4/31	0.277851256388385	3	FACETS	1	0.933	1			1	CLONAL	2	TRUE	NA	0.22	3		306	234	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054537	42054537	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007356-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	13	219	0	ENST00000219905.7:c.7721C>A	p.Ser2574Tyr	p.S2574Y	ENST00000219905	NM_001164273.1	2574	tCc/tAc	22/24	0.298515779510162	3	FACETS	0.653	0.466	0.88	0.326	0.233	0.44	SUBCLONAL	1	TRUE	1	0.22	3		219	201	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427026	49427027	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007356-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	47	360	0	ENST00000301067.7:c.11461dup	p.Gln3821ProfsTer191	p.Q3821Pfs*191	ENST00000301067	NM_003482.3	3821	cag/cCag	39/54	0.29749391804392	7	FACETS	0.981	0.837	1	0.736	0.627	0.853	CLONAL	3	TRUE	3	0.22	7		360	225	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967315	134967315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs904442404	NA	P-0007356-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	46	344	0	ENST00000398015.3:c.2654C>T	p.Pro885Leu	p.P885L	ENST00000398015	NM_004441.4	885	cCg/cTg	14/16	0.277851256388385	3	FACETS	0.951	0.808	1			1	CLONAL	2	TRUE	NA	0.22	3		344	244	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0007552-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	22	459	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		459	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0007631-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	179	475	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.723230539989237	1	FACETS	0.968	0.911	1	0.968	0.911	1	CLONAL	1	TRUE	0	0.738529016694476	1		475	316	SUCCESS
APC	324	MSKCC	GRCh37	5	112174670	112174670	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007631-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	34	429	0	ENST00000257430.4:c.3379C>T	p.Gln1127Ter	p.Q1127*	ENST00000257430	NM_000038.5	1127	Cag/Tag	16/16	1	2	FACETS	0.912	0.766	1	0.912	0.766	1	CLONAL	1	TRUE	1	0.738529016694476	2		429	101	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923778	131923778	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007631-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	18	286	0	ENST00000265335.6:c.1048C>T	p.Gln350Ter	p.Q350*	ENST00000265335		350	Cag/Tag	7/25	1	2	FACETS	0.594	0.457	0.749	0.594	0.457	0.749	SUBCLONAL	1	TRUE	1	0.738529016694476	2		286	82	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508461	106508461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762164881	NA	P-0007631-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	103	380	1	ENST00000359195.3:c.455G>A	p.Arg152Gln	p.R152Q	ENST00000359195	NM_002649.2	152	cGg/cAg	2/11	1	2	FACETS	0.85	0.77	0.934	0.85	0.77	0.934	CLONAL	1	TRUE	1	0.738529016694476	2		381	328	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18747474	18747474	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs561351298	NA	P-0007631-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	18	284	0	ENST00000266497.5:c.3935C>G	p.Thr1312Arg	p.T1312R	ENST00000266497		1312	aCa/aGa	28/31	1	2	FACETS	0.774	0.601	0.963	0.774	0.601	0.963	CLONAL	1	TRUE	1	0.738529016694476	2		284	63	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231488893	231488894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs567805129	NA	P-0007631-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	29	372	2	ENST00000295050.7:c.1263dup	p.Ile422TyrfsTer11	p.I422Yfs*11	ENST00000295050	NM_032018.5	419	aat/aaTt	5/5	1	2	FACETS	0.958	0.794	1	0.958	0.794	1	CLONAL	1	TRUE	1	0.738529016694476	2		374	82	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057892	27057893	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0007631-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	211	546	0	ENST00000324856.7:c.1601dup	p.Tyr534Ter	p.Y534*	ENST00000324856	NM_006015.4	534	tac/tAac	3/20	1	2	FACETS	0.896	0.836	0.956	0.896	0.836	0.956	CLONAL	1	TRUE	1	0.738529016694476	2		546	638	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0007816-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	66	382	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.859	0.746	0.98	0.859	0.746	0.98	CLONAL	1	TRUE	1	0.284142688694605	2		382	541	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044718	47044719	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0007816-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	95	494	0	ENST00000377604.3:c.2119_2120del	p.Gln707AlafsTer12	p.Q707Afs*12	ENST00000377604	NM_001204468.1	706	agACag/agag	19/24	1	2	FACETS	0.9	0.801	1	0.9	0.801	1	CLONAL	1	TRUE	1	0.284142688694605	2		494	743	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0009897-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	259	471	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.801140303744789	1	FACETS	0.766	0.726	0.806	0.766	0.726	0.806	SUBCLONAL	1	TRUE	0	0.801140303744789	1		471	506	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0009897-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	117	268	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	NA	2	FACETS	0.885	0.808	0.964			1	INDETERMINATE	1	TRUE	NA	0.801140303744789	2		268	330	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009897-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	75	463	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.801140303744789	1	FACETS	0.305	0.269	0.344	0.305	0.269	0.344	SUBCLONAL	1	TRUE	0	0.801140303744789	1		463	368	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287262	33287262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009897-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	188	175	0	ENST00000374542.5:c.1835C>T	p.Ser612Phe	p.S612F	ENST00000374542	NM_001141970.1	612	tCc/tTc	6/8	1	2	FACETS	0.532	0.492	0.574	0.532	0.492	0.574	SUBCLONAL	1	TRUE	1	0.801140303744789	2		175	882	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0009897-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	305	262	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.542850921078843	2	FACETS	1	0.994	1	0.67	0.639	0.701	CLONAL	1	TRUE	0	0.801140303744789	2		262	568	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998985	11998985	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009897-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	76	75	0	ENST00000353533.5:c.487C>T	p.Gln163Ter	p.Q163*	ENST00000353533	NM_003010.3	163	Cag/Tag	4/11	0.801140303744789	1	FACETS	0.338	0.299	0.38	0.338	0.299	0.38	SUBCLONAL	1	TRUE	0	0.801140303744789	1		75	336	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729733	41729733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009897-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	199	162	0	ENST00000242208.4:c.796G>A	p.Glu266Lys	p.E266K	ENST00000242208	NM_002192.2	266	Gag/Aag	3/3	1	2	FACETS	0.776	0.723	0.831	0.776	0.723	0.831	SUBCLONAL	1	TRUE	1	0.801140303744789	2		162	640	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835733	68835733	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009897-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	304	145	0	ENST00000261769.5:c.324A>C	p.Arg108Ser	p.R108S	ENST00000261769	NM_004360.3	108	agA/agC	3/16	0.801140303744789	1	FACETS	0.991	0.951	1	0.991	0.951	1	CLONAL	1	TRUE	0	0.801140303744789	1		145	459	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835740	68835752	+	frameshift_variant	Frame_Shift_Del	DEL	TCCACCAAAGTCA	TCCACCAAAGTCA	-	novel	NA	P-0009897-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	299	149	0	ENST00000261769.5:c.331_343del	p.Ser111ArgfsTer2	p.S111Rfs*2	ENST00000261769	NM_004360.3	111	TCCACCAAAGTCAcg/cg	3/16	0.801140303744789	1	FACETS	0.968	0.928	1	0.968	0.928	1	CLONAL	1	TRUE	0	0.801140303744789	1		149	462	SUCCESS
AR	367	MSKCC	GRCh37	X	66765025	66765025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1335991486	NA	P-0009897-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	59	164	0	ENST00000374690.3:c.37C>T	p.Arg13Trp	p.R13W	ENST00000374690	NM_000044.3	13	Cgg/Tgg	1/8	0.362531795215853	1	FACETS	0.173	0.149	0.2	0.173	0.149	0.2	INDETERMINATE	1	TRUE	0	0.801140303744789	1		164	510	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061313	38061313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1204900727	NA	P-0009897-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	61	184	0	ENST00000250448.2:c.676G>A	p.Asp226Asn	p.D226N	ENST00000250448	NM_004496.3	226	Gac/Aac	2/2	0.801140303744789	4	FACETS	0.235	0.201	0.271			1	SUBCLONAL	1	TRUE	NA	0.801140303744789	4		184	1168	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152373128	152373128	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009897-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	171	95	0	ENST00000359321.1:c.37G>C	p.Glu13Gln	p.E13Q	ENST00000359321	NM_005431.1	13	Gag/Cag	1/3	1	2	FACETS	0.793	0.735	0.854	0.793	0.735	0.854	SUBCLONAL	1	TRUE	1	0.801140303744789	2		95	538	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023423	27023423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009897-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	157	166	0	ENST00000324856.7:c.529C>T	p.Gln177Ter	p.Q177*	ENST00000324856	NM_006015.4	177	Caa/Taa	1/20	0.245977190236318	1	FACETS	0.51	0.471	0.549	0.51	0.471	0.549	INDETERMINATE	1	TRUE	0	0.801140303744789	1		166	461	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910632	50910632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1354117345	NA	P-0009897-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	173	194	0	ENST00000440232.2:c.1735G>A	p.Glu579Lys	p.E579K	ENST00000440232	NM_002691.3	579	Gag/Aag	14/27	1	2	FACETS	0.679	0.628	0.732	0.679	0.628	0.732	SUBCLONAL	1	TRUE	1	0.801140303744789	2		194	636	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040727	16040727	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0009897-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	147	46	0	ENST00000268712.3:c.1408-1G>C		p.X470_splice	ENST00000268712	NM_006311.3	470			0.801140303744789	1	FACETS	0.791	0.738	0.844	0.791	0.738	0.844	SUBCLONAL	1	TRUE	0	0.801140303744789	1		46	278	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486070	29486070	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs746824139	NA	P-0009897-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	183	106	0	ENST00000356175.3:c.247C>T	p.Gln83Ter	p.Q83*	ENST00000356175	NM_000267.3	83	Cag/Tag	3/57	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.801140303744789	2		106	428	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67462903	67462903	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009897-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	166	153	0	ENST00000327367.4:c.619C>G	p.Leu207Val	p.L207V	ENST00000327367	NM_005902.3	207	Cta/Gta	5/9	1	2	FACETS	0.66	0.609	0.713	0.66	0.609	0.713	SUBCLONAL	1	TRUE	1	0.801140303744789	2		153	628	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289152	33289152	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009897-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	238	207	0	ENST00000374542.5:c.400C>T	p.Leu134Phe	p.L134F	ENST00000374542	NM_001141970.1	134	Ctc/Ttc	3/8	1	2	FACETS	0.582	0.543	0.622	0.582	0.543	0.622	SUBCLONAL	1	TRUE	1	0.801140303744789	2		207	1021	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730888	40730888	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1338443808	NA	P-0009897-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	82	169	0	ENST00000373198.4:c.3647G>C	p.Gly1216Ala	p.G1216A	ENST00000373198	NM_133170.3	1216	gGg/gCg	27/32	1	2	FACETS	0.286	0.252	0.323	0.286	0.252	0.323	SUBCLONAL	1	TRUE	1	0.801140303744789	2		169	715	SUCCESS
APC	324	MSKCC	GRCh37	5	112176017	112176017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009897-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	198	143	0	ENST00000257430.4:c.4726G>A	p.Glu1576Lys	p.E1576K	ENST00000257430	NM_000038.5	1576	Gaa/Aaa	16/16	0.219275664828149	2	FACETS	0.687	0.639	0.738	0.344	0.319	0.369	INDETERMINATE	1	TRUE	0	0.801140303744789	2		143	719	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033233	69033233	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009897-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	153	82	0	ENST00000288368.4:c.3673C>T	p.Leu1225Phe	p.L1225F	ENST00000288368	NM_024870.2	1225	Ctt/Ttt	30/40	1	2	FACETS	0.678	0.624	0.735	0.678	0.624	0.735	SUBCLONAL	1	TRUE	1	0.801140303744789	2		82	563	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231489036	231489036	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009897-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	221	134	0	ENST00000295050.7:c.1399C>T	p.Gln467Ter	p.Q467*	ENST00000295050	NM_032018.5	467	Cag/Tag	5/5	0.792359905233415	3	FACETS	0.807	0.751	0.864	0.403	0.375	0.432	CLONAL	1	TRUE	1	0.801140303744789	3		134	958	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623089	52623089	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009897-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	215	125	0	ENST00000394830.3:c.2962G>C	p.Ala988Pro	p.A988P	ENST00000394830	NM_018313.4	988	Gct/Cct	19/30	0.245977190236318	1	FACETS	0.529	0.495	0.564	0.529	0.495	0.564	INDETERMINATE	1	TRUE	0	0.801140303744789	1		125	608	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123708	46123708	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009897-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	157	163	0	ENST00000334344.6:c.89G>A	p.Arg30Lys	p.R30K	ENST00000334344	NM_152641.2	30	aGa/aAa	1/21	0.180509477332645	3	FACETS	0.9	0.828	0.975	0.45	0.414	0.488	INDETERMINATE	1	TRUE	1	0.801140303744789	3		163	610	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216611	7216611	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0009897-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	72	168	0	ENST00000380728.2:c.725-1G>A		p.X242_splice	ENST00000380728		242			0.801140303744789	1	FACETS	0.238	0.208	0.27	0.238	0.208	0.27	SUBCLONAL	1	TRUE	0	0.801140303744789	1		168	453	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47600488	47600488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1474105869	NA	P-0009897-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	171	152	0	ENST00000430070.2:c.16G>A	p.Ala6Thr	p.A6T	ENST00000430070	NM_018095.4	6	Gca/Aca	1/4	1	2	FACETS	0.775	0.717	0.834	0.775	0.717	0.834	SUBCLONAL	1	TRUE	1	0.801140303744789	2		152	551	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934176	48934176	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009897-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	48	59	0	ENST00000267163.4:c.631del	p.Asp211IlefsTer3	p.D211Ifs*3	ENST00000267163	NM_000321.2	211	Gat/at	7/27	0.577758838342154	1	FACETS	0.192	0.162	0.224	0.192	0.162	0.224	SUBCLONAL	1	TRUE	0	0.801140303744789	1		59	375	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0010177-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	23	411	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.786	0.613	0.987	0.786	0.613	0.987	CLONAL	1	TRUE	1	0.18	2		411	325	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604656	48604656	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010177-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	17	430	0	ENST00000342988.3:c.1478A>G	p.Asp493Gly	p.D493G	ENST00000342988	NM_005359.5	493	gAt/gGt	12/12	1	2	FACETS	0.594	0.443	0.774	0.594	0.443	0.774	SUBCLONAL	1	TRUE	1	0.18	2		430	318	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058649	47058650	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0010177-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	29	406	0	ENST00000409792.3:c.7628dup	p.Tyr2543Ter	p.Y2543*	ENST00000409792	NM_014159.6	2543	tac/taAc	21/21	1	2	FACETS	0.808	0.648	0.989	0.808	0.648	0.989	CLONAL	1	TRUE	1	0.18	2		406	399	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717717	89717717	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011363-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	158	315	0	ENST00000371953.3:c.743del	p.Pro248LeufsTer8	p.P248Lfs*8	ENST00000371953	NM_000314.4	248	Cct/ct	7/9	0.748201862078487	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.761087590462016	2		315	202	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441795	49441795	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011363-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	151	337	0	ENST00000301067.7:c.4189T>A	p.Cys1397Ser	p.C1397S	ENST00000301067	NM_003482.3	1397	Tgt/Agt	14/54	0.608150184307262	4	FACETS	0.934	0.865	1	0.934	0.865	1	CLONAL	2	TRUE	2	0.761087590462016	4		337	374	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445017	49445017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011363-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	168	494	0	ENST00000301067.7:c.2449C>T	p.Pro817Ser	p.P817S	ENST00000301067	NM_003482.3	817	Cct/Tct	10/54	0.608150184307262	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	2	0.761087590462016	4		494	362	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061212	38061212	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0011363-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	109	486	0	ENST00000250448.2:c.777C>G	p.Tyr259Ter	p.Y259*	ENST00000250448	NM_004496.3	259	taC/taG	2/2	0.408711920762448	4	FACETS	1	0.966	1	1	0.966	1	INDETERMINATE	2	TRUE	2	0.761087590462016	4		486	229	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55962458	55962458	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011363-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	151	320	0	ENST00000263923.4:c.2666T>C	p.Leu889Pro	p.L889P	ENST00000263923	NM_002253.2	889	cTc/cCc	19/30	0.759905132660252	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	2	0.761087590462016	4		320	336	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932611	39932611	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011363-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	229	279	0	ENST00000378444.4:c.1988C>T	p.Pro663Leu	p.P663L	ENST00000378444	NM_001123385.1	663	cCt/cTt	4/15	0.662487142786235	2	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.761087590462016	2		279	262	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124448	94124449	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAAA	novel	NA	P-0011363-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	153	308	0	ENST00000369303.4:c.134_135insTTTT	p.Leu45PhefsTer16	p.L45Ffs*16	ENST00000369303	NM_004440.3	45	ttg/ttTTTTg	2/17	0.761087590462016	2	FACETS	0.985	0.937	1	0.985	0.937	1	CLONAL	2	TRUE	0	0.761087590462016	2		308	204	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124441	94124443	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	TCC	TCC	CT	novel	NA	P-0011363-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	145	298	0	ENST00000369303.4:c.140_142delinsAG	p.Trp47Ter	p.W47*	ENST00000369303	NM_004440.3	47	tGGAtt/tAGtt	2/17	0.761087590462016	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.761087590462016	2		298	184	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875052	151875052	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011363-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	184	323	0	ENST00000262189.6:c.7486G>T	p.Glu2496Ter	p.E2496*	ENST00000262189	NM_170606.2	2496	Gag/Tag	38/59	0.341812864155659	6	FACETS	1	0.986	1	0.821	0.765	0.879	INDETERMINATE	2	TRUE	3	0.761087590462016	6		323	495	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914489	32915455	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTTTTCTGAAATAGAAGATAGTACCAAGCAAGTCTTTTCCAAAGTATTGTTTAAAAGTAACGAACATTCAGACCAGCTCACAAGAGAAGAAAATACTGCTATACGTACTCCAGAACATTTAATATCCCAAAAAGGCTTTTCATATAATGTGGTAAATTCATCTGCTTTCTCTGGATTTAGTACAGCAAGTGGAAAGCAAGTTTCCATTTTAGAAAGTTCCTTACACAAAGTTAAGGGAGTGTTAGAGGAATTTGATTTAATCAGAACTGAGCATAGTCTTCACTATTCACCTACGTCTAGACAAAATGTATCAAAAATACTTCCTCGTGTTGATAAGAGAAACCCAGAGCACTGTGTAAACTCAGAAATGGAAAAAACCTGCAGTAAAGAATTTAAATTATCAAATAACTTAAATGTTGAAGGTGGTTCTTCAGAAAATAATCACTCTATTAAAGTTTCTCCATATCTCTCTCAATTTCAACAAGACAAACAACAGTTGGTATTAGGAACCAAAGTGTCACTTGTTGAGAACATTCATGTTTTGGGAAAAGAACAGGCTTCACCTAAAAACGTAAAAATGGAAATTGGTAAAACTGAAACTTTTTCTGATGTTCCTGTGAAAACAAATATAGAAGTTTGTTCTACTTACTCCAAAGATTCAGAAAACTACTTTGAAACAGAAGCAGTAGAAATTGCTAAAGCTTTTATGGAAGATGATGAACTGACAGATTCTAAACTGCCAAGTCATGCCACACATTCTCTTTTTACATGTCCCGAAAATGAGGAAATGGTTTTGTCAAATTCAAGAATTGGAAAAAGAAGAGGAGAGCCCCTTATCTTAGTGGGTAAGTGTTCATTTTTACCTTTCGTGTTGCCAATCACTATTTTTAAAGTGTTTATTCAGTAGACTTGGTATGCTAACAATTAAGAGTGTTATAAACTATGTCTTTTCAGCCATTTTTGTGTA	GTTTTCTGAAATAGAAGATAGTACCAAGCAAGTCTTTTCCAAAGTATTGTTTAAAAGTAACGAACATTCAGACCAGCTCACAAGAGAAGAAAATACTGCTATACGTACTCCAGAACATTTAATATCCCAAAAAGGCTTTTCATATAATGTGGTAAATTCATCTGCTTTCTCTGGATTTAGTACAGCAAGTGGAAAGCAAGTTTCCATTTTAGAAAGTTCCTTACACAAAGTTAAGGGAGTGTTAGAGGAATTTGATTTAATCAGAACTGAGCATAGTCTTCACTATTCACCTACGTCTAGACAAAATGTATCAAAAATACTTCCTCGTGTTGATAAGAGAAACCCAGAGCACTGTGTAAACTCAGAAATGGAAAAAACCTGCAGTAAAGAATTTAAATTATCAAATAACTTAAATGTTGAAGGTGGTTCTTCAGAAAATAATCACTCTATTAAAGTTTCTCCATATCTCTCTCAATTTCAACAAGACAAACAACAGTTGGTATTAGGAACCAAAGTGTCACTTGTTGAGAACATTCATGTTTTGGGAAAAGAACAGGCTTCACCTAAAAACGTAAAAATGGAAATTGGTAAAACTGAAACTTTTTCTGATGTTCCTGTGAAAACAAATATAGAAGTTTGTTCTACTTACTCCAAAGATTCAGAAAACTACTTTGAAACAGAAGCAGTAGAAATTGCTAAAGCTTTTATGGAAGATGATGAACTGACAGATTCTAAACTGCCAAGTCATGCCACACATTCTCTTTTTACATGTCCCGAAAATGAGGAAATGGTTTTGTCAAATTCAAGAATTGGAAAAAGAAGAGGAGAGCCCCTTATCTTAGTGGGTAAGTGTTCATTTTTACCTTTCGTGTTGCCAATCACTATTTTTAAAGTGTTTATTCAGTAGACTTGGTATGCTAACAATTAAGAGTGTTATAAACTATGTCTTTTCAGCCATTTTTGTGTA	-	novel	NA	P-0011363-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	23	513	0	ENST00000380152.3:c.5999_6841+124del		p.X2000_splice	ENST00000380152		2000		11/27	0.748201862078487	2	FACETS	0.209	0.163	0.262	0.105	0.081	0.131	SUBCLONAL	1	TRUE	0	0.761087590462016	2		513	289	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914734	32915533	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGAATTTGATTTAATCAGAACTGAGCATAGTCTTCACTATTCACCTACGTCTAGACAAAATGTATCAAAAATACTTCCTCGTGTTGATAAGAGAAACCCAGAGCACTGTGTAAACTCAGAAATGGAAAAAACCTGCAGTAAAGAATTTAAATTATCAAATAACTTAAATGTTGAAGGTGGTTCTTCAGAAAATAATCACTCTATTAAAGTTTCTCCATATCTCTCTCAATTTCAACAAGACAAACAACAGTTGGTATTAGGAACCAAAGTGTCACTTGTTGAGAACATTCATGTTTTGGGAAAAGAACAGGCTTCACCTAAAAACGTAAAAATGGAAATTGGTAAAACTGAAACTTTTTCTGATGTTCCTGTGAAAACAAATATAGAAGTTTGTTCTACTTACTCCAAAGATTCAGAAAACTACTTTGAAACAGAAGCAGTAGAAATTGCTAAAGCTTTTATGGAAGATGATGAACTGACAGATTCTAAACTGCCAAGTCATGCCACACATTCTCTTTTTACATGTCCCGAAAATGAGGAAATGGTTTTGTCAAATTCAAGAATTGGAAAAAGAAGAGGAGAGCCCCTTATCTTAGTGGGTAAGTGTTCATTTTTACCTTTCGTGTTGCCAATCACTATTTTTAAAGTGTTTATTCAGTAGACTTGGTATGCTAACAATTAAGAGTGTTATAAACTATGTCTTTTCAGCCATTTTTGTGTAGTCAGTTTGGGGGAGTATGGTTTGATATACAGATACACAGATTCAGTATTCGTATACAGATTTGATATCTTGGTATAC	AGGAATTTGATTTAATCAGAACTGAGCATAGTCTTCACTATTCACCTACGTCTAGACAAAATGTATCAAAAATACTTCCTCGTGTTGATAAGAGAAACCCAGAGCACTGTGTAAACTCAGAAATGGAAAAAACCTGCAGTAAAGAATTTAAATTATCAAATAACTTAAATGTTGAAGGTGGTTCTTCAGAAAATAATCACTCTATTAAAGTTTCTCCATATCTCTCTCAATTTCAACAAGACAAACAACAGTTGGTATTAGGAACCAAAGTGTCACTTGTTGAGAACATTCATGTTTTGGGAAAAGAACAGGCTTCACCTAAAAACGTAAAAATGGAAATTGGTAAAACTGAAACTTTTTCTGATGTTCCTGTGAAAACAAATATAGAAGTTTGTTCTACTTACTCCAAAGATTCAGAAAACTACTTTGAAACAGAAGCAGTAGAAATTGCTAAAGCTTTTATGGAAGATGATGAACTGACAGATTCTAAACTGCCAAGTCATGCCACACATTCTCTTTTTACATGTCCCGAAAATGAGGAAATGGTTTTGTCAAATTCAAGAATTGGAAAAAGAAGAGGAGAGCCCCTTATCTTAGTGGGTAAGTGTTCATTTTTACCTTTCGTGTTGCCAATCACTATTTTTAAAGTGTTTATTCAGTAGACTTGGTATGCTAACAATTAAGAGTGTTATAAACTATGTCTTTTCAGCCATTTTTGTGTAGTCAGTTTGGGGGAGTATGGTTTGATATACAGATACACAGATTCAGTATTCGTATACAGATTTGATATCTTGGTATAC	-	novel	NA	P-0011363-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	90	471	0	ENST00000380152.3:c.6244_6841+202del		p.X2082_splice	ENST00000380152		2082		11/27	0.748201862078487	2	FACETS	1	0.982	1	0.676	0.617	0.734	CLONAL	1	TRUE	0	0.761087590462016	2		471	175	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46508733	46509545	+	splice_acceptor_variant,coding_sequence_variant,3_prime_UTR_variant	Splice_Site	DEL	GATGCTGAAGCCTAAATTATGTTGGTAAGAAACAAAATACCTTCAGTTGAAGGTTTTTTTTATCATCTTGGCTTAGATTATTTAAATGAAATCCCAAGCCTCCCCATTTTCCTTTGGTTGTCTTTTTCATCAAATCCCATTCTATCACAAAACCTAAACAGCCTTCTTCGTGGGGGGAAGAGAGACTGCCAAAGCAAAACACAACTCCCAGCAGAGCCATGCCCCTGCTGCACTCTCAAGAGTTAGATTTTAAAAAGACATGGTCTCTTCAGAGGCTTCCAAATACAACCCCACCCGCTATAACCATCAAGCCTAATATTCTGTTGAGGGTGTCTGGCTAAACAAAACAAAAACCCCAATGAAACAGACTTTCAAAAAAAACATCTGCTTCCAGCTTAGTATGTCAGTGCAGCGGCATGGCTGAGTCCTAGAGAACCTCAGGCCTCTAATGCCCCCATCCCGGCCGGCTGCTGCTCGGCCTCTCCACTTCACATTCACAAAATCACTTCTTGTGCAAAACAAGCAGTCTATGTAGAAAGAATGCCCTCATCGTAGTCTAATAAAAACTGTAGAAAAAAATGCCAGAGAACCACCTCTCTTCCCACTTCCTCTTTATCTGCAAAGCGAGGGCATCTGTGCATGAACAGGGTAGGCAAGCCTGACGTTGAGGGAGTCGTTGTGCTGAACCAAGGATGTCTGCTGGTAATGGAGCACTAGCTCCTTCAGAGAGCTGTACAGGTTGTAGGGCTCTGCAAAGCCATAGCCCCGAGCAGTGCTGTAGATCACACAGTGCTTCACTTCCCCATCGGCCCT	GATGCTGAAGCCTAAATTATGTTGGTAAGAAACAAAATACCTTCAGTTGAAGGTTTTTTTTATCATCTTGGCTTAGATTATTTAAATGAAATCCCAAGCCTCCCCATTTTCCTTTGGTTGTCTTTTTCATCAAATCCCATTCTATCACAAAACCTAAACAGCCTTCTTCGTGGGGGGAAGAGAGACTGCCAAAGCAAAACACAACTCCCAGCAGAGCCATGCCCCTGCTGCACTCTCAAGAGTTAGATTTTAAAAAGACATGGTCTCTTCAGAGGCTTCCAAATACAACCCCACCCGCTATAACCATCAAGCCTAATATTCTGTTGAGGGTGTCTGGCTAAACAAAACAAAAACCCCAATGAAACAGACTTTCAAAAAAAACATCTGCTTCCAGCTTAGTATGTCAGTGCAGCGGCATGGCTGAGTCCTAGAGAACCTCAGGCCTCTAATGCCCCCATCCCGGCCGGCTGCTGCTCGGCCTCTCCACTTCACATTCACAAAATCACTTCTTGTGCAAAACAAGCAGTCTATGTAGAAAGAATGCCCTCATCGTAGTCTAATAAAAACTGTAGAAAAAAATGCCAGAGAACCACCTCTCTTCCCACTTCCTCTTTATCTGCAAAGCGAGGGCATCTGTGCATGAACAGGGTAGGCAAGCCTGACGTTGAGGGAGTCGTTGTGCTGAACCAAGGATGTCTGCTGGTAATGGAGCACTAGCTCCTTCAGAGAGCTGTACAGGTTGTAGGGCTCTGCAAAGCCATAGCCCCGAGCAGTGCTGTAGATCACACAGTGCTTCACTTCCCCATCGGCCCT	-	novel	NA	P-0011363-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1	115	0	0	ENST00000262741.5:c.1188-2_*612del		p.X396_splice	ENST00000262741	NM_003629.3	396		10/10	0.558215037313237	4	FACETS		NA	1	1	0.993	1	NA	5	TRUE	2	0.761087590462016	4		0	116	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367106	40367196	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTCCGCTCCCTGCGGGAGGGAAGGGGGGACGTGCTGACCGGGTGCCGGCCGGGCGAAGGAGGTGTCCCCGGGTCCCTCGGCACAGTCGGC	TGTCCGCTCCCTGCGGGAGGGAAGGGGGGACGTGCTGACCGGGTGCCGGCCGGGCGAAGGAGGTGTCCCCGGGTCCCTCGGCACAGTCGGC	-	novel	NA	P-0011363-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	68	510	0	ENST00000397332.2:c.82-81_91del		p.X28_splice	ENST00000397332	NM_001033082.2	28		2/3	0.558215037313237	4	FACETS	1	0.906	1	0.519	0.455	0.587	CLONAL	1	TRUE	2	0.761087590462016	4		510	303	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439688	51439696	+	inframe_deletion	In_Frame_Del	DEL	ACTTTACAG	ACTTTACAG	-	novel	NA	P-0013119-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	98	661	0	ENST00000262662.1:c.258_266del	p.Gln87_Leu89del	p.Q87_L89del	ENST00000262662		85	ACTTTACAG/-	4/4	1	2	FACETS	0.44	0.393	0.489	0.44	0.393	0.489	SUBCLONAL	1	TRUE	1	0.81	2		661	550	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922966	44922966	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0014507-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	34	504	0	ENST00000377967.4:c.1827C>G	p.Tyr609Ter	p.Y609*	ENST00000377967	NM_021140.2	609	taC/taG	16/29	0.347027215268195	1	FACETS	0.78	0.655	0.913	1	0.957	1	CLONAL	2	TRUE	0	0.346391563807531	1		504	104	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339981	70339981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014507-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	47	410	0	ENST00000374080.3:c.514G>A	p.Glu172Lys	p.E172K	ENST00000374080		172	Gag/Aag	4/45	0.347027215268195	0	FACETS	0.758	0.674	0.839			1	SUBCLONAL	3	TRUE	0	0.346391563807531	0		410	78	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799625	3799626	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	novel	NA	P-0014507-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	20	247	0	ENST00000262367.5:c.3836+2dup		p.X1279_splice	ENST00000262367	NM_004380.2	1279			0.347027215268195	1	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	0	0.346391563807531	1		247	81	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828074	72828074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766287350	NA	P-0014507-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	31	476	0	ENST00000268489.5:c.8507C>T	p.Ser2836Phe	p.S2836F	ENST00000268489	NM_006885.3	2836	tCc/tTc	9/10	0.347027215268195	0	FACETS	0.661	0.564	0.757			1	SUBCLONAL	3	TRUE	0	0.346391563807531	0		476	59	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572947	7572947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014507-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	36	436	0	ENST00000269305.4:c.1162G>A	p.Glu388Lys	p.E388K	ENST00000269305	NM_001126112.2	388	Gaa/Aaa	11/11	0.346391563807531	7	FACETS	0.93	0.779	1	0.558	0.467	0.656	CLONAL	3	TRUE	2	0.346391563807531	7		436	139	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259307	36259307	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014507-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	26	489	0	ENST00000300305.3:c.184G>A	p.Asp62Asn	p.D62N	ENST00000300305		62	Gac/Aac	3/8	0.346391563807531	5	FACETS	0.905	0.728	1	0.453	0.364	0.551	CLONAL	2	TRUE	1	0.346391563807531	5		489	126	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938567	44938567	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014507-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	16	337	0	ENST00000377967.4:c.3115C>T	p.Gln1039Ter	p.Q1039*	ENST00000377967	NM_021140.2	1039	Cag/Tag	20/29	0.347027215268195	1	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	0	0.346391563807531	1		337	54	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51507917	51507917	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014507-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	17	337	0	ENST00000260433.2:c.841G>T	p.Glu281Ter	p.E281*	ENST00000260433		281	Gag/Tag	7/10	0.347027215268195	3	FACETS	1	0.885	1	0.662	0.503	0.842	CLONAL	1	TRUE	1	0.346391563807531	3		337	87	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367055	40367055	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014507-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	39	582	0	ENST00000397332.2:c.142G>T	p.Asp48Tyr	p.D48Y	ENST00000397332	NM_001033082.2	48	Gat/Tat	2/3	0.347027215268195	4	FACETS	1	0.877	1	0.523	0.441	0.61	CLONAL	2	TRUE	0	0.346391563807531	4		582	145	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	78	350	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.847338198965715	2		350	168	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	190	348	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.847338198965715	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.847338198965715	1		348	230	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	202	380	0	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.847338198965715	2		380	397	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	70	148	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.241888426043626	3	FACETS	1	0.978	1	0.726	0.649	0.804	INDETERMINATE	1	TRUE	1	0.847338198965715	3		148	162	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	474	287	0	ENST00000267101.3:c.273G>A	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atA	3/28	0.741896119551745	3	FACETS	0.998	0.979	1	1	0.998	1	CLONAL	3	TRUE	1	0.847338198965715	3		287	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352697	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	212	394	0	ENST00000269305.4:c.587G>A	p.Arg196Gln	p.R196Q	ENST00000269305	NM_001126112.2	196	cGa/cAa	6/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.847338198965715	2		394	410	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564113	139564113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1304820249	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	160	314	0	ENST00000308874.7:c.253C>T	p.Arg85Cys	p.R85C	ENST00000308874		85	Cgc/Tgc	5/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.847338198965715	2		314	362	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641037	3641037	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	242	360	0	ENST00000294008.3:c.2602G>C	p.Glu868Gln	p.E868Q	ENST00000294008	NM_032444.2	868	Gaa/Caa	12/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.847338198965715	2		360	534	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097665	27097665	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	444	376	0	ENST00000324856.7:c.3254C>G	p.Ser1085Ter	p.S1085*	ENST00000324856	NM_006015.4	1085	tCa/tGa	12/20	0.847338198965715	3	FACETS	0.977	0.956	0.996	0.977	0.956	0.996	CLONAL	3	TRUE	0	0.847338198965715	3		376	509	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870205	44870205	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	31	122	0	ENST00000377967.4:c.385-1G>C		p.X129_splice	ENST00000377967	NM_021140.2	129			1	1	FACETS	0.322	0.265	0.384	0.322	0.265	0.384	SUBCLONAL	1	TRUE	0	0.847338198965715	1		122	131	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483351	120483351	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	160	319	0	ENST00000256646.2:c.3010G>C	p.Asp1004His	p.D1004H	ENST00000256646	NM_024408.3	1004	Gat/Cat	19/34	0.241888426043626	3	FACETS	1	0.989	1	0.691	0.642	0.741	INDETERMINATE	1	TRUE	1	0.847338198965715	3		319	389	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56477614	56477614	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	192	318	0	ENST00000267101.3:c.162G>C	p.Glu54Asp	p.E54D	ENST00000267101	NM_001982.3	54	gaG/gaC	2/28	0.741896119551745	3	FACETS	1	0.989	1	0.648	0.605	0.692	CLONAL	1	TRUE	1	0.847338198965715	3		318	498	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375412	15375412	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	194	393	0	ENST00000263377.2:c.1015C>T	p.Gln339Ter	p.Q339*	ENST00000263377	NM_058243.2	339	Cag/Tag	6/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.847338198965715	2		393	437	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286791	33286791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369424162	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	220	376	0	ENST00000374542.5:c.2146C>T	p.Arg716Trp	p.R716W	ENST00000374542	NM_001141970.1	716	Cgg/Tgg	7/8	1	2	FACETS	0.993	0.933	1	0.993	0.933	1	CLONAL	1	TRUE	1	0.847338198965715	2		376	523	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641221	93641221	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	143	245	0	ENST00000375746.1:c.1567G>T	p.Glu523Ter	p.E523*	ENST00000375746	NM_001174167.1	523	Gaa/Taa	11/14	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.847338198965715	2		245	320	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555125	106555125	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	184	333	0	ENST00000369096.4:c.2242G>A	p.Asp748Asn	p.D748N	ENST00000369096	NM_001198.3	748	Gac/Aac	7/7	1	2	FACETS	0.903	0.841	0.965	0.903	0.841	0.965	CLONAL	1	TRUE	1	0.847338198965715	2		333	481	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444668	49444668	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs727503988	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	64	388	0	ENST00000301067.7:c.2797+1G>A		p.X933_splice	ENST00000301067	NM_003482.3	933			0.741896119551745	3	FACETS	0.38	0.329	0.435	0.19	0.164	0.218	SUBCLONAL	1	TRUE	1	0.847338198965715	3		388	566	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427203	49427203	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	178	381	0	ENST00000301067.7:c.11285G>C	p.Gly3762Ala	p.G3762A	ENST00000301067	NM_003482.3	3762	gGa/gCa	39/54	0.741896119551745	3	FACETS	1	0.988	1	0.649	0.604	0.694	CLONAL	1	TRUE	1	0.847338198965715	3		381	461	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188582	11188582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	393	284	0	ENST00000361445.4:c.5839G>A	p.Asp1947Asn	p.D1947N	ENST00000361445	NM_004958.3	1947	Gat/Aat	42/58	0.847338198965715	3	FACETS	0.998	0.977	1	0.998	0.977	1	CLONAL	3	TRUE	0	0.847338198965715	3		284	441	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482379	56482379	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	148	347	0	ENST00000267101.3:c.927G>C	p.Lys309Asn	p.K309N	ENST00000267101	NM_001982.3	309	aaG/aaC	8/28	0.741896119551745	3	FACETS	1	0.934	1	0.509	0.468	0.551	CLONAL	1	TRUE	1	0.847338198965715	3		347	489	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641100	93641100	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	159	298	0	ENST00000375746.1:c.1446G>A	p.Met482Ile	p.M482I	ENST00000375746	NM_001174167.1	482	atG/atA	11/14	1	2	FACETS	0.988	0.917	1	0.988	0.917	1	CLONAL	1	TRUE	1	0.847338198965715	2		298	380	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641113	93641113	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	162	283	0	ENST00000375746.1:c.1459G>T	p.Glu487Ter	p.E487*	ENST00000375746	NM_001174167.1	487	Gag/Tag	11/14	1	2	FACETS	0.98	0.911	1	0.98	0.911	1	CLONAL	1	TRUE	1	0.847338198965715	2		283	390	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434603	128434603	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	129	263	0	ENST00000265960.3:c.251C>G	p.Ser84Ter	p.S84*	ENST00000265960	NM_001006617.1	84	tCa/tGa	2/12	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.847338198965715	2		263	299	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910852	32910852	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	128	313	0	ENST00000380152.3:c.2360G>C	p.Arg787Thr	p.R787T	ENST00000380152		787	aGa/aCa	11/27	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.847338198965715	2		313	281	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663664	29663664	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	151	300	0	ENST00000356175.3:c.6096G>C	p.Arg2032Ser	p.R2032S	ENST00000356175	NM_000267.3	2032	agG/agC	41/57	0.241888426043626	3	FACETS	1	0.99	1	0.733	0.68	0.787	INDETERMINATE	1	TRUE	1	0.847338198965715	3		300	346	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803569	+	missense_variant	Missense_Mutation	DNP	CC	CC	GT	novel	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	140	351	0	ENST00000260795.2:c.746_747delinsGT	p.Ser249Cys	p.S249C	ENST00000260795		249	tCC/tGT	6/17	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.847338198965715	2		351	318	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061339	38061339	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	167	320	0	ENST00000250448.2:c.650C>G	p.Ser217Cys	p.S217C	ENST00000250448	NM_004496.3	217	tCc/tGc	2/2	0.847338198965715	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.847338198965715	1		320	224	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845616	151845616	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	204	374	0	ENST00000262189.6:c.13396C>T	p.His4466Tyr	p.H4466Y	ENST00000262189	NM_170606.2	4466	Cac/Tac	52/59	0.241888426043626	3	FACETS	1	0.991	1	0.702	0.658	0.747	INDETERMINATE	1	TRUE	1	0.847338198965715	3		374	488	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478952	56478952	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	177	288	0	ENST00000267101.3:c.408G>C	p.Leu136Phe	p.L136F	ENST00000267101	NM_001982.3	136	ttG/ttC	3/28	0.741896119551745	3	FACETS	1	0.983	1	0.592	0.55	0.636	CLONAL	1	TRUE	1	0.847338198965715	3		288	502	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31946758	31946758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	156	244	0	ENST00000375333.2:c.646G>A	p.Glu216Lys	p.E216K	ENST00000375333	NM_032454.1	216	Gag/Aag	4/8	1	2	FACETS	0.979	0.909	1	0.979	0.909	1	CLONAL	1	TRUE	1	0.847338198965715	2		244	376	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31421399	31421399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	113	295	0	ENST00000344624.3:c.3505C>T	p.His1169Tyr	p.H1169Y	ENST00000344624		1169	Cat/Tat	27/33	1	2	FACETS	0.992	0.908	1	0.992	0.908	1	CLONAL	1	TRUE	1	0.847338198965715	2		295	269	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1691342	1691342	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs370139181	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	177	285	0	ENST00000378625.1:c.264-1G>C		p.X88_splice	ENST00000378625	NM_001198994.1	88			0.847338198965715	3	FACETS	1	0.989	1	0.455	0.423	0.486	CLONAL	1	TRUE	0	0.847338198965715	3		285	436	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27173297	27173297	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	146	282	0	ENST00000380036.4:c.838del	p.Cys280ValfsTer69	p.C280Vfs*69	ENST00000380036	NM_000459.3	280	Tgt/gt	6/23	0.847338198965715	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.847338198965715	1		282	197	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929244	44929277	+	frameshift_variant	Frame_Shift_Del	DEL	GCCTTGTTGATGGGAAAAGCCAATAACAATGTGG	GCCTTGTTGATGGGAAAAGCCAATAACAATGTGG	-	novel	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	24	172	0	ENST00000377967.4:c.2345_2378del	p.Ala782ValfsTer74	p.A782Vfs*74	ENST00000377967	NM_021140.2	782	GCCTTGTTGATGGGAAAAGCCAATAACAATGTGGgt/gt	17/29	1	1	FACETS	0.219	0.173	0.271	0.219	0.173	0.271	SUBCLONAL	1	TRUE	0	0.847338198965715	1		172	149	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139867	55139867	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	148	331	0	ENST00000257290.5:c.1528G>C	p.Glu510Gln	p.E510Q	ENST00000257290	NM_006206.4	510	Gag/Cag	10/23	1	2	FACETS	0.949	0.878	1	0.949	0.878	1	CLONAL	1	TRUE	1	0.847338198965715	2		331	368	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480402	56480402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200978269	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	231	306	0	ENST00000267101.3:c.509G>A	p.Arg170Gln	p.R170Q	ENST00000267101	NM_001982.3	170	cGa/cAa	4/28	0.741896119551745	3	FACETS	1	0.991	1	0.66	0.62	0.701	CLONAL	1	TRUE	1	0.847338198965715	3		306	588	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624360	21624360	+	splice_donor_variant	Splice_Site	SNP	A	A	T	rs879752320	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	109	286	0	ENST00000421138.2:c.1667+2T>A		p.X556_splice	ENST00000421138		556			NA	2	FACETS	0.794	0.722	0.869			1	INDETERMINATE	1	TRUE	NA	0.847338198965715	2		286	324	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286817	33286817	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs915933778	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	254	381	0	ENST00000374542.5:c.2120C>T	p.Ser707Phe	p.S707F	ENST00000374542	NM_001141970.1	707	tCc/tTc	7/8	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.847338198965715	2		381	584	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680575	30680575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	175	315	0	ENST00000376406.3:c.1144G>A	p.Glu382Lys	p.E382K	ENST00000376406	NM_014641.2	382	Gaa/Aaa	5/15	1	2	FACETS	0.998	0.93	1	0.998	0.93	1	CLONAL	1	TRUE	1	0.847338198965715	2		315	414	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	142	350	0				ENST00000310581	NM_198253.2	-/1132			0.227974543854235	2	FACETS	1	0.976	1	0.559	0.519	0.599	INDETERMINATE	1	TRUE	0	0.882048642649076	2		350	288	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871249	12871249	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	91	337	0	ENST00000228872.4:c.475+1G>A		p.X159_splice	ENST00000228872	NM_004064.3	159			0.250916311916462	3	FACETS	0.664	0.592	0.739	0.332	0.296	0.37	INDETERMINATE	1	TRUE	1	0.882048642649076	3		337	448	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	102	421	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.348456063689593	2	FACETS	0.545	0.491	0.603	0.273	0.245	0.302	INDETERMINATE	1	TRUE	0	0.882048642649076	2		421	424	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591085	67591085	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519839	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	191	372	0	ENST00000274335.5:c.1678G>T	p.Asp560Tyr	p.D560Y	ENST00000274335		560	Gac/Tac	12/15	0.227974543854235	2	FACETS	1	0.987	1	0.597	0.561	0.632	INDETERMINATE	1	TRUE	0	0.882048642649076	2		372	363	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210961	133210961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	164	418	0	ENST00000320574.5:c.5815G>A	p.Asp1939Asn	p.D1939N	ENST00000320574	NM_006231.2	1939	Gac/Aac	43/49	0.250916311916462	3	FACETS	1	0.937	1	0.507	0.469	0.547	INDETERMINATE	1	TRUE	1	0.882048642649076	3		418	528	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157758	106157758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	17	476	0	ENST00000380013.4:c.2659G>A	p.Glu887Lys	p.E887K	ENST00000380013	NM_001127208.2	887	Gag/Aag	3/11	0.610668228150898	1	FACETS	0.073	0.054	0.096	0.073	0.054	0.096	SUBCLONAL	1	TRUE	0	0.882048642649076	1		476	295	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	116	521	0	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	0.370853790666156	3	FACETS	0.542	0.489	0.598	0.271	0.244	0.299	INDETERMINATE	1	TRUE	1	0.882048642649076	3		521	699	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390537	139390537	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1289429344	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	133	518	0	ENST00000277541.6:c.7654G>A	p.Glu2552Lys	p.E2552K	ENST00000277541	NM_017617.3	2552	Gag/Aag	34/34	1	2	FACETS	0.63	0.575	0.686	0.63	0.575	0.686	SUBCLONAL	1	TRUE	1	0.882048642649076	2		518	479	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211886	123211886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	50	530	1	ENST00000218089.9:c.2753C>T	p.Thr918Ile	p.T918I	ENST00000218089	NM_001042749.1	918	aCc/aTc	27/35	NA	2	FACETS	0.386	0.329	0.447			1	INDETERMINATE	1	TRUE	NA	0.882048642649076	2		531	294	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156719	20156719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	14	315	0	ENST00000379607.5:c.38G>A	p.Arg13His	p.R13H	ENST00000379607	NM_001412.3	13	cGc/cAc	2/7	1	2	FACETS	0.139	0.1	0.186	0.139	0.1	0.186	SUBCLONAL	1	TRUE	1	0.882048642649076	2		315	228	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220485	1220485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	60	540	0	ENST00000326873.7:c.578C>T	p.Ser193Phe	p.S193F	ENST00000326873	NM_000455.4	193	tCc/tTc	4/10	0.221737949380503	4	FACETS	0.396	0.341	0.457	0.198	0.17	0.229	INDETERMINATE	1	TRUE	2	0.882048642649076	4		540	646	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421582	32421582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	101	431	0	ENST00000332351.3:c.1010C>T	p.Thr337Ile	p.T337I	ENST00000332351	NM_024426.4	337	aCa/aTa	6/10	0.36232533536672	3	FACETS	0.5	0.447	0.556	0.25	0.223	0.278	INDETERMINATE	1	TRUE	1	0.882048642649076	3		431	660	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792471	33792471	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	44	398	0	ENST00000498907.2:c.850G>A	p.Glu284Lys	p.E284K	ENST00000498907	NM_004364.3	284	Gag/Aag	1/1	0.882048642649076	1	FACETS	0.219	0.184	0.256	0.219	0.184	0.256	SUBCLONAL	1	TRUE	0	0.882048642649076	1		398	255	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563317	21563317	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	140	586	0	ENST00000382592.4:c.602C>T	p.Pro201Leu	p.P201L	ENST00000382592	NM_014572.2	201	cCc/cTc	4/8	1	2	FACETS	0.498	0.455	0.544	0.498	0.455	0.544	SUBCLONAL	1	TRUE	1	0.882048642649076	2		586	637	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523054	25523054	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199643287	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	253	470	1	ENST00000264709.3:c.131C>T	p.Thr44Met	p.T44M	ENST00000264709	NM_175629.2	44	aCg/aTg	3/23	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.882048642649076	2		471	504	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162252	47162252	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	158	460	0	ENST00000409792.3:c.3874C>T	p.Gln1292Ter	p.Q1292*	ENST00000409792	NM_014159.6	1292	Cag/Tag	3/21	1	2	FACETS	0.648	0.597	0.7	0.648	0.597	0.7	SUBCLONAL	1	TRUE	1	0.882048642649076	2		460	553	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911229	32911229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	39	382	0	ENST00000380152.3:c.2737G>A	p.Asp913Asn	p.D913N	ENST00000380152		913	Gac/Aac	11/27	1	2	FACETS	0.35	0.291	0.413	0.35	0.291	0.413	SUBCLONAL	1	TRUE	1	0.882048642649076	2		382	253	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86658471	86658471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	25	325	0	ENST00000274376.6:c.1436G>A	p.Gly479Asp	p.G479D	ENST00000274376	NM_002890.2	479	gGt/gAt	10/25	0.227974543854235	2	FACETS	0.286	0.227	0.354	0.143	0.113	0.177	INDETERMINATE	1	TRUE	0	0.882048642649076	2		325	198	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227963	123227963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752627195	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	19	301	0	ENST00000218089.9:c.3674G>A	p.Gly1225Glu	p.G1225E	ENST00000218089	NM_001042749.1	1225	gGa/gAa	33/35	NA	2	FACETS	0.184	0.14	0.236			1	INDETERMINATE	1	TRUE	NA	0.882048642649076	2		301	234	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142907	30142907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	50	493	1	ENST00000389048.3:c.619G>A	p.Ala207Thr	p.A207T	ENST00000389048	NM_004304.4	207	Gca/Aca	1/29	1	2	FACETS	0.237	0.201	0.277	0.237	0.201	0.277	SUBCLONAL	1	TRUE	1	0.882048642649076	2		494	478	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851287	63851287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	114	534	0	ENST00000279873.7:c.2065C>T	p.Pro689Ser	p.P689S	ENST00000279873	NM_032199.2	689	Cca/Tca	10/10	0.250916311916462	3	FACETS	0.568	0.512	0.627	0.284	0.256	0.314	INDETERMINATE	1	TRUE	1	0.882048642649076	3		534	656	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38975702	38975702	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	105	406	1	ENST00000357387.3:c.826G>A	p.Asp276Asn	p.D276N	ENST00000357387	NM_152756.3	276	Gac/Aac	10/38	0.227974543854235	2	FACETS	0.513	0.462	0.567	0.257	0.231	0.284	INDETERMINATE	1	TRUE	0	0.882048642649076	2		407	464	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794522	42794523	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	255	503	0	ENST00000575354.2:c.1604_1605del	p.Ser535CysfsTer154	p.S535Cfs*154	ENST00000575354	NM_015125.3	534	tcCTct/tcct	10/20	0.882048642649076	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.882048642649076	1		503	306	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132532	11132532	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	340	520	0	ENST00000358026.2:c.2748C>G	p.Asn916Lys	p.N916K	ENST00000358026	NM_001128849.1	916	aaC/aaG	19/36	0.221737949380503	4	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	2	TRUE	2	0.882048642649076	4		520	696	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945461	17945461	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	71	459	0	ENST00000458235.1:c.2269C>T	p.Gln757Ter	p.Q757*	ENST00000458235	NM_000215.3	757	Caa/Taa	17/24	0.221737949380503	4	FACETS	0.499	0.436	0.568	0.25	0.218	0.284	INDETERMINATE	1	TRUE	2	0.882048642649076	4		459	607	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118613	17118613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	79	368	0	ENST00000285071.4:c.1318G>A	p.Glu440Lys	p.E440K	ENST00000285071	NM_144997.5	440	Gag/Aag	12/14	0.370853790666156	3	FACETS	0.486	0.428	0.548	0.243	0.214	0.274	INDETERMINATE	1	TRUE	1	0.882048642649076	3		368	531	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080301	5080301	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	26	386	0	ENST00000381652.3:c.2204A>G	p.Asp735Gly	p.D735G	ENST00000381652	NM_004972.3	735	gAc/gGc	17/25	NA	2	FACETS	0.195	0.154	0.242			1	INDETERMINATE	1	TRUE	NA	0.882048642649076	2		386	302	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528339	157528339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	96	484	0	ENST00000346085.5:c.6064G>A	p.Asp2022Asn	p.D2022N	ENST00000346085	NM_020732.3	2022	Gat/Aat	20/20	1	2	FACETS	0.416	0.372	0.463	0.416	0.372	0.463	SUBCLONAL	1	TRUE	1	0.882048642649076	2		484	523	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874000	123874000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112525458	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	62	547	0	ENST00000330479.4:c.31C>T	p.Arg11Cys	p.R11C	ENST00000330479	NM_020382.3	11	Cgc/Tgc	2/9	0.250916311916462	3	FACETS	0.346	0.299	0.398	0.173	0.149	0.199	INDETERMINATE	1	TRUE	1	0.882048642649076	3		547	585	SUCCESS
REST	5978	MSKCC	GRCh37	4	57776968	57776968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	56	487	0	ENST00000309042.7:c.164C>T	p.Thr55Ile	p.T55I	ENST00000309042	NM_005612.4	55	aCt/aTt	2/4	0.610668228150898	1	FACETS	0.178	0.153	0.205	0.178	0.153	0.205	SUBCLONAL	1	TRUE	0	0.882048642649076	1		487	399	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515117	149515117	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	102	462	0	ENST00000261799.4:c.364+1G>A		p.X122_splice	ENST00000261799	NM_002609.3	122			0.227974543854235	2	FACETS	0.433	0.388	0.48	0.217	0.194	0.24	INDETERMINATE	1	TRUE	0	0.882048642649076	2		462	534	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409787	139409787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	114	426	0	ENST00000277541.6:c.1969G>A	p.Asp657Asn	p.D657N	ENST00000277541	NM_017617.3	657	Gac/Aac	12/34	1	2	FACETS	0.542	0.49	0.596	0.542	0.49	0.596	SUBCLONAL	1	TRUE	1	0.882048642649076	2		426	477	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959974	38959974	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	60	419	0	ENST00000357387.3:c.1958C>T	p.Thr653Ile	p.T653I	ENST00000357387	NM_152756.3	653	aCc/aTc	21/38	0.227974543854235	2	FACETS	0.411	0.356	0.47	0.206	0.178	0.235	INDETERMINATE	1	TRUE	0	0.882048642649076	2		419	331	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21336800	21336800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1445710752	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	40	507	0	ENST00000215739.8:c.140C>T	p.Pro47Leu	p.P47L	ENST00000215739	NM_006767.3	47	cCc/cTc	1/21	0.250916311916462	3	FACETS	0.215	0.178	0.257	0.108	0.089	0.129	INDETERMINATE	1	TRUE	1	0.882048642649076	3		507	607	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293628	1293628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	42	496	0	ENST00000310581.5:c.1373C>T	p.Pro458Leu	p.P458L	ENST00000310581	NM_198253.2	458	cCc/cTc	2/16	0.227974543854235	2	FACETS	0.213	0.178	0.252	0.107	0.089	0.126	INDETERMINATE	1	TRUE	0	0.882048642649076	2		496	447	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12632304	12632304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	100	407	0	ENST00000251849.4:c.1363G>A	p.Gly455Arg	p.G455R	ENST00000251849	NM_002880.3	455	Gga/Aga	12/17	1	2	FACETS	0.497	0.446	0.551	0.497	0.446	0.551	SUBCLONAL	1	TRUE	1	0.882048642649076	2		407	456	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51520106	51520106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs990878332	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	45	337	0	ENST00000260433.2:c.321G>A	p.Met107Ile	p.M107I	ENST00000260433		107	atG/atA	4/10	1	2	FACETS	0.233	0.196	0.275	0.233	0.196	0.275	SUBCLONAL	1	TRUE	1	0.882048642649076	2		337	437	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007089	152007089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	36	381	0	ENST00000262189.6:c.811G>A	p.Val271Met	p.V271M	ENST00000262189	NM_170606.2	271	Gtg/Atg	6/59	0.189891018499074	4	FACETS	0.271	0.222	0.326	0.135	0.111	0.163	INDETERMINATE	1	TRUE	2	0.882048642649076	4		381	567	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977204	85977204	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	35	274	0	ENST00000263360.6:c.806G>A	p.Arg269Lys	p.R269K	ENST00000263360	NM_003797.3	269	aGa/aAa	8/12	0.36232533536672	3	FACETS	0.719	0.598	0.851	0.36	0.299	0.426	INDETERMINATE	1	TRUE	1	0.882048642649076	3		274	159	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36826873	36826873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	57	464	0	ENST00000373129.3:c.61G>A	p.Gly21Arg	p.G21R	ENST00000373129	NM_032017.1	21	Gga/Aga	3/12	0.882048642649076	1	FACETS	0.216	0.186	0.248	0.216	0.186	0.248	SUBCLONAL	1	TRUE	0	0.882048642649076	1		464	335	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47079263	47079264	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	32	397	0	ENST00000409792.3:c.7242_7243del	p.Gln2414HisfsTer14	p.Q2414Hfs*14	ENST00000409792	NM_014159.6	2414	caGAct/cact	18/21	1	2	FACETS	0.159	0.129	0.194	0.159	0.129	0.194	SUBCLONAL	1	TRUE	1	0.882048642649076	2		397	455	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245256	53245259	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CTTT	CTTT	-	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	106	519	0	ENST00000375401.3:c.778_781del	p.Lys260IlefsTer11	p.K260Ifs*11	ENST00000375401	NM_004187.3	260	AAAGat/at	6/26	1	2	FACETS	0.407	0.365	0.45	0.407	0.365	0.45	SUBCLONAL	1	TRUE	1	0.882048642649076	2		519	591	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43766879	43766879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	51	430	0	ENST00000382044.4:c.1172G>A	p.Gly391Glu	p.G391E	ENST00000382044	NM_001141980.1	391	gGg/gAg	10/28	1	2	FACETS	0.255	0.216	0.297	0.255	0.216	0.297	SUBCLONAL	1	TRUE	1	0.882048642649076	2		430	454	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438524	52438524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1270349297	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	80	504	0	ENST00000460680.1:c.1195G>A	p.Asp399Asn	p.D399N	ENST00000460680	NM_004656.3	399	Gat/Aat	12/17	1	2	FACETS	0.344	0.303	0.387	0.344	0.303	0.387	SUBCLONAL	1	TRUE	1	0.882048642649076	2		504	528	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277218	41277218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	40	405	0	ENST00000349496.5:c.1687G>A	p.Gly563Arg	p.G563R	ENST00000349496	NM_001904.3	563	Ggg/Agg	11/15	1	2	FACETS	0.185	0.153	0.22	0.185	0.153	0.22	SUBCLONAL	1	TRUE	1	0.882048642649076	2		405	490	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437282	52437282	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1389012731	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	40	529	0	ENST00000460680.1:c.1762C>T	p.Pro588Ser	p.P588S	ENST00000460680	NM_004656.3	588	Cca/Tca	14/17	1	2	FACETS	0.175	0.145	0.209	0.175	0.145	0.209	SUBCLONAL	1	TRUE	1	0.882048642649076	2		529	518	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342644	70342644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	99	413	0	ENST00000374080.3:c.1405G>A	p.Glu469Lys	p.E469K	ENST00000374080		469	Gaa/Aaa	10/45	1	2	FACETS	0.437	0.391	0.485	0.437	0.391	0.485	SUBCLONAL	1	TRUE	1	0.882048642649076	2		413	514	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73110173	73110173	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	33	193	0	ENST00000356692.5:c.382-1G>A		p.X128_splice	ENST00000356692		128			1	2	FACETS	0.58	0.481	0.687	0.58	0.481	0.687	SUBCLONAL	1	TRUE	1	0.882048642649076	2		193	129	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169991129	169991129	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	36	269	0	ENST00000295797.4:c.646+1G>A		p.X216_splice	ENST00000295797	NM_002740.5	216			1	2	FACETS	0.265	0.218	0.317	0.265	0.218	0.317	SUBCLONAL	1	TRUE	1	0.882048642649076	2		269	308	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74868281	74868281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	65	312	0	ENST00000284811.8:c.13G>A	p.Glu5Lys	p.E5K	ENST00000284811		5	Gag/Aag	3/4	0.189891018499074	4	FACETS	0.665	0.579	0.758	0.333	0.289	0.379	INDETERMINATE	1	TRUE	2	0.882048642649076	4		312	417	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	493268	493268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	30	378	0	ENST00000399788.2:c.295G>A	p.Glu99Lys	p.E99K	ENST00000399788	NM_001042603.1	99	Gaa/Aaa	3/28	0.250916311916462	3	FACETS	0.244	0.196	0.298	0.122	0.098	0.149	INDETERMINATE	1	TRUE	1	0.882048642649076	3		378	402	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573480	48573480	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	108	508	0	ENST00000342988.3:c.64A>G	p.Ser22Gly	p.S22G	ENST00000342988	NM_005359.5	22	Agt/Ggt	2/12	0.250916311916462	3	FACETS	0.784	0.708	0.864	0.392	0.354	0.432	INDETERMINATE	1	TRUE	1	0.882048642649076	3		508	450	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391356	84391356	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	60	312	0	ENST00000321945.7:c.476G>A	p.Gly159Glu	p.G159E	ENST00000321945	NM_139076.2	159	gGa/gAa	5/9	0.610668228150898	1	FACETS	0.411	0.36	0.464	0.411	0.36	0.464	SUBCLONAL	1	TRUE	0	0.882048642649076	1		312	185	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379655	17379655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	78	427	0	ENST00000359435.4:c.40G>A	p.Glu14Lys	p.E14K	ENST00000359435	NM_001033549.1	14	Gag/Aag	2/9	0.221737949380503	4	FACETS	0.563	0.495	0.636	0.282	0.247	0.318	INDETERMINATE	1	TRUE	2	0.882048642649076	4		427	591	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256961	16256961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	59	467	0	ENST00000375759.3:c.4226G>A	p.Arg1409Lys	p.R1409K	ENST00000375759	NM_015001.2	1409	aGg/aAg	11/15	0.882048642649076	1	FACETS	0.289	0.251	0.329	0.289	0.251	0.329	SUBCLONAL	1	TRUE	0	0.882048642649076	1		467	259	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639980	3639980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	38	507	0	ENST00000294008.3:c.3659G>A	p.Gly1220Glu	p.G1220E	ENST00000294008	NM_032444.2	1220	gGg/gAg	12/15	1	2	FACETS	0.186	0.153	0.222	0.186	0.153	0.222	SUBCLONAL	1	TRUE	1	0.882048642649076	2		507	464	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342587	118342587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555035610	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	125	448	0	ENST00000534358.1:c.713G>A	p.Gly238Glu	p.G238E	ENST00000534358	NM_005933.3	238	gGa/gAa	3/36	0.36232533536672	3	FACETS	0.937	0.854	1	0.468	0.427	0.511	INDETERMINATE	1	TRUE	1	0.882048642649076	3		448	436	SUCCESS
APC	324	MSKCC	GRCh37	5	112176651	112176651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	93	474	0	ENST00000257430.4:c.5360C>T	p.Thr1787Ile	p.T1787I	ENST00000257430	NM_000038.5	1787	aCa/aTa	16/16	0.227974543854235	2	FACETS	0.558	0.5	0.619	0.279	0.25	0.31	INDETERMINATE	1	TRUE	0	0.882048642649076	2		474	378	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554244	29554244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1597713272	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	32	347	0	ENST00000356175.3:c.2260G>A	p.Ala754Thr	p.A754T	ENST00000356175	NM_000267.3	754	Gca/Aca	19/57	0.370853790666156	3	FACETS	0.226	0.183	0.274	0.113	0.091	0.137	INDETERMINATE	1	TRUE	1	0.882048642649076	3		347	463	SUCCESS
REST	5978	MSKCC	GRCh37	4	57797728	57797728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	27	474	0	ENST00000309042.7:c.2704G>A	p.Ala902Thr	p.A902T	ENST00000309042	NM_005612.4	902	Gca/Aca	4/4	0.610668228150898	1	FACETS	0.109	0.086	0.135	0.109	0.086	0.135	SUBCLONAL	1	TRUE	0	0.882048642649076	1		474	314	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55232973	55232973	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	76	394	0	ENST00000275493.2:c.1723G>A	p.Gly575Arg	p.G575R	ENST00000275493	NM_005228.3	575	Gga/Aga	15/28	0.189891018499074	4	FACETS	0.647	0.569	0.731	0.324	0.284	0.366	INDETERMINATE	1	TRUE	2	0.882048642649076	4		394	501	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134190	41134190	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	30	455	0	ENST00000379561.5:c.1438G>A	p.Val480Ile	p.V480I	ENST00000379561	NM_002015.3	480	Gtt/Att	2/3	1	2	FACETS	0.113	0.091	0.139	0.113	0.091	0.139	SUBCLONAL	1	TRUE	1	0.882048642649076	2		455	600	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763377	59763377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	22	462	0	ENST00000259008.2:c.2725C>T	p.Leu909Phe	p.L909F	ENST00000259008	NM_032043.2	909	Ctt/Ttt	19/20	0.370853790666156	3	FACETS	0.229	0.177	0.289	0.114	0.088	0.145	INDETERMINATE	1	TRUE	1	0.882048642649076	3		462	314	SUCCESS
AR	367	MSKCC	GRCh37	X	66765817	66765817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	105	584	0	ENST00000374690.3:c.829C>T	p.Pro277Ser	p.P277S	ENST00000374690	NM_000044.3	277	Ccc/Tcc	1/8	1	2	FACETS	0.429	0.385	0.475	0.429	0.385	0.475	SUBCLONAL	1	TRUE	1	0.882048642649076	2		584	555	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595980	52595980	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	111	396	2	ENST00000394830.3:c.3935C>T	p.Thr1312Ile	p.T1312I	ENST00000394830	NM_018313.4	1312	aCc/aTc	26/30	1	2	FACETS	0.591	0.535	0.649	0.591	0.535	0.649	SUBCLONAL	1	TRUE	1	0.882048642649076	2		398	426	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513787	41513787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	30	409	0	ENST00000263253.7:c.691G>A	p.Gly231Arg	p.G231R	ENST00000263253	NM_001429.3	231	Gga/Aga	2/31	0.250916311916462	3	FACETS	0.193	0.155	0.236	0.096	0.077	0.118	INDETERMINATE	1	TRUE	1	0.882048642649076	3		409	509	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628745	187628745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759685155	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	21	493	0	ENST00000441802.2:c.2237C>T	p.Thr746Ile	p.T746I	ENST00000441802	NM_005245.3	746	aCt/aTt	2/27	0.610668228150898	1	FACETS	0.077	0.059	0.098	0.077	0.059	0.098	SUBCLONAL	1	TRUE	0	0.882048642649076	1		493	346	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67632210	67632210	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2103753620	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	17	366	0	ENST00000272342.5:c.2396C>T	p.Pro799Leu	p.P799L	ENST00000272342	NM_019002.3	799	cCa/cTa	5/6	1	2	FACETS	0.165	0.123	0.214	0.165	0.123	0.214	SUBCLONAL	1	TRUE	1	0.882048642649076	2		366	234	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57470727	57470727	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	99	378	0	ENST00000371085.3:c.200G>A	p.Gly67Glu	p.G67E	ENST00000371085	NM_000516.4	67	gGg/gAg	2/13	0.370853790666156	3	FACETS	0.597	0.534	0.663	0.298	0.267	0.332	INDETERMINATE	1	TRUE	1	0.882048642649076	3		378	542	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059247	27059247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	86	358	0	ENST00000324856.7:c.1884G>A	p.Met628Ile	p.M628I	ENST00000324856	NM_006015.4	628	atG/atA	4/20	0.882048642649076	1	FACETS	0.371	0.332	0.412	0.371	0.332	0.412	SUBCLONAL	1	TRUE	0	0.882048642649076	1		358	294	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660609	190660609	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016383-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	78	401	0	ENST00000441310.2:c.247G>A	p.Asp83Asn	p.D83N	ENST00000441310	NM_000534.4	83	Gat/Aat	3/13	0.348456063689593	2	FACETS	0.44	0.388	0.495	0.22	0.194	0.248	INDETERMINATE	1	TRUE	0	0.882048642649076	2		401	402	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	103	350	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.99	0.906	1	0.99	0.906	1	CLONAL	1	TRUE	1	0.920328838082467	2		350	226	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0017301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	259	306	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.920328838082467	2		306	543	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791826	42791826	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	292	412	0	ENST00000575354.2:c.712T>C	p.Trp238Arg	p.W238R	ENST00000575354	NM_015125.3	238	Tgg/Cgg	5/20	0.920328838082467	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.920328838082467	1		412	340	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0017301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	293	421	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.920328838082467	2		421	624	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391901	139391901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	226	416	0	ENST00000277541.6:c.6290C>T	p.Pro2097Leu	p.P2097L	ENST00000277541	NM_017617.3	2097	cCg/cTg	34/34	0.920328838082467	1	FACETS	0.997	0.965	1	0.997	0.965	1	CLONAL	1	TRUE	0	0.920328838082467	1		416	266	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78435588	78435607	+	splice_donor_variant,intron_variant	Splice_Site	DEL	AATACTTAGAGTATAACTTA	AATACTTAGAGTATAACTTA	GT	novel	NA	P-0017301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	212	187	0	ENST00000370768.2:c.211+2_211+21delinsAC		p.X71_splice	ENST00000370768	NM_003902.3	71			0.920328838082467	1	FACETS	0.96	0.925	0.992	0.96	0.925	0.992	CLONAL	1	TRUE	0	0.920328838082467	1		187	259	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913399	NA	P-0018178-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	36	460	0	ENST00000349496.5:c.100G>C	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Cga	3/15	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.17	2		460	369	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796934	78796936	+	inframe_deletion	In_Frame_Del	DEL	TTT	TTT	-	novel	NA	P-0018178-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	20	400	0	ENST00000306801.3:c.1050_1052del	p.Phe350del	p.F350del	ENST00000306801	NM_020761.2	349	aaTTTt/aat	9/34	1	2	FACETS	0.759	0.58	0.968	0.759	0.58	0.968	CLONAL	1	TRUE	1	0.17	2		400	310	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933743	49933743	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772397266	NA	P-0019023-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	28	583	0	ENST00000296474.3:c.2534G>A	p.Arg845Gln	p.R845Q	ENST00000296474	NM_002447.2	845	cGa/cAa	10/20	1	2	FACETS	0.565	0.451	0.696	0.565	0.451	0.696	SUBCLONAL	1	TRUE	1	0.21	2		583	472	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46276064	46276064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370656650	NA	P-0019023-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	10	0	0	ENST00000371998.3:c.3500C>T	p.Pro1167Leu	p.P1167L	ENST00000371998		1167	cCc/cTc	18/23	1	2	FACETS	0.205	0.138	0.29	0.205	0.138	0.29	SUBCLONAL	1	TRUE	1	0.21	2		0	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0019781-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	336	539	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.769369436056748	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.790392697155317	1		539	495	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420209	88420209	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019781-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	186	251	0	ENST00000360948.2:c.2477C>A	p.Ala826Asp	p.A826D	ENST00000360948	NM_001012338.2	826	gCt/gAt	19/19	1	2	FACETS	0.909	0.846	0.972	0.909	0.846	0.972	CLONAL	1	TRUE	1	0.790392697155317	2		251	518	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262240	115262240	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019781-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	27	211	0	ENST00000438362.2:c.2314C>G	p.Arg772Gly	p.R772G	ENST00000438362	NM_001242891.1	772	Cgc/Ggc	18/20	1	2	FACETS	0.142	0.112	0.176	0.142	0.112	0.176	SUBCLONAL	1	TRUE	1	0.790392697155317	2		211	481	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856318	111856318	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019781-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	189	283	0	ENST00000341259.2:c.369G>C	p.Glu123Asp	p.E123D	ENST00000341259	NM_005475.2	123	gaG/gaC	2/8	0.790392697155317	3	FACETS	1	0.938	1	0.505	0.469	0.543	CLONAL	1	TRUE	1	0.790392697155317	3		283	660	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0021837-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	145	479	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.654415215489431	2		479	416	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0021837-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	184	133	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.654415215489431	2		133	453	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0021837-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	89	116	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	1	2	FACETS	0.938	0.842	1	0.938	0.842	1	CLONAL	1	TRUE	1	0.654415215489431	2		116	290	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342150	70342150	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021837-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	135	189	0	ENST00000374080.3:c.1202C>G	p.Pro401Arg	p.P401R	ENST00000374080		401	cCg/cGg	8/45	0.209070531110101	1	FACETS	0.682	0.626	0.74	0.682	0.626	0.74	INDETERMINATE	1	TRUE	0	0.654415215489431	1		189	407	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0022083-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	114	347	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.351926111021625	2		347	605	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0022174-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	127	252	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.372689813517289	5	FACETS	0.984	0.917	1	0.984	0.917	1	CLONAL	5	TRUE	0	0.372689813517289	5		253	216	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0022174-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	129	284	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.259098862301275	3	FACETS	1	0.951	1	0.704	0.644	0.765	CLONAL	2	TRUE	0	0.372689813517289	3		284	389	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0022174-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	21	148	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.378600156685592	4	FACETS	0.859	0.688	1	1	0.91	1	CLONAL	3	TRUE	2	0.372689813517289	4		148	60	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074269	30074269	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022174-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	56	291	0	ENST00000338641.4:c.1531G>C	p.Asp511His	p.D511H	ENST00000338641	NM_000268.3	511	Gat/Cat	14/16	0.291348289361377	4	FACETS	1	0.907	1	0.357	0.307	0.412	CLONAL	1	TRUE	1	0.372689813517289	4		291	385	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001374	150001376	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs753305883	NA	P-0022174-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	86	242	0	ENST00000253339.5:c.2228_2230del	p.Leu743del	p.L743del	ENST00000253339		743	cTTCga/cga	4/7	0.316366603781734	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.372689813517289	2		242	187	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151892994	151892994	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0022174-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	76	176	0	ENST00000262189.6:c.4376C>G	p.Ser1459Ter	p.S1459*	ENST00000262189	NM_170606.2	1459	tCa/tGa	28/59	0.378600156685592	4	FACETS	0.915	0.818	1	1	0.976	1	CLONAL	3	TRUE	2	0.372689813517289	4		176	204	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936103	178936103	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022174-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	25	163	0	ENST00000263967.3:c.1645G>C	p.Asp549His	p.D549H	ENST00000263967	NM_006218.2	549	Gat/Cat	10/21	0.378600156685592	4	FACETS	1	0.9	1	1	0.9	1	CLONAL	2	TRUE	2	0.372689813517289	4		163	78	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023066	27023067	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0022174-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	178	235	0	ENST00000324856.7:c.172_173del	p.Ser58ArgfsTer52	p.S58Rfs*52	ENST00000324856	NM_006015.4	58	AGc/c	1/20	0.378600156685592	3	FACETS	0.849	0.791	0.908	0.849	0.791	0.908	CLONAL	3	TRUE	0	0.372689813517289	3		235	445	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098795	47098795	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022174-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	135	281	0	ENST00000409792.3:c.6479del	p.Pro2160ArgfsTer88	p.P2160Rfs*88	ENST00000409792	NM_014159.6	2160	cCg/cg	15/21	0.259098862301275	3	FACETS	0.888	0.812	0.966	0.592	0.541	0.644	CLONAL	2	TRUE	0	0.372689813517289	3		281	484	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522422	157522422	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022174-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	161	289	0	ENST00000346085.5:c.4694A>T	p.Asn1565Ile	p.N1565I	ENST00000346085	NM_020732.3	1565	aAc/aTc	18/20	0.316366603781734	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	0	0.372689813517289	2		289	425	SUCCESS
AR	367	MSKCC	GRCh37	X	66766134	66766135	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCCCAC	novel	NA	P-0022174-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	37	309	0	ENST00000374690.3:c.1147_1152dup	p.Pro383_His384dup	p.P383_H384dup	ENST00000374690	NM_000044.3	383	-/CCCCAC	1/8	0.308519764456617	1	FACETS	0.472	0.39	0.564	0.472	0.39	0.564	SUBCLONAL	1	TRUE	0	0.372689813517289	1		309	342	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60795992	60795992	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022174-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	124	280	0	ENST00000333681.4:c.586G>T	p.Asp196Tyr	p.D196Y	ENST00000333681		196	Gat/Tat	3/3	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.372689813517289	NA		280	482	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948584	54948584	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022174-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	81	228	0	ENST00000312783.6:c.734C>G	p.Ser245Cys	p.S245C	ENST00000312783	NM_198436.1	245	tCt/tGt	8/10	0.378600156685592	4	FACETS	0.893	0.794	0.998	0.893	0.794	0.998	CLONAL	2	TRUE	2	0.372689813517289	4		228	334	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263916	104263916	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022174-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	118	212	0	ENST00000369902.3:c.7G>C	p.Glu3Gln	p.E3Q	ENST00000369902	NM_016169.3	3	Gag/Cag	1/12	0.205685600926971	4	FACETS	0.923	0.838	1	0.615	0.558	0.675	INDETERMINATE	2	TRUE	1	0.372689813517289	4		212	471	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900962	114900962	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022174-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	129	249	0	ENST00000543371.1:c.572T>G	p.Val191Gly	p.V191G	ENST00000543371	NM_001198531.1	191	gTg/gGg	6/14	0.205685600926971	4	FACETS	1	0.952	1	0.709	0.647	0.772	INDETERMINATE	2	TRUE	1	0.372689813517289	4		249	447	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568841	212568843	+	missense_variant	Missense_Mutation	TNP	CTT	CTT	ATG	novel	NA	P-0022174-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	14	232	0	ENST00000342788.4:c.1275_1277delinsCAT	p.Arg426Ile	p.R426I	ENST00000342788	NM_005235.2	425	ggAAGa/ggCATa	11/28	0.361133736575673	3	FACETS	0.602	0.438	0.799	0.301	0.219	0.4	SUBCLONAL	1	TRUE	1	0.372689813517289	3		232	148	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0024073-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	139	665	0	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.496384459309858	2		665	536	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475339	40475339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749943696	NA	P-0024073-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	107	486	0	ENST00000264657.5:c.1687G>A	p.Val563Ile	p.V563I	ENST00000264657	NM_139276.2	563	Gtc/Atc	19/24	1	2	FACETS	0.98	0.885	1	0.98	0.885	1	CLONAL	1	TRUE	1	0.496384459309858	2		486	440	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940952	49940952	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1439972260	NA	P-0024073-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	80	525	0	ENST00000296474.3:c.91C>T	p.Arg31Cys	p.R31C	ENST00000296474	NM_002447.2	31	Cgc/Tgc	1/20	1	2	FACETS	0.71	0.627	0.798	0.71	0.627	0.798	SUBCLONAL	1	TRUE	1	0.496384459309858	2		525	454	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5239031	5239031	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024073-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	60	452	0	ENST00000357368.4:c.1748A>T	p.Asp583Val	p.D583V	ENST00000357368	NM_002850.3	583	gAc/gTc	13/38	0.266751330053582	0	FACETS	0.389	0.337	0.444			1	INDETERMINATE	1	TRUE	0	0.496384459309858	0		452	313	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0026764-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	195	385	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.677564362027179	2	FACETS	1	0.984	1	0.587	0.548	0.626	CLONAL	1	TRUE	0	0.677859085692423	2		385	490	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845839	72845839	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026764-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	381	376	0	ENST00000268489.5:c.3628C>T	p.Arg1210Ter	p.R1210*	ENST00000268489	NM_006885.3	1210	Cga/Tga	6/10	0.677564362027179	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.677859085692423	2		376	538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519998	NA	P-0026764-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	460	475	0	ENST00000269305.4:c.581T>C	p.Leu194Pro	p.L194P	ENST00000269305	NM_001126112.2	194	cTt/cCt	6/11	0.677564362027179	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.677859085692423	2		475	615	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627369	14627369	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026764-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	250	419	0	ENST00000254322.2:c.701A>G	p.Asp234Gly	p.D234G	ENST00000254322	NM_006145.1	234	gAt/gGt	2/3	0.677564362027179	3	FACETS	1	0.985	1	0.578	0.542	0.615	CLONAL	1	TRUE	1	0.677859085692423	3		419	854	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952073	178952073	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519937	NA	P-0026764-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	337	360	0	ENST00000263967.3:c.3128T>C	p.Met1043Thr	p.M1043T	ENST00000263967	NM_006218.2	1043	aTg/aCg	21/21	0.677564362027179	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.677859085692423	2		360	478	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394736	45394736	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026764-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	124	298	0	ENST00000262160.6:c.613A>C	p.Asn205His	p.N205H	ENST00000262160	NM_005901.5	205	Aac/Cac	5/11	0.66906430609668	3	FACETS	1	0.912	1	0.334	0.304	0.366	CLONAL	1	TRUE	0	0.677859085692423	3		298	489	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124481105	124481105	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026764-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	106	317	0	ENST00000357628.3:c.1291G>C	p.Gly431Arg	p.G431R	ENST00000357628	NM_015450.2	431	Gga/Cga	14/19	0.677564362027179	4	FACETS	0.958	0.861	1	0.479	0.43	0.53	CLONAL	1	TRUE	2	0.677859085692423	4		317	548	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0026764-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	153	385	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.748726499982475	2	FACETS	0.979	0.905	1	0.489	0.452	0.527	CLONAL	1	TRUE	0	0.746115943670255	2		385	419	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845839	72845839	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026764-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	291	376	0	ENST00000268489.5:c.3628C>T	p.Arg1210Ter	p.R1210*	ENST00000268489	NM_006885.3	1210	Cga/Tga	6/10	0.748726499982475	2	FACETS	0.963	0.927	0.998	0.963	0.927	0.998	CLONAL	2	TRUE	0	0.746115943670255	2		376	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519998	NA	P-0026764-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	438	475	0	ENST00000269305.4:c.581T>C	p.Leu194Pro	p.L194P	ENST00000269305	NM_001126112.2	194	cTt/cCt	6/11	0.748726499982475	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.746115943670255	2		475	540	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627369	14627369	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026764-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	152	419	0	ENST00000254322.2:c.701A>G	p.Asp234Gly	p.D234G	ENST00000254322	NM_006145.1	234	gAt/gGt	2/3	0.748726499982475	3	FACETS	0.875	0.803	0.95	0.438	0.401	0.475	CLONAL	1	TRUE	1	0.746115943670255	3		419	639	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952073	178952073	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519937	NA	P-0026764-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	290	360	0	ENST00000263967.3:c.3128T>C	p.Met1043Thr	p.M1043T	ENST00000263967	NM_006218.2	1043	aTg/aCg	21/21	0.748726499982475	2	FACETS	0.999	0.963	1	0.999	0.963	1	CLONAL	2	TRUE	0	0.746115943670255	2		360	389	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124481105	124481105	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026764-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	117	317	0	ENST00000357628.3:c.1291G>C	p.Gly431Arg	p.G431R	ENST00000357628	NM_015450.2	431	Gga/Cga	14/19	0.748726499982475	3	FACETS	0.997	0.906	1	0.498	0.453	0.546	CLONAL	1	TRUE	1	0.746115943670255	3		317	432	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165557	47165557	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs563907746	NA	P-0026764-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	166	479	0	ENST00000409792.3:c.569C>T	p.Pro190Leu	p.P190L	ENST00000409792	NM_014159.6	190	cCg/cTg	3/21	1	2	FACETS	0.923	0.855	0.993	0.923	0.855	0.993	CLONAL	1	TRUE	1	0.746115943670255	2		479	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882019	NA	P-0027832-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	256	576	2	ENST00000269305.4:c.455del	p.Pro152ArgfsTer18	p.P152Rfs*18	ENST00000269305	NM_001126112.2	152	cCg/cg	5/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.526190504063137	2		578	816	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220717	1220717	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0027832-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	298	464	0	ENST00000326873.7:c.734+1G>A		p.X245_splice	ENST00000326873	NM_000455.4	245			0.528906196308288	2	FACETS	0.968	0.921	1	0.968	0.921	1	CLONAL	2	TRUE	0	0.526190504063137	2		464	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0027832-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	176	397	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.526190504063137	2		397	619	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602878	10602878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027832-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	392	548	0	ENST00000171111.5:c.700C>T	p.Arg234Trp	p.R234W	ENST00000171111	NM_203500.1	234	Cgg/Tgg	3/6	0.528906196308288	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.526190504063137	2		548	734	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233073	69233073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027832-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	168	456	0	ENST00000462284.1:c.938C>T	p.Ser313Leu	p.S313L	ENST00000462284	NM_002392.5	313	tCa/tTa	11/11	1	2	FACETS	0.938	0.865	1	0.938	0.865	1	CLONAL	1	TRUE	1	0.526190504063137	2		456	681	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900314	3900314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567361652	NA	P-0027832-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	187	505	0	ENST00000262367.5:c.782C>T	p.Ala261Val	p.A261V	ENST00000262367	NM_004380.2	261	gCa/gTa	2/31	0.528906196308288	3	FACETS	1	0.973	1	0.554	0.513	0.597	CLONAL	1	TRUE	1	0.526190504063137	3		505	810	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31472312	31472312	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027832-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	196	519	0	ENST00000344624.3:c.2099A>G	p.His700Arg	p.H700R	ENST00000344624		700	cAc/cGc	14/33	0.526190504063137	5	FACETS	1	0.981	1	0.235	0.217	0.254	CLONAL	1	TRUE	0	0.526190504063137	5		519	1133	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685294	86685294	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027832-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	310	357	0	ENST00000274376.6:c.3010G>T	p.Ala1004Ser	p.A1004S	ENST00000274376	NM_002890.2	1004	Gct/Tct	24/25	0.528906196308288	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.526190504063137	2		357	567	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462508	92462508	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027832-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	1034	568	0	ENST00000265734.4:c.130C>A	p.Arg44Ser	p.R44S	ENST00000265734	NM_001259.6	44	Cgc/Agc	2/8	0.526190504063137	9	FACETS	0.937	0.915	0.959	0.937	0.915	0.959	CLONAL	7	TRUE	2	0.526190504063137	9		568	1703	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528742	8528742	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027832-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	335	450	0	ENST00000356435.5:c.390G>T	p.Met130Ile	p.M130I	ENST00000356435		130	atG/atT	4/35	0.528906196308288	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.526190504063137	2		450	627	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657113	215657113	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1559437094	NA	P-0027832-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	164	495	0	ENST00000260947.4:c.272G>A	p.Trp91Ter	p.W91*	ENST00000260947	NM_000465.2	91	tGg/tAg	3/11	0.528906196308288	3	FACETS	1	0.958	1	0.532	0.489	0.576	CLONAL	1	TRUE	1	0.526190504063137	3		495	740	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0028925-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	57	268	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.897	0.779	1	0.897	0.779	1	CLONAL	1	TRUE	1	0.562275061324421	2		268	226	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028925-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	141	463	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.983	0.901	1	0.983	0.901	1	CLONAL	1	TRUE	1	0.562275061324421	2		463	510	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0028925-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	124	596	3	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	1	2	FACETS	0.711	0.645	0.781	0.711	0.645	0.781	SUBCLONAL	1	TRUE	1	0.562275061324421	2		599	620	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115940	8115940	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028925-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	170	511	1	ENST00000346208.3:c.1287del	p.Phe430LeufsTer45	p.F430Lfs*45	ENST00000346208		429	tCc/tc	6/6	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.562275061324421	2		512	563	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352538	118352538	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028925-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	175	537	0	ENST00000534358.1:c.3743del	p.Ala1248GlufsTer108	p.A1248Efs*108	ENST00000534358	NM_005933.3	1248	gCa/ga	7/36	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.562275061324421	2		537	600	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177762	56177763	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028925-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	132	486	0	ENST00000399503.3:c.2739dup	p.Gly914ArgfsTer16	p.G914Rfs*16	ENST00000399503	NM_005921.1	912	gga/ggAa	14/20	1	2	FACETS	0.91	0.831	0.992	0.91	0.831	0.992	CLONAL	1	TRUE	1	0.562275061324421	2		486	516	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841834	151841834	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028925-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	134	411	0	ENST00000262189.6:c.14307G>A	p.Trp4769Ter	p.W4769*	ENST00000262189	NM_170606.2	4769	tgG/tgA	55/59	1	2	FACETS	0.931	0.851	1	0.931	0.851	1	CLONAL	1	TRUE	1	0.562275061324421	2		411	512	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964514	70964514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762086448	NA	P-0028925-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	162	506	0	ENST00000276594.2:c.1514G>A	p.Arg505His	p.R505H	ENST00000276594	NM_024504.3	505	cGc/cAc	8/8	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.562275061324421	2		506	556	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644803	67644806	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	novel	NA	P-0028925-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	301	539	0	ENST00000264010.4:c.68_71del	p.Lys23IlefsTer38	p.K23Ifs*38	ENST00000264010	NM_006565.3	23	aAGACt/at	3/12	0.562275061324421	2	FACETS	0.889	0.846	0.932	0.889	0.846	0.932	CLONAL	2	TRUE	0	0.562275061324421	2		539	602	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777996	27777996	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028925-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	184	599	0	ENST00000369163.2:c.145C>G	p.Leu49Val	p.L49V	ENST00000369163	NM_003536.2	49	Ctc/Gtc	1/1	1	2	FACETS	0.949	0.879	1	0.949	0.879	1	CLONAL	1	TRUE	1	0.562275061324421	2		599	690	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115873	8115874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0030617-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	137	381	0	ENST00000346208.3:c.1220dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tCcg	6/6	1	2	FACETS	0.973	0.89	1	0.973	0.89	1	CLONAL	1	TRUE	1	0.518574940272796	2		381	543	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397163	397163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030617-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	118	368	0	ENST00000380956.4:c.548C>T	p.Pro183Leu	p.P183L	ENST00000380956	NM_001195286.1	183	cCg/cTg	5/9	1	2	FACETS	0.921	0.836	1	0.921	0.836	1	CLONAL	1	TRUE	1	0.518574940272796	2		368	494	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561076	9561076	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030617-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	110	331	0	ENST00000353224.5:c.706C>A	p.Pro236Thr	p.P236T	ENST00000353224	NM_177990.2	236	Cct/Act	4/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.518574940272796	2		331	360	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038473	180038473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030617-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	106	307	0	ENST00000261937.6:c.3544G>A	p.Glu1182Lys	p.E1182K	ENST00000261937	NM_182925.4	1182	Gag/Aag	27/30	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.518574940272796	2		307	405	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37680948	37680948	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030617-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	50	343	0	ENST00000447079.4:c.3117C>G	p.Cys1039Trp	p.C1039W	ENST00000447079	NM_015083.1	1039	tgC/tgG	12/14	1	2	FACETS	0.402	0.341	0.468	0.402	0.341	0.468	SUBCLONAL	1	TRUE	1	0.518574940272796	2		343	480	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138141	2138141	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs45517399	NA	P-0030687-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	81	571	1	ENST00000219476.3:c.5160+1G>T		p.X1720_splice	ENST00000219476	NM_000548.3	1720			1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		572	626	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138120	2138120	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45517396	NA	P-0030687-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	121	563	0	ENST00000219476.3:c.5140C>T	p.Gln1714Ter	p.Q1714*	ENST00000219476	NM_000548.3	1714	Cag/Tag	40/42	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		563	650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578530	7578530	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs267605077	NA	P-0032118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	42	554	0	ENST00000269305.4:c.400T>C	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	Ttt/Ctt	5/11	1	2	FACETS	0.994	0.832	1	0.994	0.832	1	CLONAL	1	TRUE	1	0.22	2		554	384	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676329	37676329	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	54	498	0	ENST00000447079.4:c.3085del	p.Ala1029LeufsTer28	p.A1029Lfs*28	ENST00000447079	NM_015083.1	1028	atG/at	11/14	1	2	FACETS	0.758	0.651	0.873	1	0.967	1	SUBCLONAL	2	TRUE	1	0.22	2		498	324	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845758	151845758	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	38	523	0	ENST00000262189.6:c.13254G>T	p.Arg4418Ser	p.R4418S	ENST00000262189	NM_170606.2	4418	agG/agT	52/59	1	2	FACETS	0.909	0.753	1	0.909	0.753	1	CLONAL	1	TRUE	1	0.22	2		523	380	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785542	50785542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	43	471	0	ENST00000398568.2:c.532G>A	p.Asp178Asn	p.D178N	ENST00000398568	NM_001042412.1	178	Gac/Aac	4/18	0.110990448367343	0	FACETS	0.703	0.588	0.829			1	INDETERMINATE	1	TRUE	0	0.22	0		471	434	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785812	50785812	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	23	345	0	ENST00000398568.2:c.802G>A	p.Asp268Asn	p.D268N	ENST00000398568	NM_001042412.1	268	Gac/Aac	4/18	0.110990448367343	0	FACETS	0.722	0.565	0.902			1	INDETERMINATE	1	TRUE	0	0.22	0		345	226	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171630	36171631	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033964-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	28	179	0	ENST00000300305.3:c.934dup	p.Thr312AsnfsTer288	p.T312Nfs*288	ENST00000300305		312	acc/aAcc	7/8	0.228228202669307	3	FACETS	0.386	0.309	0.473	0.193	0.154	0.237	INDETERMINATE	1	TRUE	1	0.649945993578329	3		179	296	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540131	23540141	+	frameshift_variant	Frame_Shift_Del	DEL	GCCAGCGTCTC	GCCAGCGTCTC	-	novel	NA	P-0033964-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	53	136	0	ENST00000380871.4:c.262_272del	p.Glu88ArgfsTer16	p.E88Rfs*16	ENST00000380871	NM_006167.3	88	GAGACGCTGGCa/a	1/2	NA	2	FACETS	1	0.955	1			1	INDETERMINATE	1	TRUE	NA	0.649945993578329	2		136	134	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034421-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	95	350	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.445868575057953	2		350	408	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0034421-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	123	432	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	0.445868575057953	1	FACETS	0.997	0.909	1	0.997	0.909	1	CLONAL	1	TRUE	0	0.445868575057953	1		432	430	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0034421-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	49	148	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.445868575057953	4	FACETS	1	0.9	1	0.358	0.305	0.416	CLONAL	1	TRUE	1	0.445868575057953	4		148	296	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519824	29519824	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034421-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	145	543	0	ENST00000389048.3:c.1747C>A	p.His583Asn	p.H583N	ENST00000389048	NM_004304.4	583	Cat/Aat	9/29	0.422608440613752	3	FACETS	1	0.977	1	0.596	0.545	0.649	CLONAL	1	TRUE	1	0.445868575057953	3		543	667	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856072	151856072	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034421-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	102	433	0	ENST00000262189.6:c.11546A>G	p.Gln3849Arg	p.Q3849R	ENST00000262189	NM_170606.2	3849	cAg/cGg	44/59	0.420450312680932	3	FACETS	0.831	0.744	0.924			1	CLONAL	1	TRUE	NA	0.445868575057953	3		433	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0037300-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	423	342	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.618882956438437	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.618882956438437	1		343	706	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0037300-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	219	500	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.618882956438437	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.618882956438437	1		500	482	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037300-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	131	380	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	0.600699392946869	2	FACETS	0.897	0.835	0.959	0.897	0.835	0.959	CLONAL	2	TRUE	0	0.618882956438437	2		380	236	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871249	12871249	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0037300-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	243	337	0	ENST00000228872.4:c.475+1G>A		p.X159_splice	ENST00000228872	NM_004064.3	159			0.46837499644983	1	FACETS	0.932	0.878	0.986	0.932	0.878	0.986	CLONAL	1	TRUE	0	0.618882956438437	1		337	582	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455118	50455118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200163039	NA	P-0037300-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	362	509	0	ENST00000331340.3:c.665G>A	p.Arg222His	p.R222H	ENST00000331340	NM_006060.4	222	cGc/cAc	6/8	0.100545026437522	6	FACETS	1	0.986	1	1	0.986	1	INDETERMINATE	3	TRUE	3	0.618882956438437	6		509	804	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508683	106508683	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1490061702	NA	P-0037300-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	319	629	0	ENST00000359195.3:c.677G>A	p.Arg226His	p.R226H	ENST00000359195	NM_002649.2	226	cGc/cAc	2/11	0.217167495864544	1	FACETS	0.785	0.743	0.827	0.785	0.743	0.827	INDETERMINATE	1	TRUE	0	0.618882956438437	1		629	907	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197070	26197070	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	rs1038639688	NA	P-0037300-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	76	645	0	ENST00000356476.2:c.409T>C	p.Ter137GlnextTer?	p.*137Qext*?	ENST00000356476		137	Taa/Caa	1/1	0.618882956438437	3	FACETS	0.25	0.218	0.284	0.125	0.109	0.142	SUBCLONAL	1	TRUE	1	0.618882956438437	3		645	1287	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349981	89349981	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037300-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	187	713	0	ENST00000301030.4:c.2969A>G	p.Asp990Gly	p.D990G	ENST00000301030	NM_001256183.1	990	gAc/gGc	9/13	0.189288182853018	2	FACETS	0.44	0.405	0.476	0.22	0.202	0.238	INDETERMINATE	1	TRUE	0	0.618882956438437	2		713	1374	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436612	110436612	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037300-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1505	112	647	0	ENST00000375856.3:c.1789G>T	p.Glu597Ter	p.E597*	ENST00000375856	NM_003749.2	597	Gaa/Taa	1/2	0.618882956438437	3	FACETS	0.293	0.262	0.326	0.147	0.131	0.163	SUBCLONAL	1	TRUE	1	0.618882956438437	3		647	1617	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189854	66189854	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037300-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	104	466	0	ENST00000273854.3:c.3092T>G	p.Val1031Gly	p.V1031G	ENST00000273854	NM_004439.5	1031	gTa/gGa	18/18	0.618882956438437	3	FACETS	0.719	0.645	0.797	0.24	0.215	0.266	SUBCLONAL	1	TRUE	0	0.618882956438437	3		466	612	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52649468	52649469	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	C	novel	NA	P-0037300-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	44	394	0	ENST00000394830.3:c.1822_1823insG	p.Tyr608Ter	p.Y608*	ENST00000394830	NM_018313.4	608	tat/tGat	16/30	0.572731775416559	1	FACETS	0.3	0.253	0.353	0.3	0.253	0.353	SUBCLONAL	1	TRUE	0	0.618882956438437	1		394	327	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115903	8115903	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs553192156	NA	P-0037300-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	174	726	0	ENST00000346208.3:c.1249A>C	p.Thr417Pro	p.T417P	ENST00000346208		417	Acc/Ccc	6/6	0.364454910462714	1	FACETS	0.354	0.325	0.384	0.354	0.325	0.384	INDETERMINATE	1	TRUE	0	0.618882956438437	1		726	1096	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138452225	138452225	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037300-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	51	376	0	ENST00000289153.2:c.1028T>C	p.Leu343Pro	p.L343P	ENST00000289153	NM_006219.2	343	cTt/cCt	6/22	0.386029990452474	3	FACETS	0.519	0.442	0.603	0.173	0.147	0.201	SUBCLONAL	1	TRUE	0	0.618882956438437	3		376	416	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907262	32907262	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037300-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	89	593	0	ENST00000380152.3:c.1648del	p.Glu550ArgfsTer8	p.E550Rfs*8	ENST00000380152		549	aaG/aa	10/27	0.151776698624919	4	FACETS	0.964	0.858	1	0.482	0.429	0.538	INDETERMINATE	1	TRUE	2	0.618882956438437	4		593	483	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0037864-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	302	303	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.938139307646319	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.938139307646319	1		303	324	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001523	150001523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264217871	NA	P-0037864-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	67	368	0	ENST00000253339.5:c.2081G>A	p.Arg694His	p.R694H	ENST00000253339		694	cGt/cAt	4/7	0.938139307646319	1	FACETS	0.387	0.342	0.433	0.387	0.342	0.433	SUBCLONAL	1	TRUE	0	0.938139307646319	1		368	196	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402316	402316	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037864-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	82	366	0	ENST00000399788.2:c.4475A>T	p.Lys1492Ile	p.K1492I	ENST00000399788	NM_001042603.1	1492	aAa/aTa	27/28	0.938139307646319	4	FACETS	0.464	0.409	0.524	0.155	0.136	0.175	SUBCLONAL	1	TRUE	1	0.938139307646319	4		366	730	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0039058-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	138	389	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.500816483743989	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	FALSE	2	0.574993876053246	4		389	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039058-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	425	548	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.53523752107246	5	FACETS	0.932	0.903	0.96	0.932	0.903	0.96	CLONAL	5	FALSE	0	0.574993876053246	5		548	591	SUCCESS
APC	324	MSKCC	GRCh37	5	112175536	112175536	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039058-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	173	525	0	ENST00000257430.4:c.4245del	p.Ser1415ArgfsTer4	p.S1415Rfs*4	ENST00000257430	NM_000038.5	1415	agT/ag	16/16	0.567508725032927	3	FACETS	0.938	0.874	1	0.938	0.874	1	CLONAL	2	FALSE	1	0.574993876053246	3		525	413	SUCCESS
APC	324	MSKCC	GRCh37	5	112173730	112173730	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039058-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	80	358	0	ENST00000257430.4:c.2442del	p.Phe814LeufsTer6	p.F814Lfs*6	ENST00000257430	NM_000038.5	813	aaT/aa	16/16	0.567508725032927	3	FACETS	0.976	0.865	1	0.488	0.432	0.547	CLONAL	1	FALSE	1	0.574993876053246	3		358	367	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114546	73114547	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	novel	NA	P-0039058-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	93	358	0	ENST00000356692.5:c.929_930del		p.X310_splice	ENST00000356692		310			0.553231378611507	4	FACETS	0.98	0.885	1	0.98	0.885	1	CLONAL	2	FALSE	2	0.574993876053246	4		358	260	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675097	40675097	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039058-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	113	417	0	ENST00000249776.8:c.61G>T	p.Glu21Ter	p.E21*	ENST00000249776	NM_033286.3	21	Gag/Tag	1/9	0.567508725032927	3	FACETS	1	0.982	1	0.673	0.611	0.737	CLONAL	1	FALSE	1	0.574993876053246	3		417	376	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251986	153251986	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039058-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	95	432	0	ENST00000281708.4:c.1020del	p.Val341Ter	p.V341*	ENST00000281708	NM_033632.3	340	aaA/aa	7/12	0.574993876053246	5	FACETS	0.834	0.749	0.923	0.556	0.499	0.616	CLONAL	2	FALSE	2	0.574993876053246	5		432	369	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0039410-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	85	0	0				ENST00000310581	NM_198253.2	-/1132			0.601972663929486	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.927806011890936	3		0	114	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0039410-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	323	389	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.927806011890936	7	FACETS	1	0.975	1	1	0.975	1	CLONAL	6	TRUE	1	0.927806011890936	7		389	384	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0039410-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	61	418	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.859	0.76	0.961	0.859	0.76	0.961	CLONAL	1	TRUE	1	0.927806011890936	2		418	153	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971187	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0039410-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1	107	574	0	ENST00000304494.5:c.171_172delinsTT	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	57	gcCCga/gcTTga	2/3	0.919552788101968	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.927806011890936	2		574	108	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222727	5222727	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746980740	NA	P-0039410-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	51	460	0	ENST00000357368.4:c.3076C>T	p.Arg1026Cys	p.R1026C	ENST00000357368	NM_002850.3	1026	Cgc/Tgc	18/38	0.927806011890936	3	FACETS	1	0.896	1	0.519	0.45	0.591	CLONAL	1	TRUE	1	0.927806011890936	3		460	155	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477813	140477813	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs180177037	NA	P-0039410-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	287	360	0	ENST00000288602.6:c.1495A>G	p.Lys499Glu	p.K499E	ENST00000288602	NM_004333.4	499	Aaa/Gaa	12/18	0.927806011890936	7	FACETS	1	0.973	1	0.686	0.654	0.717	CLONAL	4	TRUE	1	0.927806011890936	7		360	499	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956771	68956771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774302685	NA	P-0039410-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	259	396	0	ENST00000288368.4:c.889C>T	p.Arg297Cys	p.R297C	ENST00000288368	NM_024870.2	297	Cgt/Tgt	8/40	0.396738853234117	6	FACETS	0.888	0.845	0.93	1	0.991	1	INDETERMINATE	4	TRUE	3	0.927806011890936	6		396	449	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504382	149504382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039410-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	45	447	0	ENST00000261799.4:c.1820G>A	p.Gly607Asp	p.G607D	ENST00000261799	NM_002609.3	607	gGc/gAc	13/23	0.57754487645881	3	FACETS	1	0.909	1	0.538	0.463	0.617	CLONAL	1	TRUE	1	0.927806011890936	3		447	132	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677912	117677912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765109582	NA	P-0039410-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	61	459	0	ENST00000368508.3:c.4021G>A	p.Ala1341Thr	p.A1341T	ENST00000368508	NM_002944.2	1341	Gct/Act	25/43	1	2	FACETS	0.832	0.735	0.932	0.832	0.735	0.932	CLONAL	1	TRUE	1	0.927806011890936	2		459	158	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870265	44870265	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0039410-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	52	309	0	ENST00000377967.4:c.443+1G>C		p.X148_splice	ENST00000377967	NM_021140.2	148			0.571461529647906	4	FACETS	1	0.874	1	0.338	0.291	0.388	CLONAL	1	TRUE	1	0.927806011890936	4		309	213	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575168	48575168	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0039604-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	101	488	0	ENST00000342988.3:c.362T>G	p.Leu121Ter	p.L121*	ENST00000342988	NM_005359.5	121	tTa/tGa	3/12	0.803120387901788	1	FACETS	0.99	0.921	1	0.99	0.921	1	CLONAL	1	TRUE	0	0.803120387901788	1		488	152	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220640	1220640	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690940	NA	P-0039604-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	137	567	0	ENST00000326873.7:c.658C>T	p.Gln220Ter	p.Q220*	ENST00000326873	NM_000455.4	220	Cag/Tag	5/10	0.803120387901788	1	FACETS	0.888	0.83	0.944	0.888	0.83	0.944	CLONAL	1	TRUE	0	0.803120387901788	1		567	230	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374366	31374366	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757657111	NA	P-0039604-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	161	710	0	ENST00000328111.2:c.365G>A	p.Arg122His	p.R122H	ENST00000328111	NM_006892.3	122	cGt/cAt	5/23	0.529950407273487	3	FACETS	0.972	0.896	1			1	CLONAL	1	TRUE	NA	0.803120387901788	3		710	578	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0039604-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	142	519	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.803120387901788	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.803120387901788	1		519	206	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467978	50467978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039604-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	140	614	0	ENST00000331340.3:c.1213G>A	p.Glu405Lys	p.E405K	ENST00000331340	NM_006060.4	405	Gag/Aag	8/8	0.803120387901788	3	FACETS	1	0.953	1	0.528	0.484	0.573	CLONAL	1	TRUE	1	0.803120387901788	3		614	463	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222222	53222222	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782534108	NA	P-0039604-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	56	550	0	ENST00000375401.3:c.4610C>T	p.Ser1537Leu	p.S1537L	ENST00000375401	NM_004187.3	1537	tCg/tTg	26/26	NA	2	FACETS	0.332	0.285	0.383			1	INDETERMINATE	1	TRUE	NA	0.803120387901788	2		550	420	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222613	69222613	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039604-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	134	577	0	ENST00000462284.1:c.586T>C	p.Ser196Pro	p.S196P	ENST00000462284	NM_002392.5	196	Tcc/Ccc	8/11	1	2	FACETS	0.976	0.899	1	0.976	0.899	1	CLONAL	1	TRUE	1	0.803120387901788	2		577	342	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144877	11144877	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0039604-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	146	531	0	ENST00000358026.2:c.3951+1G>C		p.X1317_splice	ENST00000358026	NM_001128849.1	1317			0.803120387901788	1	FACETS	0.967	0.91	1	0.967	0.91	1	CLONAL	1	TRUE	0	0.803120387901788	1		531	225	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662432	117662432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039604-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	146	581	0	ENST00000368508.3:c.4945C>T	p.His1649Tyr	p.H1649Y	ENST00000368508	NM_002944.2	1649	Cat/Tat	30/43	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.803120387901788	2		581	315	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	124	539	1	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.59097829939881	3	FACETS	0.785	0.72	0.851	0.523	0.48	0.568	SUBCLONAL	2	TRUE	0	0.644629723225974	3		540	324	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028689	12028689	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0039898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	179	342	0	ENST00000353533.5:c.891+1G>C		p.X297_splice	ENST00000353533	NM_003010.3	297			0.644629723225974	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.644629723225974	2		342	272	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0039994-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	41	313	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.290197004810573	3	FACETS	0.935	0.79	1	0.935	0.79	1	CLONAL	2	TRUE	1	0.290197004810573	3		313	173	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0039994-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	21	368	2	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.263899198028451	4	FACETS	0.943	0.751	1	0.943	0.751	1	CLONAL	3	TRUE	1	0.290197004810573	4		370	66	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551085	41551085	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039994-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	6	0	0	ENST00000263253.7:c.3229C>T	p.Gln1077Ter	p.Q1077*	ENST00000263253	NM_001429.3	1077	Caa/Taa	17/31	1	2	FACETS	0.492	0.296	0.753	0.492	0.296	0.753	SUBCLONAL	1	TRUE	1	0.290197004810573	2		0	84	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420927	49420928	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0039994-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	11	337	0	ENST00000301067.7:c.14821_14822del	p.Leu4941GlyfsTer2	p.L4941Gfs*2	ENST00000301067	NM_003482.3	4941	TTg/g	48/54	0.211870591935933	3	FACETS	0.904	0.631	1	0.452	0.315	0.618	CLONAL	1	TRUE	1	0.290197004810573	3		337	96	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299836	15299836	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039994-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	11	346	0	ENST00000263388.2:c.1342G>T	p.Asp448Tyr	p.D448Y	ENST00000263388	NM_000435.2	448	Gac/Tac	8/33	1	2	FACETS	0.852	0.595	1	0.852	0.595	1	CLONAL	1	TRUE	1	0.290197004810573	2		346	89	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31511180	31511180	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755611158	NA	P-0039994-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	41	276	0	ENST00000344624.3:c.1394C>T	p.Pro465Leu	p.P465L	ENST00000344624		465	cCg/cTg	6/33	0.287689970520997	2	FACETS	0.856	0.734	0.984	1	0.95	1	CLONAL	3	TRUE	0	0.290197004810573	2		276	110	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250145	110250145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039994-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	10	321	0	ENST00000374672.4:c.530C>T	p.Ser177Phe	p.S177F	ENST00000374672	NM_004235.4	177	tCc/tTc	3/5	0.2106028035302	4	FACETS	0.78	0.532	1	0.39	0.266	0.544	CLONAL	1	TRUE	2	0.290197004810573	4		321	114	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643728	52643728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039994-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	8	0	0	ENST00000394830.3:c.2168C>T	p.Ser723Phe	p.S723F	ENST00000394830	NM_018313.4	723	tCt/tTt	17/30	0.211870591935933	3	FACETS	0.658	0.427	0.952	0.329	0.213	0.476	SUBCLONAL	1	TRUE	1	0.290197004810573	3		0	96	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662381	117662381	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039994-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	12	335	0	ENST00000368508.3:c.4996G>C	p.Val1666Leu	p.V1666L	ENST00000368508	NM_002944.2	1666	Gtt/Ctt	30/43	0.290197004810573	1	FACETS	1	0.788	1	1	0.788	1	CLONAL	1	TRUE	0	0.290197004810573	1		335	63	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292751	62292751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039994-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	15	326	0	ENST00000360203.5:c.203C>T	p.Ser68Phe	p.S68F	ENST00000360203	NM_001283009.1	68	tCt/tTt	3/35	0.170929800561367	2	FACETS	1	0.784	1	0.533	0.395	0.693	INDETERMINATE	1	TRUE	0	0.290197004810573	2		326	97	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0043892-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	77	432	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.263539102621728	1	FACETS	0.931	0.819	1	0.931	0.819	1	CLONAL	1	TRUE	0	0.2735585811831	1		432	522	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0043892-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	137	377	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.273590595119504	4	FACETS	0.993	0.912	1	1	0.988	1	CLONAL	3	TRUE	2	0.2735585811831	4		377	428	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866987936	NA	P-0043892-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	63	500	0	ENST00000281708.4:c.1436G>T	p.Arg479Leu	p.R479L	ENST00000281708	NM_033632.3	479	cGa/cTa	10/12	1	2	FACETS	0.903	0.782	1	0.903	0.782	1	CLONAL	1	TRUE	1	0.2735585811831	2		500	510	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112217	115112217	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766332681	NA	P-0043892-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	67	600	0	ENST00000257566.3:c.1523C>T	p.Ala508Val	p.A508V	ENST00000257566	NM_016569.3	508	gCg/gTg	7/8	0.239151063994252	2	FACETS	0.827	0.719	0.944	0.414	0.359	0.472	CLONAL	1	TRUE	0	0.2735585811831	2		600	592	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103409	77103409	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043892-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	31	454	0	ENST00000356341.3:c.157C>T	p.Arg53Ter	p.R53*	ENST00000356341	NM_002576.4	53	Cga/Tga	2/15	1	2	FACETS	0.445	0.359	0.543	0.445	0.359	0.543	SUBCLONAL	1	TRUE	1	0.2735585811831	2		454	509	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143348	30143348	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1031804606	NA	P-0043892-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	67	538	0	ENST00000389048.3:c.178G>T	p.Val60Leu	p.V60L	ENST00000389048	NM_004304.4	60	Gtg/Ttg	1/29	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.2735585811831	2		538	485	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53254035	53254035	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043892-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	69	267	0	ENST00000375401.3:c.37G>T	p.Glu13Ter	p.E13*	ENST00000375401	NM_004187.3	13	Gag/Tag	1/26	1	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.2735585811831	1		267	338	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949078	151949078	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043892-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	78	453	0	ENST00000262189.6:c.1567G>T	p.Glu523Ter	p.E523*	ENST00000262189	NM_170606.2	523	Gag/Tag	11/59	0.273590595119504	3	FACETS	1	0.952	1	0.582	0.512	0.657	CLONAL	1	TRUE	1	0.2735585811831	3		453	557	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057089	180057089	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043892-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	32	632	0	ENST00000261937.6:c.530G>T	p.Trp177Leu	p.W177L	ENST00000261937	NM_182925.4	177	tGg/tTg	5/30	1	2	FACETS	0.46	0.372	0.559	0.46	0.372	0.559	SUBCLONAL	1	TRUE	1	0.2735585811831	2		632	509	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400269	139400269	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043892-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	64	586	0	ENST00000277541.6:c.4079del	p.Gly1360AlafsTer85	p.G1360Afs*85	ENST00000277541	NM_017617.3	1360	gGc/gc	25/34	1	2	FACETS	0.733	0.635	0.84	0.733	0.635	0.84	SUBCLONAL	1	TRUE	1	0.2735585811831	2		586	638	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470959	25470959	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043892-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	74	600	0	ENST00000264709.3:c.802G>T	p.Asp268Tyr	p.D268Y	ENST00000264709	NM_175629.2	268	Gat/Tat	7/23	1	2	FACETS	0.815	0.713	0.924	0.815	0.713	0.924	CLONAL	1	TRUE	1	0.2735585811831	2		600	664	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188275	32188275	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043892-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	113	670	0	ENST00000375023.3:c.1066C>A	p.Leu356Met	p.L356M	ENST00000375023	NM_004557.3	356	Ctg/Atg	6/30	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.2735585811831	2		670	707	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390147	89390147	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043892-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	71	441	0	ENST00000336596.2:c.896A>T	p.Asp299Val	p.D299V	ENST00000336596	NM_005233.5	299	gAt/gTt	4/17	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.2735585811831	NA		441	461	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172025	32172025	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043892-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	77	619	0	ENST00000375023.3:c.3007T>G	p.Cys1003Gly	p.C1003G	ENST00000375023	NM_004557.3	1003	Tgt/Ggt	19/30	1	2	FACETS	0.845	0.742	0.956	0.845	0.742	0.956	CLONAL	1	TRUE	1	0.2735585811831	2		619	666	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472516	88472516	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043892-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	76	624	0	ENST00000360948.2:c.2039T>A	p.Leu680Gln	p.L680Q	ENST00000360948	NM_001012338.2	680	cTg/cAg	16/19	0.2735585811831	1	FACETS	0.944	0.83	1	0.944	0.83	1	CLONAL	1	TRUE	0	0.2735585811831	1		624	508	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484184	8484184	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043892-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	43	516	0	ENST00000356435.5:c.3348del	p.Lys1117ArgfsTer7	p.K1117Rfs*7	ENST00000356435		1116	ggG/gg	19/35	1	2	FACETS	0.644	0.539	0.761	0.644	0.539	0.761	SUBCLONAL	1	TRUE	1	0.2735585811831	2		516	488	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615056	43615056	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043892-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	60	723	1	ENST00000355710.3:c.2470C>A	p.Pro824Thr	p.P824T	ENST00000355710	NM_020975.4	824	Cct/Act	14/20	1	2	FACETS	0.66	0.568	0.76	0.66	0.568	0.76	SUBCLONAL	1	TRUE	1	0.2735585811831	2		724	665	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31239089	31239089	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043892-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	95	585	0	ENST00000376228.5:c.380T>A	p.Leu127Gln	p.L127Q	ENST00000376228	NM_002117.5	127	cTg/cAg	3/8	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.2735585811831	2		585	669	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591620	38591623	+	frameshift_variant	Frame_Shift_Del	DEL	TCAA	TCAA	AAG	novel	NA	P-0043892-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	52	387	0	ENST00000299084.4:c.79_82delinsAAG	p.Ser27LysfsTer13	p.S27Kfs*13	ENST00000299084	NM_152594.2	27	TCAAgt/AAGgt	2/7	0.2735585811831				0.764	1				CLONAL	1	TRUE	0	0.2735585811831	1		387	367	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347185	89347185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046083-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	73	465	0	ENST00000301030.4:c.5765C>T	p.Ala1922Val	p.A1922V	ENST00000301030	NM_001256183.1	1922	gCc/gTc	9/13	0.750883125743336	3	FACETS	1	0.942	1	0.549	0.487	0.613	CLONAL	1	TRUE	1	0.793851492639179	3		465	234	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0047742-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	357	483	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.596301303067996	5	FACETS	1	0.994	1	0.894	0.867	0.921	CLONAL	4	TRUE	0	0.714258044004955	5		483	463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577095	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519984	NA	P-0047742-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	185	339	1	ENST00000269305.4:c.843C>A	p.Asp281Glu	p.D281E	ENST00000269305	NM_001126112.2	281	gaC/gaA	8/11	0.584035535439403	2	FACETS	0.863	0.816	0.91	0.863	0.816	0.91	CLONAL	2	TRUE	0	0.714258044004955	2		340	300	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161739	56161751	+	frameshift_variant	Frame_Shift_Del	DEL	TTCACGCATGTCA	TTCACGCATGTCA	-	novel	NA	P-0047742-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	169	305	0	ENST00000399503.3:c.1236_1248del	p.Ser413IlefsTer19	p.S413Ifs*19	ENST00000399503	NM_005921.1	412	gtTTCACGCATGTCA/gt	6/20	0.53994785773841	4	FACETS	0.84	0.779	0.902	0.84	0.779	0.902	CLONAL	2	TRUE	2	0.714258044004955	4		305	483	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189433	56189439	+	frameshift_variant	Frame_Shift_Del	DEL	TTAGAAC	TTAGAAC	-	novel	NA	P-0047742-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	198	336	0	ENST00000399503.3:c.4467_4473del	p.Leu1489PhefsTer13	p.L1489Ffs*13	ENST00000399503	NM_005921.1	1489	TTAGAACtt/tt	20/20	0.53994785773841	4	FACETS	0.964	0.902	1	0.964	0.902	1	CLONAL	2	TRUE	2	0.714258044004955	4		336	493	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341290	341290	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047742-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	50	225	0	ENST00000262320.3:c.2194C>A	p.Gln732Lys	p.Q732K	ENST00000262320	NM_003502.3	732	Cag/Aag	9/11	0.569744812837806	5	FACETS	0.843	0.718	0.979	0.281	0.239	0.327	CLONAL	1	TRUE	2	0.714258044004955	5		225	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0048768-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	40	394	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	0.898	0.745	1	0.898	0.745	1	CLONAL	1	TRUE	1	0.162050196602984	2		394	550	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0048768-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	329	522	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.162050196602984	8	FACETS	0.958	0.911	1	0.958	0.911	1	CLONAL	8	TRUE	0	0.162050196602984	8		522	787	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0048868-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	83	264	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.857873092355296	3	FACETS	0.988	0.882	1	0.494	0.441	0.549	CLONAL	1	TRUE	1	0.857873092355296	3		264	280	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565575	41565575	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048868-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	55	328	0	ENST00000263253.7:c.4241A>G	p.Tyr1414Cys	p.Y1414C	ENST00000263253	NM_001429.3	1414	tAt/tGt	26/31	1	2	FACETS	0.884	0.775	0.997	0.884	0.775	0.997	CLONAL	1	TRUE	1	0.857873092355296	2		328	145	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741256	145741256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766026341	NA	P-0048868-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	77	781	0	ENST00000428558.2:c.1150C>T	p.Arg384Trp	p.R384W	ENST00000428558	NM_004260.3	384	Cgg/Tgg	6/22	1	2	FACETS	0.93	0.834	1	0.93	0.834	1	CLONAL	1	TRUE	1	0.857873092355296	2		781	193	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797221	135797221	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs118203417	NA	P-0048868-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	137	478	2	ENST00000298552.3:c.648del	p.Phe216LeufsTer8	p.F216Lfs*8	ENST00000298552	NM_001162426.1	216	ttT/tt	7/23	0.851700326257082	2	FACETS	0.956	0.913	0.995	0.956	0.913	0.995	CLONAL	2	TRUE	0	0.857873092355296	2		480	167	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508535	106508535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049135-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	13	168	0	ENST00000359195.3:c.529C>T	p.Arg177Cys	p.R177C	ENST00000359195	NM_002649.2	177	Cgc/Tgc	2/11	0.336078778650835	3	FACETS	0.505	0.361	0.679	0.252	0.18	0.34	SUBCLONAL	1	TRUE	1	0.336078778650835	3		168	179	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026133	71026133	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs775136381	NA	P-0049135-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	53	273	1	ENST00000318789.4:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000318789	NM_032682.5	497	Cga/Tga	17/21	0.336078778650835	2	FACETS	0.914	0.806	1	1	0.969	1	CLONAL	3	TRUE	0	0.336078778650835	2		274	115	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	220	382	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.760842690743831	3	FACETS	0.993	0.939	1	0.993	0.939	1	CLONAL	2	TRUE	1	0.760842690743831	3		382	402	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	136	313	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.760842690743831	2		313	289	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298790	15298790	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs926266778	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	22	443	1	ENST00000263388.2:c.1508C>T	p.Thr503Met	p.T503M	ENST00000263388	NM_000435.2	503	aCg/aTg	10/33	1	2	FACETS	0.243	0.189	0.306	0.243	0.189	0.306	SUBCLONAL	1	TRUE	1	0.760842690743831	2		444	238	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888199	112888199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918454	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	10	424	0	ENST00000351677.2:c.215C>T	p.Ala72Val	p.A72V	ENST00000351677	NM_002834.3	72	gCc/gTc	3/16	1	2	FACETS	0.08	0.054	0.114	0.08	0.054	0.114	SUBCLONAL	1	TRUE	1	0.760842690743831	2		424	327	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057727	27057727	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	30	522	0	ENST00000324856.7:c.1435C>T	p.Gln479Ter	p.Q479*	ENST00000324856	NM_006015.4	479	Cag/Tag	3/20	1	2	FACETS	0.232	0.187	0.283	0.232	0.187	0.283	SUBCLONAL	1	TRUE	1	0.760842690743831	2		522	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	100	380	0	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	0.760842690743831	1	FACETS	0.975	0.901	1	0.975	0.901	1	CLONAL	1	TRUE	0	0.760842690743831	1		380	167	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641555	47641555	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1114167845	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	66	212	0	ENST00000233146.2:c.940C>T	p.Gln314Ter	p.Q314*	ENST00000233146	NM_000251.2	314	Cag/Tag	5/16	0.197747778237736	3	FACETS	1	0.925	1	0.535	0.471	0.602	INDETERMINATE	1	TRUE	1	0.760842690743831	3		212	224	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099397	27099397	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	19	466	0	ENST00000324856.7:c.3634C>G	p.Gln1212Glu	p.Q1212E	ENST00000324856	NM_006015.4	1212	Cag/Gag	14/20	1	2	FACETS	0.162	0.122	0.208	0.162	0.122	0.208	SUBCLONAL	1	TRUE	1	0.760842690743831	2		466	309	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468236	50468236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	136	528	0	ENST00000331340.3:c.1471G>A	p.Glu491Lys	p.E491K	ENST00000331340	NM_006060.4	491	Gag/Aag	8/8	0.760842690743831	3	FACETS	1	0.971	1	0.565	0.518	0.613	CLONAL	1	TRUE	1	0.760842690743831	3		528	437	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101683	27101683	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	54	470	0	ENST00000324856.7:c.4965G>T	p.Gln1655His	p.Q1655H	ENST00000324856	NM_006015.4	1655	caG/caT	18/20	1	2	FACETS	0.448	0.385	0.516	0.448	0.385	0.516	SUBCLONAL	1	TRUE	1	0.760842690743831	2		470	317	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955394	48955394	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886043247	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	161	338	0	ENST00000267163.4:c.1510C>T	p.Gln504Ter	p.Q504*	ENST00000267163	NM_000321.2	504	Cag/Tag	17/27	0.760842690743831	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.760842690743831	1		338	239	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063313	67063313	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	62	288	0	ENST00000412916.2:c.3G>A	p.Met1?	p.M1?	ENST00000412916		1	atG/atA	1/6	0.760842690743831	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.760842690743831	1		288	89	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781092	135781092	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	73	502	0	ENST00000298552.3:c.1873G>T	p.Glu625Ter	p.E625*	ENST00000298552	NM_001162426.1	625	Gag/Tag	15/23	0.760842690743831	2	FACETS	0.813	0.722	0.909	0.407	0.361	0.455	CLONAL	1	TRUE	0	0.760842690743831	2		502	236	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982373	201982373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398134258	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	145	360	0	ENST00000359651.3:c.752G>A	p.Arg251Gln	p.R251Q	ENST00000359651		251	cGa/cAa	6/8	0.195912066602382	4	FACETS	1	0.933	1	1	0.933	1	INDETERMINATE	2	TRUE	2	0.760842690743831	4		360	333	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021677	69021677	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	38	341	0	ENST00000288368.4:c.2965C>T	p.Gln989Ter	p.Q989*	ENST00000288368	NM_024870.2	989	Cag/Tag	25/40	0.227614692399494	3	FACETS	0.42	0.348	0.5	0.21	0.174	0.25	INDETERMINATE	1	TRUE	1	0.760842690743831	3		341	328	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038881	12038881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	77	412	0	ENST00000396373.4:c.1174G>A	p.Glu392Lys	p.E392K	ENST00000396373	NM_001987.4	392	Gag/Aag	7/8	0.606377302123799	5	FACETS	0.709	0.623	0.802			1	SUBCLONAL	1	TRUE	NA	0.760842690743831	5		412	611	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849484	68849484	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	67	451	0	ENST00000261769.5:c.1387G>C	p.Glu463Gln	p.E463Q	ENST00000261769	NM_004360.3	463	Gag/Cag	10/16	0.760842690743831	1	FACETS	0.515	0.454	0.578	0.515	0.454	0.578	SUBCLONAL	1	TRUE	0	0.760842690743831	1		451	212	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195910	102195910	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	29	439	0	ENST00000263464.3:c.670G>C	p.Glu224Gln	p.E224Q	ENST00000263464	NM_001165.4	224	Gaa/Caa	2/9	0.760842690743831	1	FACETS	0.16	0.128	0.196	0.16	0.128	0.196	SUBCLONAL	1	TRUE	0	0.760842690743831	1		439	295	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428273	72428273	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	33	357	0	ENST00000477973.2:c.619C>G	p.Leu207Val	p.L207V	ENST00000477973	NM_012234.5	207	Ctg/Gtg	3/4	0.760842690743831	1	FACETS	0.245	0.201	0.295	0.245	0.201	0.295	SUBCLONAL	1	TRUE	0	0.760842690743831	1		357	219	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39239334	39239334	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	64	317	0	ENST00000402219.2:c.2323G>C	p.Asp775His	p.D775H	ENST00000402219	NM_005633.3	775	Gac/Cac	14/23	0.309940850473803	2	FACETS	0.504	0.439	0.573	0.252	0.219	0.287	INDETERMINATE	1	TRUE	0	0.760842690743831	2		317	334	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271277	153271277	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	42	241	0	ENST00000281708.4:c.502-1G>C		p.X168_splice	ENST00000281708	NM_033632.3	168			0.760842690743831	1	FACETS	0.279	0.235	0.328	0.279	0.235	0.328	SUBCLONAL	1	TRUE	0	0.760842690743831	1		241	245	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598311	28598311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1480732926	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	17	501	0	ENST00000253063.3:c.283C>T	p.Arg95Cys	p.R95C	ENST00000253063	NM_031459.4	95	Cgc/Tgc	3/10	1	2	FACETS	0.154	0.115	0.201	0.154	0.115	0.201	SUBCLONAL	1	TRUE	1	0.760842690743831	2		501	290	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113100	209113100	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	125	411	0	ENST00000345146.2:c.407G>T	p.Gly136Val	p.G136V	ENST00000345146	NM_005896.2	136	gGg/gTg	4/10	0.760842690743831	1	FACETS	0.974	0.908	1	0.974	0.908	1	CLONAL	1	TRUE	0	0.760842690743831	1		411	209	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543909	41543909	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	110	398	0	ENST00000263253.7:c.2200C>T	p.Gln734Ter	p.Q734*	ENST00000263253	NM_001429.3	734	Cag/Tag	12/31	0.760842690743831	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.760842690743831	1		398	177	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437088	110437088	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1021390879	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	39	364	0	ENST00000375856.3:c.1313C>G	p.Ser438Trp	p.S438W	ENST00000375856	NM_003749.2	438	tCg/tGg	1/2	0.197747778237736	3	FACETS	0.868	0.731	1	0.434	0.365	0.509	INDETERMINATE	1	TRUE	1	0.760842690743831	3		364	163	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663743	241663743	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201625211	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	17	262	0	ENST00000366560.3:c.1384C>T	p.His462Tyr	p.H462Y	ENST00000366560	NM_000143.3	462	Cat/Tat	9/10	0.171004451240941	4	FACETS	0.259	0.193	0.337	0.129	0.096	0.169	INDETERMINATE	1	TRUE	2	0.760842690743831	4		262	304	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69143584	69143584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142298071	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	114	311	0	ENST00000288368.4:c.4792G>A	p.Glu1598Lys	p.E1598K	ENST00000288368	NM_024870.2	1598	Gag/Aag	40/40	0.227614692399494	3	FACETS	1	0.986	1	0.741	0.679	0.805	INDETERMINATE	1	TRUE	1	0.760842690743831	3		311	279	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	401990	401990	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	208	449	0	ENST00000399788.2:c.4801G>C	p.Glu1601Gln	p.E1601Q	ENST00000399788	NM_001042603.1	1601	Gag/Cag	27/28	0.760842690743831	3	FACETS	1	0.987	1	0.618	0.577	0.66	CLONAL	1	TRUE	1	0.760842690743831	3		449	611	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235903	133235903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1482283883	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	108	538	0	ENST00000320574.5:c.3253G>A	p.Glu1085Lys	p.E1085K	ENST00000320574	NM_006231.2	1085	Gag/Aag	26/49	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.760842690743831	2		538	251	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40460253	40460253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	100	452	0	ENST00000345506.4:c.1964C>T	p.Ser655Phe	p.S655F	ENST00000345506	NM_003152.3	655	tCc/tTc	17/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.760842690743831	2		452	219	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40880956	40880956	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	142	324	0	ENST00000428826.2:c.4G>A	p.Glu2Lys	p.E2K	ENST00000428826		2	Gaa/Aaa	3/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.760842690743831	2		324	296	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621158	1621158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1250135870	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	95	441	0	ENST00000344749.5:c.988G>A	p.Asp330Asn	p.D330N	ENST00000344749	NM_001136139.2	330	Gat/Aat	12/19	0.449188320927048	1	FACETS	0.823	0.753	0.893	0.823	0.753	0.893	INDETERMINATE	1	TRUE	0	0.760842690743831	1		441	188	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52677318	52677318	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	142	380	0	ENST00000394830.3:c.941C>T	p.Ser314Leu	p.S314L	ENST00000394830	NM_018313.4	314	tCa/tTa	10/30	0.760842690743831	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.760842690743831	1		380	195	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260159	149260162	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	95	379	0	ENST00000360632.3:c.731_734del	p.Arg244LysfsTer11	p.R244Kfs*11	ENST00000360632	NM_015472.4	244	aGAGAa/aa	4/7	0.197747778237736	3	FACETS	1	0.974	1	0.622	0.562	0.685	INDETERMINATE	1	TRUE	1	0.760842690743831	3		379	277	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067083	143067083	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	156	371	0	ENST00000262992.4:c.1630G>T	p.Glu544Ter	p.E544*	ENST00000262992	NM_001101669.1	544	Gaa/Taa	16/24	0.760842690743831	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.760842690743831	1		371	211	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233636	233636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1337704280	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	27	71	0	ENST00000264932.6:c.940G>A	p.Glu314Lys	p.E314K	ENST00000264932	NM_004168.2	314	Gag/Aag	8/15	0.363604388229751	4	FACETS	1	0.94	1	0.484	0.396	0.579	INDETERMINATE	1	TRUE	1	0.760842690743831	4		71	86	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323241	31323241	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	147	538	0	ENST00000412585.2:c.748C>G	p.Gln250Glu	p.Q250E	ENST00000412585	NM_005514.6	250	Cag/Gag	4/8	0.760842690743831	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.760842690743831	1		538	222	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878742	151878742	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	135	508	0	ENST00000262189.6:c.6203C>G	p.Ser2068Cys	p.S2068C	ENST00000262189	NM_170606.2	2068	tCt/tGt	36/59	0.197747778237736	3	FACETS	1	0.986	1	0.684	0.63	0.74	INDETERMINATE	1	TRUE	1	0.760842690743831	3		508	358	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169596	27169596	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	200	418	0	ENST00000380036.4:c.597C>A	p.Phe199Leu	p.F199L	ENST00000380036	NM_000459.3	199	ttC/ttA	4/23	0.760842690743831	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.760842690743831	1		418	270	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760004	133760004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	85	430	0	ENST00000318560.5:c.2327C>T	p.Thr776Ile	p.T776I	ENST00000318560	NM_005157.4	776	aCc/aTc	11/11	0.760842690743831	2	FACETS	1	0.984	1	0.725	0.663	0.787	CLONAL	1	TRUE	0	0.760842690743831	2		430	154	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599209	28599209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	35	490	0	ENST00000253063.3:c.655G>A	p.Glu219Lys	p.E219K	ENST00000253063	NM_031459.4	219	Gag/Aag	5/10	1	2	FACETS	0.424	0.35	0.505	0.424	0.35	0.505	SUBCLONAL	1	TRUE	1	0.760842690743831	2		490	217	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473711	67473711	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	112	406	0	ENST00000327367.4:c.791C>A	p.Ser264Tyr	p.S264Y	ENST00000327367	NM_005902.3	264	tCc/tAc	6/9	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.760842690743831	2		406	233	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39576601	39576601	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	38	273	0	ENST00000262039.4:c.892-1G>C		p.X298_splice	ENST00000262039	NM_002647.2	298			0.227614692399494	3	FACETS	0.37	0.306	0.441	0.185	0.153	0.221	INDETERMINATE	1	TRUE	1	0.760842690743831	3		273	373	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779413	3779413	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	78	494	0	ENST00000262367.5:c.5635C>T	p.Gln1879Ter	p.Q1879*	ENST00000262367	NM_004380.2	1879	Cag/Tag	31/31	1	2	FACETS	0.919	0.822	1	0.919	0.822	1	CLONAL	1	TRUE	1	0.760842690743831	2		494	223	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941137	36941137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	60	468	0	ENST00000361632.4:c.202G>A	p.Glu68Lys	p.E68K	ENST00000361632		68	Gag/Aag	3/16	1	2	FACETS	0.548	0.476	0.625	0.548	0.476	0.625	SUBCLONAL	1	TRUE	1	0.760842690743831	2		468	288	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129785	108129785	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587778067	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	54	319	0	ENST00000278616.4:c.2449G>C	p.Asp817His	p.D817H	ENST00000278616	NM_000051.3	817	Gat/Cat	16/63	0.760842690743831	1	FACETS	0.419	0.362	0.479	0.419	0.362	0.479	SUBCLONAL	1	TRUE	0	0.760842690743831	1		319	210	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86546569	86546569	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	71	470	0	ENST00000262426.4:c.1018G>A	p.Asp340Asn	p.D340N	ENST00000262426	NM_001451.2	340	Gac/Aac	2/2	0.760842690743831	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.760842690743831	1		470	114	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217723	7217723	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs112452916	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	74	517	0	ENST00000380728.2:c.205-1G>A		p.X69_splice	ENST00000380728		69			0.760842690743831	1	FACETS	0.482	0.428	0.539	0.482	0.428	0.539	SUBCLONAL	1	TRUE	0	0.760842690743831	1		517	250	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38194859	38194859	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	32	311	0	ENST00000317025.8:c.874C>T	p.Pro292Ser	p.P292S	ENST00000317025	NM_023034.1	292	Ccc/Tcc	4/24	0.227614692399494	3	FACETS	0.318	0.258	0.386	0.159	0.129	0.193	INDETERMINATE	1	TRUE	1	0.760842690743831	3		311	365	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37055971	37055971	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1559534445	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	32	304	0	ENST00000231790.2:c.726G>A	p.Met242Ile	p.M242I	ENST00000231790	NM_000249.3	242	atG/atA	9/19	0.760842690743831	1	FACETS	0.305	0.25	0.365	0.305	0.25	0.365	SUBCLONAL	1	TRUE	0	0.760842690743831	1		304	171	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818230	32818230	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	69	477	0	ENST00000354258.4:c.1295C>G	p.Ser432Trp	p.S432W	ENST00000354258	NM_000593.5	432	tCg/tGg	5/11	0.726997371742416	2	FACETS	0.662	0.583	0.746	0.331	0.291	0.373	SUBCLONAL	1	TRUE	0	0.760842690743831	2		477	274	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49399964	49399964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	36	405	0	ENST00000418115.1:c.373G>A	p.Glu125Lys	p.E125K	ENST00000418115	NM_001664.2	125	Gag/Aag	4/5	0.760842690743831	1	FACETS	0.324	0.269	0.384	0.324	0.269	0.384	SUBCLONAL	1	TRUE	0	0.760842690743831	1		405	181	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217641	7217641	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	63	476	0	ENST00000380728.2:c.286G>T	p.Glu96Ter	p.E96*	ENST00000380728		96	Gag/Tag	4/11	0.760842690743831	1	FACETS	0.45	0.394	0.509	0.45	0.394	0.509	SUBCLONAL	1	TRUE	0	0.760842690743831	1		476	228	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588942	67588942	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	61	361	0	ENST00000274335.5:c.1033del	p.Glu345LysfsTer28	p.E345Kfs*28	ENST00000274335		345	Gaa/aa	8/15	0.227614692399494	3	FACETS	0.698	0.606	0.797	0.349	0.303	0.399	INDETERMINATE	1	TRUE	1	0.760842690743831	3		361	317	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129419	64129419	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	15	521	0	ENST00000334205.4:c.851G>C	p.Arg284Pro	p.R284P	ENST00000334205	NM_003942.2	284	cGa/cCa	8/17	0.16023090620599	3	FACETS	0.235	0.171	0.31	0.117	0.085	0.155	INDETERMINATE	1	TRUE	1	0.760842690743831	3		521	232	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416910	416910	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	126	515	0	ENST00000399788.2:c.3640C>G	p.Leu1214Val	p.L1214V	ENST00000399788	NM_001042603.1	1214	Ctt/Gtt	23/28	0.760842690743831	3	FACETS	0.943	0.859	1	0.471	0.429	0.515	CLONAL	1	TRUE	1	0.760842690743831	3		515	485	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737166	145737166	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	42	449	0	ENST00000428558.2:c.3400G>C	p.Asp1134His	p.D1134H	ENST00000428558	NM_004260.3	1134	Gat/Cat	21/22	0.227614692399494	3	FACETS	0.842	0.713	0.981	0.421	0.356	0.491	INDETERMINATE	1	TRUE	1	0.760842690743831	3		449	181	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347533	89347533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	21	467	0	ENST00000301030.4:c.5417G>A	p.Gly1806Glu	p.G1806E	ENST00000301030	NM_001256183.1	1806	gGa/gAa	9/13	0.760842690743831	1	FACETS	0.285	0.222	0.356	0.285	0.222	0.356	SUBCLONAL	1	TRUE	0	0.760842690743831	1		467	120	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202171	138202171	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	28	400	0	ENST00000237289.4:c.2089-1G>A		p.X697_splice	ENST00000237289	NM_001270507.1	697			0.760842690743831	1	FACETS	0.198	0.159	0.243	0.198	0.159	0.243	SUBCLONAL	1	TRUE	0	0.760842690743831	1		400	230	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670570	134670570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	28	471	0	ENST00000398015.3:c.481G>A	p.Glu161Lys	p.E161K	ENST00000398015	NM_004441.4	161	Gaa/Aaa	3/16	1	2	FACETS	0.27	0.216	0.33	0.27	0.216	0.33	SUBCLONAL	1	TRUE	1	0.760842690743831	2		471	273	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69210668	69210668	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	48	316	0	ENST00000462284.1:c.251C>G	p.Ser84Ter	p.S84*	ENST00000462284	NM_002392.5	84	tCa/tGa	4/11	0.64532148603691	4	FACETS	0.5	0.423	0.585			1	SUBCLONAL	1	TRUE	NA	0.760842690743831	4		316	444	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939835	49939835	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	32	381	0	ENST00000296474.3:c.1208C>G	p.Ser403Trp	p.S403W	ENST00000296474	NM_002447.2	403	tCg/tGg	1/20	0.760842690743831	1	FACETS	0.314	0.258	0.376	0.314	0.258	0.376	SUBCLONAL	1	TRUE	0	0.760842690743831	1		381	166	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677914	58677914	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1362214093	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	20	405	0	ENST00000305921.3:c.139C>A	p.Gln47Lys	p.Q47K	ENST00000305921	NM_003620.3	47	Cag/Aag	1/6	1	2	FACETS	0.208	0.159	0.265	0.208	0.159	0.265	SUBCLONAL	1	TRUE	1	0.760842690743831	2		405	253	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66735679	66735679	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	107	328	0	ENST00000307102.5:c.500G>A	p.Gly167Glu	p.G167E	ENST00000307102	NM_002755.3	167	gGa/gAa	4/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.760842690743831	2		328	236	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195755	102195755	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	21	454	0	ENST00000263464.3:c.515G>T	p.Arg172Ile	p.R172I	ENST00000263464	NM_001165.4	172	aGa/aTa	2/9	0.760842690743831	1	FACETS	0.114	0.087	0.145	0.114	0.087	0.145	SUBCLONAL	1	TRUE	0	0.760842690743831	1		454	300	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434676	128434676	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	114	434	0	ENST00000265960.3:c.178G>C	p.Glu60Gln	p.E60Q	ENST00000265960	NM_001006617.1	60	Gag/Cag	2/12	0.760842690743831	2	FACETS	1	0.963	1	0.547	0.501	0.594	CLONAL	1	TRUE	0	0.760842690743831	2		434	274	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630490	67630490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	82	358	0	ENST00000272342.5:c.676G>A	p.Glu226Lys	p.E226K	ENST00000272342	NM_019002.3	226	Gag/Aag	5/6	1	2	FACETS	0.519	0.46	0.582	0.519	0.46	0.582	SUBCLONAL	1	TRUE	1	0.760842690743831	2		358	415	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932149	36932149	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	15	508	0	ENST00000361632.4:c.2320C>A	p.Gln774Lys	p.Q774K	ENST00000361632		774	Cag/Aag	16/16	1	2	FACETS	0.164	0.12	0.218	0.164	0.12	0.218	SUBCLONAL	1	TRUE	1	0.760842690743831	2		508	240	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265808	16265808	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	25	337	0	ENST00000375759.3:c.10881G>C	p.Gln3627His	p.Q3627H	ENST00000375759	NM_015001.2	3627	caG/caC	15/15	1	2	FACETS	0.27	0.214	0.335	0.27	0.214	0.335	SUBCLONAL	1	TRUE	1	0.760842690743831	2		337	243	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020895	26020895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	28	569	0	ENST00000357647.3:c.178G>A	p.Glu60Lys	p.E60K	ENST00000357647	NM_003529.2	60	Gaa/Aaa	1/1	0.760842690743831	1	FACETS	0.124	0.099	0.153	0.124	0.099	0.153	SUBCLONAL	1	TRUE	0	0.760842690743831	1		569	368	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14016034	14016034	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	77	312	0	ENST00000311895.7:c.354C>G	p.Phe118Leu	p.F118L	ENST00000311895	NM_005236.2	118	ttC/ttG	2/11	1	2	FACETS	0.639	0.565	0.715	0.639	0.565	0.715	SUBCLONAL	1	TRUE	1	0.760842690743831	2		312	317	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50757260	50757260	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	137	356	0	ENST00000307179.4:c.558G>C	p.Lys186Asn	p.K186N	ENST00000307179		186	aaG/aaC	7/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.760842690743831	2		356	285	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651981	36651981	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	56	467	0	ENST00000244741.5:c.103G>C	p.Asp35His	p.D35H	ENST00000244741	NM_000389.4	35	Gat/Cat	2/3	0.760842690743831	1	FACETS	0.47	0.409	0.535	0.47	0.409	0.535	SUBCLONAL	1	TRUE	0	0.760842690743831	1		467	194	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212197	5212197	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	33	448	0	ENST00000357368.4:c.4834G>C	p.Glu1612Gln	p.E1612Q	ENST00000357368	NM_002850.3	1612	Gag/Cag	32/38	0.449188320927048	1	FACETS	0.311	0.256	0.371	0.311	0.256	0.371	INDETERMINATE	1	TRUE	0	0.760842690743831	1		448	173	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752797	57752797	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	33	392	0	ENST00000274289.3:c.1131C>G	p.Asp377Glu	p.D377E	ENST00000274289	NM_006622.3	377	gaC/gaG	8/14	0.227614692399494	3	FACETS	0.389	0.317	0.469	0.194	0.158	0.235	INDETERMINATE	1	TRUE	1	0.760842690743831	3		392	308	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80088610	80088610	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	66	372	0	ENST00000265081.6:c.2602G>A	p.Asp868Asn	p.D868N	ENST00000265081	NM_002439.4	868	Gat/Aat	19/24	0.227614692399494	3	FACETS	0.651	0.568	0.74	0.325	0.284	0.37	INDETERMINATE	1	TRUE	1	0.760842690743831	3		372	368	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223048	5223048	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	65	475	0	ENST00000357368.4:c.2755G>T	p.Glu919Ter	p.E919*	ENST00000357368	NM_002850.3	919	Gag/Tag	18/38	0.449188320927048	1	FACETS	0.756	0.675	0.838	0.756	0.675	0.838	INDETERMINATE	1	TRUE	0	0.760842690743831	1		475	140	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74000799	74000799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	126	492	0	ENST00000318443.5:c.1489G>A	p.Glu497Lys	p.E497K	ENST00000318443	NM_001024736.1	497	Gag/Aag	7/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.760842690743831	2		492	256	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526236	31526236	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	97	422	0	ENST00000344624.3:c.804T>A	p.Asp268Glu	p.D268E	ENST00000344624		268	gaT/gaA	2/33	0.508076727596781	4	FACETS	1	0.963	1	0.386	0.346	0.427	CLONAL	1	TRUE	1	0.760842690743831	4		422	388	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80160727	80160727	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs959058934	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	27	353	0	ENST00000265081.6:c.3096C>G	p.Phe1032Leu	p.F1032L	ENST00000265081	NM_002439.4	1032	ttC/ttG	22/24	0.227614692399494	3	FACETS	0.274	0.218	0.338	0.137	0.109	0.169	INDETERMINATE	1	TRUE	1	0.760842690743831	3		353	358	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29197739	29197739	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	43	435	0	ENST00000240100.2:c.455C>A	p.Ser152Tyr	p.S152Y	ENST00000240100	NM_001394.6	152	tCc/tAc	2/4	0.760842690743831	1	FACETS	0.511	0.437	0.59	0.511	0.437	0.59	SUBCLONAL	1	TRUE	0	0.760842690743831	1		435	137	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945674	38945674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1050685229	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	169	362	0	ENST00000357387.3:c.4552G>A	p.Asp1518Asn	p.D1518N	ENST00000357387	NM_152756.3	1518	Gat/Aat	34/38	0.508076727596781	4	FACETS	1	0.99	1	0.491	0.454	0.529	CLONAL	1	TRUE	1	0.760842690743831	4		362	531	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227896	123227896	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	41	130	0	ENST00000218089.9:c.3607G>C	p.Asp1203His	p.D1203H	ENST00000218089	NM_001042749.1	1203	Gat/Cat	33/35	1	1	FACETS	0.371	0.313	0.434	0.371	0.313	0.434	SUBCLONAL	1	TRUE	0	0.760842690743831	1		130	180	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989098	41989098	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	144	485	0	ENST00000219905.7:c.1890G>C	p.Lys630Asn	p.K630N	ENST00000219905	NM_001164273.1	630	aaG/aaC	3/24	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.760842690743831	2		485	291	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906633	32906633	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	164	399	0	ENST00000380152.3:c.1018G>C	p.Glu340Gln	p.E340Q	ENST00000380152		340	Gaa/Caa	10/27	0.760842690743831	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.760842690743831	1		399	249	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830922	156830922	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	62	404	0	ENST00000524377.1:c.196G>C	p.Glu66Gln	p.E66Q	ENST00000524377	NM_002529.3	66	Gag/Cag	1/17	0.760842690743831	3	FACETS	0.934	0.816	1	0.467	0.408	0.529	CLONAL	1	TRUE	1	0.760842690743831	3		404	241	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124487023	124487023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	22	262	0	ENST00000357628.3:c.979G>A	p.Glu327Lys	p.E327K	ENST00000357628	NM_015450.2	327	Gaa/Aaa	12/19	0.760842690743831	1	FACETS	0.199	0.155	0.249	0.199	0.155	0.249	SUBCLONAL	1	TRUE	0	0.760842690743831	1		262	180	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263961	16263961	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	21	487	0	ENST00000375759.3:c.10330C>A	p.Pro3444Thr	p.P3444T	ENST00000375759	NM_015001.2	3444	Cca/Aca	12/15	1	2	FACETS	0.174	0.134	0.221	0.174	0.134	0.221	SUBCLONAL	1	TRUE	1	0.760842690743831	2		487	317	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23640584	23640584	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	111	312	0	ENST00000261584.4:c.2527G>A	p.Glu843Lys	p.E843K	ENST00000261584	NM_024675.3	843	Gag/Aag	6/13	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.760842690743831	2		312	268	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976576	18976576	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	10	433	0	ENST00000262803.5:c.3226G>A	p.Glu1076Lys	p.E1076K	ENST00000262803	NM_002911.3	1076	Gag/Aag	22/24	1	2	FACETS	0.158	0.107	0.222	0.158	0.107	0.222	SUBCLONAL	1	TRUE	1	0.760842690743831	2		433	166	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205127	38205127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760270480	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	171	401	0	ENST00000317025.8:c.563C>T	p.Ser188Leu	p.S188L	ENST00000317025	NM_023034.1	188	tCa/tTa	2/24	0.227614692399494	3	FACETS	0.762	0.71	0.815	0.762	0.71	0.815	INDETERMINATE	2	TRUE	1	0.760842690743831	3		401	407	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259110	16259110	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	56	525	0	ENST00000375759.3:c.6375G>C	p.Glu2125Asp	p.E2125D	ENST00000375759	NM_015001.2	2125	gaG/gaC	11/15	1	2	FACETS	0.447	0.385	0.514	0.447	0.385	0.514	SUBCLONAL	1	TRUE	1	0.760842690743831	2		525	329	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670622	67670622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1264086135	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	108	404	0	ENST00000264010.4:c.1867G>A	p.Glu623Lys	p.E623K	ENST00000264010	NM_006565.3	623	Gag/Aag	11/12	0.760842690743831	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.760842690743831	1		404	142	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205331	38205331	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1257561902	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	34	493	0	ENST00000317025.8:c.359G>C	p.Arg120Thr	p.R120T	ENST00000317025	NM_023034.1	120	aGa/aCa	2/24	0.227614692399494	3	FACETS	0.287	0.234	0.346	0.143	0.117	0.173	INDETERMINATE	1	TRUE	1	0.760842690743831	3		493	430	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40739806	40739806	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	32	414	0	ENST00000392038.2:c.1419C>G	p.Phe473Leu	p.F473L	ENST00000392038	NM_001626.4	473	ttC/ttG	14/14	1	2	FACETS	0.447	0.366	0.537	0.447	0.366	0.537	SUBCLONAL	1	TRUE	1	0.760842690743831	2		414	188	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551868	150551868	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	24	422	0	ENST00000369026.2:c.139G>C	p.Glu47Gln	p.E47Q	ENST00000369026	NM_021960.4	47	Gag/Cag	1/3	0.760842690743831	3	FACETS	0.243	0.19	0.304	0.122	0.095	0.152	SUBCLONAL	1	TRUE	1	0.760842690743831	3		422	358	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266517	115266517	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	143	345	0	ENST00000438362.2:c.1998G>C	p.Glu666Asp	p.E666D	ENST00000438362	NM_001242891.1	666	gaG/gaC	16/20	0.760842690743831	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.760842690743831	1		345	210	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485740	40485740	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	125	413	0	ENST00000264657.5:c.1000G>C	p.Asp334His	p.D334H	ENST00000264657	NM_139276.2	334	Gac/Cac	10/24	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.760842690743831	2		413	273	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0049492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	23	268	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.572217751151664	4	FACETS	0.828	0.667	1	0.828	0.667	1	CLONAL	2	FALSE	2	0.658266890600849	4		268	70	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0049492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	332	522	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.658266890600849	5	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	FALSE	2	0.658266890600849	5		522	629	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059194	27059194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	101	341	0	ENST00000324856.7:c.1831C>T	p.Gln611Ter	p.Q611*	ENST00000324856	NM_006015.4	611	Cag/Tag	4/20	0.516513300325778	4	FACETS	0.998	0.908	1	0.998	0.908	1	CLONAL	2	FALSE	2	0.658266890600849	4		341	255	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874147	151874148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs747256476	NA	P-0049492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	50	523	9	ENST00000262189.6:c.8390dup	p.Glu2798GlyfsTer11	p.E2798Gfs*11	ENST00000262189	NM_170606.2	2797	aag/aaAg	38/59	0.516513300325778	4	FACETS	1	0.958	1	0.666	0.574	0.765	CLONAL	1	FALSE	2	0.658266890600849	4		532	189	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961818	15961818	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs542449256	NA	P-0049492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	117	459	1	ENST00000268712.3:c.5977C>T	p.Gln1993Ter	p.Q1993*	ENST00000268712	NM_006311.3	1993	Cag/Tag	38/46	0.617940619467845	2	FACETS	0.831	0.769	0.892	0.831	0.769	0.892	CLONAL	2	FALSE	0	0.658266890600849	2		460	214	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233111	46233111	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0049492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	66	374	0	ENST00000334344.6:c.1331-1G>C		p.X444_splice	ENST00000334344	NM_152641.2	444			0.516513300325778	4	FACETS	0.853	0.754	0.955	0.853	0.754	0.955	CLONAL	2	FALSE	2	0.658266890600849	4		374	195	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640028	3640028	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	137	497	0	ENST00000294008.3:c.3611C>A	p.Ser1204Tyr	p.S1204Y	ENST00000294008	NM_032444.2	1204	tCc/tAc	12/15	0.516513300325778	4	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	FALSE	2	0.658266890600849	4		497	331	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31239786	31239786	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs769594453	NA	P-0049492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	187	407	0	ENST00000376228.5:c.63G>C	p.Glu21Asp	p.E21D	ENST00000376228	NM_002117.5	21	gaG/gaC	1/8	0.572217751151664	4	FACETS	0.929	0.875	0.983	1	0.992	1	CLONAL	3	FALSE	2	0.658266890600849	4		407	338	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47679261	47679261	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	118	389	0	ENST00000347630.2:c.946C>G	p.Gln316Glu	p.Q316E	ENST00000347630	NM_001007230.1	316	Cag/Gag	10/11	0.658266890600849	5	FACETS	0.842	0.766	0.922	0.561	0.51	0.615	CLONAL	2	FALSE	2	0.658266890600849	5		389	423	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314613	30314613	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	139	488	0	ENST00000262643.3:c.1162C>A	p.Pro388Thr	p.P388T	ENST00000262643	NM_001238.2	388	Cct/Act	12/12	0.572217751151664	4	FACETS	0.995	0.918	1	0.995	0.918	1	CLONAL	2	FALSE	2	0.658266890600849	4		488	352	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578242	7578242	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	149	570	0	ENST00000269305.4:c.607del	p.Val203TrpfsTer44	p.V203Wfs*44	ENST00000269305	NM_001126112.2	203	Gtg/tg	6/11	0.617940619467845	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	FALSE	0	0.658266890600849	2		570	219	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128206865	128206865	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	79	398	0	ENST00000265960.3:c.1358T>G	p.Phe453Cys	p.F453C	ENST00000265960	NM_001006617.1	453	tTt/tGt	11/12	0.658266890600849	12	FACETS	1	0.969	1			1	CLONAL	1	FALSE	NA	0.658266890600849	12		398	776	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224280	36224280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs907427931	NA	P-0049492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	141	468	0	ENST00000222270.7:c.6830G>A	p.Arg2277His	p.R2277H	ENST00000222270	NM_014727.1	2277	cGc/cAc	28/37	0.572217751151664	4	FACETS	0.963	0.888	1	0.963	0.888	1	CLONAL	2	FALSE	2	0.658266890600849	4		468	369	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239387	123239387	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	110	417	0	ENST00000358487.5:c.2450G>T	p.Gly817Val	p.G817V	ENST00000358487	NM_000141.4	817	gGc/gTc	18/18	0.516513300325778	4	FACETS	0.997	0.91	1	0.997	0.91	1	CLONAL	2	FALSE	2	0.658266890600849	4		417	278	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99482493	99482493	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	145	441	0	ENST00000268035.6:c.3361G>T	p.Asp1121Tyr	p.D1121Y	ENST00000268035	NM_000875.3	1121	Gac/Tac	18/21	0.285988058090595	5	FACETS	1	0.984	1	0.831	0.769	0.895	INDETERMINATE	2	FALSE	2	0.658266890600849	5		441	351	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962786	2962786	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	95	335	0	ENST00000396946.4:c.2122G>T	p.Glu708Ter	p.E708*	ENST00000396946	NM_032415.4	708	Gag/Tag	16/25	0.516513300325778	4	FACETS	0.981	0.889	1	0.981	0.889	1	CLONAL	2	FALSE	2	0.658266890600849	4		335	244	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426678	212426678	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	115	568	0	ENST00000342788.4:c.2437G>C	p.Asp813His	p.D813H	ENST00000342788	NM_005235.2	813	Gat/Cat	20/28	0.297225679247245	4	FACETS	1	0.973	1	1	0.973	1	INDETERMINATE	2	FALSE	2	0.658266890600849	4		568	254	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637559	23637559	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	121	356	0	ENST00000261584.4:c.2746G>A	p.Glu916Lys	p.E916K	ENST00000261584	NM_024675.3	916	Gag/Aag	7/13	0.516513300325778	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	FALSE	2	0.658266890600849	4		356	283	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197085	26197085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	198	630	0	ENST00000356476.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000356476		132	Cgt/Tgt	1/1	0.572217751151664	4	FACETS	0.922	0.861	0.984	0.922	0.861	0.984	CLONAL	2	FALSE	2	0.658266890600849	4		630	541	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307484	118307484	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	119	392	0	ENST00000534358.1:c.257C>A	p.Ser86Ter	p.S86*	ENST00000534358	NM_005933.3	86	tCg/tAg	1/36	0.297225679247245	4	FACETS	1	0.953	1	1	0.953	1	INDETERMINATE	2	FALSE	2	0.658266890600849	4		392	284	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410745	63410745	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	100	522	0	ENST00000330258.3:c.2422A>T	p.Thr808Ser	p.T808S	ENST00000330258	NM_152424.3	808	Acc/Tcc	2/2	0.658266890600849	2	FACETS	0.932	0.862	1	0.932	0.862	1	CLONAL	2	FALSE	0	0.658266890600849	2		522	163	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635695	47635695	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0049492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	45	352	0	ENST00000233146.2:c.366+1G>C		p.X122_splice	ENST00000233146	NM_000251.2	122			0.297225679247245	4	FACETS	1	0.94	1	0.609	0.519	0.706	INDETERMINATE	1	FALSE	2	0.658266890600849	4		352	186	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491348	2491348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1310989468	NA	P-0049492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	158	518	0	ENST00000355716.4:c.391G>A	p.Asp131Asn	p.D131N	ENST00000355716	NM_003820.2	131	Gac/Aac	4/8	0.516513300325778	4	FACETS	0.95	0.88	1	0.95	0.88	1	CLONAL	2	FALSE	2	0.658266890600849	4		518	419	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813467	32813467	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	141	435	0	ENST00000354258.4:c.2316C>G	p.Ile772Met	p.I772M	ENST00000354258	NM_000593.5	772	atC/atG	11/11	0.572217751151664	4	FACETS	0.932	0.859	1	0.932	0.859	1	CLONAL	2	FALSE	2	0.658266890600849	4		435	381	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89839718	89839718	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	173	456	0	ENST00000389301.3:c.1975G>C	p.Glu659Gln	p.E659Q	ENST00000389301	NM_000135.2	659	Gag/Cag	22/43	0.622771634901038	2	FACETS	0.935	0.882	0.987	0.935	0.882	0.987	CLONAL	2	FALSE	0	0.658266890600849	2		456	281	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73110178	73110178	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	59	271	0	ENST00000356692.5:c.386T>C	p.Val129Ala	p.V129A	ENST00000356692		129	gTg/gCg	5/9	0.622771634901038	2	FACETS	0.954	0.862	1	0.954	0.862	1	CLONAL	2	FALSE	0	0.658266890600849	2		271	94	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394958	394958	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	151	479	0	ENST00000380956.4:c.354C>G	p.Ile118Met	p.I118M	ENST00000380956	NM_001195286.1	118	atC/atG	3/9	0.572217751151664	4	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	FALSE	2	0.658266890600849	4		479	380	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0050988-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	78	451	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	0.159895942167021	2	FACETS	0.868	0.769	0.973	0.868	0.769	0.973	CLONAL	2	FALSE	0	0.261952103378702	2		451	343	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209247	98209247	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050988-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	36	601	0	ENST00000331920.6:c.4291G>C	p.Glu1431Gln	p.E1431Q	ENST00000331920	NM_000264.3	1431	Gag/Cag	23/24	1	2	FACETS	0.616	0.506	0.739	0.616	0.506	0.739	SUBCLONAL	1	FALSE	1	0.261952103378702	2		601	446	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578179	7578179	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1555525707	NA	P-0050988-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	11	638	0	ENST00000269305.4:c.670G>A	p.Glu224Lys	p.E224K	ENST00000269305	NM_001126112.2	224	Gag/Aag	6/11	1	2	FACETS	0.163	0.112	0.228	0.163	0.112	0.228	SUBCLONAL	1	FALSE	1	0.261952103378702	2		638	515	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949163	44949163	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050988-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	31	420	0	ENST00000377967.4:c.3724G>T	p.Gly1242Cys	p.G1242C	ENST00000377967	NM_021140.2	1242	Ggt/Tgt	25/29	1	2	FACETS	0.698	0.565	0.848	0.698	0.565	0.848	SUBCLONAL	1	FALSE	1	0.261952103378702	2		420	339	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80168986	80168986	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050988-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	22	513	0	ENST00000265081.6:c.3182G>C	p.Arg1061Thr	p.R1061T	ENST00000265081	NM_002439.4	1061	aGa/aCa	23/24	1	2	FACETS	0.463	0.358	0.584	0.463	0.358	0.584	SUBCLONAL	1	FALSE	1	0.261952103378702	2		513	363	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042329	42042329	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050988-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	38	652	0	ENST00000219905.7:c.6524G>A	p.Arg2175Lys	p.R2175K	ENST00000219905	NM_001164273.1	2175	aGa/aAa	17/24	1	2	FACETS	0.464	0.383	0.556	0.464	0.383	0.556	SUBCLONAL	1	FALSE	1	0.261952103378702	2		652	625	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514822	44514822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050988-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	31	582	0	ENST00000291552.4:c.425C>T	p.Ala142Val	p.A142V	ENST00000291552	NM_006758.2	142	gCc/gTc	6/8	1	2	FACETS	0.403	0.324	0.491	0.403	0.324	0.491	SUBCLONAL	1	FALSE	1	0.261952103378702	2		582	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578400	7578400	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs751477326	NA	P-0051960-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	88	447	0	ENST00000269305.4:c.530C>G	p.Pro177Arg	p.P177R	ENST00000269305	NM_001126112.2	177	cCc/cGc	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		447	417	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907792	76907792	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051960-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	27	168	0	ENST00000373344.5:c.4369G>T	p.Glu1457Ter	p.E1457*	ENST00000373344	NM_000489.3	1457	Gag/Tag	15/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		168	134	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714412	40714412	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051960-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	74	374	0	ENST00000373198.4:c.3985G>A	p.Glu1329Lys	p.E1329K	ENST00000373198	NM_133170.3	1329	Gag/Aag	29/32	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		374	402	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434073	49434074	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1555192051	NA	P-0051960-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	27	426	0	ENST00000301067.7:c.7479dup	p.Phe2494ValfsTer12	p.F2494Vfs*12	ENST00000301067	NM_003482.3	2493	-/G	31/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		426	360	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498492	89498492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051960-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	47	364	0	ENST00000336596.2:c.2464G>A	p.Glu822Lys	p.E822K	ENST00000336596	NM_005233.5	822	Gag/Aag	14/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		364	208	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912785	100912785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051960-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	19	307	0	ENST00000325455.5:c.2537C>T	p.Ser846Leu	p.S846L	ENST00000325455	NM_001202474.3	846	tCa/tTa	7/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		307	240	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568841	212568841	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051960-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	18	324	0	ENST00000342788.4:c.1277G>T	p.Arg426Ile	p.R426I	ENST00000342788	NM_005235.2	426	aGa/aTa	11/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		324	170	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950720	38950720	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051960-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	34	379	0	ENST00000357387.3:c.3230G>A	p.Gly1077Glu	p.G1077E	ENST00000357387	NM_152756.3	1077	gGa/gAa	31/38	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		379	227	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231077	98231077	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051960-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	117	427	0	ENST00000331920.6:c.2206G>T	p.Ala736Ser	p.A736S	ENST00000331920	NM_000264.3	736	Gct/Tct	14/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		427	358	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939091	48939091	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051960-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	22	229	0	ENST00000267163.4:c.923C>G	p.Ser308Cys	p.S308C	ENST00000267163	NM_000321.2	308	tCt/tGt	9/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		229	145	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527734	157527734	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051960-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	35	426	0	ENST00000346085.5:c.5459A>T	p.Gln1820Leu	p.Q1820L	ENST00000346085	NM_020732.3	1820	cAg/cTg	20/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		426	357	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771154	161771154	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051960-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	31	314	0	ENST00000366898.1:c.1375G>T	p.Gly459Trp	p.G459W	ENST00000366898	NM_004562.2	459	Ggg/Tgg	12/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		314	293	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212252696	212252696	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051960-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	29	369	2	ENST00000342788.4:c.3157C>A	p.Pro1053Thr	p.P1053T	ENST00000342788	NM_005235.2	1053	Cct/Act	26/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		371	203	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879272	56879272	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0051960-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	70	332	0	ENST00000519728.1:c.791-2A>T		p.X264_splice	ENST00000519728	NM_002350.3	264			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		332	352	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162735793	162735793	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051960-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	23	435	0	ENST00000367921.3:c.1102G>A	p.Ala368Thr	p.A368T	ENST00000367921	NM_006182.2	368	Gct/Act	10/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		435	302	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858152	40858152	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051960-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	36	355	0	ENST00000428826.2:c.1712A>T	p.Gln571Leu	p.Q571L	ENST00000428826		571	cAa/cTa	16/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		355	416	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282725	1282725	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051960-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	101	420	0	ENST00000310581.5:c.1588C>G	p.Pro530Ala	p.P530A	ENST00000310581	NM_198253.2	530	Ccg/Gcg	3/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		420	386	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141453	11141453	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051960-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	68	430	0	ENST00000358026.2:c.3430G>T	p.Glu1144Ter	p.E1144*	ENST00000358026	NM_001128849.1	1144	Gag/Tag	25/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		430	352	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279366	38279366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051960-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	46	447	0	ENST00000425967.3:c.1123G>T	p.Gly375Cys	p.G375C	ENST00000425967	NM_001174067.1	375	Ggt/Tgt	9/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		447	291	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222200	2222200	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051960-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	90	512	0	ENST00000398665.3:c.3033del	p.Gly1013ValfsTer55	p.G1013Vfs*55	ENST00000398665	NM_032482.2	1011	cGg/cg	24/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		512	370	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306511	41306511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051960-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	20	292	0	ENST00000373198.4:c.1148G>A	p.Cys383Tyr	p.C383Y	ENST00000373198	NM_133170.3	383	tGt/tAt	7/32	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		292	307	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465603	99465603	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1391007042	NA	P-0051960-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	40	405	0	ENST00000268035.6:c.2428G>T	p.Ala810Ser	p.A810S	ENST00000268035	NM_000875.3	810	Gct/Tct	11/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		405	300	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422042	81422042	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051960-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	62	389	0	ENST00000298171.2:c.18G>C	p.Leu6Phe	p.L6F	ENST00000298171	NM_000369.2	6	ttG/ttC	1/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		389	327	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771144	161771144	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051960-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	28	307	0	ENST00000366898.1:c.1385G>C	p.Trp462Ser	p.W462S	ENST00000366898	NM_004562.2	462	tGg/tCg	12/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		307	259	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858660	9858660	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051960-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	18	483	0	ENST00000330684.3:c.2741G>T	p.Arg914Ile	p.R914I	ENST00000330684	NM_001134407.1	914	aGa/aTa	13/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		483	256	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245316	53245316	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051960-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	36	194	0	ENST00000375401.3:c.721del	p.Ala241GlnfsTer5	p.A241Qfs*5	ENST00000375401	NM_004187.3	241	Gca/ca	6/26	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		194	147	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419971	41419971	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051960-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	33	433	0	ENST00000373198.4:c.350C>A	p.Pro117Gln	p.P117Q	ENST00000373198	NM_133170.3	117	cCa/cAa	3/32	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		433	421	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306996	65306997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052411-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	374	543	7	ENST00000342505.4:c.2580dup	p.Pro861ThrfsTer4	p.P861Tfs*4	ENST00000342505	NM_002227.2	860	-/A	19/25	0.874158306892142	1	FACETS	0.894	0.863	0.924	0.894	0.863	0.924	CLONAL	1	TRUE	0	0.874158306892142	1		550	539	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0052411-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	417	378	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.874158306892142	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.874158306892142	1		378	518	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435252	56435252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs538022572	NA	P-0052411-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	374	689	1	ENST00000407977.2:c.1885G>A	p.Ala629Thr	p.A629T	ENST00000407977		629	Gcc/Acc	9/10	0.783847385210115	3	FACETS	0.988	0.938	1	0.494	0.469	0.52	CLONAL	1	TRUE	1	0.874158306892142	3		690	1244	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360550	70360550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052411-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	348	532	0	ENST00000374080.3:c.6110G>A	p.Gly2037Asp	p.G2037D	ENST00000374080		2037	gGc/gAc	42/45	1	2	FACETS	0.927	0.882	0.973	0.927	0.882	0.973	CLONAL	1	TRUE	1	0.874158306892142	2		532	859	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946172	71946172	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs746052590	NA	P-0052411-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	325	506	1	ENST00000298229.2:c.2428C>A	p.Leu810Met	p.L810M	ENST00000298229	NM_001567.3	810	Ctg/Atg	22/28	0.368227573995545	1	FACETS	0.661	0.631	0.692	0.661	0.631	0.692	INDETERMINATE	1	TRUE	0	0.874158306892142	1		507	633	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265175	5265175	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052411-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	37	552	0	ENST00000357368.4:c.412G>C	p.Asp138His	p.D138H	ENST00000357368	NM_002850.3	138	Gac/Cac	5/38	1	2	FACETS	0.115	0.094	0.138	0.115	0.094	0.138	SUBCLONAL	1	TRUE	1	0.874158306892142	2		552	737	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631718	67631725	+	frameshift_variant	Frame_Shift_Del	DEL	GTATATGT	GTATATGT	-	novel	NA	P-0052411-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	69	495	0	ENST00000272342.5:c.1905_1912del	p.Ser635ArgfsTer4	p.S635Rfs*4	ENST00000272342	NM_019002.3	635	aGTATATGT/a	5/6	0.617331993191042	3	FACETS	0.235	0.204	0.269	0.118	0.102	0.135	SUBCLONAL	1	TRUE	1	0.874158306892142	3		495	964	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053061-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	80	350	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.843	0.744	0.949	0.843	0.744	0.949	CLONAL	1	TRUE	1	0.352707060450956	2		350	538	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0053061-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	55	268	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.352707060450956	2		268	299	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0053061-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	150	508	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.943	0.862	1	0.943	0.862	1	CLONAL	1	TRUE	1	0.352707060450956	2		508	902	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910507	32910507	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053061-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	113	468	0	ENST00000380152.3:c.2015G>C	p.Arg672Thr	p.R672T	ENST00000380152		672	aGa/aCa	11/27	0.352707060450956	3	FACETS	1	0.958	1	0.559	0.504	0.618	CLONAL	1	TRUE	1	0.352707060450956	3		468	674	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772092	135772092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053061-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	139	607	0	ENST00000298552.3:c.3025G>A	p.Glu1009Lys	p.E1009K	ENST00000298552	NM_001162426.1	1009	Gaa/Aaa	23/23	0.352707060450956	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.352707060450956	1		607	622	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099397	27099397	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053061-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	123	570	0	ENST00000324856.7:c.3634C>T	p.Gln1212Ter	p.Q1212*	ENST00000324856	NM_006015.4	1212	Cag/Tag	14/20	0.32018704555853	1	FACETS	0.915	0.829	1	0.915	0.829	1	CLONAL	1	TRUE	0	0.352707060450956	1		570	628	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870260	44870260	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053061-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	83	351	0	ENST00000377967.4:c.439C>T	p.Gln147Ter	p.Q147*	ENST00000377967	NM_021140.2	147	Cag/Tag	5/29	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.352707060450956	2		351	450	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948640	71948640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053061-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	183	724	0	ENST00000298229.2:c.3352G>A	p.Asp1118Asn	p.D1118N	ENST00000298229	NM_001567.3	1118	Gac/Aac	26/28	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.352707060450956	2		724	1017	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434094	121434094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1206311303	NA	P-0053061-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	165	646	0	ENST00000257555.6:c.985G>A	p.Glu329Lys	p.E329K	ENST00000257555		329	Gag/Aag	5/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.352707060450956	2		646	855	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36024580	36024580	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0053061-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	134	573	0	ENST00000358208.4:c.569C>G	p.Ser190Ter	p.S190*	ENST00000358208		190	tCa/tGa	6/12	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.352707060450956	2		573	754	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875639	35875639	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053061-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	132	442	0	ENST00000303115.3:c.826C>G	p.Leu276Val	p.L276V	ENST00000303115	NM_002185.3	276	Ctc/Gtc	7/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.352707060450956	2		442	590	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942017	44942018	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0053061-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	123	425	0	ENST00000377967.4:c.3268_3269dup	p.Ser1091TyrfsTer14	p.S1091Yfs*14	ENST00000377967	NM_021140.2	1089	-/CT	22/29	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.352707060450956	2		425	616	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124487023	124487023	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053061-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	64	343	0	ENST00000357628.3:c.979G>C	p.Glu327Gln	p.E327Q	ENST00000357628	NM_015450.2	327	Gaa/Caa	12/19	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.352707060450956	2		343	345	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0053890-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	100	0	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.820595949127159	2		0	219	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0053890-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	150	508	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.978	0.905	1	0.978	0.905	1	CLONAL	1	TRUE	1	0.820595949127159	2		508	374	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195112	123195112	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053890-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	158	353	0	ENST00000218089.9:c.1455G>A	p.Trp485Ter	p.W485*	ENST00000218089	NM_001042749.1	485	tgG/tgA	16/35	1	2	FACETS	0.944	0.875	1	0.944	0.875	1	CLONAL	1	TRUE	1	0.820595949127159	2		353	408	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442667	442667	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053890-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	236	436	0	ENST00000399788.2:c.1639G>A	p.Glu547Lys	p.E547K	ENST00000399788	NM_001042603.1	547	Gag/Aag	12/28	1	2	FACETS	0.977	0.919	1	0.977	0.919	1	CLONAL	1	TRUE	1	0.820595949127159	2		436	589	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427447	49427447	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053890-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	170	556	1	ENST00000301067.7:c.11041C>T	p.Gln3681Ter	p.Q3681*	ENST00000301067	NM_003482.3	3681	Cag/Tag	39/54	1	2	FACETS	0.921	0.855	0.987	0.921	0.855	0.987	CLONAL	1	TRUE	1	0.820595949127159	2		557	450	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427964	49427965	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053890-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	164	412	0	ENST00000301067.7:c.10625dup	p.Cys3543ValfsTer13	p.C3543Vfs*13	ENST00000301067	NM_003482.3	3542	ctg/ctTg	38/54	1	2	FACETS	0.902	0.837	0.969	0.902	0.837	0.969	CLONAL	1	TRUE	1	0.820595949127159	2		412	443	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848560	151848565	+	inframe_deletion	In_Frame_Del	DEL	CCGCAC	CCGCAC	-	novel	NA	P-0053890-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	180	410	0	ENST00000262189.6:c.12628_12633del	p.Val4210_Arg4211del	p.V4210_R4211del	ENST00000262189	NM_170606.2	4210	GTGCGG/-	50/59	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.820595949127159	2		410	412	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998939	100998939	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054557-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	99	641	0	ENST00000325455.5:c.863C>T	p.Pro288Leu	p.P288L	ENST00000325455	NM_001202474.3	288	cCg/cTg	1/8	0.464585103666239	2	FACETS	0.547	0.491	0.605	0.273	0.245	0.303	INDETERMINATE	1	TRUE	0	0.883011754198726	2		641	410	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158414	108158414	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054557-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	324	421	0	ENST00000278616.4:c.4081C>G	p.Gln1361Glu	p.Q1361E	ENST00000278616	NM_000051.3	1361	Cag/Gag	27/63	0.464585103666239	2	FACETS	0.826	0.797	0.854	0.826	0.797	0.854	INDETERMINATE	2	TRUE	0	0.883011754198726	2		421	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0054557-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	428	324	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.887910953399557	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.883011754198726	3		324	456	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984220	7984220	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1373779217	NA	P-0054557-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	206	562	0	ENST00000319144.4:c.509G>C	p.Arg170Pro	p.R170P	ENST00000319144	NM_001139.2	170	cGc/cCc	4/15	0.887910953399557	3	FACETS	1	0.988	1	0.417	0.39	0.444	CLONAL	1	TRUE	0	0.883011754198726	3		562	538	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654802	29654802	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1436590774	NA	P-0054557-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	218	583	0	ENST00000356175.3:c.5491G>A	p.Gly1831Arg	p.G1831R	ENST00000356175	NM_000267.3	1831	Ggg/Agg	37/57	1	2	FACETS	0.963	0.904	1	0.963	0.904	1	CLONAL	1	TRUE	1	0.883011754198726	2		583	513	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214067	36214067	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054557-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	235	581	0	ENST00000222270.7:c.2893C>T	p.Arg965Ter	p.R965*	ENST00000222270	NM_014727.1	965	Cga/Tga	6/37	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.883011754198726	2		581	498	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37622747	37622747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141308774	NA	P-0054557-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	231	519	0	ENST00000249071.6:c.545C>T	p.Thr182Met	p.T182M	ENST00000249071	NM_002872.4	182	aCg/aTg	6/7	0.887910953399557	2	FACETS	1	0.994	1	0.733	0.698	0.767	CLONAL	1	TRUE	0	0.883011754198726	2		519	357	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191642	10191642	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054557-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	297	447	0	ENST00000256474.2:c.635G>T	p.Gly212Val	p.G212V	ENST00000256474	NM_000551.3	212	gGa/gTa	3/3	0.887910953399557	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.883011754198726	2		447	304	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155613	106155613	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054557-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	318	529	0	ENST00000380013.4:c.514A>T	p.Ser172Cys	p.S172C	ENST00000380013	NM_001127208.2	172	Agt/Tgt	3/11	0.52540632882843	1	FACETS	0.896	0.863	0.928	0.896	0.863	0.928	INDETERMINATE	1	TRUE	0	0.883011754198726	1		529	449	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903714	41903714	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054557-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	437	600	0	ENST00000372991.4:c.843del	p.Ser282AlafsTer22	p.S282Afs*22	ENST00000372991	NM_001760.3	281	acC/ac	5/5	0.887910953399557	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.883011754198726	2		600	486	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93973591	93973591	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054557-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	92	362	0	ENST00000369303.4:c.1785G>C	p.Glu595Asp	p.E595D	ENST00000369303	NM_004440.3	595	gaG/gaC	9/17	0.711259105283238	3	FACETS	0.713	0.638	0.793	0.357	0.319	0.397	SUBCLONAL	1	TRUE	1	0.883011754198726	3		362	421	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93973607	93973607	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054557-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	98	373	0	ENST00000369303.4:c.1769A>G	p.Gln590Arg	p.Q590R	ENST00000369303	NM_004440.3	590	cAa/cGa	9/17	0.711259105283238	3	FACETS	0.693	0.621	0.768	0.346	0.31	0.384	SUBCLONAL	1	TRUE	1	0.883011754198726	3		373	462	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647564	117647564	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054557-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	214	561	0	ENST00000368508.3:c.5380A>C	p.Asn1794His	p.N1794H	ENST00000368508	NM_002944.2	1794	Aat/Cat	33/43	0.711259105283238	3	FACETS	1	0.973	1	0.538	0.503	0.575	CLONAL	1	TRUE	1	0.883011754198726	3		561	649	SUCCESS
APC	324	MSKCC	GRCh37	5	112174268	112174268	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0054752-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	20	454	0	ENST00000257430.4:c.2977A>T	p.Lys993Ter	p.K993*	ENST00000257430	NM_000038.5	993	Aag/Tag	16/16	1	2	FACETS	0.6	0.459	0.764	0.6	0.459	0.764	SUBCLONAL	1	TRUE	1	0.24	2		454	278	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247243	153247243	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054752-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	13	410	0	ENST00000281708.4:c.1559A>G	p.Asp520Gly	p.D520G	ENST00000281708	NM_033632.3	520	gAt/gGt	10/12	1	2	FACETS	0.3	0.213	0.407	0.3	0.213	0.407	SUBCLONAL	1	TRUE	1	0.24	2		410	361	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87366908	87366908	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054752-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	30	346	0	ENST00000277120.3:c.1304C>T	p.Ala435Val	p.A435V	ENST00000277120		435	gCt/gTt	12/19	1	2	FACETS	1	0.813	1	1	0.813	1	CLONAL	1	TRUE	1	0.24	2		346	249	SUCCESS
APC	324	MSKCC	GRCh37	5	112175429	112175430	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCCACTCATGTTTAG	novel	NA	P-0054752-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	32	401	0	ENST00000257430.4:c.4140_4155dup	p.Arg1386ProfsTer5	p.R1386Pfs*5	ENST00000257430	NM_000038.5	1380	acc/aCCCCACTCATGTTTAGcc	16/16	1	2	FACETS	0.777	0.632	0.941	0.777	0.632	0.941	CLONAL	1	TRUE	1	0.24	2		401	343	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562888	21562888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759368766	NA	P-0055363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	122	694	1	ENST00000382592.4:c.1031C>T	p.Pro344Leu	p.P344L	ENST00000382592	NM_014572.2	344	cCg/cTg	4/8	0.47617399081707	4	FACETS	1	0.919	1	0.339	0.306	0.373	CLONAL	1	TRUE	1	0.55232490639288	4		695	675	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578529	7578612	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAAGC	AACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAAGC	-	novel	NA	P-0055363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	237	786	0	ENST00000269305.4:c.376-58_401del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	0.427196102915015	3	FACETS	1	0.987	1	0.762	0.72	0.804	CLONAL	2	TRUE	0	0.55232490639288	3		786	479	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562888	21562888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759368766	NA	P-0055363-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	67	694	1	ENST00000382592.4:c.1031C>T	p.Pro344Leu	p.P344L	ENST00000382592	NM_014572.2	344	cCg/cTg	4/8	0.241142707707774	3	FACETS	0.424	0.367	0.487	0.212	0.183	0.244	SUBCLONAL	1	TRUE	1	0.32	3		695	1145	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578529	7578612	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAAGC	AACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAAGC	-	novel	NA	P-0055363-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1286	146	786	0	ENST00000269305.4:c.376-58_401del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	1	2	FACETS	0.637	0.579	0.698	0.637	0.579	0.698	SUBCLONAL	1	TRUE	1	0.32	2		786	1432	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942685	48942685	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913301	NA	P-0056653-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	114	276	0	ENST00000267163.4:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000267163	NM_000321.2	358	Cga/Tga	11/27	0.373574531693217	2	FACETS	0.957	0.873	1	0.957	0.873	1	CLONAL	2	TRUE	0	0.373574531693217	2		276	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577524	7577524	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056859-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	221	295	0	ENST00000269305.4:c.757A>G	p.Thr253Ala	p.T253A	ENST00000269305	NM_001126112.2	253	Acc/Gcc	7/11	0.59571761739507	2	FACETS	0.951	0.901	1	0.951	0.901	1	CLONAL	2	TRUE	0	0.602230616598499	2		295	386	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107183	27107183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056859-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	168	351	0	ENST00000324856.7:c.6794C>T	p.Pro2265Leu	p.P2265L	ENST00000324856	NM_006015.4	2265	cCg/cTg	20/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.602230616598499	2		351	532	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643583	38643583	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056859-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	296	289	0	ENST00000299084.4:c.1053A>T	p.Lys351Asn	p.K351N	ENST00000299084	NM_152594.2	351	aaA/aaT	7/7	0.602230616598499	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.602230616598499	3		289	615	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934274	68934274	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056859-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	86	234	0	ENST00000288368.4:c.340G>T	p.Asp114Tyr	p.D114Y	ENST00000288368	NM_024870.2	114	Gac/Tac	4/40	0.428389872980493	3	FACETS	0.927	0.825	1	0.463	0.412	0.517	CLONAL	1	TRUE	1	0.602230616598499	3		234	401	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316389	14316389	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	2958	336	0	ENST00000256196.4:c.216A>C	p.Gln72His	p.Q72H	ENST00000256196		72	caA/caC	3/6	0.754673131202216	20	FACETS	1	0.997	1			1	CLONAL	19	TRUE	NA	0.754673131202216	20		336	3194	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631824	90631824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	173	457	0	ENST00000330062.3:c.529G>A	p.Asp177Asn	p.D177N	ENST00000330062	NM_002168.2	177	Gac/Aac	4/11	0.221620705074553	5	FACETS	0.764	0.706	0.823	0.305	0.282	0.33	INDETERMINATE	2	TRUE	0	0.754673131202216	5		457	640	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642722	3642722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	325	307	0	ENST00000294008.3:c.2305G>A	p.Glu769Lys	p.E769K	ENST00000294008	NM_032444.2	769	Gag/Aag	11/15	0.757069168992985	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.754673131202216	2		307	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750600586	NA	P-0057013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	527	375	1	ENST00000269305.4:c.413C>T	p.Ala138Val	p.A138V	ENST00000269305	NM_001126112.2	138	gCc/gTc	5/11	0.757069168992985	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.754673131202216	3		376	612	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213285	36213285	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	302	394	0	ENST00000222270.7:c.2482G>T	p.Glu828Ter	p.E828*	ENST00000222270	NM_014727.1	828	Gag/Tag	4/37	0.757069168992985	5	FACETS	1	0.987	1	0.751	0.712	0.792	CLONAL	2	TRUE	2	0.754673131202216	5		394	757	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393213	393213	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	132	340	0	ENST00000380956.4:c.61A>T	p.Asn21Tyr	p.N21Y	ENST00000380956	NM_001195286.1	21	Aac/Tac	2/9	0.757069168992985	5	FACETS	0.815	0.739	0.895			1	CLONAL	1	TRUE	NA	0.754673131202216	5		340	915	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004789	150004789	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	194	416	0	ENST00000253339.5:c.1436C>G	p.Ser479Cys	p.S479C	ENST00000253339		479	tCt/tGt	3/7	0.757069168992985	3	FACETS	1	0.983	1	0.586	0.545	0.628	CLONAL	1	TRUE	1	0.754673131202216	3		416	604	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559231	141559231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	386	378	0	ENST00000220592.5:c.1570G>A	p.Gly524Ser	p.G524S	ENST00000220592	NM_012154.3	524	Ggc/Agc	12/19	0.757069168992985	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.754673131202216	3		378	455	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760132	133760132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373527910	NA	P-0057013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	190	396	0	ENST00000318560.5:c.2455C>T	p.Arg819Trp	p.R819W	ENST00000318560	NM_005157.4	819	Cgg/Tgg	11/11	0.290800261054638	5	FACETS	1	0.985	1	0.793	0.742	0.846	INDETERMINATE	2	TRUE	2	0.754673131202216	5		396	451	SUCCESS
AR	367	MSKCC	GRCh37	X	66766228	66766228	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	323	159	0	ENST00000374690.3:c.1240C>A	p.Leu414Met	p.L414M	ENST00000374690	NM_000044.3	414	Ctg/Atg	1/8	0.660802597010896	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.754673131202216	2		159	357	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258990	153258995	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGGG	CTGGGG	A	novel	NA	P-0057013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	229	326	0	ENST00000281708.4:c.820_825delinsT	p.Pro274PhefsTer11	p.P274Ffs*11	ENST00000281708	NM_033632.3	274	CCCCAG/T	5/12	0.757069168992985	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.754673131202216	2		326	288	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259319	89259319	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	120	343	0	ENST00000336596.2:c.463A>G	p.Met155Val	p.M155V	ENST00000336596	NM_005233.5	155	Atg/Gtg	3/17	0.754673131202216	8	FACETS	0.951	0.857	1			1	CLONAL	1	TRUE	NA	0.754673131202216	8		343	1092	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576488	67576488	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	19	327	0	ENST00000274335.5:c.767A>C	p.Lys256Thr	p.K256T	ENST00000274335		256	aAa/aCa	5/15	0.757069168992985	3	FACETS	0.195	0.148	0.251	0.098	0.074	0.126	SUBCLONAL	1	TRUE	1	0.754673131202216	3		327	355	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194110	94194110	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773469981	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	170	381	0	ENST00000323929.3:c.1318G>A	p.Ala440Thr	p.A440T	ENST00000323929	NM_005591.3	440	Gca/Aca	12/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.920346251233543	2		381	361	SUCCESS
APC	324	MSKCC	GRCh37	5	112116551	112116551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748193367	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	169	487	2	ENST00000257430.4:c.596C>T	p.Ala199Val	p.A199V	ENST00000257430	NM_000038.5	199	gCg/gTg	6/16	1	2	FACETS	0.947	0.882	1	0.947	0.882	1	CLONAL	1	TRUE	1	0.920346251233543	2		489	388	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790490	3790490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1207183178	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	286	541	1	ENST00000262367.5:c.4043G>A	p.Arg1348His	p.R1348H	ENST00000262367	NM_004380.2	1348	cGc/cAc	24/31	1	2	FACETS	0.991	0.94	1	0.991	0.94	1	CLONAL	1	TRUE	1	0.920346251233543	2		542	627	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874147	151874148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs747256476	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	209	523	9	ENST00000262189.6:c.8390dup	p.Glu2798GlyfsTer11	p.E2798Gfs*11	ENST00000262189	NM_170606.2	2797	aag/aaAg	38/59	1	2	FACETS	0.726	0.677	0.775	0.726	0.677	0.775	SUBCLONAL	1	TRUE	1	0.920346251233543	2		532	626	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	305	400	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.947	0.899	0.995	0.947	0.899	0.995	CLONAL	1	TRUE	1	0.920346251233543	2		400	700	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	347	403	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.920346251233543	2		404	752	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813315	102813315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761462868	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	50	726	1	ENST00000307046.8:c.374G>A	p.Arg125His	p.R125H	ENST00000307046	NM_001111285.1	125	cGc/cAc	3/4	1	2	FACETS	0.17	0.144	0.199	0.17	0.144	0.199	SUBCLONAL	1	TRUE	1	0.920346251233543	2		727	638	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260601	10260601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573248196	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	264	606	0	ENST00000340748.4:c.2261C>T	p.Ala754Val	p.A754V	ENST00000340748		754	gCg/gTg	24/40	1	2	FACETS	0.966	0.913	1	0.966	0.913	1	CLONAL	1	TRUE	1	0.920346251233543	2		606	594	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972893	32972893	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	32	510	0	ENST00000380152.3:c.10248del	p.Lys3416AsnfsTer11	p.K3416Nfs*11	ENST00000380152		3415	Aaa/aa	27/27	1	2	FACETS	0.136	0.11	0.166	0.136	0.11	0.166	SUBCLONAL	1	TRUE	1	0.920346251233543	2		510	510	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073683	8073683	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	361	683	0	ENST00000377482.5:c.976T>G	p.Ser326Ala	p.S326A	ENST00000377482	NM_018948.3	326	Tca/Gca	4/4	1	2	FACETS	0.956	0.911	1	0.956	0.911	1	CLONAL	1	TRUE	1	0.920346251233543	2		683	821	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780046	9780046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776965614	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	188	726	0	ENST00000377346.4:c.1310G>A	p.Arg437His	p.R437H	ENST00000377346	NM_005026.3	437	cGc/cAc	10/24	1	2	FACETS	0.566	0.524	0.609	0.566	0.524	0.609	SUBCLONAL	1	TRUE	1	0.920346251233543	2		726	722	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11168277	11168277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	142	550	3	ENST00000361445.4:c.7595C>T	p.Ala2532Val	p.A2532V	ENST00000361445	NM_004958.3	2532	gCg/gTg	57/58	1	2	FACETS	0.478	0.436	0.521	0.478	0.436	0.521	SUBCLONAL	1	TRUE	1	0.920346251233543	2		553	646	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187719	11187719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767904339	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	295	620	0	ENST00000361445.4:c.6178C>T	p.Arg2060Trp	p.R2060W	ENST00000361445	NM_004958.3	2060	Cgg/Tgg	44/58	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.920346251233543	2		620	635	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217233	11217233	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190665412	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	312	612	2	ENST00000361445.4:c.4445G>A	p.Arg1482His	p.R1482H	ENST00000361445	NM_004958.3	1482	cGc/cAc	30/58	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.920346251233543	2		614	668	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298605	11298605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	207	626	0	ENST00000361445.4:c.1856G>A	p.Arg619His	p.R619H	ENST00000361445	NM_004958.3	619	cGc/cAc	12/58	1	2	FACETS	0.612	0.57	0.656	0.612	0.57	0.656	SUBCLONAL	1	TRUE	1	0.920346251233543	2		626	735	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317015	11317015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759750826	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	284	676	0	ENST00000361445.4:c.479G>A	p.Arg160His	p.R160H	ENST00000361445	NM_004958.3	160	cGc/cAc	4/58	1	2	FACETS	0.966	0.915	1	0.966	0.915	1	CLONAL	1	TRUE	1	0.920346251233543	2		676	639	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245500	16245500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	206	510	0	ENST00000375759.3:c.1475C>T	p.Ala492Val	p.A492V	ENST00000375759	NM_015001.2	492	gCt/gTt	7/15	1	2	FACETS	0.984	0.924	1	0.984	0.924	1	CLONAL	1	TRUE	1	0.920346251233543	2		510	455	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255169	16255170	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	382	779	1	ENST00000375759.3:c.2439dup	p.Val814SerfsTer7	p.V814Sfs*7	ENST00000375759	NM_015001.2	812	gaa/gAaa	11/15	1	2	FACETS	0.986	0.942	1	0.986	0.942	1	CLONAL	1	TRUE	1	0.920346251233543	2		780	842	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255882	16255883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	91	628	0	ENST00000375759.3:c.3154dup	p.Ile1052AsnfsTer7	p.I1052Nfs*7	ENST00000375759	NM_015001.2	1049	-/A	11/15	1	2	FACETS	0.265	0.235	0.298	0.265	0.235	0.298	SUBCLONAL	1	TRUE	1	0.920346251233543	2		628	745	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257359	16257359	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	381	623	1	ENST00000375759.3:c.4624C>T	p.Arg1542Ter	p.R1542*	ENST00000375759	NM_015001.2	1542	Cga/Tga	11/15	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.920346251233543	2		624	741	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258436	16258436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	117	714	0	ENST00000375759.3:c.5701C>T	p.Arg1901Cys	p.R1901C	ENST00000375759	NM_015001.2	1901	Cgc/Tgc	11/15	1	2	FACETS	0.301	0.271	0.333	0.301	0.271	0.333	SUBCLONAL	1	TRUE	1	0.920346251233543	2		714	845	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258440	16258440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1440008576	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	186	720	0	ENST00000375759.3:c.5705G>A	p.Arg1902Gln	p.R1902Q	ENST00000375759	NM_015001.2	1902	cGg/cAg	11/15	1	2	FACETS	0.486	0.449	0.524	0.486	0.449	0.524	SUBCLONAL	1	TRUE	1	0.920346251233543	2		720	832	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259759	16259759	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	361	735	0	ENST00000375759.3:c.7024C>T	p.Arg2342Ter	p.R2342*	ENST00000375759	NM_015001.2	2342	Cga/Tga	11/15	1	2	FACETS	0.979	0.934	1	0.979	0.934	1	CLONAL	1	TRUE	1	0.920346251233543	2		735	801	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265331	16265331	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs889756630	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	308	713	0	ENST00000375759.3:c.10823C>T	p.Ala3608Val	p.A3608V	ENST00000375759	NM_015001.2	3608	gCg/gTg	14/15	1	2	FACETS	0.928	0.881	0.976	0.928	0.881	0.976	CLONAL	1	TRUE	1	0.920346251233543	2		713	721	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089625	27089625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776905750	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	178	766	0	ENST00000324856.7:c.2581G>A	p.Ala861Thr	p.A861T	ENST00000324856	NM_006015.4	861	Gcc/Acc	8/20	1	2	FACETS	0.467	0.431	0.505	0.467	0.431	0.505	SUBCLONAL	1	TRUE	1	0.920346251233543	2		766	828	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106846	27106846	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781033223	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	44	758	1	ENST00000324856.7:c.6457C>T	p.Arg2153Cys	p.R2153C	ENST00000324856	NM_006015.4	2153	Cgc/Tgc	20/20	1	2	FACETS	0.123	0.102	0.146	0.123	0.102	0.146	SUBCLONAL	1	TRUE	1	0.920346251233543	2		759	777	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598362	28598362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770770051	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	320	644	0	ENST00000253063.3:c.334C>T	p.Arg112Cys	p.R112C	ENST00000253063	NM_031459.4	112	Cgc/Tgc	3/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.920346251233543	2		644	683	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598910	28598910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758133085	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	369	796	1	ENST00000253063.3:c.470G>A	p.Arg157His	p.R157H	ENST00000253063	NM_031459.4	157	cGc/cAc	4/10	1	2	FACETS	0.972	0.927	1	0.972	0.927	1	CLONAL	1	TRUE	1	0.920346251233543	2		797	825	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28607255	28607255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs988053889	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	308	560	0	ENST00000253063.3:c.1385C>T	p.Ala462Val	p.A462V	ENST00000253063	NM_031459.4	462	gCg/gTg	10/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.920346251233543	2		560	616	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36823932	36823932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs945529881	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	285	541	2	ENST00000373129.3:c.250C>T	p.Arg84Trp	p.R84W	ENST00000373129	NM_032017.1	84	Cgg/Tgg	5/12	1	2	FACETS	0.978	0.927	1	0.978	0.927	1	CLONAL	1	TRUE	1	0.920346251233543	2		543	633	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521581	46521581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs552393862	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	262	527	0	ENST00000262741.5:c.827G>A	p.Arg276His	p.R276H	ENST00000262741	NM_003629.3	276	cGt/cAt	7/10	1	2	FACETS	0.997	0.943	1	0.997	0.943	1	CLONAL	1	TRUE	1	0.920346251233543	2		527	571	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521582	46521582	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775105727	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	261	519	2	ENST00000262741.5:c.826C>T	p.Arg276Cys	p.R276C	ENST00000262741	NM_003629.3	276	Cgt/Tgt	7/10	1	2	FACETS	0.997	0.943	1	0.997	0.943	1	CLONAL	1	TRUE	1	0.920346251233543	2		521	569	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726526	46726526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761573792	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	338	733	0	ENST00000371975.4:c.605G>A	p.Arg202His	p.R202H	ENST00000371975	NM_003579.3	202	cGc/cAc	7/18	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.920346251233543	2		733	723	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332824	65332824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773295622	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	275	606	0	ENST00000342505.4:c.715C>T	p.Arg239Trp	p.R239W	ENST00000342505	NM_002227.2	239	Cgg/Tgg	7/25	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.920346251233543	2		606	574	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78422338	78422338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1244295456	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	276	538	0	ENST00000370768.2:c.1624G>A	p.Ala542Thr	p.A542T	ENST00000370768	NM_003902.3	542	Gct/Act	17/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.920346251233543	2		538	577	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849143	156849143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775191394	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	316	639	0	ENST00000524377.1:c.2035G>A	p.Asp679Asn	p.D679N	ENST00000524377	NM_002529.3	679	Gac/Aac	15/17	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.920346251233543	2		639	680	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161310401	161310401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760572684	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	290	490	0	ENST00000367975.2:c.197C>T	p.Ala66Val	p.A66V	ENST00000367975	NM_003001.3	66	gCg/gTg	4/6	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.920346251233543	2		490	601	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326493	161326493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	162	286	0	ENST00000367975.2:c.268C>A	p.Leu90Met	p.L90M	ENST00000367975	NM_003001.3	90	Ctg/Atg	5/6	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.920346251233543	2		286	296	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740264	162740264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756149068	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	287	638	0	ENST00000367921.3:c.1466G>A	p.Arg489Gln	p.R489Q	ENST00000367921	NM_006182.2	489	cGa/cAa	12/18	1	2	FACETS	0.987	0.936	1	0.987	0.936	1	CLONAL	1	TRUE	1	0.920346251233543	2		638	632	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163297320	163297320	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	187	492	0	ENST00000271452.3:c.166G>A	p.Val56Ile	p.V56I	ENST00000271452	NM_145697.2	56	Gta/Ata	3/14	1	2	FACETS	0.979	0.917	1	0.979	0.917	1	CLONAL	1	TRUE	1	0.920346251233543	2		492	415	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648329	206648329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55721947	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	293	603	0	ENST00000367120.3:c.350G>A	p.Arg117His	p.R117H	ENST00000367120	NM_014002.3	117	cGc/cAc	5/22	1	2	FACETS	0.972	0.922	1	0.972	0.922	1	CLONAL	1	TRUE	1	0.920346251233543	2		603	655	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649566	206649566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1464747771	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	41	638	0	ENST00000367120.3:c.401G>A	p.Arg134His	p.R134H	ENST00000367120	NM_014002.3	134	cGc/cAc	6/22	1	2	FACETS	0.12	0.1	0.144	0.12	0.1	0.144	SUBCLONAL	1	TRUE	1	0.920346251233543	2		638	740	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206667312	206667312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781860835	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	112	637	3	ENST00000367120.3:c.2105G>A	p.Arg702His	p.R702H	ENST00000367120	NM_014002.3	702	cGc/cAc	21/22	1	2	FACETS	0.345	0.31	0.382	0.345	0.31	0.382	SUBCLONAL	1	TRUE	1	0.920346251233543	2		640	705	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944310	206944310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755490123	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	298	621	0	ENST00000423557.1:c.320C>T	p.Ala107Val	p.A107V	ENST00000423557	NM_000572.2	107	gCg/gTg	3/5	1	2	FACETS	0.939	0.89	0.987	0.939	0.89	0.987	CLONAL	1	TRUE	1	0.920346251233543	2		621	690	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230459314	230459314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs578048672	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	85	674	0	ENST00000391860.1:c.1087G>A	p.Ala363Thr	p.A363T	ENST00000391860	NM_001258311.1	363	Gcc/Acc	7/7	1	2	FACETS	0.249	0.22	0.281	0.249	0.22	0.281	SUBCLONAL	1	TRUE	1	0.920346251233543	2		674	741	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63817039	63817039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1269760932	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	281	532	1	ENST00000279873.7:c.1010C>T	p.Thr337Met	p.T337M	ENST00000279873	NM_032199.2	337	aCg/aTg	6/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.920346251233543	2		533	568	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332272	70332273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1446158817	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	236	568	0	ENST00000373644.4:c.184dup	p.Thr62AsnfsTer4	p.T62Nfs*4	ENST00000373644	NM_030625.2	59	-/A	2/12	1	2	FACETS	0.811	0.762	0.862	0.811	0.762	0.862	CLONAL	1	TRUE	1	0.920346251233543	2		568	632	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88677065	88677065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765530074	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	179	349	0	ENST00000372037.3:c.850C>T	p.Arg284Cys	p.R284C	ENST00000372037	NM_004329.2	284	Cgc/Tgc	9/13	1	2	FACETS	0.977	0.913	1	0.977	0.913	1	CLONAL	1	TRUE	1	0.920346251233543	2		349	398	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653833	89653833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1085308042	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	153	447	0	ENST00000371953.3:c.131G>A	p.Gly44Asp	p.G44D	ENST00000371953	NM_000314.4	44	gGc/gAc	2/9	1	2	FACETS	0.958	0.89	1	0.958	0.89	1	CLONAL	1	TRUE	1	0.920346251233543	2		447	347	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717754	89717754	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	164	404	0	ENST00000371953.3:c.779A>C	p.Lys260Thr	p.K260T	ENST00000371953	NM_000314.4	260	aAa/aCa	7/9	1	2	FACETS	0.857	0.795	0.919	0.857	0.795	0.919	CLONAL	1	TRUE	1	0.920346251233543	2		404	416	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263973	104263974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776579	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	186	461	4	ENST00000369902.3:c.71dup	p.Ala25GlyfsTer23	p.A25Gfs*23	ENST00000369902	NM_016169.3	22	gcc/gCcc	1/12	1	2	FACETS	0.883	0.824	0.942	0.883	0.824	0.942	CLONAL	1	TRUE	1	0.920346251233543	2		465	458	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309777	104309777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745958724	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	539	487	0	ENST00000369902.3:c.368G>A	p.Arg123His	p.R123H	ENST00000369902	NM_016169.3	123	cGt/cAt	3/12	1	2	FACETS	1	0.993	1	1	0.998	1	CLONAL	2	TRUE	1	0.920346251233543	2		487	578	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114901004	114901004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	356	707	0	ENST00000543371.1:c.614C>T	p.Thr205Met	p.T205M	ENST00000543371	NM_001198531.1	205	aCg/aTg	6/14	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.920346251233543	2		707	715	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911638	114911638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1427214163	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	287	453	0	ENST00000543371.1:c.1156C>T	p.Arg386Trp	p.R386W	ENST00000543371	NM_001198531.1	386	Cgg/Tgg	10/14	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.920346251233543	2		453	548	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279681	123279681	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	360	676	0	ENST00000358487.5:c.751C>T	p.Arg251Ter	p.R251*	ENST00000358487	NM_000141.4	251	Cga/Tga	7/18	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.920346251233543	2		676	774	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310859	123310859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759750319	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	347	572	0	ENST00000358487.5:c.569G>A	p.Arg190Gln	p.R190Q	ENST00000358487	NM_000141.4	190	cGg/cAg	5/18	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.920346251233543	2		572	713	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533881	533881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs727503093	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	362	737	0	ENST00000451590.1:c.175G>A	p.Ala59Thr	p.A59T	ENST00000451590	NM_001130442.1	59	Gcc/Acc	3/5	1	2	FACETS	0.952	0.908	0.997	0.952	0.908	0.997	CLONAL	1	TRUE	1	0.920346251233543	2		737	826	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154281	2154281	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	315	791	1	ENST00000434045.2:c.647C>A	p.Ala216Asp	p.A216D	ENST00000434045	NM_001127598.1	216	gCt/gAt	5/5	1	2	FACETS	0.964	0.916	1	0.964	0.916	1	CLONAL	1	TRUE	1	0.920346251233543	2		792	710	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156699	2156699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs975030738	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	359	785	0	ENST00000434045.2:c.223G>A	p.Ala75Thr	p.A75T	ENST00000434045	NM_001127598.1	75	Gcc/Acc	3/5	1	2	FACETS	0.962	0.917	1	0.962	0.917	1	CLONAL	1	TRUE	1	0.920346251233543	2		785	811	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136016	64136016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	33	631	1	ENST00000334205.4:c.1277G>A	p.Arg426His	p.R426H	ENST00000334205	NM_003942.2	426	cGc/cAc	11/17	1	2	FACETS	0.11	0.089	0.133	0.11	0.089	0.133	SUBCLONAL	1	TRUE	1	0.920346251233543	2		632	654	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200474	67200474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	331	772	0	ENST00000312629.5:c.668G>A	p.Gly223Asp	p.G223D	ENST00000312629	NM_003952.2	223	gGc/gAc	8/15	1	2	FACETS	0.915	0.87	0.961	0.915	0.87	0.961	CLONAL	1	TRUE	1	0.920346251233543	2		772	786	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202072	67202072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372739497	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	325	669	0	ENST00000312629.5:c.1175C>T	p.Pro392Leu	p.P392L	ENST00000312629	NM_003952.2	392	cCg/cTg	14/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.920346251233543	2		669	699	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625219	69625219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	313	654	1	ENST00000334134.2:c.574C>T	p.Arg192Trp	p.R192W	ENST00000334134	NM_005247.2	192	Cgg/Tgg	3/3	1	2	FACETS	0.997	0.948	1	0.997	0.948	1	CLONAL	1	TRUE	1	0.920346251233543	2		655	682	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103553	77103553	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1214886996	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	315	615	0	ENST00000356341.3:c.13G>A	p.Gly5Ser	p.G5S	ENST00000356341	NM_002576.4	5	Ggc/Agc	2/15	1	2	FACETS	0.981	0.932	1	0.981	0.932	1	CLONAL	1	TRUE	1	0.920346251233543	2		615	698	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102080254	102080254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193100333	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	186	496	0	ENST00000282441.5:c.991C>T	p.Arg331Trp	p.R331W	ENST00000282441	NM_001130145.2	331	Cgg/Tgg	6/9	1	2	FACETS	0.9	0.841	0.961	0.9	0.841	0.961	CLONAL	1	TRUE	1	0.920346251233543	2		496	449	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117799	108117799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202160435	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	26	489	0	ENST00000278616.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000278616	NM_000051.3	337	cGt/cAt	8/63	1	2	FACETS	0.122	0.096	0.152	0.122	0.096	0.152	SUBCLONAL	1	TRUE	1	0.920346251233543	2		489	464	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121507	108121507	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	276	563	0	ENST00000278616.4:c.1315C>A	p.Leu439Ile	p.L439I	ENST00000278616	NM_000051.3	439	Cta/Ata	10/63	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.920346251233543	2		563	583	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124551	108124552	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	138	428	0	ENST00000278616.4:c.1914dup	p.Asp639ArgfsTer2	p.D639Rfs*2	ENST00000278616	NM_000051.3	637	caa/cAaa	13/63	1	2	FACETS	0.828	0.763	0.895	0.828	0.763	0.895	CLONAL	1	TRUE	1	0.920346251233543	2		428	362	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143471	108143471	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761590782	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	34	535	0	ENST00000278616.4:c.3176C>T	p.Ala1059Val	p.A1059V	ENST00000278616	NM_000051.3	1059	gCc/gTc	22/63	1	2	FACETS	0.16	0.13	0.194	0.16	0.13	0.194	SUBCLONAL	1	TRUE	1	0.920346251233543	2		535	461	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158382	108158382	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781785	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	207	514	0	ENST00000278616.4:c.4049C>T	p.Thr1350Met	p.T1350M	ENST00000278616	NM_000051.3	1350	aCg/aTg	27/63	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.920346251233543	2		514	435	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196144	108196144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879254132	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	201	470	0	ENST00000278616.4:c.6680G>A	p.Arg2227His	p.R2227H	ENST00000278616	NM_000051.3	2227	cGc/cAc	46/63	1	2	FACETS	0.937	0.878	0.997	0.937	0.878	0.997	CLONAL	1	TRUE	1	0.920346251233543	2		470	466	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118339535	118339535	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555034779	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	290	537	0	ENST00000534358.1:c.478C>T	p.Arg160Ter	p.R160*	ENST00000534358	NM_005933.3	160	Cga/Tga	2/36	1	2	FACETS	0.967	0.916	1	0.967	0.916	1	CLONAL	1	TRUE	1	0.920346251233543	2		537	652	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347553	118347553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555037629	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	303	555	0	ENST00000534358.1:c.3190C>T	p.Arg1064Ter	p.R1064*	ENST00000534358	NM_005933.3	1064	Cga/Tga	4/36	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.920346251233543	2		555	629	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377081	118377081	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559663507	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	382	628	1	ENST00000534358.1:c.10474G>A	p.Ala3492Thr	p.A3492T	ENST00000534358	NM_005933.3	3492	Gct/Act	27/36	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.920346251233543	2		629	788	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142446	119142446	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs267602720	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	30	450	0	ENST00000264033.4:c.445C>T	p.Arg149Ter	p.R149*	ENST00000264033	NM_005188.3	149	Cga/Tga	3/16	1	2	FACETS	0.133	0.106	0.162	0.133	0.106	0.162	SUBCLONAL	1	TRUE	1	0.920346251233543	2		450	492	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149290	119149290	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140627020	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	180	618	0	ENST00000264033.4:c.1298C>T	p.Pro433Leu	p.P433L	ENST00000264033	NM_005188.3	433	cCg/cTg	9/16	1	2	FACETS	0.56	0.518	0.604	0.56	0.518	0.604	SUBCLONAL	1	TRUE	1	0.920346251233543	2		618	698	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125513750	125513750	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	242	509	0	ENST00000428830.2:c.878A>G	p.His293Arg	p.H293R	ENST00000428830	NM_001114121.2	293	cAc/cGc	9/14	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.920346251233543	2		509	517	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022454	12022454	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753079378	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	397	854	0	ENST00000396373.4:c.560C>T	p.Thr187Met	p.T187M	ENST00000396373	NM_001987.4	187	aCg/aTg	5/8	1	2	FACETS	0.993	0.949	1	0.993	0.949	1	CLONAL	1	TRUE	1	0.920346251233543	2		854	869	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534717	18534717	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	207	588	0	ENST00000266497.5:c.1775C>A	p.Ser592Tyr	p.S592Y	ENST00000266497		592	tCt/tAt	12/31	NA	2	FACETS	1	0.943	1			1	INDETERMINATE	1	TRUE	NA	0.920346251233543	2		588	448	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793409	18793409	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	196	492	0	ENST00000266497.5:c.4106T>G	p.Leu1369Arg	p.L1369R	ENST00000266497		1369	cTt/cGt	30/31	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.920346251233543	2		492	406	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205284	46205284	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	233	473	0	ENST00000334344.6:c.368C>A	p.Pro123His	p.P123H	ENST00000334344	NM_152641.2	123	cCt/cAt	4/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.920346251233543	2		473	471	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424427	49424427	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs577303074	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	86	607	0	ENST00000301067.7:c.13796C>T	p.Ala4599Val	p.A4599V	ENST00000301067	NM_003482.3	4599	gCg/gTg	41/54	1	2	FACETS	0.321	0.284	0.36	0.321	0.284	0.36	SUBCLONAL	1	TRUE	1	0.920346251233543	2		607	583	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427950	49427950	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775632051	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	114	579	0	ENST00000301067.7:c.10640G>A	p.Arg3547His	p.R3547H	ENST00000301067	NM_003482.3	3547	cGc/cAc	38/54	1	2	FACETS	0.399	0.36	0.44	0.399	0.36	0.44	SUBCLONAL	1	TRUE	1	0.920346251233543	2		579	621	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431709	49431709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752428122	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	84	791	0	ENST00000301067.7:c.9430G>A	p.Ala3144Thr	p.A3144T	ENST00000301067	NM_003482.3	3144	Gca/Aca	34/54	1	2	FACETS	0.255	0.224	0.287	0.255	0.224	0.287	SUBCLONAL	1	TRUE	1	0.920346251233543	2		791	717	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487211	56487211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776335440	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	37	528	0	ENST00000267101.3:c.1357C>T	p.Arg453Cys	p.R453C	ENST00000267101	NM_001982.3	453	Cgt/Tgt	12/28	1	2	FACETS	0.141	0.116	0.17	0.141	0.116	0.17	SUBCLONAL	1	TRUE	1	0.920346251233543	2		528	570	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489570	56489570	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1377374701	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	275	636	0	ENST00000267101.3:c.2035C>T	p.Arg679Ter	p.R679*	ENST00000267101	NM_001982.3	679	Cga/Tga	17/28	1	2	FACETS	0.914	0.864	0.964	0.914	0.864	0.964	CLONAL	1	TRUE	1	0.920346251233543	2		636	654	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495050	56495050	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758743468	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	188	605	0	ENST00000267101.3:c.3407G>A	p.Arg1136His	p.R1136H	ENST00000267101	NM_001982.3	1136	cGc/cAc	27/28	1	2	FACETS	0.533	0.493	0.574	0.533	0.493	0.574	SUBCLONAL	1	TRUE	1	0.920346251233543	2		605	767	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861837	57861837	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs759838377	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	312	663	1	ENST00000228682.2:c.1138C>T	p.Arg380Ter	p.R380*	ENST00000228682	NM_005269.2	380	Cga/Tga	10/12	1	2	FACETS	0.996	0.946	1	0.996	0.946	1	CLONAL	1	TRUE	1	0.920346251233543	2		664	681	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856188	111856188	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	355	724	0	ENST00000341259.2:c.239G>A	p.Arg80His	p.R80H	ENST00000341259	NM_005475.2	80	cGc/cAc	2/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.920346251233543	2		724	738	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885176	111885176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374931521	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	100	686	0	ENST00000341259.2:c.1064C>T	p.Thr355Met	p.T355M	ENST00000341259	NM_005475.2	355	aCg/aTg	6/8	1	2	FACETS	0.312	0.278	0.347	0.312	0.278	0.347	SUBCLONAL	1	TRUE	1	0.920346251233543	2		686	697	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426830	121426830	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201934320	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	339	627	1	ENST00000257555.6:c.521C>T	p.Ala174Val	p.A174V	ENST00000257555		174	gCg/gTg	2/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.920346251233543	2		628	717	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879626	123879626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376869233	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	190	397	0	ENST00000330479.4:c.322G>A	p.Ala108Thr	p.A108T	ENST00000330479	NM_020382.3	108	Gcc/Acc	4/9	1	2	FACETS	0.938	0.878	1	0.938	0.878	1	CLONAL	1	TRUE	1	0.920346251233543	2		397	440	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219579	133219579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542430685	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	269	613	0	ENST00000320574.5:c.4555C>T	p.Arg1519Cys	p.R1519C	ENST00000320574	NM_006231.2	1519	Cgc/Tgc	36/49	1	2	FACETS	0.992	0.94	1	0.992	0.94	1	CLONAL	1	TRUE	1	0.920346251233543	2		613	589	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226444	133226444	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772686048	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	209	535	0	ENST00000320574.5:c.3614C>T	p.Pro1205Leu	p.P1205L	ENST00000320574	NM_006231.2	1205	cCg/cTg	30/49	1	2	FACETS	0.962	0.904	1	0.962	0.904	1	CLONAL	1	TRUE	1	0.920346251233543	2		535	472	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237682	133237682	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	325	533	0	ENST00000320574.5:c.2933A>G	p.Glu978Gly	p.E978G	ENST00000320574	NM_006231.2	978	gAa/gGa	25/49	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.920346251233543	2		533	679	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250243	133250243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374920539	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	289	732	0	ENST00000320574.5:c.1277C>T	p.Ala426Val	p.A426V	ENST00000320574	NM_006231.2	426	gCg/gTg	13/49	1	2	FACETS	0.987	0.937	1	0.987	0.937	1	CLONAL	1	TRUE	1	0.920346251233543	2		732	636	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562441	21562441	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1176877473	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	294	687	0	ENST00000382592.4:c.1478C>T	p.Ala493Val	p.A493V	ENST00000382592	NM_014572.2	493	gCg/gTg	4/8	1	2	FACETS	0.962	0.913	1	0.962	0.913	1	CLONAL	1	TRUE	1	0.920346251233543	2		687	664	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562753	21562753	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339653606	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	285	715	0	ENST00000382592.4:c.1166C>T	p.Pro389Leu	p.P389L	ENST00000382592	NM_014572.2	389	cCg/cTg	4/8	1	2	FACETS	0.931	0.882	0.981	0.931	0.882	0.981	CLONAL	1	TRUE	1	0.920346251233543	2		715	665	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562756	21562756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs12867400	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	282	704	0	ENST00000382592.4:c.1163C>T	p.Ala388Val	p.A388V	ENST00000382592	NM_014572.2	388	gCg/gTg	4/8	1	2	FACETS	0.923	0.874	0.973	0.923	0.874	0.973	CLONAL	1	TRUE	1	0.920346251233543	2		704	664	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26974623	26974623	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	92	434	0	ENST00000381527.3:c.967C>T	p.Arg323Ter	p.R323*	ENST00000381527	NM_001260.1	323	Cga/Tga	10/13	1	2	FACETS	0.506	0.453	0.562	0.506	0.453	0.562	SUBCLONAL	1	TRUE	1	0.920346251233543	2		434	395	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28882996	28882996	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867799392	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	229	499	0	ENST00000282397.4:c.3704C>T	p.Ala1235Val	p.A1235V	ENST00000282397	NM_002019.4	1235	gCc/gTc	28/30	1	2	FACETS	0.97	0.914	1	0.97	0.914	1	CLONAL	1	TRUE	1	0.920346251233543	2		499	513	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005423	29005423	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	214	479	0	ENST00000282397.4:c.838C>T	p.Arg280Ter	p.R280*	ENST00000282397	NM_002019.4	280	Cga/Tga	7/30	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.920346251233543	2		479	451	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906627	32906627	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358396	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	248	563	0	ENST00000380152.3:c.1012G>A	p.Ala338Thr	p.A338T	ENST00000380152		338	Gct/Act	10/27	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.920346251233543	2		563	530	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912891	32912891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793495	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	239	583	0	ENST00000380152.3:c.4399C>T	p.His1467Tyr	p.H1467Y	ENST00000380152		1467	Cat/Tat	11/27	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.920346251233543	2		583	508	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913873	32913873	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	182	639	0	ENST00000380152.3:c.5381T>C	p.Val1794Ala	p.V1794A	ENST00000380152		1794	gTa/gCa	11/27	1	2	FACETS	0.96	0.897	1	0.96	0.897	1	CLONAL	1	TRUE	1	0.920346251233543	2		639	412	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968994	32968995	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	268	644	0	ENST00000380152.3:c.9430dup	p.Ser3144PhefsTer6	p.S3144Ffs*6	ENST00000380152		3142	gat/gaTt	25/27	1	2	FACETS	0.976	0.923	1	0.976	0.923	1	CLONAL	1	TRUE	1	0.920346251233543	2		644	597	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134687	41134687	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760747458	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	293	698	0	ENST00000379561.5:c.941G>A	p.Arg314His	p.R314H	ENST00000379561	NM_002015.3	314	cGc/cAc	2/3	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.920346251233543	2		698	626	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936995	48936995	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778842	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	103	499	1	ENST00000267163.4:c.763C>T	p.Arg255Ter	p.R255*	ENST00000267163	NM_000321.2	255	Cga/Tga	8/27	1	2	FACETS	0.474	0.426	0.525	0.474	0.426	0.525	SUBCLONAL	1	TRUE	1	0.920346251233543	2		500	472	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953730	48953730	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs3092891	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	61	304	0	ENST00000267163.4:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000267163	NM_000321.2	445	Cga/Tga	14/27	1	2	FACETS	0.393	0.341	0.449	0.393	0.341	0.449	SUBCLONAL	1	TRUE	1	0.920346251233543	2		304	337	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335545	73335546	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	183	521	0	ENST00000377767.4:c.2625dup	p.Glu876Ter	p.E876*	ENST00000377767	NM_014953.3	875	-/T	19/21	1	2	FACETS	0.837	0.78	0.895	0.837	0.78	0.895	CLONAL	1	TRUE	1	0.920346251233543	2		521	475	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514688	103514688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	344	699	1	ENST00000355739.4:c.1189G>A	p.Asp397Asn	p.D397N	ENST00000355739	NM_000123.3	397	Gat/Aat	8/15	1	2	FACETS	0.94	0.895	0.986	0.94	0.895	0.986	CLONAL	1	TRUE	1	0.920346251233543	2		700	795	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515036	103515036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775996769	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	317	628	0	ENST00000355739.4:c.1537G>A	p.Ala513Thr	p.A513T	ENST00000355739	NM_000123.3	513	Gca/Aca	8/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.920346251233543	2		628	665	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515141	103515141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770246574	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	322	677	0	ENST00000355739.4:c.1642G>A	p.Glu548Lys	p.E548K	ENST00000355739	NM_000123.3	548	Gaa/Aaa	8/15	1	2	FACETS	0.971	0.923	1	0.971	0.923	1	CLONAL	1	TRUE	1	0.920346251233543	2		677	721	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30047521	30047521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	19	441	0	ENST00000331968.5:c.2480G>A	p.Arg827His	p.R827H	ENST00000331968	NM_002742.2	827	cGc/cAc	17/18	1	2	FACETS	0.115	0.087	0.148	0.115	0.087	0.148	SUBCLONAL	1	TRUE	1	0.920346251233543	2		441	360	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108091	30108091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80271647	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	193	433	0	ENST00000331968.5:c.716C>T	p.Ser239Leu	p.S239L	ENST00000331968	NM_002742.2	239	tCg/tTg	5/18	1	2	FACETS	0.987	0.925	1	0.987	0.925	1	CLONAL	1	TRUE	1	0.920346251233543	2		433	425	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023147	33023147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	304	650	0	ENST00000300177.4:c.256C>T	p.Arg86Cys	p.R86C	ENST00000300177	NM_001191322.1	86	Cgc/Tgc	2/2	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.920346251233543	2		650	648	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988691	41988691	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	74	594	0	ENST00000219905.7:c.1483C>T	p.Arg495Ter	p.R495*	ENST00000219905	NM_001164273.1	495	Cga/Tga	3/24	1	2	FACETS	0.272	0.238	0.308	0.272	0.238	0.308	SUBCLONAL	1	TRUE	1	0.920346251233543	2		594	592	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040892	42040892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463241547	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	319	607	0	ENST00000219905.7:c.5270G>A	p.Arg1757His	p.R1757H	ENST00000219905	NM_001164273.1	1757	cGt/cAt	16/24	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.920346251233543	2		607	685	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058651	42058651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	249	593	0	ENST00000219905.7:c.8371G>A	p.Glu2791Lys	p.E2791K	ENST00000219905	NM_001164273.1	2791	Gaa/Aaa	24/24	1	2	FACETS	0.987	0.933	1	0.987	0.933	1	CLONAL	1	TRUE	1	0.920346251233543	2		593	548	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784573	43784573	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	254	544	0	ENST00000382044.4:c.101G>A	p.Ser34Asn	p.S34N	ENST00000382044	NM_001141980.1	34	aGc/aAc	2/28	1	2	FACETS	0.932	0.88	0.985	0.932	0.88	0.985	CLONAL	1	TRUE	1	0.920346251233543	2		544	592	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	264	590	7	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.885	0.836	0.935	0.885	0.836	0.935	CLONAL	1	TRUE	1	0.920346251233543	2		597	648	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251184	99251184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182472366	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	39	634	0	ENST00000268035.6:c.488C>T	p.Ala163Val	p.A163V	ENST00000268035	NM_000875.3	163	gCg/gTg	2/21	1	2	FACETS	0.123	0.101	0.148	0.123	0.101	0.148	SUBCLONAL	1	TRUE	1	0.920346251233543	2		634	688	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347744	347744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771607500	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	244	694	0	ENST00000262320.3:c.1762G>A	p.Ala588Thr	p.A588T	ENST00000262320	NM_003502.3	588	Gcc/Acc	6/11	1	2	FACETS	0.959	0.905	1	0.959	0.905	1	CLONAL	1	TRUE	1	0.920346251233543	2		694	553	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348031	348031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765982081	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	423	773	0	ENST00000262320.3:c.1475G>A	p.Arg492His	p.R492H	ENST00000262320	NM_003502.3	492	cGc/cAc	6/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.920346251233543	2		773	872	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354393	354393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1488869543	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	165	551	0	ENST00000262320.3:c.1165G>A	p.Ala389Thr	p.A389T	ENST00000262320	NM_003502.3	389	Gcg/Acg	5/11	1	2	FACETS	0.527	0.486	0.571	0.527	0.486	0.571	SUBCLONAL	1	TRUE	1	0.920346251233543	2		551	680	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100464	2100464	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767626323	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	317	455	1	ENST00000219476.3:c.202G>A	p.Ala68Thr	p.A68T	ENST00000219476	NM_000548.3	68	Gca/Aca	3/42	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.920346251233543	2		456	618	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2125862	2125862	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500975	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	264	573	1	ENST00000219476.3:c.2608G>A	p.Ala870Thr	p.A870T	ENST00000219476	NM_000548.3	870	Gcc/Acc	23/42	1	2	FACETS	0.994	0.941	1	0.994	0.941	1	CLONAL	1	TRUE	1	0.920346251233543	2		574	577	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138462	2138462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758450326	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	315	685	0	ENST00000219476.3:c.5275G>A	p.Ala1759Thr	p.A1759T	ENST00000219476	NM_000548.3	1759	Gcc/Acc	42/42	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.920346251233543	2		685	669	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223334	2223334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757410464	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	337	761	0	ENST00000326181.6:c.946C>T	p.Arg316Cys	p.R316C	ENST00000326181	NM_032271.2	316	Cgc/Tgc	10/21	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.920346251233543	2		761	726	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639300	3639300	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371090786	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	326	736	0	ENST00000294008.3:c.4339G>A	p.Gly1447Ser	p.G1447S	ENST00000294008	NM_032444.2	1447	Ggc/Agc	12/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.920346251233543	2		736	674	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639525	3639525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369846826	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	38	730	0	ENST00000294008.3:c.4114C>T	p.Arg1372Trp	p.R1372W	ENST00000294008	NM_032444.2	1372	Cgg/Tgg	12/15	1	2	FACETS	0.118	0.097	0.142	0.118	0.097	0.142	SUBCLONAL	1	TRUE	1	0.920346251233543	2		730	699	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656601	3656601	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1395992833	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	337	662	0	ENST00000294008.3:c.634C>T	p.Arg212Ter	p.R212*	ENST00000294008	NM_032444.2	212	Cga/Tga	3/15	1	2	FACETS	0.965	0.918	1	0.965	0.918	1	CLONAL	1	TRUE	1	0.920346251233543	2		662	759	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828787	3828787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1013334018	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	368	634	0	ENST00000262367.5:c.1855G>A	p.Ala619Thr	p.A619T	ENST00000262367	NM_004380.2	619	Gca/Aca	9/31	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.920346251233543	2		634	763	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843551	3843551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763070109	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	340	648	0	ENST00000262367.5:c.1052G>A	p.Arg351His	p.R351H	ENST00000262367	NM_004380.2	351	cGc/cAc	4/31	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.920346251233543	2		648	716	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916205	9916205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555491654	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	274	673	0	ENST00000330684.3:c.2084G>A	p.Arg695Gln	p.R695Q	ENST00000330684	NM_001134407.1	695	cGg/cAg	10/13	1	2	FACETS	0.933	0.883	0.984	0.933	0.883	0.984	CLONAL	1	TRUE	1	0.920346251233543	2		673	638	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274042	10274042	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184494228	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	327	697	1	ENST00000330684.3:c.227G>A	p.Arg76His	p.R76H	ENST00000330684	NM_001134407.1	76	cGc/cAc	2/13	1	2	FACETS	0.992	0.944	1	0.992	0.944	1	CLONAL	1	TRUE	1	0.920346251233543	2		698	716	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274102	10274102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	333	649	0	ENST00000330684.3:c.167G>A	p.Gly56Asp	p.G56D	ENST00000330684	NM_001134407.1	56	gGc/gAc	2/13	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.920346251233543	2		649	716	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026109	14026109	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	239	571	0	ENST00000311895.7:c.1069A>C	p.Ile357Leu	p.I357L	ENST00000311895	NM_005236.2	357	Ata/Cta	6/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.920346251233543	2		571	518	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645178	67645178	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	309	592	0	ENST00000264010.4:c.443C>T	p.Ala148Val	p.A148V	ENST00000264010	NM_006565.3	148	gCg/gTg	3/12	1	2	FACETS	0.952	0.904	1	0.952	0.904	1	CLONAL	1	TRUE	1	0.920346251233543	2		592	705	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645920	67645920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567609067	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	182	573	0	ENST00000264010.4:c.848G>A	p.Arg283His	p.R283H	ENST00000264010	NM_006565.3	283	cGt/cAt	4/12	1	2	FACETS	0.559	0.517	0.602	0.559	0.517	0.602	SUBCLONAL	1	TRUE	1	0.920346251233543	2		573	708	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660469	67660469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	46	470	0	ENST00000264010.4:c.1369C>T	p.Arg457Ter	p.R457*	ENST00000264010	NM_006565.3	457	Cga/Tga	8/12	1	2	FACETS	0.173	0.145	0.203	0.173	0.145	0.203	SUBCLONAL	1	TRUE	1	0.920346251233543	2		470	579	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663371	67663371	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139828150	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	143	610	0	ENST00000264010.4:c.1772C>T	p.Thr591Met	p.T591M	ENST00000264010	NM_006565.3	591	aCg/aTg	10/12	1	2	FACETS	0.476	0.435	0.519	0.476	0.435	0.519	SUBCLONAL	1	TRUE	1	0.920346251233543	2		610	653	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847351	68847351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs570930882	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	271	557	0	ENST00000261769.5:c.1273G>A	p.Val425Ile	p.V425I	ENST00000261769	NM_004360.3	425	Gtc/Atc	9/16	1	2	FACETS	0.919	0.869	0.969	0.919	0.869	0.969	CLONAL	1	TRUE	1	0.920346251233543	2		557	641	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867356	68867356	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369126891	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	40	590	0	ENST00000261769.5:c.2603G>A	p.Arg868His	p.R868H	ENST00000261769	NM_004360.3	868	cGc/cAc	16/16	1	2	FACETS	0.125	0.104	0.15	0.125	0.104	0.15	SUBCLONAL	1	TRUE	1	0.920346251233543	2		590	693	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821664	72821664	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	262	607	0	ENST00000268489.5:c.10511T>C	p.Val3504Ala	p.V3504A	ENST00000268489	NM_006885.3	3504	gTc/gCc	10/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.920346251233543	2		607	530	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991508	72991508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755878058	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	98	570	1	ENST00000268489.5:c.2537G>A	p.Arg846His	p.R846H	ENST00000268489	NM_006885.3	846	cGc/cAc	2/10	1	2	FACETS	0.313	0.279	0.349	0.313	0.279	0.349	SUBCLONAL	1	TRUE	1	0.920346251233543	2		571	680	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993866	72993866	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761842147	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	338	731	0	ENST00000268489.5:c.179G>A	p.Arg60His	p.R60H	ENST00000268489	NM_006885.3	60	cGc/cAc	2/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.920346251233543	2		731	726	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349211	89349211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755642596	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	342	648	1	ENST00000301030.4:c.3739G>A	p.Ala1247Thr	p.A1247T	ENST00000301030	NM_001256183.1	1247	Gct/Act	9/13	1	2	FACETS	0.986	0.939	1	0.986	0.939	1	CLONAL	1	TRUE	1	0.920346251233543	2		649	754	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352037	89352037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138353708	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	308	631	0	ENST00000301030.4:c.913G>A	p.Ala305Thr	p.A305T	ENST00000301030	NM_001256183.1	305	Gca/Aca	9/13	1	2	FACETS	0.937	0.89	0.986	0.937	0.89	0.986	CLONAL	1	TRUE	1	0.920346251233543	2		631	714	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845389	89845389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769158149	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	341	677	0	ENST00000389301.3:c.1738G>A	p.Val580Met	p.V580M	ENST00000389301	NM_000135.2	580	Gtg/Atg	19/43	1	2	FACETS	0.945	0.9	0.991	0.945	0.9	0.991	CLONAL	1	TRUE	1	0.920346251233543	2		677	784	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216092	7216092	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	253	620	0	ENST00000380728.2:c.967C>T	p.Arg323Ter	p.R323*	ENST00000380728		323	Cga/Tga	11/11	1	2	FACETS	0.938	0.886	0.991	0.938	0.886	0.991	CLONAL	1	TRUE	1	0.920346251233543	2		620	586	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984220	7984220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	142	621	0	ENST00000319144.4:c.509G>A	p.Arg170His	p.R170H	ENST00000319144	NM_001139.2	170	cGc/cAc	4/15	1	2	FACETS	0.468	0.427	0.51	0.468	0.427	0.51	SUBCLONAL	1	TRUE	1	0.920346251233543	2		621	660	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961914	15961914	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	199	420	0	ENST00000268712.3:c.5882-1G>T		p.X1961_splice	ENST00000268712	NM_006311.3	1961			1	2	FACETS	0.888	0.831	0.946	0.888	0.831	0.946	CLONAL	1	TRUE	1	0.920346251233543	2		420	487	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15967420	15967420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762776993	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	340	568	1	ENST00000268712.3:c.5183G>A	p.Arg1728Gln	p.R1728Q	ENST00000268712	NM_006311.3	1728	cGg/cAg	35/46	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.920346251233543	2		569	687	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983373	15983373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200574326	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	253	511	0	ENST00000268712.3:c.3406G>A	p.Ala1136Thr	p.A1136T	ENST00000268712	NM_006311.3	1136	Gca/Aca	26/46	1	2	FACETS	0.887	0.836	0.938	0.887	0.836	0.938	CLONAL	1	TRUE	1	0.920346251233543	2		511	620	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649125	37649125	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	233	471	0	ENST00000447079.4:c.2230G>T	p.Ala744Ser	p.A744S	ENST00000447079	NM_015083.1	744	Gcc/Tcc	4/14	1	2	FACETS	0.896	0.843	0.95	0.896	0.843	0.95	CLONAL	1	TRUE	1	0.920346251233543	2		471	565	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	253	678	5	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	0.79	0.743	0.837	0.79	0.743	0.837	SUBCLONAL	1	TRUE	1	0.920346251233543	2		683	696	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459723	40459723	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	301	652	1	ENST00000345506.4:c.1888G>A	p.Ala630Thr	p.A630T	ENST00000345506	NM_003152.3	630	Gcc/Acc	16/20	1	2	FACETS	0.932	0.884	0.98	0.932	0.884	0.98	CLONAL	1	TRUE	1	0.920346251233543	2		653	702	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870501	40870501	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768296055	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	305	587	0	ENST00000428826.2:c.902G>A	p.Arg301His	p.R301H	ENST00000428826		301	cGc/cAc	9/21	1	2	FACETS	0.986	0.937	1	0.986	0.937	1	CLONAL	1	TRUE	1	0.920346251233543	2		587	672	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870630	40870630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777571053	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	232	574	0	ENST00000428826.2:c.773G>A	p.Arg258Gln	p.R258Q	ENST00000428826		258	cGa/cAa	9/21	1	2	FACETS	0.937	0.882	0.992	0.937	0.882	0.992	CLONAL	1	TRUE	1	0.920346251233543	2		574	538	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699306	47699306	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	199	464	0	ENST00000347630.2:c.200+2T>G		p.X67_splice	ENST00000347630	NM_001007230.1	67			1	2	FACETS	0.983	0.922	1	0.983	0.922	1	CLONAL	1	TRUE	1	0.920346251233543	2		464	440	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	277	589	0	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	0.98	0.929	1	0.98	0.929	1	CLONAL	1	TRUE	1	0.920346251233543	2		589	614	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926512	59926512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61757643	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	173	437	0	ENST00000259008.2:c.485G>A	p.Arg162Gln	p.R162Q	ENST00000259008	NM_032043.2	162	cGa/cAa	5/20	1	2	FACETS	0.945	0.881	1	0.945	0.881	1	CLONAL	1	TRUE	1	0.920346251233543	2		437	398	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796992	78796992	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144071963	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	276	579	0	ENST00000306801.3:c.1105C>T	p.Arg369Cys	p.R369C	ENST00000306801	NM_020761.2	369	Cgt/Tgt	9/34	1	2	FACETS	0.98	0.928	1	0.98	0.928	1	CLONAL	1	TRUE	1	0.920346251233543	2		579	612	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867522	78867522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770546124	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	337	656	0	ENST00000306801.3:c.2258C>T	p.Ala753Val	p.A753V	ENST00000306801	NM_020761.2	753	gCg/gTg	20/34	1	2	FACETS	0.979	0.932	1	0.979	0.932	1	CLONAL	1	TRUE	1	0.920346251233543	2		656	748	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56401614	56401614	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs888212988	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	89	456	0	ENST00000348428.3:c.1475+1G>A		p.X492_splice	ENST00000348428	NM_006785.3	492			1	2	FACETS	0.4	0.356	0.447	0.4	0.356	0.447	SUBCLONAL	1	TRUE	1	0.920346251233543	2		456	483	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223061	1223061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782267	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	392	678	0	ENST00000326873.7:c.998G>A	p.Arg333His	p.R333H	ENST00000326873	NM_000455.4	333	cGc/cAc	8/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.920346251233543	2		678	825	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208010	5208010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	354	748	0	ENST00000357368.4:c.5701C>T	p.Arg1901Trp	p.R1901W	ENST00000357368	NM_002850.3	1901	Cgg/Tgg	37/38	1	2	FACETS	0.936	0.891	0.981	0.936	0.891	0.981	CLONAL	1	TRUE	1	0.920346251233543	2		748	822	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212441	5212441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	379	702	0	ENST00000357368.4:c.4676G>A	p.Gly1559Asp	p.G1559D	ENST00000357368	NM_002850.3	1559	gGc/gAc	31/38	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.920346251233543	2		702	801	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238951	5238951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237159914	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	356	658	1	ENST00000357368.4:c.1828C>T	p.Arg610Trp	p.R610W	ENST00000357368	NM_002850.3	610	Cgg/Tgg	13/38	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.920346251233543	2		659	689	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117407	7117407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746000108	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	270	592	1	ENST00000302850.5:c.3809G>A	p.Arg1270His	p.R1270H	ENST00000302850	NM_000208.2	1270	cGc/cAc	22/22	1	2	FACETS	0.973	0.921	1	0.973	0.921	1	CLONAL	1	TRUE	1	0.920346251233543	2		593	603	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132295	7132295	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs575954707	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	319	654	2	ENST00000302850.5:c.2716G>A	p.Ala906Thr	p.A906T	ENST00000302850	NM_000208.2	906	Gct/Act	14/22	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.920346251233543	2		656	692	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142908	7142908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471585411	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	696	622	0	ENST00000302850.5:c.2461G>A	p.Glu821Lys	p.E821K	ENST00000302850	NM_000208.2	821	Gag/Aag	12/22	1	2	FACETS	1	0.997	1	1	0.998	1	CLONAL	2	TRUE	1	0.920346251233543	2		622	727	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184534	7184534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775222338	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	99	558	0	ENST00000302850.5:c.767G>A	p.Arg256His	p.R256H	ENST00000302850	NM_000208.2	256	cGc/cAc	3/22	1	2	FACETS	0.328	0.293	0.366	0.328	0.293	0.366	SUBCLONAL	1	TRUE	1	0.920346251233543	2		558	655	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302857	15302857	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140914494	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	326	801	0	ENST00000263388.2:c.593C>T	p.Ala198Val	p.A198V	ENST00000263388	NM_000435.2	198	gCg/gTg	4/33	1	2	FACETS	0.963	0.915	1	0.963	0.915	1	CLONAL	1	TRUE	1	0.920346251233543	2		801	736	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349666	15349666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200976853	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	341	720	0	ENST00000263377.2:c.3908C>T	p.Ala1303Val	p.A1303V	ENST00000263377	NM_058243.2	1303	gCg/gTg	19/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.920346251233543	2		720	726	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18960916	18960916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	276	564	0	ENST00000262803.5:c.494G>A	p.Cys165Tyr	p.C165Y	ENST00000262803	NM_002911.3	165	tGc/tAc	4/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.920346251233543	2		564	584	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967089	18967089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334288478	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	256	495	0	ENST00000262803.5:c.1804G>A	p.Ala602Thr	p.A602T	ENST00000262803	NM_002911.3	602	Gca/Aca	13/24	1	2	FACETS	0.933	0.881	0.986	0.933	0.881	0.986	CLONAL	1	TRUE	1	0.920346251233543	2		495	596	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976208	18976208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	385	745	1	ENST00000262803.5:c.2968C>T	p.Pro990Ser	p.P990S	ENST00000262803	NM_002911.3	990	Cca/Tca	21/24	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.920346251233543	2		746	798	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312915	30312915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1411284279	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	299	613	0	ENST00000262643.3:c.718C>T	p.Arg240Cys	p.R240C	ENST00000262643	NM_001238.2	240	Cgt/Tgt	9/12	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.920346251233543	2		613	644	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216702	36216702	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748120825	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	326	653	0	ENST00000222270.7:c.3868C>T	p.Arg1290Cys	p.R1290C	ENST00000222270	NM_014727.1	1290	Cgc/Tgc	13/37	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.920346251233543	2		653	707	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762911	40762911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	322	611	0	ENST00000392038.2:c.97G>A	p.Gly33Ser	p.G33S	ENST00000392038	NM_001626.4	33	Ggc/Agc	3/14	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.920346251233543	2		611	699	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765753	41765753	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761731744	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	295	601	0	ENST00000301178.4:c.2629G>A	p.Ala877Thr	p.A877T	ENST00000301178	NM_021913.4	877	Gct/Act	20/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.920346251233543	2		601	611	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793541	42793541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1256145408	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	284	577	0	ENST00000575354.2:c.1343G>A	p.Gly448Glu	p.G448E	ENST00000575354	NM_015125.3	448	gGg/gAg	8/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.920346251233543	2		577	604	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796484	42796484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780624177	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	342	663	0	ENST00000575354.2:c.3041C>T	p.Ala1014Val	p.A1014V	ENST00000575354	NM_015125.3	1014	gCg/gTg	13/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.920346251233543	2		663	704	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797191	42797191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778202	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	341	742	0	ENST00000575354.2:c.3553G>A	p.Ala1185Thr	p.A1185T	ENST00000575354	NM_015125.3	1185	Gcc/Acc	15/20	1	2	FACETS	0.951	0.905	0.997	0.951	0.905	0.997	CLONAL	1	TRUE	1	0.920346251233543	2		742	779	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422059	47422059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	338	634	0	ENST00000404338.3:c.127G>A	p.Val43Met	p.V43M	ENST00000404338	NM_004491.4	43	Gtg/Atg	1/6	1	2	FACETS	0.974	0.927	1	0.974	0.927	1	CLONAL	1	TRUE	1	0.920346251233543	2		634	754	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422062	47422062	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774121374	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	175	623	0	ENST00000404338.3:c.130C>T	p.Arg44Cys	p.R44C	ENST00000404338	NM_004491.4	44	Cgc/Tgc	1/6	1	2	FACETS	0.507	0.468	0.548	0.507	0.468	0.548	SUBCLONAL	1	TRUE	1	0.920346251233543	2		623	750	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910249	50910249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777866589	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	69	445	0	ENST00000440232.2:c.1504G>A	p.Asp502Asn	p.D502N	ENST00000440232	NM_002691.3	502	Gac/Aac	13/27	1	2	FACETS	0.286	0.249	0.326	0.286	0.249	0.326	SUBCLONAL	1	TRUE	1	0.920346251233543	2		445	524	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912061	50912061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149569984	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	117	614	0	ENST00000440232.2:c.1795G>A	p.Ala599Thr	p.A599T	ENST00000440232	NM_002691.3	599	Gcc/Acc	15/27	1	2	FACETS	0.374	0.337	0.412	0.374	0.337	0.412	SUBCLONAL	1	TRUE	1	0.920346251233543	2		614	680	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912440	50912440	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	279	573	0	ENST00000440232.2:c.1954C>T	p.Arg652Trp	p.R652W	ENST00000440232	NM_002691.3	652	Cgg/Tgg	16/27	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.920346251233543	2		573	573	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723002	52723002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	316	630	0	ENST00000322088.6:c.1187G>A	p.Gly396Asp	p.G396D	ENST00000322088	NM_014225.5	396	gGc/gAc	10/15	1	2	FACETS	0.988	0.939	1	0.988	0.939	1	CLONAL	1	TRUE	1	0.920346251233543	2		630	695	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52729039	52729039	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	313	678	0	ENST00000322088.6:c.1731C>A	p.Tyr577Ter	p.Y577*	ENST00000322088	NM_014225.5	577	taC/taA	14/15	1	2	FACETS	0.937	0.89	0.985	0.937	0.89	0.985	CLONAL	1	TRUE	1	0.920346251233543	2		678	726	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468900	25468900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566390868	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	249	531	0	ENST00000264709.3:c.1463G>A	p.Arg488Gln	p.R488Q	ENST00000264709	NM_175629.2	488	cGg/cAg	12/23	1	2	FACETS	0.975	0.921	1	0.975	0.921	1	CLONAL	1	TRUE	1	0.920346251233543	2		531	555	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469940	25469940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1347653303	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	294	567	0	ENST00000264709.3:c.1102G>A	p.Ala368Thr	p.A368T	ENST00000264709	NM_175629.2	368	Gcc/Acc	9/23	1	2	FACETS	0.958	0.908	1	0.958	0.908	1	CLONAL	1	TRUE	1	0.920346251233543	2		567	667	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965049	25965049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780551383	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	297	655	0	ENST00000435504.4:c.4157C>T	p.Ala1386Val	p.A1386V	ENST00000435504		1386	gCg/gTg	13/13	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.920346251233543	2		655	624	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443675	29443675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1034835558	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	300	571	0	ENST00000389048.3:c.3542G>A	p.Arg1181His	p.R1181H	ENST00000389048	NM_004304.4	1181	cGc/cAc	23/29	1	2	FACETS	0.943	0.895	0.992	0.943	0.895	0.992	CLONAL	1	TRUE	1	0.920346251233543	2		571	691	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028225	48028225	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63749999	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	277	598	0	ENST00000234420.5:c.3103C>T	p.Arg1035Ter	p.R1035*	ENST00000234420	NM_000179.2	1035	Cga/Tga	4/10	1	2	FACETS	0.907	0.857	0.956	0.907	0.857	0.956	CLONAL	1	TRUE	1	0.920346251233543	2		598	664	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147533	61147533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561660110	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	130	271	0	ENST00000295025.8:c.938G>A	p.Arg313His	p.R313H	ENST00000295025	NM_002908.2	313	cGc/cAc	9/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.920346251233543	2		271	229	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719525	61719525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	225	606	0	ENST00000401558.2:c.1658G>A	p.Arg553His	p.R553H	ENST00000401558	NM_003400.3	553	cGt/cAt	15/25	1	2	FACETS	0.984	0.926	1	0.984	0.926	1	CLONAL	1	TRUE	1	0.920346251233543	2		606	497	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172091	99172091	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776893699	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	364	717	0	ENST00000074304.5:c.1657C>T	p.Arg553Trp	p.R553W	ENST00000074304	NM_001134224.1	553	Cgg/Tgg	17/26	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.920346251233543	2		717	779	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185083	99185083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764302181	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	101	543	1	ENST00000074304.5:c.2485C>T	p.Arg829Trp	p.R829W	ENST00000074304	NM_001134224.1	829	Cgg/Tgg	23/26	1	2	FACETS	0.375	0.335	0.416	0.375	0.335	0.416	SUBCLONAL	1	TRUE	1	0.920346251233543	2		544	586	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193461	99193461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	310	585	0	ENST00000074304.5:c.2656C>T	p.Arg886Cys	p.R886C	ENST00000074304	NM_001134224.1	886	Cgc/Tgc	25/26	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.920346251233543	2		585	667	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015293	128015293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770995913	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	170	542	0	ENST00000285398.2:c.2228G>A	p.Arg743His	p.R743H	ENST00000285398	NM_000122.1	743	cGc/cAc	15/15	1	2	FACETS	0.535	0.493	0.578	0.535	0.493	0.578	SUBCLONAL	1	TRUE	1	0.920346251233543	2		542	691	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617517	158617517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	38	641	0	ENST00000263640.3:c.1139G>A	p.Arg380His	p.R380H	ENST00000263640	NM_001105.4	380	cGc/cAc	9/11	1	2	FACETS	0.116	0.095	0.14	0.116	0.095	0.14	SUBCLONAL	1	TRUE	1	0.920346251233543	2		641	710	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634719	158634719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755732603	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	176	656	1	ENST00000263640.3:c.467G>A	p.Arg156His	p.R156H	ENST00000263640	NM_001105.4	156	cGc/cAc	5/11	1	2	FACETS	0.479	0.442	0.518	0.479	0.442	0.518	SUBCLONAL	1	TRUE	1	0.920346251233543	2		657	798	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578341	212578341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1216559792	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	191	518	1	ENST00000342788.4:c.916C>T	p.Arg306Cys	p.R306C	ENST00000342788	NM_005235.2	306	Cgt/Tgt	8/28	1	2	FACETS	0.97	0.908	1	0.97	0.908	1	CLONAL	1	TRUE	1	0.920346251233543	2		519	428	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215595163	215595163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377227840	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	164	499	0	ENST00000260947.4:c.1973G>A	p.Arg658His	p.R658H	ENST00000260947	NM_000465.2	658	cGc/cAc	10/11	1	2	FACETS	0.873	0.811	0.937	0.873	0.811	0.937	CLONAL	1	TRUE	1	0.920346251233543	2		499	408	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439742	220439742	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257387062	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	392	784	0	ENST00000243786.2:c.595C>T	p.Arg199Cys	p.R199C	ENST00000243786	NM_002191.3	199	Cgc/Tgc	2/2	1	2	FACETS	0.978	0.935	1	0.978	0.935	1	CLONAL	1	TRUE	1	0.920346251233543	2		784	871	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400261	225400261	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	195	434	0	ENST00000264414.4:c.362A>G	p.Asp121Gly	p.D121G	ENST00000264414	NM_003590.4	121	gAc/gGc	3/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.920346251233543	2		434	404	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660213	227660213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372681714	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	305	740	0	ENST00000305123.5:c.3242G>A	p.Arg1081His	p.R1081H	ENST00000305123	NM_005544.2	1081	cGc/cAc	1/2	1	2	FACETS	0.928	0.881	0.976	0.928	0.881	0.976	CLONAL	1	TRUE	1	0.920346251233543	2		740	714	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661977	227661977	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	317	750	0	ENST00000305123.5:c.1478G>A	p.Arg493His	p.R493H	ENST00000305123	NM_005544.2	493	cGc/cAc	1/2	1	2	FACETS	0.966	0.918	1	0.966	0.918	1	CLONAL	1	TRUE	1	0.920346251233543	2		750	713	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662527	227662527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1428460249	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	389	727	3	ENST00000305123.5:c.928G>A	p.Ala310Thr	p.A310T	ENST00000305123	NM_005544.2	310	Gcc/Acc	1/2	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.920346251233543	2		730	832	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561268	9561268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749763005	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	281	637	0	ENST00000353224.5:c.514G>A	p.Val172Ile	p.V172I	ENST00000353224	NM_177990.2	172	Gta/Ata	4/10	1	2	FACETS	0.957	0.907	1	0.957	0.907	1	CLONAL	1	TRUE	1	0.920346251233543	2		637	638	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253828	30253828	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768665664	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	146	633	0	ENST00000307677.4:c.626G>A	p.Arg209His	p.R209H	ENST00000307677	NM_138578.1	209	cGc/cAc	3/3	1	2	FACETS	0.458	0.419	0.499	0.458	0.419	0.499	SUBCLONAL	1	TRUE	1	0.920346251233543	2		633	693	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021634	31021634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137920574	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	39	656	0	ENST00000375687.4:c.1633C>T	p.Arg545Cys	p.R545C	ENST00000375687	NM_015338.5	545	Cgt/Tgt	12/13	1	2	FACETS	0.114	0.094	0.137	0.114	0.094	0.137	SUBCLONAL	1	TRUE	1	0.920346251233543	2		656	741	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022422	31022422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370230857	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	336	759	1	ENST00000375687.4:c.1907C>T	p.Ala636Val	p.A636V	ENST00000375687	NM_015338.5	636	gCg/gTg	13/13	1	2	FACETS	0.983	0.936	1	0.983	0.936	1	CLONAL	1	TRUE	1	0.920346251233543	2		760	743	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023430	31023430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	283	632	0	ENST00000375687.4:c.2915G>A	p.Gly972Asp	p.G972D	ENST00000375687	NM_015338.5	972	gGc/gAc	13/13	1	2	FACETS	0.994	0.942	1	0.994	0.942	1	CLONAL	1	TRUE	1	0.920346251233543	2		632	619	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395677	31395677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1267164985	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	316	663	0	ENST00000328111.2:c.2530G>A	p.Ala844Thr	p.A844T	ENST00000328111	NM_006892.3	844	Gcc/Acc	23/23	1	2	FACETS	0.98	0.931	1	0.98	0.931	1	CLONAL	1	TRUE	1	0.920346251233543	2		663	701	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031609	36031609	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479989919	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	164	684	1	ENST00000358208.4:c.1438C>T	p.Arg480Trp	p.R480W	ENST00000358208		480	Cgg/Tgg	12/12	1	2	FACETS	0.517	0.475	0.559	0.517	0.475	0.559	SUBCLONAL	1	TRUE	1	0.920346251233543	2		685	690	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944608	40944608	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs752116362	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	271	535	0	ENST00000373198.4:c.1894C>T	p.Arg632Ter	p.R632*	ENST00000373198	NM_133170.3	632	Cga/Tga	12/32	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.920346251233543	2		535	559	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101119	41101119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755381090	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	292	705	2	ENST00000373198.4:c.1237G>A	p.Ala413Thr	p.A413T	ENST00000373198	NM_133170.3	413	Gcg/Acg	8/32	1	2	FACETS	0.948	0.899	0.998	0.948	0.899	0.998	CLONAL	1	TRUE	1	0.920346251233543	2		707	669	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385240	41385240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	276	577	0	ENST00000373198.4:c.721C>T	p.Arg241Cys	p.R241C	ENST00000373198	NM_133170.3	241	Cgt/Tgt	6/32	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.920346251233543	2		577	583	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256409	46256409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754382773	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	264	675	0	ENST00000371998.3:c.637G>A	p.Ala213Thr	p.A213T	ENST00000371998		213	Gcc/Acc	7/23	1	2	FACETS	0.931	0.88	0.983	0.931	0.88	0.983	CLONAL	1	TRUE	1	0.920346251233543	2		675	616	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262365	46262365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766234778	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	242	539	0	ENST00000371998.3:c.949C>T	p.Arg317Cys	p.R317C	ENST00000371998		317	Cgt/Tgt	9/23	1	2	FACETS	0.931	0.877	0.985	0.931	0.877	0.985	CLONAL	1	TRUE	1	0.920346251233543	2		539	565	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164889	36164889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1358657401	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	352	733	0	ENST00000300305.3:c.986C>T	p.Ala329Val	p.A329V	ENST00000300305		329	gCg/gTg	8/8	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.920346251233543	2		733	738	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206809	36206809	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	335	668	0	ENST00000300305.3:c.703G>A	p.Ala235Thr	p.A235T	ENST00000300305		235	Gcc/Acc	6/8	1	2	FACETS	0.978	0.931	1	0.978	0.931	1	CLONAL	1	TRUE	1	0.920346251233543	2		668	744	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651216	45651216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200793282	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	363	637	0	ENST00000407780.3:c.809C>T	p.Ala270Val	p.A270V	ENST00000407780	NM_001283052.1	270	gCg/gTg	5/7	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.920346251233543	2		637	742	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656769	45656769	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	297	581	0	ENST00000407780.3:c.387G>T	p.Glu129Asp	p.E129D	ENST00000407780	NM_001283052.1	129	gaG/gaT	3/7	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.920346251233543	2		581	582	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095881	29095881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143611747	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	72	465	0	ENST00000328354.6:c.953G>A	p.Arg318His	p.R318H	ENST00000328354	NM_007194.3	318	cGc/cAc	9/15	1	2	FACETS	0.271	0.236	0.308	0.271	0.236	0.308	SUBCLONAL	1	TRUE	1	0.920346251233543	2		465	578	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067867	30067867	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771675702	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	332	590	0	ENST00000338641.4:c.1052G>A	p.Arg351His	p.R351H	ENST00000338641	NM_000268.3	351	cGc/cAc	11/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.920346251233543	2		590	691	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070875	30070875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776109136	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	274	566	0	ENST00000338641.4:c.1391C>T	p.Ala464Val	p.A464V	ENST00000338641	NM_000268.3	464	gCg/gTg	13/16	1	2	FACETS	0.916	0.866	0.966	0.916	0.866	0.966	CLONAL	1	TRUE	1	0.920346251233543	2		566	650	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627983	37627983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375471633	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	330	613	0	ENST00000249071.6:c.277G>A	p.Val93Ile	p.V93I	ENST00000249071	NM_002872.4	93	Gtc/Atc	4/7	1	2	FACETS	0.957	0.911	1	0.957	0.911	1	CLONAL	1	TRUE	1	0.920346251233543	2		613	749	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513352	41513352	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	93	678	0	ENST00000263253.7:c.256C>T	p.Arg86Ter	p.R86*	ENST00000263253	NM_001429.3	86	Cga/Tga	2/31	1	2	FACETS	0.29	0.258	0.325	0.29	0.258	0.325	SUBCLONAL	1	TRUE	1	0.920346251233543	2		678	696	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574502	41574502	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	339	712	0	ENST00000263253.7:c.6787C>T	p.Arg2263Ter	p.R2263*	ENST00000263253	NM_001429.3	2263	Cga/Tga	31/31	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.920346251233543	2		712	727	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458536	12458536	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs780238349	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	295	672	2	ENST00000287820.6:c.1153C>T	p.Arg385Ter	p.R385*	ENST00000287820	NM_015869.4	385	Cga/Tga	6/7	1	2	FACETS	0.92	0.872	0.968	0.92	0.872	0.968	CLONAL	1	TRUE	1	0.920346251233543	2		674	697	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660217	12660217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	276	537	0	ENST00000251849.4:c.4G>A	p.Glu2Lys	p.E2K	ENST00000251849	NM_002880.3	2	Gag/Aag	2/17	1	2	FACETS	0.972	0.921	1	0.972	0.921	1	CLONAL	1	TRUE	1	0.920346251233543	2		537	617	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180279	38180279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	184	712	1	ENST00000396334.3:c.127C>T	p.Arg43Trp	p.R43W	ENST00000396334	NM_002468.4	43	Cgg/Tgg	1/5	1	2	FACETS	0.592	0.549	0.637	0.592	0.549	0.637	SUBCLONAL	1	TRUE	1	0.920346251233543	2		713	675	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266963	41266963	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770795614	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	344	776	0	ENST00000349496.5:c.634C>T	p.Arg212Cys	p.R212C	ENST00000349496	NM_001904.3	212	Cgt/Tgt	5/15	1	2	FACETS	0.99	0.943	1	0.99	0.943	1	CLONAL	1	TRUE	1	0.920346251233543	2		776	755	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274839	41274839	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	202	530	3	ENST00000349496.5:c.1089G>A	p.Met363Ile	p.M363I	ENST00000349496	NM_001904.3	363	atG/atA	8/15	1	2	FACETS	0.92	0.862	0.979	0.92	0.862	0.979	CLONAL	1	TRUE	1	0.920346251233543	2		533	477	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098912	47098912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	307	619	0	ENST00000409792.3:c.6362G>A	p.Arg2121His	p.R2121H	ENST00000409792	NM_014159.6	2121	cGc/cAc	15/21	1	2	FACETS	0.988	0.939	1	0.988	0.939	1	CLONAL	1	TRUE	1	0.920346251233543	2		619	675	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143033	47143033	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	198	359	0	ENST00000409792.3:c.4930G>A	p.Gly1644Arg	p.G1644R	ENST00000409792	NM_014159.6	1644	Gga/Aga	8/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.920346251233543	2		359	399	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164413	47164414	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	213	557	0	ENST00000409792.3:c.1712dup	p.Asn571LysfsTer10	p.N571Kfs*10	ENST00000409792	NM_014159.6	571	aat/aaAt	3/21	1	2	FACETS	0.872	0.817	0.927	0.872	0.817	0.927	CLONAL	1	TRUE	1	0.920346251233543	2		557	531	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49724695	49724695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	175	477	0	ENST00000449682.2:c.494G>A	p.Gly165Asp	p.G165D	ENST00000449682	NM_020998.3	165	gGc/gAc	5/18	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.920346251233543	2		477	380	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927986	49927986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372063160	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	278	602	0	ENST00000296474.3:c.3742C>T	p.Arg1248Cys	p.R1248C	ENST00000296474	NM_002447.2	1248	Cgc/Tgc	18/20	1	2	FACETS	0.925	0.875	0.975	0.925	0.875	0.975	CLONAL	1	TRUE	1	0.920346251233543	2		602	653	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927994	49927994	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772999107	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	302	611	0	ENST00000296474.3:c.3734G>A	p.Arg1245His	p.R1245H	ENST00000296474	NM_002447.2	1245	cGc/cAc	18/20	1	2	FACETS	0.987	0.937	1	0.987	0.937	1	CLONAL	1	TRUE	1	0.920346251233543	2		611	665	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437440	52437440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761596789	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	290	676	0	ENST00000460680.1:c.1721C>T	p.Ala574Val	p.A574V	ENST00000460680	NM_004656.3	574	gCg/gTg	13/17	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.920346251233543	2		676	605	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643362	52643362	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs774153419	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	251	527	0	ENST00000394830.3:c.2534T>C	p.Phe845Ser	p.F845S	ENST00000394830	NM_018313.4	845	tTt/tCt	17/30	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.920346251233543	2		527	521	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027093	71027093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200629338	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	440	747	0	ENST00000318789.4:c.1234G>A	p.Ala412Thr	p.A412T	ENST00000318789	NM_032682.5	412	Gcc/Acc	15/21	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.920346251233543	2		747	767	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259196	89259196	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	284	596	0	ENST00000336596.2:c.340G>T	p.Gly114Ter	p.G114*	ENST00000336596	NM_005233.5	114	Gga/Tga	3/17	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.920346251233543	2		596	574	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390123	89390123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355784567	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	248	555	0	ENST00000336596.2:c.872C>T	p.Pro291Leu	p.P291L	ENST00000336596	NM_005233.5	291	cCg/cTg	4/17	1	2	FACETS	0.936	0.883	0.989	0.936	0.883	0.989	CLONAL	1	TRUE	1	0.920346251233543	2		555	576	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873100	134873100	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	224	481	0	ENST00000398015.3:c.1404G>T	p.Glu468Asp	p.E468D	ENST00000398015	NM_004441.4	468	gaG/gaT	6/16	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.920346251233543	2		481	479	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911607	134911607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1384145752	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	262	595	0	ENST00000398015.3:c.2072G>A	p.Arg691Gln	p.R691Q	ENST00000398015	NM_004441.4	691	cGg/cAg	11/16	1	2	FACETS	0.884	0.834	0.934	0.884	0.834	0.934	CLONAL	1	TRUE	1	0.920346251233543	2		595	644	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920370	134920370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542190087	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	311	613	0	ENST00000398015.3:c.2185G>A	p.Ala729Thr	p.A729T	ENST00000398015	NM_004441.4	729	Gct/Act	12/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.920346251233543	2		613	665	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453566	138453566	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	203	541	0	ENST00000289153.2:c.882A>C	p.Glu294Asp	p.E294D	ENST00000289153	NM_006219.2	294	gaA/gaC	5/22	1	2	FACETS	0.941	0.882	1	0.941	0.882	1	CLONAL	1	TRUE	1	0.920346251233543	2		541	469	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204007	142204007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369309229	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	203	522	0	ENST00000350721.4:c.6196C>T	p.Arg2066Trp	p.R2066W	ENST00000350721	NM_001184.3	2066	Cgg/Tgg	36/47	1	2	FACETS	0.85	0.795	0.906	0.85	0.795	0.906	CLONAL	1	TRUE	1	0.920346251233543	2		522	519	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149238690	149238690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765794546	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	263	690	0	ENST00000360632.3:c.1105G>A	p.Val369Ile	p.V369I	ENST00000360632	NM_015472.4	369	Gtt/Att	7/7	1	2	FACETS	0.922	0.871	0.973	0.922	0.871	0.973	CLONAL	1	TRUE	1	0.920346251233543	2		690	620	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916875	178916875	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	245	619	0	ENST00000263967.3:c.262C>T	p.Arg88Ter	p.R88*	ENST00000263967	NM_006218.2	88	Cga/Tga	2/21	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.920346251233543	2		619	526	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928310	178928310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	198	526	0	ENST00000263967.3:c.1496C>T	p.Ser499Phe	p.S499F	ENST00000263967	NM_006218.2	499	tCt/tTt	9/21	1	2	FACETS	0.857	0.801	0.914	0.857	0.801	0.914	CLONAL	1	TRUE	1	0.920346251233543	2		526	502	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183540	185183540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	240	467	0	ENST00000265026.3:c.1394C>T	p.Ala465Val	p.A465V	ENST00000265026	NM_004721.4	465	gCg/gTg	9/14	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.920346251233543	2		467	501	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184657	185184657	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs56408536	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	293	584	0	ENST00000265026.3:c.1549C>T	p.Arg517Ter	p.R517*	ENST00000265026	NM_004721.4	517	Cga/Tga	10/14	1	2	FACETS	0.984	0.934	1	0.984	0.934	1	CLONAL	1	TRUE	1	0.920346251233543	2		584	647	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198177	185198177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs889834349	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	322	647	0	ENST00000265026.3:c.2659G>A	p.Asp887Asn	p.D887N	ENST00000265026	NM_004721.4	887	Gac/Aac	13/14	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.920346251233543	2		647	690	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440335	187440335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	251	538	0	ENST00000232014.4:c.2032C>T	p.Arg678Cys	p.R678C	ENST00000232014	NM_001130845.1	678	Cgc/Tgc	10/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.920346251233543	2		538	545	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586503	189586503	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs143591434	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	157	576	0	ENST00000264731.3:c.1127G>A	p.Arg376His	p.R376H	ENST00000264731	NM_003722.4	376	cGc/cAc	8/14	1	2	FACETS	0.583	0.537	0.631	0.583	0.537	0.631	SUBCLONAL	1	TRUE	1	0.920346251233543	2		576	585	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803663	1803663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	370	675	0	ENST00000260795.2:c.841G>A	p.Ala281Thr	p.A281T	ENST00000260795		281	Gca/Aca	6/17	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.920346251233543	2		675	782	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1918645	1918645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372805518	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	304	480	0	ENST00000382891.5:c.808G>A	p.Ala270Thr	p.A270T	ENST00000382891	NM_133335.3	270	Gcc/Acc	4/22	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.920346251233543	2		480	602	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1978262	1978262	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	328	707	3	ENST00000382891.5:c.3682C>T	p.Arg1228Cys	p.R1228C	ENST00000382891	NM_133335.3	1228	Cgc/Tgc	21/22	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.920346251233543	2		710	699	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133559	55133559	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	379	582	0	ENST00000257290.5:c.863A>G	p.Tyr288Cys	p.Y288C	ENST00000257290	NM_006206.4	288	tAc/tGc	6/23	0.148878911547719	4	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.920346251233543	4		582	714	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161380	55161380	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376544204	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	290	497	0	ENST00000257290.5:c.3211G>A	p.Asp1071Asn	p.D1071N	ENST00000257290	NM_006206.4	1071	Gac/Aac	23/23	0.148878911547719	4	FACETS	0.889	0.842	0.936			1	INDETERMINATE	2	TRUE	NA	0.920346251233543	4		497	681	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575594	55575594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs73137716	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	162	333	0	ENST00000288135.5:c.1120G>A	p.Val374Ile	p.V374I	ENST00000288135	NM_000222.2	374	Gta/Ata	7/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.920346251233543	2		333	325	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808246	99808246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776434815	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	180	417	0	ENST00000280892.6:c.443G>A	p.Arg148His	p.R148H	ENST00000280892	NM_001130678.1	148	cGc/cAc	5/7	1	2	FACETS	0.995	0.931	1	0.995	0.931	1	CLONAL	1	TRUE	1	0.920346251233543	2		417	393	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156139	106156139	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755979073	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	320	717	0	ENST00000380013.4:c.1040C>T	p.Ala347Val	p.A347V	ENST00000380013	NM_001127208.2	347	gCg/gTg	3/11	1	2	FACETS	0.964	0.917	1	0.964	0.917	1	CLONAL	1	TRUE	1	0.920346251233543	2		717	721	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244049	153244049	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	330	686	0	ENST00000281708.4:c.2108A>G	p.Asp703Gly	p.D703G	ENST00000281708	NM_033632.3	703	gAt/gGt	12/12	1	2	FACETS	0.988	0.94	1	0.988	0.94	1	CLONAL	1	TRUE	1	0.920346251233543	2		686	726	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245429	153245429	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	251	564	0	ENST00000281708.4:c.1762G>T	p.Glu588Ter	p.E588*	ENST00000281708	NM_033632.3	588	Gaa/Taa	11/12	1	2	FACETS	0.997	0.942	1	0.997	0.942	1	CLONAL	1	TRUE	1	0.920346251233543	2		564	547	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534484	187534484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748020206	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	259	553	0	ENST00000441802.2:c.9242C>T	p.Thr3081Met	p.T3081M	ENST00000441802	NM_005245.3	3081	aCg/aTg	13/27	1	2	FACETS	0.972	0.919	1	0.972	0.919	1	CLONAL	1	TRUE	1	0.920346251233543	2		553	579	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540874	187540874	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs562612394	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	320	697	0	ENST00000441802.2:c.6866C>T	p.Ala2289Val	p.A2289V	ENST00000441802	NM_005245.3	2289	gCg/gTg	10/27	1	2	FACETS	0.959	0.912	1	0.959	0.912	1	CLONAL	1	TRUE	1	0.920346251233543	2		697	725	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541603	187541603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	334	706	0	ENST00000441802.2:c.6137C>T	p.Ala2046Val	p.A2046V	ENST00000441802	NM_005245.3	2046	gCg/gTg	10/27	1	2	FACETS	0.948	0.901	0.994	0.948	0.901	0.994	CLONAL	1	TRUE	1	0.920346251233543	2		706	766	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542455	187542455	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376944386	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	352	718	0	ENST00000441802.2:c.5285C>T	p.Ala1762Val	p.A1762V	ENST00000441802	NM_005245.3	1762	gCg/gTg	10/27	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.920346251233543	2		718	749	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542860	187542860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767331775	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	134	581	0	ENST00000441802.2:c.4880G>A	p.Arg1627Gln	p.R1627Q	ENST00000441802	NM_005245.3	1627	cGa/cAa	10/27	1	2	FACETS	0.511	0.466	0.558	0.511	0.466	0.558	SUBCLONAL	1	TRUE	1	0.920346251233543	2		581	570	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628026	187628026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750746155	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	284	637	0	ENST00000441802.2:c.2956G>A	p.Val986Ile	p.V986I	ENST00000441802	NM_005245.3	986	Gtc/Atc	2/27	1	2	FACETS	0.912	0.863	0.961	0.912	0.863	0.961	CLONAL	1	TRUE	1	0.920346251233543	2		637	677	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630542	187630542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	300	679	0	ENST00000441802.2:c.440C>T	p.Pro147Leu	p.P147L	ENST00000441802	NM_005245.3	147	cCg/cTg	2/27	1	2	FACETS	0.939	0.891	0.988	0.939	0.891	0.988	CLONAL	1	TRUE	1	0.920346251233543	2		679	694	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251198	251198	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	115	242	0	ENST00000264932.6:c.1643A>G	p.His548Arg	p.H548R	ENST00000264932	NM_004168.2	548	cAc/cGc	12/15	1	2	FACETS	0.98	0.9	1	0.98	0.9	1	CLONAL	1	TRUE	1	0.920346251233543	2		242	255	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410922	31410922	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1396439517	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	324	620	0	ENST00000344624.3:c.3598G>A	p.Ala1200Thr	p.A1200T	ENST00000344624		1200	Gcc/Acc	28/33	1	2	FACETS	0.983	0.935	1	0.983	0.935	1	CLONAL	1	TRUE	1	0.920346251233543	2		620	716	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31504712	31504712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369576938	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	258	535	0	ENST00000344624.3:c.1618G>A	p.Ala540Thr	p.A540T	ENST00000344624		540	Gca/Aca	8/33	1	2	FACETS	0.901	0.851	0.953	0.901	0.851	0.953	CLONAL	1	TRUE	1	0.920346251233543	2		535	622	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947452	38947452	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1406752443	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	114	609	0	ENST00000357387.3:c.4228C>T	p.Arg1410Trp	p.R1410W	ENST00000357387	NM_152756.3	1410	Cgg/Tgg	32/38	1	2	FACETS	0.456	0.412	0.502	0.456	0.412	0.502	SUBCLONAL	1	TRUE	1	0.920346251233543	2		609	543	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963091	38963091	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	184	484	0	ENST00000357387.3:c.1453C>T	p.Arg485Ter	p.R485*	ENST00000357387	NM_152756.3	485	Cga/Tga	17/38	1	2	FACETS	0.883	0.824	0.943	0.883	0.824	0.943	CLONAL	1	TRUE	1	0.920346251233543	2		484	453	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155654	56155654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746479827	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	305	533	0	ENST00000399503.3:c.746G>A	p.Arg249His	p.R249H	ENST00000399503	NM_005921.1	249	cGc/cAc	3/20	1	2	FACETS	0.969	0.92	1	0.969	0.92	1	CLONAL	1	TRUE	1	0.920346251233543	2		533	684	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176540	56176540	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1305030339	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	30	507	1	ENST00000399503.3:c.2090G>A	p.Arg697His	p.R697H	ENST00000399503	NM_005921.1	697	cGc/cAc	12/20	1	2	FACETS	0.118	0.094	0.145	0.118	0.094	0.145	SUBCLONAL	1	TRUE	1	0.920346251233543	2		508	553	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178617	56178617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763984353	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	273	665	0	ENST00000399503.3:c.3590C>T	p.Ala1197Val	p.A1197V	ENST00000399503	NM_005921.1	1197	gCg/gTg	14/20	1	2	FACETS	0.883	0.834	0.932	0.883	0.834	0.932	CLONAL	1	TRUE	1	0.920346251233543	2		665	672	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591092	67591092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554051268	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	216	538	1	ENST00000274335.5:c.1685G>A	p.Arg562His	p.R562H	ENST00000274335		562	cGt/cAt	12/15	1	2	FACETS	0.926	0.869	0.983	0.926	0.869	0.983	CLONAL	1	TRUE	1	0.920346251233543	2		539	507	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679558	86679558	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561328441	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	148	406	0	ENST00000274376.6:c.2719C>T	p.Pro907Ser	p.P907S	ENST00000274376	NM_002890.2	907	Cct/Tct	21/25	1	2	FACETS	0.987	0.916	1	0.987	0.916	1	CLONAL	1	TRUE	1	0.920346251233543	2		406	326	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685330	86685330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	253	467	0	ENST00000274376.6:c.3046C>T	p.Arg1016Cys	p.R1016C	ENST00000274376	NM_002890.2	1016	Cgt/Tgt	24/25	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.920346251233543	2		467	502	SUCCESS
APC	324	MSKCC	GRCh37	5	112178606	112178606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1311878041	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	94	634	0	ENST00000257430.4:c.7315C>T	p.Arg2439Cys	p.R2439C	ENST00000257430	NM_000038.5	2439	Cgc/Tgc	16/16	1	2	FACETS	0.357	0.318	0.398	0.357	0.318	0.398	SUBCLONAL	1	TRUE	1	0.920346251233543	2		634	572	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924403	131924403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1184353235	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	223	469	0	ENST00000265335.6:c.1076G>A	p.Arg359His	p.R359H	ENST00000265335		359	cGc/cAc	8/25	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.920346251233543	2		469	454	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522563	176522563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777277309	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	357	764	0	ENST00000292408.4:c.1660G>A	p.Ala554Thr	p.A554T	ENST00000292408	NM_213647.1	554	Gcc/Acc	13/18	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.920346251233543	2		764	750	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707759	176707759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	377	673	0	ENST00000439151.2:c.5816G>A	p.Arg1939His	p.R1939H	ENST00000439151	NM_022455.4	1939	cGc/cAc	18/23	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.920346251233543	2		673	773	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052965	180052965	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367879842	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	301	776	0	ENST00000261937.6:c.1325C>T	p.Ala442Val	p.A442V	ENST00000261937	NM_182925.4	442	gCc/gTc	10/30	1	2	FACETS	0.94	0.891	0.989	0.94	0.891	0.989	CLONAL	1	TRUE	1	0.920346251233543	2		776	696	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407527	407527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs908661692	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	520	572	1	ENST00000380956.4:c.1285G>A	p.Asp429Asn	p.D429N	ENST00000380956	NM_001195286.1	429	Gat/Aat	9/9	0.920346251233543	2	FACETS	0.991	0.975	1	0.991	0.975	1	CLONAL	2	TRUE	0	0.920346251233543	2		573	570	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681678	30681678	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	362	738	0	ENST00000376406.3:c.419T>C	p.Val140Ala	p.V140A	ENST00000376406	NM_014641.2	140	gTc/gCc	3/15	1	2	FACETS	0.985	0.939	1	0.985	0.939	1	CLONAL	1	TRUE	1	0.920346251233543	2		738	799	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31238891	31238891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61759943	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	43	557	0	ENST00000376228.5:c.578G>A	p.Arg193His	p.R193H	ENST00000376228	NM_002117.5	193	cGc/cAc	3/8	1	2	FACETS	0.183	0.153	0.217	0.183	0.153	0.217	SUBCLONAL	1	TRUE	1	0.920346251233543	2		557	510	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652083	36652083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748758330	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	165	832	1	ENST00000244741.5:c.205C>T	p.Arg69Trp	p.R69W	ENST00000244741	NM_000389.4	69	Cgg/Tgg	2/3	1	2	FACETS	0.466	0.428	0.505	0.466	0.428	0.505	SUBCLONAL	1	TRUE	1	0.920346251233543	2		833	770	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94129005	94129005	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	146	572	0	ENST00000369303.4:c.55C>T	p.Leu19Phe	p.L19F	ENST00000369303	NM_004440.3	19	Ctc/Ttc	1/17	1	2	FACETS	0.52	0.476	0.566	0.52	0.476	0.566	SUBCLONAL	1	TRUE	1	0.920346251233543	2		572	610	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642495	117642495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs9489124	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	72	775	0	ENST00000368508.3:c.5704G>A	p.Glu1902Lys	p.E1902K	ENST00000368508	NM_002944.2	1902	Gaa/Aaa	35/43	1	2	FACETS	0.205	0.179	0.234	0.205	0.179	0.234	SUBCLONAL	1	TRUE	1	0.920346251233543	2		775	763	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678076	117678076	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs373090808	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	157	459	0	ENST00000368508.3:c.3857G>A	p.Arg1286His	p.R1286H	ENST00000368508	NM_002944.2	1286	cGc/cAc	25/43	1	2	FACETS	0.975	0.907	1	0.975	0.907	1	CLONAL	1	TRUE	1	0.920346251233543	2		459	350	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710983	117710983	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	245	609	0	ENST00000368508.3:c.1289G>A	p.Gly430Asp	p.G430D	ENST00000368508	NM_002944.2	430	gGc/gAc	12/43	1	2	FACETS	0.98	0.926	1	0.98	0.926	1	CLONAL	1	TRUE	1	0.920346251233543	2		609	543	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528952	157528952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263114512	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	300	611	0	ENST00000346085.5:c.6677C>T	p.Ser2226Leu	p.S2226L	ENST00000346085	NM_020732.3	2226	tCg/tTg	20/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.920346251233543	2		611	620	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2969651	2969651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	307	552	0	ENST00000396946.4:c.1628C>T	p.Pro543Leu	p.P543L	ENST00000396946	NM_032415.4	543	cCc/cTc	12/25	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.920346251233543	2		552	632	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431650	6431650	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	153	310	1	ENST00000356142.4:c.203G>A	p.Arg68His	p.R68H	ENST00000356142	NM_018890.3	68	cGc/cAc	3/7	1	2	FACETS	0.998	0.928	1	0.998	0.928	1	CLONAL	1	TRUE	1	0.920346251233543	2		311	333	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455117	50455117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	117	518	0	ENST00000331340.3:c.664C>T	p.Arg222Cys	p.R222C	ENST00000331340	NM_006060.4	222	Cgc/Tgc	6/8	1	2	FACETS	0.51	0.462	0.56	0.51	0.462	0.56	SUBCLONAL	1	TRUE	1	0.920346251233543	2		518	499	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468224	50468224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	286	694	0	ENST00000331340.3:c.1459C>T	p.Arg487Cys	p.R487C	ENST00000331340	NM_006060.4	487	Cgt/Tgt	8/8	1	2	FACETS	0.925	0.876	0.974	0.925	0.876	0.974	CLONAL	1	TRUE	1	0.920346251233543	2		694	672	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224316	55224316	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	286	667	0	ENST00000275493.2:c.1097G>T	p.Ser366Ile	p.S366I	ENST00000275493	NM_005228.3	366	aGt/aTt	9/28	1	2	FACETS	0.967	0.916	1	0.967	0.916	1	CLONAL	1	TRUE	1	0.920346251233543	2		667	643	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240785	55240785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1417155613	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	89	688	0	ENST00000275493.2:c.2029C>T	p.Arg677Cys	p.R677C	ENST00000275493	NM_005228.3	677	Cgc/Tgc	17/28	1	2	FACETS	0.273	0.242	0.307	0.273	0.242	0.307	SUBCLONAL	1	TRUE	1	0.920346251233543	2		688	708	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509906	106509906	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	275	605	0	ENST00000359195.3:c.1900A>G	p.Asn634Asp	p.N634D	ENST00000359195	NM_002649.2	634	Aac/Gac	2/11	1	2	FACETS	0.996	0.944	1	0.996	0.944	1	CLONAL	1	TRUE	1	0.920346251233543	2		605	600	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124481102	124481102	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs758341603	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	185	483	0	ENST00000357628.3:c.1294C>T	p.Arg432Ter	p.R432*	ENST00000357628	NM_015450.2	432	Cga/Tga	14/19	1	2	FACETS	0.966	0.904	1	0.966	0.904	1	CLONAL	1	TRUE	1	0.920346251233543	2		483	416	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876974	151876974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750213944	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	276	650	0	ENST00000262189.6:c.7387C>T	p.Arg2463Cys	p.R2463C	ENST00000262189	NM_170606.2	2463	Cgt/Tgt	37/59	1	2	FACETS	0.913	0.863	0.963	0.913	0.863	0.963	CLONAL	1	TRUE	1	0.920346251233543	2		650	657	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878749	151878749	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1211949081	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	165	680	0	ENST00000262189.6:c.6196C>T	p.Arg2066Ter	p.R2066*	ENST00000262189	NM_170606.2	2066	Cga/Tga	36/59	1	2	FACETS	0.549	0.506	0.594	0.549	0.506	0.594	SUBCLONAL	1	TRUE	1	0.920346251233543	2		680	653	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902290	151902290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301632462	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	28	103	0	ENST00000262189.6:c.3862C>T	p.Arg1288Trp	p.R1288W	ENST00000262189	NM_170606.2	1288	Cgg/Tgg	25/59	1	2	FACETS	0.534	0.435	0.642	0.534	0.435	0.642	SUBCLONAL	1	TRUE	1	0.920346251233543	2		103	114	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38314904	38314904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1383262590	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	71	534	0	ENST00000425967.3:c.160G>A	p.Ala54Thr	p.A54T	ENST00000425967	NM_001174067.1	54	Gct/Act	3/19	1	2	FACETS	0.282	0.246	0.32	0.282	0.246	0.32	SUBCLONAL	1	TRUE	1	0.920346251233543	2		534	548	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965451	68965451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	231	571	0	ENST00000288368.4:c.1063G>A	p.Ala355Thr	p.A355T	ENST00000288368	NM_024870.2	355	Gct/Act	9/40	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.920346251233543	2		571	495	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136840	69136840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746734356	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	274	481	0	ENST00000288368.4:c.4754G>A	p.Arg1585Gln	p.R1585Q	ENST00000288368	NM_024870.2	1585	cGg/cAg	39/40	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.920346251233543	2		481	575	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978590	70978590	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	287	662	0	ENST00000276594.2:c.1063G>T	p.Glu355Ter	p.E355*	ENST00000276594	NM_024504.3	355	Gag/Tag	5/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.920346251233543	2		662	608	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542668	141542668	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1201563583	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	287	630	0	ENST00000220592.5:c.2318G>A	p.Arg773His	p.R773H	ENST00000220592	NM_012154.3	773	cGt/cAt	18/19	1	2	FACETS	0.976	0.925	1	0.976	0.925	1	CLONAL	1	TRUE	1	0.920346251233543	2		630	639	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141582934	141582934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199834249	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	304	588	0	ENST00000220592.5:c.313C>T	p.Pro105Ser	p.P105S	ENST00000220592	NM_012154.3	105	Ccc/Tcc	3/19	1	2	FACETS	0.967	0.918	1	0.967	0.918	1	CLONAL	1	TRUE	1	0.920346251233543	2		588	683	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739479	145739479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748941688	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	331	725	0	ENST00000428558.2:c.1891C>T	p.Arg631Cys	p.R631C	ENST00000428558	NM_004260.3	631	Cgc/Tgc	12/22	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.920346251233543	2		725	714	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2047322	2047322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	84	145	0	ENST00000349721.2:c.884C>T	p.Ala295Val	p.A295V	ENST00000349721	NM_003070.3	295	gCg/gTg	5/34	1	2	FACETS	0.927	0.837	1	0.927	0.837	1	CLONAL	1	TRUE	1	0.920346251233543	2		145	197	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2104068	2104068	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747313863	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	81	591	2	ENST00000349721.2:c.3191C>T	p.Ala1064Val	p.A1064V	ENST00000349721	NM_003070.3	1064	gCg/gTg	23/34	1	2	FACETS	0.301	0.265	0.339	0.301	0.265	0.339	SUBCLONAL	1	TRUE	1	0.920346251233543	2		593	585	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2181578	2181578	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	55	448	0	ENST00000349721.2:c.4261C>T	p.Arg1421Ter	p.R1421*	ENST00000349721	NM_003070.3	1421	Cga/Tga	30/34	1	2	FACETS	0.26	0.222	0.301	0.26	0.222	0.301	SUBCLONAL	1	TRUE	1	0.920346251233543	2		448	460	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022009	5022009	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	238	549	0	ENST00000381652.3:c.22A>G	p.Met8Val	p.M8V	ENST00000381652	NM_004972.3	8	Atg/Gtg	3/25	1	2	FACETS	0.974	0.919	1	0.974	0.919	1	CLONAL	1	TRUE	1	0.920346251233543	2		549	531	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633320	8633320	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866980874	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	236	490	0	ENST00000356435.5:c.349C>T	p.Arg117Trp	p.R117W	ENST00000356435		117	Cgg/Tgg	3/35	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.920346251233543	2		490	483	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22008862	22008862	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	305	606	0	ENST00000276925.6:c.91C>T	p.Arg31Ter	p.R31*	ENST00000276925	NM_004936.3	31	Cga/Tga	1/2	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.920346251233543	2		606	596	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342871	87342871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200996090	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	70	561	0	ENST00000277120.3:c.1156G>A	p.Asp386Asn	p.D386N	ENST00000277120		386	Gat/Aat	9/19	1	2	FACETS	0.268	0.233	0.305	0.268	0.233	0.305	SUBCLONAL	1	TRUE	1	0.920346251233543	2		561	568	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606311	93606311	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	271	698	0	ENST00000375746.1:c.131G>T	p.Ser44Ile	p.S44I	ENST00000375746	NM_001174167.1	44	aGc/aTc	2/14	1	2	FACETS	0.97	0.918	1	0.97	0.918	1	CLONAL	1	TRUE	1	0.920346251233543	2		698	607	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93627378	93627378	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs201994789	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	174	447	0	ENST00000375746.1:c.845C>T	p.Ala282Val	p.A282V	ENST00000375746	NM_001174167.1	282	gCg/gTg	6/14	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.920346251233543	2		447	359	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128268655	128268655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370425781	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	283	491	0	ENST00000265960.3:c.1000G>A	p.Ala334Thr	p.A334T	ENST00000265960	NM_001006617.1	334	Gcc/Acc	8/12	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.920346251233543	2		491	612	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759443	133759443	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376925416	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	334	619	0	ENST00000318560.5:c.1766G>A	p.Arg589His	p.R589H	ENST00000318560	NM_005157.4	589	cGc/cAc	11/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.920346251233543	2		619	695	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779130	135779130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	317	580	0	ENST00000298552.3:c.2116C>T	p.Arg706Cys	p.R706C	ENST00000298552	NM_001162426.1	706	Cgt/Tgt	17/23	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.920346251233543	2		580	639	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391832	139391832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766836819	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	390	766	2	ENST00000277541.6:c.6359G>A	p.Arg2120His	p.R2120H	ENST00000277541	NM_017617.3	2120	cGc/cAc	34/34	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.920346251233543	2		768	791	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399128	139399128	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372830543	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	291	547	0	ENST00000277541.6:c.5015G>A	p.Arg1672His	p.R1672H	ENST00000277541	NM_017617.3	1672	cGc/cAc	26/34	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.920346251233543	2		547	597	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409061	139409061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561126575	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	335	691	0	ENST00000277541.6:c.2108G>A	p.Arg703His	p.R703H	ENST00000277541	NM_017617.3	703	cGc/cAc	13/34	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.920346251233543	2		691	722	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564423	139564423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143734077	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	276	668	1	ENST00000308874.7:c.371G>A	p.Arg124His	p.R124H	ENST00000308874		124	cGc/cAc	6/10	1	2	FACETS	0.934	0.884	0.985	0.934	0.884	0.985	CLONAL	1	TRUE	1	0.920346251233543	2		669	642	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802537	139802537	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373483375	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	300	572	0	ENST00000247668.2:c.382C>T	p.Arg128Cys	p.R128C	ENST00000247668	NM_021138.3	128	Cgc/Tgc	5/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.920346251233543	2		572	626	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911648	39911648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752359195	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	269	438	0	ENST00000378444.4:c.4982G>A	p.Arg1661Gln	p.R1661Q	ENST00000378444	NM_001123385.1	1661	cGa/cAa	15/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.920346251233543	2		438	548	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933583	39933583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778095	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	378	725	0	ENST00000378444.4:c.1016C>T	p.Pro339Leu	p.P339L	ENST00000378444	NM_001123385.1	339	cCg/cTg	4/15	1	2	FACETS	0.978	0.934	1	0.978	0.934	1	CLONAL	1	TRUE	1	0.920346251233543	2		725	840	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936039	44936039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	161	442	0	ENST00000377967.4:c.2800G>A	p.Asp934Asn	p.D934N	ENST00000377967	NM_021140.2	934	Gac/Aac	18/29	1	2	FACETS	0.972	0.905	1	0.972	0.905	1	CLONAL	1	TRUE	1	0.920346251233543	2		442	360	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223488	53223488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	261	667	0	ENST00000375401.3:c.3871C>T	p.Arg1291Cys	p.R1291C	ENST00000375401	NM_004187.3	1291	Cgc/Tgc	23/26	1	2	FACETS	0.941	0.889	0.993	0.941	0.889	0.993	CLONAL	1	TRUE	1	0.920346251233543	2		667	603	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224207	53224207	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202160290	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	38	649	0	ENST00000375401.3:c.3344G>A	p.Arg1115His	p.R1115H	ENST00000375401	NM_004187.3	1115	cGc/cAc	22/26	1	2	FACETS	0.116	0.095	0.139	0.116	0.095	0.139	SUBCLONAL	1	TRUE	1	0.920346251233543	2		649	711	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226066	53226066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556837402	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	159	642	0	ENST00000375401.3:c.2783C>T	p.Ala928Val	p.A928V	ENST00000375401	NM_004187.3	928	gCg/gTg	19/26	1	2	FACETS	0.543	0.5	0.588	0.543	0.5	0.588	SUBCLONAL	1	TRUE	1	0.920346251233543	2		642	636	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230758	53230758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782683492	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	256	589	0	ENST00000375401.3:c.2035C>T	p.Arg679Cys	p.R679C	ENST00000375401	NM_004187.3	679	Cgt/Tgt	14/26	1	2	FACETS	0.983	0.929	1	0.983	0.929	1	CLONAL	1	TRUE	1	0.920346251233543	2		589	566	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410063	63410063	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	329	812	0	ENST00000330258.3:c.3104A>G	p.Asn1035Ser	p.N1035S	ENST00000330258	NM_152424.3	1035	aAc/aGc	2/2	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.920346251233543	2		812	689	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340903	70340904	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	321	671	0	ENST00000374080.3:c.641dup	p.Cys215LeufsTer11	p.C215Lfs*11	ENST00000374080		212	-/G	5/45	1	2	FACETS	0.919	0.873	0.966	0.919	0.873	0.966	CLONAL	1	TRUE	1	0.920346251233543	2		671	759	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938647	76938647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533271695	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	24	564	0	ENST00000373344.5:c.2101C>T	p.Arg701Cys	p.R701C	ENST00000373344	NM_000489.3	701	Cgt/Tgt	9/35	1	2	FACETS	0.116	0.09	0.146	0.116	0.09	0.146	SUBCLONAL	1	TRUE	1	0.920346251233543	2		564	450	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939492	76939492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374958282	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	135	698	1	ENST00000373344.5:c.1256C>T	p.Ala419Val	p.A419V	ENST00000373344	NM_000489.3	419	gCg/gTg	9/35	1	2	FACETS	0.562	0.513	0.612	0.562	0.513	0.612	SUBCLONAL	1	TRUE	1	0.920346251233543	2		699	522	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630191	100630191	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	260	555	0	ENST00000308731.7:c.82C>T	p.Arg28Cys	p.R28C	ENST00000308731	NM_000061.2	28	Cgc/Tgc	2/19	1	2	FACETS	0.961	0.908	1	0.961	0.908	1	CLONAL	1	TRUE	1	0.920346251233543	2		555	588	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265313	10265313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762421501	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	322	761	0	ENST00000340748.4:c.1733C>T	p.Thr578Ile	p.T578I	ENST00000340748		578	aCa/aTa	20/40	1	2	FACETS	0.929	0.883	0.976	0.929	0.883	0.976	CLONAL	1	TRUE	1	0.920346251233543	2		761	753	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194653	29194654	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	105	613	2	ENST00000240100.2:c.1074dup	p.Thr359HisfsTer91	p.T359Hfs*91	ENST00000240100	NM_001394.6	358	-/C	4/4	1	2	FACETS	0.459	0.413	0.508	0.459	0.413	0.508	SUBCLONAL	1	TRUE	1	0.920346251233543	2		615	497	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073345	8073345	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	61	656	0	ENST00000377482.5:c.1314G>T	p.Lys438Asn	p.K438N	ENST00000377482	NM_018948.3	438	aaG/aaT	4/4	1	2	FACETS	0.17	0.146	0.197	0.17	0.146	0.197	SUBCLONAL	1	TRUE	1	0.920346251233543	2		656	778	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16235856	16235856	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	297	487	0	ENST00000375759.3:c.922C>T	p.Arg308Ter	p.R308*	ENST00000375759	NM_015001.2	308	Cga/Tga	4/15	1	2	FACETS	0.999	0.949	1	0.999	0.949	1	CLONAL	1	TRUE	1	0.920346251233543	2		487	646	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245446	16245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	211	500	0	ENST00000375759.3:c.1421G>A	p.Gly474Glu	p.G474E	ENST00000375759	NM_015001.2	474	gGa/gAa	7/15	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.920346251233543	2		500	454	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058587	72058587	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	249	510	0	ENST00000357731.5:c.853A>G	p.Thr285Ala	p.T285A	ENST00000357731	NM_173808.2	285	Acc/Gcc	6/7	1	2	FACETS	0.993	0.938	1	0.993	0.938	1	CLONAL	1	TRUE	1	0.920346251233543	2		510	545	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471700	120471700	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	38	630	0	ENST00000256646.2:c.3791A>G	p.Asp1264Gly	p.D1264G	ENST00000256646	NM_024408.3	1264	gAc/gGc	23/34	1	2	FACETS	0.113	0.092	0.135	0.113	0.092	0.135	SUBCLONAL	1	TRUE	1	0.920346251233543	2		630	734	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150915098	150915098	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	277	515	1	ENST00000271640.5:c.607C>T	p.Arg203Ter	p.R203*	ENST00000271640	NM_001145415.1	203	Cga/Tga	6/22	1	2	FACETS	0.982	0.93	1	0.982	0.93	1	CLONAL	1	TRUE	1	0.920346251233543	2		516	613	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958498	175958498	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1447615910	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	192	465	0	ENST00000367669.3:c.1847C>T	p.Ala616Val	p.A616V	ENST00000367669	NM_022457.5	616	gCc/gTc	16/20	1	2	FACETS	0.97	0.909	1	0.97	0.909	1	CLONAL	1	TRUE	1	0.920346251233543	2		465	430	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054984	176054984	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	214	474	0	ENST00000367669.3:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000367669	NM_022457.5	357	Cga/Tga	10/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.920346251233543	2		474	462	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104547	193104547	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs952579366	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	196	497	0	ENST00000367435.3:c.334G>A	p.Ala112Thr	p.A112T	ENST00000367435	NM_024529.4	112	Gct/Act	4/17	1	2	FACETS	0.955	0.895	1	0.955	0.895	1	CLONAL	1	TRUE	1	0.920346251233543	2		497	446	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612752	228612752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	430	932	0	ENST00000366696.1:c.275C>T	p.Ala92Val	p.A92V	ENST00000366696	NM_003493.2	92	gCg/gTg	1/1	1	2	FACETS	0.899	0.86	0.939	0.899	0.86	0.939	CLONAL	1	TRUE	1	0.920346251233543	2		932	1039	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230493044	230493045	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	189	610	0	ENST00000391860.1:c.9dup	p.Ser4GlnfsTer139	p.S4Qfs*139	ENST00000391860	NM_001258311.1	3	-/C	2/7	1	2	FACETS	0.525	0.486	0.566	0.525	0.486	0.566	SUBCLONAL	1	TRUE	1	0.920346251233543	2		610	782	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231483640	231483640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766305995	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	251	520	0	ENST00000295050.7:c.419G>A	p.Arg140His	p.R140H	ENST00000295050	NM_032018.5	140	cGc/cAc	3/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.920346251233543	2		520	511	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10781720	10781720	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs751168503	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	103	441	0	ENST00000361367.2:c.593C>T	p.Ala198Val	p.A198V	ENST00000361367	NM_014633.3	198	gCg/gTg	6/25	1	2	FACETS	0.438	0.393	0.485	0.438	0.393	0.485	SUBCLONAL	1	TRUE	1	0.920346251233543	2		441	511	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10795559	10795559	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs761302085	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	57	474	0	ENST00000361367.2:c.2728C>T	p.Arg910Cys	p.R910C	ENST00000361367	NM_014633.3	910	Cgt/Tgt	22/25	1	2	FACETS	0.229	0.196	0.264	0.229	0.196	0.264	SUBCLONAL	1	TRUE	1	0.920346251233543	2		474	542	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94910940	94910940	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	222	487	0	ENST00000536441.1:c.1190A>G	p.Asp397Gly	p.D397G	ENST00000536441	NM_144665.3	397	gAc/gGc	8/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.920346251233543	2		487	433	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344350	118344350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs997896404	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	340	671	0	ENST00000534358.1:c.2476C>T	p.Pro826Ser	p.P826S	ENST00000534358	NM_005933.3	826	Cca/Tca	3/36	1	2	FACETS	0.958	0.912	1	0.958	0.912	1	CLONAL	1	TRUE	1	0.920346251233543	2		671	771	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125513690	125513691	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	198	420	0	ENST00000428830.2:c.823dup	p.Arg275LysfsTer18	p.R275Kfs*18	ENST00000428830	NM_001114121.2	273	gca/gcAa	9/14	1	2	FACETS	0.937	0.878	0.997	0.937	0.878	0.997	CLONAL	1	TRUE	1	0.920346251233543	2		420	459	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025983	1025983	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	161	521	0	ENST00000358495.3:c.547C>T	p.Pro183Ser	p.P183S	ENST00000358495	NM_134424.2	183	Cct/Tct	8/12	1	2	FACETS	0.516	0.475	0.559	0.516	0.475	0.559	SUBCLONAL	1	TRUE	1	0.920346251233543	2		521	678	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644488	21644488	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	260	638	0	ENST00000421138.2:c.179A>C	p.Glu60Ala	p.E60A	ENST00000421138		60	gAa/gCa	4/16	1	2	FACETS	0.961	0.908	1	0.961	0.908	1	CLONAL	1	TRUE	1	0.920346251233543	2		638	588	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428649	49428649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	40	674	0	ENST00000301067.7:c.10301G>A	p.Gly3434Asp	p.G3434D	ENST00000301067	NM_003482.3	3434	gGc/gAc	35/54	1	2	FACETS	0.132	0.109	0.157	0.132	0.109	0.157	SUBCLONAL	1	TRUE	1	0.920346251233543	2		674	660	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214724	133214724	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	179	513	0	ENST00000320574.5:c.5554C>T	p.Leu1852Phe	p.L1852F	ENST00000320574	NM_006231.2	1852	Ctc/Ttc	41/49	1	2	FACETS	0.549	0.508	0.592	0.549	0.508	0.592	SUBCLONAL	1	TRUE	1	0.920346251233543	2		513	708	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622509	28622509	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	30	507	0	ENST00000241453.7:c.1108del	p.Ser370LeufsTer64	p.S370Lfs*64	ENST00000241453	NM_004119.2	370	Tct/ct	9/24	1	2	FACETS	0.134	0.108	0.165	0.134	0.108	0.165	SUBCLONAL	1	TRUE	1	0.920346251233543	2		507	485	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30095704	30095704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	70	336	0	ENST00000331968.5:c.1784G>A	p.Gly595Glu	p.G595E	ENST00000331968	NM_002742.2	595	gGa/gAa	12/18	1	2	FACETS	0.417	0.365	0.472	0.417	0.365	0.472	SUBCLONAL	1	TRUE	1	0.920346251233543	2		336	365	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961468	41961468	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	39	565	0	ENST00000219905.7:c.376G>A	p.Asp126Asn	p.D126N	ENST00000219905	NM_001164273.1	126	Gat/Aat	2/24	1	2	FACETS	0.138	0.113	0.165	0.138	0.113	0.165	SUBCLONAL	1	TRUE	1	0.920346251233543	2		565	616	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50774185	50774185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755591528	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	298	614	0	ENST00000307179.4:c.1726C>T	p.Pro576Ser	p.P576S	ENST00000307179		576	Cca/Tca	11/20	1	2	FACETS	0.983	0.933	1	0.983	0.933	1	CLONAL	1	TRUE	1	0.920346251233543	2		614	659	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51514597	51514597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761722363	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	291	608	1	ENST00000260433.2:c.577C>T	p.Arg193Cys	p.R193C	ENST00000260433		193	Cgt/Tgt	5/10	1	2	FACETS	0.993	0.942	1	0.993	0.942	1	CLONAL	1	TRUE	1	0.920346251233543	2		609	637	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303484	91303484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs538728271	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	247	446	0	ENST00000355112.3:c.1195G>A	p.Glu399Lys	p.E399K	ENST00000355112	NM_000057.2	399	Gaa/Aaa	6/22	1	2	FACETS	0.992	0.937	1	0.992	0.937	1	CLONAL	1	TRUE	1	0.920346251233543	2		446	541	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656624	3656624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1410797507	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	146	685	0	ENST00000294008.3:c.611G>A	p.Arg204His	p.R204H	ENST00000294008	NM_032444.2	204	cGc/cAc	3/15	1	2	FACETS	0.442	0.404	0.482	0.442	0.404	0.482	SUBCLONAL	1	TRUE	1	0.920346251233543	2		685	718	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133261	30133261	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	78	662	0	ENST00000263025.4:c.237G>T	p.Gln79His	p.Q79H	ENST00000263025	NM_002746.2	79	caG/caT	2/9	1	2	FACETS	0.21	0.183	0.238	0.21	0.183	0.238	SUBCLONAL	1	TRUE	1	0.920346251233543	2		662	809	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56857715	56857715	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767522635	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	159	594	2	ENST00000308159.5:c.751C>T	p.Arg251Cys	p.R251C	ENST00000308159	NM_014669.4	251	Cgc/Tgc	8/22	1	2	FACETS	0.496	0.456	0.538	0.496	0.456	0.538	SUBCLONAL	1	TRUE	1	0.920346251233543	2		596	696	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828890	72828891	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	297	678	0	ENST00000268489.5:c.7690dup	p.Gln2564ProfsTer15	p.Q2564Pfs*15	ENST00000268489	NM_006885.3	2564	cag/cCag	9/10	1	2	FACETS	0.915	0.868	0.964	0.915	0.868	0.964	CLONAL	1	TRUE	1	0.920346251233543	2		678	705	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346414	89346414	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	286	673	0	ENST00000301030.4:c.6536T>C	p.Val2179Ala	p.V2179A	ENST00000301030	NM_001256183.1	2179	gTt/gCt	9/13	1	2	FACETS	0.93	0.881	0.98	0.93	0.881	0.98	CLONAL	1	TRUE	1	0.920346251233543	2		673	668	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684056	29684056	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	244	493	0	ENST00000356175.3:c.7754A>G	p.Asp2585Gly	p.D2585G	ENST00000356175	NM_000267.3	2585	gAt/gGt	52/57	1	2	FACETS	0.999	0.943	1	0.999	0.943	1	CLONAL	1	TRUE	1	0.920346251233543	2		493	531	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428309	33428309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458813748	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	270	633	0	ENST00000345365.6:c.814C>T	p.Pro272Ser	p.P272S	ENST00000345365	NM_002878.3	272	Ccc/Tcc	9/10	1	2	FACETS	0.945	0.894	0.996	0.945	0.894	0.996	CLONAL	1	TRUE	1	0.920346251233543	2		633	621	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38793803	38793803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	296	539	0	ENST00000348513.6:c.178C>T	p.Pro60Ser	p.P60S	ENST00000348513	NM_003079.4	60	Cca/Tca	5/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.920346251233543	2		539	585	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554359	63554359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	299	723	0	ENST00000307078.5:c.380C>T	p.Thr127Ile	p.T127I	ENST00000307078	NM_004655.3	127	aCt/aTt	2/11	1	2	FACETS	0.9	0.853	0.948	0.9	0.853	0.948	CLONAL	1	TRUE	1	0.920346251233543	2		723	722	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78938119	78938119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1320914484	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	271	595	0	ENST00000306801.3:c.3997C>T	p.Arg1333Cys	p.R1333C	ENST00000306801	NM_020761.2	1333	Cgt/Tgt	34/34	1	2	FACETS	0.933	0.883	0.984	0.933	0.883	0.984	CLONAL	1	TRUE	1	0.920346251233543	2		595	631	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106947	11106947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	394	749	0	ENST00000358026.2:c.1652C>T	p.Ala551Val	p.A551V	ENST00000358026	NM_001128849.1	551	gCc/gTc	10/36	1	2	FACETS	0.998	0.954	1	0.998	0.954	1	CLONAL	1	TRUE	1	0.920346251233543	2		749	858	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910339	50910339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765276497	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	167	632	0	ENST00000440232.2:c.1594G>A	p.Ala532Thr	p.A532T	ENST00000440232	NM_002691.3	532	Gcc/Acc	13/27	1	2	FACETS	0.579	0.534	0.625	0.579	0.534	0.625	SUBCLONAL	1	TRUE	1	0.920346251233543	2		632	627	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966325	25966325	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	76	709	0	ENST00000435504.4:c.2881G>T	p.Asp961Tyr	p.D961Y	ENST00000435504		961	Gat/Tat	13/13	1	2	FACETS	0.237	0.207	0.268	0.237	0.207	0.268	SUBCLONAL	1	TRUE	1	0.920346251233543	2		709	698	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672710	47672710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	65	523	0	ENST00000233146.2:c.1300G>A	p.Ala434Thr	p.A434T	ENST00000233146	NM_000251.2	434	Gca/Aca	8/16	1	2	FACETS	0.296	0.256	0.338	0.296	0.256	0.338	SUBCLONAL	1	TRUE	1	0.920346251233543	2		523	478	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719795	61719795	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	228	583	0	ENST00000401558.2:c.1473G>T	p.Trp491Cys	p.W491C	ENST00000401558	NM_003400.3	491	tgG/tgT	14/25	1	2	FACETS	0.995	0.937	1	0.995	0.937	1	CLONAL	1	TRUE	1	0.920346251233543	2		583	498	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67626325	67626325	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532275210	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	164	526	0	ENST00000272342.5:c.248C>T	p.Ala83Val	p.A83V	ENST00000272342	NM_019002.3	83	gCg/gTg	2/6	1	2	FACETS	0.961	0.895	1	0.961	0.895	1	CLONAL	1	TRUE	1	0.920346251233543	2		526	371	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719136	190719136	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	174	530	0	ENST00000441310.2:c.1138T>C	p.Tyr380His	p.Y380H	ENST00000441310	NM_000534.4	380	Tat/Cat	9/13	1	2	FACETS	0.99	0.924	1	0.99	0.924	1	CLONAL	1	TRUE	1	0.920346251233543	2		530	382	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104646	209104646	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	35	576	0	ENST00000345146.2:c.932C>A	p.Thr311Asn	p.T311N	ENST00000345146	NM_005896.2	311	aCt/aAt	8/10	1	2	FACETS	0.122	0.099	0.147	0.122	0.099	0.147	SUBCLONAL	1	TRUE	1	0.920346251233543	2		576	625	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113209	209113209	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs777129475	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	124	652	0	ENST00000345146.2:c.298C>T	p.Arg100Ter	p.R100*	ENST00000345146	NM_005896.2	100	Cga/Tga	4/10	1	2	FACETS	0.39	0.353	0.429	0.39	0.353	0.429	SUBCLONAL	1	TRUE	1	0.920346251233543	2		652	691	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440155	220440155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	316	679	0	ENST00000243786.2:c.1008G>T	p.Arg336Ser	p.R336S	ENST00000243786	NM_002191.3	336	agG/agT	2/2	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.920346251233543	2		679	641	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662904	227662904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	286	620	0	ENST00000305123.5:c.551G>A	p.Arg184His	p.R184H	ENST00000305123	NM_005544.2	184	cGc/cAc	1/2	1	2	FACETS	0.94	0.891	0.99	0.94	0.891	0.99	CLONAL	1	TRUE	1	0.920346251233543	2		620	661	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29107925	29107925	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	102	468	0	ENST00000328354.6:c.764A>G	p.Lys255Arg	p.K255R	ENST00000328354	NM_007194.3	255	aAg/aGg	6/15	1	2	FACETS	0.493	0.443	0.545	0.493	0.443	0.545	SUBCLONAL	1	TRUE	1	0.920346251233543	2		468	450	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475400	12475400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	49	620	0	ENST00000287820.6:c.1274G>A	p.Arg425His	p.R425H	ENST00000287820	NM_015869.4	425	cGc/cAc	7/7	1	2	FACETS	0.177	0.149	0.207	0.177	0.149	0.207	SUBCLONAL	1	TRUE	1	0.920346251233543	2		620	603	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732997	30732997	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057524810	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	284	717	0	ENST00000295754.5:c.1610G>A	p.Arg537His	p.R537H	ENST00000295754	NM_003242.5	537	cGc/cAc	7/7	1	2	FACETS	0.952	0.902	1	0.952	0.902	1	CLONAL	1	TRUE	1	0.920346251233543	2		717	648	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940112	49940112	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs201805638	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	176	737	0	ENST00000296474.3:c.931G>C	p.Ala311Pro	p.A311P	ENST00000296474	NM_002447.2	311	Gcc/Ccc	1/20	1	2	FACETS	0.512	0.472	0.553	0.512	0.472	0.553	SUBCLONAL	1	TRUE	1	0.920346251233543	2		737	747	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990397	69990397	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	196	448	0	ENST00000394351.3:c.356T>C	p.Val119Ala	p.V119A	ENST00000394351	NM_000248.3	119	gTa/gCa	4/9	1	2	FACETS	0.957	0.897	1	0.957	0.897	1	CLONAL	1	TRUE	1	0.920346251233543	2		448	445	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247427	71247427	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs935869094	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	313	571	0	ENST00000318789.4:c.106C>T	p.Arg36Trp	p.R36W	ENST00000318789	NM_032682.5	36	Cgg/Tgg	6/21	1	2	FACETS	0.95	0.902	0.998	0.95	0.902	0.998	CLONAL	1	TRUE	1	0.920346251233543	2		571	716	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204659	128204659	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	329	664	0	ENST00000341105.2:c.782G>T	p.Ser261Ile	p.S261I	ENST00000341105	NM_032638.4	261	aGc/aTc	3/6	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.920346251233543	2		664	705	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803141	1803141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1286097899	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	327	752	1	ENST00000260795.2:c.493G>A	p.Ala165Thr	p.A165T	ENST00000260795		165	Gcc/Acc	4/17	1	2	FACETS	0.994	0.946	1	0.994	0.946	1	CLONAL	1	TRUE	1	0.920346251233543	2		753	715	SUCCESS
REST	5978	MSKCC	GRCh37	4	57777463	57777463	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751325926	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	355	694	1	ENST00000309042.7:c.659G>A	p.Arg220His	p.R220H	ENST00000309042	NM_005612.4	220	cGc/cAc	2/4	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.920346251233543	2		695	728	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384014	84384015	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	244	529	0	ENST00000321945.7:c.837dup	p.Leu280SerfsTer13	p.L280Sfs*13	ENST00000321945	NM_139076.2	279	-/T	9/9	1	2	FACETS	0.947	0.893	1	0.947	0.893	1	CLONAL	1	TRUE	1	0.920346251233543	2		529	560	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144336730	144336730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762061638	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	211	458	0	ENST00000262995.4:c.173G>A	p.Arg58His	p.R58H	ENST00000262995	NM_207123.2	58	cGt/cAt	2/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.920346251233543	2		458	454	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540118	187540118	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	33	637	0	ENST00000441802.2:c.7622A>G	p.Tyr2541Cys	p.Y2541C	ENST00000441802	NM_005245.3	2541	tAc/tGc	10/27	1	2	FACETS	0.127	0.103	0.154	0.127	0.103	0.154	SUBCLONAL	1	TRUE	1	0.920346251233543	2		637	565	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251197	251198	+	missense_variant	Missense_Mutation	DNP	CA	CA	TG	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	115	242	0	ENST00000264932.6:c.1642_1643inv	p.His548Cys	p.H548C	ENST00000264932	NM_004168.2	548	CAc/TGc	12/15	1	2	FACETS	0.98	0.9	1	0.98	0.9	1	CLONAL	1	TRUE	1	0.920346251233543	2		242	255	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449441	31449441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	244	616	0	ENST00000344624.3:c.2768G>A	p.Arg923Gln	p.R923Q	ENST00000344624		923	cGg/cAg	19/33	1	2	FACETS	0.921	0.868	0.974	0.921	0.868	0.974	CLONAL	1	TRUE	1	0.920346251233543	2		616	576	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435792	149435792	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	290	659	0	ENST00000286301.3:c.2432T>C	p.Val811Ala	p.V811A	ENST00000286301	NM_005211.3	811	gTc/gCc	18/22	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.920346251233543	2		659	603	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158450	26158450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866232051	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	307	605	2	ENST00000289316.2:c.53C>T	p.Ala18Val	p.A18V	ENST00000289316	NM_138720.2	18	gCg/gTg	1/2	0.920346251233543	2	FACETS	0.967	0.918	1	0.483	0.459	0.508	CLONAL	1	TRUE	0	0.920346251233543	2		607	690	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839868	27839868	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	750	823	0	ENST00000328488.2:c.226G>A	p.Ala76Thr	p.A76T	ENST00000328488	NM_003533.2	76	Gca/Aca	1/1	0.920346251233543	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.920346251233543	2		823	807	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670951	30670951	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761516200	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	71	636	2	ENST00000376406.3:c.5795G>A	p.Arg1932His	p.R1932H	ENST00000376406	NM_014641.2	1932	cGc/cAc	12/15	1	2	FACETS	0.212	0.185	0.242	0.212	0.185	0.242	SUBCLONAL	1	TRUE	1	0.920346251233543	2		638	727	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675406	30675406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201740735	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	374	784	3	ENST00000376406.3:c.2950G>A	p.Val984Ile	p.V984I	ENST00000376406	NM_014641.2	984	Gta/Ata	8/15	1	2	FACETS	0.989	0.944	1	0.989	0.944	1	CLONAL	1	TRUE	1	0.920346251233543	2		787	822	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120218	94120218	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	292	663	0	ENST00000369303.4:c.832+1G>A		p.X278_splice	ENST00000369303	NM_004440.3	278			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.920346251233543	2		663	587	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519757	137519757	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	32	529	0	ENST00000367739.4:c.881C>T	p.Ala294Val	p.A294V	ENST00000367739	NM_000416.2	294	gCt/gTt	7/7	1	2	FACETS	0.147	0.119	0.179	0.147	0.119	0.179	SUBCLONAL	1	TRUE	1	0.920346251233543	2		529	472	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523608	106523608	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	257	520	0	ENST00000359195.3:c.2760G>T	p.Lys920Asn	p.K920N	ENST00000359195	NM_002649.2	920	aaG/aaT	8/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.920346251233543	2		520	546	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124482943	124482943	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372317646	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	175	488	0	ENST00000357628.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000357628	NM_015450.2	361	Cgc/Tgc	13/19	1	2	FACETS	0.948	0.885	1	0.948	0.885	1	CLONAL	1	TRUE	1	0.920346251233543	2		488	401	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124503462	124503462	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	268	505	1	ENST00000357628.3:c.488A>G	p.Asp163Gly	p.D163G	ENST00000357628	NM_015450.2	163	gAc/gGc	8/19	1	2	FACETS	0.976	0.923	1	0.976	0.923	1	CLONAL	1	TRUE	1	0.920346251233543	2		506	597	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860740	151860740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	338	751	0	ENST00000262189.6:c.9922C>T	p.Pro3308Ser	p.P3308S	ENST00000262189	NM_170606.2	3308	Cca/Tca	43/59	1	2	FACETS	0.922	0.877	0.967	0.922	0.877	0.967	CLONAL	1	TRUE	1	0.920346251233543	2		751	797	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38186919	38186919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1418991870	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	210	479	0	ENST00000317025.8:c.1558G>A	p.Asp520Asn	p.D520N	ENST00000317025	NM_023034.1	520	Gat/Aat	6/24	1	2	FACETS	0.842	0.788	0.896	0.842	0.788	0.896	CLONAL	1	TRUE	1	0.920346251233543	2		479	542	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205058	38205058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142206759	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	43	581	0	ENST00000317025.8:c.632G>A	p.Arg211His	p.R211H	ENST00000317025	NM_023034.1	211	cGc/cAc	2/24	1	2	FACETS	0.164	0.137	0.194	0.164	0.137	0.194	SUBCLONAL	1	TRUE	1	0.920346251233543	2		581	570	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274911	38274911	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	156	538	0	ENST00000425967.3:c.1669T>C	p.Ser557Pro	p.S557P	ENST00000425967	NM_001174067.1	557	Tca/Cca	13/19	1	2	FACETS	0.553	0.508	0.599	0.553	0.508	0.599	SUBCLONAL	1	TRUE	1	0.920346251233543	2		538	613	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859926	117859926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	138	557	0	ENST00000297338.2:c.1709C>T	p.Ala570Val	p.A570V	ENST00000297338	NM_006265.2	570	gCt/gTt	14/14	1	2	FACETS	0.562	0.514	0.611	0.562	0.514	0.611	SUBCLONAL	1	TRUE	1	0.920346251233543	2		557	534	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141569590	141569590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs534512549	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	286	589	0	ENST00000220592.5:c.694G>A	p.Glu232Lys	p.E232K	ENST00000220592	NM_012154.3	232	Gag/Aag	6/19	1	2	FACETS	0.901	0.853	0.949	0.901	0.853	0.949	CLONAL	1	TRUE	1	0.920346251233543	2		589	690	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2073320	2073320	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1319646165	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	267	612	0	ENST00000349721.2:c.1855G>A	p.Ala619Thr	p.A619T	ENST00000349721	NM_003070.3	619	Gcc/Acc	11/34	1	2	FACETS	0.925	0.875	0.977	0.925	0.875	0.977	CLONAL	1	TRUE	1	0.920346251233543	2		612	627	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2088539	2088539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	184	424	0	ENST00000349721.2:c.2809C>T	p.Arg937Cys	p.R937C	ENST00000349721	NM_003070.3	937	Cgt/Tgt	19/34	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.920346251233543	2		424	376	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2182165	2182165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774671393	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	249	440	0	ENST00000349721.2:c.4384C>T	p.Arg1462Trp	p.R1462W	ENST00000349721	NM_003070.3	1462	Cgg/Tgg	31/34	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.920346251233543	2		440	502	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126352	5126352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139127951	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	53	446	0	ENST00000381652.3:c.3197G>A	p.Gly1066Asp	p.G1066D	ENST00000381652	NM_004972.3	1066	gGc/gAc	24/25	1	2	FACETS	0.309	0.264	0.357	0.309	0.264	0.357	SUBCLONAL	1	TRUE	1	0.920346251233543	2		446	373	SUCCESS
MTAP	4507	MSKCC	GRCh37	9	21816747	21816747	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	154	408	0	ENST00000380172.4:c.155A>C	p.Asn52Thr	p.N52T	ENST00000380172	NM_002451.3	52	aAt/aCt	3/8	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.920346251233543	2		408	329	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430554	80430554	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	47	292	0	ENST00000286548.4:c.454C>T	p.Gln152Ter	p.Q152*	ENST00000286548	NM_002072.3	152	Caa/Taa	3/7	1	2	FACETS	0.448	0.382	0.52	0.448	0.382	0.52	SUBCLONAL	1	TRUE	1	0.920346251233543	2		292	228	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229497	98229497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762855028	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	90	695	0	ENST00000331920.6:c.2461G>A	p.Asp821Asn	p.D821N	ENST00000331920	NM_000264.3	821	Gac/Aac	15/24	1	2	FACETS	0.272	0.241	0.305	0.272	0.241	0.305	SUBCLONAL	1	TRUE	1	0.920346251233543	2		695	720	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912013	127912013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	108	554	0	ENST00000373547.4:c.857G>A	p.Arg286Gln	p.R286Q	ENST00000373547	NM_002721.4	286	cGg/cAg	7/7	1	2	FACETS	0.374	0.336	0.414	0.374	0.336	0.414	SUBCLONAL	1	TRUE	1	0.920346251233543	2		554	627	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137320998	137320998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771637845	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	80	660	0	ENST00000481739.1:c.955G>A	p.Ala319Thr	p.A319T	ENST00000481739	NM_002957.4	319	Gcc/Acc	7/10	1	2	FACETS	0.266	0.234	0.3	0.266	0.234	0.3	SUBCLONAL	1	TRUE	1	0.920346251233543	2		660	654	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345906	70345906	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	213	487	0	ENST00000374080.3:c.2443C>T	p.Arg815Trp	p.R815W	ENST00000374080		815	Cgg/Tgg	18/45	1	2	FACETS	0.892	0.836	0.948	0.892	0.836	0.948	CLONAL	1	TRUE	1	0.920346251233543	2		487	519	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347807	70347807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	338	652	0	ENST00000374080.3:c.3046C>T	p.Arg1016Cys	p.R1016C	ENST00000374080		1016	Cgc/Tgc	22/45	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.920346251233543	2		652	686	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615707	100615707	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	158	590	0	ENST00000308731.7:c.625G>A	p.Ala209Thr	p.A209T	ENST00000308731	NM_000061.2	209	Gca/Aca	8/19	1	2	FACETS	0.557	0.513	0.604	0.557	0.513	0.604	SUBCLONAL	1	TRUE	1	0.920346251233543	2		590	616	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0057194-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	173	264	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.908787933614533	5	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	2	0.908787933614533	5		264	270	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0057194-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	112	294	0	ENST00000269305.4:c.375+1del		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.906129487784537	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.908787933614533	2		294	123	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539540	187539540	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057194-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	59	353	0	ENST00000441802.2:c.8200C>A	p.Leu2734Ile	p.L2734I	ENST00000441802	NM_005245.3	2734	Ctt/Att	10/27	0.906129487784537	2	FACETS	0.792	0.696	0.891	0.396	0.348	0.446	SUBCLONAL	1	TRUE	0	0.908787933614533	2		353	164	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293562	1293562	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs776712013	NA	P-0057194-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	236	400	0	ENST00000310581.5:c.1439C>G	p.Ser480Cys	p.S480C	ENST00000310581	NM_198253.2	480	tCc/tGc	2/16	0.908787933614533	6	FACETS	1	0.985	1			1	CLONAL	3	TRUE	NA	0.908787933614533	6		400	441	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294000	1294000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1420805598	NA	P-0057194-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	205	485	0	ENST00000310581.5:c.1001C>T	p.Ser334Phe	p.S334F	ENST00000310581	NM_198253.2	334	tCc/tTc	2/16	0.908787933614533	6	FACETS	1	0.972	1			1	CLONAL	3	TRUE	NA	0.908787933614533	6		485	402	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294550	1294550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057194-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	151	480	0	ENST00000310581.5:c.451C>T	p.His151Tyr	p.H151Y	ENST00000310581	NM_198253.2	151	Cac/Tac	2/16	0.908787933614533	6	FACETS	0.988	0.919	1			1	CLONAL	3	TRUE	NA	0.908787933614533	6		480	316	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295417	1295417	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0057194-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	250	424	0				ENST00000310581	NM_198253.2	-/1132			0.804569054503895	3	FACETS	0.928	0.883	0.973			1	CLONAL	2	TRUE	NA	0.908787933614533	3		424	431	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391859	139391859	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057194-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	76	490	0	ENST00000277541.6:c.6332G>C	p.Arg2111Thr	p.R2111T	ENST00000277541	NM_017617.3	2111	aGg/aCg	34/34	0.904867707898256	3	FACETS	1	0.946	1	0.367	0.327	0.408	CLONAL	1	TRUE	0	0.908787933614533	3		490	221	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70355035	70355035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057194-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	26	357	0	ENST00000374080.3:c.4957C>T	p.Pro1653Ser	p.P1653S	ENST00000374080		1653	Cca/Tca	36/45	0.908787933614533	6	FACETS	0.354	0.279	0.439	0.088	0.069	0.11	SUBCLONAL	1	TRUE	2	0.908787933614533	6		357	456	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	59	403	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.599	0.521	0.681	0.599	0.521	0.681	SUBCLONAL	1	TRUE	1	0.831077219899272	2		404	237	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	78	182	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.873	0.781	0.968	0.873	0.781	0.968	CLONAL	1	TRUE	1	0.831077219899272	2		182	215	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	84	356	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.906	0.815	1	0.906	0.815	1	CLONAL	1	TRUE	1	0.831077219899272	2		356	223	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446222	29446223	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	54	153	0	ENST00000389048.3:c.3344dup	p.Asn1115LysfsTer18	p.N1115Kfs*18	ENST00000389048	NM_004304.4	1115	aac/aaAc	20/29	1	2	FACETS	0.76	0.661	0.863	0.76	0.661	0.863	SUBCLONAL	1	TRUE	1	0.831077219899272	2		153	171	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	103	813	7	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	0.81194868602012	4	FACETS	0.908	0.816	1	0.303	0.272	0.335	CLONAL	1	TRUE	1	0.831077219899272	4		820	500	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971095	21971096	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	69	139	0	ENST00000304494.5:c.262dup	p.Glu88GlyfsTer32	p.E88Gfs*32	ENST00000304494	NM_000077.4	88	gag/gGag	2/3	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.831077219899272	2		139	156	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796882	42796883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761345552	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	84	240	0	ENST00000575354.2:c.3347dup	p.Ser1117LysfsTer34	p.S1117Kfs*34	ENST00000575354	NM_015125.3	1114	gcc/gCcc	14/20	1	2	FACETS	0.915	0.823	1	0.915	0.823	1	CLONAL	1	TRUE	1	0.831077219899272	2		240	221	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106803	27106804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	68	210	0	ENST00000324856.7:c.6420dup	p.Phe2141LeufsTer9	p.F2141Lfs*9	ENST00000324856	NM_006015.4	2138	-/C	20/20	1	2	FACETS	0.783	0.693	0.877	0.783	0.693	0.877	SUBCLONAL	1	TRUE	1	0.831077219899272	2		210	209	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405953	157405954	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1554294674	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	80	166	0	ENST00000346085.5:c.2201dup	p.Ser736IlefsTer27	p.S736Ifs*27	ENST00000346085	NM_020732.3	732	ccg/ccGg	6/20	1	2	FACETS	0.83	0.743	0.92	0.83	0.743	0.92	CLONAL	1	TRUE	1	0.831077219899272	2		166	232	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661663	227661664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761880048	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	62	179	2	ENST00000305123.5:c.1791dup	p.His598AlafsTer13	p.H598Afs*13	ENST00000305123	NM_005544.2	597	-/G	1/2	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.831077219899272	2		181	145	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266112	41266112	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913228	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	89	141	0	ENST00000349496.5:c.109T>C	p.Ser37Pro	p.S37P	ENST00000349496	NM_001904.3	37	Tct/Cct	3/15	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.831077219899272	2		141	212	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991757	72991758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760959844	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	48	168	0	ENST00000268489.5:c.2287dup	p.Glu763GlyfsTer26	p.E763Gfs*26	ENST00000268489	NM_006885.3	763	gag/gGag	2/10	1	2	FACETS	0.618	0.53	0.711	0.618	0.53	0.711	SUBCLONAL	1	TRUE	1	0.831077219899272	2		168	187	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405777	70405778	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	68	154	0	ENST00000373644.4:c.3297dup	p.Val1100SerfsTer2	p.V1100Sfs*2	ENST00000373644	NM_030625.2	1097	-/A	4/12	1	2	FACETS	0.779	0.689	0.873	0.779	0.689	0.873	SUBCLONAL	1	TRUE	1	0.831077219899272	2		154	210	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99136537	99136537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746072331	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	58	141	0	ENST00000074304.5:c.26G>A	p.Arg9His	p.R9H	ENST00000074304	NM_001134224.1	9	cGc/cAc	3/26	1	2	FACETS	0.883	0.776	0.994	0.883	0.776	0.994	CLONAL	1	TRUE	1	0.831077219899272	2		141	158	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922363	178922363	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	42	84	0	ENST00000263967.3:c.1132T>C	p.Cys378Arg	p.C378R	ENST00000263967	NM_006218.2	378	Tgt/Cgt	6/21	1	2	FACETS	0.972	0.838	1	0.972	0.838	1	CLONAL	1	TRUE	1	0.831077219899272	2		84	104	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231610	5231611	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	17	161	0	ENST00000357368.4:c.1865dup	p.Gln623SerfsTer4	p.Q623Sfs*4	ENST00000357368	NM_002850.3	622	cct/ccCt	14/38	0.241316876350806	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.831077219899272	0		161	57	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936057	71936058	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs878853122	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	34	119	0	ENST00000298229.2:c.35dup	p.Ala13ArgfsTer62	p.A13Rfs*62	ENST00000298229	NM_001567.3	10	ccg/ccGg	1/28	1	2	FACETS	0.731	0.611	0.858	0.731	0.611	0.858	SUBCLONAL	1	TRUE	1	0.831077219899272	2		119	112	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511205	148511205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	83	121	0	ENST00000320356.2:c.1697G>A	p.Arg566His	p.R566H	ENST00000320356	NM_004456.4	566	cGc/cAc	15/20	1	2	FACETS	0.925	0.832	1	0.925	0.832	1	CLONAL	1	TRUE	1	0.831077219899272	2		121	216	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273905	10273905	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	52	156	0	ENST00000330684.3:c.364G>A	p.Val122Ile	p.V122I	ENST00000330684	NM_001134407.1	122	Gtc/Atc	2/13	1	2	FACETS	0.907	0.792	1	0.907	0.792	1	CLONAL	1	TRUE	1	0.831077219899272	2		156	138	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800429	32800429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750440758	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	78	162	0	ENST00000374899.4:c.1118G>A	p.Arg373His	p.R373H	ENST00000374899	NM_018833.2	373	cGc/cAc	6/12	1	2	FACETS	0.925	0.829	1	0.925	0.829	1	CLONAL	1	TRUE	1	0.831077219899272	2		162	203	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749137	43749137	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	70	124	0	ENST00000382044.4:c.1669T>C	p.Ser557Pro	p.S557P	ENST00000382044	NM_001141980.1	557	Tct/Cct	12/28	1	2	FACETS	0.906	0.806	1	0.906	0.806	1	CLONAL	1	TRUE	1	0.831077219899272	2		124	186	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38949853	38949853	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	98	148	0	ENST00000357387.3:c.4097T>C	p.Met1366Thr	p.M1366T	ENST00000357387	NM_152756.3	1366	aTg/aCg	31/38	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.831077219899272	2		148	212	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224219	36224219	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	35	104	0	ENST00000222270.7:c.6773del	p.Pro2258LeufsTer3	p.P2258Lfs*3	ENST00000222270	NM_014727.1	2257	Ccc/cc	28/37	1	2	FACETS	0.906	0.766	1	0.906	0.766	1	CLONAL	1	TRUE	1	0.831077219899272	2		104	93	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164805	36164805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745561479	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	110	233	0	ENST00000300305.3:c.1070C>T	p.Pro357Leu	p.P357L	ENST00000300305		357	cCg/cTg	8/8	1	2	FACETS	0.963	0.879	1	0.963	0.879	1	CLONAL	1	TRUE	1	0.831077219899272	2		233	275	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023099	33023099	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	48	169	0	ENST00000300177.4:c.211del	p.Glu71ArgfsTer13	p.E71Rfs*13	ENST00000300177	NM_001191322.1	70	Ggg/gg	2/2	1	2	FACETS	0.786	0.679	0.898	0.786	0.679	0.898	SUBCLONAL	1	TRUE	1	0.831077219899272	2		169	147	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40458407	40458407	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	14	30	0	ENST00000345506.4:c.1622G>A	p.Ser541Asn	p.S541N	ENST00000345506	NM_003152.3	541	aGc/aAc	14/20	0.801831297806376	3	FACETS	0.917	0.721	1	0.917	0.721	1	CLONAL	2	TRUE	1	0.831077219899272	3		30	26	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4123821	4123821	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs774968670	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	68	104	0	ENST00000262948.5:c.52A>G	p.Ile18Val	p.I18V	ENST00000262948	NM_030662.3	18	Atc/Gtc	1/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.831077219899272	2		104	154	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257772	198257772	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	106	144	0	ENST00000335508.6:c.3680T>A	p.Ile1227Asn	p.I1227N	ENST00000335508	NM_012433.2	1227	aTt/aAt	24/25	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.831077219899272	2		144	224	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1940178	1940178	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	41	39	0	ENST00000382891.5:c.1675A>G	p.Arg559Gly	p.R559G	ENST00000382891	NM_133335.3	559	Aga/Gga	8/22	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.831077219899272	2		39	90	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750539	41750539	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	49	178	0	ENST00000226382.2:c.89A>G	p.Tyr30Cys	p.Y30C	ENST00000226382	NM_003924.3	30	tAt/tGt	1/3	1	2	FACETS	0.746	0.644	0.854	0.746	0.644	0.854	SUBCLONAL	1	TRUE	1	0.831077219899272	2		178	158	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5029897	5029897	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	56	110	0	ENST00000381652.3:c.341A>G	p.Tyr114Cys	p.Y114C	ENST00000381652	NM_004972.3	114	tAc/tGc	4/25	1	2	FACETS	0.881	0.772	0.993	0.881	0.772	0.993	CLONAL	1	TRUE	1	0.831077219899272	2		110	153	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	66	288	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.951	0.845	1	0.951	0.845	1	CLONAL	1	TRUE	1	0.831077219899272	2		288	167	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1747262	1747262	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756284066	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	88	148	0	ENST00000378609.4:c.136C>T	p.Arg46Cys	p.R46C	ENST00000378609	NM_002074.3	46	Cgc/Tgc	5/12	1	2	FACETS	0.941	0.85	1	0.941	0.85	1	CLONAL	1	TRUE	1	0.831077219899272	2		148	225	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27183487	27183487	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	13	133	0	ENST00000380036.4:c.1061A>G	p.Asp354Gly	p.D354G	ENST00000380036	NM_000459.3	354	gAt/gGt	8/23	1	2	FACETS	0.192	0.137	0.258	0.192	0.137	0.258	SUBCLONAL	1	TRUE	1	0.831077219899272	2		133	163	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79966027	79966027	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	96	131	0	ENST00000265081.6:c.691C>T	p.Pro231Ser	p.P231S	ENST00000265081	NM_002439.4	231	Ccg/Tcg	4/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.831077219899272	2		131	204	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854987	76854987	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	84	168	0	ENST00000373344.5:c.5849A>C	p.Asn1950Thr	p.N1950T	ENST00000373344	NM_000489.3	1950	aAt/aCt	25/35	0.830949673836547	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.831077219899272	1		168	116	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124503669	124503669	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057871-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	48	123	0	ENST00000357628.3:c.281A>G	p.Gln94Arg	p.Q94R	ENST00000357628	NM_015450.2	94	cAg/cGg	8/19	1	2	FACETS	0.813	0.703	0.929	0.813	0.703	0.929	CLONAL	1	TRUE	1	0.831077219899272	2		123	142	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577093	7577093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882008	NA	P-0058038-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	39	500	0	ENST00000269305.4:c.845G>A	p.Arg282Gln	p.R282Q	ENST00000269305	NM_001126112.2	282	cGg/cAg	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		500	470	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524486	44524486	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058038-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	185	387	0	ENST00000291552.4:c.71T>C	p.Ile24Thr	p.I24T	ENST00000291552	NM_006758.2	24	aTt/aCt	2/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		387	437	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1688556	1688556	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs944291919	NA	P-0058038-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	245	525	0	ENST00000378625.1:c.769A>G	p.Ile257Val	p.I257V	ENST00000378625	NM_001198994.1	257	Atc/Gtc	6/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		525	639	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560459	65560459	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058038-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	207	439	0	ENST00000358664.4:c.138G>T	p.Leu46Phe	p.L46F	ENST00000358664	NM_002382.4	46	ttG/ttT	3/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		439	294	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776892	76776893	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0058582-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	146	257	0	ENST00000373344.5:c.7058_7059dup	p.Ile2354Ter	p.I2354*	ENST00000373344	NM_000489.3	2353	-/TA	33/35	1	1	FACETS	0.94	0.882	0.996	1	0.993	1	CLONAL	2	TRUE	0	0.496848986675031	1		257	235	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027156	49027159	+	frameshift_variant	Frame_Shift_Del	DEL	CAAT	CAAT	-	novel	NA	P-0058608-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	117	430	0	ENST00000267163.4:c.1726_1729del	p.Ser576ArgfsTer34	p.S576Rfs*34	ENST00000267163	NM_000321.2	575	CAATca/ca	18/27	0.318042693692672	2	FACETS	1	0.984	1	0.701	0.639	0.766	CLONAL	1	TRUE	0	0.450885310150635	2		430	370	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533131	63533131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1305562386	NA	P-0058608-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	52	484	0	ENST00000307078.5:c.1763C>T	p.Pro588Leu	p.P588L	ENST00000307078	NM_004655.3	588	cCg/cTg	7/11	0.319868216986317	3	FACETS	0.613	0.523	0.712	0.307	0.261	0.356	SUBCLONAL	1	TRUE	1	0.450885310150635	3		484	461	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339062	65339070	+	inframe_deletion	In_Frame_Del	DEL	CAGATACTC	CAGATACTC	-	novel	NA	P-0058643-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	20	335	0	ENST00000342505.4:c.466_474del	p.Glu156_Leu158del	p.E156_L158del	ENST00000342505	NM_002227.2	156	GAGTATCTG/-	5/25	1	2	FACETS	0.661	0.505	0.845	0.661	0.505	0.845	SUBCLONAL	1	TRUE	1	0.16	2		335	378	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112764367	112764367	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058643-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	28	198	0	ENST00000369452.4:c.976C>G	p.Leu326Val	p.L326V	ENST00000369452	NM_007373.3	326	Ctt/Gtt	5/9	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.16	2		198	309	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908221	28908221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058643-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	25	258	0	ENST00000282397.4:c.2534C>T	p.Ser845Leu	p.S845L	ENST00000282397	NM_002019.4	845	tCa/tTa	18/30	1	2	FACETS	0.847	0.667	1	0.847	0.667	1	CLONAL	1	TRUE	1	0.16	2		258	369	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32890645	32890645	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058643-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	16	219	0	ENST00000380152.3:c.48G>C	p.Lys16Asn	p.K16N	ENST00000380152		16	aaG/aaC	2/27	1	2	FACETS	0.699	0.517	0.918	0.699	0.517	0.918	SUBCLONAL	1	TRUE	1	0.16	2		219	286	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90645594	90645594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1234438811	NA	P-0058643-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	14	225	0	ENST00000330062.3:c.29C>T	p.Ser10Leu	p.S10L	ENST00000330062	NM_002168.2	10	tCg/tTg	1/11	1	2	FACETS	0.72	0.52	0.962	0.72	0.52	0.962	CLONAL	1	TRUE	1	0.16	2		225	243	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866444	37866444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058643-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	31	309	0	ENST00000269571.5:c.749C>T	p.Ser250Phe	p.S250F	ENST00000269571		250	tCt/tTt	6/27	1	2	FACETS	0.994	0.804	1	0.994	0.804	1	CLONAL	1	TRUE	1	0.16	2		309	390	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204917	128204917	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058643-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	46	281	0	ENST00000341105.2:c.524C>T	p.Pro175Leu	p.P175L	ENST00000341105	NM_032638.4	175	cCc/cTc	3/6	0.220526579115066	3	FACETS	0.88	0.743	1	0.88	0.743	1	CLONAL	2	TRUE	1	0.16	3		281	353	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860435	151860435	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058643-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	38	373	0	ENST00000262189.6:c.10227G>C	p.Glu3409Asp	p.E3409D	ENST00000262189	NM_170606.2	3409	gaG/gaC	43/59	1	2	FACETS	1	0.832	1	1	0.832	1	CLONAL	1	TRUE	1	0.16	2		373	472	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416770	121416770	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058643-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	33	344	0	ENST00000257555.6:c.199A>G	p.Thr67Ala	p.T67A	ENST00000257555		67	Act/Gct	1/10	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.16	2		344	388	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473627	67473627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058643-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	11	0	0	ENST00000327367.4:c.707C>T	p.Ser236Phe	p.S236F	ENST00000327367	NM_005902.3	236	tCc/tTc	6/9	1	2	FACETS	0.41	0.282	0.571	0.41	0.282	0.571	SUBCLONAL	1	TRUE	1	0.16	2		0	335	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592045	67592045	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058643-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	11	0	0	ENST00000274335.5:c.1861G>T	p.Glu621Ter	p.E621*	ENST00000274335		621	Gag/Tag	14/15	1	2	FACETS	0.379	0.26	0.527	0.379	0.26	0.527	SUBCLONAL	1	TRUE	1	0.16	2		0	363	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741498	39741498	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058643-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	7	0	0	ENST00000361337.2:c.1385G>T	p.Arg462Leu	p.R462L	ENST00000361337	NM_003286.2	462	cGa/cTa	14/21	1	2	FACETS	0.231	0.143	0.349	0.231	0.143	0.349	SUBCLONAL	1	TRUE	1	0.16	2		0	378	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151602	55151602	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058643-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	5	0	0	ENST00000257290.5:c.2388G>C	p.Leu796Phe	p.L796F	ENST00000257290	NM_006206.4	796	ttG/ttC	17/23	1	2	FACETS	0.218	0.122	0.352	0.218	0.122	0.352	SUBCLONAL	1	TRUE	1	0.16	2		0	287	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143191873	143191873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059459-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	958	358	0	ENST00000262992.4:c.558G>T	p.Met186Ile	p.M186I	ENST00000262992	NM_001101669.1	186	atG/atT	8/24	0.667582461866838	7	FACETS	1	0.988	1			1	CLONAL	6	TRUE	NA	0.667582461866838	7		358	1264	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092823	27092823	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0059459-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	165	371	0	ENST00000324856.7:c.2844T>A	p.Tyr948Ter	p.Y948*	ENST00000324856	NM_006015.4	948	taT/taA	9/20	1	2	FACETS	0.902	0.833	0.973	0.902	0.833	0.973	CLONAL	1	TRUE	1	0.667582461866838	2		371	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578450	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0059459-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	309	539	0	ENST00000269305.4:c.480_481delinsTT	p.Met160_Ala161delinsIleSer	p.M160_A161delinsIS	ENST00000269305	NM_001126112.2	160	atGGcc/atTTcc	5/11	0.194236293310677	3	FACETS	1	0.984	1			1	INDETERMINATE	2	TRUE	NA	0.667582461866838	3		539	578	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628717	21628717	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059459-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	167	373	0	ENST00000421138.2:c.991A>T	p.Thr331Ser	p.T331S	ENST00000421138		331	Acg/Tcg	10/16	0.567429108546515	2	FACETS	0.89	0.838	0.942	0.89	0.838	0.942	CLONAL	2	TRUE	0	0.667582461866838	2		373	281	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042208	42042208	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059459-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	252	469	0	ENST00000219905.7:c.6404del	p.Lys2135ArgfsTer44	p.K2135Rfs*44	ENST00000219905	NM_001164273.1	2135	Aag/ag	17/24	0.571057114944325	2	FACETS	0.819	0.777	0.86	0.819	0.777	0.86	CLONAL	2	TRUE	0	0.667582461866838	2		469	461	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656655	3656655	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059459-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	167	454	0	ENST00000294008.3:c.580A>T	p.Thr194Ser	p.T194S	ENST00000294008	NM_032444.2	194	Aca/Tca	3/15	1	2	FACETS	0.921	0.852	0.993	0.921	0.852	0.993	CLONAL	1	TRUE	1	0.667582461866838	2		454	543	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991359	72991359	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059459-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	133	402	0	ENST00000268489.5:c.2686G>T	p.Ala896Ser	p.A896S	ENST00000268489	NM_006885.3	896	Gcc/Tcc	2/10	NA	2	FACETS	0.832	0.76	0.906			1	INDETERMINATE	1	TRUE	NA	0.667582461866838	2		402	479	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61305006	61305006	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059459-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	57	300	0	ENST00000341074.5:c.1120A>T	p.Arg374Trp	p.R374W	ENST00000341074	NM_002974.2	374	Agg/Tgg	8/8	1	2	FACETS	0.739	0.642	0.843	0.739	0.642	0.843	SUBCLONAL	1	TRUE	1	0.667582461866838	2		300	231	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968301	18968301	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059459-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	255	384	0	ENST00000262803.5:c.2141A>C	p.Asn714Thr	p.N714T	ENST00000262803	NM_002911.3	714	aAc/aCc	15/24	0.571057114944325	2	FACETS	0.792	0.752	0.833	0.792	0.752	0.833	SUBCLONAL	2	TRUE	0	0.667582461866838	2		384	482	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795437	39795437	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059459-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	270	453	0	ENST00000288319.7:c.283G>T	p.Gly95Cys	p.G95C	ENST00000288319	NM_182918.3	95	Ggc/Tgc	3/10	0.567429108546515	2	FACETS	0.822	0.782	0.862	0.822	0.782	0.862	CLONAL	2	TRUE	0	0.667582461866838	2		453	492	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970998	55970998	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059459-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	132	386	0	ENST00000263923.4:c.1799C>A	p.Thr600Lys	p.T600K	ENST00000263923	NM_002253.2	600	aCa/aAa	13/30	0.188510532382403	1	FACETS	0.61	0.558	0.663	0.61	0.558	0.663	INDETERMINATE	1	TRUE	0	0.667582461866838	1		386	432	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931820	68931820	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059459-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	286	369	0	ENST00000288368.4:c.250C>G	p.His84Asp	p.H84D	ENST00000288368	NM_024870.2	84	Cat/Gat	3/40	0.667582461866838	6	FACETS	1	0.983	1	0.556	0.524	0.589	CLONAL	2	TRUE	2	0.667582461866838	6		369	900	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123022477	123022477	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059459-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	99	318	0	ENST00000355640.3:c.886G>T	p.Asp296Tyr	p.D296Y	ENST00000355640		296	Gat/Tat	3/7	0.662308586432673	1	FACETS	0.8	0.727	0.874	0.8	0.727	0.874	SUBCLONAL	1	TRUE	0	0.667582461866838	1		318	247	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797503	45797503	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059459-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	149	499	0	ENST00000450313.1:c.1016G>T	p.Cys339Phe	p.C339F	ENST00000450313	NM_012222.2	339	tGc/tTc	12/16	1	2	FACETS	0.759	0.697	0.824	0.759	0.697	0.824	SUBCLONAL	1	TRUE	1	0.667582461866838	2		499	588	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61325767	61325767	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059459-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	36	90	0	ENST00000283752.5:c.449G>T	p.Trp150Leu	p.W150L	ENST00000283752	NM_006919.2	150	tGg/tTg	5/8	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.667582461866838	2		90	107	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059525-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	21	350	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.811	0.63	1	0.811	0.63	1	CLONAL	1	TRUE	1	0.35	2		350	148	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059525-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	58	227	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	0.294462000872468	1	FACETS	0.863	0.746	0.988	0.863	0.746	0.988	CLONAL	1	TRUE	0	0.35	1		227	317	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933594	39933594	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059525-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	45	327	0	ENST00000378444.4:c.1005del	p.Ser336ArgfsTer42	p.S336Rfs*42	ENST00000378444	NM_001123385.1	335	ccC/cc	4/15	0.214564155396245	3	FACETS	1	0.859	1	0.509	0.43	0.595	CLONAL	1	TRUE	1	0.35	3		327	297	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534287	534288	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0059525-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	46	284	0	ENST00000451590.1:c.35_36delinsTT	p.Gly12Val	p.G12V	ENST00000451590	NM_001130442.1	12	gGC/gTT	2/5	1	2	FACETS	0.929	0.787	1	0.929	0.787	1	CLONAL	1	TRUE	1	0.35	2		284	283	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707902	43707903	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0059525-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	55	291	0	ENST00000382044.4:c.4978_4979del	p.Glu1660LysfsTer19	p.E1660Kfs*19	ENST00000382044	NM_001141980.1	1660	GAa/a	23/28	1	2	FACETS	0.829	0.712	0.956	0.829	0.712	0.956	CLONAL	1	TRUE	1	0.35	2		291	379	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597460	10597461	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0059525-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	25	204	0	ENST00000171111.5:c.1742_1743del	p.Val581GlyfsTer37	p.V581Gfs*37	ENST00000171111	NM_203500.1	581	gTG/g	6/6	1	2	FACETS	0.501	0.396	0.622	0.501	0.396	0.622	SUBCLONAL	1	TRUE	1	0.35	2		204	285	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244757	46244758	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0059525-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	46	282	0	ENST00000334344.6:c.2851_2852del	p.Pro951SerfsTer16	p.P951Sfs*16	ENST00000334344	NM_152641.2	951	CCa/a	15/21	1	2	FACETS	0.797	0.674	0.931	0.797	0.674	0.931	CLONAL	1	TRUE	1	0.35	2		282	330	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0060003-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	49	288	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.120313690026127	3	FACETS	1	0.891	1	1	0.891	1	CLONAL	2	TRUE	1	0.120313690026127	3		288	407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0060003-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	62	536	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.120313690026127	3	FACETS	1	0.965	1	0.704	0.607	0.81	CLONAL	1	TRUE	1	0.120313690026127	3		536	776	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910335	29910335	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200058378	NA	P-0060003-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	69	419	0	ENST00000376809.5:c.5C>T	p.Ala2Val	p.A2V	ENST00000376809	NM_002116.7	2	gCc/gTc	1/8	0.120313690026127	3	FACETS	0.894	0.778	1	0.894	0.778	1	CLONAL	2	TRUE	1	0.120313690026127	3		419	680	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614898	23614898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060213-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	77	277	0	ENST00000261584.4:c.3443C>T	p.Thr1148Ile	p.T1148I	ENST00000261584	NM_024675.3	1148	aCt/aTt	13/13	1	2	FACETS	0.879	0.776	0.99	0.879	0.776	0.99	CLONAL	1	TRUE	1	0.41298847101339	2		277	424	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505040	149505063	+	inframe_deletion	In_Frame_Del	DEL	GTGGAGTCATAGGGCAGCTGCATG	GTGGAGTCATAGGGCAGCTGCATG	-	novel	NA	P-0060213-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	300	311	0	ENST00000261799.4:c.1752_1775del	p.Met585_Thr592del	p.M585_T592del	ENST00000261799	NM_002609.3	584	ccCATGCAGCTGCCCTATGACTCCACg/ccg	12/23	0.274796348902524	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	TRUE	0	0.41298847101339	3		311	572	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339214	70339271	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGCCTCAGGATGAACTGACGGCCTTGAATGTAAAACAAGGTTTCAATAACCAGCCTG	CTGCCTCAGGATGAACTGACGGCCTTGAATGTAAAACAAGGTTTCAATAACCAGCCTG	-	novel	NA	P-0060213-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	84	234	0	ENST00000374080.3:c.100-6_151del		p.X34_splice	ENST00000374080		34		2/45	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.41298847101339	2		234	301	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0060301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	170	252	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.305366419953283	4	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.475711693210131	4		253	803	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0060301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	246	506	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.157664503956765	2	FACETS	1	0.988	1	0.606	0.568	0.646	INDETERMINATE	1	TRUE	0	0.475711693210131	2		506	853	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0060301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	122	149	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	0.232575346223072	3	FACETS	1	0.983	1	0.689	0.626	0.753	INDETERMINATE	1	TRUE	1	0.475711693210131	3		149	461	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519927	NA	P-0060301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	143	169	0	ENST00000263967.3:c.1625A>C	p.Glu542Ala	p.E542A	ENST00000263967	NM_006218.2	542	gAa/gCa	10/21	0.232575346223072	3	FACETS	1	0.986	1	0.689	0.631	0.749	INDETERMINATE	1	TRUE	1	0.475711693210131	3		169	540	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245725	41245725	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs397508911	NA	P-0060301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	168	378	0	ENST00000357654.3:c.1823del	p.Lys608ArgfsTer4	p.K608Rfs*4	ENST00000357654	NM_007294.3	608	aAg/ag	10/23	1	2	FACETS	0.79	0.726	0.857	0.79	0.726	0.857	SUBCLONAL	1	TRUE	1	0.475711693210131	2		378	894	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008985	152009007	+	frameshift_variant	Frame_Shift_Del	DEL	TGCTTACACTTACACAAGATACT	TGCTTACACTTACACAAGATACT	-	novel	NA	P-0060301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	235	370	0	ENST00000262189.6:c.615_637del	p.Val206ProfsTer6	p.V206Pfs*6	ENST00000262189	NM_170606.2	205	atAGTATCTTGTGTAAGTGTAAGCAcc/atcc	5/59	0.232575346223072	3	FACETS	1	0.99	1	0.659	0.615	0.704	INDETERMINATE	1	TRUE	1	0.475711693210131	3		370	928	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665377	117665377	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	61	388	0	ENST00000368508.3:c.4370T>G	p.Leu1457Arg	p.L1457R	ENST00000368508	NM_002944.2	1457	cTt/cGt	27/43	0.475711693210131	1	FACETS	0.243	0.208	0.28	0.243	0.208	0.28	SUBCLONAL	1	TRUE	0	0.475711693210131	1		388	806	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974719	21974724	+	inframe_deletion	In_Frame_Del	DEL	CGCCCC	CGCCCC	-	novel	NA	P-0060654-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	36	562	0	ENST00000304494.5:c.103_108del	p.Gly35_Ala36del	p.G35_A36del	ENST00000304494	NM_000077.4	35	GGGGCG/-	1/3	1	2	FACETS	0.81	0.664	0.975	0.81	0.664	0.975	CLONAL	1	TRUE	1	0.12	2		562	741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587781845	NA	P-0060654-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	33	580	0	ENST00000269305.4:c.511G>T	p.Glu171Ter	p.E171*	ENST00000269305	NM_001126112.2	171	Gag/Tag	5/11	1	2	FACETS	0.653	0.53	0.793	0.653	0.53	0.793	SUBCLONAL	1	TRUE	1	0.12	2		580	842	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30682927	30682927	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060654-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	63	448	0	ENST00000376406.3:c.26G>A	p.Trp9Ter	p.W9*	ENST00000376406	NM_014641.2	9	tGg/tAg	2/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.12	2		448	709	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602799	10602799	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060654-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	29	601	0	ENST00000171111.5:c.779G>C	p.Arg260Pro	p.R260P	ENST00000171111	NM_203500.1	260	cGa/cCa	3/6	1	2	FACETS	0.573	0.458	0.705	0.573	0.458	0.705	SUBCLONAL	1	TRUE	1	0.12	2		601	844	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130504	29130504	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876661109	NA	P-0061277-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	26	534	0	ENST00000328354.6:c.206A>G	p.Gln69Arg	p.Q69R	ENST00000328354	NM_007194.3	69	cAg/cGg	2/15	1	2	FACETS	0.346	0.274	0.43	0.346	0.274	0.43	SUBCLONAL	1	TRUE	1	0.33	2		534	455	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753286	42753286	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061456-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	213	553	0	ENST00000222329.4:c.978del	p.Ser327AlafsTer70	p.S327Afs*70	ENST00000222329	NM_006494.2	326	ctC/ct	4/4	0.179114693714924	3	FACETS	1	0.985	1	0.787	0.736	0.838	INDETERMINATE	2	TRUE	0	0.363447143827322	3		553	587	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138646	37138646	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061456-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	43	483	0	ENST00000373509.5:c.180C>G	p.Asp60Glu	p.D60E	ENST00000373509	NM_002648.3	60	gaC/gaG	2/6	0.369748507709691	2	FACETS	0.491	0.411	0.58	0.245	0.205	0.29	SUBCLONAL	1	TRUE	0	0.363447143827322	2		483	482	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873580	35873580	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0061456-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	110	401	0	ENST00000303115.3:c.538-2A>G		p.X180_splice	ENST00000303115	NM_002185.3	180			0.369748507709691	3	FACETS	1	0.978	1	0.66	0.595	0.728	CLONAL	1	TRUE	1	0.363447143827322	3		401	542	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061665-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	89	350	0				ENST00000310581	NM_198253.2	-/1132			0.274430567023819	2	FACETS	0.59	0.529	0.655	0.295	0.264	0.328	INDETERMINATE	1	TRUE	0	0.96	2		350	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0061665-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	32	324	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.118	0.095	0.143	0.118	0.095	0.143	SUBCLONAL	1	TRUE	1	0.96	2		324	567	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777635	9777635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773473376	NA	P-0061665-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	74	700	0	ENST00000377346.4:c.971G>A	p.Arg324His	p.R324H	ENST00000377346	NM_005026.3	324	cGc/cAc	8/24	1	2	FACETS	0.205	0.179	0.233	0.205	0.179	0.233	SUBCLONAL	1	TRUE	1	0.96	2		700	752	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056214	27056214	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061665-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	105	673	0	ENST00000324856.7:c.1210C>T	p.Gln404Ter	p.Q404*	ENST00000324856	NM_006015.4	404	Caa/Taa	2/20	1	2	FACETS	0.376	0.337	0.416	0.376	0.337	0.416	SUBCLONAL	1	TRUE	1	0.96	2		673	582	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941653	48941653	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0061665-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	22	285	0	ENST00000267163.4:c.963C>G	p.Tyr321Ter	p.Y321*	ENST00000267163	NM_000321.2	321	taC/taG	10/27	1	2	FACETS	0.253	0.197	0.317	0.253	0.197	0.317	SUBCLONAL	1	TRUE	1	0.96	2		285	181	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0061665-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	122	547	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	1	2	FACETS	0.406	0.368	0.446	0.406	0.368	0.446	SUBCLONAL	1	TRUE	1	0.96	2		547	626	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0061789-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	230	453	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.93033047353305	2		453	472	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274897	41274897	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061789-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	264	481	0	ENST00000349496.5:c.1147T>C	p.Trp383Arg	p.W383R	ENST00000349496	NM_001904.3	383	Tgg/Cgg	8/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.93033047353305	2		481	548	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170166	32170166	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061789-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	36	495	0	ENST00000375023.3:c.3442G>A	p.Glu1148Lys	p.E1148K	ENST00000375023	NM_004557.3	1148	Gag/Aag	21/30	1	2	FACETS	0.194	0.16	0.233	0.194	0.16	0.233	SUBCLONAL	1	TRUE	1	0.93033047353305	2		495	398	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412956	63412956	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061789-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	19	232	0	ENST00000330258.3:c.211A>C	p.Ser71Arg	p.S71R	ENST00000330258	NM_152424.3	71	Agt/Cgt	2/2	1	1	FACETS	0.075	0.057	0.097	0.075	0.057	0.097	SUBCLONAL	1	TRUE	0	0.93033047353305	1		232	290	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179197	123179197	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062142-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	75	197	0	ENST00000218089.9:c.646C>T	p.Arg216Ter	p.R216*	ENST00000218089	NM_001042749.1	216	Cga/Tga	8/35	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		197	196	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062499-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	225	350	0				ENST00000310581	NM_198253.2	-/1132			0.367052716719304	9	FACETS	0.949	0.901	0.995	1	0.984	1	CLONAL	8	FALSE	2	0.367052716719304	9		350	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0062499-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	140	401	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	1	2	FACETS	0.84	0.771	0.911	1	0.99	1	CLONAL	2	FALSE	1	0.367052716719304	2		401	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0062499-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	145	369	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	1	2	FACETS	0.835	0.768	0.905	1	0.99	1	CLONAL	2	FALSE	1	0.367052716719304	2		369	473	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295247	1295247	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0062499-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	240	313	0				ENST00000310581	NM_198253.2	-/1132			0.367052716719304	9	FACETS	1	0.962	1	1	0.99	1	CLONAL	8	FALSE	2	0.367052716719304	9		313	370	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444177	49444177	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0062499-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	24	543	0	ENST00000301067.7:c.3194C>G	p.Ser1065Ter	p.S1065*	ENST00000301067	NM_003482.3	1065	tCa/tGa	11/54	1	2	FACETS	0.338	0.264	0.423	0.338	0.264	0.423	SUBCLONAL	1	FALSE	1	0.367052716719304	2		543	387	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47004903	47004903	+	intron_variant	Intron	SNP	C	C	T	novel	NA	P-0062499-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	175	310	0	ENST00000377604.3:c.-126+19C>T		p.*42*	ENST00000377604	NM_001204468.1	-/163			0.185876899996811	2	FACETS	0.876	0.829	0.923			1	INDETERMINATE	4	FALSE	NA	0.367052716719304	2		310	272	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324917	31324917	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs776780353	NA	P-0062499-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	146	394	0	ENST00000412585.2:c.19C>T	p.Arg7Ter	p.R7*	ENST00000412585	NM_005514.6	7	Cga/Tga	1/8	1	2	FACETS	1	0.982	1	1	0.993	1	CLONAL	2	FALSE	1	0.367052716719304	2		394	332	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752745	42752745	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062499-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	36	394	0	ENST00000222329.4:c.1519G>A	p.Glu507Lys	p.E507K	ENST00000222329	NM_006494.2	507	Gag/Aag	4/4	1	2	FACETS	0.584	0.481	0.698	0.584	0.481	0.698	SUBCLONAL	1	FALSE	1	0.367052716719304	2		394	336	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955452	48955452	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0062499-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	89	299	0	ENST00000267163.4:c.1568T>G	p.Leu523Ter	p.L523*	ENST00000267163	NM_000321.2	523	tTa/tGa	17/27	0.367052716719304	1	FACETS	0.947	0.858	1	1	0.987	1	CLONAL	2	FALSE	0	0.367052716719304	1		299	209	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102198795	102198795	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062499-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	79	252	0	ENST00000263464.3:c.966G>C	p.Leu322Phe	p.L322F	ENST00000263464	NM_001165.4	322	ttG/ttC	4/9	0.111840289933723	0	FACETS	1	0.895	1			1	INDETERMINATE	1	FALSE	0	0.367052716719304	0		252	271	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50786466	50786466	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062499-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	43	234	0	ENST00000307179.4:c.2647G>C	p.Asp883His	p.D883H	ENST00000307179		883	Gat/Cat	16/20	0.367052716719304	1	FACETS	0.797	0.673	0.933	0.797	0.673	0.933	CLONAL	1	FALSE	0	0.367052716719304	1		234	240	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61722598	61722598	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062499-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	83	272	0	ENST00000401558.2:c.1039C>G	p.Leu347Val	p.L347V	ENST00000401558	NM_003400.3	347	Ctt/Gtt	11/25	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.367052716719304	2		272	309	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41521961	41521961	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1226998471	NA	P-0062499-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	124	289	0	ENST00000263253.7:c.823C>G	p.Gln275Glu	p.Q275E	ENST00000263253	NM_001429.3	275	Cag/Gag	3/31	0.304507238352611	0	FACETS	0.648	0.602	0.693			1	SUBCLONAL	3	FALSE	0	0.367052716719304	0		289	220	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673284	30673284	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062499-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	201	561	0	ENST00000376406.3:c.3676C>T	p.Gln1226Ter	p.Q1226*	ENST00000376406	NM_014641.2	1226	Cag/Tag	10/15	1	2	FACETS	0.836	0.779	0.895	1	0.993	1	CLONAL	2	FALSE	1	0.367052716719304	2		561	655	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124491962	124491962	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1444104997	NA	P-0062499-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	69	221	0	ENST00000357628.3:c.913G>A	p.Val305Ile	p.V305I	ENST00000357628	NM_015450.2	305	Gtt/Att	11/19	1	2	FACETS	0.895	0.793	1	1	0.981	1	CLONAL	2	FALSE	1	0.367052716719304	2		221	210	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031939	26031939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062499-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	26	547	0	ENST00000244661.2:c.350G>A	p.Arg117Gln	p.R117Q	ENST00000244661	NM_003537.3	117	cGa/cAa	1/1	1	2	FACETS	0.276	0.218	0.343	0.276	0.218	0.343	SUBCLONAL	1	FALSE	1	0.367052716719304	2		547	513	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799213	42799213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749265824	NA	P-0062499-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	27	336	0	ENST00000575354.2:c.4697C>T	p.Ser1566Phe	p.S1566F	ENST00000575354	NM_015125.3	1566	tCt/tTt	20/20	1	2	FACETS	0.506	0.403	0.622	0.506	0.403	0.622	SUBCLONAL	1	FALSE	1	0.367052716719304	2		336	291	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794521	42794521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062499-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	39	448	0	ENST00000575354.2:c.1601C>T	p.Ser534Phe	p.S534F	ENST00000575354	NM_015125.3	534	tCc/tTc	10/20	1	2	FACETS	0.597	0.496	0.709	0.597	0.496	0.709	SUBCLONAL	1	FALSE	1	0.367052716719304	2		448	356	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324508	31324508	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs137854683	NA	P-0062499-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	26	365	0	ENST00000412585.2:c.300G>C	p.Glu100Asp	p.E100D	ENST00000412585	NM_005514.6	100	gaG/gaC	2/8	1	2	FACETS	0.422	0.334	0.522	0.422	0.334	0.522	SUBCLONAL	1	FALSE	1	0.367052716719304	2		365	336	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681114	30681114	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062499-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	66	352	0	ENST00000376406.3:c.605C>A	p.Ser202Tyr	p.S202Y	ENST00000376406	NM_014641.2	202	tCc/tAc	5/15	1	2	FACETS	0.908	0.792	1	0.908	0.792	1	CLONAL	1	FALSE	1	0.367052716719304	2		352	396	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185020	32185020	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062499-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	30	406	0	ENST00000375023.3:c.1648G>C	p.Glu550Gln	p.E550Q	ENST00000375023	NM_004557.3	550	Gag/Cag	10/30	1	2	FACETS	0.447	0.36	0.545	0.447	0.36	0.545	SUBCLONAL	1	FALSE	1	0.367052716719304	2		406	366	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs17849781	NA	P-0062608-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	174	594	0	ENST00000269305.4:c.832C>G	p.Pro278Ala	p.P278A	ENST00000269305	NM_001126112.2	278	Cct/Gct	8/11	0.756817116363038	2	FACETS	0.977	0.932	1	0.977	0.932	1	CLONAL	2	TRUE	0	0.767356420293162	2		594	232	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447410	12447410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766913119	NA	P-0062608-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	166	588	0	ENST00000287820.6:c.649G>A	p.Glu217Lys	p.E217K	ENST00000287820	NM_015869.4	217	Gag/Aag	5/7	0.766943620476177	5	FACETS	1	0.942	1	0.407	0.377	0.438	CLONAL	2	TRUE	0	0.767356420293162	5		588	457	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199454	16199454	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062608-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	192	594	0	ENST00000375759.3:c.227C>A	p.Thr76Lys	p.T76K	ENST00000375759	NM_015001.2	76	aCg/aAg	2/15	0.766943620476177	3	FACETS	0.984	0.927	1	0.984	0.927	1	CLONAL	2	TRUE	1	0.767356420293162	3		594	352	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244217	46244217	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062608-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	23	649	0	ENST00000334344.6:c.2311C>G	p.Gln771Glu	p.Q771E	ENST00000334344	NM_152641.2	771	Cag/Gag	15/21	0.635110993661454	3	FACETS	0.301	0.234	0.377			1	SUBCLONAL	1	TRUE	NA	0.767356420293162	3		649	276	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156492	106156492	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062608-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	178	647	0	ENST00000380013.4:c.1393C>G	p.Pro465Ala	p.P465A	ENST00000380013	NM_001127208.2	465	Cca/Gca	3/11	0.766943620476177	3	FACETS	0.973	0.914	1	0.973	0.914	1	CLONAL	2	TRUE	1	0.767356420293162	3		647	330	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633109	3633109	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062608-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	63	578	0	ENST00000294008.3:c.5142G>C	p.Leu1714Phe	p.L1714F	ENST00000294008	NM_032444.2	1714	ttG/ttC	14/15	0.750426455597413	3	FACETS	0.891	0.779	1	0.445	0.389	0.505	CLONAL	1	TRUE	1	0.767356420293162	3		578	255	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932848	39932848	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062608-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	173	358	0	ENST00000378444.4:c.1751G>A	p.Ser584Asn	p.S584N	ENST00000378444	NM_001123385.1	584	aGc/aAc	4/15	0.699717639464971	2	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.767356420293162	2		358	206	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0062883-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	107	426	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.346557355637299	2	FACETS	0.788	0.715	0.864	0.788	0.715	0.864	SUBCLONAL	2	TRUE	0	0.398128318075488	2		426	341	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0062883-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	34	469	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.833	0.687	0.995	0.833	0.687	0.995	CLONAL	1	TRUE	1	0.398128318075488	2		470	205	SUCCESS
APC	324	MSKCC	GRCh37	5	112174835	112174835	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0062883-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	149	503	0	ENST00000257430.4:c.3544A>T	p.Lys1182Ter	p.K1182*	ENST00000257430	NM_000038.5	1182	Aaa/Taa	16/16	0.398128318075488	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.398128318075488	2		503	325	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775955	9775955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062883-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	128	511	0	ENST00000377346.4:c.419G>A	p.Arg140His	p.R140H	ENST00000377346	NM_005026.3	140	cGc/cAc	5/24	0.346557355637299	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	0	0.398128318075488	2		511	314	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508328	106508328	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs769318398	NA	P-0062883-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	73	502	0	ENST00000359195.3:c.322G>T	p.Glu108Ter	p.E108*	ENST00000359195	NM_002649.2	108	Gag/Tag	2/11	0.362775393110099	3	FACETS	1	0.967	1	0.647	0.57	0.728	CLONAL	1	TRUE	1	0.398128318075488	3		502	340	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165199	47165199	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062883-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	41	435	0	ENST00000409792.3:c.927G>C	p.Lys309Asn	p.K309N	ENST00000409792	NM_014159.6	309	aaG/aaC	3/21	0.346557355637299	2	FACETS	0.827	0.694	0.973	0.414	0.347	0.487	CLONAL	1	TRUE	0	0.398128318075488	2		435	249	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925325	114925325	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062883-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	102	370	1	ENST00000543371.1:c.1403A>T	p.Lys468Met	p.K468M	ENST00000543371	NM_001198531.1	468	aAg/aTg	14/14	0.346557355637299	2	FACETS	0.945	0.859	1	0.945	0.859	1	CLONAL	2	TRUE	0	0.398128318075488	2		371	271	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249455	153249468	+	frameshift_variant	Frame_Shift_Del	DEL	CCGATCTGTAGATC	CCGATCTGTAGATC	-	novel	NA	P-0062883-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	26	426	0	ENST00000281708.4:c.1310_1323del	p.Gly437AspfsTer30	p.G437Dfs*30	ENST00000281708	NM_033632.3	437	gGATCTACAGATCGG/g	9/12	1	2	FACETS	0.625	0.498	0.769	0.625	0.498	0.769	SUBCLONAL	1	TRUE	1	0.398128318075488	2		426	209	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675862	30675862	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063049-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	57	345	0	ENST00000376406.3:c.2494G>T	p.Glu832Ter	p.E832*	ENST00000376406	NM_014641.2	832	Gag/Tag	8/15	0.276230113687902	2	FACETS	0.257	0.22	0.298	0.129	0.11	0.149	INDETERMINATE	1	TRUE	0	0.727376302528254	2		345	609	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625194	69625194	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063049-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	424	259	0	ENST00000334134.2:c.599G>T	p.Arg200Ile	p.R200I	ENST00000334134	NM_005247.2	200	aGa/aTa	3/3	0.727669004212328	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.727376302528254	2		259	513	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281481	15281482	+	inframe_insertion,splice_region_variant	In_Frame_Ins	INS	-	-	CCCGCACGTCCCGCAGTGGGTACGGGAAGTCCAGGCGCTCCACCG	novel	NA	P-0063049-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	173	267	0	ENST00000263388.2:c.4847_4891dup	p.Ala1616_Arg1630dup	p.A1616_R1630dup	ENST00000263388	NM_000435.2	1616	ggg/gCGGTGGAGCGCCTGGACTTCCCGTACCCACTGCGGGACGTGCGGGgg		0.31085749024861	5	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.727376302528254	5		267	848	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986944	36986944	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852694	NA	P-0063252-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	115	306	0	ENST00000354822.5:c.745C>T	p.Gln249Ter	p.Q249*	ENST00000354822	NM_001079668.2	249	Cag/Tag	3/3	0.466142917750107	1	FACETS	0.855	0.776	0.936	0.855	0.776	0.936	CLONAL	1	TRUE	0	0.491523619398892	1		306	413	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456475	89456475	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063252-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	75	220	0	ENST00000336596.2:c.1651G>T	p.Val551Leu	p.V551L	ENST00000336596	NM_005233.5	551	Gta/Tta	8/17	0.23570060190206	1	FACETS	0.603	0.531	0.679	0.603	0.531	0.679	INDETERMINATE	1	TRUE	0	0.491523619398892	1		220	382	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457350	67457351	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063252-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	199	360	0	ENST00000327367.4:c.325dup	p.Cys109LeufsTer2	p.C109Lfs*2	ENST00000327367	NM_005902.3	108	-/T	2/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.491523619398892	2		360	751	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975361	13975361	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063252-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	117	258	0	ENST00000405192.2:c.526C>G	p.Pro176Ala	p.P176A	ENST00000405192	NM_001163147.1	176	Cca/Gca	7/12	1	2	FACETS	0.818	0.74	0.9	0.818	0.74	0.9	CLONAL	1	TRUE	1	0.491523619398892	2		258	582	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0063288-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	32	504	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.16648286808456	1	FACETS	0.707	0.573	0.86	0.707	0.573	0.86	SUBCLONAL	1	TRUE	0	0.14	1		504	601	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797247	135797247	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063288-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	45	492	0	ENST00000298552.3:c.622A>T	p.Ser208Cys	p.S208C	ENST00000298552	NM_001162426.1	208	Agt/Tgt	7/23	1	2	FACETS	0.994	0.834	1	0.994	0.834	1	CLONAL	1	TRUE	1	0.14	2		492	647	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399202	139399202	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063288-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	32	545	0	ENST00000277541.6:c.4941G>T	p.Gln1647His	p.Q1647H	ENST00000277541	NM_017617.3	1647	caG/caT	26/34	1	2	FACETS	0.819	0.664	0.996	0.819	0.664	0.996	CLONAL	1	TRUE	1	0.14	2		545	558	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0063354-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	61	252	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.812	0.702	0.932	1	0.973	1	CLONAL	2	TRUE	1	0.161480238153056	2		253	465	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221313	1221314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs121913321	NA	P-0063354-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	113	502	0	ENST00000326873.7:c.842dup	p.Leu282AlafsTer3	p.L282Afs*3	ENST00000326873	NM_000455.4	279	ggc/ggCc	6/10	0.158122987905853	2	FACETS	0.922	0.83	1	0.922	0.83	1	CLONAL	2	TRUE	0	0.161480238153056	2		502	759	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207627	2207627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063354-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	130	408	0	ENST00000398665.3:c.911C>T	p.Ser304Leu	p.S304L	ENST00000398665	NM_032482.2	304	tCg/tTg	11/28	0.158122987905853	2	FACETS	0.836	0.76	0.915	1	0.978	1	CLONAL	3	TRUE	0	0.161480238153056	2		408	642	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837895	156837895	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0063354-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	78	447	0	ENST00000524377.1:c.429-1G>T		p.X143_splice	ENST00000524377	NM_002529.3	143			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.161480238153056	2		447	798	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602928	10602928	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063354-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	130	394	0	ENST00000171111.5:c.650A>C	p.Gln217Pro	p.Q217P	ENST00000171111	NM_203500.1	217	cAa/cCa	3/6	0.158122987905853	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.161480238153056	2		394	670	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65311199	65311199	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0063354-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	66	359	0	ENST00000342505.4:c.2112C>G	p.Tyr704Ter	p.Y704*	ENST00000342505	NM_002227.2	704	taC/taG	15/25	0.161480238153056	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.161480238153056	1		359	602	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980328	201980328	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063354-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	77	527	0	ENST00000359651.3:c.64G>T	p.Glu22Ter	p.E22*	ENST00000359651		22	Gag/Tag	1/8	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.161480238153056	2		527	750	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242002	105242002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063354-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	43	374	0	ENST00000349310.3:c.422C>T	p.Pro141Leu	p.P141L	ENST00000349310	NM_001014432.1	141	cCc/cTc	6/15	0.161480238153056	1	FACETS	0.859	0.718	1	0.859	0.718	1	CLONAL	1	TRUE	0	0.161480238153056	1		374	570	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124491940	124491940	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063354-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	35	260	0	ENST00000357628.3:c.935A>T	p.Asp312Val	p.D312V	ENST00000357628	NM_015450.2	312	gAc/gTc	11/19	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.161480238153056	2		260	390	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129701	11129701	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0063354-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	101	425	0	ENST00000358026.2:c.2505+2T>C		p.X835_splice	ENST00000358026	NM_001128849.1	835			0.158122987905853	2	FACETS	0.941	0.842	1	0.941	0.842	1	CLONAL	2	TRUE	0	0.161480238153056	2		425	665	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223201	2223201	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063354-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	74	454	0	ENST00000326181.6:c.813C>A	p.Asn271Lys	p.N271K	ENST00000326181	NM_032271.2	271	aaC/aaA	10/21	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.161480238153056	2		454	721	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0063851-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	41	508	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.97	0.814	1	0.97	0.814	1	CLONAL	1	FALSE	1	0.343609437465504	2		508	246	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0063851-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	20	148	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.962	0.745	1	0.962	0.745	1	CLONAL	1	FALSE	1	0.343609437465504	2		148	121	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938447	44938447	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063851-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	34	331	0	ENST00000377967.4:c.2995G>T	p.Glu999Ter	p.E999*	ENST00000377967	NM_021140.2	999	Gaa/Taa	20/29	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	FALSE	1	0.343609437465504	2		331	174	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651906	36651906	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063851-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	30	505	0	ENST00000244741.5:c.28C>T	p.Gln10Ter	p.Q10*	ENST00000244741	NM_000389.4	10	Cag/Tag	2/3	0.111057443373676	4	FACETS	0.782	0.632	0.952	0.391	0.316	0.476	INDETERMINATE	1	FALSE	2	0.343609437465504	4		505	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0063858-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	838	389	0	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.525146538072691	5	FACETS	0.973	0.953	0.993	0.973	0.953	0.993	CLONAL	5	FALSE	0	0.586694581460147	5		389	1104	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829753	76829756	+	frameshift_variant	Frame_Shift_Del	DEL	CTTC	CTTC	-	novel	NA	P-0063858-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	181	324	0	ENST00000373344.5:c.6285_6288del	p.Lys2096SerfsTer12	p.K2096Sfs*12	ENST00000373344	NM_000489.3	2095	agGAAG/ag	28/35	0.565307334026165	2	FACETS	0.884	0.83	0.938	0.884	0.83	0.938	CLONAL	2	FALSE	0	0.586694581460147	2		324	349	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0064523-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	112	268	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.299878397651664	6	FACETS	0.9	0.819	0.985	0.675	0.614	0.739	CLONAL	3	TRUE	2	0.448046469455778	6		268	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0064523-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	203	548	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.448046469455778	1	FACETS	0.771	0.723	0.819	1	0.993	1	SUBCLONAL	2	TRUE	0	0.448046469455778	1		548	456	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527973	103527973	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0064523-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	74	454	0	ENST00000355739.4:c.3281C>G	p.Ser1094Ter	p.S1094*	ENST00000355739	NM_000123.3	1094	tCa/tGa	15/15	0.438815009048189	3	FACETS	0.757	0.664	0.857	0.252	0.221	0.286	SUBCLONAL	1	TRUE	0	0.448046469455778	3		454	534	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411952	116411980	+	frameshift_variant	Frame_Shift_Del	DEL	TTTGGATAGGCTTGTAAGTGCCCGAAGTG	TTTGGATAGGCTTGTAAGTGCCCGAAGTG	-	novel	NA	P-0064523-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	262	574	0	ENST00000397752.3:c.2938_2966del	p.Leu980LysfsTer10	p.L980Kfs*10	ENST00000397752	NM_000245.2	979	caTTTGGATAGGCTTGTAAGTGCCCGAAGTGta/cata	14/21	0.448046469455778	2	FACETS	0.931	0.879	0.984	0.931	0.879	0.984	CLONAL	2	TRUE	0	0.448046469455778	2		574	628	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417833	32417833	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064523-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	142	439	0	ENST00000332351.3:c.1219C>A	p.His407Asn	p.H407N	ENST00000332351	NM_024426.4	407	Cac/Aac	7/10	0.448046469455778	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.448046469455778	1		439	405	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143369	30143369	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064523-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	44	423	0	ENST00000389048.3:c.157A>T	p.Ser53Cys	p.S53C	ENST00000389048	NM_004304.4	53	Agt/Tgt	1/29	0.448046469455778	2	FACETS	0.67	0.565	0.785	0.335	0.282	0.393	SUBCLONAL	1	TRUE	0	0.448046469455778	2		423	293	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230406	46230406	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064523-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	112	453	0	ENST00000334344.6:c.740G>T	p.Arg247Leu	p.R247L	ENST00000334344	NM_152641.2	247	cGt/cTt	7/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.448046469455778	2		453	391	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992998	72992998	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064523-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	75	490	0	ENST00000268489.5:c.1047C>G	p.His349Gln	p.H349Q	ENST00000268489	NM_006885.3	349	caC/caG	2/10	1	2	FACETS	0.603	0.529	0.683	0.603	0.529	0.683	SUBCLONAL	1	TRUE	1	0.448046469455778	2		490	555	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273181	115273181	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064523-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	84	564	0	ENST00000438362.2:c.1277T>G	p.Leu426Arg	p.L426R	ENST00000438362	NM_001242891.1	426	cTg/cGg	11/20	0.448046469455778	1	FACETS	0.628	0.557	0.704	0.628	0.557	0.704	SUBCLONAL	1	TRUE	0	0.448046469455778	1		564	463	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902584	1902584	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs752556934	NA	P-0064523-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	197	577	0	ENST00000382891.5:c.203A>G	p.His68Arg	p.H68R	ENST00000382891	NM_133335.3	68	cAc/cGc	2/22	0.448046469455778	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.448046469455778	1		577	515	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422618	47422618	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0064523-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	150	440	0	ENST00000404338.3:c.686C>G	p.Ser229Ter	p.S229*	ENST00000404338	NM_004491.4	229	tCa/tGa	1/6	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.448046469455778	2		440	484	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715371	117715371	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064523-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	107	377	0	ENST00000368508.3:c.1118C>G	p.Ser373Cys	p.S373C	ENST00000368508	NM_002944.2	373	tCc/tGc	10/43	0.15644436902554	3	FACETS	0.805	0.729	0.884	0.805	0.729	0.884	INDETERMINATE	2	TRUE	1	0.448046469455778	3		377	363	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876161	35876161	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064523-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	195	504	0	ENST00000303115.3:c.953A>T	p.Asp318Val	p.D318V	ENST00000303115	NM_002185.3	318	gAt/gTt	8/8	0.250554451377066	3	FACETS	0.933	0.869	0.998	0.933	0.869	0.998	INDETERMINATE	2	TRUE	1	0.448046469455778	3		504	571	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55335648	55335648	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064523-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	66	409	0	ENST00000284073.2:c.203C>G	p.Thr68Arg	p.T68R	ENST00000284073	NM_138962.2	68	aCg/aGg	4/14	0.15644436902554	3	FACETS	0.71	0.617	0.81	0.355	0.308	0.405	INDETERMINATE	1	TRUE	1	0.448046469455778	3		409	508	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983608	7983608	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064557-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	66	395	0	ENST00000319144.4:c.699G>C	p.Trp233Cys	p.W233C	ENST00000319144	NM_001139.2	233	tgG/tgC	6/15	0.137660928682832	4	FACETS	0.897	0.787	1	1	0.968	1	CLONAL	3	TRUE	2	0.216031682326515	4		395	276	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0064684-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	166	268	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.541380359945563	6	FACETS	0.945	0.889	1	0.945	0.889	1	CLONAL	4	TRUE	2	0.841306242029183	6		268	280	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119789	70119789	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064684-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	170	446	0	ENST00000245479.2:c.791G>C	p.Arg264Thr	p.R264T	ENST00000245479	NM_000346.3	264	aGa/aCa	3/3	0.605126770343596	4	FACETS	1	0.956	1	0.527	0.486	0.57	CLONAL	1	TRUE	2	0.841306242029183	4		446	706	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953937	32953937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80359152	NA	P-0064684-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	44	449	0	ENST00000380152.3:c.9004G>A	p.Glu3002Lys	p.E3002K	ENST00000380152		3002	Gaa/Aaa	23/27	0.387618476919188	3	FACETS	0.505	0.426	0.592	0.168	0.142	0.198	INDETERMINATE	1	TRUE	0	0.841306242029183	3		449	294	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944527	40944527	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs371433526	NA	P-0064684-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	118	506	0	ENST00000373198.4:c.1975G>T	p.Asp659Tyr	p.D659Y	ENST00000373198	NM_133170.3	659	Gat/Tat	12/32	0.728585667642419	6	FACETS	0.705	0.634	0.779	0.176	0.158	0.195	SUBCLONAL	1	TRUE	2	0.841306242029183	6		506	1068	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710657	114710657	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064684-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	157	449	0	ENST00000543371.1:c.142C>G	p.Leu48Val	p.L48V	ENST00000543371	NM_001198531.1	48	Cta/Gta	1/14	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.841306242029183	2		449	364	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224384	36224384	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs868232650	NA	P-0064684-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	184	645	0	ENST00000222270.7:c.6934C>G	p.Gln2312Glu	p.Q2312E	ENST00000222270	NM_014727.1	2312	Cag/Gag	28/37	NA	2	FACETS	0.898	0.837	0.961			1	INDETERMINATE	1	TRUE	NA	0.841306242029183	2		645	487	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256583	16256583	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0064684-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	155	606	0	ENST00000375759.3:c.3848C>G	p.Ser1283Ter	p.S1283*	ENST00000375759	NM_015001.2	1283	tCa/tGa	11/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.841306242029183	2		606	348	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868120	56868120	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064684-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	190	525	0	ENST00000308159.5:c.1618G>C	p.Glu540Gln	p.E540Q	ENST00000308159	NM_014669.4	540	Gag/Cag	14/22	0.841306242029183	2	FACETS	1	0.978	1	0.549	0.515	0.584	CLONAL	1	TRUE	0	0.841306242029183	2		525	411	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022919	31022919	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064684-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	156	531	0	ENST00000375687.4:c.2404G>A	p.Glu802Lys	p.E802K	ENST00000375687	NM_015338.5	802	Gag/Aag	13/13	NA	2	FACETS	0.716	0.66	0.774			1	INDETERMINATE	1	TRUE	NA	0.841306242029183	2		531	518	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023612	31023612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064684-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	156	523	0	ENST00000375687.4:c.3097G>A	p.Glu1033Lys	p.E1033K	ENST00000375687	NM_015338.5	1033	Gag/Aag	13/13	NA	2	FACETS	0.722	0.665	0.78			1	INDETERMINATE	1	TRUE	NA	0.841306242029183	2		523	514	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778071	27778071	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064684-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	204	675	0	ENST00000369163.2:c.220G>A	p.Glu74Lys	p.E74K	ENST00000369163	NM_003536.2	74	Gag/Aag	1/1	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.841306242029183	2		675	460	SUCCESS
PHF6	84295	MSKCC	GRCh37	X	133547523	133547523	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064684-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	80	349	0	ENST00000332070.3:c.421G>A	p.Asp141Asn	p.D141N	ENST00000332070	NM_032458.2	141	Gat/Aat	6/10	0.743201576607369	1	FACETS	0.984	0.912	1	0.984	0.912	1	CLONAL	1	TRUE	0	0.841306242029183	1		349	112	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1258736	1258736	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064684-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	148	445	0	ENST00000310581.5:c.3009G>T	p.Lys1003Asn	p.K1003N	ENST00000310581	NM_198253.2	1003	aaG/aaT	13/16	0.827797882227702	3	FACETS	0.954	0.877	1	0.477	0.438	0.517	CLONAL	1	TRUE	1	0.841306242029183	3		445	524	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231868	36231871	+	protein_altering_variant	In_Frame_Del	DEL	GCTT	GCTT	C	novel	NA	P-0064684-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	169	563	0	ENST00000300305.3:c.513_516delinsG	p.Ser172del	p.S172del	ENST00000300305		171	aaAAGC/aaG	5/8	0.490542337101625	4	FACETS	1	0.968	1	0.547	0.505	0.591	INDETERMINATE	1	TRUE	2	0.841306242029183	4		563	676	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100425	8100425	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	131	467	1	ENST00000346208.3:c.404del	p.Pro135ArgfsTer60	p.P135Rfs*60	ENST00000346208		133	taC/ta	3/6	1	2	FACETS	0.872	0.791	0.957	0.872	0.791	0.957	CLONAL	1	TRUE	1	0.343785154999604	2		468	874	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	98	397	1	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	1	2	FACETS	0.738	0.658	0.823	0.738	0.658	0.823	SUBCLONAL	1	TRUE	1	0.343785154999604	2		398	773	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	96	341	0	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	0.285557739479072	3	FACETS	0.769	0.684	0.859	0.385	0.342	0.43	SUBCLONAL	1	TRUE	1	0.343785154999604	3		341	851	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	108	413	1	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.758	0.68	0.841	0.758	0.68	0.841	SUBCLONAL	1	TRUE	1	0.343785154999604	2		414	829	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	218	441	5	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	0.285557739479072	3	FACETS	0.864	0.805	0.925	0.864	0.805	0.925	CLONAL	2	TRUE	1	0.343785154999604	3		446	860	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	235	707	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.794	0.742	0.847	1	0.993	1	SUBCLONAL	2	TRUE	1	0.343785154999604	2		711	861	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	86	307	0	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.87	0.771	0.976	0.87	0.771	0.976	CLONAL	1	TRUE	1	0.343785154999604	2		307	575	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	75	344	0	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	0.722	0.633	0.818	0.722	0.633	0.818	SUBCLONAL	1	TRUE	1	0.343785154999604	2		344	604	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	142	450	0	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.899	0.819	0.983	0.899	0.819	0.983	CLONAL	1	TRUE	1	0.343785154999604	2		450	919	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	102	334	0	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.343785154999604	2		334	586	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209616	98209617	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761353734	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	48	381	0	ENST00000331920.6:c.3921dup	p.Arg1308GlnfsTer17	p.R1308Qfs*17	ENST00000331920	NM_000264.3	1307	-/C	23/24	1	2	FACETS	0.44	0.372	0.517	0.44	0.372	0.517	SUBCLONAL	1	TRUE	1	0.343785154999604	2		381	634	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347983	347983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760961378	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	122	456	0	ENST00000262320.3:c.1523del	p.Gly508ValfsTer197	p.G508Vfs*197	ENST00000262320	NM_003502.3	508	gGt/gt	6/11	1	2	FACETS	0.81	0.732	0.893	0.81	0.732	0.893	CLONAL	1	TRUE	1	0.343785154999604	2		456	876	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154241	2154242	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755455183	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	88	421	2	ENST00000434045.2:c.686dup	p.Glu230ArgfsTer50	p.E230Rfs*50	ENST00000434045	NM_001127598.1	229	cca/ccCa	5/5	1	2	FACETS	0.603	0.533	0.678	0.603	0.533	0.678	SUBCLONAL	1	TRUE	1	0.343785154999604	2		423	849	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919935	50919935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1044937882	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	92	370	0	ENST00000440232.2:c.3022C>T	p.Arg1008Cys	p.R1008C	ENST00000440232	NM_002691.3	1008	Cgc/Tgc	24/27	1	2	FACETS	0.83	0.738	0.928	0.83	0.738	0.928	CLONAL	1	TRUE	1	0.343785154999604	2		370	645	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604806	48604806	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	142	370	0	ENST00000342988.3:c.1628T>C	p.Met543Thr	p.M543T	ENST00000342988	NM_005359.5	543	aTg/aCg	12/12	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.343785154999604	2		370	744	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574679	41574679	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	146	481	0	ENST00000263253.7:c.6970del	p.His2324ThrfsTer29	p.H2324Tfs*29	ENST00000263253	NM_001429.3	2322	Ccc/cc	31/31	1	2	FACETS	0.932	0.851	1	0.932	0.851	1	CLONAL	1	TRUE	1	0.343785154999604	2		481	911	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259288	36259288	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs927005033	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	127	360	0	ENST00000300305.3:c.203C>T	p.Ala68Val	p.A68V	ENST00000300305		68	gCc/gTc	3/8	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.343785154999604	2		360	731	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940112	49940112	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760002850	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	123	394	1	ENST00000296474.3:c.931del	p.Ala311ProfsTer27	p.A311Pfs*27	ENST00000296474	NM_002447.2	311	Gcc/cc	1/20	1	2	FACETS	0.865	0.782	0.953	0.865	0.782	0.953	CLONAL	1	TRUE	1	0.343785154999604	2		395	827	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741986	40741986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	125	425	0	ENST00000392038.2:c.986G>A	p.Arg329Gln	p.R329Q	ENST00000392038	NM_001626.4	329	cGg/cAg	11/14	1	2	FACETS	0.849	0.768	0.934	0.849	0.768	0.934	CLONAL	1	TRUE	1	0.343785154999604	2		425	857	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431874	49431874	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	134	446	5	ENST00000301067.7:c.9265del	p.Val3089TrpfsTer30	p.V3089Wfs*30	ENST00000301067	NM_003482.3	3089	Gtg/tg	34/54	0.285557739479072	3	FACETS	0.974	0.884	1	0.487	0.442	0.535	CLONAL	1	TRUE	1	0.343785154999604	3		451	938	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817720	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	103	353	0	ENST00000262367.5:c.3250dup	p.Ile1084AsnfsTer3	p.I1084Nfs*3	ENST00000262367	NM_004380.2	1084	atc/aAtc		1	2	FACETS	0.951	0.853	1	0.951	0.853	1	CLONAL	1	TRUE	1	0.343785154999604	2		353	630	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110004	115110004	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1201751425	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	97	402	0	ENST00000257566.3:c.1874G>A	p.Arg625His	p.R625H	ENST00000257566	NM_016569.3	625	cGc/cAc	8/8	0.285557739479072	3	FACETS	0.872	0.778	0.973	0.436	0.389	0.487	CLONAL	1	TRUE	1	0.343785154999604	3		402	758	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440135	49440136	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	192	401	0	ENST00000301067.7:c.4490_4491del	p.His1497LeufsTer30	p.H1497Lfs*30	ENST00000301067	NM_003482.3	1497	cAC/c	16/54	0.285557739479072	3	FACETS	1	0.989	1	0.711	0.658	0.767	CLONAL	1	TRUE	1	0.343785154999604	3		401	920	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278818	1278818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs939537185	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	130	388	0	ENST00000310581.5:c.2224C>T	p.Arg742Cys	p.R742C	ENST00000310581	NM_198253.2	742	Cgt/Tgt	6/16	1	2	FACETS	0.929	0.843	1	0.929	0.843	1	CLONAL	1	TRUE	1	0.343785154999604	2		388	814	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910608	50910608	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	135	386	0	ENST00000440232.2:c.1711C>T	p.Pro571Ser	p.P571S	ENST00000440232	NM_002691.3	571	Ccc/Tcc	14/27	1	2	FACETS	0.928	0.844	1	0.928	0.844	1	CLONAL	1	TRUE	1	0.343785154999604	2		386	846	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518464	69518464	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318349402	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	84	249	0	ENST00000294312.3:c.181C>T	p.Arg61Cys	p.R61C	ENST00000294312	NM_005117.2	61	Cgc/Tgc	1/3	1	2	FACETS	0.942	0.834	1	0.942	0.834	1	CLONAL	1	TRUE	1	0.343785154999604	2		249	519	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10791848	10791848	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs138881233	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	107	399	2	ENST00000361367.2:c.2201A>G	p.Gln734Arg	p.Q734R	ENST00000361367	NM_014633.3	734	cAg/cGg	17/25	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.343785154999604	2		401	609	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803480	32803480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	115	370	0	ENST00000374899.4:c.679G>A	p.Glu227Lys	p.E227K	ENST00000374899	NM_018833.2	227	Gag/Aag	4/12	0.343785154999604	3	FACETS	0.818	0.736	0.906	0.409	0.368	0.453	CLONAL	1	TRUE	1	0.343785154999604	3		370	958	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021095	31021095	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	114	365	0	ENST00000375687.4:c.1094T>C	p.Leu365Ser	p.L365S	ENST00000375687	NM_015338.5	365	tTg/tCg	12/13	0.278368808233416	2	FACETS	0.893	0.804	0.986	0.446	0.402	0.493	CLONAL	1	TRUE	0	0.343785154999604	2		365	743	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396658	396658	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	121	402	0	ENST00000262320.3:c.368G>A	p.Gly123Asp	p.G123D	ENST00000262320	NM_003502.3	123	gGc/gAc	2/11	1	2	FACETS	0.869	0.785	0.958	0.869	0.785	0.958	CLONAL	1	TRUE	1	0.343785154999604	2		402	810	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027089	48027089	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	95	360	0	ENST00000234420.5:c.1967C>A	p.Pro656His	p.P656H	ENST00000234420	NM_000179.2	656	cCc/cAc	4/10	1	2	FACETS	0.815	0.726	0.91	0.815	0.726	0.91	CLONAL	1	TRUE	1	0.343785154999604	2		360	678	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403346	139403346	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	101	373	0	ENST00000277541.6:c.3147G>T	p.Gln1049His	p.Q1049H	ENST00000277541	NM_017617.3	1049	caG/caT	19/34	1	2	FACETS	0.823	0.736	0.915	0.823	0.736	0.915	CLONAL	1	TRUE	1	0.343785154999604	2		373	714	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246305	41246305	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782770	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	89	381	0	ENST00000357654.3:c.1243G>T	p.Val415Phe	p.V415F	ENST00000357654	NM_007294.3	415	Gtt/Ttt	10/23	1	2	FACETS	0.945	0.84	1	0.945	0.84	1	CLONAL	1	TRUE	1	0.343785154999604	2		381	548	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261238	16261238	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	116	397	0	ENST00000375759.3:c.8503A>G	p.Ser2835Gly	p.S2835G	ENST00000375759	NM_015001.2	2835	Agc/Ggc	11/15	1	2	FACETS	0.799	0.719	0.883	0.799	0.719	0.883	SUBCLONAL	1	TRUE	1	0.343785154999604	2		397	845	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127681	64127681	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	128	366	0	ENST00000334205.4:c.177del	p.Lys60SerfsTer5	p.K60Sfs*5	ENST00000334205	NM_003942.2	58	gcG/gc	3/17	1	2	FACETS	0.96	0.87	1	0.96	0.87	1	CLONAL	1	TRUE	1	0.343785154999604	2		366	776	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31939894	31939894	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	105	394	0	ENST00000375333.2:c.121G>A	p.Gly41Ser	p.G41S	ENST00000375333	NM_032454.1	41	Ggc/Agc	1/8	0.343785154999604	3	FACETS	0.645	0.576	0.718	0.322	0.288	0.359	SUBCLONAL	1	TRUE	1	0.343785154999604	3		394	1110	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454561	99454561	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	90	329	0	ENST00000268035.6:c.1480C>A	p.His494Asn	p.H494N	ENST00000268035	NM_000875.3	494	Cat/Aat	7/21	1	2	FACETS	0.886	0.787	0.991	0.886	0.787	0.991	CLONAL	1	TRUE	1	0.343785154999604	2		329	591	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687398	37687398	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	120	380	0	ENST00000447079.4:c.4302G>T	p.Glu1434Asp	p.E1434D	ENST00000447079	NM_015083.1	1434	gaG/gaT	14/14	1	2	FACETS	0.907	0.819	0.999	0.907	0.819	0.999	CLONAL	1	TRUE	1	0.343785154999604	2		380	770	SUCCESS
APC	324	MSKCC	GRCh37	5	112173970	112173970	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	78	377	0	ENST00000257430.4:c.2679A>C	p.Glu893Asp	p.E893D	ENST00000257430	NM_000038.5	893	gaA/gaC	16/16	1	2	FACETS	0.639	0.561	0.723	0.639	0.561	0.723	SUBCLONAL	1	TRUE	1	0.343785154999604	2		377	710	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89355069	89355069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1464294383	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	109	363	0	ENST00000301030.4:c.611C>T	p.Ala204Val	p.A204V	ENST00000301030	NM_001256183.1	204	gCg/gTg	7/13	1	2	FACETS	0.819	0.736	0.908	0.819	0.736	0.908	CLONAL	1	TRUE	1	0.343785154999604	2		363	774	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148646	20148647	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCA	novel	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	26	240	0	ENST00000379607.5:c.414_416dup	p.Asp138dup	p.D138dup	ENST00000379607	NM_001412.3	138	gaa/gaTGAa	6/7	1	2	FACETS	0.377	0.298	0.468	0.377	0.298	0.468	SUBCLONAL	1	TRUE	1	0.343785154999604	2		240	401	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76919001	76919001	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	82	331	0	ENST00000373344.5:c.3990A>T	p.Glu1330Asp	p.E1330D	ENST00000373344	NM_000489.3	1330	gaA/gaT	12/35	1	2	FACETS	0.8	0.707	0.901	0.8	0.707	0.901	CLONAL	1	TRUE	1	0.343785154999604	2		331	596	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52722983	52722984	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	88	394	0	ENST00000322088.6:c.1172_1173del	p.Val391GlufsTer22	p.V391Efs*22	ENST00000322088	NM_014225.5	390	TGt/t	10/15	1	2	FACETS	0.621	0.549	0.697	0.621	0.549	0.697	SUBCLONAL	1	TRUE	1	0.343785154999604	2		394	825	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133748303	133748303	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1167422184	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	110	346	0	ENST00000318560.5:c.964A>G	p.Asn322Asp	p.N322D	ENST00000318560	NM_005157.4	322	Aac/Gac	6/11	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.343785154999604	2		346	627	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29280041	29280041	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	163	452	0	ENST00000544604.2:c.287G>C	p.Gly96Ala	p.G96A	ENST00000544604	NM_001206998.1	96	gGc/gCc	1/9	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.343785154999604	2		452	932	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404749	70404749	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065034-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	88	341	0	ENST00000373644.4:c.2263A>G	p.Thr755Ala	p.T755A	ENST00000373644	NM_030625.2	755	Acc/Gcc	4/12	1	2	FACETS	0.924	0.821	1	0.924	0.821	1	CLONAL	1	TRUE	1	0.343785154999604	2		341	554	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0065087-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	120	288	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.628290540855509	4	FACETS	1	0.981	1			1	CLONAL	2	TRUE	NA	0.628290540855509	4		288	254	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0065087-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	356	371	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.473814241454658	3	FACETS	1	0.994	1	0.821	0.787	0.854	CLONAL	2	TRUE	0	0.628290540855509	3		371	605	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101909953	101909953	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065087-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	119	290	0	ENST00000374994.4:c.1273C>T	p.Gln425Ter	p.Q425*	ENST00000374994	NM_004612.2	425	Caa/Taa	8/9	0.603290857654953	2	FACETS	0.981	0.915	1	0.981	0.915	1	CLONAL	2	TRUE	0	0.628290540855509	2		290	193	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956125	55956125	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065087-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	13	337	0	ENST00000263923.4:c.3190G>T	p.Asp1064Tyr	p.D1064Y	ENST00000263923	NM_002253.2	1064	Gat/Tat	23/30	0.628290540855509	1	FACETS	0.116	0.083	0.158	0.116	0.083	0.158	SUBCLONAL	1	TRUE	0	0.628290540855509	1		337	244	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630451	67630457	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAGGA	AAGAGGA	-	novel	NA	P-0065087-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	47	304	0	ENST00000272342.5:c.638_644del	p.Lys213IlefsTer7	p.K213Ifs*7	ENST00000272342	NM_019002.3	213	AAGAGGAat/at	5/6	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.628290540855509	2		304	131	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440727	56440727	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065087-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	453	491	1	ENST00000407977.2:c.491T>G	p.Ile164Ser	p.I164S	ENST00000407977		164	aTc/aGc	5/10	0.610211499197321	2	FACETS	0.956	0.922	0.99	0.956	0.922	0.99	CLONAL	2	TRUE	0	0.628290540855509	2		492	754	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484858	57485003	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTTTGTGGAGTGACCGCCCACCCCCTGCGCTTGCCCAGGAGGCCCTGGTCTGCACTGTTTATAGAGAAGAACCCCGTGCAAGCATTCCAGACCCCTGGCCGAAAGCGCGCTTCTCCCAAGCATTCACACGGCCTCCCTTCTTGT	AGGTTTGTGGAGTGACCGCCCACCCCCTGCGCTTGCCCAGGAGGCCCTGGTCTGCACTGTTTATAGAGAAGAACCCCGTGCAAGCATTCCAGACCCCTGGCCGAAAGCGCGCTTCTCCCAAGCATTCACACGGCCTCCCTTCTTGT	-	novel	NA	P-0065538-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	19	0	0	ENST00000371085.3:c.839+1_840-1del		p.X280_splice	ENST00000371085	NM_000516.4	280		10/13	0.2507425495344	3	FACETS	0.229	0.173	0.296	0.115	0.086	0.148	SUBCLONAL	1	FALSE	1	0.3	3		0	635	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307953	11307957	+	frameshift_variant	Frame_Shift_Del	DEL	TCCCA	TCCCA	CCCC	novel	NA	P-0065538-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	31	478	0	ENST00000361445.4:c.1035_1039delinsGGGG	p.Phe345LeufsTer21	p.F345Lfs*21	ENST00000361445	NM_004958.3	345	ttTGGGAcc/ttGGGGcc	7/58	1	2	FACETS	0.415	0.335	0.506	0.415	0.335	0.506	SUBCLONAL	1	FALSE	1	0.3	2		478	498	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065657-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	136	350	0				ENST00000310581	NM_198253.2	-/1132			0.348910514063505	4	FACETS	0.964	0.882	1	0.964	0.882	1	CLONAL	2	TRUE	2	0.389901823373372	4		350	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0065657-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	407	544	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.389901823373372	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	0	0.389901823373372	3		544	800	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937023	48937024	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065657-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	169	451	0	ENST00000267163.4:c.795dup	p.Gln266ThrfsTer5	p.Q266Tfs*5	ENST00000267163	NM_000321.2	264	gca/gcAa	8/27	0.389901823373372	2	FACETS	0.951	0.882	1	0.951	0.882	1	CLONAL	2	TRUE	0	0.389901823373372	2		451	456	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0065817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	117	501	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.244276704147746	3	FACETS	0.876	0.791	0.966	0.876	0.791	0.966	CLONAL	2	TRUE	1	0.21	3		501	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0065817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	110	437	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.29648908637249	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.21	1		437	629	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629376	187629376	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs888101917	NA	P-0065817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	62	492	0	ENST00000441802.2:c.1606C>G	p.Leu536Val	p.L536V	ENST00000441802	NM_005245.3	536	Ctg/Gtg	2/27	0.29648908637249	1	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	0	0.21	1		492	510	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61305053	61305053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	87	430	0	ENST00000341074.5:c.1073C>T	p.Ser358Leu	p.S358L	ENST00000341074	NM_002974.2	358	tCa/tTa	8/8	0.29648908637249	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.21	1		430	513	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108024	30108024	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	47	350	0	ENST00000331968.5:c.783G>C	p.Lys261Asn	p.K261N	ENST00000331968	NM_002742.2	261	aaG/aaC	5/18	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.21	2		350	378	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997727	149997727	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	67	386	0	ENST00000253339.5:c.2740C>T	p.Pro914Ser	p.P914S	ENST00000253339		914	Ccc/Tcc	5/7	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.21	2		386	508	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859619	57859619	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	34	523	0	ENST00000228682.2:c.673G>C	p.Glu225Gln	p.E225Q	ENST00000228682	NM_005269.2	225	Gag/Cag	7/12	1	2	FACETS	0.525	0.428	0.635	0.525	0.428	0.635	SUBCLONAL	1	TRUE	1	0.21	2		523	617	SUCCESS
ATR	545	MSKCC	GRCh37	3	142216012	142216012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	27	353	0	ENST00000350721.4:c.5581G>A	p.Glu1861Lys	p.E1861K	ENST00000350721	NM_001184.3	1861	Gag/Aag	33/47	1	2	FACETS	0.591	0.47	0.73	0.591	0.47	0.73	SUBCLONAL	1	TRUE	1	0.21	2		353	435	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001583	150001583	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	24	401	0	ENST00000253339.5:c.2021C>G	p.Ser674Cys	p.S674C	ENST00000253339		674	tCt/tGt	4/7	1	2	FACETS	0.708	0.555	0.883	0.708	0.555	0.883	SUBCLONAL	1	TRUE	1	0.21	2		401	323	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293714	1293714	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	71	445	0	ENST00000310581.5:c.1287G>T	p.Glu429Asp	p.E429D	ENST00000310581	NM_198253.2	429	gaG/gaT	2/16	0.274585123175238	4	FACETS	1	0.951	1	0.396	0.346	0.451	CLONAL	1	TRUE	1	0.21	4		445	688	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277080	18277080	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	27	371	0	ENST00000222254.8:c.1527C>G	p.Phe509Leu	p.F509L	ENST00000222254	NM_005027.3	509	ttC/ttG	12/16	1	2	FACETS	0.507	0.403	0.627	0.507	0.403	0.627	SUBCLONAL	1	TRUE	1	0.21	2		371	507	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281712	49281712	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	62	471	0	ENST00000282018.3:c.759G>C	p.Leu253Phe	p.L253F	ENST00000282018	NM_020377.2	253	ttG/ttC	1/1	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.21	2		471	586	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505604	186505604	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	49	394	0	ENST00000323963.5:c.1012G>C	p.Asp338His	p.D338H	ENST00000323963		338	Gat/Cat	10/11	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.21	2		394	407	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569689	41569689	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	65	624	0	ENST00000263253.7:c.4680G>C	p.Lys1560Asn	p.K1560N	ENST00000263253	NM_001429.3	1560	aaG/aaC	29/31	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.21	2		624	550	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424582	47424582	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	65	487	0	ENST00000404338.3:c.2650C>G	p.Gln884Glu	p.Q884E	ENST00000404338	NM_004491.4	884	Cag/Gag	1/6	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.21	2		487	573	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0065928-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	100	500	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.636181670706178	3	FACETS	1	0.976	1	0.78	0.719	0.841	CLONAL	2	TRUE	0	0.636181670706178	3		500	177	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0065928-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	96	403	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.376407536480874	3	FACETS	0.839	0.775	0.902	0.839	0.775	0.902	INDETERMINATE	3	TRUE	0	0.636181670706178	3		404	158	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850736	63850736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149466999	NA	P-0065928-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	70	523	1	ENST00000279873.7:c.1514C>T	p.Ala505Val	p.A505V	ENST00000279873	NM_032199.2	505	gCg/gTg	10/10	0.636181670706178	3	FACETS	1	0.97	1	0.659	0.584	0.738	CLONAL	1	TRUE	1	0.636181670706178	3		524	220	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920422	114920422	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065928-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	84	392	2	ENST00000543371.1:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000543371	NM_001198531.1	455	Cga/Tga	13/14	0.636181670706178	3	FACETS	0.956	0.866	1	0.956	0.866	1	CLONAL	2	TRUE	1	0.636181670706178	3		394	182	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029445	16029446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065928-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	91	452	4	ENST00000268712.3:c.1584dup	p.Glu529ArgfsTer7	p.E529Rfs*7	ENST00000268712	NM_006311.3	528	-/A	15/46	0.376407536480874	3	FACETS	0.924	0.839	1	0.616	0.559	0.673	INDETERMINATE	2	TRUE	0	0.636181670706178	3		456	204	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575186	48575186	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065928-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	61	369	0	ENST00000342988.3:c.380G>C	p.Cys127Ser	p.C127S	ENST00000342988	NM_005359.5	127	tGt/tCt	3/12	0.544034239710231	2	FACETS	0.813	0.727	0.898	0.813	0.727	0.898	CLONAL	2	TRUE	0	0.636181670706178	2		369	118	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366308	15366308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065928-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	50	464	1	ENST00000263377.2:c.1847G>A	p.Arg616Gln	p.R616Q	ENST00000263377	NM_058243.2	616	cGg/cAg	10/20	0.231121664190183	5	FACETS	1	0.912	1	0.711	0.617	0.809	INDETERMINATE	2	TRUE	2	0.636181670706178	5		465	144	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906394	50906394	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556862476	NA	P-0065983-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	62	505	0	ENST00000440232.2:c.1055G>A	p.Arg352His	p.R352H	ENST00000440232	NM_002691.3	352	cGc/cAc	9/27	1	2	FACETS	0.818	0.709	0.936	0.818	0.709	0.936	CLONAL	1	TRUE	1	0.36	2		505	421	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923593	39923594	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0065983-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	83	159	0	ENST00000378444.4:c.3497_3498del	p.Ser1166Ter	p.S1166*	ENST00000378444	NM_001123385.1	1166	tCT/t	7/15	1	1	FACETS	0.811	0.728	0.897	1	0.983	1	CLONAL	2	TRUE	0	0.36	1		159	233	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176176029	176176029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs989823943	NA	P-0066000-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	559	247	0	ENST00000367669.3:c.86C>T	p.Ser29Leu	p.S29L	ENST00000367669	NM_022457.5	29	tCg/tTg	1/20	0.934450210903146	6	FACETS	0.955	0.925	0.984	0.955	0.925	0.984	CLONAL	4	TRUE	2	0.934450210903146	6		247	899	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003853	57003853	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	C	C	A	rs1000614668	NA	P-0066000-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	295	378	0	ENST00000257254.3:c.626G>T	p.Gly209Val	p.G209V	ENST00000257254		209	gGc/gTc	1/2	0.815776545775231	4	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	2	0.934450210903146	4		378	609	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025530	1025530	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377410286	NA	P-0066000-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	236	307	0	ENST00000358495.3:c.845C>T	p.Pro282Leu	p.P282L	ENST00000358495	NM_134424.2	282	cCg/cTg	9/12	0.934588849863656	4	FACETS	1	0.975	1			1	CLONAL	2	TRUE	NA	0.934450210903146	4		307	464	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778736	3778737	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0066000-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	197	366	2	ENST00000262367.5:c.6311_6312delinsTT	p.Arg2104Leu	p.R2104L	ENST00000262367	NM_004380.2	2104	cGC/cTT	31/31	0.815776545775231	4	FACETS	0.96	0.9	1	0.96	0.9	1	CLONAL	2	TRUE	2	0.934450210903146	4		368	425	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649416	23649416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs515726129	NA	P-0066000-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	178	269	0	ENST00000261584.4:c.83A>G	p.Tyr28Cys	p.Y28C	ENST00000261584	NM_024675.3	28	tAc/tGc	2/13	0.90692254400375	4	FACETS	1	0.98	1			1	CLONAL	2	TRUE	NA	0.934450210903146	4		269	333	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842735	68842735	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201511530	NA	P-0066000-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	175	288	0	ENST00000261769.5:c.671G>A	p.Arg224His	p.R224H	ENST00000261769	NM_004360.3	224	cGc/cAc	5/16	0.904082491012856	3	FACETS	0.878	0.825	0.93	0.878	0.825	0.93	CLONAL	2	TRUE	1	0.934450210903146	3		288	313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578558	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCTTGTTGAGGGCAGGGGAGTACTGT	ATCTTGTTGAGGGCAGGGGAGTACTGT	-	novel	NA	P-0066000-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	160	332	0	ENST00000269305.4:c.376-4_398del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	0.930364625627923	2	FACETS	0.941	0.908	0.97	0.941	0.908	0.97	CLONAL	2	TRUE	0	0.934450210903146	2		332	182	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11999013	11999013	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0066000-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	140	276	0	ENST00000353533.5:c.513+2T>C		p.X171_splice	ENST00000353533	NM_003010.3	171			0.930364625627923	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.934450210903146	2		276	149	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075172	16075172	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066000-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	253	301	0	ENST00000268712.3:c.380del	p.Leu127CysfsTer3	p.L127Cfs*3	ENST00000268712	NM_006311.3	127	tTg/tg	4/46	0.930364625627923	2	FACETS	0.96	0.935	0.982	0.96	0.935	0.982	CLONAL	2	TRUE	0	0.934450210903146	2		301	282	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068433	26068433	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0066000-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	112	211	0	ENST00000435504.4:c.58-1G>C		p.X20_splice	ENST00000435504		20			0.921363024433083	4	FACETS	0.906	0.83	0.982	0.906	0.83	0.982	CLONAL	2	TRUE	2	0.934450210903146	4		211	256	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936313	49936313	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066000-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	329	423	0	ENST00000296474.3:c.1535C>G	p.Ala512Gly	p.A512G	ENST00000296474	NM_002447.2	512	gCc/gGc	3/20	0.921363024433083	4	FACETS	0.993	0.946	1	0.993	0.946	1	CLONAL	2	TRUE	2	0.934450210903146	4		423	686	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0066000-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	336	355	2	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	0.644403444757061	6	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	3	0.934450210903146	6		357	660	SUCCESS
ALB	213	MSKCC	GRCh37	4	74283279	74283279	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066000-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	214	248	0	ENST00000295897.4:c.1321C>A	p.Gln441Lys	p.Q441K	ENST00000295897	NM_000477.5	441	Caa/Aaa	11/15	0.929532115727984	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.934450210903146	2		248	229	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963123	38963123	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066000-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	225	305	0	ENST00000357387.3:c.1421A>G	p.Asn474Ser	p.N474S	ENST00000357387	NM_152756.3	474	aAc/aGc	17/38	0.921363024433083	4	FACETS	0.976	0.92	1	0.976	0.92	1	CLONAL	2	TRUE	2	0.934450210903146	4		305	477	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880512	155880512	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066000-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	254	346	0	ENST00000368323.3:c.41G>C	p.Ser14Thr	p.S14T	ENST00000368323	NM_006912.5	14	aGc/aCc	2/6	0.934450210903146	6	FACETS	0.896	0.841	0.953	0.448	0.42	0.477	CLONAL	2	TRUE	2	0.934450210903146	6		346	870	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864302	117864302	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs771943412	NA	P-0066000-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	358	285	0	ENST00000297338.2:c.1355A>T	p.Gln452Leu	p.Q452L	ENST00000297338	NM_006265.2	452	cAg/cTg	11/14	0.914127847444364	5	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	2	0.934450210903146	5		285	605	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111475	8111479	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAC	CAGAC	-	novel	NA	P-0066026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	369	379	0	ENST00000346208.3:c.963_967del	p.Gln321HisfsTer29	p.Q321Hfs*29	ENST00000346208		321	CAGACc/c	5/6	0.465921818105398	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.465921818105398	3		379	859	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0066026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	146	361	0	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	0.455970844756029	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.465921818105398	1		361	443	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11168251	11168251	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	120	309	0	ENST00000361445.4:c.7621T>G	p.Cys2541Gly	p.C2541G	ENST00000361445	NM_004958.3	2541	Tgc/Ggc	57/58	1	2	FACETS	0.981	0.89	1	0.981	0.89	1	CLONAL	1	TRUE	1	0.465921818105398	2		309	525	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753434	42753435	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0066026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	227	533	0	ENST00000222329.4:c.829dup	p.Tyr277LeufsTer32	p.Y277Lfs*32	ENST00000222329	NM_006494.2	277	tac/tTac	4/4	0.231984092666299	1	FACETS	0.914	0.853	0.976	0.914	0.853	0.976	INDETERMINATE	1	TRUE	0	0.465921818105398	1		533	818	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193477	99193477	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	109	434	0	ENST00000074304.5:c.2672G>A	p.Arg891Gln	p.R891Q	ENST00000074304	NM_001134224.1	891	cGg/cAg	25/26	1	2	FACETS	0.794	0.715	0.878	0.794	0.715	0.878	SUBCLONAL	1	TRUE	1	0.465921818105398	2		434	589	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067390	37067390	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	131	406	0	ENST00000231790.2:c.1301T>A	p.Leu434His	p.L434H	ENST00000231790	NM_000249.3	434	cTc/cAc	12/19	0.460096472635547	4	FACETS	0.912	0.827	1			1	CLONAL	1	TRUE	NA	0.465921818105398	4		406	904	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352372	70352372	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066131-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	75	362	0	ENST00000374080.3:c.4399C>T	p.Arg1467Ter	p.R1467*	ENST00000374080		1467	Cga/Tga	31/45	1	1	FACETS	0.961	0.851	1	1	0.983	1	CLONAL	2	FALSE	0	0.243115605678167	1		362	282	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913233	NA	P-0066131-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	440	795	0	ENST00000451590.1:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000451590	NM_001130442.1	61	cAg/cTg	3/5	0.243115605678167	5	FACETS	1	0.989	1	1	0.996	1	CLONAL	6	FALSE	0	0.243115605678167	5		795	770	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	53	397	1	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	1	2	FACETS	0.609	0.519	0.707	0.609	0.519	0.707	SUBCLONAL	1	TRUE	1	0.310406598383164	2		398	561	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306996	65306997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	93	543	7	ENST00000342505.4:c.2580dup	p.Pro861ThrfsTer4	p.P861Tfs*4	ENST00000342505	NM_002227.2	860	-/A	19/25	1	2	FACETS	0.976	0.869	1	0.976	0.869	1	CLONAL	1	TRUE	1	0.310406598383164	2		550	614	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	81	711	1	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.888	0.783	1	0.888	0.783	1	CLONAL	1	TRUE	1	0.310406598383164	2		712	588	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528120	103528120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376411022	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	93	342	0	ENST00000355739.4:c.3428C>T	p.Ala1143Val	p.A1143V	ENST00000355739	NM_000123.3	1143	gCg/gTg	15/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.310406598383164	2		342	489	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	85	342	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.310406598383164	2		342	492	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	30	273	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	1	2	FACETS	0.786	0.636	0.954	0.786	0.636	0.954	CLONAL	1	TRUE	1	0.310406598383164	2		273	246	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	95	418	2	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.943	0.841	1	0.943	0.841	1	CLONAL	1	TRUE	1	0.310406598383164	2		420	649	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	85	423	0	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.92	0.815	1	0.92	0.815	1	CLONAL	1	TRUE	1	0.310406598383164	2		423	595	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057936	27057937	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1415146710	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	82	292	0	ENST00000324856.7:c.1650dup	p.Tyr551LeufsTer72	p.Y551Lfs*72	ENST00000324856	NM_006015.4	548	-/C	3/20	1	2	FACETS	0.863	0.762	0.972	0.863	0.762	0.972	CLONAL	1	TRUE	1	0.310406598383164	2		292	612	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699369	117699369	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374822982	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	73	387	0	ENST00000369458.3:c.272C>T	p.Ser91Leu	p.S91L	ENST00000369458	NM_024626.3	91	tCg/tTg	3/6	1	2	FACETS	0.814	0.712	0.923	0.814	0.712	0.923	CLONAL	1	TRUE	1	0.310406598383164	2		387	578	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239673	105239673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	86	459	0	ENST00000349310.3:c.872C>T	p.Thr291Ile	p.T291I	ENST00000349310	NM_001014432.1	291	aCa/aTa	11/15	1	2	FACETS	0.991	0.879	1	0.991	0.879	1	CLONAL	1	TRUE	1	0.310406598383164	2		459	559	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	93	341	0	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.310406598383164	2		341	569	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288710	15288710	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	54	276	0	ENST00000263388.2:c.4029del	p.Cys1344ValfsTer76	p.C1344Vfs*76	ENST00000263388	NM_000435.2	1343	ccC/cc	24/33	1	2	FACETS	0.918	0.787	1	0.918	0.787	1	CLONAL	1	TRUE	1	0.310406598383164	2		276	379	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	101	395	0	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.310406598383164	2		395	633	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	65	227	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	0.941	0.818	1	0.941	0.818	1	CLONAL	1	TRUE	1	0.310406598383164	2		227	445	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	81	394	3	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	1	2	FACETS	0.935	0.825	1	0.935	0.825	1	CLONAL	1	TRUE	1	0.310406598383164	2		397	558	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785964	135785964	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs118203506	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	79	375	2	ENST00000298552.3:c.1257del	p.Arg420GlyfsTer20	p.R420Gfs*20	ENST00000298552	NM_001162426.1	419	ccC/cc	12/23	1	2	FACETS	0.867	0.764	0.978	0.867	0.764	0.978	CLONAL	1	TRUE	1	0.310406598383164	2		377	587	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349641	89349641	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs772267579	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	51	370	1	ENST00000301030.4:c.3309del	p.Asp1104MetfsTer214	p.D1104Mfs*214	ENST00000301030	NM_001256183.1	1103	aaA/aa	9/13	1	2	FACETS	0.725	0.617	0.844	0.725	0.617	0.844	SUBCLONAL	1	TRUE	1	0.310406598383164	2		371	453	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755478	133755478	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355584861	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	92	573	0	ENST00000318560.5:c.1447C>T	p.Arg483Trp	p.R483W	ENST00000318560	NM_005157.4	483	Cgg/Tgg	9/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.310406598383164	2		573	509	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954975	2954975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368119340	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	88	560	5	ENST00000396946.4:c.2735G>A	p.Arg912Gln	p.R912Q	ENST00000396946	NM_032415.4	912	cGg/cAg	21/25	1	2	FACETS	0.906	0.803	1	0.906	0.803	1	CLONAL	1	TRUE	1	0.310406598383164	2		565	626	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466018	69466018	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	78	503	2	ENST00000227507.2:c.856A>G	p.Thr286Ala	p.T286A	ENST00000227507	NM_053056.2	286	Aca/Gca	5/5	1	2	FACETS	0.915	0.806	1	0.915	0.806	1	CLONAL	1	TRUE	1	0.310406598383164	2		505	549	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855889	45855889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769085031	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	91	443	2	ENST00000391945.4:c.1921C>T	p.Arg641Trp	p.R641W	ENST00000391945	NM_000400.3	641	Cgg/Tgg	21/23	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.310406598383164	2		445	567	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	76	362	0	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	1	2	FACETS	0.864	0.758	0.976	0.864	0.758	0.976	CLONAL	1	TRUE	1	0.310406598383164	2		362	567	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614463	38614463	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	34	346	0	ENST00000299084.4:c.234del	p.Asp79ThrfsTer42	p.D79Tfs*42	ENST00000299084	NM_152594.2	77	Aaa/aa	3/7	1	2	FACETS	0.969	0.798	1	0.969	0.798	1	CLONAL	1	TRUE	1	0.310406598383164	2		346	226	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692793	89692793	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786204927	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	26	163	0	ENST00000371953.3:c.277C>A	p.His93Asn	p.H93N	ENST00000371953	NM_000314.4	93	Cat/Aat	5/9	1	2	FACETS	0.738	0.587	0.909	0.738	0.587	0.909	CLONAL	1	TRUE	1	0.310406598383164	2		163	227	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453399	40453399	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs759027671	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	77	435	5	ENST00000345506.4:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000345506	NM_003152.3	366	Ccc/cc	10/20	1	2	FACETS	0.982	0.865	1	0.982	0.865	1	CLONAL	1	TRUE	1	0.310406598383164	2		440	505	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610078	43610078	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536038262	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	109	428	0	ENST00000355710.3:c.2030G>A	p.Arg677Gln	p.R677Q	ENST00000355710	NM_020975.4	677	cGg/cAg	11/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.310406598383164	2		428	631	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902121	50902121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs9282830	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	70	339	1	ENST00000440232.2:c.13C>T	p.Arg5Trp	p.R5W	ENST00000440232	NM_002691.3	5	Cgg/Tgg	2/27	1	2	FACETS	0.919	0.803	1	0.919	0.803	1	CLONAL	1	TRUE	1	0.310406598383164	2		340	491	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437530	56437531	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	76	386	0	ENST00000407977.2:c.931dup	p.Leu311ProfsTer132	p.L311Pfs*132	ENST00000407977		311	ctc/cCtc	8/10	1	2	FACETS	0.915	0.804	1	0.915	0.804	1	CLONAL	1	TRUE	1	0.310406598383164	2		386	535	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371716	55371716	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	106	405	0	ENST00000297316.4:c.406A>G	p.Lys136Glu	p.K136E	ENST00000297316	NM_022454.3	136	Aag/Gag	2/2	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.310406598383164	2		405	546	SUCCESS
APC	324	MSKCC	GRCh37	5	112116551	112116551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748193367	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	25	487	2	ENST00000257430.4:c.596C>T	p.Ala199Val	p.A199V	ENST00000257430	NM_000038.5	199	gCg/gTg	6/16	1	2	FACETS	0.546	0.431	0.678	0.546	0.431	0.678	SUBCLONAL	1	TRUE	1	0.310406598383164	2		489	295	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324675	31324675	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	70	347	0	ENST00000412585.2:c.133del	p.Arg45AlafsTer14	p.R45Afs*14	ENST00000412585	NM_005514.6	45	Cgc/gc	2/8	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.310406598383164	2		347	441	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	129	395	0	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.310406598383164	2		395	593	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	81	547	0	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	1	2	FACETS	0.954	0.842	1	0.954	0.842	1	CLONAL	1	TRUE	1	0.310406598383164	2		547	547	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456681	32456681	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	84	357	0	ENST00000332351.3:c.211T>G	p.Ser71Ala	p.S71A	ENST00000332351	NM_024426.4	71	Tcc/Gcc	1/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.310406598383164	2		357	429	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911267	29911287	+	inframe_deletion	In_Frame_Del	DEL	TGGAGTGGCTCCGCAGATACC	TGGAGTGGCTCCGCAGATACC	-	novel	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	41	124	0	ENST00000376809.5:c.571_591del	p.Trp191_Glu197del	p.W191_E197del	ENST00000376809	NM_002116.7	189	gTGGAGTGGCTCCGCAGATACCtg/gtg	3/8	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.310406598383164	2		124	214	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713321	40713321	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	70	348	0	ENST00000373198.4:c.4193+1del		p.X1398_splice	ENST00000373198	NM_133170.3	1398			1	2	FACETS	0.893	0.78	1	0.893	0.78	1	CLONAL	1	TRUE	1	0.310406598383164	2		348	505	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799219	88799219	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	63	379	0	ENST00000360948.2:c.166del	p.Leu56SerfsTer30	p.L56Sfs*30	ENST00000360948	NM_001012338.2	56	Ctc/tc	2/19	1	2	FACETS	0.753	0.652	0.863	0.753	0.652	0.863	SUBCLONAL	1	TRUE	1	0.310406598383164	2		379	539	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371788	55371788	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	91	442	0	ENST00000297316.4:c.478G>T	p.Ala160Ser	p.A160S	ENST00000297316	NM_022454.3	160	Gct/Tct	2/2	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.310406598383164	2		442	495	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427419	49427419	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	96	430	0	ENST00000301067.7:c.11069G>T	p.Gly3690Val	p.G3690V	ENST00000301067	NM_003482.3	3690	gGa/gTa	39/54	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.310406598383164	2		430	614	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346158	89346159	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	92	480	0	ENST00000301030.4:c.6791_6792del	p.Pro2264ArgfsTer8	p.P2264Rfs*8	ENST00000301030	NM_001256183.1	2264	cCC/c	9/13	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.310406598383164	2		480	560	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912861	29912861	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	79	374	0	ENST00000376809.5:c.1038G>T	p.Gln346His	p.Q346H	ENST00000376809	NM_002116.7	346	caG/caT	6/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.310406598383164	2		374	442	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847286	68847286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	82	330	0	ENST00000261769.5:c.1208C>T	p.Ala403Val	p.A403V	ENST00000261769	NM_004360.3	403	gCc/gTc	9/16	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.310406598383164	2		330	526	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200103	123200103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	29	301	0	ENST00000218089.9:c.2175G>A	p.Met725Ile	p.M725I	ENST00000218089	NM_001042749.1	725	atG/atA	22/35	1	2	FACETS	0.76	0.612	0.925	0.76	0.612	0.925	CLONAL	1	TRUE	1	0.310406598383164	2		301	246	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231488718	231488718	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	65	355	0	ENST00000295050.7:c.1085del	p.Asn362ThrfsTer18	p.N362Tfs*18	ENST00000295050	NM_032018.5	361	Aaa/aa	5/5	1	2	FACETS	0.91	0.791	1	0.91	0.791	1	CLONAL	1	TRUE	1	0.310406598383164	2		355	460	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639192	3639192	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	107	422	0	ENST00000294008.3:c.4447A>G	p.Thr1483Ala	p.T1483A	ENST00000294008	NM_032444.2	1483	Act/Gct	12/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.310406598383164	2		422	594	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874068	151874068	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	77	372	0	ENST00000262189.6:c.8470del	p.Thr2824ArgfsTer39	p.T2824Rfs*39	ENST00000262189	NM_170606.2	2824	Acg/cg	38/59	1	2	FACETS	0.945	0.831	1	0.945	0.831	1	CLONAL	1	TRUE	1	0.310406598383164	2		372	525	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145341	61145341	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	47	216	0	ENST00000295025.8:c.551C>T	p.Ala184Val	p.A184V	ENST00000295025	NM_002908.2	184	gCa/gTa	6/11	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.310406598383164	2		216	286	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228613016	228613016	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs374675557	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	93	455	0	ENST00000366696.1:c.11C>A	p.Thr4Asn	p.T4N	ENST00000366696	NM_003493.2	4	aCc/aAc	1/1	1	2	FACETS	0.873	0.777	0.976	0.873	0.777	0.976	CLONAL	1	TRUE	1	0.310406598383164	2		455	686	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165992	47165993	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	58	319	0	ENST00000409792.3:c.133dup	p.Met45AsnfsTer8	p.M45Nfs*8	ENST00000409792	NM_014159.6	45	atg/aAtg	3/21	1	2	FACETS	0.896	0.772	1	0.896	0.772	1	CLONAL	1	TRUE	1	0.310406598383164	2		319	417	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563137	21563137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1317445610	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	78	437	0	ENST00000382592.4:c.782C>T	p.Pro261Leu	p.P261L	ENST00000382592	NM_014572.2	261	cCt/cTt	4/8	1	2	FACETS	0.897	0.79	1	0.897	0.79	1	CLONAL	1	TRUE	1	0.310406598383164	2		437	560	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553309	41553309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	84	325	0	ENST00000263253.7:c.3398G>A	p.Arg1133Gln	p.R1133Q	ENST00000263253	NM_001429.3	1133	cGg/cAg	18/31	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.310406598383164	2		325	495	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318755	163318755	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	42	308	0	ENST00000271452.3:c.1150del	p.Arg384GlufsTer8	p.R384Efs*8	ENST00000271452	NM_145697.2	382	gAa/ga	13/14	1	2	FACETS	0.984	0.827	1	0.984	0.827	1	CLONAL	1	TRUE	1	0.310406598383164	2		308	275	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870346	155870346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	96	304	0	ENST00000368323.3:c.493G>A	p.Ala165Thr	p.A165T	ENST00000368323	NM_006912.5	165	Gct/Act	6/6	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.310406598383164	2		304	512	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717668	89717669	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	61	312	0	ENST00000371953.3:c.694dup	p.Thr232AsnfsTer11	p.T232Nfs*11	ENST00000371953	NM_000314.4	231	-/A	7/9	1	2	FACETS	0.961	0.832	1	0.961	0.832	1	CLONAL	1	TRUE	1	0.310406598383164	2		312	409	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118904	70118904	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	107	482	4	ENST00000245479.2:c.476A>G	p.Glu159Gly	p.E159G	ENST00000245479	NM_000346.3	159	gAg/gGg	2/3	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.310406598383164	2		486	639	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066232-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	90	288	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.968	0.871	1	0.968	0.871	1	CLONAL	1	TRUE	1	0.67372947173027	2		288	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0066232-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	165	400	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.664595574910446	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.67372947173027	1		400	298	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881542	48881542	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066232-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	102	276	0	ENST00000267163.4:c.264G>T	p.Leu88Phe	p.L88F	ENST00000267163	NM_000321.2	88	ttG/ttT	2/27	0.67372947173027	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.67372947173027	1		276	194	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066936	30066936	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066232-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	95	282	0	ENST00000331968.5:c.2195G>T	p.Arg732Leu	p.R732L	ENST00000331968	NM_002742.2	732	cGg/cTg	16/18	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.67372947173027	2		282	277	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0066259-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	181	252	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.236398429880689	7	FACETS	1	0.937	1	1	0.937	1	CLONAL	5	TRUE	2	0.236398429880689	7		253	484	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440643	56440643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139557480	NA	P-0066259-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	29	474	0	ENST00000407977.2:c.575C>T	p.Pro192Leu	p.P192L	ENST00000407977		192	cCg/cTg	5/10	0.233639612197281	3	FACETS	0.536	0.429	0.658	0.268	0.214	0.329	SUBCLONAL	1	TRUE	1	0.236398429880689	3		474	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0066259-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	147	472	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.236398429880689	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.236398429880689	2		472	542	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372752	81372752	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768451705	NA	P-0066259-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	41	413	0	ENST00000222390.5:c.782G>A	p.Arg261His	p.R261H	ENST00000222390	NM_000601.4	261	cGc/cAc	7/18	0.214647099857643	4	FACETS	0.736	0.612	0.874	0.368	0.306	0.437	SUBCLONAL	1	TRUE	2	0.236398429880689	4		413	583	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991522	72991522	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066259-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	67	389	0	ENST00000268489.5:c.2523G>T	p.Gln841His	p.Q841H	ENST00000268489	NM_006885.3	841	caG/caT	2/10	0.233639612197281	3	FACETS	1	0.907	1	0.527	0.458	0.602	CLONAL	1	TRUE	1	0.236398429880689	3		389	601	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249312	110249312	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066259-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	59	382	0	ENST00000374672.4:c.1261A>G	p.Thr421Ala	p.T421A	ENST00000374672	NM_004235.4	421	Aca/Gca	4/5	0.233639612197281	3	FACETS	1	0.94	1	0.585	0.504	0.673	CLONAL	1	TRUE	1	0.236398429880689	3		382	477	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970985	21970997	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGATGGCCCAG	CGCGATGGCCCAG	-	novel	NA	P-0066259-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	64	592	0	ENST00000304494.5:c.361_373del	p.Leu121MetfsTer21	p.L121Mfs*21	ENST00000304494	NM_000077.4	121	CTGGGCCATCGCGat/at	2/3	0.236398429880689	1	FACETS	0.922	0.799	1	0.922	0.799	1	CLONAL	1	TRUE	0	0.236398429880689	1		592	518	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685315	89685315	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1554897280	NA	P-0066332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	96	293	0	ENST00000371953.3:c.209+1G>A		p.X70_splice	ENST00000371953	NM_000314.4	70			0.51096042609912	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.51096042609912	1		293	270	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578186	7578199	+	frameshift_variant	Frame_Shift_Del	DEL	CTCATAGGGCACCA	CTCATAGGGCACCA	AGGTGTGGTGGTG	novel	NA	P-0066332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	305	586	2	ENST00000269305.4:c.650_663delinsCACCACCACACCT	p.Val217AlafsTer30	p.V217Afs*30	ENST00000269305	NM_001126112.2	217	gTGGTGCCCTATGAG/gCACCACCACACCT	6/11	0.493909013842624	2	FACETS	0.906	0.861	0.951	0.906	0.861	0.951	CLONAL	2	TRUE	0	0.51096042609912	2		588	659	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155726	106155726	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	62	560	0	ENST00000380013.4:c.627T>G	p.Asn209Lys	p.N209K	ENST00000380013	NM_001127208.2	209	aaT/aaG	3/11	0.239186352351409	3	FACETS	0.425	0.366	0.489	0.212	0.183	0.245	INDETERMINATE	1	TRUE	1	0.51096042609912	3		560	717	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0066476-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	38	622	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	1	0.834	1	1	0.966	1	CLONAL	2	TRUE	1	0.09	2		622	419	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0066476-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	4	260	1	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.7	0.367	1	0.7	0.367	1	SUBCLONAL	1	TRUE	1	0.09	2		261	127	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925688	114925688	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066476-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	20	0	0	ENST00000543371.1:c.1766C>G	p.Thr589Ser	p.T589S	ENST00000543371	NM_001198531.1	589	aCc/aGc	14/14	1	2	FACETS	1	0.781	1	1	0.781	1	CLONAL	1	TRUE	1	0.09	2		0	434	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627187	86627187	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066476-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	12	0	0	ENST00000274376.6:c.562A>G	p.Arg188Gly	p.R188G	ENST00000274376	NM_002890.2	188	Aga/Gga	2/25	1	2	FACETS	0.811	0.568	1	0.811	0.568	1	CLONAL	1	TRUE	1	0.09	2		0	329	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609930	117609930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144393305	NA	P-0066476-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	6	0	0	ENST00000368508.3:c.6769G>A	p.Asp2257Asn	p.D2257N	ENST00000368508	NM_002944.2	2257	Gac/Aac	43/43	1	2	FACETS	0.794	0.474	1	0.794	0.474	1	CLONAL	1	TRUE	1	0.09	2		0	168	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47108587	47108587	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066476-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	4	0	0	ENST00000409792.3:c.6082A>C	p.Lys2028Gln	p.K2028Q	ENST00000409792	NM_014159.6	2028	Aaa/Caa	13/21	1	2	FACETS	0.597	0.312	1	0.597	0.312	1	SUBCLONAL	1	TRUE	1	0.09	2		0	149	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0066754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	56	252	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.873	0.75	1	1	0.973	1	CLONAL	2	TRUE	1	0.14	2		253	458	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0066754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	15	114	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	TRUE	1	0.14	2		114	175	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577557	7577557	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519982	NA	P-0066754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	17	403	0	ENST00000269305.4:c.724T>C	p.Cys242Arg	p.C242R	ENST00000269305	NM_001126112.2	242	Tgc/Cgc	7/11	1	2	FACETS	0.425	0.316	0.556	0.425	0.316	0.556	SUBCLONAL	1	TRUE	1	0.14	2		403	571	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	39	358	0	ENST00000263967.3:c.3012G>T	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atT	21/21	1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	TRUE	1	0.14	2		358	546	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605204	46605204	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1459319402	NA	P-0066754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	22	361	1	ENST00000263734.3:c.1421G>C	p.Ser474Thr	p.S474T	ENST00000263734	NM_001430.4	474	aGc/aCc	10/16	1	2	FACETS	0.731	0.565	0.924	0.731	0.565	0.924	CLONAL	1	TRUE	1	0.14	2		362	430	SUCCESS
EED	8726	MSKCC	GRCh37	11	85979543	85979543	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1131692173	NA	P-0066754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	38	252	0	ENST00000263360.6:c.906A>C	p.Arg302Ser	p.R302S	ENST00000263360	NM_003797.3	302	agA/agC	9/12	1	2	FACETS	0.996	0.822	1	0.996	0.822	1	CLONAL	1	TRUE	1	0.14	2		252	545	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089631	27089631	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	58	548	0	ENST00000324856.7:c.2587A>G	p.Met863Val	p.M863V	ENST00000324856	NM_006015.4	863	Atg/Gtg	8/20	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.14	2		548	701	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524668	137524668	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	27	299	0	ENST00000367739.4:c.701T>G	p.Val234Gly	p.V234G	ENST00000367739	NM_000416.2	234	gTt/gGt	5/7	1	2	FACETS	0.779	0.619	0.963	0.779	0.619	0.963	CLONAL	1	TRUE	1	0.14	2		299	495	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380757	118380758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0066754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	38	364	0	ENST00000534358.1:c.11001dup	p.Pro3668ThrfsTer8	p.P3668Tfs*8	ENST00000534358	NM_005933.3	3665	-/A	30/36	1	2	FACETS	0.881	0.727	1	0.881	0.727	1	CLONAL	1	TRUE	1	0.14	2		364	616	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589847	212589847	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1476386458	NA	P-0066754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	32	399	0	ENST00000342788.4:c.695G>A	p.Arg232Gln	p.R232Q	ENST00000342788	NM_005235.2	232	cGa/cAa	6/28	1	2	FACETS	0.751	0.608	0.913	0.751	0.608	0.913	CLONAL	1	TRUE	1	0.14	2		399	609	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066821-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	40	350	0				ENST00000310581	NM_198253.2	-/1132			0.226587908229375	2	FACETS	0.922	0.784	1	1	0.955	1	CLONAL	3	TRUE	0	0.229495897604307	2		350	126	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0066821-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	91	580	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.184092247365115	3	FACETS	0.872	0.781	0.966	0.872	0.781	0.966	CLONAL	3	TRUE	0	0.229495897604307	3		580	338	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578397	7578398	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0066821-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	82	570	0	ENST00000269305.4:c.532dup	p.His178ProfsTer3	p.H178Pfs*3	ENST00000269305	NM_001126112.2	178	cac/cCac	5/11	0.184092247365115	3	FACETS	1	0.957	1	0.772	0.686	0.862	CLONAL	2	TRUE	0	0.229495897604307	3		570	344	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0066821-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	99	527	0	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	0.229495897604307	2	FACETS	0.943	0.852	1	1	0.982	1	CLONAL	3	TRUE	0	0.229495897604307	2		527	305	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280627	41280627	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066821-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	22	491	0	ENST00000349496.5:c.2141del	p.Pro714LeufsTer21	p.P714Lfs*21	ENST00000349496	NM_001904.3	714	Cct/ct	15/15	1	2	FACETS	0.554	0.429	0.699	0.554	0.429	0.699	SUBCLONAL	1	TRUE	1	0.229495897604307	2		491	346	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180473	94180475	+	inframe_deletion	In_Frame_Del	DEL	TGC	TGC	-	novel	NA	P-0066821-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	71	387	0	ENST00000323929.3:c.1693_1695del	p.Ala565del	p.A565del	ENST00000323929	NM_005591.3	565	GCA/-	15/20	0.146765641975037	4	FACETS	0.878	0.77	0.995	0.878	0.77	0.995	CLONAL	2	TRUE	2	0.229495897604307	4		387	433	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143326466	143326466	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066821-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	73	371	0	ENST00000262992.4:c.148C>G	p.Leu50Val	p.L50V	ENST00000262992	NM_001101669.1	50	Ctc/Gtc	4/24	0.112268369138797	4	FACETS	1	0.95	1	1	0.95	1	INDETERMINATE	2	TRUE	2	0.229495897604307	4		371	340	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653048	29653048	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0066821-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	61	505	0	ENST00000356175.3:c.4983T>A	p.Cys1661Ter	p.C1661*	ENST00000356175	NM_000267.3	1661	tgT/tgA	36/57	0.112268369138797	4	FACETS	1	0.966	1	0.709	0.613	0.813	INDETERMINATE	1	TRUE	2	0.229495897604307	4		505	461	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259613	89259613	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066821-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	80	485	0	ENST00000336596.2:c.757C>A	p.Pro253Thr	p.P253T	ENST00000336596	NM_005233.5	253	Ccc/Acc	3/17	0.109536807729542	3	FACETS	1	0.926	1	0.706	0.626	0.791	INDETERMINATE	2	TRUE	0	0.229495897604307	3		485	367	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851193	63851193	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066821-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	45	507	0	ENST00000279873.7:c.1971C>G	p.Phe657Leu	p.F657L	ENST00000279873	NM_032199.2	657	ttC/ttG	10/10	0.229495897604307	3	FACETS	1	0.879	1	0.527	0.443	0.619	CLONAL	1	TRUE	1	0.229495897604307	3		507	415	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066821-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	42	350	0				ENST00000310581	NM_198253.2	-/1132			0.160170111638568	1	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	0	0.23	1		350	292	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0066821-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	72	580	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.23	2		580	626	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578397	7578398	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0066821-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	65	570	0	ENST00000269305.4:c.532dup	p.His178ProfsTer3	p.H178Pfs*3	ENST00000269305	NM_001126112.2	178	cac/cCac	5/11	1	2	FACETS	0.889	0.77	1	0.889	0.77	1	CLONAL	1	TRUE	1	0.23	2		570	636	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0066821-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	61	527	0	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	0.160170111638568	1	FACETS	0.901	0.778	1	0.901	0.778	1	CLONAL	1	TRUE	0	0.23	1		527	521	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280627	41280627	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066821-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	36	491	0	ENST00000349496.5:c.2141del	p.Pro714LeufsTer21	p.P714Lfs*21	ENST00000349496	NM_001904.3	714	Cct/ct	15/15	1	2	FACETS	0.626	0.514	0.752	0.626	0.514	0.752	SUBCLONAL	1	TRUE	1	0.23	2		491	500	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180473	94180475	+	inframe_deletion	In_Frame_Del	DEL	TGC	TGC	-	novel	NA	P-0066821-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	56	387	0	ENST00000323929.3:c.1693_1695del	p.Ala565del	p.A565del	ENST00000323929	NM_005591.3	565	GCA/-	15/20	1	2	FACETS	0.976	0.837	1	0.976	0.837	1	CLONAL	1	TRUE	1	0.23	2		387	499	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143326466	143326466	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066821-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	40	371	0	ENST00000262992.4:c.148C>G	p.Leu50Val	p.L50V	ENST00000262992	NM_001101669.1	50	Ctc/Gtc	4/24	0.115415059322302	1	FACETS	0.724	0.602	0.86	0.724	0.602	0.86	INDETERMINATE	1	TRUE	0	0.23	1		371	425	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653048	29653048	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0066821-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	41	505	0	ENST00000356175.3:c.4983T>A	p.Cys1661Ter	p.C1661*	ENST00000356175	NM_000267.3	1661	tgT/tgA	36/57	1	2	FACETS	0.585	0.487	0.696	0.585	0.487	0.696	SUBCLONAL	1	TRUE	1	0.23	2		505	609	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259613	89259613	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066821-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	42	485	0	ENST00000336596.2:c.757C>A	p.Pro253Thr	p.P253T	ENST00000336596	NM_005233.5	253	Ccc/Acc	3/17	1	2	FACETS	0.784	0.654	0.927	0.784	0.654	0.927	CLONAL	1	TRUE	1	0.23	2		485	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0066857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	263	857	0	ENST00000269305.4:c.613dup	p.Tyr205LeufsTer4	p.Y205Lfs*4	ENST00000269305	NM_001126112.2	205	tat/tTat	6/11	0.404607812474542	2	FACETS	0.98	0.925	1	0.98	0.925	1	CLONAL	2	TRUE	0	0.413346967644396	2		857	649	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219005	36219005	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	40	756	0	ENST00000222270.7:c.4504G>A	p.Glu1502Lys	p.E1502K	ENST00000222270	NM_014727.1	1502	Gaa/Aaa	19/37	0.404607812474542	2	FACETS	0.364	0.302	0.434	0.182	0.151	0.217	SUBCLONAL	1	TRUE	0	0.413346967644396	2		756	531	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035238	6035238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1805322	NA	P-0066857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	68	790	0	ENST00000265849.7:c.830C>T	p.Thr277Met	p.T277M	ENST00000265849	NM_000535.5	277	aCg/aTg	8/15	0.289181873306123	3	FACETS	0.589	0.512	0.672	0.295	0.256	0.336	SUBCLONAL	1	TRUE	1	0.413346967644396	3		790	674	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900329	101900329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	31	580	0	ENST00000374994.4:c.763C>T	p.Arg255Cys	p.R255C	ENST00000374994	NM_004612.2	255	Cgt/Tgt	4/9	0.394837960669464	3	FACETS	0.37	0.299	0.451	0.185	0.149	0.226	SUBCLONAL	1	TRUE	1	0.413346967644396	3		580	489	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390794	139390794	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	209	903	0	ENST00000277541.6:c.7397del	p.Thr2466SerfsTer11	p.T2466Sfs*11	ENST00000277541	NM_017617.3	2466	aCg/ag	34/34	0.404607812474542	2	FACETS	0.924	0.865	0.984	0.924	0.865	0.984	CLONAL	2	TRUE	0	0.413346967644396	2		903	547	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134566	41134566	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	62	783	0	ENST00000379561.5:c.1062G>C	p.Lys354Asn	p.K354N	ENST00000379561	NM_002015.3	354	aaG/aaC	2/3	0.235265188055085	3	FACETS	0.636	0.55	0.73	0.318	0.275	0.365	INDETERMINATE	1	TRUE	1	0.413346967644396	3		783	569	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0066894-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	18	207	0	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			0.169632635298614	2	FACETS	0.605	0.456	0.78	0.302	0.228	0.39	SUBCLONAL	1	TRUE	0	0.243045193547602	2		207	245	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579398	7579398	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066894-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	68	490	0	ENST00000269305.4:c.289del	p.Val97SerfsTer26	p.V97Sfs*26	ENST00000269305	NM_001126112.2	97	Gtc/tc	4/11	NA	2	FACETS	1	0.879	1			1	INDETERMINATE	1	TRUE	NA	0.243045193547602	2		490	554	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599105	28599105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066894-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	48	478	1	ENST00000253063.3:c.551C>T	p.Thr184Ile	p.T184I	ENST00000253063	NM_031459.4	184	aCc/aTc	5/10	1	2	FACETS	0.676	0.571	0.792	0.676	0.571	0.792	SUBCLONAL	1	TRUE	1	0.243045193547602	2		479	584	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0066894-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	115	207	0	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			0.786921160288182	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.794967979326282	1		207	145	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579398	7579398	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066894-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	327	490	0	ENST00000269305.4:c.289del	p.Val97SerfsTer26	p.V97Sfs*26	ENST00000269305	NM_001126112.2	97	Gtc/tc	4/11	0.755993798627401	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.794967979326282	1		490	477	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599105	28599105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066894-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	311	478	1	ENST00000253063.3:c.551C>T	p.Thr184Ile	p.T184I	ENST00000253063	NM_031459.4	184	aCc/aTc	5/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.794967979326282	2		479	720	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464578	25464578	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0066895-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	231	280	0	ENST00000264709.3:c.1937-2A>T		p.X646_splice	ENST00000264709	NM_175629.2	646			1	2	FACETS	0.994	0.936	1	0.994	0.936	1	CLONAL	1	TRUE	1	0.88	2		280	528	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922889	39922890	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0066895-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	252	135	0	ENST00000378444.4:c.3818_3819del	p.Glu1273ValfsTer3	p.E1273Vfs*3	ENST00000378444	NM_001123385.1	1273	gAG/g	8/15	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.88	1		135	286	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356728	70356728	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0066895-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	261	177	0	ENST00000374080.3:c.5401del		p.X1801_splice	ENST00000374080		1801			1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.88	1		177	293	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	76	385	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.997	0.883	1	0.997	0.883	1	CLONAL	1	TRUE	1	0.5	2		385	305	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	63	830	2	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	1	2	FACETS	0.726	0.632	0.828	0.726	0.632	0.828	SUBCLONAL	1	TRUE	1	0.5	2		832	347	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	29	482	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.58	0.469	0.704	0.58	0.469	0.704	SUBCLONAL	1	TRUE	1	0.5	2		482	200	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	66	665	0	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	1	2	FACETS	0.719	0.628	0.817	0.719	0.628	0.817	SUBCLONAL	1	TRUE	1	0.5	2		665	367	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	73	215	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.5	2		215	211	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	75	480	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.971	0.859	1	0.971	0.859	1	CLONAL	1	TRUE	1	0.5	2		480	309	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149251	119149251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267606708	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	10	641	0	ENST00000264033.4:c.1259G>A	p.Arg420Gln	p.R420Q	ENST00000264033	NM_005188.3	420	cGa/cAa	9/16	1	2	FACETS	0.109	0.073	0.154	0.109	0.073	0.154	SUBCLONAL	1	TRUE	1	0.5	2		641	367	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518099	8518099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764400127	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	115	788	2	ENST00000356435.5:c.1292C>T	p.Ser431Leu	p.S431L	ENST00000356435		431	tCg/tTg	10/35	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.5	2		790	384	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500303	99500303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61740868	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	78	875	0	ENST00000268035.6:c.3736C>T	p.Arg1246Cys	p.R1246C	ENST00000268035	NM_000875.3	1246	Cgc/Tgc	21/21	1	2	FACETS	0.926	0.82	1	0.926	0.82	1	CLONAL	1	TRUE	1	0.5	2		875	337	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431664	431664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	17	551	1	ENST00000399788.2:c.2345G>A	p.Arg782Gln	p.R782Q	ENST00000399788	NM_001042603.1	782	cGa/cAa	17/28	1	2	FACETS	0.238	0.177	0.31	0.238	0.177	0.31	SUBCLONAL	1	TRUE	1	0.5	2		552	286	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606679	29606679	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs865931787	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	107	894	1	ENST00000389048.3:c.1201C>T	p.Arg401Ter	p.R401*	ENST00000389048	NM_004304.4	401	Cga/Tga	5/29	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.5	2		895	373	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021428	42021428	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	12	787	3	ENST00000219905.7:c.3724C>T	p.Arg1242Ter	p.R1242*	ENST00000219905	NM_001164273.1	1242	Cga/Tga	11/24	1	2	FACETS	0.136	0.095	0.186	0.136	0.095	0.186	SUBCLONAL	1	TRUE	1	0.5	2		790	354	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	20	664	0	ENST00000349496.5:c.101G>A	p.Gly34Glu	p.G34E	ENST00000349496	NM_001904.3	34	gGa/gAa	3/15	0.0766075867460878	3	FACETS	0.218	0.166	0.279	0.109	0.083	0.14	INDETERMINATE	1	TRUE	1	0.5	3		664	459	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670875	134670875	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	24	1108	0	ENST00000398015.3:c.786G>T	p.Glu262Asp	p.E262D	ENST00000398015	NM_004441.4	262	gaG/gaT	3/16	1	2	FACETS	0.337	0.264	0.42	0.337	0.264	0.42	SUBCLONAL	1	TRUE	1	0.5	2		1108	285	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459558	50459558	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	31	816	0	ENST00000331340.3:c.847C>A	p.Leu283Ile	p.L283I	ENST00000331340	NM_006060.4	283	Ctt/Att	7/8	1	2	FACETS	0.324	0.262	0.394	0.324	0.262	0.394	SUBCLONAL	1	TRUE	1	0.5	2		816	383	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845627	63845627	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	128	858	0	ENST00000279873.7:c.1366G>T	p.Glu456Ter	p.E456*	ENST00000279873	NM_032199.2	456	Gaa/Taa	9/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.5	2		858	417	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39725963	39725963	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	78	428	0	ENST00000361337.2:c.834C>A	p.Phe278Leu	p.F278L	ENST00000361337	NM_003286.2	278	ttC/ttA	10/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.5	2		428	248	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253151	133253151	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	108	722	0	ENST00000320574.5:c.890C>A	p.Ser297Tyr	p.S297Y	ENST00000320574	NM_006231.2	297	tCc/tAc	9/49	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.5	2		722	331	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218125	36218125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1345863391	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	30	1033	4	ENST00000222270.7:c.4072G>A	p.Ala1358Thr	p.A1358T	ENST00000222270	NM_014727.1	1358	Gca/Aca	15/37	1	2	FACETS	0.35	0.282	0.427	0.35	0.282	0.427	SUBCLONAL	1	TRUE	1	0.5	2		1037	343	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574179	46574179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756121061	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	22	796	0	ENST00000263734.3:c.194G>A	p.Arg65Gln	p.R65Q	ENST00000263734	NM_001430.4	65	cGa/cAa	2/16	1	2	FACETS	0.275	0.213	0.347	0.275	0.213	0.347	SUBCLONAL	1	TRUE	1	0.5	2		796	320	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745593	162745593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769532262	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	21	833	0	ENST00000367921.3:c.2008G>A	p.Glu670Lys	p.E670K	ENST00000367921	NM_006182.2	670	Gag/Aag	15/18	1	2	FACETS	0.24	0.184	0.305	0.24	0.184	0.305	SUBCLONAL	1	TRUE	1	0.5	2		833	350	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061726	38061726	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	8	1407	4	ENST00000250448.2:c.263del	p.Gly88AlafsTer6	p.G88Afs*6	ENST00000250448	NM_004496.3	88	gGc/gc	2/2	1	2	FACETS	0.098	0.062	0.144	0.098	0.062	0.144	SUBCLONAL	1	TRUE	1	0.5	2		1411	327	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109313998	109313998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199611315	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	48	402	0	ENST00000436639.2:c.1225C>T	p.Arg409Cys	p.R409C	ENST00000436639	NM_014454.2	409	Cgt/Tgt	7/10	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.5	2		402	181	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443676	29443676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56315533	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	37	1118	0	ENST00000389048.3:c.3541C>T	p.Arg1181Cys	p.R1181C	ENST00000389048	NM_004304.4	1181	Cgc/Tgc	23/29	1	2	FACETS	0.339	0.279	0.405	0.339	0.279	0.405	SUBCLONAL	1	TRUE	1	0.5	2		1118	437	SUCCESS
APC	324	MSKCC	GRCh37	5	112177377	112177377	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	71	684	0	ENST00000257430.4:c.6086C>A	p.Ser2029Tyr	p.S2029Y	ENST00000257430	NM_000038.5	2029	tCt/tAt	16/16	1	2	FACETS	0.91	0.801	1	0.91	0.801	1	CLONAL	1	TRUE	1	0.5	2		684	312	SUCCESS
APC	324	MSKCC	GRCh37	5	112175925	112175925	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs863225356	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	57	761	0	ENST00000257430.4:c.4634C>A	p.Ser1545Ter	p.S1545*	ENST00000257430	NM_000038.5	1545	tCa/tAa	16/16	1	2	FACETS	0.555	0.477	0.639	0.555	0.477	0.639	SUBCLONAL	1	TRUE	1	0.5	2		761	411	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410597	63410597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758807218	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	66	1058	0	ENST00000330258.3:c.2570G>A	p.Arg857Gln	p.R857Q	ENST00000330258	NM_152424.3	857	cGa/cAa	2/2	0.158005653542985	1	FACETS	0.545	0.476	0.62	0.545	0.476	0.62	INDETERMINATE	1	TRUE	0	0.5	1		1058	363	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738258	133738258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753573200	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	36	1078	0	ENST00000318560.5:c.658C>T	p.Arg220Cys	p.R220C	ENST00000318560	NM_005157.4	220	Cgc/Tgc	4/11	1	2	FACETS	0.367	0.302	0.44	0.367	0.302	0.44	SUBCLONAL	1	TRUE	1	0.5	2		1078	392	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143181669	143181669	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	14	508	1	ENST00000262992.4:c.664G>T	p.Asp222Tyr	p.D222Y	ENST00000262992	NM_001101669.1	222	Gat/Tat	9/24	1	2	FACETS	0.221	0.16	0.296	0.221	0.16	0.296	SUBCLONAL	1	TRUE	1	0.5	2		509	253	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004302	150004302	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs35163691	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	22	503	2	ENST00000253339.5:c.1923C>A	p.Phe641Leu	p.F641L	ENST00000253339		641	ttC/ttA	3/7	1	2	FACETS	0.312	0.242	0.393	0.312	0.242	0.393	SUBCLONAL	1	TRUE	1	0.5	2		505	282	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597981	43597981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765654609	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	19	1110	0	ENST00000355710.3:c.529C>T	p.Arg177Trp	p.R177W	ENST00000355710	NM_020975.4	177	Cgg/Tgg	3/20	1	2	FACETS	0.211	0.16	0.272	0.211	0.16	0.272	SUBCLONAL	1	TRUE	1	0.5	2		1110	360	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911328	32911328	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs80358534	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	58	658	0	ENST00000380152.3:c.2836G>T	p.Asp946Tyr	p.D946Y	ENST00000380152		946	Gat/Tat	11/27	1	2	FACETS	0.879	0.762	1	0.879	0.762	1	CLONAL	1	TRUE	1	0.5	2		658	264	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378245	15378245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	60	495	0	ENST00000263377.2:c.541C>T	p.Arg181Cys	p.R181C	ENST00000263377	NM_058243.2	181	Cgt/Tgt	4/20	1	2	FACETS	0.702	0.608	0.803	0.702	0.608	0.803	SUBCLONAL	1	TRUE	1	0.5	2		495	342	SUCCESS
APC	324	MSKCC	GRCh37	5	112179153	112179153	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	15	602	0	ENST00000257430.4:c.7862C>A	p.Ser2621Tyr	p.S2621Y	ENST00000257430	NM_000038.5	2621	tCt/tAt	16/16	1	2	FACETS	0.228	0.166	0.302	0.228	0.166	0.302	SUBCLONAL	1	TRUE	1	0.5	2		602	263	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553365	41553365	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	89	773	0	ENST00000263253.7:c.3454G>T	p.Glu1152Ter	p.E1152*	ENST00000263253	NM_001429.3	1152	Gaa/Taa	18/31	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.5	2		773	306	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123888136	123888136	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	21	743	0	ENST00000330479.4:c.614G>T	p.Arg205Ile	p.R205I	ENST00000330479	NM_020382.3	205	aGa/aTa	6/9	1	2	FACETS	0.214	0.164	0.273	0.214	0.164	0.273	SUBCLONAL	1	TRUE	1	0.5	2		743	392	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831910	72831910	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	23	907	0	ENST00000268489.5:c.4671G>T	p.Lys1557Asn	p.K1557N	ENST00000268489	NM_006885.3	1557	aaG/aaT	9/10	1	2	FACETS	0.231	0.179	0.29	0.231	0.179	0.29	SUBCLONAL	1	TRUE	1	0.5	2		907	399	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10789919	10789919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1391585643	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	21	624	2	ENST00000361367.2:c.1990C>T	p.Arg664Cys	p.R664C	ENST00000361367	NM_014633.3	664	Cgt/Tgt	16/25	1	2	FACETS	0.305	0.235	0.387	0.305	0.235	0.387	SUBCLONAL	1	TRUE	1	0.5	2		626	275	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423060	47423060	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	23	875	0	ENST00000404338.3:c.1128C>A	p.Phe376Leu	p.F376L	ENST00000404338	NM_004491.4	376	ttC/ttA	1/6	1	2	FACETS	0.217	0.169	0.274	0.217	0.169	0.274	SUBCLONAL	1	TRUE	1	0.5	2		875	423	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039557	180039557	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	16	1137	0	ENST00000261937.6:c.3486C>A	p.Phe1162Leu	p.F1162L	ENST00000261937	NM_182925.4	1162	ttC/ttA	26/30	1	2	FACETS	0.213	0.157	0.28	0.213	0.157	0.28	SUBCLONAL	1	TRUE	1	0.5	2		1137	300	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423779	47423779	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	37	739	0	ENST00000404338.3:c.1847T>G	p.Ile616Ser	p.I616S	ENST00000404338	NM_004491.4	616	aTt/aGt	1/6	1	2	FACETS	0.365	0.3	0.436	0.365	0.3	0.436	SUBCLONAL	1	TRUE	1	0.5	2		739	406	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681183	86681183	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	66	472	0	ENST00000274376.6:c.2824A>C	p.Asn942His	p.N942H	ENST00000274376	NM_002890.2	942	Aat/Cat	22/25	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.5	2		472	225	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435083	18435083	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	41	736	0	ENST00000266497.5:c.68A>C	p.Glu23Ala	p.E23A	ENST00000266497		23	gAa/gCa	1/31	1	2	FACETS	0.667	0.559	0.784	0.667	0.559	0.784	SUBCLONAL	1	TRUE	1	0.5	2		736	246	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934177	49934177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226314814	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	27	710	0	ENST00000296474.3:c.2330C>T	p.Pro777Leu	p.P777L	ENST00000296474	NM_002447.2	777	cCc/cTc	8/20	0.0766075867460878	3	FACETS	0.392	0.312	0.484	0.196	0.156	0.242	INDETERMINATE	1	TRUE	1	0.5	3		710	344	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38178611	38178611	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	16	537	0	ENST00000317025.8:c.1788G>T	p.Lys596Asn	p.K596N	ENST00000317025	NM_023034.1	596	aaG/aaT	8/24	1	2	FACETS	0.213	0.157	0.28	0.213	0.157	0.28	SUBCLONAL	1	TRUE	1	0.5	2		537	300	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143288	108143288	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	22	517	0	ENST00000278616.4:c.3107T>G	p.Phe1036Cys	p.F1036C	ENST00000278616	NM_000051.3	1036	tTc/tGc	21/63	1	2	FACETS	0.331	0.257	0.417	0.331	0.257	0.417	SUBCLONAL	1	TRUE	1	0.5	2		517	266	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243506	46243506	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	26	539	1	ENST00000334344.6:c.1859C>A	p.Ser620Tyr	p.S620Y	ENST00000334344	NM_152641.2	620	tCt/tAt	14/21	1	2	FACETS	0.324	0.257	0.401	0.324	0.257	0.401	SUBCLONAL	1	TRUE	1	0.5	2		540	321	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487153	56487153	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	112	719	2	ENST00000267101.3:c.1299G>T	p.Met433Ile	p.M433I	ENST00000267101	NM_001982.3	433	atG/atT	12/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.5	2		721	384	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226579970	226579970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	124	773	0	ENST00000366794.5:c.332G>A	p.Gly111Asp	p.G111D	ENST00000366794	NM_001618.3	111	gGt/gAt	3/23	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.5	2		773	384	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772322	56772322	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	35	551	0	ENST00000337432.4:c.176A>C	p.Glu59Ala	p.E59A	ENST00000337432	NM_058216.2	59	gAa/gCa	2/9	1	2	FACETS	0.393	0.323	0.472	0.393	0.323	0.472	SUBCLONAL	1	TRUE	1	0.5	2		551	356	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210830	133210830	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	70	808	0	ENST00000320574.5:c.5946T>G	p.Ile1982Met	p.I1982M	ENST00000320574	NM_006231.2	1982	atT/atG	43/49	1	2	FACETS	0.78	0.684	0.882	0.78	0.684	0.882	SUBCLONAL	1	TRUE	1	0.5	2		808	359	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911850	32911850	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	64	438	0	ENST00000380152.3:c.3358G>T	p.Glu1120Ter	p.E1120*	ENST00000380152		1120	Gaa/Taa	11/27	1	2	FACETS	0.924	0.808	1	0.924	0.808	1	CLONAL	1	TRUE	1	0.5	2		438	277	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123022548	123022548	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	11	405	0	ENST00000355640.3:c.957A>C	p.Gln319His	p.Q319H	ENST00000355640		319	caA/caC	3/7	0.158005653542985	1	FACETS	0.169	0.117	0.234	0.169	0.117	0.234	INDETERMINATE	1	TRUE	0	0.5	1		405	195	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041049	29041049	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	27	429	0	ENST00000282397.4:c.379T>G	p.Phe127Val	p.F127V	ENST00000282397	NM_002019.4	127	Ttt/Gtt	3/30	1	2	FACETS	0.411	0.328	0.505	0.411	0.328	0.505	SUBCLONAL	1	TRUE	1	0.5	2		429	263	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247527	53247527	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	89	875	0	ENST00000375401.3:c.282A>C	p.Glu94Asp	p.E94D	ENST00000375401	NM_004187.3	94	gaA/gaC	3/26	0.158005653542985	1	FACETS	0.797	0.713	0.885	0.797	0.713	0.885	INDETERMINATE	1	TRUE	0	0.5	1		875	335	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39690063	39690063	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	30	574	0	ENST00000361337.2:c.88G>T	p.Asp30Tyr	p.D30Y	ENST00000361337	NM_003286.2	30	Gat/Tat	3/21	1	2	FACETS	0.331	0.267	0.404	0.331	0.267	0.404	SUBCLONAL	1	TRUE	1	0.5	2		574	362	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260824	16260844	+	inframe_deletion	In_Frame_Del	DEL	GTGAATGTTCTTACGGGGCCA	GTGAATGTTCTTACGGGGCCA	-	rs752734364	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	27	1247	0	ENST00000375759.3:c.8100_8120del	p.Gly2702_Thr2708del	p.G2702_T2708del	ENST00000375759	NM_015001.2	2697	GTGAATGTTCTTACGGGGCCA/-	11/15	1	2	FACETS	0.238	0.189	0.294	0.238	0.189	0.294	SUBCLONAL	1	TRUE	1	0.5	2		1247	454	SUCCESS
ATM	472	MSKCC	GRCh37	11	108154985	108154985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782035	NA	P-0066956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	19	440	0	ENST00000278616.4:c.3778G>A	p.Val1260Met	p.V1260M	ENST00000278616	NM_000051.3	1260	Gtg/Atg	26/63	1	2	FACETS	0.332	0.252	0.425	0.332	0.252	0.425	SUBCLONAL	1	TRUE	1	0.5	2		440	229	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50782642	50782659	+	inframe_deletion	In_Frame_Del	DEL	CTCCCCAGATATAACCCA	CTCCCCAGATATAACCCA	-	novel	NA	P-0066982-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	266	638	0	ENST00000307179.4:c.2154_2171del	p.Ser719_Gln724del	p.S719_Q724del	ENST00000307179		718	tcCTCCCCAGATATAACCCAg/tcg	14/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		638	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0067035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	157	394	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.420702895311535	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.428534076121722	1		394	552	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0067035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	111	382	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.319512704456685	3	FACETS	0.962	0.866	1	0.481	0.433	0.532	CLONAL	1	TRUE	1	0.428534076121722	3		382	654	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0067035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	133	448	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.428534076121722	1	FACETS	0.888	0.811	0.969	0.888	0.811	0.969	CLONAL	1	TRUE	0	0.428534076121722	1		448	549	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949966	44949966	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0067035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	100	480	0	ENST00000377967.4:c.3737-2A>G		p.X1246_splice	ENST00000377967	NM_021140.2	1246			0.428534076121722	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.428534076121722	1		480	330	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0067038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	143	678	4	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.614152531606343	1	FACETS	0.927	0.857	0.998	0.927	0.857	0.998	CLONAL	1	TRUE	0	0.614152531606343	1		682	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0067038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	120	432	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	0.59094192285458	1	FACETS	0.964	0.885	1	0.964	0.885	1	CLONAL	1	TRUE	0	0.614152531606343	1		432	281	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40739826	40739826	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142926499	NA	P-0067038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	133	650	2	ENST00000392038.2:c.1399C>T	p.Arg467Trp	p.R467W	ENST00000392038	NM_001626.4	467	Cgg/Tgg	14/14	0.614152531606343	7	FACETS	0.888	0.804	0.976			1	CLONAL	1	TRUE	NA	0.614152531606343	7		652	1237	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0067038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	147	482	6	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.614152531606343	4	FACETS	1	0.96	1			1	CLONAL	2	TRUE	NA	0.614152531606343	4		488	365	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138400853	138400854	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	46	437	1	ENST00000289153.2:c.2459dup	p.Leu820PhefsTer33	p.L820Ffs*33	ENST00000289153	NM_006219.2	820	ttg/ttTg	17/22	1	2	FACETS	0.986	0.846	1	0.986	0.846	1	CLONAL	1	TRUE	1	0.614152531606343	2		438	152	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0067056-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	191	621	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		621	490	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347973	128347973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757433296	NA	P-0067056-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	136	532	0	ENST00000265960.3:c.532G>A	p.Asp178Asn	p.D178N	ENST00000265960	NM_001006617.1	178	Gat/Aat	5/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		532	487	SUCCESS
FH	2271	MSKCC	GRCh37	1	241676902	241676902	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0067056-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	171	365	0	ENST00000366560.3:c.378+1del		p.X126_splice	ENST00000366560	NM_000143.3	126			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		365	492	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242699	46242699	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067056-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	94	481	0	ENST00000334344.6:c.1661G>T	p.Ser554Ile	p.S554I	ENST00000334344	NM_152641.2	554	aGt/aTt	13/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		481	305	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963030	38963030	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067056-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	117	513	0	ENST00000357387.3:c.1514A>C	p.His505Pro	p.H505P	ENST00000357387	NM_152756.3	505	cAc/cCc	17/38	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		513	412	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0067090-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	26	414	0	ENST00000311936.3:c.180_181delinsAA	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggAAaa	3/5	0.162501859459145	2	FACETS	1	0.858	1	0.55	0.438	0.677	CLONAL	1	TRUE	0	0.223868849521314	2		414	211	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067093-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	34	350	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		350	146	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0067111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	130	426	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.445364223908403	2	FACETS	0.859	0.79	0.929	0.859	0.79	0.929	CLONAL	2	TRUE	0	0.454690082252702	2		426	333	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946973	71946973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375841975	NA	P-0067111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	159	696	0	ENST00000298229.2:c.2822C>T	p.Thr941Met	p.T941M	ENST00000298229	NM_001567.3	941	aCg/aTg	25/28	0.454690082252702	4	FACETS	0.992	0.915	1	0.992	0.915	1	CLONAL	2	TRUE	2	0.454690082252702	4		696	513	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653866	89653868	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	GGT	GGT	-	novel	NA	P-0067111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	30	340	0	ENST00000371953.3:c.164_164+2del		p.X55_splice	ENST00000371953	NM_000314.4	55		2/9	0.445364223908403	2	FACETS	0.985	0.829	1	0.985	0.829	1	CLONAL	2	TRUE	0	0.454690082252702	2		340	67	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0067129-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	24	288	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.186424300841134	5	FACETS	0.87	0.69	1	0.58	0.46	0.714	CLONAL	2	TRUE	2	0.277111421473017	5		288	141	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0067129-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	56	645	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.258398341952452	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	2	TRUE	0	0.277111421473017	2		645	192	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0067133-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	116	328	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	0.383513023447384	5	FACETS	0.868	0.785	0.955	0.579	0.523	0.637	CLONAL	2	TRUE	2	0.383513023447384	5		328	549	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998508	100998508	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067133-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	40	374	0	ENST00000325455.5:c.1294T>A	p.Ser432Thr	p.S432T	ENST00000325455	NM_001202474.3	432	Tcc/Acc	1/8	0.368821529506167	4	FACETS	0.937	0.782	1	0.469	0.391	0.554	CLONAL	1	TRUE	2	0.383513023447384	4		374	308	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405851	157405851	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067133-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	75	421	0	ENST00000346085.5:c.2093C>T	p.Ser698Leu	p.S698L	ENST00000346085	NM_020732.3	698	tCa/tTa	6/20	0.349052665884932	2	FACETS	0.707	0.621	0.8	0.354	0.31	0.4	SUBCLONAL	1	TRUE	0	0.383513023447384	2		421	553	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067172-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	297	350	0				ENST00000310581	NM_198253.2	-/1132			0.535946580518534	6	FACETS	0.959	0.921	0.997	0.959	0.921	0.997	CLONAL	5	TRUE	1	0.627542902326535	6		350	445	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033844	49033844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853294	NA	P-0067172-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	183	333	0	ENST00000267163.4:c.1981C>T	p.Arg661Trp	p.R661W	ENST00000267163	NM_000321.2	661	Cgg/Tgg	20/27	0.316609711056925	2	FACETS	0.876	0.824	0.927	0.876	0.824	0.927	INDETERMINATE	2	TRUE	0	0.627542902326535	2		333	333	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493442	56493442	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067172-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	381	499	0	ENST00000267101.3:c.2850T>G	p.Ile950Met	p.I950M	ENST00000267101	NM_001982.3	950	atT/atG	24/28	0.52475219377285	4	FACETS	0.905	0.874	0.935			1	CLONAL	4	TRUE	NA	0.627542902326535	4		499	546	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651933	36651934	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0067172-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	153	585	0	ENST00000244741.5:c.56dup	p.Arg20ProfsTer16	p.R20Pfs*16	ENST00000244741	NM_000389.4	19	cgc/cGgc	2/3	0.320026913591817	1	FACETS	0.951	0.883	1	0.951	0.883	1	INDETERMINATE	1	TRUE	0	0.627542902326535	1		585	352	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652068	36652092	+	frameshift_variant	Frame_Shift_Del	DEL	GCCTGGGAGCGTGTGCGGGGCCTTG	GCCTGGGAGCGTGTGCGGGGCCTTG	-	novel	NA	P-0067172-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	105	654	0	ENST00000244741.5:c.195_219del	p.Trp65CysfsTer75	p.W65Cfs*75	ENST00000244741	NM_000389.4	64	GCCTGGGAGCGTGTGCGGGGCCTTGgc/gc	2/3	0.320026913591817	1	FACETS	0.576	0.52	0.634	0.576	0.52	0.634	INDETERMINATE	1	TRUE	0	0.627542902326535	1		654	399	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324105	31324106	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067172-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	24	330	0	ENST00000412585.2:c.457_458insT	p.Asp153ValfsTer24	p.D153Vfs*24	ENST00000412585	NM_005514.6	153	gac/gTac	3/8	0.320026913591817	1	FACETS	0.314	0.248	0.389	0.314	0.248	0.389	INDETERMINATE	1	TRUE	0	0.627542902326535	1		330	167	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039500	49039511	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCAAGGTGTGTG	TCAAGGTGTGTG	-	novel	NA	P-0067172-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	57	448	0	ENST00000267163.4:c.2486_2489+8del		p.X829_splice	ENST00000267163	NM_000321.2	829		23/27	0.316609711056925	2	FACETS	0.596	0.514	0.683	0.298	0.257	0.342	INDETERMINATE	1	TRUE	0	0.627542902326535	2		448	305	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0067191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	174	395	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		395	567	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935322	36935323	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs747437399	NA	P-0067191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	153	652	2	ENST00000361632.4:c.1404dup	p.Ser469GlnfsTer5	p.S469Qfs*5	ENST00000361632		468	-/C	10/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		654	875	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922084	39922085	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0067191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	194	644	0	ENST00000378444.4:c.4087_4088del	p.Cys1363GlnfsTer45	p.C1363Qfs*45	ENST00000378444	NM_001123385.1	1363	TGc/c	9/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		644	554	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589591	67589593	+	inframe_deletion	In_Frame_Del	DEL	TAT	TAT	-	novel	NA	P-0067191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	11	424	0	ENST00000274335.5:c.1354_1356del	p.Tyr452del	p.Y452del	ENST00000274335		452	TAT/-	10/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		424	308	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424112	47424112	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	165	589	0	ENST00000404338.3:c.2180A>G	p.Lys727Arg	p.K727R	ENST00000404338	NM_004491.4	727	aAa/aGa	1/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		589	701	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996162	73996163	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGGCC	novel	NA	P-0067191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	221	850	0	ENST00000318443.5:c.897_901dup	p.Arg301GlnfsTer27	p.R301Qfs*27	ENST00000318443	NM_001024736.1	299	gaa/gaAGGCCa	5/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		850	705	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578213	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs864309495	NA	P-0067222-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	724	464	0	ENST00000269305.4:c.636del	p.Arg213AspfsTer34	p.R213Dfs*34	ENST00000269305	NM_001126112.2	212	ttT/tt	6/11	0.818127746971258	3	FACETS	1	0.998	1	1	0.998	1	CLONAL	3	TRUE	0	0.813153316541209	3		464	767	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546656	9546656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067222-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	121	481	0	ENST00000353224.5:c.1366G>A	p.Gly456Arg	p.G456R	ENST00000353224	NM_177990.2	456	Ggg/Agg	5/10	0.664876634242461	5	FACETS	0.731	0.66	0.806	0.244	0.22	0.269	SUBCLONAL	1	TRUE	2	0.813153316541209	5		481	904	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664924	138664924	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067222-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	148	379	0	ENST00000330315.3:c.641C>G	p.Pro214Arg	p.P214R	ENST00000330315	NM_023067.3	214	cCc/cGc	1/1	0.818127746971258	4	FACETS	1	0.929	1			1	CLONAL	1	TRUE	NA	0.813153316541209	4		379	650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579437	7579437	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067308-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	256	401	0	ENST00000269305.4:c.250del	p.Ala84ProfsTer39	p.A84Pfs*39	ENST00000269305	NM_001126112.2	84	Gcc/cc	4/11	0.418416637934618	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.418416637934618	2		401	558	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777856	27777856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778245917	NA	P-0067308-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	98	411	0	ENST00000369163.2:c.5C>T	p.Ala2Val	p.A2V	ENST00000369163	NM_003536.2	2	gCg/gTg	1/1	0.354093955541124	5	FACETS	1	0.968	1	0.405	0.362	0.451	CLONAL	1	TRUE	2	0.418416637934618	5		411	627	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89839775	89839775	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067308-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	98	360	0	ENST00000389301.3:c.1918A>T	p.Arg640Trp	p.R640W	ENST00000389301	NM_000135.2	640	Agg/Tgg	22/43	0.240097537035483	5	FACETS	1	0.967	1	0.403	0.36	0.449	INDETERMINATE	1	TRUE	2	0.418416637934618	5		360	630	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849047	156849047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142870382	NA	P-0067308-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	90	387	0	ENST00000524377.1:c.1939G>A	p.Val647Met	p.V647M	ENST00000524377	NM_002529.3	647	Gtg/Atg	15/17	0.161691901130285	5	FACETS	1	0.955	1	0.383	0.34	0.428	INDETERMINATE	1	TRUE	2	0.418416637934618	5		387	610	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845668	72845668	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067308-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	88	376	0	ENST00000268489.5:c.3672G>C	p.Gln1224His	p.Q1224H	ENST00000268489	NM_006885.3	1224	caG/caC	7/10	0.418416637934618	3	FACETS	0.822	0.729	0.921	0.411	0.364	0.461	CLONAL	1	TRUE	1	0.418416637934618	3		376	619	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322263	31322537	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGCTGTGAGAGACACATCAGAGCCCTGGGCACTGTCGCTGCCTGGAGTAGAACAAAAACAGGACCTGGTCAGAGCCCGCAGGAGACGTGGGACAGGAGGAATTATGGGGTGGGTGAGCTCCTCCACACTCCCACCCCCACCACTTACACGCAGCCTGAGAGTAGCTCCCTCCTTTTCCACCTGTGGGAAGAAAATGTCCTGTGAGGGCACTGGGAGGAAGCAGGGCCATGAGATCTTAGAGGAACCTCCTAGTCTTGGACCCAAAAGGAATTTCC	AGCTGTGAGAGACACATCAGAGCCCTGGGCACTGTCGCTGCCTGGAGTAGAACAAAAACAGGACCTGGTCAGAGCCCGCAGGAGACGTGGGACAGGAGGAATTATGGGGTGGGTGAGCTCCTCCACACTCCCACCCCCACCACTTACACGCAGCCTGAGAGTAGCTCCCTCCTTTTCCACCTGTGGGAAGAAAATGTCCTGTGAGGGCACTGGGAGGAAGCAGGGCCATGAGATCTTAGAGGAACCTCCTAGTCTTGGACCCAAAAGGAATTTCC	-	novel	NA	P-0067308-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	38	235	0	ENST00000412585.2:c.1013-95_1086del		p.X338_splice	ENST00000412585	NM_005514.6	338		6-7/8	0.354093955541124	5	FACETS	0.571	0.471	0.682	0.19	0.157	0.228	SUBCLONAL	1	TRUE	2	0.418416637934618	5		235	518	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0067339-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	56	288	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.886	0.759	1	1	0.974	1	CLONAL	2	TRUE	1	0.12	2		288	527	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974741	21974815	+	frameshift_variant	Frame_Shift_Del	DEL	CGCACCTCCTCTACCCGACCCCGGGCCGCGGCCGTGGCCAGCCAGTCAGCCGAAGGCTCCATGCTGCTCCCCGCC	CGCACCTCCTCTACCCGACCCCGGGCCGCGGCCGTGGCCAGCCAGTCAGCCGAAGGCTCCATGCTGCTCCCCGCC	GA	novel	NA	P-0067339-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	39	728	2	ENST00000304494.5:c.12_86delinsTC	p.Ala5ArgfsTer24	p.A5Rfs*24	ENST00000304494	NM_000077.4	4	gcGGCGGGGAGCAGCATGGAGCCTTCGGCTGACTGGCTGGCCACGGCCGCGGCCCGGGGTCGGGTAGAGGAGGTGCGg/gcTCg	1/3	1	2	FACETS	0.967	0.8	1	0.967	0.8	1	CLONAL	1	TRUE	1	0.12	2		730	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0067358-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	247	407	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.927005214384327	1	FACETS	0.986	0.956	1	0.986	0.956	1	CLONAL	1	TRUE	0	0.927005214384327	1		407	290	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939798	76939798	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067358-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	200	377	0	ENST00000373344.5:c.950del	p.Pro317GlnfsTer15	p.P317Qfs*15	ENST00000373344	NM_000489.3	317	cCa/ca	9/35	0.249214759505312	1	FACETS	0.559	0.525	0.593	0.559	0.525	0.593	INDETERMINATE	1	TRUE	0	0.927005214384327	1		377	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0067375-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	160	471	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.316116640736203	3	FACETS	1	0.984	1	0.809	0.751	0.868	CLONAL	2	TRUE	0	0.397019990644239	3		471	398	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266831	18266831	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1011337615	NA	P-0067375-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	69	371	0	ENST00000222254.8:c.142G>C	p.Glu48Gln	p.E48Q	ENST00000222254	NM_005027.3	48	Gag/Cag	2/16	0.396898670448555	4	FACETS	1	0.922	1	0.538	0.47	0.612	CLONAL	1	TRUE	2	0.397019990644239	4		371	451	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564895	226564895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067375-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	68	362	0	ENST00000366794.5:c.1855G>A	p.Glu619Lys	p.E619K	ENST00000366794	NM_001618.3	619	Gaa/Aaa	13/23	0.389681529979129	3	FACETS	0.918	0.802	1	0.306	0.267	0.348	CLONAL	1	TRUE	0	0.397019990644239	3		362	447	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281303	46281303	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0067375-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	60	325	0	ENST00000371998.3:c.4100C>G	p.Ser1367Ter	p.S1367*	ENST00000371998		1367	tCa/tGa	21/23	0.396898670448555	4	FACETS	0.9	0.777	1	0.3	0.259	0.345	CLONAL	1	TRUE	1	0.397019990644239	4		325	469	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234468	41234468	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067375-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	75	388	0	ENST00000357654.3:c.4310C>G	p.Ser1437Cys	p.S1437C	ENST00000357654	NM_007294.3	1437	tCt/tGt	12/23	0.396898670448555	2	FACETS	1	0.901	1	0.512	0.451	0.576	CLONAL	1	TRUE	0	0.397019990644239	2		388	369	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299135	15299135	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067375-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	88	375	0	ENST00000263388.2:c.1403T>G	p.Val468Gly	p.V468G	ENST00000263388	NM_000435.2	468	gTg/gGg	9/33	0.396898670448555	4	FACETS	1	0.973	1	0.662	0.589	0.739	CLONAL	1	TRUE	2	0.397019990644239	4		375	468	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262240	115262240	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067375-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	132	352	0	ENST00000438362.2:c.2314del	p.Arg772AlafsTer32	p.R772Afs*32	ENST00000438362	NM_001242891.1	772	Cgc/gc	18/20	0.396898670448555	3	FACETS	0.977	0.895	1	0.651	0.597	0.707	CLONAL	2	TRUE	0	0.397019990644239	3		352	408	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200481	67200497	+	frameshift_variant	Frame_Shift_Del	DEL	CACTCACACCTTCTGCG	CACTCACACCTTCTGCG	-	novel	NA	P-0067375-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	74	439	0	ENST00000312629.5:c.675_691del	p.Thr226HisfsTer3	p.T226Hfs*3	ENST00000312629	NM_003952.2	225	gtCACTCACACCTTCTGCGgc/gtgc	8/15	0.396898670448555	3	FACETS	0.91	0.799	1	0.455	0.399	0.515	CLONAL	1	TRUE	1	0.397019990644239	3		439	491	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326768	62326768	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067375-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	37	422	0	ENST00000360203.5:c.3587G>C	p.Gly1196Ala	p.G1196A	ENST00000360203	NM_001283009.1	1196	gGc/gCc	34/35	0.396898670448555	4	FACETS	0.441	0.362	0.528	0.147	0.12	0.176	SUBCLONAL	1	TRUE	1	0.397019990644239	4		422	591	SUCCESS
APC	324	MSKCC	GRCh37	5	112163677	112163677	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0067379-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	59	254	0	ENST00000257430.4:c.1600A>T	p.Lys534Ter	p.K534*	ENST00000257430	NM_000038.5	534	Aaa/Taa	13/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.274374121869417	2		254	295	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0067379-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	118	473	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.274374121869417	2	FACETS	0.923	0.838	1	0.923	0.838	1	CLONAL	2	TRUE	0	0.274374121869417	2		473	466	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236087	108236087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781894	NA	P-0067379-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	124	448	0	ENST00000278616.4:c.9023G>A	p.Arg3008His	p.R3008H	ENST00000278616	NM_000051.3	3008	cGt/cAt	63/63	0.274374121869417	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.274374121869417	2		448	383	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511172	148511172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554486390	NA	P-0067379-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	89	358	0	ENST00000320356.2:c.1730C>T	p.Pro577Leu	p.P577L	ENST00000320356	NM_004456.4	577	cCg/cTg	15/20	0.167495263459823	4	FACETS	0.854	0.76	0.954	0.854	0.76	0.954	CLONAL	2	TRUE	2	0.274374121869417	4		358	484	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288569	33288569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266548613	NA	P-0067379-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	54	376	0	ENST00000374542.5:c.983G>A	p.Arg328His	p.R328H	ENST00000374542	NM_001141970.1	328	cGt/cAt	3/8	0.207159297943759	2	FACETS	1	0.894	1	0.526	0.451	0.608	CLONAL	1	TRUE	0	0.274374121869417	2		376	374	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046339	180046339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067379-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	43	338	0	ENST00000261937.6:c.2675C>T	p.Ala892Val	p.A892V	ENST00000261937	NM_182925.4	892	gCg/gTg	19/30	0.207159297943759	2	FACETS	1	0.895	1	0.542	0.456	0.637	CLONAL	1	TRUE	0	0.274374121869417	2		338	289	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425499	47425500	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0067379-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	137	423	0	ENST00000404338.3:c.3569_3570del	p.Glu1190GlyfsTer9	p.E1190Gfs*9	ENST00000404338	NM_004491.4	1189	aaAGag/aaag	1/6	0.274374121869417	3	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	1	0.274374121869417	3		423	560	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807538	36807539	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067379-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	31	407	0	ENST00000373129.3:c.1125dup	p.Glu376Ter	p.E376*	ENST00000373129	NM_032017.1	375	-/T	12/12	1	2	FACETS	0.546	0.441	0.664	0.546	0.441	0.664	SUBCLONAL	1	TRUE	1	0.274374121869417	2		407	414	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	76	478	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	1	2	FACETS	0.815	0.715	0.923	1	0.978	1	CLONAL	2	TRUE	1	0.14	2		478	666	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456314	99456325	+	inframe_deletion	In_Frame_Del	DEL	GCGGCTCCAACA	GCGGCTCCAACA	-	novel	NA	P-0067403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	77	442	0	ENST00000268035.6:c.1633_1644del	p.Gly545_Ser548del	p.G545_S548del	ENST00000268035	NM_000875.3	544	tGCGGCTCCAACAgc/tgc	8/21	0.139399713782263	3	FACETS	0.91	0.799	1	0.91	0.799	1	CLONAL	2	TRUE	1	0.14	3		442	647	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099560	157099560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1583024172	NA	P-0067403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	26	441	0	ENST00000346085.5:c.497C>T	p.Ala166Val	p.A166V	ENST00000346085	NM_020732.3	166	gCt/gTt	1/20	1	2	FACETS	0.797	0.63	0.989	0.797	0.63	0.989	CLONAL	1	TRUE	1	0.14	2		441	466	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081691	143081691	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	30	343	0	ENST00000262992.4:c.1383C>A	p.Phe461Leu	p.F461L	ENST00000262992	NM_001101669.1	461	ttC/ttA	15/24	1	2	FACETS	0.965	0.777	1	0.965	0.777	1	CLONAL	1	TRUE	1	0.14	2		343	444	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152043	11152043	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755455174	NA	P-0067403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	42	444	0	ENST00000358026.2:c.4327C>T	p.Arg1443Trp	p.R1443W	ENST00000358026	NM_001128849.1	1443	Cgg/Tgg	31/36	1	2	FACETS	0.933	0.778	1	0.933	0.778	1	CLONAL	1	TRUE	1	0.14	2		444	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0067415-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	309	437	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.693633115431719	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.693633115431719	2		437	408	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435293	49435293	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067415-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	264	352	0	ENST00000301067.7:c.6260del	p.Gln2087ArgfsTer7	p.Q2087Rfs*7	ENST00000301067	NM_003482.3	2087	cAg/cg	31/54	0.693633115431719	2	FACETS	0.949	0.908	0.989	0.949	0.908	0.989	CLONAL	2	TRUE	0	0.693633115431719	2		352	401	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046290	180046290	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067415-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	21	256	0	ENST00000261937.6:c.2724C>A	p.Asn908Lys	p.N908K	ENST00000261937	NM_182925.4	908	aaC/aaA	19/30	0.693633115431719	2	FACETS	0.21	0.161	0.266	0.105	0.08	0.133	SUBCLONAL	1	TRUE	0	0.693633115431719	2		256	289	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147551	47147551	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067445-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	149	496	0	ENST00000409792.3:c.4775G>T	p.Arg1592Leu	p.R1592L	ENST00000409792	NM_014159.6	1592	cGa/cTa	6/21	0.563067194844974	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	0	0.555596482099197	1		496	311	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188230	10188241	+	inframe_deletion	In_Frame_Del	DEL	CACGATGGGCTT	CACGATGGGCTT	-	novel	NA	P-0067445-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	81	286	0	ENST00000256474.2:c.374_385del	p.His125_Leu128del	p.H125_L128del	ENST00000256474	NM_000551.3	125	CACGATGGGCTT/-	2/3	0.563067194844974	1	FACETS	0.936	0.839	1	0.936	0.839	1	CLONAL	1	FALSE	0	0.555596482099197	1		286	225	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52692291	52692298	+	frameshift_variant	Frame_Shift_Del	DEL	AGAAGCTG	AGAAGCTG	-	novel	NA	P-0067445-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	82	353	0	ENST00000394830.3:c.562_569del	p.Gln188Ter	p.Q188*	ENST00000394830	NM_018313.4	188	CAGCTTCTt/t	6/30	0.563067194844974	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	FALSE	0	0.555596482099197	1		353	205	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884002	37884002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1299958872	NA	P-0067445-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	168	558	0	ENST00000269571.5:c.3473C>T	p.Pro1158Leu	p.P1158L	ENST00000269571		1158	cCt/cTt	27/27	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	FALSE	NA	0.555596482099197	2		558	495	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572594	64572594	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs386134249	NA	P-0067445-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	155	597	1	ENST00000312049.6:c.1262G>A	p.Cys421Tyr	p.C421Y	ENST00000312049	NM_130799.2	421	tGc/tAc	9/10	0.121555448048051	4	FACETS	0.849	0.783	0.918	0.849	0.783	0.918	INDETERMINATE	2	FALSE	2	0.555596482099197	4		598	511	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817517	39817517	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067445-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	70	396	0	ENST00000288319.7:c.46C>A	p.Gln16Lys	p.Q16K	ENST00000288319	NM_182918.3	16	Cag/Aag	2/10	0.178253140203013	0	FACETS	0.423	0.372	0.475			1	INDETERMINATE	1	FALSE	0	0.555596482099197	0		396	265	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051642	30051643	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCAGA	novel	NA	P-0067453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	93	369	0	ENST00000338641.4:c.580_584dup	p.His195GlnfsTer16	p.H195Qfs*16	ENST00000338641	NM_000268.3	192	-/GCAGA	6/16	0.819220182699103	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.819220182699103	1		369	126	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178627	108178627	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0067494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	12	361	0	ENST00000278616.4:c.5678C>G	p.Ser1893Ter	p.S1893*	ENST00000278616	NM_000051.3	1893	tCa/tGa	38/63	1	2	FACETS	0.769	0.548	1	0.769	0.548	1	CLONAL	1	FALSE	1	0.354461731953231	2		361	88	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57474042	57474042	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0067494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	40	361	0	ENST00000371085.3:c.257+2T>C		p.X86_splice	ENST00000371085	NM_000516.4	86			0.354461731953231	7	FACETS	0.917	0.762	1			1	CLONAL	1	FALSE	NA	0.354461731953231	7		361	464	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564279	86564279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	43	404	0	ENST00000274376.6:c.11C>T	p.Ala4Val	p.A4V	ENST00000274376	NM_002890.2	4	gCc/gTc	1/25	1	2	FACETS	0.733	0.616	0.862	0.733	0.616	0.862	SUBCLONAL	1	FALSE	1	0.354461731953231	2		404	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0067509-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	100	544	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		544	310	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041402	47041402	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0067509-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	31	291	0	ENST00000377604.3:c.1746T>G	p.Tyr582Ter	p.Y582*	ENST00000377604	NM_001204468.1	582	taT/taG	16/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		291	158	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190359	32190359	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067509-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	74	452	0	ENST00000375023.3:c.380G>A	p.Cys127Tyr	p.C127Y	ENST00000375023	NM_004557.3	127	tGt/tAt	3/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		452	318	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909237	41909237	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067509-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	67	455	1	ENST00000372991.4:c.151del	p.Glu51ArgfsTer32	p.E51Rfs*32	ENST00000372991	NM_001760.3	51	Gag/ag	1/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		456	328	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0067525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	20	515	1	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.342567233576535	6	FACETS	0.253	0.193	0.325	0.063	0.048	0.082	SUBCLONAL	1	TRUE	2	0.450746240449298	6		516	666	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577555	7577555	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs375874539	NA	P-0067525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	267	568	0	ENST00000269305.4:c.726C>G	p.Cys242Trp	p.C242W	ENST00000269305	NM_001126112.2	242	tgC/tgG	7/11	0.409169255150061	3	FACETS	0.908	0.861	0.955	0.908	0.861	0.955	CLONAL	3	TRUE	0	0.450746240449298	3		568	533	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936096	178936096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	39	189	0	ENST00000263967.3:c.1638G>C	p.Gln546His	p.Q546H	ENST00000263967	NM_006218.2	546	caG/caC	10/21	0.451284681262371	4	FACETS	1	0.927	1	0.402	0.336	0.474	CLONAL	1	TRUE	1	0.450746240449298	4		189	208	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219384	1219384	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0067525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	166	649	0	ENST00000326873.7:c.436A>T	p.Lys146Ter	p.K146*	ENST00000326873	NM_000455.4	146	Aag/Tag	3/10	0.451284681262371	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.450746240449298	1		649	523	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591916	48591916	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	318	631	0	ENST00000342988.3:c.1079A>T	p.Asp360Val	p.D360V	ENST00000342988	NM_005359.5	360	gAt/gTt	9/12	0.243458335429794	3	FACETS	1	0.978	1			1	INDETERMINATE	3	TRUE	NA	0.450746240449298	3		631	556	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101008	41101008	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	88	574	0	ENST00000373198.4:c.1348C>T	p.Arg450Ter	p.R450*	ENST00000373198	NM_133170.3	450	Cga/Tga	8/32	0.222472953480626	4	FACETS	0.79	0.7	0.887	0.395	0.35	0.444	INDETERMINATE	1	TRUE	2	0.450746240449298	4		574	717	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217293	66217294	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0067525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	85	530	0	ENST00000273854.3:c.2321_2322del	p.Val774AspfsTer19	p.V774Dfs*19	ENST00000273854	NM_004439.5	774	gTG/g	14/18	1	2	FACETS	0.902	0.802	1	0.902	0.802	1	CLONAL	1	TRUE	1	0.450746240449298	2		530	418	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725040	162725040	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs149052593	NA	P-0067525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	251	666	0	ENST00000367921.3:c.512A>G	p.Asp171Gly	p.D171G	ENST00000367921	NM_006182.2	171	gAc/gGc	6/18	0.313377492729229	4	FACETS	1	0.978	1	0.541	0.509	0.575	CLONAL	2	TRUE	0	0.450746240449298	4		666	746	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419087	419087	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs764882331	NA	P-0067525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	30	617	0	ENST00000399788.2:c.3260A>G	p.Lys1087Arg	p.K1087R	ENST00000399788	NM_001042603.1	1087	aAa/aGa	22/28	0.370751095096054	4	FACETS	0.342	0.274	0.419	0.171	0.137	0.21	SUBCLONAL	1	TRUE	2	0.450746240449298	4		617	565	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415885	49415885	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	91	676	0	ENST00000301067.7:c.16462T>A	p.Phe5488Ile	p.F5488I	ENST00000301067	NM_003482.3	5488	Ttt/Att	53/54	0.370751095096054	4	FACETS	0.745	0.661	0.835	0.373	0.33	0.418	SUBCLONAL	1	TRUE	2	0.450746240449298	4		676	786	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46597072	46597073	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TG	TG	-	novel	NA	P-0067525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	37	458	0	ENST00000263734.3:c.886+2_886+3del		p.X296_splice	ENST00000263734	NM_001430.4	296		7/16	0.27914387183379	4	FACETS	0.46	0.378	0.551	0.23	0.189	0.276	SUBCLONAL	1	TRUE	2	0.450746240449298	4		458	518	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032593	12032594	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0067525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	192	549	0	ENST00000353533.5:c.1030_1031del	p.Val344GlnfsTer8	p.V344Qfs*8	ENST00000353533	NM_003010.3	343	ttTGtc/tttc	9/11	0.381399262131131	3	FACETS	1	0.988	1	0.825	0.773	0.877	CLONAL	2	TRUE	0	0.450746240449298	3		549	422	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143060	30143060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761318889	NA	P-0067525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	253	841	0	ENST00000389048.3:c.466G>A	p.Gly156Arg	p.G156R	ENST00000389048	NM_004304.4	156	Ggg/Agg	1/29	0.27914387183379	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.450746240449298	4		841	793	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880254	37880254	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	176	613	0	ENST00000269571.5:c.2298A>T	p.Glu766Asp	p.E766D	ENST00000269571		766	gaA/gaT	19/27	0.423664800394354	4	FACETS	0.768	0.709	0.829	0.512	0.472	0.553	SUBCLONAL	2	TRUE	1	0.450746240449298	4		613	738	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468000	50468000	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	97	686	0	ENST00000331340.3:c.1235T>A	p.Ile412Asn	p.I412N	ENST00000331340	NM_006060.4	412	aTc/aAc	8/8	0.450746240449298	5	FACETS	0.784	0.698	0.876	0.261	0.232	0.292	SUBCLONAL	1	TRUE	2	0.450746240449298	5		686	920	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336247	73336247	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	149	401	0	ENST00000377767.4:c.2156A>T	p.Lys719Met	p.K719M	ENST00000377767	NM_014953.3	719	aAg/aTg	17/21	0.451284681262371	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	1	0.450746240449298	3		401	389	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662526	227662526	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	257	797	0	ENST00000305123.5:c.929C>A	p.Ala310Asp	p.A310D	ENST00000305123	NM_005544.2	310	gCc/gAc	1/2	0.342567233576535	6	FACETS	1	0.974	1	0.537	0.503	0.572	CLONAL	2	TRUE	2	0.450746240449298	6		797	1010	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045484	47045493	+	frameshift_variant	Frame_Shift_Del	DEL	TGCAGCTGAA	TGCAGCTGAA	-	novel	NA	P-0067525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	220	748	0	ENST00000377604.3:c.2451_2460del	p.Ala819GlufsTer25	p.A819Efs*25	ENST00000377604	NM_001204468.1	817	cgTGCAGCTGAA/cg	22/24	0.378833094089503	2	FACETS	0.833	0.781	0.886	0.833	0.781	0.886	CLONAL	2	TRUE	0	0.450746240449298	2		748	586	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0067530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	81	473	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.328502689846993	2	FACETS	1	0.978	1	0.713	0.637	0.793	CLONAL	1	TRUE	0	0.430154551263385	2		473	264	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0067530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	223	542	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.128952934609082	5	FACETS	0.991	0.93	1			1	INDETERMINATE	3	TRUE	NA	0.430154551263385	5		542	574	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274899	41274899	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	76	450	0	ENST00000349496.5:c.1149G>T	p.Trp383Cys	p.W383C	ENST00000349496	NM_001904.3	383	tgG/tgT	8/15	0.264141739406906	3	FACETS	0.91	0.81	1	0.91	0.81	1	CLONAL	2	TRUE	1	0.430154551263385	3		450	236	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686382	30686382	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	69	567	0	ENST00000295754.5:c.238C>G	p.Pro80Ala	p.P80A	ENST00000295754	NM_003242.5	80	Cca/Gca	2/7	0.264141739406906	3	FACETS	0.837	0.731	0.95	0.418	0.365	0.475	CLONAL	1	TRUE	1	0.430154551263385	3		567	466	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230461114	230461114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779820889	NA	P-0067530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	37	364	1	ENST00000391860.1:c.976G>A	p.Val326Met	p.V326M	ENST00000391860	NM_001258311.1	326	Gtg/Atg	6/7	0.430154551263385	3	FACETS	0.458	0.378	0.549	0.229	0.189	0.275	SUBCLONAL	1	TRUE	1	0.430154551263385	3		365	456	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039417	49039417	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	20	458	0	ENST00000267163.4:c.2402G>C	p.Gly801Ala	p.G801A	ENST00000267163	NM_000321.2	801	gGa/gCa	23/27	0.430154551263385	5	FACETS	0.624	0.478	0.795	0.208	0.159	0.265	SUBCLONAL	1	TRUE	2	0.430154551263385	5		458	245	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754793	29754793	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	56	519	0	ENST00000389048.3:c.1142C>G	p.Pro381Arg	p.P381R	ENST00000389048	NM_004304.4	381	cCa/cGa	4/29	0.130651390472853	3	FACETS	0.766	0.658	0.883	0.383	0.329	0.442	INDETERMINATE	1	TRUE	1	0.430154551263385	3		519	413	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821832	72821832	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	44	558	0	ENST00000268489.5:c.10343G>C	p.Ser3448Thr	p.S3448T	ENST00000268489	NM_006885.3	3448	aGt/aCt	10/10	0.264141739406906	3	FACETS	0.459	0.384	0.541	0.229	0.192	0.271	SUBCLONAL	1	TRUE	1	0.430154551263385	3		558	542	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575157	48575158	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0067530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	29	324	0	ENST00000342988.3:c.353_354dup	p.Phe119ArgfsTer4	p.F119Rfs*4	ENST00000342988	NM_005359.5	117	-/GC	3/12	0.430154551263385	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.430154551263385	1		324	89	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196238	108196239	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCTATACT	novel	NA	P-0067539-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	19	240	0	ENST00000278616.4:c.6775_6782dup	p.Ala2262LeufsTer51	p.A2262Lfs*51	ENST00000278616	NM_000051.3	2258	-/TCTATACT	46/63	1	2	FACETS	0.384	0.292	0.493	0.384	0.292	0.493	SUBCLONAL	1	TRUE	1	0.390699304834972	2		240	253	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	181	586	2	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.992	0.921	1	0.992	0.921	1	CLONAL	1	TRUE	1	0.641334034641133	2		588	569	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	93	397	1	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	1	2	FACETS	0.382	0.339	0.427	0.382	0.339	0.427	SUBCLONAL	1	TRUE	1	0.641334034641133	2		398	760	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	297	545	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.641334034641133	1	FACETS	0.983	0.934	1	0.983	0.934	1	CLONAL	1	TRUE	0	0.641334034641133	1		545	640	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	238	413	1	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	0.641334034641133	1	FACETS	0.92	0.867	0.974	0.92	0.867	0.974	CLONAL	1	TRUE	0	0.641334034641133	1		414	548	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023769	27023769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	117	377	0	ENST00000324856.7:c.879del	p.Thr294ProfsTer69	p.T294Pfs*69	ENST00000324856	NM_006015.4	292	aCc/ac	1/20	1	2	FACETS	0.53	0.478	0.584	0.53	0.478	0.584	SUBCLONAL	1	TRUE	1	0.641334034641133	2		377	689	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874637	35874637	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	185	326	1	ENST00000303115.3:c.799del	p.Arg267GlyfsTer28	p.R267Gfs*28	ENST00000303115	NM_002185.3	265	Aaa/aa	6/8	1	2	FACETS	0.859	0.796	0.923	0.859	0.796	0.923	CLONAL	1	TRUE	1	0.641334034641133	2		327	672	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	177	441	5	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	0.608	0.56	0.658	0.608	0.56	0.658	SUBCLONAL	1	TRUE	1	0.641334034641133	2		446	908	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262742	16262742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769028117	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	263	359	0	ENST00000375759.3:c.10007G>A	p.Arg3336Gln	p.R3336Q	ENST00000375759	NM_015001.2	3336	cGg/cAg	11/15	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.641334034641133	2		359	815	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422959	45422959	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	218	332	1	ENST00000262160.6:c.169C>T	p.Arg57Ter	p.R57*	ENST00000262160	NM_005901.5	57	Cga/Tga	2/11	0.641334034641133	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.641334034641133	1		333	440	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043349	6043349	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781716	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	42	76	0	ENST00000265849.7:c.325del	p.Glu109LysfsTer3	p.E109Kfs*3	ENST00000265849	NM_000535.5	109	Gaa/aa	4/15	1	2	FACETS	0.748	0.634	0.872	0.748	0.634	0.872	SUBCLONAL	1	TRUE	1	0.641334034641133	2		76	175	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262680	16262680	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	220	336	1	ENST00000375759.3:c.9950del	p.Pro3317ArgfsTer83	p.P3317Rfs*83	ENST00000375759	NM_015001.2	3315	caC/ca	11/15	1	2	FACETS	0.911	0.851	0.973	0.911	0.851	0.973	CLONAL	1	TRUE	1	0.641334034641133	2		337	753	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119910	70119910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1297203260	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	251	391	0	ENST00000245479.2:c.916del	p.Val306CysfsTer77	p.V306Cfs*77	ENST00000245479	NM_000346.3	304	ccG/cc	3/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.641334034641133	2		391	739	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752695	42752695	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1366176199	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	224	321	1	ENST00000222329.4:c.1569del	p.Leu525SerfsTer6	p.L525Sfs*6	ENST00000222329	NM_006494.2	523	ggG/gg	4/4	1	2	FACETS	0.916	0.855	0.977	0.916	0.855	0.977	CLONAL	1	TRUE	1	0.641334034641133	2		322	763	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449577	32449577	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1060501253	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	187	340	1	ENST00000332351.3:c.797del	p.Pro266ArgfsTer20	p.P266Rfs*20	ENST00000332351	NM_024426.4	266	cCg/cg	3/10	1	2	FACETS	0.894	0.83	0.961	0.894	0.83	0.961	CLONAL	1	TRUE	1	0.641334034641133	2		341	652	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185545	27185545	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1564083506	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	287	405	0	ENST00000380036.4:c.1250del	p.Pro417LeufsTer10	p.P417Lfs*10	ENST00000380036	NM_000459.3	415	ctC/ct	9/23	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.641334034641133	2		405	871	SUCCESS
APC	324	MSKCC	GRCh37	5	112102099	112102099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750503329	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	106	180	0	ENST00000257430.4:c.212G>A	p.Arg71His	p.R71H	ENST00000257430	NM_000038.5	71	cGt/cAt	3/16	0.641334034641133	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.641334034641133	1		180	222	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478756	57478757	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	44	348	0	ENST00000371085.3:c.348dup	p.Val117ArgfsTer23	p.V117Rfs*23	ENST00000371085	NM_000516.4	114	-/C	5/13	1	2	FACETS	0.169	0.141	0.2	0.169	0.141	0.2	SUBCLONAL	1	TRUE	1	0.641334034641133	2		348	814	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685289	89685289	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554897267	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	171	234	4	ENST00000371953.3:c.188del	p.Asn63ThrfsTer36	p.N63Tfs*36	ENST00000371953	NM_000314.4	62	Aaa/aa	3/9	0.641334034641133	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.641334034641133	1		238	354	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861951	57861951	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564218374	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	241	427	0	ENST00000228682.2:c.1252C>T	p.Arg418Trp	p.R418W	ENST00000228682	NM_005269.2	418	Cgg/Tgg	10/12	1	2	FACETS	0.971	0.91	1	0.971	0.91	1	CLONAL	1	TRUE	1	0.641334034641133	2		427	774	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240069	41240069	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1482440466	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	81	181	1	ENST00000379561.5:c.281T>C	p.Val94Ala	p.V94A	ENST00000379561	NM_002015.3	94	gTg/gCg	1/3	1	2	FACETS	0.692	0.614	0.775	0.692	0.614	0.775	SUBCLONAL	1	TRUE	1	0.641334034641133	2		182	365	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55991439	55991439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424357101	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	211	300	2	ENST00000263923.4:c.22G>A	p.Ala8Thr	p.A8T	ENST00000263923	NM_002253.2	8	Gcc/Acc	1/30	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.641334034641133	2		302	581	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553542	106553542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	237	386	2	ENST00000369096.4:c.1507G>A	p.Ala503Thr	p.A503T	ENST00000369096	NM_001198.3	503	Gcc/Acc	5/7	0.641334034641133	1	FACETS	0.903	0.851	0.956	0.903	0.851	0.956	CLONAL	1	TRUE	0	0.641334034641133	1		388	556	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149498371	149498371	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776607612	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	239	410	0	ENST00000261799.4:c.2843G>A	p.Arg948Gln	p.R948Q	ENST00000261799	NM_002609.3	948	cGg/cAg	21/23	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.641334034641133	2		410	732	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042170	6042170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758561884	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	104	390	0	ENST00000265849.7:c.451C>T	p.Arg151Cys	p.R151C	ENST00000265849	NM_000535.5	151	Cgc/Tgc	5/15	1	2	FACETS	0.403	0.361	0.449	0.403	0.361	0.449	SUBCLONAL	1	TRUE	1	0.641334034641133	2		390	804	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3634841	3634841	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs752736478	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	245	382	0	ENST00000294008.3:c.4668del	p.Val1558CysfsTer3	p.V1558Cfs*3	ENST00000294008	NM_032444.2	1556	ccC/cc	13/15	1	2	FACETS	0.907	0.85	0.966	0.907	0.85	0.966	CLONAL	1	TRUE	1	0.641334034641133	2		382	842	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246658	41246658	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	257	356	3	ENST00000357654.3:c.890T>G	p.Met297Arg	p.M297R	ENST00000357654	NM_007294.3	297	aTg/aGg	10/23	1	2	FACETS	0.997	0.937	1	0.997	0.937	1	CLONAL	1	TRUE	1	0.641334034641133	2		359	804	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103421	2103421	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	179	263	0	ENST00000219476.3:c.304C>G	p.Leu102Val	p.L102V	ENST00000219476	NM_000548.3	102	Ctg/Gtg	4/42	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.641334034641133	2		263	553	SUCCESS
APC	324	MSKCC	GRCh37	5	112176152	112176153	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	273	423	0	ENST00000257430.4:c.4865dup	p.Asn1622LysfsTer10	p.N1622Kfs*10	ENST00000257430	NM_000038.5	1621	caa/cAaa	16/16	0.641334034641133	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.641334034641133	1		423	536	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732930	44732931	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	226	142	0	ENST00000377967.4:c.136_137del	p.Arg46GlyfsTer18	p.R46Gfs*18	ENST00000377967	NM_021140.2	45	GAg/g	1/29	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.641334034641133	1		142	357	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846128	68846128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	128	330	0	ENST00000261769.5:c.1099G>A	p.Asp367Asn	p.D367N	ENST00000261769	NM_004360.3	367	Gac/Aac	8/16	0.641334034641133	1	FACETS	0.573	0.523	0.626	0.573	0.523	0.626	SUBCLONAL	1	TRUE	0	0.641334034641133	1		330	473	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536920	120536920	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	83	311	0	ENST00000229340.5:c.266A>G	p.Asp89Gly	p.D89G	ENST00000229340	NM_006861.6	89	gAc/gGc	4/6	1	2	FACETS	0.379	0.334	0.427	0.379	0.334	0.427	SUBCLONAL	1	TRUE	1	0.641334034641133	2		311	683	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350021	15350021	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	256	367	0	ENST00000263377.2:c.3631A>G	p.Thr1211Ala	p.T1211A	ENST00000263377	NM_058243.2	1211	Acc/Gcc	18/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.641334034641133	2		367	751	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374889	149374889	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	215	325	3	ENST00000360632.3:c.205T>A	p.Ser69Thr	p.S69T	ENST00000360632	NM_015472.4	69	Tcg/Acg	2/7	1	2	FACETS	0.927	0.865	0.991	0.927	0.865	0.991	CLONAL	1	TRUE	1	0.641334034641133	2		328	723	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6222272	6222277	+	inframe_deletion	In_Frame_Del	DEL	AGGAGG	AGGAGG	-	novel	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	245	462	0	ENST00000252674.7:c.965_970del	p.Ser322_Ser323del	p.S322_S323del	ENST00000252674	NM_005934.3	322	tCCTCCTtc/ttc	6/12	1	2	FACETS	0.903	0.846	0.962	0.903	0.846	0.962	CLONAL	1	TRUE	1	0.641334034641133	2		462	846	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618449	37618449	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	292	362	0	ENST00000447079.4:c.125A>G	p.His42Arg	p.H42R	ENST00000447079	NM_015083.1	42	cAc/cGc	1/14	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.641334034641133	2		362	890	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554462	63554462	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	291	445	1	ENST00000307078.5:c.277T>C	p.Tyr93His	p.Y93H	ENST00000307078	NM_004655.3	93	Tac/Cac	2/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.641334034641133	2		446	818	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745708	745708	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	101	306	0	ENST00000314574.4:c.724G>T	p.Glu242Ter	p.E242*	ENST00000314574	NM_005433.3	242	Gaa/Taa	6/12	0.335750415032512	1	FACETS	0.433	0.389	0.48	0.433	0.389	0.48	INDETERMINATE	1	TRUE	0	0.641334034641133	1		306	494	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670439	30670439	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1338281774	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	318	380	0	ENST00000376406.3:c.5993G>A	p.Gly1998Asp	p.G1998D	ENST00000376406	NM_014641.2	1998	gGc/gAc	14/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.641334034641133	2		380	898	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639158	176639158	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	260	429	1	ENST00000439151.2:c.3758T>C	p.Ile1253Thr	p.I1253T	ENST00000439151	NM_022455.4	1253	aTt/aCt	5/23	1	2	FACETS	0.996	0.936	1	0.996	0.936	1	CLONAL	1	TRUE	1	0.641334034641133	2		430	814	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874778	151874778	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	242	350	0	ENST00000262189.6:c.7760A>T	p.Asn2587Ile	p.N2587I	ENST00000262189	NM_170606.2	2587	aAt/aTt	38/59	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.641334034641133	2		350	745	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10785376	10785376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	235	343	2	ENST00000361367.2:c.1144G>A	p.Gly382Ser	p.G382S	ENST00000361367	NM_014633.3	382	Ggc/Agc	9/25	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.641334034641133	2		345	681	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138560	11138560	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	111	382	0	ENST00000358026.2:c.3316A>G	p.Thr1106Ala	p.T1106A	ENST00000358026	NM_001128849.1	1106	Acc/Gcc	24/36	1	2	FACETS	0.424	0.38	0.469	0.424	0.38	0.469	SUBCLONAL	1	TRUE	1	0.641334034641133	2		382	817	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807364	36807364	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750541903	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	198	270	2	ENST00000373129.3:c.1300C>T	p.Arg434Trp	p.R434W	ENST00000373129	NM_032017.1	434	Cgg/Tgg	12/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.641334034641133	2		272	579	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988377	41988377	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	261	335	0	ENST00000219905.7:c.1169A>G	p.Asp390Gly	p.D390G	ENST00000219905	NM_001164273.1	390	gAc/gGc	3/24	0.641334034641133	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.641334034641133	1		335	549	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433549	138433549	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	187	317	0	ENST00000289153.2:c.1063G>A	p.Ala355Thr	p.A355T	ENST00000289153	NM_006219.2	355	Gct/Act	7/22	1	2	FACETS	0.95	0.882	1	0.95	0.882	1	CLONAL	1	TRUE	1	0.641334034641133	2		317	614	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014151	70014151	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	229	393	2	ENST00000394351.3:c.1012A>G	p.Thr338Ala	p.T338A	ENST00000394351	NM_000248.3	338	Aca/Gca	9/9	1	2	FACETS	0.921	0.862	0.983	0.921	0.862	0.983	CLONAL	1	TRUE	1	0.641334034641133	2		395	775	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213930	36213930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756802660	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	147	398	0	ENST00000222270.7:c.2756C>T	p.Pro919Leu	p.P919L	ENST00000222270	NM_014727.1	919	cCg/cTg	6/37	1	2	FACETS	0.572	0.522	0.623	0.572	0.522	0.623	SUBCLONAL	1	TRUE	1	0.641334034641133	2		398	802	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582079	95582079	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	223	388	1	ENST00000393063.1:c.1832del	p.Phe611SerfsTer6	p.F611Sfs*6	ENST00000393063	NM_030621.3	611	tTc/tc	12/28	1	2	FACETS	0.879	0.821	0.939	0.879	0.821	0.939	CLONAL	1	TRUE	1	0.641334034641133	2		389	791	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262460	16262460	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	109	228	1	ENST00000375759.3:c.9729del	p.Thr3244ProfsTer40	p.T3244Pfs*40	ENST00000375759	NM_015001.2	3242	gCc/gc	11/15	1	2	FACETS	0.716	0.646	0.789	0.716	0.646	0.789	SUBCLONAL	1	TRUE	1	0.641334034641133	2		229	475	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388003	31388003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752495145	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	303	352	0	ENST00000328111.2:c.1804G>A	p.Val602Ile	p.V602I	ENST00000328111	NM_006892.3	602	Gtc/Atc	17/23	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.641334034641133	2		352	822	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573678	41573678	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	297	439	1	ENST00000263253.7:c.5963G>T	p.Gly1988Val	p.G1988V	ENST00000263253	NM_001429.3	1988	gGg/gTg	31/31	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.641334034641133	2		440	885	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519118	103519118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774567443	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	190	330	1	ENST00000355739.4:c.2456G>A	p.Arg819Gln	p.R819Q	ENST00000355739	NM_000123.3	819	cGg/cAg	11/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.641334034641133	2		331	566	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676268	37676268	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	243	272	0	ENST00000447079.4:c.3023G>T	p.Arg1008Leu	p.R1008L	ENST00000447079	NM_015083.1	1008	cGg/cTg	11/14	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.641334034641133	2		272	757	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131356	202131356	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	227	329	2	ENST00000358485.4:c.324G>T	p.Gln108His	p.Q108H	ENST00000358485	NM_001080125.1	108	caG/caT	2/9	1	2	FACETS	0.993	0.929	1	0.993	0.929	1	CLONAL	1	TRUE	1	0.641334034641133	2		331	713	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0067542-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	143	264	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.166551800637757	3	FACETS	0.899	0.825	0.975	0.899	0.825	0.975	CLONAL	3	TRUE	0	0.2472009419114	3		264	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882025	NA	P-0067542-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	126	488	0	ENST00000269305.4:c.646G>T	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ttg	6/11	0.229704796765056	2	FACETS	0.909	0.826	0.995	0.909	0.826	0.995	CLONAL	2	TRUE	0	0.2472009419114	2		488	561	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067556-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	30	350	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	FALSE	1	0.306659023697463	2		350	156	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074281	30074281	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067556-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	76	270	0	ENST00000338641.4:c.1544del	p.Lys515SerfsTer7	p.K515Sfs*7	ENST00000338641	NM_000268.3	515	Aag/ag	14/16	0.306659023697463	0	FACETS	1	0.934	1			1	CLONAL	1	FALSE	0	0.306659023697463	0		270	318	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099385	4099385	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067573-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	21	399	0	ENST00000262948.5:c.733T>A	p.Ser245Thr	p.S245T	ENST00000262948	NM_030662.3	245	Tcg/Acg	7/11	1	2	FACETS	0.683	0.528	0.862	0.683	0.528	0.862	SUBCLONAL	1	FALSE	1	0.3	2		399	205	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0067577-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	17	646	0	ENST00000269305.4:c.560-1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		646	357	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	205	350	0				ENST00000310581	NM_198253.2	-/1132			0.220280336807361	5	FACETS	1	0.963	1	1	0.963	1	CLONAL	3	TRUE	2	0.331947754019853	5		350	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	159	539	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.331947754019853	2		539	878	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	542	313	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.331947754019853	6	FACETS	1	0.992	1			1	CLONAL	4	TRUE	NA	0.331947754019853	6		313	1224	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410626	32410626	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	48	432	0	ENST00000332351.3:c.1532C>G	p.Thr511Ser	p.T511S	ENST00000332351	NM_024426.4	511	aCc/aGc	10/10	0.208106879442025	1	FACETS	0.402	0.339	0.471	0.402	0.339	0.471	SUBCLONAL	1	TRUE	0	0.331947754019853	1		432	600	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414212	32414212	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	47	392	0	ENST00000332351.3:c.1339G>A	p.Gly447Ser	p.G447S	ENST00000332351	NM_024426.4	447	Ggt/Agt	8/10	0.208106879442025	1	FACETS	0.457	0.385	0.536	0.457	0.385	0.536	SUBCLONAL	1	TRUE	0	0.331947754019853	1		392	517	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	72	278	0	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.331947754019853	2		278	415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	219	524	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.331947754019853	2		524	887	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873455	45873455	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	205	383	0	ENST00000391945.4:c.41A>G	p.Tyr14Cys	p.Y14C	ENST00000391945	NM_000400.3	14	tAc/tGc	2/23	0.240110020584923	3	FACETS	0.973	0.906	1	0.973	0.906	1	CLONAL	2	TRUE	1	0.331947754019853	3		383	740	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113377	209113377	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	200	406	0	ENST00000345146.2:c.130T>G	p.Leu44Val	p.L44V	ENST00000345146	NM_005896.2	44	Tta/Gta	4/10	0.25673334997296	2	FACETS	0.967	0.901	1	0.967	0.901	1	CLONAL	2	TRUE	0	0.331947754019853	2		406	623	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659979	227659979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1310675277	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	70	533	0	ENST00000305123.5:c.3476C>T	p.Ala1159Val	p.A1159V	ENST00000305123	NM_005544.2	1159	gCc/gTc	1/2	0.25673334997296	2	FACETS	0.564	0.491	0.643	0.282	0.245	0.322	SUBCLONAL	1	TRUE	0	0.331947754019853	2		533	748	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572357	41572357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	85	484	0	ENST00000263253.7:c.4886C>T	p.Ala1629Val	p.A1629V	ENST00000263253	NM_001429.3	1629	gCg/gTg	30/31	1	2	FACETS	0.663	0.585	0.746	0.663	0.585	0.746	SUBCLONAL	1	TRUE	1	0.331947754019853	2		484	773	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391234	89391234	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1317883302	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	56	404	0	ENST00000336596.2:c.1300C>T	p.Gln434Ter	p.Q434*	ENST00000336596	NM_005233.5	434	Cag/Tag	5/17	0.330041009650021	3	FACETS	0.588	0.503	0.681	0.294	0.251	0.341	SUBCLONAL	1	TRUE	1	0.331947754019853	3		404	669	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664864	138664893	+	inframe_deletion	In_Frame_Del	DEL	GCGGCTGCAGCCGCAGCTGCTGCAGCCGCT	GCGGCTGCAGCCGCAGCTGCTGCAGCCGCT	-	rs387906321	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	103	322	0	ENST00000330315.3:c.672_701del	p.Ala225_Ala234del	p.A225_A234del	ENST00000330315	NM_023067.3	224	gcAGCGGCTGCAGCAGCTGCGGCTGCAGCCGCg/gcg	1/1	0.297827247408042	4	FACETS	1	0.98	1	0.699	0.627	0.776	CLONAL	1	TRUE	2	0.331947754019853	4		322	591	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	161	432	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.331947754019853	3	FACETS	0.77	0.708	0.835	0.77	0.708	0.835	SUBCLONAL	2	TRUE	1	0.331947754019853	3		432	734	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958612	38958612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	67	406	0	ENST00000357387.3:c.2353C>T	p.His785Tyr	p.H785Y	ENST00000357387	NM_152756.3	785	Cat/Tat	24/38	0.162816254697133	3	FACETS	0.756	0.656	0.863	0.378	0.328	0.432	INDETERMINATE	1	TRUE	1	0.331947754019853	3		406	623	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845580	151845580	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1287135873	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	46	521	0	ENST00000262189.6:c.13432C>T	p.Arg4478Ter	p.R4478*	ENST00000262189	NM_170606.2	4478	Cga/Tga	52/59	1	2	FACETS	0.355	0.298	0.418	0.355	0.298	0.418	SUBCLONAL	1	TRUE	1	0.331947754019853	2		521	781	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105638	27105650	+	frameshift_variant	Frame_Shift_Del	DEL	TCAGCAAGGTGTC	TCAGCAAGGTGTC	-	novel	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	93	538	0	ENST00000324856.7:c.5250_5262del	p.Phe1750LeufsTer16	p.F1750Lfs*16	ENST00000324856	NM_006015.4	1750	tTCAGCAAGGTGTCt/tt	20/20	0.174353548337445	2	FACETS	0.708	0.629	0.793	0.354	0.314	0.397	INDETERMINATE	1	TRUE	0	0.331947754019853	2		538	791	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699369	117699369	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	285	485	0	ENST00000369458.3:c.272C>G	p.Ser91Trp	p.S91W	ENST00000369458	NM_024626.3	91	tCg/tGg	3/6	0.256096272016273	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.331947754019853	3		485	862	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514337	69514337	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	71	436	0	ENST00000294312.3:c.344A>T	p.Tyr115Phe	p.Y115F	ENST00000294312	NM_005117.2	115	tAc/tTc	3/3	1	2	FACETS	0.689	0.601	0.783	0.689	0.601	0.783	SUBCLONAL	1	TRUE	1	0.331947754019853	2		436	621	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998987	100998987	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	38	458	0	ENST00000325455.5:c.815A>G	p.Asp272Gly	p.D272G	ENST00000325455	NM_001202474.3	272	gAt/gGt	1/8	0.331947754019853	3	FACETS	0.379	0.312	0.454	0.189	0.156	0.227	SUBCLONAL	1	TRUE	1	0.331947754019853	3		458	705	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947630	48947630	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	96	269	0	ENST00000267163.4:c.1215+2T>C		p.X405_splice	ENST00000267163	NM_000321.2	405			1	2	FACETS	0.773	0.695	0.856	1	0.983	1	SUBCLONAL	2	TRUE	1	0.331947754019853	2		269	374	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781240	3781240	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	50	487	0	ENST00000262367.5:c.5125G>A	p.Glu1709Lys	p.E1709K	ENST00000262367	NM_004380.2	1709	Gag/Aag	30/31	0.208106879442025	1	FACETS	0.339	0.287	0.397	0.339	0.287	0.397	SUBCLONAL	1	TRUE	0	0.331947754019853	1		487	741	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828062	3828062	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375125948	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	67	462	0	ENST00000262367.5:c.2063C>T	p.Pro688Leu	p.P688L	ENST00000262367	NM_004380.2	688	cCg/cTg	10/31	0.208106879442025	1	FACETS	0.521	0.453	0.595	0.521	0.453	0.595	SUBCLONAL	1	TRUE	0	0.331947754019853	1		462	646	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679593	33679593	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	155	528	0	ENST00000308377.4:c.2488A>G	p.Met830Val	p.M830V	ENST00000308377	NM_152270.3	830	Atg/Gtg	5/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.331947754019853	2		528	815	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732339	74732339	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	79	539	0	ENST00000359995.5:c.570G>C	p.Arg190Ser	p.R190S	ENST00000359995	NM_001195427.1	190	agG/agC	2/3	0.240110020584923	3	FACETS	0.599	0.525	0.678	0.299	0.262	0.339	SUBCLONAL	1	TRUE	1	0.331947754019853	3		539	927	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288477	15288477	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	104	385	0	ENST00000263388.2:c.4262T>A	p.Val1421Glu	p.V1421E	ENST00000263388	NM_000435.2	1421	gTg/gAg	24/33	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.331947754019853	2		385	557	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051199	128051199	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	164	484	0	ENST00000285398.2:c.124G>C	p.Ala42Pro	p.A42P	ENST00000285398	NM_000122.1	42	Gcg/Ccg	2/15	0.208106879442025	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.331947754019853	1		484	660	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660634	190660634	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	58	440	0	ENST00000441310.2:c.272G>T	p.Gly91Val	p.G91V	ENST00000441310	NM_000534.4	91	gGt/gTt	3/13	NA	2	FACETS	0.516	0.443	0.596			1	INDETERMINATE	1	TRUE	NA	0.331947754019853	2		440	677	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548234	41548234	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	44	473	1	ENST00000263253.7:c.3022G>T	p.Glu1008Ter	p.E1008*	ENST00000263253	NM_001429.3	1008	Gaa/Taa	16/31	1	2	FACETS	0.386	0.323	0.457	0.386	0.323	0.457	SUBCLONAL	1	TRUE	1	0.331947754019853	2		474	686	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143043290	143043290	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	59	341	0	ENST00000262992.4:c.2126C>T	p.Thr709Ile	p.T709I	ENST00000262992	NM_001101669.1	709	aCa/aTa	19/24	1	2	FACETS	0.648	0.557	0.746	0.648	0.557	0.746	SUBCLONAL	1	TRUE	1	0.331947754019853	2		341	549	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111794	56111794	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	88	305	0	ENST00000399503.3:c.394G>T	p.Asp132Tyr	p.D132Y	ENST00000399503	NM_005921.1	132	Gac/Tac	1/20	0.208106879442025	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.331947754019853	1		305	398	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271294	26271294	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	112	634	0	ENST00000305910.3:c.319G>T	p.Asp107Tyr	p.D107Y	ENST00000305910	NM_003534.2	107	Gat/Tat	1/1	0.331947754019853	3	FACETS	0.783	0.703	0.868	0.391	0.351	0.434	SUBCLONAL	1	TRUE	1	0.331947754019853	3		634	1005	SUCCESS
MET	4233	MSKCC	GRCh37	7	116422059	116422059	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	29	336	0	ENST00000397752.3:c.3540T>A	p.Asp1180Glu	p.D1180E	ENST00000397752	NM_000245.2	1180	gaT/gaA	18/21	1	2	FACETS	0.325	0.26	0.4	0.325	0.26	0.4	SUBCLONAL	1	TRUE	1	0.331947754019853	2		336	537	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341532	70341532	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067579-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	69	286	0	ENST00000374080.3:c.967C>T	p.Gln323Ter	p.Q323*	ENST00000374080		323	Cag/Tag	7/45	1	1	FACETS	0.867	0.758	0.983	0.867	0.758	0.983	CLONAL	1	TRUE	0	0.331947754019853	1		286	400	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0067599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	356	471	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.460968447259807	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.46720440477517	2		471	689	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	281	418	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	0.460968447259807	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.46720440477517	2		418	573	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057627	180057627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756234174	NA	P-0067599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	191	460	0	ENST00000261937.6:c.328G>A	p.Val110Ile	p.V110I	ENST00000261937	NM_182925.4	110	Gtc/Atc	3/30	0.46720440477517	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.46720440477517	1		460	480	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077558	30077558	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	85	391	0	ENST00000338641.4:c.1705G>A	p.Gly569Ser	p.G569S	ENST00000338641	NM_000268.3	569	Ggt/Agt	15/16	0.46720440477517	1	FACETS	0.591	0.524	0.662	0.591	0.524	0.662	SUBCLONAL	1	TRUE	0	0.46720440477517	1		391	472	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333991	70333993	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	rs903550402	NA	P-0067599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	51	372	0	ENST00000373644.4:c.1902_1904del	p.Val635del	p.V635del	ENST00000373644	NM_030625.2	632	tcTGTt/tct	2/12	0.319971024014273	1	FACETS	0.334	0.284	0.389	0.334	0.284	0.389	SUBCLONAL	1	TRUE	0	0.46720440477517	1		372	501	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500768	8500768	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757479150	NA	P-0067599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	130	368	0	ENST00000356435.5:c.2114G>A	p.Arg705Gln	p.R705Q	ENST00000356435		705	cGa/cAa	13/35	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.46720440477517	2		368	503	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500758	8500758	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	103	372	0	ENST00000356435.5:c.2124A>T	p.Glu708Asp	p.E708D	ENST00000356435		708	gaA/gaT	13/35	1	2	FACETS	0.932	0.838	1	0.932	0.838	1	CLONAL	1	TRUE	1	0.46720440477517	2		372	473	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21350151	21350151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780915875	NA	P-0067599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	114	471	0	ENST00000215739.8:c.2059G>A	p.Ala687Thr	p.A687T	ENST00000215739	NM_006767.3	687	Gcc/Acc	17/21	0.32395290140338	0	FACETS	0.557	0.504	0.612			1	SUBCLONAL	1	TRUE	0	0.46720440477517	0		471	467	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39575887	39575887	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	99	319	0	ENST00000262039.4:c.820G>T	p.Ala274Ser	p.A274S	ENST00000262039	NM_002647.2	274	Gcc/Tcc	8/25	0.205260569266317	1	FACETS	0.695	0.624	0.771	0.695	0.624	0.771	INDETERMINATE	1	TRUE	0	0.46720440477517	1		319	467	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813351	102813351	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	38	433	0	ENST00000307046.8:c.338A>C	p.Lys113Thr	p.K113T	ENST00000307046	NM_001111285.1	113	aAg/aCg	3/4	0.460968447259807	2	FACETS	0.262	0.216	0.314	0.131	0.108	0.157	SUBCLONAL	1	TRUE	0	0.46720440477517	2		433	621	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979330	93979330	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	31	393	0	ENST00000369303.4:c.1498G>T	p.Ala500Ser	p.A500S	ENST00000369303	NM_004440.3	500	Gcc/Tcc	7/17	0.232530942894771	3	FACETS	0.376	0.304	0.458	0.188	0.152	0.229	INDETERMINATE	1	TRUE	1	0.46720440477517	3		393	435	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0067599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	58	411	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.185642938060377	3	FACETS	0.562	0.482	0.65	0.187	0.16	0.217	INDETERMINATE	1	TRUE	0	0.33983941420185	3		411	710	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197834	123197834	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0067599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	45	228	0	ENST00000218089.9:c.1958C>G	p.Ser653Ter	p.S653*	ENST00000218089	NM_001042749.1	653	tCa/tGa	20/35	0.33983941420185	1	FACETS	0.44	0.369	0.517	0.44	0.369	0.517	SUBCLONAL	1	TRUE	0	0.33983941420185	1		228	500	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271747	15271747	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs773656789	NA	P-0067599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	69	461	0	ENST00000263388.2:c.6692del	p.Pro2231GlnfsTer15	p.P2231Qfs*15	ENST00000263388	NM_000435.2	2231	cCa/ca	33/33	1	2	FACETS	0.501	0.435	0.572	0.501	0.435	0.572	SUBCLONAL	1	TRUE	1	0.33983941420185	2		461	811	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714387	40714387	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	107	353	0	ENST00000373198.4:c.4010G>T	p.Arg1337Leu	p.R1337L	ENST00000373198	NM_133170.3	1337	cGc/cTc	29/32	0.235342971512674	1	FACETS	0.749	0.672	0.83	0.749	0.672	0.83	SUBCLONAL	1	TRUE	0	0.33983941420185	1		353	698	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796223	45796223	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781668	NA	P-0067599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	71	269	0	ENST00000450313.1:c.1483C>T	p.Arg495Cys	p.R495C	ENST00000450313	NM_012222.2	495	Cgt/Tgt	15/16	0.21395188598396	1	FACETS	0.564	0.492	0.641	0.564	0.492	0.641	SUBCLONAL	1	TRUE	0	0.33983941420185	1		269	615	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257668	16257668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs541126378	NA	P-0067599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	64	385	0	ENST00000375759.3:c.4933G>A	p.Val1645Ile	p.V1645I	ENST00000375759	NM_015001.2	1645	Gta/Ata	11/15	0.21395188598396	1	FACETS	0.413	0.357	0.474	0.413	0.357	0.474	SUBCLONAL	1	TRUE	0	0.33983941420185	1		385	757	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0067599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	120	459	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.189738687728044	3	FACETS	0.777	0.704	0.852	0.777	0.704	0.852	INDETERMINATE	2	TRUE	1	0.33983941420185	3		459	532	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230486756	230486756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375905173	NA	P-0067599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	52	313	0	ENST00000391860.1:c.497G>A	p.Arg166Gln	p.R166Q	ENST00000391860	NM_001258311.1	166	cGg/cAg	3/7	0.269331401608482	3	FACETS	0.466	0.395	0.543	0.155	0.131	0.181	SUBCLONAL	1	TRUE	0	0.33983941420185	3		313	769	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992384	72992384	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1006215604	NA	P-0067599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	71	376	0	ENST00000268489.5:c.1661C>G	p.Ser554Cys	p.S554C	ENST00000268489	NM_006885.3	554	tCt/tGt	2/10	1	2	FACETS	0.541	0.472	0.617	0.541	0.472	0.617	SUBCLONAL	1	TRUE	1	0.33983941420185	2		376	772	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649054	37649054	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	169	304	0	ENST00000447079.4:c.2159G>T	p.Gly720Val	p.G720V	ENST00000447079	NM_015083.1	720	gGg/gTg	4/14	0.189738687728044	3	FACETS	0.804	0.741	0.869	0.804	0.741	0.869	INDETERMINATE	2	TRUE	1	0.33983941420185	3		304	724	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446637	29446637	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	51	359	0	ENST00000544604.2:c.2468G>T	p.Arg823Leu	p.R823L	ENST00000544604	NM_001206998.1	823	cGg/cTg	8/9	0.21395188598396	1	FACETS	0.406	0.344	0.473	0.406	0.344	0.473	SUBCLONAL	1	TRUE	0	0.33983941420185	1		359	614	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743858	40743858	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	91	275	0	ENST00000373198.4:c.3137G>T	p.Arg1046Leu	p.R1046L	ENST00000373198	NM_133170.3	1046	cGc/cTc	23/32	0.235342971512674	1	FACETS	0.836	0.744	0.933	0.836	0.744	0.933	CLONAL	1	TRUE	0	0.33983941420185	1		275	532	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643821	38643821	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	49	335	0	ENST00000299084.4:c.1291G>T	p.Glu431Ter	p.E431*	ENST00000299084	NM_152594.2	431	Gag/Tag	7/7	0.33983941420185	1	FACETS	0.424	0.358	0.496	0.424	0.358	0.496	SUBCLONAL	1	TRUE	0	0.33983941420185	1		335	565	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31448715	31448716	+	splice_acceptor_variant	Splice_Site	DNP	CT	CT	TA	novel	NA	P-0067599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	182	235	2	ENST00000344624.3:c.2822-2_2822-1delinsTA		p.X941_splice	ENST00000344624		941			0.185642938060377	3	FACETS	0.923	0.854	0.993	0.615	0.569	0.662	INDETERMINATE	2	TRUE	0	0.33983941420185	3		237	679	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20153892	20153892	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	38	166	0	ENST00000379607.5:c.168G>C	p.Lys56Asn	p.K56N	ENST00000379607	NM_001412.3	56	aaG/aaC	3/7	0.33983941420185	1	FACETS	0.436	0.36	0.52	0.436	0.36	0.52	SUBCLONAL	1	TRUE	0	0.33983941420185	1		166	426	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075179	16075179	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	49	323	0	ENST00000268712.3:c.373G>A	p.Ala125Thr	p.A125T	ENST00000268712	NM_006311.3	125	Gcg/Acg	4/46	0.240936786542044	1	FACETS	0.396	0.335	0.464	0.396	0.335	0.464	SUBCLONAL	1	TRUE	0	0.33983941420185	1		323	604	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781307	9781307	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0067599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	46	324	0	ENST00000377346.4:c.1811+1G>A		p.X604_splice	ENST00000377346	NM_005026.3	604			0.21395188598396	1	FACETS	0.462	0.389	0.543	0.462	0.389	0.543	SUBCLONAL	1	TRUE	0	0.33983941420185	1		324	486	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034479	47034479	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	95	277	0	ENST00000377604.3:c.565del	p.Glu189LysfsTer77	p.E189Kfs*77	ENST00000377604	NM_001204468.1	188	atG/at	6/24	0.33983941420185	1	FACETS	0.871	0.778	0.969	0.871	0.778	0.969	CLONAL	1	TRUE	0	0.33983941420185	1		277	533	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753671	42753671	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	70	415	0	ENST00000222329.4:c.593A>T	p.Glu198Val	p.E198V	ENST00000222329	NM_006494.2	198	gAa/gTa	4/4	1	2	FACETS	0.505	0.439	0.576	0.505	0.439	0.576	SUBCLONAL	1	TRUE	1	0.33983941420185	2		415	816	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	124	385	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.998	0.91	1	0.998	0.91	1	CLONAL	1	TRUE	1	0.586327152956765	2		385	424	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	45	150	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.919	0.785	1	0.919	0.785	1	CLONAL	1	TRUE	1	0.586327152956765	2		150	167	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	148	418	2	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.586327152956765	2		420	494	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	157	470	5	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.586327152956765	2		475	534	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	135	351	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.586327152956765	2		351	404	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	25	450	0	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	0.586327152956765	1	FACETS	0.192	0.151	0.239	0.192	0.151	0.239	SUBCLONAL	1	TRUE	0	0.586327152956765	1		450	314	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033844	49033844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853294	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	126	333	0	ENST00000267163.4:c.1981C>T	p.Arg661Trp	p.R661W	ENST00000267163	NM_000321.2	661	Cgg/Tgg	20/27	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.586327152956765	2		333	404	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230461114	230461114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779820889	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	93	364	1	ENST00000391860.1:c.976G>A	p.Val326Met	p.V326M	ENST00000391860	NM_001258311.1	326	Gtg/Atg	6/7	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.586327152956765	2		365	307	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	158	429	0	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.586327152956765	2		429	505	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	25	255	2	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	2	FACETS	0.508	0.404	0.625	0.508	0.404	0.625	SUBCLONAL	1	TRUE	1	0.586327152956765	2		257	168	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645687	12645687	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397516828	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	153	366	0	ENST00000251849.4:c.782C>G	p.Pro261Arg	p.P261R	ENST00000251849	NM_002880.3	261	cCt/cGt	7/17	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.586327152956765	2		366	467	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040642	16040642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	114	318	0	ENST00000268712.3:c.1492C>T	p.Arg498Cys	p.R498C	ENST00000268712	NM_006311.3	498	Cgc/Tgc	14/46	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.586327152956765	2		318	366	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257789	133257789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143626223	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	144	397	0	ENST00000320574.5:c.139C>T	p.Arg47Trp	p.R47W	ENST00000320574	NM_006231.2	47	Cgg/Tgg	2/49	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.586327152956765	2		397	408	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430936	181430936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	150	514	0	ENST00000325404.1:c.788C>T	p.Ala263Val	p.A263V	ENST00000325404	NM_003106.3	263	gCg/gTg	1/1	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.586327152956765	2		514	461	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521975	157521975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144424476	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	189	471	0	ENST00000346085.5:c.4247G>A	p.Arg1416His	p.R1416H	ENST00000346085	NM_020732.3	1416	cGc/cAc	18/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.586327152956765	2		471	505	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717712	89717712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782350	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	122	301	0	ENST00000371953.3:c.737C>T	p.Pro246Leu	p.P246L	ENST00000371953	NM_000314.4	246	cCg/cTg	7/9	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.586327152956765	2		301	357	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692900	89692900	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	90	258	0	ENST00000371953.3:c.384G>T	p.Lys128Asn	p.K128N	ENST00000371953	NM_000314.4	128	aaG/aaT	5/9	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.586327152956765	2		258	289	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380338	14380339	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCCCACGCC	novel	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	106	362	0	ENST00000256196.4:c.70_78dup	p.Gly24_Gly26dup	p.G24_G26dup	ENST00000256196		24	-/GGCGTGGGC	1/6	1	2	FACETS	0.942	0.851	1	0.942	0.851	1	CLONAL	1	TRUE	1	0.586327152956765	2		362	384	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350753	89350753	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886041791	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	122	432	0	ENST00000301030.4:c.2197C>T	p.Arg733Ter	p.R733*	ENST00000301030	NM_001256183.1	733	Cga/Tga	9/13	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.586327152956765	2		432	388	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220027	5220027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202004674	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	140	460	1	ENST00000357368.4:c.3688G>A	p.Gly1230Ser	p.G1230S	ENST00000357368	NM_002850.3	1230	Ggc/Agc	22/38	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.586327152956765	2		461	396	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048156	180048156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747033940	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	130	481	0	ENST00000261937.6:c.2117C>T	p.Ala706Val	p.A706V	ENST00000261937	NM_182925.4	706	gCg/gTg	14/30	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.586327152956765	2		481	411	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087486	27087487	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	126	490	0	ENST00000324856.7:c.2060_2061insA	p.His688SerfsTer129	p.H688Sfs*129	ENST00000324856	NM_006015.4	687	cct/ccAt	5/20	0.586327152956765	1	FACETS	0.873	0.8	0.947	0.873	0.8	0.947	CLONAL	1	TRUE	0	0.586327152956765	1		490	348	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109843	115109843	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751621934	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	136	449	0	ENST00000257566.3:c.2035G>A	p.Ala679Thr	p.A679T	ENST00000257566	NM_016569.3	679	Gcc/Acc	8/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.586327152956765	2		449	410	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986526	36986526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	138	498	1	ENST00000354822.5:c.1163G>A	p.Gly388Asp	p.G388D	ENST00000354822	NM_001079668.2	388	gGc/gAc	3/3	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.586327152956765	2		499	431	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998081	169998081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138560118	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	138	305	0	ENST00000295797.4:c.772C>T	p.Arg258Trp	p.R258W	ENST00000295797	NM_002740.5	258	Cgg/Tgg	9/18	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.586327152956765	2		305	392	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551951	150551951	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1490867890	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	137	416	0	ENST00000369026.2:c.56C>G	p.Ala19Gly	p.A19G	ENST00000369026	NM_021960.4	19	gCc/gGc	1/3	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.586327152956765	2		416	423	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47503884	47503884	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	111	386	0	ENST00000404338.3:c.4444del	p.Gln1482SerfsTer317	p.Q1482Sfs*317	ENST00000404338	NM_004491.4	1480	aCc/ac	6/6	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.586327152956765	2		386	370	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920141	1920141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1211896693	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	140	453	0	ENST00000382891.5:c.1201C>T	p.Arg401Trp	p.R401W	ENST00000382891	NM_133335.3	401	Cgg/Tgg	5/22	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.586327152956765	2		453	473	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230492905	230492905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs534656022	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	142	423	0	ENST00000391860.1:c.149C>T	p.Thr50Met	p.T50M	ENST00000391860	NM_001258311.1	50	aCg/aTg	2/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.586327152956765	2		423	417	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185195174	185195174	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	113	345	0	ENST00000265026.3:c.2491C>T	p.Arg831Ter	p.R831*	ENST00000265026	NM_004721.4	831	Cga/Tga	12/14	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.586327152956765	2		345	367	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94923007	94923007	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	84	369	0	ENST00000536441.1:c.461del	p.Asn154IlefsTer9	p.N154Ifs*9	ENST00000536441	NM_144665.3	154	aAt/at	4/10	1	2	FACETS	0.779	0.693	0.869	0.779	0.693	0.869	SUBCLONAL	1	TRUE	1	0.586327152956765	2		369	368	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003839	57003839	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	76	438	0	ENST00000257254.3:c.640T>G	p.Phe214Val	p.F214V	ENST00000257254		214	Ttc/Gtc	1/2	1	2	FACETS	0.564	0.496	0.636	0.564	0.496	0.636	SUBCLONAL	1	TRUE	1	0.586327152956765	2		438	460	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511661	66511661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356757839	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	143	372	1	ENST00000358598.2:c.121G>A	p.Ala41Thr	p.A41T	ENST00000358598	NM_212471.2	41	Gct/Act	2/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.586327152956765	2		373	392	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344128	70344128	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	128	363	0	ENST00000374080.3:c.1864G>T	p.Gly622Trp	p.G622W	ENST00000374080		622	Ggg/Tgg	13/45	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.586327152956765	2		363	383	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295123	15295123	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1343309010	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	22	402	0	ENST00000263388.2:c.2549T>C	p.Ile850Thr	p.I850T	ENST00000263388	NM_000435.2	850	aTc/aCc	16/33	1	2	FACETS	0.191	0.147	0.242	0.191	0.147	0.242	SUBCLONAL	1	TRUE	1	0.586327152956765	2		402	393	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919710	96919710	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	129	344	0	ENST00000258439.3:c.553G>T	p.Gly185Ter	p.G185*	ENST00000258439	NM_001193304.2	185	Gga/Tga	4/4	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.586327152956765	2		344	403	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836582	89836582	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1354855145	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	145	474	0	ENST00000389301.3:c.2308C>T	p.Arg770Cys	p.R770C	ENST00000389301	NM_000135.2	770	Cgt/Tgt	25/43	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.586327152956765	2		474	439	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742649	39742649	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	155	391	0	ENST00000361337.2:c.1492A>T	p.Thr498Ser	p.T498S	ENST00000361337	NM_003286.2	498	Aca/Tca	15/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.586327152956765	2		391	461	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200146	128200146	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	111	400	1	ENST00000341105.2:c.1159A>G	p.Thr387Ala	p.T387A	ENST00000341105	NM_032638.4	387	Acc/Gcc	6/6	1	2	FACETS	0.893	0.809	0.981	0.893	0.809	0.981	CLONAL	1	TRUE	1	0.586327152956765	2		401	424	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286823	33286823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143737807	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	146	541	1	ENST00000374542.5:c.2114G>A	p.Arg705Gln	p.R705Q	ENST00000374542	NM_001141970.1	705	cGg/cAg	7/8	1	2	FACETS	0.992	0.912	1	0.992	0.912	1	CLONAL	1	TRUE	1	0.586327152956765	2		542	502	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984859	72984859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756019082	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	134	413	0	ENST00000268489.5:c.2725G>A	p.Gly909Ser	p.G909S	ENST00000268489	NM_006885.3	909	Ggt/Agt	3/10	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.586327152956765	2		413	444	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411908	63411908	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	175	520	0	ENST00000330258.3:c.1259A>T	p.Asn420Ile	p.N420I	ENST00000330258	NM_152424.3	420	aAt/aTt	2/2	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.586327152956765	2		520	494	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215324	5215324	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	143	440	0	ENST00000357368.4:c.4294C>T	p.Arg1432Cys	p.R1432C	ENST00000357368	NM_002850.3	1432	Cgt/Tgt	28/38	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.586327152956765	2		440	437	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134159	41134159	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140386357	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	153	421	0	ENST00000379561.5:c.1469G>A	p.Arg490Gln	p.R490Q	ENST00000379561	NM_002015.3	490	cGg/cAg	2/3	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.586327152956765	2		421	477	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527374	157527374	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs149841055	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	133	409	0	ENST00000346085.5:c.5099A>G	p.Glu1700Gly	p.E1700G	ENST00000346085	NM_020732.3	1700	gAa/gGa	20/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.586327152956765	2		409	387	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416212	416212	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs753142023	NA	P-0067603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	151	425	0	ENST00000399788.2:c.3974T>C	p.Val1325Ala	p.V1325A	ENST00000399788	NM_001042603.1	1325	gTg/gCg	24/28	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.586327152956765	2		425	474	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0067609-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	108	459	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.300637980048966	3	FACETS	0.904	0.816	0.996	0.904	0.816	0.996	CLONAL	2	TRUE	1	0.3	3		459	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057519990	NA	P-0067609-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	174	533	1	ENST00000269305.4:c.796G>T	p.Gly266Ter	p.G266*	ENST00000269305	NM_001126112.2	266	Gga/Tga	8/11	0.300637980048966	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.3	2		534	534	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911593	114911593	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067609-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	154	509	0	ENST00000543371.1:c.1111G>T	p.Glu371Ter	p.E371*	ENST00000543371	NM_001198531.1	371	Gag/Tag	10/14	0.2325990751857	3	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	1	0.3	3		509	577	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61322931	61322931	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067609-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	58	319	0	ENST00000283752.5:c.1133C>A	p.Thr378Asn	p.T378N	ENST00000283752	NM_006919.2	378	aCc/aAc	8/8	0.300637980048966	2	FACETS	1	0.962	1	0.671	0.581	0.768	CLONAL	1	TRUE	0	0.3	2		319	288	SUCCESS
APC	324	MSKCC	GRCh37	5	112175248	112175255	+	frameshift_variant	Frame_Shift_Del	DEL	TGTGAGCG	TGTGAGCG	-	novel	NA	P-0067609-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	218	523	1	ENST00000257430.4:c.3957_3964del	p.Val1320SerfsTer9	p.V1320Sfs*9	ENST00000257430	NM_000038.5	1319	ccTGTGAGCGaa/ccaa	16/16	0.294449014153101	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	3	TRUE	0	0.3	3		524	541	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0067611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	129	306	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		306	307	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717715	89717716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587782341	NA	P-0067611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	138	304	0	ENST00000371953.3:c.741dup	p.Pro248ThrfsTer5	p.P248Tfs*5	ENST00000371953	NM_000314.4	247	tta/ttAa	7/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		304	361	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057773	27057774	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	126	544	0	ENST00000324856.7:c.1482dup	p.His495SerfsTer128	p.H495Sfs*128	ENST00000324856	NM_006015.4	494	cct/ccTt	3/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		544	333	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183864	10183864	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	25	467	0	ENST00000256474.2:c.333del	p.Tyr112ThrfsTer47	p.Y112Tfs*47	ENST00000256474	NM_000551.3	111	agC/ag	1/3	1	2	FACETS	0.845	0.668	1	0.845	0.668	1	CLONAL	1	FALSE	1	0.227531115361396	2		467	260	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240738	53240738	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	32	208	0	ENST00000375401.3:c.1342G>T	p.Glu448Ter	p.E448*	ENST00000375401	NM_004187.3	448	Gaa/Taa	10/26	1	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	0	0.227531115361396	1		208	169	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	211	350	0				ENST00000310581	NM_198253.2	-/1132			0.353344589762817	8	FACETS	1	0.971	1	1	0.971	1	CLONAL	7	TRUE	1	0.353344589762817	8		350	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	243	559	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.353344589762817	3	FACETS	1	0.977	1	1	0.994	1	CLONAL	4	TRUE	0	0.353344589762817	3		559	388	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0067614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	107	268	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.353344589762817	6	FACETS	1	0.922	1	1	0.922	1	CLONAL	4	TRUE	2	0.353344589762817	6		268	256	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030486	49030486	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0067614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	105	405	0	ENST00000267163.4:c.1960+1G>A		p.X654_splice	ENST00000267163	NM_000321.2	654			0.353344589762817	1	FACETS	1	0.981	1	1	0.991	1	CLONAL	2	TRUE	0	0.353344589762817	1		405	198	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215674233	215674233	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs864622206	NA	P-0067614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	77	367	0	ENST00000260947.4:c.61C>G	p.Arg21Gly	p.R21G	ENST00000260947	NM_000465.2	21	Cgt/Ggt	1/11	1	2	FACETS	0.861	0.767	0.96	1	0.982	1	CLONAL	2	TRUE	1	0.353344589762817	2		367	253	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059176	27059176	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	112	336	0	ENST00000324856.7:c.1813C>T	p.Gln605Ter	p.Q605*	ENST00000324856	NM_006015.4	605	Caa/Taa	4/20	0.353344589762817	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.353344589762817	3		336	309	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917056	50917056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	129	579	0	ENST00000440232.2:c.2308G>A	p.Glu770Lys	p.E770K	ENST00000440232	NM_002691.3	770	Gag/Aag	19/27	0.317870753499349	3	FACETS	0.889	0.818	0.962	0.889	0.818	0.962	CLONAL	3	TRUE	0	0.353344589762817	3		579	322	SUCCESS
RET	5979	MSKCC	GRCh37	10	43572711	43572711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	34	371	0	ENST00000355710.3:c.5C>T	p.Ala2Val	p.A2V	ENST00000355710	NM_020975.4	2	gCg/gTg	1/20	NA	2	FACETS	0.819	0.674	0.98			1	INDETERMINATE	1	TRUE	NA	0.353344589762817	2		371	235	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641147	117641147	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370269692	NA	P-0067614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	42	595	0	ENST00000368508.3:c.5824C>T	p.Arg1942Trp	p.R1942W	ENST00000368508	NM_002944.2	1942	Cgg/Tgg	36/43	0.353344589762817	3	FACETS	0.553	0.461	0.655	0.276	0.23	0.328	SUBCLONAL	1	TRUE	1	0.353344589762817	3		595	506	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511274	157511274	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	104	508	0	ENST00000346085.5:c.3792G>C	p.Met1264Ile	p.M1264I	ENST00000346085	NM_020732.3	1264	atG/atC	15/20	0.353344589762817	3	FACETS	1	0.979	1	0.683	0.614	0.756	CLONAL	1	TRUE	1	0.353344589762817	3		508	507	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2115634	2115634	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	70	426	0	ENST00000219476.3:c.1714C>T	p.Gln572Ter	p.Q572*	ENST00000219476	NM_000548.3	572	Cag/Tag	16/42	0.296100977005635	4	FACETS	1	0.967	1	0.441	0.386	0.5	CLONAL	1	TRUE	1	0.353344589762817	4		426	405	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372495	118372495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	99	550	0	ENST00000534358.1:c.6428C>T	p.Ser2143Leu	p.S2143L	ENST00000534358	NM_005933.3	2143	tCa/tTa	26/36	1	2	FACETS	0.81	0.73	0.893	1	0.985	1	CLONAL	2	TRUE	1	0.353344589762817	2		550	346	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451413	70451413	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	100	490	0	ENST00000373644.4:c.6253G>C	p.Asp2085His	p.D2085H	ENST00000373644	NM_030625.2	2085	Gac/Cac	12/12	0.353344589762817	3	FACETS	0.814	0.732	0.9	0.814	0.732	0.9	CLONAL	2	TRUE	1	0.353344589762817	3		490	409	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858147	9858147	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	21	518	0	ENST00000330684.3:c.3254A>C	p.Asn1085Thr	p.N1085T	ENST00000330684	NM_001134407.1	1085	aAc/aCc	13/13	0.296100977005635	4	FACETS	0.421	0.324	0.535	0.14	0.108	0.179	SUBCLONAL	1	TRUE	1	0.353344589762817	4		518	382	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6214028	6214028	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1285224641	NA	P-0067614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	18	433	0	ENST00000252674.7:c.1329G>C	p.Glu443Asp	p.E443D	ENST00000252674	NM_005934.3	443	gaG/gaC	9/12	0.317870753499349	3	FACETS	0.472	0.356	0.609	0.157	0.118	0.203	SUBCLONAL	1	TRUE	0	0.353344589762817	3		433	254	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22008871	22008871	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	85	473	0	ENST00000276925.6:c.82G>C	p.Glu28Gln	p.E28Q	ENST00000276925	NM_004936.3	28	Gag/Cag	1/2	0.174089336005536	4	FACETS	1	0.965	1	0.617	0.546	0.691	INDETERMINATE	1	TRUE	2	0.353344589762817	4		473	528	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158390	108158390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	30	412	0	ENST00000278616.4:c.4057G>A	p.Glu1353Lys	p.E1353K	ENST00000278616	NM_000051.3	1353	Gag/Aag	27/63	1	2	FACETS	0.832	0.676	1	0.832	0.676	1	CLONAL	1	TRUE	1	0.353344589762817	2		412	204	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346796	89346796	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	59	519	0	ENST00000301030.4:c.6154G>T	p.Glu2052Ter	p.E2052*	ENST00000301030	NM_001256183.1	2052	Gag/Tag	9/13	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.353344589762817	2		519	265	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31485039	31485039	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	273	367	0	ENST00000344624.3:c.1945del	p.Ser649HisfsTer38	p.S649Hfs*38	ENST00000344624		649	Tca/ca	12/33	0.353344589762817	8	FACETS	0.945	0.9	0.99	0.945	0.9	0.99	CLONAL	7	TRUE	1	0.353344589762817	8		367	481	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89828361	89828361	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	57	278	0	ENST00000389301.3:c.2848G>A	p.Glu950Lys	p.E950K	ENST00000389301	NM_000135.2	950	Gaa/Aaa	29/43	1	2	FACETS	0.906	0.792	1	1	0.978	1	CLONAL	2	TRUE	1	0.353344589762817	2		278	178	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532463	63532463	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	77	558	0	ENST00000307078.5:c.2116G>C	p.Glu706Gln	p.E706Q	ENST00000307078	NM_004655.3	706	Gag/Cag	8/11	0.353344589762817	3	FACETS	1	0.961	1	0.405	0.357	0.456	CLONAL	1	TRUE	0	0.353344589762817	3		558	422	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641293	12641293	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	41	426	0	ENST00000251849.4:c.1005G>C	p.Gln335His	p.Q335H	ENST00000251849	NM_002880.3	335	caG/caC	10/17	0.353344589762817	5	FACETS	0.915	0.764	1	0.229	0.191	0.271	CLONAL	1	TRUE	1	0.353344589762817	5		426	388	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971351	15971351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	69	528	0	ENST00000268712.3:c.4598C>T	p.Ser1533Phe	p.S1533F	ENST00000268712	NM_006311.3	1533	tCt/tTt	32/46	0.353344589762817	3	FACETS	1	0.915	1	0.354	0.309	0.402	CLONAL	1	TRUE	0	0.353344589762817	3		528	433	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89871712	89871712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148419748	NA	P-0067614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	25	513	0	ENST00000389301.3:c.685G>A	p.Asp229Asn	p.D229N	ENST00000389301	NM_000135.2	229	Gac/Aac	7/43	1	2	FACETS	0.476	0.376	0.592	0.476	0.376	0.592	SUBCLONAL	1	TRUE	1	0.353344589762817	2		513	297	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0067615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	34	288	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.977	0.807	1	0.977	0.807	1	CLONAL	1	FALSE	1	0.380202478408484	2		288	183	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0067615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	28	378	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.380202478408484	1	FACETS	0.858	0.696	1	0.858	0.696	1	CLONAL	1	FALSE	0	0.380202478408484	1		378	139	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044470	12044470	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	37	336	2	ENST00000353533.5:c.1095del	p.Phe366LeufsTer3	p.F366Lfs*3	ENST00000353533	NM_003010.3	365	Ccc/cc	11/11	0.380202478408484	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	FALSE	0	0.380202478408484	1		338	133	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877000	151877000	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	26	475	0	ENST00000262189.6:c.7361G>C	p.Arg2454Thr	p.R2454T	ENST00000262189	NM_170606.2	2454	aGa/aCa	37/59	1	2	FACETS	0.674	0.537	0.828	0.674	0.537	0.828	SUBCLONAL	1	FALSE	1	0.380202478408484	2		475	203	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0067616-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	182	382	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.601496260552218	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	0	0.679523266125488	3		382	223	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0067616-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	61	448	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.679523266125488	1	FACETS	0.98	0.875	1	0.98	0.875	1	CLONAL	1	TRUE	0	0.679523266125488	1		448	121	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0067616-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	263	400	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.601496260552218	3	FACETS	0.877	0.84	0.914	0.877	0.84	0.914	CLONAL	3	TRUE	0	0.679523266125488	3		400	394	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878061	48878062	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1131690852	NA	P-0067616-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	316	472	1	ENST00000267163.4:c.19dup	p.Arg7ProfsTer24	p.R7Pfs*24	ENST00000267163	NM_000321.2	5	acc/aCcc	1/27	0.679523266125488	2	FACETS	1	0.994	1	0.66	0.627	0.693	CLONAL	1	TRUE	0	0.679523266125488	2		473	705	SUCCESS
APC	324	MSKCC	GRCh37	5	112173933	112173933	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs535344579	NA	P-0067616-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	86	455	0	ENST00000257430.4:c.2642C>T	p.Ser881Phe	p.S881F	ENST00000257430	NM_000038.5	881	tCc/tTc	16/16	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.679523266125488	2		455	238	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180584	56180584	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	106	436	0	ENST00000399503.3:c.3913A>G	p.Asn1305Asp	p.N1305D	ENST00000399503	NM_005921.1	1305	Aac/Gac	16/20	1	2	FACETS	0.915	0.826	1	1	0.987	1	CLONAL	2	TRUE	1	0.275173082741533	2		436	421	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177769	56177770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	122	494	0	ENST00000399503.3:c.2744dup	p.Leu915PhefsTer15	p.L915Ffs*15	ENST00000399503	NM_005921.1	914	-/T	14/20	1	2	FACETS	0.888	0.807	0.973	1	0.988	1	CLONAL	2	TRUE	1	0.275173082741533	2		494	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0067618-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	234	510	0	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	0.902506348787117	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.902506348787117	1		510	266	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481620	56481620	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067618-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	219	595	0	ENST00000267101.3:c.655T>G	p.Phe219Val	p.F219V	ENST00000267101	NM_001982.3	219	Ttt/Gtt	6/28	1	2	FACETS	0.982	0.924	1	0.982	0.924	1	CLONAL	1	TRUE	1	0.902506348787117	2		595	494	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250449	26250449	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067618-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	236	663	0	ENST00000446824.2:c.385C>T	p.Arg129Cys	p.R129C	ENST00000446824	NM_021018.2	129	Cgc/Tgc	1/1	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.902506348787117	2		663	511	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589168	67589168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	67	328	0	ENST00000274335.5:c.1156C>T	p.Arg386Ter	p.R386*	ENST00000274335		386	Cga/Tga	9/15	0.4047543265357	1	FACETS	0.798	0.708	0.891	0.798	0.708	0.891	SUBCLONAL	1	TRUE	0	0.633913998968643	1		328	181	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0067620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	252	452	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.633913998968643	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.633913998968643	1		452	449	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509127	66509127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145126637	NA	P-0067620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	27	262	2	ENST00000273854.3:c.200G>A	p.Arg67His	p.R67H	ENST00000273854	NM_004439.5	67	cGc/cAc	2/18	0.377438925902784	1	FACETS	0.32	0.256	0.391	0.32	0.256	0.391	INDETERMINATE	1	TRUE	0	0.633913998968643	1		264	182	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727443	66727457	+	inframe_deletion	In_Frame_Del	DEL	TCTTACCCAGAAGCA	TCTTACCCAGAAGCA	-	novel	NA	P-0067620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	123	366	0	ENST00000307102.5:c.159_173del	p.Phe53_Gln58delinsLeu	p.F53_Q58delinsL	ENST00000307102	NM_002755.3	53	ttTCTTACCCAGAAGCAg/ttg	2/11	1	2	FACETS	0.833	0.758	0.911	0.833	0.758	0.911	CLONAL	1	TRUE	1	0.633913998968643	2		366	466	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610169	10610169	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	194	431	0	ENST00000171111.5:c.541C>T	p.Pro181Ser	p.P181S	ENST00000171111	NM_203500.1	181	Ccc/Tcc	2/6	0.633913998968643	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.633913998968643	1		431	372	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726631	46726631	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	94	424	1	ENST00000371975.4:c.710G>A	p.Arg237Lys	p.R237K	ENST00000371975	NM_003579.3	237	aGg/aAg	7/18	0.377438925902784	1	FACETS	0.444	0.397	0.494	0.444	0.397	0.494	INDETERMINATE	1	TRUE	0	0.633913998968643	1		425	456	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0067625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	111	459	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		459	296	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602452	10602452	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	212	1219	0	ENST00000171111.5:c.1126G>C	p.Ala376Pro	p.A376P	ENST00000171111	NM_203500.1	376	Gcc/Ccc	3/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1219	313	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981721	101981721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564561654	NA	P-0067625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	172	960	1	ENST00000282441.5:c.142C>T	p.Pro48Ser	p.P48S	ENST00000282441	NM_001130145.2	48	Ccc/Tcc	1/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		961	409	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836626	89836626	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	223	883	0	ENST00000389301.3:c.2264G>T	p.Gly755Val	p.G755V	ENST00000389301	NM_000135.2	755	gGa/gTa	25/43	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		883	516	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124465403	124465403	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	66	340	0	ENST00000357628.3:c.1695C>A	p.Phe565Leu	p.F565L	ENST00000357628	NM_015450.2	565	ttC/ttA	18/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		340	194	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385250	4385250	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	232	852	0	ENST00000261254.3:c.275C>A	p.Pro92Gln	p.P92Q	ENST00000261254	NM_001759.3	92	cCg/cAg	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		852	511	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643561	52643561	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs751804410	NA	P-0067625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	147	775	0	ENST00000394830.3:c.2335C>G	p.Gln779Glu	p.Q779E	ENST00000394830	NM_018313.4	779	Caa/Gaa	17/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		775	307	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858060	9858060	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	221	1013	0	ENST00000330684.3:c.3341G>T	p.Arg1114Ile	p.R1114I	ENST00000330684	NM_001134407.1	1114	aGa/aTa	13/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1013	521	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293148	212293148	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	133	534	0	ENST00000342788.4:c.2704G>T	p.Asp902Tyr	p.D902Y	ENST00000342788	NM_005235.2	902	Gac/Tac	22/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		534	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577098	7577098	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	314	409	0	ENST00000269305.4:c.840A>T	p.Arg280Ser	p.R280S	ENST00000269305	NM_001126112.2	280	agA/agT	8/11	0.936057257995754	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.936057257995754	1		409	333	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671683	67671683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	292	438	0	ENST00000264010.4:c.2092G>A	p.Glu698Lys	p.E698K	ENST00000264010	NM_006565.3	698	Gag/Aag	12/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.936057257995754	2		438	603	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690608	88690608	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	269	307	0	ENST00000360948.2:c.422C>A	p.Thr141Lys	p.T141K	ENST00000360948	NM_001012338.2	141	aCa/aAa	5/19	1	2	FACETS	0.989	0.937	1	0.989	0.937	1	CLONAL	1	TRUE	1	0.936057257995754	2		307	581	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965549	90965549	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	226	401	0	ENST00000265433.3:c.1768A>G	p.Arg590Gly	p.R590G	ENST00000265433	NM_002485.4	590	Aga/Gga	11/16	0.230686698917312	3	FACETS	1	0.991	1	0.655	0.616	0.695	INDETERMINATE	1	TRUE	1	0.936057257995754	3		401	541	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40476787	40476789	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0067636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	546	435	0	ENST00000264657.5:c.1540_1542del	p.Ser514del	p.S514del	ENST00000264657	NM_139276.2	514	TCC/-	17/24	0.936057257995754	3	FACETS	0.933	0.902	0.963	0.933	0.902	0.963	CLONAL	2	TRUE	1	0.936057257995754	3		435	918	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3794897	3794897	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	244	350	0	ENST00000262367.5:c.3980A>C	p.Lys1327Thr	p.K1327T	ENST00000262367	NM_004380.2	1327	aAg/aCg	23/31	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.936057257995754	2		350	511	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436705	110436705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	282	421	0	ENST00000375856.3:c.1696G>A	p.Asp566Asn	p.D566N	ENST00000375856	NM_003749.2	566	Gac/Aac	1/2	1	2	FACETS	0.955	0.905	1	0.955	0.905	1	CLONAL	1	TRUE	1	0.936057257995754	2		421	631	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965528	90965528	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs864622167	NA	P-0067636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	235	366	0	ENST00000265433.3:c.1789A>G	p.Ile597Val	p.I597V	ENST00000265433	NM_002485.4	597	Ata/Gta	11/16	0.230686698917312	3	FACETS	1	0.992	1	0.68	0.64	0.72	INDETERMINATE	1	TRUE	1	0.936057257995754	3		366	542	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256888	41256888	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	339	294	0	ENST00000357654.3:c.298G>C	p.Glu100Gln	p.E100Q	ENST00000357654	NM_007294.3	100	Gag/Cag	5/23	0.936057257995754	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.936057257995754	3		294	529	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	166	350	0				ENST00000310581	NM_198253.2	-/1132			0.501046436500952	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.494837178149394	3		350	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0067637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	244	396	1	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.501046436500952	2	FACETS	0.896	0.856	0.935	1	0.994	1	CLONAL	3	TRUE	0	0.494837178149394	2		397	367	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519893	NA	P-0067637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	110	368	0	ENST00000267101.3:c.310G>T	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ttg	3/28	0.501046436500952	3	FACETS	1	0.973	1	0.609	0.551	0.671	CLONAL	1	TRUE	1	0.494837178149394	3		368	455	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59820440	59820440	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1298345650	NA	P-0067637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	81	385	0	ENST00000259008.2:c.2313C>G	p.Phe771Leu	p.F771L	ENST00000259008	NM_032043.2	771	ttC/ttG	16/20	0.496689596242056	4	FACETS	1	0.917	1	0.523	0.462	0.587	CLONAL	1	TRUE	2	0.494837178149394	4		385	468	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80088662	80088662	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	28	299	0	ENST00000265081.6:c.2654C>T	p.Ser885Leu	p.S885L	ENST00000265081	NM_002439.4	885	tCa/tTa	19/24	0.370336702353794	3	FACETS	0.554	0.444	0.677	0.277	0.222	0.339	SUBCLONAL	1	TRUE	1	0.494837178149394	3		299	255	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370210	40370210	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	123	500	0	ENST00000293328.3:c.1128G>T	p.Glu376Asp	p.E376D	ENST00000293328	NM_012448.3	376	gaG/gaT	9/19	0.501046436500952	3	FACETS	1	0.975	1	0.606	0.55	0.663	CLONAL	1	TRUE	1	0.494837178149394	3		500	512	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522816	67522816	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	100	393	0	ENST00000274335.5:c.313G>A	p.Glu105Lys	p.E105K	ENST00000274335		105	Gaa/Aaa	1/15	0.370336702353794	3	FACETS	1	0.977	1	0.653	0.588	0.721	CLONAL	1	TRUE	1	0.494837178149394	3		393	386	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258268	16258268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776167964	NA	P-0067637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	100	542	0	ENST00000375759.3:c.5533G>A	p.Glu1845Lys	p.E1845K	ENST00000375759	NM_015001.2	1845	Gag/Aag	11/15	0.135860949970354	3	FACETS	1	0.934	1	0.527	0.473	0.584	INDETERMINATE	1	TRUE	1	0.494837178149394	3		542	478	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61729143	61729143	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	55	269	0	ENST00000401558.2:c.396G>C	p.Met132Ile	p.M132I	ENST00000401558	NM_003400.3	132	atG/atC	6/25	0.501046436500952	4	FACETS	0.998	0.858	1	0.499	0.429	0.575	CLONAL	1	TRUE	2	0.494837178149394	4		269	333	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	41	350	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.282728441686972	2		350	249	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0067637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	66	396	1	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.282728441686972	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.282728441686972	1		397	342	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519893	NA	P-0067637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	22	368	0	ENST00000267101.3:c.310G>T	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ttg	3/28	1	2	FACETS	0.459	0.355	0.579	0.459	0.355	0.579	SUBCLONAL	1	TRUE	1	0.282728441686972	2		368	339	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80088662	80088662	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	19	299	0	ENST00000265081.6:c.2654C>T	p.Ser885Leu	p.S885L	ENST00000265081	NM_002439.4	885	tCa/tTa	19/24	1	2	FACETS	0.416	0.315	0.535	0.416	0.315	0.535	SUBCLONAL	1	TRUE	1	0.282728441686972	2		299	323	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370210	40370210	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	41	500	0	ENST00000293328.3:c.1128G>T	p.Glu376Asp	p.E376D	ENST00000293328	NM_012448.3	376	gaG/gaT	9/19	1	2	FACETS	0.709	0.591	0.84	0.709	0.591	0.84	SUBCLONAL	1	TRUE	1	0.282728441686972	2		500	409	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522816	67522816	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	29	393	0	ENST00000274335.5:c.313G>A	p.Glu105Lys	p.E105K	ENST00000274335		105	Gaa/Aaa	1/15	1	2	FACETS	0.575	0.461	0.703	0.575	0.461	0.703	SUBCLONAL	1	TRUE	1	0.282728441686972	2		393	357	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258268	16258268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776167964	NA	P-0067637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	29	542	0	ENST00000375759.3:c.5533G>A	p.Glu1845Lys	p.E1845K	ENST00000375759	NM_015001.2	1845	Gag/Aag	11/15	0.282728441686972	1	FACETS	0.456	0.366	0.559	0.456	0.366	0.559	SUBCLONAL	1	TRUE	0	0.282728441686972	1		542	386	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61729143	61729143	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	22	269	0	ENST00000401558.2:c.396G>C	p.Met132Ile	p.M132I	ENST00000401558	NM_003400.3	132	atG/atC	6/25	1	2	FACETS	0.596	0.463	0.75	0.596	0.463	0.75	SUBCLONAL	1	TRUE	1	0.282728441686972	2		269	261	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260162	10260162	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	24	481	0	ENST00000340748.4:c.2505C>G	p.Ile835Met	p.I835M	ENST00000340748		835	atC/atG	25/40	1	2	FACETS	0.441	0.345	0.552	0.441	0.345	0.552	SUBCLONAL	1	TRUE	1	0.282728441686972	2		481	385	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513686	41513686	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	63	513	0	ENST00000263253.7:c.590G>C	p.Gly197Ala	p.G197A	ENST00000263253	NM_001429.3	197	gGa/gCa	2/31	0.282728441686972	1	FACETS	0.997	0.866	1	0.997	0.866	1	CLONAL	1	TRUE	0	0.282728441686972	1		513	384	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609937	43609937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767405	NA	P-0067637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	48	583	0	ENST00000355710.3:c.1889G>A	p.Cys630Tyr	p.C630Y	ENST00000355710	NM_020975.4	630	tGc/tAc	11/20	1	2	FACETS	0.668	0.565	0.782	0.668	0.565	0.782	SUBCLONAL	1	TRUE	1	0.282728441686972	2		583	508	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438710	49438710	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	22	403	0	ENST00000301067.7:c.4780G>T	p.Glu1594Ter	p.E1594*	ENST00000301067	NM_003482.3	1594	Gaa/Taa	19/54	1	2	FACETS	0.416	0.322	0.526	0.416	0.322	0.526	SUBCLONAL	1	TRUE	1	0.282728441686972	2		403	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0067638-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	281	546	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	0.579257527995036	4	FACETS	0.964	0.926	1	0.964	0.926	1	CLONAL	4	FALSE	0	0.575857118150189	4		546	399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0067638-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	243	395	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.579257527995036	4	FACETS	0.972	0.931	1	0.972	0.931	1	CLONAL	4	FALSE	0	0.575857118150189	4		395	342	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0067638-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	110	284	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.579257527995036	4	FACETS	0.861	0.791	0.932	0.861	0.791	0.932	CLONAL	3	FALSE	1	0.575857118150189	4		284	233	SUCCESS
APC	324	MSKCC	GRCh37	5	112175162	112175162	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561588104	NA	P-0067638-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	63	387	0	ENST00000257430.4:c.3871C>T	p.Gln1291Ter	p.Q1291*	ENST00000257430	NM_000038.5	1291	Cag/Tag	16/16	0.435141461798056	3	FACETS	1	0.964	1	0.646	0.567	0.73	CLONAL	1	FALSE	1	0.575857118150189	3		387	218	SUCCESS
APC	324	MSKCC	GRCh37	5	112116538	112116538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs749479682	NA	P-0067638-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	91	349	0	ENST00000257430.4:c.583C>T	p.Gln195Ter	p.Q195*	ENST00000257430	NM_000038.5	195	Caa/Taa	6/16	0.435141461798056	3	FACETS	0.917	0.83	1	0.917	0.83	1	CLONAL	2	FALSE	1	0.575857118150189	3		349	222	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576013	29576013	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0067638-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	214	369	0	ENST00000356175.3:c.3986C>G	p.Ser1329Ter	p.S1329*	ENST00000356175	NM_000267.3	1329	tCa/tGa	30/57	0.578173256621738	4	FACETS	1	0.982	1			1	CLONAL	4	FALSE	NA	0.575857118150189	4		369	280	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636645	73636647	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0067638-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	447	522	0	ENST00000377687.4:c.913_915del	p.Pro305del	p.P305del	ENST00000377687	NM_001730.3	303	tCACca/tca	2/4	0.575857118150189	8	FACETS	1	0.985	1			1	CLONAL	5	FALSE	NA	0.575857118150189	8		522	809	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0067639-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	18	440	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.488	0.367	0.63	0.488	0.367	0.63	SUBCLONAL	1	TRUE	1	0.26	2		440	284	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183787	10183787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123481	NA	P-0067640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	125	494	0	ENST00000256474.2:c.256C>T	p.Pro86Ser	p.P86S	ENST00000256474	NM_000551.3	86	Ccc/Tcc	1/3	0.572616528478638	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.572616528478638	1		494	299	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2077641	2077641	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	114	436	0	ENST00000349721.2:c.2049A>T	p.Gln683His	p.Q683H	ENST00000349721	NM_003070.3	683	caA/caT	14/34	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.572616528478638	2		436	368	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216414	36216415	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0067640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	69	577	0	ENST00000222270.7:c.3680dup	p.Phe1228IlefsTer77	p.F1228Ifs*77	ENST00000222270	NM_014727.1	1226	cac/caCc	12/37	1	2	FACETS	0.424	0.369	0.482	0.424	0.369	0.482	SUBCLONAL	1	TRUE	1	0.572616528478638	2		577	569	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474597	138474597	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	10	330	0	ENST00000289153.2:c.396A>C	p.Lys132Asn	p.K132N	ENST00000289153	NM_006219.2	132	aaA/aaC	2/22	0.572616528478638	1	FACETS	0.167	0.113	0.235	0.167	0.113	0.235	SUBCLONAL	1	TRUE	0	0.572616528478638	1		330	149	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610423	10610423	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067641-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	149	483	0	ENST00000171111.5:c.287A>G	p.His96Arg	p.H96R	ENST00000171111	NM_203500.1	96	cAc/cGc	2/6	0.604351445318331	1	FACETS	0.975	0.903	1	0.975	0.903	1	CLONAL	1	TRUE	0	0.604351445318331	1		483	353	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222001	1222001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067641-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	108	354	0	ENST00000326873.7:c.916C>T	p.His306Tyr	p.H306Y	ENST00000326873	NM_000455.4	306	Cac/Tac	7/10	0.604351445318331	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.604351445318331	1		354	242	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637496	47637496	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067641-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	42	349	1	ENST00000233146.2:c.630G>T	p.Met210Ile	p.M210I	ENST00000233146	NM_000251.2	210	atG/atT	3/16	1	2	FACETS	0.302	0.252	0.358	0.302	0.252	0.358	SUBCLONAL	1	TRUE	1	0.604351445318331	2		350	460	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683506	29683506	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067641-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	116	338	0	ENST00000356175.3:c.7581A>G	p.Ile2527Met	p.I2527M	ENST00000356175	NM_000267.3	2527	atA/atG	51/57	1	2	FACETS	0.962	0.875	1	0.962	0.875	1	CLONAL	1	TRUE	1	0.604351445318331	2		338	399	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701195	43701195	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067641-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	24	434	0	ENST00000382044.4:c.5500G>T	p.Val1834Phe	p.V1834F	ENST00000382044	NM_001141980.1	1834	Gtc/Ttc	26/28	1	2	FACETS	0.167	0.13	0.209	0.167	0.13	0.209	SUBCLONAL	1	TRUE	1	0.604351445318331	2		434	477	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211749	2211749	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0067641-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	137	381	0	ENST00000398665.3:c.1466-1G>C		p.X489_splice	ENST00000398665	NM_032482.2	489			0.604351445318331	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.604351445318331	1		381	309	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0067642-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	146	378	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		378	435	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771319	68771319	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1555509622	NA	P-0067642-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	124	393	0	ENST00000261769.5:c.1A>G	p.Met1?	p.M1?	ENST00000261769	NM_004360.3	1	Atg/Gtg	1/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		393	208	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0067643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	146	432	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.469684580808066	1	FACETS	0.859	0.793	0.927	0.859	0.793	0.927	CLONAL	1	TRUE	0	0.599587924617965	1		432	397	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445149	49445149	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	193	667	2	ENST00000301067.7:c.2317del	p.Gln773SerfsTer157	p.Q773Sfs*157	ENST00000301067	NM_003482.3	773	Cag/ag	10/54	1	2	FACETS	0.833	0.772	0.895	0.833	0.772	0.895	CLONAL	1	TRUE	1	0.599587924617965	2		669	773	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894230	NA	P-0067643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	134	392	0	ENST00000451590.1:c.35G>T	p.Gly12Val	p.G12V	ENST00000451590	NM_001130442.1	12	gGc/gTc	2/5	0.599587924617965	1	FACETS	0.862	0.793	0.933	0.862	0.793	0.933	CLONAL	1	TRUE	0	0.599587924617965	1		392	363	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813376	102813376	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs747403094	NA	P-0067643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	171	427	0	ENST00000307046.8:c.313C>A	p.Leu105Met	p.L105M	ENST00000307046	NM_001111285.1	105	Ctg/Atg	3/4	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.599587924617965	2		427	525	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266695	41266695	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	163	426	0	ENST00000349496.5:c.492C>A	p.Asp164Glu	p.D164E	ENST00000349496	NM_001904.3	164	gaC/gaA	4/15	0.599587924617965	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.599587924617965	1		426	364	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455124	50455124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1432192241	NA	P-0067643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	120	308	0	ENST00000331340.3:c.671A>G	p.His224Arg	p.H224R	ENST00000331340	NM_006060.4	224	cAc/cGc	6/8	1	2	FACETS	0.929	0.845	1	0.929	0.845	1	CLONAL	1	TRUE	1	0.599587924617965	2		308	431	SUCCESS
AR	367	MSKCC	GRCh37	X	66765695	66765695	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	209	561	0	ENST00000374690.3:c.707C>G	p.Ala236Gly	p.A236G	ENST00000374690	NM_000044.3	236	gCc/gGc	1/8	1	2	FACETS	0.985	0.918	1	0.985	0.918	1	CLONAL	1	TRUE	1	0.599587924617965	2		561	708	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124481189	124481189	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	99	340	0	ENST00000357628.3:c.1207G>T	p.Asp403Tyr	p.D403Y	ENST00000357628	NM_015450.2	403	Gat/Tat	14/19	0.599587924617965	1	FACETS	0.91	0.827	0.996	0.91	0.827	0.996	CLONAL	1	TRUE	0	0.599587924617965	1		340	254	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577599	7577600	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1567550002	NA	P-0067645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	64	360	0	ENST00000269305.4:c.681dup	p.Asp228Ter	p.D228*	ENST00000269305	NM_001126112.2	227	-/T	7/11	0.280619935721302	1	FACETS	0.777	0.675	0.887	0.777	0.675	0.887	SUBCLONAL	1	TRUE	0	0.31	1		360	449	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859701	57859701	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	35	354	0	ENST00000228682.2:c.755T>C	p.Leu252Pro	p.L252P	ENST00000228682	NM_005269.2	252	cTg/cCg	7/12	1	2	FACETS	0.391	0.319	0.471	0.391	0.319	0.471	SUBCLONAL	1	TRUE	1	0.31	2		354	578	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542720	187542720	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	16	441	0	ENST00000441802.2:c.5020G>A	p.Val1674Ile	p.V1674I	ENST00000441802	NM_005245.3	1674	Gtt/Att	10/27	1	2	FACETS	0.975	0.723	1	0.975	0.723	1	CLONAL	1	TRUE	1	0.17	2		441	193	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0067651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	13	288	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.292293586308426	4	FACETS	0.631	0.453	0.845	0.316	0.226	0.423	SUBCLONAL	1	TRUE	2	0.48	4		288	127	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587780070	NA	P-0067660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	198	428	0	ENST00000269305.4:c.535C>G	p.His179Asp	p.H179D	ENST00000269305	NM_001126112.2	179	Cat/Gat	5/11	0.21087025555964	2	FACETS	0.854	0.796	0.914	0.854	0.796	0.914	INDETERMINATE	2	TRUE	0	0.381853721489619	2		428	607	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218467	1218467	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	146	309	0	ENST00000326873.7:c.343del	p.Asp115MetfsTer14	p.D115Mfs*14	ENST00000326873	NM_000455.4	114	gtG/gt	2/10	0.35028056286221	2	FACETS	0.815	0.75	0.883	0.815	0.75	0.883	CLONAL	2	TRUE	0	0.381853721489619	2		309	469	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051100	128051100	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs774644406	NA	P-0067660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	135	312	0	ENST00000285398.2:c.223C>A	p.Pro75Thr	p.P75T	ENST00000285398	NM_000122.1	75	Ccc/Acc	2/15	0.272390609647509	3	FACETS	0.751	0.685	0.819	0.751	0.685	0.819	SUBCLONAL	2	TRUE	1	0.381853721489619	3		312	561	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913237	NA	P-0067663-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	135	265	0	ENST00000369535.4:c.35G>C	p.Gly12Ala	p.G12A	ENST00000369535	NM_002524.4	12	gGt/gCt	2/7	0.408960790167472	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.408960790167472	1		265	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577586	7577586	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587781589	NA	P-0067663-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	196	301	0	ENST00000269305.4:c.695T>C	p.Ile232Thr	p.I232T	ENST00000269305	NM_001126112.2	232	aTc/aCc	7/11	0.343216030879803	2	FACETS	0.932	0.871	0.995	0.932	0.871	0.995	CLONAL	2	TRUE	0	0.408960790167472	2		301	514	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156986	89156986	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067663-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	122	236	0	ENST00000336596.2:c.88G>A	p.Val30Ile	p.V30I	ENST00000336596	NM_005233.5	30	Gtc/Atc	1/17	0.123052361349132	4	FACETS	0.902	0.821	0.987	0.902	0.821	0.987	INDETERMINATE	2	TRUE	2	0.408960790167472	4		236	466	SUCCESS
APC	324	MSKCC	GRCh37	5	112173730	112173730	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	178	358	0	ENST00000257430.4:c.2442del	p.Phe814LeufsTer6	p.F814Lfs*6	ENST00000257430	NM_000038.5	813	aaT/aa	16/16	0.331972212389584	2	FACETS	0.96	0.892	1	0.96	0.892	1	CLONAL	2	TRUE	0	0.349041476883001	2		358	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578281	7578281	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660254	NA	P-0067668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	273	523	0	ENST00000269305.4:c.568C>A	p.Pro190Thr	p.P190T	ENST00000269305	NM_001126112.2	190	Cct/Act	6/11	0.353019241387538	3	FACETS	1	0.987	1	0.767	0.723	0.813	CLONAL	2	TRUE	0	0.349041476883001	3		523	798	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677990	58677990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1375271471	NA	P-0067668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	64	375	0	ENST00000305921.3:c.215C>T	p.Ala72Val	p.A72V	ENST00000305921	NM_003620.3	72	gCc/gTc	1/6	0.324981696293001	4	FACETS	0.646	0.558	0.741	0.215	0.186	0.247	SUBCLONAL	1	TRUE	1	0.349041476883001	4		375	766	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509408	46509410	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	rs1557544840	NA	P-0067668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	118	460	0	ENST00000262741.5:c.1321_1323del	p.Asn441del	p.N441del	ENST00000262741	NM_003629.3	441	AAC/-	10/10	0.33422594629866	2	FACETS	0.959	0.866	1	0.48	0.433	0.529	CLONAL	1	TRUE	0	0.349041476883001	2		460	705	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40761150	40761150	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	87	410	0	ENST00000392038.2:c.202C>G	p.Pro68Ala	p.P68A	ENST00000392038	NM_001626.4	68	Ccg/Gcg	4/14	0.353019241387538	4	FACETS	0.911	0.806	1	0.456	0.403	0.512	CLONAL	1	TRUE	2	0.349041476883001	4		410	738	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212365	36212365	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067687-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	195	547	0	ENST00000222270.7:c.2116C>T	p.Arg706Ter	p.R706*	ENST00000222270	NM_014727.1	706	Cga/Tga	3/37	0.765628464698876	4	FACETS	0.931	0.87	0.993	0.931	0.87	0.993	CLONAL	2	TRUE	2	0.765628464698876	4		547	483	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	117	483	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.61	2		483	379	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379820	17379820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199925580	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	44	532	0	ENST00000359435.4:c.205G>A	p.Gly69Ser	p.G69S	ENST00000359435	NM_001033549.1	69	Ggc/Agc	2/9	1	2	FACETS	0.375	0.315	0.441	0.375	0.315	0.441	SUBCLONAL	1	TRUE	1	0.61	2		532	385	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	89	577	5	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.605	0.539	0.676	0.605	0.539	0.676	SUBCLONAL	1	TRUE	1	0.61	2		582	482	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	175	606	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.61	2		606	490	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665096	138665096	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs758370933	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	60	404	0	ENST00000330315.3:c.469C>G	p.Pro157Ala	p.P157A	ENST00000330315	NM_023067.3	157	Ccc/Gcc	1/1	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.61	2		404	187	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614463	38614463	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	19	346	0	ENST00000299084.4:c.234del	p.Asp79ThrfsTer42	p.D79Tfs*42	ENST00000299084	NM_152594.2	77	Aaa/aa	3/7	1	2	FACETS	0.232	0.176	0.298	0.232	0.176	0.298	SUBCLONAL	1	TRUE	1	0.61	2		346	268	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	79	547	0	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	1	2	FACETS	0.627	0.554	0.705	0.627	0.554	0.705	SUBCLONAL	1	TRUE	1	0.61	2		547	413	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	118	707	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.992	0.903	1	0.992	0.903	1	CLONAL	1	TRUE	1	0.61	2		711	390	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	151	570	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.61	2		570	481	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141874	108141874	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587781558	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	120	426	1	ENST00000278616.4:c.2921+1G>A		p.X974_splice	ENST00000278616	NM_000051.3	974			1	2	FACETS	0.921	0.839	1	0.921	0.839	1	CLONAL	1	TRUE	1	0.61	2		427	427	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	109	590	7	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.792	0.716	0.872	0.792	0.716	0.872	SUBCLONAL	1	TRUE	1	0.61	2		597	451	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429978	78429978	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	111	552	1	ENST00000370768.2:c.901del	p.Ile301TyrfsTer22	p.I301Yfs*22	ENST00000370768	NM_003902.3	301	Ata/ta	11/20	1	2	FACETS	0.822	0.743	0.903	0.822	0.743	0.903	CLONAL	1	TRUE	1	0.61	2		553	443	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468085	120468085	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	152	595	0	ENST00000256646.2:c.4354G>T	p.Gly1452Trp	p.G1452W	ENST00000256646	NM_024408.3	1452	Ggg/Tgg	25/34	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.61	2		595	446	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099338	193099338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	21	365	0	ENST00000367435.3:c.272G>A	p.Arg91Gln	p.R91Q	ENST00000367435	NM_024529.4	91	cGa/cAa	3/17	1	2	FACETS	0.188	0.144	0.239	0.188	0.144	0.239	SUBCLONAL	1	TRUE	1	0.61	2		365	366	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231488894	231488894	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	119	541	0	ENST00000295050.7:c.1263del	p.Phe421LeufsTer7	p.F421Lfs*7	ENST00000295050	NM_032018.5	419	aaT/aa	5/5	1	2	FACETS	0.895	0.814	0.979	0.895	0.814	0.979	CLONAL	1	TRUE	1	0.61	2		541	436	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100720	8100720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	38	495	0	ENST00000346208.3:c.694G>A	p.Gly232Arg	p.G232R	ENST00000346208		232	Gga/Aga	3/6	1	2	FACETS	0.402	0.333	0.478	0.402	0.333	0.478	SUBCLONAL	1	TRUE	1	0.61	2		495	310	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649927	88649927	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1564714834	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	63	308	0	ENST00000372037.3:c.176T>A	p.Leu59Ter	p.L59*	ENST00000372037	NM_004329.2	59	tTa/tAa	4/13	1	2	FACETS	0.804	0.703	0.911	0.804	0.703	0.911	CLONAL	1	TRUE	1	0.61	2		308	257	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946996	71946996	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs754591389	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	22	510	0	ENST00000298229.2:c.2845C>T	p.Arg949Ter	p.R949*	ENST00000298229	NM_001567.3	949	Cga/Tga	25/28	1	2	FACETS	0.223	0.173	0.282	0.223	0.173	0.282	SUBCLONAL	1	TRUE	1	0.61	2		510	323	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	92	419	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.61	2		419	287	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433950	49433950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780306423	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	21	602	0	ENST00000301067.7:c.7603C>T	p.Arg2535Cys	p.R2535C	ENST00000301067	NM_003482.3	2535	Cgt/Tgt	31/54	1	2	FACETS	0.169	0.13	0.215	0.169	0.13	0.215	SUBCLONAL	1	TRUE	1	0.61	2		602	407	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959366	26959366	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1418353379	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	112	396	0	ENST00000381527.3:c.533G>A	p.Arg178Gln	p.R178Q	ENST00000381527	NM_001260.1	178	cGa/cAa	6/13	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.61	2		396	353	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134571	41134571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760394095	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	107	550	0	ENST00000379561.5:c.1057G>A	p.Ala353Thr	p.A353T	ENST00000379561	NM_002015.3	353	Gca/Aca	2/3	1	2	FACETS	0.841	0.76	0.926	0.841	0.76	0.926	CLONAL	1	TRUE	1	0.61	2		550	417	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435499	110435499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	27	486	0	ENST00000375856.3:c.2902G>A	p.Asp968Asn	p.D968N	ENST00000375856	NM_003749.2	968	Gac/Aac	1/2	1	2	FACETS	0.29	0.231	0.358	0.29	0.231	0.358	SUBCLONAL	1	TRUE	1	0.61	2		486	305	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1023835002	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	96	459	0	ENST00000558401.1:c.1A>G	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Gtg	1/4	1	2	FACETS	0.848	0.762	0.939	0.848	0.762	0.939	CLONAL	1	TRUE	1	0.61	2		459	371	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003812	45003812	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	126	525	0	ENST00000558401.1:c.67+1G>A		p.X23_splice	ENST00000558401	NM_004048.2	23			1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.61	2		525	403	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354328	354328	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	84	396	0	ENST00000262320.3:c.1230G>T	p.Glu410Asp	p.E410D	ENST00000262320	NM_003502.3	410	gaG/gaT	5/11	1	2	FACETS	0.874	0.78	0.973	0.874	0.78	0.973	CLONAL	1	TRUE	1	0.61	2		396	315	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647124	2647124	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	23	382	0	ENST00000342085.4:c.1402G>T	p.Gly468Cys	p.G468C	ENST00000342085	NM_002613.4	468	Ggt/Tgt	13/14	1	2	FACETS	0.222	0.173	0.279	0.222	0.173	0.279	SUBCLONAL	1	TRUE	1	0.61	2		382	340	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639657	3639657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1394177026	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	131	687	0	ENST00000294008.3:c.3982G>A	p.Val1328Ile	p.V1328I	ENST00000294008	NM_032444.2	1328	Gtc/Atc	12/15	1	2	FACETS	0.972	0.889	1	0.972	0.889	1	CLONAL	1	TRUE	1	0.61	2		687	442	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821998	72821998	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	154	633	0	ENST00000268489.5:c.10177C>T	p.Gln3393Ter	p.Q3393*	ENST00000268489	NM_006885.3	3393	Cag/Tag	10/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.61	2		633	454	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829643	72829643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763494543	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	38	498	0	ENST00000268489.5:c.6938G>A	p.Arg2313His	p.R2313H	ENST00000268489	NM_006885.3	2313	cGt/cAt	9/10	1	2	FACETS	0.352	0.291	0.419	0.352	0.291	0.419	SUBCLONAL	1	TRUE	1	0.61	2		498	354	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984418	72984418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	117	530	0	ENST00000268489.5:c.3166C>T	p.Arg1056Trp	p.R1056W	ENST00000268489	NM_006885.3	1056	Cgg/Tgg	3/10	1	2	FACETS	0.94	0.855	1	0.94	0.855	1	CLONAL	1	TRUE	1	0.61	2		530	408	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992316	72992316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs62640001	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	121	657	2	ENST00000268489.5:c.1729G>A	p.Val577Ile	p.V577I	ENST00000268489	NM_006885.3	577	Gtc/Atc	2/10	1	2	FACETS	0.866	0.788	0.948	0.866	0.788	0.948	CLONAL	1	TRUE	1	0.61	2		659	458	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347087	89347087	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762574237	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	115	637	0	ENST00000301030.4:c.5863G>A	p.Glu1955Lys	p.E1955K	ENST00000301030	NM_001256183.1	1955	Gag/Aag	9/13	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.61	2		637	377	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349640	89349641	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs772267579	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	126	529	12	ENST00000301030.4:c.3309dup	p.Asp1104ArgfsTer2	p.D1104Rfs*2	ENST00000301030	NM_001256183.1	1103	-/A	9/13	1	2	FACETS	0.847	0.771	0.925	0.847	0.771	0.925	CLONAL	1	TRUE	1	0.61	2		541	488	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120031	70120031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	26	511	0	ENST00000245479.2:c.1037del	p.Pro346ArgfsTer37	p.P346Rfs*37	ENST00000245479	NM_000346.3	345	Ccc/cc	3/3	1	2	FACETS	0.312	0.248	0.386	0.312	0.248	0.386	SUBCLONAL	1	TRUE	1	0.61	2		511	273	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622369	1622369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143406385	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	52	523	0	ENST00000344749.5:c.595G>A	p.Ala199Thr	p.A199T	ENST00000344749	NM_001136139.2	199	Gcc/Acc	9/19	1	2	FACETS	0.49	0.419	0.567	0.49	0.419	0.567	SUBCLONAL	1	TRUE	1	0.61	2		523	348	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10264977	10264977	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1486893166	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	96	538	0	ENST00000340748.4:c.1963G>A	p.Val655Ile	p.V655I	ENST00000340748		655	Gtc/Atc	21/40	1	2	FACETS	0.92	0.828	1	0.92	0.828	1	CLONAL	1	TRUE	1	0.61	2		538	342	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367894	15367894	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	44	457	0	ENST00000263377.2:c.1432A>G	p.Lys478Glu	p.K478E	ENST00000263377	NM_058243.2	478	Aag/Gag	8/20	1	2	FACETS	0.429	0.361	0.504	0.429	0.361	0.504	SUBCLONAL	1	TRUE	1	0.61	2		457	336	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765523	41765523	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199709000	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	104	548	0	ENST00000301178.4:c.2399G>A	p.Arg800Gln	p.R800Q	ENST00000301178	NM_021913.4	800	cGg/cAg	20/20	1	2	FACETS	0.84	0.758	0.926	0.84	0.758	0.926	CLONAL	1	TRUE	1	0.61	2		548	406	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422684	47422684	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1298488368	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	144	501	0	ENST00000404338.3:c.752G>A	p.Arg251Gln	p.R251Q	ENST00000404338	NM_004491.4	251	cGg/cAg	1/6	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.61	2		501	423	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193506	99193506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	37	618	0	ENST00000074304.5:c.2701C>T	p.Arg901Cys	p.R901C	ENST00000074304	NM_001134224.1	901	Cgt/Tgt	25/26	1	2	FACETS	0.282	0.232	0.338	0.282	0.232	0.338	SUBCLONAL	1	TRUE	1	0.61	2		618	430	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038133	128038133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369244363	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	115	437	0	ENST00000285398.2:c.1417G>A	p.Glu473Lys	p.E473K	ENST00000285398	NM_000122.1	473	Gaa/Aaa	9/15	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.61	2		437	362	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523270	9523270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367986819	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	104	482	0	ENST00000353224.5:c.1967G>A	p.Arg656Gln	p.R656Q	ENST00000353224	NM_177990.2	656	cGg/cAg	9/10	1	2	FACETS	0.888	0.802	0.978	0.888	0.802	0.978	CLONAL	1	TRUE	1	0.61	2		482	384	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374365	31374365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768468807	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	120	579	0	ENST00000328111.2:c.364C>T	p.Arg122Cys	p.R122C	ENST00000328111	NM_006892.3	122	Cgt/Tgt	5/23	1	2	FACETS	0.976	0.889	1	0.976	0.889	1	CLONAL	1	TRUE	1	0.61	2		579	403	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386388	31386388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	112	580	2	ENST00000328111.2:c.1613G>A	p.Arg538His	p.R538H	ENST00000328111	NM_006892.3	538	cGc/cAc	15/23	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.61	2		582	350	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40738973	40738973	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	83	426	0	ENST00000373198.4:c.3311G>T	p.Ser1104Ile	p.S1104I	ENST00000373198	NM_133170.3	1104	aGt/aTt	24/32	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.61	2		426	269	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739099	40739099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536918490	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	88	438	0	ENST00000373198.4:c.3185G>A	p.Arg1062His	p.R1062H	ENST00000373198	NM_133170.3	1062	cGc/cAc	24/32	1	2	FACETS	0.931	0.834	1	0.931	0.834	1	CLONAL	1	TRUE	1	0.61	2		438	310	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231782	36231782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs74315450	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	136	663	0	ENST00000300305.3:c.602G>A	p.Arg201Gln	p.R201Q	ENST00000300305		201	cGa/cAa	5/8	1	2	FACETS	0.886	0.811	0.965	0.886	0.811	0.965	CLONAL	1	TRUE	1	0.61	2		663	503	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627233	12627233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs941573221	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	129	373	0	ENST00000251849.4:c.1483C>T	p.Arg495Cys	p.R495C	ENST00000251849	NM_002880.3	495	Cgc/Tgc	14/17	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.61	2		373	399	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438494	52438494	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756443059	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	26	477	0	ENST00000460680.1:c.1225G>A	p.Val409Met	p.V409M	ENST00000460680	NM_004656.3	409	Gtg/Atg	12/17	1	2	FACETS	0.232	0.183	0.287	0.232	0.183	0.287	SUBCLONAL	1	TRUE	1	0.61	2		477	368	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851646	134851646	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757558701	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	96	495	0	ENST00000398015.3:c.1052G>A	p.Arg351Gln	p.R351Q	ENST00000398015	NM_004441.4	351	cGg/cAg	5/16	1	2	FACETS	0.974	0.878	1	0.974	0.878	1	CLONAL	1	TRUE	1	0.61	2		495	323	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748123	41748123	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	46	398	0	ENST00000226382.2:c.646G>A	p.Gly216Ser	p.G216S	ENST00000226382	NM_003924.3	216	Ggc/Agc	3/3	1	2	FACETS	0.591	0.502	0.689	0.591	0.502	0.689	SUBCLONAL	1	TRUE	1	0.61	2		398	255	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244280	153244280	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	155	438	1	ENST00000281708.4:c.1877C>T	p.Ala626Val	p.A626V	ENST00000281708	NM_033632.3	626	gCt/gTt	12/12	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.61	2		439	477	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510101	187510101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375425015	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	106	519	0	ENST00000441802.2:c.13412C>T	p.Ala4471Val	p.A4471V	ENST00000441802	NM_005245.3	4471	gCg/gTg	27/27	1	2	FACETS	0.833	0.752	0.918	0.833	0.752	0.918	CLONAL	1	TRUE	1	0.61	2		519	417	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526444	31526444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs974715206	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	37	518	0	ENST00000344624.3:c.596G>A	p.Ser199Asn	p.S199N	ENST00000344624		199	aGc/aAc	2/33	1	2	FACETS	0.305	0.251	0.365	0.305	0.251	0.365	SUBCLONAL	1	TRUE	1	0.61	2		518	398	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592108	67592108	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1419325070	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	108	452	0	ENST00000274335.5:c.1924C>T	p.Arg642Ter	p.R642*	ENST00000274335		642	Cga/Tga	14/15	1	2	FACETS	0.922	0.835	1	0.922	0.835	1	CLONAL	1	TRUE	1	0.61	2		452	384	SUCCESS
APC	324	MSKCC	GRCh37	5	112170862	112170862	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1060503318	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	118	396	0	ENST00000257430.4:c.1958G>T	p.Arg653Met	p.R653M	ENST00000257430	NM_000038.5	653	aGg/aTg	15/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.61	2		396	348	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058747	180058748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755445139	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	91	581	0	ENST00000261937.6:c.89dup	p.Thr31AspfsTer15	p.T31Dfs*15	ENST00000261937	NM_182925.4	30	ccg/ccCg	2/30	1	2	FACETS	0.722	0.645	0.804	0.722	0.645	0.804	SUBCLONAL	1	TRUE	1	0.61	2		581	413	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402605	20402605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775788562	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	80	539	0	ENST00000346618.3:c.142G>A	p.Ala48Thr	p.A48T	ENST00000346618	NM_001949.4	48	Gcc/Acc	1/7	1	2	FACETS	0.927	0.825	1	0.927	0.825	1	CLONAL	1	TRUE	1	0.61	2		539	283	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287520	33287520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141395832	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	146	588	0	ENST00000374542.5:c.1577G>A	p.Arg526His	p.R526H	ENST00000374542	NM_001141970.1	526	cGc/cAc	6/8	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.61	2		588	476	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517377	157517377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	106	403	0	ENST00000346085.5:c.3941C>T	p.Pro1314Leu	p.P1314L	ENST00000346085	NM_020732.3	1314	cCc/cTc	16/20	1	2	FACETS	0.968	0.876	1	0.968	0.876	1	CLONAL	1	TRUE	1	0.61	2		403	359	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431649	6431649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	84	298	0	ENST00000356142.4:c.202C>T	p.Arg68Cys	p.R68C	ENST00000356142	NM_018890.3	68	Cgc/Tgc	3/7	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.61	2		298	236	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2060867	2060867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	134	560	0	ENST00000349721.2:c.1573C>T	p.Arg525Cys	p.R525C	ENST00000349721	NM_003070.3	525	Cgt/Tgt	9/34	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.61	2		560	397	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8733794	8733794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs949202374	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	110	463	1	ENST00000356435.5:c.50G>A	p.Arg17His	p.R17H	ENST00000356435		17	cGc/cAc	1/35	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.61	2		464	353	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401847	139401847	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs548083258	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	43	657	0	ENST00000277541.6:c.3553G>A	p.Asp1185Asn	p.D1185N	ENST00000277541	NM_017617.3	1185	Gac/Aac	22/34	1	2	FACETS	0.343	0.287	0.405	0.343	0.287	0.405	SUBCLONAL	1	TRUE	1	0.61	2		657	411	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139811026	139811026	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	129	457	0	ENST00000247668.2:c.637C>T	p.Arg213Ter	p.R213*	ENST00000247668	NM_021138.3	213	Cga/Tga	7/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.61	2		457	399	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15821890	15821890	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188867560	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	110	438	0	ENST00000307771.7:c.283G>A	p.Ala95Thr	p.A95T	ENST00000307771	NM_005089.3	95	Gcg/Acg	4/11	1	2	FACETS	0.988	0.897	1	0.988	0.897	1	CLONAL	1	TRUE	1	0.61	2		438	365	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921559	39921559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746716983	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	128	439	0	ENST00000378444.4:c.4261C>T	p.Arg1421Cys	p.R1421C	ENST00000378444	NM_001123385.1	1421	Cgc/Tgc	10/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.61	2		439	377	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411276	63411276	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	113	621	0	ENST00000330258.3:c.1891C>T	p.Arg631Ter	p.R631*	ENST00000330258	NM_152424.3	631	Cga/Tga	2/2	1	2	FACETS	0.891	0.808	0.977	0.891	0.808	0.977	CLONAL	1	TRUE	1	0.61	2		621	416	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412151	63412151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	110	594	0	ENST00000330258.3:c.1016G>A	p.Ser339Asn	p.S339N	ENST00000330258	NM_152424.3	339	aGt/aAt	2/2	1	2	FACETS	0.88	0.796	0.966	0.88	0.796	0.966	CLONAL	1	TRUE	1	0.61	2		594	410	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946462	2946462	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758055212	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	88	509	0	ENST00000396946.4:c.3275G>A	p.Arg1092Gln	p.R1092Q	ENST00000396946	NM_032415.4	1092	cGa/cAa	25/25	1	2	FACETS	0.767	0.685	0.854	0.767	0.685	0.854	SUBCLONAL	1	TRUE	1	0.61	2		509	376	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258437	16258437	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1308982924	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	182	621	0	ENST00000375759.3:c.5702G>A	p.Arg1901His	p.R1901H	ENST00000375759	NM_015001.2	1901	cGc/cAc	11/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.61	2		621	542	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471692	120471692	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	148	521	0	ENST00000256646.2:c.3799G>A	p.Glu1267Lys	p.E1267K	ENST00000256646	NM_024408.3	1267	Gag/Aag	23/34	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.61	2		521	466	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724571	162724571	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	131	583	0	ENST00000367921.3:c.343G>T	p.Ala115Ser	p.A115S	ENST00000367921	NM_006182.2	115	Gcc/Tcc	5/18	1	2	FACETS	0.936	0.855	1	0.936	0.855	1	CLONAL	1	TRUE	1	0.61	2		583	459	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10794724	10794724	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	45	450	0	ENST00000361367.2:c.2631G>T	p.Gln877His	p.Q877H	ENST00000361367	NM_014633.3	877	caG/caT	21/25	1	2	FACETS	0.387	0.326	0.455	0.387	0.326	0.455	SUBCLONAL	1	TRUE	1	0.61	2		450	381	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212926	94212926	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	16	385	0	ENST00000323929.3:c.316T>G	p.Phe106Val	p.F106V	ENST00000323929	NM_005591.3	106	Ttt/Gtt	5/20	1	2	FACETS	0.186	0.137	0.244	0.186	0.137	0.244	SUBCLONAL	1	TRUE	1	0.61	2		385	282	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375914	118375914	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	138	576	0	ENST00000534358.1:c.9307C>A	p.Gln3103Lys	p.Q3103K	ENST00000534358	NM_005933.3	3103	Caa/Aaa	27/36	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.61	2		576	430	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431963	49431963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	114	626	0	ENST00000301067.7:c.9176C>T	p.Thr3059Ile	p.T3059I	ENST00000301067	NM_003482.3	3059	aCt/aTt	34/54	1	2	FACETS	0.912	0.827	0.999	0.912	0.827	0.999	CLONAL	1	TRUE	1	0.61	2		626	410	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027238	49027238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	105	358	0	ENST00000267163.4:c.1805C>T	p.Ala602Val	p.A602V	ENST00000267163	NM_000321.2	602	gCa/gTa	18/27	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.61	2		358	313	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518137	103518137	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	126	563	1	ENST00000355739.4:c.2075A>G	p.Glu692Gly	p.E692G	ENST00000355739	NM_000123.3	692	gAa/gGa	9/15	1	2	FACETS	0.941	0.859	1	0.941	0.859	1	CLONAL	1	TRUE	1	0.61	2		564	439	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241991	105241991	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1166659979	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	39	474	0	ENST00000349310.3:c.433G>A	p.Val145Met	p.V145M	ENST00000349310	NM_001014432.1	145	Gtg/Atg	6/15	1	2	FACETS	0.356	0.296	0.423	0.356	0.296	0.423	SUBCLONAL	1	TRUE	1	0.61	2		474	359	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701222	43701222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	134	551	0	ENST00000382044.4:c.5473G>A	p.Ala1825Thr	p.A1825T	ENST00000382044	NM_001141980.1	1825	Gcc/Acc	26/28	1	2	FACETS	0.974	0.892	1	0.974	0.892	1	CLONAL	1	TRUE	1	0.61	2		551	451	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713297	43713297	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	129	572	0	ENST00000382044.4:c.4176G>T	p.Gln1392His	p.Q1392H	ENST00000382044	NM_001141980.1	1392	caG/caT	20/28	1	2	FACETS	0.979	0.895	1	0.979	0.895	1	CLONAL	1	TRUE	1	0.61	2		572	432	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2089941	2089941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	40	559	0	ENST00000219066.1:c.923C>T	p.Ala308Val	p.A308V	ENST00000219066	NM_002528.5	308	gCc/gTc	6/6	1	2	FACETS	0.315	0.261	0.374	0.315	0.261	0.374	SUBCLONAL	1	TRUE	1	0.61	2		559	417	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222540	2222540	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	125	525	0	ENST00000326181.6:c.734T>C	p.Met245Thr	p.M245T	ENST00000326181	NM_032271.2	245	aTg/aCg	9/21	1	2	FACETS	0.901	0.821	0.983	0.901	0.821	0.983	CLONAL	1	TRUE	1	0.61	2		525	455	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223788	2223788	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	80	510	0	ENST00000326181.6:c.1087-1G>T		p.X363_splice	ENST00000326181	NM_032271.2	363			1	2	FACETS	0.863	0.767	0.963	0.863	0.767	0.963	CLONAL	1	TRUE	1	0.61	2		510	304	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639473	3639473	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773210318	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	105	617	0	ENST00000294008.3:c.4166C>T	p.Ala1389Val	p.A1389V	ENST00000294008	NM_032444.2	1389	gCg/gTg	12/15	1	2	FACETS	0.867	0.783	0.955	0.867	0.783	0.955	CLONAL	1	TRUE	1	0.61	2		617	397	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646711	23646711	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148102335	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	116	484	0	ENST00000261584.4:c.1156A>G	p.Thr386Ala	p.T386A	ENST00000261584	NM_024675.3	386	Acc/Gcc	4/13	1	2	FACETS	0.944	0.858	1	0.944	0.858	1	CLONAL	1	TRUE	1	0.61	2		484	403	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50818243	50818243	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs758765051	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	21	470	0	ENST00000398568.2:c.1821A>T	p.Leu607Phe	p.L607F	ENST00000398568	NM_001042412.1	607	ttA/ttT	11/18	1	2	FACETS	0.172	0.132	0.219	0.172	0.132	0.219	SUBCLONAL	1	TRUE	1	0.61	2		470	400	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829115	72829115	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	110	534	0	ENST00000268489.5:c.7466C>A	p.Pro2489His	p.P2489H	ENST00000268489	NM_006885.3	2489	cCt/cAt	9/10	1	2	FACETS	0.871	0.789	0.957	0.871	0.789	0.957	CLONAL	1	TRUE	1	0.61	2		534	414	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544957	86544957	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	18	467	0	ENST00000262426.4:c.782C>A	p.Ala261Asp	p.A261D	ENST00000262426	NM_001451.2	261	gCc/gAc	1/2	1	2	FACETS	0.213	0.16	0.276	0.213	0.16	0.276	SUBCLONAL	1	TRUE	1	0.61	2		467	277	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89355018	89355018	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	131	553	0	ENST00000301030.4:c.662T>C	p.Leu221Pro	p.L221P	ENST00000301030	NM_001256183.1	221	cTg/cCg	7/13	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.61	2		553	428	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216421	7216421	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	145	650	0	ENST00000380728.2:c.827C>A	p.Pro276His	p.P276H	ENST00000380728		276	cCc/cAc	10/11	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.61	2		650	470	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110540	8110540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	101	466	1	ENST00000585124.1:c.352G>A	p.Val118Met	p.V118M	ENST00000585124	NM_004217.3	118	Gtg/Atg	5/9	1	2	FACETS	0.91	0.821	1	0.91	0.821	1	CLONAL	1	TRUE	1	0.61	2		467	364	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679852	33679852	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	137	597	0	ENST00000308377.4:c.2229del	p.Glu744LysfsTer4	p.E744Kfs*4	ENST00000308377	NM_152270.3	743	aaA/aa	5/5	1	2	FACETS	0.944	0.864	1	0.944	0.864	1	CLONAL	1	TRUE	1	0.61	2		597	476	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858200	59858200	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs766516963	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	110	429	0	ENST00000259008.2:c.1794+1G>A		p.X598_splice	ENST00000259008	NM_032043.2	598			1	2	FACETS	0.97	0.879	1	0.97	0.879	1	CLONAL	1	TRUE	1	0.61	2		429	372	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6216521	6216521	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	74	441	0	ENST00000252674.7:c.1202C>A	p.Pro401His	p.P401H	ENST00000252674	NM_005934.3	401	cCc/cAc	8/12	1	2	FACETS	0.909	0.805	1	0.909	0.805	1	CLONAL	1	TRUE	1	0.61	2		441	267	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6230592	6230592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196954792	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	104	436	1	ENST00000252674.7:c.409C>T	p.Arg137Trp	p.R137W	ENST00000252674	NM_005934.3	137	Cgg/Tgg	4/12	1	2	FACETS	0.983	0.889	1	0.983	0.889	1	CLONAL	1	TRUE	1	0.61	2		437	347	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251514	10251514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	135	542	0	ENST00000340748.4:c.3418C>T	p.Arg1140Trp	p.R1140W	ENST00000340748		1140	Cgg/Tgg	31/40	1	2	FACETS	0.936	0.857	1	0.936	0.857	1	CLONAL	1	TRUE	1	0.61	2		542	473	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096951	11096951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138689221	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	111	593	0	ENST00000358026.2:c.442G>A	p.Gly148Arg	p.G148R	ENST00000358026	NM_001128849.1	148	Ggg/Agg	4/36	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.61	2		593	348	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284952	15284952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	24	529	0	ENST00000263388.2:c.4663G>A	p.Val1555Ile	p.V1555I	ENST00000263388	NM_000435.2	1555	Gtc/Atc	25/33	1	2	FACETS	0.22	0.172	0.275	0.22	0.172	0.275	SUBCLONAL	1	TRUE	1	0.61	2		529	358	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213908	36213908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1166009631	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	124	547	0	ENST00000222270.7:c.2734G>A	p.Ala912Thr	p.A912T	ENST00000222270	NM_014727.1	912	Gcg/Acg	6/37	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.61	2		547	375	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905940	50905940	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	113	584	0	ENST00000440232.2:c.912G>A	p.Trp304Ter	p.W304*	ENST00000440232	NM_002691.3	304	tgG/tgA	8/27	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.61	2		584	347	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416361	29416361	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1335258939	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	127	571	0	ENST00000389048.3:c.4592del	p.Gly1531ValfsTer27	p.G1531Vfs*27	ENST00000389048	NM_004304.4	1531	gGt/gt	29/29	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.61	2		571	416	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67632273	67632273	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	91	458	0	ENST00000272342.5:c.2459A>C	p.Lys820Thr	p.K820T	ENST00000272342	NM_019002.3	820	aAg/aCg	5/6	1	2	FACETS	0.935	0.839	1	0.935	0.839	1	CLONAL	1	TRUE	1	0.61	2		458	319	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096552	178096552	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776472261	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	128	547	0	ENST00000397062.3:c.779C>T	p.Thr260Ile	p.T260I	ENST00000397062	NM_006164.4	260	aCa/aTa	5/5	1	2	FACETS	0.935	0.853	1	0.935	0.853	1	CLONAL	1	TRUE	1	0.61	2		547	449	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251728	212251728	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	109	562	0	ENST00000342788.4:c.3331C>A	p.Leu1111Ile	p.L1111I	ENST00000342788	NM_005235.2	1111	Cta/Ata	27/28	1	2	FACETS	0.867	0.785	0.953	0.867	0.785	0.953	CLONAL	1	TRUE	1	0.61	2		562	412	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661482	227661482	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	40	639	0	ENST00000305123.5:c.1973A>G	p.Asp658Gly	p.D658G	ENST00000305123	NM_005544.2	658	gAc/gGc	1/2	1	2	FACETS	0.391	0.326	0.464	0.391	0.326	0.464	SUBCLONAL	1	TRUE	1	0.61	2		639	335	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252958	36252958	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	166	482	0	ENST00000300305.3:c.404G>A	p.Gly135Asp	p.G135D	ENST00000300305		135	gGc/gAc	4/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.61	2		482	476	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839732	42839732	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	147	574	0	ENST00000398585.3:c.1507G>A	p.Ala503Thr	p.A503T	ENST00000398585	NM_001135099.1	503	Gcc/Acc	13/14	1	2	FACETS	0.98	0.901	1	0.98	0.901	1	CLONAL	1	TRUE	1	0.61	2		574	492	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032780	30032780	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1185209056	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	137	548	0	ENST00000338641.4:c.155G>A	p.Arg52Gln	p.R52Q	ENST00000338641	NM_000268.3	52	cGg/cAg	2/16	1	2	FACETS	0.904	0.827	0.983	0.904	0.827	0.983	CLONAL	1	TRUE	1	0.61	2		548	497	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069385	30069385	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	113	535	0	ENST00000338641.4:c.1250T>C	p.Ile417Thr	p.I417T	ENST00000338641	NM_000268.3	417	aTt/aCt	12/16	1	2	FACETS	0.95	0.863	1	0.95	0.863	1	CLONAL	1	TRUE	1	0.61	2		535	390	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191551	10191551	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs778205243	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	103	478	0	ENST00000256474.2:c.544A>G	p.Arg182Gly	p.R182G	ENST00000256474	NM_000551.3	182	Agg/Ggg	3/3	1	2	FACETS	0.828	0.746	0.913	0.828	0.746	0.913	CLONAL	1	TRUE	1	0.61	2		478	408	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936039	49936039	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	143	668	0	ENST00000296474.3:c.1631G>A	p.Gly544Asp	p.G544D	ENST00000296474	NM_002447.2	544	gGc/gAc	4/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.61	2		668	436	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014295	70014295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756044021	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	100	520	0	ENST00000394351.3:c.1156G>A	p.Val386Ile	p.V386I	ENST00000394351	NM_000248.3	386	Gtc/Atc	9/9	1	2	FACETS	0.824	0.741	0.91	0.824	0.741	0.91	CLONAL	1	TRUE	1	0.61	2		520	398	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247445	71247445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs913003790	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	125	488	0	ENST00000318789.4:c.88G>A	p.Gly30Ser	p.G30S	ENST00000318789	NM_032682.5	30	Ggc/Agc	6/21	1	2	FACETS	0.934	0.851	1	0.934	0.851	1	CLONAL	1	TRUE	1	0.61	2		488	439	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920371	134920371	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	117	547	0	ENST00000398015.3:c.2186C>T	p.Ala729Val	p.A729V	ENST00000398015	NM_004441.4	729	gCt/gTt	12/16	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.61	2		547	379	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374673	149374673	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1377588889	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	95	445	0	ENST00000360632.3:c.421T>A	p.Tyr141Asn	p.Y141N	ENST00000360632	NM_015472.4	141	Tac/Aac	2/7	1	2	FACETS	0.935	0.841	1	0.935	0.841	1	CLONAL	1	TRUE	1	0.61	2		445	333	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980551	1980551	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	127	597	0	ENST00000382891.5:c.4013C>A	p.Thr1338Asn	p.T1338N	ENST00000382891	NM_133335.3	1338	aCt/aAt	22/22	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.61	2		597	397	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984780	55984780	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	100	431	0	ENST00000263923.4:c.349T>C	p.Tyr117His	p.Y117H	ENST00000263923	NM_002253.2	117	Tat/Cat	3/30	1	2	FACETS	0.901	0.812	0.993	0.901	0.812	0.993	CLONAL	1	TRUE	1	0.61	2		431	364	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539699	187539699	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	26	569	0	ENST00000441802.2:c.8041C>A	p.Pro2681Thr	p.P2681T	ENST00000441802	NM_005245.3	2681	Cca/Aca	10/27	1	2	FACETS	0.193	0.152	0.24	0.193	0.152	0.24	SUBCLONAL	1	TRUE	1	0.61	2		569	442	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251215	251215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs9809219	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	47	227	0	ENST00000264932.6:c.1660C>T	p.Arg554Trp	p.R554W	ENST00000264932	NM_004168.2	554	Cgg/Tgg	12/15	1	2	FACETS	0.79	0.676	0.913	0.79	0.676	0.913	CLONAL	1	TRUE	1	0.61	2		227	195	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177542	56177542	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	140	507	0	ENST00000399503.3:c.2515G>T	p.Glu839Ter	p.E839*	ENST00000399503	NM_005921.1	839	Gaa/Taa	14/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.61	2		507	446	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685255	86685255	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs144692925	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	106	428	0	ENST00000274376.6:c.2971C>A	p.Leu991Met	p.L991M	ENST00000274376	NM_002890.2	991	Ctg/Atg	24/25	1	2	FACETS	0.86	0.777	0.947	0.86	0.777	0.947	CLONAL	1	TRUE	1	0.61	2		428	404	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158413	26158413	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	110	496	0	ENST00000289316.2:c.16A>C	p.Lys6Gln	p.K6Q	ENST00000289316	NM_138720.2	6	Aag/Cag	1/2	1	2	FACETS	0.884	0.8	0.971	0.884	0.8	0.971	CLONAL	1	TRUE	1	0.61	2		496	408	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188755	32188755	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	109	682	0	ENST00000375023.3:c.799G>T	p.Gly267Cys	p.G267C	ENST00000375023	NM_004557.3	267	Ggt/Tgt	4/30	1	2	FACETS	0.909	0.823	0.999	0.909	0.823	0.999	CLONAL	1	TRUE	1	0.61	2		682	393	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90947820	90947820	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	18	276	0	ENST00000265433.3:c.2255G>A	p.Arg752Lys	p.R752K	ENST00000265433	NM_002485.4	752	aGg/aAg	16/16	1	2	FACETS	0.26	0.196	0.335	0.26	0.196	0.335	SUBCLONAL	1	TRUE	1	0.61	2		276	227	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965779	90965779	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	29	453	0	ENST00000265433.3:c.1538C>A	p.Pro513His	p.P513H	ENST00000265433	NM_002485.4	513	cCt/cAt	11/16	1	2	FACETS	0.291	0.233	0.356	0.291	0.233	0.356	SUBCLONAL	1	TRUE	1	0.61	2		453	327	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205078	123205078	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	30	430	0	ENST00000218089.9:c.2438T>C	p.Leu813Ser	p.L813S	ENST00000218089	NM_001042749.1	813	tTa/tCa	25/35	1	2	FACETS	0.294	0.237	0.359	0.294	0.237	0.359	SUBCLONAL	1	TRUE	1	0.61	2		430	334	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180790	106180790	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067708-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	118	366	0	ENST00000380013.4:c.3818G>C	p.Cys1273Ser	p.C1273S	ENST00000380013	NM_001127208.2	1273	tGt/tCt	7/11	0.620994229172836	1	FACETS	0.978	0.899	1	0.978	0.899	1	CLONAL	1	TRUE	0	0.620994229172836	1		366	268	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702568	52702569	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067708-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	80	352	0	ENST00000394830.3:c.329dup	p.Asn110LysfsTer6	p.N110Kfs*6	ENST00000394830	NM_018313.4	110	aat/aaAt	4/30	0.620994229172836	1	FACETS	0.897	0.807	0.99	0.897	0.807	0.99	CLONAL	1	TRUE	0	0.620994229172836	1		352	198	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256162	41256162	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067708-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	37	374	0	ENST00000357654.3:c.418A>C	p.Ser140Arg	p.S140R	ENST00000357654	NM_007294.3	140	Agt/Cgt	6/23	1	2	FACETS	0.271	0.223	0.324	0.271	0.223	0.324	SUBCLONAL	1	TRUE	1	0.620994229172836	2		374	440	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191473	10191474	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATAC	novel	NA	P-0067708-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	128	345	0	ENST00000256474.2:c.467_470dup	p.Leu158TyrfsTer17	p.L158Yfs*17	ENST00000256474	NM_000551.3	156	tat/tATACat	3/3	0.620994229172836	1	FACETS	0.814	0.747	0.883	0.814	0.747	0.883	CLONAL	1	TRUE	0	0.620994229172836	1		345	349	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797309	135797309	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067708-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	155	500	0	ENST00000298552.3:c.560T>G	p.Leu187Arg	p.L187R	ENST00000298552	NM_001162426.1	187	cTc/cGc	7/23	0.620994229172836	1	FACETS	0.8	0.74	0.862	0.8	0.74	0.862	SUBCLONAL	1	TRUE	0	0.620994229172836	1		500	430	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0067721-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	113	371	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.610334313392348	2	FACETS	1	0.969	1	0.57	0.52	0.622	CLONAL	1	TRUE	0	0.62140133690349	2		371	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0067721-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	80	368	2	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.610334313392348	2	FACETS	0.698	0.618	0.782	0.349	0.309	0.391	SUBCLONAL	1	TRUE	0	0.62140133690349	2		370	369	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0067721-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	132	302	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.154343402857427	3	FACETS	1	0.984	1	0.666	0.61	0.724	INDETERMINATE	1	TRUE	1	0.62140133690349	3		302	418	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219785	36219785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067721-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	184	422	1	ENST00000222270.7:c.4682C>T	p.Ser1561Leu	p.S1561L	ENST00000222270	NM_014727.1	1561	tCa/tTa	20/37	0.578240161798804	3	FACETS	0.835	0.778	0.892	0.835	0.778	0.892	CLONAL	2	TRUE	1	0.62140133690349	3		423	465	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105634	27105643	+	frameshift_variant	Frame_Shift_Del	DEL	AGGTTCAGCA	AGGTTCAGCA	-	novel	NA	P-0067721-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	124	374	0	ENST00000324856.7:c.5249_5258del	p.Phe1750CysfsTer17	p.F1750Cfs*17	ENST00000324856	NM_006015.4	1749	AGGTTCAGCAag/ag	20/20	0.62140133690349	1	FACETS	0.917	0.843	0.992	0.917	0.843	0.992	CLONAL	1	TRUE	0	0.62140133690349	1		374	300	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52649414	52649414	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	45	329	0	ENST00000394830.3:c.1877del	p.Gly626AlafsTer16	p.G626Afs*16	ENST00000394830	NM_018313.4	626	gGc/gc	16/30	1	2	FACETS	0.823	0.693	0.965	0.823	0.693	0.965	CLONAL	1	TRUE	1	0.280502042570597	2		329	390	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437235	52437266	+	frameshift_variant	Frame_Shift_Del	DEL	GACCTCCTTCTCCACTGGGCTGCTGGACCCCT	GACCTCCTTCTCCACTGGGCTGCTGGACCCCT	-	novel	NA	P-0067723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	32	456	0	ENST00000460680.1:c.1778_1809del	p.Gln593ArgfsTer39	p.Q593Rfs*39	ENST00000460680	NM_004656.3	593	cAGGGGTCCAGCAGCCCAGTGGAGAAGGAGGTC/c	14/17	1	2	FACETS	0.622	0.505	0.753	0.622	0.505	0.753	SUBCLONAL	1	TRUE	1	0.280502042570597	2		456	367	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161894	47161895	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	51	427	0	ENST00000409792.3:c.4231dup	p.Ile1411AsnfsTer4	p.I1411Nfs*4	ENST00000409792	NM_014159.6	1411	ata/aAta	3/21	1	2	FACETS	0.794	0.676	0.923	0.794	0.676	0.923	CLONAL	1	TRUE	1	0.280502042570597	2		427	458	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067724-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	54	350	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.846	0.734	0.965	0.846	0.734	0.965	CLONAL	1	TRUE	1	0.657775859015202	2		350	194	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982373	201982373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398134258	NA	P-0067724-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	192	360	0	ENST00000359651.3:c.752G>A	p.Arg251Gln	p.R251Q	ENST00000359651		251	cGa/cAa	6/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.657775859015202	2		360	522	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249341	110249341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067724-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	141	315	0	ENST00000374672.4:c.1232C>T	p.Ser411Phe	p.S411F	ENST00000374672	NM_004235.4	411	tCc/tTc	4/5	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.657775859015202	2		315	407	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055994	180055994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067724-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	111	222	0	ENST00000261937.6:c.991C>T	p.Pro331Ser	p.P331S	ENST00000261937	NM_182925.4	331	Ccc/Tcc	8/30	1	2	FACETS	0.9	0.817	0.986	0.9	0.817	0.986	CLONAL	1	TRUE	1	0.657775859015202	2		222	375	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290034	15290034	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258221482	NA	P-0067724-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	144	346	0	ENST00000263388.2:c.3520C>T	p.Pro1174Ser	p.P1174S	ENST00000263388	NM_000435.2	1174	Ccc/Tcc	22/33	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.657775859015202	2		346	429	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294603	1294603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067724-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	92	300	0	ENST00000310581.5:c.398G>A	p.Gly133Glu	p.G133E	ENST00000310581	NM_198253.2	133	gGg/gAg	2/16	1	2	FACETS	0.84	0.754	0.93	0.84	0.754	0.93	CLONAL	1	TRUE	1	0.657775859015202	2		300	333	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515276	149515276	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067724-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	158	371	0	ENST00000261799.4:c.206C>T	p.Pro69Leu	p.P69L	ENST00000261799	NM_002609.3	69	cCc/cTc	3/23	1	2	FACETS	0.961	0.887	1	0.961	0.887	1	CLONAL	1	TRUE	1	0.657775859015202	2		371	500	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244466	41244466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357049	NA	P-0067724-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	175	359	0	ENST00000357654.3:c.3082C>T	p.Arg1028Cys	p.R1028C	ENST00000357654	NM_007294.3	1028	Cgt/Tgt	10/23	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.657775859015202	2		359	502	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866303	42866303	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067724-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	170	350	0	ENST00000398585.3:c.329C>T	p.Ser110Phe	p.S110F	ENST00000398585	NM_001135099.1	110	tCc/tTc	3/14	0.657775859015202	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.657775859015202	1		350	304	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155462	47155462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067724-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	137	308	0	ENST00000409792.3:c.4619C>T	p.Ser1540Phe	p.S1540F	ENST00000409792	NM_014159.6	1540	tCc/tTc	5/21	1	2	FACETS	0.945	0.866	1	0.945	0.866	1	CLONAL	1	TRUE	1	0.657775859015202	2		308	441	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342400	118342400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067724-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	154	308	0	ENST00000534358.1:c.526C>T	p.Arg176Cys	p.R176C	ENST00000534358	NM_005933.3	176	Cgt/Tgt	3/36	0.657775859015202	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.657775859015202	1		308	302	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713418	40713418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067724-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	180	371	0	ENST00000373198.4:c.4097C>T	p.Pro1366Leu	p.P1366L	ENST00000373198	NM_133170.3	1366	cCc/cTc	30/32	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.657775859015202	2		371	511	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944530	40944530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067724-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	154	270	0	ENST00000373198.4:c.1972C>T	p.Leu658Phe	p.L658F	ENST00000373198	NM_133170.3	658	Ctc/Ttc	12/32	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.657775859015202	2		270	439	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166224	118166224	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067724-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	186	360	0	ENST00000369448.3:c.734T>C	p.Leu245Pro	p.L245P	ENST00000369448	NM_017709.3	245	cTc/cCc	2/2	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.657775859015202	2		360	532	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258744	115258745	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0067724-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	145	224	0	ENST00000369535.4:c.37_38delinsAA	p.Gly13Asn	p.G13N	ENST00000369535	NM_002524.4	13	GGt/AAt	2/7	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.657775859015202	2		224	425	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120034	70120034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1462690222	NA	P-0067724-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	113	196	0	ENST00000245479.2:c.1036C>T	p.Pro346Ser	p.P346S	ENST00000245479	NM_000346.3	346	Ccg/Tcg	3/3	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.657775859015202	2		196	300	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560139	29560139	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067724-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	184	336	0	ENST00000356175.3:c.3616G>T	p.Glu1206Ter	p.E1206*	ENST00000356175	NM_000267.3	1206	Gag/Tag	27/57	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.657775859015202	2		336	492	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143460	108143460	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0067724-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	153	313	0	ENST00000278616.4:c.3165T>A	p.Tyr1055Ter	p.Y1055*	ENST00000278616	NM_000051.3	1055	taT/taA	22/63	0.657775859015202	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.657775859015202	1		313	294	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426810	49426810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067724-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	168	348	0	ENST00000301067.7:c.11678C>T	p.Pro3893Leu	p.P3893L	ENST00000301067	NM_003482.3	3893	cCc/cTc	39/54	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.657775859015202	2		348	459	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668765	52668765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067724-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	162	323	0	ENST00000394830.3:c.1154C>T	p.Pro385Leu	p.P385L	ENST00000394830	NM_018313.4	385	cCt/cTt	12/30	1	2	FACETS	0.975	0.902	1	0.975	0.902	1	CLONAL	1	TRUE	1	0.657775859015202	2		323	505	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604227	189604227	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775037738	NA	P-0067724-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	148	349	0	ENST00000264731.3:c.1394C>T	p.Pro465Leu	p.P465L	ENST00000264731	NM_003722.4	465	cCt/cTt	11/14	1	2	FACETS	0.985	0.907	1	0.985	0.907	1	CLONAL	1	TRUE	1	0.657775859015202	2		349	457	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67626730	67626730	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067724-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	112	255	0	ENST00000272342.5:c.401C>T	p.Ser134Leu	p.S134L	ENST00000272342	NM_019002.3	134	tCa/tTa	3/6	1	2	FACETS	0.867	0.786	0.95	0.867	0.786	0.95	CLONAL	1	TRUE	1	0.657775859015202	2		255	393	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741701	145741701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561010978	NA	P-0067724-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	142	324	0	ENST00000428558.2:c.802C>T	p.Pro268Ser	p.P268S	ENST00000428558	NM_004260.3	268	Ccc/Tcc	5/22	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.657775859015202	2		324	424	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525011	187525011	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067724-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	190	293	0	ENST00000441802.2:c.10669G>A	p.Glu3557Lys	p.E3557K	ENST00000441802	NM_005245.3	3557	Gaa/Aaa	19/27	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.657775859015202	2		293	503	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39542543	39542543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368674895	NA	P-0067724-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	187	309	0	ENST00000262039.4:c.347C>T	p.Pro116Leu	p.P116L	ENST00000262039	NM_002647.2	116	cCc/cTc	3/25	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.657775859015202	2		309	528	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067727-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	139	350	0				ENST00000310581	NM_198253.2	-/1132			0.60261658235598	3	FACETS	1	0.933	1	1	0.933	1	CLONAL	2	TRUE	1	0.60261658235598	3		350	298	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023715	27023716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0067727-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	182	465	0	ENST00000324856.7:c.827dup	p.Gly277ArgfsTer123	p.G277Rfs*123	ENST00000324856	NM_006015.4	274	atg/atGg	1/20	0.273420778493963	2	FACETS	1	0.987	1	0.628	0.585	0.672	INDETERMINATE	1	TRUE	0	0.60261658235598	2		465	481	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2208937	2208937	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067727-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	62	296	0	ENST00000398665.3:c.967G>C	p.Glu323Gln	p.E323Q	ENST00000398665	NM_032482.2	323	Gaa/Caa	12/28	NA	2	FACETS	1	0.885	1			1	INDETERMINATE	1	TRUE	NA	0.60261658235598	2		296	204	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073911	8073911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753335514	NA	P-0067727-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	124	465	0	ENST00000377482.5:c.748C>T	p.His250Tyr	p.H250Y	ENST00000377482	NM_018948.3	250	Cat/Tat	4/4	0.322827287923381	3	FACETS	1	0.968	1	0.569	0.517	0.622	INDETERMINATE	1	TRUE	1	0.60261658235598	3		465	471	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101358	27101358	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067727-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	56	448	0	ENST00000324856.7:c.4642del	p.His1548MetfsTer17	p.H1548Mfs*17	ENST00000324856	NM_006015.4	1547	tCc/tc	18/20	0.273420778493963	2	FACETS	0.439	0.377	0.507	0.22	0.188	0.254	INDETERMINATE	1	TRUE	0	0.60261658235598	2		448	423	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436332	52436332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067727-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	94	501	0	ENST00000460680.1:c.2162C>T	p.Ser721Phe	p.S721F	ENST00000460680	NM_004656.3	721	tCt/tTt	17/17	0.322827287923381	3	FACETS	0.896	0.801	0.996	0.448	0.4	0.498	INDETERMINATE	1	TRUE	1	0.60261658235598	3		501	453	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575461	64575461	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1431991249	NA	P-0067727-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	80	558	0	ENST00000312049.6:c.556T>A	p.Phe186Ile	p.F186I	ENST00000312049	NM_130799.2	186	Ttt/Att	3/10	NA	2	FACETS	0.506	0.446	0.57			1	INDETERMINATE	1	TRUE	NA	0.60261658235598	2		558	525	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866444	37866444	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067727-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	143	529	0	ENST00000269571.5:c.749C>A	p.Ser250Tyr	p.S250Y	ENST00000269571		250	tCt/tAt	6/27	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.60261658235598	2		529	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578400	7578400	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs751477326	NA	P-0067733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	99	447	0	ENST00000269305.4:c.530C>G	p.Pro177Arg	p.P177R	ENST00000269305	NM_001126112.2	177	cCc/cGc	5/11	0.24200453030473	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	0	0.24200453030473	1		447	522	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952146	178952147	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587776802	NA	P-0067733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	55	359	0	ENST00000263967.3:c.3203dup	p.Asn1068LysfsTer5	p.N1068Kfs*5	ENST00000263967	NM_006218.2	1067	-/A	21/21	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.24200453030473	2		359	355	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0067736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	241	536	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.316750159209866	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	3	TRUE	0	0.373091294769716	3		536	509	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816452	32816452	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765271187	NA	P-0067736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	62	408	0	ENST00000354258.4:c.1723C>T	p.Arg575Cys	p.R575C	ENST00000354258	NM_000593.5	575	Cgc/Tgc	7/11	0.314379526328117	5	FACETS	0.951	0.822	1	0.317	0.274	0.364	CLONAL	1	TRUE	2	0.373091294769716	5		408	545	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820180	139820180	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	48	417	0	ENST00000247668.2:c.1333G>C	p.Asp445His	p.D445H	ENST00000247668	NM_021138.3	445	Gac/Cac	11/11	1	2	FACETS	0.648	0.549	0.757	0.648	0.549	0.757	SUBCLONAL	1	TRUE	1	0.373091294769716	2		417	397	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38157087	38157087	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0067736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	41	425	0	ENST00000317025.8:c.2633C>G	p.Ser878Ter	p.S878*	ENST00000317025	NM_023034.1	878	tCa/tGa	15/24	0.373091294769716	1	FACETS	0.777	0.653	0.913	0.777	0.653	0.913	CLONAL	1	TRUE	0	0.373091294769716	1		425	230	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061885	38061885	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	67	450	0	ENST00000250448.2:c.104A>C	p.Asn35Thr	p.N35T	ENST00000250448	NM_004496.3	35	aAc/aCc	2/2	0.358445664832171	4	FACETS	1	0.906	1	0.262	0.228	0.299	CLONAL	1	TRUE	0	0.373091294769716	4		450	470	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948174	71948174	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	54	413	0	ENST00000298229.2:c.2886G>C	p.Lys962Asn	p.K962N	ENST00000298229	NM_001567.3	962	aaG/aaC	26/28	0.373091294769716	6	FACETS	0.782	0.668	0.909	0.156	0.133	0.182	CLONAL	1	TRUE	1	0.373091294769716	6		413	646	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184714	185184714	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	53	456	0	ENST00000265026.3:c.1606A>G	p.Lys536Glu	p.K536E	ENST00000265026	NM_004721.4	536	Aaa/Gaa	10/14	0.271442798637398	3	FACETS	0.692	0.591	0.803	0.231	0.197	0.268	SUBCLONAL	1	TRUE	0	0.373091294769716	3		456	487	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155544	56155606	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GGTAAAACCAATCCCAGTTAAAGGAGATGGATCTGAAATGAATCACTTAGCAGCTGAGTCTCC	GGTAAAACCAATCCCAGTTAAAGGAGATGGATCTGAAATGAATCACTTAGCAGCTGAGTCTCC	-	novel	NA	P-0067736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	54	308	0	ENST00000399503.3:c.636_698del	p.Val213_Pro233del	p.V213_P233del	ENST00000399503	NM_005921.1	212	gtGGTAAAACCAATCCCAGTTAAAGGAGATGGATCTGAAATGAATCACTTAGCAGCTGAGTCTCCa/gta	3/20	0.373091294769716	2	FACETS	0.988	0.85	1	0.494	0.425	0.569	CLONAL	1	TRUE	0	0.373091294769716	2		308	293	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933465	36933484	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCAGCCTGGCTGGCAGCC	CCCCAGCCTGGCTGGCAGCC	-	novel	NA	P-0067736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	83	535	0	ENST00000361632.4:c.1803_1822del	p.Met601IlefsTer96	p.M601Ifs*96	ENST00000361632		601	atGGCTGCCAGCCAGGCTGGGGcc/atcc	13/16	0.199633912742351	3	FACETS	1	0.893	1	0.336	0.297	0.378	INDETERMINATE	1	TRUE	0	0.373091294769716	3		535	523	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933244	36933244	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	57	419	0	ENST00000361632.4:c.1873del	p.Glu625SerfsTer177	p.E625Sfs*177	ENST00000361632		625	Gag/ag	14/16	0.199633912742351	3	FACETS	0.872	0.75	1	0.291	0.25	0.335	INDETERMINATE	1	TRUE	0	0.373091294769716	3		419	416	SUCCESS
ALK	238	MSKCC	GRCh37	2	29497976	29497978	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0067739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	98	475	0	ENST00000389048.3:c.2028_2030del	p.Phe677del	p.F677del	ENST00000389048	NM_004304.4	676	atCTTt/att	11/29	0.389565271788072	3	FACETS	1	0.898	1	0.502	0.449	0.558	CLONAL	1	TRUE	1	0.414078216243792	3		475	569	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189300	99189300	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	91	438	0	ENST00000074304.5:c.2556G>C	p.Gln852His	p.Q852H	ENST00000074304	NM_001134224.1	852	caG/caC	24/26	0.374486897648147	4	FACETS	0.973	0.865	1	0.486	0.432	0.544	CLONAL	1	TRUE	2	0.414078216243792	4		438	639	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480500	57480507	+	stop_gained,protein_altering_variant	Nonsense_Mutation	DEL	CTCCAACG	CTCCAACG	TT	novel	NA	P-0067739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	110	486	1	ENST00000371085.3:c.495_502delinsTT	p.Ser166_Glu168delinsTer	p.S166_E168delins*	ENST00000371085	NM_000516.4	165	cgCTCCAACGag/cgTTag	6/13	0.414078216243792	6	FACETS	1	0.952	1	0.276	0.247	0.306	CLONAL	1	TRUE	2	0.414078216243792	6		487	881	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968924	32968924	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067740-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	95	542	0	ENST00000380152.3:c.9356del	p.Leu3119Ter	p.L3119*	ENST00000380152		3119	Tta/ta	25/27	0.319120143193941	1	FACETS	0.793	0.708	0.884	0.793	0.708	0.884	SUBCLONAL	1	TRUE	0	0.337869802832967	1		542	589	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112227	115112228	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCGAAGCCGGCCT	novel	NA	P-0067740-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	61	688	0	ENST00000257566.3:c.1512_1513insAGGCCGGCTTCGCC	p.Pro505ArgfsTer132	p.P505Rfs*132	ENST00000257566	NM_016569.3	504	-/AGGCCGGCTTCGCC	7/8	1	2	FACETS	0.549	0.473	0.631	0.549	0.473	0.631	SUBCLONAL	1	TRUE	1	0.337869802832967	2		688	658	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275362	142275363	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATTC	novel	NA	P-0067740-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	93	477	0	ENST00000350721.4:c.1937_1940dup	p.Ile647MetfsTer5	p.I647Mfs*5	ENST00000350721	NM_001184.3	647	ata/atGAATa	9/47	1	2	FACETS	0.936	0.834	1	0.936	0.834	1	CLONAL	1	TRUE	1	0.337869802832967	2		477	588	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0067741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	132	288	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.999	0.917	1	0.999	0.917	1	CLONAL	1	TRUE	1	0.674001132983802	2		288	392	SUCCESS
APC	324	MSKCC	GRCh37	5	112175751	112175752	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1114167577	NA	P-0067741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	192	604	0	ENST00000257430.4:c.4463dup	p.Leu1488PhefsTer26	p.L1488Ffs*26	ENST00000257430	NM_000038.5	1487	act/acTt	16/16	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.674001132983802	2		604	543	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855543	45855543	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs140296400	NA	P-0067741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	227	600	0	ENST00000391945.4:c.2114A>G	p.Asn705Ser	p.N705S	ENST00000391945	NM_000400.3	705	aAc/aGc	22/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.674001132983802	2		600	604	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032401	10032401	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs78631453	NA	P-0067741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	191	472	0	ENST00000330684.3:c.422C>T	p.Thr141Met	p.T141M	ENST00000330684	NM_001134407.1	141	aCg/aTg	3/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.674001132983802	2		472	474	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119780	70119781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0067741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	249	501	0	ENST00000245479.2:c.788dup	p.Arg264GlnfsTer32	p.R264Qfs*32	ENST00000245479	NM_000346.3	261	gag/gaGg	3/3	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.674001132983802	2		501	592	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881329	37881329	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	256	600	0	ENST00000269571.5:c.2521C>A	p.Leu841Ile	p.L841I	ENST00000269571		841	Ctc/Atc	21/27	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.674001132983802	2		600	635	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410088	139410088	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763886355	NA	P-0067741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	261	638	0	ENST00000277541.6:c.1750G>A	p.Val584Ile	p.V584I	ENST00000277541	NM_017617.3	584	Gtc/Atc	11/34	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.674001132983802	2		638	648	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982141	201982142	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	617	594	0	ENST00000359651.3:c.666dup	p.Asp223Ter	p.D223*	ENST00000359651		222	act/acTt	5/8	0.349806205597455	6	FACETS	0.978	0.947	1			1	INDETERMINATE	4	TRUE	NA	0.674001132983802	6		594	1099	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267003	41267003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144087793	NA	P-0067741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	276	647	0	ENST00000349496.5:c.674G>A	p.Arg225His	p.R225H	ENST00000349496	NM_001904.3	225	cGt/cAt	5/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.674001132983802	2		647	730	SUCCESS
APC	324	MSKCC	GRCh37	5	112155002	112155002	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	178	504	0	ENST00000257430.4:c.1273G>T	p.Glu425Ter	p.E425*	ENST00000257430	NM_000038.5	425	Gaa/Taa	10/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.674001132983802	2		504	482	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101186	27101186	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	494	684	0	ENST00000324856.7:c.4468G>T	p.Glu1490Ter	p.E1490*	ENST00000324856	NM_006015.4	1490	Gag/Tag	18/20	0.674001132983802	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.674001132983802	2		684	677	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762491	41762491	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1441087022	NA	P-0067741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	221	528	2	ENST00000301178.4:c.2171G>A	p.Arg724His	p.R724H	ENST00000301178	NM_021913.4	724	cGt/cAt	18/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.674001132983802	2		530	580	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871314	35871314	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs200751605	NA	P-0067741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	130	371	0	ENST00000303115.3:c.536C>T	p.Thr179Met	p.T179M	ENST00000303115	NM_002185.3	179	aCg/aTg	4/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.674001132983802	2		371	344	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120310	70120311	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CACAGTAA	novel	NA	P-0067741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	268	620	0	ENST00000245479.2:c.1319_1320insACACAGTA	p.Tyr440Ter	p.Y440*	ENST00000245479	NM_000346.3	438	tca/tCACAGTAAca	3/3	1	2	FACETS	0.997	0.938	1	0.997	0.938	1	CLONAL	1	TRUE	1	0.674001132983802	2		620	798	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564558	55564558	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	192	493	0	ENST00000288135.5:c.446A>C	p.Lys149Thr	p.K149T	ENST00000288135	NM_000222.2	149	aAg/aCg	3/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.674001132983802	2		493	512	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562675	21562675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1460912842	NA	P-0067741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	202	672	1	ENST00000382592.4:c.1244G>A	p.Arg415Gln	p.R415Q	ENST00000382592	NM_014572.2	415	cGg/cAg	4/8	0.674001132983802	3	FACETS	1	0.983	1	0.587	0.546	0.628	CLONAL	1	TRUE	1	0.674001132983802	3		673	683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0067742-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	188	395	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.3	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.33	3		395	574	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30102152	30102152	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs775376594	NA	P-0067742-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	16	330	0	ENST00000331968.5:c.1315C>T	p.Arg439Trp	p.R439W	ENST00000331968	NM_002742.2	439	Cgg/Tgg	9/18	1	2	FACETS	0.345	0.255	0.453	0.345	0.255	0.453	SUBCLONAL	1	TRUE	1	0.33	2		330	281	SUCCESS
APC	324	MSKCC	GRCh37	5	112175416	112175417	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067742-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	43	457	0	ENST00000257430.4:c.4126dup	p.Tyr1376LeufsTer10	p.Y1376Lfs*10	ENST00000257430	NM_000038.5	1375	-/T	16/16	1	2	FACETS	0.609	0.51	0.718	0.609	0.51	0.718	SUBCLONAL	1	TRUE	1	0.33	2		457	428	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21652495	21652495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201737130	NA	P-0067742-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	16	269	0	ENST00000421138.2:c.10G>A	p.Val4Ile	p.V4I	ENST00000421138		4	Gtt/Att	3/16	0.277207573135795	3	FACETS	0.388	0.286	0.51	0.194	0.143	0.255	SUBCLONAL	1	TRUE	1	0.33	3		269	291	SUCCESS
APC	324	MSKCC	GRCh37	5	112174796	112174798	+	frameshift_variant	Frame_Shift_Del	DEL	GAG	GAG	AA	novel	NA	P-0067742-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	34	503	0	ENST00000257430.4:c.3505_3507delinsAA	p.Glu1169LysfsTer13	p.E1169Kfs*13	ENST00000257430	NM_000038.5	1169	GAG/AA	16/16	1	2	FACETS	0.582	0.476	0.701	0.582	0.476	0.701	SUBCLONAL	1	TRUE	1	0.33	2		503	354	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	37	678	7	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.777	0.641	0.93	0.777	0.641	0.93	CLONAL	1	TRUE	1	0.220409202385078	2		685	432	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	108	624	0	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	1	0.909	1	1	0.988	1	CLONAL	2	TRUE	1	0.220409202385078	2		624	486	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307393	118307394	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1555138552	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	11	292	0	ENST00000534358.1:c.173dup	p.Ala59GlyfsTer88	p.A59Gfs*88	ENST00000534358	NM_005933.3	56	tcc/tCcc	1/36	1	2	FACETS	0.745	0.517	1	0.745	0.517	1	CLONAL	1	TRUE	1	0.220409202385078	2		292	134	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	76	556	4	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.864	0.762	0.973	1	0.981	1	CLONAL	2	TRUE	1	0.220409202385078	2		560	399	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	102	577	5	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.841	0.755	0.933	1	0.985	1	CLONAL	2	TRUE	1	0.220409202385078	2		582	550	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	83	638	1	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.899	0.797	1	1	0.983	1	CLONAL	2	TRUE	1	0.220409202385078	2		639	419	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	102	707	5	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	1	2	FACETS	0.916	0.823	1	1	0.986	1	CLONAL	2	TRUE	1	0.220409202385078	2		712	505	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	102	441	5	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	0.767	0.688	0.852	1	0.983	1	SUBCLONAL	2	TRUE	1	0.220409202385078	2		446	603	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	203	707	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.884	0.827	0.942	1	0.995	1	CLONAL	4	TRUE	1	0.220409202385078	2		711	521	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	89	573	5	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.945	1	1	0.987	1	CLONAL	2	TRUE	1	0.220409202385078	2		578	370	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	76	284	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.977	0.863	1	1	0.983	1	CLONAL	2	TRUE	1	0.220409202385078	2		284	353	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	80	307	0	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.220409202385078	2		307	491	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1687996	1687996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200152611	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	77	639	0	ENST00000378625.1:c.880G>A	p.Ala294Thr	p.A294T	ENST00000378625	NM_001198994.1	294	Gcc/Acc	7/14	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.220409202385078	2		639	588	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776087	9776087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755725121	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	21	601	0	ENST00000377346.4:c.551G>A	p.Arg184Gln	p.R184Q	ENST00000377346	NM_005026.3	184	cGg/cAg	5/24	1	2	FACETS	0.459	0.353	0.584	0.459	0.353	0.584	SUBCLONAL	1	TRUE	1	0.220409202385078	2		601	415	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059236	27059236	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	89	434	0	ENST00000324856.7:c.1873C>T	p.Gln625Ter	p.Q625*	ENST00000324856	NM_006015.4	625	Caa/Taa	4/20	1	2	FACETS	0.859	0.765	0.959	1	0.983	1	CLONAL	2	TRUE	1	0.220409202385078	2		434	470	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400830	72400830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	86	486	1	ENST00000357731.5:c.341G>A	p.Gly114Asp	p.G114D	ENST00000357731	NM_173808.2	114	gGc/gAc	2/7	1	2	FACETS	0.925	0.822	1	1	0.984	1	CLONAL	2	TRUE	1	0.220409202385078	2		487	422	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852118	63852118	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	80	583	0	ENST00000279873.7:c.2901del	p.Lys967AsnfsTer15	p.K967Nfs*15	ENST00000279873	NM_032199.2	966	Aaa/aa	10/10	1	2	FACETS	0.764	0.675	0.859	1	0.978	1	SUBCLONAL	2	TRUE	1	0.220409202385078	2		583	475	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420204	49420204	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	82	676	0	ENST00000301067.7:c.15545del	p.Gly5182AlafsTer61	p.G5182Afs*61	ENST00000301067	NM_003482.3	5182	gGc/gc	48/54	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.220409202385078	2		676	535	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	164	535	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	0.217593511196625	2	FACETS	0.925	0.855	0.998	1	0.988	1	CLONAL	3	TRUE	0	0.220409202385078	2		535	536	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467143	99467143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369599027	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	31	490	0	ENST00000268035.6:c.2524C>T	p.Pro842Ser	p.P842S	ENST00000268035	NM_000875.3	842	Cca/Tca	12/21	0.217593511196625	2	FACETS	0.642	0.519	0.782	0.321	0.259	0.391	SUBCLONAL	1	TRUE	0	0.220409202385078	2		490	438	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127724	2127724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397515306	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	105	615	0	ENST00000219476.3:c.2963G>A	p.Arg988His	p.R988H	ENST00000219476	NM_000548.3	988	cGc/cAc	26/42	1	2	FACETS	0.959	0.863	1	1	0.987	1	CLONAL	2	TRUE	1	0.220409202385078	2		615	497	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136823	2136823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	33	682	0	ENST00000219476.3:c.4940C>T	p.Ser1647Phe	p.S1647F	ENST00000219476	NM_000548.3	1647	tCc/tTc	38/42	1	2	FACETS	0.574	0.466	0.695	0.574	0.466	0.695	SUBCLONAL	1	TRUE	1	0.220409202385078	2		682	522	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783767	50783767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375455772	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	43	507	0	ENST00000398568.2:c.158G>A	p.Arg53His	p.R53H	ENST00000398568	NM_001042412.1	53	cGt/cAt	3/18	1	2	FACETS	0.759	0.635	0.897	0.759	0.635	0.897	SUBCLONAL	1	TRUE	1	0.220409202385078	2		507	514	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827474	72827474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749152788	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	50	542	0	ENST00000268489.5:c.9107G>A	p.Arg3036Gln	p.R3036Q	ENST00000268489	NM_006885.3	3036	cGg/cAg	9/10	1	2	FACETS	0.856	0.726	0.999	0.856	0.726	0.999	CLONAL	1	TRUE	1	0.220409202385078	2		542	530	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	51	586	5	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	0.815	0.692	0.949	0.815	0.692	0.949	CLONAL	1	TRUE	1	0.220409202385078	2		591	568	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222490	2222490	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs995952663	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	100	584	0	ENST00000398665.3:c.3322C>T	p.Arg1108Ter	p.R1108*	ENST00000398665	NM_032482.2	1108	Cga/Tga	24/28	1	2	FACETS	1	0.922	1	1	0.988	1	CLONAL	2	TRUE	1	0.220409202385078	2		584	440	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214637	5214637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757423838	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	98	649	0	ENST00000357368.4:c.4429C>T	p.Arg1477Cys	p.R1477C	ENST00000357368	NM_002850.3	1477	Cgt/Tgt	29/38	1	2	FACETS	1	0.922	1	1	0.987	1	CLONAL	2	TRUE	1	0.220409202385078	2		649	431	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6213975	6213976	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs772076449	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	30	545	0	ENST00000252674.7:c.1381dup	p.Gln461ProfsTer23	p.Q461Pfs*23	ENST00000252674	NM_005934.3	461	cag/cCag	9/12	1	2	FACETS	0.861	0.696	1	0.861	0.696	1	CLONAL	1	TRUE	1	0.220409202385078	2		545	316	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311682	15311684	+	inframe_deletion	In_Frame_Del	DEL	CGG	CGG	-	rs894374843	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	68	818	8	ENST00000263388.2:c.33_35del	p.Arg13del	p.R13del	ENST00000263388	NM_000435.2	11	cgCCGt/cgt	1/33	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.220409202385078	2		826	451	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974351	18974351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1249690376	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	106	677	0	ENST00000262803.5:c.2705C>T	p.Pro902Leu	p.P902L	ENST00000262803	NM_002911.3	902	cCg/cTg	19/24	1	2	FACETS	0.945	0.851	1	1	0.987	1	CLONAL	2	TRUE	1	0.220409202385078	2		677	509	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	55	885	0	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.938	0.803	1	0.938	0.803	1	CLONAL	1	TRUE	1	0.220409202385078	2		885	532	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224183	36224183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771130237	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	37	452	0	ENST00000222270.7:c.6733G>A	p.Val2245Met	p.V2245M	ENST00000222270	NM_014727.1	2245	Gtg/Atg	28/37	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.220409202385078	2		452	261	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867709	45867709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200895828	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	67	820	3	ENST00000391945.4:c.691G>A	p.Val231Met	p.V231M	ENST00000391945	NM_000400.3	231	Gtg/Atg	8/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.220409202385078	2		823	450	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025856	48025857	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs267608041	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	43	555	0	ENST00000234420.5:c.741dup	p.Arg248ThrfsTer8	p.R248Tfs*8	ENST00000234420	NM_000179.2	245	ata/atAa	4/10	1	2	FACETS	0.706	0.59	0.834	0.706	0.59	0.834	SUBCLONAL	1	TRUE	1	0.220409202385078	2		555	553	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660670	190660670	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	33	490	0	ENST00000441310.2:c.308T>C	p.Ile103Thr	p.I103T	ENST00000441310	NM_000534.4	103	aTa/aCa	3/13	1	2	FACETS	0.504	0.409	0.611	0.504	0.409	0.611	SUBCLONAL	1	TRUE	1	0.220409202385078	2		490	594	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108185	209108185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751364381	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	55	392	0	ENST00000345146.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000345146	NM_005896.2	222	Cgt/Tgt	6/10	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.220409202385078	2		392	468	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989591	212989592	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1553563398	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	78	441	0	ENST00000342788.4:c.119_120del	p.Ser40Ter	p.S40*	ENST00000342788	NM_005235.2	40	tCT/t	2/28	1	2	FACETS	0.819	0.723	0.922	1	0.98	1	CLONAL	2	TRUE	1	0.220409202385078	2		441	432	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661664	227661664	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs761880048	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	85	660	18	ENST00000305123.5:c.1791del	p.His598ThrfsTer38	p.H598Tfs*38	ENST00000305123	NM_005544.2	597	ggG/gg	1/2	1	2	FACETS	1	0.916	1	1	0.986	1	CLONAL	2	TRUE	1	0.220409202385078	2		678	373	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21345972	21345972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1346699262	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	43	710	0	ENST00000215739.8:c.847C>T	p.Arg283Trp	p.R283W	ENST00000215739	NM_006767.3	283	Cgg/Tgg	9/21	1	2	FACETS	0.889	0.744	1	0.889	0.744	1	CLONAL	1	TRUE	1	0.220409202385078	2		710	439	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374245	138374245	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	25	485	0	ENST00000289153.2:c.3199G>T	p.Asp1067Tyr	p.D1067Y	ENST00000289153	NM_006219.2	1067	Gac/Tac	22/22	1	2	FACETS	0.462	0.363	0.576	0.462	0.363	0.576	SUBCLONAL	1	TRUE	1	0.220409202385078	2		485	491	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446270	187446270	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	34	625	1	ENST00000232014.4:c.1418del	p.Pro473ArgfsTer117	p.P473Rfs*117	ENST00000232014	NM_001130845.1	473	cCg/cg	6/10	1	2	FACETS	0.635	0.518	0.766	0.635	0.518	0.766	SUBCLONAL	1	TRUE	1	0.220409202385078	2		626	486	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106194022	106194022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	117	486	1	ENST00000380013.4:c.4484C>T	p.Ala1495Val	p.A1495V	ENST00000380013	NM_001127208.2	1495	gCc/gTc	10/11	1	2	FACETS	0.892	0.807	0.982	1	0.988	1	CLONAL	2	TRUE	1	0.220409202385078	2		487	595	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178258	56178258	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	53	562	0	ENST00000399503.3:c.3236del	p.Asn1079IlefsTer3	p.N1079Ifs*3	ENST00000399503	NM_005921.1	1077	tcA/tc	14/20	1	2	FACETS	0.966	0.824	1	0.966	0.824	1	CLONAL	1	TRUE	1	0.220409202385078	2		562	498	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520241	176520241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	38	652	0	ENST00000292408.4:c.1160C>T	p.Ala387Val	p.A387V	ENST00000292408	NM_213647.1	387	gCc/gTc	9/18	1	2	FACETS	0.758	0.626	0.905	0.758	0.626	0.905	CLONAL	1	TRUE	1	0.220409202385078	2		652	455	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402540	20402540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	41	525	1	ENST00000346618.3:c.77C>T	p.Ala26Val	p.A26V	ENST00000346618	NM_001949.4	26	gCc/gTc	1/7	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.220409202385078	2		526	351	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323262	31323262	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs77665001	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	60	314	0	ENST00000412585.2:c.727C>T	p.Arg243Trp	p.R243W	ENST00000412585	NM_005514.6	243	Cgg/Tgg	4/8	1	2	FACETS	0.939	0.815	1	1	0.978	1	CLONAL	2	TRUE	1	0.220409202385078	2		314	290	SUCCESS
MTAP	4507	MSKCC	GRCh37	9	21854745	21854745	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	80	539	0	ENST00000380172.4:c.571del	p.Ala191ArgfsTer6	p.A191Rfs*6	ENST00000380172	NM_002451.3	189	tGg/tg	6/8	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.220409202385078	2		539	486	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128420047	128420047	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	76	428	1	ENST00000265960.3:c.381del	p.Lys127AsnfsTer20	p.K127Nfs*20	ENST00000265960	NM_001006617.1	127	aaA/aa	4/12	1	2	FACETS	0.809	0.713	0.912	1	0.979	1	CLONAL	2	TRUE	1	0.220409202385078	2		429	426	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs753143066	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	34	447	6	ENST00000295797.4:c.826dup	p.Thr276AsnfsTer16	p.T276Nfs*16	ENST00000295797	NM_002740.5	273	tta/ttAa	9/18	1	2	FACETS	0.637	0.52	0.77	0.637	0.52	0.77	SUBCLONAL	1	TRUE	1	0.220409202385078	2		453	484	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821613	72821618	+	inframe_deletion	In_Frame_Del	DEL	CCGCCA	CCGCCA	-	rs761344900	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	27	739	0	ENST00000268489.5:c.10557_10562del	p.Gly3526_Gly3527del	p.G3526_G3527del	ENST00000268489	NM_006885.3	3519	ggTGGCGGc/ggc	10/10	1	2	FACETS	0.595	0.473	0.734	0.595	0.473	0.734	SUBCLONAL	1	TRUE	1	0.220409202385078	2		739	412	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1685629	1685629	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	104	716	0	ENST00000378625.1:c.1397del	p.Pro466ArgfsTer15	p.P466Rfs*15	ENST00000378625	NM_001198994.1	466	cCg/cg	12/14	1	2	FACETS	1	0.917	1	1	0.988	1	CLONAL	2	TRUE	1	0.220409202385078	2		716	462	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150900312	150900312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772551762	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	107	590	0	ENST00000271640.5:c.122G>A	p.Arg41Gln	p.R41Q	ENST00000271640	NM_001145415.1	41	cGg/cAg	2/22	1	2	FACETS	0.858	0.772	0.948	1	0.986	1	CLONAL	2	TRUE	1	0.220409202385078	2		590	566	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10776563	10776563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141469100	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	101	539	0	ENST00000361367.2:c.203G>A	p.Arg68His	p.R68H	ENST00000361367	NM_014633.3	68	cGt/cAt	3/25	1	2	FACETS	0.817	0.732	0.906	1	0.984	1	CLONAL	2	TRUE	1	0.220409202385078	2		539	561	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572273	64572273	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765306552	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	125	876	0	ENST00000312049.6:c.1366C>T	p.Arg456Cys	p.R456C	ENST00000312049	NM_130799.2	456	Cgc/Tgc	10/10	1	2	FACETS	0.895	0.812	0.981	1	0.988	1	CLONAL	2	TRUE	1	0.220409202385078	2		876	634	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129773	108129773	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	100	418	0	ENST00000278616.4:c.2437A>G	p.Asn813Asp	p.N813D	ENST00000278616	NM_000051.3	813	Aat/Gat	16/63	1	2	FACETS	0.851	0.763	0.944	1	0.985	1	CLONAL	2	TRUE	1	0.220409202385078	2		418	533	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287243	46287244	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	29	596	0	ENST00000334344.6:c.5192dup	p.Ala1732GlyfsTer28	p.A1732Gfs*28	ENST00000334344	NM_152641.2	1730	caa/cAaa	19/21	1	2	FACETS	0.511	0.409	0.627	0.511	0.409	0.627	SUBCLONAL	1	TRUE	1	0.220409202385078	2		596	515	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123868747	123868747	+	start_lost	Translation_Start_Site	SNP	T	T	C	rs771910601	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	68	550	0	ENST00000330479.4:c.2T>C	p.Met1?	p.M1?	ENST00000330479	NM_020382.3	1	aTg/aCg	1/9	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.220409202385078	2		550	414	SUCCESS
SCG5	6447	MSKCC	GRCh37	15	32976815	32976815	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	80	457	0	ENST00000300175.4:c.434A>G	p.Gln145Arg	p.Q145R	ENST00000300175	NM_001144757.1	145	cAg/cGg	4/6	1	2	FACETS	0.86	0.761	0.966	1	0.981	1	CLONAL	2	TRUE	1	0.220409202385078	2		457	422	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322588	30322588	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	38	379	0	ENST00000322652.5:c.1601A>C	p.Lys534Thr	p.K534T	ENST00000322652	NM_015355.2	534	aAa/aCa	14/16	1	2	FACETS	0.866	0.717	1	0.866	0.717	1	CLONAL	1	TRUE	1	0.220409202385078	2		379	398	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41222956	41222956	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	89	602	0	ENST00000357654.3:c.4975C>A	p.Pro1659Thr	p.P1659T	ENST00000357654	NM_007294.3	1659	Cca/Aca	15/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.220409202385078	2		602	546	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245274	41245275	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80357681	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	131	537	0	ENST00000357654.3:c.2273dup	p.Leu758PhefsTer4	p.L758Ffs*4	ENST00000357654	NM_007294.3	758	ttg/ttTg	10/23	1	2	FACETS	1	0.911	1	1	0.99	1	CLONAL	2	TRUE	1	0.220409202385078	2		537	594	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39613805	39613805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1289206436	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	35	378	0	ENST00000262039.4:c.1723G>A	p.Ala575Thr	p.A575T	ENST00000262039	NM_002647.2	575	Gca/Aca	16/25	1	2	FACETS	0.782	0.641	0.94	0.782	0.641	0.94	CLONAL	1	TRUE	1	0.220409202385078	2		378	406	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265694	10265694	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs199473692	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	48	633	0	ENST00000340748.4:c.1483T>C	p.Tyr495His	p.Y495H	ENST00000340748		495	Tat/Cat	19/40	1	2	FACETS	0.961	0.814	1	0.961	0.814	1	CLONAL	1	TRUE	1	0.220409202385078	2		633	453	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752717	42752718	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	44	642	0	ENST00000222329.4:c.1546dup	p.Glu516GlyfsTer18	p.E516Gfs*18	ENST00000222329	NM_006494.2	516	gag/gGag	4/4	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.220409202385078	2		642	341	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568829	212568829	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	67	379	0	ENST00000342788.4:c.1289G>T	p.Ser430Ile	p.S430I	ENST00000342788	NM_005235.2	430	aGt/aTt	11/28	1	2	FACETS	0.817	0.714	0.928	1	0.976	1	CLONAL	2	TRUE	1	0.220409202385078	2		379	372	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023763	31023763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	33	565	0	ENST00000375687.4:c.3248C>T	p.Ala1083Val	p.A1083V	ENST00000375687	NM_015338.5	1083	gCc/gTc	13/13	1	2	FACETS	0.673	0.548	0.814	0.673	0.548	0.814	SUBCLONAL	1	TRUE	1	0.220409202385078	2		565	445	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37081762	37081762	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	178	447	0	ENST00000231790.2:c.1644C>A	p.Tyr548Ter	p.Y548*	ENST00000231790	NM_000249.3	548	taC/taA	14/19	0.220409202385078	2	FACETS	0.893	0.832	0.956	1	0.993	1	CLONAL	4	TRUE	0	0.220409202385078	2		447	452	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138431137	138431137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	101	370	0	ENST00000289153.2:c.1312G>A	p.Val438Ile	p.V438I	ENST00000289153	NM_006219.2	438	Gta/Ata	8/22	1	2	FACETS	0.951	0.854	1	1	0.987	1	CLONAL	2	TRUE	1	0.220409202385078	2		370	482	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383988	84383988	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs35378950	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	33	425	0	ENST00000321945.7:c.864del	p.Pro289GlnfsTer13	p.P289Qfs*13	ENST00000321945	NM_139076.2	288	ttT/tt	9/9	1	2	FACETS	0.587	0.477	0.711	0.587	0.477	0.711	SUBCLONAL	1	TRUE	1	0.220409202385078	2		425	510	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245464	153245464	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1429385222	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	70	529	0	ENST00000281708.4:c.1727C>T	p.Thr576Met	p.T576M	ENST00000281708	NM_033632.3	576	aCg/aTg	11/12	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.220409202385078	2		529	447	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323135	31323135	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	61	783	1	ENST00000412585.2:c.854T>C	p.Val285Ala	p.V285A	ENST00000412585	NM_005514.6	285	gTa/gCa	4/8	1	2	FACETS	0.94	0.811	1	0.94	0.811	1	CLONAL	1	TRUE	1	0.220409202385078	2		784	589	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020387	69020387	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	42	485	0	ENST00000288368.4:c.2759A>G	p.Gln920Arg	p.Q920R	ENST00000288368	NM_024870.2	920	cAg/cGg	24/40	0.220409202385078	5	FACETS	0.871	0.727	1	0.174	0.145	0.207	CLONAL	1	TRUE	0	0.220409202385078	5		485	582	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128246848	128246848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139882483	NA	P-0067746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	85	497	0	ENST00000265960.3:c.1081G>A	p.Gly361Arg	p.G361R	ENST00000265960	NM_001006617.1	361	Ggg/Agg	9/12	1	2	FACETS	0.821	0.728	0.919	1	0.981	1	CLONAL	2	TRUE	1	0.220409202385078	2		497	470	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415537	152415537	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519714	NA	P-0067774-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	134	502	0	ENST00000206249.3:c.1387T>C	p.Ser463Pro	p.S463P	ENST00000206249	NM_000125.3	463	Tcc/Ccc	7/8	0.405125802643909	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	3	TRUE	0	0.458081208350186	3		502	233	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778090	135778090	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203673	NA	P-0067774-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	51	501	0	ENST00000298552.3:c.2293C>T	p.Gln765Ter	p.Q765*	ENST00000298552	NM_001162426.1	765	Cag/Tag	18/23	0.458081208350186	1	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	0	0.458081208350186	1		501	166	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832898	3832898	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067776-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	232	360	0	ENST00000262367.5:c.1360C>T	p.Gln454Ter	p.Q454*	ENST00000262367	NM_004380.2	454	Caa/Taa	6/31	0.491764921241542	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.491764921241542	3		360	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0067776-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	402	468	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.491764921241542	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	TRUE	0	0.491764921241542	3		468	671	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556657	41556657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067776-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	240	394	0	ENST00000263253.7:c.3602G>A	p.Cys1201Tyr	p.C1201Y	ENST00000263253	NM_001429.3	1201	tGt/tAt	20/31	0.409580718854372	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.491764921241542	3		394	587	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41022124	41022124	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067776-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	45	296	0	ENST00000267868.3:c.848C>G	p.Pro283Arg	p.P283R	ENST00000267868	NM_002875.4	283	cCc/cGc	9/10	NA	2	FACETS	0.495	0.417	0.58			1	INDETERMINATE	1	TRUE	NA	0.491764921241542	2		296	370	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525600	187525601	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0067776-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	183	385	0	ENST00000441802.2:c.10478dup	p.Gln3494AlafsTer27	p.Q3494Afs*27	ENST00000441802	NM_005245.3	3493	ccg/ccCg	18/27	0.491764921241542	3	FACETS	0.815	0.757	0.874	0.815	0.757	0.874	CLONAL	2	TRUE	1	0.491764921241542	3		385	569	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526672	31526672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067776-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	300	406	0	ENST00000344624.3:c.368C>T	p.Pro123Leu	p.P123L	ENST00000344624		123	cCa/cTa	2/33	0.428171107187531	5	FACETS	0.961	0.911	1	0.961	0.911	1	CLONAL	3	TRUE	2	0.491764921241542	5		406	735	SUCCESS
APC	324	MSKCC	GRCh37	5	112175331	112175331	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067776-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	52	329	0	ENST00000257430.4:c.4040C>G	p.Ala1347Gly	p.A1347G	ENST00000257430	NM_000038.5	1347	gCc/gGc	16/16	0.491764921241542	3	FACETS	0.531	0.452	0.617	0.177	0.15	0.206	SUBCLONAL	1	TRUE	0	0.491764921241542	3		329	496	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670395	30670395	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067776-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	109	396	0	ENST00000376406.3:c.6037C>G	p.Gln2013Glu	p.Q2013E	ENST00000376406	NM_014641.2	2013	Cag/Gag	14/15	0.212816796083683	5	FACETS	1	0.921	1	0.343	0.308	0.381	INDETERMINATE	1	TRUE	2	0.491764921241542	5		396	748	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2054650	2054650	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067776-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	87	308	0	ENST00000349721.2:c.1100C>G	p.Ser367Cys	p.S367C	ENST00000349721	NM_003070.3	367	tCt/tGt	6/34	0.234626606138461	4	FACETS	0.881	0.781	0.988	0.441	0.39	0.494	INDETERMINATE	1	TRUE	2	0.491764921241542	4		308	599	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0067777-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	257	252	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.486263683058551	5	FACETS	1	0.973	1	1	0.973	1	CLONAL	4	TRUE	1	0.486263683058551	5		253	442	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034487	47034487	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067777-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	246	321	0	ENST00000377604.3:c.572A>G	p.Asn191Ser	p.N191S	ENST00000377604	NM_001204468.1	191	aAt/aGt	6/24	0.486263683058551	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	0	0.486263683058551	3		321	408	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578466	+	missense_variant	Missense_Mutation	TNP	GGG	GGG	AGT	novel	NA	P-0067777-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	340	555	0	ENST00000269305.4:c.464_466delinsACT	p.Thr155_Arg156delinsAsnCys	p.T155_R156delinsNC	ENST00000269305	NM_001126112.2	155	aCCCgc/aACTgc	5/11	0.486263683058551	3	FACETS	0.921	0.881	0.962	0.921	0.881	0.962	CLONAL	3	TRUE	0	0.486263683058551	3		555	629	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274835	142274835	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067777-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	228	354	0	ENST00000350721.4:c.2225G>A	p.Cys742Tyr	p.C742Y	ENST00000350721	NM_001184.3	742	tGt/tAt	10/47	0.486263683058551	5	FACETS	0.999	0.94	1	0.999	0.94	1	CLONAL	3	TRUE	2	0.486263683058551	5		354	541	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170817124	170817124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067777-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	60	209	0	ENST00000296930.5:c.128C>T	p.Ser43Phe	p.S43F	ENST00000296930	NM_002520.6	43	tCt/tTt	2/11	0.486263683058551	4	FACETS	1	0.941	1	0.579	0.502	0.661	CLONAL	1	TRUE	2	0.486263683058551	4		209	317	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0067778-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	22	395	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.202750103886534	3	FACETS	0.824	0.639	1			1	CLONAL	1	FALSE	NA	0.202926239714337	3		395	290	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156409	106156409	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067778-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	13	560	0	ENST00000380013.4:c.1310A>G	p.Tyr437Cys	p.Y437C	ENST00000380013	NM_001127208.2	437	tAc/tGc	3/11	0.202750103886534	1	FACETS	0.584	0.417	0.787	0.584	0.417	0.787	SUBCLONAL	1	FALSE	0	0.202926239714337	1		560	197	SUCCESS
BLM	641	MSKCC	GRCh37	15	91298147	91298147	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067778-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	84	429	0	ENST00000355112.3:c.1066G>T	p.Glu356Ter	p.E356*	ENST00000355112	NM_000057.2	356	Gaa/Taa	5/22	0.202926239714337	7	FACETS	1	0.932	1			1	CLONAL	4	FALSE	NA	0.202926239714337	7		429	295	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735658	204735658	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0067778-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	14	434	0	ENST00000302823.3:c.457+2T>C		p.X153_splice	ENST00000302823	NM_005214.4	153			1	2	FACETS	0.585	0.423	0.781	0.585	0.423	0.781	SUBCLONAL	1	FALSE	1	0.202926239714337	2		434	236	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847235	68847245	+	protein_altering_variant	In_Frame_Del	DEL	AGAACGAGGCT	AGAACGAGGCT	TG	novel	NA	P-0067778-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	24	421	1	ENST00000261769.5:c.1157_1167delinsTG	p.Glu386_Ala389delinsVal	p.E386_A389delinsV	ENST00000261769	NM_004360.3	386	gAGAACGAGGCT/gTG	9/16	0.202750103886534	1	FACETS	1	0.79	1	1	0.79	1	CLONAL	1	FALSE	0	0.202926239714337	1		422	212	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0067780-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	448	388	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.621407294125419	2		388	628	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952006	178952006	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067780-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	348	367	0	ENST00000263967.3:c.3061T>C	p.Tyr1021His	p.Y1021H	ENST00000263967	NM_006218.2	1021	Tac/Cac	21/21	0.340649316575693	2	FACETS	0.874	0.836	0.911	0.874	0.836	0.911	INDETERMINATE	2	TRUE	0	0.621407294125419	2		367	641	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189377	56189377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067780-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	105	332	0	ENST00000399503.3:c.4409C>T	p.Ala1470Val	p.A1470V	ENST00000399503	NM_005921.1	1470	gCt/gTt	20/20	0.397391905065126	1	FACETS	0.458	0.412	0.506	0.458	0.412	0.506	SUBCLONAL	1	TRUE	0	0.621407294125419	1		332	509	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391421	139391421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377112509	NA	P-0067780-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	208	467	0	ENST00000277541.6:c.6770C>T	p.Ala2257Val	p.A2257V	ENST00000277541	NM_017617.3	2257	gCg/gTg	34/34	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.621407294125419	2		467	668	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181849	56181849	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067780-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	91	306	0	ENST00000399503.3:c.4073C>T	p.Ser1358Leu	p.S1358L	ENST00000399503	NM_005921.1	1358	tCg/tTg	17/20	0.397391905065126	1	FACETS	0.433	0.386	0.483	0.433	0.386	0.483	SUBCLONAL	1	TRUE	0	0.621407294125419	1		306	466	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55334876	55334876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067780-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	261	305	0	ENST00000284073.2:c.153G>A	p.Met51Ile	p.M51I	ENST00000284073	NM_138962.2	51	atG/atA	3/14	0.621407294125419	7	FACETS	1	0.992	1			1	CLONAL	1	TRUE	NA	0.621407294125419	7		305	1472	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55334866	55334866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067780-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	264	281	0	ENST00000284073.2:c.143G>A	p.Arg48Lys	p.R48K	ENST00000284073	NM_138962.2	48	aGa/aAa	3/14	0.621407294125419	7	FACETS	0.767	0.717	0.818			1	SUBCLONAL	2	TRUE	NA	0.621407294125419	7		281	1415	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496924	29496927	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs786201874	NA	P-0067780-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	150	244	0	ENST00000356175.3:c.499_502del	p.Cys167GlnfsTer10	p.C167Qfs*10	ENST00000356175	NM_000267.3	165	acTGTT/ac	5/57	0.632027457987579	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.621407294125419	1		244	288	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	69	350	0				ENST00000310581	NM_198253.2	-/1132			0.151387631521282	3	FACETS	1	0.97	1	0.7	0.612	0.795	INDETERMINATE	1	TRUE	1	0.265774653695973	3		350	420	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0067783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	61	313	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.733	0.632	0.843	0.733	0.632	0.843	SUBCLONAL	1	TRUE	1	0.265774653695973	2		313	626	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577543	7577543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1019340046	NA	P-0067783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	32	461	1	ENST00000269305.4:c.738G>A	p.Met246Ile	p.M246I	ENST00000269305	NM_001126112.2	246	atG/atA	7/11	1	2	FACETS	0.43	0.348	0.523	0.43	0.348	0.523	SUBCLONAL	1	TRUE	1	0.265774653695973	2		462	560	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360602	118360602	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	58	386	0	ENST00000534358.1:c.4575G>A	p.Trp1525Ter	p.W1525*	ENST00000534358	NM_005933.3	1525	tgG/tgA	12/36	1	2	FACETS	0.767	0.659	0.885	0.767	0.659	0.885	SUBCLONAL	1	TRUE	1	0.265774653695973	2		386	569	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946303	81946304	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0067783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	34	467	0	ENST00000359376.3:c.2036_2037delinsAA	p.Ser679Ter	p.S679*	ENST00000359376	NM_002661.3	679	tCC/tAA	19/33	0.265774653695973	1	FACETS	0.424	0.346	0.513	0.424	0.346	0.513	SUBCLONAL	1	TRUE	0	0.265774653695973	1		467	523	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198262841	198262841	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0067783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	37	391	0	ENST00000335508.6:c.3135-1G>A		p.X1045_splice	ENST00000335508	NM_012433.2	1045			0.200513498236013	2	FACETS	0.524	0.432	0.628	0.262	0.216	0.314	SUBCLONAL	1	TRUE	0	0.265774653695973	2		391	531	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402587	20402587	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067784-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	86	375	0	ENST00000346618.3:c.124C>T	p.Pro42Ser	p.P42S	ENST00000346618	NM_001949.4	42	Ccc/Tcc	1/7	0.405966264493907	3	FACETS	1	0.961	1	0.574	0.515	0.635	INDETERMINATE	1	TRUE	1	0.80972604474262	3		375	260	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943769	71943769	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067784-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	179	479	0	ENST00000298229.2:c.1812G>T	p.Trp604Cys	p.W604C	ENST00000298229	NM_001567.3	604	tgG/tgT	15/28	0.80972604474262	2	FACETS	1	0.99	1	0.666	0.625	0.706	CLONAL	1	TRUE	0	0.80972604474262	2		479	332	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796240	42796240	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067784-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	98	379	0	ENST00000575354.2:c.2889C>G	p.Ile963Met	p.I963M	ENST00000575354	NM_015125.3	963	atC/atG	12/20	1	2	FACETS	0.927	0.841	1	0.927	0.841	1	CLONAL	1	TRUE	1	0.80972604474262	2		379	261	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61305220	61305220	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067784-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	78	325	0	ENST00000341074.5:c.906G>C	p.Met302Ile	p.M302I	ENST00000341074	NM_002974.2	302	atG/atC	8/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.80972604474262	2		325	157	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0067800-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	20	421	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.322648242973627	1	FACETS	0.776	0.612	0.954	1	0.928	1	CLONAL	2	FALSE	0	0.322648242973627	1		421	67	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578206	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs886039484	NA	P-0067800-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	71	509	0	ENST00000269305.4:c.643A>G	p.Ser215Gly	p.S215G	ENST00000269305	NM_001126112.2	215	Agt/Ggt	6/11	0.322648242973627	2	FACETS	1	0.915	1	1	0.986	1	CLONAL	4	FALSE	0	0.322648242973627	2		509	110	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944121	71944121	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067800-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	12	468	0	ENST00000298229.2:c.1954G>T	p.Glu652Ter	p.E652*	ENST00000298229	NM_001567.3	652	Gag/Tag	17/28	0.322648242973627	3	FACETS	0.554	0.39	0.753	0.277	0.195	0.377	SUBCLONAL	1	FALSE	1	0.322648242973627	3		468	156	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238398	98238398	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759078774	NA	P-0067801-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	31	395	0	ENST00000331920.6:c.1646C>T	p.Ala549Val	p.A549V	ENST00000331920	NM_000264.3	549	gCc/gTc	12/24	0.873149643040747	1	FACETS	0.102	0.082	0.125	0.102	0.082	0.125	SUBCLONAL	1	TRUE	0	0.873149643040747	1		395	392	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442804	442804	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067801-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	215	394	0	ENST00000399788.2:c.1502A>C	p.Lys501Thr	p.K501T	ENST00000399788	NM_001042603.1	501	aAg/aCg	12/28	NA	2	FACETS	0.697	0.65	0.744			1	INDETERMINATE	1	TRUE	NA	0.873149643040747	2		394	707	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696637	47696637	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067801-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	18	417	0	ENST00000347630.2:c.311T>G	p.Phe104Cys	p.F104C	ENST00000347630	NM_001007230.1	104	tTc/tGc	5/11	1	2	FACETS	0.774	0.588	0.989	0.774	0.588	0.989	CLONAL	1	TRUE	1	0.329927719311803	2		417	141	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0067802-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	546	373	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.889913777926914	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.889913777926914	2		373	592	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0067802-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	264	446	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.939	0.887	0.991	0.939	0.887	0.991	CLONAL	1	TRUE	1	0.889913777926914	2		446	632	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652129	36652129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34916193	NA	P-0067802-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	198	478	0	ENST00000244741.5:c.251G>A	p.Arg84Gln	p.R84Q	ENST00000244741	NM_000389.4	84	cGa/cAa	2/3	1	2	FACETS	0.876	0.819	0.934	0.876	0.819	0.934	CLONAL	1	TRUE	1	0.889913777926914	2		478	508	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916948	178916948	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs863225460	NA	P-0067802-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	124	382	1	ENST00000263967.3:c.335T>A	p.Ile112Asn	p.I112N	ENST00000263967	NM_006218.2	112	aTc/aAc	2/21	0.122454711305409	3	FACETS	1	0.987	1	0.732	0.675	0.79	INDETERMINATE	1	TRUE	1	0.889913777926914	3		383	275	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250914	153250914	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067802-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	105	315	0	ENST00000281708.4:c.1146T>A	p.His382Gln	p.H382Q	ENST00000281708	NM_033632.3	382	caT/caA	8/12	0.592167046505444	1	FACETS	0.766	0.71	0.82	0.766	0.71	0.82	SUBCLONAL	1	TRUE	0	0.889913777926914	1		315	171	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562333	176562333	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067802-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	272	474	0	ENST00000439151.2:c.229G>T	p.Asp77Tyr	p.D77Y	ENST00000439151	NM_022455.4	77	Gat/Tat	2/23	1	2	FACETS	0.945	0.893	0.997	0.945	0.893	0.997	CLONAL	1	TRUE	1	0.889913777926914	2		474	647	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47440565	47440565	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067802-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	258	421	1	ENST00000404338.3:c.3726G>A	p.Trp1242Ter	p.W1242*	ENST00000404338	NM_004491.4	1242	tgG/tgA	2/6	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.889913777926914	2		422	567	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004778	150004778	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067802-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	194	474	0	ENST00000253339.5:c.1447G>C	p.Ala483Pro	p.A483P	ENST00000253339		483	Gct/Cct	3/7	0.233684324740646	1	FACETS	0.484	0.452	0.517	0.484	0.452	0.517	INDETERMINATE	1	TRUE	0	0.889913777926914	1		474	500	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266958	18266958	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067802-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	237	378	0	ENST00000222254.8:c.269C>T	p.Pro90Leu	p.P90L	ENST00000222254	NM_005027.3	90	cCa/cTa	2/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.889913777926914	2		378	507	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0067804-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	98	284	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.25446476111714	3	FACETS	0.813	0.728	0.902	0.813	0.728	0.902	CLONAL	2	TRUE	1	0.276603957385361	3		284	496	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186838	108186838	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067804-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	64	339	0	ENST00000278616.4:c.6196C>T	p.Gln2066Ter	p.Q2066*	ENST00000278616	NM_000051.3	2066	Cag/Tag	42/63	0.276603957385361	1	FACETS	0.847	0.735	0.967	0.847	0.735	0.967	CLONAL	1	TRUE	0	0.276603957385361	1		339	471	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591889	48591889	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067804-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	15	400	0	ENST00000342988.3:c.1052A>G	p.Asp351Gly	p.D351G	ENST00000342988	NM_005359.5	351	gAt/gGt	9/12	0.276603957385361	1	FACETS	0.152	0.11	0.203	0.152	0.11	0.203	SUBCLONAL	1	TRUE	0	0.276603957385361	1		400	615	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604668	48604668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067804-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	45	360	0	ENST00000342988.3:c.1490G>A	p.Arg497His	p.R497H	ENST00000342988	NM_005359.5	497	cGc/cAc	12/12	0.276603957385361	1	FACETS	0.537	0.451	0.632	0.537	0.451	0.632	SUBCLONAL	1	TRUE	0	0.276603957385361	1		360	522	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909673	50909673	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771858429	NA	P-0067804-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	113	364	0	ENST00000440232.2:c.1393C>T	p.Arg465Trp	p.R465W	ENST00000440232	NM_002691.3	465	Cgg/Tgg	12/27	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.276603957385361	2		364	615	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524341	187524341	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067804-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	63	357	0	ENST00000441802.2:c.11339G>A	p.Cys3780Tyr	p.C3780Y	ENST00000441802	NM_005245.3	3780	tGt/tAt	19/27	1	2	FACETS	0.742	0.641	0.851	0.742	0.641	0.851	SUBCLONAL	1	TRUE	1	0.276603957385361	2		357	614	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220540	123220540	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067804-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	46	306	0	ENST00000218089.9:c.3201del	p.Ser1068GlnfsTer37	p.S1068Qfs*37	ENST00000218089	NM_001042749.1	1066	cGg/cg	30/35	1	2	FACETS	0.64	0.538	0.751	0.64	0.538	0.751	SUBCLONAL	1	TRUE	1	0.276603957385361	2		306	520	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538913	23538913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	151	398	0	ENST00000380871.4:c.526C>T	p.Arg176Cys	p.R176C	ENST00000380871	NM_006167.3	176	Cgc/Tgc	2/2	1	2	FACETS	0.904	0.831	0.98	0.904	0.831	0.98	CLONAL	1	TRUE	1	0.593136143169436	2		398	563	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860325	42860326	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGATTCT	novel	NA	P-0067806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	172	311	0	ENST00000398585.3:c.545_551dup	p.Cys185GlufsTer46	p.C185Efs*46	ENST00000398585	NM_001135099.1	184	cgg/cgAGAATCGg	5/14	1	2	FACETS	0.902	0.833	0.973	0.902	0.833	0.973	CLONAL	1	TRUE	1	0.593136143169436	2		311	643	SUCCESS
PHF6	84295	MSKCC	GRCh37	X	133527979	133527979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770811341	NA	P-0067806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1204	174	504	0	ENST00000332070.3:c.415G>A	p.Glu139Lys	p.E139K	ENST00000332070	NM_032458.2	139	Gaa/Aaa	5/10	0.593136143169436	5	FACETS	0.805	0.739	0.874	0.268	0.246	0.292	CLONAL	1	TRUE	2	0.593136143169436	5		504	1378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0067807-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	380	395	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.37871589029852	4	FACETS	0.986	0.945	1	0.986	0.945	1	CLONAL	4	TRUE	0	0.386785799047181	4		395	691	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467086	25467086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757492795	NA	P-0067807-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	185	451	0	ENST00000264709.3:c.1789C>T	p.Arg597Trp	p.R597W	ENST00000264709	NM_175629.2	597	Cgg/Tgg	15/23	0.292098239426443	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.386785799047181	4		451	604	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86676413	86676413	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs863223719	NA	P-0067807-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	51	402	0	ENST00000274376.6:c.2690+1G>A		p.X897_splice	ENST00000274376	NM_002890.2	897			0.195858287656529	4	FACETS	1	0.957	1	0.672	0.576	0.776	INDETERMINATE	1	TRUE	2	0.386785799047181	4		402	272	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259208	89259208	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067807-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	68	465	0	ENST00000336596.2:c.352G>T	p.Glu118Ter	p.E118*	ENST00000336596	NM_005233.5	118	Gag/Tag	3/17	0.386785799047181	2	FACETS	0.948	0.829	1	0.474	0.414	0.538	CLONAL	1	TRUE	0	0.386785799047181	2		465	371	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0067808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	60	389	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		389	210	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714236	43714236	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	73	574	0	ENST00000382044.4:c.3917del	p.Asp1306ValfsTer61	p.D1306Vfs*61	ENST00000382044	NM_001141980.1	1306	gAt/gt	19/28	0.507430058189357	1	FACETS	0.488	0.428	0.552	0.488	0.428	0.552	SUBCLONAL	1	FALSE	0	0.507430058189357	1		574	440	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786775	3786775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	40	445	2	ENST00000262367.5:c.4436G>A	p.Gly1479Glu	p.G1479E	ENST00000262367	NM_004380.2	1479	gGa/gAa	27/31	1	2	FACETS	0.38	0.316	0.451	0.38	0.316	0.451	SUBCLONAL	1	FALSE	1	0.507430058189357	2		447	415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0067814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	146	471	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.265445752110986	2	FACETS	1	0.987	1	0.72	0.661	0.78	CLONAL	1	TRUE	0	0.405588294523171	2		471	500	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0067814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	191	418	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.30016494481515	2	FACETS	0.859	0.8	0.92	0.859	0.8	0.92	CLONAL	2	TRUE	0	0.405588294523171	2		418	548	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026095	71026095	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	51	315	0	ENST00000318789.4:c.1527G>A	p.Trp509Ter	p.W509*	ENST00000318789	NM_032682.5	509	tgG/tgA	17/21	0.30016494481515	2	FACETS	0.66	0.563	0.766	0.33	0.281	0.383	SUBCLONAL	1	TRUE	0	0.405588294523171	2		315	381	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249016	55249017	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCCACG	rs397517114	NA	P-0067814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	276	506	0	ENST00000275493.2:c.2315_2320dup	p.His773_Val774insAlaHis	p.H773_V774insAH	ENST00000275493	NM_005228.3	772	ccc/cCCCACGcc	20/28	0.405588294523171	5	FACETS	0.894	0.843	0.947	0.894	0.843	0.947	CLONAL	3	TRUE	2	0.405588294523171	5		506	816	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410526	63410526	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs750449400	NA	P-0067814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	83	315	0	ENST00000330258.3:c.2641C>T	p.Arg881Ter	p.R881*	ENST00000330258	NM_152424.3	881	Cga/Tga	2/2	0.337434882856494	2	FACETS	0.907	0.804	1			1	CLONAL	1	TRUE	NA	0.405588294523171	2		315	451	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521276	8521276	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0067814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	37	347	0	ENST00000356435.5:c.961+1G>T		p.X321_splice	ENST00000356435		321			0.304991552256681	3	FACETS	0.524	0.432	0.626	0.175	0.144	0.209	SUBCLONAL	1	TRUE	0	0.405588294523171	3		347	419	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545791	106545791	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	132	357	0	ENST00000359195.3:c.3268C>G	p.Leu1090Val	p.L1090V	ENST00000359195	NM_002649.2	1090	Ctt/Gtt	11/11	0.254694654551737	4	FACETS	0.85	0.776	0.928	0.85	0.776	0.928	CLONAL	2	TRUE	2	0.405588294523171	4		357	538	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845343	42845343	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1313725740	NA	P-0067814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	35	520	0	ENST00000398585.3:c.919C>T	p.Gln307Ter	p.Q307*	ENST00000398585	NM_001135099.1	307	Cag/Tag	9/14	0.304991552256681	3	FACETS	0.358	0.292	0.432	0.119	0.097	0.144	SUBCLONAL	1	TRUE	0	0.405588294523171	3		520	580	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983465	90983465	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0067814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	114	372	0	ENST00000265433.3:c.638C>G	p.Ser213Ter	p.S213*	ENST00000265433	NM_002485.4	213	tCa/tGa	6/16	0.350403570548439	4	FACETS	0.79	0.715	0.869	0.79	0.715	0.869	SUBCLONAL	2	TRUE	2	0.405588294523171	4		372	500	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623894	28623894	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs766677410	NA	P-0067814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	69	473	0	ENST00000241453.7:c.760C>T	p.Gln254Ter	p.Q254*	ENST00000241453	NM_004119.2	254	Cag/Tag	7/24	0.299529058401593	2	FACETS	0.712	0.621	0.809	0.356	0.31	0.405	SUBCLONAL	1	TRUE	0	0.405588294523171	2		473	478	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0067815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	190	453	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	0.266848034797056	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.328220274502018	4		453	673	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398262	25398262	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913538	NA	P-0067815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	59	314	0	ENST00000311936.3:c.57G>C	p.Leu19Phe	p.L19F	ENST00000311936	NM_004985.3	19	ttG/ttC	2/5	0.204084878047011	4	FACETS	0.946	0.815	1	0.473	0.407	0.544	CLONAL	1	TRUE	2	0.328220274502018	4		314	505	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239387	123239387	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	77	404	1	ENST00000358487.5:c.2450G>A	p.Gly817Asp	p.G817D	ENST00000358487	NM_000141.4	817	gGc/gAc	18/18	0.266848034797056	4	FACETS	0.969	0.851	1	0.485	0.425	0.548	CLONAL	1	TRUE	2	0.328220274502018	4		405	643	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0067815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	70	353	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	0.266848034797056	4	FACETS	0.978	0.854	1	0.489	0.427	0.557	CLONAL	1	TRUE	2	0.328220274502018	4		353	579	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0067815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	101	403	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	0.266848034797056	4	FACETS	1	0.933	1	0.53	0.474	0.59	CLONAL	1	TRUE	2	0.328220274502018	4		403	771	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876565	35876565	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs141919625	NA	P-0067815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	81	439	0	ENST00000303115.3:c.1357T>C	p.Ser453Pro	p.S453P	ENST00000303115	NM_002185.3	453	Tcc/Ccc	8/8	0.328220274502018	6	FACETS	0.958	0.843	1			1	CLONAL	1	TRUE	NA	0.328220274502018	6		439	853	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665360	138665360	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	54	485	0	ENST00000330315.3:c.205G>C	p.Glu69Gln	p.E69Q	ENST00000330315	NM_023067.3	69	Gag/Cag	1/1	0.266848034797056	4	FACETS	0.832	0.711	0.965	0.416	0.355	0.483	CLONAL	1	TRUE	2	0.328220274502018	4		485	525	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856356	45856356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	61	485	0	ENST00000391945.4:c.1816G>A	p.Glu606Lys	p.E606K	ENST00000391945	NM_000400.3	606	Gag/Aag	19/23	0.107675814824426	5	FACETS	1	0.964	1	0.34	0.294	0.389	INDETERMINATE	1	TRUE	1	0.328220274502018	5		485	408	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149245664	149245664	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	82	402	0	ENST00000360632.3:c.864G>C	p.Met288Ile	p.M288I	ENST00000360632	NM_015472.4	288	atG/atC	5/7	0.306115561922412	2	FACETS	0.927	0.819	1	0.464	0.409	0.521	CLONAL	1	TRUE	0	0.328220274502018	2		402	539	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274631	198274631	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	70	440	0	ENST00000335508.6:c.767C>G	p.Pro256Arg	p.P256R	ENST00000335508	NM_012433.2	256	cCt/cGt	7/25	0.266848034797056	4	FACETS	0.861	0.75	0.981	0.431	0.375	0.491	CLONAL	1	TRUE	2	0.328220274502018	4		440	658	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020724	26020724	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1426138687	NA	P-0067815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	84	443	0	ENST00000357647.3:c.7C>T	p.Arg3Cys	p.R3C	ENST00000357647	NM_003529.2	3	Cgc/Tgc	1/1	0.328220274502018	3	FACETS	0.958	0.847	1	0.479	0.423	0.539	CLONAL	1	TRUE	1	0.328220274502018	3		443	622	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150933591	150933591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149404089	NA	P-0067815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	73	426	0	ENST00000271640.5:c.3053G>A	p.Arg1018Gln	p.R1018Q	ENST00000271640	NM_001145415.1	1018	cGa/cAa	16/22	0.304123077317098	3	FACETS	1	0.944	1	0.567	0.497	0.641	CLONAL	1	TRUE	1	0.328220274502018	3		426	457	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231474157	231474157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	61	394	1	ENST00000295050.7:c.28C>T	p.Arg10Trp	p.R10W	ENST00000295050	NM_032018.5	10	Cgg/Tgg	1/5	0.304123077317098	3	FACETS	0.903	0.781	1	0.452	0.39	0.518	CLONAL	1	TRUE	1	0.328220274502018	3		395	479	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796789	135796789	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	159	318	0	ENST00000298552.3:c.698del	p.Leu233Ter	p.L233*	ENST00000298552	NM_001162426.1	233	tTa/ta	8/23	0.328220274502018	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.328220274502018	2		318	408	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63968028	63968028	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	76	498	0	ENST00000398590.3:c.919C>G	p.Leu307Val	p.L307V	ENST00000398590	NM_001177387.1	307	Ctg/Gtg	7/14	0.266848034797056	4	FACETS	0.863	0.756	0.977	0.431	0.378	0.489	CLONAL	1	TRUE	2	0.328220274502018	4		498	713	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976702	55976702	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	102	416	0	ENST00000263923.4:c.1123C>G	p.His375Asp	p.H375D	ENST00000263923	NM_002253.2	375	Cac/Gac	9/30	0.306115561922412	2	FACETS	1	0.974	1	0.633	0.568	0.701	CLONAL	1	TRUE	0	0.328220274502018	2		416	491	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054689	13054759	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	GAGGAAGATGTCCCCGGCCAGGCCAAGGACGAGCTGTAGAGAGGCCTGCCTCCAGGGCTGGACTGAGGCCT	GAGGAAGATGTCCCCGGCCAGGCCAAGGACGAGCTGTAGAGAGGCCTGCCTCCAGGGCTGGACTGAGGCCT	-	novel	NA	P-0067815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	162	510	0	ENST00000316448.5:c.1219_*35del		p.*407*	ENST00000316448	NM_004343.3	406		9/9	0.107675814824426	5	FACETS	1	0.982	1	0.613	0.565	0.663	INDETERMINATE	2	TRUE	1	0.328220274502018	5		510	601	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497702	125497702	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	88	370	0	ENST00000428830.2:c.266G>C	p.Gly89Ala	p.G89A	ENST00000428830	NM_001114121.2	89	gGa/gCa	3/14	0.304123077317098	3	FACETS	1	0.906	1	0.512	0.454	0.573	CLONAL	1	TRUE	1	0.328220274502018	3		370	610	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851387	63851387	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	94	475	0	ENST00000279873.7:c.2165T>G	p.Leu722Arg	p.L722R	ENST00000279873	NM_032199.2	722	cTg/cGg	10/10	0.266848034797056	4	FACETS	0.947	0.842	1	0.474	0.421	0.53	CLONAL	1	TRUE	2	0.328220274502018	4		475	803	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639452	3639452	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	66	511	0	ENST00000294008.3:c.4187G>C	p.Gly1396Ala	p.G1396A	ENST00000294008	NM_032444.2	1396	gGa/gCa	12/15	0.204084878047011	4	FACETS	0.869	0.754	0.993	0.434	0.377	0.497	CLONAL	1	TRUE	2	0.328220274502018	4		511	615	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0067816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	56	678	7	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.237	0.202	0.274	0.237	0.202	0.274	SUBCLONAL	1	TRUE	1	0.721426799885739	2		685	656	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0067816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	43	418	2	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.172	0.143	0.204	0.172	0.143	0.204	SUBCLONAL	1	TRUE	1	0.721426799885739	2		420	693	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0067816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	161	497	0	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	1	2	FACETS	0.712	0.655	0.77	0.712	0.655	0.77	SUBCLONAL	1	TRUE	1	0.721426799885739	2		497	627	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0067816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	74	148	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.721426799885739	2		148	192	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0067816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	136	469	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.721426799885739	2		470	354	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216477	108216477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587782558	NA	P-0067816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	84	256	0	ENST00000278616.4:c.8432del	p.Lys2811SerfsTer46	p.K2811Sfs*46	ENST00000278616	NM_000051.3	2809	cAa/ca	58/63	0.721103675831145	2	FACETS	0.978	0.879	1	0.489	0.439	0.541	CLONAL	1	TRUE	0	0.721426799885739	2		256	238	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28931588	NA	P-0067816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	17	509	0	ENST00000349496.5:c.94G>C	p.Asp32His	p.D32H	ENST00000349496	NM_001904.3	32	Gac/Cac	3/15	1	2	FACETS	0.074	0.055	0.098	0.074	0.055	0.098	SUBCLONAL	1	TRUE	1	0.721426799885739	2		509	634	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	46	463	0	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.16	0.134	0.189	0.16	0.134	0.189	SUBCLONAL	1	TRUE	1	0.721426799885739	2		463	795	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101259	27101259	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	40	526	0	ENST00000324856.7:c.4541del	p.Thr1514ArgfsTer13	p.T1514Rfs*13	ENST00000324856	NM_006015.4	1514	aCg/ag	18/20	1	2	FACETS	0.188	0.155	0.224	0.188	0.155	0.224	SUBCLONAL	1	TRUE	1	0.721426799885739	2		526	591	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753011	57753012	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	40	458	6	ENST00000274289.3:c.1004dup	p.Leu335PhefsTer12	p.L335Ffs*12	ENST00000274289	NM_006622.3	335	ttg/ttTg	7/14	1	2	FACETS	0.218	0.181	0.26	0.218	0.181	0.26	SUBCLONAL	1	TRUE	1	0.721426799885739	2		464	508	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057947	27057948	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	284	515	0	ENST00000324856.7:c.1656dup	p.Gln553ThrfsTer70	p.Q553Tfs*70	ENST00000324856	NM_006015.4	552	tca/tcAa	3/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.721426799885739	2		515	699	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296203	15296204	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CA	CA	-	novel	NA	P-0067816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	238	524	0	ENST00000263388.2:c.2160_2161del	p.Cys720Ter	p.C720*	ENST00000263388	NM_000435.2	720	tgTGag/tgag	14/33	1	2	FACETS	0.948	0.889	1	0.948	0.889	1	CLONAL	1	TRUE	1	0.721426799885739	2		524	696	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692892	89692892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554898129	NA	P-0067816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	100	256	0	ENST00000371953.3:c.376G>A	p.Ala126Thr	p.A126T	ENST00000371953	NM_000314.4	126	Gct/Act	5/9	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.721426799885739	2		256	227	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525662	187525662	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774876401	NA	P-0067816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	168	384	0	ENST00000441802.2:c.10417G>A	p.Gly3473Ser	p.G3473S	ENST00000441802	NM_005245.3	3473	Ggt/Agt	18/27	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.721426799885739	2		384	445	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348056	348056	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758201257	NA	P-0067816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	74	554	0	ENST00000262320.3:c.1450C>T	p.Arg484Cys	p.R484C	ENST00000262320	NM_003502.3	484	Cgc/Tgc	6/11	1	2	FACETS	0.331	0.289	0.375	0.331	0.289	0.375	SUBCLONAL	1	TRUE	1	0.721426799885739	2		554	620	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344435	118344435	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	95	483	1	ENST00000534358.1:c.2565del	p.Glu856ArgfsTer93	p.E856Rfs*93	ENST00000534358	NM_005933.3	854	gCc/gc	3/36	0.721103675831145	2	FACETS	0.342	0.304	0.382	0.171	0.152	0.191	SUBCLONAL	1	TRUE	0	0.721426799885739	2		484	770	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206609	108206609	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs762154857	NA	P-0067816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	157	407	0	ENST00000278616.4:c.8189A>G	p.Gln2730Arg	p.Q2730R	ENST00000278616	NM_000051.3	2730	cAg/cGg	56/63	0.721103675831145	2	FACETS	1	0.962	1	0.531	0.492	0.571	CLONAL	1	TRUE	0	0.721426799885739	2		407	410	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054630	5054630	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772744665	NA	P-0067816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	170	482	0	ENST00000381652.3:c.682C>T	p.Arg228Ter	p.R228*	ENST00000381652	NM_004972.3	228	Cga/Tga	7/25	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.721426799885739	2		482	387	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041200	47041200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	50	531	0	ENST00000377604.3:c.1628C>T	p.Thr543Ile	p.T543I	ENST00000377604	NM_001204468.1	543	aCc/aTc	15/24	1	2	FACETS	0.214	0.181	0.251	0.214	0.181	0.251	SUBCLONAL	1	TRUE	1	0.721426799885739	2		531	647	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359677	40359677	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	190	332	0	ENST00000293328.3:c.1976G>A	p.Arg659His	p.R659H	ENST00000293328	NM_012448.3	659	cGc/cAc	16/19	1	2	FACETS	0.99	0.923	1	0.99	0.923	1	CLONAL	1	TRUE	1	0.721426799885739	2		332	532	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756664	756664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	34	467	0	ENST00000314574.4:c.164G>A	p.Ser55Asn	p.S55N	ENST00000314574	NM_005433.3	55	aGc/aAc	2/12	1	2	FACETS	0.155	0.126	0.188	0.155	0.126	0.188	SUBCLONAL	1	TRUE	1	0.721426799885739	2		467	609	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268950	55268950	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	286	503	0	ENST00000275493.2:c.3016G>A	p.Asp1006Asn	p.D1006N	ENST00000275493	NM_005228.3	1006	Gac/Aac	25/28	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.721426799885739	2		503	676	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976400	18976400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768863545	NA	P-0067816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	219	491	0	ENST00000262803.5:c.3050G>A	p.Arg1017His	p.R1017H	ENST00000262803	NM_002911.3	1017	cGt/cAt	22/24	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.721426799885739	2		491	594	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720853	176720853	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	190	480	1	ENST00000439151.2:c.6484C>A	p.His2162Asn	p.H2162N	ENST00000439151	NM_022455.4	2162	Cat/Aat	23/23	1	2	FACETS	0.822	0.763	0.882	0.822	0.763	0.882	CLONAL	1	TRUE	1	0.721426799885739	2		481	641	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160433	108160433	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	124	346	0	ENST00000278616.4:c.4341T>A	p.Ser1447Arg	p.S1447R	ENST00000278616	NM_000051.3	1447	agT/agA	29/63	0.721103675831145	2	FACETS	1	0.926	1	0.506	0.463	0.549	CLONAL	1	TRUE	0	0.721426799885739	2		346	340	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675490	40675490	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746725876	NA	P-0067816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	104	387	0	ENST00000249776.8:c.276del	p.Ser93LeufsTer3	p.S93Lfs*3	ENST00000249776	NM_033286.3	91	Ccc/cc	2/9	1	2	FACETS	0.541	0.486	0.599	0.541	0.486	0.599	SUBCLONAL	1	TRUE	1	0.721426799885739	2		387	533	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121820	2121820	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1213719461	NA	P-0067816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	126	551	0	ENST00000219476.3:c.1982G>C	p.Gly661Ala	p.G661A	ENST00000219476	NM_000548.3	661	gGc/gCc	19/42	1	2	FACETS	0.603	0.548	0.661	0.603	0.548	0.661	SUBCLONAL	1	TRUE	1	0.721426799885739	2		551	579	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220159	36220159	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0067816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	235	530	0	ENST00000222270.7:c.4879A>T	p.Lys1627Ter	p.K1627*	ENST00000222270	NM_014727.1	1627	Aag/Tag	22/37	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.721426799885739	2		530	623	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111995711	111995711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	215	425	0	ENST00000368678.4:c.1387C>T	p.Pro463Ser	p.P463S	ENST00000368678		463	Cca/Tca	12/13	1	2	FACETS	0.99	0.926	1	0.99	0.926	1	CLONAL	1	TRUE	1	0.721426799885739	2		425	602	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0067817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	141	288	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.997	0.913	1	0.997	0.913	1	CLONAL	1	TRUE	1	0.521687591551839	2		288	542	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0067817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	56	448	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.521687591551839	1	FACETS	0.274	0.234	0.317	0.274	0.234	0.317	SUBCLONAL	1	TRUE	0	0.521687591551839	1		448	579	SUCCESS
RET	5979	MSKCC	GRCh37	10	43598017	43598017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1210452561	NA	P-0067817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	58	597	0	ENST00000355710.3:c.565C>T	p.Arg189Cys	p.R189C	ENST00000355710	NM_020975.4	189	Cgc/Tgc	3/20	1	2	FACETS	0.256	0.219	0.297	0.256	0.219	0.297	SUBCLONAL	1	TRUE	1	0.521687591551839	2		597	867	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930087	68930087	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	38	398	0	ENST00000288368.4:c.148T>G	p.Leu50Val	p.L50V	ENST00000288368	NM_024870.2	50	Tta/Gta	2/40	1	2	FACETS	0.217	0.179	0.261	0.217	0.179	0.261	SUBCLONAL	1	TRUE	1	0.521687591551839	2		398	670	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581304	48581305	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	37	509	0	ENST00000342988.3:c.609dup	p.Ser204IlefsTer2	p.S204Ifs*2	ENST00000342988	NM_005359.5	203	cca/ccAa	5/12	0.521687591551839	1	FACETS	0.165	0.136	0.199	0.165	0.136	0.199	SUBCLONAL	1	TRUE	0	0.521687591551839	1		509	634	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446339	70446339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374692138	NA	P-0067817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	166	581	0	ENST00000373644.4:c.5279C>T	p.Ala1760Val	p.A1760V	ENST00000373644	NM_030625.2	1760	gCg/gTg	11/12	1	2	FACETS	0.721	0.662	0.782	0.721	0.662	0.782	SUBCLONAL	1	TRUE	1	0.521687591551839	2		581	883	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0067818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	394	512	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	0.751057041090928	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.751057041090928	2		512	493	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523145	176523145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746619070	NA	P-0067818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	184	697	0	ENST00000292408.4:c.1909G>A	p.Val637Ile	p.V637I	ENST00000292408	NM_213647.1	637	Gtc/Atc	14/18	1	2	FACETS	0.814	0.755	0.874	0.814	0.755	0.874	CLONAL	1	TRUE	1	0.751057041090928	2		697	602	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271835	15271835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748776589	NA	P-0067818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	214	657	0	ENST00000263388.2:c.6604G>A	p.Val2202Ile	p.V2202I	ENST00000263388	NM_000435.2	2202	Gtc/Atc	33/33	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.751057041090928	2		657	558	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021760	69021760	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	135	445	0	ENST00000288368.4:c.3048A>C	p.Lys1016Asn	p.K1016N	ENST00000288368	NM_024870.2	1016	aaA/aaC	25/40	0.437186615634034	5	FACETS	0.963	0.876	1	0.321	0.292	0.352	INDETERMINATE	1	TRUE	2	0.751057041090928	5		445	794	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082695	16082695	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	83	209	0	ENST00000281043.3:c.509G>A	p.Arg170His	p.R170H	ENST00000281043	NM_005378.4	170	cGc/cAc	2/3	0.751057041090928	3	FACETS	1	0.964	1	0.591	0.529	0.656	CLONAL	1	TRUE	1	0.751057041090928	3		209	257	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16235857	16235857	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752245407	NA	P-0067818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	226	446	0	ENST00000375759.3:c.923G>A	p.Arg308Gln	p.R308Q	ENST00000375759	NM_015001.2	308	cGa/cAa	4/15	0.751057041090928	3	FACETS	1	0.984	1	0.581	0.543	0.619	CLONAL	1	TRUE	1	0.751057041090928	3		446	713	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22142985	22142985	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	250	409	0	ENST00000215832.6:c.722T>C	p.Leu241Ser	p.L241S	ENST00000215832	NM_002745.4	241	tTg/tCg	5/9	0.751057041090928	3	FACETS	0.881	0.833	0.928	0.881	0.833	0.928	CLONAL	2	TRUE	1	0.751057041090928	3		409	520	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526627	106526627	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	138	455	0	ENST00000359195.3:c.2920A>C	p.Ser974Arg	p.S974R	ENST00000359195	NM_002649.2	974	Agt/Cgt	10/11	0.615027632689271	4	FACETS	1	0.952	1	0.532	0.485	0.58	CLONAL	1	TRUE	2	0.751057041090928	4		455	605	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0067819-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	12	400	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.567	0.397	0.779	0.567	0.397	0.779	SUBCLONAL	1	TRUE	1	0.1	2		400	423	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0067819-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	21	453	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	1	2	FACETS	0.827	0.635	1	0.827	0.635	1	CLONAL	1	TRUE	1	0.1	2		453	508	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339230	70339230	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067819-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	11	166	0	ENST00000374080.3:c.107T>C	p.Leu36Pro	p.L36P	ENST00000374080		36	cTg/cCg	2/45	1	1	FACETS	0.941	0.65	1	0.941	0.65	1	CLONAL	1	TRUE	0	0.1	1		166	222	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0067820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	141	389	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.899	0.822	0.979	0.899	0.822	0.979	CLONAL	1	TRUE	1	0.526394763998603	2		389	596	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0067820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	130	471	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.526394763998603	2		473	494	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857725	9857725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	184	554	0	ENST00000330684.3:c.3676G>A	p.Gly1226Ser	p.G1226S	ENST00000330684	NM_001134407.1	1226	Ggc/Agc	13/13	1	2	FACETS	0.864	0.799	0.932	0.864	0.799	0.932	CLONAL	1	TRUE	1	0.526394763998603	2		554	809	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317623	163317623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747173543	NA	P-0067820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	155	387	0	ENST00000271452.3:c.1019C>T	p.Ser340Leu	p.S340L	ENST00000271452	NM_145697.2	340	tCg/tTg	12/14	1	2	FACETS	0.986	0.907	1	0.986	0.907	1	CLONAL	1	TRUE	1	0.526394763998603	2		387	597	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273218	115273218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	166	440	0	ENST00000438362.2:c.1240C>T	p.Arg414Cys	p.R414C	ENST00000438362	NM_001242891.1	414	Cgt/Tgt	11/20	1	2	FACETS	0.953	0.878	1	0.953	0.878	1	CLONAL	1	TRUE	1	0.526394763998603	2		440	662	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031669	69031669	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	142	441	0	ENST00000288368.4:c.3424G>A	p.Asp1142Asn	p.D1142N	ENST00000288368	NM_024870.2	1142	Gat/Aat	28/40	1	2	FACETS	0.803	0.733	0.875	0.803	0.733	0.875	CLONAL	1	TRUE	1	0.526394763998603	2		441	672	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471052	25471052	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	376	580	1	ENST00000264709.3:c.709C>T	p.Gln237Ter	p.Q237*	ENST00000264709	NM_175629.2	237	Cag/Tag	7/23	0.526394763998603	2	FACETS	0.985	0.943	1	0.985	0.943	1	CLONAL	2	TRUE	0	0.526394763998603	2		581	725	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726618	41726618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	181	501	0	ENST00000301178.4:c.163C>T	p.Arg55Trp	p.R55W	ENST00000301178	NM_021913.4	55	Cgg/Tgg	2/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.526394763998603	2		501	622	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130306	11130306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	146	433	0	ENST00000358026.2:c.2545C>T	p.Arg849Trp	p.R849W	ENST00000358026	NM_001128849.1	849	Cgg/Tgg	18/36	1	2	FACETS	0.932	0.854	1	0.932	0.854	1	CLONAL	1	TRUE	1	0.526394763998603	2		433	595	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395668	45395668	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	152	416	0	ENST00000262160.6:c.466A>G	p.Lys156Glu	p.K156E	ENST00000262160	NM_005901.5	156	Aaa/Gaa	4/11	1	2	FACETS	0.971	0.892	1	0.971	0.892	1	CLONAL	1	TRUE	1	0.526394763998603	2		416	595	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710989	117710989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	170	418	0	ENST00000368508.3:c.1283G>A	p.Arg428Lys	p.R428K	ENST00000368508	NM_002944.2	428	aGa/aAa	12/43	0.526394763998603	1	FACETS	0.991	0.92	1	0.991	0.92	1	CLONAL	1	TRUE	0	0.526394763998603	1		418	480	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858164	152858164	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	191	258	0	ENST00000406277.2:c.451C>T	p.Gln151Ter	p.Q151*	ENST00000406277	NM_152274.4	151	Cag/Tag	6/7	1	1	FACETS	0.751	0.707	0.795	1	0.993	1	SUBCLONAL	2	TRUE	0	0.526394763998603	1		258	356	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082328	16082328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	336	498	0	ENST00000281043.3:c.142G>A	p.Asp48Asn	p.D48N	ENST00000281043	NM_005378.4	48	Gac/Aac	2/3	0.526394763998603	2	FACETS	0.893	0.851	0.935	0.893	0.851	0.935	CLONAL	2	TRUE	0	0.526394763998603	2		498	715	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636154	28636154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	117	488	0	ENST00000241453.7:c.218G>A	p.Gly73Glu	p.G73E	ENST00000241453	NM_004119.2	73	gGg/gAg	3/24	1	2	FACETS	0.779	0.704	0.856	0.779	0.704	0.856	SUBCLONAL	1	TRUE	1	0.526394763998603	2		488	571	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576099	29576099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555617359	NA	P-0067820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	168	392	0	ENST00000356175.3:c.4072C>T	p.Pro1358Ser	p.P1358S	ENST00000356175	NM_000267.3	1358	Ccc/Tcc	30/57	1	2	FACETS	0.885	0.816	0.958	0.885	0.816	0.958	CLONAL	1	TRUE	1	0.526394763998603	2		392	721	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690366	33690366	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	200	468	0	ENST00000308377.4:c.461C>T	p.Thr154Ile	p.T154I	ENST00000308377	NM_152270.3	154	aCc/aTc	2/5	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.526394763998603	2		468	740	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0067824-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	108	453	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	1	2	FACETS	0.856	0.773	0.942	0.856	0.773	0.942	CLONAL	1	TRUE	1	0.585718450289491	2		453	431	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0067824-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	133	322	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.585718450289491	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.585718450289491	1		322	267	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0067824-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	45	268	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.692	0.588	0.805	0.692	0.588	0.805	SUBCLONAL	1	TRUE	1	0.585718450289491	2		268	222	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874147	151874148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs747256476	NA	P-0067824-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	107	523	9	ENST00000262189.6:c.8390dup	p.Glu2798GlyfsTer11	p.E2798Gfs*11	ENST00000262189	NM_170606.2	2797	aag/aaAg	38/59	1	2	FACETS	0.772	0.696	0.852	0.772	0.696	0.852	SUBCLONAL	1	TRUE	1	0.585718450289491	2		532	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587782289	NA	P-0067824-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	120	433	0	ENST00000269305.4:c.706T>A	p.Tyr236Asn	p.Y236N	ENST00000269305	NM_001126112.2	236	Tac/Aac	7/11	0.585718450289491	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.585718450289491	1		433	284	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730832	40730832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs914506046	NA	P-0067824-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	135	562	0	ENST00000373198.4:c.3703C>T	p.Arg1235Cys	p.R1235C	ENST00000373198	NM_133170.3	1235	Cgc/Tgc	27/32	0.0941457146693128	5	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.585718450289491	5		562	695	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324601	62324601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146221660	NA	P-0067824-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	199	500	1	ENST00000360203.5:c.2957G>A	p.Arg986Gln	p.R986Q	ENST00000360203	NM_001283009.1	986	cGa/cAa	30/35	0.585718450289491	4	FACETS	0.88	0.82	0.942	0.88	0.82	0.942	CLONAL	2	TRUE	2	0.585718450289491	4		501	612	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	47	426	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.28339153155989	3	FACETS	0.833	0.705	0.972	0.416	0.352	0.486	CLONAL	1	TRUE	1	0.391298281582083	3		426	345	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932242	36932242	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	102	877	0	ENST00000361632.4:c.2227C>T	p.Gln743Ter	p.Q743*	ENST00000361632		743	Cag/Tag	16/16	0.195030412976451	4	FACETS	0.822	0.74	0.909	0.822	0.74	0.909	INDETERMINATE	2	TRUE	2	0.391298281582083	4		877	441	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333641	70333641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	98	770	0	ENST00000373644.4:c.1546C>T	p.Pro516Ser	p.P516S	ENST00000373644	NM_030625.2	516	Cca/Tca	2/12	0.195030412976451	4	FACETS	0.822	0.738	0.91	0.822	0.738	0.91	INDETERMINATE	2	TRUE	2	0.391298281582083	4		770	424	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575376	64575376	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	126	801	0	ENST00000312049.6:c.641G>T	p.Gly214Val	p.G214V	ENST00000312049	NM_130799.2	214	gGt/gTt	3/10	0.227237882396761	4	FACETS	0.885	0.806	0.968	0.885	0.806	0.968	INDETERMINATE	2	TRUE	2	0.391298281582083	4		801	506	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811604	102811604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	59	722	0	ENST00000307046.8:c.580G>A	p.Gly194Arg	p.G194R	ENST00000307046	NM_001111285.1	194	Gga/Aga	4/4	0.28339153155989	3	FACETS	0.854	0.737	0.981	0.427	0.368	0.491	CLONAL	1	TRUE	1	0.391298281582083	3		722	422	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675118	40675118	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	98	732	0	ENST00000249776.8:c.82C>T	p.Pro28Ser	p.P28S	ENST00000249776	NM_033286.3	28	Ccg/Tcg	1/9	0.28339153155989	3	FACETS	1	0.982	1	0.749	0.673	0.828	CLONAL	1	TRUE	1	0.391298281582083	3		732	400	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74003508	74003508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	78	621	0	ENST00000318443.5:c.1579G>A	p.Glu527Lys	p.E527K	ENST00000318443	NM_001024736.1	527	Gaa/Aaa	9/10	1	2	FACETS	0.982	0.867	1	0.982	0.867	1	CLONAL	1	TRUE	1	0.391298281582083	2		621	406	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250997	99250997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	67	772	0	ENST00000268035.6:c.301C>T	p.Pro101Ser	p.P101S	ENST00000268035	NM_000875.3	101	Ccc/Tcc	2/21	0.28339153155989	3	FACETS	1	0.913	1	0.529	0.462	0.601	CLONAL	1	TRUE	1	0.391298281582083	3		772	387	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640578	3640578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138344471	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	150	969	0	ENST00000294008.3:c.3061C>T	p.Arg1021Cys	p.R1021C	ENST00000294008	NM_032444.2	1021	Cgc/Tgc	12/15	0.28339153155989	3	FACETS	0.926	0.852	1	0.926	0.852	1	CLONAL	2	TRUE	1	0.391298281582083	3		969	495	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646443	23646443	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039479	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	64	719	0	ENST00000261584.4:c.1424C>T	p.Ser475Leu	p.S475L	ENST00000261584	NM_024675.3	475	tCa/tTa	4/13	0.28339153155989	3	FACETS	0.789	0.684	0.902	0.394	0.342	0.451	CLONAL	1	TRUE	1	0.391298281582083	3		719	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781371	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	122	815	0	ENST00000269305.4:c.328C>T	p.Arg110Cys	p.R110C	ENST00000269305	NM_001126112.2	110	Cgt/Tgt	4/11	0.28339153155989	3	FACETS	0.818	0.744	0.894	0.818	0.744	0.894	CLONAL	2	TRUE	1	0.391298281582083	3		815	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579395	7579395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	138	859	0	ENST00000269305.4:c.292C>T	p.Pro98Ser	p.P98S	ENST00000269305	NM_001126112.2	98	Cct/Tct	4/11	0.28339153155989	3	FACETS	0.882	0.808	0.958	0.882	0.808	0.958	CLONAL	2	TRUE	1	0.391298281582083	3		859	478	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082895	16082895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1412185126	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	73	495	0	ENST00000281043.3:c.709C>T	p.Pro237Ser	p.P237S	ENST00000281043	NM_005378.4	237	Ccg/Tcg	2/3	0.195030412976451	4	FACETS	1	0.959	1	1	0.959	1	INDETERMINATE	2	TRUE	2	0.391298281582083	4		495	221	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416111	29416111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	127	735	0	ENST00000389048.3:c.4842C>A	p.Ser1614Arg	p.S1614R	ENST00000389048	NM_004304.4	1614	agC/agA	29/29	0.195030412976451	4	FACETS	0.982	0.896	1	0.982	0.896	1	INDETERMINATE	2	TRUE	2	0.391298281582083	4		735	460	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659851	227659851	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	56	330	0	ENST00000305123.5:c.3604C>T	p.Pro1202Ser	p.P1202S	ENST00000305123	NM_005544.2	1202	Ccc/Tcc	1/2	0.195030412976451	4	FACETS	1	0.935	1	1	0.935	1	INDETERMINATE	2	TRUE	2	0.391298281582083	4		330	178	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911166	40911166	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	88	410	0	ENST00000373198.4:c.2140-1G>A		p.X714_splice	ENST00000373198	NM_133170.3	714			0.195030412976451	4	FACETS	1	0.895	1	1	0.895	1	INDETERMINATE	2	TRUE	2	0.391298281582083	4		410	313	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101129	41101130	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	99	806	0	ENST00000373198.4:c.1226_1227delinsTT	p.Pro409Leu	p.P409L	ENST00000373198	NM_133170.3	409	cCC/cTT	8/32	0.195030412976451	4	FACETS	0.813	0.73	0.9	0.813	0.73	0.9	INDETERMINATE	2	TRUE	2	0.391298281582083	4		806	433	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259388	89259388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	201	712	0	ENST00000336596.2:c.532G>A	p.Gly178Arg	p.G178R	ENST00000336596	NM_005233.5	178	Gga/Aga	3/17	0.391298281582083	5	FACETS	0.945	0.882	1	0.945	0.882	1	CLONAL	3	TRUE	2	0.391298281582083	5		712	575	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851570	134851570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	89	568	0	ENST00000398015.3:c.976C>T	p.Pro326Ser	p.P326S	ENST00000398015	NM_004441.4	326	Ccc/Tcc	5/16	0.195030412976451	4	FACETS	0.896	0.802	0.996	0.896	0.802	0.996	INDETERMINATE	2	TRUE	2	0.391298281582083	4		568	353	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356361	66356361	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772108237	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	62	744	0	ENST00000273854.3:c.1136C>T	p.Pro379Leu	p.P379L	ENST00000273854	NM_004439.5	379	cCg/cTg	5/18	1	2	FACETS	0.854	0.741	0.975	0.854	0.741	0.975	CLONAL	1	TRUE	1	0.391298281582083	2		744	371	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549515	187549515	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs577375480	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	79	677	0	ENST00000441802.2:c.4603C>T	p.Arg1535Ter	p.R1535*	ENST00000441802	NM_005245.3	1535	Cga/Tga	9/27	0.391298281582083	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.391298281582083	1		677	303	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295230	+	upstream_gene_variant	5'Flank	TNP	GGG	GGG	AGA	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	41	562	0				ENST00000310581	NM_198253.2	-/1132			0.28339153155989	3	FACETS	1	0.955	1	0.712	0.601	0.831	CLONAL	1	TRUE	1	0.391298281582083	3		562	176	SUCCESS
APC	324	MSKCC	GRCh37	5	112174307	112174307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253876	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	46	772	0	ENST00000257430.4:c.3016C>T	p.His1006Tyr	p.H1006Y	ENST00000257430	NM_000038.5	1006	Cat/Tat	16/16	0.28339153155989	3	FACETS	0.959	0.813	1	0.48	0.406	0.56	CLONAL	1	TRUE	1	0.391298281582083	3		772	293	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964400	93964400	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1051471746	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	88	494	0	ENST00000369303.4:c.2497G>A	p.Gly833Arg	p.G833R	ENST00000369303	NM_004440.3	833	Gga/Aga	14/17	0.28339153155989	3	FACETS	0.87	0.779	0.965	0.87	0.779	0.965	CLONAL	2	TRUE	1	0.391298281582083	3		494	309	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983048	111983048	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	60	747	0	ENST00000368678.4:c.1499G>A	p.Trp500Ter	p.W500*	ENST00000368678		500	tGg/tAg	13/13	0.28339153155989	3	FACETS	0.801	0.691	0.919	0.4	0.345	0.46	CLONAL	1	TRUE	1	0.391298281582083	3		747	458	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700229	117700229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	79	541	0	ENST00000368508.3:c.2590G>A	p.Gly864Arg	p.G864R	ENST00000368508	NM_002944.2	864	Gga/Aga	17/43	0.28339153155989	3	FACETS	0.891	0.793	0.993	0.891	0.793	0.993	CLONAL	2	TRUE	1	0.391298281582083	3		541	271	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997874	149997874	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	110	622	0	ENST00000253339.5:c.2594-1G>A		p.X865_splice	ENST00000253339		865			0.28339153155989	3	FACETS	0.834	0.755	0.916	0.834	0.755	0.916	CLONAL	2	TRUE	1	0.391298281582083	3		622	403	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	160	518	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.214371189957827	5	FACETS	0.899	0.836	0.962	0.719	0.669	0.77	INDETERMINATE	4	TRUE	0	0.391298281582083	5		518	361	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335633	81335633	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	100	590	0	ENST00000222390.5:c.1727G>A	p.Gly576Glu	p.G576E	ENST00000222390	NM_000601.4	576	gGa/gAa	15/18	0.189990216826209	2	FACETS	0.824	0.745	0.906	0.824	0.745	0.906	INDETERMINATE	2	TRUE	0	0.391298281582083	2		590	310	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381466	81381466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	35	543	1	ENST00000222390.5:c.595G>A	p.Glu199Lys	p.E199K	ENST00000222390	NM_000601.4	199	Gaa/Aaa	5/18	0.189990216826209	2	FACETS	0.572	0.47	0.685	0.286	0.235	0.343	INDETERMINATE	1	TRUE	0	0.391298281582083	2		544	313	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486089	8486089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	122	794	0	ENST00000356435.5:c.2728G>A	p.Glu910Lys	p.E910K	ENST00000356435		910	Gag/Aag	17/35	0.195030412976451	4	FACETS	0.927	0.843	1	0.927	0.843	1	INDETERMINATE	2	TRUE	2	0.391298281582083	4		794	468	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	108	795	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.195030412976451	4	FACETS	0.904	0.817	0.994	0.904	0.817	0.994	INDETERMINATE	2	TRUE	2	0.391298281582083	4		795	425	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971116	21971116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552823	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	133	859	0	ENST00000304494.5:c.242C>T	p.Pro81Leu	p.P81L	ENST00000304494	NM_000077.4	81	cCc/cTc	2/3	0.195030412976451	4	FACETS	1	0.932	1	1	0.932	1	INDETERMINATE	2	TRUE	2	0.391298281582083	4		859	463	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430562	80430562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	40	300	0	ENST00000286548.4:c.446G>A	p.Arg149Gln	p.R149Q	ENST00000286548	NM_002072.3	149	cGa/cAa	3/7	0.28339153155989	3	FACETS	0.994	0.846	1	0.994	0.846	1	CLONAL	2	TRUE	1	0.391298281582083	3		300	123	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412381	139412381	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	53	804	0	ENST00000277541.6:c.1264C>T	p.Pro422Ser	p.P422S	ENST00000277541	NM_017617.3	422	Ccc/Tcc	8/34	0.28339153155989	3	FACETS	0.841	0.72	0.973	0.421	0.36	0.487	CLONAL	1	TRUE	1	0.391298281582083	3		804	385	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814824	139814824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755691522	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	48	863	0	ENST00000247668.2:c.817G>A	p.Glu273Lys	p.E273K	ENST00000247668	NM_021138.3	273	Gag/Aag	8/11	0.28339153155989	3	FACETS	0.671	0.568	0.784	0.336	0.284	0.392	SUBCLONAL	1	TRUE	1	0.391298281582083	3		863	437	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237641	16237641	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	96	558	0	ENST00000375759.3:c.1088G>T	p.Gly363Val	p.G363V	ENST00000375759	NM_015001.2	363	gGa/gTa	5/15	0.195030412976451	4	FACETS	0.864	0.775	0.957	0.864	0.775	0.957	INDETERMINATE	2	TRUE	2	0.391298281582083	4		558	395	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807552	36807552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	98	725	0	ENST00000373129.3:c.1112C>T	p.Ser371Phe	p.S371F	ENST00000373129	NM_032017.1	371	tCc/tTc	12/12	0.195030412976451	4	FACETS	0.801	0.719	0.887	0.801	0.719	0.887	INDETERMINATE	2	TRUE	2	0.391298281582083	4		725	435	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400938	72400938	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	104	685	0	ENST00000357731.5:c.233T>A	p.Ile78Asn	p.I78N	ENST00000357731	NM_173808.2	78	aTt/aAt	2/7	0.195030412976451	4	FACETS	0.818	0.737	0.903	0.818	0.737	0.903	INDETERMINATE	2	TRUE	2	0.391298281582083	4		685	452	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843668	156843668	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	44	950	1	ENST00000524377.1:c.1094A>G	p.Asn365Ser	p.N365S	ENST00000524377	NM_002529.3	365	aAc/aGc	8/17	0.391298281582083	4	FACETS	0.594	0.498	0.7	0.198	0.166	0.234	SUBCLONAL	1	TRUE	1	0.391298281582083	4		951	527	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980328	201980328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	214	789	0	ENST00000359651.3:c.64G>A	p.Glu22Lys	p.E22K	ENST00000359651		22	Gag/Aag	1/8	0.391298281582083	3	FACETS	0.838	0.786	0.891	1	0.989	1	CLONAL	3	TRUE	1	0.391298281582083	3		789	520	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332310	70332310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	131	682	0	ENST00000373644.4:c.215G>A	p.Ser72Asn	p.S72N	ENST00000373644	NM_030625.2	72	aGc/aAc	2/12	0.195030412976451	4	FACETS	0.953	0.87	1	0.953	0.87	1	INDETERMINATE	2	TRUE	2	0.391298281582083	4		682	489	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572253	64572254	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	96	1080	1	ENST00000312049.6:c.1385_1386delinsTT	p.Ala462Val	p.A462V	ENST00000312049	NM_130799.2	462	gCC/gTT	10/10	0.227237882396761	4	FACETS	1	0.978	1	0.699	0.626	0.777	INDETERMINATE	1	TRUE	2	0.391298281582083	4		1081	488	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180397	94180397	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1215450873	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	107	628	0	ENST00000323929.3:c.1771C>T	p.Gln591Ter	p.Q591*	ENST00000323929	NM_005591.3	591	Caa/Taa	15/20	0.227237882396761	4	FACETS	0.942	0.851	1	0.942	0.851	1	INDETERMINATE	2	TRUE	2	0.391298281582083	4		628	404	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344191	118344192	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	139	847	1	ENST00000534358.1:c.2317_2318delinsTT	p.Pro773Leu	p.P773L	ENST00000534358	NM_005933.3	773	CCg/TTg	3/36	0.227237882396761	4	FACETS	0.767	0.701	0.837	0.767	0.701	0.837	INDETERMINATE	2	TRUE	2	0.391298281582083	4		848	644	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544148	18544149	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	81	568	0	ENST00000266497.5:c.1965_1966delinsT	p.Lys655AsnfsTer39	p.K655Nfs*39	ENST00000266497		655	aaACat/aaTat	13/31	0.341682244403205	2	FACETS	0.87	0.779	0.964	0.87	0.779	0.964	CLONAL	2	TRUE	0	0.391298281582083	2		568	238	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624522	21624522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	101	675	0	ENST00000421138.2:c.1507G>A	p.Ala503Thr	p.A503T	ENST00000421138		503	Gca/Aca	14/16	0.341682244403205	2	FACETS	1	0.982	1	0.731	0.66	0.805	CLONAL	1	TRUE	0	0.391298281582083	2		675	353	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426023	49426024	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	136	905	0	ENST00000301067.7:c.12464_12465delinsTT	p.Pro4155Leu	p.P4155L	ENST00000301067	NM_003482.3	4155	cCC/cTT	39/54	0.28339153155989	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.391298281582083	3		905	378	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448415	49448415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765815816	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	65	784	0	ENST00000301067.7:c.296C>T	p.Pro99Leu	p.P99L	ENST00000301067	NM_003482.3	99	cCt/cTt	3/54	0.28339153155989	3	FACETS	0.966	0.841	1	0.483	0.42	0.551	CLONAL	1	TRUE	1	0.391298281582083	3		784	411	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	359988	359989	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	53	670	0	ENST00000262320.3:c.1100_1101delinsTT	p.Pro367Leu	p.P367L	ENST00000262320	NM_003502.3	367	cCC/cTT	4/11	0.28339153155989	3	FACETS	0.967	0.829	1	0.483	0.414	0.558	CLONAL	1	TRUE	1	0.391298281582083	3		670	335	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670698	67670698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	70	650	0	ENST00000264010.4:c.1943C>T	p.Ala648Val	p.A648V	ENST00000264010	NM_006565.3	648	gCc/gTc	11/12	1	2	FACETS	0.922	0.808	1	0.922	0.808	1	CLONAL	1	TRUE	1	0.391298281582083	2		650	388	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032540	12032540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	40	439	0	ENST00000353533.5:c.976C>T	p.Pro326Ser	p.P326S	ENST00000353533	NM_003010.3	326	Ccg/Tcg	9/11	0.28339153155989	3	FACETS	0.978	0.818	1	0.489	0.409	0.577	CLONAL	1	TRUE	1	0.391298281582083	3		439	250	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679306	29679306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1336098547	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	97	622	0	ENST00000356175.3:c.7426C>T	p.Pro2476Ser	p.P2476S	ENST00000356175	NM_000267.3	2476	Ccc/Tcc	50/57	0.227237882396761	4	FACETS	0.871	0.782	0.964	0.871	0.782	0.964	INDETERMINATE	2	TRUE	2	0.391298281582083	4		622	396	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40447769	40447769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	176	920	0	ENST00000345506.4:c.508G>A	p.Glu170Lys	p.E170K	ENST00000345506	NM_003152.3	170	Gag/Aag	6/20	0.227237882396761	4	FACETS	0.941	0.87	1	0.941	0.87	1	INDETERMINATE	2	TRUE	2	0.391298281582083	4		920	665	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533757	63533757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793954	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	103	913	0	ENST00000307078.5:c.1397C>T	p.Ser466Phe	p.S466F	ENST00000307078	NM_004655.3	466	tCc/tTc	6/11	0.227237882396761	4	FACETS	0.766	0.689	0.847	0.766	0.689	0.847	INDETERMINATE	2	TRUE	2	0.391298281582083	4		913	478	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226890	2226891	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	62	926	2	ENST00000398665.3:c.4370_4371delinsAT	p.Ser1457Tyr	p.S1457Y	ENST00000398665	NM_032482.2	1457	tCC/tAT	27/28	0.195030412976451	4	FACETS	1	0.901	1	0.524	0.454	0.599	INDETERMINATE	1	TRUE	2	0.391298281582083	4		928	421	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243948	5243948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	100	699	0	ENST00000357368.4:c.1534C>T	p.Leu512Phe	p.L512F	ENST00000357368	NM_002850.3	512	Ctc/Ttc	11/38	0.195030412976451	4	FACETS	0.776	0.697	0.86	0.776	0.697	0.86	INDETERMINATE	2	TRUE	2	0.391298281582083	4		699	458	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300083	15300083	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	76	826	0	ENST00000263388.2:c.1192+1G>A		p.X398_splice	ENST00000263388	NM_000435.2	398			0.195030412976451	4	FACETS	1	0.967	1	0.643	0.567	0.725	INDETERMINATE	1	TRUE	2	0.391298281582083	4		826	420	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376235	15376235	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	73	524	0	ENST00000263377.2:c.779C>T	p.Pro260Leu	p.P260L	ENST00000263377	NM_058243.2	260	cCa/cTa	5/20	0.195030412976451	4	FACETS	0.927	0.82	1	0.927	0.82	1	INDETERMINATE	2	TRUE	2	0.391298281582083	4		524	280	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793194	33793194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	32	611	0	ENST00000498907.2:c.127C>T	p.Pro43Ser	p.P43S	ENST00000498907	NM_004364.3	43	Ccc/Tcc	1/1	0.28339153155989	3	FACETS	0.877	0.717	1	0.438	0.358	0.528	CLONAL	1	TRUE	1	0.391298281582083	3		611	223	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210766	36210766	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	49	918	0	ENST00000222270.7:c.517C>T	p.Pro173Ser	p.P173S	ENST00000222270	NM_014727.1	173	Ccc/Tcc	3/37	0.28339153155989	3	FACETS	0.632	0.535	0.738	0.316	0.267	0.369	SUBCLONAL	1	TRUE	1	0.391298281582083	3		918	474	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791382	42791382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	131	810	0	ENST00000575354.2:c.442C>T	p.His148Tyr	p.H148Y	ENST00000575354	NM_015125.3	148	Cat/Tat	3/20	0.28339153155989	3	FACETS	0.859	0.785	0.936	0.859	0.785	0.936	CLONAL	2	TRUE	1	0.391298281582083	3		810	466	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797272	42797272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751126298	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	49	883	0	ENST00000575354.2:c.3634C>T	p.Pro1212Ser	p.P1212S	ENST00000575354	NM_015125.3	1212	Cca/Tca	15/20	0.28339153155989	3	FACETS	0.77	0.654	0.897	0.385	0.327	0.449	SUBCLONAL	1	TRUE	1	0.391298281582083	3		883	389	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799121	42799122	+	missense_variant	Missense_Mutation	DNP	CC	CC	GT	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	25	648	0	ENST00000575354.2:c.4605_4606delinsGT	p.Pro1536Ser	p.P1536S	ENST00000575354	NM_015125.3	1535	ctCCct/ctGTct	20/20	0.28339153155989	3	FACETS	0.568	0.449	0.704	0.284	0.224	0.352	SUBCLONAL	1	TRUE	1	0.391298281582083	3		648	269	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523009	25523009	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	76	658	0	ENST00000264709.3:c.176C>A	p.Pro59Gln	p.P59Q	ENST00000264709	NM_175629.2	59	cCg/cAg	3/23	0.195030412976451	4	FACETS	1	0.969	1	0.657	0.579	0.741	INDETERMINATE	1	TRUE	2	0.391298281582083	4		658	411	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523013	25523013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	81	665	0	ENST00000264709.3:c.172C>T	p.Pro58Ser	p.P58S	ENST00000264709	NM_175629.2	58	Ccc/Tcc	3/23	0.195030412976451	4	FACETS	1	0.974	1	0.687	0.609	0.771	INDETERMINATE	1	TRUE	2	0.391298281582083	4		665	419	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561309	9561309	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs760330867	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	90	730	0	ENST00000353224.5:c.473C>A	p.Pro158Gln	p.P158Q	ENST00000353224	NM_177990.2	158	cCg/cAg	4/10	0.195030412976451	4	FACETS	1	0.98	1	0.739	0.659	0.823	INDETERMINATE	1	TRUE	2	0.391298281582083	4		730	433	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624790	9624790	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	82	685	0	ENST00000353224.5:c.187C>T	p.Gln63Ter	p.Q63*	ENST00000353224	NM_177990.2	63	Cag/Tag	3/10	0.195030412976451	4	FACETS	1	0.978	1	0.738	0.655	0.826	INDETERMINATE	1	TRUE	2	0.391298281582083	4		685	395	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022636	31022637	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	99	873	1	ENST00000375687.4:c.2121_2122delinsTT	p.Gln708Ter	p.Q708*	ENST00000375687	NM_015338.5	707	acCCag/acTTag	13/13	0.195030412976451	4	FACETS	1	0.98	1	0.708	0.635	0.786	INDETERMINATE	1	TRUE	2	0.391298281582083	4		874	497	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022680	36022680	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	114	548	0	ENST00000358208.4:c.553G>A	p.Gly185Ser	p.G185S	ENST00000358208		185	Ggt/Agt	5/12	0.195030412976451	4	FACETS	0.972	0.882	1	0.972	0.882	1	INDETERMINATE	2	TRUE	2	0.391298281582083	4		548	417	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979295	40979295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	96	652	2	ENST00000373198.4:c.1838C>T	p.Pro613Leu	p.P613L	ENST00000373198	NM_133170.3	613	cCc/cTc	11/32	0.195030412976451	4	FACETS	0.809	0.725	0.897	0.809	0.725	0.897	INDETERMINATE	2	TRUE	2	0.391298281582083	4		654	422	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121060	29121060	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	110	673	1	ENST00000328354.6:c.497A>C	p.Asn166Thr	p.N166T	ENST00000328354	NM_007194.3	166	aAt/aCt	4/15	0.28339153155989	3	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	1	0.391298281582083	3		674	321	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573446	41573446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761000930	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	124	1017	0	ENST00000263253.7:c.5731C>T	p.Pro1911Ser	p.P1911S	ENST00000263253	NM_001429.3	1911	Cct/Tct	31/31	0.28339153155989	3	FACETS	0.804	0.732	0.879	0.804	0.732	0.879	CLONAL	2	TRUE	1	0.391298281582083	3		1017	471	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12647761	12647761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	77	585	0	ENST00000251849.4:c.619C>T	p.Pro207Ser	p.P207S	ENST00000251849	NM_002880.3	207	Cca/Tca	6/17	0.391298281582083	5	FACETS	1	0.968	1	0.435	0.382	0.49	CLONAL	1	TRUE	2	0.391298281582083	5		585	479	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598213	52598213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	146	658	0	ENST00000394830.3:c.3653C>T	p.Ser1218Phe	p.S1218F	ENST00000394830	NM_018313.4	1218	tCc/tTc	24/30	0.391298281582083	5	FACETS	0.893	0.817	0.972	0.595	0.545	0.648	CLONAL	2	TRUE	2	0.391298281582083	5		658	663	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146667	185146668	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	119	698	0	ENST00000265026.3:c.298_299delinsAA	p.Gly100Lys	p.G100K	ENST00000265026	NM_004721.4	100	GGg/AAg	2/14	0.195030412976451	4	FACETS	0.848	0.769	0.93	0.848	0.769	0.93	INDETERMINATE	2	TRUE	2	0.391298281582083	4		698	499	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526137	189526137	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1381645678	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	121	873	0	ENST00000264731.3:c.401A>G	p.Tyr134Cys	p.Y134C	ENST00000264731	NM_003722.4	134	tAt/tGt	4/14	0.195030412976451	4	FACETS	1	0.984	1	0.716	0.649	0.786	INDETERMINATE	1	TRUE	2	0.391298281582083	4		873	601	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133769	55133769	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs772538462	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	52	714	0	ENST00000257290.5:c.982A>G	p.Asn328Asp	p.N328D	ENST00000257290	NM_006206.4	328	Aac/Gac	7/23	1	2	FACETS	0.766	0.655	0.886	0.766	0.655	0.886	SUBCLONAL	1	TRUE	1	0.391298281582083	2		714	347	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55143591	55143591	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1560482703	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	51	642	0	ENST00000257290.5:c.1823T>C	p.Val608Ala	p.V608A	ENST00000257290	NM_006206.4	608	gTt/gCt	13/23	1	2	FACETS	0.663	0.565	0.77	0.663	0.565	0.77	SUBCLONAL	1	TRUE	1	0.391298281582083	2		642	393	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796102	57796102	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	62	647	0	ENST00000309042.7:c.1078C>A	p.Pro360Thr	p.P360T	ENST00000309042	NM_005612.4	360	Cct/Act	4/4	1	2	FACETS	0.898	0.78	1	0.898	0.78	1	CLONAL	1	TRUE	1	0.391298281582083	2		647	353	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534476	187534476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	60	697	0	ENST00000441802.2:c.9250C>T	p.Pro3084Ser	p.P3084S	ENST00000441802	NM_005245.3	3084	Ccc/Tcc	13/27	0.391298281582083	1	FACETS	0.817	0.709	0.932	0.817	0.709	0.932	CLONAL	1	TRUE	0	0.391298281582083	1		697	302	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873732	35873732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	106	621	0	ENST00000303115.3:c.688G>A	p.Glu230Lys	p.E230K	ENST00000303115	NM_002185.3	230	Gag/Aag	5/8	0.28339153155989	3	FACETS	0.883	0.799	0.97	0.883	0.799	0.97	CLONAL	2	TRUE	1	0.391298281582083	3		621	367	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752845	57752845	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	61	646	0	ENST00000274289.3:c.1083G>C	p.Lys361Asn	p.K361N	ENST00000274289	NM_006622.3	361	aaG/aaC	8/14	0.28339153155989	3	FACETS	1	0.882	1	0.509	0.441	0.582	CLONAL	1	TRUE	1	0.391298281582083	3		646	366	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682650	86682653	+	frameshift_variant	Frame_Shift_Del	DEL	ACAT	ACAT	CTA	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	67	590	2	ENST00000274376.6:c.2855_2858delinsCTA	p.Tyr952SerfsTer16	p.Y952Sfs*16	ENST00000274376	NM_002890.2	952	tACATg/tCTAg	23/25	0.28339153155989	3	FACETS	0.784	0.689	0.885	0.784	0.689	0.885	SUBCLONAL	2	TRUE	1	0.391298281582083	3		592	261	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682652	86682653	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	39	592	0	ENST00000274376.6:c.2858dup	p.Met953IlefsTer21	p.M953Ifs*21	ENST00000274376	NM_002890.2	953	atg/aTtg	23/25	0.28339153155989	3	FACETS	0.924	0.771	1	0.462	0.385	0.546	CLONAL	1	TRUE	1	0.391298281582083	3		592	258	SUCCESS
APC	324	MSKCC	GRCh37	5	112176848	112176848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561601033	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	60	716	0	ENST00000257430.4:c.5557C>T	p.Pro1853Ser	p.P1853S	ENST00000257430	NM_000038.5	1853	Cct/Tct	16/16	0.28339153155989	3	FACETS	0.919	0.795	1	0.459	0.397	0.527	CLONAL	1	TRUE	1	0.391298281582083	3		716	399	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449601	149449601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	108	745	0	ENST00000286301.3:c.1345G>A	p.Val449Ile	p.V449I	ENST00000286301	NM_005211.3	449	Gtc/Atc	10/22	0.28339153155989	3	FACETS	0.788	0.712	0.867	0.788	0.712	0.867	SUBCLONAL	2	TRUE	1	0.391298281582083	3		745	419	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631248	176631249	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	118	638	0	ENST00000439151.2:c.1191_1192delinsTT	p.Leu398Phe	p.L398F	ENST00000439151	NM_022455.4	397	gtCCtt/gtTTtt	4/23	0.28339153155989	3	FACETS	0.767	0.696	0.841	0.767	0.696	0.841	SUBCLONAL	2	TRUE	1	0.391298281582083	3		638	470	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638532	176638533	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	142	850	0	ENST00000439151.2:c.3132_3133delinsTT	p.Arg1045Cys	p.R1045C	ENST00000439151	NM_022455.4	1044	aaCCgt/aaTTgt	5/23	0.28339153155989	3	FACETS	0.768	0.703	0.835	0.768	0.703	0.835	SUBCLONAL	2	TRUE	1	0.391298281582083	3		850	565	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271408	26271408	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs200234697	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	137	1075	0	ENST00000305910.3:c.205C>T	p.Gln69Ter	p.Q69*	ENST00000305910	NM_003534.2	69	Caa/Taa	1/1	0.28339153155989	3	FACETS	1	0.986	1	0.726	0.663	0.791	CLONAL	1	TRUE	1	0.391298281582083	3		1075	577	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166203	32166203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	89	631	0	ENST00000375023.3:c.4751G>A	p.Gly1584Glu	p.G1584E	ENST00000375023	NM_004557.3	1584	gGa/gAa	26/30	0.28339153155989	3	FACETS	1	0.979	1	0.727	0.649	0.809	CLONAL	1	TRUE	1	0.391298281582083	3		631	374	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289241	33289242	+	missense_variant	Missense_Mutation	DNP	TC	TC	CT	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	84	731	0	ENST00000374542.5:c.310_311delinsAG	p.Glu104Arg	p.E104R	ENST00000374542	NM_001141970.1	104	GAg/AGg	3/8	0.28339153155989	3	FACETS	1	0.978	1	0.729	0.649	0.813	CLONAL	1	TRUE	1	0.391298281582083	3		731	352	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652206	36652206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	120	680	0	ENST00000244741.5:c.328C>T	p.His110Tyr	p.H110Y	ENST00000244741	NM_000389.4	110	Cat/Tat	2/3	0.28339153155989	3	FACETS	0.841	0.765	0.92	0.841	0.765	0.92	CLONAL	2	TRUE	1	0.391298281582083	3		680	436	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974330	93974330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	66	489	0	ENST00000369303.4:c.1724G>A	p.Gly575Asp	p.G575D	ENST00000369303	NM_004440.3	575	gGc/gAc	8/17	0.28339153155989	3	FACETS	1	0.974	1	0.747	0.655	0.844	CLONAL	1	TRUE	1	0.391298281582083	3		489	270	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641186	117641186	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	125	865	0	ENST00000368508.3:c.5785C>A	p.Pro1929Thr	p.P1929T	ENST00000368508	NM_002944.2	1929	Cca/Aca	36/43	0.28339153155989	3	FACETS	0.88	0.803	0.96	0.88	0.803	0.96	CLONAL	2	TRUE	1	0.391298281582083	3		865	434	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662646	117662646	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753442951	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	92	757	0	ENST00000368508.3:c.4819C>T	p.Pro1607Ser	p.P1607S	ENST00000368508	NM_002944.2	1607	Cct/Tct	29/43	0.28339153155989	3	FACETS	1	0.973	1	0.648	0.579	0.721	CLONAL	1	TRUE	1	0.391298281582083	3		757	434	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137522022	137522022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746134574	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	76	522	0	ENST00000367739.4:c.857C>T	p.Ser286Phe	p.S286F	ENST00000367739	NM_000416.2	286	tCc/tTc	6/7	0.28339153155989	3	FACETS	0.844	0.749	0.944	0.844	0.749	0.944	CLONAL	2	TRUE	1	0.391298281582083	3		522	275	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099866	157099866	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	47	570	0	ENST00000346085.5:c.803C>T	p.Ser268Phe	p.S268F	ENST00000346085	NM_020732.3	268	tCc/tTc	1/20	0.28339153155989	3	FACETS	1	0.936	1	0.596	0.507	0.692	CLONAL	1	TRUE	1	0.391298281582083	3		570	241	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162475203	162475203	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	94	566	0	ENST00000366898.1:c.538C>T	p.Pro180Ser	p.P180S	ENST00000366898	NM_004562.2	180	Cca/Tca	5/12	0.28339153155989	3	FACETS	0.774	0.694	0.858	0.774	0.694	0.858	SUBCLONAL	2	TRUE	1	0.391298281582083	3		566	371	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374316	81374316	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	63	483	0	ENST00000222390.5:c.746G>A	p.Arg249Lys	p.R249K	ENST00000222390	NM_000601.4	249	aGa/aAa	6/18	0.189990216826209	2	FACETS	1	0.956	1	0.612	0.535	0.694	INDETERMINATE	1	TRUE	0	0.391298281582083	2		483	263	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508625	106508625	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	105	702	0	ENST00000359195.3:c.619C>T	p.Leu207Phe	p.L207F	ENST00000359195	NM_002649.2	207	Ctc/Ttc	2/11	0.189990216826209	2	FACETS	0.839	0.76	0.919	0.839	0.76	0.919	INDETERMINATE	2	TRUE	0	0.391298281582083	2		702	320	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879441	151879441	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239127912	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	35	815	0	ENST00000262189.6:c.5504C>T	p.Pro1835Leu	p.P1835L	ENST00000262189	NM_170606.2	1835	cCc/cTc	36/59	0.189990216826209	2	FACETS	0.453	0.371	0.544	0.226	0.185	0.272	INDETERMINATE	1	TRUE	0	0.391298281582083	2		815	395	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90960112	90960112	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	63	428	0	ENST00000265433.3:c.1854T>G	p.Asn618Lys	p.N618K	ENST00000265433	NM_002485.4	618	aaT/aaG	12/16	0.312202166992018	3	FACETS	1	0.972	1	0.74	0.647	0.839	CLONAL	1	TRUE	1	0.391298281582083	3		428	260	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741821	145741821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1316434470	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	44	824	0	ENST00000428558.2:c.682C>T	p.Leu228Phe	p.L228F	ENST00000428558	NM_004260.3	228	Ctt/Ttt	5/22	0.312202166992018	3	FACETS	0.671	0.563	0.789	0.335	0.281	0.395	SUBCLONAL	1	TRUE	1	0.391298281582083	3		824	401	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2084126	2084126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1004796796	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	101	612	0	ENST00000349721.2:c.2456G>A	p.Arg819Gln	p.R819Q	ENST00000349721	NM_003070.3	819	cGg/cAg	17/34	0.195030412976451	4	FACETS	0.824	0.741	0.911	0.824	0.741	0.911	INDETERMINATE	2	TRUE	2	0.391298281582083	4		612	436	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484176	8484176	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	147	642	0	ENST00000356435.5:c.3356A>G	p.Asn1119Ser	p.N1119S	ENST00000356435		1119	aAc/aGc	19/35	0.195030412976451	4	FACETS	1	0.972	1	1	0.972	1	INDETERMINATE	2	TRUE	2	0.391298281582083	4		642	465	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500798	8500798	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	133	659	0	ENST00000356435.5:c.2084C>T	p.Pro695Leu	p.P695L	ENST00000356435		695	cCt/cTt	13/35	0.195030412976451	4	FACETS	0.967	0.884	1	0.967	0.884	1	INDETERMINATE	2	TRUE	2	0.391298281582083	4		659	489	SUCCESS
MTAP	4507	MSKCC	GRCh37	9	21859322	21859322	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	112	510	0	ENST00000380172.4:c.711A>T	p.Leu237Phe	p.L237F	ENST00000380172	NM_002451.3	237	ttA/ttT	7/8	0.195030412976451	4	FACETS	0.918	0.831	1	0.918	0.831	1	INDETERMINATE	2	TRUE	2	0.391298281582083	4		510	434	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759653	133759653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	103	751	0	ENST00000318560.5:c.1976C>T	p.Ser659Phe	p.S659F	ENST00000318560	NM_005157.4	659	tCc/tTc	11/11	0.28339153155989	3	FACETS	0.833	0.751	0.917	0.833	0.751	0.917	CLONAL	2	TRUE	1	0.391298281582083	3		751	378	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771828	135771828	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	56	824	0	ENST00000298552.3:c.3289del	p.Arg1097ValfsTer13	p.R1097Vfs*13	ENST00000298552	NM_001162426.1	1097	Cgt/gt	23/23	0.28339153155989	3	FACETS	0.847	0.728	0.976	0.424	0.364	0.488	CLONAL	1	TRUE	1	0.391298281582083	3		824	404	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395029	139395029	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	38	566	0	ENST00000277541.6:c.5909C>T	p.Ser1970Phe	p.S1970F	ENST00000277541	NM_017617.3	1970	tCt/tTt	31/34	0.28339153155989	3	FACETS	0.697	0.578	0.83	0.349	0.289	0.415	SUBCLONAL	1	TRUE	1	0.391298281582083	3		566	333	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412632	139412632	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	64	808	0	ENST00000277541.6:c.1212C>A	p.Tyr404Ter	p.Y404*	ENST00000277541	NM_017617.3	404	taC/taA	7/34	0.28339153155989	3	FACETS	0.838	0.727	0.957	0.419	0.363	0.479	CLONAL	1	TRUE	1	0.391298281582083	3		808	467	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038826	47038826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	123	360	0	ENST00000377604.3:c.833C>T	p.Ala278Val	p.A278V	ENST00000377604	NM_001204468.1	278	gCc/gTc	9/24	0.245062687112548	2	FACETS	0.975	0.906	1			1	CLONAL	3	TRUE	NA	0.391298281582083	2		360	215	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0067836-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	52	148	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.473363822074856	4	FACETS	0.962	0.823	1	0.321	0.274	0.371	CLONAL	1	TRUE	1	0.493947033062616	4		148	327	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522598	157522598	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554236040	NA	P-0067836-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	59	442	0	ENST00000346085.5:c.4870C>T	p.Arg1624Ter	p.R1624*	ENST00000346085	NM_020732.3	1624	Cga/Tga	18/20	0.433709464688258	2	FACETS	0.38	0.326	0.438	0.19	0.163	0.219	SUBCLONAL	1	TRUE	0	0.493947033062616	2		442	629	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520006	NA	P-0067836-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	526	474	0	ENST00000269305.4:c.821T>C	p.Val274Ala	p.V274A	ENST00000269305	NM_001126112.2	274	gTt/gCt	8/11	0.493978974669815	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.493947033062616	3		474	864	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509612	106509612	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067836-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	59	507	0	ENST00000359195.3:c.1606C>A	p.Pro536Thr	p.P536T	ENST00000359195	NM_002649.2	536	Cct/Act	2/11	0.493978974669815	3	FACETS	0.352	0.302	0.407	0.176	0.151	0.204	SUBCLONAL	1	TRUE	1	0.493947033062616	3		507	846	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321535	62321535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067836-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	184	555	0	ENST00000360203.5:c.2237C>T	p.Ala746Val	p.A746V	ENST00000360203	NM_001283009.1	746	gCc/gTc	25/35	0.308557382574488	4	FACETS	1	0.971	1	0.554	0.511	0.599	CLONAL	1	TRUE	2	0.493947033062616	4		555	1005	SUCCESS
ALB	213	MSKCC	GRCh37	4	74285330	74285330	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs76587671	NA	P-0067836-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	61	386	1	ENST00000295897.4:c.1759G>A	p.Asp587Asn	p.D587N	ENST00000295897	NM_000477.5	587	Gat/Aat	13/15	1	2	FACETS	0.477	0.412	0.548	0.477	0.412	0.548	SUBCLONAL	1	TRUE	1	0.493947033062616	2		387	518	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1296105	1296105	+	upstream_gene_variant	5'Flank	SNP	G	G	C	novel	NA	P-0067836-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	88	626	0				ENST00000310581	NM_198253.2	-/1132			0.493978974669815	2	FACETS	0.48	0.424	0.538	0.24	0.212	0.269	SUBCLONAL	1	TRUE	0	0.493947033062616	2		626	743	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163741	32163741	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067836-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	446	479	0	ENST00000375023.3:c.5485C>G	p.His1829Asp	p.H1829D	ENST00000375023	NM_004557.3	1829	Cac/Gac	30/30	0.493947033062616	5	FACETS	0.969	0.928	1	0.969	0.928	1	CLONAL	3	TRUE	2	0.493947033062616	5		479	1081	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0067837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	281	459	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.834645301469507	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.834645301469507	1		459	366	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941682	48941754	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAGATGCAAGATTATTTTTGGATCATGATAAAACTCTTCAGACTGATTCTATAGACAGGTATTGCACATGGTA	TAGATGCAAGATTATTTTTGGATCATGATAAAACTCTTCAGACTGATTCTATAGACAGGTATTGCACATGGTA	-	novel	NA	P-0067837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	157	310	0	ENST00000267163.4:c.994_1049+17del		p.X332_splice	ENST00000267163	NM_000321.2	332		10/27	0.834645301469507	1	FACETS	0.856	0.805	0.906	0.856	0.805	0.906	CLONAL	1	TRUE	0	0.834645301469507	1		310	256	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0067838-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	137	437	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.688037898428004	3	FACETS	1	0.987	1	0.702	0.646	0.76	CLONAL	1	TRUE	1	0.688037898428004	3		437	381	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143275	108143275	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067838-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	20	501	0	ENST00000278616.4:c.3094A>G	p.Arg1032Gly	p.R1032G	ENST00000278616	NM_000051.3	1032	Agg/Ggg	21/63	1	2	FACETS	0.186	0.142	0.238	0.186	0.142	0.238	SUBCLONAL	1	TRUE	1	0.688037898428004	2		501	312	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435607	18435607	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067838-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	53	582	0	ENST00000266497.5:c.592G>T	p.Val198Leu	p.V198L	ENST00000266497		198	Gtg/Ttg	1/31	1	2	FACETS	0.371	0.317	0.43	0.371	0.317	0.43	SUBCLONAL	1	TRUE	1	0.688037898428004	2		582	415	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675348	30675348	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067838-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	166	778	0	ENST00000376406.3:c.3008A>T	p.Gln1003Leu	p.Q1003L	ENST00000376406	NM_014641.2	1003	cAg/cTg	8/15	1	2	FACETS	0.433	0.397	0.471	0.433	0.397	0.471	SUBCLONAL	1	TRUE	1	0.688037898428004	2		778	1115	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000358	42000358	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067838-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	37	442	0	ENST00000219905.7:c.2377A>C	p.Lys793Gln	p.K793Q	ENST00000219905	NM_001164273.1	793	Aag/Cag	7/24	1	2	FACETS	0.27	0.222	0.322	0.27	0.222	0.322	SUBCLONAL	1	TRUE	1	0.688037898428004	2		442	399	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356258	66356258	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs780756647	NA	P-0067839-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	84	695	0	ENST00000273854.3:c.1239G>T	p.Arg413Ser	p.R413S	ENST00000273854	NM_004439.5	413	agG/agT	5/18	1	2	FACETS	0.268	0.237	0.303	0.268	0.237	0.303	SUBCLONAL	1	TRUE	1	0.837726104636367	2		695	747	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981845	201981845	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748393735	NA	P-0067839-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	284	721	1	ENST00000359651.3:c.556G>A	p.Ala186Thr	p.A186T	ENST00000359651		186	Gca/Aca	4/8	1	2	FACETS	0.984	0.931	1	0.984	0.931	1	CLONAL	1	TRUE	1	0.837726104636367	2		722	689	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92404053	92404056	+	frameshift_variant	Frame_Shift_Del	DEL	AAGT	AAGT	-	novel	NA	P-0067839-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	223	544	0	ENST00000265734.4:c.323_326del	p.Tyr108TrpfsTer14	p.Y108Wfs*14	ENST00000265734	NM_001259.6	108	tACTTg/tg	3/8	1	2	FACETS	0.99	0.93	1	0.99	0.93	1	CLONAL	1	TRUE	1	0.837726104636367	2		544	538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067839-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	291	674	0	ENST00000269305.4:c.817del	p.Arg273ValfsTer72	p.R273Vfs*72	ENST00000269305	NM_001126112.2	273	Cgt/gt	8/11	0.837726104636367	1	FACETS	0.997	0.959	1	0.997	0.959	1	CLONAL	1	TRUE	0	0.837726104636367	1		674	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0067840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	530	478	2	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.398619300792847	6	FACETS	1	0.989	1	1	0.989	1	CLONAL	6	TRUE	0	0.398619300792847	6		480	766	SUCCESS
APC	324	MSKCC	GRCh37	5	112163701	112163701	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	99	307	0	ENST00000257430.4:c.1624C>T	p.Gln542Ter	p.Q542*	ENST00000257430	NM_000038.5	542	Cag/Tag	13/16	0.178003923853775	4	FACETS	1	0.921	1	1	0.921	1	INDETERMINATE	2	TRUE	2	0.398619300792847	4		307	339	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503787	186503789	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs1560084666	NA	P-0067840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	96	434	0	ENST00000323963.5:c.470_472del	p.Val157del	p.V157del	ENST00000323963		155	aTTGtt/att	5/11	0.301591141888363	4	FACETS	1	0.953	1	0.562	0.502	0.627	CLONAL	1	TRUE	2	0.398619300792847	4		434	599	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910883	114910883	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1477809102	NA	P-0067840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	185	421	0	ENST00000543371.1:c.1001+1G>A		p.X334_splice	ENST00000543371	NM_001198531.1	334			0.398619300792847	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.398619300792847	3		421	497	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443491	49443491	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067841-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	324	646	0	ENST00000301067.7:c.3880T>A	p.Ser1294Thr	p.S1294T	ENST00000301067	NM_003482.3	1294	Tcc/Acc	11/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		646	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579514	7579514	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	293	648	0	ENST00000269305.4:c.173del	p.Pro58GlnfsTer65	p.P58Qfs*65	ENST00000269305	NM_001126112.2	58	cCa/ca	4/11	0.424631170908905	3	FACETS	1	0.992	1	0.802	0.763	0.842	CLONAL	2	TRUE	0	0.528913594389311	3		648	582	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845590	128845590	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772693769	NA	P-0067842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	86	505	0	ENST00000249373.3:c.887G>A	p.Arg296His	p.R296H	ENST00000249373	NM_005631.4	296	cGt/cAt	4/12	0.528913594389311	4	FACETS	0.894	0.793	1	0.298	0.264	0.334	CLONAL	1	TRUE	1	0.528913594389311	4		505	556	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241971	72241971	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	127	436	0	ENST00000357731.5:c.419A>T	p.Lys140Met	p.K140M	ENST00000357731	NM_173808.2	140	aAg/aTg	3/7	0.424631170908905	3	FACETS	0.771	0.705	0.838	0.514	0.47	0.559	SUBCLONAL	2	TRUE	0	0.528913594389311	3		436	394	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21342336	21342338	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs1278587866	NA	P-0067842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	171	471	0	ENST00000215739.8:c.441_443del	p.Lys147del	p.K147del	ENST00000215739	NM_006767.3	146	ttGAAg/ttg	5/21	0.139613587427842	5	FACETS	1	0.985	1	0.618	0.574	0.663	INDETERMINATE	2	TRUE	1	0.528913594389311	5		471	469	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0067844-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	181	515	1	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.532414621940388	3	FACETS	0.922	0.859	0.986	0.922	0.859	0.986	CLONAL	2	TRUE	1	0.532414621940388	3		516	467	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934245	81934245	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067844-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	35	584	0	ENST00000359376.3:c.1222C>T	p.His408Tyr	p.H408Y	ENST00000359376	NM_002661.3	408	Cac/Tac	14/33	0.243658512729847	4	FACETS	0.301	0.246	0.364	0.151	0.123	0.182	INDETERMINATE	1	TRUE	2	0.532414621940388	4		584	669	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578504	7578562	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGA	AGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGA	-	novel	NA	P-0067844-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	272	807	0	ENST00000269305.4:c.376-8_426del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	0.532414621940388	2	FACETS	0.893	0.847	0.94	0.893	0.847	0.94	CLONAL	2	TRUE	0	0.532414621940388	2		807	572	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639596	47639596	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067844-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	50	489	0	ENST00000233146.2:c.689C>A	p.Ala230Asp	p.A230D	ENST00000233146	NM_000251.2	230	gCt/gAt	4/16	0.532414621940388	3	FACETS	0.634	0.54	0.737	0.317	0.27	0.369	SUBCLONAL	1	TRUE	1	0.532414621940388	3		489	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0067847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	210	394	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.690233006357679	1	FACETS	0.991	0.935	1	0.991	0.935	1	CLONAL	1	TRUE	0	0.690233006357679	1		394	402	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054325	42054325	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0067847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	162	325	0	ENST00000219905.7:c.7511-2A>G		p.X2504_splice	ENST00000219905	NM_001164273.1	2504			1	2	FACETS	0.976	0.903	1	0.976	0.903	1	CLONAL	1	TRUE	1	0.690233006357679	2		325	481	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	97	350	0				ENST00000310581	NM_198253.2	-/1132			0.577345208209531	4	FACETS	1	0.978	1	0.809	0.743	0.873	CLONAL	2	TRUE	1	0.84138294057271	4		350	175	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0067848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	236	324	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.84138294057271	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.84138294057271	3		324	362	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0067848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	112	572	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	0.84138294057271	3	FACETS	0.948	0.86	1	0.474	0.43	0.52	CLONAL	1	TRUE	1	0.84138294057271	3		572	399	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916747	48916747	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690915	NA	P-0067848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	279	315	0	ENST00000267163.4:c.277C>T	p.Gln93Ter	p.Q93*	ENST00000267163	NM_000321.2	93	Caa/Taa	3/27	0.548847011118176	3	FACETS	1	0.996	1			1	CLONAL	3	TRUE	NA	0.84138294057271	3		315	288	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905585	50905585	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs553342844	NA	P-0067848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	14	631	0	ENST00000440232.2:c.713C>T	p.Thr238Met	p.T238M	ENST00000440232	NM_002691.3	238	aCg/aTg	6/27	1	2	FACETS	0.151	0.109	0.201	0.151	0.109	0.201	SUBCLONAL	1	TRUE	1	0.84138294057271	2		631	221	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	230998	230998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs940845256	NA	P-0067848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	92	405	0	ENST00000264932.6:c.778G>A	p.Gly260Arg	p.G260R	ENST00000264932	NM_004168.2	260	Ggg/Agg	7/15	0.577345208209531	4	FACETS	1	0.965	1	0.392	0.352	0.435	CLONAL	1	TRUE	1	0.84138294057271	4		405	342	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278106	142278106	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	130	352	0	ENST00000350721.4:c.1719G>C	p.Leu573Phe	p.L573F	ENST00000350721	NM_001184.3	573	ttG/ttC	7/47	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.84138294057271	2		352	287	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023726	27023726	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	87	496	0	ENST00000324856.7:c.833del	p.Gly278AlafsTer85	p.G278Afs*85	ENST00000324856	NM_006015.4	278	Ggc/gc	1/20	1	2	FACETS	0.989	0.895	1	0.989	0.895	1	CLONAL	1	TRUE	1	0.84138294057271	2		496	209	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912703	32912703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41293489	NA	P-0067848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	213	467	0	ENST00000380152.3:c.4211C>T	p.Ser1404Leu	p.S1404L	ENST00000380152		1404	tCa/tTa	11/27	0.740827604853182	4	FACETS	0.89	0.834	0.946	0.593	0.556	0.631	CLONAL	2	TRUE	1	0.84138294057271	4		467	524	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625151	69625151	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	88	441	0	ENST00000334134.2:c.642G>T	p.Lys214Asn	p.K214N	ENST00000334134	NM_005247.2	214	aaG/aaT	3/3	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.84138294057271	2		441	202	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094321	193094321	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	146	412	0	ENST00000367435.3:c.211C>G	p.His71Asp	p.H71D	ENST00000367435	NM_024529.4	71	Cat/Gat	2/17	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.84138294057271	2		412	290	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711222	61711222	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	30	402	0	ENST00000401558.2:c.2527G>C	p.Glu843Gln	p.E843Q	ENST00000401558	NM_003400.3	843	Gaa/Caa	21/25	0.697292141695637	1	FACETS	0.228	0.185	0.276	0.228	0.185	0.276	SUBCLONAL	1	TRUE	0	0.84138294057271	1		402	181	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0067849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	43	252	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.781	0.653	0.923	0.781	0.653	0.923	CLONAL	1	FALSE	1	0.207719946933141	2		253	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0067849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	56	317	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	1	2	FACETS	0.953	0.816	1	0.953	0.816	1	CLONAL	1	FALSE	1	0.207719946933141	2		317	566	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473708	67473708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906855	NA	P-0067849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	36	353	0	ENST00000327367.4:c.788C>T	p.Pro263Leu	p.P263L	ENST00000327367	NM_005902.3	263	cCc/cTc	6/9	1	2	FACETS	0.565	0.464	0.68	0.565	0.464	0.68	SUBCLONAL	1	FALSE	1	0.207719946933141	2		353	613	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955394	48955394	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	44	245	0	ENST00000267163.4:c.1510C>A	p.Gln504Lys	p.Q504K	ENST00000267163	NM_000321.2	504	Cag/Aag	17/27	0.193898112171206	3	FACETS	0.966	0.81	1			1	CLONAL	1	FALSE	NA	0.207719946933141	3		245	484	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992689	68992689	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	31	345	0	ENST00000288368.4:c.1654A>T	p.Ser552Cys	p.S552C	ENST00000288368	NM_024870.2	552	Agc/Tgc	16/40	0.207719946933141	1	FACETS	0.564	0.456	0.687	0.564	0.456	0.687	SUBCLONAL	1	FALSE	0	0.207719946933141	1		345	474	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423598	88423598	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	286	419	0	ENST00000360948.2:c.2237A>C	p.Lys746Thr	p.K746T	ENST00000360948	NM_001012338.2	746	aAg/aCg	18/19	0.227702294671742	3	FACETS	0.868	0.82	0.916	0.868	0.82	0.916	INDETERMINATE	2	TRUE	1	0.579157871924342	3		419	734	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573663	48573663	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	180	395	0	ENST00000342988.3:c.247C>T	p.Gln83Ter	p.Q83*	ENST00000342988	NM_005359.5	83	Cag/Tag	2/12	0.573223362819833	1	FACETS	0.973	0.906	1	0.973	0.906	1	CLONAL	1	TRUE	0	0.579157871924342	1		395	454	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563387	21563387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528026146	NA	P-0067850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	189	542	0	ENST00000382592.4:c.532G>A	p.Asp178Asn	p.D178N	ENST00000382592	NM_014572.2	178	Gat/Aat	4/8	1	2	FACETS	0.887	0.822	0.954	0.887	0.822	0.954	CLONAL	1	TRUE	1	0.579157871924342	2		542	736	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438150	438150	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	965	446	0	ENST00000399788.2:c.1819C>T	p.Arg607Cys	p.R607C	ENST00000399788	NM_001042603.1	607	Cgc/Tgc	14/28	0.579157871924342	4	FACETS	1	0.997	1			1	CLONAL	4	TRUE	NA	0.579157871924342	4		446	1207	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260232	19260232	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	35	460	0	ENST00000162023.5:c.61T>G	p.Phe21Val	p.F21V	ENST00000162023		21	Ttc/Gtc	7/13	1	2	FACETS	0.214	0.174	0.258	0.214	0.174	0.258	SUBCLONAL	1	TRUE	1	0.579157871924342	2		460	566	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138291	2138300	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCGGCTCC	GCCCGGCTCC	-	novel	NA	P-0067850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	75	467	0	ENST00000219476.3:c.5227_5236del	p.Arg1743ThrfsTer80	p.R1743Tfs*80	ENST00000219476	NM_000548.3	1742	GCCCGGCTCCgc/gc	41/42	0.579157871924342	1	FACETS	0.466	0.41	0.525	0.466	0.41	0.525	SUBCLONAL	1	TRUE	0	0.579157871924342	1		467	395	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233243	46233244	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	414	452	0	ENST00000334344.6:c.1464dup	p.Val489SerfsTer32	p.V489Sfs*32	ENST00000334344	NM_152641.2	488	caa/cAaa	11/21	0.57496815348944	2	FACETS	0.987	0.949	1	0.987	0.949	1	CLONAL	2	TRUE	0	0.579157871924342	2		452	724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0067851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	157	445	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	0.389369908679377	1	FACETS	0.946	0.87	1	0.946	0.87	1	CLONAL	1	TRUE	0	0.420045012481582	1		445	624	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930609	32930609	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs80358972	NA	P-0067851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	127	388	0	ENST00000380152.3:c.7480C>T	p.Arg2494Ter	p.R2494*	ENST00000380152		2494	Cga/Tga	15/27	0.420045012481582	1	FACETS	0.937	0.853	1	0.937	0.853	1	CLONAL	1	TRUE	0	0.420045012481582	1		388	510	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486112	29486112	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0067851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	93	325	0	ENST00000356175.3:c.288+1G>A		p.X96_splice	ENST00000356175	NM_000267.3	96			0.389369908679377	1	FACETS	0.961	0.862	1	0.961	0.862	1	CLONAL	1	TRUE	0	0.420045012481582	1		325	364	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295990	1295990	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0067851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	168	572	0				ENST00000310581	NM_198253.2	-/1132			0.285267707381277	4	FACETS	1	0.955	1	0.529	0.486	0.575	CLONAL	1	TRUE	2	0.420045012481582	4		572	1073	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421819	49421819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	122	539	0	ENST00000301067.7:c.14488C>T	p.Pro4830Ser	p.P4830S	ENST00000301067	NM_003482.3	4830	Cca/Tca	46/54	0.36298058251775	1	FACETS	0.633	0.573	0.697	0.633	0.573	0.697	SUBCLONAL	1	TRUE	0	0.420045012481582	1		539	725	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21342302	21342302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1425031926	NA	P-0067851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	99	376	0	ENST00000215739.8:c.404G>A	p.Gly135Asp	p.G135D	ENST00000215739	NM_006767.3	135	gGt/gAt	5/21	0.389369908679377	1	FACETS	0.818	0.734	0.907	0.818	0.734	0.907	CLONAL	1	TRUE	0	0.420045012481582	1		376	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0067852-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	54	324	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.17899728385697	2		324	563	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796458	57796458	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067852-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	32	436	0	ENST00000309042.7:c.1434G>C	p.Lys478Asn	p.K478N	ENST00000309042	NM_005612.4	478	aaG/aaC	4/4	1	2	FACETS	0.615	0.498	0.748	0.615	0.498	0.748	SUBCLONAL	1	TRUE	1	0.17899728385697	2		436	581	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0067853-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	21	252	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.815	0.637	1	1	0.93	1	CLONAL	2	TRUE	1	0.23	2		253	112	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374979	45374980	+	stop_gained,inframe_insertion	Nonsense_Mutation	INS	-	-	TAC	novel	NA	P-0067853-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	10	419	0	ENST00000262160.6:c.863_864insGTA	p.Glu288_Thr289insTer	p.E288_T289ins*	ENST00000262160	NM_005901.5	288	gaa/gaGTAa	8/11	0.166833336701853	1	FACETS	0.546	0.371	0.764	0.546	0.371	0.764	SUBCLONAL	1	TRUE	0	0.23	1		419	141	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604776	48604776	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs377767382	NA	P-0067853-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	22	459	0	ENST00000342988.3:c.1598T>C	p.Leu533Pro	p.L533P	ENST00000342988	NM_005359.5	533	cTc/cCc	12/12	0.166833336701853	1	FACETS	1	0.792	1	1	0.792	1	CLONAL	1	TRUE	0	0.23	1		459	167	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913508	32913508	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067853-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	10	460	0	ENST00000380152.3:c.5016C>A	p.Tyr1672Ter	p.Y1672*	ENST00000380152		1672	taC/taA	11/27	0.166833336701853	0	FACETS	0.563	0.383	0.785			1	SUBCLONAL	1	TRUE	0	0.23	0		460	119	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193181543	193181903	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTCCTGCAGCTACCACCTCTTTAATAACCATGCTTAATGCAAAAGACCTTCTACAGGACCTGAAGTAAGTAATTTATTAAACTATCCTGTACGTAGGATATTGAGATACCATTGGAAAATAGTAGTTACTGAATCAGTATTACTTATTTGGAAAAAACAAAATTTCGGTTTCTGTGCTATAGGCCTTACACATAGTATGAAGCATACATTTTCAAAACAGAATATATTCTTTTATATTTGGATCCTTTAGGGAAAGTTACAGAAACTTCTGGCTAAAGTCCTAATGAAAAAAGGTACTATCGTATTAACTTTTAATATGAATTGTTTTCTTTTGATGATTTTCTCTGAGAGAGCTTGAGG	ATTCCTGCAGCTACCACCTCTTTAATAACCATGCTTAATGCAAAAGACCTTCTACAGGACCTGAAGTAAGTAATTTATTAAACTATCCTGTACGTAGGATATTGAGATACCATTGGAAAATAGTAGTTACTGAATCAGTATTACTTATTTGGAAAAAACAAAATTTCGGTTTCTGTGCTATAGGCCTTACACATAGTATGAAGCATACATTTTCAAAACAGAATATATTCTTTTATATTTGGATCCTTTAGGGAAAGTTACAGAAACTTCTGGCTAAAGTCCTAATGAAAAAAGGTACTATCGTATTAACTTTTAATATGAATTGTTTTCTTTTGATGATTTTCTCTGAGAGAGCTTGAGG	-	novel	NA	P-0067853-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	10	381	0	ENST00000367435.3:c.1091_1154+297del		p.X364_splice	ENST00000367435	NM_024529.4	364		13/17	1	2	FACETS	0.776	0.529	1	0.776	0.529	1	CLONAL	1	TRUE	1	0.23	2		381	112	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478922	56478922	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067853-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	15	336	0	ENST00000267101.3:c.378C>G	p.Asn126Lys	p.N126K	ENST00000267101	NM_001982.3	126	aaC/aaG	3/28	1	2	FACETS	0.659	0.483	0.869	0.659	0.483	0.869	SUBCLONAL	1	TRUE	1	0.23	2		336	198	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954975	2954975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368119340	NA	P-0067854-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	24	560	5	ENST00000396946.4:c.2735G>A	p.Arg912Gln	p.R912Q	ENST00000396946	NM_032415.4	912	cGg/cAg	21/25	0.208599026446717	2	FACETS	1	0.929	1	0.735	0.585	0.903	CLONAL	1	TRUE	0	0.256990576684735	2		565	127	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0067854-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	11	570	0	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	0.191489849679251	1	FACETS	0.424	0.293	0.586	0.424	0.293	0.586	SUBCLONAL	1	TRUE	0	0.256990576684735	1		570	176	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0067854-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	9	443	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	0.256990576684735	3	FACETS	0.507	0.336	0.723	0.253	0.168	0.362	SUBCLONAL	1	TRUE	1	0.256990576684735	3		443	156	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917794	29917794	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201750304	NA	P-0067854-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	13	499	0	ENST00000389048.3:c.874C>T	p.Arg292Cys	p.R292C	ENST00000389048	NM_004304.4	292	Cgc/Tgc	3/29	0.256990576684735	0	FACETS	0.549	0.394	0.735			1	SUBCLONAL	1	TRUE	0	0.256990576684735	0		499	137	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578244	7578252	+	inframe_deletion	In_Frame_Del	DEL	CGCAAATTT	CGCAAATTT	-	novel	NA	P-0067854-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	8	514	0	ENST00000269305.4:c.597_605del	p.Asn200_Arg202del	p.N200_R202del	ENST00000269305	NM_001126112.2	199	ggAAATTTGCGt/ggt	6/11	1	2	FACETS	0.537	0.347	0.78	0.537	0.347	0.78	SUBCLONAL	1	TRUE	1	0.256990576684735	2		514	116	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150900239	150900239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767435466	NA	P-0067855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	40	480	0	ENST00000271640.5:c.49G>A	p.Val17Met	p.V17M	ENST00000271640	NM_001145415.1	17	Gtg/Atg	2/22	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.74	NA		480	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0067856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	416	395	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.779971587312899	2	FACETS	0.98	0.952	1	0.98	0.952	1	CLONAL	2	TRUE	0	0.779971587312899	2		395	544	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856097	111856097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1013978345	NA	P-0067856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	298	418	0	ENST00000341259.2:c.148C>T	p.Arg50Trp	p.R50W	ENST00000341259	NM_005475.2	50	Cgg/Tgg	2/8	0.751659397845093	2	FACETS	0.912	0.877	0.945	0.912	0.877	0.945	CLONAL	2	TRUE	0	0.779971587312899	2		418	419	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465902	69465902	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1417190579	NA	P-0067856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	191	459	0	ENST00000227507.2:c.740G>T	p.Cys247Phe	p.C247F	ENST00000227507	NM_053056.2	247	tGc/tTc	5/5	1	2	FACETS	0.915	0.853	0.979	0.915	0.853	0.979	CLONAL	1	TRUE	1	0.779971587312899	2		459	535	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0067857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	145	252	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.193551070581209	4	FACETS	1	0.988	1	0.748	0.684	0.813	INDETERMINATE	1	TRUE	2	0.461753953502741	4		253	614	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0067857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	159	360	1	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	0.142799988343466	4	FACETS	0.801	0.737	0.868	0.801	0.737	0.868	INDETERMINATE	2	TRUE	2	0.461753953502741	4		361	628	SUCCESS
APC	324	MSKCC	GRCh37	5	112175755	112175755	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	223	404	1	ENST00000257430.4:c.4464del	p.Leu1488PhefsTer19	p.L1488Ffs*19	ENST00000257430	NM_000038.5	1488	ttA/tt	16/16	0.167910486206008	2	FACETS	1	0.99	1	0.672	0.628	0.717	INDETERMINATE	1	TRUE	0	0.461753953502741	2		405	719	SUCCESS
APC	324	MSKCC	GRCh37	5	112174112	112174112	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	84	405	3	ENST00000257430.4:c.2821G>T	p.Glu941Ter	p.E941*	ENST00000257430	NM_000038.5	941	Gaa/Taa	16/16	0.167910486206008	2	FACETS	0.54	0.477	0.607	0.27	0.238	0.304	INDETERMINATE	1	TRUE	0	0.461753953502741	2		408	674	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247168	153247168	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1560758208	NA	P-0067857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	167	365	1	ENST00000281708.4:c.1634A>G	p.Tyr545Cys	p.Y545C	ENST00000281708	NM_033632.3	545	tAt/tGt	10/12	0.461753953502741	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.461753953502741	1		366	501	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120346	70120347	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCTA	novel	NA	P-0067857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	164	470	0	ENST00000245479.2:c.1350_1353dup	p.Tyr452LeufsTer127	p.Y452Lfs*127	ENST00000245479	NM_000346.3	450	tcc/tCCTAcc	3/3	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.461753953502741	2		470	699	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244171	41244172	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0067857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	174	398	0	ENST00000357654.3:c.3376_3377del	p.Pro1126IlefsTer6	p.P1126Ifs*6	ENST00000357654	NM_007294.3	1126	CCa/a	10/23	1	2	FACETS	0.949	0.875	1	0.949	0.875	1	CLONAL	1	TRUE	1	0.461753953502741	2		398	794	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129427	64129427	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367990117	NA	P-0067857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	115	419	0	ENST00000334205.4:c.859G>A	p.Ala287Thr	p.A287T	ENST00000334205	NM_003942.2	287	Gcg/Acg	8/17	0.150387896163472	2	FACETS	0.669	0.603	0.739	0.335	0.301	0.37	INDETERMINATE	1	TRUE	0	0.461753953502741	2		419	744	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579543	7579544	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACGAT	novel	NA	P-0067857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	161	481	0	ENST00000269305.4:c.143_144insATCGT	p.Asp48GlufsTer77	p.D48Efs*77	ENST00000269305	NM_001126112.2	48	gac/gaATCGTc	4/11	0.315447519085008	1	FACETS	0.956	0.882	1	0.956	0.882	1	CLONAL	1	TRUE	0	0.461753953502741	1		481	561	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120229	70120229	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	199	434	1	ENST00000245479.2:c.1231C>T	p.Gln411Ter	p.Q411*	ENST00000245479	NM_000346.3	411	Cag/Tag	3/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.461753953502741	2		435	746	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969913	161969913	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs780996466	NA	P-0067857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	90	341	0	ENST00000366898.1:c.1056C>A	p.Cys352Ter	p.C352*	ENST00000366898	NM_004562.2	352	tgC/tgA	9/12	1	2	FACETS	0.744	0.662	0.831	0.744	0.662	0.831	SUBCLONAL	1	TRUE	1	0.461753953502741	2		341	524	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0067868-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	122	457	0	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	1	2	FACETS	0.803	0.727	0.882	0.803	0.727	0.882	CLONAL	1	TRUE	1	0.466823903754966	2		457	651	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0067868-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	180	480	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.466823903754966	2		480	707	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0067868-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	197	592	0	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.466823903754966	2		592	773	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067868-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	89	482	0	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	1	2	FACETS	0.527	0.467	0.592	0.527	0.467	0.592	SUBCLONAL	1	TRUE	1	0.466823903754966	2		482	723	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193172951	193172951	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067868-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	135	359	0	ENST00000367435.3:c.999G>T	p.Gln333His	p.Q333H	ENST00000367435	NM_024529.4	333	caG/caT	11/17	0.229891317727511	1	FACETS	0.789	0.72	0.86	0.789	0.72	0.86	INDETERMINATE	1	TRUE	0	0.466823903754966	1		359	562	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0067870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	261	400	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.317951844674981	3	FACETS	1	0.989	1	0.797	0.753	0.842	CLONAL	2	TRUE	0	0.442885512412309	3		400	602	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285870	38285870	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs780153672	NA	P-0067870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	52	493	0	ENST00000425967.3:c.541C>T	p.Pro181Ser	p.P181S	ENST00000425967	NM_001174067.1	181	Ccc/Tcc	5/19	0.447752515876512	1	FACETS	0.552	0.472	0.639	0.552	0.472	0.639	SUBCLONAL	1	TRUE	0	0.442885512412309	1		493	331	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280031	66280031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867811974	NA	P-0067870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	128	490	0	ENST00000273854.3:c.1658G>A	p.Arg553Gln	p.R553Q	ENST00000273854	NM_004439.5	553	cGa/cAa	7/18	0.447752515876512	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.442885512412309	1		490	314	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136799	2136799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137854153	NA	P-0067870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	70	618	0	ENST00000219476.3:c.4916G>A	p.Arg1639His	p.R1639H	ENST00000219476	NM_000548.3	1639	cGc/cAc	38/42	0.447752515876512	1	FACETS	0.436	0.38	0.496	0.436	0.38	0.496	SUBCLONAL	1	TRUE	0	0.442885512412309	1		618	565	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941715	48941716	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0067870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	14	327	0	ENST00000267163.4:c.1027_1028del	p.Leu343SerfsTer3	p.L343Sfs*3	ENST00000267163	NM_000321.2	342	aCT/a	10/27	0.447752515876512	1	FACETS	0.807	0.599	1	0.807	0.599	1	CLONAL	1	TRUE	0	0.442885512412309	1		327	61	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48922000	48922000	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1566187856	NA	P-0067870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	34	339	0	ENST00000267163.4:c.539+1G>A		p.X180_splice	ENST00000267163	NM_000321.2	180			0.447752515876512	1	FACETS	0.808	0.689	0.928	1	0.963	1	CLONAL	2	TRUE	0	0.442885512412309	1		339	74	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949076	44949076	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	31	335	0	ENST00000377967.4:c.3637C>T	p.Arg1213Ter	p.R1213*	ENST00000377967	NM_021140.2	1213	Cga/Tga	25/29	0.447752515876512	2	FACETS	0.737	0.601	0.887			1	SUBCLONAL	1	TRUE	NA	0.442885512412309	2		335	190	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442567	52442567	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1253151209	NA	P-0067870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	294	535	0	ENST00000460680.1:c.178C>T	p.Arg60Ter	p.R60*	ENST00000460680	NM_004656.3	60	Cga/Tga	4/17	0.423445069562229	2	FACETS	0.875	0.827	0.922	0.875	0.827	0.922	CLONAL	2	TRUE	0	0.442885512412309	2		535	759	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441974	6441974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	73	303	0	ENST00000356142.4:c.533C>T	p.Ala178Val	p.A178V	ENST00000356142	NM_018890.3	178	gCg/gTg	7/7	0.434999606056671	2	FACETS	0.822	0.722	0.928	0.411	0.361	0.464	CLONAL	1	TRUE	0	0.442885512412309	2		303	401	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590478	67590478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	51	453	0	ENST00000274335.5:c.1540C>T	p.Arg514Cys	p.R514C	ENST00000274335		514	Cgt/Tgt	11/15	0.367557497941445	2	FACETS	0.837	0.717	0.967	0.419	0.358	0.484	CLONAL	1	TRUE	0	0.442885512412309	2		453	275	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602293	10602293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1320679251	NA	P-0067870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	224	594	0	ENST00000171111.5:c.1285G>A	p.Gly429Ser	p.G429S	ENST00000171111	NM_203500.1	429	Ggc/Agc	3/6	0.423445069562229	2	FACETS	1	0.992	1	0.725	0.678	0.773	CLONAL	1	TRUE	0	0.442885512412309	2		594	698	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984856	9984856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	144	441	0	ENST00000330684.3:c.1109G>A	p.Arg370Gln	p.R370Q	ENST00000330684	NM_001134407.1	370	cGg/cAg	4/13	0.447752515876512	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.442885512412309	1		441	372	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752723	42752723	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1410725157	NA	P-0067870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	343	519	0	ENST00000222329.4:c.1541G>A	p.Arg514His	p.R514H	ENST00000222329	NM_006494.2	514	cGt/cAt	4/4	0.317951844674981	3	FACETS	0.901	0.86	0.942	0.901	0.86	0.942	CLONAL	3	TRUE	0	0.442885512412309	3		519	700	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47724984	47724984	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373478289	NA	P-0067870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	118	571	0	ENST00000449228.1:c.760G>A	p.Ala254Thr	p.A254T	ENST00000449228	NM_001127240.2	254	Gcg/Acg	4/4	0.317951844674981	3	FACETS	0.997	0.901	1	0.332	0.3	0.366	CLONAL	1	TRUE	0	0.442885512412309	3		571	653	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725208	49725208	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752708882	NA	P-0067870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	32	116	0	ENST00000449682.2:c.217C>T	p.Arg73Cys	p.R73C	ENST00000449682	NM_020998.3	73	Cgc/Tgc	2/18	0.423445069562229	2	FACETS	0.84	0.69	1	0.42	0.345	0.503	CLONAL	1	TRUE	0	0.442885512412309	2		116	172	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041765	14041765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	70	516	0	ENST00000311895.7:c.2312C>T	p.Ser771Phe	p.S771F	ENST00000311895	NM_005236.2	771	tCc/tTc	11/11	0.423445069562229	2	FACETS	0.579	0.505	0.658	0.289	0.252	0.329	SUBCLONAL	1	TRUE	0	0.442885512412309	2		516	546	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607771	46607771	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375135104	NA	P-0067870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	293	554	0	ENST00000263734.3:c.1960G>A	p.Val654Ile	p.V654I	ENST00000263734	NM_001430.4	654	Gtc/Atc	12/16	0.447752515876512	1	FACETS	0.804	0.762	0.845	1	0.995	1	CLONAL	2	TRUE	0	0.442885512412309	1		554	641	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044484	128044484	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	237	461	0	ENST00000285398.2:c.1137G>T	p.Lys379Asn	p.K379N	ENST00000285398	NM_000122.1	379	aaG/aaT	8/15	0.367557497941445	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.442885512412309	2		461	525	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222958	5222958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781437725	NA	P-0067870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	214	601	0	ENST00000357368.4:c.2845C>T	p.Arg949Cys	p.R949C	ENST00000357368	NM_002850.3	949	Cgc/Tgc	18/38	0.447752515876512	1	FACETS	0.855	0.805	0.905	1	0.994	1	CLONAL	2	TRUE	0	0.442885512412309	1		601	440	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29497003	29497003	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397514641	NA	P-0067870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	61	353	0	ENST00000356175.3:c.574C>T	p.Arg192Ter	p.R192*	ENST00000356175	NM_000267.3	192	Cga/Tga	5/57	0.423445069562229	2	FACETS	0.9	0.796	1	0.9	0.796	1	CLONAL	2	TRUE	0	0.442885512412309	2		353	153	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214625	133214625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748008084	NA	P-0067870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	108	523	0	ENST00000320574.5:c.5653G>A	p.Ala1885Thr	p.A1885T	ENST00000320574	NM_006231.2	1885	Gct/Act	41/49	0.369508038886811	1	FACETS	0.715	0.644	0.79	0.715	0.644	0.79	SUBCLONAL	1	TRUE	0	0.442885512412309	1		523	531	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119660	108119660	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	35	418	0	ENST00000278616.4:c.1066G>C	p.Val356Leu	p.V356L	ENST00000278616	NM_000051.3	356	Gtt/Ctt	9/63	0.434999606056671	2	FACETS	0.681	0.562	0.813	0.341	0.281	0.407	SUBCLONAL	1	TRUE	0	0.442885512412309	2		418	232	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0067875-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	73	288	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.903	0.793	1	0.903	0.793	1	CLONAL	1	TRUE	1	0.352157531113759	2		288	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0067875-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	119	429	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.31605412638229	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.352157531113759	1		429	530	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099336	157099362	+	inframe_deletion	In_Frame_Del	DEL	CCACCACCACCACCATGCCCACCACCT	CCACCACCACCACCATGCCCACCACCT	-	rs1225430487	NA	P-0067875-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	50	433	0	ENST00000346085.5:c.286_312del	p.His96_His104del	p.H96_H104del	ENST00000346085	NM_020732.3	91	caCCACCACCACCACCATGCCCACCACCTc/cac	1/20	1	2	FACETS	0.543	0.461	0.633	0.543	0.461	0.633	SUBCLONAL	1	TRUE	1	0.352157531113759	2		433	523	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0067875-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	100	288	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.392279012355435	3	FACETS	0.793	0.714	0.875	0.793	0.714	0.875	SUBCLONAL	2	TRUE	1	0.395542836005966	3		288	382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0067875-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	33	429	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	1	2	FACETS	0.293	0.238	0.356	0.293	0.238	0.356	SUBCLONAL	1	TRUE	1	0.395542836005966	2		429	569	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41818373	41818373	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0067876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	96	469	0	ENST00000373198.4:c.1A>G	p.Met1?	p.M1?	ENST00000373198	NM_133170.3	1	Atg/Gtg	1/32	0.829401466827499	1	FACETS	0.516	0.467	0.565	0.516	0.467	0.565	SUBCLONAL	1	TRUE	0	0.851731809969464	1		469	251	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589527	69589527	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	45	699	0	ENST00000168712.1:c.326C>A	p.Ala109Glu	p.A109E	ENST00000168712	NM_002007.2	109	gCg/gAg	1/3	0.38891549319097	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.851731809969464	0		699	322	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067877-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	46	350	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.948	0.806	1	0.948	0.806	1	CLONAL	1	TRUE	1	0.407686976457424	2		350	238	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0067877-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	40	306	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.502	0.417	0.595	0.502	0.417	0.595	SUBCLONAL	1	TRUE	1	0.407686976457424	2		306	391	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0067878-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	13	242	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.739	0.527	0.996	0.739	0.527	0.996	CLONAL	1	TRUE	1	0.17	2		242	207	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0067878-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	24	360	1	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.902	0.708	1	0.902	0.708	1	CLONAL	1	TRUE	1	0.17	2		361	313	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0067878-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	27	258	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	1	2	FACETS	0.986	0.786	1	0.986	0.786	1	CLONAL	1	TRUE	1	0.17	2		258	322	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188050	151188050	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519949	NA	P-0067878-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	17	252	0	ENST00000262187.5:c.103T>A	p.Tyr35Asn	p.Y35N	ENST00000262187	NM_005614.3	35	Tac/Aac	2/8	1	2	FACETS	0.749	0.559	0.974	0.749	0.559	0.974	CLONAL	1	TRUE	1	0.17	2		252	267	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370985	55370985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067878-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	24	334	0	ENST00000297316.4:c.287C>G	p.Ala96Gly	p.A96G	ENST00000297316	NM_022454.3	96	gCc/gGc	1/2	1	2	FACETS	0.974	0.765	1	0.974	0.765	1	CLONAL	1	TRUE	1	0.17	2		334	290	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845642	63845642	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1564647852	NA	P-0067878-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	28	324	0	ENST00000279873.7:c.1384del	p.Gln462ArgfsTer17	p.Q462Rfs*17	ENST00000279873	NM_032199.2	461	Ccc/cc	9/10	1	2	FACETS	0.849	0.678	1	0.849	0.678	1	CLONAL	1	TRUE	1	0.17	2		324	388	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119562158	119562158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067878-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	31	341	0	ENST00000316626.5:c.1178C>T	p.Pro393Leu	p.P393L	ENST00000316626		393	cCt/cTt	11/12	1	2	FACETS	0.784	0.634	0.955	0.784	0.634	0.955	CLONAL	1	TRUE	1	0.17	2		341	465	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424400	47424412	+	protein_altering_variant	In_Frame_Del	DEL	AACTACCAATCGG	AACTACCAATCGG	CACT	novel	NA	P-0067878-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	38	420	1	ENST00000404338.3:c.2468_2480delinsCACT	p.Glu823_Gly827delinsAlaLeu	p.E823_G827delinsAL	ENST00000404338	NM_004491.4	823	gAACTACCAATCGGa/gCACTa	1/6	1	2	FACETS	0.887	0.733	1	0.887	0.733	1	CLONAL	1	TRUE	1	0.17	2		421	504	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0067879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	43	351	0	ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	4/10	0.272249931546896	3	FACETS	0.746	0.624	0.88	0.373	0.312	0.44	SUBCLONAL	1	TRUE	1	0.291726276713387	3		351	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0067880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	326	313	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	3	TRUE	NA	0.587705122145183	2		313	362	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417817	138417817	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	45	296	0	ENST00000289153.2:c.1702A>T	p.Ile568Phe	p.I568F	ENST00000289153	NM_006219.2	568	Att/Ttt	11/22	0.353113700296676	3	FACETS	0.375	0.314	0.441	0.125	0.104	0.147	SUBCLONAL	1	TRUE	0	0.587705122145183	3		296	529	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945590	71945590	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	20	270	0	ENST00000298229.2:c.2346G>T	p.Glu782Asp	p.E782D	ENST00000298229	NM_001567.3	782	gaG/gaT	21/28	0.54577505944888	1	FACETS	0.195	0.149	0.249	0.195	0.149	0.249	SUBCLONAL	1	TRUE	0	0.587705122145183	1		270	246	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779073	3779073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	68	397	0	ENST00000262367.5:c.5975G>A	p.Gly1992Glu	p.G1992E	ENST00000262367	NM_004380.2	1992	gGg/gAg	31/31	0.362616410258668	2	FACETS	0.562	0.49	0.638	0.281	0.245	0.319	SUBCLONAL	1	TRUE	0	0.587705122145183	2		397	412	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593600	55593650	+	inframe_deletion	In_Frame_Del	DEL	CAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGAC	CAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGAC	-	novel	NA	P-0067881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	224	440	0	ENST00000288135.5:c.1667_1717del	p.Gln556_Asp572del	p.Q556_D572del	ENST00000288135	NM_000222.2	556	CAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGAC/-	11/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.803277095946261	2		440	512	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599341	55599341	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519761	NA	P-0067881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	140	356	0	ENST00000288135.5:c.2467T>G	p.Tyr823Asp	p.Y823D	ENST00000288135	NM_000222.2	823	Tat/Gat	17/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.803277095946261	2		356	340	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922154	100922154	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0067881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	105	279	0	ENST00000325455.5:c.2357+1G>T		p.X786_splice	ENST00000325455	NM_001202474.3	786			1	2	FACETS	0.975	0.889	1	0.975	0.889	1	CLONAL	1	FALSE	1	0.803277095946261	2		279	268	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0067882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	206	403	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.122545520709145	6	FACETS	0.977	0.937	1			1	INDETERMINATE	6	TRUE	NA	0.55190189562327	6		404	268	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467697	66467697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779449792	NA	P-0067882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	168	310	0	ENST00000273854.3:c.572G>A	p.Arg191His	p.R191H	ENST00000273854	NM_004439.5	191	cGt/cAt	3/18	0.557200076530219	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	0	0.55190189562327	3		310	229	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319854	8319854	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	59	259	0	ENST00000356435.5:c.5647C>T	p.Arg1883Ter	p.R1883*	ENST00000356435		1883	Cga/Tga	34/35	0.542038735809135	3	FACETS	0.928	0.805	1	0.464	0.402	0.53	CLONAL	1	TRUE	1	0.55190189562327	3		259	294	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852532	63852532	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	17	277	0	ENST00000279873.7:c.3310C>T	p.Gln1104Ter	p.Q1104*	ENST00000279873	NM_032199.2	1104	Cag/Tag	10/10	0.557200076530219	3	FACETS	0.322	0.24	0.419	0.161	0.12	0.21	SUBCLONAL	1	TRUE	1	0.55190189562327	3		277	244	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139218	108139218	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	13	302	0	ENST00000278616.4:c.2720G>C	p.Cys907Ser	p.C907S	ENST00000278616	NM_000051.3	907	tGt/tCt	18/63	0.542038735809135	3	FACETS	0.253	0.18	0.341	0.126	0.09	0.171	SUBCLONAL	1	TRUE	1	0.55190189562327	3		302	238	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992921	72992921	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs79835643	NA	P-0067882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	37	309	0	ENST00000268489.5:c.1124G>A	p.Gly375Glu	p.G375E	ENST00000268489	NM_006885.3	375	gGg/gAg	2/10	0.233357122431449	2	FACETS	0.677	0.564	0.801	0.339	0.282	0.401	INDETERMINATE	1	TRUE	0	0.55190189562327	2		309	198	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101011	26101036	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCCCTTCGCTCCCTCCCCCTTACCG	TCCCCTTCGCTCCCTCCCCCTTACCG	-	novel	NA	P-0067882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	148	199	0	ENST00000435504.4:c.56_57+24del		p.X19_splice	ENST00000435504		19		1/13	0.204177577229745	3	FACETS	1	0.985	1	0.815	0.76	0.869	INDETERMINATE	2	TRUE	0	0.55190189562327	3		199	280	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864350	162864350	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	43	250	0	ENST00000366898.1:c.163A>G	p.Thr55Ala	p.T55A	ENST00000366898	NM_004562.2	55	Act/Gct	2/12	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.55190189562327	2		250	125	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414863	56414863	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067890-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	151	467	0	ENST00000348428.3:c.2264A>G	p.Asp755Gly	p.D755G	ENST00000348428	NM_006785.3	755	gAc/gGc	17/17	1	2	FACETS	0.913	0.838	0.99	0.913	0.838	0.99	CLONAL	1	TRUE	1	0.559672858497359	2		467	591	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0067891-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	16	342	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.516	0.38	0.678	0.516	0.38	0.678	SUBCLONAL	1	TRUE	1	0.17	2		342	365	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0067891-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	18	459	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.811	0.611	1	0.811	0.611	1	CLONAL	1	TRUE	1	0.17	2		459	261	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0067891-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	12	302	0	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	1	2	FACETS	0.477	0.334	0.653	0.477	0.334	0.653	SUBCLONAL	1	TRUE	1	0.17	2		302	296	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0067891-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	22	335	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	1	2	FACETS	1	0.782	1	1	0.782	1	CLONAL	1	TRUE	1	0.17	2		335	257	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0067891-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	62	358	0	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	1	2	FACETS	0.87	0.754	0.996	1	0.976	1	CLONAL	2	TRUE	1	0.17	2		358	419	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750945	128750945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067891-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	21	434	0	ENST00000377970.2:c.482C>T	p.Ser161Leu	p.S161L	ENST00000377970	NM_002467.4	161	tCa/tTa	2/3	1	2	FACETS	0.797	0.614	1	0.797	0.614	1	CLONAL	1	TRUE	1	0.17	2		434	310	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067891-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	33	417	0	ENST00000397062.3:c.246A>C	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaC	2/5	1	2	FACETS	0.722	0.587	0.874	0.722	0.587	0.874	SUBCLONAL	1	TRUE	1	0.17	2		417	538	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976426	25976426	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067891-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	24	293	0	ENST00000435504.4:c.1119C>A	p.Phe373Leu	p.F373L	ENST00000435504		373	ttC/ttA	11/13	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.17	2		293	243	SUCCESS
AR	367	MSKCC	GRCh37	X	66765796	66765796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067891-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	24	564	0	ENST00000374690.3:c.808G>A	p.Ala270Thr	p.A270T	ENST00000374690	NM_000044.3	270	Gcc/Acc	1/8	1	2	FACETS	0.598	0.468	0.749	0.598	0.468	0.749	SUBCLONAL	1	TRUE	1	0.17	2		564	472	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685305	89685305	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067891-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	14	274	0	ENST00000371953.3:c.200T>G	p.Ile67Arg	p.I67R	ENST00000371953	NM_000314.4	67	aTa/aGa	3/9	1	2	FACETS	0.828	0.599	1	0.828	0.599	1	CLONAL	1	TRUE	1	0.17	2		274	199	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717730	89717757	+	frameshift_variant	Frame_Shift_Del	DEL	ATATCAAAGTAGAGTTCTTCCACAAACA	ATATCAAAGTAGAGTTCTTCCACAAACA	-	novel	NA	P-0067891-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	25	289	0	ENST00000371953.3:c.755_782del	p.Asp252GlyfsTer5	p.D252Gfs*5	ENST00000371953	NM_000314.4	252	gATATCAAAGTAGAGTTCTTCCACAAACAg/gg	7/9	1	2	FACETS	0.961	0.759	1	0.961	0.759	1	CLONAL	1	TRUE	1	0.17	2		289	306	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0067893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	48	252	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.334262741754807	2		253	239	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0067893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	79	400	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.932	0.822	1	0.932	0.822	1	CLONAL	1	TRUE	1	0.334262741754807	2		400	507	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117790	70117790	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	81	547	0	ENST00000245479.2:c.258G>A	p.Trp86Ter	p.W86*	ENST00000245479	NM_000346.3	86	tgG/tgA	1/3	1	2	FACETS	0.952	0.841	1	0.952	0.841	1	CLONAL	1	TRUE	1	0.334262741754807	2		547	509	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820959	36820959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139999382	NA	P-0067893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	97	489	0	ENST00000373129.3:c.418G>A	p.Val140Ile	p.V140I	ENST00000373129	NM_032017.1	140	Gtc/Atc	6/12	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.334262741754807	2		489	547	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341120	8341120	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	66	434	0	ENST00000356435.5:c.5096A>G	p.Tyr1699Cys	p.Y1699C	ENST00000356435		1699	tAc/tGc	30/35	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.334262741754807	2		434	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0067894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	423	342	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.62758678124001	4	FACETS	0.934	0.905	0.963	0.934	0.905	0.963	CLONAL	4	TRUE	0	0.62758678124001	4		343	587	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913384	NA	P-0067894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	231	350	0	ENST00000304494.5:c.262G>T	p.Glu88Ter	p.E88*	ENST00000304494	NM_000077.4	88	Gag/Tag	2/3	0.537341310867754	2	FACETS	0.911	0.864	0.957	0.911	0.864	0.957	CLONAL	2	TRUE	0	0.62758678124001	2		350	404	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453136	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	rs397516897	NA	P-0067894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	222	296	0	ENST00000288602.6:c.1799_1801del	p.Val600_Lys601delinsGlu	p.V600_K601delinsE	ENST00000288602	NM_004333.4	600	gTGAaa/gaa	15/18	0.62758678124001	3	FACETS	0.84	0.797	0.882	0.84	0.797	0.882	CLONAL	3	TRUE	0	0.62758678124001	3		296	369	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272090	15272090	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	238	434	0	ENST00000263388.2:c.6349del	p.Ser2117ProfsTer32	p.S2117Pfs*32	ENST00000263388	NM_000435.2	2117	Tcc/cc	33/33	0.537341310867754	2	FACETS	0.905	0.859	0.951	0.905	0.859	0.951	CLONAL	2	TRUE	0	0.62758678124001	2		434	419	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10787954	10787954	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	101	300	0	ENST00000361367.2:c.1603T>G	p.Leu535Val	p.L535V	ENST00000361367	NM_014633.3	535	Ttg/Gtg	13/25	0.528125269925533	4	FACETS	0.811	0.733	0.892	0.811	0.733	0.892	CLONAL	2	TRUE	2	0.62758678124001	4		300	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0067896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	398	395	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.812091956175522	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.808041286248061	2		395	427	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	486	378	1	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	0.688681233727382	3	FACETS	1	0.998	1			1	CLONAL	3	TRUE	NA	0.808041286248061	3		379	506	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266036	41266036	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	257	380	0	ENST00000349496.5:c.33C>A	p.Asp11Glu	p.D11E	ENST00000349496	NM_001904.3	11	gaC/gaA	3/15	0.634585226646603	4	FACETS	0.873	0.822	0.923	0.873	0.822	0.923	CLONAL	2	TRUE	2	0.808041286248061	4		380	659	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28601501	28601502	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0067897-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	30	455	0	ENST00000253063.3:c.1189_1190del	p.Ile397ProfsTer9	p.I397Pfs*9	ENST00000253063	NM_031459.4	396	TAt/t	8/10	1	2	FACETS	0.14	0.112	0.171	0.14	0.112	0.171	SUBCLONAL	1	TRUE	1	0.773542785256783	2		455	556	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430791	181430791	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067897-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	33	551	0	ENST00000325404.1:c.643A>G	p.Thr215Ala	p.T215A	ENST00000325404	NM_003106.3	215	Acc/Gcc	1/1	1	2	FACETS	0.177	0.143	0.214	0.177	0.143	0.214	SUBCLONAL	1	TRUE	1	0.773542785256783	2		551	483	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0067902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	44	148	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.339709594921943	1	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	0	0.339709594921943	1		148	202	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685287	89685287	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs398123316	NA	P-0067902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	49	214	0	ENST00000371953.3:c.182A>T	p.His61Leu	p.H61L	ENST00000371953	NM_000314.4	61	cAt/cTt	3/9	0.339709594921943	1	FACETS	0.849	0.724	0.985	0.849	0.724	0.985	CLONAL	1	TRUE	0	0.339709594921943	1		214	282	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228572	36228572	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	33	535	0	ENST00000222270.7:c.7586C>G	p.Ser2529Cys	p.S2529C	ENST00000222270	NM_014727.1	2529	tCc/tGc	34/37	1	2	FACETS	0.325	0.264	0.395	0.325	0.264	0.395	SUBCLONAL	1	TRUE	1	0.339709594921943	2		535	597	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636638	73636638	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	98	603	0	ENST00000377687.4:c.905del	p.Pro302ArgfsTer21	p.P302Rfs*21	ENST00000377687	NM_001730.3	301	Ccc/cc	2/4	1	2	FACETS	0.882	0.788	0.982	0.882	0.788	0.982	CLONAL	1	TRUE	1	0.339709594921943	2		603	654	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534654	140534654	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	100	427	0	ENST00000288602.6:c.259A>T	p.Ser87Cys	p.S87C	ENST00000288602	NM_004333.4	87	Agc/Tgc	3/18	0.339709594921943	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.339709594921943	1		427	446	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060659	38060659	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	51	686	0	ENST00000250448.2:c.1330G>A	p.Val444Met	p.V444M	ENST00000250448	NM_004496.3	444	Gtg/Atg	2/2	1	2	FACETS	0.371	0.314	0.433	0.371	0.314	0.433	SUBCLONAL	1	TRUE	1	0.339709594921943	2		686	810	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849830	151849830	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	85	414	0	ENST00000262189.6:c.12486del	p.Leu4163Ter	p.L4163*	ENST00000262189	NM_170606.2	4162	cgG/cg	49/59	0.339709594921943	1	FACETS	0.857	0.76	0.959	0.857	0.76	0.959	CLONAL	1	TRUE	0	0.339709594921943	1		414	485	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556707	41556727	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	GACCCTTCCCAGCCTCAAACG	GACCCTTCCCAGCCTCAAACG	-	novel	NA	P-0067902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	82	456	0	ENST00000263253.7:c.3652_3671+1del		p.X1218_splice	ENST00000263253	NM_001429.3	1218		20/31	0.339709594921943	1	FACETS	0.808	0.715	0.907	0.808	0.715	0.907	CLONAL	1	TRUE	0	0.339709594921943	1		456	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0067903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	602	394	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.873728329900336	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.874241660421719	2		394	680	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104710	193104712	+	inframe_deletion	In_Frame_Del	DEL	ACG	ACG	-	novel	NA	P-0067903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	400	365	0	ENST00000367435.3:c.415_417del	p.Arg139del	p.R139del	ENST00000367435	NM_024529.4	138	ccACGa/cca	5/17	0.797173872728666	3	FACETS	1	0.967	1			1	CLONAL	2	TRUE	NA	0.874241660421719	3		365	654	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677218	29677227	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGAAGTTC	GAAGAAGTTC	-	novel	NA	P-0067903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	183	371	0	ENST00000356175.3:c.7280_7289del	p.Glu2427ValfsTer5	p.E2427Vfs*5	ENST00000356175	NM_000267.3	2426	GAAGAAGTTCga/ga	49/57	0.76305003082924	6	FACETS	0.994	0.916	1			1	CLONAL	1	TRUE	NA	0.874241660421719	6		371	1158	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553279	106553279	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	301	560	0	ENST00000369096.4:c.1244T>G	p.Leu415Trp	p.L415W	ENST00000369096	NM_001198.3	415	tTg/tGg	5/7	1	2	FACETS	0.943	0.894	0.993	0.943	0.894	0.993	CLONAL	1	TRUE	1	0.874241660421719	2		560	730	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	137	539	1	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.656240498952331	2		540	371	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115873	8115874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0067904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	147	381	0	ENST00000346208.3:c.1220dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tCcg	6/6	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.656240498952331	2		381	400	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692800	89692800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204856	NA	P-0067904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	45	234	0	ENST00000371953.3:c.284C>T	p.Pro95Leu	p.P95L	ENST00000371953	NM_000314.4	95	cCa/cTa	5/9	0.656240498952331	1	FACETS	0.931	0.811	1	0.931	0.811	1	CLONAL	1	TRUE	0	0.656240498952331	1		234	99	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944516	71944516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293622519	NA	P-0067904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	134	553	0	ENST00000298229.2:c.2072G>A	p.Arg691Gln	p.R691Q	ENST00000298229	NM_001567.3	691	cGg/cAg	18/28	0.656240498952331	1	FACETS	0.998	0.925	1	0.998	0.925	1	CLONAL	1	TRUE	0	0.656240498952331	1		553	275	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100689	8100690	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TACCCGCCCTACGTGCCCGAGTACAGCTCCGGACTCT	novel	NA	P-0067904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	73	492	0	ENST00000346208.3:c.665_701dup	p.Phe234LeufsTer81	p.F234Lfs*81	ENST00000346208		221	-/TACCCGCCCTACGTGCCCGAGTACAGCTCCGGACTCT	3/6	1	2	FACETS	0.596	0.525	0.673	0.596	0.525	0.673	SUBCLONAL	1	TRUE	1	0.656240498952331	2		492	373	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955538	48955538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913303	NA	P-0067905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	8	418	0	ENST00000267163.4:c.1654C>T	p.Arg552Ter	p.R552*	ENST00000267163	NM_000321.2	552	Cga/Tga	17/27	1	2	FACETS	0.156	0.1	0.229	0.156	0.1	0.229	SUBCLONAL	1	TRUE	1	0.34	2		418	302	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485290	8485290	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	59	421	0	ENST00000356435.5:c.3090G>T	p.Met1030Ile	p.M1030I	ENST00000356435		1030	atG/atT	18/35	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.34	2		421	307	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937751	44937751	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0067905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	24	162	0	ENST00000377967.4:c.2938+1G>T		p.X980_splice	ENST00000377967	NM_021140.2	980			1	1	FACETS	0.868	0.689	1	0.868	0.689	1	CLONAL	1	TRUE	0	0.34	1		162	135	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0067906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	170	536	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.51135030805261	1	FACETS	0.97	0.899	1	0.97	0.899	1	CLONAL	1	TRUE	0	0.510857205652337	1		536	511	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974744	21974775	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTCCTCTACCCGACCCCGGGCCGCGGCCGT	ACCTCCTCTACCCGACCCCGGGCCGCGGCCGT	-	novel	NA	P-0067906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	200	509	0	ENST00000304494.5:c.52_83del	p.Thr18AlafsTer15	p.T18Afs*15	ENST00000304494	NM_000077.4	18	ACGGCCGCGGCCCGGGGTCGGGTAGAGGAGGTg/g	1/3	0.51135030805261	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.510857205652337	1		509	439	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198390	108198390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762427092	NA	P-0067906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	103	368	0	ENST00000278616.4:c.6994C>T	p.Leu2332Phe	p.L2332F	ENST00000278616	NM_000051.3	2332	Ctt/Ttt	48/63	0.166788252686929	2	FACETS	1	0.953	1	0.546	0.493	0.602	INDETERMINATE	1	TRUE	0	0.510857205652337	2		368	369	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930121	68930121	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	230	366	0	ENST00000288368.4:c.182T>G	p.Val61Gly	p.V61G	ENST00000288368	NM_024870.2	61	gTt/gGt	2/40	0.51135030805261	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.510857205652337	3		366	529	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587125	212587125	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	23	372	0	ENST00000342788.4:c.876A>T	p.Lys292Asn	p.K292N	ENST00000342788	NM_005235.2	292	aaA/aaT	7/28	0.51135030805261	2	FACETS	0.225	0.174	0.283	0.112	0.087	0.142	SUBCLONAL	1	TRUE	0	0.510857205652337	2		372	401	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0067908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	170	324	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.358473515027744	5	FACETS	1	0.935	1			1	CLONAL	3	TRUE	NA	0.358473515027744	5		324	482	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970971	21970971	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	101	623	0	ENST00000304494.5:c.387C>A	p.Tyr129Ter	p.Y129*	ENST00000304494	NM_000077.4	129	taC/taA	2/3	0.260055746956015	2	FACETS	1	0.899	1	0.501	0.449	0.556	CLONAL	1	TRUE	0	0.358473515027744	2		623	562	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467874	66467874	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	27	447	0	ENST00000273854.3:c.395T>G	p.Phe132Cys	p.F132C	ENST00000273854	NM_004439.5	132	tTt/tGt	3/18	1	2	FACETS	0.837	0.672	1	0.837	0.672	1	CLONAL	1	TRUE	1	0.358473515027744	2		447	180	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219860	133219860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758114596	NA	P-0067908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	96	514	0	ENST00000320574.5:c.4501G>A	p.Gly1501Arg	p.G1501R	ENST00000320574	NM_006231.2	1501	Ggg/Agg	35/49	0.361327247491068	3	FACETS	1	0.97	1	0.62	0.555	0.69	CLONAL	1	TRUE	1	0.358473515027744	3		514	509	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046349	180046349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	64	444	0	ENST00000261937.6:c.2665G>A	p.Glu889Lys	p.E889K	ENST00000261937	NM_182925.4	889	Gag/Aag	19/30	NA	2	FACETS	0.97	0.845	1			1	INDETERMINATE	1	TRUE	NA	0.358473515027744	2		444	368	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926932	112926932	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	80	367	0	ENST00000351677.2:c.1552G>C	p.Val518Leu	p.V518L	ENST00000351677	NM_002834.3	518	Gtc/Ctc	13/16	0.361327247491068	3	FACETS	1	0.961	1	0.602	0.532	0.677	CLONAL	1	TRUE	1	0.358473515027744	3		367	437	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610513	215610513	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	68	414	0	ENST00000260947.4:c.1743A>T	p.Gln581His	p.Q581H	ENST00000260947	NM_000465.2	581	caA/caT	8/11	NA	2	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.358473515027744	2		414	260	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413104	139413121	+	inframe_deletion	In_Frame_Del	DEL	GTGGAAGCAGGCGGCGCT	GTGGAAGCAGGCGGCGCT	-	novel	NA	P-0067908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	46	459	0	ENST00000277541.6:c.1021_1038del	p.Ser341_His346del	p.S341_H346del	ENST00000277541	NM_017617.3	341	AGCGCCGCCTGCTTCCAC/-	6/34	0.350950875905538	5	FACETS	0.611	0.513	0.719	0.204	0.171	0.24	SUBCLONAL	1	TRUE	2	0.358473515027744	5		459	646	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0067909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	212	440	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.499146171455017	4	FACETS	0.981	0.917	1	0.981	0.917	1	CLONAL	2	TRUE	2	0.55594376255173	4		440	605	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0067909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	78	508	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.566	0.498	0.638	0.566	0.498	0.638	SUBCLONAL	1	TRUE	1	0.55594376255173	2		508	496	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0067909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	244	371	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	0.512115628811842	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.55594376255173	2		371	434	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0067909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	24	540	0	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	0.177	0.138	0.222	0.177	0.138	0.222	SUBCLONAL	1	TRUE	1	0.55594376255173	2		540	487	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912690	32912690	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	95	483	0	ENST00000380152.3:c.4198C>G	p.His1400Asp	p.H1400D	ENST00000380152		1400	Cat/Gat	11/27	1	2	FACETS	0.874	0.784	0.969	0.874	0.784	0.969	CLONAL	1	TRUE	1	0.55594376255173	2		483	391	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165131	47165131	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	115	474	0	ENST00000409792.3:c.995C>T	p.Ser332Leu	p.S332L	ENST00000409792	NM_014159.6	332	tCa/tTa	3/21	0.53067582857866	2	FACETS	0.855	0.774	0.939	0.427	0.387	0.47	CLONAL	1	TRUE	0	0.55594376255173	2		474	484	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165300	47165300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	122	531	0	ENST00000409792.3:c.826G>A	p.Asp276Asn	p.D276N	ENST00000409792	NM_014159.6	276	Gat/Aat	3/21	0.53067582857866	2	FACETS	0.842	0.765	0.923	0.421	0.382	0.462	CLONAL	1	TRUE	0	0.55594376255173	2		531	521	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445016	49445016	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	88	525	0	ENST00000301067.7:c.2450del	p.Pro817LeufsTer113	p.P817Lfs*113	ENST00000301067	NM_003482.3	817	cCt/ct	10/54	0.114477539792455	4	FACETS	0.818	0.726	0.917	0.409	0.363	0.459	INDETERMINATE	1	TRUE	2	0.55594376255173	4		525	602	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041893	14041893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	160	518	0	ENST00000311895.7:c.2440G>A	p.Glu814Lys	p.E814K	ENST00000311895	NM_005236.2	814	Gag/Aag	11/11	0.541526037670258	3	FACETS	0.974	0.895	1	0.487	0.447	0.529	CLONAL	1	TRUE	1	0.55594376255173	3		518	755	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165321	47165321	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	129	523	0	ENST00000409792.3:c.805C>G	p.Gln269Glu	p.Q269E	ENST00000409792	NM_014159.6	269	Caa/Gaa	3/21	0.53067582857866	2	FACETS	0.899	0.82	0.982	0.45	0.41	0.491	CLONAL	1	TRUE	0	0.55594376255173	2		523	516	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165290	47165290	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	118	535	0	ENST00000409792.3:c.836C>T	p.Ser279Leu	p.S279L	ENST00000409792	NM_014159.6	279	tCa/tTa	3/21	0.53067582857866	2	FACETS	0.807	0.731	0.886	0.404	0.365	0.443	CLONAL	1	TRUE	0	0.55594376255173	2		535	526	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164427	47164427	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	114	452	0	ENST00000409792.3:c.1699G>C	p.Asp567His	p.D567H	ENST00000409792	NM_014159.6	567	Gat/Cat	3/21	0.53067582857866	2	FACETS	0.976	0.886	1	0.488	0.443	0.536	CLONAL	1	TRUE	0	0.55594376255173	2		452	420	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0067910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	74	377	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.786	0.689	0.889	0.786	0.689	0.889	SUBCLONAL	1	TRUE	1	0.36506044911631	2		377	516	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47440567	47440567	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	57	404	0	ENST00000404338.3:c.3728A>T	p.Glu1243Val	p.E1243V	ENST00000404338	NM_004491.4	1243	gAg/gTg	2/6	0.242244264313314	3	FACETS	0.805	0.692	0.927			1	CLONAL	1	TRUE	NA	0.36506044911631	3		404	459	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176700747	176700747	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	84	341	0	ENST00000439151.2:c.5584A>C	p.Lys1862Gln	p.K1862Q	ENST00000439151	NM_022455.4	1862	Aag/Cag	17/23	1	2	FACETS	0.939	0.832	1	0.939	0.832	1	CLONAL	1	TRUE	1	0.36506044911631	2		341	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0067911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	98	426	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.293734161678027	2	FACETS	0.776	0.698	0.856	0.776	0.698	0.856	SUBCLONAL	2	TRUE	0	0.36	2		426	351	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247516	123247516	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519795	NA	P-0067911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	74	385	0	ENST00000358487.5:c.1975A>G	p.Lys659Glu	p.K659E	ENST00000358487	NM_000141.4	659	Aag/Gag	14/18	0.302062282975703	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.36	1		385	302	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342932	118342932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	45	457	0	ENST00000534358.1:c.1058G>A	p.Arg353Gln	p.R353Q	ENST00000534358	NM_005933.3	353	cGa/cAa	3/36	1	2	FACETS	0.491	0.413	0.578	0.491	0.413	0.578	SUBCLONAL	1	TRUE	1	0.36	2		457	509	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	81	471	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	1	2	FACETS	0.976	0.863	1	0.976	0.863	1	CLONAL	1	TRUE	1	0.36	2		471	461	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0067911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	120	468	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	0.241167955429618	3	FACETS	0.878	0.798	0.961	0.878	0.798	0.961	CLONAL	2	TRUE	1	0.36	3		468	448	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047963	180047963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	27	582	0	ENST00000261937.6:c.2212G>A	p.Val738Met	p.V738M	ENST00000261937	NM_182925.4	738	Gtg/Atg	15/30	0.253643780130165	1	FACETS	0.278	0.22	0.343	0.278	0.22	0.343	SUBCLONAL	1	TRUE	0	0.36	1		582	443	SUCCESS
ATM	472	MSKCC	GRCh37	11	108126945	108126945	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	47	332	0	ENST00000278616.4:c.2128A>T	p.Thr710Ser	p.T710S	ENST00000278616	NM_000051.3	710	Aca/Tca	14/63	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.36	2		332	249	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923235	26923235	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	43	444	0	ENST00000381527.3:c.231C>G	p.Asn77Lys	p.N77K	ENST00000381527	NM_001260.1	77	aaC/aaG	3/13	1	2	FACETS	0.534	0.447	0.631	0.534	0.447	0.631	SUBCLONAL	1	TRUE	1	0.36	2		444	447	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571448	95571448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373412959	NA	P-0067911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	46	380	0	ENST00000393063.1:c.3229G>A	p.Asp1077Asn	p.D1077N	ENST00000393063	NM_030621.3	1077	Gat/Aat	21/28	1	2	FACETS	0.617	0.521	0.724	0.617	0.521	0.724	SUBCLONAL	1	TRUE	1	0.36	2		380	414	SUCCESS
APC	324	MSKCC	GRCh37	5	112179200	112179200	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060503272	NA	P-0067911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	39	497	0	ENST00000257430.4:c.7909G>A	p.Gly2637Ser	p.G2637S	ENST00000257430	NM_000038.5	2637	Ggt/Agt	16/16	0.253643780130165	1	FACETS	0.479	0.397	0.569	0.479	0.397	0.569	SUBCLONAL	1	TRUE	0	0.36	1		497	371	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0067912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3467	2886	313	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.167435268578738	153	FACETS	1	0.984	1			1	CLONAL	74	TRUE	NA	0.167435268578738	153		313	6353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0067912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	35	471	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.864	0.713	1	1	0.958	1	CLONAL	2	TRUE	1	0.167435268578738	2		471	242	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439655	220439655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	24	429	0	ENST00000243786.2:c.508G>A	p.Gly170Ser	p.G170S	ENST00000243786	NM_002191.3	170	Ggc/Agc	2/2	0.167435268578738	3	FACETS	0.878	0.688	1	0.439	0.344	0.548	CLONAL	1	TRUE	1	0.167435268578738	3		429	354	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0067913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	229	450	1	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.684187389489216	2		451	555	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0067914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	20	288	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.223	0.17	0.285	0.223	0.17	0.285	SUBCLONAL	1	TRUE	1	0.46	2		288	390	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0067914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	119	342	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.46	2		342	419	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0067914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	119	377	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.956	0.867	1	0.956	0.867	1	CLONAL	1	TRUE	1	0.46	2		377	541	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106648	27106648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553153748	NA	P-0067914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	27	503	0	ENST00000324856.7:c.6259G>A	p.Gly2087Arg	p.G2087R	ENST00000324856	NM_006015.4	2087	Gga/Aga	20/20	1	2	FACETS	0.205	0.162	0.253	0.205	0.162	0.253	SUBCLONAL	1	TRUE	1	0.46	2		503	574	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020768	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs926053251	NA	P-0067914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	117	372	0	ENST00000358127.4:c.77T>G	p.Val26Gly	p.V26G	ENST00000358127	NM_001280556.1	26	gTt/gGt	2/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.46	2		372	448	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	10	375	0	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	1	2	FACETS	0.091	0.061	0.13	0.091	0.061	0.13	SUBCLONAL	1	TRUE	1	0.46	2		375	476	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933744	49933744	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs750582514	NA	P-0067914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	109	475	0	ENST00000296474.3:c.2533C>T	p.Arg845Ter	p.R845*	ENST00000296474	NM_002447.2	845	Cga/Tga	10/20	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.46	2		475	470	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653859	89653861	+	inframe_deletion	In_Frame_Del	DEL	GTA	GTA	-	rs1554893831	NA	P-0067914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	82	279	0	ENST00000371953.3:c.160_162del	p.Val54del	p.V54del	ENST00000371953	NM_000314.4	53	GTA/-	2/9	1	2	FACETS	0.961	0.853	1	0.961	0.853	1	CLONAL	1	TRUE	1	0.46	2		279	371	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692838	89692839	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	37	122	0	ENST00000371953.3:c.324dup	p.Asp109Ter	p.D109*	ENST00000371953	NM_000314.4	108	ctt/cTtt	5/9	1	2	FACETS	0.958	0.8	1	0.958	0.8	1	CLONAL	1	TRUE	1	0.46	2		122	168	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422683	49422683	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	119	433	0	ENST00000301067.7:c.14310del	p.Val4771SerfsTer26	p.V4771Sfs*26	ENST00000301067	NM_003482.3	4770	ccT/cc	45/54	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.46	2		433	512	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344690	70344694	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TCTCA	TCTCA	-	novel	NA	P-0067914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	110	356	0	ENST00000374080.3:c.2051_2055del	p.Ser685ValfsTer8	p.S685Vfs*8	ENST00000374080		684	tTCTCA/t	14/45	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.46	2		356	416	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164839	36164839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1378698695	NA	P-0067914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	148	536	0	ENST00000300305.3:c.1036C>T	p.Arg346Cys	p.R346C	ENST00000300305		346	Cgc/Tgc	8/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.46	2		536	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0067915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	243	536	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.896279690029167	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.896279690029167	1		536	287	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914714	32914714	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555284601	NA	P-0067915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	150	489	0	ENST00000380152.3:c.6222C>G	p.His2074Gln	p.H2074Q	ENST00000380152		2074	caC/caG	11/27	0.896279690029167	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.896279690029167	1		489	184	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0067916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	159	415	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	0.607983317795217	1	FACETS	0.948	0.88	1	0.948	0.88	1	CLONAL	1	TRUE	0	0.607983317795217	1		415	384	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912120	114912120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	153	314	0	ENST00000543371.1:c.1190C>T	p.Ala397Val	p.A397V	ENST00000543371	NM_001198531.1	397	gCg/gTg	11/14	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.607983317795217	2		314	464	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090515	5090516	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0067916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	63	312	0	ENST00000381652.3:c.2832_2833del	p.His944GlnfsTer47	p.H944Qfs*47	ENST00000381652	NM_004972.3	944	cAT/c	21/25	0.607983317795217	1	FACETS	0.896	0.793	1	0.896	0.793	1	CLONAL	1	TRUE	0	0.607983317795217	1		312	161	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111481	8111484	+	frameshift_variant	Frame_Shift_Ins	INS	ACCA	ACCA	TTTCG	novel	NA	P-0067916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	161	363	2	ENST00000346208.3:c.967_970delinsTTTCG	p.Thr323PhefsTer29	p.T323Ffs*29	ENST00000346208		323	ACCAca/TTTCGca	5/6	1	2	FACETS	0.954	0.88	1	0.954	0.88	1	CLONAL	1	TRUE	1	0.607983317795217	2		365	555	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	11	380	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	0.236	0.162	0.329	0.236	0.162	0.329	SUBCLONAL	1	TRUE	1	0.29	2		380	321	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921566	178921566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793349	NA	P-0067917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	34	336	0	ENST00000263967.3:c.1048G>A	p.Asp350Asn	p.D350N	ENST00000263967	NM_006218.2	350	Gac/Aac	5/21	1	2	FACETS	0.728	0.596	0.876	0.728	0.596	0.876	SUBCLONAL	1	TRUE	1	0.29	2		336	322	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0067917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	64	452	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	1	2	FACETS	0.964	0.837	1	0.964	0.837	1	CLONAL	1	TRUE	1	0.29	2		452	458	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584513	48584514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs377767334	NA	P-0067917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	62	459	0	ENST00000342988.3:c.692dup	p.Ser232GlnfsTer3	p.S232Qfs*3	ENST00000342988	NM_005359.5	229	ctg/ctGg	6/12	0.3	1	FACETS	0.955	0.828	1	0.955	0.828	1	CLONAL	1	TRUE	0	0.29	1		459	383	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740623	58740624	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs763475304	NA	P-0067917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	71	511	1	ENST00000305921.3:c.1535dup	p.Asn512LysfsTer16	p.N512Kfs*16	ENST00000305921	NM_003620.3	510	caa/cAaa	6/6	1	2	FACETS	0.953	0.833	1	0.953	0.833	1	CLONAL	1	TRUE	1	0.29	2		512	514	SUCCESS
APC	324	MSKCC	GRCh37	5	112136997	112136997	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	54	347	0	ENST00000257430.4:c.751G>T	p.Glu251Ter	p.E251*	ENST00000257430	NM_000038.5	251	Gaa/Taa	8/16	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.29	2		347	367	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761412	59761415	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	rs786203717	NA	P-0067917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	61	372	0	ENST00000259008.2:c.2992_2995del	p.Lys998GlufsTer60	p.K998Efs*60	ENST00000259008	NM_032043.2	998	AAGAga/ga	20/20	1	2	FACETS	0.96	0.831	1	0.96	0.831	1	CLONAL	1	TRUE	1	0.29	2		372	438	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856052	111856052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758024019	NA	P-0067917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	57	521	0	ENST00000341259.2:c.103G>A	p.Val35Ile	p.V35I	ENST00000341259	NM_005475.2	35	Gta/Ata	2/8	1	2	FACETS	0.912	0.785	1	0.912	0.785	1	CLONAL	1	TRUE	1	0.29	2		521	431	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903714	114903715	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0067917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	59	386	0	ENST00000543371.1:c.721_722dup	p.Tyr242ArgfsTer10	p.Y242Rfs*10	ENST00000543371	NM_001198531.1	240	tcc/tCCcc	7/14	1	2	FACETS	0.908	0.783	1	0.908	0.783	1	CLONAL	1	TRUE	1	0.29	2		386	448	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247878	59247886	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	CTTTCAAGG	CTTTCAAGG	TCAAGGTTTTCACTTTTTCACT	novel	NA	P-0067917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	74	507	0	ENST00000371222.2:c.857_865delinsAGTGAAAAAGTGAAAACCTTGA	p.Thr286LysfsTer2	p.T286Kfs*2	ENST00000371222	NM_002228.3	286	aCCTTGAAAGct/aAGTGAAAAAGTGAAAACCTTGAct	1/1	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.29	2		507	501	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565575	41565575	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	111	328	0	ENST00000263253.7:c.4241A>G	p.Tyr1414Cys	p.Y1414C	ENST00000263253	NM_001429.3	1414	tAt/tGt	26/31	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.464485033380547	2		328	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0067918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	224	491	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.464485033380547	2		491	890	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499832	8499832	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	141	391	1	ENST00000356435.5:c.2137G>T	p.Gly713Cys	p.G713C	ENST00000356435		713	Ggt/Tgt	14/35	0.464485033380547	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.464485033380547	1		392	429	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971133	21971133	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	217	490	0	ENST00000304494.5:c.225del	p.Ala76ProfsTer70	p.A76Pfs*70	ENST00000304494	NM_000077.4	75	ccC/cc	2/3	0.464485033380547	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.464485033380547	1		490	683	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023099	33023099	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	309	429	0	ENST00000300177.4:c.208G>T	p.Gly70Trp	p.G70W	ENST00000300177	NM_001191322.1	70	Ggg/Tgg	2/2	0.439188998352594	2	FACETS	0.956	0.908	1	0.956	0.908	1	CLONAL	2	TRUE	0	0.464485033380547	2		429	696	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352025	89352025	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	202	427	1	ENST00000301030.4:c.925G>T	p.Ala309Ser	p.A309S	ENST00000301030	NM_001256183.1	309	Gca/Tca	9/13	0.464485033380547	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.464485033380547	1		428	571	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641086	117641086	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	140	466	0	ENST00000368508.3:c.5885G>T	p.Gly1962Val	p.G1962V	ENST00000368508	NM_002944.2	1962	gGa/gTa	36/43	0.464485033380547	1	FACETS	0.828	0.758	0.901	0.828	0.758	0.901	CLONAL	1	TRUE	0	0.464485033380547	1		466	559	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003403	57003403	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	173	490	1	ENST00000257254.3:c.1076G>A	p.Gly359Asp	p.G359D	ENST00000257254		359	gGc/gAc	1/2	1	2	FACETS	0.877	0.808	0.949	0.877	0.808	0.949	CLONAL	1	TRUE	1	0.464485033380547	2		491	849	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960214	151960214	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	10	96	0	ENST00000262189.6:c.1186C>T	p.Gln396Ter	p.Q396*	ENST00000262189	NM_170606.2	396	Caa/Taa	9/59	1	2	FACETS	0.245	0.166	0.344	0.245	0.166	0.344	SUBCLONAL	1	TRUE	1	0.464485033380547	2		96	176	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941475	71941475	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	181	471	0	ENST00000298229.2:c.1160G>C	p.Arg387Pro	p.R387P	ENST00000298229	NM_001567.3	387	cGg/cCg	10/28	1	2	FACETS	0.945	0.873	1	0.945	0.873	1	CLONAL	1	TRUE	1	0.464485033380547	2		471	825	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056071	26056071	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	203	440	0	ENST00000343677.2:c.586A>G	p.Lys196Glu	p.K196E	ENST00000343677	NM_005319.3	196	Aag/Gag	1/1	0.464485033380547	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.464485033380547	1		440	647	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226504	41226504	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1567778299	NA	P-0067918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	159	485	0	ENST00000357654.3:c.4519A>G	p.Arg1507Gly	p.R1507G	ENST00000357654	NM_007294.3	1507	Agg/Ggg	14/23	1	2	FACETS	0.935	0.859	1	0.935	0.859	1	CLONAL	1	TRUE	1	0.464485033380547	2		485	732	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612882	228612882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752880989	NA	P-0067918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	341	656	0	ENST00000366696.1:c.145C>T	p.Leu49Phe	p.L49F	ENST00000366696	NM_003493.2	49	Ctt/Ttt	1/1	0.221737921385506	1	FACETS	1	0.976	1	1	0.976	1	INDETERMINATE	1	TRUE	0	0.464485033380547	1		656	1073	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872998	35873004	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CAGGAAC	CAGGAAC	-	novel	NA	P-0067919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	136	214	0	ENST00000216797.5:c.228_234del	p.Phe77ThrfsTer11	p.F77Tfs*11	ENST00000216797	NM_020529.2	76	tcGTTCCTG/tc	2/6	0.64592884404788	1	FACETS	0.929	0.859	0.999	0.929	0.859	0.999	CLONAL	1	TRUE	0	0.64592884404788	1		214	307	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843634	156843634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201035170	NA	P-0067920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	421	568	0	ENST00000524377.1:c.1060G>A	p.Val354Ile	p.V354I	ENST00000524377	NM_002529.3	354	Gtc/Atc	8/17	0.608318147159879	3	FACETS	0.985	0.943	1	0.985	0.943	1	CLONAL	2	TRUE	1	0.628397948682471	3		568	894	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50763921	50763921	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	139	321	0	ENST00000307179.4:c.778G>C	p.Asp260His	p.D260H	ENST00000307179		260	Gac/Cac	8/20	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.628397948682471	2		321	439	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158476	26158476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776467875	NA	P-0067920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	160	414	0	ENST00000289316.2:c.79G>A	p.Gly27Arg	p.G27R	ENST00000289316	NM_138720.2	27	Ggg/Agg	1/2	1	2	FACETS	0.961	0.887	1	0.961	0.887	1	CLONAL	1	TRUE	1	0.628397948682471	2		414	530	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144798	11144801	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GGAG	GGAG	-	novel	NA	P-0067920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	150	344	0	ENST00000358026.2:c.3874_3877del		p.X1292_splice	ENST00000358026	NM_001128849.1	1292		28/36	0.628397948682471	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.628397948682471	1		344	310	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289995	15289995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	34	550	0	ENST00000263388.2:c.3559G>A	p.Gly1187Ser	p.G1187S	ENST00000263388	NM_000435.2	1187	Ggt/Agt	22/33	0.628397948682471	1	FACETS	0.166	0.135	0.201	0.166	0.135	0.201	SUBCLONAL	1	TRUE	0	0.628397948682471	1		550	447	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150923058	150923058	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1196294465	NA	P-0067921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	62	409	0	ENST00000271640.5:c.1705G>T	p.Glu569Ter	p.E569*	ENST00000271640	NM_001145415.1	569	Gag/Tag	13/22	1	2	FACETS	0.642	0.557	0.734	0.642	0.557	0.734	SUBCLONAL	1	TRUE	1	0.480209837244463	2		409	402	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312721	30312721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868405846	NA	P-0067921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	55	351	0	ENST00000262643.3:c.702G>A	p.Met234Ile	p.M234I	ENST00000262643	NM_001238.2	234	atG/atA	8/12	1	2	FACETS	0.566	0.485	0.653	0.566	0.485	0.653	SUBCLONAL	1	TRUE	1	0.480209837244463	2		351	405	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56402475	56402475	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0067921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	41	267	0	ENST00000348428.3:c.1517T>A	p.Leu506Ter	p.L506*	ENST00000348428	NM_006785.3	506	tTg/tAg	13/17	0.3111573879796	1	FACETS	0.507	0.425	0.597	0.507	0.425	0.597	SUBCLONAL	1	TRUE	0	0.480209837244463	1		267	256	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120806017	120806017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	33	418	0	ENST00000257552.2:c.160G>A	p.Asp54Asn	p.D54N	ENST00000257552	NM_002442.3	54	Gac/Aac	3/15	1	2	FACETS	0.341	0.278	0.413	0.341	0.278	0.413	SUBCLONAL	1	TRUE	1	0.480209837244463	2		418	403	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374293	138374293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	15	370	0	ENST00000289153.2:c.3151G>A	p.Glu1051Lys	p.E1051K	ENST00000289153	NM_006219.2	1051	Gaa/Aaa	22/22	0.443382973155476	3	FACETS	0.112	0.081	0.149	0.056	0.04	0.075	SUBCLONAL	1	TRUE	1	0.547757797515361	3		370	625	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982157	201982157	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	75	437	0	ENST00000359651.3:c.684del	p.Ser229AlafsTer25	p.S229Afs*25	ENST00000359651		227	ttC/tt	5/8	0.458115942320555	1	FACETS	0.349	0.306	0.395	0.349	0.306	0.395	SUBCLONAL	1	TRUE	0	0.547757797515361	1		437	570	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028656	12028656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	89	312	0	ENST00000353533.5:c.859C>T	p.Arg287Cys	p.R287C	ENST00000353533	NM_003010.3	287	Cgc/Tgc	8/11	0.547757797515361	1	FACETS	0.704	0.63	0.782	0.704	0.63	0.782	SUBCLONAL	1	TRUE	0	0.547757797515361	1		312	335	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981100	201981101	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0067922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	143	385	0	ENST00000359651.3:c.184dup	p.Glu62GlyfsTer30	p.E62Gfs*30	ENST00000359651		60	ttg/ttGg	2/8	0.458115942320555	1	FACETS	0.602	0.55	0.655	0.602	0.55	0.655	SUBCLONAL	1	TRUE	0	0.547757797515361	1		385	630	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845820	151845820	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	57	404	0	ENST00000262189.6:c.13192G>C	p.Asp4398His	p.D4398H	ENST00000262189	NM_170606.2	4398	Gac/Cac	52/59	1	2	FACETS	0.46	0.396	0.531	0.46	0.396	0.531	SUBCLONAL	1	TRUE	1	0.547757797515361	2		404	452	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984413	201984413	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	154	372	0	ENST00000359651.3:c.1078G>T	p.Gly360Cys	p.G360C	ENST00000359651		360	Ggc/Tgc	8/8	0.458115942320555	1	FACETS	0.619	0.568	0.671	0.619	0.568	0.671	SUBCLONAL	1	TRUE	0	0.547757797515361	1		372	660	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577077	7577103	+	inframe_deletion	In_Frame_Del	DEL	CTCTTCCTCTGTGCGCCGGTCTCTCCC	CTCTTCCTCTGTGCGCCGGTCTCTCCC	-	novel	NA	P-0067922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	201	379	0	ENST00000269305.4:c.835_861del	p.Gly279_Glu287del	p.G279_E287del	ENST00000269305	NM_001126112.2	279	GGGAGAGACCGGCGCACAGAGGAAGAG/-	8/11	0.547757797515361	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.547757797515361	1		379	461	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950067	38950067	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	116	443	0	ENST00000357387.3:c.3883A>G	p.Thr1295Ala	p.T1295A	ENST00000357387	NM_152756.3	1295	Acg/Gcg	31/38	1	2	FACETS	0.647	0.584	0.713	0.647	0.584	0.713	SUBCLONAL	1	TRUE	1	0.547757797515361	2		443	655	SUCCESS
APC	324	MSKCC	GRCh37	5	112176063	112176063	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	103	476	0	ENST00000257430.4:c.4772del	p.Ala1591GlufsTer59	p.A1591Efs*59	ENST00000257430	NM_000038.5	1591	gCa/ga	16/16	0.547757797515361	1	FACETS	0.518	0.465	0.574	0.518	0.465	0.574	SUBCLONAL	1	TRUE	0	0.547757797515361	1		476	527	SUCCESS
APC	324	MSKCC	GRCh37	5	112103015	112103015	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0067922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	58	363	0	ENST00000257430.4:c.350C>G	p.Ser117Ter	p.S117*	ENST00000257430	NM_000038.5	117	tCa/tGa	4/16	0.547757797515361	1	FACETS	0.387	0.334	0.445	0.387	0.334	0.445	SUBCLONAL	1	TRUE	0	0.547757797515361	1		363	397	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231610	5231611	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	19	161	0	ENST00000357368.4:c.1865dup	p.Gln623SerfsTer4	p.Q623Sfs*4	ENST00000357368	NM_002850.3	622	cct/ccCt	14/38	1	2	FACETS	0.842	0.645	1	0.842	0.645	1	CLONAL	1	TRUE	1	0.322206376983307	2		161	140	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	108	624	0	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.322206376983307	2		624	463	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	58	389	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.322206376983307	2		389	273	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	17	176	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	1	0.322206376983307	2		176	90	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	120	389	0	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	1	2	FACETS	0.906	0.825	0.99	1	0.989	1	CLONAL	2	TRUE	1	0.322206376983307	2		389	411	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	206	707	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.901	0.845	0.957	1	0.995	1	CLONAL	3	TRUE	1	0.322206376983307	2		711	473	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29279846	29279846	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	18	104	0	ENST00000544604.2:c.92del	p.Leu31ArgfsTer91	p.L31Rfs*91	ENST00000544604	NM_001206998.1	31	cTg/cg	1/9	1	2	FACETS	0.859	0.654	1	0.859	0.654	1	CLONAL	1	TRUE	1	0.322206376983307	2		104	130	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	44	307	0	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.843	0.71	0.989	0.843	0.71	0.989	CLONAL	1	TRUE	1	0.322206376983307	2		307	324	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	35	260	1	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.322206376983307	2		261	162	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255142	16255143	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	rs764595221	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	147	525	5	ENST00000375759.3:c.2417_2418del	p.Arg806ThrfsTer14	p.R806Tfs*14	ENST00000375759	NM_015001.2	803	GAg/g	11/15	1	2	FACETS	0.773	0.709	0.84	1	0.988	1	SUBCLONAL	2	TRUE	1	0.322206376983307	2		530	590	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	75	460	3	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.322206376983307	2		463	345	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097790	27097790	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	39	424	0	ENST00000324856.7:c.3379C>T	p.Gln1127Ter	p.Q1127*	ENST00000324856	NM_006015.4	1127	Cag/Tag	12/20	1	2	FACETS	0.557	0.461	0.663	0.557	0.461	0.663	SUBCLONAL	1	TRUE	1	0.322206376983307	2		424	435	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	64	275	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.798	0.699	0.902	1	0.976	1	CLONAL	2	TRUE	1	0.322206376983307	2		275	249	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138187	64138187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1418251990	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	41	476	2	ENST00000334205.4:c.2110G>A	p.Ala704Thr	p.A704T	ENST00000334205	NM_003942.2	704	Gcc/Acc	16/17	1	2	FACETS	0.593	0.494	0.703	0.593	0.494	0.703	SUBCLONAL	1	TRUE	1	0.322206376983307	2		478	429	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572092	64572093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767319284	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	107	577	1	ENST00000312049.6:c.1546dup	p.Arg516ProfsTer15	p.R516Pfs*15	ENST00000312049	NM_130799.2	516	cgg/cCgg	10/10	1	2	FACETS	0.785	0.709	0.864	1	0.985	1	SUBCLONAL	2	TRUE	1	0.322206376983307	2		578	423	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457951	69457951	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	74	507	0	ENST00000227507.2:c.355del	p.Leu119Ter	p.L119*	ENST00000227507	NM_053056.2	117	atC/at	2/5	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.322206376983307	2		507	390	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589686	69589686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756925670	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	38	796	0	ENST00000168712.1:c.167C>T	p.Ala56Val	p.A56V	ENST00000168712	NM_002007.2	56	gCg/gTg	1/3	1	2	FACETS	0.47	0.388	0.562	0.47	0.388	0.562	SUBCLONAL	1	TRUE	1	0.322206376983307	2		796	502	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	94	592	0	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.322206376983307	2		592	435	SUCCESS
CBL	867	MSKCC	GRCh37	11	119168162	119168162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763213265	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	95	395	0	ENST00000264033.4:c.2222C>T	p.Ala741Val	p.A741V	ENST00000264033	NM_005188.3	741	gCg/gTg	14/16	1	2	FACETS	0.806	0.723	0.892	1	0.984	1	CLONAL	2	TRUE	1	0.322206376983307	2		395	366	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	95	575	3	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.322206376983307	2		578	503	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444000	49444000	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	35	591	0	ENST00000301067.7:c.3371del	p.Pro1124LeufsTer40	p.P1124Lfs*40	ENST00000301067	NM_003482.3	1124	cCt/ct	11/54	1	2	FACETS	0.475	0.389	0.572	0.475	0.389	0.572	SUBCLONAL	1	TRUE	1	0.322206376983307	2		591	457	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112323	115112324	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	rs1381943852	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	111	475	0	ENST00000257566.3:c.1416_1417del	p.Leu473ProfsTer218	p.L473Pfs*218	ENST00000257566	NM_016569.3	472	gcGCtc/gctc	7/8	1	2	FACETS	0.863	0.783	0.947	1	0.987	1	CLONAL	2	TRUE	1	0.322206376983307	2		475	399	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911358	32911358	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507645	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	36	464	0	ENST00000380152.3:c.2870del	p.Asn957IlefsTer3	p.N957Ifs*3	ENST00000380152		956	Aaa/aa	11/27	1	2	FACETS	0.887	0.733	1	0.887	0.733	1	CLONAL	1	TRUE	1	0.322206376983307	2		464	252	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	67	380	2	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.322206376983307	2		382	284	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354312	354312	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1432410713	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	79	389	0	ENST00000262320.3:c.1246G>A	p.Val416Met	p.V416M	ENST00000262320	NM_003502.3	416	Gtg/Atg	5/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.322206376983307	2		389	328	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	128	489	0	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.322206376983307	2		489	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28934577	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	103	387	1	ENST00000269305.4:c.770T>C	p.Leu257Pro	p.L257P	ENST00000269305	NM_001126112.2	257	cTg/cCg	7/11	1	2	FACETS	0.811	0.732	0.894	1	0.985	1	CLONAL	2	TRUE	1	0.322206376983307	2		388	394	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435456	56435456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756000629	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	100	570	1	ENST00000407977.2:c.1681C>T	p.Arg561Trp	p.R561W	ENST00000407977		561	Cgg/Tgg	9/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.322206376983307	2		571	489	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885829	59885829	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	70	341	1	ENST00000259008.2:c.917del	p.Asn306ThrfsTer32	p.N306Tfs*32	ENST00000259008	NM_032043.2	306	aAc/ac	7/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.322206376983307	2		342	291	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096931	11096931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502073	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	101	517	0	ENST00000358026.2:c.422C>T	p.Ser141Leu	p.S141L	ENST00000358026	NM_001128849.1	141	tCg/tTg	4/36	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.322206376983307	2		517	444	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216189	36216189	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	105	592	1	ENST00000222270.7:c.3602del	p.Pro1201ArgfsTer154	p.P1201Rfs*154	ENST00000222270	NM_014727.1	1199	ggC/gg	11/37	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.322206376983307	2		593	466	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	81	508	1	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.322206376983307	2		509	426	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467502	25467502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	61	501	0	ENST00000264709.3:c.1574C>T	p.Ala525Val	p.A525V	ENST00000264709	NM_175629.2	525	gCg/gTg	14/23	1	2	FACETS	0.876	0.758	1	0.876	0.758	1	CLONAL	1	TRUE	1	0.322206376983307	2		501	432	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150001	202150001	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	121	468	0	ENST00000358485.4:c.1442T>C	p.Ile481Thr	p.I481T	ENST00000358485	NM_001080125.1	481	aTc/aCc	8/9	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.322206376983307	2		468	505	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764346	39764347	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	34	416	0	ENST00000288319.7:c.765dup	p.Arg256GlnfsTer29	p.R256Qfs*29	ENST00000288319	NM_182918.3	255	-/C	7/10	1	2	FACETS	0.505	0.412	0.609	0.505	0.412	0.609	SUBCLONAL	1	TRUE	1	0.322206376983307	2		416	418	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157644	106157644	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	44	459	0	ENST00000380013.4:c.2545A>G	p.Thr849Ala	p.T849A	ENST00000380013	NM_001127208.2	849	Aca/Gca	3/11	1	2	FACETS	0.74	0.622	0.87	0.74	0.622	0.87	SUBCLONAL	1	TRUE	1	0.322206376983307	2		459	369	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144258384	144258385	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755581817	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	61	438	1	ENST00000262995.4:c.50dup	p.Glu18GlyfsTer34	p.E18Gfs*34	ENST00000262995	NM_207123.2	15	tcc/tCcc	1/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.322206376983307	2		439	308	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20486919	20486919	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs376318599	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	49	266	0	ENST00000346618.3:c.885-1C>T		p.X295_splice	ENST00000346618	NM_001949.4	295			1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.322206376983307	2		266	259	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100577	157100577	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1289149988	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	52	282	1	ENST00000346085.5:c.1518del	p.Gly507AspfsTer16	p.G507Dfs*16	ENST00000346085	NM_020732.3	505	aCc/ac	1/20	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.322206376983307	2		283	280	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971174	13971174	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	94	497	0	ENST00000405192.2:c.755del	p.Pro252LeufsTer3	p.P252Lfs*3	ENST00000405192	NM_001163147.1	252	cCt/ct	8/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.322206376983307	2		497	479	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508193	106508193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373644334	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	81	488	2	ENST00000359195.3:c.187G>A	p.Gly63Ser	p.G63S	ENST00000359195	NM_002649.2	63	Ggc/Agc	2/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.322206376983307	2		490	417	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509661	106509661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1182076194	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	101	500	0	ENST00000359195.3:c.1655G>A	p.Arg552His	p.R552H	ENST00000359195	NM_002649.2	552	cGc/cAc	2/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.322206376983307	2		500	467	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	107	506	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.322206376983307	2		506	445	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187221	38187222	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	99	472	1	ENST00000317025.8:c.1255dup	p.Thr419AsnfsTer28	p.T419Nfs*28	ENST00000317025	NM_023034.1	419	acc/aAcc	6/24	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.322206376983307	2		473	473	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992720	68992721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs764112302	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	58	396	3	ENST00000288368.4:c.1693dup	p.Ser565PhefsTer3	p.S565Ffs*3	ENST00000288368	NM_024870.2	562	cgt/cgTt	16/40	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.322206376983307	2		399	249	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981632	70981632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	99	435	0	ENST00000276594.2:c.464C>T	p.Ala155Val	p.A155V	ENST00000276594	NM_024504.3	155	gCg/gTg	2/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.322206376983307	2		435	442	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981892	70981892	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	90	576	0	ENST00000276594.2:c.204del	p.Phe69SerfsTer10	p.F69Sfs*10	ENST00000276594	NM_024504.3	68	ccC/cc	2/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.322206376983307	2		576	445	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971194	21971194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561034503	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	108	435	0	ENST00000304494.5:c.164G>A	p.Gly55Asp	p.G55D	ENST00000304494	NM_000077.4	55	gGc/gAc	2/3	1	2	FACETS	0.769	0.694	0.846	1	0.984	1	SUBCLONAL	2	TRUE	1	0.322206376983307	2		435	436	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624492	93624492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	83	353	0	ENST00000375746.1:c.583C>T	p.Arg195Ter	p.R195*	ENST00000375746	NM_001174167.1	195	Cga/Tga	4/14	1	2	FACETS	0.785	0.699	0.876	1	0.981	1	SUBCLONAL	2	TRUE	1	0.322206376983307	2		353	328	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110251257	110251257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	88	357	0	ENST00000374672.4:c.80C>T	p.Pro27Leu	p.P27L	ENST00000374672	NM_004235.4	27	cCg/cTg	2/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.322206376983307	2		357	419	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390617	139390617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567323027	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	114	575	0	ENST00000277541.6:c.7574C>T	p.Pro2525Leu	p.P2525L	ENST00000277541	NM_017617.3	2525	cCg/cTg	34/34	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.322206376983307	2		575	506	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040987	47040987	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	54	316	0	ENST00000377604.3:c.1517G>A	p.Gly506Asp	p.G506D	ENST00000377604	NM_001204468.1	506	gGc/gAc	14/24	1	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.322206376983307	1		316	257	SUCCESS
AR	367	MSKCC	GRCh37	X	66765826	66765826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	13	286	0	ENST00000374690.3:c.838C>T	p.Arg280Cys	p.R280C	ENST00000374690	NM_000044.3	280	Cgt/Tgt	1/8	1	1	FACETS	0.304	0.216	0.41	0.304	0.216	0.41	SUBCLONAL	1	TRUE	0	0.322206376983307	1		286	223	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254888	16254888	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	58	480	0	ENST00000375759.3:c.2153A>G	p.Glu718Gly	p.E718G	ENST00000375759	NM_015001.2	718	gAg/gGg	11/15	1	2	FACETS	0.652	0.56	0.752	0.652	0.56	0.752	SUBCLONAL	1	TRUE	1	0.322206376983307	2		480	552	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260425	16260425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	132	566	1	ENST00000375759.3:c.7690G>A	p.Ala2564Thr	p.A2564T	ENST00000375759	NM_015001.2	2564	Gct/Act	11/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.322206376983307	2		567	547	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36819990	36819990	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	36	332	0	ENST00000373129.3:c.598C>A	p.Leu200Met	p.L200M	ENST00000373129	NM_032017.1	200	Ctg/Atg	7/12	1	2	FACETS	0.633	0.521	0.758	0.633	0.521	0.758	SUBCLONAL	1	TRUE	1	0.322206376983307	2		332	353	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150923130	150923130	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	85	509	0	ENST00000271640.5:c.1777C>T	p.Gln593Ter	p.Q593*	ENST00000271640	NM_001145415.1	593	Cag/Tag	13/22	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.322206376983307	2		509	439	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426848	70426848	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	100	409	1	ENST00000373644.4:c.4508G>A	p.Arg1503Gln	p.R1503Q	ENST00000373644	NM_030625.2	1503	cGg/cAg	7/12	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.322206376983307	2		410	465	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903694	114903694	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	28	336	0	ENST00000543371.1:c.698C>A	p.Pro233His	p.P233H	ENST00000543371	NM_001198531.1	233	cCt/cAt	7/14	1	2	FACETS	0.479	0.383	0.588	0.479	0.383	0.588	SUBCLONAL	1	TRUE	1	0.322206376983307	2		336	363	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741555	17741555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760979284	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	81	420	0	ENST00000250003.3:c.226C>T	p.Arg76Cys	p.R76C	ENST00000250003	NM_002478.4	76	Cgt/Tgt	1/3	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.322206376983307	2		420	345	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77930333	77930333	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	113	460	0	ENST00000361507.4:c.2016G>T	p.Lys672Asn	p.K672N	ENST00000361507	NM_080491.2	672	aaG/aaT	10/10	1	2	FACETS	0.864	0.784	0.947	1	0.987	1	CLONAL	2	TRUE	1	0.322206376983307	2		460	406	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424529	49424529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749198835	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	41	521	0	ENST00000301067.7:c.13694C>T	p.Thr4565Met	p.T4565M	ENST00000301067	NM_003482.3	4565	aCg/aTg	41/54	1	2	FACETS	0.597	0.498	0.708	0.597	0.498	0.708	SUBCLONAL	1	TRUE	1	0.322206376983307	2		521	426	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28624262	28624262	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	94	411	0	ENST00000241453.7:c.712G>T	p.Gly238Cys	p.G238C	ENST00000241453	NM_004119.2	238	Ggc/Tgc	6/24	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.322206376983307	2		411	390	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937059	48937059	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	56	347	0	ENST00000267163.4:c.827T>C	p.Val276Ala	p.V276A	ENST00000267163	NM_000321.2	276	gTt/gCt	8/27	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.322206376983307	2		347	264	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132970	30132970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	40	379	0	ENST00000331968.5:c.631G>A	p.Gly211Arg	p.G211R	ENST00000331968	NM_002742.2	211	Ggg/Agg	4/18	1	2	FACETS	0.573	0.477	0.681	0.573	0.477	0.681	SUBCLONAL	1	TRUE	1	0.322206376983307	2		379	433	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50791109	50791109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs960428350	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	85	428	1	ENST00000307179.4:c.3181G>A	p.Gly1061Ser	p.G1061S	ENST00000307179		1061	Ggt/Agt	20/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.322206376983307	2		429	389	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862838	9862838	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	25	483	0	ENST00000330684.3:c.2465A>G	p.Tyr822Cys	p.Y822C	ENST00000330684	NM_001134407.1	822	tAc/tGc	12/13	1	2	FACETS	0.389	0.306	0.484	0.389	0.306	0.484	SUBCLONAL	1	TRUE	1	0.322206376983307	2		483	399	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348770	11348770	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	32	363	1	ENST00000332029.2:c.566A>G	p.Glu189Gly	p.E189G	ENST00000332029	NM_003745.1	189	gAg/gGg	2/2	1	2	FACETS	0.595	0.483	0.72	0.595	0.483	0.72	SUBCLONAL	1	TRUE	1	0.322206376983307	2		364	334	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014135	14014135	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	85	398	0	ENST00000311895.7:c.113G>T	p.Gly38Val	p.G38V	ENST00000311895	NM_005236.2	38	gGg/gTg	1/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.322206376983307	2		398	387	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544519	86544519	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	104	506	0	ENST00000262426.4:c.344G>T	p.Arg115Leu	p.R115L	ENST00000262426	NM_001451.2	115	cGg/cTg	1/2	1	2	FACETS	0.912	0.825	1	1	0.987	1	CLONAL	2	TRUE	1	0.322206376983307	2		506	354	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131252	17131252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	147	539	0	ENST00000285071.4:c.200C>T	p.Ala67Val	p.A67V	ENST00000285071	NM_144997.5	67	gCc/gTc	4/14	1	2	FACETS	0.773	0.709	0.84	1	0.988	1	SUBCLONAL	2	TRUE	1	0.322206376983307	2		539	590	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208350	5208350	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	116	482	0	ENST00000357368.4:c.5540A>G	p.Gln1847Arg	p.Q1847R	ENST00000357368	NM_002850.3	1847	cAg/cGg	36/38	1	2	FACETS	0.87	0.79	0.952	1	0.988	1	CLONAL	2	TRUE	1	0.322206376983307	2		482	414	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7152863	7152863	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	112	400	0	ENST00000302850.5:c.2105A>G	p.Tyr702Cys	p.Y702C	ENST00000302850	NM_000208.2	702	tAt/tGt	10/22	1	2	FACETS	0.783	0.709	0.86	1	0.985	1	SUBCLONAL	2	TRUE	1	0.322206376983307	2		400	444	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132470	11132470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	48	570	0	ENST00000358026.2:c.2686G>A	p.Val896Met	p.V896M	ENST00000358026	NM_001128849.1	896	Gtg/Atg	19/36	1	2	FACETS	0.622	0.526	0.728	0.622	0.526	0.728	SUBCLONAL	1	TRUE	1	0.322206376983307	2		570	479	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15280959	15280959	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	66	489	0	ENST00000263388.2:c.5137C>A	p.Leu1713Met	p.L1713M	ENST00000263388	NM_000435.2	1713	Ctg/Atg	28/33	1	2	FACETS	0.845	0.735	0.963	0.845	0.735	0.963	CLONAL	1	TRUE	1	0.322206376983307	2		489	485	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281241	15281241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	111	607	0	ENST00000263388.2:c.5015G>A	p.Ser1672Asn	p.S1672N	ENST00000263388	NM_000435.2	1672	aGc/aAc	27/33	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.322206376983307	2		607	525	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266898	18266898	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	46	460	0	ENST00000222254.8:c.209T>A	p.Phe70Tyr	p.F70Y	ENST00000222254	NM_005027.3	70	tTc/tAc	2/16	1	2	FACETS	0.751	0.634	0.88	0.751	0.634	0.88	SUBCLONAL	1	TRUE	1	0.322206376983307	2		460	380	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18964112	18964112	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	30	458	0	ENST00000262803.5:c.1109T>G	p.Leu370Arg	p.L370R	ENST00000262803	NM_002911.3	370	cTt/cGt	8/24	1	2	FACETS	0.45	0.362	0.549	0.45	0.362	0.549	SUBCLONAL	1	TRUE	1	0.322206376983307	2		458	414	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213525	36213525	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	95	538	0	ENST00000222270.7:c.2627C>A	p.Ala876Asp	p.A876D	ENST00000222270	NM_014727.1	876	gCt/gAt	5/37	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.322206376983307	2		538	434	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214353	36214353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	92	449	1	ENST00000222270.7:c.3007C>T	p.Arg1003Trp	p.R1003W	ENST00000222270	NM_014727.1	1003	Cgg/Tgg	7/37	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.322206376983307	2		450	392	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224291	36224291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	102	500	0	ENST00000222270.7:c.6841G>A	p.Val2281Met	p.V2281M	ENST00000222270	NM_014727.1	2281	Gtg/Atg	28/37	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.322206376983307	2		500	424	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753323	42753323	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs766445497	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	50	543	1	ENST00000222329.4:c.941T>G	p.Leu314Arg	p.L314R	ENST00000222329	NM_006494.2	314	cTg/cGg	4/4	1	2	FACETS	0.675	0.573	0.786	0.675	0.573	0.786	SUBCLONAL	1	TRUE	1	0.322206376983307	2		544	460	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791000	42791000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	83	459	1	ENST00000575354.2:c.145C>T	p.Pro49Ser	p.P49S	ENST00000575354	NM_015125.3	49	Cct/Tct	2/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.322206376983307	2		460	391	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50916774	50916774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1244269995	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	26	487	0	ENST00000440232.2:c.2246C>T	p.Ala749Val	p.A749V	ENST00000440232	NM_002691.3	749	gCc/gTc	18/27	1	2	FACETS	0.451	0.357	0.558	0.451	0.357	0.558	SUBCLONAL	1	TRUE	1	0.322206376983307	2		487	358	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637494	47637494	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	23	380	0	ENST00000233146.2:c.628A>T	p.Met210Leu	p.M210L	ENST00000233146	NM_000251.2	210	Atg/Ttg	3/16	1	2	FACETS	0.363	0.283	0.457	0.363	0.283	0.457	SUBCLONAL	1	TRUE	1	0.322206376983307	2		380	393	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637500	47637500	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	21	393	0	ENST00000233146.2:c.636del	p.Lys212AsnfsTer2	p.K212Nfs*2	ENST00000233146	NM_000251.2	212	Aaa/aa	3/16	1	2	FACETS	0.33	0.253	0.42	0.33	0.253	0.42	SUBCLONAL	1	TRUE	1	0.322206376983307	2		393	395	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21347134	21347134	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	106	472	1	ENST00000215739.8:c.1201T>C	p.Tyr401His	p.Y401H	ENST00000215739	NM_006767.3	401	Tac/Cac	11/21	1	2	FACETS	0.778	0.702	0.857	1	0.984	1	SUBCLONAL	2	TRUE	1	0.322206376983307	2		473	423	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713732	30713732	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	116	576	0	ENST00000295754.5:c.1057T>C	p.Ser353Pro	p.S353P	ENST00000295754	NM_003242.5	353	Tcc/Ccc	4/7	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.322206376983307	2		576	512	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215203	142215203	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	23	163	0	ENST00000350721.4:c.5898G>T	p.Lys1966Asn	p.K1966N	ENST00000350721	NM_001184.3	1966	aaG/aaT	34/47	1	2	FACETS	0.933	0.735	1	0.933	0.735	1	CLONAL	1	TRUE	1	0.322206376983307	2		163	153	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467415	66467415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758504916	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	108	429	1	ENST00000273854.3:c.854C>T	p.Pro285Leu	p.P285L	ENST00000273854	NM_004439.5	285	cCc/cTc	3/18	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.322206376983307	2		430	503	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293745	1293745	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	120	536	0	ENST00000310581.5:c.1256T>C	p.Val419Ala	p.V419A	ENST00000310581	NM_198253.2	419	gTc/gCc	2/16	1	2	FACETS	0.763	0.693	0.836	1	0.986	1	SUBCLONAL	2	TRUE	1	0.322206376983307	2		536	488	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405085	405085	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	91	364	3	ENST00000380956.4:c.1167G>T	p.Glu389Asp	p.E389D	ENST00000380956	NM_001195286.1	389	gaG/gaT	8/9	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.322206376983307	2		367	414	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001086	150001086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	78	402	0	ENST00000253339.5:c.2518G>A	p.Gly840Ser	p.G840S	ENST00000253339		840	Ggt/Agt	4/7	1	2	FACETS	0.802	0.711	0.896	1	0.98	1	CLONAL	2	TRUE	1	0.322206376983307	2		402	302	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382239	152382239	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	60	327	0	ENST00000206249.3:c.1349C>A	p.Ser450Tyr	p.S450Y	ENST00000206249	NM_000125.3	450	tCt/tAt	6/8	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.322206376983307	2		327	268	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099593	157099593	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	71	394	0	ENST00000346085.5:c.530C>T	p.Pro177Leu	p.P177L	ENST00000346085	NM_020732.3	177	cCg/cTg	1/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.322206376983307	2		394	326	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969885	161969885	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	81	378	0	ENST00000366898.1:c.1083+1del		p.X361_splice	ENST00000366898	NM_004562.2	361			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.322206376983307	2		378	345	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90960095	90960095	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782297	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	54	293	0	ENST00000265433.3:c.1871G>A	p.Arg624His	p.R624H	ENST00000265433	NM_002485.4	624	cGt/cAt	12/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.322206376983307	2		293	224	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2047292	2047292	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	28	98	0	ENST00000349721.2:c.854G>A	p.Gly285Asp	p.G285D	ENST00000349721	NM_003070.3	285	gGc/gAc	5/34	1	2	FACETS	0.988	0.812	1	1	0.959	1	CLONAL	2	TRUE	1	0.322206376983307	2		98	88	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126448	5126448	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	60	322	0	ENST00000381652.3:c.3291+2T>C		p.X1097_splice	ENST00000381652	NM_004972.3	1097			1	2	FACETS	0.769	0.671	0.874	1	0.973	1	SUBCLONAL	2	TRUE	1	0.322206376983307	2		322	242	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910580	29910581	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	T	novel	NA	P-0067923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	98	419	0	ENST00000376809.5:c.120_121delinsT	p.Arg41AlafsTer36	p.R41Afs*36	ENST00000376809	NM_002116.7	40	ggCCgc/ggTgc	2/8	1	2	FACETS	0.882	0.794	0.973	1	0.986	1	CLONAL	2	TRUE	1	0.322206376983307	2		419	345	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0067924-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	237	504	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.315077695949351	2	FACETS	1	0.971	1	1	0.994	1	CLONAL	3	TRUE	0	0.33268027284843	2		504	457	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0067925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	47	148	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.289678289389884	2	FACETS	0.922	0.813	1	1	0.977	1	CLONAL	4	FALSE	0	0.289678289389884	2		148	88	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0067925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	37	396	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	0.598	0.493	0.716	0.598	0.493	0.716	SUBCLONAL	1	FALSE	1	0.289678289389884	2		396	427	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665213	138665213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	165	439	0	ENST00000330315.3:c.352G>A	p.Glu118Lys	p.E118K	ENST00000330315	NM_023067.3	118	Gag/Aag	1/1	0.289678289389884	2	FACETS	1	0.949	1	1	0.994	1	CLONAL	4	FALSE	0	0.289678289389884	2		439	282	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092809	27092809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	97	350	0	ENST00000324856.7:c.2830C>T	p.Gln944Ter	p.Q944*	ENST00000324856	NM_006015.4	944	Cag/Tag	9/20	0.286041140223418	3	FACETS	0.896	0.817	0.976	1	0.988	1	CLONAL	4	FALSE	1	0.289678289389884	3		350	214	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911760	26911760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	27	279	0	ENST00000381527.3:c.185C>T	p.Ser62Leu	p.S62L	ENST00000381527	NM_001260.1	62	tCg/tTg	2/13	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	FALSE	1	0.289678289389884	2		279	129	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806153	1806153	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28931615	NA	P-0067925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	193	412	0	ENST00000260795.2:c.1172C>A	p.Ala391Glu	p.A391E	ENST00000260795		391	gCg/gAg	8/17	1	2	FACETS	0.976	0.913	1	1	0.995	1	CLONAL	3	FALSE	1	0.289678289389884	2		412	455	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291911	15291911	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	139	482	0	ENST00000263388.2:c.2855C>T	p.Pro952Leu	p.P952L	ENST00000263388	NM_000435.2	952	cCc/cTc	18/33	0.183430323382417	4	FACETS	1	0.938	1	1	0.989	1	CLONAL	3	FALSE	2	0.289678289389884	4		482	403	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574053	46574053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1320324950	NA	P-0067925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	125	410	0	ENST00000263734.3:c.68C>T	p.Ala23Val	p.A23V	ENST00000263734	NM_001430.4	23	gCg/gTg	2/16	1	2	FACETS	0.844	0.773	0.916	1	0.992	1	CLONAL	3	FALSE	1	0.289678289389884	2		410	341	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426373	49426373	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	127	496	0	ENST00000301067.7:c.12115G>T	p.Glu4039Ter	p.E4039*	ENST00000301067	NM_003482.3	4039	Gag/Tag	39/54	0.289678289389884	4	FACETS	1	0.942	1	1	0.988	1	CLONAL	3	FALSE	2	0.289678289389884	4		496	364	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723510	49723510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748083669	NA	P-0067925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	19	44	0	ENST00000449682.2:c.1132G>A	p.Asp378Asn	p.D378N	ENST00000449682	NM_020998.3	378	Gac/Aac	9/18	1	2	FACETS	1	0.815	1	1	0.954	1	CLONAL	3	FALSE	1	0.289678289389884	2		44	43	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023525	27023525	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	108	376	0	ENST00000324856.7:c.631C>T	p.Gln211Ter	p.Q211*	ENST00000324856	NM_006015.4	211	Cag/Tag	1/20	0.286041140223418	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	FALSE	1	0.289678289389884	3		376	369	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458323	12458323	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	37	430	0	ENST00000287820.6:c.940C>G	p.Gln314Glu	p.Q314E	ENST00000287820	NM_015869.4	314	Cag/Gag	6/7	1	2	FACETS	0.669	0.552	0.799	0.669	0.552	0.799	SUBCLONAL	1	FALSE	1	0.289678289389884	2		430	382	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281446	49281446	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	14	410	0	ENST00000282018.3:c.493C>A	p.Leu165Ile	p.L165I	ENST00000282018	NM_020377.2	165	Ctt/Att	1/1	1	2	FACETS	0.597	0.433	0.793	0.597	0.433	0.793	SUBCLONAL	1	FALSE	1	0.289678289389884	2		410	162	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202486	123202490	+	frameshift_variant	Frame_Shift_Del	DEL	AATAC	AATAC	-	novel	NA	P-0067925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	33	143	0	ENST00000218089.9:c.2338_2342del	p.Asn780TyrfsTer3	p.N780Yfs*3	ENST00000218089	NM_001042749.1	780	AATACt/t	24/35	1	1	FACETS	0.886	0.769	0.998	1	0.976	1	CLONAL	4	FALSE	0	0.289678289389884	1		143	55	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10785293	10785293	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs112593026	NA	P-0067925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	61	429	0	ENST00000361367.2:c.1061G>A	p.Arg354Gln	p.R354Q	ENST00000361367	NM_014633.3	354	cGa/cAa	9/25	1	2	FACETS	0.942	0.834	1	1	0.985	1	CLONAL	3	FALSE	1	0.289678289389884	2		429	149	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023066	150023066	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	47	407	0	ENST00000253339.5:c.197G>A	p.Arg66Lys	p.R66K	ENST00000253339		66	aGa/aAa	1/7	1	2	FACETS	0.995	0.855	1	1	0.975	1	CLONAL	2	FALSE	1	0.289678289389884	2		407	163	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349010	89349010	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	32	468	0	ENST00000301030.4:c.3940G>A	p.Glu1314Lys	p.E1314K	ENST00000301030	NM_001256183.1	1314	Gag/Aag	9/13	1	2	FACETS	0.516	0.419	0.626	0.516	0.419	0.626	SUBCLONAL	1	FALSE	1	0.289678289389884	2		468	428	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963036	38963036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1411741331	NA	P-0067925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	35	330	1	ENST00000357387.3:c.1508C>T	p.Ala503Val	p.A503V	ENST00000357387	NM_152756.3	503	gCa/gTa	17/38	1	2	FACETS	0.902	0.753	1	1	0.963	1	CLONAL	2	FALSE	1	0.289678289389884	2		331	134	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10793128	10793128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	15	352	0	ENST00000361367.2:c.2409G>A	p.Met803Ile	p.M803I	ENST00000361367	NM_014633.3	803	atG/atA	19/25	1	2	FACETS	0.503	0.368	0.664	0.503	0.368	0.664	SUBCLONAL	1	FALSE	1	0.289678289389884	2		352	206	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457924	69457924	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs751995000	NA	P-0067925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	35	396	0	ENST00000227507.2:c.324C>A	p.Phe108Leu	p.F108L	ENST00000227507	NM_053056.2	108	ttC/ttA	2/5	1	2	FACETS	0.52	0.426	0.625	0.52	0.426	0.625	SUBCLONAL	1	FALSE	1	0.289678289389884	2		396	465	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723107	49723107	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	122	219	0	ENST00000449682.2:c.1309G>C	p.Asp437His	p.D437H	ENST00000449682	NM_020998.3	437	Gat/Cat	11/18	1	2	FACETS	1	0.972	1	1	0.993	1	CLONAL	3	FALSE	1	0.289678289389884	2		219	251	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526299	189526299	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	285	464	0	ENST00000264731.3:c.563A>G	p.Lys188Arg	p.K188R	ENST00000264731	NM_003722.4	188	aAg/aGg	4/14	0.289678289389884	2	FACETS	1	0.978	1	1	0.996	1	CLONAL	4	FALSE	0	0.289678289389884	2		464	474	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463597	25463597	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	95	399	0	ENST00000264709.3:c.2085C>G	p.Ile695Met	p.I695M	ENST00000264709	NM_175629.2	695	atC/atG	18/23	1	2	FACETS	0.942	0.847	1	1	0.986	1	CLONAL	2	FALSE	1	0.289678289389884	2		399	348	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38792777	38792777	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	73	320	0	ENST00000348513.6:c.239T>A	p.Val80Asp	p.V80D	ENST00000348513	NM_003079.4	80	gTc/gAc	6/11	0.154539003857091	2	FACETS	1	0.952	1	1	0.983	1	INDETERMINATE	3	FALSE	0	0.289678289389884	2		320	153	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422643	49422644	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	175	454	0	ENST00000301067.7:c.14349dup	p.Val4784SerfsTer33	p.V4784Sfs*33	ENST00000301067	NM_003482.3	4783	-/A	45/54	0.289678289389884	4	FACETS	1	0.98	1	1	0.992	1	CLONAL	3	FALSE	2	0.289678289389884	4		454	453	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280063	18280063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067926-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	104	322	0	ENST00000222254.8:c.2146G>A	p.Val716Met	p.V716M	ENST00000222254	NM_005027.3	716	Gtg/Atg	16/16	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.422791285761435	2		322	472	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244119	153244119	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067926-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	155	421	0	ENST00000281708.4:c.2038A>T	p.Thr680Ser	p.T680S	ENST00000281708	NM_033632.3	680	Aca/Tca	12/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.422791285761435	2		421	662	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579355	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519997	NA	P-0067927-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	19	406	0	ENST00000269305.4:c.332T>G	p.Leu111Arg	p.L111R	ENST00000269305	NM_001126112.2	111	cTg/cGg	4/11	1	2	FACETS	0.534	0.404	0.689	0.534	0.404	0.689	SUBCLONAL	1	TRUE	1	0.12	2		406	593	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6027032	6027032	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs748698776	NA	P-0067927-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	19	240	0	ENST00000265849.7:c.1364C>G	p.Ser455Cys	p.S455C	ENST00000265849	NM_000535.5	455	tCt/tGt	11/15	1	2	FACETS	0.856	0.649	1	0.856	0.649	1	CLONAL	1	TRUE	1	0.12	2		240	370	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850653	63850653	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067928-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	209	421	0	ENST00000279873.7:c.1433del	p.Leu478Ter	p.L478*	ENST00000279873	NM_032199.2	477	acT/ac	10/10	1	2	FACETS	0.981	0.918	1	0.981	0.918	1	CLONAL	1	TRUE	1	0.771767033533449	2		421	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0067929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	79	371	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.44105010574082	1	FACETS	0.333	0.295	0.373	0.333	0.295	0.373	INDETERMINATE	1	TRUE	0	0.863923507839371	1		371	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0067929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	185	545	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.44105010574082	1	FACETS	0.667	0.626	0.707	0.667	0.626	0.707	INDETERMINATE	1	TRUE	0	0.863923507839371	1		545	365	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0067929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	185	446	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.998	0.933	1	0.998	0.933	1	CLONAL	1	TRUE	1	0.863923507839371	2		446	429	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259412	89259412	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	154	499	0	ENST00000336596.2:c.556G>T	p.Val186Phe	p.V186F	ENST00000336596	NM_005233.5	186	Gtt/Ttt	3/17	0.366363785502642	1	FACETS	0.523	0.485	0.563	0.523	0.485	0.563	INDETERMINATE	1	TRUE	0	0.863923507839371	1		499	387	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885902	59885902	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	123	470	0	ENST00000259008.2:c.844A>G	p.Thr282Ala	p.T282A	ENST00000259008	NM_032043.2	282	Act/Gct	7/20	1	2	FACETS	0.622	0.566	0.68	0.622	0.566	0.68	SUBCLONAL	1	TRUE	1	0.863923507839371	2		470	458	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492620	56492620	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	185	440	0	ENST00000267101.3:c.2770C>G	p.Leu924Val	p.L924V	ENST00000267101	NM_001982.3	924	Cta/Gta	23/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.863923507839371	2		440	418	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030945	36030953	+	inframe_deletion	In_Frame_Del	DEL	TGGGCTGGC	TGGGCTGGC	-	novel	NA	P-0067929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	57	473	0	ENST00000358208.4:c.1225_1233del	p.Gly409_Ala411del	p.G409_A411del	ENST00000358208		408	ttTGGGCTGGCt/ttt	10/12	0.180988176066021	3	FACETS	0.379	0.326	0.438	0.19	0.163	0.219	INDETERMINATE	1	TRUE	1	0.863923507839371	3		473	498	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	71	227	0	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.881	0.783	0.983	0.881	0.783	0.983	CLONAL	1	TRUE	1	0.79	2		227	204	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	84	385	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.79	2		385	205	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	127	418	2	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.794	0.726	0.864	0.794	0.726	0.864	SUBCLONAL	1	TRUE	1	0.79	2		420	405	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057936	27057937	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1415146710	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	27	292	0	ENST00000324856.7:c.1650dup	p.Tyr551LeufsTer72	p.Y551Lfs*72	ENST00000324856	NM_006015.4	548	-/C	3/20	1	2	FACETS	0.187	0.149	0.231	0.187	0.149	0.231	SUBCLONAL	1	TRUE	1	0.79	2		292	365	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	53	215	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.808	0.703	0.919	0.808	0.703	0.919	CLONAL	1	TRUE	1	0.79	2		215	166	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	111	372	1	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	2	FACETS	0.801	0.727	0.876	0.801	0.727	0.876	CLONAL	1	TRUE	1	0.79	2		373	351	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521298	187521299	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	115	300	0	ENST00000441802.2:c.11856dup	p.Gly3953TrpfsTer19	p.G3953Wfs*19	ENST00000441802	NM_005245.3	3952	-/T	22/27	1	2	FACETS	0.951	0.869	1	0.951	0.869	1	CLONAL	1	TRUE	1	0.79	2		300	306	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426123	138426123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217537873	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	51	188	0	ENST00000289153.2:c.1408G>A	p.Glu470Lys	p.E470K	ENST00000289153	NM_006219.2	470	Gaa/Aaa	9/22	1	2	FACETS	0.916	0.797	1	0.916	0.797	1	CLONAL	1	TRUE	1	0.79	2		188	141	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	39	333	0	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.279	0.231	0.332	0.279	0.231	0.332	SUBCLONAL	1	TRUE	1	0.79	2		333	354	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101054	27101054	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	35	270	0	ENST00000324856.7:c.4336C>T	p.Arg1446Ter	p.R1446*	ENST00000324856	NM_006015.4	1446	Cga/Tga	18/20	1	2	FACETS	0.306	0.251	0.366	0.306	0.251	0.366	SUBCLONAL	1	TRUE	1	0.79	2		270	290	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884011	37884011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150680317	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	145	357	1	ENST00000269571.5:c.3482G>A	p.Arg1161Gln	p.R1161Q	ENST00000269571		1161	cGa/cAa	27/27	1	2	FACETS	0.922	0.851	0.995	0.922	0.851	0.995	CLONAL	1	TRUE	1	0.79	2		358	398	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	160	289	0	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.79	2		289	404	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541541	187541541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs980333559	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	135	311	0	ENST00000441802.2:c.6199G>A	p.Val2067Met	p.V2067M	ENST00000441802	NM_005245.3	2067	Gtg/Atg	10/27	1	2	FACETS	0.911	0.838	0.987	0.911	0.838	0.987	CLONAL	1	TRUE	1	0.79	2		311	375	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	177	570	0	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	1	2	FACETS	0.916	0.852	0.982	0.916	0.852	0.982	CLONAL	1	TRUE	1	0.79	2		570	489	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937219	36937219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140159756	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	139	323	0	ENST00000361632.4:c.1100G>A	p.Arg367Gln	p.R367Q	ENST00000361632		367	cGg/cAg	9/16	1	2	FACETS	0.936	0.862	1	0.936	0.862	1	CLONAL	1	TRUE	1	0.79	2		323	376	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729775	41729775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	129	286	0	ENST00000242208.4:c.754G>A	p.Ala252Thr	p.A252T	ENST00000242208	NM_002192.2	252	Gcc/Acc	3/3	1	2	FACETS	0.987	0.907	1	0.987	0.907	1	CLONAL	1	TRUE	1	0.79	2		286	331	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792016	42792016	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1199661448	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	141	322	0	ENST00000575354.2:c.820C>T	p.Arg274Ter	p.R274*	ENST00000575354	NM_015125.3	274	Cga/Tga	6/20	1	2	FACETS	0.989	0.913	1	0.989	0.913	1	CLONAL	1	TRUE	1	0.79	2		322	361	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226899	2226899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762029066	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	151	345	0	ENST00000398665.3:c.4379C>T	p.Thr1460Met	p.T1460M	ENST00000398665	NM_032482.2	1460	aCg/aTg	27/28	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.79	2		345	370	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943380	71943380	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1394942069	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	123	269	0	ENST00000298229.2:c.1712G>A	p.Arg571Gln	p.R571Q	ENST00000298229	NM_001567.3	571	cGg/cAg	14/28	1	2	FACETS	0.921	0.844	1	0.921	0.844	1	CLONAL	1	TRUE	1	0.79	2		269	338	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136030	64136030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1380280944	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	96	256	0	ENST00000334205.4:c.1291C>T	p.Arg431Cys	p.R431C	ENST00000334205	NM_003942.2	431	Cgc/Tgc	11/17	1	2	FACETS	0.894	0.808	0.982	0.894	0.808	0.982	CLONAL	1	TRUE	1	0.79	2		256	272	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69000005	69000005	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561299451	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	55	259	0	ENST00000288368.4:c.2074C>T	p.Arg692Trp	p.R692W	ENST00000288368	NM_024870.2	692	Cgg/Tgg	19/40	1	2	FACETS	0.378	0.325	0.436	0.378	0.325	0.436	SUBCLONAL	1	TRUE	1	0.79	2		259	368	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442578	52442578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1294552464	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	153	255	1	ENST00000460680.1:c.167G>A	p.Arg56His	p.R56H	ENST00000460680	NM_004656.3	56	cGc/cAc	4/17	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.79	2		256	387	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367845	15367845	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265135334	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	134	205	0	ENST00000263377.2:c.1481C>T	p.Ser494Leu	p.S494L	ENST00000263377	NM_058243.2	494	tCg/tTg	8/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.79	2		205	328	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941843	71941843	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514511	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	114	279	0	ENST00000298229.2:c.1201C>T	p.Arg401Trp	p.R401W	ENST00000298229	NM_001567.3	401	Cgg/Tgg	11/28	1	2	FACETS	0.925	0.844	1	0.925	0.844	1	CLONAL	1	TRUE	1	0.79	2		279	312	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852527	42852527	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs748560513	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	120	268	0	ENST00000398585.3:c.559C>T	p.Arg187Cys	p.R187C	ENST00000398585	NM_001135099.1	187	Cgc/Tgc	6/14	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.79	2		268	302	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591593	38591593	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs750777752	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	82	182	0	ENST00000299084.4:c.52C>T	p.Arg18Ter	p.R18*	ENST00000299084	NM_152594.2	18	Cga/Tga	2/7	1	2	FACETS	0.821	0.734	0.91	0.821	0.734	0.91	CLONAL	1	TRUE	1	0.79	2		182	253	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508977	106508977	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760224981	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	113	291	0	ENST00000359195.3:c.971C>T	p.Pro324Leu	p.P324L	ENST00000359195	NM_002649.2	324	cCa/cTa	2/11	1	2	FACETS	0.875	0.797	0.955	0.875	0.797	0.955	CLONAL	1	TRUE	1	0.79	2		291	327	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593308	67593308	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	29	255	0	ENST00000274335.5:c.2054A>G	p.Tyr685Cys	p.Y685C	ENST00000274335		685	tAt/tGt	15/15	1	2	FACETS	0.213	0.171	0.261	0.213	0.171	0.261	SUBCLONAL	1	TRUE	1	0.79	2		255	345	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624294	89624294	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	91	176	1	ENST00000371953.3:c.68T>C	p.Leu23Ser	p.L23S	ENST00000371953	NM_000314.4	23	tTa/tCa	1/9	1	2	FACETS	0.989	0.894	1	0.989	0.894	1	CLONAL	1	TRUE	1	0.79	2		177	233	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245483	133245483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200471266	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	148	252	0	ENST00000320574.5:c.1837G>A	p.Val613Ile	p.V613I	ENST00000320574	NM_006231.2	613	Gtt/Att	17/49	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.79	2		252	372	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144336667	144336667	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746261423	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	29	260	0	ENST00000262995.4:c.110G>A	p.Arg37His	p.R37H	ENST00000262995	NM_207123.2	37	cGt/cAt	2/11	1	2	FACETS	0.38	0.308	0.462	0.38	0.308	0.462	SUBCLONAL	1	TRUE	1	0.79	2		260	193	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864024	97864024	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs104886457	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	91	210	0	ENST00000289081.3:c.1642C>T	p.Arg548Ter	p.R548*	ENST00000289081	NM_000136.2	548	Cga/Tga	15/15	1	2	FACETS	0.964	0.871	1	0.964	0.871	1	CLONAL	1	TRUE	1	0.79	2		210	239	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499631	18499631	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	20	279	0	ENST00000266497.5:c.1486G>A	p.Val496Ile	p.V496I	ENST00000266497		496	Gtc/Atc	10/31	1	2	FACETS	0.181	0.138	0.231	0.181	0.138	0.231	SUBCLONAL	1	TRUE	1	0.79	2		279	280	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123875244	123875244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	17	48	0	ENST00000330479.4:c.200G>A	p.Arg67His	p.R67H	ENST00000330479	NM_020382.3	67	cGt/cAt	3/9	1	2	FACETS	0.878	0.684	1	0.878	0.684	1	CLONAL	1	TRUE	1	0.79	2		48	49	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21340156	21340156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1327974340	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	125	228	0	ENST00000215739.8:c.290G>A	p.Arg97Gln	p.R97Q	ENST00000215739	NM_006767.3	97	cGg/cAg	3/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.79	2		228	285	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729616	41729616	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	155	334	0	ENST00000242208.4:c.913C>A	p.His305Asn	p.H305N	ENST00000242208	NM_002192.2	305	Cat/Aat	3/3	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.79	2		334	391	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181968	38181968	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	188	273	0	ENST00000396334.3:c.592A>G	p.Thr198Ala	p.T198A	ENST00000396334	NM_002468.4	198	Aca/Gca	3/5	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.79	2		273	449	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15838392	15838392	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	97	174	0	ENST00000307771.7:c.890T>C	p.Leu297Pro	p.L297P	ENST00000307771	NM_005089.3	297	cTg/cCg	10/11	1	2	FACETS	0.978	0.887	1	0.978	0.887	1	CLONAL	1	TRUE	1	0.79	2		174	251	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118365108	118365108	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	73	177	0	ENST00000534358.1:c.5284A>G	p.Ile1762Val	p.I1762V	ENST00000534358	NM_005933.3	1762	Att/Gtt	17/36	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.79	2		177	174	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210468	2210468	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	96	268	0	ENST00000398665.3:c.1075G>A	p.Gly359Ser	p.G359S	ENST00000398665	NM_032482.2	359	Ggc/Agc	13/28	1	2	FACETS	0.972	0.881	1	0.972	0.881	1	CLONAL	1	TRUE	1	0.79	2		268	250	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163273	32163273	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	126	306	0	ENST00000375023.3:c.5953T>C	p.Cys1985Arg	p.C1985R	ENST00000375023	NM_004557.3	1985	Tgt/Cgt	30/30	1	2	FACETS	0.837	0.766	0.911	0.837	0.766	0.911	CLONAL	1	TRUE	1	0.79	2		306	381	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21351038	21351038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767013106	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	150	332	1	ENST00000215739.8:c.2273C>T	p.Ala758Val	p.A758V	ENST00000215739	NM_006767.3	758	gCg/gTg	19/21	1	2	FACETS	0.989	0.915	1	0.989	0.915	1	CLONAL	1	TRUE	1	0.79	2		333	384	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62323153	62323153	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751636582	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	123	207	0	ENST00000360203.5:c.2615G>A	p.Arg872Gln	p.R872Q	ENST00000360203	NM_001283009.1	872	cGa/cAa	28/35	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.79	2		207	275	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1936913	1936913	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	138	228	0	ENST00000382891.5:c.1598A>G	p.Gln533Arg	p.Q533R	ENST00000382891	NM_133335.3	533	cAg/cGg	7/22	1	2	FACETS	0.905	0.833	0.979	0.905	0.833	0.979	CLONAL	1	TRUE	1	0.79	2		228	386	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562726	21562726	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	126	309	0	ENST00000382592.4:c.1193C>A	p.Pro398His	p.P398H	ENST00000382592	NM_014572.2	398	cCt/cAt	4/8	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.79	2		309	314	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140324	50140324	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	23	263	0	ENST00000246792.3:c.217G>T	p.Asp73Tyr	p.D73Y	ENST00000246792	NM_006270.3	73	Gat/Tat	2/6	1	2	FACETS	0.178	0.138	0.224	0.178	0.138	0.224	SUBCLONAL	1	TRUE	1	0.79	2		263	327	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191139	185191139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs994247483	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	124	290	0	ENST00000265026.3:c.2020G>A	p.Gly674Ser	p.G674S	ENST00000265026	NM_004721.4	674	Ggc/Agc	11/14	1	2	FACETS	0.937	0.859	1	0.937	0.859	1	CLONAL	1	TRUE	1	0.79	2		290	335	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984840	72984840	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	152	269	0	ENST00000268489.5:c.2744T>C	p.Met915Thr	p.M915T	ENST00000268489	NM_006885.3	915	aTg/aCg	3/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.79	2		269	336	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986486	36986486	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	110	295	0	ENST00000354822.5:c.1203G>A	p.Trp401Ter	p.W401*	ENST00000354822	NM_001079668.2	401	tgG/tgA	3/3	1	2	FACETS	0.977	0.892	1	0.977	0.892	1	CLONAL	1	TRUE	1	0.79	2		295	285	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271584	26271584	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	160	336	0	ENST00000305910.3:c.29A>G	p.Lys10Arg	p.K10R	ENST00000305910	NM_003534.2	10	aAg/aGg	1/1	1	2	FACETS	0.921	0.853	0.99	0.921	0.853	0.99	CLONAL	1	TRUE	1	0.79	2		336	440	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78882729	78882729	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	112	206	0	ENST00000306801.3:c.2520G>T	p.Lys840Asn	p.K840N	ENST00000306801	NM_020761.2	840	aaG/aaT	21/34	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.79	2		206	279	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62305396	62305396	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202157063	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	157	334	0	ENST00000360203.5:c.869C>T	p.Ala290Val	p.A290V	ENST00000360203	NM_001283009.1	290	gCg/gTg	10/35	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.79	2		334	367	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247270	153247270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	60	268	0	ENST00000281708.4:c.1532G>A	p.Gly511Asp	p.G511D	ENST00000281708	NM_033632.3	511	gGc/gAc	10/12	1	2	FACETS	0.415	0.359	0.475	0.415	0.359	0.475	SUBCLONAL	1	TRUE	1	0.79	2		268	366	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828356	72828356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	155	280	0	ENST00000268489.5:c.8225G>A	p.Gly2742Asp	p.G2742D	ENST00000268489	NM_006885.3	2742	gGc/gAc	9/10	1	2	FACETS	0.974	0.902	1	0.974	0.902	1	CLONAL	1	TRUE	1	0.79	2		280	403	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63661960	63661960	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	151	234	1	ENST00000279873.7:c.64T>C	p.Tyr22His	p.Y22H	ENST00000279873	NM_032199.2	22	Tac/Cac	2/10	1	2	FACETS	0.902	0.833	0.972	0.902	0.833	0.972	CLONAL	1	TRUE	1	0.79	2		235	424	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525100	9525100	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	141	241	0	ENST00000353224.5:c.1785A>C	p.Lys595Asn	p.K595N	ENST00000353224	NM_177990.2	595	aaA/aaC	8/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.79	2		241	336	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935659	15935659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745396360	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	160	294	0	ENST00000268712.3:c.7274C>T	p.Ala2425Val	p.A2425V	ENST00000268712	NM_006311.3	2425	gCc/gTc	46/46	1	2	FACETS	0.969	0.898	1	0.969	0.898	1	CLONAL	1	TRUE	1	0.79	2		294	418	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599131	28599131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1245263209	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	151	318	0	ENST00000253063.3:c.577G>A	p.Glu193Lys	p.E193K	ENST00000253063	NM_031459.4	193	Gag/Aag	5/10	1	2	FACETS	0.985	0.912	1	0.985	0.912	1	CLONAL	1	TRUE	1	0.79	2		318	388	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940388	13940388	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	79	224	0	ENST00000405192.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000405192	NM_001163147.1	373	tAc/tGc	11/12	1	2	FACETS	0.775	0.691	0.863	0.775	0.691	0.863	SUBCLONAL	1	TRUE	1	0.79	2		224	258	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612810	228612810	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148579172	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	213	435	0	ENST00000366696.1:c.217C>T	p.Arg73Cys	p.R73C	ENST00000366696	NM_003493.2	73	Cgc/Tgc	1/1	1	2	FACETS	0.98	0.919	1	0.98	0.919	1	CLONAL	1	TRUE	1	0.79	2		435	550	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161169	56161169	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	66	186	0	ENST00000399503.3:c.1038C>A	p.Asn346Lys	p.N346K	ENST00000399503	NM_005921.1	346	aaC/aaA	5/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.79	2		186	151	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981462	63981462	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772012460	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	184	355	0	ENST00000398590.3:c.1964C>T	p.Thr655Met	p.T655M	ENST00000398590	NM_001177387.1	655	aCg/aTg	12/14	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.79	2		355	453	SUCCESS
MTAP	4507	MSKCC	GRCh37	9	21818081	21818081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751881433	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	113	221	0	ENST00000380172.4:c.227C>T	p.Ala76Val	p.A76V	ENST00000380172	NM_002451.3	76	gCg/gTg	4/8	1	2	FACETS	0.95	0.868	1	0.95	0.868	1	CLONAL	1	TRUE	1	0.79	2		221	301	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509763	187509763	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs750900612	NA	P-0067930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	36	280	0	ENST00000441802.2:c.13750C>T	p.Gln4584Ter	p.Q4584*	ENST00000441802	NM_005245.3	4584	Cag/Tag	27/27	1	2	FACETS	0.238	0.195	0.285	0.238	0.195	0.285	SUBCLONAL	1	TRUE	1	0.79	2		280	383	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457939	69457939	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1546	100	323	0	ENST00000227507.2:c.339G>A	p.Met113Ile	p.M113I	ENST00000227507	NM_053056.2	113	atG/atA	2/5	0.601702472449219	16	FACETS	1	0.926	1			1	CLONAL	1	TRUE	NA	0.601702472449219	16		323	1646	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143235887	143235887	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	55	205	0	ENST00000262992.4:c.401A>G	p.Lys134Arg	p.K134R	ENST00000262992	NM_001101669.1	134	aAg/aGg	6/24	0.601702472449219	3	FACETS	0.817	0.704	0.939	0.409	0.352	0.47	CLONAL	1	TRUE	1	0.601702472449219	3		205	291	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs760043106	NA	P-0067932-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	96	596	0	ENST00000269305.4:c.584T>G	p.Ile195Ser	p.I195S	ENST00000269305	NM_001126112.2	195	aTc/aGc	6/11	0.421727676890085	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	FALSE	1	0.421727676890085	3		596	256	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584537	187584537	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067932-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	21	475	0	ENST00000441802.2:c.3496C>G	p.Pro1166Ala	p.P1166A	ENST00000441802	NM_005245.3	1166	Cca/Gca	3/27	0.191287543781968	3	FACETS	0.928	0.723	1	0.464	0.361	0.58	INDETERMINATE	1	FALSE	1	0.421727676890085	3		475	130	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589556	67589597	+	inframe_deletion	In_Frame_Del	DEL	ATAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACA	ATAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACA	-	novel	NA	P-0067932-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	56	343	0	ENST00000274335.5:c.1319_1360del	p.Asp440_Thr454delinsAla	p.D440_T454delinsA	ENST00000274335		440	gATAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACAct/gct	10/15	0.421727676890085	3	FACETS	0.946	0.826	1	0.946	0.826	1	CLONAL	2	FALSE	1	0.421727676890085	3		343	170	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061240	38061240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	175	484	0	ENST00000250448.2:c.749C>T	p.Ser250Phe	p.S250F	ENST00000250448	NM_004496.3	250	tCc/tTc	2/2	0.398399678691169	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	3	TRUE	0	0.432716193452153	3		484	316	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0067938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	132	483	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.432716193452153	5	FACETS	1	0.927	1	1	0.927	1	CLONAL	3	TRUE	2	0.432716193452153	5		483	333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0067938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	130	407	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.377569543178642	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	0	0.432716193452153	2		407	297	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553350	41553350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	59	438	0	ENST00000263253.7:c.3439G>A	p.Glu1147Lys	p.E1147K	ENST00000263253	NM_001429.3	1147	Gag/Aag	18/31	0.377569543178642	2	FACETS	0.931	0.807	1	0.465	0.403	0.532	CLONAL	1	TRUE	0	0.432716193452153	2		438	293	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750740	57750740	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	62	330	0	ENST00000274289.3:c.1864C>T	p.Gln622Ter	p.Q622*	ENST00000274289	NM_006622.3	622	Cag/Tag	13/14	0.431318436148582	3	FACETS	0.92	0.798	1	0.46	0.399	0.525	CLONAL	1	TRUE	1	0.432716193452153	3		330	379	SUCCESS
APC	324	MSKCC	GRCh37	5	112177920	112177920	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0067938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	75	375	0	ENST00000257430.4:c.6629C>G	p.Ser2210Ter	p.S2210*	ENST00000257430	NM_000038.5	2210	tCa/tGa	16/16	0.422812197726021	2	FACETS	1	0.905	1	0.514	0.454	0.578	CLONAL	1	TRUE	0	0.432716193452153	2		375	337	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846111	151846111	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1299251851	NA	P-0067938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	200	491	1	ENST00000262189.6:c.12901C>G	p.Pro4301Ala	p.P4301A	ENST00000262189	NM_170606.2	4301	Ccc/Gcc	52/59	0.433410840536217	5	FACETS	0.959	0.896	1	0.959	0.896	1	CLONAL	3	TRUE	2	0.432716193452153	5		492	530	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846118	151846120	+	frameshift_variant	Frame_Shift_Ins	INS	TTT	TTT	GAAG	novel	NA	P-0067938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	177	492	1	ENST00000262189.6:c.12892_12894delinsCTTC	p.Lys4298LeufsTer17	p.K4298Lfs*17	ENST00000262189	NM_170606.2	4298	AAA/CTTC	52/59	0.433410840536217	5	FACETS	0.882	0.819	0.946	0.882	0.819	0.946	CLONAL	3	TRUE	2	0.432716193452153	5		493	510	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007149	152007149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	129	327	0	ENST00000262189.6:c.751G>A	p.Ala251Thr	p.A251T	ENST00000262189	NM_170606.2	251	Gct/Act	6/59	0.433410840536217	5	FACETS	0.956	0.872	1	0.638	0.581	0.696	CLONAL	2	TRUE	2	0.432716193452153	5		327	514	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293430	1293430	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	21	356	0	ENST00000310581.5:c.1571C>A	p.Pro524Gln	p.P524Q	ENST00000310581	NM_198253.2	524	cCa/cAa	2/16	0.433410840536217	5	FACETS	0.507	0.39	0.642	0.169	0.13	0.214	SUBCLONAL	1	TRUE	2	0.432716193452153	5		356	316	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123040837	123040837	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0067938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	50	312	0	ENST00000355640.3:c.1301-1G>C		p.X434_splice	ENST00000355640		434			0.160302579805594	5	FACETS	1	0.94	1	0.402	0.343	0.466	INDETERMINATE	1	TRUE	2	0.432716193452153	5		312	316	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945296	54945296	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	22	171	0	ENST00000312783.6:c.1130T>C	p.Val377Ala	p.V377A	ENST00000312783	NM_198436.1	377	gTa/gCa	10/10	0.374490427080732	5	FACETS	0.776	0.604	0.974	0.194	0.151	0.244	CLONAL	1	TRUE	1	0.432716193452153	5		171	216	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061240	38061240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067938-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	697	484	0	ENST00000250448.2:c.749C>T	p.Ser250Phe	p.S250F	ENST00000250448	NM_004496.3	250	tCc/tTc	2/2	0.861889658565097	5	FACETS	0.992	0.969	1	0.992	0.969	1	CLONAL	4	TRUE	1	0.860826527686973	5		484	935	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0067938-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	551	483	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.861889658565097	5	FACETS	1	0.989	1	1	0.989	1	CLONAL	4	TRUE	1	0.860826527686973	5		483	716	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0067938-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	507	407	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.861889658565097	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.860826527686973	3		407	558	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553350	41553350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067938-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	79	438	0	ENST00000263253.7:c.3439G>A	p.Glu1147Lys	p.E1147K	ENST00000263253	NM_001429.3	1147	Gag/Aag	18/31	0.849853110113219	2	FACETS	0.971	0.874	1	0.486	0.437	0.536	CLONAL	1	TRUE	0	0.860826527686973	2		438	189	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750740	57750740	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067938-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	82	330	0	ENST00000274289.3:c.1864C>T	p.Gln622Ter	p.Q622*	ENST00000274289	NM_006622.3	622	Cag/Tag	13/14	0.861889658565097	3	FACETS	0.93	0.829	1	0.465	0.414	0.518	CLONAL	1	TRUE	1	0.860826527686973	3		330	293	SUCCESS
APC	324	MSKCC	GRCh37	5	112177920	112177920	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0067938-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	100	375	0	ENST00000257430.4:c.6629C>G	p.Ser2210Ter	p.S2210*	ENST00000257430	NM_000038.5	2210	tCa/tGa	16/16	0.855154056789085	2	FACETS	1	0.949	1	0.528	0.482	0.575	CLONAL	1	TRUE	0	0.860826527686973	2		375	220	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846111	151846111	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1299251851	NA	P-0067938-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	671	491	1	ENST00000262189.6:c.12901C>G	p.Pro4301Ala	p.P4301A	ENST00000262189	NM_170606.2	4301	Ccc/Gcc	52/59	0.861889658565097	6	FACETS	0.968	0.94	0.996	0.968	0.94	0.996	CLONAL	4	TRUE	2	0.860826527686973	6		492	1096	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846118	151846120	+	frameshift_variant	Frame_Shift_Ins	INS	TTT	TTT	GAAG	novel	NA	P-0067938-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	613	492	1	ENST00000262189.6:c.12892_12894delinsCTTC	p.Lys4298LeufsTer17	p.K4298Lfs*17	ENST00000262189	NM_170606.2	4298	AAA/CTTC	52/59	0.861889658565097	6	FACETS	0.926	0.897	0.954	0.926	0.897	0.954	CLONAL	4	TRUE	2	0.860826527686973	6		493	1047	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007149	152007149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067938-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	226	327	0	ENST00000262189.6:c.751G>A	p.Ala251Thr	p.A251T	ENST00000262189	NM_170606.2	251	Gct/Act	6/59	0.861889658565097	6	FACETS	1	0.967	1	0.525	0.492	0.56	CLONAL	2	TRUE	2	0.860826527686973	6		327	680	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184041	123184041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1375196362	NA	P-0067938-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	76	364	0	ENST00000218089.9:c.899C>T	p.Ala300Val	p.A300V	ENST00000218089	NM_001042749.1	300	gCg/gTg	11/35	0.375339435130521	4	FACETS	1	0.938	1			1	INDETERMINATE	1	TRUE	NA	0.860826527686973	4		364	301	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420539	49420539	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0067938-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	162	524	0	ENST00000301067.7:c.15210T>G	p.Tyr5070Ter	p.Y5070*	ENST00000301067	NM_003482.3	5070	taT/taG	48/54	1	2	FACETS	0.934	0.867	1	0.934	0.867	1	CLONAL	1	TRUE	1	0.860826527686973	2		524	403	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440134	49440135	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0067938-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	161	485	0	ENST00000301067.7:c.4491_4492del	p.His1497GlnfsTer30	p.H1497Qfs*30	ENST00000301067	NM_003482.3	1497	caCTgt/cagt	16/54	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.860826527686973	2		485	357	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913381	NA	P-0067939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	351	483	1	ENST00000304494.5:c.322G>T	p.Asp108Tyr	p.D108Y	ENST00000304494	NM_000077.4	108	Gat/Tat	2/3	0.543752403725104	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.543752403725104	3		484	500	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439989	56439989	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	125	471	0	ENST00000407977.2:c.603C>G	p.Ile201Met	p.I201M	ENST00000407977		201	atC/atG	6/10	0.457778050697195	3	FACETS	0.856	0.776	0.94	0.428	0.388	0.47	CLONAL	1	TRUE	1	0.543752403725104	3		471	683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579849	7579849	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	224	433	0	ENST00000269305.4:c.64del	p.Leu22TyrfsTer22	p.L22Yfs*22	ENST00000269305	NM_001126112.2	22	Cta/ta	2/11	0.543752403725104	2	FACETS	0.949	0.897	1	0.949	0.897	1	CLONAL	2	TRUE	0	0.543752403725104	2		433	434	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809240	243809240	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs374658863	NA	P-0067939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	41	460	0	ENST00000263826.5:c.384A>G	p.Ile128Met	p.I128M	ENST00000263826	NM_005465.4	128	atA/atG	4/13	0.0766576507733503	6	FACETS	1	0.937	1			1	INDETERMINATE	1	TRUE	NA	0.543752403725104	6		460	250	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602314	10602314	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	283	580	0	ENST00000171111.5:c.1264G>C	p.Asp422His	p.D422H	ENST00000171111	NM_203500.1	422	Gat/Cat	3/6	0.486110922152886	3	FACETS	0.964	0.921	1	0.964	0.921	1	CLONAL	3	TRUE	0	0.543752403725104	3		580	458	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	69061268	69061268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1233273666	NA	P-0067939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	68	221	0	ENST00000487270.1:c.1103C>T	p.Pro368Leu	p.P368L	ENST00000487270	NM_133509.3	368	cCt/cTt	11/11	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.543752403725104	2		221	240	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907689	76907689	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	91	389	0	ENST00000373344.5:c.4472C>G	p.Thr1491Arg	p.T1491R	ENST00000373344	NM_000489.3	1491	aCa/aGa	15/35	0.543752403725104	2	FACETS	0.976	0.875	1	0.488	0.437	0.541	CLONAL	1	TRUE	0	0.543752403725104	2		389	343	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630777	187630777	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	78	522	0	ENST00000441802.2:c.205del	p.Glu69LysfsTer2	p.E69Kfs*2	ENST00000441802	NM_005245.3	69	Gaa/aa	2/27	1	2	FACETS	0.834	0.739	0.935	0.834	0.739	0.935	CLONAL	1	TRUE	1	0.543752403725104	2		522	344	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294131	1294132	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0067939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	167	524	0	ENST00000310581.5:c.869_870del	p.Ser290TrpfsTer248	p.S290Wfs*248	ENST00000310581	NM_198253.2	290	tCT/t	2/16	0.543752403725104	5	FACETS	0.851	0.785	0.92	0.568	0.523	0.613	CLONAL	2	TRUE	2	0.543752403725104	5		524	655	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351683	89351683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	71	514	0	ENST00000301030.4:c.1267G>A	p.Gly423Arg	p.G423R	ENST00000301030	NM_001256183.1	423	Gga/Aga	9/13	0.523651534383922	3	FACETS	0.524	0.457	0.596	0.175	0.152	0.199	SUBCLONAL	1	TRUE	0	0.543752403725104	3		514	634	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47724958	47724958	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0067939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	223	461	0	ENST00000449228.1:c.786G>C	p.Ter262TyrextTer61	p.*262Yext*61	ENST00000449228	NM_001127240.2	262	taG/taC	4/4	0.543752403725104	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.543752403725104	2		461	387	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394382	162394382	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	11	442	0	ENST00000366898.1:c.686T>A	p.Ile229Asn	p.I229N	ENST00000366898	NM_004562.2	229	aTc/aAc	6/12	0.543752403725104	1	FACETS	0.136	0.093	0.188	0.136	0.093	0.188	SUBCLONAL	1	TRUE	0	0.543752403725104	1		442	217	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10257146	10257156	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGGGGATTT	CCTGGGGATTT	-	novel	NA	P-0067939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	157	450	0	ENST00000340748.4:c.2717_2727del	p.Glu906GlyfsTer10	p.E906Gfs*10	ENST00000340748		906	gAAATCCCCAGG/g	27/40	0.486110922152886	3	FACETS	1	0.988	1	0.474	0.437	0.513	CLONAL	1	TRUE	0	0.543752403725104	3		450	516	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790674	89790675	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTGGCTT	novel	NA	P-0067939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	180	502	0	ENST00000336032.3:c.64_70dup	p.Ser24PhefsTer186	p.S24Ffs*186	ENST00000336032	NM_006813.2	21	ctt/cTTGGCTTtt	1/2	0.506521794816139	2	FACETS	0.77	0.718	0.822	0.77	0.718	0.822	SUBCLONAL	2	TRUE	0	0.543752403725104	2		502	430	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597959	43597959	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	44	585	0	ENST00000355710.3:c.507G>T	p.Glu169Asp	p.E169D	ENST00000355710	NM_020975.4	169	gaG/gaT	3/20	0.543752403725104	2	FACETS	0.379	0.318	0.446	0.19	0.159	0.223	SUBCLONAL	1	TRUE	0	0.543752403725104	2		585	427	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713346	40713346	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	58	525	0	ENST00000373198.4:c.4169A>C	p.Glu1390Ala	p.E1390A	ENST00000373198	NM_133170.3	1390	gAg/gCg	30/32	0.373877683216581	3	FACETS	0.447	0.384	0.516	0.149	0.128	0.172	SUBCLONAL	1	TRUE	0	0.543752403725104	3		525	607	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400182	139400182	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1159134576	NA	P-0067939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	85	496	1	ENST00000277541.6:c.4166G>A	p.Ser1389Asn	p.S1389N	ENST00000277541	NM_017617.3	1389	aGc/aAc	25/34	1	2	FACETS	0.689	0.611	0.771	0.689	0.611	0.771	SUBCLONAL	1	TRUE	1	0.543752403725104	2		497	454	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0067960-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	375	313	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.3	6	FACETS	0.978	0.933	1	1	0.992	1	CLONAL	6	TRUE	1	0.21	6		313	864	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509360	46509360	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067960-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	72	507	0	ENST00000262741.5:c.1371del	p.Ser458ArgfsTer33	p.S458Rfs*33	ENST00000262741	NM_003629.3	457	ccC/cc	10/10	0.241174090209809	3	FACETS	1	0.951	1	0.592	0.517	0.673	CLONAL	1	TRUE	1	0.21	3		507	640	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983013	149983013	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067960-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	51	494	0	ENST00000253339.5:c.3245G>C	p.Arg1082Thr	p.R1082T	ENST00000253339		1082	aGg/aCg	7/7	0.3	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.21	1		494	352	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15976857	15976857	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067960-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	19	308	0	ENST00000268712.3:c.3697A>G	p.Arg1233Gly	p.R1233G	ENST00000268712	NM_006311.3	1233	Agg/Ggg	28/46	1	2	FACETS	0.665	0.505	0.853	0.665	0.505	0.853	SUBCLONAL	1	TRUE	1	0.21	2		308	272	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0067966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	350	597	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.736499524234296	3	FACETS	1	0.981	1	0.537	0.509	0.567	CLONAL	1	TRUE	1	0.74	3		597	1206	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912660	NA	P-0067966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	42	671	0	ENST00000269305.4:c.839G>T	p.Arg280Ile	p.R280I	ENST00000269305	NM_001126112.2	280	aGa/aTa	8/11	1	2	FACETS	0.111	0.092	0.133	0.111	0.092	0.133	SUBCLONAL	1	TRUE	1	0.74	2		671	1019	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519833	29519833	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	55	609	0	ENST00000389048.3:c.1738del	p.Met580TrpfsTer11	p.M580Wfs*11	ENST00000389048	NM_004304.4	580	Atg/tg	9/29	1	2	FACETS	0.152	0.129	0.177	0.152	0.129	0.177	SUBCLONAL	1	TRUE	1	0.74	2		609	977	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044923	47044923	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	30	363	0	ENST00000377604.3:c.2249del	p.Glu750GlyfsTer52	p.E750Gfs*52	ENST00000377604	NM_001204468.1	750	gAg/gg	20/24	1	1	FACETS	0.103	0.083	0.127	0.103	0.083	0.127	SUBCLONAL	1	TRUE	0	0.74	1		363	494	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600408	10600408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1412883238	NA	P-0067967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	80	654	0	ENST00000171111.5:c.1447C>T	p.Arg483Cys	p.R483C	ENST00000171111	NM_203500.1	483	Cgc/Tgc	4/6	0.143073093571413	0	FACETS	0.315	0.28	0.352			1	INDETERMINATE	1	TRUE	0	0.62	0		654	311	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17354324	17354324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	55	511	0	ENST00000375499.3:c.460G>A	p.Glu154Lys	p.E154K	ENST00000375499	NM_003000.2	154	Gag/Aag	5/8	1	2	FACETS	0.939	0.816	1	0.939	0.816	1	CLONAL	1	TRUE	1	0.62	2		511	189	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164972	47164972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1012081309	NA	P-0067967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	74	550	0	ENST00000409792.3:c.1154G>A	p.Arg385Lys	p.R385K	ENST00000409792	NM_014159.6	385	aGa/aAa	3/21	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.62	2		550	227	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1040386	1040386	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	80	416	0	ENST00000358495.3:c.186G>C	p.Lys62Asn	p.K62N	ENST00000358495	NM_134424.2	62	aaG/aaC	3/12	1	2	FACETS	0.981	0.875	1	0.981	0.875	1	CLONAL	1	TRUE	1	0.62	2		416	263	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878933	151878933	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	84	558	0	ENST00000262189.6:c.6012del	p.Ser2004ArgfsTer28	p.S2004Rfs*28	ENST00000262189	NM_170606.2	2004	agT/ag	36/59	1	2	FACETS	0.961	0.859	1	0.961	0.859	1	CLONAL	1	TRUE	1	0.62	2		558	282	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874024	151874025	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	52	618	0	ENST00000262189.6:c.8513_8514insT	p.Glu2838AspfsTer3	p.E2838Dfs*3	ENST00000262189	NM_170606.2	2838	gaa/gaTa	38/59	1	2	FACETS	0.948	0.821	1	0.948	0.821	1	CLONAL	1	TRUE	1	0.62	2		618	177	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141568614	141568614	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs755874332	NA	P-0067967-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	134	512	0	ENST00000220592.5:c.848A>G	p.Asn283Ser	p.N283S	ENST00000220592	NM_012154.3	283	aAt/aGt	7/19	1	2	FACETS	0.681	0.623	0.742	0.681	0.623	0.742	SUBCLONAL	1	TRUE	1	0.81613056764583	2		512	482	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347524	118347540	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAAAGTGACTCATCA	AAGAAAGTGACTCATCA	-	novel	NA	P-0067967-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	127	447	0	ENST00000534358.1:c.3161_3177del	p.Gln1054ArgfsTer10	p.Q1054Rfs*10	ENST00000534358	NM_005933.3	1054	cAAGAAAGTGACTCATCA/c	4/36	0.12212143245565	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.81613056764583	0		447	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0067968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	72	426	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.3614352602866	2		426	359	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0067968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	17	409	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.324798455824883	1	FACETS	0.445	0.334	0.576	0.445	0.334	0.576	SUBCLONAL	1	TRUE	0	0.3614352602866	1		410	173	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0067968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	9	317	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	1	2	FACETS	0.145	0.095	0.209	0.145	0.095	0.209	SUBCLONAL	1	TRUE	1	0.3614352602866	2		317	344	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413072	139413072	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	63	522	0	ENST00000277541.6:c.1070T>C	p.Phe357Ser	p.F357S	ENST00000277541	NM_017617.3	357	tTc/tCc	6/34	0.3614352602866	1	FACETS	0.863	0.751	0.982	0.863	0.751	0.982	CLONAL	1	TRUE	0	0.3614352602866	1		522	331	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628314	187628314	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	21	537	0	ENST00000441802.2:c.2668G>C	p.Glu890Gln	p.E890Q	ENST00000441802	NM_005245.3	890	Gag/Cag	2/27	0.3614352602866	1	FACETS	0.27	0.208	0.344	0.27	0.208	0.344	SUBCLONAL	1	TRUE	0	0.3614352602866	1		537	352	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59871091	59871091	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0067968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	36	402	0	ENST00000259008.2:c.1341-1G>A		p.X447_splice	ENST00000259008	NM_032043.2	447			1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.3614352602866	2		402	189	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443643	49443643	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	60	576	0	ENST00000301067.7:c.3728G>T	p.Gly1243Val	p.G1243V	ENST00000301067	NM_003482.3	1243	gGg/gTg	11/54	1	2	FACETS	0.808	0.698	0.926	0.808	0.698	0.926	CLONAL	1	TRUE	1	0.3614352602866	2		576	411	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639969	3639969	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	48	550	0	ENST00000294008.3:c.3670G>T	p.Glu1224Ter	p.E1224*	ENST00000294008	NM_032444.2	1224	Gag/Tag	12/15	0.11444098366341	0	FACETS	0.493	0.418	0.575			1	INDETERMINATE	1	TRUE	0	0.3614352602866	0		550	344	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281500	198281500	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	55	484	0	ENST00000335508.6:c.631A>G	p.Thr211Ala	p.T211A	ENST00000335508	NM_012433.2	211	Act/Gct	6/25	1	2	FACETS	0.665	0.569	0.768	0.665	0.569	0.768	SUBCLONAL	1	TRUE	1	0.3614352602866	2		484	458	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151919134	151919134	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	33	444	0	ENST00000262189.6:c.3451T>C	p.Cys1151Arg	p.C1151R	ENST00000262189	NM_170606.2	1151	Tgt/Cgt	22/59	0.3614352602866	1	FACETS	0.901	0.743	1	0.901	0.743	1	CLONAL	1	TRUE	0	0.3614352602866	1		444	166	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512304	120512304	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	84	677	0	ENST00000256646.2:c.938del	p.Gly313AlafsTer83	p.G313Afs*83	ENST00000256646	NM_024408.3	313	gGc/gc	6/34	0.11444098366341	0	FACETS	0.658	0.584	0.737			1	INDETERMINATE	1	TRUE	0	0.3614352602866	0		677	451	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979286	40979286	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	176	473	0	ENST00000373198.4:c.1847C>A	p.Ser616Tyr	p.S616Y	ENST00000373198	NM_133170.3	616	tCc/tAc	11/32	0.238197137801498	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.3614352602866	2		473	473	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426325	49426325	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	52	590	0	ENST00000301067.7:c.12163C>A	p.Pro4055Thr	p.P4055T	ENST00000301067	NM_003482.3	4055	Cct/Act	39/54	1	2	FACETS	0.666	0.568	0.773	0.666	0.568	0.773	SUBCLONAL	1	TRUE	1	0.3614352602866	2		590	432	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481674	56481674	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	76	670	0	ENST00000267101.3:c.709G>T	p.Gly237Cys	p.G237C	ENST00000267101	NM_001982.3	237	Ggc/Tgc	6/28	1	2	FACETS	0.883	0.777	0.997	0.883	0.777	0.997	CLONAL	1	TRUE	1	0.3614352602866	2		670	476	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436231	110436231	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	39	560	0	ENST00000375856.3:c.2170G>T	p.Gly724Trp	p.G724W	ENST00000375856	NM_003749.2	724	Ggg/Tgg	1/2	0.150365360003804	0	FACETS	0.436	0.363	0.517			1	INDETERMINATE	1	TRUE	0	0.3614352602866	0		560	316	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0067968-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	148	156	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.652184257711599	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.698651380831138	2		156	205	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682691	86682691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067968-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	26	139	0	ENST00000274376.6:c.2896C>T	p.Arg966Cys	p.R966C	ENST00000274376	NM_002890.2	966	Cgt/Tgt	23/25	0.698651380831138	1	FACETS	0.757	0.625	0.894	0.757	0.625	0.894	SUBCLONAL	1	TRUE	0	0.698651380831138	1		139	64	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841253	15841253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375322183	NA	P-0067968-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	135	88	0	ENST00000307771.7:c.1337G>A	p.Arg446Gln	p.R446Q	ENST00000307771	NM_005089.3	446	cGg/cAg	11/11	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.698651380831138	1		88	171	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248787	212248787	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0067968-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	46	115	0	ENST00000342788.4:c.3482-2A>G		p.X1161_splice	ENST00000342788	NM_005235.2	1161			0.353319850905683	1	FACETS	0.832	0.725	0.94	0.832	0.725	0.94	INDETERMINATE	1	TRUE	0	0.698651380831138	1		115	103	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433707	49433707	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067968-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	91	255	0	ENST00000301067.7:c.7846del	p.Leu2616CysfsTer75	p.L2616Cfs*75	ENST00000301067	NM_003482.3	2616	Ctg/tg	31/54	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.698651380831138	2		255	218	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431339	49431339	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067968-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	49	210	0	ENST00000301067.7:c.9800C>A	p.Ser3267Ter	p.S3267*	ENST00000301067	NM_003482.3	3267	tCa/tAa	34/54	1	2	FACETS	0.626	0.536	0.723	0.626	0.536	0.723	SUBCLONAL	1	TRUE	1	0.698651380831138	2		210	224	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395222	139395222	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779880917	NA	P-0067968-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	54	223	0	ENST00000277541.6:c.5716G>A	p.Ala1906Thr	p.A1906T	ENST00000277541	NM_017617.3	1906	Gcg/Acg	31/34	0.698651380831138	1	FACETS	0.585	0.509	0.665	0.585	0.509	0.665	SUBCLONAL	1	TRUE	0	0.698651380831138	1		223	172	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508393	106508393	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs780713089	NA	P-0067968-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	112	191	0	ENST00000359195.3:c.387C>A	p.His129Gln	p.H129Q	ENST00000359195	NM_002649.2	129	caC/caA	2/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.698651380831138	2		191	278	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225629	26225629	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067968-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	131	248	0	ENST00000360408.1:c.247C>A	p.Leu83Met	p.L83M	ENST00000360408	NM_003532.2	83	Ctg/Atg	1/1	1	2	FACETS	0.972	0.891	1	0.972	0.891	1	CLONAL	1	TRUE	1	0.698651380831138	2		248	386	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536247	106536247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067968-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	61	168	0	ENST00000369096.4:c.214G>A	p.Asp72Asn	p.D72N	ENST00000369096	NM_001198.3	72	Gat/Aat	2/7	1	2	FACETS	0.592	0.515	0.674	0.592	0.515	0.674	SUBCLONAL	1	TRUE	1	0.698651380831138	2		168	295	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867498	35867498	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1337027587	NA	P-0067968-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	42	118	0	ENST00000303115.3:c.312G>C	p.Lys104Asn	p.K104N	ENST00000303115	NM_002185.3	104	aaG/aaC	3/8	1	2	FACETS	0.977	0.837	1	0.977	0.837	1	CLONAL	1	TRUE	1	0.698651380831138	2		118	123	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825553	50825553	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067968-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	33	133	0	ENST00000398568.2:c.2184G>T	p.Gln728His	p.Q728H	ENST00000398568	NM_001042412.1	728	caG/caT	14/18	1	2	FACETS	0.843	0.703	0.994	0.843	0.703	0.994	CLONAL	1	TRUE	1	0.698651380831138	2		133	112	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376613	118376613	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067968-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	103	199	0	ENST00000534358.1:c.10006G>T	p.Gly3336Cys	p.G3336C	ENST00000534358	NM_005933.3	3336	Ggc/Tgc	27/36	0.353319850905683	1	FACETS	0.764	0.696	0.833	0.764	0.696	0.833	INDETERMINATE	1	TRUE	0	0.698651380831138	1		199	251	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858446	27858446	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067968-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	121	223	0	ENST00000359303.2:c.125A>G	p.Tyr42Cys	p.Y42C	ENST00000359303	NM_003535.2	42	tAc/tGc	1/1	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.698651380831138	2		223	325	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068923	30068923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067968-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	23	129	0	ENST00000331968.5:c.2006T>C	p.Met669Thr	p.M669T	ENST00000331968	NM_002742.2	669	aTg/aCg	14/18	1	2	FACETS	0.604	0.479	0.743	0.604	0.479	0.743	SUBCLONAL	1	TRUE	1	0.698651380831138	2		129	109	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0067969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	260	403	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.517798215752871	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.51818701632144	2		404	438	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0067970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	22	288	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.742	0.576	0.933	0.742	0.576	0.933	CLONAL	1	TRUE	1	0.242072632792305	2		288	245	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0067970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	37	425	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.878	0.726	1	0.878	0.726	1	CLONAL	1	TRUE	1	0.242072632792305	2		425	348	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413009	49413009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519953	NA	P-0067970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	49	429	0	ENST00000418115.1:c.14G>A	p.Arg5Gln	p.R5Q	ENST00000418115	NM_001664.2	5	cGg/cAg	2/5	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.242072632792305	2		429	382	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129840	55129840	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1167372221	NA	P-0067970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	22	592	0	ENST00000257290.5:c.374A>T	p.Asp125Val	p.D125V	ENST00000257290	NM_006206.4	125	gAt/gTt	4/23	1	2	FACETS	0.608	0.471	0.766	0.608	0.471	0.766	SUBCLONAL	1	TRUE	1	0.242072632792305	2		592	299	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212680	36212680	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	40	517	0	ENST00000222270.7:c.2431C>T	p.Gln811Ter	p.Q811*	ENST00000222270	NM_014727.1	811	Cag/Tag	3/37	1	2	FACETS	0.879	0.732	1	0.879	0.732	1	CLONAL	1	TRUE	1	0.242072632792305	2		517	376	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448390	56448390	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	28	593	0	ENST00000407977.2:c.257A>G	p.His86Arg	p.H86R	ENST00000407977		86	cAc/cGc	3/10	1	2	FACETS	0.636	0.508	0.781	0.636	0.508	0.781	SUBCLONAL	1	TRUE	1	0.242072632792305	2		593	364	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108098	30108098	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	17	366	0	ENST00000331968.5:c.709T>A	p.Ser237Thr	p.S237T	ENST00000331968	NM_002742.2	237	Tca/Aca	5/18	1	2	FACETS	0.532	0.397	0.692	0.532	0.397	0.692	SUBCLONAL	1	TRUE	1	0.242072632792305	2		366	264	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	140	813	7	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.848	0.776	0.924	0.848	0.776	0.924	CLONAL	1	TRUE	1	0.58	2		820	569	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	114	288	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.58	2		288	343	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	22	586	2	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.28	0.217	0.353	0.28	0.217	0.353	SUBCLONAL	1	TRUE	1	0.58	2		588	271	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	17	256	3	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	0.399	0.3	0.515	0.399	0.3	0.515	SUBCLONAL	1	TRUE	1	0.58	2		259	147	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	121	711	1	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.848	0.77	0.929	0.848	0.77	0.929	CLONAL	1	TRUE	1	0.58	2		712	492	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	37	187	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.851	0.713	0.999	0.851	0.713	0.999	CLONAL	1	TRUE	1	0.58	2		187	150	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	324	707	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.876	0.835	0.916	1	0.996	1	CLONAL	2	TRUE	1	0.58	2		711	638	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	145	773	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.58	2		773	492	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	134	400	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.58	2		400	418	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357069	70357069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200279192	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	174	318	0	ENST00000374080.3:c.5584C>T	p.Arg1862Cys	p.R1862C	ENST00000374080		1862	Cgc/Tgc	39/45	1	1	FACETS	0.792	0.749	0.834	1	0.993	1	SUBCLONAL	2	TRUE	0	0.58	1		318	269	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654642	67654642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	62	508	0	ENST00000264010.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000264010	NM_006565.3	377	Cgt/Tgt	6/12	1	2	FACETS	0.398	0.344	0.457	0.398	0.344	0.457	SUBCLONAL	1	TRUE	1	0.58	2		508	537	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	111	585	1	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	1	2	FACETS	0.886	0.802	0.974	0.886	0.802	0.974	CLONAL	1	TRUE	1	0.58	2		586	432	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	96	351	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	0.887	0.797	0.982	0.887	0.797	0.982	CLONAL	1	TRUE	1	0.58	2		351	373	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440943	56440943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786205215	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	176	241	0	ENST00000407977.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000407977		132	Cga/Tga	4/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.58	2		241	522	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582120	189582120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	169	607	1	ENST00000264731.3:c.679G>A	p.Ala227Thr	p.A227T	ENST00000264731	NM_003722.4	227	Gcc/Acc	5/14	1	2	FACETS	0.989	0.914	1	0.989	0.914	1	CLONAL	1	TRUE	1	0.58	2		608	589	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942685	48942685	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913301	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	73	276	0	ENST00000267163.4:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000267163	NM_000321.2	358	Cga/Tga	11/27	1	2	FACETS	0.767	0.676	0.864	0.767	0.676	0.864	SUBCLONAL	1	TRUE	1	0.58	2		276	328	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256956	41256956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357209	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	28	408	0	ENST00000357654.3:c.230C>T	p.Thr77Met	p.T77M	ENST00000357654	NM_007294.3	77	aCg/aTg	5/23	1	2	FACETS	0.255	0.204	0.314	0.255	0.204	0.314	SUBCLONAL	1	TRUE	1	0.58	2		408	378	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	107	573	5	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.887	0.801	0.976	0.887	0.801	0.976	CLONAL	1	TRUE	1	0.58	2		578	416	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513527	149513527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	120	606	0	ENST00000261799.4:c.676C>T	p.Arg226Cys	p.R226C	ENST00000261799	NM_002609.3	226	Cgc/Tgc	5/23	1	2	FACETS	0.922	0.838	1	0.922	0.838	1	CLONAL	1	TRUE	1	0.58	2		606	449	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856553	111856553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	98	688	0	ENST00000341259.2:c.604C>T	p.Arg202Cys	p.R202C	ENST00000341259	NM_005475.2	202	Cgc/Tgc	2/8	0.198192463069365	3	FACETS	1	0.974	1	0.63	0.567	0.695	INDETERMINATE	1	TRUE	1	0.58	3		688	346	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741492	17741492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	114	596	0	ENST00000250003.3:c.163G>A	p.Ala55Thr	p.A55T	ENST00000250003	NM_002478.4	55	Gcg/Acg	1/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.58	2		596	337	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271208	38271208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765900637	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	73	517	1	ENST00000425967.3:c.2500G>A	p.Glu834Lys	p.E834K	ENST00000425967	NM_001174067.1	834	Gag/Aag	19/19	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.58	2		518	235	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285832	198285832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775351918	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	101	478	0	ENST00000335508.6:c.221C>T	p.Thr74Met	p.T74M	ENST00000335508	NM_012433.2	74	aCg/aTg	3/25	1	2	FACETS	0.898	0.809	0.99	0.898	0.809	0.99	CLONAL	1	TRUE	1	0.58	2		478	388	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181311	123181311	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs774761933	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	99	207	0	ENST00000218089.9:c.775C>T	p.Arg259Ter	p.R259*	ENST00000218089	NM_001042749.1	259	Cga/Tga	9/35	1	1	FACETS	0.757	0.701	0.812	1	0.987	1	SUBCLONAL	2	TRUE	0	0.58	1		207	160	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931468	131931468	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369560280	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	62	455	1	ENST00000265335.6:c.2173C>T	p.Arg725Trp	p.R725W	ENST00000265335		725	Cgg/Tgg	13/25	1	2	FACETS	0.433	0.374	0.496	0.433	0.374	0.496	SUBCLONAL	1	TRUE	1	0.58	2		456	494	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437427	110437427	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	84	539	0	ENST00000375856.3:c.974A>G	p.His325Arg	p.H325R	ENST00000375856	NM_003749.2	325	cAc/cGc	1/2	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.58	2		539	280	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249393	110249393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747114701	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	145	708	0	ENST00000374672.4:c.1180G>A	p.Ala394Thr	p.A394T	ENST00000374672	NM_004235.4	394	Gcc/Acc	4/5	1	2	FACETS	0.969	0.89	1	0.969	0.89	1	CLONAL	1	TRUE	1	0.58	2		708	516	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070923	30070923	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145666157	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	106	548	0	ENST00000338641.4:c.1439C>T	p.Thr480Met	p.T480M	ENST00000338641	NM_000268.3	480	aCg/aTg	13/16	1	2	FACETS	0.988	0.894	1	0.988	0.894	1	CLONAL	1	TRUE	1	0.58	2		548	370	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137271	64137271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	116	727	0	ENST00000334205.4:c.1703C>T	p.Thr568Met	p.T568M	ENST00000334205	NM_003942.2	568	aCg/aTg	14/17	1	2	FACETS	0.983	0.893	1	0.983	0.893	1	CLONAL	1	TRUE	1	0.58	2		727	407	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163377	47163377	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	40	523	0	ENST00000409792.3:c.2749del	p.Ser917ValfsTer5	p.S917Vfs*5	ENST00000409792	NM_014159.6	917	Agt/gt	3/21	1	2	FACETS	0.366	0.304	0.434	0.366	0.304	0.434	SUBCLONAL	1	TRUE	1	0.58	2		523	377	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589576	67589576	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1289537429	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	85	411	0	ENST00000274335.5:c.1344del	p.Lys448AsnfsTer32	p.K448Nfs*32	ENST00000274335		447	Aaa/aa	10/15	1	2	FACETS	0.922	0.823	1	0.922	0.823	1	CLONAL	1	TRUE	1	0.58	2		411	318	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119767	70119767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	18	586	0	ENST00000245479.2:c.769C>T	p.Arg257Cys	p.R257C	ENST00000245479	NM_000346.3	257	Cgc/Tgc	3/3	1	2	FACETS	0.195	0.146	0.252	0.195	0.146	0.252	SUBCLONAL	1	TRUE	1	0.58	2		586	319	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	92	637	1	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	1	2	FACETS	0.764	0.683	0.85	0.764	0.683	0.85	SUBCLONAL	1	TRUE	1	0.58	2		638	415	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495715	56495715	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	114	604	0	ENST00000267101.3:c.3910del	p.His1304MetfsTer7	p.H1304Mfs*7	ENST00000267101	NM_001982.3	1302	gCc/gc	28/28	0.198192463069365	3	FACETS	1	0.973	1	0.599	0.544	0.657	INDETERMINATE	1	TRUE	1	0.58	3		604	423	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209267	133209267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs5745021	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	103	709	0	ENST00000320574.5:c.6119C>T	p.Ala2040Val	p.A2040V	ENST00000320574	NM_006231.2	2040	gCg/gTg	44/49	1	2	FACETS	0.92	0.83	1	0.92	0.83	1	CLONAL	1	TRUE	1	0.58	2		709	386	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346613	89346613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370535812	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	127	681	0	ENST00000301030.4:c.6337G>A	p.Gly2113Ser	p.G2113S	ENST00000301030	NM_001256183.1	2113	Ggc/Agc	9/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.58	2		681	365	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917610	151917610	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	36	293	0	ENST00000262189.6:c.3710G>A	p.Arg1237Gln	p.R1237Q	ENST00000262189	NM_170606.2	1237	cGa/cAa	23/59	1	2	FACETS	0.552	0.457	0.656	0.552	0.457	0.656	SUBCLONAL	1	TRUE	1	0.58	2		293	225	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522059	157522059	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770643408	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	147	768	0	ENST00000346085.5:c.4331C>T	p.Pro1444Leu	p.P1444L	ENST00000346085	NM_020732.3	1444	cCg/cTg	18/20	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.58	2		768	502	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268382	198268382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	112	488	0	ENST00000335508.6:c.1646G>A	p.Arg549His	p.R549H	ENST00000335508	NM_012433.2	549	cGt/cAt	12/25	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.58	2		488	376	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352576	89352576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762710349	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	43	517	0	ENST00000301030.4:c.763C>T	p.Arg255Trp	p.R255W	ENST00000301030	NM_001256183.1	255	Cgg/Tgg	8/13	1	2	FACETS	0.377	0.316	0.445	0.377	0.316	0.445	SUBCLONAL	1	TRUE	1	0.58	2		517	393	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317159	11317159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	30	686	0	ENST00000361445.4:c.335G>A	p.Arg112Gln	p.R112Q	ENST00000361445	NM_004958.3	112	cGg/cAg	4/58	1	2	FACETS	0.242	0.194	0.296	0.242	0.194	0.296	SUBCLONAL	1	TRUE	1	0.58	2		686	428	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597990	43597990	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs76449634	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	128	736	1	ENST00000355710.3:c.538C>T	p.Arg180Ter	p.R180*	ENST00000355710	NM_020975.4	180	Cga/Tga	3/20	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.58	2		737	434	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526792	31526792	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	95	489	1	ENST00000344624.3:c.248del	p.Pro83HisfsTer25	p.P83Hfs*25	ENST00000344624		83	cCa/ca	2/33	1	2	FACETS	0.996	0.896	1	0.996	0.896	1	CLONAL	1	TRUE	1	0.58	2		490	329	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570799	226570799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1407958928	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	61	741	0	ENST00000366794.5:c.1097C>T	p.Ala366Val	p.A366V	ENST00000366794	NM_001618.3	366	gCg/gTg	8/23	1	2	FACETS	0.335	0.289	0.385	0.335	0.289	0.385	SUBCLONAL	1	TRUE	1	0.58	2		741	628	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155301	185155301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140999720	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	165	532	0	ENST00000265026.3:c.542C>T	p.Ala181Val	p.A181V	ENST00000265026	NM_004721.4	181	gCg/gTg	3/14	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.58	2		532	549	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502242	157502242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	55	638	0	ENST00000346085.5:c.3275C>T	p.Ala1092Val	p.A1092V	ENST00000346085	NM_020732.3	1092	gCc/gTc	12/20	1	2	FACETS	0.34	0.291	0.395	0.34	0.291	0.395	SUBCLONAL	1	TRUE	1	0.58	2		638	557	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213366	36213366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866223177	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	113	675	0	ENST00000222270.7:c.2563C>T	p.Arg855Trp	p.R855W	ENST00000222270	NM_014727.1	855	Cgg/Tgg	4/37	1	2	FACETS	0.923	0.837	1	0.923	0.837	1	CLONAL	1	TRUE	1	0.58	2		675	422	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199813	138199813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1373396587	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	133	719	0	ENST00000237289.4:c.1231C>T	p.Arg411Trp	p.R411W	ENST00000237289	NM_001270507.1	411	Cgg/Tgg	7/9	1	2	FACETS	0.767	0.699	0.838	0.767	0.699	0.838	SUBCLONAL	1	TRUE	1	0.58	2		719	598	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813315	102813315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761462868	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	138	726	1	ENST00000307046.8:c.374G>A	p.Arg125His	p.R125H	ENST00000307046	NM_001111285.1	125	cGc/cAc	3/4	0.198192463069365	3	FACETS	1	0.982	1	0.634	0.581	0.689	INDETERMINATE	1	TRUE	1	0.58	3		727	484	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15938168	15938168	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775915024	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	108	538	0	ENST00000268712.3:c.7046G>A	p.Arg2349Gln	p.R2349Q	ENST00000268712	NM_006311.3	2349	cGg/cAg	45/46	1	2	FACETS	0.715	0.644	0.789	0.715	0.644	0.789	SUBCLONAL	1	TRUE	1	0.58	2		538	521	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522560	176522560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201831200	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	111	758	0	ENST00000292408.4:c.1657G>A	p.Ala553Thr	p.A553T	ENST00000292408	NM_213647.1	553	Gcc/Acc	13/18	1	2	FACETS	0.934	0.846	1	0.934	0.846	1	CLONAL	1	TRUE	1	0.58	2		758	410	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81927346	81927346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	98	441	0	ENST00000359376.3:c.1019C>T	p.Ser340Leu	p.S340L	ENST00000359376	NM_002661.3	340	tCg/tTg	12/33	1	2	FACETS	0.934	0.84	1	0.934	0.84	1	CLONAL	1	TRUE	1	0.58	2		441	362	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31464360	31464360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755033541	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	115	540	0	ENST00000344624.3:c.2557C>T	p.Arg853Cys	p.R853C	ENST00000344624		853	Cgt/Tgt	17/33	0.157938377599221	1	FACETS	0.62	0.562	0.681	0.62	0.562	0.681	INDETERMINATE	1	TRUE	0	0.58	1		540	454	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985524	60985524	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	141	692	1	ENST00000333681.4:c.376G>A	p.Ala126Thr	p.A126T	ENST00000333681		126	Gcg/Acg	2/3	1	2	FACETS	0.916	0.839	0.995	0.916	0.839	0.995	CLONAL	1	TRUE	1	0.58	2		693	531	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691872	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs79375991	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	220	578	15	ENST00000295754.5:c.383del	p.Lys128SerfsTer35	p.K128Sfs*35	ENST00000295754	NM_003242.5	125	gAa/ga	3/7	1	2	FACETS	0.756	0.71	0.801	1	0.993	1	SUBCLONAL	2	TRUE	1	0.58	2		593	502	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	158	688	1	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.58	2		689	491	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759811	133759811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1312773585	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	31	617	0	ENST00000318560.5:c.2134C>T	p.Arg712Cys	p.R712C	ENST00000318560	NM_005157.4	712	Cgc/Tgc	11/11	1	2	FACETS	0.355	0.288	0.431	0.355	0.288	0.431	SUBCLONAL	1	TRUE	1	0.58	2		617	301	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29279846	29279846	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	20	104	0	ENST00000544604.2:c.92del	p.Leu31ArgfsTer91	p.L31Rfs*91	ENST00000544604	NM_001206998.1	31	cTg/cg	1/9	1	2	FACETS	0.519	0.401	0.653	0.519	0.401	0.653	SUBCLONAL	1	TRUE	1	0.58	2		104	133	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29383127	29383127	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	144	662	0	ENST00000544604.2:c.364G>T	p.Gly122Ter	p.G122*	ENST00000544604	NM_001206998.1	122	Gga/Tga	2/9	1	2	FACETS	0.977	0.897	1	0.977	0.897	1	CLONAL	1	TRUE	1	0.58	2		662	508	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020669	37020669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	112	540	0	ENST00000358127.4:c.176G>A	p.Arg59Gln	p.R59Q	ENST00000358127	NM_001280556.1	59	cGg/cAg	2/10	1	2	FACETS	0.92	0.833	1	0.92	0.833	1	CLONAL	1	TRUE	1	0.58	2		540	420	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943411	17943411	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	122	668	0	ENST00000458235.1:c.2597G>T	p.Arg866Met	p.R866M	ENST00000458235	NM_000215.3	866	aGg/aTg	19/24	1	2	FACETS	0.96	0.875	1	0.96	0.875	1	CLONAL	1	TRUE	1	0.58	2		668	438	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250785	26250785	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	40	754	0	ENST00000446824.2:c.49C>A	p.Pro17Thr	p.P17T	ENST00000446824	NM_021018.2	17	Ccg/Acg	1/1	1	2	FACETS	0.185	0.153	0.221	0.185	0.153	0.221	SUBCLONAL	1	TRUE	1	0.58	2		754	745	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165725	118165725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1211776583	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	171	759	0	ENST00000369448.3:c.235G>A	p.Val79Ile	p.V79I	ENST00000369448	NM_017709.3	79	Gtt/Att	2/2	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.58	2		759	572	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260601	10260601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573248196	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	112	606	0	ENST00000340748.4:c.2261C>T	p.Ala754Val	p.A754V	ENST00000340748		754	gCg/gTg	24/40	1	2	FACETS	0.926	0.839	1	0.926	0.839	1	CLONAL	1	TRUE	1	0.58	2		606	417	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131394	202131394	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	41	618	0	ENST00000358485.4:c.362T>G	p.Leu121Arg	p.L121R	ENST00000358485	NM_001080125.1	121	cTg/cGg	2/9	1	2	FACETS	0.292	0.242	0.346	0.292	0.242	0.346	SUBCLONAL	1	TRUE	1	0.58	2		618	485	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916765	48916766	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	93	432	0	ENST00000267163.4:c.299dup	p.Ile101AsnfsTer9	p.I101Nfs*9	ENST00000267163	NM_000321.2	99	tgg/tGgg	3/27	1	2	FACETS	0.987	0.887	1	0.987	0.887	1	CLONAL	1	TRUE	1	0.58	2		432	325	SUCCESS
MTAP	4507	MSKCC	GRCh37	9	21818116	21818116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	111	580	0	ENST00000380172.4:c.262C>T	p.His88Tyr	p.H88Y	ENST00000380172	NM_002451.3	88	Cat/Tat	4/8	1	2	FACETS	0.936	0.848	1	0.936	0.848	1	CLONAL	1	TRUE	1	0.58	2		580	409	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150935485	150935485	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1558028405	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	167	639	0	ENST00000271640.5:c.3331del	p.Glu1111LysfsTer41	p.E1111Kfs*41	ENST00000271640	NM_001145415.1	1109	gaG/ga	19/22	1	2	FACETS	0.93	0.859	1	0.93	0.859	1	CLONAL	1	TRUE	1	0.58	2		639	619	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2093680	2093680	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	34	603	0	ENST00000219066.1:c.597C>A	p.His199Gln	p.H199Q	ENST00000219066	NM_002528.5	199	caC/caA	4/6	1	2	FACETS	0.273	0.222	0.329	0.273	0.222	0.329	SUBCLONAL	1	TRUE	1	0.58	2		603	430	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230468739	230468739	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	31	695	1	ENST00000391860.1:c.779G>A	p.Gly260Asp	p.G260D	ENST00000391860	NM_001258311.1	260	gGc/gAc	5/7	1	2	FACETS	0.227	0.183	0.277	0.227	0.183	0.277	SUBCLONAL	1	TRUE	1	0.58	2		696	471	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842737	68842737	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555515290	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	141	494	0	ENST00000261769.5:c.673A>G	p.Ile225Val	p.I225V	ENST00000261769	NM_004360.3	225	Att/Gtt	5/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.58	2		494	429	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570094	212570094	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	94	492	0	ENST00000342788.4:c.1147G>T	p.Ala383Ser	p.A383S	ENST00000342788	NM_005235.2	383	Gcc/Tcc	10/28	1	2	FACETS	0.789	0.706	0.875	0.789	0.706	0.875	SUBCLONAL	1	TRUE	1	0.58	2		492	411	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63967927	63967927	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369372603	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	145	610	1	ENST00000398590.3:c.818C>T	p.Ala273Val	p.A273V	ENST00000398590	NM_001177387.1	273	gCg/gTg	7/14	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.58	2		611	470	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539963	187539963	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1008654148	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	40	597	1	ENST00000441802.2:c.7777G>A	p.Ala2593Thr	p.A2593T	ENST00000441802	NM_005245.3	2593	Gca/Aca	10/27	1	2	FACETS	0.302	0.251	0.36	0.302	0.251	0.36	SUBCLONAL	1	TRUE	1	0.58	2		598	456	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380692	118380692	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	115	525	0	ENST00000534358.1:c.10930A>C	p.Asn3644His	p.N3644H	ENST00000534358	NM_005933.3	3644	Aat/Cat	30/36	1	2	FACETS	0.994	0.903	1	0.994	0.903	1	CLONAL	1	TRUE	1	0.58	2		525	399	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650855	93650855	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	44	526	2	ENST00000375746.1:c.1781C>A	p.Pro594His	p.P594H	ENST00000375746	NM_001174167.1	594	cCt/cAt	13/14	1	2	FACETS	0.333	0.279	0.392	0.333	0.279	0.392	SUBCLONAL	1	TRUE	1	0.58	2		528	456	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295424	1295424	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1265237635	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	17	732	0				ENST00000310581	NM_198253.2	-/1132			0.157938377599221	1	FACETS	0.127	0.094	0.165	0.127	0.094	0.165	INDETERMINATE	1	TRUE	0	0.58	1		732	329	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393201	393201	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	33	672	0	ENST00000380956.4:c.49G>A	p.Val17Met	p.V17M	ENST00000380956	NM_001195286.1	17	Gtg/Atg	2/9	1	2	FACETS	0.318	0.259	0.384	0.318	0.259	0.384	SUBCLONAL	1	TRUE	1	0.58	2		672	358	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858011	152858011	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	32	334	0	ENST00000406277.2:c.604G>A	p.Gly202Arg	p.G202R	ENST00000406277	NM_152274.4	202	Gga/Aga	6/7	1	1	FACETS	0.426	0.349	0.511	0.426	0.349	0.511	SUBCLONAL	1	TRUE	0	0.58	1		334	184	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984460	72984460	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	50	679	0	ENST00000268489.5:c.3124T>C	p.Cys1042Arg	p.C1042R	ENST00000268489	NM_006885.3	1042	Tgc/Cgc	3/10	1	2	FACETS	0.399	0.339	0.465	0.399	0.339	0.465	SUBCLONAL	1	TRUE	1	0.58	2		679	432	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29002047	29002047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	91	458	0	ENST00000282397.4:c.1118G>A	p.Gly373Glu	p.G373E	ENST00000282397	NM_002019.4	373	gGg/gAg	9/30	1	2	FACETS	0.869	0.778	0.965	0.869	0.778	0.965	CLONAL	1	TRUE	1	0.58	2		458	361	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456525	32456526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	15	542	0	ENST00000332351.3:c.366_367insA	p.Ala123SerfsTer76	p.A123Sfs*76	ENST00000332351	NM_024426.4	122	-/A	1/10	1	2	FACETS	0.287	0.211	0.379	0.287	0.211	0.379	SUBCLONAL	1	TRUE	1	0.58	2		542	180	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77934482	77934482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395405019	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	40	558	0	ENST00000361507.4:c.1543C>T	p.Arg515Cys	p.R515C	ENST00000361507	NM_080491.2	515	Cgc/Tgc	6/10	1	2	FACETS	0.311	0.258	0.369	0.311	0.258	0.369	SUBCLONAL	1	TRUE	1	0.58	2		558	444	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881538	111881538	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	131	660	0	ENST00000393256.3:c.219del	p.Phe73LeufsTer11	p.F73Lfs*11	ENST00000393256	NM_006538.4	72	ccT/cc	2/4	1	2	FACETS	0.933	0.852	1	0.933	0.852	1	CLONAL	1	TRUE	1	0.58	2		660	484	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420197	88420197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	100	571	1	ENST00000360948.2:c.2489C>T	p.Ala830Val	p.A830V	ENST00000360948	NM_001012338.2	830	gCc/gTc	19/19	1	2	FACETS	0.88	0.792	0.971	0.88	0.792	0.971	CLONAL	1	TRUE	1	0.58	2		572	392	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100080	157100082	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs765410747	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	102	715	1	ENST00000346085.5:c.1026_1028del	p.Ala350del	p.A350del	ENST00000346085	NM_020732.3	339	gtGGCg/gtg	1/20	1	2	FACETS	0.902	0.813	0.995	0.902	0.813	0.995	CLONAL	1	TRUE	1	0.58	2		716	390	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10790030	10790030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1335030370	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	107	489	0	ENST00000361367.2:c.2101G>A	p.Val701Ile	p.V701I	ENST00000361367	NM_014633.3	701	Gtt/Att	16/25	1	2	FACETS	0.876	0.792	0.965	0.876	0.792	0.965	CLONAL	1	TRUE	1	0.58	2		489	421	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993367	72993367	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	142	679	1	ENST00000268489.5:c.678del	p.Val227SerfsTer19	p.V227Sfs*19	ENST00000268489	NM_006885.3	226	ccC/cc	2/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.58	2		680	413	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2047291	2047291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1482605809	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	15	138	0	ENST00000349721.2:c.853G>A	p.Gly285Ser	p.G285S	ENST00000349721	NM_003070.3	285	Ggc/Agc	5/34	1	2	FACETS	0.414	0.305	0.542	0.414	0.305	0.542	SUBCLONAL	1	TRUE	1	0.58	2		138	125	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2047369	2047369	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1431146434	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	17	375	0	ENST00000349721.2:c.931G>A	p.Ala311Thr	p.A311T	ENST00000349721	NM_003070.3	311	Gcc/Acc	5/34	1	2	FACETS	0.22	0.164	0.286	0.22	0.164	0.286	SUBCLONAL	1	TRUE	1	0.58	2		375	267	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804197	46804198	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	157	600	0	ENST00000290295.7:c.809_810del	p.Lys270ArgfsTer51	p.K270Rfs*51	ENST00000290295	NM_006361.5	270	aAA/a	2/2	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.58	2		600	489	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250084	39250084	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	49	513	0	ENST00000402219.2:c.1485del	p.Phe495LeufsTer22	p.F495Lfs*22	ENST00000402219	NM_005633.3	495	ttT/tt	10/23	1	2	FACETS	0.503	0.428	0.585	0.503	0.428	0.585	SUBCLONAL	1	TRUE	1	0.58	2		513	336	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028842	47028842	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	18	303	0	ENST00000377604.3:c.146G>A	p.Gly49Asp	p.G49D	ENST00000377604	NM_001204468.1	49	gGc/gAc	3/24	0.3	2	FACETS	0.265	0.2	0.342	0.133	0.1	0.171	INDETERMINATE	1	TRUE	0	0.58	2		303	234	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240966	133240966	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs903152944	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	106	643	0	ENST00000320574.5:c.2551G>A	p.Glu851Lys	p.E851K	ENST00000320574	NM_006231.2	851	Gag/Aag	22/49	1	2	FACETS	0.872	0.788	0.961	0.872	0.788	0.961	CLONAL	1	TRUE	1	0.58	2		643	419	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705485	47705496	+	inframe_deletion	In_Frame_Del	DEL	TAGCATGGGCTA	TAGCATGGGCTA	-	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	73	553	0	ENST00000233146.2:c.2287_2298del	p.Ala763_Ile766del	p.A763_I766del	ENST00000233146	NM_000251.2	762	tTAGCATGGGCTAta/tta	14/16	1	2	FACETS	0.784	0.691	0.882	0.784	0.691	0.882	SUBCLONAL	1	TRUE	1	0.58	2		553	321	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831161	72831161	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	27	658	0	ENST00000268489.5:c.5420T>C	p.Phe1807Ser	p.F1807S	ENST00000268489	NM_006885.3	1807	tTc/tCc	9/10	1	2	FACETS	0.272	0.216	0.336	0.272	0.216	0.336	SUBCLONAL	1	TRUE	1	0.58	2		658	342	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546150	41546150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150389014	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	59	621	0	ENST00000263253.7:c.2765C>T	p.Ala922Val	p.A922V	ENST00000263253	NM_001429.3	922	gCg/gTg	14/31	1	2	FACETS	0.406	0.35	0.467	0.406	0.35	0.467	SUBCLONAL	1	TRUE	1	0.58	2		621	501	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	364600	364600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	150	624	0	ENST00000262320.3:c.962G>A	p.Ser321Asn	p.S321N	ENST00000262320	NM_003502.3	321	aGc/aAc	3/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.58	2		624	465	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206896	36206896	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	21	390	0	ENST00000300305.3:c.616C>T	p.His206Tyr	p.H206Y	ENST00000300305		206	Cat/Tat	6/8	1	2	FACETS	0.231	0.177	0.293	0.231	0.177	0.293	SUBCLONAL	1	TRUE	1	0.58	2		390	314	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919691	96919691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200327514	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	121	595	0	ENST00000258439.3:c.572C>T	p.Thr191Met	p.T191M	ENST00000258439	NM_001193304.2	191	aCg/aTg	4/4	1	2	FACETS	0.979	0.892	1	0.979	0.892	1	CLONAL	1	TRUE	1	0.58	2		595	426	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457258	25457258	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	142	633	0	ENST00000264709.3:c.2629G>A	p.Val877Ile	p.V877I	ENST00000264709	NM_175629.2	877	Gtc/Atc	23/23	1	2	FACETS	0.962	0.882	1	0.962	0.882	1	CLONAL	1	TRUE	1	0.58	2		633	509	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245424	46245424	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	155	713	0	ENST00000334344.6:c.3518C>T	p.Thr1173Ile	p.T1173I	ENST00000334344	NM_152641.2	1173	aCc/aTc	15/21	0.198192463069365	3	FACETS	1	0.986	1	0.666	0.613	0.719	INDETERMINATE	1	TRUE	1	0.58	3		713	518	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740379	46740379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs550980888	NA	P-0067973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	44	565	0	ENST00000371975.4:c.1859G>A	p.Arg620His	p.R620H	ENST00000371975	NM_003579.3	620	cGc/cAc	16/18	1	2	FACETS	0.346	0.29	0.407	0.346	0.29	0.407	SUBCLONAL	1	TRUE	1	0.58	2		565	439	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0067974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	42	252	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.113251360886919	4	FACETS	1	0.927	1	0.599	0.502	0.705	INDETERMINATE	1	TRUE	2	0.282024396968827	4		253	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0067974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	91	400	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.216425747904582	3	FACETS	0.894	0.798	0.994	0.894	0.798	0.994	CLONAL	2	TRUE	1	0.282024396968827	3		400	412	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0067974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	38	390	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	0.282024396968827	1	FACETS	0.812	0.675	0.964	0.812	0.675	0.964	CLONAL	1	TRUE	0	0.282024396968827	1		390	285	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645751	12645751	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	41	459	0	ENST00000251849.4:c.718T>G	p.Phe240Val	p.F240V	ENST00000251849	NM_002880.3	240	Ttt/Gtt	7/17	0.216425747904582	3	FACETS	0.829	0.692	0.982	0.415	0.346	0.491	CLONAL	1	TRUE	1	0.282024396968827	3		459	400	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285209	15285209	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	42	519	0	ENST00000263388.2:c.4406C>T	p.Pro1469Leu	p.P1469L	ENST00000263388	NM_000435.2	1469	cCg/cTg	25/33	0.257301781307762	2	FACETS	0.914	0.766	1	0.457	0.383	0.538	CLONAL	1	TRUE	0	0.282024396968827	2		519	326	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0067975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	408	440	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.689272697643382	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.699867035756811	3		440	743	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577594	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	153	472	0	ENST00000269305.4:c.687del	p.Cys229Ter	p.C229*	ENST00000269305	NM_001126112.2	229	tgT/tg	7/11	0.656163492549313	1	FACETS	0.851	0.791	0.911	0.851	0.791	0.911	CLONAL	1	TRUE	0	0.699867035756811	1		472	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0067977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	502	612	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.828612700205339	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.828336532568954	1		612	684	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090396	77090396	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0067977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	337	455	0	ENST00000356341.3:c.329C>G	p.Ser110Ter	p.S110*	ENST00000356341	NM_002576.4	110	tCa/tGa	4/15	0.810410204534026	4	FACETS	1	0.975	1	0.352	0.332	0.372	CLONAL	1	TRUE	1	0.828336532568954	4		455	1410	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592267	29592291	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAATTCAAGGCTTTGAAAACGTT	AAGAATTCAAGGCTTTGAAAACGTT	-	novel	NA	P-0067977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	15	338	0	ENST00000356175.3:c.4685_4709del	p.Glu1562ValfsTer33	p.E1562Vfs*33	ENST00000356175	NM_000267.3	1561	gAAGAATTCAAGGCTTTGAAAACGTTa/ga	35/57	0.828612700205339	1	FACETS	0.092	0.067	0.122	0.092	0.067	0.122	SUBCLONAL	1	TRUE	0	0.828336532568954	1		338	230	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732247	74732247	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	351	491	0	ENST00000359995.5:c.662C>G	p.Ser221Cys	p.S221C	ENST00000359995	NM_001195427.1	221	tCt/tGt	2/3	0.828612700205339	2	FACETS	0.969	0.921	1	0.484	0.46	0.508	CLONAL	1	TRUE	0	0.828336532568954	2		491	875	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650608	48650609	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0067977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	376	684	0	ENST00000376670.3:c.581_582del	p.Leu194ProfsTer6	p.L194Pfs*6	ENST00000376670	NM_002049.3	193	aCT/a	3/6	0.787602134418711	1	FACETS	0.941	0.907	0.974	0.941	0.907	0.974	CLONAL	1	TRUE	0	0.828336532568954	1		684	565	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	195	350	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		350	561	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	710	557	0	ENST00000269571.5:c.829G>C	p.Asp277His	p.D277H	ENST00000269571		277	Gac/Cac	7/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		557	1295	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156713	20156713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	18	190	0	ENST00000379607.5:c.44G>A	p.Gly15Asp	p.G15D	ENST00000379607	NM_001412.3	15	gGt/gAt	2/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		190	311	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0067978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	251	436	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		436	452	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120633	94120633	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	124	414	0	ENST00000369303.4:c.418G>A	p.Glu140Lys	p.E140K	ENST00000369303	NM_004440.3	140	Gaa/Aaa	3/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		414	711	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844107	68844107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	207	438	0	ENST00000261769.5:c.695C>T	p.Ser232Phe	p.S232F	ENST00000261769	NM_004360.3	232	tCt/tTt	6/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		438	589	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475599	12475599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	265	393	0	ENST00000287820.6:c.1473G>A	p.Met491Ile	p.M491I	ENST00000287820	NM_015869.4	491	atG/atA	7/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		393	665	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714297	43714297	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	359	421	0	ENST00000382044.4:c.3856C>T	p.Gln1286Ter	p.Q1286*	ENST00000382044	NM_001141980.1	1286	Cag/Tag	19/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		421	748	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197716	66197716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	261	369	0	ENST00000273854.3:c.2983G>A	p.Asp995Asn	p.D995N	ENST00000273854	NM_004439.5	995	Gac/Aac	17/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		369	791	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439945	49439945	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	259	542	0	ENST00000301067.7:c.4596del	p.Gly1533AlafsTer29	p.G1533Afs*29	ENST00000301067	NM_003482.3	1532	gcA/gc	17/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		542	785	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120710	94120710	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	148	443	0	ENST00000369303.4:c.341G>C	p.Gly114Ala	p.G114A	ENST00000369303	NM_004440.3	114	gGa/gCa	3/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		443	781	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107042	27107042	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	45	583	0	ENST00000324856.7:c.6653T>C	p.Met2218Thr	p.M2218T	ENST00000324856	NM_006015.4	2218	aTg/aCg	20/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		583	838	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802692	135802692	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0067978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	217	367	0	ENST00000298552.3:c.107-1G>C		p.X36_splice	ENST00000298552	NM_001162426.1	36			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		367	411	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946124	55946124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	219	399	0	ENST00000263923.4:c.4055G>A	p.Ser1352Asn	p.S1352N	ENST00000263923	NM_002253.2	1352	aGc/aAc	30/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		399	677	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0067979-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	140	288	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.931	1	1	0.994	1	CLONAL	5	TRUE	1	0.14	2		288	395	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0067979-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	198	606	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.977	1	1	0.996	1	CLONAL	5	TRUE	1	0.14	2		606	515	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0067979-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	74	403	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.913	0.8	1	1	0.981	1	CLONAL	2	TRUE	1	0.14	2		404	579	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0067979-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	112	457	0	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	1	2	FACETS	0.962	0.871	1	1	0.992	1	CLONAL	4	TRUE	1	0.14	2		457	416	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514500	41514500	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067979-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	51	451	0	ENST00000373198.4:c.161G>T	p.Trp54Leu	p.W54L	ENST00000373198	NM_133170.3	54	tGg/tTg	2/32	0.0650284665710794	4	FACETS	0.885	0.753	1	0.885	0.753	1	INDETERMINATE	2	TRUE	2	0.14	4		451	469	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650777	48650777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387907207	NA	P-0067979-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	238	744	0	ENST00000376670.3:c.646C>T	p.Arg216Trp	p.R216W	ENST00000376670	NM_002049.3	216	Cgg/Tgg	4/6	1	2	FACETS	0.92	0.865	0.976	1	0.996	1	CLONAL	6	TRUE	1	0.14	2		744	616	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129267	152129267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775435150	NA	P-0067979-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	122	631	0	ENST00000206249.3:c.220G>A	p.Gly74Ser	p.G74S	ENST00000206249	NM_000125.3	74	Ggt/Agt	1/8	1	2	FACETS	0.997	0.908	1	1	0.992	1	CLONAL	4	TRUE	1	0.14	2		631	437	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604784	48604798	+	inframe_deletion	In_Frame_Del	DEL	CTAGACGAAGTACTT	CTAGACGAAGTACTT	-	novel	NA	P-0067979-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	28	542	0	ENST00000342988.3:c.1607_1621del	p.Leu536_Leu540del	p.L536_L540del	ENST00000342988	NM_005359.5	536	CTAGACGAAGTACTT/-	12/12	0.3	1	FACETS	0.867	0.692	1	0.867	0.692	1	CLONAL	1	TRUE	0	0.14	1		542	429	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0067981-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	117	446	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.773509939003279	2		446	301	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067981-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	168	495	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	0.773509939003279	6	FACETS	0.881	0.813	0.951	0.44	0.406	0.476	CLONAL	2	TRUE	2	0.773509939003279	6		495	628	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067981-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	363	378	1	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	0.772482621716234	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	1	0.773509939003279	4		379	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs985033810	NA	P-0067981-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	232	516	1	ENST00000269305.4:c.731G>T	p.Gly244Val	p.G244V	ENST00000269305	NM_001126112.2	244	gGc/gTc	7/11	0.772482621716234	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.773509939003279	2		517	271	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821268	72821269	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0067981-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	171	590	0	ENST00000268489.5:c.10906_10907del	p.Ser3636LeufsTer29	p.S3636Lfs*29	ENST00000268489	NM_006885.3	3636	TCc/c	10/10	0.772482621716234	2	FACETS	0.965	0.92	1	0.965	0.92	1	CLONAL	2	TRUE	0	0.773509939003279	2		590	229	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066880	30066880	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067981-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	169	545	0	ENST00000331968.5:c.2251G>T	p.Ala751Ser	p.A751S	ENST00000331968	NM_002742.2	751	Gct/Tct	16/18	0.754309381586802	4	FACETS	0.903	0.84	0.968	0.903	0.84	0.968	CLONAL	2	TRUE	2	0.773509939003279	4		545	429	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990627	7990627	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067981-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	70	283	0	ENST00000319144.4:c.134T>A	p.Phe45Tyr	p.F45Y	ENST00000319144	NM_001139.2	45	tTt/tAt	1/15	0.772482621716234	2	FACETS	0.826	0.732	0.925	0.413	0.366	0.463	CLONAL	1	TRUE	0	0.773509939003279	2		283	219	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0067982-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	64	0	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		0	191	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0067982-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	114	389	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		389	333	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873660	35873660	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs201559094	NA	P-0067982-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	72	460	2	ENST00000303115.3:c.616C>T	p.Arg206Ter	p.R206*	ENST00000303115	NM_002185.3	206	Cga/Tga	5/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		462	316	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112494	115112494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067982-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	135	567	0	ENST00000257566.3:c.1246C>T	p.Leu416Phe	p.L416F	ENST00000257566	NM_016569.3	416	Ctt/Ttt	7/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		567	458	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8339047	8339047	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067982-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	45	376	0	ENST00000356435.5:c.5254G>A	p.Glu1752Lys	p.E1752K	ENST00000356435		1752	Gag/Aag	32/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		376	194	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259780	142259780	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067982-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	34	420	0	ENST00000350721.4:c.3547C>T	p.Arg1183Ter	p.R1183*	ENST00000350721	NM_001184.3	1183	Cga/Tga	18/47	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		420	266	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37055963	37055963	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067982-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	19	362	0	ENST00000231790.2:c.718T>C	p.Phe240Leu	p.F240L	ENST00000231790	NM_000249.3	240	Ttc/Ctc	9/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		362	226	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582089	189582089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767553568	NA	P-0067982-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	82	539	0	ENST00000264731.3:c.648G>A	p.Met216Ile	p.M216I	ENST00000264731	NM_003722.4	216	atG/atA	5/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		539	500	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191512	10191512	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067986-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	10	376	0	ENST00000256474.2:c.505C>G	p.Leu169Val	p.L169V	ENST00000256474	NM_000551.3	169	Cta/Gta	3/3	1	2	FACETS	0.277	0.187	0.392	0.277	0.187	0.392	SUBCLONAL	1	TRUE	1	0.18	2		376	401	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067988-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	48	350	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.974	0.84	1	0.974	0.84	1	CLONAL	1	TRUE	1	0.623539721060902	2		350	158	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200961	108200961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782310	NA	P-0067988-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	110	413	0	ENST00000278616.4:c.7328G>A	p.Arg2443Gln	p.R2443Q	ENST00000278616	NM_000051.3	2443	cGa/cAa	50/63	1	2	FACETS	0.951	0.863	1	0.951	0.863	1	CLONAL	1	TRUE	1	0.623539721060902	2		413	371	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141874	108141874	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587781558	NA	P-0067988-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	125	426	1	ENST00000278616.4:c.2921+1G>A		p.X974_splice	ENST00000278616	NM_000051.3	974			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.623539721060902	2		427	349	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98002971	98002971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067988-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	17	316	0	ENST00000289081.3:c.305C>T	p.Pro102Leu	p.P102L	ENST00000289081	NM_000136.2	102	cCa/cTa	4/15	1	2	FACETS	0.171	0.127	0.224	0.171	0.127	0.224	SUBCLONAL	1	TRUE	1	0.623539721060902	2		316	318	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526300	189526300	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067988-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	245	525	0	ENST00000264731.3:c.564G>T	p.Lys188Asn	p.K188N	ENST00000264731	NM_003722.4	188	aaG/aaT	4/14	0.617767968888685	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.623539721060902	3		525	490	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	88	350	0				ENST00000310581	NM_198253.2	-/1132			0.154467650539776	0	FACETS	0.342	0.307	0.378			1	INDETERMINATE	1	TRUE	0	0.666284110192488	0		350	258	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0067988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	152	293	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	0.558753088442826	3	FACETS	0.983	0.902	1	0.491	0.451	0.533	CLONAL	1	TRUE	1	0.666284110192488	3		293	619	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119842	70119842	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	61	241	0	ENST00000245479.2:c.844G>A	p.Val282Ile	p.V282I	ENST00000245479	NM_000346.3	282	Gtc/Atc	3/3	1	2	FACETS	0.491	0.425	0.562	0.491	0.425	0.562	SUBCLONAL	1	TRUE	1	0.666284110192488	2		241	373	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629996	187629996	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	162	318	0	ENST00000441802.2:c.986del	p.Pro329LeufsTer27	p.P329Lfs*27	ENST00000441802	NM_005245.3	329	cCt/ct	2/27	0.666284110192488	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.666284110192488	1		318	312	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564594	86564594	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	59	374	0	ENST00000274376.6:c.326G>T	p.Gly109Val	p.G109V	ENST00000274376	NM_002890.2	109	gGa/gTa	1/25	1	2	FACETS	0.299	0.257	0.345	0.299	0.257	0.345	SUBCLONAL	1	TRUE	1	0.666284110192488	2		374	592	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176700744	176700744	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886041218	NA	P-0067989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	10	352	0	ENST00000439151.2:c.5581C>T	p.Arg1861Ter	p.R1861*	ENST00000439151	NM_022455.4	1861	Cga/Tga	17/23	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		352	154	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723154	49723154	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1234245343	NA	P-0067989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	10	471	0	ENST00000449682.2:c.1262C>T	p.Thr421Ile	p.T421I	ENST00000449682	NM_020998.3	421	aCc/aTc	11/18	0.142324467319185	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		471	188	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856230	111856230	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	167	437	0	ENST00000341259.2:c.281G>C	p.Arg94Pro	p.R94P	ENST00000341259	NM_005475.2	94	cGt/cCt	2/8	0.266938057674159	3	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	1	0.298121109641161	3		437	635	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183763	10183763	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1559425925	NA	P-0067990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	85	467	0	ENST00000256474.2:c.233del	p.Asn78IlefsTer81	p.N78Ifs*81	ENST00000256474	NM_000551.3	78	Aat/at	1/3	0.298121109641161	1	FACETS	0.965	0.855	1	0.965	0.855	1	CLONAL	1	TRUE	0	0.298121109641161	1		467	503	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627466	37627466	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	93	383	0	ENST00000447079.4:c.1381G>T	p.Glu461Ter	p.E461*	ENST00000447079	NM_015083.1	461	Gaa/Taa	2/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		383	259	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266408	55266408	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0067991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	103	366	0	ENST00000275493.2:c.2702-2A>T		p.X901_splice	ENST00000275493	NM_005228.3	901			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		366	251	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805441	46805441	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	161	468	0	ENST00000290295.7:c.515G>C	p.Trp172Ser	p.W172S	ENST00000290295	NM_006361.5	172	tGg/tCg	1/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		468	406	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332919	152332919	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	55	343	0	ENST00000206249.3:c.1225C>A	p.Leu409Ile	p.L409I	ENST00000206249	NM_000125.3	409	Ctc/Atc	5/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		343	181	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512254	120512254	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	166	481	0	ENST00000256646.2:c.988T>G	p.Trp330Gly	p.W330G	ENST00000256646	NM_024408.3	330	Tgg/Ggg	6/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		481	400	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618647	37618656	+	frameshift_variant	Frame_Shift_Del	DEL	TGCACAAACA	TGCACAAACA	-	novel	NA	P-0067991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	137	493	0	ENST00000447079.4:c.324_333del	p.His109ValfsTer12	p.H109Vfs*12	ENST00000447079	NM_015083.1	108	cTGCACAAACAt/ct	1/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		493	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577086	7577087	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0067993-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	167	498	0	ENST00000269305.4:c.851_852del	p.Thr284ArgfsTer21	p.T284Rfs*21	ENST00000269305	NM_001126112.2	284	aCA/a	8/11	0.409360219630834	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.409360219630834	1		498	621	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937268	76937268	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067993-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	18	256	0	ENST00000373344.5:c.3480A>T	p.Glu1160Asp	p.E1160D	ENST00000373344	NM_000489.3	1160	gaA/gaT	9/35	1	1	FACETS	0.328	0.248	0.423	0.328	0.248	0.423	SUBCLONAL	1	TRUE	0	0.409360219630834	1		256	213	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930087	68930087	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067993-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	104	409	0	ENST00000288368.4:c.148T>A	p.Leu50Ile	p.L50I	ENST00000288368	NM_024870.2	50	Tta/Ata	2/40	0.20069687131507	1	FACETS	0.971	0.876	1	0.971	0.876	1	INDETERMINATE	1	TRUE	0	0.409360219630834	1		409	416	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0067994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	17	288	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.908	0.677	1	0.908	0.677	1	CLONAL	1	TRUE	1	0.12	2		288	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0067994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	32	645	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	1	2	FACETS	0.995	0.806	1	0.995	0.806	1	CLONAL	1	TRUE	1	0.12	2		645	536	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0067994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	24	411	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.93	0.728	1	0.93	0.728	1	CLONAL	1	TRUE	1	0.12	2		411	430	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	15	410	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	1	2	FACETS	0.591	0.431	0.785	0.591	0.431	0.785	SUBCLONAL	1	TRUE	1	0.12	2		410	423	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	81	350	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.270706454936371	2		350	401	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0068015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	137	252	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.270706454936371	4	FACETS	0.999	0.923	1	0.999	0.923	1	CLONAL	4	TRUE	0	0.270706454936371	4		253	322	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572820	41572826	+	frameshift_variant	Frame_Shift_Del	DEL	ACCACAA	ACCACAA	-	novel	NA	P-0068015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	40	376	0	ENST00000263253.7:c.5106_5112del	p.Asp1702GlufsTer5	p.D1702Efs*5	ENST00000263253	NM_001429.3	1702	gACCACAAa/ga	31/31	1	2	FACETS	0.519	0.431	0.618	0.519	0.431	0.618	SUBCLONAL	1	TRUE	1	0.270706454936371	2		376	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0068016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	38	426	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.568750683667849	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.561259248273579	1		426	69	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744078	39744078	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs372925211	NA	P-0068016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	37	369	0	ENST00000361337.2:c.1706A>G	p.Asn569Ser	p.N569S	ENST00000361337	NM_003286.2	569	aAt/aGt	16/21	0.188024624394483	2	FACETS	1	0.939	1	0.622	0.527	0.722	INDETERMINATE	1	TRUE	0	0.561259248273579	2		369	106	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877094	89877117	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GATTTGCAATCTCAAATTTACCTG	GATTTGCAATCTCAAATTTACCTG	-	novel	NA	P-0068016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	24	269	0	ENST00000389301.3:c.520_522+21del		p.X174_splice	ENST00000389301	NM_000135.2	174		5/43	0.359881686979119	4	FACETS	1	0.922	1	0.454	0.364	0.554	CLONAL	1	TRUE	1	0.561259248273579	4		269	98	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534747	18534791	+	inframe_deletion	In_Frame_Del	DEL	AGCCTCCCGTAGAAATGATAACTCCAGGAGTGTGGGATGTAAGTC	AGCCTCCCGTAGAAATGATAACTCCAGGAGTGTGGGATGTAAGTC	-	novel	NA	P-0068016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	21	375	0	ENST00000266497.5:c.1809_1853del	p.Pro604_Pro618del	p.P604_P618del	ENST00000266497		602	gAGCCTCCCGTAGAAATGATAACTCCAGGAGTGTGGGATGTAAGTCag/gag	12/31	0.310191441034885	3	FACETS	1	0.899	1	0.63	0.499	0.774	INDETERMINATE	1	TRUE	1	0.561259248273579	3		375	76	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188829	32188879	+	inframe_deletion	In_Frame_Del	DEL	CCCCTAGGAGGGCAGGGTCCTGCCCGCAGCTCACAACGTGGACCCTCCTGC	CCCCTAGGAGGGCAGGGTCCTGCCCGCAGCTCACAACGTGGACCCTCCTGC	-	novel	NA	P-0068016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	18	516	0	ENST00000375023.3:c.675_725del	p.Gln226_Gly242del	p.Q226_G242del	ENST00000375023	NM_004557.3	225	ggGCAGGAGGGTCCACGTTGTGAGCTGCGGGCAGGACCCTGCCCTCCTAGGGGc/ggc	4/30	0.261982435913018	4	FACETS	1	0.803	1	0.527	0.404	0.667	INDETERMINATE	1	TRUE	2	0.561259248273579	4		516	95	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932797	39932797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs895548545	NA	P-0068016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	16	473	0	ENST00000378444.4:c.1802C>T	p.Pro601Leu	p.P601L	ENST00000378444	NM_001123385.1	601	cCc/cTc	4/15	0.188024624394483	2	FACETS	0.588	0.441	0.757	0.294	0.22	0.379	INDETERMINATE	1	TRUE	0	0.561259248273579	2		473	97	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	370	508	0	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.484444881357582	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.484444881357582	2		508	691	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163889	152163889	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	170	482	0	ENST00000206249.3:c.610G>T	p.Gly204Cys	p.G204C	ENST00000206249	NM_000125.3	204	Ggc/Tgc	2/8	0.484444881357582	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.484444881357582	1		482	469	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638674	176638674	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1562212423	NA	P-0068017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	161	502	0	ENST00000439151.2:c.3274C>T	p.Gln1092Ter	p.Q1092*	ENST00000439151	NM_022455.4	1092	Cag/Tag	5/23	0.484444881357582	1	FACETS	0.993	0.918	1	0.993	0.918	1	CLONAL	1	TRUE	0	0.484444881357582	1		502	507	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561041	9561041	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	146	528	0	ENST00000353224.5:c.741G>T	p.Lys247Asn	p.K247N	ENST00000353224	NM_177990.2	247	aaG/aaT	4/10	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.484444881357582	2		528	595	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325688	87325688	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	246	416	0	ENST00000277120.3:c.565C>A	p.Leu189Met	p.L189M	ENST00000277120		189	Ctg/Atg	6/19	0.484444881357582	2	FACETS	0.994	0.94	1	0.994	0.94	1	CLONAL	2	TRUE	0	0.484444881357582	2		416	511	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460439	149460439	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	159	515	0	ENST00000286301.3:c.198C>G	p.Ser66Arg	p.S66R	ENST00000286301	NM_005211.3	66	agC/agG	3/22	0.484444881357582	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.484444881357582	1		515	464	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870307	155870307	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	167	509	1	ENST00000368323.3:c.532C>A	p.Leu178Ile	p.L178I	ENST00000368323	NM_006912.5	178	Ctt/Att	6/6	1	2	FACETS	0.988	0.91	1	0.988	0.91	1	CLONAL	1	TRUE	1	0.484444881357582	2		510	698	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665395	182665395	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	326	281	0	ENST00000292782.4:c.546G>T	p.Trp182Cys	p.W182C	ENST00000292782	NM_020640.2	182	tgG/tgT	5/7	0.44706932903499	4	FACETS	0.922	0.877	0.968	0.922	0.877	0.968	CLONAL	3	TRUE	1	0.484444881357582	4		281	722	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446175	49446175	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	153	491	0	ENST00000301067.7:c.1291del	p.Glu431ArgfsTer4	p.E431Rfs*4	ENST00000301067	NM_003482.3	431	Gag/ag	10/54	1	2	FACETS	0.953	0.874	1	0.953	0.874	1	CLONAL	1	TRUE	1	0.484444881357582	2		491	663	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412697	63412697	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	136	209	0	ENST00000330258.3:c.470A>G	p.Glu157Gly	p.E157G	ENST00000330258	NM_152424.3	157	gAg/gGg	2/2	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.484444881357582	1		209	287	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828147	243828147	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	158	362	0	ENST00000263826.5:c.211A>T	p.Thr71Ser	p.T71S	ENST00000263826	NM_005465.4	71	Aca/Tca	3/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.484444881357582	2		362	592	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420031	49420031	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	195	575	0	ENST00000301067.7:c.15718G>C	p.Glu5240Gln	p.E5240Q	ENST00000301067	NM_003482.3	5240	Gag/Cag	48/54	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.484444881357582	2		575	724	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448481	49448481	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747186162	NA	P-0068017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	145	476	0	ENST00000301067.7:c.230A>G	p.His77Arg	p.H77R	ENST00000301067	NM_003482.3	77	cAc/cGc	3/54	1	2	FACETS	0.944	0.864	1	0.944	0.864	1	CLONAL	1	TRUE	1	0.484444881357582	2		476	634	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970985	21970986	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0068017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	157	518	0	ENST00000304494.5:c.372_373del	p.Asp125CysfsTer16	p.D125Cfs*16	ENST00000304494	NM_000077.4	124	cgCGat/cgat	2/3	0.484444881357582	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.484444881357582	1		518	452	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0068018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	20	288	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.206288015678881	3	FACETS	0.764	0.59	0.963	0.764	0.59	0.963	CLONAL	2	TRUE	1	0.206288015678881	3		288	140	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572955	41572955	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	25	624	0	ENST00000263253.7:c.5240A>G	p.Gln1747Arg	p.Q1747R	ENST00000263253	NM_001429.3	1747	cAg/cGg	31/31	0.206288015678881	3	FACETS	0.948	0.757	1	0.948	0.757	1	CLONAL	2	TRUE	1	0.206288015678881	3		624	141	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535416	187535416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs756123882	NA	P-0068018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	13	464	0	ENST00000441802.2:c.9158G>T	p.Arg3053Leu	p.R3053L	ENST00000441802	NM_005245.3	3053	cGc/cTc	12/27	0.16371234632209	0	FACETS	1	0.77	1			1	CLONAL	1	TRUE	0	0.206288015678881	0		464	93	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499516	89499516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773476878	NA	P-0068018-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	46	460	1	ENST00000336596.2:c.2686G>A	p.Ala896Thr	p.A896T	ENST00000336596	NM_005233.5	896	Gca/Aca	15/17	1	2	FACETS	0.874	0.738	1	0.874	0.738	1	CLONAL	1	TRUE	1	0.28	2		461	376	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411902	116411902	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0068018-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	112	604	0	ENST00000397752.3:c.2888-1G>A		p.X963_splice	ENST00000397752	NM_000245.2	963			0.292470506879819	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.28	3		604	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0068018-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	83	418	0	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.28	2		418	482	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012358	29012359	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0068018-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	22	319	2	ENST00000282397.4:c.512dup	p.Phe172ValfsTer4	p.F172Vfs*4	ENST00000282397	NM_002019.4	171	aag/aaAg	4/30	0.244044601806389	0	FACETS	0.647	0.505	0.809			1	SUBCLONAL	1	TRUE	0	0.28	0		321	175	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141426	11141426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068018-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	88	554	0	ENST00000358026.2:c.3403C>T	p.Arg1135Trp	p.R1135W	ENST00000358026	NM_001128849.1	1135	Cgg/Tgg	25/36	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.28	2		554	481	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144049	11144051	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0068018-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	89	581	0	ENST00000358026.2:c.3634_3636del	p.Glu1212del	p.E1212del	ENST00000358026	NM_001128849.1	1210	gtGGAg/gtg	26/36	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.28	2		581	514	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620117	21620117	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068018-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	59	551	0	ENST00000382592.4:c.49C>G	p.Gln17Glu	p.Q17E	ENST00000382592	NM_014572.2	17	Cag/Gag	2/8	1	2	FACETS	0.926	0.799	1	0.926	0.799	1	CLONAL	1	TRUE	1	0.28	2		551	455	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411454	63411454	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068018-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	95	695	0	ENST00000330258.3:c.1713G>T	p.Trp571Cys	p.W571C	ENST00000330258	NM_152424.3	571	tgG/tgT	2/2	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.28	2		695	518	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480483	89480483	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068018-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	30	478	0	ENST00000336596.2:c.2320G>T	p.Asp774Tyr	p.D774Y	ENST00000336596	NM_005233.5	774	Gac/Tac	13/17	1	2	FACETS	0.661	0.534	0.806	0.661	0.534	0.806	SUBCLONAL	1	TRUE	1	0.28	2		478	324	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339606	116339607	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0068018-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	70	541	0	ENST00000397752.3:c.468_469delinsTT	p.Glu157Ter	p.E157*	ENST00000397752	NM_000245.2	156	tcGGag/tcTTag	2/21	0.292470506879819	3	FACETS	1	0.919	1	0.536	0.468	0.609	CLONAL	1	TRUE	1	0.28	3		541	532	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222201	53222201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782529520	NA	P-0068018-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	59	570	0	ENST00000375401.3:c.4631C>T	p.Thr1544Ile	p.T1544I	ENST00000375401	NM_004187.3	1544	aCt/aTt	26/26	1	2	FACETS	0.91	0.785	1	0.91	0.785	1	CLONAL	1	TRUE	1	0.28	2		570	463	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044958	47044958	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068018-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	73	641	0	ENST00000377604.3:c.2284del	p.Leu762CysfsTer40	p.L762Cfs*40	ENST00000377604	NM_001204468.1	762	Ctg/tg	20/24	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.28	2		641	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0068019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	271	378	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.597067681583557	3	FACETS	0.94	0.906	0.972	0.94	0.906	0.972	CLONAL	3	FALSE	0	0.745703751568218	3		378	354	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207009	1207009	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	609	338	0	ENST00000326873.7:c.97G>T	p.Glu33Ter	p.E33*	ENST00000326873	NM_000455.4	33	Gag/Tag	1/10	0.745703751568218	8	FACETS	0.961	0.944	0.976			1	CLONAL	8	FALSE	NA	0.745703751568218	8		338	688	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55974004	55974004	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	400	304	0	ENST00000263923.4:c.1312G>T	p.Gly438Cys	p.G438C	ENST00000263923	NM_002253.2	438	Ggc/Tgc	10/30	0.620694844216306	5	FACETS	1	0.995	1	0.891	0.866	0.916	CLONAL	4	FALSE	0	0.745703751568218	5		304	510	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993579	72993579	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	219	366	0	ENST00000268489.5:c.466G>T	p.Ala156Ser	p.A156S	ENST00000268489	NM_006885.3	156	Gcc/Tcc	2/10	0.682706696237583	5	FACETS	0.883	0.831	0.934	0.883	0.831	0.934	CLONAL	3	FALSE	2	0.745703751568218	5		366	470	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239686	105239686	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	77	338	0	ENST00000349310.3:c.859C>T	p.His287Tyr	p.H287Y	ENST00000349310	NM_001014432.1	287	Cac/Tac	11/15	0.745703751568218	7	FACETS	0.96	0.844	1	0.192	0.168	0.218	CLONAL	1	FALSE	2	0.745703751568218	7		338	616	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670604	134670605	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0068019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	74	310	0	ENST00000398015.3:c.520dup	p.Tyr174LeufsTer87	p.Y174Lfs*87	ENST00000398015	NM_004441.4	172	ggt/ggTt	3/16	0.745703751568218	12	FACETS	0.806	0.703	0.918	0.101	0.087	0.115	CLONAL	1	FALSE	4	0.745703751568218	12		310	1164	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606031	81606031	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	181	287	0	ENST00000298171.2:c.701C>T	p.Ser234Phe	p.S234F	ENST00000298171	NM_000369.2	234	tCt/tTt	9/10	0.719605343070962	5	FACETS	0.897	0.833	0.964	0.598	0.555	0.643	CLONAL	2	FALSE	2	0.745703751568218	5		287	573	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279440	1279440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1376041056	NA	P-0068019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	54	274	0	ENST00000310581.5:c.2096C>T	p.Ala699Val	p.A699V	ENST00000310581	NM_198253.2	699	gCc/gTc	5/16	0.745703751568218	6	FACETS	0.898	0.769	1	0.224	0.192	0.26	CLONAL	1	FALSE	2	0.745703751568218	6		274	402	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068435	16068435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	22	74	0	ENST00000268712.3:c.476C>T	p.Pro159Leu	p.P159L	ENST00000268712	NM_006311.3	159	cCa/cTa	5/46	0.713152163708765	5	FACETS	0.899	0.705	1			1	CLONAL	1	FALSE	NA	0.745703751568218	5		74	139	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2220221	2220221	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	322	318	0	ENST00000398665.3:c.2806G>C	p.Gly936Arg	p.G936R	ENST00000398665	NM_032482.2	936	Ggc/Cgc	23/28	0.74817638814776	3	FACETS	1	0.988	1			1	CLONAL	3	FALSE	NA	0.745703751568218	3		318	383	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215971	36215971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068020-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	16	498	0	ENST00000222270.7:c.3511G>A	p.Val1171Ile	p.V1171I	ENST00000222270	NM_014727.1	1171	Gtc/Atc	10/37	0.359331764652452	3	FACETS	0.265	0.195	0.349	0.133	0.097	0.175	SUBCLONAL	1	TRUE	1	0.464593248126902	3		498	320	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39762932	39762932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1401427882	NA	P-0068020-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	19	377	0	ENST00000288319.7:c.904C>T	p.Arg302Cys	p.R302C	ENST00000288319	NM_182918.3	302	Cgc/Tgc	9/10	1	2	FACETS	0.413	0.315	0.528	0.413	0.315	0.528	SUBCLONAL	1	TRUE	1	0.464593248126902	2		377	198	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191470	10191470	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs5030817	NA	P-0068020-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	42	393	0	ENST00000256474.2:c.464-1G>A		p.X155_splice	ENST00000256474	NM_000551.3	155			0.307497792864649	1	FACETS	0.549	0.461	0.644	0.549	0.461	0.644	SUBCLONAL	1	TRUE	0	0.464593248126902	1		393	253	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144879	47144879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068020-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	38	416	0	ENST00000409792.3:c.4874G>A	p.Arg1625His	p.R1625H	ENST00000409792	NM_014159.6	1625	cGt/cAt	7/21	0.344145721381396	1	FACETS	0.528	0.439	0.625	0.528	0.439	0.625	SUBCLONAL	1	TRUE	0	0.464593248126902	1		416	238	SUCCESS
PHF6	84295	MSKCC	GRCh37	X	133547547	133547547	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068020-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	38	407	0	ENST00000332070.3:c.445del	p.His149MetfsTer69	p.H149Mfs*69	ENST00000332070	NM_032458.2	149	Cat/at	6/10	1	2	FACETS	0.684	0.57	0.81	0.684	0.57	0.81	SUBCLONAL	1	TRUE	1	0.464593248126902	2		407	239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934574	NA	P-0068021-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	71	382	0	ENST00000269305.4:c.844C>G	p.Arg282Gly	p.R282G	ENST00000269305	NM_001126112.2	282	Cgg/Ggg	8/11	0.320809384298905	1	FACETS	0.994	0.872	1	0.994	0.872	1	CLONAL	1	FALSE	0	0.320809384298905	1		382	374	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876425	35876425	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068021-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	58	428	0	ENST00000303115.3:c.1217T>G	p.Leu406Arg	p.L406R	ENST00000303115	NM_002185.3	406	cTt/cGt	8/8	0.320809384298905	6	FACETS	1	0.909	1	0.215	0.185	0.249	CLONAL	1	FALSE	1	0.320809384298905	6		428	551	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143350349	143350349	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs944466060	NA	P-0068021-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	23	212	0	ENST00000262992.4:c.113A>T	p.Glu38Val	p.E38V	ENST00000262992	NM_001101669.1	38	gAa/gTa	3/24	1	2	FACETS	0.902	0.71	1	0.902	0.71	1	CLONAL	1	FALSE	1	0.320809384298905	2		212	159	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736285	243736285	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068021-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	71	350	0	ENST00000263826.5:c.762A>C	p.Glu254Asp	p.E254D	ENST00000263826	NM_005465.4	254	gaA/gaC	8/13	0.166924926343821	3	FACETS	1	0.959	1	0.411	0.36	0.465	INDETERMINATE	1	FALSE	0	0.320809384298905	3		350	417	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212252718	212252718	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs865897799	NA	P-0068021-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	21	335	0	ENST00000342788.4:c.3136-1G>A		p.X1046_splice	ENST00000342788	NM_005235.2	1046			1	2	FACETS	0.504	0.388	0.637	0.504	0.388	0.637	SUBCLONAL	1	FALSE	1	0.320809384298905	2		335	260	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	102	356	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.801	0.717	0.891	0.801	0.717	0.891	CLONAL	1	TRUE	1	0.368943099815169	2		356	690	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	95	427	1	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.653	0.581	0.73	0.653	0.581	0.73	SUBCLONAL	1	TRUE	1	0.368943099815169	2		428	789	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755427	39755427	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	68	492	0	ENST00000288319.7:c.1338del	p.Phe446LeufsTer59	p.F446Lfs*59	ENST00000288319	NM_182918.3	446	ttT/tt	10/10	1	2	FACETS	0.496	0.431	0.567	0.496	0.431	0.567	SUBCLONAL	1	TRUE	1	0.368943099815169	2		492	743	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	43	341	0	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	0.368943099815169	3	FACETS	0.363	0.303	0.431	0.182	0.151	0.216	SUBCLONAL	1	TRUE	1	0.368943099815169	3		341	760	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	85	389	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.682	0.603	0.766	0.682	0.603	0.766	SUBCLONAL	1	TRUE	1	0.368943099815169	2		389	676	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	28	371	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	1	2	FACETS	0.258	0.205	0.318	0.258	0.205	0.318	SUBCLONAL	1	TRUE	1	0.368943099815169	2		371	589	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	81	367	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	1	2	FACETS	0.652	0.575	0.736	0.652	0.575	0.736	SUBCLONAL	1	TRUE	1	0.368943099815169	2		367	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	134	514	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	1	2	FACETS	0.969	0.881	1	0.969	0.881	1	CLONAL	1	TRUE	1	0.368943099815169	2		514	750	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053022	180053023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750808726	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	33	426	0	ENST00000261937.6:c.1267dup	p.Gln423ProfsTer4	p.Q423Pfs*4	ENST00000261937	NM_182925.4	423	cag/cCag	10/30	0.183910235531701	0	FACETS	0.205	0.166	0.249			1	INDETERMINATE	1	TRUE	0	0.368943099815169	0		426	551	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	74	370	1	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	1	2	FACETS	0.653	0.572	0.741	0.653	0.572	0.741	SUBCLONAL	1	TRUE	1	0.368943099815169	2		371	614	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422384	47422384	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	62	357	2	ENST00000377045.4:c.23del	p.Pro8LeufsTer26	p.P8Lfs*26	ENST00000377045	NM_001654.4	6	ggC/gg	2/16	0.368943099815169	1	FACETS	0.657	0.57	0.752	0.657	0.57	0.752	SUBCLONAL	1	TRUE	0	0.368943099815169	1		359	417	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944382	131944382	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs748536322	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	74	334	3	ENST00000265335.6:c.2801del	p.Asn934IlefsTer6	p.N934Ifs*6	ENST00000265335		932	Aaa/aa	17/25	1	2	FACETS	0.662	0.58	0.75	0.662	0.58	0.75	SUBCLONAL	1	TRUE	1	0.368943099815169	2		337	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	81	453	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	1	2	FACETS	0.601	0.529	0.678	0.601	0.529	0.678	SUBCLONAL	1	TRUE	1	0.368943099815169	2		453	731	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972893	32972893	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	79	510	0	ENST00000380152.3:c.10248del	p.Lys3416AsnfsTer11	p.K3416Nfs*11	ENST00000380152		3415	Aaa/aa	27/27	0.266452618595007	3	FACETS	0.663	0.582	0.75	0.332	0.291	0.375	SUBCLONAL	1	TRUE	1	0.368943099815169	3		510	765	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131457	202131459	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	69	440	0	ENST00000358485.4:c.430_432del	p.Glu144del	p.E144del	ENST00000358485	NM_001080125.1	142	aAGGag/aag	2/9	1	2	FACETS	0.516	0.449	0.589	0.516	0.449	0.589	SUBCLONAL	1	TRUE	1	0.368943099815169	2		440	725	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151290	202151290	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	75	373	0	ENST00000358485.4:c.1596del	p.Lys532AsnfsTer73	p.K532Nfs*73	ENST00000358485	NM_001080125.1	530	agA/ag	9/9	1	2	FACETS	0.653	0.572	0.739	0.653	0.572	0.739	SUBCLONAL	1	TRUE	1	0.368943099815169	2		373	623	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446294	70446294	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144991411	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	118	467	0	ENST00000373644.4:c.5234C>T	p.Thr1745Met	p.T1745M	ENST00000373644	NM_030625.2	1745	aCg/aTg	11/12	1	2	FACETS	0.83	0.749	0.915	0.83	0.749	0.915	CLONAL	1	TRUE	1	0.368943099815169	2		467	771	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972428	81972428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1341635199	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	75	367	0	ENST00000359376.3:c.3221C>T	p.Pro1074Leu	p.P1074L	ENST00000359376	NM_002661.3	1074	cCc/cTc	29/33	1	2	FACETS	0.76	0.667	0.86	0.76	0.667	0.86	SUBCLONAL	1	TRUE	1	0.368943099815169	2		367	535	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	98	307	0	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.701	0.625	0.782	0.701	0.625	0.782	SUBCLONAL	1	TRUE	1	0.368943099815169	2		307	758	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22412959	22412959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	62	232	0	ENST00000344548.3:c.206C>T	p.Pro69Leu	p.P69L	ENST00000344548	NM_001039802.1	69	cCg/cTg	5/7	1	2	FACETS	0.818	0.709	0.935	0.818	0.709	0.935	CLONAL	1	TRUE	1	0.368943099815169	2		232	411	SUCCESS
APC	324	MSKCC	GRCh37	5	112128170	112128170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768233232	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	90	299	0	ENST00000257430.4:c.673G>A	p.Glu225Lys	p.E225K	ENST00000257430	NM_000038.5	225	Gaa/Aaa	7/16	1	2	FACETS	0.797	0.708	0.892	0.797	0.708	0.892	SUBCLONAL	1	TRUE	1	0.368943099815169	2		299	612	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229299	55229299	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767193132	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	77	447	2	ENST00000275493.2:c.1606G>A	p.Val536Met	p.V536M	ENST00000275493	NM_005228.3	536	Gtg/Atg	13/28	1	2	FACETS	0.66	0.58	0.747	0.66	0.58	0.747	SUBCLONAL	1	TRUE	1	0.368943099815169	2		449	632	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660046	227660046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3731594	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	94	441	0	ENST00000305123.5:c.3409G>A	p.Asp1137Asn	p.D1137N	ENST00000305123	NM_005544.2	1137	Gat/Aat	1/2	1	2	FACETS	0.704	0.626	0.787	0.704	0.626	0.787	SUBCLONAL	1	TRUE	1	0.368943099815169	2		441	724	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250494	110250494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	65	302	0	ENST00000374672.4:c.181C>T	p.Arg61Cys	p.R61C	ENST00000374672	NM_004235.4	61	Cgc/Tgc	3/5	1	2	FACETS	0.718	0.623	0.819	0.718	0.623	0.819	SUBCLONAL	1	TRUE	1	0.368943099815169	2		302	491	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612184	189612184	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	100	467	0	ENST00000264731.3:c.1936C>A	p.Leu646Ile	p.L646I	ENST00000264731	NM_003722.4	646	Ctc/Atc	14/14	1	2	FACETS	0.805	0.72	0.896	0.805	0.72	0.896	CLONAL	1	TRUE	1	0.368943099815169	2		467	673	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849598	68849598	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368690400	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	115	473	0	ENST00000261769.5:c.1501G>A	p.Val501Met	p.V501M	ENST00000261769	NM_004360.3	501	Gtg/Atg	10/16	1	2	FACETS	0.798	0.719	0.882	0.798	0.719	0.882	SUBCLONAL	1	TRUE	1	0.368943099815169	2		473	781	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566520	41566520	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	28	340	0	ENST00000263253.7:c.4397G>T	p.Trp1466Leu	p.W1466L	ENST00000263253	NM_001429.3	1466	tGg/tTg	27/31	1	2	FACETS	0.228	0.181	0.282	0.228	0.181	0.282	SUBCLONAL	1	TRUE	1	0.368943099815169	2		340	665	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467088	25467088	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs899717364	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	85	396	0	ENST00000264709.3:c.1787G>A	p.Arg596Gln	p.R596Q	ENST00000264709	NM_175629.2	596	cGg/cAg	15/23	1	2	FACETS	0.774	0.685	0.869	0.774	0.685	0.869	SUBCLONAL	1	TRUE	1	0.368943099815169	2		396	595	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526603	106526603	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1277491292	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	58	333	0	ENST00000359195.3:c.2896G>A	p.Gly966Arg	p.G966R	ENST00000359195	NM_002649.2	966	Ggg/Agg	10/11	1	2	FACETS	0.519	0.445	0.599	0.519	0.445	0.599	SUBCLONAL	1	TRUE	1	0.368943099815169	2		333	606	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228046	36228046	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	192	497	0	ENST00000222270.7:c.7432C>T	p.Gln2478Ter	p.Q2478*	ENST00000222270	NM_014727.1	2478	Cag/Tag	33/37	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.368943099815169	2		497	799	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007825	45007826	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	76	466	0	ENST00000558401.1:c.275_276del	p.Pro92HisfsTer2	p.P92Hfs*2	ENST00000558401	NM_004048.2	91	aCC/a	2/4	1	2	FACETS	0.501	0.439	0.569	0.501	0.439	0.569	SUBCLONAL	1	TRUE	1	0.368943099815169	2		466	822	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489800	40489800	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356637796	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	75	423	0	ENST00000264657.5:c.626C>T	p.Ala209Val	p.A209V	ENST00000264657	NM_139276.2	209	gCg/gTg	7/24	1	2	FACETS	0.59	0.517	0.669	0.59	0.517	0.669	SUBCLONAL	1	TRUE	1	0.368943099815169	2		423	689	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932002	36932002	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	99	517	0	ENST00000361632.4:c.2467C>T	p.Gln823Ter	p.Q823*	ENST00000361632		823	Cag/Tag	16/16	1	2	FACETS	0.783	0.7	0.872	0.783	0.7	0.872	SUBCLONAL	1	TRUE	1	0.368943099815169	2		517	685	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557785	187557785	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	87	453	0	ENST00000441802.2:c.3926T>G	p.Val1309Gly	p.V1309G	ENST00000441802	NM_005245.3	1309	gTt/gGt	5/27	1	2	FACETS	0.621	0.549	0.697	0.621	0.549	0.697	SUBCLONAL	1	TRUE	1	0.368943099815169	2		453	760	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326285	62326285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746445840	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	146	365	0	ENST00000360203.5:c.3301G>A	p.Ala1101Thr	p.A1101T	ENST00000360203	NM_001283009.1	1101	Gcc/Acc	32/35	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.368943099815169	2		365	635	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18962988	18962988	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	64	414	0	ENST00000262803.5:c.856del	p.Asp286ThrfsTer35	p.D286Tfs*35	ENST00000262803	NM_002911.3	285	gtG/gt	6/24	1	2	FACETS	0.535	0.462	0.613	0.535	0.462	0.613	SUBCLONAL	1	TRUE	1	0.368943099815169	2		414	649	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991260	41991260	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	93	356	0	ENST00000219905.7:c.2093-2A>G		p.X698_splice	ENST00000219905	NM_001164273.1	698			1	2	FACETS	0.765	0.681	0.855	0.765	0.681	0.855	SUBCLONAL	1	TRUE	1	0.368943099815169	2		356	659	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759749	133759749	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	65	336	0	ENST00000318560.5:c.2072G>A	p.Ser691Asn	p.S691N	ENST00000318560	NM_005157.4	691	aGc/aAc	11/11	1	2	FACETS	0.727	0.631	0.829	0.727	0.631	0.829	SUBCLONAL	1	TRUE	1	0.368943099815169	2		336	485	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302868	15302869	+	stop_gained	Nonsense_Mutation	DNP	AC	AC	CT	novel	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	66	432	1	ENST00000263388.2:c.581_582delinsAG	p.Cys194Ter	p.C194*	ENST00000263388	NM_000435.2	194	tGT/tAG	4/33	1	2	FACETS	0.607	0.527	0.694	0.607	0.527	0.694	SUBCLONAL	1	TRUE	1	0.368943099815169	2		433	589	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420111	49420111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775381331	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	92	443	0	ENST00000301067.7:c.15638C>T	p.Thr5213Met	p.T5213M	ENST00000301067	NM_003482.3	5213	aCg/aTg	48/54	0.368943099815169	3	FACETS	0.81	0.72	0.907	0.405	0.36	0.454	CLONAL	1	TRUE	1	0.368943099815169	3		443	729	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781200	161781200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766915327	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	76	389	0	ENST00000366898.1:c.1205G>A	p.Arg402His	p.R402H	ENST00000366898	NM_004562.2	402	cGt/cAt	11/12	1	2	FACETS	0.668	0.586	0.756	0.668	0.586	0.756	SUBCLONAL	1	TRUE	1	0.368943099815169	2		389	617	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624285	89624285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064795967	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	65	274	0	ENST00000371953.3:c.59G>A	p.Gly20Glu	p.G20E	ENST00000371953	NM_000314.4	20	gGa/gAa	1/9	1	2	FACETS	0.756	0.657	0.863	0.756	0.657	0.863	SUBCLONAL	1	TRUE	1	0.368943099815169	2		274	466	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038862	12038862	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	212	397	0	ENST00000396373.4:c.1155del	p.Asn385LysfsTer5	p.N385Kfs*5	ENST00000396373	NM_001987.4	385	aaC/aa	7/8	0.368367326765493	5	FACETS	1	0.943	1	0.677	0.63	0.726	CLONAL	2	TRUE	2	0.368943099815169	5		397	879	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447415	12447415	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	96	418	0	ENST00000287820.6:c.654G>T	p.Lys218Asn	p.K218N	ENST00000287820	NM_015869.4	218	aaG/aaT	5/7	1	2	FACETS	0.687	0.611	0.767	0.687	0.611	0.767	SUBCLONAL	1	TRUE	1	0.368943099815169	2		418	758	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300040	137300040	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	82	358	1	ENST00000481739.1:c.325C>T	p.Pro109Ser	p.P109S	ENST00000481739	NM_002957.4	109	Ccc/Tcc	3/10	1	2	FACETS	0.86	0.76	0.966	0.86	0.76	0.966	CLONAL	1	TRUE	1	0.368943099815169	2		359	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0068023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	166	403	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.328125318981456	2	FACETS	0.951	0.879	1	0.951	0.879	1	CLONAL	2	TRUE	0	0.328125318981456	2		404	532	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21968242	21968242	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0068023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	93	324	0	ENST00000304494.5:c.458-1G>A		p.X153_splice	ENST00000304494	NM_000077.4	153			1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.328125318981456	2		324	504	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434521	140434521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777533608	NA	P-0068023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	70	308	0	ENST00000288602.6:c.2177G>A	p.Arg726His	p.R726H	ENST00000288602	NM_004333.4	726	cGc/cAc	18/18	1	2	FACETS	0.936	0.818	1	0.936	0.818	1	CLONAL	1	TRUE	1	0.328125318981456	2		308	456	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213841	66213841	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	23	329	0	ENST00000273854.3:c.2589T>G	p.Ser863Arg	p.S863R	ENST00000273854	NM_004439.5	863	agT/agG	15/18	1	2	FACETS	0.46	0.358	0.576	0.46	0.358	0.576	SUBCLONAL	1	TRUE	1	0.328125318981456	2		329	305	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241895	72241895	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	58	366	0	ENST00000357731.5:c.495A>C	p.Lys165Asn	p.K165N	ENST00000357731	NM_173808.2	165	aaA/aaC	3/7	1	2	FACETS	0.897	0.774	1	0.897	0.774	1	CLONAL	1	TRUE	1	0.328125318981456	2		366	394	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252155	226252155	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068024-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	129	160	0	ENST00000366813.1:c.103G>C	p.Gly35Arg	p.G35R	ENST00000366813		35	Ggg/Cgg	1/3	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		160	317	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	83	408	0	ENST00000269305.4:c.853G>T	p.Glu285Ter	p.E285*	ENST00000269305	NM_001126112.2	285	Gag/Tag	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		408	287	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0068025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	72	303	0	ENST00000269305.4:c.782+1G>C		p.X261_splice	ENST00000269305	NM_001126112.2	261			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		303	221	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0068025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	165	0	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		0	287	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0068025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	44	284	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		284	227	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0068025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	69	148	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		148	216	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870888	12870888	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	102	413	0	ENST00000228872.4:c.115G>T	p.Glu39Ter	p.E39*	ENST00000228872	NM_004064.3	39	Gaa/Taa	1/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		413	402	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954221	48954221	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0068025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	84	217	0	ENST00000267163.4:c.1421+1G>T		p.X474_splice	ENST00000267163	NM_000321.2	474			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		217	119	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249013	55249013	+	protein_altering_variant	In_Frame_Ins	INS	A	A	GGGG	novel	NA	P-0068025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	96	449	0	ENST00000275493.2:c.2311delinsGGGG	p.Asn771delinsGlyAsp	p.N771delinsGD	ENST00000275493	NM_005228.3	771	Aac/GGGGac	20/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		449	315	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111807	56111807	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	25	213	0	ENST00000399503.3:c.407C>G	p.Ser136Trp	p.S136W	ENST00000399503	NM_005921.1	136	tCg/tGg	1/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		213	229	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145689	11145689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318154109	NA	P-0068025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	64	428	0	ENST00000358026.2:c.4051G>A	p.Asp1351Asn	p.D1351N	ENST00000358026	NM_001128849.1	1351	Gac/Aac	29/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		428	281	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0068026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	23	354	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.221014673475667	3	FACETS	1	0.862	1	1	0.862	1	CLONAL	2	TRUE	1	0.15	3		354	146	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0068027-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	23	389	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.782	0.611	0.98	0.782	0.611	0.98	CLONAL	1	TRUE	1	0.21	2		389	280	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068027-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	47	227	0	ENST00000262160.6:c.1391C>A	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tAa	11/11	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.21	2		227	381	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312660	30312660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146187350	NA	P-0068027-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	29	222	0	ENST00000262643.3:c.641C>T	p.Ala214Val	p.A214V	ENST00000262643	NM_001238.2	214	gCg/gTg	8/12	1	2	FACETS	0.903	0.726	1	0.903	0.726	1	CLONAL	1	TRUE	1	0.21	2		222	306	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482870	67482870	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068027-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	78	240	0	ENST00000327367.4:c.1274C>G	p.Ser425Cys	p.S425C	ENST00000327367	NM_005902.3	425	tCt/tGt	9/9	1	2	FACETS	0.955	0.844	1	1	0.983	1	CLONAL	2	TRUE	1	0.21	2		240	389	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999618	100999618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762965993	NA	P-0068027-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	26	274	0	ENST00000325455.5:c.184C>T	p.Arg62Trp	p.R62W	ENST00000325455	NM_001202474.3	62	Cgg/Tgg	1/8	1	2	FACETS	0.904	0.718	1	0.904	0.718	1	CLONAL	1	TRUE	1	0.21	2		274	274	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2949714	2949714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068027-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	30	229	0	ENST00000396946.4:c.3230G>A	p.Arg1077Gln	p.R1077Q	ENST00000396946	NM_032415.4	1077	cGg/cAg	24/25	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.21	2		229	261	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372070	45372071	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATAT	novel	NA	P-0068027-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	37	201	0	ENST00000262160.6:c.1095_1098dup	p.Gly367IlefsTer10	p.G367Ifs*10	ENST00000262160	NM_005901.5	366	-/ATAT	9/11	1	2	FACETS	0.837	0.69	1	0.837	0.69	1	CLONAL	1	TRUE	1	0.21	2		201	421	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445223	29445223	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068027-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	41	249	0	ENST00000389048.3:c.3502G>T	p.Ala1168Ser	p.A1168S	ENST00000389048	NM_004304.4	1168	Gcc/Tcc	22/29	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.21	2		249	350	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956777	68956777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771902674	NA	P-0068027-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	24	206	0	ENST00000288368.4:c.895C>T	p.Arg299Trp	p.R299W	ENST00000288368	NM_024870.2	299	Cgg/Tgg	8/40	0.165560635559084	3	FACETS	0.577	0.451	0.722	0.288	0.225	0.361	SUBCLONAL	1	TRUE	1	0.21	3		206	438	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356379	66356379	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068027-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	31	257	0	ENST00000273854.3:c.1118T>C	p.Val373Ala	p.V373A	ENST00000273854	NM_004439.5	373	gTc/gCc	5/18	1	2	FACETS	0.703	0.568	0.855	0.703	0.568	0.855	SUBCLONAL	1	TRUE	1	0.21	2		257	420	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068029-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	22	350	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.514	0.399	0.646	0.514	0.399	0.646	SUBCLONAL	1	FALSE	1	0.333255218145875	2		350	257	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846113	151846113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068029-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	253	375	0	ENST00000262189.6:c.12899C>T	p.Ser4300Phe	p.S4300F	ENST00000262189	NM_170606.2	4300	tCt/tTt	52/59	0.274227831924762	4	FACETS	1	0.989	1	0.828	0.777	0.88	CLONAL	2	FALSE	1	0.333255218145875	4		375	815	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027690	152027690	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068029-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	209	321	0	ENST00000262189.6:c.385A>G	p.Ile129Val	p.I129V	ENST00000262189	NM_170606.2	129	Atc/Gtc	3/59	0.274227831924762	4	FACETS	1	0.987	1	0.823	0.768	0.88	CLONAL	2	FALSE	1	0.333255218145875	4		321	677	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219904	36219904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761847081	NA	P-0068029-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	40	407	0	ENST00000222270.7:c.4706C>T	p.Pro1569Leu	p.P1569L	ENST00000222270	NM_014727.1	1569	cCg/cTg	21/37	1	2	FACETS	0.389	0.322	0.464	0.389	0.322	0.464	SUBCLONAL	1	FALSE	1	0.333255218145875	2		407	617	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139804381	139804381	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767031937	NA	P-0068029-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	43	262	0	ENST00000247668.2:c.538G>A	p.Glu180Lys	p.E180K	ENST00000247668	NM_021138.3	180	Gag/Aag	6/11	1	2	FACETS	0.502	0.42	0.593	0.502	0.42	0.593	SUBCLONAL	1	FALSE	1	0.333255218145875	2		262	514	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983042	201983204	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCGGCATGAAGGCGTCTTCAAGTTCCTGCGCTCCGAGGCTGTGGCCCAACTATGGGGCCAAAAGAAAAAGAACAGCAACATGACCTACGAGAAGCTGAGCCGGGCCATGAGGTGAGCTGGCGGCCAGGACCCTCACGATACAGCCGGACATGGGGACAGGCGC	TCGGCATGAAGGCGTCTTCAAGTTCCTGCGCTCCGAGGCTGTGGCCCAACTATGGGGCCAAAAGAAAAAGAACAGCAACATGACCTACGAGAAGCTGAGCCGGGCCATGAGGTGAGCTGGCGGCCAGGACCCTCACGATACAGCCGGACATGGGGACAGGCGC	-	novel	NA	P-0068029-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	43	343	0	ENST00000359651.3:c.893_1001+54del		p.X298_splice	ENST00000359651		298		7/8	1	2	FACETS	0.458	0.382	0.541	0.458	0.382	0.541	SUBCLONAL	1	FALSE	1	0.333255218145875	2		343	564	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482437	56482437	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068030-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	40	379	0	ENST00000267101.3:c.985A>G	p.Lys329Glu	p.K329E	ENST00000267101	NM_001982.3	329	Aaa/Gaa	8/28	1	2	FACETS	0.769	0.637	0.917	0.769	0.637	0.917	CLONAL	1	TRUE	1	0.14	2		379	743	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405932	49405932	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068030-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	37	296	0	ENST00000418115.1:c.206T>C	p.Leu69Pro	p.L69P	ENST00000418115	NM_001664.2	69	cTg/cCg	3/5	1	2	FACETS	0.789	0.649	0.947	0.789	0.649	0.947	CLONAL	1	TRUE	1	0.14	2		296	670	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713863	30713863	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068030-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	59	373	0	ENST00000295754.5:c.1188T>G	p.Cys396Trp	p.C396W	ENST00000295754	NM_003242.5	396	tgT/tgG	4/7	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.14	2		373	787	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	47	350	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.975	0.83	1	0.975	0.83	1	CLONAL	1	TRUE	1	0.398416402421317	2		350	242	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	58	268	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.398416402421317	2		268	258	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174908	11174908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	94	447	0	ENST00000361445.4:c.7126C>T	p.Pro2376Ser	p.P2376S	ENST00000361445	NM_004958.3	2376	Cca/Tca	52/58	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.398416402421317	2		447	466	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101349	27101349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326693674	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	101	576	0	ENST00000324856.7:c.4631C>T	p.Ser1544Leu	p.S1544L	ENST00000324856	NM_006015.4	1544	tCg/tTg	18/20	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.398416402421317	2		576	503	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610149	43610149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1199456015	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	98	645	0	ENST00000355710.3:c.2101G>A	p.Glu701Lys	p.E701K	ENST00000355710	NM_020975.4	701	Gag/Aag	11/20	0.398416402421317	1	FACETS	0.945	0.848	1	0.945	0.848	1	CLONAL	1	TRUE	0	0.398416402421317	1		645	417	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860033	57860033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	111	518	0	ENST00000228682.2:c.773G>A	p.Ser258Asn	p.S258N	ENST00000228682	NM_005269.2	258	aGc/aAc	8/12	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.398416402421317	2		518	543	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857197	9857197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866121846	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	134	631	0	ENST00000330684.3:c.4204C>T	p.Arg1402Trp	p.R1402W	ENST00000330684	NM_001134407.1	1402	Cgg/Tgg	13/13	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.398416402421317	2		631	628	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858351	9858351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	108	555	0	ENST00000330684.3:c.3050C>T	p.Ser1017Phe	p.S1017F	ENST00000330684	NM_001134407.1	1017	tCc/tTc	13/13	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.398416402421317	2		555	530	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274248	10274248	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555491563	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	99	534	0	ENST00000330684.3:c.21G>A	p.Trp7Ter	p.W7*	ENST00000330684	NM_001134407.1	7	tgG/tgA	2/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.398416402421317	2		534	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	116	545	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.398416402421317	1	FACETS	0.992	0.9	1	0.992	0.9	1	CLONAL	1	TRUE	0	0.398416402421317	1		545	470	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719881	52719881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373680053	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	106	579	0	ENST00000322088.6:c.1093C>T	p.Leu365Phe	p.L365F	ENST00000322088	NM_014225.5	365	Ctc/Ttc	9/15	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.398416402421317	2		579	531	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419992	41419992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	110	632	0	ENST00000373198.4:c.329C>T	p.Ser110Phe	p.S110F	ENST00000373198	NM_133170.3	110	tCc/tTc	3/32	1	2	FACETS	0.974	0.878	1	0.974	0.878	1	CLONAL	1	TRUE	1	0.398416402421317	2		632	567	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247418	71247418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752297898	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	126	544	0	ENST00000318789.4:c.115G>A	p.Gly39Arg	p.G39R	ENST00000318789	NM_032682.5	39	Gga/Aga	6/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.398416402421317	2		544	581	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169999038	169999038	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	68	379	0	ENST00000295797.4:c.967C>T	p.Gln323Ter	p.Q323*	ENST00000295797	NM_002740.5	323	Cag/Tag	10/18	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.398416402421317	2		379	334	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604206	189604206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	102	507	0	ENST00000264731.3:c.1373C>T	p.Ser458Leu	p.S458L	ENST00000264731	NM_003722.4	458	tCa/tTa	11/14	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.398416402421317	2		507	497	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286943	33286943	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	143	761	0	ENST00000374542.5:c.1994C>T	p.Thr665Ile	p.T665I	ENST00000374542	NM_001141970.1	665	aCc/aTc	7/8	0.354858767593789	3	FACETS	1	0.974	1	0.587	0.536	0.641	CLONAL	1	TRUE	1	0.398416402421317	3		761	733	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965658	93965658	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751194338	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	81	465	0	ENST00000369303.4:c.2270G>A	p.Arg757Lys	p.R757K	ENST00000369303	NM_004440.3	757	aGg/aAg	13/17	1	2	FACETS	0.973	0.861	1	0.973	0.861	1	CLONAL	1	TRUE	1	0.398416402421317	2		465	418	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674329	117674329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	72	360	0	ENST00000368508.3:c.4145G>A	p.Gly1382Glu	p.G1382E	ENST00000368508	NM_002944.2	1382	gGa/gAa	26/43	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.398416402421317	2		360	343	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	CT	rs121913227	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	151	461	0	ENST00000288602.6:c.1798_1799delinsAG	p.Val600Arg	p.V600R	ENST00000288602	NM_004333.4	600	GTg/AGg	15/18	0.395290660117497	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	1	0.398416402421317	3		461	437	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845814	151845814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	108	617	0	ENST00000262189.6:c.13198C>T	p.Arg4400Trp	p.R4400W	ENST00000262189	NM_170606.2	4400	Cgg/Tgg	52/59	0.395290660117497	3	FACETS	0.993	0.892	1	0.496	0.446	0.55	CLONAL	1	TRUE	1	0.398416402421317	3		617	655	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372065	55372065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	85	649	0	ENST00000297316.4:c.755G>A	p.Ser252Asn	p.S252N	ENST00000297316	NM_022454.3	252	aGc/aAc	2/2	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.398416402421317	2		649	407	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030872	69030872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	92	454	0	ENST00000288368.4:c.3414G>A	p.Met1138Ile	p.M1138I	ENST00000288368	NM_024870.2	1138	atG/atA	27/40	1	2	FACETS	0.941	0.839	1	0.941	0.839	1	CLONAL	1	TRUE	1	0.398416402421317	2		454	491	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521516	8521516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748982864	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	93	478	0	ENST00000356435.5:c.722C>T	p.Pro241Leu	p.P241L	ENST00000356435		241	cCa/cTa	9/35	0.398416402421317	1	FACETS	0.974	0.872	1	0.974	0.872	1	CLONAL	1	TRUE	0	0.398416402421317	1		478	384	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974679	21974679	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs864622636	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	82	630	0	ENST00000304494.5:c.148C>T	p.Gln50Ter	p.Q50*	ENST00000304494	NM_000077.4	50	Cag/Tag	1/3	0.398416402421317	1	FACETS	0.975	0.867	1	0.975	0.867	1	CLONAL	1	TRUE	0	0.398416402421317	1		630	338	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240002	53240002	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	104	279	0	ENST00000375401.3:c.1439C>A	p.Pro480Gln	p.P480Q	ENST00000375401	NM_004187.3	480	cCg/cAg	11/26	1	1	FACETS	0.857	0.782	0.933	1	0.988	1	CLONAL	2	TRUE	0	0.398416402421317	1		279	244	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36824367	36824367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	91	524	0	ENST00000373129.3:c.169G>A	p.Asp57Asn	p.D57N	ENST00000373129	NM_032017.1	57	Gat/Aat	4/12	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.398416402421317	2		524	456	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65312418	65312418	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	98	537	0	ENST00000342505.4:c.1901C>T	p.Ala634Val	p.A634V	ENST00000342505	NM_002227.2	634	gCc/gTc	14/25	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.398416402421317	2		537	469	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132087	176132087	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	73	400	0	ENST00000367669.3:c.680G>T	p.Gly227Val	p.G227V	ENST00000367669	NM_022457.5	227	gGa/gTa	5/20	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.398416402421317	2		400	357	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094246	193094246	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	71	420	0	ENST00000367435.3:c.136G>A	p.Gly46Arg	p.G46R	ENST00000367435	NM_024529.4	46	Gga/Aga	2/17	1	2	FACETS	0.835	0.731	0.945	0.835	0.731	0.945	CLONAL	1	TRUE	1	0.398416402421317	2		420	427	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102033213	102033213	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	106	549	0	ENST00000282441.5:c.599A>T	p.Gln200Leu	p.Q200L	ENST00000282441	NM_001130145.2	200	cAg/cTg	3/9	0.236336121809064	1	FACETS	0.792	0.712	0.876	0.792	0.712	0.876	INDETERMINATE	1	TRUE	0	0.398416402421317	1		549	538	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715723	18715723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	93	538	0	ENST00000266497.5:c.3554C>T	p.Ala1185Val	p.A1185V	ENST00000266497		1185	gCc/gTc	25/31	0.236336121809064	1	FACETS	0.842	0.753	0.936	0.842	0.753	0.936	INDETERMINATE	1	TRUE	0	0.398416402421317	1		538	444	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432426	49432427	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	114	701	1	ENST00000301067.7:c.8712_8713delinsTT	p.Arg2905Cys	p.R2905C	ENST00000301067	NM_003482.3	2904	ccCCgt/ccTTgt	34/54	1	2	FACETS	0.957	0.864	1	0.957	0.864	1	CLONAL	1	TRUE	1	0.398416402421317	2		702	598	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26974635	26974635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	91	427	0	ENST00000381527.3:c.979G>A	p.Glu327Lys	p.E327K	ENST00000381527	NM_001260.1	327	Gaa/Aaa	10/13	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.398416402421317	2		427	391	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134716	41134716	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	105	591	0	ENST00000379561.5:c.912T>G	p.Asn304Lys	p.N304K	ENST00000379561	NM_002015.3	304	aaT/aaG	2/3	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.398416402421317	2		591	527	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519018	103519018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	79	527	0	ENST00000355739.4:c.2356G>A	p.Ala786Thr	p.A786T	ENST00000355739	NM_000123.3	786	Gct/Act	11/15	1	2	FACETS	0.889	0.785	1	0.889	0.785	1	CLONAL	1	TRUE	1	0.398416402421317	2		527	446	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729174	66729174	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	98	579	0	ENST00000307102.5:c.382G>A	p.Gly128Ser	p.G128S	ENST00000307102	NM_002755.3	128	Ggc/Agc	3/11	1	2	FACETS	0.874	0.782	0.971	0.874	0.782	0.971	CLONAL	1	TRUE	1	0.398416402421317	2		579	563	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858181	9858181	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	108	621	0	ENST00000330684.3:c.3220C>T	p.Pro1074Ser	p.P1074S	ENST00000330684	NM_001134407.1	1074	Cct/Tct	13/13	1	2	FACETS	0.913	0.821	1	0.913	0.821	1	CLONAL	1	TRUE	1	0.398416402421317	2		621	594	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337257	89337257	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	64	397	0	ENST00000301030.4:c.7774C>T	p.Gln2592Ter	p.Q2592*	ENST00000301030	NM_001256183.1	2592	Cag/Tag	12/13	1	2	FACETS	0.942	0.821	1	0.942	0.821	1	CLONAL	1	TRUE	1	0.398416402421317	2		397	341	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627716	37627716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1391374274	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	114	494	0	ENST00000447079.4:c.1631C>T	p.Pro544Leu	p.P544L	ENST00000447079	NM_015083.1	544	cCt/cTt	2/14	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.398416402421317	2		494	475	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855484	45855484	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	97	580	0	ENST00000391945.4:c.2173G>A	p.Ala725Thr	p.A725T	ENST00000391945	NM_000400.3	725	Gca/Aca	22/23	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.398416402421317	2		580	484	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543629	29543629	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	110	593	0	ENST00000389048.3:c.1534C>T	p.Gln512Ter	p.Q512*	ENST00000389048	NM_004304.4	512	Cag/Tag	7/29	1	2	FACETS	0.964	0.868	1	0.964	0.868	1	CLONAL	1	TRUE	1	0.398416402421317	2		593	573	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380558	31380558	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	94	544	0	ENST00000328111.2:c.1048C>A	p.Pro350Thr	p.P350T	ENST00000328111	NM_006892.3	350	Ccc/Acc	9/23	1	2	FACETS	0.853	0.761	0.951	0.853	0.761	0.951	CLONAL	1	TRUE	1	0.398416402421317	2		544	553	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627313	37627313	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	122	629	0	ENST00000249071.6:c.406C>T	p.Pro136Ser	p.P136S	ENST00000249071	NM_002872.4	136	Ccc/Tcc	5/7	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.398416402421317	2		629	610	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098501	47098502	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	128	649	0	ENST00000409792.3:c.6772_6773delinsTT	p.Pro2258Leu	p.P2258L	ENST00000409792	NM_014159.6	2258	CCa/TTa	15/21	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.398416402421317	2		649	619	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169977843	169977843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	90	368	0	ENST00000295797.4:c.310C>T	p.His104Tyr	p.H104Y	ENST00000295797	NM_002740.5	104	Cat/Tat	3/18	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.398416402421317	2		368	376	SUCCESS
ALB	213	MSKCC	GRCh37	4	74270115	74270115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs74821926	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	74	411	0	ENST00000295897.4:c.71G>A	p.Arg24Gln	p.R24Q	ENST00000295897	NM_000477.5	24	cGa/cAa	1/15	1	2	FACETS	0.899	0.791	1	0.899	0.791	1	CLONAL	1	TRUE	1	0.398416402421317	2		411	413	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609906	117609906	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201673653	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	82	491	0	ENST00000368508.3:c.6793G>T	p.Glu2265Ter	p.E2265*	ENST00000368508	NM_002944.2	2265	Gaa/Taa	43/43	1	2	FACETS	0.994	0.881	1	0.994	0.881	1	CLONAL	1	TRUE	1	0.398416402421317	2		491	414	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846048	128846048	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	113	584	0	ENST00000249373.3:c.978G>T	p.Met326Ile	p.M326I	ENST00000249373	NM_005631.4	326	atG/atT	5/12	0.395290660117497	3	FACETS	1	0.904	1	0.502	0.452	0.554	CLONAL	1	TRUE	1	0.398416402421317	3		584	678	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151871282	151871282	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1295108695	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	91	405	1	ENST00000262189.6:c.9308C>T	p.Ala3103Val	p.A3103V	ENST00000262189	NM_170606.2	3103	gCc/gTc	39/59	0.395290660117497	3	FACETS	1	0.967	1	0.607	0.542	0.677	CLONAL	1	TRUE	1	0.398416402421317	3		406	451	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56854524	56854524	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	82	448	0	ENST00000519728.1:c.106C>T	p.Pro36Ser	p.P36S	ENST00000519728	NM_002350.3	36	Cca/Tca	2/13	1	2	FACETS	0.874	0.773	0.981	0.874	0.773	0.981	CLONAL	1	TRUE	1	0.398416402421317	2		448	471	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2096745	2096745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	88	439	0	ENST00000349721.2:c.2972G>A	p.Gly991Asp	p.G991D	ENST00000349721	NM_003070.3	991	gGt/gAt	20/34	0.398416402421317	1	FACETS	0.975	0.87	1	0.975	0.87	1	CLONAL	1	TRUE	0	0.398416402421317	1		439	363	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	41	350	0				ENST00000310581	NM_198253.2	-/1132			0.264973607476135	3	FACETS	1	0.955	1	0.727	0.61	0.855	CLONAL	1	TRUE	1	0.264973607476135	3		350	241	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0068032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	141	719	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.264973607476135	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.264973607476135	2		719	498	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231439	46231439	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	136	602	0	ENST00000334344.6:c.1279G>T	p.Glu427Ter	p.E427*	ENST00000334344	NM_152641.2	427	Gaa/Taa	10/21	0.243980271730864	4	FACETS	1	0.936	1	0.688	0.627	0.751	CLONAL	2	TRUE	1	0.264973607476135	4		602	629	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629110	14629110	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs768130288	NA	P-0068032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	49	432	0	ENST00000254322.2:c.52G>T	p.Glu18Ter	p.E18*	ENST00000254322	NM_006145.1	18	Gag/Tag	1/3	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.264973607476135	2		432	322	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46725680	46725680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145938974	NA	P-0068032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	119	641	0	ENST00000371975.4:c.316C>T	p.Arg106Cys	p.R106C	ENST00000371975	NM_003579.3	106	Cgc/Tgc	5/18	0.264973607476135	1	FACETS	0.879	0.799	0.963	1	0.988	1	CLONAL	2	TRUE	0	0.264973607476135	1		641	443	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656778	45656778	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	57	623	0	ENST00000407780.3:c.378G>C	p.Leu126Phe	p.L126F	ENST00000407780	NM_001283052.1	126	ttG/ttC	3/7	0.25381427653123	3	FACETS	1	0.896	1	0.526	0.452	0.607	CLONAL	1	TRUE	1	0.264973607476135	3		623	463	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682125	37682125	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3862	247	552	1	ENST00000447079.4:c.3316G>A	p.Asp1106Asn	p.D1106N	ENST00000447079	NM_015083.1	1106	Gac/Aac	13/14	0.264973607476135	63	FACETS	1	0.951	1			1	CLONAL	4	TRUE	NA	0.264973607476135	63		553	4109	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641476	23641476	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	70	659	0	ENST00000261584.4:c.1999G>C	p.Glu667Gln	p.E667Q	ENST00000261584	NM_024675.3	667	Gaa/Caa	5/13	0.25381427653123	3	FACETS	1	0.937	1	0.561	0.49	0.638	CLONAL	1	TRUE	1	0.264973607476135	3		659	533	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866663	78866663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	127	508	0	ENST00000306801.3:c.2236G>A	p.Glu746Lys	p.E746K	ENST00000306801	NM_020761.2	746	Gag/Aag	19/34	0.264973607476135	1	FACETS	1	0.918	1	1	0.99	1	CLONAL	2	TRUE	0	0.264973607476135	1		508	414	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088787	27088788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0068033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	153	631	0	ENST00000324856.7:c.2401_2402dup	p.Gln802ValfsTer32	p.Q802Vfs*32	ENST00000324856	NM_006015.4	799	cag/caGGg	7/20	0.35408583079964	2	FACETS	0.973	0.899	1	0.973	0.899	1	CLONAL	2	TRUE	0	0.364828574544202	2		631	431	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447298	49447298	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	100	660	0	ENST00000301067.7:c.800G>A	p.Gly267Asp	p.G267D	ENST00000301067	NM_003482.3	267	gGc/gAc	6/54	0.364828574544202	5	FACETS	0.92	0.821	1	0.307	0.273	0.342	CLONAL	1	TRUE	2	0.364828574544202	5		660	922	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839809	42839809	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	147	566	0	ENST00000398585.3:c.1430A>T	p.Asp477Val	p.D477V	ENST00000398585	NM_001135099.1	477	gAc/gTc	13/14	0.3282774693794	2	FACETS	0.944	0.87	1	0.944	0.87	1	CLONAL	2	TRUE	0	0.364828574544202	2		566	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782329	NA	P-0068034-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	50	468	0	ENST00000269305.4:c.746G>C	p.Arg249Thr	p.R249T	ENST00000269305	NM_001126112.2	249	aGg/aCg	7/11	0.244523876733588	1	FACETS	0.774	0.657	0.901	0.774	0.657	0.901	CLONAL	1	TRUE	0	0.244523876733588	1		468	464	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0068034-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	36	354	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.969	0.799	1	0.969	0.799	1	CLONAL	1	TRUE	1	0.244523876733588	2		354	304	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143316	30143316	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068034-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	31	574	0	ENST00000389048.3:c.210C>G	p.Asp70Glu	p.D70E	ENST00000389048	NM_004304.4	70	gaC/gaG	1/29	1	2	FACETS	0.629	0.509	0.765	0.629	0.509	0.765	SUBCLONAL	1	TRUE	1	0.244523876733588	2		574	403	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378571	25378571	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068034-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	34	382	1	ENST00000311936.3:c.427G>A	p.Glu143Lys	p.E143K	ENST00000311936	NM_004985.3	143	Gaa/Aaa	4/5	1	2	FACETS	0.624	0.509	0.752	0.624	0.509	0.752	SUBCLONAL	1	TRUE	1	0.244523876733588	2		383	446	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971048	21971052	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGC	GCCGC	-	novel	NA	P-0068034-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	57	554	0	ENST00000304494.5:c.306_310del	p.Arg103GlyfsTer15	p.R103Gfs*15	ENST00000304494	NM_000077.4	102	gcGCGGCtg/gctg	2/3	0.244523876733588	1	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	0	0.244523876733588	1		554	409	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231755	66231755	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068034-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	25	369	0	ENST00000273854.3:c.1945A>G	p.Thr649Ala	p.T649A	ENST00000273854	NM_004439.5	649	Act/Gct	11/18	0.244523876733588	1	FACETS	0.69	0.546	0.856	0.69	0.546	0.856	SUBCLONAL	1	TRUE	0	0.244523876733588	1		369	260	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0068035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	41	403	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.443	0.367	0.528	0.443	0.367	0.528	SUBCLONAL	1	TRUE	1	0.17	2		404	1089	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973853	131973853	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	48	563	0	ENST00000265335.6:c.3556G>T	p.Val1186Leu	p.V1186L	ENST00000265335		1186	Gtg/Ttg	23/25	1	2	FACETS	0.714	0.602	0.838	0.714	0.602	0.838	SUBCLONAL	1	TRUE	1	0.17	2		563	791	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956956	2956956	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs750486472	NA	P-0068036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	128	717	0	ENST00000396946.4:c.2671C>T	p.Arg891Ter	p.R891*	ENST00000396946	NM_032415.4	891	Cga/Tga	20/25	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.334889985615905	2		717	638	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7119467	7119467	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	144	762	0	ENST00000302850.5:c.3787G>C	p.Glu1263Gln	p.E1263Q	ENST00000302850	NM_000208.2	1263	Gag/Cag	21/22	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.334889985615905	2		762	754	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881392	37881392	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	109	910	0	ENST00000269571.5:c.2584A>G	p.Thr862Ala	p.T862A	ENST00000269571		862	Aca/Gca	21/27	1	2	FACETS	0.811	0.728	0.899	0.811	0.728	0.899	CLONAL	1	TRUE	1	0.334889985615905	2		910	803	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217180	66217180	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	89	711	0	ENST00000273854.3:c.2435T>C	p.Leu812Pro	p.L812P	ENST00000273854	NM_004439.5	812	cTt/cCt	14/18	1	2	FACETS	0.799	0.709	0.896	0.799	0.709	0.896	SUBCLONAL	1	TRUE	1	0.334889985615905	2		711	665	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164865	123164865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	169	331	0	ENST00000218089.9:c.178G>A	p.Gly60Arg	p.G60R	ENST00000218089	NM_001042749.1	60	Gga/Aga	5/35	1	1	FACETS	1	0.939	1	1	0.993	1	CLONAL	2	TRUE	0	0.334889985615905	1		331	416	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101427	27101427	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	71	573	0	ENST00000324856.7:c.4709C>G	p.Ser1570Cys	p.S1570C	ENST00000324856	NM_006015.4	1570	tCt/tGt	18/20	1	2	FACETS	0.938	0.821	1	0.938	0.821	1	CLONAL	1	TRUE	1	0.334889985615905	2		573	452	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100378	27100378	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	175	826	0	ENST00000324856.7:c.4090C>T	p.Gln1364Ter	p.Q1364*	ENST00000324856	NM_006015.4	1364	Cag/Tag	17/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.334889985615905	2		826	847	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912288	29912288	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	119	1041	0	ENST00000376809.5:c.907C>T	p.Gln303Ter	p.Q303*	ENST00000376809	NM_002116.7	303	Cag/Tag	5/8	0.334889985615905	1	FACETS	0.797	0.72	0.879	0.797	0.72	0.879	SUBCLONAL	1	TRUE	0	0.334889985615905	1		1041	742	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877449	40877449	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs201441123	NA	P-0068036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	141	815	0	ENST00000373198.4:c.2247G>T	p.Gln749His	p.Q749H	ENST00000373198	NM_133170.3	749	caG/caT	15/32	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.334889985615905	2		815	770	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0068036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	125	284	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.334889985615905	2		284	577	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781146	161781146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531247345	NA	P-0068036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	112	727	1	ENST00000366898.1:c.1259G>A	p.Arg420His	p.R420H	ENST00000366898	NM_004562.2	420	cGc/cAc	11/12	0.244629628535166	3	FACETS	1	0.961	1	0.566	0.509	0.626	CLONAL	1	TRUE	1	0.334889985615905	3		728	690	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73633662	73633662	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	26	547	2	ENST00000377687.4:c.197A>G	p.Gln66Arg	p.Q66R	ENST00000377687	NM_001730.3	66	cAg/cGg	1/4	1	2	FACETS	0.429	0.34	0.531	0.429	0.34	0.531	SUBCLONAL	1	TRUE	1	0.334889985615905	2		549	362	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97897720	97897720	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	129	657	0	ENST00000289081.3:c.751G>A	p.Glu251Lys	p.E251K	ENST00000289081	NM_000136.2	251	Gaa/Aaa	8/15	0.334889985615905	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.334889985615905	1		657	582	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361184	66361184	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	134	792	0	ENST00000273854.3:c.988G>T	p.Glu330Ter	p.E330*	ENST00000273854	NM_004439.5	330	Gag/Tag	4/18	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.334889985615905	2		792	713	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2191335	2191335	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	79	852	0	ENST00000349721.2:c.4664A>T	p.Lys1555Met	p.K1555M	ENST00000349721	NM_003070.3	1555	aAg/aTg	33/34	1	2	FACETS	0.601	0.528	0.68	0.601	0.528	0.68	SUBCLONAL	1	TRUE	1	0.334889985615905	2		852	785	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396631	30396631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	32	573	0	ENST00000331968.5:c.88G>A	p.Gly30Arg	p.G30R	ENST00000331968	NM_002742.2	30	Ggg/Agg	1/18	1	2	FACETS	0.387	0.313	0.47	0.387	0.313	0.47	SUBCLONAL	1	TRUE	1	0.334889985615905	2		573	494	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680458	30680458	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	193	854	0	ENST00000376406.3:c.1261G>C	p.Glu421Gln	p.E421Q	ENST00000376406	NM_014641.2	421	Gag/Cag	5/15	0.334889985615905	1	FACETS	0.773	0.719	0.828	1	0.991	1	SUBCLONAL	2	TRUE	0	0.334889985615905	1		854	621	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99439989	99439989	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	119	627	0	ENST00000268035.6:c.957G>A	p.Met319Ile	p.M319I	ENST00000268035	NM_000875.3	319	atG/atA	4/21	0.244629628535166	3	FACETS	1	0.968	1	0.584	0.528	0.644	CLONAL	1	TRUE	1	0.334889985615905	3		627	710	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900155	101900155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	70	548	0	ENST00000374994.4:c.589G>T	p.Val197Phe	p.V197F	ENST00000374994	NM_004612.2	197	Gtt/Ttt	4/9	0.334889985615905	1	FACETS	0.686	0.6	0.78	0.686	0.6	0.78	SUBCLONAL	1	TRUE	0	0.334889985615905	1		548	507	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412542	80412542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1402276757	NA	P-0068036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	126	703	0	ENST00000286548.4:c.499G>A	p.Val167Ile	p.V167I	ENST00000286548	NM_002072.3	167	Gta/Ata	4/7	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.334889985615905	2		703	674	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332558	153332558	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	122	800	0	ENST00000281708.4:c.398G>C	p.Arg133Thr	p.R133T	ENST00000281708	NM_033632.3	133	aGa/aCa	2/12	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.334889985615905	2		800	696	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196850	108196850	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	77	677	0	ENST00000278616.4:c.6873G>A	p.Trp2291Ter	p.W2291*	ENST00000278616	NM_000051.3	2291	tgG/tgA	47/63	1	2	FACETS	0.689	0.605	0.78	0.689	0.605	0.78	SUBCLONAL	1	TRUE	1	0.334889985615905	2		677	667	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801476	1801476	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	74	796	0	ENST00000260795.2:c.382G>T	p.Ala128Ser	p.A128S	ENST00000260795		128	Gct/Tct	3/17	1	2	FACETS	0.694	0.607	0.787	0.694	0.607	0.787	SUBCLONAL	1	TRUE	1	0.334889985615905	2		796	637	SUCCESS
AR	367	MSKCC	GRCh37	X	66941782	66941782	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	84	340	0	ENST00000374690.3:c.2426A>C	p.Lys809Thr	p.K809T	ENST00000374690	NM_000044.3	809	aAa/aCa	6/8	1	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.334889985615905	1		340	291	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828165	243828165	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	107	464	0	ENST00000263826.5:c.193G>A	p.Glu65Lys	p.E65K	ENST00000263826	NM_005465.4	65	Gaa/Aaa	3/13	0.244629628535166	3	FACETS	1	0.97	1	0.608	0.546	0.673	CLONAL	1	TRUE	1	0.334889985615905	3		464	614	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950488	68950488	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	40	602	0	ENST00000288368.4:c.800T>A	p.Leu267His	p.L267H	ENST00000288368	NM_024870.2	267	cTt/cAt	7/40	0.334889985615905	3	FACETS	0.369	0.305	0.44	0.184	0.152	0.22	SUBCLONAL	1	TRUE	1	0.334889985615905	3		602	756	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	95	350	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.439110350581773	2		350	411	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755478	133755478	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355584861	NA	P-0068037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	55	573	0	ENST00000318560.5:c.1447C>T	p.Arg483Trp	p.R483W	ENST00000318560	NM_005157.4	483	Cgg/Tgg	9/11	0.196498911810789	2	FACETS	0.36	0.307	0.418	0.18	0.153	0.209	INDETERMINATE	1	TRUE	0	0.439110350581773	2		573	696	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0068037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	44	407	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.417	0.349	0.491	0.417	0.349	0.491	SUBCLONAL	1	TRUE	1	0.439110350581773	2		407	481	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418243	139418243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1333041588	NA	P-0068037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	237	635	0	ENST00000277541.6:c.329C>T	p.Pro110Leu	p.P110L	ENST00000277541	NM_017617.3	110	cCc/cTc	3/34	0.196498911810789	2	FACETS	0.751	0.704	0.799	0.751	0.704	0.799	INDETERMINATE	2	TRUE	0	0.439110350581773	2		635	719	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519920	NA	P-0068037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	152	599	0	ENST00000397062.3:c.85G>C	p.Asp29His	p.D29H	ENST00000397062	NM_006164.4	29	Gat/Cat	2/5	1	2	FACETS	0.946	0.867	1	0.946	0.867	1	CLONAL	1	TRUE	1	0.439110350581773	2		599	732	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347908	347908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146189916	NA	P-0068037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	201	805	0	ENST00000262320.3:c.1598G>A	p.Arg533Gln	p.R533Q	ENST00000262320	NM_003502.3	533	cGa/cAa	6/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.439110350581773	2		805	822	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482606	56482606	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	17	573	0	ENST00000267101.3:c.1063A>C	p.Thr355Pro	p.T355P	ENST00000267101	NM_001982.3	355	Acc/Ccc	9/28	1	2	FACETS	0.106	0.078	0.139	0.106	0.078	0.139	SUBCLONAL	1	TRUE	1	0.439110350581773	2		573	730	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971155	21971192	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCT	GCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCT	-	novel	NA	P-0068037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	294	618	0	ENST00000304494.5:c.166_203del	p.Ser56GlyfsTer51	p.S56Gfs*51	ENST00000304494	NM_000077.4	56	AGCGCCCGAGTGGCGGAGCTGCTGCTGCTCCACGGCGCg/g	2/3	0.439110350581773	2	FACETS	0.985	0.933	1	0.985	0.933	1	CLONAL	2	TRUE	0	0.439110350581773	2		618	680	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441554	6441554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	53	181	0	ENST00000356142.4:c.401C>T	p.Thr134Ile	p.T134I	ENST00000356142	NM_018890.3	134	aCt/aTt	6/7	1	2	FACETS	0.981	0.845	1	0.981	0.845	1	CLONAL	1	TRUE	1	0.439110350581773	2		181	246	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911124	29911134	+	frameshift_variant	Frame_Shift_Del	DEL	CTACGACGGCA	CTACGACGGCA	GCG	novel	NA	P-0068037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	180	570	2	ENST00000376809.5:c.423_433delinsGCG	p.Tyr142ArgfsTer32	p.Y142Rfs*32	ENST00000376809	NM_002116.7	141	gcCTACGACGGCAag/gcGCGag	3/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.439110350581773	2		572	636	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0068038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	729	382	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.422429137355937	5	FACETS	0.94	0.912	0.967	0.94	0.912	0.967	CLONAL	4	TRUE	1	0.537953524104695	5		382	1303	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106764	27106765	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0068038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	179	680	0	ENST00000324856.7:c.6376dup	p.Ser2126LysfsTer24	p.S2126Kfs*24	ENST00000324856	NM_006015.4	2125	-/A	20/20	0.265902646517757	1	FACETS	0.459	0.422	0.497	0.459	0.422	0.497	INDETERMINATE	1	TRUE	0	0.537953524104695	1		680	1060	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569689	41569689	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	162	624	0	ENST00000263253.7:c.4680G>C	p.Lys1560Asn	p.K1560N	ENST00000263253	NM_001429.3	1560	aaG/aaC	29/31	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.356506089478385	2		624	813	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519934	NA	P-0068039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	85	449	0	ENST00000263967.3:c.333G>C	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaC	2/21	0.356506089478385	3	FACETS	0.927	0.821	1	0.464	0.41	0.521	CLONAL	1	TRUE	1	0.356506089478385	3		449	606	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948136	178948136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	117	542	0	ENST00000263967.3:c.2908G>A	p.Glu970Lys	p.E970K	ENST00000263967	NM_006218.2	970	Gaa/Aaa	20/21	0.356506089478385	3	FACETS	1	0.924	1	0.514	0.464	0.568	CLONAL	1	TRUE	1	0.356506089478385	3		542	752	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961059	55961059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530419081	NA	P-0068039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	107	523	0	ENST00000263923.4:c.2881C>T	p.Arg961Trp	p.R961W	ENST00000263923	NM_002253.2	961	Cgg/Tgg	21/30	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.356506089478385	2		523	593	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149961	202149962	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs587776665	NA	P-0068039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	146	705	0	ENST00000358485.4:c.1405_1406del	p.Val469PhefsTer28	p.V469Ffs*28	ENST00000358485	NM_001080125.1	468	TGt/t	8/9	1	2	FACETS	0.943	0.86	1	0.943	0.86	1	CLONAL	1	TRUE	1	0.356506089478385	2		705	869	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323216	31323216	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	198	802	0	ENST00000412585.2:c.773G>C	p.Arg258Thr	p.R258T	ENST00000412585	NM_005514.6	258	aGa/aCa	4/8	NA	3	FACETS	1	0.985	1	0.621	0.574	0.669	INDETERMINATE	1	TRUE	1	0.356506089478385	3		802	1054	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323241	31323241	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	192	771	0	ENST00000412585.2:c.748C>T	p.Gln250Ter	p.Q250*	ENST00000412585	NM_005514.6	250	Cag/Tag	4/8	NA	3	FACETS	1	0.984	1	0.621	0.574	0.67	INDETERMINATE	1	TRUE	1	0.356506089478385	3		771	1022	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118370083	118370083	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	110	542	0	ENST00000534358.1:c.6027G>C	p.Leu2009Phe	p.L2009F	ENST00000534358	NM_005933.3	2009	ttG/ttC	23/36	1	2	FACETS	0.948	0.853	1	0.948	0.853	1	CLONAL	1	TRUE	1	0.356506089478385	2		542	651	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885962	59885962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	151	634	0	ENST00000259008.2:c.784G>A	p.Glu262Lys	p.E262K	ENST00000259008	NM_032043.2	262	Gag/Aag	7/20	NA	3	FACETS	1	0.986	1	0.703	0.644	0.764	INDETERMINATE	1	TRUE	1	0.356506089478385	3		634	710	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288612	33288612	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	105	603	0	ENST00000374542.5:c.940C>G	p.Gln314Glu	p.Q314E	ENST00000374542	NM_001141970.1	314	Cag/Gag	3/8	NA	3	FACETS	0.961	0.862	1	0.481	0.431	0.534	INDETERMINATE	1	TRUE	1	0.356506089478385	3		603	722	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325194	123325194	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	134	651	0	ENST00000358487.5:c.134C>G	p.Ser45Cys	p.S45C	ENST00000358487	NM_000141.4	45	tCt/tGt	3/18	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.356506089478385	2		651	701	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242900	142242900	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	123	553	0	ENST00000350721.4:c.4087G>A	p.Ala1363Thr	p.A1363T	ENST00000350721	NM_001184.3	1363	Gcg/Acg	22/47	0.356506089478385	3	FACETS	1	0.926	1	0.514	0.465	0.566	CLONAL	1	TRUE	1	0.356506089478385	3		553	791	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618339	37618339	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	162	630	0	ENST00000447079.4:c.15G>C	p.Glu5Asp	p.E5D	ENST00000447079	NM_015083.1	5	gaG/gaC	1/14	NA	3	FACETS	1	0.985	1	0.664	0.61	0.721	INDETERMINATE	1	TRUE	1	0.356506089478385	3		630	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs587780073	NA	P-0068040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	187	608	0	ENST00000269305.4:c.701A>C	p.Tyr234Ser	p.Y234S	ENST00000269305	NM_001126112.2	234	tAc/tCc	7/11	0.392992989632968	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.392992989632968	1		608	631	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912175	29912175	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs41547331	NA	P-0068040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	90	269	0	ENST00000376809.5:c.895+1G>A		p.X299_splice	ENST00000376809	NM_002116.7	299			0.392992989632968	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.392992989632968	1		269	263	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1268637	1268637	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	57	553	0	ENST00000310581.5:c.2580C>A	p.Asp860Glu	p.D860E	ENST00000310581	NM_198253.2	860	gaC/gaA	9/16	0.269259747506003	1	FACETS	0.387	0.332	0.448	0.387	0.332	0.448	SUBCLONAL	1	TRUE	0	0.392992989632968	1		553	602	SUCCESS
APC	324	MSKCC	GRCh37	5	112174956	112174956	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	84	598	0	ENST00000257430.4:c.3665C>T	p.Ser1222Leu	p.S1222L	ENST00000257430	NM_000038.5	1222	tCa/tTa	16/16	0.269259747506003	1	FACETS	0.517	0.456	0.581	0.517	0.456	0.581	SUBCLONAL	1	TRUE	0	0.392992989632968	1		598	665	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306532	41306560	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGGCCCTGGCGGTCCCGTACCCCCCTC	GGAGGCCCTGGCGGTCCCGTACCCCCCTC	-	novel	NA	P-0068040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	29	545	0	ENST00000373198.4:c.1099_1127del	p.Glu367ProfsTer43	p.E367Pfs*43	ENST00000373198	NM_133170.3	367	GAGGGGGGTACGGGACCGCCAGGGCCTCCc/c	7/32	1	2	FACETS	0.287	0.229	0.352	0.287	0.229	0.352	SUBCLONAL	1	TRUE	1	0.392992989632968	2		545	515	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0068041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	162	606	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.168937261458115	2	FACETS	1	0.987	1	0.692	0.635	0.751	INDETERMINATE	1	FALSE	0	0.286219798230602	2		606	818	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0068041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	82	465	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	FALSE	1	0.286219798230602	2		465	555	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117835	70117836	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0068041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	49	820	0	ENST00000245479.2:c.305dup	p.Pro103AlafsTer149	p.P103Afs*149	ENST00000245479	NM_000346.3	101	-/A	1/3	0.281645021616227	0	FACETS	0.418	0.353	0.489			1	SUBCLONAL	1	FALSE	0	0.286219798230602	0		820	585	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	140	714	0	ENST00000342988.3:c.1067C>G	p.Pro356Arg	p.P356R	ENST00000342988	NM_005359.5	356	cCt/cGt	9/12	0.286219798230602	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	0	0.286219798230602	1		714	691	SUCCESS
APC	324	MSKCC	GRCh37	5	112164585	112164585	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123116	NA	P-0068041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	44	628	0	ENST00000257430.4:c.1659G>A	p.Trp553Ter	p.W553*	ENST00000257430	NM_000038.5	553	tgG/tgA	14/16	0.168937261458115	2	FACETS	0.485	0.406	0.573	0.242	0.203	0.287	INDETERMINATE	1	FALSE	0	0.286219798230602	2		628	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578525	7578525	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519976	NA	P-0068041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	251	765	0	ENST00000269305.4:c.405C>G	p.Cys135Trp	p.C135W	ENST00000269305	NM_001126112.2	135	tgC/tgG	5/11	0.286219798230602	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	FALSE	0	0.286219798230602	2		765	836	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411796	63411797	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0068041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	137	822	0	ENST00000330258.3:c.1370dup	p.Ser458GlufsTer2	p.S458Efs*2	ENST00000330258	NM_152424.3	457	cag/caAg	2/2	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.286219798230602	2		822	801	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861493	152861493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1442543413	NA	P-0068041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	79	629	0	ENST00000406277.2:c.259C>T	p.Arg87Trp	p.R87W	ENST00000406277	NM_152274.4	87	Cgg/Tgg	4/7	NA		FACETS		0.751	0.963				INDETERMINATE	1	FALSE	NA	0.286219798230602	2		629	647	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646363	3646363	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs551757021	NA	P-0068041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	118	688	0	ENST00000294008.3:c.1715T>A	p.Val572Glu	p.V572E	ENST00000294008	NM_032444.2	572	gTg/gAg	8/15	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.286219798230602	2		688	775	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593646	55593647	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGACCCAACACAACTTCCTTATGACTCACA	novel	NA	P-0068042-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	88	518	0	ENST00000288135.5:c.1736_1737insCTCACAAGACCCAACACAACTTCCTTATGA	p.Asp579_His580insSerGlnAspProThrGlnLeuProTyrAsp	p.D579_H580insSQDPTQLPYD	ENST00000288135	NM_000222.2	571	ata/atAGACCCAACACAACTTCCTTATGACTCACAa	11/21	0.574553899900769	1	FACETS	0.673	0.602	0.747	0.673	0.602	0.747	SUBCLONAL	1	TRUE	0	0.587974148615865	1		518	314	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0068044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	40	451	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	1	2	FACETS	1	0.881	1	1	0.97	1	CLONAL	2	FALSE	1	0.13665572703698	2		451	274	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115727	108115727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747727055	NA	P-0068044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	16	382	0	ENST00000278616.4:c.875C>T	p.Pro292Leu	p.P292L	ENST00000278616	NM_000051.3	292	cCg/cTg	7/63	1	2	FACETS	0.887	0.656	1	0.887	0.656	1	CLONAL	1	FALSE	1	0.13665572703698	2		382	264	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830958	72830958	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	67	575	0	ENST00000268489.5:c.5623del	p.Glu1875LysfsTer39	p.E1875Kfs*39	ENST00000268489	NM_006885.3	1875	Gaa/aa	9/10	1	2	FACETS	1	0.95	1	1	0.983	1	CLONAL	2	FALSE	1	0.13665572703698	2		575	414	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115982	8115983	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0068045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	94	409	0	ENST00000346208.3:c.1330dup	p.Ter444LeufsTer63	p.*444Lfs*63	ENST00000346208		443	ggt/ggTt	6/6	0.590421841573612	3	FACETS	0.888	0.795	0.986	0.444	0.397	0.493	CLONAL	1	TRUE	1	0.64916806168766	3		409	432	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229315	55229315	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	86	500	0	ENST00000275493.2:c.1622T>A	p.Leu541His	p.L541H	ENST00000275493	NM_005228.3	541	cTt/cAt	13/28	0.64916806168766	3	FACETS	0.679	0.602	0.76	0.339	0.301	0.38	SUBCLONAL	1	TRUE	1	0.64916806168766	3		500	517	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821371	72821371	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1344062004	NA	P-0068045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	63	233	0	ENST00000268489.5:c.10804G>A	p.Ala3602Thr	p.A3602T	ENST00000268489	NM_006885.3	3602	Gcc/Acc	10/10	1	2	FACETS	0.966	0.849	1	0.966	0.849	1	CLONAL	1	TRUE	1	0.64916806168766	2		233	201	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0068047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	84	357	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.897	0.799	1	0.897	0.799	1	CLONAL	1	TRUE	1	0.522962209377455	2		357	358	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0068047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	195	395	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.522962209377455	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.522962209377455	1		395	477	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	181	570	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.522962209377455	2		570	625	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515306	149515306	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202213873	NA	P-0068047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	173	494	0	ENST00000261799.4:c.176C>T	p.Pro59Leu	p.P59L	ENST00000261799	NM_002609.3	59	cCg/cTg	3/23	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.522962209377455	2		494	630	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89478319	89478319	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0068047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	73	350	0	ENST00000336596.2:c.2136+2T>C		p.X712_splice	ENST00000336596	NM_005233.5	712			1	2	FACETS	0.859	0.757	0.967	0.859	0.757	0.967	CLONAL	1	TRUE	1	0.522962209377455	2		350	325	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80037300	80037300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	92	343	0	ENST00000265081.6:c.1586C>T	p.Ser529Leu	p.S529L	ENST00000265081	NM_002439.4	529	tCa/tTa	11/24	1	2	FACETS	0.856	0.765	0.951	0.856	0.765	0.951	CLONAL	1	TRUE	1	0.522962209377455	2		343	411	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974700	21974701	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0068048-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	114	350	0	ENST00000304494.5:c.126_127del	p.Asn42LysfsTer77	p.N42Kfs*77	ENST00000304494	NM_000077.4	42	aaTAgt/aagt	1/3	0.558947302936817	1	FACETS	0.954	0.871	1	0.954	0.871	1	CLONAL	1	TRUE	0	0.558947302936817	1		350	308	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313279	65313279	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068048-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	36	313	0	ENST00000342505.4:c.1835C>T	p.Ser612Phe	p.S612F	ENST00000342505	NM_002227.2	612	tCt/tTt	13/25	1	2	FACETS	0.353	0.29	0.423	0.353	0.29	0.423	SUBCLONAL	1	TRUE	1	0.558947302936817	2		313	365	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227632	36227632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758032213	NA	P-0068048-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	37	322	0	ENST00000222270.7:c.7201G>A	p.Asp2401Asn	p.D2401N	ENST00000222270	NM_014727.1	2401	Gat/Aat	31/37	1	2	FACETS	0.271	0.223	0.324	0.271	0.223	0.324	SUBCLONAL	1	TRUE	1	0.558947302936817	2		322	489	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134242	41134242	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	36	397	0	ENST00000379561.5:c.1386G>T	p.Leu462Phe	p.L462F	ENST00000379561	NM_002015.3	462	ttG/ttT	2/3	1	2	FACETS	0.686	0.564	0.824	0.686	0.564	0.824	SUBCLONAL	1	TRUE	1	0.22	2		397	477	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0068051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	138	411	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.419293777734615	2		411	566	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0068051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	100	400	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.968	0.868	1	0.968	0.868	1	CLONAL	1	TRUE	1	0.419293777734615	2		400	493	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440943	56440943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786205215	NA	P-0068051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	262	241	0	ENST00000407977.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000407977		132	Cga/Tga	4/10	0.419293777734615	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.419293777734615	2		241	547	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0068051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	115	284	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.419293777734615	2		284	477	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120512	70120513	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCTC	novel	NA	P-0068051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	161	265	0	ENST00000245479.2:c.1515_1518dup	p.Thr507AlafsTer72	p.T507Afs*72	ENST00000245479	NM_000346.3	505	cag/caGCTCg	3/3	0.419293777734615	2	FACETS	1	0.986	1	0.667	0.614	0.72	CLONAL	1	TRUE	0	0.419293777734615	2		265	576	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794791	242794791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	76	187	0	ENST00000334409.5:c.418G>A	p.Ala140Thr	p.A140T	ENST00000334409	NM_005018.2	140	Gca/Aca	2/5	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.419293777734615	2		187	344	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0068052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	235	457	0	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	0.433412466757004	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.433412466757004	2		457	523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578546	7578547	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0068052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	291	318	0	ENST00000269305.4:c.383dup	p.Ala129CysfsTer20	p.A129Cfs*20	ENST00000269305	NM_001126112.2	128	cct/ccCt	5/11	0.385037479934767	3	FACETS	0.838	0.795	0.881	0.838	0.795	0.881	CLONAL	3	TRUE	0	0.433412466757004	3		318	650	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	44	350	0				ENST00000310581	NM_198253.2	-/1132			0.473985963314445	3	FACETS	1	0.913	1	0.555	0.471	0.644	CLONAL	1	TRUE	1	0.538596237975408	3		350	187	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0068053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	246	288	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.538596237975408	4	FACETS	0.972	0.92	1	0.972	0.92	1	CLONAL	3	TRUE	1	0.538596237975408	4		288	482	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179197	123179197	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	167	197	0	ENST00000218089.9:c.646C>T	p.Arg216Ter	p.R216*	ENST00000218089	NM_001042749.1	216	Cga/Tga	8/35	0.324165819076249	2	FACETS	0.883	0.839	0.926			1	CLONAL	3	TRUE	NA	0.538596237975408	2		197	234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573987	7573987	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397516434	NA	P-0068053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	197	409	0	ENST00000269305.4:c.1040C>A	p.Ala347Asp	p.A347D	ENST00000269305	NM_001126112.2	347	gCc/gAc	10/11	0.538596237975408	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.538596237975408	2		409	348	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572904	41572904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	86	499	0	ENST00000263253.7:c.5189C>T	p.Ser1730Phe	p.S1730F	ENST00000263253	NM_001429.3	1730	tCt/tTt	31/31	0.32630375488189	5	FACETS	1	0.93	1	0.356	0.315	0.399	CLONAL	1	TRUE	2	0.538596237975408	5		499	541	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120657	115120657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	85	476	0	ENST00000257566.3:c.349C>T	p.His117Tyr	p.H117Y	ENST00000257566	NM_016569.3	117	Cac/Tac	1/8	0.501869859042042	4	FACETS	0.804	0.712	0.903	0.268	0.237	0.301	CLONAL	1	TRUE	1	0.538596237975408	4		476	604	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871757	12871757	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0068053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	297	450	0	ENST00000228872.4:c.476-2A>G		p.X159_splice	ENST00000228872	NM_004064.3	159			0.501869859042042	4	FACETS	0.967	0.92	1	0.967	0.92	1	CLONAL	3	TRUE	1	0.538596237975408	4		450	585	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346786	225346786	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	55	368	0	ENST00000264414.4:c.1852C>T	p.Gln618Ter	p.Q618*	ENST00000264414	NM_003590.4	618	Caa/Taa	14/16	1	2	FACETS	0.636	0.547	0.732	0.636	0.547	0.732	SUBCLONAL	1	TRUE	1	0.538596237975408	2		368	321	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143235873	143235873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	79	321	0	ENST00000262992.4:c.415G>A	p.Glu139Lys	p.E139K	ENST00000262992	NM_001101669.1	139	Gaa/Aaa	6/24	0.538596237975408	3	FACETS	0.936	0.827	1	0.468	0.413	0.525	CLONAL	1	TRUE	1	0.538596237975408	3		321	398	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99473531	99473531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	158	341	0	ENST00000268035.6:c.2953G>A	p.Asp985Asn	p.D985N	ENST00000268035	NM_000875.3	985	Gat/Aat	15/21	0.462777028867235	5	FACETS	1	0.93	1			1	CLONAL	2	TRUE	NA	0.538596237975408	5		341	526	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650332	48650332	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200599207	NA	P-0068053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	176	243	0	ENST00000376670.3:c.302C>T	p.Thr101Met	p.T101M	ENST00000376670	NM_002049.3	101	aCg/aTg	3/6	0.324165819076249	2	FACETS	0.848	0.804	0.89			1	CLONAL	3	TRUE	NA	0.538596237975408	2		243	257	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739611	41739611	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	104	264	0	ENST00000242208.4:c.362C>T	p.Ser121Leu	p.S121L	ENST00000242208	NM_002192.2	121	tCg/tTg	2/3	0.473291598909216	5	FACETS	1	0.924	1	0.682	0.618	0.75	CLONAL	2	TRUE	2	0.538596237975408	5		264	341	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929371	44929371	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	83	298	0	ENST00000377967.4:c.2471C>T	p.Ser824Leu	p.S824L	ENST00000377967	NM_021140.2	824	tCa/tTa	17/29	0.324165819076249	2	FACETS	1	0.92	1			1	CLONAL	1	TRUE	NA	0.538596237975408	2		298	297	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135804258	135804258	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0068053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	291	473	0	ENST00000298552.3:c.2T>C	p.Met1?	p.M1?	ENST00000298552	NM_001162426.1	1	aTg/aCg	3/23	0.538596237975408	3	FACETS	0.979	0.937	1	0.979	0.937	1	CLONAL	3	TRUE	0	0.538596237975408	3		473	467	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713315	30713315	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764821003	NA	P-0068053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	51	478	0	ENST00000295754.5:c.640G>A	p.Glu214Lys	p.E214K	ENST00000295754	NM_003242.5	214	Gag/Aag	4/7	0.538596237975408	6	FACETS	0.539	0.457	0.629	0.135	0.114	0.158	SUBCLONAL	1	TRUE	2	0.538596237975408	6		478	730	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541229	187541229	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1579333329	NA	P-0068053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	120	528	0	ENST00000441802.2:c.6511C>G	p.Pro2171Ala	p.P2171A	ENST00000441802	NM_005245.3	2171	Ccg/Gcg	10/27	0.538596237975408	3	FACETS	1	0.973	1	0.595	0.541	0.652	CLONAL	1	TRUE	1	0.538596237975408	3		528	475	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90645570	90645570	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	102	261	0	ENST00000330062.3:c.53G>T	p.Arg18Leu	p.R18L	ENST00000330062	NM_002168.2	18	cGg/cTg	1/11	0.462777028867235	5	FACETS	0.984	0.889	1			1	CLONAL	2	TRUE	NA	0.538596237975408	5		261	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0068054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	94	403	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.202868832588844	1	FACETS	0.987	0.883	1	1	0.986	1	CLONAL	2	TRUE	0	0.202868832588844	1		404	422	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828867	26828867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	55	436	0	ENST00000381527.3:c.89G>A	p.Gly30Asp	p.G30D	ENST00000381527	NM_001260.1	30	gGc/gAc	1/13	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.202868832588844	2		436	477	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168996	32168996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs8192573	NA	P-0068054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	68	517	0	ENST00000375023.3:c.4037G>A	p.Arg1346Gln	p.R1346Q	ENST00000375023	NM_004557.3	1346	cGg/cAg	22/30	0.202868832588844	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.202868832588844	1		517	418	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335129	65335129	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	51	530	0	ENST00000342505.4:c.512C>A	p.Ala171Asp	p.A171D	ENST00000342505	NM_002227.2	171	gCt/gAt	6/25	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.202868832588844	2		530	432	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003454	57003454	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	57	541	0	ENST00000257254.3:c.1025A>T	p.Lys342Met	p.K342M	ENST00000257254		342	aAg/aTg	1/2	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.202868832588844	2		541	458	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0068056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	151	400	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.610910131708843	3	FACETS	0.865	0.801	0.93	0.865	0.801	0.93	CLONAL	2	TRUE	1	0.610910131708843	3		400	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0068056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	167	403	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.946	0.874	1	0.946	0.874	1	CLONAL	1	TRUE	1	0.610910131708843	2		404	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501195	NA	P-0068056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	195	413	0	ENST00000269305.4:c.313G>A	p.Gly105Ser	p.G105S	ENST00000269305	NM_001126112.2	105	Ggc/Agc	4/11	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.610910131708843	2		413	631	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946227	81946227	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1295648437	NA	P-0068056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	170	332	0	ENST00000359376.3:c.1960G>A	p.Gly654Arg	p.G654R	ENST00000359376	NM_002661.3	654	Gga/Aga	19/33	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.610910131708843	2		332	514	SUCCESS
APC	324	MSKCC	GRCh37	5	112162804	112162804	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0068056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	104	250	0	ENST00000257430.4:c.1412del		p.X471_splice	ENST00000257430	NM_000038.5	471			1	2	FACETS	0.938	0.848	1	0.938	0.848	1	CLONAL	1	TRUE	1	0.610910131708843	2		250	363	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244167	153244167	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	431	370	0	ENST00000281708.4:c.1990G>T	p.Glu664Ter	p.E664*	ENST00000281708	NM_033632.3	664	Gag/Tag	12/12	0.610910131708843	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.610910131708843	2		370	697	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983140	201983141	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0068056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	181	323	0	ENST00000359651.3:c.990_991dup	p.Arg331ProfsTer4	p.R331Pfs*4	ENST00000359651		330	agc/agCCc	7/8	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.610910131708843	2		323	582	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679838	88679838	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs542205293	NA	P-0068056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	122	267	0	ENST00000360948.2:c.625C>A	p.Leu209Ile	p.L209I	ENST00000360948	NM_001012338.2	209	Ctt/Att	7/19	1	2	FACETS	0.916	0.834	1	0.916	0.834	1	CLONAL	1	TRUE	1	0.610910131708843	2		267	436	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856004	151856004	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201674711	NA	P-0068056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	172	333	0	ENST00000262189.6:c.11614G>A	p.Glu3872Lys	p.E3872K	ENST00000262189	NM_170606.2	3872	Gaa/Aaa	44/59	1	2	FACETS	0.888	0.821	0.958	0.888	0.821	0.958	CLONAL	1	TRUE	1	0.610910131708843	2		333	634	SUCCESS
APC	324	MSKCC	GRCh37	5	112175356	112175420	+	frameshift_variant	Frame_Shift_Del	DEL	TTCAGGAGCGAAATCTCCCTCCAAAAGTGGTGCTCAGACACCCAAAAGTCCACCTGAACACTATG	TTCAGGAGCGAAATCTCCCTCCAAAAGTGGTGCTCAGACACCCAAAAGTCCACCTGAACACTATG	-	novel	NA	P-0068056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	138	313	0	ENST00000257430.4:c.4073_4137del	p.Ala1358AspfsTer6	p.A1358Dfs*6	ENST00000257430	NM_000038.5	1355	tcTTCAGGAGCGAAATCTCCCTCCAAAAGTGGTGCTCAGACACCCAAAAGTCCACCTGAACACTATGtt/tctt	16/16	1	2	FACETS	0.949	0.87	1	0.949	0.87	1	CLONAL	1	TRUE	1	0.610910131708843	2		313	476	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264335	30264335	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	52	180	0	ENST00000322652.5:c.70G>T	p.Gly24Cys	p.G24C	ENST00000322652	NM_015355.2	24	Ggc/Tgc	1/16	1	2	FACETS	0.803	0.692	0.921	0.803	0.692	0.921	CLONAL	1	TRUE	1	0.610910131708843	2		180	212	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0068058-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	77	288	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.259667448161953	4	FACETS	1	0.951	1	0.762	0.674	0.854	CLONAL	2	TRUE	1	0.259667448161953	4		288	327	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0068058-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	65	400	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.259667448161953	2		400	464	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249348	110249348	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068058-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	75	440	0	ENST00000374672.4:c.1225A>C	p.Lys409Gln	p.K409Q	ENST00000374672	NM_004235.4	409	Aag/Cag	4/5	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.259667448161953	2		440	443	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933345	39933346	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0068058-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	107	615	0	ENST00000378444.4:c.1253_1254del	p.Arg418LysfsTer21	p.R418Kfs*21	ENST00000378444	NM_001123385.1	418	aGA/a	4/15	1	2	FACETS	0.818	0.737	0.903	1	0.985	1	CLONAL	2	TRUE	1	0.259667448161953	2		615	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0068060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	39	471	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.326656143235845	3	FACETS	1	0.93	1	0.41	0.342	0.484	CLONAL	1	TRUE	0	0.32666564035048	3		471	226	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591121	67591121	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1390357148	NA	P-0068060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	12	345	0	ENST00000274335.5:c.1714C>T	p.Gln572Ter	p.Q572*	ENST00000274335		572	Cag/Tag	12/15	0.174517240055656	3	FACETS	1	0.841	1	0.432	0.309	0.575	INDETERMINATE	1	TRUE	0	0.32666564035048	3		345	66	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986940	36986941	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0068060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	49	432	0	ENST00000354822.5:c.747_748dup	p.Ala250GlyfsTer46	p.A250Gfs*46	ENST00000354822	NM_001079668.2	250	gcc/gGGcc	3/3	0.174517240055656	3	FACETS	0.98	0.844	1	0.654	0.562	0.75	INDETERMINATE	2	TRUE	0	0.32666564035048	3		432	178	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385197	41385197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	15	391	0	ENST00000373198.4:c.764C>T	p.Ala255Val	p.A255V	ENST00000373198	NM_133170.3	255	gCa/gTa	6/32	0.32666564035048	3	FACETS	0.632	0.464	0.832	0.316	0.232	0.416	SUBCLONAL	1	TRUE	1	0.32666564035048	3		391	169	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0068069-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	289	342	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.379796853075123	3	FACETS	0.905	0.859	0.951	0.905	0.859	0.951	CLONAL	3	TRUE	0	0.421352328190102	3		343	612	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0068069-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	122	465	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	0.408560624887069	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.421352328190102	3		465	318	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100462	8100462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752779081	NA	P-0068069-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	199	724	2	ENST00000346208.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000346208		146	Gcc/Acc	3/6	0.421352328190102	3	FACETS	0.916	0.854	0.981	0.916	0.854	0.981	CLONAL	2	TRUE	1	0.421352328190102	3		726	624	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911632	114911632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068069-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	64	432	0	ENST00000543371.1:c.1150C>T	p.Leu384Phe	p.L384F	ENST00000543371	NM_001198531.1	384	Ctt/Ttt	10/14	0.421352328190102	3	FACETS	0.793	0.688	0.906	0.396	0.344	0.453	CLONAL	1	TRUE	1	0.421352328190102	3		432	464	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56872967	56872967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068069-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	71	411	1	ENST00000308159.5:c.2122G>A	p.Asp708Asn	p.D708N	ENST00000308159	NM_014669.4	708	Gat/Aat	19/22	0.408560624887069	3	FACETS	1	0.954	1	0.591	0.52	0.668	CLONAL	1	TRUE	1	0.421352328190102	3		412	345	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223060	5223060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1379163672	NA	P-0068069-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	235	728	0	ENST00000357368.4:c.2743G>A	p.Glu915Lys	p.E915K	ENST00000357368	NM_002850.3	915	Gag/Aag	18/38	0.408560624887069	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.421352328190102	3		728	630	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498457	89498457	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068069-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	100	564	0	ENST00000336596.2:c.2429A>G	p.Tyr810Cys	p.Y810C	ENST00000336596	NM_005233.5	810	tAt/tGt	14/17	0.408560624887069	3	FACETS	1	0.97	1	0.61	0.547	0.676	CLONAL	1	TRUE	1	0.421352328190102	3		564	471	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0068084-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	57	288	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.4	2		288	272	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0068084-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	109	506	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.4	2		506	472	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249341	110249341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068084-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	75	315	0	ENST00000374672.4:c.1232C>T	p.Ser411Phe	p.S411F	ENST00000374672	NM_004235.4	411	tCc/tTc	4/5	1	2	FACETS	0.805	0.707	0.909	0.805	0.707	0.909	CLONAL	1	TRUE	1	0.4	2		315	466	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526817	31526817	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs762001670	NA	P-0068084-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	81	562	0	ENST00000344624.3:c.223C>T	p.Arg75Ter	p.R75*	ENST00000344624		75	Cga/Tga	2/33	1	2	FACETS	0.902	0.798	1	0.902	0.798	1	CLONAL	1	TRUE	1	0.4	2		562	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0068085-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	17	395	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.37	0.275	0.485	0.37	0.275	0.485	SUBCLONAL	1	TRUE	1	0.14	2		395	656	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519912	NA	P-0068085-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	12	280	0	ENST00000374080.3:c.3670C>G	p.Leu1224Val	p.L1224V	ENST00000374080		1224	Ctc/Gtc	26/45	1	1	FACETS	0.415	0.29	0.57	0.415	0.29	0.57	SUBCLONAL	1	TRUE	0	0.14	1		280	384	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022724	31022724	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068086-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	95	741	0	ENST00000375687.4:c.2209G>T	p.Val737Phe	p.V737F	ENST00000375687	NM_015338.5	737	Gtt/Ttt	13/13	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.527851301199527	2		741	332	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0068087-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	306	348	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.260070315394904	3	FACETS	1	0.986	1	1	0.986	1	INDETERMINATE	2	TRUE	1	0.459884798845986	3		348	736	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0068087-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	391	576	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	0.459884798845986	3	FACETS	0.895	0.857	0.933	0.895	0.857	0.933	CLONAL	3	TRUE	0	0.459884798845986	3		576	779	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271581	26271581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068087-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	192	703	0	ENST00000305910.3:c.32C>T	p.Ser11Phe	p.S11F	ENST00000305910	NM_003534.2	11	tCc/tTc	1/1	0.283166546334581	5	FACETS	1	0.988	1	0.454	0.419	0.49	CLONAL	1	TRUE	2	0.459884798845986	5		703	1036	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36989309	36989309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1312549716	NA	P-0068087-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	195	499	2	ENST00000354822.5:c.26C>T	p.Ala9Val	p.A9V	ENST00000354822	NM_001079668.2	9	gCg/gTg	1/3	0.369501115872842	2	FACETS	0.76	0.708	0.813	0.76	0.708	0.813	SUBCLONAL	2	TRUE	0	0.459884798845986	2		501	558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577074	7577097	+	protein_altering_variant	In_Frame_Del	DEL	ATTCTCTTCCTCTGTGCGCCGGTC	ATTCTCTTCCTCTGTGCGCCGGTC	CCCTTTCTTGTG	novel	NA	P-0068087-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	360	566	1	ENST00000269305.4:c.841_864delinsCACAAGAAAGGG	p.Asp281_Asn288delinsHisLysLysGly	p.D281_N288delinsHKKG	ENST00000269305	NM_001126112.2	281	GACCGGCGCACAGAGGAAGAGAAT/CACAAGAAAGGG	8/11	0.447718902962939	3	FACETS	1	0.993	1	0.831	0.793	0.87	CLONAL	2	TRUE	0	0.459884798845986	3		567	772	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0068088-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	107	288	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.21583618183841	3	FACETS	0.806	0.731	0.883	0.806	0.731	0.883	INDETERMINATE	2	TRUE	1	0.503710459662926	3		288	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691039	NA	P-0068088-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	169	.	.	ENST00000269305.4:c.919+1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.503710459662926	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.503710459662926	1		0	486	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350121	81350121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068088-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	49	345	0	ENST00000222390.5:c.1211C>T	p.Ser404Phe	p.S404F	ENST00000222390	NM_000601.4	404	tCc/tTc	10/18	1	2	FACETS	0.52	0.442	0.606	0.52	0.442	0.606	SUBCLONAL	1	TRUE	1	0.503710459662926	2		345	374	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164975	47164975	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068088-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	173	488	0	ENST00000409792.3:c.1151A>C	p.Glu384Ala	p.E384A	ENST00000409792	NM_014159.6	384	gAa/gCa	3/21	0.503710459662926	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.503710459662926	1		488	397	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677783	58677783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068088-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2195	310	531	0	ENST00000305921.3:c.8G>A	p.Gly3Glu	p.G3E	ENST00000305921	NM_003620.3	3	gGg/gAg	1/6	0.503710459662926	15	FACETS	1	0.968	1			1	CLONAL	2	TRUE	NA	0.503710459662926	15		531	2505	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677825	58677825	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068088-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2467	371	571	0	ENST00000305921.3:c.50G>A	p.Gly17Glu	p.G17E	ENST00000305921	NM_003620.3	17	gGg/gAg	1/6	0.503710459662926	15	FACETS	1	0.984	1			1	CLONAL	2	TRUE	NA	0.503710459662926	15		571	2838	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627577	37627577	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068090-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	269	494	0	ENST00000447079.4:c.1492del	p.Gln498ArgfsTer9	p.Q498Rfs*9	ENST00000447079	NM_015083.1	498	Cag/ag	2/14	0.425209727957142	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	FALSE	1	0.425209727957142	3		494	748	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508136	106508136	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068090-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	45	510	0	ENST00000359195.3:c.130C>A	p.Leu44Met	p.L44M	ENST00000359195	NM_002649.2	44	Ctg/Atg	2/11	NA	2	FACETS	0.362	0.304	0.427			1	INDETERMINATE	1	FALSE	NA	0.425209727957142	2		510	584	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736330	243736330	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068090-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	111	456	0	ENST00000263826.5:c.717del	p.Glu240SerfsTer38	p.E240Sfs*38	ENST00000263826	NM_005465.4	239	agA/ag	8/13	NA	2	FACETS	0.885	0.798	0.977			1	INDETERMINATE	1	FALSE	NA	0.425209727957142	2		456	590	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673791	37673792	+	missense_variant	Missense_Mutation	DNP	TA	TA	GT	novel	NA	P-0068090-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	91	369	1	ENST00000447079.4:c.2945_2946delinsGT	p.Leu982Arg	p.L982R	ENST00000447079	NM_015083.1	982	cTA/cGT	10/14	0.425209727957142	3	FACETS	0.812	0.722	0.909	0.406	0.361	0.455	CLONAL	1	FALSE	1	0.425209727957142	3		370	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0068093-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	84	426	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.333744920557549	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.333744920557549	1		426	386	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0068093-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	63	354	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.333744920557549	2		354	342	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954272	32954273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359752	NA	P-0068093-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	98	367	2	ENST00000380152.3:c.9253dup	p.Thr3085AsnfsTer26	p.T3085Nfs*26	ENST00000380152		3082	-/A	24/27	0.324713412449044	2	FACETS	1	0.981	1	0.725	0.651	0.802	CLONAL	1	TRUE	0	0.333744920557549	2		369	405	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782893	66782893	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068093-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	67	334	0	ENST00000307102.5:c.1122G>C	p.Trp374Cys	p.W374C	ENST00000307102	NM_002755.3	374	tgG/tgC	11/11	1	2	FACETS	0.954	0.832	1	0.954	0.832	1	CLONAL	1	TRUE	1	0.333744920557549	2		334	421	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551798	150551798	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs771154790	NA	P-0068093-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	82	536	0	ENST00000369026.2:c.209C>A	p.Thr70Lys	p.T70K	ENST00000369026	NM_021960.4	70	aCg/aAg	1/3	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.333744920557549	2		536	470	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715664	30715664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068093-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	75	442	0	ENST00000295754.5:c.1322C>T	p.Ser441Phe	p.S441F	ENST00000295754	NM_003242.5	441	tCc/tTc	5/7	0.333744920557549	1	FACETS	0.929	0.818	1	0.929	0.818	1	CLONAL	1	TRUE	0	0.333744920557549	1		442	403	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0068094-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	76	0	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.955	0.849	1	0.955	0.849	1	CLONAL	1	TRUE	1	0.6525932560496	2		0	244	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0068094-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	258	374	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.64571826798369	2	FACETS	0.981	0.937	1	0.981	0.937	1	CLONAL	2	TRUE	0	0.6525932560496	2		374	403	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711894	89711894	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068094-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	118	278	0	ENST00000371953.3:c.512A>T	p.Gln171Leu	p.Q171L	ENST00000371953	NM_000314.4	171	cAg/cTg	6/9	0.6525932560496	1	FACETS	0.952	0.876	1	0.952	0.876	1	CLONAL	1	TRUE	0	0.6525932560496	1		278	256	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540652	NA	P-0068095-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	27	430	0	ENST00000269305.4:c.743G>C	p.Arg248Pro	p.R248P	ENST00000269305	NM_001126112.2	248	cGg/cCg	7/11	0.189131566166428	1	FACETS	0.632	0.504	0.779	0.632	0.504	0.779	SUBCLONAL	1	FALSE	0	0.238714582599162	1		430	315	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068095-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	80	459	0	ENST00000256196.4:c.68G>A	p.Gly23Asp	p.G23D	ENST00000256196		23	gGc/gAc	1/6	0.140044518091934	1	FACETS	1	0.972	1	1	0.972	1	INDETERMINATE	1	FALSE	0	0.238714582599162	1		459	438	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091797	29091797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780168	NA	P-0068095-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	13	321	0	ENST00000328354.6:c.1160C>T	p.Thr387Ile	p.T387I	ENST00000328354	NM_007194.3	387	aCc/aTc	11/15	0.140026543501207	0	FACETS	0.727	0.523	0.971			1	INDETERMINATE	1	FALSE	0	0.238714582599162	0		321	114	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592101	55592102	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0068095-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	24	401	0	ENST00000288135.5:c.1425_1426delinsTT	p.Gln475_Ser476delinsHisCys	p.Q475_S476delinsHC	ENST00000288135	NM_000222.2	475	caGAgt/caTTgt	9/21	0.207800467550065	0	FACETS	1	0.903	1			1	CLONAL	1	FALSE	0	0.238714582599162	0		401	122	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188252	10188252	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1559428134	NA	P-0068096-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	96	356	0	ENST00000256474.2:c.397del	p.Thr133LeufsTer26	p.T133Lfs*26	ENST00000256474	NM_000551.3	132	cAa/ca	2/3	0.455715590130443	2	FACETS	0.801	0.725	0.879	0.801	0.725	0.879	CLONAL	2	TRUE	0	0.455715590130443	2		356	263	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584504	52584504	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068096-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	127	420	0	ENST00000394830.3:c.4509C>A	p.Tyr1503Ter	p.Y1503*	ENST00000394830	NM_018313.4	1503	taC/taA	29/30	0.455715590130443	2	FACETS	0.964	0.889	1	0.964	0.889	1	CLONAL	2	TRUE	0	0.455715590130443	2		420	289	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182698277	182698277	+	start_lost,splice_region_variant	Translation_Start_Site	SNP	T	T	A	novel	NA	P-0068096-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	88	431	0	ENST00000292782.4:c.1A>T	p.Met1?	p.M1?	ENST00000292782	NM_020640.2	1	Atg/Ttg	1/7	0.409858936035688	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.455715590130443	4		431	242	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0068097-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	86	432	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.154033300012624	2	FACETS	0.962	0.855	1	0.962	0.855	1	CLONAL	2	TRUE	0	0.202801936235375	2		432	441	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178459	56178460	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0068097-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	45	321	0	ENST00000399503.3:c.3433dup	p.Thr1145AsnfsTer6	p.T1145Nfs*6	ENST00000399503	NM_005921.1	1144	-/A	14/20	0.202801936235375	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.202801936235375	1		321	311	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141036	55141036	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121908586	NA	P-0068099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	108	365	0	ENST00000257290.5:c.1682T>A	p.Val561Asp	p.V561D	ENST00000257290	NM_006206.4	561	gTc/gAc	12/23	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.575073861416214	2		365	348	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26927858	26927877	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTTTTTTCTTTCTTTCAGC	ATTTTTTTCTTTCTTTCAGC	-	novel	NA	P-0068099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	94	294	0	ENST00000381527.3:c.316-17_318del		p.X106_splice	ENST00000381527	NM_001260.1	106		4/13	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.575073861416214	2		294	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0068100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	251	342	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.307584443875805	3	FACETS	0.97	0.914	1	0.97	0.914	1	CLONAL	3	FALSE	0	0.307584443875805	3		343	647	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162040	22162040	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	40	425	0	ENST00000215832.6:c.215T>C	p.Ile72Thr	p.I72T	ENST00000215832	NM_002745.4	72	aTa/aCa	2/9	0.273489101376366	3	FACETS	0.56	0.465	0.666	0.187	0.155	0.222	SUBCLONAL	1	FALSE	0	0.307584443875805	3		425	536	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047524	49047527	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	GGGG	GGGG	-	novel	NA	P-0068100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	57	243	0	ENST00000267163.4:c.2518_2520+1del		p.X840_splice	ENST00000267163	NM_000321.2	840		24/27	0.304592513207923	2	FACETS	0.792	0.687	0.903	0.792	0.687	0.903	CLONAL	2	FALSE	0	0.307584443875805	2		243	234	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0068101-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	156	313	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.218092479166316	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.218092479166316	3		313	679	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921551	178921551	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068101-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	47	317	0	ENST00000263967.3:c.1033A>T	p.Asn345Tyr	p.N345Y	ENST00000263967	NM_006218.2	345	Aat/Tat	5/21	0.168942855320311	3	FACETS	1	0.947	1	0.646	0.547	0.755	CLONAL	1	TRUE	1	0.218092479166316	3		317	370	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0068101-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	22	383	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.643	0.498	0.81	0.643	0.498	0.81	SUBCLONAL	1	TRUE	1	0.218092479166316	2		383	314	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807539	36807539	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068101-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	54	429	0	ENST00000373129.3:c.1125T>G	p.Phe375Leu	p.F375L	ENST00000373129	NM_032017.1	375	ttT/ttG	12/12	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.218092479166316	2		429	489	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0068102-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	13	483	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.795	1	1	0.795	1	CLONAL	1	TRUE	1	0.12	2		483	189	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0068102-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	10	342	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.7	0.474	0.986	0.7	0.474	0.986	SUBCLONAL	1	TRUE	1	0.12	2		342	238	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0068102-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	17	497	0	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	1	2	FACETS	0.902	0.673	1	0.902	0.673	1	CLONAL	1	TRUE	1	0.12	2		497	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579361	7579361	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1064796722	NA	P-0068117-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	23	619	0	ENST00000269305.4:c.326T>G	p.Phe109Cys	p.F109C	ENST00000269305	NM_001126112.2	109	tTc/tGc	4/11	1	2	FACETS	0.684	0.531	0.862	0.684	0.531	0.862	SUBCLONAL	1	FALSE	1	0.103989618165174	2		619	647	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720801	89720802	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0068118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	13	160	0	ENST00000371953.3:c.954dup	p.Thr319TyrfsTer6	p.T319Yfs*6	ENST00000371953	NM_000314.4	318	ctt/cTtt	8/9	0.368367177504543	1	FACETS	0.278	0.199	0.373	0.278	0.199	0.373	SUBCLONAL	1	TRUE	0	0.509148215952535	1		160	137	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0068118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	250	336	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.501380987814719	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.509148215952535	1		336	675	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47421976	47421976	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs758574203	NA	P-0068118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	148	634	0	ENST00000404338.3:c.44A>G	p.Asn15Ser	p.N15S	ENST00000404338	NM_004491.4	15	aAc/aGc	1/6	NA	2	FACETS	0.72	0.658	0.784			1	INDETERMINATE	1	TRUE	NA	0.509148215952535	2		634	808	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842632	68842632	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068119-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	39	642	0	ENST00000261769.5:c.568T>A	p.Tyr190Asn	p.Y190N	ENST00000261769	NM_004360.3	190	Tac/Aac	5/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		642	718	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0068120-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	132	389	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.15303985298942	3	FACETS	0.857	0.781	0.937	0.857	0.781	0.937	INDETERMINATE	2	TRUE	1	0.287866792796411	3		389	612	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971370	13971370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748346103	NA	P-0068120-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	113	485	0	ENST00000405192.2:c.559C>T	p.Arg187Cys	p.R187C	ENST00000405192	NM_001163147.1	187	Cgc/Tgc	8/12	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.287866792796411	2		485	696	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724241	112724241	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068120-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	96	527	0	ENST00000369452.4:c.125A>G	p.Glu42Gly	p.E42G	ENST00000369452	NM_007373.3	42	gAa/gGa	2/9	0.287866792796411	1	FACETS	0.812	0.724	0.906	0.812	0.724	0.906	CLONAL	1	TRUE	0	0.287866792796411	1		527	703	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31448660	31448660	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068120-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	60	421	0	ENST00000344624.3:c.2876C>T	p.Pro959Leu	p.P959L	ENST00000344624		959	cCc/cTc	20/33	1	2	FACETS	0.861	0.743	0.989	0.861	0.743	0.989	CLONAL	1	TRUE	1	0.287866792796411	2		421	484	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061220	38061228	+	inframe_deletion	In_Frame_Del	DEL	CGTTCTCGA	CGTTCTCGA	-	novel	NA	P-0068121-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	348	759	0	ENST00000250448.2:c.761_769del	p.Phe254_Gly257delinsCys	p.F254_G257delinsC	ENST00000250448	NM_004496.3	254	tTCGAGAACGgc/tgc	2/2	0.504666184318094	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	FALSE	2	0.561171232659174	4		759	834	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539249	187539249	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068121-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	233	678	0	ENST00000441802.2:c.8491A>G	p.Ile2831Val	p.I2831V	ENST00000441802	NM_005245.3	2831	Atc/Gtc	10/27	0.504666184318094	4	FACETS	0.888	0.832	0.946	0.888	0.832	0.946	CLONAL	2	FALSE	2	0.561171232659174	4		678	730	SUCCESS
SCG5	6447	MSKCC	GRCh37	15	32988801	32988801	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068121-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	154	466	0	ENST00000300175.4:c.630T>G	p.Asp210Glu	p.D210E	ENST00000300175	NM_001144757.1	210	gaT/gaG	6/6	0.135239287076907	4	FACETS	1	0.973	1	0.738	0.684	0.793	INDETERMINATE	2	FALSE	1	0.561171232659174	4		466	387	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0068122-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	48	354	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.288723477706919	2		354	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579315	7579316	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1267047192	NA	P-0068122-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	66	592	0	ENST00000269305.4:c.371dup	p.Cys124TrpfsTer25	p.C124Wfs*25	ENST00000269305	NM_001126112.2	124	tgc/tgGc	4/11	0.288723477706919	1	FACETS	0.993	0.866	1	0.993	0.866	1	CLONAL	1	TRUE	0	0.288723477706919	1		592	394	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439945	56439945	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068122-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	105	595	0	ENST00000407977.2:c.647C>A	p.Ser216Ter	p.S216*	ENST00000407977		216	tCg/tAg	6/10	0.288723477706919	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.288723477706919	1		595	455	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349771	15349771	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781555424	NA	P-0068122-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	67	644	0	ENST00000263377.2:c.3803C>T	p.Ala1268Val	p.A1268V	ENST00000263377	NM_058243.2	1268	gCg/gTg	19/20	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.288723477706919	2		644	426	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0068123-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	46	306	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.452	0.381	0.53	0.452	0.381	0.53	SUBCLONAL	1	TRUE	1	0.47	2		306	433	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61706101	61706101	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068123-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	40	276	0	ENST00000401558.2:c.3070G>A	p.Glu1024Lys	p.E1024K	ENST00000401558	NM_003400.3	1024	Gaa/Aaa	25/25	1	2	FACETS	0.401	0.333	0.476	0.401	0.333	0.476	SUBCLONAL	1	TRUE	1	0.47	2		276	425	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0068123-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	305	622	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.47	2		622	894	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36846881	36846881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs865878221	NA	P-0068125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	21	608	0	ENST00000358127.4:c.1058C>T	p.Ser353Leu	p.S353L	ENST00000358127	NM_001280556.1	353	tCg/tTg	9/10	0.33416728518579	2	FACETS	0.306	0.235	0.389	0.153	0.117	0.195	SUBCLONAL	1	TRUE	0	0.374411480509149	2		608	366	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577514	7577514	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	106	527	0	ENST00000269305.4:c.767del	p.Thr256AsnfsTer89	p.T256Nfs*89	ENST00000269305	NM_001126112.2	256	aCa/aa	7/11	0.271051000418023	2	FACETS	0.8	0.724	0.878	0.8	0.724	0.878	SUBCLONAL	2	TRUE	0	0.374411480509149	2		527	354	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971026	21971038	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCAGGCATCGC	CCCCAGGCATCGC	-	novel	NA	P-0068125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	187	610	0	ENST00000304494.5:c.320_332del	p.Arg107ProfsTer35	p.R107Pfs*35	ENST00000304494	NM_000077.4	107	cGCGATGCCTGGGGc/cc	2/3	0.33416728518579	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.374411480509149	2		610	447	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646913	37646913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1316574941	NA	P-0068125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	32	508	0	ENST00000447079.4:c.2035G>A	p.Asp679Asn	p.D679N	ENST00000447079	NM_015083.1	679	Gat/Aat	3/14	0.271051000418023	2	FACETS	0.362	0.293	0.44	0.181	0.146	0.22	SUBCLONAL	1	TRUE	0	0.374411480509149	2		508	472	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105592	27105592	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	193	594	0	ENST00000324856.7:c.5203G>T	p.Glu1735Ter	p.E1735*	ENST00000324856	NM_006015.4	1735	Gag/Tag	20/20	0.221625096212095	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.221628526576967	2		594	824	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412365	139412365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	107	670	1	ENST00000277541.6:c.1280G>A	p.Gly427Asp	p.G427D	ENST00000277541	NM_017617.3	427	gGc/gAc	8/34	1	2	FACETS	0.978	0.876	1	0.978	0.876	1	CLONAL	1	TRUE	1	0.221628526576967	2		671	987	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964925	55964925	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	69	385	0	ENST00000263923.4:c.2312C>A	p.Thr771Lys	p.T771K	ENST00000263923	NM_002253.2	771	aCg/aAg	16/30	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.221628526576967	2		385	563	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900209	101900209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068135-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	236	402	0	ENST00000374994.4:c.643C>T	p.Arg215Ter	p.R215*	ENST00000374994	NM_004612.2	215	Cga/Tga	4/9	0.835804619152198	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.9159436503722	1		402	269	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729259	41729259	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068135-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	185	360	0	ENST00000242208.4:c.1270G>C	p.Gly424Arg	p.G424R	ENST00000242208	NM_002192.2	424	Ggg/Cgg	3/3	0.639828948196384	3	FACETS	1	0.976	1	0.555	0.516	0.594	CLONAL	1	TRUE	1	0.9159436503722	3		360	531	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268778	98268820	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAACTTGCCGCAGTTTTTTTGAATGTAACAACCCAGTTTAA	AAGAACTTGCCGCAGTTTTTTTGAATGTAACAACCCAGTTTAA	-	novel	NA	P-0068135-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	274	413	0	ENST00000331920.6:c.263_305del	p.Phe88TrpfsTer15	p.F88Wfs*15	ENST00000331920	NM_000264.3	88	tTTAAACTGGGTTGTTACATTCAAAAAAACTGCGGCAAGTTCTTg/tg	2/24	0.835804619152198	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.9159436503722	1		413	303	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0068139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	158	264	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		264	516	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912580	NA	P-0068139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	30	398	0	ENST00000342988.3:c.1157G>A	p.Gly386Asp	p.G386D	ENST00000342988	NM_005359.5	386	gGt/gAt	10/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		398	430	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929053	44929053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1224090700	NA	P-0068139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	19	198	0	ENST00000377967.4:c.2153G>A	p.Ser718Asn	p.S718N	ENST00000377967	NM_021140.2	718	aGc/aAc	17/29	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		198	231	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201885	152201885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778449608	NA	P-0068139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	22	312	2	ENST00000206249.3:c.739G>A	p.Glu247Lys	p.E247K	ENST00000206249	NM_000125.3	247	Gaa/Aaa	3/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		314	340	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504305	149504305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780819031	NA	P-0068139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	57	401	1	ENST00000261799.4:c.1897G>A	p.Val633Ile	p.V633I	ENST00000261799	NM_002609.3	633	Gtc/Atc	13/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		402	337	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461149	120461149	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	145	417	0	ENST00000256646.2:c.5809C>G	p.Leu1937Val	p.L1937V	ENST00000256646	NM_024408.3	1937	Cta/Gta	32/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		417	555	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460387	149460387	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	30	490	0	ENST00000286301.3:c.250T>A	p.Cys84Ser	p.C84S	ENST00000286301	NM_005211.3	84	Tgc/Agc	3/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		490	409	SUCCESS
APC	324	MSKCC	GRCh37	5	112116497	112116506	+	frameshift_variant	Frame_Shift_Del	DEL	AAACAGATAT	AAACAGATAT	-	novel	NA	P-0068139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	38	320	0	ENST00000257430.4:c.542_551del	p.Gln181ArgfsTer21	p.Q181Rfs*21	ENST00000257430	NM_000038.5	181	cAAACAGATATg/cg	6/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		320	219	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73649732	73649952	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCCTTCTTTCGCTTGGCCAAGATTTTTTTTTTCTTTGAAATTCCTTCTCCGGTGTTATCTAGGATGTTTGCATTACAAGCAGGCCGCTTTACCTCCTTTGTTCGTTGTCACAGGTGAAAAGCCATACAAGTGTACCTGGGAAGGCTGCGACTGGAGGTTCGCGCGATCGGATGAGCTGACCCGCCACTACCGGAAGCACACAGGCGCCAAGCCCTTCCAG	TTCCTTCTTTCGCTTGGCCAAGATTTTTTTTTTCTTTGAAATTCCTTCTCCGGTGTTATCTAGGATGTTTGCATTACAAGCAGGCCGCTTTACCTCCTTTGTTCGTTGTCACAGGTGAAAAGCCATACAAGTGTACCTGGGAAGGCTGCGACTGGAGGTTCGCGCGATCGGATGAGCTGACCCGCCACTACCGGAAGCACACAGGCGCCAAGCCCTTCCAG	-	novel	NA	P-0068139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	12	92	0	ENST00000377687.4:c.1196-113_1303del		p.X399_splice	ENST00000377687	NM_001730.3	399		4/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		92	114	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461032	120461032	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	166	431	0	ENST00000256646.2:c.5926C>T	p.His1976Tyr	p.H1976Y	ENST00000256646	NM_024408.3	1976	Cat/Tat	32/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		431	580	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648390	30648391	+	missense_variant	Missense_Mutation	DNP	GC	GC	CT	novel	NA	P-0068139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	54	402	0	ENST00000295754.5:c.15_16delinsCT	p.Leu6Phe	p.L6F	ENST00000295754	NM_003242.5	5	ctGCtc/ctCTtc	1/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		402	314	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420831	49420831	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	109	552	0	ENST00000301067.7:c.14918A>G	p.Asp4973Gly	p.D4973G	ENST00000301067	NM_003482.3	4973	gAt/gGt	48/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		552	571	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0068155-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	102	536	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	1	2	FACETS	0.805	0.72	0.896	0.805	0.72	0.896	CLONAL	1	TRUE	1	0.32	2		536	792	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0068155-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	104	348	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.3	1	FACETS	0.777	0.696	0.862	0.777	0.696	0.862	SUBCLONAL	1	TRUE	0	0.32	1		348	703	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443697	29443697	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs281864719	NA	P-0068155-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	108	447	0	ENST00000389048.3:c.3520T>G	p.Phe1174Val	p.F1174V	ENST00000389048	NM_004304.4	1174	Ttc/Gtc	23/29	NA	2	FACETS	1	0.918	1			1	INDETERMINATE	1	TRUE	NA	0.32	2		447	659	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445213	29445213	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519698	NA	P-0068155-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	65	520	0	ENST00000389048.3:c.3512T>A	p.Ile1171Asn	p.I1171N	ENST00000389048	NM_004304.4	1171	aTc/aAc	22/29	NA	2	FACETS	0.644	0.558	0.737			1	INDETERMINATE	1	TRUE	NA	0.32	2		520	631	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735470	40735470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761910971	NA	P-0068168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	90	663	0	ENST00000373198.4:c.3403G>A	p.Val1135Met	p.V1135M	ENST00000373198	NM_133170.3	1135	Gtg/Atg	25/32	0.761131179882216	9	FACETS	0.904	0.8	1	0.113	0.1	0.127	CLONAL	1	FALSE	1	0.761131179882216	9		663	959	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587781702	NA	P-0068168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	249	761	0	ENST00000269305.4:c.920-1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.761131179882216	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	FALSE	0	0.761131179882216	2		761	319	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696404	47696404	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	495	625	1	ENST00000347630.2:c.419A>T	p.Asp140Val	p.D140V	ENST00000347630	NM_001007230.1	140	gAt/gTt	6/11	0.761131179882216	6	FACETS	0.994	0.967	1	0.994	0.967	1	CLONAL	5	FALSE	1	0.761131179882216	6		626	660	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326803	62326803	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	85	880	0	ENST00000360203.5:c.3622C>A	p.Pro1208Thr	p.P1208T	ENST00000360203	NM_001283009.1	1208	Cct/Act	34/35	0.669154585053433	5	FACETS	0.986	0.875	1	0.247	0.218	0.277	CLONAL	1	FALSE	1	0.761131179882216	5		880	485	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165632	118165632	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	222	730	0	ENST00000369448.3:c.142C>G	p.Leu48Val	p.L48V	ENST00000369448	NM_017709.3	48	Ctg/Gtg	2/2	0.761131179882216	5	FACETS	0.964	0.902	1	0.643	0.601	0.685	CLONAL	2	FALSE	2	0.761131179882216	5		730	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0068170-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	472	400	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.403157776491468	1	FACETS	1	0.995	1	1	0.998	1	CLONAL	3	TRUE	0	0.39632665528991	1		400	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863224683	NA	P-0068170-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	172	589	0	ENST00000269305.4:c.388C>T	p.Leu130Phe	p.L130F	ENST00000269305	NM_001126112.2	130	Ctc/Ttc	5/11	0.403157776491468	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.39632665528991	1		589	580	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438640	49438640	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1374905609	NA	P-0068170-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	116	577	1	ENST00000301067.7:c.4850G>A	p.Arg1617Gln	p.R1617Q	ENST00000301067	NM_003482.3	1617	cGg/cAg	19/54	1	2	FACETS	0.923	0.834	1	0.923	0.834	1	CLONAL	1	TRUE	1	0.39632665528991	2		578	634	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258006	16258006	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068170-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	34	581	0	ENST00000375759.3:c.5271G>C	p.Gln1757His	p.Q1757H	ENST00000375759	NM_015001.2	1757	caG/caC	11/15	0.369751621148868	2	FACETS	0.278	0.226	0.336	0.139	0.113	0.168	SUBCLONAL	1	TRUE	0	0.39632665528991	2		581	618	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0068171-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	27	288	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.18	2		288	258	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578537	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs879254214	NA	P-0068171-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	45	508	0	ENST00000269305.4:c.393_395del	p.Asn131del	p.N131del	ENST00000269305	NM_001126112.2	131	aaCAAg/aag	5/11	1	2	FACETS	0.921	0.773	1	0.921	0.773	1	CLONAL	1	TRUE	1	0.18	2		508	543	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448310	56448310	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567880628	NA	P-0068171-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	48	589	0	ENST00000407977.2:c.337C>T	p.Arg113Ter	p.R113*	ENST00000407977		113	Cga/Tga	3/10	1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	1	0.18	2		589	531	SUCCESS
H3C13	653604	MSKCC	GRCh37	1	149784876	149784876	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1187192600	NA	P-0068171-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	16	263	0	ENST00000331491.1:c.361A>T	p.Met121Leu	p.M121L	ENST00000331491	NM_001123375.2	121	Atg/Ttg	1/1	1	2	FACETS	0.651	0.481	0.854	0.651	0.481	0.854	SUBCLONAL	1	TRUE	1	0.18	2		263	273	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593609	55593611	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	rs121913685	NA	P-0068172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	189	452	0	ENST00000288135.5:c.1679_1681del	p.Val560del	p.V560del	ENST00000288135	NM_000222.2	559	GTT/-	11/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		452	480	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0068173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	15	0	0				ENST00000310581	NM_198253.2	-/1132			0.0816449036827738	0	FACETS	0.337	0.247	0.445			1	INDETERMINATE	1	TRUE	0	0.31	0		0	198	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691178	18691178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	27	352	0	ENST00000266497.5:c.3289G>A	p.Glu1097Lys	p.E1097K	ENST00000266497		1097	Gaa/Aaa	23/31	1	2	FACETS	0.337	0.267	0.417	0.337	0.267	0.417	SUBCLONAL	1	TRUE	1	0.31	2		352	517	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524338	148524338	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771139896	NA	P-0068173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	107	331	0	ENST00000320356.2:c.646C>T	p.Arg216Trp	p.R216W	ENST00000320356	NM_004456.4	216	Cgg/Tgg	7/20	0.307106342314759	3	FACETS	1	0.976	1	0.644	0.579	0.713	CLONAL	1	TRUE	1	0.31	3		331	619	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295824	212295825	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0068173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	35	310	0	ENST00000342788.4:c.2488_2489delinsAA	p.Gly830Lys	p.G830K	ENST00000342788	NM_005235.2	830	GGa/AAa	21/28	1	2	FACETS	0.478	0.392	0.576	0.478	0.392	0.576	SUBCLONAL	1	TRUE	1	0.31	2		310	472	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409047	4409047	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	27	376	0	ENST00000261254.3:c.742G>A	p.Glu248Lys	p.E248K	ENST00000261254	NM_001759.3	248	Gag/Aag	5/5	1	2	FACETS	0.387	0.307	0.478	0.387	0.307	0.478	SUBCLONAL	1	TRUE	1	0.31	2		376	450	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100943	41100943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	37	416	0	ENST00000373198.4:c.1413G>A	p.Met471Ile	p.M471I	ENST00000373198	NM_133170.3	471	atG/atA	8/32	1	2	FACETS	0.546	0.45	0.654	0.546	0.45	0.654	SUBCLONAL	1	TRUE	1	0.31	2		416	437	SUCCESS
APC	324	MSKCC	GRCh37	5	112175618	112175618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	45	457	0	ENST00000257430.4:c.4327C>T	p.Pro1443Ser	p.P1443S	ENST00000257430	NM_000038.5	1443	Cct/Tct	16/16	1	2	FACETS	0.531	0.446	0.625	0.531	0.446	0.625	SUBCLONAL	1	TRUE	1	0.31	2		457	547	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251941	8251941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	33	464	0	ENST00000335790.3:c.136G>A	p.Glu46Lys	p.E46K	ENST00000335790	NM_002315.2	46	Gaa/Aaa	2/4	1	2	FACETS	0.482	0.392	0.583	0.482	0.392	0.583	SUBCLONAL	1	TRUE	1	0.31	2		464	442	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131364	17131364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	51	476	0	ENST00000285071.4:c.88C>T	p.Pro30Ser	p.P30S	ENST00000285071	NM_144997.5	30	Cct/Tct	4/14	1	2	FACETS	0.634	0.539	0.738	0.634	0.539	0.738	SUBCLONAL	1	TRUE	1	0.31	2		476	519	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245740	41245740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	40	438	0	ENST00000357654.3:c.1808C>T	p.Ser603Leu	p.S603L	ENST00000357654	NM_007294.3	603	tCa/tTa	10/23	1	2	FACETS	0.488	0.405	0.58	0.488	0.405	0.58	SUBCLONAL	1	TRUE	1	0.31	2		438	529	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949069	151949069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776295921	NA	P-0068173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	48	355	0	ENST00000262189.6:c.1576C>T	p.Arg526Cys	p.R526C	ENST00000262189	NM_170606.2	526	Cgt/Tgt	11/59	0.307106342314759	3	FACETS	0.596	0.503	0.699	0.298	0.251	0.35	SUBCLONAL	1	TRUE	1	0.31	3		355	600	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732506	74732506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1419789271	NA	P-0068173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	36	419	0	ENST00000359995.5:c.403C>T	p.Arg135Cys	p.R135C	ENST00000359995	NM_001195427.1	135	Cgt/Tgt	2/3	1	2	FACETS	0.525	0.432	0.63	0.525	0.432	0.63	SUBCLONAL	1	TRUE	1	0.31	2		419	442	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969900	161969900	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	31	363	0	ENST00000366898.1:c.1069G>A	p.Gly357Ser	p.G357S	ENST00000366898	NM_004562.2	357	Ggc/Agc	9/12	1	2	FACETS	0.508	0.41	0.618	0.508	0.41	0.618	SUBCLONAL	1	TRUE	1	0.31	2		363	394	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416948	416948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384215	NA	P-0068173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	44	488	0	ENST00000399788.2:c.3602C>T	p.Ser1201Phe	p.S1201F	ENST00000399788	NM_001042603.1	1201	tCc/tTc	23/28	0.307106342314759	2	FACETS	0.472	0.395	0.557			1	SUBCLONAL	1	TRUE	NA	0.31	2		488	602	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69456227	69456227	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	38	383	0	ENST00000227507.2:c.146A>T	p.Gln49Leu	p.Q49L	ENST00000227507	NM_053056.2	49	cAg/cTg	1/5	1	2	FACETS	0.599	0.496	0.715	0.599	0.496	0.715	SUBCLONAL	1	TRUE	1	0.31	2		383	409	SUCCESS
BTK	695	MSKCC	GRCh37	X	100604888	100604888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782709592	NA	P-0068173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	29	315	0	ENST00000308731.7:c.1965G>A	p.Met655Ile	p.M655I	ENST00000308731	NM_000061.2	655	atG/atA	19/19	1	2	FACETS	0.557	0.447	0.681	0.557	0.447	0.681	SUBCLONAL	1	TRUE	1	0.31	2		315	336	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206667318	206667318	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	32	423	0	ENST00000367120.3:c.2111T>G	p.Ile704Ser	p.I704S	ENST00000367120	NM_014002.3	704	aTc/aGc	21/22	1	2	FACETS	0.44	0.357	0.535	0.44	0.357	0.535	SUBCLONAL	1	TRUE	1	0.31	2		423	469	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220182	36220183	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0068173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	39	432	0	ENST00000222270.7:c.4902_4903delinsTT	p.Arg1635Ter	p.R1635*	ENST00000222270	NM_014727.1	1634	gcCCga/gcTTga	22/37	1	2	FACETS	0.592	0.491	0.705	0.592	0.491	0.705	SUBCLONAL	1	TRUE	1	0.31	2		432	425	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316175	11316175	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	54	462	0	ENST00000361445.4:c.579C>A	p.Asn193Lys	p.N193K	ENST00000361445	NM_004958.3	193	aaC/aaA	5/58	1	2	FACETS	0.697	0.596	0.807	0.697	0.596	0.807	SUBCLONAL	1	TRUE	1	0.31	2		462	500	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076941	41076941	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	36	320	0	ENST00000373198.4:c.1479C>G	p.Ile493Met	p.I493M	ENST00000373198	NM_133170.3	493	atC/atG	9/32	1	2	FACETS	0.652	0.537	0.781	0.652	0.537	0.781	SUBCLONAL	1	TRUE	1	0.31	2		320	356	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218078	36218080	+	frameshift_variant	Frame_Shift_Del	DEL	CAC	CAC	TA	novel	NA	P-0068173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	44	360	1	ENST00000222270.7:c.4025_4027delinsTA	p.Thr1342IlefsTer13	p.T1342Ifs*13	ENST00000222270	NM_014727.1	1342	aCACgc/aTAgc	15/37	1	2	FACETS	0.745	0.626	0.876	0.745	0.626	0.876	SUBCLONAL	1	TRUE	1	0.31	2		361	381	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183825	10183825	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068175-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	125	416	0	ENST00000256474.2:c.294C>A	p.Tyr98Ter	p.Y98*	ENST00000256474	NM_000551.3	98	taC/taA	1/3	0.44291429820607	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.44291429820607	1		416	309	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281837	49281837	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068175-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	31	465	0	ENST00000282018.3:c.884C>G	p.Ala295Gly	p.A295G	ENST00000282018	NM_020377.2	295	gCa/gGa	1/1	1	2	FACETS	0.31	0.251	0.378	0.31	0.251	0.378	SUBCLONAL	1	TRUE	1	0.44291429820607	2		465	451	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339011	225339011	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068175-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	78	381	0	ENST00000264414.4:c.2258A>G	p.Tyr753Cys	p.Y753C	ENST00000264414	NM_003590.4	753	tAt/tGt	16/16	0.44291429820607	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.44291429820607	1		381	239	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573429	48573429	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068175-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	79	386	0	ENST00000342988.3:c.13T>C	p.Ser5Pro	p.S5P	ENST00000342988	NM_005359.5	5	Tct/Cct	2/12	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.44291429820607	2		386	346	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0068181-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	61	306	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.247266419959526	2		306	467	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0068181-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	60	273	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.247266419959526	2		273	458	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589579	67589596	+	inframe_deletion	In_Frame_Del	DEL	AAATTACATGAATATAAC	AAATTACATGAATATAAC	-	novel	NA	P-0068181-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	30	242	0	ENST00000274335.5:c.1343_1360del	p.Lys448_Asn453del	p.K448_N453del	ENST00000274335		448	AAATTACATGAATATAAC/-	10/15	1	2	FACETS	0.526	0.423	0.643	0.526	0.423	0.643	SUBCLONAL	1	TRUE	1	0.247266419959526	2		242	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0068181-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	117	451	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.247266419959526	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.247266419959526	1		451	596	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1936871	1936871	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068181-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	60	299	0	ENST00000382891.5:c.1556G>A	p.Gly519Asp	p.G519D	ENST00000382891	NM_133335.3	519	gGt/gAt	7/22	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.247266419959526	2		299	458	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684327	29684401	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAATTCTTTATGAATACTTAGCAGAGGCCAGTGTTGTGTTTCCCAAAGTCTTTCCTGTTGTGTAAGTATCTCCTT	GAATTCTTTATGAATACTTAGCAGAGGCCAGTGTTGTGTTTCCCAAAGTCTTTCCTGTTGTGTAAGTATCTCCTT	-	novel	NA	P-0068181-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	63	275	0	ENST00000356175.3:c.7847_7907+14del		p.X2616_splice	ENST00000356175	NM_000267.3	2616		53/57	0.247266419959526	1	FACETS	0.981	0.851	1	0.981	0.851	1	CLONAL	1	TRUE	0	0.247266419959526	1		275	455	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857899	9857899	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068181-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	39	391	0	ENST00000330684.3:c.3502A>T	p.Asn1168Tyr	p.N1168Y	ENST00000330684	NM_001134407.1	1168	Aac/Tac	13/13	1	2	FACETS	0.485	0.401	0.58	0.485	0.401	0.58	SUBCLONAL	1	TRUE	1	0.247266419959526	2		391	650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0068182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	117	426	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.376356869164806	1	FACETS	0.975	0.884	1	0.975	0.884	1	CLONAL	1	TRUE	0	0.382733364148813	1		426	507	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0068182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	717	0	0				ENST00000310581	NM_198253.2	-/1132			0.382733364148813	6	FACETS	1	0.992	1	1	0.997	1	CLONAL	6	TRUE	1	0.382733364148813	6		0	1055	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0068182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	38	262	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.30641845879616	0	FACETS	0.311	0.257	0.371			1	SUBCLONAL	1	TRUE	0	0.382733364148813	0		262	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0068182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	42	380	0	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	0.376356869164806	1	FACETS	0.259	0.215	0.307	0.259	0.215	0.307	SUBCLONAL	1	TRUE	0	0.382733364148813	1		380	686	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0068182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	125	148	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.382733364148813	3	FACETS	0.91	0.838	0.983	1	0.986	1	CLONAL	3	TRUE	1	0.382733364148813	3		148	285	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494257	140494257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1181422421	NA	P-0068182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	60	412	0	ENST00000288602.6:c.991C>T	p.Leu331Phe	p.L331F	ENST00000288602	NM_004333.4	331	Ctc/Ttc	8/18	1	2	FACETS	0.406	0.349	0.469	0.406	0.349	0.469	SUBCLONAL	1	TRUE	1	0.382733364148813	2		412	772	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453132	140453132	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913365	NA	P-0068182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	54	315	0	ENST00000288602.6:c.1803A>T	p.Lys601Asn	p.K601N	ENST00000288602	NM_004333.4	601	aaA/aaT	15/18	1	2	FACETS	0.535	0.457	0.621	0.535	0.457	0.621	SUBCLONAL	1	TRUE	1	0.382733364148813	2		315	527	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790512	3790512	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	97	348	0	ENST00000262367.5:c.4021C>T	p.Arg1341Ter	p.R1341*	ENST00000262367	NM_004380.2	1341	Cga/Tga	24/31	0.376356869164806	1	FACETS	0.751	0.671	0.835	0.751	0.671	0.835	SUBCLONAL	1	TRUE	0	0.382733364148813	1		348	546	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0068182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	256	396	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	0.887	0.834	0.941	1	0.995	1	CLONAL	2	TRUE	1	0.382733364148813	2		396	754	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90645594	90645594	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	70	238	0	ENST00000330062.3:c.29C>A	p.Ser10Ter	p.S10*	ENST00000330062	NM_002168.2	10	tCg/tAg	1/11	1	2	FACETS	0.676	0.59	0.769	0.676	0.59	0.769	SUBCLONAL	1	TRUE	1	0.382733364148813	2		238	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577065	7577065	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs372613518	NA	P-0068182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	53	376	0	ENST00000269305.4:c.873G>C	p.Lys291Asn	p.K291N	ENST00000269305	NM_001126112.2	291	aaG/aaC	8/11	0.376356869164806	1	FACETS	0.311	0.264	0.362	0.311	0.264	0.362	SUBCLONAL	1	TRUE	0	0.382733364148813	1		376	720	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539027	23539027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751677679	NA	P-0068182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	94	380	0	ENST00000380871.4:c.412G>A	p.Glu138Lys	p.E138K	ENST00000380871	NM_006167.3	138	Gag/Aag	2/2	1	2	FACETS	0.6	0.534	0.672	0.6	0.534	0.672	SUBCLONAL	1	TRUE	1	0.382733364148813	2		380	818	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129632	11129632	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs113895708	NA	P-0068182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	306	346	0	ENST00000358026.2:c.2439-1G>C		p.X813_splice	ENST00000358026	NM_001128849.1	813			1	2	FACETS	0.953	0.902	1	1	0.996	1	CLONAL	2	TRUE	1	0.382733364148813	2		346	839	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992232	11992232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772696896	NA	P-0068182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	236	331	0	ENST00000396373.4:c.322C>T	p.His108Tyr	p.H108Y	ENST00000396373	NM_001987.4	108	Cat/Tat	3/8	0.376356869164806	1	FACETS	0.918	0.865	0.972	1	0.995	1	CLONAL	2	TRUE	0	0.382733364148813	1		331	543	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681015	30681015	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0068182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	174	369	0	ENST00000376406.3:c.704C>G	p.Ser235Ter	p.S235*	ENST00000376406	NM_014641.2	235	tCa/tGa	5/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.382733364148813	2		369	834	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692796	89692797	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TATG	novel	NA	P-0068182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	20	217	0	ENST00000371953.3:c.280_281insTATG	p.Asn94IlefsTer2	p.N94Ifs*2	ENST00000371953	NM_000314.4	94	aac/aTATGac	5/9	0.30641845879616	0	FACETS	0.233	0.178	0.297			1	SUBCLONAL	1	TRUE	0	0.382733364148813	0		217	277	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788627	3788627	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	82	308	0	ENST00000262367.5:c.4327del	p.Arg1443ValfsTer16	p.R1443Vfs*16	ENST00000262367	NM_004380.2	1443	Cgt/gt	26/31	0.376356869164806	1	FACETS	0.683	0.604	0.768	0.683	0.604	0.768	SUBCLONAL	1	TRUE	0	0.382733364148813	1		308	507	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950587	79950587	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	122	334	0	ENST00000265081.6:c.41C>G	p.Ser14Cys	p.S14C	ENST00000265081	NM_002439.4	14	tCc/tGc	1/24	1	2	FACETS	0.917	0.83	1	0.917	0.83	1	CLONAL	1	TRUE	1	0.382733364148813	2		334	695	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942765	15942765	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	244	393	0	ENST00000268712.3:c.6937G>T	p.Asp2313Tyr	p.D2313Y	ENST00000268712	NM_006311.3	2313	Gac/Tac	44/46	0.376356869164806	1	FACETS	0.908	0.856	0.96	1	0.995	1	CLONAL	2	TRUE	0	0.382733364148813	1		393	568	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939052	48939053	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0068182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	114	196	0	ENST00000267163.4:c.884_885insG	p.Asn295LysfsTer15	p.N295Kfs*15	ENST00000267163	NM_000321.2	295	aat/aaGt	9/27	0.35062618077421	0	FACETS	0.786	0.723	0.848			1	SUBCLONAL	2	TRUE	0	0.382733364148813	0		196	234	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494154	140494154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	44	431	0	ENST00000288602.6:c.1094C>T	p.Ser365Leu	p.S365L	ENST00000288602	NM_004333.4	365	tCa/tTa	8/18	1	2	FACETS	0.269	0.224	0.318	0.269	0.224	0.318	SUBCLONAL	1	TRUE	1	0.382733364148813	2		431	855	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636663	73636664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0068182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	55	459	0	ENST00000377687.4:c.927dup	p.Gly310TrpfsTer5	p.G310Wfs*5	ENST00000377687	NM_001730.3	309	cct/ccTt	2/4	1	2	FACETS	0.294	0.25	0.342	0.294	0.25	0.342	SUBCLONAL	1	TRUE	1	0.382733364148813	2		459	977	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0068183-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	61	478	2	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.169877020250861	3	FACETS	0.998	0.873	1	0.666	0.582	0.754	INDETERMINATE	2	TRUE	0	0.310985760063877	3		480	227	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513282	44513287	+	inframe_deletion	In_Frame_Del	DEL	CCACCG	CCACCG	-	rs745888281	NA	P-0068183-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	11	321	0	ENST00000291552.4:c.648_653del	p.Gly222_Gly223del	p.G222_G223del	ENST00000291552	NM_006758.2	216	ggCGGTGGt/ggt	8/8	1	2	FACETS	0.244	0.168	0.339	0.244	0.168	0.339	SUBCLONAL	1	TRUE	1	0.310985760063877	2		321	290	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692779	89692780	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0068183-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	40	205	0	ENST00000371953.3:c.264dup	p.Pro89SerfsTer3	p.P89Sfs*3	ENST00000371953	NM_000314.4	88	tat/taTt	5/9	0.224867932636364	3	FACETS	0.971	0.821	1	0.648	0.547	0.755	CLONAL	2	TRUE	0	0.310985760063877	3		205	153	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303481	30303481	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068183-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	22	326	0	ENST00000262643.3:c.19G>C	p.Glu7Gln	p.E7Q	ENST00000262643	NM_001238.2	7	Gag/Cag	2/12	0.31036869795201	3	FACETS	0.87	0.678	1	0.435	0.339	0.545	CLONAL	1	TRUE	1	0.310985760063877	3		326	188	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65312412	65312412	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068183-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	19	286	0	ENST00000342505.4:c.1907T>G	p.Phe636Cys	p.F636C	ENST00000342505	NM_002227.2	636	tTc/tGc	14/25	0.273639689321929	3	FACETS	0.72	0.549	0.92	0.36	0.274	0.46	CLONAL	1	TRUE	1	0.310985760063877	3		286	196	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039489	49039505	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TGACTCCAAGATCAAGG	TGACTCCAAGATCAAGG	-	novel	NA	P-0068183-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	57	256	0	ENST00000267163.4:c.2476_2489+3del		p.X826_splice	ENST00000267163	NM_000321.2	826		23/27	0.310985760063877	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	2	TRUE	0	0.310985760063877	2		256	174	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557744	21557744	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068183-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	70	326	0	ENST00000382592.4:c.2101A>G	p.Lys701Glu	p.K701E	ENST00000382592	NM_014572.2	701	Aaa/Gaa	5/8	0.282932018863374	3	FACETS	0.916	0.807	1			1	CLONAL	2	TRUE	NA	0.310985760063877	3		326	284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0068184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	405	403	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.622576405074313	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.622576405074313	2		404	605	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249503	153249503	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	237	298	0	ENST00000281708.4:c.1275G>C	p.Trp425Cys	p.W425C	ENST00000281708	NM_033632.3	425	tgG/tgC	9/12	0.30915175245341	3	FACETS	1	0.982	1	0.723	0.684	0.762	INDETERMINATE	2	TRUE	0	0.622576405074313	3		298	460	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044919	47044919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	105	424	2	ENST00000377604.3:c.2245C>T	p.Arg749Trp	p.R749W	ENST00000377604	NM_001204468.1	749	Cgg/Tgg	20/24	0.368305172718944	1	FACETS	0.506	0.456	0.559	0.506	0.456	0.559	INDETERMINATE	1	TRUE	0	0.622576405074313	1		426	459	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528086	29528086	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs864622107	NA	P-0068184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	98	140	0	ENST00000356175.3:c.1094C>G	p.Ser365Ter	p.S365*	ENST00000356175	NM_000267.3	365	tCa/tGa	10/57	0.622576405074313	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.622576405074313	2		140	146	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672276	30672276	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	226	459	0	ENST00000376406.3:c.4684A>G	p.Arg1562Gly	p.R1562G	ENST00000376406	NM_014641.2	1562	Agg/Ggg	10/15	0.610998535665747	3	FACETS	1	0.963	1	0.524	0.489	0.561	CLONAL	1	TRUE	1	0.622576405074313	3		459	908	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	133	539	1	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.742142566631559	2	FACETS	1	0.963	1	0.538	0.495	0.581	CLONAL	1	TRUE	0	0.74225012658966	2		540	333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0068185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	179	395	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.744503516544425	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.74225012658966	2		395	233	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406543	70406543	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	55	314	4	ENST00000373644.4:c.4057C>G	p.Leu1353Val	p.L1353V	ENST00000373644	NM_030625.2	1353	Ctc/Gtc	4/12	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.74225012658966	2		318	122	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524993	187524993	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	27	369	1	ENST00000441802.2:c.10687G>T	p.Val3563Phe	p.V3563F	ENST00000441802	NM_005245.3	3563	Gtc/Ttc	19/27	0.438848651216165	1	FACETS	0.305	0.245	0.371	0.305	0.245	0.371	INDETERMINATE	1	TRUE	0	0.74225012658966	1		370	150	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761336	59761336	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	122	369	10	ENST00000259008.2:c.3071G>A	p.Gly1024Glu	p.G1024E	ENST00000259008	NM_032043.2	1024	gGg/gAg	20/20	0.74225012658966	8	FACETS	1	0.967	1	0.283	0.257	0.31	CLONAL	2	TRUE	0	0.74225012658966	8		379	468	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761037	59761037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	37	306	3	ENST00000259008.2:c.3370G>A	p.Glu1124Lys	p.E1124K	ENST00000259008	NM_032043.2	1124	Gaa/Aaa	20/20	0.74225012658966	8	FACETS	1	0.862	1	0.131	0.108	0.156	CLONAL	1	TRUE	0	0.74225012658966	8		309	307	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761287	59761287	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	125	361	14	ENST00000259008.2:c.3120G>T	p.Lys1040Asn	p.K1040N	ENST00000259008	NM_032043.2	1040	aaG/aaT	20/20	0.74225012658966	8	FACETS	0.856	0.782	0.934	0.321	0.293	0.351	CLONAL	3	TRUE	0	0.74225012658966	8		375	423	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761343	59761343	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782808	NA	P-0068185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	110	360	11	ENST00000259008.2:c.3064G>A	p.Glu1022Lys	p.E1022K	ENST00000259008	NM_032043.2	1022	Gag/Aag	20/20	0.74225012658966	8	FACETS	1	0.93	1	0.259	0.233	0.285	CLONAL	2	TRUE	0	0.74225012658966	8		371	462	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	13	350	0				ENST00000310581	NM_198253.2	-/1132			0.221248049866395	1	FACETS	0.763	0.547	1	0.763	0.547	1	CLONAL	1	TRUE	0	0.221248049866395	1		350	137	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478786	56478786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324972550	NA	P-0068186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	43	339	0	ENST00000267101.3:c.242G>A	p.Arg81Gln	p.R81Q	ENST00000267101	NM_001982.3	81	cGa/cAa	3/28	1	2	FACETS	0.997	0.844	1	1	0.971	1	CLONAL	2	TRUE	1	0.221248049866395	2		339	195	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489582	56489582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56387488	NA	P-0068186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	17	411	2	ENST00000267101.3:c.2047C>T	p.Arg683Trp	p.R683W	ENST00000267101	NM_001982.3	683	Cgg/Tgg	17/28	1	2	FACETS	0.549	0.409	0.714	0.549	0.409	0.714	SUBCLONAL	1	TRUE	1	0.221248049866395	2		413	280	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101586	27101586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1420328983	NA	P-0068186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	34	357	0	ENST00000324856.7:c.4868C>T	p.Ser1623Leu	p.S1623L	ENST00000324856	NM_006015.4	1623	tCg/tTg	18/20	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.221248049866395	2		357	273	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806623	1806623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	56	419	0	ENST00000260795.2:c.1339G>A	p.Glu447Lys	p.E447K	ENST00000260795		447	Gag/Aag	9/17	1	2	FACETS	0.798	0.688	0.917	1	0.971	1	CLONAL	2	TRUE	1	0.221248049866395	2		419	317	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105682	27105682	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	32	425	0	ENST00000324856.7:c.5293G>T	p.Glu1765Ter	p.E1765*	ENST00000324856	NM_006015.4	1765	Gaa/Taa	20/20	1	2	FACETS	1	0.826	1	1	0.826	1	CLONAL	1	TRUE	1	0.221248049866395	2		425	285	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	493255	493255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	28	313	0	ENST00000399788.2:c.308C>T	p.Ser103Phe	p.S103F	ENST00000399788	NM_001042603.1	103	tCt/tTt	3/28	0.221248049866395	0	FACETS	1	0.833	1			1	CLONAL	1	TRUE	0	0.221248049866395	0		313	190	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401406	139401406	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	27	395	0	ENST00000277541.6:c.3663C>A	p.Asn1221Lys	p.N1221K	ENST00000277541	NM_017617.3	1221	aaC/aaA	23/34	1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	TRUE	1	0.221248049866395	2		395	229	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633400	8633400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760713741	NA	P-0068186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	20	348	0	ENST00000356435.5:c.269C>T	p.Pro90Leu	p.P90L	ENST00000356435		90	cCg/cTg	3/35	0.221248049866395	1	FACETS	1	0.789	1	1	0.789	1	CLONAL	1	TRUE	0	0.221248049866395	1		348	157	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061902	38061903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0068186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	93	413	0	ENST00000250448.2:c.86dup	p.Val31GlyfsTer196	p.V31Gfs*196	ENST00000250448	NM_004496.3	29	gtc/gtTc	2/2	0.178906919928945	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.221248049866395	3		413	377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	71	373	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.909	0.796	1	0.909	0.796	1	CLONAL	1	TRUE	1	0.353406294311339	2		373	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	110	371	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.353406294311339	2		371	525	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	90	492	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.353406294311339	1	FACETS	0.971	0.866	1	0.971	0.866	1	CLONAL	1	TRUE	0	0.353406294311339	1		492	432	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	87	564	5	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.873	0.774	0.978	0.873	0.774	0.978	CLONAL	1	TRUE	1	0.353406294311339	2		569	564	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	96	678	7	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.353406294311339	2		685	518	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042266	6042266	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs587781913	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	70	396	0	ENST00000265849.7:c.355G>A	p.Asp119Asn	p.D119N	ENST00000265849	NM_000535.5	119	Gat/Aat	5/15	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.353406294311339	2		396	382	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	36	160	1	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.353406294311339	1	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	0	0.353406294311339	1		161	162	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306569	41306569	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	46	451	0	ENST00000373198.4:c.1090C>T	p.Arg364Ter	p.R364*	ENST00000373198	NM_133170.3	364	Cga/Tga	7/32	0.353406294311339	1	FACETS	0.604	0.51	0.706	0.604	0.51	0.706	SUBCLONAL	1	TRUE	0	0.353406294311339	1		451	355	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951852	2951852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770667388	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	97	497	0	ENST00000396946.4:c.3098C>T	p.Ala1033Val	p.A1033V	ENST00000396946	NM_032415.4	1033	gCg/gTg	23/25	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.353406294311339	2		497	506	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281551	15281551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	76	464	0	ENST00000263388.2:c.4822G>A	p.Ala1608Thr	p.A1608T	ENST00000263388	NM_000435.2	1608	Gct/Act	26/33	1	2	FACETS	0.96	0.845	1	0.96	0.845	1	CLONAL	1	TRUE	1	0.353406294311339	2		464	448	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155778	106155779	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs759055581	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	71	582	0	ENST00000380013.4:c.685dup	p.Thr229AsnfsTer25	p.T229Nfs*25	ENST00000380013	NM_001127208.2	227	gaa/gAaa	3/11	1	2	FACETS	0.771	0.674	0.875	0.771	0.674	0.875	SUBCLONAL	1	TRUE	1	0.353406294311339	2		582	521	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412545	80412545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	71	407	0	ENST00000286548.4:c.496C>T	p.Arg166Cys	p.R166C	ENST00000286548	NM_002072.3	166	Cgc/Tgc	4/7	1	2	FACETS	0.877	0.768	0.994	0.877	0.768	0.994	CLONAL	1	TRUE	1	0.353406294311339	2		407	458	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238356	98238356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	75	442	0	ENST00000331920.6:c.1688C>T	p.Ala563Val	p.A563V	ENST00000331920	NM_000264.3	563	gCg/gTg	12/24	1	2	FACETS	0.847	0.744	0.958	0.847	0.744	0.958	CLONAL	1	TRUE	1	0.353406294311339	2		442	501	SUCCESS
APC	324	MSKCC	GRCh37	5	112170772	112170772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765557332	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	70	486	1	ENST00000257430.4:c.1868G>A	p.Arg623Gln	p.R623Q	ENST00000257430	NM_000038.5	623	cGg/cAg	15/16	1	2	FACETS	0.852	0.745	0.967	0.852	0.745	0.967	CLONAL	1	TRUE	1	0.353406294311339	2		487	465	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029521	14029521	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202186213	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	72	545	0	ENST00000311895.7:c.1732G>A	p.Val578Met	p.V578M	ENST00000311895	NM_005236.2	578	Gtg/Atg	8/11	1	2	FACETS	0.787	0.689	0.892	0.787	0.689	0.892	SUBCLONAL	1	TRUE	1	0.353406294311339	2		545	518	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17125941	17125941	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367843558	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	66	472	0	ENST00000285071.4:c.653G>A	p.Arg218His	p.R218H	ENST00000285071	NM_144997.5	218	cGt/cAt	7/14	1	2	FACETS	0.752	0.653	0.857	0.752	0.653	0.857	SUBCLONAL	1	TRUE	1	0.353406294311339	2		472	497	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504349	149504349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139554380	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	26	437	2	ENST00000261799.4:c.1853C>T	p.Thr618Met	p.T618M	ENST00000261799	NM_002609.3	618	aCg/aTg	13/23	1	2	FACETS	0.365	0.289	0.453	0.365	0.289	0.453	SUBCLONAL	1	TRUE	1	0.353406294311339	2		439	403	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070324	37070324	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63749795	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	82	465	0	ENST00000231790.2:c.1459C>T	p.Arg487Ter	p.R487*	ENST00000231790	NM_000249.3	487	Cga/Tga	13/19	0.353406294311339	1	FACETS	0.912	0.808	1	0.912	0.808	1	CLONAL	1	TRUE	0	0.353406294311339	1		465	419	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775601	39775601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146705250	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	105	511	0	ENST00000288319.7:c.419G>A	p.Arg140Gln	p.R140Q	ENST00000288319	NM_182918.3	140	cGg/cAg	4/10	0.353406294311339	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.353406294311339	1		511	437	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499772	8499772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773166856	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	102	482	1	ENST00000356435.5:c.2197C>T	p.Arg733Cys	p.R733C	ENST00000356435		733	Cgc/Tgc	14/35	0.353406294311339	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.353406294311339	1		483	398	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933872	39933872	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1274186244	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	86	607	0	ENST00000378444.4:c.727C>T	p.Arg243Cys	p.R243C	ENST00000378444	NM_001123385.1	243	Cgc/Tgc	4/15	1	2	FACETS	0.817	0.723	0.916	0.817	0.723	0.916	CLONAL	1	TRUE	1	0.353406294311339	2		607	596	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154755	2154755	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	105	522	1	ENST00000434045.2:c.466G>A	p.Val156Met	p.V156M	ENST00000434045	NM_001127598.1	156	Gtg/Atg	4/5	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.353406294311339	2		523	526	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793208	139793208	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561210418	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	64	340	0	ENST00000247668.2:c.16G>A	p.Val6Met	p.V6M	ENST00000247668	NM_021138.3	6	Gtg/Atg	2/11	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.353406294311339	2		340	344	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172271	99172271	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	108	600	0	ENST00000074304.5:c.1837C>T	p.His613Tyr	p.H613Y	ENST00000074304	NM_001134224.1	613	Cat/Tat	17/26	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.353406294311339	2		600	596	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445095	49445095	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	90	558	1	ENST00000301067.7:c.2371del	p.Gln791ArgfsTer139	p.Q791Rfs*139	ENST00000301067	NM_003482.3	791	Cag/ag	10/54	1	2	FACETS	0.928	0.825	1	0.928	0.825	1	CLONAL	1	TRUE	1	0.353406294311339	2		559	549	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729108	66729108	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752994941	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	93	511	0	ENST00000307102.5:c.316G>A	p.Ala106Thr	p.A106T	ENST00000307102	NM_002755.3	106	Gca/Aca	3/11	1	2	FACETS	0.959	0.855	1	0.959	0.855	1	CLONAL	1	TRUE	1	0.353406294311339	2		511	549	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119971	70119971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	68	457	0	ENST00000245479.2:c.973G>A	p.Ala325Thr	p.A325T	ENST00000245479	NM_000346.3	325	Gcg/Acg	3/3	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.353406294311339	2		457	359	SUCCESS
AR	367	MSKCC	GRCh37	X	66941694	66941694	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	65	440	0	ENST00000374690.3:c.2338C>T	p.Arg780Trp	p.R780W	ENST00000374690	NM_000044.3	780	Cgg/Tgg	6/8	1	2	FACETS	0.859	0.748	0.98	0.859	0.748	0.98	CLONAL	1	TRUE	1	0.353406294311339	2		440	428	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161293426	161293426	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs201286421	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	79	361	0	ENST00000367975.2:c.43C>T	p.Arg15Ter	p.R15*	ENST00000367975	NM_003001.3	15	Cga/Tga	2/6	1	2	FACETS	0.931	0.822	1	0.931	0.822	1	CLONAL	1	TRUE	1	0.353406294311339	2		361	480	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831345	89831346	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs878853663	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	80	549	2	ENST00000389301.3:c.2730_2731del	p.Trp911AspfsTer31	p.W911Dfs*31	ENST00000389301	NM_000135.2	910	ctCTgg/ctgg	28/43	1	2	FACETS	0.765	0.674	0.862	0.765	0.674	0.862	SUBCLONAL	1	TRUE	1	0.353406294311339	2		551	592	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67646012	67646013	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	88	415	4	ENST00000264010.4:c.950_951dup	p.Gly318GlnfsTer16	p.G318Qfs*16	ENST00000264010	NM_006565.3	314	aac/aACac	4/12	1	2	FACETS	0.96	0.853	1	0.96	0.853	1	CLONAL	1	TRUE	1	0.353406294311339	2		419	519	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344036	118344036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	95	543	0	ENST00000534358.1:c.2162G>A	p.Arg721Gln	p.R721Q	ENST00000534358	NM_005933.3	721	cGa/cAa	3/36	1	2	FACETS	0.893	0.797	0.996	0.893	0.797	0.996	CLONAL	1	TRUE	1	0.353406294311339	2		543	602	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880926	134880926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371083718	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	77	441	0	ENST00000398015.3:c.1489C>T	p.Arg497Trp	p.R497W	ENST00000398015	NM_004441.4	497	Cgg/Tgg	7/16	0.312079944949622	3	FACETS	0.973	0.856	1	0.486	0.428	0.549	CLONAL	1	TRUE	1	0.353406294311339	3		441	527	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376920	118376920	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782425634	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	88	586	0	ENST00000534358.1:c.10313C>T	p.Thr3438Met	p.T3438M	ENST00000534358	NM_005933.3	3438	aCg/aTg	27/36	1	2	FACETS	0.874	0.776	0.978	0.874	0.776	0.978	CLONAL	1	TRUE	1	0.353406294311339	2		586	570	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170150	32170150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	86	579	0	ENST00000375023.3:c.3458G>A	p.Gly1153Glu	p.G1153E	ENST00000375023	NM_004557.3	1153	gGg/gAg	21/30	0.353406294311339	1	FACETS	0.943	0.838	1	0.943	0.838	1	CLONAL	1	TRUE	0	0.353406294311339	1		579	425	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417590	139417590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750242131	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	102	516	0	ENST00000277541.6:c.454G>A	p.Gly152Ser	p.G152S	ENST00000277541	NM_017617.3	152	Ggt/Agt	4/34	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.353406294311339	2		516	525	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111982980	111982980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	64	472	1	ENST00000368678.4:c.1567G>A	p.Ala523Thr	p.A523T	ENST00000368678		523	Gcg/Acg	13/13	1	2	FACETS	0.753	0.653	0.861	0.753	0.653	0.861	SUBCLONAL	1	TRUE	1	0.353406294311339	2		473	481	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530103	63530103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398258340	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	88	437	0	ENST00000307078.5:c.2332C>T	p.Arg778Trp	p.R778W	ENST00000307078	NM_004655.3	778	Cgg/Tgg	10/11	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.353406294311339	2		437	461	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563168	21563168	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766080720	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	73	606	0	ENST00000382592.4:c.751G>A	p.Ala251Thr	p.A251T	ENST00000382592	NM_014572.2	251	Gcg/Acg	4/8	0.353406294311339	1	FACETS	0.786	0.69	0.888	0.786	0.69	0.888	SUBCLONAL	1	TRUE	0	0.353406294311339	1		606	433	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977548	2977548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751008087	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	64	292	0	ENST00000396946.4:c.1136G>A	p.Arg379Gln	p.R379Q	ENST00000396946	NM_032415.4	379	cGg/cAg	8/25	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.353406294311339	2		292	319	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909557	50909557	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1004124075	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	95	543	0	ENST00000440232.2:c.1361G>A	p.Arg454His	p.R454H	ENST00000440232	NM_002691.3	454	cGc/cAc	11/27	1	2	FACETS	0.996	0.889	1	0.996	0.889	1	CLONAL	1	TRUE	1	0.353406294311339	2		543	540	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502704	149502704	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375978065	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	86	514	1	ENST00000261799.4:c.2084G>A	p.Arg695His	p.R695H	ENST00000261799	NM_002609.3	695	cGc/cAc	15/23	1	2	FACETS	0.932	0.827	1	0.932	0.827	1	CLONAL	1	TRUE	1	0.353406294311339	2		515	522	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28595718	28595718	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	86	499	0	ENST00000253063.3:c.115C>T	p.Arg39Ter	p.R39*	ENST00000253063	NM_031459.4	39	Cga/Tga	2/10	1	2	FACETS	0.875	0.776	0.981	0.875	0.776	0.981	CLONAL	1	TRUE	1	0.353406294311339	2		499	556	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15821902	15821902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs181618355	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	76	451	0	ENST00000307771.7:c.295C>T	p.Arg99Trp	p.R99W	ENST00000307771	NM_005089.3	99	Cgg/Tgg	4/11	1	2	FACETS	0.96	0.845	1	0.96	0.845	1	CLONAL	1	TRUE	1	0.353406294311339	2		451	448	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225698	26225698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	101	686	0	ENST00000360408.1:c.316G>A	p.Glu106Lys	p.E106K	ENST00000360408	NM_003532.2	106	Gag/Aag	1/1	0.353406294311339	1	FACETS	0.84	0.753	0.932	0.84	0.753	0.932	CLONAL	1	TRUE	0	0.353406294311339	1		686	560	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101854	11101854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377549345	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	79	511	0	ENST00000358026.2:c.1274G>A	p.Arg425Gln	p.R425Q	ENST00000358026	NM_001128849.1	425	cGg/cAg	8/36	1	2	FACETS	0.86	0.758	0.969	0.86	0.758	0.969	CLONAL	1	TRUE	1	0.353406294311339	2		511	520	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379820	17379820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199925580	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	67	532	0	ENST00000359435.4:c.205G>A	p.Gly69Ser	p.G69S	ENST00000359435	NM_001033549.1	69	Ggc/Agc	2/9	1	2	FACETS	0.814	0.709	0.926	0.814	0.709	0.926	CLONAL	1	TRUE	1	0.353406294311339	2		532	466	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470521	25470521	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	91	506	0	ENST00000264709.3:c.953G>T	p.Arg318Leu	p.R318L	ENST00000264709	NM_175629.2	318	cGg/cTg	8/23	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.353406294311339	2		506	479	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212185	5212185	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	73	498	0	ENST00000357368.4:c.4846G>A	p.Asp1616Asn	p.D1616N	ENST00000357368	NM_002850.3	1616	Gat/Aat	32/38	0.312079944949622	3	FACETS	0.768	0.672	0.872	0.384	0.336	0.436	SUBCLONAL	1	TRUE	1	0.353406294311339	3		498	633	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931831	68931831	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	78	411	0	ENST00000288368.4:c.261C>G	p.Phe87Leu	p.F87L	ENST00000288368	NM_024870.2	87	ttC/ttG	3/40	0.309493214053896	5	FACETS	1	0.924	1	0.268	0.235	0.303	CLONAL	1	TRUE	1	0.353406294311339	5		411	631	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006806	47006806	+	5_prime_UTR_variant	5'UTR	SNP	G	G	A	rs782371765	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	31	509	0	ENST00000377604.3:c.-75G>A		p.*25*	ENST00000377604	NM_001204468.1	-/852		2/24	1	2	FACETS	0.316	0.254	0.385	0.316	0.254	0.385	SUBCLONAL	1	TRUE	1	0.353406294311339	2		509	556	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637473	47637473	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587779973	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	73	409	0	ENST00000233146.2:c.607G>A	p.Gly203Arg	p.G203R	ENST00000233146	NM_000251.2	203	Gga/Aga	3/16	1	2	FACETS	0.838	0.735	0.949	0.838	0.735	0.949	CLONAL	1	TRUE	1	0.353406294311339	2		409	493	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960126	151960126	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	65	321	0	ENST00000262189.6:c.1274T>C	p.Val425Ala	p.V425A	ENST00000262189	NM_170606.2	425	gTa/gCa	9/59	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.353406294311339	2		321	296	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451245	70451245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	85	596	0	ENST00000373644.4:c.6085G>A	p.Ala2029Thr	p.A2029T	ENST00000373644	NM_030625.2	2029	Gct/Act	12/12	1	2	FACETS	0.909	0.806	1	0.909	0.806	1	CLONAL	1	TRUE	1	0.353406294311339	2		596	529	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920699	96920699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746831347	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	61	397	0	ENST00000258439.3:c.281G>A	p.Arg94Gln	p.R94Q	ENST00000258439	NM_001193304.2	94	cGg/cAg	3/4	1	2	FACETS	0.805	0.696	0.922	0.805	0.696	0.922	CLONAL	1	TRUE	1	0.353406294311339	2		397	429	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328398	137328398	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	78	518	0	ENST00000481739.1:c.1327G>A	p.Gly443Arg	p.G443R	ENST00000481739	NM_002957.4	443	Ggg/Agg	10/10	1	2	FACETS	0.867	0.764	0.978	0.867	0.764	0.978	CLONAL	1	TRUE	1	0.353406294311339	2		518	509	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931821	68931821	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	66	412	0	ENST00000288368.4:c.251A>G	p.His84Arg	p.H84R	ENST00000288368	NM_024870.2	84	cAt/cGt	3/40	0.309493214053896	5	FACETS	0.934	0.811	1	0.233	0.202	0.267	CLONAL	1	TRUE	1	0.353406294311339	5		412	612	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209336	133209336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144178150	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	90	530	0	ENST00000320574.5:c.6050G>A	p.Arg2017His	p.R2017H	ENST00000320574	NM_006231.2	2017	cGc/cAc	44/49	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.353406294311339	2		530	506	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224594	108224594	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	55	405	0	ENST00000278616.4:c.8773G>T	p.Gly2925Cys	p.G2925C	ENST00000278616	NM_000051.3	2925	Ggt/Tgt	60/63	1	2	FACETS	0.867	0.745	0.999	0.867	0.745	0.999	CLONAL	1	TRUE	1	0.353406294311339	2		405	359	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62317172	62317172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770158407	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	80	557	0	ENST00000360203.5:c.1295G>A	p.Arg432Gln	p.R432Q	ENST00000360203	NM_001283009.1	432	cGg/cAg	16/35	1	2	FACETS	0.909	0.803	1	0.909	0.803	1	CLONAL	1	TRUE	1	0.353406294311339	2		557	498	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090416	77090416	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	98	426	0	ENST00000356341.3:c.309G>T	p.Trp103Cys	p.W103C	ENST00000356341	NM_002576.4	103	tgG/tgT	4/15	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.353406294311339	2		426	513	SUCCESS
SCG5	6447	MSKCC	GRCh37	15	32983959	32983959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1401047581	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	69	390	0	ENST00000300175.4:c.538C>T	p.Arg180Trp	p.R180W	ENST00000300175	NM_001144757.1	180	Cgg/Tgg	5/6	1	2	FACETS	0.872	0.762	0.99	0.872	0.762	0.99	CLONAL	1	TRUE	1	0.353406294311339	2		390	448	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178355	56178355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1038244253	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	58	415	0	ENST00000399503.3:c.3328G>A	p.Glu1110Lys	p.E1110K	ENST00000399503	NM_005921.1	1110	Gag/Aag	14/20	1	2	FACETS	0.825	0.711	0.948	0.825	0.711	0.948	CLONAL	1	TRUE	1	0.353406294311339	2		415	398	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51503214	51503214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121434534	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	78	471	0	ENST00000260433.2:c.1303C>T	p.Arg435Cys	p.R435C	ENST00000260433		435	Cgt/Tgt	10/10	1	2	FACETS	0.905	0.797	1	0.905	0.797	1	CLONAL	1	TRUE	1	0.353406294311339	2		471	488	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322622	109322622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756253993	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	63	456	0	ENST00000436639.2:c.415C>T	p.Arg139Cys	p.R139C	ENST00000436639	NM_014454.2	139	Cgt/Tgt	3/10	1	2	FACETS	0.775	0.672	0.886	0.775	0.672	0.886	SUBCLONAL	1	TRUE	1	0.353406294311339	2		456	460	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804363	46804363	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	91	472	0	ENST00000290295.7:c.644G>A	p.Arg215His	p.R215H	ENST00000290295	NM_006361.5	215	cGc/cAc	2/2	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.353406294311339	2		472	468	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0068192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	38	206	0	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	0.293108975059469	1	FACETS	0.723	0.6	0.859	0.723	0.6	0.859	SUBCLONAL	1	TRUE	0	0.293108975059469	1		206	306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0068192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	15	303	0	ENST00000269305.4:c.782+1G>C		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.293108975059469	1	FACETS	0.204	0.148	0.271	0.204	0.148	0.271	SUBCLONAL	1	TRUE	0	0.293108975059469	1		303	428	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100074	27100074	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	88	533	0	ENST00000324856.7:c.3871del	p.Glu1291SerfsTer4	p.E1291Sfs*4	ENST00000324856	NM_006015.4	1290	acG/ac	16/20	1	2	FACETS	0.852	0.755	0.956	0.852	0.755	0.956	CLONAL	1	TRUE	1	0.293108975059469	2		533	705	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439742	140439742	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	37	251	0	ENST00000288602.6:c.1997T>C	p.Ile666Thr	p.I666T	ENST00000288602	NM_004333.4	666	aTt/aCt	17/18	1	2	FACETS	0.83	0.687	0.989	0.83	0.687	0.989	CLONAL	1	TRUE	1	0.293108975059469	2		251	304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0068193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	247	426	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.820336594972504	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.820336594972504	2		426	286	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597402	10597402	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	323	451	0	ENST00000171111.5:c.1801C>G	p.Arg601Gly	p.R601G	ENST00000171111	NM_203500.1	601	Cgg/Ggg	6/6	0.820336594972504	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.820336594972504	2		451	364	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120114	70120115	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0068194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	17	464	3	ENST00000245479.2:c.1121dup	p.Gln375AlafsTer203	p.Q375Afs*203	ENST00000245479	NM_000346.3	372	-/C	3/3	0.65515154684305	1	FACETS	0.436	0.332	0.554	0.436	0.332	0.554	SUBCLONAL	1	TRUE	0	0.65515154684305	1		467	80	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923667	72923667	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1292211543	NA	P-0068194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	75	506	0	ENST00000268489.5:c.3411G>C	p.Gln1137His	p.Q1137H	ENST00000268489	NM_006885.3	1137	caG/caC	4/10	0.65515154684305	1	FACETS	0.74	0.661	0.822	0.74	0.661	0.822	SUBCLONAL	1	TRUE	0	0.65515154684305	1		506	208	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913514	NA	P-0068195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	122	481	0	ENST00000288135.5:c.2466T>G	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaG	17/21	0.516233485607556	2	FACETS	1	0.973	1	0.585	0.533	0.638	CLONAL	1	TRUE	0	0.516233485607556	2		481	404	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031376	11031376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	179	733	0	ENST00000327064.4:c.1376C>T	p.Thr459Ile	p.T459I	ENST00000327064	NM_199141.1	459	aCc/aTc	12/16	0.516233485607556	3	FACETS	1	0.926	1	0.502	0.463	0.543	CLONAL	1	TRUE	1	0.516233485607556	3		733	869	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969324	44969324	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	41	229	0	ENST00000377967.4:c.4006G>T	p.Val1336Leu	p.V1336L	ENST00000377967	NM_021140.2	1336	Gtg/Ttg	28/29	0.494765177077574	2	FACETS	0.567	0.475	0.669			1	SUBCLONAL	1	TRUE	NA	0.516233485607556	2		229	280	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332109	70332109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777837034	NA	P-0068196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	108	381	0	ENST00000373644.4:c.14G>A	p.Arg5His	p.R5H	ENST00000373644	NM_030625.2	5	cGc/cAc	2/12	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.33	2		381	620	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0068197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	353	599	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	0.963	0.918	1	0.963	0.918	1	CLONAL	1	TRUE	1	0.952472364291225	2		599	770	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799063	42799065	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs751580245	NA	P-0068197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	302	474	0	ENST00000575354.2:c.4550_4552del	p.Lys1517del	p.K1517del	ENST00000575354	NM_015125.3	1516	cAGAag/cag	20/20	0.952472364291225	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.952472364291225	1		474	330	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775614	9775614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766440014	NA	P-0068197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	17	439	0	ENST00000377346.4:c.157G>A	p.Ala53Thr	p.A53T	ENST00000377346	NM_005026.3	53	Gcc/Acc	4/24	0.952472364291225	1	FACETS	0.071	0.053	0.093	0.071	0.053	0.093	SUBCLONAL	1	TRUE	0	0.952472364291225	1		439	263	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413067	139413069	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0068197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	306	452	0	ENST00000277541.6:c.1073_1075del	p.Tyr358del	p.Y358del	ENST00000277541	NM_017617.3	358	tACTgc/tgc	6/34	0.752405879276319	1	FACETS	0.996	0.973	1	0.996	0.973	1	CLONAL	1	TRUE	0	0.952472364291225	1		452	338	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0068197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	157	0	0				ENST00000310581	NM_198253.2	-/1132			0.289715105452128	1	FACETS	0.517	0.481	0.553	0.517	0.481	0.553	INDETERMINATE	1	TRUE	0	0.952472364291225	1		0	334	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746003	162746003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs896311138	NA	P-0068197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	255	456	1	ENST00000367921.3:c.2126G>A	p.Arg709Gln	p.R709Q	ENST00000367921	NM_006182.2	709	cGa/cAa	16/18	1	2	FACETS	0.824	0.776	0.872	0.824	0.776	0.872	CLONAL	1	TRUE	1	0.952472364291225	2		457	650	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353850	68353853	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	novel	NA	P-0068197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	.	304	449	0	ENST00000487270.1:c.692_695del	p.Arg231ThrfsTer11	p.R231Tfs*11	ENST00000487270	NM_133509.3	229	AAAGaa/aa	7/11	0.952472364291225	1	FACETS		NA	1			1	NA	NA	TRUE	0	0.952472364291225	1		449	304	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164162	47164163	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0068197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	253	400	0	ENST00000409792.3:c.1963_1964del	p.Leu655IlefsTer2	p.L655Ifs*2	ENST00000409792	NM_014159.6	655	TTa/a	3/21	1	2	FACETS	0.877	0.827	0.927	0.877	0.827	0.927	CLONAL	1	TRUE	1	0.952472364291225	2		400	606	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176133007	176133007	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	265	334	0	ENST00000367669.3:c.586C>G	p.Gln196Glu	p.Q196E	ENST00000367669	NM_022457.5	196	Cag/Gag	4/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.952472364291225	2		334	490	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10283823	10283825	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0068197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	197	389	0	ENST00000340748.4:c.661_663del	p.Glu221del	p.E221del	ENST00000340748		221	GAA/-	8/40	1	2	FACETS	0.705	0.657	0.754	0.705	0.657	0.754	SUBCLONAL	1	TRUE	1	0.952472364291225	2		389	587	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0068207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	49	377	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	0.334424043174365	4	FACETS	0.738	0.625	0.863	0.369	0.312	0.432	SUBCLONAL	1	TRUE	2	0.33	4		377	535	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476310	88476310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760692815	NA	P-0068207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	33	330	0	ENST00000360948.2:c.1822G>A	p.Gly608Ser	p.G608S	ENST00000360948	NM_001012338.2	608	Ggc/Agc	15/19	0.334424043174365	1	FACETS	0.425	0.346	0.514	0.425	0.346	0.514	SUBCLONAL	1	TRUE	0	0.33	1		330	393	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043465	180043465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1451816005	NA	P-0068207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	24	384	1	ENST00000261937.6:c.3121C>T	p.Arg1041Trp	p.R1041W	ENST00000261937	NM_182925.4	1041	Cgg/Tgg	23/30	1	2	FACETS	0.328	0.256	0.41	0.328	0.256	0.41	SUBCLONAL	1	TRUE	1	0.33	2		385	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579419	7579419	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	52	414	0	ENST00000269305.4:c.268del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	90	Tcc/cc	4/11	0.334424043174365	4	FACETS	0.708	0.602	0.824			1	SUBCLONAL	1	TRUE	NA	0.33	4		414	592	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604707	48604707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs377767371	NA	P-0068207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	41	386	0	ENST00000342988.3:c.1529G>T	p.Gly510Val	p.G510V	ENST00000342988	NM_005359.5	510	gGa/gTa	12/12	0.274303561100004	4	FACETS	0.744	0.62	0.882	0.372	0.31	0.441	SUBCLONAL	1	TRUE	2	0.33	4		386	444	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14027792	14027792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555395802	NA	P-0068207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	39	277	0	ENST00000405192.2:c.52C>T	p.Arg18Cys	p.R18C	ENST00000405192	NM_001163147.1	18	Cgt/Tgt	3/12	0.274303561100004	4	FACETS	0.77	0.639	0.917	0.385	0.319	0.459	CLONAL	1	TRUE	2	0.33	4		277	408	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21349316	21349316	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs765095992	NA	P-0068207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	38	410	0	ENST00000215739.8:c.1942+1G>T		p.X648_splice	ENST00000215739	NM_006767.3	648			0.334424043174365	3	FACETS	0.555	0.459	0.664	0.278	0.229	0.332	SUBCLONAL	1	TRUE	1	0.33	3		410	483	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659761	227659761	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	38	284	0	ENST00000305123.5:c.3694A>T	p.Ile1232Phe	p.I1232F	ENST00000305123	NM_005544.2	1232	Atc/Ttc	1/2	0.334424043174365	3	FACETS	0.519	0.428	0.62	0.259	0.214	0.31	SUBCLONAL	1	TRUE	1	0.33	3		284	517	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026566	48026566	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750909	NA	P-0068210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	153	461	0	ENST00000234420.5:c.1444C>T	p.Arg482Ter	p.R482*	ENST00000234420	NM_000179.2	482	Cga/Tga	4/10	0.613380735755625	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		461	661	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	37	350	0				ENST00000310581	NM_198253.2	-/1132			0.328033308785585	3	FACETS	0.804	0.665	0.958	0.402	0.332	0.479	CLONAL	1	TRUE	1	0.333674762227389	3		350	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	55	559	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.167931614887621	0	FACETS	0.364	0.311	0.422			1	INDETERMINATE	1	TRUE	0	0.333674762227389	0		559	603	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971029	21971029	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519852	NA	P-0068211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	177	376	2	ENST00000304494.5:c.329G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tGg/tAg	2/3	0.333674762227389	1	FACETS	0.993	0.925	1	1	0.993	1	CLONAL	2	TRUE	0	0.333674762227389	1		378	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577088	7577088	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1204379654	NA	P-0068211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	67	395	0	ENST00000269305.4:c.850A>C	p.Thr284Pro	p.T284P	ENST00000269305	NM_001126112.2	284	Aca/Cca	8/11	0.167931614887621	0	FACETS	0.473	0.411	0.54			1	INDETERMINATE	1	TRUE	0	0.333674762227389	0		395	566	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125395	7125395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs185736681	NA	P-0068211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	102	387	0	ENST00000302850.5:c.3157C>T	p.Arg1053Cys	p.R1053C	ENST00000302850	NM_000208.2	1053	Cgc/Tgc	17/22	0.333674762227389	1	FACETS	0.85	0.762	0.944	0.85	0.762	0.944	CLONAL	1	TRUE	0	0.333674762227389	1		387	599	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791726	42791726	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	130	422	0	ENST00000575354.2:c.612G>C	p.Met204Ile	p.M204I	ENST00000575354	NM_015125.3	204	atG/atC	5/20	0.333674762227389	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.333674762227389	1		422	536	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475322	40475336	+	inframe_deletion	In_Frame_Del	DEL	GATATTGTCCAGCCA	GATATTGTCCAGCCA	-	novel	NA	P-0068211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	56	366	0	ENST00000264657.5:c.1690_1704del	p.Trp564_Ile568del	p.W564_I568del	ENST00000264657	NM_139276.2	564	TGGCTGGACAATATC/-	19/24	0.205492841307528	1	FACETS	0.538	0.461	0.622	0.538	0.461	0.622	SUBCLONAL	1	TRUE	0	0.333674762227389	1		366	520	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438022	49438022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1157281284	NA	P-0068211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	49	415	0	ENST00000301067.7:c.5149C>T	p.Gln1717Ter	p.Q1717*	ENST00000301067	NM_003482.3	1717	Cag/Tag	21/54	0.205492841307528	1	FACETS	0.423	0.358	0.495	0.423	0.358	0.495	SUBCLONAL	1	TRUE	0	0.333674762227389	1		415	578	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622684	158622684	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0068211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	115	332	0	ENST00000263640.3:c.815C>G	p.Ser272Ter	p.S272*	ENST00000263640	NM_001105.4	272	tCa/tGa	8/11	0.205492841307528	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.333674762227389	1		332	528	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254887	16254887	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	374	443	0	ENST00000375759.3:c.2152G>T	p.Glu718Ter	p.E718*	ENST00000375759	NM_015001.2	718	Gag/Tag	11/15	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.800136701397524	2		443	736	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159098	143159098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1321044670	NA	P-0068213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	21	222	0	ENST00000262992.4:c.755G>A	p.Arg252Gln	p.R252Q	ENST00000262992	NM_001101669.1	252	cGa/cAa	10/24	0.284310160030876	1	FACETS	0.477	0.38	0.582	0.477	0.38	0.582	INDETERMINATE	1	TRUE	0	0.800136701397524	1		222	66	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020487	14020487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913050	NA	P-0068213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	12	360	0	ENST00000311895.7:c.458G>A	p.Arg153His	p.R153H	ENST00000311895	NM_005236.2	153	cGc/cAc	3/11	1	2	FACETS	0.256	0.181	0.347	0.256	0.181	0.347	SUBCLONAL	1	TRUE	1	0.800136701397524	2		360	117	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256363	16256363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	254	443	0	ENST00000375759.3:c.3628G>A	p.Glu1210Lys	p.E1210K	ENST00000375759	NM_015001.2	1210	Gag/Aag	11/15	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.800136701397524	2		443	501	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225535	26225535	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1701	237	516	0	ENST00000360408.1:c.153G>C	p.Glu51Asp	p.E51D	ENST00000360408	NM_003532.2	51	gaG/gaC	1/1	0.751447631564653	4	FACETS	0.55	0.511	0.591	0.275	0.255	0.296	SUBCLONAL	1	TRUE	2	0.800136701397524	4		516	1938	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255565	16255565	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	296	447	0	ENST00000375759.3:c.2830G>T	p.Gly944Trp	p.G944W	ENST00000375759	NM_015001.2	944	Ggg/Tgg	11/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.800136701397524	2		447	671	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254594	16254594	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	184	334	0	ENST00000375759.3:c.1859G>T	p.Arg620Leu	p.R620L	ENST00000375759	NM_015001.2	620	cGa/cTa	11/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.800136701397524	2		334	379	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533460	533461	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCTTGGCCGAGGTC	novel	NA	P-0068213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	99	435	0	ENST00000451590.1:c.429_442dup	p.Thr148ArgfsTer29	p.T148Rfs*29	ENST00000451590	NM_001130442.1	148	acc/aGACCTCGGCCAAGAcc	4/5	0.800136701397524	1	FACETS	0.21	0.187	0.235	0.21	0.187	0.235	SUBCLONAL	1	TRUE	0	0.800136701397524	1		435	706	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0068214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	298	622	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	0.943	0.898	0.987	1	0.997	1	CLONAL	3	TRUE	1	0.373677370881866	2		622	564	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241688	55241688	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	41	397	0	ENST00000275493.2:c.2136C>G	p.Phe712Leu	p.F712L	ENST00000275493	NM_005228.3	712	ttC/ttG	18/28	0.148042287141245	3	FACETS	0.631	0.526	0.747	0.315	0.263	0.374	INDETERMINATE	1	TRUE	1	0.373677370881866	3		397	413	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278821	1278821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150819225	NA	P-0068214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	94	413	0	ENST00000310581.5:c.2221G>A	p.Val741Met	p.V741M	ENST00000310581	NM_198253.2	741	Gtg/Atg	6/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.373677370881866	2		413	368	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984923	101984923	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587777249	NA	P-0068214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	124	276	0	ENST00000282441.5:c.370C>T	p.Arg124Ter	p.R124*	ENST00000282441	NM_001130145.2	124	Cga/Tga	2/9	0.382084377708545	1	FACETS	1	0.971	1	1	0.992	1	CLONAL	2	TRUE	0	0.373677370881866	1		276	245	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870779	12870779	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	129	346	0	ENST00000228872.4:c.8del	p.Asn3ThrfsTer39	p.N3Tfs*39	ENST00000228872	NM_004064.3	2	tcA/tc	1/3	0.109049870845603	4	FACETS	1	0.972	1	1	0.972	1	INDETERMINATE	2	TRUE	2	0.373677370881866	4		346	414	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467803	99467803	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	30	400	0	ENST00000268035.6:c.2672C>G	p.Ala891Gly	p.A891G	ENST00000268035	NM_000875.3	891	gCc/gGc	13/21	0.148042287141245	3	FACETS	0.402	0.323	0.492	0.201	0.161	0.246	INDETERMINATE	1	TRUE	1	0.373677370881866	3		400	474	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117159	7117159	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs74495977	NA	P-0068215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	58	341	0	ENST00000302850.5:c.4057C>T	p.Arg1353Trp	p.R1353W	ENST00000302850	NM_000208.2	1353	Cgg/Tgg	22/22	0.254894585078077	3	FACETS	0.791	0.684	0.906	0.791	0.684	0.906	CLONAL	2	TRUE	1	0.254417623137514	3		341	325	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676264	37676271	+	frameshift_variant	Frame_Shift_Del	DEL	AAGCGGTG	AAGCGGTG	-	novel	NA	P-0068215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	91	330	0	ENST00000447079.4:c.3019_3026del	p.Lys1007HisfsTer3	p.K1007Hfs*3	ENST00000447079	NM_015083.1	1007	AAGCGGTGc/c	11/14	0.254417623137514	11	FACETS	1	0.927	1	0.465	0.416	0.516	CLONAL	4	TRUE	2	0.254417623137514	11		330	367	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230601	46230601	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	57	340	0	ENST00000334344.6:c.850C>T	p.Gln284Ter	p.Q284*	ENST00000334344	NM_152641.2	284	Cag/Tag	8/21	0.254894585078077	3	FACETS	1	0.905	1	1	0.974	1	CLONAL	3	TRUE	1	0.254417623137514	3		340	162	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061150	38061197	+	inframe_deletion	In_Frame_Del	DEL	CTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGC	CTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGC	-	novel	NA	P-0068215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	300	318	0	ENST00000250448.2:c.792_839del	p.Lys264_Ser280delinsAsn	p.K264_S280delinsN	ENST00000250448	NM_004496.3	264	aaGCGCTTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGc/aac	2/2	0.254417623137514	23	FACETS	0.985	0.938	1			1	CLONAL	15	TRUE	NA	0.254417623137514	23		318	586	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667805	37667805	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	279	266	0	ENST00000447079.4:c.2691del	p.Thr898LeufsTer11	p.T898Lfs*11	ENST00000447079	NM_015083.1	897	aTt/at	8/14	0.254417623137514	11	FACETS	1	0.982	1	1	0.994	1	CLONAL	11	TRUE	2	0.254417623137514	11		266	410	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204032	142204033	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTG	novel	NA	P-0068215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	51	333	0	ENST00000350721.4:c.6168_6170dup	p.Asn2056dup	p.N2056dup	ENST00000350721	NM_001184.3	2056	aaa/aaCAAa	36/47	NA	2	FACETS	1	0.958	1			1	INDETERMINATE	1	TRUE	NA	0.254417623137514	2		333	294	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0068217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	145	437	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.227842691053449	3	FACETS	0.998	0.916	1	0.665	0.611	0.722	CLONAL	2	TRUE	0	0.33292121776609	3		437	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0068217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	202	361	0	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	0.332049938897272	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.33292121776609	2		361	555	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261245	16261246	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0068217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	134	491	0	ENST00000375759.3:c.8516dup	p.Ala2840GlyfsTer7	p.A2840Gfs*7	ENST00000375759	NM_015001.2	2837	atc/atCc	11/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.33292121776609	2		491	717	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55238872	55238872	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	78	260	0	ENST00000275493.2:c.1885A>C	p.Thr629Pro	p.T629P	ENST00000275493	NM_005228.3	629	Act/Cct	16/28	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.33292121776609	2		260	461	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124510965	124510965	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	78	246	0	ENST00000357628.3:c.255G>T	p.Lys85Asn	p.K85N	ENST00000357628	NM_015450.2	85	aaG/aaT	7/19	0.33292121776609	4	FACETS	1	0.953	1	0.584	0.514	0.659	CLONAL	1	TRUE	2	0.33292121776609	4		246	535	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729914	30729914	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1444024775	NA	P-0068217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	97	385	1	ENST00000295754.5:c.1435C>T	p.Arg479Trp	p.R479W	ENST00000295754	NM_003242.5	479	Cgg/Tgg	6/7	NA	2	FACETS	1	0.898	1			1	INDETERMINATE	1	TRUE	NA	0.33292121776609	2		386	580	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528082	103528082	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	173	396	0	ENST00000355739.4:c.3390G>T	p.Gln1130His	p.Q1130H	ENST00000355739	NM_000123.3	1130	caG/caT	15/15	0.328146125957687	3	FACETS	0.891	0.823	0.962	0.891	0.823	0.962	CLONAL	2	TRUE	1	0.33292121776609	3		396	680	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156608	55156608	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs981559406	NA	P-0068217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	134	417	0	ENST00000257290.5:c.3009G>T	p.Trp1003Cys	p.W1003C	ENST00000257290	NM_006206.4	1003	tgG/tgT	22/23	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.33292121776609	2		417	713	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431654	431654	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	191	369	0	ENST00000399788.2:c.2355G>C	p.Arg785Ser	p.R785S	ENST00000399788	NM_001042603.1	785	agG/agC	17/28	0.227842691053449	3	FACETS	1	0.955	1	0.692	0.642	0.742	CLONAL	2	TRUE	0	0.33292121776609	3		369	645	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934022	39934022	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	126	448	0	ENST00000378444.4:c.577A>T	p.Asn193Tyr	p.N193Y	ENST00000378444	NM_001123385.1	193	Aat/Tat	4/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.33292121776609	2		448	683	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790065	40790065	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs780417311	NA	P-0068217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	95	413	0	ENST00000373198.4:c.2666G>T	p.Arg889Leu	p.R889L	ENST00000373198	NM_133170.3	889	cGg/cTg	18/32	0.214554558486971	1	FACETS	0.725	0.646	0.809	0.725	0.646	0.809	SUBCLONAL	1	TRUE	0	0.33292121776609	1		413	656	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044534	128044534	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	114	366	0	ENST00000285398.2:c.1087G>T	p.Val363Leu	p.V363L	ENST00000285398	NM_000122.1	363	Gtg/Ttg	8/15	0.328146125957687	3	FACETS	1	0.952	1	0.546	0.492	0.604	CLONAL	1	TRUE	1	0.33292121776609	3		366	731	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0068235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	75	268	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.510456773566005	4	FACETS	0.969	0.852	1			1	CLONAL	1	TRUE	NA	0.510456773566005	4		268	458	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0068235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	327	433	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	0.510456773566005	3	FACETS	0.964	0.915	1	0.643	0.61	0.676	CLONAL	2	TRUE	0	0.510456773566005	3		433	834	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52685790	52685790	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs201022657	NA	P-0068235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	130	362	0	ENST00000394830.3:c.682A>G	p.Ile228Val	p.I228V	ENST00000394830	NM_018313.4	228	Ata/Gta	7/30	1	2	FACETS	0.898	0.818	0.982	0.898	0.818	0.982	CLONAL	1	TRUE	1	0.510456773566005	2		362	567	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131505	202131505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	298	421	0	ENST00000358485.4:c.473C>T	p.Ser158Phe	p.S158F	ENST00000358485	NM_001080125.1	158	tCt/tTt	2/9	0.489618563538997	2	FACETS	0.942	0.895	0.988	0.942	0.895	0.988	CLONAL	2	TRUE	0	0.510456773566005	2		421	620	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0068235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	88	299	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	0.827	0.737	0.922	0.827	0.737	0.922	CLONAL	1	TRUE	1	0.510456773566005	2		299	417	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099233	157099233	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1478614436	NA	P-0068235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	151	519	0	ENST00000346085.5:c.170C>T	p.Ser57Leu	p.S57L	ENST00000346085	NM_020732.3	57	tCg/tTg	1/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.510456773566005	2		519	571	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853113	151853113	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	153	451	0	ENST00000262189.6:c.11842C>T	p.Gln3948Ter	p.Q3948*	ENST00000262189	NM_170606.2	3948	Cag/Tag	46/59	0.495598546831032	1	FACETS	0.911	0.84	0.985	0.911	0.84	0.985	CLONAL	1	TRUE	0	0.510456773566005	1		451	490	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230472949	230472949	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	111	459	0	ENST00000391860.1:c.635G>A	p.Arg212Lys	p.R212K	ENST00000391860	NM_001258311.1	212	aGg/aAg	4/7	1	2	FACETS	0.828	0.748	0.913	0.828	0.748	0.913	CLONAL	1	TRUE	1	0.510456773566005	2		459	525	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095857	178095857	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	375	463	0	ENST00000397062.3:c.1474G>C	p.Glu492Gln	p.E492Q	ENST00000397062	NM_006164.4	492	Gaa/Caa	5/5	0.510456773566005	3	FACETS	0.988	0.942	1	0.659	0.628	0.691	CLONAL	2	TRUE	0	0.510456773566005	3		463	933	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63898281	63898281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	133	391	0	ENST00000398590.3:c.7G>A	p.Glu3Lys	p.E3K	ENST00000398590	NM_001177387.1	3	Gag/Aag	3/14	1	2	FACETS	0.998	0.912	1	0.998	0.912	1	CLONAL	1	TRUE	1	0.510456773566005	2		391	522	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095893	178095893	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	326	438	0	ENST00000397062.3:c.1438G>C	p.Asp480His	p.D480H	ENST00000397062	NM_006164.4	480	Gac/Cac	5/5	0.510456773566005	3	FACETS	0.908	0.861	0.956	0.605	0.574	0.637	CLONAL	2	TRUE	0	0.510456773566005	3		438	883	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096064	178096064	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	362	538	0	ENST00000397062.3:c.1267G>C	p.Glu423Gln	p.E423Q	ENST00000397062	NM_006164.4	423	Gag/Cag	5/5	0.510456773566005	3	FACETS	0.907	0.863	0.953	0.605	0.575	0.635	CLONAL	2	TRUE	0	0.510456773566005	3		538	981	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056334	180056334	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	133	599	0	ENST00000261937.6:c.910G>T	p.Asp304Tyr	p.D304Y	ENST00000261937	NM_182925.4	304	Gac/Tac	7/30	1	2	FACETS	0.921	0.84	1	0.921	0.84	1	CLONAL	1	TRUE	1	0.510456773566005	2		599	566	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	401981	401981	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	142	466	0	ENST00000399788.2:c.4810G>C	p.Asp1604His	p.D1604H	ENST00000399788	NM_001042603.1	1604	Gat/Cat	27/28	1	2	FACETS	0.867	0.792	0.944	0.867	0.792	0.944	CLONAL	1	TRUE	1	0.510456773566005	2		466	642	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095700	178095700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	393	508	0	ENST00000397062.3:c.1631G>A	p.Gly544Glu	p.G544E	ENST00000397062	NM_006164.4	544	gGa/gAa	5/5	0.510456773566005	3	FACETS	1	0.976	1	0.69	0.658	0.722	CLONAL	2	TRUE	0	0.510456773566005	3		508	934	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63898290	63898290	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	123	363	0	ENST00000398590.3:c.16G>T	p.Ala6Ser	p.A6S	ENST00000398590	NM_001177387.1	6	Gcg/Tcg	3/14	1	2	FACETS	0.978	0.889	1	0.978	0.889	1	CLONAL	1	TRUE	1	0.510456773566005	2		363	493	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721874	176721874	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	200	561	0	ENST00000439151.2:c.7505G>A	p.Arg2502Lys	p.R2502K	ENST00000439151	NM_022455.4	2502	aGa/aAa	23/23	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.510456773566005	2		561	715	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958456	90958456	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	95	351	0	ENST00000265433.3:c.1982C>T	p.Ser661Leu	p.S661L	ENST00000265433	NM_002485.4	661	tCa/tTa	13/16	1	2	FACETS	0.8	0.716	0.889	0.8	0.716	0.889	SUBCLONAL	1	TRUE	1	0.510456773566005	2		351	465	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0068236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	96	0	0				ENST00000310581	NM_198253.2	-/1132			0.35143150035415	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	0	0.437665307641575	1		0	294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578493	7578493	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1206165503	NA	P-0068236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	237	522	0	ENST00000269305.4:c.437G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tGg/tAg	5/11	0.415956150266388	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	FALSE	0	0.437665307641575	2		522	531	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050656	69050656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752015034	NA	P-0068236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	40	306	0	ENST00000288368.4:c.3991G>A	p.Glu1331Lys	p.E1331K	ENST00000288368	NM_024870.2	1331	Gaa/Aaa	33/40	0.213140165394287	0	FACETS	0.323	0.269	0.383			1	INDETERMINATE	1	FALSE	0	0.437665307641575	0		306	318	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272119	15272119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	104	468	0	ENST00000263388.2:c.6320C>T	p.Ser2107Phe	p.S2107F	ENST00000263388	NM_000435.2	2107	tCc/tTc	33/33	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	FALSE	1	0.437665307641575	2		468	468	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561131	9561131	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1463915700	NA	P-0068236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	109	442	0	ENST00000353224.5:c.651G>A	p.Trp217Ter	p.W217*	ENST00000353224	NM_177990.2	217	tgG/tgA	4/10	0.232594555968011	1	FACETS	0.837	0.756	0.922	0.837	0.756	0.922	INDETERMINATE	1	FALSE	0	0.437665307641575	1		442	465	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223526	36223526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	124	614	0	ENST00000222270.7:c.6076G>A	p.Glu2026Lys	p.E2026K	ENST00000222270	NM_014727.1	2026	Gag/Aag	28/37	1	2	FACETS	0.977	0.887	1	0.977	0.887	1	CLONAL	1	FALSE	1	0.437665307641575	2		614	580	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61323158	61323158	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	48	321	0	ENST00000283752.5:c.906G>T	p.Met302Ile	p.M302I	ENST00000283752	NM_006919.2	302	atG/atT	8/8	0.232594555968011	1	FACETS	0.49	0.415	0.571	0.49	0.415	0.571	INDETERMINATE	1	FALSE	0	0.437665307641575	1		321	350	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661877	29661877	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	184	394	0	ENST00000356175.3:c.5771G>C	p.Cys1924Ser	p.C1924S	ENST00000356175	NM_000267.3	1924	tGt/tCt	39/57	0.415956150266388	2	FACETS	0.953	0.89	1	0.953	0.89	1	CLONAL	2	FALSE	0	0.437665307641575	2		394	441	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513323	41513323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	129	431	0	ENST00000263253.7:c.227C>T	p.Ser76Phe	p.S76F	ENST00000263253	NM_001429.3	76	tCt/tTt	2/31	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.437665307641575	2		431	536	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357585	70357585	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1195178209	NA	P-0068236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	116	268	0	ENST00000374080.3:c.5836C>T	p.Pro1946Ser	p.P1946S	ENST00000374080		1946	Cct/Tct	41/45	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	0	0.437665307641575	1		268	281	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641166	117641166	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	76	502	0	ENST00000368508.3:c.5805A>T	p.Glu1935Asp	p.E1935D	ENST00000368508	NM_002944.2	1935	gaA/gaT	36/43	0.232594555968011	1	FACETS	0.481	0.422	0.544	0.481	0.422	0.544	INDETERMINATE	1	FALSE	0	0.437665307641575	1		502	564	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661897	29661897	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199474791	NA	P-0068236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	185	393	0	ENST00000356175.3:c.5791T>C	p.Trp1931Arg	p.W1931R	ENST00000356175	NM_000267.3	1931	Tgg/Cgg	39/57	0.415956150266388	2	FACETS	0.89	0.83	0.951	0.89	0.83	0.951	CLONAL	2	FALSE	0	0.437665307641575	2		393	475	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61323136	61323136	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	60	361	0	ENST00000283752.5:c.928G>T	p.Gly310Trp	p.G310W	ENST00000283752	NM_006919.2	310	Ggg/Tgg	8/8	0.232594555968011	1	FACETS	0.522	0.451	0.599	0.522	0.451	0.599	INDETERMINATE	1	FALSE	0	0.437665307641575	1		361	410	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056316	26056316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs562552825	NA	P-0068236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	128	462	0	ENST00000343677.2:c.341G>A	p.Gly114Glu	p.G114E	ENST00000343677	NM_005319.3	114	gGg/gAg	1/1	0.232594555968011	1	FACETS	0.88	0.802	0.962	0.88	0.802	0.962	INDETERMINATE	1	FALSE	0	0.437665307641575	1		462	519	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056757	102056757	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068237-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	149	245	0	ENST00000282441.5:c.697C>G	p.Pro233Ala	p.P233A	ENST00000282441	NM_001130145.2	233	Cct/Gct	4/9	NA	2	FACETS	1	0.949	1			1	INDETERMINATE	1	TRUE	NA	0.783085831569499	2		245	369	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0068238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	44	288	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.669	0.564	0.785	0.669	0.564	0.785	SUBCLONAL	1	TRUE	1	0.433819286764283	2		288	303	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935607	13935607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751525538	NA	P-0068238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	77	532	0	ENST00000405192.2:c.1249C>T	p.Arg417Cys	p.R417C	ENST00000405192	NM_001163147.1	417	Cgt/Tgt	12/12	1	2	FACETS	0.749	0.66	0.844	0.749	0.66	0.844	SUBCLONAL	1	TRUE	1	0.433819286764283	2		532	474	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771219	161771219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149953814	NA	P-0068238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	70	401	0	ENST00000366898.1:c.1310C>T	p.Pro437Leu	p.P437L	ENST00000366898	NM_004562.2	437	cCg/cTg	12/12	0.400877329827569	1	FACETS	0.739	0.649	0.835	0.739	0.649	0.835	SUBCLONAL	1	TRUE	0	0.433819286764283	1		401	342	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699455	117699455	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1360680576	NA	P-0068238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	254	469	1	ENST00000369458.3:c.186C>G	p.Ile62Met	p.I62M	ENST00000369458	NM_024626.3	62	atC/atG	3/6	0.22137594008315	6	FACETS	1	0.964	1			1	INDETERMINATE	3	TRUE	NA	0.433819286764283	6		470	705	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0068239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	394	510	0	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	0.469555677071357	5	FACETS	0.981	0.947	1	0.981	0.947	1	CLONAL	5	TRUE	0	0.469555677071357	5		510	583	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026449	6026449	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	27	44	1	ENST00000265849.7:c.1947G>T	p.Arg649Ser	p.R649S	ENST00000265849	NM_000535.5	649	agG/agT	11/15	0.469555677071357	6	FACETS	1	0.885	1	0.82	0.679	0.967	CLONAL	3	TRUE	2	0.469555677071357	6		45	68	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55339528	55339528	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	44	339	1	ENST00000284073.2:c.287C>A	p.Ala96Glu	p.A96E	ENST00000284073	NM_138962.2	96	gCa/gAa	5/14	0.438975136950362	3	FACETS	0.634	0.533	0.745	0.211	0.177	0.249	SUBCLONAL	1	TRUE	0	0.469555677071357	3		340	365	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098816	178098816	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068240-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	173	456	0	ENST00000397062.3:c.229G>C	p.Asp77His	p.D77H	ENST00000397062	NM_006164.4	77	Gat/Cat	2/5	0.133529783840425	3	FACETS	1	0.989	1	0.697	0.647	0.749	INDETERMINATE	1	TRUE	1	0.685251347252566	3		456	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782082	NA	P-0068240-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	167	370	0	ENST00000269305.4:c.745A>T	p.Arg249Trp	p.R249W	ENST00000269305	NM_001126112.2	249	Agg/Tgg	7/11	0.685251347252566	2	FACETS	0.963	0.911	1	0.963	0.911	1	CLONAL	2	TRUE	0	0.685251347252566	2		370	253	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374398	81374398	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068240-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	124	323	0	ENST00000222390.5:c.664C>A	p.Leu222Ile	p.L222I	ENST00000222390	NM_000601.4	222	Ctc/Atc	6/18	0.3032748766101	3	FACETS	1	0.977	1	0.604	0.552	0.659	INDETERMINATE	1	TRUE	1	0.685251347252566	3		323	402	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740288	162740288	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068240-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	168	476	0	ENST00000367921.3:c.1490G>T	p.Gly497Val	p.G497V	ENST00000367921	NM_006182.2	497	gGg/gTg	12/18	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.685251347252566	2		476	377	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505117	149505117	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068240-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	190	440	0	ENST00000261799.4:c.1698G>A	p.Trp566Ter	p.W566*	ENST00000261799	NM_002609.3	566	tgG/tgA	12/23	0.65987672790012	2	FACETS	0.937	0.888	0.984	0.937	0.888	0.984	CLONAL	2	TRUE	0	0.685251347252566	2		440	296	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111520	8111521	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0068240-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	102	384	0	ENST00000346208.3:c.1006_1007delinsAA	p.Pro336Asn	p.P336N	ENST00000346208		336	CCt/AAt	5/6	0.685251347252566	1	FACETS	0.988	0.908	1	0.988	0.908	1	CLONAL	1	TRUE	0	0.685251347252566	1		384	198	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719733	190719733	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068240-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	181	377	0	ENST00000441310.2:c.1735G>T	p.Ala579Ser	p.A579S	ENST00000441310	NM_000534.4	579	Gct/Tct	9/13	0.133529783840425	3	FACETS	1	0.991	1	0.75	0.698	0.802	INDETERMINATE	1	TRUE	1	0.685251347252566	3		377	473	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417801	32417801	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0068240-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	110	343	0	ENST00000332351.3:c.1249+2T>C		p.X417_splice	ENST00000332351	NM_024426.4	417			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.685251347252566	2		343	293	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911293	32911293	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068240-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	94	418	0	ENST00000380152.3:c.2801G>T	p.Gly934Val	p.G934V	ENST00000380152		934	gGt/gTt	11/27	0.352008599191912	2	FACETS	0.529	0.472	0.589	0.264	0.236	0.295	INDETERMINATE	1	TRUE	0	0.685251347252566	2		418	519	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100069	11100069	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0068240-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	219	498	0	ENST00000358026.2:c.1195A>T	p.Lys399Ter	p.K399*	ENST00000358026	NM_001128849.1	399	Aaa/Taa	7/36	0.685251347252566	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.685251347252566	2		498	300	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682982	241682983	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1060500900	NA	P-0068240-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	103	392	0	ENST00000366560.3:c.40dup	p.Leu14ProfsTer42	p.L14Pfs*42	ENST00000366560	NM_000143.3	14	ctc/cCtc	1/10	NA	2	FACETS	0.995	0.903	1			1	INDETERMINATE	1	TRUE	NA	0.685251347252566	2		392	302	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068241-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	83	350	0				ENST00000310581	NM_198253.2	-/1132			0.184400474373583	2	FACETS	0.82	0.725	0.921	0.82	0.725	0.921	CLONAL	2	TRUE	0	0.184400474373583	2		350	549	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874261	155874261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352822	NA	P-0068241-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	172	417	2	ENST00000368323.3:c.270G>A	p.Met90Ile	p.M90I	ENST00000368323	NM_006912.5	90	atG/atA	5/6	0.184400474373583	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.184400474373583	3		419	921	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247165	153247165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068241-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	40	306	0	ENST00000281708.4:c.1637C>T	p.Ser546Leu	p.S546L	ENST00000281708	NM_033632.3	546	tCa/tTa	10/12	1	2	FACETS	0.836	0.694	0.994	0.836	0.694	0.994	CLONAL	1	TRUE	1	0.184400474373583	2		306	519	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867571	45867571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068241-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	55	534	0	ENST00000391945.4:c.737C>T	p.Ser246Phe	p.S246F	ENST00000391945	NM_000400.3	246	tCc/tTc	9/23	1	2	FACETS	0.569	0.485	0.662	0.569	0.485	0.662	SUBCLONAL	1	TRUE	1	0.184400474373583	2		534	1048	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788605	3788605	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068241-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	46	386	0	ENST00000262367.5:c.4349A>G	p.Tyr1450Cys	p.Y1450C	ENST00000262367	NM_004380.2	1450	tAc/tGc	26/31	1	2	FACETS	0.83	0.698	0.976	0.83	0.698	0.976	CLONAL	1	TRUE	1	0.184400474373583	2		386	601	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845371	89845371	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201212806	NA	P-0068241-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	54	496	3	ENST00000389301.3:c.1756G>A	p.Ala586Thr	p.A586T	ENST00000389301	NM_000135.2	586	Gcc/Acc	19/43	1	2	FACETS	0.693	0.59	0.806	0.693	0.59	0.806	SUBCLONAL	1	TRUE	1	0.184400474373583	2		499	845	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572934	7572934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068241-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	48	461	0	ENST00000269305.4:c.1175C>T	p.Ser392Leu	p.S392L	ENST00000269305	NM_001126112.2	392	tCa/tTa	11/11	1	2	FACETS	0.655	0.552	0.769	0.655	0.552	0.769	SUBCLONAL	1	TRUE	1	0.184400474373583	2		461	795	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922769	44922769	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068241-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	98	203	0	ENST00000377967.4:c.1630C>T	p.Gln544Ter	p.Q544*	ENST00000377967	NM_021140.2	544	Cag/Tag	16/29	0.164383563947084	2	FACETS	1	0.968	1			1	CLONAL	2	TRUE	NA	0.184400474373583	2		203	442	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068252	30068252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068241-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	65	285	0	ENST00000331968.5:c.2147C>T	p.Ser716Leu	p.S716L	ENST00000331968	NM_002742.2	716	tCa/tTa	15/18	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.184400474373583	2		285	497	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195712	102195712	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs141741107	NA	P-0068241-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	78	469	0	ENST00000263464.3:c.472A>G	p.Met158Val	p.M158V	ENST00000263464	NM_001165.4	158	Atg/Gtg	2/9	1	2	FACETS	0.983	0.862	1	0.983	0.862	1	CLONAL	1	TRUE	1	0.184400474373583	2		469	861	SUCCESS
MET	4233	MSKCC	GRCh37	7	116381011	116381011	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068241-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	131	404	0	ENST00000397752.3:c.1633T>C	p.Cys545Arg	p.C545R	ENST00000397752	NM_000245.2	545	Tgt/Cgt	5/21	1	2	FACETS	0.782	0.709	0.859	1	0.986	1	SUBCLONAL	2	TRUE	1	0.184400474373583	2		404	908	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195797	102195797	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068241-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	85	490	0	ENST00000263464.3:c.557C>G	p.Pro186Arg	p.P186R	ENST00000263464	NM_001165.4	186	cCa/cGa	2/9	1	2	FACETS	0.893	0.788	1	0.893	0.788	1	CLONAL	1	TRUE	1	0.184400474373583	2		490	1032	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245401	153245401	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068241-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	127	372	0	ENST00000281708.4:c.1790G>T	p.Gly597Val	p.G597V	ENST00000281708	NM_033632.3	597	gGg/gTg	11/12	1	2	FACETS	1	0.972	1	1	0.991	1	CLONAL	2	TRUE	1	0.184400474373583	2		372	586	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29280015	29280030	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCGGGGCCACGCTC	GGCCGGGGCCACGCTC	-	novel	NA	P-0068241-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	75	473	0	ENST00000544604.2:c.261_276del	p.Gly89ProfsTer28	p.G89Pfs*28	ENST00000544604	NM_001206998.1	87	cgGGCCGGGGCCACGCTC/cg	1/9	0.163369575573612	2	FACETS	0.687	0.6	0.782	0.344	0.3	0.391	SUBCLONAL	1	TRUE	0	0.184400474373583	2		473	1184	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946110	13946110	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068241-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	107	333	0	ENST00000405192.2:c.986A>G	p.His329Arg	p.H329R	ENST00000405192	NM_001163147.1	329	cAt/cGt	10/12	0.184400474373583	3	FACETS	0.949	0.852	1	0.949	0.852	1	CLONAL	2	TRUE	1	0.184400474373583	3		333	668	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16097845	16097845	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068241-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	28	231	0	ENST00000268712.3:c.39C>A	p.Phe13Leu	p.F13L	ENST00000268712	NM_006311.3	13	ttC/ttA	2/46	1	2	FACETS	0.773	0.617	0.95	0.773	0.617	0.95	CLONAL	1	TRUE	1	0.184400474373583	2		231	393	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518575	69518575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068241-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	38	363	0	ENST00000294312.3:c.70C>T	p.Pro24Ser	p.P24S	ENST00000294312	NM_005117.2	24	Ccc/Tcc	1/3	1	2	FACETS	0.69	0.57	0.826	0.69	0.57	0.826	SUBCLONAL	1	TRUE	1	0.184400474373583	2		363	597	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50731334	50731334	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068241-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	28	287	0	ENST00000307179.4:c.64A>G	p.Lys22Glu	p.K22E	ENST00000307179		22	Aag/Gag	2/20	1	2	FACETS	0.986	0.79	1	0.986	0.79	1	CLONAL	1	TRUE	1	0.184400474373583	2		287	308	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881344	111881344	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068241-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	132	342	0	ENST00000393256.3:c.22G>T	p.Val8Leu	p.V8L	ENST00000393256	NM_006538.4	8	Gta/Tta	2/4	1	2	FACETS	1	0.93	1	1	0.99	1	CLONAL	2	TRUE	1	0.184400474373583	2		342	697	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0068243-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	188	288	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.383711987858821	4	FACETS	0.842	0.785	0.899	0.842	0.785	0.899	CLONAL	3	TRUE	1	0.443073620094619	4		288	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0068243-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	259	395	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.386506463066826	2	FACETS	0.814	0.766	0.863	0.814	0.766	0.863	CLONAL	2	TRUE	0	0.443073620094619	2		395	718	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0068257-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	103	437	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.608219868178047	2		437	299	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345997	70345997	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750730080	NA	P-0068257-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	36	205	0	ENST00000374080.3:c.2534C>T	p.Thr845Met	p.T845M	ENST00000374080		845	aCg/aTg	18/45	0.608219868178047	2	FACETS	0.3	0.247	0.36			1	SUBCLONAL	1	TRUE	NA	0.608219868178047	2		205	394	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119831	108119831	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0068257-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	99	235	0	ENST00000278616.4:c.1235+2T>G		p.X412_splice	ENST00000278616	NM_000051.3	412			1	2	FACETS	0.996	0.899	1	0.996	0.899	1	CLONAL	1	TRUE	1	0.608219868178047	2		235	327	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434609	128434609	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068257-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	49	275	0	ENST00000265960.3:c.245G>T	p.Arg82Ile	p.R82I	ENST00000265960	NM_001006617.1	82	aGa/aTa	2/12	0.263722205858117	2	FACETS	0.569	0.485	0.66	0.285	0.242	0.33	INDETERMINATE	1	TRUE	0	0.608219868178047	2		275	283	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752723	128752723	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068257-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	219	432	0	ENST00000377970.2:c.884G>C	p.Gly295Ala	p.G295A	ENST00000377970	NM_002467.4	295	gGa/gCa	3/3	0.608219868178047	3	FACETS	1	0.979	1	0.559	0.521	0.598	CLONAL	1	TRUE	1	0.608219868178047	3		432	840	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391608	139391608	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068257-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	68	546	0	ENST00000277541.6:c.6583G>T	p.Gly2195Cys	p.G2195C	ENST00000277541	NM_017617.3	2195	Ggc/Tgc	34/34	0.263722205858117	2	FACETS	0.553	0.483	0.628	0.277	0.241	0.314	INDETERMINATE	1	TRUE	0	0.608219868178047	2		546	404	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435630	18435630	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs758726931	NA	P-0068257-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	103	411	0	ENST00000266497.5:c.615G>T	p.Leu205Phe	p.L205F	ENST00000266497		205	ttG/ttT	1/31	1	2	FACETS	0.962	0.87	1	0.962	0.87	1	CLONAL	1	TRUE	1	0.608219868178047	2		411	352	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95598921	95598921	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1595466234	NA	P-0068257-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	105	306	0	ENST00000393063.1:c.238G>T	p.Glu80Ter	p.E80*	ENST00000393063	NM_030621.3	80	Gag/Tag	4/28	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.608219868178047	2		306	324	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748154	72748154	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs368350763	NA	P-0068257-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	159	318	0	ENST00000357731.5:c.24G>C	p.Gln8His	p.Q8H	ENST00000357731	NM_173808.2	8	caG/caC	1/7	0.384392925485816	1	FACETS	0.914	0.848	0.981	0.914	0.848	0.981	CLONAL	1	TRUE	0	0.608219868178047	1		318	398	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562787	176562787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068257-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	219	499	1	ENST00000439151.2:c.683C>T	p.Pro228Leu	p.P228L	ENST00000439151	NM_022455.4	228	cCa/cTa	2/23	0.608219868178047	3	FACETS	1	0.976	1	0.55	0.512	0.589	CLONAL	1	TRUE	1	0.608219868178047	3		500	854	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134622	41134622	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068257-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	179	459	0	ENST00000379561.5:c.1006G>T	p.Asp336Tyr	p.D336Y	ENST00000379561	NM_002015.3	336	Gat/Tat	2/3	0.608219868178047	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.608219868178047	1		459	334	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206683	108206683	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068257-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	79	270	0	ENST00000278616.4:c.8263T>C	p.Tyr2755His	p.Y2755H	ENST00000278616	NM_000051.3	2755	Tat/Cat	56/63	1	2	FACETS	0.866	0.769	0.967	0.866	0.769	0.967	CLONAL	1	TRUE	1	0.608219868178047	2		270	300	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0068258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	24	288	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.517	0.406	0.646	0.517	0.406	0.646	SUBCLONAL	1	FALSE	1	0.284553565136664	2		288	326	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090050	37090050	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	35	470	0	ENST00000231790.2:c.1939G>C	p.Val647Leu	p.V647L	ENST00000231790	NM_000249.3	647	Gtg/Ctg	17/19	1	2	FACETS	0.433	0.354	0.522	0.433	0.354	0.522	SUBCLONAL	1	FALSE	1	0.284553565136664	2		470	568	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273961	10273961	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	60	566	0	ENST00000330684.3:c.308A>G	p.Asp103Gly	p.D103G	ENST00000330684	NM_001134407.1	103	gAc/gGc	2/13	1	2	FACETS	0.675	0.581	0.777	0.675	0.581	0.777	SUBCLONAL	1	FALSE	1	0.284553565136664	2		566	625	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045907	26045907	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	71	818	0	ENST00000540144.1:c.269T>G	p.Val90Gly	p.V90G	ENST00000540144	NM_003531.2	90	gTg/gGg	1/1	1	2	FACETS	0.523	0.455	0.597	0.523	0.455	0.597	SUBCLONAL	1	FALSE	1	0.284553565136664	2		818	954	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150936756	150936756	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	53	553	0	ENST00000271640.5:c.3792C>A	p.Asp1264Glu	p.D1264E	ENST00000271640	NM_001145415.1	1264	gaC/gaA	22/22	1	2	FACETS	0.454	0.386	0.529	0.454	0.386	0.529	SUBCLONAL	1	FALSE	1	0.284553565136664	2		553	821	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051638	30051638	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068259-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	149	219	0	ENST00000338641.4:c.572G>A	p.Trp191Ter	p.W191*	ENST00000338641	NM_000268.3	191	tGg/tAg	6/16	0.514592963563175	1	FACETS	0.956	0.881	1	0.956	0.881	1	CLONAL	1	TRUE	0	0.514592963563175	1		219	450	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150934631	150934632	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0068259-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	177	128	0	ENST00000271640.5:c.3156dup	p.Val1053SerfsTer4	p.V1053Sfs*4	ENST00000271640	NM_001145415.1	1052	tca/tcAa	17/22	0.513222862082011	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.514592963563175	2		128	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0068260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	80	403	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.238575046338356	1	FACETS	0.87	0.766	0.982	0.87	0.766	0.982	CLONAL	1	TRUE	0	0.238575046338356	1		404	679	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024573	31024573	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	68	418	1	ENST00000375687.4:c.4058G>T	p.Arg1353Met	p.R1353M	ENST00000375687	NM_015338.5	1353	aGg/aTg	13/13	1	2	FACETS	0.8	0.695	0.913	0.8	0.695	0.913	CLONAL	1	TRUE	1	0.238575046338356	2		419	713	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261277	16261277	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	54	465	0	ENST00000375759.3:c.8542C>T	p.Gln2848Ter	p.Q2848*	ENST00000375759	NM_015001.2	2848	Cag/Tag	11/15	1	2	FACETS	0.719	0.613	0.834	0.719	0.613	0.834	SUBCLONAL	1	TRUE	1	0.238575046338356	2		465	630	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268460	142268460	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	29	295	0	ENST00000350721.4:c.3032C>T	p.Ser1011Phe	p.S1011F	ENST00000350721	NM_001184.3	1011	tCt/tTt	15/47	1	2	FACETS	0.782	0.629	0.955	0.782	0.629	0.955	CLONAL	1	TRUE	1	0.238575046338356	2		295	311	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293709	1293709	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1164823749	NA	P-0068260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	59	479	0	ENST00000310581.5:c.1292C>T	p.Pro431Leu	p.P431L	ENST00000310581	NM_198253.2	431	cCc/cTc	2/16	1	2	FACETS	0.692	0.594	0.798	0.692	0.594	0.798	SUBCLONAL	1	TRUE	1	0.238575046338356	2		479	715	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47088039	47088039	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	81	348	0	ENST00000409792.3:c.7036del	p.Val2346TyrfsTer7	p.V2346Yfs*7	ENST00000409792	NM_014159.6	2346	Gta/ta	16/21	0.238575046338356	1	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	0	0.238575046338356	1		348	587	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187412	38187412	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0068260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	40	302	0	ENST00000317025.8:c.1066-1G>A		p.X356_splice	ENST00000317025	NM_023034.1	356			1	2	FACETS	0.838	0.698	0.995	0.838	0.698	0.995	CLONAL	1	TRUE	1	0.238575046338356	2		302	400	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0068261-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	152	403	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.629560732858072	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.629560732858072	1		404	296	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099187	157099195	+	inframe_deletion	In_Frame_Del	DEL	GCGGCGGCA	GCGGCGGCA	-	rs769480864	NA	P-0068261-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	204	579	0	ENST00000346085.5:c.133_141del	p.Ala45_Ala47del	p.A45_A47del	ENST00000346085	NM_020732.3	42	GCGGCGGCA/-	1/20	0.629663675263944	3	FACETS	0.822	0.77	0.876	0.822	0.77	0.876	CLONAL	2	TRUE	1	0.629560732858072	3		579	518	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661221	227661221	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068261-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	93	570	1	ENST00000305123.5:c.2234G>T	p.Ser745Ile	p.S745I	ENST00000305123	NM_005544.2	745	aGc/aTc	1/2	0.272334750275453	1	FACETS	0.448	0.4	0.498	0.448	0.4	0.498	INDETERMINATE	1	TRUE	0	0.629560732858072	1		571	452	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090434	37090434	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068261-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	102	382	0	ENST00000231790.2:c.2029A>C	p.Ser677Arg	p.S677R	ENST00000231790	NM_000249.3	677	Agt/Cgt	18/19	1	2	FACETS	0.918	0.829	1	0.918	0.829	1	CLONAL	1	TRUE	1	0.629560732858072	2		382	353	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074412	8074412	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068261-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	116	490	1	ENST00000377482.5:c.247G>T	p.Glu83Ter	p.E83*	ENST00000377482	NM_018948.3	83	Gaa/Taa	4/4	0.629560732858072	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.629560732858072	1		491	240	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587261	212587261	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0068261-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	81	364	0	ENST00000342788.4:c.742-2A>T		p.X248_splice	ENST00000342788	NM_005235.2	248			0.272334750275453	1	FACETS	0.732	0.655	0.811	0.732	0.655	0.811	INDETERMINATE	1	TRUE	0	0.629560732858072	1		364	241	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0068262-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	289	448	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.758812468476708	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.758812468476708	1		448	465	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0068262-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	159	284	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.917	0.848	0.987	0.917	0.848	0.987	CLONAL	1	TRUE	1	0.758812468476708	2		284	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0068262-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	333	544	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.747254848931858	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.758812468476708	1		544	542	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0068262-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	246	382	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	1	2	FACETS	0.963	0.906	1	0.963	0.906	1	CLONAL	1	TRUE	1	0.758812468476708	2		382	673	SUCCESS
APC	324	MSKCC	GRCh37	5	112174268	112174268	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0068262-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	262	454	0	ENST00000257430.4:c.2977A>T	p.Lys993Ter	p.K993*	ENST00000257430	NM_000038.5	993	Aag/Tag	16/16	1	2	FACETS	0.97	0.914	1	0.97	0.914	1	CLONAL	1	TRUE	1	0.758812468476708	2		454	712	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257037	16257037	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068262-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	129	434	0	ENST00000375759.3:c.4302T>G	p.Phe1434Leu	p.F1434L	ENST00000375759	NM_015001.2	1434	ttT/ttG	11/15	1	2	FACETS	0.417	0.378	0.458	0.417	0.378	0.458	SUBCLONAL	1	TRUE	1	0.758812468476708	2		434	816	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0068263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	90	264	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.116127383436905	5	FACETS	0.824	0.734	0.919	0.55	0.489	0.613	INDETERMINATE	2	TRUE	2	0.353111064177605	5		264	473	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0068264-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	77	440	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.934	0.828	1	0.934	0.828	1	CLONAL	1	TRUE	1	0.526589498711307	2		440	313	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099098	27099098	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068264-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	390	472	0	ENST00000324856.7:c.3514C>T	p.Gln1172Ter	p.Q1172*	ENST00000324856	NM_006015.4	1172	Cag/Tag	13/20	0.30134765824956	5	FACETS	0.868	0.827	0.909			1	INDETERMINATE	3	TRUE	NA	0.526589498711307	5		472	1018	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510160	149510160	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772355478	NA	P-0068264-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	178	389	0	ENST00000261799.4:c.1309C>T	p.Arg437Cys	p.R437C	ENST00000261799	NM_002609.3	437	Cgt/Tgt	9/23	1	2	FACETS	0.78	0.719	0.843	0.78	0.719	0.843	SUBCLONAL	1	TRUE	1	0.526589498711307	2		389	867	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023855	27023856	+	frameshift_variant	Frame_Shift_Ins	INS	CA	CA	GGC	novel	NA	P-0068264-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	103	500	0	ENST00000324856.7:c.961_962delinsGGC	p.Gln321GlyfsTer79	p.Q321Gfs*79	ENST00000324856	NM_006015.4	321	CAg/GGCg	1/20	1	2	FACETS	0.625	0.56	0.694	0.625	0.56	0.694	SUBCLONAL	1	TRUE	1	0.526589498711307	2		500	626	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022248	31022248	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068264-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	111	359	0	ENST00000375687.4:c.1733G>T	p.Arg578Leu	p.R578L	ENST00000375687	NM_015338.5	578	cGt/cTt	13/13	1	2	FACETS	0.952	0.861	1	0.952	0.861	1	CLONAL	1	TRUE	1	0.526589498711307	2		359	443	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589207	67589208	+	protein_altering_variant	In_Frame_Ins	INS	-	-	AAG	novel	NA	P-0068264-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	36	352	0	ENST00000274335.5:c.1195_1196insAAG	p.Ser399delinsLysGly	p.S399delinsKG	ENST00000274335		399	agt/aAAGgt	9/15	1	2	FACETS	0.743	0.618	0.88	0.743	0.618	0.88	SUBCLONAL	1	TRUE	1	0.526589498711307	2		352	184	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913400	NA	P-0068268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	129	338	0	ENST00000349496.5:c.98C>A	p.Ser33Tyr	p.S33Y	ENST00000349496	NM_001904.3	33	tCt/tAt	3/15	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.595537814005346	2		338	428	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0068268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	174	242	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.560657563120959	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.595537814005346	3		242	364	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717608	89717608	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0068268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	102	239	0	ENST00000371953.3:c.635-2A>C		p.X212_splice	ENST00000371953	NM_000314.4	212			0.560657563120959	3	FACETS	1	0.937	1	0.528	0.475	0.583	CLONAL	1	TRUE	1	0.595537814005346	3		239	421	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	118	351	0	ENST00000267101.3:c.850G>C	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Cga	7/28	0.334059676914648	3	FACETS	1	0.984	1	0.708	0.646	0.773	INDETERMINATE	1	TRUE	1	0.595537814005346	3		351	363	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588819	67589710	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGATTTTGCTGTGAACCTAAAACTGCTCTAAAAAATAGCCTATTTTAAAAAATATAAATCTGTGGTCACTAAACCTTAAGATGAGCATTGTTTTGTGTTTTCATTTCAGGGAAGAAGTGAATGAAAAACTTCGAGATACAGCAGACGGGACCTTTTTGGTACGAGATGCGTCTACTAAAATGCATGGTGATTATACTCTTACACTAAGGTAAGCCAGGGAATATAGCTGAAATTAGGGTTTTGGGCTGATATTAAAACATATTTCCTTATTCCAAAATGTTAATACCTTTATTTTTATATTGTTTTTACAGGAAAGGGGGAAATAACAAATTAATCAAAATATTTCATCGAGATGGGAAATATGGCTTCTCTGACCCATTAACCTTCAGTTCTGTGGTTGAATTAATAAACCACTACCGGAATGAATCTCTAGCTCAGTATAATCCCAAATTGGATGTGAAATTACTTTATCCAGTATCCAAATACCAACAGGTAATAAAAACTGAATGAATTATCCAGTTACGATGTTTAGACAAGATCCTTTTAATACTTAGAAAACATTTGAAGCAGATGAATTACATGTAATCAAGTCTAAAAAACTTGACACTCGTAATTACATAATTGCAATTTTAAAGATGTTTCCATGTCAGCTATTTTGTTAAACAATTGTTATTTGATTAAATACCTTATCCATTGAATTTATTTTAATCTTTCTAGGATCAAGTTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACACTCAGTTTCAAGAAAAAAGTCGAGAATATGATAGATTATATGAAGAATATACCCGCACATCCCAGGTGAGTTTTCTATGAAAATCAGATTAAAAAATAAGAGTTCTAAACTTT	TTGATTTTGCTGTGAACCTAAAACTGCTCTAAAAAATAGCCTATTTTAAAAAATATAAATCTGTGGTCACTAAACCTTAAGATGAGCATTGTTTTGTGTTTTCATTTCAGGGAAGAAGTGAATGAAAAACTTCGAGATACAGCAGACGGGACCTTTTTGGTACGAGATGCGTCTACTAAAATGCATGGTGATTATACTCTTACACTAAGGTAAGCCAGGGAATATAGCTGAAATTAGGGTTTTGGGCTGATATTAAAACATATTTCCTTATTCCAAAATGTTAATACCTTTATTTTTATATTGTTTTTACAGGAAAGGGGGAAATAACAAATTAATCAAAATATTTCATCGAGATGGGAAATATGGCTTCTCTGACCCATTAACCTTCAGTTCTGTGGTTGAATTAATAAACCACTACCGGAATGAATCTCTAGCTCAGTATAATCCCAAATTGGATGTGAAATTACTTTATCCAGTATCCAAATACCAACAGGTAATAAAAACTGAATGAATTATCCAGTTACGATGTTTAGACAAGATCCTTTTAATACTTAGAAAACATTTGAAGCAGATGAATTACATGTAATCAAGTCTAAAAAACTTGACACTCGTAATTACATAATTGCAATTTTAAAGATGTTTCCATGTCAGCTATTTTGTTAAACAATTGTTATTTGATTAAATACCTTATCCATTGAATTTATTTTAATCTTTCTAGGATCAAGTTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACACTCAGTTTCAAGAAAAAAGTCGAGAATATGATAGATTATATGAAGAATATACCCGCACATCCCAGGTGAGTTTTCTATGAAAATCAGATTAAAAAATAAGAGTTCTAAACTTT	-	novel	NA	P-0068268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	14	109	0	ENST00000274335.5:c.1020-109_1425+49del		p.X340_splice	ENST00000274335		340		8-10/15	1	2	FACETS	0.25	0.181	0.333	0.25	0.181	0.333	SUBCLONAL	1	TRUE	1	0.595537814005346	2		109	188	SUCCESS
ATM	472	MSKCC	GRCh37	11	108168047	108168047	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	160	226	0	ENST00000278616.4:c.4944del	p.Val1649SerfsTer11	p.V1649Sfs*11	ENST00000278616	NM_000051.3	1648	gTt/gt	33/63	0.595537814005346	2	FACETS	0.97	0.91	1	0.97	0.91	1	CLONAL	2	TRUE	0	0.595537814005346	2		226	277	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589595	67589596	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAC	novel	NA	P-0068268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	130	251	0	ENST00000274335.5:c.1359_1361dup	p.Thr454dup	p.T454dup	ENST00000274335		454	aac/aaCACc	10/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.595537814005346	2		251	362	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0068270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	65	288	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.279839209407846	4	FACETS	1	0.933	1	0.732	0.642	0.828	CLONAL	2	TRUE	1	0.302075032980104	4		288	255	SUCCESS
APC	324	MSKCC	GRCh37	5	112175447	112175447	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0068270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	107	434	0	ENST00000257430.4:c.4156A>T	p.Arg1386Ter	p.R1386*	ENST00000257430	NM_000038.5	1386	Aga/Tga	16/16	0.225699424860963	3	FACETS	0.99	0.894	1	0.66	0.596	0.726	CLONAL	2	TRUE	0	0.302075032980104	3		434	412	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94926629	94926629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	53	297	0	ENST00000536441.1:c.136G>A	p.Glu46Lys	p.E46K	ENST00000536441	NM_144665.3	46	Gag/Aag	2/10	0.244835387730709	3	FACETS	1	0.95	1	0.629	0.539	0.726	CLONAL	1	TRUE	1	0.302075032980104	3		297	321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577520	7577520	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	84	434	0	ENST00000269305.4:c.761T>C	p.Ile254Thr	p.I254T	ENST00000269305	NM_001126112.2	254	aTc/aCc	7/11	0.248099478043831	2	FACETS	0.833	0.742	0.928	0.833	0.742	0.928	CLONAL	2	TRUE	0	0.302075032980104	2		434	334	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555262	226555262	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	64	474	0	ENST00000366794.5:c.2325C>A	p.Tyr775Ter	p.Y775*	ENST00000366794	NM_001618.3	775	taC/taA	17/23	0.244835387730709	3	FACETS	1	0.923	1	0.546	0.474	0.623	CLONAL	1	TRUE	1	0.302075032980104	3		474	447	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054566	13054566	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	56	552	0	ENST00000316448.5:c.1093C>T	p.Gln365Ter	p.Q365*	ENST00000316448	NM_004343.3	365	Cag/Tag	9/9	0.302075032980104	3	FACETS	0.772	0.661	0.892	0.386	0.33	0.446	SUBCLONAL	1	TRUE	1	0.302075032980104	3		552	553	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127235	17127235	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0068270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	96	465	0	ENST00000285071.4:c.618+1G>A		p.X206_splice	ENST00000285071	NM_144997.5	206			0.248099478043831	2	FACETS	0.987	0.889	1	0.987	0.889	1	CLONAL	2	TRUE	0	0.302075032980104	2		465	322	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145721	61145721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766053281	NA	P-0068270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	40	382	0	ENST00000295025.8:c.833G>A	p.Arg278Lys	p.R278K	ENST00000295025	NM_002908.2	278	aGa/aAa	7/11	0.244835387730709	3	FACETS	0.756	0.629	0.898	0.378	0.314	0.449	SUBCLONAL	1	TRUE	1	0.302075032980104	3		382	403	SUCCESS
AR	367	MSKCC	GRCh37	X	66766351	66766386	+	inframe_deletion	In_Frame_Del	DEL	GGTGGTGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	GGTGGTGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	-	novel	NA	P-0068270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	46	377	2	ENST00000374690.3:c.1365_1400del	p.Gly462_Gly473del	p.G462_G473del	ENST00000374690	NM_000044.3	455	GGTGGTGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC/-	1/8	0.289055855978298	2	FACETS	0.765	0.653	0.886	0.765	0.653	0.886	SUBCLONAL	2	TRUE	0	0.302075032980104	2		379	199	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0068281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	45	342	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.612	0.515	0.72	0.612	0.515	0.72	SUBCLONAL	1	TRUE	1	0.315438622572651	2		343	466	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592097	67592098	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0068281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	27	399	0	ENST00000274335.5:c.1914dup	p.Arg639AlafsTer15	p.R639Afs*15	ENST00000274335		638	ttg/ttGg	14/15	1	2	FACETS	0.405	0.321	0.5	0.405	0.321	0.5	SUBCLONAL	1	TRUE	1	0.315438622572651	2		399	423	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592357	29592357	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1555619423	NA	P-0068281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	24	329	0	ENST00000356175.3:c.4772G>T	p.Arg1591Met	p.R1591M	ENST00000356175	NM_000267.3	1591	aGg/aTg	35/57	1	2	FACETS	0.506	0.397	0.631	0.506	0.397	0.631	SUBCLONAL	1	TRUE	1	0.315438622572651	2		329	301	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	170	350	0				ENST00000310581	NM_198253.2	-/1132			0.286366731371024	3	FACETS	0.808	0.754	0.862	0.808	0.754	0.862	INDETERMINATE	2	TRUE	1	0.794689582225488	3		350	370	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	113	288	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.974	0.89	1	0.974	0.89	1	CLONAL	1	TRUE	1	0.794689582225488	2		288	292	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830872	156830872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	193	373	0	ENST00000524377.1:c.146G>A	p.Arg49Gln	p.R49Q	ENST00000524377	NM_002529.3	49	cGa/cAa	1/17	1	2	FACETS	0.973	0.909	1	0.973	0.909	1	CLONAL	1	TRUE	1	0.794689582225488	2		373	499	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	20	268	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.416	0.322	0.523	0.416	0.322	0.523	SUBCLONAL	1	TRUE	1	0.794689582225488	2		268	121	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641161	23641161	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	73	428	0	ENST00000261584.4:c.2314G>A	p.Asp772Asn	p.D772N	ENST00000261584	NM_024675.3	772	Gat/Aat	5/13	1	2	FACETS	0.246	0.215	0.28	0.246	0.215	0.28	SUBCLONAL	1	TRUE	1	0.794689582225488	2		428	746	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287238	38287238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140382957	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	367	419	0	ENST00000425967.3:c.419C>T	p.Ser140Leu	p.S140L	ENST00000425967	NM_001174067.1	140	tCg/tTg	4/19	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.794689582225488	2		419	672	SUCCESS
AR	367	MSKCC	GRCh37	X	66765159	66765185	+	inframe_deletion	In_Frame_Del	DEL	GCAGCAGCAGCAGCAGCAGCAGCAGCA	GCAGCAGCAGCAGCAGCAGCAGCAGCA	-	rs3032358	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	34	108	0	ENST00000374690.3:c.213_239del	p.Gln72_Gln80del	p.Q72_Q80del	ENST00000374690	NM_000044.3	57	ctGCAGCAGCAGCAGCAGCAGCAGCAGCAg/ctg	1/8	1	1	FACETS	0.288	0.238	0.343	0.288	0.238	0.343	SUBCLONAL	1	TRUE	0	0.794689582225488	1		108	179	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	241	418	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	0.916	0.861	0.973	0.916	0.861	0.973	CLONAL	1	TRUE	1	0.794689582225488	2		418	662	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	58	221	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	1	1	FACETS	0.263	0.227	0.301	0.263	0.227	0.301	SUBCLONAL	1	TRUE	0	0.794689582225488	1		221	335	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166770	32166770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs947409717	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	31	431	0	ENST00000375023.3:c.4468C>T	p.Arg1490Trp	p.R1490W	ENST00000375023	NM_004557.3	1490	Cgg/Tgg	24/30	1	2	FACETS	0.13	0.105	0.159	0.13	0.105	0.159	SUBCLONAL	1	TRUE	1	0.794689582225488	2		431	599	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872366	45872366	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	314	397	0	ENST00000391945.4:c.145A>G	p.Thr49Ala	p.T49A	ENST00000391945	NM_000400.3	49	Aca/Gca	3/23	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.794689582225488	2		397	717	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780851	9780851	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	46	386	0	ENST00000377346.4:c.1573G>C	p.Glu525Gln	p.E525Q	ENST00000377346	NM_005026.3	525	Gag/Cag	13/24	1	2	FACETS	0.236	0.198	0.277	0.236	0.198	0.277	SUBCLONAL	1	TRUE	1	0.794689582225488	2		386	491	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665280	138665280	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	232	420	0	ENST00000330315.3:c.285G>C	p.Lys95Asn	p.K95N	ENST00000330315	NM_023067.3	95	aaG/aaC	1/1	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.794689582225488	2		420	529	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110013	115110013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	79	372	0	ENST00000257566.3:c.1865C>T	p.Ser622Leu	p.S622L	ENST00000257566	NM_016569.3	622	tCg/tTg	8/8	1	2	FACETS	0.381	0.335	0.429	0.381	0.335	0.429	SUBCLONAL	1	TRUE	1	0.794689582225488	2		372	522	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907687	111907687	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373945451	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	47	347	0	ENST00000393256.3:c.461G>A	p.Arg154His	p.R154H	ENST00000393256	NM_006538.4	154	cGt/cAt	3/4	1	2	FACETS	0.227	0.192	0.267	0.227	0.192	0.267	SUBCLONAL	1	TRUE	1	0.794689582225488	2		347	520	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864663	68864663	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773560075	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	59	264	0	ENST00000288368.4:c.34G>A	p.Glu12Lys	p.E12K	ENST00000288368	NM_024870.2	12	Gag/Aag	1/40	1	2	FACETS	0.454	0.393	0.52	0.454	0.393	0.52	SUBCLONAL	1	TRUE	1	0.794689582225488	2		264	327	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548294	41548294	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	54	438	0	ENST00000263253.7:c.3082G>C	p.Asp1028His	p.D1028H	ENST00000263253	NM_001429.3	1028	Gac/Cac	16/31	1	2	FACETS	0.236	0.201	0.274	0.236	0.201	0.274	SUBCLONAL	1	TRUE	1	0.794689582225488	2		438	577	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205277	61205277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	69	415	0	ENST00000301761.2:c.217G>A	p.Glu73Lys	p.E73K	ENST00000301761	NM_017841.2	73	Gag/Aag	2/4	1	2	FACETS	0.276	0.24	0.315	0.276	0.24	0.315	SUBCLONAL	1	TRUE	1	0.794689582225488	2		415	629	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873661	37873661	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	109	419	0	ENST00000269571.5:c.1826C>G	p.Ser609Cys	p.S609C	ENST00000269571		609	tCc/tGc	15/27	1	2	FACETS	0.468	0.421	0.517	0.468	0.421	0.517	SUBCLONAL	1	TRUE	1	0.794689582225488	2		419	586	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425839	49425839	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	97	453	0	ENST00000301067.7:c.12649C>T	p.Gln4217Ter	p.Q4217*	ENST00000301067	NM_003482.3	4217	Cag/Tag	39/54	1	2	FACETS	0.396	0.353	0.441	0.396	0.353	0.441	SUBCLONAL	1	TRUE	1	0.794689582225488	2		453	617	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156150	106156150	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	60	462	0	ENST00000380013.4:c.1051G>A	p.Glu351Lys	p.E351K	ENST00000380013	NM_001127208.2	351	Gaa/Aaa	3/11	1	2	FACETS	0.207	0.178	0.239	0.207	0.178	0.239	SUBCLONAL	1	TRUE	1	0.794689582225488	2		462	728	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129776	108129776	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	29	330	0	ENST00000278616.4:c.2440G>T	p.Asp814Tyr	p.D814Y	ENST00000278616	NM_000051.3	814	Gac/Tac	16/63	1	2	FACETS	0.199	0.16	0.244	0.199	0.16	0.244	SUBCLONAL	1	TRUE	1	0.794689582225488	2		330	366	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748070	72748070	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	49	378	0	ENST00000357731.5:c.108G>C	p.Gln36His	p.Q36H	ENST00000357731	NM_173808.2	36	caG/caC	1/7	1	2	FACETS	0.209	0.176	0.245	0.209	0.176	0.245	SUBCLONAL	1	TRUE	1	0.794689582225488	2		378	590	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412929	49412929	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	57	364	0	ENST00000418115.1:c.94G>C	p.Glu32Gln	p.E32Q	ENST00000418115	NM_001664.2	32	Gag/Cag	2/5	1	2	FACETS	0.217	0.186	0.251	0.217	0.186	0.251	SUBCLONAL	1	TRUE	1	0.794689582225488	2		364	661	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294414	1294414	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779999492	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	57	468	0	ENST00000310581.5:c.587G>A	p.Arg196His	p.R196H	ENST00000310581	NM_198253.2	196	cGt/cAt	2/16	0.286366731371024	3	FACETS	0.306	0.262	0.354	0.153	0.131	0.177	INDETERMINATE	1	TRUE	1	0.794689582225488	3		468	655	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426459	49426459	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1341534320	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	134	508	0	ENST00000301067.7:c.12029C>G	p.Ser4010Cys	p.S4010C	ENST00000301067	NM_003482.3	4010	tCt/tGt	39/54	1	2	FACETS	0.431	0.391	0.472	0.431	0.391	0.472	SUBCLONAL	1	TRUE	1	0.794689582225488	2		508	783	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955531	90955531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	172	321	0	ENST00000265433.3:c.2134C>T	p.His712Tyr	p.H712Y	ENST00000265433	NM_002485.4	712	Cat/Tat	14/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.794689582225488	2		321	391	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158464	26158464	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs916752202	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	264	482	0	ENST00000289316.2:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000289316	NM_138720.2	23	Cag/Tag	1/2	1	2	FACETS	0.977	0.922	1	0.977	0.922	1	CLONAL	1	TRUE	1	0.794689582225488	2		482	680	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398262	25398262	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913538	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	22	314	0	ENST00000311936.3:c.57G>C	p.Leu19Phe	p.L19F	ENST00000311936	NM_004985.3	19	ttG/ttC	2/5	1	2	FACETS	0.194	0.15	0.245	0.194	0.15	0.245	SUBCLONAL	1	TRUE	1	0.794689582225488	2		314	285	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032069	26032069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	318	597	0	ENST00000244661.2:c.220G>A	p.Glu74Lys	p.E74K	ENST00000244661	NM_003537.3	74	Gaa/Aaa	1/1	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.794689582225488	2		597	786	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479971	50479971	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	254	346	1	ENST00000394963.4:c.205A>G	p.Met69Val	p.M69V	ENST00000394963	NM_003076.4	69	Atg/Gtg	2/13	1	2	FACETS	0.996	0.938	1	0.996	0.938	1	CLONAL	1	TRUE	1	0.794689582225488	2		347	642	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424446	49424446	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	91	435	0	ENST00000301067.7:c.13777G>C	p.Gly4593Arg	p.G4593R	ENST00000301067	NM_003482.3	4593	Ggg/Cgg	41/54	1	2	FACETS	0.428	0.381	0.478	0.428	0.381	0.478	SUBCLONAL	1	TRUE	1	0.794689582225488	2		435	535	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056284	27056284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745637145	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	306	464	0	ENST00000324856.7:c.1280C>T	p.Pro427Leu	p.P427L	ENST00000324856	NM_006015.4	427	cCg/cTg	2/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.794689582225488	2		464	726	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774795	73774795	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	268	404	0	ENST00000254810.4:c.292G>A	p.Glu98Lys	p.E98K	ENST00000254810	NM_005324.3	98	Gaa/Aaa	4/4	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.794689582225488	2		404	657	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342931	118342931	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	64	421	0	ENST00000534358.1:c.1057C>G	p.Arg353Gly	p.R353G	ENST00000534358	NM_005933.3	353	Cga/Gga	3/36	1	2	FACETS	0.227	0.196	0.261	0.227	0.196	0.261	SUBCLONAL	1	TRUE	1	0.794689582225488	2		421	709	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37083771	37083771	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	63	303	0	ENST00000231790.2:c.1680C>G	p.Phe560Leu	p.F560L	ENST00000231790	NM_000249.3	560	ttC/ttG	15/19	1	2	FACETS	0.373	0.323	0.427	0.373	0.323	0.427	SUBCLONAL	1	TRUE	1	0.794689582225488	2		303	425	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144359658	144359658	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	106	423	0	ENST00000262995.4:c.1100C>G	p.Ser367Ter	p.S367*	ENST00000262995	NM_207123.2	367	tCa/tGa	4/11	1	2	FACETS	0.439	0.395	0.487	0.439	0.395	0.487	SUBCLONAL	1	TRUE	1	0.794689582225488	2		423	607	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641470	23641470	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	276	452	0	ENST00000261584.4:c.2005G>A	p.Glu669Lys	p.E669K	ENST00000261584	NM_024675.3	669	Gag/Aag	5/13	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.794689582225488	2		452	609	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432917	432917	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	209	411	0	ENST00000399788.2:c.1999G>C	p.Glu667Gln	p.E667Q	ENST00000399788	NM_001042603.1	667	Gaa/Caa	15/28	1	2	FACETS	0.918	0.858	0.979	0.918	0.858	0.979	CLONAL	1	TRUE	1	0.794689582225488	2		411	573	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819803	170819803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	65	209	0	ENST00000296930.5:c.442G>A	p.Gly148Ser	p.G148S	ENST00000296930	NM_002520.6	148	Ggt/Agt	5/11	0.559880676166141	1	FACETS	0.476	0.419	0.536	0.476	0.419	0.536	SUBCLONAL	1	TRUE	0	0.794689582225488	1		209	207	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984929	101984929	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	173	273	0	ENST00000282441.5:c.376C>G	p.His126Asp	p.H126D	ENST00000282441	NM_001130145.2	126	Cat/Gat	2/9	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.794689582225488	2		273	364	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94926665	94926665	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	173	333	0	ENST00000536441.1:c.100C>T	p.Gln34Ter	p.Q34*	ENST00000536441	NM_144665.3	34	Caa/Taa	2/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.794689582225488	2		333	414	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47595142	47595142	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	134	425	0	ENST00000430070.2:c.945G>A	p.Trp315Ter	p.W315*	ENST00000430070	NM_018095.4	315	tgG/tgA	4/4	0.497514072294663	1	FACETS	0.39	0.356	0.425	0.39	0.356	0.425	SUBCLONAL	1	TRUE	0	0.794689582225488	1		425	521	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121299	29121299	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	26	480	0	ENST00000328354.6:c.376G>C	p.Asp126His	p.D126H	ENST00000328354	NM_007194.3	126	Gat/Cat	3/15	1	2	FACETS	0.133	0.104	0.165	0.133	0.104	0.165	SUBCLONAL	1	TRUE	1	0.794689582225488	2		480	493	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658947	3658947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	216	347	0	ENST00000294008.3:c.19G>A	p.Glu7Lys	p.E7K	ENST00000294008	NM_032444.2	7	Gag/Aag	2/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.794689582225488	2		347	496	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054733	5054733	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	207	466	0	ENST00000381652.3:c.785A>G	p.Gln262Arg	p.Q262R	ENST00000381652	NM_004972.3	262	cAg/cGg	7/25	0.794689582225488	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.794689582225488	1		466	263	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427111	49427111	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	385	511	0	ENST00000301067.7:c.11377C>T	p.Gln3793Ter	p.Q3793*	ENST00000301067	NM_003482.3	3793	Caa/Taa	39/54	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.794689582225488	2		511	649	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600525	43600525	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	96	354	0	ENST00000355710.3:c.751G>T	p.Glu251Ter	p.E251*	ENST00000355710	NM_020975.4	251	Gag/Tag	4/20	0.497514072294663	1	FACETS	0.354	0.317	0.393	0.354	0.317	0.393	SUBCLONAL	1	TRUE	0	0.794689582225488	1		354	411	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267719	7267719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	338	486	1	ENST00000302850.5:c.289G>A	p.Glu97Lys	p.E97K	ENST00000302850	NM_000208.2	97	Gag/Aag	2/22	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.794689582225488	2		487	724	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335035	81335035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	172	363	0	ENST00000222390.5:c.1792G>A	p.Asp598Asn	p.D598N	ENST00000222390	NM_000601.4	598	Gat/Aat	16/18	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.794689582225488	2		363	398	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981769	101981769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	51	384	0	ENST00000282441.5:c.190G>A	p.Asp64Asn	p.D64N	ENST00000282441	NM_001130145.2	64	Gac/Aac	1/9	1	2	FACETS	0.269	0.228	0.313	0.269	0.228	0.313	SUBCLONAL	1	TRUE	1	0.794689582225488	2		384	478	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900117	151900117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	81	384	0	ENST00000262189.6:c.3994G>A	p.Asp1332Asn	p.D1332N	ENST00000262189	NM_170606.2	1332	Gat/Aat	26/59	1	2	FACETS	0.918	0.824	1	0.918	0.824	1	CLONAL	1	TRUE	1	0.794689582225488	2		384	222	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075244	16075244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	33	411	0	ENST00000268712.3:c.308C>T	p.Ser103Leu	p.S103L	ENST00000268712	NM_006311.3	103	tCa/tTa	4/46	0.794689582225488	1	FACETS	0.155	0.126	0.187	0.155	0.126	0.187	SUBCLONAL	1	TRUE	0	0.794689582225488	1		411	323	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691947	30691947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	226	416	0	ENST00000295754.5:c.449C>T	p.Ser150Leu	p.S150L	ENST00000295754	NM_003242.5	150	tCa/tTa	3/7	1	2	FACETS	0.993	0.932	1	0.993	0.932	1	CLONAL	1	TRUE	1	0.794689582225488	2		416	573	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196970	123196990	+	inframe_deletion	In_Frame_Del	DEL	CTGTAGATGCAGAAAAGGTGA	CTGTAGATGCAGAAAAGGTGA	-	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	87	185	0	ENST00000218089.9:c.1738_1758del	p.Val580_Thr586del	p.V580_T586del	ENST00000218089	NM_001042749.1	579	tCTGTAGATGCAGAAAAGGTGAct/tct	19/35	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.794689582225488	1		185	93	SUCCESS
ATM	472	MSKCC	GRCh37	11	108159738	108159738	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	27	311	0	ENST00000278616.4:c.4144C>G	p.Pro1382Ala	p.P1382A	ENST00000278616	NM_000051.3	1382	Cca/Gca	28/63	1	2	FACETS	0.282	0.225	0.346	0.282	0.225	0.346	SUBCLONAL	1	TRUE	1	0.794689582225488	2		311	241	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342944	118342944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	68	436	0	ENST00000534358.1:c.1070C>T	p.Pro357Leu	p.P357L	ENST00000534358	NM_005933.3	357	cCa/cTa	3/36	1	2	FACETS	0.243	0.211	0.278	0.243	0.211	0.278	SUBCLONAL	1	TRUE	1	0.794689582225488	2		436	703	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643563	38643563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	41	452	0	ENST00000299084.4:c.1033G>A	p.Glu345Lys	p.E345K	ENST00000299084	NM_152594.2	345	Gaa/Aaa	7/7	1	2	FACETS	0.173	0.144	0.206	0.173	0.144	0.206	SUBCLONAL	1	TRUE	1	0.794689582225488	2		452	595	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786036	3786036	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	268	323	0	ENST00000262367.5:c.4728+1G>T		p.X1576_splice	ENST00000262367	NM_004380.2	1576			1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.794689582225488	2		323	526	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186750	11186750	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764978010	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	261	347	0	ENST00000361445.4:c.6455G>A	p.Arg2152His	p.R2152H	ENST00000361445	NM_004958.3	2152	cGc/cAc	46/58	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.794689582225488	2		347	557	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199594	16199594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	338	400	0	ENST00000375759.3:c.367C>T	p.His123Tyr	p.H123Y	ENST00000375759	NM_015001.2	123	Cat/Tat	2/15	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.794689582225488	2		400	709	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473790	67473790	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	33	288	0	ENST00000327367.4:c.870C>G	p.Ile290Met	p.I290M	ENST00000327367	NM_005902.3	290	atC/atG	6/9	1	2	FACETS	0.202	0.164	0.244	0.202	0.164	0.244	SUBCLONAL	1	TRUE	1	0.794689582225488	2		288	412	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509488	149509488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs914677813	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	201	458	0	ENST00000261799.4:c.1411G>A	p.Glu471Lys	p.E471K	ENST00000261799	NM_002609.3	471	Gaa/Aaa	10/23	0.559880676166141	1	FACETS	0.696	0.653	0.739	0.696	0.653	0.739	SUBCLONAL	1	TRUE	0	0.794689582225488	1		458	438	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599336	55599336	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	18	398	0	ENST00000288135.5:c.2462C>T	p.Ser821Phe	p.S821F	ENST00000288135	NM_000222.2	821	tCt/tTt	17/21	1	2	FACETS	0.129	0.097	0.168	0.129	0.097	0.168	SUBCLONAL	1	TRUE	1	0.794689582225488	2		398	350	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465399	120465399	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	123	384	0	ENST00000256646.2:c.4862C>T	p.Ser1621Phe	p.S1621F	ENST00000256646	NM_024408.3	1621	tCt/tTt	27/34	1	2	FACETS	0.49	0.444	0.538	0.49	0.444	0.538	SUBCLONAL	1	TRUE	1	0.794689582225488	2		384	632	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459510	40459510	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	227	428	0	ENST00000345506.4:c.1771G>A	p.Asp591Asn	p.D591N	ENST00000345506	NM_003152.3	591	Gat/Aat	15/20	1	2	FACETS	0.923	0.866	0.981	0.923	0.866	0.981	CLONAL	1	TRUE	1	0.794689582225488	2		428	619	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166367	118166367	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	331	490	0	ENST00000369448.3:c.877C>T	p.Gln293Ter	p.Q293*	ENST00000369448	NM_017709.3	293	Caa/Taa	2/2	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.794689582225488	2		490	750	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247869	59247869	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	305	501	0	ENST00000371222.2:c.874T>A	p.Ser292Thr	p.S292T	ENST00000371222	NM_002228.3	292	Tcg/Acg	1/1	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.794689582225488	2		501	708	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600603	43600603	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1027662469	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	113	350	0	ENST00000355710.3:c.829G>A	p.Asp277Asn	p.D277N	ENST00000355710	NM_020975.4	277	Gac/Aac	4/20	0.497514072294663	1	FACETS	0.427	0.388	0.469	0.427	0.388	0.469	SUBCLONAL	1	TRUE	0	0.794689582225488	1		350	401	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7174610	7174610	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	242	381	0	ENST00000302850.5:c.1107C>G	p.Ile369Met	p.I369M	ENST00000302850	NM_000208.2	369	atC/atG	4/22	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.794689582225488	2		381	559	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667523	29667523	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	225	308	0	ENST00000356175.3:c.6859G>T	p.Asp2287Tyr	p.D2287Y	ENST00000356175	NM_000267.3	2287	Gac/Tac	46/57	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.794689582225488	2		308	474	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437343	121437343	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	117	400	0	ENST00000257555.6:c.1681C>T	p.Gln561Ter	p.Q561*	ENST00000257555		561	Cag/Tag	9/10	1	2	FACETS	0.495	0.447	0.545	0.495	0.447	0.545	SUBCLONAL	1	TRUE	1	0.794689582225488	2		400	595	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123892075	123892075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	22	223	0	ENST00000330479.4:c.884G>A	p.Arg295Lys	p.R295K	ENST00000330479	NM_020382.3	295	aGa/aAa	8/9	1	2	FACETS	0.167	0.129	0.211	0.167	0.129	0.211	SUBCLONAL	1	TRUE	1	0.794689582225488	2		223	331	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161807	47161807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	342	450	1	ENST00000409792.3:c.4319C>T	p.Pro1440Leu	p.P1440L	ENST00000409792	NM_014159.6	1440	cCa/cTa	3/21	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.794689582225488	2		451	735	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150935579	150935579	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	287	373	0	ENST00000271640.5:c.3421G>A	p.Glu1141Lys	p.E1141K	ENST00000271640	NM_001145415.1	1141	Gaa/Aaa	19/22	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.794689582225488	2		373	639	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287238	46287238	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	112	445	0	ENST00000334344.6:c.5183G>C	p.Arg1728Thr	p.R1728T	ENST00000334344	NM_152641.2	1728	aGa/aCa	19/21	1	2	FACETS	0.438	0.394	0.484	0.438	0.394	0.484	SUBCLONAL	1	TRUE	1	0.794689582225488	2		445	644	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342889	118342889	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	58	441	0	ENST00000534358.1:c.1015C>G	p.Pro339Ala	p.P339A	ENST00000534358	NM_005933.3	339	Cca/Gca	3/36	1	2	FACETS	0.211	0.181	0.244	0.211	0.181	0.244	SUBCLONAL	1	TRUE	1	0.794689582225488	2		441	692	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148513849	148513849	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	214	336	0	ENST00000320356.2:c.1432G>A	p.Glu478Lys	p.E478K	ENST00000320356	NM_004456.4	478	Gaa/Aaa	12/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.794689582225488	2		336	480	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424435	49424436	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCAAAGG	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	84	434	0	ENST00000301067.7:c.13781_13787dup	p.Ser4597LeufsTer11	p.S4597Lfs*11	ENST00000301067	NM_003482.3	4596	gga/ggCCTTTGGa	41/54	1	2	FACETS	0.4	0.354	0.449	0.4	0.354	0.449	SUBCLONAL	1	TRUE	1	0.794689582225488	2		434	529	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266903	41266903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	85	469	0	ENST00000349496.5:c.574C>T	p.Pro192Ser	p.P192S	ENST00000349496	NM_001904.3	192	Cct/Tct	5/15	1	2	FACETS	0.292	0.258	0.329	0.292	0.258	0.329	SUBCLONAL	1	TRUE	1	0.794689582225488	2		469	733	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219381	1219381	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	59	334	0	ENST00000326873.7:c.433G>T	p.Glu145Ter	p.E145*	ENST00000326873	NM_000455.4	145	Gag/Tag	3/10	0.300583050449216	1	FACETS	0.596	0.514	0.684	0.596	0.514	0.684	SUBCLONAL	1	TRUE	0	0.37520583426437	1		334	429	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600364	10600364	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	59	456	0	ENST00000171111.5:c.1491G>A	p.Trp497Ter	p.W497*	ENST00000171111	NM_203500.1	497	tgG/tgA	4/6	0.344653214204078	1	FACETS	0.575	0.496	0.661	0.575	0.496	0.661	SUBCLONAL	1	TRUE	0	0.37520583426437	1		456	444	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259111	89259111	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	50	381	0	ENST00000336596.2:c.255C>A	p.Asn85Lys	p.N85K	ENST00000336596	NM_005233.5	85	aaC/aaA	3/17	1	2	FACETS	0.751	0.639	0.872	0.751	0.639	0.872	SUBCLONAL	1	TRUE	1	0.37520583426437	2		381	355	SUCCESS
AR	367	MSKCC	GRCh37	X	66766261	66766261	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	42	344	0	ENST00000374690.3:c.1273G>T	p.Gly425Trp	p.G425W	ENST00000374690	NM_000044.3	425	Ggg/Tgg	1/8	0.230111464329686	1	FACETS	0.592	0.497	0.698	0.592	0.497	0.698	SUBCLONAL	1	TRUE	0	0.37520583426437	1		344	307	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061486	38061486	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	63	380	0	ENST00000250448.2:c.503A>T	p.His168Leu	p.H168L	ENST00000250448	NM_004496.3	168	cAc/cTc	2/2	1	2	FACETS	0.848	0.736	0.968	0.848	0.736	0.968	CLONAL	1	TRUE	1	0.37520583426437	2		380	396	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923417	9923417	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	47	382	0	ENST00000330684.3:c.1870G>C	p.Gly624Arg	p.G624R	ENST00000330684	NM_001134407.1	624	Ggg/Cgg	9/13	0.318117077878597	1	FACETS	0.611	0.518	0.713	0.611	0.518	0.713	SUBCLONAL	1	TRUE	0	0.37520583426437	1		382	333	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145645	11145645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	66	382	0	ENST00000358026.2:c.4007G>T	p.Arg1336Leu	p.R1336L	ENST00000358026	NM_001128849.1	1336	cGc/cTc	29/36	0.344653214204078	1	FACETS	0.772	0.674	0.878	0.772	0.674	0.878	SUBCLONAL	1	TRUE	0	0.37520583426437	1		382	370	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47491296	47491296	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	60	292	0	ENST00000404338.3:c.3877G>T	p.Glu1293Ter	p.E1293*	ENST00000404338	NM_004491.4	1293	Gag/Tag	3/6	1	2	FACETS	0.927	0.803	1	0.927	0.803	1	CLONAL	1	TRUE	1	0.37520583426437	2		292	345	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568653	41568653	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	32	378	0	ENST00000263253.7:c.4603A>C	p.Asn1535His	p.N1535H	ENST00000263253	NM_001429.3	1535	Aat/Cat	28/31	1	2	FACETS	0.636	0.519	0.768	0.636	0.519	0.768	SUBCLONAL	1	TRUE	1	0.37520583426437	2		378	268	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259018	89259018	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	40	335	0	ENST00000336596.2:c.162G>T	p.Glu54Asp	p.E54D	ENST00000336596	NM_005233.5	54	gaG/gaT	3/17	1	2	FACETS	0.826	0.691	0.975	0.826	0.691	0.975	CLONAL	1	TRUE	1	0.37520583426437	2		335	258	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484366	8484366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	56	323	0	ENST00000356435.5:c.3166G>A	p.Asp1056Asn	p.D1056N	ENST00000356435		1056	Gat/Aat	19/35	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.37520583426437	2		323	290	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913548	39913548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs768510508	NA	P-0068283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	41	345	0	ENST00000378444.4:c.4780G>T	p.Ala1594Ser	p.A1594S	ENST00000378444	NM_001123385.1	1594	Gcc/Tcc	13/15	1	2	FACETS	0.65	0.543	0.768	0.65	0.543	0.768	SUBCLONAL	1	TRUE	1	0.37520583426437	2		345	336	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044699	47044700	+	splice_acceptor_variant	Splice_Site	INS	-	-	G	novel	NA	P-0068283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	76	495	0	ENST00000377604.3:c.2102dup		p.X701_splice	ENST00000377604	NM_001204468.1	701			0.230111464329686	1	FACETS	0.65	0.572	0.735	0.65	0.572	0.735	SUBCLONAL	1	TRUE	0	0.37520583426437	1		495	506	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939735	76939735	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	41	374	0	ENST00000373344.5:c.1013C>A	p.Ser338Tyr	p.S338Y	ENST00000373344	NM_000489.3	338	tCt/tAt	9/35	0.230111464329686	1	FACETS	0.614	0.514	0.724	0.614	0.514	0.724	SUBCLONAL	1	TRUE	0	0.37520583426437	1		374	289	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1296255	1296255	+	upstream_gene_variant	5'Flank	SNP	A	A	G	novel	NA	P-0068284-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	22	407	2				ENST00000310581	NM_198253.2	-/1132			0.782030713267673	2	FACETS	0.138	0.107	0.175	0.069	0.053	0.088	SUBCLONAL	1	TRUE	0	0.782030713267673	2		409	407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0068285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	252	333	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.862500873690001	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.862500873690001	1		333	301	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144819	58144819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150281463	NA	P-0068285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	240	494	1	ENST00000257904.6:c.409G>A	p.Val137Ile	p.V137I	ENST00000257904	NM_000075.3	137	Gtt/Att	4/8	1	2	FACETS	0.95	0.894	1	0.95	0.894	1	CLONAL	1	TRUE	1	0.862500873690001	2		495	586	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006006	22006006	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749530069	NA	P-0068285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	211	455	0	ENST00000276925.6:c.397C>T	p.Arg133Cys	p.R133C	ENST00000276925	NM_004936.3	133	Cgc/Tgc	2/2	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.862500873690001	2		455	478	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940490	29940490	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	164	412	0	ENST00000389048.3:c.741G>T	p.Trp247Cys	p.W247C	ENST00000389048	NM_004304.4	247	tgG/tgT	2/29	0.862500873690001	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.862500873690001	1		412	203	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917639	94917639	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	177	446	0	ENST00000536441.1:c.882G>C	p.Lys294Asn	p.K294N	ENST00000536441	NM_144665.3	294	aaG/aaC	6/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.862500873690001	2		446	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0068286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	138	342	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.241513017982425	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.241513017982425	3		343	565	SUCCESS
APC	324	MSKCC	GRCh37	5	112173830	112173831	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0068286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	89	401	0	ENST00000257430.4:c.2544dup	p.Asp849ArgfsTer2	p.D849Rfs*2	ENST00000257430	NM_000038.5	847	gaa/gAaa	16/16	0.241513017982425	2	FACETS	0.905	0.808	1	0.905	0.808	1	CLONAL	2	TRUE	0	0.241513017982425	2		401	407	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549094	87549094	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	59	345	0	ENST00000277120.3:c.1651C>T	p.Arg551Ter	p.R551*	ENST00000277120		551	Cga/Tga	15/19	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.241513017982425	2		345	436	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456460	89456460	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1221318412	NA	P-0068286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	55	342	1	ENST00000336596.2:c.1636G>A	p.Ala546Thr	p.A546T	ENST00000336596	NM_005233.5	546	Gcc/Acc	8/17	0.037177668279903	3	FACETS	0.773	0.665	0.89	0.773	0.665	0.89	INDETERMINATE	2	TRUE	1	0.241513017982425	3		343	330	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023715	27023716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0068286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	72	465	0	ENST00000324856.7:c.827dup	p.Gly277ArgfsTer123	p.G277Rfs*123	ENST00000324856	NM_006015.4	274	atg/atGg	1/20	0.241513017982425	2	FACETS	0.879	0.774	0.991	0.879	0.774	0.991	CLONAL	2	TRUE	0	0.241513017982425	2		465	339	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086004	16086008	+	frameshift_variant	Frame_Shift_Del	DEL	CGCAA	CGCAA	-	novel	NA	P-0068286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	30	401	0	ENST00000281043.3:c.1182_1186del	p.Asn395ProfsTer19	p.N395Pfs*19	ENST00000281043	NM_005378.4	394	CGCAAc/c	3/3	0.234605847086251	3	FACETS	0.626	0.504	0.764	0.313	0.252	0.382	SUBCLONAL	1	TRUE	1	0.241513017982425	3		401	445	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120308	70120309	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0068286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	130	401	0	ENST00000245479.2:c.1312_1313dup	p.Gln439HisfsTer32	p.Q439Hfs*32	ENST00000245479	NM_000346.3	437	cgc/cgCTc	3/3	0.241513017982425	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.241513017982425	3		401	494	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871294	35871294	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	91	343	0	ENST00000303115.3:c.516A>T	p.Glu172Asp	p.E172D	ENST00000303115	NM_002185.3	172	gaA/gaT	4/8	0.241513017982425	3	FACETS	1	0.934	1	0.707	0.632	0.786	CLONAL	2	TRUE	0	0.241513017982425	3		343	398	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271595	26271595	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs930444048	NA	P-0068286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	69	441	0	ENST00000305910.3:c.18G>T	p.Gln6His	p.Q6H	ENST00000305910	NM_003534.2	6	caG/caT	1/1	0.159042550816135	4	FACETS	1	0.937	1	0.564	0.491	0.643	CLONAL	1	TRUE	2	0.241513017982425	4		441	629	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577569	7577570	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAT	novel	NA	P-0068286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	30	362	0	ENST00000269305.4:c.709_711dup	p.Met237dup	p.M237dup	ENST00000269305	NM_001126112.2	237	-/ATG	7/11	0.241513017982425	3	FACETS	0.604	0.486	0.738	0.302	0.243	0.369	SUBCLONAL	1	TRUE	1	0.241513017982425	3		362	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0068287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	206	471	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.437878829634699	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.437878829634699	2		471	453	SUCCESS
APC	324	MSKCC	GRCh37	5	112154967	112154968	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs879254088	NA	P-0068287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	204	414	0	ENST00000257430.4:c.1239dup	p.Arg414ThrfsTer5	p.R414Tfs*5	ENST00000257430	NM_000038.5	413	ata/atAa	10/16	0.437878829634699	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	0	0.437878829634699	2		414	461	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771347	68771348	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs587782476	NA	P-0068287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	25	216	0	ENST00000261769.5:c.44_46dup	p.Leu15dup	p.L15dup	ENST00000261769	NM_004360.3	15	gcg/gcGCTg	1/16	0.429080602375776	3	FACETS	0.616	0.488	0.762	0.308	0.244	0.381	SUBCLONAL	1	TRUE	1	0.437878829634699	3		216	226	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21337317	21337317	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs886041418	NA	P-0068287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	23	397	0	ENST00000215739.8:c.202C>T	p.Arg68Cys	p.R68C	ENST00000215739	NM_006767.3	68	Cgc/Tgc	2/21	0.437878829634699	2	FACETS	0.274	0.213	0.344	0.137	0.106	0.172	SUBCLONAL	1	TRUE	0	0.437878829634699	2		397	384	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584726	48584726	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	41	467	0	ENST00000342988.3:c.804G>A	p.Trp268Ter	p.W268*	ENST00000342988	NM_005359.5	268	tgG/tgA	7/12	0.437878829634699	1	FACETS	0.434	0.362	0.513	0.434	0.362	0.513	SUBCLONAL	1	TRUE	0	0.437878829634699	1		467	337	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906516	32906516	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	106	389	0	ENST00000380152.3:c.901G>C	p.Asp301His	p.D301H	ENST00000380152		301	Gat/Cat	10/27	0.417225510086741	4	FACETS	0.838	0.763	0.914	1	0.978	1	CLONAL	3	TRUE	2	0.437878829634699	4		389	277	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562612	21562612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253168141	NA	P-0068287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	51	343	0	ENST00000382592.4:c.1307C>T	p.Thr436Met	p.T436M	ENST00000382592	NM_014572.2	436	aCg/aTg	4/8	0.437878829634699	10	FACETS	0.852	0.723	0.995			1	CLONAL	1	TRUE	NA	0.437878829634699	10		343	752	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549143	87549143	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	156	408	0	ENST00000277120.3:c.1700A>T	p.Lys567Ile	p.K567I	ENST00000277120		567	aAa/aTa	15/19	0.437878829634699	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.437878829634699	2		408	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934574	NA	P-0068289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	104	382	0	ENST00000269305.4:c.844C>G	p.Arg282Gly	p.R282G	ENST00000269305	NM_001126112.2	282	Cgg/Ggg	8/11	0.227419892318245	5	FACETS	0.879	0.792	0.971			1	CLONAL	3	TRUE	NA	0.227419892318245	5		382	465	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21968233	21968233	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	109	358	0	ENST00000304494.5:c.466del	p.Asp156IlefsTer37	p.D156Ifs*37	ENST00000304494	NM_000077.4	156	Gat/at	3/3	0.227723457957822	3	FACETS	0.892	0.807	0.98	0.892	0.807	0.98	CLONAL	3	TRUE	0	0.227419892318245	3		358	399	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988270	36988270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	73	342	0	ENST00000354822.5:c.383C>T	p.Pro128Leu	p.P128L	ENST00000354822	NM_001079668.2	128	cCg/cTg	2/3	0.227723457957822	4	FACETS	0.962	0.851	1	0.962	0.851	1	CLONAL	3	TRUE	1	0.227419892318245	4		342	273	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819207	3819207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	37	394	0	ENST00000262367.5:c.3028C>T	p.Pro1010Ser	p.P1010S	ENST00000262367	NM_004380.2	1010	Cct/Tct	15/31	0.127499556193549	3	FACETS	0.929	0.767	1	0.465	0.383	0.555	INDETERMINATE	1	TRUE	1	0.227419892318245	3		394	390	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983281	149983281	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	45	481	0	ENST00000253339.5:c.2977G>T	p.Glu993Ter	p.E993*	ENST00000253339		993	Gaa/Taa	7/7	0.181766438648422	4	FACETS	0.789	0.666	0.923	0.526	0.444	0.615	CLONAL	2	TRUE	1	0.227419892318245	4		481	308	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38788459	38788459	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	60	327	0	ENST00000348513.6:c.702A>T	p.Leu234Phe	p.L234F	ENST00000348513	NM_003079.4	234	ttA/ttT	8/11	0.227419892318245	5	FACETS	1	0.904	1	0.702	0.608	0.803	CLONAL	2	TRUE	2	0.227419892318245	5		327	336	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6027078	6027078	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs762894051	NA	P-0068289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	25	144	0	ENST00000265849.7:c.1318C>G	p.Pro440Ala	p.P440A	ENST00000265849	NM_000535.5	440	Cca/Gca	11/15	0.227723457957822	5	FACETS	1	0.816	1	0.683	0.544	0.837	CLONAL	2	TRUE	2	0.227419892318245	5		144	144	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343503	343503	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1328741594	NA	P-0068289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	55	368	0	ENST00000262320.3:c.2171C>T	p.Ala724Val	p.A724V	ENST00000262320	NM_003502.3	724	gCa/gTa	8/11	0.127499556193549	3	FACETS	0.799	0.687	0.92	0.799	0.687	0.92	INDETERMINATE	2	TRUE	1	0.227419892318245	3		368	337	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371866	55371866	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	16	378	0	ENST00000297316.4:c.556C>T	p.Gln186Ter	p.Q186*	ENST00000297316	NM_022454.3	186	Cag/Tag	2/2	0.227723457957822	1	FACETS	0.549	0.407	0.719	0.549	0.407	0.719	SUBCLONAL	1	TRUE	0	0.227419892318245	1		378	227	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57004166	57004166	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	24	475	0	ENST00000257254.3:c.313A>T	p.Ser105Cys	p.S105C	ENST00000257254		105	Agc/Tgc	1/2	0.192326582160022	2	FACETS	0.524	0.41	0.655	0.262	0.205	0.328	SUBCLONAL	1	TRUE	0	0.227419892318245	2		475	403	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791989	42791989	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	45	494	0	ENST00000575354.2:c.793C>G	p.Pro265Ala	p.P265A	ENST00000575354	NM_015125.3	265	Cca/Gca	6/20	0.227419892318245	6	FACETS	0.966	0.811	1	0.322	0.27	0.38	CLONAL	1	TRUE	3	0.227419892318245	6		494	596	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109833	115109833	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs753103762	NA	P-0068289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	102	401	0	ENST00000257566.3:c.2045C>A	p.Ala682Asp	p.A682D	ENST00000257566	NM_016569.3	682	gCc/gAc	8/8	0.227723457957822	4	FACETS	0.953	0.86	1	0.953	0.86	1	CLONAL	3	TRUE	1	0.227419892318245	4		401	385	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196935	108196935	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1565521026	NA	P-0068289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	53	387	0	ENST00000278616.4:c.6958G>T	p.Asp2320Tyr	p.D2320Y	ENST00000278616	NM_000051.3	2320	Gat/Tat	47/63	0.151252732871252	4	FACETS	0.792	0.678	0.916	0.792	0.678	0.916	CLONAL	2	TRUE	2	0.227419892318245	4		387	361	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47440581	47440582	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0068289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	55	353	0	ENST00000404338.3:c.3742_3743delinsTT	p.Gly1248Leu	p.G1248L	ENST00000404338	NM_004491.4	1248	GGg/TTg	2/6	0.227419892318245	6	FACETS	1	0.958	1	0.449	0.384	0.52	CLONAL	1	TRUE	3	0.227419892318245	6		353	522	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800459	32800459	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	119	452	0	ENST00000374899.4:c.1088G>T	p.Arg363Leu	p.R363L	ENST00000374899	NM_018833.2	363	cGg/cTg	6/12	0.2274779902764	3	FACETS	1	0.94	1	0.7	0.634	0.769	CLONAL	2	TRUE	0	0.227419892318245	3		452	555	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387719	17387719	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0068289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	106	394	0	ENST00000359435.4:c.786+1G>T		p.X262_splice	ENST00000359435	NM_001033549.1	262			0.216841070033191	4	FACETS	1	0.973	1	0.822	0.741	0.907	CLONAL	2	TRUE	1	0.227419892318245	4		394	464	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372161	55372161	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	15	391	0	ENST00000297316.4:c.851C>G	p.Pro284Arg	p.P284R	ENST00000297316	NM_022454.3	284	cCg/cGg	2/2	0.227723457957822	1	FACETS	0.415	0.303	0.549	0.415	0.303	0.549	SUBCLONAL	1	TRUE	0	0.227419892318245	1		391	282	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2132493	2132493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201135184	NA	P-0068290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	26	304	1	ENST00000219476.3:c.3871G>A	p.Val1291Ile	p.V1291I	ENST00000219476	NM_000548.3	1291	Gtt/Att	32/42	1	2	FACETS	0.673	0.535	0.83	0.673	0.535	0.83	SUBCLONAL	1	FALSE	1	0.307985390113224	2		305	251	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046489	69046489	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	50	378	0	ENST00000288368.4:c.3962A>G	p.Gln1321Arg	p.Q1321R	ENST00000288368	NM_024870.2	1321	cAg/cGg	32/40	0.21062542682074	2	FACETS	1	0.956	1	0.663	0.567	0.765	CLONAL	1	FALSE	0	0.307985390113224	2		378	245	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023478	27023478	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	51	340	0	ENST00000324856.7:c.584del	p.Tyr195SerfsTer37	p.Y195Sfs*37	ENST00000324856	NM_006015.4	195	tAc/tc	1/20	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	FALSE	1	0.307985390113224	2		340	286	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249852	110249852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1348583597	NA	P-0068290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	31	401	0	ENST00000374672.4:c.823C>T	p.Pro275Ser	p.P275S	ENST00000374672	NM_004235.4	275	Ccc/Tcc	3/5	1	2	FACETS	0.643	0.521	0.78	0.643	0.521	0.78	SUBCLONAL	1	FALSE	1	0.307985390113224	2		401	313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0068291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	199	426	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.720023078190837	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.720023078190837	1		426	330	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0068291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	203	425	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.720023078190837	2		425	552	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0068291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	61	403	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.411009958143907	1	FACETS	0.317	0.275	0.362	0.317	0.275	0.362	INDETERMINATE	1	TRUE	0	0.720023078190837	1		403	342	SUCCESS
APC	324	MSKCC	GRCh37	5	112175235	112175235	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	196	481	0	ENST00000257430.4:c.3944C>A	p.Ser1315Ter	p.S1315*	ENST00000257430	NM_000038.5	1315	tCa/tAa	16/16	0.411009958143907	1	FACETS	0.814	0.763	0.865	0.814	0.763	0.865	INDETERMINATE	1	TRUE	0	0.720023078190837	1		481	428	SUCCESS
AR	367	MSKCC	GRCh37	X	66765139	66765139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758522275	NA	P-0068291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	231	149	0	ENST00000374690.3:c.151G>A	p.Gly51Ser	p.G51S	ENST00000374690	NM_000044.3	51	Ggc/Agc	1/8	0.521340697030294	2	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.720023078190837	2		149	269	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244214	153244214	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	244	575	0	ENST00000281708.4:c.1943T>G	p.Leu648Arg	p.L648R	ENST00000281708	NM_033632.3	648	cTa/cGa	12/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.720023078190837	2		575	614	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187463174	187463199	+	splice_donor_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	GGCGGCAGCAACAGCAATAATCACCT	GGCGGCAGCAACAGCAATAATCACCT	-	novel	NA	P-0068291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	31	297	0	ENST00000406870.2:c.-51_-50+24del		p.X17_splice	ENST00000406870	NM_001706.4	17		1/10	1	2	FACETS	0.25	0.202	0.304	0.25	0.202	0.304	SUBCLONAL	1	TRUE	1	0.720023078190837	2		297	344	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727138	40727138	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	383	481	0	ENST00000373198.4:c.3826del	p.Val1276TrpfsTer17	p.V1276Wfs*17	ENST00000373198	NM_133170.3	1276	Gtg/tg	28/32	0.258449424887714	3	FACETS	0.974	0.932	1			1	INDETERMINATE	2	TRUE	NA	0.720023078190837	3		481	743	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0068293-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	34	437	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.825	0.681	0.983	0.825	0.681	0.983	CLONAL	1	TRUE	1	0.445639450688553	2		437	185	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979319	40979319	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1217327426	NA	P-0068293-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	81	350	0	ENST00000373198.4:c.1814C>T	p.Thr605Met	p.T605M	ENST00000373198	NM_133170.3	605	aCg/aTg	11/32	0.445639450688553	1	FACETS	0.971	0.865	1	0.971	0.865	1	CLONAL	1	TRUE	0	0.445639450688553	1		350	291	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356311	70356311	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1042718707	NA	P-0068293-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	24	384	0	ENST00000374080.3:c.5206G>A	p.Ala1736Thr	p.A1736T	ENST00000374080		1736	Gcc/Acc	37/45	1	2	FACETS	0.344	0.27	0.43	0.344	0.27	0.43	SUBCLONAL	1	TRUE	1	0.445639450688553	2		384	313	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120623	94120623	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068293-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	160	458	0	ENST00000369303.4:c.428A>C	p.Tyr143Ser	p.Y143S	ENST00000369303	NM_004440.3	143	tAt/tCt	3/17	0.301075922312856	3	FACETS	1	0.965	1	0.712	0.66	0.765	CLONAL	2	TRUE	0	0.445639450688553	3		458	411	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401556	401556	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068293-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	42	484	0	ENST00000380956.4:c.878C>G	p.Pro293Arg	p.P293R	ENST00000380956	NM_001195286.1	293	cCc/cGc	7/9	0.301075922312856	3	FACETS	0.605	0.506	0.714	0.202	0.168	0.238	SUBCLONAL	1	TRUE	0	0.445639450688553	3		484	381	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450300	50450300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	243	479	0	ENST00000331340.3:c.484C>T	p.Arg162Trp	p.R162W	ENST00000331340	NM_006060.4	162	Cgg/Tgg	5/8	0.549798972046386	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.643159690459976	4		479	604	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0068296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	68	371	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.911	0.804	1	0.911	0.804	1	CLONAL	1	TRUE	1	0.643159690459976	2		371	232	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256561	115256562	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0068296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	197	350	1	ENST00000369535.4:c.149_150delinsTT	p.Thr50Ile	p.T50I	ENST00000369535	NM_002524.4	50	aCC/aTT	3/7	0.643159690459976	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.643159690459976	3		351	383	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023830	27023831	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0068296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	86	425	0	ENST00000324856.7:c.941dup	p.Asp315ArgfsTer85	p.D315Rfs*85	ENST00000324856	NM_006015.4	312	-/G	1/20	0.643159690459976	3	FACETS	0.94	0.837	1	0.47	0.418	0.524	CLONAL	1	TRUE	1	0.643159690459976	3		425	376	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023943	27023943	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	195	374	0	ENST00000324856.7:c.1049C>A	p.Ser350Ter	p.S350*	ENST00000324856	NM_006015.4	350	tCg/tAg	1/20	0.643159690459976	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.643159690459976	3		374	355	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414251	32414251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121907910	NA	P-0068296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	132	472	1	ENST00000332351.3:c.1300C>T	p.Arg434Cys	p.R434C	ENST00000332351	NM_024426.4	434	Cgt/Tgt	8/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.643159690459976	2		473	371	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716366	18716366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs935135637	NA	P-0068296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	277	479	0	ENST00000266497.5:c.3713C>T	p.Ser1238Leu	p.S1238L	ENST00000266497		1238	tCa/tTa	26/31	0.643159690459976	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.643159690459976	3		479	522	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601986	43601986	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs749883001	NA	P-0068296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	120	465	0	ENST00000355710.3:c.1030G>C	p.Gly344Arg	p.G344R	ENST00000355710	NM_020975.4	344	Ggc/Cgc	5/20	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.643159690459976	2		465	365	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425086	49425086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761717148	NA	P-0068296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	141	549	0	ENST00000301067.7:c.13402C>T	p.Arg4468Trp	p.R4468W	ENST00000301067	NM_003482.3	4468	Cgg/Tgg	39/54	0.643159690459976	3	FACETS	1	0.936	1	0.514	0.47	0.559	CLONAL	1	TRUE	1	0.643159690459976	3		549	564	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932395	36932395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376317083	NA	P-0068296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	262	574	3	ENST00000361632.4:c.2074C>T	p.Pro692Ser	p.P692S	ENST00000361632		692	Ccc/Tcc	16/16	0.643159690459976	3	FACETS	0.991	0.939	1	0.991	0.939	1	CLONAL	2	TRUE	1	0.643159690459976	3		577	543	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31237859	31237859	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs281860581	NA	P-0068296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	503	590	0	ENST00000376228.5:c.899C>T	p.Pro300Leu	p.P300L	ENST00000376228	NM_002117.5	300	cCa/cTa	5/8	0.588111690231025	5	FACETS	0.937	0.906	0.968	0.937	0.906	0.968	CLONAL	4	TRUE	1	0.643159690459976	5		590	820	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347299	89347299	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526636	NA	P-0068296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	290	573	0	ENST00000301030.4:c.5651C>T	p.Ser1884Leu	p.S1884L	ENST00000301030	NM_001256183.1	1884	tCa/tTa	9/13	0.643159690459976	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.643159690459976	3		573	562	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258748	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0068296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	182	355	2	ENST00000369535.4:c.34_35delinsAA	p.Gly12Asn	p.G12N	ENST00000369535	NM_002524.4	12	GGt/AAt	2/7	0.643159690459976	3	FACETS	0.901	0.842	0.961	0.901	0.842	0.961	CLONAL	2	TRUE	1	0.643159690459976	3		357	415	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561249	9561249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	296	530	0	ENST00000353224.5:c.533G>A	p.Gly178Glu	p.G178E	ENST00000353224	NM_177990.2	178	gGg/gAg	4/10	0.301742201995714	6	FACETS	0.98	0.928	1	0.98	0.928	1	INDETERMINATE	3	TRUE	3	0.643159690459976	6		530	716	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410757	63410757	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	154	242	0	ENST00000330258.3:c.2410C>T	p.Pro804Ser	p.P804S	ENST00000330258	NM_152424.3	804	Cct/Tct	2/2	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.643159690459976	1		242	228	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273408	38273408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	119	504	0	ENST00000425967.3:c.1927G>A	p.Glu643Lys	p.E643K	ENST00000425967	NM_001174067.1	643	Gag/Aag	14/19	0.54450659256792	4	FACETS	0.984	0.89	1	0.328	0.296	0.361	CLONAL	1	TRUE	1	0.643159690459976	4		504	618	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10785951	10785951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	156	562	0	ENST00000361367.2:c.1381C>T	p.His461Tyr	p.H461Y	ENST00000361367	NM_014633.3	461	Cat/Tat	11/25	1	2	FACETS	0.99	0.914	1	0.99	0.914	1	CLONAL	1	TRUE	1	0.643159690459976	2		562	490	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882012	36882013	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0068296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	188	416	0	ENST00000358127.4:c.1000_1001delinsAA	p.Gly334Lys	p.G334K	ENST00000358127	NM_001280556.1	334	GGg/AAg	8/10	0.643159690459976	2	FACETS	0.978	0.925	1	0.978	0.925	1	CLONAL	2	TRUE	0	0.643159690459976	2		416	299	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740458	58740458	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	138	508	0	ENST00000305921.3:c.1363G>T	p.Glu455Ter	p.E455*	ENST00000305921	NM_003620.3	455	Gag/Tag	6/6	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.643159690459976	2		508	421	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272394	38272394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	136	539	0	ENST00000425967.3:c.1973G>A	p.Arg658Lys	p.R658K	ENST00000425967	NM_001174067.1	658	aGg/aAg	15/19	0.54450659256792	4	FACETS	0.984	0.897	1	0.328	0.299	0.359	CLONAL	1	TRUE	1	0.643159690459976	4		539	706	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950210	38950210	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	133	564	0	ENST00000357387.3:c.3740C>T	p.Thr1247Ile	p.T1247I	ENST00000357387	NM_152756.3	1247	aCt/aTt	31/38	1	2	FACETS	0.971	0.889	1	0.971	0.889	1	CLONAL	1	TRUE	1	0.643159690459976	2		564	426	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719892	52719893	+	missense_variant	Missense_Mutation	DNP	CT	CT	TC	novel	NA	P-0068296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	97	516	0	ENST00000322088.6:c.1104_1105delinsTC	p.Phe369Leu	p.F369L	ENST00000322088	NM_014225.5	368	ctCTtc/ctTCtc	9/15	0.643159690459976	3	FACETS	0.783	0.701	0.87	0.392	0.35	0.435	SUBCLONAL	1	TRUE	1	0.643159690459976	3		516	509	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612278	1612278	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0068296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	247	470	0	ENST00000344749.5:c.1741A>T	p.Lys581Ter	p.K581*	ENST00000344749	NM_001136139.2	581	Aaa/Taa	18/19	0.643159690459976	3	FACETS	0.94	0.888	0.992	0.94	0.888	0.992	CLONAL	2	TRUE	1	0.643159690459976	3		470	540	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31015994	31015994	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	263	470	0	ENST00000375687.4:c.316G>C	p.Ala106Pro	p.A106P	ENST00000375687	NM_015338.5	106	Gct/Cct	5/13	0.301742201995714	6	FACETS	1	0.951	1	1	0.951	1	INDETERMINATE	3	TRUE	3	0.643159690459976	6		470	619	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305335	65305335	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	145	544	1	ENST00000342505.4:c.2793C>G	p.Asn931Lys	p.N931K	ENST00000342505	NM_002227.2	931	aaC/aaG	20/25	0.643159690459976	3	FACETS	1	0.929	1	0.508	0.465	0.552	CLONAL	1	TRUE	1	0.643159690459976	3		545	587	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272163	142272163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	117	447	0	ENST00000350721.4:c.2711C>T	p.Ser904Phe	p.S904F	ENST00000350721	NM_001184.3	904	tCt/tTt	13/47	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.643159690459976	2		447	324	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4123786	4123787	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0068296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	98	312	0	ENST00000262948.5:c.86_87delinsTT	p.Ala29Val	p.A29V	ENST00000262948	NM_030662.3	29	gCC/gTT	1/11	0.643159690459976	3	FACETS	1	0.949	1	0.544	0.49	0.601	CLONAL	1	TRUE	1	0.643159690459976	3		312	370	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978327	2978327	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	226	423	0	ENST00000396946.4:c.1003G>A	p.Glu335Lys	p.E335K	ENST00000396946	NM_032415.4	335	Gag/Aag	7/25	0.643159690459976	4	FACETS	0.966	0.906	1	0.966	0.906	1	CLONAL	2	TRUE	2	0.643159690459976	4		423	598	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902646	50902646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	145	532	0	ENST00000440232.2:c.221C>T	p.Ala74Val	p.A74V	ENST00000440232	NM_002691.3	74	gCc/gTc	3/27	0.643159690459976	3	FACETS	1	0.971	1	0.562	0.516	0.61	CLONAL	1	TRUE	1	0.643159690459976	3		532	530	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231488446	231488446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772330427	NA	P-0068296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	124	507	0	ENST00000295050.7:c.809G>A	p.Gly270Glu	p.G270E	ENST00000295050	NM_032018.5	270	gGg/gAg	5/5	0.643159690459976	5	FACETS	1	0.922	1	0.255	0.231	0.281	CLONAL	1	TRUE	1	0.643159690459976	5		507	742	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129036	2129036	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1317631053	NA	P-0068296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	122	449	0	ENST00000219476.3:c.2970G>T	p.Arg990Ser	p.R990S	ENST00000219476	NM_000548.3	990	agG/agT	27/42	0.643159690459976	3	FACETS	1	0.937	1	0.519	0.472	0.568	CLONAL	1	TRUE	1	0.643159690459976	3		449	483	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	41	350	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.922	0.776	1	0.922	0.776	1	CLONAL	1	TRUE	1	0.425490339920371	2		350	209	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692885	89692885	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	39	226	0	ENST00000371953.3:c.369C>A	p.His123Gln	p.H123Q	ENST00000371953	NM_000314.4	123	caC/caA	5/9	0.425490339920371	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.425490339920371	1		226	126	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037865	49037865	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0068299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	25	277	0	ENST00000267163.4:c.2107-2A>G		p.X703_splice	ENST00000267163	NM_000321.2	703			0.425490339920371	1	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	0	0.425490339920371	1		277	74	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0068299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	16	385	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	1	2	FACETS	0.177	0.13	0.233	0.177	0.13	0.233	SUBCLONAL	1	TRUE	1	0.425490339920371	2		385	426	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449397	31449397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776471094	NA	P-0068299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	85	343	0	ENST00000344624.3:c.2812C>T	p.Arg938Trp	p.R938W	ENST00000344624		938	Cgg/Tgg	19/33	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.425490339920371	2		343	359	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69032446	69032446	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	70	338	0	ENST00000288368.4:c.3520A>G	p.Asn1174Asp	p.N1174D	ENST00000288368	NM_024870.2	1174	Aat/Gat	29/40	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.425490339920371	2		338	315	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272526	11272526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	70	474	0	ENST00000361445.4:c.3404C>T	p.Ala1135Val	p.A1135V	ENST00000361445	NM_004958.3	1135	gCg/gTg	23/58	1	2	FACETS	0.825	0.72	0.938	0.825	0.72	0.938	CLONAL	1	TRUE	1	0.308623560707271	2		474	550	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	67	504	0	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	0.676	0.587	0.773	0.676	0.587	0.773	SUBCLONAL	1	TRUE	1	0.308623560707271	2		504	642	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521525	46521525	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	63	334	0	ENST00000262741.5:c.883del	p.Met295Ter	p.M295*	ENST00000262741	NM_003629.3	295	Atg/tg	7/10	1	2	FACETS	0.947	0.822	1	0.947	0.822	1	CLONAL	1	TRUE	1	0.308623560707271	2		334	431	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100425	8100425	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	41	467	1	ENST00000346208.3:c.404del	p.Pro135ArgfsTer60	p.P135Rfs*60	ENST00000346208		133	taC/ta	3/6	1	2	FACETS	0.378	0.314	0.45	0.378	0.314	0.45	SUBCLONAL	1	TRUE	1	0.308623560707271	2		468	703	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100728	8100728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs771019738	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	81	646	2	ENST00000346208.3:c.708del	p.Ser237AlafsTer28	p.S237Afs*28	ENST00000346208		234	ttC/tt	3/6	1	2	FACETS	0.976	0.861	1	0.976	0.861	1	CLONAL	1	TRUE	1	0.308623560707271	2		648	538	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332376	70332376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	28	466	0	ENST00000373644.4:c.281C>T	p.Pro94Leu	p.P94L	ENST00000373644	NM_030625.2	94	cCa/cTa	2/12	1	2	FACETS	0.357	0.285	0.44	0.357	0.285	0.44	SUBCLONAL	1	TRUE	1	0.308623560707271	2		466	508	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	42	624	0	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.436	0.363	0.517	0.436	0.363	0.517	SUBCLONAL	1	TRUE	1	0.308623560707271	2		624	624	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307393	118307394	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1555138552	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	28	292	0	ENST00000534358.1:c.173dup	p.Ala59GlyfsTer88	p.A59Gfs*88	ENST00000534358	NM_005933.3	56	tcc/tCcc	1/36	1	2	FACETS	0.677	0.543	0.829	0.677	0.543	0.829	SUBCLONAL	1	TRUE	1	0.308623560707271	2		292	268	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs770248150	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	37	361	0	ENST00000311936.3:c.351A>T	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaT	4/5	1	2	FACETS	0.81	0.671	0.965	0.81	0.671	0.965	CLONAL	1	TRUE	1	0.308623560707271	2		361	296	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872461	35872461	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	73	647	0	ENST00000216797.5:c.442del	p.Leu148TyrfsTer16	p.L148Yfs*16	ENST00000216797	NM_020529.2	148	Cta/ta	3/6	1	2	FACETS	0.712	0.623	0.809	0.712	0.623	0.809	SUBCLONAL	1	TRUE	1	0.308623560707271	2		647	664	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987109	36987109	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	37	595	0	ENST00000354822.5:c.580C>T	p.Arg194Cys	p.R194C	ENST00000354822	NM_001079668.2	194	Cgc/Tgc	3/3	1	2	FACETS	0.478	0.393	0.572	0.478	0.393	0.572	SUBCLONAL	1	TRUE	1	0.308623560707271	2		595	502	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052635	42052635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	34	524	1	ENST00000219905.7:c.7306C>T	p.Arg2436Cys	p.R2436C	ENST00000219905	NM_001164273.1	2436	Cgt/Tgt	20/24	1	2	FACETS	0.337	0.274	0.408	0.337	0.274	0.408	SUBCLONAL	1	TRUE	1	0.308623560707271	2		525	654	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347929	347929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141699962	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	111	735	0	ENST00000262320.3:c.1577C>T	p.Ala526Val	p.A526V	ENST00000262320	NM_003502.3	526	gCg/gTg	6/11	1	2	FACETS	0.971	0.873	1	0.971	0.873	1	CLONAL	1	TRUE	1	0.308623560707271	2		735	741	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273878	10273878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	70	508	0	ENST00000330684.3:c.391G>A	p.Ala131Thr	p.A131T	ENST00000330684	NM_001134407.1	131	Gca/Aca	2/13	1	2	FACETS	0.879	0.768	0.999	0.879	0.768	0.999	CLONAL	1	TRUE	1	0.308623560707271	2		508	516	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821425	72821425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769841511	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	35	525	0	ENST00000268489.5:c.10750G>A	p.Ala3584Thr	p.A3584T	ENST00000268489	NM_006885.3	3584	Gca/Aca	10/10	1	2	FACETS	0.391	0.32	0.472	0.391	0.32	0.472	SUBCLONAL	1	TRUE	1	0.308623560707271	2		525	580	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944279	81944279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747373917	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	75	525	0	ENST00000359376.3:c.1888C>T	p.Arg630Trp	p.R630W	ENST00000359376	NM_002661.3	630	Cgg/Tgg	18/33	1	2	FACETS	0.902	0.792	1	0.902	0.792	1	CLONAL	1	TRUE	1	0.308623560707271	2		525	539	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351215	89351215	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs143817649	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	36	529	0	ENST00000301030.4:c.1735T>C	p.Tyr579His	p.Y579H	ENST00000301030	NM_001256183.1	579	Tac/Cac	9/13	1	2	FACETS	0.356	0.292	0.429	0.356	0.292	0.429	SUBCLONAL	1	TRUE	1	0.308623560707271	2		529	655	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89862422	89862422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1467900630	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	91	459	0	ENST00000389301.3:c.898G>A	p.Gly300Arg	p.G300R	ENST00000389301	NM_000135.2	300	Gga/Aga	11/43	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.308623560707271	2		459	515	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968279	15968279	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	67	543	0	ENST00000268712.3:c.5006del	p.Gly1669GlufsTer93	p.G1669Efs*93	ENST00000268712	NM_006311.3	1669	gGa/ga	34/46	1	2	FACETS	0.845	0.735	0.963	0.845	0.735	0.963	CLONAL	1	TRUE	1	0.308623560707271	2		543	514	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59793411	59793411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375082407	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	54	265	0	ENST00000259008.2:c.2393G>A	p.Arg798Gln	p.R798Q	ENST00000259008	NM_032043.2	798	cGa/cAa	17/20	0.285548024629484	2	FACETS	0.961	0.835	1	0.961	0.835	1	CLONAL	2	TRUE	0	0.308623560707271	2		265	182	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	204	666	0	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	0.285548024629484	2	FACETS	0.899	0.837	0.964	0.899	0.837	0.964	CLONAL	2	TRUE	0	0.308623560707271	2		666	735	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533732	63533733	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGG	rs570443161	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	60	725	0	ENST00000307078.5:c.1419_1421dup	p.His474dup	p.H474dup	ENST00000307078	NM_004655.3	474	cat/caCCAt	6/11	0.285548024629484	2	FACETS	0.507	0.436	0.585	0.253	0.218	0.293	SUBCLONAL	1	TRUE	0	0.308623560707271	2		725	767	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	29	586	2	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.341	0.273	0.419	0.341	0.273	0.419	SUBCLONAL	1	TRUE	1	0.308623560707271	2		588	551	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166282	7166282	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	40	538	0	ENST00000302850.5:c.1744G>T	p.Gly582Cys	p.G582C	ENST00000302850	NM_000208.2	582	Ggt/Tgt	8/22	1	2	FACETS	0.396	0.328	0.472	0.396	0.328	0.472	SUBCLONAL	1	TRUE	1	0.308623560707271	2		538	654	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7174602	7174602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	78	493	1	ENST00000302850.5:c.1115G>A	p.Arg372Gln	p.R372Q	ENST00000302850	NM_000208.2	372	cGa/cAa	4/22	1	2	FACETS	0.869	0.764	0.98	0.869	0.764	0.98	CLONAL	1	TRUE	1	0.308623560707271	2		494	582	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272244	15272244	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1168179879	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	34	607	0	ENST00000263388.2:c.6195G>C	p.Arg2065Ser	p.R2065S	ENST00000263388	NM_000435.2	2065	agG/agC	33/33	1	2	FACETS	0.428	0.349	0.517	0.428	0.349	0.517	SUBCLONAL	1	TRUE	1	0.308623560707271	2		607	515	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743932	41743933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs778012871	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	92	652	0	ENST00000301178.4:c.874dup	p.His292ProfsTer47	p.H292Pfs*47	ENST00000301178	NM_021913.4	289	-/C	7/20	1	2	FACETS	0.877	0.779	0.981	0.877	0.779	0.981	CLONAL	1	TRUE	1	0.308623560707271	2		652	680	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	10	256	3	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	0.356	0.241	0.5	0.356	0.241	0.5	SUBCLONAL	1	TRUE	1	0.308623560707271	2		259	182	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485820	57485820	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	80	524	0	ENST00000371085.3:c.1121G>A	p.Arg374His	p.R374H	ENST00000371085	NM_000516.4	374	cGt/cAt	13/13	1	2	FACETS	0.781	0.687	0.881	0.781	0.687	0.881	SUBCLONAL	1	TRUE	1	0.308623560707271	2		524	664	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	71	510	4	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	0.299135396311543	2	FACETS	0.825	0.72	0.937	0.412	0.36	0.469	CLONAL	1	TRUE	0	0.308623560707271	2		514	558	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274910	41274910	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	119	525	0	ENST00000349496.5:c.1160A>T	p.Asn387Ile	p.N387I	ENST00000349496	NM_001904.3	387	aAt/aTt	8/15	0.299135396311543	2	FACETS	0.812	0.737	0.89	0.812	0.737	0.89	CLONAL	2	TRUE	0	0.308623560707271	2		525	475	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125832	47125832	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	67	397	0	ENST00000409792.3:c.5438del	p.Asn1813IlefsTer25	p.N1813Ifs*25	ENST00000409792	NM_014159.6	1813	aAt/at	12/21	0.299135396311543	2	FACETS	0.914	0.796	1	0.457	0.398	0.521	CLONAL	1	TRUE	0	0.308623560707271	2		397	475	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851558	134851558	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs770155473	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	55	416	0	ENST00000398015.3:c.964G>A	p.Val322Ile	p.V322I	ENST00000398015	NM_004441.4	322	Gtc/Atc	5/16	1	2	FACETS	0.762	0.652	0.881	0.762	0.652	0.881	SUBCLONAL	1	TRUE	1	0.308623560707271	2		416	468	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884864	134884864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257672576	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	94	448	0	ENST00000398015.3:c.1640C>T	p.Ala547Val	p.A547V	ENST00000398015	NM_004441.4	547	gCg/gTg	8/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.308623560707271	2		448	545	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683417	182683417	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	49	361	0	ENST00000292782.4:c.128A>T	p.Asn43Ile	p.N43I	ENST00000292782	NM_020640.2	43	aAt/aTt	2/7	1	2	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	1	0.308623560707271	2		361	317	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957419	1957419	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	72	484	0	ENST00000382891.5:c.2523del		p.X841_splice	ENST00000382891	NM_133335.3	841			1	2	FACETS	0.91	0.796	1	0.91	0.796	1	CLONAL	1	TRUE	1	0.308623560707271	2		484	513	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	106	694	7	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	1	2	FACETS	0.961	0.862	1	0.961	0.862	1	CLONAL	1	TRUE	1	0.308623560707271	2		701	715	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604659	55604659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139694927	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	56	463	0	ENST00000288135.5:c.2867G>A	p.Arg956Gln	p.R956Q	ENST00000288135	NM_000222.2	956	cGg/cAg	21/21	1	2	FACETS	0.603	0.516	0.698	0.603	0.516	0.698	SUBCLONAL	1	TRUE	1	0.308623560707271	2		463	602	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510158	187510158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs932754737	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	34	550	0	ENST00000441802.2:c.13355C>T	p.Pro4452Leu	p.P4452L	ENST00000441802	NM_005245.3	4452	cCg/cTg	27/27	1	2	FACETS	0.33	0.269	0.4	0.33	0.269	0.4	SUBCLONAL	1	TRUE	1	0.308623560707271	2		550	667	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235282	235282	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	69	290	0	ENST00000264932.6:c.1088A>G	p.His363Arg	p.H363R	ENST00000264932	NM_004168.2	363	cAc/cGc	9/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.308623560707271	2		290	369	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871286	35871286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145210284	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	42	388	0	ENST00000303115.3:c.508C>T	p.Arg170Cys	p.R170C	ENST00000303115	NM_002185.3	170	Cgc/Tgc	4/8	1	2	FACETS	0.752	0.629	0.887	0.752	0.629	0.887	SUBCLONAL	1	TRUE	1	0.308623560707271	2		388	362	SUCCESS
APC	324	MSKCC	GRCh37	5	112178033	112178033	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs773874693	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	81	505	0	ENST00000257430.4:c.6747del	p.Gly2250AlafsTer29	p.G2250Afs*29	ENST00000257430	NM_000038.5	2248	Aaa/aa	16/16	1	2	FACETS	0.849	0.749	0.957	0.849	0.749	0.957	CLONAL	1	TRUE	1	0.308623560707271	2		505	618	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322412	31322412	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs756666358	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	84	490	0	ENST00000412585.2:c.1043C>T	p.Ala348Val	p.A348V	ENST00000412585	NM_005514.6	348	gCg/gTg	6/8	1	2	FACETS	0.915	0.809	1	0.915	0.809	1	CLONAL	1	TRUE	1	0.308623560707271	2		490	595	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324917	31324917	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	105	631	0	ENST00000412585.2:c.19del	p.Arg7GlufsTer13	p.R7Efs*13	ENST00000412585	NM_005514.6	7	Cga/ga	1/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.308623560707271	2		631	599	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903745	41903746	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	69	649	0	ENST00000372991.4:c.811dup	p.Arg271ProfsTer53	p.R271Pfs*53	ENST00000372991	NM_001760.3	271	cgg/cCgg	5/5	1	2	FACETS	0.682	0.593	0.777	0.682	0.593	0.777	SUBCLONAL	1	TRUE	1	0.308623560707271	2		649	656	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129249	152129249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771540162	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	104	631	0	ENST00000206249.3:c.202G>A	p.Ala68Thr	p.A68T	ENST00000206249	NM_000125.3	68	Gcc/Acc	1/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.308623560707271	2		631	570	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	35	556	4	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.439	0.359	0.529	0.439	0.359	0.529	SUBCLONAL	1	TRUE	1	0.308623560707271	2		560	517	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	65	397	1	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	1	2	FACETS	0.677	0.587	0.775	0.677	0.587	0.775	SUBCLONAL	1	TRUE	1	0.308623560707271	2		398	622	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482927	140482927	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	33	567	0	ENST00000288602.6:c.1208del	p.Pro403LeufsTer8	p.P403Lfs*8	ENST00000288602	NM_004333.4	403	cCt/ct	10/18	1	2	FACETS	0.349	0.284	0.424	0.349	0.284	0.424	SUBCLONAL	1	TRUE	1	0.308623560707271	2		567	612	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211580	98211580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762040036	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	76	543	0	ENST00000331920.6:c.3575G>A	p.Arg1192His	p.R1192H	ENST00000331920	NM_000264.3	1192	cGc/cAc	22/24	1	2	FACETS	0.947	0.833	1	0.947	0.833	1	CLONAL	1	TRUE	1	0.308623560707271	2		543	520	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300039	137300040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755912201	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	43	491	2	ENST00000481739.1:c.331dup	p.Leu111ProfsTer70	p.L111Pfs*70	ENST00000481739	NM_002957.4	108	-/C	3/10	1	2	FACETS	0.546	0.457	0.646	0.546	0.457	0.646	SUBCLONAL	1	TRUE	1	0.308623560707271	2		493	510	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652527	48652527	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	76	597	0	ENST00000376670.3:c.1203del	p.Thr402ProfsTer30	p.T402Pfs*30	ENST00000376670	NM_002049.3	400	Ccc/cc	6/6	1	2	FACETS	0.936	0.823	1	0.936	0.823	1	CLONAL	1	TRUE	1	0.308623560707271	2		597	526	SUCCESS
AR	367	MSKCC	GRCh37	X	66765242	66765243	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCA	rs753526329	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	30	581	0	ENST00000374690.3:c.271_273dup	p.Gln91dup	p.Q91dup	ENST00000374690	NM_000044.3	91	agg/agGCAg	1/8	1	2	FACETS	0.342	0.275	0.419	0.342	0.275	0.419	SUBCLONAL	1	TRUE	1	0.308623560707271	2		581	568	SUCCESS
AR	367	MSKCC	GRCh37	X	66765779	66765779	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	97	675	0	ENST00000374690.3:c.796del	p.Asp266IlefsTer30	p.D266Ifs*30	ENST00000374690	NM_000044.3	264	cGg/cg	1/8	1	2	FACETS	0.923	0.824	1	0.923	0.824	1	CLONAL	1	TRUE	1	0.308623560707271	2		675	681	SUCCESS
AR	367	MSKCC	GRCh37	X	66943627	66943627	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	25	502	0	ENST00000374690.3:c.2707C>T	p.Gln903Ter	p.Q903*	ENST00000374690	NM_000044.3	903	Caa/Taa	8/8	1	2	FACETS	0.343	0.269	0.427	0.343	0.269	0.427	SUBCLONAL	1	TRUE	1	0.308623560707271	2		502	473	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776918	76776918	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	22	440	0	ENST00000373344.5:c.7034T>C	p.Val2345Ala	p.V2345A	ENST00000373344	NM_000489.3	2345	gTg/gCg	33/35	1	2	FACETS	0.471	0.365	0.593	0.471	0.365	0.593	SUBCLONAL	1	TRUE	1	0.308623560707271	2		440	303	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938724	76938724	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	43	501	0	ENST00000373344.5:c.2024C>A	p.Ser675Tyr	p.S675Y	ENST00000373344	NM_000489.3	675	tCt/tAt	9/35	1	2	FACETS	0.728	0.61	0.857	0.728	0.61	0.857	SUBCLONAL	1	TRUE	1	0.308623560707271	2		501	383	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099975	27099975	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	47	734	0	ENST00000324856.7:c.3854A>G	p.Tyr1285Cys	p.Y1285C	ENST00000324856	NM_006015.4	1285	tAt/tGt	15/20	1	2	FACETS	0.41	0.345	0.483	0.41	0.345	0.483	SUBCLONAL	1	TRUE	1	0.308623560707271	2		734	742	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981801	201981801	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	33	617	0	ENST00000359651.3:c.512A>G	p.Asp171Gly	p.D171G	ENST00000359651		171	gAc/gGc	4/8	1	2	FACETS	0.351	0.285	0.425	0.351	0.285	0.425	SUBCLONAL	1	TRUE	1	0.308623560707271	2		617	610	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600641	43600641	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	34	684	0	ENST00000355710.3:c.867G>T	p.Glu289Asp	p.E289D	ENST00000355710	NM_020975.4	289	gaG/gaT	4/20	1	2	FACETS	0.357	0.29	0.431	0.357	0.29	0.431	SUBCLONAL	1	TRUE	1	0.308623560707271	2		684	618	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57004244	57004244	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	C	C	T	rs144634263	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	102	695	0	ENST00000257254.3:c.235G>A	p.Val79Met	p.V79M	ENST00000257254		79	Gtg/Atg	1/2	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.308623560707271	2		695	647	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205214	61205214	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	71	487	0	ENST00000301761.2:c.154T>G	p.Leu52Val	p.L52V	ENST00000301761	NM_017841.2	52	Ttg/Gtg	2/4	1	2	FACETS	0.941	0.823	1	0.941	0.823	1	CLONAL	1	TRUE	1	0.308623560707271	2		487	489	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77937618	77937618	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	56	425	0	ENST00000361507.4:c.1100del	p.Gly367AlafsTer60	p.G367Afs*60	ENST00000361507	NM_080491.2	367	gGc/gc	4/10	1	2	FACETS	0.819	0.703	0.945	0.819	0.703	0.945	CLONAL	1	TRUE	1	0.308623560707271	2		425	443	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922270	100922270	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	18	361	0	ENST00000325455.5:c.2242A>T	p.Ile748Leu	p.I748L	ENST00000325455	NM_001202474.3	748	Ata/Tta	5/8	1	2	FACETS	0.498	0.376	0.643	0.498	0.376	0.643	SUBCLONAL	1	TRUE	1	0.308623560707271	2		361	234	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164181	108164181	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs781275128	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	20	339	0	ENST00000278616.4:c.4753A>G	p.Arg1585Gly	p.R1585G	ENST00000278616	NM_000051.3	1585	Aga/Gga	31/63	1	2	FACETS	0.369	0.282	0.472	0.369	0.282	0.472	SUBCLONAL	1	TRUE	1	0.308623560707271	2		339	351	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437673	49437673	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	43	686	0	ENST00000301067.7:c.5297A>G	p.Asp1766Gly	p.D1766G	ENST00000301067	NM_003482.3	1766	gAc/gGc	22/54	1	2	FACETS	0.365	0.304	0.433	0.365	0.304	0.433	SUBCLONAL	1	TRUE	1	0.308623560707271	2		686	763	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856677	111856677	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	35	539	0	ENST00000341259.2:c.728C>A	p.Pro243His	p.P243H	ENST00000341259	NM_005475.2	243	cCc/cAc	2/8	1	2	FACETS	0.428	0.35	0.516	0.428	0.35	0.516	SUBCLONAL	1	TRUE	1	0.308623560707271	2		539	530	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209307	133209307	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	36	647	0	ENST00000320574.5:c.6079A>G	p.Arg2027Gly	p.R2027G	ENST00000320574	NM_006231.2	2027	Agg/Ggg	44/49	1	2	FACETS	0.386	0.316	0.464	0.386	0.316	0.464	SUBCLONAL	1	TRUE	1	0.308623560707271	2		647	605	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636038	73636038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754308838	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	67	476	0	ENST00000377687.4:c.301C>T	p.Pro101Ser	p.P101S	ENST00000377687	NM_001730.3	101	Cct/Tct	2/4	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.308623560707271	2		476	411	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778903	3778903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	77	636	0	ENST00000262367.5:c.6145G>A	p.Ala2049Thr	p.A2049T	ENST00000262367	NM_004380.2	2049	Gct/Act	31/31	1	2	FACETS	0.863	0.759	0.975	0.863	0.759	0.975	CLONAL	1	TRUE	1	0.308623560707271	2		636	578	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439959	56439960	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	171	548	0	ENST00000407977.2:c.632_633del	p.Val211AspfsTer47	p.V211Dfs*47	ENST00000407977		211	gTG/g	6/10	0.285548024629484	2	FACETS	0.891	0.823	0.961	0.891	0.823	0.961	CLONAL	2	TRUE	0	0.308623560707271	2		548	622	SUCCESS
YES1	7525	MSKCC	GRCh37	18	739786	739786	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	17	318	0	ENST00000314574.4:c.1086del	p.Gly363GlufsTer6	p.G363Efs*6	ENST00000314574	NM_005433.3	362	gaA/ga	9/12	1	2	FACETS	0.362	0.27	0.472	0.362	0.27	0.472	SUBCLONAL	1	TRUE	1	0.308623560707271	2		318	304	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285152	15285152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	99	640	0	ENST00000263388.2:c.4463G>A	p.Cys1488Tyr	p.C1488Y	ENST00000263388	NM_000435.2	1488	tGc/tAc	25/33	1	2	FACETS	0.917	0.819	1	0.917	0.819	1	CLONAL	1	TRUE	1	0.308623560707271	2		640	700	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312960	30312960	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	72	532	0	ENST00000262643.3:c.763C>T	p.Gln255Ter	p.Q255*	ENST00000262643	NM_001238.2	255	Cag/Tag	9/12	1	2	FACETS	0.87	0.762	0.987	0.87	0.762	0.987	CLONAL	1	TRUE	1	0.308623560707271	2		532	536	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798821	42798821	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	71	542	0	ENST00000575354.2:c.4393C>T	p.Arg1465Cys	p.R1465C	ENST00000575354	NM_015125.3	1465	Cgc/Tgc	19/20	1	2	FACETS	0.937	0.82	1	0.937	0.82	1	CLONAL	1	TRUE	1	0.308623560707271	2		542	491	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423682	47423682	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750559194	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	91	540	1	ENST00000404338.3:c.1750C>T	p.Arg584Trp	p.R584W	ENST00000404338	NM_004491.4	584	Cgg/Tgg	1/6	1	2	FACETS	0.932	0.828	1	0.932	0.828	1	CLONAL	1	TRUE	1	0.308623560707271	2		541	633	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445446	29445446	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs759177019	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	99	539	0	ENST00000389048.3:c.3387G>T	p.Glu1129Asp	p.E1129D	ENST00000389048	NM_004304.4	1129	gaG/gaT	21/29	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.308623560707271	2		539	565	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630515	67630515	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1676110017	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	18	427	0	ENST00000272342.5:c.701A>G	p.Asn234Ser	p.N234S	ENST00000272342	NM_019002.3	234	aAt/aGt	5/6	1	2	FACETS	0.362	0.272	0.469	0.362	0.272	0.469	SUBCLONAL	1	TRUE	1	0.308623560707271	2		427	322	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251734	212251734	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	91	574	0	ENST00000342788.4:c.3325G>T	p.Gly1109Cys	p.G1109C	ENST00000342788	NM_005235.2	1109	Ggc/Tgc	27/28	1	2	FACETS	0.86	0.764	0.962	0.86	0.764	0.962	CLONAL	1	TRUE	1	0.308623560707271	2		574	686	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29115469	29115469	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1250779080	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	16	288	0	ENST00000328354.6:c.597del	p.Phe199LeufsTer6	p.F199Lfs*6	ENST00000328354	NM_007194.3	199	ttT/tt	5/15	1	2	FACETS	0.337	0.248	0.442	0.337	0.248	0.442	SUBCLONAL	1	TRUE	1	0.308623560707271	2		288	308	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29438490	29438490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376766629	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	76	411	0	ENST00000544604.2:c.434G>A	p.Arg145Gln	p.R145Q	ENST00000544604	NM_001206998.1	145	cGa/cAa	3/9	1	2	FACETS	0.892	0.784	1	0.892	0.784	1	CLONAL	1	TRUE	1	0.308623560707271	2		411	552	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29438495	29438496	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	71	410	0	ENST00000544604.2:c.440dup	p.Gln148ThrfsTer10	p.Q148Tfs*10	ENST00000544604	NM_001206998.1	147	gta/gTta	3/9	1	2	FACETS	0.809	0.706	0.919	0.809	0.706	0.919	CLONAL	1	TRUE	1	0.308623560707271	2		410	569	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421214	12421214	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1010142067	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	85	461	0	ENST00000287820.6:c.94G>T	p.Val32Phe	p.V32F	ENST00000287820	NM_015869.4	32	Gtt/Ttt	2/7	0.299135396311543	2	FACETS	0.966	0.856	1	0.483	0.428	0.542	CLONAL	1	TRUE	0	0.308623560707271	2		461	570	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035133	37035133	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1575377175	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	36	428	0	ENST00000231790.2:c.95T>A	p.Ile32Asn	p.I32N	ENST00000231790	NM_000249.3	32	aTc/aAc	1/19	0.299135396311543	2	FACETS	0.415	0.34	0.499	0.208	0.17	0.25	SUBCLONAL	1	TRUE	0	0.308623560707271	2		428	562	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37092115	37092115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	126	444	0	ENST00000231790.2:c.2242del	p.Asp748IlefsTer35	p.D748Ifs*35	ENST00000231790	NM_000249.3	748	Gat/at	19/19	0.299135396311543	2	FACETS	0.963	0.879	1	0.963	0.879	1	CLONAL	2	TRUE	0	0.308623560707271	2		444	424	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119562182	119562182	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	33	458	0	ENST00000316626.5:c.1154C>A	p.Pro385His	p.P385H	ENST00000316626		385	cCt/cAt	11/12	1	2	FACETS	0.396	0.322	0.48	0.396	0.322	0.48	SUBCLONAL	1	TRUE	1	0.308623560707271	2		458	540	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806174	1806174	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	48	672	0	ENST00000260795.2:c.1193T>C	p.Leu398Pro	p.L398P	ENST00000260795		398	cTg/cCg	8/17	1	2	FACETS	0.474	0.4	0.556	0.474	0.4	0.556	SUBCLONAL	1	TRUE	1	0.308623560707271	2		672	656	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057325	180057325	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	32	570	0	ENST00000261937.6:c.413C>A	p.Pro138Gln	p.P138Q	ENST00000261937	NM_182925.4	138	cCa/cAa	4/30	1	2	FACETS	0.443	0.359	0.538	0.443	0.359	0.538	SUBCLONAL	1	TRUE	1	0.308623560707271	2		570	468	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41905047	41905047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149279084	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	73	580	0	ENST00000372991.4:c.500G>A	p.Arg167Gln	p.R167Q	ENST00000372991	NM_001760.3	167	cGg/cAg	3/5	1	2	FACETS	0.705	0.616	0.801	0.705	0.616	0.801	SUBCLONAL	1	TRUE	1	0.308623560707271	2		580	671	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790678	89790678	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	38	562	0	ENST00000336032.3:c.65G>A	p.Gly22Asp	p.G22D	ENST00000336032	NM_006813.2	22	gGc/gAc	1/2	1	2	FACETS	0.428	0.353	0.512	0.428	0.353	0.512	SUBCLONAL	1	TRUE	1	0.308623560707271	2		562	575	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124532383	124532383	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	15	336	0	ENST00000357628.3:c.61A>G	p.Thr21Ala	p.T21A	ENST00000357628	NM_015450.2	21	Aca/Gca	6/19	1	2	FACETS	0.351	0.256	0.465	0.351	0.256	0.465	SUBCLONAL	1	TRUE	1	0.308623560707271	2		336	277	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511107	148511107	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	32	451	1	ENST00000320356.2:c.1795T>C	p.Trp599Arg	p.W599R	ENST00000320356	NM_004456.4	599	Tgg/Cgg	15/20	1	2	FACETS	0.332	0.268	0.404	0.332	0.268	0.404	SUBCLONAL	1	TRUE	1	0.308623560707271	2		452	625	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841941	151841941	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1221863211	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	31	544	0	ENST00000262189.6:c.14200A>G	p.Thr4734Ala	p.T4734A	ENST00000262189	NM_170606.2	4734	Acc/Gcc	55/59	1	2	FACETS	0.325	0.261	0.396	0.325	0.261	0.396	SUBCLONAL	1	TRUE	1	0.308623560707271	2		544	619	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007082	152007082	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	25	358	0	ENST00000262189.6:c.818T>C	p.Val273Ala	p.V273A	ENST00000262189	NM_170606.2	273	gTg/gCg	6/59	1	2	FACETS	0.346	0.272	0.432	0.346	0.272	0.432	SUBCLONAL	1	TRUE	1	0.308623560707271	2		358	468	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2161821	2161821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148991905	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	86	512	0	ENST00000349721.2:c.4117G>A	p.Ala1373Thr	p.A1373T	ENST00000349721	NM_003070.3	1373	Gct/Act	28/34	1	2	FACETS	0.818	0.724	0.919	0.818	0.724	0.919	CLONAL	1	TRUE	1	0.308623560707271	2		512	681	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250037	110250037	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	22	500	0	ENST00000374672.4:c.638T>C	p.Ile213Thr	p.I213T	ENST00000374672	NM_004235.4	213	aTt/aCt	3/5	1	2	FACETS	0.353	0.273	0.446	0.353	0.273	0.446	SUBCLONAL	1	TRUE	1	0.308623560707271	2		500	404	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418415	139418415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757497167	NA	P-0068305-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	64	532	0	ENST00000277541.6:c.157G>A	p.Val53Met	p.V53M	ENST00000277541	NM_017617.3	53	Gtg/Atg	3/34	1	2	FACETS	0.799	0.693	0.914	0.799	0.693	0.914	CLONAL	1	TRUE	1	0.308623560707271	2		532	519	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0068311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	612	437	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		437	881	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913384	NA	P-0068311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	139	350	0	ENST00000304494.5:c.262G>T	p.Glu88Ter	p.E88*	ENST00000304494	NM_000077.4	88	Gag/Tag	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		350	484	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366981	15366982	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0068311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	65	542	0	ENST00000263377.2:c.1644dup	p.Glu549ArgfsTer13	p.E549Rfs*13	ENST00000263377	NM_058243.2	548	-/A	9/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		542	501	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511735	46511735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	103	379	0	ENST00000262741.5:c.1042G>A	p.Glu348Lys	p.E348K	ENST00000262741	NM_003629.3	348	Gaa/Aaa	9/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		379	368	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484362	8484362	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	87	393	0	ENST00000356435.5:c.3170G>T	p.Gly1057Val	p.G1057V	ENST00000356435		1057	gGg/gTg	19/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		393	440	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748318	41748318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	69	445	0	ENST00000226382.2:c.451G>A	p.Ala151Thr	p.A151T	ENST00000226382	NM_003924.3	151	Gcc/Acc	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		445	386	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741864	17741864	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	41	423	0	ENST00000250003.3:c.535T>C	p.Tyr179His	p.Y179H	ENST00000250003	NM_002478.4	179	Tat/Cat	1/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		423	331	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602964	55602964	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	61	385	0	ENST00000288135.5:c.2674C>A	p.Pro892Thr	p.P892T	ENST00000288135	NM_000222.2	892	Cct/Act	19/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		385	404	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124492007	124492007	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0068311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	149	306	0	ENST00000357628.3:c.870-2A>G		p.X290_splice	ENST00000357628	NM_015450.2	290			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		306	415	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624409	140624427	+	frameshift_variant	Frame_Shift_Del	DEL	CCGGCGCCGGCGCCGGCCT	CCGGCGCCGGCGCCGGCCT	-	novel	NA	P-0068311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	88	339	0	ENST00000288602.6:c.77_95del	p.Glu26AlafsTer22	p.E26Afs*22	ENST00000288602	NM_004333.4	26	gAGGCCGGCGCCGGCGCCGGc/gc	1/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		339	425	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300792	137300792	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	114	482	0	ENST00000481739.1:c.437A>T	p.His146Leu	p.H146L	ENST00000481739	NM_002957.4	146	cAc/cTc	4/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		482	461	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912835	50912835	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	223	553	0	ENST00000440232.2:c.2066G>T	p.Arg689Leu	p.R689L	ENST00000440232	NM_002691.3	689	cGg/cTg	17/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		553	540	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019927	123019927	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	52	551	0	ENST00000355640.3:c.415T>A	p.Tyr139Asn	p.Y139N	ENST00000355640		139	Tat/Aat	2/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		551	505	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650417	48650417	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	110	611	0	ENST00000376670.3:c.387C>A	p.Ser129Arg	p.S129R	ENST00000376670	NM_002049.3	129	agC/agA	3/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		611	532	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934339	39934339	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	133	506	0	ENST00000378444.4:c.260A>T	p.Asn87Ile	p.N87I	ENST00000378444	NM_001123385.1	87	aAc/aTc	4/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		506	539	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202414	123202414	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	63	259	0	ENST00000218089.9:c.2266G>T	p.Glu756Ter	p.E756*	ENST00000218089	NM_001042749.1	756	Gag/Tag	24/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		259	318	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842344	151842344	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs749571160	NA	P-0068317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	51	322	2	ENST00000262189.6:c.14068C>T	p.Arg4690Ter	p.R4690*	ENST00000262189	NM_170606.2	4690	Cga/Tga	54/59	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.16	2		324	465	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484212	8484212	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	31	368	0	ENST00000356435.5:c.3320T>C	p.Val1107Ala	p.V1107A	ENST00000356435		1107	gTa/gCa	19/35	1	2	FACETS	1	0.838	1	1	0.838	1	CLONAL	1	TRUE	1	0.16	2		368	373	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150902505	150902505	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587721669	NA	P-0068317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	31	321	0	ENST00000271640.5:c.323G>A	p.Arg108Gln	p.R108Q	ENST00000271640	NM_001145415.1	108	cGg/cAg	3/22	1	2	FACETS	0.873	0.705	1	0.873	0.705	1	CLONAL	1	TRUE	1	0.16	2		321	444	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852460	63852460	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1231090488	NA	P-0068317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	22	410	0	ENST00000279873.7:c.3238G>A	p.Gly1080Ser	p.G1080S	ENST00000279873	NM_032199.2	1080	Ggt/Agt	10/10	1	2	FACETS	0.712	0.551	0.9	0.712	0.551	0.9	SUBCLONAL	1	TRUE	1	0.16	2		410	386	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446314	29446314	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	23	513	0	ENST00000389048.3:c.3253A>T	p.Thr1085Ser	p.T1085S	ENST00000389048	NM_004304.4	1085	Acc/Tcc	20/29	1	2	FACETS	0.642	0.499	0.807	0.642	0.499	0.807	SUBCLONAL	1	TRUE	1	0.16	2		513	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0068320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	216	395	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.809238777927098	2	FACETS	0.981	0.944	1	0.981	0.944	1	CLONAL	2	TRUE	0	0.809238777927098	2		395	272	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949076	44949076	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	113	335	0	ENST00000377967.4:c.3637C>T	p.Arg1213Ter	p.R1213*	ENST00000377967	NM_021140.2	1213	Cga/Tga	25/29	0.809238777927098	3	FACETS	1	0.977	1	0.609	0.555	0.665	CLONAL	1	TRUE	1	0.809238777927098	3		335	322	SUCCESS
AR	367	MSKCC	GRCh37	X	66765149	66765151	+	inframe_deletion	In_Frame_Del	DEL	TGC	TGC	-	rs752055010	NA	P-0068320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	11	233	0	ENST00000374690.3:c.170_172del	p.Leu57del	p.L57del	ENST00000374690	NM_000044.3	54	tTGCtg/ttg	1/8	0.809238777927098	3	FACETS	0.212	0.146	0.293	0.106	0.073	0.147	SUBCLONAL	1	TRUE	1	0.809238777927098	3		233	180	SUCCESS
APC	324	MSKCC	GRCh37	5	112175606	112175606	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	242	403	0	ENST00000257430.4:c.4316del	p.Pro1439LeufsTer34	p.P1439Lfs*34	ENST00000257430	NM_000038.5	1439	Cct/ct	16/16	0.809238777927098	2	FACETS	0.929	0.892	0.963	0.929	0.892	0.963	CLONAL	2	TRUE	0	0.809238777927098	2		403	322	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059447	42059447	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753335816	NA	P-0068320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	127	364	0	ENST00000219905.7:c.9167C>T	p.Ser3056Leu	p.S3056L	ENST00000219905	NM_001164273.1	3056	tCg/tTg	24/24	0.70406272990855	3	FACETS	1	0.953	1	0.532	0.486	0.58	CLONAL	1	TRUE	1	0.809238777927098	3		364	414	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286812	212286812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	75	317	0	ENST00000342788.4:c.2884G>A	p.Asp962Asn	p.D962N	ENST00000342788	NM_005235.2	962	Gac/Aac	24/28	1	2	FACETS	0.997	0.893	1	0.997	0.893	1	CLONAL	1	TRUE	1	0.809238777927098	2		317	186	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	84	403	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	0.20653482568658	3	FACETS	0.899	0.797	1	0.599	0.531	0.672	CLONAL	2	TRUE	0	0.20653482568658	3		404	499	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650071	93650071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1486347243	NA	P-0068321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	104	308	0	ENST00000375746.1:c.1622C>T	p.Pro541Leu	p.P541L	ENST00000375746	NM_001174167.1	541	cCg/cTg	12/14	0.20653482568658	4	FACETS	0.918	0.827	1	0.918	0.827	1	CLONAL	3	TRUE	1	0.20653482568658	4		308	441	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799299	42799300	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1158987717	NA	P-0068321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	19	122	1	ENST00000575354.2:c.4790dup	p.Pro1598ThrfsTer16	p.P1598Tfs*16	ENST00000575354	NM_015125.3	1595	tcc/tCcc	20/20	0.163269973970958	4	FACETS	1	0.87	1	0.617	0.47	0.786	CLONAL	1	TRUE	2	0.20653482568658	4		123	180	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032794	30032794	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434259	NA	P-0068321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	78	402	0	ENST00000338641.4:c.169C>T	p.Arg57Ter	p.R57*	ENST00000338641	NM_000268.3	57	Cga/Tga	2/16	0.20653482568658	3	FACETS	0.842	0.742	0.949	0.561	0.494	0.633	CLONAL	2	TRUE	0	0.20653482568658	3		402	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0068321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	89	279	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.20653482568658	3	FACETS	1	0.96	1	0.775	0.691	0.863	CLONAL	2	TRUE	0	0.20653482568658	3		279	409	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0068321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	53	272	0	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	0.20653482568658	3	FACETS	0.976	0.839	1	0.976	0.839	1	CLONAL	2	TRUE	1	0.20653482568658	3		272	290	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222308	2222308	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750329755	NA	P-0068321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	96	368	1	ENST00000326181.6:c.592G>A	p.Gly198Arg	p.G198R	ENST00000326181	NM_032271.2	198	Ggg/Agg	8/21	0.20653482568658	3	FACETS	1	0.925	1	0.695	0.622	0.772	CLONAL	2	TRUE	0	0.20653482568658	3		369	492	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134598	2134598	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45517340	NA	P-0068321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	127	458	0	ENST00000219476.3:c.4375C>T	p.Arg1459Ter	p.R1459*	ENST00000219476	NM_000548.3	1459	Cga/Tga	34/42	0.20653482568658	3	FACETS	1	0.961	1	0.737	0.669	0.807	CLONAL	2	TRUE	0	0.20653482568658	3		458	614	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37056036	37056036	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs267607789	NA	P-0068321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	77	247	0	ENST00000231790.2:c.790+1G>A		p.X264_splice	ENST00000231790	NM_000249.3	264			0.20653482568658	3	FACETS	0.911	0.808	1	0.911	0.808	1	CLONAL	3	TRUE	0	0.20653482568658	3		247	301	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436560	110436560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567423781	NA	P-0068321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	103	356	0	ENST00000375856.3:c.1841C>T	p.Pro614Leu	p.P614L	ENST00000375856	NM_003749.2	614	cCg/cTg	1/2	0.20653482568658	3	FACETS	1	0.919	1	1	0.919	1	CLONAL	2	TRUE	1	0.20653482568658	3		356	536	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663356	67663356	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	43	409	1	ENST00000264010.4:c.1760del	p.Asn587MetfsTer44	p.N587Mfs*44	ENST00000264010	NM_006565.3	586	gAa/ga	10/12	0.20653482568658	3	FACETS	0.945	0.791	1	0.315	0.263	0.372	CLONAL	1	TRUE	0	0.20653482568658	3		410	486	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687371	117687371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748148750	NA	P-0068321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	94	377	0	ENST00000368508.3:c.2680C>T	p.Arg894Trp	p.R894W	ENST00000368508	NM_002944.2	894	Cgg/Tgg	18/43	0.20653482568658	3	FACETS	1	0.964	1	0.786	0.703	0.873	CLONAL	2	TRUE	0	0.20653482568658	3		377	426	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058477	42058477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760533003	NA	P-0068321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	107	456	0	ENST00000219905.7:c.8197G>A	p.Val2733Ile	p.V2733I	ENST00000219905	NM_001164273.1	2733	Gtt/Att	24/24	0.20653482568658	3	FACETS	1	0.923	1	0.687	0.618	0.759	CLONAL	2	TRUE	0	0.20653482568658	3		456	555	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176516607	176516607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545721160	NA	P-0068321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	58	333	0	ENST00000292408.4:c.4C>T	p.Arg2Trp	p.R2W	ENST00000292408	NM_213647.1	2	Cgg/Tgg	2/18	0.20653482568658	3	FACETS	0.759	0.655	0.873	0.759	0.655	0.873	SUBCLONAL	2	TRUE	1	0.20653482568658	3		333	408	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655248	45655248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs533193731	NA	P-0068321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	95	390	0	ENST00000407780.3:c.604G>A	p.Val202Met	p.V202M	ENST00000407780	NM_001283052.1	202	Gtg/Atg	4/7	0.20653482568658	3	FACETS	0.972	0.869	1	0.972	0.869	1	CLONAL	2	TRUE	1	0.20653482568658	3		390	522	SUCCESS
MET	4233	MSKCC	GRCh37	7	116381018	116381018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761951444	NA	P-0068321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	112	334	0	ENST00000397752.3:c.1640G>A	p.Arg547Gln	p.R547Q	ENST00000397752	NM_000245.2	547	cGa/cAa	5/21	0.20653482568658	5	FACETS	1	0.959	1	0.749	0.675	0.827	CLONAL	2	TRUE	2	0.20653482568658	5		334	632	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617690	39617690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141329274	NA	P-0068321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	72	355	0	ENST00000262039.4:c.1874C>T	p.Thr625Met	p.T625M	ENST00000262039	NM_002647.2	625	aCg/aTg	17/25	0.20653482568658	3	FACETS	1	0.938	1	0.737	0.648	0.831	CLONAL	2	TRUE	0	0.20653482568658	3		355	348	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271264	38271264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746602135	NA	P-0068321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	86	386	0	ENST00000425967.3:c.2444G>A	p.Arg815Gln	p.R815Q	ENST00000425967	NM_001174067.1	815	cGg/cAg	19/19	0.20653482568658	3	FACETS	0.857	0.76	0.96	0.571	0.507	0.64	CLONAL	2	TRUE	0	0.20653482568658	3		386	536	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106558	27106558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	43	454	0	ENST00000324856.7:c.6169C>T	p.Arg2057Trp	p.R2057W	ENST00000324856	NM_006015.4	2057	Cgg/Tgg	20/20	0.20653482568658	3	FACETS	0.771	0.644	0.912	0.257	0.214	0.304	CLONAL	1	TRUE	0	0.20653482568658	3		454	596	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268930	55268930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149248025	NA	P-0068321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	114	468	0	ENST00000275493.2:c.2996G>A	p.Arg999His	p.R999H	ENST00000275493	NM_005228.3	999	cGt/cAt	25/28	0.20653482568658	3	FACETS	1	0.936	1	0.699	0.631	0.77	CLONAL	2	TRUE	0	0.20653482568658	3		468	581	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918912	76918912	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	62	330	0	ENST00000373344.5:c.4079C>A	p.Pro1360His	p.P1360H	ENST00000373344	NM_000489.3	1360	cCt/cAt	12/35	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.20653482568658	2		330	444	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120496255	120496255	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	80	384	0	ENST00000256646.2:c.2276del	p.Asn759MetfsTer18	p.N759Mfs*18	ENST00000256646	NM_024408.3	759	aAt/at	14/34	0.20653482568658	3	FACETS	0.843	0.744	0.949	0.562	0.496	0.633	CLONAL	2	TRUE	0	0.20653482568658	3		384	507	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440558	49440558	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	93	387	0	ENST00000301067.7:c.4252C>A	p.Leu1418Met	p.L1418M	ENST00000301067	NM_003482.3	1418	Ctg/Atg	15/54	0.20653482568658	3	FACETS	1	0.929	1	0.702	0.627	0.781	CLONAL	2	TRUE	0	0.20653482568658	3		387	472	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100676	67100677	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0068321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	86	353	0	ENST00000412916.2:c.374_375del	p.Leu125ArgfsTer3	p.L125Rfs*3	ENST00000412916		125	cTG/c	4/6	0.20653482568658	3	FACETS	1	0.931	1	0.709	0.63	0.792	CLONAL	2	TRUE	0	0.20653482568658	3		353	432	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279307	18279307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1333755424	NA	P-0068321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	74	340	0	ENST00000222254.8:c.1759C>T	p.Arg587Trp	p.R587W	ENST00000222254	NM_005027.3	587	Cgg/Tgg	14/16	0.20653482568658	5	FACETS	0.913	0.801	1	0.609	0.534	0.689	CLONAL	2	TRUE	2	0.20653482568658	5		340	514	SUCCESS
MAD2L2	10459	MSKCC	GRCh37	1	11734849	11734849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759967644	NA	P-0068321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	63	253	0	ENST00000235310.3:c.619G>A	p.Ala207Thr	p.A207T	ENST00000235310		207	Gct/Act	11/11	0.20653482568658	3	FACETS	1	0.905	1	0.699	0.609	0.795	CLONAL	2	TRUE	0	0.20653482568658	3		253	321	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	15	350	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.428	0.313	0.566	0.428	0.313	0.566	SUBCLONAL	1	TRUE	1	0.32	2		350	219	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0068322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	14	293	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	0.242	0.174	0.324	0.242	0.174	0.324	SUBCLONAL	1	TRUE	1	0.32	2		293	362	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0068322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	49	336	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	1	2	FACETS	0.682	0.578	0.796	0.682	0.578	0.796	SUBCLONAL	1	TRUE	1	0.32	2		336	449	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0068322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	9	148	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.439	0.292	0.626	0.439	0.292	0.626	SUBCLONAL	1	TRUE	1	0.32	2		148	128	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276903	15276903	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0068322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	41	312	0	ENST00000263388.2:c.5363-1G>T		p.X1788_splice	ENST00000263388	NM_000435.2	1788			1	2	FACETS	0.593	0.494	0.703	0.593	0.494	0.703	SUBCLONAL	1	TRUE	1	0.32	2		312	432	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186501416	186501416	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	22	203	0	ENST00000323963.5:c.17C>T	p.Ala6Val	p.A6V	ENST00000323963		6	gCg/gTg	1/11	1	2	FACETS	0.372	0.287	0.47	0.372	0.287	0.47	SUBCLONAL	1	TRUE	1	0.32	2		203	370	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44920573	44920574	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0068322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	17	212	0	ENST00000377967.4:c.1336dup	p.Ser446PhefsTer2	p.S446Ffs*2	ENST00000377967	NM_021140.2	445	act/acTt	14/29	1	2	FACETS	0.354	0.264	0.461	0.354	0.264	0.461	SUBCLONAL	1	TRUE	1	0.32	2		212	300	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70967542	70967542	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	39	273	0	ENST00000276594.2:c.1481G>T	p.Cys494Phe	p.C494F	ENST00000276594	NM_024504.3	494	tGt/tTt	7/8	1	2	FACETS	0.677	0.562	0.804	0.677	0.562	0.804	SUBCLONAL	1	TRUE	1	0.32	2		273	360	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89825019	89825019	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	67	321	1	ENST00000389301.3:c.2947A>G	p.Ile983Val	p.I983V	ENST00000389301	NM_000135.2	983	Att/Gtt	30/43	1	2	FACETS	0.823	0.716	0.938	0.823	0.716	0.938	CLONAL	1	TRUE	1	0.32	2		322	509	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661393	227661393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751466820	NA	P-0068323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	121	363	0	ENST00000305123.5:c.2062G>A	p.Ala688Thr	p.A688T	ENST00000305123	NM_005544.2	688	Gcc/Acc	1/2	0.256599529877556	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.256599529877556	2		363	390	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089759	5089759	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs572395683	NA	P-0068323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	88	258	0	ENST00000381652.3:c.2657A>G	p.His886Arg	p.H886R	ENST00000381652	NM_004972.3	886	cAt/cGt	20/25	0.256599529877556	4	FACETS	1	0.956	1	0.57	0.509	0.635	CLONAL	2	TRUE	0	0.256599529877556	4		258	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579300	7579325	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGGCAACTGACCGTGCAAGTCACAG	AGGGCAACTGACCGTGCAAGTCACAG	-	novel	NA	P-0068323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	80	284	0	ENST00000269305.4:c.362_375+12del		p.X121_splice	ENST00000269305	NM_001126112.2	121		4/11	0.201671658128787	2	FACETS	0.974	0.866	1	0.974	0.866	1	CLONAL	2	TRUE	0	0.256599529877556	2		284	320	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163298698	163298698	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs375054079	NA	P-0068323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	34	305	0	ENST00000271452.3:c.337+1G>T		p.X113_splice	ENST00000271452	NM_145697.2	113			0.256599529877556	3	FACETS	1	0.944	1	0.475	0.391	0.567	CLONAL	1	TRUE	0	0.256599529877556	3		305	210	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38991145	38991145	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	45	267	0	ENST00000357387.3:c.489T>A	p.Ser163Arg	p.S163R	ENST00000357387	NM_152756.3	163	agT/agA	7/38	0.256599529877556	2	FACETS	0.872	0.742	1	0.872	0.742	1	CLONAL	2	TRUE	0	0.256599529877556	2		267	201	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556780	29556965	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTTTCATCTCTCTAGGGGGTCTGTCTTCTGGGCATTGATGGCAAATCATTAATGTATTTGTTCTTTCTTTAGGTTTTATTGACTGATACCAATACTCAATTTGTAGAACAAACCATAGCTATAATGAAGAACTTGCTAGATAATCATACTGAAGGCAGCTCTGAACATCTAGGGCAAGCTAGCAT	AGTTTCATCTCTCTAGGGGGTCTGTCTTCTGGGCATTGATGGCAAATCATTAATGTATTTGTTCTTTCTTTAGGTTTTATTGACTGATACCAATACTCAATTTGTAGAACAAACCATAGCTATAATGAAGAACTTGCTAGATAATCATACTGAAGGCAGCTCTGAACATCTAGGGCAAGCTAGCAT	-	novel	NA	P-0068323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	35	238	0	ENST00000356175.3:c.2851-73_2963del		p.X951_splice	ENST00000356175	NM_000267.3	951		22/57	0.201671658128787	2	FACETS	1	0.936	1	0.659	0.545	0.785	CLONAL	1	TRUE	0	0.256599529877556	2		238	207	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853060	151853061	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	T	novel	NA	P-0068323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	70	333	0	ENST00000262189.6:c.11894_11895delinsA	p.Gly3965AspfsTer22	p.G3965Dfs*22	ENST00000262189	NM_170606.2	3965	gGC/gA	46/59	0.175995485199822	4	FACETS	1	0.972	1	0.728	0.636	0.826	CLONAL	1	TRUE	2	0.256599529877556	4		333	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0068325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	228	342	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.473368867811859	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.473368867811859	2		343	441	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214612	5214612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139132124	NA	P-0068325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	173	336	1	ENST00000357368.4:c.4454C>T	p.Ala1485Val	p.A1485V	ENST00000357368	NM_002850.3	1485	gCg/gTg	29/38	0.237198506987282	5	FACETS	0.87	0.808	0.933	0.87	0.808	0.933	INDETERMINATE	3	TRUE	2	0.473368867811859	5		337	479	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0068325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	105	300	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.368300599966576	4	FACETS	1	0.922	1	1	0.922	1	CLONAL	2	TRUE	2	0.473368867811859	4		300	321	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119689	108119689	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	76	274	0	ENST00000278616.4:c.1095G>T	p.Glu365Asp	p.E365D	ENST00000278616	NM_000051.3	365	gaG/gaT	9/63	0.278865868645313	5	FACETS	0.845	0.747	0.948	0.563	0.498	0.632	INDETERMINATE	2	TRUE	2	0.473368867811859	5		274	325	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416649	416649	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	164	360	0	ENST00000399788.2:c.3901C>A	p.Gln1301Lys	p.Q1301K	ENST00000399788	NM_001042603.1	1301	Caa/Aaa	23/28	0.473368867811859	2	FACETS	0.888	0.826	0.951	0.888	0.826	0.951	CLONAL	2	TRUE	0	0.473368867811859	2		360	390	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550407	39550407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773653046	NA	P-0068325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	109	300	0	ENST00000262039.4:c.518G>A	p.Ser173Asn	p.S173N	ENST00000262039	NM_002647.2	173	aGc/aAc	4/25	0.457608815961377	2	FACETS	0.847	0.773	0.922	0.847	0.773	0.922	CLONAL	2	TRUE	0	0.473368867811859	2		300	272	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268817	98268817	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	150	325	0	ENST00000331920.6:c.266A>T	p.Lys89Ile	p.K89I	ENST00000331920	NM_000264.3	89	aAa/aTa	2/24	0.278865868645313	5	FACETS	1	0.983	1	0.827	0.763	0.892	INDETERMINATE	2	TRUE	2	0.473368867811859	5		325	437	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939391	76939391	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	96	359	0	ENST00000373344.5:c.1357G>T	p.Glu453Ter	p.E453*	ENST00000373344	NM_000489.3	453	Gaa/Taa	9/35	0.237198506987282	5	FACETS	1	0.92	1	0.684	0.615	0.755	INDETERMINATE	2	TRUE	2	0.473368867811859	5		359	338	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	108	350	0				ENST00000310581	NM_198253.2	-/1132			0.430893709790291	7	FACETS	1	0.969	1	0.913	0.845	0.981	CLONAL	5	TRUE	1	0.430893709790291	7		350	190	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026133	71026133	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs775136381	NA	P-0068326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	74	273	1	ENST00000318789.4:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000318789	NM_032682.5	497	Cga/Tga	17/21	0.430893709790291	6	FACETS	0.963	0.85	1	0.482	0.425	0.542	CLONAL	2	TRUE	2	0.430893709790291	6		274	332	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0068326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	111	313	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.430893709790291	5	FACETS	1	0.961	1	0.74	0.671	0.812	CLONAL	2	TRUE	2	0.430893709790291	5		313	382	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0068326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	54	272	0	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	0.33637945524201	3	FACETS	0.846	0.746	0.948	0.846	0.746	0.948	CLONAL	3	TRUE	0	0.430893709790291	3		272	120	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326473	161326473	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1227520085	NA	P-0068326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	33	208	0	ENST00000367975.2:c.248C>G	p.Ser83Cys	p.S83C	ENST00000367975	NM_003001.3	83	tCt/tGt	5/6	0.430893709790291	13	FACETS	0.93	0.756	1			1	CLONAL	1	TRUE	NA	0.430893709790291	13		208	555	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450814	70450814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776722537	NA	P-0068326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	45	378	2	ENST00000373644.4:c.5654C>T	p.Ser1885Leu	p.S1885L	ENST00000373644	NM_030625.2	1885	tCg/tTg	12/12	0.430893709790291	5	FACETS	0.877	0.739	1	0.292	0.246	0.343	CLONAL	1	TRUE	2	0.430893709790291	5		380	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1555525429	NA	P-0068326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	124	287	0	ENST00000269305.4:c.782+1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.292637138926681	5	FACETS	0.891	0.822	0.96	0.712	0.657	0.768	CLONAL	4	TRUE	0	0.430893709790291	5		287	266	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180614	32180614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	231	264	0	ENST00000375023.3:c.2513G>A	p.Gly838Glu	p.G838E	ENST00000375023	NM_004557.3	838	gGa/gAa	16/30	0.430893709790291	9	FACETS	1	0.955	1			1	CLONAL	7	TRUE	NA	0.430893709790291	9		264	382	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776328	76776328	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	53	166	0	ENST00000373344.5:c.7138C>T	p.Gln2380Ter	p.Q2380*	ENST00000373344	NM_000489.3	2380	Cag/Tag	34/35	0.430893709790291	2	FACETS	1	0.922	1			1	CLONAL	3	TRUE	NA	0.430893709790291	2		166	80	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432491	49432491	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	65	357	0	ENST00000301067.7:c.8648A>G	p.Asn2883Ser	p.N2883S	ENST00000301067	NM_003482.3	2883	aAt/aGt	34/54	0.261878007356349	5	FACETS	0.916	0.803	1	0.611	0.535	0.691	CLONAL	2	TRUE	2	0.430893709790291	5		357	271	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608514	28608514	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0068326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	28	332	0	ENST00000241453.7:c.1628C>G	p.Ser543Ter	p.S543*	ENST00000241453	NM_004119.2	543	tCa/tGa	13/24	0.272772901823438	3	FACETS	0.981	0.793	1	0.491	0.396	0.595	CLONAL	1	TRUE	1	0.430893709790291	3		332	161	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864775	37864775	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	97	371	0	ENST00000269571.5:c.427C>G	p.Arg143Gly	p.R143G	ENST00000269571		143	Cga/Gga	3/27	0.430893709790291	5	FACETS	0.994	0.893	1	0.662	0.595	0.732	CLONAL	2	TRUE	2	0.430893709790291	5		371	373	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28605747	28605747	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	56	338	0	ENST00000253063.3:c.1351G>C	p.Glu451Gln	p.E451Q	ENST00000253063	NM_031459.4	451	Gag/Cag	9/10	0.430893709790291	5	FACETS	1	0.947	1	0.405	0.349	0.466	CLONAL	1	TRUE	2	0.430893709790291	5		338	352	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77991826	77991826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	166	397	0	ENST00000361507.4:c.197G>A	p.Cys66Tyr	p.C66Y	ENST00000361507	NM_080491.2	66	tGt/tAt	2/10	0.430893709790291	6	FACETS	1	0.944	1	1	0.944	1	CLONAL	3	TRUE	3	0.430893709790291	6		397	468	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	896813	896813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	43	376	0	ENST00000166345.3:c.292C>T	p.His98Tyr	p.H98Y	ENST00000166345	NM_004237.3	98	Cac/Tac	3/13	0.430893709790291	7	FACETS	0.971	0.813	1	0.162	0.135	0.191	CLONAL	1	TRUE	1	0.430893709790291	7		376	427	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41258472	41258472	+	splice_donor_variant	Splice_Site	SNP	C	C	G	rs80358042	NA	P-0068326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	29	257	0	ENST00000357654.3:c.212+1G>C		p.X71_splice	ENST00000357654	NM_007294.3	71			0.430893709790291	5	FACETS	1	0.909	1	0.408	0.33	0.495	CLONAL	1	TRUE	2	0.430893709790291	5		257	181	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169999023	169999024	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0068326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	20	252	0	ENST00000295797.4:c.953_954dup	p.His319CysfsTer15	p.H319Cfs*15	ENST00000295797	NM_002740.5	318	ctg/cTGtg	10/18	0.181057499677317	4	FACETS	0.942	0.728	1	0.314	0.242	0.396	INDETERMINATE	1	TRUE	1	0.430893709790291	4		252	141	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486089	29486089	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555605392	NA	P-0068326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	18	272	0	ENST00000356175.3:c.266C>A	p.Thr89Lys	p.T89K	ENST00000356175	NM_000267.3	89	aCa/aAa	3/57	0.430893709790291	5	FACETS	0.804	0.609	1	0.268	0.203	0.344	CLONAL	1	TRUE	2	0.430893709790291	5		272	171	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0068363-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	111	409	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.807440900625666	1	FACETS	0.922	0.858	0.984	0.922	0.858	0.984	CLONAL	1	TRUE	0	0.815127130675701	1		410	175	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552143	29552144	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1555613558	NA	P-0068363-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	111	394	0	ENST00000356175.3:c.1882dup	p.Tyr628LeufsTer6	p.Y628Lfs*6	ENST00000356175	NM_000267.3	626	ctt/cTtt	17/57	1	2	FACETS	0.854	0.777	0.932	0.854	0.777	0.932	CLONAL	1	TRUE	1	0.815127130675701	2		394	319	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676179	29676181	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0068363-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	118	433	0	ENST00000356175.3:c.7169_7171del	p.Arg2390del	p.R2390del	ENST00000356175	NM_000267.3	2390	AGA/-	48/57	1	2	FACETS	0.919	0.841	0.999	0.919	0.841	0.999	CLONAL	1	TRUE	1	0.815127130675701	2		433	315	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721213	39721213	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs781633039	NA	P-0068363-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	150	399	0	ENST00000361337.2:c.716A>G	p.Lys239Arg	p.K239R	ENST00000361337	NM_003286.2	239	aAg/aGg	9/21	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.815127130675701	2		399	363	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851688	134851688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068363-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	180	482	0	ENST00000398015.3:c.1094C>T	p.Ala365Val	p.A365V	ENST00000398015	NM_004441.4	365	gCa/gTa	5/16	1	2	FACETS	0.936	0.871	1	0.936	0.871	1	CLONAL	1	TRUE	1	0.815127130675701	2		482	472	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834552	156834552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540521894	NA	P-0068364-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	130	688	0	ENST00000524377.1:c.320C>T	p.Ala107Val	p.A107V	ENST00000524377	NM_002529.3	107	gCg/gTg	3/17	0.215030044187432	3	FACETS	1	0.942	1	0.526	0.477	0.577	INDETERMINATE	1	TRUE	1	0.374952105207045	3		688	783	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579321	7579322	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs587780067	NA	P-0068364-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	306	538	0	ENST00000269305.4:c.365_366del	p.Val122AspfsTer26	p.V122Dfs*26	ENST00000269305	NM_001126112.2	122	gTG/g	4/11	0.276584626660099	3	FACETS	0.879	0.834	0.925	0.879	0.834	0.925	CLONAL	3	TRUE	0	0.374952105207045	3		538	735	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121058	3121058	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1427351200	NA	P-0068364-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	115	667	0	ENST00000078429.4:c.961G>A	p.Asp321Asn	p.D321N	ENST00000078429	NM_002067.2	321	Gac/Aac	7/7	0.299731914232404	2	FACETS	0.969	0.875	1	0.485	0.437	0.534	CLONAL	1	TRUE	0	0.374952105207045	2		667	633	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40743960	40743960	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068364-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	52	627	0	ENST00000392038.2:c.747G>T	p.Glu249Asp	p.E249D	ENST00000392038	NM_001626.4	249	gaG/gaT	9/14	0.336488125332608	4	FACETS	0.425	0.361	0.496	0.106	0.09	0.124	SUBCLONAL	1	TRUE	0	0.374952105207045	4		627	897	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31015995	31015995	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068364-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	182	537	0	ENST00000375687.4:c.317C>A	p.Ala106Asp	p.A106D	ENST00000375687	NM_015338.5	106	gCt/gAt	5/13	0.270770315845681	5	FACETS	0.788	0.727	0.852	0.315	0.291	0.341	SUBCLONAL	2	TRUE	0	0.374952105207045	5		537	962	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591074	67591081	+	frameshift_variant	Frame_Shift_Del	DEL	ATCGAGAA	ATCGAGAA	-	novel	NA	P-0068364-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	45	436	0	ENST00000274335.5:c.1669_1676del	p.Arg557Ter	p.R557*	ENST00000274335		556	tATCGAGAA/t	12/15	0.336873909368662	2	FACETS	0.535	0.449	0.628	0.267	0.224	0.314	SUBCLONAL	1	TRUE	0	0.374952105207045	2		436	449	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971086	21971086	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068364-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	241	531	0	ENST00000304494.5:c.272del	p.Leu91ArgfsTer55	p.L91Rfs*55	ENST00000304494	NM_000077.4	91	cTg/cg	2/3	0.374952105207045	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.374952105207045	2		531	637	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0068367-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	18	176	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.28988772550723	3	FACETS	1	0.907	1	0.726	0.557	0.917	CLONAL	1	TRUE	1	0.327884660021782	3		176	88	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951847	2951847	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868687398	NA	P-0068367-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	41	649	0	ENST00000396946.4:c.3103G>A	p.Glu1035Lys	p.E1035K	ENST00000396946	NM_032415.4	1035	Gaa/Aaa	23/25	0.279096252257901	0	FACETS	0.31	0.257	0.368			1	SUBCLONAL	1	TRUE	0	0.327884660021782	0		649	543	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63810716	63810716	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068367-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	31	517	0	ENST00000279873.7:c.803T>G	p.Val268Gly	p.V268G	ENST00000279873	NM_032199.2	268	gTt/gGt	5/10	0.28988772550723	3	FACETS	0.483	0.39	0.588	0.241	0.195	0.294	SUBCLONAL	1	TRUE	1	0.327884660021782	3		517	456	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665639	86665716	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TTTTCAGATAGTAGTTCAGCACTTTAGTGAAGAACATTACATCTTTTACTTTGCAGGAGAAACTCCAGAACAAGCAGA	TTTTCAGATAGTAGTTCAGCACTTTAGTGAAGAACATTACATCTTTTACTTTGCAGGAGAAACTCCAGAACAAGCAGA	-	novel	NA	P-0068367-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	23	380	0	ENST00000274376.6:c.1620_1697del	p.Cys540_Glu566delinsTrp	p.C540_E566delinsW	ENST00000274376	NM_002890.2	540	tgTTTTCAGATAGTAGTTCAGCACTTTAGTGAAGAACATTACATCTTTTACTTTGCAGGAGAAACTCCAGAACAAGCAGAg/tgg	12/25	0.256243822279157	2	FACETS	0.861	0.677	1	0.43	0.338	0.535	CLONAL	1	TRUE	0	0.327884660021782	2		380	163	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998354	100998354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068367-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	26	571	0	ENST00000325455.5:c.1448C>T	p.Pro483Leu	p.P483L	ENST00000325455	NM_001202474.3	483	cCg/cTg	1/8	1	2	FACETS	0.475	0.376	0.588	0.475	0.376	0.588	SUBCLONAL	1	TRUE	1	0.327884660021782	2		571	334	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740839	58740839	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	202	440	0	ENST00000305921.3:c.1744C>T	p.Arg582Cys	p.R582C	ENST00000305921	NM_003620.3	582	Cgc/Tgc	6/6	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.54640399471482	2		440	700	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163441	47163444	+	frameshift_variant	Frame_Shift_Del	DEL	TAGA	TAGA	-	novel	NA	P-0068368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	161	423	0	ENST00000409792.3:c.2682_2685del	p.Ser894ArgfsTer4	p.S894Rfs*4	ENST00000409792	NM_014159.6	894	agTCTA/ag	3/21	0.544826825634047	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.54640399471482	1		423	417	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437748	52437748	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	201	451	0	ENST00000460680.1:c.1413del	p.Ser473ValfsTer98	p.S473Vfs*98	ENST00000460680	NM_004656.3	471	gcT/gc	13/17	0.544826825634047	1	FACETS	0.999	0.934	1	0.999	0.934	1	CLONAL	1	TRUE	0	0.54640399471482	1		451	535	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541663	120541663	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	418	471	0	ENST00000229340.5:c.194C>A	p.Ala65Glu	p.A65E	ENST00000229340	NM_006861.6	65	gCg/gAg	3/6	0.529114694639457	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.54640399471482	2		471	754	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322955	31322955	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	268	506	0	ENST00000412585.2:c.941G>C	p.Gly314Ala	p.G314A	ENST00000412585	NM_005514.6	314	gGc/gCc	5/8	1	2	FACETS	0.958	0.899	1	0.958	0.899	1	CLONAL	1	TRUE	1	0.54640399471482	2		506	1024	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183813	10183813	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	188	351	0	ENST00000256474.2:c.282del	p.Glu94AspfsTer65	p.E94Dfs*65	ENST00000256474	NM_000551.3	94	gaG/ga	1/3	0.544826825634047	1	FACETS	0.962	0.896	1	0.962	0.896	1	CLONAL	1	TRUE	0	0.54640399471482	1		351	520	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39774530	39774530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	61	448	0	ENST00000288319.7:c.622G>A	p.Val208Ile	p.V208I	ENST00000288319	NM_182918.3	208	Gtt/Att	5/10	0.359019445619063	4	FACETS	1	0.926	1	0.554	0.479	0.634	CLONAL	1	FALSE	2	0.359019445619063	4		448	417	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0068370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	210	252	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.520546252081549	5	FACETS	1	0.958	1	0.769	0.723	0.816	CLONAL	3	TRUE	1	0.520546252081549	5		253	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0068370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	188	313	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	0.520546252081549	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.520546252081549	2		313	350	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66520159	66520159	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	314	468	0	ENST00000358598.2:c.443A>G	p.Asp148Gly	p.D148G	ENST00000358598	NM_212471.2	148	gAt/gGt	5/11	0.520546252081549	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.520546252081549	3		468	483	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456475	32456477	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs1262223289	NA	P-0068370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	58	515	0	ENST00000332351.3:c.415_417del	p.Phe139del	p.F139del	ENST00000332351	NM_024426.4	139	TTC/-	1/10	0.520546252081549	3	FACETS	0.774	0.668	0.888	0.387	0.334	0.444	SUBCLONAL	1	TRUE	1	0.520546252081549	3		515	363	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157293	106157293	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs199638510	NA	P-0068370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	118	508	0	ENST00000380013.4:c.2194C>G	p.Pro732Ala	p.P732A	ENST00000380013	NM_001127208.2	732	Cca/Gca	3/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.520546252081549	2		508	417	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511713	66511713	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	83	355	1	ENST00000358598.2:c.173A>T	p.Glu58Val	p.E58V	ENST00000358598	NM_212471.2	58	gAg/gTg	2/11	0.60413168474771	2	FACETS	0.824	0.751	0.897	0.824	0.751	0.897	CLONAL	2	TRUE	0	0.653706520848932	2		356	154	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955063	1955063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	106	426	0	ENST00000382891.5:c.2150G>A	p.Cys717Tyr	p.C717Y	ENST00000382891	NM_133335.3	717	tGt/tAt	12/22	0.60413168474771	2	FACETS	0.943	0.875	1	0.943	0.875	1	CLONAL	2	TRUE	0	0.653706520848932	2		426	172	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29442846	29442846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	133	431	0	ENST00000544604.2:c.887G>A	p.Cys296Tyr	p.C296Y	ENST00000544604	NM_001206998.1	296	tGt/tAt	6/9	0.60413168474771	2	FACETS	0.837	0.779	0.895	0.837	0.779	0.895	CLONAL	2	TRUE	0	0.653706520848932	2		431	243	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941703	48941703	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	77	247	0	ENST00000267163.4:c.1013A>G	p.Asp338Gly	p.D338G	ENST00000267163	NM_000321.2	338	gAt/gGt	10/27	0.581435893594673	3	FACETS	0.922	0.85	0.99	0.922	0.85	0.99	CLONAL	3	TRUE	0	0.653706520848932	3		247	113	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342404	70342404	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	156	494	0	ENST00000374080.3:c.1295G>C	p.Gly432Ala	p.G432A	ENST00000374080		432	gGa/gCa	9/45	0.541618839870718	4	FACETS	0.972	0.9	1	0.972	0.9	1	CLONAL	2	TRUE	2	0.653706520848932	4		494	406	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526255	189526255	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068372-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	60	667	0	ENST00000264731.3:c.521del	p.Pro174ArgfsTer25	p.P174Rfs*25	ENST00000264731	NM_003722.4	173	ggC/gg	4/14	0.187298851447262	3	FACETS	0.96	0.827	1	0.48	0.413	0.553	CLONAL	1	TRUE	1	0.232500427983187	3		667	600	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0068373-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	155	504	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.371616696062264	3	FACETS	0.894	0.833	0.956	0.894	0.833	0.956	INDETERMINATE	2	TRUE	1	0.720940147079848	3		504	327	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	142	350	0				ENST00000310581	NM_198253.2	-/1132			0.620661350440894	3	FACETS	0.94	0.871	1	0.94	0.871	1	CLONAL	2	TRUE	1	0.620661350440894	3		350	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578213	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs864309495	NA	P-0068416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	306	464	0	ENST00000269305.4:c.636del	p.Arg213AspfsTer34	p.R213Dfs*34	ENST00000269305	NM_001126112.2	212	ttT/tt	6/11	0.620661350440894	2	FACETS	0.943	0.901	0.984	0.943	0.901	0.984	CLONAL	2	TRUE	0	0.620661350440894	2		464	523	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978895	25978895	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	202	351	0	ENST00000435504.4:c.1028T>G	p.Leu343Arg	p.L343R	ENST00000435504		343	cTc/cGc	10/13	0.225183695595919	4	FACETS	0.875	0.823	0.926	0.656	0.617	0.695	INDETERMINATE	3	TRUE	0	0.620661350440894	4		351	402	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172211	99172211	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	97	800	0	ENST00000074304.5:c.1777C>T	p.Pro593Ser	p.P593S	ENST00000074304	NM_001134224.1	593	Ccc/Tcc	17/26	0.225183695595919	4	FACETS	0.829	0.74	0.923	0.207	0.185	0.231	INDETERMINATE	1	TRUE	0	0.620661350440894	4		800	611	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862885	117862885	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1281760771	NA	P-0068416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	189	392	0	ENST00000297338.2:c.1592A>G	p.Lys531Arg	p.K531R	ENST00000297338	NM_006265.2	531	aAg/aGg	12/14	0.620661350440894	7	FACETS	0.984	0.911	1	0.492	0.455	0.53	CLONAL	2	TRUE	3	0.620661350440894	7		392	790	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973820	15973820	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	257	526	0	ENST00000268712.3:c.4172A>G	p.Asp1391Gly	p.D1391G	ENST00000268712	NM_006311.3	1391	gAc/gGc	31/46	0.620661350440894	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.620661350440894	2		526	408	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145308	58145308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1595110976	NA	P-0068416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	65	668	0	ENST00000257904.6:c.193G>A	p.Ala65Thr	p.A65T	ENST00000257904	NM_000075.3	65	Gct/Act	2/8	0.620661350440894	3	FACETS	0.334	0.289	0.383	0.167	0.144	0.192	SUBCLONAL	1	TRUE	1	0.620661350440894	3		668	822	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821389	32821389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781627254	NA	P-0068416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	238	685	0	ENST00000354258.4:c.205C>T	p.Pro69Ser	p.P69S	ENST00000354258	NM_000593.5	69	Ccc/Tcc	1/11	0.620661350440894	6	FACETS	0.855	0.799	0.914	0.428	0.399	0.457	CLONAL	2	TRUE	2	0.620661350440894	6		685	1005	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371708	225371708	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	72	495	0	ENST00000264414.4:c.896T>G	p.Met299Arg	p.M299R	ENST00000264414	NM_003590.4	299	aTg/aGg	7/16	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.369431931068356	2		495	381	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0068420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	30	411	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.331	0.266	0.405	0.331	0.266	0.405	SUBCLONAL	1	TRUE	1	0.396649556663999	2		411	457	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242478	55242478	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913229	NA	P-0068420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	85	382	0	ENST00000275493.2:c.2248G>C	p.Ala750Pro	p.A750P	ENST00000275493	NM_005228.3	750	Gca/Cca	19/28	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.396649556663999	2		382	374	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038529	47038529	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	20	248	0	ENST00000377604.3:c.691G>T	p.Glu231Ter	p.E231*	ENST00000377604	NM_001204468.1	231	Gag/Tag	8/24	1	1	FACETS	0.394	0.303	0.501	0.394	0.303	0.501	SUBCLONAL	1	TRUE	0	0.396649556663999	1		248	205	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242474	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGA	GAATTAAGA	-	rs121913436	NA	P-0068420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	80	392	0	ENST00000275493.2:c.2239_2247del	p.Leu747_Glu749del	p.L747_E749del	ENST00000275493	NM_005228.3	746	GAATTAAGA/-	19/28	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.396649556663999	2		392	375	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352585	70352694	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CACAGTCTCCCTTTTCTCCTCTCCTCTTCTCTCCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTTTCTCTTGTCTCTAG	CACAGTCTCCCTTTTCTCCTCTCCTCTTCTCTCCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTTTCTCTTGTCTCTAG	-	novel	NA	P-0068420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	49	64	0	ENST00000374080.3:c.4416-108_4417del		p.X1472_splice	ENST00000374080		1472			1	1	FACETS	0.88	0.79	0.965	1	0.983	1	CLONAL	3	TRUE	0	0.396649556663999	1		64	75	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266735	18266735	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80233027	NA	P-0068436-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	67	417	1	ENST00000222254.8:c.46C>T	p.Arg16Cys	p.R16C	ENST00000222254	NM_005027.3	16	Cgc/Tgc	2/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		418	642	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044700	47044700	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0068436-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	97	544	0	ENST00000377604.3:c.2101-1G>T		p.X701_splice	ENST00000377604	NM_001204468.1	701			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		544	859	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0068436-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	37	437	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		437	353	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526603	106526603	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068436-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	46	252	0	ENST00000359195.3:c.2896G>T	p.Gly966Trp	p.G966W	ENST00000359195	NM_002649.2	966	Ggg/Tgg	10/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		252	450	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219916	133219916	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068436-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	42	436	0	ENST00000320574.5:c.4445G>T	p.Gly1482Val	p.G1482V	ENST00000320574	NM_006231.2	1482	gGg/gTg	35/49	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		436	633	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158515	26158515	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068436-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	64	330	0	ENST00000289316.2:c.118G>C	p.Val40Leu	p.V40L	ENST00000289316	NM_138720.2	40	Gtg/Ctg	1/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		330	728	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215325	123215325	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068436-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	27	243	0	ENST00000218089.9:c.2871A>C	p.Leu957Phe	p.L957F	ENST00000218089	NM_001042749.1	957	ttA/ttC	28/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		243	421	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143134	30143134	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068436-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	63	461	0	ENST00000389048.3:c.392C>A	p.Ser131Tyr	p.S131Y	ENST00000389048	NM_004304.4	131	tCc/tAc	1/29	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		461	713	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578213	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs864309495	NA	P-0068437-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	77	464	0	ENST00000269305.4:c.636del	p.Arg213AspfsTer34	p.R213Dfs*34	ENST00000269305	NM_001126112.2	212	ttT/tt	6/11	1	2	FACETS	0.274	0.241	0.311	0.274	0.241	0.311	SUBCLONAL	1	TRUE	1	0.849249895271018	2		464	661	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0068437-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	178	504	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.849249895271018	2		504	398	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058036	27058036	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068437-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	291	403	0	ENST00000324856.7:c.1747del	p.Gln583SerfsTer36	p.Q583Sfs*36	ENST00000324856	NM_006015.4	582	Ccc/cc	3/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.849249895271018	2		403	608	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148716	20148727	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	TTGATTTTAGCT	TTGATTTTAGCT	A	novel	NA	P-0068437-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	58	184	0	ENST00000379607.5:c.338-2_347delinsT		p.X113_splice	ENST00000379607	NM_001412.3	113		6/7	1	2	FACETS	0.767	0.672	0.867	0.767	0.672	0.867	SUBCLONAL	1	TRUE	1	0.849249895271018	2		184	178	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068440-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	41	350	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.59	2		350	139	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770587	40770587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776338672	NA	P-0068440-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	89	324	0	ENST00000373198.4:c.2795G>A	p.Arg932His	p.R932H	ENST00000373198	NM_133170.3	932	cGc/cAc	19/32	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.59	2		324	239	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0068440-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	67	389	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.59	2		389	201	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0068442-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	140	440	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.481594891968575	1	FACETS	0.326	0.299	0.354	0.326	0.299	0.354	INDETERMINATE	1	TRUE	0	0.967495287387096	1		440	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578440	7578440	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0068442-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	447	439	0	ENST00000269305.4:c.490A>T	p.Lys164Ter	p.K164*	ENST00000269305	NM_001126112.2	164	Aag/Tag	5/11	0.967455848842105	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.967495287387096	1		439	466	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946283	55946283	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0068442-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	231	392	0	ENST00000263923.4:c.3896C>G	p.Ser1299Ter	p.S1299*	ENST00000263923	NM_002253.2	1299	tCa/tGa	30/30	0.220058273509694	3	FACETS	0.669	0.623	0.716	0.335	0.311	0.358	INDETERMINATE	1	TRUE	1	0.967495287387096	3		392	1059	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258986	16258986	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068442-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	219	400	0	ENST00000375759.3:c.6251G>A	p.Arg2084Lys	p.R2084K	ENST00000375759	NM_015001.2	2084	aGg/aAg	11/15	0.967495287387096	2	FACETS	0.649	0.606	0.692	0.324	0.303	0.346	SUBCLONAL	1	TRUE	0	0.967495287387096	2		400	698	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	77	385	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.818	0.721	0.921	0.818	0.721	0.921	CLONAL	1	TRUE	1	0.43	2		385	438	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073435	8073435	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1365672479	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	105	746	0	ENST00000377482.5:c.1224A>C	p.Glu408Asp	p.E408D	ENST00000377482	NM_018948.3	408	gaA/gaC	4/4	1	2	FACETS	0.86	0.773	0.952	0.86	0.773	0.952	CLONAL	1	TRUE	1	0.43	2		746	568	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	87	976	2	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	1	2	FACETS	0.797	0.707	0.891	0.797	0.707	0.891	SUBCLONAL	1	TRUE	1	0.43	2		978	508	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245461	16245461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465789087	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	88	640	2	ENST00000375759.3:c.1436C>T	p.Ala479Val	p.A479V	ENST00000375759	NM_015001.2	479	gCg/gTg	7/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.43	2		642	329	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254645	16254645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149954308	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	118	948	0	ENST00000375759.3:c.1910G>A	p.Arg637Gln	p.R637Q	ENST00000375759	NM_015001.2	637	cGa/cAa	11/15	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.43	2		948	500	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023197	27023197	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	53	682	0	ENST00000324856.7:c.303G>T	p.Lys101Asn	p.K101N	ENST00000324856	NM_006015.4	101	aaG/aaT	1/20	1	2	FACETS	0.841	0.722	0.97	0.841	0.722	0.97	CLONAL	1	TRUE	1	0.43	2		682	293	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094449	27094449	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	113	812	0	ENST00000324856.7:c.3157C>T	p.Arg1053Cys	p.R1053C	ENST00000324856	NM_006015.4	1053	Cgc/Tgc	11/20	1	2	FACETS	0.912	0.824	1	0.912	0.824	1	CLONAL	1	TRUE	1	0.43	2		812	576	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101624	27101624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1283627889	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	129	1228	0	ENST00000324856.7:c.4906C>T	p.Arg1636Trp	p.R1636W	ENST00000324856	NM_006015.4	1636	Cgg/Tgg	18/20	1	2	FACETS	0.998	0.908	1	0.998	0.908	1	CLONAL	1	TRUE	1	0.43	2		1228	601	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106342	27106342	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	140	983	0	ENST00000324856.7:c.5953T>C	p.Ser1985Pro	p.S1985P	ENST00000324856	NM_006015.4	1985	Tcc/Ccc	20/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.43	2		983	582	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	131	965	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.43	2		965	583	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531836	46531836	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	56	394	0	ENST00000262741.5:c.511G>T	p.Glu171Ter	p.E171*	ENST00000262741	NM_003629.3	171	Gaa/Taa	5/10	1	2	FACETS	0.901	0.778	1	0.901	0.778	1	CLONAL	1	TRUE	1	0.43	2		394	289	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462920	120462920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372061331	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	114	1030	1	ENST00000256646.2:c.5411C>T	p.Ser1804Leu	p.S1804L	ENST00000256646	NM_024408.3	1804	tCg/tTg	30/34	1	2	FACETS	0.932	0.842	1	0.932	0.842	1	CLONAL	1	TRUE	1	0.43	2		1031	569	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830872	156830872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	62	373	0	ENST00000524377.1:c.146G>A	p.Arg49Gln	p.R49Q	ENST00000524377	NM_002529.3	49	cGa/cAa	1/17	1	2	FACETS	0.817	0.71	0.932	0.817	0.71	0.932	CLONAL	1	TRUE	1	0.43	2		373	353	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163313556	163313556	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	77	537	0	ENST00000271452.3:c.703G>T	p.Glu235Ter	p.E235*	ENST00000271452	NM_145697.2	235	Gaa/Taa	10/14	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.43	2		537	316	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648328	206648328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782549877	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	107	920	0	ENST00000367120.3:c.349C>T	p.Arg117Cys	p.R117C	ENST00000367120	NM_014002.3	117	Cgc/Tgc	5/22	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.43	2		920	487	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63662043	63662043	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	111	780	1	ENST00000279873.7:c.147G>T	p.Lys49Asn	p.K49N	ENST00000279873	NM_032199.2	49	aaG/aaT	2/10	1	2	FACETS	0.839	0.756	0.927	0.839	0.756	0.927	CLONAL	1	TRUE	1	0.43	2		781	615	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851033	63851033	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202205668	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	111	1011	1	ENST00000279873.7:c.1811C>T	p.Pro604Leu	p.P604L	ENST00000279873	NM_032199.2	604	cCg/cTg	10/10	1	2	FACETS	0.887	0.8	0.979	0.887	0.8	0.979	CLONAL	1	TRUE	1	0.43	2		1012	582	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406295	70406295	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762257556	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	86	829	1	ENST00000373644.4:c.3809C>T	p.Thr1270Met	p.T1270M	ENST00000373644	NM_030625.2	1270	aCg/aTg	4/12	1	2	FACETS	0.855	0.759	0.956	0.855	0.759	0.956	CLONAL	1	TRUE	1	0.43	2		830	468	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406432	70406432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779743688	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	119	956	0	ENST00000373644.4:c.3946G>A	p.Asp1316Asn	p.D1316N	ENST00000373644	NM_030625.2	1316	Gat/Aat	4/12	1	2	FACETS	0.886	0.801	0.974	0.886	0.801	0.974	CLONAL	1	TRUE	1	0.43	2		956	625	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406445	70406445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781773145	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	112	899	5	ENST00000373644.4:c.3959G>A	p.Arg1320Gln	p.R1320Q	ENST00000373644	NM_030625.2	1320	cGg/cAg	4/12	1	2	FACETS	0.854	0.77	0.943	0.854	0.77	0.943	CLONAL	1	TRUE	1	0.43	2		904	610	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624245	89624245	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554890335	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	32	188	0	ENST00000371953.3:c.19G>T	p.Glu7Ter	p.E7*	ENST00000371953	NM_000314.4	7	Gag/Tag	1/9	1	2	FACETS	0.96	0.79	1	0.96	0.79	1	CLONAL	1	TRUE	1	0.43	2		188	155	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692940	89692940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746152219	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	85	759	2	ENST00000371953.3:c.424C>T	p.Arg142Trp	p.R142W	ENST00000371953	NM_000314.4	142	Cgg/Tgg	5/9	1	2	FACETS	0.924	0.821	1	0.924	0.821	1	CLONAL	1	TRUE	1	0.43	2		761	428	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717746	89717746	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1554825245	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	87	422	0	ENST00000371953.3:c.771C>A	p.Phe257Leu	p.F257L	ENST00000371953	NM_000314.4	257	ttC/ttA	7/9	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.43	2		422	371	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720870	89720870	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1554825652	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	52	272	0	ENST00000371953.3:c.1021T>G	p.Phe341Val	p.F341V	ENST00000371953	NM_000314.4	341	Ttt/Gtt	8/9	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.43	2		272	199	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710672	114710672	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs184454375	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	96	533	0	ENST00000543371.1:c.157G>A	p.Glu53Lys	p.E53K	ENST00000543371	NM_001198531.1	53	Gaa/Aaa	1/14	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.43	2		533	443	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243238	123243238	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs868056281	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	135	1257	2	ENST00000358487.5:c.2275C>T	p.Arg759Ter	p.R759*	ENST00000358487	NM_000141.4	759	Cga/Tga	17/18	1	2	FACETS	0.984	0.897	1	0.984	0.897	1	CLONAL	1	TRUE	1	0.43	2		1259	638	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47598975	47598975	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	118	907	2	ENST00000430070.2:c.625G>T	p.Asp209Tyr	p.D209Y	ENST00000430070	NM_018095.4	209	Gat/Tat	2/4	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.43	2		909	533	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912815	100912815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1000609240	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	11	692	0	ENST00000325455.5:c.2507G>A	p.Arg836Gln	p.R836Q	ENST00000325455	NM_001202474.3	836	cGa/cAa	7/8	1	2	FACETS	0.127	0.087	0.177	0.127	0.087	0.177	SUBCLONAL	1	TRUE	1	0.43	2		692	404	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922293	100922293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149186732	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	46	623	0	ENST00000325455.5:c.2219G>A	p.Arg740Gln	p.R740Q	ENST00000325455	NM_001202474.3	740	cGa/cAa	5/8	1	2	FACETS	0.839	0.712	0.977	0.839	0.712	0.977	CLONAL	1	TRUE	1	0.43	2		623	255	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195745	102195745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	129	900	0	ENST00000263464.3:c.505G>A	p.Glu169Lys	p.E169K	ENST00000263464	NM_001165.4	169	Gaa/Aaa	2/9	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.43	2		900	545	SUCCESS
ATM	472	MSKCC	GRCh37	11	108128229	108128229	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1555075658	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	63	615	0	ENST00000278616.4:c.2272G>T	p.Glu758Ter	p.E758*	ENST00000278616	NM_000051.3	758	Gaa/Taa	15/63	1	2	FACETS	0.91	0.793	1	0.91	0.793	1	CLONAL	1	TRUE	1	0.43	2		615	322	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163444	108163444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	79	652	0	ENST00000278616.4:c.4535C>T	p.Ala1512Val	p.A1512V	ENST00000278616	NM_000051.3	1512	gCt/gTt	30/63	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.43	2		652	342	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342392	118342392	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	73	714	0	ENST00000534358.1:c.518G>A	p.Arg173Gln	p.R173Q	ENST00000534358	NM_005933.3	173	cGa/cAa	3/36	1	2	FACETS	0.862	0.758	0.973	0.862	0.758	0.973	CLONAL	1	TRUE	1	0.43	2		714	394	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422312	422312	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	47	820	2	ENST00000399788.2:c.2946G>T	p.Lys982Asn	p.K982N	ENST00000399788	NM_001042603.1	982	aaG/aaT	20/28	1	2	FACETS	0.463	0.391	0.543	0.463	0.391	0.543	SUBCLONAL	1	TRUE	1	0.43	2		822	472	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231466	46231466	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	84	772	0	ENST00000334344.6:c.1306A>C	p.Ile436Leu	p.I436L	ENST00000334344	NM_152641.2	436	Att/Ctt	10/21	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.43	2		772	385	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285669	46285669	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1368075571	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	99	795	0	ENST00000334344.6:c.5029C>T	p.Arg1677Ter	p.R1677*	ENST00000334344	NM_152641.2	1677	Cga/Tga	17/21	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.43	2		795	456	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424512	49424512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756908474	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	89	997	0	ENST00000301067.7:c.13711G>A	p.Ala4571Thr	p.A4571T	ENST00000301067	NM_003482.3	4571	Gcc/Acc	41/54	1	2	FACETS	0.943	0.84	1	0.943	0.84	1	CLONAL	1	TRUE	1	0.43	2		997	439	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813334	102813334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1430553116	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	116	1250	0	ENST00000307046.8:c.355C>T	p.Arg119Cys	p.R119C	ENST00000307046	NM_001111285.1	119	Cgc/Tgc	3/4	1	2	FACETS	0.988	0.894	1	0.988	0.894	1	CLONAL	1	TRUE	1	0.43	2		1250	546	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112919929	112919929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1214510641	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	42	259	0	ENST00000351677.2:c.1144G>A	p.Val382Ile	p.V382I	ENST00000351677	NM_002834.3	382	Gtc/Atc	10/16	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.43	2		259	168	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118758	115118758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	99	1059	0	ENST00000257566.3:c.583G>A	p.Glu195Lys	p.E195K	ENST00000257566	NM_016569.3	195	Gaa/Aaa	2/8	1	2	FACETS	0.83	0.743	0.922	0.83	0.743	0.922	CLONAL	1	TRUE	1	0.43	2		1059	555	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536873	120536873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	83	739	1	ENST00000229340.5:c.313G>A	p.Glu105Lys	p.E105K	ENST00000229340	NM_006861.6	105	Gaa/Aaa	4/6	1	2	FACETS	0.963	0.855	1	0.963	0.855	1	CLONAL	1	TRUE	1	0.43	2		740	401	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225525	133225525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762090058	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	167	845	0	ENST00000320574.5:c.4139C>T	p.Ser1380Leu	p.S1380L	ENST00000320574	NM_006231.2	1380	tCg/tTg	32/49	1	2	FACETS	0.907	0.843	0.973	1	0.992	1	CLONAL	2	TRUE	1	0.43	2		845	428	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233948	133233948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778212434	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	91	1044	0	ENST00000320574.5:c.3446C>T	p.Ala1149Val	p.A1149V	ENST00000320574	NM_006231.2	1149	gCg/gTg	28/49	1	2	FACETS	0.809	0.721	0.903	0.809	0.721	0.903	CLONAL	1	TRUE	1	0.43	2		1044	523	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	99	893	0	ENST00000320574.5:c.1231G>C	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ctg	13/49	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.43	2		893	451	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21565530	21565530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	110	1106	2	ENST00000382592.4:c.356G>A	p.Arg119Gln	p.R119Q	ENST00000382592	NM_014572.2	119	cGa/cAa	3/8	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.43	2		1108	476	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896980	28896980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371199947	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	81	777	0	ENST00000282397.4:c.2900C>T	p.Ala967Val	p.A967V	ENST00000282397	NM_002019.4	967	gCg/gTg	21/30	1	2	FACETS	0.755	0.667	0.849	0.755	0.667	0.849	SUBCLONAL	1	TRUE	1	0.43	2		777	499	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945129	32945129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80359104	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	94	734	0	ENST00000380152.3:c.8524C>T	p.Arg2842Cys	p.R2842C	ENST00000380152		2842	Cgc/Tgc	20/27	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.43	2		734	380	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937017	48937017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752342013	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	76	697	2	ENST00000267163.4:c.785G>A	p.Arg262Gln	p.R262Q	ENST00000267163	NM_000321.2	262	cGg/cAg	8/27	1	2	FACETS	0.787	0.693	0.888	0.787	0.693	0.888	SUBCLONAL	1	TRUE	1	0.43	2		699	449	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955517	48955517	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	59	637	0	ENST00000267163.4:c.1633G>T	p.Glu545Ter	p.E545*	ENST00000267163	NM_000321.2	545	Gaa/Taa	17/27	1	2	FACETS	0.839	0.727	0.96	0.839	0.727	0.96	CLONAL	1	TRUE	1	0.43	2		637	327	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347916	73347916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139907646	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	74	682	0	ENST00000377767.4:c.1145G>A	p.Arg382Gln	p.R382Q	ENST00000377767	NM_014953.3	382	cGa/cAa	8/21	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.43	2		682	341	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435798	110435798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1240854451	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	74	1198	0	ENST00000375856.3:c.2603C>T	p.Ser868Leu	p.S868L	ENST00000375856	NM_003749.2	868	tCg/tTg	1/2	1	2	FACETS	0.854	0.751	0.963	0.854	0.751	0.963	CLONAL	1	TRUE	1	0.43	2		1198	403	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135325	30135325	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	83	814	0	ENST00000331968.5:c.493G>T	p.Glu165Ter	p.E165*	ENST00000331968	NM_002742.2	165	Gaa/Taa	3/18	1	2	FACETS	0.766	0.678	0.86	0.766	0.678	0.86	SUBCLONAL	1	TRUE	1	0.43	2		814	504	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060728	38060728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	119	1138	1	ENST00000250448.2:c.1261G>A	p.Glu421Lys	p.E421K	ENST00000250448	NM_004496.3	421	Gaa/Aaa	2/2	1	2	FACETS	0.98	0.887	1	0.98	0.887	1	CLONAL	1	TRUE	1	0.43	2		1139	565	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060842	38060842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285265540	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	105	1341	2	ENST00000250448.2:c.1147G>A	p.Glu383Lys	p.E383K	ENST00000250448	NM_004496.3	383	Gag/Aag	2/2	1	2	FACETS	0.898	0.807	0.993	0.898	0.807	0.993	CLONAL	1	TRUE	1	0.43	2		1343	544	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748312	43748312	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	54	814	0	ENST00000382044.4:c.2494G>T	p.Glu832Ter	p.E832*	ENST00000382044	NM_001141980.1	832	Gag/Tag	12/28	1	2	FACETS	0.499	0.427	0.579	0.499	0.427	0.579	SUBCLONAL	1	TRUE	1	0.43	2		814	503	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678572	88678572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1161765368	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	66	1165	1	ENST00000360948.2:c.964G>A	p.Glu322Lys	p.E322K	ENST00000360948	NM_001012338.2	322	Gag/Aag	9/19	1	2	FACETS	0.682	0.594	0.777	0.682	0.594	0.777	SUBCLONAL	1	TRUE	1	0.43	2		1166	450	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293070	91293070	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs569086568	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	88	808	0	ENST00000355112.3:c.572G>T	p.Arg191Ile	p.R191I	ENST00000355112	NM_000057.2	191	aGa/aTa	3/22	1	2	FACETS	0.902	0.802	1	0.902	0.802	1	CLONAL	1	TRUE	1	0.43	2		808	454	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312713	91312713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1279814185	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	87	625	1	ENST00000355112.3:c.2452C>T	p.Arg818Cys	p.R818C	ENST00000355112	NM_000057.2	818	Cgc/Tgc	12/22	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.43	2		626	398	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636803	2636803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	110	948	2	ENST00000342085.4:c.1252G>A	p.Asp418Asn	p.D418N	ENST00000342085	NM_002613.4	418	Gat/Aat	11/14	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.43	2		950	499	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647143	2647143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	79	861	0	ENST00000342085.4:c.1421G>A	p.Arg474Gln	p.R474Q	ENST00000342085	NM_002613.4	474	cGa/cAa	13/14	1	2	FACETS	0.835	0.738	0.939	0.835	0.738	0.939	CLONAL	1	TRUE	1	0.43	2		861	440	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632602	3632602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377329498	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	83	1241	3	ENST00000294008.3:c.5246C>T	p.Ala1749Val	p.A1749V	ENST00000294008	NM_032444.2	1749	gCg/gTg	15/15	1	2	FACETS	0.848	0.752	0.951	0.848	0.752	0.951	CLONAL	1	TRUE	1	0.43	2		1244	455	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640200	3640200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs974413437	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	78	880	0	ENST00000294008.3:c.3439G>A	p.Glu1147Lys	p.E1147K	ENST00000294008	NM_032444.2	1147	Gaa/Aaa	12/15	1	2	FACETS	0.838	0.739	0.943	0.838	0.739	0.943	CLONAL	1	TRUE	1	0.43	2		880	433	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647460	3647460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776394340	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	104	1300	0	ENST00000294008.3:c.1603G>A	p.Ala535Thr	p.A535T	ENST00000294008	NM_032444.2	535	Gca/Aca	7/15	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.43	2		1300	455	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652140	3652140	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759447034	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	97	1010	1	ENST00000294008.3:c.929G>A	p.Arg310Gln	p.R310Q	ENST00000294008	NM_032444.2	310	cGa/cAa	4/15	1	2	FACETS	0.908	0.813	1	0.908	0.813	1	CLONAL	1	TRUE	1	0.43	2		1011	497	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790490	3790490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1207183178	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	99	541	1	ENST00000262367.5:c.4043G>A	p.Arg1348His	p.R1348H	ENST00000262367	NM_004380.2	1348	cGc/cAc	24/31	1	2	FACETS	0.83	0.743	0.922	0.83	0.743	0.922	CLONAL	1	TRUE	1	0.43	2		542	555	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900884	3900884	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	51	806	2	ENST00000262367.5:c.212C>A	p.Ser71Ter	p.S71*	ENST00000262367	NM_004380.2	71	tCg/tAg	2/31	1	2	FACETS	0.425	0.361	0.496	0.425	0.361	0.496	SUBCLONAL	1	TRUE	1	0.43	2		808	558	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274007	10274007	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	31	1205	0	ENST00000330684.3:c.262G>A	p.Asp88Asn	p.D88N	ENST00000330684	NM_001134407.1	88	Gac/Aac	2/13	1	2	FACETS	0.316	0.255	0.385	0.316	0.255	0.385	SUBCLONAL	1	TRUE	1	0.43	2		1205	456	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641409	23641409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749602688	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	83	865	2	ENST00000261584.4:c.2066C>T	p.Ser689Leu	p.S689L	ENST00000261584	NM_024675.3	689	tCg/tTg	5/13	1	2	FACETS	0.781	0.692	0.877	0.781	0.692	0.877	SUBCLONAL	1	TRUE	1	0.43	2		867	494	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646626	23646626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749461008	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	87	716	0	ENST00000261584.4:c.1241G>A	p.Arg414Gln	p.R414Q	ENST00000261584	NM_024675.3	414	cGa/cAa	4/13	1	2	FACETS	0.874	0.777	0.977	0.874	0.777	0.977	CLONAL	1	TRUE	1	0.43	2		716	463	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821082	72821082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458157669	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	45	765	0	ENST00000268489.5:c.11093C>T	p.Thr3698Met	p.T3698M	ENST00000268489	NM_006885.3	3698	aCg/aTg	10/10	1	2	FACETS	0.43	0.361	0.506	0.43	0.361	0.506	SUBCLONAL	1	TRUE	1	0.43	2		765	487	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992568	72992568	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	110	1065	2	ENST00000268489.5:c.1477G>T	p.Gly493Ter	p.G493*	ENST00000268489	NM_006885.3	493	Gga/Tga	2/10	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.43	2		1067	505	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347552	89347552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369218399	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	73	1199	1	ENST00000301030.4:c.5398G>A	p.Glu1800Lys	p.E1800K	ENST00000301030	NM_001256183.1	1800	Gag/Aag	9/13	1	2	FACETS	0.781	0.685	0.882	0.781	0.685	0.882	SUBCLONAL	1	TRUE	1	0.43	2		1200	435	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349799	89349799	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	99	701	1	ENST00000301030.4:c.3151G>T	p.Glu1051Ter	p.E1051*	ENST00000301030	NM_001256183.1	1051	Gaa/Taa	9/13	1	2	FACETS	0.973	0.873	1	0.973	0.873	1	CLONAL	1	TRUE	1	0.43	2		702	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	118	1096	0	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	1	2	FACETS	0.989	0.896	1	0.989	0.896	1	CLONAL	1	TRUE	1	0.43	2		1096	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579348	7579348	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	36	993	0	ENST00000269305.4:c.339C>A	p.Phe113Leu	p.F113L	ENST00000269305	NM_001126112.2	113	ttC/ttA	4/11	1	2	FACETS	0.287	0.235	0.346	0.287	0.235	0.346	SUBCLONAL	1	TRUE	1	0.43	2		993	583	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013719	12013719	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	68	595	0	ENST00000353533.5:c.661G>T	p.Glu221Ter	p.E221*	ENST00000353533	NM_003010.3	221	Gaa/Taa	6/11	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.43	2		595	312	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	115	830	2	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	1	2	FACETS	0.9	0.813	0.992	0.9	0.813	0.992	CLONAL	1	TRUE	1	0.43	2		832	594	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	70	482	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.852	0.747	0.965	0.852	0.747	0.965	CLONAL	1	TRUE	1	0.43	2		482	382	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701036	29701036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1475978079	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	100	879	0	ENST00000356175.3:c.8320G>A	p.Asp2774Asn	p.D2774N	ENST00000356175	NM_000267.3	2774	Gac/Aac	57/57	1	2	FACETS	0.938	0.841	1	0.938	0.841	1	CLONAL	1	TRUE	1	0.43	2		879	496	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690456	33690456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770564755	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	110	1095	0	ENST00000308377.4:c.371G>A	p.Arg124His	p.R124H	ENST00000308377	NM_152270.3	124	cGc/cAc	2/5	1	2	FACETS	0.815	0.733	0.9	0.815	0.733	0.9	CLONAL	1	TRUE	1	0.43	2		1095	628	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474351	40474351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780466766	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	120	842	2	ENST00000264657.5:c.2050G>A	p.Gly684Arg	p.G684R	ENST00000264657	NM_139276.2	684	Gga/Aga	21/24	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.43	2		844	495	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244664	41244664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80356955	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	108	912	0	ENST00000357654.3:c.2884G>A	p.Glu962Lys	p.E962K	ENST00000357654	NM_007294.3	962	Gaa/Aaa	10/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.43	2		912	402	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696405	47696405	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	79	819	2	ENST00000347630.2:c.418G>T	p.Asp140Tyr	p.D140Y	ENST00000347630	NM_001007230.1	140	Gat/Tat	6/11	1	2	FACETS	0.785	0.693	0.883	0.785	0.693	0.883	SUBCLONAL	1	TRUE	1	0.43	2		821	468	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770859	59770859	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1060501736	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	65	668	0	ENST00000259008.2:c.2507G>T	p.Arg836Ile	p.R836I	ENST00000259008	NM_032043.2	836	aGa/aTa	18/20	1	2	FACETS	0.911	0.795	1	0.911	0.795	1	CLONAL	1	TRUE	1	0.43	2		668	332	SUCCESS
YES1	7525	MSKCC	GRCh37	18	751726	751726	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1010928891	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	14	368	0	ENST00000314574.4:c.350G>T	p.Arg117Ile	p.R117I	ENST00000314574	NM_005433.3	117	aGa/aTa	3/12	1	2	FACETS	0.256	0.185	0.343	0.256	0.185	0.343	SUBCLONAL	1	TRUE	1	0.43	2		368	254	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570433	39570433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747825815	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	49	477	0	ENST00000262039.4:c.629G>A	p.Arg210Gln	p.R210Q	ENST00000262039	NM_002647.2	210	cGa/cAa	6/25	1	2	FACETS	0.747	0.636	0.868	0.747	0.636	0.868	SUBCLONAL	1	TRUE	1	0.43	2		477	305	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39623702	39623702	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	62	561	0	ENST00000262039.4:c.2109T>G	p.Phe703Leu	p.F703L	ENST00000262039	NM_002647.2	703	ttT/ttG	20/25	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.43	2		561	233	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581268	48581268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752575871	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	114	1028	0	ENST00000342988.3:c.572C>T	p.Ser191Leu	p.S191L	ENST00000342988	NM_005359.5	191	tCg/tTg	5/12	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.43	2		1028	521	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267389	7267389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767658477	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	95	1051	0	ENST00000302850.5:c.619G>A	p.Glu207Lys	p.E207K	ENST00000302850	NM_000208.2	207	Gaa/Aaa	2/22	1	2	FACETS	0.837	0.747	0.931	0.837	0.747	0.931	CLONAL	1	TRUE	1	0.43	2		1051	528	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299878	15299878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	108	1120	1	ENST00000263388.2:c.1300G>A	p.Glu434Lys	p.E434K	ENST00000263388	NM_000435.2	434	Gag/Aag	8/33	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.43	2		1121	496	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943652	17943652	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	93	1094	0	ENST00000458235.1:c.2437G>T	p.Asp813Tyr	p.D813Y	ENST00000458235	NM_000215.3	813	Gac/Tac	18/24	1	2	FACETS	0.801	0.714	0.893	0.801	0.714	0.893	CLONAL	1	TRUE	1	0.43	2		1094	540	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228800	36228800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393734909	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	95	1102	0	ENST00000222270.7:c.7699C>T	p.Arg2567Cys	p.R2567C	ENST00000222270	NM_014727.1	2567	Cgt/Tgt	35/37	1	2	FACETS	0.817	0.729	0.909	0.817	0.729	0.909	CLONAL	1	TRUE	1	0.43	2		1102	541	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905304	50905304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	101	1342	4	ENST00000440232.2:c.512C>T	p.Ala171Val	p.A171V	ENST00000440232	NM_002691.3	171	gCc/gTc	5/27	1	2	FACETS	0.965	0.866	1	0.965	0.866	1	CLONAL	1	TRUE	1	0.43	2		1346	487	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964903	25964903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561088610	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	106	966	2	ENST00000435504.4:c.4303C>T	p.Arg1435Trp	p.R1435W	ENST00000435504		1435	Cgg/Tgg	13/13	1	2	FACETS	0.87	0.782	0.962	0.87	0.782	0.962	CLONAL	1	TRUE	1	0.43	2		968	567	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965013	25965013	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs190294224	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	119	867	3	ENST00000435504.4:c.4193C>T	p.Ser1398Leu	p.S1398L	ENST00000435504		1398	tCg/tTg	13/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.43	2		870	508	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982356	25982356	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	155	542	0	ENST00000435504.4:c.934C>T	p.Arg312Ter	p.R312*	ENST00000435504		312	Cga/Tga	9/13	1	2	FACETS	0.832	0.77	0.897	1	0.991	1	CLONAL	2	TRUE	1	0.43	2		542	433	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416493	29416493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1182539285	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	106	1032	0	ENST00000389048.3:c.4460C>T	p.Ser1487Leu	p.S1487L	ENST00000389048	NM_004304.4	1487	tCg/tTg	29/29	1	2	FACETS	0.83	0.746	0.919	0.83	0.746	0.919	CLONAL	1	TRUE	1	0.43	2		1032	594	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702296	47702296	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1361816581	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	83	670	2	ENST00000233146.2:c.1892G>T	p.Arg631Ile	p.R631I	ENST00000233146	NM_000251.2	631	aGa/aTa	12/16	1	2	FACETS	0.902	0.8	1	0.902	0.8	1	CLONAL	1	TRUE	1	0.43	2		672	428	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	80	684	2	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.43	2		686	332	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715794	61715794	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	93	634	0	ENST00000401558.2:c.2135G>T	p.Arg712Ile	p.R712I	ENST00000401558	NM_003400.3	712	aGa/aTa	18/25	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.43	2		634	425	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736158	204736158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs963824682	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	114	912	0	ENST00000302823.3:c.515C>T	p.Ser172Leu	p.S172L	ENST00000302823	NM_005214.4	172	tCg/tTg	3/4	1	2	FACETS	0.929	0.839	1	0.929	0.839	1	CLONAL	1	TRUE	1	0.43	2		912	571	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530085	212530085	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561997094	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	88	878	0	ENST00000342788.4:c.1834C>T	p.Arg612Trp	p.R612W	ENST00000342788	NM_005235.2	612	Cgg/Tgg	15/28	1	2	FACETS	0.751	0.667	0.84	0.751	0.667	0.84	SUBCLONAL	1	TRUE	1	0.43	2		878	545	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989562	212989562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755026855	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	101	858	1	ENST00000342788.4:c.149G>A	p.Arg50His	p.R50H	ENST00000342788	NM_005235.2	50	cGc/cAc	2/28	1	2	FACETS	0.888	0.797	0.985	0.888	0.797	0.985	CLONAL	1	TRUE	1	0.43	2		859	529	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379426	225379426	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	78	731	0	ENST00000264414.4:c.442C>T	p.Arg148Ter	p.R148*	ENST00000264414	NM_003590.4	148	Cga/Tga	4/16	1	2	FACETS	0.921	0.814	1	0.921	0.814	1	CLONAL	1	TRUE	1	0.43	2		731	394	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023108	31023108	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147895689	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	117	916	0	ENST00000375687.4:c.2593G>A	p.Glu865Lys	p.E865K	ENST00000375687	NM_015338.5	865	Gaa/Aaa	13/13	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.43	2		916	522	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770617	40770617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749916516	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	103	933	0	ENST00000373198.4:c.2765C>T	p.Ser922Leu	p.S922L	ENST00000373198	NM_133170.3	922	tCg/tTg	19/32	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.43	2		933	469	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306638	41306638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	67	805	1	ENST00000373198.4:c.1021G>A	p.Asp341Asn	p.D341N	ENST00000373198	NM_133170.3	341	Gac/Aac	7/32	1	2	FACETS	0.781	0.682	0.888	0.781	0.682	0.888	SUBCLONAL	1	TRUE	1	0.43	2		806	399	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256699	46256699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749607074	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	99	614	0	ENST00000371998.3:c.755G>A	p.Arg252His	p.R252H	ENST00000371998		252	cGc/cAc	8/23	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.43	2		614	391	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164712	36164712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	122	1352	0	ENST00000300305.3:c.1163C>T	p.Ser388Leu	p.S388L	ENST00000300305		388	tCg/tTg	8/8	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.43	2		1352	493	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231773	36231773	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1569061762	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	17	1293	0	ENST00000300305.3:c.611G>A	p.Arg204Gln	p.R204Q	ENST00000300305		204	cGa/cAa	5/8	1	2	FACETS	0.119	0.088	0.156	0.119	0.088	0.156	SUBCLONAL	1	TRUE	1	0.43	2		1293	666	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755585	39755585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	104	1250	1	ENST00000288319.7:c.1180G>A	p.Gly394Arg	p.G394R	ENST00000288319	NM_182918.3	394	Ggg/Agg	10/10	1	2	FACETS	0.934	0.839	1	0.934	0.839	1	CLONAL	1	TRUE	1	0.43	2		1251	518	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655428	45655428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372772395	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	107	1152	0	ENST00000407780.3:c.424G>A	p.Val142Ile	p.V142I	ENST00000407780	NM_001283052.1	142	Gtc/Atc	4/7	1	2	FACETS	0.999	0.901	1	0.999	0.901	1	CLONAL	1	TRUE	1	0.43	2		1152	498	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537100	41537100	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	100	820	0	ENST00000263253.7:c.1927G>T	p.Glu643Ter	p.E643*	ENST00000263253	NM_001429.3	643	Gaa/Taa	10/31	1	2	FACETS	0.898	0.805	0.996	0.898	0.805	0.996	CLONAL	1	TRUE	1	0.43	2		820	518	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732958	30732958	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	116	1051	2	ENST00000295754.5:c.1571A>G	p.Asp524Gly	p.D524G	ENST00000295754	NM_003242.5	524	gAc/gGc	7/7	1	2	FACETS	0.979	0.886	1	0.979	0.886	1	CLONAL	1	TRUE	1	0.43	2		1053	551	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147533	47147533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	126	1223	0	ENST00000409792.3:c.4793G>A	p.Arg1598Gln	p.R1598Q	ENST00000409792	NM_014159.6	1598	cGa/cAa	6/21	1	2	FACETS	0.987	0.896	1	0.987	0.896	1	CLONAL	1	TRUE	1	0.43	2		1223	594	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164118	47164118	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	60	618	0	ENST00000409792.3:c.2008G>T	p.Glu670Ter	p.E670*	ENST00000409792	NM_014159.6	670	Gaa/Taa	3/21	1	2	FACETS	0.936	0.813	1	0.936	0.813	1	CLONAL	1	TRUE	1	0.43	2		618	298	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723053	49723053	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	35	329	0	ENST00000449682.2:c.1363G>A	p.Asp455Asn	p.D455N	ENST00000449682	NM_020998.3	455	Gac/Aac	11/18	1	2	FACETS	0.963	0.8	1	0.963	0.8	1	CLONAL	1	TRUE	1	0.43	2		329	169	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014163	70014163	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868519483	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	104	1035	0	ENST00000394351.3:c.1024G>A	p.Asp342Asn	p.D342N	ENST00000394351	NM_000248.3	342	Gat/Aat	9/9	1	2	FACETS	0.844	0.758	0.935	0.844	0.758	0.935	CLONAL	1	TRUE	1	0.43	2		1035	573	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499516	89499516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773476878	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	83	460	1	ENST00000336596.2:c.2686G>A	p.Ala896Thr	p.A896T	ENST00000336596	NM_005233.5	896	Gca/Aca	15/17	1	2	FACETS	0.837	0.742	0.939	0.837	0.742	0.939	CLONAL	1	TRUE	1	0.43	2		461	461	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960059	134960059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	83	1140	1	ENST00000398015.3:c.2416G>A	p.Asp806Asn	p.D806N	ENST00000398015	NM_004441.4	806	Gac/Aac	13/16	1	2	FACETS	0.704	0.623	0.792	0.704	0.623	0.792	SUBCLONAL	1	TRUE	1	0.43	2		1141	548	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968251	134968251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373797543	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	94	1043	0	ENST00000398015.3:c.2764G>A	p.Ala922Thr	p.A922T	ENST00000398015	NM_004441.4	922	Gcc/Acc	15/16	1	2	FACETS	0.856	0.764	0.953	0.856	0.764	0.953	CLONAL	1	TRUE	1	0.43	2		1043	511	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279197	142279197	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs200968047	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	81	611	0	ENST00000350721.4:c.1449G>T	p.Lys483Asn	p.K483N	ENST00000350721	NM_001184.3	483	aaG/aaT	6/47	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.43	2		611	355	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260151	149260151	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1307297959	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	89	807	1	ENST00000360632.3:c.742C>T	p.Arg248Ter	p.R248*	ENST00000360632	NM_015472.4	248	Cga/Tga	4/7	1	2	FACETS	0.924	0.823	1	0.924	0.823	1	CLONAL	1	TRUE	1	0.43	2		808	448	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178943785	178943785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	76	544	0	ENST00000263967.3:c.2452C>T	p.Arg818Cys	p.R818C	ENST00000263967	NM_006218.2	818	Cgt/Tgt	17/21	1	2	FACETS	0.996	0.88	1	0.996	0.88	1	CLONAL	1	TRUE	1	0.43	2		544	355	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947119	178947119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199943173	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	101	777	4	ENST00000263967.3:c.2555G>A	p.Arg852Gln	p.R852Q	ENST00000263967	NM_006218.2	852	cGa/cAa	18/21	1	2	FACETS	0.898	0.806	0.996	0.898	0.806	0.996	CLONAL	1	TRUE	1	0.43	2		781	523	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952075	178952075	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	90	760	0	ENST00000263967.3:c.3130A>C	p.Asn1044His	p.N1044H	ENST00000263967	NM_006218.2	1044	Aat/Cat	21/21	1	2	FACETS	0.945	0.843	1	0.945	0.843	1	CLONAL	1	TRUE	1	0.43	2		760	443	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430749	181430749	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	82	1138	0	ENST00000325404.1:c.601G>A	p.Asp201Asn	p.D201N	ENST00000325404	NM_003106.3	201	Gac/Aac	1/1	1	2	FACETS	0.76	0.672	0.853	0.76	0.672	0.853	SUBCLONAL	1	TRUE	1	0.43	2		1138	502	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665375	182665375	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	43	446	0	ENST00000292782.4:c.566G>T	p.Arg189Ile	p.R189I	ENST00000292782	NM_020640.2	189	aGa/aTa	5/7	1	2	FACETS	0.758	0.638	0.888	0.758	0.638	0.888	SUBCLONAL	1	TRUE	1	0.43	2		446	264	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451405	187451405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	92	795	0	ENST00000232014.4:c.77G>A	p.Arg26Gln	p.R26Q	ENST00000232014	NM_001130845.1	26	cGg/cAg	3/10	1	2	FACETS	0.698	0.621	0.78	0.698	0.621	0.78	SUBCLONAL	1	TRUE	1	0.43	2		795	613	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526268	189526268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	37	1330	1	ENST00000264731.3:c.532G>A	p.Asp178Asn	p.D178N	ENST00000264731	NM_003722.4	178	Gac/Aac	4/14	1	2	FACETS	0.255	0.209	0.306	0.255	0.209	0.306	SUBCLONAL	1	TRUE	1	0.43	2		1331	675	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612250	189612250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749906547	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	101	905	1	ENST00000264731.3:c.2002C>T	p.Arg668Cys	p.R668C	ENST00000264731	NM_003722.4	668	Cgc/Tgc	14/14	1	2	FACETS	0.985	0.885	1	0.985	0.885	1	CLONAL	1	TRUE	1	0.43	2		906	477	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747912	41747912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	74	1087	0	ENST00000226382.2:c.857C>T	p.Ser286Leu	p.S286L	ENST00000226382	NM_003924.3	286	tCg/tTg	3/3	1	2	FACETS	0.878	0.773	0.99	0.878	0.773	0.99	CLONAL	1	TRUE	1	0.43	2		1087	392	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748320	41748320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	82	1004	0	ENST00000226382.2:c.449G>A	p.Arg150His	p.R150H	ENST00000226382	NM_003924.3	150	cGc/cAc	3/3	1	2	FACETS	0.82	0.726	0.92	0.82	0.726	0.92	CLONAL	1	TRUE	1	0.43	2		1004	465	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131211	55131211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772605262	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	91	698	0	ENST00000257290.5:c.754G>A	p.Glu252Lys	p.E252K	ENST00000257290	NM_006206.4	252	Gaa/Aaa	5/23	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.43	2		698	394	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146636	55146636	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	80	665	0	ENST00000257290.5:c.2310G>T	p.Lys770Asn	p.K770N	ENST00000257290	NM_006206.4	770	aaG/aaT	16/23	1	2	FACETS	0.961	0.852	1	0.961	0.852	1	CLONAL	1	TRUE	1	0.43	2		665	387	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561767	55561767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780349712	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	110	909	1	ENST00000288135.5:c.157G>A	p.Glu53Lys	p.E53K	ENST00000288135	NM_000222.2	53	Gag/Aag	2/21	1	2	FACETS	0.867	0.781	0.958	0.867	0.781	0.958	CLONAL	1	TRUE	1	0.43	2		910	590	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604673	55604673	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773828910	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	83	946	0	ENST00000288135.5:c.2881G>A	p.Gly961Ser	p.G961S	ENST00000288135	NM_000222.2	961	Ggc/Agc	21/21	1	2	FACETS	0.735	0.65	0.826	0.735	0.65	0.826	SUBCLONAL	1	TRUE	1	0.43	2		946	525	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961109	55961109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374755237	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	86	667	2	ENST00000263923.4:c.2831G>A	p.Arg944Gln	p.R944Q	ENST00000263923	NM_002253.2	944	cGa/cAa	21/30	1	2	FACETS	0.868	0.771	0.97	0.868	0.771	0.97	CLONAL	1	TRUE	1	0.43	2		669	461	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968610	55968610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374980446	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	89	824	0	ENST00000263923.4:c.2053G>A	p.Glu685Lys	p.E685K	ENST00000263923	NM_002253.2	685	Gaa/Aaa	14/30	1	2	FACETS	0.879	0.782	0.981	0.879	0.782	0.981	CLONAL	1	TRUE	1	0.43	2		824	471	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130126	143130126	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769344936	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	77	755	0	ENST00000262992.4:c.890G>A	p.Arg297Gln	p.R297Q	ENST00000262992	NM_001101669.1	297	cGa/cAa	11/24	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.43	2		755	334	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516861	187516861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763565837	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	105	814	2	ENST00000441802.2:c.13120G>A	p.Glu4374Lys	p.E4374K	ENST00000441802	NM_005245.3	4374	Gaa/Aaa	26/27	1	2	FACETS	0.954	0.858	1	0.954	0.858	1	CLONAL	1	TRUE	1	0.43	2		816	512	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629340	187629340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769413470	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	135	909	2	ENST00000441802.2:c.1642C>T	p.Arg548Cys	p.R548C	ENST00000441802	NM_005245.3	548	Cgc/Tgc	2/27	1	2	FACETS	0.984	0.897	1	0.984	0.897	1	CLONAL	1	TRUE	1	0.43	2		911	638	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31448657	31448657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757002340	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	72	614	0	ENST00000344624.3:c.2879C>T	p.Ser960Leu	p.S960L	ENST00000344624		960	tCg/tTg	20/33	1	2	FACETS	0.9	0.791	1	0.9	0.791	1	CLONAL	1	TRUE	1	0.43	2		614	372	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31451710	31451710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1466433904	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	59	659	0	ENST00000344624.3:c.2612G>A	p.Arg871His	p.R871H	ENST00000344624		871	cGc/cAc	18/33	1	2	FACETS	0.937	0.812	1	0.937	0.812	1	CLONAL	1	TRUE	1	0.43	2		659	293	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31466354	31466354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376262500	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	67	854	0	ENST00000344624.3:c.2401C>T	p.Arg801Cys	p.R801C	ENST00000344624		801	Cgc/Tgc	16/33	1	2	FACETS	0.693	0.603	0.788	0.693	0.603	0.788	SUBCLONAL	1	TRUE	1	0.43	2		854	450	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31472277	31472277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	102	854	0	ENST00000344624.3:c.2134G>A	p.Ala712Thr	p.A712T	ENST00000344624		712	Gcc/Acc	14/33	1	2	FACETS	0.897	0.805	0.994	0.897	0.805	0.994	CLONAL	1	TRUE	1	0.43	2		854	529	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871287	35871287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149161098	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	69	500	0	ENST00000303115.3:c.509G>A	p.Arg170His	p.R170H	ENST00000303115	NM_002185.3	170	cGc/cAc	4/8	1	2	FACETS	0.823	0.72	0.933	0.823	0.72	0.933	CLONAL	1	TRUE	1	0.43	2		500	390	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950138	38950138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573790456	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	94	911	3	ENST00000357387.3:c.3812C>T	p.Thr1271Met	p.T1271M	ENST00000357387	NM_152756.3	1271	aCg/aTg	31/38	1	2	FACETS	0.838	0.748	0.933	0.838	0.748	0.933	CLONAL	1	TRUE	1	0.43	2		914	522	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950199	38950199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	86	719	2	ENST00000357387.3:c.3751G>A	p.Asp1251Asn	p.D1251N	ENST00000357387	NM_152756.3	1251	Gac/Aac	31/38	1	2	FACETS	0.911	0.81	1	0.911	0.81	1	CLONAL	1	TRUE	1	0.43	2		721	439	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950622	38950622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748585755	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	93	759	0	ENST00000357387.3:c.3328C>T	p.Arg1110Cys	p.R1110C	ENST00000357387	NM_152756.3	1110	Cgt/Tgt	31/38	1	2	FACETS	0.97	0.867	1	0.97	0.867	1	CLONAL	1	TRUE	1	0.43	2		759	446	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170877	56170877	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	94	884	2	ENST00000399503.3:c.1705G>A	p.Val569Ile	p.V569I	ENST00000399503	NM_005921.1	569	Gtt/Att	10/20	1	2	FACETS	0.862	0.77	0.96	0.862	0.77	0.96	CLONAL	1	TRUE	1	0.43	2		886	507	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752361	57752361	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	26	490	0	ENST00000274289.3:c.1212G>T	p.Lys404Asn	p.K404N	ENST00000274289	NM_006622.3	404	aaG/aaT	9/14	1	2	FACETS	0.33	0.261	0.408	0.33	0.261	0.408	SUBCLONAL	1	TRUE	1	0.43	2		490	367	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591303	67591303	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	90	776	1	ENST00000274335.5:c.1801G>T	p.Glu601Ter	p.E601*	ENST00000274335		601	Gaa/Taa	13/15	1	2	FACETS	0.956	0.852	1	0.956	0.852	1	CLONAL	1	TRUE	1	0.43	2		777	438	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961137	79961137	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs569679162	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	104	659	0	ENST00000265081.6:c.534G>T	p.Lys178Asn	p.K178N	ENST00000265081	NM_002439.4	178	aaG/aaT	3/24	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.43	2		659	418	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80071522	80071522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	34	521	0	ENST00000265081.6:c.2263G>A	p.Glu755Lys	p.E755K	ENST00000265081	NM_002439.4	755	Gaa/Aaa	16/24	1	2	FACETS	0.575	0.472	0.69	0.575	0.472	0.69	SUBCLONAL	1	TRUE	1	0.43	2		521	275	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670711	86670711	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	56	519	0	ENST00000274376.6:c.1989G>T	p.Lys663Asn	p.K663N	ENST00000274376	NM_002890.2	663	aaG/aaT	15/25	1	2	FACETS	0.904	0.781	1	0.904	0.781	1	CLONAL	1	TRUE	1	0.43	2		519	288	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672759	86672759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	174	808	0	ENST00000274376.6:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000274376	NM_002890.2	749	cGa/cAa	17/25	1	2	FACETS	1	0.95	1	1	0.993	1	CLONAL	2	TRUE	1	0.43	2		808	396	SUCCESS
APC	324	MSKCC	GRCh37	5	112116593	112116593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1235428754	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	62	565	0	ENST00000257430.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000257430	NM_000038.5	213	cGa/cAa	6/16	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.43	2		565	284	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	27	800	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	1	2	FACETS	0.237	0.188	0.293	0.237	0.188	0.293	SUBCLONAL	1	TRUE	1	0.43	2		800	530	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149498372	149498372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	103	1021	1	ENST00000261799.4:c.2842C>T	p.Arg948Trp	p.R948W	ENST00000261799	NM_002609.3	948	Cgg/Tgg	21/23	1	2	FACETS	0.925	0.831	1	0.925	0.831	1	CLONAL	1	TRUE	1	0.43	2		1022	518	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043973	180043973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149033942	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	82	1160	2	ENST00000261937.6:c.3023C>T	p.Pro1008Leu	p.P1008L	ENST00000261937	NM_182925.4	1008	cCg/cTg	22/30	1	2	FACETS	0.991	0.879	1	0.991	0.879	1	CLONAL	1	TRUE	1	0.43	2		1162	385	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057699	180057699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	85	1101	0	ENST00000261937.6:c.256G>A	p.Gly86Ser	p.G86S	ENST00000261937	NM_182925.4	86	Ggc/Agc	3/30	1	2	FACETS	0.869	0.771	0.972	0.869	0.771	0.972	CLONAL	1	TRUE	1	0.43	2		1101	455	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394891	394891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	86	987	0	ENST00000380956.4:c.287G>A	p.Arg96His	p.R96H	ENST00000380956	NM_001195286.1	96	cGc/cAc	3/9	1	2	FACETS	0.71	0.63	0.797	0.71	0.63	0.797	SUBCLONAL	1	TRUE	1	0.43	2		987	563	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395937	395937	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	67	1151	0	ENST00000380956.4:c.492+2T>C		p.X164_splice	ENST00000380956	NM_001195286.1	164			1	2	FACETS	0.691	0.602	0.786	0.691	0.602	0.786	SUBCLONAL	1	TRUE	1	0.43	2		1151	451	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405111	405111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	41	846	0	ENST00000380956.4:c.1193G>T	p.Arg398Ile	p.R398I	ENST00000380956	NM_001195286.1	398	aGa/aTa	8/9	1	2	FACETS	0.433	0.361	0.514	0.433	0.361	0.514	SUBCLONAL	1	TRUE	1	0.43	2		846	440	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671519	30671519	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	107	931	0	ENST00000376406.3:c.5441C>A	p.Ser1814Tyr	p.S1814Y	ENST00000376406	NM_014641.2	1814	tCt/tAt	10/15	1	2	FACETS	0.786	0.706	0.871	0.786	0.706	0.871	SUBCLONAL	1	TRUE	1	0.43	2		931	633	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31237824	31237824	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs12209550	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	123	1084	0	ENST00000376228.5:c.934G>A	p.Val312Ile	p.V312I	ENST00000376228	NM_002117.5	312	Gtt/Att	5/8	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.43	2		1084	551	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956553	93956553	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1035177735	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	104	812	0	ENST00000369303.4:c.2683C>T	p.Arg895Ter	p.R895*	ENST00000369303	NM_004440.3	895	Cga/Tga	15/17	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.43	2		812	480	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024169	112024169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465963577	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	85	730	2	ENST00000368678.4:c.616C>T	p.Arg206Cys	p.R206C	ENST00000368678		206	Cgc/Tgc	7/13	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.43	2		732	372	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662727	117662727	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	71	833	0	ENST00000368508.3:c.4738G>T	p.Glu1580Ter	p.E1580*	ENST00000368508	NM_002944.2	1580	Gaa/Taa	29/43	0.3	1	FACETS	0.668	0.586	0.756	0.668	0.586	0.756	SUBCLONAL	1	TRUE	0	0.43	1		833	388	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525012	157525012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1022849043	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	101	878	0	ENST00000346085.5:c.4907C>T	p.Ala1636Val	p.A1636V	ENST00000346085	NM_020732.3	1636	gCg/gTg	19/20	1	2	FACETS	0.943	0.847	1	0.943	0.847	1	CLONAL	1	TRUE	1	0.43	2		878	498	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954942	2954942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371300769	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	109	1361	0	ENST00000396946.4:c.2768C>T	p.Ser923Leu	p.S923L	ENST00000396946	NM_032415.4	923	tCg/tTg	21/25	1	2	FACETS	0.957	0.862	1	0.957	0.862	1	CLONAL	1	TRUE	1	0.43	2		1361	530	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976790	2976790	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1053219257	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	92	961	1	ENST00000396946.4:c.1222C>T	p.Arg408Cys	p.R408C	ENST00000396946	NM_032415.4	408	Cgc/Tgc	9/25	1	2	FACETS	0.849	0.757	0.946	0.849	0.757	0.946	CLONAL	1	TRUE	1	0.43	2		962	504	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355326	81355326	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	61	725	1	ENST00000222390.5:c.1048C>T	p.Arg350Ter	p.R350*	ENST00000222390	NM_000601.4	350	Cga/Tga	9/18	1	2	FACETS	0.788	0.683	0.901	0.788	0.683	0.901	CLONAL	1	TRUE	1	0.43	2		726	360	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374327	81374327	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	70	767	0	ENST00000222390.5:c.735C>A	p.Phe245Leu	p.F245L	ENST00000222390	NM_000601.4	245	ttC/ttA	6/18	1	2	FACETS	0.917	0.805	1	0.917	0.805	1	CLONAL	1	TRUE	1	0.43	2		767	355	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381528	81381528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776090604	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	78	750	2	ENST00000222390.5:c.533G>A	p.Arg178Gln	p.R178Q	ENST00000222390	NM_000601.4	178	cGa/cAa	5/18	1	2	FACETS	0.86	0.759	0.967	0.86	0.759	0.967	CLONAL	1	TRUE	1	0.43	2		752	422	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381529	81381529	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	74	742	2	ENST00000222390.5:c.532C>T	p.Arg178Ter	p.R178*	ENST00000222390	NM_000601.4	178	Cga/Tga	5/18	1	2	FACETS	0.821	0.722	0.927	0.821	0.722	0.927	CLONAL	1	TRUE	1	0.43	2		744	419	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509138	106509138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753981231	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	110	964	0	ENST00000359195.3:c.1132G>A	p.Asp378Asn	p.D378N	ENST00000359195	NM_002649.2	378	Gac/Aac	2/11	1	2	FACETS	0.939	0.847	1	0.939	0.847	1	CLONAL	1	TRUE	1	0.43	2		964	545	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506448	148506448	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	21	519	0	ENST00000320356.2:c.2064A>C	p.Lys688Asn	p.K688N	ENST00000320356	NM_004456.4	688	aaA/aaC	18/20	1	2	FACETS	0.254	0.195	0.323	0.254	0.195	0.323	SUBCLONAL	1	TRUE	1	0.43	2		519	385	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152009026	152009026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369725088	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	68	611	2	ENST00000262189.6:c.596G>A	p.Arg199Gln	p.R199Q	ENST00000262189	NM_170606.2	199	cGa/cAa	5/59	1	2	FACETS	0.988	0.867	1	0.988	0.867	1	CLONAL	1	TRUE	1	0.43	2		613	320	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031690	69031690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371787029	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	94	726	0	ENST00000288368.4:c.3445C>T	p.Arg1149Cys	p.R1149C	ENST00000288368	NM_024870.2	1149	Cgc/Tgc	28/40	1	2	FACETS	0.974	0.871	1	0.974	0.871	1	CLONAL	1	TRUE	1	0.43	2		726	449	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066739	5066739	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1340580425	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	55	619	0	ENST00000381652.3:c.1276C>T	p.Arg426Ter	p.R426*	ENST00000381652	NM_004972.3	426	Cga/Tga	10/25	1	2	FACETS	0.792	0.681	0.911	0.792	0.681	0.911	CLONAL	1	TRUE	1	0.43	2		619	323	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457091	5457091	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143235887	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	68	646	2	ENST00000381577.3:c.65C>T	p.Thr22Met	p.T22M	ENST00000381577	NM_014143.3	22	aCg/aTg	3/7	1	2	FACETS	0.853	0.746	0.967	0.853	0.746	0.967	CLONAL	1	TRUE	1	0.43	2		648	371	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485948	8485948	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	84	749	0	ENST00000356435.5:c.2869C>A	p.Leu957Ile	p.L957I	ENST00000356435		957	Ctt/Att	17/35	1	2	FACETS	0.831	0.737	0.931	0.831	0.737	0.931	CLONAL	1	TRUE	1	0.43	2		749	470	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549189	87549189	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	100	479	0	ENST00000277120.3:c.1746G>T	p.Lys582Asn	p.K582N	ENST00000277120		582	aaG/aaT	15/19	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.43	2		479	424	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249824	110249824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	71	815	0	ENST00000374672.4:c.851C>T	p.Ser284Leu	p.S284L	ENST00000374672	NM_004235.4	284	tCg/tTg	3/5	1	2	FACETS	0.845	0.741	0.955	0.845	0.741	0.955	CLONAL	1	TRUE	1	0.43	2		815	391	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915943	127915943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781486938	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	96	768	2	ENST00000373547.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000373547	NM_002721.4	180	Gaa/Aaa	6/7	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.43	2		770	439	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399799	139399799	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554727954	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	113	1314	0	ENST00000277541.6:c.4549G>A	p.Asp1517Asn	p.D1517N	ENST00000277541	NM_017617.3	1517	Gac/Aac	25/34	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.43	2		1314	442	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317422	1317422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759127718	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	85	895	0	ENST00000400841.2:c.643C>T	p.Arg215Trp	p.R215W	ENST00000400841		215	Cgg/Tgg	5/6	1	2	FACETS	0.896	0.796	1	0.896	0.796	1	CLONAL	1	TRUE	1	0.43	2		895	441	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922118	39922118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768842901	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	101	1003	1	ENST00000378444.4:c.4054G>A	p.Asp1352Asn	p.D1352N	ENST00000378444	NM_001123385.1	1352	Gac/Aac	9/15	1	2	FACETS	0.761	0.682	0.846	0.761	0.682	0.846	SUBCLONAL	1	TRUE	1	0.43	2		1004	617	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933164	39933164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763751220	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	124	985	0	ENST00000378444.4:c.1435G>A	p.Gly479Arg	p.G479R	ENST00000378444	NM_001123385.1	479	Gga/Aga	4/15	1	2	FACETS	0.932	0.845	1	0.932	0.845	1	CLONAL	1	TRUE	1	0.43	2		985	619	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937668	44937668	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	54	428	0	ENST00000377967.4:c.2856C>A	p.Phe952Leu	p.F952L	ENST00000377967	NM_021140.2	952	ttC/ttA	19/29	1	2	FACETS	0.9	0.775	1	0.9	0.775	1	CLONAL	1	TRUE	1	0.43	2		428	279	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969391	44969391	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	81	648	0	ENST00000377967.4:c.4073G>C	p.Cys1358Ser	p.C1358S	ENST00000377967	NM_021140.2	1358	tGc/tCc	28/29	1	2	FACETS	0.949	0.841	1	0.949	0.841	1	CLONAL	1	TRUE	1	0.43	2		648	397	SUCCESS
AR	367	MSKCC	GRCh37	X	66765598	66765598	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	93	1106	0	ENST00000374690.3:c.610G>A	p.Glu204Lys	p.E204K	ENST00000374690	NM_000044.3	204	Gaa/Aaa	1/8	1	2	FACETS	0.874	0.78	0.973	0.874	0.78	0.973	CLONAL	1	TRUE	1	0.43	2		1106	495	SUCCESS
AR	367	MSKCC	GRCh37	X	66942740	66942740	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852577	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	55	736	2	ENST00000374690.3:c.2521C>T	p.Arg841Cys	p.R841C	ENST00000374690	NM_000044.3	841	Cgt/Tgt	7/8	1	2	FACETS	0.752	0.647	0.866	0.752	0.647	0.866	SUBCLONAL	1	TRUE	1	0.43	2		738	340	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342421	70342421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771266719	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	125	884	0	ENST00000374080.3:c.1312C>T	p.Arg438Cys	p.R438C	ENST00000374080		438	Cgc/Tgc	9/45	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.43	2		884	542	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342687	70342687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	93	780	0	ENST00000374080.3:c.1448G>A	p.Arg483Gln	p.R483Q	ENST00000374080		483	cGa/cAa	10/45	1	2	FACETS	0.89	0.795	0.991	0.89	0.795	0.991	CLONAL	1	TRUE	1	0.43	2		780	486	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352372	70352372	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	107	362	0	ENST00000374080.3:c.4399C>T	p.Arg1467Ter	p.R1467*	ENST00000374080		1467	Cga/Tga	31/45	1	2	FACETS	0.944	0.85	1	0.944	0.85	1	CLONAL	1	TRUE	1	0.43	2		362	527	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937683	76937683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781811015	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	94	832	2	ENST00000373344.5:c.3065G>A	p.Arg1022Gln	p.R1022Q	ENST00000373344	NM_000489.3	1022	cGa/cAa	9/35	1	2	FACETS	0.93	0.831	1	0.93	0.831	1	CLONAL	1	TRUE	1	0.43	2		834	470	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185195	123185195	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	76	530	2	ENST00000218089.9:c.1147G>T	p.Glu383Ter	p.E383*	ENST00000218089	NM_001042749.1	383	Gaa/Taa	13/35	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.43	2		532	338	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307972	11307972	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	127	990	0	ENST00000361445.4:c.1020A>C	p.Gln340His	p.Q340H	ENST00000361445	NM_004958.3	340	caA/caC	7/58	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.43	2		990	526	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257479	16257479	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	96	864	0	ENST00000375759.3:c.4744C>A	p.Leu1582Met	p.L1582M	ENST00000375759	NM_015001.2	1582	Ctg/Atg	11/15	1	2	FACETS	0.902	0.807	1	0.902	0.807	1	CLONAL	1	TRUE	1	0.43	2		864	495	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261314	16261314	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	122	926	0	ENST00000375759.3:c.8579C>A	p.Ser2860Tyr	p.S2860Y	ENST00000375759	NM_015001.2	2860	tCt/tAt	11/15	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.43	2		926	531	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803805	43803805	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	104	708	2	ENST00000372470.3:c.115A>G	p.Lys39Glu	p.K39E	ENST00000372470	NM_005373.2	39	Aag/Gag	2/12	1	2	FACETS	0.977	0.879	1	0.977	0.879	1	CLONAL	1	TRUE	1	0.43	2		710	495	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796853	45796853	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	94	807	0	ENST00000450313.1:c.1476+1G>A		p.X492_splice	ENST00000450313	NM_012222.2	492			1	2	FACETS	0.892	0.797	0.993	0.892	0.797	0.993	CLONAL	1	TRUE	1	0.43	2		807	490	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45805911	45805911	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	103	673	0	ENST00000450313.1:c.16T>C	p.Ser6Pro	p.S6P	ENST00000450313	NM_012222.2	6	Tcc/Ccc	1/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.43	2		673	385	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873205	71873205	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	78	851	0	ENST00000357731.5:c.989T>C	p.Phe330Ser	p.F330S	ENST00000357731	NM_173808.2	330	tTc/tCc	7/7	1	2	FACETS	0.806	0.711	0.907	0.806	0.711	0.907	CLONAL	1	TRUE	1	0.43	2		851	450	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115272919	115272920	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	74	815	0	ENST00000438362.2:c.1453dup	p.Ser485PhefsTer4	p.S485Ffs*4	ENST00000438362	NM_001242891.1	485	tcc/tTcc	12/20	1	2	FACETS	0.756	0.664	0.855	0.756	0.664	0.855	SUBCLONAL	1	TRUE	1	0.43	2		815	455	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458270	120458270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs75831573	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	112	1207	0	ENST00000256646.2:c.7075C>T	p.Pro2359Ser	p.P2359S	ENST00000256646	NM_024408.3	2359	Ccc/Tcc	34/34	1	2	FACETS	0.958	0.865	1	0.958	0.865	1	CLONAL	1	TRUE	1	0.43	2		1207	544	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480002	120480002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	129	961	0	ENST00000256646.2:c.3425C>T	p.Thr1142Ile	p.T1142I	ENST00000256646	NM_024408.3	1142	aCt/aTt	21/34	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.43	2		961	587	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176118155	176118155	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	65	463	0	ENST00000367669.3:c.818G>A	p.Arg273Lys	p.R273K	ENST00000367669	NM_022457.5	273	aGa/aAa	6/20	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.43	2		463	288	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663776	241663776	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1558396320	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	43	261	2	ENST00000366560.3:c.1351G>T	p.Glu451Ter	p.E451*	ENST00000366560	NM_000143.3	451	Gag/Tag	9/10	1	2	FACETS	0.917	0.775	1	0.917	0.775	1	CLONAL	1	TRUE	1	0.43	2		263	218	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243778419	243778419	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	45	642	0	ENST00000263826.5:c.606C>A	p.Asn202Lys	p.N202K	ENST00000263826	NM_005465.4	202	aaC/aaA	6/13	1	2	FACETS	0.654	0.552	0.766	0.654	0.552	0.766	SUBCLONAL	1	TRUE	1	0.43	2		642	320	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608411	43608411	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs748905470	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	115	1384	0	ENST00000355710.3:c.1759C>T	p.Arg587Trp	p.R587W	ENST00000355710	NM_020975.4	587	Cgg/Tgg	9/20	1	2	FACETS	0.867	0.783	0.955	0.867	0.783	0.955	CLONAL	1	TRUE	1	0.43	2		1384	617	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446152	70446152	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	90	761	2	ENST00000373644.4:c.5092G>A	p.Val1698Ile	p.V1698I	ENST00000373644	NM_030625.2	1698	Gtt/Att	11/12	1	2	FACETS	0.936	0.835	1	0.936	0.835	1	CLONAL	1	TRUE	1	0.43	2		763	447	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724157	112724157	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	78	632	0	ENST00000369452.4:c.41A>G	p.Lys14Arg	p.K14R	ENST00000369452	NM_007373.3	14	aAa/aGa	2/9	1	2	FACETS	0.864	0.763	0.971	0.864	0.763	0.971	CLONAL	1	TRUE	1	0.43	2		632	420	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417847	32417847	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	91	689	0	ENST00000332351.3:c.1205A>G	p.Tyr402Cys	p.Y402C	ENST00000332351	NM_024426.4	402	tAt/tGt	7/10	1	2	FACETS	0.887	0.791	0.989	0.887	0.791	0.989	CLONAL	1	TRUE	1	0.43	2		689	477	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197324	94197324	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	58	509	0	ENST00000323929.3:c.1180G>T	p.Asp394Tyr	p.D394Y	ENST00000323929	NM_005591.3	394	Gac/Tac	11/20	1	2	FACETS	0.773	0.668	0.887	0.773	0.668	0.887	SUBCLONAL	1	TRUE	1	0.43	2		509	349	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375597	118375597	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	90	968	0	ENST00000534358.1:c.8990T>G	p.Phe2997Cys	p.F2997C	ENST00000534358	NM_005933.3	2997	tTt/tGt	27/36	1	2	FACETS	0.861	0.767	0.961	0.861	0.767	0.961	CLONAL	1	TRUE	1	0.43	2		968	486	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431678	431678	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	75	693	0	ENST00000399788.2:c.2331G>T	p.Glu777Asp	p.E777D	ENST00000399788	NM_001042603.1	777	gaG/gaT	17/28	1	2	FACETS	0.883	0.778	0.995	0.883	0.778	0.995	CLONAL	1	TRUE	1	0.43	2		693	395	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231445	46231445	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	76	869	0	ENST00000334344.6:c.1285G>T	p.Gly429Ter	p.G429*	ENST00000334344	NM_152641.2	429	Gga/Tga	10/21	1	2	FACETS	0.877	0.773	0.988	0.877	0.773	0.988	CLONAL	1	TRUE	1	0.43	2		869	403	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233112	46233112	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	26	471	1	ENST00000334344.6:c.1331A>G	p.Asp444Gly	p.D444G	ENST00000334344	NM_152641.2	444	gAc/gGc	11/21	1	2	FACETS	0.34	0.269	0.421	0.34	0.269	0.421	SUBCLONAL	1	TRUE	1	0.43	2		472	356	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421038	49421038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751628871	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	91	1043	2	ENST00000301067.7:c.14711G>A	p.Arg4904Gln	p.R4904Q	ENST00000301067	NM_003482.3	4904	cGa/cAa	48/54	1	2	FACETS	0.91	0.812	1	0.91	0.812	1	CLONAL	1	TRUE	1	0.43	2		1045	465	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120802539	120802539	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	80	720	0	ENST00000257552.2:c.287T>C	p.Phe96Ser	p.F96S	ENST00000257552	NM_002442.3	96	tTc/tCc	5/15	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.43	2		720	358	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120806034	120806034	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	73	895	0	ENST00000257552.2:c.143A>C	p.Glu48Ala	p.E48A	ENST00000257552	NM_002442.3	48	gAg/gCg	3/15	1	2	FACETS	0.765	0.671	0.865	0.765	0.671	0.865	SUBCLONAL	1	TRUE	1	0.43	2		895	444	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28885818	28885818	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	54	743	0	ENST00000282397.4:c.3544T>C	p.Phe1182Leu	p.F1182L	ENST00000282397	NM_002019.4	1182	Ttt/Ctt	27/30	1	2	FACETS	0.775	0.666	0.893	0.775	0.666	0.893	SUBCLONAL	1	TRUE	1	0.43	2		743	324	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28963943	28963943	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	23	791	0	ENST00000282397.4:c.1959T>G	p.Ile653Met	p.I653M	ENST00000282397	NM_002019.4	653	atT/atG	13/30	1	2	FACETS	0.253	0.197	0.319	0.253	0.197	0.319	SUBCLONAL	1	TRUE	1	0.43	2		791	422	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32905075	32905075	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	86	523	1	ENST00000380152.3:c.701C>T	p.Ser234Phe	p.S234F	ENST00000380152		234	tCc/tTc	9/27	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.43	2		524	380	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907197	32907197	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	59	731	0	ENST00000380152.3:c.1582A>C	p.Asn528His	p.N528H	ENST00000380152		528	Aac/Cac	10/27	1	2	FACETS	0.702	0.606	0.805	0.702	0.606	0.805	SUBCLONAL	1	TRUE	1	0.43	2		731	391	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913298	32913298	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	88	815	0	ENST00000380152.3:c.4806A>C	p.Lys1602Asn	p.K1602N	ENST00000380152		1602	aaA/aaC	11/27	1	2	FACETS	0.876	0.78	0.979	0.876	0.78	0.979	CLONAL	1	TRUE	1	0.43	2		815	467	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941649	48941649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760787104	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	26	430	0	ENST00000267163.4:c.959G>A	p.Arg320Gln	p.R320Q	ENST00000267163	NM_000321.2	320	cGa/cAa	10/27	1	2	FACETS	0.547	0.435	0.674	0.547	0.435	0.674	SUBCLONAL	1	TRUE	1	0.43	2		430	221	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281041	49281041	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	72	766	0	ENST00000282018.3:c.88A>T	p.Asn30Tyr	p.N30Y	ENST00000282018	NM_020377.2	30	Aac/Tac	1/1	1	2	FACETS	0.766	0.672	0.867	0.766	0.672	0.867	SUBCLONAL	1	TRUE	1	0.43	2		766	437	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281940	49281940	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	134	892	2	ENST00000282018.3:c.987G>T	p.Lys329Asn	p.K329N	ENST00000282018	NM_020377.2	329	aaG/aaT	1/1	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.43	2		894	560	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337744	73337744	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	51	685	0	ENST00000377767.4:c.1972G>T	p.Glu658Ter	p.E658*	ENST00000377767	NM_014953.3	658	Gaa/Taa	16/21	1	2	FACETS	0.748	0.639	0.866	0.748	0.639	0.866	SUBCLONAL	1	TRUE	1	0.43	2		685	317	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105616	30105616	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	105	1025	0	ENST00000331968.5:c.1070T>C	p.Met357Thr	p.M357T	ENST00000331968	NM_002742.2	357	aTg/aCg	7/18	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.43	2		1025	480	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572113	95572113	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	70	627	0	ENST00000393063.1:c.2995C>A	p.Leu999Ile	p.L999I	ENST00000393063	NM_030621.3	999	Ctt/Att	20/28	1	2	FACETS	0.826	0.724	0.936	0.826	0.724	0.936	CLONAL	1	TRUE	1	0.43	2		627	394	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105237151	105237151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	101	968	0	ENST00000349310.3:c.1294G>A	p.Glu432Lys	p.E432K	ENST00000349310	NM_001014432.1	432	Gag/Aag	14/15	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.43	2		968	451	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989196	41989196	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	72	754	0	ENST00000219905.7:c.1988T>C	p.Val663Ala	p.V663A	ENST00000219905	NM_001164273.1	663	gTt/gCt	3/24	1	2	FACETS	0.935	0.823	1	0.935	0.823	1	CLONAL	1	TRUE	1	0.43	2		754	358	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51510846	51510846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	83	534	0	ENST00000260433.2:c.635C>T	p.Ala212Val	p.A212V	ENST00000260433		212	gCt/gTt	6/10	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.43	2		534	375	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358412	91358412	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	67	769	0	ENST00000355112.3:c.4157C>A	p.Ser1386Tyr	p.S1386Y	ENST00000355112	NM_000057.2	1386	tCt/tAt	22/22	1	2	FACETS	0.726	0.633	0.826	0.726	0.633	0.826	SUBCLONAL	1	TRUE	1	0.43	2		769	429	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99452029	99452029	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	109	945	1	ENST00000268035.6:c.1363T>G	p.Cys455Gly	p.C455G	ENST00000268035	NM_000875.3	455	Tgt/Ggt	6/21	1	2	FACETS	0.885	0.797	0.977	0.885	0.797	0.977	CLONAL	1	TRUE	1	0.43	2		946	573	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862890	9862890	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	88	986	0	ENST00000330684.3:c.2413A>G	p.Asn805Asp	p.N805D	ENST00000330684	NM_001134407.1	805	Aac/Gac	12/13	1	2	FACETS	0.789	0.701	0.882	0.789	0.701	0.882	SUBCLONAL	1	TRUE	1	0.43	2		986	519	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9927982	9927982	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	84	672	0	ENST00000330684.3:c.1757G>T	p.Arg586Ile	p.R586I	ENST00000330684	NM_001134407.1	586	aGa/aTa	8/13	1	2	FACETS	0.992	0.881	1	0.992	0.881	1	CLONAL	1	TRUE	1	0.43	2		672	394	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041713	14041713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs535728795	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	90	860	1	ENST00000311895.7:c.2260C>T	p.Arg754Cys	p.R754C	ENST00000311895	NM_005236.2	754	Cgt/Tgt	11/11	1	2	FACETS	0.772	0.687	0.863	0.772	0.687	0.863	SUBCLONAL	1	TRUE	1	0.43	2		861	542	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829730	72829730	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	84	946	0	ENST00000268489.5:c.6851G>A	p.Arg2284Gln	p.R2284Q	ENST00000268489	NM_006885.3	2284	cGa/cAa	9/10	1	2	FACETS	0.807	0.715	0.905	0.807	0.715	0.905	CLONAL	1	TRUE	1	0.43	2		946	484	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935626	15935626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	126	848	0	ENST00000268712.3:c.7307C>T	p.Ser2436Leu	p.S2436L	ENST00000268712	NM_006311.3	2436	tCg/tTg	46/46	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.43	2		848	562	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17129583	17129583	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	95	1241	0	ENST00000285071.4:c.303G>T	p.Glu101Asp	p.E101D	ENST00000285071	NM_144997.5	101	gaG/gaT	5/14	1	2	FACETS	0.891	0.796	0.991	0.891	0.796	0.991	CLONAL	1	TRUE	1	0.43	2		1241	496	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496944	29496944	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	54	448	0	ENST00000356175.3:c.515T>C	p.Val172Ala	p.V172A	ENST00000356175	NM_000267.3	172	gTt/gCt	5/57	1	2	FACETS	0.766	0.658	0.883	0.766	0.658	0.883	SUBCLONAL	1	TRUE	1	0.43	2		448	328	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560176	29560176	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659541	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	131	752	0	ENST00000356175.3:c.3653A>G	p.Gln1218Arg	p.Q1218R	ENST00000356175	NM_000267.3	1218	cAa/cGa	27/57	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.43	2		752	593	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325679	30325679	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	61	477	0	ENST00000322652.5:c.1877T>G	p.Phe626Cys	p.F626C	ENST00000322652	NM_015355.2	626	tTt/tGt	16/16	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.43	2		477	283	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33681013	33681013	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs901071190	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	85	794	0	ENST00000308377.4:c.1264G>T	p.Gly422Ter	p.G422*	ENST00000308377	NM_152270.3	422	Gga/Tga	4/5	1	2	FACETS	0.869	0.771	0.972	0.869	0.771	0.972	CLONAL	1	TRUE	1	0.43	2		794	455	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690728	33690729	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	94	911	0	ENST00000308377.4:c.98dup	p.Leu34AlafsTer35	p.L34Afs*35	ENST00000308377	NM_152270.3	33	aag/aaAg	2/5	1	2	FACETS	0.755	0.673	0.842	0.755	0.673	0.842	SUBCLONAL	1	TRUE	1	0.43	2		911	579	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38787170	38787170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745448272	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	109	673	0	ENST00000348513.6:c.823G>A	p.Gly275Ser	p.G275S	ENST00000348513	NM_003079.4	275	Ggt/Agt	10/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.43	2		673	396	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437576	56437576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318890868	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	99	910	0	ENST00000407977.2:c.886C>T	p.Arg296Cys	p.R296C	ENST00000407977		296	Cgt/Tgt	8/10	1	2	FACETS	0.905	0.811	1	0.905	0.811	1	CLONAL	1	TRUE	1	0.43	2		910	509	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554027	63554027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1279069233	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	104	926	2	ENST00000307078.5:c.712G>A	p.Asp238Asn	p.D238N	ENST00000307078	NM_004655.3	238	Gac/Aac	2/11	1	2	FACETS	0.881	0.791	0.976	0.881	0.791	0.976	CLONAL	1	TRUE	1	0.43	2		928	549	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519893	66519893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	60	676	2	ENST00000358598.2:c.376G>A	p.Ala126Thr	p.A126T	ENST00000358598	NM_212471.2	126	Gcc/Acc	4/11	1	2	FACETS	0.777	0.673	0.89	0.777	0.673	0.89	SUBCLONAL	1	TRUE	1	0.43	2		678	359	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348517	56348517	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	83	789	0	ENST00000348428.3:c.325T>G	p.Phe109Val	p.F109V	ENST00000348428	NM_006785.3	109	Ttc/Gtc	2/17	1	2	FACETS	0.781	0.692	0.877	0.781	0.692	0.877	SUBCLONAL	1	TRUE	1	0.43	2		789	494	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1206986	1206986	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	87	869	0	ENST00000326873.7:c.74T>G	p.Phe25Cys	p.F25C	ENST00000326873	NM_000455.4	25	tTc/tGc	1/10	1	2	FACETS	0.935	0.832	1	0.935	0.832	1	CLONAL	1	TRUE	1	0.43	2		869	433	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170584	7170584	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757634971	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	104	914	1	ENST00000302850.5:c.1447G>A	p.Asp483Asn	p.D483N	ENST00000302850	NM_000208.2	483	Gac/Aac	6/22	1	2	FACETS	0.87	0.781	0.963	0.87	0.781	0.963	CLONAL	1	TRUE	1	0.43	2		915	556	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031419	11031419	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	112	1018	0	ENST00000327064.4:c.1419C>A	p.Phe473Leu	p.F473L	ENST00000327064	NM_199141.1	473	ttC/ttA	12/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.43	2		1018	463	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313367	30313367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757767972	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	89	872	0	ENST00000262643.3:c.967G>A	p.Asp323Asn	p.D323N	ENST00000262643	NM_001238.2	323	Gac/Aac	11/12	1	2	FACETS	0.813	0.723	0.909	0.813	0.723	0.909	CLONAL	1	TRUE	1	0.43	2		872	509	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085623	16085623	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	27	722	3	ENST00000281043.3:c.799G>T	p.Asp267Tyr	p.D267Y	ENST00000281043	NM_005378.4	267	Gat/Tat	3/3	1	2	FACETS	0.3	0.239	0.371	0.3	0.239	0.371	SUBCLONAL	1	TRUE	1	0.43	2		725	418	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46608806	46608806	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	97	754	0	ENST00000263734.3:c.2117T>C	p.Leu706Pro	p.L706P	ENST00000263734	NM_001430.4	706	cTg/cCg	13/16	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.43	2		754	431	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027284	48027284	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660319	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	92	748	0	ENST00000234420.5:c.2162G>T	p.Arg721Ile	p.R721I	ENST00000234420	NM_000179.2	721	aGa/aTa	4/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.43	2		748	374	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032789	48032789	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	76	648	0	ENST00000234420.5:c.3589A>C	p.Thr1197Pro	p.T1197P	ENST00000234420	NM_000179.2	1197	Act/Cct	7/10	1	2	FACETS	0.869	0.766	0.978	0.869	0.766	0.978	CLONAL	1	TRUE	1	0.43	2		648	407	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033447	48033447	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	93	744	0	ENST00000234420.5:c.3751T>C	p.Ser1251Pro	p.S1251P	ENST00000234420	NM_000179.2	1251	Tca/Cca	8/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.43	2		744	379	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67632320	67632320	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	78	513	0	ENST00000272342.5:c.2506A>G	p.Asn836Asp	p.N836D	ENST00000272342	NM_019002.3	836	Aat/Gat	5/6	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.43	2		513	328	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99137160	99137160	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	90	529	0	ENST00000074304.5:c.117A>C	p.Gln39His	p.Q39H	ENST00000074304	NM_001134224.1	39	caA/caC	4/26	1	2	FACETS	0.92	0.82	1	0.92	0.82	1	CLONAL	1	TRUE	1	0.43	2		529	455	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156090	99156090	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1312525188	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	99	920	0	ENST00000074304.5:c.770A>G	p.His257Arg	p.H257R	ENST00000074304	NM_001134224.1	257	cAc/cGc	10/26	1	2	FACETS	0.908	0.814	1	0.908	0.814	1	CLONAL	1	TRUE	1	0.43	2		920	507	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881584	111881584	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	37	879	0	ENST00000393256.3:c.262C>A	p.Leu88Met	p.L88M	ENST00000393256	NM_006538.4	88	Ctg/Atg	2/4	1	2	FACETS	0.299	0.246	0.358	0.299	0.246	0.358	SUBCLONAL	1	TRUE	1	0.43	2		879	576	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873268	136873268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	107	821	0	ENST00000241393.3:c.230G>A	p.Arg77Lys	p.R77K	ENST00000241393	NM_003467.2	77	aGg/aAg	2/2	1	2	FACETS	0.816	0.733	0.903	0.816	0.733	0.903	CLONAL	1	TRUE	1	0.43	2		821	610	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225343021	225343021	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	81	805	0	ENST00000264414.4:c.2071A>G	p.Thr691Ala	p.T691A	ENST00000264414	NM_003590.4	691	Aca/Gca	15/16	1	2	FACETS	0.912	0.808	1	0.912	0.808	1	CLONAL	1	TRUE	1	0.43	2		805	413	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661749	227661749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372100778	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	77	984	1	ENST00000305123.5:c.1706C>T	p.Pro569Leu	p.P569L	ENST00000305123	NM_005544.2	569	cCg/cTg	1/2	1	2	FACETS	0.82	0.722	0.923	0.82	0.722	0.923	CLONAL	1	TRUE	1	0.43	2		985	437	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729941	39729941	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	83	755	0	ENST00000361337.2:c.1256A>G	p.Asn419Ser	p.N419S	ENST00000361337	NM_003286.2	419	aAc/aGc	13/21	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.43	2		755	372	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750347	39750347	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	101	703	3	ENST00000361337.2:c.1962G>T	p.Lys654Asn	p.K654N	ENST00000361337	NM_003286.2	654	aaG/aaT	19/21	1	2	FACETS	0.997	0.896	1	0.997	0.896	1	CLONAL	1	TRUE	1	0.43	2		706	471	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730937	40730937	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	111	1127	0	ENST00000373198.4:c.3598A>G	p.Thr1200Ala	p.T1200A	ENST00000373198	NM_133170.3	1200	Acc/Gcc	27/32	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.43	2		1127	481	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46275828	46275828	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	108	817	0	ENST00000371998.3:c.3264A>C	p.Leu1088Phe	p.L1088F	ENST00000371998		1088	ttA/ttC	18/23	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.43	2		817	475	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29439389	29439389	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1445903020	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	86	816	2	ENST00000544604.2:c.604C>T	p.Arg202Ter	p.R202*	ENST00000544604	NM_001206998.1	202	Cga/Tga	4/9	1	2	FACETS	0.818	0.726	0.916	0.818	0.726	0.916	CLONAL	1	TRUE	1	0.43	2		818	489	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37092046	37092046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138584384	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	97	799	0	ENST00000231790.2:c.2173C>T	p.Arg725Cys	p.R725C	ENST00000231790	NM_000249.3	725	Cgc/Tgc	19/19	1	2	FACETS	0.97	0.869	1	0.97	0.869	1	CLONAL	1	TRUE	1	0.43	2		799	465	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155376	47155376	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	91	609	0	ENST00000409792.3:c.4705G>T	p.Asp1569Tyr	p.D1569Y	ENST00000409792	NM_014159.6	1569	Gac/Tac	5/21	1	2	FACETS	0.987	0.881	1	0.987	0.881	1	CLONAL	1	TRUE	1	0.43	2		609	429	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164329	47164329	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	72	582	0	ENST00000409792.3:c.1797A>C	p.Glu599Asp	p.E599D	ENST00000409792	NM_014159.6	599	gaA/gaC	3/21	1	2	FACETS	0.803	0.705	0.908	0.803	0.705	0.908	CLONAL	1	TRUE	1	0.43	2		582	417	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164581	47164581	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	81	592	0	ENST00000409792.3:c.1545A>T	p.Glu515Asp	p.E515D	ENST00000409792	NM_014159.6	515	gaA/gaT	3/21	1	2	FACETS	0.933	0.826	1	0.933	0.826	1	CLONAL	1	TRUE	1	0.43	2		592	404	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259366	89259366	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	31	796	0	ENST00000336596.2:c.510A>C	p.Glu170Asp	p.E170D	ENST00000336596	NM_005233.5	170	gaA/gaC	3/17	1	2	FACETS	0.304	0.245	0.37	0.304	0.245	0.37	SUBCLONAL	1	TRUE	1	0.43	2		796	475	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391202	89391202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	30	721	0	ENST00000336596.2:c.1268G>A	p.Arg423Lys	p.R423K	ENST00000336596	NM_005233.5	423	aGa/aAa	5/17	1	2	FACETS	0.251	0.202	0.308	0.251	0.202	0.308	SUBCLONAL	1	TRUE	1	0.43	2		721	555	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448492	89448492	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs374626393	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	59	812	0	ENST00000336596.2:c.1456A>G	p.Ile486Val	p.I486V	ENST00000336596	NM_005233.5	486	Att/Gtt	7/17	1	2	FACETS	0.586	0.505	0.674	0.586	0.505	0.674	SUBCLONAL	1	TRUE	1	0.43	2		812	468	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176536	142176536	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	53	736	0	ENST00000350721.4:c.7565G>A	p.Gly2522Glu	p.G2522E	ENST00000350721	NM_001184.3	2522	gGa/gAa	45/47	1	2	FACETS	0.664	0.569	0.769	0.664	0.569	0.769	SUBCLONAL	1	TRUE	1	0.43	2		736	371	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212126	142212126	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	82	667	0	ENST00000350721.4:c.5926C>A	p.Leu1976Ile	p.L1976I	ENST00000350721	NM_001184.3	1976	Ctt/Att	35/47	1	2	FACETS	0.963	0.854	1	0.963	0.854	1	CLONAL	1	TRUE	1	0.43	2		667	396	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149238634	149238634	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	103	805	1	ENST00000360632.3:c.1161G>T	p.Glu387Asp	p.E387D	ENST00000360632	NM_015472.4	387	gaG/gaT	7/7	1	2	FACETS	0.976	0.877	1	0.976	0.877	1	CLONAL	1	TRUE	1	0.43	2		806	491	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683373	182683373	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	77	567	0	ENST00000292782.4:c.172G>T	p.Gly58Ter	p.G58*	ENST00000292782	NM_020640.2	58	Gga/Tga	2/7	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.43	2		567	344	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146718	185146718	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	98	819	0	ENST00000265026.3:c.349A>C	p.Lys117Gln	p.K117Q	ENST00000265026	NM_004721.4	117	Aag/Cag	2/14	1	2	FACETS	0.829	0.741	0.921	0.829	0.741	0.921	CLONAL	1	TRUE	1	0.43	2		819	550	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564536	55564536	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	95	937	0	ENST00000288135.5:c.424G>T	p.Glu142Ter	p.E142*	ENST00000288135	NM_000222.2	142	Gaa/Taa	3/21	1	2	FACETS	0.846	0.756	0.942	0.846	0.756	0.942	CLONAL	1	TRUE	1	0.43	2		937	522	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599294	55599294	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	21	778	0	ENST00000288135.5:c.2420A>G	p.Lys807Arg	p.K807R	ENST00000288135	NM_000222.2	807	aAg/aGg	17/21	1	2	FACETS	0.292	0.224	0.37	0.292	0.224	0.37	SUBCLONAL	1	TRUE	1	0.43	2		778	335	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968641	55968641	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	98	678	2	ENST00000263923.4:c.2022G>T	p.Glu674Asp	p.E674D	ENST00000263923	NM_002253.2	674	gaG/gaT	14/30	1	2	FACETS	0.889	0.796	0.987	0.889	0.796	0.987	CLONAL	1	TRUE	1	0.43	2		680	513	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981172	55981172	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	31	706	0	ENST00000263923.4:c.527G>A	p.Arg176Lys	p.R176K	ENST00000263923	NM_002253.2	176	aGa/aAa	5/30	1	2	FACETS	0.455	0.368	0.552	0.455	0.368	0.552	SUBCLONAL	1	TRUE	1	0.43	2		706	317	SUCCESS
REST	5978	MSKCC	GRCh37	4	57797767	57797767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372214552	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	116	723	0	ENST00000309042.7:c.2743G>A	p.Glu915Lys	p.E915K	ENST00000309042	NM_005612.4	915	Gaa/Aaa	4/4	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.43	2		723	417	SUCCESS
ALB	213	MSKCC	GRCh37	4	74280772	74280772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771966334	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	94	586	0	ENST00000295897.4:c.1079G>A	p.Arg360Lys	p.R360K	ENST00000295897	NM_000477.5	360	aGa/aAa	9/15	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.43	2		586	433	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142950057	142950057	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374251810	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	78	632	0	ENST00000262992.4:c.2653C>T	p.Arg885Cys	p.R885C	ENST00000262992	NM_001101669.1	885	Cgc/Tgc	24/24	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.43	2		632	348	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045823	143045823	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	88	768	0	ENST00000262992.4:c.1811T>G	p.Phe604Cys	p.F604C	ENST00000262992	NM_001101669.1	604	tTt/tGt	17/24	1	2	FACETS	0.793	0.705	0.887	0.793	0.705	0.887	SUBCLONAL	1	TRUE	1	0.43	2		768	516	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253834	153253834	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	82	526	0	ENST00000281708.4:c.899A>G	p.Asp300Gly	p.D300G	ENST00000281708	NM_033632.3	300	gAc/gGc	6/12	1	2	FACETS	0.963	0.854	1	0.963	0.854	1	CLONAL	1	TRUE	1	0.43	2		526	396	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871274	35871274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776941426	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	76	494	0	ENST00000303115.3:c.496G>A	p.Asp166Asn	p.D166N	ENST00000303115	NM_002185.3	166	Gat/Aat	4/8	1	2	FACETS	0.906	0.799	1	0.906	0.799	1	CLONAL	1	TRUE	1	0.43	2		494	390	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876415	35876415	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	89	957	0	ENST00000303115.3:c.1207G>A	p.Asp403Asn	p.D403N	ENST00000303115	NM_002185.3	403	Gac/Aac	8/8	1	2	FACETS	0.784	0.697	0.876	0.784	0.697	0.876	SUBCLONAL	1	TRUE	1	0.43	2		957	528	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876507	35876507	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs200165388	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	49	1044	0	ENST00000303115.3:c.1299G>C	p.Gln433His	p.Q433H	ENST00000303115	NM_002185.3	433	caG/caC	8/8	1	2	FACETS	0.504	0.427	0.589	0.504	0.427	0.589	SUBCLONAL	1	TRUE	1	0.43	2		1044	452	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945025	38945025	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	84	653	0	ENST00000357387.3:c.4779A>C	p.Glu1593Asp	p.E1593D	ENST00000357387	NM_152756.3	1593	gaA/gaC	35/38	1	2	FACETS	0.977	0.868	1	0.977	0.868	1	CLONAL	1	TRUE	1	0.43	2		653	400	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38975689	38975689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs551282093	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	101	977	0	ENST00000357387.3:c.839G>A	p.Arg280Gln	p.R280Q	ENST00000357387	NM_152756.3	280	cGa/cAa	10/38	1	2	FACETS	0.925	0.83	1	0.925	0.83	1	CLONAL	1	TRUE	1	0.43	2		977	508	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685287	86685287	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	125	768	0	ENST00000274376.6:c.3003T>G	p.Ile1001Met	p.I1001M	ENST00000274376	NM_002890.2	1001	atT/atG	24/25	1	2	FACETS	0.989	0.898	1	0.989	0.898	1	CLONAL	1	TRUE	1	0.43	2		768	588	SUCCESS
APC	324	MSKCC	GRCh37	5	112178526	112178526	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	66	639	0	ENST00000257430.4:c.7235A>C	p.Lys2412Thr	p.K2412T	ENST00000257430	NM_000038.5	2412	aAa/aCa	16/16	1	2	FACETS	0.89	0.777	1	0.89	0.777	1	CLONAL	1	TRUE	1	0.43	2		639	345	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495471	149495471	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs888526507	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	82	1250	1	ENST00000261799.4:c.3176C>T	p.Ser1059Phe	p.S1059F	ENST00000261799	NM_002609.3	1059	tCc/tTc	23/23	1	2	FACETS	0.77	0.681	0.865	0.77	0.681	0.865	SUBCLONAL	1	TRUE	1	0.43	2		1251	495	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709541	176709541	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	100	616	1	ENST00000439151.2:c.5968G>T	p.Glu1990Ter	p.E1990*	ENST00000439151	NM_022455.4	1990	Gaa/Taa	19/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.43	2		617	360	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26046008	26046008	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	121	1104	4	ENST00000540144.1:c.370G>T	p.Asp124Tyr	p.D124Y	ENST00000540144	NM_003531.2	124	Gat/Tat	1/1	1	2	FACETS	0.989	0.897	1	0.989	0.897	1	CLONAL	1	TRUE	1	0.43	2		1108	569	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250434	26250434	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	146	1115	2	ENST00000446824.2:c.400G>T	p.Glu134Ter	p.E134*	ENST00000446824	NM_021018.2	134	Gag/Tag	1/1	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.43	2		1117	642	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680154	30680154	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	101	894	0	ENST00000376406.3:c.1565A>T	p.Asn522Ile	p.N522I	ENST00000376406	NM_014641.2	522	aAc/aTc	5/15	1	2	FACETS	0.74	0.662	0.822	0.74	0.662	0.822	SUBCLONAL	1	TRUE	1	0.43	2		894	635	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180999	32180999	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	82	787	0	ENST00000375023.3:c.2351A>G	p.Asn784Ser	p.N784S	ENST00000375023	NM_004557.3	784	aAc/aGc	15/30	1	2	FACETS	0.881	0.78	0.987	0.881	0.78	0.987	CLONAL	1	TRUE	1	0.43	2		787	433	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909377	41909377	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	70	778	0	ENST00000372991.4:c.11T>A	p.Leu4Gln	p.L4Q	ENST00000372991	NM_001760.3	4	cTg/cAg	1/5	1	2	FACETS	0.859	0.753	0.972	0.859	0.753	0.972	CLONAL	1	TRUE	1	0.43	2		778	379	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120589	94120589	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	82	694	0	ENST00000369303.4:c.462T>A	p.Ser154Arg	p.S154R	ENST00000369303	NM_004440.3	154	agT/agA	3/17	1	2	FACETS	0.861	0.762	0.965	0.861	0.762	0.965	CLONAL	1	TRUE	1	0.43	2		694	443	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642498	117642498	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	145	953	0	ENST00000368508.3:c.5701A>C	p.Asn1901His	p.N1901H	ENST00000368508	NM_002944.2	1901	Aac/Cac	35/43	0.3	1	FACETS	0.782	0.715	0.852	0.782	0.715	0.852	SUBCLONAL	1	TRUE	0	0.43	1		953	677	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679020	117679020	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1562310695	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	67	589	0	ENST00000368508.3:c.3801G>T	p.Lys1267Asn	p.K1267N	ENST00000368508	NM_002944.2	1267	aaG/aaT	24/43	0.3	1	FACETS	0.693	0.606	0.786	0.693	0.606	0.786	SUBCLONAL	1	TRUE	0	0.43	1		589	353	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710541	117710541	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	116	817	3	ENST00000368508.3:c.1731G>A	p.Trp577Ter	p.W577*	ENST00000368508	NM_002944.2	577	tgG/tgA	12/43	0.3	1	FACETS	0.787	0.712	0.866	0.787	0.712	0.866	SUBCLONAL	1	TRUE	0	0.43	1		820	538	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527978	157527978	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	131	1218	0	ENST00000346085.5:c.5703T>G	p.Ser1901Arg	p.S1901R	ENST00000346085	NM_020732.3	1901	agT/agG	20/20	1	2	FACETS	0.963	0.876	1	0.963	0.876	1	CLONAL	1	TRUE	1	0.43	2		1218	633	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683607	162683607	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	84	905	0	ENST00000366898.1:c.362T>C	p.Val121Ala	p.V121A	ENST00000366898	NM_004562.2	121	gTc/gCc	3/12	1	2	FACETS	0.821	0.728	0.92	0.821	0.728	0.92	CLONAL	1	TRUE	1	0.43	2		905	476	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210092	55210092	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	88	661	0	ENST00000275493.2:c.202A>G	p.Thr68Ala	p.T68A	ENST00000275493	NM_005228.3	68	Acc/Gcc	2/28	1	2	FACETS	0.934	0.832	1	0.934	0.832	1	CLONAL	1	TRUE	1	0.43	2		661	438	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55260490	55260490	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	53	712	0	ENST00000275493.2:c.2657T>A	p.Ile886Asn	p.I886N	ENST00000275493	NM_005228.3	886	aTt/aAt	22/28	1	2	FACETS	0.838	0.72	0.966	0.838	0.72	0.966	CLONAL	1	TRUE	1	0.43	2		712	294	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346553	81346553	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	80	703	0	ENST00000222390.5:c.1400C>A	p.Ser467Tyr	p.S467Y	ENST00000222390	NM_000601.4	467	tCt/tAt	11/18	1	2	FACETS	0.899	0.795	1	0.899	0.795	1	CLONAL	1	TRUE	1	0.43	2		703	414	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515194	148515194	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	144	839	0	ENST00000320356.2:c.1015T>G	p.Phe339Val	p.F339V	ENST00000320356	NM_004456.4	339	Ttt/Gtt	10/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.43	2		839	558	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148526843	148526843	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	51	547	0	ENST00000320356.2:c.461A>G	p.Asp154Gly	p.D154G	ENST00000320356	NM_004456.4	154	gAt/gGt	5/20	1	2	FACETS	0.835	0.715	0.965	0.835	0.715	0.965	CLONAL	1	TRUE	1	0.43	2		547	284	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880099	151880099	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	61	777	0	ENST00000262189.6:c.5225A>T	p.Gln1742Leu	p.Q1742L	ENST00000262189	NM_170606.2	1742	cAa/cTa	35/59	1	2	FACETS	0.786	0.681	0.898	0.786	0.681	0.898	SUBCLONAL	1	TRUE	1	0.43	2		777	361	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152357816	152357816	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	63	572	1	ENST00000359321.1:c.91C>A	p.Leu31Met	p.L31M	ENST00000359321	NM_005431.1	31	Ctg/Atg	2/3	1	2	FACETS	0.832	0.724	0.949	0.832	0.724	0.949	CLONAL	1	TRUE	1	0.43	2		573	352	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152357825	152357825	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	68	579	0	ENST00000359321.1:c.82G>T	p.Glu28Ter	p.E28*	ENST00000359321	NM_005431.1	28	Gaa/Taa	2/3	1	2	FACETS	0.85	0.744	0.964	0.85	0.744	0.964	CLONAL	1	TRUE	1	0.43	2		579	372	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146159	38146159	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	131	882	0	ENST00000317025.8:c.3347A>G	p.Asn1116Ser	p.N1116S	ENST00000317025	NM_023034.1	1116	aAc/aGc	19/24	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.43	2		882	568	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38184284	38184284	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	70	676	0	ENST00000317025.8:c.1672A>C	p.Ser558Arg	p.S558R	ENST00000317025	NM_023034.1	558	Agt/Cgt	7/24	1	2	FACETS	0.733	0.641	0.832	0.733	0.641	0.832	SUBCLONAL	1	TRUE	1	0.43	2		676	444	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285438	38285438	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	34	686	0	ENST00000425967.3:c.714+1G>C		p.X238_splice	ENST00000425967	NM_001174067.1	238			1	2	FACETS	0.3	0.244	0.362	0.3	0.244	0.362	SUBCLONAL	1	TRUE	1	0.43	2		686	528	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965589	90965589	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	94	646	0	ENST00000265433.3:c.1728T>G	p.Ile576Met	p.I576M	ENST00000265433	NM_002485.4	576	atT/atG	11/16	1	2	FACETS	0.978	0.875	1	0.978	0.875	1	CLONAL	1	TRUE	1	0.43	2		646	447	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2161873	2161873	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	109	823	0	ENST00000349721.2:c.4169T>G	p.Ile1390Ser	p.I1390S	ENST00000349721	NM_003070.3	1390	aTc/aGc	28/34	1	2	FACETS	0.925	0.834	1	0.925	0.834	1	CLONAL	1	TRUE	1	0.43	2		823	548	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054861	5054861	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	64	612	0	ENST00000381652.3:c.913G>T	p.Glu305Ter	p.E305*	ENST00000381652	NM_004972.3	305	Gaa/Taa	7/25	1	2	FACETS	0.899	0.784	1	0.899	0.784	1	CLONAL	1	TRUE	1	0.43	2		612	331	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376069	8376069	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	67	661	0	ENST00000356435.5:c.4528G>T	p.Glu1510Ter	p.E1510*	ENST00000356435		1510	Gaa/Taa	28/35	1	2	FACETS	0.833	0.728	0.946	0.833	0.728	0.946	CLONAL	1	TRUE	1	0.43	2		661	374	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376075	8376075	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	38	656	0	ENST00000356435.5:c.4522A>G	p.Lys1508Glu	p.K1508E	ENST00000356435		1508	Aag/Gag	28/35	1	2	FACETS	0.476	0.394	0.568	0.476	0.394	0.568	SUBCLONAL	1	TRUE	1	0.43	2		656	371	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430665	80430665	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	72	466	2	ENST00000286548.4:c.343G>T	p.Glu115Ter	p.E115*	ENST00000286548	NM_002072.3	115	Gaa/Taa	3/7	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.43	2		468	247	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941875	44941875	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	83	595	1	ENST00000377967.4:c.3199T>C	p.Ser1067Pro	p.S1067P	ENST00000377967	NM_021140.2	1067	Tcg/Ccg	21/29	1	2	FACETS	0.942	0.836	1	0.942	0.836	1	CLONAL	1	TRUE	1	0.43	2		596	410	SUCCESS
AR	367	MSKCC	GRCh37	X	66931496	66931496	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	110	1002	0	ENST00000374690.3:c.2138T>G	p.Leu713Arg	p.L713R	ENST00000374690	NM_000044.3	713	cTt/cGt	4/8	1	2	FACETS	0.885	0.798	0.977	0.885	0.798	0.977	CLONAL	1	TRUE	1	0.43	2		1002	578	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341595	70341595	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	102	1101	0	ENST00000374080.3:c.1030A>G	p.Thr344Ala	p.T344A	ENST00000374080		344	Act/Gct	7/45	1	2	FACETS	0.849	0.761	0.941	0.849	0.761	0.941	CLONAL	1	TRUE	1	0.43	2		1101	559	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814187	76814187	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	74	628	0	ENST00000373344.5:c.6457C>T	p.Arg2153Cys	p.R2153C	ENST00000373344	NM_000489.3	2153	Cgc/Tgc	29/35	1	2	FACETS	0.986	0.87	1	0.986	0.87	1	CLONAL	1	TRUE	1	0.43	2		628	349	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855039	76855039	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	69	775	0	ENST00000373344.5:c.5797A>T	p.Lys1933Ter	p.K1933*	ENST00000373344	NM_000489.3	1933	Aaa/Taa	25/35	1	2	FACETS	0.734	0.642	0.834	0.734	0.642	0.834	SUBCLONAL	1	TRUE	1	0.43	2		775	437	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019937	123019937	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	98	666	0	ENST00000355640.3:c.425G>A	p.Arg142Lys	p.R142K	ENST00000355640		142	aGa/aAa	2/7	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.43	2		666	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0068451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	193	546	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	0.242792958045626	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.243909857188977	2		546	690	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986603	36986652	+	frameshift_variant	Frame_Shift_Del	DEL	GTGCGCCAGGTCCGGAGACTGGCCTGCGCTGCCTGGCTGGTGGCCCGGGT	GTGCGCCAGGTCCGGAGACTGGCCTGCGCTGCCTGGCTGGTGGCCCGGGT	-	novel	NA	P-0068451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	115	411	0	ENST00000354822.5:c.1037_1086del	p.His346ProfsTer76	p.H346Pfs*76	ENST00000354822	NM_001079668.2	346	cACCCGGGCCACCAGCCAGGCAGCGCAGGCCAGTCTCCGGACCTGGCGCAC/c	3/3	0.243909857188977	2	FACETS	0.956	0.866	1	0.956	0.866	1	CLONAL	2	TRUE	0	0.243909857188977	2		411	493	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187753	11187753	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	93	412	0	ENST00000361445.4:c.6144T>G	p.Phe2048Leu	p.F2048L	ENST00000361445	NM_004958.3	2048	ttT/ttG	44/58	0.235133299468941	3	FACETS	1	0.972	1	0.65	0.578	0.726	CLONAL	1	TRUE	1	0.243909857188977	3		412	658	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959477	26959477	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	49	300	0	ENST00000381527.3:c.644T>C	p.Ile215Thr	p.I215T	ENST00000381527	NM_001260.1	215	aTt/aCt	6/13	0.108440470023092	4	FACETS	0.856	0.729	0.993	0.856	0.729	0.993	INDETERMINATE	2	TRUE	2	0.243909857188977	4		300	292	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	443428	443428	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	22	418	0	ENST00000399788.2:c.1469A>T	p.Tyr490Phe	p.Y490F	ENST00000399788	NM_001042603.1	490	tAt/tTt	11/28	0.242792958045626	2	FACETS	0.548	0.425	0.692	0.274	0.212	0.346	SUBCLONAL	1	TRUE	0	0.243909857188977	2		418	329	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401404	139401404	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	67	429	0	ENST00000277541.6:c.3665T>G	p.Val1222Gly	p.V1222G	ENST00000277541	NM_017617.3	1222	gTg/gGg	23/34	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.243909857188977	2		429	540	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752803	128752803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068452-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	813	553	0	ENST00000377970.2:c.964C>T	p.His322Tyr	p.H322Y	ENST00000377970	NM_002467.4	322	Cac/Tac	3/3	0.80125520105793	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.80125520105793	3		553	1378	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602763	10602763	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs774469695	NA	P-0068452-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	719	540	0	ENST00000171111.5:c.815G>T	p.Arg272Leu	p.R272L	ENST00000171111	NM_203500.1	272	cGc/cTc	3/6	0.80125520105793	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.80125520105793	2		540	877	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0068452-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	151	320	1	ENST00000311936.3:c.34_35delinsTT	p.Gly12Phe	p.G12F	ENST00000311936	NM_004985.3	12	GGt/TTt	2/5	1	2	FACETS	0.849	0.783	0.916	0.849	0.783	0.916	CLONAL	1	TRUE	1	0.80125520105793	2		321	444	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272523	142272523	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068452-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	255	412	0	ENST00000350721.4:c.2592G>T	p.Glu864Asp	p.E864D	ENST00000350721	NM_001184.3	864	gaG/gaT	12/47	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.80125520105793	2		412	616	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459525	50459525	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068452-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	224	415	0	ENST00000331340.3:c.814G>T	p.Ala272Ser	p.A272S	ENST00000331340	NM_006060.4	272	Gcc/Tcc	7/8	0.140008382913329	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.80125520105793	0		415	591	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276224	15276224	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068452-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	303	486	0	ENST00000263388.2:c.5770G>C	p.Glu1924Gln	p.E1924Q	ENST00000263388	NM_000435.2	1924	Gag/Cag	31/33	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.80125520105793	2		486	733	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433647	149433647	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068452-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	229	394	0	ENST00000286301.3:c.2904C>A	p.Asn968Lys	p.N968K	ENST00000286301	NM_005211.3	968	aaC/aaA	22/22	1	2	FACETS	0.919	0.862	0.977	0.919	0.862	0.977	CLONAL	1	TRUE	1	0.80125520105793	2		394	622	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472461	88472461	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068452-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	270	569	0	ENST00000360948.2:c.2094C>A	p.Phe698Leu	p.F698L	ENST00000360948	NM_001012338.2	698	ttC/ttA	16/19	NA	2	FACETS	0.997	0.941	1			1	INDETERMINATE	1	TRUE	NA	0.80125520105793	2		569	676	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892175	9892175	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068452-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	158	593	0	ENST00000330684.3:c.2315A>T	p.Lys772Met	p.K772M	ENST00000330684	NM_001134407.1	772	aAg/aTg	11/13	NA	2	FACETS	0.61	0.561	0.662			1	INDETERMINATE	1	TRUE	NA	0.80125520105793	2		593	646	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098548	108098549	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0068452-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	192	474	0	ENST00000278616.4:c.120dup	p.Lys41Ter	p.K41*	ENST00000278616	NM_000051.3	40	att/aTtt	3/63	0.80125520105793	1	FACETS	0.918	0.868	0.966	0.918	0.868	0.966	CLONAL	1	TRUE	0	0.80125520105793	1		474	313	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94209455	94209455	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068452-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	170	314	0	ENST00000323929.3:c.659G>T	p.Arg220Met	p.R220M	ENST00000323929	NM_005591.3	220	aGg/aTg	7/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.80125520105793	2		314	408	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112745425	112745425	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs374067666	NA	P-0068452-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	201	414	0	ENST00000369452.4:c.743A>G	p.Asn248Ser	p.N248S	ENST00000369452	NM_007373.3	248	aAt/aGt	3/9	1	2	FACETS	0.982	0.918	1	0.982	0.918	1	CLONAL	1	TRUE	1	0.80125520105793	2		414	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0068453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	580	284	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.938878528928155	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.938878528928155	2		284	597	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653834	89653834	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	254	290	3	ENST00000371953.3:c.132del	p.Val45TyrfsTer9	p.V45Yfs*9	ENST00000371953	NM_000314.4	44	ggC/gg	2/9	0.938878528928155	3	FACETS	0.993	0.974	1	0.993	0.974	1	CLONAL	3	TRUE	0	0.938878528928155	3		293	267	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866359	37866359	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	501	411	0	ENST00000269571.5:c.664G>T	p.Gly222Cys	p.G222C	ENST00000269571		222	Ggt/Tgt	6/27	0.938878528928155	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.938878528928155	3		411	774	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253800	153253800	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	219	334	0	ENST00000281708.4:c.933G>A	p.Trp311Ter	p.W311*	ENST00000281708	NM_033632.3	311	tgG/tgA	6/12	0.938878528928155	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.938878528928155	2		334	226	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29449588	29449588	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	250	284	1	ENST00000544604.2:c.2789A>G	p.Asp930Gly	p.D930G	ENST00000544604	NM_001206998.1	930	gAc/gGc	9/9	1	2	FACETS	0.999	0.945	1	0.999	0.945	1	CLONAL	1	TRUE	1	0.938878528928155	2		285	533	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170016870	170016870	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	136	216	0	ENST00000295797.4:c.1675G>T	p.Glu559Ter	p.E559*	ENST00000295797	NM_002740.5	559	Gaa/Taa	17/18	0.863375326244692	4	FACETS	1	0.952	1	0.531	0.485	0.578	CLONAL	1	TRUE	2	0.938878528928155	4		216	529	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945972	17945972	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	718	505	0	ENST00000458235.1:c.1967C>A	p.Ala656Asp	p.A656D	ENST00000458235	NM_000215.3	656	gCt/gAt	15/24	0.938878528928155	3	FACETS	0.989	0.962	1	0.989	0.962	1	CLONAL	2	TRUE	1	0.938878528928155	3		505	1136	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31238907	31238907	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	67	175	1	ENST00000376228.5:c.562T>C	p.Cys188Arg	p.C188R	ENST00000376228	NM_002117.5	188	Tgc/Cgc	3/8	0.878947599058841	3	FACETS	0.643	0.563	0.729	0.322	0.281	0.365	SUBCLONAL	1	TRUE	1	0.938878528928155	3		176	326	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0068453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	166	437	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.217135451030071	6	FACETS	1	0.972	1	0.881	0.815	0.948	CLONAL	4	TRUE	1	0.217135451030071	6		437	498	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0068453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	93	432	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.217135451030071	2		432	682	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480499	123480499	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs148554414	NA	P-0068453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	91	327	0	ENST00000371139.4:c.7G>T	p.Ala3Ser	p.A3S	ENST00000371139	NM_001114937.2	3	Gca/Tca	1/4	NA	2	FACETS	0.759	0.676	0.848			1	INDETERMINATE	2	TRUE	NA	0.217135451030071	2		327	552	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127387	55127387	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	76	492	0	ENST00000257290.5:c.175T>A	p.Tyr59Asn	p.Y59N	ENST00000257290	NM_006206.4	59	Tac/Aac	3/23	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.217135451030071	2		492	663	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112074	115112074	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	143	499	0	ENST00000257566.3:c.1666C>A	p.Leu556Met	p.L556M	ENST00000257566	NM_016569.3	556	Ctg/Atg	7/8	0.217135451030071	1	FACETS	0.878	0.802	0.956	1	0.99	1	CLONAL	2	TRUE	0	0.217135451030071	1		499	669	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909490	50909490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774130423	NA	P-0068453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	73	517	2	ENST00000440232.2:c.1294C>T	p.Arg432Trp	p.R432W	ENST00000440232	NM_002691.3	432	Cgg/Tgg	11/27	NA	2	FACETS	0.93	0.813	1			1	INDETERMINATE	1	TRUE	NA	0.217135451030071	2		519	723	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332070	81332070	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	62	301	0	ENST00000222390.5:c.2014del	p.Asp672IlefsTer13	p.D672Ifs*13	ENST00000222390	NM_000601.4	672	Gat/at	18/18	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.217135451030071	2		301	392	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50784990	50784990	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs146125856	NA	P-0068453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	19	235	0	ENST00000307179.4:c.2327T>C	p.Leu776Pro	p.L776P	ENST00000307179		776	cTt/cCt	15/20	0.175272263392008	1	FACETS	0.46	0.349	0.591	0.46	0.349	0.591	SUBCLONAL	1	TRUE	0	0.217135451030071	1		235	339	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798120	45798120	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	42	559	0	ENST00000450313.1:c.731G>T	p.Cys244Phe	p.C244F	ENST00000450313	NM_012222.2	244	tGc/tTc	9/16	1	2	FACETS	0.543	0.452	0.644	0.543	0.452	0.644	SUBCLONAL	1	TRUE	1	0.217135451030071	2		559	713	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678344	88678344	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	32	419	0	ENST00000360948.2:c.1192G>T	p.Glu398Ter	p.E398*	ENST00000360948	NM_001012338.2	398	Gag/Tag	9/19	0.175272263392008	1	FACETS	0.457	0.37	0.556	0.457	0.37	0.556	SUBCLONAL	1	TRUE	0	0.217135451030071	1		419	575	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696465	47696465	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	45	479	0	ENST00000347630.2:c.358C>G	p.Gln120Glu	p.Q120E	ENST00000347630	NM_001007230.1	120	Caa/Gaa	6/11	1	2	FACETS	0.632	0.53	0.745	0.632	0.53	0.745	SUBCLONAL	1	TRUE	1	0.217135451030071	2		479	656	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522599	67522605	+	frameshift_variant	Frame_Shift_Del	DEL	GAATAAA	GAATAAA	-	novel	NA	P-0068453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	94	393	0	ENST00000274335.5:c.97_103del	p.Asn33GlyfsTer3	p.N33Gfs*3	ENST00000274335		32	gtGAATAAA/gt	1/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.217135451030071	2		393	593	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012357	29012358	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0068453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	57	301	0	ENST00000282397.4:c.513_513+1delinsTT		p.X171_splice	ENST00000282397	NM_002019.4	171		4/30	0.217135451030071	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.217135451030071	1		301	391	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21639478	21639478	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	70	298	0	ENST00000421138.2:c.436G>C	p.Asp146His	p.D146H	ENST00000421138		146	Gac/Cac	6/16	0.217135451030071	1	FACETS	0.845	0.742	0.955	1	0.979	1	CLONAL	2	TRUE	0	0.217135451030071	1		298	340	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865749	57865749	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	127	516	0	ENST00000228682.2:c.3226C>A	p.Pro1076Thr	p.P1076T	ENST00000228682	NM_005269.2	1076	Cct/Act	12/12	0.217135451030071	3	FACETS	1	0.983	1	0.702	0.635	0.772	CLONAL	1	TRUE	1	0.217135451030071	3		516	924	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015673	27015673	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	87	454	0	ENST00000335756.4:c.260A>T	p.Gln87Leu	p.Q87L	ENST00000335756	NM_001809.3	87	cAa/cTa	3/5	1	2	FACETS	0.997	0.882	1	0.997	0.882	1	CLONAL	1	TRUE	1	0.217135451030071	2		454	804	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115831	8115832	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0068453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	62	410	2	ENST00000346208.3:c.1177_1178delinsAA	p.Pro393Lys	p.P393K	ENST00000346208		393	CCg/AAg	6/6	1	2	FACETS	0.89	0.768	1	0.89	0.768	1	CLONAL	1	TRUE	1	0.217135451030071	2		412	642	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163566	47163566	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	62	352	0	ENST00000409792.3:c.2560C>T	p.Gln854Ter	p.Q854*	ENST00000409792	NM_014159.6	854	Cag/Tag	3/21	0.217135451030071	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.217135451030071	1		352	413	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865108	57865108	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	72	427	1	ENST00000228682.2:c.2585C>A	p.Ser862Ter	p.S862*	ENST00000228682	NM_005269.2	862	tCa/tAa	12/12	0.217135451030071	3	FACETS	0.926	0.808	1	0.463	0.404	0.527	CLONAL	1	TRUE	1	0.217135451030071	3		428	794	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928980	44928980	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	75	316	0	ENST00000377967.4:c.2080G>T	p.Ala694Ser	p.A694S	ENST00000377967	NM_021140.2	694	Gct/Tct	17/29	0.175272263392008	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.217135451030071	1		316	496	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446111	70446111	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0068453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	73	291	0	ENST00000373644.4:c.5053-2A>G		p.X1685_splice	ENST00000373644	NM_030625.2	1685			1	2	FACETS	0.771	0.677	0.872	1	0.976	1	SUBCLONAL	2	TRUE	1	0.217135451030071	2		291	436	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028073	69028073	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	56	420	0	ENST00000288368.4:c.3232G>T	p.Gly1078Ter	p.G1078*	ENST00000288368	NM_024870.2	1078	Gga/Tga	26/40	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.217135451030071	2		420	490	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573665	48573702	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTTAGTCTTATAAGAGTTTTTCTATACCCTCTATGGT	GGTTAGTCTTATAAGAGTTTTTCTATACCCTCTATGGT	-	novel	NA	P-0068453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	54	361	0	ENST00000342988.3:c.249+2_249+39del		p.X83_splice	ENST00000342988	NM_005359.5	83		2/12	0.217135451030071	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.217135451030071	1		361	370	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206892	162206892	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	84	442	0	ENST00000366898.1:c.783A>T	p.Leu261Phe	p.L261F	ENST00000366898	NM_004562.2	261	ttA/ttT	7/12	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.217135451030071	2		442	640	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622086	43622086	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0068453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	81	437	0	ENST00000355710.3:c.3103G>T	p.Glu1035Ter	p.E1035*	ENST00000355710	NM_020975.4	1035	Gag/Tag	19/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.217135451030071	2		437	633	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524818	137524818	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	53	303	0	ENST00000367739.4:c.551A>C	p.Gln184Pro	p.Q184P	ENST00000367739	NM_000416.2	184	cAg/cCg	5/7	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.217135451030071	2		303	402	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339492	116339492	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	124	435	0	ENST00000397752.3:c.354G>T	p.Met118Ile	p.M118I	ENST00000397752	NM_000245.2	118	atG/atT	2/21	1	2	FACETS	0.846	0.767	0.929	1	0.987	1	CLONAL	2	TRUE	1	0.217135451030071	2		435	675	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42842656	42842656	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1430677365	NA	P-0068453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	78	384	0	ENST00000398585.3:c.1201G>T	p.Val401Leu	p.V401L	ENST00000398585	NM_001135099.1	401	Gtg/Ttg	11/14	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.217135451030071	2		384	554	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942068	81942068	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	67	433	0	ENST00000359376.3:c.1605G>T	p.Lys535Asn	p.K535N	ENST00000359376	NM_002661.3	535	aaG/aaT	17/33	1	2	FACETS	0.921	0.8	1	0.921	0.8	1	CLONAL	1	TRUE	1	0.217135451030071	2		433	670	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272159	142272160	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0068453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	69	363	1	ENST00000350721.4:c.2714_2715delinsTT	p.Gly905Val	p.G905V	ENST00000350721	NM_001184.3	905	gGA/gTT	13/47	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.217135451030071	2		364	504	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0068457-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	101	504	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.915	0.821	1	0.915	0.821	1	CLONAL	1	TRUE	1	0.44	2		504	502	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557628	95557628	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068457-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	127	553	0	ENST00000393063.1:c.5439G>T	p.Glu1813Asp	p.E1813D	ENST00000393063	NM_030621.3	1813	gaG/gaT	26/28	1	2	FACETS	0.999	0.908	1	0.999	0.908	1	CLONAL	1	TRUE	1	0.44	2		553	578	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570058	95570058	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs184830847	NA	P-0068457-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	120	552	0	ENST00000393063.1:c.3675C>G	p.Tyr1225Ter	p.Y1225*	ENST00000393063	NM_030621.3	1225	taC/taG	22/28	1	2	FACETS	0.87	0.787	0.957	0.87	0.787	0.957	CLONAL	1	TRUE	1	0.44	2		552	627	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	13	350	0				ENST00000310581	NM_198253.2	-/1132			0.197429448895263	1	FACETS	0.634	0.454	0.85	0.634	0.454	0.85	SUBCLONAL	1	TRUE	0	0.25403655059347	1		350	141	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916653	178916653	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	16	119	0	ENST00000263967.3:c.40C>G	p.His14Asp	p.H14D	ENST00000263967	NM_006218.2	14	Cac/Gac	2/21	1	2	FACETS	0.666	0.494	0.871	0.666	0.494	0.871	SUBCLONAL	1	TRUE	1	0.25403655059347	2		119	189	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715637	30715637	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	47	128	0	ENST00000295754.5:c.1295C>T	p.Ser432Phe	p.S432F	ENST00000295754	NM_003242.5	432	tCc/tTc	5/7	1	2	FACETS	0.771	0.656	0.895	1	0.965	1	SUBCLONAL	2	TRUE	1	0.25403655059347	2		128	240	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191503	10191503	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	25	138	0	ENST00000256474.2:c.496del	p.Val166SerfsTer4	p.V166Sfs*4	ENST00000256474	NM_000551.3	166	Gtc/tc	3/3	NA	2	FACETS	0.989	0.785	1			1	INDETERMINATE	1	TRUE	NA	0.25403655059347	2		138	199	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436690	52436690	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	39	170	0	ENST00000460680.1:c.1984del	p.Ile662LeufsTer30	p.I662Lfs*30	ENST00000460680	NM_004656.3	662	Att/tt	16/17	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.25403655059347	2		170	229	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577157	7577157	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1060501207	NA	P-0068474-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	53	131	0	ENST00000269305.4:c.783-2A>G		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.177422813261641	2	FACETS	1	0.958	1	0.657	0.566	0.754	INDETERMINATE	1	TRUE	0	0.340510755256016	2		131	237	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989592	212989592	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068474-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	13	175	0	ENST00000342788.4:c.119C>G	p.Ser40Cys	p.S40C	ENST00000342788	NM_005235.2	40	tCt/tGt	2/28	1	2	FACETS	0.314	0.224	0.425	0.314	0.224	0.425	SUBCLONAL	1	TRUE	1	0.340510755256016	2		175	243	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346340	73346340	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068474-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	11	129	0	ENST00000377767.4:c.1460A>T	p.Asp487Val	p.D487V	ENST00000377767	NM_014953.3	487	gAc/gTc	10/21	NA	2	FACETS	0.687	0.48	0.939			1	INDETERMINATE	1	TRUE	NA	0.340510755256016	2		129	94	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577136	7577136	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068474-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	62	165	0	ENST00000269305.4:c.802A>T	p.Asn268Tyr	p.N268Y	ENST00000269305	NM_001126112.2	268	Aac/Tac	8/11	0.177422813261641	2	FACETS	1	0.965	1	0.667	0.582	0.758	INDETERMINATE	1	TRUE	0	0.340510755256016	2		165	273	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231197	142231197	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068474-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	27	146	0	ENST00000350721.4:c.4757A>G	p.Asp1586Gly	p.D1586G	ENST00000350721	NM_001184.3	1586	gAc/gGc	27/47	0.340510755256016	3	FACETS	0.675	0.538	0.83			1	SUBCLONAL	1	TRUE	NA	0.340510755256016	3		146	275	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80088604	80088604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068474-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	13	157	0	ENST00000265081.6:c.2596G>A	p.Val866Met	p.V866M	ENST00000265081	NM_002439.4	866	Gtg/Atg	19/24	1	2	FACETS	0.48	0.344	0.645	0.48	0.344	0.645	SUBCLONAL	1	TRUE	1	0.340510755256016	2		157	159	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046580	42046636	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTAGGTGTGCTTGCCACTCAATACATTATTTACTTTTATAATGATGTATTTCAGAA	TTTAGGTGTGCTTGCCACTCAATACATTATTTACTTTTATAATGATGTATTTCAGAA	-	novel	NA	P-0068474-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	29	81	0	ENST00000219905.7:c.7009-54_7011del		p.X2337_splice	ENST00000219905	NM_001164273.1	2337		18/24	0.177422813261641	2	FACETS	1	0.885	1	0.564	0.458	0.681	INDETERMINATE	1	TRUE	0	0.340510755256016	2		81	151	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219347	1219349	+	frameshift_variant	Frame_Shift_Del	DEL	GTG	GTG	TT	novel	NA	P-0068474-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	67	192	0	ENST00000326873.7:c.399_401delinsTT	p.Cys134LeufsTer27	p.C134Lfs*27	ENST00000326873	NM_000455.4	133	gtGTGt/gtTTt	3/10	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	1	TRUE	NA	0.340510755256016	2		192	296	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012765	36012765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068475-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	42	169	0	ENST00000358208.4:c.209C>T	p.Ser70Leu	p.S70L	ENST00000358208		70	tCg/tTg	2/12	1	2	FACETS	0.743	0.627	0.868	0.743	0.627	0.868	SUBCLONAL	1	TRUE	1	0.568097737052943	2		169	199	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591149	+	inframe_deletion	In_Frame_Del	DEL	GACGAGAGACCAATACTT	GACGAGAGACCAATACTT	-	novel	NA	P-0068475-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	71	134	0	ENST00000274335.5:c.1727_1744del	p.Thr576_Leu581del	p.T576_L581del	ENST00000274335		575	aaGACGAGAGACCAATACTTg/aag	12/15	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.568097737052943	2		134	229	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555098	106555098	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068475-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	29	204	0	ENST00000369096.4:c.2215G>T	p.Ala739Ser	p.A739S	ENST00000369096	NM_001198.3	739	Gct/Tct	7/7	1	2	FACETS	0.328	0.264	0.401	0.328	0.264	0.401	SUBCLONAL	1	TRUE	1	0.568097737052943	2		204	311	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31238901	31238901	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068475-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	36	195	0	ENST00000376228.5:c.568G>T	p.Glu190Ter	p.E190*	ENST00000376228	NM_002117.5	190	Gag/Tag	3/8	1	2	FACETS	0.618	0.513	0.734	0.618	0.513	0.734	SUBCLONAL	1	TRUE	1	0.568097737052943	2		195	205	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742693	39742693	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068475-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	91	193	0	ENST00000361337.2:c.1536C>G	p.Ile512Met	p.I512M	ENST00000361337	NM_003286.2	512	atC/atG	15/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.568097737052943	2		193	255	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707807	176707807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068475-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	69	189	0	ENST00000439151.2:c.5864G>A	p.Gly1955Asp	p.G1955D	ENST00000439151	NM_022455.4	1955	gGt/gAt	18/23	1	2	FACETS	0.896	0.789	1	0.896	0.789	1	CLONAL	1	TRUE	1	0.568097737052943	2		189	271	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0068476-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	26	437	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.26	2		437	167	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578242	7578242	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882003	NA	P-0068476-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	35	216	0	ENST00000269305.4:c.607G>T	p.Val203Leu	p.V203L	ENST00000269305	NM_001126112.2	203	Gtg/Ttg	6/11	1	2	FACETS	1	0.831	1	1	0.831	1	CLONAL	1	TRUE	1	0.26	2		216	267	SUCCESS
APC	324	MSKCC	GRCh37	5	112175328	112175328	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068476-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	46	166	0	ENST00000257430.4:c.4037C>A	p.Ser1346Ter	p.S1346*	ENST00000257430	NM_000038.5	1346	tCa/tAa	16/16	0.3	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.26	1		166	243	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511155	148511155	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068476-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	20	170	0	ENST00000320356.2:c.1747C>T	p.Arg583Ter	p.R583*	ENST00000320356	NM_004456.4	583	Cga/Tga	15/20	1	2	FACETS	0.62	0.475	0.789	0.62	0.475	0.789	SUBCLONAL	1	TRUE	1	0.26	2		170	248	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666636	206666636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782318549	NA	P-0068476-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	18	213	0	ENST00000367120.3:c.1970G>A	p.Arg657Gln	p.R657Q	ENST00000367120	NM_014002.3	657	cGa/cAa	20/22	1	2	FACETS	0.519	0.391	0.67	0.519	0.391	0.67	SUBCLONAL	1	TRUE	1	0.26	2		213	267	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6036994	6036994	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782633	NA	P-0068476-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	15	117	0	ENST00000265849.7:c.766G>A	p.Gly256Ser	p.G256S	ENST00000265849	NM_000535.5	256	Ggt/Agt	7/15	1	2	FACETS	0.5	0.365	0.66	0.5	0.365	0.66	SUBCLONAL	1	TRUE	1	0.26	2		117	231	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057638	180057638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068476-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	45	220	0	ENST00000261937.6:c.317C>T	p.Thr106Ile	p.T106I	ENST00000261937	NM_182925.4	106	aCa/aTa	3/30	0.3	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.26	1		220	231	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435948	49435948	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1247545411	NA	P-0068476-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	24	225	0	ENST00000301067.7:c.6033G>T	p.Glu2011Asp	p.E2011D	ENST00000301067	NM_003482.3	2011	gaG/gaT	28/54	1	2	FACETS	0.776	0.61	0.965	0.776	0.61	0.965	CLONAL	1	TRUE	1	0.26	2		225	238	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350593	15350593	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157242729	NA	P-0068476-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	29	181	0	ENST00000263377.2:c.3322G>A	p.Val1108Met	p.V1108M	ENST00000263377	NM_058243.2	1108	Gtg/Atg	16/20	1	2	FACETS	0.918	0.74	1	0.918	0.74	1	CLONAL	1	TRUE	1	0.26	2		181	243	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	71	350	0				ENST00000310581	NM_198253.2	-/1132			0.289127021847348	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.289127021847348	1		350	281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	235	559	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	1	2	FACETS	1	0.954	1	1	0.995	1	CLONAL	2	TRUE	1	0.289127021847348	2		559	794	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023633	27023634	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCGGCTC	novel	NA	P-0068485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	72	498	0	ENST00000324856.7:c.741_747dup	p.Lys250ArgfsTer152	p.K250Rfs*152	ENST00000324856	NM_006015.4	247	gcc/gCCGGCTCcc	1/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.289127021847348	2		498	397	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879903	37879903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	1079	566	0	ENST00000269571.5:c.2198C>T	p.Thr733Ile	p.T733I	ENST00000269571		733	aCa/aTa	18/27	0.289127021847348	12	FACETS	0.973	0.952	0.995			1	CLONAL	11	TRUE	NA	0.289127021847348	12		566	1705	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402595	20402595	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	85	520	0	ENST00000346618.3:c.132C>G	p.Phe44Leu	p.F44L	ENST00000346618	NM_001949.4	44	ttC/ttG	1/7	0.289127021847348	5	FACETS	1	0.967	1	0.317	0.28	0.357	CLONAL	1	TRUE	1	0.289127021847348	5		520	664	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082599	16082599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	47	308	0	ENST00000281043.3:c.413G>A	p.Arg138His	p.R138H	ENST00000281043	NM_005378.4	138	cGc/cAc	2/3	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.289127021847348	2		308	256	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207488	29207488	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1188486918	NA	P-0068485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	84	360	0	ENST00000240100.2:c.308C>T	p.Ser103Leu	p.S103L	ENST00000240100	NM_001394.6	103	tCg/tTg	1/4	1	2	FACETS	0.775	0.689	0.865	1	0.98	1	SUBCLONAL	2	TRUE	1	0.289127021847348	2		360	375	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118370627	118370627	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	88	399	0	ENST00000534358.1:c.6157C>T	p.Gln2053Ter	p.Q2053*	ENST00000534358	NM_005933.3	2053	Cag/Tag	24/36	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.289127021847348	2		399	467	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947579	48947579	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0068485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	143	375	0	ENST00000267163.4:c.1166T>G	p.Leu389Ter	p.L389*	ENST00000267163	NM_000321.2	389	tTa/tGa	12/27	0.289127021847348	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.289127021847348	2		375	424	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860735	3860735	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	120	458	0	ENST00000262367.5:c.844C>T	p.Gln282Ter	p.Q282*	ENST00000262367	NM_004380.2	282	Caa/Taa	3/31	0.289127021847348	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.289127021847348	1		458	543	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440664	56440664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	109	508	0	ENST00000407977.2:c.554G>A	p.Arg185Lys	p.R185K	ENST00000407977		185	aGg/aAg	5/10	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.289127021847348	2		508	724	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900674	3900674	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs573905785	NA	P-0068485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	205	527	0	ENST00000262367.5:c.422C>G	p.Ser141Cys	p.S141C	ENST00000262367	NM_004380.2	141	tCt/tGt	2/31	0.289127021847348	1	FACETS	1	0.965	1	1	0.994	1	CLONAL	2	TRUE	0	0.289127021847348	1		527	578	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981646	63981657	+	inframe_deletion	In_Frame_Del	DEL	CTCTTCCTCCTC	CTCTTCCTCCTC	-	rs752651112	NA	P-0068485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	122	614	0	ENST00000398590.3:c.2163_2174del	p.Ser725_Ser728del	p.S725_S728del	ENST00000398590	NM_001177387.1	716	caCTCTTCCTCCTCc/cac	12/14	0.19652779220846	2	FACETS	1	0.975	1	0.615	0.557	0.677	CLONAL	1	TRUE	0	0.289127021847348	2		614	686	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619082	37619082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1313	184	518	0	ENST00000447079.4:c.758C>T	p.Ser253Phe	p.S253F	ENST00000447079	NM_015083.1	253	tCt/tTt	1/14	0.289127021847348	12	FACETS	1	0.948	1			1	CLONAL	2	TRUE	NA	0.289127021847348	12		518	1497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578286	+	inframe_deletion	In_Frame_Del	DEL	GAGGAGGGGCCA	GAGGAGGGGCCA	-	novel	NA	P-0068485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	153	670	0	ENST00000269305.4:c.563_574del	p.Leu188_Pro191del	p.L188_P191del	ENST00000269305	NM_001126112.2	188	cTGGCCCCTCCTCag/cag	6/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.289127021847348	2		670	812	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782651	9782651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	255	374	0	ENST00000377346.4:c.2413G>A	p.Gly805Arg	p.G805R	ENST00000377346	NM_005026.3	805	Ggg/Agg	19/24	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.811374573212711	2		374	503	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115279452	115279452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	210	330	0	ENST00000438362.2:c.565C>T	p.Pro189Ser	p.P189S	ENST00000438362	NM_001242891.1	189	Cct/Tct	6/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.811374573212711	2		330	431	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244815	46244815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	358	552	0	ENST00000334344.6:c.2909C>T	p.Pro970Leu	p.P970L	ENST00000334344	NM_152641.2	970	cCa/cTa	15/21	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.811374573212711	2		552	728	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955482	48955482	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	195	374	0	ENST00000267163.4:c.1600del	p.Ser534ValfsTer9	p.S534Vfs*9	ENST00000267163	NM_000321.2	533	gAa/ga	17/27	0.811374573212711	3	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.811374573212711	3		374	604	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73351584	73351584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	334	399	0	ENST00000377767.4:c.628C>T	p.Arg210Cys	p.R210C	ENST00000377767	NM_014953.3	210	Cgt/Tgt	4/21	0.791503140376733	4	FACETS	1	0.992	1	0.637	0.602	0.672	CLONAL	1	TRUE	2	0.811374573212711	4		399	1171	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42002918	42002918	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	232	399	0	ENST00000219905.7:c.2455C>T	p.Arg819Cys	p.R819C	ENST00000219905	NM_001164273.1	819	Cgt/Tgt	8/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.811374573212711	2		399	506	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459909	99459909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	297	444	0	ENST00000268035.6:c.2005C>T	p.Pro669Ser	p.P669S	ENST00000268035	NM_000875.3	669	Ccc/Tcc	10/21	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.811374573212711	2		444	646	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640758	3640758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	313	543	0	ENST00000294008.3:c.2881C>T	p.Pro961Ser	p.P961S	ENST00000294008	NM_032444.2	961	Cct/Tct	12/15	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.811374573212711	2		543	667	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857163	9857163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	315	520	0	ENST00000330684.3:c.4238C>T	p.Ser1413Phe	p.S1413F	ENST00000330684	NM_001134407.1	1413	tCc/tTc	13/13	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.811374573212711	2		520	620	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867355	68867355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622630	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	328	463	0	ENST00000261769.5:c.2602C>T	p.Arg868Cys	p.R868C	ENST00000261769	NM_004360.3	868	Cgc/Tgc	16/16	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.811374573212711	2		463	665	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	354	408	0	ENST00000269305.4:c.853G>T	p.Glu285Ter	p.E285*	ENST00000269305	NM_001126112.2	285	Gag/Tag	8/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.811374573212711	2		408	768	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	376	587	0	ENST00000269305.4:c.532C>T	p.His178Tyr	p.H178Y	ENST00000269305	NM_001126112.2	178	Cac/Tac	5/11	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.811374573212711	2		587	782	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519980	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	376	578	0	ENST00000269305.4:c.528C>G	p.Cys176Trp	p.C176W	ENST00000269305	NM_001126112.2	176	tgC/tgG	5/11	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.811374573212711	2		578	774	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110130	8110130	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs531140672	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	349	464	0	ENST00000585124.1:c.475C>T	p.Arg159Cys	p.R159C	ENST00000585124	NM_004217.3	159	Cgc/Tgc	6/9	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.811374573212711	2		464	747	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654766	29654766	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	399	527	0	ENST00000356175.3:c.5455C>T	p.Pro1819Ser	p.P1819S	ENST00000356175	NM_000267.3	1819	Ccc/Tcc	37/57	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.811374573212711	2		527	726	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37865642	37865642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	297	461	0	ENST00000269571.5:c.511G>A	p.Asp171Asn	p.D171N	ENST00000269571		171	Gac/Aac	4/27	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.811374573212711	2		461	662	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37865693	37865693	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765706190	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	374	476	0	ENST00000269571.5:c.562C>T	p.Arg188Cys	p.R188C	ENST00000269571		188	Cgc/Tgc	4/27	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.811374573212711	2		476	732	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492701	56492701	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	358	465	0	ENST00000407977.2:c.238G>T	p.Gly80Ter	p.G80*	ENST00000407977		80	Gga/Tga	2/10	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.811374573212711	2		465	696	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353986	15353986	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	80	131	0	ENST00000263377.2:c.2894C>T	p.Ser965Phe	p.S965F	ENST00000263377	NM_058243.2	965	tCt/tTt	14/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.811374573212711	2		131	179	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133480	55133480	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376265745	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	213	400	0	ENST00000257290.5:c.784G>A	p.Glu262Lys	p.E262K	ENST00000257290	NM_006206.4	262	Gaa/Aaa	6/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.811374573212711	2		400	494	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467644	66467644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202165566	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	298	454	1	ENST00000273854.3:c.625G>A	p.Gly209Arg	p.G209R	ENST00000273854	NM_004439.5	209	Gga/Aga	3/18	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.811374573212711	2		455	616	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155902	106155902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	374	501	0	ENST00000380013.4:c.803C>T	p.Ser268Leu	p.S268L	ENST00000380013	NM_001127208.2	268	tCg/tTg	3/11	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.811374573212711	2		501	765	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950648	38950648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776074870	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	225	489	0	ENST00000357387.3:c.3302C>T	p.Ser1101Leu	p.S1101L	ENST00000357387	NM_152756.3	1101	tCg/tTg	31/38	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.811374573212711	2		489	446	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911116	29911116	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs199474504	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	329	465	0	ENST00000376809.5:c.415C>T	p.Gln139Ter	p.Q139*	ENST00000376809	NM_002116.7	139	Cag/Tag	3/8	1	2	FACETS	0.754	0.722	0.784	1	0.996	1	SUBCLONAL	2	TRUE	1	0.811374573212711	2		465	538	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138201268	138201268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1490946222	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	326	492	1	ENST00000237289.4:c.1967C>T	p.Pro656Leu	p.P656L	ENST00000237289	NM_001270507.1	656	cCg/cTg	8/9	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.811374573212711	2		493	769	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426907	6426907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	162	327	0	ENST00000356142.4:c.100C>T	p.Pro34Ser	p.P34S	ENST00000356142	NM_018890.3	34	Cct/Tct	2/7	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.811374573212711	2		327	390	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331980	81331980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1383506132	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	145	438	0	ENST00000222390.5:c.2104C>T	p.Arg702Cys	p.R702C	ENST00000222390	NM_000601.4	702	Cgt/Tgt	18/18	1	2	FACETS	0.894	0.824	0.965	0.894	0.824	0.965	CLONAL	1	TRUE	1	0.811374573212711	2		438	400	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057697	27057698	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	389	529	0	ENST00000324856.7:c.1405_1406delinsTT	p.Pro469Leu	p.P469L	ENST00000324856	NM_006015.4	469	CCa/TTa	3/20	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.811374573212711	2		529	819	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120509113	120509113	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	285	420	0	ENST00000256646.2:c.1454-1G>A		p.X485_splice	ENST00000256646	NM_024408.3	485			1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.811374573212711	2		420	530	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843686	156843686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	429	582	0	ENST00000524377.1:c.1112C>T	p.Ser371Phe	p.S371F	ENST00000524377	NM_002529.3	371	tCc/tTc	8/17	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.811374573212711	2		582	850	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100483	8100483	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	257	508	0	ENST00000346208.3:c.457T>A	p.Phe153Ile	p.F153I	ENST00000346208		153	Ttc/Atc	3/6	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.811374573212711	2		508	555	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352747	118352747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	376	516	0	ENST00000534358.1:c.3952G>A	p.Glu1318Lys	p.E1318K	ENST00000534358	NM_005933.3	1318	Gaa/Aaa	7/36	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.811374573212711	2		516	684	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416492	49416492	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	328	534	0	ENST00000301067.7:c.16219C>T	p.Gln5407Ter	p.Q5407*	ENST00000301067	NM_003482.3	5407	Cag/Tag	51/54	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.811374573212711	2		534	706	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432452	49432452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	329	507	0	ENST00000301067.7:c.8687C>T	p.Pro2896Leu	p.P2896L	ENST00000301067	NM_003482.3	2896	cCt/cTt	34/54	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.811374573212711	2		507	675	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493524	56493524	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	410	507	0	ENST00000267101.3:c.2932A>T	p.Ile978Leu	p.I978L	ENST00000267101	NM_001982.3	978	Ata/Tta	24/28	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.811374573212711	2		507	792	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859675	57859676	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	333	498	0	ENST00000228682.2:c.729_730delinsTT	p.Gln244Ter	p.Q244*	ENST00000228682	NM_005269.2	243	agCCag/agTTag	7/12	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.811374573212711	2		498	743	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112103	115112103	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	324	533	0	ENST00000257566.3:c.1637T>A	p.Val546Asp	p.V546D	ENST00000257566	NM_016569.3	546	gTt/gAt	7/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.811374573212711	2		533	713	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26970431	26970431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	110	267	0	ENST00000381527.3:c.800G>A	p.Trp267Ter	p.W267*	ENST00000381527	NM_001260.1	267	tGg/tAg	8/13	NA	2	FACETS	0.997	0.911	1			1	INDETERMINATE	1	TRUE	NA	0.811374573212711	2		267	272	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89815087	89815087	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	268	382	0	ENST00000389301.3:c.3328C>T	p.His1110Tyr	p.H1110Y	ENST00000389301	NM_000135.2	1110	Cac/Tac	33/43	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.811374573212711	2		382	531	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649081	37649082	+	missense_variant	Missense_Mutation	DNP	TT	TT	AG	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	274	408	0	ENST00000447079.4:c.2186_2187delinsAG	p.Ile729Lys	p.I729K	ENST00000447079	NM_015083.1	729	aTT/aAG	4/14	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.811374573212711	2		408	615	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55693415	55693415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1198633816	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	399	407	0	ENST00000284073.2:c.622G>A	p.Asp208Asn	p.D208N	ENST00000284073	NM_138962.2	208	Gac/Aac	9/14	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.811374573212711	2		407	766	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752452	55752452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369406659	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	356	404	0	ENST00000284073.2:c.910C>T	p.Pro304Ser	p.P304S	ENST00000284073	NM_138962.2	304	Cca/Tca	12/14	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.811374573212711	2		404	648	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39575950	39575950	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	187	361	0	ENST00000262039.4:c.883C>T	p.Gln295Ter	p.Q295*	ENST00000262039	NM_002647.2	295	Cag/Tag	8/25	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.811374573212711	2		361	437	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61325834	61325834	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	123	207	0	ENST00000283752.5:c.382C>T	p.Gln128Ter	p.Q128*	ENST00000283752	NM_006919.2	128	Cag/Tag	5/8	0.811374573212711	6	FACETS	0.979	0.886	1	0.196	0.177	0.216	CLONAL	1	TRUE	1	0.811374573212711	6		207	812	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17389825	17389825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs2073944993	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	281	460	0	ENST00000359435.4:c.958G>A	p.Asp320Asn	p.D320N	ENST00000359435	NM_001033549.1	320	Gat/Aat	9/9	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.811374573212711	2		460	589	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953144	17953144	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	290	441	0	ENST00000458235.1:c.842G>A	p.Trp281Ter	p.W281*	ENST00000458235	NM_000215.3	281	tGg/tAg	6/24	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.811374573212711	2		441	568	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274172	18274172	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	367	466	0	ENST00000222254.8:c.1390T>C	p.Tyr464His	p.Y464H	ENST00000222254	NM_005027.3	464	Tat/Cat	11/16	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.811374573212711	2		466	734	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744447	41744447	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	236	499	0	ENST00000301178.4:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000301178	NM_021913.4	356	cCc/cTc	8/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.811374573212711	2		499	483	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606980	47606981	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	272	393	0	ENST00000263735.4:c.730_731delinsTT	p.Pro244Phe	p.P244F	ENST00000263735	NM_002354.2	244	CCt/TTt	7/9	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.811374573212711	2		393	593	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636878	158636878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	273	475	0	ENST00000263640.3:c.302G>A	p.Arg101Lys	p.R101K	ENST00000263640	NM_001105.4	101	aGg/aAg	4/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.811374573212711	2		475	604	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202123063	202123063	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	361	573	0	ENST00000358485.4:c.109G>T	p.Gly37Trp	p.G37W	ENST00000358485	NM_001080125.1	37	Ggg/Tgg	1/9	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.811374573212711	2		573	728	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543581	9543581	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	268	405	0	ENST00000353224.5:c.1573T>A	p.Phe525Ile	p.F525I	ENST00000353224	NM_177990.2	525	Ttt/Att	6/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.811374573212711	2		405	543	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713427	30713427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	232	595	0	ENST00000295754.5:c.752G>A	p.Gly251Glu	p.G251E	ENST00000295754	NM_003242.5	251	gGg/gAg	4/7	0.326356969088221	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.811374573212711	0		595	525	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612084	189612085	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	289	522	0	ENST00000264731.3:c.1836_1837delinsTT	p.Pro613Ser	p.P613S	ENST00000264731	NM_003722.4	612	tcCCct/tcTTct	14/14	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.811374573212711	2		522	639	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133743	55133744	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	242	491	0	ENST00000257290.5:c.956_957delinsTT	p.Pro319Leu	p.P319L	ENST00000257290	NM_006206.4	319	cCC/cTT	7/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.811374573212711	2		491	560	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948184	55948184	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	170	286	0	ENST00000263923.4:c.3787G>C	p.Val1263Leu	p.V1263L	ENST00000263923	NM_002253.2	1263	Gtt/Ctt	29/30	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.811374573212711	2		286	328	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294207	1294207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	312	490	0	ENST00000310581.5:c.794C>T	p.Pro265Leu	p.P265L	ENST00000310581	NM_198253.2	265	cCg/cTg	2/16	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.811374573212711	2		490	618	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609786	117609786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	256	407	0	ENST00000368508.3:c.6913G>A	p.Glu2305Lys	p.E2305K	ENST00000368508	NM_002944.2	2305	Gaa/Aaa	43/43	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.811374573212711	2		407	558	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117739636	117739636	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	195	348	0	ENST00000368508.3:c.157C>A	p.Leu53Met	p.L53M	ENST00000368508	NM_002944.2	53	Ctg/Atg	2/43	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.811374573212711	2		348	423	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004622	150004623	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	400	545	0	ENST00000253339.5:c.1602_1603delinsAA	p.Gly535Arg	p.G535R	ENST00000253339		534	gaGGga/gaAAga	3/7	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.811374573212711	2		545	843	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879416	56879417	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	201	395	1	ENST00000519728.1:c.933_934delinsAA	p.Glu312Lys	p.E312K	ENST00000519728	NM_002350.3	311	agGGag/agAAag	9/13	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.811374573212711	2		396	466	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158101	27158101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	306	472	0	ENST00000380036.4:c.325G>A	p.Glu109Lys	p.E109K	ENST00000380036	NM_000459.3	109	Gag/Aag	2/23	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.811374573212711	2		472	703	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845374	76845374	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0068486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	201	213	0	ENST00000373344.5:c.6147G>C	p.Leu2049Phe	p.L2049F	ENST00000373344	NM_000489.3	2049	ttG/ttC	27/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.811374573212711	1		213	207	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278106	41278106	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0068491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	45	474	0	ENST00000349496.5:c.1982G>C	p.Arg661Pro	p.R661P	ENST00000349496	NM_001904.3	661	cGa/cCa	13/15	1	2	FACETS	0.146	0.122	0.173	0.146	0.122	0.173	SUBCLONAL	1	TRUE	1	0.888230175310808	2		474	693	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754656	57754659	+	frameshift_variant	Frame_Shift_Del	DEL	TTTC	TTTC	-	novel	NA	P-0068491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	180	357	0	ENST00000274289.3:c.388_391del	p.Glu130Ter	p.E130*	ENST00000274289	NM_006622.3	130	GAAAta/ta	3/14	1	2	FACETS	0.855	0.796	0.915	0.855	0.796	0.915	CLONAL	1	TRUE	1	0.888230175310808	2		357	474	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446002	49446002	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	409	667	0	ENST00000301067.7:c.1464del	p.Leu489TrpfsTer441	p.L489Wfs*441	ENST00000301067	NM_003482.3	488	ccG/cc	10/54	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.888230175310808	2		667	919	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431176	49431177	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0068491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	364	574	0	ENST00000301067.7:c.9962dup	p.Gln3322ThrfsTer101	p.Q3322Tfs*101	ENST00000301067	NM_003482.3	3321	cga/cgGa	34/54	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.888230175310808	2		574	767	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142582	119142582	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	256	480	0	ENST00000264033.4:c.581T>C	p.Phe194Ser	p.F194S	ENST00000264033	NM_005188.3	194	tTt/tCt	3/16	1	2	FACETS	0.975	0.921	1	0.975	0.921	1	CLONAL	1	TRUE	1	0.888230175310808	2		480	591	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287212	33287213	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1268651006	NA	P-0068492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	229	485	0	ENST00000374542.5:c.1884dup	p.Cys629LeufsTer29	p.C629Lfs*29	ENST00000374542	NM_001141970.1	628	-/C	6/8	0.520908256147505	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.520908256147505	1		485	616	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186787	108186787	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	159	434	0	ENST00000278616.4:c.6145T>A	p.Tyr2049Asn	p.Y2049N	ENST00000278616	NM_000051.3	2049	Tat/Aat	42/63	0.520908256147505	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.520908256147505	1		434	444	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410627	32410627	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	252	392	0	ENST00000332351.3:c.1531A>T	p.Thr511Ser	p.T511S	ENST00000332351	NM_024426.4	511	Acc/Tcc	10/10	0.520908256147505	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.520908256147505	1		392	625	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068493-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	24	350	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.671	0.537	0.82			1	INDETERMINATE	1	TRUE	NA	0.694258966336533	2		350	103	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0068493-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	172	602	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.480998030458877	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.694258966336533	1		602	253	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0068493-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14232	343	471	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.694258966336533	71	FACETS	0.846	0.793	0.901	0.024	0.022	0.026	CLONAL	2	TRUE	0	0.694258966336533	71		471	14575	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923160	48923161	+	splice_donor_variant	Splice_Site	INS	-	-	T	rs1131690895	NA	P-0068493-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	112	259	0	ENST00000267163.4:c.607+2dup		p.X203_splice	ENST00000267163	NM_000321.2	203			0.694258966336533	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.694258966336533	1		259	189	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710659	40710659	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0068493-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	105	428	0	ENST00000373198.4:c.4194-2A>G		p.X1398_splice	ENST00000373198	NM_133170.3	1398			0.694258966336533	3	FACETS	1	0.953	1	0.545	0.492	0.599	CLONAL	1	TRUE	1	0.694258966336533	3		428	374	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593594	55593608	+	inframe_deletion	In_Frame_Del	DEL	GAAGTACAGTGGAAG	GAAGTACAGTGGAAG	-	novel	NA	P-0068497-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	281	605	0	ENST00000288135.5:c.1661_1675del	p.Glu554_Lys558del	p.E554_K558del	ENST00000288135	NM_000222.2	554	GAAGTACAGTGGAAG/-	11/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.782769801452459	2		605	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0068499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	134	371	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		371	491	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	71	446	0	ENST00000256196.4:c.68G>T	p.Gly23Val	p.G23V	ENST00000256196		23	gGc/gTc	1/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		446	294	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950466	68950466	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	26	387	0	ENST00000288368.4:c.778A>G	p.Ile260Val	p.I260V	ENST00000288368	NM_024870.2	260	Att/Gtt	7/40	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		387	345	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0068501-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	71	350	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		350	463	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0068502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	156	252	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.512289080870411	4	FACETS	1	0.984	1	0.807	0.75	0.866	CLONAL	2	TRUE	1	0.540771079750368	4		253	367	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405953	49405953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	241	482	0	ENST00000418115.1:c.185G>A	p.Gly62Glu	p.G62E	ENST00000418115	NM_001664.2	62	gGg/gAg	3/5	0.53990901151917	2	FACETS	1	0.98	1	0.554	0.519	0.59	CLONAL	1	TRUE	0	0.540771079750368	2		482	804	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207162	1207162	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs137853076	NA	P-0068502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	971	516	0	ENST00000326873.7:c.250A>T	p.Lys84Ter	p.K84*	ENST00000326873	NM_000455.4	84	Aag/Tag	1/10	0.540771079750368	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.540771079750368	3		516	1413	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577505	7577505	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs745425759	NA	P-0068502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	604	412	0	ENST00000269305.4:c.776A>T	p.Asp259Val	p.D259V	ENST00000269305	NM_001126112.2	259	gAc/gTc	7/11	0.540771079750368	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.540771079750368	2		412	929	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194110	94194110	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773469981	NA	P-0068502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	102	381	0	ENST00000323929.3:c.1318G>A	p.Ala440Thr	p.A440T	ENST00000323929	NM_005591.3	440	Gca/Aca	12/20	0.281566405501931	5	FACETS	1	0.939	1	0.701	0.634	0.77	INDETERMINATE	2	TRUE	2	0.540771079750368	5		381	325	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599757	10600058	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGACCTTGTTTCTAAAAAAAAAAAAAAAAAAAAAAAAAAGGAAAGCAAAAGCAAAAGCAGTCCACAAAAGATGGGCTAGTCAGGACTCTTCCCCGCCCCCAGGGCCTCACCAAGGACGTAGATTCTCCCCTGGTGGACAGTGATCCCCAGGGCACTTCGCCGGTGCTTCATGGGGGCTACGAAAGTCCACGTCTCTGTTTCCACATCGTAGCGCTCCACGCTGTTCAGCTGGTCCTGACCATCATAGCCCCCAGCAGCATAGATACAGTTGTGCAGGACGCAGACGCCTAAAGGGCACCAT	GAGACCTTGTTTCTAAAAAAAAAAAAAAAAAAAAAAAAAAGGAAAGCAAAAGCAAAAGCAGTCCACAAAAGATGGGCTAGTCAGGACTCTTCCCCGCCCCCAGGGCCTCACCAAGGACGTAGATTCTCCCCTGGTGGACAGTGATCCCCAGGGCACTTCGCCGGTGCTTCATGGGGGCTACGAAAGTCCACGTCTCTGTTTCCACATCGTAGCGCTCCACGCTGTTCAGCTGGTCCTGACCATCATAGCCCCCAGCAGCATAGATACAGTTGTGCAGGACGCAGACGCCTAAAGGGCACCAT	-	novel	NA	P-0068502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	256	112	0	ENST00000171111.5:c.1532-14_1708+111del		p.X511_splice	ENST00000171111	NM_203500.1	511		5/6	0.540771079750368	3	FACETS	0.961	0.929	0.99	1	0.995	1	CLONAL	4	TRUE	0	0.540771079750368	3		112	313	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958418	90958419	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGATGGATT	novel	NA	P-0068502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	34	372	0	ENST00000265433.3:c.2019_2020insAATCCATCG	p.Asn671_Ser673dup	p.N671_S673dup	ENST00000265433	NM_002485.4	671	-/AATCCATCG	13/16	0.540771079750368	3	FACETS	0.579	0.475	0.695	0.289	0.237	0.348	SUBCLONAL	1	TRUE	1	0.540771079750368	3		372	276	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	110	564	5	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.813	0.732	0.899	0.813	0.732	0.899	CLONAL	1	FALSE	1	0.422691190790434	2		569	640	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	13	256	3	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	0.263	0.187	0.355	0.263	0.187	0.355	SUBCLONAL	1	FALSE	1	0.422691190790434	2		259	234	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073398	8073398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201286989	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	156	525	0	ENST00000377482.5:c.1261G>A	p.Ala421Thr	p.A421T	ENST00000377482	NM_018948.3	421	Gcc/Acc	4/4	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.422691190790434	2		525	670	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303627	65303627	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	118	404	0	ENST00000342505.4:c.3128G>T	p.Ser1043Ile	p.S1043I	ENST00000342505	NM_002227.2	1043	aGc/aTc	22/25	1	2	FACETS	0.966	0.874	1	0.966	0.874	1	CLONAL	1	FALSE	1	0.422691190790434	2		404	578	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306996	65306997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	118	543	7	ENST00000342505.4:c.2580dup	p.Pro861ThrfsTer4	p.P861Tfs*4	ENST00000342505	NM_002227.2	860	-/A	19/25	1	2	FACETS	0.729	0.658	0.804	0.729	0.658	0.804	SUBCLONAL	1	FALSE	1	0.422691190790434	2		550	766	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843514	156843514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137994522	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	123	517	0	ENST00000524377.1:c.940C>T	p.Arg314Cys	p.R314C	ENST00000524377	NM_002529.3	314	Cgc/Tgc	8/17	1	2	FACETS	0.893	0.809	0.981	0.893	0.809	0.981	CLONAL	1	FALSE	1	0.422691190790434	2		517	652	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900984	114900984	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778855667	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	157	516	0	ENST00000543371.1:c.598del	p.Leu200SerfsTer25	p.L200Sfs*25	ENST00000543371	NM_001198531.1	198	caC/ca	6/14	1	2	FACETS	0.893	0.818	0.971	0.893	0.818	0.971	CLONAL	1	FALSE	1	0.422691190790434	2		516	832	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943783	71943783	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	98	595	0	ENST00000298229.2:c.1826A>G	p.Asn609Ser	p.N609S	ENST00000298229	NM_001567.3	609	aAc/aGc	15/28	1	2	FACETS	0.643	0.574	0.717	0.643	0.574	0.717	SUBCLONAL	1	FALSE	1	0.422691190790434	2		595	721	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102033248	102033248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867350713	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	167	567	0	ENST00000282441.5:c.634G>A	p.Val212Ile	p.V212I	ENST00000282441	NM_001130145.2	212	Gtc/Atc	3/9	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	FALSE	1	0.422691190790434	2		567	786	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390460	118390461	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	128	513	0	ENST00000534358.1:c.11280dup	p.Asn3762GlufsTer9	p.N3762Efs*9	ENST00000534358	NM_005933.3	3758	-/C	32/36	1	2	FACETS	0.749	0.679	0.822	0.749	0.679	0.822	SUBCLONAL	1	FALSE	1	0.422691190790434	2		513	809	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170274	119170274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057518072	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	130	472	0	ENST00000264033.4:c.2504G>A	p.Arg835Gln	p.R835Q	ENST00000264033	NM_005188.3	835	cGg/cAg	16/16	1	2	FACETS	0.738	0.669	0.81	0.738	0.669	0.81	SUBCLONAL	1	FALSE	1	0.422691190790434	2		472	834	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	86	227	0	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.769	0.682	0.862	0.769	0.682	0.862	SUBCLONAL	1	FALSE	1	0.422691190790434	2		227	529	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	158	559	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.945	0.867	1	0.945	0.867	1	CLONAL	1	FALSE	1	0.422691190790434	2		559	791	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112892398	112892398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143433437	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	126	381	0	ENST00000351677.2:c.556C>T	p.Arg186Trp	p.R186W	ENST00000351677	NM_002834.3	186	Cgg/Tgg	5/16	1	2	FACETS	0.976	0.886	1	0.976	0.886	1	CLONAL	1	FALSE	1	0.422691190790434	2		381	611	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112940045	112940045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150730493	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	150	418	0	ENST00000351677.2:c.1697C>T	p.Thr566Met	p.T566M	ENST00000351677	NM_002834.3	566	aCg/aTg	14/16	1	2	FACETS	0.948	0.867	1	0.948	0.867	1	CLONAL	1	FALSE	1	0.422691190790434	2		418	749	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562564	21562564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1452154404	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	83	400	1	ENST00000382592.4:c.1355C>T	p.Pro452Leu	p.P452L	ENST00000382592	NM_014572.2	452	cCg/cTg	4/8	0.318698779324379	3	FACETS	1	0.941	1	0.548	0.486	0.614	CLONAL	1	FALSE	1	0.422691190790434	3		401	434	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636193	28636193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777905087	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	128	477	0	ENST00000241453.7:c.179C>T	p.Pro60Leu	p.P60L	ENST00000241453	NM_004119.2	60	cCg/cTg	3/24	0.318698779324379	3	FACETS	0.815	0.738	0.896	0.408	0.369	0.448	CLONAL	1	FALSE	1	0.422691190790434	3		477	900	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134019	41134019	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146488369	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	107	599	0	ENST00000379561.5:c.1609C>T	p.Arg537Cys	p.R537C	ENST00000379561	NM_002015.3	537	Cgt/Tgt	2/3	0.318698779324379	3	FACETS	0.687	0.615	0.763	0.343	0.307	0.382	SUBCLONAL	1	FALSE	1	0.422691190790434	3		599	893	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134267	41134267	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1028000118	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	115	492	0	ENST00000379561.5:c.1361A>G	p.Gln454Arg	p.Q454R	ENST00000379561	NM_002015.3	454	cAg/cGg	2/3	0.318698779324379	3	FACETS	0.907	0.817	1	0.453	0.408	0.501	CLONAL	1	FALSE	1	0.422691190790434	3		492	727	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994794	73994794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747338278	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	130	434	1	ENST00000318443.5:c.278C>T	p.Thr93Met	p.T93M	ENST00000318443	NM_001024736.1	93	aCg/aTg	3/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.422691190790434	2		435	516	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679814	88679814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753910026	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	117	383	0	ENST00000360948.2:c.649G>A	p.Val217Ile	p.V217I	ENST00000360948	NM_001012338.2	217	Gtc/Atc	7/19	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	1	0.422691190790434	2		383	535	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341596	89341596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	130	361	0	ENST00000301030.4:c.7474G>A	p.Ala2492Thr	p.A2492T	ENST00000301030	NM_001256183.1	2492	Gca/Aca	10/13	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.422691190790434	2		361	571	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553478	29553478	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781807	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	171	447	0	ENST00000356175.3:c.2033del	p.Pro678ArgfsTer10	p.P678Rfs*10	ENST00000356175	NM_000267.3	676	aCc/ac	18/57	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.422691190790434	2		447	757	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637944	39637944	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	125	461	1	ENST00000262039.4:c.2366del	p.Gly789AlafsTer27	p.G789Afs*27	ENST00000262039	NM_002647.2	787	atG/at	22/25	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	1	0.422691190790434	2		462	549	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622410	1622410	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	118	367	0	ENST00000344749.5:c.554A>G	p.Tyr185Cys	p.Y185C	ENST00000344749	NM_001136139.2	185	tAc/tGc	9/19	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	1	0.422691190790434	2		367	527	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223454	2223454	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	178	471	0	ENST00000398665.3:c.3565C>T	p.Pro1189Ser	p.P1189S	ENST00000398665	NM_032482.2	1189	Cca/Tca	25/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.422691190790434	2		471	716	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252720	10252720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377078524	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	165	498	0	ENST00000340748.4:c.3245G>A	p.Arg1082His	p.R1082H	ENST00000340748		1082	cGc/cAc	29/40	1	2	FACETS	0.959	0.882	1	0.959	0.882	1	CLONAL	1	FALSE	1	0.422691190790434	2		498	814	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224340	36224340	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1568382485	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	171	531	0	ENST00000222270.7:c.6895del	p.Arg2299GlyfsTer26	p.R2299Gfs*26	ENST00000222270	NM_014727.1	2297	gCc/gc	28/37	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.422691190790434	2		531	776	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	48	427	1	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.286	0.241	0.336	0.286	0.241	0.336	SUBCLONAL	1	FALSE	1	0.422691190790434	2		428	794	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753584	42753584	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	119	514	0	ENST00000222329.4:c.680A>G	p.His227Arg	p.H227R	ENST00000222329	NM_006494.2	227	cAt/cGt	4/4	1	2	FACETS	0.766	0.692	0.844	0.766	0.692	0.844	SUBCLONAL	1	FALSE	1	0.422691190790434	2		514	735	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792017	42792017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	154	594	0	ENST00000575354.2:c.821G>A	p.Arg274Gln	p.R274Q	ENST00000575354	NM_015125.3	274	cGa/cAa	6/20	1	2	FACETS	0.991	0.909	1	0.991	0.909	1	CLONAL	1	FALSE	1	0.422691190790434	2		594	735	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910259	50910259	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1043752384	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	139	415	1	ENST00000440232.2:c.1514G>A	p.Arg505His	p.R505H	ENST00000440232	NM_002691.3	505	cGc/cAc	13/27	0.420455165241139	2	FACETS	1	0.958	1	0.54	0.493	0.589	CLONAL	1	FALSE	0	0.422691190790434	2		416	609	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085972	16085972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs998174759	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	143	442	0	ENST00000281043.3:c.1148G>A	p.Arg383His	p.R383H	ENST00000281043	NM_005378.4	383	cGc/cAc	3/3	1	2	FACETS	0.978	0.893	1	0.978	0.893	1	CLONAL	1	FALSE	1	0.422691190790434	2		442	692	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222520	39222520	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	29	452	1	ENST00000402219.2:c.3090del	p.Lys1030AsnfsTer6	p.K1030Nfs*6	ENST00000402219	NM_005633.3	1030	aaA/aa	20/23	1	2	FACETS	0.253	0.202	0.311	0.253	0.202	0.311	SUBCLONAL	1	FALSE	1	0.422691190790434	2		453	543	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46587791	46587791	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	80	451	1	ENST00000263734.3:c.475del	p.Ser159AlafsTer12	p.S159Afs*12	ENST00000263734	NM_001430.4	157	Aaa/aa	5/16	1	2	FACETS	0.705	0.622	0.794	0.705	0.622	0.794	SUBCLONAL	1	FALSE	1	0.422691190790434	2		452	537	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46602969	46602969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs574490008	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	154	495	0	ENST00000263734.3:c.1027G>A	p.Val343Ile	p.V343I	ENST00000263734	NM_001430.4	343	Gtc/Atc	8/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.422691190790434	2		495	668	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	130	577	5	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.879	0.798	0.963	0.879	0.798	0.963	CLONAL	1	FALSE	1	0.422691190790434	2		582	700	SUCCESS
REL	5966	MSKCC	GRCh37	2	61121667	61121667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs955883570	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	113	485	0	ENST00000295025.8:c.289C>T	p.Arg97Cys	p.R97C	ENST00000295025	NM_002908.2	97	Cgc/Tgc	3/11	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	FALSE	1	0.422691190790434	2		485	523	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212484000	212484000	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1369649105	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	54	352	0	ENST00000342788.4:c.2203G>A	p.Gly735Ser	p.G735S	ENST00000342788	NM_005235.2	735	Ggt/Agt	19/28	1	2	FACETS	0.706	0.605	0.815	0.706	0.605	0.815	SUBCLONAL	1	FALSE	1	0.422691190790434	2		352	362	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	171	711	1	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.994	0.916	1	0.994	0.916	1	CLONAL	1	FALSE	1	0.422691190790434	2		712	814	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755427	39755427	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	113	492	0	ENST00000288319.7:c.1338del	p.Phe446LeufsTer59	p.F446Lfs*59	ENST00000288319	NM_182918.3	446	ttT/tt	10/10	1	2	FACETS	0.712	0.641	0.787	0.712	0.641	0.787	SUBCLONAL	1	FALSE	1	0.422691190790434	2		492	751	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176338	24176338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	102	353	0	ENST00000263121.7:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000263121	NM_003073.3	377	Cgt/Tgt	9/9	1	2	FACETS	0.912	0.819	1	0.912	0.819	1	CLONAL	1	FALSE	1	0.422691190790434	2		353	529	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	157	453	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	FALSE	1	0.422691190790434	2		453	713	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723037	49723037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767971831	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	83	271	0	ENST00000449682.2:c.1379G>A	p.Arg460Gln	p.R460Q	ENST00000449682	NM_020998.3	460	cGa/cAa	11/18	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	FALSE	1	0.422691190790434	2		271	373	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934243	49934243	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1407832113	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	174	524	4	ENST00000296474.3:c.2264del	p.Gly755ValfsTer19	p.G755Vfs*19	ENST00000296474	NM_002447.2	755	gGt/gt	8/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.422691190790434	2		528	760	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	120	385	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	FALSE	1	0.422691190790434	2		385	557	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	101	306	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.422691190790434	2		306	435	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602952	55602952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1237984655	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	105	450	0	ENST00000288135.5:c.2662C>T	p.Arg888Trp	p.R888W	ENST00000288135	NM_000222.2	888	Cgg/Tgg	19/21	1	2	FACETS	0.843	0.758	0.934	0.843	0.758	0.934	CLONAL	1	FALSE	1	0.422691190790434	2		450	589	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467590	66467590	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746706656	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	119	478	0	ENST00000273854.3:c.679C>T	p.Arg227Cys	p.R227C	ENST00000273854	NM_004439.5	227	Cgt/Tgt	3/18	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	FALSE	1	0.422691190790434	2		478	560	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193762	106193762	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	114	468	0	ENST00000380013.4:c.4227del	p.Lys1409AsnfsTer39	p.K1409Nfs*39	ENST00000380013	NM_001127208.2	1408	ggA/gg	10/11	1	2	FACETS	0.844	0.761	0.931	0.844	0.761	0.931	CLONAL	1	FALSE	1	0.422691190790434	2		468	639	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538991	187538991	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	162	592	0	ENST00000441802.2:c.8749C>T	p.Arg2917Ter	p.R2917*	ENST00000441802	NM_005245.3	2917	Cga/Tga	10/27	1	2	FACETS	0.935	0.858	1	0.935	0.858	1	CLONAL	1	FALSE	1	0.422691190790434	2		592	820	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	106	357	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.954	0.858	1	0.954	0.858	1	CLONAL	1	FALSE	1	0.422691190790434	2		357	526	SUCCESS
APC	324	MSKCC	GRCh37	5	112162944	112162944	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	89	349	0	ENST00000257430.4:c.1548G>T	p.Lys516Asn	p.K516N	ENST00000257430	NM_000038.5	516	aaG/aaT	12/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	1	0.422691190790434	2		349	384	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163553	32163554	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs777647776	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	24	451	2	ENST00000375023.3:c.5672dup	p.Gly1892ArgfsTer24	p.G1892Rfs*24	ENST00000375023	NM_004557.3	1891	ggc/ggGc	30/30	1	2	FACETS	0.25	0.195	0.313	0.25	0.195	0.313	SUBCLONAL	1	FALSE	1	0.422691190790434	2		453	454	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288200	33288200	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	176	507	0	ENST00000374542.5:c.1208C>T	p.Ser403Phe	p.S403F	ENST00000374542	NM_001141970.1	403	tCc/tTc	4/8	1	2	FACETS	0.977	0.901	1	0.977	0.901	1	CLONAL	1	FALSE	1	0.422691190790434	2		507	852	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005515	150005515	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	37	502	0	ENST00000253339.5:c.710del	p.Pro237HisfsTer6	p.P237Hfs*6	ENST00000253339		237	cCa/ca	3/7	1	2	FACETS	0.253	0.208	0.304	0.253	0.208	0.304	SUBCLONAL	1	FALSE	1	0.422691190790434	2		502	692	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946337	2946337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759681668	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	120	464	1	ENST00000396946.4:c.3400G>A	p.Val1134Ile	p.V1134I	ENST00000396946	NM_032415.4	1134	Gtt/Att	25/25	0.387811903051993	3	FACETS	0.998	0.903	1	0.499	0.451	0.55	CLONAL	1	FALSE	1	0.422691190790434	3		465	689	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962854	2962854	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	86	417	0	ENST00000396946.4:c.2054del	p.Gly685AlafsTer31	p.G685Afs*31	ENST00000396946	NM_032415.4	685	gGc/gc	16/25	0.387811903051993	3	FACETS	0.808	0.716	0.907	0.404	0.358	0.454	CLONAL	1	FALSE	1	0.422691190790434	3		417	610	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956748	68956748	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	78	386	0	ENST00000288368.4:c.866C>T	p.Thr289Ile	p.T289I	ENST00000288368	NM_024870.2	289	aCa/aTa	8/40	0.387811903051993	3	FACETS	0.735	0.647	0.831	0.368	0.323	0.416	SUBCLONAL	1	FALSE	1	0.422691190790434	3		386	608	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992721	68992721	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs764112302	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	48	491	2	ENST00000288368.4:c.1693del	p.Ser565ArgfsTer10	p.S565Rfs*10	ENST00000288368	NM_024870.2	562	cgT/cg	16/40	0.387811903051993	3	FACETS	0.413	0.348	0.485	0.207	0.174	0.243	SUBCLONAL	1	FALSE	1	0.422691190790434	3		493	666	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499763	8499763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745717615	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	208	479	0	ENST00000356435.5:c.2206G>A	p.Val736Met	p.V736M	ENST00000356435		736	Gtg/Atg	14/35	0.318698779324379	3	FACETS	0.844	0.787	0.903	0.844	0.787	0.903	CLONAL	2	FALSE	1	0.422691190790434	3		479	706	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650071	93650071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1486347243	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	139	308	0	ENST00000375746.1:c.1622C>T	p.Pro541Leu	p.P541L	ENST00000375746	NM_001174167.1	541	cCg/cTg	12/14	0.318698779324379	3	FACETS	1	0.964	1	0.556	0.506	0.607	CLONAL	1	FALSE	1	0.422691190790434	3		308	717	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	248	638	1	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	0.318698779324379	3	FACETS	0.953	0.895	1	0.953	0.895	1	CLONAL	2	FALSE	1	0.422691190790434	3		639	746	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137325984	137325984	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753474465	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	145	448	2	ENST00000481739.1:c.1172C>T	p.Ala391Val	p.A391V	ENST00000481739	NM_002957.4	391	gCg/gTg	9/10	0.318698779324379	3	FACETS	1	0.96	1	0.543	0.496	0.593	CLONAL	1	FALSE	1	0.422691190790434	3		450	765	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396913	139396913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768040014	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	117	379	0	ENST00000277541.6:c.5195C>T	p.Ala1732Val	p.A1732V	ENST00000277541	NM_017617.3	1732	gCg/gTg	28/34	0.318698779324379	3	FACETS	1	0.948	1	0.536	0.485	0.591	CLONAL	1	FALSE	1	0.422691190790434	3		379	625	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222456	53222456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	38	286	0	ENST00000375401.3:c.4376G>A	p.Arg1459Gln	p.R1459Q	ENST00000375401	NM_004187.3	1459	cGg/cAg	26/26	1	1	FACETS	0.413	0.342	0.492	0.413	0.342	0.492	SUBCLONAL	1	FALSE	0	0.422691190790434	1		286	343	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544224	86544224	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	29	510	0	ENST00000262426.4:c.49G>A	p.Gly17Ser	p.G17S	ENST00000262426	NM_001451.2	17	Ggc/Agc	1/2	1	2	FACETS	0.279	0.224	0.343	0.279	0.224	0.343	SUBCLONAL	1	FALSE	1	0.422691190790434	2		510	491	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	132	461	2	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.964	0.877	1	0.964	0.877	1	CLONAL	1	FALSE	1	0.422691190790434	2		463	648	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1720657	1720657	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	50	499	0	ENST00000378609.4:c.751A>G	p.Arg251Gly	p.R251G	ENST00000378609	NM_002074.3	251	Agg/Ggg	10/12	1	2	FACETS	0.308	0.261	0.361	0.308	0.261	0.361	SUBCLONAL	1	FALSE	1	0.422691190790434	2		499	767	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332788	65332788	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	98	488	0	ENST00000342505.4:c.751T>A	p.Phe251Ile	p.F251I	ENST00000342505	NM_002227.2	251	Ttt/Att	7/25	1	2	FACETS	0.814	0.728	0.905	0.814	0.728	0.905	CLONAL	1	FALSE	1	0.422691190790434	2		488	570	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165602	118165602	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs921184290	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	149	517	0	ENST00000369448.3:c.112C>T	p.Arg38Ter	p.R38*	ENST00000369448	NM_017709.3	38	Cga/Tga	2/2	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	FALSE	1	0.422691190790434	2		517	701	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120469204	120469204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	158	507	0	ENST00000256646.2:c.3923G>A	p.Cys1308Tyr	p.C1308Y	ENST00000256646	NM_024408.3	1308	tGt/tAt	24/34	1	2	FACETS	0.909	0.834	0.988	0.909	0.834	0.988	CLONAL	1	FALSE	1	0.422691190790434	2		507	822	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741936	162741936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55973200	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	134	483	0	ENST00000367921.3:c.1627G>A	p.Val543Ile	p.V543I	ENST00000367921	NM_006182.2	543	Gtc/Atc	13/18	1	2	FACETS	0.972	0.886	1	0.972	0.886	1	CLONAL	1	FALSE	1	0.422691190790434	2		483	652	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226574076	226574076	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	116	391	0	ENST00000366794.5:c.785A>C	p.Lys262Thr	p.K262T	ENST00000366794	NM_001618.3	262	aAg/aCg	6/23	1	2	FACETS	0.759	0.685	0.838	0.759	0.685	0.838	SUBCLONAL	1	FALSE	1	0.422691190790434	2		391	723	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230561443	230561443	+	5_prime_UTR_variant	5'UTR	DEL	G	G	-	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	132	587	0	ENST00000391860.1:c.-114del		p.*38*	ENST00000391860	NM_001258311.1	-/409		1/7	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.422691190790434	2		587	578	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421513	32421513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769934402	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	111	513	0	ENST00000332351.3:c.1079G>A	p.Gly360Asp	p.G360D	ENST00000332351	NM_024426.4	360	gGt/gAt	6/10	1	2	FACETS	0.706	0.635	0.781	0.706	0.635	0.781	SUBCLONAL	1	FALSE	1	0.422691190790434	2		513	744	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939470	71939470	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	136	614	0	ENST00000298229.2:c.325C>A	p.Leu109Ile	p.L109I	ENST00000298229	NM_001567.3	109	Ctt/Att	3/28	1	2	FACETS	0.806	0.734	0.883	0.806	0.734	0.883	CLONAL	1	FALSE	1	0.422691190790434	2		614	798	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186775	108186775	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	32	489	1	ENST00000278616.4:c.6133G>T	p.Ala2045Ser	p.A2045S	ENST00000278616	NM_000051.3	2045	Gcc/Tcc	42/63	1	2	FACETS	0.252	0.204	0.307	0.252	0.204	0.307	SUBCLONAL	1	FALSE	1	0.422691190790434	2		490	600	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415595	49415595	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	175	461	0	ENST00000301067.7:c.16582G>T	p.Gly5528Ter	p.G5528*	ENST00000301067	NM_003482.3	5528	Gga/Tga	54/54	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.422691190790434	2		461	701	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865366	57865366	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	97	598	0	ENST00000228682.2:c.2843A>G	p.Tyr948Cys	p.Y948C	ENST00000228682	NM_005269.2	948	tAt/tGt	12/12	1	2	FACETS	0.619	0.552	0.691	0.619	0.552	0.691	SUBCLONAL	1	FALSE	1	0.422691190790434	2		598	741	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856179	111856179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219220572	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	121	444	1	ENST00000341259.2:c.230G>A	p.Arg77His	p.R77H	ENST00000341259	NM_005475.2	77	cGc/cAc	2/8	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	FALSE	1	0.422691190790434	2		445	563	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120535114	120535114	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	143	485	0	ENST00000229340.5:c.541C>A	p.Gln181Lys	p.Q181K	ENST00000229340	NM_006861.6	181	Cag/Aag	6/6	1	2	FACETS	0.819	0.747	0.895	0.819	0.747	0.895	CLONAL	1	FALSE	1	0.422691190790434	2		485	826	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103510665	103510665	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	71	449	0	ENST00000355739.4:c.569C>A	p.Ser190Tyr	p.S190Y	ENST00000355739	NM_000123.3	190	tCt/tAt	6/15	0.318698779324379	3	FACETS	0.796	0.696	0.904	0.398	0.348	0.452	CLONAL	1	FALSE	1	0.422691190790434	3		449	511	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986835	36986835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	69	456	0	ENST00000354822.5:c.854C>T	p.Pro285Leu	p.P285L	ENST00000354822	NM_001079668.2	285	cCg/cTg	3/3	1	2	FACETS	0.684	0.598	0.778	0.684	0.598	0.778	SUBCLONAL	1	FALSE	1	0.422691190790434	2		456	477	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005545	42005545	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	177	542	0	ENST00000219905.7:c.3281C>T	p.Ser1094Phe	p.S1094F	ENST00000219905	NM_001164273.1	1094	tCc/tTc	9/24	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.422691190790434	2		542	784	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042739	42042739	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1477260954	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	91	514	0	ENST00000219905.7:c.6934A>G	p.Thr2312Ala	p.T2312A	ENST00000219905	NM_001164273.1	2312	Act/Gct	17/24	1	2	FACETS	0.751	0.669	0.84	0.751	0.669	0.84	SUBCLONAL	1	FALSE	1	0.422691190790434	2		514	573	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647489	3647489	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756369289	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	121	526	0	ENST00000294008.3:c.1574G>A	p.Arg525His	p.R525H	ENST00000294008	NM_032444.2	525	cGc/cAc	7/15	1	2	FACETS	0.805	0.728	0.886	0.805	0.728	0.886	CLONAL	1	FALSE	1	0.422691190790434	2		526	711	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828099	72828099	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	37	547	0	ENST00000268489.5:c.8482A>G	p.Thr2828Ala	p.T2828A	ENST00000268489	NM_006885.3	2828	Act/Gct	9/10	1	2	FACETS	0.241	0.198	0.289	0.241	0.198	0.289	SUBCLONAL	1	FALSE	1	0.422691190790434	2		547	727	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544782	86544782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1362905724	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	97	455	0	ENST00000262426.4:c.607G>A	p.Val203Met	p.V203M	ENST00000262426	NM_001451.2	203	Gtg/Atg	1/2	1	2	FACETS	0.925	0.828	1	0.925	0.828	1	CLONAL	1	FALSE	1	0.422691190790434	2		455	496	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346678	89346678	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	98	576	0	ENST00000301030.4:c.6272A>G	p.Gln2091Arg	p.Q2091R	ENST00000301030	NM_001256183.1	2091	cAg/cGg	9/13	1	2	FACETS	0.737	0.659	0.821	0.737	0.659	0.821	SUBCLONAL	1	FALSE	1	0.422691190790434	2		576	629	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845349	89845349	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	72	545	0	ENST00000389301.3:c.1776+2T>C		p.X592_splice	ENST00000389301	NM_000135.2	592			1	2	FACETS	0.37	0.322	0.422	0.37	0.322	0.422	SUBCLONAL	1	FALSE	1	0.422691190790434	2		545	921	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556296	29556296	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	66	515	0	ENST00000356175.3:c.2663A>G	p.Asp888Gly	p.D888G	ENST00000356175	NM_000267.3	888	gAt/gGt	21/57	1	2	FACETS	0.509	0.441	0.582	0.509	0.441	0.582	SUBCLONAL	1	FALSE	1	0.422691190790434	2		515	614	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557370	29557370	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	90	359	0	ENST00000356175.3:c.3083A>G	p.Asp1028Gly	p.D1028G	ENST00000356175	NM_000267.3	1028	gAc/gGc	23/57	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.422691190790434	2		359	375	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264348	30264353	+	inframe_deletion	In_Frame_Del	DEL	CGGCGG	CGGCGG	-	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	54	321	0	ENST00000322652.5:c.86_91del	p.Ala29_Ala30del	p.A29_A30del	ENST00000322652	NM_015355.2	28	tCGGCGGcg/tcg	1/16	1	2	FACETS	0.765	0.657	0.882	0.765	0.657	0.882	SUBCLONAL	1	FALSE	1	0.422691190790434	2		321	334	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492734	56492734	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	115	512	0	ENST00000407977.2:c.205T>C	p.Phe69Leu	p.F69L	ENST00000407977		69	Ttt/Ctt	2/10	1	2	FACETS	0.773	0.697	0.853	0.773	0.697	0.853	SUBCLONAL	1	FALSE	1	0.422691190790434	2		512	704	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761282	59761282	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555572828	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	120	559	0	ENST00000259008.2:c.3125A>G	p.Glu1042Gly	p.E1042G	ENST00000259008	NM_032043.2	1042	gAa/gGa	20/20	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	FALSE	1	0.422691190790434	2		559	560	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375005	45375005	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	129	475	0	ENST00000262160.6:c.838T>C	p.Tyr280His	p.Y280H	ENST00000262160	NM_005901.5	280	Tat/Cat	8/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.422691190790434	2		475	557	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220481	1220481	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	122	486	0	ENST00000326873.7:c.574A>G	p.Ile192Val	p.I192V	ENST00000326873	NM_000455.4	192	Atc/Gtc	4/10	1	2	FACETS	0.854	0.773	0.939	0.854	0.773	0.939	CLONAL	1	FALSE	1	0.422691190790434	2		486	676	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220098	5220098	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs142918634	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	130	520	0	ENST00000357368.4:c.3617G>T	p.Arg1206Leu	p.R1206L	ENST00000357368	NM_002850.3	1206	cGg/cTg	22/38	1	2	FACETS	0.938	0.853	1	0.938	0.853	1	CLONAL	1	FALSE	1	0.422691190790434	2		520	656	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262222	10262222	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	152	525	0	ENST00000340748.4:c.2070-1G>T		p.X690_splice	ENST00000340748		690			1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	FALSE	1	0.422691190790434	2		525	713	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030316	11030316	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	44	480	0	ENST00000327064.4:c.1066A>G	p.Thr356Ala	p.T356A	ENST00000327064	NM_199141.1	356	Acg/Gcg	9/16	1	2	FACETS	0.3	0.251	0.355	0.3	0.251	0.355	SUBCLONAL	1	FALSE	1	0.422691190790434	2		480	694	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136122	11136122	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	133	448	0	ENST00000358026.2:c.3106A>G	p.Met1036Val	p.M1036V	ENST00000358026	NM_001128849.1	1036	Atg/Gtg	22/36	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	FALSE	1	0.422691190790434	2		448	619	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297713	15297713	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	167	408	0	ENST00000263388.2:c.1927T>C	p.Cys643Arg	p.C643R	ENST00000263388	NM_000435.2	643	Tgt/Cgt	12/33	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.422691190790434	2		408	756	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18963812	18963812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	155	395	0	ENST00000262803.5:c.989C>T	p.Thr330Ile	p.T330I	ENST00000262803	NM_002911.3	330	aCt/aTt	7/24	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.422691190790434	2		395	672	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313432	30313432	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	135	453	0	ENST00000262643.3:c.1035del	p.Lys345AsnfsTer2	p.K345Nfs*2	ENST00000262643	NM_001238.2	344	tcA/tc	11/12	1	2	FACETS	0.909	0.827	0.994	0.909	0.827	0.994	CLONAL	1	FALSE	1	0.422691190790434	2		453	703	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214406	36214406	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	108	417	0	ENST00000222270.7:c.3058+2T>C		p.X1020_splice	ENST00000222270	NM_014727.1	1020			1	2	FACETS	0.705	0.633	0.781	0.705	0.633	0.781	SUBCLONAL	1	FALSE	1	0.422691190790434	2		417	725	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52725352	52725352	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	86	546	0	ENST00000322088.6:c.1519G>A	p.Val507Met	p.V507M	ENST00000322088	NM_014225.5	507	Gtg/Atg	13/15	0.420455165241139	2	FACETS	0.564	0.498	0.634	0.282	0.249	0.317	SUBCLONAL	1	FALSE	0	0.422691190790434	2		546	722	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637426	47637426	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs63751444	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	149	429	0	ENST00000233146.2:c.560T>G	p.Leu187Arg	p.L187R	ENST00000233146	NM_000251.2	187	cTt/cGt	3/16	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.422691190790434	2		429	604	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030648	48030648	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs866793892	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	140	567	0	ENST00000234420.5:c.3262T>C	p.Phe1088Leu	p.F1088L	ENST00000234420	NM_000179.2	1088	Ttc/Ctc	5/10	1	2	FACETS	0.978	0.893	1	0.978	0.893	1	CLONAL	1	FALSE	1	0.422691190790434	2		567	677	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631622	67631622	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1038834210	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	88	628	1	ENST00000272342.5:c.1808A>G	p.Asp603Gly	p.D603G	ENST00000272342	NM_019002.3	603	gAt/gGt	5/6	1	2	FACETS	0.789	0.701	0.882	0.789	0.701	0.882	SUBCLONAL	1	FALSE	1	0.422691190790434	2		629	528	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919836	96919836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772153618	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	156	439	0	ENST00000258439.3:c.427G>A	p.Val143Ile	p.V143I	ENST00000258439	NM_001193304.2	143	Gtc/Atc	4/4	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	FALSE	1	0.422691190790434	2		439	725	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182562	99182562	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	102	455	0	ENST00000074304.5:c.2365G>T	p.Gly789Cys	p.G789C	ENST00000074304	NM_001134224.1	789	Ggc/Tgc	22/26	1	2	FACETS	0.751	0.672	0.834	0.751	0.672	0.834	SUBCLONAL	1	FALSE	1	0.422691190790434	2		455	643	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158656001	158656001	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	106	445	2	ENST00000263640.3:c.5T>C	p.Val2Ala	p.V2A	ENST00000263640	NM_001105.4	2	gTa/gCa	3/11	1	2	FACETS	0.9	0.81	0.996	0.9	0.81	0.996	CLONAL	1	FALSE	1	0.422691190790434	2		447	557	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097266	178097266	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	117	446	0	ENST00000397062.3:c.448C>A	p.His150Asn	p.H150N	ENST00000397062	NM_006164.4	150	Cac/Aac	4/5	1	2	FACETS	0.861	0.778	0.948	0.861	0.778	0.948	CLONAL	1	FALSE	1	0.422691190790434	2		446	643	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812237	212812237	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	76	480	0	ENST00000342788.4:c.339T>A	p.Asp113Glu	p.D113E	ENST00000342788	NM_005235.2	113	gaT/gaA	3/28	1	2	FACETS	0.782	0.688	0.882	0.782	0.688	0.882	SUBCLONAL	1	FALSE	1	0.422691190790434	2		480	460	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017236	31017236	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	134	370	0	ENST00000375687.4:c.565+2T>C		p.X189_splice	ENST00000375687	NM_015338.5	189			1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	FALSE	1	0.422691190790434	2		370	628	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324333	62324333	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	38	553	0	ENST00000360203.5:c.2828C>A	p.Pro943His	p.P943H	ENST00000360203	NM_001283009.1	943	cCc/cAc	29/35	1	2	FACETS	0.264	0.217	0.316	0.264	0.217	0.316	SUBCLONAL	1	FALSE	1	0.422691190790434	2		553	681	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206823	36206823	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	41	493	1	ENST00000300305.3:c.689A>G	p.Gln230Arg	p.Q230R	ENST00000300305		230	cAg/cGg	6/8	1	2	FACETS	0.263	0.218	0.313	0.263	0.218	0.313	SUBCLONAL	1	FALSE	1	0.422691190790434	2		494	739	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29445584	29445584	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1177396156	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	147	507	0	ENST00000544604.2:c.1415A>G	p.Tyr472Cys	p.Y472C	ENST00000544604	NM_001206998.1	472	tAc/tGc	8/9	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.422691190790434	2		507	654	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446003	29446003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764157636	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	91	443	0	ENST00000544604.2:c.1834G>A	p.Gly612Ser	p.G612S	ENST00000544604	NM_001206998.1	612	Ggc/Agc	8/9	1	2	FACETS	0.815	0.726	0.91	0.815	0.726	0.91	CLONAL	1	FALSE	1	0.422691190790434	2		443	528	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732950	30732950	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1553631968	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	148	520	0	ENST00000295754.5:c.1563G>A	p.Trp521Ter	p.W521*	ENST00000295754	NM_003242.5	521	tgG/tgA	7/7	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	FALSE	1	0.422691190790434	2		520	698	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936091	49936091	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	146	609	0	ENST00000296474.3:c.1579T>C	p.Cys527Arg	p.C527R	ENST00000296474	NM_002447.2	527	Tgc/Cgc	4/20	1	2	FACETS	0.834	0.762	0.91	0.834	0.762	0.91	CLONAL	1	FALSE	1	0.422691190790434	2		609	828	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102851	71102851	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	105	502	0	ENST00000318789.4:c.356A>G	p.Gln119Arg	p.Q119R	ENST00000318789	NM_032682.5	119	cAa/cGa	8/21	1	2	FACETS	0.735	0.659	0.815	0.735	0.659	0.815	SUBCLONAL	1	FALSE	1	0.422691190790434	2		502	676	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665354	138665354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	33	473	0	ENST00000330315.3:c.211G>A	p.Ala71Thr	p.A71T	ENST00000330315	NM_023067.3	71	Gcg/Acg	1/1	1	2	FACETS	0.268	0.217	0.325	0.268	0.217	0.325	SUBCLONAL	1	FALSE	1	0.422691190790434	2		473	583	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131188	55131188	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	106	425	0	ENST00000257290.5:c.731A>T	p.Asp244Val	p.D244V	ENST00000257290	NM_006206.4	244	gAc/gTc	5/23	1	2	FACETS	0.854	0.768	0.946	0.854	0.768	0.946	CLONAL	1	FALSE	1	0.422691190790434	2		425	587	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467793	66467793	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	91	456	0	ENST00000273854.3:c.476A>C	p.Asp159Ala	p.D159A	ENST00000273854	NM_004439.5	159	gAt/gCt	3/18	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	FALSE	1	0.422691190790434	2		456	422	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268161	153268161	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs746085490	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	180	528	0	ENST00000281708.4:c.647A>G	p.Asn216Ser	p.N216S	ENST00000281708	NM_033632.3	216	aAt/aGt	4/12	1	2	FACETS	0.966	0.891	1	0.966	0.891	1	CLONAL	1	FALSE	1	0.422691190790434	2		528	882	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295459	1295459	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	129	534	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	1	0.422691190790434	2		535	575	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295725	1295725	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	167	534	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.422691190790434	2		534	661	SUCCESS
APC	324	MSKCC	GRCh37	5	112174815	112174815	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	28	549	0	ENST00000257430.4:c.3524A>C	p.Gln1175Pro	p.Q1175P	ENST00000257430	NM_000038.5	1175	cAg/cCg	16/16	1	2	FACETS	0.248	0.197	0.306	0.248	0.197	0.306	SUBCLONAL	1	FALSE	1	0.422691190790434	2		549	534	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931319	131931319	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	88	403	0	ENST00000265335.6:c.2024A>T	p.Asp675Val	p.D675V	ENST00000265335		675	gAc/gTc	13/25	1	2	FACETS	0.713	0.633	0.799	0.713	0.633	0.799	SUBCLONAL	1	FALSE	1	0.422691190790434	2		403	584	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401427	401427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	108	416	0	ENST00000380956.4:c.749G>A	p.Cys250Tyr	p.C250Y	ENST00000380956	NM_001195286.1	250	tGc/tAc	7/9	1	2	FACETS	0.877	0.789	0.969	0.877	0.789	0.969	CLONAL	1	FALSE	1	0.422691190790434	2		416	583	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197432	26197432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	141	607	0	ENST00000356476.2:c.47C>T	p.Ala16Val	p.A16V	ENST00000356476		16	gCg/gTg	1/1	1	2	FACETS	0.919	0.839	1	0.919	0.839	1	CLONAL	1	FALSE	1	0.422691190790434	2		607	726	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683870	117683870	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	64	426	0	ENST00000368508.3:c.3277A>T	p.Ile1093Phe	p.I1093F	ENST00000368508	NM_002944.2	1093	Att/Ttt	21/43	1	2	FACETS	0.621	0.538	0.709	0.621	0.538	0.709	SUBCLONAL	1	FALSE	1	0.422691190790434	2		426	488	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192427	138192427	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	114	429	0	ENST00000237289.4:c.63A>G	p.Ile21Met	p.I21M	ENST00000237289	NM_001270507.1	21	atA/atG	2/9	1	2	FACETS	0.995	0.9	1	0.995	0.9	1	CLONAL	1	FALSE	1	0.422691190790434	2		429	542	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874419	151874419	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	235	483	0	ENST00000262189.6:c.8119del	p.Val2707LeufsTer6	p.V2707Lfs*6	ENST00000262189	NM_170606.2	2707	Gtt/tt	38/59	0.387811903051993	3	FACETS	0.905	0.848	0.964	0.905	0.848	0.964	CLONAL	2	FALSE	1	0.422691190790434	3		483	744	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983513	90983513	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	44	293	0	ENST00000265433.3:c.590A>T	p.Tyr197Phe	p.Y197F	ENST00000265433	NM_002485.4	197	tAc/tTc	6/16	0.387811903051993	3	FACETS	0.653	0.549	0.768	0.327	0.274	0.384	SUBCLONAL	1	FALSE	1	0.422691190790434	3		293	386	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878862	117878862	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	107	467	0	ENST00000297338.2:c.107A>G	p.Asn36Ser	p.N36S	ENST00000297338	NM_006265.2	36	aAt/aGt	2/14	0.387811903051993	3	FACETS	0.852	0.764	0.944	0.426	0.382	0.472	CLONAL	1	FALSE	1	0.422691190790434	3		467	720	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341700	8341700	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	73	461	0	ENST00000356435.5:c.4940A>G	p.Glu1647Gly	p.E1647G	ENST00000356435		1647	gAa/gGa	29/35	0.318698779324379	3	FACETS	0.833	0.731	0.944	0.417	0.365	0.472	CLONAL	1	FALSE	1	0.422691190790434	3		461	502	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449805	8449805	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs756024990	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	90	440	0	ENST00000356435.5:c.3908G>T	p.Ser1303Ile	p.S1303I	ENST00000356435		1303	aGc/aTc	23/35	0.318698779324379	3	FACETS	0.744	0.661	0.834	0.372	0.33	0.417	SUBCLONAL	1	FALSE	1	0.422691190790434	3		440	693	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139794080	139794080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	127	494	0	ENST00000247668.2:c.223G>A	p.Glu75Lys	p.E75K	ENST00000247668	NM_021138.3	75	Gag/Aag	3/11	0.318698779324379	3	FACETS	0.774	0.701	0.852	0.387	0.35	0.426	SUBCLONAL	1	FALSE	1	0.422691190790434	3		494	940	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732840	44732840	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	17	200	0	ENST00000377967.4:c.43G>A	p.Ala15Thr	p.A15T	ENST00000377967	NM_021140.2	15	Gcc/Acc	1/29	1	1	FACETS	0.257	0.192	0.334	0.257	0.192	0.334	SUBCLONAL	1	FALSE	0	0.422691190790434	1		200	247	SUCCESS
PHF6	84295	MSKCC	GRCh37	X	133549116	133549116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	97	187	0	ENST00000332070.3:c.800C>T	p.Thr267Ile	p.T267I	ENST00000332070	NM_032458.2	267	aCt/aTt	8/10	1	1	FACETS	0.896	0.819	0.974	1	0.988	1	CLONAL	2	FALSE	0	0.422691190790434	1		187	202	SUCCESS
AR	367	MSKCC	GRCh37	X	66765171	66765172	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAA	novel	NA	P-0068503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	14	160	0	ENST00000374690.3:c.185_186insACA	p.Gln80dup	p.Q80dup	ENST00000374690	NM_000044.3	80	-/CAA	1/8	1	1	FACETS	0.212	0.152	0.283	0.212	0.152	0.283	SUBCLONAL	1	FALSE	0	0.422691190790434	1		160	247	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	102	288	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.187919652472657	2	FACETS	0.836	0.752	0.923	1	0.974	1	CLONAL	3	TRUE	0	0.187919652472657	2		288	433	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	45	638	1	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	0.187855805171076	3	FACETS	0.844	0.708	0.994	0.422	0.354	0.497	CLONAL	1	TRUE	1	0.187919652472657	3		639	621	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	203	606	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.877	0.815	0.942	1	0.995	1	CLONAL	3	TRUE	1	0.187919652472657	2		606	821	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070349	37070349	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs63750855	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	57	551	0	ENST00000231790.2:c.1489del	p.Arg497GlyfsTer11	p.R497Gfs*11	ENST00000231790	NM_000249.3	495	aCc/ac	13/19	1	2	FACETS	0.886	0.759	1	0.886	0.759	1	CLONAL	1	TRUE	1	0.187919652472657	2		551	685	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	133	322	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.918	0.838	1	1	0.992	1	CLONAL	3	TRUE	1	0.187919652472657	2		322	514	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	62	496	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.187919652472657	2		496	529	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528120	103528120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376411022	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	88	342	0	ENST00000355739.4:c.3428C>T	p.Ala1143Val	p.A1143V	ENST00000355739	NM_000123.3	1143	gCg/gTg	15/15	0.187855805171076	3	FACETS	1	0.978	1	0.745	0.66	0.835	CLONAL	1	TRUE	1	0.187919652472657	3		342	688	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023327	27023327	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	28	405	0	ENST00000324856.7:c.437del	p.Pro146GlnfsTer86	p.P146Qfs*86	ENST00000324856	NM_006015.4	145	Ccc/cc	1/20	1	2	FACETS	0.895	0.716	1	0.895	0.716	1	CLONAL	1	TRUE	1	0.187919652472657	2		405	333	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007834	45007834	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	69	519	0	ENST00000558401.1:c.285del	p.Asp96MetfsTer7	p.D96Mfs*7	ENST00000558401	NM_004048.2	94	gAa/ga	2/4	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.187919652472657	2		519	710	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	65	528	0	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	0.147775651318722	3	FACETS	0.982	0.85	1	0.491	0.425	0.563	CLONAL	1	TRUE	1	0.187919652472657	3		528	771	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119752	70119753	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	22	391	0	ENST00000245479.2:c.755dup	p.Lys253GlufsTer43	p.K253Efs*43	ENST00000245479	NM_000346.3	252	ctg/cTtg	3/3	1	2	FACETS	0.734	0.569	0.926	0.734	0.569	0.926	CLONAL	1	TRUE	1	0.187919652472657	2		391	319	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285913	38285914	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCA	rs138489552	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	35	517	0	ENST00000425967.3:c.495_497dup	p.Asp166dup	p.D166dup	ENST00000425967	NM_001174067.1	166	gac/gaTGAc	5/19	0.187919652472657	2	FACETS	0.619	0.506	0.746	0.309	0.253	0.373	SUBCLONAL	1	TRUE	0	0.187919652472657	2		517	602	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214065	108214074	+	frameshift_variant	Frame_Shift_Del	DEL	TTTCAGTGCC	TTTCAGTGCC	-	rs786202800	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	115	487	0	ENST00000278616.4:c.8395_8404del	p.Phe2799LysfsTer4	p.F2799Kfs*4	ENST00000278616	NM_000051.3	2795	gaTTTCAGTGCC/ga	57/63	0.187919652472657	0	FACETS	0.811	0.732	0.893			1	CLONAL	2	TRUE	0	0.187919652472657	0		487	613	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961103	55961103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140041720	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	37	406	1	ENST00000263923.4:c.2837G>A	p.Arg946His	p.R946H	ENST00000263923	NM_002253.2	946	cGt/cAt	21/30	1	2	FACETS	0.659	0.542	0.79	0.659	0.542	0.79	SUBCLONAL	1	TRUE	1	0.187919652472657	2		407	598	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239441	123239442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	71	599	0	ENST00000358487.5:c.2395dup	p.Ser799PhefsTer22	p.S799Ffs*22	ENST00000358487	NM_000141.4	799	tct/tTct	18/18	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.187919652472657	2		599	686	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	70	707	5	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.187919652472657	2		712	645	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482439	56482446	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTGGGT	AGGTGGGT	-	novel	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	122	521	0	ENST00000267101.3:c.988+2_988+9del		p.X330_splice	ENST00000267101	NM_001982.3	330		8/28	0.187919652472657	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.187919652472657	2		521	608	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665096	138665096	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs758370933	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	48	404	0	ENST00000330315.3:c.469C>G	p.Pro157Ala	p.P157A	ENST00000330315	NM_023067.3	157	Ccc/Gcc	1/1	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.187919652472657	2		404	413	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633518	69633518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	46	531	0	ENST00000334134.2:c.184G>A	p.Gly62Ser	p.G62S	ENST00000334134	NM_005247.2	62	Ggc/Agc	1/3	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.187919652472657	2		531	392	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798864	135798864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372215435	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	87	457	0	ENST00000298552.3:c.379G>A	p.Val127Ile	p.V127I	ENST00000298552	NM_001162426.1	127	Gtt/Att	6/23	0.187855805171076	3	FACETS	0.817	0.724	0.916	0.817	0.724	0.916	CLONAL	2	TRUE	1	0.187919652472657	3		457	620	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738804	145738804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs190061994	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	81	755	0	ENST00000428558.2:c.2261G>A	p.Arg754Gln	p.R754Q	ENST00000428558	NM_004260.3	754	cGg/cAg	14/22	0.187919652472657	5	FACETS	1	0.912	1	0.524	0.46	0.593	CLONAL	1	TRUE	3	0.187919652472657	5		755	1055	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681139	37681139	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	63	475	0	ENST00000447079.4:c.3307+1G>A		p.X1103_splice	ENST00000447079	NM_015083.1	1103			1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.187919652472657	2		475	653	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430744	181430744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	71	597	0	ENST00000325404.1:c.596G>A	p.Arg199His	p.R199H	ENST00000325404	NM_003106.3	199	cGc/cAc	1/1	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.187919652472657	2		597	572	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	74	400	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.187919652472657	2	FACETS	0.909	0.799	1	0.909	0.799	1	CLONAL	2	TRUE	0	0.187919652472657	2		400	433	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110710	2110710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559727962	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	60	505	0	ENST00000219476.3:c.1015G>A	p.Val339Ile	p.V339I	ENST00000219476	NM_000548.3	339	Gtc/Atc	11/42	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.187919652472657	2		505	559	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38139034	38139034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201914561	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	43	449	0	ENST00000317025.8:c.3569G>A	p.Arg1190Gln	p.R1190Q	ENST00000317025	NM_023034.1	1190	cGa/cAa	20/24	0.187919652472657	2	FACETS	0.792	0.662	0.936	0.396	0.331	0.468	CLONAL	1	TRUE	0	0.187919652472657	2		449	578	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47599086	47599086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148905856	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	44	589	0	ENST00000430070.2:c.514C>T	p.Arg172Trp	p.R172W	ENST00000430070	NM_018095.4	172	Cgg/Tgg	2/4	1	2	FACETS	0.695	0.581	0.821	0.695	0.581	0.821	SUBCLONAL	1	TRUE	1	0.187919652472657	2		589	674	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044524	12044524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	60	435	0	ENST00000353533.5:c.1150del	p.Ile384SerfsTer29	p.I384Sfs*29	ENST00000353533	NM_003010.3	383	Aaa/aa	11/11	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.187919652472657	2		435	543	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438322	110438322	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	42	438	0	ENST00000375856.3:c.79A>G	p.Asn27Asp	p.N27D	ENST00000375856	NM_003749.2	27	Aac/Gac	1/2	0.187855805171076	3	FACETS	1	0.872	1	0.526	0.439	0.622	CLONAL	1	TRUE	1	0.187919652472657	3		438	465	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137294	64137294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	58	576	0	ENST00000334205.4:c.1726G>A	p.Ala576Thr	p.A576T	ENST00000334205	NM_003942.2	576	Gct/Act	14/17	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.187919652472657	2		576	568	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104014	69104014	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	41	429	0	ENST00000288368.4:c.4404T>A	p.Tyr1468Ter	p.Y1468*	ENST00000288368	NM_024870.2	1468	taT/taA	36/40	0.187919652472657	5	FACETS	0.862	0.716	1	0.431	0.358	0.512	CLONAL	1	TRUE	3	0.187919652472657	5		429	649	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246187	46246196	+	frameshift_variant	Frame_Shift_Del	DEL	TGTGAGCAGT	TGTGAGCAGT	-	novel	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	54	464	0	ENST00000334344.6:c.4281_4290del	p.Val1428TyrfsTer22	p.V1428Yfs*22	ENST00000334344	NM_152641.2	1427	tcTGTGAGCAGT/tc	15/21	0.187919652472657	2	FACETS	0.971	0.829	1	0.485	0.414	0.563	CLONAL	1	TRUE	0	0.187919652472657	2		464	592	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265519	198265519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	79	410	0	ENST00000335508.6:c.2638G>A	p.Gly880Arg	p.G880R	ENST00000335508	NM_012433.2	880	Gga/Aga	18/25	0.187855805171076	3	FACETS	0.879	0.775	0.991	0.879	0.775	0.991	CLONAL	2	TRUE	1	0.187919652472657	3		410	523	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253855	153253855	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	39	308	0	ENST00000281708.4:c.878T>C	p.Leu293Pro	p.L293P	ENST00000281708	NM_033632.3	293	cTt/cCt	6/12	1	2	FACETS	0.993	0.824	1	0.993	0.824	1	CLONAL	1	TRUE	1	0.187919652472657	2		308	418	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347126	89347126	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	60	555	0	ENST00000301030.4:c.5824G>A	p.Val1942Ile	p.V1942I	ENST00000301030	NM_001256183.1	1942	Gtc/Atc	9/13	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.187919652472657	2		555	560	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77931466	77931466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145573768	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	64	548	1	ENST00000361507.4:c.1786G>A	p.Val596Ile	p.V596I	ENST00000361507	NM_080491.2	596	Gtt/Att	9/10	1	2	FACETS	0.989	0.855	1	0.989	0.855	1	CLONAL	1	TRUE	1	0.187919652472657	2		549	689	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32439125	32439125	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	47	464	0	ENST00000332351.3:c.948G>T	p.Lys316Asn	p.K316N	ENST00000332351	NM_024426.4	316	aaG/aaT	4/10	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.187919652472657	2		464	471	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332815	70332815	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	56	459	0	ENST00000373644.4:c.724del	p.Met242CysfsTer29	p.M242Cfs*29	ENST00000373644	NM_030625.2	240	ccA/cc	2/12	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.187919652472657	2		459	561	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009361	69009361	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	182	430	0	ENST00000288368.4:c.2478C>A	p.Asp826Glu	p.D826E	ENST00000288368	NM_024870.2	826	gaC/gaA	22/40	0.187919652472657	5	FACETS	1	0.966	1	1	0.991	1	CLONAL	3	TRUE	3	0.187919652472657	5		430	768	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80169095	80169095	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	51	395	0	ENST00000265081.6:c.3291A>G	p.Ile1097Met	p.I1097M	ENST00000265081	NM_002439.4	1097	atA/atG	23/24	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.187919652472657	2		395	458	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412291	63412291	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	59	348	0	ENST00000330258.3:c.876G>T	p.Lys292Asn	p.K292N	ENST00000330258	NM_152424.3	292	aaG/aaT	2/2	1	1	FACETS	0.842	0.728	0.964	1	0.974	1	CLONAL	2	TRUE	0	0.187919652472657	1		348	338	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189500	94189500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767097795	NA	P-0068504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	49	328	0	ENST00000323929.3:c.1505G>A	p.Arg502His	p.R502H	ENST00000323929	NM_005591.3	502	cGt/cAt	14/20	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.187919652472657	2		328	499	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343540	343540	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0068505-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	20	570	0	ENST00000262320.3:c.2134C>T	p.Arg712Ter	p.R712*	ENST00000262320	NM_003502.3	712	Cga/Tga	8/11	0.637482352478234	1	FACETS	0.108	0.082	0.138	0.108	0.082	0.138	SUBCLONAL	1	TRUE	0	0.638574482874826	1		570	395	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368458	225368458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1312027878	NA	P-0068505-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	346	421	0	ENST00000264414.4:c.1288C>T	p.Arg430Cys	p.R430C	ENST00000264414	NM_003590.4	430	Cgt/Tgt	9/16	0.595449975688447	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.638574482874826	4		421	852	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971057	21971058	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0068505-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	607	570	0	ENST00000304494.5:c.300dup	p.Gly101ArgfsTer19	p.G101Rfs*19	ENST00000304494	NM_000077.4	100	-/C	2/3	0.635626626494603	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	0	0.638574482874826	3		570	835	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584529	52584531	+	inframe_deletion	In_Frame_Del	DEL	TGG	TGG	-	novel	NA	P-0068505-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	413	601	0	ENST00000394830.3:c.4482_4484del	p.Gln1495del	p.Q1495del	ENST00000394830	NM_018313.4	1494	acCCAg/acg	29/30	0.637482352478234	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.638574482874826	2		601	634	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306790	41306790	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068505-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	348	508	0	ENST00000373198.4:c.869C>A	p.Thr290Lys	p.T290K	ENST00000373198	NM_133170.3	290	aCg/aAg	7/32	0.595449975688447	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.638574482874826	4		508	849	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685534	29685553	+	frameshift_variant	Frame_Shift_Del	DEL	ATCATTGTGCCAAGATCCAA	ATCATTGTGCCAAGATCCAA	-	novel	NA	P-0068505-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	311	507	0	ENST00000356175.3:c.7946_7965del	p.Ser2649PhefsTer16	p.S2649Ffs*16	ENST00000356175	NM_000267.3	2648	ttATCATTGTGCCAAGATCCAAat/ttat	54/57	0.595449975688447	4	FACETS	0.927	0.877	0.977	0.927	0.877	0.977	CLONAL	2	TRUE	2	0.638574482874826	4		507	861	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422752	47422761	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGACAAGT	AAAGACAAGT	-	novel	NA	P-0068505-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	360	505	0	ENST00000404338.3:c.821_830del	p.Lys274MetfsTer5	p.K274Mfs*5	ENST00000404338	NM_004491.4	274	AAAGACAAGTat/at	1/6	0.637482352478234	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.638574482874826	2		505	522	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649626	48649626	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0068505-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	398	290	0	ENST00000376670.3:c.110G>T	p.Gly37Val	p.G37V	ENST00000376670	NM_002049.3	37	gGg/gTg	2/6	0.598639176033586	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.638574482874826	2		290	504	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391151	89391151	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0068505-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	320	491	0	ENST00000336596.2:c.1217C>A	p.Thr406Asn	p.T406N	ENST00000336596	NM_005233.5	406	aCc/aAc	5/17	0.541924881060075	4	FACETS	0.976	0.926	1	0.976	0.926	1	CLONAL	2	TRUE	2	0.638574482874826	4		491	841	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577585	7577587	+	missense_variant	Missense_Mutation	TNP	GAT	GAT	AAA	novel	NA	P-0068505-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	352	528	0	ENST00000269305.4:c.694_696delinsTTT	p.Ile232Phe	p.I232F	ENST00000269305	NM_001126112.2	232	ATC/TTT	7/11	0.637482352478234	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.638574482874826	2		528	517	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163744	72163744	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1248852117	NA	P-0068506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	47	451	0	ENST00000357731.5:c.614C>T	p.Ala205Val	p.A205V	ENST00000357731	NM_173808.2	205	gCg/gTg	4/7	0.181755997953943	3	FACETS	0.535	0.45	0.629	0.267	0.225	0.315	SUBCLONAL	1	TRUE	1	0.29	3		451	694	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15978853	15978853	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1278600466	NA	P-0068506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	39	452	0	ENST00000268712.3:c.3665A>G	p.Tyr1222Cys	p.Y1222C	ENST00000268712	NM_006311.3	1222	tAt/tGt	27/46	0.3	1	FACETS	0.505	0.419	0.602	0.505	0.419	0.602	SUBCLONAL	1	TRUE	0	0.29	1		452	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577101	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCTGTGCGCCGGTCTCTC	CCTCTGTGCGCCGGTCTCTC	-	novel	NA	P-0068506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	85	571	0	ENST00000269305.4:c.837_856del	p.Asp281GlufsTer18	p.D281Efs*18	ENST00000269305	NM_001126112.2	279	ggGAGAGACCGGCGCACAGAGGaa/ggaa	8/11	0.3	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.29	1		571	469	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510829	120510829	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0068506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	104	509	0	ENST00000256646.2:c.1135T>C	p.Cys379Arg	p.C379R	ENST00000256646	NM_024408.3	379	Tgc/Cgc	7/34	0.181755997953943	3	FACETS	1	0.972	1	0.625	0.56	0.694	CLONAL	1	TRUE	1	0.29	3		509	657	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0068507-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	77	150	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.606726490833261	4	FACETS	1	0.913	1	0.347	0.306	0.39	CLONAL	1	TRUE	1	0.606726490833261	4		150	392	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713238	43713238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1273385388	NA	P-0068507-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	168	496	0	ENST00000382044.4:c.4235G>A	p.Arg1412Gln	p.R1412Q	ENST00000382044	NM_001141980.1	1412	cGg/cAg	20/28	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.606726490833261	2		496	493	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62009557	62009557	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0068507-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	136	442	0	ENST00000392795.3:c.65C>T	p.Ser22Leu	p.S22L	ENST00000392795	NM_001039933.1	22	tCa/tTa	1/6	0.606726490833261	3	FACETS	1	0.978	1	0.604	0.552	0.657	CLONAL	1	TRUE	1	0.606726490833261	3		442	484	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521031	187521051	+	splice_donor_variant,intron_variant	Splice_Site	DEL	TGGCAACATTACGGAGCCCAC	TGGCAACATTACGGAGCCCAC	-	novel	NA	P-0068507-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	110	404	0	ENST00000441802.2:c.12103+1_12103+21del		p.X4035_splice	ENST00000441802	NM_005245.3	4035			0.176324061041423	1	FACETS	0.622	0.563	0.683	0.622	0.563	0.683	INDETERMINATE	1	TRUE	0	0.606726490833261	1		404	406	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115966	8115967	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0068508-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	56	492	0	ENST00000346208.3:c.1313_1314dup	p.Val439TrpfsTer37	p.V439Wfs*37	ENST00000346208		438	atg/aTGtg	6/6	1	2	FACETS	0.487	0.416	0.564	0.487	0.416	0.564	SUBCLONAL	1	FALSE	1	0.348110001093593	2		492	661	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467833	66467833	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0068508-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	54	412	0	ENST00000273854.3:c.436A>G	p.Thr146Ala	p.T146A	ENST00000273854	NM_004439.5	146	Acc/Gcc	3/18	1	2	FACETS	0.559	0.477	0.648	0.559	0.477	0.648	SUBCLONAL	1	FALSE	1	0.348110001093593	2		412	555	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130141	143130141	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1561488767	NA	P-0068508-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	38	351	0	ENST00000262992.4:c.875A>G	p.His292Arg	p.H292R	ENST00000262992	NM_001101669.1	292	cAt/cGt	11/24	1	2	FACETS	0.43	0.355	0.514	0.43	0.355	0.514	SUBCLONAL	1	FALSE	1	0.348110001093593	2		351	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0068560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	13	511	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	1	2	FACETS	0.105	0.074	0.142	0.105	0.074	0.142	SUBCLONAL	1	TRUE	1	0.463174687532125	2		511	537	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0068560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	51	252	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.857	0.735	0.988	0.857	0.735	0.988	CLONAL	1	TRUE	1	0.463174687532125	2		253	257	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0000836-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	183	529	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	0.395083841476927	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.394085122668328	3		529	522	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004667-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	53	317	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.799	0.692	0.911	0.799	0.692	0.911	CLONAL	1	TRUE	1	0.725175413363502	2		317	183	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653808	89653808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004667-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	278	262	0	ENST00000371953.3:c.106G>A	p.Gly36Arg	p.G36R	ENST00000371953	NM_000314.4	36	Gga/Aga	2/9	0.725175413363502	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.725175413363502	2		262	380	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031691	69031691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748595305	NA	P-0004667-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	172	354	0	ENST00000288368.4:c.3446G>A	p.Arg1149His	p.R1149H	ENST00000288368	NM_024870.2	1149	cGc/cAc	28/40	1	2	FACETS	0.962	0.893	1	0.962	0.893	1	CLONAL	1	TRUE	1	0.725175413363502	2		354	493	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601927	43601927	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004667-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	23	515	0	ENST00000355710.3:c.973del	p.Ala325ProfsTer88	p.A325Pfs*88	ENST00000355710	NM_020975.4	324	tGg/tg	5/20	1	2	FACETS	0.15	0.117	0.189	0.15	0.117	0.189	SUBCLONAL	1	TRUE	1	0.725175413363502	2		515	422	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	112	317	0				ENST00000310581	NM_198253.2	-/1132			0.273620530698253	3	FACETS	0.753	0.688	0.819	0.753	0.688	0.819	INDETERMINATE	2	TRUE	1	0.703259484946242	3		317	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0006254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	12	613	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.682577005381432	1	FACETS	0.076	0.053	0.105	0.076	0.053	0.105	SUBCLONAL	1	TRUE	0	0.703259484946242	1		613	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577595	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0006254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	113	544	0	ENST00000269305.4:c.686_687del	p.Cys229TyrfsTer10	p.C229Yfs*10	ENST00000269305	NM_001126112.2	229	tGT/t	7/11	0.682577005381432	1	FACETS	0.814	0.747	0.882	0.814	0.747	0.882	CLONAL	1	TRUE	0	0.703259484946242	1		544	256	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913233	32913233	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	181	625	0	ENST00000380152.3:c.4741G>T	p.Glu1581Ter	p.E1581*	ENST00000380152		1581	Gag/Tag	11/27	1	2	FACETS	0.948	0.881	1	0.948	0.881	1	CLONAL	1	TRUE	1	0.703259484946242	2		625	543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577599	7577599	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	26	528	0	ENST00000269305.4:c.682G>C	p.Asp228His	p.D228H	ENST00000269305	NM_001126112.2	228	Gac/Cac	7/11	0.682577005381432	1	FACETS	0.19	0.151	0.235	0.19	0.151	0.235	SUBCLONAL	1	TRUE	0	0.703259484946242	1		528	252	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499477	89499477	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752560194	NA	P-0006254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	130	587	0	ENST00000336596.2:c.2647C>T	p.Arg883Trp	p.R883W	ENST00000336596	NM_005233.5	883	Cgg/Tgg	15/17	1	2	FACETS	0.8	0.731	0.872	0.8	0.731	0.872	SUBCLONAL	1	TRUE	1	0.703259484946242	2		587	462	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981084	201981084	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0006254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	216	549	0	ENST00000359651.3:c.164-1G>C		p.X55_splice	ENST00000359651		55			1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.703259484946242	2		549	607	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598203	28598203	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	146	621	0	ENST00000253063.3:c.175G>A	p.Glu59Lys	p.E59K	ENST00000253063	NM_031459.4	59	Gag/Aag	3/10	1	2	FACETS	0.927	0.853	1	0.927	0.853	1	CLONAL	1	TRUE	1	0.703259484946242	2		621	448	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194789	30194789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761853569	NA	P-0006254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	137	604	0	ENST00000331968.5:c.356C>T	p.Ala119Val	p.A119V	ENST00000331968	NM_002742.2	119	gCg/gTg	2/18	1	2	FACETS	0.854	0.783	0.928	0.854	0.783	0.928	CLONAL	1	TRUE	1	0.703259484946242	2		604	456	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599875	28599875	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	110	495	0	ENST00000253063.3:c.757G>C	p.Glu253Gln	p.E253Q	ENST00000253063	NM_031459.4	253	Gag/Cag	6/10	1	2	FACETS	0.798	0.723	0.876	0.798	0.723	0.876	SUBCLONAL	1	TRUE	1	0.703259484946242	2		495	392	SUCCESS
APC	324	MSKCC	GRCh37	5	112173429	112173429	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs137854570	NA	P-0006254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	290	591	0	ENST00000257430.4:c.2138C>G	p.Ser713Ter	p.S713*	ENST00000257430	NM_000038.5	713	tCa/tGa	16/16	0.703259484946242	2	FACETS	0.927	0.888	0.965	0.927	0.888	0.965	CLONAL	2	TRUE	0	0.703259484946242	2		591	445	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601365	28601365	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	98	418	0	ENST00000241453.7:c.2067G>C	p.Leu689Phe	p.L689F	ENST00000241453	NM_004119.2	689	ttG/ttC	17/24	0.575304746911567	1	FACETS	0.541	0.488	0.597	0.541	0.488	0.597	SUBCLONAL	1	TRUE	0	0.703259484946242	1		418	334	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349141	89349141	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	157	633	0	ENST00000301030.4:c.3809C>T	p.Ser1270Phe	p.S1270F	ENST00000301030	NM_001256183.1	1270	tCc/tTc	9/13	1	2	FACETS	0.936	0.864	1	0.936	0.864	1	CLONAL	1	TRUE	1	0.703259484946242	2		633	477	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405872	70405872	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0006254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	122	607	0	ENST00000373644.4:c.3386C>G	p.Ser1129Ter	p.S1129*	ENST00000373644	NM_030625.2	1129	tCa/tGa	4/12	1	2	FACETS	0.83	0.756	0.906	0.83	0.756	0.906	CLONAL	1	TRUE	1	0.703259484946242	2		607	418	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250525	110250525	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	86	422	0	ENST00000374672.4:c.150C>A	p.His50Gln	p.H50Q	ENST00000374672	NM_004235.4	50	caC/caA	3/5	1	2	FACETS	0.883	0.791	0.978	0.883	0.791	0.978	CLONAL	1	TRUE	1	0.703259484946242	2		422	277	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030450	49030450	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs587778865	NA	P-0006254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	147	518	0	ENST00000267163.4:c.1925T>A	p.Leu642Ter	p.L642*	ENST00000267163	NM_000321.2	642	tTg/tAg	19/27	0.702605845480641	1	FACETS	0.935	0.87	0.999	0.935	0.87	0.999	CLONAL	1	TRUE	0	0.703259484946242	1		518	290	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324537	62324537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	178	660	0	ENST00000360203.5:c.2893G>A	p.Glu965Lys	p.E965K	ENST00000360203	NM_001283009.1	965	Gag/Aag	30/35	1	2	FACETS	0.983	0.913	1	0.983	0.913	1	CLONAL	1	TRUE	1	0.703259484946242	2		660	515	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	240568	240568	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	17	57	0	ENST00000264932.6:c.1528G>C	p.Glu510Gln	p.E510Q	ENST00000264932	NM_004168.2	510	Gaa/Caa	11/15	0.374601239235539	5	FACETS	0.965	0.73	1	0.322	0.243	0.412	INDETERMINATE	1	TRUE	2	0.703259484946242	5		57	103	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223911	36223911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	158	697	0	ENST00000222270.7:c.6461C>T	p.Ala2154Val	p.A2154V	ENST00000222270	NM_014727.1	2154	gCc/gTc	28/37	1	2	FACETS	0.897	0.828	0.968	0.897	0.828	0.968	CLONAL	1	TRUE	1	0.703259484946242	2		697	501	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673794	30673794	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	27	551	0	ENST00000376406.3:c.3166C>T	p.Gln1056Ter	p.Q1056*	ENST00000376406	NM_014641.2	1056	Cag/Tag	10/15	1	2	FACETS	0.151	0.12	0.188	0.151	0.12	0.188	SUBCLONAL	1	TRUE	1	0.703259484946242	2		551	507	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346214	70346214	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	134	310	0	ENST00000374080.3:c.2565G>C	p.Gln855His	p.Q855H	ENST00000374080		855	caG/caC	19/45	1	1	FACETS	0.988	0.919	1	0.988	0.919	1	CLONAL	1	TRUE	0	0.703259484946242	1		310	250	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981246	201981246	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	270	684	0	ENST00000359651.3:c.325G>T	p.Glu109Ter	p.E109*	ENST00000359651		109	Gag/Tag	2/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.703259484946242	2		684	709	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224023	36224023	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	142	640	0	ENST00000222270.7:c.6573C>G	p.Ile2191Met	p.I2191M	ENST00000222270	NM_014727.1	2191	atC/atG	28/37	1	2	FACETS	0.822	0.755	0.893	0.822	0.755	0.893	CLONAL	1	TRUE	1	0.703259484946242	2		640	491	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2123882	2123882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	138	570	1	ENST00000349721.2:c.3926G>A	p.Arg1309His	p.R1309H	ENST00000349721	NM_003070.3	1309	cGc/cAc	27/34	1	2	FACETS	0.863	0.791	0.936	0.863	0.791	0.936	CLONAL	1	TRUE	1	0.703259484946242	2		571	455	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261508	16261508	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs780306504	NA	P-0006254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	157	662	0	ENST00000375759.3:c.8773C>G	p.Gln2925Glu	p.Q2925E	ENST00000375759	NM_015001.2	2925	Cag/Gag	11/15	0.551171259121681	4	FACETS	1	0.971	1			1	CLONAL	1	TRUE	NA	0.703259484946242	4		662	676	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099259	4099259	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	139	536	2	ENST00000262948.5:c.859G>T	p.Glu287Ter	p.E287*	ENST00000262948	NM_030662.3	287	Gaa/Taa	7/11	1	2	FACETS	0.919	0.844	0.996	0.919	0.844	0.996	CLONAL	1	TRUE	1	0.703259484946242	2		538	430	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771535	112771535	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	161	586	0	ENST00000369452.4:c.1708C>G	p.Gln570Glu	p.Q570E	ENST00000369452	NM_007373.3	570	Cag/Gag	9/9	1	2	FACETS	0.925	0.855	0.997	0.925	0.855	0.997	CLONAL	1	TRUE	1	0.703259484946242	2		586	495	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1932378	1932378	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	120	593	0	ENST00000382891.5:c.1436C>T	p.Ser479Leu	p.S479L	ENST00000382891	NM_133335.3	479	tCa/tTa	6/22	0.682577005381432	1	FACETS	0.664	0.608	0.723	0.664	0.608	0.723	SUBCLONAL	1	TRUE	0	0.703259484946242	1		593	333	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099436	27099439	+	frameshift_variant	Frame_Shift_Del	DEL	TCCT	TCCT	-	novel	NA	P-0006254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	36	667	0	ENST00000324856.7:c.3673_3676del	p.Ser1225MetfsTer11	p.S1225Mfs*11	ENST00000324856	NM_006015.4	1225	TCCTat/at	14/20	1	2	FACETS	0.185	0.152	0.223	0.185	0.152	0.223	SUBCLONAL	1	TRUE	1	0.703259484946242	2		667	552	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673703	37673703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009401-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	158	520	0	ENST00000447079.4:c.2857G>A	p.Gly953Ser	p.G953S	ENST00000447079	NM_015083.1	953	Ggt/Agt	10/14	0.582318917385741	3	FACETS	1	0.986	1	0.667	0.615	0.721	CLONAL	1	TRUE	1	0.581007453721461	3		520	526	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618989	37618990	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0009401-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	356	647	0	ENST00000447079.4:c.670dup	p.His224ProfsTer6	p.H224Pfs*6	ENST00000447079	NM_015083.1	222	agc/agCc	1/14	0.582318917385741	3	FACETS	0.938	0.893	0.983	0.938	0.893	0.983	CLONAL	2	TRUE	1	0.581007453721461	3		647	843	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944841	31944842	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0009401-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	159	574	0	ENST00000340398.3:c.259_260del	p.Ala87SerfsTer9	p.A87Sfs*9	ENST00000340398	NM_001013699.2	87	GCa/a	1/1	1	2	FACETS	0.754	0.692	0.818	0.754	0.692	0.818	SUBCLONAL	1	TRUE	1	0.581007453721461	2		574	726	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880998	37880998	+	protein_altering_variant	In_Frame_Ins	INS	G	G	TTGT	novel	NA	P-0010841-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	277	389	0	ENST00000269571.5:c.2327delinsTTGT	p.Gly776delinsValVal	p.G776delinsVV	ENST00000269571		776	gGt/gTTGTt	20/27	0.760922788325414	3	FACETS	0.927	0.881	0.974	0.927	0.881	0.974	CLONAL	2	TRUE	1	0.760663443470446	3		389	542	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21336844	21336844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010841-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	131	368	0	ENST00000215739.8:c.184G>A	p.Glu62Lys	p.E62K	ENST00000215739	NM_006767.3	62	Gag/Aag	1/21	1	2	FACETS	0.909	0.834	0.986	0.909	0.834	0.986	CLONAL	1	TRUE	1	0.760663443470446	2		368	379	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157495216	157495216	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010841-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	124	348	0	ENST00000346085.5:c.3100G>C	p.Glu1034Gln	p.E1034Q	ENST00000346085	NM_020732.3	1034	Gaa/Caa	11/20	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.760663443470446	2		348	323	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285607	46285607	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010841-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	58	289	0	ENST00000334344.6:c.4968del	p.Glu1656AspfsTer45	p.E1656Dfs*45	ENST00000334344	NM_152641.2	1656	gAa/ga	17/21	NA	2	FACETS	0.398	0.343	0.458			1	INDETERMINATE	1	TRUE	NA	0.760663443470446	2		289	383	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205150	61205172	+	frameshift_variant	Frame_Shift_Del	DEL	ATTCAGACGCTTCTACAGAGGTG	ATTCAGACGCTTCTACAGAGGTG	-	novel	NA	P-0010841-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	49	256	0	ENST00000301761.2:c.91_113del	p.Phe31GlnfsTer11	p.F31Qfs*11	ENST00000301761	NM_017841.2	30	tcATTCAGACGCTTCTACAGAGGTGac/tcac	2/4	1	2	FACETS	0.376	0.319	0.437	0.376	0.319	0.437	SUBCLONAL	1	TRUE	1	0.760663443470446	2		256	343	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458958	120458959	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0010841-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	48	399	0	ENST00000256646.2:c.6386_6387del	p.Ser2129LysfsTer8	p.S2129Kfs*8	ENST00000256646	NM_024408.3	2129	aGT/a	34/34	1	2	FACETS	0.324	0.275	0.379	0.324	0.275	0.379	SUBCLONAL	1	TRUE	1	0.760663443470446	2		399	389	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880998	37880998	+	protein_altering_variant	In_Frame_Ins	INS	G	G	TTGT	novel	NA	P-0010841-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	43	389	0	ENST00000269571.5:c.2327delinsTTGT	p.Gly776delinsValVal	p.G776delinsVV	ENST00000269571		776	gGt/gTTGTt	20/27	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.17	2		389	497	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21336844	21336844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010841-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	24	368	0	ENST00000215739.8:c.184G>A	p.Glu62Lys	p.E62K	ENST00000215739	NM_006767.3	62	Gag/Aag	1/21	0.087800153668946	0	FACETS	0.512	0.4	0.641			1	INDETERMINATE	1	TRUE	0	0.17	0		368	458	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0012824-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	324	455	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.871572428087986	5	FACETS	0.999	0.955	1	0.999	0.955	1	CLONAL	3	TRUE	2	0.866484546573502	5		455	574	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012824-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	418	384	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.601671454837025	6	FACETS	0.927	0.892	0.962	1	0.995	1	CLONAL	4	TRUE	3	0.866484546573502	6		384	711	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115699	8115834	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAGATTAACAGACCCCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGG	TAGATTAACAGACCCCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGG	-	novel	NA	P-0012824-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	172	404	0	ENST00000346208.3:c.1048-3_1180del		p.X350_splice	ENST00000346208		350		6/6	0.632098901564178	6	FACETS	0.95	0.879	1			1	CLONAL	2	TRUE	NA	0.866484546573502	6		404	571	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31448685	31448685	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012824-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	89	423	0	ENST00000344624.3:c.2851C>A	p.Arg951Ser	p.R951S	ENST00000344624		951	Cgc/Agc	20/33	0.871572428087986	3	FACETS	1	0.958	1	0.562	0.505	0.62	CLONAL	1	TRUE	1	0.866484546573502	3		423	262	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793431	242793431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376257658	NA	P-0014400-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	110	429	0	ENST00000334409.5:c.646G>A	p.Val216Met	p.V216M	ENST00000334409	NM_005018.2	216	Gtg/Atg	5/5	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.450738982926093	2		429	445	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696448	47696448	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014400-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	89	374	0	ENST00000347630.2:c.375T>G	p.Phe125Leu	p.F125L	ENST00000347630	NM_001007230.1	125	ttT/ttG	6/11	1	2	FACETS	0.849	0.756	0.948	0.849	0.756	0.948	CLONAL	1	TRUE	1	0.450738982926093	2		374	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0014400-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	105	507	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.332100632798439	1	FACETS	0.826	0.745	0.911	0.826	0.745	0.911	CLONAL	1	TRUE	0	0.450738982926093	1		507	437	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591825	48591825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767342	NA	P-0014400-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	78	212	0	ENST00000342988.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000342988	NM_005359.5	330	Gaa/Aaa	9/12	0.450738982926093	1	FACETS	0.775	0.686	0.869	0.775	0.686	0.869	SUBCLONAL	1	TRUE	0	0.450738982926093	1		212	346	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061012	38061033	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGCCGGCGCGCCCTCTAGCT	GGGGCCGGCGCGCCCTCTAGCT	-	novel	NA	P-0014400-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	109	430	0	ENST00000250448.2:c.956_977del	p.Gln319ProfsTer24	p.Q319Pfs*24	ENST00000250448	NM_004496.3	319	cAGCTAGAGGGCGCGCCGGCCCCc/cc	2/2	0.104130620304396	0	FACETS	0.694	0.628	0.761			1	INDETERMINATE	1	TRUE	0	0.450738982926093	0		430	383	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591140	67591141	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0014400-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	94	373	0	ENST00000274335.5:c.1735dup	p.Gln579ProfsTer23	p.Q579Pfs*23	ENST00000274335		578	gac/gaCc	12/15	0.432188002477615	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.450738982926093	1		373	314	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336612	81336612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014400-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	55	286	0	ENST00000222390.5:c.1610C>T	p.Pro537Leu	p.P537L	ENST00000222390	NM_000601.4	537	cCt/cTt	14/18	NA	2	FACETS	0.957	0.827	1			1	INDETERMINATE	1	TRUE	NA	0.450738982926093	2		286	255	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392116	118392116	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014400-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	130	420	0	ENST00000534358.1:c.11627A>G	p.Lys3876Arg	p.K3876R	ENST00000534358	NM_005933.3	3876	aAg/aGg	35/36	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.450738982926093	2		420	528	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449577	32449577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014400-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	81	386	0	ENST00000332351.3:c.797C>T	p.Pro266Leu	p.P266L	ENST00000332351	NM_024426.4	266	cCg/cTg	3/10	0.235909009349814	1	FACETS	0.763	0.677	0.854	0.763	0.677	0.854	INDETERMINATE	1	TRUE	0	0.450738982926093	1		386	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0014506-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	87	413	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.143024098017841	3	FACETS	0.802	0.714	0.897	0.535	0.476	0.598	INDETERMINATE	2	TRUE	0	0.270506348822153	3		413	455	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0014506-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	91	468	0	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	0.270506348822153	3	FACETS	0.791	0.705	0.882	0.791	0.705	0.882	SUBCLONAL	2	TRUE	1	0.270506348822153	3		468	483	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971097	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0014506-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	52	456	1	ENST00000304494.5:c.261_262delinsAA	p.Glu88Lys	p.E88K	ENST00000304494	NM_000077.4	87	cgGGag/cgAAag	2/3	0.270506348822153	1	FACETS	0.969	0.829	1	0.969	0.829	1	CLONAL	1	TRUE	0	0.270506348822153	1		457	343	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166772	32166772	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753820483	NA	P-0014506-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	37	454	0	ENST00000375023.3:c.4466G>A	p.Arg1489Gln	p.R1489Q	ENST00000375023	NM_004557.3	1489	cGa/cAa	24/30	0.270506348822153	4	FACETS	0.644	0.53	0.771	0.215	0.176	0.257	SUBCLONAL	1	TRUE	1	0.270506348822153	4		454	540	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916260	9916260	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014506-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	24	532	0	ENST00000330684.3:c.2029T>G	p.Ser677Ala	p.S677A	ENST00000330684	NM_001134407.1	677	Tcc/Gcc	10/13	0.270506348822153	4	FACETS	0.555	0.435	0.695	0.278	0.217	0.348	SUBCLONAL	1	TRUE	2	0.270506348822153	4		532	406	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449569	149449569	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014506-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	27	539	0	ENST00000286301.3:c.1377C>G	p.Ser459Arg	p.S459R	ENST00000286301	NM_005211.3	459	agC/agG	10/22	0.121676671684601	4	FACETS	0.478	0.379	0.591	0.239	0.189	0.296	INDETERMINATE	1	TRUE	2	0.270506348822153	4		539	531	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564747	139564747	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014506-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	71	396	0	ENST00000308874.7:c.536A>G	p.Lys179Arg	p.K179R	ENST00000308874		179	aAg/aGg	7/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.270506348822153	2		396	378	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636396	21636396	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014506-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	19	459	0	ENST00000421138.2:c.614A>G	p.Glu205Gly	p.E205G	ENST00000421138		205	gAg/gGg	7/16	1	2	FACETS	0.639	0.486	0.817	0.639	0.486	0.817	SUBCLONAL	1	TRUE	1	0.270506348822153	2		459	220	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631422	117631422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014506-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	18	305	0	ENST00000368508.3:c.6256C>T	p.Leu2086Phe	p.L2086F	ENST00000368508	NM_002944.2	2086	Ctt/Ttt	40/43	1	2	FACETS	0.48	0.362	0.621	0.48	0.362	0.621	SUBCLONAL	1	TRUE	1	0.270506348822153	2		305	277	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856353	45856353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014506-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	32	428	0	ENST00000391945.4:c.1819G>A	p.Gly607Arg	p.G607R	ENST00000391945	NM_000400.3	607	Gga/Aga	19/23	0.270506348822153	3	FACETS	0.588	0.477	0.714	0.294	0.238	0.357	SUBCLONAL	1	TRUE	1	0.270506348822153	3		428	457	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410683	63410683	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014506-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	26	493	0	ENST00000330258.3:c.2484C>A	p.Phe828Leu	p.F828L	ENST00000330258	NM_152424.3	828	ttC/ttA	2/2	0.270506348822153	1	FACETS	0.42	0.332	0.52	0.42	0.332	0.52	SUBCLONAL	1	TRUE	0	0.270506348822153	1		493	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0014577-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	124	369	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.256163892900612	2	FACETS	0.979	0.892	1	0.979	0.892	1	CLONAL	2	TRUE	0	0.272888966832896	2		369	464	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627730	37627730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763665826	NA	P-0014577-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	122	463	0	ENST00000447079.4:c.1645C>T	p.Pro549Ser	p.P549S	ENST00000447079	NM_015083.1	549	Ccc/Tcc	2/14	0.256163892900612	2	FACETS	0.909	0.826	0.995	0.909	0.826	0.995	CLONAL	2	TRUE	0	0.272888966832896	2		463	492	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099957	157099957	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0014577-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	110	520	0	ENST00000346085.5:c.894T>A	p.Tyr298Ter	p.Y298*	ENST00000346085	NM_020732.3	298	taT/taA	1/20	0.272888966832896	5	FACETS	0.93	0.837	1	0.62	0.558	0.685	CLONAL	2	TRUE	2	0.272888966832896	5		520	611	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923382	36923382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014577-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	132	393	1	ENST00000358127.4:c.880C>T	p.Pro294Ser	p.P294S	ENST00000358127	NM_001280556.1	294	Cca/Tca	7/10	0.218076046632206	5	FACETS	1	0.977	1	0.813	0.741	0.888	CLONAL	2	TRUE	2	0.272888966832896	5		394	559	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650080	93650080	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014577-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	134	398	1	ENST00000375746.1:c.1631T>C	p.Ile544Thr	p.I544T	ENST00000375746	NM_001174167.1	544	aTc/aCc	12/14	0.218076046632206	5	FACETS	1	0.92	1	0.675	0.614	0.738	CLONAL	2	TRUE	2	0.272888966832896	5		399	684	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1795762	1795762	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014577-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	56	558	0	ENST00000260795.2:c.101G>C	p.Arg34Pro	p.R34P	ENST00000260795		34	cGa/cCa	1/17	0.209600506904179	2	FACETS	0.839	0.72	0.969	0.42	0.36	0.485	CLONAL	1	TRUE	0	0.272888966832896	2		558	489	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43769919	43769919	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014577-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	75	422	0	ENST00000382044.4:c.827C>G	p.Ala276Gly	p.A276G	ENST00000382044	NM_001141980.1	276	gCt/gGt	8/28	0.209600506904179	2	FACETS	1	0.912	1	0.523	0.459	0.592	CLONAL	1	TRUE	0	0.272888966832896	2		422	525	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589564	67589571	+	protein_altering_variant	In_Frame_Del	DEL	GAAGCTGT	GAAGCTGT	AA	novel	NA	P-0014577-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	49	291	1	ENST00000274335.5:c.1327_1334delinsAA	p.Glu443_Val445delinsLys	p.E443_V445delinsK	ENST00000274335		443	GAAGCTGTa/AAa	10/15	0.256163892900612	2	FACETS	1	0.918	1	0.561	0.477	0.652	CLONAL	1	TRUE	0	0.272888966832896	2		292	320	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183755	10183757	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs5030648	NA	P-0014618-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	18	414	0	ENST00000256474.2:c.227_229del	p.Phe76del	p.F76del	ENST00000256474	NM_000551.3	75	aTCTtc/atc	1/3	1	2	FACETS	0.824	0.62	1	0.824	0.62	1	CLONAL	1	TRUE	1	0.13	2		414	336	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37061937	37061941	+	frameshift_variant	Frame_Shift_Del	DEL	AGGAT	AGGAT	-	novel	NA	P-0014618-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	26	421	0	ENST00000231790.2:c.1021_1025del	p.Arg341ValfsTer19	p.R341Vfs*19	ENST00000231790	NM_000249.3	341	AGGATg/g	11/19	1	2	FACETS	0.952	0.754	1	0.952	0.754	1	CLONAL	1	TRUE	1	0.13	2		421	420	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2111998	2111998	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs45517157	NA	P-0014812-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	157	427	0	ENST00000219476.3:c.1246G>T	p.Asp416Tyr	p.D416Y	ENST00000219476	NM_000548.3	416	Gac/Tac	12/42	1	2	FACETS	0.862	0.795	0.931	1	0.993	1	CLONAL	3	TRUE	1	0.23	2		427	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0015111-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	204	638	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.584660920248856	2	FACETS	0.975	0.921	1	0.975	0.921	1	CLONAL	2	TRUE	0	0.584660920248856	2		638	358	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0015111-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	126	390	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.584660920248856	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.584660920248856	3		392	248	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569823	67569823	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1230037871	NA	P-0015111-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	64	330	0	ENST00000274335.5:c.484C>T	p.Arg162Ter	p.R162*	ENST00000274335		162	Cga/Tga	3/15	0.584660920248856	4	FACETS	0.807	0.701	0.921	0.269	0.233	0.307	CLONAL	1	TRUE	1	0.584660920248856	4		330	430	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589556	67589585	+	inframe_deletion	In_Frame_Del	DEL	ATAATATTGAAGCTGTAGGGAAAAAATTAC	ATAATATTGAAGCTGTAGGGAAAAAATTAC	-	novel	NA	P-0015111-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	81	238	0	ENST00000274335.5:c.1321_1350del	p.Asn441_His450del	p.N441_H450del	ENST00000274335		440	gATAATATTGAAGCTGTAGGGAAAAAATTACat/gat	10/15	0.584660920248856	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	1	0.584660920248856	4		238	127	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872936	35872936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184836139	NA	P-0015111-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	110	396	0	ENST00000216797.5:c.296G>A	p.Gly99Glu	p.G99E	ENST00000216797	NM_020529.2	99	gGa/gAa	2/6	0.567047271345665	4	FACETS	0.681	0.612	0.756	0.341	0.306	0.378	SUBCLONAL	1	TRUE	2	0.584660920248856	4		396	875	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911627	134911627	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015111-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	103	420	0	ENST00000398015.3:c.2092G>C	p.Glu698Gln	p.E698Q	ENST00000398015	NM_004441.4	698	Gag/Cag	11/16	0.584660920248856	7	FACETS	0.984	0.88	1	0.197	0.176	0.22	CLONAL	1	TRUE	2	0.584660920248856	7		420	881	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215271	142215271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015111-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	75	365	0	ENST00000350721.4:c.5830C>T	p.Leu1944Phe	p.L1944F	ENST00000350721	NM_001184.3	1944	Ctc/Ttc	34/47	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.584660920248856	NA		365	660	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199663	138199663	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015111-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	105	483	0	ENST00000237289.4:c.1081G>T	p.Glu361Ter	p.E361*	ENST00000237289	NM_001270507.1	361	Gag/Tag	7/9	0.584660920248856	5	FACETS	0.931	0.835	1	0.31	0.278	0.345	CLONAL	1	TRUE	2	0.584660920248856	5		483	724	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250656	26250656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015111-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	226	555	0	ENST00000446824.2:c.178G>A	p.Glu60Lys	p.E60K	ENST00000446824	NM_021018.2	60	Gag/Aag	1/1	0.584660920248856	5	FACETS	0.831	0.775	0.888	0.554	0.517	0.592	CLONAL	2	TRUE	2	0.584660920248856	5		555	873	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99192868	99192868	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs775802966	NA	P-0015111-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	69	288	0	ENST00000268035.6:c.58T>C	p.Ser20Pro	p.S20P	ENST00000268035	NM_000875.3	20	Tcc/Ccc	1/21	0.584660920248856	4	FACETS	0.689	0.601	0.784	0.23	0.2	0.262	SUBCLONAL	1	TRUE	1	0.584660920248856	4		288	543	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544795	86544795	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015111-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	94	424	0	ENST00000262426.4:c.620C>G	p.Ala207Gly	p.A207G	ENST00000262426	NM_001451.2	207	gCc/gGc	1/2	0.584660920248856	3	FACETS	0.93	0.832	1	0.465	0.416	0.517	CLONAL	1	TRUE	1	0.584660920248856	3		424	447	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942105	71942105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015111-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	116	492	0	ENST00000298229.2:c.1369G>A	p.Glu457Lys	p.E457K	ENST00000298229	NM_001567.3	457	Gag/Aag	12/28	0.577092489900723	5	FACETS	0.955	0.861	1	0.318	0.287	0.352	CLONAL	1	TRUE	2	0.584660920248856	5		492	780	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553550	106553550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015111-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	39	469	0	ENST00000369096.4:c.1515G>T	p.Met505Ile	p.M505I	ENST00000369096	NM_001198.3	505	atG/atT	5/7	0.537282388417596	5	FACETS	0.337	0.278	0.403	0.112	0.092	0.135	SUBCLONAL	1	TRUE	2	0.584660920248856	5		469	743	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422943	49422943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015111-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	111	521	0	ENST00000301067.7:c.14152G>A	p.Glu4718Lys	p.E4718K	ENST00000301067	NM_003482.3	4718	Gag/Aag	44/54	0.567047271345665	4	FACETS	0.862	0.776	0.953	0.431	0.388	0.477	CLONAL	1	TRUE	2	0.584660920248856	4		521	698	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257774	133257774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs115452881	NA	P-0015535-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	53	480	0	ENST00000320574.5:c.154C>T	p.Arg52Trp	p.R52W	ENST00000320574	NM_006231.2	52	Cgg/Tgg	2/49	1	2	FACETS	0.204	0.174	0.238	0.204	0.174	0.238	SUBCLONAL	1	TRUE	1	0.869938639967876	2		480	596	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533881	533881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs727503093	NA	P-0015535-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	58	590	0	ENST00000451590.1:c.175G>A	p.Ala59Thr	p.A59T	ENST00000451590	NM_001130442.1	59	Gcc/Acc	3/5	1	2	FACETS	0.191	0.164	0.221	0.191	0.164	0.221	SUBCLONAL	1	TRUE	1	0.869938639967876	2		590	698	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249934	39249945	+	inframe_deletion	In_Frame_Del	DEL	CTGTAAAGATAT	CTGTAAAGATAT	-	novel	NA	P-0015535-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	44	484	0	ENST00000402219.2:c.1624_1635del	p.Ile542_Gln545del	p.I542_Q545del	ENST00000402219	NM_005633.3	542	ATATCTTTACAG/-	10/23	1	2	FACETS	0.159	0.133	0.188	0.159	0.133	0.188	SUBCLONAL	1	TRUE	1	0.869938639967876	2		484	636	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0015535-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	56	171	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.951	0.822	1	0.951	0.822	1	CLONAL	1	TRUE	1	0.420523687299735	2		171	280	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845618	68845618	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015535-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	112	437	0	ENST00000261769.5:c.864del	p.Asp288GlufsTer6	p.D288Efs*6	ENST00000261769	NM_004360.3	288	gaC/ga	7/16	0.413307342918628	1	FACETS	0.969	0.878	1	0.969	0.878	1	CLONAL	1	TRUE	0	0.420523687299735	1		437	434	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995270	15995270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015535-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	105	476	0	ENST00000268712.3:c.2923G>A	p.Glu975Lys	p.E975K	ENST00000268712	NM_006311.3	975	Gag/Aag	22/46	1	2	FACETS	0.884	0.794	0.978	0.884	0.794	0.978	CLONAL	1	TRUE	1	0.420523687299735	2		476	565	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0015535-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	113	482	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	0.931	0.841	1	0.931	0.841	1	CLONAL	1	TRUE	1	0.420523687299735	2		482	577	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573663	48573663	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015535-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	76	462	0	ENST00000342988.3:c.247C>T	p.Gln83Ter	p.Q83*	ENST00000342988	NM_005359.5	83	Cag/Tag	2/12	0.420523687299735	1	FACETS	0.78	0.689	0.877	0.78	0.689	0.877	SUBCLONAL	1	TRUE	0	0.420523687299735	1		462	366	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095620	178095620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015535-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	130	557	0	ENST00000397062.3:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000397062	NM_006164.4	571	Gaa/Aaa	5/5	1	2	FACETS	0.942	0.857	1	0.942	0.857	1	CLONAL	1	TRUE	1	0.420523687299735	2		557	656	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265310	16265310	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015535-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	98	501	0	ENST00000375759.3:c.10802C>G	p.Thr3601Ser	p.T3601S	ENST00000375759	NM_015001.2	3601	aCt/aGt	14/15	0.307193664545364	1	FACETS	0.858	0.77	0.95	0.858	0.77	0.95	CLONAL	1	TRUE	0	0.420523687299735	1		501	429	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170545	108170545	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015535-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	112	433	1	ENST00000278616.4:c.5110G>T	p.Glu1704Ter	p.E1704*	ENST00000278616	NM_000051.3	1704	Gaa/Taa	34/63	0.413307342918628	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.420523687299735	1		434	382	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118355620	118355620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015535-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	28	405	0	ENST00000534358.1:c.4262G>A	p.Gly1421Glu	p.G1421E	ENST00000534358	NM_005933.3	1421	gGa/gAa	10/36	0.413307342918628	1	FACETS	0.264	0.21	0.324	0.264	0.21	0.324	SUBCLONAL	1	TRUE	0	0.420523687299735	1		405	399	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21643307	21643307	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015535-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	57	326	0	ENST00000421138.2:c.220C>G	p.Pro74Ala	p.P74A	ENST00000421138		74	Cca/Gca	5/16	1	2	FACETS	0.777	0.67	0.892	0.777	0.67	0.892	SUBCLONAL	1	TRUE	1	0.420523687299735	2		326	349	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272344	21272344	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015535-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	94	513	0	ENST00000354336.3:c.122C>G	p.Ser41Cys	p.S41C	ENST00000354336	NM_005207.3	41	tCt/tGt	1/3	0.378314682732219	1	FACETS	0.731	0.653	0.813	0.731	0.653	0.813	SUBCLONAL	1	TRUE	0	0.420523687299735	1		513	483	SUCCESS
APC	324	MSKCC	GRCh37	5	112177862	112177862	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015535-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	94	492	0	ENST00000257430.4:c.6572del	p.Gly2191GlufsTer8	p.G2191Efs*8	ENST00000257430	NM_000038.5	2191	Gga/ga	16/16	1	2	FACETS	0.836	0.746	0.931	0.836	0.746	0.931	CLONAL	1	TRUE	1	0.420523687299735	2		492	535	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805599	89805599	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021299-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	175	508	0	ENST00000389301.3:c.4109C>A	p.Ala1370Asp	p.A1370D	ENST00000389301	NM_000135.2	1370	gCt/gAt	41/43	1	2	FACETS	0.919	0.857	0.982	1	0.995	1	CLONAL	4	TRUE	1	0.229421861628313	2		508	415	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099403	157099426	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAGCAA	CAGCAGCAGCAGCAGCAGCAGCAA	-	rs770869529	NA	P-0021299-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	85	650	0	ENST00000346085.5:c.369_392del	p.Gln124_Gln131del	p.Q124_Q131del	ENST00000346085	NM_020732.3	114	CAGCAGCAGCAGCAGCAGCAGCAA/-	1/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.229421861628313	2		650	549	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845959	151845959	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021299-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	151	562	0	ENST00000262189.6:c.13053del	p.Lys4351AsnfsTer5	p.K4351Nfs*5	ENST00000262189	NM_170606.2	4351	aaA/aa	52/59	1	2	FACETS	1	0.963	1	1	0.994	1	CLONAL	3	TRUE	1	0.229421861628313	2		562	410	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856070	151856070	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021299-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	197	448	0	ENST00000262189.6:c.11548C>T	p.Arg3850Ter	p.R3850*	ENST00000262189	NM_170606.2	3850	Cga/Tga	44/59	1	2	FACETS	1	0.945	1	1	0.995	1	CLONAL	4	TRUE	1	0.229421861628313	2		448	426	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0026316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	121	583	1	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.6162088309241	1	FACETS	0.888	0.814	0.963	0.888	0.814	0.963	CLONAL	1	TRUE	0	0.6162088309241	1		584	306	SUCCESS
AR	367	MSKCC	GRCh37	X	66943552	66943552	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137852578	NA	P-0026316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	220	238	0	ENST00000374690.3:c.2632A>G	p.Thr878Ala	p.T878A	ENST00000374690	NM_000044.3	878	Act/Gct	8/8	0.6162088309241	2	FACETS	0.85	0.817	0.881			1	CLONAL	3	TRUE	NA	0.6162088309241	2		238	280	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0026316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	121	517	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.6162088309241	2		517	381	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435069	49435073	+	frameshift_variant	Frame_Shift_Del	DEL	TGAGG	TGAGG	-	novel	NA	P-0026316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	238	461	0	ENST00000301067.7:c.6480_6484del	p.Phe2160LeufsTer40	p.F2160Lfs*40	ENST00000301067	NM_003482.3	2160	ttCCTCAag/ttag	31/54	0.600446113698839	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.6162088309241	3		461	476	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830100	72830101	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0026316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	100	538	0	ENST00000268489.5:c.6480dup	p.Arg2161AlafsTer5	p.R2161Afs*5	ENST00000268489	NM_006885.3	2160	-/G	9/10	1	2	FACETS	0.889	0.801	0.981	0.889	0.801	0.981	CLONAL	1	TRUE	1	0.6162088309241	2		538	365	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132522	11132522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778175819	NA	P-0026316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	117	612	0	ENST00000358026.2:c.2738C>T	p.Pro913Leu	p.P913L	ENST00000358026	NM_001128849.1	913	cCg/cTg	19/36	1	2	FACETS	0.883	0.802	0.967	0.883	0.802	0.967	CLONAL	1	TRUE	1	0.6162088309241	2		612	430	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124499118	124499118	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	123	374	1	ENST00000357628.3:c.595C>A	p.Gln199Lys	p.Q199K	ENST00000357628	NM_015450.2	199	Caa/Aaa	9/19	0.600446113698839	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.6162088309241	3		375	237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0027119-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	95	469	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.415163991771155	2		469	411	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0027119-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	157	439	0				ENST00000310581	NM_198253.2	-/1132			0.415163991771155	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.415163991771155	3		439	371	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0028030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	79	496	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	1	2	FACETS	0.621	0.545	0.703	0.621	0.545	0.703	SUBCLONAL	1	TRUE	1	0.283405597732709	2		496	898	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0028030-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	156	496	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	0.357728425777783	3	FACETS	0.979	0.896	1	0.49	0.448	0.534	CLONAL	1	TRUE	1	0.357728425777783	3		496	1050	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941640	48941640	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028030-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	79	286	0	ENST00000267163.4:c.950T>G	p.Leu317Arg	p.L317R	ENST00000267163	NM_000321.2	317	cTt/cGt	10/27	0.357728425777783	1	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	0	0.357728425777783	1		286	360	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492725	56492725	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028030-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	133	475	0	ENST00000407977.2:c.214G>T	p.Val72Phe	p.V72F	ENST00000407977		72	Gtt/Ttt	2/10	0.351093255904982	4	FACETS	0.89	0.807	0.979	0.297	0.269	0.327	CLONAL	1	TRUE	1	0.357728425777783	4		475	1134	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978779	13978787	+	frameshift_variant	Frame_Shift_Del	DEL	TAAAGGGCT	TAAAGGGCT	C	novel	NA	P-0028030-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	148	375	0	ENST00000405192.2:c.320_328delinsG	p.Gln107ArgfsTer16	p.Q107Rfs*16	ENST00000405192	NM_001163147.1	107	cAGCCCTTTAaa/cGaa	6/12	0.357728425777783	3	FACETS	1	0.974	1	0.586	0.535	0.639	CLONAL	1	TRUE	1	0.357728425777783	3		375	833	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472553	88472553	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs761075951	NA	P-0028083-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	52	286	0	ENST00000360948.2:c.2002G>T	p.Val668Leu	p.V668L	ENST00000360948	NM_001012338.2	668	Gtg/Ttg	16/19	1	2	FACETS	0.631	0.538	0.734	0.631	0.538	0.734	SUBCLONAL	1	TRUE	1	0.324240868881797	2		286	508	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481403	140481403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913357	NA	P-0028083-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	56	228	0	ENST00000288602.6:c.1405G>A	p.Gly469Arg	p.G469R	ENST00000288602	NM_004333.4	469	Gga/Aga	11/18	1	2	FACETS	0.954	0.821	1	0.954	0.821	1	CLONAL	1	TRUE	1	0.324240868881797	2		228	362	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58700932	58700932	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028083-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	85	275	0	ENST00000305921.3:c.523G>T	p.Ala175Ser	p.A175S	ENST00000305921	NM_003620.3	175	Gcc/Tcc	2/6	0.324240868881797	3	FACETS	0.997	0.883	1	0.499	0.441	0.56	CLONAL	1	TRUE	1	0.324240868881797	3		275	611	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115888	8115889	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0030342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	40	466	0	ENST00000346208.3:c.1236dup	p.Ser413GlnfsTer94	p.S413Qfs*94	ENST00000346208		412	tcc/tCcc	6/6	0.0827348986212105	0	FACETS	0.614	0.509	0.733			1	INDETERMINATE	1	TRUE	0	0.14	0		466	800	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023895	27023895	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	42	490	0	ENST00000324856.7:c.1001C>A	p.Ser334Ter	p.S334*	ENST00000324856	NM_006015.4	334	tCg/tAg	1/20	1	2	FACETS	0.803	0.669	0.953	0.803	0.669	0.953	CLONAL	1	TRUE	1	0.14	2		490	747	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577068	7577071	+	frameshift_variant	Frame_Shift_Del	DEL	GCGG	GCGG	-	novel	NA	P-0030342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	34	479	0	ENST00000269305.4:c.867_870del	p.Lys292GlyfsTer52	p.K292Gfs*52	ENST00000269305	NM_001126112.2	289	ctCCGC/ct	8/11	1	2	FACETS	0.66	0.537	0.799	0.66	0.537	0.799	SUBCLONAL	1	TRUE	1	0.14	2		479	736	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230468752	230468752	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	33	473	0	ENST00000391860.1:c.766A>T	p.Ser256Cys	p.S256C	ENST00000391860	NM_001258311.1	256	Agt/Tgt	5/7	1	2	FACETS	0.788	0.641	0.956	0.788	0.641	0.956	CLONAL	1	TRUE	1	0.14	2		473	598	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809338	243809338	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	31	319	0	ENST00000263826.5:c.286G>A	p.Glu96Lys	p.E96K	ENST00000263826	NM_005465.4	96	Gaa/Aaa	4/13	1	2	FACETS	0.769	0.62	0.938	0.769	0.62	0.938	CLONAL	1	TRUE	1	0.14	2		319	576	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674306	117674306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243900066	NA	P-0030342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	26	310	0	ENST00000368508.3:c.4168G>A	p.Val1390Met	p.V1390M	ENST00000368508	NM_002944.2	1390	Gtg/Atg	26/43	0.3	1	FACETS	0.68	0.537	0.844	0.68	0.537	0.844	SUBCLONAL	1	TRUE	0	0.14	1		310	508	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839443	27839751	+	coding_sequence_variant,3_prime_UTR_variant	In_Frame_Del	DEL	GTGATAATCCTTATCAGTAGGAACAGGTTCTGTATGTGAAATTGATTTAGCATACCAACAGCCTGTGACCTGACTCCTGCATTATAGTGTGTTGGGCCACTACCACGTTTTGTCCACAGCTTGTATTTAACATGGAGCTAAGACACGTCTCAAAAGCTACAGCTTCCTTTTGGTGACAATTGAGGGGCTCTGAAAAGAGCCTTTTGGGGTTGGACAGACTTCTTGGGCTGATAGGAATATTTATGCCCTCTCCCCTCGGATGCGGCGCGCAAGCTGGATGTCTTTAGGCATAATAGTGACGCGTTTGGC	GTGATAATCCTTATCAGTAGGAACAGGTTCTGTATGTGAAATTGATTTAGCATACCAACAGCCTGTGACCTGACTCCTGCATTATAGTGTGTTGGGCCACTACCACGTTTTGTCCACAGCTTGTATTTAACATGGAGCTAAGACACGTCTCAAAAGCTACAGCTTCCTTTTGGTGACAATTGAGGGGCTCTGAAAAGAGCCTTTTGGGGTTGGACAGACTTCTTGGGCTGATAGGAATATTTATGCCCTCTCCCCTCGGATGCGGCGCGCAAGCTGGATGTCTTTAGGCATAATAGTGACGCGTTTGGC	-	novel	NA	P-0030342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	25	25	0				ENST00000328488	NM_003533.2	115		1/1	1	2	FACETS	0.35	0.274	0.438	0.35	0.274	0.438	SUBCLONAL	1	TRUE	1	0.14	2		25	1021	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0031299-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	209	405	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.399792393253292	6	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	FALSE	3	0.399792393253292	6		405	586	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0031299-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	71	455	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.29635852967721	4	FACETS	1	0.968	1	0.334	0.293	0.378	CLONAL	1	FALSE	0	0.399792393253292	4		455	372	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241678	55241678	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517085	NA	P-0031299-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	235	563	0	ENST00000275493.2:c.2126A>C	p.Glu709Ala	p.E709A	ENST00000275493	NM_005228.3	709	gAa/gCa	18/28	0.399792393253292	6	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	FALSE	3	0.399792393253292	6		563	647	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519975	NA	P-0031299-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	216	637	0	ENST00000269305.4:c.403T>A	p.Cys135Ser	p.C135S	ENST00000269305	NM_001126112.2	135	Tgc/Agc	5/11	0.360494578356272	3	FACETS	0.893	0.839	0.947	0.893	0.839	0.947	CLONAL	3	FALSE	0	0.399792393253292	3		637	484	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026891	6026891	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031299-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	15	192	0	ENST00000265849.7:c.1505A>G	p.Asp502Gly	p.D502G	ENST00000265849	NM_000535.5	502	gAt/gGt	11/15	0.399792393253292	6	FACETS	0.475	0.347	0.63	0.158	0.115	0.21	SUBCLONAL	1	FALSE	3	0.399792393253292	6		192	284	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729968	30729968	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs863223852	NA	P-0031299-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	51	475	0	ENST00000295754.5:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000295754	NM_003242.5	497	Cga/Tga	6/7	0.317014096443198	2	FACETS	0.69	0.588	0.8	0.345	0.294	0.4	SUBCLONAL	1	FALSE	0	0.399792393253292	2		475	370	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575209	48575209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767326	NA	P-0033093-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	407	286	0	ENST00000342988.3:c.403C>T	p.Arg135Ter	p.R135*	ENST00000342988	NM_005359.5	135	Cga/Tga	3/12	0.943848296315771	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.943848296315771	3		286	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0033093-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	613	529	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.943848296315771	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.943848296315771	2		529	627	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0033093-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	51	424	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.260863649713226	3	FACETS	0.75	0.646	0.862	0.375	0.323	0.431	INDETERMINATE	1	TRUE	1	0.943848296315771	3		424	212	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0033093-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	168	410	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.764879594163637	1	FACETS	0.694	0.654	0.733	0.694	0.654	0.733	SUBCLONAL	1	TRUE	0	0.943848296315771	1		410	271	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371734	55371734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033093-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	55	533	0	ENST00000297316.4:c.424C>T	p.Arg142Cys	p.R142C	ENST00000297316	NM_022454.3	142	Cgc/Tgc	2/2	0.943848296315771	1	FACETS	0.18	0.154	0.208	0.18	0.154	0.208	SUBCLONAL	1	TRUE	0	0.943848296315771	1		533	342	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942662	48942662	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0033093-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	286	239	0	ENST00000267163.4:c.1050-1G>T		p.X350_splice	ENST00000267163	NM_000321.2	350			0.943848296315771	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.943848296315771	3		239	296	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236684	236684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033093-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	147	249	0	ENST00000264932.6:c.1402G>A	p.Ala468Thr	p.A468T	ENST00000264932	NM_004168.2	468	Gcc/Acc	10/15	0.901469748465408	4	FACETS	1	0.963	1	0.362	0.332	0.394	CLONAL	1	TRUE	1	0.943848296315771	4		249	557	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230493055	230493055	+	5_prime_UTR_variant	5'UTR	SNP	T	T	A	novel	NA	P-0033093-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	161	546	0	ENST00000391860.1:c.-2A>T		p.*1*	ENST00000391860	NM_001258311.1	46/455		2/7	0.943848296315771	1	FACETS	0.548	0.511	0.584	0.548	0.511	0.584	SUBCLONAL	1	TRUE	0	0.943848296315771	1		546	329	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034906-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	48	317	0				ENST00000310581	NM_198253.2	-/1132			0.22898582166165	7	FACETS	1	0.896	1	0.18	0.152	0.211	CLONAL	1	TRUE	1	0.22898582166165	7		317	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0034906-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	72	372	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.174715187127391	1	FACETS	0.866	0.757	0.984	0.866	0.757	0.984	CLONAL	1	TRUE	0	0.22898582166165	1		372	643	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013691	12013691	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0034906-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	44	142	0	ENST00000353533.5:c.634-1G>C		p.X212_splice	ENST00000353533	NM_003010.3	212			0.174715187127391	1	FACETS	0.917	0.771	1	0.917	0.771	1	CLONAL	1	TRUE	0	0.22898582166165	1		142	371	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785992	135785992	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0034906-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	64	291	0	ENST00000298552.3:c.1229C>G	p.Ser410Ter	p.S410*	ENST00000298552	NM_001162426.1	410	tCa/tGa	12/23	0.225763331048027	1	FACETS	0.95	0.824	1	0.95	0.824	1	CLONAL	1	TRUE	0	0.22898582166165	1		291	521	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606412	93606412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773659676	NA	P-0034906-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	58	344	0	ENST00000375746.1:c.232G>A	p.Gly78Ser	p.G78S	ENST00000375746	NM_001174167.1	78	Ggt/Agt	2/14	0.225763331048027	1	FACETS	0.969	0.834	1	0.969	0.834	1	CLONAL	1	TRUE	0	0.22898582166165	1		344	463	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983140	201983141	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034906-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	62	286	0	ENST00000359651.3:c.991dup	p.Arg331ProfsTer140	p.R331Pfs*140	ENST00000359651		330	agc/agCc	7/8	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.22898582166165	2		286	518	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264275	30264275	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034906-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	30	133	0	ENST00000322652.5:c.10C>G	p.Gln4Glu	p.Q4E	ENST00000322652	NM_015355.2	4	Cag/Gag	1/16	0.22898582166165	3	FACETS	1	0.822	1	0.509	0.411	0.619	CLONAL	1	TRUE	1	0.22898582166165	3		133	287	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288499	15288499	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393495970	NA	P-0034906-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	45	269	0	ENST00000263388.2:c.4240G>A	p.Gly1414Ser	p.G1414S	ENST00000263388	NM_000435.2	1414	Ggc/Agc	24/33	1	2	FACETS	0.864	0.727	1	0.864	0.727	1	CLONAL	1	TRUE	1	0.22898582166165	2		269	455	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983111	201983111	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034906-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	53	313	0	ENST00000359651.3:c.960del	p.Asn321ThrfsTer4	p.N321Tfs*4	ENST00000359651		320	aaG/aa	7/8	1	2	FACETS	0.845	0.72	0.981	0.845	0.72	0.981	CLONAL	1	TRUE	1	0.22898582166165	2		313	548	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366206	15366206	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034906-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	62	318	0	ENST00000263377.2:c.1949A>G	p.Asp650Gly	p.D650G	ENST00000263377	NM_058243.2	650	gAc/gGc	10/20	1	2	FACETS	0.952	0.822	1	0.952	0.822	1	CLONAL	1	TRUE	1	0.22898582166165	2		318	569	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798190	32798190	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034906-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	54	353	0	ENST00000374899.4:c.1489G>T	p.Glu497Ter	p.E497*	ENST00000374899	NM_018833.2	497	Gag/Tag	9/12	0.225763331048027	1	FACETS	0.883	0.755	1	0.883	0.755	1	CLONAL	1	TRUE	0	0.22898582166165	1		353	473	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137540382	137540382	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	rs1468647789	NA	P-0034906-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	97	316	0	ENST00000367739.4:c.83C>G	p.Ser28Ter	p.S28*	ENST00000367739	NM_000416.2	28	tCa/tGa	1/7	0.22898582166165	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.22898582166165	1		316	560	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170531	11170531	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034906-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	72	388	0	ENST00000358026.2:c.4834G>C	p.Glu1612Gln	p.E1612Q	ENST00000358026	NM_001128849.1	1612	Gag/Cag	34/36	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.22898582166165	2		388	622	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1296366	1296366	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0034906-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	37	208	0				ENST00000310581	NM_198253.2	-/1132			0.22898582166165	7	FACETS	0.742	0.61	0.89	0.124	0.101	0.149	SUBCLONAL	1	TRUE	1	0.22898582166165	7		208	685	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057811	27057811	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034990-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	166	768	0	ENST00000324856.7:c.1519C>T	p.Gln507Ter	p.Q507*	ENST00000324856	NM_006015.4	507	Caa/Taa	3/20	0.633628943737742	1	FACETS	0.911	0.848	0.975	0.911	0.848	0.975	CLONAL	1	TRUE	0	0.633628943737742	1		768	393	SUCCESS
RET	5979	MSKCC	GRCh37	10	43614996	43614996	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs79658334	NA	P-0034990-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	120	585	0	ENST00000355710.3:c.2410G>A	p.Val804Met	p.V804M	ENST00000355710	NM_020975.4	804	Gtg/Atg	14/20	1	2	FACETS	0.933	0.85	1	0.933	0.85	1	CLONAL	1	TRUE	1	0.633628943737742	2		585	406	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971732	18971732	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034990-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	108	546	0	ENST00000262803.5:c.2398C>T	p.Arg800Cys	p.R800C	ENST00000262803	NM_002911.3	800	Cgc/Tgc	17/24	1	2	FACETS	0.911	0.826	1	0.911	0.826	1	CLONAL	1	TRUE	1	0.633628943737742	2		546	374	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615002	43615002	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034990-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	119	595	0	ENST00000355710.3:c.2416T>C	p.Tyr806His	p.Y806H	ENST00000355710	NM_020975.4	806	Tac/Cac	14/20	1	2	FACETS	0.914	0.832	0.999	0.914	0.832	0.999	CLONAL	1	TRUE	1	0.633628943737742	2		595	411	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400176	139400176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238653760	NA	P-0121496-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	176	667	0	ENST00000277541.6:c.4172G>A	p.Cys1391Tyr	p.C1391Y	ENST00000277541	NM_017617.3	1391	tGc/tAc	25/34	0.80664735147208	2	FACETS	0.974	0.907	1	0.487	0.453	0.521	CLONAL	1	NA	0	0.817902998858392	2		667	442	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001498	150001498	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0121496-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	105	471	0	ENST00000253339.5:c.2106G>C	p.Lys702Asn	p.K702N	ENST00000253339		702	aaG/aaC	4/7	0.817902998858392	1	FACETS	0.733	0.674	0.793	0.733	0.674	0.793	SUBCLONAL	1	NA	0	0.817902998858392	1		471	207	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443696	29443696	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0121496-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	20	515	0	ENST00000389048.3:c.3521T>C	p.Phe1174Ser	p.F1174S	ENST00000389048	NM_004304.4	1174	tTc/tCc	23/29	0.817902998858392	4	FACETS	0.147	0.112	0.189	0.049	0.037	0.063	SUBCLONAL	1	NA	1	0.817902998858392	4		515	604	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425547	49425548	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0121496-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	176	660	0	ENST00000301067.7:c.12940_12941del	p.Pro4314SerfsTer19	p.P4314Sfs*19	ENST00000301067	NM_003482.3	4314	CCt/t	39/54	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	NA	1	0.817902998858392	2		660	427	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324014	123324014	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0121496-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	19	420	0	ENST00000358487.5:c.454+2T>C		p.X152_splice	ENST00000358487	NM_000141.4	152			1	2	FACETS	0.14	0.106	0.181	0.14	0.106	0.181	SUBCLONAL	1	NA	1	0.817902998858392	2		420	331	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729695	162729695	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035844-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	46	302	0	ENST00000367921.3:c.781A>G	p.Asn261Asp	p.N261D	ENST00000367921	NM_006182.2	261	Aac/Gac	8/18	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.337242601677099	2		302	264	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625224	69625225	+	missense_variant	Missense_Mutation	DNP	AT	AT	GC	novel	NA	P-0035844-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	28	279	0	ENST00000334134.2:c.568_569delinsGC	p.Met190Ala	p.M190A	ENST00000334134	NM_005247.2	190	ATg/GCg	3/3	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.337242601677099	2		279	144	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098369	108098369	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035844-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	28	237	0	ENST00000278616.4:c.18T>A	p.Asn6Lys	p.N6K	ENST00000278616	NM_000051.3	6	aaT/aaA	2/63	1	2	FACETS	0.791	0.636	0.964	0.791	0.636	0.964	CLONAL	1	TRUE	1	0.337242601677099	2		237	210	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0036885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	209	333	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.726038836941027	2		333	528	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565575	41565575	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	293	366	0	ENST00000263253.7:c.4241A>G	p.Tyr1414Cys	p.Y1414C	ENST00000263253	NM_001429.3	1414	tAt/tGt	26/31	0.598296020891637	3	FACETS	0.958	0.912	1	0.958	0.912	1	CLONAL	2	TRUE	1	0.726038836941027	3		366	574	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100324	157100324	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	107	270	0	ENST00000346085.5:c.1261C>T	p.Gln421Ter	p.Q421*	ENST00000346085	NM_020732.3	421	Cag/Tag	1/20	1	2	FACETS	0.93	0.845	1	0.93	0.845	1	CLONAL	1	TRUE	1	0.726038836941027	2		270	317	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572974	7572974	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	170	403	0	ENST00000269305.4:c.1135del	p.Arg379AlafsTer43	p.R379Afs*43	ENST00000269305	NM_001126112.2	379	Cgc/gc	11/11	0.665480387469458	1	FACETS	0.929	0.871	0.987	0.929	0.871	0.987	CLONAL	1	TRUE	0	0.726038836941027	1		403	321	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555341	106555341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1382807606	NA	P-0036885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	157	333	0	ENST00000369096.4:c.2458G>A	p.Val820Ile	p.V820I	ENST00000369096	NM_001198.3	820	Gtt/Att	7/7	1	2	FACETS	0.936	0.865	1	0.936	0.865	1	CLONAL	1	TRUE	1	0.726038836941027	2		333	462	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425631	49425631	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	155	471	0	ENST00000301067.7:c.12857del	p.Pro4286HisfsTer98	p.P4286Hfs*98	ENST00000301067	NM_003482.3	4286	cCa/ca	39/54	1	2	FACETS	0.91	0.84	0.982	0.91	0.84	0.982	CLONAL	1	TRUE	1	0.726038836941027	2		471	469	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33680154	33680154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs776928711	NA	P-0036885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	159	359	1	ENST00000308377.4:c.1927A>G	p.Arg643Gly	p.R643G	ENST00000308377	NM_152270.3	643	Aga/Gga	5/5	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.726038836941027	2		360	408	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442591	52442606	+	frameshift_variant	Frame_Shift_Del	DEL	ATTTGAACAGGAAGAT	ATTTGAACAGGAAGAT	-	novel	NA	P-0036885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	217	505	0	ENST00000460680.1:c.139_154del	p.Ile47GlyfsTer20	p.I47Gfs*20	ENST00000460680	NM_004656.3	47	ATCTTCCTGTTCAAATgg/gg	4/17	0.726038836941027	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.726038836941027	1		505	368	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47599146	47599146	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1345707150	NA	P-0036885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	182	450	0	ENST00000430070.2:c.454C>T	p.Arg152Trp	p.R152W	ENST00000430070	NM_018095.4	152	Cgg/Tgg	2/4	1	2	FACETS	0.995	0.926	1	0.995	0.926	1	CLONAL	1	TRUE	1	0.726038836941027	2		450	504	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652236	48652236	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	159	371	0	ENST00000376670.3:c.907C>A	p.Gln303Lys	p.Q303K	ENST00000376670	NM_002049.3	303	Cag/Aag	6/6	1	2	FACETS	0.912	0.843	0.984	0.912	0.843	0.984	CLONAL	1	TRUE	1	0.726038836941027	2		371	480	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037957-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	74	314	4	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.326984403941454	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.419008815513976	4		318	207	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591892	48591892	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037957-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	102	491	0	ENST00000342988.3:c.1055G>C	p.Gly352Ala	p.G352A	ENST00000342988	NM_005359.5	352	gGa/gCa	9/12	0.419008815513976	2	FACETS	0.97	0.883	1	0.97	0.883	1	CLONAL	2	TRUE	0	0.419008815513976	2		491	251	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422959	45422959	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037957-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	146	447	0	ENST00000262160.6:c.169C>T	p.Arg57Ter	p.R57*	ENST00000262160	NM_005901.5	57	Cga/Tga	2/11	0.419008815513976	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.419008815513976	2		447	315	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118881	70118882	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0037957-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	114	609	0	ENST00000245479.2:c.454dup	p.Arg152ProfsTer100	p.R152Pfs*100	ENST00000245479	NM_000346.3	151	-/C	2/3	0.289120662738272	4	FACETS	0.906	0.822	0.994	0.906	0.822	0.994	CLONAL	2	TRUE	2	0.419008815513976	4		609	426	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046509	69046509	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs557338072	NA	P-0037957-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	44	420	0	ENST00000288368.4:c.3982T>G	p.Leu1328Val	p.L1328V	ENST00000288368	NM_024870.2	1328	Ttg/Gtg	32/40	0.419008815513976	5	FACETS	1	0.885	1	0.266	0.223	0.312	CLONAL	1	TRUE	1	0.419008815513976	5		420	322	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418849	116418849	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037957-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	52	356	0	ENST00000397752.3:c.3360A>C	p.Glu1120Asp	p.E1120D	ENST00000397752	NM_000245.2	1120	gaA/gaC	17/21	0.396432223582726	3	FACETS	1	0.93	1	0.571	0.49	0.658	CLONAL	1	TRUE	1	0.419008815513976	3		356	263	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479846	67479846	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs886038836	NA	P-0037957-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	228	405	0	ENST00000327367.4:c.1153A>G	p.Arg385Gly	p.R385G	ENST00000327367	NM_005902.3	385	Agg/Ggg	8/9	0.418504190325581	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	4	TRUE	0	0.419008815513976	4		405	384	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505106	149505106	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037957-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	81	476	0	ENST00000261799.4:c.1709A>T	p.Glu570Val	p.E570V	ENST00000261799	NM_002609.3	570	gAg/gTg	12/23	0.396432223582726	3	FACETS	1	0.969	1	0.641	0.568	0.717	CLONAL	1	TRUE	1	0.419008815513976	3		476	365	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128501	30128501	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037957-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	50	508	0	ENST00000263025.4:c.881A>C	p.Lys294Thr	p.K294T	ENST00000263025	NM_002746.2	294	aAg/aCg	6/9	0.136408783853222	5	FACETS	1	0.912	1			1	INDETERMINATE	1	TRUE	NA	0.419008815513976	5		508	353	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027899	48027899	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037957-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	52	408	0	ENST00000234420.5:c.2777T>G	p.Leu926Arg	p.L926R	ENST00000234420	NM_000179.2	926	cTt/cGt	4/10	0.289120662738272	4	FACETS	1	0.918	1	0.554	0.474	0.64	CLONAL	1	TRUE	2	0.419008815513976	4		408	318	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55962464	55962464	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037957-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	41	336	0	ENST00000263923.4:c.2660A>C	p.Lys887Thr	p.K887T	ENST00000263923	NM_002253.2	887	aAg/aCg	19/30	0.396432223582726	3	FACETS	1	0.853	1	0.508	0.426	0.597	CLONAL	1	TRUE	1	0.419008815513976	3		336	233	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172074	99172074	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037957-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	56	521	0	ENST00000074304.5:c.1640A>C	p.Lys547Thr	p.K547T	ENST00000074304	NM_001134224.1	547	aAg/aCg	17/26	0.289120662738272	4	FACETS	0.97	0.834	1	0.485	0.417	0.559	CLONAL	1	TRUE	2	0.419008815513976	4		521	391	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62317201	62317201	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037957-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	56	498	0	ENST00000360203.5:c.1324A>G	p.Ser442Gly	p.S442G	ENST00000360203	NM_001283009.1	442	Agc/Ggc	16/35	0.326984403941454	4	FACETS	1	0.865	1	0.503	0.432	0.579	CLONAL	1	TRUE	2	0.419008815513976	4		498	377	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815556	139815556	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037957-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	52	417	0	ENST00000247668.2:c.1027T>A	p.Leu343Met	p.L343M	ENST00000247668	NM_021138.3	343	Ttg/Atg	9/11	0.326984403941454	4	FACETS	0.934	0.798	1	0.467	0.399	0.541	CLONAL	1	TRUE	2	0.419008815513976	4		417	377	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731103	162731103	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037957-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	58	532	0	ENST00000367921.3:c.958T>G	p.Phe320Val	p.F320V	ENST00000367921	NM_006182.2	320	Ttc/Gtc	9/18	0.289120662738272	4	FACETS	0.883	0.76	1	0.441	0.38	0.508	CLONAL	1	TRUE	2	0.419008815513976	4		532	445	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0038882-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	41	525	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.164466318682173	3	FACETS	0.607	0.505	0.72	0.303	0.252	0.36	INDETERMINATE	1	TRUE	1	0.32	3		527	490	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591895	48591895	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs377767346	NA	P-0038882-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	34	477	0	ENST00000342988.3:c.1058A>G	p.Tyr353Cys	p.Y353C	ENST00000342988	NM_005359.5	353	tAc/tGc	9/12	1	2	FACETS	0.491	0.401	0.592	0.491	0.401	0.592	SUBCLONAL	1	TRUE	1	0.32	2		477	433	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982157	201982158	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	G	novel	NA	P-0038882-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	73	503	0	ENST00000359651.3:c.681_682delinsG	p.Phe227LeufsTer27	p.F227Lfs*27	ENST00000359651		227	ttCCcc/ttGcc	5/8	0.326500161775148	3	FACETS	0.888	0.784	0.998	0.888	0.784	0.998	CLONAL	2	TRUE	1	0.32	3		503	298	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441231	52441231	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038882-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	25	517	0	ENST00000460680.1:c.539T>C	p.Leu180Pro	p.L180P	ENST00000460680	NM_004656.3	180	cTc/cCc	7/17	1	2	FACETS	0.395	0.31	0.491	0.395	0.31	0.491	SUBCLONAL	1	TRUE	1	0.32	2		517	396	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0040999-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	124	329	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.253008887659286	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.253008887659286	2		329	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0040999-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	102	529	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.150754445592263	4	FACETS	1	0.935	1	0.527	0.474	0.584	INDETERMINATE	2	TRUE	0	0.253008887659286	4		529	479	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0041570-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	12	314	4	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.778	0.546	1	0.778	0.546	1	CLONAL	1	TRUE	1	0.12	2		318	257	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577523	7577524	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041570-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	26	424	0	ENST00000269305.4:c.757dup	p.Thr253AsnfsTer11	p.T253Nfs*11	ENST00000269305	NM_001126112.2	253	acc/aAcc	7/11	1	2	FACETS	0.965	0.763	1	0.965	0.763	1	CLONAL	1	TRUE	1	0.12	2		424	449	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907032	101907032	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041570-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	24	304	0	ENST00000374994.4:c.992A>G	p.His331Arg	p.H331R	ENST00000374994	NM_004612.2	331	cAt/cGt	6/9	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.12	2		304	335	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562618	95562618	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041570-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	28	544	0	ENST00000393063.1:c.4639G>C	p.Asp1547His	p.D1547H	ENST00000393063	NM_030621.3	1547	Gac/Cac	24/28	1	2	FACETS	0.894	0.713	1	0.894	0.713	1	CLONAL	1	TRUE	1	0.12	2		544	522	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243941	46243941	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041570-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	24	510	0	ENST00000334344.6:c.2035C>T	p.Gln679Ter	p.Q679*	ENST00000334344	NM_152641.2	679	Caa/Taa	15/21	1	2	FACETS	0.903	0.707	1	0.903	0.707	1	CLONAL	1	TRUE	1	0.12	2		510	443	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602763	10602763	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs774469695	NA	P-0042066-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	88	489	0	ENST00000171111.5:c.815G>T	p.Arg272Leu	p.R272L	ENST00000171111	NM_203500.1	272	cGc/cTc	3/6	0.310043385192198	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.310043385192198	1		489	340	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041247	47041247	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042066-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	88	233	0	ENST00000377604.3:c.1675G>T	p.Glu559Ter	p.E559*	ENST00000377604	NM_001204468.1	559	Gaa/Taa	15/24	0.310043385192198	2	FACETS	1	0.973	1			1	CLONAL	2	TRUE	NA	0.310043385192198	2		233	229	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155254	55155254	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042066-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	37	380	0	ENST00000257290.5:c.2853G>C	p.Glu951Asp	p.E951D	ENST00000257290	NM_006206.4	951	gaG/gaC	21/23	0.225062571276926	3	FACETS	0.801	0.662	0.956	0.401	0.331	0.478	CLONAL	1	TRUE	1	0.310043385192198	3		380	344	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223059	1223060	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0042066-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	88	423	0	ENST00000326873.7:c.998_999del	p.Arg333GlnfsTer26	p.R333Qfs*26	ENST00000326873	NM_000455.4	332	tgGCgc/tggc	8/10	0.310043385192198	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.310043385192198	1		423	367	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215969	41215969	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1800747	NA	P-0042066-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	70	259	0	ENST00000357654.3:c.5075-1G>A		p.X1692_splice	ENST00000357654	NM_007294.3	1692			0.225062571276926	3	FACETS	0.833	0.732	0.94	0.833	0.732	0.94	CLONAL	2	TRUE	1	0.310043385192198	3		259	313	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499364	89499364	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs572288873	NA	P-0042066-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	51	386	0	ENST00000336596.2:c.2534C>A	p.Pro845His	p.P845H	ENST00000336596	NM_005233.5	845	cCc/cAc	15/17	0.225062571276926	3	FACETS	0.782	0.665	0.91	0.391	0.332	0.455	CLONAL	1	TRUE	1	0.310043385192198	3		386	486	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42050003	42050003	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042066-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	41	173	0	ENST00000219905.7:c.7157C>G	p.Ser2386Cys	p.S2386C	ENST00000219905	NM_001164273.1	2386	tCt/tGt	19/24	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.310043385192198	2		173	257	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556461	29556461	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042066-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	75	261	0	ENST00000356175.3:c.2828A>C	p.Lys943Thr	p.K943T	ENST00000356175	NM_000267.3	943	aAg/aCg	21/57	0.225062571276926	3	FACETS	1	0.968	1	0.656	0.577	0.74	CLONAL	1	TRUE	1	0.310043385192198	3		261	426	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201912	67201912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042066-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	51	444	0	ENST00000312629.5:c.1112C>T	p.Pro371Leu	p.P371L	ENST00000312629	NM_003952.2	371	cCt/cTt	13/15	1	2	FACETS	0.833	0.71	0.967	0.833	0.71	0.967	CLONAL	1	TRUE	1	0.310043385192198	2		444	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0042732-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	258	574	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		574	268	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0042732-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	0	270	364	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		364	270	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952100	178952100	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042732-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	139	373	0	ENST00000263967.3:c.3155C>A	p.Thr1052Lys	p.T1052K	ENST00000263967	NM_006218.2	1052	aCa/aAa	21/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		373	269	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640155	3640155	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042732-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	48	489	0	ENST00000294008.3:c.3484G>C	p.Glu1162Gln	p.E1162Q	ENST00000294008	NM_032444.2	1162	Gag/Cag	12/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		489	523	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77930434	77930434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042732-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	186	448	0	ENST00000361507.4:c.1915G>A	p.Glu639Lys	p.E639K	ENST00000361507	NM_080491.2	639	Gag/Aag	10/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		448	379	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184406	7184406	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042732-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	124	403	0	ENST00000302850.5:c.895del	p.Gln299ArgfsTer23	p.Q299Rfs*23	ENST00000302850	NM_000208.2	299	Cag/ag	3/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		403	257	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61710009	61710148	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGACCTCCCAAAGTGCTGGGATTATAGGCGTGAGGCCCTGTGCCCAGCTGGCACTTAACATTTAAATCGTATTAAATTCTTACCAGCAGTATGTGAAGTGTCTGTCACAACAGAAAAGATATGCTGGAGAATATCACAAA	CGACCTCCCAAAGTGCTGGGATTATAGGCGTGAGGCCCTGTGCCCAGCTGGCACTTAACATTTAAATCGTATTAAATTCTTACCAGCAGTATGTGAAGTGTCTGTCACAACAGAAAAGATATGCTGGAGAATATCACAAA	-	novel	NA	P-0042732-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	61	117	0	ENST00000401558.2:c.2756_2812+83del		p.X919_splice	ENST00000401558	NM_003400.3	919		22/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		117	177	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0042732-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	144	574	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		574	422	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0042732-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	186	364	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		364	345	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952100	178952100	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042732-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	60	373	0	ENST00000263967.3:c.3155C>A	p.Thr1052Lys	p.T1052K	ENST00000263967	NM_006218.2	1052	aCa/aAa	21/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		373	303	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77930434	77930434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042732-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	79	448	0	ENST00000361507.4:c.1915G>A	p.Glu639Lys	p.E639K	ENST00000361507	NM_080491.2	639	Gag/Aag	10/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		448	368	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184406	7184406	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042732-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	135	403	0	ENST00000302850.5:c.895del	p.Gln299ArgfsTer23	p.Q299Rfs*23	ENST00000302850	NM_000208.2	299	Cag/ag	3/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		403	430	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61710009	61710148	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGACCTCCCAAAGTGCTGGGATTATAGGCGTGAGGCCCTGTGCCCAGCTGGCACTTAACATTTAAATCGTATTAAATTCTTACCAGCAGTATGTGAAGTGTCTGTCACAACAGAAAAGATATGCTGGAGAATATCACAAA	CGACCTCCCAAAGTGCTGGGATTATAGGCGTGAGGCCCTGTGCCCAGCTGGCACTTAACATTTAAATCGTATTAAATTCTTACCAGCAGTATGTGAAGTGTCTGTCACAACAGAAAAGATATGCTGGAGAATATCACAAA	-	novel	NA	P-0042732-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	29	117	0	ENST00000401558.2:c.2756_2812+83del		p.X919_splice	ENST00000401558	NM_003400.3	919		22/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		117	182	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241722	55241722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1051753269	NA	P-0042732-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	120	361	0	ENST00000275493.2:c.2170G>A	p.Gly724Ser	p.G724S	ENST00000275493	NM_005228.3	724	Ggc/Agc	18/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		361	412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555525585	NA	P-0042898-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	559	273	0	ENST00000269305.4:c.673-2A>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.754546988798603	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	4	FALSE	0	0.773488986170833	4		273	640	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044470	12044470	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042898-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	55	247	0	ENST00000353533.5:c.1093C>T	p.Pro365Ser	p.P365S	ENST00000353533	NM_003010.3	365	Ccc/Tcc	11/11	0.754546988798603	4	FACETS	0.493	0.421	0.57	0.123	0.105	0.143	SUBCLONAL	1	FALSE	0	0.773488986170833	4		247	512	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222211	53222211	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042898-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	60	385	0	ENST00000375401.3:c.4621T>C	p.Ser1541Pro	p.S1541P	ENST00000375401	NM_004187.3	1541	Tcc/Ccc	26/26	0.63679350221111	5	FACETS	0.42	0.361	0.485	0.14	0.12	0.162	SUBCLONAL	1	FALSE	2	0.773488986170833	5		385	798	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778944	9778944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042898-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	386	630	0	ENST00000377346.4:c.1213C>T	p.Arg405Cys	p.R405C	ENST00000377346	NM_005026.3	405	Cgc/Tgc	9/24	0.774952663466793	2	FACETS	0.998	0.968	1	0.998	0.968	1	CLONAL	2	FALSE	0	0.773488986170833	2		630	500	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755599	39755599	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042898-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	153	433	0	ENST00000288319.7:c.1166A>C	p.Lys389Thr	p.K389T	ENST00000288319	NM_182918.3	389	aAg/aCg	10/10	NA	2	FACETS	0.664	0.61	0.72			1	INDETERMINATE	1	FALSE	NA	0.773488986170833	2		433	596	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188384	32188384	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042898-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	192	445	0	ENST00000375023.3:c.957G>T	p.Glu319Asp	p.E319D	ENST00000375023	NM_004557.3	319	gaG/gaT	6/30	0.336619877374793	3	FACETS	1	0.96	1			1	INDETERMINATE	1	FALSE	NA	0.773488986170833	3		445	657	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55270234	55270234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042898-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	52	387	0	ENST00000275493.2:c.3187G>A	p.Asp1063Asn	p.D1063N	ENST00000275493	NM_005228.3	1063	Gac/Aac	27/28	0.44739707899056	6	FACETS	0.352	0.298	0.411	0.117	0.099	0.137	INDETERMINATE	1	FALSE	3	0.773488986170833	6		387	974	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61708321	61708321	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042898-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	77	198	0	ENST00000401558.2:c.3068A>C	p.Lys1023Thr	p.K1023T	ENST00000401558	NM_003400.3	1023	aAg/aCg	24/25	0.774952663466793	5	FACETS	0.615	0.54	0.697	0.205	0.18	0.233	SUBCLONAL	1	FALSE	2	0.773488986170833	5		198	699	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0043051-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	104	288	0				ENST00000310581	NM_198253.2	-/1132			0.928875877282749	4	FACETS	0.9	0.822	0.979	0.9	0.822	0.979	CLONAL	2	TRUE	2	0.928875877282749	4		288	240	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249853	133249853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854842	NA	P-0043051-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	121	394	0	ENST00000320574.5:c.1370C>T	p.Thr457Met	p.T457M	ENST00000320574	NM_006231.2	457	aCg/aTg	14/49	1	2	FACETS	0.976	0.898	1	0.976	0.898	1	CLONAL	1	TRUE	1	0.928875877282749	2		394	267	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112491	115112495	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGG	AAAGG	-	novel	NA	P-0043051-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	105	478	0	ENST00000257566.3:c.1245_1249del	p.Leu416ArgfsTer3	p.L416Rfs*3	ENST00000257566	NM_016569.3	415	caCCTTTtc/catc	7/8	1	2	FACETS	0.95	0.868	1	0.95	0.868	1	CLONAL	1	TRUE	1	0.928875877282749	2		478	238	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043877-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	47	317	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.768	0.661	0.879	0.768	0.661	0.879	SUBCLONAL	1	TRUE	1	0.838840078698536	2		317	146	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0043877-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	184	420	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.838840078698536	2		420	406	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220476	123220476	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043877-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	58	170	0	ENST00000218089.9:c.3133C>T	p.Arg1045Ter	p.R1045*	ENST00000218089	NM_001042749.1	1045	Cga/Tga	30/35	0.734654482809926	0	FACETS		NA	1			1	NA	1	TRUE	NA	0.838840078698536	0		170	75	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115747	108115747	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043877-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	55	275	0	ENST00000278616.4:c.895G>T	p.Glu299Ter	p.E299*	ENST00000278616	NM_000051.3	299	Gaa/Taa	7/63	0.838840078698536	1	FACETS	0.952	0.864	1	0.952	0.864	1	CLONAL	1	TRUE	0	0.838840078698536	1		275	80	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983066	201983066	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043877-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	351	442	0	ENST00000359651.3:c.916del	p.Leu306CysfsTer19	p.L306Cfs*19	ENST00000359651		305	ttC/tt	7/8	0.425716842950527	3	FACETS	1	0.995	1	0.827	0.799	0.853	INDETERMINATE	2	TRUE	0	0.838840078698536	3		442	479	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961586	18961586	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043877-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	125	377	1	ENST00000262803.5:c.719C>A	p.Ser240Tyr	p.S240Y	ENST00000262803	NM_002911.3	240	tCc/tAc	5/24	0.15801621356513	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.838840078698536	0		378	303	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622190	117622190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs565633598	NA	P-0043877-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	62	278	0	ENST00000368508.3:c.6680A>G	p.Tyr2227Cys	p.Y2227C	ENST00000368508	NM_002944.2	2227	tAt/tGt	42/43	1	2	FACETS	0.808	0.711	0.908	0.808	0.711	0.908	CLONAL	1	TRUE	1	0.838840078698536	2		278	183	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73649902	73649902	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043877-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	124	396	0	ENST00000377687.4:c.1252G>A	p.Asp418Asn	p.D418N	ENST00000377687	NM_001730.3	418	Gat/Aat	4/4	0.267925153020229	1	FACETS	0.554	0.508	0.6	0.554	0.508	0.6	INDETERMINATE	1	TRUE	0	0.838840078698536	1		396	310	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405085	70405085	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043877-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	62	380	0	ENST00000373644.4:c.2599C>G	p.Pro867Ala	p.P867A	ENST00000373644	NM_030625.2	867	Cca/Gca	4/12	0.267925153020229	1	FACETS	0.413	0.362	0.466	0.413	0.362	0.466	INDETERMINATE	1	TRUE	0	0.838840078698536	1		380	208	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874535	151874535	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043877-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	76	337	0	ENST00000262189.6:c.8003C>G	p.Ser2668Cys	p.S2668C	ENST00000262189	NM_170606.2	2668	tCt/tGt	38/59	0.433657544136805	1	FACETS	0.489	0.437	0.544	0.489	0.437	0.544	INDETERMINATE	1	TRUE	0	0.838840078698536	1		337	215	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699264	18699264	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043877-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	107	318	0	ENST00000266497.5:c.3365A>G	p.Tyr1122Cys	p.Y1122C	ENST00000266497		1122	tAt/tGt	24/31	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.838840078698536	2		318	246	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411318	63411318	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043877-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	81	299	0	ENST00000330258.3:c.1849G>C	p.Glu617Gln	p.E617Q	ENST00000330258	NM_152424.3	617	Gaa/Caa	2/2	0.734654482809926	0	FACETS		NA	1			1	NA	1	TRUE	NA	0.838840078698536	0		299	109	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790433	3790434	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0043877-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	168	370	0	ENST00000262367.5:c.4099_4100del	p.Lys1367AspfsTer20	p.K1367Dfs*20	ENST00000262367	NM_004380.2	1367	AAg/g	24/31	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.838840078698536	2		370	371	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928885	44928885	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043877-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	143	155	0	ENST00000377967.4:c.1986del	p.Thr663LeufsTer28	p.T663Lfs*28	ENST00000377967	NM_021140.2	662	tCc/tc	17/29	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.838840078698536	1		155	168	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991763	72991763	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs569425024	NA	P-0044290-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	31	436	0	ENST00000268489.5:c.2282G>T	p.Gly761Val	p.G761V	ENST00000268489	NM_006885.3	761	gGg/gTg	2/10	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.21	2		436	262	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0044352-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	76	376	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.35	2		376	409	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949007	44949013	+	frameshift_variant	Frame_Shift_Del	DEL	ATGGGTT	ATGGGTT	-	novel	NA	P-0044352-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	64	358	0	ENST00000377967.4:c.3568_3574del	p.Met1190LeufsTer29	p.M1190Lfs*29	ENST00000377967	NM_021140.2	1190	ATGGGTTct/ct	25/29	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.35	2		358	333	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245192	46245192	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045222-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	51	312	0	ENST00000334344.6:c.3286C>T	p.Gln1096Ter	p.Q1096*	ENST00000334344	NM_152641.2	1096	Cag/Tag	15/21	0.262452965572057	6	FACETS	0.908	0.77	1			1	CLONAL	1	TRUE	NA	0.262452965572057	6		312	653	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047393	128047393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139690693	NA	P-0045222-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	66	235	0	ENST00000285398.2:c.529G>A	p.Val177Ile	p.V177I	ENST00000285398	NM_000122.1	177	Gtt/Att	5/15	0.210056804687366	2	FACETS	1	0.973	1	0.744	0.65	0.844	CLONAL	1	TRUE	0	0.262452965572057	2		235	338	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602659	10602659	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045222-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	44	332	0	ENST00000171111.5:c.919G>A	p.Glu307Lys	p.E307K	ENST00000171111	NM_203500.1	307	Gag/Aag	3/6	0.262452965572057	1	FACETS	0.859	0.723	1	0.859	0.723	1	CLONAL	1	TRUE	0	0.262452965572057	1		332	339	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204631	128204631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045222-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	48	293	0	ENST00000341105.2:c.810C>A	p.Phe270Leu	p.F270L	ENST00000341105	NM_032638.4	270	ttC/ttA	3/6	0.262470052782543	3	FACETS	1	0.868	1	0.513	0.435	0.599	CLONAL	1	TRUE	1	0.262452965572057	3		293	403	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129622	47129623	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0045222-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	39	253	0	ENST00000409792.3:c.5257dup	p.Thr1753AsnfsTer36	p.T1753Nfs*36	ENST00000409792	NM_014159.6	1753	acc/aAcc	10/21	0.234502964426761	1	FACETS	0.906	0.755	1	0.906	0.755	1	CLONAL	1	TRUE	0	0.262452965572057	1		253	285	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814689	139814689	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045222-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	51	245	0	ENST00000247668.2:c.682G>C	p.Glu228Gln	p.E228Q	ENST00000247668	NM_021138.3	228	Gag/Cag	8/11	0.234502964426761	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.262452965572057	1		245	291	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900912	3900912	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045222-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	47	270	0	ENST00000262367.5:c.184G>C	p.Asp62His	p.D62H	ENST00000262367	NM_004380.2	62	Gat/Cat	2/31	1	2	FACETS	0.953	0.806	1	0.953	0.806	1	CLONAL	1	TRUE	1	0.262452965572057	2		270	376	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244108	41244108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045222-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	58	295	0	ENST00000357654.3:c.3440C>T	p.Ser1147Phe	p.S1147F	ENST00000357654	NM_007294.3	1147	tCt/tTt	10/23	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.262452965572057	2		295	406	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170528	11170528	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045222-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	47	310	2	ENST00000358026.2:c.4831G>T	p.Glu1611Ter	p.E1611*	ENST00000358026	NM_001128849.1	1611	Gaa/Taa	34/36	0.262452965572057	1	FACETS	0.963	0.817	1	0.963	0.817	1	CLONAL	1	TRUE	0	0.262452965572057	1		312	323	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673683	30673683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045222-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	33	322	0	ENST00000376406.3:c.3277C>T	p.Pro1093Ser	p.P1093S	ENST00000376406	NM_014641.2	1093	Ccc/Tcc	10/15	0.240367292472406	2	FACETS	0.683	0.557	0.825	0.342	0.278	0.413	SUBCLONAL	1	TRUE	0	0.262452965572057	2		322	368	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049112-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	92	317	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.872	0.783	0.965	1	0.985	1	CLONAL	2	TRUE	1	0.324745759164727	2		317	325	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0049112-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	36	424	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.981	0.813	1	0.981	0.813	1	CLONAL	1	TRUE	1	0.324745759164727	2		424	226	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850341	128850341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121918347	NA	P-0049112-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	86	521	0	ENST00000249373.3:c.1604G>T	p.Trp535Leu	p.W535L	ENST00000249373	NM_005631.4	535	tGg/tTg	9/12	1	2	FACETS	0.996	0.883	1	0.996	0.883	1	CLONAL	1	TRUE	1	0.324745759164727	2		521	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0049112-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	177	513	0	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	1	2	FACETS	1	0.959	1	1	0.993	1	CLONAL	2	TRUE	1	0.324745759164727	2		513	520	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220640	1220640	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690940	NA	P-0049130-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	76	536	0	ENST00000326873.7:c.658C>T	p.Gln220Ter	p.Q220*	ENST00000326873	NM_000455.4	220	Cag/Tag	5/10	0.198361163776995	4	FACETS	0.88	0.781	0.982			1	CLONAL	4	FALSE	NA	0.198361163776995	4		536	261	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200976	108200976	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1275267580	NA	P-0049130-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	54	414	0	ENST00000278616.4:c.7343A>T	p.Asp2448Val	p.D2448V	ENST00000278616	NM_000051.3	2448	gAt/gTt	50/63	0.198361163776995	3	FACETS	0.988	0.856	1	0.988	0.856	1	CLONAL	3	FALSE	0	0.198361163776995	3		414	202	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314622	30314622	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049130-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	35	439	0	ENST00000262643.3:c.1171A>T	p.Ser391Cys	p.S391C	ENST00000262643	NM_001238.2	391	Agt/Tgt	12/12	0.198361163776995	3	FACETS	0.915	0.756	1	0.915	0.756	1	CLONAL	2	FALSE	1	0.198361163776995	3		439	212	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793446	242793446	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049130-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	34	415	0	ENST00000334409.5:c.631G>T	p.Glu211Ter	p.E211*	ENST00000334409	NM_005018.2	211	Gag/Tag	5/5	0.187769634301375	4	FACETS	0.838	0.689	1	0.838	0.689	1	CLONAL	2	FALSE	2	0.198361163776995	4		415	245	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141111	55141111	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049130-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	49	454	0	ENST00000257290.5:c.1757G>C	p.Trp586Ser	p.W586S	ENST00000257290	NM_006206.4	586	tGg/tCg	12/23	0.190805538704181	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	FALSE	1	0.198361163776995	3		454	220	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392026	81392026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049130-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	10	352	0	ENST00000222390.5:c.251G>T	p.Cys84Phe	p.C84F	ENST00000222390	NM_000601.4	84	tGc/tTc	2/18	0.198361163776995	3	FACETS	1	0.745	1	0.554	0.378	0.771	CLONAL	1	FALSE	1	0.198361163776995	3		352	100	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0049130-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	17	321	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.187769634301375	4	FACETS	1	0.889	1	0.694	0.522	0.895	CLONAL	1	FALSE	2	0.198361163776995	4		321	148	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764146326	NA	P-0049651-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	44	418	0	ENST00000269305.4:c.841G>T	p.Asp281Tyr	p.D281Y	ENST00000269305	NM_001126112.2	281	Gac/Tac	8/11	1	2	FACETS	0.759	0.635	0.897	0.759	0.635	0.897	SUBCLONAL	1	TRUE	1	0.18	2		418	644	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423407	116423407	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913671	NA	P-0049651-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	43	303	0	ENST00000397752.3:c.3682G>C	p.Asp1228His	p.D1228H	ENST00000397752	NM_000245.2	1228	Gac/Cac	19/21	0.164746636906546	2	FACETS	0.915	0.766	1	0.458	0.383	0.541	CLONAL	1	TRUE	0	0.18	2		303	522	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411891	116411924	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCTGTTTTAAGATCTGGGCAGTGAATTAGTTCG	CTCTGTTTTAAGATCTGGGCAGTGAATTAGTTCG	-	novel	NA	P-0049651-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	126	476	0	ENST00000397752.3:c.2888-10_2911del		p.X963_splice	ENST00000397752	NM_000245.2	963		14/21	0.164746636906546	2	FACETS	0.908	0.823	0.998	0.908	0.823	0.998	CLONAL	2	TRUE	0	0.18	2		476	771	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459840	149459840	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049651-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	40	366	0	ENST00000286301.3:c.367G>T	p.Ala123Ser	p.A123S	ENST00000286301	NM_005211.3	123	Gca/Tca	4/22	1	2	FACETS	0.675	0.56	0.805	0.675	0.56	0.805	SUBCLONAL	1	TRUE	1	0.18	2		366	658	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472607	88472607	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049651-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	17	0	0	ENST00000360948.2:c.1948G>T	p.Glu650Ter	p.E650*	ENST00000360948	NM_001012338.2	650	Gag/Tag	16/19	1	2	FACETS	0.319	0.236	0.417	0.319	0.236	0.417	SUBCLONAL	1	TRUE	1	0.18	2		0	593	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051772-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	76	317	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.9	0.802	1	0.9	0.802	1	CLONAL	1	TRUE	1	0.747439897487468	2		317	226	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0051772-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	171	328	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	0.885	0.82	0.951	0.885	0.82	0.951	CLONAL	1	TRUE	1	0.747439897487468	2		328	517	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275782	38275782	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051772-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	181	408	0	ENST00000425967.3:c.1487T>G	p.Leu496Arg	p.L496R	ENST00000425967	NM_001174067.1	496	cTt/cGt	11/19	1	2	FACETS	0.973	0.905	1	0.973	0.905	1	CLONAL	1	TRUE	1	0.747439897487468	2		408	498	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0051772-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	381	506	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	0.744659352153585	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.747439897487468	2		506	502	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566491	41566493	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	novel	NA	P-0051772-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	200	359	0	ENST00000263253.7:c.4368_4370del	p.Ile1457del	p.I1457del	ENST00000263253	NM_001429.3	1456	aaGATa/aaa	27/31	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.747439897487468	2		359	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0052695-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	157	455	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.323481174220451	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.323481174220451	1		455	561	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653807	89653807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554893782	NA	P-0052695-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	109	263	0	ENST00000371953.3:c.105G>A	p.Met35Ile	p.M35I	ENST00000371953	NM_000314.4	35	atG/atA	2/9	0.295554899608065	2	FACETS	0.98	0.889	1	0.98	0.889	1	CLONAL	2	TRUE	0	0.323481174220451	2		263	344	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463287	25463287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761934754	NA	P-0052695-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	29	418	1	ENST00000264709.3:c.2206C>T	p.Arg736Cys	p.R736C	ENST00000264709	NM_175629.2	736	Cgc/Tgc	19/23	1	2	FACETS	0.342	0.274	0.42	0.342	0.274	0.42	SUBCLONAL	1	TRUE	1	0.323481174220451	2		419	524	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114169	115114169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773465537	NA	P-0052695-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	135	382	0	ENST00000257566.3:c.1048G>A	p.Ala350Thr	p.A350T	ENST00000257566	NM_016569.3	350	Gcc/Acc	6/8	0.163817235507918	3	FACETS	0.872	0.796	0.951	0.872	0.796	0.951	INDETERMINATE	2	TRUE	1	0.323481174220451	3		382	556	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741849	162741849	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052695-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	54	400	0	ENST00000367921.3:c.1540G>C	p.Gly514Arg	p.G514R	ENST00000367921	NM_006182.2	514	Ggc/Cgc	13/18	1	2	FACETS	0.669	0.572	0.775	0.669	0.572	0.775	SUBCLONAL	1	TRUE	1	0.323481174220451	2		400	499	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423508	88423508	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052695-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	46	310	0	ENST00000360948.2:c.2327A>T	p.Asn776Ile	p.N776I	ENST00000360948	NM_001012338.2	776	aAc/aTc	18/19	1	2	FACETS	0.771	0.651	0.902	0.771	0.651	0.902	CLONAL	1	TRUE	1	0.323481174220451	2		310	369	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680740	88680740	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052695-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	36	359	0	ENST00000360948.2:c.517C>A	p.Leu173Ile	p.L173I	ENST00000360948	NM_001012338.2	173	Ctc/Atc	6/19	1	2	FACETS	0.636	0.524	0.761	0.636	0.524	0.761	SUBCLONAL	1	TRUE	1	0.323481174220451	2		359	350	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93973599	93973599	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052695-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	97	263	0	ENST00000369303.4:c.1777G>C	p.Asp593His	p.D593H	ENST00000369303	NM_004440.3	593	Gat/Cat	9/17	0.239628180301678	3	FACETS	0.965	0.868	1	0.965	0.868	1	CLONAL	2	TRUE	1	0.323481174220451	3		263	361	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989680	68989680	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052695-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	84	380	0	ENST00000288368.4:c.1618T>C	p.Cys540Arg	p.C540R	ENST00000288368	NM_024870.2	540	Tgt/Cgt	15/40	0.163817235507918	3	FACETS	1	0.961	1	0.601	0.532	0.674	INDETERMINATE	1	TRUE	1	0.323481174220451	3		380	502	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981857	70981857	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052695-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	152	440	0	ENST00000276594.2:c.239C>A	p.Pro80Gln	p.P80Q	ENST00000276594	NM_024504.3	80	cCg/cAg	2/8	0.163817235507918	3	FACETS	1	0.92	1	1	0.92	1	INDETERMINATE	2	TRUE	1	0.323481174220451	3		440	546	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5077512	5077512	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0052695-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	45	263	0	ENST00000381652.3:c.1924A>T	p.Lys642Ter	p.K642*	ENST00000381652	NM_004972.3	642	Aaa/Taa	15/25	0.323481174220451	1	FACETS	0.842	0.712	0.983	0.842	0.712	0.983	CLONAL	1	TRUE	0	0.323481174220451	1		263	277	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180601	56180602	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	T	novel	NA	P-0052695-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	55	256	0	ENST00000399503.3:c.3930_3931delinsT	p.Leu1310PhefsTer26	p.L1310Ffs*26	ENST00000399503	NM_005921.1	1310	ttGGga/ttTga	16/20	0.323481174220451	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	0	0.323481174220451	1		256	269	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30733020	30733020	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052695-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	46	454	0	ENST00000295754.5:c.1633G>T	p.Asp545Tyr	p.D545Y	ENST00000295754	NM_003242.5	545	Gac/Tac	7/7	0.323481174220451	1	FACETS	0.46	0.387	0.541	0.46	0.387	0.541	SUBCLONAL	1	TRUE	0	0.323481174220451	1		454	518	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0053890-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	200	439	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.894323869785037	2		439	396	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0053890-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	309	344	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.989	0.939	1	0.989	0.939	1	CLONAL	1	TRUE	1	0.894323869785037	2		344	699	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195112	123195112	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053890-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	173	313	0	ENST00000218089.9:c.1455G>A	p.Trp485Ter	p.W485*	ENST00000218089	NM_001042749.1	485	tgG/tgA	16/35	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.894323869785037	2		313	350	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442667	442667	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053890-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	253	453	0	ENST00000399788.2:c.1639G>A	p.Glu547Lys	p.E547K	ENST00000399788	NM_001042603.1	547	Gag/Aag	12/28	NA	2	FACETS	0.974	0.919	1			1	INDETERMINATE	1	TRUE	NA	0.894323869785037	2		453	581	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427447	49427447	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053890-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	330	531	0	ENST00000301067.7:c.11041C>T	p.Gln3681Ter	p.Q3681*	ENST00000301067	NM_003482.3	3681	Cag/Tag	39/54	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.894323869785037	2		531	726	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427964	49427965	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053890-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	301	447	0	ENST00000301067.7:c.10625dup	p.Cys3543ValfsTer13	p.C3543Vfs*13	ENST00000301067	NM_003482.3	3542	ctg/ctTg	38/54	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.894323869785037	2		447	577	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848560	151848565	+	inframe_deletion	In_Frame_Del	DEL	CCGCAC	CCGCAC	-	novel	NA	P-0053890-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	175	398	0	ENST00000262189.6:c.12628_12633del	p.Val4210_Arg4211del	p.V4210_R4211del	ENST00000262189	NM_170606.2	4210	GTGCGG/-	50/59	1	2	FACETS	0.964	0.899	1	0.964	0.899	1	CLONAL	1	TRUE	1	0.894323869785037	2		398	406	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012396	29012396	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1475917029	NA	P-0054365-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	144	366	0	ENST00000282397.4:c.475C>T	p.Arg159Trp	p.R159W	ENST00000282397	NM_002019.4	159	Cgg/Tgg	4/30	0.650841988936536	3	FACETS	1	0.975	1	0.578	0.53	0.627	CLONAL	1	TRUE	1	0.646885718681444	3		366	510	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578572	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGTACTGTAGGAAGAGGAAGGA	GAGTACTGTAGGAAGAGGAAGGA	-	novel	NA	P-0054365-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	235	505	0	ENST00000269305.4:c.376-18_380del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	0.618464121156358	3	FACETS	0.89	0.849	0.931	0.89	0.849	0.931	CLONAL	3	TRUE	0	0.646885718681444	3		505	360	SUCCESS
REST	5978	MSKCC	GRCh37	4	57798145	57798145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054365-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	105	399	0	ENST00000309042.7:c.3121G>A	p.Glu1041Lys	p.E1041K	ENST00000309042	NM_005612.4	1041	Gaa/Aaa	4/4	0.310074335531711	5	FACETS	1	0.964	1	0.388	0.348	0.429	INDETERMINATE	1	TRUE	2	0.646885718681444	5		399	550	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0055424-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	13	171	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		171	271	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0055424-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	30	395	11	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		406	483	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055424-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	19	455	1	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		456	457	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042539	42042539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055424-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	34	409	0	ENST00000219905.7:c.6734G>A	p.Ser2245Asn	p.S2245N	ENST00000219905	NM_001164273.1	2245	aGt/aAt	17/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		409	670	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0055427-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	188	475	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.3096929355666	4	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	2	0.31	4		475	767	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793159	42793159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055427-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	65	534	0	ENST00000575354.2:c.1051C>T	p.Arg351Trp	p.R351W	ENST00000575354	NM_015125.3	351	Cgg/Tgg	7/20	0.297947402015925	3	FACETS	0.636	0.551	0.73	0.318	0.275	0.365	SUBCLONAL	1	TRUE	1	0.31	3		534	761	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0055427-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	108	518	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.201853518551743	3	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.31	3		518	647	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282578	1282578	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055427-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	75	410	0	ENST00000310581.5:c.1735A>G	p.Ser579Gly	p.S579G	ENST00000310581	NM_198253.2	579	Agt/Ggt	3/16	1	2	FACETS	0.877	0.769	0.992	0.877	0.769	0.992	CLONAL	1	TRUE	1	0.31	2		410	552	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740872	58740872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055427-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	52	428	0	ENST00000305921.3:c.1777C>T	p.Pro593Ser	p.P593S	ENST00000305921	NM_003620.3	593	Cct/Tct	6/6	0.19523869030998	3	FACETS	0.732	0.624	0.852	0.366	0.312	0.426	SUBCLONAL	1	TRUE	1	0.31	3		428	529	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499508	89499508	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055427-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	71	485	0	ENST00000336596.2:c.2678G>T	p.Ser893Ile	p.S893I	ENST00000336596	NM_005233.5	893	aGt/aTt	15/17	0.3096929355666	1	FACETS	0.904	0.792	1	0.904	0.792	1	CLONAL	1	TRUE	0	0.31	1		485	428	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045627	47045657	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACCACTCATGCTGTGCACCGCCCCTGCAGA	GACCACTCATGCTGTGCACCGCCCCTGCAGA	-	novel	NA	P-0055427-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	90	506	0	ENST00000377604.3:c.2538-27_2541del		p.X846_splice	ENST00000377604	NM_001204468.1	846		23/24	0.221342514724564	2	FACETS	0.955	0.849	1	0.478	0.424	0.534	CLONAL	1	TRUE	0	0.31	2		506	608	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612085	189612085	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055427-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	117	519	0	ENST00000264731.3:c.1837C>G	p.Pro613Ala	p.P613A	ENST00000264731	NM_003722.4	613	Cct/Gct	14/14	0.241951801833469	2	FACETS	1	0.977	1	0.638	0.576	0.702	CLONAL	1	TRUE	0	0.31	2		519	592	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055498-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	15	317	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.803	0.588	1	0.803	0.588	1	CLONAL	1	TRUE	1	0.15	2		317	249	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0055498-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	37	305	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.15	2		305	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780068	NA	P-0055498-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	32	555	0	ENST00000269305.4:c.472C>T	p.Arg158Cys	p.R158C	ENST00000269305	NM_001126112.2	158	Cgc/Tgc	5/11	1	2	FACETS	0.819	0.664	0.995	0.819	0.664	0.995	CLONAL	1	TRUE	1	0.15	2		555	521	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856005	111856005	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778291950	NA	P-0055498-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	27	408	1	ENST00000341259.2:c.56C>T	p.Pro19Leu	p.P19L	ENST00000341259	NM_005475.2	19	cCg/cTg	2/8	1	2	FACETS	0.947	0.754	1	0.947	0.754	1	CLONAL	1	TRUE	1	0.15	2		409	380	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831350	72831350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs967087904	NA	P-0055498-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	36	459	0	ENST00000268489.5:c.5231C>T	p.Thr1744Met	p.T1744M	ENST00000268489	NM_006885.3	1744	aCg/aTg	9/10	1	2	FACETS	0.892	0.732	1	0.892	0.732	1	CLONAL	1	TRUE	1	0.15	2		459	538	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984771	55984771	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055498-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	30	305	0	ENST00000263923.4:c.358G>T	p.Asp120Tyr	p.D120Y	ENST00000263923	NM_002253.2	120	Gat/Tat	3/30	1	2	FACETS	1	0.833	1	1	0.833	1	CLONAL	1	TRUE	1	0.15	2		305	386	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055606-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	328	384	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.764328993754047	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.790079236632291	1		384	469	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506975	186506975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055606-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	242	494	0	ENST00000323963.5:c.1141G>A	p.Asp381Asn	p.D381N	ENST00000323963		381	Gac/Aac	11/11	1	2	FACETS	0.965	0.907	1	0.965	0.907	1	CLONAL	1	TRUE	1	0.790079236632291	2		494	635	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518095	176518095	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055606-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	288	616	0	ENST00000292408.4:c.593G>T	p.Gly198Val	p.G198V	ENST00000292408	NM_213647.1	198	gGa/gTa	5/18	1	2	FACETS	0.979	0.925	1	0.979	0.925	1	CLONAL	1	TRUE	1	0.790079236632291	2		616	745	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120669	115120669	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055606-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	618	603	0	ENST00000257566.3:c.337T>C	p.Trp113Arg	p.W113R	ENST00000257566	NM_016569.3	113	Tgg/Cgg	1/8	0.77158657491359	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.790079236632291	2		603	778	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0056533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	119	638	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.33279645489375	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.33279645489375	1		638	590	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778944	9778944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	77	630	0	ENST00000377346.4:c.1213C>T	p.Arg405Cys	p.R405C	ENST00000377346	NM_005026.3	405	Cgc/Tgc	9/24	1	2	FACETS	0.867	0.762	0.978	0.867	0.762	0.978	CLONAL	1	TRUE	1	0.33279645489375	2		630	534	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0056533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	72	424	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.894	0.783	1	0.894	0.783	1	CLONAL	1	TRUE	1	0.33279645489375	2		424	484	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927405	178927405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	62	364	0	ENST00000263967.3:c.1168G>A	p.Asp390Asn	p.D390N	ENST00000263967	NM_006218.2	390	Gat/Aat	7/21	1	2	FACETS	0.896	0.776	1	0.896	0.776	1	CLONAL	1	TRUE	1	0.33279645489375	2		364	416	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150031	202150031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167464002	NA	P-0057262-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	8	351	1	ENST00000358485.4:c.1472G>A	p.Arg491Gln	p.R491Q	ENST00000358485	NM_001080125.1	491	cGa/cAa	8/9	0.293810780439159	1	FACETS	0.073	0.047	0.107	0.073	0.047	0.107	INDETERMINATE	1	TRUE	0	0.861875716168137	1		352	144	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1427441061	NA	P-0057262-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	147	480	0	ENST00000269305.4:c.560-2A>G		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.861875716168137	3	FACETS	0.951	0.914	0.984	0.951	0.914	0.984	CLONAL	3	TRUE	0	0.861875716168137	3		480	171	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586404	189586404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908841	NA	P-0057262-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	42	311	0	ENST00000264731.3:c.1028G>A	p.Arg343Gln	p.R343Q	ENST00000264731	NM_003722.4	343	cGg/cAg	8/14	0.287236022253861	1	FACETS	0.321	0.271	0.373	0.321	0.271	0.373	INDETERMINATE	1	TRUE	0	0.861875716168137	1		311	173	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130570	29130570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057262-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	35	371	0	ENST00000328354.6:c.140C>T	p.Pro47Leu	p.P47L	ENST00000328354	NM_007194.3	47	cCa/cTa	2/15	0.245373442599902	3	FACETS	0.581	0.481	0.691	0.291	0.24	0.346	INDETERMINATE	1	TRUE	1	0.861875716168137	3		371	200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0057435-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	52	533	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.311589829656052	3	FACETS	1	0.95	1	0.79	0.691	0.892	CLONAL	2	FALSE	0	0.398787749127157	3		533	132	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61197642	61197663	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACTTCGTCGCTGGTGAGGAGA	GACTTCGTCGCTGGTGAGGAGA	-	novel	NA	P-0057435-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	41	474	0	ENST00000301761.2:c.26_36+11del		p.X9_splice	ENST00000301761	NM_017841.2	9		1/4	0.244351090630179	2	FACETS	0.875	0.735	1	0.437	0.367	0.514	CLONAL	1	FALSE	0	0.398787749127157	2		474	235	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470474	25470474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024296111	NA	P-0057435-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	33	522	0	ENST00000264709.3:c.1000G>A	p.Gly334Ser	p.G334S	ENST00000264709	NM_175629.2	334	Ggc/Agc	8/23	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	FALSE	1	0.398787749127157	2		522	160	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579366	7579366	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs770776262	NA	P-0057737-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	98	575	5	ENST00000269305.4:c.321C>A	p.Tyr107Ter	p.Y107*	ENST00000269305	NM_001126112.2	107	taC/taA	4/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.19	2		580	813	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508389	106508389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758375337	NA	P-0057737-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	55	574	0	ENST00000359195.3:c.383C>T	p.Thr128Met	p.T128M	ENST00000359195	NM_002649.2	128	aCg/aTg	2/11	0.168608155426773	3	FACETS	0.835	0.713	0.969	0.418	0.356	0.485	CLONAL	1	TRUE	1	0.19	3		574	759	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117782	108117782	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057737-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	13	191	1	ENST00000278616.4:c.993G>C	p.Lys331Asn	p.K331N	ENST00000278616	NM_000051.3	331	aaG/aaC	8/63	1	2	FACETS	0.541	0.385	0.731	0.541	0.385	0.731	SUBCLONAL	1	TRUE	1	0.19	2		192	253	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217275	7217275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057737-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	110	577	0	ENST00000380728.2:c.430C>T	p.Leu144Phe	p.L144F	ENST00000380728		144	Ctc/Ttc	6/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.19	2		577	836	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585394	29585437	+	frameshift_variant	Frame_Shift_Del	DEL	CGGTGCAGTAGGAAGTGCCATGTTCCTCAGATTTATCAATCCTG	CGGTGCAGTAGGAAGTGCCATGTTCCTCAGATTTATCAATCCTG	-	novel	NA	P-0057737-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	48	485	0	ENST00000356175.3:c.4144_4187del	p.Gly1382HisfsTer6	p.G1382Hfs*6	ENST00000356175	NM_000267.3	1381	atCGGTGCAGTAGGAAGTGCCATGTTCCTCAGATTTATCAATCCTGcc/atcc	31/57	0.3	3	FACETS	1	0.909	1	0.554	0.469	0.649	CLONAL	1	TRUE	1	0.19	3		485	499	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943769	9943769	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057737-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	47	610	1	ENST00000330684.3:c.1172C>A	p.Pro391His	p.P391H	ENST00000330684	NM_001134407.1	391	cCc/cAc	5/13	1	2	FACETS	0.712	0.599	0.836	0.712	0.599	0.836	SUBCLONAL	1	TRUE	1	0.19	2		611	695	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861083	35861083	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	74	78	0	ENST00000303115.3:c.212T>G	p.Phe71Cys	p.F71C	ENST00000303115	NM_002185.3	71	tTt/tGt	2/8	1	2	FACETS	0.783	0.688	0.884	0.783	0.688	0.884	SUBCLONAL	1	TRUE	1	0.426826143081714	2		78	443	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141496	11141496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	73	180	0	ENST00000358026.2:c.3473C>T	p.Ala1158Val	p.A1158V	ENST00000358026	NM_001128849.1	1158	gCt/gTt	25/36	1	2	FACETS	0.48	0.419	0.545	0.48	0.419	0.545	SUBCLONAL	1	TRUE	1	0.426826143081714	2		180	713	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149452892	149452892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	46	143	1	ENST00000286301.3:c.1054G>A	p.Ala352Thr	p.A352T	ENST00000286301	NM_005211.3	352	Gct/Act	7/22	1	2	FACETS	0.303	0.254	0.357	0.303	0.254	0.357	SUBCLONAL	1	TRUE	1	0.426826143081714	2		144	711	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0059466-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	306	475	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.549710900508215	6	FACETS	1	0.983	1	1	0.983	1	INDETERMINATE	3	TRUE	3	0.923980208263028	6		475	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0059466-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	218	389	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.923980208263028	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.923980208263028	2		389	231	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387080	31387080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1007955291	NA	P-0059466-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	98	501	0	ENST00000328111.2:c.1705G>A	p.Ala569Thr	p.A569T	ENST00000328111	NM_006892.3	569	Gca/Aca	16/23	0.923980208263028	3	FACETS	0.546	0.488	0.607	0.273	0.244	0.304	SUBCLONAL	1	TRUE	1	0.923980208263028	3		501	568	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035956	47035956	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0059466-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	121	391	0	ENST00000377604.3:c.634A>T	p.Lys212Ter	p.K212*	ENST00000377604	NM_001204468.1	212	Aag/Tag	7/24	0.33165056547631	3	FACETS	0.832	0.771	0.894	0.555	0.514	0.596	INDETERMINATE	2	TRUE	0	0.923980208263028	3		391	230	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584473	189584473	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059466-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	97	376	0	ENST00000264731.3:c.769C>T	p.Gln257Ter	p.Q257*	ENST00000264731	NM_003722.4	257	Cag/Tag	6/14	1	2	FACETS	0.897	0.816	0.98	0.897	0.816	0.98	CLONAL	1	TRUE	1	0.923980208263028	2		376	234	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422184	47422184	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059466-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	70	450	0	ENST00000404338.3:c.252G>C	p.Glu84Asp	p.E84D	ENST00000404338	NM_004491.4	84	gaG/gaC	1/6	0.481675085944434	3	FACETS	0.673	0.591	0.76	0.224	0.197	0.254	INDETERMINATE	1	TRUE	0	0.923980208263028	3		450	329	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045685	26045685	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059466-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	182	589	0	ENST00000540144.1:c.47C>G	p.Ala16Gly	p.A16G	ENST00000540144	NM_003531.2	16	gCt/gGt	1/1	0.862488489507588	6	FACETS	0.976	0.899	1	0.325	0.299	0.352	CLONAL	1	TRUE	3	0.923980208263028	6		589	1150	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690456	33690456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770564755	NA	P-0059466-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	82	496	0	ENST00000308377.4:c.371G>A	p.Arg124His	p.R124H	ENST00000308377	NM_152270.3	124	cGc/cAc	2/5	0.923980208263028	2	FACETS	0.519	0.461	0.58	0.259	0.23	0.29	SUBCLONAL	1	TRUE	0	0.923980208263028	2		496	342	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100603	102100614	+	inframe_deletion	In_Frame_Del	DEL	CTTAATGACATG	CTTAATGACATG	-	novel	NA	P-0059466-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	102	459	0	ENST00000282441.5:c.1447_1458del	p.Leu483_Met486del	p.L483_M486del	ENST00000282441	NM_001130145.2	483	CTTAATGACATG/-	9/9	0.923980208263028	2	FACETS	0.549	0.495	0.606	0.275	0.247	0.303	SUBCLONAL	1	TRUE	0	0.923980208263028	2		459	402	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0059536-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	16	314	4	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.259389967844503	4	FACETS	0.811	0.598	1	0.406	0.299	0.534	CLONAL	1	TRUE	2	0.11	4		318	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0059536-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	23	471	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	1	2	FACETS	1	0.784	1	1	0.784	1	CLONAL	1	TRUE	1	0.11	2		471	415	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs763804037	NA	P-0059536-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	19	470	0	ENST00000304494.5:c.143C>G	p.Pro48Arg	p.P48R	ENST00000304494	NM_000077.4	48	cCg/cGg	1/3	1	2	FACETS	0.996	0.755	1	0.996	0.755	1	CLONAL	1	TRUE	1	0.11	2		470	347	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586236	48586236	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs1555686071	NA	P-0059536-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	10	335	0	ENST00000342988.3:c.905G>A	p.Trp302Ter	p.W302*	ENST00000342988	NM_005359.5	302	tGg/tAg	8/12	1	2	FACETS	0.942	0.638	1	0.942	0.638	1	CLONAL	1	TRUE	1	0.11	2		335	193	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967584	26967584	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059536-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	13	381	0	ENST00000381527.3:c.727A>G	p.Thr243Ala	p.T243A	ENST00000381527	NM_001260.1	243	Act/Gct	7/13	0.104285201524157	0	FACETS	0.859	0.612	1			1	CLONAL	1	TRUE	0	0.11	0		381	245	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0059805-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1297	143	418	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.36125545557907	13	FACETS	0.821	0.746	0.9	0.137	0.124	0.15	CLONAL	2	TRUE	1	0.36125545557907	13		418	1440	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984475	7984475	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059805-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	40	428	0	ENST00000319144.4:c.383T>C	p.Val128Ala	p.V128A	ENST00000319144	NM_001139.2	128	gTc/gCc	3/15	0.282349717865527	3	FACETS	0.572	0.475	0.68	0.286	0.237	0.34	SUBCLONAL	1	TRUE	1	0.36125545557907	3		428	457	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972913	55972913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059805-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	58	378	0	ENST00000263923.4:c.1477G>A	p.Gly493Arg	p.G493R	ENST00000263923	NM_002253.2	493	Gga/Aga	11/30	0.182991346363705	3	FACETS	0.856	0.737	0.985	0.428	0.368	0.493	INDETERMINATE	1	TRUE	1	0.36125545557907	3		378	443	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727513	88727513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374069724	NA	P-0059805-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	20	481	0	ENST00000360948.2:c.266G>A	p.Arg89His	p.R89H	ENST00000360948	NM_001012338.2	89	cGc/cAc	3/19	0.36125545557907	1	FACETS	0.238	0.181	0.304	0.238	0.181	0.304	SUBCLONAL	1	TRUE	0	0.36125545557907	1		481	382	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332807	70332807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059805-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	44	449	1	ENST00000373644.4:c.712G>T	p.Gly238Cys	p.G238C	ENST00000373644	NM_030625.2	238	Ggt/Tgt	2/12	1	2	FACETS	0.557	0.468	0.656	0.557	0.468	0.656	SUBCLONAL	1	TRUE	1	0.36125545557907	2		450	437	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420305	88420305	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059805-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	44	448	0	ENST00000360948.2:c.2381T>C	p.Val794Ala	p.V794A	ENST00000360948	NM_001012338.2	794	gTc/gCc	19/19	0.36125545557907	1	FACETS	0.414	0.347	0.488	0.414	0.347	0.488	SUBCLONAL	1	TRUE	0	0.36125545557907	1		448	482	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923453	9923453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059805-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	54	488	0	ENST00000330684.3:c.1834G>A	p.Val612Met	p.V612M	ENST00000330684	NM_001134407.1	612	Gtg/Atg	9/13	NA	2	FACETS	0.618	0.528	0.716			1	INDETERMINATE	1	TRUE	NA	0.36125545557907	2		488	484	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663748	29663795	+	inframe_deletion	In_Frame_Del	DEL	AGCACGCTACATGCTGATGCTGTCCTTCAACAATTCCCTTGATGTGGC	AGCACGCTACATGCTGATGCTGTCCTTCAACAATTCCCTTGATGTGGC	-	novel	NA	P-0059805-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	61	451	0	ENST00000356175.3:c.6183_6230del	p.Arg2062_Ala2077del	p.R2062_A2077del	ENST00000356175	NM_000267.3	2060	ttAGCACGCTACATGCTGATGCTGTCCTTCAACAATTCCCTTGATGTGGCa/tta	41/57	0.182991346363705	3	FACETS	0.797	0.689	0.915	0.399	0.344	0.458	INDETERMINATE	1	TRUE	1	0.36125545557907	3		451	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0059971-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	70	477	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.21310584682931	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	0	0.21310584682931	1		477	562	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630697	67630697	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs189478486	NA	P-0059971-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	29	389	0	ENST00000272342.5:c.883G>C	p.Gly295Arg	p.G295R	ENST00000272342	NM_019002.3	295	Gga/Cga	5/6	0.21310584682931	3	FACETS	0.521	0.417	0.64	0.261	0.208	0.32	SUBCLONAL	1	TRUE	1	0.21310584682931	3		389	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578464	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060043-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	248	531	0	ENST00000269305.4:c.466del	p.Arg156AlafsTer14	p.R156Afs*14	ENST00000269305	NM_001126112.2	156	Cgc/gc	5/11	0.496906255946552	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.511060310496461	2		531	464	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422254	422254	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1448384274	NA	P-0060043-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	73	344	0	ENST00000399788.2:c.3004C>G	p.Arg1002Gly	p.R1002G	ENST00000399788	NM_001042603.1	1002	Cga/Gga	20/28	1	2	FACETS	0.876	0.773	0.986	0.876	0.773	0.986	CLONAL	1	TRUE	1	0.511060310496461	2		344	326	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437770	49437770	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060043-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	110	571	0	ENST00000301067.7:c.5200del	p.Asp1734ThrfsTer12	p.D1734Tfs*12	ENST00000301067	NM_003482.3	1734	Gac/ac	22/54	1	2	FACETS	0.957	0.865	1	0.957	0.865	1	CLONAL	1	TRUE	1	0.511060310496461	2		571	450	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041151	112041151	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060043-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	115	469	1	ENST00000368678.4:c.104C>A	p.Thr35Asn	p.T35N	ENST00000368678		35	aCc/aAc	3/13	0.457601945846662	3	FACETS	1	0.96	1	0.557	0.504	0.613	CLONAL	1	TRUE	1	0.511060310496461	3		470	507	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812269	212812269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201152419	NA	P-0060672-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	25	298	0	ENST00000342788.4:c.307C>T	p.Arg103Cys	p.R103C	ENST00000342788	NM_005235.2	103	Cgc/Tgc	3/28	0.516755385578928	3	FACETS	0.886	0.709	1	0.443	0.354	0.542	CLONAL	1	TRUE	1	0.559860153333668	3		298	129	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0060672-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	82	249	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.349341245953618	2	FACETS	0.939	0.854	1	0.939	0.854	1	CLONAL	2	TRUE	0	0.559860153333668	2		249	156	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352697	NA	P-0060672-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	122	349	0	ENST00000269305.4:c.587G>A	p.Arg196Gln	p.R196Q	ENST00000269305	NM_001126112.2	196	cGa/cAa	6/11	0.559860153333668	2	FACETS	0.995	0.924	1	0.995	0.924	1	CLONAL	2	TRUE	0	0.559860153333668	2		349	219	SUCCESS
APC	324	MSKCC	GRCh37	5	112173854	112173854	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060672-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	25	338	0	ENST00000257430.4:c.2563G>T	p.Glu855Ter	p.E855*	ENST00000257430	NM_000038.5	855	Gaa/Taa	16/16	0.516755385578928	3	FACETS	0.706	0.561	0.868	0.353	0.28	0.434	SUBCLONAL	1	TRUE	1	0.559860153333668	3		338	162	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876314	35876314	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060672-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	34	269	0	ENST00000303115.3:c.1106G>A	p.Cys369Tyr	p.C369Y	ENST00000303115	NM_002185.3	369	tGc/tAc	8/8	0.516755385578928	3	FACETS	0.733	0.604	0.876	0.367	0.302	0.438	SUBCLONAL	1	TRUE	1	0.559860153333668	3		269	212	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0060804-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	49	366	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.182043013504359	3	FACETS	1	0.937	1	0.6	0.51	0.699	CLONAL	1	FALSE	1	0.253266755190017	3		366	363	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216624	108216626	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs786203976	NA	P-0061332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	21	292	0	ENST00000278616.4:c.8578_8580del	p.Ser2860del	p.S2860del	ENST00000278616	NM_000051.3	2858	aCTTct/act	58/63	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	FALSE	1	0.275386360584058	2		292	107	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123543	108123543	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0061332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	18	236	0	ENST00000278616.4:c.1803-1G>T		p.X601_splice	ENST00000278616	NM_000051.3	601			1	2	FACETS	0.902	0.684	1	0.902	0.684	1	CLONAL	1	FALSE	1	0.275386360584058	2		236	145	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624257	89624258	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0061332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	18	120	0	ENST00000371953.3:c.32_33del	p.Arg11LysfsTer32	p.R11Kfs*32	ENST00000371953	NM_000314.4	11	AGa/a	1/9	1	2	FACETS	0.908	0.731	1	1	0.955	1	CLONAL	4	FALSE	1	0.275386360584058	2		120	36	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870180	155870180	+	stop_lost	Nonstop_Mutation	SNP	C	C	A	novel	NA	P-0061332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	23	279	0	ENST00000368323.3:c.659G>T	p.Ter220LeuextTer24	p.*220Lext*24	ENST00000368323	NM_006912.5	220	tGa/tTa	6/6	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	FALSE	1	0.275386360584058	2		279	113	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	58	317	0				ENST00000310581	NM_198253.2	-/1132			0.3	2	FACETS	0.796	0.689	0.912			1	CLONAL	1	TRUE	NA	0.47	2		317	310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	132	661	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.47	2		661	560	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	34	213	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	1	1	FACETS	0.427	0.351	0.512	0.427	0.351	0.512	SUBCLONAL	1	TRUE	0	0.47	1		213	259	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519920	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	40	530	0	ENST00000397062.3:c.85G>C	p.Asp29His	p.D29H	ENST00000397062	NM_006164.4	29	Gat/Cat	2/5	1	2	FACETS	0.86	0.722	1	0.86	0.722	1	CLONAL	1	TRUE	1	0.47	2		530	198	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884903	134884903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377220159	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	119	353	0	ENST00000398015.3:c.1679C>T	p.Ser560Phe	p.S560F	ENST00000398015	NM_004441.4	560	tCt/tTt	8/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.47	2		353	472	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740479	58740479	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	62	483	0	ENST00000305921.3:c.1384C>T	p.Gln462Ter	p.Q462*	ENST00000305921	NM_003620.3	462	Caa/Taa	6/6	1	2	FACETS	0.783	0.68	0.893	0.783	0.68	0.893	SUBCLONAL	1	TRUE	1	0.47	2		483	337	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	81	636	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.47	2		636	332	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100959	41100959	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	130	520	0	ENST00000373198.4:c.1397A>G	p.Asn466Ser	p.N466S	ENST00000373198	NM_133170.3	466	aAc/aGc	8/32	1	2	FACETS	0.967	0.881	1	0.967	0.881	1	CLONAL	1	TRUE	1	0.47	2		520	572	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645275	67645276	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	140	550	0	ENST00000264010.4:c.544dup	p.Glu182GlyfsTer9	p.E182Gfs*9	ENST00000264010	NM_006565.3	180	-/G	3/12	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.47	2		550	519	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859570	57859570	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1566559716	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	114	620	0	ENST00000228682.2:c.625-1G>A		p.X209_splice	ENST00000228682	NM_005269.2	209			1	2	FACETS	0.928	0.839	1	0.928	0.839	1	CLONAL	1	TRUE	1	0.47	2		620	523	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244595	41244595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555588649	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	49	510	0	ENST00000357654.3:c.2953C>T	p.Pro985Ser	p.P985S	ENST00000357654	NM_007294.3	985	Ccc/Tcc	10/23	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.47	2		510	198	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032291	10032291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	96	504	0	ENST00000330684.3:c.532C>T	p.Pro178Ser	p.P178S	ENST00000330684	NM_001134407.1	178	Cct/Tct	3/13	1	2	FACETS	0.946	0.847	1	0.946	0.847	1	CLONAL	1	TRUE	1	0.47	2		504	432	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222832	36222832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	130	496	0	ENST00000222270.7:c.5461C>T	p.Pro1821Ser	p.P1821S	ENST00000222270	NM_014727.1	1821	Cca/Tca	27/37	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.47	2		496	541	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856098	111856098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	125	522	0	ENST00000341259.2:c.149G>A	p.Arg50Gln	p.R50Q	ENST00000341259	NM_005475.2	50	cGg/cAg	2/8	1	2	FACETS	0.834	0.756	0.915	0.834	0.756	0.915	CLONAL	1	TRUE	1	0.47	2		522	638	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956787	68956787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs934598745	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	21	367	0	ENST00000288368.4:c.905C>T	p.Thr302Met	p.T302M	ENST00000288368	NM_024870.2	302	aCg/aTg	8/40	1	2	FACETS	0.253	0.194	0.322	0.253	0.194	0.322	SUBCLONAL	1	TRUE	1	0.47	2		367	353	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218449	36218449	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs267605436	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	41	461	0	ENST00000222270.7:c.4228C>T	p.Gln1410Ter	p.Q1410*	ENST00000222270	NM_014727.1	1410	Cag/Tag	16/37	1	2	FACETS	0.357	0.297	0.423	0.357	0.297	0.423	SUBCLONAL	1	TRUE	1	0.47	2		461	489	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447443	12447443	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	110	497	0	ENST00000287820.6:c.682G>A	p.Asp228Asn	p.D228N	ENST00000287820	NM_015869.4	228	Gat/Aat	5/7	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.47	2		497	456	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534285	534285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894226	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	107	449	0	ENST00000451590.1:c.38G>A	p.Gly13Asp	p.G13D	ENST00000451590	NM_001130442.1	13	gGt/gAt	2/5	1	2	FACETS	0.856	0.771	0.946	0.856	0.771	0.946	CLONAL	1	TRUE	1	0.47	2		449	532	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874157	151874158	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	52	482	2	ENST00000262189.6:c.8380_8381delinsTT	p.Pro2794Leu	p.P2794L	ENST00000262189	NM_170606.2	2794	CCa/TTa	38/59	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.47	2		484	211	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144378878	144378878	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779785762	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	46	339	0	ENST00000262995.4:c.1631G>A	p.Arg544Gln	p.R544Q	ENST00000262995	NM_207123.2	544	cGa/cAa	7/11	1	2	FACETS	0.833	0.708	0.968	0.833	0.708	0.968	CLONAL	1	TRUE	1	0.47	2		339	235	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30733030	30733030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755070814	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	109	515	0	ENST00000295754.5:c.1643C>T	p.Ser548Leu	p.S548L	ENST00000295754	NM_003242.5	548	tCg/tTg	7/7	1	2	FACETS	0.913	0.824	1	0.913	0.824	1	CLONAL	1	TRUE	1	0.47	2		515	508	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954974	2954975	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	134	565	0	ENST00000396946.4:c.2735_2736delinsAA	p.Arg912Gln	p.R912Q	ENST00000396946	NM_032415.4	912	cGG/cAA	21/25	1	2	FACETS	0.995	0.908	1	0.995	0.908	1	CLONAL	1	TRUE	1	0.47	2		565	573	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413277	139413277	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	104	374	0	ENST00000277541.6:c.866-1G>A		p.X289_splice	ENST00000277541	NM_017617.3	289			1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.47	2		374	427	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29195817	29195818	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	72	483	0	ENST00000240100.2:c.780_781delinsAA	p.Met260_Glu261delinsIleLys	p.M260_E261delinsIK	ENST00000240100	NM_001394.6	260	atGGaa/atAAaa	3/4	1	2	FACETS	0.808	0.71	0.913	0.808	0.71	0.913	CLONAL	1	TRUE	1	0.47	2		483	379	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008555	70008555	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	103	469	0	ENST00000394351.3:c.842T>A	p.Leu281Ter	p.L281*	ENST00000394351	NM_000248.3	281	tTg/tAg	8/9	1	2	FACETS	0.858	0.771	0.949	0.858	0.771	0.949	CLONAL	1	TRUE	1	0.47	2		469	511	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73633706	73633706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	45	355	0	ENST00000377687.4:c.241C>T	p.Pro81Ser	p.P81S	ENST00000377687	NM_001730.3	81	Cct/Tct	1/4	1	2	FACETS	0.48	0.404	0.564	0.48	0.404	0.564	SUBCLONAL	1	TRUE	1	0.47	2		355	399	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216982	2216983	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	127	523	1	ENST00000398665.3:c.2437_2438delinsTT	p.Pro813Phe	p.P813F	ENST00000398665	NM_032482.2	813	CCc/TTc	21/28	1	2	FACETS	0.983	0.894	1	0.983	0.894	1	CLONAL	1	TRUE	1	0.47	2		524	550	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131211	17131211	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	113	548	0	ENST00000285071.4:c.241A>T	p.Met81Leu	p.M81L	ENST00000285071	NM_144997.5	81	Atg/Ttg	4/14	1	2	FACETS	0.87	0.785	0.958	0.87	0.785	0.958	CLONAL	1	TRUE	1	0.47	2		548	553	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047318	77047318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	30	472	0	ENST00000356341.3:c.1226G>A	p.Gly409Glu	p.G409E	ENST00000356341	NM_002576.4	409	gGa/gAa	13/15	1	2	FACETS	0.323	0.26	0.395	0.323	0.26	0.395	SUBCLONAL	1	TRUE	1	0.47	2		472	395	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393350	139393382	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CCCTGTTGTTCTGCATATCTTTGTTAGCCCCGT	CCCTGTTGTTCTGCATATCTTTGTTAGCCCCGT	-	novel	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	114	503	0	ENST00000277541.6:c.6149_6180+1del		p.X2050_splice	ENST00000277541	NM_017617.3	2050		33/34	1	2	FACETS	0.888	0.803	0.978	0.888	0.803	0.978	CLONAL	1	TRUE	1	0.47	2		503	546	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120479898	120479916	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCTCACCTCGCATCTGTA	TCCTCACCTCGCATCTGTA	-	novel	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	106	459	0	ENST00000256646.2:c.3511_3522+7del		p.X1171_splice	ENST00000256646	NM_024408.3	1171		21/34	1	2	FACETS	0.94	0.847	1	0.94	0.847	1	CLONAL	1	TRUE	1	0.47	2		459	480	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347923	89347923	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780866636	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	114	502	0	ENST00000301030.4:c.5027C>T	p.Ser1676Phe	p.S1676F	ENST00000301030	NM_001256183.1	1676	tCc/tTc	9/13	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.47	2		502	481	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608117	28608117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	59	471	0	ENST00000241453.7:c.1849G>A	p.Gly617Arg	p.G617R	ENST00000241453	NM_004119.2	617	Gga/Aga	15/24	0.155081065742107	0	FACETS	0.416	0.36	0.476			1	INDETERMINATE	1	TRUE	0	0.47	0		471	320	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170834729	170834729	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	26	362	0	ENST00000296930.5:c.797C>G	p.Ala266Gly	p.A266G	ENST00000296930	NM_002520.6	266	gCc/gGc	10/11	1	2	FACETS	0.622	0.496	0.762	0.622	0.496	0.762	SUBCLONAL	1	TRUE	1	0.47	2		362	178	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376911	118376911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	38	543	0	ENST00000534358.1:c.10304C>T	p.Thr3435Ile	p.T3435I	ENST00000534358	NM_005933.3	3435	aCt/aTt	27/36	1	2	FACETS	0.281	0.232	0.337	0.281	0.232	0.337	SUBCLONAL	1	TRUE	1	0.47	2		543	575	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022477	31022479	+	frameshift_variant	Frame_Shift_Del	DEL	CAC	CAC	TA	novel	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	159	548	0	ENST00000375687.4:c.1962_1964delinsTA	p.Asp656MetfsTer47	p.D656Mfs*47	ENST00000375687	NM_015338.5	654	gcCACc/gcTAc	13/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.47	2		548	580	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916122	9916122	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1355678094	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	76	439	0	ENST00000330684.3:c.2167G>A	p.Gly723Arg	p.G723R	ENST00000330684	NM_001134407.1	723	Ggg/Agg	10/13	1	2	FACETS	0.84	0.741	0.945	0.84	0.741	0.945	CLONAL	1	TRUE	1	0.47	2		439	385	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518798	176518798	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	133	535	0	ENST00000292408.4:c.716T>A	p.Leu239Gln	p.L239Q	ENST00000292408	NM_213647.1	239	cTa/cAa	6/18	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.47	2		535	509	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124503414	124503414	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	19	337	0	ENST00000357628.3:c.536T>G	p.Phe179Cys	p.F179C	ENST00000357628	NM_015450.2	179	tTt/tGt	8/19	1	2	FACETS	0.298	0.226	0.383	0.298	0.226	0.383	SUBCLONAL	1	TRUE	1	0.47	2		337	271	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961579	54961579	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	65	411	0	ENST00000312783.6:c.53C>T	p.Pro18Leu	p.P18L	ENST00000312783	NM_198436.1	18	cCa/cTa	4/10	1	2	FACETS	0.951	0.832	1	0.951	0.832	1	CLONAL	1	TRUE	1	0.47	2		411	291	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257664	19257664	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	113	584	0	ENST00000162023.5:c.562T>C	p.Ser188Pro	p.S188P	ENST00000162023		188	Tca/Cca	10/13	1	2	FACETS	0.921	0.833	1	0.921	0.833	1	CLONAL	1	TRUE	1	0.47	2		584	522	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120509093	120509093	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	56	482	0	ENST00000256646.2:c.1473T>A	p.Cys491Ter	p.C491*	ENST00000256646	NM_024408.3	491	tgT/tgA	9/34	1	2	FACETS	0.792	0.683	0.909	0.792	0.683	0.909	CLONAL	1	TRUE	1	0.47	2		482	301	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435705	110435705	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	109	505	0	ENST00000375856.3:c.2696C>T	p.Pro899Leu	p.P899L	ENST00000375856	NM_003749.2	899	cCc/cTc	1/2	1	2	FACETS	0.928	0.837	1	0.928	0.837	1	CLONAL	1	TRUE	1	0.47	2		505	500	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062486-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	33	317	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.386401546154037	2		317	155	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820810	36820810	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062486-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	53	486	0	ENST00000373129.3:c.567C>A	p.His189Gln	p.H189Q	ENST00000373129	NM_032017.1	189	caC/caA	6/12	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.386401546154037	2		486	269	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717721	89717721	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062486-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	41	293	0	ENST00000371953.3:c.746T>C	p.Val249Ala	p.V249A	ENST00000371953	NM_000314.4	249	gTg/gCg	7/9	0.386401546154037	1	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	0	0.386401546154037	1		293	158	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410687	63410687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062486-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	64	319	1	ENST00000330258.3:c.2480A>G	p.Glu827Gly	p.E827G	ENST00000330258	NM_152424.3	827	gAg/gGg	2/2	1	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.386401546154037	1		320	208	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670340	134670340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415689583	NA	P-0062812-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	36	398	0	ENST00000398015.3:c.251G>A	p.Arg84His	p.R84H	ENST00000398015	NM_004441.4	84	cGc/cAc	3/16	1	2	FACETS	0.845	0.696	1	0.845	0.696	1	CLONAL	1	TRUE	1	0.242149717406592	2		398	352	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119810	108119810	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062812-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	40	338	0	ENST00000278616.4:c.1216G>T	p.Asp406Tyr	p.D406Y	ENST00000278616	NM_000051.3	406	Gat/Tat	9/63	1	2	FACETS	0.849	0.707	1	0.849	0.707	1	CLONAL	1	TRUE	1	0.242149717406592	2		338	389	SUCCESS
ATM	472	MSKCC	GRCh37	11	108128247	108128247	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0062812-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	19	349	0	ENST00000278616.4:c.2290A>T	p.Lys764Ter	p.K764*	ENST00000278616	NM_000051.3	764	Aaa/Taa	15/63	1	2	FACETS	0.445	0.337	0.572	0.445	0.337	0.572	SUBCLONAL	1	TRUE	1	0.242149717406592	2		349	353	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0062834-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	76	375	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.487	0.428	0.55	0.487	0.428	0.55	SUBCLONAL	1	TRUE	1	0.61	2		375	512	SUCCESS
APC	324	MSKCC	GRCh37	5	112175022	112175022	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062834-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	173	480	0	ENST00000257430.4:c.3734del	p.Lys1245ArgfsTer20	p.K1245Rfs*20	ENST00000257430	NM_000038.5	1244	cAa/ca	16/16	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.61	2		480	565	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266086	41266097	+	inframe_deletion	In_Frame_Del	DEL	AGTCTTACCTGG	AGTCTTACCTGG	-	rs1553630102	NA	P-0062948-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	20	405	0	ENST00000349496.5:c.84_95del	p.Gln28_Asp32delinsHis	p.Q28_D32delinsH	ENST00000349496	NM_001904.3	28	cAGTCTTACCTGGac/cac	3/15	1	2	FACETS	0.173	0.131	0.222	0.173	0.131	0.222	SUBCLONAL	1	TRUE	1	0.52	2		405	445	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519920	NA	P-0063246-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	968	530	0	ENST00000397062.3:c.85G>C	p.Asp29His	p.D29H	ENST00000397062	NM_006164.4	29	Gat/Cat	2/5	0.521281179773142	10	FACETS	0.996	0.974	1			1	CLONAL	8	TRUE	NA	0.521281179773142	10		530	1438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579366	7579366	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs770776262	NA	P-0063246-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	289	575	5	ENST00000269305.4:c.321C>A	p.Tyr107Ter	p.Y107*	ENST00000269305	NM_001126112.2	107	taC/taA	4/11	0.470128764754163	3	FACETS	0.98	0.928	1	0.98	0.928	1	CLONAL	2	TRUE	1	0.521281179773142	3		580	713	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578412	7578412	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519747	NA	P-0063246-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	143	567	3	ENST00000269305.4:c.518T>C	p.Val173Ala	p.V173A	ENST00000269305	NM_001126112.2	173	gTg/gCg	5/11	0.470128764754163	3	FACETS	0.932	0.851	1	0.466	0.425	0.509	CLONAL	1	TRUE	1	0.521281179773142	3		570	742	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951082	48951082	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063246-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	272	274	4	ENST00000267163.4:c.1244del	p.Ile415AsnfsTer2	p.I415Nfs*2	ENST00000267163	NM_000321.2	415	aTa/aa	13/27	0.510250639665555	4	FACETS	0.985	0.944	1	0.985	0.944	1	CLONAL	4	TRUE	0	0.521281179773142	4		278	403	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244192	133244192	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063246-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	142	493	0	ENST00000320574.5:c.2216T>A	p.Val739Glu	p.V739E	ENST00000320574	NM_006231.2	739	gTg/gAg	20/49	0.470128764754163	3	FACETS	1	0.944	1	0.522	0.477	0.569	CLONAL	1	TRUE	1	0.521281179773142	3		493	658	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911664	134911664	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063246-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	137	441	0	ENST00000398015.3:c.2129G>T	p.Arg710Met	p.R710M	ENST00000398015	NM_004441.4	710	aGg/aTg	11/16	0.495788136504002	2	FACETS	1	0.929	1	0.508	0.465	0.553	CLONAL	1	TRUE	0	0.521281179773142	2		441	517	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100562	102100562	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063246-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	106	487	0	ENST00000282441.5:c.1406A>C	p.Glu469Ala	p.E469A	ENST00000282441	NM_001130145.2	469	gAg/gCg	9/9	0.456069861303509	4	FACETS	0.885	0.794	0.981	0.443	0.397	0.491	CLONAL	1	TRUE	2	0.521281179773142	4		487	699	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416656	121416656	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063246-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	105	381	2	ENST00000257555.6:c.85G>T	p.Ala29Ser	p.A29S	ENST00000257555		29	Gca/Tca	1/10	0.470128764754163	3	FACETS	0.902	0.811	0.998	0.451	0.405	0.499	CLONAL	1	TRUE	1	0.521281179773142	3		383	563	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922615	56922615	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063246-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	34	450	0	ENST00000519728.1:c.1485C>G	p.Ser495Arg	p.S495R	ENST00000519728	NM_002350.3	495	agC/agG	13/13	0.495540542118378	3	FACETS	0.271	0.221	0.328	0.136	0.11	0.164	SUBCLONAL	1	TRUE	1	0.521281179773142	3		450	606	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348696	118348696	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063246-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	103	392	0	ENST00000534358.1:c.3349G>T	p.Ala1117Ser	p.A1117S	ENST00000534358	NM_005933.3	1117	Gct/Tct	5/36	0.456069861303509	4	FACETS	0.938	0.841	1	0.469	0.42	0.521	CLONAL	1	TRUE	2	0.521281179773142	4		392	641	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913396	NA	P-0063283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	119	417	1	ENST00000349496.5:c.95A>G	p.Asp32Gly	p.D32G	ENST00000349496	NM_001904.3	32	gAc/gGc	3/15	1	2	FACETS	0.982	0.89	1	0.982	0.89	1	CLONAL	1	TRUE	1	0.425129194913957	2		418	570	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0063283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	45	247	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.425129194913957	2		247	197	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439664	220439664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs992068119	NA	P-0063283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	92	478	0	ENST00000243786.2:c.517C>T	p.Pro173Ser	p.P173S	ENST00000243786	NM_002191.3	173	Ccc/Tcc	2/2	1	2	FACETS	0.801	0.714	0.894	0.801	0.714	0.894	CLONAL	1	TRUE	1	0.425129194913957	2		478	540	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0063318-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	85	439	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.611251609423343	2		439	254	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878116	48878116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063318-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	157	556	0	ENST00000267163.4:c.68C>T	p.Pro23Leu	p.P23L	ENST00000267163	NM_000321.2	23	cCg/cTg	1/27	0.611251609423343	1	FACETS	0.896	0.831	0.963	0.896	0.831	0.963	CLONAL	1	TRUE	0	0.611251609423343	1		556	398	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249012	55249013	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGTTA	novel	NA	P-0063318-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	344	516	0	ENST00000275493.2:c.2310_2311insGGGTTA	p.Asp770_Asn771insGlyLeu	p.D770_N771insGL	ENST00000275493	NM_005228.3	770	-/GGGTTA	20/28	0.611251609423343	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.611251609423343	2		516	563	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759904	63759904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063318-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	72	450	0	ENST00000279873.7:c.557G>A	p.Arg186Gln	p.R186Q	ENST00000279873	NM_032199.2	186	cGg/cAg	4/10	1	2	FACETS	0.44	0.384	0.499	0.44	0.384	0.499	SUBCLONAL	1	TRUE	1	0.611251609423343	2		450	536	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288732	11288732	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063318-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	168	461	0	ENST00000361445.4:c.3023T>C	p.Ile1008Thr	p.I1008T	ENST00000361445	NM_004958.3	1008	aTc/aCc	19/58	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.611251609423343	2		461	499	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944567	32944567	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063318-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	87	329	1	ENST00000380152.3:c.8360G>C	p.Arg2787Pro	p.R2787P	ENST00000380152		2787	cGc/cCc	19/27	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.611251609423343	2		330	282	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574361	41574361	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1333876461	NA	P-0063318-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	142	602	0	ENST00000263253.7:c.6646G>A	p.Gly2216Arg	p.G2216R	ENST00000263253	NM_001429.3	2216	Gga/Aga	31/31	NA	2	FACETS	0.882	0.808	0.958			1	INDETERMINATE	1	TRUE	NA	0.611251609423343	2		602	527	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045118	47045118	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063318-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	247	288	0	ENST00000377604.3:c.2359A>G	p.Asn787Asp	p.N787D	ENST00000377604	NM_001204468.1	787	Aac/Gac	21/24	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.611251609423343	1		288	376	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348681	118348681	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	19	245	0	ENST00000534358.1:c.3335-1G>A		p.X1112_splice	ENST00000534358	NM_005933.3	1112			0.542126899828898	1	FACETS	0.46	0.354	0.581	0.46	0.354	0.581	SUBCLONAL	1	TRUE	0	0.542126899828898	1		245	111	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032080	48032080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752212361	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	48	383	0	ENST00000234420.5:c.3470G>A	p.Gly1157Asp	p.G1157D	ENST00000234420	NM_000179.2	1157	gGt/gAt	6/10	0.541809374796712	1	FACETS	0.782	0.673	0.898	0.782	0.673	0.898	SUBCLONAL	1	TRUE	0	0.542126899828898	1		383	165	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982138	93982138	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	17	361	0	ENST00000369303.4:c.1327C>T	p.Pro443Ser	p.P443S	ENST00000369303	NM_004440.3	443	Ccc/Tcc	6/17	0.542126899828898	1	FACETS	0.204	0.152	0.265	0.204	0.152	0.265	SUBCLONAL	1	TRUE	0	0.542126899828898	1		361	224	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101092	41101092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs724159837	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	16	446	0	ENST00000373198.4:c.1264C>T	p.Leu422Phe	p.L422F	ENST00000373198	NM_133170.3	422	Ctc/Ttc	8/32	1	2	FACETS	0.214	0.158	0.281	0.214	0.158	0.281	SUBCLONAL	1	TRUE	1	0.542126899828898	2		446	276	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115769	8115769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	59	435	0	ENST00000346208.3:c.1115C>T	p.Ser372Phe	p.S372F	ENST00000346208		372	tCc/tTc	6/6	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.542126899828898	2		435	206	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861010	35861010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	13	362	0	ENST00000303115.3:c.139G>A	p.Glu47Lys	p.E47K	ENST00000303115	NM_002185.3	47	Gaa/Aaa	2/8	0.542126899828898	3	FACETS	0.243	0.173	0.328	0.121	0.086	0.164	SUBCLONAL	1	TRUE	1	0.542126899828898	3		362	251	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259288	36259288	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs927005033	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	13	412	0	ENST00000300305.3:c.203C>T	p.Ala68Val	p.A68V	ENST00000300305		68	gCc/gTc	3/8	0.542126899828898	1	FACETS	0.243	0.174	0.326	0.243	0.174	0.326	SUBCLONAL	1	TRUE	0	0.542126899828898	1		412	144	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980608	1980608	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753305456	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	17	452	0	ENST00000382891.5:c.4070G>A	p.Gly1357Asp	p.G1357D	ENST00000382891	NM_133335.3	1357	gGc/gAc	22/22	1	2	FACETS	0.248	0.185	0.323	0.248	0.185	0.323	SUBCLONAL	1	TRUE	1	0.542126899828898	2		452	253	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955217	17955217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	15	378	0	ENST00000458235.1:c.10C>T	p.Pro4Ser	p.P4S	ENST00000458235	NM_000215.3	4	Cca/Tca	2/24	1	2	FACETS	0.243	0.177	0.321	0.243	0.177	0.321	SUBCLONAL	1	TRUE	1	0.542126899828898	2		378	228	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984919	9984919	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	14	299	0	ENST00000330684.3:c.1046C>T	p.Ser349Phe	p.S349F	ENST00000330684	NM_001134407.1	349	tCc/tTc	4/13	0.542126899828898	1	FACETS	0.271	0.197	0.359	0.271	0.197	0.359	SUBCLONAL	1	TRUE	0	0.542126899828898	1		299	139	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993399	72993399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243611387	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	10	417	0	ENST00000268489.5:c.646C>T	p.Pro216Ser	p.P216S	ENST00000268489	NM_006885.3	216	Ccg/Tcg	2/10	0.542126899828898	1	FACETS	0.14	0.094	0.197	0.14	0.094	0.197	SUBCLONAL	1	TRUE	0	0.542126899828898	1		417	192	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866480	56866480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	18	408	0	ENST00000519728.1:c.727C>T	p.Pro243Ser	p.P243S	ENST00000519728	NM_002350.3	243	Ccc/Tcc	8/13	0.541809374796712	1	FACETS	0.234	0.176	0.301	0.234	0.176	0.301	SUBCLONAL	1	TRUE	0	0.542126899828898	1		408	207	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132924	30132924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	22	351	0	ENST00000331968.5:c.677C>T	p.Ala226Val	p.A226V	ENST00000331968	NM_002742.2	226	gCc/gTc	4/18	1	2	FACETS	0.267	0.207	0.337	0.267	0.207	0.337	SUBCLONAL	1	TRUE	1	0.542126899828898	2		351	304	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405923	70405923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	15	376	0	ENST00000373644.4:c.3437C>T	p.Thr1146Ile	p.T1146I	ENST00000373644	NM_030625.2	1146	aCc/aTc	4/12	1	2	FACETS	0.253	0.185	0.334	0.253	0.185	0.334	SUBCLONAL	1	TRUE	1	0.542126899828898	2		376	219	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260152	10260152	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	48	476	1	ENST00000340748.4:c.2515C>T	p.Pro839Ser	p.P839S	ENST00000340748		839	Ccc/Tcc	25/40	1	2	FACETS	0.621	0.529	0.722	0.621	0.529	0.722	SUBCLONAL	1	TRUE	1	0.542126899828898	2		477	285	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829017	128829017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	11	259	0	ENST00000249373.3:c.25G>A	p.Gly9Arg	p.G9R	ENST00000249373	NM_005631.4	9	Ggg/Agg	1/12	0.542126899828898	1	FACETS	0.58	0.412	0.776	0.58	0.412	0.776	SUBCLONAL	1	TRUE	0	0.542126899828898	1		259	51	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487269	56487269	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	179	386	0	ENST00000267101.3:c.1415A>G	p.Lys472Arg	p.K472R	ENST00000267101	NM_001982.3	472	aAg/aGg	12/28	0.541849799638226	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.542126899828898	2		386	320	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36989327	36989327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749986225	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	20	344	0	ENST00000354822.5:c.8C>T	p.Ser3Phe	p.S3F	ENST00000354822	NM_001079668.2	3	tCc/tTc	1/3	1	2	FACETS	0.294	0.225	0.374	0.294	0.225	0.374	SUBCLONAL	1	TRUE	1	0.542126899828898	2		344	251	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523094	176523094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	19	506	0	ENST00000292408.4:c.1858G>A	p.Val620Met	p.V620M	ENST00000292408	NM_213647.1	620	Gtg/Atg	14/18	0.542126899828898	3	FACETS	0.263	0.199	0.338	0.131	0.099	0.169	SUBCLONAL	1	TRUE	1	0.542126899828898	3		506	339	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32890665	32890665	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs81002796	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	14	304	0	ENST00000380152.3:c.67+1G>A		p.X23_splice	ENST00000380152		23			0.542126899828898	3	FACETS	0.257	0.186	0.344	0.129	0.093	0.172	SUBCLONAL	1	TRUE	1	0.542126899828898	3		304	255	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216786	7216786	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs748835899	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	19	434	0	ENST00000380728.2:c.637C>T	p.Pro213Ser	p.P213S	ENST00000380728		213	Cct/Tct	8/11	0.486850314864563	2	FACETS	0.253	0.192	0.325	0.127	0.096	0.163	SUBCLONAL	1	TRUE	0	0.542126899828898	2		434	277	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088742	27088742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747693064	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	13	415	0	ENST00000324856.7:c.2351G>A	p.Gly784Asp	p.G784D	ENST00000324856	NM_006015.4	784	gGc/gAc	7/20	0.542126899828898	1	FACETS	0.162	0.115	0.219	0.162	0.115	0.219	SUBCLONAL	1	TRUE	0	0.542126899828898	1		415	216	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728857	190728857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	35	350	0	ENST00000441310.2:c.2245C>T	p.Pro749Ser	p.P749S	ENST00000441310	NM_000534.4	749	Cca/Tca	10/13	0.541809374796712	1	FACETS	0.668	0.557	0.787	0.668	0.557	0.787	SUBCLONAL	1	TRUE	0	0.542126899828898	1		350	141	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435713	56435713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	12	440	0	ENST00000407977.2:c.1424C>T	p.Ser475Phe	p.S475F	ENST00000407977		475	tCc/tTc	9/10	0.224471920169971	1	FACETS	0.154	0.108	0.21	0.154	0.108	0.21	INDETERMINATE	1	TRUE	0	0.542126899828898	1		440	210	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626410	12626410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	12	461	0	ENST00000251849.4:c.1739C>T	p.Ala580Val	p.A580V	ENST00000251849	NM_002880.3	580	gCa/gTa	16/17	0.541849799638226	2	FACETS	0.191	0.134	0.261	0.095	0.067	0.131	SUBCLONAL	1	TRUE	0	0.542126899828898	2		461	232	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867270	45867270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	41	435	0	ENST00000391945.4:c.923C>T	p.Pro308Leu	p.P308L	ENST00000391945	NM_000400.3	308	cCc/cTc	10/23	1	2	FACETS	0.764	0.644	0.894	0.764	0.644	0.894	SUBCLONAL	1	TRUE	1	0.542126899828898	2		435	198	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999074	100999074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763110021	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	40	463	0	ENST00000325455.5:c.728C>T	p.Ala243Val	p.A243V	ENST00000325455	NM_001202474.3	243	gCt/gTt	1/8	0.542126899828898	1	FACETS	0.854	0.726	0.989	0.854	0.726	0.989	CLONAL	1	TRUE	0	0.542126899828898	1		463	126	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274802	123274829	+	frameshift_variant	Frame_Shift_Del	DEL	GGAAGCTGTAATCTCCTTTTCTCTTCCA	GGAAGCTGTAATCTCCTTTTCTCTTCCA	-	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	60	387	0	ENST00000358487.5:c.1089_1116del	p.Gly364GlnfsTer6	p.G364Qfs*6	ENST00000358487	NM_000141.4	363	ccTGGAAGAGAAAAGGAGATTACAGCTTCC/cc	9/18	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.542126899828898	2		387	215	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968855	15968855	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	51	358	1	ENST00000268712.3:c.4895C>T	p.Ala1632Val	p.A1632V	ENST00000268712	NM_006311.3	1632	gCc/gTc	33/46	0.224471920169971	1	FACETS	0.527	0.452	0.609	0.527	0.452	0.609	INDETERMINATE	1	TRUE	0	0.542126899828898	1		359	260	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295860	1295860	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	14	510	1				ENST00000310581	NM_198253.2	-/1132			0.190847196752389	0	FACETS	0.113	0.081	0.151			1	INDETERMINATE	1	TRUE	0	0.542126899828898	0		511	209	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288987	33288987	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	92	447	0	ENST00000374542.5:c.565del	p.Gln189SerfsTer40	p.Q189Sfs*40	ENST00000374542	NM_001141970.1	189	Cag/ag	3/8	0.542126899828898	1	FACETS	0.79	0.71	0.874	0.79	0.71	0.874	SUBCLONAL	1	TRUE	0	0.542126899828898	1		447	313	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367530	40367530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	13	570	0	ENST00000397332.2:c.31C>T	p.Pro11Ser	p.P11S	ENST00000397332	NM_001033082.2	11	Ccg/Tcg	1/3	0.542126899828898	1	FACETS	0.206	0.147	0.277	0.206	0.147	0.277	SUBCLONAL	1	TRUE	0	0.542126899828898	1		570	170	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422182	47422182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	45	358	0	ENST00000404338.3:c.250G>A	p.Glu84Lys	p.E84K	ENST00000404338	NM_004491.4	84	Gag/Aag	1/6	1	2	FACETS	0.719	0.61	0.837	0.719	0.61	0.837	SUBCLONAL	1	TRUE	1	0.542126899828898	2		358	231	SUCCESS
APC	324	MSKCC	GRCh37	5	112179510	112179510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1580691275	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	42	418	0	ENST00000257430.4:c.8219C>T	p.Pro2740Leu	p.P2740L	ENST00000257430	NM_000038.5	2740	cCa/cTa	16/16	0.542126899828898	3	FACETS	0.727	0.61	0.854	0.363	0.305	0.427	SUBCLONAL	1	TRUE	1	0.542126899828898	3		418	271	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341692	8341692	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	16	347	0	ENST00000356435.5:c.4947+1G>A		p.X1649_splice	ENST00000356435		1649			1	2	FACETS	0.301	0.223	0.394	0.301	0.223	0.394	SUBCLONAL	1	TRUE	1	0.542126899828898	2		347	196	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555246	106555246	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	15	373	0	ENST00000369096.4:c.2363G>A	p.Gly788Glu	p.G788E	ENST00000369096	NM_001198.3	788	gGg/gAg	7/7	0.542126899828898	1	FACETS	0.265	0.195	0.349	0.265	0.195	0.349	SUBCLONAL	1	TRUE	0	0.542126899828898	1		373	152	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357580	89357580	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	18	376	0	ENST00000301030.4:c.238C>T	p.Pro80Ser	p.P80S	ENST00000301030	NM_001256183.1	80	Cct/Tct	5/13	0.542126899828898	1	FACETS	0.308	0.233	0.395	0.308	0.233	0.395	SUBCLONAL	1	TRUE	0	0.542126899828898	1		376	157	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549767	226549767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs78381515	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	12	315	0	ENST00000366794.5:c.2866C>T	p.Pro956Ser	p.P956S	ENST00000366794	NM_001618.3	956	Cct/Tct	22/23	0.542126899828898	1	FACETS	0.288	0.204	0.39	0.288	0.204	0.39	SUBCLONAL	1	TRUE	0	0.542126899828898	1		315	112	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253844	153253844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	42	216	0	ENST00000281708.4:c.889G>A	p.Glu297Lys	p.E297K	ENST00000281708	NM_033632.3	297	Gaa/Aaa	6/12	1	2	FACETS	0.896	0.759	1	0.896	0.759	1	CLONAL	1	TRUE	1	0.542126899828898	2		216	173	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350550	15350550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1314825758	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	15	290	0	ENST00000263377.2:c.3365G>A	p.Ser1122Asn	p.S1122N	ENST00000263377	NM_058243.2	1122	aGc/aAc	16/20	1	2	FACETS	0.301	0.22	0.397	0.301	0.22	0.397	SUBCLONAL	1	TRUE	1	0.542126899828898	2		290	184	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425331	49425331	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778416089	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	13	459	0	ENST00000301067.7:c.13157C>T	p.Thr4386Ile	p.T4386I	ENST00000301067	NM_003482.3	4386	aCc/aTc	39/54	0.541849799638226	2	FACETS	0.201	0.143	0.271	0.1	0.071	0.136	SUBCLONAL	1	TRUE	0	0.542126899828898	2		459	239	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10778386	10778386	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	12	268	0	ENST00000361367.2:c.592+1G>A		p.X198_splice	ENST00000361367	NM_014633.3	198			0.542126899828898	1	FACETS	0.262	0.185	0.356	0.262	0.185	0.356	SUBCLONAL	1	TRUE	0	0.542126899828898	1		268	123	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846060	151846060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	20	405	0	ENST00000262189.6:c.12952G>A	p.Val4318Ile	p.V4318I	ENST00000262189	NM_170606.2	4318	Gtc/Atc	52/59	1	2	FACETS	0.207	0.158	0.265	0.207	0.158	0.265	SUBCLONAL	1	TRUE	1	0.542126899828898	2		405	356	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176684147	176684147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	17	368	0	ENST00000439151.2:c.4961C>T	p.Ser1654Phe	p.S1654F	ENST00000439151	NM_022455.4	1654	tCt/tTt	13/23	0.542126899828898	3	FACETS	0.304	0.227	0.396	0.152	0.113	0.198	SUBCLONAL	1	TRUE	1	0.542126899828898	3		368	262	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983983	15983983	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	26	427	0	ENST00000268712.3:c.3236C>T	p.Pro1079Leu	p.P1079L	ENST00000268712	NM_006311.3	1079	cCc/cTc	24/46	0.224471920169971	1	FACETS	0.246	0.195	0.304	0.246	0.195	0.304	INDETERMINATE	1	TRUE	0	0.542126899828898	1		427	284	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112893838	112893838	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	21	279	0	ENST00000351677.2:c.727G>A	p.Val243Ile	p.V243I	ENST00000351677	NM_002834.3	243	Gtc/Atc	6/16	0.541849799638226	2	FACETS	0.561	0.437	0.703	0.281	0.218	0.352	SUBCLONAL	1	TRUE	0	0.542126899828898	2		279	138	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627720	14627720	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	24	503	0	ENST00000254322.2:c.350G>A	p.Gly117Glu	p.G117E	ENST00000254322	NM_006145.1	117	gGg/gAg	2/3	1	2	FACETS	0.253	0.198	0.316	0.253	0.198	0.316	SUBCLONAL	1	TRUE	1	0.542126899828898	2		503	350	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56792520	56792520	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770597885	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	69	334	0	ENST00000308159.5:c.250G>A	p.Ala84Thr	p.A84T	ENST00000308159	NM_014669.4	84	Gcc/Acc	3/22	0.542126899828898	1	FACETS	0.884	0.783	0.989	0.884	0.783	0.989	CLONAL	1	TRUE	0	0.542126899828898	1		334	210	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770848	59770848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1412270207	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	34	325	0	ENST00000259008.2:c.2518G>A	p.Gly840Arg	p.G840R	ENST00000259008	NM_032043.2	840	Gga/Aga	18/20	0.224471920169971	1	FACETS	0.703	0.586	0.83	0.703	0.586	0.83	INDETERMINATE	1	TRUE	0	0.542126899828898	1		325	130	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543364	65543364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	16	363	0	ENST00000358664.4:c.313G>A	p.Ala105Thr	p.A105T	ENST00000358664	NM_002382.4	105	Gcg/Acg	5/5	1	2	FACETS	0.224	0.165	0.294	0.224	0.165	0.294	SUBCLONAL	1	TRUE	1	0.542126899828898	2		363	264	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254972	16254972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	31	334	0	ENST00000375759.3:c.2237G>A	p.Arg746Lys	p.R746K	ENST00000375759	NM_015001.2	746	aGg/aAg	11/15	0.542126899828898	1	FACETS	0.301	0.244	0.365	0.301	0.244	0.365	SUBCLONAL	1	TRUE	0	0.542126899828898	1		334	277	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352046	70352046	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	13	260	0	ENST00000374080.3:c.4243C>T	p.Pro1415Ser	p.P1415S	ENST00000374080		1415	Cct/Tct	30/45	1	1	FACETS	0.267	0.191	0.358	0.267	0.191	0.358	SUBCLONAL	1	TRUE	0	0.542126899828898	1		260	131	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484765	57484765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	85	396	0	ENST00000371085.3:c.745G>A	p.Ala249Thr	p.A249T	ENST00000371085	NM_000516.4	249	Gcc/Acc	10/13	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.542126899828898	2		396	301	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58701043	58701043	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1021050144	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	18	355	0	ENST00000305921.3:c.634G>A	p.Glu212Lys	p.E212K	ENST00000305921	NM_003620.3	212	Gag/Aag	2/6	0.224471920169971	1	FACETS	0.22	0.166	0.284	0.22	0.166	0.284	INDETERMINATE	1	TRUE	0	0.542126899828898	1		355	220	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613176	52613176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	14	306	0	ENST00000394830.3:c.3352C>T	p.Pro1118Ser	p.P1118S	ENST00000394830	NM_018313.4	1118	Cca/Tca	22/30	0.541809374796712	1	FACETS	0.26	0.188	0.345	0.26	0.188	0.345	SUBCLONAL	1	TRUE	0	0.542126899828898	1		306	145	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714158	43714158	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	21	434	0	ENST00000382044.4:c.3995G>A	p.Ser1332Asn	p.S1332N	ENST00000382044	NM_001141980.1	1332	aGt/aAt	19/28	0.542126899828898	1	FACETS	0.235	0.181	0.298	0.235	0.181	0.298	SUBCLONAL	1	TRUE	0	0.542126899828898	1		434	240	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319363	62319363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	14	447	0	ENST00000360203.5:c.1555G>A	p.Gly519Ser	p.G519S	ENST00000360203	NM_001283009.1	519	Ggc/Agc	18/35	1	2	FACETS	0.194	0.14	0.26	0.194	0.14	0.26	SUBCLONAL	1	TRUE	1	0.542126899828898	2		447	266	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961334	15961334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775984069	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	14	399	0	ENST00000268712.3:c.6055C>T	p.Pro2019Ser	p.P2019S	ENST00000268712	NM_006311.3	2019	Cca/Tca	39/46	0.224471920169971	1	FACETS	0.169	0.122	0.226	0.169	0.122	0.226	INDETERMINATE	1	TRUE	0	0.542126899828898	1		399	223	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588802	52588802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	23	379	0	ENST00000394830.3:c.4226G>A	p.Gly1409Glu	p.G1409E	ENST00000394830	NM_018313.4	1409	gGg/gAg	27/30	0.541809374796712	1	FACETS	0.29	0.227	0.363	0.29	0.227	0.363	SUBCLONAL	1	TRUE	0	0.542126899828898	1		379	213	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053158	180053158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	15	502	0	ENST00000261937.6:c.1211C>T	p.Ser404Phe	p.S404F	ENST00000261937	NM_182925.4	404	tCc/tTc	9/30	1	2	FACETS	0.232	0.169	0.306	0.232	0.169	0.306	SUBCLONAL	1	TRUE	1	0.542126899828898	2		502	239	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485695	40485695	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368454926	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	16	375	0	ENST00000264657.5:c.1045G>A	p.Val349Ile	p.V349I	ENST00000264657	NM_139276.2	349	Gtc/Atc	10/24	0.224471920169971	1	FACETS	0.154	0.114	0.203	0.154	0.114	0.203	INDETERMINATE	1	TRUE	0	0.542126899828898	1		375	279	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041657	42041657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	17	409	0	ENST00000219905.7:c.5852G>A	p.Gly1951Glu	p.G1951E	ENST00000219905	NM_001164273.1	1951	gGa/gAa	17/24	0.542126899828898	1	FACETS	0.291	0.218	0.376	0.291	0.218	0.376	SUBCLONAL	1	TRUE	0	0.542126899828898	1		409	157	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971189	13971189	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1159668213	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	67	409	0	ENST00000405192.2:c.740G>A	p.Ser247Asn	p.S247N	ENST00000405192	NM_001163147.1	247	aGc/aAc	8/12	1	2	FACETS	0.861	0.756	0.973	0.861	0.756	0.973	CLONAL	1	TRUE	1	0.542126899828898	2		409	287	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524719	103524719	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771139049	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	13	344	0	ENST00000355739.4:c.2850G>A	p.Trp950Ter	p.W950*	ENST00000355739	NM_000123.3	950	tgG/tgA	13/15	0.541809374796712	1	FACETS	0.185	0.132	0.249	0.185	0.132	0.249	SUBCLONAL	1	TRUE	0	0.542126899828898	1		344	189	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807994	1807994	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	19	577	0	ENST00000260795.2:c.1970C>T	p.Pro657Leu	p.P657L	ENST00000260795		657	cCc/cTc	14/17	1	2	FACETS	0.316	0.24	0.404	0.316	0.24	0.404	SUBCLONAL	1	TRUE	1	0.542126899828898	2		577	222	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16021341	16021341	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	18	336	0	ENST00000268712.3:c.1916G>A	p.Gly639Asp	p.G639D	ENST00000268712	NM_006311.3	639	gGt/gAt	18/46	0.224471920169971	1	FACETS	0.266	0.201	0.342	0.266	0.201	0.342	INDETERMINATE	1	TRUE	0	0.542126899828898	1		336	182	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212442	5212442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	16	433	0	ENST00000357368.4:c.4675G>A	p.Gly1559Ser	p.G1559S	ENST00000357368	NM_002850.3	1559	Ggc/Agc	31/38	1	2	FACETS	0.253	0.187	0.332	0.253	0.187	0.332	SUBCLONAL	1	TRUE	1	0.542126899828898	2		433	233	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10800417	10800417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	35	404	0	ENST00000361367.2:c.3287C>T	p.Pro1096Leu	p.P1096L	ENST00000361367	NM_014633.3	1096	cCc/cTc	25/25	0.542126899828898	1	FACETS	0.426	0.352	0.508	0.426	0.352	0.508	SUBCLONAL	1	TRUE	0	0.542126899828898	1		404	221	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912985	32912985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555283809	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	55	389	0	ENST00000380152.3:c.4493G>A	p.Gly1498Asp	p.G1498D	ENST00000380152		1498	gGt/gAt	11/27	0.542126899828898	3	FACETS	1	0.918	1	0.544	0.47	0.623	CLONAL	1	TRUE	1	0.542126899828898	3		389	237	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528095	103528095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	31	329	0	ENST00000355739.4:c.3403G>A	p.Glu1135Lys	p.E1135K	ENST00000355739	NM_000123.3	1135	Gaa/Aaa	15/15	0.541809374796712	1	FACETS	0.361	0.293	0.436	0.361	0.293	0.436	SUBCLONAL	1	TRUE	0	0.542126899828898	1		329	231	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037164	71037164	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	17	427	0	ENST00000318789.4:c.1127C>T	p.Pro376Leu	p.P376L	ENST00000318789	NM_032682.5	376	cCc/cTc	14/21	0.541809374796712	1	FACETS	0.155	0.115	0.202	0.155	0.115	0.202	SUBCLONAL	1	TRUE	0	0.542126899828898	1		427	295	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084080	47084080	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	55	434	0	ENST00000409792.3:c.7209del	p.Lys2404ArgfsTer7	p.K2404Rfs*7	ENST00000409792	NM_014159.6	2403	ggG/gg	17/21	0.541809374796712	1	FACETS	0.831	0.724	0.944	0.831	0.724	0.944	CLONAL	1	TRUE	0	0.542126899828898	1		434	178	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619193	1619193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	13	517	0	ENST00000344749.5:c.1367C>T	p.Thr456Ile	p.T456I	ENST00000344749	NM_001136139.2	456	aCc/aTc	16/19	1	2	FACETS	0.185	0.132	0.251	0.185	0.132	0.251	SUBCLONAL	1	TRUE	1	0.542126899828898	2		517	259	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756620	756620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	15	399	0	ENST00000314574.4:c.208C>T	p.Pro70Ser	p.P70S	ENST00000314574	NM_005433.3	70	Cct/Tct	2/12	1	2	FACETS	0.249	0.182	0.33	0.249	0.182	0.33	SUBCLONAL	1	TRUE	1	0.542126899828898	2		399	222	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317072	11317072	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1266943208	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	12	417	0	ENST00000361445.4:c.422C>T	p.Thr141Ile	p.T141I	ENST00000361445	NM_004958.3	141	aCc/aTc	4/58	0.542126899828898	1	FACETS	0.17	0.119	0.232	0.17	0.119	0.232	SUBCLONAL	1	TRUE	0	0.542126899828898	1		417	190	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451278	70451278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	25	442	0	ENST00000373644.4:c.6118C>T	p.His2040Tyr	p.H2040Y	ENST00000373644	NM_030625.2	2040	Cat/Tat	12/12	1	2	FACETS	0.279	0.22	0.348	0.279	0.22	0.348	SUBCLONAL	1	TRUE	1	0.542126899828898	2		442	330	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248408	212248408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367568427	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	88	415	0	ENST00000342788.4:c.3859G>A	p.Glu1287Lys	p.E1287K	ENST00000342788	NM_005235.2	1287	Gag/Aag	28/28	0.541809374796712	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.542126899828898	1		415	217	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909686	76909686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	13	126	0	ENST00000373344.5:c.4219G>A	p.Ala1407Thr	p.A1407T	ENST00000373344	NM_000489.3	1407	Gca/Aca	14/35	1	1	FACETS	0.376	0.271	0.5	0.376	0.271	0.5	SUBCLONAL	1	TRUE	0	0.542126899828898	1		126	93	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942207	71942207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	19	385	0	ENST00000298229.2:c.1471G>A	p.Glu491Lys	p.E491K	ENST00000298229	NM_001567.3	491	Gag/Aag	12/28	0.542126899828898	1	FACETS	0.219	0.166	0.281	0.219	0.166	0.281	SUBCLONAL	1	TRUE	0	0.542126899828898	1		385	233	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497242	149497242	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	15	365	0	ENST00000261799.4:c.3076C>T	p.Pro1026Ser	p.P1026S	ENST00000261799	NM_002609.3	1026	Cct/Tct	22/23	0.542126899828898	3	FACETS	0.234	0.171	0.311	0.117	0.085	0.156	SUBCLONAL	1	TRUE	1	0.542126899828898	3		365	300	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108251	8108251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148715809	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	30	397	0	ENST00000585124.1:c.973C>T	p.Pro325Ser	p.P325S	ENST00000585124	NM_004217.3	325	Cct/Tct	9/9	0.486850314864563	2	FACETS	0.302	0.243	0.368	0.151	0.121	0.184	SUBCLONAL	1	TRUE	0	0.542126899828898	2		397	367	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182511	99182511	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	23	358	0	ENST00000074304.5:c.2314G>A	p.Val772Ile	p.V772I	ENST00000074304	NM_001134224.1	772	Gtc/Atc	22/26	0.541809374796712	1	FACETS	0.305	0.239	0.38	0.305	0.239	0.38	SUBCLONAL	1	TRUE	0	0.542126899828898	1		358	203	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33680980	33680980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140112516	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	13	365	0	ENST00000308377.4:c.1297C>T	p.Pro433Ser	p.P433S	ENST00000308377	NM_152270.3	433	Cct/Tct	4/5	0.224471920169971	1	FACETS	0.181	0.129	0.244	0.181	0.129	0.244	INDETERMINATE	1	TRUE	0	0.542126899828898	1		365	193	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46275845	46275845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	17	359	0	ENST00000371998.3:c.3281C>T	p.Ala1094Val	p.A1094V	ENST00000371998		1094	gCt/gTt	18/23	1	2	FACETS	0.318	0.238	0.413	0.318	0.238	0.413	SUBCLONAL	1	TRUE	1	0.542126899828898	2		359	197	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620045	21620045	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	23	450	0	ENST00000382592.4:c.121C>T	p.Pro41Ser	p.P41S	ENST00000382592	NM_014572.2	41	Cca/Tca	2/8	0.542126899828898	3	FACETS	0.249	0.194	0.314	0.125	0.096	0.157	SUBCLONAL	1	TRUE	1	0.542126899828898	3		450	433	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2086836	2086836	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	44	394	0	ENST00000349721.2:c.2534G>A	p.Trp845Ter	p.W845*	ENST00000349721	NM_003070.3	845	tGg/tAg	18/34	1	2	FACETS	0.812	0.689	0.944	0.812	0.689	0.944	CLONAL	1	TRUE	1	0.542126899828898	2		394	200	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884499	151884499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1457412767	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	17	339	0	ENST00000262189.6:c.4856C>T	p.Ala1619Val	p.A1619V	ENST00000262189	NM_170606.2	1619	gCt/gTt	33/59	1	2	FACETS	0.32	0.239	0.415	0.32	0.239	0.415	SUBCLONAL	1	TRUE	1	0.542126899828898	2		339	196	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659783	88659783	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	13	232	0	ENST00000372037.3:c.431-1G>A		p.X144_splice	ENST00000372037	NM_004329.2	144			1	2	FACETS	0.393	0.282	0.526	0.393	0.282	0.526	SUBCLONAL	1	TRUE	1	0.542126899828898	2		232	122	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349692	70349692	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	69	226	0	ENST00000374080.3:c.3854G>A	p.Ser1285Asn	p.S1285N	ENST00000374080		1285	aGc/aAc	27/45	1	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.542126899828898	1		226	138	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936729	78936729	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	25	416	0	ENST00000306801.3:c.3811G>A	p.Gly1271Ser	p.G1271S	ENST00000306801	NM_020761.2	1271	Ggc/Agc	33/34	0.224471920169971	1	FACETS	0.294	0.232	0.364	0.294	0.232	0.364	INDETERMINATE	1	TRUE	0	0.542126899828898	1		416	229	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953453	32953453	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs81002812	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	23	387	0	ENST00000380152.3:c.8755-1G>A		p.X2919_splice	ENST00000380152		2919			0.542126899828898	3	FACETS	0.394	0.307	0.493	0.197	0.153	0.247	SUBCLONAL	1	TRUE	1	0.542126899828898	3		387	274	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295073	1295073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	16	420	0	ENST00000310581.5:c.32G>A	p.Arg11His	p.R11H	ENST00000310581	NM_198253.2	11	cGc/cAc	1/16	0.190847196752389	0	FACETS	0.233	0.174	0.302			1	INDETERMINATE	1	TRUE	0	0.542126899828898	0		420	116	SUCCESS
BLM	641	MSKCC	GRCh37	15	91328273	91328273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	14	366	0	ENST00000355112.3:c.2785G>A	p.Glu929Lys	p.E929K	ENST00000355112	NM_000057.2	929	Gaa/Aaa	14/22	0.542126899828898	1	FACETS	0.19	0.137	0.254	0.19	0.137	0.254	SUBCLONAL	1	TRUE	0	0.542126899828898	1		366	198	SUCCESS
APC	324	MSKCC	GRCh37	5	112176488	112176488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1441448668	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	34	357	0	ENST00000257430.4:c.5197C>T	p.Pro1733Ser	p.P1733S	ENST00000257430	NM_000038.5	1733	Ccc/Tcc	16/16	0.542126899828898	3	FACETS	0.745	0.614	0.89	0.373	0.307	0.445	SUBCLONAL	1	TRUE	1	0.542126899828898	3		357	214	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438364	110438364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	23	236	0	ENST00000375856.3:c.37G>A	p.Ala13Thr	p.A13T	ENST00000375856	NM_003749.2	13	Gcg/Acg	1/2	0.541809374796712	1	FACETS	0.631	0.502	0.773	0.631	0.502	0.773	SUBCLONAL	1	TRUE	0	0.542126899828898	1		236	98	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95595836	95595836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	13	268	0	ENST00000393063.1:c.707C>T	p.Thr236Ile	p.T236I	ENST00000393063	NM_030621.3	236	aCt/aTt	7/28	1	2	FACETS	0.243	0.174	0.328	0.243	0.174	0.328	SUBCLONAL	1	TRUE	1	0.542126899828898	2		268	197	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114736	108114736	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	51	317	0	ENST00000278616.4:c.553G>A	p.Val185Ile	p.V185I	ENST00000278616	NM_000051.3	185	Gtt/Att	6/63	0.542126899828898	1	FACETS	0.868	0.753	0.989	0.868	0.753	0.989	CLONAL	1	TRUE	0	0.542126899828898	1		317	158	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935735	15935735	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	16	372	0	ENST00000268712.3:c.7198C>T	p.Pro2400Ser	p.P2400S	ENST00000268712	NM_006311.3	2400	Ccg/Tcg	46/46	0.224471920169971	1	FACETS	0.146	0.107	0.192	0.146	0.107	0.192	INDETERMINATE	1	TRUE	0	0.542126899828898	1		372	295	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2111871	2111871	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	24	350	0	ENST00000219476.3:c.1120-1G>A		p.X374_splice	ENST00000219476	NM_000548.3	374			0.542126899828898	1	FACETS	0.386	0.305	0.478	0.386	0.305	0.478	SUBCLONAL	1	TRUE	0	0.542126899828898	1		350	167	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423743	47423743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	11	408	0	ENST00000404338.3:c.1811G>A	p.Gly604Asp	p.G604D	ENST00000404338	NM_004491.4	604	gGc/gAc	1/6	1	2	FACETS	0.192	0.132	0.267	0.192	0.132	0.267	SUBCLONAL	1	TRUE	1	0.542126899828898	2		408	211	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987070	36987070	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	16	373	0	ENST00000354822.5:c.619G>A	p.Glu207Lys	p.E207K	ENST00000354822	NM_001079668.2	207	Gag/Aag	3/3	1	2	FACETS	0.356	0.264	0.464	0.356	0.264	0.464	SUBCLONAL	1	TRUE	1	0.542126899828898	2		373	166	SUCCESS
REL	5966	MSKCC	GRCh37	2	61144099	61144099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	21	291	0	ENST00000295025.8:c.482G>A	p.Gly161Asp	p.G161D	ENST00000295025	NM_002908.2	161	gGt/gAt	5/11	0.541809374796712	1	FACETS	0.392	0.305	0.492	0.392	0.305	0.492	SUBCLONAL	1	TRUE	0	0.542126899828898	1		291	144	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434470	110434470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761038860	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	52	402	0	ENST00000375856.3:c.3931C>T	p.Pro1311Ser	p.P1311S	ENST00000375856	NM_003749.2	1311	Ccc/Tcc	1/2	0.541809374796712	1	FACETS	0.804	0.696	0.917	0.804	0.696	0.917	CLONAL	1	TRUE	0	0.542126899828898	1		402	174	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437250	220437250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349744536	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	21	436	0	ENST00000243786.2:c.154G>A	p.Asp52Asn	p.D52N	ENST00000243786	NM_002191.3	52	Gac/Aac	1/2	0.541809374796712	1	FACETS	0.317	0.246	0.4	0.317	0.246	0.4	SUBCLONAL	1	TRUE	0	0.542126899828898	1		436	178	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518092	103518092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	32	419	0	ENST00000355739.4:c.2030C>T	p.Pro677Leu	p.P677L	ENST00000355739	NM_000123.3	677	cCc/cTc	9/15	0.541809374796712	1	FACETS	0.388	0.317	0.467	0.388	0.317	0.467	SUBCLONAL	1	TRUE	0	0.542126899828898	1		419	222	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741635	145741635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	20	461	0	ENST00000428558.2:c.868G>A	p.Gly290Arg	p.G290R	ENST00000428558	NM_004260.3	290	Ggg/Agg	5/22	0.541809374796712	1	FACETS	0.34	0.262	0.43	0.34	0.262	0.43	SUBCLONAL	1	TRUE	0	0.542126899828898	1		461	158	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197481	27197481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	51	369	0	ENST00000380036.4:c.1793C>T	p.Thr598Ile	p.T598I	ENST00000380036	NM_000459.3	598	aCt/aTt	12/23	1	2	FACETS	0.694	0.595	0.802	0.694	0.595	0.802	SUBCLONAL	1	TRUE	1	0.542126899828898	2		369	271	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206783	102206783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	21	335	0	ENST00000263464.3:c.1411G>A	p.Ala471Thr	p.A471T	ENST00000263464	NM_001165.4	471	Gcc/Acc	7/9	0.542126899828898	1	FACETS	0.367	0.285	0.461	0.367	0.285	0.461	SUBCLONAL	1	TRUE	0	0.542126899828898	1		335	154	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31015988	31015988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	24	393	0	ENST00000375687.4:c.310G>A	p.Asp104Asn	p.D104N	ENST00000375687	NM_015338.5	104	Gac/Aac	5/13	1	2	FACETS	0.243	0.19	0.303	0.243	0.19	0.303	SUBCLONAL	1	TRUE	1	0.542126899828898	2		393	365	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222323	2222323	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	10	438	0	ENST00000398665.3:c.3155G>A	p.Gly1052Asp	p.G1052D	ENST00000398665	NM_032482.2	1052	gGt/gAt	24/28	1	2	FACETS	0.192	0.13	0.27	0.192	0.13	0.27	SUBCLONAL	1	TRUE	1	0.542126899828898	2		438	192	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828528	72828528	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	30	416	0	ENST00000268489.5:c.8053G>A	p.Val2685Ile	p.V2685I	ENST00000268489	NM_006885.3	2685	Gta/Ata	9/10	0.542126899828898	1	FACETS	0.427	0.347	0.516	0.427	0.347	0.516	SUBCLONAL	1	TRUE	0	0.542126899828898	1		416	189	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2110364	2110364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	34	376	0	ENST00000349721.2:c.3403C>T	p.Leu1135Phe	p.L1135F	ENST00000349721	NM_003070.3	1135	Ctt/Ttt	24/34	1	2	FACETS	0.434	0.356	0.521	0.434	0.356	0.521	SUBCLONAL	1	TRUE	1	0.542126899828898	2		376	289	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313032	30313032	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	15	402	0	ENST00000262643.3:c.835G>A	p.Ala279Thr	p.A279T	ENST00000262643	NM_001238.2	279	Gca/Aca	9/12	1	2	FACETS	0.256	0.187	0.339	0.256	0.187	0.339	SUBCLONAL	1	TRUE	1	0.542126899828898	2		402	216	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119220	3119220	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	14	472	0	ENST00000078429.4:c.752G>A	p.Ser251Asn	p.S251N	ENST00000078429	NM_002067.2	251	aGc/aAc	6/7	1	2	FACETS	0.207	0.149	0.276	0.207	0.149	0.276	SUBCLONAL	1	TRUE	1	0.542126899828898	2		472	250	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310466	65310466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	16	483	0	ENST00000342505.4:c.2222G>A	p.Gly741Asp	p.G741D	ENST00000342505	NM_002227.2	741	gGc/gAc	16/25	0.542126899828898	1	FACETS	0.218	0.162	0.286	0.218	0.162	0.286	SUBCLONAL	1	TRUE	0	0.542126899828898	1		483	197	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932198	39932198	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747433153	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	13	193	0	ENST00000378444.4:c.2401G>A	p.Asp801Asn	p.D801N	ENST00000378444	NM_001123385.1	801	Gac/Aac	4/15	1	1	FACETS	0.324	0.233	0.432	0.324	0.233	0.432	SUBCLONAL	1	TRUE	0	0.542126899828898	1		193	108	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61305161	61305161	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	30	478	0	ENST00000341074.5:c.965G>A	p.Gly322Asp	p.G322D	ENST00000341074	NM_002974.2	322	gGt/gAt	8/8	1	2	FACETS	0.358	0.289	0.436	0.358	0.289	0.436	SUBCLONAL	1	TRUE	1	0.542126899828898	2		478	309	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077559	30077559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781488145	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	19	386	0	ENST00000338641.4:c.1706G>A	p.Gly569Asp	p.G569D	ENST00000338641	NM_000268.3	569	gGt/gAt	15/16	0.542126899828898	1	FACETS	0.341	0.26	0.433	0.341	0.26	0.433	SUBCLONAL	1	TRUE	0	0.542126899828898	1		386	150	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973940	55973940	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1228182220	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	18	416	0	ENST00000263923.4:c.1376A>G	p.Tyr459Cys	p.Y459C	ENST00000263923	NM_002253.2	459	tAt/tGt	10/30	1	2	FACETS	0.241	0.181	0.311	0.241	0.181	0.311	SUBCLONAL	1	TRUE	1	0.542126899828898	2		416	276	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	360038	360038	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	10	421	0	ENST00000262320.3:c.1051C>T	p.Gln351Ter	p.Q351*	ENST00000262320	NM_003502.3	351	Cag/Tag	4/11	0.542126899828898	1	FACETS	0.147	0.099	0.207	0.147	0.099	0.207	SUBCLONAL	1	TRUE	0	0.542126899828898	1		421	183	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460377	149460377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	24	370	0	ENST00000286301.3:c.260C>T	p.Pro87Leu	p.P87L	ENST00000286301	NM_005211.3	87	cCt/cTt	3/22	0.542126899828898	3	FACETS	0.361	0.283	0.45	0.18	0.141	0.225	SUBCLONAL	1	TRUE	1	0.542126899828898	3		370	312	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778885	9778885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	22	475	0	ENST00000377346.4:c.1154C>T	p.Pro385Leu	p.P385L	ENST00000377346	NM_005026.3	385	cCc/cTc	9/24	0.542126899828898	1	FACETS	0.275	0.214	0.346	0.275	0.214	0.346	SUBCLONAL	1	TRUE	0	0.542126899828898	1		475	215	SUCCESS
APC	324	MSKCC	GRCh37	5	112178183	112178183	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	21	405	0	ENST00000257430.4:c.6892G>A	p.Ala2298Thr	p.A2298T	ENST00000257430	NM_000038.5	2298	Gca/Aca	16/16	0.542126899828898	3	FACETS	0.303	0.233	0.385	0.151	0.116	0.193	SUBCLONAL	1	TRUE	1	0.542126899828898	3		405	325	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867284	68867284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063734-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	14	383	0	ENST00000261769.5:c.2531G>A	p.Ser844Asn	p.S844N	ENST00000261769	NM_004360.3	844	aGt/aAt	16/16	0.542126899828898	1	FACETS	0.197	0.142	0.263	0.197	0.142	0.263	SUBCLONAL	1	TRUE	0	0.542126899828898	1		383	191	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470559	25470559	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs761839006	NA	P-0063940-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	234	390	0	ENST00000264709.3:c.915G>A	p.Trp305Ter	p.W305*	ENST00000264709	NM_175629.2	305	tgG/tgA	8/23	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	1	0.37	2		390	531	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465962	69465962	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs377271027	NA	P-0064179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	157	595	0	ENST00000227507.2:c.800A>G	p.Asp267Gly	p.D267G	ENST00000227507	NM_053056.2	267	gAc/gGc	5/5	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.652036214638726	2		595	351	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948520	71948520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777553838	NA	P-0064179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	171	652	1	ENST00000298229.2:c.3232C>T	p.Arg1078Trp	p.R1078W	ENST00000298229	NM_001567.3	1078	Cgg/Tgg	26/28	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.652036214638726	2		653	374	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122592	108122592	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs2227924	NA	P-0064179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	154	492	0	ENST00000278616.4:c.1636C>G	p.Leu546Val	p.L546V	ENST00000278616	NM_000051.3	546	Ctg/Gtg	11/63	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.652036214638726	2		492	357	SUCCESS
ATM	472	MSKCC	GRCh37	11	108138045	108138045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3218673	NA	P-0064179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	133	388	0	ENST00000278616.4:c.2614C>T	p.Pro872Ser	p.P872S	ENST00000278616	NM_000051.3	872	Cct/Tct	17/63	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.652036214638726	2		388	287	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050906	49050906	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	105	493	0	ENST00000267163.4:c.2590G>T	p.Glu864Ter	p.E864*	ENST00000267163	NM_000321.2	864	Gaa/Taa	25/27	0.652036214638726	1	FACETS	0.743	0.676	0.813	0.743	0.676	0.813	SUBCLONAL	1	FALSE	0	0.652036214638726	1		493	292	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0064179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	104	395	0	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.652036214638726	3	FACETS	1	0.969	1	0.393	0.355	0.432	CLONAL	1	FALSE	0	0.652036214638726	3		395	359	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416194	29416194	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs765866043	NA	P-0064179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	108	605	0	ENST00000389048.3:c.4759C>T	p.Gln1587Ter	p.Q1587*	ENST00000389048	NM_004304.4	1587	Cag/Tag	29/29	1	2	FACETS	0.828	0.749	0.91	0.828	0.749	0.91	CLONAL	1	FALSE	1	0.652036214638726	2		605	400	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503853	149503853	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	131	519	0	ENST00000261799.4:c.1983C>A	p.His661Gln	p.H661Q	ENST00000261799	NM_002609.3	661	caC/caA	14/23	0.652036214638726	1	FACETS	0.854	0.787	0.923	0.854	0.787	0.923	CLONAL	1	FALSE	0	0.652036214638726	1		519	317	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523334	176523334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769459268	NA	P-0064179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	231	629	1	ENST00000292408.4:c.1991G>A	p.Arg664Gln	p.R664Q	ENST00000292408	NM_213647.1	664	cGg/cAg	15/18	1	2	FACETS	0.82	0.776	0.864	1	0.994	1	CLONAL	2	FALSE	1	0.652036214638726	2		630	432	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100023	157100024	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGA	rs747790383	NA	P-0064179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	62	629	0	ENST00000346085.5:c.983_985dup	p.Gly328dup	p.G328dup	ENST00000346085	NM_020732.3	328	-/GGA	1/20	1	2	FACETS	0.743	0.649	0.843	0.743	0.649	0.843	SUBCLONAL	1	FALSE	1	0.652036214638726	2		629	256	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981395	70981395	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0064179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	97	477	2	ENST00000276594.2:c.700+1G>A		p.X234_splice	ENST00000276594	NM_024504.3	234			1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	FALSE	1	0.652036214638726	2		479	294	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0064274-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	34	270	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.196370106407353	3	FACETS	1	0.928	1			1	CLONAL	1	TRUE	NA	0.19629141041013	3		270	296	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0064274-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	27	529	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	0.7	0.557	0.864	0.7	0.557	0.864	SUBCLONAL	1	TRUE	1	0.19629141041013	2		529	393	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0064471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	158	855	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	1	2	FACETS	0.967	0.891	1	0.967	0.891	1	CLONAL	1	TRUE	1	0.569060298745067	2		855	574	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445101	89445101	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs370552845	NA	P-0064471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	161	874	0	ENST00000336596.2:c.1421A>G	p.Tyr474Cys	p.Y474C	ENST00000336596	NM_005233.5	474	tAc/tGc	6/17	0.270580386574067	1	FACETS	0.707	0.651	0.763	0.707	0.651	0.763	INDETERMINATE	1	TRUE	0	0.569060298745067	1		874	573	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441425	52441425	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	270	1360	0	ENST00000460680.1:c.427del	p.Ser143AlafsTer44	p.S143Afs*44	ENST00000460680	NM_004656.3	143	Agc/gc	6/17	0.569060298745067	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.569060298745067	1		1360	609	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064599-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	21	317	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.331	0.254	0.421	0.331	0.254	0.421	SUBCLONAL	1	TRUE	1	0.312380740237582	2		317	406	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88651892	88651892	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1589764265	NA	P-0064599-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	29	342	0	ENST00000372037.3:c.239G>T	p.Gly80Val	p.G80V	ENST00000372037	NM_004329.2	80	gGa/gTa	5/13	0.181065291327926	3	FACETS	0.574	0.461	0.703	0.287	0.23	0.352	INDETERMINATE	1	TRUE	1	0.312380740237582	3		342	374	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417160	417160	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064599-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	45	525	0	ENST00000399788.2:c.3390C>G	p.Phe1130Leu	p.F1130L	ENST00000399788	NM_001042603.1	1130	ttC/ttG	23/28	1	2	FACETS	0.567	0.476	0.667	0.567	0.476	0.667	SUBCLONAL	1	TRUE	1	0.312380740237582	2		525	508	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209274	133209274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs181570274	NA	P-0064599-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	110	578	0	ENST00000320574.5:c.6112G>A	p.Glu2038Lys	p.E2038K	ENST00000320574	NM_006231.2	2038	Gag/Aag	44/49	NA	2	FACETS	1	0.962	1			1	INDETERMINATE	1	TRUE	NA	0.312380740237582	2		578	617	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047527	49047527	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587778850	NA	P-0064599-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	66	354	0	ENST00000267163.4:c.2520+1G>A		p.X840_splice	ENST00000267163	NM_000321.2	840			0.241466588506602	2	FACETS	1	0.947	1	0.584	0.509	0.663	CLONAL	1	TRUE	0	0.312380740237582	2		354	362	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66777418	66777418	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064599-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	45	536	0	ENST00000307102.5:c.784C>G	p.Pro262Ala	p.P262A	ENST00000307102	NM_002755.3	262	Ccc/Gcc	7/11	0.118100563112982	4	FACETS	0.483	0.404	0.57	0.241	0.202	0.285	INDETERMINATE	1	TRUE	2	0.312380740237582	4		536	783	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573991	7573991	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567542019	NA	P-0064599-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	104	496	0	ENST00000269305.4:c.1036G>T	p.Glu346Ter	p.E346*	ENST00000269305	NM_001126112.2	346	Gag/Tag	10/11	0.171727158155644	2	FACETS	1	0.979	1	0.684	0.615	0.756	INDETERMINATE	1	TRUE	0	0.312380740237582	2		496	487	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808880	1808880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755526507	NA	P-0064599-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	64	607	0	ENST00000260795.2:c.2312C>T	p.Ser771Phe	p.S771F	ENST00000260795		771	tCc/tTc	17/17	0.312380740237582	1	FACETS	0.619	0.536	0.708	0.619	0.536	0.708	SUBCLONAL	1	TRUE	0	0.312380740237582	1		607	559	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637208	176637208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064599-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	54	596	0	ENST00000439151.2:c.1808C>T	p.Ser603Phe	p.S603F	ENST00000439151	NM_022455.4	603	tCt/tTt	5/23	0.233223896782406	2	FACETS	0.559	0.477	0.65	0.28	0.238	0.325	SUBCLONAL	1	TRUE	0	0.312380740237582	2		596	618	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675671	30675671	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064599-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	33	526	0	ENST00000376406.3:c.2685G>C	p.Glu895Asp	p.E895D	ENST00000376406	NM_014641.2	895	gaG/gaC	8/15	0.134477934593404	3	FACETS	0.392	0.318	0.476	0.131	0.106	0.159	INDETERMINATE	1	TRUE	0	0.312380740237582	3		526	623	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673000	30673000	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064599-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	32	0	0	ENST00000376406.3:c.3960G>C	p.Lys1320Asn	p.K1320N	ENST00000376406	NM_014641.2	1320	aaG/aaC	10/15	0.134477934593404	3	FACETS	0.302	0.244	0.368	0.101	0.081	0.123	INDETERMINATE	1	TRUE	0	0.312380740237582	3		0	784	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180498	38180498	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064599-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	21	0	0	ENST00000396334.3:c.346C>A	p.Leu116Met	p.L116M	ENST00000396334	NM_002468.4	116	Ctg/Atg	1/5	0.181065291327926	3	FACETS	0.276	0.211	0.351	0.138	0.105	0.176	INDETERMINATE	1	TRUE	1	0.312380740237582	3		0	564	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681186	86681186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064716-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	13	322	0	ENST00000274376.6:c.2827C>T	p.Leu943Phe	p.L943F	ENST00000274376	NM_002890.2	943	Ctt/Ttt	22/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		322	117	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042185	42042186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0064716-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	16	541	0	ENST00000219905.7:c.6381_6382dup	p.Ser2128LysfsTer52	p.S2128Kfs*52	ENST00000219905	NM_001164273.1	2127	tca/tcAAa	17/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		541	125	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957037	1957037	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064716-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	26	477	0	ENST00000382891.5:c.2488A>T	p.Asn830Tyr	p.N830Y	ENST00000382891	NM_133335.3	830	Aac/Tac	13/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		477	187	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691896	30691897	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTTCATGTGTTCC	novel	NA	P-0065009-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	34	448	0	ENST00000295754.5:c.399_411dup	p.Cys138LeufsTer6	p.C138Lfs*6	ENST00000295754	NM_003242.5	133	ttc/ttCTTCATGTGTTCCc	3/7	0.244820854324027	1	FACETS	0.58	0.474	0.7	0.58	0.474	0.7	SUBCLONAL	1	TRUE	0	0.244820854324027	1		448	420	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0065029-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	17	375	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.712	0.531	0.929	0.712	0.531	0.929	CLONAL	1	TRUE	1	0.14	2		375	341	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065029-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	33	359	0	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	1	2	FACETS	0.871	0.708	1	0.871	0.708	1	CLONAL	1	TRUE	1	0.14	2		359	541	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352387	143352387	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065029-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	21	275	0	ENST00000262992.4:c.26C>T	p.Ser9Leu	p.S9L	ENST00000262992	NM_001101669.1	9	tCa/tTa	2/24	1	2	FACETS	0.765	0.588	0.972	0.765	0.588	0.972	CLONAL	1	TRUE	1	0.14	2		275	392	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0065101-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	38	314	4	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.194205748387748	5	FACETS	0.987	0.821	1	0.987	0.821	1	CLONAL	2	FALSE	3	0.194205748387748	5		318	256	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105745	27105745	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065101-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	85	425	0	ENST00000324856.7:c.5356G>T	p.Glu1786Ter	p.E1786*	ENST00000324856	NM_006015.4	1786	Gag/Tag	20/20	0.176415286532139	3	FACETS	0.99	0.878	1	0.99	0.878	1	CLONAL	2	FALSE	1	0.194205748387748	3		425	485	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944160	71944160	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201836862	NA	P-0065101-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	79	449	0	ENST00000298229.2:c.1993C>T	p.Arg665Trp	p.R665W	ENST00000298229	NM_001567.3	665	Cgg/Tgg	17/28	0.194205748387748	4	FACETS	0.975	0.86	1	0.975	0.86	1	CLONAL	2	FALSE	2	0.194205748387748	4		449	498	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047135	77047135	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065101-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	75	327	1	ENST00000356341.3:c.1409T>C	p.Leu470Pro	p.L470P	ENST00000356341	NM_002576.4	470	cTg/cCg	13/15	0.194205748387748	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	FALSE	2	0.194205748387748	4		328	383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540654	NA	P-0065101-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	96	412	0	ENST00000269305.4:c.329G>A	p.Arg110His	p.R110H	ENST00000269305	NM_001126112.2	110	cGt/cAt	4/11	0.189743284214194	4	FACETS	1	0.97	1			1	CLONAL	2	FALSE	NA	0.194205748387748	4		412	479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579400	7579400	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065101-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	101	429	0	ENST00000269305.4:c.287del	p.Ser96LeufsTer27	p.S96Lfs*27	ENST00000269305	NM_001126112.2	96	tCt/tt	4/11	0.189743284214194	4	FACETS	1	0.97	1			1	CLONAL	2	FALSE	NA	0.194205748387748	4		429	507	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0065101-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	62	342	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.179033309578128	2	FACETS	0.91	0.79	1	0.91	0.79	1	CLONAL	2	FALSE	0	0.194205748387748	2		342	351	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573270	55573270	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065101-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	18	263	0	ENST00000288135.5:c.932G>T	p.Gly311Val	p.G311V	ENST00000288135	NM_000222.2	311	gGa/gTa	6/21	1	2	FACETS	0.922	0.697	1	0.922	0.697	1	CLONAL	1	FALSE	1	0.194205748387748	2		263	201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577123	7577123	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876660333	NA	P-0065221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	327	360	0	ENST00000269305.4:c.815T>A	p.Val272Glu	p.V272E	ENST00000269305	NM_001126112.2	272	gTg/gAg	8/11	0.538290744422458	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	0	0.539019809549861	3		360	505	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729843	41729843	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	84	424	0	ENST00000242208.4:c.686G>T	p.Arg229Leu	p.R229L	ENST00000242208	NM_002192.2	229	cGg/cTg	3/3	0.51223467451795	4	FACETS	0.854	0.755	0.958	0.427	0.377	0.479	CLONAL	1	TRUE	2	0.539019809549861	4		424	562	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627628	14627628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	216	596	0	ENST00000254322.2:c.442C>T	p.Arg148Cys	p.R148C	ENST00000254322	NM_006145.1	148	Cgc/Tgc	2/3	0.456195911539118	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.539019809549861	4		596	544	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658713	3658713	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	96	479	0	ENST00000294008.3:c.253C>T	p.Gln85Ter	p.Q85*	ENST00000294008	NM_032444.2	85	Cag/Tag	2/15	0.538290744422458	2	FACETS	0.854	0.766	0.947	0.427	0.383	0.474	CLONAL	1	TRUE	0	0.539019809549861	2		479	417	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371916	55371916	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	61	590	0	ENST00000297316.4:c.606C>A	p.His202Gln	p.H202Q	ENST00000297316	NM_022454.3	202	caC/caA	2/2	0.50640396683942	3	FACETS	0.945	0.822	1	0.473	0.411	0.539	CLONAL	1	TRUE	1	0.539019809549861	3		590	304	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549199	226549199	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	81	310	0	ENST00000366794.5:c.3007C>A	p.Leu1003Met	p.L1003M	ENST00000366794	NM_001618.3	1003	Ctg/Atg	23/23	0.51223467451795	4	FACETS	1	0.908	1	0.515	0.455	0.578	CLONAL	1	TRUE	2	0.539019809549861	4		310	449	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246493817	246493817	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0065221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	71	327	0	ENST00000388985.4:c.359C>G	p.Ser120Ter	p.S120*	ENST00000388985		120	tCa/tGa	4/12	0.51223467451795	4	FACETS	0.876	0.767	0.993	0.438	0.383	0.497	CLONAL	1	TRUE	2	0.539019809549861	4		327	463	SUCCESS
APC	324	MSKCC	GRCh37	5	112102045	112102081	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGTATTGAAGATGAAGCTATGGCTTCTTCTGGACA	GAAGTATTGAAGATGAAGCTATGGCTTCTTCTGGACA	-	novel	NA	P-0065221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	128	179	0	ENST00000257430.4:c.160_196del	p.Ser54LeufsTer4	p.S54Lfs*4	ENST00000257430	NM_000038.5	53	gGAAGTATTGAAGATGAAGCTATGGCTTCTTCTGGACAg/gg	3/16	0.538290744422458	2	FACETS	0.935	0.866	1	0.935	0.866	1	CLONAL	2	TRUE	0	0.539019809549861	2		179	254	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0065339-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	29	321	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.51	0.411	0.622	0.51	0.411	0.622	SUBCLONAL	1	FALSE	1	0.445613654282887	2		321	255	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	229	789	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.283877904002668	2	FACETS	0.693	0.646	0.742	0.347	0.323	0.371	INDETERMINATE	1	TRUE	0	0.647584310831131	2		790	1020	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	38	177	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.567	0.473	0.67	0.567	0.473	0.67	SUBCLONAL	1	TRUE	1	0.647584310831131	2		178	207	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	100	342	4	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.916	0.827	1	0.916	0.827	1	CLONAL	1	TRUE	1	0.647584310831131	2		346	337	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928078	178928080	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs587776933	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	54	196	0	ENST00000263967.3:c.1359_1361del	p.Glu453del	p.E453del	ENST00000263967	NM_006218.2	452	ttAGAa/tta	8/21	1	2	FACETS	0.719	0.621	0.823	0.719	0.621	0.823	SUBCLONAL	1	TRUE	1	0.647584310831131	2		196	232	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	172	490	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.962	0.891	1	0.962	0.891	1	CLONAL	1	TRUE	1	0.647584310831131	2		490	552	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760024	133760024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	211	535	1	ENST00000318560.5:c.2352del	p.Arg785GlyfsTer3	p.R785Gfs*3	ENST00000318560	NM_005157.4	783	Ccc/cc	11/11	1	2	FACETS	0.993	0.927	1	0.993	0.927	1	CLONAL	1	TRUE	1	0.647584310831131	2		536	656	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	272	642	5	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.94	0.884	0.997	0.94	0.884	0.997	CLONAL	1	TRUE	1	0.647584310831131	2		647	894	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	90	257	0	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.647584310831131	2		257	260	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624877	9624877	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1359466621	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	220	525	0	ENST00000353224.5:c.100G>A	p.Gly34Ser	p.G34S	ENST00000353224	NM_177990.2	34	Ggc/Agc	3/10	1	2	FACETS	0.962	0.899	1	0.962	0.899	1	CLONAL	1	TRUE	1	0.647584310831131	2		525	706	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717769	89717770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	50	190	0	ENST00000371953.3:c.800dup	p.Asp268GlyfsTer30	p.D268Gfs*30	ENST00000371953	NM_000314.4	265	cta/ctAa	7/9	1	2	FACETS	0.83	0.715	0.952	0.83	0.715	0.952	CLONAL	1	TRUE	1	0.647584310831131	2		190	186	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	217	525	0	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	0.987	0.922	1	0.987	0.922	1	CLONAL	1	TRUE	1	0.647584310831131	2		525	679	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519886	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	115	483	0	ENST00000349496.5:c.97T>C	p.Ser33Pro	p.S33P	ENST00000349496	NM_001904.3	33	Tct/Cct	3/15	1	2	FACETS	0.575	0.519	0.634	0.575	0.519	0.634	SUBCLONAL	1	TRUE	1	0.647584310831131	2		483	618	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917490	178917490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	37	171	0	ENST00000263967.3:c.365G>A	p.Gly122Asp	p.G122D	ENST00000263967	NM_006218.2	122	gGc/gAc	3/21	1	2	FACETS	0.728	0.609	0.856	0.728	0.609	0.856	SUBCLONAL	1	TRUE	1	0.647584310831131	2		171	157	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436026	56436026	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771831816	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	188	808	1	ENST00000407977.2:c.1111C>T	p.Arg371Ter	p.R371*	ENST00000407977		371	Cga/Tga	9/10	0.283877904002668	2	FACETS	0.572	0.528	0.618	0.286	0.264	0.309	INDETERMINATE	1	TRUE	0	0.647584310831131	2		809	1015	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797777	42797777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778206	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	301	691	0	ENST00000575354.2:c.3829C>T	p.Arg1277Cys	p.R1277C	ENST00000575354	NM_015125.3	1277	Cgc/Tgc	16/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.647584310831131	2		691	918	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275669	41275669	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764576683	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	237	483	0	ENST00000349496.5:c.1564G>A	p.Ala522Thr	p.A522T	ENST00000349496	NM_001904.3	522	Gca/Aca	10/15	1	2	FACETS	0.997	0.935	1	0.997	0.935	1	CLONAL	1	TRUE	1	0.647584310831131	2		483	734	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248285	59248285	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	152	726	1	ENST00000371222.2:c.458del	p.Gly153AlafsTer29	p.G153Afs*29	ENST00000371222	NM_002228.3	153	gGc/gc	1/1	1	2	FACETS	0.611	0.56	0.665	0.611	0.56	0.665	SUBCLONAL	1	TRUE	1	0.647584310831131	2		727	768	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717719	89717720	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs780264945	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	87	257	0	ENST00000371953.3:c.750_751del	p.Cys250TrpfsTer2	p.C250Wfs*2	ENST00000371953	NM_000314.4	248	ccTGtg/cctg	7/9	1	2	FACETS	0.949	0.851	1	0.949	0.851	1	CLONAL	1	TRUE	1	0.647584310831131	2		257	283	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670324	134670324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775406650	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	111	535	1	ENST00000398015.3:c.235C>T	p.Arg79Trp	p.R79W	ENST00000398015	NM_004441.4	79	Cgg/Tgg	3/16	1	2	FACETS	0.45	0.404	0.498	0.45	0.404	0.498	SUBCLONAL	1	TRUE	1	0.647584310831131	2		536	762	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023715	27023716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	200	624	1	ENST00000324856.7:c.827dup	p.Gly277ArgfsTer123	p.G277Rfs*123	ENST00000324856	NM_006015.4	274	atg/atGg	1/20	1	2	FACETS	0.848	0.789	0.91	0.848	0.789	0.91	CLONAL	1	TRUE	1	0.647584310831131	2		625	728	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867268	68867268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780121	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	95	539	0	ENST00000261769.5:c.2515G>A	p.Gly839Ser	p.G839S	ENST00000261769	NM_004360.3	839	Ggt/Agt	16/16	1	2	FACETS	0.37	0.329	0.414	0.37	0.329	0.414	SUBCLONAL	1	TRUE	1	0.647584310831131	2		539	792	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523008	25523009	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	rs769876640	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	155	586	0	ENST00000264709.3:c.176dup	p.Val60GlyfsTer5	p.V60Gfs*5	ENST00000264709	NM_175629.2	59	ccg/ccCg	3/23	1	2	FACETS	0.574	0.526	0.625	0.574	0.526	0.625	SUBCLONAL	1	TRUE	1	0.647584310831131	2		586	834	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178136	56178139	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	novel	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	46	481	0	ENST00000399503.3:c.3110_3113del	p.Lys1037ThrfsTer44	p.K1037Tfs*44	ENST00000399503	NM_005921.1	1037	AAAGac/ac	14/20	1	2	FACETS	0.274	0.23	0.322	0.274	0.23	0.322	SUBCLONAL	1	TRUE	1	0.647584310831131	2		481	519	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2039776	2039777	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCAG	rs113070757	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	130	653	18	ENST00000349721.2:c.702_707dup	p.Gln237_Gln238dup	p.Q237_Q238dup	ENST00000349721	NM_003070.3	237	-/CAGCAG	4/34	1	2	FACETS	0.441	0.399	0.484	0.441	0.399	0.484	SUBCLONAL	1	TRUE	1	0.647584310831131	2		671	911	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307283	65307283	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	61	461	0	ENST00000342505.4:c.2405A>G	p.Lys802Arg	p.K802R	ENST00000342505	NM_002227.2	802	aAa/aGa	18/25	1	2	FACETS	0.368	0.318	0.423	0.368	0.318	0.423	SUBCLONAL	1	TRUE	1	0.647584310831131	2		461	512	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94209512	94209512	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	159	126	0	ENST00000323929.3:c.602T>C	p.Leu201Ser	p.L201S	ENST00000323929	NM_005591.3	201	tTg/tCg	7/20	0.383623682889972	3	FACETS	0.903	0.853	0.951	0.903	0.853	0.951	INDETERMINATE	3	TRUE	0	0.647584310831131	3		126	240	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120785317	120785317	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	270	632	0	ENST00000257552.2:c.791C>A	p.Ala264Asp	p.A264D	ENST00000257552	NM_002442.3	264	gCc/gAc	12/15	1	2	FACETS	0.996	0.938	1	0.996	0.938	1	CLONAL	1	TRUE	1	0.647584310831131	2		632	837	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434873	110434873	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	115	708	0	ENST00000375856.3:c.3528del	p.Val1177TrpfsTer82	p.V1177Wfs*82	ENST00000375856	NM_003749.2	1176	tcC/tc	1/2	0.647584310831131	2	FACETS	0.375	0.337	0.416	0.188	0.168	0.208	SUBCLONAL	1	TRUE	0	0.647584310831131	2		708	946	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383748	15383748	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	265	698	0	ENST00000263377.2:c.163A>G	p.Lys55Glu	p.K55E	ENST00000263377	NM_058243.2	55	Aag/Gag	2/20	1	2	FACETS	0.961	0.903	1	0.961	0.903	1	CLONAL	1	TRUE	1	0.647584310831131	2		698	852	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29444420	29444420	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	116	633	1	ENST00000544604.2:c.956G>A	p.Cys319Tyr	p.C319Y	ENST00000544604	NM_001206998.1	319	tGc/tAc	7/9	0.377887016981847	1	FACETS	0.32	0.289	0.354	0.32	0.289	0.354	INDETERMINATE	1	TRUE	0	0.647584310831131	1		634	756	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035101	37035101	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs63750822	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	246	576	0	ENST00000231790.2:c.67del	p.Glu23LysfsTer13	p.E23Kfs*13	ENST00000231790	NM_000249.3	21	gcG/gc	1/19	1	2	FACETS	0.984	0.923	1	0.984	0.923	1	CLONAL	1	TRUE	1	0.647584310831131	2		576	772	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144359709	144359709	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55997904	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	175	412	0	ENST00000262995.4:c.1151G>A	p.Arg384His	p.R384H	ENST00000262995	NM_207123.2	384	cGt/cAt	4/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.647584310831131	2		412	479	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202341	138202341	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	233	632	0	ENST00000237289.4:c.2262del	p.Glu755LysfsTer61	p.E755Kfs*61	ENST00000237289	NM_001270507.1	753	gCc/gc	9/9	1	2	FACETS	0.842	0.787	0.898	0.842	0.787	0.898	CLONAL	1	TRUE	1	0.647584310831131	2		632	855	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285914	38285916	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	rs138489552	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	138	494	10	ENST00000425967.3:c.495_497del	p.Asp166del	p.D166del	ENST00000425967	NM_001174067.1	165	gaTGAc/gac	5/19	1	2	FACETS	0.87	0.797	0.945	0.87	0.797	0.945	CLONAL	1	TRUE	1	0.647584310831131	2		504	490	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352313	70352313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	93	585	1	ENST00000374080.3:c.4340C>T	p.Ala1447Val	p.A1447V	ENST00000374080		1447	gCt/gTt	31/45	0.468498323210772	1	FACETS	0.308	0.274	0.344	0.308	0.274	0.344	SUBCLONAL	1	TRUE	0	0.647584310831131	1		586	631	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053022	180053023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750808726	NA	P-0065588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	42	456	2	ENST00000261937.6:c.1267dup	p.Gln423ProfsTer4	p.Q423Pfs*4	ENST00000261937	NM_182925.4	423	cag/cCag	10/30	1	2	FACETS	0.902	0.758	1	0.902	0.758	1	CLONAL	1	TRUE	1	0.339851059588173	2		458	274	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016647	12016648	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0065588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	46	395	0	ENST00000353533.5:c.783_784del	p.Asp263CysfsTer4	p.D263Cfs*4	ENST00000353533	NM_003010.3	261	acAAga/acga	7/11	0.339851059588173	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.339851059588173	1		395	183	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0065652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	193	477	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.291305591113263	2	FACETS	0.909	0.845	0.976	0.909	0.845	0.976	CLONAL	2	TRUE	0	0.310750400746548	2		477	683	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235962	133235962	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	118	506	0	ENST00000320574.5:c.3194G>C	p.Gly1065Ala	p.G1065A	ENST00000320574	NM_006231.2	1065	gGa/gCa	26/49	0.303585476050508	3	FACETS	0.977	0.881	1	0.489	0.44	0.54	CLONAL	1	TRUE	1	0.310750400746548	3		506	898	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0065679-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	77	333	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.306908316604157	1	FACETS	0.946	0.837	1	0.946	0.837	1	CLONAL	1	TRUE	0	0.378293909937818	1		333	349	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508761	29508761	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065679-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	68	313	1	ENST00000356175.3:c.688G>T	p.Glu230Ter	p.E230*	ENST00000356175	NM_000267.3	230	Gaa/Taa	7/57	0.378293909937818	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.378293909937818	1		314	247	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056141	26056141	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065679-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	112	418	0	ENST00000343677.2:c.516G>C	p.Lys172Asn	p.K172N	ENST00000343677	NM_005319.3	172	aaG/aaC	1/1	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.378293909937818	2		418	585	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245421	41245421	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397508939	NA	P-0065679-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	238	439	0	ENST00000357654.3:c.2127del	p.Phe709LeufsTer27	p.F709Lfs*27	ENST00000357654	NM_007294.3	709	ttT/tt	10/23	0.235865192365121	3	FACETS	0.927	0.874	0.981			1	CLONAL	3	TRUE	NA	0.378293909937818	3		439	538	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594075	55594075	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1560418178	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	105	419	0	ENST00000288135.5:c.1861G>A	p.Ala621Thr	p.A621T	ENST00000288135	NM_000222.2	621	Gct/Act	12/21	1	2	FACETS	0.993	0.892	1	0.993	0.892	1	CLONAL	1	TRUE	1	0.35	2		419	604	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	12	525	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.121	0.084	0.166	0.121	0.084	0.166	SUBCLONAL	1	TRUE	1	0.35	2		527	568	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	77	372	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.35	2		372	425	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679887	33679887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200734680	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	103	589	0	ENST00000308377.4:c.2194C>T	p.Arg732Cys	p.R732C	ENST00000308377	NM_152270.3	732	Cgc/Tgc	5/5	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.35	2		589	573	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412637	63412637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779222316	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	79	511	0	ENST00000330258.3:c.530G>A	p.Arg177His	p.R177H	ENST00000330258	NM_152424.3	177	cGc/cAc	2/2	1	2	FACETS	0.91	0.803	1	0.91	0.803	1	CLONAL	1	TRUE	1	0.35	2		511	496	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778765	9778765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	44	511	0	ENST00000377346.4:c.1034C>T	p.Ala345Val	p.A345V	ENST00000377346	NM_005026.3	345	gCc/gTc	9/24	1	2	FACETS	0.495	0.415	0.584	0.495	0.415	0.584	SUBCLONAL	1	TRUE	1	0.35	2		511	508	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780196	9780196	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28730674	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	104	614	0	ENST00000377346.4:c.1366A>G	p.Thr456Ala	p.T456A	ENST00000377346	NM_005026.3	456	Acg/Gcg	11/24	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.35	2		614	543	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784052	9784052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	78	496	0	ENST00000377346.4:c.2620G>A	p.Glu874Lys	p.E874K	ENST00000377346	NM_005026.3	874	Gag/Aag	21/24	1	2	FACETS	0.993	0.876	1	0.993	0.876	1	CLONAL	1	TRUE	1	0.35	2		496	449	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298557	11298557	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	91	598	0	ENST00000361445.4:c.1904A>G	p.His635Arg	p.H635R	ENST00000361445	NM_004958.3	635	cAc/cGc	12/58	1	2	FACETS	0.917	0.816	1	0.917	0.816	1	CLONAL	1	TRUE	1	0.35	2		598	567	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259759	16259759	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	116	591	0	ENST00000375759.3:c.7024C>T	p.Arg2342Ter	p.R2342*	ENST00000375759	NM_015001.2	2342	Cga/Tga	11/15	1	2	FACETS	0.94	0.848	1	0.94	0.848	1	CLONAL	1	TRUE	1	0.35	2		591	705	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22405002	22405002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	11	83	0	ENST00000344548.3:c.31G>A	p.Asp11Asn	p.D11N	ENST00000344548	NM_001039802.1	11	Gat/Aat	3/7	1	2	FACETS	0.849	0.596	1	0.849	0.596	1	CLONAL	1	TRUE	1	0.35	2		83	74	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480612	120480612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61752485	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	88	448	0	ENST00000256646.2:c.3205C>T	p.Arg1069Trp	p.R1069W	ENST00000256646	NM_024408.3	1069	Cgg/Tgg	20/34	1	2	FACETS	0.921	0.818	1	0.921	0.818	1	CLONAL	1	TRUE	1	0.35	2		448	546	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150936128	150936128	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764341148	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	90	565	0	ENST00000271640.5:c.3580C>T	p.Arg1194Cys	p.R1194C	ENST00000271640	NM_001145415.1	1194	Cgt/Tgt	20/22	1	2	FACETS	0.853	0.758	0.954	0.853	0.758	0.954	CLONAL	1	TRUE	1	0.35	2		565	603	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725055	162725055	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	91	490	0	ENST00000367921.3:c.527T>C	p.Val176Ala	p.V176A	ENST00000367921	NM_006182.2	176	gTg/gCg	6/18	1	2	FACETS	0.84	0.747	0.939	0.84	0.747	0.939	CLONAL	1	TRUE	1	0.35	2		490	619	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163297296	163297296	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1205244475	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	56	407	0	ENST00000271452.3:c.142A>G	p.Ile48Val	p.I48V	ENST00000271452	NM_145697.2	48	Atc/Gtc	3/14	1	2	FACETS	0.856	0.736	0.985	0.856	0.736	0.985	CLONAL	1	TRUE	1	0.35	2		407	374	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981297	201981297	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs756079277	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	92	582	0	ENST00000359651.3:c.376C>T	p.Arg126Ter	p.R126*	ENST00000359651		126	Cga/Tga	2/8	1	2	FACETS	0.968	0.863	1	0.968	0.863	1	CLONAL	1	TRUE	1	0.35	2		582	543	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649568	206649568	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1211870723	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	77	613	0	ENST00000367120.3:c.403G>A	p.Asp135Asn	p.D135N	ENST00000367120	NM_014002.3	135	Gac/Aac	6/22	1	2	FACETS	0.765	0.673	0.865	0.765	0.673	0.865	SUBCLONAL	1	TRUE	1	0.35	2		613	575	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658601	206658601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879953097	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	85	594	0	ENST00000367120.3:c.1574G>A	p.Arg525Gln	p.R525Q	ENST00000367120	NM_014002.3	525	cGg/cAg	15/22	1	2	FACETS	0.835	0.739	0.937	0.835	0.739	0.937	CLONAL	1	TRUE	1	0.35	2		594	582	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851963	63851963	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779966636	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	102	571	1	ENST00000279873.7:c.2741C>T	p.Pro914Leu	p.P914L	ENST00000279873	NM_032199.2	914	cCg/cTg	10/10	1	2	FACETS	0.988	0.886	1	0.988	0.886	1	CLONAL	1	TRUE	1	0.35	2		572	590	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405958	70405958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370887665	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	87	555	0	ENST00000373644.4:c.3472C>T	p.Arg1158Trp	p.R1158W	ENST00000373644	NM_030625.2	1158	Cgg/Tgg	4/12	1	2	FACETS	0.841	0.746	0.943	0.841	0.746	0.943	CLONAL	1	TRUE	1	0.35	2		555	591	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653803	89653803	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	36	284	0	ENST00000371953.3:c.101C>A	p.Ala34Asp	p.A34D	ENST00000371953	NM_000314.4	34	gCt/gAt	2/9	1	2	FACETS	0.709	0.585	0.847	0.709	0.585	0.847	SUBCLONAL	1	TRUE	1	0.35	2		284	290	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717712	89717712	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	72	369	0	ENST00000371953.3:c.737C>A	p.Pro246Gln	p.P246Q	ENST00000371953	NM_000314.4	246	cCg/cAg	7/9	1	2	FACETS	0.957	0.839	1	0.957	0.839	1	CLONAL	1	TRUE	1	0.35	2		369	430	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720870	89720870	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1554825652	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	35	153	0	ENST00000371953.3:c.1021T>G	p.Phe341Val	p.F341V	ENST00000371953	NM_000314.4	341	Ttt/Gtt	8/9	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.35	2		153	188	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104359244	104359244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	71	441	0	ENST00000369902.3:c.965C>T	p.Pro322Leu	p.P322L	ENST00000369902	NM_016169.3	322	cCt/cTt	8/12	1	2	FACETS	0.802	0.701	0.91	0.802	0.701	0.91	CLONAL	1	TRUE	1	0.35	2		441	506	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910844	114910844	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	123	473	0	ENST00000543371.1:c.963G>T	p.Gln321His	p.Q321H	ENST00000543371	NM_001198531.1	321	caG/caT	9/14	1	2	FACETS	0.965	0.874	1	0.965	0.874	1	CLONAL	1	TRUE	1	0.35	2		473	728	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310820	123310820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747502397	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	94	530	0	ENST00000358487.5:c.608G>A	p.Arg203His	p.R203H	ENST00000358487	NM_000141.4	203	cGc/cAc	5/18	1	2	FACETS	0.966	0.862	1	0.966	0.862	1	CLONAL	1	TRUE	1	0.35	2		530	556	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	532659	532659	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	89	546	0	ENST00000451590.1:c.547A>C	p.Ser183Arg	p.S183R	ENST00000451590	NM_001130442.1	183	Agc/Cgc	5/5	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.35	2		546	507	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204911	94204911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1418567615	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	35	337	0	ENST00000323929.3:c.674G>A	p.Ser225Asn	p.S225N	ENST00000323929	NM_005591.3	225	aGt/aAt	8/20	1	2	FACETS	0.749	0.617	0.896	0.749	0.617	0.896	SUBCLONAL	1	TRUE	1	0.35	2		337	267	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150313	108150313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	70	372	0	ENST00000278616.4:c.3380C>T	p.Ala1127Val	p.A1127V	ENST00000278616	NM_000051.3	1127	gCt/gTt	23/63	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.35	2		372	393	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160446	108160446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	85	387	0	ENST00000278616.4:c.4354G>A	p.Asp1452Asn	p.D1452N	ENST00000278616	NM_000051.3	1452	Gat/Aat	29/63	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.35	2		387	475	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186586	108186586	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	71	455	0	ENST00000278616.4:c.6043C>A	p.Pro2015Thr	p.P2015T	ENST00000278616	NM_000051.3	2015	Cca/Aca	41/63	1	2	FACETS	0.869	0.76	0.985	0.869	0.76	0.985	CLONAL	1	TRUE	1	0.35	2		455	467	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374115	118374115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	92	523	0	ENST00000534358.1:c.7508C>T	p.Ala2503Val	p.A2503V	ENST00000534358	NM_005933.3	2503	gCt/gTt	27/36	1	2	FACETS	0.851	0.757	0.95	0.851	0.757	0.95	CLONAL	1	TRUE	1	0.35	2		523	618	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155956	119155956	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	124	646	0	ENST00000264033.4:c.1621G>T	p.Asp541Tyr	p.D541Y	ENST00000264033	NM_005188.3	541	Gat/Tat	11/16	1	2	FACETS	0.937	0.849	1	0.937	0.849	1	CLONAL	1	TRUE	1	0.35	2		646	756	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402268	402268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs539682097	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	90	457	0	ENST00000399788.2:c.4523G>A	p.Arg1508Gln	p.R1508Q	ENST00000399788	NM_001042603.1	1508	cGg/cAg	27/28	1	2	FACETS	0.872	0.775	0.975	0.872	0.775	0.975	CLONAL	1	TRUE	1	0.35	2		457	590	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636384	21636384	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	59	443	0	ENST00000421138.2:c.626A>G	p.Glu209Gly	p.E209G	ENST00000421138		209	gAa/gGa	7/16	1	2	FACETS	0.837	0.722	0.96	0.837	0.722	0.96	CLONAL	1	TRUE	1	0.35	2		443	403	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246566	46246566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	100	538	0	ENST00000334344.6:c.4660G>A	p.Val1554Ile	p.V1554I	ENST00000334344	NM_152641.2	1554	Gtt/Att	15/21	1	2	FACETS	0.989	0.885	1	0.989	0.885	1	CLONAL	1	TRUE	1	0.35	2		538	578	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420716	49420716	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	85	633	0	ENST00000301067.7:c.15033G>T	p.Glu5011Asp	p.E5011D	ENST00000301067	NM_003482.3	5011	gaG/gaT	48/54	1	2	FACETS	0.814	0.72	0.913	0.814	0.72	0.913	CLONAL	1	TRUE	1	0.35	2		633	597	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495651	56495651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	86	594	0	ENST00000267101.3:c.3841G>A	p.Ala1281Thr	p.A1281T	ENST00000267101	NM_001982.3	1281	Gcc/Acc	28/28	1	2	FACETS	0.991	0.879	1	0.991	0.879	1	CLONAL	1	TRUE	1	0.35	2		594	496	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861838	57861838	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381253752	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	95	605	0	ENST00000228682.2:c.1139G>A	p.Arg380Gln	p.R380Q	ENST00000228682	NM_005269.2	380	cGa/cAa	10/12	1	2	FACETS	0.93	0.829	1	0.93	0.829	1	CLONAL	1	TRUE	1	0.35	2		605	584	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813315	102813315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761462868	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	76	579	0	ENST00000307046.8:c.374G>A	p.Arg125His	p.R125H	ENST00000307046	NM_001111285.1	125	cGc/cAc	3/4	1	2	FACETS	0.747	0.656	0.845	0.747	0.656	0.845	SUBCLONAL	1	TRUE	1	0.35	2		579	581	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856589	111856589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	39	534	0	ENST00000341259.2:c.640G>A	p.Gly214Arg	p.G214R	ENST00000341259	NM_005475.2	214	Ggg/Agg	2/8	1	2	FACETS	0.58	0.482	0.69	0.58	0.482	0.69	SUBCLONAL	1	TRUE	1	0.35	2		534	384	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	75	544	0	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	1	2	FACETS	0.895	0.786	1	0.895	0.786	1	CLONAL	1	TRUE	1	0.35	2		544	479	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256623	133256623	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555230189	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	67	446	0	ENST00000320574.5:c.340C>T	p.Arg114Ter	p.R114*	ENST00000320574	NM_006231.2	114	Cga/Tga	5/49	1	2	FACETS	0.728	0.633	0.83	0.728	0.633	0.83	SUBCLONAL	1	TRUE	1	0.35	2		446	526	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001914	29001915	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	88	377	0	ENST00000282397.4:c.1250dup	p.Asn417LysfsTer56	p.N417Kfs*56	ENST00000282397	NM_002019.4	417	aac/aaAc	9/30	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.35	2		377	458	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906651	32906651	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	70	426	0	ENST00000380152.3:c.1036A>C	p.Asn346His	p.N346H	ENST00000380152		346	Aac/Cac	10/27	1	2	FACETS	0.877	0.767	0.995	0.877	0.767	0.995	CLONAL	1	TRUE	1	0.35	2		426	456	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911973	32911973	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	79	448	0	ENST00000380152.3:c.3481G>T	p.Asp1161Tyr	p.D1161Y	ENST00000380152		1161	Gat/Tat	11/27	1	2	FACETS	0.94	0.83	1	0.94	0.83	1	CLONAL	1	TRUE	1	0.35	2		448	480	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913630	32913630	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	64	346	0	ENST00000380152.3:c.5138A>C	p.Asn1713Thr	p.N1713T	ENST00000380152		1713	aAt/aCt	11/27	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.35	2		346	346	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913646	32913646	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	56	328	0	ENST00000380152.3:c.5154T>A	p.Asn1718Lys	p.N1718K	ENST00000380152		1718	aaT/aaA	11/27	1	2	FACETS	0.97	0.836	1	0.97	0.836	1	CLONAL	1	TRUE	1	0.35	2		328	330	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32931894	32931894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358990	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	58	369	0	ENST00000380152.3:c.7633G>A	p.Val2545Ile	p.V2545I	ENST00000380152		2545	Gtt/Att	16/27	1	2	FACETS	0.735	0.633	0.846	0.735	0.633	0.846	SUBCLONAL	1	TRUE	1	0.35	2		369	451	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134924	41134924	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	96	480	0	ENST00000379561.5:c.704C>A	p.Ser235Tyr	p.S235Y	ENST00000379561	NM_002015.3	235	tCt/tAt	2/3	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.35	2		480	524	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347875	73347875	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs917054849	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	66	453	0	ENST00000377767.4:c.1186C>T	p.Arg396Trp	p.R396W	ENST00000377767	NM_014953.3	396	Cgg/Tgg	8/21	1	2	FACETS	0.787	0.685	0.898	0.787	0.685	0.898	SUBCLONAL	1	TRUE	1	0.35	2		453	479	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504519	103504519	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1331207226	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	49	396	0	ENST00000355739.4:c.140G>A	p.Gly47Glu	p.G47E	ENST00000355739	NM_000123.3	47	gGg/gAg	2/15	1	2	FACETS	0.725	0.616	0.845	0.725	0.616	0.845	SUBCLONAL	1	TRUE	1	0.35	2		396	386	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582133	95582133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752424727	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	93	508	0	ENST00000393063.1:c.1778C>T	p.Ser593Leu	p.S593L	ENST00000393063	NM_030621.3	593	tCg/tTg	12/28	1	2	FACETS	0.982	0.876	1	0.982	0.876	1	CLONAL	1	TRUE	1	0.35	2		508	541	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034744	42034744	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs752630480	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	97	429	0	ENST00000219905.7:c.4586C>T	p.Ala1529Val	p.A1529V	ENST00000219905	NM_001164273.1	1529	gCg/gTg	15/24	1	2	FACETS	0.895	0.8	0.997	0.895	0.8	0.997	CLONAL	1	TRUE	1	0.35	2		429	619	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748994	43748994	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1445164930	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	93	572	0	ENST00000382044.4:c.1812T>G	p.Ile604Met	p.I604M	ENST00000382044	NM_001141980.1	604	atT/atG	12/28	1	2	FACETS	0.907	0.808	1	0.907	0.808	1	CLONAL	1	TRUE	1	0.35	2		572	586	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007661	45007661	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	66	460	0	ENST00000558401.1:c.108G>T	p.Glu36Asp	p.E36D	ENST00000558401	NM_004048.2	36	gaG/gaT	2/4	1	2	FACETS	0.734	0.638	0.837	0.734	0.638	0.837	SUBCLONAL	1	TRUE	1	0.35	2		460	514	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341244	341244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773933232	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	81	439	0	ENST00000262320.3:c.2240C>T	p.Ala747Val	p.A747V	ENST00000262320	NM_003502.3	747	gCg/gTg	9/11	1	2	FACETS	0.937	0.828	1	0.937	0.828	1	CLONAL	1	TRUE	1	0.35	2		439	494	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2125806	2125806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1596364874	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	65	514	0	ENST00000219476.3:c.2552C>T	p.Ala851Val	p.A851V	ENST00000219476	NM_000548.3	851	gCc/gTc	23/42	1	2	FACETS	0.771	0.669	0.88	0.771	0.669	0.88	SUBCLONAL	1	TRUE	1	0.35	2		514	482	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2215916	2215916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	72	498	0	ENST00000326181.6:c.118G>A	p.Ala40Thr	p.A40T	ENST00000326181	NM_032271.2	40	Gcc/Acc	3/21	1	2	FACETS	0.829	0.726	0.94	0.829	0.726	0.94	CLONAL	1	TRUE	1	0.35	2		498	496	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778421	3778421	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	76	626	0	ENST00000262367.5:c.6627G>T	p.Gln2209His	p.Q2209H	ENST00000262367	NM_004380.2	2209	caG/caT	31/31	1	2	FACETS	0.735	0.645	0.831	0.735	0.645	0.831	SUBCLONAL	1	TRUE	1	0.35	2		626	591	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857769	9857769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	86	679	0	ENST00000330684.3:c.3632C>T	p.Ser1211Phe	p.S1211F	ENST00000330684	NM_001134407.1	1211	tCc/tTc	13/13	1	2	FACETS	0.71	0.628	0.798	0.71	0.628	0.798	SUBCLONAL	1	TRUE	1	0.35	2		679	692	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923507	9923507	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs367543140	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	64	420	0	ENST00000330684.3:c.1780C>T	p.Pro594Ser	p.P594S	ENST00000330684	NM_001134407.1	594	Ccc/Tcc	9/13	1	2	FACETS	0.863	0.749	0.984	0.863	0.749	0.984	CLONAL	1	TRUE	1	0.35	2		420	424	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832265	72832265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267604632	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	110	549	0	ENST00000268489.5:c.4316G>A	p.Arg1439Gln	p.R1439Q	ENST00000268489	NM_006885.3	1439	cGa/cAa	9/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.35	2		549	573	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983378	15983378	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs780562500	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	71	475	0	ENST00000268712.3:c.3401G>A	p.Gly1134Asp	p.G1134D	ENST00000268712	NM_006311.3	1134	gGt/gAt	26/46	1	2	FACETS	0.944	0.827	1	0.944	0.827	1	CLONAL	1	TRUE	1	0.35	2		475	430	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989628	15989628	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs907509452	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	96	503	0	ENST00000268712.3:c.3145C>A	p.Pro1049Thr	p.P1049T	ENST00000268712	NM_006311.3	1049	Cca/Aca	23/46	1	2	FACETS	0.863	0.769	0.961	0.863	0.769	0.961	CLONAL	1	TRUE	1	0.35	2		503	636	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995263	15995263	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	83	483	0	ENST00000268712.3:c.2930G>T	p.Arg977Leu	p.R977L	ENST00000268712	NM_006311.3	977	cGg/cTg	22/46	1	2	FACETS	0.916	0.81	1	0.916	0.81	1	CLONAL	1	TRUE	1	0.35	2		483	518	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559758	29559758	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	106	495	0	ENST00000356175.3:c.3355G>T	p.Glu1119Ter	p.E1119*	ENST00000356175	NM_000267.3	1119	Gaa/Taa	26/57	1	2	FACETS	0.966	0.868	1	0.966	0.868	1	CLONAL	1	TRUE	1	0.35	2		495	627	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676159	29676159	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771706364	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	62	422	0	ENST00000356175.3:c.7148C>T	p.Ala2383Val	p.A2383V	ENST00000356175	NM_000267.3	2383	gCt/gTt	48/57	1	2	FACETS	0.76	0.658	0.871	0.76	0.658	0.871	SUBCLONAL	1	TRUE	1	0.35	2		422	466	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677324	29677324	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	45	368	0	ENST00000356175.3:c.7382A>G	p.Asp2461Gly	p.D2461G	ENST00000356175	NM_000267.3	2461	gAc/gGc	49/57	1	2	FACETS	0.887	0.75	1	0.887	0.75	1	CLONAL	1	TRUE	1	0.35	2		368	290	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55704608	55704608	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765095480	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	53	420	0	ENST00000284073.2:c.671C>T	p.Ala224Val	p.A224V	ENST00000284073	NM_138962.2	224	gCg/gTg	10/14	1	2	FACETS	0.609	0.52	0.707	0.609	0.52	0.707	SUBCLONAL	1	TRUE	1	0.35	2		420	497	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492863	56492863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	82	614	0	ENST00000407977.2:c.76G>A	p.Gly26Arg	p.G26R	ENST00000407977		26	Gga/Aga	2/10	1	2	FACETS	0.715	0.631	0.806	0.715	0.631	0.806	SUBCLONAL	1	TRUE	1	0.35	2		614	655	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117869	70117869	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	110	592	0	ENST00000245479.2:c.337A>G	p.Met113Val	p.M113V	ENST00000245479	NM_000346.3	113	Atg/Gtg	1/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.35	2		592	500	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573651	48573651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	64	500	0	ENST00000342988.3:c.235G>A	p.Asp79Asn	p.D79N	ENST00000342988	NM_005359.5	79	Gat/Aat	2/12	1	2	FACETS	0.841	0.73	0.96	0.841	0.73	0.96	CLONAL	1	TRUE	1	0.35	2		500	435	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212456	5212456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1191088838	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	78	552	0	ENST00000357368.4:c.4661C>T	p.Ala1554Val	p.A1554V	ENST00000357368	NM_002850.3	1554	gCg/gTg	31/38	1	2	FACETS	0.806	0.709	0.909	0.806	0.709	0.909	CLONAL	1	TRUE	1	0.35	2		552	553	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267839	7267839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886044001	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	107	475	0	ENST00000302850.5:c.169G>A	p.Glu57Lys	p.E57K	ENST00000302850	NM_000208.2	57	Gaa/Aaa	2/22	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.35	2		475	547	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350470	15350470	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs779348570	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	63	497	0	ENST00000263377.2:c.3445C>T	p.Arg1149Trp	p.R1149W	ENST00000263377	NM_058243.2	1149	Cgg/Tgg	16/20	1	2	FACETS	0.847	0.735	0.968	0.847	0.735	0.968	CLONAL	1	TRUE	1	0.35	2		497	425	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218684	36218684	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	91	665	1	ENST00000222270.7:c.4388C>A	p.Ser1463Tyr	p.S1463Y	ENST00000222270	NM_014727.1	1463	tCt/tAt	17/37	1	2	FACETS	0.852	0.758	0.953	0.852	0.758	0.953	CLONAL	1	TRUE	1	0.35	2		666	610	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765472	41765472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775504685	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	70	457	0	ENST00000301178.4:c.2348C>T	p.Ser783Leu	p.S783L	ENST00000301178	NM_021913.4	783	tCg/tTg	20/20	1	2	FACETS	0.81	0.708	0.92	0.81	0.708	0.92	CLONAL	1	TRUE	1	0.35	2		457	494	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793156	42793156	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	71	620	0	ENST00000575354.2:c.1048G>C	p.Ala350Pro	p.A350P	ENST00000575354	NM_015125.3	350	Gcc/Ccc	7/20	1	2	FACETS	0.648	0.566	0.737	0.648	0.566	0.737	SUBCLONAL	1	TRUE	1	0.35	2		620	626	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856014	45856014	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751084702	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	76	504	0	ENST00000391945.4:c.1892G>A	p.Arg631His	p.R631H	ENST00000391945	NM_000400.3	631	cGc/cAc	20/23	1	2	FACETS	0.8	0.703	0.904	0.8	0.703	0.904	CLONAL	1	TRUE	1	0.35	2		504	543	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425371	47425371	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1420876999	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	94	524	0	ENST00000404338.3:c.3439C>T	p.Arg1147Cys	p.R1147C	ENST00000404338	NM_004491.4	1147	Cgc/Tgc	1/6	1	2	FACETS	0.903	0.805	1	0.903	0.805	1	CLONAL	1	TRUE	1	0.35	2		524	595	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917793	29917793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149145987	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	71	477	1	ENST00000389048.3:c.875G>A	p.Arg292His	p.R292H	ENST00000389048	NM_004304.4	292	cGc/cAc	3/29	1	2	FACETS	0.843	0.738	0.957	0.843	0.738	0.957	CLONAL	1	TRUE	1	0.35	2		478	481	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027958	48027958	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1558666905	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	64	532	0	ENST00000234420.5:c.2836G>T	p.Glu946Ter	p.E946*	ENST00000234420	NM_000179.2	946	Gaa/Taa	4/10	1	2	FACETS	0.754	0.654	0.862	0.754	0.654	0.862	SUBCLONAL	1	TRUE	1	0.35	2		532	485	SUCCESS
REL	5966	MSKCC	GRCh37	2	61108979	61108979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	63	420	0	ENST00000295025.8:c.4G>A	p.Ala2Thr	p.A2T	ENST00000295025	NM_002908.2	2	Gcc/Acc	1/11	1	2	FACETS	0.776	0.673	0.887	0.776	0.673	0.887	SUBCLONAL	1	TRUE	1	0.35	2		420	464	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198272772	198272772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1360040192	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	65	428	0	ENST00000335508.6:c.1189C>T	p.Arg397Cys	p.R397C	ENST00000335508	NM_012433.2	397	Cgc/Tgc	9/25	1	2	FACETS	0.889	0.773	1	0.889	0.773	1	CLONAL	1	TRUE	1	0.35	2		428	418	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660166	227660166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775121566	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	108	674	0	ENST00000305123.5:c.3289C>T	p.Arg1097Trp	p.R1097W	ENST00000305123	NM_005544.2	1097	Cgg/Tgg	1/2	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.35	2		674	574	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31372563	31372563	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	70	429	0	ENST00000328111.2:c.205-1G>T		p.X69_splice	ENST00000328111	NM_006892.3	69			1	2	FACETS	0.988	0.865	1	0.988	0.865	1	CLONAL	1	TRUE	1	0.35	2		429	405	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742794	39742794	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	90	453	0	ENST00000361337.2:c.1637G>A	p.Arg546Gln	p.R546Q	ENST00000361337	NM_003286.2	546	cGa/cAa	15/21	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.35	2		453	508	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958111	54958111	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	98	453	0	ENST00000312783.6:c.496A>C	p.Lys166Gln	p.K166Q	ENST00000312783	NM_198436.1	166	Aaa/Caa	6/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.35	2		453	489	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57470712	57470712	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	56	443	0	ENST00000371085.3:c.185T>G	p.Ile62Ser	p.I62S	ENST00000371085	NM_000516.4	62	aTc/aGc	2/13	1	2	FACETS	0.661	0.567	0.764	0.661	0.567	0.764	SUBCLONAL	1	TRUE	1	0.35	2		443	484	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160245	22160245	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	75	493	0	ENST00000215832.6:c.386T>G	p.Phe129Cys	p.F129C	ENST00000215832	NM_002745.4	129	tTt/tGt	3/9	1	2	FACETS	0.812	0.713	0.918	0.812	0.713	0.918	CLONAL	1	TRUE	1	0.35	2		493	528	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553263	41553263	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	44	491	0	ENST00000263253.7:c.3352G>C	p.Val1118Leu	p.V1118L	ENST00000263253	NM_001429.3	1118	Gtc/Ctc	18/31	1	2	FACETS	0.597	0.501	0.703	0.597	0.501	0.703	SUBCLONAL	1	TRUE	1	0.35	2		491	421	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47108598	47108598	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	57	308	0	ENST00000409792.3:c.6071G>A	p.Arg2024Gln	p.R2024Q	ENST00000409792	NM_014159.6	2024	cGa/cAa	13/21	1	2	FACETS	0.984	0.849	1	0.984	0.849	1	CLONAL	1	TRUE	1	0.35	2		308	331	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940321	49940321	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	97	658	0	ENST00000296474.3:c.722A>G	p.His241Arg	p.H241R	ENST00000296474	NM_002447.2	241	cAt/cGt	1/20	1	2	FACETS	0.872	0.778	0.971	0.872	0.778	0.971	CLONAL	1	TRUE	1	0.35	2		658	636	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651490	52651490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	79	438	0	ENST00000394830.3:c.1606C>T	p.Pro536Ser	p.P536S	ENST00000394830	NM_018313.4	536	Cca/Tca	15/30	1	2	FACETS	0.894	0.788	1	0.894	0.788	1	CLONAL	1	TRUE	1	0.35	2		438	505	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202843	128202843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	97	607	0	ENST00000341105.2:c.877C>T	p.Arg293Trp	p.R293W	ENST00000341105	NM_032638.4	293	Cgg/Tgg	4/6	1	2	FACETS	0.858	0.766	0.956	0.858	0.766	0.956	CLONAL	1	TRUE	1	0.35	2		607	646	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279165	142279165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	82	374	0	ENST00000350721.4:c.1481C>T	p.Ala494Val	p.A494V	ENST00000350721	NM_001184.3	494	gCt/gTt	6/47	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.35	2		374	439	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948136	178948136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	83	401	0	ENST00000263967.3:c.2908G>A	p.Glu970Lys	p.E970K	ENST00000263967	NM_006218.2	970	Gaa/Aaa	20/21	1	2	FACETS	0.954	0.845	1	0.954	0.845	1	CLONAL	1	TRUE	1	0.35	2		401	497	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952076	178952076	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	67	521	0	ENST00000263967.3:c.3131A>C	p.Asn1044Thr	p.N1044T	ENST00000263967	NM_006218.2	1044	aAt/aCt	21/21	1	2	FACETS	0.96	0.838	1	0.96	0.838	1	CLONAL	1	TRUE	1	0.35	2		521	399	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430918	181430918	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	84	689	0	ENST00000325404.1:c.770C>A	p.Ser257Tyr	p.S257Y	ENST00000325404	NM_003106.3	257	tCt/tAt	1/1	1	2	FACETS	0.825	0.729	0.926	0.825	0.729	0.926	CLONAL	1	TRUE	1	0.35	2		689	582	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612028	189612028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs900140738	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	77	497	0	ENST00000264731.3:c.1780C>T	p.Arg594Ter	p.R594*	ENST00000264731	NM_003722.4	594	Cga/Tga	14/14	1	2	FACETS	0.856	0.753	0.966	0.856	0.753	0.966	CLONAL	1	TRUE	1	0.35	2		497	514	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141026	55141026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765680542	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	85	433	0	ENST00000257290.5:c.1672C>T	p.Arg558Cys	p.R558C	ENST00000257290	NM_006206.4	558	Cgc/Tgc	12/23	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.35	2		433	463	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161380	55161380	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376544204	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	84	498	0	ENST00000257290.5:c.3211G>A	p.Asp1071Asn	p.D1071N	ENST00000257290	NM_006206.4	1071	Gac/Aac	23/23	1	2	FACETS	0.99	0.877	1	0.99	0.877	1	CLONAL	1	TRUE	1	0.35	2		498	485	SUCCESS
REST	5978	MSKCC	GRCh37	4	57798146	57798146	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs369445358	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	104	494	0	ENST00000309042.7:c.3122A>C	p.Glu1041Ala	p.E1041A	ENST00000309042	NM_005612.4	1041	gAa/gCa	4/4	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.35	2		494	507	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808250	99808250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs17850950	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	45	247	0	ENST00000280892.6:c.439G>A	p.Asp147Asn	p.D147N	ENST00000280892	NM_001130678.1	147	Gat/Aat	5/7	1	2	FACETS	0.932	0.788	1	0.932	0.788	1	CLONAL	1	TRUE	1	0.35	2		247	276	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156813	106156813	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	119	618	0	ENST00000380013.4:c.1714T>G	p.Phe572Val	p.F572V	ENST00000380013	NM_001127208.2	572	Ttt/Gtt	3/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.35	2		618	622	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538214	187538214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750202307	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	80	472	0	ENST00000441802.2:c.9020C>T	p.Ala3007Val	p.A3007V	ENST00000441802	NM_005245.3	3007	gCg/gTg	11/27	1	2	FACETS	0.975	0.861	1	0.975	0.861	1	CLONAL	1	TRUE	1	0.35	2		472	469	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628173	187628173	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs547340067	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	86	557	0	ENST00000441802.2:c.2809C>T	p.Arg937Ter	p.R937*	ENST00000441802	NM_005245.3	937	Cga/Tga	2/27	1	2	FACETS	0.956	0.848	1	0.956	0.848	1	CLONAL	1	TRUE	1	0.35	2		557	514	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293661	1293661	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	73	680	0	ENST00000310581.5:c.1340G>A	p.Arg447His	p.R447H	ENST00000310581	NM_198253.2	447	cGc/cAc	2/16	1	2	FACETS	0.793	0.695	0.899	0.793	0.695	0.899	SUBCLONAL	1	TRUE	1	0.35	2		680	526	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179496	56179496	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	95	402	0	ENST00000399503.3:c.3809C>A	p.Ala1270Asp	p.A1270D	ENST00000399503	NM_005921.1	1270	gCt/gAt	15/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.35	2		402	480	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752771	57752771	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	39	323	0	ENST00000274289.3:c.1156+1G>A		p.X386_splice	ENST00000274289	NM_006622.3	386			1	2	FACETS	0.602	0.5	0.716	0.602	0.5	0.716	SUBCLONAL	1	TRUE	1	0.35	2		323	370	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589583	67589583	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	62	234	0	ENST00000274335.5:c.1346T>C	p.Leu449Ser	p.L449S	ENST00000274335		449	tTa/tCa	10/15	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.35	2		234	339	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80037311	80037311	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1321121530	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	53	332	0	ENST00000265081.6:c.1597G>A	p.Glu533Lys	p.E533K	ENST00000265081	NM_002439.4	533	Gaa/Aaa	11/24	1	2	FACETS	0.834	0.714	0.965	0.834	0.714	0.965	CLONAL	1	TRUE	1	0.35	2		332	363	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645121	86645121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	47	466	0	ENST00000274376.6:c.1193G>A	p.Arg398Gln	p.R398Q	ENST00000274376	NM_002890.2	398	cGa/cAa	8/25	1	2	FACETS	0.694	0.587	0.811	0.694	0.587	0.811	SUBCLONAL	1	TRUE	1	0.35	2		466	387	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925472	131925472	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	47	338	0	ENST00000265335.6:c.1395G>T	p.Gln465His	p.Q465H	ENST00000265335		465	caG/caT	9/25	1	2	FACETS	0.795	0.673	0.927	0.795	0.673	0.927	CLONAL	1	TRUE	1	0.35	2		338	338	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673238	30673238	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	89	509	0	ENST00000376406.3:c.3722A>G	p.Glu1241Gly	p.E1241G	ENST00000376406	NM_014641.2	1241	gAa/gGa	10/15	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.35	2		509	505	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289199	33289199	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	103	526	0	ENST00000374542.5:c.353G>T	p.Ser118Ile	p.S118I	ENST00000374542	NM_001141970.1	118	aGc/aTc	3/8	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.35	2		526	560	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066574	94066574	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	95	564	0	ENST00000369303.4:c.1185A>C	p.Leu395Phe	p.L395F	ENST00000369303	NM_004440.3	395	ttA/ttC	5/17	1	2	FACETS	0.92	0.821	1	0.92	0.821	1	CLONAL	1	TRUE	1	0.35	2		564	590	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6038753	6038753	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	80	477	0	ENST00000265849.7:c.691T>G	p.Phe231Val	p.F231V	ENST00000265849	NM_000535.5	231	Ttt/Gtt	6/15	1	2	FACETS	0.905	0.799	1	0.905	0.799	1	CLONAL	1	TRUE	1	0.35	2		477	505	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729739	41729739	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	82	520	0	ENST00000242208.4:c.790G>T	p.Glu264Ter	p.E264*	ENST00000242208	NM_002192.2	264	Gaa/Taa	3/3	1	2	FACETS	0.891	0.787	1	0.891	0.787	1	CLONAL	1	TRUE	1	0.35	2		520	526	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334734	81334734	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	73	433	0	ENST00000222390.5:c.1982C>T	p.Ala661Val	p.A661V	ENST00000222390	NM_000601.4	661	gCt/gTt	17/18	1	2	FACETS	0.988	0.868	1	0.988	0.868	1	CLONAL	1	TRUE	1	0.35	2		433	422	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124499018	124499018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	48	294	0	ENST00000357628.3:c.695C>T	p.Ser232Phe	p.S232F	ENST00000357628	NM_015450.2	232	tCt/tTt	9/19	1	2	FACETS	0.863	0.733	1	0.863	0.733	1	CLONAL	1	TRUE	1	0.35	2		294	318	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148504761	148504761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397515548	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	75	353	0	ENST00000320356.2:c.2233G>A	p.Glu745Lys	p.E745K	ENST00000320356	NM_004456.4	745	Gaa/Aaa	20/20	1	2	FACETS	0.924	0.812	1	0.924	0.812	1	CLONAL	1	TRUE	1	0.35	2		353	464	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506483	148506483	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1229491969	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	59	349	0	ENST00000320356.2:c.2030-1G>T		p.X677_splice	ENST00000320356	NM_004456.4	677			1	2	FACETS	0.777	0.67	0.892	0.777	0.67	0.892	SUBCLONAL	1	TRUE	1	0.35	2		349	434	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949634	151949634	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	53	374	0	ENST00000262189.6:c.1466A>C	p.Lys489Thr	p.K489T	ENST00000262189	NM_170606.2	489	aAa/aCa	10/59	1	2	FACETS	0.714	0.61	0.827	0.714	0.61	0.827	SUBCLONAL	1	TRUE	1	0.35	2		374	424	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012410	152012410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	75	370	0	ENST00000262189.6:c.403G>A	p.Ala135Thr	p.A135T	ENST00000262189	NM_170606.2	135	Gct/Act	4/59	1	2	FACETS	0.934	0.821	1	0.934	0.821	1	CLONAL	1	TRUE	1	0.35	2		370	459	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069564	69069564	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	59	313	0	ENST00000288368.4:c.4239G>T	p.Glu1413Asp	p.E1413D	ENST00000288368	NM_024870.2	1413	gaG/gaT	35/40	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.35	2		313	313	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141569616	141569616	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	78	508	0	ENST00000220592.5:c.668C>T	p.Ala223Val	p.A223V	ENST00000220592	NM_012154.3	223	gCg/gTg	6/19	1	2	FACETS	0.777	0.683	0.877	0.777	0.683	0.877	SUBCLONAL	1	TRUE	1	0.35	2		508	574	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740713	145740713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776602501	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	108	708	0	ENST00000428558.2:c.1387G>A	p.Ala463Thr	p.A463T	ENST00000428558	NM_004260.3	463	Gca/Aca	7/22	1	2	FACETS	0.961	0.864	1	0.961	0.864	1	CLONAL	1	TRUE	1	0.35	2		708	642	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2056778	2056778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs865840815	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	103	578	1	ENST00000349721.2:c.1280G>A	p.Arg427His	p.R427H	ENST00000349721	NM_003070.3	427	cGc/cAc	7/34	1	2	FACETS	0.903	0.809	1	0.903	0.809	1	CLONAL	1	TRUE	1	0.35	2		579	652	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080657	5080657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774709145	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	46	350	0	ENST00000381652.3:c.2408G>A	p.Arg803Gln	p.R803Q	ENST00000381652	NM_004972.3	803	cGa/cAa	18/25	1	2	FACETS	0.659	0.556	0.772	0.659	0.556	0.772	SUBCLONAL	1	TRUE	1	0.35	2		350	399	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971142	21971142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1563889729	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	88	623	0	ENST00000579755.1:c.259C>T	p.Arg87Cys	p.R87C	ENST00000579755		87	Cgc/Tgc	2/3	1	2	FACETS	0.973	0.864	1	0.973	0.864	1	CLONAL	1	TRUE	1	0.35	2		623	517	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206740	27206740	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200750146	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	59	448	0	ENST00000380036.4:c.2525G>A	p.Arg842His	p.R842H	ENST00000380036	NM_000459.3	842	cGc/cAc	15/23	1	2	FACETS	0.6	0.516	0.691	0.6	0.516	0.691	SUBCLONAL	1	TRUE	1	0.35	2		448	562	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87338508	87338508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	61	441	0	ENST00000277120.3:c.604G>A	p.Ala202Thr	p.A202T	ENST00000277120		202	Gcc/Acc	7/19	1	2	FACETS	0.726	0.628	0.833	0.726	0.628	0.833	SUBCLONAL	1	TRUE	1	0.35	2		441	480	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894991	101894991	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	74	423	0	ENST00000374994.4:c.544T>C	p.Tyr182His	p.Y182H	ENST00000374994	NM_004612.2	182	Tat/Cat	3/9	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.35	2		423	415	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730388	133730388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	88	497	0	ENST00000318560.5:c.454C>T	p.Arg152Cys	p.R152C	ENST00000318560	NM_005157.4	152	Cgt/Tgt	3/11	1	2	FACETS	0.961	0.854	1	0.961	0.854	1	CLONAL	1	TRUE	1	0.35	2		497	523	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759980	133759980	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	66	467	0	ENST00000318560.5:c.2303G>A	p.Gly768Glu	p.G768E	ENST00000318560	NM_005157.4	768	gGg/gAg	11/11	1	2	FACETS	0.802	0.698	0.915	0.802	0.698	0.915	CLONAL	1	TRUE	1	0.35	2		467	470	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802685	135802685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	104	431	0	ENST00000298552.3:c.113G>A	p.Gly38Asp	p.G38D	ENST00000298552	NM_001162426.1	38	gGc/gAc	4/23	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.35	2		431	534	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410574	63410574	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	82	639	0	ENST00000330258.3:c.2593G>A	p.Gly865Ser	p.G865S	ENST00000330258	NM_152424.3	865	Ggt/Agt	2/2	1	2	FACETS	0.877	0.775	0.986	0.877	0.775	0.986	CLONAL	1	TRUE	1	0.35	2		639	534	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76764017	76764017	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	81	551	0	ENST00000373344.5:c.7291G>T	p.Ala2431Ser	p.A2431S	ENST00000373344	NM_000489.3	2431	Gca/Tca	35/35	1	2	FACETS	0.86	0.76	0.968	0.86	0.76	0.968	CLONAL	1	TRUE	1	0.35	2		551	538	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776364	76776364	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	78	429	0	ENST00000373344.5:c.7102C>A	p.Gln2368Lys	p.Q2368K	ENST00000373344	NM_000489.3	2368	Caa/Aaa	34/35	1	2	FACETS	0.982	0.866	1	0.982	0.866	1	CLONAL	1	TRUE	1	0.35	2		429	454	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938406	76938406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	97	429	0	ENST00000373344.5:c.2342G>A	p.Arg781Gln	p.R781Q	ENST00000373344	NM_000489.3	781	cGa/cAa	9/35	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.35	2		429	469	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185216	123185216	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	51	326	0	ENST00000218089.9:c.1168G>T	p.Ala390Ser	p.A390S	ENST00000218089	NM_001042749.1	390	Gca/Tca	13/35	1	2	FACETS	0.842	0.719	0.976	0.842	0.719	0.976	CLONAL	1	TRUE	1	0.35	2		326	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0065754-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	141	415	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.213585169271411	6	FACETS	0.918	0.842	0.998	0.735	0.673	0.798	CLONAL	4	TRUE	1	0.213585169271411	6		415	513	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425600	47425600	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065754-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	99	410	0	ENST00000404338.3:c.3669del	p.Arg1224GlyfsTer28	p.R1224Gfs*28	ENST00000404338	NM_004491.4	1223	aGg/ag	1/6	0.212456420887483	4	FACETS	1	0.968	1			1	CLONAL	2	TRUE	NA	0.213585169271411	4		410	467	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274090	18274091	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0065754-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	91	518	0	ENST00000222254.8:c.1308_1309delinsAT	p.Asp437Tyr	p.D437Y	ENST00000222254	NM_005027.3	436	gaGGac/gaATac	11/16	0.213585169271411	4	FACETS	0.835	0.743	0.934	0.835	0.743	0.934	CLONAL	2	TRUE	2	0.213585169271411	4		518	619	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940463	49940463	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065754-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	48	581	0	ENST00000296474.3:c.580G>T	p.Ala194Ser	p.A194S	ENST00000296474	NM_002447.2	194	Gcc/Tcc	1/20	0.213585169271411	2	FACETS	0.791	0.668	0.927	0.396	0.334	0.464	CLONAL	1	TRUE	0	0.213585169271411	2		581	568	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0065854-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	25	329	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.82372289455298	2	FACETS	0.187	0.147	0.232	0.093	0.073	0.116	SUBCLONAL	1	TRUE	0	0.826386589179029	2		329	324	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241679	55241681	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	rs397517086	NA	P-0065854-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	1046	435	0	ENST00000275493.2:c.2127_2129del	p.Glu709_Thr710delinsAsp	p.E709_T710delinsD	ENST00000275493	NM_005228.3	709	gaAACt/gat	18/28	0.826386589179029	7	FACETS	1	0.989	1	1	0.989	1	CLONAL	6	TRUE	1	0.826386589179029	7		435	1284	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183770	10183770	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065854-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	213	463	0	ENST00000256474.2:c.239G>C	p.Ser80Thr	p.S80T	ENST00000256474	NM_000551.3	80	aGt/aCt	1/3	0.826386589179029	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.826386589179029	1		463	277	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468387	89468387	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065854-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	139	295	0	ENST00000336596.2:c.1921A>G	p.Lys641Glu	p.K641E	ENST00000336596	NM_005233.5	641	Aaa/Gaa	11/17	0.826386589179029	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.826386589179029	1		295	195	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304251	65304251	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065854-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	140	388	0	ENST00000342505.4:c.2864T>C	p.Ile955Thr	p.I955T	ENST00000342505	NM_002227.2	955	aTc/aCc	21/25	0.826386589179029	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.826386589179029	1		388	193	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149982932	149982932	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065854-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	143	366	1	ENST00000253339.5:c.3326A>G	p.Gln1109Arg	p.Q1109R	ENST00000253339		1109	cAg/cGg	7/7	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.826386589179029	2		367	292	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140911	37140911	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1583399317	NA	P-0065854-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	235	465	0	ENST00000373509.5:c.747C>G	p.Ile249Met	p.I249M	ENST00000373509	NM_002648.3	249	atC/atG	5/6	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.826386589179029	2		465	494	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0065926-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	37	314	4	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.885	0.735	1	0.885	0.735	1	CLONAL	1	TRUE	1	0.354218416739282	2		318	236	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220433	1220433	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065926-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	108	349	0	ENST00000326873.7:c.526G>T	p.Asp176Tyr	p.D176Y	ENST00000326873	NM_000455.4	176	Gac/Tac	4/10	0.354218416739282	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.354218416739282	1		349	476	SUCCESS
APC	324	MSKCC	GRCh37	5	112177234	112177234	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065926-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	40	346	0	ENST00000257430.4:c.5943del	p.Asn1981LysfsTer63	p.N1981Kfs*63	ENST00000257430	NM_000038.5	1981	aaT/aa	16/16	0.354218416739282	1	FACETS	0.841	0.705	0.989	0.841	0.705	0.989	CLONAL	1	TRUE	0	0.354218416739282	1		346	221	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0066010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	109	450	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.401874120976138	1	FACETS	0.94	0.85	1	0.94	0.85	1	CLONAL	1	TRUE	0	0.418653137603223	1		450	438	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354402	354402	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	180	379	0	ENST00000262320.3:c.1156C>T	p.Gln386Ter	p.Q386*	ENST00000262320	NM_003502.3	386	Cag/Tag	5/11	0.379908182079154	2	FACETS	0.876	0.815	0.938	0.876	0.815	0.938	CLONAL	2	TRUE	0	0.418653137603223	2		379	491	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636050	73636050	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs148819017	NA	P-0066010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	81	371	0	ENST00000377687.4:c.313A>G	p.Ile105Val	p.I105V	ENST00000377687	NM_001730.3	105	Ata/Gta	2/4	1	2	FACETS	0.946	0.838	1	0.946	0.838	1	CLONAL	1	TRUE	1	0.418653137603223	2		371	409	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636027	73636027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773515015	NA	P-0066010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	77	352	0	ENST00000377687.4:c.290C>T	p.Thr97Ile	p.T97I	ENST00000377687	NM_001730.3	97	aCa/aTa	2/4	1	2	FACETS	0.929	0.82	1	0.929	0.82	1	CLONAL	1	TRUE	1	0.418653137603223	2		352	396	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598230	28598230	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs372078521	NA	P-0066010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	105	415	0	ENST00000253063.3:c.202G>C	p.Glu68Gln	p.E68Q	ENST00000253063	NM_031459.4	68	Gag/Cag	3/10	0.386292325429586	1	FACETS	0.97	0.875	1	0.97	0.875	1	CLONAL	1	TRUE	0	0.418653137603223	1		415	409	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285854	87285854	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	82	373	0	ENST00000277120.3:c.191A>C	p.Asp64Ala	p.D64A	ENST00000277120		64	gAt/gCt	2/19	0.339386940982328	0	FACETS	0.737	0.656	0.821			1	SUBCLONAL	1	TRUE	0	0.418653137603223	0		373	309	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51510773	51510773	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	65	342	0	ENST00000260433.2:c.708G>T	p.Lys236Asn	p.K236N	ENST00000260433		236	aaG/aaT	6/10	1	2	FACETS	0.961	0.84	1	0.961	0.84	1	CLONAL	1	TRUE	1	0.418653137603223	2		342	323	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222481	53222481	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	87	246	0	ENST00000375401.3:c.4351C>T	p.Arg1451Trp	p.R1451W	ENST00000375401	NM_004187.3	1451	Cgg/Tgg	26/26	1	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.418653137603223	1		246	250	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066043-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	84	314	4	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.208746433217485	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	2	0.229234046374169	4		318	395	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989058	41989058	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066043-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	79	425	0	ENST00000219905.7:c.1850C>T	p.Pro617Leu	p.P617L	ENST00000219905	NM_001164273.1	617	cCa/cTa	3/24	0.175946445019735	2	FACETS	0.907	0.803	1	0.907	0.803	1	CLONAL	2	TRUE	0	0.229234046374169	2		425	380	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219389	1219389	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066043-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	74	420	0	ENST00000326873.7:c.443del	p.Phe148SerfsTer13	p.F148Sfs*13	ENST00000326873	NM_000455.4	147	cgT/cg	3/10	0.229234046374169	1	FACETS	0.919	0.812	1	1	0.982	1	CLONAL	2	TRUE	0	0.229234046374169	1		420	311	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211843	2211843	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0066043-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	48	342	0	ENST00000398665.3:c.1557+2T>G		p.X519_splice	ENST00000398665	NM_032482.2	519			0.229234046374169	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.229234046374169	1		342	253	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610181	10610181	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066043-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	83	415	0	ENST00000171111.5:c.529C>T	p.Gln177Ter	p.Q177*	ENST00000171111	NM_203500.1	177	Cag/Tag	2/6	0.229234046374169	1	FACETS	1	0.925	1	1	0.986	1	CLONAL	2	TRUE	0	0.229234046374169	1		415	306	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506913	186506913	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0066043-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	54	308	0	ENST00000323963.5:c.1080-1G>A		p.X360_splice	ENST00000323963		360			0.226220962737309	2	FACETS	1	0.941	1	0.599	0.513	0.693	CLONAL	1	TRUE	0	0.229234046374169	2		308	393	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127484	55127484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs538480165	NA	P-0066043-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	43	454	0	ENST00000257290.5:c.272C>T	p.Ser91Leu	p.S91L	ENST00000257290	NM_006206.4	91	tCg/tTg	3/23	0.180229434551137	3	FACETS	1	0.856	1	0.511	0.428	0.603	CLONAL	1	TRUE	1	0.229234046374169	3		454	409	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066043-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	82	314	4	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.187833275408605	4	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	2	0.209739016188578	4		318	434	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989058	41989058	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066043-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	103	425	0	ENST00000219905.7:c.1850C>T	p.Pro617Leu	p.P617L	ENST00000219905	NM_001164273.1	617	cCa/cTa	3/24	0.209739016188578	3	FACETS	0.967	0.868	1	0.967	0.868	1	CLONAL	2	TRUE	1	0.209739016188578	3		425	561	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219389	1219389	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066043-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	168	420	0	ENST00000326873.7:c.443del	p.Phe148SerfsTer13	p.F148Sfs*13	ENST00000326873	NM_000455.4	147	cgT/cg	3/10	0.198987274351726	3	FACETS	0.894	0.828	0.961	1	0.982	1	CLONAL	4	TRUE	0	0.209739016188578	3		420	495	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211843	2211843	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0066043-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	134	342	0	ENST00000398665.3:c.1557+2T>G		p.X519_splice	ENST00000398665	NM_032482.2	519			0.198987274351726	3	FACETS	0.999	0.914	1	0.999	0.914	1	CLONAL	3	TRUE	0	0.209739016188578	3		342	471	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610181	10610181	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066043-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	104	415	0	ENST00000171111.5:c.529C>T	p.Gln177Ter	p.Q177*	ENST00000171111	NM_203500.1	177	Cag/Tag	2/6	0.209739016188578	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	0	0.209739016188578	2		415	473	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506913	186506913	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0066043-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	42	308	0	ENST00000323963.5:c.1080-1G>A		p.X360_splice	ENST00000323963		360			0.209739016188578	2	FACETS	1	0.846	1	0.506	0.423	0.597	CLONAL	1	TRUE	0	0.209739016188578	2		308	396	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0066059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	317	455	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.54355254836611	3	FACETS	0.978	0.939	1	0.978	0.939	1	CLONAL	3	TRUE	0	0.567339744050389	3		455	489	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791719	42791719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	143	628	0	ENST00000575354.2:c.605G>A	p.Arg202Gln	p.R202Q	ENST00000575354	NM_015125.3	202	cGg/cAg	5/20	0.541095716031049	3	FACETS	0.936	0.856	1	0.468	0.428	0.511	CLONAL	1	TRUE	1	0.567339744050389	3		628	691	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652804	212652804	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138433638	NA	P-0066059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	144	414	0	ENST00000342788.4:c.502C>T	p.Arg168Trp	p.R168W	ENST00000342788	NM_005235.2	168	Cgg/Tgg	4/28	0.49967448537095	4	FACETS	0.906	0.834	0.981	0.906	0.834	0.981	CLONAL	2	TRUE	2	0.567339744050389	4		414	439	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912159	114912159	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	222	406	0	ENST00000543371.1:c.1229A>G	p.His410Arg	p.H410R	ENST00000543371	NM_001198531.1	410	cAt/cGt	11/14	0.541095716031049	3	FACETS	0.975	0.917	1	0.975	0.917	1	CLONAL	2	TRUE	1	0.567339744050389	3		406	515	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2218099	2218100	+	missense_variant	Missense_Mutation	DNP	AG	AG	TT	novel	NA	P-0066059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	126	601	0	ENST00000326181.6:c.161_162delinsTT	p.Lys54Ile	p.K54I	ENST00000326181	NM_032271.2	54	aAG/aTT	4/21	0.541095716031049	3	FACETS	0.879	0.797	0.964	0.439	0.398	0.482	CLONAL	1	TRUE	1	0.567339744050389	3		601	649	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578223	7578236	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTCATCCAAATA	CTGTCATCCAAATA	-	novel	NA	P-0066059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	322	572	0	ENST00000269305.4:c.613_626del	p.Tyr205LysfsTer6	p.Y205Kfs*6	ENST00000269305	NM_001126112.2	205	TATTTGGATGACAGa/a	6/11	0.551060361827853	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.567339744050389	2		572	548	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760994	133760994	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	125	500	0	ENST00000318560.5:c.3317G>T	p.Ser1106Ile	p.S1106I	ENST00000318560	NM_005157.4	1106	aGt/aTt	11/11	0.541095716031049	3	FACETS	0.991	0.9	1	0.495	0.45	0.543	CLONAL	1	TRUE	1	0.567339744050389	3		500	571	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56792489	56792490	+	missense_variant	Missense_Mutation	DNP	CA	CA	TT	novel	NA	P-0066059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	126	452	2	ENST00000308159.5:c.219_220delinsTT	p.Ile74Phe	p.I74F	ENST00000308159	NM_014669.4	73	caCAtc/caTTtc	3/22	0.567339744050389	6	FACETS	1	0.961	1			1	CLONAL	1	TRUE	NA	0.567339744050389	6		454	848	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317944	8317944	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0066059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	43	457	0	ENST00000356435.5:c.5671-2A>T		p.X1891_splice	ENST00000356435		1891			0.541095716031049	3	FACETS	0.427	0.357	0.504	0.213	0.178	0.252	SUBCLONAL	1	TRUE	1	0.567339744050389	3		457	456	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0066090-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	395	270	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.452111582310746	7	FACETS	1	0.984	1	1	0.984	1	CLONAL	5	TRUE	2	0.452111582310746	7		270	711	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0066090-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	206	529	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.421072088288619	2	FACETS	0.873	0.817	0.929	0.873	0.817	0.929	CLONAL	2	TRUE	0	0.452111582310746	2		529	522	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110665	8110665	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066090-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	185	540	0	ENST00000585124.1:c.227A>G	p.Asp76Gly	p.D76G	ENST00000585124	NM_004217.3	76	gAc/gGc	5/9	0.421072088288619	2	FACETS	0.884	0.824	0.944	0.884	0.824	0.944	CLONAL	2	TRUE	0	0.452111582310746	2		540	463	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0066144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	155	516	0	ENST00000311936.3:c.180_181delinsAA	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggAAaa	3/5	0.319458006726844	3	FACETS	1	0.986	1	0.668	0.614	0.723	CLONAL	1	TRUE	1	0.528938555168656	3		516	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7590694	7590694	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0066144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	179	583	0	ENST00000269305.4:c.-29+1G>T		p.X10_splice	ENST00000269305	NM_001126112.2	10			0.528938555168656	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.528938555168656	1		583	440	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412637	63412637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779222316	NA	P-0066144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	133	511	0	ENST00000330258.3:c.530G>A	p.Arg177His	p.R177H	ENST00000330258	NM_152424.3	177	cGc/cAc	2/2	1	2	FACETS	0.858	0.782	0.937	0.858	0.782	0.937	CLONAL	1	TRUE	1	0.528938555168656	2		511	586	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591885	48591885	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	134	599	0	ENST00000342988.3:c.1048G>T	p.Val350Phe	p.V350F	ENST00000342988	NM_005359.5	350	Gtt/Ttt	9/12	0.528938555168656	1	FACETS	0.879	0.806	0.954	0.879	0.806	0.954	CLONAL	1	TRUE	0	0.528938555168656	1		599	424	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190708784	190708784	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	80	405	0	ENST00000441310.2:c.677A>G	p.Gln226Arg	p.Q226R	ENST00000441310	NM_000534.4	226	cAg/cGg	6/13	0.139584587164383	4	FACETS	1	0.956	1	0.582	0.516	0.653	INDETERMINATE	1	TRUE	2	0.528938555168656	4		405	397	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035257	6035257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	162	660	0	ENST00000265849.7:c.811G>A	p.Gly271Ser	p.G271S	ENST00000265849	NM_000535.5	271	Ggt/Agt	8/15	1	2	FACETS	0.914	0.841	0.99	0.914	0.841	0.99	CLONAL	1	TRUE	1	0.528938555168656	2		660	670	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183752	10183752	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs5030803	NA	P-0066250-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	34	312	0	ENST00000256474.2:c.221T>A	p.Val74Asp	p.V74D	ENST00000256474	NM_000551.3	74	gTc/gAc	1/3	0.3	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.21	1		312	213	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084127	47084127	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066250-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	42	574	0	ENST00000409792.3:c.7162del	p.Thr2388ProfsTer23	p.T2388Pfs*23	ENST00000409792	NM_014159.6	2388	Acc/cc	17/21	0.3	1	FACETS	0.899	0.76	1	1	0.968	1	CLONAL	2	TRUE	0	0.21	1		574	199	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168745	56168745	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066250-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	44	285	0	ENST00000399503.3:c.1599G>C	p.Arg533Ser	p.R533S	ENST00000399503	NM_005921.1	533	agG/agC	9/20	0.193524335170611	3	FACETS	0.965	0.816	1	0.965	0.816	1	CLONAL	2	TRUE	1	0.21	3		285	240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0066292-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	302	529	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.374819464958421	3	FACETS	0.965	0.913	1	0.965	0.913	1	CLONAL	2	TRUE	1	0.50708973867637	3		529	774	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044901	47044901	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066292-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	163	614	0	ENST00000377604.3:c.2227G>T	p.Glu743Ter	p.E743*	ENST00000377604	NM_001204468.1	743	Gag/Tag	20/24	0.385590002105776	5	FACETS	0.859	0.787	0.936			1	CLONAL	1	TRUE	NA	0.50708973867637	5		614	1317	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858738	9858738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149698593	NA	P-0066292-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	73	524	0	ENST00000330684.3:c.2663C>T	p.Thr888Met	p.T888M	ENST00000330684	NM_001134407.1	888	aCg/aTg	13/13	0.50708973867637	3	FACETS	0.428	0.373	0.487	0.143	0.124	0.163	SUBCLONAL	1	TRUE	0	0.50708973867637	3		524	843	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0066292-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	1221	315	0	ENST00000311936.3:c.34_35delinsTT	p.Gly12Phe	p.G12F	ENST00000311936	NM_004985.3	12	GGt/TTt	2/5	0.50708973867637	15	FACETS	1	0.993	1	0.945	0.928	0.962	CLONAL	12	TRUE	2	0.50708973867637	15		315	1684	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245434	153245434	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066292-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	205	455	0	ENST00000281708.4:c.1757G>T	p.Gly586Val	p.G586V	ENST00000281708	NM_033632.3	586	gGa/gTa	11/12	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.50708973867637	2		455	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579375	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0066292-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	148	601	0	ENST00000269305.4:c.312_313delinsTA	p.Gln104_Gly105delinsHisSer	p.Q104_G105delinsHS	ENST00000269305	NM_001126112.2	104	caGGgc/caTAgc	4/11	0.374819464958421	3	FACETS	0.941	0.86	1	0.47	0.43	0.513	CLONAL	1	TRUE	1	0.50708973867637	3		601	778	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293432	1293432	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066292-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	151	430	0	ENST00000310581.5:c.1569C>A	p.Ser523Arg	p.S523R	ENST00000310581	NM_198253.2	523	agC/agA	2/16	0.48653578980143	3	FACETS	1	0.974	1	0.574	0.527	0.624	CLONAL	1	TRUE	1	0.50708973867637	3		430	650	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33434399	33434399	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066292-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	116	532	0	ENST00000345365.6:c.331A>T	p.Ser111Cys	p.S111C	ENST00000345365	NM_002878.3	111	Agc/Tgc	4/10	1	2	FACETS	0.749	0.676	0.825	0.749	0.676	0.825	SUBCLONAL	1	TRUE	1	0.50708973867637	2		532	611	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242663	46242663	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066292-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	168	392	0	ENST00000334344.6:c.1625G>C	p.Arg542Pro	p.R542P	ENST00000334344	NM_152641.2	542	cGa/cCa	13/21	0.104965253342403	3	FACETS	0.829	0.768	0.892			1	INDETERMINATE	2	TRUE	NA	0.50708973867637	3		392	501	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784059	120784059	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066292-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	140	619	1	ENST00000257552.2:c.926G>T	p.Gly309Val	p.G309V	ENST00000257552	NM_002442.3	309	gGg/gTg	13/15	1	2	FACETS	0.721	0.657	0.788	0.721	0.657	0.788	SUBCLONAL	1	TRUE	1	0.50708973867637	2		620	766	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660535	227660535	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066292-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	221	590	0	ENST00000305123.5:c.2920A>G	p.Ser974Gly	p.S974G	ENST00000305123	NM_005544.2	974	Agc/Ggc	1/2	0.50708973867637	2	FACETS	1	0.987	1	0.606	0.566	0.647	CLONAL	1	TRUE	0	0.50708973867637	2		590	719	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1331523	1331523	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066292-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	66	428	0	ENST00000400841.2:c.5G>T	p.Gly2Val	p.G2V	ENST00000400841		2	gGg/gTg	1/6	1	2	FACETS	0.387	0.336	0.443	0.387	0.336	0.443	SUBCLONAL	1	TRUE	1	0.50708973867637	2		428	672	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951867	2951867	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066292-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	135	551	0	ENST00000396946.4:c.3083A>T	p.Glu1028Val	p.E1028V	ENST00000396946	NM_032415.4	1028	gAg/gTg	23/25	0.50708973867637	3	FACETS	0.83	0.755	0.909	0.415	0.377	0.455	CLONAL	1	TRUE	1	0.50708973867637	3		551	804	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63661961	63661961	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066292-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	85	552	0	ENST00000279873.7:c.65A>G	p.Tyr22Cys	p.Y22C	ENST00000279873	NM_032199.2	22	tAc/tGc	2/10	0.438943973764078	1	FACETS	0.437	0.387	0.491	0.437	0.387	0.491	SUBCLONAL	1	TRUE	0	0.50708973867637	1		552	572	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068299	30068299	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066292-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	46	358	0	ENST00000331968.5:c.2100A>T	p.Lys700Asn	p.K700N	ENST00000331968	NM_002742.2	700	aaA/aaT	15/18	0.413515989805448	4	FACETS	0.46	0.387	0.541	0.153	0.129	0.181	SUBCLONAL	1	TRUE	1	0.50708973867637	4		358	594	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068916	30068916	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066292-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	116	414	0	ENST00000331968.5:c.2013G>T	p.Leu671Phe	p.L671F	ENST00000331968	NM_002742.2	671	ttG/ttT	14/18	0.413515989805448	4	FACETS	0.928	0.837	1	0.309	0.279	0.342	CLONAL	1	TRUE	1	0.50708973867637	4		414	743	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514859	103514859	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066292-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	393	581	0	ENST00000355739.4:c.1360G>T	p.Ala454Ser	p.A454S	ENST00000355739	NM_000123.3	454	Gca/Tca	8/15	0.50708973867637	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.50708973867637	3		581	866	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874059	151874059	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066299-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	33	458	0	ENST00000262189.6:c.8479C>G	p.Leu2827Val	p.L2827V	ENST00000262189	NM_170606.2	2827	Ctg/Gtg	38/59	0.157234029400661	6	FACETS	1	0.901	1	0.388	0.317	0.467	INDETERMINATE	1	TRUE	3	0.336641536666178	6		458	282	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	134	317	0				ENST00000310581	NM_198253.2	-/1132			0.506179989722602	1	FACETS	0.797	0.737	0.857	0.797	0.737	0.857	SUBCLONAL	1	TRUE	0	0.727846588076189	1		317	294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0066335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	247	493	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	0.727846588076189	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.727846588076189	1		493	385	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12647734	12647734	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	73	399	0	ENST00000251849.4:c.646C>T	p.Arg216Cys	p.R216C	ENST00000251849	NM_002880.3	216	Cgt/Tgt	6/17	1	2	FACETS	0.489	0.43	0.553	0.489	0.43	0.553	SUBCLONAL	1	TRUE	1	0.727846588076189	2		399	410	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120789192	120789192	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	79	360	0	ENST00000257552.2:c.745G>C	p.Glu249Gln	p.E249Q	ENST00000257552	NM_002442.3	249	Gag/Cag	11/15	0.341728314153238	2	FACETS	0.526	0.464	0.591	0.263	0.232	0.296	INDETERMINATE	1	TRUE	0	0.727846588076189	2		360	413	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505476	157505476	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	96	422	0	ENST00000346085.5:c.3457G>C	p.Glu1153Gln	p.E1153Q	ENST00000346085	NM_020732.3	1153	Gag/Cag	13/20	0.348983249701674	3	FACETS	0.519	0.463	0.579	0.26	0.231	0.29	INDETERMINATE	1	TRUE	1	0.727846588076189	3		422	693	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894230	NA	P-0066335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	211	389	0	ENST00000451590.1:c.35G>A	p.Gly12Asp	p.G12D	ENST00000451590	NM_001130442.1	12	gGc/gAc	2/5	0.394256737909244	1	FACETS	0.788	0.74	0.836	0.788	0.74	0.836	INDETERMINATE	1	TRUE	0	0.727846588076189	1		389	468	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37882077	37882077	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	100	357	0	ENST00000269571.5:c.2843C>A	p.Thr948Asn	p.T948N	ENST00000269571		948	aCc/aAc	23/27	0.50308693128296	3	FACETS	0.549	0.49	0.611	0.274	0.245	0.306	SUBCLONAL	1	TRUE	1	0.727846588076189	3		357	683	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67197010	67197010	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs374406780	NA	P-0066335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	179	348	0	ENST00000312629.5:c.253C>T	p.Arg85Ter	p.R85*	ENST00000312629	NM_003952.2	85	Cga/Tga	4/15	1	2	FACETS	0.951	0.884	1	0.951	0.884	1	CLONAL	1	TRUE	1	0.727846588076189	2		348	517	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189097	38189097	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	72	384	0	ENST00000317025.8:c.917G>C	p.Arg306Pro	p.R306P	ENST00000317025	NM_023034.1	306	cGa/cCa	5/24	0.394256737909244	1	FACETS	0.371	0.326	0.419	0.371	0.326	0.419	INDETERMINATE	1	TRUE	0	0.727846588076189	1		384	339	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21350131	21350131	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	234	509	0	ENST00000215739.8:c.2039C>T	p.Ala680Val	p.A680V	ENST00000215739	NM_006767.3	680	gCc/gTc	17/21	0.163874363475857	3	FACETS	1	0.988	1	0.408	0.382	0.435	INDETERMINATE	1	TRUE	0	0.727846588076189	3		509	716	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955516	48955533	+	inframe_deletion	In_Frame_Del	DEL	AGAAATGATAAAACATTT	AGAAATGATAAAACATTT	-	novel	NA	P-0066335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	147	328	0	ENST00000267163.4:c.1636_1653del	p.Met546_Glu551del	p.M546_E551del	ENST00000267163	NM_000321.2	544	agAGAAATGATAAAACATTTa/aga	17/27	0.727846588076189	1	FACETS	0.955	0.892	1	0.955	0.892	1	CLONAL	1	TRUE	0	0.727846588076189	1		328	269	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456508	29456508	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	105	530	0	ENST00000389048.3:c.2410G>C	p.Glu804Gln	p.E804Q	ENST00000389048	NM_004304.4	804	Gaa/Caa	14/29	1	2	FACETS	0.46	0.413	0.51	0.46	0.413	0.51	SUBCLONAL	1	TRUE	1	0.727846588076189	2		530	627	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650144	206650144	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	112	530	0	ENST00000367120.3:c.664A>T	p.Ile222Phe	p.I222F	ENST00000367120	NM_014002.3	222	Atc/Ttc	7/22	0.348983249701674	3	FACETS	0.531	0.477	0.587	0.265	0.238	0.294	INDETERMINATE	1	TRUE	1	0.727846588076189	3		530	791	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885887	59885887	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	96	474	0	ENST00000259008.2:c.859G>C	p.Glu287Gln	p.E287Q	ENST00000259008	NM_032043.2	287	Gag/Cag	7/20	0.459161232773627	3	FACETS	0.546	0.487	0.609	0.273	0.243	0.305	SUBCLONAL	1	TRUE	1	0.727846588076189	3		474	659	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878577	151878577	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0066335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	128	508	0	ENST00000262189.6:c.6368C>G	p.Ser2123Ter	p.S2123*	ENST00000262189	NM_170606.2	2123	tCa/tGa	36/59	1	2	FACETS	0.653	0.594	0.714	0.653	0.594	0.714	SUBCLONAL	1	TRUE	1	0.727846588076189	2		508	539	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845395	156845395	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	128	747	0	ENST00000524377.1:c.1438G>T	p.Glu480Ter	p.E480*	ENST00000524377	NM_002529.3	480	Gag/Tag	12/17	0.348983249701674	3	FACETS	0.514	0.465	0.566	0.257	0.232	0.283	INDETERMINATE	1	TRUE	1	0.727846588076189	3		747	933	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405581	70405581	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	100	461	0	ENST00000373644.4:c.3095C>G	p.Ser1032Cys	p.S1032C	ENST00000373644	NM_030625.2	1032	tCc/tGc	4/12	0.394256737909244	1	FACETS	0.437	0.393	0.483	0.437	0.393	0.483	INDETERMINATE	1	TRUE	0	0.727846588076189	1		461	400	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0066344-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	436	594	0	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	0.673798033925244	3	FACETS	0.916	0.889	0.942	0.916	0.889	0.942	CLONAL	3	TRUE	0	0.749646335779407	3		594	582	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941730	48941742	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTATAGACAGGTA	CTATAGACAGGTA	-	novel	NA	P-0066344-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	190	253	0	ENST00000267163.4:c.1040_1049+3del		p.X347_splice	ENST00000267163	NM_000321.2	347		10/27	0.749646335779407	3	FACETS	0.96	0.92	0.997	0.96	0.92	0.997	CLONAL	3	TRUE	0	0.749646335779407	3		253	242	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485439	57485439	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs3205253	NA	P-0066344-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	273	462	0	ENST00000371085.3:c.1021A>G	p.Ile341Val	p.I341V	ENST00000371085	NM_000516.4	341	Att/Gtt	12/13	0.564075735993862	4	FACETS	0.954	0.901	1	0.954	0.901	1	CLONAL	2	TRUE	2	0.749646335779407	4		462	668	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0066345-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	190	410	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.25306167464727	3	FACETS	0.953	0.887	1	0.953	0.887	1	CLONAL	3	TRUE	0	0.273274541844567	3		410	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203436	NA	P-0066345-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	187	684	0	ENST00000269305.4:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269305	NM_001126112.2	163	Tac/Cac	5/11	0.196454764697876	3	FACETS	0.96	0.889	1	0.64	0.592	0.69	CLONAL	2	TRUE	0	0.273274541844567	3		684	810	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724542	162724542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1041487062	NA	P-0066345-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	123	712	0	ENST00000367921.3:c.314G>A	p.Arg105His	p.R105H	ENST00000367921	NM_006182.2	105	cGc/cAc	5/18	0.11261234242353	4	FACETS	1	0.98	1	0.663	0.599	0.73	INDETERMINATE	1	TRUE	2	0.273274541844567	4		712	865	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877861	151877861	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066345-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	68	600	0	ENST00000262189.6:c.7084T>G	p.Ser2362Ala	p.S2362A	ENST00000262189	NM_170606.2	2362	Tca/Gca	36/59	0.25306167464727	3	FACETS	0.738	0.641	0.843	0.246	0.213	0.281	SUBCLONAL	1	TRUE	0	0.273274541844567	3		600	767	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2060868	2060868	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066345-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	36	541	0	ENST00000349721.2:c.1574G>A	p.Arg525His	p.R525H	ENST00000349721	NM_003070.3	525	cGt/cAt	9/34	0.187706814888942	2	FACETS	0.384	0.315	0.462	0.192	0.157	0.231	SUBCLONAL	1	TRUE	0	0.273274541844567	2		541	686	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721044	61721044	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066345-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	35	546	0	ENST00000401558.2:c.1230G>T	p.Leu410Phe	p.L410F	ENST00000401558	NM_003400.3	410	ttG/ttT	12/25	0.225264721352767	2	FACETS	0.378	0.309	0.457	0.189	0.154	0.229	SUBCLONAL	1	TRUE	0	0.273274541844567	2		546	677	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796805	135796805	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203427	NA	P-0066355-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	137	365	0	ENST00000298552.3:c.682C>T	p.Arg228Ter	p.R228*	ENST00000298552	NM_001162426.1	228	Cga/Tga	8/23	1	2	FACETS	0.998	0.916	1	0.998	0.916	1	CLONAL	1	TRUE	1	0.63688731685055	2		365	431	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135777074	135777074	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066355-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	108	349	0	ENST00000298552.3:c.2404del	p.Asp802ThrfsTer5	p.D802Tfs*5	ENST00000298552	NM_001162426.1	802	Gac/ac	19/23	1	2	FACETS	0.961	0.871	1	0.961	0.871	1	CLONAL	1	TRUE	1	0.63688731685055	2		349	353	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0066367-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	22	513	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.202876435887739	4	FACETS	1	0.807	1	0.686	0.539	0.852	CLONAL	2	FALSE	1	0.208200927605416	4		513	124	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866528	117866529	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0066379-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	232	392	0	ENST00000297338.2:c.1116_1117del	p.Ser374PhefsTer9	p.S374Ffs*9	ENST00000297338	NM_006265.2	372	ctGTtt/cttt	9/14	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		392	528	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653843	89653904	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAACAATATTGATGATGTAGTAAGGTAAGAATGCTTTGATTTTCTATTTCAAATATTGATGT	GAACAATATTGATGATGTAGTAAGGTAAGAATGCTTTGATTTTCTATTTCAAATATTGATGT	-	novel	NA	P-0066380-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	13	339	0	ENST00000371953.3:c.141_164+38del		p.X47_splice	ENST00000371953	NM_000314.4	47		2/9	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		339	167	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0066393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	55	270	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.16488508740495	3	FACETS	1	0.964	1	0.716	0.615	0.826	CLONAL	1	TRUE	1	0.219716072036821	3		270	388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0066393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	65	389	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.219716072036821	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.219716072036821	1		389	398	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95573978	95573978	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	25	416	0	ENST00000393063.1:c.2771del	p.Leu924Ter	p.L924*	ENST00000393063	NM_030621.3	924	tTa/ta	18/28	1	2	FACETS	0.528	0.415	0.658	0.528	0.415	0.658	SUBCLONAL	1	TRUE	1	0.219716072036821	2		416	431	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398286	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0066409-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	348	271	0	ENST00000311936.3:c.33_34delinsCT	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	11	gcTGgt/gcCTgt	2/5	0.456763341679646	7	FACETS	0.989	0.946	1	0.989	0.946	1	CLONAL	5	TRUE	2	0.456763341679646	7		271	660	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0066409-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	163	529	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.336054099785851	3	FACETS	1	0.986	1	0.821	0.765	0.877	CLONAL	2	TRUE	0	0.456763341679646	3		529	356	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61725918	61725918	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066409-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	81	343	0	ENST00000401558.2:c.649C>G	p.Gln217Glu	p.Q217E	ENST00000401558	NM_003400.3	217	Caa/Gaa	9/25	0.45801796480922	4	FACETS	0.885	0.78	0.996	0.295	0.26	0.332	CLONAL	1	TRUE	1	0.456763341679646	4		343	584	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041266	47041266	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0066409-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	79	251	0	ENST00000377604.3:c.1693+1G>T		p.X565_splice	ENST00000377604	NM_001204468.1	565			0.134816143885479	2	FACETS	0.956	0.861	1			1	INDETERMINATE	2	TRUE	NA	0.456763341679646	2		251	181	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971133	21971133	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066409-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	154	460	0	ENST00000304494.5:c.225del	p.Ala76ProfsTer70	p.A76Pfs*70	ENST00000304494	NM_000077.4	75	ccC/cc	2/3	0.455797695913029	2	FACETS	0.972	0.903	1	0.972	0.903	1	CLONAL	2	TRUE	0	0.456763341679646	2		460	347	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525066	9525066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066409-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	58	411	0	ENST00000353224.5:c.1819C>T	p.Pro607Ser	p.P607S	ENST00000353224	NM_177990.2	607	Ccc/Tcc	8/10	0.45801796480922	3	FACETS	0.687	0.592	0.791	0.344	0.296	0.396	SUBCLONAL	1	TRUE	1	0.456763341679646	3		411	454	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439564	51439564	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0066409-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	149	299	0	ENST00000262662.1:c.130-1G>T		p.X44_splice	ENST00000262662		44			0.45801796480922	3	FACETS	0.966	0.891	1	0.966	0.891	1	CLONAL	2	TRUE	1	0.456763341679646	3		299	415	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911540	101911540	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066409-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	53	323	0	ENST00000374994.4:c.1465A>C	p.Lys489Gln	p.K489Q	ENST00000374994	NM_004612.2	489	Aag/Cag	9/9	0.45801796480922	3	FACETS	0.766	0.656	0.886	0.255	0.218	0.296	SUBCLONAL	1	TRUE	0	0.456763341679646	3		323	372	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530121	212530121	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066409-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	83	393	0	ENST00000342788.4:c.1798G>C	p.Ala600Pro	p.A600P	ENST00000342788	NM_005235.2	600	Gca/Cca	15/28	0.45801796480922	4	FACETS	0.959	0.848	1	0.32	0.282	0.36	CLONAL	1	TRUE	1	0.456763341679646	4		393	552	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590658	189590658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751698974	NA	P-0066409-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	67	354	0	ENST00000264731.3:c.1223G>A	p.Arg408His	p.R408H	ENST00000264731	NM_003722.4	408	cGt/cAt	10/14	0.134816143885479	3	FACETS	0.86	0.75	0.978			1	INDETERMINATE	1	TRUE	NA	0.456763341679646	3		354	419	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332369	70332369	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066409-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	32	325	0	ENST00000373644.4:c.274C>T	p.Gln92Ter	p.Q92*	ENST00000373644	NM_030625.2	92	Cag/Tag	2/12	0.350561929444377	2	FACETS	0.525	0.428	0.633	0.262	0.214	0.317	SUBCLONAL	1	TRUE	0	0.456763341679646	2		325	267	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56792532	56792532	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066409-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	63	342	0	ENST00000308159.5:c.262G>T	p.Glu88Ter	p.E88*	ENST00000308159	NM_014669.4	88	Gag/Tag	3/22	0.45801796480922	3	FACETS	0.73	0.633	0.835	0.365	0.316	0.418	SUBCLONAL	1	TRUE	1	0.456763341679646	3		342	464	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261046	16261046	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066409-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	93	469	0	ENST00000375759.3:c.8311A>G	p.Thr2771Ala	p.T2771A	ENST00000375759	NM_015001.2	2771	Aca/Gca	11/15	0.170496856977525	3	FACETS	1	0.963	1	0.588	0.526	0.654	INDETERMINATE	1	TRUE	1	0.456763341679646	3		469	425	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446848	49446848	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066409-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	294	459	0	ENST00000301067.7:c.962G>T	p.Arg321Leu	p.R321L	ENST00000301067	NM_003482.3	321	cGg/cTg	8/54	0.456763341679646	5	FACETS	0.951	0.9	1	0.951	0.9	1	CLONAL	3	TRUE	2	0.456763341679646	5		459	760	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955577	55955577	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs374457339	NA	P-0066409-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	141	319	0	ENST00000263923.4:c.3368C>A	p.Thr1123Asn	p.T1123N	ENST00000263923	NM_002253.2	1123	aCt/aAt	25/30	0.45801796480922	4	FACETS	0.988	0.908	1	0.988	0.908	1	CLONAL	2	TRUE	2	0.456763341679646	4		319	455	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980876	40980876	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066409-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	65	336	0	ENST00000373198.4:c.1610G>T	p.Ser537Ile	p.S537I	ENST00000373198	NM_133170.3	537	aGc/aTc	10/32	1	2	FACETS	0.749	0.652	0.853	0.749	0.652	0.853	SUBCLONAL	1	TRUE	1	0.456763341679646	2		336	380	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934361	81934361	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066409-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	65	326	0	ENST00000359376.3:c.1338G>C	p.Gln446His	p.Q446H	ENST00000359376	NM_002661.3	446	caG/caC	14/33	0.170496856977525	3	FACETS	0.953	0.83	1	0.476	0.415	0.542	INDETERMINATE	1	TRUE	1	0.456763341679646	3		326	367	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753695	42753695	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066409-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	216	461	0	ENST00000222329.4:c.569G>T	p.Ser190Ile	p.S190I	ENST00000222329	NM_006494.2	190	aGt/aTt	4/4	0.45801796480922	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.456763341679646	4		461	641	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965858	90965858	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066409-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	146	311	0	ENST00000265433.3:c.1459T>A	p.Cys487Ser	p.C487S	ENST00000265433	NM_002485.4	487	Tgt/Agt	11/16	0.336054099785851	3	FACETS	1	0.982	1	0.793	0.735	0.852	CLONAL	2	TRUE	0	0.456763341679646	3		311	330	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124532377	124532377	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066409-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	369	327	0	ENST00000357628.3:c.67G>T	p.Val23Phe	p.V23F	ENST00000357628	NM_015450.2	23	Gtc/Ttc	6/19	0.456763341679646	6	FACETS	1	0.98	1	1	0.98	1	CLONAL	5	TRUE	1	0.456763341679646	6		327	600	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	53	317	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.948	0.821	1	1	0.976	1	CLONAL	2	TRUE	1	0.291331200432232	2		317	192	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	134	420	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.291331200432232	6	FACETS	1	0.979	1			1	CLONAL	2	TRUE	NA	0.291331200432232	6		420	585	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57470707	57470707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	31	365	0	ENST00000371085.3:c.180G>A	p.Met60Ile	p.M60I	ENST00000371085	NM_000516.4	60	atG/atA	2/13	0.197688827369478	3	FACETS	0.504	0.407	0.614	0.252	0.203	0.307	SUBCLONAL	1	TRUE	1	0.291331200432232	3		365	484	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922340	178922340	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	47	252	0	ENST00000263967.3:c.1109A>G	p.Asn370Ser	p.N370S	ENST00000263967	NM_006218.2	370	aAt/aGt	6/21	0.197688827369478	3	FACETS	0.807	0.688	0.936	0.807	0.688	0.936	CLONAL	2	TRUE	1	0.291331200432232	3		252	229	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662172	227662172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770740222	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	97	465	0	ENST00000305123.5:c.1283C>T	p.Ser428Leu	p.S428L	ENST00000305123	NM_005544.2	428	tCg/tTg	1/2	0.291331200432232	2	FACETS	0.802	0.72	0.889	0.802	0.72	0.889	CLONAL	2	TRUE	0	0.291331200432232	2		465	415	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856356	45856356	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	117	418	0	ENST00000391945.4:c.1816G>C	p.Glu606Gln	p.E606Q	ENST00000391945	NM_000400.3	606	Gag/Cag	19/23	0.197688827369478	3	FACETS	0.986	0.902	1	1	0.986	1	CLONAL	3	TRUE	1	0.291331200432232	3		418	311	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882362	89882362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	51	382	0	ENST00000389301.3:c.112G>A	p.Glu38Lys	p.E38K	ENST00000389301	NM_000135.2	38	Gaa/Aaa	2/43	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.291331200432232	2		382	330	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374320	81374320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	20	262	0	ENST00000222390.5:c.742G>A	p.Glu248Lys	p.E248K	ENST00000222390	NM_000601.4	248	Gaa/Aaa	6/18	0.158562214477042	5	FACETS	0.569	0.434	0.726	0.19	0.144	0.242	INDETERMINATE	1	TRUE	2	0.291331200432232	5		262	347	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069459	30069459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	19	404	0	ENST00000338641.4:c.1324G>A	p.Glu442Lys	p.E442K	ENST00000338641	NM_000268.3	442	Gag/Aag	12/16	1	2	FACETS	0.444	0.337	0.569	0.444	0.337	0.569	SUBCLONAL	1	TRUE	1	0.291331200432232	2		404	294	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675071	40675071	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	33	385	0	ENST00000249776.8:c.35T>G	p.Val12Gly	p.V12G	ENST00000249776	NM_033286.3	12	gTt/gGt	1/9	1	2	FACETS	0.558	0.454	0.675	0.558	0.454	0.675	SUBCLONAL	1	TRUE	1	0.291331200432232	2		385	406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs878854073	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	82	364	0	ENST00000269305.4:c.673-1G>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.136773773185707	3	FACETS	1	0.897	1	1	0.897	1	INDETERMINATE	2	TRUE	1	0.291331200432232	3		364	320	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577497	7577497	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	67	341	0	ENST00000269305.4:c.782+2T>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.136773773185707	3	FACETS	1	0.967	1	0.677	0.591	0.769	INDETERMINATE	1	TRUE	1	0.291331200432232	3		341	389	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205786	128205786	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	62	434	0	ENST00000341105.2:c.89C>A	p.Ala30Glu	p.A30E	ENST00000341105	NM_032638.4	30	gCg/gAg	2/6	0.197688827369478	3	FACETS	1	0.96	1	0.647	0.561	0.739	CLONAL	1	TRUE	1	0.291331200432232	3		434	377	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2111921	2111921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	63	446	0	ENST00000219476.3:c.1169C>T	p.Thr390Met	p.T390M	ENST00000219476	NM_000548.3	390	aCg/aTg	12/42	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.291331200432232	2		446	360	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641076	3641076	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	53	411	0	ENST00000294008.3:c.2563T>G	p.Tyr855Asp	p.Y855D	ENST00000294008	NM_032444.2	855	Tat/Gat	12/15	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.291331200432232	2		411	302	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190546	32190546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751511627	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	95	434	0	ENST00000375023.3:c.193C>T	p.Pro65Ser	p.P65S	ENST00000375023	NM_004557.3	65	Cct/Tct	3/30	0.196632889116989	5	FACETS	0.987	0.882	1	0.658	0.588	0.731	CLONAL	2	TRUE	2	0.291331200432232	5		434	475	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67624756	67624756	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	19	349	0	ENST00000272342.5:c.176G>C	p.Arg59Pro	p.R59P	ENST00000272342	NM_019002.3	59	cGa/cCa	1/6	0.291331200432232	3	FACETS	0.412	0.312	0.529	0.206	0.156	0.265	SUBCLONAL	1	TRUE	1	0.291331200432232	3		349	363	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921476	178921477	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	33	305	0	ENST00000263967.3:c.958_959delinsTT	p.Gly320Leu	p.G320L	ENST00000263967	NM_006218.2	320	GGa/TTa	5/21	0.197688827369478	3	FACETS	0.848	0.693	1	0.424	0.346	0.511	CLONAL	1	TRUE	1	0.291331200432232	3		305	306	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913085	44913085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	46	129	0	ENST00000377967.4:c.760C>T	p.His254Tyr	p.H254Y	ENST00000377967	NM_021140.2	254	Cac/Tac	10/29	0.291331200432232	2	FACETS	1	0.92	1			1	CLONAL	2	TRUE	NA	0.291331200432232	2		129	143	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366901	15366901	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	42	405	0	ENST00000263377.2:c.1725A>T	p.Lys575Asn	p.K575N	ENST00000263377	NM_058243.2	575	aaA/aaT	9/20	0.136773773185707	3	FACETS	0.81	0.677	0.956	0.405	0.338	0.478	INDETERMINATE	1	TRUE	1	0.291331200432232	3		405	408	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069468	30069468	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	20	378	0	ENST00000338641.4:c.1333G>C	p.Glu445Gln	p.E445Q	ENST00000338641	NM_000268.3	445	Gag/Cag	12/16	1	2	FACETS	0.497	0.381	0.634	0.497	0.381	0.634	SUBCLONAL	1	TRUE	1	0.291331200432232	2		378	276	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158268	106158268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	113	430	0	ENST00000380013.4:c.3169G>A	p.Glu1057Lys	p.E1057K	ENST00000380013	NM_001127208.2	1057	Gaa/Aaa	3/11	0.197688827369478	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.291331200432232	3		430	405	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004838	16004838	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	74	366	0	ENST00000268712.3:c.2416G>A	p.Glu806Lys	p.E806K	ENST00000268712	NM_006311.3	806	Gaa/Aaa	20/46	0.136773773185707	3	FACETS	1	0.964	1	0.634	0.557	0.717	INDETERMINATE	1	TRUE	1	0.291331200432232	3		366	459	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441969	52442001	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTACCTCAGGGCTGAAACCCTTGGTGAAGTCC	CCTACCTCAGGGCTGAAACCCTTGGTGAAGTCC	-	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	102	321	0	ENST00000460680.1:c.348_375+5del		p.X116_splice	ENST00000460680	NM_004656.3	116		5/17	0.196632889116989	5	FACETS	1	0.96	1	0.757	0.681	0.837	CLONAL	2	TRUE	2	0.291331200432232	5		321	443	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547368	106547368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572233387	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	109	457	1	ENST00000369096.4:c.605G>A	p.Arg202Gln	p.R202Q	ENST00000369096	NM_001198.3	202	cGg/cAg	4/7	0.179673832270594	2	FACETS	1	0.984	1	0.75	0.676	0.827	CLONAL	1	TRUE	0	0.291331200432232	2		458	499	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64286793	64286793	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	22	306	0	ENST00000370651.3:c.8G>C	p.Arg3Pro	p.R3P	ENST00000370651	NM_003463.4	3	cGa/cCa	2/6	0.179673832270594	2	FACETS	0.447	0.346	0.564	0.223	0.173	0.282	SUBCLONAL	1	TRUE	0	0.291331200432232	2		306	338	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21351012	21351012	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	70	436	0	ENST00000215739.8:c.2247C>G	p.Tyr749Ter	p.Y749*	ENST00000215739	NM_006767.3	749	taC/taG	19/21	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.291331200432232	2		436	398	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659275	86659275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	40	321	0	ENST00000274376.6:c.1564C>T	p.Leu522Phe	p.L522F	ENST00000274376	NM_002890.2	522	Ctc/Ttc	11/25	1	2	FACETS	0.825	0.687	0.976	0.825	0.687	0.976	CLONAL	1	TRUE	1	0.291331200432232	2		321	333	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461417	138461417	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	20	270	0	ENST00000289153.2:c.604C>G	p.His202Asp	p.H202D	ENST00000289153	NM_006219.2	202	Cat/Gat	3/22	0.197688827369478	3	FACETS	0.614	0.471	0.782	0.307	0.235	0.391	SUBCLONAL	1	TRUE	1	0.291331200432232	3		270	256	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224537	39224537	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	35	303	0	ENST00000402219.2:c.2821G>C	p.Glu941Gln	p.E941Q	ENST00000402219	NM_005633.3	941	Gaa/Caa	18/23	0.291331200432232	3	FACETS	0.906	0.745	1	0.453	0.372	0.543	CLONAL	1	TRUE	1	0.291331200432232	3		303	304	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268736	46268737	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGTTCCT	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	90	496	0	ENST00000371998.3:c.3024_3030dup	p.Pro1011PhefsTer19	p.P1011Ffs*19	ENST00000371998		1007	-/GGTTCCT	16/23	0.197688827369478	3	FACETS	1	0.972	1	0.647	0.575	0.723	CLONAL	1	TRUE	1	0.291331200432232	3		496	547	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582153	95582153	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	20	387	0	ENST00000393063.1:c.1758G>C	p.Leu586Phe	p.L586F	ENST00000393063	NM_030621.3	586	ttG/ttC	12/28	0.291331200432232	2	FACETS	0.407	0.311	0.52	0.204	0.155	0.26	SUBCLONAL	1	TRUE	0	0.291331200432232	2		387	337	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791322	42791322	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	24	460	0	ENST00000575354.2:c.382G>A	p.Glu128Lys	p.E128K	ENST00000575354	NM_015125.3	128	Gag/Aag	3/20	0.291331200432232	5	FACETS	0.548	0.429	0.686			1	SUBCLONAL	1	TRUE	NA	0.291331200432232	5		460	432	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694625	176694625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200423668	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	53	413	0	ENST00000439151.2:c.5209G>A	p.Asp1737Asn	p.D1737N	ENST00000439151	NM_022455.4	1737	Gat/Aat	15/23	1	2	FACETS	0.868	0.742	1	0.868	0.742	1	CLONAL	1	TRUE	1	0.291331200432232	2		413	419	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540379	187540379	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	28	459	0	ENST00000441802.2:c.7361G>T	p.Arg2454Leu	p.R2454L	ENST00000441802	NM_005245.3	2454	cGg/cTg	10/27	0.197688827369478	3	FACETS	0.512	0.409	0.63	0.256	0.204	0.315	SUBCLONAL	1	TRUE	1	0.291331200432232	3		459	430	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774072	56774072	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	27	443	0	ENST00000337432.4:c.423T>A	p.Asp141Glu	p.D141E	ENST00000337432	NM_058216.2	141	gaT/gaA	3/9	0.197688827369478	3	FACETS	0.528	0.42	0.652	0.264	0.21	0.326	SUBCLONAL	1	TRUE	1	0.291331200432232	3		443	402	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933216	100933216	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	30	317	0	ENST00000325455.5:c.2174A>T	p.Gln725Leu	p.Q725L	ENST00000325455	NM_001202474.3	725	cAa/cTa	4/8	0.136773773185707	3	FACETS	0.583	0.469	0.711	0.291	0.234	0.356	INDETERMINATE	1	TRUE	1	0.291331200432232	3		317	405	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595599	55595599	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	46	313	0	ENST00000288135.5:c.2089C>G	p.His697Asp	p.H697D	ENST00000288135	NM_000222.2	697	Cat/Gat	14/21	0.197688827369478	3	FACETS	0.83	0.706	0.963	0.83	0.706	0.963	CLONAL	2	TRUE	1	0.291331200432232	3		313	218	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075146	16075146	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	110	392	0	ENST00000268712.3:c.406G>C	p.Gly136Arg	p.G136R	ENST00000268712	NM_006311.3	136	Ggg/Cgg	4/46	0.136773773185707	3	FACETS	0.758	0.683	0.836	0.758	0.683	0.836	INDETERMINATE	2	TRUE	1	0.291331200432232	3		392	571	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962583	100962583	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	63	304	0	ENST00000325455.5:c.1814G>C	p.Gly605Ala	p.G605A	ENST00000325455	NM_001202474.3	605	gGa/gCa	3/8	0.136773773185707	3	FACETS	0.753	0.656	0.857	0.753	0.656	0.857	INDETERMINATE	2	TRUE	1	0.291331200432232	3		304	329	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259853	142259853	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	78	356	0	ENST00000350721.4:c.3474G>C	p.Leu1158Phe	p.L1158F	ENST00000350721	NM_001184.3	1158	ttG/ttC	18/47	0.197688827369478	3	FACETS	1	0.976	1	0.737	0.651	0.829	CLONAL	1	TRUE	1	0.291331200432232	3		356	416	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816142	89816142	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	64	385	0	ENST00000389301.3:c.3235A>T	p.Lys1079Ter	p.K1079*	ENST00000389301	NM_000135.2	1079	Aaa/Taa	32/43	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.291331200432232	2		385	331	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056333	27056337	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCC	CGGCC	-	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	90	405	0	ENST00000324856.7:c.1329_1333del	p.Gly444LeufsTer177	p.G444Lfs*177	ENST00000324856	NM_006015.4	443	ggCGGCCtc/ggtc	2/20	0.179673832270594	2	FACETS	1	0.973	1	0.652	0.581	0.727	CLONAL	1	TRUE	0	0.291331200432232	2		405	474	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061304	38061304	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	24	442	0	ENST00000250448.2:c.685G>C	p.Val229Leu	p.V229L	ENST00000250448	NM_004496.3	229	Gtc/Ctc	2/2	0.291331200432232	2	FACETS	0.441	0.345	0.551	0.22	0.172	0.276	SUBCLONAL	1	TRUE	0	0.291331200432232	2		442	374	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713667	52713667	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	126	424	0	ENST00000394830.3:c.61G>A	p.Asp21Asn	p.D21N	ENST00000394830	NM_018313.4	21	Gat/Aat	2/30	0.196632889116989	5	FACETS	1	0.961	1	0.737	0.67	0.807	CLONAL	2	TRUE	2	0.291331200432232	5		424	562	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345806	152345806	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	59	334	0	ENST00000359321.1:c.764T>C	p.Leu255Ser	p.L255S	ENST00000359321	NM_005431.1	255	tTa/tCa	3/3	0.158562214477042	5	FACETS	0.893	0.773	1	0.595	0.515	0.681	INDETERMINATE	2	TRUE	2	0.291331200432232	5		334	326	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0066436-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	17	270	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.634	0.472	0.827	0.634	0.472	0.827	SUBCLONAL	1	TRUE	1	0.14	2		270	383	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098975	178098975	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1328994103	NA	P-0066436-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	26	418	0	ENST00000397062.3:c.70T>C	p.Trp24Arg	p.W24R	ENST00000397062	NM_006164.4	24	Tgg/Cgg	2/5	1	2	FACETS	0.638	0.504	0.793	0.638	0.504	0.793	SUBCLONAL	1	TRUE	1	0.14	2		418	582	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0066504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	560	270	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.280941483469338	8	FACETS	1	0.98	1	1	0.995	1	CLONAL	8	TRUE	1	0.280941483469338	8		270	905	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0066504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	365	409	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.280941483469338	2	FACETS	1	0.985	1	1	0.997	1	CLONAL	4	TRUE	0	0.280941483469338	2		410	617	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618715	37618716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0066504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	229	553	0	ENST00000447079.4:c.397dup	p.Ser133LysfsTer24	p.S133Kfs*24	ENST00000447079	NM_015083.1	131	gaa/gAaa	1/14	1	2	FACETS	0.906	0.845	0.968	1	0.994	1	CLONAL	2	TRUE	1	0.280941483469338	2		553	900	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55704606	55704606	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	37	364	0	ENST00000284073.2:c.670del	p.Ala224ArgfsTer76	p.A224Rfs*76	ENST00000284073	NM_138962.2	223	gtG/gt	10/14	1	2	FACETS	0.453	0.373	0.544	0.453	0.373	0.544	SUBCLONAL	1	TRUE	1	0.280941483469338	2		364	581	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0066573-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	10	410	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		410	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0066574-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	97	529	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.331532710630373	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	3	TRUE	0	0.329817594026048	3		529	216	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101267	27101268	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0066574-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	40	455	0	ENST00000324856.7:c.4555dup	p.Gln1519ProfsTer13	p.Q1519Pfs*13	ENST00000324856	NM_006015.4	1517	gcc/gCcc	18/20	0.331532710630373	1	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	0	0.329817594026048	1		455	196	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448579	89448579	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066574-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	56	460	0	ENST00000336596.2:c.1543G>C	p.Ala515Pro	p.A515P	ENST00000336596	NM_005233.5	515	Gct/Cct	7/17	0.31332600040381	4	FACETS	0.953	0.834	1	0.953	0.834	1	CLONAL	3	TRUE	1	0.329817594026048	4		460	158	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664918	138664918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs565208053	NA	P-0066574-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	15	294	0	ENST00000330315.3:c.647C>T	p.Ala216Val	p.A216V	ENST00000330315	NM_023067.3	216	gCc/gTc	1/1	0.329817594026048	6	FACETS	0.712	0.522	0.94			1	CLONAL	1	TRUE	NA	0.329817594026048	6		294	212	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131151	55131151	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs758580911	NA	P-0066574-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	22	380	0	ENST00000257290.5:c.694G>T	p.Val232Leu	p.V232L	ENST00000257290	NM_006206.4	232	Gtg/Ttg	5/23	0.285194635722957	2	FACETS	1	0.868	1	0.575	0.452	0.713	CLONAL	1	TRUE	0	0.329817594026048	2		380	116	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190717486	190717486	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066577-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	50	396	0	ENST00000441310.2:c.805C>T	p.Gln269Ter	p.Q269*	ENST00000441310	NM_000534.4	269	Caa/Taa	7/13	1	2	FACETS	0.805	0.683	0.938	0.805	0.683	0.938	CLONAL	1	TRUE	1	0.26	2		396	478	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180405	32180405	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0066577-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	70	609	0	ENST00000375023.3:c.2527-1G>C		p.X843_splice	ENST00000375023	NM_004557.3	843			1	2	FACETS	0.988	0.863	1	0.988	0.863	1	CLONAL	1	TRUE	1	0.26	2		609	545	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363307	40363307	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066577-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	40	639	0	ENST00000397332.2:c.922G>C	p.Glu308Gln	p.E308Q	ENST00000397332	NM_001033082.2	308	Gag/Cag	3/3	0.3	1	FACETS	0.442	0.367	0.527	0.442	0.367	0.527	SUBCLONAL	1	TRUE	0	0.26	1		639	605	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41554474	41554474	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066577-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	69	437	0	ENST00000263253.7:c.3560G>T	p.Arg1187Leu	p.R1187L	ENST00000263253	NM_001429.3	1187	cGt/cTt	19/31	1	2	FACETS	0.99	0.864	1	0.99	0.864	1	CLONAL	1	TRUE	1	0.26	2		437	536	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974767	21974775	+	inframe_deletion	In_Frame_Del	DEL	CGCGGCCGT	CGCGGCCGT	-	novel	NA	P-0066577-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	60	583	0	ENST00000304494.5:c.52_60del	p.Thr18_Ala20del	p.T18_A20del	ENST00000304494	NM_000077.4	18	ACGGCCGCG/-	1/3	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.26	2		583	458	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691947	30691947	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0066577-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	86	526	0	ENST00000295754.5:c.449C>G	p.Ser150Ter	p.S150*	ENST00000295754	NM_003242.5	150	tCa/tGa	3/7	0.3	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.26	1		526	525	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231763	66231763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs865862638	NA	P-0066577-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	23	386	0	ENST00000273854.3:c.1937G>A	p.Gly646Glu	p.G646E	ENST00000273854	NM_004439.5	646	gGa/gAa	11/18	0.201451077116278	2	FACETS	0.461	0.359	0.579	0.23	0.179	0.29	SUBCLONAL	1	TRUE	0	0.26	2		386	384	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915145	131915145	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066577-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	65	408	0	ENST00000265335.6:c.502G>C	p.Glu168Gln	p.E168Q	ENST00000265335		168	Gaa/Caa	4/25	0.201451077116278	2	FACETS	1	0.964	1	0.663	0.578	0.755	CLONAL	1	TRUE	0	0.26	2		408	377	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536187	41536187	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066577-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	66	463	0	ENST00000263253.7:c.1804G>C	p.Asp602His	p.D602H	ENST00000263253	NM_001429.3	602	Gac/Cac	9/31	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.26	2		463	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0066586-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	193	396	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.094566500123495	5	FACETS	0.897	0.843	0.952			1	INDETERMINATE	4	TRUE	NA	0.474386241938026	5		396	388	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0066586-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	76	375	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.476039804473666	3	FACETS	0.901	0.804	1	0.901	0.804	1	CLONAL	2	TRUE	1	0.474386241938026	3		375	220	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961055	55961055	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1229432573	NA	P-0066586-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	68	460	0	ENST00000263923.4:c.2885G>A	p.Arg962His	p.R962H	ENST00000263923	NM_002253.2	962	cGc/cAc	21/30	NA	2	FACETS	0.719	0.628	0.816			1	INDETERMINATE	1	TRUE	NA	0.474386241938026	2		460	399	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410117	63410117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066586-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	177	634	0	ENST00000330258.3:c.3050G>A	p.Gly1017Glu	p.G1017E	ENST00000330258	NM_152424.3	1017	gGg/gAg	2/2	NA	2	FACETS	0.88	0.82	0.94			1	INDETERMINATE	2	TRUE	NA	0.474386241938026	2		634	424	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0066595-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	56	171	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.227011876754217	4	FACETS	0.893	0.774	1	0.893	0.774	1	CLONAL	3	TRUE	1	0.227011876754217	4		171	226	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0066595-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	44	308	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.883	0.741	1	0.883	0.741	1	CLONAL	1	TRUE	1	0.227011876754217	2		308	439	SUCCESS
EED	8726	MSKCC	GRCh37	11	85963189	85963189	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0066595-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	17	207	0	ENST00000263360.6:c.268-1G>A		p.X90_splice	ENST00000263360	NM_003797.3	90			0.223909352441497	1	FACETS	0.667	0.499	0.865	0.667	0.499	0.865	SUBCLONAL	1	TRUE	0	0.227011876754217	1		207	199	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252865	36252865	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066595-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	34	281	0	ENST00000300305.3:c.497G>T	p.Arg166Leu	p.R166L	ENST00000300305		166	cGa/cTa	4/8	1	2	FACETS	0.692	0.565	0.834	0.692	0.565	0.834	SUBCLONAL	1	TRUE	1	0.227011876754217	2		281	433	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374308	138374308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066595-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	57	348	0	ENST00000289153.2:c.3136G>A	p.Asp1046Asn	p.D1046N	ENST00000289153	NM_006219.2	1046	Gat/Aat	22/22	0.227011876754217	4	FACETS	0.977	0.837	1	0.326	0.279	0.377	CLONAL	1	TRUE	1	0.227011876754217	4		348	631	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230468590	230468590	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066595-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	56	418	0	ENST00000391860.1:c.928G>T	p.Gly310Ter	p.G310*	ENST00000391860	NM_001258311.1	310	Gga/Tga	5/7	0.222481196422325	3	FACETS	0.983	0.842	1	0.491	0.421	0.568	CLONAL	1	TRUE	1	0.227011876754217	3		418	559	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196471	67196471	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs546014798	NA	P-0066595-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	52	309	0	ENST00000312629.5:c.97G>C	p.Glu33Gln	p.E33Q	ENST00000312629	NM_003952.2	33	Gag/Cag	2/15	1	2	FACETS	0.969	0.826	1	0.969	0.826	1	CLONAL	1	TRUE	1	0.227011876754217	2		309	473	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207738	102207738	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066595-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	24	345	0	ENST00000263464.3:c.1720C>T	p.His574Tyr	p.H574Y	ENST00000263464	NM_001165.4	574	Cat/Tat	9/9	0.223909352441497	1	FACETS	0.531	0.416	0.664	0.531	0.416	0.664	SUBCLONAL	1	TRUE	0	0.227011876754217	1		345	353	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913535	NA	P-0066595-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	43	260	0	ENST00000311936.3:c.37G>C	p.Gly13Arg	p.G13R	ENST00000311936	NM_004985.3	13	Ggc/Cgc	2/5	1	2	FACETS	0.949	0.796	1	0.949	0.796	1	CLONAL	1	TRUE	1	0.227011876754217	2		260	399	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643378	38643378	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066595-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	72	343	0	ENST00000299084.4:c.848C>G	p.Ser283Cys	p.S283C	ENST00000299084	NM_152594.2	283	tCt/tGt	7/7	0.223909352441497	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.227011876754217	1		343	454	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89880961	89880961	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066595-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	27	334	0	ENST00000389301.3:c.250G>C	p.Glu84Gln	p.E84Q	ENST00000389301	NM_000135.2	84	Gag/Cag	3/43	1	2	FACETS	0.564	0.448	0.696	0.564	0.448	0.696	SUBCLONAL	1	TRUE	1	0.227011876754217	2		334	422	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158322	106158322	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066595-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	56	373	0	ENST00000380013.4:c.3223G>A	p.Asp1075Asn	p.D1075N	ENST00000380013	NM_001127208.2	1075	Gat/Aat	3/11	1	2	FACETS	0.973	0.834	1	0.973	0.834	1	CLONAL	1	TRUE	1	0.227011876754217	2		373	507	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637847	176637847	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066595-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	53	318	0	ENST00000439151.2:c.2447C>G	p.Ser816Cys	p.S816C	ENST00000439151	NM_022455.4	816	tCt/tGt	5/23	1	2	FACETS	0.94	0.802	1	0.94	0.802	1	CLONAL	1	TRUE	1	0.227011876754217	2		318	497	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001128	150001128	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066595-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	51	335	0	ENST00000253339.5:c.2476C>G	p.His826Asp	p.H826D	ENST00000253339		826	Cat/Gat	4/7	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.227011876754217	2		335	401	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874698	151874698	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs750597117	NA	P-0066595-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	71	427	1	ENST00000262189.6:c.7840G>T	p.Gly2614Cys	p.G2614C	ENST00000262189	NM_170606.2	2614	Ggt/Tgt	38/59	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.227011876754217	2		428	567	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70967609	70967609	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1462829390	NA	P-0066595-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	48	320	0	ENST00000276594.2:c.1414C>G	p.Gln472Glu	p.Q472E	ENST00000276594	NM_024504.3	472	Caa/Gaa	7/8	1	2	FACETS	0.942	0.797	1	0.942	0.797	1	CLONAL	1	TRUE	1	0.227011876754217	2		320	449	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0066607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	161	439	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.470199855916287	2		439	574	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807889	1807889	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs78311289	NA	P-0066607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	294	828	0	ENST00000260795.2:c.1948A>G	p.Lys650Glu	p.K650E	ENST00000260795		650	Aag/Gag	13/17	0.181784780942443	1	FACETS	0.879	0.828	0.932	0.879	0.828	0.932	INDETERMINATE	1	TRUE	0	0.470199855916287	1		828	1088	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	213	667	0	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.470199855916287	2		667	864	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	94	374	0	ENST00000335508.6:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000335508	NM_012433.2	902	Gaa/Aaa	18/25	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.470199855916287	2		374	348	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	142	317	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.470199855916287	2		317	565	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328377	137328377	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	394	544	0	ENST00000481739.1:c.1306C>G	p.Leu436Val	p.L436V	ENST00000481739	NM_002957.4	436	Ctc/Gtc	10/10	0.470199855916287	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.470199855916287	2		544	793	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241979	39241979	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	80	343	0	ENST00000402219.2:c.1867T>A	p.Phe623Ile	p.F623I	ENST00000402219	NM_005633.3	623	Ttt/Att	11/23	1	2	FACETS	0.975	0.865	1	0.975	0.865	1	CLONAL	1	TRUE	1	0.470199855916287	2		343	349	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940480	76940480	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	86	197	0	ENST00000373344.5:c.613A>G	p.Met205Val	p.M205V	ENST00000373344	NM_000489.3	205	Atg/Gtg	8/35	1	1	FACETS	0.79	0.718	0.863	1	0.985	1	SUBCLONAL	2	TRUE	0	0.470199855916287	1		197	177	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965402	68965405	+	frameshift_variant	Frame_Shift_Del	DEL	GTTT	GTTT	-	novel	NA	P-0066607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	70	453	0	ENST00000288368.4:c.1020_1023del	p.Cys341TrpfsTer16	p.C341Wfs*16	ENST00000288368	NM_024870.2	338	tgGTTT/tg	9/40	1	2	FACETS	0.728	0.637	0.825	0.728	0.637	0.825	SUBCLONAL	1	TRUE	1	0.470199855916287	2		453	409	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56432306	56432306	+	stop_lost	Nonstop_Mutation	SNP	A	A	T	novel	NA	P-0066607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	132	357	0	ENST00000407977.2:c.2350T>A	p.Ter784ArgextTer5	p.*784Rext*5	ENST00000407977		784	Tga/Aga	10/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.470199855916287	2		357	534	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225365008	225365134	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAATGTTCAAATTCATTTTTAATTTTGAACACTTACTTGTACACAGTGATACAAAGTCTGATTTTGATTTACCTTCTGAATATCTCAAAAGCATGTCTTGGTGCTGGTGGGATGTTGCACTTTGGTG	TAATGTTCAAATTCATTTTTAATTTTGAACACTTACTTGTACACAGTGATACAAAGTCTGATTTTGATTTACCTTCTGAATATCTCAAAAGCATGTCTTGGTGCTGGTGGGATGTTGCACTTTGGTG	-	novel	NA	P-0066607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	126	243	0	ENST00000264414.4:c.1556_1610+72del		p.X519_splice	ENST00000264414	NM_003590.4	519		11/16	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.470199855916287	2		243	370	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619267	37619267	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs747011911	NA	P-0066607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	179	612	0	ENST00000447079.4:c.943A>G	p.Arg315Gly	p.R315G	ENST00000447079	NM_015083.1	315	Aga/Gga	1/14	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.470199855916287	2		612	754	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255558	16255558	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	197	512	0	ENST00000375759.3:c.2823G>C	p.Lys941Asn	p.K941N	ENST00000375759	NM_015001.2	941	aaG/aaC	11/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.470199855916287	2		512	751	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753984	57753984	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	133	407	0	ENST00000274289.3:c.640A>G	p.Asn214Asp	p.N214D	ENST00000274289	NM_006622.3	214	Aat/Gat	5/14	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.470199855916287	2		407	539	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871872	12871872	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs375717769	NA	P-0066607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	150	437	0	ENST00000228872.4:c.589C>A	p.Gln197Lys	p.Q197K	ENST00000228872	NM_004064.3	197	Caa/Aaa	2/3	1	2	FACETS	0.955	0.875	1	0.955	0.875	1	CLONAL	1	TRUE	1	0.470199855916287	2		437	668	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051608	30051650	+	frameshift_variant	Frame_Shift_Del	DEL	CGGAAATGTGGGAGGAGAGAATTACTGCTTGGTACGCAGAGCA	CGGAAATGTGGGAGGAGAGAATTACTGCTTGGTACGCAGAGCA	-	novel	NA	P-0066607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	75	397	0	ENST00000338641.4:c.543_585del	p.Met183AlafsTer12	p.M183Afs*12	ENST00000338641	NM_000268.3	181	cCGGAAATGTGGGAGGAGAGAATTACTGCTTGGTACGCAGAGCAc/cc	6/16	0.470199855916287	1	FACETS	0.665	0.586	0.748	0.665	0.586	0.748	SUBCLONAL	1	TRUE	0	0.470199855916287	1		397	367	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922721	44922722	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0066607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	274	241	0	ENST00000377967.4:c.1583_1584del	p.Thr528SerfsTer2	p.T528Sfs*2	ENST00000377967	NM_021140.2	528	ACa/a	16/29	0.431018327970706	2	FACETS	0.865	0.826	0.904			1	CLONAL	3	TRUE	NA	0.470199855916287	2		241	449	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77930437	77930437	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	170	510	0	ENST00000361507.4:c.1912G>T	p.Asp638Tyr	p.D638Y	ENST00000361507	NM_080491.2	638	Gat/Tat	10/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.470199855916287	2		510	667	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765733	41765733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	164	601	0	ENST00000301178.4:c.2609C>T	p.Pro870Leu	p.P870L	ENST00000301178	NM_021913.4	870	cCt/cTt	20/20	1	2	FACETS	0.888	0.816	0.962	0.888	0.816	0.962	CLONAL	1	TRUE	1	0.470199855916287	2		601	786	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203604	108203604	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs754002355	NA	P-0066607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	86	459	0	ENST00000278616.4:c.7904C>A	p.Ala2635Asp	p.A2635D	ENST00000278616	NM_000051.3	2635	gCc/gAc	53/63	0.470199855916287	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.470199855916287	1		459	254	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59870985	59870985	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs759360709	NA	P-0066607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	66	398	0	ENST00000259008.2:c.1446C>G	p.Ile482Met	p.I482M	ENST00000259008	NM_032043.2	482	atC/atG	10/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.470199855916287	2		398	245	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661483	227661483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751198979	NA	P-0066607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	191	642	0	ENST00000305123.5:c.1972G>A	p.Asp658Asn	p.D658N	ENST00000305123	NM_005544.2	658	Gac/Aac	1/2	1	2	FACETS	0.908	0.84	0.978	0.908	0.84	0.978	CLONAL	1	TRUE	1	0.470199855916287	2		642	895	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591825	48591825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767342	NA	P-0066612-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	181	212	0	ENST00000342988.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000342988	NM_005359.5	330	Gaa/Aaa	9/12	0.515419165641578	1	FACETS	0.995	0.925	1	0.995	0.925	1	CLONAL	1	TRUE	0	0.515419165641578	1		212	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0066612-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	140	166	1	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.479441123351232	1	FACETS	0.94	0.864	1	0.94	0.864	1	CLONAL	1	TRUE	0	0.515419165641578	1		167	429	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032474	12032474	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066612-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	77	131	0	ENST00000353533.5:c.910C>T	p.Arg304Ter	p.R304*	ENST00000353533	NM_003010.3	304	Cga/Tga	9/11	0.479441123351232	1	FACETS	0.732	0.649	0.819	0.732	0.649	0.819	SUBCLONAL	1	TRUE	0	0.515419165641578	1		131	303	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0066612-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	162	144	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.505143366181175	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.515419165641578	1		144	461	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057023	180057023	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066612-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	131	244	0	ENST00000261937.6:c.596A>G	p.His199Arg	p.H199R	ENST00000261937	NM_182925.4	199	cAc/cGc	5/30	0.282610418902286	0	FACETS	0.524	0.479	0.571			1	INDETERMINATE	1	TRUE	0	0.515419165641578	0		244	470	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265203	5265203	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066612-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	90	197	0	ENST00000357368.4:c.384C>A	p.Asp128Glu	p.D128E	ENST00000357368	NM_002850.3	128	gaC/gaA	5/38	1	2	FACETS	0.917	0.819	1	0.917	0.819	1	CLONAL	1	TRUE	1	0.515419165641578	2		197	381	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544555	86544555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066612-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	23	264	0	ENST00000262426.4:c.380C>T	p.Ala127Val	p.A127V	ENST00000262426	NM_001451.2	127	gCc/gTc	1/2	1	2	FACETS	0.201	0.156	0.253	0.201	0.156	0.253	SUBCLONAL	1	TRUE	1	0.515419165641578	2		264	445	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627402	37627402	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066612-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	33	222	0	ENST00000249071.6:c.317C>G	p.Pro106Arg	p.P106R	ENST00000249071	NM_002872.4	106	cCc/cGc	5/7	1	2	FACETS	0.208	0.168	0.252	0.208	0.168	0.252	SUBCLONAL	1	TRUE	1	0.515419165641578	2		222	617	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207065	1207073	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGGACCT	GGGGGACCT	TACC	novel	NA	P-0066612-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	145	213	0	ENST00000326873.7:c.153_161delinsTACC	p.Met51IlefsTer110	p.M51Ifs*110	ENST00000326873	NM_000455.4	51	atGGGGGACCTg/atTACCg	1/10	0.479441123351232	1	FACETS	0.847	0.778	0.918	0.847	0.778	0.918	CLONAL	1	TRUE	0	0.515419165641578	1		213	493	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037501	12037501	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	140	338	0	ENST00000396373.4:c.1132C>T	p.Arg378Ter	p.R378*	ENST00000396373	NM_001987.4	378	Cga/Tga	6/8	0.709389774101182	3	FACETS	0.883	0.807	0.962	0.441	0.403	0.481	CLONAL	1	TRUE	1	0.713580315852495	3		338	603	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166387	7166387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747554207	NA	P-0066636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	215	376	0	ENST00000302850.5:c.1639G>A	p.Gly547Arg	p.G547R	ENST00000302850	NM_000208.2	547	Ggg/Agg	8/22	0.709389774101182	3	FACETS	1	0.981	1	0.568	0.53	0.607	CLONAL	1	TRUE	1	0.713580315852495	3		376	720	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998369	100998392	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGCGAACGGGCCCTGCTGG	GGCGGCGCGAACGGGCCCTGCTGG	-	novel	NA	P-0066636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	105	339	0	ENST00000325455.5:c.1410_1433del	p.Gln471_Pro478del	p.Q471_P478del	ENST00000325455	NM_001202474.3	470	ccCCAGCAGGGCCCGTTCGCGCCGCCg/ccg	1/8	0.696286312641379	2	FACETS	0.931	0.845	1	0.466	0.422	0.511	CLONAL	1	TRUE	0	0.713580315852495	2		339	316	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130118	143130118	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	53	262	0	ENST00000262992.4:c.898G>A	p.Val300Ile	p.V300I	ENST00000262992	NM_001101669.1	300	Gtc/Atc	11/24	0.690711234977003	3	FACETS	0.969	0.838	1	0.484	0.419	0.555	CLONAL	1	TRUE	1	0.713580315852495	3		262	208	SUCCESS
EED	8726	MSKCC	GRCh37	11	85961442	85961442	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	199	321	0	ENST00000263360.6:c.219G>T	p.Trp73Cys	p.W73C	ENST00000263360	NM_003797.3	73	tgG/tgT	2/12	0.705683201157057	2	FACETS	0.975	0.929	1	0.975	0.929	1	CLONAL	2	TRUE	0	0.713580315852495	2		321	286	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435963	110435963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	164	487	0	ENST00000375856.3:c.2438C>T	p.Pro813Leu	p.P813L	ENST00000375856	NM_003749.2	813	cCc/cTc	1/2	0.708613558329743	3	FACETS	0.877	0.807	0.95	0.439	0.403	0.475	CLONAL	1	TRUE	1	0.713580315852495	3		487	711	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61324083	61324083	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	38	267	0	ENST00000283752.5:c.750A>C	p.Glu250Asp	p.E250D	ENST00000283752	NM_006919.2	250	gaA/gaC	7/8	0.708613558329743	3	FACETS	0.715	0.597	0.844	0.358	0.298	0.422	SUBCLONAL	1	TRUE	1	0.713580315852495	3		267	202	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0066659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	24	270	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.171480183933727	3	FACETS	0.855	0.67	1	0.427	0.335	0.535	CLONAL	1	TRUE	1	0.16	3		270	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0066659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	25	288	0	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	0.3	2	FACETS	1	0.826	1			1	CLONAL	1	TRUE	NA	0.16	2		288	297	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554292	63554293	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0066659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	29	375	0	ENST00000307078.5:c.446dup	p.Lys150GlufsTer18	p.K150Efs*18	ENST00000307078	NM_004655.3	149	ctg/ctTg	2/11	1	2	FACETS	0.918	0.737	1	0.918	0.737	1	CLONAL	1	TRUE	1	0.16	2		375	395	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0066660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	89	329	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.454427557105173	2		329	387	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0066660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	74	305	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.964	0.85	1	0.964	0.85	1	CLONAL	1	TRUE	1	0.454427557105173	2		305	338	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0066660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	69	332	1	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	0.88	0.772	0.996	0.88	0.772	0.996	CLONAL	1	TRUE	1	0.454427557105173	2		333	345	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487277	56487277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035001455	NA	P-0066660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	102	414	1	ENST00000267101.3:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000267101	NM_001982.3	475	Cgg/Tgg	12/28	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.454427557105173	2		415	397	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370985	55370985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	126	357	0	ENST00000297316.4:c.287C>G	p.Ala96Gly	p.A96G	ENST00000297316	NM_022454.3	96	gCc/gGc	1/2	0.436832112679576	3	FACETS	0.922	0.844	1	0.922	0.844	1	CLONAL	2	TRUE	1	0.454427557105173	3		357	369	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380346	14380346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	115	612	0	ENST00000256196.4:c.71G>A	p.Gly24Asp	p.G24D	ENST00000256196		24	gGc/gAc	1/6	0.389332605666891	2	FACETS	0.888	0.813	0.964	0.888	0.813	0.964	CLONAL	2	TRUE	0	0.454427557105173	2		612	285	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431257	49431267	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCTGGGCAG	GGCCTGGGCAG	-	novel	NA	P-0066660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	70	572	0	ENST00000301067.7:c.9872_9882del	p.Pro3291HisfsTer6	p.P3291Hfs*6	ENST00000301067	NM_003482.3	3291	cCTGCCCAGGCC/c	34/54	1	2	FACETS	0.705	0.617	0.8	0.705	0.617	0.8	SUBCLONAL	1	TRUE	1	0.454427557105173	2		572	437	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110086	115110086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1314719430	NA	P-0066660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	63	367	0	ENST00000257566.3:c.1792G>A	p.Gly598Arg	p.G598R	ENST00000257566	NM_016569.3	598	Gga/Aga	8/8	1	2	FACETS	0.963	0.84	1	0.963	0.84	1	CLONAL	1	TRUE	1	0.454427557105173	2		367	288	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133685	41133685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1216360372	NA	P-0066660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	88	464	0	ENST00000379561.5:c.1943C>T	p.Thr648Met	p.T648M	ENST00000379561	NM_002015.3	648	aCg/aTg	2/3	1	2	FACETS	0.92	0.82	1	0.92	0.82	1	CLONAL	1	TRUE	1	0.454427557105173	2		464	421	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141426	11141426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	78	449	0	ENST00000358026.2:c.3403C>T	p.Arg1135Trp	p.R1135W	ENST00000358026	NM_001128849.1	1135	Cgg/Tgg	25/36	1	2	FACETS	0.911	0.805	1	0.911	0.805	1	CLONAL	1	TRUE	1	0.454427557105173	2		449	377	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105746	27105766	+	inframe_deletion	In_Frame_Del	DEL	AGGAGATAGCCTTTTCAGGCA	AGGAGATAGCCTTTTCAGGCA	-	novel	NA	P-0066660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	90	500	0	ENST00000324856.7:c.5361_5381del	p.Glu1787_Lys1793del	p.E1787_K1793del	ENST00000324856	NM_006015.4	1786	gAGGAGATAGCCTTTTCAGGCAag/gag	20/20	1	2	FACETS	0.908	0.81	1	0.908	0.81	1	CLONAL	1	TRUE	1	0.454427557105173	2		500	436	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371721	55371721	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	76	483	0	ENST00000297316.4:c.411C>A	p.Tyr137Ter	p.Y137*	ENST00000297316	NM_022454.3	137	taC/taA	2/2	0.436832112679576	3	FACETS	0.968	0.853	1	0.484	0.426	0.546	CLONAL	1	TRUE	1	0.454427557105173	3		483	424	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422337	47422337	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1202657284	NA	P-0066660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	76	441	0	ENST00000404338.3:c.405C>A	p.Cys135Ter	p.C135*	ENST00000404338	NM_004491.4	135	tgC/tgA	1/6	1	2	FACETS	0.878	0.775	0.988	0.878	0.775	0.988	CLONAL	1	TRUE	1	0.454427557105173	2		441	381	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105772	27105772	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0066660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	98	535	0	ENST00000324856.7:c.5383A>T	p.Lys1795Ter	p.K1795*	ENST00000324856	NM_006015.4	1795	Aag/Tag	20/20	1	2	FACETS	0.961	0.862	1	0.961	0.862	1	CLONAL	1	TRUE	1	0.454427557105173	2		535	449	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937990	76937990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	67	381	0	ENST00000373344.5:c.2758G>A	p.Gly920Ser	p.G920S	ENST00000373344	NM_000489.3	920	Ggt/Agt	9/35	1	2	FACETS	0.812	0.71	0.922	0.812	0.71	0.922	CLONAL	1	TRUE	1	0.454427557105173	2		381	363	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78831689	78831689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755927307	NA	P-0066662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	166	339	0	ENST00000306801.3:c.1498G>A	p.Ala500Thr	p.A500T	ENST00000306801	NM_020761.2	500	Gca/Aca	13/34	0.546124672733841	4	FACETS	1	0.956	1	0.53	0.487	0.576	CLONAL	1	TRUE	2	0.546124672733841	4		339	886	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47205152	47205404	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCGGGCCTGCTGCGGCCCCGGCCAAGCGGCTCGAAGTGGCGGCGCGGGCCTGCTCCCGACACCGACCGCGCGAGGCCACCGTGGGCCTGTTACTCCTCGCGCCGGCCCGCGCCGCCACCCGTCAGGACGCGCCGCCCTCGGCTGGGGATAAGGCGGCCGACAGCAGCGGGGGGCCGCGGAGCTGATACTTACTCAGGGGTCGGGTGCTCCGGGTCGTAGAAATCCCCCATCTTCGGAGGCGGCTGCGGCTGCA	GCGGGCCTGCTGCGGCCCCGGCCAAGCGGCTCGAAGTGGCGGCGCGGGCCTGCTCCCGACACCGACCGCGCGAGGCCACCGTGGGCCTGTTACTCCTCGCGCCGGCCCGCGCCGCCACCCGTCAGGACGCGCCGCCCTCGGCTGGGGATAAGGCGGCCGACAGCAGCGGGGGGCCGCGGAGCTGATACTTACTCAGGGGTCGGGTGCTCCGGGTCGTAGAAATCCCCCATCTTCGGAGGCGGCTGCGGCTGCA	-	novel	NA	P-0066662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	54	50	0	ENST00000409792.3:c.11_71+192del		p.X4_splice	ENST00000409792	NM_014159.6	4		1/21	0.546124672733841	1	FACETS	1	0.975	1	1	0.985	1	CLONAL	2	TRUE	0	0.546124672733841	1		50	63	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118852	115118859	+	frameshift_variant	Frame_Shift_Del	DEL	ATAACGAC	ATAACGAC	-	novel	NA	P-0066662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	255	422	0	ENST00000257566.3:c.482_489del	p.Cys161Ter	p.C161*	ENST00000257566	NM_016569.3	161	tGTCGTTAT/t	2/8	0.531509103954745	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.546124672733841	3		422	576	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0066664-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	11	270	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.273917086857316	3	FACETS	0.428	0.296	0.591	0.214	0.148	0.296	SUBCLONAL	1	TRUE	1	0.34	3		270	177	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579327	7579327	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066664-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	41	438	0	ENST00000269305.4:c.360G>C	p.Lys120Asn	p.K120N	ENST00000269305	NM_001126112.2	120	aaG/aaC	4/11	1	2	FACETS	0.459	0.381	0.544	0.459	0.381	0.544	SUBCLONAL	1	TRUE	1	0.34	2		438	526	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851754	134851754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56396912	NA	P-0066664-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	37	491	0	ENST00000398015.3:c.1160C>T	p.Thr387Met	p.T387M	ENST00000398015	NM_004441.4	387	aCg/aTg	5/16	1	2	FACETS	0.45	0.37	0.539	0.45	0.37	0.539	SUBCLONAL	1	TRUE	1	0.34	2		491	484	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505130	149505130	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066664-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	24	440	0	ENST00000261799.4:c.1685A>G	p.Tyr562Cys	p.Y562C	ENST00000261799	NM_002609.3	562	tAc/tGc	12/23	1	2	FACETS	0.298	0.233	0.373	0.298	0.233	0.373	SUBCLONAL	1	TRUE	1	0.34	2		440	474	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974744	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAGCAGCGCCCGCA	CCTCCAGCAGCGCCCGCA	-	novel	NA	P-0066664-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	26	445	0	ENST00000304494.5:c.83_100del	p.Val28_Glu33del	p.V28_E33del	ENST00000304494	NM_000077.4	28	gTGCGGGCGCTGCTGGAGGcg/gcg	1/3	1	2	FACETS	0.306	0.241	0.38	0.306	0.241	0.38	SUBCLONAL	1	TRUE	1	0.34	2		445	500	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589268	67589268	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066664-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	14	308	0	ENST00000274335.5:c.1256A>G	p.Lys419Arg	p.K419R	ENST00000274335		419	aAa/aGa	9/15	1	2	FACETS	0.508	0.369	0.676	0.508	0.369	0.676	SUBCLONAL	1	TRUE	1	0.34	2		308	162	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244278	153244278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	114	365	1	ENST00000281708.4:c.1879G>A	p.Val627Met	p.V627M	ENST00000281708	NM_033632.3	627	Gtg/Atg	12/12	1	2	FACETS	0.991	0.895	1	0.991	0.895	1	CLONAL	1	TRUE	1	0.38341861281823	2		366	600	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413060	63413060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769613326	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	115	212	0	ENST00000330258.3:c.107C>T	p.Ala36Val	p.A36V	ENST00000330258	NM_152424.3	36	gCg/gTg	2/2	1	1	FACETS	0.797	0.729	0.868	1	0.987	1	SUBCLONAL	2	TRUE	0	0.38341861281823	1		212	304	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	121	393	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.38341861281823	2		393	621	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	182	319	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.995	0.927	1	1	0.993	1	CLONAL	2	TRUE	1	0.38341861281823	2		325	477	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515136	148515136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	36	393	1	ENST00000320356.2:c.1073G>A	p.Arg358His	p.R358H	ENST00000320356	NM_004456.4	358	cGc/cAc	10/20	0.229623076693324	3	FACETS	0.341	0.279	0.411	0.171	0.139	0.206	INDETERMINATE	1	TRUE	1	0.38341861281823	3		394	656	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	102	276	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.38341861281823	2		276	463	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	24	91	2	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	1	FACETS	0.85	0.677	1	0.85	0.677	1	CLONAL	1	TRUE	0	0.38341861281823	1		93	119	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	83	239	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.38341861281823	2		239	399	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470559	25470559	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs761839006	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	47	390	0	ENST00000264709.3:c.915G>A	p.Trp305Ter	p.W305*	ENST00000264709	NM_175629.2	305	tgG/tgA	8/23	0.361919063144079	2	FACETS	0.421	0.354	0.494	0.21	0.177	0.247	SUBCLONAL	1	TRUE	0	0.38341861281823	2		390	583	SUCCESS
AR	367	MSKCC	GRCh37	X	66766237	66766237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	98	161	0	ENST00000374690.3:c.1249G>A	p.Ala417Thr	p.A417T	ENST00000374690	NM_000044.3	417	Gcg/Acg	1/8	1	1	FACETS	0.864	0.786	0.945	1	0.987	1	CLONAL	2	TRUE	0	0.38341861281823	1		161	239	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	142	418	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.38341861281823	2		418	657	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	44	317	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	0.398	0.333	0.47	0.398	0.333	0.47	SUBCLONAL	1	TRUE	1	0.38341861281823	2		317	577	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782032	9782032	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	111	368	0	ENST00000377346.4:c.2059del		p.X687_splice	ENST00000377346	NM_005026.3	687			1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.38341861281823	2		368	529	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255154	16255154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766167369	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	150	524	0	ENST00000375759.3:c.2419C>T	p.Arg807Cys	p.R807C	ENST00000375759	NM_015001.2	807	Cgc/Tgc	11/15	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.38341861281823	2		524	770	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259207	16259207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	145	475	0	ENST00000375759.3:c.6472C>T	p.Pro2158Ser	p.P2158S	ENST00000375759	NM_015001.2	2158	Ccg/Tcg	11/15	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.38341861281823	2		475	719	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101174	27101174	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	124	442	0	ENST00000324856.7:c.4456C>T	p.Gln1486Ter	p.Q1486*	ENST00000324856	NM_006015.4	1486	Cag/Tag	18/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.38341861281823	2		442	610	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852245	63852245	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1376484834	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	107	417	0	ENST00000279873.7:c.3023C>T	p.Ala1008Val	p.A1008V	ENST00000279873	NM_032199.2	1008	gCg/gTg	10/10	1	2	FACETS	0.946	0.851	1	0.946	0.851	1	CLONAL	1	TRUE	1	0.38341861281823	2		417	590	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205158	61205158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777442412	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	108	350	1	ENST00000301761.2:c.98G>A	p.Arg33His	p.R33H	ENST00000301761	NM_017841.2	33	cGc/cAc	2/4	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.38341861281823	2		351	531	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422242	422242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769792722	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	75	364	0	ENST00000399788.2:c.3016G>A	p.Ala1006Thr	p.A1006T	ENST00000399788	NM_001042603.1	1006	Gct/Act	20/28	1	2	FACETS	0.642	0.563	0.728	0.642	0.563	0.728	SUBCLONAL	1	TRUE	1	0.38341861281823	2		364	609	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432787	432787	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	121	396	0	ENST00000399788.2:c.2129C>A	p.Pro710His	p.P710H	ENST00000399788	NM_001042603.1	710	cCc/cAc	15/28	1	2	FACETS	0.894	0.809	0.984	0.894	0.809	0.984	CLONAL	1	TRUE	1	0.38341861281823	2		396	706	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004254	29004254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143093353	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	115	365	0	ENST00000282397.4:c.1039G>A	p.Val347Ile	p.V347I	ENST00000282397	NM_002019.4	347	Gta/Ata	8/30	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.38341861281823	2		365	515	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954300	48954300	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1461382798	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	18	201	0	ENST00000267163.4:c.1422-1G>A		p.X474_splice	ENST00000267163	NM_000321.2	474			1	2	FACETS	0.228	0.171	0.296	0.228	0.171	0.296	SUBCLONAL	1	TRUE	1	0.38341861281823	2		201	412	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51503148	51503148	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs72552260	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	32	368	0	ENST00000260433.2:c.1369C>T	p.Arg457Ter	p.R457*	ENST00000260433		457	Cga/Tga	10/10	1	2	FACETS	0.307	0.248	0.373	0.307	0.248	0.373	SUBCLONAL	1	TRUE	1	0.38341861281823	2		368	544	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420199	88420199	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	66	361	0	ENST00000360948.2:c.2487G>T	p.Lys829Asn	p.K829N	ENST00000360948	NM_001012338.2	829	aaG/aaT	19/19	1	2	FACETS	0.639	0.555	0.729	0.639	0.555	0.729	SUBCLONAL	1	TRUE	1	0.38341861281823	2		361	539	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788626	3788626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	106	365	0	ENST00000262367.5:c.4328G>A	p.Arg1443His	p.R1443H	ENST00000262367	NM_004380.2	1443	cGt/cAt	26/31	1	2	FACETS	0.967	0.869	1	0.967	0.869	1	CLONAL	1	TRUE	1	0.38341861281823	2		365	572	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807914	3807914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	114	413	0	ENST00000262367.5:c.3505C>T	p.Arg1169Cys	p.R1169C	ENST00000262367	NM_004380.2	1169	Cgc/Tgc	18/31	1	2	FACETS	0.991	0.895	1	0.991	0.895	1	CLONAL	1	TRUE	1	0.38341861281823	2		413	600	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832376	72832376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	117	408	1	ENST00000268489.5:c.4205G>A	p.Arg1402His	p.R1402H	ENST00000268489	NM_006885.3	1402	cGc/cAc	9/10	1	2	FACETS	0.96	0.867	1	0.96	0.867	1	CLONAL	1	TRUE	1	0.38341861281823	2		409	636	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832445	72832445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753592536	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	102	408	0	ENST00000268489.5:c.4136C>T	p.Thr1379Met	p.T1379M	ENST00000268489	NM_006885.3	1379	aCg/aTg	9/10	1	2	FACETS	0.888	0.796	0.986	0.888	0.796	0.986	CLONAL	1	TRUE	1	0.38341861281823	2		408	599	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544659	86544659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	48	475	0	ENST00000262426.4:c.484G>A	p.Gly162Ser	p.G162S	ENST00000262426	NM_001451.2	162	Ggc/Agc	1/2	1	2	FACETS	0.405	0.342	0.475	0.405	0.342	0.475	SUBCLONAL	1	TRUE	1	0.38341861281823	2		475	618	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347224	89347224	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780224924	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	116	450	0	ENST00000301030.4:c.5726C>T	p.Pro1909Leu	p.P1909L	ENST00000301030	NM_001256183.1	1909	cCg/cTg	9/13	1	2	FACETS	0.974	0.88	1	0.974	0.88	1	CLONAL	1	TRUE	1	0.38341861281823	2		450	621	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435080	56435080	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	151	504	0	ENST00000407977.2:c.2057C>A	p.Pro686His	p.P686H	ENST00000407977		686	cCc/cAc	9/10	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.38341861281823	2		504	774	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285038	15285038	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	109	363	0	ENST00000263388.2:c.4577G>A	p.Arg1526His	p.R1526H	ENST00000263388	NM_000435.2	1526	cGt/cAt	25/33	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.38341861281823	2		363	536	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274078	18274078	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	143	432	1	ENST00000222254.8:c.1296G>T	p.Gln432His	p.Q432H	ENST00000222254	NM_005027.3	432	caG/caT	11/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.38341861281823	2		433	673	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280012	18280012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1438495093	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	26	317	0	ENST00000222254.8:c.2095G>A	p.Ala699Thr	p.A699T	ENST00000222254	NM_005027.3	699	Gcc/Acc	16/16	1	2	FACETS	0.295	0.233	0.367	0.295	0.233	0.367	SUBCLONAL	1	TRUE	1	0.38341861281823	2		317	459	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798822	42798822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	119	380	1	ENST00000575354.2:c.4394G>A	p.Arg1465His	p.R1465H	ENST00000575354	NM_015125.3	1465	cGc/cAc	19/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.38341861281823	2		381	527	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855837	45855837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762141272	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	128	429	0	ENST00000391945.4:c.1973G>A	p.Arg658His	p.R658H	ENST00000391945	NM_000400.3	658	cGc/cAc	21/23	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.38341861281823	2		429	649	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128028956	128028956	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775316471	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	86	364	0	ENST00000285398.2:c.1901G>A	p.Arg634His	p.R634H	ENST00000285398	NM_000122.1	634	cGt/cAt	12/15	1	2	FACETS	0.888	0.788	0.995	0.888	0.788	0.995	CLONAL	1	TRUE	1	0.38341861281823	2		364	505	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175869	24175869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555881572	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	122	430	0	ENST00000263121.7:c.1097G>A	p.Arg366His	p.R366H	ENST00000263121	NM_003073.3	366	cGc/cAc	8/9	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.38341861281823	2		430	554	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573002	41573002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266719702	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	67	497	0	ENST00000263253.7:c.5287C>T	p.Arg1763Trp	p.R1763W	ENST00000263253	NM_001429.3	1763	Cgg/Tgg	31/31	1	2	FACETS	0.486	0.422	0.556	0.486	0.422	0.556	SUBCLONAL	1	TRUE	1	0.38341861281823	2		497	719	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	115	373	0	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	1	2	FACETS	0.961	0.868	1	0.961	0.868	1	CLONAL	1	TRUE	1	0.38341861281823	2		373	624	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098912	47098912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	37	410	0	ENST00000409792.3:c.6362G>A	p.Arg2121His	p.R2121H	ENST00000409792	NM_014159.6	2121	cGc/cAc	15/21	1	2	FACETS	0.298	0.245	0.358	0.298	0.245	0.358	SUBCLONAL	1	TRUE	1	0.38341861281823	2		410	647	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164711	47164711	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201984344	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	147	387	0	ENST00000409792.3:c.1415G>A	p.Arg472His	p.R472H	ENST00000409792	NM_014159.6	472	cGt/cAt	3/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.38341861281823	2		387	674	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440347	187440347	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1202633041	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	74	293	0	ENST00000232014.4:c.2020C>T	p.Arg674Ter	p.R674*	ENST00000232014	NM_001130845.1	674	Cga/Tga	10/10	1	2	FACETS	0.791	0.694	0.895	0.791	0.694	0.895	SUBCLONAL	1	TRUE	1	0.38341861281823	2		293	488	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980493	1980493	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	54	443	0	ENST00000382891.5:c.3955G>A	p.Gly1319Arg	p.G1319R	ENST00000382891	NM_133335.3	1319	Ggg/Agg	22/22	1	2	FACETS	0.446	0.381	0.518	0.446	0.381	0.518	SUBCLONAL	1	TRUE	1	0.38341861281823	2		443	631	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796069	57796069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1419352292	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	128	311	0	ENST00000309042.7:c.1045C>T	p.Arg349Cys	p.R349C	ENST00000309042	NM_005612.4	349	Cgc/Tgc	4/4	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.38341861281823	2		311	529	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356134	66356134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756357402	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	112	386	0	ENST00000273854.3:c.1363C>T	p.Arg455Trp	p.R455W	ENST00000273854	NM_004439.5	455	Cgg/Tgg	5/18	1	2	FACETS	0.997	0.899	1	0.997	0.899	1	CLONAL	1	TRUE	1	0.38341861281823	2		386	586	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	136	454	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.38341861281823	2		454	674	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293593	1293593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1482602039	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	29	392	0	ENST00000310581.5:c.1408C>T	p.Arg470Cys	p.R470C	ENST00000310581	NM_198253.2	470	Cgc/Tgc	2/16	1	2	FACETS	0.291	0.233	0.358	0.291	0.233	0.358	SUBCLONAL	1	TRUE	1	0.38341861281823	2		392	519	SUCCESS
APC	324	MSKCC	GRCh37	5	112175171	112175171	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085373	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	72	360	0	ENST00000257430.4:c.3880C>T	p.Gln1294Ter	p.Q1294*	ENST00000257430	NM_000038.5	1294	Cag/Tag	16/16	1	2	FACETS	0.551	0.481	0.626	0.551	0.481	0.626	SUBCLONAL	1	TRUE	1	0.38341861281823	2		360	682	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456962	149456962	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764483518	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	202	429	0	ENST00000286301.3:c.766C>T	p.Arg256Cys	p.R256C	ENST00000286301	NM_005211.3	256	Cgt/Tgt	6/22	1	2	FACETS	0.786	0.732	0.842	1	0.992	1	SUBCLONAL	2	TRUE	1	0.38341861281823	2		429	670	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502666	149502666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749226501	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	78	475	0	ENST00000261799.4:c.2122C>T	p.Arg708Cys	p.R708C	ENST00000261799	NM_002609.3	708	Cgc/Tgc	15/23	1	2	FACETS	0.694	0.611	0.784	0.694	0.611	0.784	SUBCLONAL	1	TRUE	1	0.38341861281823	2		475	586	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394896	394896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	34	386	1	ENST00000380956.4:c.292C>T	p.Arg98Trp	p.R98W	ENST00000380956	NM_001195286.1	98	Cgg/Tgg	3/9	0.268007986830722	2	FACETS	0.31	0.252	0.374	0.155	0.126	0.187	SUBCLONAL	1	TRUE	0	0.38341861281823	2		387	573	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323362	31323363	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748204482	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	133	322	0	ENST00000412585.2:c.626dup	p.Thr211AspfsTer10	p.T211Dfs*10	ENST00000412585	NM_005514.6	209	cca/ccCa	4/8	0.285981612191307	2	FACETS	1	0.986	1	0.723	0.661	0.787	CLONAL	1	TRUE	0	0.38341861281823	2		322	480	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068123	94068123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778426683	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	27	277	0	ENST00000369303.4:c.839G>A	p.Gly280Asp	p.G280D	ENST00000369303	NM_004440.3	280	gGc/gAc	4/17	1	2	FACETS	0.316	0.251	0.39	0.316	0.251	0.39	SUBCLONAL	1	TRUE	1	0.38341861281823	2		277	446	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2966388	2966388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145836432	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	94	298	0	ENST00000396946.4:c.1792G>A	p.Ala598Thr	p.A598T	ENST00000396946	NM_032415.4	598	Gcc/Acc	14/25	0.308133797338306	4	FACETS	1	0.94	1	0.361	0.322	0.403	CLONAL	1	TRUE	1	0.38341861281823	4		298	626	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968244	2968244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161484391	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	102	383	0	ENST00000396946.4:c.1742C>T	p.Ala581Val	p.A581V	ENST00000396946	NM_032415.4	581	gCg/gTg	13/25	0.308133797338306	4	FACETS	1	0.948	1	0.365	0.327	0.406	CLONAL	1	TRUE	1	0.38341861281823	4		383	672	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340050	116340050	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	36	318	0	ENST00000397752.3:c.917del	p.Lys306ArgfsTer28	p.K306Rfs*28	ENST00000397752	NM_000245.2	304	agA/ag	2/21	0.229623076693324	3	FACETS	0.408	0.335	0.491	0.204	0.167	0.246	INDETERMINATE	1	TRUE	1	0.38341861281823	3		318	548	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285950	38285950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1307187624	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	133	390	0	ENST00000425967.3:c.461C>T	p.Ala154Val	p.A154V	ENST00000425967	NM_001174067.1	154	gCt/gTt	5/19	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.38341861281823	2		390	611	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737070	145737070	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779410033	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	116	387	0	ENST00000428558.2:c.3496G>A	p.Gly1166Ser	p.G1166S	ENST00000428558	NM_004260.3	1166	Ggc/Agc	21/22	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.38341861281823	2		387	555	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211415	98211415	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	101	344	1	ENST00000331920.6:c.3740C>T	p.Ala1247Val	p.A1247V	ENST00000331920	NM_000264.3	1247	gCg/gTg	22/24	1	2	FACETS	0.963	0.864	1	0.963	0.864	1	CLONAL	1	TRUE	1	0.38341861281823	2		345	547	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133761001	133761003	+	missense_variant	Missense_Mutation	TNP	AGC	AGC	GGT	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	96	364	0	ENST00000318560.5:c.3324_3326delinsGGT	p.Ala1109Val	p.A1109V	ENST00000318560	NM_005157.4	1108	ccAGCg/ccGGTg	11/11	1	2	FACETS	0.936	0.837	1	0.936	0.837	1	CLONAL	1	TRUE	1	0.38341861281823	2		364	535	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812576	43812576	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	124	422	0	ENST00000372470.3:c.1279T>C	p.Tyr427His	p.Y427H	ENST00000372470	NM_005373.2	427	Tac/Cac	8/12	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.38341861281823	2		422	616	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279651	123279651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	114	495	0	ENST00000358487.5:c.781G>A	p.Gly261Arg	p.G261R	ENST00000358487	NM_000141.4	261	Gga/Aga	7/18	1	2	FACETS	0.892	0.804	0.984	0.892	0.804	0.984	CLONAL	1	TRUE	1	0.38341861281823	2		495	667	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572092	64572092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1565637104	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	38	460	0	ENST00000312049.6:c.1547G>A	p.Arg516Gln	p.R516Q	ENST00000312049	NM_130799.2	516	cGg/cAg	10/10	1	2	FACETS	0.326	0.269	0.39	0.326	0.269	0.39	SUBCLONAL	1	TRUE	1	0.38341861281823	2		460	608	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518076	69518076	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	35	305	0	ENST00000294312.3:c.289A>C	p.Ser97Arg	p.S97R	ENST00000294312	NM_005117.2	97	Agc/Cgc	2/3	1	2	FACETS	0.389	0.319	0.469	0.389	0.319	0.469	SUBCLONAL	1	TRUE	1	0.38341861281823	2		305	469	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427968	49427968	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	47	359	0	ENST00000301067.7:c.10622C>A	p.Ala3541Asp	p.A3541D	ENST00000301067	NM_003482.3	3541	gCt/gAt	38/54	1	2	FACETS	0.428	0.36	0.502	0.428	0.36	0.502	SUBCLONAL	1	TRUE	1	0.38341861281823	2		359	573	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435952	49435952	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	42	429	0	ENST00000301067.7:c.6029A>G	p.Glu2010Gly	p.E2010G	ENST00000301067	NM_003482.3	2010	gAg/gGg	28/54	1	2	FACETS	0.356	0.297	0.423	0.356	0.297	0.423	SUBCLONAL	1	TRUE	1	0.38341861281823	2		429	615	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885214	111885214	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	52	425	0	ENST00000341259.2:c.1102C>A	p.Pro368Thr	p.P368T	ENST00000341259	NM_005475.2	368	Ccc/Acc	6/8	1	2	FACETS	0.389	0.33	0.453	0.389	0.33	0.453	SUBCLONAL	1	TRUE	1	0.38341861281823	2		425	698	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123875244	123875244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	27	70	0	ENST00000330479.4:c.200G>A	p.Arg67His	p.R67H	ENST00000330479	NM_020382.3	67	cGt/cAt	3/9	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.38341861281823	2		70	107	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936740	32936740	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs80359015	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	117	362	0	ENST00000380152.3:c.7886G>A	p.Trp2629Ter	p.W2629*	ENST00000380152		2629	tGg/tAg	17/27	1	2	FACETS	0.994	0.899	1	0.994	0.899	1	CLONAL	1	TRUE	1	0.38341861281823	2		362	614	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954359	48954359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	27	276	0	ENST00000267163.4:c.1480G>A	p.Val494Ile	p.V494I	ENST00000267163	NM_000321.2	494	Gta/Ata	16/27	1	2	FACETS	0.277	0.219	0.342	0.277	0.219	0.342	SUBCLONAL	1	TRUE	1	0.38341861281823	2		276	509	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436765	110436765	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	93	422	0	ENST00000375856.3:c.1636G>T	p.Asp546Tyr	p.D546Y	ENST00000375856	NM_003749.2	546	Gac/Tac	1/2	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.38341861281823	2		422	472	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566250	95566250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780488568	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	121	347	1	ENST00000393063.1:c.4073G>A	p.Arg1358His	p.R1358H	ENST00000393063	NM_030621.3	1358	cGc/cAc	23/28	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.38341861281823	2		348	550	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022925	33022925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	52	348	0	ENST00000300177.4:c.34C>T	p.Leu12Phe	p.L12F	ENST00000300177	NM_001191322.1	12	Ctt/Ttt	2/2	1	2	FACETS	0.502	0.427	0.584	0.502	0.427	0.584	SUBCLONAL	1	TRUE	1	0.38341861281823	2		348	540	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134968	2134968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747613240	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	40	411	0	ENST00000219476.3:c.4510C>T	p.Leu1504Phe	p.L1504F	ENST00000219476	NM_000548.3	1504	Ctc/Ttc	35/42	1	2	FACETS	0.326	0.27	0.389	0.326	0.27	0.389	SUBCLONAL	1	TRUE	1	0.38341861281823	2		411	640	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831494	72831494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	116	441	0	ENST00000268489.5:c.5087C>T	p.Pro1696Leu	p.P1696L	ENST00000268489	NM_006885.3	1696	cCt/cTt	9/10	1	2	FACETS	0.935	0.845	1	0.935	0.845	1	CLONAL	1	TRUE	1	0.38341861281823	2		441	647	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944325	81944325	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	96	332	0	ENST00000359376.3:c.1934C>A	p.Pro645Gln	p.P645Q	ENST00000359376	NM_002661.3	645	cCg/cAg	18/33	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.38341861281823	2		332	463	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89833632	89833632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	73	291	0	ENST00000389301.3:c.2518G>A	p.Ala840Thr	p.A840T	ENST00000389301	NM_000135.2	840	Gca/Aca	27/43	1	2	FACETS	0.727	0.637	0.823	0.727	0.637	0.823	SUBCLONAL	1	TRUE	1	0.38341861281823	2		291	524	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552243	29552243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151138158	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	90	298	0	ENST00000356175.3:c.1976G>A	p.Arg659Gln	p.R659Q	ENST00000356175	NM_000267.3	659	cGg/cAg	17/57	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.38341861281823	2		298	444	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38788563	38788563	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	90	327	0	ENST00000348513.6:c.598C>A	p.His200Asn	p.H200N	ENST00000348513	NM_003079.4	200	Cac/Aac	8/11	1	2	FACETS	0.858	0.763	0.959	0.858	0.763	0.959	CLONAL	1	TRUE	1	0.38341861281823	2		327	547	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256975	41256975	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397508940	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	30	280	0	ENST00000357654.3:c.213-2A>G		p.X71_splice	ENST00000357654	NM_007294.3	71			1	2	FACETS	0.317	0.255	0.388	0.317	0.255	0.388	SUBCLONAL	1	TRUE	1	0.38341861281823	2		280	494	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096967	11096967	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs539710314	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	43	388	0	ENST00000358026.2:c.458C>T	p.Pro153Leu	p.P153L	ENST00000358026	NM_001128849.1	153	cCg/cTg	4/36	1	2	FACETS	0.379	0.316	0.448	0.379	0.316	0.448	SUBCLONAL	1	TRUE	1	0.38341861281823	2		388	592	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18943071	18943071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	70	489	0	ENST00000262803.5:c.53C>T	p.Thr18Met	p.T18M	ENST00000262803	NM_002911.3	18	aCg/aTg	1/24	1	2	FACETS	0.581	0.507	0.662	0.581	0.507	0.662	SUBCLONAL	1	TRUE	1	0.38341861281823	2		489	628	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745195	41745195	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	95	328	0	ENST00000301178.4:c.1261G>A	p.Val421Ile	p.V421I	ENST00000301178	NM_021913.4	421	Gta/Ata	9/20	1	2	FACETS	0.968	0.865	1	0.968	0.865	1	CLONAL	1	TRUE	1	0.38341861281823	2		328	512	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793076	42793076	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	33	404	0	ENST00000575354.2:c.968T>A	p.Leu323His	p.L323H	ENST00000575354	NM_015125.3	323	cTc/cAc	7/20	1	2	FACETS	0.304	0.247	0.369	0.304	0.247	0.369	SUBCLONAL	1	TRUE	1	0.38341861281823	2		404	566	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149926	202149926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	56	472	0	ENST00000358485.4:c.1367C>T	p.Ala456Val	p.A456V	ENST00000358485	NM_001080125.1	456	gCt/gTt	8/9	1	2	FACETS	0.405	0.346	0.47	0.405	0.346	0.47	SUBCLONAL	1	TRUE	1	0.38341861281823	2		472	721	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164749	36164749	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	48	528	0	ENST00000300305.3:c.1126C>T	p.Arg376Cys	p.R376C	ENST00000300305		376	Cgc/Tgc	8/8	1	2	FACETS	0.392	0.331	0.46	0.392	0.331	0.46	SUBCLONAL	1	TRUE	1	0.38341861281823	2		528	638	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125310	47125310	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	132	370	0	ENST00000409792.3:c.5960T>C	p.Val1987Ala	p.V1987A	ENST00000409792	NM_014159.6	1987	gTg/gCg	12/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.38341861281823	2		370	613	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63898596	63898596	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs564106533	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	124	518	0	ENST00000398590.3:c.322G>T	p.Asp108Tyr	p.D108Y	ENST00000398590	NM_001177387.1	108	Gac/Tac	3/14	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.38341861281823	2		518	632	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665421	138665421	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1449136816	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	85	337	0	ENST00000330315.3:c.144G>T	p.Lys48Asn	p.K48N	ENST00000330315	NM_023067.3	48	aaG/aaT	1/1	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.38341861281823	2		337	438	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146512	185146512	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	124	361	0	ENST00000265026.3:c.146del	p.Lys49ArgfsTer8	p.K49Rfs*8	ENST00000265026	NM_004721.4	48	gAa/ga	2/14	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.38341861281823	2		361	614	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1952820	1952820	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	36	431	0	ENST00000382891.5:c.1903G>A	p.Glu635Lys	p.E635K	ENST00000382891	NM_133335.3	635	Gag/Aag	10/22	1	2	FACETS	0.304	0.249	0.366	0.304	0.249	0.366	SUBCLONAL	1	TRUE	1	0.38341861281823	2		431	618	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31495445	31495445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	33	399	0	ENST00000344624.3:c.1703C>T	p.Ala568Val	p.A568V	ENST00000344624		568	gCt/gTt	9/33	1	2	FACETS	0.3	0.244	0.364	0.3	0.244	0.364	SUBCLONAL	1	TRUE	1	0.38341861281823	2		399	573	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520705	176520705	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141384037	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	28	342	0	ENST00000292408.4:c.1448G>A	p.Arg483His	p.R483H	ENST00000292408	NM_213647.1	483	cGt/cAt	11/18	1	2	FACETS	0.29	0.231	0.357	0.29	0.231	0.357	SUBCLONAL	1	TRUE	1	0.38341861281823	2		342	504	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858300	27858300	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	46	554	1	ENST00000359303.2:c.271A>G	p.Met91Val	p.M91V	ENST00000359303	NM_003535.2	91	Atg/Gtg	1/1	0.268007986830722	2	FACETS	0.303	0.254	0.357	0.151	0.127	0.179	SUBCLONAL	1	TRUE	0	0.38341861281823	2		555	793	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324080	31324080	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs41546015	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	20	217	0	ENST00000412585.2:c.483C>G	p.Asp161Glu	p.D161E	ENST00000412585	NM_005514.6	161	gaC/gaG	3/8	0.285981612191307	2	FACETS	0.369	0.282	0.47	0.184	0.141	0.235	SUBCLONAL	1	TRUE	0	0.38341861281823	2		217	283	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026663	6026663	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750770	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	97	389	0	ENST00000265849.7:c.1733G>A	p.Arg578His	p.R578H	ENST00000265849	NM_000535.5	578	cGt/cAt	11/15	0.308133797338306	4	FACETS	0.863	0.769	0.964	0.288	0.256	0.322	CLONAL	1	TRUE	1	0.38341861281823	4		389	811	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739742	145739742	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755865911	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	99	405	0	ENST00000428558.2:c.1709G>A	p.Arg570Gln	p.R570Q	ENST00000428558	NM_004260.3	570	cGg/cAg	11/22	1	2	FACETS	0.872	0.78	0.97	0.872	0.78	0.97	CLONAL	1	TRUE	1	0.38341861281823	2		405	592	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139563011	139563011	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs548014889	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	114	397	1	ENST00000308874.7:c.83G>A	p.Arg28His	p.R28H	ENST00000308874		28	cGt/cAt	4/10	1	2	FACETS	0.953	0.86	1	0.953	0.86	1	CLONAL	1	TRUE	1	0.38341861281823	2		398	624	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045185	47045185	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	121	182	0	ENST00000377604.3:c.2426T>C	p.Met809Thr	p.M809T	ENST00000377604	NM_001204468.1	809	aTg/aCg	21/24	1	1	FACETS	0.818	0.749	0.887	1	0.988	1	CLONAL	2	TRUE	0	0.38341861281823	1		182	312	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217318	123217318	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	27	159	0	ENST00000218089.9:c.2972G>A	p.Ser991Asn	p.S991N	ENST00000218089	NM_001042749.1	991	aGc/aAc	29/35	1	1	FACETS	0.44	0.351	0.54	0.44	0.351	0.54	SUBCLONAL	1	TRUE	0	0.38341861281823	1		159	259	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50784990	50784990	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs146125856	NA	P-0066699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	22	317	3	ENST00000307179.4:c.2327T>C	p.Leu776Pro	p.L776P	ENST00000307179		776	cTt/cCt	15/20	1	2	FACETS	0.277	0.215	0.35	0.277	0.215	0.35	SUBCLONAL	1	TRUE	1	0.521966667111357	2		320	304	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188043	151188043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	157	335	0	ENST00000262187.5:c.110C>T	p.Pro37Leu	p.P37L	ENST00000262187	NM_005614.3	37	cCa/cTa	2/8	0.130743913140804	6	FACETS	0.888	0.827	0.951			1	INDETERMINATE	4	TRUE	NA	0.521966667111357	6		335	346	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	180	789	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.382069392277255	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.382069392277255	2		790	458	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882049	36882050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs780753361	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	22	481	0	ENST00000358127.4:c.963dup	p.Ala322ArgfsTer19	p.A322Rfs*19	ENST00000358127	NM_001280556.1	321	-/C	8/10	1	2	FACETS	0.309	0.239	0.39	0.309	0.239	0.39	SUBCLONAL	1	TRUE	1	0.382069392277255	2		481	373	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	16	478	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.275	0.202	0.361	0.275	0.202	0.361	SUBCLONAL	1	TRUE	1	0.382069392277255	2		478	305	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	79	518	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.382069392277255	2		518	399	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	26	589	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.445	0.353	0.55	0.445	0.353	0.55	SUBCLONAL	1	TRUE	1	0.382069392277255	2		590	306	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	59	337	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.78	0.682	0.883	1	0.974	1	SUBCLONAL	2	TRUE	1	0.382069392277255	2		338	198	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	53	177	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.382069392277255	2		178	276	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784077	120784077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1210006090	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	83	582	2	ENST00000257552.2:c.908G>A	p.Arg303His	p.R303H	ENST00000257552	NM_002442.3	303	cGc/cAc	13/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.382069392277255	2		584	355	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306960	65306960	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	69	531	0	ENST00000342505.4:c.2617C>T	p.Arg873Cys	p.R873C	ENST00000342505	NM_002227.2	873	Cgc/Tgc	19/25	1	2	FACETS	0.896	0.784	1	0.896	0.784	1	CLONAL	1	TRUE	1	0.382069392277255	2		531	403	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437288	220437288	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1190141661	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	64	497	0	ENST00000243786.2:c.197del	p.Gly66AlafsTer61	p.G66Afs*61	ENST00000243786	NM_002191.3	64	ctG/ct	1/2	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.382069392277255	2		497	335	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491375	2491375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760189429	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	19	531	0	ENST00000355716.4:c.418G>A	p.Ala140Thr	p.A140T	ENST00000355716	NM_003820.2	140	Gct/Act	4/8	1	2	FACETS	0.294	0.223	0.378	0.294	0.223	0.378	SUBCLONAL	1	TRUE	1	0.382069392277255	2		531	338	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088787	27088788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	69	537	0	ENST00000324856.7:c.2402dup	p.Gln802SerfsTer15	p.Q802Sfs*15	ENST00000324856	NM_006015.4	799	cag/caGg	7/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.382069392277255	2		537	298	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101402	27101402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	49	286	0	ENST00000324856.7:c.4689del	p.Met1564Ter	p.M1564*	ENST00000324856	NM_006015.4	1562	Ccc/cc	18/20	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.382069392277255	2		286	213	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804274	43804274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1215318596	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	28	540	0	ENST00000372470.3:c.274G>A	p.Val92Met	p.V92M	ENST00000372470	NM_005373.2	92	Gtg/Atg	3/12	1	2	FACETS	0.3	0.239	0.369	0.3	0.239	0.369	SUBCLONAL	1	TRUE	1	0.382069392277255	2		540	489	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107230	193107230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	51	405	0	ENST00000367435.3:c.439C>T	p.Arg147Cys	p.R147C	ENST00000367435	NM_024529.4	147	Cgc/Tgc	6/17	1	2	FACETS	0.981	0.841	1	0.981	0.841	1	CLONAL	1	TRUE	1	0.382069392277255	2		405	272	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100637	8100637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755917839	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	83	574	0	ENST00000346208.3:c.611G>A	p.Ser204Asn	p.S204N	ENST00000346208		204	aGc/aAc	3/6	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.382069392277255	2		574	380	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615014	43615014	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764784013	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	18	514	0	ENST00000355710.3:c.2428G>A	p.Gly810Ser	p.G810S	ENST00000355710	NM_020975.4	810	Ggc/Agc	14/20	1	2	FACETS	0.297	0.223	0.385	0.297	0.223	0.385	SUBCLONAL	1	TRUE	1	0.382069392277255	2		514	317	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	23	157	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.382069392277255	2		157	103	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136190	64136190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777217932	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	81	482	0	ENST00000334205.4:c.1349C>T	p.Thr450Met	p.T450M	ENST00000334205	NM_003942.2	450	aCg/aTg	12/17	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.382069392277255	2		482	407	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944515	71944515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878853123	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	62	488	0	ENST00000298229.2:c.2071C>T	p.Arg691Trp	p.R691W	ENST00000298229	NM_001567.3	691	Cgg/Tgg	18/28	1	2	FACETS	0.963	0.837	1	0.963	0.837	1	CLONAL	1	TRUE	1	0.382069392277255	2		488	337	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426345	49426345	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs527255553	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	20	597	0	ENST00000301067.7:c.12143C>T	p.Pro4048Leu	p.P4048L	ENST00000301067	NM_003482.3	4048	cCg/cTg	39/54	1	2	FACETS	0.274	0.209	0.351	0.274	0.209	0.351	SUBCLONAL	1	TRUE	1	0.382069392277255	2		597	382	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861162	57861162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564027387	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	87	533	0	ENST00000228682.2:c.959C>T	p.Thr320Met	p.T320M	ENST00000228682	NM_005269.2	320	aCg/aTg	9/12	1	2	FACETS	0.981	0.873	1	0.981	0.873	1	CLONAL	1	TRUE	1	0.382069392277255	2		533	464	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112226	115112226	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	37	484	0	ENST00000257566.3:c.1514C>T	p.Pro505Leu	p.P505L	ENST00000257566	NM_016569.3	505	cCg/cTg	7/8	1	2	FACETS	0.784	0.651	0.931	0.784	0.651	0.931	CLONAL	1	TRUE	1	0.382069392277255	2		484	247	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033823	49033823	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	13	435	0	ENST00000267163.4:c.1961-1G>C		p.X654_splice	ENST00000267163	NM_000321.2	654			1	2	FACETS	0.273	0.194	0.369	0.273	0.194	0.369	SUBCLONAL	1	TRUE	1	0.382069392277255	2		435	249	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436354	110436354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	76	625	0	ENST00000375856.3:c.2047G>A	p.Val683Met	p.V683M	ENST00000375856	NM_003749.2	683	Gtg/Atg	1/2	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.382069392277255	2		625	348	SUCCESS
BLM	641	MSKCC	GRCh37	15	91328183	91328183	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779884	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	21	435	0	ENST00000355112.3:c.2695C>T	p.Arg899Ter	p.R899*	ENST00000355112	NM_000057.2	899	Cga/Tga	14/22	1	2	FACETS	0.306	0.235	0.389	0.306	0.235	0.389	SUBCLONAL	1	TRUE	1	0.382069392277255	2		435	359	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639453	3639453	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376437029	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	72	556	0	ENST00000294008.3:c.4186G>A	p.Gly1396Arg	p.G1396R	ENST00000294008	NM_032444.2	1396	Gga/Aga	12/15	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.382069392277255	2		556	337	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857075	9857075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	59	454	0	ENST00000330684.3:c.4326del	p.Arg1443GlyfsTer3	p.R1443Gfs*3	ENST00000330684	NM_001134407.1	1442	ccC/cc	13/13	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.382069392277255	2		454	278	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645357	67645357	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	77	588	0	ENST00000264010.4:c.626del	p.Lys209ArgfsTer13	p.K209Rfs*13	ENST00000264010	NM_006565.3	208	Aaa/aa	3/12	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.382069392277255	2		588	388	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244243	5244243	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1390768500	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	80	516	3	ENST00000357368.4:c.1239del	p.Ser414AlafsTer30	p.S414Afs*30	ENST00000357368	NM_002850.3	413	ccC/cc	11/38	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.382069392277255	2		519	390	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248546	10248546	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374047326	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	58	470	0	ENST00000340748.4:c.4207G>A	p.Ala1403Thr	p.A1403T	ENST00000340748		1403	Gca/Aca	35/40	1	2	FACETS	0.955	0.826	1	0.955	0.826	1	CLONAL	1	TRUE	1	0.382069392277255	2		470	318	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15364986	15364986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768842514	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	82	454	0	ENST00000263377.2:c.2135C>T	p.Ser712Phe	p.S712F	ENST00000263377	NM_058243.2	712	tCt/tTt	11/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.382069392277255	2		454	367	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	84	604	4	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.979	0.869	1	0.979	0.869	1	CLONAL	1	TRUE	1	0.382069392277255	2		608	449	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	75	575	2	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.382069392277255	2		577	378	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47503884	47503884	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	58	480	1	ENST00000404338.3:c.4444del	p.Gln1482SerfsTer317	p.Q1482Sfs*317	ENST00000404338	NM_004491.4	1480	aCc/ac	6/6	1	2	FACETS	0.767	0.661	0.881	0.767	0.661	0.881	SUBCLONAL	1	TRUE	1	0.382069392277255	2		481	396	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912134	50912134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781327088	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	66	504	0	ENST00000440232.2:c.1868G>A	p.Arg623Gln	p.R623Q	ENST00000440232	NM_002691.3	623	cGg/cAg	15/27	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.382069392277255	2		504	343	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919960	50919960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1440946792	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	27	424	2	ENST00000440232.2:c.3047G>A	p.Arg1016His	p.R1016H	ENST00000440232	NM_002691.3	1016	cGc/cAc	24/27	1	2	FACETS	0.403	0.32	0.497	0.403	0.32	0.497	SUBCLONAL	1	TRUE	1	0.382069392277255	2		426	351	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443577	29443577	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758172315	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	77	495	0	ENST00000389048.3:c.3640C>T	p.Arg1214Cys	p.R1214C	ENST00000389048	NM_004304.4	1214	Cgc/Tgc	23/29	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.382069392277255	2		495	363	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451801	29451801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745317944	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	38	251	0	ENST00000389048.3:c.2764G>A	p.Gly922Arg	p.G922R	ENST00000389048	NM_004304.4	922	Gga/Aga	16/29	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.382069392277255	2		251	168	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693886	47693886	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	68	398	0	ENST00000233146.2:c.1600del	p.Arg534ValfsTer9	p.R534Vfs*9	ENST00000233146	NM_000251.2	534	Cgt/gt	10/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.382069392277255	2		398	299	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026783	48026783	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881791	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	52	555	0	ENST00000234420.5:c.1661G>A	p.Arg554His	p.R554H	ENST00000234420	NM_000179.2	554	cGt/cAt	4/10	1	2	FACETS	0.83	0.71	0.96	0.83	0.71	0.96	CLONAL	1	TRUE	1	0.382069392277255	2		555	328	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622516	158622516	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906589	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	30	421	0	ENST00000263640.3:c.983G>A	p.Gly328Glu	p.G328E	ENST00000263640	NM_001105.4	328	gGg/gAg	8/11	1	2	FACETS	0.567	0.458	0.689	0.567	0.458	0.689	SUBCLONAL	1	TRUE	1	0.382069392277255	2		421	277	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191563	10191563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367545984	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	88	487	0	ENST00000256474.2:c.556G>A	p.Glu186Lys	p.E186K	ENST00000256474	NM_000551.3	186	Gaa/Aaa	3/3	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.382069392277255	2		487	395	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164793	47164793	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1306620044	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	67	517	0	ENST00000409792.3:c.1333C>T	p.Arg445Cys	p.R445C	ENST00000409792	NM_014159.6	445	Cgc/Tgc	3/21	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.382069392277255	2		517	326	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391024	89391024	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	64	453	0	ENST00000336596.2:c.1095del	p.Lys365AsnfsTer6	p.K365Nfs*6	ENST00000336596	NM_005233.5	364	Aaa/aa	5/17	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.382069392277255	2		453	290	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374298	138374298	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	51	453	0	ENST00000289153.2:c.3146T>G	p.Leu1049Arg	p.L1049R	ENST00000289153	NM_006219.2	1049	cTc/cGc	22/22	1	2	FACETS	0.957	0.819	1	0.957	0.819	1	CLONAL	1	TRUE	1	0.382069392277255	2		453	279	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	49	257	0	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	1	2	FACETS	0.852	0.726	0.989	0.852	0.726	0.989	CLONAL	1	TRUE	1	0.382069392277255	2		257	301	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181431	185181431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377513650	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	73	373	0	ENST00000265026.3:c.1372C>T	p.Arg458Cys	p.R458C	ENST00000265026	NM_004721.4	458	Cgc/Tgc	8/14	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.382069392277255	2		373	295	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957419	1957419	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	73	419	1	ENST00000382891.5:c.2523del		p.X841_splice	ENST00000382891	NM_133335.3	841			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.382069392277255	2		420	294	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280287	1280287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147521473	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	22	566	0	ENST00000310581.5:c.1936C>T	p.Arg646Cys	p.R646C	ENST00000310581	NM_198253.2	646	Cgc/Tgc	4/16	1	2	FACETS	0.284	0.219	0.359	0.284	0.219	0.359	SUBCLONAL	1	TRUE	1	0.382069392277255	2		566	406	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420001	152420001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763337967	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	91	528	1	ENST00000206249.3:c.1688C>T	p.Thr563Met	p.T563M	ENST00000206249	NM_000125.3	563	aCg/aTg	8/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.382069392277255	2		529	371	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501294	140501294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	60	289	0	ENST00000288602.6:c.778C>T	p.Arg260Cys	p.R260C	ENST00000288602	NM_004333.4	260	Cgc/Tgc	6/18	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.382069392277255	2		289	263	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873975	151873975	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	91	540	0	ENST00000262189.6:c.8563C>T	p.Gln2855Ter	p.Q2855*	ENST00000262189	NM_170606.2	2855	Cag/Tag	38/59	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.382069392277255	2		540	322	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864925	117864925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149171113	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	52	430	0	ENST00000297338.2:c.1184C>T	p.Pro395Leu	p.P395L	ENST00000297338	NM_006265.2	395	cCg/cTg	10/14	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.382069392277255	2		430	268	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	66	493	3	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.857	0.747	0.975	0.857	0.747	0.975	CLONAL	1	TRUE	1	0.382069392277255	2		496	403	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932474	39932474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398124312	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	105	618	0	ENST00000378444.4:c.2125G>A	p.Gly709Ser	p.G709S	ENST00000378444	NM_001123385.1	709	Ggc/Agc	4/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.382069392277255	2		618	422	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030469	47030469	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556772646	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	70	493	0	ENST00000377604.3:c.244C>T	p.Arg82Trp	p.R82W	ENST00000377604	NM_001204468.1	82	Cgg/Tgg	4/24	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.382069392277255	2		493	357	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360705	70360705	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1210702033	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	93	563	0	ENST00000374080.3:c.6265C>T	p.Arg2089Trp	p.R2089W	ENST00000374080		2089	Cgg/Tgg	42/45	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.382069392277255	2		563	400	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611048	100611048	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs128621201	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	56	471	0	ENST00000308731.7:c.1558C>T	p.Arg520Ter	p.R520*	ENST00000308731	NM_000061.2	520	Cga/Tga	15/19	1	2	FACETS	0.823	0.709	0.947	0.823	0.709	0.947	CLONAL	1	TRUE	1	0.382069392277255	2		471	356	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020315	123020315	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1431863732	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	66	446	0	ENST00000355640.3:c.803G>A	p.Arg268Gln	p.R268Q	ENST00000355640		268	cGg/cAg	2/7	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.382069392277255	2		446	258	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377271	118377271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	94	562	1	ENST00000534358.1:c.10664G>A	p.Gly3555Asp	p.G3555D	ENST00000534358	NM_005933.3	3555	gGc/gAc	27/36	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.382069392277255	2		563	398	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420045	49420045	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	96	542	0	ENST00000301067.7:c.15704A>G	p.Asn5235Ser	p.N5235S	ENST00000301067	NM_003482.3	5235	aAc/aGc	48/54	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.382069392277255	2		542	394	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21565544	21565544	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	93	534	0	ENST00000382592.4:c.343-1G>T		p.X115_splice	ENST00000382592	NM_014572.2	115			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.382069392277255	2		534	331	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061672	38061672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	50	573	0	ENST00000250448.2:c.317C>T	p.Thr106Met	p.T106M	ENST00000250448	NM_004496.3	106	aCg/aTg	2/2	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.382069392277255	2		573	242	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347544	91347544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	86	455	0	ENST00000355112.3:c.3706C>T	p.His1236Tyr	p.H1236Y	ENST00000355112	NM_000057.2	1236	Cat/Tat	19/22	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.382069392277255	2		455	321	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989706	15989706	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767556915	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	24	545	0	ENST00000268712.3:c.3067C>T	p.Arg1023Trp	p.R1023W	ENST00000268712	NM_006311.3	1023	Cgg/Tgg	23/46	1	2	FACETS	0.263	0.205	0.329	0.263	0.205	0.329	SUBCLONAL	1	TRUE	1	0.382069392277255	2		545	478	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47421960	47421960	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	92	553	0	ENST00000404338.3:c.28C>T	p.Arg10Ter	p.R10*	ENST00000404338	NM_004491.4	10	Cga/Tga	1/6	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.382069392277255	2		553	360	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606195	47606195	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	50	332	0	ENST00000263735.4:c.657+2T>C		p.X219_splice	ENST00000263735	NM_002354.2	219			1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.382069392277255	2		332	205	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275726	41275726	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	105	516	0	ENST00000349496.5:c.1621G>A	p.Val541Ile	p.V541I	ENST00000349496	NM_001904.3	541	Gtt/Att	10/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.382069392277255	2		516	461	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201788	66201788	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	70	444	0	ENST00000273854.3:c.2714C>T	p.Ala905Val	p.A905V	ENST00000273854	NM_004439.5	905	gCt/gTt	16/18	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.382069392277255	2		444	317	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295931	1295931	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	99	710	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.382069392277255	2		710	378	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31437367	31437367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	17	455	0	ENST00000344624.3:c.2921C>T	p.Ala974Val	p.A974V	ENST00000344624		974	gCt/gTt	21/33	1	2	FACETS	0.301	0.224	0.392	0.301	0.224	0.392	SUBCLONAL	1	TRUE	1	0.382069392277255	2		455	296	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402750	20402750	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs111421935	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	51	463	0	ENST00000346618.3:c.287G>A	p.Gly96Asp	p.G96D	ENST00000346618	NM_001949.4	96	gGc/gAc	1/7	0.166384520294223	3	FACETS	1	0.943	1	0.605	0.518	0.698	INDETERMINATE	1	TRUE	1	0.382069392277255	3		463	263	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370998	55370998	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	82	437	0	ENST00000297316.4:c.300G>T	p.Lys100Asn	p.K100N	ENST00000297316	NM_022454.3	100	aaG/aaT	1/2	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.382069392277255	2		437	372	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032546	47032546	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782792881	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	78	449	0	ENST00000377604.3:c.452C>T	p.Ser151Leu	p.S151L	ENST00000377604	NM_001204468.1	151	tCg/tTg	5/24	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.382069392277255	2		449	367	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229226	123229226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	66	483	0	ENST00000218089.9:c.3710C>T	p.Pro1237Leu	p.P1237L	ENST00000218089	NM_001042749.1	1237	cCa/cTa	34/35	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.382069392277255	2		483	281	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40771150	40771150	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066725-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	115	600	0	ENST00000392038.2:c.25G>T	p.Glu9Ter	p.E9*	ENST00000392038	NM_001626.4	9	Gaa/Taa	2/14	1	2	FACETS	0.932	0.849	1	0.932	0.849	1	CLONAL	1	TRUE	1	0.69906026581905	2		600	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0066755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	165	477	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.401377232107522	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.427703576870917	1		477	599	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0066755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	240	418	1	ENST00000257430.4:c.3919dup	p.Ile1307AsnfsTer8	p.I1307Nfs*8	ENST00000257430	NM_000038.5	1306	gaa/gAaa	16/16	0.386210712324966	2	FACETS	0.805	0.756	0.856	0.805	0.756	0.856	CLONAL	2	TRUE	0	0.427703576870917	2		419	697	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	203	314	4	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.177798152877429	3	FACETS	1	0.952	1	0.682	0.637	0.728	INDETERMINATE	2	TRUE	0	0.427703576870917	3		318	563	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0066755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	101	439	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.427703576870917	2		439	412	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0066755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	139	409	5	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.427703576870917	2		414	626	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0066755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	250	390	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.358210630761886	2	FACETS	0.934	0.88	0.988	0.934	0.88	0.988	CLONAL	2	TRUE	0	0.427703576870917	2		392	626	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459290	120459290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1430961661	NA	P-0066755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	113	452	3	ENST00000256646.2:c.6055C>T	p.Arg2019Trp	p.R2019W	ENST00000256646	NM_024408.3	2019	Cgg/Tgg	34/34	1	2	FACETS	0.785	0.707	0.867	0.785	0.707	0.867	SUBCLONAL	1	TRUE	1	0.427703576870917	2		455	673	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21345972	21345972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1346699262	NA	P-0066755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	155	575	5	ENST00000215739.8:c.847C>T	p.Arg283Trp	p.R283W	ENST00000215739	NM_006767.3	283	Cgg/Tgg	9/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.427703576870917	2		580	654	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0066764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	90	415	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.215955194242148	2	FACETS	0.988	0.881	1	0.988	0.881	1	CLONAL	2	TRUE	0	0.215955194242148	2		415	422	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163313641	163313641	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	13	348	0	ENST00000271452.3:c.788A>T	p.Gln263Leu	p.Q263L	ENST00000271452	NM_145697.2	263	cAg/cTg	10/14	0.215955194242148	3	FACETS	0.554	0.395	0.748	0.277	0.197	0.374	SUBCLONAL	1	TRUE	1	0.215955194242148	3		348	241	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184761	32184761	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	66	608	0	ENST00000375023.3:c.1822C>A	p.Pro608Thr	p.P608T	ENST00000375023	NM_004557.3	608	Cca/Aca	11/30	0.211997807692601	3	FACETS	1	0.928	1	0.552	0.479	0.632	CLONAL	1	TRUE	1	0.215955194242148	3		608	613	SUCCESS
AR	367	MSKCC	GRCh37	X	66765988	66765988	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	34	576	0	ENST00000374690.3:c.1000G>C	p.Gly334Arg	p.G334R	ENST00000374690	NM_000044.3	334	Ggg/Cgg	1/8	0.215955194242148	3	FACETS	0.691	0.564	0.834	0.345	0.282	0.417	SUBCLONAL	1	TRUE	1	0.215955194242148	3		576	505	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	840	789	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		790	1180	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	183	377	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		377	474	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	130	329	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		329	763	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216477	108216477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587782558	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	163	376	0	ENST00000278616.4:c.8432del	p.Lys2811SerfsTer46	p.K2811Sfs*46	ENST00000278616	NM_000051.3	2809	cAa/ca	58/63	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		376	393	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	255	319	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		325	726	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	135	177	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		178	737	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	198	625	0	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		625	1091	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21344765	21344765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869320686	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	376	530	1	ENST00000215739.8:c.742G>A	p.Gly248Arg	p.G248R	ENST00000215739	NM_006767.3	248	Gga/Aga	8/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		531	995	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	229	524	13	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		537	722	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	345	528	2	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		530	957	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	302	529	4	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		533	1053	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	307	511	1	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		512	811	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	446	661	0	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		661	1134	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101627	27101627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1023142691	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	414	610	0	ENST00000324856.7:c.4909C>T	p.Arg1637Trp	p.R1637W	ENST00000324856	NM_006015.4	1637	Cgg/Tgg	18/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		610	1081	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804359	43804359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749391587	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	337	500	0	ENST00000372470.3:c.359G>A	p.Arg120Gln	p.R120Q	ENST00000372470	NM_005373.2	120	cGg/cAg	3/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		500	861	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652330	206652330	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	193	649	6	ENST00000367120.3:c.1042del	p.Arg348AspfsTer32	p.R348Dfs*32	ENST00000367120	NM_014002.3	346	gCc/gc	10/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		655	1215	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606766	43606766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs539995816	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	368	725	0	ENST00000355710.3:c.1375G>A	p.Glu459Lys	p.E459K	ENST00000355710	NM_020975.4	459	Gag/Aag	7/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		725	1032	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405743	70405743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	55	517	0	ENST00000373644.4:c.3257C>T	p.Ser1086Leu	p.S1086L	ENST00000373644	NM_030625.2	1086	tCg/tTg	4/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		517	733	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659788	88659789	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	173	316	0	ENST00000372037.3:c.441dup	p.Asp148Ter	p.D148*	ENST00000372037	NM_004329.2	145	-/T	7/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		316	474	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911638	114911638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1427214163	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	320	413	0	ENST00000543371.1:c.1156C>T	p.Arg386Trp	p.R386W	ENST00000543371	NM_001198531.1	386	Cgg/Tgg	10/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		413	804	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465988	69465990	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs753296543	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	301	581	14	ENST00000227507.2:c.839_841del	p.Glu280del	p.E280del	ENST00000227507	NM_053056.2	276	GAG/-	5/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		595	1007	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588241	69588241	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs533842802	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	280	440	0	ENST00000168712.1:c.457G>A	p.Asp153Asn	p.D153N	ENST00000168712	NM_002007.2	153	Gat/Aat	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		440	760	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625435	69625435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376445217	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	354	522	0	ENST00000334134.2:c.358C>T	p.Arg120Trp	p.R120W	ENST00000334134	NM_005247.2	120	Cgg/Tgg	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		522	853	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369217	118369217	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	344	550	0	ENST00000534358.1:c.5935C>T	p.Arg1979Ter	p.R1979*	ENST00000534358	NM_005933.3	1979	Cga/Tga	22/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		550	910	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427491	427491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774366438	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	235	592	0	ENST00000399788.2:c.2678G>A	p.Arg893Gln	p.R893Q	ENST00000399788	NM_001042603.1	893	cGa/cAa	19/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		592	1031	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541709	120541709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	376	600	0	ENST00000229340.5:c.148G>A	p.Val50Met	p.V50M	ENST00000229340	NM_006861.6	50	Gtg/Atg	3/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		600	1024	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563051	21563051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	182	615	0	ENST00000382592.4:c.868C>T	p.Pro290Ser	p.P290S	ENST00000382592	NM_014572.2	290	Ccc/Tcc	4/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		615	950	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039144	49039144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764520289	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	156	311	1	ENST00000267163.4:c.2222G>A	p.Arg741His	p.R741H	ENST00000267163	NM_000321.2	741	cGt/cAt	22/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		312	456	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	382	610	0	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		610	1080	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655481	67655481	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs34679888	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	289	548	1	ENST00000264010.4:c.1348del	p.Ser450ValfsTer61	p.S450Vfs*61	ENST00000264010	NM_006565.3	448	cgA/cg	7/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		549	722	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	380	642	5	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		647	996	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830616	72830616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149779567	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	342	584	0	ENST00000268489.5:c.5965G>A	p.Gly1989Ser	p.G1989S	ENST00000268489	NM_006885.3	1989	Ggc/Agc	9/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		584	883	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832575	72832575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751584946	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	319	458	0	ENST00000268489.5:c.4006G>A	p.Ala1336Thr	p.A1336T	ENST00000268489	NM_006885.3	1336	Gca/Aca	9/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		458	804	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544978	86544978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	244	462	0	ENST00000262426.4:c.803C>T	p.Ala268Val	p.A268V	ENST00000262426	NM_001451.2	268	gCg/gTg	1/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		462	686	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348058	89348058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886568838	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	403	575	0	ENST00000301030.4:c.4892G>A	p.Arg1631Gln	p.R1631Q	ENST00000301030	NM_001256183.1	1631	cGg/cAg	9/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		575	993	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351514	89351514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754010341	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	373	670	0	ENST00000301030.4:c.1436C>T	p.Ser479Leu	p.S479L	ENST00000301030	NM_001256183.1	479	tCg/tTg	9/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		670	986	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579399	7579401	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs878854068	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	104	659	0	ENST00000269305.4:c.286_288del	p.Ser96del	p.S96del	ENST00000269305	NM_001126112.2	96	TCT/-	4/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		659	1120	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556292	29556292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1251621684	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	384	546	3	ENST00000356175.3:c.2659G>A	p.Ala887Thr	p.A887T	ENST00000356175	NM_000267.3	887	Gca/Aca	21/57	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		549	977	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	377	418	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		418	1024	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508715	38508715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758973243	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	372	492	0	ENST00000254066.5:c.763G>A	p.Ala255Thr	p.A255T	ENST00000254066	NM_000964.3	255	Gcc/Acc	6/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		492	904	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526179	63526179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755508971	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	407	584	0	ENST00000307078.5:c.2447C>T	p.Ala816Val	p.A816V	ENST00000307078	NM_004655.3	816	gCg/gTg	11/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		584	1046	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533939	63533940	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs771001164	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	123	496	2	ENST00000307078.5:c.1214_1215del	p.Glu405GlyfsTer56	p.E405Gfs*56	ENST00000307078	NM_004655.3	405	gAG/g	6/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		498	814	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554672	63554672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	219	599	0	ENST00000307078.5:c.67C>T	p.Arg23Trp	p.R23W	ENST00000307078	NM_004655.3	23	Cgg/Tgg	2/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		599	1118	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7152776	7152776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	189	574	0	ENST00000302850.5:c.2192C>T	p.Thr731Met	p.T731M	ENST00000302850	NM_000208.2	731	aCg/aTg	10/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		574	963	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097625	11097625	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	606	556	0	ENST00000358026.2:c.810del	p.Met272CysfsTer31	p.M272Cfs*31	ENST00000358026	NM_001128849.1	269	Ccc/cc	5/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		556	850	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355326	15355326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775700444	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	367	280	0	ENST00000263377.2:c.2297C>T	p.Pro766Leu	p.P766L	ENST00000263377	NM_058243.2	766	cCg/cTg	13/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		280	510	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375418	15375418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471575560	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	749	592	0	ENST00000263377.2:c.1009G>A	p.Asp337Asn	p.D337N	ENST00000263377	NM_058243.2	337	Gac/Aac	6/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		592	1017	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257890	19257890	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1386180499	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	182	539	0	ENST00000162023.5:c.496C>T	p.Arg166Cys	p.R166C	ENST00000162023		166	Cgc/Tgc	9/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		539	1057	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	354	583	0	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		583	985	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215571	36215571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	335	417	0	ENST00000222270.7:c.3368G>A	p.Arg1123Gln	p.R1123Q	ENST00000222270	NM_014727.1	1123	cGg/cAg	9/37	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		417	836	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52725442	52725442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767299944	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	410	653	0	ENST00000322088.6:c.1609C>T	p.Arg537Cys	p.R537C	ENST00000322088	NM_014225.5	537	Cgc/Tgc	13/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		653	1085	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972669	25972669	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369844902	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	390	531	0	ENST00000435504.4:c.1756C>T	p.Arg586Cys	p.R586C	ENST00000435504		586	Cgt/Tgt	12/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		531	1050	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656951	47656951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63749849	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	249	449	0	ENST00000233146.2:c.1147C>T	p.Arg383Ter	p.R383*	ENST00000233146	NM_000251.2	383	Cga/Tga	7/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		449	653	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661664	227661664	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs761880048	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	296	574	9	ENST00000305123.5:c.1791del	p.His598ThrfsTer38	p.H598Tfs*38	ENST00000305123	NM_005544.2	597	ggG/gg	1/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		583	863	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024812	31024812	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	367	629	0	ENST00000375687.4:c.4297C>A	p.Gln1433Lys	p.Q1433K	ENST00000375687	NM_015338.5	1433	Caa/Aaa	13/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		629	1020	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36024634	36024634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867236697	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	197	555	1	ENST00000358208.4:c.623G>A	p.Arg208His	p.R208H	ENST00000358208		208	cGc/cAc	6/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		556	875	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729866	39729868	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	343	545	0	ENST00000361337.2:c.1188_1190del	p.Pro397del	p.P397del	ENST00000361337	NM_003286.2	394	tCTCct/tct	13/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		545	926	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385153	41385153	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776806194	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	222	515	0	ENST00000373198.4:c.808C>T	p.Arg270Cys	p.R270C	ENST00000373198	NM_133170.3	270	Cgc/Tgc	6/32	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		515	643	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553308	41553308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1203250209	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	340	531	0	ENST00000263253.7:c.3397C>T	p.Arg1133Trp	p.R1133W	ENST00000263253	NM_001429.3	1133	Cgg/Tgg	18/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		531	870	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981832	63981832	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	351	536	0	ENST00000398590.3:c.2340del	p.Thr781ProfsTer11	p.T781Pfs*11	ENST00000398590	NM_001177387.1	778	ggC/gg	12/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		536	1071	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967254	134967254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758204492	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	159	611	1	ENST00000398015.3:c.2593C>T	p.Arg865Trp	p.R865W	ENST00000398015	NM_004441.4	865	Cgg/Tgg	14/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		612	985	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803419	1803419	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	447	580	1	ENST00000260795.2:c.688G>A	p.Val230Met	p.V230M	ENST00000260795		230	Gtg/Atg	5/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		581	1027	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467573	66467573	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	300	573	0	ENST00000273854.3:c.696del	p.Lys232AsnfsTer36	p.K232Nfs*36	ENST00000273854	NM_004439.5	232	aaA/aa	3/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		573	785	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524146	187524146	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368616927	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	309	529	0	ENST00000441802.2:c.11393C>T	p.Pro3798Leu	p.P3798L	ENST00000441802	NM_005245.3	3798	cCg/cTg	20/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		529	907	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524869	187524869	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	386	646	0	ENST00000441802.2:c.10811del	p.Lys3604SerfsTer2	p.K3604Sfs*2	ENST00000441802	NM_005245.3	3604	aAg/ag	19/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		646	1027	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950546	38950546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371456052	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	266	560	0	ENST00000357387.3:c.3404C>T	p.Thr1135Met	p.T1135M	ENST00000357387	NM_152756.3	1135	aCg/aTg	31/38	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		560	688	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170877	56170877	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	298	512	0	ENST00000399503.3:c.1705G>A	p.Val569Ile	p.V569I	ENST00000399503	NM_005921.1	569	Gtt/Att	10/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		512	800	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931452	131931452	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507178	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	315	453	17	ENST00000265335.6:c.2165del	p.Lys722ArgfsTer14	p.K722Rfs*14	ENST00000265335		719	ctA/ct	13/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		470	850	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149516579	149516579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465066628	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	363	488	0	ENST00000261799.4:c.32C>T	p.Ala11Val	p.A11V	ENST00000261799	NM_002609.3	11	gCc/gTc	2/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		488	910	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180641	32180641	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1186558705	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	262	379	0	ENST00000375023.3:c.2486G>A	p.Arg829His	p.R829H	ENST00000375023	NM_004557.3	829	cGc/cAc	16/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		379	680	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803059	32803059	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs61736923	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	213	528	0	ENST00000374899.4:c.817C>T	p.Arg273Ter	p.R273*	ENST00000374899	NM_018833.2	273	Cga/Tga	5/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		528	1085	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289545	33289545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1436067809	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	209	501	0	ENST00000374542.5:c.158C>T	p.Ser53Leu	p.S53L	ENST00000374542	NM_001141970.1	53	tCg/tTg	2/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		501	956	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528849	157528849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761204913	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	217	630	0	ENST00000346085.5:c.6574G>A	p.Val2192Ile	p.V2192I	ENST00000346085	NM_020732.3	2192	Gta/Ata	20/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		630	1066	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946306	2946306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573740263	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	281	508	0	ENST00000396946.4:c.3431G>A	p.Arg1144His	p.R1144H	ENST00000396946	NM_032415.4	1144	cGc/cAc	25/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		508	800	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962960	2962960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745349548	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	268	474	0	ENST00000396946.4:c.1948C>T	p.Arg650Trp	p.R650W	ENST00000396946	NM_032415.4	650	Cgg/Tgg	16/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		474	737	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223603	55223603	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1343888047	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	155	461	0	ENST00000275493.2:c.970C>T	p.Arg324Cys	p.R324C	ENST00000275493	NM_005228.3	324	Cgc/Tgc	8/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		461	847	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850271	128850271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1018551272	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	336	435	0	ENST00000249373.3:c.1534C>T	p.Arg512Cys	p.R512C	ENST00000249373	NM_005631.4	512	Cgc/Tgc	9/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		435	858	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	176	635	1	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		636	927	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500844	8500845	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	148	518	0	ENST00000356435.5:c.2037dup	p.Trp680MetfsTer3	p.W680Mfs*3	ENST00000356435		679	-/A	13/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		518	813	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97869475	97869475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149917017	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	400	552	0	ENST00000289081.3:c.1406C>T	p.Thr469Met	p.T469M	ENST00000289081	NM_000136.2	469	aCg/aTg	14/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		552	972	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399315	139399315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369467132	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	140	493	2	ENST00000277541.6:c.4828G>A	p.Ala1610Thr	p.A1610T	ENST00000277541	NM_017617.3	1610	Gca/Aca	26/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		495	847	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651631	48651631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	194	273	0	ENST00000376670.3:c.797C>T	p.Thr266Met	p.T266M	ENST00000376670	NM_002049.3	266	aCg/aTg	5/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		273	548	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228288	53228288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1569264240	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	384	262	0	ENST00000375401.3:c.2114G>A	p.Arg705His	p.R705H	ENST00000375401	NM_004187.3	705	cGc/cAc	15/26	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		262	485	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820890	36820890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753697977	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	359	596	1	ENST00000373129.3:c.487G>A	p.Val163Ile	p.V163I	ENST00000373129	NM_032017.1	163	Gtc/Atc	6/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		597	997	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36826927	36826927	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs12086307	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	275	482	0	ENST00000373129.3:c.7C>T	p.Arg3Trp	p.R3W	ENST00000373129	NM_032017.1	3	Cgg/Tgg	3/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		482	878	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165725	118165725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1211776583	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	438	649	0	ENST00000369448.3:c.235G>A	p.Val79Ile	p.V79I	ENST00000369448	NM_017709.3	79	Gtt/Att	2/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		649	1052	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746095	162746095	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	344	585	0	ENST00000367921.3:c.2218T>C	p.Tyr740His	p.Y740H	ENST00000367921	NM_006182.2	740	Tat/Cat	16/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		585	1157	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091463	193091463	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	461	460	0	ENST00000367435.3:c.131+2T>C		p.X44_splice	ENST00000367435	NM_024529.4	44			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		460	1009	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578283	226578283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	362	595	0	ENST00000366794.5:c.445C>T	p.Pro149Ser	p.P149S	ENST00000366794	NM_001618.3	149	Cca/Tca	4/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		595	1136	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681287	88681287	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	279	416	0	ENST00000372037.3:c.1177G>T	p.Glu393Ter	p.E393*	ENST00000372037	NM_004329.2	393	Gaa/Taa	11/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		416	692	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128026	64128026	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	371	600	1	ENST00000334205.4:c.428del	p.Gly143ValfsTer20	p.G143Vfs*20	ENST00000334205	NM_003942.2	142	Ggg/gg	4/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		601	991	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435203	18435203	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	276	606	0	ENST00000266497.5:c.188T>C	p.Phe63Ser	p.F63S	ENST00000266497		63	tTt/tCt	1/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		606	684	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244727	46244727	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	339	644	0	ENST00000334344.6:c.2821C>T	p.Pro941Ser	p.P941S	ENST00000334344	NM_152641.2	941	Cca/Tca	15/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		644	982	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481633	56481633	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	228	629	1	ENST00000267101.3:c.668C>A	p.Pro223His	p.P223H	ENST00000267101	NM_001982.3	223	cCc/cAc	6/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		630	1167	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811645	102811645	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	320	598	0	ENST00000307046.8:c.539G>T	p.Arg180Met	p.R180M	ENST00000307046	NM_001111285.1	180	aGg/aTg	4/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		598	877	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29068976	29068976	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	204	406	0	ENST00000282397.4:c.5T>C	p.Val2Ala	p.V2A	ENST00000282397	NM_002019.4	2	gTc/gCc	1/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		406	604	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434788	110434788	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	344	577	0	ENST00000375856.3:c.3613C>T	p.Arg1205Ter	p.R1205*	ENST00000375856	NM_003749.2	1205	Cga/Tga	1/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		577	863	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986953	36986953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	259	542	0	ENST00000354822.5:c.736del	p.Met246Ter	p.M246*	ENST00000354822	NM_001079668.2	246	Atg/tg	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		542	715	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50773879	50773879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	134	583	1	ENST00000307179.4:c.1420G>A	p.Glu474Lys	p.E474K	ENST00000307179		474	Gaa/Aaa	11/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		584	759	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472577	88472577	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	286	567	0	ENST00000360948.2:c.1978G>T	p.Ala660Ser	p.A660S	ENST00000360948	NM_001012338.2	660	Gcc/Tcc	16/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		567	822	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857370	9857370	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1596374520	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	146	599	0	ENST00000330684.3:c.4031T>C	p.Phe1344Ser	p.F1344S	ENST00000330684	NM_001134407.1	1344	tTc/tCc	13/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		599	784	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042012	14042012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	189	571	0	ENST00000311895.7:c.2563del	p.Met855CysfsTer4	p.M855Cfs*4	ENST00000311895	NM_005236.2	853	ttA/tt	11/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		571	1004	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646734	23646734	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	137	526	0	ENST00000261584.4:c.1133C>A	p.Pro378His	p.P378H	ENST00000261584	NM_024675.3	378	cCt/cAt	4/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		526	793	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983163	7983163	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	280	452	0	ENST00000319144.4:c.851C>A	p.Pro284Gln	p.P284Q	ENST00000319144	NM_001139.2	284	cCa/cAa	7/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		452	762	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456566	40456566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	448	599	0	ENST00000345506.4:c.1276C>T	p.Arg426Cys	p.R426C	ENST00000345506	NM_003152.3	426	Cgt/Tgt	12/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		599	1122	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40871138	40871138	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	230	411	0	ENST00000428826.2:c.752A>G	p.Asp251Gly	p.D251G	ENST00000428826		251	gAt/gGt	8/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		411	643	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584764	48584764	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	195	597	0	ENST00000342988.3:c.842C>A	p.Pro281His	p.P281H	ENST00000342988	NM_005359.5	281	cCt/cAt	7/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		597	1092	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170522	11170522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	568	632	0	ENST00000358026.2:c.4825G>A	p.Glu1609Lys	p.E1609K	ENST00000358026	NM_001128849.1	1609	Gag/Aag	34/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		632	1004	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47491278	47491278	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771708442	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	322	464	1	ENST00000404338.3:c.3859G>A	p.Gly1287Arg	p.G1287R	ENST00000404338	NM_004491.4	1287	Ggg/Agg	3/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		465	830	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47503649	47503649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	171	590	0	ENST00000404338.3:c.4204C>T	p.Pro1402Ser	p.P1402S	ENST00000404338	NM_004491.4	1402	Ccc/Tcc	6/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		590	1000	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523037	25523037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1438813586	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	328	569	0	ENST00000264709.3:c.148C>T	p.Arg50Trp	p.R50W	ENST00000264709	NM_175629.2	50	Cgg/Tgg	3/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		569	867	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285256	212285256	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	215	502	0	ENST00000342788.4:c.3045T>A	p.Asp1015Glu	p.D1015E	ENST00000342788	NM_005235.2	1015	gaT/gaA	25/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		502	596	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030895	36030895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	356	463	0	ENST00000358208.4:c.1174G>A	p.Ala392Thr	p.A392T	ENST00000358208		392	Gca/Aca	10/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		463	881	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21350125	21350125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752699291	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	179	559	0	ENST00000215739.8:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000215739	NM_006767.3	678	cGg/cAg	17/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		559	959	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29279819	29279819	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	94	96	0	ENST00000544604.2:c.65del	p.Arg22ProfsTer100	p.R22Pfs*100	ENST00000544604	NM_001206998.1	22	cGc/cc	1/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		96	254	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29279819	29279819	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	19	96	0	ENST00000544604.2:c.65G>C	p.Arg22Pro	p.R22P	ENST00000544604	NM_001206998.1	22	cGc/cCc	1/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		96	254	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446611	29446611	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	272	453	0	ENST00000544604.2:c.2442del	p.Pro815ArgfsTer11	p.P815Rfs*11	ENST00000544604	NM_001206998.1	814	ccA/cc	8/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		453	752	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573240	41573240	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	387	651	0	ENST00000263253.7:c.5525G>T	p.Gly1842Val	p.G1842V	ENST00000263253	NM_001429.3	1842	gGg/gTg	31/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		651	990	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165909	47165909	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778611476	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	330	589	0	ENST00000409792.3:c.217G>T	p.Val73Leu	p.V73L	ENST00000409792	NM_014159.6	73	Gtg/Ttg	3/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		589	912	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188985	142188985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	72	438	0	ENST00000350721.4:c.6262C>T	p.Pro2088Ser	p.P2088S	ENST00000350721	NM_001184.3	2088	Cca/Tca	37/47	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		438	309	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805506	1805506	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	164	522	0	ENST00000260795.2:c.1018C>A	p.Leu340Met	p.L340M	ENST00000260795		340	Ctg/Atg	7/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		522	847	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595592	55595592	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	153	446	0	ENST00000288135.5:c.2082G>T	p.Gln694His	p.Q694H	ENST00000288135	NM_000222.2	694	caG/caT	14/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		446	406	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56171057	56171057	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	165	523	0	ENST00000399503.3:c.1885G>T	p.Gly629Ter	p.G629*	ENST00000399503	NM_005921.1	629	Gga/Tga	10/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		523	957	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592109	67592109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143171832	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	316	447	0	ENST00000274335.5:c.1925G>A	p.Arg642Gln	p.R642Q	ENST00000274335		642	cGa/cAa	14/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		447	900	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43746204	43746204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367757959	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	342	594	0	ENST00000523873.1:c.323G>A	p.Arg108Gln	p.R108Q	ENST00000523873		108	cGg/cAg	4/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		594	965	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555024	106555024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367573477	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	401	602	0	ENST00000369096.4:c.2141C>T	p.Pro714Leu	p.P714L	ENST00000369096	NM_001198.3	714	cCg/cTg	7/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		602	1020	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527329	157527329	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	305	530	1	ENST00000346085.5:c.5054A>T	p.Glu1685Val	p.E1685V	ENST00000346085	NM_020732.3	1685	gAg/gTg	20/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		531	779	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080638	5080638	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs528871831	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	222	452	0	ENST00000381652.3:c.2389T>C	p.Ser797Pro	p.S797P	ENST00000381652	NM_004972.3	797	Tct/Cct	18/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		452	548	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209256	98209256	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	299	544	0	ENST00000331920.6:c.4282G>T	p.Glu1428Ter	p.E1428*	ENST00000331920	NM_000264.3	1428	Gaa/Taa	23/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		544	867	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128322030	128322030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243805016	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	302	494	0	ENST00000265960.3:c.730G>A	p.Asp244Asn	p.D244N	ENST00000265960	NM_001006617.1	244	Gat/Aat	6/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		494	863	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401089	139401089	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs767910707	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	333	561	0	ENST00000277541.6:c.3904C>T	p.Arg1302Cys	p.R1302C	ENST00000277541	NM_017617.3	1302	Cgc/Tgc	24/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		561	859	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793289	139793289	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	322	402	0	ENST00000247668.2:c.97C>A	p.Leu33Met	p.L33M	ENST00000247668	NM_021138.3	33	Ctg/Atg	2/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		402	868	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841253	15841253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375322183	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	226	289	0	ENST00000307771.7:c.1337G>A	p.Arg446Gln	p.R446Q	ENST00000307771	NM_005089.3	446	cGg/cAg	11/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		289	627	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349008	70349008	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	356	255	0	ENST00000374080.3:c.3520C>T	p.Arg1174Cys	p.R1174C	ENST00000374080		1174	Cgc/Tgc	25/45	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		255	454	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354652	70354652	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	201	262	0	ENST00000374080.3:c.4817T>C	p.Met1606Thr	p.M1606T	ENST00000374080		1606	aTg/aCg	35/45	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		262	529	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220615	2220615	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	rs774508592	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	154	481	0	ENST00000326181.6:c.237del	p.Ile80SerfsTer48	p.I80Sfs*48	ENST00000326181	NM_032271.2	78	Ccc/cc	5/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.47981975292	2		481	532	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	239	789	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.47981975292	2		790	783	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	120	418	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.237430895999375	3	FACETS	0.773	0.704	0.845	0.773	0.704	0.845	INDETERMINATE	2	TRUE	1	0.47981975292	3		418	401	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	242	477	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.47981975292	2		477	689	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	39	476	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.298	0.246	0.355	0.298	0.246	0.355	SUBCLONAL	1	TRUE	1	0.47981975292	2		476	546	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	55	565	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.305	0.26	0.355	0.305	0.26	0.355	SUBCLONAL	1	TRUE	1	0.47981975292	2		565	751	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	52	91	2	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	2	FACETS	0.803	0.689	0.925	0.803	0.689	0.925	CLONAL	1	TRUE	1	0.47981975292	2		93	270	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913396	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	144	403	0	ENST00000349496.5:c.95A>T	p.Asp32Val	p.D32V	ENST00000349496	NM_001904.3	32	gAc/gTc	3/15	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.47981975292	2		403	592	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	11	235	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.222	0.153	0.307	0.222	0.153	0.307	SUBCLONAL	1	TRUE	1	0.47981975292	2		235	207	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539027	23539027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751677679	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	204	565	0	ENST00000380871.4:c.412G>A	p.Glu138Lys	p.E138K	ENST00000380871	NM_006167.3	138	Gag/Aag	2/2	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.47981975292	2		565	625	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	73	671	1	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.47981975292	3	FACETS	0.409	0.357	0.466	0.205	0.178	0.233	SUBCLONAL	1	TRUE	1	0.47981975292	3		672	922	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	353	528	2	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	0.47981975292	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.47981975292	3		530	800	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023295	27023295	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	92	415	1	ENST00000324856.7:c.401C>T	p.Ala134Val	p.A134V	ENST00000324856	NM_006015.4	134	gCg/gTg	1/20	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.47981975292	2		416	364	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115272979	115272979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	19	448	0	ENST00000438362.2:c.1394C>T	p.Ser465Leu	p.S465L	ENST00000438362	NM_001242891.1	465	tCa/tTa	12/20	1	2	FACETS	0.217	0.164	0.279	0.217	0.164	0.279	SUBCLONAL	1	TRUE	1	0.47981975292	2		448	365	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653395	206653395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374485120	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	60	499	1	ENST00000367120.3:c.1279C>T	p.Arg427Trp	p.R427W	ENST00000367120	NM_014002.3	427	Cgg/Tgg	12/22	1	2	FACETS	0.368	0.316	0.424	0.368	0.316	0.424	SUBCLONAL	1	TRUE	1	0.47981975292	2		500	680	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149355	119149356	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATG	rs397507494	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	102	465	1	ENST00000264033.4:c.1380_1382dup	p.Asp460dup	p.D460dup	ENST00000264033	NM_005188.3	460	tat/tATGat	9/16	1	2	FACETS	0.861	0.773	0.953	0.861	0.773	0.953	CLONAL	1	TRUE	1	0.47981975292	2		466	494	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123712	46123712	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	128	445	0	ENST00000334344.6:c.92+1G>A		p.X31_splice	ENST00000334344	NM_152641.2	31			0.47981975292	3	FACETS	1	0.912	1	0.502	0.456	0.55	CLONAL	1	TRUE	1	0.47981975292	3		445	659	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244967	46244967	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	227	542	0	ENST00000334344.6:c.3065del	p.Pro1022HisfsTer38	p.P1022Hfs*38	ENST00000334344	NM_152641.2	1021	Ccc/cc	15/21	0.47981975292	3	FACETS	0.773	0.722	0.825	0.773	0.722	0.825	SUBCLONAL	2	TRUE	1	0.47981975292	3		542	759	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433806	49433806	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	53	639	0	ENST00000301067.7:c.7747G>A	p.Ala2583Thr	p.A2583T	ENST00000301067	NM_003482.3	2583	Gcc/Acc	31/54	0.47981975292	3	FACETS	0.315	0.268	0.368	0.158	0.134	0.184	SUBCLONAL	1	TRUE	1	0.47981975292	3		639	869	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	40	484	1	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	0.47981975292	3	FACETS	0.283	0.234	0.338	0.142	0.117	0.169	SUBCLONAL	1	TRUE	1	0.47981975292	3		485	730	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444091	49444091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1053550290	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	54	545	0	ENST00000301067.7:c.3280C>T	p.Leu1094Phe	p.L1094F	ENST00000301067	NM_003482.3	1094	Ctc/Ttc	11/54	0.47981975292	3	FACETS	0.368	0.314	0.428	0.184	0.157	0.214	SUBCLONAL	1	TRUE	1	0.47981975292	3		545	758	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856545	111856545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157707616	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	251	514	2	ENST00000341259.2:c.596C>T	p.Ala199Val	p.A199V	ENST00000341259	NM_005475.2	199	gCg/gTg	2/8	0.47981975292	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.47981975292	3		516	615	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885901	111885901	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	53	552	2	ENST00000341259.2:c.1527del	p.Leu510SerfsTer38	p.L510Sfs*38	ENST00000341259	NM_005475.2	508	cGg/cg	8/8	0.47981975292	3	FACETS	0.31	0.263	0.362	0.155	0.131	0.181	SUBCLONAL	1	TRUE	1	0.47981975292	3		554	883	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115111984	115111984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	53	512	0	ENST00000257566.3:c.1756G>A	p.Val586Ile	p.V586I	ENST00000257566	NM_016569.3	586	Gtc/Atc	7/8	0.47981975292	3	FACETS	0.332	0.282	0.387	0.166	0.141	0.194	SUBCLONAL	1	TRUE	1	0.47981975292	3		512	826	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426748	121426748	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	99	567	0	ENST00000257555.6:c.439C>T	p.His147Tyr	p.H147Y	ENST00000257555		147	Cac/Tac	2/10	0.47981975292	3	FACETS	0.557	0.497	0.622	0.279	0.248	0.311	SUBCLONAL	1	TRUE	1	0.47981975292	3		567	918	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563168	21563168	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766080720	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	168	638	0	ENST00000382592.4:c.751G>A	p.Ala251Thr	p.A251T	ENST00000382592	NM_014572.2	251	Gcg/Acg	4/8	0.0536818949404091	6	FACETS	0.863	0.794	0.935	0.575	0.529	0.623	INDETERMINATE	2	TRUE	3	0.47981975292	6		638	795	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435573	110435573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	103	506	0	ENST00000375856.3:c.2828C>T	p.Ala943Val	p.A943V	ENST00000375856	NM_003749.2	943	gCc/gTc	1/2	0.0536818949404091	6	FACETS	1	0.981	1	0.489	0.439	0.543	INDETERMINATE	1	TRUE	3	0.47981975292	6		506	573	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358697	67358697	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	30	412	0	ENST00000327367.4:c.205A>T	p.Arg69Trp	p.R69W	ENST00000327367	NM_005902.3	69	Agg/Tgg	1/9	1	2	FACETS	0.292	0.235	0.357	0.292	0.235	0.357	SUBCLONAL	1	TRUE	1	0.47981975292	2		412	428	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396382	396382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200741961	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	203	491	0	ENST00000262320.3:c.644C>T	p.Ser215Leu	p.S215L	ENST00000262320	NM_003502.3	215	tCg/tTg	2/11	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.47981975292	2		491	579	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857805	9857805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	195	543	1	ENST00000330684.3:c.3596C>T	p.Pro1199Leu	p.P1199L	ENST00000330684	NM_001134407.1	1199	cCg/cTg	13/13	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.47981975292	2		544	726	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993509	72993509	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	173	626	2	ENST00000268489.5:c.536del	p.Gly179AlafsTer22	p.G179Afs*22	ENST00000268489	NM_006885.3	179	gGc/gc	2/10	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.47981975292	2		628	704	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857935	89857935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11646374	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	47	467	0	ENST00000389301.3:c.1235C>T	p.Ala412Val	p.A412V	ENST00000389301	NM_000135.2	412	gCg/gTg	14/43	1	2	FACETS	0.299	0.251	0.351	0.299	0.251	0.351	SUBCLONAL	1	TRUE	1	0.47981975292	2		467	656	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	45	427	0	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	1	2	FACETS	0.334	0.28	0.393	0.334	0.28	0.393	SUBCLONAL	1	TRUE	1	0.47981975292	2		427	562	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	190	463	3	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.47981975292	2		466	602	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131402	17131402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398124537	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	33	539	0	ENST00000285071.4:c.50G>A	p.Arg17His	p.R17H	ENST00000285071	NM_144997.5	17	cGc/cAc	4/14	1	2	FACETS	0.21	0.17	0.255	0.21	0.17	0.255	SUBCLONAL	1	TRUE	1	0.47981975292	2		539	656	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683984	29683985	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1135402907	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	114	348	0	ENST00000356175.3:c.7684_7685del	p.Arg2562AspfsTer12	p.R2562Dfs*12	ENST00000356175	NM_000267.3	2561	cAG/c	52/57	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.47981975292	2		348	335	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37856539	37856540	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	129	529	0	ENST00000269571.5:c.54dup	p.Gly19ArgfsTer91	p.G19Rfs*91	ENST00000269571		16	-/C	1/27	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.47981975292	2		529	500	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532653	63532654	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1301294410	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	200	534	2	ENST00000307078.5:c.1925dup	p.Ala643GlyfsTer64	p.A643Gfs*64	ENST00000307078	NM_004655.3	642	aag/aaAg	8/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.47981975292	2		536	693	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745962	745963	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	20	349	0	ENST00000314574.4:c.559_560del	p.Ser187Ter	p.S187*	ENST00000314574	NM_005433.3	187	AGt/t	5/12	1	2	FACETS	0.281	0.214	0.358	0.281	0.214	0.358	SUBCLONAL	1	TRUE	1	0.47981975292	2		349	297	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395646	45395646	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	72	341	0	ENST00000262160.6:c.488A>G	p.Asn163Ser	p.N163S	ENST00000262160	NM_005901.5	163	aAc/aGc	4/11	1	2	FACETS	0.82	0.721	0.926	0.82	0.721	0.926	CLONAL	1	TRUE	1	0.47981975292	2		341	366	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223103	1223103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782058	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	154	502	1	ENST00000326873.7:c.1040C>T	p.Ala347Val	p.A347V	ENST00000326873	NM_000455.4	347	gCg/gTg	8/10	1	2	FACETS	0.997	0.915	1	0.997	0.915	1	CLONAL	1	TRUE	1	0.47981975292	2		503	644	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115015	3115015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	57	544	0	ENST00000078429.4:c.550G>A	p.Val184Met	p.V184M	ENST00000078429	NM_002067.2	184	Gtg/Atg	4/7	1	2	FACETS	0.361	0.309	0.418	0.361	0.309	0.418	SUBCLONAL	1	TRUE	1	0.47981975292	2		544	658	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4102403	4102403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457335620	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	46	451	0	ENST00000262948.5:c.499G>A	p.Glu167Lys	p.E167K	ENST00000262948	NM_030662.3	167	Gag/Aag	4/11	1	2	FACETS	0.379	0.319	0.445	0.379	0.319	0.445	SUBCLONAL	1	TRUE	1	0.47981975292	2		451	506	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024650	11024650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	53	498	0	ENST00000327064.4:c.767C>T	p.Ser256Leu	p.S256L	ENST00000327064	NM_199141.1	256	tCg/tTg	6/16	1	2	FACETS	0.43	0.366	0.499	0.43	0.366	0.499	SUBCLONAL	1	TRUE	1	0.47981975292	2		498	514	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272336	15272337	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs771517374	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	150	546	2	ENST00000263388.2:c.6102dup	p.Gly2035ArgfsTer60	p.G2035Rfs*60	ENST00000263388	NM_000435.2	2034	-/C	33/33	1	2	FACETS	0.904	0.828	0.982	0.904	0.828	0.982	CLONAL	1	TRUE	1	0.47981975292	2		548	692	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288901	15288901	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs958354298	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	138	412	0	ENST00000263388.2:c.3838C>T	p.Pro1280Ser	p.P1280S	ENST00000263388	NM_000435.2	1280	Ccg/Tcg	24/33	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.47981975292	2		412	476	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384726	17384726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368554117	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	167	417	0	ENST00000359435.4:c.358G>A	p.Ala120Thr	p.A120T	ENST00000359435	NM_001033549.1	120	Gcc/Acc	4/9	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.47981975292	2		417	656	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222961	36222961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	205	593	0	ENST00000222270.7:c.5590C>T	p.Arg1864Ter	p.R1864*	ENST00000222270	NM_014727.1	1864	Cga/Tga	27/37	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.47981975292	2		593	638	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797278	42797278	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs968289754	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	177	623	0	ENST00000575354.2:c.3640C>T	p.Arg1214Ter	p.R1214*	ENST00000575354	NM_015125.3	1214	Cga/Tga	15/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.47981975292	2		623	573	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910306	50910306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1341055535	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	56	511	1	ENST00000440232.2:c.1561C>T	p.Arg521Trp	p.R521W	ENST00000440232	NM_002691.3	521	Cgg/Tgg	13/27	1	2	FACETS	0.376	0.322	0.436	0.376	0.322	0.436	SUBCLONAL	1	TRUE	1	0.47981975292	2		512	620	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978890	25978890	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	97	255	0	ENST00000435504.4:c.1033G>T	p.Glu345Ter	p.E345*	ENST00000435504		345	Gaa/Taa	10/13	0.477875949824103	3	FACETS	1	0.959	1	0.568	0.509	0.63	CLONAL	1	TRUE	1	0.47981975292	3		255	441	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278407	39278407	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	22	300	0	ENST00000402219.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000402219	NM_005633.3	248	Cgc/Tgc	6/23	0.477875949824103	3	FACETS	0.366	0.283	0.461	0.183	0.141	0.231	SUBCLONAL	1	TRUE	1	0.47981975292	3		300	311	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	rs267608078	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	39	463	0	ENST00000234420.5:c.3260_3261dup	p.Phe1088ProfsTer3	p.F1088Pfs*3	ENST00000234420	NM_000179.2	1085	acc/aCCcc	5/10	0.477875949824103	3	FACETS	0.312	0.258	0.373	0.156	0.129	0.187	SUBCLONAL	1	TRUE	1	0.47981975292	3		463	646	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919673	96919673	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1231066976	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	141	481	0	ENST00000258439.3:c.590G>A	p.Arg197His	p.R197H	ENST00000258439	NM_001193304.2	197	cGc/cAc	4/4	0.477875949824103	3	FACETS	1	0.921	1	0.505	0.46	0.551	CLONAL	1	TRUE	1	0.47981975292	3		481	722	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131511	202131511	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs376330981	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	61	426	0	ENST00000358485.4:c.479A>G	p.Tyr160Cys	p.Y160C	ENST00000358485	NM_001080125.1	160	tAc/tGc	2/9	0.477875949824103	3	FACETS	0.393	0.338	0.453	0.197	0.169	0.227	SUBCLONAL	1	TRUE	1	0.47981975292	3		426	802	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295773	212295773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1299031105	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	102	435	1	ENST00000342788.4:c.2540G>A	p.Arg847His	p.R847H	ENST00000342788	NM_005235.2	847	cGt/cAt	21/28	0.477875949824103	3	FACETS	1	0.97	1	0.602	0.541	0.665	CLONAL	1	TRUE	1	0.47981975292	3		436	438	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437288	220437288	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1190141661	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	49	497	0	ENST00000243786.2:c.197del	p.Gly66AlafsTer61	p.G66Afs*61	ENST00000243786	NM_002191.3	64	ctG/ct	1/2	0.477875949824103	3	FACETS	0.344	0.29	0.403	0.172	0.145	0.202	SUBCLONAL	1	TRUE	1	0.47981975292	3		497	736	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661129	227661129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781654199	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	47	640	0	ENST00000305123.5:c.2326C>T	p.Arg776Cys	p.R776C	ENST00000305123	NM_005544.2	776	Cgc/Tgc	1/2	0.477875949824103	3	FACETS	0.308	0.259	0.363	0.154	0.129	0.182	SUBCLONAL	1	TRUE	1	0.47981975292	3		640	788	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	244	535	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.902	0.85	0.954	1	0.995	1	CLONAL	2	TRUE	1	0.47981975292	2		536	564	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610568	52610568	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	18	322	0	ENST00000394830.3:c.3605C>T	p.Thr1202Ile	p.T1202I	ENST00000394830	NM_018313.4	1202	aCa/aTa	23/30	1	2	FACETS	0.245	0.184	0.317	0.245	0.184	0.317	SUBCLONAL	1	TRUE	1	0.47981975292	2		322	306	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027087	71027087	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	185	507	0	ENST00000318789.4:c.1240del	p.Leu414Ter	p.L414*	ENST00000318789	NM_032682.5	414	Ctg/tg	15/21	1	2	FACETS	0.963	0.89	1	0.963	0.89	1	CLONAL	1	TRUE	1	0.47981975292	2		507	801	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202767	128202767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	148	485	0	ENST00000341105.2:c.953C>T	p.Ala318Val	p.A318V	ENST00000341105	NM_032638.4	318	gCc/gTc	4/6	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.47981975292	2		485	580	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155052	55155052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	199	459	1	ENST00000257290.5:c.2761G>A	p.Ala921Thr	p.A921T	ENST00000257290	NM_006206.4	921	Gct/Act	20/23	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.47981975292	2		460	665	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295960	1295960	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	254	695	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.47981975292	2		695	798	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149516594	149516594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150173975	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	126	457	0	ENST00000261799.4:c.17C>T	p.Ala6Val	p.A6V	ENST00000261799	NM_002609.3	6	gCg/gTg	2/23	1	2	FACETS	0.94	0.854	1	0.94	0.854	1	CLONAL	1	TRUE	1	0.47981975292	2		457	559	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053023	180053023	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	147	580	1	ENST00000261937.6:c.1267del	p.Gln423ArgfsTer70	p.Q423Rfs*70	ENST00000261937	NM_182925.4	423	Cag/ag	10/30	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.47981975292	2		581	599	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056575	26056575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs75040909	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	135	467	0	ENST00000343677.2:c.82G>A	p.Ala28Thr	p.A28T	ENST00000343677	NM_005319.3	28	Gct/Act	1/1	0.317715322073391	2	FACETS	0.868	0.791	0.949	0.434	0.395	0.475	CLONAL	1	TRUE	0	0.47981975292	2		467	648	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911274	29911274	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs199474568	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	28	373	0	ENST00000376809.5:c.573G>A	p.Trp191Ter	p.W191*	ENST00000376809	NM_002116.7	191	tgG/tgA	3/8	0.317715322073391	2	FACETS	0.309	0.246	0.38	0.154	0.123	0.19	SUBCLONAL	1	TRUE	0	0.47981975292	2		373	378	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129358	152129358	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	36	492	0	ENST00000206249.3:c.311C>T	p.Ser104Phe	p.S104F	ENST00000206249	NM_000125.3	104	tCt/tTt	1/8	0.317715322073391	2	FACETS	0.266	0.218	0.32	0.133	0.109	0.16	SUBCLONAL	1	TRUE	0	0.47981975292	2		492	564	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521890	157521890	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1199179337	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	331	552	0	ENST00000346085.5:c.4162G>A	p.Glu1388Lys	p.E1388K	ENST00000346085	NM_020732.3	1388	Gag/Aag	18/20	0.317715322073391	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.47981975292	2		552	675	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508725	106508725	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	204	536	2	ENST00000359195.3:c.723del	p.Gly242AlafsTer17	p.G242Afs*17	ENST00000359195	NM_002649.2	240	aCc/ac	2/11	0.237430895999375	3	FACETS	1	0.988	1	0.646	0.6	0.693	INDETERMINATE	1	TRUE	1	0.47981975292	3		538	816	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845086	128845086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761395599	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	131	443	0	ENST00000249373.3:c.580G>A	p.Glu194Lys	p.E194K	ENST00000249373	NM_005631.4	194	Gaa/Aaa	3/12	0.237430895999375	3	FACETS	0.954	0.867	1	0.477	0.433	0.523	INDETERMINATE	1	TRUE	1	0.47981975292	3		443	710	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884924	151884924	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	40	416	2	ENST00000262189.6:c.4669del	p.Ser1557HisfsTer6	p.S1557Hfs*6	ENST00000262189	NM_170606.2	1557	Tca/ca	32/59	0.237430895999375	3	FACETS	0.439	0.364	0.522	0.219	0.182	0.261	INDETERMINATE	1	TRUE	1	0.47981975292	3		418	471	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271461	38271461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374473310	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	153	618	0	ENST00000425967.3:c.2360G>A	p.Arg787His	p.R787H	ENST00000425967	NM_001174067.1	787	cGc/cAc	18/19	1	2	FACETS	0.992	0.911	1	0.992	0.911	1	CLONAL	1	TRUE	1	0.47981975292	2		618	643	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370715	55370715	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479682835	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	616	496	0	ENST00000297316.4:c.17C>T	p.Ala6Val	p.A6V	ENST00000297316	NM_022454.3	6	gCg/gTg	1/2	0.47981975292	6	FACETS	1	0.995	1	1	0.995	1	CLONAL	5	TRUE	1	0.47981975292	6		496	920	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212857	27212857	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs906836493	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	364	483	0	ENST00000380036.4:c.2839G>A	p.Asp947Asn	p.D947N	ENST00000380036	NM_000459.3	947	Gac/Aac	17/23	0.47981975292	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.47981975292	3		483	803	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606436	93606436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201455170	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	112	513	0	ENST00000375746.1:c.256G>A	p.Ala86Thr	p.A86T	ENST00000375746	NM_001174167.1	86	Gcc/Acc	2/14	0.47981975292	3	FACETS	0.714	0.642	0.79	0.357	0.321	0.395	SUBCLONAL	1	TRUE	1	0.47981975292	3		513	811	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759683	133759683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	35	569	0	ENST00000318560.5:c.2006C>T	p.Pro669Leu	p.P669L	ENST00000318560	NM_005157.4	669	cCc/cTc	11/11	0.47981975292	3	FACETS	0.276	0.225	0.333	0.138	0.112	0.167	SUBCLONAL	1	TRUE	1	0.47981975292	3		569	656	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391799	139391799	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1455334351	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	313	576	0	ENST00000277541.6:c.6392del	p.Gly2131AlafsTer117	p.G2131Afs*117	ENST00000277541	NM_017617.3	2131	gGc/gc	34/34	0.47981975292	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.47981975292	3		576	742	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	106	369	3	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	0.47981975292	3	FACETS	0.991	0.891	1	0.495	0.445	0.548	CLONAL	1	TRUE	1	0.47981975292	3		372	553	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139804418	139804418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746259933	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	161	418	0	ENST00000247668.2:c.575G>A	p.Cys192Tyr	p.C192Y	ENST00000247668	NM_021138.3	192	tGc/tAc	6/11	0.47981975292	3	FACETS	1	0.973	1	0.567	0.521	0.615	CLONAL	1	TRUE	1	0.47981975292	3		418	734	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030472	47030472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782522553	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	136	462	1	ENST00000377604.3:c.247C>T	p.Arg83Trp	p.R83W	ENST00000377604	NM_001204468.1	83	Cgg/Tgg	4/24	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.47981975292	2		463	523	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1686012	1686012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754601133	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	68	556	0	ENST00000378625.1:c.1249G>A	p.Asp417Asn	p.D417N	ENST00000378625	NM_001198994.1	417	Gat/Aat	10/14	1	2	FACETS	0.446	0.387	0.509	0.446	0.387	0.509	SUBCLONAL	1	TRUE	1	0.47981975292	2		556	636	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190678	11190678	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	55	587	0	ENST00000361445.4:c.5521A>G	p.Thr1841Ala	p.T1841A	ENST00000361445	NM_004958.3	1841	Act/Gct	39/58	1	2	FACETS	0.295	0.252	0.343	0.295	0.252	0.343	SUBCLONAL	1	TRUE	1	0.47981975292	2		587	777	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11314015	11314015	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	52	441	0	ENST00000361445.4:c.721G>A	p.Ala241Thr	p.A241T	ENST00000361445	NM_004958.3	241	Gca/Aca	6/58	1	2	FACETS	0.366	0.311	0.426	0.366	0.311	0.426	SUBCLONAL	1	TRUE	1	0.47981975292	2		441	592	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11314023	11314023	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	48	431	0	ENST00000361445.4:c.713T>A	p.Phe238Tyr	p.F238Y	ENST00000361445	NM_004958.3	238	tTt/tAt	6/58	1	2	FACETS	0.337	0.284	0.395	0.337	0.284	0.395	SUBCLONAL	1	TRUE	1	0.47981975292	2		431	594	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263949	16263949	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	68	588	0	ENST00000375759.3:c.10318A>T	p.Lys3440Ter	p.K3440*	ENST00000375759	NM_015001.2	3440	Aag/Tag	12/15	1	2	FACETS	0.344	0.298	0.393	0.344	0.298	0.393	SUBCLONAL	1	TRUE	1	0.47981975292	2		588	824	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367020	40367020	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	37	612	0	ENST00000397332.2:c.177C>G	p.Ile59Met	p.I59M	ENST00000397332	NM_001033082.2	59	atC/atG	2/3	1	2	FACETS	0.288	0.237	0.346	0.288	0.237	0.346	SUBCLONAL	1	TRUE	1	0.47981975292	2		612	535	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797090	45797090	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	62	583	0	ENST00000450313.1:c.1323+2T>C		p.X441_splice	ENST00000450313	NM_012222.2	441			1	2	FACETS	0.396	0.341	0.455	0.396	0.341	0.455	SUBCLONAL	1	TRUE	1	0.47981975292	2		583	653	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430774	78430775	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	34	438	0	ENST00000370768.2:c.614dup	p.Glu206ArgfsTer4	p.E206Rfs*4	ENST00000370768	NM_003902.3	205	gga/ggGa	8/20	1	2	FACETS	0.313	0.255	0.378	0.313	0.255	0.378	SUBCLONAL	1	TRUE	1	0.47981975292	2		438	453	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150923392	150923392	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	27	419	0	ENST00000271640.5:c.2039T>A	p.Leu680Ter	p.L680*	ENST00000271640	NM_001145415.1	680	tTg/tAg	13/22	1	2	FACETS	0.243	0.192	0.3	0.243	0.192	0.3	SUBCLONAL	1	TRUE	1	0.47981975292	2		419	464	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150936829	150936829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	189	447	0	ENST00000271640.5:c.3865C>T	p.Arg1289Cys	p.R1289C	ENST00000271640	NM_001145415.1	1289	Cgt/Tgt	22/22	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.47981975292	2		447	626	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729684	162729684	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	42	460	0	ENST00000367921.3:c.770T>C	p.Val257Ala	p.V257A	ENST00000367921	NM_006182.2	257	gTg/gCg	8/18	1	2	FACETS	0.284	0.236	0.337	0.284	0.236	0.337	SUBCLONAL	1	TRUE	1	0.47981975292	2		460	617	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163309172	163309172	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	51	311	0	ENST00000271452.3:c.511T>A	p.Ser171Thr	p.S171T	ENST00000271452	NM_145697.2	171	Tct/Act	8/14	1	2	FACETS	0.844	0.724	0.973	0.844	0.724	0.973	CLONAL	1	TRUE	1	0.47981975292	2		311	252	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012922	176012922	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	52	322	0	ENST00000367669.3:c.1454T>A	p.Leu485Gln	p.L485Q	ENST00000367669	NM_022457.5	485	cTg/cAg	13/20	1	2	FACETS	0.85	0.73	0.979	0.85	0.73	0.979	CLONAL	1	TRUE	1	0.47981975292	2		322	255	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650159	206650159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	131	503	0	ENST00000367120.3:c.679C>T	p.Pro227Ser	p.P227S	ENST00000367120	NM_014002.3	227	Cca/Tca	7/22	1	2	FACETS	0.783	0.712	0.858	0.783	0.712	0.858	SUBCLONAL	1	TRUE	1	0.47981975292	2		503	697	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231488883	231488884	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	102	406	0	ENST00000295050.7:c.1251dup	p.Asp418Ter	p.D418*	ENST00000295050	NM_032018.5	416	gtt/gTtt	5/5	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.47981975292	2		406	378	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097829	8097829	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	46	476	0	ENST00000346208.3:c.211A>C	p.Thr71Pro	p.T71P	ENST00000346208		71	Acg/Ccg	2/6	1	2	FACETS	0.336	0.282	0.395	0.336	0.282	0.395	SUBCLONAL	1	TRUE	1	0.47981975292	2		476	571	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851198	63851198	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	39	529	0	ENST00000279873.7:c.1976A>G	p.Asp659Gly	p.D659G	ENST00000279873	NM_032199.2	659	gAc/gGc	10/10	1	2	FACETS	0.26	0.215	0.311	0.26	0.215	0.311	SUBCLONAL	1	TRUE	1	0.47981975292	2		529	625	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851941	63851941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	62	502	0	ENST00000279873.7:c.2719G>A	p.Asp907Asn	p.D907N	ENST00000279873	NM_032199.2	907	Gat/Aat	10/10	1	2	FACETS	0.384	0.331	0.442	0.384	0.331	0.442	SUBCLONAL	1	TRUE	1	0.47981975292	2		502	673	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742945	17742945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	132	502	0	ENST00000250003.3:c.853G>A	p.Ala285Thr	p.A285T	ENST00000250003	NM_002478.4	285	Gct/Act	3/3	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.47981975292	2		502	524	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205726	108205726	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	79	313	0	ENST00000278616.4:c.8041G>T	p.Val2681Leu	p.V2681L	ENST00000278616	NM_000051.3	2681	Gtg/Ttg	55/63	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.47981975292	2		313	324	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156004	119156004	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	67	599	0	ENST00000264033.4:c.1669G>A	p.Glu557Lys	p.E557K	ENST00000264033	NM_005188.3	557	Gaa/Aaa	11/16	1	2	FACETS	0.361	0.313	0.414	0.361	0.313	0.414	SUBCLONAL	1	TRUE	1	0.47981975292	2		599	773	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170283	119170283	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs144191570	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	42	459	0	ENST00000264033.4:c.2513G>C	p.Gly838Ala	p.G838A	ENST00000264033	NM_005188.3	838	gGc/gCc	16/16	1	2	FACETS	0.237	0.197	0.282	0.237	0.197	0.282	SUBCLONAL	1	TRUE	1	0.47981975292	2		459	739	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644557	21644557	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	198	332	0	ENST00000421138.2:c.110A>T	p.Gln37Leu	p.Q37L	ENST00000421138		37	cAg/cTg	4/16	0.47981975292	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.47981975292	3		332	454	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231336	46231336	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	58	395	0	ENST00000334344.6:c.1176T>A	p.Cys392Ter	p.C392*	ENST00000334344	NM_152641.2	392	tgT/tgA	10/21	0.47981975292	3	FACETS	0.964	0.834	1	0.482	0.417	0.552	CLONAL	1	TRUE	1	0.47981975292	3		395	311	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287459	46287459	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	22	327	0	ENST00000334344.6:c.5318C>T	p.Ala1773Val	p.A1773V	ENST00000334344	NM_152641.2	1773	gCc/gTc	20/21	0.47981975292	3	FACETS	0.352	0.273	0.444	0.176	0.136	0.222	SUBCLONAL	1	TRUE	1	0.47981975292	3		327	323	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432467	49432467	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	56	555	0	ENST00000301067.7:c.8672G>T	p.Gly2891Val	p.G2891V	ENST00000301067	NM_003482.3	2891	gGg/gTg	34/54	0.47981975292	3	FACETS	0.374	0.319	0.434	0.187	0.159	0.217	SUBCLONAL	1	TRUE	1	0.47981975292	3		555	774	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145034	58145034	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs759535768	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	48	503	0	ENST00000257904.6:c.310C>A	p.Leu104Met	p.L104M	ENST00000257904	NM_000075.3	104	Ctg/Atg	3/8	0.47981975292	3	FACETS	0.297	0.25	0.35	0.149	0.125	0.175	SUBCLONAL	1	TRUE	1	0.47981975292	3		503	834	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112940024	112940024	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	286	378	0	ENST00000351677.2:c.1676C>A	p.Pro559His	p.P559H	ENST00000351677	NM_002834.3	559	cCt/cAt	14/16	0.47981975292	3	FACETS	0.934	0.882	0.987	0.934	0.882	0.987	CLONAL	2	TRUE	1	0.47981975292	3		378	791	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219146	133219146	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	41	536	0	ENST00000320574.5:c.4898T>A	p.Ile1633Asn	p.I1633N	ENST00000320574	NM_006231.2	1633	aTc/aAc	37/49	0.47981975292	3	FACETS	0.295	0.245	0.351	0.148	0.122	0.176	SUBCLONAL	1	TRUE	1	0.47981975292	3		536	718	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252093	133252093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	95	532	0	ENST00000320574.5:c.1117G>A	p.Glu373Lys	p.E373K	ENST00000320574	NM_006231.2	373	Gag/Aag	12/49	0.47981975292	3	FACETS	0.618	0.55	0.691	0.309	0.275	0.346	SUBCLONAL	1	TRUE	1	0.47981975292	3		532	794	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636474	73636474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	148	559	0	ENST00000377687.4:c.737C>T	p.Thr246Ile	p.T246I	ENST00000377687	NM_001730.3	246	aCa/aTa	2/4	0.0536818949404091	6	FACETS	1	0.986	1	0.477	0.435	0.52	INDETERMINATE	1	TRUE	3	0.47981975292	6		559	845	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50788153	50788153	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	74	270	0	ENST00000307179.4:c.2767G>T	p.Val923Phe	p.V923F	ENST00000307179		923	Gtt/Ttt	17/20	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.47981975292	2		270	294	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112576	2112576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45517163	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	83	542	1	ENST00000219476.3:c.1336C>T	p.Gln446Ter	p.Q446*	ENST00000219476	NM_000548.3	446	Cag/Tag	13/42	1	2	FACETS	0.593	0.524	0.667	0.593	0.524	0.667	SUBCLONAL	1	TRUE	1	0.47981975292	2		543	583	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779369	3779369	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	223	636	1	ENST00000262367.5:c.5679del	p.Thr1894HisfsTer21	p.T1894Hfs*21	ENST00000262367	NM_004380.2	1893	ccC/cc	31/31	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.47981975292	2		637	712	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864594	56864594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	43	358	0	ENST00000308159.5:c.1082G>A	p.Arg361Lys	p.R361K	ENST00000308159	NM_014669.4	361	aGa/aAa	10/22	1	2	FACETS	0.341	0.285	0.404	0.341	0.285	0.404	SUBCLONAL	1	TRUE	1	0.47981975292	2		358	525	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665042	29665042	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs1060500356	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	30	313	0	ENST00000356175.3:c.6642-1G>C		p.X2214_splice	ENST00000356175	NM_000267.3	2214			1	2	FACETS	0.465	0.376	0.565	0.465	0.376	0.565	SUBCLONAL	1	TRUE	1	0.47981975292	2		313	269	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246359	41246359	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	41	473	0	ENST00000357654.3:c.1189G>A	p.Asp397Asn	p.D397N	ENST00000357654	NM_007294.3	397	Gac/Aac	10/23	1	2	FACETS	0.412	0.343	0.488	0.412	0.343	0.488	SUBCLONAL	1	TRUE	1	0.47981975292	2		473	415	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56809900	56809900	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	25	333	0	ENST00000337432.4:c.1021A>G	p.Ile341Val	p.I341V	ENST00000337432	NM_058216.2	341	Atc/Gtc	8/9	1	2	FACETS	0.392	0.309	0.486	0.392	0.309	0.486	SUBCLONAL	1	TRUE	1	0.47981975292	2		333	266	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533446	63533446	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	68	469	0	ENST00000307078.5:c.1708T>C	p.Phe570Leu	p.F570L	ENST00000307078	NM_004655.3	570	Ttt/Ctt	6/11	1	2	FACETS	0.417	0.363	0.477	0.417	0.363	0.477	SUBCLONAL	1	TRUE	1	0.47981975292	2		469	679	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61306900	61306900	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	22	408	0	ENST00000341074.5:c.580A>T	p.Asn194Tyr	p.N194Y	ENST00000341074	NM_002974.2	194	Aac/Tac	6/8	1	2	FACETS	0.253	0.195	0.319	0.253	0.195	0.319	SUBCLONAL	1	TRUE	1	0.47981975292	2		408	363	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226504	1226504	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782493	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	117	481	0	ENST00000326873.7:c.1160C>T	p.Pro387Leu	p.P387L	ENST00000326873	NM_000455.4	387	cCc/cTc	9/10	1	2	FACETS	0.913	0.827	1	0.913	0.827	1	CLONAL	1	TRUE	1	0.47981975292	2		481	534	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612429	1612429	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	116	340	0	ENST00000344749.5:c.1590T>A	p.Ser530Arg	p.S530R	ENST00000344749	NM_001136139.2	530	agT/agA	18/19	1	2	FACETS	0.941	0.852	1	0.941	0.852	1	CLONAL	1	TRUE	1	0.47981975292	2		340	514	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222953	5222953	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	39	589	0	ENST00000357368.4:c.2850G>A	p.Trp950Ter	p.W950*	ENST00000357368	NM_002850.3	950	tgG/tgA	18/38	1	2	FACETS	0.297	0.245	0.354	0.297	0.245	0.354	SUBCLONAL	1	TRUE	1	0.47981975292	2		589	548	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6222692	6222692	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776746658	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	160	451	0	ENST00000252674.7:c.550G>A	p.Ala184Thr	p.A184T	ENST00000252674	NM_005934.3	184	Gcc/Acc	6/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.47981975292	2		451	565	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250974	10250974	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	85	478	0	ENST00000340748.4:c.3506T>C	p.Met1169Thr	p.M1169T	ENST00000340748		1169	aTg/aCg	32/40	1	2	FACETS	0.654	0.579	0.733	0.654	0.579	0.733	SUBCLONAL	1	TRUE	1	0.47981975292	2		478	542	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254635	10254635	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	129	401	0	ENST00000340748.4:c.2875C>A	p.Pro959Thr	p.P959T	ENST00000340748		959	Cca/Aca	28/40	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.47981975292	2		401	536	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291097	10291097	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	82	803	2	ENST00000340748.4:c.374C>T	p.Ala125Val	p.A125V	ENST00000340748		125	gCc/gTc	4/40	1	2	FACETS	0.313	0.275	0.354	0.313	0.275	0.354	SUBCLONAL	1	TRUE	1	0.47981975292	2		805	1093	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135059	11135059	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	69	426	0	ENST00000358026.2:c.3026G>T	p.Arg1009Leu	p.R1009L	ENST00000358026	NM_001128849.1	1009	cGc/cTc	21/36	1	2	FACETS	0.529	0.461	0.602	0.529	0.461	0.602	SUBCLONAL	1	TRUE	1	0.47981975292	2		426	544	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143988	11143988	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	110	483	0	ENST00000358026.2:c.3569C>G	p.Ala1190Gly	p.A1190G	ENST00000358026	NM_001128849.1	1190	gCc/gGc	26/36	1	2	FACETS	0.735	0.661	0.812	0.735	0.661	0.812	SUBCLONAL	1	TRUE	1	0.47981975292	2		483	624	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288768	15288768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	104	367	0	ENST00000263388.2:c.3971G>A	p.Cys1324Tyr	p.C1324Y	ENST00000263388	NM_000435.2	1324	tGc/tAc	24/33	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.47981975292	2		367	408	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967735	18967735	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	128	471	0	ENST00000262803.5:c.1874T>A	p.Leu625Gln	p.L625Q	ENST00000262803	NM_002911.3	625	cTg/cAg	14/24	1	2	FACETS	0.906	0.824	0.992	0.906	0.824	0.992	CLONAL	1	TRUE	1	0.47981975292	2		471	589	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42384752	42384752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs953006206	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	147	297	0	ENST00000221972.3:c.514G>A	p.Glu172Lys	p.E172K	ENST00000221972	NM_021601.3	172	Gag/Aag	4/5	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.47981975292	2		297	433	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752879	42752879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	55	683	0	ENST00000222329.4:c.1385C>T	p.Ala462Val	p.A462V	ENST00000222329	NM_006494.2	462	gCa/gTa	4/4	1	2	FACETS	0.302	0.258	0.351	0.302	0.258	0.351	SUBCLONAL	1	TRUE	1	0.47981975292	2		683	758	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082259	16082259	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886041290	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	35	416	0	ENST00000281043.3:c.73C>T	p.Gln25Ter	p.Q25*	ENST00000281043	NM_005378.4	25	Cag/Tag	2/3	0.477875949824103	3	FACETS	0.296	0.242	0.357	0.148	0.121	0.179	SUBCLONAL	1	TRUE	1	0.47981975292	3		416	611	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085630	16085630	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	37	435	0	ENST00000281043.3:c.806A>G	p.Glu269Gly	p.E269G	ENST00000281043	NM_005378.4	269	gAa/gGa	3/3	0.477875949824103	3	FACETS	0.335	0.276	0.402	0.168	0.138	0.201	SUBCLONAL	1	TRUE	1	0.47981975292	3		435	570	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965769	25965769	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	65	493	0	ENST00000435504.4:c.3437C>A	p.Pro1146His	p.P1146H	ENST00000435504		1146	cCt/cAt	13/13	0.477875949824103	3	FACETS	0.436	0.377	0.5	0.218	0.188	0.25	SUBCLONAL	1	TRUE	1	0.47981975292	3		493	770	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982412	25982412	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	44	359	0	ENST00000435504.4:c.878C>G	p.Ser293Ter	p.S293*	ENST00000435504		293	tCa/tGa	9/13	0.477875949824103	3	FACETS	0.333	0.278	0.394	0.166	0.139	0.197	SUBCLONAL	1	TRUE	1	0.47981975292	3		359	683	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131237	202131237	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	38	393	0	ENST00000358485.4:c.205A>T	p.Ile69Phe	p.I69F	ENST00000358485	NM_001080125.1	69	Att/Ttt	2/9	0.477875949824103	3	FACETS	0.326	0.268	0.39	0.163	0.134	0.195	SUBCLONAL	1	TRUE	1	0.47981975292	3		393	603	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375208	31375208	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	421	593	0	ENST00000328111.2:c.608del	p.Pro203ArgfsTer23	p.P203Rfs*23	ENST00000328111	NM_006892.3	202	tCc/tc	6/23	0.104546743420274	4	FACETS	0.85	0.813	0.888	1	0.994	1	INDETERMINATE	3	TRUE	2	0.47981975292	4		593	1018	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306629	41306629	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	80	336	0	ENST00000373198.4:c.1030A>T	p.Asn344Tyr	p.N344Y	ENST00000373198	NM_133170.3	344	Aac/Tac	7/32	0.104546743420274	4	FACETS	0.909	0.802	1	0.454	0.401	0.512	INDETERMINATE	1	TRUE	2	0.47981975292	4		336	543	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62309699	62309699	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	189	413	0	ENST00000360203.5:c.1037G>T	p.Ser346Ile	p.S346I	ENST00000360203	NM_001283009.1	346	aGc/aTc	12/35	0.104546743420274	4	FACETS	0.758	0.702	0.816	0.758	0.702	0.816	INDETERMINATE	2	TRUE	2	0.47981975292	4		413	769	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21346528	21346528	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368589786	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	168	535	0	ENST00000215739.8:c.1019G>A	p.Arg340Gln	p.R340Q	ENST00000215739	NM_006767.3	340	cGa/cAa	10/21	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.47981975292	2		535	693	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29090039	29090039	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	35	96	0	ENST00000328354.6:c.1442T>C	p.Leu481Ser	p.L481S	ENST00000328354	NM_007194.3	481	tTa/tCa	13/15	1	2	FACETS	0.838	0.696	0.994	0.838	0.696	0.994	CLONAL	1	TRUE	1	0.47981975292	2		96	174	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29445207	29445208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	230	467	0	ENST00000544604.2:c.1046_1047dup	p.Glu350TrpfsTer14	p.E350Wfs*14	ENST00000544604	NM_001206998.1	346	-/GT	8/9	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.47981975292	2		467	737	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523675	41523675	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	51	476	0	ENST00000263253.7:c.1091G>C	p.Cys364Ser	p.C364S	ENST00000263253	NM_001429.3	364	tGc/tCc	4/31	1	2	FACETS	0.314	0.266	0.366	0.314	0.266	0.366	SUBCLONAL	1	TRUE	1	0.47981975292	2		476	678	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266200	41266200	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	113	464	0	ENST00000349496.5:c.197G>T	p.Trp66Leu	p.W66L	ENST00000349496	NM_001904.3	66	tGg/tTg	3/15	1	2	FACETS	0.948	0.857	1	0.948	0.857	1	CLONAL	1	TRUE	1	0.47981975292	2		464	497	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143028	47143028	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	94	249	0	ENST00000409792.3:c.4935A>T	p.Gln1645His	p.Q1645H	ENST00000409792	NM_014159.6	1645	caA/caT	8/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.47981975292	2		249	294	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935045	49935045	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	58	611	0	ENST00000296474.3:c.1954C>T	p.Pro652Ser	p.P652S	ENST00000296474	NM_002447.2	652	Cct/Tct	6/20	1	2	FACETS	0.311	0.266	0.36	0.311	0.266	0.36	SUBCLONAL	1	TRUE	1	0.47981975292	2		611	778	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280204	142280206	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	100	348	0	ENST00000350721.4:c.1228_1230del	p.Glu410del	p.E410del	ENST00000350721	NM_001184.3	410	GAG/-	5/47	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.47981975292	2		348	370	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169977768	169977768	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	19	285	0	ENST00000295797.4:c.235A>G	p.Thr79Ala	p.T79A	ENST00000295797	NM_002740.5	79	Aca/Gca	3/18	1	2	FACETS	0.234	0.177	0.301	0.234	0.177	0.301	SUBCLONAL	1	TRUE	1	0.47981975292	2		285	338	SUCCESS
REST	5978	MSKCC	GRCh37	4	57777453	57777453	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376611047	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	193	526	0	ENST00000309042.7:c.649C>T	p.Arg217Cys	p.R217C	ENST00000309042	NM_005612.4	217	Cgc/Tgc	2/4	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.47981975292	2		526	598	SUCCESS
ALB	213	MSKCC	GRCh37	4	74274489	74274489	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	27	356	0	ENST00000295897.4:c.449C>T	p.Ala150Val	p.A150V	ENST00000295897	NM_000477.5	150	gCt/gTt	4/15	1	2	FACETS	0.25	0.198	0.309	0.25	0.198	0.309	SUBCLONAL	1	TRUE	1	0.47981975292	2		356	450	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143181697	143181697	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	17	304	0	ENST00000262992.4:c.636T>G	p.Cys212Trp	p.C212W	ENST00000262992	NM_001101669.1	212	tgT/tgG	9/24	1	2	FACETS	0.212	0.158	0.277	0.212	0.158	0.277	SUBCLONAL	1	TRUE	1	0.47981975292	2		304	334	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540453	187540453	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	34	493	0	ENST00000441802.2:c.7287T>G	p.Ile2429Met	p.I2429M	ENST00000441802	NM_005245.3	2429	atT/atG	10/27	1	2	FACETS	0.239	0.194	0.289	0.239	0.194	0.289	SUBCLONAL	1	TRUE	1	0.47981975292	2		493	593	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630303	187630303	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	177	528	0	ENST00000441802.2:c.679C>A	p.Arg227Ser	p.R227S	ENST00000441802	NM_005245.3	227	Cgt/Agt	2/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.47981975292	2		528	633	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630371	187630371	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	45	493	0	ENST00000441802.2:c.611T>C	p.Ile204Thr	p.I204T	ENST00000441802	NM_005245.3	204	aTa/aCa	2/27	1	2	FACETS	0.331	0.277	0.39	0.331	0.277	0.39	SUBCLONAL	1	TRUE	1	0.47981975292	2		493	567	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526244	31526244	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	138	457	0	ENST00000344624.3:c.796A>T	p.Arg266Ter	p.R266*	ENST00000344624		266	Aga/Tga	2/33	1	2	FACETS	0.931	0.85	1	0.931	0.85	1	CLONAL	1	TRUE	1	0.47981975292	2		457	618	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526981	31526981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1206389569	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	166	399	0	ENST00000344624.3:c.59G>A	p.Arg20Gln	p.R20Q	ENST00000344624		20	cGa/cAa	2/33	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.47981975292	2		399	543	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953178	38953178	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	21	297	0	ENST00000357387.3:c.2806T>A	p.Ser936Thr	p.S936T	ENST00000357387	NM_152756.3	936	Tca/Aca	29/38	1	2	FACETS	0.281	0.216	0.357	0.281	0.216	0.357	SUBCLONAL	1	TRUE	1	0.47981975292	2		297	311	SUCCESS
APC	324	MSKCC	GRCh37	5	112174409	112174409	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587782306	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	67	429	0	ENST00000257430.4:c.3118A>T	p.Arg1040Trp	p.R1040W	ENST00000257430	NM_000038.5	1040	Agg/Tgg	16/16	1	2	FACETS	0.898	0.787	1	0.898	0.787	1	CLONAL	1	TRUE	1	0.47981975292	2		429	311	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433672	149433672	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776645465	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	25	361	1	ENST00000286301.3:c.2879C>T	p.Ala960Val	p.A960V	ENST00000286301	NM_005211.3	960	gCc/gTc	22/22	1	2	FACETS	0.265	0.208	0.33	0.265	0.208	0.33	SUBCLONAL	1	TRUE	1	0.47981975292	2		362	393	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405095	405095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	102	316	0	ENST00000380956.4:c.1177G>A	p.Asp393Asn	p.D393N	ENST00000380956	NM_001195286.1	393	Gac/Aac	8/9	0.317715322073391	2	FACETS	0.826	0.741	0.914	0.413	0.37	0.457	CLONAL	1	TRUE	0	0.47981975292	2		316	515	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911269	29911269	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs199474566	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	30	336	0	ENST00000376809.5:c.568G>C	p.Glu190Gln	p.E190Q	ENST00000376809	NM_002116.7	190	Gag/Cag	3/8	0.317715322073391	2	FACETS	0.379	0.306	0.462	0.189	0.153	0.231	SUBCLONAL	1	TRUE	0	0.47981975292	2		336	330	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31238918	31238918	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	11	192	0	ENST00000376228.5:c.551T>C	p.Leu184Pro	p.L184P	ENST00000376228	NM_002117.5	184	cTg/cCg	3/8	0.317715322073391	2	FACETS	0.252	0.174	0.348	0.126	0.087	0.174	SUBCLONAL	1	TRUE	0	0.47981975292	2		192	182	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178588	32178588	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	41	477	0	ENST00000375023.3:c.2806T>C	p.Ser936Pro	p.S936P	ENST00000375023	NM_004557.3	936	Tcc/Ccc	18/30	0.317715322073391	2	FACETS	0.275	0.228	0.327	0.137	0.114	0.164	SUBCLONAL	1	TRUE	0	0.47981975292	2		477	622	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800570	32800570	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	42	508	0	ENST00000374899.4:c.977C>G	p.Ala326Gly	p.A326G	ENST00000374899	NM_018833.2	326	gCc/gGc	6/12	0.317715322073391	2	FACETS	0.227	0.188	0.27	0.113	0.094	0.135	SUBCLONAL	1	TRUE	0	0.47981975292	2		508	772	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288684	33288684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	29	440	0	ENST00000374542.5:c.868C>T	p.Leu290Phe	p.L290F	ENST00000374542	NM_001141970.1	290	Ctt/Ttt	3/8	0.317715322073391	2	FACETS	0.238	0.19	0.292	0.119	0.095	0.146	SUBCLONAL	1	TRUE	0	0.47981975292	2		440	508	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846110	128846110	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1584662459	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	62	558	0	ENST00000249373.3:c.1040G>C	p.Gly347Ala	p.G347A	ENST00000249373	NM_005631.4	347	gGc/gCc	5/12	0.237430895999375	3	FACETS	0.392	0.338	0.452	0.196	0.169	0.226	INDETERMINATE	1	TRUE	1	0.47981975292	3		558	817	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624415	140624415	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	24	324	0	ENST00000288602.6:c.89G>C	p.Gly30Ala	p.G30A	ENST00000288602	NM_004333.4	30	gGc/gCc	1/18	0.237430895999375	3	FACETS	0.335	0.262	0.419	0.168	0.131	0.21	INDETERMINATE	1	TRUE	1	0.47981975292	3		324	370	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873964	151873966	+	inframe_deletion	In_Frame_Del	DEL	AGC	AGC	-	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	48	439	0	ENST00000262189.6:c.8572_8574del	p.Ala2858del	p.A2858del	ENST00000262189	NM_170606.2	2858	GCT/-	38/59	0.237430895999375	3	FACETS	0.465	0.393	0.545	0.233	0.196	0.273	INDETERMINATE	1	TRUE	1	0.47981975292	3		439	533	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874847	151874847	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	148	469	0	ENST00000262189.6:c.7691G>T	p.Arg2564Met	p.R2564M	ENST00000262189	NM_170606.2	2564	aGg/aTg	38/59	0.237430895999375	3	FACETS	1	0.957	1	0.536	0.491	0.584	INDETERMINATE	1	TRUE	1	0.47981975292	3		469	713	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877887	151877887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375772772	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	47	453	0	ENST00000262189.6:c.7058C>T	p.Ser2353Phe	p.S2353F	ENST00000262189	NM_170606.2	2353	tCc/tTc	36/59	0.237430895999375	3	FACETS	0.344	0.289	0.405	0.172	0.144	0.203	INDETERMINATE	1	TRUE	1	0.47981975292	3		453	706	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540144	23540144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	125	416	0	ENST00000380871.4:c.259G>A	p.Ala87Thr	p.A87T	ENST00000380871	NM_006167.3	87	Gcc/Acc	1/2	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.47981975292	2		416	496	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864644	68864644	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	69	312	0	ENST00000288368.4:c.15C>G	p.Ser5Arg	p.S5R	ENST00000288368	NM_024870.2	5	agC/agG	1/40	0.47981975292	6	FACETS	0.788	0.686	0.899	0.158	0.137	0.18	SUBCLONAL	1	TRUE	1	0.47981975292	6		312	715	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859897	117859897	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	62	371	0	ENST00000297338.2:c.1738A>G	p.Ser580Gly	p.S580G	ENST00000297338	NM_006265.2	580	Agt/Ggt	14/14	0.47981975292	6	FACETS	0.52	0.448	0.599	0.104	0.089	0.12	SUBCLONAL	1	TRUE	1	0.47981975292	6		371	974	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2047365	2047365	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	23	238	0	ENST00000349721.2:c.927G>T	p.Gln309His	p.Q309H	ENST00000349721	NM_003070.3	309	caG/caT	5/34	0.47981975292	3	FACETS	0.314	0.245	0.395	0.157	0.122	0.198	SUBCLONAL	1	TRUE	1	0.47981975292	3		238	378	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460412	8460412	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	67	331	0	ENST00000356435.5:c.3874A>G	p.Arg1292Gly	p.R1292G	ENST00000356435		1292	Agg/Ggg	22/35	0.47981975292	3	FACETS	0.904	0.79	1	0.452	0.395	0.514	CLONAL	1	TRUE	1	0.47981975292	3		331	383	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637110	93637110	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	44	376	0	ENST00000375746.1:c.1160A>T	p.Lys387Met	p.K387M	ENST00000375746	NM_001174167.1	387	aAg/aTg	9/14	0.47981975292	3	FACETS	0.375	0.314	0.443	0.188	0.157	0.222	SUBCLONAL	1	TRUE	1	0.47981975292	3		376	606	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249854	110249854	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758232150	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	209	536	0	ENST00000374672.4:c.821G>A	p.Cys274Tyr	p.C274Y	ENST00000374672	NM_004235.4	274	tGc/tAc	3/5	0.47981975292	3	FACETS	0.961	0.899	1	0.961	0.899	1	CLONAL	2	TRUE	1	0.47981975292	3		536	562	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759836	133759836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	47	489	0	ENST00000318560.5:c.2159C>T	p.Ser720Phe	p.S720F	ENST00000318560	NM_005157.4	720	tCc/tTc	11/11	0.47981975292	3	FACETS	0.395	0.333	0.464	0.197	0.166	0.232	SUBCLONAL	1	TRUE	1	0.47981975292	3		489	615	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396239	139396239	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	57	531	0	ENST00000277541.6:c.5599G>T	p.Val1867Phe	p.V1867F	ENST00000277541	NM_017617.3	1867	Gtt/Ttt	30/34	0.47981975292	3	FACETS	0.354	0.302	0.41	0.177	0.151	0.205	SUBCLONAL	1	TRUE	1	0.47981975292	3		531	833	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413920	139413920	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1564200790	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	133	453	0	ENST00000277541.6:c.840C>G	p.Asn280Lys	p.N280K	ENST00000277541	NM_017617.3	280	aaC/aaG	5/34	0.47981975292	3	FACETS	0.811	0.736	0.889	0.405	0.368	0.445	CLONAL	1	TRUE	1	0.47981975292	3		453	848	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918346	44918346	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	10	282	0	ENST00000377967.4:c.971T>A	p.Ile324Lys	p.I324K	ENST00000377967	NM_021140.2	324	aTa/aAa	11/29	1	2	FACETS	0.215	0.145	0.302	0.215	0.145	0.302	SUBCLONAL	1	TRUE	1	0.47981975292	2		282	194	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538941	187538942	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0066776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	167	472	0	ENST00000441802.2:c.8798_8799insC	p.Gln2933HisfsTer14	p.Q2933Hfs*14	ENST00000441802	NM_005245.3	2933	caa/caCa	10/27	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.47981975292	2		472	586	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166860	32166860	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066778-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	72	490	0	ENST00000375023.3:c.4378C>A	p.Leu1460Met	p.L1460M	ENST00000375023	NM_004557.3	1460	Ctg/Atg	24/30	1	2	FACETS	0.789	0.691	0.894	0.789	0.691	0.894	SUBCLONAL	1	TRUE	1	0.372477271740024	2		490	490	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	155	317	0				ENST00000310581	NM_198253.2	-/1132			0.34929172461388	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	2	0.462341694712747	4		317	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0066796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	298	552	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.469160033544073	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.462341694712747	2		552	528	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516921	187516921	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	90	432	0	ENST00000441802.2:c.13060C>T	p.Gln4354Ter	p.Q4354*	ENST00000441802	NM_005245.3	4354	Cag/Tag	26/27	0.202100918540302	2	FACETS	0.701	0.624	0.784	0.351	0.312	0.392	INDETERMINATE	1	TRUE	0	0.462341694712747	2		432	555	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456514	29456514	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	99	522	0	ENST00000389048.3:c.2404G>C	p.Glu802Gln	p.E802Q	ENST00000389048	NM_004304.4	802	Gaa/Caa	14/29	0.469160033544073	3	FACETS	0.789	0.705	0.879	0.395	0.352	0.44	SUBCLONAL	1	TRUE	1	0.462341694712747	3		522	668	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999201	100999201	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	257	575	0	ENST00000325455.5:c.601G>C	p.Glu201Gln	p.E201Q	ENST00000325455	NM_001202474.3	201	Gag/Cag	1/8	0.469160033544073	3	FACETS	0.968	0.911	1	0.968	0.911	1	CLONAL	2	TRUE	1	0.462341694712747	3		575	707	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216704	7216707	+	frameshift_variant	Frame_Shift_Del	DEL	TGAG	TGAG	-	rs758044036	NA	P-0066796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	306	562	0	ENST00000380728.2:c.716_719del	p.Thr239ArgfsTer105	p.T239Rfs*105	ENST00000380728		239	aCTCAg/ag	8/11	0.469160033544073	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.462341694712747	2		562	575	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344440	118344440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	225	570	0	ENST00000534358.1:c.2566G>A	p.Glu856Lys	p.E856K	ENST00000534358	NM_005933.3	856	Gag/Aag	3/36	0.469160033544073	3	FACETS	1	0.99	1	0.686	0.64	0.734	CLONAL	1	TRUE	1	0.462341694712747	3		570	873	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528210	103528210	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	50	471	0	ENST00000355739.4:c.3518G>C	p.Arg1173Thr	p.R1173T	ENST00000355739	NM_000123.3	1173	aGa/aCa	15/15	0.469160033544073	3	FACETS	0.43	0.364	0.503	0.215	0.182	0.252	SUBCLONAL	1	TRUE	1	0.462341694712747	3		471	619	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853881	59853881	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	358	425	0	ENST00000259008.2:c.1978C>G	p.Leu660Val	p.L660V	ENST00000259008	NM_032043.2	660	Ctc/Gtc	14/20	0.435927839256083	5	FACETS	0.899	0.859	0.94	0.899	0.859	0.94	CLONAL	4	TRUE	1	0.462341694712747	5		425	729	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422721	49422744	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGGTTTGGTATCTGGGAAGACTG	AAGGTTTGGTATCTGGGAAGACTG	-	novel	NA	P-0066796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	374	549	0	ENST00000301067.7:c.14252-3_14272del		p.X4751_splice	ENST00000301067	NM_003482.3	4751		45/54	0.467458613678697	5	FACETS	0.971	0.924	1			1	CLONAL	3	TRUE	NA	0.462341694712747	5		549	941	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481424	56481424	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs56107455	NA	P-0066796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	52	540	0	ENST00000267101.3:c.611C>T	p.Thr204Ile	p.T204I	ENST00000267101	NM_001982.3	204	aCa/aTa	5/28	0.469160033544073	3	FACETS	0.425	0.361	0.495	0.212	0.18	0.248	SUBCLONAL	1	TRUE	1	0.462341694712747	3		540	652	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722266	176722266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758475990	NA	P-0066796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	249	592	0	ENST00000439151.2:c.7897C>T	p.Arg2633Trp	p.R2633W	ENST00000439151	NM_022455.4	2633	Cgg/Tgg	23/23	0.161237705574066	4	FACETS	0.949	0.89	1	0.949	0.89	1	INDETERMINATE	2	TRUE	2	0.462341694712747	4		592	830	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472212	472212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369614089	NA	P-0066796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	86	441	0	ENST00000399788.2:c.589C>T	p.Leu197Phe	p.L197F	ENST00000399788	NM_001042603.1	197	Ctc/Ttc	5/28	0.327060114558282	5	FACETS	0.801	0.707	0.9	0.267	0.235	0.3	CLONAL	1	TRUE	2	0.462341694712747	5		441	787	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31379512	31379512	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	200	372	0	ENST00000328111.2:c.919G>C	p.Glu307Gln	p.E307Q	ENST00000328111	NM_006892.3	307	Gag/Cag	8/23	0.327060114558282	5	FACETS	1	0.968	1	0.712	0.662	0.763	CLONAL	2	TRUE	2	0.462341694712747	5		372	686	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371747	55371841	+	frameshift_variant	Frame_Shift_Del	DEL	AGCGGCTGAAGCGGGTGGAGGGCGGCTTCCTGCACGGCCTGGCTGAGCCGCAGGCGGCCGCGCTGGGCCCCGAGGGCGGCCGCGTGGCCATGGAC	AGCGGCTGAAGCGGGTGGAGGGCGGCTTCCTGCACGGCCTGGCTGAGCCGCAGGCGGCCGCGCTGGGCCCCGAGGGCGGCCGCGTGGCCATGGAC	-	novel	NA	P-0066796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	40	511	0	ENST00000297316.4:c.437_531del	p.Lys146ArgfsTer187	p.K146Rfs*187	ENST00000297316	NM_022454.3	146	aAGCGGCTGAAGCGGGTGGAGGGCGGCTTCCTGCACGGCCTGGCTGAGCCGCAGGCGGCCGCGCTGGGCCCCGAGGGCGGCCGCGTGGCCATGGAC/a	2/2	0.34929172461388	4	FACETS	0.329	0.272	0.392	0.164	0.136	0.196	SUBCLONAL	1	TRUE	2	0.462341694712747	4		511	770	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120611999	120611999	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	18	122	0	ENST00000256646.2:c.22C>G	p.Leu8Val	p.L8V	ENST00000256646	NM_024408.3	8	Ctg/Gtg	1/34	0.436627201020237	3	FACETS	0.864	0.659	1	0.432	0.329	0.549	CLONAL	1	TRUE	1	0.462341694712747	3		122	111	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169547	27169547	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	499	478	0	ENST00000380036.4:c.548C>A	p.Pro183His	p.P183H	ENST00000380036	NM_000459.3	183	cCc/cAc	4/23	0.469160033544073	3	FACETS	0.878	0.85	0.905	1	0.995	1	CLONAL	4	TRUE	0	0.462341694712747	3		478	757	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107135	27107135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	136	600	0	ENST00000324856.7:c.6746C>T	p.Ser2249Leu	p.S2249L	ENST00000324856	NM_006015.4	2249	tCa/tTa	20/20	0.202100918540302	2	FACETS	0.817	0.744	0.894	0.409	0.372	0.447	INDETERMINATE	1	TRUE	0	0.462341694712747	2		600	720	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163707	32163707	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	271	494	0	ENST00000375023.3:c.5519T>G	p.Phe1840Cys	p.F1840C	ENST00000375023	NM_004557.3	1840	tTc/tGc	30/30	0.309594094448493	4	FACETS	0.896	0.847	0.945	1	0.993	1	CLONAL	3	TRUE	2	0.462341694712747	4		494	638	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665284	176665284	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	212	425	0	ENST00000439151.2:c.3968C>A	p.Ser1323Tyr	p.S1323Y	ENST00000439151	NM_022455.4	1323	tCt/tAt	7/23	0.161237705574066	4	FACETS	1	0.976	1	1	0.976	1	INDETERMINATE	2	TRUE	2	0.462341694712747	4		425	613	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63965770	63965770	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	262	537	0	ENST00000398590.3:c.679G>C	p.Glu227Gln	p.E227Q	ENST00000398590	NM_001177387.1	227	Gag/Cag	6/14	0.285654984450852	5	FACETS	1	0.99	1	0.832	0.783	0.882	CLONAL	2	TRUE	2	0.462341694712747	5		537	769	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38545409	38545409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	78	347	0	ENST00000299084.4:c.23C>T	p.Ser8Phe	p.S8F	ENST00000299084	NM_152594.2	8	tCt/tTt	1/7	0.202100918540302	2	FACETS	0.935	0.827	1	0.467	0.413	0.525	INDETERMINATE	1	TRUE	0	0.462341694712747	2		347	361	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169559	27169559	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	501	481	0	ENST00000380036.4:c.560G>C	p.Gly187Ala	p.G187A	ENST00000380036	NM_000459.3	187	gGa/gCa	4/23	0.469160033544073	3	FACETS	0.884	0.856	0.911	1	0.996	1	CLONAL	4	TRUE	0	0.462341694712747	3		481	755	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820601	44820601	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066796-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	177	428	0	ENST00000377967.4:c.298G>T	p.Gly100Cys	p.G100C	ENST00000377967	NM_021140.2	100	Ggt/Tgt	3/29	0.469160033544073	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.462341694712747	1		428	451	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066812-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	24	642	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.766	0.621	0.92	1	0.939	1	CLONAL	2	FALSE	1	0.44138906949001	2		643	71	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066812-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	25	547	1	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	FALSE	1	0.44138906949001	2		548	88	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272337	15272337	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs771517374	NA	P-0066812-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	20	712	0	ENST00000263388.2:c.6102del	p.Gly2035ValfsTer50	p.G2035Vfs*50	ENST00000263388	NM_000435.2	2034	ccC/cc	33/33	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	1	0.44138906949001	2		712	62	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066812-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	26	589	3	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	FALSE	1	0.44138906949001	2		592	98	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0066812-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	17	470	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.951	0.725	1	0.951	0.725	1	CLONAL	1	FALSE	1	0.44138906949001	2		470	81	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857275	9857275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426934537	NA	P-0066812-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	13	639	0	ENST00000330684.3:c.4126C>T	p.Arg1376Cys	p.R1376C	ENST00000330684	NM_001134407.1	1376	Cgc/Tgc	13/13	1	2	FACETS	0.92	0.672	1	0.92	0.672	1	CLONAL	1	FALSE	1	0.44138906949001	2		639	64	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86648973	86648973	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0066812-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	11	297	0	ENST00000274376.6:c.1254-1G>A		p.X418_splice	ENST00000274376	NM_002890.2	418			1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	FALSE	1	0.44138906949001	2		297	34	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520183	9520183	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781425219	NA	P-0066812-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	12	502	0	ENST00000353224.5:c.2086G>A	p.Gly696Arg	p.G696R	ENST00000353224	NM_177990.2	696	Gga/Aga	10/10	0.184103205083595	1	FACETS	0.847	0.614	1	0.847	0.614	1	INDETERMINATE	1	FALSE	0	0.44138906949001	1		502	50	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778953	9778955	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs1259321686	NA	P-0066812-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	12	566	0	ENST00000377346.4:c.1228_1230del	p.Lys410del	p.K410del	ENST00000377346	NM_005026.3	408	AAG/-	9/24	1	2	FACETS	0.85	0.61	1	0.85	0.61	1	CLONAL	1	FALSE	1	0.44138906949001	2		566	64	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092946	27092946	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0066812-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	29	452	0	ENST00000324856.7:c.2879-2A>G		p.X960_splice	ENST00000324856	NM_006015.4	960			1	2	FACETS	0.792	0.656	0.935	1	0.952	1	CLONAL	2	FALSE	1	0.44138906949001	2		452	83	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829902	72829902	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066812-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	26	474	0	ENST00000268489.5:c.6679del	p.Arg2227GlyfsTer28	p.R2227Gfs*28	ENST00000268489	NM_006885.3	2227	Cgg/gg	9/10	0.44138906949001	1	FACETS	0.918	0.771	1	1	0.959	1	CLONAL	2	FALSE	0	0.44138906949001	1		474	50	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344715	65344715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766239143	NA	P-0066812-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	20	507	0	ENST00000342505.4:c.322C>T	p.Arg108Trp	p.R108W	ENST00000342505	NM_002227.2	108	Cgg/Tgg	4/25	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	FALSE	1	0.44138906949001	2		507	70	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593379	67593380	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0066812-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	31	544	0	ENST00000274335.5:c.2128dup	p.Leu710ProfsTer31	p.L710Pfs*31	ENST00000274335		709	tcc/tCcc	15/15	1	2	FACETS	0.763	0.636	0.899	1	0.952	1	SUBCLONAL	2	FALSE	1	0.44138906949001	2		544	92	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591291	67591291	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066812-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	44	454	0	ENST00000274335.5:c.1789T>A	p.Trp597Arg	p.W597R	ENST00000274335		597	Tgg/Agg	13/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.44138906949001	2		454	134	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220168	36220168	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066812-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	35	611	0	ENST00000222270.7:c.4888C>T	p.His1630Tyr	p.H1630Y	ENST00000222270	NM_014727.1	1630	Cat/Tat	22/37	1	2	FACETS	0.785	0.662	0.915	1	0.959	1	CLONAL	2	FALSE	1	0.44138906949001	2		611	101	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685268	89685268	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs1085308043	NA	P-0066813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	16	167	0	ENST00000371953.3:c.165-2A>T		p.X55_splice	ENST00000371953	NM_000314.4	55			0.462952745470163	5	FACETS	0.33	0.243	0.433	0.11	0.081	0.145	SUBCLONAL	1	FALSE	2	0.716352169311669	5		167	281	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8501056	8501056	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs905180868	NA	P-0066813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	76	429	0	ENST00000356435.5:c.1826C>T	p.Pro609Leu	p.P609L	ENST00000356435		609	cCg/cTg	13/35	0.479519132397612	4	FACETS	0.984	0.883	1	0.984	0.883	1	CLONAL	2	FALSE	2	0.716352169311669	4		429	185	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717776	89717776	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	rs1060500110	NA	P-0066813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	20	271	0	ENST00000371953.3:c.801+1del		p.K267fs	ENST00000371953	NM_000314.4	267	aaG/aa	7/9	0.462952745470163	5	FACETS	0.393	0.3	0.501	0.131	0.1	0.167	SUBCLONAL	1	FALSE	2	0.716352169311669	5		271	295	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095755	178095755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543741573	NA	P-0066813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	83	424	0	ENST00000397062.3:c.1576G>A	p.Glu526Lys	p.E526K	ENST00000397062	NM_006164.4	526	Gag/Aag	5/5	0.716352169311669	6	FACETS	0.938	0.829	1			1	CLONAL	1	FALSE	NA	0.716352169311669	6		424	601	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390865	139390868	+	frameshift_variant	Frame_Shift_Del	DEL	GTCT	GTCT	-	novel	NA	P-0066813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	235	660	0	ENST00000277541.6:c.7323_7326del	p.Asp2442CysfsTer34	p.D2442Cfs*34	ENST00000277541	NM_017617.3	2441	gcAGAC/gc	34/34	0.724894642465724	3	FACETS	0.958	0.921	0.994	0.958	0.921	0.994	CLONAL	3	FALSE	0	0.716352169311669	3		660	310	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929403	44929412	+	frameshift_variant	Frame_Shift_Del	DEL	CAGACAACCA	CAGACAACCA	-	novel	NA	P-0066813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	221	567	0	ENST00000377967.4:c.2505_2514del	p.Thr837ValfsTer27	p.T837Vfs*27	ENST00000377967	NM_021140.2	835	CAGACAACCAca/ca	17/29	0.615893433838649	3	FACETS	1	0.991	1			1	CLONAL	3	FALSE	NA	0.716352169311669	3		567	258	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183863	10183863	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869025631	NA	P-0066814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	79	512	0	ENST00000256474.2:c.332G>A	p.Ser111Asn	p.S111N	ENST00000256474	NM_000551.3	111	aGc/aAc	1/3	0.465964574856142	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	0	0.465964574856142	1		512	239	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952064	178952064	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	74	478	0	ENST00000263967.3:c.3119T>A	p.Met1040Lys	p.M1040K	ENST00000263967	NM_006218.2	1040	aTg/aAg	21/21	0.379886619001609	3	FACETS	1	0.93	1	0.702	0.628	0.778	CLONAL	2	FALSE	0	0.465964574856142	3		478	186	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94169002	94169002	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1591640825	NA	P-0066814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	37	370	0	ENST00000323929.3:c.1990C>G	p.Gln664Glu	p.Q664E	ENST00000323929	NM_005591.3	664	Caa/Gaa	18/20	0.38819144582557	1	FACETS	0.896	0.753	1	0.896	0.753	1	CLONAL	1	FALSE	0	0.465964574856142	1		370	136	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52685823	52685824	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	22	407	0	ENST00000394830.3:c.648dup	p.Tyr217IlefsTer9	p.Y217Ifs*9	ENST00000394830	NM_018313.4	216	-/A	7/30	0.465964574856142	1	FACETS	0.873	0.694	1	0.873	0.694	1	CLONAL	1	FALSE	0	0.465964574856142	1		407	83	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539985	187539987	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	novel	NA	P-0066814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	102	541	0	ENST00000441802.2:c.7753_7755del	p.Ile2585del	p.I2585del	ENST00000441802	NM_005245.3	2585	ATC/-	10/27	0.379886619001609	3	FACETS	1	0.977	1	0.814	0.744	0.885	CLONAL	2	FALSE	0	0.465964574856142	3		541	221	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304027	91304027	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	30	620	0	ENST00000355112.3:c.1424G>A	p.Gly475Glu	p.G475E	ENST00000355112	NM_000057.2	475	gGa/gAa	7/22	1	2	FACETS	0.66	0.536	0.798	0.66	0.536	0.798	SUBCLONAL	1	FALSE	1	0.465964574856142	2		620	195	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0066815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	111	270	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.360722840354144	4	FACETS	0.901	0.829	0.973	0.901	0.829	0.973	CLONAL	4	TRUE	0	0.372476208099706	4		270	227	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579395	7579395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	143	460	1	ENST00000269305.4:c.292C>T	p.Pro98Ser	p.P98S	ENST00000269305	NM_001126112.2	98	Cct/Tct	4/11	0.344304082439282	2	FACETS	0.984	0.908	1	0.984	0.908	1	CLONAL	2	TRUE	0	0.372476208099706	2		461	390	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597488	10597488	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	125	305	0	ENST00000171111.5:c.1715A>G	p.Tyr572Cys	p.Y572C	ENST00000171111	NM_203500.1	572	tAt/tGt	6/6	0.366002551010109	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.372476208099706	2		305	324	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332010	81332010	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	31	342	0	ENST00000222390.5:c.2074G>C	p.Val692Leu	p.V692L	ENST00000222390	NM_000601.4	692	Gtt/Ctt	18/18	0.356268692208279	3	FACETS	0.806	0.655	0.975	0.403	0.327	0.488	CLONAL	1	TRUE	1	0.372476208099706	3		342	245	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0066816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	196	529	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.407804481032385	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.407804481032385	2		529	444	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494644	2494644	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	79	526	0	ENST00000355716.4:c.784C>T	p.Pro262Ser	p.P262S	ENST00000355716	NM_003820.2	262	Ccg/Tcg	8/8	1	2	FACETS	0.947	0.838	1	0.947	0.838	1	CLONAL	1	TRUE	1	0.407804481032385	2		526	409	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510339	187510339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs192910004	NA	P-0066816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	151	402	0	ENST00000441802.2:c.13174G>A	p.Val4392Ile	p.V4392I	ENST00000441802	NM_005245.3	4392	Gtt/Att	27/27	0.407804481032385	2	FACETS	0.959	0.888	1	0.959	0.888	1	CLONAL	2	TRUE	0	0.407804481032385	2		402	386	SUCCESS
AR	367	MSKCC	GRCh37	X	66942785	66942785	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	104	391	0	ENST00000374690.3:c.2566C>G	p.Arg856Gly	p.R856G	ENST00000374690	NM_000044.3	856	Cgc/Ggc	7/8	0.407804481032385	2	FACETS	1	0.974	1	0.622	0.561	0.686	CLONAL	1	TRUE	0	0.407804481032385	2		391	410	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946263	81946263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	87	555	0	ENST00000359376.3:c.1996G>A	p.Asp666Asn	p.D666N	ENST00000359376	NM_002661.3	666	Gac/Aac	19/33	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.407804481032385	2		555	417	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089694	5089694	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	124	265	0	ENST00000381652.3:c.2592G>T	p.Glu864Asp	p.E864D	ENST00000381652	NM_004972.3	864	gaG/gaT	20/25	1	2	FACETS	0.923	0.846	1	1	0.993	1	CLONAL	4	TRUE	1	0.2	2		265	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0066818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	185	477	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.618909699545009	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.632155764174104	2		477	285	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	87	317	0				ENST00000310581	NM_198253.2	-/1132			0.618909699545009	2	FACETS	0.962	0.885	1	0.962	0.885	1	CLONAL	2	TRUE	0	0.632155764174104	2		317	143	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519874	NA	P-0066818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	34	279	0	ENST00000356142.4:c.85C>A	p.Pro29Thr	p.P29T	ENST00000356142	NM_018890.3	29	Cct/Act	2/7	0.504085691706016	4	FACETS	0.813	0.669	0.971	0.271	0.223	0.324	CLONAL	1	TRUE	1	0.632155764174104	4		279	216	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598357	28598357	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748874332	NA	P-0066818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	30	335	0	ENST00000253063.3:c.329C>T	p.Ser110Phe	p.S110F	ENST00000253063	NM_031459.4	110	tCc/tTc	3/10	0.439359247408674	2	FACETS	0.298	0.24	0.363	0.149	0.12	0.182	SUBCLONAL	1	TRUE	0	0.632155764174104	2		335	319	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204501339	204501339	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	14	246	0	ENST00000367182.3:c.308G>T	p.Arg103Ile	p.R103I	ENST00000367182	NM_001278516.1	103	aGa/aTa	5/11	0.23366745368313	4	FACETS	0.408	0.296	0.544	0.136	0.098	0.182	INDETERMINATE	1	TRUE	1	0.632155764174104	4		246	177	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243708829	243708829	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	44	231	0	ENST00000263826.5:c.1234G>T	p.Asp412Tyr	p.D412Y	ENST00000263826	NM_005465.4	412	Gat/Tat	11/13	0.23366745368313	4	FACETS	1	0.959	1	0.473	0.404	0.547	INDETERMINATE	1	TRUE	1	0.632155764174104	4		231	160	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604656	43604656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	148	319	0	ENST00000355710.3:c.1241G>A	p.Arg414Lys	p.R414K	ENST00000355710	NM_020975.4	414	aGg/aAg	6/20	0.215951642610272	5	FACETS	1	0.973	1			1	INDETERMINATE	2	TRUE	NA	0.632155764174104	5		319	407	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195568	102195568	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	53	364	0	ENST00000263464.3:c.328C>T	p.Gln110Ter	p.Q110*	ENST00000263464	NM_001165.4	110	Cag/Tag	2/9	0.538815053802282	2	FACETS	0.576	0.495	0.664	0.288	0.247	0.332	SUBCLONAL	1	TRUE	0	0.632155764174104	2		364	291	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175580	108175580	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0066818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	17	284	0	ENST00000278616.4:c.5674+1G>A		p.X1892_splice	ENST00000278616	NM_000051.3	1892			0.369846445824933	1	FACETS	0.177	0.132	0.23	0.177	0.132	0.23	INDETERMINATE	1	TRUE	0	0.632155764174104	1		284	208	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348681	118348681	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0066818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	11	245	0	ENST00000534358.1:c.3335-1G>A		p.X1112_splice	ENST00000534358	NM_005933.3	1112			0.538815053802282	2	FACETS	0.168	0.116	0.233	0.084	0.058	0.117	SUBCLONAL	1	TRUE	0	0.632155764174104	2		245	207	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362470	118362470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	17	295	0	ENST00000534358.1:c.4831G>A	p.Glu1611Lys	p.E1611K	ENST00000534358	NM_005933.3	1611	Gag/Aag	15/36	0.538815053802282	2	FACETS	0.224	0.167	0.292	0.112	0.083	0.146	SUBCLONAL	1	TRUE	0	0.632155764174104	2		295	240	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419007	419007	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	18	302	0	ENST00000399788.2:c.3340G>C	p.Glu1114Gln	p.E1114Q	ENST00000399788	NM_001042603.1	1114	Gag/Cag	22/28	0.270479806759096	3	FACETS	0.347	0.262	0.447	0.116	0.087	0.149	INDETERMINATE	1	TRUE	0	0.632155764174104	3		302	216	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865093	57865095	+	frameshift_variant	Frame_Shift_Del	DEL	CCC	CCC	A	novel	NA	P-0066818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	123	289	0	ENST00000228682.2:c.2570_2572delinsA	p.Pro857GlnfsTer14	p.P857Qfs*14	ENST00000228682	NM_005269.2	857	cCCCaa/cAaa	12/12	0.179124540227806	3	FACETS	0.862	0.792	0.933	0.575	0.528	0.622	INDETERMINATE	2	TRUE	0	0.632155764174104	3		289	297	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042693	42042693	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	74	395	0	ENST00000219905.7:c.6888C>G	p.Phe2296Leu	p.F2296L	ENST00000219905	NM_001164273.1	2296	ttC/ttG	17/24	0.325206048324714	2	FACETS	0.773	0.683	0.867	0.386	0.341	0.434	INDETERMINATE	1	TRUE	0	0.632155764174104	2		395	303	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346823	91346823	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	15	352	0	ENST00000355112.3:c.3431G>A	p.Arg1144Lys	p.R1144K	ENST00000355112	NM_000057.2	1144	aGa/aAa	18/22	0.369846445824933	1	FACETS	0.192	0.141	0.253	0.192	0.141	0.253	INDETERMINATE	1	TRUE	0	0.632155764174104	1		352	169	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16022773	16022774	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0066818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	38	314	0	ENST00000268712.3:c.1878_1879del	p.Arg627MetfsTer10	p.R627Mfs*10	ENST00000268712	NM_006311.3	626	tcTCga/tcga	17/46	0.618909699545009	2	FACETS	0.589	0.492	0.696	0.295	0.246	0.348	SUBCLONAL	1	TRUE	0	0.632155764174104	2		314	204	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732535	74732535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	120	254	0	ENST00000359995.5:c.374G>A	p.Arg125His	p.R125H	ENST00000359995	NM_001195427.1	125	cGt/cAt	2/3	0.632155764174104	4	FACETS	0.761	0.693	0.832	0.761	0.693	0.832	SUBCLONAL	2	TRUE	2	0.632155764174104	4		254	407	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217827	2217827	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	125	310	0	ENST00000398665.3:c.2601C>G	p.Ile867Met	p.I867M	ENST00000398665	NM_032482.2	867	atC/atG	22/28	0.236549579790293	2	FACETS	1	0.984	1	0.653	0.6	0.706	INDETERMINATE	1	TRUE	0	0.632155764174104	2		310	303	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288703	15288703	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	28	218	0	ENST00000263388.2:c.4036C>A	p.His1346Asn	p.H1346N	ENST00000263388	NM_000435.2	1346	Cac/Aac	24/33	0.236549579790293	2	FACETS	0.406	0.326	0.496	0.203	0.163	0.248	INDETERMINATE	1	TRUE	0	0.632155764174104	2		218	218	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872380	45872380	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	32	349	0	ENST00000391945.4:c.131C>A	p.Ser44Ter	p.S44*	ENST00000391945	NM_000400.3	44	tCa/tAa	3/23	0.632155764174104	5	FACETS	0.343	0.278	0.417	0.114	0.092	0.139	SUBCLONAL	1	TRUE	2	0.632155764174104	5		349	575	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966681	25966681	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	19	353	0	ENST00000435504.4:c.2525C>T	p.Ser842Leu	p.S842L	ENST00000435504		842	tCa/tTa	13/13	0.504085691706016	4	FACETS	0.283	0.214	0.364	0.094	0.071	0.122	SUBCLONAL	1	TRUE	1	0.632155764174104	4		353	347	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264275	46264275	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200950152	NA	P-0066818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	236	307	0	ENST00000371998.3:c.1322C>T	p.Ser441Leu	p.S441L	ENST00000371998		441	tCa/tTa	11/23	0.632155764174104	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.632155764174104	3		307	437	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24135807	24135807	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	171	332	0	ENST00000263121.7:c.294G>C	p.Glu98Asp	p.E98D	ENST00000263121	NM_003073.3	98	gaG/gaC	3/9	0.325206048324714	2	FACETS	0.902	0.848	0.955	0.902	0.848	0.955	INDETERMINATE	2	TRUE	0	0.632155764174104	2		332	300	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051666	30051666	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1555993352	NA	P-0066818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	69	262	0	ENST00000338641.4:c.599+1G>T		p.X200_splice	ENST00000338641	NM_000268.3	200			0.325206048324714	2	FACETS	0.763	0.671	0.861	0.382	0.335	0.431	INDETERMINATE	1	TRUE	0	0.632155764174104	2		262	286	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397710	49397710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	141	290	0	ENST00000418115.1:c.514G>A	p.Glu172Lys	p.E172K	ENST00000418115	NM_001664.2	172	Gaa/Aaa	5/5	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.632155764174104	2		290	331	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157113	106157113	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	155	370	0	ENST00000380013.4:c.2014C>T	p.His672Tyr	p.H672Y	ENST00000380013	NM_001127208.2	672	Cat/Tat	3/11	0.632155764174104	3	FACETS	0.984	0.916	1	0.984	0.916	1	CLONAL	2	TRUE	1	0.632155764174104	3		370	328	SUCCESS
APC	324	MSKCC	GRCh37	5	112137018	112137018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	30	256	0	ENST00000257430.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000257430	NM_000038.5	258	Gag/Aag	8/16	0.618909699545009	2	FACETS	0.463	0.376	0.56	0.231	0.188	0.28	SUBCLONAL	1	TRUE	0	0.632155764174104	2		256	205	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138201378	138201378	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	18	264	0	ENST00000237289.4:c.2077G>C	p.Glu693Gln	p.E693Q	ENST00000237289	NM_001270507.1	693	Gaa/Caa	8/9	1	2	FACETS	0.25	0.188	0.322	0.25	0.188	0.322	SUBCLONAL	1	TRUE	1	0.632155764174104	2		264	228	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415163	116415163	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	52	256	0	ENST00000397752.3:c.3257G>C	p.Arg1086Thr	p.R1086T	ENST00000397752	NM_000245.2	1086	aGa/aCa	15/21	0.632155764174104	3	FACETS	0.779	0.668	0.898	0.389	0.334	0.449	SUBCLONAL	1	TRUE	1	0.632155764174104	3		256	278	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950475	68950475	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371711855	NA	P-0066818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	98	318	0	ENST00000288368.4:c.787C>T	p.Arg263Trp	p.R263W	ENST00000288368	NM_024870.2	263	Cgg/Tgg	7/40	0.239170524134665	3	FACETS	0.907	0.826	0.989	0.605	0.55	0.659	INDETERMINATE	2	TRUE	0	0.632155764174104	3		318	225	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021764	69021764	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	23	334	0	ENST00000288368.4:c.3052G>C	p.Glu1018Gln	p.E1018Q	ENST00000288368	NM_024870.2	1018	Gaa/Caa	25/40	0.239170524134665	3	FACETS	0.296	0.23	0.371	0.099	0.076	0.124	INDETERMINATE	1	TRUE	0	0.632155764174104	3		334	324	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70967607	70967609	+	missense_variant	Missense_Mutation	TNP	TTG	TTG	CTT	novel	NA	P-0066818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	63	287	0	ENST00000276594.2:c.1414_1416delinsAAG	p.Gln472Lys	p.Q472K	ENST00000276594	NM_024504.3	472	CAA/AAG	7/8	0.239170524134665	3	FACETS	0.937	0.818	1	0.312	0.272	0.355	INDETERMINATE	1	TRUE	0	0.632155764174104	3		287	280	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0066820-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	46	270	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.974	0.821	1	0.974	0.821	1	CLONAL	1	TRUE	1	0.19	2		270	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0066820-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	61	507	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	1	2	FACETS	0.891	0.767	1	0.891	0.767	1	CLONAL	1	TRUE	1	0.19	2		507	721	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041585	47041585	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066820-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	64	495	1	ENST00000377604.3:c.1810C>T	p.Gln604Ter	p.Q604*	ENST00000377604	NM_001204468.1	604	Cag/Tag	17/24	1	2	FACETS	0.836	0.722	0.959	0.836	0.722	0.959	CLONAL	1	TRUE	1	0.19	2		496	806	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292808	62292808	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066820-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	46	419	0	ENST00000360203.5:c.260C>T	p.Ser87Leu	p.S87L	ENST00000360203	NM_001283009.1	87	tCa/tTa	3/35	0.149192759415644	1	FACETS	0.578	0.485	0.681	0.578	0.485	0.681	SUBCLONAL	1	TRUE	0	0.19	1		419	758	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226595602	226595602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066820-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	41	353	0	ENST00000366794.5:c.29G>A	p.Arg10Gln	p.R10Q	ENST00000366794	NM_001618.3	10	cGa/cAa	1/23	1	2	FACETS	0.773	0.643	0.918	0.773	0.643	0.918	CLONAL	1	TRUE	1	0.19	2		353	558	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505354	25505354	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066820-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	38	388	0	ENST00000264709.3:c.404G>T	p.Gly135Val	p.G135V	ENST00000264709	NM_175629.2	135	gGc/gTc	4/23	1	2	FACETS	0.656	0.541	0.785	0.656	0.541	0.785	SUBCLONAL	1	TRUE	1	0.19	2		388	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0066833-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	385	486	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.914234630904111	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.91484012388815	1		486	407	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024321	31024321	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747065583	NA	P-0066833-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	367	504	0	ENST00000375687.4:c.3806C>T	p.Ser1269Leu	p.S1269L	ENST00000375687	NM_015338.5	1269	tCg/tTg	13/13	1	2	FACETS	0.963	0.919	1	0.963	0.919	1	CLONAL	1	TRUE	1	0.91484012388815	2		504	833	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133234458	133234458	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066833-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	469	389	0	ENST00000320574.5:c.3374G>T	p.Arg1125Leu	p.R1125L	ENST00000320574	NM_006231.2	1125	cGa/cTa	27/49	0.914234630904111	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.91484012388815	2		389	499	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39311757	39311757	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0066833-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	383	406	0	ENST00000373001.3:c.902T>A	p.Leu301Ter	p.L301*	ENST00000373001	NM_022157.3	301	tTa/tAa	6/7	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.91484012388815	2		406	764	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0066834-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	114	221	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	1	FACETS	0.782	0.714	0.852	1	0.987	1	SUBCLONAL	2	TRUE	0	0.386662684192969	1		221	304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578226	7578226	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1464727668	NA	P-0066834-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	193	549	0	ENST00000269305.4:c.623A>T	p.Asp208Val	p.D208V	ENST00000269305	NM_001126112.2	208	gAc/gTc	6/11	0.386662684192969	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.386662684192969	1		549	684	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136804	69136804	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066834-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	101	335	0	ENST00000288368.4:c.4718T>G	p.Val1573Gly	p.V1573G	ENST00000288368	NM_024870.2	1573	gTt/gGt	39/40	0.386662684192969	1	FACETS	0.722	0.646	0.801	0.722	0.646	0.801	SUBCLONAL	1	TRUE	0	0.386662684192969	1		335	584	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146472	185146472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066834-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	158	415	0	ENST00000265026.3:c.103G>A	p.Gly35Arg	p.G35R	ENST00000265026	NM_004721.4	35	Ggg/Agg	2/14	0.163100189697613	3	FACETS	1	0.985	1	0.669	0.614	0.726	INDETERMINATE	1	TRUE	1	0.386662684192969	3		415	729	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631150	67631150	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066834-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	119	380	0	ENST00000272342.5:c.1336G>C	p.Asp446His	p.D446H	ENST00000272342	NM_019002.3	446	Gat/Cat	5/6	1	2	FACETS	0.95	0.859	1	0.95	0.859	1	CLONAL	1	TRUE	1	0.386662684192969	2		380	648	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	109	611	1	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	0.256749933309908	1	FACETS	0.461	0.414	0.51	0.461	0.414	0.51	INDETERMINATE	1	TRUE	0	0.536765094767098	1		612	645	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	89	789	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.298327508839449	1	FACETS	0.408	0.362	0.457	0.408	0.362	0.457	INDETERMINATE	1	TRUE	0	0.536765094767098	1		790	594	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882049	36882050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs780753361	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	62	481	0	ENST00000358127.4:c.963dup	p.Ala322ArgfsTer19	p.A322Rfs*19	ENST00000358127	NM_001280556.1	321	-/C	8/10	0.298327508839449	1	FACETS	0.313	0.27	0.359	0.313	0.27	0.359	INDETERMINATE	1	TRUE	0	0.536765094767098	1		481	540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	99	412	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.298327508839449	1	FACETS	0.465	0.415	0.516	0.465	0.415	0.516	INDETERMINATE	1	TRUE	0	0.536765094767098	1		412	581	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	73	574	0	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.425	0.371	0.483	0.425	0.371	0.483	SUBCLONAL	1	TRUE	1	0.536765094767098	2		574	640	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	57	319	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.452	0.388	0.521	0.452	0.388	0.521	SUBCLONAL	1	TRUE	1	0.536765094767098	2		325	470	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	85	177	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.763	0.678	0.853	0.763	0.678	0.853	SUBCLONAL	1	TRUE	1	0.536765094767098	2		178	415	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	48	383	2	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.406	0.344	0.475	0.406	0.344	0.475	SUBCLONAL	1	TRUE	1	0.536765094767098	2		385	440	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	97	418	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	1	2	FACETS	0.798	0.715	0.885	0.798	0.715	0.885	SUBCLONAL	1	TRUE	1	0.536765094767098	2		418	453	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991949	72991949	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs753977275	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	69	497	4	ENST00000268489.5:c.2096del	p.Gly699AlafsTer125	p.G699Afs*125	ENST00000268489	NM_006885.3	699	gGc/gc	2/10	1	2	FACETS	0.467	0.407	0.531	0.467	0.407	0.531	SUBCLONAL	1	TRUE	1	0.536765094767098	2		501	551	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927443	245927443	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	76	416	0	ENST00000388985.4:c.1085del	p.Phe362SerfsTer12	p.F362Sfs*12	ENST00000388985		362	tTc/tc	11/12	NA	2	FACETS	0.532	0.468	0.602			1	INDETERMINATE	1	TRUE	NA	0.536765094767098	2		416	532	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	49	369	3	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	1	2	FACETS	0.482	0.409	0.561	0.482	0.409	0.561	SUBCLONAL	1	TRUE	1	0.536765094767098	2		372	379	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258889	16258889	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	53	627	3	ENST00000375759.3:c.6158del	p.Asn2053ThrfsTer11	p.N2053Tfs*11	ENST00000375759	NM_015001.2	2052	Aaa/aa	11/15	0.256749933309908	1	FACETS	0.204	0.173	0.237	0.204	0.173	0.237	INDETERMINATE	1	TRUE	0	0.536765094767098	1		630	709	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023135	27023135	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	35	421	0	ENST00000324856.7:c.245del	p.Gly82ValfsTer19	p.G82Vfs*19	ENST00000324856	NM_006015.4	81	Ggg/gg	1/20	0.256749933309908	1	FACETS	0.338	0.278	0.405	0.338	0.278	0.405	INDETERMINATE	1	TRUE	0	0.536765094767098	1		421	282	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429978	78429978	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	67	462	1	ENST00000370768.2:c.901del	p.Ile301TyrfsTer22	p.I301Yfs*22	ENST00000370768	NM_003902.3	301	Ata/ta	11/20	0.256749933309908	1	FACETS	0.391	0.34	0.446	0.391	0.34	0.446	INDETERMINATE	1	TRUE	0	0.536765094767098	1		463	467	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600466	43600466	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	83	504	0	ENST00000355710.3:c.692G>T	p.Arg231Leu	p.R231L	ENST00000355710	NM_020975.4	231	cGc/cTc	4/20	1	2	FACETS	0.574	0.507	0.645	0.574	0.507	0.645	SUBCLONAL	1	TRUE	1	0.536765094767098	2		504	539	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943741	71943742	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	115	632	0	ENST00000298229.2:c.1789_1790del	p.Leu597AlafsTer32	p.L597Afs*32	ENST00000298229	NM_001567.3	595	aTC/a	15/28	0.298327508839449	1	FACETS	0.52	0.469	0.573	0.52	0.469	0.573	INDETERMINATE	1	TRUE	0	0.536765094767098	1		632	603	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948544	71948544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200480750	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	94	592	0	ENST00000298229.2:c.3256C>T	p.Arg1086Cys	p.R1086C	ENST00000298229	NM_001567.3	1086	Cgt/Tgt	26/28	0.298327508839449	1	FACETS	0.541	0.483	0.601	0.541	0.483	0.601	INDETERMINATE	1	TRUE	0	0.536765094767098	1		592	474	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022376	12022376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	92	638	0	ENST00000396373.4:c.486del	p.Arg163GlyfsTer46	p.R163Gfs*46	ENST00000396373	NM_001987.4	161	aCc/ac	5/8	1	2	FACETS	0.455	0.404	0.51	0.455	0.404	0.51	SUBCLONAL	1	TRUE	1	0.536765094767098	2		638	753	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244454	46244454	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs751704736	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	78	573	0	ENST00000334344.6:c.2552del	p.Pro851HisfsTer4	p.P851Hfs*4	ENST00000334344	NM_152641.2	850	Ccc/cc	15/21	1	2	FACETS	0.454	0.399	0.513	0.454	0.399	0.513	SUBCLONAL	1	TRUE	1	0.536765094767098	2		573	640	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426774	49426774	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1334139538	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	94	577	2	ENST00000301067.7:c.11714A>T	p.Gln3905Leu	p.Q3905L	ENST00000301067	NM_003482.3	3905	cAg/cTg	39/54	1	2	FACETS	0.448	0.399	0.502	0.448	0.399	0.502	SUBCLONAL	1	TRUE	1	0.536765094767098	2		579	781	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440431	49440431	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1240601136	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	98	552	0	ENST00000301067.7:c.4379del	p.Pro1460HisfsTer46	p.P1460Hfs*46	ENST00000301067	NM_003482.3	1460	cCa/ca	15/54	1	2	FACETS	0.514	0.458	0.573	0.514	0.458	0.573	SUBCLONAL	1	TRUE	1	0.536765094767098	2		552	711	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563293	21563293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367963331	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	76	585	0	ENST00000382592.4:c.626G>A	p.Arg209Gln	p.R209Q	ENST00000382592	NM_014572.2	209	cGg/cAg	4/8	0.116063573457319	6	FACETS	0.772	0.676	0.875			1	INDETERMINATE	1	TRUE	NA	0.536765094767098	6		585	761	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133898	41133898	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	40	489	0	ENST00000379561.5:c.1730del	p.Gly577AlafsTer5	p.G577Afs*5	ENST00000379561	NM_002015.3	577	gGc/gc	2/3	0.536765094767098	2	FACETS	0.231	0.192	0.276	0.116	0.096	0.138	SUBCLONAL	1	TRUE	0	0.536765094767098	2		489	644	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353757	68353757	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs774910383	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	23	340	0	ENST00000487270.1:c.592G>T	p.Glu198Ter	p.E198*	ENST00000487270	NM_133509.3	198	Gaa/Taa	7/11	0.244121076208798	2	FACETS	0.311	0.242	0.389	0.155	0.121	0.195	INDETERMINATE	1	TRUE	0	0.536765094767098	2		340	276	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054540	42054541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	27	368	0	ENST00000219905.7:c.7731dup	p.Asp2578ArgfsTer45	p.D2578Rfs*45	ENST00000219905	NM_001164273.1	2575	aga/agAa	22/24	1	2	FACETS	0.25	0.199	0.309	0.25	0.199	0.309	SUBCLONAL	1	TRUE	1	0.536765094767098	2		368	402	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857391	9857391	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	70	524	0	ENST00000330684.3:c.4010C>T	p.Ser1337Leu	p.S1337L	ENST00000330684	NM_001134407.1	1337	tCg/tTg	13/13	0.244121076208798	2	FACETS	0.466	0.406	0.53	0.233	0.203	0.265	INDETERMINATE	1	TRUE	0	0.536765094767098	2		524	560	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028690	12028690	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	48	436	0	ENST00000353533.5:c.891+2T>C		p.X297_splice	ENST00000353533	NM_003010.3	297			0.298327508839449	1	FACETS	0.277	0.234	0.324	0.277	0.234	0.324	INDETERMINATE	1	TRUE	0	0.536765094767098	1		436	472	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	73	428	0	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	0.298327508839449	1	FACETS	0.368	0.322	0.417	0.368	0.322	0.417	INDETERMINATE	1	TRUE	0	0.536765094767098	1		428	541	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440943	56440943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786205215	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	81	516	0	ENST00000407977.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000407977		132	Cga/Tga	4/10	0.298327508839449	1	FACETS	0.431	0.381	0.485	0.431	0.381	0.485	INDETERMINATE	1	TRUE	0	0.536765094767098	1		516	512	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899179	78899179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760865448	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	106	479	0	ENST00000306801.3:c.2818G>A	p.Asp940Asn	p.D940N	ENST00000306801	NM_020761.2	940	Gac/Aac	24/34	0.298327508839449	1	FACETS	0.523	0.47	0.578	0.523	0.47	0.578	INDETERMINATE	1	TRUE	0	0.536765094767098	1		479	553	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917074	50917074	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780138978	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	82	552	0	ENST00000440232.2:c.2326C>T	p.Arg776Trp	p.R776W	ENST00000440232	NM_002691.3	776	Cgg/Tgg	19/27	1	2	FACETS	0.458	0.404	0.516	0.458	0.404	0.516	SUBCLONAL	1	TRUE	1	0.536765094767098	2		552	667	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156050	99156050	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866440781	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	40	483	1	ENST00000074304.5:c.730C>T	p.Arg244Trp	p.R244W	ENST00000074304	NM_001134224.1	244	Cgg/Tgg	10/26	1	2	FACETS	0.305	0.253	0.363	0.305	0.253	0.363	SUBCLONAL	1	TRUE	1	0.536765094767098	2		484	489	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212522482	212522482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	61	461	0	ENST00000342788.4:c.1943C>T	p.Ala648Val	p.A648V	ENST00000342788	NM_005235.2	648	gCt/gTt	16/28	1	2	FACETS	0.46	0.397	0.528	0.46	0.397	0.528	SUBCLONAL	1	TRUE	1	0.536765094767098	2		461	494	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21336680	21336681	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs587777613	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	57	494	4	ENST00000215739.8:c.27dup	p.Gln10AlafsTer24	p.Q10Afs*24	ENST00000215739	NM_006767.3	7	acg/acGg	1/21	0.298327508839449	1	FACETS	0.404	0.347	0.464	0.404	0.347	0.464	INDETERMINATE	1	TRUE	0	0.536765094767098	1		498	385	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412914	49412914	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	105	516	0	ENST00000418115.1:c.109A>G	p.Thr37Ala	p.T37A	ENST00000418115	NM_001664.2	37	Aca/Gca	2/5	0.182660057575417	2	FACETS	0.69	0.62	0.764	0.345	0.31	0.382	INDETERMINATE	1	TRUE	0	0.536765094767098	2		516	567	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261555	142261555	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	31	427	1	ENST00000350721.4:c.3402del	p.Phe1134LeufsTer6	p.F1134Lfs*6	ENST00000350721	NM_001184.3	1134	ttT/tt	17/47	1	2	FACETS	0.292	0.236	0.355	0.292	0.236	0.355	SUBCLONAL	1	TRUE	1	0.536765094767098	2		428	396	SUCCESS
APC	324	MSKCC	GRCh37	5	112176193	112176193	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	75	556	0	ENST00000257430.4:c.4906del	p.Asp1636MetfsTer14	p.D1636Mfs*14	ENST00000257430	NM_000038.5	1634	ccG/cc	16/16	1	2	FACETS	0.426	0.373	0.483	0.426	0.373	0.483	SUBCLONAL	1	TRUE	1	0.536765094767098	2		556	656	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931452	131931453	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	65	439	1	ENST00000265335.6:c.2164_2165del	p.Lys722GlyfsTer5	p.K722Gfs*5	ENST00000265335		719	ctAAaa/ctaa	13/25	1	2	FACETS	0.46	0.399	0.526	0.46	0.399	0.526	SUBCLONAL	1	TRUE	1	0.536765094767098	2		440	526	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505029	149505029	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	64	510	0	ENST00000261799.4:c.1786C>T	p.Pro596Ser	p.P596S	ENST00000261799	NM_002609.3	596	Ccg/Tcg	12/23	1	2	FACETS	0.463	0.401	0.53	0.463	0.401	0.53	SUBCLONAL	1	TRUE	1	0.536765094767098	2		510	515	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512395	149512395	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	65	569	0	ENST00000261799.4:c.1045C>A	p.Leu349Met	p.L349M	ENST00000261799	NM_002609.3	349	Ctg/Atg	7/23	1	2	FACETS	0.387	0.335	0.443	0.387	0.335	0.443	SUBCLONAL	1	TRUE	1	0.536765094767098	2		569	626	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513488	149513488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465364786	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	95	610	0	ENST00000261799.4:c.715G>A	p.Gly239Arg	p.G239R	ENST00000261799	NM_002609.3	239	Ggg/Agg	5/23	1	2	FACETS	0.578	0.516	0.645	0.578	0.516	0.645	SUBCLONAL	1	TRUE	1	0.536765094767098	2		610	612	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520268	176520268	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	29	486	0	ENST00000292408.4:c.1187A>G	p.His396Arg	p.H396R	ENST00000292408	NM_213647.1	396	cAc/cGc	9/18	1	2	FACETS	0.225	0.18	0.276	0.225	0.18	0.276	SUBCLONAL	1	TRUE	1	0.536765094767098	2		486	480	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048737	180048737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144803521	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	41	539	0	ENST00000261937.6:c.1825G>A	p.Asp609Asn	p.D609N	ENST00000261937	NM_182925.4	609	Gac/Aac	13/30	1	2	FACETS	0.288	0.24	0.342	0.288	0.24	0.342	SUBCLONAL	1	TRUE	1	0.536765094767098	2		539	530	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051002	180051002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs566339142	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	53	530	0	ENST00000261937.6:c.1481C>T	p.Thr494Met	p.T494M	ENST00000261937	NM_182925.4	494	aCg/aTg	11/30	1	2	FACETS	0.356	0.304	0.414	0.356	0.304	0.414	SUBCLONAL	1	TRUE	1	0.536765094767098	2		530	554	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30682856	30682856	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113702536	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	88	541	0	ENST00000376406.3:c.97C>T	p.Arg33Trp	p.R33W	ENST00000376406	NM_014641.2	33	Cgg/Tgg	2/15	1	2	FACETS	0.571	0.507	0.64	0.571	0.507	0.64	SUBCLONAL	1	TRUE	1	0.536765094767098	2		541	574	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908284	41908284	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	33	439	0	ENST00000372991.4:c.238del	p.Leu80TrpfsTer3	p.L80Wfs*3	ENST00000372991	NM_001760.3	80	Ctg/tg	2/5	1	2	FACETS	0.251	0.204	0.305	0.251	0.204	0.305	SUBCLONAL	1	TRUE	1	0.536765094767098	2		439	489	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129338	152129338	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1361952517	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	55	473	0	ENST00000206249.3:c.296del	p.Pro99HisfsTer10	p.P99Hfs*10	ENST00000206249	NM_000125.3	97	ttC/tt	1/8	1	2	FACETS	0.477	0.408	0.551	0.477	0.408	0.551	SUBCLONAL	1	TRUE	1	0.536765094767098	2		473	430	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509636	106509636	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867282260	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	111	527	0	ENST00000359195.3:c.1630C>T	p.Arg544Ter	p.R544*	ENST00000359195	NM_002649.2	544	Cga/Tga	2/11	1	2	FACETS	0.637	0.574	0.704	0.637	0.574	0.704	SUBCLONAL	1	TRUE	1	0.536765094767098	2		527	649	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403178	116403178	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	64	546	0	ENST00000397752.3:c.2443del	p.Leu815Ter	p.L815*	ENST00000397752	NM_000245.2	813	ctC/ct	11/21	1	2	FACETS	0.47	0.408	0.538	0.47	0.408	0.538	SUBCLONAL	1	TRUE	1	0.536765094767098	2		546	507	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372313	55372313	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	37	618	0	ENST00000297316.4:c.1007del	p.Pro336LeufsTer51	p.P336Lfs*51	ENST00000297316	NM_022454.3	335	Ccc/cc	2/2	1	2	FACETS	0.232	0.191	0.279	0.232	0.191	0.279	SUBCLONAL	1	TRUE	1	0.536765094767098	2		618	593	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748399150	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	93	483	2	ENST00000220592.5:c.1806del	p.Ala603ProfsTer92	p.A603Pfs*92	ENST00000220592	NM_012154.3	602	ccC/cc	14/19	1	2	FACETS	0.528	0.47	0.59	0.528	0.47	0.59	SUBCLONAL	1	TRUE	1	0.536765094767098	2		485	656	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5465595	5465595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148141792	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	84	541	0	ENST00000381577.3:c.779G>A	p.Arg260His	p.R260H	ENST00000381577	NM_014143.3	260	cGt/cAt	5/7	0.298327508839449	1	FACETS	0.439	0.388	0.492	0.439	0.388	0.492	INDETERMINATE	1	TRUE	0	0.536765094767098	1		541	522	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006027	22006027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371415045	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	79	545	0	ENST00000276925.6:c.376C>T	p.Arg126Cys	p.R126C	ENST00000276925	NM_004936.3	126	Cgc/Tgc	2/2	0.298327508839449	1	FACETS	0.478	0.421	0.537	0.478	0.421	0.537	INDETERMINATE	1	TRUE	0	0.536765094767098	1		545	451	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020769	37020769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	75	490	2	ENST00000358127.4:c.76del	p.Val26PhefsTer3	p.V26Ffs*3	ENST00000358127	NM_001280556.1	26	Gtt/tt	2/10	0.298327508839449	1	FACETS	0.392	0.344	0.443	0.392	0.344	0.443	INDETERMINATE	1	TRUE	0	0.536765094767098	1		492	522	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156686	20156687	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	59	375	0	ENST00000379607.5:c.70dup	p.Arg24LysfsTer64	p.R24Kfs*64	ENST00000379607	NM_001412.3	24	aga/aAga	2/7	1	2	FACETS	0.457	0.394	0.526	0.457	0.394	0.526	SUBCLONAL	1	TRUE	1	0.536765094767098	2		375	481	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258778	16258778	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	40	575	0	ENST00000375759.3:c.6043A>G	p.Thr2015Ala	p.T2015A	ENST00000375759	NM_015001.2	2015	Act/Gct	11/15	0.256749933309908	1	FACETS	0.181	0.149	0.215	0.181	0.149	0.215	INDETERMINATE	1	TRUE	0	0.536765094767098	1		575	604	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363057	40363057	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	79	432	0	ENST00000397332.2:c.1172T>C	p.Leu391Pro	p.L391P	ENST00000397332	NM_001033082.2	391	cTc/cCc	3/3	0.256749933309908	1	FACETS	0.466	0.411	0.525	0.466	0.411	0.525	INDETERMINATE	1	TRUE	0	0.536765094767098	1		432	462	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874223	155874223	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	62	550	0	ENST00000368323.3:c.308C>A	p.Thr103Lys	p.T103K	ENST00000368323	NM_006912.5	103	aCg/aAg	5/6	0.256749933309908	1	FACETS	0.256	0.22	0.294	0.256	0.22	0.294	INDETERMINATE	1	TRUE	0	0.536765094767098	1		550	661	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956216	175956216	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	29	364	0	ENST00000367669.3:c.1996C>A	p.Leu666Met	p.L666M	ENST00000367669	NM_022457.5	666	Ctg/Atg	18/20	1	2	FACETS	0.424	0.341	0.517	0.424	0.341	0.517	SUBCLONAL	1	TRUE	1	0.536765094767098	2		364	255	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650084	206650084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	67	552	1	ENST00000367120.3:c.604G>A	p.Val202Met	p.V202M	ENST00000367120	NM_014002.3	202	Gtg/Atg	7/22	1	2	FACETS	0.404	0.351	0.461	0.404	0.351	0.461	SUBCLONAL	1	TRUE	1	0.536765094767098	2		553	618	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555994	226555994	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	43	486	0	ENST00000366794.5:c.2183A>G	p.Gln728Arg	p.Q728R	ENST00000366794	NM_001618.3	728	cAg/cGg	16/23	1	2	FACETS	0.287	0.24	0.34	0.287	0.24	0.34	SUBCLONAL	1	TRUE	1	0.536765094767098	2		486	558	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10785256	10785256	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	36	461	0	ENST00000361367.2:c.1024C>T	p.Leu342Phe	p.L342F	ENST00000361367	NM_014633.3	342	Ctc/Ttc	9/25	0.298327508839449	1	FACETS	0.225	0.184	0.27	0.225	0.184	0.27	INDETERMINATE	1	TRUE	0	0.536765094767098	1		461	437	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924702	94924702	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	90	577	0	ENST00000536441.1:c.208G>A	p.Gly70Ser	p.G70S	ENST00000536441	NM_144665.3	70	Ggt/Agt	3/10	0.298327508839449	1	FACETS	0.453	0.403	0.507	0.453	0.403	0.507	INDETERMINATE	1	TRUE	0	0.536765094767098	1		577	541	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	401959	401959	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	137	503	0	ENST00000399788.2:c.4832C>T	p.Ala1611Val	p.A1611V	ENST00000399788	NM_001042603.1	1611	gCa/gTa	27/28	1	2	FACETS	0.645	0.587	0.705	0.645	0.587	0.705	SUBCLONAL	1	TRUE	1	0.536765094767098	2		503	792	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218289	133218289	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	43	473	0	ENST00000320574.5:c.5322G>T	p.Gln1774His	p.Q1774H	ENST00000320574	NM_006231.2	1774	caG/caT	39/49	1	2	FACETS	0.292	0.244	0.345	0.292	0.244	0.345	SUBCLONAL	1	TRUE	1	0.536765094767098	2		473	549	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50774176	50774176	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	60	498	2	ENST00000307179.4:c.1720del	p.Arg574GlyfsTer20	p.R574Gfs*20	ENST00000307179		573	Aaa/aa	11/20	1	2	FACETS	0.427	0.368	0.492	0.427	0.368	0.492	SUBCLONAL	1	TRUE	1	0.536765094767098	2		500	523	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2111977	2111977	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	60	525	1	ENST00000219476.3:c.1225G>T	p.Glu409Ter	p.E409*	ENST00000219476	NM_000548.3	409	Gaa/Taa	12/42	0.244121076208798	2	FACETS	0.356	0.306	0.41	0.178	0.153	0.205	INDETERMINATE	1	TRUE	0	0.536765094767098	2		526	628	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544326	86544326	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	45	499	0	ENST00000262426.4:c.151T>C	p.Tyr51His	p.Y51H	ENST00000262426	NM_001451.2	51	Tat/Cat	1/2	1	2	FACETS	0.4	0.337	0.47	0.4	0.337	0.47	SUBCLONAL	1	TRUE	1	0.536765094767098	2		499	419	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435540	56435552	+	frameshift_variant	Frame_Shift_Del	DEL	AGGAACGAGGCCG	AGGAACGAGGCCG	-	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	81	484	0	ENST00000407977.2:c.1585_1597del	p.Arg529TrpfsTer167	p.R529Wfs*167	ENST00000407977		529	CGGCCTCGTTCCTtg/tg	9/10	0.298327508839449	1	FACETS	0.457	0.404	0.514	0.457	0.404	0.514	INDETERMINATE	1	TRUE	0	0.536765094767098	1		484	483	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110270	3110270	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	98	572	0	ENST00000078429.4:c.260T>C	p.Met87Thr	p.M87T	ENST00000078429	NM_002067.2	87	aTg/aCg	2/7	1	2	FACETS	0.536	0.479	0.597	0.536	0.479	0.597	SUBCLONAL	1	TRUE	1	0.536765094767098	2		572	681	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366327	15366327	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1309211158	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	76	469	0	ENST00000263377.2:c.1828A>G	p.Met610Val	p.M610V	ENST00000263377	NM_058243.2	610	Atg/Gtg	10/20	1	2	FACETS	0.489	0.429	0.553	0.489	0.429	0.553	SUBCLONAL	1	TRUE	1	0.536765094767098	2		469	579	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799056	42799056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	84	484	0	ENST00000575354.2:c.4540G>A	p.Val1514Met	p.V1514M	ENST00000575354	NM_015125.3	1514	Gtg/Atg	20/20	1	2	FACETS	0.555	0.491	0.623	0.555	0.491	0.623	SUBCLONAL	1	TRUE	1	0.536765094767098	2		484	564	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61717845	61717845	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	26	468	0	ENST00000401558.2:c.1954C>T	p.His652Tyr	p.H652Y	ENST00000401558	NM_003400.3	652	Cac/Tac	17/25	1	2	FACETS	0.199	0.157	0.247	0.199	0.157	0.247	SUBCLONAL	1	TRUE	1	0.536765094767098	2		468	487	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131516	202131516	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	62	513	0	ENST00000358485.4:c.482+2T>C		p.X161_splice	ENST00000358485	NM_001080125.1	161			1	2	FACETS	0.343	0.296	0.395	0.343	0.296	0.395	SUBCLONAL	1	TRUE	1	0.536765094767098	2		513	673	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29383140	29383140	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	53	524	0	ENST00000544604.2:c.377T>C	p.Leu126Pro	p.L126P	ENST00000544604	NM_001206998.1	126	cTg/cCg	2/9	0.298327508839449	1	FACETS	0.262	0.223	0.304	0.262	0.223	0.304	INDETERMINATE	1	TRUE	0	0.536765094767098	1		524	552	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446437	29446437	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	53	507	0	ENST00000544604.2:c.2268G>T	p.Gln756His	p.Q756H	ENST00000544604	NM_001206998.1	756	caG/caT	8/9	0.298327508839449	1	FACETS	0.37	0.317	0.429	0.37	0.317	0.429	INDETERMINATE	1	TRUE	0	0.536765094767098	1		507	390	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933740	49933740	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	90	549	0	ENST00000296474.3:c.2537G>T	p.Gly846Val	p.G846V	ENST00000296474	NM_002447.2	846	gGg/gTg	10/20	0.182660057575417	2	FACETS	0.597	0.53	0.667	0.298	0.265	0.334	INDETERMINATE	1	TRUE	0	0.536765094767098	2		549	562	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643884	52643884	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	27	444	0	ENST00000394830.3:c.2012A>T	p.Asn671Ile	p.N671I	ENST00000394830	NM_018313.4	671	aAc/aTc	17/30	0.182660057575417	2	FACETS	0.24	0.19	0.296	0.12	0.095	0.148	INDETERMINATE	1	TRUE	0	0.536765094767098	2		444	420	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156937	89156937	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	54	451	0	ENST00000336596.2:c.39C>A	p.Cys13Ter	p.C13*	ENST00000336596	NM_005233.5	13	tgC/tgA	1/17	1	2	FACETS	0.517	0.443	0.598	0.517	0.443	0.598	SUBCLONAL	1	TRUE	1	0.536765094767098	2		451	389	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443315	187443315	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	64	534	0	ENST00000232014.4:c.1811G>A	p.Cys604Tyr	p.C604Y	ENST00000232014	NM_001130845.1	604	tGc/tAc	8/10	1	2	FACETS	0.387	0.335	0.444	0.387	0.335	0.444	SUBCLONAL	1	TRUE	1	0.536765094767098	2		534	616	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84406216	84406216	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs549027065	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	53	380	0	ENST00000321945.7:c.10G>A	p.Glu4Lys	p.E4K	ENST00000321945	NM_139076.2	4	Gag/Aag	1/9	1	2	FACETS	0.598	0.513	0.691	0.598	0.513	0.691	SUBCLONAL	1	TRUE	1	0.536765094767098	2		380	330	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1296155	1296155	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	70	569	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.419	0.365	0.478	0.419	0.365	0.478	SUBCLONAL	1	TRUE	1	0.536765094767098	2		569	622	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021115	26021116	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	rs770926417	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	88	561	0	ENST00000357647.3:c.403_404del	p.Arg135GlyfsTer?	p.R135Gfs*?	ENST00000357647	NM_003529.2	133	gGA/g	1/1	1	2	FACETS	0.531	0.47	0.595	0.531	0.47	0.595	SUBCLONAL	1	TRUE	1	0.536765094767098	2		561	618	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197288	26197288	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	82	674	0	ENST00000356476.2:c.191G>C	p.Arg64Pro	p.R64P	ENST00000356476		64	cGc/cCc	1/1	1	2	FACETS	0.481	0.424	0.542	0.481	0.424	0.542	SUBCLONAL	1	TRUE	1	0.536765094767098	2		674	635	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31238107	31238107	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	42	682	0	ENST00000376228.5:c.775C>A	p.Pro259Thr	p.P259T	ENST00000376228	NM_002117.5	259	Cca/Aca	4/8	1	2	FACETS	0.206	0.171	0.244	0.206	0.171	0.244	SUBCLONAL	1	TRUE	1	0.536765094767098	2		682	761	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31238166	31238166	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	20	277	0	ENST00000376228.5:c.716T>C	p.Leu239Pro	p.L239P	ENST00000376228	NM_002117.5	239	cTg/cCg	4/8	1	2	FACETS	0.273	0.209	0.348	0.273	0.209	0.348	SUBCLONAL	1	TRUE	1	0.536765094767098	2		277	273	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350101	81350101	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1382781839	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	39	360	0	ENST00000222390.5:c.1231A>G	p.Thr411Ala	p.T411A	ENST00000222390	NM_000601.4	411	Aca/Gca	10/18	1	2	FACETS	0.456	0.379	0.541	0.456	0.379	0.541	SUBCLONAL	1	TRUE	1	0.536765094767098	2		360	319	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864231	151864231	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	59	303	0	ENST00000262189.6:c.9750G>T	p.Gln3250His	p.Q3250H	ENST00000262189	NM_170606.2	3250	caG/caT	42/59	1	2	FACETS	0.534	0.46	0.613	0.534	0.46	0.613	SUBCLONAL	1	TRUE	1	0.536765094767098	2		303	412	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874668	151874668	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	72	550	0	ENST00000262189.6:c.7870G>T	p.Asp2624Tyr	p.D2624Y	ENST00000262189	NM_170606.2	2624	Gat/Tat	38/59	1	2	FACETS	0.398	0.347	0.453	0.398	0.347	0.453	SUBCLONAL	1	TRUE	1	0.536765094767098	2		550	674	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960109	151960109	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	53	337	0	ENST00000262189.6:c.1291A>G	p.Lys431Glu	p.K431E	ENST00000262189	NM_170606.2	431	Aaa/Gaa	9/59	1	2	FACETS	0.676	0.581	0.779	0.676	0.581	0.779	SUBCLONAL	1	TRUE	1	0.536765094767098	2		337	292	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370883	55370883	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	54	421	0	ENST00000297316.4:c.185C>A	p.Ala62Asp	p.A62D	ENST00000297316	NM_022454.3	62	gCc/gAc	1/2	1	2	FACETS	0.41	0.35	0.475	0.41	0.35	0.475	SUBCLONAL	1	TRUE	1	0.536765094767098	2		421	491	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2047307	2047307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1284404989	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	21	115	1	ENST00000349721.2:c.869C>T	p.Ala290Val	p.A290V	ENST00000349721	NM_003070.3	290	gCg/gTg	5/34	NA	2	FACETS	1	0.793	1			1	INDETERMINATE	1	TRUE	NA	0.536765094767098	2		116	78	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211512	98211512	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	45	445	0	ENST00000331920.6:c.3643C>T	p.His1215Tyr	p.H1215Y	ENST00000331920	NM_000264.3	1215	Cac/Tac	22/24	1	2	FACETS	0.342	0.287	0.403	0.342	0.287	0.403	SUBCLONAL	1	TRUE	1	0.536765094767098	2		445	490	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760191	133760191	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	46	425	0	ENST00000318560.5:c.2514G>T	p.Lys838Asn	p.K838N	ENST00000318560	NM_005157.4	838	aaG/aaT	11/11	1	2	FACETS	0.398	0.335	0.467	0.398	0.335	0.467	SUBCLONAL	1	TRUE	1	0.536765094767098	2		425	431	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815667	139815667	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	43	484	0	ENST00000247668.2:c.1138G>T	p.Ala380Ser	p.A380S	ENST00000247668	NM_021138.3	380	Gcc/Tcc	9/11	1	2	FACETS	0.325	0.272	0.384	0.325	0.272	0.384	SUBCLONAL	1	TRUE	1	0.536765094767098	2		484	493	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874010	123874011	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGC	rs780061449	NA	P-0066835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	27	570	0	ENST00000330479.4:c.62_64dup	p.Ala21dup	p.A21dup	ENST00000330479	NM_020382.3	21	gag/gaGGCg	2/9	1	2	FACETS	0.196	0.156	0.243	0.196	0.156	0.243	SUBCLONAL	1	TRUE	1	0.536765094767098	2		570	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0066836-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	59	477	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.316289783307673	1	FACETS	0.667	0.575	0.767	0.667	0.575	0.767	SUBCLONAL	1	TRUE	0	0.316289783307673	1		477	471	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066836-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	42	314	4	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.316289783307673	2		318	232	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555310	226555310	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0066836-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	78	520	0	ENST00000366794.5:c.2278-1G>C		p.X760_splice	ENST00000366794	NM_001618.3	760			1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.316289783307673	2		520	460	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431029	181431055	+	inframe_deletion	In_Frame_Del	DEL	TGTCCCAGCACTACCAGAGCGGCCCGG	TGTCCCAGCACTACCAGAGCGGCCCGG	-	novel	NA	P-0066836-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	66	599	0	ENST00000325404.1:c.883_909del	p.Ser295_Val303del	p.S295_V303del	ENST00000325404	NM_003106.3	294	aTGTCCCAGCACTACCAGAGCGGCCCGGtg/atg	1/1	0.170279275085538	4	FACETS	0.969	0.842	1	0.484	0.421	0.554	INDETERMINATE	1	TRUE	2	0.316289783307673	4		599	567	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519920	NA	P-0066837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	218	530	0	ENST00000397062.3:c.85G>C	p.Asp29His	p.D29H	ENST00000397062	NM_006164.4	29	Gat/Cat	2/5	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.721107645392633	2		530	581	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955522	48955522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	188	425	0	ENST00000267163.4:c.1638G>A	p.Met546Ile	p.M546I	ENST00000267163	NM_000321.2	546	atG/atA	17/27	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.721107645392633	2		425	486	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955544	48955544	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	171	426	0	ENST00000267163.4:c.1660G>A	p.Glu554Lys	p.E554K	ENST00000267163	NM_000321.2	554	Gaa/Aaa	17/27	1	2	FACETS	0.988	0.917	1	0.988	0.917	1	CLONAL	1	TRUE	1	0.721107645392633	2		426	480	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66781559	66781559	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1301109791	NA	P-0066837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	184	496	0	ENST00000307102.5:c.967C>G	p.Pro323Ala	p.P323A	ENST00000307102	NM_002755.3	323	Cca/Gca	9/11	1	2	FACETS	0.898	0.835	0.964	0.898	0.835	0.964	CLONAL	1	TRUE	1	0.721107645392633	2		496	568	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244426	41244426	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397509035	NA	P-0066837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	216	555	0	ENST00000357654.3:c.3122C>T	p.Ser1041Leu	p.S1041L	ENST00000357654	NM_007294.3	1041	tCa/tTa	10/23	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.721107645392633	2		555	575	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575152	48575152	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	201	506	0	ENST00000342988.3:c.346C>T	p.Gln116Ter	p.Q116*	ENST00000342988	NM_005359.5	116	Cag/Tag	3/12	0.706341068645811	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.721107645392633	1		506	337	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636794	8636794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	188	581	0	ENST00000356435.5:c.115G>A	p.Gly39Arg	p.G39R	ENST00000356435		39	Gga/Aga	2/35	0.721107645392633	1	FACETS	0.921	0.866	0.976	0.921	0.866	0.976	CLONAL	1	TRUE	0	0.721107645392633	1		581	362	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243569	41243569	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs876659720	NA	P-0066837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	249	661	0	ENST00000357654.3:c.3979C>T	p.Gln1327Ter	p.Q1327*	ENST00000357654	NM_007294.3	1327	Cag/Tag	10/23	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.721107645392633	2		661	660	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243655	41243655	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs80357440	NA	P-0066837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	238	640	0	ENST00000357654.3:c.3893C>A	p.Ser1298Ter	p.S1298*	ENST00000357654	NM_007294.3	1298	tCa/tAa	10/23	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.721107645392633	2		640	660	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2047264	2047264	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066839-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	37	164	0	ENST00000349721.2:c.826C>A	p.Gln276Lys	p.Q276K	ENST00000349721	NM_003070.3	276	Cag/Aag	5/34	0.78906579568675	7	FACETS	0.537	0.442	0.644	0.077	0.063	0.092	SUBCLONAL	1	TRUE	0	0.78906579568675	7		164	519	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	346	789	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.882	0.837	0.927	0.882	0.837	0.927	CLONAL	1	TRUE	1	0.81	2		790	969	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	344	642	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.911	0.865	0.958	0.911	0.865	0.958	CLONAL	1	TRUE	1	0.81	2		643	932	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	303	418	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.81	2		418	681	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	299	519	2	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.8	0.755	0.846	0.8	0.755	0.846	SUBCLONAL	1	TRUE	1	0.81	2		521	923	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	85	206	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.726	0.65	0.806	0.726	0.65	0.806	SUBCLONAL	1	TRUE	1	0.81	2		206	289	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	493	177	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.876	0.85	0.901	1	0.998	1	CLONAL	2	TRUE	1	0.81	2		178	695	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	261	545	3	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.79	0.742	0.838	0.79	0.742	0.838	SUBCLONAL	1	TRUE	1	0.81	2		548	816	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216189	36216189	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	318	581	0	ENST00000222270.7:c.3602del	p.Pro1201ArgfsTer154	p.P1201Rfs*154	ENST00000222270	NM_014727.1	1199	ggC/gg	11/37	1	2	FACETS	0.925	0.876	0.974	0.925	0.876	0.974	CLONAL	1	TRUE	1	0.81	2		581	849	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	336	545	4	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.969	0.92	1	0.969	0.92	1	CLONAL	1	TRUE	1	0.81	2		549	856	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981832	63981832	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	319	536	0	ENST00000398590.3:c.2340del	p.Thr781ProfsTer11	p.T781Pfs*11	ENST00000398590	NM_001177387.1	778	ggC/gg	12/14	1	2	FACETS	0.867	0.82	0.913	0.867	0.82	0.913	CLONAL	1	TRUE	1	0.81	2		536	909	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	309	535	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.891	0.843	0.94	0.891	0.843	0.94	CLONAL	1	TRUE	1	0.81	2		536	856	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440431	49440431	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1240601136	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	271	552	0	ENST00000301067.7:c.4379del	p.Pro1460HisfsTer46	p.P1460Hfs*46	ENST00000301067	NM_003482.3	1460	cCa/ca	15/54	1	2	FACETS	0.759	0.714	0.805	0.759	0.714	0.805	SUBCLONAL	1	TRUE	1	0.81	2		552	882	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255883	16255883	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	338	485	0	ENST00000375759.3:c.3154del	p.Ile1052SerfsTer40	p.I1052Sfs*40	ENST00000375759	NM_015001.2	1050	Aaa/aa	11/15	1	2	FACETS	0.98	0.931	1	0.98	0.931	1	CLONAL	1	TRUE	1	0.81	2		485	852	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830849	156830849	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1174707423	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	274	455	0	ENST00000524377.1:c.127del	p.His43ThrfsTer26	p.H43Tfs*26	ENST00000524377	NM_002529.3	41	tgC/tg	1/17	1	2	FACETS	0.923	0.871	0.976	0.923	0.871	0.976	CLONAL	1	TRUE	1	0.81	2		455	733	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846308	156846308	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	287	496	0	ENST00000524377.1:c.1753del	p.Leu585CysfsTer73	p.L585Cfs*73	ENST00000524377	NM_002529.3	583	cgC/cg	14/17	1	2	FACETS	0.93	0.879	0.982	0.93	0.879	0.982	CLONAL	1	TRUE	1	0.81	2		496	762	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652329	206652330	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782347019	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	310	544	1	ENST00000367120.3:c.1042dup	p.Arg348ProfsTer8	p.R348Pfs*8	ENST00000367120	NM_014002.3	346	gcc/gCcc	10/22	1	2	FACETS	0.888	0.84	0.936	0.888	0.84	0.936	CLONAL	1	TRUE	1	0.81	2		545	862	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333864	70333864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528233201	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	352	522	0	ENST00000373644.4:c.1769G>A	p.Arg590Gln	p.R590Q	ENST00000373644	NM_030625.2	590	cGa/cAa	2/12	1	2	FACETS	0.977	0.929	1	0.977	0.929	1	CLONAL	1	TRUE	1	0.81	2		522	890	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771514	112771514	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1564732148	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	303	489	0	ENST00000369452.4:c.1692del	p.Pro565LeufsTer8	p.P565Lfs*8	ENST00000369452	NM_007373.3	563	Ggg/gg	9/9	1	2	FACETS	0.935	0.885	0.986	0.935	0.885	0.986	CLONAL	1	TRUE	1	0.81	2		489	800	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998658	100998658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	293	564	0	ENST00000325455.5:c.1144C>T	p.Pro382Ser	p.P382S	ENST00000325455	NM_001202474.3	382	Ccg/Tcg	1/8	1	2	FACETS	0.924	0.874	0.975	0.924	0.874	0.975	CLONAL	1	TRUE	1	0.81	2		564	783	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998925	100998925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	292	478	0	ENST00000325455.5:c.877C>T	p.Arg293Cys	p.R293C	ENST00000325455	NM_001202474.3	293	Cgc/Tgc	1/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.81	2		478	691	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307394	118307394	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	105	228	2	ENST00000534358.1:c.173del	p.Pro58ArgfsTer92	p.P58Rfs*92	ENST00000534358	NM_005933.3	56	tCc/tc	1/36	1	2	FACETS	0.894	0.813	0.978	0.894	0.813	0.978	CLONAL	1	TRUE	1	0.81	2		230	290	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	305	618	0	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	1	2	FACETS	0.768	0.725	0.812	0.768	0.725	0.812	SUBCLONAL	1	TRUE	1	0.81	2		618	981	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373592	118373592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782489222	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	349	522	0	ENST00000534358.1:c.6985C>T	p.Pro2329Ser	p.P2329S	ENST00000534358	NM_005933.3	2329	Cct/Tct	27/36	1	2	FACETS	0.992	0.943	1	0.992	0.943	1	CLONAL	1	TRUE	1	0.81	2		522	869	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885574	111885574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773486842	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	325	504	0	ENST00000341259.2:c.1351G>A	p.Gly451Ser	p.G451S	ENST00000341259	NM_005475.2	451	Ggc/Agc	7/8	1	2	FACETS	0.986	0.936	1	0.986	0.936	1	CLONAL	1	TRUE	1	0.81	2		504	814	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209267	133209267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs5745021	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	299	514	0	ENST00000320574.5:c.6119C>T	p.Ala2040Val	p.A2040V	ENST00000320574	NM_006231.2	2040	gCg/gTg	44/49	1	2	FACETS	0.951	0.9	1	0.951	0.9	1	CLONAL	1	TRUE	1	0.81	2		514	776	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220099	133220100	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs758487568	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	338	512	11	ENST00000320574.5:c.4337_4338del	p.Val1446GlyfsTer3	p.V1446Gfs*3	ENST00000320574	NM_006231.2	1446	gTG/g	34/49	1	2	FACETS	0.997	0.948	1	0.997	0.948	1	CLONAL	1	TRUE	1	0.81	2		523	837	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245023	133245024	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs752846614	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	321	548	0	ENST00000320574.5:c.2091dup	p.Phe699ValfsTer11	p.F699Vfs*11	ENST00000320574	NM_006231.2	697	-/C	19/49	1	2	FACETS	0.881	0.834	0.928	0.881	0.834	0.928	CLONAL	1	TRUE	1	0.81	2		548	900	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73995362	73995362	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763918983	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	244	445	0	ENST00000318443.5:c.668G>A	p.Arg223His	p.R223H	ENST00000318443	NM_001024736.1	223	cGc/cAc	4/10	1	2	FACETS	0.924	0.869	0.98	0.924	0.869	0.98	CLONAL	1	TRUE	1	0.81	2		445	652	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99460060	99460060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs544049409	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	288	450	0	ENST00000268035.6:c.2156G>A	p.Arg719His	p.R719H	ENST00000268035	NM_000875.3	719	cGc/cAc	10/21	1	2	FACETS	0.965	0.912	1	0.965	0.912	1	CLONAL	1	TRUE	1	0.81	2		450	737	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500474	99500474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45475702	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	366	572	0	ENST00000268035.6:c.3907G>A	p.Val1303Ile	p.V1303I	ENST00000268035	NM_000875.3	1303	Gtc/Atc	21/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.81	2		572	858	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828389	72828389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750838080	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	330	544	0	ENST00000268489.5:c.8192G>A	p.Arg2731Gln	p.R2731Q	ENST00000268489	NM_006885.3	2731	cGg/cAg	9/10	1	2	FACETS	0.979	0.93	1	0.979	0.93	1	CLONAL	1	TRUE	1	0.81	2		544	832	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979514	7979514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141010860	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	294	474	1	ENST00000319144.4:c.1511C>T	p.Ala504Val	p.A504V	ENST00000319144	NM_001139.2	504	gCg/gTg	11/15	1	2	FACETS	0.99	0.938	1	0.99	0.938	1	CLONAL	1	TRUE	1	0.81	2		475	733	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979987	7979987	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746723399	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	291	501	1	ENST00000319144.4:c.1350del	p.Leu451SerfsTer16	p.L451Sfs*16	ENST00000319144	NM_001139.2	450	ggG/gg	10/15	1	2	FACETS	0.927	0.876	0.979	0.927	0.876	0.979	CLONAL	1	TRUE	1	0.81	2		502	775	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	236	505	3	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	1	2	FACETS	0.762	0.713	0.811	0.762	0.713	0.811	SUBCLONAL	1	TRUE	1	0.81	2		508	765	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40468917	40468917	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs869312892	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	253	375	0	ENST00000264657.5:c.2147C>T	p.Thr716Met	p.T716M	ENST00000264657	NM_139276.2	716	aCg/aTg	23/24	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.81	2		375	621	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435513	56435513	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	318	473	0	ENST00000407977.2:c.1624del	p.Thr542ProfsTer158	p.T542Pfs*158	ENST00000407977		542	Acc/cc	9/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.81	2		473	782	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740727	58740727	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	318	544	1	ENST00000305921.3:c.1636del	p.Leu546Ter	p.L546*	ENST00000305921	NM_003620.3	544	ggC/gg	6/6	1	2	FACETS	0.892	0.845	0.94	0.892	0.845	0.94	CLONAL	1	TRUE	1	0.81	2		545	880	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530042	63530042	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	245	391	0	ENST00000307078.5:c.2393del	p.Lys798ArgfsTer63	p.K798Rfs*63	ENST00000307078	NM_004655.3	798	aAg/ag	10/11	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.81	2		391	603	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099225	4099225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200371894	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	40	443	0	ENST00000262948.5:c.893C>T	p.Pro298Leu	p.P298L	ENST00000262948	NM_030662.3	298	cCg/cTg	7/11	1	2	FACETS	0.144	0.119	0.172	0.144	0.119	0.172	SUBCLONAL	1	TRUE	1	0.81	2		443	687	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221081	5221081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199805837	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	372	576	0	ENST00000357368.4:c.3385G>A	p.Ala1129Thr	p.A1129T	ENST00000357368	NM_002850.3	1129	Gcc/Acc	20/38	1	2	FACETS	0.99	0.943	1	0.99	0.943	1	CLONAL	1	TRUE	1	0.81	2		576	928	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5225777	5225777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751437578	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	328	415	0	ENST00000357368.4:c.2455G>A	p.Ala819Thr	p.A819T	ENST00000357368	NM_002850.3	819	Gct/Act	17/38	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.81	2		415	759	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031737	11031737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753354844	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	367	593	0	ENST00000327064.4:c.1549G>A	p.Ala517Thr	p.A517T	ENST00000327064	NM_199141.1	517	Gcc/Acc	14/16	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.81	2		593	900	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222925	36222925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746346674	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	342	636	0	ENST00000222270.7:c.5554G>A	p.Ala1852Thr	p.A1852T	ENST00000222270	NM_014727.1	1852	Gcc/Acc	27/37	1	2	FACETS	0.978	0.93	1	0.978	0.93	1	CLONAL	1	TRUE	1	0.81	2		636	863	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991736	25991736	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs530632623	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	282	420	0	ENST00000435504.4:c.506C>T	p.Ala169Val	p.A169V	ENST00000435504		169	gCg/gTg	7/13	1	2	FACETS	0.953	0.9	1	0.953	0.9	1	CLONAL	1	TRUE	1	0.81	2		420	731	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446386	29446386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371521416	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	319	540	0	ENST00000389048.3:c.3181C>T	p.Arg1061Trp	p.R1061W	ENST00000389048	NM_004304.4	1061	Cgg/Tgg	20/29	1	2	FACETS	0.929	0.88	0.978	0.929	0.88	0.978	CLONAL	1	TRUE	1	0.81	2		540	848	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151290	202151290	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	281	382	0	ENST00000358485.4:c.1596del	p.Lys532AsnfsTer73	p.K532Nfs*73	ENST00000358485	NM_001080125.1	530	agA/ag	9/9	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.81	2		382	692	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403254	213403254	+	frameshift_variant,start_lost,start_retained_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	208	434	0	ENST00000342788.4:c.1del	p.Met1?	p.M1?	ENST00000342788	NM_005235.2	1	Atg/tg	1/28	1	2	FACETS	0.836	0.781	0.893	0.836	0.781	0.893	CLONAL	1	TRUE	1	0.81	2		434	614	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546626	9546626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751328296	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	334	517	1	ENST00000353224.5:c.1396G>A	p.Ala466Thr	p.A466T	ENST00000353224	NM_177990.2	466	Gcc/Acc	5/10	1	2	FACETS	0.973	0.924	1	0.973	0.924	1	CLONAL	1	TRUE	1	0.81	2		518	848	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385068	31385068	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	293	464	0	ENST00000328111.2:c.1453C>T	p.Arg485Ter	p.R485*	ENST00000328111	NM_006892.3	485	Cga/Tga	14/23	1	2	FACETS	0.987	0.934	1	0.987	0.934	1	CLONAL	1	TRUE	1	0.81	2		464	733	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595976	52595977	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	286	400	0	ENST00000394830.3:c.3938dup	p.Ser1315ValfsTer26	p.S1315Vfs*26	ENST00000394830	NM_018313.4	1313	cca/ccCa	26/30	1	2	FACETS	0.865	0.817	0.915	0.865	0.817	0.915	CLONAL	1	TRUE	1	0.81	2		400	816	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119666150	119666150	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	245	408	0	ENST00000316626.5:c.331C>T	p.Arg111Ter	p.R111*	ENST00000316626		111	Cga/Tga	3/12	1	2	FACETS	0.992	0.934	1	0.992	0.934	1	CLONAL	1	TRUE	1	0.81	2		408	610	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144258384	144258385	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755581817	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	217	413	0	ENST00000262995.4:c.50dup	p.Glu18GlyfsTer34	p.E18Gfs*34	ENST00000262995	NM_207123.2	15	tcc/tCcc	1/11	1	2	FACETS	0.908	0.85	0.967	0.908	0.85	0.967	CLONAL	1	TRUE	1	0.81	2		413	590	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279524	1279524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774381540	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	246	428	0	ENST00000310581.5:c.2012G>A	p.Arg671Gln	p.R671Q	ENST00000310581	NM_198253.2	671	cGg/cAg	5/16	1	2	FACETS	0.969	0.912	1	0.969	0.912	1	CLONAL	1	TRUE	1	0.81	2		428	627	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468080	31468080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458058411	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	295	461	1	ENST00000344624.3:c.2332C>T	p.Arg778Cys	p.R778C	ENST00000344624		778	Cgc/Tgc	15/33	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.81	2		462	728	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685330	86685330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	46	367	0	ENST00000274376.6:c.3046C>T	p.Arg1016Cys	p.R1016C	ENST00000274376	NM_002890.2	1016	Cgt/Tgt	24/25	1	2	FACETS	0.187	0.156	0.22	0.187	0.156	0.22	SUBCLONAL	1	TRUE	1	0.81	2		367	609	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323288	31323288	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	194	284	0	ENST00000412585.2:c.701C>A	p.Pro234His	p.P234H	ENST00000412585	NM_005514.6	234	cCt/cAt	4/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.81	2		284	450	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188297	32188297	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs753855314	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	402	619	0	ENST00000375023.3:c.1044del	p.Gly349AlafsTer49	p.G349Afs*49	ENST00000375023	NM_004557.3	348	ggC/gg	6/30	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.81	2		619	925	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983042	111983042	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	273	552	8	ENST00000368678.4:c.1505del	p.Lys502ArgfsTer53	p.K502Rfs*53	ENST00000368678		502	aAg/ag	13/13	1	2	FACETS	0.843	0.794	0.892	0.843	0.794	0.892	CLONAL	1	TRUE	1	0.81	2		560	800	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372128	55372128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	274	501	0	ENST00000297316.4:c.818G>A	p.Arg273Gln	p.R273Q	ENST00000297316	NM_022454.3	273	cGa/cAa	2/2	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.81	2		501	655	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2039777	2039782	+	inframe_deletion	In_Frame_Del	DEL	CAGCAG	CAGCAG	-	rs113070757	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	205	532	12	ENST00000349721.2:c.702_707del	p.Gln237_Gln238del	p.Q237_Q238del	ENST00000349721	NM_003070.3	223	CAGCAG/-	4/34	1	2	FACETS	0.646	0.601	0.693	0.646	0.601	0.693	SUBCLONAL	1	TRUE	1	0.81	2		544	783	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22008918	22008918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	224	408	0	ENST00000276925.6:c.35del	p.Gly12AlafsTer15	p.G12Afs*15	ENST00000276925	NM_004936.3	12	gGc/gc	1/2	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.81	2		408	541	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395053	139395053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1484525055	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	287	414	2	ENST00000277541.6:c.5885G>A	p.Arg1962His	p.R1962H	ENST00000277541	NM_017617.3	1962	cGc/cAc	31/34	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.81	2		416	670	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841230	15841231	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGCCGG	rs752736259	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	184	621	0	ENST00000307771.7:c.1338_1343dup	p.Ser447_Arg448dup	p.S447_R448dup	ENST00000307771	NM_005089.3	447	-/AGCCGG	11/11	1	2	FACETS	0.501	0.463	0.542	0.501	0.463	0.542	SUBCLONAL	1	TRUE	1	0.81	2		621	906	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933617	39933617	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	303	561	1	ENST00000378444.4:c.982del	p.Asp328ThrfsTer50	p.D328Tfs*50	ENST00000378444	NM_001123385.1	328	Gac/ac	4/15	1	2	FACETS	0.918	0.869	0.968	0.918	0.869	0.968	CLONAL	1	TRUE	1	0.81	2		562	815	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411366	63411366	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	386	639	0	ENST00000330258.3:c.1801C>T	p.Arg601Ter	p.R601*	ENST00000330258	NM_152424.3	601	Cga/Tga	2/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.81	2		639	903	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412124	63412124	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	302	618	0	ENST00000330258.3:c.1043del	p.Gly348AlafsTer16	p.G348Afs*16	ENST00000330258	NM_152424.3	348	gGc/gc	2/2	1	2	FACETS	0.925	0.875	0.976	0.925	0.875	0.976	CLONAL	1	TRUE	1	0.81	2		618	806	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357069	70357069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200279192	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	322	553	0	ENST00000374080.3:c.5584C>T	p.Arg1862Cys	p.R1862C	ENST00000374080		1862	Cgc/Tgc	39/45	1	2	FACETS	0.951	0.902	1	0.951	0.902	1	CLONAL	1	TRUE	1	0.81	2		553	836	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743856	46743856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762444770	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	382	508	0	ENST00000371975.4:c.2146C>T	p.Arg716Trp	p.R716W	ENST00000371975	NM_003579.3	716	Cgg/Tgg	18/18	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.81	2		508	897	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746044	162746044	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	362	550	0	ENST00000367921.3:c.2167A>C	p.Thr723Pro	p.T723P	ENST00000367921	NM_006182.2	723	Aca/Cca	16/18	1	2	FACETS	0.96	0.913	1	0.96	0.913	1	CLONAL	1	TRUE	1	0.81	2		550	931	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206646613	206646613	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	324	468	0	ENST00000367120.3:c.43C>A	p.Leu15Met	p.L15M	ENST00000367120	NM_014002.3	15	Ctg/Atg	3/22	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.81	2		468	785	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230492744	230492744	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	316	455	0	ENST00000391860.1:c.310G>A	p.Ala104Thr	p.A104T	ENST00000391860	NM_001258311.1	104	Gcc/Acc	2/7	1	2	FACETS	0.995	0.944	1	0.995	0.944	1	CLONAL	1	TRUE	1	0.81	2		455	784	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100444	8100444	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	369	625	0	ENST00000346208.3:c.418T>G	p.Ser140Ala	p.S140A	ENST00000346208		140	Tcc/Gcc	3/6	1	2	FACETS	0.996	0.948	1	0.996	0.948	1	CLONAL	1	TRUE	1	0.81	2		625	915	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852194	63852194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	323	470	0	ENST00000279873.7:c.2972G>A	p.Gly991Asp	p.G991D	ENST00000279873	NM_032199.2	991	gGc/gAc	10/10	1	2	FACETS	0.968	0.918	1	0.968	0.918	1	CLONAL	1	TRUE	1	0.81	2		470	824	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178686	108178686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659487	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	286	429	0	ENST00000278616.4:c.5737G>A	p.Val1913Met	p.V1913M	ENST00000278616	NM_000051.3	1913	Gtg/Atg	38/63	1	2	FACETS	0.956	0.903	1	0.956	0.903	1	CLONAL	1	TRUE	1	0.81	2		429	739	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426551	49426551	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	437	652	0	ENST00000301067.7:c.11937C>A	p.Asn3979Lys	p.N3979K	ENST00000301067	NM_003482.3	3979	aaC/aaA	39/54	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.81	2		652	1010	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813342	102813342	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	287	523	0	ENST00000307046.8:c.347A>C	p.Lys116Thr	p.K116T	ENST00000307046	NM_001111285.1	116	aAg/aCg	3/4	1	2	FACETS	0.892	0.843	0.943	0.892	0.843	0.943	CLONAL	1	TRUE	1	0.81	2		523	794	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219884	133219884	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748522633	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	336	515	0	ENST00000320574.5:c.4477G>A	p.Ala1493Thr	p.A1493T	ENST00000320574	NM_006231.2	1493	Gca/Aca	35/49	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.81	2		515	819	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225574	133225574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770024304	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	341	547	0	ENST00000320574.5:c.4090C>T	p.Arg1364Cys	p.R1364C	ENST00000320574	NM_006231.2	1364	Cgt/Tgt	32/49	1	2	FACETS	0.999	0.949	1	0.999	0.949	1	CLONAL	1	TRUE	1	0.81	2		547	843	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562051	21562051	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	325	474	0	ENST00000382592.4:c.1868G>T	p.Arg623Leu	p.R623L	ENST00000382592	NM_014572.2	623	cGg/cTg	4/8	1	2	FACETS	0.93	0.882	0.979	0.93	0.882	0.979	CLONAL	1	TRUE	1	0.81	2		474	863	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916810	48916810	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	171	346	0	ENST00000267163.4:c.340T>C	p.Ser114Pro	p.S114P	ENST00000267163	NM_000321.2	114	Tcg/Ccg	3/27	1	2	FACETS	0.936	0.87	1	0.936	0.87	1	CLONAL	1	TRUE	1	0.81	2		346	451	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996180	73996180	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	301	519	0	ENST00000318443.5:c.914G>A	p.Ser305Asn	p.S305N	ENST00000318443	NM_001024736.1	305	aGc/aAc	5/10	1	2	FACETS	0.963	0.912	1	0.963	0.912	1	CLONAL	1	TRUE	1	0.81	2		519	772	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134383	2134383	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	347	576	0	ENST00000219476.3:c.4160C>A	p.Ser1387Tyr	p.S1387Y	ENST00000219476	NM_000548.3	1387	tCc/tAc	34/42	1	2	FACETS	0.965	0.917	1	0.965	0.917	1	CLONAL	1	TRUE	1	0.81	2		576	888	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636752	2636752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1043839627	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	360	525	0	ENST00000342085.4:c.1201G>A	p.Asp401Asn	p.D401N	ENST00000342085	NM_002613.4	401	Gac/Aac	11/14	1	2	FACETS	0.97	0.923	1	0.97	0.923	1	CLONAL	1	TRUE	1	0.81	2		525	916	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964988	15964988	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	345	529	0	ENST00000268712.3:c.5608A>C	p.Thr1870Pro	p.T1870P	ENST00000268712	NM_006311.3	1870	Acc/Ccc	37/46	1	2	FACETS	0.927	0.88	0.974	0.927	0.88	0.974	CLONAL	1	TRUE	1	0.81	2		529	919	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33680051	33680051	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs755740719	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	243	326	0	ENST00000308377.4:c.2030A>G	p.Asp677Gly	p.D677G	ENST00000308377	NM_152270.3	677	gAt/gGt	5/5	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.81	2		326	583	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353877	40353877	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	342	466	0	ENST00000293328.3:c.2243A>G	p.Asp748Gly	p.D748G	ENST00000293328	NM_012448.3	748	gAc/gGc	19/19	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.81	2		466	826	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58725286	58725286	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	316	486	0	ENST00000305921.3:c.860A>G	p.Glu287Gly	p.E287G	ENST00000305921	NM_003620.3	287	gAa/gGa	4/6	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.81	2		486	763	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622129	1622129	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	292	573	0	ENST00000344749.5:c.746T>C	p.Leu249Pro	p.L249P	ENST00000344749	NM_001136139.2	249	cTc/cCc	10/19	1	2	FACETS	0.945	0.894	0.997	0.945	0.894	0.997	CLONAL	1	TRUE	1	0.81	2		573	763	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125526	7125526	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	323	513	0	ENST00000302850.5:c.3026C>A	p.Ser1009Tyr	p.S1009Y	ENST00000302850	NM_000208.2	1009	tCt/tAt	17/22	1	2	FACETS	0.989	0.939	1	0.989	0.939	1	CLONAL	1	TRUE	1	0.81	2		513	806	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350809	15350809	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200117669	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	252	442	0	ENST00000263377.2:c.3194C>T	p.Pro1065Leu	p.P1065L	ENST00000263377	NM_058243.2	1065	cCg/cTg	15/20	1	2	FACETS	0.977	0.92	1	0.977	0.92	1	CLONAL	1	TRUE	1	0.81	2		442	637	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798108	42798108	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	340	532	0	ENST00000575354.2:c.4062C>A	p.Asp1354Glu	p.D1354E	ENST00000575354	NM_015125.3	1354	gaC/gaA	17/20	1	2	FACETS	0.995	0.945	1	0.995	0.945	1	CLONAL	1	TRUE	1	0.81	2		532	844	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467185	25467185	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	346	508	0	ENST00000264709.3:c.1690G>A	p.Asp564Asn	p.D564N	ENST00000264709	NM_175629.2	564	Gac/Aac	15/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.81	2		508	818	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145621	61145621	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	325	432	0	ENST00000295025.8:c.736del	p.Thr246LeufsTer12	p.T246Lfs*12	ENST00000295025	NM_002908.2	245	Aaa/aa	7/11	1	2	FACETS	0.959	0.91	1	0.959	0.91	1	CLONAL	1	TRUE	1	0.81	2		432	837	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136290	202136290	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	289	464	0	ENST00000358485.4:c.537del	p.Phe179LeufsTer18	p.F179Lfs*18	ENST00000358485	NM_001080125.1	178	tcT/tc	3/9	1	2	FACETS	0.948	0.896	1	0.948	0.896	1	CLONAL	1	TRUE	1	0.81	2		464	753	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728846	39728846	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	322	447	0	ENST00000361337.2:c.1126C>T	p.Arg376Ter	p.R376*	ENST00000361337	NM_003286.2	376	Cga/Tga	12/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.81	2		447	774	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436633	52436633	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	328	482	0	ENST00000460680.1:c.2041A>G	p.Met681Val	p.M681V	ENST00000460680	NM_004656.3	681	Atg/Gtg	16/17	1	2	FACETS	0.966	0.917	1	0.966	0.917	1	CLONAL	1	TRUE	1	0.81	2		482	838	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165573	185165574	+	splice_region_variant,intron_variant	Splice_Region	DEL	AA	AA	-	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	241	335	0	ENST00000265026.3:c.852-3_852-2del		p.X284_splice	ENST00000265026	NM_004721.4	284			1	2	FACETS	0.903	0.848	0.958	0.903	0.848	0.958	CLONAL	1	TRUE	1	0.81	2		335	659	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191528	185191528	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	328	496	1	ENST00000265026.3:c.2413del	p.Thr805GlnfsTer19	p.T805Qfs*19	ENST00000265026	NM_004721.4	803	cgA/cg	11/14	1	2	FACETS	0.922	0.875	0.971	0.922	0.875	0.971	CLONAL	1	TRUE	1	0.81	2		497	878	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383899	84383899	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs769962886	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	297	485	0	ENST00000321945.7:c.953A>G	p.Asp318Gly	p.D318G	ENST00000321945	NM_139076.2	318	gAt/gGt	9/9	1	2	FACETS	0.978	0.926	1	0.978	0.926	1	CLONAL	1	TRUE	1	0.81	2		485	750	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950583	79950583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	237	409	0	ENST00000265081.6:c.37G>A	p.Ala13Thr	p.A13T	ENST00000265081	NM_002439.4	13	Gcc/Acc	1/24	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.81	2		409	579	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20487020	20487020	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	274	413	0	ENST00000346618.3:c.985C>T	p.Pro329Ser	p.P329S	ENST00000346618	NM_001949.4	329	Cct/Tct	5/7	1	2	FACETS	0.968	0.914	1	0.968	0.914	1	CLONAL	1	TRUE	1	0.81	2		413	699	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020821	26020821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758782004	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	385	661	0	ENST00000357647.3:c.104G>A	p.Gly35Asp	p.G35D	ENST00000357647	NM_003529.2	35	gGc/gAc	1/1	1	2	FACETS	0.994	0.948	1	0.994	0.948	1	CLONAL	1	TRUE	1	0.81	2		661	956	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045763	26045763	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	372	575	0	ENST00000540144.1:c.125A>G	p.Tyr42Cys	p.Y42C	ENST00000540144	NM_003531.2	42	tAc/tGc	1/1	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.81	2		575	893	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271549	26271549	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	337	577	0	ENST00000305910.3:c.64G>A	p.Ala22Thr	p.A22T	ENST00000305910	NM_003534.2	22	Gcc/Acc	1/1	1	2	FACETS	0.939	0.892	0.987	0.939	0.892	0.987	CLONAL	1	TRUE	1	0.81	2		577	886	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910601	29910623	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCGTGGGCTACGTGGACGACA	CGCCGTGGGCTACGTGGACGACA	-	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	195	472	0	ENST00000376809.5:c.144_166del	p.Gly50ArgfsTer41	p.G50Rfs*41	ENST00000376809	NM_002116.7	47	atCGCCGTGGGCTACGTGGACGACAcg/atcg	2/8	1	2	FACETS	0.686	0.637	0.736	0.686	0.637	0.736	SUBCLONAL	1	TRUE	1	0.81	2		472	702	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324901	31324901	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1386205687	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	185	422	0	ENST00000412585.2:c.35T>C	p.Leu12Pro	p.L12P	ENST00000412585	NM_005514.6	12	cTg/cCg	1/8	1	2	FACETS	0.659	0.611	0.709	0.659	0.611	0.709	SUBCLONAL	1	TRUE	1	0.81	2		422	693	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729612	41729612	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1202073030	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	344	586	0	ENST00000242208.4:c.917G>A	p.Arg306His	p.R306H	ENST00000242208	NM_002192.2	306	cGc/cAc	3/3	1	2	FACETS	0.967	0.919	1	0.967	0.919	1	CLONAL	1	TRUE	1	0.81	2		586	878	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829092	128829092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	224	339	0	ENST00000249373.3:c.100G>A	p.Gly34Arg	p.G34R	ENST00000249373	NM_005631.4	34	Ggg/Agg	1/12	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.81	2		339	495	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145736923	145736923	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1375776479	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	296	498	0	ENST00000428558.2:c.3518C>T	p.Pro1173Leu	p.P1173L	ENST00000428558	NM_004260.3	1173	cCg/cTg	22/22	1	2	FACETS	0.984	0.931	1	0.984	0.931	1	CLONAL	1	TRUE	1	0.81	2		498	743	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5462933	5462933	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	322	461	0	ENST00000381577.3:c.494T>C	p.Val165Ala	p.V165A	ENST00000381577	NM_014143.3	165	gTc/gCc	4/7	1	2	FACETS	0.998	0.947	1	0.998	0.947	1	CLONAL	1	TRUE	1	0.81	2		461	797	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994178	21994178	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	267	494	0	ENST00000579755.1:c.153G>T	p.Arg51Ser	p.R51S	ENST00000579755		51	agG/agT	1/3	1				0.864	0.97				CLONAL	1	TRUE	1	0.81	2		494	719	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882000	36882000	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	258	426	0	ENST00000358127.4:c.1012+1G>A		p.X338_splice	ENST00000358127	NM_001280556.1	338			1	2	FACETS	0.913	0.859	0.967	0.913	0.859	0.967	CLONAL	1	TRUE	1	0.81	2		426	698	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759569	133759569	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	372	565	0	ENST00000318560.5:c.1892G>T	p.Arg631Ile	p.R631I	ENST00000318560	NM_005157.4	631	aGa/aTa	11/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.81	2		565	899	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399885	139399885	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	314	532	0	ENST00000277541.6:c.4463A>C	p.Lys1488Thr	p.K1488T	ENST00000277541	NM_017617.3	1488	aAg/aCg	25/34	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.81	2		532	761	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342365	70342365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	325	461	2	ENST00000374080.3:c.1256C>T	p.Ala419Val	p.A419V	ENST00000374080		419	gCa/gTa	9/45	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.81	2		463	794	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690847	89690847	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776667	NA	P-0066841-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	23	283	0	ENST00000371953.3:c.253+1G>A		p.X85_splice	ENST00000371953	NM_000314.4	85			0.535289991557086	1	FACETS	0.176	0.136	0.221	0.176	0.136	0.221	SUBCLONAL	1	TRUE	0	0.539060798580814	1		283	355	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720833	89720833	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066841-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	42	164	0	ENST00000371953.3:c.986del	p.Asn329IlefsTer15	p.N329Ifs*15	ENST00000371953	NM_000314.4	328	gcA/gc	8/9	0.535289991557086	1	FACETS	0.527	0.444	0.617	0.527	0.444	0.617	SUBCLONAL	1	TRUE	0	0.539060798580814	1		164	216	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	164	317	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		317	416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	373	567	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		567	765	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514311	69514311	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	108	466	0	ENST00000294312.3:c.370G>A	p.Glu124Lys	p.E124K	ENST00000294312	NM_005117.2	124	Gag/Aag	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		466	669	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77043819	77043819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371644543	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	255	488	0	ENST00000356341.3:c.1507G>A	p.Glu503Lys	p.E503K	ENST00000356341	NM_002576.4	503	Gag/Aag	14/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		488	723	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650625	18650625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	105	485	0	ENST00000266497.5:c.2836G>A	p.Glu946Lys	p.E946K	ENST00000266497		946	Gaa/Aaa	20/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		485	533	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243514	46243514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140086050	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	112	423	0	ENST00000334344.6:c.1867C>T	p.Arg623Cys	p.R623C	ENST00000334344	NM_152641.2	623	Cgt/Tgt	14/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		423	571	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926248	112926248	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs121918468	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	140	405	0	ENST00000351677.2:c.1381G>A	p.Ala461Thr	p.A461T	ENST00000351677	NM_002834.3	461	Gct/Act	12/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		405	659	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219278	133219278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	118	472	0	ENST00000320574.5:c.4766C>T	p.Ser1589Phe	p.S1589F	ENST00000320574	NM_006231.2	1589	tCc/tTc	37/49	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		472	662	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066721	30066721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1263767545	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	119	403	1	ENST00000331968.5:c.2410C>T	p.Pro804Ser	p.P804S	ENST00000331968	NM_002742.2	804	Ccc/Tcc	16/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		404	659	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576115	88576115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	126	433	0	ENST00000360948.2:c.1558G>A	p.Gly520Arg	p.G520R	ENST00000360948	NM_001012338.2	520	Gga/Aga	13/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		433	603	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434578	99434578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199789940	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	146	434	0	ENST00000268035.6:c.665G>A	p.Arg222Gln	p.R222Q	ENST00000268035	NM_000875.3	222	cGg/cAg	3/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		434	570	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819257	3819257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767573846	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	327	514	0	ENST00000262367.5:c.2978C>T	p.Pro993Leu	p.P993L	ENST00000262367	NM_004380.2	993	cCt/cTt	15/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		514	678	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821815	72821815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770453754	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	324	590	0	ENST00000268489.5:c.10360G>A	p.Asp3454Asn	p.D3454N	ENST00000268489	NM_006885.3	3454	Gac/Aac	10/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		590	806	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81927346	81927346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	110	348	0	ENST00000359376.3:c.1019C>T	p.Ser340Leu	p.S340L	ENST00000359376	NM_002661.3	340	tCg/tTg	12/33	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		348	597	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17120454	17120454	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	151	468	0	ENST00000285071.4:c.1105C>T	p.Leu369Phe	p.L369F	ENST00000285071	NM_144997.5	369	Ctc/Ttc	10/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		468	637	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214893	36214894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	236	472	0	ENST00000222270.7:c.3325dup	p.Arg1109ProfsTer4	p.R1109Pfs*4	ENST00000222270	NM_014727.1	1107	acc/aCcc	8/37	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		472	961	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281904	39281904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886041241	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	95	355	0	ENST00000402219.2:c.571G>A	p.Glu191Lys	p.E191K	ENST00000402219	NM_005633.3	191	Gaa/Aaa	5/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		355	510	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149861	99149861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	141	460	0	ENST00000074304.5:c.173C>T	p.Pro58Leu	p.P58L	ENST00000074304	NM_001134224.1	58	cCa/cTa	5/26	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		460	662	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538374	9538374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868564987	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	163	494	0	ENST00000353224.5:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000353224	NM_177990.2	542	Gaa/Aaa	7/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		494	761	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561040	9561040	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	264	518	0	ENST00000353224.5:c.742G>A	p.Glu248Lys	p.E248K	ENST00000353224	NM_177990.2	248	Gag/Aag	4/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		518	830	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733255	40733255	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	155	546	0	ENST00000373198.4:c.3551G>A	p.Arg1184Lys	p.R1184K	ENST00000373198	NM_133170.3	1184	aGg/aAg	26/32	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		546	898	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743871	40743871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	254	405	0	ENST00000373198.4:c.3124G>A	p.Glu1042Lys	p.E1042K	ENST00000373198	NM_133170.3	1042	Gaa/Aaa	23/32	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		405	747	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944422	40944422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	261	498	0	ENST00000373198.4:c.2080C>T	p.Pro694Ser	p.P694S	ENST00000373198	NM_133170.3	694	Cct/Tct	12/32	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		498	881	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	142	494	0	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		494	827	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973958	55973958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769193899	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	314	527	0	ENST00000263923.4:c.1358C>T	p.Pro453Leu	p.P453L	ENST00000263923	NM_002253.2	453	cCg/cTg	10/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		527	727	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106194076	106194076	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	47	397	0	ENST00000380013.4:c.4537+1G>A		p.X1513_splice	ENST00000380013	NM_001127208.2	1513			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		397	626	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628824	187628824	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	159	510	0	ENST00000441802.2:c.2158C>G	p.Leu720Val	p.L720V	ENST00000441802	NM_005245.3	720	Ctt/Gtt	2/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		510	765	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564686	86564686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751440049	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	76	591	0	ENST00000274376.6:c.418C>T	p.Pro140Ser	p.P140S	ENST00000274376	NM_002890.2	140	Ccc/Tcc	1/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		591	798	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441389	149441389	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	273	515	0	ENST00000286301.3:c.1650G>A	p.Trp550Ter	p.W550*	ENST00000286301	NM_005211.3	550	tgG/tgA	12/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		515	702	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043925	180043925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	54	471	0	ENST00000261937.6:c.3071G>A	p.Gly1024Glu	p.G1024E	ENST00000261937	NM_182925.4	1024	gGg/gAg	22/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		471	605	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909291	41909291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778979671	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	123	460	0	ENST00000372991.4:c.97C>T	p.Arg33Cys	p.R33C	ENST00000372991	NM_001760.3	33	Cgc/Tgc	1/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		460	660	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553584	106553584	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	177	463	0	ENST00000369096.4:c.1549C>T	p.Pro517Ser	p.P517S	ENST00000369096	NM_001198.3	517	Ccc/Tcc	5/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		463	644	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459558	50459558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	237	396	0	ENST00000331340.3:c.847C>T	p.Leu283Phe	p.L283F	ENST00000331340	NM_006060.4	283	Ctt/Ttt	7/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		396	1087	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392143	81392143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	157	421	0	ENST00000222390.5:c.134C>T	p.Ser45Leu	p.S45L	ENST00000222390	NM_000601.4	45	tCa/tTa	2/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		421	869	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340339	116340339	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	158	381	0	ENST00000397752.3:c.1200+1G>A		p.X400_splice	ENST00000397752	NM_000245.2	400			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		381	811	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418998	116418998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369838973	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	52	376	0	ENST00000397752.3:c.3509G>A	p.Arg1170Gln	p.R1170Q	ENST00000397752	NM_000245.2	1170	cGa/cAa	17/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		376	857	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992692	68992692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529924687	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	151	443	0	ENST00000288368.4:c.1657G>A	p.Glu553Lys	p.E553K	ENST00000288368	NM_024870.2	553	Gaa/Aaa	16/40	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		443	676	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158095	27158095	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	151	567	0	ENST00000380036.4:c.319C>T	p.Arg107Ter	p.R107*	ENST00000380036	NM_000459.3	107	Cga/Tga	2/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		567	614	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27220088	27220088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760667841	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	129	452	0	ENST00000380036.4:c.3145G>A	p.Glu1049Lys	p.E1049K	ENST00000380036	NM_000459.3	1049	Gag/Aag	21/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		452	586	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932176	36932176	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	211	585	0	ENST00000361632.4:c.2293G>A	p.Gly765Arg	p.G765R	ENST00000361632		765	Ggg/Agg	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		585	880	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731068	162731068	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	178	501	1	ENST00000367921.3:c.923C>T	p.Ser308Phe	p.S308F	ENST00000367921	NM_006182.2	308	tCt/tTt	9/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		502	889	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552720	226552720	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1479824551	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	70	525	1	ENST00000366794.5:c.2641C>T	p.Pro881Ser	p.P881S	ENST00000366794	NM_001618.3	881	Ccg/Tcg	19/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		526	898	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123353290	123353291	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	155	663	0	ENST00000358487.5:c.41_42delinsTT	p.Thr14Ile	p.T14I	ENST00000358487	NM_000141.4	14	aCC/aTT	2/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		663	803	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377252	118377252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	300	561	0	ENST00000534358.1:c.10645C>T	p.Pro3549Ser	p.P3549S	ENST00000534358	NM_005933.3	3549	Cct/Tct	27/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		561	755	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148923	119148923	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	194	442	0	ENST00000264033.4:c.1143T>G	p.Cys381Trp	p.C381W	ENST00000264033	NM_005188.3	381	tgT/tgG	8/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		442	522	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406367	406367	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	95	465	0	ENST00000399788.2:c.4075-1G>A		p.X1359_splice	ENST00000399788	NM_001042603.1	1359			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		465	622	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428260	49428260	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	144	537	0	ENST00000301067.7:c.10441-1G>A		p.X3481_splice	ENST00000301067	NM_003482.3	3481			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		537	785	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858611	57858611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774885952	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	171	508	0	ENST00000228682.2:c.349C>T	p.Pro117Ser	p.P117S	ENST00000228682	NM_005269.2	117	Cca/Tca	4/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		508	715	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865417	57865417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	195	618	0	ENST00000228682.2:c.2894C>T	p.Pro965Leu	p.P965L	ENST00000228682	NM_005269.2	965	cCc/cTc	12/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		618	852	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219916	133219916	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1555222946	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	246	513	0	ENST00000320574.5:c.4445G>A	p.Gly1482Glu	p.G1482E	ENST00000320574	NM_006231.2	1482	gGg/gAg	35/49	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		513	747	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911607	32911607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	46	375	0	ENST00000380152.3:c.3115C>T	p.Pro1039Ser	p.P1039S	ENST00000380152		1039	Cct/Tct	11/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		375	440	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281623	49281623	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	169	471	0	ENST00000282018.3:c.670A>C	p.Ile224Leu	p.I224L	ENST00000282018	NM_020377.2	224	Atc/Ctc	1/1	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		471	701	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472654	88472654	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	118	522	0	ENST00000360948.2:c.1901C>T	p.Pro634Leu	p.P634L	ENST00000360948	NM_001012338.2	634	cCa/cTa	16/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		522	529	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50830411	50830411	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	275	452	0	ENST00000398568.2:c.2854T>A	p.Tyr952Asn	p.Y952N	ENST00000398568	NM_001042412.1	952	Tac/Aac	18/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		452	719	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842367	68842367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777714207	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	131	464	0	ENST00000261769.5:c.428C>T	p.Pro143Leu	p.P143L	ENST00000261769	NM_004360.3	143	cCc/cTc	4/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		464	815	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347302	89347302	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	315	572	0	ENST00000301030.4:c.5648T>C	p.Phe1883Ser	p.F1883S	ENST00000301030	NM_001256183.1	1883	tTc/tCc	9/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		572	810	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348074	89348074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	334	557	0	ENST00000301030.4:c.4876C>T	p.Pro1626Ser	p.P1626S	ENST00000301030	NM_001256183.1	1626	Ccg/Tcg	9/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		557	791	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548946	29548946	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	50	165	0	ENST00000356175.3:c.1720A>G	p.Ser574Gly	p.S574G	ENST00000356175	NM_000267.3	574	Agc/Ggc	15/57	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		165	187	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559105	29559105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	56	157	0	ENST00000356175.3:c.3212C>T	p.Ala1071Val	p.A1071V	ENST00000356175	NM_000267.3	1071	gCa/gTa	25/57	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		157	272	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587446	29587446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	100	423	0	ENST00000356175.3:c.4427C>T	p.Ser1476Phe	p.S1476F	ENST00000356175	NM_000267.3	1476	tCc/tTc	33/57	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		423	620	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652974	29652974	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	123	560	0	ENST00000356175.3:c.4909T>G	p.Phe1637Val	p.F1637V	ENST00000356175	NM_000267.3	1637	Ttt/Gtt	36/57	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		560	721	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690283	33690283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754434472	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	168	529	0	ENST00000308377.4:c.544C>T	p.Pro182Ser	p.P182S	ENST00000308377	NM_152270.3	182	Cct/Tct	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		529	762	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690643	33690643	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs758613276	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	218	567	1	ENST00000308377.4:c.184C>T	p.Arg62Ter	p.R62*	ENST00000308377	NM_152270.3	62	Cga/Tga	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		568	770	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682459	37682459	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	216	481	0	ENST00000447079.4:c.3650T>G	p.Leu1217Arg	p.L1217R	ENST00000447079	NM_015083.1	1217	cTg/cGg	13/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		481	712	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272242	15272243	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	119	522	2	ENST00000263388.2:c.6196_6197delinsTT	p.Pro2066Phe	p.P2066F	ENST00000263388	NM_000435.2	2066	CCc/TTc	33/33	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		524	648	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257458	19257458	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	150	577	0	ENST00000162023.5:c.676-1G>A		p.X226_splice	ENST00000162023		226			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		577	836	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312689	30312689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751127659	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	341	474	0	ENST00000262643.3:c.670G>A	p.Asp224Asn	p.D224N	ENST00000262643	NM_001238.2	224	Gat/Aat	8/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		474	879	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211952	36211952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242797965	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	316	510	0	ENST00000222270.7:c.1703C>T	p.Thr568Ile	p.T568I	ENST00000222270	NM_014727.1	568	aCc/aTc	3/37	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		510	1188	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719888	52719889	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	138	532	1	ENST00000322088.6:c.1100_1101delinsTT	p.Pro367Leu	p.P367L	ENST00000322088	NM_014225.5	367	cCC/cTT	9/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		533	985	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285882	39285882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	91	360	0	ENST00000402219.2:c.277G>A	p.Ala93Thr	p.A93T	ENST00000402219	NM_005633.3	93	Gct/Act	3/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		360	486	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116271	209116271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	90	420	0	ENST00000345146.2:c.5C>T	p.Ser2Phe	p.S2F	ENST00000345146	NM_005896.2	2	tCc/tTc	3/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		420	599	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251820	212251820	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	123	543	0	ENST00000342788.4:c.3239C>T	p.Pro1080Leu	p.P1080L	ENST00000342788	NM_005235.2	1080	cCc/cTc	27/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		543	739	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439720	220439721	+	missense_variant	Missense_Mutation	DNP	CC	CC	TG	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	80	562	0	ENST00000243786.2:c.573_574delinsTG	p.Pro192Ala	p.P192A	ENST00000243786	NM_002191.3	191	caCCcc/caTGcc	2/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		562	783	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164539	36164539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	111	493	0	ENST00000300305.3:c.1336C>T	p.Leu446Phe	p.L446F	ENST00000300305		446	Ctc/Ttc	8/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		493	650	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866447	42866447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	308	602	0	ENST00000398585.3:c.185C>T	p.Pro62Leu	p.P62L	ENST00000398585	NM_001135099.1	62	cCc/cTc	3/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		602	923	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21344754	21344754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	298	448	0	ENST00000215739.8:c.731C>T	p.Ser244Phe	p.S244F	ENST00000215739	NM_006767.3	244	tCt/tTt	8/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		448	764	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272217	142272217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	85	381	0	ENST00000350721.4:c.2657C>T	p.Pro886Leu	p.P886L	ENST00000350721	NM_001184.3	886	cCa/cTa	13/47	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		381	661	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156410	106156411	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	64	551	0	ENST00000380013.4:c.1311_1312delinsTT	p.Pro438Ser	p.P438S	ENST00000380013	NM_001127208.2	437	taCCcc/taTTcc	3/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		551	811	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158442	106158442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	64	466	0	ENST00000380013.4:c.3343C>T	p.Pro1115Ser	p.P1115S	ENST00000380013	NM_001127208.2	1115	Cct/Tct	3/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		466	643	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032257	26032257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	116	478	0	ENST00000244661.2:c.32C>T	p.Ser11Phe	p.S11F	ENST00000244661	NM_003537.3	11	tCc/tTc	1/1	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		478	846	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271492	26271492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	155	631	0	ENST00000305910.3:c.121C>T	p.Arg41Cys	p.R41C	ENST00000305910	NM_003534.2	41	Cgc/Tgc	1/1	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		631	1102	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553223	106553224	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	100	636	0	ENST00000369096.4:c.1188_1189delinsTT	p.His397Tyr	p.H397Y	ENST00000369096	NM_001198.3	396	ccCCac/ccTTac	5/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		636	644	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609777	117609777	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	161	479	0	ENST00000368508.3:c.6922G>A	p.Glu2308Lys	p.E2308K	ENST00000368508	NM_002944.2	2308	Gaa/Aaa	43/43	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		479	621	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397726	116397726	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	118	475	1	ENST00000397752.3:c.2000G>A	p.Gly667Asp	p.G667D	ENST00000397752	NM_000245.2	667	gGt/gAt	8/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		476	1009	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439625	140439625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1257391548	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	69	252	0	ENST00000288602.6:c.2114C>T	p.Pro705Leu	p.P705L	ENST00000288602	NM_004333.4	705	cCa/cTa	17/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		252	601	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194568	29194568	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	59	518	0	ENST00000240100.2:c.1160C>T	p.Pro387Leu	p.P387L	ENST00000240100	NM_001394.6	387	cCc/cTc	4/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		518	810	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992746	68992746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	155	488	0	ENST00000288368.4:c.1711G>A	p.Gly571Arg	p.G571R	ENST00000288368	NM_024870.2	571	Gga/Aga	16/40	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		488	713	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5055790	5055790	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	68	331	0	ENST00000381652.3:c.1056+2T>G		p.X352_splice	ENST00000381652	NM_004972.3	352			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		331	346	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486212	8486212	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	240	508	0	ENST00000356435.5:c.2605A>G	p.Thr869Ala	p.T869A	ENST00000356435		869	Act/Gct	17/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		508	573	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970915	21970917	+	frameshift_variant	Frame_Shift_Del	DEL	GCG	GCG	CA	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	234	447	0	ENST00000304494.5:c.441_443delinsTG	p.Ala148GlyfsTer45	p.A148Gfs*45	ENST00000304494	NM_000077.4	147	gcCGCg/gcTGg	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		447	518	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293632	137293632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759150362	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	143	586	0	ENST00000481739.1:c.183G>A	p.Met61Ile	p.M61I	ENST00000481739	NM_002957.4	61	atG/atA	2/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		586	666	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611877	100611877	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	135	246	0	ENST00000308731.7:c.1244T>G	p.Val415Gly	p.V415G	ENST00000308731	NM_000061.2	415	gTa/gGa	14/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		246	312	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188971	11188971	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	27	426	0	ENST00000361445.4:c.5752G>T	p.Asp1918Tyr	p.D1918Y	ENST00000361445	NM_004958.3	1918	Gat/Tat	41/58	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		426	458	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21348525	21348525	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1331354829	NA	P-0066843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	224	517	0	ENST00000215739.8:c.1582C>T	p.Leu528Phe	p.L528F	ENST00000215739	NM_006767.3	528	Ctc/Ttc	14/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		517	1358	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0066845-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	233	415	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		415	531	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409824	63409824	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066845-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	136	594	0	ENST00000330258.3:c.3343G>T	p.Glu1115Ter	p.E1115*	ENST00000330258	NM_152424.3	1115	Gag/Tag	2/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		594	652	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983059	111983059	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066845-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	91	549	0	ENST00000368678.4:c.1488G>C	p.Met496Ile	p.M496I	ENST00000368678		496	atG/atC	13/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		549	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578484	7578485	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1064793929	NA	P-0066863-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	285	574	0	ENST00000269305.4:c.445dup	p.Ser149PhefsTer32	p.S149Ffs*32	ENST00000269305	NM_001126112.2	149	tcc/tTcc	5/11	0.545001693970643	2	FACETS	0.992	0.944	1	0.992	0.944	1	CLONAL	2	TRUE	0	0.538071701192728	2		574	534	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42861436	42861437	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0066863-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	129	342	0	ENST00000398585.3:c.433_434del	p.Phe145HisfsTer23	p.F145Hfs*23	ENST00000398585	NM_001135099.1	145	TTc/c	4/14	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.538071701192728	2		342	369	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753648	42753649	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCGG	novel	NA	P-0066863-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	240	496	0	ENST00000222329.4:c.612_615dup	p.Ala206ProfsTer24	p.A206Pfs*24	ENST00000222329	NM_006494.2	205	-/CCGC	4/4	0.503121244494309	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	2	0.538071701192728	4		496	662	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0066864-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	207	389	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.482801362972165	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.481394384955711	2		389	364	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031402	11031402	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066864-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	206	503	0	ENST00000327064.4:c.1402G>C	p.Asp468His	p.D468H	ENST00000327064	NM_199141.1	468	Gat/Cat	12/16	0.482469011951306	4	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	2	0.481394384955711	4		503	632	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670944	30670954	+	frameshift_variant	Frame_Shift_Del	DEL	TGTCCGGCGGA	TGTCCGGCGGA	-	novel	NA	P-0066864-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	95	436	0	ENST00000376406.3:c.5792_5802del	p.Ile1931SerfsTer33	p.I1931Sfs*33	ENST00000376406	NM_014641.2	1931	aTCCGCCGGACA/a	12/15	0.482801362972165	3	FACETS	0.881	0.786	0.981	0.44	0.393	0.491	CLONAL	1	TRUE	1	0.481394384955711	3		436	556	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820993	32820993	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066864-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	48	427	0	ENST00000354258.4:c.601G>C	p.Val201Leu	p.V201L	ENST00000354258	NM_000593.5	201	Gtt/Ctt	1/11	0.482801362972165	3	FACETS	0.439	0.37	0.514	0.219	0.185	0.257	SUBCLONAL	1	TRUE	1	0.481394384955711	3		427	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0066868-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	265	412	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.731628240438456	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.731628240438456	1		412	423	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910404	29910404	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0066868-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	205	430	0	ENST00000376809.5:c.73+1G>C		p.X25_splice	ENST00000376809	NM_002116.7	25			0.231694444910464	3	FACETS	1	0.99	1	0.679	0.634	0.724	INDETERMINATE	1	TRUE	1	0.731628240438456	3		430	564	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551600	150551600	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066868-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	252	395	0	ENST00000369026.2:c.407A>G	p.Lys136Arg	p.K136R	ENST00000369026	NM_021960.4	136	aAg/aGg	1/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.731628240438456	2		395	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0066869-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	390	567	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.855213161493332	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.855213161493332	2		567	428	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0066869-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	40	403	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	0.855213161493332	5	FACETS	0.293	0.243	0.35	0.098	0.081	0.117	SUBCLONAL	1	TRUE	2	0.855213161493332	5		403	728	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030487	49030487	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0066869-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	407	373	0	ENST00000267163.4:c.1960+2T>G		p.X654_splice	ENST00000267163	NM_000321.2	654			0.855213161493332	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.855213161493332	3		373	442	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042647	42042648	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0066869-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	181	563	0	ENST00000219905.7:c.6843dup	p.Gln2282ThrfsTer14	p.Q2282Tfs*14	ENST00000219905	NM_001164273.1	2281	ata/atAa	17/24	1	2	FACETS	0.991	0.925	1	0.991	0.925	1	CLONAL	1	TRUE	1	0.855213161493332	2		563	427	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1646363	1646363	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143529809	NA	P-0066869-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	77	490	0	ENST00000344749.5:c.136G>A	p.Gly46Arg	p.G46R	ENST00000344749	NM_001136139.2	46	Gga/Aga	3/19	0.855213161493332	2	FACETS	0.641	0.569	0.716	0.32	0.284	0.358	SUBCLONAL	1	TRUE	0	0.855213161493332	2		490	281	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0066870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	254	171	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		171	353	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652097	36652098	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0066870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	163	403	0	ENST00000244741.5:c.222dup	p.Lys75GlnfsTer14	p.K75Qfs*14	ENST00000244741	NM_000389.4	73	-/C	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		403	511	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539177	187539177	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	129	440	0	ENST00000441802.2:c.8563G>T	p.Glu2855Ter	p.E2855*	ENST00000441802	NM_005245.3	2855	Gaa/Taa	10/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		440	418	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982087	93982087	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	116	371	0	ENST00000369303.4:c.1378G>T	p.Glu460Ter	p.E460*	ENST00000369303	NM_004440.3	460	Gag/Tag	6/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		371	561	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008984	152008984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	103	367	0	ENST00000262189.6:c.638C>T	p.Thr213Ile	p.T213I	ENST00000262189	NM_170606.2	213	aCc/aTc	5/59	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		367	421	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615079	100615079	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	23	150	0	ENST00000308731.7:c.836A>T	p.Tyr279Phe	p.Y279F	ENST00000308731	NM_000061.2	279	tAt/tTt	9/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		150	73	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391244	139391245	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	141	431	0	ENST00000277541.6:c.6946dup	p.Ser2316LysfsTer38	p.S2316Kfs*38	ENST00000277541	NM_017617.3	2316	agc/aAgc	34/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		431	719	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197259	26197259	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	242	534	0	ENST00000356476.2:c.220G>T	p.Glu74Ter	p.E74*	ENST00000356476		74	Gag/Tag	1/1	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		534	612	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557740	187557740	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0066870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	60	302	0	ENST00000441802.2:c.3971C>G	p.Ser1324Ter	p.S1324*	ENST00000441802	NM_005245.3	1324	tCa/tGa	5/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		302	260	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383471	31383471	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	139	426	0	ENST00000328111.2:c.1268A>T	p.Asp423Val	p.D423V	ENST00000328111	NM_006892.3	423	gAt/gTt	12/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		426	464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0066871-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	554	396	1	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	0.786284824115835	2	FACETS	0.981	0.957	1	0.981	0.957	1	CLONAL	2	TRUE	0	0.786284824115835	2		397	718	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862901	117862902	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066871-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	160	282	0	ENST00000297338.2:c.1575dup	p.Glu526ArgfsTer11	p.E526Rfs*11	ENST00000297338	NM_006265.2	525	-/A	12/14	0.388306186617697	3	FACETS	0.88	0.81	0.953	0.44	0.405	0.477	INDETERMINATE	1	TRUE	1	0.786284824115835	3		282	644	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1688623	1688623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066871-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	207	306	0	ENST00000378625.1:c.702G>A	p.Met234Ile	p.M234I	ENST00000378625	NM_001198994.1	234	atG/atA	6/14	0.786284824115835	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.786284824115835	1		306	312	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426643	49426647	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGC	GAAGC	-	novel	NA	P-0066871-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	393	586	0	ENST00000301067.7:c.11841_11845del	p.Leu3948ThrfsTer62	p.L3948Tfs*62	ENST00000301067	NM_003482.3	3947	caGCTTCaa/caaa	39/54	1	2	FACETS	0.907	0.864	0.951	0.907	0.864	0.951	CLONAL	1	TRUE	1	0.786284824115835	2		586	1102	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436881	49436881	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066871-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	274	410	0	ENST00000301067.7:c.5622del	p.Leu1875Ter	p.L1875*	ENST00000301067	NM_003482.3	1874	gaC/ga	25/54	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.786284824115835	2		410	685	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881511	48881512	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0066871-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	486	340	0	ENST00000267163.4:c.234_235del	p.Trp78Ter	p.W78*	ENST00000267163	NM_000321.2	78	tGG/t	2/27	0.786284824115835	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.786284824115835	2		340	606	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436209	110436209	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318843123	NA	P-0066871-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	223	408	0	ENST00000375856.3:c.2192C>T	p.Ser731Leu	p.S731L	ENST00000375856	NM_003749.2	731	tCg/tTg	1/2	0.786284824115835	2	FACETS	0.77	0.719	0.821	0.385	0.359	0.411	SUBCLONAL	1	TRUE	0	0.786284824115835	2		408	737	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188151	142188179	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CATATAAAAAGGTAAAAGACCCTTTTACC	CATATAAAAAGGTAAAAGACCCTTTTACC	-	novel	NA	P-0066871-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	116	202	0	ENST00000350721.4:c.6552_6552+28del		p.X2184_splice	ENST00000350721	NM_001184.3	2184		38/47	1	2	FACETS	0.9	0.821	0.98	0.9	0.821	0.98	CLONAL	1	TRUE	1	0.786284824115835	2		202	328	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522551	176522551	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774571806	NA	P-0066872-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	105	638	0	ENST00000292408.4:c.1648G>A	p.Val550Met	p.V550M	ENST00000292408	NM_213647.1	550	Gtg/Atg	13/18	0.293124586846461	4	FACETS	1	0.976	1	0.647	0.581	0.716	CLONAL	1	TRUE	2	0.427448565962853	4		638	542	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0066873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	143	305	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.280292718648717	2	FACETS	0.981	0.9	1	0.981	0.9	1	CLONAL	2	TRUE	0	0.280292718648717	2		305	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0066873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	177	410	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.218113571627202	2	FACETS	1	0.989	1	0.735	0.678	0.795	CLONAL	1	TRUE	0	0.280292718648717	2		410	859	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857549	57857549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	141	360	1	ENST00000228682.2:c.79del	p.Ala27ProfsTer51	p.A27Pfs*51	ENST00000228682	NM_005269.2	25	caG/ca	2/12	0.201867917106537	3	FACETS	1	0.982	1	0.65	0.592	0.711	CLONAL	1	TRUE	1	0.280292718648717	3		361	882	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980879	40980879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs192708116	NA	P-0066873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	89	380	0	ENST00000373198.4:c.1607C>T	p.Ser536Leu	p.S536L	ENST00000373198	NM_133170.3	536	tCg/tTg	10/32	0.210991402225419	5	FACETS	0.745	0.659	0.839	0.248	0.219	0.28	SUBCLONAL	1	TRUE	2	0.280292718648717	5		380	1210	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44896898	44896898	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0066873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	79	264	0	ENST00000377967.4:c.620-2A>T		p.X207_splice	ENST00000377967	NM_021140.2	207			0.206340091214274	2	FACETS	1	0.975	1	0.712	0.629	0.799	CLONAL	1	TRUE	0	0.280292718648717	2		264	396	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911460	101911460	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0066873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	174	297	0	ENST00000374994.4:c.1387-2A>T		p.X463_splice	ENST00000374994	NM_004612.2	463			0.280292718648717	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.280292718648717	2		297	568	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857727	9857727	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0066873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	188	474	0	ENST00000330684.3:c.3674C>G	p.Ser1225Ter	p.S1225*	ENST00000330684	NM_001134407.1	1225	tCa/tGa	13/13	0.201867917106537	3	FACETS	1	0.99	1	0.748	0.691	0.808	CLONAL	1	TRUE	1	0.280292718648717	3		474	1022	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869523	102869523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	68	380	0	ENST00000307046.8:c.118C>T	p.Leu40Phe	p.L40F	ENST00000307046	NM_001111285.1	40	Ctc/Ttc	2/4	0.201867917106537	3	FACETS	0.687	0.597	0.785	0.344	0.298	0.393	SUBCLONAL	1	TRUE	1	0.280292718648717	3		380	805	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206942002	206942002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	132	321	0	ENST00000423557.1:c.516G>A	p.Met172Ile	p.M172I	ENST00000423557	NM_000572.2	172	atG/atA	5/5	0.201867917106537	3	FACETS	0.762	0.692	0.834	0.762	0.692	0.834	SUBCLONAL	2	TRUE	1	0.280292718648717	3		321	705	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752964	42752964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749808726	NA	P-0066873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	207	424	0	ENST00000222329.4:c.1300G>A	p.Glu434Lys	p.E434K	ENST00000222329	NM_006494.2	434	Gag/Aag	4/4	0.174114314996012	4	FACETS	0.834	0.773	0.897	0.834	0.773	0.897	CLONAL	2	TRUE	2	0.280292718648717	4		424	1134	SUCCESS
ATM	472	MSKCC	GRCh37	11	108181023	108181023	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	112	298	0	ENST00000278616.4:c.5899A>T	p.Met1967Leu	p.M1967L	ENST00000278616	NM_000051.3	1967	Atg/Ttg	39/63	0.196762951405044	5	FACETS	0.938	0.846	1	0.625	0.564	0.69	CLONAL	2	TRUE	2	0.280292718648717	5		298	605	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273995	10273995	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	158	480	0	ENST00000330684.3:c.274G>T	p.Gly92Trp	p.G92W	ENST00000330684	NM_001134407.1	92	Ggg/Tgg	2/13	0.201867917106537	3	FACETS	1	0.988	1	0.734	0.672	0.798	CLONAL	1	TRUE	1	0.280292718648717	3		480	876	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248600	212248600	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	28	468	0	ENST00000342788.4:c.3667A>C	p.Lys1223Gln	p.K1223Q	ENST00000342788	NM_005235.2	1223	Aag/Cag	28/28	0.201867917106537	3	FACETS	0.239	0.19	0.295	0.119	0.095	0.148	SUBCLONAL	1	TRUE	1	0.280292718648717	3		468	954	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755579	39755579	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	223	446	0	ENST00000288319.7:c.1186G>T	p.Ala396Ser	p.A396S	ENST00000288319	NM_182918.3	396	Gcc/Tcc	10/10	0.201867917106537	3	FACETS	0.849	0.79	0.91	0.849	0.79	0.91	CLONAL	2	TRUE	1	0.280292718648717	3		446	1068	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845223	151845223	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	221	412	1	ENST00000262189.6:c.13789C>A	p.Arg4597Ser	p.R4597S	ENST00000262189	NM_170606.2	4597	Cgc/Agc	52/59	0.196762951405044	5	FACETS	0.992	0.922	1	0.661	0.615	0.71	CLONAL	2	TRUE	2	0.280292718648717	5		413	1129	SUCCESS
REST	5978	MSKCC	GRCh37	4	57777079	57777079	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	188	382	0	ENST00000309042.7:c.275G>T	p.Gly92Val	p.G92V	ENST00000309042	NM_005612.4	92	gGa/gTa	2/4	0.201867917106537	3	FACETS	0.884	0.818	0.953	0.884	0.818	0.953	CLONAL	2	TRUE	1	0.280292718648717	3		382	865	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911956	94911956	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	53	300	0	ENST00000536441.1:c.974C>G	p.Ser325Cys	p.S325C	ENST00000536441	NM_144665.3	325	tCt/tGt	7/10	0.196762951405044	5	FACETS	0.77	0.655	0.895	0.257	0.218	0.299	SUBCLONAL	1	TRUE	2	0.280292718648717	5		300	698	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3827626	3827626	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	120	285	0	ENST00000262367.5:c.2146C>T	p.Gln716Ter	p.Q716*	ENST00000262367	NM_004380.2	716	Caa/Taa	11/31	0.201867917106537	3	FACETS	0.78	0.706	0.857	0.78	0.706	0.857	SUBCLONAL	2	TRUE	1	0.280292718648717	3		285	626	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508657	106508657	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	148	422	0	ENST00000359195.3:c.651C>A	p.Asn217Lys	p.N217K	ENST00000359195	NM_002649.2	217	aaC/aaA	2/11	0.196762951405044	5	FACETS	1	0.987	1	0.495	0.451	0.541	CLONAL	1	TRUE	2	0.280292718648717	5		422	1010	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146725	185146725	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	89	459	0	ENST00000265026.3:c.356A>G	p.Gln119Arg	p.Q119R	ENST00000265026	NM_004721.4	119	cAg/cGg	2/14	0.212106448896499	4	FACETS	0.814	0.72	0.915	0.271	0.24	0.305	CLONAL	1	TRUE	1	0.280292718648717	4		459	999	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645906	215645906	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758140052	NA	P-0066873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	80	435	0	ENST00000260947.4:c.692C>T	p.Ser231Phe	p.S231F	ENST00000260947	NM_000465.2	231	tCc/tTc	4/11	0.201867917106537	3	FACETS	0.798	0.701	0.901	0.399	0.35	0.451	CLONAL	1	TRUE	1	0.280292718648717	3		435	816	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220659	1220659	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	163	394	0	ENST00000326873.7:c.677A>T	p.Asn226Ile	p.N226I	ENST00000326873	NM_000455.4	226	aAc/aTc	5/10	0.206340091214274	2	FACETS	0.801	0.737	0.868	0.801	0.737	0.868	CLONAL	2	TRUE	0	0.280292718648717	2		394	726	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251717	212251718	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	A	novel	NA	P-0066873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	173	450	0	ENST00000342788.4:c.3341_3342delinsT	p.Pro1114LeufsTer38	p.P1114Lfs*38	ENST00000342788	NM_005235.2	1114	cCA/cT	27/28	0.201867917106537	3	FACETS	1	0.986	1	0.674	0.62	0.731	CLONAL	1	TRUE	1	0.280292718648717	3		450	1044	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0066874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	150	389	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.195465229823436	3	FACETS	0.889	0.815	0.965	0.889	0.815	0.965	CLONAL	3	FALSE	0	0.195465229823436	3		389	632	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321286	1321286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780766655	NA	P-0066874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	75	535	0	ENST00000400841.2:c.469G>A	p.Asp157Asn	p.D157N	ENST00000400841		157	Gac/Aac	4/6	0.194698859592673	2	FACETS	0.818	0.719	0.924			1	CLONAL	2	FALSE	NA	0.195465229823436	2		535	469	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376302	118376302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1052748793	NA	P-0066874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	84	685	0	ENST00000534358.1:c.9695G>A	p.Arg3232Gln	p.R3232Q	ENST00000534358	NM_005933.3	3232	cGa/cAa	27/36	0.195465229823436	5	FACETS	1	0.973	1	0.461	0.407	0.52	CLONAL	1	FALSE	2	0.195465229823436	5		685	803	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134270	11134270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs797045981	NA	P-0066874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	97	463	0	ENST00000358026.2:c.2936G>A	p.Arg979Gln	p.R979Q	ENST00000358026	NM_001128849.1	979	cGa/cAa	20/36	NA	2	FACETS	1	0.909	1			1	INDETERMINATE	2	FALSE	NA	0.195465229823436	2		463	488	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197147	106197148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0066874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	58	575	0	ENST00000380013.4:c.5481dup	p.Gln1828AlafsTer18	p.Q1828Afs*18	ENST00000380013	NM_001127208.2	1827	aag/aaGg	11/11	1	2	FACETS	0.973	0.836	1	0.973	0.836	1	CLONAL	1	FALSE	1	0.195465229823436	2		575	610	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158666	26158666	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	21	50	0	ENST00000289316.2:c.269T>C	p.Ile90Thr	p.I90T	ENST00000289316	NM_138720.2	90	aTc/aCc	1/2	0.195465229823436	4	FACETS	1	0.875	1	1	0.875	1	CLONAL	3	FALSE	1	0.195465229823436	4		50	74	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317920	8317920	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200610422	NA	P-0066874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	115	536	0	ENST00000356435.5:c.5693G>A	p.Arg1898His	p.R1898H	ENST00000356435		1898	cGt/cAt	35/35	0.153923167261584	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	FALSE	0	0.195465229823436	2		536	526	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs1057519842	NA	P-0066875-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	137	422	0	ENST00000274335.5:c.1727_1729del	p.Thr576del	p.T576del	ENST00000274335		575	aaGACg/aag	12/15	1	2	FACETS	0.97	0.889	1	0.97	0.889	1	CLONAL	1	TRUE	1	0.629119194257817	2		422	449	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101259	27101259	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066875-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	142	478	0	ENST00000324856.7:c.4541del	p.Thr1514ArgfsTer13	p.T1514Rfs*13	ENST00000324856	NM_006015.4	1514	aCg/ag	18/20	1	2	FACETS	0.885	0.812	0.961	0.885	0.812	0.961	CLONAL	1	TRUE	1	0.629119194257817	2		478	510	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692809	89692809	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs781647403	NA	P-0066875-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	83	202	0	ENST00000371953.3:c.293T>G	p.Leu98Arg	p.L98R	ENST00000371953	NM_000314.4	98	cTa/cGa	5/9	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.629119194257817	2		202	233	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188085	151188085	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867628277	NA	P-0066875-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	104	377	0	ENST00000262187.5:c.68C>T	p.Thr23Met	p.T23M	ENST00000262187	NM_005614.3	23	aCg/aTg	2/8	1	2	FACETS	0.865	0.782	0.953	0.865	0.782	0.953	CLONAL	1	TRUE	1	0.629119194257817	2		377	382	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942835	44942835	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066875-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	154	395	0	ENST00000377967.4:c.3416del	p.Pro1139GlnfsTer19	p.P1139Qfs*19	ENST00000377967	NM_021140.2	1139	Cca/ca	23/29	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.629119194257817	2		395	419	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655348	67655349	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0066875-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	146	455	0	ENST00000264010.4:c.1213_1214del	p.Lys405AlafsTer3	p.K405Afs*3	ENST00000264010	NM_006565.3	404	gAA/g	7/12	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.629119194257817	2		455	433	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266093	41266107	+	inframe_deletion	In_Frame_Del	DEL	CCTGGACTCTGGAAT	CCTGGACTCTGGAAT	-	novel	NA	P-0066875-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	18	467	0	ENST00000349496.5:c.92_106del	p.Leu31_Ile35del	p.L31_I35del	ENST00000349496	NM_001904.3	30	taCCTGGACTCTGGAATc/tac	3/15	1	2	FACETS	0.078	0.058	0.102	0.078	0.058	0.102	SUBCLONAL	1	TRUE	1	0.629119194257817	2		467	733	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437750	110437750	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066875-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	143	407	0	ENST00000375856.3:c.651C>A	p.Tyr217Ter	p.Y217*	ENST00000375856	NM_003749.2	217	taC/taA	1/2	1	2	FACETS	0.971	0.892	1	0.971	0.892	1	CLONAL	1	TRUE	1	0.629119194257817	2		407	468	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653782	89653783	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0066875-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	94	324	0	ENST00000371953.3:c.80_81insC	p.Ile28TyrfsTer16	p.I28Yfs*16	ENST00000371953	NM_000314.4	27	tat/taCt	2/9	1	2	FACETS	0.917	0.824	1	0.917	0.824	1	CLONAL	1	TRUE	1	0.629119194257817	2		324	326	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023207	27023207	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	TT	novel	NA	P-0066875-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	76	403	0	ENST00000324856.7:c.313delinsTT	p.Gly105LeufsTer6	p.G105Lfs*6	ENST00000324856	NM_006015.4	105	Ggg/TTgg	1/20	1	2	FACETS	0.888	0.788	0.993	0.888	0.788	0.993	CLONAL	1	TRUE	1	0.629119194257817	2		403	272	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0066876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	332	465	0	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	0.836429987157687	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.84077926393913	2		465	386	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	55	480	0	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	1	2	FACETS	0.828	0.708	0.959	0.828	0.708	0.959	CLONAL	1	FALSE	1	0.233445598346005	2		480	569	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	39	454	0	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	0.603	0.499	0.719	0.603	0.499	0.719	SUBCLONAL	1	FALSE	1	0.233445598346005	2		454	554	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736166	204736166	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	28	369	2	ENST00000302823.3:c.529del	p.Tyr177IlefsTer10	p.Y177Ifs*10	ENST00000302823	NM_005214.4	175	Ttt/tt	3/4	1	2	FACETS	0.606	0.484	0.745	0.606	0.484	0.745	SUBCLONAL	1	FALSE	1	0.233445598346005	2		371	396	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779211	3779211	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783507	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	23	268	0	ENST00000262367.5:c.5837del	p.Pro1946HisfsTer30	p.P1946Hfs*30	ENST00000262367	NM_004380.2	1946	cCa/ca	31/31	1	2	FACETS	0.614	0.479	0.77	0.614	0.479	0.77	SUBCLONAL	1	FALSE	1	0.233445598346005	2		268	321	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	37	565	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.739	0.609	0.884	0.739	0.609	0.884	SUBCLONAL	1	FALSE	1	0.233445598346005	2		565	429	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	42	439	0	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	0.707	0.59	0.837	0.707	0.59	0.837	SUBCLONAL	1	FALSE	1	0.233445598346005	2		439	509	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	45	404	0	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	1	2	FACETS	0.776	0.652	0.913	0.776	0.652	0.913	CLONAL	1	FALSE	1	0.233445598346005	2		404	497	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021817	71021817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs797045586	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	25	353	0	ENST00000318789.4:c.1541G>A	p.Arg514His	p.R514H	ENST00000318789	NM_032682.5	514	cGt/cAt	18/21	1	2	FACETS	0.736	0.581	0.913	0.736	0.581	0.913	CLONAL	1	FALSE	1	0.233445598346005	2		353	291	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699360	47699360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	17	312	0	ENST00000347630.2:c.148G>A	p.Glu50Lys	p.E50K	ENST00000347630	NM_001007230.1	50	Gaa/Aaa	4/11	1	2	FACETS	0.832	0.624	1	0.832	0.624	1	CLONAL	1	FALSE	1	0.233445598346005	2		312	175	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276755	15276755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138265894	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	61	466	1	ENST00000263388.2:c.5510G>A	p.Arg1837His	p.R1837H	ENST00000263388	NM_000435.2	1837	cGt/cAt	30/33	1	2	FACETS	0.98	0.847	1	0.98	0.847	1	CLONAL	1	FALSE	1	0.233445598346005	2		467	533	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352609	68352609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548280411	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	17	317	0	ENST00000487270.1:c.476G>A	p.Arg159His	p.R159H	ENST00000487270	NM_133509.3	159	cGt/cAt	6/11	1	2	FACETS	1	0.755	1	1	0.755	1	CLONAL	1	FALSE	1	0.233445598346005	2		317	145	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016550	12016550	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	23	290	0	ENST00000353533.5:c.686A>T	p.Asp229Val	p.D229V	ENST00000353533	NM_003010.3	229	gAt/gTt	7/11	1	2	FACETS	0.767	0.599	0.959	0.767	0.599	0.959	CLONAL	1	FALSE	1	0.233445598346005	2		290	257	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272337	15272337	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs771517374	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	55	712	0	ENST00000263388.2:c.6102del	p.Gly2035ValfsTer50	p.G2035Vfs*50	ENST00000263388	NM_000435.2	2034	ccC/cc	33/33	1	2	FACETS	0.913	0.782	1	0.913	0.782	1	CLONAL	1	FALSE	1	0.233445598346005	2		712	516	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39746809	39746809	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	28	298	0	ENST00000361337.2:c.1823C>T	p.Pro608Leu	p.P608L	ENST00000361337	NM_003286.2	608	cCg/cTg	18/21	1	2	FACETS	0.819	0.656	1	0.819	0.656	1	CLONAL	1	FALSE	1	0.233445598346005	2		298	293	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711908	89711910	+	inframe_deletion	In_Frame_Del	DEL	TAT	TAT	-	rs587780711	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	11	343	1	ENST00000371953.3:c.532_534del	p.Tyr178del	p.Y178del	ENST00000371953	NM_000314.4	176	TAT/-	6/9	1	2	FACETS	0.645	0.447	0.889	0.645	0.447	0.889	SUBCLONAL	1	FALSE	1	0.233445598346005	2		344	146	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	82	589	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.233445598346005	2		590	477	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897002	28897002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554058758	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	37	394	0	ENST00000282397.4:c.2878G>A	p.Val960Ile	p.V960I	ENST00000282397	NM_002019.4	960	Gtc/Atc	21/30	0.233445598346005	0	FACETS	0.597	0.492	0.714			1	SUBCLONAL	1	FALSE	0	0.233445598346005	0		394	407	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	55	480	2	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	1	2	FACETS	0.915	0.783	1	0.915	0.783	1	CLONAL	1	FALSE	1	0.233445598346005	2		482	515	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211521	98211521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559827048	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	53	393	0	ENST00000331920.6:c.3634G>A	p.Gly1212Ser	p.G1212S	ENST00000331920	NM_000264.3	1212	Ggc/Agc	22/24	1	2	FACETS	0.923	0.788	1	0.923	0.788	1	CLONAL	1	FALSE	1	0.233445598346005	2		393	492	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594075	55594075	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1560418178	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	30	419	0	ENST00000288135.5:c.1861G>A	p.Ala621Thr	p.A621T	ENST00000288135	NM_000222.2	621	Gct/Act	12/21	1	2	FACETS	0.676	0.545	0.825	0.676	0.545	0.825	SUBCLONAL	1	FALSE	1	0.233445598346005	2		419	380	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672814	86672816	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	novel	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	13	414	0	ENST00000274376.6:c.2307_2309del	p.Leu770del	p.L770del	ENST00000274376	NM_002890.2	767	tcGTTg/tcg	17/25	1	2	FACETS	0.692	0.495	0.929	0.692	0.495	0.929	SUBCLONAL	1	FALSE	1	0.233445598346005	2		414	161	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106074	27106074	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	39	459	0	ENST00000324856.7:c.5688del	p.Pro1898HisfsTer25	p.P1898Hfs*25	ENST00000324856	NM_006015.4	1895	gaG/ga	20/20	1	2	FACETS	0.609	0.504	0.726	0.609	0.504	0.726	SUBCLONAL	1	FALSE	1	0.233445598346005	2		459	549	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439919	51439919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	37	307	0	ENST00000262662.1:c.488del	p.Gly163GlufsTer24	p.G163Efs*24	ENST00000262662		162	Ggg/gg	4/4	1	2	FACETS	0.805	0.664	0.961	0.805	0.664	0.961	CLONAL	1	FALSE	1	0.233445598346005	2		307	394	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391424	139391424	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759225800	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	42	395	0	ENST00000277541.6:c.6767C>T	p.Ala2256Val	p.A2256V	ENST00000277541	NM_017617.3	2256	gCg/gTg	34/34	1	2	FACETS	0.839	0.701	0.991	0.839	0.701	0.991	CLONAL	1	FALSE	1	0.233445598346005	2		395	429	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155301	185155301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140999720	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	43	349	0	ENST00000265026.3:c.542C>T	p.Ala181Val	p.A181V	ENST00000265026	NM_004721.4	181	gCg/gTg	3/14	1	2	FACETS	0.764	0.64	0.903	0.764	0.64	0.903	CLONAL	1	FALSE	1	0.233445598346005	2		349	482	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342401	70342401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	55	377	0	ENST00000374080.3:c.1292G>A	p.Arg431Gln	p.R431Q	ENST00000374080		431	cGg/cAg	9/45	1	2	FACETS	0.812	0.695	0.941	0.812	0.695	0.941	CLONAL	1	FALSE	1	0.233445598346005	2		377	580	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150933119	150933119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	32	386	0	ENST00000271640.5:c.2581G>A	p.Glu861Lys	p.E861K	ENST00000271640	NM_001145415.1	861	Gag/Aag	16/22	1	2	FACETS	0.731	0.594	0.886	0.731	0.594	0.886	SUBCLONAL	1	FALSE	1	0.233445598346005	2		386	375	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981291	63981291	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	49	491	2	ENST00000398590.3:c.1793C>T	p.Thr598Ile	p.T598I	ENST00000398590	NM_001177387.1	598	aCc/aTc	12/14	1	2	FACETS	0.789	0.668	0.922	0.789	0.668	0.922	CLONAL	1	FALSE	1	0.233445598346005	2		493	532	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347708	89347708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746152599	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	54	400	0	ENST00000301030.4:c.5242G>A	p.Val1748Met	p.V1748M	ENST00000301030	NM_001256183.1	1748	Gtg/Atg	9/13	1	2	FACETS	0.794	0.677	0.921	0.794	0.677	0.921	CLONAL	1	FALSE	1	0.233445598346005	2		400	583	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311638	30311638	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138463303	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	16	304	0	ENST00000262643.3:c.492G>C	p.Glu164Asp	p.E164D	ENST00000262643	NM_001238.2	164	gaG/gaC	7/12	1	2	FACETS	0.729	0.541	0.952	0.729	0.541	0.952	CLONAL	1	FALSE	1	0.233445598346005	2		304	188	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067422	37067422	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	86	427	0	ENST00000231790.2:c.1333C>T	p.Gln445Ter	p.Q445*	ENST00000231790	NM_000249.3	445	Cag/Tag	12/19	1	2	FACETS	0.833	0.741	0.932	1	0.982	1	CLONAL	2	FALSE	1	0.233445598346005	2		427	442	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47600695	47600695	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	20	335	0	ENST00000263735.4:c.170T>G	p.Val57Gly	p.V57G	ENST00000263735	NM_002354.2	57	gTc/gGc	2/9	0.233445598346005	1	FACETS	0.983	0.758	1	0.983	0.758	1	CLONAL	1	FALSE	0	0.233445598346005	1		335	154	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628839	187628839	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	21	387	0	ENST00000441802.2:c.2143C>T	p.Gln715Ter	p.Q715*	ENST00000441802	NM_005245.3	715	Cag/Tag	2/27	1	2	FACETS	0.59	0.454	0.748	0.59	0.454	0.748	SUBCLONAL	1	FALSE	1	0.233445598346005	2		387	305	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349967	15349967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	33	380	0	ENST00000263377.2:c.3685C>T	p.Arg1229Cys	p.R1229C	ENST00000263377	NM_058243.2	1229	Cgc/Tgc	18/20	1	2	FACETS	0.625	0.509	0.757	0.625	0.509	0.757	SUBCLONAL	1	FALSE	1	0.233445598346005	2		380	452	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991550	72991550	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	33	414	0	ENST00000268489.5:c.2495T>C	p.Met832Thr	p.M832T	ENST00000268489	NM_006885.3	832	aTg/aCg	2/10	1	2	FACETS	0.644	0.524	0.779	0.644	0.524	0.779	SUBCLONAL	1	FALSE	1	0.233445598346005	2		414	439	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128246770	128246770	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	45	295	0	ENST00000265960.3:c.1159A>G	p.Lys387Glu	p.K387E	ENST00000265960	NM_001006617.1	387	Aaa/Gaa	9/12	1	2	FACETS	0.957	0.806	1	0.957	0.806	1	CLONAL	1	FALSE	1	0.233445598346005	2		295	403	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593321	67593322	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	45	410	0	ENST00000274335.5:c.2071_2072del	p.Leu691GlufsTer49	p.L691Efs*49	ENST00000274335		689	agCTct/agct	15/15	1	2	FACETS	0.826	0.694	0.971	0.826	0.694	0.971	CLONAL	1	FALSE	1	0.233445598346005	2		410	467	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3634847	3634847	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066885-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	44	384	0	ENST00000294008.3:c.4662G>T	p.Leu1554Phe	p.L1554F	ENST00000294008	NM_032444.2	1554	ttG/ttT	13/15	1	2	FACETS	0.802	0.673	0.945	0.802	0.673	0.945	CLONAL	1	FALSE	1	0.233445598346005	2		384	470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0066886-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	222	524	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.354816185991108	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.354408701108635	2		524	592	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484049	50484049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066886-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	88	399	0	ENST00000394963.4:c.899G>A	p.Arg300His	p.R300H	ENST00000394963	NM_003076.4	300	cGc/cAc	8/13	NA	2	FACETS	0.928	0.825	1			1	INDETERMINATE	1	TRUE	NA	0.354408701108635	2		399	535	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258683	16258683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559309170	NA	P-0066886-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	116	548	1	ENST00000375759.3:c.5948C>T	p.Ser1983Leu	p.S1983L	ENST00000375759	NM_015001.2	1983	tCg/tTg	11/15	0.134207506958914	5	FACETS	1	0.976	1	0.424	0.382	0.468	INDETERMINATE	1	TRUE	2	0.354408701108635	5		549	789	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127453	55127453	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066886-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	87	452	0	ENST00000257290.5:c.241T>C	p.Phe81Leu	p.F81L	ENST00000257290	NM_006206.4	81	Ttt/Ctt	3/23	0.354816185991108	3	FACETS	0.914	0.81	1	0.457	0.405	0.513	CLONAL	1	TRUE	1	0.354408701108635	3		452	632	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274878	142274878	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066886-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	85	368	0	ENST00000350721.4:c.2182T>A	p.Leu728Ile	p.L728I	ENST00000350721	NM_001184.3	728	Tta/Ata	10/47	0.314381274240338	4	FACETS	1	0.953	1	0.575	0.509	0.645	CLONAL	1	TRUE	2	0.354408701108635	4		368	565	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0066889-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	114	322	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		322	335	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913514	NA	P-0066889-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	166	373	0	ENST00000288135.5:c.2466T>A	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaA	17/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		373	342	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342509	118342509	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066889-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	164	404	0	ENST00000534358.1:c.635A>G	p.Lys212Arg	p.K212R	ENST00000534358	NM_005933.3	212	aAg/aGg	3/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		404	410	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120508155	120508155	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066889-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	141	390	0	ENST00000256646.2:c.1602T>A	p.Asp534Glu	p.D534E	ENST00000256646	NM_024408.3	534	gaT/gaA	10/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		390	198	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593605	55593613	+	inframe_deletion	In_Frame_Del	DEL	GAAGGTTGT	GAAGGTTGT	-	novel	NA	P-0066908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	195	262	0	ENST00000288135.5:c.1671_1679del	p.Trp557_Val560delinsCys	p.W557_V560delinsC	ENST00000288135	NM_000222.2	557	tgGAAGGTTGTt/tgt	11/21	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.851906100972213	2		262	438	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624846	9624846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	212	309	0	ENST00000353224.5:c.131C>T	p.Ala44Val	p.A44V	ENST00000353224	NM_177990.2	44	gCa/gTa	3/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.851906100972213	2		309	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0066909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	279	458	1	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.504911488914887	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.500136910332764	2		459	505	SUCCESS
APC	324	MSKCC	GRCh37	5	112175772	112175772	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	208	447	0	ENST00000257430.4:c.4483del	p.Ser1495ValfsTer12	p.S1495Vfs*12	ENST00000257430	NM_000038.5	1494	gAa/ga	16/16	0.477929807589736	3	FACETS	0.938	0.878	1	0.938	0.878	1	CLONAL	2	TRUE	1	0.500136910332764	3		447	554	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0066909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	223	334	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	2	TRUE	NA	0.500136910332764	2		334	425	SUCCESS
APC	324	MSKCC	GRCh37	5	112174207	112174207	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	126	459	0	ENST00000257430.4:c.2917del	p.Tyr973MetfsTer7	p.Y973Mfs*7	ENST00000257430	NM_000038.5	972	ggT/gg	16/16	0.477929807589736	3	FACETS	1	0.948	1	0.531	0.482	0.582	CLONAL	1	TRUE	1	0.500136910332764	3		459	593	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976856	2976857	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGA	novel	NA	P-0066909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	84	450	0	ENST00000396946.4:c.1153_1155dup	p.Ser385dup	p.S385dup	ENST00000396946	NM_032415.4	385	-/TCC	9/25	0.504911488914887	4	FACETS	0.728	0.643	0.819	0.243	0.214	0.273	SUBCLONAL	1	TRUE	1	0.500136910332764	4		450	692	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0066910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	75	496	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	0.620141456236343	3	FACETS	1	0.892	1	0.504	0.446	0.566	CLONAL	1	TRUE	1	0.639652814248873	3		496	307	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106586	27106586	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	91	502	0	ENST00000324856.7:c.6197A>T	p.Asn2066Ile	p.N2066I	ENST00000324856	NM_006015.4	2066	aAc/aTc	20/20	0.615869551884067	5	FACETS	1	0.977	1	0.454	0.406	0.506	CLONAL	1	TRUE	2	0.639652814248873	5		502	409	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944872	31944872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	33	258	0	ENST00000340398.3:c.229G>A	p.Asp77Asn	p.D77N	ENST00000340398	NM_001013699.2	77	Gat/Aat	1/1	0.639652814248873	7	FACETS	0.755	0.616	0.912			1	CLONAL	1	TRUE	NA	0.639652814248873	7		258	355	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830778	72830778	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	52	401	0	ENST00000268489.5:c.5803C>A	p.Arg1935Ser	p.R1935S	ENST00000268489	NM_006885.3	1935	Cgc/Agc	9/10	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.639652814248873	2		401	158	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993717	72993717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	10	499	0	ENST00000268489.5:c.328G>A	p.Glu110Lys	p.E110K	ENST00000268489	NM_006885.3	110	Gag/Aag	2/10	1	2	FACETS	0.192	0.13	0.269	0.192	0.13	0.269	SUBCLONAL	1	TRUE	1	0.639652814248873	2		499	163	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115930	8115931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCAGCCTGTCCTTTGGACCACA	novel	NA	P-0066911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	30	449	0	ENST00000346208.3:c.1280_1301dup	p.His434GlnfsTer80	p.H434Qfs*80	ENST00000346208		426	tcc/tCCAGCCTGTCCTTTGGACCACAcc	6/6	1	2	FACETS	0.602	0.485	0.736	0.602	0.485	0.736	SUBCLONAL	1	TRUE	1	0.222857946714768	2		449	447	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565875	55565875	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	22	305	0	ENST00000288135.5:c.699C>G	p.Cys233Trp	p.C233W	ENST00000288135	NM_000222.2	233	tgC/tgG	4/21	1	2	FACETS	0.862	0.671	1	0.862	0.671	1	CLONAL	1	TRUE	1	0.222857946714768	2		305	229	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	14	317	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	0.847	0.614	1	0.847	0.614	1	CLONAL	1	TRUE	0	0.17	1		317	178	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593613	55593613	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913521	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	33	319	0	ENST00000288135.5:c.1679T>A	p.Val560Asp	p.V560D	ENST00000288135	NM_000222.2	560	gTt/gAt	11/21	1	2	FACETS	0.901	0.734	1	0.901	0.734	1	CLONAL	1	TRUE	1	0.17	2		319	431	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609813	117609813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761155034	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	32	337	0	ENST00000368508.3:c.6886G>A	p.Glu2296Lys	p.E2296K	ENST00000368508	NM_002944.2	2296	Gaa/Aaa	43/43	1	2	FACETS	0.776	0.629	0.943	0.776	0.629	0.943	CLONAL	1	TRUE	1	0.17	2		337	485	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285905	38285905	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	22	344	0	ENST00000425967.3:c.506C>T	p.Ser169Leu	p.S169L	ENST00000425967	NM_001174067.1	169	tCa/tTa	5/19	1	2	FACETS	0.667	0.516	0.843	0.667	0.516	0.843	SUBCLONAL	1	TRUE	1	0.17	2		344	388	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197255	106197255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1222260506	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	35	342	0	ENST00000380013.4:c.5588C>T	p.Ala1863Val	p.A1863V	ENST00000380013	NM_001127208.2	1863	gCc/gTc	11/11	1	2	FACETS	0.82	0.672	0.988	0.82	0.672	0.988	CLONAL	1	TRUE	1	0.17	2		342	502	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	40	374	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	1	2	FACETS	0.883	0.733	1	0.883	0.733	1	CLONAL	1	TRUE	1	0.17	2		374	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579395	7579395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	35	460	1	ENST00000269305.4:c.292C>T	p.Pro98Ser	p.P98S	ENST00000269305	NM_001126112.2	98	Cct/Tct	4/11	1	2	FACETS	0.793	0.649	0.955	0.793	0.649	0.955	CLONAL	1	TRUE	1	0.17	2		461	519	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536947	120536947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	22	291	0	ENST00000229340.5:c.239G>A	p.Gly80Glu	p.G80E	ENST00000229340	NM_006861.6	80	gGg/gAg	4/6	1	2	FACETS	0.681	0.527	0.86	0.681	0.527	0.86	SUBCLONAL	1	TRUE	1	0.17	2		291	380	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266828	198266828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs16865307	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	46	253	0	ENST00000335508.6:c.2104C>T	p.Arg702Trp	p.R702W	ENST00000335508	NM_012433.2	702	Cgg/Tgg	15/25	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.17	2		253	526	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381466	81381466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	70	275	0	ENST00000222390.5:c.595G>A	p.Glu199Lys	p.E199K	ENST00000222390	NM_000601.4	199	Gaa/Aaa	5/18	0.163063576998838	3	FACETS	0.806	0.704	0.917	0.806	0.704	0.917	CLONAL	2	TRUE	1	0.17	3		275	554	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658412	117658412	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	38	380	0	ENST00000368508.3:c.5171C>T	p.Ser1724Leu	p.S1724L	ENST00000368508	NM_002944.2	1724	tCa/tTa	31/43	1	2	FACETS	0.961	0.795	1	0.961	0.795	1	CLONAL	1	TRUE	1	0.17	2		380	465	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560970	9560970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781706438	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	38	324	0	ENST00000353224.5:c.812C>T	p.Ser271Leu	p.S271L	ENST00000353224	NM_177990.2	271	tCg/tTg	4/10	1	2	FACETS	0.957	0.791	1	0.957	0.791	1	CLONAL	1	TRUE	1	0.17	2		324	467	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100947	41100947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372070542	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	39	365	0	ENST00000373198.4:c.1409G>A	p.Arg470Gln	p.R470Q	ENST00000373198	NM_133170.3	470	cGa/cAa	8/32	1	2	FACETS	0.923	0.765	1	0.923	0.765	1	CLONAL	1	TRUE	1	0.17	2		365	497	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263844	16263844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	28	427	0	ENST00000375759.3:c.10213C>T	p.Pro3405Ser	p.P3405S	ENST00000375759	NM_015001.2	3405	Cca/Tca	12/15	1	2	FACETS	0.648	0.517	0.799	0.648	0.517	0.799	SUBCLONAL	1	TRUE	1	0.17	2		427	508	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164604	36164604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1476276192	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	32	268	0	ENST00000300305.3:c.1271C>T	p.Ser424Leu	p.S424L	ENST00000300305		424	tCg/tTg	8/8	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.17	2		268	320	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355565	15355565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	46	323	0	ENST00000263377.2:c.2167C>T	p.Pro723Ser	p.P723S	ENST00000263377	NM_058243.2	723	Ccg/Tcg	12/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.17	2		323	441	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875648	35875648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	29	268	0	ENST00000303115.3:c.835C>T	p.His279Tyr	p.H279Y	ENST00000303115	NM_002185.3	279	Cat/Tat	7/8	1	2	FACETS	0.731	0.586	0.896	0.731	0.586	0.896	SUBCLONAL	1	TRUE	1	0.17	2		268	467	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349757	15349757	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	26	427	0	ENST00000263377.2:c.3817C>T	p.Arg1273Trp	p.R1273W	ENST00000263377	NM_058243.2	1273	Cgg/Tgg	19/20	1	2	FACETS	0.748	0.592	0.927	0.748	0.592	0.927	CLONAL	1	TRUE	1	0.17	2		427	409	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443642	29443642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113994089	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	38	357	0	ENST00000389048.3:c.3575G>A	p.Arg1192Gln	p.R1192Q	ENST00000389048	NM_004304.4	1192	cGg/cAg	23/29	1	2	FACETS	0.87	0.718	1	0.87	0.718	1	CLONAL	1	TRUE	1	0.17	2		357	514	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268128	153268128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	41	274	0	ENST00000281708.4:c.680C>T	p.Ser227Phe	p.S227F	ENST00000281708	NM_033632.3	227	tCt/tTt	4/12	1	2	FACETS	0.843	0.701	1	0.843	0.701	1	CLONAL	1	TRUE	1	0.17	2		274	572	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341587	89341587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	24	265	0	ENST00000301030.4:c.7483C>T	p.Pro2495Ser	p.P2495S	ENST00000301030	NM_001256183.1	2495	Ccc/Tcc	10/13	1	2	FACETS	0.891	0.699	1	0.891	0.699	1	CLONAL	1	TRUE	1	0.17	2		265	317	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622363	1622363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	18	321	0	ENST00000344749.5:c.601C>T	p.Pro201Ser	p.P201S	ENST00000344749	NM_001136139.2	201	Ccg/Tcg	9/19	1	2	FACETS	0.648	0.487	0.838	0.648	0.487	0.838	SUBCLONAL	1	TRUE	1	0.17	2		321	327	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868350	45868350	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs765679315	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	32	361	0	ENST00000391945.4:c.427C>G	p.Arg143Gly	p.R143G	ENST00000391945	NM_000400.3	143	Cgg/Ggg	6/23	1	2	FACETS	0.905	0.735	1	0.905	0.735	1	CLONAL	1	TRUE	1	0.17	2		361	416	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593301	67593301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	29	317	0	ENST00000274335.5:c.2047G>A	p.Glu683Lys	p.E683K	ENST00000274335		683	Gag/Aag	15/15	1	2	FACETS	0.604	0.483	0.742	0.604	0.483	0.742	SUBCLONAL	1	TRUE	1	0.17	2		317	565	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758775	41758775	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374737642	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	28	356	0	ENST00000301178.4:c.1829G>A	p.Arg610Gln	p.R610Q	ENST00000301178	NM_021913.4	610	cGa/cAa	16/20	1	2	FACETS	0.656	0.523	0.808	0.656	0.523	0.808	SUBCLONAL	1	TRUE	1	0.17	2		356	502	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458329	12458329	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1364613522	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	32	362	0	ENST00000287820.6:c.946C>T	p.Arg316Cys	p.R316C	ENST00000287820	NM_015869.4	316	Cgc/Tgc	6/7	1	2	FACETS	0.678	0.549	0.825	0.678	0.549	0.825	SUBCLONAL	1	TRUE	1	0.17	2		362	555	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321393	1321393	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265666508	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	22	335	1	ENST00000400841.2:c.362C>T	p.Ser121Phe	p.S121F	ENST00000400841		121	tCc/tTc	4/6	1	1	FACETS	0.555	0.429	0.701	0.555	0.429	0.701	SUBCLONAL	1	TRUE	0	0.17	1		336	427	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11181313	11181313	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	25	226	0	ENST00000361445.4:c.6923C>T	p.Pro2308Leu	p.P2308L	ENST00000361445	NM_004958.3	2308	cCc/cTc	49/58	1	2	FACETS	0.705	0.555	0.878	0.705	0.555	0.878	SUBCLONAL	1	TRUE	1	0.17	2		226	417	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69012043	69012043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	28	275	0	ENST00000288368.4:c.2680G>A	p.Glu894Lys	p.E894K	ENST00000288368	NM_024870.2	894	Gaa/Aaa	23/40	1	2	FACETS	0.79	0.631	0.972	0.79	0.631	0.972	CLONAL	1	TRUE	1	0.17	2		275	417	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445991	49445991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265398099	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	44	416	0	ENST00000301067.7:c.1475C>T	p.Ser492Leu	p.S492L	ENST00000301067	NM_003482.3	492	tCg/tTg	10/54	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.17	2		416	460	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552934	106552934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	46	399	0	ENST00000369096.4:c.899C>T	p.Pro300Leu	p.P300L	ENST00000369096	NM_001198.3	300	cCc/cTc	5/7	1	2	FACETS	0.863	0.726	1	0.863	0.726	1	CLONAL	1	TRUE	1	0.17	2		399	627	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760671	59760671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	29	184	0	ENST00000259008.2:c.3736C>T	p.Pro1246Ser	p.P1246S	ENST00000259008	NM_032043.2	1246	Cct/Tct	20/20	1	2	FACETS	0.774	0.62	0.948	0.774	0.62	0.948	CLONAL	1	TRUE	1	0.17	2		184	441	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80160665	80160665	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	32	291	1	ENST00000265081.6:c.3034C>T	p.Pro1012Ser	p.P1012S	ENST00000265081	NM_002439.4	1012	Ccg/Tcg	22/24	1	2	FACETS	0.818	0.664	0.993	0.818	0.664	0.993	CLONAL	1	TRUE	1	0.17	2		292	460	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692941	89692941	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753630034	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	32	313	0	ENST00000371953.3:c.425G>A	p.Arg142Gln	p.R142Q	ENST00000371953	NM_000314.4	142	cGg/cAg	5/9	1	2	FACETS	0.817	0.662	0.991	0.817	0.662	0.991	CLONAL	1	TRUE	1	0.17	2		313	461	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678605	88678605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774363821	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	28	344	0	ENST00000360948.2:c.931G>A	p.Glu311Lys	p.E311K	ENST00000360948	NM_001012338.2	311	Gag/Aag	9/19	1	2	FACETS	0.856	0.684	1	0.856	0.684	1	CLONAL	1	TRUE	1	0.17	2		344	385	SUCCESS
H3C13	653604	MSKCC	GRCh37	1	149784855	149784856	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	28	238	0	ENST00000331491.1:c.381_382delinsAA	p.Ala128Thr	p.A128T	ENST00000331491	NM_001123375.2	127	ttGGcc/ttAAcc	1/1	1	2	FACETS	1	0.818	1	1	0.818	1	CLONAL	1	TRUE	1	0.17	2		238	322	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097246	11097246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1366344437	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	29	317	0	ENST00000358026.2:c.737C>T	p.Pro246Leu	p.P246L	ENST00000358026	NM_001128849.1	246	cCt/cTt	4/36	1	2	FACETS	0.859	0.69	1	0.859	0.69	1	CLONAL	1	TRUE	1	0.17	2		317	397	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32971171	32971183	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ACAAGCTTCTGGT	ACAAGCTTCTGGT	-	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	28	297	0	ENST00000380152.3:c.9639_9648+3del		p.X3213_splice	ENST00000380152		3213		26/27	1	2	FACETS	0.786	0.628	0.967	0.786	0.628	0.967	CLONAL	1	TRUE	1	0.17	2		297	419	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1941461	1941461	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	28	301	0	ENST00000382891.5:c.1837T>C	p.Phe613Leu	p.F613L	ENST00000382891	NM_133335.3	613	Ttt/Ctt	9/22	1	2	FACETS	0.62	0.495	0.764	0.62	0.495	0.764	SUBCLONAL	1	TRUE	1	0.17	2		301	531	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206880	102206880	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756933731	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	35	309	0	ENST00000263464.3:c.1508G>A	p.Gly503Glu	p.G503E	ENST00000263464	NM_001165.4	503	gGa/gAa	7/9	1	2	FACETS	0.738	0.604	0.889	0.738	0.604	0.889	SUBCLONAL	1	TRUE	1	0.17	2		309	558	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099384	4099384	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	36	319	1	ENST00000262948.5:c.734C>T	p.Ser245Leu	p.S245L	ENST00000262948	NM_030662.3	245	tCg/tTg	7/11	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.17	2		320	391	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51504630	51504630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747645435	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	32	364	0	ENST00000260433.2:c.1150G>A	p.Asp384Asn	p.D384N	ENST00000260433		384	Gat/Aat	9/10	1	2	FACETS	0.691	0.56	0.84	0.691	0.56	0.84	SUBCLONAL	1	TRUE	1	0.17	2		364	545	SUCCESS
APC	324	MSKCC	GRCh37	5	112175102	112175102	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1580640499	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	27	254	0	ENST00000257430.4:c.3811T>C	p.Phe1271Leu	p.F1271L	ENST00000257430	NM_000038.5	1271	Ttt/Ctt	16/16	1	2	FACETS	0.68	0.54	0.841	0.68	0.54	0.841	SUBCLONAL	1	TRUE	1	0.17	2		254	467	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157173	106157173	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	41	346	0	ENST00000380013.4:c.2074G>T	p.Glu692Ter	p.E692*	ENST00000380013	NM_001127208.2	692	Gaa/Taa	3/11	1	2	FACETS	0.887	0.738	1	0.887	0.738	1	CLONAL	1	TRUE	1	0.17	2		346	544	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101909964	101909965	+	stop_gained	Nonsense_Mutation	DNP	TT	TT	AA	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	31	266	0	ENST00000374994.4:c.1284_1285inv	p.Tyr428_Tyr429delinsTer	p.Y428_Y429delins*	ENST00000374994	NM_004612.2	428	taTTat/taAAat	8/9	1	2	FACETS	0.836	0.676	1	0.836	0.676	1	CLONAL	1	TRUE	1	0.17	2		266	436	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263347	123263347	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	26	262	0	ENST00000358487.5:c.1396T>A	p.Tyr466Asn	p.Y466N	ENST00000358487	NM_000141.4	466	Tat/Aat	10/18	1	2	FACETS	0.774	0.613	0.96	0.774	0.613	0.96	CLONAL	1	TRUE	1	0.17	2		262	395	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99162507	99162507	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	26	301	0	ENST00000074304.5:c.1025G>T	p.Arg342Met	p.R342M	ENST00000074304	NM_001134224.1	342	aGg/aTg	12/26	1	2	FACETS	0.683	0.54	0.847	0.683	0.54	0.847	SUBCLONAL	1	TRUE	1	0.17	2		301	448	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339013	225339013	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	41	280	0	ENST00000264414.4:c.2256A>T	p.Glu752Asp	p.E752D	ENST00000264414	NM_003590.4	752	gaA/gaT	16/16	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.17	2		280	443	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885829	111885830	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	39	400	0	ENST00000341259.2:c.1451_1452delinsAA	p.Trp484Ter	p.W484*	ENST00000341259	NM_005475.2	484	tGG/tAA	8/8	1	2	FACETS	0.861	0.713	1	0.861	0.713	1	CLONAL	1	TRUE	1	0.17	2		400	533	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56866209	56866209	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	33	307	0	ENST00000308159.5:c.1254G>T	p.Leu418Phe	p.L418F	ENST00000308159	NM_014669.4	418	ttG/ttT	12/22	1	2	FACETS	0.797	0.649	0.965	0.797	0.649	0.965	CLONAL	1	TRUE	1	0.17	2		307	487	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650877	37650878	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	38	294	1	ENST00000447079.4:c.2349_2350delinsTT	p.Arg784Ter	p.R784*	ENST00000447079	NM_015083.1	783	caCCga/caTTga	5/14	1	2	FACETS	0.887	0.733	1	0.887	0.733	1	CLONAL	1	TRUE	1	0.17	2		295	504	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170010	32170010	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168803342	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	36	338	0	ENST00000375023.3:c.3598G>A	p.Gly1200Arg	p.G1200R	ENST00000375023	NM_004557.3	1200	Gga/Aga	21/30	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.17	2		338	374	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124464035	124464035	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	30	269	0	ENST00000357628.3:c.1886T>C	p.Val629Ala	p.V629A	ENST00000357628	NM_015450.2	629	gTt/gCt	19/19	0.163063576998838	3	FACETS	0.825	0.664	1	0.413	0.332	0.504	CLONAL	1	TRUE	1	0.17	3		269	464	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561095	9561095	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	41	330	0	ENST00000353224.5:c.687T>A	p.Asp229Glu	p.D229E	ENST00000353224	NM_177990.2	229	gaT/gaA	4/10	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.17	2		330	466	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336340	80336340	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	31	325	0	ENST00000286548.4:c.979C>T	p.His327Tyr	p.H327Y	ENST00000286548	NM_002072.3	327	Cac/Tac	7/7	1	2	FACETS	0.689	0.556	0.84	0.689	0.556	0.84	SUBCLONAL	1	TRUE	1	0.17	2		325	529	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349676	89349676	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	27	361	0	ENST00000301030.4:c.3274C>A	p.Pro1092Thr	p.P1092T	ENST00000301030	NM_001256183.1	1092	Cct/Act	9/13	1	2	FACETS	0.72	0.572	0.89	0.72	0.572	0.89	SUBCLONAL	1	TRUE	1	0.17	2		361	441	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27190530	27190530	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	91	294	0	ENST00000380036.4:c.1331T>C	p.Leu444Pro	p.L444P	ENST00000380036	NM_000459.3	444	cTt/cCt	10/23	1	2	FACETS	1	0.915	1	1	0.986	1	CLONAL	2	TRUE	1	0.17	2		294	519	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944944	31944944	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144139961	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	29	213	0	ENST00000340398.3:c.157C>T	p.Arg53Cys	p.R53C	ENST00000340398	NM_001013699.2	53	Cgt/Tgt	1/1	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.17	2		213	314	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279441	1279441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	16	283	0	ENST00000310581.5:c.2095G>A	p.Ala699Thr	p.A699T	ENST00000310581	NM_198253.2	699	Gcc/Acc	5/16	0.3	1	FACETS	0.622	0.459	0.816	0.622	0.459	0.816	SUBCLONAL	1	TRUE	0	0.17	1		283	277	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332746	65332746	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	39	382	0	ENST00000342505.4:c.793G>A	p.Asp265Asn	p.D265N	ENST00000342505	NM_002227.2	265	Gac/Aac	7/25	1	2	FACETS	0.772	0.639	0.922	0.772	0.639	0.922	CLONAL	1	TRUE	1	0.17	2		382	594	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007132	62007132	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	25	300	0	ENST00000392795.3:c.550A>G	p.Lys184Glu	p.K184E	ENST00000392795	NM_001039933.1	184	Aag/Gag	4/6	1	2	FACETS	0.826	0.651	1	0.826	0.651	1	CLONAL	1	TRUE	1	0.17	2		300	356	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251586	212251586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	34	334	0	ENST00000342788.4:c.3473C>T	p.Pro1158Leu	p.P1158L	ENST00000342788	NM_005235.2	1158	cCc/cTc	27/28	1	2	FACETS	0.905	0.739	1	0.905	0.739	1	CLONAL	1	TRUE	1	0.17	2		334	442	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207804	102207804	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	27	239	0	ENST00000263464.3:c.1786A>C	p.Lys596Gln	p.K596Q	ENST00000263464	NM_001165.4	596	Aag/Cag	9/9	1	2	FACETS	0.827	0.658	1	0.827	0.658	1	CLONAL	1	TRUE	1	0.17	2		239	384	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144361398	144361398	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	50	345	0	ENST00000262995.4:c.1448C>T	p.Ser483Phe	p.S483F	ENST00000262995	NM_207123.2	483	tCc/tTc	6/11	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.17	2		345	507	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748914	41748914	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	33	356	0	ENST00000301178.4:c.1439G>C	p.Arg480Pro	p.R480P	ENST00000301178	NM_021913.4	480	cGt/cCt	11/20	1	2	FACETS	0.758	0.617	0.918	0.758	0.617	0.918	CLONAL	1	TRUE	1	0.17	2		356	512	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43806129	43806129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	36	348	0	ENST00000372470.3:c.925G>A	p.Ala309Thr	p.A309T	ENST00000372470	NM_005373.2	309	Gct/Act	6/12	1	2	FACETS	0.776	0.637	0.932	0.776	0.637	0.932	CLONAL	1	TRUE	1	0.17	2		348	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0066913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	359	638	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.545940914756584	4	FACETS	1	0.984	1			1	CLONAL	4	TRUE	NA	0.543561368305241	4		638	494	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	385	346	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.483866460225127	5	FACETS	0.998	0.96	1	0.998	0.96	1	CLONAL	4	TRUE	1	0.543561368305241	5		346	644	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354411	354411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140809342	NA	P-0066913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	195	309	0	ENST00000262320.3:c.1147G>A	p.Val383Met	p.V383M	ENST00000262320	NM_003502.3	383	Gtg/Atg	5/11	0.331973831322859	5	FACETS	1	0.97	1	0.716	0.667	0.767	CLONAL	2	TRUE	2	0.543561368305241	5		309	606	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106696	2106696	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	129	320	0	ENST00000219476.3:c.700G>C	p.Glu234Gln	p.E234Q	ENST00000219476	NM_000548.3	234	Gag/Cag	8/42	0.331973831322859	5	FACETS	1	0.986	1	0.491	0.447	0.537	CLONAL	1	TRUE	2	0.543561368305241	5		320	585	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022405	26022405	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0066913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	110	270	0	ENST00000435504.4:c.253-1G>A		p.X85_splice	ENST00000435504		85			0.545940914756584	3	FACETS	1	0.978	1	0.642	0.581	0.705	CLONAL	1	TRUE	1	0.543561368305241	3		270	401	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627793	37627793	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	502	381	0	ENST00000447079.4:c.1708C>T	p.Gln570Ter	p.Q570*	ENST00000447079	NM_015083.1	570	Cag/Tag	2/14	0.545940914756584	4	FACETS	1	0.992	1			1	CLONAL	4	TRUE	NA	0.543561368305241	4		381	677	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726743	41726743	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	84	343	0	ENST00000301178.4:c.288G>C	p.Trp96Cys	p.W96C	ENST00000301178	NM_021913.4	96	tgG/tgC	2/20	0.545940914756584	4	FACETS	0.887	0.785	0.995	0.296	0.261	0.332	CLONAL	1	TRUE	1	0.543561368305241	4		343	538	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422289	47422326	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTGCTGCGACCAAGCTTGCATCAGCTGAAAAACTCA	AGCTGCTGCGACCAAGCTTGCATCAGCTGAAAAACTCA	C	novel	NA	P-0066913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	498	344	0	ENST00000404338.3:c.357_394delinsC	p.Arg119SerfsTer40	p.R119Sfs*40	ENST00000404338	NM_004491.4	119	agAGCTGCTGCGACCAAGCTTGCATCAGCTGAAAAACTCAtg/agCtg	1/6	0.543561368305241	6	FACETS	0.972	0.94	1	0.972	0.94	1	CLONAL	5	TRUE	1	0.543561368305241	6		344	787	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0066914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	60	376	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	0.6	0.517	0.69	0.6	0.517	0.69	SUBCLONAL	1	TRUE	1	0.381676893154152	2		376	524	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	65	410	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	1	2	FACETS	0.697	0.605	0.795	0.697	0.605	0.795	SUBCLONAL	1	TRUE	1	0.381676893154152	2		410	489	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239505	123239505	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1388165238	NA	P-0066914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	277	431	0	ENST00000358487.5:c.2332C>T	p.Gln778Ter	p.Q778*	ENST00000358487	NM_000141.4	778	Cag/Tag	18/18	0.290747580611249	3	FACETS	0.854	0.807	0.901	0.854	0.807	0.901	CLONAL	3	TRUE	0	0.381676893154152	3		431	675	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425928	49425928	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	98	475	0	ENST00000301067.7:c.12560G>C	p.Gly4187Ala	p.G4187A	ENST00000301067	NM_003482.3	4187	gGg/gCg	39/54	1	2	FACETS	0.895	0.8	0.995	0.895	0.8	0.995	CLONAL	1	TRUE	1	0.381676893154152	2		475	574	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589564	67589602	+	inframe_deletion	In_Frame_Del	DEL	GAAGCTGTAGGGAAAAAATTACATGAATATAACACTCAG	GAAGCTGTAGGGAAAAAATTACATGAATATAACACTCAG	-	novel	NA	P-0066914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	59	274	0	ENST00000274335.5:c.1327_1365del	p.Glu443_Gln455del	p.E443_Q455del	ENST00000274335		443	GAAGCTGTAGGGAAAAAATTACATGAATATAACACTCAG/-	10/15	1	2	FACETS	0.907	0.784	1	0.907	0.784	1	CLONAL	1	TRUE	1	0.381676893154152	2		274	341	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	132	384	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.504356267179779	2		384	508	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035932	47035932	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	97	306	0	ENST00000377604.3:c.610A>G	p.Met204Val	p.M204V	ENST00000377604	NM_001204468.1	204	Atg/Gtg	7/24	1	2	FACETS	0.984	0.884	1	0.984	0.884	1	CLONAL	1	TRUE	1	0.504356267179779	2		306	391	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855991	76855992	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	TA	novel	NA	P-0066918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	46	261	0	ENST00000373344.5:c.5608_5609delinsTA	p.Ala1870Ter	p.A1870*	ENST00000373344	NM_000489.3	1870	GCa/TAa	23/35	1	2	FACETS	0.825	0.702	0.958	0.825	0.702	0.958	CLONAL	1	TRUE	1	0.504356267179779	2		261	221	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	223	317	0				ENST00000310581	NM_198253.2	-/1132			0.673919567770054	6	FACETS	0.919	0.876	0.962	0.919	0.876	0.962	CLONAL	5	FALSE	1	0.673919567770054	6		317	338	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279582	1279582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1228165704	NA	P-0066919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	82	247	0	ENST00000310581.5:c.1954G>A	p.Glu652Lys	p.E652K	ENST00000310581	NM_198253.2	652	Gag/Aag	5/16	0.673919567770054	6	FACETS	1	0.919	1	0.21	0.185	0.237	CLONAL	1	FALSE	1	0.673919567770054	6		247	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	248	289	0	ENST00000269305.4:c.775G>C	p.Asp259His	p.D259H	ENST00000269305	NM_001126112.2	259	Gac/Cac	7/11	0.621388756368259	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	FALSE	0	0.673919567770054	3		289	323	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270530	98270530	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs751977093	NA	P-0066919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	33	213	2	ENST00000331920.6:c.114del	p.Leu39CysfsTer41	p.L39Cfs*41	ENST00000331920	NM_000264.3	38	ggG/gg	1/24	0.673919567770054	3	FACETS	0.633	0.519	0.758	0.316	0.259	0.379	SUBCLONAL	1	FALSE	1	0.673919567770054	3		215	207	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436145	56436145	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	36	287	0	ENST00000407977.2:c.992C>G	p.Ser331Cys	p.S331C	ENST00000407977		331	tCt/tGt	9/10	0.661488753334443	5	FACETS	0.387	0.317	0.465	0.129	0.105	0.155	SUBCLONAL	1	FALSE	2	0.673919567770054	5		287	555	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602926	10602926	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	96	300	0	ENST00000171111.5:c.652G>C	p.Glu218Gln	p.E218Q	ENST00000171111	NM_203500.1	218	Gag/Cag	3/6	0.668138594251754	4	FACETS	0.937	0.838	1	0.468	0.419	0.521	CLONAL	1	FALSE	2	0.673919567770054	4		300	509	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49051519	49051519	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1566241180	NA	P-0066919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	40	157	0	ENST00000267163.4:c.2692C>T	p.Gln898Ter	p.Q898*	ENST00000267163	NM_000321.2	898	Cag/Tag	26/27	0.673919567770054	1	FACETS	0.856	0.737	0.977	0.856	0.737	0.977	CLONAL	1	FALSE	0	0.673919567770054	1		157	92	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11177127	11177127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	77	293	0	ENST00000361445.4:c.6950G>A	p.Arg2317Lys	p.R2317K	ENST00000361445	NM_004958.3	2317	aGa/aAa	50/58	0.649502486351145	4	FACETS	1	0.904	1	0.342	0.302	0.384	CLONAL	1	FALSE	1	0.673919567770054	4		293	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0066919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	265	321	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.621388756368259	3	FACETS	0.91	0.873	0.947	0.91	0.873	0.947	CLONAL	3	FALSE	0	0.673919567770054	3		321	385	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651978	36651979	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0066919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	215	344	0	ENST00000244741.5:c.102_103del	p.Cys34Ter	p.C34*	ENST00000244741	NM_000389.4	34	TGt/t	2/3	0.673919567770054	3	FACETS	0.956	0.901	1	0.956	0.901	1	CLONAL	2	FALSE	1	0.673919567770054	3		344	446	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627485	14627485	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	98	271	0	ENST00000254322.2:c.585G>C	p.Lys195Asn	p.K195N	ENST00000254322	NM_006145.1	195	aaG/aaC	2/3	0.668138594251754	4	FACETS	1	0.966	1	0.588	0.528	0.651	CLONAL	1	FALSE	2	0.673919567770054	4		271	414	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262523	10262523	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	67	237	0	ENST00000340748.4:c.1972G>T	p.Val658Leu	p.V658L	ENST00000340748		658	Gtg/Ttg	22/40	0.668138594251754	4	FACETS	0.791	0.69	0.899	0.395	0.345	0.45	SUBCLONAL	1	FALSE	2	0.673919567770054	4		237	421	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984919	9984919	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	49	256	0	ENST00000330684.3:c.1046C>G	p.Ser349Cys	p.S349C	ENST00000330684	NM_001134407.1	349	tCc/tGc	4/13	0.300055307992507	4	FACETS	0.863	0.736	1	0.216	0.184	0.251	INDETERMINATE	1	FALSE	0	0.673919567770054	4		256	282	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430306	181430306	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	68	174	0	ENST00000325404.1:c.158G>C	p.Arg53Pro	p.R53P	ENST00000325404	NM_003106.3	53	cGc/cCc	1/1	0.337838928506254	5	FACETS	0.867	0.765	0.974	0.578	0.51	0.65	INDETERMINATE	2	FALSE	2	0.673919567770054	5		174	234	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724442	43724442	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	98	308	0	ENST00000382044.4:c.3625G>T	p.Glu1209Ter	p.E1209*	ENST00000382044	NM_001141980.1	1209	Gag/Tag	17/28	0.673919567770054	3	FACETS	0.951	0.854	1	0.475	0.427	0.526	CLONAL	1	FALSE	1	0.673919567770054	3		308	409	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212400	5212400	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0066919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	118	361	0	ENST00000357368.4:c.4717A>T	p.Arg1573Ter	p.R1573*	ENST00000357368	NM_002850.3	1573	Aga/Tga	31/38	0.673919567770054	3	FACETS	1	0.967	1	0.567	0.515	0.62	CLONAL	1	FALSE	1	0.673919567770054	3		361	413	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521515	187521515	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs1560921893	NA	P-0066919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	59	209	0	ENST00000441802.2:c.11641-1G>C		p.X3881_splice	ENST00000441802	NM_005245.3	3881			0.673919567770054	3	FACETS	0.887	0.77	1	0.443	0.385	0.506	CLONAL	1	FALSE	1	0.673919567770054	3		209	264	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481612	56481612	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	242	356	0	ENST00000267101.3:c.647G>C	p.Gly216Ala	p.G216A	ENST00000267101	NM_001982.3	216	gGt/gCt	6/28	0.673919567770054	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	FALSE	1	0.673919567770054	3		356	431	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039327	47039328	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0066919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	203	166	0	ENST00000377604.3:c.955dup	p.Ala319GlyfsTer62	p.A319Gfs*62	ENST00000377604	NM_001204468.1	317	ctg/ctGg	10/24	0.666555927819555	2	FACETS	1	0.989	1			1	CLONAL	2	FALSE	NA	0.673919567770054	2		166	271	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486100	8486100	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	183	339	0	ENST00000356435.5:c.2717A>C	p.Glu906Ala	p.E906A	ENST00000356435		906	gAg/gCg	17/35	0.673919567770054	3	FACETS	0.924	0.865	0.983	0.924	0.865	0.983	CLONAL	2	FALSE	1	0.673919567770054	3		339	393	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039435	49039437	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CAC	CAC	AA	novel	NA	P-0066919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	89	286	0	ENST00000267163.4:c.2420_2422delinsAA	p.Ser807Ter	p.S807*	ENST00000267163	NM_000321.2	807	tCACcc/tAAcc	23/27	0.673919567770054	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	0	0.673919567770054	1		286	154	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1650233	1650233	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	105	279	0	ENST00000344749.5:c.15G>C	p.Gln5His	p.Q5H	ENST00000344749	NM_001136139.2	5	caG/caC	2/19	0.673919567770054	3	FACETS	1	0.96	1	0.56	0.506	0.616	CLONAL	1	FALSE	1	0.673919567770054	3		279	372	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0066921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	399	329	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.468393742351957	4	FACETS	1	0.993	1			1	CLONAL	3	TRUE	NA	0.609695108480949	4		329	629	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770587	40770587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776338672	NA	P-0066921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	31	287	0	ENST00000373198.4:c.2795G>A	p.Arg932His	p.R932H	ENST00000373198	NM_133170.3	932	cGc/cAc	19/32	0.306940311812372	5	FACETS	0.348	0.28	0.424	0.116	0.093	0.142	INDETERMINATE	1	TRUE	2	0.609695108480949	5		287	560	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175440	108175440	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	118	254	0	ENST00000278616.4:c.5535G>C	p.Leu1845Phe	p.L1845F	ENST00000278616	NM_000051.3	1845	ttG/ttC	37/63	0.356975254055048	6	FACETS	0.767	0.694	0.843	0.384	0.347	0.422	INDETERMINATE	2	TRUE	2	0.609695108480949	6		254	560	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177054	56177055	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs1311306052	NA	P-0066921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	148	281	0	ENST00000399503.3:c.2326_2327del	p.Ile776CysfsTer4	p.I776Cfs*4	ENST00000399503	NM_005921.1	775	cAT/c	13/20	0.296082584553533	4	FACETS	0.944	0.871	1	0.944	0.871	1	INDETERMINATE	2	TRUE	2	0.609695108480949	4		281	414	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111509	56111519	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGCGGCTGC	CCCGCGGCTGC	-	novel	NA	P-0066921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	256	310	0	ENST00000399503.3:c.110_120del	p.Pro37ArgfsTer35	p.P37Rfs*35	ENST00000399503	NM_005921.1	37	CCCGCGGCTGCc/c	1/20	0.296082584553533	4	FACETS	1	0.974	1	1	0.974	1	INDETERMINATE	2	TRUE	2	0.609695108480949	4		310	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579559	7579560	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0066921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	170	364	0	ENST00000269305.4:c.127_128del	p.Leu43AspfsTer8	p.L43Dfs*8	ENST00000269305	NM_001126112.2	43	TTg/g	4/11	0.612337881273934	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.609695108480949	1		364	281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0066930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	212	389	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.518723678255949	4	FACETS	0.894	0.84	0.948	0.894	0.84	0.948	CLONAL	3	TRUE	1	0.518723678255949	4		389	463	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013744	12013744	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0066930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	102	243	0	ENST00000353533.5:c.685+1G>C		p.X229_splice	ENST00000353533	NM_003010.3	229			0.243811673149525	4	FACETS	1	0.956	1	0.794	0.731	0.857	INDETERMINATE	3	TRUE	0	0.518723678255949	4		243	188	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171734	36171743	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGGATGGT	TGGGGATGGT	-	novel	NA	P-0066930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	91	373	0	ENST00000300305.3:c.822_831del	p.Gln274HisfsTer34	p.Q274Hfs*34	ENST00000300305		274	caACCATCCCCA/ca	7/8	0.518723678255949	3	FACETS	1	0.913	1	0.342	0.305	0.381	CLONAL	1	TRUE	0	0.518723678255949	3		373	431	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129632	11129632	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs113895708	NA	P-0066930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	56	283	0	ENST00000358026.2:c.2439-1G>C		p.X813_splice	ENST00000358026	NM_001128849.1	813			0.392480468817693	4	FACETS	1	0.89	1	0.519	0.447	0.596	CLONAL	1	TRUE	2	0.518723678255949	4		283	316	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714159	43714159	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	81	358	0	ENST00000382044.4:c.3994A>T	p.Ser1332Cys	p.S1332C	ENST00000382044	NM_001141980.1	1332	Agt/Tgt	19/28	0.514369693051505	4	FACETS	0.986	0.872	1	0.247	0.218	0.277	CLONAL	1	TRUE	0	0.518723678255949	4		358	481	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026121	14026121	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1397638551	NA	P-0066930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	111	313	0	ENST00000311895.7:c.1081A>G	p.Met361Val	p.M361V	ENST00000311895	NM_005236.2	361	Atg/Gtg	6/11	0.518723678255949	4	FACETS	1	0.933	1	1	0.933	1	CLONAL	2	TRUE	2	0.518723678255949	4		313	316	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357114	89357114	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	43	698	0	ENST00000301030.4:c.520C>T	p.Arg174Ter	p.R174*	ENST00000301030	NM_001256183.1	174	Cga/Tga	6/13	0.638621323426151	1	FACETS	0.126	0.105	0.15	0.126	0.105	0.15	SUBCLONAL	1	TRUE	0	0.83571576009361	1		698	474	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0066936-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	268	301	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.783168888794179	2		301	610	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557630	95557630	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066936-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	284	419	0	ENST00000393063.1:c.5437G>C	p.Glu1813Gln	p.E1813Q	ENST00000393063	NM_030621.3	1813	Gag/Cag	26/28	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.783168888794179	2		419	664	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422237	47422237	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066936-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	262	391	0	ENST00000404338.3:c.305A>G	p.Asp102Gly	p.D102G	ENST00000404338	NM_004491.4	102	gAt/gGt	1/6	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.783168888794179	2		391	609	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95583994	95583994	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0066936-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	274	314	0	ENST00000393063.1:c.1474A>T	p.Lys492Ter	p.K492*	ENST00000393063	NM_030621.3	492	Aaa/Taa	10/28	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.783168888794179	2		314	555	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066937-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	109	314	4	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.353675445313869	2		318	531	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0066937-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	89	298	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	0.353675445313869	1	FACETS	0.975	0.869	1	0.975	0.869	1	CLONAL	1	TRUE	0	0.353675445313869	1		298	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0066937-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	149	383	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.353675445313869	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.353675445313869	1		383	673	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916923	178916923	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066937-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	16	345	0	ENST00000263967.3:c.310C>G	p.Pro104Ala	p.P104A	ENST00000263967	NM_006218.2	104	Cca/Gca	2/21	1	2	FACETS	0.149	0.109	0.197	0.149	0.109	0.197	SUBCLONAL	1	TRUE	1	0.353675445313869	2		345	607	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913113	44913114	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0066937-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	107	304	0	ENST00000377967.4:c.790_791dup	p.Lys265ProfsTer61	p.K265Pfs*61	ENST00000377967	NM_021140.2	263	gcc/gcCAc	10/29	0.353675445313869	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.353675445313869	1		304	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0066938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	37	503	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.196112202987615	3	FACETS	0.44	0.361	0.529			1	SUBCLONAL	1	TRUE	NA	0.196112202987615	3		503	941	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802587	135802587	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0066938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	39	297	0	ENST00000298552.3:c.210+1del		p.X70_splice	ENST00000298552	NM_001162426.1	70			0.184294590666996	3	FACETS	0.739	0.611	0.882	0.369	0.305	0.441	SUBCLONAL	1	TRUE	1	0.196112202987615	3		297	591	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205235	38205235	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	166	426	0	ENST00000317025.8:c.455A>G	p.Glu152Gly	p.E152G	ENST00000317025	NM_023034.1	152	gAa/gGa	2/24	0.196112202987615	7	FACETS	0.947	0.868	1			1	CLONAL	2	TRUE	NA	0.196112202987615	7		426	1332	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205229	38205229	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	156	396	0	ENST00000317025.8:c.461A>C	p.Lys154Thr	p.K154T	ENST00000317025	NM_023034.1	154	aAa/aCa	2/24	0.196112202987615	7	FACETS	0.971	0.887	1			1	CLONAL	2	TRUE	NA	0.196112202987615	7		396	1221	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802596	135802596	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	40	315	0	ENST00000298552.3:c.202C>A	p.His68Asn	p.H68N	ENST00000298552	NM_001162426.1	68	Cat/Aat	4/23	0.184294590666996	3	FACETS	0.725	0.601	0.863	0.362	0.3	0.432	SUBCLONAL	1	TRUE	1	0.196112202987615	3		315	618	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0066939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	105	418	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.458411557164109	2		418	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577111	7577120	+	frameshift_variant	Frame_Shift_Del	DEL	GCACAAACAC	GCACAAACAC	-	novel	NA	P-0066939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	174	433	0	ENST00000269305.4:c.818_827del	p.Arg273ProfsTer69	p.R273Pfs*69	ENST00000269305	NM_001126112.2	273	cGTGTTTGTGCc/cc	8/11	0.458411557164109	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.458411557164109	1		433	522	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972855	55972855	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	61	326	0	ENST00000263923.4:c.1535A>C	p.Lys512Thr	p.K512T	ENST00000263923	NM_002253.2	512	aAa/aCa	11/30	0.295496987178515	1	FACETS	0.798	0.696	0.907	0.798	0.696	0.907	CLONAL	1	TRUE	0	0.458411557164109	1		326	257	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744053	39744053	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	67	359	0	ENST00000361337.2:c.1681G>T	p.Glu561Ter	p.E561*	ENST00000361337	NM_003286.2	561	Gag/Tag	16/21	0.215355014522519	1	FACETS	0.486	0.423	0.553	0.486	0.423	0.553	INDETERMINATE	1	TRUE	0	0.458411557164109	1		359	464	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0066940-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	19	117	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	0.606	0.463	0.77	0.606	0.463	0.77	SUBCLONAL	1	TRUE	1	0.41	2		117	153	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066940-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	63	314	4	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.976	0.85	1	0.976	0.85	1	CLONAL	1	TRUE	1	0.41	2		318	315	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0066940-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	67	414	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	1	2	FACETS	0.805	0.702	0.915	0.805	0.702	0.915	CLONAL	1	TRUE	1	0.41	2		414	406	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089704	27089705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0066940-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	108	480	0	ENST00000324856.7:c.2661dup	p.Gly888ArgfsTer48	p.G888Rfs*48	ENST00000324856	NM_006015.4	887	cca/ccAa	8/20	1	2	FACETS	0.851	0.765	0.942	0.851	0.765	0.942	CLONAL	1	TRUE	1	0.41	2		480	619	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692892	89692892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554898129	NA	P-0066940-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	58	213	0	ENST00000371953.3:c.376G>A	p.Ala126Thr	p.A126T	ENST00000371953	NM_000314.4	126	Gct/Act	5/9	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.41	2		213	281	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629102	86629102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066940-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	93	261	0	ENST00000274376.6:c.847C>T	p.Arg283Cys	p.R283C	ENST00000274376	NM_002890.2	283	Cgt/Tgt	4/25	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.41	2		261	423	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922321	178922321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066940-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	60	222	0	ENST00000263967.3:c.1090G>A	p.Gly364Arg	p.G364R	ENST00000263967	NM_006218.2	364	Gga/Aga	6/21	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.41	2		222	289	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023420	27023420	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066940-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	60	335	0	ENST00000324856.7:c.526C>T	p.Gln176Ter	p.Q176*	ENST00000324856	NM_006015.4	176	Caa/Taa	1/20	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.41	2		335	277	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645877	67645877	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066940-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	114	350	0	ENST00000264010.4:c.805G>T	p.Glu269Ter	p.E269*	ENST00000264010	NM_006565.3	269	Gag/Tag	4/12	1	2	FACETS	0.979	0.884	1	0.979	0.884	1	CLONAL	1	TRUE	1	0.41	2		350	568	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212357	36212357	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066940-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	108	457	0	ENST00000222270.7:c.2108del	p.Ser703ThrfsTer25	p.S703Tfs*25	ENST00000222270	NM_014727.1	703	aGc/ac	3/37	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.41	2		457	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0066941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	237	412	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.594397016421647	2	FACETS	0.993	0.945	1	0.993	0.945	1	CLONAL	2	TRUE	0	0.605500110159837	2		412	394	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0066941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	182	270	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.605500110159837	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.605500110159837	3		270	369	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958791	55958791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	24	309	0	ENST00000263923.4:c.3062C>T	p.Ser1021Leu	p.S1021L	ENST00000263923	NM_002253.2	1021	tCg/tTg	22/30	1	2	FACETS	0.238	0.186	0.298	0.238	0.186	0.298	SUBCLONAL	1	TRUE	1	0.605500110159837	2		309	333	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23640560	23640560	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	98	332	0	ENST00000261584.4:c.2551A>G	p.Asn851Asp	p.N851D	ENST00000261584	NM_024675.3	851	Aac/Gac	6/13	0.605500110159837	4	FACETS	1	0.9	1	0.335	0.3	0.372	CLONAL	1	TRUE	1	0.605500110159837	4		332	517	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374882	45374882	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs776149698	NA	P-0066942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	136	404	0	ENST00000262160.6:c.961C>T	p.Arg321Ter	p.R321*	ENST00000262160	NM_005901.5	321	Cga/Tga	8/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.461093439095403	2		404	480	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0066942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	179	270	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.455247558704594	3	FACETS	0.995	0.926	1	0.995	0.926	1	CLONAL	2	TRUE	1	0.461093439095403	3		270	480	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0066942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	136	464	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.898	0.818	0.981	0.898	0.818	0.981	CLONAL	1	TRUE	1	0.461093439095403	2		464	657	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321697	30321697	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	97	351	0	ENST00000322652.5:c.1552G>A	p.Gly518Arg	p.G518R	ENST00000322652	NM_015355.2	518	Gga/Aga	13/16	1	2	FACETS	0.848	0.759	0.942	0.848	0.759	0.942	CLONAL	1	TRUE	1	0.461093439095403	2		351	496	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479810	67479810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863223746	NA	P-0066942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	282	383	0	ENST00000327367.4:c.1117C>T	p.Arg373Cys	p.R373C	ENST00000327367	NM_005902.3	373	Cgc/Tgc	8/9	0.45809981286865	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.461093439095403	2		383	603	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174395	11174395	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	116	334	0	ENST00000361445.4:c.7280T>G	p.Leu2427Arg	p.L2427R	ENST00000361445	NM_004958.3	2427	cTg/cGg	53/58	1	2	FACETS	0.944	0.854	1	0.944	0.854	1	CLONAL	1	TRUE	1	0.461093439095403	2		334	533	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411576	63411576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	155	214	0	ENST00000330258.3:c.1591C>T	p.Arg531Ter	p.R531*	ENST00000330258	NM_152424.3	531	Cga/Tga	2/2	1	1	FACETS	0.856	0.799	0.913	1	0.992	1	CLONAL	2	TRUE	0	0.461093439095403	1		214	302	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593520	48593520	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	147	342	0	ENST00000342988.3:c.1271A>T	p.Asp424Val	p.D424V	ENST00000342988	NM_005359.5	424	gAt/gTt	10/12	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.461093439095403	2		342	615	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956574	93956574	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	134	413	0	ENST00000369303.4:c.2662G>T	p.Gly888Ter	p.G888*	ENST00000369303	NM_004440.3	888	Gga/Tga	15/17	NA	2	FACETS	1	0.952	1			1	INDETERMINATE	1	TRUE	NA	0.461093439095403	2		413	547	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2086876	2086876	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	157	501	0	ENST00000349721.2:c.2574T>G	p.Asn858Lys	p.N858K	ENST00000349721	NM_003070.3	858	aaT/aaG	18/34	0.461093439095403	3	FACETS	0.984	0.901	1	0.492	0.45	0.535	CLONAL	1	TRUE	1	0.461093439095403	3		501	852	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919803	96919803	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	164	408	0	ENST00000258439.3:c.460A>G	p.Ile154Val	p.I154V	ENST00000258439	NM_001193304.2	154	Atc/Gtc	4/4	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.461093439095403	2		408	663	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604781	48604785	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCT	CTCCT	-	novel	NA	P-0066942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	156	381	0	ENST00000342988.3:c.1603_1607del	p.Leu535ArgfsTer40	p.L535Rfs*40	ENST00000342988	NM_005359.5	535	CTCCTa/a	12/12	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.461093439095403	2		381	662	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132644	67132644	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	112	351	0	ENST00000412916.2:c.527C>A	p.Ser176Tyr	p.S176Y	ENST00000412916		176	tCc/tAc	6/6	1	2	FACETS	0.943	0.852	1	0.943	0.852	1	CLONAL	1	TRUE	1	0.461093439095403	2		351	515	SUCCESS
APC	324	MSKCC	GRCh37	5	112174210	112174210	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0066942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	126	495	0	ENST00000257430.4:c.2919T>A	p.Tyr973Ter	p.Y973*	ENST00000257430	NM_000038.5	973	taT/taA	16/16	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.461093439095403	2		495	523	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0066943-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	142	375	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.505413273773107	2		375	493	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936338	78936338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1212387005	NA	P-0066943-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	191	541	0	ENST00000306801.3:c.3770C>T	p.Thr1257Met	p.T1257M	ENST00000306801	NM_020761.2	1257	aCg/aTg	32/34	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.505413273773107	2		541	737	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0066943-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	198	652	0	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	0.505413273773107	1	FACETS	0.935	0.871	1	0.935	0.871	1	CLONAL	1	TRUE	0	0.505413273773107	1		652	626	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265479	152265479	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766779326	NA	P-0066943-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	193	487	0	ENST00000206249.3:c.932C>T	p.Thr311Met	p.T311M	ENST00000206249	NM_000125.3	311	aCg/aTg	4/8	0.505413273773107	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.505413273773107	1		487	548	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591846	48591846	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066943-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	177	592	0	ENST00000342988.3:c.1009G>T	p.Glu337Ter	p.E337*	ENST00000342988	NM_005359.5	337	Gag/Tag	9/12	0.505413273773107	1	FACETS	0.977	0.906	1	0.977	0.906	1	CLONAL	1	TRUE	0	0.505413273773107	1		592	536	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742485	17742485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066943-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	152	431	1	ENST00000250003.3:c.667C>T	p.Arg223Trp	p.R223W	ENST00000250003	NM_002478.4	223	Cgg/Tgg	2/3	1	2	FACETS	0.946	0.868	1	0.946	0.868	1	CLONAL	1	TRUE	1	0.505413273773107	2		432	636	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971102	21971104	+	missense_variant	Missense_Mutation	TNP	CAG	CAG	GAA	novel	NA	P-0066943-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	168	448	0	ENST00000304494.5:c.254_256delinsTTC	p.Ala85_Ala86delinsValPro	p.A85_A86delinsVP	ENST00000304494	NM_000077.4	85	gCTGcc/gTTCcc	2/3	0.505413273773107	1	FACETS	0.976	0.904	1	0.976	0.904	1	CLONAL	1	TRUE	0	0.505413273773107	1		448	509	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	127	305	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.46	2		305	474	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	162	530	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.9	0.826	0.976	0.9	0.826	0.976	CLONAL	1	TRUE	1	0.46	2		530	783	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	125	382	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	0.945	0.859	1	0.945	0.859	1	CLONAL	1	TRUE	1	0.46	2		382	575	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	75	276	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.881	0.777	0.992	0.881	0.777	0.992	CLONAL	1	TRUE	1	0.46	2		276	370	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724120	61724120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781425578	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	142	389	0	ENST00000401558.2:c.782G>A	p.Arg261Gln	p.R261Q	ENST00000401558	NM_003400.3	261	cGa/cAa	10/25	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.46	2		389	617	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	137	448	0	ENST00000394830.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000394830	NM_018313.4	710	Cga/Tga	17/30	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.46	2		448	593	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257144	16257144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775010663	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	147	499	0	ENST00000375759.3:c.4409G>A	p.Arg1470Gln	p.R1470Q	ENST00000375759	NM_015001.2	1470	cGa/cAa	11/15	1	2	FACETS	0.933	0.854	1	0.933	0.854	1	CLONAL	1	TRUE	1	0.46	2		499	685	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805714	43805714	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs993195285	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	165	442	0	ENST00000372470.3:c.770G>A	p.Arg257His	p.R257H	ENST00000372470	NM_005373.2	257	cGc/cAc	5/12	1	2	FACETS	0.934	0.859	1	0.934	0.859	1	CLONAL	1	TRUE	1	0.46	2		442	768	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241873	72241873	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1252345844	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	102	416	0	ENST00000357731.5:c.517C>T	p.Arg173Ter	p.R173*	ENST00000357731	NM_173808.2	173	Cga/Tga	3/7	1	2	FACETS	0.826	0.741	0.915	0.826	0.741	0.915	CLONAL	1	TRUE	1	0.46	2		416	537	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733503	85733503	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	183	490	0	ENST00000370580.1:c.509C>A	p.Ser170Tyr	p.S170Y	ENST00000370580	NM_003921.4	170	tCt/tAt	3/3	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.46	2		490	761	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746018	162746018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	142	493	0	ENST00000367921.3:c.2141G>A	p.Arg714Gln	p.R714Q	ENST00000367921	NM_006182.2	714	cGa/cAa	16/18	1	2	FACETS	0.957	0.875	1	0.957	0.875	1	CLONAL	1	TRUE	1	0.46	2		493	645	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518415	204518415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs913129198	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	166	508	0	ENST00000367182.3:c.1078C>T	p.Pro360Ser	p.P360S	ENST00000367182	NM_001278516.1	360	Cct/Tct	11/11	1	2	FACETS	0.93	0.856	1	0.93	0.856	1	CLONAL	1	TRUE	1	0.46	2		508	776	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552729	226552729	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746139482	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	163	492	0	ENST00000366794.5:c.2632C>T	p.Arg878Trp	p.R878W	ENST00000366794	NM_001618.3	878	Cgg/Tgg	19/23	1	2	FACETS	0.872	0.801	0.946	0.872	0.801	0.946	CLONAL	1	TRUE	1	0.46	2		492	813	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663891	241663891	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	67	158	0	ENST00000366560.3:c.1237-1G>T		p.X413_splice	ENST00000366560	NM_000143.3	413			1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.46	2		158	259	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405608	70405608	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	129	439	1	ENST00000373644.4:c.3122G>T	p.Arg1041Ile	p.R1041I	ENST00000373644	NM_030625.2	1041	aGa/aTa	4/12	1	2	FACETS	0.874	0.794	0.957	0.874	0.794	0.957	CLONAL	1	TRUE	1	0.46	2		440	642	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88677032	88677032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782400	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	43	153	1	ENST00000372037.3:c.817C>T	p.Arg273Ter	p.R273*	ENST00000372037	NM_004329.2	273	Cga/Tga	9/13	1	2	FACETS	0.87	0.735	1	0.87	0.735	1	CLONAL	1	TRUE	1	0.46	2		154	215	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685272	89685272	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs748031178	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	111	342	0	ENST00000371953.3:c.167T>G	p.Phe56Cys	p.F56C	ENST00000371953	NM_000314.4	56	tTt/tGt	3/9	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.46	2		342	447	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112760262	112760262	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	77	331	0	ENST00000369452.4:c.931G>T	p.Glu311Ter	p.E311*	ENST00000369452	NM_007373.3	311	Gaa/Taa	4/9	1	2	FACETS	0.917	0.811	1	0.917	0.811	1	CLONAL	1	TRUE	1	0.46	2		331	365	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	123	432	0	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	1	2	FACETS	0.905	0.821	0.993	0.905	0.821	0.993	CLONAL	1	TRUE	1	0.46	2		432	591	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132927	64132927	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145356210	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	147	452	0	ENST00000334205.4:c.1061G>A	p.Arg354Gln	p.R354Q	ENST00000334205	NM_003942.2	354	cGa/cAa	9/17	1	2	FACETS	0.888	0.812	0.967	0.888	0.812	0.967	CLONAL	1	TRUE	1	0.46	2		452	720	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924618	94924618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1400088899	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	153	495	0	ENST00000536441.1:c.292C>T	p.Arg98Cys	p.R98C	ENST00000536441	NM_144665.3	98	Cgc/Tgc	3/10	1	2	FACETS	0.974	0.893	1	0.974	0.893	1	CLONAL	1	TRUE	1	0.46	2		495	683	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155078	108155078	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	98	352	0	ENST00000278616.4:c.3871C>A	p.Leu1291Ile	p.L1291I	ENST00000278616	NM_000051.3	1291	Ctt/Att	26/63	1	2	FACETS	0.91	0.816	1	0.91	0.816	1	CLONAL	1	TRUE	1	0.46	2		352	468	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160488	108160488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730881369	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	31	401	1	ENST00000278616.4:c.4396C>T	p.Arg1466Ter	p.R1466*	ENST00000278616	NM_000051.3	1466	Cga/Tga	29/63	1	2	FACETS	0.272	0.22	0.332	0.272	0.22	0.332	SUBCLONAL	1	TRUE	1	0.46	2		402	495	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196225	108196225	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	55	342	0	ENST00000278616.4:c.6761A>G	p.His2254Arg	p.H2254R	ENST00000278616	NM_000051.3	2254	cAc/cGc	46/63	1	2	FACETS	0.504	0.432	0.584	0.504	0.432	0.584	SUBCLONAL	1	TRUE	1	0.46	2		342	474	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118339501	118339501	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	140	426	0	ENST00000534358.1:c.444C>A	p.Phe148Leu	p.F148L	ENST00000534358	NM_005933.3	148	ttC/ttA	2/36	1	2	FACETS	0.925	0.845	1	0.925	0.845	1	CLONAL	1	TRUE	1	0.46	2		426	658	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552613	18552613	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1371859788	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	119	434	0	ENST00000266497.5:c.2024G>T	p.Arg675Ile	p.R675I	ENST00000266497		675	aGa/aTa	14/31	1	2	FACETS	0.948	0.859	1	0.948	0.859	1	CLONAL	1	TRUE	1	0.46	2		434	546	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431709	49431709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752428122	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	153	571	1	ENST00000301067.7:c.9430G>A	p.Ala3144Thr	p.A3144T	ENST00000301067	NM_003482.3	3144	Gca/Aca	34/54	1	2	FACETS	0.867	0.795	0.943	0.867	0.795	0.943	CLONAL	1	TRUE	1	0.46	2		572	767	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50488298	50488298	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	133	440	0	ENST00000394963.4:c.1212G>T	p.Met404Ile	p.M404I	ENST00000394963	NM_003076.4	404	atG/atT	10/13	1	2	FACETS	0.88	0.801	0.963	0.88	0.801	0.963	CLONAL	1	TRUE	1	0.46	2		440	657	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226041	133226041	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373170535	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	154	464	0	ENST00000320574.5:c.3856C>T	p.Arg1286Cys	p.R1286C	ENST00000320574	NM_006231.2	1286	Cgc/Tgc	31/49	1	2	FACETS	0.98	0.9	1	0.98	0.9	1	CLONAL	1	TRUE	1	0.46	2		464	683	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249857	133249857	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1565972665	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	131	404	0	ENST00000320574.5:c.1366G>C	p.Ala456Pro	p.A456P	ENST00000320574	NM_006231.2	456	Gcc/Ccc	14/49	1	2	FACETS	0.931	0.847	1	0.931	0.847	1	CLONAL	1	TRUE	1	0.46	2		404	612	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939073	48939073	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1208736713	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	64	280	0	ENST00000267163.4:c.905C>A	p.Ser302Tyr	p.S302Y	ENST00000267163	NM_000321.2	302	tCt/tAt	9/27	1	2	FACETS	0.872	0.761	0.991	0.872	0.761	0.991	CLONAL	1	TRUE	1	0.46	2		280	319	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942686	48942686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767011440	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	87	335	0	ENST00000267163.4:c.1073G>A	p.Arg358Gln	p.R358Q	ENST00000267163	NM_000321.2	358	cGa/cAa	11/27	1	2	FACETS	0.953	0.849	1	0.953	0.849	1	CLONAL	1	TRUE	1	0.46	2		335	397	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506670	103506670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1372959301	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	120	450	0	ENST00000355739.4:c.413G>A	p.Arg138Gln	p.R138Q	ENST00000355739	NM_000123.3	138	cGa/cAa	4/15	1	2	FACETS	0.831	0.752	0.914	0.831	0.752	0.914	CLONAL	1	TRUE	1	0.46	2		450	628	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023435	33023435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	156	460	0	ENST00000300177.4:c.544G>A	p.Asp182Asn	p.D182N	ENST00000300177	NM_001191322.1	182	Gat/Aat	2/2	1	2	FACETS	0.888	0.814	0.964	0.888	0.814	0.964	CLONAL	1	TRUE	1	0.46	2		460	764	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007743	45007743	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	146	481	0	ENST00000558401.1:c.190G>T	p.Glu64Ter	p.E64*	ENST00000558401	NM_004048.2	64	Gag/Tag	2/4	1	2	FACETS	0.823	0.752	0.898	0.823	0.752	0.898	CLONAL	1	TRUE	1	0.46	2		481	771	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457330	67457330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	195	519	1	ENST00000327367.4:c.304G>A	p.Glu102Lys	p.E102K	ENST00000327367	NM_005902.3	102	Gag/Aag	2/9	1	2	FACETS	0.939	0.87	1	0.939	0.87	1	CLONAL	1	TRUE	1	0.46	2		520	903	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473723	67473723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223740	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	153	428	0	ENST00000327367.4:c.803G>A	p.Arg268His	p.R268H	ENST00000327367	NM_005902.3	268	cGc/cAc	6/9	1	2	FACETS	0.913	0.836	0.992	0.913	0.836	0.992	CLONAL	1	TRUE	1	0.46	2		428	729	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472489	88472489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144852342	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	111	525	0	ENST00000360948.2:c.2066C>T	p.Ala689Val	p.A689V	ENST00000360948	NM_001012338.2	689	gCg/gTg	16/19	0.3	0	FACETS	0.422	0.38	0.467			1	SUBCLONAL	1	TRUE	0	0.46	0		525	617	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346808	91346808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771776126	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	126	414	0	ENST00000355112.3:c.3416G>A	p.Arg1139Gln	p.R1139Q	ENST00000355112	NM_000057.2	1139	cGa/cAa	18/22	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.46	2		414	536	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3794921	3794921	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1252438256	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	111	357	0	ENST00000262367.5:c.3956G>A	p.Arg1319Gln	p.R1319Q	ENST00000262367	NM_004380.2	1319	cGa/cAa	23/31	1	2	FACETS	0.85	0.766	0.937	0.85	0.766	0.937	CLONAL	1	TRUE	1	0.46	2		357	568	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828383	72828383	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1277890729	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	137	512	0	ENST00000268489.5:c.8198G>A	p.Arg2733His	p.R2733H	ENST00000268489	NM_006885.3	2733	cGt/cAt	9/10	1	2	FACETS	0.834	0.76	0.912	0.834	0.76	0.912	CLONAL	1	TRUE	1	0.46	2		512	714	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829497	72829497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761486040	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	108	409	0	ENST00000268489.5:c.7084G>A	p.Asp2362Asn	p.D2362N	ENST00000268489	NM_006885.3	2362	Gac/Aac	9/10	1	2	FACETS	0.749	0.673	0.829	0.749	0.673	0.829	SUBCLONAL	1	TRUE	1	0.46	2		409	627	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993099	72993099	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	144	489	0	ENST00000268489.5:c.946A>C	p.Ile316Leu	p.I316L	ENST00000268489	NM_006885.3	316	Att/Ctt	2/10	1	2	FACETS	0.84	0.768	0.917	0.84	0.768	0.917	CLONAL	1	TRUE	1	0.46	2		489	745	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929510	81929510	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	145	492	0	ENST00000359376.3:c.1171G>T	p.Asp391Tyr	p.D391Y	ENST00000359376	NM_002661.3	391	Gac/Tac	13/33	1	2	FACETS	0.916	0.838	0.998	0.916	0.838	0.998	CLONAL	1	TRUE	1	0.46	2		492	688	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438156	56438156	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs141997049	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	169	438	0	ENST00000407977.2:c.837C>A	p.Phe279Leu	p.F279L	ENST00000407977		279	ttC/ttA	7/10	1	2	FACETS	0.952	0.877	1	0.952	0.877	1	CLONAL	1	TRUE	1	0.46	2		438	772	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372045	45372045	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	131	408	0	ENST00000262160.6:c.1124A>C	p.Lys375Thr	p.K375T	ENST00000262160	NM_005901.5	375	aAa/aCa	9/11	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.46	2		408	569	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375002	45375002	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	126	481	0	ENST00000262160.6:c.841G>T	p.Glu281Ter	p.E281*	ENST00000262160	NM_005901.5	281	Gaa/Taa	8/11	1	2	FACETS	0.971	0.883	1	0.971	0.883	1	CLONAL	1	TRUE	1	0.46	2		481	564	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210815	2210815	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200004531	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	147	453	0	ENST00000398665.3:c.1312G>A	p.Ala438Thr	p.A438T	ENST00000398665	NM_032482.2	438	Gct/Act	14/28	1	2	FACETS	0.997	0.913	1	0.997	0.913	1	CLONAL	1	TRUE	1	0.46	2		453	641	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210733	5210733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779302415	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	124	501	0	ENST00000357368.4:c.5318C>T	p.Ser1773Leu	p.S1773L	ENST00000357368	NM_002850.3	1773	tCg/tTg	34/38	1	2	FACETS	0.767	0.695	0.843	0.767	0.695	0.843	SUBCLONAL	1	TRUE	1	0.46	2		501	703	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212224	5212224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151279682	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	36	515	0	ENST00000357368.4:c.4807G>A	p.Asp1603Asn	p.D1603N	ENST00000357368	NM_002850.3	1603	Gac/Aac	32/38	1	2	FACETS	0.223	0.182	0.268	0.223	0.182	0.268	SUBCLONAL	1	TRUE	1	0.46	2		515	703	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265175	5265175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147257283	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	164	455	0	ENST00000357368.4:c.412G>A	p.Asp138Asn	p.D138N	ENST00000357368	NM_002850.3	138	Gac/Aac	5/38	1	2	FACETS	0.971	0.894	1	0.971	0.894	1	CLONAL	1	TRUE	1	0.46	2		455	734	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10292746	10292746	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	121	304	0	ENST00000340748.4:c.88G>T	p.Asp30Tyr	p.D30Y	ENST00000340748		30	Gat/Tat	2/40	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.46	2		304	525	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425290	47425290	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178800275	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	188	526	0	ENST00000404338.3:c.3358C>T	p.Arg1120Trp	p.R1120W	ENST00000404338	NM_004491.4	1120	Cgg/Tgg	1/6	1	2	FACETS	0.938	0.868	1	0.938	0.868	1	CLONAL	1	TRUE	1	0.46	2		526	871	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068357	26068357	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	173	289	0	ENST00000435504.4:c.133G>T	p.Glu45Ter	p.E45*	ENST00000435504		45	Gaa/Taa	2/13	1	2	FACETS	0.969	0.905	1	1	0.993	1	CLONAL	2	TRUE	1	0.46	2		289	388	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606678	29606678	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs188859061	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	129	473	0	ENST00000389048.3:c.1202G>A	p.Arg401Gln	p.R401Q	ENST00000389048	NM_004304.4	401	cGa/cAa	5/29	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.46	2		473	530	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	98	356	0	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.46	2		356	415	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	14	426	0	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	0.105	0.075	0.142	0.105	0.075	0.142	SUBCLONAL	1	TRUE	1	0.46	2		426	578	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921750	111921750	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs185078669	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	140	438	0	ENST00000393256.3:c.539G>A	p.Arg180Gln	p.R180Q	ENST00000393256	NM_006538.4	180	cGa/cAa	4/4	1	2	FACETS	0.934	0.853	1	0.934	0.853	1	CLONAL	1	TRUE	1	0.46	2		438	652	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038133	128038133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369244363	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	114	363	0	ENST00000285398.2:c.1417G>A	p.Glu473Lys	p.E473K	ENST00000285398	NM_000122.1	473	Gaa/Aaa	9/15	1	2	FACETS	0.777	0.701	0.857	0.777	0.701	0.857	SUBCLONAL	1	TRUE	1	0.46	2		363	638	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131192	202131192	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	105	427	0	ENST00000358485.4:c.160C>A	p.Leu54Ile	p.L54I	ENST00000358485	NM_001080125.1	54	Ctc/Atc	2/9	1	2	FACETS	0.769	0.69	0.851	0.769	0.69	0.851	SUBCLONAL	1	TRUE	1	0.46	2		427	594	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136279	202136279	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	103	447	0	ENST00000358485.4:c.523G>T	p.Glu175Ter	p.E175*	ENST00000358485	NM_001080125.1	175	Gaa/Taa	3/9	1	2	FACETS	0.722	0.647	0.801	0.722	0.647	0.801	SUBCLONAL	1	TRUE	1	0.46	2		447	620	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483964	212483964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	66	407	0	ENST00000342788.4:c.2239C>T	p.Pro747Ser	p.P747S	ENST00000342788	NM_005235.2	747	Cct/Tct	19/28	1	2	FACETS	0.867	0.758	0.983	0.867	0.758	0.983	CLONAL	1	TRUE	1	0.46	2		407	331	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368470	225368470	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	101	381	0	ENST00000264414.4:c.1276G>T	p.Asp426Tyr	p.D426Y	ENST00000264414	NM_003590.4	426	Gat/Tat	9/16	1	2	FACETS	0.924	0.83	1	0.924	0.83	1	CLONAL	1	TRUE	1	0.46	2		381	475	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775575	39775575	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	150	533	0	ENST00000288319.7:c.445G>T	p.Glu149Ter	p.E149*	ENST00000288319	NM_182918.3	149	Gaa/Taa	4/10	1	2	FACETS	0.911	0.834	0.991	0.911	0.834	0.991	CLONAL	1	TRUE	1	0.46	2		533	716	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275192	41275192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	219	499	0	ENST00000349496.5:c.1358G>A	p.Arg453Gln	p.R453Q	ENST00000349496	NM_001904.3	453	cGg/cAg	9/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.46	2		499	856	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127805	47127805	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	150	410	0	ENST00000409792.3:c.5278-1G>T		p.X1760_splice	ENST00000409792	NM_014159.6	1760			1	2	FACETS	0.919	0.841	0.999	0.919	0.841	0.999	CLONAL	1	TRUE	1	0.46	2		410	710	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164118	47164118	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	115	456	0	ENST00000409792.3:c.2008G>T	p.Glu670Ter	p.E670*	ENST00000409792	NM_014159.6	670	Gaa/Taa	3/21	1	2	FACETS	0.893	0.807	0.983	0.893	0.807	0.983	CLONAL	1	TRUE	1	0.46	2		456	560	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164366	47164366	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1299511576	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	41	446	0	ENST00000409792.3:c.1760C>A	p.Ser587Tyr	p.S587Y	ENST00000409792	NM_014159.6	587	tCt/tAt	3/21	1	2	FACETS	0.362	0.301	0.43	0.362	0.301	0.43	SUBCLONAL	1	TRUE	1	0.46	2		446	492	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670597	134670597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1330628001	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	123	470	0	ENST00000398015.3:c.508C>T	p.Arg170Trp	p.R170W	ENST00000398015	NM_004441.4	170	Cgg/Tgg	3/16	0.3	1	FACETS	0.728	0.66	0.798	0.728	0.66	0.798	SUBCLONAL	1	TRUE	0	0.46	1		470	566	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426050	138426050	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	97	350	0	ENST00000289153.2:c.1481A>C	p.Lys494Thr	p.K494T	ENST00000289153	NM_006219.2	494	aAa/aCa	9/22	1	2	FACETS	0.884	0.792	0.981	0.884	0.792	0.981	CLONAL	1	TRUE	1	0.46	2		350	477	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	127	464	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	0.861	0.782	0.944	0.861	0.782	0.944	CLONAL	1	TRUE	1	0.46	2		464	641	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129932	55129934	+	missense_variant	Missense_Mutation	TNP	GAG	GAG	AAT	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	151	459	0	ENST00000257290.5:c.466_468delinsAAT	p.Glu156Asn	p.E156N	ENST00000257290	NM_006206.4	156	GAG/AAT	4/23	0.0900906161516501	0	FACETS	0.501	0.459	0.545			1	INDETERMINATE	1	TRUE	0	0.46	0		459	708	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133597	55133597	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	133	464	0	ENST00000257290.5:c.901G>T	p.Glu301Ter	p.E301*	ENST00000257290	NM_006206.4	301	Gaa/Taa	6/23	0.0900906161516501	0	FACETS	0.507	0.462	0.554			1	INDETERMINATE	1	TRUE	0	0.46	0		464	616	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136799	55136799	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	73	290	0	ENST00000257290.5:c.1122-1G>T		p.X374_splice	ENST00000257290	NM_006206.4	374			0.0900906161516501	0	FACETS	0.458	0.403	0.517			1	INDETERMINATE	1	TRUE	0	0.46	0		290	374	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604643	55604643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745651409	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	128	434	0	ENST00000288135.5:c.2851G>A	p.Val951Ile	p.V951I	ENST00000288135	NM_000222.2	951	Gta/Ata	21/21	0.0900906161516501	0	FACETS	0.479	0.435	0.524			1	INDETERMINATE	1	TRUE	0	0.46	0		434	628	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156325	106156325	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	55	566	0	ENST00000380013.4:c.1226C>A	p.Pro409His	p.P409H	ENST00000380013	NM_001127208.2	409	cCt/cAt	3/11	1	2	FACETS	0.297	0.253	0.345	0.297	0.253	0.345	SUBCLONAL	1	TRUE	1	0.46	2		566	805	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244184	153244184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759610249	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	185	501	0	ENST00000281708.4:c.1973G>A	p.Arg658Gln	p.R658Q	ENST00000281708	NM_033632.3	658	cGa/cAa	12/12	1	2	FACETS	0.974	0.9	1	0.974	0.9	1	CLONAL	1	TRUE	1	0.46	2		501	826	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251990	153251990	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	106	372	0	ENST00000281708.4:c.1016G>T	p.Arg339Ile	p.R339I	ENST00000281708	NM_033632.3	339	aGa/aTa	7/12	1	2	FACETS	0.954	0.86	1	0.954	0.86	1	CLONAL	1	TRUE	1	0.46	2		372	483	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510219	187510219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276553545	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	137	424	1	ENST00000441802.2:c.13294G>A	p.Glu4432Lys	p.E4432K	ENST00000441802	NM_005245.3	4432	Gaa/Aaa	27/27	1	2	FACETS	0.801	0.729	0.876	0.801	0.729	0.876	CLONAL	1	TRUE	1	0.46	2		425	744	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534362	187534362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375701023	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	136	422	0	ENST00000441802.2:c.9364G>A	p.Ala3122Thr	p.A3122T	ENST00000441802	NM_005245.3	3122	Gcc/Acc	13/27	1	2	FACETS	0.851	0.775	0.93	0.851	0.775	0.93	CLONAL	1	TRUE	1	0.46	2		422	695	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584530	187584530	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200633985	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	185	469	0	ENST00000441802.2:c.3503C>T	p.Ser1168Leu	p.S1168L	ENST00000441802	NM_005245.3	1168	tCg/tTg	3/27	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.46	2		469	679	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295845	1295845	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	179	608	0				ENST00000310581	NM_198253.2	-/1132			0.0900906161516501	0	FACETS	0.497	0.459	0.537			1	INDETERMINATE	1	TRUE	0	0.46	0		608	845	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409261	31409261	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	154	476	0	ENST00000344624.3:c.3756C>A	p.Phe1252Leu	p.F1252L	ENST00000344624		1252	ttC/ttA	30/33	0.0900906161516501	0	FACETS	0.572	0.525	0.621			1	INDETERMINATE	1	TRUE	0	0.46	0		476	632	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867477	35867477	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	86	393	0	ENST00000303115.3:c.291G>T	p.Lys97Asn	p.K97N	ENST00000303115	NM_002185.3	97	aaG/aaT	3/8	1	2	FACETS	0.719	0.638	0.806	0.719	0.638	0.806	SUBCLONAL	1	TRUE	1	0.46	2		393	520	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945757	38945757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1032272899	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	107	419	0	ENST00000357387.3:c.4469C>T	p.Thr1490Met	p.T1490M	ENST00000357387	NM_152756.3	1490	aCg/aTg	34/38	1	2	FACETS	0.802	0.721	0.887	0.802	0.721	0.887	CLONAL	1	TRUE	1	0.46	2		419	580	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947466	38947466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	126	451	0	ENST00000357387.3:c.4214G>A	p.Arg1405Gln	p.R1405Q	ENST00000357387	NM_152756.3	1405	cGa/cAa	32/38	1	2	FACETS	0.954	0.867	1	0.954	0.867	1	CLONAL	1	TRUE	1	0.46	2		451	574	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950648	38950648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776074870	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	11	504	0	ENST00000357387.3:c.3302C>T	p.Ser1101Leu	p.S1101L	ENST00000357387	NM_152756.3	1101	tCg/tTg	31/38	1	2	FACETS	0.089	0.061	0.124	0.089	0.061	0.124	SUBCLONAL	1	TRUE	1	0.46	2		504	539	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590466	67590466	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	130	414	0	ENST00000274335.5:c.1528G>T	p.Glu510Ter	p.E510*	ENST00000274335		510	Gaa/Taa	11/15	0.0900906161516501	3	FACETS	1	0.972	1	0.582	0.53	0.637	INDETERMINATE	1	TRUE	1	0.46	3		414	597	SUCCESS
APC	324	MSKCC	GRCh37	5	112103015	112103015	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1064793535	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	138	415	0	ENST00000257430.4:c.350C>A	p.Ser117Ter	p.S117*	ENST00000257430	NM_000038.5	117	tCa/tAa	4/16	1	2	FACETS	0.94	0.858	1	0.94	0.858	1	CLONAL	1	TRUE	1	0.46	2		415	638	SUCCESS
APC	324	MSKCC	GRCh37	5	112175103	112175103	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	78	460	0	ENST00000257430.4:c.3812T>G	p.Phe1271Cys	p.F1271C	ENST00000257430	NM_000038.5	1271	tTt/tGt	16/16	1	2	FACETS	0.573	0.504	0.647	0.573	0.504	0.647	SUBCLONAL	1	TRUE	1	0.46	2		460	592	SUCCESS
APC	324	MSKCC	GRCh37	5	112175166	112175166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371113837	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	111	453	0	ENST00000257430.4:c.3875C>T	p.Thr1292Met	p.T1292M	ENST00000257430	NM_000038.5	1292	aCg/aTg	16/16	1	2	FACETS	0.695	0.626	0.769	0.695	0.626	0.769	SUBCLONAL	1	TRUE	1	0.46	2		453	694	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407567	407567	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	119	351	0	ENST00000380956.4:c.1325G>A	p.Arg442Lys	p.R442K	ENST00000380956	NM_001195286.1	442	aGa/aAa	9/9	1	2	FACETS	0.984	0.892	1	0.984	0.892	1	CLONAL	1	TRUE	1	0.46	2		351	526	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323184	31323184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2308488	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	194	601	0	ENST00000412585.2:c.805G>A	p.Ala269Thr	p.A269T	ENST00000412585	NM_005514.6	269	Gca/Aca	4/8	1	2	FACETS	0.834	0.772	0.899	0.834	0.772	0.899	CLONAL	1	TRUE	1	0.46	2		601	1011	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555167	106555167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747743863	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	152	491	1	ENST00000369096.4:c.2284G>A	p.Val762Met	p.V762M	ENST00000369096	NM_001198.3	762	Gtg/Atg	7/7	0.3	3	FACETS	0.985	0.902	1			1	CLONAL	1	TRUE	NA	0.46	3		492	825	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663635	117663635	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs755903627	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	88	369	0	ENST00000368508.3:c.4597A>C	p.Lys1533Gln	p.K1533Q	ENST00000368508	NM_002944.2	1533	Aaa/Caa	28/43	0.122063018292711	0	FACETS	0.52	0.464	0.58			1	INDETERMINATE	1	TRUE	0	0.46	0		369	397	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199594	138199594	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	164	497	0	ENST00000237289.4:c.1012G>T	p.Glu338Ter	p.E338*	ENST00000237289	NM_001270507.1	338	Gaa/Taa	7/9	0.3	3	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.46	3		497	648	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150022982	150022982	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	117	419	0	ENST00000253339.5:c.281C>A	p.Ser94Tyr	p.S94Y	ENST00000253339		94	tCt/tAt	1/7	0.3	3	FACETS	1	0.943	1			1	CLONAL	1	TRUE	NA	0.46	3		419	590	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026397	6026397	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	59	222	0	ENST00000265849.7:c.1999G>T	p.Glu667Ter	p.E667*	ENST00000265849	NM_000535.5	667	Gag/Tag	11/15	1	2	FACETS	0.744	0.643	0.852	0.744	0.643	0.852	SUBCLONAL	1	TRUE	1	0.46	2		222	345	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508609	106508609	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	88	409	0	ENST00000359195.3:c.603G>A	p.Trp201Ter	p.W201*	ENST00000359195	NM_002649.2	201	tgG/tgA	2/11	1	2	FACETS	0.683	0.606	0.765	0.683	0.606	0.765	SUBCLONAL	1	TRUE	1	0.46	2		409	560	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509539	106509539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	143	495	0	ENST00000359195.3:c.1533G>T	p.Glu511Asp	p.E511D	ENST00000359195	NM_002649.2	511	gaG/gaT	2/11	1	2	FACETS	0.828	0.756	0.903	0.828	0.756	0.903	CLONAL	1	TRUE	1	0.46	2		495	751	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523708	148523708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520183	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	106	374	0	ENST00000320356.2:c.745G>A	p.Glu249Lys	p.E249K	ENST00000320356	NM_004456.4	249	Gaa/Aaa	8/20	1	2	FACETS	0.836	0.752	0.925	0.836	0.752	0.925	CLONAL	1	TRUE	1	0.46	2		374	551	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879084	151879084	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	161	544	0	ENST00000262189.6:c.5861C>A	p.Ser1954Tyr	p.S1954Y	ENST00000262189	NM_170606.2	1954	tCt/tAt	36/59	1	2	FACETS	0.962	0.884	1	0.962	0.884	1	CLONAL	1	TRUE	1	0.46	2		544	728	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69012038	69012038	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	86	406	0	ENST00000288368.4:c.2675G>T	p.Arg892Ile	p.R892I	ENST00000288368	NM_024870.2	892	aGa/aTa	23/40	0.122063018292711	0	FACETS	0.496	0.441	0.554			1	INDETERMINATE	1	TRUE	0	0.46	0		406	407	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964514	70964514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762086448	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	153	555	2	ENST00000276594.2:c.1514G>A	p.Arg505His	p.R505H	ENST00000276594	NM_024504.3	505	cGc/cAc	8/8	0.122063018292711	0	FACETS	0.495	0.453	0.538			1	INDETERMINATE	1	TRUE	0	0.46	0		557	726	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141569503	141569503	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	129	386	0	ENST00000220592.5:c.781G>T	p.Glu261Ter	p.E261*	ENST00000220592	NM_012154.3	261	Gaa/Taa	6/19	1	2	FACETS	0.876	0.797	0.96	0.876	0.797	0.96	CLONAL	1	TRUE	1	0.46	2		386	640	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2191349	2191349	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs747368303	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	133	525	0	ENST00000349721.2:c.4678C>T	p.Arg1560Ter	p.R1560*	ENST00000349721	NM_003070.3	1560	Cga/Tga	33/34	1	2	FACETS	0.784	0.712	0.858	0.784	0.712	0.858	SUBCLONAL	1	TRUE	1	0.46	2		525	738	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054649	5054649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373174105	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	105	455	0	ENST00000381652.3:c.701G>A	p.Arg234His	p.R234H	ENST00000381652	NM_004972.3	234	cGc/cAc	7/25	1	2	FACETS	0.849	0.763	0.939	0.849	0.763	0.939	CLONAL	1	TRUE	1	0.46	2		455	538	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090791	5090791	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	106	463	0	ENST00000381652.3:c.2939G>T	p.Arg980Ile	p.R980I	ENST00000381652	NM_004972.3	980	aGa/aTa	22/25	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.46	2		463	444	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465627	8465627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	57	433	0	ENST00000356435.5:c.3553G>A	p.Glu1185Lys	p.E1185K	ENST00000356435		1185	Gaa/Aaa	21/35	1	2	FACETS	0.457	0.392	0.528	0.457	0.392	0.528	SUBCLONAL	1	TRUE	1	0.46	2		433	542	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239843	98239843	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1398130707	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	123	361	0	ENST00000331920.6:c.1489G>A	p.Ala497Thr	p.A497T	ENST00000331920	NM_000264.3	497	Gct/Act	10/24	1	2	FACETS	0.878	0.796	0.964	0.878	0.796	0.964	CLONAL	1	TRUE	1	0.46	2		361	609	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128432165	128432165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1371596131	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	82	317	0	ENST00000265960.3:c.281G>A	p.Arg94Gln	p.R94Q	ENST00000265960	NM_001006617.1	94	cGa/cAa	3/12	1	2	FACETS	0.778	0.689	0.873	0.778	0.689	0.873	SUBCLONAL	1	TRUE	1	0.46	2		317	458	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875930	76875930	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	99	217	0	ENST00000373344.5:c.5205G>T	p.Met1735Ile	p.M1735I	ENST00000373344	NM_000489.3	1735	atG/atT	20/35	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.46	1		217	248	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938028	76938028	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143413618	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	15	270	1	ENST00000373344.5:c.2720G>A	p.Arg907Gln	p.R907Q	ENST00000373344	NM_000489.3	907	cGa/cAa	9/35	1	1	FACETS	0.149	0.109	0.199	0.149	0.109	0.199	SUBCLONAL	1	TRUE	0	0.46	1		271	336	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220477	123220477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1372684971	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	136	232	0	ENST00000218089.9:c.3134G>A	p.Arg1045Gln	p.R1045Q	ENST00000218089	NM_001042749.1	1045	cGa/cAa	30/35	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.46	1		232	349	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074308	8074308	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	198	507	0	ENST00000377482.5:c.351A>C	p.Lys117Asn	p.K117N	ENST00000377482	NM_018948.3	117	aaA/aaC	4/4	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.46	2		507	832	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11177109	11177109	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	119	376	0	ENST00000361445.4:c.6968C>A	p.Ser2323Tyr	p.S2323Y	ENST00000361445	NM_004958.3	2323	tCt/tAt	50/58	1	2	FACETS	0.827	0.748	0.909	0.827	0.748	0.909	CLONAL	1	TRUE	1	0.46	2		376	626	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307976	11307976	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	179	445	0	ENST00000361445.4:c.1016A>G	p.His339Arg	p.H339R	ENST00000361445	NM_004958.3	339	cAc/cGc	7/58	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.46	2		445	746	SUCCESS
MAD2L2	10459	MSKCC	GRCh37	1	11736936	11736936	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	118	404	0	ENST00000235310.3:c.301G>T	p.Glu101Ter	p.E101*	ENST00000235310		101	Gag/Tag	7/11	1	2	FACETS	0.747	0.675	0.823	0.747	0.675	0.823	SUBCLONAL	1	TRUE	1	0.46	2		404	687	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255568	16255568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs956946321	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	43	463	0	ENST00000375759.3:c.2833C>T	p.Leu945Phe	p.L945F	ENST00000375759	NM_015001.2	945	Ctt/Ttt	11/15	1	2	FACETS	0.234	0.195	0.277	0.234	0.195	0.277	SUBCLONAL	1	TRUE	1	0.46	2		463	800	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059192	27059192	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	137	341	0	ENST00000324856.7:c.1829C>T	p.Ser610Phe	p.S610F	ENST00000324856	NM_006015.4	610	tCt/tTt	4/20	1	2	FACETS	0.98	0.894	1	0.98	0.894	1	CLONAL	1	TRUE	1	0.46	2		341	608	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363236	40363236	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	152	503	0	ENST00000397332.2:c.993C>A	p.Phe331Leu	p.F331L	ENST00000397332	NM_001033082.2	331	ttC/ttA	3/3	1	2	FACETS	0.842	0.771	0.916	0.842	0.771	0.916	CLONAL	1	TRUE	1	0.46	2		503	785	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78425883	78425883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	138	462	0	ENST00000370768.2:c.1562C>T	p.Ala521Val	p.A521V	ENST00000370768	NM_003902.3	521	gCt/gTt	16/20	1	2	FACETS	0.78	0.711	0.853	0.78	0.711	0.853	SUBCLONAL	1	TRUE	1	0.46	2		462	769	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150913815	150913815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	121	332	0	ENST00000271640.5:c.458C>T	p.Ala153Val	p.A153V	ENST00000271640	NM_001145415.1	153	gCt/gTt	5/22	1	2	FACETS	0.884	0.801	0.971	0.884	0.801	0.971	CLONAL	1	TRUE	1	0.46	2		332	595	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150915099	150915099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371182642	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	150	465	0	ENST00000271640.5:c.608G>A	p.Arg203Gln	p.R203Q	ENST00000271640	NM_001145415.1	203	cGa/cAa	6/22	1	2	FACETS	0.865	0.792	0.941	0.865	0.792	0.941	CLONAL	1	TRUE	1	0.46	2		465	754	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176104197	176104197	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs2149730404	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	104	360	0	ENST00000367669.3:c.917T>C	p.Val306Ala	p.V306A	ENST00000367669	NM_022457.5	306	gTc/gCc	8/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.46	2		360	402	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63700053	63700053	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	193	409	0	ENST00000279873.7:c.388A>C	p.Lys130Gln	p.K130Q	ENST00000279873	NM_032199.2	130	Aaa/Caa	3/10	1	2	FACETS	0.959	0.888	1	0.959	0.888	1	CLONAL	1	TRUE	1	0.46	2		409	875	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57004162	57004162	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	136	460	0	ENST00000257254.3:c.317G>T	p.Ser106Ile	p.S106I	ENST00000257254		106	aGc/aTc	1/2	0.185398855874445	1	FACETS	0.668	0.608	0.73	0.668	0.608	0.73	INDETERMINATE	1	TRUE	0	0.46	1		460	682	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94170371	94170371	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745614941	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	65	274	0	ENST00000323929.3:c.1898G>A	p.Arg633Gln	p.R633Q	ENST00000323929	NM_005591.3	633	cGa/cAa	17/20	1	2	FACETS	0.88	0.769	0.999	0.88	0.769	0.999	CLONAL	1	TRUE	1	0.46	2		274	321	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194110	94194110	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773469981	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	76	298	0	ENST00000323929.3:c.1318G>A	p.Ala440Thr	p.A440T	ENST00000323929	NM_005591.3	440	Gca/Aca	12/20	1	2	FACETS	0.995	0.88	1	0.995	0.88	1	CLONAL	1	TRUE	1	0.46	2		298	332	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212851	94212851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368403414	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	77	369	0	ENST00000323929.3:c.391G>A	p.Asp131Asn	p.D131N	ENST00000323929	NM_005591.3	131	Gat/Aat	5/20	1	2	FACETS	0.87	0.768	0.977	0.87	0.768	0.977	CLONAL	1	TRUE	1	0.46	2		369	385	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343711	118343711	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	150	429	0	ENST00000534358.1:c.1837C>T	p.Arg613Ter	p.R613*	ENST00000534358	NM_005933.3	613	Cga/Tga	3/36	1	2	FACETS	0.871	0.797	0.948	0.871	0.797	0.948	CLONAL	1	TRUE	1	0.46	2		429	749	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376311	118376311	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	148	508	0	ENST00000534358.1:c.9704A>C	p.Lys3235Thr	p.K3235T	ENST00000534358	NM_005933.3	3235	aAa/aCa	27/36	1	2	FACETS	0.885	0.81	0.964	0.885	0.81	0.964	CLONAL	1	TRUE	1	0.46	2		508	727	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125513761	125513761	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	116	448	0	ENST00000428830.2:c.889A>T	p.Asn297Tyr	p.N297Y	ENST00000428830	NM_001114121.2	297	Aat/Tat	9/14	1	2	FACETS	0.917	0.83	1	0.917	0.83	1	CLONAL	1	TRUE	1	0.46	2		448	550	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514053	125514053	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	103	508	0	ENST00000428830.2:c.991A>C	p.Ser331Arg	p.S331R	ENST00000428830	NM_001114121.2	331	Agc/Cgc	10/14	1	2	FACETS	0.671	0.601	0.746	0.671	0.601	0.746	SUBCLONAL	1	TRUE	1	0.46	2		508	667	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552625	18552625	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	155	438	0	ENST00000266497.5:c.2036T>G	p.Phe679Cys	p.F679C	ENST00000266497		679	tTt/tGt	14/31	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.46	2		438	558	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636322	21636322	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	83	405	0	ENST00000421138.2:c.688G>T	p.Asp230Tyr	p.D230Y	ENST00000421138		230	Gat/Tat	7/16	1	2	FACETS	0.771	0.683	0.865	0.771	0.683	0.865	SUBCLONAL	1	TRUE	1	0.46	2		405	468	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231331	46231331	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	127	416	0	ENST00000334344.6:c.1171A>G	p.Ile391Val	p.I391V	ENST00000334344	NM_152641.2	391	Att/Gtt	10/21	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.46	2		416	523	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28644727	28644727	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	128	416	0	ENST00000241453.7:c.66del	p.Phe22LeufsTer11	p.F22Lfs*11	ENST00000241453	NM_004119.2	22	ttT/tt	2/24	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.46	2		416	550	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906931	32906931	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	137	471	0	ENST00000380152.3:c.1316T>G	p.Phe439Cys	p.F439C	ENST00000380152		439	tTt/tGt	10/27	1	2	FACETS	0.947	0.864	1	0.947	0.864	1	CLONAL	1	TRUE	1	0.46	2		471	629	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506181	103506181	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	127	385	0	ENST00000355739.4:c.339T>G	p.Phe113Leu	p.F113L	ENST00000355739	NM_000123.3	113	ttT/ttG	3/15	1	2	FACETS	0.928	0.844	1	0.928	0.844	1	CLONAL	1	TRUE	1	0.46	2		385	595	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574747	95574747	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1131691210	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	113	451	0	ENST00000393063.1:c.2350G>T	p.Glu784Ter	p.E784*	ENST00000393063	NM_030621.3	784	Gaa/Taa	16/28	1	2	FACETS	0.892	0.805	0.982	0.892	0.805	0.982	CLONAL	1	TRUE	1	0.46	2		451	551	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95595941	95595941	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749484792	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	101	404	0	ENST00000393063.1:c.602G>A	p.Arg201His	p.R201H	ENST00000393063	NM_030621.3	201	cGc/cAc	7/28	1	2	FACETS	0.963	0.865	1	0.963	0.865	1	CLONAL	1	TRUE	1	0.46	2		404	456	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41023252	41023252	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	100	365	0	ENST00000267868.3:c.897-1G>T		p.X299_splice	ENST00000267868	NM_002875.4	299			1	2	FACETS	0.736	0.658	0.817	0.736	0.658	0.817	SUBCLONAL	1	TRUE	1	0.46	2		365	591	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042423	42042423	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	176	484	0	ENST00000219905.7:c.6618G>T	p.Lys2206Asn	p.K2206N	ENST00000219905	NM_001164273.1	2206	aaG/aaT	17/24	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.46	2		484	713	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748744	43748744	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs753789253	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	137	504	0	ENST00000382044.4:c.2062A>C	p.Asn688His	p.N688H	ENST00000382044	NM_001141980.1	688	Aat/Cat	12/28	1	2	FACETS	0.889	0.811	0.971	0.889	0.811	0.971	CLONAL	1	TRUE	1	0.46	2		504	670	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007799	45007799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	159	472	0	ENST00000558401.1:c.246C>A	p.Phe82Leu	p.F82L	ENST00000558401	NM_004048.2	82	ttC/ttA	2/4	1	2	FACETS	0.874	0.802	0.949	0.874	0.802	0.949	CLONAL	1	TRUE	1	0.46	2		472	791	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50757338	50757338	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	26	129	0	ENST00000307179.4:c.636T>A	p.Asp212Glu	p.D212E	ENST00000307179		212	gaT/gaA	7/20	1	2	FACETS	0.661	0.528	0.81	0.661	0.528	0.81	SUBCLONAL	1	TRUE	1	0.46	2		129	171	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50757355	50757355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	16	56	0	ENST00000307179.4:c.653C>T	p.Ser218Phe	p.S218F	ENST00000307179		218	tCt/tTt	7/20	1	2	FACETS	0.809	0.609	1	0.809	0.609	1	CLONAL	1	TRUE	1	0.46	2		56	86	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50788096	50788096	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	83	343	0	ENST00000307179.4:c.2710T>G	p.Phe904Val	p.F904V	ENST00000307179		904	Ttt/Gtt	17/20	1	2	FACETS	0.725	0.641	0.813	0.725	0.641	0.813	SUBCLONAL	1	TRUE	1	0.46	2		343	498	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454570	99454570	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	41	432	0	ENST00000268035.6:c.1489T>A	p.Ser497Thr	p.S497T	ENST00000268035	NM_000875.3	497	Tcc/Acc	7/21	1	2	FACETS	0.275	0.228	0.327	0.275	0.228	0.327	SUBCLONAL	1	TRUE	1	0.46	2		432	648	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857314	68857314	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747235838	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	140	378	0	ENST00000261769.5:c.1949T>C	p.Ile650Thr	p.I650T	ENST00000261769	NM_004360.3	650	aTc/aCc	13/16	1	2	FACETS	0.971	0.887	1	0.971	0.887	1	CLONAL	1	TRUE	1	0.46	2		378	627	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351594	89351594	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	160	535	0	ENST00000301030.4:c.1356T>G	p.Asn452Lys	p.N452K	ENST00000301030	NM_001256183.1	452	aaT/aaG	9/13	1	2	FACETS	0.838	0.769	0.91	0.838	0.769	0.91	CLONAL	1	TRUE	1	0.46	2		535	830	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813006	89813006	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	164	429	0	ENST00000389301.3:c.3499T>G	p.Leu1167Val	p.L1167V	ENST00000389301	NM_000135.2	1167	Ttg/Gtg	35/43	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.46	2		429	669	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677314	29677314	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	78	329	0	ENST00000356175.3:c.7372C>A	p.His2458Asn	p.H2458N	ENST00000356175	NM_000267.3	2458	Cat/Aat	49/57	1	2	FACETS	0.8	0.706	0.9	0.8	0.706	0.9	SUBCLONAL	1	TRUE	1	0.46	2		329	424	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679514	33679514	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs939685161	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	109	276	0	ENST00000308377.4:c.2567G>T	p.Arg856Leu	p.R856L	ENST00000308377	NM_152270.3	856	cGa/cTa	5/5	1	2	FACETS	0.942	0.85	1	0.942	0.85	1	CLONAL	1	TRUE	1	0.46	2		276	503	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33680112	33680112	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	51	273	0	ENST00000308377.4:c.1969G>T	p.Glu657Ter	p.E657*	ENST00000308377	NM_152270.3	657	Gaa/Taa	5/5	1	2	FACETS	0.632	0.539	0.733	0.632	0.539	0.733	SUBCLONAL	1	TRUE	1	0.46	2		273	351	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40864329	40864329	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	149	447	0	ENST00000428826.2:c.1379T>C	p.Leu460Pro	p.L460P	ENST00000428826		460	cTg/cCg	12/21	1	2	FACETS	0.942	0.862	1	0.942	0.862	1	CLONAL	1	TRUE	1	0.46	2		447	688	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245425	41245425	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs80357182	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	141	517	0	ENST00000357654.3:c.2123C>A	p.Ser708Tyr	p.S708Y	ENST00000357654	NM_007294.3	708	tCt/tAt	10/23	1	2	FACETS	0.93	0.85	1	0.93	0.85	1	CLONAL	1	TRUE	1	0.46	2		517	659	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006834	62006834	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	128	499	0	ENST00000392795.3:c.554A>G	p.Asp185Gly	p.D185G	ENST00000392795	NM_001039933.1	185	gAt/gGt	5/6	1	2	FACETS	0.777	0.705	0.853	0.777	0.705	0.853	SUBCLONAL	1	TRUE	1	0.46	2		499	716	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584329	39584329	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	107	420	0	ENST00000262039.4:c.994A>C	p.Lys332Gln	p.K332Q	ENST00000262039	NM_002647.2	332	Aaa/Caa	10/25	1	2	FACETS	0.866	0.78	0.957	0.866	0.78	0.957	CLONAL	1	TRUE	1	0.46	2		420	537	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15379822	15379822	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	165	425	0	ENST00000263377.2:c.317A>G	p.Asp106Gly	p.D106G	ENST00000263377	NM_058243.2	106	gAt/gGt	3/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.46	2		425	669	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462559	29462559	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	122	405	0	ENST00000389048.3:c.2342A>G	p.Asp781Gly	p.D781G	ENST00000389048	NM_004304.4	781	gAc/gGc	13/29	1	2	FACETS	0.878	0.796	0.964	0.878	0.796	0.964	CLONAL	1	TRUE	1	0.46	2		405	604	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145606	61145606	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs766677940	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	115	456	0	ENST00000295025.8:c.718G>T	p.Val240Leu	p.V240L	ENST00000295025	NM_002908.2	240	Gta/Tta	7/11	1	2	FACETS	0.742	0.669	0.818	0.742	0.669	0.818	SUBCLONAL	1	TRUE	1	0.46	2		456	674	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61712937	61712937	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	133	403	0	ENST00000401558.2:c.2474C>T	p.Ala825Val	p.A825V	ENST00000401558	NM_003400.3	825	gCt/gTt	20/25	1	2	FACETS	0.975	0.889	1	0.975	0.889	1	CLONAL	1	TRUE	1	0.46	2		403	593	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630589	67630589	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1345206133	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	162	506	0	ENST00000272342.5:c.775A>G	p.Thr259Ala	p.T259A	ENST00000272342	NM_019002.3	259	Acc/Gcc	5/6	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.46	2		506	675	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736148	204736148	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	115	479	0	ENST00000302823.3:c.505G>A	p.Ala169Thr	p.A169T	ENST00000302823	NM_005214.4	169	Gca/Aca	3/4	1	2	FACETS	0.731	0.659	0.807	0.731	0.659	0.807	SUBCLONAL	1	TRUE	1	0.46	2		479	684	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543625	9543625	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	98	464	0	ENST00000353224.5:c.1529A>G	p.Tyr510Cys	p.Y510C	ENST00000353224	NM_177990.2	510	tAc/tGc	6/10	1	2	FACETS	0.757	0.677	0.841	0.757	0.677	0.841	SUBCLONAL	1	TRUE	1	0.46	2		464	563	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31020738	31020738	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	112	423	0	ENST00000375687.4:c.1035G>T	p.Lys345Asn	p.K345N	ENST00000375687	NM_015338.5	345	aaG/aaT	11/13	1	2	FACETS	0.851	0.768	0.939	0.851	0.768	0.939	CLONAL	1	TRUE	1	0.46	2		423	572	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386297	31386297	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1300094609	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	41	493	0	ENST00000328111.2:c.1522G>T	p.Val508Leu	p.V508L	ENST00000328111	NM_006892.3	508	Gtg/Ttg	15/23	1	2	FACETS	0.237	0.197	0.283	0.237	0.197	0.283	SUBCLONAL	1	TRUE	1	0.46	2		493	751	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39704921	39704921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778237366	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	137	479	0	ENST00000361337.2:c.266G>A	p.Arg89Gln	p.R89Q	ENST00000361337	NM_003286.2	89	cGa/cAa	4/21	1	2	FACETS	0.83	0.756	0.907	0.83	0.756	0.907	CLONAL	1	TRUE	1	0.46	2		479	718	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39709875	39709875	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	110	328	0	ENST00000361337.2:c.502G>A	p.Glu168Lys	p.E168K	ENST00000361337	NM_003286.2	168	Gaa/Aaa	7/21	1	2	FACETS	0.873	0.787	0.963	0.873	0.787	0.963	CLONAL	1	TRUE	1	0.46	2		328	548	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288152	21288152	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	188	462	0	ENST00000354336.3:c.397G>T	p.Asp133Tyr	p.D133Y	ENST00000354336	NM_005207.3	133	Gat/Tat	2/3	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.46	2		462	803	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513431	41513431	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752713674	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	149	471	0	ENST00000263253.7:c.335G>A	p.Ser112Asn	p.S112N	ENST00000263253	NM_001429.3	112	aGt/aAt	2/31	1	2	FACETS	0.789	0.721	0.86	0.789	0.721	0.86	SUBCLONAL	1	TRUE	1	0.46	2		471	821	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125638	47125638	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs138568145	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	160	483	0	ENST00000409792.3:c.5632T>C	p.Phe1878Leu	p.F1878L	ENST00000409792	NM_014159.6	1878	Ttt/Ctt	12/21	1	2	FACETS	0.94	0.864	1	0.94	0.864	1	CLONAL	1	TRUE	1	0.46	2		483	740	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144864	47144864	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	109	415	0	ENST00000409792.3:c.4889G>T	p.Ser1630Ile	p.S1630I	ENST00000409792	NM_014159.6	1630	aGc/aTc	7/21	1	2	FACETS	0.887	0.8	0.979	0.887	0.8	0.979	CLONAL	1	TRUE	1	0.46	2		415	534	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637695	52637695	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	82	394	0	ENST00000394830.3:c.2621A>C	p.Lys874Thr	p.K874T	ENST00000394830	NM_018313.4	874	aAa/aCa	18/30	1	2	FACETS	0.731	0.646	0.82	0.731	0.646	0.82	SUBCLONAL	1	TRUE	1	0.46	2		394	488	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696238	52696238	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	136	484	0	ENST00000394830.3:c.439A>G	p.Thr147Ala	p.T147A	ENST00000394830	NM_018313.4	147	Aca/Gca	5/30	1	2	FACETS	0.852	0.776	0.931	0.852	0.776	0.931	CLONAL	1	TRUE	1	0.46	2		484	694	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008431	70008431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	129	385	0	ENST00000394351.3:c.718C>T	p.Arg240Cys	p.R240C	ENST00000394351	NM_000248.3	240	Cgc/Tgc	8/9	1	2	FACETS	0.962	0.875	1	0.962	0.875	1	CLONAL	1	TRUE	1	0.46	2		385	583	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799436	72799436	+	stop_lost	Nonstop_Mutation	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	160	410	0	ENST00000325599.8:c.1733G>T	p.Ter578LeuextTer9	p.*578Lext*9	ENST00000325599	NM_018130.2	578	tGa/tTa	11/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.46	2		410	657	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259557	89259557	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	137	501	0	ENST00000336596.2:c.701C>A	p.Ser234Tyr	p.S234Y	ENST00000336596	NM_005233.5	234	tCt/tAt	3/17	0.3	1	FACETS	0.788	0.72	0.859	0.788	0.72	0.859	SUBCLONAL	1	TRUE	0	0.46	1		501	582	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468528	89468528	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1489618254	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	35	391	0	ENST00000336596.2:c.2062G>A	p.Val688Ile	p.V688I	ENST00000336596	NM_005233.5	688	Gtt/Att	11/17	0.3	1	FACETS	0.248	0.203	0.298	0.248	0.203	0.298	SUBCLONAL	1	TRUE	0	0.46	1		391	473	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480298	89480298	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	27	376	0	ENST00000336596.2:c.2137-2A>G		p.X713_splice	ENST00000336596	NM_005233.5	713			0.3	1	FACETS	0.211	0.167	0.261	0.211	0.167	0.261	SUBCLONAL	1	TRUE	0	0.46	1		376	429	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374266	138374266	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	118	378	0	ENST00000289153.2:c.3178A>G	p.Met1060Val	p.M1060V	ENST00000289153	NM_006219.2	1060	Atg/Gtg	22/22	1	2	FACETS	0.834	0.754	0.918	0.834	0.754	0.918	CLONAL	1	TRUE	1	0.46	2		378	615	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170015132	170015132	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	166	420	0	ENST00000295797.4:c.1538T>G	p.Phe513Cys	p.F513C	ENST00000295797	NM_002740.5	513	tTt/tGt	16/18	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.46	2		420	622	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178943809	178943809	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	100	358	0	ENST00000263967.3:c.2476A>C	p.Asn826His	p.N826H	ENST00000263967	NM_006218.2	826	Aat/Cat	17/21	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.46	2		358	405	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455609	189455609	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	134	448	0	ENST00000264731.3:c.143A>C	p.Glu48Ala	p.E48A	ENST00000264731	NM_003722.4	48	gAa/gCa	2/14	1	2	FACETS	0.987	0.901	1	0.987	0.901	1	CLONAL	1	TRUE	1	0.46	2		448	590	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749415	41749415	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	96	313	0	ENST00000226382.2:c.380C>A	p.Thr127Asn	p.T127N	ENST00000226382	NM_003924.3	127	aCt/aAt	2/3	0.0900906161516501	0	FACETS	0.493	0.441	0.548			1	INDETERMINATE	1	TRUE	0	0.46	0		313	457	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592115	55592115	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	109	378	0	ENST00000288135.5:c.1439C>A	p.Ser480Tyr	p.S480Y	ENST00000288135	NM_000222.2	480	tCt/tAt	9/21	0.0900906161516501	0	FACETS	0.501	0.451	0.553			1	INDETERMINATE	1	TRUE	0	0.46	0		378	511	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964394	55964394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	114	466	0	ENST00000263923.4:c.2419G>A	p.Asp807Asn	p.D807N	ENST00000263923	NM_002253.2	807	Gat/Aat	17/30	0.0900906161516501	0	FACETS	0.455	0.411	0.502			1	INDETERMINATE	1	TRUE	0	0.46	0		466	588	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976642	55976642	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	134	447	0	ENST00000263923.4:c.1183A>C	p.Asn395His	p.N395H	ENST00000263923	NM_002253.2	395	Aat/Cat	9/30	0.0900906161516501	0	FACETS	0.543	0.495	0.593			1	INDETERMINATE	1	TRUE	0	0.46	0		447	579	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796501	57796501	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs749881609	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	129	554	0	ENST00000309042.7:c.1477C>T	p.Arg493Ter	p.R493*	ENST00000309042	NM_005612.4	493	Cga/Tga	4/4	0.0900906161516501	0	FACETS	0.506	0.461	0.554			1	INDETERMINATE	1	TRUE	0	0.46	0		554	598	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230870	66230870	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	84	418	0	ENST00000273854.3:c.2101G>T	p.Glu701Ter	p.E701*	ENST00000273854	NM_004439.5	701	Gaa/Taa	12/18	0.0900906161516501	0	FACETS	0.54	0.481	0.603			1	INDETERMINATE	1	TRUE	0	0.46	0		418	365	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144390320	144390320	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757720830	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	128	422	0	ENST00000262995.4:c.2153C>T	p.Thr718Met	p.T718M	ENST00000262995	NM_207123.2	718	aCg/aTg	11/11	1	2	FACETS	0.898	0.816	0.983	0.898	0.816	0.983	CLONAL	1	TRUE	1	0.46	2		422	620	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332762	153332762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	159	558	0	ENST00000281708.4:c.194G>A	p.Arg65Lys	p.R65K	ENST00000281708	NM_033632.3	65	aGa/aAa	2/12	1	2	FACETS	0.901	0.827	0.978	0.901	0.827	0.978	CLONAL	1	TRUE	1	0.46	2		558	767	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549905	187549905	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	130	354	0	ENST00000441802.2:c.4336G>T	p.Val1446Leu	p.V1446L	ENST00000441802	NM_005245.3	1446	Gta/Tta	8/27	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.46	2		354	498	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584515	187584515	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	177	461	0	ENST00000441802.2:c.3518A>C	p.Lys1173Thr	p.K1173T	ENST00000441802	NM_005245.3	1173	aAg/aCg	3/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.46	2		461	659	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861079	35861079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769426499	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	214	429	0	ENST00000303115.3:c.208G>A	p.Glu70Lys	p.E70K	ENST00000303115	NM_002185.3	70	Gaa/Aaa	2/8	1	2	FACETS	0.763	0.713	0.813	1	0.992	1	SUBCLONAL	2	TRUE	1	0.46	2		429	610	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161693	56161693	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	108	399	0	ENST00000399503.3:c.1190G>T	p.Ser397Ile	p.S397I	ENST00000399503	NM_005921.1	397	aGc/aTc	6/20	0.0900906161516501	3	FACETS	0.986	0.887	1	0.493	0.443	0.545	INDETERMINATE	1	TRUE	1	0.46	3		399	586	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80063769	80063769	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	106	358	0	ENST00000265081.6:c.1914C>A	p.Phe638Leu	p.F638L	ENST00000265081	NM_002439.4	638	ttC/ttA	14/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.46	2		358	385	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670084	86670084	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	86	375	0	ENST00000274376.6:c.1881A>C	p.Lys627Asn	p.K627N	ENST00000274376	NM_002890.2	627	aaA/aaC	14/25	1	2	FACETS	0.937	0.834	1	0.937	0.834	1	CLONAL	1	TRUE	1	0.46	2		375	399	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818360	170818360	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	71	184	0	ENST00000296930.5:c.190G>A	p.Ala64Thr	p.A64T	ENST00000296930	NM_002520.6	64	Gca/Aca	3/11	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.46	2		184	277	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058713	180058713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777334601	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	135	436	0	ENST00000261937.6:c.124G>A	p.Asp42Asn	p.D42N	ENST00000261937	NM_182925.4	42	Gac/Aac	2/30	0.3	1	FACETS	0.763	0.696	0.833	0.763	0.696	0.833	SUBCLONAL	1	TRUE	0	0.46	1		436	592	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005679	150005679	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	137	478	0	ENST00000253339.5:c.546A>C	p.Lys182Asn	p.K182N	ENST00000253339		182	aaA/aaC	3/7	0.3	3	FACETS	0.958	0.872	1			1	CLONAL	1	TRUE	NA	0.46	3		478	765	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124503691	124503691	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	89	319	1	ENST00000357628.3:c.259C>A	p.Gln87Lys	p.Q87K	ENST00000357628	NM_015450.2	87	Caa/Aaa	8/19	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.46	2		320	382	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148544359	148544359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1400051032	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	134	386	0	ENST00000320356.2:c.32G>A	p.Gly11Glu	p.G11E	ENST00000320356	NM_004456.4	11	gGa/gAa	2/20	1	2	FACETS	0.88	0.801	0.962	0.88	0.801	0.962	CLONAL	1	TRUE	1	0.46	2		386	662	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902278	151902278	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554526666	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	34	107	0	ENST00000262189.6:c.3874C>T	p.Arg1292Ter	p.R1292*	ENST00000262189	NM_170606.2	1292	Cga/Tga	25/59	1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	1	0.46	2		107	143	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345857	152345857	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	102	454	0	ENST00000359321.1:c.713G>T	p.Arg238Met	p.R238M	ENST00000359321	NM_005431.1	238	aGg/aTg	3/3	1	2	FACETS	0.701	0.627	0.778	0.701	0.627	0.778	SUBCLONAL	1	TRUE	1	0.46	2		454	633	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187135	38187135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356401338	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	150	402	0	ENST00000317025.8:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000317025	NM_023034.1	448	Cgg/Tgg	6/24	1	2	FACETS	0.813	0.744	0.886	0.813	0.744	0.886	CLONAL	1	TRUE	1	0.46	2		402	802	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005937	69005937	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	92	422	0	ENST00000288368.4:c.2348C>A	p.Ala783Asp	p.A783D	ENST00000288368	NM_024870.2	783	gCt/gAt	21/40	0.122063018292711	0	FACETS	0.478	0.426	0.532			1	INDETERMINATE	1	TRUE	0	0.46	0		422	452	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978540	70978540	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	152	477	0	ENST00000276594.2:c.1113G>T	p.Glu371Asp	p.E371D	ENST00000276594	NM_024504.3	371	gaG/gaT	5/8	0.122063018292711	0	FACETS	0.556	0.51	0.604			1	INDETERMINATE	1	TRUE	0	0.46	0		477	642	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965606	90965606	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	88	470	0	ENST00000265433.3:c.1711A>C	p.Lys571Gln	p.K571Q	ENST00000265433	NM_002485.4	571	Aaa/Caa	11/16	1	2	FACETS	0.845	0.752	0.943	0.845	0.752	0.943	CLONAL	1	TRUE	1	0.46	2		470	453	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738125	145738125	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	166	525	0	ENST00000428558.2:c.2785C>A	p.Leu929Met	p.L929M	ENST00000428558	NM_004260.3	929	Ctg/Atg	17/22	1	2	FACETS	0.847	0.779	0.918	0.847	0.779	0.918	CLONAL	1	TRUE	1	0.46	2		525	852	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2104017	2104017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	102	360	0	ENST00000349721.2:c.3140G>A	p.Arg1047Gln	p.R1047Q	ENST00000349721	NM_003070.3	1047	cGg/cAg	23/34	1	2	FACETS	0.747	0.669	0.829	0.747	0.669	0.829	SUBCLONAL	1	TRUE	1	0.46	2		360	594	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2182150	2182150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217286722	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	97	332	0	ENST00000349721.2:c.4369C>T	p.Arg1457Cys	p.R1457C	ENST00000349721	NM_003070.3	1457	Cgt/Tgt	31/34	1	2	FACETS	0.832	0.744	0.924	0.832	0.744	0.924	CLONAL	1	TRUE	1	0.46	2		332	507	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080300	5080300	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	98	396	0	ENST00000381652.3:c.2203G>T	p.Asp735Tyr	p.D735Y	ENST00000381652	NM_004972.3	735	Gac/Tac	17/25	1	2	FACETS	0.926	0.831	1	0.926	0.831	1	CLONAL	1	TRUE	1	0.46	2		396	460	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404588	8404588	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	83	443	0	ENST00000356435.5:c.4159G>C	p.Ala1387Pro	p.A1387P	ENST00000356435		1387	Gcg/Ccg	25/35	1	2	FACETS	0.786	0.697	0.881	0.786	0.697	0.881	SUBCLONAL	1	TRUE	1	0.46	2		443	459	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636738	8636738	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	122	384	0	ENST00000356435.5:c.171G>A	p.Trp57Ter	p.W57*	ENST00000356435		57	tgG/tgA	2/35	1	2	FACETS	0.849	0.769	0.932	0.849	0.769	0.932	CLONAL	1	TRUE	1	0.46	2		384	625	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20150371	20150371	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	78	176	0	ENST00000379607.5:c.266C>T	p.Ala89Val	p.A89V	ENST00000379607	NM_001412.3	89	gCt/gTt	5/7	1	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.46	1		176	189	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916574	39916574	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	152	197	0	ENST00000378444.4:c.4429G>T	p.Glu1477Ter	p.E1477*	ENST00000378444	NM_001123385.1	1477	Gaa/Taa	11/15	0.3	2	FACETS	0.969	0.9	1	0.969	0.9	1	CLONAL	2	TRUE	0	0.46	2		197	341	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344180	70344180	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	136	211	0	ENST00000374080.3:c.1916A>C	p.Asp639Ala	p.D639A	ENST00000374080		639	gAt/gCt	13/45	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.46	1		211	347	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939686	76939686	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	138	256	0	ENST00000373344.5:c.1062G>T	p.Lys354Asn	p.K354N	ENST00000373344	NM_000489.3	354	aaG/aaT	9/35	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.46	1		256	376	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968167	68968167	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	65	357	0	ENST00000288368.4:c.1196G>T	p.Arg399Leu	p.R399L	ENST00000288368	NM_024870.2	399	cGa/cTa	10/40	0.122063018292711	0	FACETS	0.385	0.335	0.439			1	INDETERMINATE	1	TRUE	0	0.46	0		357	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913343	NA	P-0066945-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	401	467	1	ENST00000269305.4:c.817C>A	p.Arg273Ser	p.R273S	ENST00000269305	NM_001126112.2	273	Cgt/Agt	8/11	0.740203733482273	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.736094847377538	2		468	490	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227030	2227030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768112599	NA	P-0066945-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	68	435	0	ENST00000398665.3:c.4510G>A	p.Ala1504Thr	p.A1504T	ENST00000398665	NM_032482.2	1504	Gcc/Acc	27/28	0.475734238849221	3	FACETS	0.502	0.437	0.571	0.167	0.145	0.191	SUBCLONAL	1	TRUE	0	0.736094847377538	3		435	504	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615599	100615599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066946-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	63	458	0	ENST00000308731.7:c.733G>A	p.Glu245Lys	p.E245K	ENST00000308731	NM_000061.2	245	Gag/Aag	8/19	0.276741711185837	6	FACETS	0.647	0.559	0.743	0.162	0.139	0.186	INDETERMINATE	1	TRUE	2	0.674169558214195	6		458	678	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119024	70119024	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762685531	NA	P-0066946-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	137	507	0	ENST00000245479.2:c.596C>A	p.Ser199Tyr	p.S199Y	ENST00000245479	NM_000346.3	199	tCc/tAc	2/3	0.505729533377723	4	FACETS	1	0.949	1	0.529	0.482	0.578	CLONAL	1	TRUE	2	0.674169558214195	4		507	643	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0066980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	69	171	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.725	0.635	0.822	0.725	0.635	0.822	SUBCLONAL	1	TRUE	1	0.491853456029265	2		171	387	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014062	14014062	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	83	515	0	ENST00000311895.7:c.41del	p.Pro14ArgfsTer19	p.P14Rfs*19	ENST00000311895	NM_005236.2	14	Ccg/cg	1/11	1	2	FACETS	0.672	0.595	0.755	0.672	0.595	0.755	SUBCLONAL	1	TRUE	1	0.491853456029265	2		515	502	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100945	27100945	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	114	615	0	ENST00000324856.7:c.4227G>T	p.Gln1409His	p.Q1409H	ENST00000324856	NM_006015.4	1409	caG/caT	18/20	1	2	FACETS	0.782	0.706	0.862	0.782	0.706	0.862	SUBCLONAL	1	TRUE	1	0.491853456029265	2		615	593	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280023	66280023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066985-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	36	412	0	ENST00000273854.3:c.1666G>A	p.Glu556Lys	p.E556K	ENST00000273854	NM_004439.5	556	Gag/Aag	7/18	1	2	FACETS	0.644	0.529	0.773	0.644	0.529	0.773	SUBCLONAL	1	TRUE	1	0.215481347816103	2		412	519	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128848687	128848687	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1204546630	NA	P-0066991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	319	490	0	ENST00000249373.3:c.1352G>A	p.Arg451His	p.R451H	ENST00000249373	NM_005631.4	451	cGc/cAc	7/12	0.532011065137234	3	FACETS	0.866	0.82	0.912	0.866	0.82	0.912	CLONAL	2	TRUE	1	0.531966183904339	3		490	877	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114917785	114917785	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	63	492	0	ENST00000543371.1:c.1275G>C	p.Lys425Asn	p.K425N	ENST00000543371	NM_001198531.1	425	aaG/aaC	12/14	0.176298761620011	3	FACETS	0.785	0.682	0.896	0.392	0.341	0.448	INDETERMINATE	1	TRUE	1	0.531966183904339	3		492	382	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0066992-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	17	466	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.577	0.429	0.754	0.577	0.429	0.754	SUBCLONAL	1	TRUE	1	0.13	2		466	453	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0066992-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	71	663	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	1	2	FACETS	0.855	0.746	0.972	1	0.978	1	CLONAL	2	TRUE	1	0.13	2		663	639	SUCCESS
APC	324	MSKCC	GRCh37	5	112175720	112175720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066992-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	39	651	0	ENST00000257430.4:c.4429C>T	p.Gln1477Ter	p.Q1477*	ENST00000257430	NM_000038.5	1477	Cag/Tag	16/16	1	2	FACETS	0.882	0.73	1	0.882	0.73	1	CLONAL	1	TRUE	1	0.13	2		651	680	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434494	140434494	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1436193121	NA	P-0066992-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	32	497	0	ENST00000288602.6:c.2204G>A	p.Arg735Gln	p.R735Q	ENST00000288602	NM_004333.4	735	cGg/cAg	18/18	1	2	FACETS	0.879	0.712	1	0.879	0.712	1	CLONAL	1	TRUE	1	0.13	2		497	560	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375142	31375142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537913125	NA	P-0066992-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	39	714	0	ENST00000328111.2:c.539C>T	p.Thr180Met	p.T180M	ENST00000328111	NM_006892.3	180	aCg/aTg	6/23	1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	1	0.13	2		714	578	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395746	45395746	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066992-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	40	520	0	ENST00000262160.6:c.388C>T	p.Arg130Ter	p.R130*	ENST00000262160	NM_005901.5	130	Cga/Tga	4/11	1	2	FACETS	1	0.834	1	1	0.834	1	CLONAL	1	TRUE	1	0.13	2		520	612	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577111	7577120	+	frameshift_variant	Frame_Shift_Del	DEL	GCACAAACAC	GCACAAACAC	-	novel	NA	P-0066992-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	27	433	0	ENST00000269305.4:c.818_827del	p.Arg273ProfsTer69	p.R273Pfs*69	ENST00000269305	NM_001126112.2	273	cGTGTTTGTGCc/cc	8/11	1	2	FACETS	0.725	0.575	0.897	0.725	0.575	0.897	SUBCLONAL	1	TRUE	1	0.13	2		433	573	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479772	67479772	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066992-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	33	539	0	ENST00000327367.4:c.1079T>C	p.Phe360Ser	p.F360S	ENST00000327367	NM_005902.3	360	tTt/tCt	8/9	1	2	FACETS	0.967	0.786	1	0.967	0.786	1	CLONAL	1	TRUE	1	0.13	2		539	525	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066993-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	141	317	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.804667765768381	2		317	349	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7152776	7152776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066993-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	231	574	0	ENST00000302850.5:c.2192C>T	p.Thr731Met	p.T731M	ENST00000302850	NM_000208.2	731	aCg/aTg	10/22	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.804667765768381	2		574	573	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637050	93637050	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066993-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	301	585	0	ENST00000375746.1:c.1100G>T	p.Arg367Leu	p.R367L	ENST00000375746	NM_001174167.1	367	cGa/cTa	9/14	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.804667765768381	2		585	617	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0066998-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	82	652	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.311044796313695	1	FACETS	0.837	0.74	0.941	0.837	0.74	0.941	CLONAL	1	TRUE	0	0.311044796313695	1		652	532	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367798	15367798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144627512	NA	P-0066998-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	54	449	0	ENST00000263377.2:c.1528C>T	p.Arg510Trp	p.R510W	ENST00000263377	NM_058243.2	510	Cgg/Tgg	8/20	1	2	FACETS	0.786	0.672	0.909	0.786	0.672	0.909	CLONAL	1	TRUE	1	0.311044796313695	2		449	442	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865222	57865222	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066998-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	35	514	0	ENST00000228682.2:c.2699A>C	p.Asn900Thr	p.N900T	ENST00000228682	NM_005269.2	900	aAt/aCt	12/12	1	2	FACETS	0.483	0.395	0.581	0.483	0.395	0.581	SUBCLONAL	1	TRUE	1	0.311044796313695	2		514	466	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527444	29527444	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0066998-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	52	422	0	ENST00000356175.3:c.893T>A	p.Leu298Ter	p.L298*	ENST00000356175	NM_000267.3	298	tTa/tAa	9/57	0.311044796313695	1	FACETS	0.757	0.647	0.877	0.757	0.647	0.877	SUBCLONAL	1	TRUE	0	0.311044796313695	1		422	373	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941207	71941207	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066998-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	65	724	0	ENST00000298229.2:c.982A>G	p.Lys328Glu	p.K328E	ENST00000298229	NM_001567.3	328	Aag/Gag	9/28	1	2	FACETS	0.71	0.615	0.812	0.71	0.615	0.812	SUBCLONAL	1	TRUE	1	0.311044796313695	2		724	589	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0066999-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	55	635	0	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	0.259785920967042	1	FACETS	0.757	0.648	0.875	0.757	0.648	0.875	SUBCLONAL	1	TRUE	0	0.259785920967042	1		635	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0067009-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	37	375	16	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.55530725951067	1	FACETS	0.917	0.815	1	1	0.974	1	CLONAL	2	TRUE	0	0.551247523359998	1		391	53	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827951	40827951	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067009-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	28	440	13	ENST00000373198.4:c.2477C>G	p.Pro826Arg	p.P826R	ENST00000373198	NM_133170.3	826	cCc/cGc	17/32	0.327738146587047	2	FACETS	0.883	0.72	1	0.442	0.36	0.531	INDETERMINATE	1	TRUE	0	0.551247523359998	2		453	115	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878233	151878233	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067009-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	13	454	7	ENST00000262189.6:c.6712A>C	p.Met2238Leu	p.M2238L	ENST00000262189	NM_170606.2	2238	Atg/Ctg	36/59	0.540935818599657	0	FACETS	0.529	0.394	0.677			1	SUBCLONAL	1	TRUE	0	0.551247523359998	0		461	40	SUCCESS
ALB	213	MSKCC	GRCh37	4	74274486	74274486	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067009-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	10	390	3	ENST00000295897.4:c.446C>A	p.Thr149Asn	p.T149N	ENST00000295897	NM_000477.5	149	aCt/aAt	4/15	0.446179019761867	1	FACETS	0.392	0.27	0.54	0.392	0.27	0.54	SUBCLONAL	1	TRUE	0	0.551247523359998	1		393	67	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0067011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	26	308	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.477	0.377	0.592	0.477	0.377	0.592	SUBCLONAL	1	TRUE	1	0.23	2		308	474	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0067011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	109	321	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.3	3	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	1	0.23	3		321	514	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220487	123220487	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	48	499	0	ENST00000218089.9:c.3144G>T	p.Leu1048Phe	p.L1048F	ENST00000218089	NM_001042749.1	1048	ttG/ttT	30/35	0.3	3	FACETS	0.833	0.703	0.975	0.416	0.351	0.488	CLONAL	1	TRUE	1	0.23	3		499	559	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031895	26031895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1332600888	NA	P-0067011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	30	678	0	ENST00000244661.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000244661	NM_003537.3	132	Cgc/Tgc	1/1	0.161617413877034	2	FACETS	0.453	0.364	0.554	0.226	0.182	0.277	SUBCLONAL	1	TRUE	0	0.23	2		678	576	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039338	47039338	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	32	589	0	ENST00000377604.3:c.961G>C	p.Ala321Pro	p.A321P	ENST00000377604	NM_001204468.1	321	Gca/Cca	10/24	1	2	FACETS	0.586	0.475	0.711	0.586	0.475	0.711	SUBCLONAL	1	TRUE	1	0.23	2		589	475	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332751	153332751	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	33	665	0	ENST00000281708.4:c.205C>T	p.Gln69Ter	p.Q69*	ENST00000281708	NM_033632.3	69	Caa/Taa	2/12	1	2	FACETS	0.526	0.427	0.637	0.526	0.427	0.637	SUBCLONAL	1	TRUE	1	0.23	2		665	546	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045706	26045706	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769895262	NA	P-0067011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	62	612	0	ENST00000540144.1:c.68C>T	p.Thr23Ile	p.T23I	ENST00000540144	NM_003531.2	23	aCt/aTt	1/1	0.161617413877034	2	FACETS	0.943	0.814	1	0.471	0.407	0.541	CLONAL	1	TRUE	0	0.23	2		612	572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0067011-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	159	477	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.252953661048008	2	FACETS	0.807	0.746	0.869	0.807	0.746	0.869	INDETERMINATE	2	TRUE	0	0.425612988349108	2		477	463	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451339	187451339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200263685	NA	P-0067011-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	92	416	0	ENST00000232014.4:c.143C>T	p.Thr48Met	p.T48M	ENST00000232014	NM_001130845.1	48	aCg/aTg	3/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.425612988349108	2		416	370	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656567	3656567	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762475814	NA	P-0067011-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	83	507	0	ENST00000294008.3:c.668G>A	p.Arg223His	p.R223H	ENST00000294008	NM_032444.2	223	cGt/cAt	3/15	1	2	FACETS	0.782	0.692	0.877	0.782	0.692	0.877	SUBCLONAL	1	TRUE	1	0.425612988349108	2		507	499	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512600	148512600	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067011-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	8	333	2	ENST00000320356.2:c.1544A>G	p.Lys515Arg	p.K515R	ENST00000320356	NM_004456.4	515	aAg/aGg	13/20	0.207689719404683	3	FACETS	0.179	0.114	0.262	0.089	0.057	0.131	INDETERMINATE	1	TRUE	1	0.425612988349108	3		335	255	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0067011-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	41	270	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.207689719404683	3	FACETS	1	0.943	1	0.642	0.542	0.75	INDETERMINATE	1	TRUE	1	0.425612988349108	3		270	182	SUCCESS
APC	324	MSKCC	GRCh37	5	112175022	112175022	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067011-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	56	480	0	ENST00000257430.4:c.3734del	p.Lys1245ArgfsTer20	p.K1245Rfs*20	ENST00000257430	NM_000038.5	1244	cAa/ca	16/16	0.401178969405842	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.425612988349108	1		480	185	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5216748	5216748	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753417682	NA	P-0067011-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	64	427	0	ENST00000357368.4:c.4079C>T	p.Pro1360Leu	p.P1360L	ENST00000357368	NM_002850.3	1360	cCg/cTg	26/38	0.207689719404683	3	FACETS	1	0.925	1	0.544	0.474	0.619	INDETERMINATE	1	TRUE	1	0.425612988349108	3		427	335	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0067012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	91	461	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.95	0.848	1	0.95	0.848	1	CLONAL	1	TRUE	1	0.423911628647636	2		461	452	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323141	31323141	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	116	696	0	ENST00000412585.2:c.848G>A	p.Cys283Tyr	p.C283Y	ENST00000412585	NM_005514.6	283	tGc/tAc	4/8	1	2	FACETS	0.856	0.773	0.944	0.856	0.773	0.944	CLONAL	1	TRUE	1	0.423911628647636	2		696	639	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609692	117609692	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	25	439	0	ENST00000368508.3:c.7007G>T	p.Cys2336Phe	p.C2336F	ENST00000368508	NM_002944.2	2336	tGt/tTt	43/43	0.423911628647636	1	FACETS	0.301	0.237	0.374	0.301	0.237	0.374	SUBCLONAL	1	TRUE	0	0.423911628647636	1		439	309	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439226	52439226	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	135	521	0	ENST00000460680.1:c.1016del	p.Pro339GlnfsTer23	p.P339Qfs*23	ENST00000460680	NM_004656.3	339	cCa/ca	11/17	0.423911628647636	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.423911628647636	1		521	442	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs869320707	NA	P-0067013-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	84	597	0	ENST00000397752.3:c.3028+1G>T		p.X1010_splice	ENST00000397752	NM_000245.2	1010			1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.28	2		597	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121912666	NA	P-0067013-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	52	670	0	ENST00000269305.4:c.659A>C	p.Tyr220Ser	p.Y220S	ENST00000269305	NM_001126112.2	220	tAt/tCt	6/11	1	2	FACETS	0.689	0.587	0.801	0.689	0.587	0.801	SUBCLONAL	1	TRUE	1	0.28	2		670	539	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876343	35876343	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200570812	NA	P-0067013-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	52	568	0	ENST00000303115.3:c.1135G>A	p.Ala379Thr	p.A379T	ENST00000303115	NM_002185.3	379	Gcc/Acc	8/8	1	2	FACETS	0.684	0.582	0.796	0.684	0.582	0.796	SUBCLONAL	1	TRUE	1	0.28	2		568	543	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586449	189586449	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067013-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	61	502	0	ENST00000264731.3:c.1073G>T	p.Ser358Ile	p.S358I	ENST00000264731	NM_003722.4	358	aGc/aTc	8/14	1	2	FACETS	0.781	0.674	0.897	0.781	0.674	0.897	SUBCLONAL	1	TRUE	1	0.28	2		502	558	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830796	3830796	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067013-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	47	550	0	ENST00000262367.5:c.1760G>T	p.Gly587Val	p.G587V	ENST00000262367	NM_004380.2	587	gGt/gTt	8/31	1	2	FACETS	0.579	0.488	0.679	0.579	0.488	0.679	SUBCLONAL	1	TRUE	1	0.28	2		550	580	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045493	47045494	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0067013-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	44	606	0	ENST00000377604.3:c.2460_2461del	p.Arg821GlnfsTer38	p.R821Qfs*38	ENST00000377604	NM_001204468.1	820	gaACgc/gagc	22/24	1	2	FACETS	0.525	0.439	0.62	0.525	0.439	0.62	SUBCLONAL	1	TRUE	1	0.28	2		606	599	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462388	89462388	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067013-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	64	466	0	ENST00000336596.2:c.1860C>G	p.Asn620Lys	p.N620K	ENST00000336596	NM_005233.5	620	aaC/aaG	10/17	1	2	FACETS	0.909	0.788	1	0.909	0.788	1	CLONAL	1	TRUE	1	0.28	2		466	503	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0067014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	192	565	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.885	0.822	0.95	0.885	0.822	0.95	CLONAL	1	TRUE	1	0.64	2		565	678	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0067014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	189	337	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.879	0.828	0.929	1	0.994	1	CLONAL	2	TRUE	1	0.64	2		338	336	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0067014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	131	527	2	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	0.748	0.682	0.817	0.748	0.682	0.817	SUBCLONAL	1	TRUE	1	0.64	2		529	547	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	137	589	3	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.874	0.8	0.95	0.874	0.8	0.95	CLONAL	1	TRUE	1	0.64	2		592	490	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913396	NA	P-0067014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	160	417	1	ENST00000349496.5:c.95A>G	p.Asp32Gly	p.D32G	ENST00000349496	NM_001904.3	32	gAc/gGc	3/15	1	2	FACETS	0.901	0.831	0.973	0.901	0.831	0.973	CLONAL	1	TRUE	1	0.64	2		418	555	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821594	72821602	+	inframe_deletion	In_Frame_Del	DEL	GCCGCCGCC	GCCGCCGCC	-	rs374416547	NA	P-0067014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	63	550	0	ENST00000268489.5:c.10573_10581del	p.Gly3525_Gly3527del	p.G3525_G3527del	ENST00000268489	NM_006885.3	3525	GGCGGCGGC/-	10/10	1	2	FACETS	0.679	0.592	0.771	0.679	0.592	0.771	SUBCLONAL	1	TRUE	1	0.64	2		550	290	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480499	123480499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	105	437	0	ENST00000371139.4:c.7G>A	p.Ala3Thr	p.A3T	ENST00000371139	NM_001114937.2	3	Gca/Aca	1/4	1	2	FACETS	0.901	0.815	0.991	0.901	0.815	0.991	CLONAL	1	TRUE	1	0.64	2		437	364	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218928	133218928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500823	NA	P-0067014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	57	575	0	ENST00000320574.5:c.5008G>A	p.Asp1670Asn	p.D1670N	ENST00000320574	NM_006231.2	1670	Gac/Aac	38/49	1	2	FACETS	0.372	0.319	0.429	0.372	0.319	0.429	SUBCLONAL	1	TRUE	1	0.64	2		575	479	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332177	70332177	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1564947700	NA	P-0067014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	35	520	0	ENST00000373644.4:c.82C>T	p.Arg28Ter	p.R28*	ENST00000373644	NM_030625.2	28	Cga/Tga	2/12	1	2	FACETS	0.174	0.142	0.21	0.174	0.142	0.21	SUBCLONAL	1	TRUE	1	0.64	2		520	629	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560464	95560464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	160	504	0	ENST00000393063.1:c.5125G>A	p.Asp1709Asn	p.D1709N	ENST00000393063	NM_030621.3	1709	Gat/Aat	25/28	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.64	2		504	498	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552674	18552674	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	130	532	0	ENST00000266497.5:c.2087del	p.Gly696ValfsTer18	p.G696Vfs*18	ENST00000266497		695	ctG/ct	14/31	1	2	FACETS	0.919	0.84	1	0.919	0.84	1	CLONAL	1	TRUE	1	0.64	2		532	442	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594105	158594105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	29	485	0	ENST00000263640.3:c.1468C>T	p.Arg490Cys	p.R490C	ENST00000263640	NM_001105.4	490	Cgt/Tgt	11/11	1	2	FACETS	0.179	0.143	0.22	0.179	0.143	0.22	SUBCLONAL	1	TRUE	1	0.64	2		485	506	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102196070	102196070	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	176	484	0	ENST00000263464.3:c.830C>T	p.Ala277Val	p.A277V	ENST00000263464	NM_001165.4	277	gCa/gTa	2/9	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.64	2		484	548	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72866505	72866505	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	146	460	0	ENST00000325599.8:c.758T>A	p.Leu253Gln	p.L253Q	ENST00000325599	NM_018130.2	253	cTa/cAa	7/11	1	2	FACETS	0.998	0.919	1	0.998	0.919	1	CLONAL	1	TRUE	1	0.64	2		460	457	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101394	27101395	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0067014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	80	329	0	ENST00000324856.7:c.4678_4679del	p.Pro1560CysfsTer11	p.P1560Cfs*11	ENST00000324856	NM_006015.4	1559	gCC/g	18/20	1	2	FACETS	0.856	0.762	0.955	0.856	0.762	0.955	CLONAL	1	TRUE	1	0.64	2		329	292	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024840	31024840	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	139	565	0	ENST00000375687.4:c.4325G>A	p.Gly1442Glu	p.G1442E	ENST00000375687	NM_015338.5	1442	gGg/gAg	13/13	1	2	FACETS	0.879	0.806	0.955	0.879	0.806	0.955	CLONAL	1	TRUE	1	0.64	2		565	494	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119019	70119033	+	inframe_deletion	In_Frame_Del	DEL	CATCTCCCCCAACGC	CATCTCCCCCAACGC	-	novel	NA	P-0067014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	137	613	0	ENST00000245479.2:c.596_610del	p.Ser199_Ile203del	p.S199_I203del	ENST00000245479	NM_000346.3	197	caCATCTCCCCCAACGCc/cac	2/3	1	2	FACETS	0.907	0.831	0.986	0.907	0.831	0.986	CLONAL	1	TRUE	1	0.64	2		613	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0067015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	59	638	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.229012367601352	2	FACETS	0.548	0.472	0.63	0.274	0.236	0.315	INDETERMINATE	1	TRUE	0	0.464957995560942	2		638	463	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221785	55221786	+	missense_variant	Missense_Mutation	DNP	AT	AT	GA	novel	NA	P-0067015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	305	612	0	ENST00000275493.2:c.829_830delinsGA	p.Met277Glu	p.M277E	ENST00000275493	NM_005228.3	277	ATg/GAg	7/28	0.459891224310657	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.464957995560942	3		612	719	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435278	18435278	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs750826408	NA	P-0067015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	89	536	0	ENST00000266497.5:c.263A>G	p.Glu88Gly	p.E88G	ENST00000266497		88	gAa/gGa	1/31	0.347567821096135	3	FACETS	0.766	0.68	0.858	0.383	0.34	0.429	SUBCLONAL	1	TRUE	1	0.464957995560942	3		536	616	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123693	11123693	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	16	512	0	ENST00000358026.2:c.2343G>T	p.Met781Ile	p.M781I	ENST00000358026	NM_001128849.1	781	atG/atT	16/36	0.464957995560942	2	FACETS	0.153	0.112	0.202	0.076	0.056	0.101	SUBCLONAL	1	TRUE	0	0.464957995560942	2		512	450	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150936820	150936820	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	285	517	0	ENST00000271640.5:c.3856T>C	p.Cys1286Arg	p.C1286R	ENST00000271640	NM_001145415.1	1286	Tgc/Cgc	22/22	0.459891224310657	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.464957995560942	3		517	677	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058718	47058718	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	271	493	0	ENST00000409792.3:c.7560G>T	p.Glu2520Asp	p.E2520D	ENST00000409792	NM_014159.6	2520	gaG/gaT	21/21	0.464957995560942	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.464957995560942	2		493	509	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221995	1221995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201090	NA	P-0067016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	19	358	0	ENST00000326873.7:c.910C>T	p.Arg304Trp	p.R304W	ENST00000326873	NM_000455.4	304	Cgg/Tgg	7/10	1	2	FACETS	0.51	0.387	0.654	0.51	0.387	0.654	SUBCLONAL	1	TRUE	1	0.27	2		358	276	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582134	189582135	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	31	634	0	ENST00000264731.3:c.699dup	p.Ala234SerfsTer2	p.A234Sfs*2	ENST00000264731	NM_003722.4	231	-/A	5/14	1	2	FACETS	0.738	0.599	0.896	0.738	0.599	0.896	SUBCLONAL	1	TRUE	1	0.27	2		634	311	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732993	30732993	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	36	516	0	ENST00000295754.5:c.1606G>T	p.Glu536Ter	p.E536*	ENST00000295754	NM_003242.5	536	Gaa/Taa	7/7	1	2	FACETS	0.737	0.607	0.882	0.737	0.607	0.882	SUBCLONAL	1	TRUE	1	0.27	2		516	362	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045928	26045928	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	33	656	0	ENST00000540144.1:c.290G>T	p.Cys97Phe	p.C97F	ENST00000540144	NM_003531.2	97	tGt/tTt	1/1	0.141105053425406	3	FACETS	0.628	0.511	0.759	0.314	0.255	0.38	INDETERMINATE	1	TRUE	1	0.27	3		656	442	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46608822	46608822	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	28	499	0	ENST00000263734.3:c.2133G>T	p.Gln711His	p.Q711H	ENST00000263734	NM_001430.4	711	caG/caT	13/16	1	2	FACETS	0.757	0.607	0.927	0.757	0.607	0.927	CLONAL	1	TRUE	1	0.27	2		499	274	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106182959	106182959	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	11	299	0	ENST00000380013.4:c.3998T>A	p.Met1333Lys	p.M1333K	ENST00000380013	NM_001127208.2	1333	aTg/aAg	8/11	1	2	FACETS	0.595	0.413	0.819	0.595	0.413	0.819	SUBCLONAL	1	TRUE	1	0.27	2		299	137	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576277	88576277	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0067016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	39	482	0	ENST00000360948.2:c.1397-1G>T		p.X466_splice	ENST00000360948	NM_001012338.2	466			0.254424669584339	1	FACETS	0.798	0.664	0.947	0.798	0.664	0.947	CLONAL	1	TRUE	0	0.27	1		482	313	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0067017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	36	270	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.985	0.809	1	0.985	0.809	1	CLONAL	1	TRUE	1	0.16	2		270	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578400	7578400	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs751477326	NA	P-0067017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	86	625	0	ENST00000269305.4:c.530C>G	p.Pro177Arg	p.P177R	ENST00000269305	NM_001126112.2	177	cCc/cGc	5/11	0.159585319827748	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.16	1		625	762	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974676	21974676	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0067017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	117	551	0	ENST00000304494.5:c.150+1G>A		p.X50_splice	ENST00000304494	NM_000077.4	50			0.159585319827748	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	2	TRUE	0	0.16	2		551	727	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262259	115262259	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	36	425	0	ENST00000438362.2:c.2295C>A	p.Phe765Leu	p.F765L	ENST00000438362	NM_001242891.1	765	ttC/ttA	18/20	1	2	FACETS	0.775	0.635	0.931	0.775	0.635	0.931	CLONAL	1	TRUE	1	0.16	2		425	581	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573845	41573845	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	46	656	0	ENST00000263253.7:c.6130G>C	p.Gly2044Arg	p.G2044R	ENST00000263253	NM_001429.3	2044	Ggc/Cgc	31/31	1	2	FACETS	0.691	0.58	0.814	0.691	0.58	0.814	SUBCLONAL	1	TRUE	1	0.16	2		656	832	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572998	41572998	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	73	691	0	ENST00000263253.7:c.5283G>A	p.Met1761Ile	p.M1761I	ENST00000263253	NM_001429.3	1761	atG/atA	31/31	1	2	FACETS	0.979	0.854	1	0.979	0.854	1	CLONAL	1	TRUE	1	0.16	2		691	932	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573711	41573711	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	66	694	0	ENST00000263253.7:c.5996G>T	p.Gly1999Val	p.G1999V	ENST00000263253	NM_001429.3	1999	gGa/gTa	31/31	1	2	FACETS	0.963	0.834	1	0.963	0.834	1	CLONAL	1	TRUE	1	0.16	2		694	857	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864863	117864864	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	54	447	0	ENST00000297338.2:c.1245dup	p.Phe416IlefsTer6	p.F416Ifs*6	ENST00000297338	NM_006265.2	415	-/A	10/14	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.16	2		447	613	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972951	25972963	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGCTCCAAGAG	TCTGCTCCAAGAG	-	novel	NA	P-0067017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	60	565	0	ENST00000435504.4:c.1462_1474del	p.Leu488SerfsTer30	p.L488Sfs*30	ENST00000435504		488	CTCTTGGAGCAGAag/ag	12/13	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.16	2		565	696	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572860	41572860	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	58	576	0	ENST00000263253.7:c.5145G>C	p.Glu1715Asp	p.E1715D	ENST00000263253	NM_001429.3	1715	gaG/gaC	31/31	1	2	FACETS	0.94	0.806	1	0.94	0.806	1	CLONAL	1	TRUE	1	0.16	2		576	771	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0067018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	179	314	4	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.9	2		318	397	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0067018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	87	424	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.981	0.889	1	0.981	0.889	1	CLONAL	1	TRUE	1	0.9	2		424	197	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0067018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	264	470	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.973	0.92	1	0.973	0.92	1	CLONAL	1	TRUE	1	0.9	2		470	603	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100195	27100195	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	359	562	0	ENST00000324856.7:c.3991C>T	p.Gln1331Ter	p.Q1331*	ENST00000324856	NM_006015.4	1331	Cag/Tag	16/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.9	2		562	792	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466019	69466019	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	241	557	0	ENST00000227507.2:c.857C>G	p.Thr286Arg	p.T286R	ENST00000227507	NM_053056.2	286	aCa/aGa	5/5	1	2	FACETS	0.872	0.821	0.925	0.872	0.821	0.925	CLONAL	1	TRUE	1	0.9	2		557	614	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772900	135772900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780115763	NA	P-0067018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	277	459	0	ENST00000298552.3:c.2723G>A	p.Arg908Gln	p.R908Q	ENST00000298552	NM_001162426.1	908	cGg/cAg	21/23	1	2	FACETS	0.998	0.945	1	0.998	0.945	1	CLONAL	1	TRUE	1	0.9	2		459	617	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338680	70338692	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCAGGACCCCA	CCTCAGGACCCCA	-	novel	NA	P-0067018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	176	344	0	ENST00000374080.3:c.76_88del	p.Pro26AsnfsTer7	p.P26Nfs*7	ENST00000374080		26	CCTCAGGACCCCAaa/aa	1/45	1	2	FACETS	0.94	0.877	1	0.94	0.877	1	CLONAL	1	TRUE	1	0.9	2		344	416	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522337	157522337	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554235870	NA	P-0067018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	284	571	0	ENST00000346085.5:c.4609C>T	p.Gln1537Ter	p.Q1537*	ENST00000346085	NM_020732.3	1537	Cag/Tag	18/20	1	2	FACETS	0.92	0.871	0.97	0.92	0.871	0.97	CLONAL	1	TRUE	1	0.9	2		571	686	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435770	49435770	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	334	546	0	ENST00000301067.7:c.6113G>A	p.Trp2038Ter	p.W2038*	ENST00000301067	NM_003482.3	2038	tGg/tAg	29/54	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.9	2		546	692	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023206	27023223	+	frameshift_variant	Frame_Shift_Del	DEL	CGGGAACGCGGGCCCTAG	CGGGAACGCGGGCCCTAG	T	novel	NA	P-0067018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	175	405	0	ENST00000324856.7:c.312_329delinsT	p.Gly105AlafsTer6	p.G105Afs*6	ENST00000324856	NM_006015.4	104	aaCGGGAACGCGGGCCCTAGg/aaTg	1/20	1	2	FACETS	0.987	0.921	1	0.987	0.921	1	CLONAL	1	TRUE	1	0.9	2		405	394	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562641	29562641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854562	NA	P-0067019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	93	427	0	ENST00000356175.3:c.3721C>T	p.Arg1241Ter	p.R1241*	ENST00000356175	NM_000267.3	1241	Cga/Tga	28/57	0.519797098333692	1	FACETS	0.985	0.888	1	0.985	0.888	1	CLONAL	1	TRUE	0	0.519797098333692	1		427	269	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162099	47162099	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067021-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	121	466	0	ENST00000409792.3:c.4027C>T	p.Gln1343Ter	p.Q1343*	ENST00000409792	NM_014159.6	1343	Caa/Taa	3/21	0.565058053206893	4	FACETS	1	0.921	1			1	CLONAL	1	TRUE	NA	0.566210865252343	4		466	657	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067021-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	444	442	0	ENST00000269305.4:c.383del	p.Pro128LeufsTer42	p.P128Lfs*42	ENST00000269305	NM_001126112.2	128	cCt/ct	5/11	0.565058053206893	5	FACETS	0.956	0.927	0.983	0.956	0.927	0.983	CLONAL	5	TRUE	0	0.566210865252343	5		442	607	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300502	11300502	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067021-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	104	496	0	ENST00000361445.4:c.1644G>T	p.Met548Ile	p.M548I	ENST00000361445	NM_004958.3	548	atG/atT	11/58	0.508935158104163	3	FACETS	0.921	0.828	1	0.46	0.414	0.509	CLONAL	1	TRUE	1	0.566210865252343	3		496	512	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807522	1807522	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067021-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	62	523	0	ENST00000260795.2:c.1691G>C	p.Arg564Pro	p.R564P	ENST00000260795		564	cGg/cCg	12/17	0.566210865252343	5	FACETS	0.788	0.681	0.903			1	CLONAL	1	TRUE	NA	0.566210865252343	5		523	514	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754032	42754032	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1360969996	NA	P-0067021-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	132	512	0	ENST00000222329.4:c.320A>G	p.Asn107Ser	p.N107S	ENST00000222329	NM_006494.2	107	aAt/aGt	3/4	0.508935158104163	3	FACETS	1	0.942	1	0.522	0.476	0.57	CLONAL	1	TRUE	1	0.566210865252343	3		512	573	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256189	16256189	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067021-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	159	487	0	ENST00000375759.3:c.3454T>A	p.Ser1152Thr	p.S1152T	ENST00000375759	NM_015001.2	1152	Tca/Aca	11/15	0.508935158104163	3	FACETS	1	0.983	1	0.623	0.574	0.674	CLONAL	1	TRUE	1	0.566210865252343	3		487	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0067022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	268	477	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.670551375936614	2	FACETS	0.913	0.872	0.954	0.913	0.872	0.954	CLONAL	2	TRUE	0	0.677957397530673	2		477	433	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438206	110438206	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	45	267	0	ENST00000375856.3:c.195del	p.Ser66ArgfsTer27	p.S66Rfs*27	ENST00000375856	NM_003749.2	65	ggG/gg	1/2	0.656055044797679	3	FACETS	0.726	0.615	0.846	0.242	0.205	0.282	SUBCLONAL	1	TRUE	0	0.677957397530673	3		267	245	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265890	16265890	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	186	366	0	ENST00000375759.3:c.10966del	p.His3656ThrfsTer3	p.H3656Tfs*3	ENST00000375759	NM_015001.2	3655	Ccc/cc	15/15	0.39855418819293	3	FACETS	0.782	0.729	0.835	0.782	0.729	0.835	INDETERMINATE	2	TRUE	1	0.677957397530673	3		366	470	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436415	49436426	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CAAAGGGAGTCC	CAAAGGGAGTCC	A	novel	NA	P-0067022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	261	343	0	ENST00000301067.7:c.5785_5796delinsT	p.Gly1929TrpfsTer24	p.G1929Wfs*24	ENST00000301067	NM_003482.3	1929	GGACTCCCTTTG/T	27/54	0.540523330545841	5	FACETS	1	0.988	1	0.787	0.742	0.832	CLONAL	2	TRUE	2	0.677957397530673	5		343	658	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326721	62326721	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	25	398	0	ENST00000360203.5:c.3540G>C	p.Lys1180Asn	p.K1180N	ENST00000360203	NM_001283009.1	1180	aaG/aaC	34/35	0.677957397530673	3	FACETS	0.215	0.169	0.268	0.107	0.084	0.134	SUBCLONAL	1	TRUE	1	0.677957397530673	3		398	460	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	30	300	0	ENST00000295754.5:c.1583G>C	p.Arg528Pro	p.R528P	ENST00000295754	NM_003242.5	528	cGt/cCt	7/7	0.670551375936614	2	FACETS	0.221	0.177	0.27	0.11	0.088	0.135	SUBCLONAL	1	TRUE	0	0.677957397530673	2		300	401	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842379	151842379	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	72	334	0	ENST00000262189.6:c.14033T>C	p.Leu4678Pro	p.L4678P	ENST00000262189	NM_170606.2	4678	cTt/cCt	54/59	1	2	FACETS	0.607	0.534	0.685	0.607	0.534	0.685	SUBCLONAL	1	TRUE	1	0.677957397530673	2		334	350	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0067023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	259	418	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.583705680441984	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.603979390288137	4		418	621	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0067023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	152	439	0				ENST00000310581	NM_198253.2	-/1132			0.288189241020506	5	FACETS	0.906	0.841	0.972	0.906	0.841	0.972	INDETERMINATE	3	TRUE	2	0.603979390288137	5		439	353	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0067023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	91	698	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.479050095952388	0	FACETS	0.55	0.498	0.603			1	SUBCLONAL	1	TRUE	0	0.603979390288137	0		698	217	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578525	7578525	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	347	693	0	ENST00000269305.4:c.405C>A	p.Cys135Ter	p.C135*	ENST00000269305	NM_001126112.2	135	tgC/tgA	5/11	0.60313799705263	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.603979390288137	2		693	549	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596088	43596088	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	85	632	0	ENST00000355710.3:c.255G>A	p.Trp85Ter	p.W85*	ENST00000355710	NM_020975.4	85	tgG/tgA	2/20	0.422920493283982	1	FACETS	0.675	0.604	0.75	0.675	0.604	0.75	SUBCLONAL	1	TRUE	0	0.603979390288137	1		632	291	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536873	120536873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	146	649	0	ENST00000229340.5:c.313G>A	p.Glu105Lys	p.E105K	ENST00000229340	NM_006861.6	105	Gaa/Aaa	4/6	0.376240612720379	1	FACETS	0.927	0.857	0.998	0.927	0.857	0.998	CLONAL	1	TRUE	0	0.603979390288137	1		649	364	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945112	151945112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	32	352	0	ENST00000262189.6:c.2407G>A	p.Ala803Thr	p.A803T	ENST00000262189	NM_170606.2	803	Gct/Act	14/59	0.603979390288137	3	FACETS	0.63	0.515	0.758	0.315	0.257	0.379	SUBCLONAL	1	TRUE	1	0.603979390288137	3		352	219	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61305195	61305195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	107	601	0	ENST00000341074.5:c.931G>A	p.Asp311Asn	p.D311N	ENST00000341074	NM_002974.2	311	Gat/Aat	8/8	0.603979390288137	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.603979390288137	1		601	244	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376136	118376136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	219	846	0	ENST00000534358.1:c.9529C>T	p.Pro3177Ser	p.P3177S	ENST00000534358	NM_005933.3	3177	Cca/Tca	27/36	0.213626494277272	4	FACETS	0.845	0.79	0.902	0.845	0.79	0.902	INDETERMINATE	2	TRUE	2	0.603979390288137	4		846	688	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494988	56494988	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0067023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	66	715	0	ENST00000267101.3:c.3345T>A	p.Cys1115Ter	p.C1115*	ENST00000267101	NM_001982.3	1115	tgT/tgA	27/28	0.376240612720379	1	FACETS	0.355	0.309	0.404	0.355	0.309	0.404	SUBCLONAL	1	TRUE	0	0.603979390288137	1		715	430	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89176370	89176370	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	94	473	3	ENST00000336596.2:c.100G>A	p.Asp34Asn	p.D34N	ENST00000336596	NM_005233.5	34	Gat/Aat	2/17	0.270169790487391	2	FACETS	0.759	0.691	0.828	0.759	0.691	0.828	INDETERMINATE	2	TRUE	0	0.603979390288137	2		476	205	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874718	151874718	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	408	806	0	ENST00000262189.6:c.7820C>T	p.Pro2607Leu	p.P2607L	ENST00000262189	NM_170606.2	2607	cCc/cTc	38/59	0.603979390288137	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.603979390288137	3		806	749	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246550	105246552	+	missense_variant,splice_region_variant	Missense_Mutation	TNP	TCC	TCC	CTT	novel	NA	P-0067023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	241	662	0	ENST00000349310.3:c.48_50delinsAAG	p.Glu17Arg	p.E17R	ENST00000349310	NM_001014432.1	16	ggGGAg/ggAAGg	4/15	0.603979390288137	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.603979390288137	2		662	372	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0067043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	10	171	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.581	0.397	0.807	0.581	0.397	0.807	SUBCLONAL	1	TRUE	1	0.362362246669066	2		171	95	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593689	215593689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	78	374	0	ENST00000260947.4:c.2045C>T	p.Thr682Ile	p.T682I	ENST00000260947	NM_000465.2	682	aCc/aTc	11/11	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.362362246669066	2		374	401	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242486	+	inframe_deletion	In_Frame_Del	DEL	TTAAGAGAAGCAACATCT	TTAAGAGAAGCAACATCT	-	rs121913440	NA	P-0067043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	100	309	0	ENST00000275493.2:c.2239_2256del	p.Leu747_Ser752del	p.L747_S752del	ENST00000275493	NM_005228.3	747	TTAAGAGAAGCAACATCT/-	19/28	0.145219293626398	2	FACETS	0.786	0.709	0.867	0.786	0.709	0.867	INDETERMINATE	2	TRUE	0	0.362362246669066	2		309	351	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878254	151878254	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	68	431	0	ENST00000262189.6:c.6691G>C	p.Glu2231Gln	p.E2231Q	ENST00000262189	NM_170606.2	2231	Gag/Cag	36/59	1	2	FACETS	0.812	0.709	0.924	0.812	0.709	0.924	CLONAL	1	TRUE	1	0.362362246669066	2		431	462	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245624	46245624	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	72	472	0	ENST00000334344.6:c.3718G>A	p.Asp1240Asn	p.D1240N	ENST00000334344	NM_152641.2	1240	Gat/Aat	15/21	1	2	FACETS	0.866	0.759	0.98	0.866	0.759	0.98	CLONAL	1	TRUE	1	0.362362246669066	2		472	459	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007672	45007672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	92	370	0	ENST00000558401.1:c.119C>T	p.Ser40Leu	p.S40L	ENST00000558401	NM_004048.2	40	tCa/tTa	2/4	0.18605422521274	3	FACETS	1	0.969	1	0.621	0.554	0.692	INDETERMINATE	1	TRUE	1	0.362362246669066	3		370	483	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868654	56868654	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	31	271	0	ENST00000308159.5:c.1746G>A	p.Met582Ile	p.M582I	ENST00000308159	NM_014669.4	582	atG/atA	16/22	1	2	FACETS	0.663	0.539	0.803	0.663	0.539	0.803	SUBCLONAL	1	TRUE	1	0.362362246669066	2		271	258	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865287	40865287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	65	340	0	ENST00000428826.2:c.1144G>A	p.Glu382Lys	p.E382K	ENST00000428826		382	Gag/Aag	11/21	1	2	FACETS	0.738	0.641	0.843	0.738	0.641	0.843	SUBCLONAL	1	TRUE	1	0.362362246669066	2		340	486	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424731	47424731	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	71	444	0	ENST00000404338.3:c.2799C>G	p.Ile933Met	p.I933M	ENST00000404338	NM_004491.4	933	atC/atG	1/6	0.362362246669066	3	FACETS	0.991	0.868	1			1	CLONAL	1	TRUE	NA	0.362362246669066	3		444	467	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564369	86564369	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	67	434	0	ENST00000274376.6:c.101G>C	p.Cys34Ser	p.C34S	ENST00000274376	NM_002890.2	34	tGt/tCt	1/25	0.362362246669066	3	FACETS	0.715	0.621	0.816	0.357	0.31	0.408	SUBCLONAL	1	TRUE	1	0.362362246669066	3		434	611	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5463108	5463108	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	71	356	0	ENST00000381577.3:c.669A>C	p.Glu223Asp	p.E223D	ENST00000381577	NM_014143.3	223	gaA/gaC	4/7	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.362362246669066	2		356	318	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0067044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	159	439	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.818145213384971	2		439	333	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0067044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	237	341	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	0.818145213384971	3	FACETS	1	0.984	1	0.572	0.536	0.608	CLONAL	1	TRUE	1	0.818145213384971	3		341	714	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717715	89717716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587782341	NA	P-0067044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	202	310	0	ENST00000371953.3:c.741dup	p.Pro248ThrfsTer5	p.P248Tfs*5	ENST00000371953	NM_000314.4	247	tta/ttAa	7/9	0.815109106443539	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.818145213384971	1		310	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	266	487	0	ENST00000269305.4:c.497C>A	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tAa	5/11	0.760614854492658	1	FACETS	0.975	0.934	1	0.975	0.934	1	CLONAL	1	TRUE	0	0.818145213384971	1		487	394	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100414	157100414	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1438676618	NA	P-0067044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	12	128	0	ENST00000346085.5:c.1351T>C	p.Ser451Pro	p.S451P	ENST00000346085	NM_020732.3	451	Tcg/Ccg	1/20	1	2	FACETS	0.129	0.09	0.177	0.129	0.09	0.177	SUBCLONAL	1	TRUE	1	0.818145213384971	2		128	227	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039387	49039394	+	frameshift_variant	Frame_Shift_Del	DEL	AGTTTCCT	AGTTTCCT	-	novel	NA	P-0067044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	254	426	0	ENST00000267163.4:c.2376_2383del	p.Pro793ThrfsTer19	p.P793Tfs*19	ENST00000267163	NM_000321.2	791	aAGTTTCCT/a	23/27	0.815109106443539	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.818145213384971	1		426	357	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21336729	21336729	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	316	447	0	ENST00000215739.8:c.69G>T	p.Lys23Asn	p.K23N	ENST00000215739	NM_006767.3	23	aaG/aaT	1/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.818145213384971	2		447	712	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963117	38963117	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0067047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	164	356	0	ENST00000357387.3:c.1427T>G	p.Leu476Ter	p.L476*	ENST00000357387	NM_152756.3	476	tTa/tGa	17/38	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.588787214188798	2		356	452	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161938	47161939	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	127	408	0	ENST00000409792.3:c.4187dup	p.Asn1396LysfsTer2	p.N1396Kfs*2	ENST00000409792	NM_014159.6	1396	aat/aaAt	3/21	0.588787214188798	1	FACETS	0.979	0.9	1	0.979	0.9	1	CLONAL	1	TRUE	0	0.588787214188798	1		408	311	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224161	53224162	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0067047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	82	446	0	ENST00000375401.3:c.3389_3390del	p.Thr1130ArgfsTer73	p.T1130Rfs*73	ENST00000375401	NM_004187.3	1130	aCA/a	22/26	1	2	FACETS	0.89	0.792	0.992	0.89	0.792	0.992	CLONAL	1	TRUE	1	0.588787214188798	2		446	313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067048-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	33	331	0	ENST00000269305.4:c.772G>C	p.Glu258Gln	p.E258Q	ENST00000269305	NM_001126112.2	258	Gaa/Caa	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		331	494	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606815	43606815	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138624658	NA	P-0067048-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	90	501	0	ENST00000355710.3:c.1424G>A	p.Arg475Gln	p.R475Q	ENST00000355710	NM_020975.4	475	cGg/cAg	7/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		501	765	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54956587	54956587	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067048-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	60	264	0	ENST00000312783.6:c.607G>A	p.Ala203Thr	p.A203T	ENST00000312783	NM_198436.1	203	Gct/Act	7/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		264	850	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54956557	54956557	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067048-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	66	257	0	ENST00000312783.6:c.637G>A	p.Ala213Thr	p.A213T	ENST00000312783	NM_198436.1	213	Gca/Aca	7/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		257	883	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067048-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	79	409	0	ENST00000295754.5:c.1583G>T	p.Arg528Leu	p.R528L	ENST00000295754	NM_003242.5	528	cGt/cTt	7/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		409	673	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54956533	54956533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067048-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	65	224	0	ENST00000312783.6:c.661G>A	p.Glu221Lys	p.E221K	ENST00000312783	NM_198436.1	221	Gaa/Aaa	7/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		224	827	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144903	47144903	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067048-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	77	247	0	ENST00000409792.3:c.4850C>A	p.Ala1617Asp	p.A1617D	ENST00000409792	NM_014159.6	1617	gCc/gAc	7/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		247	664	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373398	118373398	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	107	541	0	ENST00000534358.1:c.6792del	p.Thr2265ProfsTer12	p.T2265Pfs*12	ENST00000534358	NM_005933.3	2264	tCc/tc	27/36	0.334679021291484	1	FACETS	0.822	0.739	0.91	0.822	0.739	0.91	CLONAL	1	TRUE	0	0.35410826466956	1		541	605	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038726	47038726	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067067-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	99	470	0	ENST00000377604.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000377604	NM_001204468.1	245	Cag/Tag	9/24	0.172224095709999	4	FACETS	0.805	0.721	0.893	0.805	0.721	0.893	INDETERMINATE	2	TRUE	2	0.31	4		470	520	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259516	+	missense_variant	Missense_Mutation	DNP	TG	TG	GT	rs1057519848	NA	P-0067067-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	168	390	0	ENST00000275493.2:c.2573_2574delinsGT	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTG/cGT	21/28	0.288365534954708	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.31	4		390	631	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939417	71939417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142516692	NA	P-0067067-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	34	616	2	ENST00000298229.2:c.272G>A	p.Arg91His	p.R91H	ENST00000298229	NM_001567.3	91	cGc/cAc	3/28	0.244856034650988	3	FACETS	0.417	0.34	0.505	0.209	0.17	0.253	SUBCLONAL	1	TRUE	1	0.31	3		618	607	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	896889	896889	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067067-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	59	494	0	ENST00000166345.3:c.368A>T	p.Asn123Ile	p.N123I	ENST00000166345	NM_004237.3	123	aAt/aTt	3/13	0.298786374181396	6	FACETS	0.684	0.587	0.791	0.137	0.117	0.159	SUBCLONAL	1	TRUE	1	0.31	6		494	901	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0067068-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	194	405	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.1996519441145	9	FACETS	0.956	0.888	1	0.683	0.634	0.733	CLONAL	5	TRUE	2	0.1996519441145	9		405	691	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0067068-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	226	446	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.1996519441145	9	FACETS	1	0.963	1	0.744	0.696	0.794	CLONAL	5	TRUE	2	0.1996519441145	9		446	738	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100943	27100943	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067068-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	43	476	0	ENST00000324856.7:c.4225C>T	p.Gln1409Ter	p.Q1409*	ENST00000324856	NM_006015.4	1409	Cag/Tag	18/20	0.1996519441145	6	FACETS	0.988	0.826	1	0.247	0.206	0.293	CLONAL	1	TRUE	2	0.1996519441145	6		476	610	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468920	25468920	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067068-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	54	325	0	ENST00000264709.3:c.1443C>A	p.Tyr481Ter	p.Y481*	ENST00000264709	NM_175629.2	481	taC/taA	12/23	0.184722857631031	4	FACETS	1	0.953	1	0.65	0.556	0.753	CLONAL	1	TRUE	2	0.1996519441145	4		325	499	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337695	73337695	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067068-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	52	169	0	ENST00000377767.4:c.2021T>A	p.Val674Asp	p.V674D	ENST00000377767	NM_014953.3	674	gTt/gAt	16/21	0.1996519441145	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	0	0.1996519441145	2		169	224	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117831	70117831	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067068-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	159	457	0	ENST00000245479.2:c.299A>C	p.Lys100Thr	p.K100T	ENST00000245479	NM_000346.3	100	aAg/aCg	1/3	0.184722857631031	4	FACETS	0.969	0.895	1	1	0.992	1	CLONAL	4	TRUE	2	0.1996519441145	4		457	493	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361215	66361215	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067068-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	51	396	0	ENST00000273854.3:c.957C>A	p.Cys319Ter	p.C319*	ENST00000273854	NM_004439.5	319	tgC/tgA	4/18	0.184722857631031	4	FACETS	1	0.91	1	0.551	0.468	0.642	CLONAL	1	TRUE	2	0.1996519441145	4		396	556	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584552	48584552	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0067069-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	327	514	0	ENST00000342988.3:c.725C>G	p.Ser242Ter	p.S242*	ENST00000342988	NM_005359.5	242	tCa/tGa	6/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		514	472	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0067078-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	29	171	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.962	0.777	1	0.962	0.777	1	CLONAL	1	TRUE	1	0.29	2		171	208	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0067078-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	80	322	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.975	0.859	1	0.975	0.859	1	CLONAL	1	TRUE	1	0.29	2		322	566	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0067078-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	55	108	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.294261363052435	3	FACETS	0.842	0.734	0.955	0.842	0.734	0.955	CLONAL	3	TRUE	0	0.29	3		108	172	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625426	69625426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067078-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	80	374	0	ENST00000334134.2:c.367G>A	p.Glu123Lys	p.E123K	ENST00000334134	NM_005247.2	123	Gag/Aag	3/3	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.29	2		374	514	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144146	11144146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067078-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	85	351	0	ENST00000358026.2:c.3727C>T	p.Arg1243Trp	p.R1243W	ENST00000358026	NM_001128849.1	1243	Cgg/Tgg	26/36	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.29	2		351	523	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370987	55370987	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067078-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	87	313	0	ENST00000297316.4:c.289G>T	p.Glu97Ter	p.E97*	ENST00000297316	NM_022454.3	97	Gag/Tag	1/2	0.282647214980955	3	FACETS	1	0.974	1	0.678	0.602	0.758	CLONAL	1	TRUE	1	0.29	3		313	507	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654655	67654655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067078-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	74	311	0	ENST00000264010.4:c.1142G>A	p.Cys381Tyr	p.C381Y	ENST00000264010	NM_006565.3	381	tGc/tAc	6/12	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.29	2		311	510	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220936	36220936	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067078-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	67	358	0	ENST00000222270.7:c.4987del	p.His1663ThrfsTer33	p.H1663Tfs*33	ENST00000222270	NM_014727.1	1662	ttC/tt	23/37	1	2	FACETS	0.926	0.806	1	0.926	0.806	1	CLONAL	1	TRUE	1	0.29	2		358	499	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023094	27023094	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067078-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	44	294	0	ENST00000324856.7:c.200del	p.Gln67ArgfsTer34	p.Q67Rfs*34	ENST00000324856	NM_006015.4	67	cAg/cg	1/20	1	2	FACETS	0.939	0.791	1	0.939	0.791	1	CLONAL	1	TRUE	1	0.29	2		294	323	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347591	89347591	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067078-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	70	366	1	ENST00000301030.4:c.5359del	p.Leu1787PhefsTer176	p.L1787Ffs*176	ENST00000301030	NM_001256183.1	1787	Ctt/tt	9/13	1	2	FACETS	0.881	0.769	1	0.881	0.769	1	CLONAL	1	TRUE	1	0.29	2		367	548	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	143	317	0				ENST00000310581	NM_198253.2	-/1132			0.313447730508326	3	FACETS	0.872	0.808	0.935	0.872	0.808	0.935	CLONAL	3	TRUE	0	0.42836796506353	3		317	310	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0067081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	249	344	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.42836796506353	3	FACETS	1	0.99	1			1	CLONAL	2	TRUE	NA	0.42836796506353	3		344	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0067081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	248	259	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.42836796506353	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	3	TRUE	0	0.42836796506353	3		259	460	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407593	407593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	173	189	0	ENST00000380956.4:c.1351G>A	p.Glu451Lys	p.E451K	ENST00000380956	NM_001195286.1	451	Gaa/Aaa	9/9	0.136709286686912	4	FACETS	0.849	0.789	0.91			1	INDETERMINATE	3	TRUE	NA	0.42836796506353	4		189	453	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220429	123220429	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	57	240	0	ENST00000218089.9:c.3086A>C	p.Gln1029Pro	p.Q1029P	ENST00000218089	NM_001042749.1	1029	cAg/cCg	30/35	0.213624904487146	2	FACETS	0.51	0.438	0.589	0.255	0.219	0.295	INDETERMINATE	1	TRUE	0	0.42836796506353	2		240	522	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221323	2221323	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	133	294	0	ENST00000326181.6:c.407G>A	p.Ser136Asn	p.S136N	ENST00000326181	NM_032271.2	136	aGc/aAc	6/21	0.121752995439828	5	FACETS	0.874	0.802	0.948	0.656	0.601	0.711	INDETERMINATE	3	TRUE	1	0.42836796506353	5		294	389	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918671	44918672	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	148	286	0	ENST00000377967.4:c.1155dup	p.Asn386Ter	p.N386*	ENST00000377967	NM_021140.2	385	agt/agTt	12/29	0.355860899745433	2	FACETS	0.769	0.709	0.832	0.769	0.709	0.832	SUBCLONAL	2	TRUE	0	0.42836796506353	2		286	449	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866609	117866609	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	286	260	0	ENST00000297338.2:c.1036G>C	p.Asp346His	p.D346H	ENST00000297338	NM_006265.2	346	Gat/Cat	9/14	0.348676467217517	4	FACETS	0.968	0.917	1	0.968	0.917	1	CLONAL	3	TRUE	1	0.42836796506353	4		260	657	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67197010	67197010	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs374406780	NA	P-0067087-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	138	348	0	ENST00000312629.5:c.253C>T	p.Arg85Ter	p.R85*	ENST00000312629	NM_003952.2	85	Cga/Tga	4/15	1	2	FACETS	0.833	0.763	0.906	1	0.989	1	CLONAL	2	TRUE	1	0.33270436288823	2		348	498	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806569	1806569	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs182935140	NA	P-0067087-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	46	463	0	ENST00000260795.2:c.1285G>A	p.Ala429Thr	p.A429T	ENST00000260795		429	Gcg/Acg	9/17	1	2	FACETS	0.665	0.561	0.779	0.665	0.561	0.779	SUBCLONAL	1	TRUE	1	0.33270436288823	2		463	416	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562981	29562981	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs376576925	NA	P-0067087-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	80	384	0	ENST00000356175.3:c.3916C>T	p.Arg1306Ter	p.R1306*	ENST00000356175	NM_000267.3	1306	Cga/Tga	29/57	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.33270436288823	2		384	362	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023246	27023261	+	frameshift_variant	Frame_Shift_Del	DEL	ACGGAGCCGCCCGGCG	ACGGAGCCGCCCGGCG	-	novel	NA	P-0067087-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	35	303	0	ENST00000324856.7:c.352_367del	p.Thr118AlafsTer109	p.T118Afs*109	ENST00000324856	NM_006015.4	118	ACGGAGCCGCCCGGCGgc/gc	1/20	0.260210985823581	1	FACETS	0.593	0.487	0.71	0.593	0.487	0.71	SUBCLONAL	1	TRUE	0	0.33270436288823	1		303	296	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111463	8111506	+	frameshift_variant	Frame_Shift_Del	DEL	TGTGCGAACTGTCAGACCACCACAACCACACTCTGGAGGAGGAA	TGTGCGAACTGTCAGACCACCACAACCACACTCTGGAGGAGGAA	-	novel	NA	P-0067087-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	101	344	0	ENST00000346208.3:c.951_994del	p.Ala318GlnfsTer19	p.A318Qfs*19	ENST00000346208		317	TGTGCGAACTGTCAGACCACCACAACCACACTCTGGAGGAGGAAt/t	5/6	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.33270436288823	2		344	436	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727098	243727098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067087-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	80	354	0	ENST00000263826.5:c.872G>A	p.Gly291Glu	p.G291E	ENST00000263826	NM_005465.4	291	gGa/gAa	9/13	0.246789268940059	3	FACETS	1	0.975	1	0.701	0.621	0.787	CLONAL	1	TRUE	1	0.33270436288823	3		354	400	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067089-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	66	317	0				ENST00000310581	NM_198253.2	-/1132			0.178274998689345	3	FACETS	0.892	0.777	1	0.892	0.777	1	CLONAL	2	FALSE	1	0.189778389584858	3		317	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579561	7579567	+	frameshift_variant	Frame_Shift_Del	DEL	ATCATCC	ATCATCC	-	novel	NA	P-0067089-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	126	447	0	ENST00000269305.4:c.120_126del	p.Met40IlefsTer2	p.M40Ifs*2	ENST00000269305	NM_001126112.2	40	atGGATGAT/at	4/11	0.189778389584858	2	FACETS	0.929	0.842	1	0.929	0.842	1	CLONAL	2	FALSE	0	0.189778389584858	2		447	715	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136321	202136321	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067089-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	55	357	0	ENST00000358485.4:c.565A>G	p.Lys189Glu	p.K189E	ENST00000358485	NM_001080125.1	189	Aaa/Gaa	3/9	0.178274998689345	3	FACETS	1	0.901	1	0.534	0.457	0.619	CLONAL	1	FALSE	1	0.189778389584858	3		357	594	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021323	31021323	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067089-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	60	393	0	ENST00000375687.4:c.1322C>G	p.Ser441Cys	p.S441C	ENST00000375687	NM_015338.5	441	tCt/tGt	12/13	0.189778389584858	5	FACETS	1	0.94	1			1	CLONAL	1	FALSE	NA	0.189778389584858	5		393	691	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435054	56435054	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067089-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	223	472	0	ENST00000407977.2:c.2083G>C	p.Glu695Gln	p.E695Q	ENST00000407977		695	Gag/Cag	9/10	0.189778389584858	5	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	FALSE	2	0.189778389584858	5		472	926	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050842	49050843	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0067089-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	325	274	0	ENST00000267163.4:c.2526_2527del	p.Lys844ValfsTer10	p.K844Vfs*10	ENST00000267163	NM_000321.2	842	tcTGag/tcag	25/27	0.189778389584858	8	FACETS	0.964	0.918	1			1	CLONAL	8	FALSE	NA	0.189778389584858	8		274	697	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317706	163317706	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067089-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	52	300	0	ENST00000271452.3:c.1102C>A	p.Gln368Lys	p.Q368K	ENST00000271452	NM_145697.2	368	Caa/Aaa	12/14	0.159081334750957	4	FACETS	1	0.957	1	0.683	0.582	0.794	CLONAL	1	FALSE	2	0.189778389584858	4		300	477	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375469	40375469	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067089-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	70	463	0	ENST00000293328.3:c.481G>C	p.Glu161Gln	p.E161Q	ENST00000293328	NM_012448.3	161	Gag/Cag	5/19	0.189778389584858	5	FACETS	1	0.875	1	0.335	0.291	0.383	CLONAL	1	FALSE	2	0.189778389584858	5		463	942	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38787915	38787915	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067089-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	78	300	0	ENST00000348513.6:c.745G>C	p.Glu249Gln	p.E249Q	ENST00000348513	NM_003079.4	249	Gag/Cag	9/11	0.189778389584858	5	FACETS	0.985	0.867	1	0.657	0.578	0.741	CLONAL	2	FALSE	2	0.189778389584858	5		300	536	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971181	21971195	+	frameshift_variant	Frame_Shift_Del	DEL	CACTCGGGCGCTGCC	CACTCGGGCGCTGCC	TGCTGCG	novel	NA	P-0067089-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	109	494	1	ENST00000304494.5:c.163_177delinsCGCAGCA	p.Gly55ArgfsTer62	p.G55Rfs*62	ENST00000304494	NM_000077.4	55	GGCAGCGCCCGAGTG/CGCAGCA	2/3	0.183325062732216	1	FACETS	0.884	0.796	0.977	1	0.987	1	CLONAL	2	FALSE	0	0.189778389584858	1		495	588	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0067090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	121	516	0	ENST00000311936.3:c.180_181delinsAA	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggAAaa	3/5	0.311038026067836	2	FACETS	0.858	0.781	0.937	0.858	0.781	0.937	CLONAL	2	TRUE	0	0.33043791190048	2		516	427	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0067099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	169	314	4	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.848897740887484	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.848897740887484	2		318	188	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873081	134873081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	136	468	1	ENST00000398015.3:c.1385G>A	p.Gly462Asp	p.G462D	ENST00000398015	NM_004441.4	462	gGc/gAc	6/16	1	2	FACETS	0.971	0.896	1	0.971	0.896	1	CLONAL	1	TRUE	1	0.848897740887484	2		469	330	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902235	50902235	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	180	535	0	ENST00000440232.2:c.127G>A	p.Glu43Lys	p.E43K	ENST00000440232	NM_002691.3	43	Gag/Aag	2/27	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.848897740887484	2		535	387	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374831	149374857	+	protein_altering_variant	In_Frame_Del	DEL	TGCGAGCGGACATGCTGGGCACCCCCA	TGCGAGCGGACATGCTGGGCACCCCCA	GCC	novel	NA	P-0067099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	126	410	0	ENST00000360632.3:c.237_263delinsGGC	p.Gly80_His88delinsAla	p.G80_H88delinsA	ENST00000360632	NM_015472.4	79	gcTGGGGGTGCCCAGCATGTCCGCTCGCAc/gcGGCc	2/7	1	2	FACETS	0.958	0.88	1	0.958	0.88	1	CLONAL	1	TRUE	1	0.848897740887484	2		410	310	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944607	40944607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766880457	NA	P-0067103-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	84	390	0	ENST00000373198.4:c.1895G>A	p.Arg632Gln	p.R632Q	ENST00000373198	NM_133170.3	632	cGa/cAa	12/32	0.384580053400384	3	FACETS	0.95	0.841	1	0.475	0.42	0.534	CLONAL	1	TRUE	1	0.384580053400384	3		390	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579849	7579849	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067103-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	111	401	0	ENST00000269305.4:c.64del	p.Leu22TyrfsTer22	p.L22Yfs*22	ENST00000269305	NM_001126112.2	22	Cta/ta	2/11	0.306919642053348	2	FACETS	0.795	0.722	0.871	0.795	0.722	0.871	SUBCLONAL	2	TRUE	0	0.384580053400384	2		401	363	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0067103-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	72	314	4	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.384580053400384	3	FACETS	0.767	0.677	0.862	0.767	0.677	0.862	SUBCLONAL	2	TRUE	1	0.384580053400384	3		318	291	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0067121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	160	469	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.480136486190345	1	FACETS	0.867	0.799	0.938	0.867	0.799	0.938	CLONAL	1	TRUE	0	0.480136486190345	1		469	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0067121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	364	652	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.472654402783283	2	FACETS	0.828	0.788	0.868	0.828	0.788	0.868	CLONAL	2	TRUE	0	0.480136486190345	2		652	916	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076870	41076870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751972373	NA	P-0067121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	101	272	0	ENST00000373198.4:c.1550C>T	p.Thr517Met	p.T517M	ENST00000373198	NM_133170.3	517	aCg/aTg	9/32	0.449318389600077	1	FACETS	0.685	0.615	0.758	0.685	0.615	0.758	SUBCLONAL	1	TRUE	0	0.480136486190345	1		272	467	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420005	41420005	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	130	425	0	ENST00000373198.4:c.316C>T	p.His106Tyr	p.H106Y	ENST00000373198	NM_133170.3	106	Cat/Tat	3/32	0.449318389600077	1	FACETS	0.575	0.522	0.63	0.575	0.522	0.63	SUBCLONAL	1	TRUE	0	0.480136486190345	1		425	716	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249456	153249456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	135	353	0	ENST00000281708.4:c.1322G>A	p.Arg441Gln	p.R441Q	ENST00000281708	NM_033632.3	441	cGg/cAg	9/12	0.480136486190345	1	FACETS	0.732	0.668	0.799	0.732	0.668	0.799	SUBCLONAL	1	TRUE	0	0.480136486190345	1		353	584	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867192	68867192	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0067121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	122	362	0	ENST00000261769.5:c.2440-1G>C		p.X814_splice	ENST00000261769	NM_004360.3	814			1	2	FACETS	0.792	0.717	0.87	0.792	0.717	0.87	SUBCLONAL	1	TRUE	1	0.480136486190345	2		362	642	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243391	46243391	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	135	375	0	ENST00000334344.6:c.1744A>G	p.Arg582Gly	p.R582G	ENST00000334344	NM_152641.2	582	Aga/Gga	14/21	1	2	FACETS	0.822	0.749	0.899	0.822	0.749	0.899	CLONAL	1	TRUE	1	0.480136486190345	2		375	684	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371721	225371721	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0067121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	134	342	0	ENST00000264414.4:c.884-1G>A		p.X295_splice	ENST00000264414	NM_003590.4	295			1	2	FACETS	0.897	0.818	0.98	0.897	0.818	0.98	CLONAL	1	TRUE	1	0.480136486190345	2		342	622	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542846	187542846	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	124	376	0	ENST00000441802.2:c.4894G>T	p.Glu1632Ter	p.E1632*	ENST00000441802	NM_005245.3	1632	Gag/Tag	10/27	0.480136486190345	1	FACETS	0.884	0.806	0.965	0.884	0.806	0.965	CLONAL	1	TRUE	0	0.480136486190345	1		376	444	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117680992	117680992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	112	315	0	ENST00000368508.3:c.3628C>T	p.His1210Tyr	p.H1210Y	ENST00000368508	NM_002944.2	1210	Cac/Tac	23/43	0.179604786351281	0	FACETS	0.458	0.414	0.505			1	INDETERMINATE	1	TRUE	0	0.480136486190345	0		315	529	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109314054	109314054	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	86	291	1	ENST00000436639.2:c.1169A>G	p.Asp390Gly	p.D390G	ENST00000436639	NM_014454.2	390	gAt/gGt	7/10	NA	2	FACETS	0.684	0.606	0.766			1	INDETERMINATE	1	TRUE	NA	0.480136486190345	2		292	524	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647416	117647416	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	111	391	0	ENST00000368508.3:c.5528G>A	p.Gly1843Glu	p.G1843E	ENST00000368508	NM_002944.2	1843	gGa/gAa	33/43	0.179604786351281	0	FACETS	0.508	0.459	0.559			1	INDETERMINATE	1	TRUE	0	0.480136486190345	0		391	473	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276642	15276642	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	186	433	0	ENST00000263388.2:c.5623C>G	p.Pro1875Ala	p.P1875A	ENST00000263388	NM_000435.2	1875	Ccc/Gcc	30/33	1	2	FACETS	0.922	0.853	0.994	0.922	0.853	0.994	CLONAL	1	TRUE	1	0.480136486190345	2		433	840	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568617	41568617	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	165	414	1	ENST00000263253.7:c.4567G>C	p.Glu1523Gln	p.E1523Q	ENST00000263253	NM_001429.3	1523	Gag/Cag	28/31	1	2	FACETS	0.806	0.74	0.874	0.806	0.74	0.874	CLONAL	1	TRUE	1	0.480136486190345	2		415	853	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596131	43596131	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	203	387	0	ENST00000355710.3:c.298A>T	p.Ser100Cys	p.S100C	ENST00000355710	NM_020975.4	100	Agc/Tgc	2/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.480136486190345	2		387	692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0067126-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	151	365	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.440412837776622	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.440412837776622	2		365	276	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519922	NA	P-0067126-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	134	444	0	ENST00000397062.3:c.235G>A	p.Glu79Lys	p.E79K	ENST00000397062	NM_006164.4	79	Gag/Aag	2/5	0.419861384041428	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.440412837776622	4		444	408	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593441	55593441	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs753212327	NA	P-0067126-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	364	425	2	ENST00000288135.5:c.1598C>A	p.Ala533Asp	p.A533D	ENST00000288135	NM_000222.2	533	gCt/gAt	10/21	0.440412837776622	23	FACETS	1	0.95	1	0.319	0.302	0.336	CLONAL	7	TRUE	1	0.440412837776622	23		427	1325	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631290	117631290	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067126-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	167	333	0	ENST00000368508.3:c.6388C>A	p.Pro2130Thr	p.P2130T	ENST00000368508	NM_002944.2	2130	Cca/Aca	40/43	0.440412837776622	6	FACETS	0.956	0.891	1	0.956	0.891	1	CLONAL	4	TRUE	2	0.440412837776622	6		333	373	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149982947	149982947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067126-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	14	420	0	ENST00000253339.5:c.3311C>T	p.Ser1104Leu	p.S1104L	ENST00000253339		1104	tCa/tTa	7/7	0.440412837776622	6	FACETS	0.441	0.318	0.59	0.11	0.079	0.148	SUBCLONAL	1	TRUE	2	0.440412837776622	6		420	271	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382135	152382135	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067126-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	9	328	0	ENST00000206249.3:c.1248del	p.Lys416AsnfsTer3	p.K416Nfs*3	ENST00000206249	NM_000125.3	415	ggA/gg	6/8	0.440412837776622	6	FACETS	0.199	0.131	0.287	0.05	0.032	0.072	SUBCLONAL	1	TRUE	2	0.440412837776622	6		328	386	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562632	176562632	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067126-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	21	507	0	ENST00000439151.2:c.528G>C	p.Glu176Asp	p.E176D	ENST00000439151	NM_022455.4	176	gaG/gaC	2/23	1	2	FACETS	0.322	0.248	0.409	0.322	0.248	0.409	SUBCLONAL	1	TRUE	1	0.440412837776622	2		507	296	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831452	72831452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067126-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	147	458	0	ENST00000268489.5:c.5129C>T	p.Ala1710Val	p.A1710V	ENST00000268489	NM_006885.3	1710	gCc/gTc	9/10	0.440412837776622	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.440412837776622	2		458	269	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183696	10183696	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	62	576	0	ENST00000256474.2:c.166del	p.Ala56ProfsTer11	p.A56Pfs*11	ENST00000256474	NM_000551.3	55	gaG/ga	1/3	0.212557454309567	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.212557454309567	1		576	433	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099930	27099930	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	64	669	0	ENST00000324856.7:c.3809A>C	p.Asn1270Thr	p.N1270T	ENST00000324856	NM_006015.4	1270	aAt/aCt	15/20	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.212557454309567	2		669	569	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003438	42003439	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0067159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	65	591	0	ENST00000219905.7:c.2977dup	p.Val993GlyfsTer42	p.V993Gfs*42	ENST00000219905	NM_001164273.1	992	cag/caGg	8/24	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.212557454309567	2		591	567	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47061245	47061251	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTACCT	CTTACCT	-	novel	NA	P-0067159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	55	512	0	ENST00000409792.3:c.7430_7431+5del		p.X2477_splice	ENST00000409792	NM_014159.6	2477		19/21	0.212557454309567	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.212557454309567	1		512	399	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845713	68845713	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	234	512	0	ENST00000261769.5:c.959A>T	p.Asn320Ile	p.N320I	ENST00000261769	NM_004360.3	320	aAc/aTc	7/16	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.678013368062919	2		512	538	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0067162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	17	314	4	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.571	0.425	0.746	0.571	0.425	0.746	SUBCLONAL	1	TRUE	1	0.13	2		318	458	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223650	36223650	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs758571377	NA	P-0067162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	34	768	0	ENST00000222270.7:c.6200G>T	p.Gly2067Val	p.G2067V	ENST00000222270	NM_014727.1	2067	gGc/gTc	28/37	1	2	FACETS	0.841	0.685	1	0.841	0.685	1	CLONAL	1	TRUE	1	0.13	2		768	622	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483922	88483922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	28	582	0	ENST00000360948.2:c.1648G>A	p.Gly550Arg	p.G550R	ENST00000360948	NM_001012338.2	550	Gga/Aga	14/19	1	2	FACETS	0.917	0.731	1	0.917	0.731	1	CLONAL	1	TRUE	1	0.13	2		582	470	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760627	133760627	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	39	734	0	ENST00000318560.5:c.2950A>T	p.Thr984Ser	p.T984S	ENST00000318560	NM_005157.4	984	Acg/Tcg	11/11	1	2	FACETS	0.976	0.807	1	0.976	0.807	1	CLONAL	1	TRUE	1	0.13	2		734	615	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544622	86544622	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	25	635	0	ENST00000262426.4:c.447G>T	p.Gln149His	p.Q149H	ENST00000262426	NM_001451.2	149	caG/caT	1/2	1	2	FACETS	0.793	0.624	0.989	0.793	0.624	0.989	CLONAL	1	TRUE	1	0.13	2		635	485	SUCCESS
AR	367	MSKCC	GRCh37	X	66765712	66765712	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs756810389	NA	P-0067162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	37	717	1	ENST00000374690.3:c.724G>T	p.Ala242Ser	p.A242S	ENST00000374690	NM_000044.3	242	Gca/Tca	1/8	1	2	FACETS	0.843	0.693	1	0.843	0.693	1	CLONAL	1	TRUE	1	0.13	2		718	675	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0067163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	33	270	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.938	0.763	1	0.938	0.763	1	CLONAL	1	TRUE	1	0.16	2		270	440	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0067163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	59	507	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	1	2	FACETS	0.952	0.817	1	0.952	0.817	1	CLONAL	1	TRUE	1	0.16	2		507	775	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374991	45374991	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	39	649	0	ENST00000262160.6:c.852G>C	p.Gln284His	p.Q284H	ENST00000262160	NM_005901.5	284	caG/caC	8/11	1	2	FACETS	0.891	0.738	1	0.891	0.738	1	CLONAL	1	TRUE	1	0.16	2		649	547	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974681	21974681	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	42	697	0	ENST00000304494.5:c.146del	p.Ile49ThrfsTer4	p.I49Tfs*4	ENST00000304494	NM_000077.4	49	aTc/ac	1/3	0.145358972672669	1	FACETS	0.846	0.705	1	0.846	0.705	1	CLONAL	1	TRUE	0	0.16	1		697	571	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140165	50140165	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	46	657	0	ENST00000246792.3:c.260A>T	p.Gln87Leu	p.Q87L	ENST00000246792	NM_006270.3	87	cAg/cTg	3/6	1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	TRUE	1	0.194304797700075	2		657	473	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0067164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	229	439	0				ENST00000310581	NM_198253.2	-/1132			0.194304797700075	10	FACETS	0.979	0.926	1	1	0.99	1	CLONAL	10	TRUE	2	0.194304797700075	10		439	428	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412045	116412045	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0067164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	117	676	0	ENST00000397752.3:c.3028+2T>G		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.194304797700075	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.194304797700075	2		676	546	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510835	157510836	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0067164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	61	624	0	ENST00000346085.5:c.3610_3611delinsTT	p.Ala1204Leu	p.A1204L	ENST00000346085	NM_020732.3	1204	GCa/TTa	14/20	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.194304797700075	2		624	529	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243951	46243951	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0067165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	49	486	0	ENST00000334344.6:c.2045C>G	p.Ser682Ter	p.S682*	ENST00000334344	NM_152641.2	682	tCa/tGa	15/21	1	2	FACETS	0.504	0.427	0.588	0.504	0.427	0.588	SUBCLONAL	1	TRUE	1	0.439879848349349	2		486	442	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425146	49425146	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	45	717	0	ENST00000301067.7:c.13342del	p.His4448ThrfsTer71	p.H4448Tfs*71	ENST00000301067	NM_003482.3	4448	Cac/ac	39/54	1	2	FACETS	0.443	0.372	0.521	0.443	0.372	0.521	SUBCLONAL	1	TRUE	1	0.439879848349349	2		717	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0067166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	364	598	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.470730641124668	3	FACETS	0.921	0.884	0.957	0.921	0.884	0.957	CLONAL	3	TRUE	0	0.550955753334175	3		598	610	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0067166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	145	559	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.550955753334175	2		559	525	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591837	48591837	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867764109	NA	P-0067166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	122	533	0	ENST00000342988.3:c.1000C>T	p.Gln334Ter	p.Q334*	ENST00000342988	NM_005359.5	334	Cag/Tag	9/12	0.550955753334175	1	FACETS	0.961	0.88	1	0.961	0.88	1	CLONAL	1	TRUE	0	0.550955753334175	1		533	334	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623152	52623152	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	124	498	0	ENST00000394830.3:c.2899G>T	p.Glu967Ter	p.E967*	ENST00000394830	NM_018313.4	967	Gaa/Taa	19/30	0.516886185776989	1	FACETS	0.843	0.77	0.918	0.843	0.77	0.918	CLONAL	1	TRUE	0	0.550955753334175	1		498	387	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509083	66509083	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	51	338	0	ENST00000273854.3:c.244G>T	p.Gly82Trp	p.G82W	ENST00000273854	NM_004439.5	82	Ggg/Tgg	2/18	0.550955753334175	1	FACETS	0.931	0.81	1	0.931	0.81	1	CLONAL	1	TRUE	0	0.550955753334175	1		338	144	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163348	32163348	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	140	691	0	ENST00000375023.3:c.5878G>C	p.Gly1960Arg	p.G1960R	ENST00000375023	NM_004557.3	1960	Ggt/Cgt	30/30	0.550955753334175	1	FACETS	0.875	0.804	0.947	0.875	0.804	0.947	CLONAL	1	TRUE	0	0.550955753334175	1		691	421	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636845	73636845	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	142	537	0	ENST00000377687.4:c.1108C>G	p.Arg370Gly	p.R370G	ENST00000377687	NM_001730.3	370	Cga/Gga	2/4	0.552468777511878	3	FACETS	1	0.933	1	0.512	0.468	0.558	CLONAL	1	TRUE	1	0.550955753334175	3		537	642	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041172	180041172	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	144	659	0	ENST00000261937.6:c.3227T>A	p.Leu1076Gln	p.L1076Q	ENST00000261937	NM_182925.4	1076	cTg/cAg	24/30	0.550955753334175	1	FACETS	0.855	0.787	0.925	0.855	0.787	0.925	CLONAL	1	TRUE	0	0.550955753334175	1		659	443	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495831	56495831	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1381182333	NA	P-0067166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	263	438	0	ENST00000267101.3:c.4021A>G	p.Arg1341Gly	p.R1341G	ENST00000267101	NM_001982.3	1341	Aga/Gga	28/28	0.470730641124668	3	FACETS	0.896	0.853	0.938	0.896	0.853	0.938	CLONAL	3	TRUE	0	0.550955753334175	3		438	453	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591686	38591686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	111	393	0	ENST00000299084.4:c.145C>T	p.His49Tyr	p.H49Y	ENST00000299084	NM_152594.2	49	Cat/Tat	2/7	0.552468777511878	1	FACETS	0.846	0.769	0.926	0.846	0.769	0.926	CLONAL	1	TRUE	0	0.550955753334175	1		393	345	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752751	42752751	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	127	620	0	ENST00000222329.4:c.1513G>C	p.Glu505Gln	p.E505Q	ENST00000222329	NM_006494.2	505	Gag/Cag	4/4	1	2	FACETS	0.917	0.835	1	0.917	0.835	1	CLONAL	1	TRUE	1	0.550955753334175	2		620	503	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28605607	28605607	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0067166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	111	517	0	ENST00000253063.3:c.1212-1G>C		p.X404_splice	ENST00000253063	NM_031459.4	404			1	2	FACETS	0.882	0.797	0.97	0.882	0.797	0.97	CLONAL	1	TRUE	1	0.550955753334175	2		517	457	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574960	41574960	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0067166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	58	450	0	ENST00000263253.7:c.7245G>C	p.Ter2415TyrextTer30	p.*2415Yext*30	ENST00000263253	NM_001429.3	2415	taG/taC	31/31	0.161863917684434	3	FACETS	0.71	0.613	0.816	0.237	0.204	0.272	INDETERMINATE	1	TRUE	0	0.550955753334175	3		450	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764146326	NA	P-0067167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	99	539	0	ENST00000269305.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000269305	NM_001126112.2	281	Gac/Aac	8/11	0.16035691133988	2	FACETS	1	0.943	1	0.542	0.484	0.604	INDETERMINATE	1	TRUE	0	0.26924309024803	2		539	678	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839724	27839724	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	100	677	0	ENST00000328488.2:c.370G>C	p.Asp124His	p.D124H	ENST00000328488	NM_003533.2	124	Gac/Cac	1/1	0.207140681628869	4	FACETS	0.931	0.83	1	0.465	0.415	0.52	CLONAL	1	TRUE	2	0.26924309024803	4		677	1013	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720860	89720860	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	12	177	0	ENST00000371953.3:c.1011T>A	p.Phe337Leu	p.F337L	ENST00000371953	NM_000314.4	337	ttT/ttA	8/9	1	2	FACETS	0.415	0.291	0.566	0.415	0.291	0.566	SUBCLONAL	1	TRUE	1	0.26924309024803	2		177	215	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679025	117679025	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	28	474	0	ENST00000368508.3:c.3796G>C	p.Val1266Leu	p.V1266L	ENST00000368508	NM_002944.2	1266	Gtg/Ctg	24/43	0.124680936315606	0	FACETS	0.421	0.336	0.517			1	INDETERMINATE	1	TRUE	0	0.26924309024803	0		474	361	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663662	29663662	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	34	439	0	ENST00000356175.3:c.6094A>T	p.Arg2032Trp	p.R2032W	ENST00000356175	NM_000267.3	2032	Agg/Tgg	41/57	1	2	FACETS	0.536	0.438	0.647	0.536	0.438	0.647	SUBCLONAL	1	TRUE	1	0.26924309024803	2		439	471	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413264	139413264	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	49	407	0	ENST00000277541.6:c.878C>T	p.Thr293Ile	p.T293I	ENST00000277541	NM_017617.3	293	aCc/aTc	6/34	0.155438691443557	3	FACETS	0.649	0.549	0.76	0.325	0.274	0.38	INDETERMINATE	1	TRUE	1	0.26924309024803	3		407	636	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104711	193104711	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	168	285	0	ENST00000367435.3:c.415C>T	p.Arg139Ter	p.R139*	ENST00000367435	NM_024529.4	139	Cga/Tga	5/17	0.569004275372803	3	FACETS	0.952	0.876	1	0.476	0.438	0.515	CLONAL	1	TRUE	1	0.569004275372803	3		285	797	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163298075	163298075	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	160	278	0	ENST00000271452.3:c.256A>T	p.Ser86Cys	p.S86C	ENST00000271452	NM_145697.2	86	Agc/Tgc	4/14	0.569004275372803	3	FACETS	1	0.939	1	0.512	0.471	0.556	CLONAL	1	TRUE	1	0.569004275372803	3		278	705	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653231	206653231	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs145306712	NA	P-0067168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	231	530	0	ENST00000367120.3:c.1202A>G	p.Lys401Arg	p.K401R	ENST00000367120	NM_014002.3	401	aAg/aGg	11/22	0.569004275372803	3	FACETS	1	0.941	1	0.505	0.47	0.54	CLONAL	1	TRUE	1	0.569004275372803	3		530	1033	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549473	21549474	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	186	422	0	ENST00000382592.4:c.2802dup	p.Pro935SerfsTer9	p.P935Sfs*9	ENST00000382592	NM_014572.2	934	-/T	8/8	0.569004275372803	1	FACETS	0.955	0.89	1	0.955	0.89	1	CLONAL	1	TRUE	0	0.569004275372803	1		422	490	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647526	23647526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567223045	NA	P-0067168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	151	352	0	ENST00000261584.4:c.341G>A	p.Gly114Glu	p.G114E	ENST00000261584	NM_024675.3	114	gGa/gAa	4/13	1	2	FACETS	0.888	0.815	0.963	0.888	0.815	0.963	CLONAL	1	TRUE	1	0.569004275372803	2		352	598	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743335	743335	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	177	364	0	ENST00000314574.4:c.805G>A	p.Ala269Thr	p.A269T	ENST00000314574	NM_005433.3	269	Gct/Act	7/12	1	2	FACETS	0.965	0.893	1	0.965	0.893	1	CLONAL	1	TRUE	1	0.569004275372803	2		364	645	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207064	1207065	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0067168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	180	455	0	ENST00000326873.7:c.152_153del	p.Met51ArgfsTer111	p.M51Rfs*111	ENST00000326873	NM_000455.4	51	aTG/a	1/10	0.569004275372803	1	FACETS	0.864	0.803	0.926	0.864	0.803	0.926	CLONAL	1	TRUE	0	0.569004275372803	1		455	524	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610484	10610490	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGCTG	GCTGCTG	-	novel	NA	P-0067168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	170	415	0	ENST00000171111.5:c.220_226del	p.Gln74CysfsTer81	p.Q74Cfs*81	ENST00000171111	NM_203500.1	74	CAGCAGCtg/tg	2/6	0.569004275372803	1	FACETS	0.908	0.842	0.974	0.908	0.842	0.974	CLONAL	1	TRUE	0	0.569004275372803	1		415	471	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133756030	133756030	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	187	408	0	ENST00000318560.5:c.1657T>C	p.Ser553Pro	p.S553P	ENST00000318560	NM_005157.4	553	Tcc/Ccc	10/11	0.569004275372803	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.569004275372803	1		408	446	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0067169-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	579	494	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.944251604345984	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.945353100654245	3		494	594	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737028	162737028	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067169-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	94	379	0	ENST00000367921.3:c.1172T>A	p.Leu391His	p.L391H	ENST00000367921	NM_006182.2	391	cTt/cAt	11/18	0.943609768261609	4	FACETS	0.594	0.529	0.664	0.198	0.176	0.222	SUBCLONAL	1	TRUE	1	0.945353100654245	4		379	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587782529	NA	P-0067170-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	177	318	0	ENST00000269305.4:c.1009C>G	p.Arg337Gly	p.R337G	ENST00000269305	NM_001126112.2	337	Cgc/Ggc	10/11	0.431437708237185	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.429430107470551	2		318	375	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517514	176517514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373397427	NA	P-0067170-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	123	400	0	ENST00000292408.4:c.215G>A	p.Arg72His	p.R72H	ENST00000292408	NM_213647.1	72	cGc/cAc	3/18	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.429430107470551	2		400	421	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424511	47424511	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067170-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	168	416	0	ENST00000377045.4:c.431G>T	p.Cys144Phe	p.C144F	ENST00000377045	NM_001654.4	144	tGt/tTt	5/16	0.33603483938179	2	FACETS	1	0.99	1	0.748	0.692	0.805	CLONAL	1	TRUE	0	0.429430107470551	2		416	523	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0067171-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	159	395	11	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.398654191248984	3	FACETS	0.978	0.904	1	0.978	0.904	1	CLONAL	2	TRUE	1	0.398654191248984	3		406	489	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063718	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0067171-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	35	335	0	ENST00000412916.2:c.165+2dup		p.X55_splice	ENST00000412916		55			1	2	FACETS	0.576	0.473	0.69	0.576	0.473	0.69	SUBCLONAL	1	TRUE	1	0.398654191248984	2		335	305	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441265	52441265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067171-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	48	508	0	ENST00000460680.1:c.505C>T	p.His169Tyr	p.H169Y	ENST00000460680	NM_004656.3	169	Cac/Tac	7/17	1	2	FACETS	0.402	0.339	0.471	0.402	0.339	0.471	SUBCLONAL	1	TRUE	1	0.398654191248984	2		508	599	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099314	27099314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067171-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	40	382	1	ENST00000324856.7:c.3551C>T	p.Ser1184Leu	p.S1184L	ENST00000324856	NM_006015.4	1184	tCa/tTa	14/20	1	2	FACETS	0.402	0.334	0.478	0.402	0.334	0.478	SUBCLONAL	1	TRUE	1	0.398654191248984	2		383	499	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	74	317	0				ENST00000310581	NM_198253.2	-/1132			0.276214096666214	4	FACETS	1	0.95	1	0.76	0.672	0.853	CLONAL	2	TRUE	1	0.276214096666214	4		317	300	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033844	49033844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853294	NA	P-0067172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	34	241	0	ENST00000267163.4:c.1981C>T	p.Arg661Trp	p.R661W	ENST00000267163	NM_000321.2	661	Cgg/Tgg	20/27	1	2	FACETS	0.746	0.611	0.897	0.746	0.611	0.897	SUBCLONAL	1	TRUE	1	0.276214096666214	2		241	330	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493442	56493442	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	107	255	0	ENST00000267101.3:c.2850T>G	p.Ile950Met	p.I950M	ENST00000267101	NM_001982.3	950	atT/atG	24/28	1	2	FACETS	0.851	0.768	0.939	1	0.986	1	CLONAL	2	TRUE	1	0.276214096666214	2		255	455	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651933	36651934	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0067172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	58	338	0	ENST00000244741.5:c.56dup	p.Arg20ProfsTer16	p.R20Pfs*16	ENST00000244741	NM_000389.4	19	cgc/cGgc	2/3	1	2	FACETS	0.765	0.657	0.882	0.765	0.657	0.882	SUBCLONAL	1	TRUE	1	0.276214096666214	2		338	549	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067172-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	45	317	0				ENST00000310581	NM_198253.2	-/1132			0.132840687002487	5	FACETS	1	0.944	1	0.32	0.27	0.375	INDETERMINATE	1	FALSE	1	0.334076457541535	5		317	316	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033844	49033844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853294	NA	P-0067172-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	39	241	0	ENST00000267163.4:c.1981C>T	p.Arg661Trp	p.R661W	ENST00000267163	NM_000321.2	661	Cgg/Tgg	20/27	1	2	FACETS	0.656	0.545	0.779	0.656	0.545	0.779	SUBCLONAL	1	FALSE	1	0.334076457541535	2		241	356	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493442	56493442	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067172-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	90	255	0	ENST00000267101.3:c.2850T>G	p.Ile950Met	p.I950M	ENST00000267101	NM_001982.3	950	atT/atG	24/28	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	1	0.334076457541535	2		255	507	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651933	36651934	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0067172-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	40	338	0	ENST00000244741.5:c.56dup	p.Arg20ProfsTer16	p.R20Pfs*16	ENST00000244741	NM_000389.4	19	cgc/cGgc	2/3	1	2	FACETS	0.355	0.294	0.423	0.355	0.294	0.423	SUBCLONAL	1	FALSE	1	0.334076457541535	2		338	675	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953760	48953760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913302	NA	P-0067173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	58	169	0	ENST00000267163.4:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000267163	NM_000321.2	455	Cga/Tga	14/27	0.691517674410308	1	FACETS	0.437	0.379	0.499	0.437	0.379	0.499	SUBCLONAL	1	TRUE	0	0.691517674410308	1		169	251	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	53	317	0				ENST00000310581	NM_198253.2	-/1132			0.267161017651846	1	FACETS	0.597	0.513	0.688	0.597	0.513	0.688	INDETERMINATE	1	TRUE	0	0.46258200024883	1		317	295	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0067174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	215	333	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.165474107201652	3	FACETS	1	0.945	1	0.673	0.63	0.716	INDETERMINATE	2	TRUE	0	0.46258200024883	3		333	567	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0067174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	92	362	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.46258200024883	1	FACETS	0.881	0.79	0.976	0.881	0.79	0.976	CLONAL	1	TRUE	0	0.46258200024883	1		362	347	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716431	18716431	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	106	313	0	ENST00000266497.5:c.3778G>A	p.Glu1260Lys	p.E1260K	ENST00000266497		1260	Gag/Aag	26/31	1	2	FACETS	0.988	0.89	1	0.988	0.89	1	CLONAL	1	TRUE	1	0.46258200024883	2		313	464	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	150	448	0	ENST00000394830.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000394830	NM_018313.4	710	Cga/Tga	17/30	0.451445415121935	2	FACETS	1	0.989	1	0.749	0.691	0.808	CLONAL	1	TRUE	0	0.46258200024883	2		448	433	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955063	55955063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	114	265	0	ENST00000263923.4:c.3482G>A	p.Gly1161Glu	p.G1161E	ENST00000263923	NM_002253.2	1161	gGa/gAa	26/30	1	2	FACETS	0.856	0.773	0.943	0.856	0.773	0.943	CLONAL	1	TRUE	1	0.46258200024883	2		265	576	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993798	72993798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1283557059	NA	P-0067174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	184	460	0	ENST00000268489.5:c.247G>A	p.Glu83Lys	p.E83K	ENST00000268489	NM_006885.3	83	Gaa/Aaa	2/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.46258200024883	2		460	713	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38964909	38964909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	42	268	0	ENST00000357387.3:c.1385C>T	p.Pro462Leu	p.P462L	ENST00000357387	NM_152756.3	462	cCc/cTc	16/38	0.267161017651846	1	FACETS	0.545	0.458	0.64	0.545	0.458	0.64	INDETERMINATE	1	TRUE	0	0.46258200024883	1		268	256	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876163	35876163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	89	357	0	ENST00000303115.3:c.955G>A	p.Glu319Lys	p.E319K	ENST00000303115	NM_002185.3	319	Gaa/Aaa	8/8	0.267161017651846	1	FACETS	0.513	0.455	0.574	0.513	0.455	0.574	INDETERMINATE	1	TRUE	0	0.46258200024883	1		357	577	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322989	31322989	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	175	496	0	ENST00000412585.2:c.907C>T	p.Gln303Ter	p.Q303*	ENST00000412585	NM_005514.6	303	Cag/Tag	5/8	1	2	FACETS	0.978	0.902	1	0.978	0.902	1	CLONAL	1	TRUE	1	0.46258200024883	2		496	774	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374844	149374844	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	87	328	0	ENST00000360632.3:c.250C>A	p.His84Asn	p.H84N	ENST00000360632	NM_015472.4	84	Cat/Aat	2/7	0.372752213419973	3	FACETS	0.663	0.586	0.744	0.331	0.293	0.372	SUBCLONAL	1	TRUE	1	0.46258200024883	3		328	699	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752392	55752392	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766409125	NA	P-0067174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	143	365	2	ENST00000284073.2:c.850G>A	p.Asp284Asn	p.D284N	ENST00000284073	NM_138962.2	284	Gat/Aat	12/14	1	2	FACETS	0.965	0.882	1	0.965	0.882	1	CLONAL	1	TRUE	1	0.46258200024883	2		367	641	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750600	128750600	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs780361249	NA	P-0067174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	152	436	0	ENST00000377970.2:c.137T>C	p.Phe46Ser	p.F46S	ENST00000377970	NM_002467.4	46	tTc/tCc	2/3	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.46258200024883	2		436	630	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007661	45007665	+	frameshift_variant	Frame_Shift_Del	DEL	GAATG	GAATG	-	novel	NA	P-0067174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	110	369	0	ENST00000558401.1:c.111_115del	p.Asn37LysfsTer18	p.N37Kfs*18	ENST00000558401	NM_004048.2	36	gaGAATGga/gaga	2/4	0.267161017651846	1	FACETS	0.89	0.805	0.977	0.89	0.805	0.977	INDETERMINATE	1	TRUE	0	0.46258200024883	1		369	411	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248618	59248618	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	376	374	0	ENST00000371222.2:c.125T>C	p.Leu42Pro	p.L42P	ENST00000371222	NM_002228.3	42	cTg/cCg	1/1	0.165474107201652	3	FACETS	1	0.986	1	0.724	0.69	0.759	INDETERMINATE	2	TRUE	0	0.46258200024883	3		374	921	SUCCESS
ALB	213	MSKCC	GRCh37	4	74283322	74283322	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	56	305	0	ENST00000295897.4:c.1364G>A	p.Gly455Glu	p.G455E	ENST00000295897	NM_000477.5	455	gGa/gAa	11/15	1	2	FACETS	0.66	0.568	0.76	0.66	0.568	0.76	SUBCLONAL	1	TRUE	1	0.46258200024883	2		305	367	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526502	31526502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	71	422	0	ENST00000344624.3:c.538C>T	p.Pro180Ser	p.P180S	ENST00000344624		180	Ccc/Tcc	2/33	0.267161017651846	1	FACETS	0.393	0.343	0.447	0.393	0.343	0.447	INDETERMINATE	1	TRUE	0	0.46258200024883	1		422	600	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619169	43619169	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	199	461	0	ENST00000355710.3:c.2852C>T	p.Pro951Leu	p.P951L	ENST00000355710	NM_020975.4	951	cCc/cTc	17/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.46258200024883	2		461	793	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940514	131940514	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs768115577	NA	P-0067174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	68	292	0	ENST00000265335.6:c.2541A>T	p.Glu847Asp	p.E847D	ENST00000265335		847	gaA/gaT	16/25	0.45741023651617	1	FACETS	0.713	0.625	0.806	0.713	0.625	0.806	SUBCLONAL	1	TRUE	0	0.46258200024883	1		292	317	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909579	50909579	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	197	450	0	ENST00000440232.2:c.1383G>C	p.Gln461His	p.Q461H	ENST00000440232	NM_002691.3	461	caG/caC	11/27	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.46258200024883	2		450	722	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0067194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	22	314	4	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		318	260	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0067194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	43	389	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		389	347	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974678	21974678	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs587778189	NA	P-0067194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	31	431	0	ENST00000304494.5:c.149A>G	p.Gln50Arg	p.Q50R	ENST00000304494	NM_000077.4	50	cAg/cGg	1/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		431	368	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720741	89720741	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs371387815	NA	P-0067195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	13	90	0	ENST00000371953.3:c.892C>T	p.Gln298Ter	p.Q298*	ENST00000371953	NM_000314.4	298	Caa/Taa	8/9	0.468967715762368	1	FACETS	0.653	0.476	0.857	0.653	0.476	0.857	SUBCLONAL	1	TRUE	0	0.468967715762368	1		90	65	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1131691023	NA	P-0067195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	147	548	0	ENST00000269305.4:c.470T>A	p.Val157Asp	p.V157D	ENST00000269305	NM_001126112.2	157	gTc/gAc	5/11	0.468967715762368	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.468967715762368	1		548	475	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259661	16259661	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0067195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	164	588	0	ENST00000375759.3:c.6926C>G	p.Ser2309Ter	p.S2309*	ENST00000375759	NM_015001.2	2309	tCa/tGa	11/15	0.468967715762368	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.468967715762368	1		588	493	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156058	106156059	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACAACT	novel	NA	P-0067195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	101	551	0	ENST00000380013.4:c.965_970dup	p.Leu322_Gln323dup	p.L322_Q323dup	ENST00000380013	NM_001127208.2	322	gaa/gaACAACTa	3/11	1	2	FACETS	0.768	0.688	0.852	0.768	0.688	0.852	SUBCLONAL	1	TRUE	1	0.468967715762368	2		551	561	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991623	72991623	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	136	545	0	ENST00000268489.5:c.2422G>C	p.Val808Leu	p.V808L	ENST00000268489	NM_006885.3	808	Gtg/Ctg	2/10	1	2	FACETS	0.983	0.897	1	0.983	0.897	1	CLONAL	1	TRUE	1	0.468967715762368	2		545	590	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156168	106156169	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCAGCAATTT	novel	NA	P-0067195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	91	525	0	ENST00000380013.4:c.1073_1082dup	p.Ala362GlnfsTer10	p.A362Qfs*10	ENST00000380013	NM_001127208.2	357	agc/aGCAGCAATTTgc	3/11	1	2	FACETS	0.698	0.621	0.78	0.698	0.621	0.78	SUBCLONAL	1	TRUE	1	0.468967715762368	2		525	556	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527490	29527520	+	frameshift_variant	Frame_Shift_Del	DEL	TAGGCAGCTGACAGAAAGTGCTGCAATTGCC	TAGGCAGCTGACAGAAAGTGCTGCAATTGCC	-	novel	NA	P-0067195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	147	392	0	ENST00000356175.3:c.940_970del	p.Arg314ValfsTer52	p.R314Vfs*52	ENST00000356175	NM_000267.3	313	agTAGGCAGCTGACAGAAAGTGCTGCAATTGCC/ag	9/57	0.468094637414601	2	FACETS	1	0.989	1	0.748	0.69	0.808	CLONAL	1	TRUE	0	0.468967715762368	2		392	419	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156288	106156288	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	169	650	0	ENST00000380013.4:c.1189A>G	p.Thr397Ala	p.T397A	ENST00000380013	NM_001127208.2	397	Aca/Gca	3/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.468967715762368	2		650	667	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158269	106158287	+	frameshift_variant	Frame_Shift_Del	DEL	AAATGTCAGGGCCAGTCAC	AAATGTCAGGGCCAGTCAC	TCT	novel	NA	P-0067195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	91	534	1	ENST00000380013.4:c.3170_3188delinsTCT	p.Glu1057ValfsTer2	p.E1057Vfs*2	ENST00000380013	NM_001127208.2	1057	gAAATGTCAGGGCCAGTCACa/gTCTa	3/11	1	2	FACETS	0.738	0.657	0.824	0.738	0.657	0.824	SUBCLONAL	1	TRUE	1	0.468967715762368	2		535	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0067196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	211	415	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.390887695461559	2	FACETS	0.902	0.846	0.959	0.902	0.846	0.959	CLONAL	2	TRUE	0	0.457536381460537	2		415	511	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0067196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	63	303	1	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.284134560912965	3	FACETS	0.857	0.744	0.978	0.428	0.372	0.489	CLONAL	1	TRUE	1	0.457536381460537	3		304	395	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440904	56440904	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1458799446	NA	P-0067196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	253	475	1	ENST00000407977.2:c.433C>T	p.Arg145Ter	p.R145*	ENST00000407977		145	Cga/Tga	4/10	0.390887695461559	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	0	0.457536381460537	2		476	552	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593507	48593507	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1367209662	NA	P-0067196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	166	375	0	ENST00000342988.3:c.1258C>T	p.Arg420Cys	p.R420C	ENST00000342988	NM_005359.5	420	Cgt/Tgt	10/12	0.394505958559675	2	FACETS	0.862	0.801	0.924	0.862	0.801	0.924	CLONAL	2	TRUE	0	0.457536381460537	2		375	421	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81557418	81557418	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	39	352	0	ENST00000298171.2:c.398T>G	p.Ile133Ser	p.I133S	ENST00000298171	NM_000369.2	133	aTt/aGt	5/10	1	2	FACETS	0.539	0.449	0.64	0.539	0.449	0.64	SUBCLONAL	1	TRUE	1	0.457536381460537	2		352	316	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70432744	70432744	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	38	392	0	ENST00000373644.4:c.4766A>C	p.Lys1589Thr	p.K1589T	ENST00000373644	NM_030625.2	1589	aAg/aCg	8/12	1	2	FACETS	0.403	0.333	0.481	0.403	0.333	0.481	SUBCLONAL	1	TRUE	1	0.457536381460537	2		392	412	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57004099	57004099	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	C	C	T	rs772893901	NA	P-0067196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	92	480	1	ENST00000257254.3:c.380G>A	p.Arg127His	p.R127H	ENST00000257254		127	cGc/cAc	1/2	0.359911504823003	1	FACETS	0.67	0.598	0.746	0.67	0.598	0.746	SUBCLONAL	1	TRUE	0	0.457536381460537	1		481	463	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294342	1294342	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	98	604	0	ENST00000310581.5:c.659G>T	p.Gly220Val	p.G220V	ENST00000310581	NM_198253.2	220	gGt/gTt	2/16	0.457536381460537	3	FACETS	0.758	0.677	0.845	0.253	0.225	0.282	SUBCLONAL	1	TRUE	0	0.457536381460537	3		604	694	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70355027	70355027	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	126	242	0	ENST00000374080.3:c.4949C>T	p.Thr1650Met	p.T1650M	ENST00000374080		1650	aCg/aTg	36/45	0.457536381460537	2	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.457536381460537	2		242	419	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176710903	176710903	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	161	390	0	ENST00000439151.2:c.6125T>G	p.Leu2042Arg	p.L2042R	ENST00000439151	NM_022455.4	2042	cTt/cGt	20/23	0.188750113574141	3	FACETS	1	0.977	1			1	INDETERMINATE	2	TRUE	NA	0.457536381460537	3		390	384	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591921	48591921	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	187	420	0	ENST00000342988.3:c.1084T>A	p.Phe362Ile	p.F362I	ENST00000342988	NM_005359.5	362	Ttt/Att	9/12	0.394505958559675	2	FACETS	0.798	0.744	0.854	0.798	0.744	0.854	SUBCLONAL	2	TRUE	0	0.457536381460537	2		420	512	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81960773	81960773	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	69	439	0	ENST00000359376.3:c.2504T>A	p.Leu835Gln	p.L835Q	ENST00000359376	NM_002661.3	835	cTa/cAa	23/33	0.457536381460537	1	FACETS	0.696	0.611	0.788	0.696	0.611	0.788	SUBCLONAL	1	TRUE	0	0.457536381460537	1		439	334	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435843	110435843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	147	549	0	ENST00000375856.3:c.2558C>T	p.Ala853Val	p.A853V	ENST00000375856	NM_003749.2	853	gCc/gTc	1/2	NA	2	FACETS	0.824	0.757	0.893			1	INDETERMINATE	1	TRUE	NA	0.710934537994115	2		549	502	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779746	3779746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	197	483	0	ENST00000262367.5:c.5302C>T	p.Arg1768Cys	p.R1768C	ENST00000262367	NM_004380.2	1768	Cgc/Tgc	31/31	0.669293193529578	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.710934537994115	1		483	325	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469793	157469793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1436675945	NA	P-0067197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	158	457	1	ENST00000346085.5:c.2587C>T	p.Pro863Ser	p.P863S	ENST00000346085	NM_020732.3	863	Ccc/Tcc	9/20	1	2	FACETS	0.852	0.785	0.92	0.852	0.785	0.92	CLONAL	1	TRUE	1	0.710934537994115	2		458	522	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577505	7577505	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	182	384	2	ENST00000269305.4:c.776del	p.Asp259AlafsTer86	p.D259Afs*86	ENST00000269305	NM_001126112.2	259	gAc/gc	7/11	0.669293193529578	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.710934537994115	1		386	320	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397771	116397771	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	43	372	0	ENST00000397752.3:c.2045T>C	p.Leu682Pro	p.L682P	ENST00000397752	NM_000245.2	682	cTa/cCa	8/21	0.241282070822458	4	FACETS	0.962	0.817	1	0.962	0.817	1	CLONAL	2	TRUE	2	0.356773502601856	4		372	170	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183711	10183728	+	inframe_deletion	In_Frame_Del	DEL	GCCCGTGCTGCGCTCGGT	GCCCGTGCTGCGCTCGGT	-	novel	NA	P-0067198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	81	442	0	ENST00000256474.2:c.181_198del	p.Pro61_Val66del	p.P61_V66del	ENST00000256474	NM_000551.3	60	cgGCCCGTGCTGCGCTCGGTg/cgg	1/3	0.356773502601856	2	FACETS	0.966	0.865	1	0.966	0.865	1	CLONAL	2	TRUE	0	0.356773502601856	2		442	235	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38792293	38792293	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	33	424	0	ENST00000348513.6:c.431A>C	p.Asn144Thr	p.N144T	ENST00000348513	NM_003079.4	144	aAt/aCt	7/11	0.32852829675435	3	FACETS	0.829	0.678	0.997	0.414	0.339	0.499	CLONAL	1	TRUE	1	0.356773502601856	3		424	263	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478087	99478104	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGATCACCATGAGCCG	GAAGATCACCATGAGCCG	CCAT	novel	NA	P-0067198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	108	429	0	ENST00000268035.6:c.2991_3008delinsCCAT	p.Glu997AspfsTer14	p.E997Dfs*14	ENST00000268035	NM_000875.3	997	gaGAAGATCACCATGAGCCGg/gaCCATg	16/21	0.32852829675435	3	FACETS	0.908	0.821	0.997	0.908	0.821	0.997	CLONAL	2	TRUE	1	0.356773502601856	3		429	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0067199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	329	574	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.47295414693679	3	FACETS	0.943	0.904	0.981	0.943	0.904	0.981	CLONAL	3	TRUE	0	0.552986667250963	3		574	537	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155203	55155203	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	78	502	0	ENST00000257290.5:c.2802C>A	p.Asn934Lys	p.N934K	ENST00000257290	NM_006206.4	934	aaC/aaA	21/23	1	2	FACETS	0.523	0.461	0.591	0.523	0.461	0.591	SUBCLONAL	1	TRUE	1	0.552986667250963	2		502	539	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923085	39923085	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	160	432	1	ENST00000378444.4:c.3623A>C	p.Gln1208Pro	p.Q1208P	ENST00000378444	NM_001123385.1	1208	cAa/cCa	8/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.552986667250963	2		433	535	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73995393	73995393	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	34	520	0	ENST00000318443.5:c.699C>G	p.Ser233Arg	p.S233R	ENST00000318443	NM_001024736.1	233	agC/agG	4/10	0.552986667250963	2	FACETS	0.274	0.224	0.331	0.137	0.112	0.166	SUBCLONAL	1	TRUE	0	0.552986667250963	2		520	448	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609746	81609746	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1291324306	NA	P-0067199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	37	504	0	ENST00000298171.2:c.1348del	p.Arg450AlafsTer24	p.R450Afs*24	ENST00000298171	NM_000369.2	448	gtC/gt	10/10	0.552986667250963	1	FACETS	0.24	0.197	0.287	0.24	0.197	0.287	SUBCLONAL	1	TRUE	0	0.552986667250963	1		504	404	SUCCESS
ATM	472	MSKCC	GRCh37	11	108126978	108126978	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	72	338	0	ENST00000278616.4:c.2161C>A	p.Leu721Ile	p.L721I	ENST00000278616	NM_000051.3	721	Ctt/Att	14/63	0.155480591491792	3	FACETS	0.817	0.717	0.923	0.408	0.358	0.462	INDETERMINATE	1	TRUE	1	0.552986667250963	3		338	407	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39746839	39746839	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	15	180	0	ENST00000361337.2:c.1853C>T	p.Ser618Phe	p.S618F	ENST00000361337	NM_003286.2	618	tCt/tTt	18/21	1	2	FACETS	0.202	0.148	0.268	0.202	0.148	0.268	SUBCLONAL	1	TRUE	1	0.552986667250963	2		180	268	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590717	95590717	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	119	450	0	ENST00000393063.1:c.1192G>C	p.Val398Leu	p.V398L	ENST00000393063	NM_030621.3	398	Gtt/Ctt	9/28	0.552986667250963	2	FACETS	0.906	0.823	0.993	0.453	0.411	0.497	CLONAL	1	TRUE	0	0.552986667250963	2		450	475	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639588	47639588	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63749897	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	21	302	0	ENST00000233146.2:c.687del	p.Ala230LeufsTer16	p.A230Lfs*16	ENST00000233146	NM_000251.2	227	agA/ag	4/16	1	2	FACETS	0.398	0.307	0.504	0.398	0.307	0.504	SUBCLONAL	1	TRUE	1	0.428895635545052	2		302	246	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	43	518	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.43	0.36	0.508	0.43	0.36	0.508	SUBCLONAL	1	TRUE	1	0.428895635545052	2		518	466	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	58	589	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.58	0.499	0.668	0.58	0.499	0.668	SUBCLONAL	1	TRUE	1	0.428895635545052	2		590	466	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	51	589	3	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.451	0.383	0.526	0.451	0.383	0.526	SUBCLONAL	1	TRUE	1	0.428895635545052	2		592	527	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100324	8100324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs904307886	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	50	640	1	ENST00000346208.3:c.298G>A	p.Gly100Ser	p.G100S	ENST00000346208		100	Ggc/Agc	3/6	1	2	FACETS	0.402	0.341	0.47	0.402	0.341	0.47	SUBCLONAL	1	TRUE	1	0.428895635545052	2		641	580	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574678	41574679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs754418509	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	55	625	1	ENST00000263253.7:c.6970dup	p.His2324ProfsTer55	p.H2324Pfs*55	ENST00000263253	NM_001429.3	2321	-/C	31/31	1	2	FACETS	0.425	0.363	0.492	0.425	0.363	0.492	SUBCLONAL	1	TRUE	1	0.428895635545052	2		626	604	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27093058	27093058	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	49	460	0	ENST00000324856.7:c.2988+1G>T		p.X996_splice	ENST00000324856	NM_006015.4	996			1	2	FACETS	0.518	0.439	0.605	0.518	0.439	0.605	SUBCLONAL	1	TRUE	1	0.428895635545052	2		460	441	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468516	89468516	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1453560937	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	34	419	0	ENST00000336596.2:c.2050C>T	p.Arg684Ter	p.R684*	ENST00000336596	NM_005233.5	684	Cga/Tga	11/17	1	2	FACETS	0.388	0.317	0.467	0.388	0.317	0.467	SUBCLONAL	1	TRUE	1	0.428895635545052	2		419	409	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444659	78444659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs908264837	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	36	505	1	ENST00000370768.2:c.30del	p.Ser11LeufsTer43	p.S11Lfs*43	ENST00000370768	NM_003902.3	10	ccC/cc	1/20	1	2	FACETS	0.322	0.264	0.387	0.322	0.264	0.387	SUBCLONAL	1	TRUE	1	0.428895635545052	2		506	521	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692792	89692792	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs779530981	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	12	230	0	ENST00000371953.3:c.276C>A	p.Asp92Glu	p.D92E	ENST00000371953	NM_000314.4	92	gaC/gaA	5/9	1	2	FACETS	0.311	0.219	0.424	0.311	0.219	0.424	SUBCLONAL	1	TRUE	1	0.428895635545052	2		230	180	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100727	8100728	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs771019738	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	28	555	0	ENST00000346208.3:c.708dup	p.Ser237GlnfsTer66	p.S237Qfs*66	ENST00000346208		234	ttc/ttCc	3/6	1	2	FACETS	0.284	0.226	0.35	0.284	0.226	0.35	SUBCLONAL	1	TRUE	1	0.428895635545052	2		555	460	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097644	8097644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762722802	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	33	461	0	ENST00000346208.3:c.26G>A	p.Arg9His	p.R9H	ENST00000346208		9	cGc/cAc	2/6	1	2	FACETS	0.408	0.332	0.493	0.408	0.332	0.493	SUBCLONAL	1	TRUE	1	0.428895635545052	2		461	377	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	51	449	0	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	1	2	FACETS	0.53	0.451	0.616	0.53	0.451	0.616	SUBCLONAL	1	TRUE	1	0.428895635545052	2		449	449	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916882	178916882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	15	437	0	ENST00000263967.3:c.269G>A	p.Cys90Tyr	p.C90Y	ENST00000263967	NM_006218.2	90	tGt/tAt	2/21	1	2	FACETS	0.214	0.156	0.284	0.214	0.156	0.284	SUBCLONAL	1	TRUE	1	0.428895635545052	2		437	327	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	27	671	1	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.248	0.197	0.307	0.248	0.197	0.307	SUBCLONAL	1	TRUE	1	0.428895635545052	2		672	507	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498442	89498442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765969815	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	25	444	0	ENST00000336596.2:c.2414G>A	p.Ser805Asn	p.S805N	ENST00000336596	NM_005233.5	805	aGc/aAc	14/17	1	2	FACETS	0.28	0.22	0.348	0.28	0.22	0.348	SUBCLONAL	1	TRUE	1	0.428895635545052	2		444	417	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100049	157100049	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1256773336	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	48	590	0	ENST00000346085.5:c.986C>G	p.Ala329Gly	p.A329G	ENST00000346085	NM_020732.3	329	gCa/gGa	1/20	1	2	FACETS	0.578	0.49	0.675	0.578	0.49	0.675	SUBCLONAL	1	TRUE	1	0.428895635545052	2		590	387	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210725	36210725	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	51	536	0	ENST00000222270.7:c.481del	p.Leu161PhefsTer6	p.L161Ffs*6	ENST00000222270	NM_014727.1	159	aCc/ac	3/37	1	2	FACETS	0.524	0.446	0.609	0.524	0.446	0.609	SUBCLONAL	1	TRUE	1	0.428895635545052	2		536	454	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033790	48033790	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs267608122	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	20	429	0	ENST00000234420.5:c.4001G>A	p.Arg1334Gln	p.R1334Q	ENST00000234420	NM_000179.2	1334	cGg/cAg	9/10	1	2	FACETS	0.369	0.282	0.469	0.369	0.282	0.469	SUBCLONAL	1	TRUE	1	0.428895635545052	2		429	253	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115269618	115269620	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs745372505	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	12	368	0	ENST00000438362.2:c.1586_1588del	p.Pro529del	p.P529del	ENST00000438362	NM_001242891.1	529	cCTCaa/caa	13/20	1	2	FACETS	0.327	0.23	0.446	0.327	0.23	0.446	SUBCLONAL	1	TRUE	1	0.428895635545052	2		368	171	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448188	49448188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1438744754	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	28	576	2	ENST00000301067.7:c.412G>A	p.Ala138Thr	p.A138T	ENST00000301067	NM_003482.3	138	Gct/Act	4/54	1	2	FACETS	0.259	0.206	0.319	0.259	0.206	0.319	SUBCLONAL	1	TRUE	1	0.428895635545052	2		578	504	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022734	12022734	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	55	685	0	ENST00000396373.4:c.844del	p.Arg282GlyfsTer34	p.R282Gfs*34	ENST00000396373	NM_001987.4	280	aaC/aa	5/8	1	2	FACETS	0.472	0.404	0.547	0.472	0.404	0.547	SUBCLONAL	1	TRUE	1	0.428895635545052	2		685	543	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100424	8100425	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs772396478	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	43	619	1	ENST00000346208.3:c.404dup	p.Ala136GlyfsTer167	p.A136Gfs*167	ENST00000346208		133	tac/taCc	3/6	1	2	FACETS	0.357	0.298	0.423	0.357	0.298	0.423	SUBCLONAL	1	TRUE	1	0.428895635545052	2		620	561	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275378	142275379	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	24	371	0	ENST00000350721.4:c.1924_1925del	p.Leu642ValfsTer8	p.L642Vfs*8	ENST00000350721	NM_001184.3	642	CTg/g	9/47	1	2	FACETS	0.361	0.283	0.451	0.361	0.283	0.451	SUBCLONAL	1	TRUE	1	0.428895635545052	2		371	310	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941029	71941029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200057735	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	43	662	0	ENST00000298229.2:c.905G>A	p.Arg302His	p.R302H	ENST00000298229	NM_001567.3	302	cGt/cAt	8/28	1	2	FACETS	0.298	0.248	0.353	0.298	0.248	0.353	SUBCLONAL	1	TRUE	1	0.428895635545052	2		662	673	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150933159	150933159	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	41	535	0	ENST00000271640.5:c.2625del	p.Cys876ValfsTer8	p.C876Vfs*8	ENST00000271640	NM_001145415.1	874	gCc/gc	16/22	0.428895635545052	3	FACETS	0.41	0.34	0.486	0.205	0.17	0.243	SUBCLONAL	1	TRUE	1	0.428895635545052	3		535	567	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874034	123874034	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs186822980	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	37	513	0	ENST00000330479.4:c.65T>C	p.Val22Ala	p.V22A	ENST00000330479	NM_020382.3	22	gTg/gCg	2/9	1	2	FACETS	0.492	0.406	0.587	0.492	0.406	0.587	SUBCLONAL	1	TRUE	1	0.428895635545052	2		513	351	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540470	187540470	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	28	554	0	ENST00000441802.2:c.7270A>G	p.Lys2424Glu	p.K2424E	ENST00000441802	NM_005245.3	2424	Aag/Gag	10/27	1	2	FACETS	0.277	0.22	0.341	0.277	0.22	0.341	SUBCLONAL	1	TRUE	1	0.428895635545052	2		554	472	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739683	41739684	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	23	445	0	ENST00000242208.4:c.289dup	p.Glu97GlyfsTer10	p.E97Gfs*10	ENST00000242208	NM_002192.2	97	gag/gGag	2/3	1	2	FACETS	0.257	0.2	0.324	0.257	0.2	0.324	SUBCLONAL	1	TRUE	1	0.428895635545052	2		445	417	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504027	186504028	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	25	390	0	ENST00000323963.5:c.593_594del	p.Tyr198Ter	p.Y198*	ENST00000323963		198	TAt/t	6/11	1	2	FACETS	0.364	0.287	0.453	0.364	0.287	0.453	SUBCLONAL	1	TRUE	1	0.428895635545052	2		390	320	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125377	7125377	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	50	524	0	ENST00000302850.5:c.3175G>T	p.Val1059Phe	p.V1059F	ENST00000302850	NM_000208.2	1059	Gtc/Ttc	17/22	1	2	FACETS	0.447	0.379	0.521	0.447	0.379	0.521	SUBCLONAL	1	TRUE	1	0.428895635545052	2		524	522	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425542	47425542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	29	525	0	ENST00000404338.3:c.3610G>A	p.Val1204Ile	p.V1204I	ENST00000404338	NM_004491.4	1204	Gtc/Atc	1/6	1	2	FACETS	0.292	0.234	0.358	0.292	0.234	0.358	SUBCLONAL	1	TRUE	1	0.428895635545052	2		525	463	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81528491	81528491	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	13	323	0	ENST00000298171.2:c.171-1G>T		p.X57_splice	ENST00000298171	NM_000369.2	57			1	2	FACETS	0.306	0.218	0.413	0.306	0.218	0.413	SUBCLONAL	1	TRUE	1	0.428895635545052	2		323	198	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121143	11121143	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	29	521	0	ENST00000358026.2:c.2210C>T	p.Ala737Val	p.A737V	ENST00000358026	NM_001128849.1	737	gCt/gTt	15/36	1	2	FACETS	0.297	0.237	0.364	0.297	0.237	0.364	SUBCLONAL	1	TRUE	1	0.428895635545052	2		521	456	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981713	63981713	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	52	601	0	ENST00000398590.3:c.2215G>T	p.Val739Leu	p.V739L	ENST00000398590	NM_001177387.1	739	Gtg/Ttg	12/14	1	2	FACETS	0.416	0.354	0.484	0.416	0.354	0.484	SUBCLONAL	1	TRUE	1	0.428895635545052	2		601	583	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334819	81334819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	25	393	0	ENST00000222390.5:c.1897C>T	p.His633Tyr	p.H633Y	ENST00000222390	NM_000601.4	633	Cat/Tat	17/18	1	2	FACETS	0.454	0.358	0.562	0.454	0.358	0.562	SUBCLONAL	1	TRUE	1	0.428895635545052	2		393	257	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692932	89692933	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	46	489	0	ENST00000371953.3:c.417_418del	p.Leu139PhefsTer40	p.L139Ffs*40	ENST00000371953	NM_000314.4	139	tTA/t	5/9	1	2	FACETS	0.786	0.666	0.916	0.786	0.666	0.916	CLONAL	1	TRUE	1	0.428895635545052	2		489	273	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991960	72991961	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	96	465	0	ENST00000268489.5:c.2084dup	p.Glu696GlyfsTer37	p.E696Gfs*37	ENST00000268489	NM_006885.3	695	ccg/ccCg	2/10	0.218424538093798	2	FACETS	0.95	0.851	1	0.475	0.425	0.528	INDETERMINATE	1	TRUE	0	0.428895635545052	2		465	471	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74868161	74868161	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	16	266	0	ENST00000284811.8:c.133A>G	p.Met45Val	p.M45V	ENST00000284811		45	Atg/Gtg	3/4	1	2	FACETS	0.329	0.243	0.431	0.329	0.243	0.431	SUBCLONAL	1	TRUE	1	0.428895635545052	2		266	227	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040963	47040963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782131895	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	32	597	0	ENST00000377604.3:c.1493G>A	p.Arg498His	p.R498H	ENST00000377604	NM_001204468.1	498	cGc/cAc	14/24	1	2	FACETS	0.322	0.26	0.391	0.322	0.26	0.391	SUBCLONAL	1	TRUE	1	0.428895635545052	2		597	464	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459961	99459961	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	32	450	0	ENST00000268035.6:c.2057A>G	p.Asn686Ser	p.N686S	ENST00000268035	NM_000875.3	686	aAc/aGc	10/21	1	2	FACETS	0.339	0.275	0.412	0.339	0.275	0.412	SUBCLONAL	1	TRUE	1	0.428895635545052	2		450	440	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542203	187542203	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1357031500	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	23	537	0	ENST00000441802.2:c.5537C>T	p.Thr1846Ile	p.T1846I	ENST00000441802	NM_005245.3	1846	aCc/aTc	10/27	1	2	FACETS	0.293	0.228	0.368	0.293	0.228	0.368	SUBCLONAL	1	TRUE	1	0.428895635545052	2		537	366	SUCCESS
H3C13	653604	MSKCC	GRCh37	1	149784843	149784843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	32	339	0	ENST00000331491.1:c.394C>T	p.Arg132Cys	p.R132C	ENST00000331491	NM_001123375.2	132	Cgc/Tgc	1/1	1	2	FACETS	0.358	0.29	0.434	0.358	0.29	0.434	SUBCLONAL	1	TRUE	1	0.428895635545052	2		339	417	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118370107	118370107	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	22	410	0	ENST00000534358.1:c.6051G>T	p.Leu2017Phe	p.L2017F	ENST00000534358	NM_005933.3	2017	ttG/ttT	23/36	1	2	FACETS	0.34	0.263	0.428	0.34	0.263	0.428	SUBCLONAL	1	TRUE	1	0.428895635545052	2		410	302	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371676	55371677	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0067201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	43	564	0	ENST00000297316.4:c.367dup	p.Arg123ProfsTer39	p.R123Pfs*39	ENST00000297316	NM_022454.3	122	-/C	2/2	1	2	FACETS	0.464	0.389	0.548	0.464	0.389	0.548	SUBCLONAL	1	TRUE	1	0.428895635545052	2		564	432	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0067202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	11	171	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.873	0.604	1	0.873	0.604	1	CLONAL	1	TRUE	1	0.15	2		171	168	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0067202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	14	117	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.15	2		117	136	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0067202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	22	270	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.971	0.753	1	0.971	0.753	1	CLONAL	1	TRUE	1	0.15	2		270	302	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106279	27106279	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	34	711	0	ENST00000324856.7:c.5890G>T	p.Glu1964Ter	p.E1964*	ENST00000324856	NM_006015.4	1964	Gag/Tag	20/20	1	2	FACETS	0.749	0.611	0.906	0.749	0.611	0.906	CLONAL	1	TRUE	1	0.15	2		711	605	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0067202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	25	710	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.571	0.448	0.713	0.571	0.448	0.713	SUBCLONAL	1	TRUE	1	0.15	2		710	584	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089626	27089626	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	34	753	0	ENST00000324856.7:c.2583del	p.Ser862ProfsTer29	p.S862Pfs*29	ENST00000324856	NM_006015.4	861	gCc/gc	8/20	1	2	FACETS	0.748	0.61	0.904	0.748	0.61	0.904	CLONAL	1	TRUE	1	0.15	2		753	606	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672233	86672233	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554049394	NA	P-0067204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	32	542	0	ENST00000274376.6:c.2035C>T	p.Arg679Ter	p.R679*	ENST00000274376	NM_002890.2	679	Cga/Tga	16/25	1	2	FACETS	0.671	0.546	0.812	0.671	0.546	0.812	SUBCLONAL	1	TRUE	1	0.28543784212592	2		542	334	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219390	1219392	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0067204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	125	707	0	ENST00000326873.7:c.442_444del	p.Phe148del	p.F148del	ENST00000326873	NM_000455.4	148	TTC/-	3/10	0.176318527783942	2	FACETS	1	0.974	1	0.606	0.549	0.666	CLONAL	1	TRUE	0	0.28543784212592	2		707	723	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782411	9782411	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	83	599	0	ENST00000377346.4:c.2344G>T	p.Asp782Tyr	p.D782Y	ENST00000377346	NM_005026.3	782	Gat/Tat	18/24	1	2	FACETS	0.851	0.751	0.959	0.851	0.751	0.959	CLONAL	1	TRUE	1	0.28543784212592	2		599	683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0067205-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	167	477	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.256556694579872	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.256556694579872	2		477	570	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0067205-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	82	631	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.256556694579872	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.256556694579872	1		631	451	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11022897	11022897	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067205-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	147	604	0	ENST00000327064.4:c.596C>T	p.Ser199Leu	p.S199L	ENST00000327064	NM_199141.1	199	tCg/tTg	5/16	0.256556694579872	3	FACETS	0.999	0.915	1	0.999	0.915	1	CLONAL	2	TRUE	1	0.256556694579872	3		604	647	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106558	27106558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067205-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	151	725	0	ENST00000324856.7:c.6169C>T	p.Arg2057Trp	p.R2057W	ENST00000324856	NM_006015.4	2057	Cgg/Tgg	20/20	1	2	FACETS	0.878	0.805	0.954	1	0.99	1	CLONAL	2	TRUE	1	0.256556694579872	2		725	670	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790170	40790170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373191879	NA	P-0067205-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	55	580	0	ENST00000373198.4:c.2561G>A	p.Arg854His	p.R854H	ENST00000373198	NM_133170.3	854	cGc/cAc	18/32	0.256556694579872	3	FACETS	0.805	0.688	0.933	0.402	0.344	0.467	CLONAL	1	TRUE	1	0.256556694579872	3		580	601	SUCCESS
AR	367	MSKCC	GRCh37	X	66941796	66941796	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067205-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	34	216	0	ENST00000374690.3:c.2440T>A	p.Phe814Ile	p.F814I	ENST00000374690	NM_000044.3	814	Ttc/Atc	6/8	0.256556694579872	2	FACETS	1	0.872	1			1	CLONAL	1	TRUE	NA	0.256556694579872	2		216	246	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785522	50785522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067205-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	65	468	0	ENST00000398568.2:c.512G>A	p.Gly171Asp	p.G171D	ENST00000398568	NM_001042412.1	171	gGt/gAt	4/18	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.256556694579872	2		468	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0067206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	18	558	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	1	2	FACETS	0.583	0.438	0.756	0.583	0.438	0.756	SUBCLONAL	1	FALSE	1	0.14496742894667	2		558	426	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911254	29911254	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs41541015	NA	P-0067206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	27	272	0	ENST00000376809.5:c.553G>C	p.Asp185His	p.D185H	ENST00000376809	NM_002116.7	185	Gat/Cat	3/8	1	2	FACETS	0.985	0.79	1	1	0.953	1	CLONAL	2	FALSE	1	0.14496742894667	2		272	189	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224208	53224208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	24	598	0	ENST00000375401.3:c.3343C>T	p.Arg1115Cys	p.R1115C	ENST00000375401	NM_004187.3	1115	Cgc/Tgc	22/26	1	2	FACETS	0.763	0.597	0.955	0.763	0.597	0.955	CLONAL	1	FALSE	1	0.14496742894667	2		598	434	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662242	227662242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	28	640	0	ENST00000305123.5:c.1213G>A	p.Asp405Asn	p.D405N	ENST00000305123	NM_005544.2	405	Gat/Aat	1/2	0.119965135322538	2	FACETS	0.92	0.735	1	0.46	0.367	0.566	CLONAL	1	FALSE	0	0.14496742894667	2		640	420	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127933401	127933401	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0067206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	14	370	0	ENST00000373547.4:c.134C>G	p.Ser45Ter	p.S45*	ENST00000373547	NM_002721.4	45	tCa/tGa	2/7	1	2	FACETS	1	0.733	1	1	0.733	1	CLONAL	1	FALSE	1	0.14496742894667	2		370	191	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094916	143094916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754383120	NA	P-0067206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	19	429	0	ENST00000262992.4:c.1228G>A	p.Ala410Thr	p.A410T	ENST00000262992	NM_001101669.1	410	Gca/Aca	14/24	0.14496742894667	1	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	FALSE	0	0.14496742894667	1		429	209	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645748	215645748	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	11	486	0	ENST00000260947.4:c.850G>A	p.Glu284Lys	p.E284K	ENST00000260947	NM_000465.2	284	Gag/Aag	4/11	0.119965135322538	2	FACETS	0.925	0.641	1	0.463	0.32	0.639	CLONAL	1	FALSE	0	0.14496742894667	2		486	164	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0067207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	61	412	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.260252511529972	1	FACETS	0.927	0.802	1	0.927	0.802	1	CLONAL	1	TRUE	0	0.260252511529972	1		412	440	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0067207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	75	375	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.948	0.839	1	1	0.983	1	CLONAL	2	TRUE	1	0.260252511529972	2		375	304	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586250	48586250	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	40	414	0	ENST00000342988.3:c.919G>T	p.Glu307Ter	p.E307*	ENST00000342988	NM_005359.5	307	Gag/Tag	8/12	0.260252511529972	1	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	0	0.260252511529972	1		414	247	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46255795	46255795	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	45	462	0	ENST00000371998.3:c.407T>C	p.Phe136Ser	p.F136S	ENST00000371998		136	tTt/tCt	6/23	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.260252511529972	2		462	329	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482839	67482839	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	57	551	0	ENST00000327367.4:c.1243G>T	p.Gly415Cys	p.G415C	ENST00000327367	NM_005902.3	415	Ggc/Tgc	9/9	1	2	FACETS	0.857	0.736	0.989	0.857	0.736	0.989	CLONAL	1	TRUE	1	0.260252511529972	2		551	511	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436858	29436858	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs863225284	NA	P-0067208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	54	339	0	ENST00000389048.3:c.3735C>A	p.Phe1245Leu	p.F1245L	ENST00000389048	NM_004304.4	1245	ttC/ttA	24/29	1	2	FACETS	0.618	0.528	0.717	0.618	0.528	0.717	SUBCLONAL	1	TRUE	1	0.323568935074317	2		339	540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574030	7574030	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	172	475	0	ENST00000269305.4:c.997del	p.Arg333ValfsTer12	p.R333Vfs*12	ENST00000269305	NM_001126112.2	333	Cgt/gt	10/11	0.472465264979349	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.472465264979349	2		475	339	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576120	88576120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147160868	NA	P-0067209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	210	545	1	ENST00000360948.2:c.1553G>A	p.Arg518His	p.R518H	ENST00000360948	NM_001012338.2	518	cGt/cAt	13/19	0.472465264979349	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.472465264979349	2		546	373	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41222967	41222967	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	201	602	0	ENST00000357654.3:c.4964C>G	p.Ser1655Cys	p.S1655C	ENST00000357654	NM_007294.3	1655	tCt/tGt	15/23	0.472465264979349	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.472465264979349	2		602	404	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512099	148512099	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	59	525	0	ENST00000320356.2:c.1579C>A	p.Pro527Thr	p.P527T	ENST00000320356	NM_004456.4	527	Ccc/Acc	14/20	0.472465264979349	8	FACETS	0.646	0.554	0.747	0.108	0.092	0.125	SUBCLONAL	1	TRUE	2	0.472465264979349	8		525	934	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0067210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	31	314	4	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.997	0.809	1	0.997	0.809	1	CLONAL	1	TRUE	1	0.209384296605148	2		318	297	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288430	15288430	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	23	538	0	ENST00000263388.2:c.4309T>C	p.Phe1437Leu	p.F1437L	ENST00000263388	NM_000435.2	1437	Ttc/Ctc	24/33	1	2	FACETS	0.621	0.484	0.779	0.621	0.484	0.779	SUBCLONAL	1	TRUE	1	0.209384296605148	2		538	354	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51535061	51535061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200111039	NA	P-0067210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	63	501	0	ENST00000260433.2:c.49G>A	p.Val17Met	p.V17M	ENST00000260433		17	Gtg/Atg	2/10	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.209384296605148	2		501	497	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143324197	143324197	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	51	386	0	ENST00000262992.4:c.266A>G	p.Asp89Gly	p.D89G	ENST00000262992	NM_001101669.1	89	gAc/gGc	5/24	0.209384296605148	1	FACETS	0.905	0.77	1	0.905	0.77	1	CLONAL	1	TRUE	0	0.209384296605148	1		386	482	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930688	32930697	+	frameshift_variant	Frame_Shift_Del	DEL	GAATCTCTCT	GAATCTCTCT	-	novel	NA	P-0067210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	89	579	0	ENST00000380152.3:c.7562_7571del	p.Ile2521LysfsTer4	p.I2521Kfs*4	ENST00000380152		2520	cGAATCTCTCTg/cg	15/27	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.209384296605148	2		579	645	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260200	19260217	+	inframe_deletion	In_Frame_Del	DEL	CTTCTTCATCAGCCCGAA	CTTCTTCATCAGCCCGAA	-	novel	NA	P-0067210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	46	526	0	ENST00000162023.5:c.76_93del	p.Phe26_Lys31del	p.F26_K31del	ENST00000162023		26	TTCGGGCTGATGAAGAAG/-	7/13	1	2	FACETS	0.776	0.653	0.912	0.776	0.653	0.912	CLONAL	1	TRUE	1	0.209384296605148	2		526	566	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594221	55594221	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913512	NA	P-0067211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	412	375	0	ENST00000288135.5:c.1924A>G	p.Lys642Glu	p.K642E	ENST00000288135	NM_000222.2	642	Aaa/Gaa	13/21	0.891371368511517	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.891371368511517	3		375	648	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710594	117710594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768790336	NA	P-0067211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	300	617	0	ENST00000368508.3:c.1678C>T	p.Arg560Cys	p.R560C	ENST00000368508	NM_002944.2	560	Cgc/Tgc	12/43	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.891371368511517	2		617	642	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	141	642	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.985	0.901	1	0.985	0.901	1	CLONAL	1	TRUE	1	0.466077854443635	2		643	614	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	110	478	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.996	0.9	1	0.996	0.9	1	CLONAL	1	TRUE	1	0.466077854443635	2		478	474	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	189	518	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.765	0.713	0.819	1	0.991	1	SUBCLONAL	2	TRUE	1	0.466077854443635	2		518	530	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380346	14380346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	111	612	0	ENST00000256196.4:c.71G>A	p.Gly24Asp	p.G24D	ENST00000256196		24	gGc/gAc	1/6	0.287076754943095	3	FACETS	0.885	0.805	0.967	0.885	0.805	0.967	CLONAL	2	TRUE	1	0.466077854443635	3		612	332	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	117	589	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.466077854443635	2		590	408	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	104	393	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.924	0.831	1	0.924	0.831	1	CLONAL	1	TRUE	1	0.466077854443635	2		393	483	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	99	177	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.841	0.754	0.933	0.841	0.754	0.933	CLONAL	1	TRUE	1	0.466077854443635	2		178	505	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	21	181	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.466077854443635	3	FACETS	0.558	0.432	0.704	0.279	0.216	0.352	SUBCLONAL	1	TRUE	1	0.466077854443635	3		181	199	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	105	341	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.466077854443635	2		341	396	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660469	67660469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	98	464	0	ENST00000264010.4:c.1369C>T	p.Arg457Ter	p.R457*	ENST00000264010	NM_006565.3	457	Cga/Tga	8/12	1	2	FACETS	0.976	0.876	1	0.976	0.876	1	CLONAL	1	TRUE	1	0.466077854443635	2		464	431	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	172	500	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	0.466077854443635	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.466077854443635	3		500	444	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399155	139399155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749490844	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	70	598	0	ENST00000277541.6:c.4988G>A	p.Arg1663Gln	p.R1663Q	ENST00000277541	NM_017617.3	1663	cGg/cAg	26/34	1	2	FACETS	0.978	0.861	1	0.978	0.861	1	CLONAL	1	TRUE	1	0.466077854443635	2		598	307	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023769	27023769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	59	715	1	ENST00000324856.7:c.879del	p.Thr294ProfsTer69	p.T294Pfs*69	ENST00000324856	NM_006015.4	292	aCc/ac	1/20	1	2	FACETS	0.799	0.692	0.913	0.799	0.692	0.913	CLONAL	1	TRUE	1	0.466077854443635	2		716	317	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	79	729	1	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.685	0.604	0.771	0.685	0.604	0.771	SUBCLONAL	1	TRUE	1	0.466077854443635	2		730	495	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874637	35874637	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	100	546	1	ENST00000303115.3:c.799del	p.Arg267GlyfsTer28	p.R267Gfs*28	ENST00000303115	NM_002185.3	265	Aaa/aa	6/8	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.466077854443635	2		547	407	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646981	23646981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	133	527	2	ENST00000261584.4:c.886del	p.Met296Ter	p.M296*	ENST00000261584	NM_024675.3	296	Atg/tg	4/13	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.466077854443635	2		529	541	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419903	41419903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761607732	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	224	705	0	ENST00000373198.4:c.418G>A	p.Gly140Arg	p.G140R	ENST00000373198	NM_133170.3	140	Ggg/Agg	3/32	0.287076754943095	3	FACETS	0.903	0.846	0.962	0.903	0.846	0.962	CLONAL	2	TRUE	1	0.466077854443635	3		705	656	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760024	133760024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	84	535	1	ENST00000318560.5:c.2352del	p.Arg785GlyfsTer3	p.R785Gfs*3	ENST00000318560	NM_005157.4	783	Ccc/cc	11/11	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.466077854443635	2		536	359	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101612	27101612	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	123	798	3	ENST00000324856.7:c.4899del	p.Met1634Ter	p.M1634*	ENST00000324856	NM_006015.4	1632	Ccc/cc	18/20	1	2	FACETS	0.855	0.776	0.939	0.855	0.776	0.939	CLONAL	1	TRUE	1	0.466077854443635	2		801	617	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434953	110434953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	88	818	0	ENST00000375856.3:c.3448G>A	p.Glu1150Lys	p.E1150K	ENST00000375856	NM_003749.2	1150	Gag/Aag	1/2	1	2	FACETS	0.912	0.813	1	0.912	0.813	1	CLONAL	1	TRUE	1	0.466077854443635	2		818	414	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210737	2210737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	98	793	0	ENST00000398665.3:c.1234G>A	p.Gly412Arg	p.G412R	ENST00000398665	NM_032482.2	412	Ggg/Agg	14/28	1	2	FACETS	0.88	0.788	0.976	0.88	0.788	0.976	CLONAL	1	TRUE	1	0.466077854443635	2		793	478	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156699	2156699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs975030738	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	239	817	1	ENST00000434045.2:c.223G>A	p.Ala75Thr	p.A75T	ENST00000434045	NM_001127598.1	75	Gcc/Acc	3/5	0.287076754943095	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.466077854443635	3		818	620	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114816	108114817	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	83	507	0	ENST00000278616.4:c.640dup	p.Ser214PhefsTer40	p.S214Ffs*40	ENST00000278616	NM_000051.3	211	-/T	6/63	1	2	FACETS	0.947	0.842	1	0.947	0.842	1	CLONAL	1	TRUE	1	0.466077854443635	2		507	376	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627257	86627257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458179717	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	123	582	0	ENST00000274376.6:c.632G>A	p.Arg211Gln	p.R211Q	ENST00000274376	NM_002890.2	211	cGg/cAg	2/25	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.466077854443635	2		582	507	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988340	36988340	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	59	600	0	ENST00000354822.5:c.313del	p.Val105CysfsTer20	p.V105Cfs*20	ENST00000354822	NM_001079668.2	105	Gtg/tg	2/3	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.466077854443635	2		600	252	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441974	6441974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	79	349	0	ENST00000356142.4:c.533C>T	p.Ala178Val	p.A178V	ENST00000356142	NM_018890.3	178	gCg/gTg	7/7	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.466077854443635	2		349	285	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112400	115112400	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770040454	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	99	826	0	ENST00000257566.3:c.1340G>A	p.Arg447His	p.R447H	ENST00000257566	NM_016569.3	447	cGc/cAc	7/8	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.466077854443635	2		826	385	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943623	9943623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758815434	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	100	529	0	ENST00000330684.3:c.1318G>A	p.Val440Ile	p.V440I	ENST00000330684	NM_001134407.1	440	Gtc/Atc	5/13	1	2	FACETS	0.869	0.779	0.963	0.869	0.779	0.963	CLONAL	1	TRUE	1	0.466077854443635	2		529	494	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371810	55371831	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGCCCCGAGGGCGGCCGCGT	TGGGCCCCGAGGGCGGCCGCGT	-	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	124	705	0	ENST00000297316.4:c.500_521del	p.Leu167ArgfsTer213	p.L167Rfs*213	ENST00000297316	NM_022454.3	167	cTGGGCCCCGAGGGCGGCCGCGTg/cg	2/2	0.448404542008138	3	FACETS	0.945	0.866	1	0.945	0.866	1	CLONAL	2	TRUE	1	0.466077854443635	3		705	347	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741372	17741372	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	35	652	0	ENST00000250003.3:c.43G>C	p.Ala15Pro	p.A15P	ENST00000250003	NM_002478.4	15	Gcc/Ccc	1/3	0.287076754943095	3	FACETS	0.418	0.342	0.503	0.209	0.171	0.252	SUBCLONAL	1	TRUE	1	0.466077854443635	3		652	443	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944516	71944516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293622519	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	101	710	0	ENST00000298229.2:c.2072G>A	p.Arg691Gln	p.R691Q	ENST00000298229	NM_001567.3	691	cGg/cAg	18/28	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.466077854443635	2		710	431	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991697	72991699	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs757316139	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	71	720	12	ENST00000268489.5:c.2346_2348del	p.Ala784del	p.A784del	ENST00000268489	NM_006885.3	782	gcGGCa/gca	2/10	1	2	FACETS	0.686	0.601	0.778	0.686	0.601	0.778	SUBCLONAL	1	TRUE	1	0.466077854443635	2		732	444	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274173	10274173	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	48	593	1	ENST00000330684.3:c.96del	p.Ala33ArgfsTer2	p.A33Rfs*2	ENST00000330684	NM_001134407.1	32	ccC/cc	2/13	1	2	FACETS	0.599	0.508	0.698	0.599	0.508	0.698	SUBCLONAL	1	TRUE	1	0.466077854443635	2		594	344	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848562	151848562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367652375	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	111	585	1	ENST00000262189.6:c.12631C>T	p.Arg4211Trp	p.R4211W	ENST00000262189	NM_170606.2	4211	Cgg/Tgg	50/59	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.466077854443635	2		586	421	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803117	1803117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1330260382	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	85	669	0	ENST00000260795.2:c.469G>A	p.Glu157Lys	p.E157K	ENST00000260795		157	Gag/Aag	4/17	1	2	FACETS	0.952	0.848	1	0.952	0.848	1	CLONAL	1	TRUE	1	0.466077854443635	2		669	383	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133009	30133009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760058972	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	112	541	0	ENST00000331968.5:c.592G>A	p.Gly198Ser	p.G198S	ENST00000331968	NM_002742.2	198	Ggt/Agt	4/18	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.466077854443635	2		541	447	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994778	73994778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11574476	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	99	741	0	ENST00000318443.5:c.262G>A	p.Ala88Thr	p.A88T	ENST00000318443	NM_001024736.1	88	Gcc/Acc	3/10	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.466077854443635	2		741	419	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138294	2138294	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45517412	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	108	778	0	ENST00000219476.3:c.5227C>T	p.Arg1743Trp	p.R1743W	ENST00000219476	NM_000548.3	1743	Cgg/Tgg	41/42	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.466077854443635	2		778	384	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226123	53226123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148661902	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	81	671	0	ENST00000375401.3:c.2726G>A	p.Arg909Gln	p.R909Q	ENST00000375401	NM_004187.3	909	cGg/cAg	19/26	1	2	FACETS	0.932	0.827	1	0.932	0.827	1	CLONAL	1	TRUE	1	0.466077854443635	2		671	373	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629102	86629102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	81	261	0	ENST00000274376.6:c.847C>T	p.Arg283Cys	p.R283C	ENST00000274376	NM_002890.2	283	Cgt/Tgt	4/25	1	2	FACETS	0.894	0.792	1	0.894	0.792	1	CLONAL	1	TRUE	1	0.466077854443635	2		261	389	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451400	187451400	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs11545363	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	95	659	0	ENST00000232014.4:c.82C>T	p.Arg28Ter	p.R28*	ENST00000232014	NM_001130845.1	28	Cga/Tga	3/10	1	2	FACETS	0.844	0.755	0.938	0.844	0.755	0.938	CLONAL	1	TRUE	1	0.466077854443635	2		659	483	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22412996	22412996	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	69	307	0	ENST00000344548.3:c.247del	p.Ser83GlnfsTer11	p.S83Qfs*11	ENST00000344548	NM_001039802.1	81	tgT/tg	5/7	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.466077854443635	2		307	260	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28595718	28595718	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	56	716	3	ENST00000253063.3:c.115C>T	p.Arg39Ter	p.R39*	ENST00000253063	NM_031459.4	39	Cga/Tga	2/10	1	2	FACETS	0.454	0.389	0.525	0.454	0.389	0.525	SUBCLONAL	1	TRUE	1	0.466077854443635	2		719	529	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412288	139412288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761629787	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	128	702	0	ENST00000277541.6:c.1357G>A	p.Val453Ile	p.V453I	ENST00000277541	NM_017617.3	453	Gtc/Atc	8/34	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.466077854443635	2		702	460	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711987	89711987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1085308053	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	178	440	0	ENST00000371953.3:c.605C>T	p.Thr202Ile	p.T202I	ENST00000371953	NM_000314.4	202	aCt/aTt	6/9	0.466077854443635	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.466077854443635	3		440	402	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425365	47425365	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	56	722	0	ENST00000404338.3:c.3433C>T	p.Arg1145Ter	p.R1145*	ENST00000404338	NM_004491.4	1145	Cga/Tga	1/6	1	2	FACETS	0.435	0.372	0.503	0.435	0.372	0.503	SUBCLONAL	1	TRUE	1	0.466077854443635	2		722	553	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446275	29446275	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	74	674	0	ENST00000544604.2:c.2111del	p.Gly704AlafsTer69	p.G704Afs*69	ENST00000544604	NM_001206998.1	702	aaG/aa	8/9	1	2	FACETS	0.905	0.798	1	0.905	0.798	1	CLONAL	1	TRUE	1	0.466077854443635	2		674	351	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228613001	228613001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373549345	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	30	899	0	ENST00000366696.1:c.26G>A	p.Arg9His	p.R9H	ENST00000366696	NM_003493.2	9	cGc/cAc	1/1	1	2	FACETS	0.229	0.183	0.28	0.229	0.183	0.28	SUBCLONAL	1	TRUE	1	0.466077854443635	2		899	563	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99136558	99136558	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	109	640	0	ENST00000074304.5:c.47C>G	p.Ala16Gly	p.A16G	ENST00000074304	NM_001134224.1	16	gCa/gGa	3/26	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.466077854443635	2		640	435	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969969	161969969	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	89	537	0	ENST00000366898.1:c.1000del	p.Arg334AlafsTer101	p.R334Afs*101	ENST00000366898	NM_004562.2	334	Cgc/gc	9/12	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.466077854443635	2		537	374	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698202	47698202	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587779108	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	236	487	0	ENST00000233146.2:c.1759+1G>A		p.X587_splice	ENST00000233146	NM_000251.2	587			0.466077854443635	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.466077854443635	2		487	440	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65323415	65323415	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	124	711	0	ENST00000342505.4:c.1382G>T	p.Gly461Val	p.G461V	ENST00000342505	NM_002227.2	461	gGg/gTg	10/25	1	2	FACETS	0.987	0.897	1	0.987	0.897	1	CLONAL	1	TRUE	1	0.466077854443635	2		711	539	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940413	31940413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	140	787	1	ENST00000375333.2:c.446C>T	p.Ala149Val	p.A149V	ENST00000375333	NM_032454.1	149	gCt/gTt	3/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.466077854443635	2		788	531	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309470	30309472	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	49	637	0	ENST00000307677.4:c.550_552del	p.Glu184del	p.E184del	ENST00000307677	NM_138578.1	184	GAG/-	2/3	0.287076754943095	3	FACETS	0.441	0.373	0.516	0.22	0.186	0.258	SUBCLONAL	1	TRUE	1	0.466077854443635	3		637	588	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939935	49939935	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	136	828	0	ENST00000296474.3:c.1108C>A	p.Pro370Thr	p.P370T	ENST00000296474	NM_002447.2	370	Ccc/Acc	1/20	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.466077854443635	2		828	579	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631985	67631985	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs775404204	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	105	636	0	ENST00000272342.5:c.2171A>G	p.Tyr724Cys	p.Y724C	ENST00000272342	NM_019002.3	724	tAt/tGt	5/6	0.466077854443635	2	FACETS	1	0.944	1	0.534	0.481	0.589	CLONAL	1	TRUE	0	0.466077854443635	2		636	422	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271171	38271171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	122	443	1	ENST00000425967.3:c.2537C>T	p.Ala846Val	p.A846V	ENST00000425967	NM_001174067.1	846	gCc/gTc	19/19	0.448404542008138	3	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	1	0.466077854443635	3		444	318	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944600	32944600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs276174906	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	101	477	0	ENST00000380152.3:c.8393C>T	p.Pro2798Leu	p.P2798L	ENST00000380152		2798	cCt/cTt	19/27	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.466077854443635	2		477	424	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346358	89346358	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1384428326	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	90	785	0	ENST00000301030.4:c.6592C>T	p.Arg2198Trp	p.R2198W	ENST00000301030	NM_001256183.1	2198	Cgg/Tgg	9/13	1	2	FACETS	0.966	0.862	1	0.966	0.862	1	CLONAL	1	TRUE	1	0.466077854443635	2		785	400	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856125	111856125	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	71	411	0	ENST00000341259.2:c.176G>A	p.Arg59His	p.R59H	ENST00000341259	NM_005475.2	59	cGc/cAc	2/8	1	2	FACETS	0.787	0.691	0.89	0.787	0.691	0.89	SUBCLONAL	1	TRUE	1	0.466077854443635	2		411	387	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298086	15298086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	35	637	0	ENST00000263388.2:c.1670G>A	p.Gly557Asp	p.G557D	ENST00000263388	NM_000435.2	557	gGt/gAt	11/33	1	2	FACETS	0.366	0.3	0.441	0.366	0.3	0.441	SUBCLONAL	1	TRUE	1	0.466077854443635	2		637	410	SUCCESS
APC	324	MSKCC	GRCh37	5	112154867	112154867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1436383065	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	117	679	0	ENST00000257430.4:c.1138C>T	p.Arg380Trp	p.R380W	ENST00000257430	NM_000038.5	380	Cgg/Tgg	10/16	1	2	FACETS	0.861	0.779	0.947	0.861	0.779	0.947	CLONAL	1	TRUE	1	0.466077854443635	2		679	583	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061597	38061597	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	88	690	1	ENST00000250448.2:c.392C>T	p.Ala131Val	p.A131V	ENST00000250448	NM_004496.3	131	gCg/gTg	2/2	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.466077854443635	2		691	333	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742022	145742022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	222	751	0	ENST00000428558.2:c.481C>T	p.Gln161Ter	p.Q161*	ENST00000428558	NM_004260.3	161	Cag/Tag	5/22	0.448404542008138	3	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	1	0.466077854443635	3		751	586	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660235	227660235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763911795	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	107	812	0	ENST00000305123.5:c.3220C>T	p.Arg1074Trp	p.R1074W	ENST00000305123	NM_005544.2	1074	Cgg/Tgg	1/2	1	2	FACETS	0.998	0.9	1	0.998	0.9	1	CLONAL	1	TRUE	1	0.466077854443635	2		812	460	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090461	5090464	+	frameshift_variant	Frame_Shift_Del	DEL	AATT	AATT	-	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	98	426	0	ENST00000381652.3:c.2782_2785del	p.Ile928TrpfsTer20	p.I928Wfs*20	ENST00000381652	NM_004972.3	926	aAATTa/aa	21/25	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.466077854443635	2		426	377	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2220213	2220213	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	23	631	0	ENST00000398665.3:c.2802del	p.Ala935GlnfsTer133	p.A935Qfs*133	ENST00000398665	NM_032482.2	933	gCc/gc	23/28	1	2	FACETS	0.24	0.187	0.302	0.24	0.187	0.302	SUBCLONAL	1	TRUE	1	0.466077854443635	2		631	411	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713464	40713464	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	42	699	0	ENST00000373198.4:c.4051G>T	p.Val1351Phe	p.V1351F	ENST00000373198	NM_133170.3	1351	Gtc/Ttc	30/32	0.287076754943095	3	FACETS	0.371	0.309	0.44	0.185	0.154	0.22	SUBCLONAL	1	TRUE	1	0.466077854443635	3		699	599	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126420	5126420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770472387	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	69	548	0	ENST00000381652.3:c.3265C>T	p.Pro1089Ser	p.P1089S	ENST00000381652	NM_004972.3	1089	Cca/Tca	24/25	1	2	FACETS	0.876	0.768	0.991	0.876	0.768	0.991	CLONAL	1	TRUE	1	0.466077854443635	2		548	338	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2093697	2093697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554393986	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	98	633	0	ENST00000219066.1:c.580G>A	p.Ala194Thr	p.A194T	ENST00000219066	NM_002528.5	194	Gcc/Acc	4/6	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.466077854443635	2		633	385	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598067	55598067	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758252647	NA	P-0067212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	86	528	0	ENST00000288135.5:c.2264C>T	p.Ala755Val	p.A755V	ENST00000288135	NM_000222.2	755	gCc/gTc	16/21	1	2	FACETS	0.879	0.782	0.981	0.879	0.782	0.981	CLONAL	1	TRUE	1	0.466077854443635	2		528	420	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005006	150005006	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	100	513	0	ENST00000253339.5:c.1219C>T	p.Gln407Ter	p.Q407*	ENST00000253339		407	Cag/Tag	3/7	0.161662434444237	1	FACETS	0.673	0.603	0.748	0.673	0.603	0.748	INDETERMINATE	1	TRUE	0	0.406547548772835	1		513	582	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0067213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	53	400	2	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	0.161662434444237	1	FACETS	0.476	0.407	0.552	0.476	0.407	0.552	INDETERMINATE	1	TRUE	0	0.406547548772835	1		402	436	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602764	10602764	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	142	418	0	ENST00000171111.5:c.814C>T	p.Arg272Cys	p.R272C	ENST00000171111	NM_203500.1	272	Cgc/Tgc	3/6	0.406547548772835	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.406547548772835	1		418	474	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032401	10032401	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs78631453	NA	P-0067213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	124	413	0	ENST00000330684.3:c.422C>T	p.Thr141Met	p.T141M	ENST00000330684	NM_001134407.1	141	aCg/aTg	3/13	0.192236354985563	2	FACETS	1	0.975	1	0.6	0.546	0.657	INDETERMINATE	1	TRUE	0	0.406547548772835	2		413	508	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729465	41729465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747474916	NA	P-0067213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	95	444	1	ENST00000242208.4:c.1064C>T	p.Pro355Leu	p.P355L	ENST00000242208	NM_002192.2	355	cCg/cTg	3/3	0.161662434444237	1	FACETS	0.854	0.765	0.948	0.854	0.765	0.948	INDETERMINATE	1	TRUE	0	0.406547548772835	1		445	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	170	378	0	ENST00000269305.4:c.734del	p.Gly245AlafsTer2	p.G245Afs*2	ENST00000269305	NM_001126112.2	245	gGc/gc	7/11	0.405739386484043	2	FACETS	0.955	0.887	1	0.955	0.887	1	CLONAL	2	TRUE	0	0.406547548772835	2		378	438	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372160	45372160	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1040132520	NA	P-0067213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	94	377	0	ENST00000262160.6:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000262160	NM_005901.5	337	Cgc/Tgc	9/11	1	2	FACETS	0.986	0.881	1	0.986	0.881	1	CLONAL	1	TRUE	1	0.406547548772835	2		377	469	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807505	36807505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200986219	NA	P-0067213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	88	422	0	ENST00000373129.3:c.1159G>A	p.Glu387Lys	p.E387K	ENST00000373129	NM_032017.1	387	Gag/Aag	12/12	0.161662434444237	1	FACETS	0.745	0.663	0.832	0.745	0.663	0.832	INDETERMINATE	1	TRUE	0	0.406547548772835	1		422	463	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851324	63851324	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	123	499	0	ENST00000279873.7:c.2102G>T	p.Gly701Val	p.G701V	ENST00000279873	NM_032199.2	701	gGg/gTg	10/10	1	2	FACETS	0.927	0.84	1	0.927	0.84	1	CLONAL	1	TRUE	1	0.406547548772835	2		499	653	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984816	11984816	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	239	364	0	ENST00000353533.5:c.362A>G	p.His121Arg	p.H121R	ENST00000353533	NM_003010.3	121	cAc/cGc	3/11	0.405739386484043	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.406547548772835	2		364	506	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259598	89259598	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	123	416	0	ENST00000336596.2:c.742G>T	p.Gly248Cys	p.G248C	ENST00000336596	NM_005233.5	248	Ggc/Tgc	3/17	0.221984290170983	1	FACETS	0.847	0.769	0.929	0.847	0.769	0.929	INDETERMINATE	1	TRUE	0	0.406547548772835	1		416	569	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32438046	32438046	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	68	345	0	ENST00000332351.3:c.991G>T	p.Gly331Trp	p.G331W	ENST00000332351	NM_024426.4	331	Ggg/Tgg	5/10	0.221984290170983	1	FACETS	0.694	0.607	0.787	0.694	0.607	0.787	INDETERMINATE	1	TRUE	0	0.406547548772835	1		345	384	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075239	16075239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	267	450	0	ENST00000268712.3:c.313G>A	p.Glu105Lys	p.E105K	ENST00000268712	NM_006311.3	105	Gaa/Aaa	4/46	0.405739386484043	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.406547548772835	2		450	581	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530141	212530141	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	86	487	0	ENST00000342788.4:c.1778G>C	p.Cys593Ser	p.C593S	ENST00000342788	NM_005235.2	593	tGt/tCt	15/28	0.406547548772835	1	FACETS	0.701	0.622	0.784	0.701	0.622	0.784	SUBCLONAL	1	TRUE	0	0.406547548772835	1		487	481	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592615	28592615	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	72	423	0	ENST00000241453.7:c.2530G>T	p.Val844Phe	p.V844F	ENST00000241453	NM_004119.2	844	Gtc/Ttc	20/24	0.161662434444237	1	FACETS	0.553	0.484	0.628	0.553	0.484	0.628	INDETERMINATE	1	TRUE	0	0.406547548772835	1		423	510	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467698	66467698	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	165	398	0	ENST00000273854.3:c.571C>A	p.Arg191Ser	p.R191S	ENST00000273854	NM_004439.5	191	Cgt/Agt	3/18	0.406547548772835	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.406547548772835	1		398	442	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55269464	55269464	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	57	598	0	ENST00000275493.2:c.3151G>T	p.Asp1051Tyr	p.D1051Y	ENST00000275493	NM_005228.3	1051	Gat/Tat	26/28	0.161662434444237	1	FACETS	0.316	0.27	0.366	0.316	0.27	0.366	INDETERMINATE	1	TRUE	0	0.406547548772835	1		598	707	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660517	227660517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148431809	NA	P-0067213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	91	429	0	ENST00000305123.5:c.2938C>T	p.Arg980Trp	p.R980W	ENST00000305123	NM_005544.2	980	Cgg/Tgg	1/2	1	2	FACETS	0.95	0.848	1	0.95	0.848	1	CLONAL	1	TRUE	1	0.406547548772835	2		429	471	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729986	41729986	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	96	466	0	ENST00000242208.4:c.543C>G	p.His181Gln	p.H181Q	ENST00000242208	NM_002192.2	181	caC/caG	3/3	0.161662434444237	1	FACETS	0.731	0.653	0.812	0.731	0.653	0.812	INDETERMINATE	1	TRUE	0	0.406547548772835	1		466	515	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856540	111856540	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	116	384	0	ENST00000341259.2:c.591G>C	p.Lys197Asn	p.K197N	ENST00000341259	NM_005475.2	197	aaG/aaC	2/8	0.406547548772835	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.406547548772835	1		384	397	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124503540	124503540	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587777475	NA	P-0067213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	242	402	0	ENST00000357628.3:c.410G>T	p.Arg137Leu	p.R137L	ENST00000357628	NM_015450.2	137	cGt/cTt	8/19	0.405739386484043	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.406547548772835	2		402	516	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804204	46804204	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	97	464	0	ENST00000290295.7:c.803G>T	p.Arg268Leu	p.R268L	ENST00000290295	NM_006361.5	268	cGg/cTg	2/2	1	2	FACETS	0.978	0.876	1	0.978	0.876	1	CLONAL	1	TRUE	1	0.406547548772835	2		464	488	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714460	40714460	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	126	445	0	ENST00000373198.4:c.3937G>T	p.Gly1313Trp	p.G1313W	ENST00000373198	NM_133170.3	1313	Ggg/Tgg	29/32	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.406547548772835	2		445	594	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28674629	28674629	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	104	591	0	ENST00000241453.7:c.19G>C	p.Asp7His	p.D7H	ENST00000241453	NM_004119.2	7	Gac/Cac	1/24	0.161662434444237	1	FACETS	0.91	0.82	1	0.91	0.82	1	INDETERMINATE	1	TRUE	0	0.406547548772835	1		591	448	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242741	66242741	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs777294375	NA	P-0067213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	159	449	1	ENST00000273854.3:c.1831G>T	p.Ala611Ser	p.A611S	ENST00000273854	NM_004439.5	611	Gct/Tct	9/18	0.406547548772835	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.406547548772835	1		450	462	SUCCESS
ATR	545	MSKCC	GRCh37	3	142241629	142241640	+	inframe_deletion	In_Frame_Del	DEL	CTCTTGTTAGCT	CTCTTGTTAGCT	-	novel	NA	P-0067213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	96	371	0	ENST00000350721.4:c.4196_4207del	p.Glu1399_Arg1402del	p.E1399_R1402del	ENST00000350721	NM_001184.3	1399	gAGCTAACAAGAGct/gct	23/47	1	2	FACETS	0.948	0.848	1	0.948	0.848	1	CLONAL	1	TRUE	1	0.406547548772835	2		371	498	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384773	17384773	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	127	404	0	ENST00000359435.4:c.405A>T	p.Lys135Asn	p.K135N	ENST00000359435	NM_001033549.1	135	aaA/aaT	4/9	0.406547548772835	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.406547548772835	1		404	465	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926576	59926576	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0067213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	108	410	0	ENST00000259008.2:c.421A>T	p.Lys141Ter	p.K141*	ENST00000259008	NM_032043.2	141	Aag/Tag	5/20	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.406547548772835	2		410	528	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861026	35861026	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	116	403	0	ENST00000303115.3:c.155A>T	p.Gln52Leu	p.Q52L	ENST00000303115	NM_002185.3	52	cAg/cTg	2/8	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.406547548772835	2		403	533	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16248785	16248785	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	68	368	0	ENST00000375759.3:c.1791C>G	p.His597Gln	p.H597Q	ENST00000375759	NM_015001.2	597	caC/caG	10/15	0.161662434444237	1	FACETS	0.565	0.492	0.642	0.565	0.492	0.642	INDETERMINATE	1	TRUE	0	0.406547548772835	1		368	472	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953840	17953840	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	113	364	0	ENST00000458235.1:c.562G>C	p.Val188Leu	p.V188L	ENST00000458235	NM_000215.3	188	Gtc/Ctc	5/24	0.406547548772835	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.406547548772835	1		364	403	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218492	1218492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690925	NA	P-0067214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	30	426	0	ENST00000326873.7:c.367C>T	p.Gln123Ter	p.Q123*	ENST00000326873	NM_000455.4	123	Cag/Tag	2/10	0.3	2	FACETS	0.518	0.417	0.634			1	SUBCLONAL	1	TRUE	NA	0.22	2		426	526	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0067214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	52	318	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.875	0.745	1	0.875	0.745	1	CLONAL	1	TRUE	1	0.22	2		318	540	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864525	56864525	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs868430124	NA	P-0067214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	54	377	0	ENST00000519728.1:c.488G>A	p.Gly163Glu	p.G163E	ENST00000519728	NM_002350.3	163	gGa/gAa	7/13	1	2	FACETS	0.842	0.719	0.977	0.842	0.719	0.977	CLONAL	1	TRUE	1	0.22	2		377	583	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392729	118392729	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	38	470	0	ENST00000534358.1:c.11761A>T	p.Ile3921Phe	p.I3921F	ENST00000534358	NM_005933.3	3921	Atc/Ttc	36/36	1	2	FACETS	0.507	0.418	0.607	0.507	0.418	0.607	SUBCLONAL	1	TRUE	1	0.22	2		470	681	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96931076	96931076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	42	458	0	ENST00000258439.3:c.44G>A	p.Arg15Gln	p.R15Q	ENST00000258439	NM_001193304.2	15	cGg/cAg	2/4	1	2	FACETS	0.834	0.696	0.986	0.834	0.696	0.986	CLONAL	1	TRUE	1	0.22	2		458	458	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596005	43596005	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	64	455	0	ENST00000355710.3:c.172G>T	p.Asp58Tyr	p.D58Y	ENST00000355710	NM_020975.4	58	Gac/Tac	2/20	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.22	2		455	524	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165703	108165703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	31	450	0	ENST00000278616.4:c.4826C>T	p.Thr1609Ile	p.T1609I	ENST00000278616	NM_000051.3	1609	aCa/aTa	32/63	1	2	FACETS	0.505	0.407	0.616	0.505	0.407	0.616	SUBCLONAL	1	TRUE	1	0.22	2		450	558	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967613	90967614	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	50	415	0	ENST00000265433.3:c.1294dup	p.Ser432PhefsTer4	p.S432Ffs*4	ENST00000265433	NM_002485.4	432	tca/tTca	10/16	1	2	FACETS	0.78	0.661	0.91	0.78	0.661	0.91	CLONAL	1	TRUE	1	0.22	2		415	583	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317464	1317464	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	42	473	0	ENST00000400841.2:c.601A>T	p.Ser201Cys	p.S201C	ENST00000400841		201	Agc/Tgc	5/6	1	2	FACETS	0.612	0.51	0.726	0.612	0.51	0.726	SUBCLONAL	1	TRUE	1	0.22	2		473	624	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456455	32456455	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	33	428	0	ENST00000332351.3:c.437G>C	p.Trp146Ser	p.W146S	ENST00000332351	NM_024426.4	146	tGg/tCg	1/10	1	2	FACETS	0.673	0.547	0.814	0.673	0.547	0.814	SUBCLONAL	1	TRUE	1	0.22	2		428	446	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110585	8110585	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	33	450	0	ENST00000585124.1:c.307G>T	p.Val103Leu	p.V103L	ENST00000585124	NM_004217.3	103	Gtg/Ttg	5/9	1	2	FACETS	0.51	0.414	0.619	0.51	0.414	0.619	SUBCLONAL	1	TRUE	1	0.22	2		450	588	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	157	317	0				ENST00000310581	NM_198253.2	-/1132			0.300898311061777	5	FACETS	1	0.983	1	0.817	0.756	0.88	INDETERMINATE	2	TRUE	2	0.508566448623559	5		317	444	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0067215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	151	471	0	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.508566448623559	2		471	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0067215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	189	507	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.449025328940798	3	FACETS	1	0.98	1	0.584	0.541	0.629	CLONAL	1	TRUE	1	0.508566448623559	3		507	798	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578464	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	315	497	0	ENST00000269305.4:c.466C>G	p.Arg156Gly	p.R156G	ENST00000269305	NM_001126112.2	156	Cgc/Ggc	5/11	0.449025328940798	3	FACETS	0.945	0.896	0.995	0.945	0.896	0.995	CLONAL	2	TRUE	1	0.508566448623559	3		497	822	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106951	27106951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	161	499	0	ENST00000324856.7:c.6562C>T	p.Gln2188Ter	p.Q2188*	ENST00000324856	NM_006015.4	2188	Cag/Tag	20/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.508566448623559	2		499	599	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037866	49037866	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs587778860	NA	P-0067215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	54	273	0	ENST00000267163.4:c.2107-1G>C		p.X703_splice	ENST00000267163	NM_000321.2	703			NA	2	FACETS	0.908	0.801	1			1	INDETERMINATE	2	TRUE	NA	0.508566448623559	2		273	117	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229612	5229612	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1246891588	NA	P-0067215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	200	338	1	ENST00000357368.4:c.2239G>A	p.Gly747Ser	p.G747S	ENST00000357368	NM_002850.3	747	Ggc/Agc	15/38	0.508566448623559	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.508566448623559	2		339	372	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132763	152132763	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	180	237	0	ENST00000262189.6:c.109C>T	p.Arg37Trp	p.R37W	ENST00000262189	NM_170606.2	37	Cgg/Tgg	1/59	0.256409494241463	4	FACETS	1	0.958	1	1	0.958	1	INDETERMINATE	2	TRUE	2	0.508566448623559	4		237	512	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040613	47040613	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1556778986	NA	P-0067215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	635	170	0	ENST00000377604.3:c.1249-1G>A		p.X417_splice	ENST00000377604	NM_001204468.1	417			0.508566448623559	6	FACETS	0.982	0.964	0.998			1	CLONAL	7	TRUE	NA	0.508566448623559	6		170	733	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401733	401733	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	314	573	0	ENST00000380956.4:c.1055G>C	p.Arg352Thr	p.R352T	ENST00000380956	NM_001195286.1	352	aGa/aCa	7/9	0.256409494241463	4	FACETS	1	0.973	1	1	0.973	1	INDETERMINATE	2	TRUE	2	0.508566448623559	4		573	893	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400945	72400945	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	114	440	0	ENST00000357731.5:c.226A>C	p.Ser76Arg	p.S76R	ENST00000357731	NM_173808.2	76	Agt/Cgt	2/7	0.471314670581762	4	FACETS	1	0.952	1	0.363	0.327	0.401	CLONAL	1	TRUE	1	0.508566448623559	4		440	621	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1688643	1688643	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	278	300	0	ENST00000378625.1:c.682G>C	p.Glu228Gln	p.E228Q	ENST00000378625	NM_001198994.1	228	Gag/Cag	6/14	0.217823459670113	6	FACETS	0.913	0.865	0.961			1	INDETERMINATE	4	TRUE	NA	0.508566448623559	6		300	604	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586425	189586425	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	129	493	1	ENST00000264731.3:c.1049G>T	p.Arg350Ile	p.R350I	ENST00000264731	NM_003722.4	350	aGa/aTa	8/14	0.193308678401178	3	FACETS	0.87	0.79	0.955	0.29	0.263	0.319	INDETERMINATE	1	TRUE	0	0.508566448623559	3		494	731	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509117	66509117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	41	365	0	ENST00000273854.3:c.210G>A	p.Met70Ile	p.M70I	ENST00000273854	NM_004439.5	70	atG/atA	2/18	1	2	FACETS	0.911	0.769	1	0.911	0.769	1	CLONAL	1	TRUE	1	0.508566448623559	2		365	177	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317639	163317639	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	104	394	0	ENST00000271452.3:c.1035G>C	p.Met345Ile	p.M345I	ENST00000271452	NM_145697.2	345	atG/atC	12/14	0.494455961012326	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.508566448623559	1		394	285	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	25	439	0				ENST00000310581	NM_198253.2	-/1132			0.280518287917136	1	FACETS	0.4	0.315	0.498	0.4	0.315	0.498	SUBCLONAL	1	TRUE	0	0.280518287917136	1		439	383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	113	415	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.929	0.836	1	0.929	0.836	1	CLONAL	1	TRUE	1	0.280518287917136	2		415	867	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370861	55370861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs973775594	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	86	428	0	ENST00000297316.4:c.163C>T	p.Pro55Ser	p.P55S	ENST00000297316	NM_022454.3	55	Ccg/Tcg	1/2	1	2	FACETS	0.994	0.88	1	0.994	0.88	1	CLONAL	1	TRUE	1	0.280518287917136	2		428	617	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919518	78919518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	107	388	2	ENST00000306801.3:c.3077C>T	p.Pro1026Leu	p.P1026L	ENST00000306801	NM_020761.2	1026	cCc/cTc	26/34	1	2	FACETS	0.907	0.813	1	0.907	0.813	1	CLONAL	1	TRUE	1	0.280518287917136	2		390	841	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974679	21974679	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs864622636	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	89	440	0	ENST00000304494.5:c.148C>T	p.Gln50Ter	p.Q50*	ENST00000304494	NM_000077.4	50	Cag/Tag	1/3	0.280518287917136	1	FACETS	0.909	0.807	1	0.909	0.807	1	CLONAL	1	TRUE	0	0.280518287917136	1		440	600	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513165	106513165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	103	422	0	ENST00000359195.3:c.2069G>A	p.Arg690Lys	p.R690K	ENST00000359195	NM_002649.2	690	aGa/aAa	4/11	0.280518287917136	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.280518287917136	1		422	594	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42053936	42053936	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	56	323	0	ENST00000219905.7:c.7399-1G>A		p.X2467_splice	ENST00000219905	NM_001164273.1	2467			1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.280518287917136	2		323	345	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164733	106164733	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1373336171	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	91	349	1	ENST00000380013.4:c.3601C>T	p.Arg1201Cys	p.R1201C	ENST00000380013	NM_001127208.2	1201	Cgc/Tgc	6/11	0.280518287917136	1	FACETS	0.906	0.805	1	0.906	0.805	1	CLONAL	1	TRUE	0	0.280518287917136	1		350	616	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991679	72991679	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867168176	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	94	500	0	ENST00000268489.5:c.2366C>T	p.Ser789Phe	p.S789F	ENST00000268489	NM_006885.3	789	tCc/tTc	2/10	1	2	FACETS	0.868	0.772	0.971	0.868	0.772	0.971	CLONAL	1	TRUE	1	0.280518287917136	2		500	772	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938390	44938390	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	53	140	0	ENST00000377967.4:c.2939-1G>A		p.X980_splice	ENST00000377967	NM_021140.2	980			1	1	FACETS	1	0.909	1	1	0.979	1	CLONAL	2	TRUE	0	0.280518287917136	1		140	154	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670237	134670237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	99	398	0	ENST00000398015.3:c.148G>A	p.Glu50Lys	p.E50K	ENST00000398015	NM_004441.4	50	Gaa/Aaa	3/16	1	2	FACETS	0.972	0.868	1	0.972	0.868	1	CLONAL	1	TRUE	1	0.280518287917136	2		398	726	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211554	98211554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	102	392	0	ENST00000331920.6:c.3601C>T	p.Pro1201Ser	p.P1201S	ENST00000331920	NM_000264.3	1201	Ccc/Tcc	22/24	0.280518287917136	1	FACETS	0.994	0.891	1	0.994	0.891	1	CLONAL	1	TRUE	0	0.280518287917136	1		392	629	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210419	36210419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs567944243	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	101	450	0	ENST00000222270.7:c.412C>T	p.Arg138Cys	p.R138C	ENST00000222270	NM_014727.1	138	Cgc/Tgc	2/37	1	2	FACETS	0.864	0.772	0.963	0.864	0.772	0.963	CLONAL	1	TRUE	1	0.280518287917136	2		450	833	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022020	5022020	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs945180127	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	78	505	0	ENST00000381652.3:c.33G>A	p.Met11Ile	p.M11I	ENST00000381652	NM_004972.3	11	atG/atA	3/25	1	2	FACETS	0.969	0.852	1	0.969	0.852	1	CLONAL	1	TRUE	1	0.280518287917136	2		505	574	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352582	118352582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	116	476	0	ENST00000534358.1:c.3787C>T	p.Pro1263Ser	p.P1263S	ENST00000534358	NM_005933.3	1263	Cca/Tca	7/36	1	2	FACETS	0.898	0.808	0.993	0.898	0.808	0.993	CLONAL	1	TRUE	1	0.280518287917136	2		476	921	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21652496	21652497	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	51	320	0	ENST00000421138.2:c.8_9delinsTT	p.Ser3Phe	p.S3F	ENST00000421138		3	tCC/tTT	3/16	1	2	FACETS	0.925	0.789	1	0.925	0.789	1	CLONAL	1	TRUE	1	0.280518287917136	2		320	393	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435340	121435341	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	58	473	0	ENST00000257555.6:c.1373_1374delinsTT	p.Thr458Ile	p.T458I	ENST00000257555		458	aCC/aTT	7/10	1	2	FACETS	0.546	0.468	0.631	0.546	0.468	0.631	SUBCLONAL	1	TRUE	1	0.280518287917136	2		473	758	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577037	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TA	novel	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	114	591	0	ENST00000269305.4:c.901_902delinsTA	p.Pro301Ter	p.P301*	ENST00000269305	NM_001126112.2	301	CCa/TAa	8/11	1	2	FACETS	0.758	0.681	0.84	0.758	0.681	0.84	SUBCLONAL	1	TRUE	1	0.280518287917136	2		591	1072	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549436	187549436	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	137	486	0	ENST00000441802.2:c.4682G>A	p.Trp1561Ter	p.W1561*	ENST00000441802	NM_005245.3	1561	tGg/tAg	9/27	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.280518287917136	2		486	940	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412390	139412390	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	92	464	0	ENST00000277541.6:c.1256-1G>A		p.X419_splice	ENST00000277541	NM_017617.3	419			0.280518287917136	1	FACETS	0.854	0.76	0.955	0.854	0.76	0.955	CLONAL	1	TRUE	0	0.280518287917136	1		464	660	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349889	70349889	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	98	256	0	ENST00000374080.3:c.3872G>C	p.Trp1291Ser	p.W1291S	ENST00000374080		1291	tGg/tCg	28/45	1	1	FACETS	0.772	0.694	0.854	1	0.983	1	SUBCLONAL	2	TRUE	0	0.280518287917136	1		256	389	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115272968	115272969	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	84	470	0	ENST00000438362.2:c.1404_1405delinsTT	p.His469Tyr	p.H469Y	ENST00000438362	NM_001242891.1	468	tcCCat/tcTTat	12/20	0.280518287917136	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.280518287917136	1		470	489	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243779	41243779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567790183	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	87	499	1	ENST00000357654.3:c.3769G>A	p.Glu1257Lys	p.E1257K	ENST00000357654	NM_007294.3	1257	Gag/Aag	10/23	1	2	FACETS	0.999	0.885	1	0.999	0.885	1	CLONAL	1	TRUE	1	0.280518287917136	2		500	621	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515205	31515205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199515305	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	62	447	0	ENST00000344624.3:c.1180G>A	p.Glu394Lys	p.E394K	ENST00000344624		394	Gag/Aag	5/33	0.280518287917136	1	FACETS	0.496	0.428	0.571	0.496	0.428	0.571	SUBCLONAL	1	TRUE	0	0.280518287917136	1		447	766	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542303	187542303	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	99	516	0	ENST00000441802.2:c.5437G>T	p.Glu1813Ter	p.E1813*	ENST00000441802	NM_005245.3	1813	Gaa/Taa	10/27	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.280518287917136	2		516	706	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038874	12038874	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	100	410	0	ENST00000396373.4:c.1167G>A	p.Met389Ile	p.M389I	ENST00000396373	NM_001987.4	389	atG/atA	7/8	1	2	FACETS	0.934	0.835	1	0.934	0.835	1	CLONAL	1	TRUE	1	0.280518287917136	2		410	763	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80024775	80024775	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753874943	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	67	338	0	ENST00000265081.6:c.1559C>T	p.Ser520Phe	p.S520F	ENST00000265081	NM_002439.4	520	tCc/tTc	10/24	0.280518287917136	1	FACETS	0.957	0.835	1	0.957	0.835	1	CLONAL	1	TRUE	0	0.280518287917136	1		338	429	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685497	29685497	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	57	325	0	ENST00000356175.3:c.7908-1G>A		p.X2636_splice	ENST00000356175	NM_000267.3	2636			1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.280518287917136	2		325	367	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68292295	68292295	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	70	334	0	ENST00000487270.1:c.198+1G>A		p.X66_splice	ENST00000487270	NM_133509.3	66			1	2	FACETS	0.954	0.833	1	0.954	0.833	1	CLONAL	1	TRUE	1	0.280518287917136	2		334	523	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461937	120461937	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	88	412	0	ENST00000256646.2:c.5779C>T	p.Gln1927Ter	p.Q1927*	ENST00000256646	NM_024408.3	1927	Cag/Tag	31/34	0.280518287917136	1	FACETS	0.928	0.824	1	0.928	0.824	1	CLONAL	1	TRUE	0	0.280518287917136	1		412	581	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528848	157528848	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	91	483	0	ENST00000346085.5:c.6573C>G	p.Ser2191Arg	p.S2191R	ENST00000346085	NM_020732.3	2191	agC/agG	20/20	1	2	FACETS	0.728	0.645	0.817	0.728	0.645	0.817	SUBCLONAL	1	TRUE	1	0.280518287917136	2		483	891	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879641	123879641	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756376927	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	67	242	0	ENST00000330479.4:c.337G>A	p.Glu113Lys	p.E113K	ENST00000330479	NM_020382.3	113	Gaa/Aaa	4/9	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.280518287917136	2		242	456	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665053	29665053	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691093	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	60	316	0	ENST00000356175.3:c.6652C>T	p.Gln2218Ter	p.Q2218*	ENST00000356175	NM_000267.3	2218	Caa/Taa	44/57	1	2	FACETS	0.979	0.846	1	0.979	0.846	1	CLONAL	1	TRUE	1	0.280518287917136	2		316	437	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354236	15354236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1459633818	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	80	393	0	ENST00000263377.2:c.2644C>T	p.Pro882Ser	p.P882S	ENST00000263377	NM_058243.2	882	Ccc/Tcc	14/20	1	2	FACETS	0.848	0.746	0.956	0.848	0.746	0.956	CLONAL	1	TRUE	1	0.280518287917136	2		393	673	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495025	56495025	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1181827941	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	133	532	0	ENST00000267101.3:c.3382G>A	p.Gly1128Arg	p.G1128R	ENST00000267101	NM_001982.3	1128	Gga/Aga	27/28	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.280518287917136	2		532	896	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205052	128205052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775918028	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	120	504	0	ENST00000341105.2:c.389C>T	p.Ala130Val	p.A130V	ENST00000341105	NM_032638.4	130	gCt/gTt	3/6	1	2	FACETS	0.994	0.897	1	0.994	0.897	1	CLONAL	1	TRUE	1	0.280518287917136	2		504	861	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139081	37139081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	92	453	0	ENST00000373509.5:c.421G>A	p.Glu141Lys	p.E141K	ENST00000373509	NM_002648.3	141	Gag/Aag	4/6	0.280518287917136	1	FACETS	0.838	0.745	0.937	0.838	0.745	0.937	CLONAL	1	TRUE	0	0.280518287917136	1		453	673	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487495	38487495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	91	421	0	ENST00000254066.5:c.25C>T	p.Pro9Ser	p.P9S	ENST00000254066	NM_000964.3	9	Ccg/Tcg	2/9	1	2	FACETS	0.907	0.806	1	0.907	0.806	1	CLONAL	1	TRUE	1	0.280518287917136	2		421	715	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238553	142238553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	92	398	0	ENST00000350721.4:c.4340C>T	p.Pro1447Leu	p.P1447L	ENST00000350721	NM_001184.3	1447	cCt/cTt	24/47	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.280518287917136	2		398	539	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0067218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	46	270	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.963	0.817	1	0.963	0.817	1	CLONAL	1	TRUE	1	0.362055582983163	2		270	264	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599929	10599929	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	60	337	0	ENST00000171111.5:c.1647del	p.Met550Ter	p.M550*	ENST00000171111	NM_203500.1	549	ccC/cc	5/6	0.362055582983163	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.362055582983163	1		337	249	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604676	48604676	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	48	343	0	ENST00000342988.3:c.1498del	p.Ile500TyrfsTer4	p.I500Yfs*4	ENST00000342988	NM_005359.5	500	Ata/ta	12/12	0.342995510260765	1	FACETS	0.912	0.779	1	0.912	0.779	1	CLONAL	1	TRUE	0	0.362055582983163	1		343	238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579357	7579364	+	frameshift_variant	Frame_Shift_Del	DEL	ACGGAAAC	ACGGAAAC	-	novel	NA	P-0067218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	60	327	0	ENST00000269305.4:c.323_330del	p.Gly108AlafsTer38	p.G108Afs*38	ENST00000269305	NM_001126112.2	108	gGTTTCCGT/g	4/11	0.342995510260765	1	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	0	0.362055582983163	1		327	271	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373280	118373282	+	inframe_deletion	In_Frame_Del	DEL	AAT	AAT	-	novel	NA	P-0067218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	49	356	0	ENST00000534358.1:c.6676_6678del	p.Asn2226del	p.N2226del	ENST00000534358	NM_005933.3	2225	AAT/-	27/36	1	2	FACETS	0.778	0.661	0.905	0.778	0.661	0.905	CLONAL	1	TRUE	1	0.362055582983163	2		356	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0067219-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	629	455	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	0.718251690637327	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.709934430874105	2		455	733	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84403327	84403327	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067219-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	77	329	0	ENST00000321945.7:c.158T>C	p.Val53Ala	p.V53A	ENST00000321945	NM_139076.2	53	gTt/gCt	2/9	NA	2	FACETS	0.676	0.598	0.757			1	INDETERMINATE	1	TRUE	NA	0.709934430874105	2		329	321	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	78	329	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.844	0.746	0.948	1	0.981	1	CLONAL	2	TRUE	1	0.241860673129528	2		329	382	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	101	409	5	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.241860673129528	2		414	581	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	25	332	1	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	1	0.803	1	1	0.803	1	CLONAL	1	TRUE	1	0.241860673129528	2		333	204	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	115	565	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.241860673129528	2		565	729	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	55	342	4	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.241860673129528	2		346	387	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918105	50918105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	147	388	0	ENST00000440232.2:c.2422C>T	p.Arg808Cys	p.R808C	ENST00000440232	NM_002691.3	808	Cgc/Tgc	20/27	1	2	FACETS	0.965	0.884	1	1	0.991	1	CLONAL	2	TRUE	1	0.241860673129528	2		388	630	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856125	111856125	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	116	411	0	ENST00000341259.2:c.176G>A	p.Arg59His	p.R59H	ENST00000341259	NM_005475.2	59	cGc/cAc	2/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.241860673129528	2		411	656	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1686864	1686864	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	44	390	0	ENST00000378625.1:c.1072A>C	p.Thr358Pro	p.T358P	ENST00000378625	NM_001198994.1	358	Acc/Ccc	9/14	1	2	FACETS	0.646	0.541	0.763	0.646	0.541	0.763	SUBCLONAL	1	TRUE	1	0.241860673129528	2		390	563	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1737924	1737924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	29	391	1	ENST00000378609.4:c.257C>T	p.Thr86Ile	p.T86I	ENST00000378609	NM_002074.3	86	aCc/aTc	6/12	1	2	FACETS	0.42	0.336	0.516	0.42	0.336	0.516	SUBCLONAL	1	TRUE	1	0.241860673129528	2		392	571	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073419	8073419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393864904	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	95	435	0	ENST00000377482.5:c.1240G>A	p.Ala414Thr	p.A414T	ENST00000377482	NM_018948.3	414	Gca/Aca	4/4	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.241860673129528	2		435	540	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074392	8074393	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	92	441	0	ENST00000377482.5:c.266dup	p.Ser90ValfsTer12	p.S90Vfs*12	ENST00000377482	NM_018948.3	89	aag/aaAg	4/4	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.241860673129528	2		441	592	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9787015	9787015	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	113	365	0	ENST00000377346.4:c.3046C>T	p.Arg1016Ter	p.R1016*	ENST00000377346	NM_005026.3	1016	Cga/Tga	24/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.241860673129528	2		365	706	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272853	11272853	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	40	391	0	ENST00000361445.4:c.3398A>C	p.Lys1133Thr	p.K1133T	ENST00000361445	NM_004958.3	1133	aAg/aCg	22/58	1	2	FACETS	0.63	0.523	0.749	0.63	0.523	0.749	SUBCLONAL	1	TRUE	1	0.241860673129528	2		391	525	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199435	16199435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	76	447	0	ENST00000375759.3:c.208G>A	p.Gly70Ser	p.G70S	ENST00000375759	NM_015001.2	70	Ggt/Agt	2/15	1	2	FACETS	0.85	0.745	0.964	0.85	0.745	0.964	CLONAL	1	TRUE	1	0.241860673129528	2		447	739	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255519	16255519	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	148	414	1	ENST00000375759.3:c.2784C>A	p.Asp928Glu	p.D928E	ENST00000375759	NM_015001.2	928	gaC/gaA	11/15	1	2	FACETS	0.913	0.836	0.993	1	0.99	1	CLONAL	2	TRUE	1	0.241860673129528	2		415	670	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256211	16256211	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	42	483	0	ENST00000375759.3:c.3476T>A	p.Ile1159Asn	p.I1159N	ENST00000375759	NM_015001.2	1159	aTt/aAt	11/15	1	2	FACETS	0.61	0.509	0.723	0.61	0.509	0.723	SUBCLONAL	1	TRUE	1	0.241860673129528	2		483	569	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256430	16256430	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760748544	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	148	505	0	ENST00000375759.3:c.3695A>G	p.His1232Arg	p.H1232R	ENST00000375759	NM_015001.2	1232	cAt/cGt	11/15	1	2	FACETS	0.802	0.733	0.874	1	0.989	1	CLONAL	2	TRUE	1	0.241860673129528	2		505	763	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258563	16258563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764002157	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	112	504	1	ENST00000375759.3:c.5828C>T	p.Ala1943Val	p.A1943V	ENST00000375759	NM_015001.2	1943	gCg/gTg	11/15	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.241860673129528	2		505	905	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259044	16259044	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	138	493	1	ENST00000375759.3:c.6309G>T	p.Arg2103Ser	p.R2103S	ENST00000375759	NM_015001.2	2103	agG/agT	11/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.241860673129528	2		494	779	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17350510	17350510	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs397516836	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	57	355	0	ENST00000375499.3:c.600G>T	p.Trp200Cys	p.W200C	ENST00000375499	NM_003000.2	200	tgG/tgT	6/8	1	2	FACETS	0.779	0.668	0.9	0.779	0.668	0.9	SUBCLONAL	1	TRUE	1	0.241860673129528	2		355	605	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17354331	17354331	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	21	375	0	ENST00000375499.3:c.453A>C	p.Lys151Asn	p.K151N	ENST00000375499	NM_003000.2	151	aaA/aaC	5/8	1	2	FACETS	0.455	0.349	0.578	0.455	0.349	0.578	SUBCLONAL	1	TRUE	1	0.241860673129528	2		375	382	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22408284	22408284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	55	304	0	ENST00000344548.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000344548	NM_001039802.1	59	Gca/Aca	4/7	1	2	FACETS	0.792	0.683	0.91	1	0.971	1	CLONAL	2	TRUE	1	0.241860673129528	2		304	287	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22412962	22412962	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	15	228	0	ENST00000344548.3:c.209T>C	p.Leu70Pro	p.L70P	ENST00000344548	NM_001039802.1	70	cTg/cCg	5/7	1	2	FACETS	0.775	0.57	1	0.775	0.57	1	CLONAL	1	TRUE	1	0.241860673129528	2		228	160	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094361	27094361	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	127	447	0	ENST00000324856.7:c.3069G>A	p.Trp1023Ter	p.W1023*	ENST00000324856	NM_006015.4	1023	tgG/tgA	11/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.241860673129528	2		447	742	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097703	27097703	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	98	452	0	ENST00000324856.7:c.3292C>A	p.Gln1098Lys	p.Q1098K	ENST00000324856	NM_006015.4	1098	Cag/Aag	12/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.241860673129528	2		452	673	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28605628	28605628	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	48	386	0	ENST00000253063.3:c.1232G>T	p.Gly411Val	p.G411V	ENST00000253063	NM_031459.4	411	gGg/gTg	9/10	1	2	FACETS	0.709	0.599	0.83	0.709	0.599	0.83	SUBCLONAL	1	TRUE	1	0.241860673129528	2		386	560	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809808	36809808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	64	368	0	ENST00000373129.3:c.797C>T	p.Thr266Ile	p.T266I	ENST00000373129	NM_032017.1	266	aCc/aTc	9/12	1	2	FACETS	0.801	0.693	0.918	0.801	0.693	0.918	CLONAL	1	TRUE	1	0.241860673129528	2		368	661	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935322	36935322	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	118	406	0	ENST00000361632.4:c.1405A>G	p.Ser469Gly	p.S469G	ENST00000361632		469	Agc/Ggc	10/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.241860673129528	2		406	673	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795109	45795109	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	79	409	0	ENST00000450313.1:c.1519G>T	p.Gly507Cys	p.G507C	ENST00000450313	NM_012222.2	507	Ggt/Tgt	16/16	1	2	FACETS	0.879	0.773	0.994	0.879	0.773	0.994	CLONAL	1	TRUE	1	0.241860673129528	2		409	743	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521641	46521641	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	22	291	0	ENST00000262741.5:c.767T>G	p.Ile256Ser	p.I256S	ENST00000262741	NM_003629.3	256	aTt/aGt	7/10	1	2	FACETS	0.6	0.465	0.757	0.6	0.465	0.757	SUBCLONAL	1	TRUE	1	0.241860673129528	2		291	303	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740226	46740226	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs201979352	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	40	374	0	ENST00000371975.4:c.1706T>C	p.Phe569Ser	p.F569S	ENST00000371975	NM_003579.3	569	tTc/tCc	16/18	1	2	FACETS	0.583	0.484	0.694	0.583	0.484	0.694	SUBCLONAL	1	TRUE	1	0.241860673129528	2		374	567	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248585	59248585	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	50	395	0	ENST00000371222.2:c.158T>G	p.Leu53Arg	p.L53R	ENST00000371222	NM_002228.3	53	cTc/cGc	1/1	1	2	FACETS	0.641	0.543	0.749	0.641	0.543	0.749	SUBCLONAL	1	TRUE	1	0.241860673129528	2		395	645	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65311305	65311305	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	51	459	0	ENST00000342505.4:c.2006T>C	p.Phe669Ser	p.F669S	ENST00000342505	NM_002227.2	669	tTt/tCt	15/25	1	2	FACETS	0.702	0.596	0.818	0.702	0.596	0.818	SUBCLONAL	1	TRUE	1	0.241860673129528	2		459	601	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400911	72400911	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	22	399	0	ENST00000357731.5:c.260T>C	p.Val87Ala	p.V87A	ENST00000357731	NM_173808.2	87	gTg/gCg	2/7	1	2	FACETS	0.413	0.32	0.523	0.413	0.32	0.523	SUBCLONAL	1	TRUE	1	0.241860673129528	2		399	440	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78426041	78426041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	37	504	0	ENST00000370768.2:c.1484G>A	p.Gly495Asp	p.G495D	ENST00000370768	NM_003902.3	495	gGc/gAc	15/20	1	2	FACETS	0.447	0.367	0.536	0.447	0.367	0.536	SUBCLONAL	1	TRUE	1	0.241860673129528	2		504	685	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690386	117690386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770820854	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	51	428	0	ENST00000369458.3:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000369458	NM_024626.3	248	cGg/cAg	5/6	1	2	FACETS	0.73	0.62	0.85	0.73	0.62	0.85	SUBCLONAL	1	TRUE	1	0.241860673129528	2		428	578	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699480	117699480	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs372329698	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	63	365	0	ENST00000369458.3:c.161T>C	p.Leu54Pro	p.L54P	ENST00000369458	NM_024626.3	54	cTg/cCg	3/6	1	2	FACETS	0.793	0.685	0.91	0.793	0.685	0.91	CLONAL	1	TRUE	1	0.241860673129528	2		365	657	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120460344	120460344	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	92	411	0	ENST00000256646.2:c.5971G>A	p.Glu1991Lys	p.E1991K	ENST00000256646	NM_024408.3	1991	Gag/Aag	33/34	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.241860673129528	2		411	607	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462060	120462060	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	53	446	0	ENST00000256646.2:c.5656C>A	p.Arg1886Ser	p.R1886S	ENST00000256646	NM_024408.3	1886	Cgc/Agc	31/34	1	2	FACETS	0.661	0.563	0.769	0.661	0.563	0.769	SUBCLONAL	1	TRUE	1	0.241860673129528	2		446	663	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120469186	120469186	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	61	379	0	ENST00000256646.2:c.3941T>C	p.Leu1314Pro	p.L1314P	ENST00000256646	NM_024408.3	1314	cTg/cCg	24/34	1	2	FACETS	0.575	0.495	0.663	0.575	0.495	0.663	SUBCLONAL	1	TRUE	1	0.241860673129528	2		379	877	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471613	120471613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201968231	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	109	331	0	ENST00000256646.2:c.3878G>A	p.Arg1293His	p.R1293H	ENST00000256646	NM_024408.3	1293	cGt/cAt	23/34	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.241860673129528	2		331	624	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150923080	150923080	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	62	362	0	ENST00000271640.5:c.1727A>G	p.His576Arg	p.H576R	ENST00000271640	NM_001145415.1	576	cAt/cGt	13/22	1	2	FACETS	0.776	0.669	0.891	0.776	0.669	0.891	SUBCLONAL	1	TRUE	1	0.241860673129528	2		362	661	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150936092	150936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	110	498	0	ENST00000271640.5:c.3544A>G	p.Met1182Val	p.M1182V	ENST00000271640	NM_001145415.1	1182	Atg/Gtg	20/22	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.241860673129528	2		498	690	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870205	155870205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs563231684	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	39	400	0	ENST00000368323.3:c.634C>T	p.Arg212Trp	p.R212W	ENST00000368323	NM_006912.5	212	Cgg/Tgg	6/6	1	2	FACETS	0.77	0.638	0.916	0.77	0.638	0.916	CLONAL	1	TRUE	1	0.241860673129528	2		400	419	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844194	156844194	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs944976553	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	64	692	0	ENST00000524377.1:c.1195+2T>C		p.X399_splice	ENST00000524377	NM_002529.3	399			1	2	FACETS	0.506	0.436	0.582	0.506	0.436	0.582	SUBCLONAL	1	TRUE	1	0.241860673129528	2		692	1046	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161298278	161298278	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	57	337	0	ENST00000367975.2:c.170C>A	p.Thr57Asn	p.T57N	ENST00000367975	NM_003001.3	57	aCt/aAt	3/6	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.241860673129528	2		337	318	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725501	162725501	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	39	354	0	ENST00000367921.3:c.613C>T	p.Pro205Ser	p.P205S	ENST00000367921	NM_006182.2	205	Cct/Tct	7/18	1	2	FACETS	0.642	0.532	0.766	0.642	0.532	0.766	SUBCLONAL	1	TRUE	1	0.241860673129528	2		354	502	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162735842	162735842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	47	404	0	ENST00000367921.3:c.1151C>A	p.Pro384His	p.P384H	ENST00000367921	NM_006182.2	384	cCc/cAc	10/18	1	2	FACETS	0.8	0.675	0.937	0.8	0.675	0.937	CLONAL	1	TRUE	1	0.241860673129528	2		404	486	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163298060	163298060	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	20	324	0	ENST00000271452.3:c.241G>T	p.Gly81Cys	p.G81C	ENST00000271452	NM_145697.2	81	Ggc/Tgc	4/14	1	2	FACETS	0.799	0.613	1	0.799	0.613	1	CLONAL	1	TRUE	1	0.241860673129528	2		324	207	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318844	163318844	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757297441	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	49	407	0	ENST00000271452.3:c.1234G>A	p.Ala412Thr	p.A412T	ENST00000271452	NM_145697.2	412	Gct/Act	13/14	1	2	FACETS	0.947	0.811	1	1	0.974	1	CLONAL	2	TRUE	1	0.241860673129528	2		407	214	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015317	176015317	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	12	268	0	ENST00000367669.3:c.1421G>T	p.Ser474Ile	p.S474I	ENST00000367669	NM_022457.5	474	aGc/aTc	12/20	1	2	FACETS	0.746	0.527	1	0.746	0.527	1	CLONAL	1	TRUE	1	0.241860673129528	2		268	133	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176118170	176118170	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	27	286	0	ENST00000367669.3:c.803T>C	p.Leu268Pro	p.L268P	ENST00000367669	NM_022457.5	268	cTc/cCc	6/20	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.241860673129528	2		286	201	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176118173	176118173	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	13	282	0	ENST00000367669.3:c.800T>C	p.Phe267Ser	p.F267S	ENST00000367669	NM_022457.5	267	tTc/tCc	6/20	1	2	FACETS	0.522	0.372	0.704	0.522	0.372	0.704	SUBCLONAL	1	TRUE	1	0.241860673129528	2		282	206	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117012	193117013	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	65	284	0	ENST00000367435.3:c.750dup	p.Ala251CysfsTer16	p.A251Cfs*16	ENST00000367435	NM_024529.4	249	att/aTtt	8/17	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.241860673129528	2		284	361	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119447	193119447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762716583	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	23	375	0	ENST00000367435.3:c.842G>A	p.Arg281His	p.R281H	ENST00000367435	NM_024529.4	281	cGc/cAc	9/17	1	2	FACETS	0.47	0.365	0.59	0.47	0.365	0.59	SUBCLONAL	1	TRUE	1	0.241860673129528	2		375	405	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981261	201981261	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	34	435	0	ENST00000359651.3:c.340T>G	p.Phe114Val	p.F114V	ENST00000359651		114	Ttt/Gtt	2/8	1	2	FACETS	0.413	0.337	0.5	0.413	0.337	0.5	SUBCLONAL	1	TRUE	1	0.241860673129528	2		435	680	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204511931	204511931	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	18	327	0	ENST00000367182.3:c.531T>A	p.Asn177Lys	p.N177K	ENST00000367182	NM_001278516.1	177	aaT/aaA	8/11	1	2	FACETS	0.528	0.397	0.682	0.528	0.397	0.682	SUBCLONAL	1	TRUE	1	0.241860673129528	2		327	282	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652424	206652424	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	62	473	0	ENST00000367120.3:c.1131C>A	p.Ser377Arg	p.S377R	ENST00000367120	NM_014002.3	377	agC/agA	10/22	1	2	FACETS	0.683	0.589	0.785	0.683	0.589	0.785	SUBCLONAL	1	TRUE	1	0.241860673129528	2		473	751	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653404	206653404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368845063	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	135	426	0	ENST00000367120.3:c.1288C>T	p.Arg430Trp	p.R430W	ENST00000367120	NM_014002.3	430	Cgg/Tgg	12/22	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.241860673129528	2		426	825	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230561616	230561616	+	upstream_gene_variant	5'Flank	SNP	C	C	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	22	357	0				ENST00000391860	NM_001258311.1	-/409			1	2	FACETS	0.415	0.321	0.525	0.415	0.321	0.525	SUBCLONAL	1	TRUE	1	0.241860673129528	2		357	438	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231474223	231474223	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373093523	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	128	398	0	ENST00000295050.7:c.94G>A	p.Val32Met	p.V32M	ENST00000295050	NM_032018.5	32	Gtg/Atg	1/5	1	2	FACETS	0.781	0.709	0.856	1	0.986	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		398	678	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680502	241680502	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	29	318	0	ENST00000366560.3:c.247G>T	p.Gly83Cys	p.G83C	ENST00000366560	NM_000143.3	83	Ggt/Tgt	2/10	1	2	FACETS	0.626	0.502	0.767	0.626	0.502	0.767	SUBCLONAL	1	TRUE	1	0.241860673129528	2		318	383	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246091256	246091256	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs566281194	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	90	343	0	ENST00000388985.4:c.679C>T	p.Arg227Ter	p.R227*	ENST00000388985		227	Cga/Tga	7/12	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.241860673129528	2		343	575	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097689	8097689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1485724723	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	63	485	0	ENST00000346208.3:c.71C>T	p.Pro24Leu	p.P24L	ENST00000346208		24	cCg/cTg	2/6	1	2	FACETS	0.709	0.612	0.814	0.709	0.612	0.814	SUBCLONAL	1	TRUE	1	0.241860673129528	2		485	735	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100334	8100334	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	42	541	0	ENST00000346208.3:c.308T>C	p.Leu103Pro	p.L103P	ENST00000346208		103	cTg/cCg	3/6	1	2	FACETS	0.464	0.386	0.551	0.464	0.386	0.551	SUBCLONAL	1	TRUE	1	0.241860673129528	2		541	749	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111496	8111496	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	79	410	0	ENST00000346208.3:c.982T>C	p.Trp328Arg	p.W328R	ENST00000346208		328	Tgg/Cgg	5/6	1	2	FACETS	0.901	0.792	1	0.901	0.792	1	CLONAL	1	TRUE	1	0.241860673129528	2		410	725	SUCCESS
RET	5979	MSKCC	GRCh37	10	43572770	43572770	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	92	353	0	ENST00000355710.3:c.64C>A	p.Leu22Ile	p.L22I	ENST00000355710	NM_020975.4	22	Cta/Ata	1/20	1	2	FACETS	0.842	0.751	0.937	1	0.983	1	CLONAL	2	TRUE	1	0.241860673129528	2		353	452	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606859	43606859	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	148	582	0	ENST00000355710.3:c.1468C>T	p.Gln490Ter	p.Q490*	ENST00000355710	NM_020975.4	490	Cag/Tag	7/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.241860673129528	2		582	866	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608300	43608300	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	125	663	0	ENST00000355710.3:c.1649-1G>T		p.X550_splice	ENST00000355710	NM_020975.4	550			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.241860673129528	2		663	804	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609042	43609042	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745418960	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	128	509	0	ENST00000355710.3:c.1798C>T	p.Arg600Trp	p.R600W	ENST00000355710	NM_020975.4	600	Cgg/Tgg	10/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.241860673129528	2		509	793	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610164	43610164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137855422	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	51	507	0	ENST00000355710.3:c.2116G>A	p.Val706Met	p.V706M	ENST00000355710	NM_020975.4	706	Gtg/Atg	11/20	1	2	FACETS	0.582	0.493	0.679	0.582	0.493	0.679	SUBCLONAL	1	TRUE	1	0.241860673129528	2		507	725	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619201	43619201	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	68	526	0	ENST00000355710.3:c.2884A>G	p.Asn962Asp	p.N962D	ENST00000355710	NM_020975.4	962	Aac/Gac	17/20	1	2	FACETS	0.737	0.64	0.842	0.737	0.64	0.842	SUBCLONAL	1	TRUE	1	0.241860673129528	2		526	763	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620387	43620387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748288493	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	36	376	0	ENST00000355710.3:c.2996C>T	p.Ala999Val	p.A999V	ENST00000355710	NM_020975.4	999	gCg/gTg	18/20	1	2	FACETS	0.442	0.362	0.532	0.442	0.362	0.532	SUBCLONAL	1	TRUE	1	0.241860673129528	2		376	673	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759978	63759978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	41	417	0	ENST00000279873.7:c.631G>A	p.Gly211Arg	p.G211R	ENST00000279873	NM_032199.2	211	Ggg/Agg	4/10	1	2	FACETS	0.454	0.377	0.54	0.454	0.377	0.54	SUBCLONAL	1	TRUE	1	0.241860673129528	2		417	747	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850676	63850676	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	40	424	0	ENST00000279873.7:c.1454C>A	p.Pro485His	p.P485H	ENST00000279873	NM_032199.2	485	cCt/cAt	10/10	1	2	FACETS	0.644	0.534	0.765	0.644	0.534	0.765	SUBCLONAL	1	TRUE	1	0.241860673129528	2		424	514	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333291	70333291	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	60	404	0	ENST00000373644.4:c.1196C>A	p.Pro399His	p.P399H	ENST00000373644	NM_030625.2	399	cCt/cAt	2/12	1	2	FACETS	0.759	0.653	0.874	0.759	0.653	0.874	SUBCLONAL	1	TRUE	1	0.241860673129528	2		404	654	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333966	70333966	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	71	382	0	ENST00000373644.4:c.1871G>A	p.Cys624Tyr	p.C624Y	ENST00000373644	NM_030625.2	624	tGt/tAt	2/12	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.241860673129528	2		382	516	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404866	70404866	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	44	402	0	ENST00000373644.4:c.2380C>A	p.Leu794Ile	p.L794I	ENST00000373644	NM_030625.2	794	Cta/Ata	4/12	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.241860673129528	2		402	328	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450828	70450828	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	42	475	0	ENST00000373644.4:c.5668G>T	p.Gly1890Cys	p.G1890C	ENST00000373644	NM_030625.2	1890	Ggt/Tgt	12/12	1	2	FACETS	0.465	0.387	0.552	0.465	0.387	0.552	SUBCLONAL	1	TRUE	1	0.241860673129528	2		475	747	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123353331	123353331	+	start_lost	Translation_Start_Site	SNP	T	T	C	rs774885289	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	41	486	0	ENST00000358487.5:c.1A>G	p.Met1?	p.M1?	ENST00000358487	NM_000141.4	1	Atg/Gtg	2/18	1	2	FACETS	0.417	0.346	0.496	0.417	0.346	0.496	SUBCLONAL	1	TRUE	1	0.241860673129528	2		486	814	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	532649	532649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	107	309	0	ENST00000451590.1:c.557G>A	p.Cys186Tyr	p.C186Y	ENST00000451590	NM_001130442.1	186	tGt/tAt	5/5	1	2	FACETS	0.756	0.68	0.837	1	0.983	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		309	585	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251838	8251838	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs766510770	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	136	421	0	ENST00000335790.3:c.239G>A	p.Arg80Lys	p.R80K	ENST00000335790	NM_002315.2	80	aGg/aAg	2/4	1	2	FACETS	0.823	0.75	0.9	1	0.988	1	CLONAL	2	TRUE	1	0.241860673129528	2		421	683	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10792100	10792100	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	51	447	0	ENST00000361367.2:c.2293G>T	p.Ala765Ser	p.A765S	ENST00000361367	NM_014633.3	765	Gct/Tct	18/25	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.241860673129528	2		447	328	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47594840	47594840	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	125	514	0	ENST00000430070.2:c.1247T>C	p.Ile416Thr	p.I416T	ENST00000430070	NM_018095.4	416	aTc/aCc	4/4	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.241860673129528	2		514	722	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77069950	77069950	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	45	428	0	ENST00000356341.3:c.590C>T	p.Thr197Ile	p.T197I	ENST00000356341	NM_002576.4	197	aCa/aTa	6/15	1	2	FACETS	0.457	0.382	0.539	0.457	0.382	0.539	SUBCLONAL	1	TRUE	1	0.241860673129528	2		428	815	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77091018	77091018	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	86	381	0	ENST00000356341.3:c.212A>G	p.Glu71Gly	p.E71G	ENST00000356341	NM_002576.4	71	gAg/gGg	3/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.241860673129528	2		381	495	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103411	77103411	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	48	496	0	ENST00000356341.3:c.155A>G	p.Asp52Gly	p.D52G	ENST00000356341	NM_002576.4	52	gAc/gGc	2/15	1	2	FACETS	0.771	0.652	0.902	0.771	0.652	0.902	CLONAL	1	TRUE	1	0.241860673129528	2		496	515	SUCCESS
EED	8726	MSKCC	GRCh37	11	85956320	85956320	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	97	374	0	ENST00000263360.6:c.49G>A	p.Ala17Thr	p.A17T	ENST00000263360	NM_003797.3	17	Gcg/Acg	1/12	1	2	FACETS	0.751	0.672	0.835	1	0.981	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		374	534	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977135	85977135	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	24	270	0	ENST00000263360.6:c.737T>C	p.Leu246Pro	p.L246P	ENST00000263360	NM_003797.3	246	cTt/cCt	8/12	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.241860673129528	2		270	137	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94169053	94169053	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	40	326	0	ENST00000323929.3:c.1939G>T	p.Asp647Tyr	p.D647Y	ENST00000323929	NM_005591.3	647	Gat/Tat	18/20	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.241860673129528	2		326	271	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94225949	94225949	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	26	312	0	ENST00000323929.3:c.19C>A	p.Leu7Ile	p.L7I	ENST00000323929	NM_005591.3	7	Ctt/Att	2/20	1	2	FACETS	0.592	0.469	0.734	0.592	0.469	0.734	SUBCLONAL	1	TRUE	1	0.241860673129528	2		312	363	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996747	100996747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	27	362	0	ENST00000325455.5:c.1780G>A	p.Ala594Thr	p.A594T	ENST00000325455	NM_001202474.3	594	Gca/Aca	2/8	1	2	FACETS	0.638	0.508	0.787	0.638	0.508	0.787	SUBCLONAL	1	TRUE	1	0.241860673129528	2		362	350	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195847	102195847	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	37	448	0	ENST00000263464.3:c.607G>T	p.Val203Leu	p.V203L	ENST00000263464	NM_001165.4	203	Gtg/Ttg	2/9	1	2	FACETS	0.44	0.361	0.528	0.44	0.361	0.528	SUBCLONAL	1	TRUE	1	0.241860673129528	2		448	696	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106524	108106524	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	16	342	0	ENST00000278616.4:c.459A>C	p.Arg153Ser	p.R153S	ENST00000278616	NM_000051.3	153	agA/agC	5/63	1	2	FACETS	0.497	0.367	0.653	0.497	0.367	0.653	SUBCLONAL	1	TRUE	1	0.241860673129528	2		342	266	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121522	108121522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	61	404	0	ENST00000278616.4:c.1330C>T	p.Pro444Ser	p.P444S	ENST00000278616	NM_000051.3	444	Ccc/Tcc	10/63	1	2	FACETS	0.938	0.81	1	0.938	0.81	1	CLONAL	1	TRUE	1	0.241860673129528	2		404	538	SUCCESS
ATM	472	MSKCC	GRCh37	11	108126963	108126963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	32	288	0	ENST00000278616.4:c.2146G>A	p.Val716Ile	p.V716I	ENST00000278616	NM_000051.3	716	Gtc/Atc	14/63	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.241860673129528	2		288	205	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129794	108129794	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	48	275	0	ENST00000278616.4:c.2458A>T	p.Lys820Ter	p.K820*	ENST00000278616	NM_000051.3	820	Aaa/Taa	16/63	1	2	FACETS	0.82	0.7	0.95	1	0.968	1	CLONAL	2	TRUE	1	0.241860673129528	2		275	242	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155073	108155073	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	30	351	0	ENST00000278616.4:c.3866A>T	p.Lys1289Met	p.K1289M	ENST00000278616	NM_000051.3	1289	aAg/aTg	26/63	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.241860673129528	2		351	211	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111958589	111958589	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	77	276	0	ENST00000375549.3:c.61C>A	p.Leu21Ile	p.L21I	ENST00000375549	NM_003002.3	21	Ctt/Att	2/4	1	2	FACETS	0.899	0.795	1	1	0.982	1	CLONAL	2	TRUE	1	0.241860673129528	2		276	354	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344293	118344293	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	115	442	0	ENST00000534358.1:c.2419G>A	p.Gly807Arg	p.G807R	ENST00000534358	NM_005933.3	807	Ggg/Agg	3/36	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.241860673129528	2		442	717	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344618	118344618	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	55	446	0	ENST00000534358.1:c.2744A>G	p.Lys915Arg	p.K915R	ENST00000534358	NM_005933.3	915	aAg/aGg	3/36	1	2	FACETS	0.664	0.567	0.77	0.664	0.567	0.77	SUBCLONAL	1	TRUE	1	0.241860673129528	2		446	685	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377172	118377172	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	52	543	0	ENST00000534358.1:c.10565C>T	p.Pro3522Leu	p.P3522L	ENST00000534358	NM_005933.3	3522	cCa/cTa	27/36	1	2	FACETS	0.553	0.469	0.645	0.553	0.469	0.645	SUBCLONAL	1	TRUE	1	0.241860673129528	2		543	778	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377199	118377199	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	148	537	0	ENST00000534358.1:c.10592C>A	p.Pro3531His	p.P3531H	ENST00000534358	NM_005933.3	3531	cCt/cAt	27/36	1	2	FACETS	0.77	0.704	0.839	1	0.988	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		537	795	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380725	118380725	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	28	400	0	ENST00000534358.1:c.10963C>T	p.Gln3655Ter	p.Q3655*	ENST00000534358	NM_005933.3	3655	Caa/Taa	30/36	1	2	FACETS	0.613	0.489	0.753	0.613	0.489	0.753	SUBCLONAL	1	TRUE	1	0.241860673129528	2		400	378	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155731	119155731	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	176	503	0	ENST00000264033.4:c.1484C>G	p.Pro495Arg	p.P495R	ENST00000264033	NM_005188.3	495	cCg/cGg	10/16	1	2	FACETS	0.839	0.774	0.908	1	0.991	1	CLONAL	2	TRUE	1	0.241860673129528	2		503	867	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170398	119170398	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	61	448	0	ENST00000264033.4:c.2628A>C	p.Lys876Asn	p.K876N	ENST00000264033	NM_005188.3	876	aaA/aaC	16/16	1	2	FACETS	0.747	0.644	0.86	0.747	0.644	0.86	SUBCLONAL	1	TRUE	1	0.241860673129528	2		448	675	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505404	125505404	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	20	381	1	ENST00000428830.2:c.700del	p.Ile234SerfsTer6	p.I234Sfs*6	ENST00000428830	NM_001114121.2	232	Aaa/aa	7/14	1	2	FACETS	0.606	0.464	0.772	0.606	0.464	0.772	SUBCLONAL	1	TRUE	1	0.241860673129528	2		382	273	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	459938	459938	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	23	301	0	ENST00000399788.2:c.1157C>T	p.Pro386Leu	p.P386L	ENST00000399788	NM_001042603.1	386	cCc/cTc	10/28	1	2	FACETS	0.674	0.527	0.845	0.674	0.527	0.845	SUBCLONAL	1	TRUE	1	0.241860673129528	2		301	282	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	461487	461487	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	16	314	0	ENST00000399788.2:c.1033T>G	p.Cys345Gly	p.C345G	ENST00000399788	NM_001042603.1	345	Tgt/Ggt	9/28	1	2	FACETS	0.485	0.358	0.636	0.485	0.358	0.636	SUBCLONAL	1	TRUE	1	0.241860673129528	2		314	273	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472133	472133	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	60	367	0	ENST00000399788.2:c.668C>A	p.Thr223Asn	p.T223N	ENST00000399788	NM_001042603.1	223	aCt/aAt	5/28	1	2	FACETS	0.773	0.665	0.89	0.773	0.665	0.89	SUBCLONAL	1	TRUE	1	0.241860673129528	2		367	642	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472227	472227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	93	341	0	ENST00000399788.2:c.574G>A	p.Val192Met	p.V192M	ENST00000399788	NM_001042603.1	192	Gtg/Atg	5/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.241860673129528	2		341	579	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475203	475203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754666448	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	62	369	0	ENST00000399788.2:c.434G>A	p.Arg145His	p.R145H	ENST00000399788	NM_001042603.1	145	cGc/cAc	4/28	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.241860673129528	2		369	358	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023201	1023201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	47	387	0	ENST00000358495.3:c.1054G>A	p.Ala352Thr	p.A352T	ENST00000358495	NM_134424.2	352	Gcc/Acc	11/12	1	2	FACETS	0.592	0.499	0.696	0.592	0.499	0.696	SUBCLONAL	1	TRUE	1	0.241860673129528	2		387	656	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037474	12037474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	55	424	0	ENST00000396373.4:c.1105C>T	p.Arg369Trp	p.R369W	ENST00000396373	NM_001987.4	369	Cgg/Tgg	6/8	1	2	FACETS	0.703	0.601	0.815	0.703	0.601	0.815	SUBCLONAL	1	TRUE	1	0.241860673129528	2		424	647	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544075	18544075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	17	363	0	ENST00000266497.5:c.1892G>A	p.Gly631Glu	p.G631E	ENST00000266497		631	gGg/gAg	13/31	1	2	FACETS	0.666	0.498	0.864	0.666	0.498	0.864	SUBCLONAL	1	TRUE	1	0.241860673129528	2		363	211	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573910	18573910	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	22	386	0	ENST00000266497.5:c.2228A>G	p.Gln743Arg	p.Q743R	ENST00000266497		743	cAa/cGa	15/31	1	2	FACETS	0.831	0.646	1	0.831	0.646	1	CLONAL	1	TRUE	1	0.241860673129528	2		386	219	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641563	18641563	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	12	323	0	ENST00000266497.5:c.2562G>T	p.Gln854His	p.Q854H	ENST00000266497		854	caG/caT	17/31	1	2	FACETS	0.447	0.314	0.611	0.447	0.314	0.611	SUBCLONAL	1	TRUE	1	0.241860673129528	2		323	222	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719908	18719908	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	14	333	0	ENST00000266497.5:c.3805T>C	p.Phe1269Leu	p.F1269L	ENST00000266497		1269	Ttt/Ctt	27/31	1	2	FACETS	0.473	0.341	0.631	0.473	0.341	0.631	SUBCLONAL	1	TRUE	1	0.241860673129528	2		333	245	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21626568	21626568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778148225	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	45	383	0	ENST00000421138.2:c.1364G>A	p.Arg455His	p.R455H	ENST00000421138		455	cGt/cAt	13/16	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.241860673129528	2		383	291	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644543	21644543	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	20	370	0	ENST00000421138.2:c.124C>A	p.Leu42Met	p.L42M	ENST00000421138		42	Ctg/Atg	4/16	1	2	FACETS	0.484	0.369	0.618	0.484	0.369	0.618	SUBCLONAL	1	TRUE	1	0.241860673129528	2		370	342	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46240674	46240674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1287100037	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	36	353	0	ENST00000334344.6:c.1534C>T	p.Pro512Ser	p.P512S	ENST00000334344	NM_152641.2	512	Cct/Tct	12/21	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.241860673129528	2		353	222	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244154	46244154	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	81	405	0	ENST00000334344.6:c.2248G>T	p.Gly750Trp	p.G750W	ENST00000334344	NM_152641.2	750	Ggg/Tgg	15/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.241860673129528	2		405	463	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244845	46244845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	58	457	0	ENST00000334344.6:c.2939C>T	p.Thr980Ile	p.T980I	ENST00000334344	NM_152641.2	980	aCt/aTt	15/21	1	2	FACETS	0.662	0.568	0.766	0.662	0.568	0.766	SUBCLONAL	1	TRUE	1	0.241860673129528	2		457	724	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245213	46245213	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	64	415	0	ENST00000334344.6:c.3307A>G	p.Ser1103Gly	p.S1103G	ENST00000334344	NM_152641.2	1103	Agt/Ggt	15/21	1	2	FACETS	0.709	0.613	0.814	0.709	0.613	0.814	SUBCLONAL	1	TRUE	1	0.241860673129528	2		415	746	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285582	46285582	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	73	367	0	ENST00000334344.6:c.4942C>T	p.Gln1648Ter	p.Q1648*	ENST00000334344	NM_152641.2	1648	Cag/Tag	17/21	1	2	FACETS	0.843	0.742	0.95	1	0.979	1	CLONAL	2	TRUE	1	0.241860673129528	2		367	358	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418699	49418699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	60	358	0	ENST00000301067.7:c.15815C>T	p.Ala5272Val	p.A5272V	ENST00000301067	NM_003482.3	5272	gCt/gTt	49/54	1	2	FACETS	0.909	0.783	1	0.909	0.783	1	CLONAL	1	TRUE	1	0.241860673129528	2		358	546	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420229	49420229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	68	439	1	ENST00000301067.7:c.15520C>T	p.Arg5174Trp	p.R5174W	ENST00000301067	NM_003482.3	5174	Cgg/Tgg	48/54	1	2	FACETS	0.749	0.65	0.855	0.749	0.65	0.855	SUBCLONAL	1	TRUE	1	0.241860673129528	2		440	751	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420554	49420554	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587783696	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	65	406	0	ENST00000301067.7:c.15195G>A	p.Trp5065Ter	p.W5065*	ENST00000301067	NM_003482.3	5065	tgG/tgA	48/54	1	2	FACETS	0.674	0.584	0.773	0.674	0.584	0.773	SUBCLONAL	1	TRUE	1	0.241860673129528	2		406	797	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420996	49420996	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	67	378	0	ENST00000301067.7:c.14753C>A	p.Pro4918His	p.P4918H	ENST00000301067	NM_003482.3	4918	cCt/cAt	48/54	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.241860673129528	2		378	552	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49423256	49423256	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	39	379	0	ENST00000301067.7:c.14003C>A	p.Thr4668Asn	p.T4668N	ENST00000301067	NM_003482.3	4668	aCt/aAt	43/54	1	2	FACETS	0.488	0.403	0.583	0.488	0.403	0.583	SUBCLONAL	1	TRUE	1	0.241860673129528	2		379	661	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424179	49424179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	45	268	0	ENST00000301067.7:c.13883C>T	p.Pro4628Leu	p.P4628L	ENST00000301067	NM_003482.3	4628	cCc/cTc	42/54	1	2	FACETS	0.74	0.622	0.87	0.74	0.622	0.87	SUBCLONAL	1	TRUE	1	0.241860673129528	2		268	503	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425616	49425616	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1267264428	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	56	459	0	ENST00000301067.7:c.12872C>T	p.Ala4291Val	p.A4291V	ENST00000301067	NM_003482.3	4291	gCc/gTc	39/54	1	2	FACETS	0.695	0.595	0.805	0.695	0.595	0.805	SUBCLONAL	1	TRUE	1	0.241860673129528	2		459	666	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426038	49426038	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	132	516	0	ENST00000301067.7:c.12450G>T	p.Gln4150His	p.Q4150H	ENST00000301067	NM_003482.3	4150	caG/caT	39/54	1	2	FACETS	0.817	0.743	0.894	1	0.988	1	CLONAL	2	TRUE	1	0.241860673129528	2		516	668	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426239	49426239	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	70	501	0	ENST00000301067.7:c.12249G>T	p.Gln4083His	p.Q4083H	ENST00000301067	NM_003482.3	4083	caG/caT	39/54	1	2	FACETS	0.827	0.72	0.942	0.827	0.72	0.942	CLONAL	1	TRUE	1	0.241860673129528	2		501	700	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431810	49431810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769315900	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	129	508	0	ENST00000301067.7:c.9329G>A	p.Arg3110His	p.R3110H	ENST00000301067	NM_003482.3	3110	cGc/cAc	34/54	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.241860673129528	2		508	724	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434659	49434659	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	61	513	0	ENST00000301067.7:c.6894C>A	p.Ser2298Arg	p.S2298R	ENST00000301067	NM_003482.3	2298	agC/agA	31/54	1	2	FACETS	0.721	0.621	0.829	0.721	0.621	0.829	SUBCLONAL	1	TRUE	1	0.241860673129528	2		513	700	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438587	49438587	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	117	419	0	ENST00000301067.7:c.4903C>A	p.Leu1635Ile	p.L1635I	ENST00000301067	NM_003482.3	1635	Ctt/Att	19/54	1	2	FACETS	0.768	0.694	0.846	1	0.985	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		419	630	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440188	49440188	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	119	420	0	ENST00000301067.7:c.4438T>C	p.Cys1480Arg	p.C1480R	ENST00000301067	NM_003482.3	1480	Tgt/Cgt	16/54	1	2	FACETS	0.762	0.689	0.838	1	0.985	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		420	646	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443602	49443602	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	43	482	0	ENST00000301067.7:c.3769C>A	p.Leu1257Ile	p.L1257I	ENST00000301067	NM_003482.3	1257	Cta/Ata	11/54	1	2	FACETS	0.547	0.457	0.648	0.547	0.457	0.648	SUBCLONAL	1	TRUE	1	0.241860673129528	2		482	650	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443784	49443784	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	57	438	0	ENST00000301067.7:c.3587C>A	p.Pro1196Gln	p.P1196Q	ENST00000301067	NM_003482.3	1196	cCa/cAa	11/54	1	2	FACETS	0.671	0.575	0.777	0.671	0.575	0.777	SUBCLONAL	1	TRUE	1	0.241860673129528	2		438	702	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444887	49444887	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs775496424	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	146	487	0	ENST00000301067.7:c.2579T>C	p.Leu860Pro	p.L860P	ENST00000301067	NM_003482.3	860	cTg/cCg	10/54	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.241860673129528	2		487	810	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445422	49445422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	134	582	0	ENST00000301067.7:c.2044C>T	p.Pro682Ser	p.P682S	ENST00000301067	NM_003482.3	682	Cct/Tct	10/54	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.241860673129528	2		582	852	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446013	49446013	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	65	575	0	ENST00000301067.7:c.1453C>A	p.Leu485Met	p.L485M	ENST00000301067	NM_003482.3	485	Ctg/Atg	10/54	1	2	FACETS	0.61	0.528	0.7	0.61	0.528	0.7	SUBCLONAL	1	TRUE	1	0.241860673129528	2		575	881	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447761	49447761	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	58	377	0	ENST00000301067.7:c.673G>A	p.Glu225Lys	p.E225K	ENST00000301067	NM_003482.3	225	Gag/Aag	5/54	1	2	FACETS	0.827	0.71	0.954	0.827	0.71	0.954	CLONAL	1	TRUE	1	0.241860673129528	2		377	580	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479178	50479178	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	91	381	0	ENST00000394963.4:c.26C>A	p.Ser9Tyr	p.S9Y	ENST00000394963	NM_003076.4	9	tCt/tAt	1/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.241860673129528	2		381	544	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480445	50480445	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	31	431	0	ENST00000394963.4:c.407G>T	p.Arg136Met	p.R136M	ENST00000394963	NM_003076.4	136	aGg/aTg	3/13	1	2	FACETS	0.678	0.549	0.825	0.678	0.549	0.825	SUBCLONAL	1	TRUE	1	0.241860673129528	2		431	378	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50488252	50488252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	53	359	0	ENST00000394963.4:c.1166G>A	p.Cys389Tyr	p.C389Y	ENST00000394963	NM_003076.4	389	tGt/tAt	10/13	1	2	FACETS	0.843	0.719	0.978	0.843	0.719	0.978	CLONAL	1	TRUE	1	0.241860673129528	2		359	520	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488226	56488226	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	115	363	0	ENST00000267101.3:c.1745G>T	p.Gly582Val	p.G582V	ENST00000267101	NM_001982.3	582	gGg/gTg	15/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.241860673129528	2		363	663	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493726	56493726	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	37	466	0	ENST00000267101.3:c.3042C>A	p.Asp1014Glu	p.D1014E	ENST00000267101	NM_001982.3	1014	gaC/gaA	25/28	1	2	FACETS	0.417	0.343	0.501	0.417	0.343	0.501	SUBCLONAL	1	TRUE	1	0.241860673129528	2		466	733	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495049	56495049	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs79759315	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	117	413	0	ENST00000267101.3:c.3406C>T	p.Arg1136Cys	p.R1136C	ENST00000267101	NM_001982.3	1136	Cgc/Tgc	27/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.241860673129528	2		413	738	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144753	58144753	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	170	533	0	ENST00000257904.6:c.475T>G	p.Phe159Val	p.F159V	ENST00000257904	NM_000075.3	159	Ttt/Gtt	4/8	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.241860673129528	2		533	939	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811738	102811738	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	61	536	0	ENST00000307046.8:c.446G>T	p.Arg149Met	p.R149M	ENST00000307046	NM_001111285.1	149	aGg/aTg	4/4	1	2	FACETS	0.662	0.57	0.762	0.662	0.57	0.762	SUBCLONAL	1	TRUE	1	0.241860673129528	2		536	762	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856553	111856553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	33	413	0	ENST00000341259.2:c.604C>T	p.Arg202Cys	p.R202C	ENST00000341259	NM_005475.2	202	Cgc/Tgc	2/8	1	2	FACETS	0.453	0.367	0.549	0.453	0.367	0.549	SUBCLONAL	1	TRUE	1	0.241860673129528	2		413	603	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110101	115110101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1182949304	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	26	325	2	ENST00000257566.3:c.1777G>A	p.Ala593Thr	p.A593T	ENST00000257566	NM_016569.3	593	Gcc/Acc	8/8	1	2	FACETS	0.419	0.331	0.521	0.419	0.331	0.521	SUBCLONAL	1	TRUE	1	0.241860673129528	2		327	513	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114183	115114183	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	57	413	0	ENST00000257566.3:c.1034C>A	p.Ala345Asp	p.A345D	ENST00000257566	NM_016569.3	345	gCt/gAt	6/8	1	2	FACETS	0.652	0.558	0.754	0.652	0.558	0.754	SUBCLONAL	1	TRUE	1	0.241860673129528	2		413	723	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784077	120784077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1210006090	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	48	582	2	ENST00000257552.2:c.908G>A	p.Arg303His	p.R303H	ENST00000257552	NM_002442.3	303	cGc/cAc	13/15	1	2	FACETS	0.568	0.479	0.666	0.568	0.479	0.666	SUBCLONAL	1	TRUE	1	0.241860673129528	2		584	699	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120789177	120789177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759088687	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	108	352	0	ENST00000257552.2:c.760C>T	p.Pro254Ser	p.P254S	ENST00000257552	NM_002442.3	254	Ccg/Tcg	11/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.241860673129528	2		352	610	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210946	133210947	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	123	424	0	ENST00000320574.5:c.5829_5830insT	p.Gly1944TrpfsTer6	p.G1944Wfs*6	ENST00000320574	NM_006231.2	1943	-/T	43/49	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.241860673129528	2		424	737	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218841	133218841	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1256635297	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	113	420	0	ENST00000320574.5:c.5095G>A	p.Ala1699Thr	p.A1699T	ENST00000320574	NM_006231.2	1699	Gct/Act	38/49	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.241860673129528	2		420	732	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219294	133219294	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463404681	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	102	390	0	ENST00000320574.5:c.4750C>T	p.Leu1584Phe	p.L1584F	ENST00000320574	NM_006231.2	1584	Ctc/Ttc	37/49	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.241860673129528	2		390	628	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133234474	133234474	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	46	330	0	ENST00000320574.5:c.3358C>T	p.Gln1120Ter	p.Q1120*	ENST00000320574	NM_006231.2	1120	Caa/Taa	27/49	1	2	FACETS	0.779	0.657	0.915	0.779	0.657	0.915	CLONAL	1	TRUE	1	0.241860673129528	2		330	488	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237642	133237642	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	58	388	0	ENST00000320574.5:c.2973G>T	p.Glu991Asp	p.E991D	ENST00000320574	NM_006231.2	991	gaG/gaT	25/49	1	2	FACETS	0.673	0.577	0.777	0.673	0.577	0.777	SUBCLONAL	1	TRUE	1	0.241860673129528	2		388	713	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250267	133250267	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	102	390	0	ENST00000320574.5:c.1253C>A	p.Pro418His	p.P418H	ENST00000320574	NM_006231.2	418	cCt/cAt	13/49	1	2	FACETS	0.77	0.69	0.853	1	0.983	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		390	548	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549076	21549076	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	90	419	0	ENST00000382592.4:c.3200A>G	p.Glu1067Gly	p.E1067G	ENST00000382592	NM_014572.2	1067	gAg/gGg	8/8	NA	2	FACETS	1	0.953	1			1	INDETERMINATE	1	TRUE	NA	0.241860673129528	2		419	653	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549149	21549149	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1444091389	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	89	524	0	ENST00000382592.4:c.3127C>T	p.Arg1043Ter	p.R1043*	ENST00000382592	NM_014572.2	1043	Cga/Tga	8/8	NA	2	FACETS	1	0.938	1			1	INDETERMINATE	1	TRUE	NA	0.241860673129528	2		524	677	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549289	21549289	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	132	506	0	ENST00000382592.4:c.2987C>A	p.Pro996His	p.P996H	ENST00000382592	NM_014572.2	996	cCc/cAc	8/8	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.241860673129528	2		506	728	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562888	21562888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759368766	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	40	441	1	ENST00000382592.4:c.1031C>T	p.Pro344Leu	p.P344L	ENST00000382592	NM_014572.2	344	cCg/cTg	4/8	NA	2	FACETS	0.48	0.398	0.572			1	INDETERMINATE	1	TRUE	NA	0.241860673129528	2		442	689	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975684	26975684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	111	518	0	ENST00000381527.3:c.1192G>A	p.Gly398Arg	p.G398R	ENST00000381527	NM_001260.1	398	Gga/Aga	12/13	0.205550790292595	0	FACETS	1	0.948	1			1	CLONAL	1	TRUE	0	0.241860673129528	0		518	643	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589802	28589802	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	59	426	0	ENST00000241453.7:c.2578C>A	p.Leu860Met	p.L860M	ENST00000241453	NM_004119.2	860	Ctg/Atg	21/24	0.205550790292595	0	FACETS	0.756	0.652	0.87			1	SUBCLONAL	1	TRUE	0	0.241860673129528	0		426	489	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610151	28610151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	42	368	0	ENST00000241453.7:c.1339G>A	p.Ala447Thr	p.A447T	ENST00000241453	NM_004119.2	447	Gca/Aca	11/24	0.205550790292595	0	FACETS	0.49	0.409	0.581			1	SUBCLONAL	1	TRUE	0	0.241860673129528	0		368	537	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913329	28913329	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	114	415	0	ENST00000282397.4:c.2464T>C	p.Phe822Leu	p.F822L	ENST00000282397	NM_002019.4	822	Ttt/Ctt	17/30	0.205550790292595	0	FACETS	1	0.971	1			1	CLONAL	1	TRUE	0	0.241860673129528	0		415	598	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964223	28964223	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1241074483	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	18	385	0	ENST00000282397.4:c.1679A>G	p.His560Arg	p.H560R	ENST00000282397	NM_002019.4	560	cAt/cGt	13/30	0.205550790292595	0	FACETS	0.392	0.295	0.506			1	SUBCLONAL	1	TRUE	0	0.241860673129528	0		385	288	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29007999	29007999	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	59	403	0	ENST00000282397.4:c.770C>T	p.Pro257Leu	p.P257L	ENST00000282397	NM_002019.4	257	cCc/cTc	6/30	0.205550790292595	0	FACETS	0.831	0.717	0.955			1	CLONAL	1	TRUE	0	0.241860673129528	0		403	445	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906601	32906601	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	52	426	0	ENST00000380152.3:c.986G>T	p.Arg329Met	p.R329M	ENST00000380152		329	aGg/aTg	10/27	0.205550790292595	0	FACETS	0.655	0.563	0.753			1	SUBCLONAL	2	TRUE	0	0.241860673129528	0		426	249	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32920963	32920963	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	19	309	0	ENST00000380152.3:c.6938-1G>T		p.X2313_splice	ENST00000380152		2313			0.205550790292595	0	FACETS	0.882	0.677	1			1	CLONAL	1	TRUE	0	0.241860673129528	0		309	135	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936981	48936981	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	18	308	0	ENST00000267163.4:c.749C>A	p.Pro250His	p.P250H	ENST00000267163	NM_000321.2	250	cCt/cAt	8/27	1	2	FACETS	0.586	0.442	0.756	0.586	0.442	0.756	SUBCLONAL	1	TRUE	1	0.241860673129528	2		308	254	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951056	48951056	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	19	232	0	ENST00000267163.4:c.1218C>A	p.Asn406Lys	p.N406K	ENST00000267163	NM_000321.2	406	aaC/aaA	13/27	1	2	FACETS	1	0.765	1	1	0.765	1	CLONAL	1	TRUE	1	0.241860673129528	2		232	157	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636682	73636682	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	130	498	0	ENST00000377687.4:c.945A>T	p.Gln315His	p.Q315H	ENST00000377687	NM_001730.3	315	caA/caT	2/4	1	2	FACETS	0.781	0.71	0.856	1	0.987	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		498	688	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103498647	103498647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	87	403	0	ENST00000355739.4:c.31G>A	p.Glu11Lys	p.E11K	ENST00000355739	NM_000123.3	11	Gag/Aag	1/15	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.241860673129528	2		403	674	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514647	103514647	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	139	460	0	ENST00000355739.4:c.1148T>C	p.Ile383Thr	p.I383T	ENST00000355739	NM_000123.3	383	aTa/aCa	8/15	1	2	FACETS	0.835	0.762	0.912	1	0.989	1	CLONAL	2	TRUE	1	0.241860673129528	2		460	688	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103520574	103520574	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	33	325	0	ENST00000355739.4:c.2645C>A	p.Pro882His	p.P882H	ENST00000355739	NM_000123.3	882	cCt/cAt	12/15	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.241860673129528	2		325	210	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434533	110434533	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	54	420	0	ENST00000375856.3:c.3868C>A	p.Leu1290Ile	p.L1290I	ENST00000375856	NM_003749.2	1290	Ctc/Atc	1/2	1	2	FACETS	0.641	0.546	0.744	0.641	0.546	0.744	SUBCLONAL	1	TRUE	1	0.241860673129528	2		420	697	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437097	110437097	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	43	313	0	ENST00000375856.3:c.1304T>C	p.Val435Ala	p.V435A	ENST00000375856	NM_003749.2	435	gTg/gCg	1/2	1	2	FACETS	0.938	0.787	1	0.938	0.787	1	CLONAL	1	TRUE	1	0.241860673129528	2		313	379	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066808	30066808	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	32	387	0	ENST00000331968.5:c.2323G>A	p.Val775Ile	p.V775I	ENST00000331968	NM_002742.2	775	Gta/Ata	16/18	1	2	FACETS	0.587	0.476	0.712	0.587	0.476	0.712	SUBCLONAL	1	TRUE	1	0.241860673129528	2		387	451	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352622	68352622	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	50	329	0	ENST00000487270.1:c.489T>A	p.Tyr163Ter	p.Y163*	ENST00000487270	NM_133509.3	163	taT/taA	6/11	1	2	FACETS	0.783	0.67	0.905	1	0.967	1	CLONAL	2	TRUE	1	0.241860673129528	2		329	264	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81534651	81534651	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	18	347	0	ENST00000298171.2:c.296A>C	p.Asn99Thr	p.N99T	ENST00000298171	NM_000369.2	99	aAt/aCt	3/10	1	2	FACETS	0.488	0.367	0.631	0.488	0.367	0.631	SUBCLONAL	1	TRUE	1	0.241860673129528	2		347	305	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610097	81610097	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	61	533	0	ENST00000298171.2:c.1695A>C	p.Lys565Asn	p.K565N	ENST00000298171	NM_000369.2	565	aaA/aaC	10/10	1	2	FACETS	0.657	0.565	0.756	0.657	0.565	0.756	SUBCLONAL	1	TRUE	1	0.241860673129528	2		533	768	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574767	95574767	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	31	380	0	ENST00000393063.1:c.2330T>C	p.Leu777Ser	p.L777S	ENST00000393063	NM_030621.3	777	tTa/tCa	16/28	1	2	FACETS	0.745	0.603	0.905	0.745	0.603	0.905	CLONAL	1	TRUE	1	0.241860673129528	2		380	344	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95579557	95579557	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	21	351	0	ENST00000393063.1:c.1912T>C	p.Cys638Arg	p.C638R	ENST00000393063	NM_030621.3	638	Tgt/Cgt	13/28	1	2	FACETS	0.73	0.563	0.922	0.73	0.563	0.922	CLONAL	1	TRUE	1	0.241860673129528	2		351	238	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95583033	95583033	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	46	362	0	ENST00000393063.1:c.1510-1G>T		p.X504_splice	ENST00000393063	NM_030621.3	504			1	2	FACETS	0.834	0.709	0.969	1	0.968	1	CLONAL	2	TRUE	1	0.241860673129528	2		362	228	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239697	105239697	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	118	418	0	ENST00000349310.3:c.848A>T	p.Asp283Val	p.D283V	ENST00000349310	NM_001014432.1	283	gAc/gTc	11/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.241860673129528	2		418	711	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239890	105239890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1297345295	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	66	429	0	ENST00000349310.3:c.730G>A	p.Val244Met	p.V244M	ENST00000349310	NM_001014432.1	244	Gtg/Atg	10/15	1	2	FACETS	0.7	0.606	0.801	0.7	0.606	0.801	SUBCLONAL	1	TRUE	1	0.241860673129528	2		429	780	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246483	105246483	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	57	394	0	ENST00000349310.3:c.117G>T	p.Lys39Asn	p.K39N	ENST00000349310	NM_001014432.1	39	aaG/aaT	4/15	1	2	FACETS	0.721	0.618	0.833	0.721	0.618	0.833	SUBCLONAL	1	TRUE	1	0.241860673129528	2		394	654	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023406	33023406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1256642631	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	53	427	0	ENST00000300177.4:c.515G>A	p.Arg172His	p.R172H	ENST00000300177	NM_001191322.1	172	cGt/cAt	2/2	1	2	FACETS	0.651	0.554	0.758	0.651	0.554	0.758	SUBCLONAL	1	TRUE	1	0.241860673129528	2		427	673	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41022092	41022092	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	91	347	0	ENST00000267868.3:c.816A>C	p.Gln272His	p.Q272H	ENST00000267868	NM_002875.4	272	caA/caC	9/10	1	2	FACETS	0.836	0.746	0.931	1	0.983	1	CLONAL	2	TRUE	1	0.241860673129528	2		347	450	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003315	42003315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780300588	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	103	509	0	ENST00000219905.7:c.2852C>T	p.Ala951Val	p.A951V	ENST00000219905	NM_001164273.1	951	gCg/gTg	8/24	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.241860673129528	2		509	609	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005461	42005461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778156846	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	175	483	0	ENST00000219905.7:c.3197G>A	p.Arg1066His	p.R1066H	ENST00000219905	NM_001164273.1	1066	cGc/cAc	9/24	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.241860673129528	2		483	996	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041872	42041872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	79	413	0	ENST00000219905.7:c.6067G>A	p.Asp2023Asn	p.D2023N	ENST00000219905	NM_001164273.1	2023	Gat/Aat	17/24	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.241860673129528	2		413	440	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052582	42052582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	149	451	0	ENST00000219905.7:c.7253C>T	p.Ala2418Val	p.A2418V	ENST00000219905	NM_001164273.1	2418	gCa/gTa	20/24	1	2	FACETS	0.844	0.772	0.919	1	0.99	1	CLONAL	2	TRUE	1	0.241860673129528	2		451	730	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058540	42058540	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	21	463	0	ENST00000219905.7:c.8260A>T	p.Ile2754Phe	p.I2754F	ENST00000219905	NM_001164273.1	2754	Att/Ttt	24/24	1	2	FACETS	0.462	0.355	0.587	0.462	0.355	0.587	SUBCLONAL	1	TRUE	1	0.241860673129528	2		463	376	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701209	43701209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	111	466	4	ENST00000382044.4:c.5486C>T	p.Pro1829Leu	p.P1829L	ENST00000382044	NM_001141980.1	1829	cCt/cTt	26/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.241860673129528	2		470	674	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708423	43708423	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	58	407	0	ENST00000382044.4:c.4873G>T	p.Asp1625Tyr	p.D1625Y	ENST00000382044	NM_001141980.1	1625	Gac/Tac	22/28	1	2	FACETS	0.841	0.723	0.971	0.841	0.723	0.971	CLONAL	1	TRUE	1	0.241860673129528	2		407	570	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724622	43724622	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	122	414	0	ENST00000382044.4:c.3445A>G	p.Ile1149Val	p.I1149V	ENST00000382044	NM_001141980.1	1149	Att/Gtt	17/28	1	2	FACETS	0.818	0.741	0.898	1	0.987	1	CLONAL	2	TRUE	1	0.241860673129528	2		414	617	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738719	43738719	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	40	430	0	ENST00000382044.4:c.2906A>G	p.His969Arg	p.H969R	ENST00000382044	NM_001141980.1	969	cAt/cGt	14/28	1	2	FACETS	0.574	0.476	0.684	0.574	0.476	0.684	SUBCLONAL	1	TRUE	1	0.241860673129528	2		430	576	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43739657	43739657	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	33	393	0	ENST00000382044.4:c.2743A>G	p.Lys915Glu	p.K915E	ENST00000382044	NM_001141980.1	915	Aaa/Gaa	13/28	1	2	FACETS	0.716	0.584	0.865	0.716	0.584	0.865	SUBCLONAL	1	TRUE	1	0.241860673129528	2		393	381	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43773181	43773181	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	35	440	0	ENST00000382044.4:c.411G>T	p.Glu137Asp	p.E137D	ENST00000382044	NM_001141980.1	137	gaG/gaT	5/28	1	2	FACETS	0.577	0.472	0.694	0.577	0.472	0.694	SUBCLONAL	1	TRUE	1	0.241860673129528	2		440	502	SUCCESS
B2M	567	MSKCC	GRCh37	15	45008537	45008537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	21	301	0	ENST00000558401.1:c.357G>A	p.Met119Ile	p.M119I	ENST00000558401	NM_004048.2	119	atG/atA	3/4	1	2	FACETS	0.541	0.416	0.686	0.541	0.416	0.686	SUBCLONAL	1	TRUE	1	0.241860673129528	2		301	321	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50769137	50769137	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	37	375	0	ENST00000307179.4:c.941A>C	p.Asn314Thr	p.N314T	ENST00000307179		314	aAt/aCt	9/20	1	2	FACETS	0.688	0.567	0.823	0.688	0.567	0.823	SUBCLONAL	1	TRUE	1	0.241860673129528	2		375	445	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50791272	50791272	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1194842774	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	23	382	0	ENST00000307179.4:c.3344A>T	p.Asp1115Val	p.D1115V	ENST00000307179		1115	gAt/gTt	20/20	1	2	FACETS	0.521	0.406	0.655	0.521	0.406	0.655	SUBCLONAL	1	TRUE	1	0.241860673129528	2		382	365	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727424	66727424	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567009054	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	112	336	0	ENST00000307102.5:c.140G>A	p.Arg47Gln	p.R47Q	ENST00000307102	NM_002755.3	47	cGa/cAa	2/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.241860673129528	2		336	650	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774125	66774125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759605592	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	112	456	0	ENST00000307102.5:c.601C>T	p.Arg201Cys	p.R201C	ENST00000307102	NM_002755.3	201	Cgt/Tgt	6/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.241860673129528	2		456	790	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479778	67479778	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	124	425	0	ENST00000327367.4:c.1085C>T	p.Ala362Val	p.A362V	ENST00000327367	NM_005902.3	362	gCt/gTt	8/9	1	2	FACETS	0.755	0.684	0.83	1	0.985	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		425	679	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996016	73996016	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	57	403	0	ENST00000318443.5:c.750G>T	p.Gln250His	p.Q250H	ENST00000318443	NM_001024736.1	250	caG/caT	5/10	1	2	FACETS	0.752	0.644	0.869	0.752	0.644	0.869	SUBCLONAL	1	TRUE	1	0.241860673129528	2		403	627	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74003485	74003485	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	53	332	0	ENST00000318443.5:c.1556C>A	p.Pro519His	p.P519H	ENST00000318443	NM_001024736.1	519	cCt/cAt	9/10	1	2	FACETS	0.686	0.584	0.798	0.686	0.584	0.798	SUBCLONAL	1	TRUE	1	0.241860673129528	2		332	639	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678508	88678508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs183806623	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	96	439	0	ENST00000360948.2:c.1028G>A	p.Arg343Gln	p.R343Q	ENST00000360948	NM_001012338.2	343	cGg/cAg	9/19	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.241860673129528	2		439	588	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295177	91295177	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	18	251	0	ENST00000355112.3:c.959+1G>A		p.X320_splice	ENST00000355112	NM_000057.2	320			1	2	FACETS	0.855	0.648	1	0.855	0.648	1	CLONAL	1	TRUE	1	0.241860673129528	2		251	174	SUCCESS
BLM	641	MSKCC	GRCh37	15	91306249	91306249	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	27	371	0	ENST00000355112.3:c.1936A>C	p.Ser646Arg	p.S646R	ENST00000355112	NM_000057.2	646	Agt/Cgt	8/22	1	2	FACETS	0.693	0.552	0.854	0.693	0.552	0.854	SUBCLONAL	1	TRUE	1	0.241860673129528	2		371	322	SUCCESS
BLM	641	MSKCC	GRCh37	15	91333968	91333968	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	44	430	0	ENST00000355112.3:c.2913G>T	p.Glu971Asp	p.E971D	ENST00000355112	NM_000057.2	971	gaG/gaT	15/22	1	2	FACETS	0.771	0.647	0.908	0.771	0.647	0.908	CLONAL	1	TRUE	1	0.241860673129528	2		430	472	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251111	99251111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	45	429	0	ENST00000268035.6:c.415G>A	p.Gly139Arg	p.G139R	ENST00000268035	NM_000875.3	139	Ggg/Agg	2/21	1	2	FACETS	0.619	0.52	0.73	0.619	0.52	0.73	SUBCLONAL	1	TRUE	1	0.241860673129528	2		429	601	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251228	99251228	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	116	418	0	ENST00000268035.6:c.532T>C	p.Cys178Arg	p.C178R	ENST00000268035	NM_000875.3	178	Tgt/Cgt	2/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.241860673129528	2		418	652	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465453	99465453	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs70958396	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	135	450	0	ENST00000268035.6:c.2278G>A	p.Ala760Thr	p.A760T	ENST00000268035	NM_000875.3	760	Gca/Aca	11/21	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.241860673129528	2		450	836	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094789	2094789	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	83	335	0	ENST00000219066.1:c.391C>T	p.Gln131Ter	p.Q131*	ENST00000219066	NM_002528.5	131	Cag/Tag	3/6	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.241860673129528	2		335	560	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103409	2103409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372321790	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	86	299	0	ENST00000219476.3:c.292C>T	p.Arg98Trp	p.R98W	ENST00000219476	NM_000548.3	98	Cgg/Tgg	4/42	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.241860673129528	2		299	501	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2107167	2107167	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	117	415	0	ENST00000219476.3:c.836T>C	p.Leu279Pro	p.L279P	ENST00000219476	NM_000548.3	279	cTc/cCc	9/42	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.241860673129528	2		415	665	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127631	2127631	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	54	556	0	ENST00000219476.3:c.2870T>C	p.Leu957Ser	p.L957S	ENST00000219476	NM_000548.3	957	tTg/tCg	26/42	1	2	FACETS	0.534	0.455	0.621	0.534	0.455	0.621	SUBCLONAL	1	TRUE	1	0.241860673129528	2		556	836	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129670	2129670	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1555511031	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	90	416	0	ENST00000219476.3:c.3397G>A	p.Gly1133Arg	p.G1133R	ENST00000219476	NM_000548.3	1133	Ggg/Agg	29/42	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.241860673129528	2		416	634	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135236	2135236	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	53	438	0	ENST00000219476.3:c.4575G>T	p.Gln1525His	p.Q1525H	ENST00000219476	NM_000548.3	1525	caG/caT	36/42	1	2	FACETS	0.717	0.611	0.834	0.717	0.611	0.834	SUBCLONAL	1	TRUE	1	0.241860673129528	2		438	611	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632695	3632695	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	55	402	0	ENST00000294008.3:c.5154-1G>T		p.X1718_splice	ENST00000294008	NM_032444.2	1718			1	2	FACETS	0.683	0.583	0.792	0.683	0.583	0.792	SUBCLONAL	1	TRUE	1	0.241860673129528	2		402	666	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640561	3640561	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	48	524	0	ENST00000294008.3:c.3078G>T	p.Gln1026His	p.Q1026H	ENST00000294008	NM_032444.2	1026	caG/caT	12/15	1	2	FACETS	0.529	0.446	0.62	0.529	0.446	0.62	SUBCLONAL	1	TRUE	1	0.241860673129528	2		524	751	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640580	3640580	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	57	549	0	ENST00000294008.3:c.3059A>G	p.His1020Arg	p.H1020R	ENST00000294008	NM_032444.2	1020	cAt/cGt	12/15	1	2	FACETS	0.599	0.513	0.694	0.599	0.513	0.694	SUBCLONAL	1	TRUE	1	0.241860673129528	2		549	787	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778941	3778941	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	58	501	1	ENST00000262367.5:c.6107C>A	p.Pro2036His	p.P2036H	ENST00000262367	NM_004380.2	2036	cCc/cAc	31/31	1	2	FACETS	0.694	0.595	0.802	0.694	0.595	0.802	SUBCLONAL	1	TRUE	1	0.241860673129528	2		502	691	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779058	3779058	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758101123	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	59	478	0	ENST00000262367.5:c.5990C>T	p.Pro1997Leu	p.P1997L	ENST00000262367	NM_004380.2	1997	cCc/cTc	31/31	1	2	FACETS	0.747	0.642	0.862	0.747	0.642	0.862	SUBCLONAL	1	TRUE	1	0.241860673129528	2		478	653	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781382	3781382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	149	410	0	ENST00000262367.5:c.4983G>A	p.Met1661Ile	p.M1661I	ENST00000262367	NM_004380.2	1661	atG/atA	30/31	1	2	FACETS	0.866	0.793	0.943	1	0.99	1	CLONAL	2	TRUE	1	0.241860673129528	2		410	711	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781810	3781810	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	149	422	0	ENST00000262367.5:c.4857G>T	p.Gln1619His	p.Q1619H	ENST00000262367	NM_004380.2	1619	caG/caT	29/31	1	2	FACETS	0.777	0.71	0.846	1	0.988	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		422	793	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807833	3807833	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	89	393	0	ENST00000262367.5:c.3586C>A	p.Leu1196Ile	p.L1196I	ENST00000262367	NM_004380.2	1196	Ctt/Att	18/31	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.241860673129528	2		393	590	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819203	3819203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	60	366	0	ENST00000262367.5:c.3032G>A	p.Gly1011Asp	p.G1011D	ENST00000262367	NM_004380.2	1011	gGt/gAt	15/31	1	2	FACETS	0.757	0.652	0.872	0.757	0.652	0.872	SUBCLONAL	1	TRUE	1	0.241860673129528	2		366	655	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831226	3831226	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398406959	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	41	308	0	ENST00000262367.5:c.1655C>T	p.Pro552Leu	p.P552L	ENST00000262367	NM_004380.2	552	cCg/cTg	7/31	1	2	FACETS	0.623	0.518	0.74	0.623	0.518	0.74	SUBCLONAL	1	TRUE	1	0.241860673129528	2		308	544	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832915	3832915	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	88	358	1	ENST00000262367.5:c.1343C>A	p.Ser448Tyr	p.S448Y	ENST00000262367	NM_004380.2	448	tCt/tAt	6/31	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.241860673129528	2		359	491	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860753	3860753	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	31	354	0	ENST00000262367.5:c.826T>C	p.Phe276Leu	p.F276L	ENST00000262367	NM_004380.2	276	Ttt/Ctt	3/31	1	2	FACETS	0.542	0.438	0.66	0.542	0.438	0.66	SUBCLONAL	1	TRUE	1	0.241860673129528	2		354	473	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024728	14024728	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	58	324	0	ENST00000311895.7:c.954A>C	p.Lys318Asn	p.K318N	ENST00000311895	NM_005236.2	318	aaA/aaC	5/11	1	2	FACETS	0.919	0.797	1	1	0.977	1	CLONAL	2	TRUE	1	0.241860673129528	2		324	261	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029115	14029115	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	80	381	0	ENST00000311895.7:c.1326G>T	p.Lys442Asn	p.K442N	ENST00000311895	NM_005236.2	442	aaG/aaT	8/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.241860673129528	2		381	501	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646629	23646629	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	41	401	0	ENST00000261584.4:c.1238C>T	p.Thr413Ile	p.T413I	ENST00000261584	NM_024675.3	413	aCa/aTa	4/13	1	2	FACETS	0.702	0.585	0.832	0.702	0.585	0.832	SUBCLONAL	1	TRUE	1	0.241860673129528	2		401	483	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128576	30128576	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	50	441	0	ENST00000263025.4:c.806T>C	p.Leu269Pro	p.L269P	ENST00000263025	NM_002746.2	269	cTg/cCg	6/9	1	2	FACETS	0.678	0.574	0.792	0.678	0.574	0.792	SUBCLONAL	1	TRUE	1	0.241860673129528	2		441	610	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50811750	50811750	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	15	307	0	ENST00000398568.2:c.1027C>A	p.Pro343Thr	p.P343T	ENST00000398568	NM_001042412.1	343	Cct/Act	7/18	1	2	FACETS	0.674	0.495	0.888	0.674	0.495	0.888	SUBCLONAL	1	TRUE	1	0.241860673129528	2		307	184	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868166	56868166	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	108	457	0	ENST00000308159.5:c.1664G>T	p.Arg555Met	p.R555M	ENST00000308159	NM_014669.4	555	aGg/aTg	14/22	1	2	FACETS	0.782	0.704	0.864	1	0.984	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		457	571	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063693	67063693	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	41	334	0	ENST00000412916.2:c.142T>C	p.Cys48Arg	p.C48R	ENST00000412916		48	Tgc/Cgc	2/6	1	2	FACETS	0.582	0.484	0.691	0.582	0.484	0.691	SUBCLONAL	1	TRUE	1	0.241860673129528	2		334	583	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644779	67644779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1304440183	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	67	488	0	ENST00000264010.4:c.44C>T	p.Thr15Ile	p.T15I	ENST00000264010	NM_006565.3	15	aCt/aTt	3/12	1	2	FACETS	0.836	0.726	0.955	0.836	0.726	0.955	CLONAL	1	TRUE	1	0.241860673129528	2		488	663	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644798	67644798	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	130	495	0	ENST00000264010.4:c.63G>T	p.Glu21Asp	p.E21D	ENST00000264010	NM_006565.3	21	gaG/gaT	3/12	1	2	FACETS	0.782	0.711	0.857	1	0.987	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		495	687	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847221	68847221	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	84	353	0	ENST00000261769.5:c.1143G>T	p.Lys381Asn	p.K381N	ENST00000261769	NM_004360.3	381	aaG/aaT	9/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.241860673129528	2		353	559	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856035	68856035	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1003012321	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	111	485	0	ENST00000261769.5:c.1843A>G	p.Ile615Val	p.I615V	ENST00000261769	NM_004360.3	615	Att/Gtt	12/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.241860673129528	2		485	612	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822135	72822135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194146935	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	112	492	1	ENST00000268489.5:c.10040C>T	p.Ala3347Val	p.A3347V	ENST00000268489	NM_006885.3	3347	gCa/gTa	10/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.241860673129528	2		493	724	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828910	72828910	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1162760672	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	111	429	0	ENST00000268489.5:c.7671G>T	p.Gln2557His	p.Q2557H	ENST00000268489	NM_006885.3	2557	caG/caT	9/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.241860673129528	2		429	770	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845865	72845865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	40	433	0	ENST00000268489.5:c.3602G>A	p.Ser1201Asn	p.S1201N	ENST00000268489	NM_006885.3	1201	aGc/aAc	6/10	1	2	FACETS	0.449	0.372	0.536	0.449	0.372	0.536	SUBCLONAL	1	TRUE	1	0.241860673129528	2		433	736	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992654	72992654	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	97	480	0	ENST00000268489.5:c.1391A>G	p.Glu464Gly	p.E464G	ENST00000268489	NM_006885.3	464	gAg/gGg	2/10	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.241860673129528	2		480	746	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942061	81942061	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	36	411	0	ENST00000359376.3:c.1598T>C	p.Phe533Ser	p.F533S	ENST00000359376	NM_002661.3	533	tTc/tCc	17/33	1	2	FACETS	0.499	0.409	0.6	0.499	0.409	0.6	SUBCLONAL	1	TRUE	1	0.241860673129528	2		411	597	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81962197	81962197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	24	373	0	ENST00000359376.3:c.2549G>A	p.Arg850Lys	p.R850K	ENST00000359376	NM_002661.3	850	aGa/aAa	24/33	1	2	FACETS	0.456	0.357	0.571	0.456	0.357	0.571	SUBCLONAL	1	TRUE	1	0.241860673129528	2		373	435	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990331	81990331	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768299957	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	74	423	0	ENST00000359376.3:c.3602G>A	p.Arg1201His	p.R1201H	ENST00000359376	NM_002661.3	1201	cGc/cAc	32/33	1	2	FACETS	0.88	0.77	0.999	0.88	0.77	0.999	CLONAL	1	TRUE	1	0.241860673129528	2		423	695	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346225	89346225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372632879	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	40	431	0	ENST00000301030.4:c.6725C>T	p.Ala2242Val	p.A2242V	ENST00000301030	NM_001256183.1	2242	gCg/gTg	9/13	1	2	FACETS	0.517	0.428	0.616	0.517	0.428	0.616	SUBCLONAL	1	TRUE	1	0.241860673129528	2		431	640	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347059	89347059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	58	489	0	ENST00000301030.4:c.5891G>A	p.Gly1964Glu	p.G1964E	ENST00000301030	NM_001256183.1	1964	gGg/gAg	9/13	1	2	FACETS	0.68	0.584	0.786	0.68	0.584	0.786	SUBCLONAL	1	TRUE	1	0.241860673129528	2		489	705	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348118	89348118	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	55	458	0	ENST00000301030.4:c.4832T>G	p.Leu1611Arg	p.L1611R	ENST00000301030	NM_001256183.1	1611	cTg/cGg	9/13	1	2	FACETS	0.661	0.565	0.767	0.661	0.565	0.767	SUBCLONAL	1	TRUE	1	0.241860673129528	2		458	688	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349291	89349291	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	121	481	0	ENST00000301030.4:c.3659G>T	p.Arg1220Met	p.R1220M	ENST00000301030	NM_001256183.1	1220	aGg/aTg	9/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.241860673129528	2		481	822	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351506	89351506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	61	494	0	ENST00000301030.4:c.1444G>A	p.Glu482Lys	p.E482K	ENST00000301030	NM_001256183.1	482	Gag/Aag	9/13	1	2	FACETS	0.727	0.626	0.837	0.727	0.626	0.837	SUBCLONAL	1	TRUE	1	0.241860673129528	2		494	694	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816234	89816234	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	61	390	0	ENST00000389301.3:c.3143T>C	p.Leu1048Pro	p.L1048P	ENST00000389301	NM_000135.2	1048	cTc/cCc	32/43	1	2	FACETS	0.72	0.62	0.828	0.72	0.62	0.828	SUBCLONAL	1	TRUE	1	0.241860673129528	2		390	701	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831398	89831398	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	98	446	0	ENST00000389301.3:c.2678G>A	p.Trp893Ter	p.W893*	ENST00000389301	NM_000135.2	893	tGg/tAg	28/43	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.241860673129528	2		446	731	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838183	89838183	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	56	461	0	ENST00000389301.3:c.2054G>T	p.Arg685Met	p.R685M	ENST00000389301	NM_000135.2	685	aGg/aTg	23/43	1	2	FACETS	0.633	0.541	0.733	0.633	0.541	0.733	SUBCLONAL	1	TRUE	1	0.241860673129528	2		461	732	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89839742	89839742	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	104	448	0	ENST00000389301.3:c.1951G>T	p.Gly651Ter	p.G651*	ENST00000389301	NM_000135.2	651	Gga/Tga	22/43	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.241860673129528	2		448	651	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990682	7990682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	39	305	0	ENST00000319144.4:c.79G>A	p.Val27Met	p.V27M	ENST00000319144	NM_001139.2	27	Gtg/Atg	1/15	1	2	FACETS	0.568	0.47	0.677	0.568	0.47	0.677	SUBCLONAL	1	TRUE	1	0.241860673129528	2		305	568	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028644	12028644	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	36	383	0	ENST00000353533.5:c.847G>T	p.Gly283Ter	p.G283*	ENST00000353533	NM_003010.3	283	Gga/Tga	8/11	1	2	FACETS	0.616	0.506	0.74	0.616	0.506	0.74	SUBCLONAL	1	TRUE	1	0.241860673129528	2		383	483	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044531	12044531	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	36	341	0	ENST00000353533.5:c.1154T>C	p.Leu385Pro	p.L385P	ENST00000353533	NM_003010.3	385	cTg/cCg	11/11	1	2	FACETS	0.68	0.559	0.815	0.68	0.559	0.815	SUBCLONAL	1	TRUE	1	0.241860673129528	2		341	438	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942951	15942951	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	98	422	0	ENST00000268712.3:c.6751G>T	p.Gly2251Cys	p.G2251C	ENST00000268712	NM_006311.3	2251	Ggc/Tgc	44/46	1	2	FACETS	0.784	0.702	0.87	1	0.983	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		422	517	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960987	15960987	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	32	310	0	ENST00000268712.3:c.6233C>T	p.Thr2078Ile	p.T2078I	ENST00000268712	NM_006311.3	2078	aCt/aTt	40/46	1	2	FACETS	0.577	0.467	0.7	0.577	0.467	0.7	SUBCLONAL	1	TRUE	1	0.241860673129528	2		310	459	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968805	15968805	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	105	401	0	ENST00000268712.3:c.4945A>G	p.Thr1649Ala	p.T1649A	ENST00000268712	NM_006311.3	1649	Acg/Gcg	33/46	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.241860673129528	2		401	632	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483086	29483086	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	28	374	0	ENST00000356175.3:c.146A>G	p.Tyr49Cys	p.Y49C	ENST00000356175	NM_000267.3	49	tAc/tGc	2/57	1	2	FACETS	0.774	0.62	0.949	0.774	0.62	0.949	CLONAL	1	TRUE	1	0.241860673129528	2		374	299	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553503	29553503	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	70	388	0	ENST00000356175.3:c.2052G>T	p.Gln684His	p.Q684H	ENST00000356175	NM_000267.3	684	caG/caT	18/57	1	2	FACETS	0.897	0.782	1	0.897	0.782	1	CLONAL	1	TRUE	1	0.241860673129528	2		388	645	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654666	29654666	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	78	444	0	ENST00000356175.3:c.5355G>T	p.Gln1785His	p.Q1785H	ENST00000356175	NM_000267.3	1785	caG/caT	37/57	1	2	FACETS	0.846	0.743	0.958	0.846	0.743	0.958	CLONAL	1	TRUE	1	0.241860673129528	2		444	762	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657466	29657466	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	35	358	0	ENST00000356175.3:c.5699A>G	p.His1900Arg	p.H1900R	ENST00000356175	NM_000267.3	1900	cAc/cGc	38/57	1	2	FACETS	0.891	0.732	1	0.891	0.732	1	CLONAL	1	TRUE	1	0.241860673129528	2		358	325	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676137	29676137	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	21	355	0	ENST00000356175.3:c.7127-1G>T		p.X2376_splice	ENST00000356175	NM_000267.3	2376			1	2	FACETS	0.591	0.455	0.749	0.591	0.455	0.749	SUBCLONAL	1	TRUE	1	0.241860673129528	2		355	294	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683557	29683558	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1060500295	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	44	392	0	ENST00000356175.3:c.7638dup	p.Lys2547GlnfsTer9	p.K2547Qfs*9	ENST00000356175	NM_000267.3	2544	-/C	51/57	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.241860673129528	2		392	272	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264493	30264493	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	79	301	0	ENST00000322652.5:c.228G>A	p.Met76Ile	p.M76I	ENST00000322652	NM_015355.2	76	atG/atA	1/16	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.241860673129528	2		301	443	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679652	33679652	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	35	438	0	ENST00000308377.4:c.2429C>A	p.Ala810Asp	p.A810D	ENST00000308377	NM_152270.3	810	gCt/gAt	5/5	1	2	FACETS	0.462	0.378	0.558	0.462	0.378	0.558	SUBCLONAL	1	TRUE	1	0.241860673129528	2		438	626	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618662	37618662	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs754105952	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	82	485	0	ENST00000447079.4:c.338A>G	p.His113Arg	p.H113R	ENST00000447079	NM_015083.1	113	cAc/cGc	1/14	1	2	FACETS	0.752	0.662	0.849	0.752	0.662	0.849	SUBCLONAL	1	TRUE	1	0.241860673129528	2		485	902	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627195	37627196	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	73	420	0	ENST00000447079.4:c.1115dup	p.Lys373GlufsTer20	p.K373Efs*20	ENST00000447079	NM_015083.1	370	-/A	2/14	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.241860673129528	2		420	436	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649087	37649087	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	31	386	0	ENST00000447079.4:c.2192G>T	p.Gly731Val	p.G731V	ENST00000447079	NM_015083.1	731	gGg/gTg	4/14	1	2	FACETS	0.668	0.54	0.812	0.668	0.54	0.812	SUBCLONAL	1	TRUE	1	0.241860673129528	2		386	384	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687471	37687472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs760014508	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	38	437	2	ENST00000447079.4:c.4382dup	p.Thr1463AsnfsTer50	p.T1463Nfs*50	ENST00000447079	NM_015083.1	1459	tgg/tGgg	14/14	1	2	FACETS	0.429	0.353	0.514	0.429	0.353	0.514	SUBCLONAL	1	TRUE	1	0.241860673129528	2		439	733	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884178	37884178	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	127	421	0	ENST00000269571.5:c.3649T>G	p.Phe1217Val	p.F1217V	ENST00000269571		1217	Ttc/Gtc	27/27	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.241860673129528	2		421	733	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38504571	38504571	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1410890791	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	42	385	0	ENST00000254066.5:c.182T>C	p.Ile61Thr	p.I61T	ENST00000254066	NM_000964.3	61	aTt/aCt	3/9	1	2	FACETS	0.637	0.531	0.755	0.637	0.531	0.755	SUBCLONAL	1	TRUE	1	0.241860673129528	2		385	545	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508730	38508730	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	34	345	0	ENST00000254066.5:c.778C>A	p.Leu260Ile	p.L260I	ENST00000254066	NM_000964.3	260	Ctc/Atc	6/9	1	2	FACETS	0.421	0.343	0.509	0.421	0.343	0.509	SUBCLONAL	1	TRUE	1	0.241860673129528	2		345	668	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38788569	38788569	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	107	318	0	ENST00000348513.6:c.592A>G	p.Arg198Gly	p.R198G	ENST00000348513	NM_003079.4	198	Aga/Gga	8/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.241860673129528	2		318	599	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40451842	40451842	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	27	82	0	ENST00000345506.4:c.624G>T	p.Gln208His	p.Q208H	ENST00000345506	NM_003152.3	208	caG/caT	7/20	1	2	FACETS	0.759	0.612	0.923	1	0.939	1	CLONAL	2	TRUE	1	0.241860673129528	2		82	147	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453327	40453327	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	126	419	0	ENST00000345506.4:c.1024C>A	p.Leu342Met	p.L342M	ENST00000345506	NM_003152.3	342	Ctg/Atg	10/20	1	2	FACETS	0.827	0.751	0.907	1	0.987	1	CLONAL	2	TRUE	1	0.241860673129528	2		419	630	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459475	40459475	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	129	392	0	ENST00000345506.4:c.1736A>C	p.Glu579Ala	p.E579A	ENST00000345506	NM_003152.3	579	gAg/gCg	15/20	1	2	FACETS	0.791	0.719	0.867	1	0.987	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		392	674	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474364	40474364	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	134	414	0	ENST00000264657.5:c.2037G>T	p.Lys679Asn	p.K679N	ENST00000264657	NM_139276.2	679	aaG/aaT	21/24	1	2	FACETS	0.795	0.723	0.87	1	0.987	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		414	697	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474386	40474386	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	104	405	0	ENST00000264657.5:c.2015A>G	p.Tyr672Cys	p.Y672C	ENST00000264657	NM_139276.2	672	tAt/tGt	21/24	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.241860673129528	2		405	621	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485692	40485692	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	33	326	0	ENST00000264657.5:c.1048A>G	p.Arg350Gly	p.R350G	ENST00000264657	NM_139276.2	350	Agg/Ggg	10/24	1	2	FACETS	0.437	0.355	0.531	0.437	0.355	0.531	SUBCLONAL	1	TRUE	1	0.241860673129528	2		326	624	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865256	40865256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	63	369	0	ENST00000428826.2:c.1175C>T	p.Thr392Ile	p.T392I	ENST00000428826		392	aCa/aTa	11/21	1	2	FACETS	0.894	0.773	1	0.894	0.773	1	CLONAL	1	TRUE	1	0.241860673129528	2		369	583	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40871123	40871123	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	56	264	0	ENST00000428826.2:c.767G>T	p.Arg256Met	p.R256M	ENST00000428826		256	aGg/aTg	8/21	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.241860673129528	2		264	338	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226539	41226539	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs80358189	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	86	470	0	ENST00000357654.3:c.4485-1G>T		p.X1495_splice	ENST00000357654	NM_007294.3	1495			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.241860673129528	2		470	524	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243030	41243030	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs397509140	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	49	421	0	ENST00000357654.3:c.4116T>A	p.Cys1372Ter	p.C1372*	ENST00000357654	NM_007294.3	1372	tgT/tgA	11/23	1	2	FACETS	0.734	0.621	0.858	0.734	0.621	0.858	SUBCLONAL	1	TRUE	1	0.241860673129528	2		421	552	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243508	41243508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80357210	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	80	421	0	ENST00000357654.3:c.4040G>A	p.Arg1347Lys	p.R1347K	ENST00000357654	NM_007294.3	1347	aGa/aAa	10/23	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.241860673129528	2		421	471	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243670	41243670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357213	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	40	444	0	ENST00000357654.3:c.3878C>T	p.Ala1293Val	p.A1293V	ENST00000357654	NM_007294.3	1293	gCt/gTt	10/23	1	2	FACETS	0.73	0.607	0.867	0.73	0.607	0.867	SUBCLONAL	1	TRUE	1	0.241860673129528	2		444	453	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699375	47699375	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	56	413	0	ENST00000347630.2:c.133C>T	p.Arg45Trp	p.R45W	ENST00000347630	NM_001007230.1	45	Cgg/Tgg	4/11	1	2	FACETS	0.764	0.659	0.877	1	0.969	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		413	303	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55704655	55704655	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	111	339	0	ENST00000284073.2:c.718C>T	p.Gln240Ter	p.Q240*	ENST00000284073	NM_138962.2	240	Cag/Tag	10/14	1	2	FACETS	0.777	0.7	0.857	1	0.984	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		339	591	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438175	56438175	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	40	458	0	ENST00000407977.2:c.818C>A	p.Ala273Asp	p.A273D	ENST00000407977		273	gCc/gAc	7/10	1	2	FACETS	0.514	0.426	0.613	0.514	0.426	0.613	SUBCLONAL	1	TRUE	1	0.241860673129528	2		458	643	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770108	56770108	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	44	356	0	ENST00000337432.4:c.104C>A	p.Ala35Asp	p.A35D	ENST00000337432	NM_058216.2	35	gCt/gAt	1/9	1	2	FACETS	0.576	0.482	0.68	0.576	0.482	0.68	SUBCLONAL	1	TRUE	1	0.241860673129528	2		356	632	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740540	58740540	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	78	434	0	ENST00000305921.3:c.1445T>C	p.Leu482Pro	p.L482P	ENST00000305921	NM_003620.3	482	cTg/cCg	6/6	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.241860673129528	2		434	489	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007723	62007723	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	119	389	0	ENST00000392795.3:c.144G>A	p.Trp48Ter	p.W48*	ENST00000392795	NM_001039933.1	48	tgG/tgA	3/6	1	2	FACETS	0.797	0.722	0.877	1	0.986	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		389	617	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530191	63530191	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	35	370	0	ENST00000307078.5:c.2244A>C	p.Lys748Asn	p.K748N	ENST00000307078	NM_004655.3	748	aaA/aaC	10/11	1	2	FACETS	0.447	0.365	0.539	0.447	0.365	0.539	SUBCLONAL	1	TRUE	1	0.241860673129528	2		370	648	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533625	63533625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367938045	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	139	404	0	ENST00000307078.5:c.1529C>T	p.Thr510Met	p.T510M	ENST00000307078	NM_004655.3	510	aCg/aTg	6/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.241860673129528	2		404	775	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545767	63545767	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	58	393	0	ENST00000307078.5:c.827G>T	p.Arg276Met	p.R276M	ENST00000307078	NM_004655.3	276	aGg/aTg	3/11	1	2	FACETS	0.838	0.72	0.967	0.838	0.72	0.967	CLONAL	1	TRUE	1	0.241860673129528	2		393	572	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554536	63554536	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	59	497	0	ENST00000307078.5:c.203G>T	p.Arg68Leu	p.R68L	ENST00000307078	NM_004655.3	68	cGg/cTg	2/11	1	2	FACETS	0.611	0.524	0.705	0.611	0.524	0.705	SUBCLONAL	1	TRUE	1	0.241860673129528	2		497	799	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796024	78796024	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	115	358	1	ENST00000306801.3:c.914G>T	p.Arg305Met	p.R305M	ENST00000306801	NM_020761.2	305	aGg/aTg	8/34	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.241860673129528	2		359	658	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796063	78796063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	134	394	0	ENST00000306801.3:c.953C>T	p.Ala318Val	p.A318V	ENST00000306801	NM_020761.2	318	gCc/gTc	8/34	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.241860673129528	2		394	774	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78882689	78882689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393327607	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	54	372	0	ENST00000306801.3:c.2480C>T	p.Ser827Leu	p.S827L	ENST00000306801	NM_020761.2	827	tCg/tTg	21/34	1	2	FACETS	0.677	0.577	0.786	0.677	0.577	0.786	SUBCLONAL	1	TRUE	1	0.241860673129528	2		372	660	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78882698	78882698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1244520756	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	119	356	0	ENST00000306801.3:c.2489C>T	p.Ala830Val	p.A830V	ENST00000306801	NM_020761.2	830	gCc/gTc	21/34	1	2	FACETS	0.756	0.683	0.832	1	0.985	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		356	651	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897410	78897410	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	145	532	0	ENST00000306801.3:c.2745G>T	p.Gln915His	p.Q915H	ENST00000306801	NM_020761.2	915	caG/caT	23/34	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.241860673129528	2		532	818	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743082	743082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	21	415	0	ENST00000314574.4:c.896C>T	p.Thr299Ile	p.T299I	ENST00000314574	NM_005433.3	299	aCc/aTc	8/12	0.241860673129528	1	FACETS	0.616	0.475	0.779	0.616	0.475	0.779	SUBCLONAL	1	TRUE	0	0.241860673129528	1		415	248	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745957	745957	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	25	410	0	ENST00000314574.4:c.565A>C	p.Thr189Pro	p.T189P	ENST00000314574	NM_005433.3	189	Aca/Cca	5/12	0.241860673129528	1	FACETS	0.794	0.628	0.982	0.794	0.628	0.982	CLONAL	1	TRUE	0	0.241860673129528	1		410	229	SUCCESS
YES1	7525	MSKCC	GRCh37	18	751766	751766	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	20	228	0	ENST00000314574.4:c.310G>A	p.Ala104Thr	p.A104T	ENST00000314574	NM_005433.3	104	Gct/Act	3/12	0.241860673129528	1	FACETS	0.831	0.639	1	0.831	0.639	1	CLONAL	1	TRUE	0	0.241860673129528	1		228	175	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39576618	39576618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	11	313	0	ENST00000262039.4:c.908C>T	p.Pro303Leu	p.P303L	ENST00000262039	NM_002647.2	303	cCa/cTa	9/25	0.241860673129528	1	FACETS	0.47	0.325	0.65	0.47	0.325	0.65	SUBCLONAL	1	TRUE	0	0.241860673129528	1		313	170	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617690	39617690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141329274	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	22	351	0	ENST00000262039.4:c.1874C>T	p.Thr625Met	p.T625M	ENST00000262039	NM_002647.2	625	aCg/aTg	17/25	0.241860673129528	1	FACETS	0.73	0.568	0.917	0.73	0.568	0.917	CLONAL	1	TRUE	0	0.241860673129528	1		351	219	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368284	45368284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	36	381	0	ENST00000262160.6:c.1318C>T	p.Leu440Phe	p.L440F	ENST00000262160	NM_005901.5	440	Ctt/Ttt	11/11	0.241860673129528	1	FACETS	0.715	0.589	0.856	0.715	0.589	0.856	SUBCLONAL	1	TRUE	0	0.241860673129528	1		381	366	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374984	45374984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	39	412	0	ENST00000262160.6:c.859G>A	p.Gly287Arg	p.G287R	ENST00000262160	NM_005901.5	287	Gga/Aga	8/11	0.241860673129528	1	FACETS	0.836	0.695	0.993	0.836	0.695	0.993	CLONAL	1	TRUE	0	0.241860673129528	1		412	339	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45423017	45423017	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	73	439	0	ENST00000262160.6:c.111A>C	p.Glu37Asp	p.E37D	ENST00000262160	NM_005901.5	37	gaA/gaC	2/11	0.241860673129528	1	FACETS	0.849	0.743	0.964	0.849	0.743	0.964	CLONAL	1	TRUE	0	0.241860673129528	1		439	625	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56338949	56338949	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	25	370	0	ENST00000348428.3:c.74C>A	p.Pro25Gln	p.P25Q	ENST00000348428	NM_006785.3	25	cCg/cAg	1/17	0.241860673129528	1	FACETS	0.412	0.324	0.514	0.412	0.324	0.514	SUBCLONAL	1	TRUE	0	0.241860673129528	1		370	441	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985626	60985626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	100	398	0	ENST00000333681.4:c.274G>A	p.Val92Met	p.V92M	ENST00000333681		92	Gtg/Atg	2/3	0.241860673129528	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.241860673129528	1		398	531	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61306889	61306889	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1290205333	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	20	441	0	ENST00000341074.5:c.591G>T	p.Glu197Asp	p.E197D	ENST00000341074	NM_002974.2	197	gaG/gaT	6/8	0.241860673129528	1	FACETS	0.591	0.453	0.752	0.591	0.453	0.752	SUBCLONAL	1	TRUE	0	0.241860673129528	1		441	246	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61306930	61306930	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	32	511	0	ENST00000341074.5:c.550G>T	p.Gly184Trp	p.G184W	ENST00000341074	NM_002974.2	184	Ggg/Tgg	6/8	0.241860673129528	1	FACETS	0.75	0.611	0.907	0.75	0.611	0.907	CLONAL	1	TRUE	0	0.241860673129528	1		511	310	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61310697	61310697	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	42	224	0	ENST00000341074.5:c.115G>T	p.Gly39Trp	p.G39W	ENST00000341074	NM_002974.2	39	Ggg/Tgg	2/8	0.241860673129528	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.241860673129528	1		224	255	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61323151	61323151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	49	333	0	ENST00000283752.5:c.913G>A	p.Val305Met	p.V305M	ENST00000283752	NM_006919.2	305	Gtg/Atg	8/8	0.241860673129528	1	FACETS	0.693	0.587	0.81	0.693	0.587	0.81	SUBCLONAL	1	TRUE	0	0.241860673129528	1		333	514	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213912	2213912	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	41	435	0	ENST00000398665.3:c.1724A>G	p.Asn575Ser	p.N575S	ENST00000398665	NM_032482.2	575	aAc/aGc	18/28	1	2	FACETS	0.466	0.387	0.554	0.466	0.387	0.554	SUBCLONAL	1	TRUE	1	0.241860673129528	2		435	728	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2214578	2214578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	43	419	0	ENST00000398665.3:c.1906C>T	p.His636Tyr	p.H636Y	ENST00000398665	NM_032482.2	636	Cac/Tac	19/28	1	2	FACETS	0.542	0.452	0.642	0.542	0.452	0.642	SUBCLONAL	1	TRUE	1	0.241860673129528	2		419	656	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216413	2216413	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	50	471	0	ENST00000398665.3:c.2057A>G	p.Asp686Gly	p.D686G	ENST00000398665	NM_032482.2	686	gAc/gGc	20/28	1	2	FACETS	0.654	0.554	0.764	0.654	0.554	0.764	SUBCLONAL	1	TRUE	1	0.241860673129528	2		471	632	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118995	3118995	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	126	442	0	ENST00000078429.4:c.679A>G	p.Met227Val	p.M227V	ENST00000078429	NM_002067.2	227	Atg/Gtg	5/7	1	2	FACETS	0.804	0.73	0.882	1	0.987	1	CLONAL	2	TRUE	1	0.241860673129528	2		442	648	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212483	5212483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754177433	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	43	377	0	ENST00000357368.4:c.4634G>A	p.Arg1545His	p.R1545H	ENST00000357368	NM_002850.3	1545	cGc/cAc	31/38	1	2	FACETS	0.524	0.437	0.62	0.524	0.437	0.62	SUBCLONAL	1	TRUE	1	0.241860673129528	2		377	679	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222721	5222721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769764410	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	33	337	0	ENST00000357368.4:c.3082C>T	p.Arg1028Trp	p.R1028W	ENST00000357368	NM_002850.3	1028	Cgg/Tgg	18/38	1	2	FACETS	0.501	0.407	0.607	0.501	0.407	0.607	SUBCLONAL	1	TRUE	1	0.241860673129528	2		337	545	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223167	5223167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	132	472	0	ENST00000357368.4:c.2636C>T	p.Ala879Val	p.A879V	ENST00000357368	NM_002850.3	879	gCc/gTc	18/38	1	2	FACETS	0.833	0.758	0.912	1	0.988	1	CLONAL	2	TRUE	1	0.241860673129528	2		472	655	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231384	5231384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778710485	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	80	416	0	ENST00000357368.4:c.2092G>A	p.Ala698Thr	p.A698T	ENST00000357368	NM_002850.3	698	Gct/Act	14/38	1	2	FACETS	0.792	0.696	0.896	0.792	0.696	0.896	SUBCLONAL	1	TRUE	1	0.241860673129528	2		416	835	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244448	5244448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	120	477	0	ENST00000357368.4:c.1034C>T	p.Ala345Val	p.A345V	ENST00000357368	NM_002850.3	345	gCc/gTc	11/38	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.241860673129528	2		477	737	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6222447	6222447	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	53	411	0	ENST00000252674.7:c.795C>A	p.Ser265Arg	p.S265R	ENST00000252674	NM_005934.3	265	agC/agA	6/12	1	2	FACETS	0.798	0.681	0.927	0.798	0.681	0.927	CLONAL	1	TRUE	1	0.241860673129528	2		411	549	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117071	7117071	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752575531	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	50	329	0	ENST00000302850.5:c.4145C>T	p.Ser1382Phe	p.S1382F	ENST00000302850	NM_000208.2	1382	tCc/tTc	22/22	1	2	FACETS	0.693	0.587	0.809	0.693	0.587	0.809	SUBCLONAL	1	TRUE	1	0.241860673129528	2		329	597	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10257150	10257150	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	121	359	0	ENST00000340748.4:c.2723C>A	p.Pro908His	p.P908H	ENST00000340748		908	cCc/cAc	27/40	1	2	FACETS	0.757	0.685	0.832	1	0.985	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		359	661	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262510	10262510	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	38	366	0	ENST00000340748.4:c.1985C>A	p.Pro662His	p.P662H	ENST00000340748		662	cCt/cAt	22/40	1	2	FACETS	0.466	0.384	0.557	0.466	0.384	0.557	SUBCLONAL	1	TRUE	1	0.241860673129528	2		366	675	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600039	10600039	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	136	341	0	ENST00000171111.5:c.1537T>C	p.Cys513Arg	p.C513R	ENST00000171111	NM_203500.1	513	Tgc/Cgc	5/6	1	2	FACETS	0.934	0.852	1	1	0.99	1	CLONAL	2	TRUE	1	0.241860673129528	2		341	602	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602724	10602724	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	143	445	0	ENST00000171111.5:c.854T>C	p.Leu285Pro	p.L285P	ENST00000171111	NM_203500.1	285	cTg/cCg	3/6	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.241860673129528	2		445	828	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098434	11098434	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758091260	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	87	332	0	ENST00000358026.2:c.952G>A	p.Val318Ile	p.V318I	ENST00000358026	NM_001128849.1	318	Gtc/Atc	6/36	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.241860673129528	2		332	542	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138614	11138614	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	86	351	1	ENST00000358026.2:c.3370C>A	p.Leu1124Ile	p.L1124I	ENST00000358026	NM_001128849.1	1124	Ctc/Atc	24/36	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.241860673129528	2		352	580	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145789	11145789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	97	404	1	ENST00000358026.2:c.4151C>T	p.Thr1384Met	p.T1384M	ENST00000358026	NM_001128849.1	1384	aCg/aTg	29/36	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.241860673129528	2		405	641	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629057	14629057	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1348811211	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	31	319	0	ENST00000254322.2:c.105G>T	p.Lys35Asn	p.K35N	ENST00000254322	NM_006145.1	35	aaG/aaT	1/3	1	2	FACETS	0.571	0.461	0.695	0.571	0.461	0.695	SUBCLONAL	1	TRUE	1	0.241860673129528	2		319	449	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288568	15288568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	30	270	0	ENST00000263388.2:c.4171G>A	p.Ala1391Thr	p.A1391T	ENST00000263388	NM_000435.2	1391	Gcc/Acc	24/33	1	2	FACETS	0.73	0.589	0.889	0.73	0.589	0.889	SUBCLONAL	1	TRUE	1	0.241860673129528	2		270	340	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291914	15291914	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451498063	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	41	463	2	ENST00000263388.2:c.2852G>A	p.Arg951His	p.R951H	ENST00000263388	NM_000435.2	951	cGt/cAt	18/33	1	2	FACETS	0.542	0.451	0.645	0.542	0.451	0.645	SUBCLONAL	1	TRUE	1	0.241860673129528	2		465	625	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349600	15349600	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	56	478	2	ENST00000263377.2:c.3974G>T	p.Arg1325Met	p.R1325M	ENST00000263377	NM_058243.2	1325	aGg/aTg	19/20	1	2	FACETS	0.707	0.605	0.819	0.707	0.605	0.819	SUBCLONAL	1	TRUE	1	0.241860673129528	2		480	655	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350579	15350579	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	92	347	0	ENST00000263377.2:c.3336G>T	p.Glu1112Asp	p.E1112D	ENST00000263377	NM_058243.2	1112	gaG/gaT	16/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.241860673129528	2		347	551	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366939	15366939	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	61	428	0	ENST00000263377.2:c.1687A>G	p.Ser563Gly	p.S563G	ENST00000263377	NM_058243.2	563	Agc/Ggc	9/20	1	2	FACETS	0.724	0.624	0.833	0.724	0.624	0.833	SUBCLONAL	1	TRUE	1	0.241860673129528	2		428	697	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367957	15367957	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	35	375	0	ENST00000263377.2:c.1369A>G	p.Met457Val	p.M457V	ENST00000263377	NM_058243.2	457	Atg/Gtg	8/20	1	2	FACETS	0.471	0.385	0.568	0.471	0.385	0.568	SUBCLONAL	1	TRUE	1	0.241860673129528	2		375	615	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387396	17387396	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	163	440	0	ENST00000359435.4:c.662C>A	p.Pro221His	p.P221H	ENST00000359435	NM_001033549.1	221	cCt/cAt	7/9	1	2	FACETS	0.816	0.749	0.885	1	0.99	1	CLONAL	2	TRUE	1	0.241860673129528	2		440	826	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943338	17943338	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	81	338	0	ENST00000458235.1:c.2670C>A	p.Ser890Arg	p.S890R	ENST00000458235	NM_000215.3	890	agC/agA	19/24	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.241860673129528	2		338	534	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952499	17952499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	103	412	0	ENST00000458235.1:c.934G>A	p.Ala312Thr	p.A312T	ENST00000458235	NM_000215.3	312	Gcc/Acc	7/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.241860673129528	2		412	703	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273097	18273097	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	126	451	0	ENST00000222254.8:c.987G>T	p.Glu329Asp	p.E329D	ENST00000222254	NM_005027.3	329	gaG/gaT	8/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.241860673129528	2		451	783	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18958600	18958600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	78	332	1	ENST00000262803.5:c.419G>A	p.Ser140Asn	p.S140N	ENST00000262803	NM_002911.3	140	aGc/aAc	3/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.241860673129528	2		333	475	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965753	18965753	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	52	466	0	ENST00000262803.5:c.1331A>G	p.Lys444Arg	p.K444R	ENST00000262803	NM_002911.3	444	aAg/aGg	10/24	1	2	FACETS	0.583	0.495	0.679	0.583	0.495	0.679	SUBCLONAL	1	TRUE	1	0.241860673129528	2		466	738	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209141	36209141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769345523	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	33	447	1	ENST00000222270.7:c.221G>A	p.Arg74His	p.R74H	ENST00000222270	NM_014727.1	74	cGc/cAc	1/37	1	2	FACETS	0.438	0.356	0.531	0.438	0.356	0.531	SUBCLONAL	1	TRUE	1	0.241860673129528	2		448	623	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209280	36209280	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	143	567	0	ENST00000222270.7:c.360G>T	p.Glu120Asp	p.E120D	ENST00000222270	NM_014727.1	120	gaG/gaT	1/37	1	2	FACETS	0.778	0.71	0.849	1	0.988	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		567	760	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211109	36211109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756303519	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	52	484	0	ENST00000222270.7:c.860G>A	p.Arg287His	p.R287H	ENST00000222270	NM_014727.1	287	cGt/cAt	3/37	1	2	FACETS	0.511	0.434	0.597	0.511	0.434	0.597	SUBCLONAL	1	TRUE	1	0.241860673129528	2		484	841	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213372	36213372	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	47	431	0	ENST00000222270.7:c.2569T>C	p.Ser857Pro	p.S857P	ENST00000222270	NM_014727.1	857	Tca/Cca	4/37	1	2	FACETS	0.618	0.52	0.726	0.618	0.52	0.726	SUBCLONAL	1	TRUE	1	0.241860673129528	2		431	629	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227707	36227707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1454808380	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	157	514	0	ENST00000222270.7:c.7276G>A	p.Val2426Ile	p.V2426I	ENST00000222270	NM_014727.1	2426	Gtt/Att	31/37	1	2	FACETS	0.784	0.719	0.852	1	0.989	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		514	828	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741927	40741927	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	138	498	0	ENST00000392038.2:c.1045C>T	p.Pro349Ser	p.P349S	ENST00000392038	NM_001626.4	349	Ccc/Tcc	11/14	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.241860673129528	2		498	787	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758823	41758823	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	55	429	0	ENST00000301178.4:c.1877G>A	p.Gly626Glu	p.G626E	ENST00000301178	NM_021913.4	626	gGa/gAa	16/20	1	2	FACETS	0.631	0.539	0.732	0.631	0.539	0.732	SUBCLONAL	1	TRUE	1	0.241860673129528	2		429	721	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792129	42792129	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	40	314	0	ENST00000575354.2:c.931+2T>G		p.X311_splice	ENST00000575354	NM_015125.3	311			1	2	FACETS	0.586	0.487	0.698	0.586	0.487	0.698	SUBCLONAL	1	TRUE	1	0.241860673129528	2		314	564	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796588	42796588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1360243390	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	89	358	0	ENST00000575354.2:c.3145G>A	p.Gly1049Ser	p.G1049S	ENST00000575354	NM_015125.3	1049	Ggc/Agc	13/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.241860673129528	2		358	617	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797418	42797418	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	52	414	1	ENST00000575354.2:c.3780G>T	p.Lys1260Asn	p.K1260N	ENST00000575354	NM_015125.3	1260	aaG/aaT	15/20	1	2	FACETS	0.6	0.509	0.699	0.6	0.509	0.699	SUBCLONAL	1	TRUE	1	0.241860673129528	2		415	717	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423623	47423623	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	58	406	0	ENST00000404338.3:c.1691C>A	p.Ala564Asp	p.A564D	ENST00000404338	NM_004491.4	564	gCt/gAt	1/6	1	2	FACETS	0.744	0.638	0.859	0.744	0.638	0.859	SUBCLONAL	1	TRUE	1	0.241860673129528	2		406	645	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424520	47424520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	63	440	0	ENST00000404338.3:c.2588G>A	p.Arg863His	p.R863H	ENST00000404338	NM_004491.4	863	cGt/cAt	1/6	1	2	FACETS	0.85	0.735	0.975	0.85	0.735	0.975	CLONAL	1	TRUE	1	0.241860673129528	2		440	613	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425058	47425058	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	35	477	0	ENST00000404338.3:c.3126A>C	p.Lys1042Asn	p.K1042N	ENST00000404338	NM_004491.4	1042	aaA/aaC	1/6	1	2	FACETS	0.473	0.387	0.57	0.473	0.387	0.57	SUBCLONAL	1	TRUE	1	0.241860673129528	2		477	612	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906448	50906448	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs868850526	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	46	367	0	ENST00000440232.2:c.1109G>T	p.Ser370Ile	p.S370I	ENST00000440232	NM_002691.3	370	aGc/aTc	9/27	1	2	FACETS	0.61	0.512	0.717	0.61	0.512	0.717	SUBCLONAL	1	TRUE	1	0.241860673129528	2		367	624	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909713	50909713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397514632	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	124	429	0	ENST00000440232.2:c.1433G>A	p.Ser478Asn	p.S478N	ENST00000440232	NM_002691.3	478	aGc/aAc	12/27	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.241860673129528	2		429	753	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457169	25457169	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	108	387	0	ENST00000264709.3:c.2718G>T	p.Lys906Asn	p.K906N	ENST00000264709	NM_175629.2	906	aaG/aaT	23/23	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.241860673129528	2		387	794	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25458616	25458616	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	45	369	0	ENST00000264709.3:c.2557A>G	p.Asn853Asp	p.N853D	ENST00000264709	NM_175629.2	853	Aat/Gat	22/23	1	2	FACETS	0.727	0.611	0.855	0.727	0.611	0.855	SUBCLONAL	1	TRUE	1	0.241860673129528	2		369	512	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467094	25467094	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	74	463	0	ENST00000264709.3:c.1781T>C	p.Leu594Pro	p.L594P	ENST00000264709	NM_175629.2	594	cTg/cCg	15/23	1	2	FACETS	0.766	0.669	0.87	0.766	0.669	0.87	SUBCLONAL	1	TRUE	1	0.241860673129528	2		463	799	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965261	25965261	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	83	342	0	ENST00000435504.4:c.3945G>T	p.Lys1315Asn	p.K1315N	ENST00000435504		1315	aaG/aaT	13/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.241860673129528	2		342	502	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966113	25966113	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	101	428	0	ENST00000435504.4:c.3093G>T	p.Gln1031His	p.Q1031H	ENST00000435504		1031	caG/caT	13/13	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.241860673129528	2		428	665	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966459	25966459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	129	443	0	ENST00000435504.4:c.2747C>T	p.Pro916Leu	p.P916L	ENST00000435504		916	cCc/cTc	13/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.241860673129528	2		443	755	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972833	25972833	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	40	445	0	ENST00000435504.4:c.1592C>A	p.Pro531His	p.P531H	ENST00000435504		531	cCt/cAt	12/13	1	2	FACETS	0.54	0.447	0.643	0.54	0.447	0.643	SUBCLONAL	1	TRUE	1	0.241860673129528	2		445	613	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994321	25994321	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	100	373	0	ENST00000435504.4:c.492G>T	p.Lys164Asn	p.K164N	ENST00000435504		164	aaG/aaT	6/13	1	2	FACETS	0.851	0.763	0.943	1	0.985	1	CLONAL	2	TRUE	1	0.241860673129528	2		373	486	SUCCESS
ALK	238	MSKCC	GRCh37	2	29448339	29448339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375889530	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	173	573	0	ENST00000389048.3:c.3160G>A	p.Gly1054Ser	p.G1054S	ENST00000389048	NM_004304.4	1054	Ggc/Agc	19/29	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.241860673129528	2		573	957	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455272	29455272	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	135	436	0	ENST00000389048.3:c.2530G>T	p.Gly844Cys	p.G844C	ENST00000389048	NM_004304.4	844	Ggt/Tgt	15/29	1	2	FACETS	0.792	0.721	0.866	1	0.987	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		436	705	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474126	29474126	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	109	417	0	ENST00000389048.3:c.2049G>T	p.Trp683Cys	p.W683C	ENST00000389048	NM_004304.4	683	tgG/tgT	12/29	1	2	FACETS	0.765	0.689	0.846	1	0.984	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		417	589	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39214693	39214693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775259671	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	41	276	0	ENST00000402219.2:c.3431C>T	p.Thr1144Ile	p.T1144I	ENST00000402219	NM_005633.3	1144	aCt/aTt	22/23	1	2	FACETS	0.779	0.65	0.923	0.779	0.65	0.923	CLONAL	1	TRUE	1	0.241860673129528	2		276	435	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39240680	39240680	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	19	304	0	ENST00000402219.2:c.2088G>T	p.Trp696Cys	p.W696C	ENST00000402219	NM_005633.3	696	tgG/tgT	13/23	1	2	FACETS	0.778	0.593	0.994	0.778	0.593	0.994	CLONAL	1	TRUE	1	0.241860673129528	2		304	202	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574029	46574029	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	111	434	0	ENST00000263734.3:c.44G>T	p.Arg15Met	p.R15M	ENST00000263734	NM_001430.4	15	aGg/aTg	2/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.241860673129528	2		434	630	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583933	46583933	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	87	363	0	ENST00000263734.3:c.440T>C	p.Leu147Pro	p.L147P	ENST00000263734	NM_001430.4	147	cTg/cCg	4/16	1	2	FACETS	0.842	0.75	0.94	1	0.983	1	CLONAL	2	TRUE	1	0.241860673129528	2		363	427	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698125	47698125	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	39	322	0	ENST00000233146.2:c.1683A>T	p.Glu561Asp	p.E561D	ENST00000233146	NM_000251.2	561	gaA/gaT	11/16	1	2	FACETS	0.881	0.739	1	1	0.965	1	CLONAL	2	TRUE	1	0.241860673129528	2		322	183	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702374	47702374	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	23	326	0	ENST00000233146.2:c.1970T>C	p.Phe657Ser	p.F657S	ENST00000233146	NM_000251.2	657	tTt/tCt	12/16	1	2	FACETS	0.616	0.48	0.772	0.616	0.48	0.772	SUBCLONAL	1	TRUE	1	0.241860673129528	2		326	309	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705648	47705648	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	56	330	0	ENST00000233146.2:c.2448G>T	p.Gln816His	p.Q816H	ENST00000233146	NM_000251.2	816	caG/caT	14/16	1	2	FACETS	0.864	0.747	0.989	1	0.974	1	CLONAL	2	TRUE	1	0.241860673129528	2		330	268	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010391	48010391	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1064795094	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	85	422	0	ENST00000234420.5:c.19C>A	p.Leu7Met	p.L7M	ENST00000234420	NM_000179.2	7	Ctg/Atg	1/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.241860673129528	2		422	486	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030786	48030786	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1114167697	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	77	415	0	ENST00000234420.5:c.3400G>C	p.Gly1134Arg	p.G1134R	ENST00000234420	NM_000179.2	1134	Gga/Cga	5/10	1	2	FACETS	0.81	0.715	0.911	1	0.979	1	CLONAL	2	TRUE	1	0.241860673129528	2		415	393	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715328	61715328	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	44	314	0	ENST00000401558.2:c.2285G>A	p.Trp762Ter	p.W762*	ENST00000401558	NM_003400.3	762	tGg/tAg	19/25	1	2	FACETS	0.827	0.7	0.964	1	0.966	1	CLONAL	2	TRUE	1	0.241860673129528	2		314	220	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721222	61721222	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	64	358	0	ENST00000401558.2:c.1052T>A	p.Leu351His	p.L351H	ENST00000401558	NM_003400.3	351	cTt/cAt	12/25	1	2	FACETS	0.916	0.8	1	1	0.979	1	CLONAL	2	TRUE	1	0.241860673129528	2		358	289	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67632410	67632410	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	40	336	0	ENST00000272342.5:c.2596G>C	p.Ala866Pro	p.A866P	ENST00000272342	NM_019002.3	866	Gct/Cct	5/6	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.241860673129528	2		336	249	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99180038	99180038	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	111	388	0	ENST00000074304.5:c.1981G>A	p.Ala661Thr	p.A661T	ENST00000074304	NM_001134224.1	661	Gcg/Acg	19/26	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.241860673129528	2		388	657	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190741997	190741997	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	15	309	0	ENST00000441310.2:c.2635-1G>T		p.X879_splice	ENST00000441310	NM_000534.4	879			1	2	FACETS	0.546	0.4	0.722	0.546	0.4	0.722	SUBCLONAL	1	TRUE	1	0.241860673129528	2		309	227	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288699	198288699	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	26	276	0	ENST00000335508.6:c.29-1G>T		p.X10_splice	ENST00000335508	NM_012433.2	10			1	2	FACETS	0.712	0.565	0.88	0.712	0.565	0.88	SUBCLONAL	1	TRUE	1	0.241860673129528	2		276	302	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137434	202137434	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	30	413	0	ENST00000358485.4:c.662G>T	p.Arg221Ile	p.R221I	ENST00000358485	NM_001080125.1	221	aGa/aTa	4/9	1	2	FACETS	0.555	0.447	0.678	0.555	0.447	0.678	SUBCLONAL	1	TRUE	1	0.241860673129528	2		413	447	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141676	202141676	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	35	447	0	ENST00000358485.4:c.964A>G	p.Thr322Ala	p.T322A	ENST00000358485	NM_001080125.1	322	Aca/Gca	7/9	1	2	FACETS	0.558	0.456	0.672	0.558	0.456	0.672	SUBCLONAL	1	TRUE	1	0.241860673129528	2		447	519	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149551	202149551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139337151	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	50	391	0	ENST00000358485.4:c.992C>T	p.Thr331Met	p.T331M	ENST00000358485	NM_001080125.1	331	aCg/aTg	8/9	1	2	FACETS	0.839	0.712	0.978	0.839	0.712	0.978	CLONAL	1	TRUE	1	0.241860673129528	2		391	493	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149634	202149635	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	98	422	0	ENST00000358485.4:c.1077dup	p.Leu360ThrfsTer6	p.L360Tfs*6	ENST00000358485	NM_001080125.1	359	caa/cAaa	8/9	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.241860673129528	2		422	555	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149973	202149973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1272714323	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	141	450	0	ENST00000358485.4:c.1414C>T	p.Arg472Ter	p.R472*	ENST00000358485	NM_001080125.1	472	Cga/Tga	8/9	1	2	FACETS	0.847	0.774	0.924	1	0.989	1	CLONAL	2	TRUE	1	0.241860673129528	2		450	688	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248503	212248503	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	81	537	0	ENST00000342788.4:c.3764A>G	p.His1255Arg	p.H1255R	ENST00000342788	NM_005235.2	1255	cAc/cGc	28/28	1	2	FACETS	0.754	0.663	0.852	0.754	0.663	0.852	SUBCLONAL	1	TRUE	1	0.241860673129528	2		537	888	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251791	212251791	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	60	451	0	ENST00000342788.4:c.3268G>T	p.Glu1090Ter	p.E1090*	ENST00000342788	NM_005235.2	1090	Gaa/Taa	27/28	1	2	FACETS	0.704	0.605	0.811	0.704	0.605	0.811	SUBCLONAL	1	TRUE	1	0.241860673129528	2		451	705	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285304	212285304	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	27	384	0	ENST00000342788.4:c.2997T>A	p.Asn999Lys	p.N999K	ENST00000342788	NM_005235.2	999	aaT/aaA	25/28	1	2	FACETS	0.693	0.552	0.854	0.693	0.552	0.854	SUBCLONAL	1	TRUE	1	0.241860673129528	2		384	322	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212484001	212484001	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	30	302	0	ENST00000342788.4:c.2203-1G>T		p.X735_splice	ENST00000342788	NM_005235.2	735			1	2	FACETS	0.775	0.632	0.933	1	0.946	1	CLONAL	2	TRUE	1	0.241860673129528	2		302	160	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589808	212589808	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	107	380	0	ENST00000342788.4:c.734A>G	p.Asp245Gly	p.D245G	ENST00000342788	NM_005235.2	245	gAc/gGc	6/28	1	2	FACETS	0.803	0.723	0.888	1	0.985	1	CLONAL	2	TRUE	1	0.241860673129528	2		380	551	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645681	215645681	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1326117428	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	32	438	0	ENST00000260947.4:c.917A>C	p.Asn306Thr	p.N306T	ENST00000260947	NM_000465.2	306	aAt/aCt	4/11	1	2	FACETS	0.748	0.607	0.905	0.748	0.607	0.905	CLONAL	1	TRUE	1	0.241860673129528	2		438	354	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645991	215645991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881415	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	49	392	0	ENST00000260947.4:c.607G>A	p.Gly203Arg	p.G203R	ENST00000260947	NM_000465.2	203	Gga/Aga	4/11	1	2	FACETS	0.931	0.79	1	0.931	0.79	1	CLONAL	1	TRUE	1	0.241860673129528	2		392	435	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440240	220440240	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	75	368	0	ENST00000243786.2:c.1093T>C	p.Cys365Arg	p.C365R	ENST00000243786	NM_002191.3	365	Tgt/Cgt	2/2	1	2	FACETS	0.972	0.852	1	0.972	0.852	1	CLONAL	1	TRUE	1	0.241860673129528	2		368	638	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661567	227661567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	115	467	0	ENST00000305123.5:c.1888G>A	p.Gly630Arg	p.G630R	ENST00000305123	NM_005544.2	630	Gga/Aga	1/2	1	2	FACETS	0.757	0.683	0.835	1	0.984	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		467	628	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661584	227661584	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	116	470	0	ENST00000305123.5:c.1871G>T	p.Ser624Ile	p.S624I	ENST00000305123	NM_005544.2	624	aGt/aTt	1/2	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.241860673129528	2		470	652	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662078	227662078	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	131	484	0	ENST00000305123.5:c.1377G>T	p.Glu459Asp	p.E459D	ENST00000305123	NM_005544.2	459	gaG/gaT	1/2	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.241860673129528	2		484	734	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662518	227662518	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	115	446	0	ENST00000305123.5:c.937C>A	p.Pro313Thr	p.P313T	ENST00000305123	NM_005544.2	313	Ccg/Acg	1/2	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.241860673129528	2		446	734	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662644	227662644	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	130	435	0	ENST00000305123.5:c.811C>A	p.Gln271Lys	p.Q271K	ENST00000305123	NM_005544.2	271	Cag/Aag	1/2	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.241860673129528	2		435	723	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546635	9546635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	76	454	0	ENST00000353224.5:c.1387G>A	p.Val463Ile	p.V463I	ENST00000353224	NM_177990.2	463	Gta/Ata	5/10	0.191881071602356	3	FACETS	0.97	0.851	1	0.485	0.425	0.55	CLONAL	1	TRUE	1	0.241860673129528	3		454	726	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021151	31021151	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	44	464	0	ENST00000375687.4:c.1150A>C	p.Ser384Arg	p.S384R	ENST00000375687	NM_015338.5	384	Agt/Cgt	12/13	0.191881071602356	3	FACETS	0.556	0.465	0.658	0.278	0.232	0.329	SUBCLONAL	1	TRUE	1	0.241860673129528	3		464	733	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023096	31023096	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1170492819	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	45	468	0	ENST00000375687.4:c.2581G>T	p.Ala861Ser	p.A861S	ENST00000375687	NM_015338.5	861	Gca/Tca	13/13	0.191881071602356	3	FACETS	0.58	0.486	0.684	0.29	0.243	0.342	SUBCLONAL	1	TRUE	1	0.241860673129528	3		468	719	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023180	31023180	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763287860	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	49	409	0	ENST00000375687.4:c.2665G>A	p.Ala889Thr	p.A889T	ENST00000375687	NM_015338.5	889	Gct/Act	13/13	0.191881071602356	3	FACETS	0.729	0.617	0.853	0.365	0.308	0.427	SUBCLONAL	1	TRUE	1	0.241860673129528	3		409	623	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024573	31024573	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	149	460	0	ENST00000375687.4:c.4058G>T	p.Arg1353Met	p.R1353M	ENST00000375687	NM_015338.5	1353	aGg/aTg	13/13	0.191881071602356	3	FACETS	0.838	0.766	0.913	0.838	0.766	0.913	CLONAL	2	TRUE	1	0.241860673129528	3		460	824	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383492	31383492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	131	426	0	ENST00000328111.2:c.1289G>A	p.Ser430Asn	p.S430N	ENST00000328111	NM_006892.3	430	aGc/aAc	12/23	0.191881071602356	3	FACETS	1	0.919	1	1	0.919	1	CLONAL	2	TRUE	1	0.241860673129528	3		426	601	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394126	31394126	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	61	248	0	ENST00000328111.2:c.2413C>T	p.Leu805Phe	p.L805F	ENST00000328111	NM_006892.3	805	Ctc/Ttc	22/23	0.191881071602356	3	FACETS	1	0.865	1	0.501	0.432	0.576	CLONAL	1	TRUE	1	0.241860673129528	3		248	564	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39706270	39706270	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	68	287	0	ENST00000361337.2:c.328T>G	p.Phe110Val	p.F110V	ENST00000361337	NM_003286.2	110	Ttc/Gtc	5/21	0.191881071602356	3	FACETS	1	0.959	1	0.628	0.547	0.715	CLONAL	1	TRUE	1	0.241860673129528	3		287	502	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728842	39728842	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	116	363	0	ENST00000361337.2:c.1122G>T	p.Lys374Asn	p.K374N	ENST00000361337	NM_003286.2	374	aaG/aaT	12/21	0.191881071602356	3	FACETS	0.763	0.688	0.841	0.763	0.688	0.841	SUBCLONAL	2	TRUE	1	0.241860673129528	3		363	705	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742782	39742782	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	88	356	0	ENST00000361337.2:c.1625C>A	p.Pro542His	p.P542H	ENST00000361337	NM_003286.2	542	cCt/cAt	15/21	0.191881071602356	3	FACETS	1	0.978	1	0.739	0.656	0.827	CLONAL	1	TRUE	1	0.241860673129528	3		356	552	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750387	39750387	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1471511396	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	58	370	0	ENST00000361337.2:c.2002G>A	p.Ala668Thr	p.A668T	ENST00000361337	NM_003286.2	668	Gct/Act	19/21	0.191881071602356	3	FACETS	0.811	0.696	0.936	0.405	0.348	0.468	CLONAL	1	TRUE	1	0.241860673129528	3		370	663	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748574	40748574	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	40	289	0	ENST00000373198.4:c.2941+1G>A		p.X981_splice	ENST00000373198	NM_133170.3	981			0.191881071602356	3	FACETS	0.764	0.635	0.909	0.382	0.317	0.455	CLONAL	1	TRUE	1	0.241860673129528	3		289	485	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944383	40944383	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	53	398	0	ENST00000373198.4:c.2119G>T	p.Ala707Ser	p.A707S	ENST00000373198	NM_133170.3	707	Gca/Tca	12/32	0.191881071602356	3	FACETS	0.785	0.669	0.912	0.392	0.334	0.456	CLONAL	1	TRUE	1	0.241860673129528	3		398	626	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076931	41076932	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	39	343	0	ENST00000373198.4:c.1488dup	p.Pro497AlafsTer3	p.P497Afs*3	ENST00000373198	NM_133170.3	496	-/G	9/32	0.191881071602356	3	FACETS	0.75	0.621	0.894	0.375	0.31	0.447	SUBCLONAL	1	TRUE	1	0.241860673129528	3		343	482	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46251001	46251001	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	58	279	0	ENST00000371998.3:c.10T>G	p.Leu4Val	p.L4V	ENST00000371998		4	Tta/Gta	3/23	0.191881071602356	3	FACETS	0.759	0.656	0.871	0.759	0.656	0.871	SUBCLONAL	2	TRUE	1	0.241860673129528	3		279	354	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485756	57485756	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	166	386	0	ENST00000371085.3:c.1057G>T	p.Gly353Ter	p.G353*	ENST00000371085	NM_000516.4	353	Gga/Tga	13/13	0.191881071602356	3	FACETS	0.999	0.919	1	0.999	0.919	1	CLONAL	2	TRUE	1	0.241860673129528	3		386	770	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485856	57485856	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	185	367	0	ENST00000371085.3:c.1157T>C	p.Met386Thr	p.M386T	ENST00000371085	NM_000516.4	386	aTg/aCg	13/13	0.191881071602356	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.241860673129528	3		367	798	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292739	62292739	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146544609	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	141	395	0	ENST00000360203.5:c.191G>A	p.Arg64Gln	p.R64Q	ENST00000360203	NM_001283009.1	64	cGa/cAa	3/35	0.191881071602356	3	FACETS	0.859	0.783	0.938	0.859	0.783	0.938	CLONAL	2	TRUE	1	0.241860673129528	3		395	761	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62294182	62294182	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	75	392	0	ENST00000360203.5:c.478A>T	p.Ile160Phe	p.I160F	ENST00000360203	NM_001283009.1	160	Atc/Ttc	6/35	0.191881071602356	3	FACETS	0.959	0.84	1	0.479	0.42	0.544	CLONAL	1	TRUE	1	0.241860673129528	3		392	725	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321795	62321795	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs776744306	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	83	300	0	ENST00000360203.5:c.2413+1G>A		p.X805_splice	ENST00000360203	NM_001283009.1	805			0.191881071602356	3	FACETS	0.787	0.696	0.883	0.787	0.696	0.883	SUBCLONAL	2	TRUE	1	0.241860673129528	3		300	489	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39762917	39762917	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	18	270	0	ENST00000288319.7:c.919G>A	p.Gly307Ser	p.G307S	ENST00000288319	NM_182918.3	307	Ggc/Agc	9/10	1	2	FACETS	0.553	0.417	0.715	0.553	0.417	0.715	SUBCLONAL	1	TRUE	1	0.241860673129528	2		270	269	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839693	42839693	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs997356304	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	66	388	0	ENST00000398585.3:c.1546G>A	p.Val516Ile	p.V516I	ENST00000398585	NM_001135099.1	516	Gta/Ata	13/14	1	2	FACETS	0.838	0.727	0.959	0.838	0.727	0.959	CLONAL	1	TRUE	1	0.241860673129528	2		388	651	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860381	42860381	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	64	397	0	ENST00000398585.3:c.496C>A	p.Pro166Thr	p.P166T	ENST00000398585	NM_001135099.1	166	Ccc/Acc	5/14	1	2	FACETS	0.741	0.641	0.85	0.741	0.641	0.85	SUBCLONAL	1	TRUE	1	0.241860673129528	2		397	714	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42870078	42870078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	43	462	0	ENST00000398585.3:c.94G>A	p.Ala32Thr	p.A32T	ENST00000398585	NM_001135099.1	32	Gct/Act	2/14	1	2	FACETS	0.615	0.514	0.728	0.615	0.514	0.728	SUBCLONAL	1	TRUE	1	0.241860673129528	2		462	578	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44515626	44515626	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	101	382	0	ENST00000291552.4:c.270G>T	p.Glu90Asp	p.E90D	ENST00000291552	NM_006758.2	90	gaG/gaT	5/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.241860673129528	2		382	573	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656888	45656888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566695508	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	69	445	0	ENST00000407780.3:c.268G>A	p.Gly90Ser	p.G90S	ENST00000407780	NM_001283052.1	90	Ggc/Agc	3/7	1	2	FACETS	0.661	0.574	0.755	0.661	0.574	0.755	SUBCLONAL	1	TRUE	1	0.241860673129528	2		445	863	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21344765	21344765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869320686	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	93	530	1	ENST00000215739.8:c.742G>A	p.Gly248Arg	p.G248R	ENST00000215739	NM_006767.3	248	Gga/Aga	8/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.241860673129528	2		531	621	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21347168	21347168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs935736801	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	145	420	0	ENST00000215739.8:c.1235G>A	p.Arg412His	p.R412H	ENST00000215739	NM_006767.3	412	cGc/cAc	11/21	1	2	FACETS	0.827	0.756	0.901	1	0.989	1	CLONAL	2	TRUE	1	0.241860673129528	2		420	725	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21348493	21348493	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	54	488	0	ENST00000215739.8:c.1550A>G	p.Glu517Gly	p.E517G	ENST00000215739	NM_006767.3	517	gAg/gGg	14/21	1	2	FACETS	0.571	0.486	0.664	0.571	0.486	0.664	SUBCLONAL	1	TRUE	1	0.241860673129528	2		488	782	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145484	24145484	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	43	430	0	ENST00000263121.7:c.503T>C	p.Phe168Ser	p.F168S	ENST00000263121	NM_003073.3	168	tTt/tCt	5/9	1	2	FACETS	0.618	0.517	0.731	0.618	0.517	0.731	SUBCLONAL	1	TRUE	1	0.241860673129528	2		430	575	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167571	24167571	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	110	373	0	ENST00000263121.7:c.955C>A	p.Leu319Met	p.L319M	ENST00000263121	NM_003073.3	319	Ctg/Atg	7/9	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.241860673129528	2		373	682	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091753	29091753	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758206293	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	49	169	0	ENST00000328354.6:c.1204G>A	p.Ala402Thr	p.A402T	ENST00000328354	NM_007194.3	402	Gct/Act	11/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.241860673129528	2		169	274	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091782	29091782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373073383	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	77	265	0	ENST00000328354.6:c.1175C>T	p.Ala392Val	p.A392V	ENST00000328354	NM_007194.3	392	gCg/gTg	11/15	1	2	FACETS	0.782	0.69	0.88	1	0.978	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		265	407	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29445385	29445385	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	51	500	2	ENST00000544604.2:c.1216A>G	p.Ser406Gly	p.S406G	ENST00000544604	NM_001206998.1	406	Agc/Ggc	8/9	1	2	FACETS	0.605	0.513	0.706	0.605	0.513	0.706	SUBCLONAL	1	TRUE	1	0.241860673129528	2		502	697	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446422	29446422	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	38	408	0	ENST00000544604.2:c.2253G>T	p.Gln751His	p.Q751H	ENST00000544604	NM_001206998.1	751	caG/caT	8/9	1	2	FACETS	0.581	0.479	0.694	0.581	0.479	0.694	SUBCLONAL	1	TRUE	1	0.241860673129528	2		408	541	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032752	30032752	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	146	390	0	ENST00000338641.4:c.127G>T	p.Gly43Trp	p.G43W	ENST00000338641	NM_000268.3	43	Ggg/Tgg	2/16	1	2	FACETS	0.872	0.798	0.95	1	0.99	1	CLONAL	2	TRUE	1	0.241860673129528	2		390	692	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537063	41537063	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	44	412	0	ENST00000263253.7:c.1890C>A	p.Tyr630Ter	p.Y630*	ENST00000263253	NM_001429.3	630	taC/taA	10/31	1	2	FACETS	0.81	0.68	0.954	0.81	0.68	0.954	CLONAL	1	TRUE	1	0.241860673129528	2		412	449	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572460	41572460	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	57	507	0	ENST00000263253.7:c.4989G>T	p.Gln1663His	p.Q1663H	ENST00000263253	NM_001429.3	1663	caG/caT	30/31	1	2	FACETS	0.541	0.463	0.627	0.541	0.463	0.627	SUBCLONAL	1	TRUE	1	0.241860673129528	2		507	871	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573564	41573564	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	142	563	0	ENST00000263253.7:c.5849G>T	p.Arg1950Met	p.R1950M	ENST00000263253	NM_001429.3	1950	aGg/aTg	31/31	1	2	FACETS	0.838	0.765	0.914	1	0.989	1	CLONAL	2	TRUE	1	0.241860673129528	2		563	701	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434213	12434213	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148195788	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	25	357	0	ENST00000287820.6:c.581G>A	p.Arg194Gln	p.R194Q	ENST00000287820	NM_015869.4	194	cGg/cAg	4/7	1	2	FACETS	0.594	0.468	0.739	0.594	0.468	0.739	SUBCLONAL	1	TRUE	1	0.241860673129528	2		357	348	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434222	12434222	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	62	358	0	ENST00000287820.6:c.590A>G	p.Lys197Arg	p.K197R	ENST00000287820	NM_015869.4	197	aAa/aGa	4/7	1	2	FACETS	0.763	0.663	0.87	1	0.972	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		358	336	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37061935	37061935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs191257018	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	113	423	0	ENST00000231790.2:c.1019C>T	p.Ser340Phe	p.S340F	ENST00000231790	NM_000249.3	340	tCc/tTc	11/19	1	2	FACETS	0.803	0.724	0.885	1	0.985	1	CLONAL	2	TRUE	1	0.241860673129528	2		423	582	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266824	41266824	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	101	397	0	ENST00000349496.5:c.496-1G>A		p.X166_splice	ENST00000349496	NM_001904.3	166			1	2	FACETS	0.856	0.768	0.948	1	0.985	1	CLONAL	2	TRUE	1	0.241860673129528	2		397	488	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267314	41267314	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	55	411	0	ENST00000349496.5:c.898T>C	p.Cys300Arg	p.C300R	ENST00000349496	NM_001904.3	300	Tgc/Cgc	6/15	1	2	FACETS	0.863	0.739	0.999	0.863	0.739	0.999	CLONAL	1	TRUE	1	0.241860673129528	2		411	527	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125276	47125276	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	28	404	0	ENST00000409792.3:c.5994G>T	p.Gln1998His	p.Q1998H	ENST00000409792	NM_014159.6	1998	caG/caT	12/21	1	2	FACETS	0.461	0.368	0.568	0.461	0.368	0.568	SUBCLONAL	1	TRUE	1	0.241860673129528	2		404	502	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125697	47125697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750379129	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	56	444	0	ENST00000409792.3:c.5573C>T	p.Pro1858Leu	p.P1858L	ENST00000409792	NM_014159.6	1858	cCt/cTt	12/21	1	2	FACETS	0.744	0.637	0.862	0.744	0.637	0.862	SUBCLONAL	1	TRUE	1	0.241860673129528	2		444	622	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158132	47158132	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	50	359	1	ENST00000409792.3:c.4567C>T	p.Arg1523Cys	p.R1523C	ENST00000409792	NM_014159.6	1523	Cgt/Tgt	4/21	1	2	FACETS	0.876	0.751	1	1	0.972	1	CLONAL	2	TRUE	1	0.241860673129528	2		360	236	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161958	47161958	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	97	398	0	ENST00000409792.3:c.4168T>C	p.Ser1390Pro	p.S1390P	ENST00000409792	NM_014159.6	1390	Tca/Cca	3/21	1	2	FACETS	0.864	0.774	0.959	1	0.985	1	CLONAL	2	TRUE	1	0.241860673129528	2		398	464	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162069	47162069	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	39	429	0	ENST00000409792.3:c.4057T>C	p.Ser1353Pro	p.S1353P	ENST00000409792	NM_014159.6	1353	Tcc/Ccc	3/21	1	2	FACETS	0.717	0.594	0.853	0.717	0.594	0.853	SUBCLONAL	1	TRUE	1	0.241860673129528	2		429	450	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164475	47164475	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	17	400	0	ENST00000409792.3:c.1651A>G	p.Ser551Gly	p.S551G	ENST00000409792	NM_014159.6	551	Agt/Ggt	3/21	1	2	FACETS	0.459	0.342	0.599	0.459	0.342	0.599	SUBCLONAL	1	TRUE	1	0.241860673129528	2		400	306	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725262	49725262	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	24	82	0	ENST00000449682.2:c.163G>A	p.Val55Met	p.V55M	ENST00000449682	NM_020998.3	55	Gtg/Atg	2/18	1	2	FACETS	0.807	0.642	0.99	1	0.938	1	CLONAL	2	TRUE	1	0.241860673129528	2		82	123	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936040	49936040	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1237486360	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	54	525	0	ENST00000296474.3:c.1630G>A	p.Gly544Ser	p.G544S	ENST00000296474	NM_002447.2	544	Ggc/Agc	4/20	1	2	FACETS	0.551	0.469	0.64	0.551	0.469	0.64	SUBCLONAL	1	TRUE	1	0.241860673129528	2		525	811	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936310	49936310	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	136	500	0	ENST00000296474.3:c.1538C>A	p.Ser513Tyr	p.S513Y	ENST00000296474	NM_002447.2	513	tCt/tAt	3/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.241860673129528	2		500	779	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437194	52437194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751746876	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	133	420	0	ENST00000460680.1:c.1850G>A	p.Arg617Lys	p.R617K	ENST00000460680	NM_004656.3	617	aGg/aAg	14/17	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.241860673129528	2		420	766	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439262	52439262	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	55	395	0	ENST00000460680.1:c.980G>A	p.Ser327Asn	p.S327N	ENST00000460680	NM_004656.3	327	aGc/aAc	11/17	1	2	FACETS	0.71	0.606	0.823	0.71	0.606	0.823	SUBCLONAL	1	TRUE	1	0.241860673129528	2		395	641	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597495	52597495	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	35	358	0	ENST00000394830.3:c.3815C>A	p.Pro1272His	p.P1272H	ENST00000394830	NM_018313.4	1272	cCt/cAt	25/30	1	2	FACETS	0.709	0.582	0.853	0.709	0.582	0.853	SUBCLONAL	1	TRUE	1	0.241860673129528	2		358	408	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620441	52620441	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	41	357	0	ENST00000394830.3:c.3312G>T	p.Lys1104Asn	p.K1104N	ENST00000394830	NM_018313.4	1104	aaG/aaT	21/30	1	2	FACETS	0.75	0.625	0.889	0.75	0.625	0.889	SUBCLONAL	1	TRUE	1	0.241860673129528	2		357	452	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643586	52643586	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	61	426	0	ENST00000394830.3:c.2310T>A	p.His770Gln	p.H770Q	ENST00000394830	NM_018313.4	770	caT/caA	17/30	1	2	FACETS	0.914	0.789	1	0.914	0.789	1	CLONAL	1	TRUE	1	0.241860673129528	2		426	552	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63898530	63898530	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	74	474	0	ENST00000398590.3:c.256A>G	p.Ser86Gly	p.S86G	ENST00000398590	NM_001177387.1	86	Agt/Ggt	3/14	1	2	FACETS	0.912	0.798	1	0.912	0.798	1	CLONAL	1	TRUE	1	0.241860673129528	2		474	671	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63973735	63973735	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	33	332	0	ENST00000398590.3:c.1096A>G	p.Thr366Ala	p.T366A	ENST00000398590	NM_001177387.1	366	Aca/Gca	9/14	1	2	FACETS	0.601	0.489	0.727	0.601	0.489	0.727	SUBCLONAL	1	TRUE	1	0.241860673129528	2		332	454	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981513	63981513	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	135	496	0	ENST00000398590.3:c.2015A>G	p.Gln672Arg	p.Q672R	ENST00000398590	NM_001177387.1	672	cAg/cGg	12/14	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.241860673129528	2		496	773	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981657	63981657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770877170	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	55	549	0	ENST00000398590.3:c.2159C>T	p.Ser720Phe	p.S720F	ENST00000398590	NM_001177387.1	720	tCc/tTc	12/14	1	2	FACETS	0.588	0.502	0.683	0.588	0.502	0.683	SUBCLONAL	1	TRUE	1	0.241860673129528	2		549	773	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981691	63981691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	138	545	1	ENST00000398590.3:c.2193G>A	p.Met731Ile	p.M731I	ENST00000398590	NM_001177387.1	731	atG/atA	12/14	1	2	FACETS	0.753	0.686	0.823	1	0.987	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		546	758	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008423	70008423	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	44	314	0	ENST00000394351.3:c.711-1G>T		p.X237_splice	ENST00000394351	NM_000248.3	237			1	2	FACETS	0.734	0.615	0.865	0.734	0.615	0.865	SUBCLONAL	1	TRUE	1	0.241860673129528	2		314	496	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015208	71015208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	78	302	0	ENST00000318789.4:c.1723-1G>T		p.X575_splice	ENST00000318789	NM_032682.5	575			1	2	FACETS	0.862	0.763	0.968	1	0.981	1	CLONAL	2	TRUE	1	0.241860673129528	2		302	374	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027093	71027093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200629338	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	174	441	0	ENST00000318789.4:c.1234G>A	p.Ala412Thr	p.A412T	ENST00000318789	NM_032682.5	412	Gcc/Acc	15/21	1	2	FACETS	0.839	0.773	0.908	1	0.991	1	CLONAL	2	TRUE	1	0.241860673129528	2		441	857	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799670	72799670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	117	420	0	ENST00000325599.8:c.1499G>A	p.Ser500Asn	p.S500N	ENST00000325599	NM_018130.2	500	aGt/aAt	11/11	1	2	FACETS	0.789	0.713	0.869	1	0.986	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		420	613	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799817	72799817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	143	381	0	ENST00000325599.8:c.1352G>A	p.Ser451Asn	p.S451N	ENST00000325599	NM_018130.2	451	aGc/aAc	11/11	1	2	FACETS	0.846	0.773	0.922	1	0.989	1	CLONAL	2	TRUE	1	0.241860673129528	2		381	699	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114293	73114293	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	27	359	0	ENST00000356692.5:c.928+1G>A		p.X310_splice	ENST00000356692		310			1	2	FACETS	0.522	0.414	0.644	0.522	0.414	0.644	SUBCLONAL	1	TRUE	1	0.241860673129528	2		359	428	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521616	89521616	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	82	358	0	ENST00000336596.2:c.2693C>A	p.Pro898Gln	p.P898Q	ENST00000336596	NM_005233.5	898	cCa/cAa	16/17	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.241860673129528	2		358	543	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119585465	119585465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	46	252	0	ENST00000316626.5:c.920G>A	p.Gly307Glu	p.G307E	ENST00000316626		307	gGa/gAa	9/12	1	2	FACETS	0.928	0.791	1	1	0.972	1	CLONAL	2	TRUE	1	0.241860673129528	2		252	205	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205867	128205867	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1220018679	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	22	318	0	ENST00000341105.2:c.8T>C	p.Val3Ala	p.V3A	ENST00000341105	NM_032638.4	3	gTg/gCg	2/6	1	2	FACETS	0.416	0.322	0.527	0.416	0.322	0.527	SUBCLONAL	1	TRUE	1	0.241860673129528	2		318	437	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851628	134851628	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	82	355	0	ENST00000398015.3:c.1034C>T	p.Pro345Leu	p.P345L	ENST00000398015	NM_004441.4	345	cCa/cTa	5/16	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.241860673129528	2		355	619	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967198	134967198	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	52	415	0	ENST00000398015.3:c.2537C>A	p.Pro846His	p.P846H	ENST00000398015	NM_004441.4	846	cCc/cAc	14/16	1	2	FACETS	0.667	0.567	0.777	0.667	0.567	0.777	SUBCLONAL	1	TRUE	1	0.241860673129528	2		415	645	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968209	134968209	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	75	445	0	ENST00000398015.3:c.2722C>A	p.Pro908Thr	p.P908T	ENST00000398015	NM_004441.4	908	Cca/Aca	15/16	1	2	FACETS	0.842	0.737	0.955	0.842	0.737	0.955	CLONAL	1	TRUE	1	0.241860673129528	2		445	737	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417912	138417912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	32	333	0	ENST00000289153.2:c.1607C>T	p.Pro536Leu	p.P536L	ENST00000289153	NM_006219.2	536	cCt/cTt	11/22	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.241860673129528	2		333	252	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433347	138433347	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	11	313	0	ENST00000289153.2:c.1265C>A	p.Pro422His	p.P422H	ENST00000289153	NM_006219.2	422	cCc/cAc	7/22	1	2	FACETS	0.448	0.309	0.62	0.448	0.309	0.62	SUBCLONAL	1	TRUE	1	0.241860673129528	2		313	203	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176458	142176458	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	64	286	0	ENST00000350721.4:c.7643A>C	p.Glu2548Ala	p.E2548A	ENST00000350721	NM_001184.3	2548	gAg/gCg	45/47	1	2	FACETS	0.83	0.724	0.943	1	0.976	1	CLONAL	2	TRUE	1	0.241860673129528	2		286	319	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176544	142176544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	22	335	0	ENST00000350721.4:c.7557G>A	p.Met2519Ile	p.M2519I	ENST00000350721	NM_001184.3	2519	atG/atA	45/47	1	2	FACETS	0.602	0.467	0.759	0.602	0.467	0.759	SUBCLONAL	1	TRUE	1	0.241860673129528	2		335	302	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212117	142212117	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	22	410	0	ENST00000350721.4:c.5935G>T	p.Gly1979Cys	p.G1979C	ENST00000350721	NM_001184.3	1979	Ggt/Tgt	35/47	1	2	FACETS	0.819	0.638	1	0.819	0.638	1	CLONAL	1	TRUE	1	0.241860673129528	2		410	222	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231123	142231123	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	41	323	0	ENST00000350721.4:c.4831A>G	p.Arg1611Gly	p.R1611G	ENST00000350721	NM_001184.3	1611	Aga/Gga	27/47	1	2	FACETS	0.723	0.602	0.857	0.723	0.602	0.857	SUBCLONAL	1	TRUE	1	0.241860673129528	2		323	469	SUCCESS
ATR	545	MSKCC	GRCh37	3	142234289	142234289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	27	290	0	ENST00000350721.4:c.4451G>A	p.Gly1484Asp	p.G1484D	ENST00000350721	NM_001184.3	1484	gGt/gAt	25/47	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.241860673129528	2		290	195	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272858	142272858	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	16	303	0	ENST00000350721.4:c.2342-1G>T		p.X781_splice	ENST00000350721	NM_001184.3	781			1	2	FACETS	0.696	0.516	0.91	0.696	0.516	0.91	SUBCLONAL	1	TRUE	1	0.241860673129528	2		303	190	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275329	142275329	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	73	382	0	ENST00000350721.4:c.1974G>T	p.Trp658Cys	p.W658C	ENST00000350721	NM_001184.3	658	tgG/tgT	9/47	1	2	FACETS	0.794	0.699	0.896	1	0.978	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		382	380	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277589	142277589	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	31	321	0	ENST00000350721.4:c.1762G>A	p.Glu588Lys	p.E588K	ENST00000350721	NM_001184.3	588	Gaa/Aaa	8/47	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.241860673129528	2		321	192	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281231	142281231	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	38	404	1	ENST00000350721.4:c.1013A>T	p.Lys338Met	p.K338M	ENST00000350721	NM_001184.3	338	aAg/aTg	4/47	1	2	FACETS	0.719	0.595	0.858	0.719	0.595	0.858	SUBCLONAL	1	TRUE	1	0.241860673129528	2		405	437	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374688	149374688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	98	326	1	ENST00000360632.3:c.406G>A	p.Ala136Thr	p.A136T	ENST00000360632	NM_015472.4	136	Gcc/Acc	2/7	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.241860673129528	2		327	557	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169940548	169940548	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	28	323	0	ENST00000295797.4:c.91T>C	p.Tyr31His	p.Y31H	ENST00000295797	NM_002740.5	31	Tac/Cac	1/18	1	2	FACETS	0.453	0.361	0.558	0.453	0.361	0.558	SUBCLONAL	1	TRUE	1	0.241860673129528	2		323	511	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928098	178928098	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	32	344	0	ENST00000263967.3:c.1376T>A	p.Ile459Asn	p.I459N	ENST00000263967	NM_006218.2	459	aTt/aAt	8/21	1	2	FACETS	1	0.832	1	1	0.832	1	CLONAL	1	TRUE	1	0.241860673129528	2		344	259	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430499	181430499	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	50	378	0	ENST00000325404.1:c.351G>T	p.Lys117Asn	p.K117N	ENST00000325404	NM_003106.3	117	aaG/aaT	1/1	1	2	FACETS	0.654	0.554	0.764	0.654	0.554	0.764	SUBCLONAL	1	TRUE	1	0.241860673129528	2		378	632	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182662920	182662920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	54	288	0	ENST00000292782.4:c.742C>T	p.Arg248Cys	p.R248C	ENST00000292782	NM_020640.2	248	Cgc/Tgc	7/7	1	2	FACETS	0.792	0.681	0.91	1	0.97	1	CLONAL	2	TRUE	1	0.241860673129528	2		288	282	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683469	182683469	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	24	323	0	ENST00000292782.4:c.76G>A	p.Ala26Thr	p.A26T	ENST00000292782	NM_020640.2	26	Gca/Aca	2/7	1	2	FACETS	0.878	0.691	1	0.878	0.691	1	CLONAL	1	TRUE	1	0.241860673129528	2		323	226	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161406	185161406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	57	348	0	ENST00000265026.3:c.833G>A	p.Arg278His	p.R278H	ENST00000265026	NM_004721.4	278	cGt/cAt	4/14	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.241860673129528	2		348	393	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167687	185167687	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	41	357	0	ENST00000265026.3:c.1011-1G>T		p.X337_splice	ENST00000265026	NM_004721.4	337			1	2	FACETS	0.605	0.504	0.719	0.605	0.504	0.719	SUBCLONAL	1	TRUE	1	0.241860673129528	2		357	560	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167690	185167691	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	102	341	0	ENST00000265026.3:c.1017dup	p.Gly340TrpfsTer41	p.G340Wfs*41	ENST00000265026	NM_004721.4	338	tct/tcTt	6/14	1	2	FACETS	0.764	0.685	0.847	1	0.983	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		341	552	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185169074	185169074	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	23	308	1	ENST00000265026.3:c.1170-1G>T		p.X390_splice	ENST00000265026	NM_004721.4	390			1	2	FACETS	0.448	0.348	0.563	0.448	0.348	0.563	SUBCLONAL	1	TRUE	1	0.241860673129528	2		309	425	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191536	185191536	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	149	423	0	ENST00000265026.3:c.2417G>T	p.Arg806Met	p.R806M	ENST00000265026	NM_004721.4	806	aGg/aTg	11/14	1	2	FACETS	0.815	0.746	0.887	1	0.989	1	CLONAL	2	TRUE	1	0.241860673129528	2		423	756	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185195175	185195175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749182070	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	48	344	0	ENST00000265026.3:c.2492G>A	p.Arg831Gln	p.R831Q	ENST00000265026	NM_004721.4	831	cGa/cAa	12/14	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.241860673129528	2		344	341	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185200142	185200143	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GA	GA	TG	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	104	369	0	ENST00000265026.3:c.2800-1_2800delinsTG		p.X934_splice	ENST00000265026	NM_004721.4	934		14/14	1	2	FACETS	0.979	0.883	1	1	0.988	1	CLONAL	2	TRUE	1	0.241860673129528	2		369	439	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185200143	185200143	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	104	369	0	ENST00000265026.3:c.2800A>G	p.Asn934Asp	p.N934D	ENST00000265026	NM_004721.4	934	Aac/Gac	14/14	1	2	FACETS	0.979	0.883	1	1	0.988	1	CLONAL	2	TRUE	1	0.241860673129528	2		369	439	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442857	187442857	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	102	408	0	ENST00000232014.4:c.1849C>A	p.Leu617Ile	p.L617I	ENST00000232014	NM_001130845.1	617	Ctc/Atc	9/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.241860673129528	2		408	602	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807669	1807669	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	141	446	0	ENST00000260795.2:c.1836+2T>C		p.X612_splice	ENST00000260795		612			1	2	FACETS	0.823	0.752	0.899	1	0.989	1	CLONAL	2	TRUE	1	0.241860673129528	2		446	708	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1932402	1932402	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	78	386	0	ENST00000382891.5:c.1460T>C	p.Leu487Pro	p.L487P	ENST00000382891	NM_133335.3	487	cTc/cCc	6/22	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.241860673129528	2		386	615	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1936871	1936871	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	54	318	0	ENST00000382891.5:c.1556G>A	p.Gly519Asp	p.G519D	ENST00000382891	NM_133335.3	519	gGt/gAt	7/22	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.241860673129528	2		318	402	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955132	1955132	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	116	422	0	ENST00000382891.5:c.2219A>G	p.His740Arg	p.H740R	ENST00000382891	NM_133335.3	740	cAt/cGt	12/22	1	2	FACETS	0.856	0.775	0.942	1	0.987	1	CLONAL	2	TRUE	1	0.241860673129528	2		422	560	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141142	55141142	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	69	350	0	ENST00000257290.5:c.1786+2T>C		p.X596_splice	ENST00000257290	NM_006206.4	596			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.241860673129528	2		350	415	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565857	55565857	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	96	307	0	ENST00000288135.5:c.681A>C	p.Glu227Asp	p.E227D	ENST00000288135	NM_000222.2	227	gaA/gaC	4/21	1	2	FACETS	1	0.949	1	1	0.988	1	CLONAL	2	TRUE	1	0.241860673129528	2		307	364	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575597	55575597	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	41	243	0	ENST00000288135.5:c.1123A>C	p.Ser375Arg	p.S375R	ENST00000288135	NM_000222.2	375	Agt/Cgt	7/21	1	2	FACETS	0.958	0.809	1	1	0.969	1	CLONAL	2	TRUE	1	0.241860673129528	2		243	177	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968562	55968562	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	90	394	0	ENST00000263923.4:c.2101T>G	p.Phe701Val	p.F701V	ENST00000263923	NM_002253.2	701	Ttt/Gtt	14/30	1	2	FACETS	0.811	0.723	0.904	1	0.982	1	CLONAL	2	TRUE	1	0.241860673129528	2		394	459	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971129	55971129	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	90	326	0	ENST00000263923.4:c.1668A>T	p.Gln556His	p.Q556H	ENST00000263923	NM_002253.2	556	caA/caT	13/30	1	2	FACETS	0.807	0.719	0.9	1	0.982	1	CLONAL	2	TRUE	1	0.241860673129528	2		326	461	SUCCESS
REST	5978	MSKCC	GRCh37	4	57797929	57797929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	98	389	0	ENST00000309042.7:c.2905C>T	p.Pro969Ser	p.P969S	ENST00000309042	NM_005612.4	969	Cca/Tca	4/4	1	2	FACETS	0.812	0.727	0.901	1	0.984	1	CLONAL	2	TRUE	1	0.241860673129528	2		389	499	SUCCESS
REST	5978	MSKCC	GRCh37	4	57798062	57798062	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	38	368	0	ENST00000309042.7:c.3038G>T	p.Ser1013Ile	p.S1013I	ENST00000309042	NM_005612.4	1013	aGc/aTc	4/4	1	2	FACETS	0.611	0.505	0.731	0.611	0.505	0.731	SUBCLONAL	1	TRUE	1	0.241860673129528	2		368	514	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201783	66201783	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747056219	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	107	435	0	ENST00000273854.3:c.2719C>T	p.Leu907Phe	p.L907F	ENST00000273854	NM_004439.5	907	Ctc/Ttc	16/18	1	2	FACETS	0.846	0.762	0.934	1	0.986	1	CLONAL	2	TRUE	1	0.241860673129528	2		435	523	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356206	66356206	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	82	450	0	ENST00000273854.3:c.1291C>A	p.Leu431Ile	p.L431I	ENST00000273854	NM_004439.5	431	Cta/Ata	5/18	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.241860673129528	2		450	664	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356430	66356430	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs943944162	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	22	403	0	ENST00000273854.3:c.1067G>A	p.Arg356Lys	p.R356K	ENST00000273854	NM_004439.5	356	aGa/aAa	5/18	1	2	FACETS	0.454	0.351	0.573	0.454	0.351	0.573	SUBCLONAL	1	TRUE	1	0.241860673129528	2		403	401	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467625	66467625	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	38	385	0	ENST00000273854.3:c.644A>G	p.Gln215Arg	p.Q215R	ENST00000273854	NM_004439.5	215	cAa/cGa	3/18	1	2	FACETS	0.709	0.586	0.846	0.709	0.586	0.846	SUBCLONAL	1	TRUE	1	0.241860673129528	2		385	443	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467662	66467662	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	44	369	0	ENST00000273854.3:c.607G>T	p.Gly203Ter	p.G203*	ENST00000273854	NM_004439.5	203	Gga/Tga	3/18	1	2	FACETS	0.856	0.719	1	0.856	0.719	1	CLONAL	1	TRUE	1	0.241860673129528	2		369	425	SUCCESS
ALB	213	MSKCC	GRCh37	4	74272366	74272366	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	24	392	0	ENST00000295897.4:c.158A>C	p.Gln53Pro	p.Q53P	ENST00000295897	NM_000477.5	53	cAg/cCg	3/15	1	2	FACETS	0.874	0.688	1	0.874	0.688	1	CLONAL	1	TRUE	1	0.241860673129528	2		392	227	SUCCESS
ALB	213	MSKCC	GRCh37	4	74272444	74272444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	23	312	0	ENST00000295897.4:c.236C>T	p.Ala79Val	p.A79V	ENST00000295897	NM_000477.5	79	gCt/gTt	3/15	1	2	FACETS	0.881	0.69	1	0.881	0.69	1	CLONAL	1	TRUE	1	0.241860673129528	2		312	216	SUCCESS
ALB	213	MSKCC	GRCh37	4	74279217	74279217	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	51	392	0	ENST00000295897.4:c.924G>T	p.Leu308Phe	p.L308F	ENST00000295897	NM_000477.5	308	ttG/ttT	8/15	1	2	FACETS	0.843	0.717	0.982	0.843	0.717	0.982	CLONAL	1	TRUE	1	0.241860673129528	2		392	500	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384046	84384046	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	19	345	0	ENST00000321945.7:c.806A>G	p.Asn269Ser	p.N269S	ENST00000321945	NM_139076.2	269	aAc/aGc	9/9	1	2	FACETS	0.734	0.559	0.939	0.734	0.559	0.939	CLONAL	1	TRUE	1	0.241860673129528	2		345	214	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84403344	84403344	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	17	309	0	ENST00000321945.7:c.141T>A	p.Asp47Glu	p.D47E	ENST00000321945	NM_139076.2	47	gaT/gaA	2/9	1	2	FACETS	0.53	0.396	0.69	0.53	0.396	0.69	SUBCLONAL	1	TRUE	1	0.241860673129528	2		309	265	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196384	106196384	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	91	447	0	ENST00000380013.4:c.4717C>T	p.Pro1573Ser	p.P1573S	ENST00000380013	NM_001127208.2	1573	Ccc/Tcc	11/11	1	2	FACETS	0.822	0.733	0.915	1	0.983	1	CLONAL	2	TRUE	1	0.241860673129528	2		447	458	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003263	143003263	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	28	292	0	ENST00000262992.4:c.2563C>A	p.Leu855Ile	p.L855I	ENST00000262992	NM_001101669.1	855	Ctt/Att	23/24	1	2	FACETS	0.601	0.48	0.739	0.601	0.48	0.739	SUBCLONAL	1	TRUE	1	0.241860673129528	2		292	385	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144258358	144258358	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	31	333	0	ENST00000262995.4:c.17T>C	p.Val6Ala	p.V6A	ENST00000262995	NM_207123.2	6	gTg/gCg	1/11	1	2	FACETS	0.579	0.468	0.705	0.579	0.468	0.705	SUBCLONAL	1	TRUE	1	0.241860673129528	2		333	443	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	31	349	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.241860673129528	2		349	235	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510212	187510212	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	103	424	0	ENST00000441802.2:c.13301A>G	p.Asp4434Gly	p.D4434G	ENST00000441802	NM_005245.3	4434	gAt/gGt	27/27	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.241860673129528	2		424	613	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518013	187518013	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	98	456	0	ENST00000441802.2:c.12681C>A	p.Phe4227Leu	p.F4227L	ENST00000441802	NM_005245.3	4227	ttC/ttA	25/27	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.241860673129528	2		456	628	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524057	187524057	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	40	360	0	ENST00000441802.2:c.11482G>T	p.Gly3828Trp	p.G3828W	ENST00000441802	NM_005245.3	3828	Ggg/Tgg	20/27	1	2	FACETS	0.628	0.521	0.747	0.628	0.521	0.747	SUBCLONAL	1	TRUE	1	0.241860673129528	2		360	527	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531065	187531065	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	37	385	0	ENST00000441802.2:c.9958A>G	p.Thr3320Ala	p.T3320A	ENST00000441802	NM_005245.3	3320	Act/Gct	15/27	1	2	FACETS	0.551	0.454	0.661	0.551	0.454	0.661	SUBCLONAL	1	TRUE	1	0.241860673129528	2		385	555	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539354	187539354	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	51	455	0	ENST00000441802.2:c.8386A>G	p.Ser2796Gly	p.S2796G	ENST00000441802	NM_005245.3	2796	Agt/Ggt	10/27	1	2	FACETS	0.816	0.693	0.95	0.816	0.693	0.95	CLONAL	1	TRUE	1	0.241860673129528	2		455	517	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539378	187539378	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	70	445	0	ENST00000441802.2:c.8362G>T	p.Glu2788Ter	p.E2788*	ENST00000441802	NM_005245.3	2788	Gag/Tag	10/27	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.241860673129528	2		445	532	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540523	187540523	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	125	449	0	ENST00000441802.2:c.7217G>T	p.Gly2406Val	p.G2406V	ENST00000441802	NM_005245.3	2406	gGg/gTg	10/27	1	2	FACETS	0.851	0.773	0.934	1	0.988	1	CLONAL	2	TRUE	1	0.241860673129528	2		449	607	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540670	187540670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530876083	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	56	483	0	ENST00000441802.2:c.7070C>T	p.Thr2357Met	p.T2357M	ENST00000441802	NM_005245.3	2357	aCg/aTg	10/27	1	2	FACETS	0.593	0.507	0.688	0.593	0.507	0.688	SUBCLONAL	1	TRUE	1	0.241860673129528	2		483	781	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540679	187540679	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	71	452	0	ENST00000441802.2:c.7061G>T	p.Arg2354Leu	p.R2354L	ENST00000441802	NM_005245.3	2354	cGg/cTg	10/27	1	2	FACETS	0.778	0.678	0.886	0.778	0.678	0.886	SUBCLONAL	1	TRUE	1	0.241860673129528	2		452	755	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542066	187542066	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs771318103	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	31	506	0	ENST00000441802.2:c.5674A>G	p.Thr1892Ala	p.T1892A	ENST00000441802	NM_005245.3	1892	Aca/Gca	10/27	1	2	FACETS	0.676	0.547	0.822	0.676	0.547	0.822	SUBCLONAL	1	TRUE	1	0.241860673129528	2		506	379	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629928	187629928	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	40	493	0	ENST00000441802.2:c.1054G>T	p.Val352Phe	p.V352F	ENST00000441802	NM_005245.3	352	Gtc/Ttc	2/27	1	2	FACETS	0.546	0.453	0.65	0.546	0.453	0.65	SUBCLONAL	1	TRUE	1	0.241860673129528	2		493	606	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630128	187630128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	61	517	1	ENST00000441802.2:c.854C>T	p.Ala285Val	p.A285V	ENST00000441802	NM_005245.3	285	gCc/gTc	2/27	1	2	FACETS	0.791	0.682	0.909	0.791	0.682	0.909	CLONAL	1	TRUE	1	0.241860673129528	2		518	638	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	223624	223624	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs142441643	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	26	285	0	ENST00000264932.6:c.91C>T	p.Arg31Ter	p.R31*	ENST00000264932	NM_004168.2	31	Cga/Tga	2/15	1	2	FACETS	0.567	0.449	0.703	0.567	0.449	0.703	SUBCLONAL	1	TRUE	1	0.241860673129528	2		285	379	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	901497	901497	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	111	365	0	ENST00000166345.3:c.486G>T	p.Lys162Asn	p.K162N	ENST00000166345	NM_004237.3	162	aaG/aaT	5/13	1	2	FACETS	0.836	0.754	0.922	1	0.986	1	CLONAL	2	TRUE	1	0.241860673129528	2		365	549	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279582	1279582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1228165704	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	106	247	0	ENST00000310581.5:c.1954G>A	p.Glu652Lys	p.E652K	ENST00000310581	NM_198253.2	652	Gag/Aag	5/16	1	2	FACETS	0.762	0.685	0.843	1	0.983	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		247	575	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1296195	1296195	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	53	442	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.547	0.465	0.637	0.547	0.465	0.637	SUBCLONAL	1	TRUE	1	0.241860673129528	2		442	801	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31405819	31405819	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	16	295	0	ENST00000344624.3:c.3959C>G	p.Ala1320Gly	p.A1320G	ENST00000344624		1320	gCg/gGg	32/33	1	2	FACETS	0.639	0.473	0.836	0.639	0.473	0.836	SUBCLONAL	1	TRUE	1	0.241860673129528	2		295	207	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31485046	31485046	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	25	350	0	ENST00000344624.3:c.1938A>T	p.Glu646Asp	p.E646D	ENST00000344624		646	gaA/gaT	12/33	1	2	FACETS	0.834	0.659	1	0.834	0.659	1	CLONAL	1	TRUE	1	0.241860673129528	2		350	248	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515295	31515295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756537138	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	62	390	0	ENST00000344624.3:c.1090C>T	p.Arg364Cys	p.R364C	ENST00000344624		364	Cgt/Tgt	5/33	1	2	FACETS	0.904	0.781	1	0.904	0.781	1	CLONAL	1	TRUE	1	0.241860673129528	2		390	567	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526214	31526214	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	47	419	0	ENST00000344624.3:c.826T>G	p.Ser276Ala	p.S276A	ENST00000344624		276	Tct/Gct	2/33	1	2	FACETS	0.564	0.475	0.663	0.564	0.475	0.663	SUBCLONAL	1	TRUE	1	0.241860673129528	2		419	689	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873586	35873586	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	37	342	0	ENST00000303115.3:c.542T>A	p.Val181Glu	p.V181E	ENST00000303115	NM_002185.3	181	gTg/gAg	5/8	1	2	FACETS	0.703	0.58	0.841	0.703	0.58	0.841	SUBCLONAL	1	TRUE	1	0.241860673129528	2		342	435	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875666	35875666	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1022245698	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	79	366	0	ENST00000303115.3:c.853C>T	p.His285Tyr	p.H285Y	ENST00000303115	NM_002185.3	285	Cat/Tat	7/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.241860673129528	2		366	501	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950436	38950436	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs781542631	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	23	387	1	ENST00000357387.3:c.3514A>G	p.Thr1172Ala	p.T1172A	ENST00000357387	NM_152756.3	1172	Act/Gct	31/38	1	2	FACETS	0.559	0.436	0.702	0.559	0.436	0.702	SUBCLONAL	1	TRUE	1	0.241860673129528	2		388	340	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38978722	38978722	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	40	288	0	ENST00000357387.3:c.784T>A	p.Tyr262Asn	p.Y262N	ENST00000357387	NM_152756.3	262	Tac/Aac	9/38	1	2	FACETS	0.803	0.674	0.943	1	0.961	1	CLONAL	2	TRUE	1	0.241860673129528	2		288	206	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155552	56155552	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	36	351	0	ENST00000399503.3:c.644C>A	p.Pro215Gln	p.P215Q	ENST00000399503	NM_005921.1	215	cCa/cAa	3/20	1	2	FACETS	0.707	0.581	0.848	0.707	0.581	0.848	SUBCLONAL	1	TRUE	1	0.241860673129528	2		351	421	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160762	56160762	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs890505345	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	29	363	0	ENST00000399503.3:c.1035+1G>A		p.X345_splice	ENST00000399503	NM_005921.1	345			1	2	FACETS	0.558	0.447	0.684	0.558	0.447	0.684	SUBCLONAL	1	TRUE	1	0.241860673129528	2		363	430	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751549	57751549	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	126	416	0	ENST00000274289.3:c.1442G>A	p.Gly481Glu	p.G481E	ENST00000274289	NM_006622.3	481	gGa/gAa	11/14	1	2	FACETS	0.792	0.718	0.869	1	0.987	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		416	658	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564386	86564386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	63	421	0	ENST00000274376.6:c.118G>A	p.Ala40Thr	p.A40T	ENST00000274376	NM_002890.2	40	Gcg/Acg	1/25	1	2	FACETS	0.94	0.814	1	0.94	0.814	1	CLONAL	1	TRUE	1	0.241860673129528	2		421	554	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86668013	86668013	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	52	358	0	ENST00000274376.6:c.1776+1G>A		p.X592_splice	ENST00000274376	NM_002890.2	592			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.241860673129528	2		358	315	SUCCESS
APC	324	MSKCC	GRCh37	5	112102080	112102080	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	20	220	0	ENST00000257430.4:c.193C>T	p.Gln65Ter	p.Q65*	ENST00000257430	NM_000038.5	65	Cag/Tag	3/16	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.241860673129528	2		220	140	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	33	316	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	0.78	0.642	0.931	1	0.951	1	CLONAL	2	TRUE	1	0.241860673129528	2		316	175	SUCCESS
APC	324	MSKCC	GRCh37	5	112173293	112173293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660307	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	28	351	0	ENST00000257430.4:c.2002C>T	p.His668Tyr	p.H668Y	ENST00000257430	NM_000038.5	668	Cac/Tac	16/16	1	2	FACETS	0.695	0.556	0.853	0.695	0.556	0.853	SUBCLONAL	1	TRUE	1	0.241860673129528	2		351	333	SUCCESS
APC	324	MSKCC	GRCh37	5	112173888	112173888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	33	422	0	ENST00000257430.4:c.2597C>T	p.Ala866Val	p.A866V	ENST00000257430	NM_000038.5	866	gCa/gTa	16/16	1	2	FACETS	0.525	0.427	0.636	0.525	0.427	0.636	SUBCLONAL	1	TRUE	1	0.241860673129528	2		422	520	SUCCESS
APC	324	MSKCC	GRCh37	5	112175748	112175748	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	45	459	0	ENST00000257430.4:c.4457A>G	p.Asp1486Gly	p.D1486G	ENST00000257430	NM_000038.5	1486	gAt/gGt	16/16	1	2	FACETS	0.633	0.531	0.746	0.633	0.531	0.746	SUBCLONAL	1	TRUE	1	0.241860673129528	2		459	588	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927570	131927570	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	15	241	0	ENST00000265335.6:c.1637C>T	p.Ala546Val	p.A546V	ENST00000265335		546	gCt/gTt	11/25	1	2	FACETS	0.77	0.566	1	0.77	0.566	1	CLONAL	1	TRUE	1	0.241860673129528	2		241	161	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939738	131939738	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	20	325	0	ENST00000265335.6:c.2524G>T	p.Val842Phe	p.V842F	ENST00000265335		842	Gtt/Ttt	15/25	1	2	FACETS	0.622	0.476	0.792	0.622	0.476	0.792	SUBCLONAL	1	TRUE	1	0.241860673129528	2		325	266	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149434864	149434864	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	59	425	0	ENST00000286301.3:c.2590A>G	p.Lys864Glu	p.K864E	ENST00000286301	NM_005211.3	864	Aag/Gag	20/22	1	2	FACETS	0.777	0.668	0.896	0.777	0.668	0.896	SUBCLONAL	1	TRUE	1	0.241860673129528	2		425	628	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149450096	149450096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	40	388	0	ENST00000286301.3:c.1121C>T	p.Ser374Phe	p.S374F	ENST00000286301	NM_005211.3	374	tCt/tTt	8/22	1	2	FACETS	0.489	0.405	0.583	0.489	0.405	0.583	SUBCLONAL	1	TRUE	1	0.241860673129528	2		388	676	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149453027	149453027	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	49	433	0	ENST00000286301.3:c.919C>T	p.Gln307Ter	p.Q307*	ENST00000286301	NM_005211.3	307	Cag/Tag	7/22	1	2	FACETS	0.613	0.518	0.718	0.613	0.518	0.718	SUBCLONAL	1	TRUE	1	0.241860673129528	2		433	661	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495393	149495393	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	54	482	0	ENST00000261799.4:c.3254A>G	p.Glu1085Gly	p.E1085G	ENST00000261799	NM_002609.3	1085	gAg/gGg	23/23	1	2	FACETS	0.63	0.537	0.732	0.63	0.537	0.732	SUBCLONAL	1	TRUE	1	0.241860673129528	2		482	709	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504311	149504311	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	29	340	0	ENST00000261799.4:c.1891G>T	p.Val631Leu	p.V631L	ENST00000261799	NM_002609.3	631	Gtg/Ttg	13/23	1	2	FACETS	0.546	0.438	0.67	0.546	0.438	0.67	SUBCLONAL	1	TRUE	1	0.241860673129528	2		340	439	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513230	149513230	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	46	443	0	ENST00000261799.4:c.853G>T	p.Asp285Tyr	p.D285Y	ENST00000261799	NM_002609.3	285	Gac/Tac	6/23	1	2	FACETS	0.53	0.445	0.624	0.53	0.445	0.624	SUBCLONAL	1	TRUE	1	0.241860673129528	2		443	718	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519321	176519321	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	101	408	0	ENST00000292408.4:c.728-1G>T		p.X243_splice	ENST00000292408	NM_213647.1	243			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.241860673129528	2		408	639	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562105	176562105	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1472886872	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	85	401	0	ENST00000439151.2:c.1A>G	p.Met1?	p.M1?	ENST00000439151	NM_022455.4	1	Atg/Gtg	2/23	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.241860673129528	2		401	579	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665339	176665339	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	44	363	0	ENST00000439151.2:c.4023G>T	p.Glu1341Asp	p.E1341D	ENST00000439151	NM_022455.4	1341	gaG/gaT	7/23	1	2	FACETS	0.484	0.405	0.573	0.484	0.405	0.573	SUBCLONAL	1	TRUE	1	0.241860673129528	2		363	751	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687092	176687092	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	63	371	0	ENST00000439151.2:c.5069C>A	p.Pro1690His	p.P1690H	ENST00000439151	NM_022455.4	1690	cCt/cAt	14/23	1	2	FACETS	0.834	0.721	0.956	0.834	0.721	0.956	CLONAL	1	TRUE	1	0.241860673129528	2		371	625	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720881	176720881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	150	520	1	ENST00000439151.2:c.6512C>T	p.Ala2171Val	p.A2171V	ENST00000439151	NM_022455.4	2171	gCa/gTa	23/23	1	2	FACETS	0.782	0.715	0.852	1	0.988	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		521	793	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720962	176720962	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	126	454	0	ENST00000439151.2:c.6593G>T	p.Gly2198Val	p.G2198V	ENST00000439151	NM_022455.4	2198	gGg/gTg	23/23	1	2	FACETS	0.765	0.694	0.84	1	0.986	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		454	681	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720998	176720998	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	58	443	0	ENST00000439151.2:c.6629C>A	p.Pro2210His	p.P2210H	ENST00000439151	NM_022455.4	2210	cCc/cAc	23/23	1	2	FACETS	0.748	0.642	0.864	0.748	0.642	0.864	SUBCLONAL	1	TRUE	1	0.241860673129528	2		443	641	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721618	176721618	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs895272851	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	42	454	0	ENST00000439151.2:c.7249A>G	p.Arg2417Gly	p.R2417G	ENST00000439151	NM_022455.4	2417	Aga/Gga	23/23	1	2	FACETS	0.451	0.375	0.536	0.451	0.375	0.536	SUBCLONAL	1	TRUE	1	0.241860673129528	2		454	770	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039520	180039520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	86	343	0	ENST00000261937.6:c.3523G>A	p.Gly1175Ser	p.G1175S	ENST00000261937	NM_182925.4	1175	Ggc/Agc	26/30	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.241860673129528	2		343	512	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043480	180043480	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	119	355	1	ENST00000261937.6:c.3106A>G	p.Arg1036Gly	p.R1036G	ENST00000261937	NM_182925.4	1036	Aga/Gga	23/30	1	2	FACETS	0.77	0.696	0.847	1	0.985	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		356	639	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407587	407587	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	29	374	0	ENST00000380956.4:c.1345A>G	p.Ile449Val	p.I449V	ENST00000380956	NM_001195286.1	449	Att/Gtt	9/9	1	2	FACETS	0.597	0.479	0.731	0.597	0.479	0.731	SUBCLONAL	1	TRUE	1	0.241860673129528	2		374	402	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045766	26045766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1042668277	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	81	501	0	ENST00000540144.1:c.128G>A	p.Arg43His	p.R43H	ENST00000540144	NM_003531.2	43	cGc/cAc	1/1	1	2	FACETS	0.792	0.696	0.894	0.792	0.696	0.894	SUBCLONAL	1	TRUE	1	0.241860673129528	2		501	846	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777873	27777873	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	45	498	0	ENST00000369163.2:c.22G>A	p.Ala8Thr	p.A8T	ENST00000369163	NM_003536.2	8	Gct/Act	1/1	1	2	FACETS	0.524	0.439	0.618	0.524	0.439	0.618	SUBCLONAL	1	TRUE	1	0.241860673129528	2		498	710	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911122	29911122	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199474506	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	56	425	0	ENST00000376809.5:c.421G>A	p.Ala141Thr	p.A141T	ENST00000376809	NM_002116.7	141	Gcc/Acc	3/8	1	2	FACETS	0.694	0.594	0.804	0.694	0.594	0.804	SUBCLONAL	1	TRUE	1	0.241860673129528	2		425	667	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29913027	29913027	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	55	388	0	ENST00000376809.5:c.1062G>T	p.Gln354His	p.Q354H	ENST00000376809	NM_002116.7	354	caG/caT	7/8	1	2	FACETS	0.633	0.541	0.735	0.633	0.541	0.735	SUBCLONAL	1	TRUE	1	0.241860673129528	2		388	718	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670940	30670940	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	65	415	0	ENST00000376406.3:c.5806A>G	p.Lys1936Glu	p.K1936E	ENST00000376406	NM_014641.2	1936	Aag/Gag	12/15	1	2	FACETS	0.726	0.629	0.832	0.726	0.629	0.832	SUBCLONAL	1	TRUE	1	0.241860673129528	2		415	740	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672930	30672930	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	55	609	0	ENST00000376406.3:c.4030C>A	p.Pro1344Thr	p.P1344T	ENST00000376406	NM_014641.2	1344	Cct/Act	10/15	1	2	FACETS	0.513	0.437	0.596	0.513	0.437	0.596	SUBCLONAL	1	TRUE	1	0.241860673129528	2		609	887	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673674	30673674	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	116	495	0	ENST00000376406.3:c.3286T>C	p.Ser1096Pro	p.S1096P	ENST00000376406	NM_014641.2	1096	Tca/Cca	10/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.241860673129528	2		495	641	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673682	30673682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372811207	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	58	510	0	ENST00000376406.3:c.3278C>T	p.Pro1093Leu	p.P1093L	ENST00000376406	NM_014641.2	1093	cCc/cTc	10/15	1	2	FACETS	0.705	0.605	0.815	0.705	0.605	0.815	SUBCLONAL	1	TRUE	1	0.241860673129528	2		510	680	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31239090	31239090	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs34592426	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	119	500	0	ENST00000376228.5:c.379C>A	p.Leu127Met	p.L127M	ENST00000376228	NM_002117.5	127	Ctg/Atg	3/8	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.241860673129528	2		500	771	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31239818	31239818	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	35	467	0	ENST00000376228.5:c.31C>A	p.Leu11Met	p.L11M	ENST00000376228	NM_002117.5	11	Ctg/Atg	1/8	1	2	FACETS	0.429	0.351	0.518	0.429	0.351	0.518	SUBCLONAL	1	TRUE	1	0.241860673129528	2		467	674	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181537	32181537	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	40	364	0	ENST00000375023.3:c.2248G>T	p.Gly750Cys	p.G750C	ENST00000375023	NM_004557.3	750	Ggc/Tgc	14/30	1	2	FACETS	0.501	0.415	0.597	0.501	0.415	0.597	SUBCLONAL	1	TRUE	1	0.241860673129528	2		364	660	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185864	32185864	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	111	369	0	ENST00000375023.3:c.1532A>T	p.Glu511Val	p.E511V	ENST00000375023	NM_004557.3	511	gAg/gTg	9/30	1	2	FACETS	0.79	0.712	0.872	1	0.985	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		369	581	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797241	32797241	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778896765	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	60	404	0	ENST00000374899.4:c.1868G>A	p.Arg623Gln	p.R623Q	ENST00000374899	NM_018833.2	623	cGa/cAa	11/12	1	2	FACETS	0.654	0.562	0.754	0.654	0.562	0.754	SUBCLONAL	1	TRUE	1	0.241860673129528	2		404	759	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818728	32818728	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs55955143	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	55	366	0	ENST00000354258.4:c.1223G>T	p.Trp408Leu	p.W408L	ENST00000354258	NM_000593.5	408	tGg/tTg	4/11	1	2	FACETS	0.809	0.692	0.937	0.809	0.692	0.937	CLONAL	1	TRUE	1	0.241860673129528	2		366	562	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287524	33287524	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	47	463	0	ENST00000374542.5:c.1573G>T	p.Gly525Ter	p.G525*	ENST00000374542	NM_001141970.1	525	Gga/Tga	6/8	1	2	FACETS	0.556	0.468	0.653	0.556	0.468	0.653	SUBCLONAL	1	TRUE	1	0.241860673129528	2		463	699	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289603	33289603	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1282674627	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	49	397	0	ENST00000374542.5:c.100C>T	p.Pro34Ser	p.P34S	ENST00000374542	NM_001141970.1	34	Cct/Tct	2/8	1	2	FACETS	0.659	0.557	0.771	0.659	0.557	0.771	SUBCLONAL	1	TRUE	1	0.241860673129528	2		397	615	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41905027	41905027	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	59	409	0	ENST00000372991.4:c.520C>T	p.Arg174Ter	p.R174*	ENST00000372991	NM_001760.3	174	Cga/Tga	3/5	1	2	FACETS	0.665	0.571	0.767	0.665	0.571	0.767	SUBCLONAL	1	TRUE	1	0.241860673129528	2		409	734	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43738986	43738986	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	47	406	0	ENST00000523873.1:c.3G>A	p.Met1?	p.M1?	ENST00000523873		1	atG/atA	1/8	1	2	FACETS	0.712	0.6	0.835	0.712	0.6	0.835	SUBCLONAL	1	TRUE	1	0.241860673129528	2		406	546	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43749697	43749697	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	64	399	0	ENST00000523873.1:c.550T>G	p.Cys184Gly	p.C184G	ENST00000523873		184	Tgt/Ggt	7/8	1	2	FACETS	0.633	0.547	0.727	0.633	0.547	0.727	SUBCLONAL	1	TRUE	1	0.241860673129528	2		399	836	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64290050	64290050	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs546134768	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	79	374	0	ENST00000370651.3:c.493G>T	p.Gly165Cys	p.G165C	ENST00000370651	NM_003463.4	165	Ggt/Tgt	6/6	1	2	FACETS	0.758	0.669	0.852	1	0.978	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		374	431	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790735	89790735	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs946884142	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	64	456	0	ENST00000336032.3:c.122C>T	p.Pro41Leu	p.P41L	ENST00000336032	NM_006813.2	41	cCt/cTt	1/2	1	2	FACETS	0.889	0.77	1	0.889	0.77	1	CLONAL	1	TRUE	1	0.241860673129528	2		456	595	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793769	89793769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	42	410	0	ENST00000336032.3:c.838G>A	p.Ala280Thr	p.A280T	ENST00000336032	NM_006813.2	280	Gct/Act	2/2	1	2	FACETS	0.851	0.712	1	0.851	0.712	1	CLONAL	1	TRUE	1	0.241860673129528	2		410	408	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554859	106554859	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	69	380	1	ENST00000369096.4:c.1976A>G	p.Tyr659Cys	p.Y659C	ENST00000369096	NM_001198.3	659	tAc/tGc	7/7	1	2	FACETS	0.805	0.7	0.918	0.805	0.7	0.918	CLONAL	1	TRUE	1	0.241860673129528	2		381	709	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111982983	111982983	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	56	377	0	ENST00000368678.4:c.1564A>G	p.Thr522Ala	p.T522A	ENST00000368678		522	Acc/Gcc	13/13	1	2	FACETS	0.63	0.539	0.73	0.63	0.539	0.73	SUBCLONAL	1	TRUE	1	0.241860673129528	2		377	735	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017660	112017660	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	20	303	0	ENST00000368678.4:c.854-1G>T		p.X285_splice	ENST00000368678		285			1	2	FACETS	0.479	0.366	0.612	0.479	0.366	0.612	SUBCLONAL	1	TRUE	1	0.241860673129528	2		303	345	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631254	117631254	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	81	340	0	ENST00000368508.3:c.6424T>A	p.Ser2142Thr	p.S2142T	ENST00000368508	NM_002944.2	2142	Tct/Act	40/43	0.170890120596729	0	FACETS	1	0.965	1			1	CLONAL	1	TRUE	0	0.241860673129528	0		340	410	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641099	117641099	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	96	520	0	ENST00000368508.3:c.5872G>T	p.Glu1958Ter	p.E1958*	ENST00000368508	NM_002944.2	1958	Gaa/Taa	36/43	0.170890120596729	0	FACETS	1	0.925	1			1	CLONAL	1	TRUE	0	0.241860673129528	0		520	576	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647516	117647516	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	42	432	0	ENST00000368508.3:c.5428T>C	p.Ser1810Pro	p.S1810P	ENST00000368508	NM_002944.2	1810	Tcc/Ccc	33/43	0.170890120596729	0	FACETS	0.725	0.607	0.856			1	SUBCLONAL	1	TRUE	0	0.241860673129528	0		432	363	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117650511	117650511	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs762317256	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	60	477	0	ENST00000368508.3:c.5347T>C	p.Tyr1783His	p.Y1783H	ENST00000368508	NM_002944.2	1783	Tac/Cac	32/43	0.170890120596729	0	FACETS	0.672	0.584	0.766			1	SUBCLONAL	2	TRUE	0	0.241860673129528	0		477	280	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686784	117686784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	34	343	1	ENST00000368508.3:c.2933G>A	p.Gly978Asp	p.G978D	ENST00000368508	NM_002944.2	978	gGt/gAt	19/43	0.170890120596729	0	FACETS	0.65	0.532	0.782			1	SUBCLONAL	1	TRUE	0	0.241860673129528	0		344	328	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704551	117704551	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	37	369	0	ENST00000368508.3:c.2425G>T	p.Val809Leu	p.V809L	ENST00000368508	NM_002944.2	809	Gtg/Ttg	16/43	0.170890120596729	0	FACETS	0.52	0.429	0.622			1	SUBCLONAL	1	TRUE	0	0.241860673129528	0		369	446	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527447	137527447	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	22	223	0	ENST00000367739.4:c.201-2A>G		p.X67_splice	ENST00000367739	NM_000416.2	67			1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.241860673129528	2		223	130	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199889	138199889	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	146	487	0	ENST00000237289.4:c.1307G>T	p.Gly436Val	p.G436V	ENST00000237289	NM_001270507.1	436	gGg/gTg	7/9	1	2	FACETS	0.787	0.719	0.858	1	0.988	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		487	767	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997792	149997792	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	56	450	0	ENST00000253339.5:c.2675A>G	p.Lys892Arg	p.K892R	ENST00000253339		892	aAg/aGg	5/7	1	2	FACETS	0.703	0.601	0.814	0.703	0.601	0.814	SUBCLONAL	1	TRUE	1	0.241860673129528	2		450	659	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001266	150001266	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	57	371	0	ENST00000253339.5:c.2338T>G	p.Phe780Val	p.F780V	ENST00000253339		780	Ttt/Gtt	4/7	1	2	FACETS	0.943	0.817	1	1	0.977	1	CLONAL	2	TRUE	1	0.241860673129528	2		371	250	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150022976	150022976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373625760	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	91	368	0	ENST00000253339.5:c.287G>A	p.Arg96Gln	p.R96Q	ENST00000253339		96	cGg/cAg	1/7	1	2	FACETS	1	0.919	1	1	0.987	1	CLONAL	2	TRUE	1	0.241860673129528	2		368	365	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163761	152163761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	97	412	0	ENST00000206249.3:c.482G>A	p.Gly161Asp	p.G161D	ENST00000206249	NM_000125.3	161	gGc/gAc	2/8	1	2	FACETS	0.77	0.689	0.856	1	0.982	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		412	521	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511344	157511344	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	101	353	0	ENST00000346085.5:c.3862G>T	p.Val1288Leu	p.V1288L	ENST00000346085	NM_020732.3	1288	Gtg/Ttg	15/20	1	2	FACETS	0.761	0.682	0.844	1	0.982	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		353	549	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527364	157527364	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	92	354	0	ENST00000346085.5:c.5089A>C	p.Ile1697Leu	p.I1697L	ENST00000346085	NM_020732.3	1697	Att/Ctt	20/20	1	2	FACETS	0.801	0.715	0.892	1	0.982	1	CLONAL	2	TRUE	1	0.241860673129528	2		354	475	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527513	157527513	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	67	434	0	ENST00000346085.5:c.5238G>T	p.Glu1746Asp	p.E1746D	ENST00000346085	NM_020732.3	1746	gaG/gaT	20/20	1	2	FACETS	0.848	0.737	0.969	0.848	0.737	0.969	CLONAL	1	TRUE	1	0.241860673129528	2		434	653	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781146	161781146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531247345	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	64	398	1	ENST00000366898.1:c.1259G>A	p.Arg420His	p.R420H	ENST00000366898	NM_004562.2	420	cGc/cAc	11/12	1	2	FACETS	0.741	0.641	0.85	0.741	0.641	0.85	SUBCLONAL	1	TRUE	1	0.241860673129528	2		399	714	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968295	2968295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1037942671	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	39	385	0	ENST00000396946.4:c.1691C>T	p.Thr564Ile	p.T564I	ENST00000396946	NM_032415.4	564	aCc/aTc	13/25	1	2	FACETS	0.465	0.384	0.555	0.465	0.384	0.555	SUBCLONAL	1	TRUE	1	0.241860673129528	2		385	694	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974190	2974190	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	61	382	0	ENST00000396946.4:c.1415A>G	p.Gln472Arg	p.Q472R	ENST00000396946	NM_032415.4	472	cAa/cGa	10/25	1	2	FACETS	0.794	0.685	0.914	0.794	0.685	0.914	CLONAL	1	TRUE	1	0.241860673129528	2		382	635	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946096	13946096	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	38	344	0	ENST00000405192.2:c.1000A>C	p.Thr334Pro	p.T334P	ENST00000405192	NM_001163147.1	334	Act/Cct	10/12	1	2	FACETS	0.659	0.544	0.787	0.659	0.544	0.787	SUBCLONAL	1	TRUE	1	0.241860673129528	2		344	477	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729489	41729489	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	62	414	0	ENST00000242208.4:c.1040C>T	p.Ala347Val	p.A347V	ENST00000242208	NM_002192.2	347	gCc/gTc	3/3	1	2	FACETS	0.805	0.695	0.925	0.805	0.695	0.925	CLONAL	1	TRUE	1	0.241860673129528	2		414	637	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739618	41739618	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	37	291	0	ENST00000242208.4:c.355C>T	p.Gln119Ter	p.Q119*	ENST00000242208	NM_002192.2	119	Cag/Tag	2/3	1	2	FACETS	0.71	0.585	0.849	0.71	0.585	0.849	SUBCLONAL	1	TRUE	1	0.241860673129528	2		291	431	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367249	50367249	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752227855	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	122	362	0	ENST00000331340.3:c.56C>T	p.Pro19Leu	p.P19L	ENST00000331340	NM_006060.4	19	cCt/cTt	3/8	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.241860673129528	2		362	700	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467693	50467693	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	116	375	0	ENST00000331340.3:c.928G>T	p.Val310Leu	p.V310L	ENST00000331340	NM_006060.4	310	Gtg/Ttg	8/8	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.241860673129528	2		375	642	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467999	50467999	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	41	451	0	ENST00000331340.3:c.1234A>G	p.Ile412Val	p.I412V	ENST00000331340	NM_006060.4	412	Atc/Gtc	8/8	1	2	FACETS	0.451	0.374	0.537	0.451	0.374	0.537	SUBCLONAL	1	TRUE	1	0.241860673129528	2		451	752	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468000	50468000	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1409620690	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	78	452	0	ENST00000331340.3:c.1235T>C	p.Ile412Thr	p.I412T	ENST00000331340	NM_006060.4	412	aTc/aCc	8/8	1	2	FACETS	0.884	0.776	0.999	0.884	0.776	0.999	CLONAL	1	TRUE	1	0.241860673129528	2		452	730	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259411	55259411	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	100	293	0	ENST00000275493.2:c.2470-1G>A		p.X824_splice	ENST00000275493	NM_005228.3	824			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.241860673129528	2		293	561	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268993	55268993	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	53	473	0	ENST00000275493.2:c.3059A>G	p.Gln1020Arg	p.Q1020R	ENST00000275493	NM_005228.3	1020	cAg/cGg	25/28	1	2	FACETS	0.563	0.478	0.655	0.563	0.478	0.655	SUBCLONAL	1	TRUE	1	0.241860673129528	2		473	779	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332000	81332000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543827901	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	51	344	0	ENST00000222390.5:c.2084G>A	p.Arg695His	p.R695H	ENST00000222390	NM_000601.4	695	cGt/cAt	18/18	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.241860673129528	2		344	308	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346628	81346628	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	35	378	0	ENST00000222390.5:c.1325A>G	p.Asn442Ser	p.N442S	ENST00000222390	NM_000601.4	442	aAt/aGt	11/18	1	2	FACETS	0.683	0.559	0.821	0.683	0.559	0.821	SUBCLONAL	1	TRUE	1	0.241860673129528	2		378	424	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403138	116403138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1209881740	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	44	405	0	ENST00000397752.3:c.2399G>A	p.Cys800Tyr	p.C800Y	ENST00000397752	NM_000245.2	800	tGt/tAt	11/21	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.241860673129528	2		405	301	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411900	116411900	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	41	563	0	ENST00000397752.3:c.2888-3A>G		p.X963_splice	ENST00000397752	NM_000245.2	963			1	2	FACETS	0.468	0.389	0.557	0.468	0.389	0.557	SUBCLONAL	1	TRUE	1	0.241860673129528	2		563	724	SUCCESS
MET	4233	MSKCC	GRCh37	7	116422079	116422079	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	23	291	0	ENST00000397752.3:c.3560A>G	p.Gln1187Arg	p.Q1187R	ENST00000397752	NM_000245.2	1187	cAa/cGa	18/21	1	2	FACETS	0.561	0.437	0.704	0.561	0.437	0.704	SUBCLONAL	1	TRUE	1	0.241860673129528	2		291	339	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124467320	124467320	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	58	357	0	ENST00000357628.3:c.1634C>T	p.Thr545Ile	p.T545I	ENST00000357628	NM_015450.2	545	aCc/aTc	17/19	1	2	FACETS	0.963	0.836	1	1	0.978	1	CLONAL	2	TRUE	1	0.241860673129528	2		357	249	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124481233	124481233	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	15	328	0	ENST00000357628.3:c.1164-1G>T		p.X388_splice	ENST00000357628	NM_015450.2	388			1	2	FACETS	0.697	0.511	0.918	0.697	0.511	0.918	SUBCLONAL	1	TRUE	1	0.241860673129528	2		328	178	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124532337	124532337	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057524691	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	20	286	0	ENST00000357628.3:c.107A>G	p.Tyr36Cys	p.Y36C	ENST00000357628	NM_015450.2	36	tAt/tGt	6/19	1	2	FACETS	0.788	0.605	1	0.788	0.605	1	CLONAL	1	TRUE	1	0.241860673129528	2		286	210	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846172	128846172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374812951	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	148	542	0	ENST00000249373.3:c.1102C>T	p.Pro368Ser	p.P368S	ENST00000249373	NM_005631.4	368	Ccc/Tcc	5/12	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.241860673129528	2		542	857	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534626	140534626	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	28	403	0	ENST00000288602.6:c.287A>G	p.Glu96Gly	p.E96G	ENST00000288602	NM_004333.4	96	gAa/gGa	3/18	1	2	FACETS	0.588	0.469	0.723	0.588	0.469	0.723	SUBCLONAL	1	TRUE	1	0.241860673129528	2		403	394	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835912	151835912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746423251	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	80	360	0	ENST00000262189.6:c.14612G>A	p.Ser4871Asn	p.S4871N	ENST00000262189	NM_170606.2	4871	aGc/aAc	58/59	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.241860673129528	2		360	501	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845787	151845787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	30	452	0	ENST00000262189.6:c.13225G>T	p.Gly4409Cys	p.G4409C	ENST00000262189	NM_170606.2	4409	Ggt/Tgt	52/59	1	2	FACETS	0.434	0.348	0.531	0.434	0.348	0.531	SUBCLONAL	1	TRUE	1	0.241860673129528	2		452	572	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845912	151845912	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	41	435	0	ENST00000262189.6:c.13100C>A	p.Pro4367His	p.P4367H	ENST00000262189	NM_170606.2	4367	cCt/cAt	52/59	1	2	FACETS	0.675	0.562	0.801	0.675	0.562	0.801	SUBCLONAL	1	TRUE	1	0.241860673129528	2		435	502	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873993	151873993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	87	420	0	ENST00000262189.6:c.8545G>A	p.Val2849Ile	p.V2849I	ENST00000262189	NM_170606.2	2849	Gtt/Att	38/59	1	2	FACETS	0.899	0.801	1	1	0.984	1	CLONAL	2	TRUE	1	0.241860673129528	2		420	400	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879598	151879598	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	49	375	1	ENST00000262189.6:c.5347C>T	p.Gln1783Ter	p.Q1783*	ENST00000262189	NM_170606.2	1783	Cag/Tag	36/59	1	2	FACETS	0.616	0.521	0.721	0.616	0.521	0.721	SUBCLONAL	1	TRUE	1	0.241860673129528	2		376	658	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949057	151949057	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	35	329	1	ENST00000262189.6:c.1588G>A	p.Gly530Ser	p.G530S	ENST00000262189	NM_170606.2	530	Ggt/Agt	11/59	1	2	FACETS	0.706	0.579	0.848	0.706	0.579	0.848	SUBCLONAL	1	TRUE	1	0.241860673129528	2		330	410	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008993	152008993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs548398268	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	69	376	0	ENST00000262189.6:c.629G>A	p.Ser210Asn	p.S210N	ENST00000262189	NM_170606.2	210	aGt/aAt	5/59	1	2	FACETS	0.813	0.712	0.92	1	0.977	1	CLONAL	2	TRUE	1	0.241860673129528	2		376	351	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38156985	38156985	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	57	372	0	ENST00000317025.8:c.2735C>A	p.Ala912Asp	p.A912D	ENST00000317025	NM_023034.1	912	gCt/gAt	15/24	1	2	FACETS	0.802	0.693	0.918	1	0.972	1	CLONAL	2	TRUE	1	0.241860673129528	2		372	294	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69011964	69011964	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	65	363	0	ENST00000288368.4:c.2601T>A	p.Cys867Ter	p.C867*	ENST00000288368	NM_024870.2	867	tgT/tgA	23/40	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.241860673129528	2		363	395	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046405	69046405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	111	433	0	ENST00000288368.4:c.3878G>A	p.Ser1293Asn	p.S1293N	ENST00000288368	NM_024870.2	1293	aGc/aAc	32/40	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.241860673129528	2		433	666	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90971007	90971007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	83	366	1	ENST00000265433.3:c.1070C>T	p.Pro357Leu	p.P357L	ENST00000265433	NM_002485.4	357	cCa/cTa	9/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.241860673129528	2		367	535	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750780	128750780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	76	440	0	ENST00000377970.2:c.317G>A	p.Gly106Glu	p.G106E	ENST00000377970	NM_002467.4	106	gGg/gAg	2/3	1	2	FACETS	0.88	0.772	0.997	0.88	0.772	0.997	CLONAL	1	TRUE	1	0.241860673129528	2		440	714	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561516	141561516	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	128	389	0	ENST00000220592.5:c.1289C>A	p.Pro430His	p.P430H	ENST00000220592	NM_012154.3	430	cCt/cAt	11/19	1	2	FACETS	0.756	0.686	0.829	1	0.986	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		389	700	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141567226	141567226	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	55	427	0	ENST00000220592.5:c.988G>T	p.Val330Phe	p.V330F	ENST00000220592	NM_012154.3	330	Gtc/Ttc	8/19	1	2	FACETS	0.671	0.573	0.778	0.671	0.573	0.778	SUBCLONAL	1	TRUE	1	0.241860673129528	2		427	678	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572709	141572709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	53	434	0	ENST00000220592.5:c.361G>A	p.Gly121Arg	p.G121R	ENST00000220592	NM_012154.3	121	Gga/Aga	4/19	1	2	FACETS	0.664	0.565	0.772	0.664	0.565	0.772	SUBCLONAL	1	TRUE	1	0.241860673129528	2		434	660	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737162	145737162	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	35	452	0	ENST00000428558.2:c.3404G>T	p.Trp1135Leu	p.W1135L	ENST00000428558	NM_004260.3	1135	tGg/tTg	21/22	1	2	FACETS	0.482	0.394	0.582	0.482	0.394	0.582	SUBCLONAL	1	TRUE	1	0.241860673129528	2		452	600	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737903	145737903	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	119	462	0	ENST00000428558.2:c.2927A>G	p.Glu976Gly	p.E976G	ENST00000428558	NM_004260.3	976	gAg/gGg	18/22	1	2	FACETS	0.758	0.686	0.834	1	0.985	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		462	649	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741383	145741383	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	136	502	1	ENST00000428558.2:c.1120C>A	p.Leu374Ile	p.L374I	ENST00000428558	NM_004260.3	374	Ctc/Atc	5/22	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.241860673129528	2		503	844	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2116049	2116049	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	50	323	0	ENST00000349721.2:c.3684G>T	p.Glu1228Asp	p.E1228D	ENST00000349721	NM_003070.3	1228	gaG/gaT	25/34	1	2	FACETS	0.756	0.641	0.882	0.756	0.641	0.882	SUBCLONAL	1	TRUE	1	0.241860673129528	2		323	547	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044455	5044455	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	31	259	0	ENST00000381652.3:c.403G>T	p.Gly135Ter	p.G135*	ENST00000381652	NM_004972.3	135	Gga/Tga	5/25	1	2	FACETS	0.99	0.804	1	0.99	0.804	1	CLONAL	1	TRUE	1	0.241860673129528	2		259	259	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5077549	5077549	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	24	281	0	ENST00000381652.3:c.1961C>A	p.Ala654Asp	p.A654D	ENST00000381652	NM_004972.3	654	gCt/gAt	15/25	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.241860673129528	2		281	161	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089680	5089680	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	23	290	0	ENST00000381652.3:c.2578T>C	p.Phe860Leu	p.F860L	ENST00000381652	NM_004972.3	860	Ttt/Ctt	20/25	1	2	FACETS	0.533	0.415	0.669	0.533	0.415	0.669	SUBCLONAL	1	TRUE	1	0.241860673129528	2		290	357	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089863	5089863	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	43	355	0	ENST00000381652.3:c.2761G>A	p.Gly921Ser	p.G921S	ENST00000381652	NM_004972.3	921	Ggt/Agt	20/25	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.241860673129528	2		355	307	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090464	5090464	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	14	315	0	ENST00000381652.3:c.2780T>G	p.Leu927Ter	p.L927*	ENST00000381652	NM_004972.3	927	tTa/tGa	21/25	1	2	FACETS	0.643	0.466	0.856	0.643	0.466	0.856	SUBCLONAL	1	TRUE	1	0.241860673129528	2		315	180	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123095	5123095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1007272721	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	30	313	0	ENST00000381652.3:c.3151A>G	p.Ile1051Val	p.I1051V	ENST00000381652	NM_004972.3	1051	Att/Gtt	23/25	1	2	FACETS	0.912	0.738	1	0.912	0.738	1	CLONAL	1	TRUE	1	0.241860673129528	2		313	272	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126709	5126709	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	26	322	0	ENST00000381652.3:c.3317G>T	p.Trp1106Leu	p.W1106L	ENST00000381652	NM_004972.3	1106	tGg/tTg	25/25	1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	TRUE	1	0.241860673129528	2		322	201	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389278	8389278	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	47	362	0	ENST00000356435.5:c.4340G>T	p.Arg1447Leu	p.R1447L	ENST00000356435		1447	cGg/cTg	26/35	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.241860673129528	2		362	267	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471029	8471029	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	28	339	0	ENST00000356435.5:c.3470C>T	p.Pro1157Leu	p.P1157L	ENST00000356435		1157	cCa/cTa	20/35	1	2	FACETS	0.669	0.535	0.822	0.669	0.535	0.822	SUBCLONAL	1	TRUE	1	0.241860673129528	2		339	346	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484333	8484333	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	60	378	0	ENST00000356435.5:c.3199G>T	p.Ala1067Ser	p.A1067S	ENST00000356435		1067	Gcc/Tcc	19/35	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.241860673129528	2		378	393	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518232	8518232	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	48	319	0	ENST00000356435.5:c.1159T>C	p.Ser387Pro	p.S387P	ENST00000356435		387	Tcg/Ccg	10/35	1	2	FACETS	0.755	0.638	0.883	0.755	0.638	0.883	SUBCLONAL	1	TRUE	1	0.241860673129528	2		319	526	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518362	8518362	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	87	339	0	ENST00000356435.5:c.1029G>A	p.Trp343Ter	p.W343*	ENST00000356435		343	tgG/tgA	10/35	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.241860673129528	2		339	519	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528614	8528614	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	32	373	2	ENST00000356435.5:c.518G>C	p.Gly173Ala	p.G173A	ENST00000356435		173	gGt/gCt	4/35	1	2	FACETS	0.62	0.503	0.752	0.62	0.503	0.752	SUBCLONAL	1	TRUE	1	0.241860673129528	2		375	427	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020676	37020676	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	36	381	0	ENST00000358127.4:c.169C>T	p.Gln57Ter	p.Q57*	ENST00000358127	NM_001280556.1	57	Cag/Tag	2/10	1	2	FACETS	0.477	0.391	0.574	0.477	0.391	0.574	SUBCLONAL	1	TRUE	1	0.241860673129528	2		381	624	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342784	87342784	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	27	438	0	ENST00000277120.3:c.1069G>A	p.Gly357Arg	p.G357R	ENST00000277120		357	Ggg/Agg	9/19	1	2	FACETS	0.445	0.353	0.55	0.445	0.353	0.55	SUBCLONAL	1	TRUE	1	0.241860673129528	2		438	502	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482256	87482256	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	107	415	0	ENST00000277120.3:c.1543G>T	p.Asp515Tyr	p.D515Y	ENST00000277120		515	Gat/Tat	14/19	1	2	FACETS	0.769	0.692	0.851	1	0.984	1	SUBCLONAL	2	TRUE	1	0.241860673129528	2		415	575	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636207	87636207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	64	426	0	ENST00000277120.3:c.2372C>T	p.Pro791Leu	p.P791L	ENST00000277120		791	cCc/cTc	19/19	1	2	FACETS	0.761	0.659	0.873	0.761	0.659	0.873	SUBCLONAL	1	TRUE	1	0.241860673129528	2		426	695	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97869482	97869482	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	118	455	0	ENST00000289081.3:c.1399C>A	p.Leu467Met	p.L467M	ENST00000289081	NM_000136.2	467	Ctg/Atg	14/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.241860673129528	2		455	726	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97873893	97873893	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	55	423	0	ENST00000289081.3:c.1181G>T	p.Trp394Leu	p.W394L	ENST00000289081	NM_000136.2	394	tGg/tTg	13/15	1	2	FACETS	0.642	0.548	0.745	0.642	0.548	0.745	SUBCLONAL	1	TRUE	1	0.241860673129528	2		423	708	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220557	98220557	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	37	398	0	ENST00000331920.6:c.2906T>A	p.Ile969Asn	p.I969N	ENST00000331920	NM_000264.3	969	aTc/aAc	18/24	1	2	FACETS	0.424	0.349	0.51	0.424	0.349	0.51	SUBCLONAL	1	TRUE	1	0.241860673129528	2		398	721	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229521	98229521	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	60	430	0	ENST00000331920.6:c.2437C>T	p.Pro813Ser	p.P813S	ENST00000331920	NM_000264.3	813	Ccg/Tcg	15/24	1	2	FACETS	0.854	0.736	0.983	0.854	0.736	0.983	CLONAL	1	TRUE	1	0.241860673129528	2		430	581	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231105	98231105	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	128	443	1	ENST00000331920.6:c.2178del	p.Cys727ValfsTer19	p.C727Vfs*19	ENST00000331920	NM_000264.3	726	ccC/cc	14/24	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.241860673129528	2		444	820	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231340	98231340	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	61	505	0	ENST00000331920.6:c.1943A>G	p.His648Arg	p.H648R	ENST00000331920	NM_000264.3	648	cAc/cGc	14/24	1	2	FACETS	0.59	0.508	0.68	0.59	0.508	0.68	SUBCLONAL	1	TRUE	1	0.241860673129528	2		505	855	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242772	98242772	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	58	428	0	ENST00000331920.6:c.845T>C	p.Leu282Pro	p.L282P	ENST00000331920	NM_000264.3	282	cTg/cCg	6/24	1	2	FACETS	0.692	0.594	0.8	0.692	0.594	0.8	SUBCLONAL	1	TRUE	1	0.241860673129528	2		428	693	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891380	101891380	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	64	327	0	ENST00000374994.4:c.341C>T	p.Thr114Ile	p.T114I	ENST00000374994	NM_004612.2	114	aCt/aTt	2/9	1	2	FACETS	0.876	0.765	0.995	1	0.978	1	CLONAL	2	TRUE	1	0.241860673129528	2		327	302	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894949	101894949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519144	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	45	393	0	ENST00000374994.4:c.502C>T	p.Arg168Cys	p.R168C	ENST00000374994	NM_004612.2	168	Cgc/Tgc	3/9	1	2	FACETS	0.778	0.654	0.915	0.778	0.654	0.915	CLONAL	1	TRUE	1	0.241860673129528	2		393	478	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300843	137300843	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	38	430	0	ENST00000481739.1:c.488T>C	p.Val163Ala	p.V163A	ENST00000481739	NM_002957.4	163	gTg/gCg	4/10	1	2	FACETS	0.486	0.401	0.582	0.486	0.401	0.582	SUBCLONAL	1	TRUE	1	0.241860673129528	2		430	646	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413145	139413145	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs895972070	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	117	445	0	ENST00000277541.6:c.997A>C	p.Ser333Arg	p.S333R	ENST00000277541	NM_017617.3	333	Agc/Cgc	6/34	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.241860673129528	2		445	668	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417356	139417356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1027492078	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	51	466	0	ENST00000277541.6:c.688G>A	p.Gly230Arg	p.G230R	ENST00000277541	NM_017617.3	230	Ggg/Agg	4/34	1	2	FACETS	0.582	0.493	0.679	0.582	0.493	0.679	SUBCLONAL	1	TRUE	1	0.241860673129528	2		466	725	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793329	139793329	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	104	367	0	ENST00000247668.2:c.137A>G	p.Gln46Arg	p.Q46R	ENST00000247668	NM_021138.3	46	cAg/cGg	2/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.241860673129528	2		367	644	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139804395	139804395	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	42	326	0	ENST00000247668.2:c.552G>T	p.Lys184Asn	p.K184N	ENST00000247668	NM_021138.3	184	aaG/aaT	6/11	1	2	FACETS	0.511	0.425	0.606	0.511	0.425	0.606	SUBCLONAL	1	TRUE	1	0.241860673129528	2		326	680	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814893	139814893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	42	413	0	ENST00000247668.2:c.886G>A	p.Val296Met	p.V296M	ENST00000247668	NM_021138.3	296	Gtg/Atg	8/11	1	2	FACETS	0.469	0.391	0.557	0.469	0.391	0.557	SUBCLONAL	1	TRUE	1	0.241860673129528	2		413	740	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815559	139815559	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	80	415	0	ENST00000247668.2:c.1030G>T	p.Glu344Ter	p.E344*	ENST00000247668	NM_021138.3	344	Gag/Tag	9/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.241860673129528	2		415	554	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913271	39913271	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	130	454	0	ENST00000378444.4:c.4844A>G	p.Asp1615Gly	p.D1615G	ENST00000378444	NM_001123385.1	1615	gAt/gGt	14/15	0.242302568138419	1	FACETS	0.928	0.847	1	1	0.99	1	CLONAL	2	TRUE	0	0.241860673129528	1		454	509	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922059	39922059	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	63	464	0	ENST00000378444.4:c.4113G>T	p.Gln1371His	p.Q1371H	ENST00000378444	NM_001123385.1	1371	caG/caT	9/15	0.242302568138419	1	FACETS	0.698	0.603	0.801	0.698	0.603	0.801	SUBCLONAL	1	TRUE	0	0.241860673129528	1		464	656	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923734	39923734	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	54	392	0	ENST00000378444.4:c.3357G>T	p.Gln1119His	p.Q1119H	ENST00000378444	NM_001123385.1	1119	caG/caT	7/15	0.242302568138419	1	FACETS	0.625	0.533	0.726	0.625	0.533	0.726	SUBCLONAL	1	TRUE	0	0.241860673129528	1		392	628	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933799	39933799	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1477989848	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	58	498	0	ENST00000378444.4:c.800T>C	p.Leu267Pro	p.L267P	ENST00000378444	NM_001123385.1	267	cTc/cCc	4/15	0.242302568138419	1	FACETS	0.619	0.531	0.715	0.619	0.531	0.715	SUBCLONAL	1	TRUE	0	0.241860673129528	1		498	681	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44894228	44894228	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	20	288	0	ENST00000377967.4:c.617A>G	p.Glu206Gly	p.E206G	ENST00000377967	NM_021140.2	206	gAa/gGa	7/29	0.242302568138419	1	FACETS	1	0.779	1	1	0.779	1	CLONAL	1	TRUE	0	0.241860673129528	1		288	144	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44921983	44921983	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	16	246	0	ENST00000377967.4:c.1517A>G	p.Gln506Arg	p.Q506R	ENST00000377967	NM_021140.2	506	cAa/cGa	15/29	0.242302568138419	1	FACETS	0.736	0.547	0.959	0.736	0.547	0.959	CLONAL	1	TRUE	0	0.241860673129528	1		246	158	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936063	44936063	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	57	288	0	ENST00000377967.4:c.2824A>G	p.Ser942Gly	p.S942G	ENST00000377967	NM_021140.2	942	Agt/Ggt	18/29	0.242302568138419	1	FACETS	0.937	0.815	1	1	0.978	1	CLONAL	2	TRUE	0	0.241860673129528	1		288	221	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938454	44938454	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	23	346	0	ENST00000377967.4:c.3002G>T	p.Arg1001Met	p.R1001M	ENST00000377967	NM_021140.2	1001	aGg/aTg	20/29	0.242302568138419	1	FACETS	0.624	0.487	0.781	0.624	0.487	0.781	SUBCLONAL	1	TRUE	0	0.241860673129528	1		346	268	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028748	47028748	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	56	430	0	ENST00000377604.3:c.52G>T	p.Ala18Ser	p.A18S	ENST00000377604	NM_001204468.1	18	Gcc/Tcc	3/24	0.242302568138419	1	FACETS	0.672	0.575	0.777	0.672	0.575	0.777	SUBCLONAL	1	TRUE	0	0.241860673129528	1		430	606	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044930	47044930	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	74	497	0	ENST00000377604.3:c.2256G>T	p.Lys752Asn	p.K752N	ENST00000377604	NM_001204468.1	752	aaG/aaT	20/24	0.242302568138419	1	FACETS	0.897	0.785	1	0.897	0.785	1	CLONAL	1	TRUE	0	0.241860673129528	1		497	600	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650731	48650731	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs781977639	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	69	479	0	ENST00000376670.3:c.600G>T	p.Glu200Asp	p.E200D	ENST00000376670	NM_002049.3	200	gaG/gaT	4/6	0.242302568138419	1	FACETS	0.782	0.681	0.892	0.782	0.681	0.892	SUBCLONAL	1	TRUE	0	0.241860673129528	1		479	641	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652302	48652302	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	152	491	0	ENST00000376670.3:c.973G>T	p.Gly325Ter	p.G325*	ENST00000376670	NM_002049.3	325	Gga/Tga	6/6	0.242302568138419	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.241860673129528	1		491	768	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223910	53223910	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	96	383	0	ENST00000375401.3:c.3449T>C	p.Phe1150Ser	p.F1150S	ENST00000375401	NM_004187.3	1150	tTc/tCc	23/26	0.242302568138419	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.241860673129528	1		383	535	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226087	53226087	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	49	431	0	ENST00000375401.3:c.2762T>C	p.Leu921Pro	p.L921P	ENST00000375401	NM_004187.3	921	cTc/cCc	19/26	0.242302568138419	1	FACETS	0.646	0.547	0.756	0.646	0.547	0.756	SUBCLONAL	1	TRUE	0	0.241860673129528	1		431	551	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413022	63413022	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	141	437	0	ENST00000330258.3:c.145C>A	p.Pro49Thr	p.P49T	ENST00000330258	NM_152424.3	49	Cca/Aca	2/2	0.242302568138419	1	FACETS	0.75	0.685	0.819	1	0.987	1	SUBCLONAL	2	TRUE	0	0.241860673129528	1		437	683	SUCCESS
AR	367	MSKCC	GRCh37	X	66766055	66766055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	29	406	0	ENST00000374690.3:c.1067C>T	p.Ala356Val	p.A356V	ENST00000374690	NM_000044.3	356	gCa/gTa	1/8	0.242302568138419	1	FACETS	0.38	0.304	0.467	0.38	0.304	0.467	SUBCLONAL	1	TRUE	0	0.241860673129528	1		406	555	SUCCESS
AR	367	MSKCC	GRCh37	X	66766237	66766237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	50	161	0	ENST00000374690.3:c.1249G>A	p.Ala417Thr	p.A417T	ENST00000374690	NM_000044.3	417	Gcg/Acg	1/8	0.242302568138419	1	FACETS	0.707	0.6	0.825	0.707	0.6	0.825	SUBCLONAL	1	TRUE	0	0.241860673129528	1		161	514	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339591	70339591	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	36	322	0	ENST00000374080.3:c.260C>T	p.Pro87Leu	p.P87L	ENST00000374080		87	cCt/cTt	3/45	0.242302568138419	1	FACETS	0.604	0.497	0.725	0.604	0.497	0.725	SUBCLONAL	1	TRUE	0	0.241860673129528	1		322	433	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345330	70345330	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	105	391	0	ENST00000374080.3:c.2356G>T	p.Gly786Trp	p.G786W	ENST00000374080		786	Ggg/Tgg	16/45	0.242302568138419	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.241860673129528	1		391	555	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348457	70348457	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	66	379	0	ENST00000374080.3:c.3364C>A	p.Leu1122Ile	p.L1122I	ENST00000374080		1122	Cta/Ata	24/45	0.242302568138419	1	FACETS	0.88	0.765	1	0.88	0.765	1	CLONAL	1	TRUE	0	0.241860673129528	1		379	545	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778867	76778867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	22	352	0	ENST00000373344.5:c.6712G>A	p.Ala2238Thr	p.A2238T	ENST00000373344	NM_000489.3	2238	Gca/Aca	31/35	0.242302568138419	1	FACETS	0.792	0.617	0.993	0.792	0.617	0.993	CLONAL	1	TRUE	0	0.241860673129528	1		352	202	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909692	76909692	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	17	287	0	ENST00000373344.5:c.4215-2A>G		p.X1405_splice	ENST00000373344	NM_000489.3	1405			0.242302568138419	1	FACETS	0.802	0.603	1	0.802	0.603	1	CLONAL	1	TRUE	0	0.241860673129528	1		287	154	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938585	76938585	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	21	383	0	ENST00000373344.5:c.2163A>T	p.Gln721His	p.Q721H	ENST00000373344	NM_000489.3	721	caA/caT	9/35	0.242302568138419	1	FACETS	0.71	0.549	0.896	0.71	0.549	0.896	SUBCLONAL	1	TRUE	0	0.241860673129528	1		383	215	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940430	76940430	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	12	317	0	ENST00000373344.5:c.662+1G>A		p.X221_splice	ENST00000373344	NM_000489.3	221			0.242302568138419	1	FACETS	0.441	0.31	0.601	0.441	0.31	0.601	SUBCLONAL	1	TRUE	0	0.241860673129528	1		317	198	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608945	100608945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	90	359	0	ENST00000308731.7:c.1663G>A	p.Val555Ile	p.V555I	ENST00000308731	NM_000061.2	555	Gta/Ata	17/19	0.242302568138419	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.241860673129528	1		359	486	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617638	100617638	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	40	389	0	ENST00000308731.7:c.431C>A	p.Pro144His	p.P144H	ENST00000308731	NM_000061.2	144	cCt/cAt	6/19	0.242302568138419	1	FACETS	0.579	0.481	0.689	0.579	0.481	0.689	SUBCLONAL	1	TRUE	0	0.241860673129528	1		389	502	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019926	123019926	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	35	399	0	ENST00000355640.3:c.414C>A	p.Asp138Glu	p.D138E	ENST00000355640		138	gaC/gaA	2/7	0.242302568138419	1	FACETS	0.615	0.504	0.739	0.615	0.504	0.739	SUBCLONAL	1	TRUE	0	0.241860673129528	1		399	414	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215254	123215254	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	15	268	0	ENST00000218089.9:c.2800A>G	p.Asn934Asp	p.N934D	ENST00000218089	NM_001042749.1	934	Aat/Gat	28/35	0.242302568138419	1	FACETS	0.661	0.485	0.869	0.661	0.485	0.869	SUBCLONAL	1	TRUE	0	0.241860673129528	1		268	165	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224541	123224541	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	22	461	0	ENST00000218089.9:c.3394T>G	p.Leu1132Val	p.L1132V	ENST00000218089	NM_001042749.1	1132	Tta/Gta	31/35	0.242302568138419	1	FACETS	0.366	0.283	0.463	0.366	0.283	0.463	SUBCLONAL	1	TRUE	0	0.241860673129528	1		461	437	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858089	152858089	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	59	438	0	ENST00000406277.2:c.526T>C	p.Tyr176His	p.Y176H	ENST00000406277	NM_152274.4	176	Tac/Cac	6/7	0.242302568138419	1	FACETS	0.731	0.628	0.842	0.731	0.628	0.842	SUBCLONAL	1	TRUE	0	0.241860673129528	1		438	587	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	176	317	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		317	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0067221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	422	383	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		383	663	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039505	49039505	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs764754259	NA	P-0067221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	443	361	0	ENST00000267163.4:c.2489+1G>A		p.X830_splice	ENST00000267163	NM_000321.2	830			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		361	680	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739100	40739100	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1158638222	NA	P-0067221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	224	357	0	ENST00000373198.4:c.3184C>T	p.Arg1062Cys	p.R1062C	ENST00000373198	NM_133170.3	1062	Cgc/Tgc	24/32	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		357	719	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106178	27106178	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	452	438	0	ENST00000324856.7:c.5789C>A	p.Ser1930Ter	p.S1930*	ENST00000324856	NM_006015.4	1930	tCa/tAa	20/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		438	1182	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578213	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs864309495	NA	P-0067222-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	551	516	0	ENST00000269305.4:c.636del	p.Arg213AspfsTer34	p.R213Dfs*34	ENST00000269305	NM_001126112.2	212	ttT/tt	6/11	0.812909244827823	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	FALSE	0	0.809513610424578	3		516	606	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546656	9546656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067222-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	144	438	0	ENST00000353224.5:c.1366G>A	p.Gly456Arg	p.G456R	ENST00000353224	NM_177990.2	456	Ggg/Agg	5/10	0.812909244827823	5	FACETS	0.848	0.773	0.927	0.283	0.257	0.309	CLONAL	1	FALSE	2	0.809513610424578	5		438	929	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664924	138664924	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067222-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	127	350	0	ENST00000330315.3:c.641C>G	p.Pro214Arg	p.P214R	ENST00000330315	NM_023067.3	214	cCc/cGc	1/1	0.651515076252144	5	FACETS	1	0.977	1	0.309	0.281	0.339	CLONAL	1	FALSE	1	0.809513610424578	5		350	562	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0067252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	33	171	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.925922101345969	4	FACETS	0.51	0.417	0.614	0.255	0.208	0.307	SUBCLONAL	1	TRUE	2	0.952948711832571	4		171	265	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782177	NA	P-0067252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	1173	512	0	ENST00000269305.4:c.644G>T	p.Ser215Ile	p.S215I	ENST00000269305	NM_001126112.2	215	aGt/aTt	6/11	0.796598147621736	3	FACETS	1	0.998	1			1	CLONAL	3	TRUE	NA	0.952948711832571	3		512	1201	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243983	53243983	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	1274	272	0	ENST00000375401.3:c.1010A>G	p.Asp337Gly	p.D337G	ENST00000375401	NM_004187.3	337	gAc/gGc	8/26	0.952948711832571	4	FACETS	1	0.999	1			1	CLONAL	4	TRUE	NA	0.952948711832571	4		272	1282	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678504	88678504	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	346	530	0	ENST00000360948.2:c.1032G>T	p.Glu344Asp	p.E344D	ENST00000360948	NM_001012338.2	344	gaG/gaT	9/19	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.952948711832571	2		530	674	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156620	2156620	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	746	559	0	ENST00000434045.2:c.302G>C	p.Cys101Ser	p.C101S	ENST00000434045	NM_001127598.1	101	tGt/tCt	3/5	0.952948711832571	2	FACETS	0.987	0.976	0.998	0.987	0.976	0.998	CLONAL	2	TRUE	0	0.952948711832571	2		559	793	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707573	176707573	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	917	483	0	ENST00000439151.2:c.5630G>T	p.Arg1877Leu	p.R1877L	ENST00000439151	NM_022455.4	1877	cGt/cTt	18/23	0.952948711832571	6	FACETS	1	0.987	1	1	0.987	1	CLONAL	4	TRUE	2	0.952948711832571	6		483	1378	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934155	48934155	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1	129	321	0	ENST00000267163.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000267163	NM_000321.2	204	Gaa/Taa	7/27	0.950634932249654	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.952948711832571	2		321	130	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524695	137524695	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs374675376	NA	P-0067252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	225	432	0	ENST00000367739.4:c.674G>T	p.Gly225Val	p.G225V	ENST00000367739	NM_000416.2	225	gGt/gTt	5/7	0.925922101345969	4	FACETS	0.798	0.749	0.848	0.798	0.749	0.848	SUBCLONAL	2	TRUE	2	0.952948711832571	4		432	578	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314940	1314940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	244	527	0	ENST00000400841.2:c.721C>T	p.Leu241Phe	p.L241F	ENST00000400841		241	Ctt/Ttt	6/6	1	1	FACETS	0.344	0.322	0.366	0.344	0.322	0.366	SUBCLONAL	1	TRUE	0	0.952948711832571	1		527	779	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141552	11141552	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	703	501	0	ENST00000358026.2:c.3529G>T	p.Asp1177Tyr	p.D1177Y	ENST00000358026	NM_001128849.1	1177	Gac/Tac	25/36	0.952948711832571	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.952948711832571	2		501	727	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714459	40714459	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs772137373	NA	P-0067252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	1274	533	0	ENST00000373198.4:c.3938G>T	p.Gly1313Val	p.G1313V	ENST00000373198	NM_133170.3	1313	gGg/gTg	29/32	0.950463688046479	4	FACETS	0.999	0.993	1	0.999	0.993	1	CLONAL	4	TRUE	0	0.952948711832571	4		533	1307	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231177	46231177	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	324	440	0	ENST00000334344.6:c.1097G>T	p.Arg366Met	p.R366M	ENST00000334344	NM_152641.2	366	aGg/aTg	9/21	0.952948711832571	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.952948711832571	2		440	330	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111562	8111562	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs112399242	NA	P-0067252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	539	389	0	ENST00000346208.3:c.1047+1G>C		p.X349_splice	ENST00000346208		349			0.952948711832571	3	FACETS	0.962	0.931	0.992	0.962	0.931	0.992	CLONAL	2	TRUE	1	0.952948711832571	3		389	868	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366749	40366749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	391	652	0	ENST00000397332.2:c.448G>A	p.Gly150Arg	p.G150R	ENST00000397332	NM_001033082.2	150	Ggg/Agg	2/3	0.952948711832571	3	FACETS	0.958	0.91	1	0.479	0.455	0.503	CLONAL	1	TRUE	1	0.952948711832571	3		652	1265	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922751	44922751	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	1255	235	0	ENST00000377967.4:c.1612G>T	p.Val538Phe	p.V538F	ENST00000377967	NM_021140.2	538	Gtc/Ttc	16/29	0.952948711832571	4	FACETS	1	0.999	1			1	CLONAL	4	TRUE	NA	0.952948711832571	4		235	1266	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918888	76918888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	416	195	0	ENST00000373344.5:c.4103G>A	p.Gly1368Asp	p.G1368D	ENST00000373344	NM_000489.3	1368	gGc/gAc	12/35	0.785709415086814	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.952948711832571	2		195	425	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023002	33023002	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	357	506	0	ENST00000300177.4:c.111C>A	p.Asp37Glu	p.D37E	ENST00000300177	NM_001191322.1	37	gaC/gaA	2/2	1	2	FACETS	0.947	0.903	0.992	0.947	0.903	0.992	CLONAL	1	TRUE	1	0.952948711832571	2		506	791	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881458	111881458	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	321	544	0	ENST00000393256.3:c.136G>T	p.Gly46Cys	p.G46C	ENST00000393256	NM_006538.4	46	Ggc/Tgc	2/4	0.814370140298136	3	FACETS	1	0.972	1	0.52	0.492	0.549	CLONAL	1	TRUE	1	0.952948711832571	3		544	956	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56798136	56798136	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	186	342	0	ENST00000337432.4:c.867G>T	p.Lys289Asn	p.K289N	ENST00000337432	NM_058216.2	289	aaG/aaT	6/9	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.952948711832571	2		342	383	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610432	81610432	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	344	513	0	ENST00000298171.2:c.2030T>A	p.Leu677His	p.L677H	ENST00000298171	NM_000369.2	677	cTc/cAc	10/10	0.952948711832571	3	FACETS	0.982	0.93	1	0.491	0.465	0.517	CLONAL	1	TRUE	1	0.952948711832571	3		513	1086	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354598	91354598	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	277	481	0	ENST00000355112.3:c.4038G>T	p.Lys1346Asn	p.K1346N	ENST00000355112	NM_000057.2	1346	aaG/aaT	21/22	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.952948711832571	2		481	581	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682988	241682988	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	671	495	0	ENST00000366560.3:c.35G>A	p.Arg12His	p.R12H	ENST00000366560	NM_000143.3	12	cGt/cAt	1/10	0.925922101345969	4	FACETS	0.984	0.952	1	0.984	0.952	1	CLONAL	2	TRUE	2	0.952948711832571	4		495	1397	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104705	69104705	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	362	583	0	ENST00000288368.4:c.4549C>G	p.Leu1517Val	p.L1517V	ENST00000288368	NM_024870.2	1517	Ctg/Gtg	37/40	0.952948711832571	3	FACETS	0.966	0.917	1	0.483	0.458	0.509	CLONAL	1	TRUE	1	0.952948711832571	3		583	1161	SUCCESS
ALB	213	MSKCC	GRCh37	4	74277780	74277780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	838	349	0	ENST00000295897.4:c.781G>A	p.Asp261Asn	p.D261N	ENST00000295897	NM_000477.5	261	Gat/Aat	7/15	0.952948711832571	3	FACETS	0.99	0.981	0.999	0.99	0.981	0.999	CLONAL	3	TRUE	0	0.952948711832571	3		349	874	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863304	56863304	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs141769918	NA	P-0067252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	232	396	0	ENST00000519728.1:c.448G>T	p.Ala150Ser	p.A150S	ENST00000519728	NM_002350.3	150	Gct/Tct	6/13	0.952948711832571	3	FACETS	1	0.978	1	0.545	0.511	0.58	CLONAL	1	TRUE	1	0.952948711832571	3		396	659	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176710849	176710849	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	1052	451	0	ENST00000439151.2:c.6071A>T	p.Gln2024Leu	p.Q2024L	ENST00000439151	NM_022455.4	2024	cAg/cTg	20/23	0.952948711832571	6	FACETS	1	0.991	1	1	0.991	1	CLONAL	4	TRUE	2	0.952948711832571	6		451	1569	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264309	30264309	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	178	264	0	ENST00000322652.5:c.44G>T	p.Gly15Val	p.G15V	ENST00000322652	NM_015355.2	15	gGg/gTg	1/16	1	2	FACETS	0.902	0.842	0.963	0.902	0.842	0.963	CLONAL	1	TRUE	1	0.952948711832571	2		264	414	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35860996	35860996	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	531	452	0	ENST00000303115.3:c.125G>T	p.Cys42Phe	p.C42F	ENST00000303115	NM_002185.3	42	tGc/tTc	2/8	0.92374834105485	6	FACETS	1	0.974	1	0.511	0.489	0.533	CLONAL	2	TRUE	2	0.952948711832571	6		452	1585	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63965625	63965625	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	308	417	0	ENST00000398590.3:c.534G>T	p.Leu178Phe	p.L178F	ENST00000398590	NM_001177387.1	178	ttG/ttT	6/14	0.952099353628194	2	FACETS	1	0.991	1	0.573	0.547	0.599	CLONAL	1	TRUE	0	0.952948711832571	2		417	564	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143044479	143044479	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4	307	354	0	ENST00000262992.4:c.1983G>T	p.Leu661Phe	p.L661F	ENST00000262992	NM_001101669.1	661	ttG/ttT	18/24	0.952099353628194	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.952948711832571	2		354	311	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0067254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	31	171	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.935	0.778	1	0.935	0.778	1	CLONAL	1	TRUE	1	0.697643217862438	2		171	95	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063666	67063685	+	frameshift_variant	Frame_Shift_Del	DEL	GAACGCCAGGCACGCTTCCA	GAACGCCAGGCACGCTTCCA	-	novel	NA	P-0067254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	144	288	0	ENST00000412916.2:c.122_141del	p.Gln41LeufsTer35	p.Q41Lfs*35	ENST00000412916		39	GAACGCCAGGCACGCTTCCAg/g	2/6	0.697643217862438	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.697643217862438	1		288	267	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611173	100611173	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555977832	NA	P-0067254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	107	304	0	ENST00000308731.7:c.1433C>T	p.Ala478Val	p.A478V	ENST00000308731	NM_000061.2	478	gCc/gTc	15/19	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.697643217862438	2		304	254	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0067255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	113	396	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.388800162739849	2	FACETS	0.942	0.863	1	0.942	0.863	1	CLONAL	2	TRUE	0	0.450906911762882	2		396	266	SUCCESS
APC	324	MSKCC	GRCh37	5	112175133	112175133	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	112	378	0	ENST00000257430.4:c.3842C>A	p.Ser1281Ter	p.S1281*	ENST00000257430	NM_000038.5	1281	tCa/tAa	16/16	0.433602477474181	3	FACETS	0.871	0.801	0.941	0.871	0.801	0.941	CLONAL	3	TRUE	0	0.450906911762882	3		378	233	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971145	13971145	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	31	324	0	ENST00000405192.2:c.784G>T	p.Asp262Tyr	p.D262Y	ENST00000405192	NM_001163147.1	262	Gat/Tat	8/12	0.391768089070018	5	FACETS	0.568	0.459	0.691	0.189	0.153	0.231	SUBCLONAL	1	TRUE	2	0.450906911762882	5		324	406	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522751	67522751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747723877	NA	P-0067255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	69	364	0	ENST00000274335.5:c.248C>T	p.Ser83Leu	p.S83L	ENST00000274335		83	tCg/tTg	1/15	0.402173437360416	3	FACETS	0.895	0.783	1	0.448	0.391	0.508	CLONAL	1	TRUE	1	0.450906911762882	3		364	419	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0067256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	12	171	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.25683717882598	3	FACETS	0.603	0.424	0.821	0.301	0.212	0.411	SUBCLONAL	1	TRUE	1	0.25683717882598	3		171	175	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849663	68849663	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs587780113	NA	P-0067256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	121	361	0	ENST00000261769.5:c.1565+1G>C		p.X522_splice	ENST00000261769	NM_004360.3	522			0.25683717882598	2	FACETS	0.998	0.907	1	0.998	0.907	1	CLONAL	2	TRUE	0	0.25683717882598	2		361	472	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16046919	16046919	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0067256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	75	222	0	ENST00000268712.3:c.1173+1G>T		p.X391_splice	ENST00000268712	NM_006311.3	391			0.139496670454517	4	FACETS	1	0.898	1			1	INDETERMINATE	3	TRUE	NA	0.25683717882598	4		222	242	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168546	56168546	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs199985393	NA	P-0067256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	59	127	0	ENST00000399503.3:c.1502A>G	p.Tyr501Cys	p.Y501C	ENST00000399503	NM_005921.1	501	tAc/tGc	8/20	0.168777631718543	4	FACETS	0.947	0.82	1	0.947	0.82	1	CLONAL	2	TRUE	2	0.25683717882598	4		127	305	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220632	1220642	+	protein_altering_variant	In_Frame_Del	DEL	CGGCTTTCCAG	CGGCTTTCCAG	GC	novel	NA	P-0067256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	158	473	1	ENST00000326873.7:c.650_660delinsGC	p.Pro217_Gln220delinsArg	p.P217_Q220delinsR	ENST00000326873	NM_000455.4	217	cCGGCTTTCCAG/cGC	5/10	0.25683717882598	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.25683717882598	2		474	504	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067257-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	122	317	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.978	0.896	1	0.978	0.896	1	CLONAL	1	TRUE	1	0.758247067460008	2		317	329	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0067257-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22312	768	848	0	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.758247067460008	43	FACETS	1	0.997	1	0.035	0.033	0.037	CLONAL	1	TRUE	1	0.758247067460008	43		848	23080	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294191	1294191	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067257-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	220	534	0	ENST00000310581.5:c.810C>A	p.Phe270Leu	p.F270L	ENST00000310581	NM_198253.2	270	ttC/ttA	2/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.758247067460008	2		534	571	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0067258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	225	349	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.47471445632748	1	FACETS	0.689	0.654	0.724	0.689	0.654	0.724	INDETERMINATE	1	TRUE	0	0.92946693271514	1		349	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1064795203	NA	P-0067258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	571	523	0	ENST00000269305.4:c.532C>G	p.His178Asp	p.H178D	ENST00000269305	NM_001126112.2	178	Cac/Gac	5/11	0.92946693271514	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.92946693271514	2		523	612	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165930	118165930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781549053	NA	P-0067258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	354	446	0	ENST00000369448.3:c.440C>T	p.Thr147Met	p.T147M	ENST00000369448	NM_017709.3	147	aCg/aTg	2/2	0.47471445632748	1	FACETS	0.722	0.693	0.749	0.722	0.693	0.749	INDETERMINATE	1	TRUE	0	0.92946693271514	1		446	565	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409163	31409163	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	133	315	0	ENST00000344624.3:c.3854A>G	p.Lys1285Arg	p.K1285R	ENST00000344624		1285	aAg/aGg	30/33	1	2	FACETS	0.55	0.502	0.6	0.55	0.502	0.6	SUBCLONAL	1	TRUE	1	0.92946693271514	2		315	520	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696711	47696713	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0067258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	566	419	0	ENST00000347630.2:c.235_237del	p.Glu79del	p.E79del	ENST00000347630	NM_001007230.1	79	GAA/-	5/11	0.92946693271514	2	FACETS	0.987	0.972	1	0.987	0.972	1	CLONAL	2	TRUE	0	0.92946693271514	2		419	617	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0067261-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	88	418	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.821	0.735	0.91	0.821	0.735	0.91	CLONAL	1	TRUE	1	0.689512731220128	2		418	311	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067261-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	83	317	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.734	0.654	0.818	0.734	0.654	0.818	SUBCLONAL	1	TRUE	1	0.689512731220128	2		317	328	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31448714	31448714	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067261-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	110	391	0	ENST00000344624.3:c.2822G>C	p.Gly941Ala	p.G941A	ENST00000344624		941	gGg/gCg	20/33	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.689512731220128	2		391	263	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0067262-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	134	329	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.532184785905315	2		329	419	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0067263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	134	482	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.924	0.843	1	1	0.99	1	CLONAL	2	TRUE	1	0.26	2		482	558	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs770248150	NA	P-0067263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	54	354	0	ENST00000311936.3:c.351A>C	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaC	4/5	0.274328045696367	3	FACETS	1	0.96	1	0.684	0.587	0.789	CLONAL	1	TRUE	1	0.26	3		354	343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0067263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	68	389	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.937	0.816	1	0.937	0.816	1	CLONAL	1	TRUE	1	0.26	2		389	558	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0067263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	104	470	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	NA	2	FACETS	0.789	0.709	0.873			1	INDETERMINATE	2	TRUE	NA	0.26	2		470	507	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0067263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	43	462	1	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	1	2	FACETS	0.654	0.547	0.772	0.654	0.547	0.772	SUBCLONAL	1	TRUE	1	0.26	2		463	506	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023159	31023159	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770209084	NA	P-0067263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	48	493	0	ENST00000375687.4:c.2644C>T	p.Gln882Ter	p.Q882*	ENST00000375687	NM_015338.5	882	Caa/Taa	13/13	0.3	4	FACETS	0.553	0.466	0.649	0.184	0.155	0.217	SUBCLONAL	1	TRUE	1	0.26	4		493	842	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31485046	31485046	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	34	355	0	ENST00000344624.3:c.1938A>C	p.Glu646Asp	p.E646D	ENST00000344624		646	gaA/gaC	12/33	1	2	FACETS	0.679	0.555	0.818	0.679	0.555	0.818	SUBCLONAL	1	TRUE	1	0.26	2		355	385	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33680061	33680061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201406101	NA	P-0067263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	20	262	0	ENST00000308377.4:c.2020C>T	p.Arg674Cys	p.R674C	ENST00000308377	NM_152270.3	674	Cgt/Tgt	5/5	0.169596204552173	3	FACETS	0.461	0.352	0.589	0.231	0.176	0.295	SUBCLONAL	1	TRUE	1	0.26	3		262	377	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859604	57859604	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1455558333	NA	P-0067263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	78	543	0	ENST00000228682.2:c.658G>T	p.Asp220Tyr	p.D220Y	ENST00000228682	NM_005269.2	220	Gac/Tac	7/12	0.274328045696367	3	FACETS	0.81	0.711	0.917	0.405	0.355	0.459	CLONAL	1	TRUE	1	0.26	3		543	837	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940202	49940202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067265-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	122	677	0	ENST00000296474.3:c.841G>A	p.Ala281Thr	p.A281T	ENST00000296474	NM_002447.2	281	Gca/Aca	1/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.371763300864051	2		677	579	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679886	33679886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746690453	NA	P-0067265-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	125	578	0	ENST00000308377.4:c.2195G>A	p.Arg732His	p.R732H	ENST00000308377	NM_152270.3	732	cGc/cAc	5/5	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.371763300864051	2		578	575	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415672	152415672	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067265-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	86	562	0	ENST00000206249.3:c.1522C>G	p.Leu508Val	p.L508V	ENST00000206249	NM_000125.3	508	Ctc/Gtc	7/8	0.371763300864051	1	FACETS	0.793	0.704	0.887	0.793	0.704	0.887	SUBCLONAL	1	TRUE	0	0.371763300864051	1		562	475	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608320	28608320	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520022	NA	P-0067265-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	113	598	0	ENST00000241453.7:c.1736T>C	p.Val579Ala	p.V579A	ENST00000241453	NM_004119.2	579	gTa/gCa	14/24	0.371763300864051	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.371763300864051	1		598	437	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574250	95574250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067265-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	75	466	0	ENST00000393063.1:c.2617G>A	p.Asp873Asn	p.D873N	ENST00000393063	NM_030621.3	873	Gat/Aat	17/28	1	2	FACETS	0.947	0.834	1	0.947	0.834	1	CLONAL	1	TRUE	1	0.371763300864051	2		466	426	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031952	26031952	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067265-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	85	650	0	ENST00000244661.2:c.337A>G	p.Ile113Val	p.I113V	ENST00000244661	NM_003537.3	113	Atc/Gtc	1/1	1	2	FACETS	0.712	0.63	0.8	0.712	0.63	0.8	SUBCLONAL	1	TRUE	1	0.371763300864051	2		650	642	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23640548	23640548	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067265-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	91	388	0	ENST00000261584.4:c.2563del	p.Leu855TyrfsTer7	p.L855Yfs*7	ENST00000261584	NM_024675.3	855	Cta/ta	6/13	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.371763300864051	2		388	418	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	42	642	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.334	0.278	0.396	0.334	0.278	0.396	SUBCLONAL	1	TRUE	1	0.442243262784402	2		643	569	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863054	56863054	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1266824391	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	95	393	2	ENST00000519728.1:c.327del	p.Glu110LysfsTer15	p.E110Kfs*15	ENST00000519728	NM_002350.3	107	acA/ac	5/13	1	2	FACETS	0.997	0.893	1	0.997	0.893	1	CLONAL	1	TRUE	1	0.442243262784402	2		395	431	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	33	377	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.614	0.503	0.738	0.614	0.503	0.738	SUBCLONAL	1	TRUE	1	0.442243262784402	2		377	243	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	27	476	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.301	0.239	0.372	0.301	0.239	0.372	SUBCLONAL	1	TRUE	1	0.442243262784402	2		476	406	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720712	89720712	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	39	105	0	ENST00000371953.3:c.867del	p.Val290Ter	p.V290*	ENST00000371953	NM_000314.4	288	gAa/ga	8/9	0.442243262784402	2	FACETS	0.794	0.676	0.918	0.794	0.676	0.918	CLONAL	2	TRUE	0	0.442243262784402	2		105	111	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	71	319	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.442243262784402	2	FACETS	0.821	0.72	0.929	0.411	0.36	0.465	CLONAL	1	TRUE	0	0.442243262784402	2		325	391	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	145	177	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.8	0.737	0.864	1	0.99	1	SUBCLONAL	2	TRUE	1	0.442243262784402	2		178	410	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	19	191	1	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	0.508	0.388	0.648	0.508	0.388	0.648	SUBCLONAL	1	TRUE	1	0.442243262784402	2		192	169	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	84	515	0	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	1	2	FACETS	0.621	0.549	0.698	0.621	0.549	0.698	SUBCLONAL	1	TRUE	1	0.442243262784402	2		515	612	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	98	342	4	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.916	0.821	1	0.916	0.821	1	CLONAL	1	TRUE	1	0.442243262784402	2		346	484	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574678	41574679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs754418509	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	110	625	1	ENST00000263253.7:c.6970dup	p.His2324ProfsTer55	p.H2324Pfs*55	ENST00000263253	NM_001429.3	2321	-/C	31/31	1	2	FACETS	0.887	0.799	0.979	0.887	0.799	0.979	CLONAL	1	TRUE	1	0.442243262784402	2		626	561	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074055	8074055	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1032815946	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	30	513	0	ENST00000377482.5:c.604C>T	p.Arg202Cys	p.R202C	ENST00000377482	NM_018948.3	202	Cgt/Tgt	4/4	1	2	FACETS	0.292	0.235	0.358	0.292	0.235	0.358	SUBCLONAL	1	TRUE	1	0.442243262784402	2		513	464	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319439	11319439	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs368184120	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	133	517	0	ENST00000361445.4:c.28A>G	p.Thr10Ala	p.T10A	ENST00000361445	NM_004958.3	10	Acc/Gcc	2/58	1	2	FACETS	0.98	0.893	1	0.98	0.893	1	CLONAL	1	TRUE	1	0.442243262784402	2		517	614	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36826852	36826852	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1253659600	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	59	441	0	ENST00000373129.3:c.82A>G	p.Asn28Asp	p.N28D	ENST00000373129	NM_032017.1	28	Aat/Gat	3/12	1	2	FACETS	0.562	0.484	0.646	0.562	0.484	0.646	SUBCLONAL	1	TRUE	1	0.442243262784402	2		441	475	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14303202	14303202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	91	363	0	ENST00000256196.4:c.473C>T	p.Ala158Val	p.A158V	ENST00000256196		158	gCa/gTa	5/6	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.442243262784402	2		363	328	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137065	64137065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767134558	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	81	483	0	ENST00000334205.4:c.1576G>A	p.Val526Met	p.V526M	ENST00000334205	NM_003942.2	526	Gtg/Atg	13/17	1	2	FACETS	0.916	0.811	1	0.916	0.811	1	CLONAL	1	TRUE	1	0.442243262784402	2		483	400	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307406	118307406	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	28	232	0	ENST00000534358.1:c.179T>C	p.Val60Ala	p.V60A	ENST00000534358	NM_005933.3	60	gTg/gCg	1/36	1	2	FACETS	0.724	0.584	0.88	0.724	0.584	0.88	SUBCLONAL	1	TRUE	1	0.442243262784402	2		232	175	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	45	627	0	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.319	0.268	0.377	0.319	0.268	0.377	SUBCLONAL	1	TRUE	1	0.442243262784402	2		627	637	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420175	420175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1036242026	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	49	496	0	ENST00000399788.2:c.3092G>A	p.Arg1031His	p.R1031H	ENST00000399788	NM_001042603.1	1031	cGc/cAc	21/28	1	2	FACETS	0.458	0.388	0.535	0.458	0.388	0.535	SUBCLONAL	1	TRUE	1	0.442243262784402	2		496	484	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	79	524	13	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.918	0.813	1	0.918	0.813	1	CLONAL	1	TRUE	1	0.442243262784402	2		537	389	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420660	49420660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	101	554	0	ENST00000301067.7:c.15089G>A	p.Arg5030His	p.R5030H	ENST00000301067	NM_003482.3	5030	cGt/cAt	48/54	1	2	FACETS	0.972	0.873	1	0.972	0.873	1	CLONAL	1	TRUE	1	0.442243262784402	2		554	470	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495511	56495511	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	108	620	0	ENST00000267101.3:c.3701C>A	p.Ser1234Tyr	p.S1234Y	ENST00000267101	NM_001982.3	1234	tCt/tAt	28/28	1	2	FACETS	0.967	0.872	1	0.967	0.872	1	CLONAL	1	TRUE	1	0.442243262784402	2		620	505	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118704	115118706	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	50	548	0	ENST00000257566.3:c.635_637del	p.Asn212del	p.N212del	ENST00000257566	NM_016569.3	212	aACAtt/att	2/8	1	2	FACETS	0.386	0.327	0.451	0.386	0.327	0.451	SUBCLONAL	1	TRUE	1	0.442243262784402	2		548	586	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	67	528	2	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.638	0.556	0.727	0.638	0.556	0.727	SUBCLONAL	1	TRUE	1	0.442243262784402	2		530	475	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435793	110435793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761634910	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	103	514	0	ENST00000375856.3:c.2608G>A	p.Val870Met	p.V870M	ENST00000375856	NM_003749.2	870	Gtg/Atg	1/2	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.442243262784402	2		514	418	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242073	105242075	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs768025881	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	103	486	1	ENST00000349310.3:c.349_351del	p.Glu117del	p.E117del	ENST00000349310	NM_001014432.1	117	GAG/-	6/15	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.442243262784402	2		487	455	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38616977	38616977	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	20	280	0	ENST00000299084.4:c.395del	p.Asn132MetfsTer20	p.N132Mfs*20	ENST00000299084	NM_152594.2	130	tcA/tc	4/7	1	2	FACETS	0.295	0.225	0.376	0.295	0.225	0.376	SUBCLONAL	1	TRUE	1	0.442243262784402	2		280	307	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007619	45007619	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs111482205	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	42	408	0	ENST00000558401.1:c.68-2A>G		p.X23_splice	ENST00000558401	NM_004048.2	23			1	2	FACETS	0.452	0.378	0.535	0.452	0.378	0.535	SUBCLONAL	1	TRUE	1	0.442243262784402	2		408	420	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820982	3820982	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	32	386	0	ENST00000262367.5:c.2469G>T	p.Gln823His	p.Q823H	ENST00000262367	NM_004380.2	823	caG/caT	14/31	1	2	FACETS	0.408	0.331	0.494	0.408	0.331	0.494	SUBCLONAL	1	TRUE	1	0.442243262784402	2		386	355	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274172	10274173	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1555491538	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	64	441	0	ENST00000330684.3:c.96dup	p.Ala33ArgfsTer105	p.A33Rfs*105	ENST00000330684	NM_001134407.1	32	-/C	2/13	1	2	FACETS	0.919	0.802	1	0.919	0.802	1	CLONAL	1	TRUE	1	0.442243262784402	2		441	315	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026103	14026104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs34607888	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	116	438	0	ENST00000311895.7:c.1069dup	p.Ile357AsnfsTer3	p.I357Nfs*3	ENST00000311895	NM_005236.2	355	gaa/gAaa	6/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.442243262784402	2		438	461	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992169	72992169	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs758458326	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	38	607	0	ENST00000268489.5:c.1876C>A	p.Leu626Ile	p.L626I	ENST00000268489	NM_006885.3	626	Ctc/Atc	2/10	1	2	FACETS	0.306	0.252	0.366	0.306	0.252	0.366	SUBCLONAL	1	TRUE	1	0.442243262784402	2		607	562	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349171	89349171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	119	576	0	ENST00000301030.4:c.3779C>T	p.Ser1260Leu	p.S1260L	ENST00000301030	NM_001256183.1	1260	tCg/tTg	9/13	1	2	FACETS	0.915	0.829	1	0.915	0.829	1	CLONAL	1	TRUE	1	0.442243262784402	2		576	588	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351595	89351595	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	127	555	1	ENST00000301030.4:c.1355del	p.Asn452IlefsTer3	p.N452Ifs*3	ENST00000301030	NM_001256183.1	452	aAt/at	9/13	1	2	FACETS	0.997	0.907	1	0.997	0.907	1	CLONAL	1	TRUE	1	0.442243262784402	2		556	576	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89815164	89815164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752642945	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	92	389	0	ENST00000389301.3:c.3251G>A	p.Arg1084His	p.R1084H	ENST00000389301	NM_000135.2	1084	cGc/cAc	33/43	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.442243262784402	2		389	376	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618327	37618327	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	57	415	0	ENST00000447079.4:c.3G>A	p.Met1?	p.M1?	ENST00000447079	NM_015083.1	1	atG/atA	1/14	1	2	FACETS	0.675	0.581	0.776	0.675	0.581	0.776	SUBCLONAL	1	TRUE	1	0.442243262784402	2		415	382	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441886	40441886	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	24	463	1	ENST00000345506.4:c.131A>G	p.Asp44Gly	p.D44G	ENST00000345506	NM_003152.3	44	gAt/gGt	4/20	1	2	FACETS	0.229	0.178	0.286	0.229	0.178	0.286	SUBCLONAL	1	TRUE	1	0.442243262784402	2		464	475	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617680	39617680	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	23	406	0	ENST00000262039.4:c.1869del	p.Phe623LeufsTer43	p.F623Lfs*43	ENST00000262039	NM_002647.2	622	Ttt/tt	17/25	1	2	FACETS	0.331	0.258	0.416	0.331	0.258	0.416	SUBCLONAL	1	TRUE	1	0.442243262784402	2		406	314	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1627381	1627381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113419714	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	97	495	2	ENST00000344749.5:c.343G>A	p.Ala115Thr	p.A115T	ENST00000344749	NM_001136139.2	115	Gca/Aca	6/19	1	2	FACETS	0.852	0.762	0.947	0.852	0.762	0.947	CLONAL	1	TRUE	1	0.442243262784402	2		497	515	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226578	2226579	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	113	658	0	ENST00000398665.3:c.4062dup	p.Ser1355LeufsTer183	p.S1355Lfs*183	ENST00000398665	NM_032482.2	1353	ttc/ttCc	27/28	1	2	FACETS	0.988	0.893	1	0.988	0.893	1	CLONAL	1	TRUE	1	0.442243262784402	2		658	517	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5258060	5258060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770748688	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	51	406	0	ENST00000357368.4:c.674G>A	p.Arg225His	p.R225H	ENST00000357368	NM_002850.3	225	cGc/cAc	8/38	1	2	FACETS	0.612	0.522	0.71	0.612	0.522	0.71	SUBCLONAL	1	TRUE	1	0.442243262784402	2		406	377	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274304	5274304	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	72	499	2	ENST00000357368.4:c.143del	p.Gly48ValfsTer17	p.G48Vfs*17	ENST00000357368	NM_002850.3	48	gGt/gt	3/38	1	2	FACETS	0.611	0.534	0.693	0.611	0.534	0.693	SUBCLONAL	1	TRUE	1	0.442243262784402	2		501	533	SUCCESS
CALR	811	MSKCC	GRCh37	19	13049990	13049991	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	56	416	0	ENST00000316448.5:c.138dup	p.Gly47TrpfsTer13	p.G47Wfs*13	ENST00000316448	NM_004343.3	45	gat/gaTt	2/9	1	2	FACETS	0.549	0.471	0.634	0.549	0.471	0.634	SUBCLONAL	1	TRUE	1	0.442243262784402	2		416	461	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353819	15353819	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	33	236	2	ENST00000263377.2:c.3061del	p.His1021IlefsTer47	p.H1021Ifs*47	ENST00000263377	NM_058243.2	1021	Cat/at	14/20	1	2	FACETS	0.672	0.551	0.806	0.672	0.551	0.806	SUBCLONAL	1	TRUE	1	0.442243262784402	2		238	222	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354007	15354008	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	14	169	0	ENST00000263377.2:c.2872dup	p.Leu958ProfsTer135	p.L958Pfs*135	ENST00000263377	NM_058243.2	958	ctg/cCtg	14/20	1	2	FACETS	0.483	0.352	0.64	0.483	0.352	0.64	SUBCLONAL	1	TRUE	1	0.442243262784402	2		169	131	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40771132	40771132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781407242	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	44	362	0	ENST00000392038.2:c.43C>T	p.Arg15Cys	p.R15C	ENST00000392038	NM_001626.4	15	Cgt/Tgt	2/14	1	2	FACETS	0.614	0.517	0.721	0.614	0.517	0.721	SUBCLONAL	1	TRUE	1	0.442243262784402	2		362	324	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796594	42796594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762323815	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	90	501	0	ENST00000575354.2:c.3151G>A	p.Ala1051Thr	p.A1051T	ENST00000575354	NM_015125.3	1051	Gcc/Acc	13/20	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.442243262784402	2		501	389	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905747	50905747	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	53	616	0	ENST00000440232.2:c.795G>A	p.Trp265Ter	p.W265*	ENST00000440232	NM_002691.3	265	tgG/tgA	7/27	1	2	FACETS	0.479	0.409	0.556	0.479	0.409	0.556	SUBCLONAL	1	TRUE	1	0.442243262784402	2		616	500	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605204	46605204	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1459319402	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	64	432	1	ENST00000263734.3:c.1421G>C	p.Ser474Thr	p.S474T	ENST00000263734	NM_001430.4	474	aGc/aCc	10/16	1	2	FACETS	0.825	0.718	0.939	0.825	0.718	0.939	CLONAL	1	TRUE	1	0.442243262784402	2		433	351	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630408	47630408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	20	516	0	ENST00000233146.2:c.78G>A	p.Met26Ile	p.M26I	ENST00000233146	NM_000251.2	26	atG/atA	1/16	1	2	FACETS	0.261	0.199	0.333	0.261	0.199	0.333	SUBCLONAL	1	TRUE	1	0.442243262784402	2		516	347	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705528	47705528	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	71	432	0	ENST00000233146.2:c.2332del	p.Cys778AlafsTer34	p.C778Afs*34	ENST00000233146	NM_000251.2	776	gcT/gc	14/16	1	2	FACETS	0.856	0.752	0.968	0.856	0.752	0.968	CLONAL	1	TRUE	1	0.442243262784402	2		432	375	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169316	99169316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1320693278	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	93	516	0	ENST00000074304.5:c.1246G>A	p.Ala416Thr	p.A416T	ENST00000074304	NM_001134224.1	416	Gcc/Acc	15/26	1	2	FACETS	0.876	0.782	0.975	0.876	0.782	0.975	CLONAL	1	TRUE	1	0.442243262784402	2		516	480	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645923	215645923	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	80	527	0	ENST00000260947.4:c.675A>C	p.Glu225Asp	p.E225D	ENST00000260947	NM_000465.2	225	gaA/gaC	4/11	1	2	FACETS	0.932	0.826	1	0.932	0.826	1	CLONAL	1	TRUE	1	0.442243262784402	2		527	388	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660376	227660376	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756650445	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	28	503	0	ENST00000305123.5:c.3079C>T	p.Pro1027Ser	p.P1027S	ENST00000305123	NM_005544.2	1027	Ccc/Tcc	1/2	1	2	FACETS	0.394	0.315	0.484	0.394	0.315	0.484	SUBCLONAL	1	TRUE	1	0.442243262784402	2		503	321	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662683	227662683	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866580419	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	43	513	0	ENST00000305123.5:c.772C>T	p.Arg258Trp	p.R258W	ENST00000305123	NM_005544.2	258	Cgg/Tgg	1/2	1	2	FACETS	0.414	0.346	0.489	0.414	0.346	0.489	SUBCLONAL	1	TRUE	1	0.442243262784402	2		513	470	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30946592	30946594	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs752094508	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	57	312	2	ENST00000375687.4:c.25_27del	p.Lys9del	p.K9del	ENST00000375687	NM_015338.5	5	cAGAag/cag	1/13	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.442243262784402	2		314	229	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	67	529	4	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.654	0.57	0.745	0.654	0.57	0.745	SUBCLONAL	1	TRUE	1	0.442243262784402	2		533	463	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259157	36259157	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	85	574	0	ENST00000300305.3:c.334C>A	p.Leu112Met	p.L112M	ENST00000300305		112	Ctg/Atg	3/8	1	2	FACETS	0.854	0.758	0.956	0.854	0.758	0.956	CLONAL	1	TRUE	1	0.442243262784402	2		574	450	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21348552	21348552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754507552	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	105	652	0	ENST00000215739.8:c.1609C>T	p.Arg537Trp	p.R537W	ENST00000215739	NM_006767.3	537	Cgg/Tgg	14/21	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.442243262784402	2		652	439	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21348891	21348891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	192	543	0	ENST00000215739.8:c.1660G>A	p.Ala554Thr	p.A554T	ENST00000215739	NM_006767.3	554	Gca/Aca	15/21	1	2	FACETS	0.984	0.921	1	1	0.994	1	CLONAL	2	TRUE	1	0.442243262784402	2		543	441	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732934	30732934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149847376	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	101	432	0	ENST00000295754.5:c.1547C>T	p.Thr516Met	p.T516M	ENST00000295754	NM_003242.5	516	aCg/aTg	7/7	1	2	FACETS	0.991	0.89	1	0.991	0.89	1	CLONAL	1	TRUE	1	0.442243262784402	2		432	461	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050377	37050378	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	66	357	0	ENST00000231790.2:c.530dup	p.Leu177PhefsTer15	p.L177Ffs*15	ENST00000231790	NM_000249.3	176	att/aTtt	6/19	1	2	FACETS	0.886	0.774	1	0.886	0.774	1	CLONAL	1	TRUE	1	0.442243262784402	2		357	337	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161957	47161958	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	95	504	0	ENST00000409792.3:c.4168dup	p.Ser1390PhefsTer8	p.S1390Ffs*8	ENST00000409792	NM_014159.6	1390	tca/tTca	3/21	1	2	FACETS	0.924	0.827	1	0.924	0.827	1	CLONAL	1	TRUE	1	0.442243262784402	2		504	465	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149243823	149243823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	58	355	0	ENST00000360632.3:c.995G>A	p.Ser332Asn	p.S332N	ENST00000360632	NM_015472.4	332	aGc/aAc	6/7	1	2	FACETS	0.673	0.58	0.773	0.673	0.58	0.773	SUBCLONAL	1	TRUE	1	0.442243262784402	2		355	390	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998128	169998128	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs753143066	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	46	354	2	ENST00000295797.4:c.826del	p.Thr276GlnfsTer7	p.T276Qfs*7	ENST00000295797	NM_002740.5	273	ttA/tt	9/18	1	2	FACETS	0.549	0.463	0.643	0.549	0.463	0.643	SUBCLONAL	1	TRUE	1	0.442243262784402	2		356	379	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170015162	170015162	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368665283	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	81	385	0	ENST00000295797.4:c.1568G>A	p.Arg523Gln	p.R523Q	ENST00000295797	NM_002740.5	523	cGa/cAa	16/18	1	2	FACETS	0.985	0.874	1	0.985	0.874	1	CLONAL	1	TRUE	1	0.442243262784402	2		385	372	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139876	55139876	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	98	414	0	ENST00000257290.5:c.1537G>C	p.Glu513Gln	p.E513Q	ENST00000257290	NM_006206.4	513	Gag/Cag	10/23	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.442243262784402	2		414	435	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286184	66286184	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	58	395	0	ENST00000273854.3:c.1502A>T	p.Glu501Val	p.E501V	ENST00000273854	NM_004439.5	501	gAg/gTg	6/18	1	2	FACETS	0.846	0.732	0.969	0.846	0.732	0.969	CLONAL	1	TRUE	1	0.442243262784402	2		395	310	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541678	187541678	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377498159	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	56	518	1	ENST00000441802.2:c.6062G>A	p.Arg2021His	p.R2021H	ENST00000441802	NM_005245.3	2021	cGc/cAc	10/27	1	2	FACETS	0.466	0.399	0.538	0.466	0.399	0.538	SUBCLONAL	1	TRUE	1	0.442243262784402	2		519	544	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	230998	230998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs940845256	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	97	406	0	ENST00000264932.6:c.778G>A	p.Gly260Arg	p.G260R	ENST00000264932	NM_004168.2	260	Ggg/Agg	7/15	1	2	FACETS	0.992	0.89	1	0.992	0.89	1	CLONAL	1	TRUE	1	0.442243262784402	2		406	442	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293773	1293773	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	96	626	0	ENST00000310581.5:c.1228A>G	p.Lys410Glu	p.K410E	ENST00000310581	NM_198253.2	410	Aag/Gag	2/16	1	2	FACETS	0.998	0.894	1	0.998	0.894	1	CLONAL	1	TRUE	1	0.442243262784402	2		626	435	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294552	1294552	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	97	520	0	ENST00000310581.5:c.449T>A	p.Val150Asp	p.V150D	ENST00000310581	NM_198253.2	150	gTt/gAt	2/16	1	2	FACETS	0.99	0.888	1	0.99	0.888	1	CLONAL	1	TRUE	1	0.442243262784402	2		520	443	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753011	57753012	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	84	514	2	ENST00000274289.3:c.1004dup	p.Leu335PhefsTer12	p.L335Ffs*12	ENST00000274289	NM_006622.3	335	ttg/ttTg	7/14	1	2	FACETS	0.82	0.728	0.919	0.82	0.728	0.919	CLONAL	1	TRUE	1	0.442243262784402	2		516	463	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564511	86564511	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	71	556	2	ENST00000274376.6:c.248del	p.Gly83GlufsTer4	p.G83Efs*4	ENST00000274376	NM_002890.2	81	ctG/ct	1/25	1	2	FACETS	0.873	0.766	0.986	0.873	0.766	0.986	CLONAL	1	TRUE	1	0.442243262784402	2		558	368	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675571	86675571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1561325048	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	24	310	0	ENST00000274376.6:c.2513del	p.Asn838MetfsTer4	p.N838Mfs*4	ENST00000274376	NM_002890.2	836	gAa/ga	19/25	1	2	FACETS	0.345	0.27	0.43	0.345	0.27	0.43	SUBCLONAL	1	TRUE	1	0.442243262784402	2		310	315	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675616	86675616	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	42	326	0	ENST00000274376.6:c.2552T>C	p.Ile851Thr	p.I851T	ENST00000274376	NM_002890.2	851	aTa/aCa	19/25	1	2	FACETS	0.559	0.468	0.659	0.559	0.468	0.659	SUBCLONAL	1	TRUE	1	0.442243262784402	2		326	340	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	70	357	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.858	0.752	0.971	0.858	0.752	0.971	CLONAL	1	TRUE	1	0.442243262784402	2		357	369	SUCCESS
APC	324	MSKCC	GRCh37	5	112175716	112175726	+	frameshift_variant	Frame_Shift_Del	DEL	AGTTCAGAGGG	AGTTCAGAGGG	-	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	91	563	0	ENST00000257430.4:c.4425_4435del	p.Val1476ProfsTer7	p.V1476Pfs*7	ENST00000257430	NM_000038.5	1475	gcAGTTCAGAGGGtc/gctc	16/16	1	2	FACETS	0.874	0.779	0.974	0.874	0.779	0.974	CLONAL	1	TRUE	1	0.442243262784402	2		563	471	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046686	180046686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	35	691	0	ENST00000261937.6:c.2626G>A	p.Val876Met	p.V876M	ENST00000261937	NM_182925.4	876	Gtg/Atg	18/30	1	2	FACETS	0.315	0.258	0.38	0.315	0.258	0.38	SUBCLONAL	1	TRUE	1	0.442243262784402	2		691	502	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056511	26056511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781230949	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	27	473	0	ENST00000343677.2:c.146C>T	p.Ala49Val	p.A49V	ENST00000343677	NM_005319.3	49	gCc/gTc	1/1	1	2	FACETS	0.285	0.226	0.353	0.285	0.226	0.353	SUBCLONAL	1	TRUE	1	0.442243262784402	2		473	428	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911159	29911159	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	24	390	0	ENST00000376809.5:c.458A>G	p.Asp153Gly	p.D153G	ENST00000376809	NM_002116.7	153	gAc/gGc	3/8	1	2	FACETS	0.342	0.268	0.428	0.342	0.268	0.428	SUBCLONAL	1	TRUE	1	0.442243262784402	2		390	317	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	26	363	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	0.361	0.286	0.446	0.361	0.286	0.446	SUBCLONAL	1	TRUE	1	0.442243262784402	2		363	326	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797286	32797286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	84	502	0	ENST00000374899.4:c.1823C>T	p.Ala608Val	p.A608V	ENST00000374899	NM_018833.2	608	gCt/gTt	11/12	1	2	FACETS	0.798	0.707	0.894	0.798	0.707	0.894	SUBCLONAL	1	TRUE	1	0.442243262784402	2		502	476	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803522	32803522	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	67	488	0	ENST00000374899.4:c.637T>C	p.Cys213Arg	p.C213R	ENST00000374899	NM_018833.2	213	Tgc/Cgc	4/12	1	2	FACETS	0.579	0.504	0.661	0.579	0.504	0.661	SUBCLONAL	1	TRUE	1	0.442243262784402	2		488	523	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289083	33289083	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	36	581	0	ENST00000374542.5:c.469G>T	p.Gly157Trp	p.G157W	ENST00000374542	NM_001141970.1	157	Ggg/Tgg	3/8	1	2	FACETS	0.29	0.238	0.349	0.29	0.238	0.349	SUBCLONAL	1	TRUE	1	0.442243262784402	2		581	561	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665221	117665221	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	66	425	0	ENST00000368508.3:c.4524+2T>C		p.X1508_splice	ENST00000368508	NM_002944.2	1508			1	2	FACETS	0.995	0.871	1	0.995	0.871	1	CLONAL	1	TRUE	1	0.442243262784402	2		425	300	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519504	137519505	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	88	493	0	ENST00000367739.4:c.1132_1133dup	p.Ser378ArgfsTer6	p.S378Rfs*6	ENST00000367739	NM_000416.2	378	agt/agAGt	7/7	1	2	FACETS	0.884	0.787	0.987	0.884	0.787	0.987	CLONAL	1	TRUE	1	0.442243262784402	2		493	450	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405991	157405991	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554294689	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	106	601	0	ENST00000346085.5:c.2233G>T	p.Gly745Ter	p.G745*	ENST00000346085	NM_020732.3	745	Gga/Tga	6/20	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.442243262784402	2		601	476	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525104	157525104	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	56	464	0	ENST00000346085.5:c.4999A>G	p.Thr1667Ala	p.T1667A	ENST00000346085	NM_020732.3	1667	Act/Gct	19/20	1	2	FACETS	0.677	0.582	0.78	0.677	0.582	0.78	SUBCLONAL	1	TRUE	1	0.442243262784402	2		464	374	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729709	41729709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768547360	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	35	554	1	ENST00000242208.4:c.820G>A	p.Gly274Arg	p.G274R	ENST00000242208	NM_002192.2	274	Gga/Aga	3/3	1	2	FACETS	0.317	0.259	0.381	0.317	0.259	0.381	SUBCLONAL	1	TRUE	1	0.442243262784402	2		555	500	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55225430	55225430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	20	372	0	ENST00000275493.2:c.1282G>A	p.Gly428Ser	p.G428S	ENST00000275493	NM_005228.3	428	Ggc/Agc	11/28	1	2	FACETS	0.24	0.183	0.307	0.24	0.183	0.307	SUBCLONAL	1	TRUE	1	0.442243262784402	2		372	377	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359017	81359017	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	66	454	0	ENST00000222390.5:c.944del	p.Gly315AlafsTer25	p.G315Afs*25	ENST00000222390	NM_000601.4	315	gGc/gc	8/18	1	2	FACETS	0.907	0.793	1	0.907	0.793	1	CLONAL	1	TRUE	1	0.442243262784402	2		454	329	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	48	511	1	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.595	0.504	0.694	0.595	0.504	0.694	SUBCLONAL	1	TRUE	1	0.442243262784402	2		512	365	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859938	151859938	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	89	587	0	ENST00000262189.6:c.10724C>T	p.Thr3575Ile	p.T3575I	ENST00000262189	NM_170606.2	3575	aCt/aTt	43/59	1	2	FACETS	0.925	0.825	1	0.925	0.825	1	CLONAL	1	TRUE	1	0.442243262784402	2		587	435	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983427	90983427	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1563561558	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	56	347	0	ENST00000265433.3:c.676del	p.Thr226HisfsTer5	p.T226Hfs*5	ENST00000265433	NM_002485.4	226	Aca/ca	6/16	1	2	FACETS	0.684	0.589	0.788	0.684	0.589	0.788	SUBCLONAL	1	TRUE	1	0.442243262784402	2		347	370	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913138	39913138	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	111	445	0	ENST00000378444.4:c.4976+1del		p.X1659_splice	ENST00000378444	NM_001123385.1	1659			0.225772584904537	3	FACETS	1	0.962	1	0.568	0.512	0.626	INDETERMINATE	1	TRUE	1	0.442243262784402	3		445	540	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424287	47424287	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	40	535	0	ENST00000377045.4:c.292A>G	p.Met98Val	p.M98V	ENST00000377045	NM_001654.4	98	Atg/Gtg	4/16	0.225772584904537	3	FACETS	0.399	0.331	0.476	0.2	0.165	0.238	INDETERMINATE	1	TRUE	1	0.442243262784402	3		535	553	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411540	63411540	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	96	546	0	ENST00000330258.3:c.1627G>T	p.Glu543Ter	p.E543*	ENST00000330258	NM_152424.3	543	Gag/Tag	2/2	0.420118360148636	1	FACETS	0.86	0.772	0.953	0.86	0.772	0.953	CLONAL	1	TRUE	0	0.442243262784402	1		546	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0067267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	81	369	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.417950119243703	3	FACETS	1	0.961	1	0.766	0.688	0.845	CLONAL	2	TRUE	0	0.417950119243703	3		369	204	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610678	10610678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	40	614	0	ENST00000171111.5:c.32G>A	p.Gly11Glu	p.G11E	ENST00000171111	NM_203500.1	11	gGg/gAg	2/6	0.347383022436105	5	FACETS	1	0.851	1	0.34	0.284	0.403	CLONAL	1	TRUE	2	0.417950119243703	5		614	305	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673312	30673312	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs754395572	NA	P-0067267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	63	941	0	ENST00000376406.3:c.3648C>A	p.Asp1216Glu	p.D1216E	ENST00000376406	NM_014641.2	1216	gaC/gaA	10/15	0.417950119243703	2	FACETS	1	0.93	1	0.55	0.48	0.624	CLONAL	1	TRUE	0	0.417950119243703	2		941	274	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028118	48028118	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	90	597	0	ENST00000234420.5:c.2996C>T	p.Thr999Ile	p.T999I	ENST00000234420	NM_000179.2	999	aCc/aTc	4/10	0.220864314180746	4	FACETS	0.934	0.845	1	0.934	0.845	1	INDETERMINATE	3	TRUE	1	0.417950119243703	4		597	218	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938203	36938203	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	80	646	0	ENST00000361632.4:c.758G>T	p.Trp253Leu	p.W253L	ENST00000361632		253	tGg/tTg	6/16	0.316558828554971	3	FACETS	0.887	0.801	0.973	0.887	0.801	0.973	CLONAL	3	TRUE	0	0.417950119243703	3		646	174	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0067268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	162	661	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.342102565772747	2	FACETS	0.877	0.816	0.937	1	0.988	1	CLONAL	3	TRUE	0	0.341299317213446	2		661	361	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0067268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	110	490	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.342102565772747	3	FACETS	0.873	0.79	0.96	0.873	0.79	0.96	CLONAL	2	TRUE	1	0.341299317213446	3		490	432	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0067269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	60	270	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.92	0.804	1	0.92	0.804	1	CLONAL	1	TRUE	1	0.606876607493263	2		270	215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0067269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	160	704	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	0.606876607493263	1	FACETS	0.993	0.923	1	0.993	0.923	1	CLONAL	1	TRUE	0	0.606876607493263	1		704	370	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686893	117686893	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs115534545	NA	P-0067269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	12	446	0	ENST00000368508.3:c.2824T>C	p.Phe942Leu	p.F942L	ENST00000368508	NM_002944.2	942	Ttt/Ctt	19/43	0.606876607493263	1	FACETS	0.136	0.095	0.186	0.136	0.095	0.186	SUBCLONAL	1	TRUE	0	0.606876607493263	1		446	202	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448297	56448298	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1567880599	NA	P-0067269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	128	626	0	ENST00000407977.2:c.349dup	p.Arg117ProfsTer8	p.R117Pfs*8	ENST00000407977		117	cgc/cCgc	3/10	0.606876607493263	1	FACETS	0.936	0.861	1	0.936	0.861	1	CLONAL	1	TRUE	0	0.606876607493263	1		626	314	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781225	161781225	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1801334	NA	P-0067269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	18	506	0	ENST00000366898.1:c.1180G>A	p.Asp394Asn	p.D394N	ENST00000366898	NM_004562.2	394	Gat/Aat	11/12	0.606876607493263	1	FACETS	0.155	0.116	0.2	0.155	0.116	0.2	SUBCLONAL	1	TRUE	0	0.606876607493263	1		506	267	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138729528	NA	P-0067287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	12	556	0	ENST00000269305.4:c.523C>T	p.Arg175Cys	p.R175C	ENST00000269305	NM_001126112.2	175	Cgc/Tgc	5/11	0.449026089786743	2	FACETS	0.101	0.07	0.139	0.05	0.035	0.07	SUBCLONAL	1	TRUE	0	0.449026089786743	2		556	531	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913381	NA	P-0067287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	178	528	0	ENST00000304494.5:c.322G>A	p.Asp108Asn	p.D108N	ENST00000304494	NM_000077.4	108	Gat/Aat	2/3	0.179483964021954	4	FACETS	0.982	0.91	1	0.982	0.91	1	INDETERMINATE	2	TRUE	2	0.449026089786743	4		528	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0067287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	228	600	0	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	0.449026089786743	2	FACETS	0.925	0.87	0.981	0.925	0.87	0.981	CLONAL	2	TRUE	0	0.449026089786743	2		600	549	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0067287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	652	509	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.449026089786743	7	FACETS	1	0.99	1	0.751	0.728	0.775	CLONAL	5	TRUE	0	0.449026089786743	7		509	1172	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807288	1807288	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs121913112	NA	P-0067287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	77	518	1	ENST00000260795.2:c.1537G>A	p.Asp513Asn	p.D513N	ENST00000260795		513	Gat/Aat	11/17	0.243718943768647	2	FACETS	0.589	0.518	0.666	0.295	0.259	0.333	INDETERMINATE	1	TRUE	0	0.449026089786743	2		519	582	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912815	100912815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1000609240	NA	P-0067287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	58	438	0	ENST00000325455.5:c.2507G>A	p.Arg836Gln	p.R836Q	ENST00000325455	NM_001202474.3	836	cGa/cAa	7/8	0.43335092446003	3	FACETS	0.889	0.767	1	0.444	0.383	0.51	CLONAL	1	TRUE	1	0.449026089786743	3		438	356	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881392	37881392	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	813	558	0	ENST00000269571.5:c.2584A>G	p.Thr862Ala	p.T862A	ENST00000269571		862	Aca/Gca	21/27	0.449026089786743	7	FACETS	1	0.993	1	1	0.993	1	CLONAL	7	TRUE	0	0.449026089786743	7		558	1064	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435832	149435832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1209791630	NA	P-0067287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	89	489	0	ENST00000286301.3:c.2392G>A	p.Gly798Arg	p.G798R	ENST00000286301	NM_005211.3	798	Ggg/Agg	18/22	0.449026089786743	2	FACETS	0.999	0.891	1	0.499	0.445	0.556	CLONAL	1	TRUE	0	0.449026089786743	2		489	397	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911971	32911971	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	138	460	0	ENST00000380152.3:c.3479G>C	p.Arg1160Thr	p.R1160T	ENST00000380152		1160	aGa/aCa	11/27	0.449026089786743	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	1	0.449026089786743	3		460	359	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578277	7578277	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	22	603	0	ENST00000269305.4:c.572del	p.Pro191LeufsTer56	p.P191Lfs*56	ENST00000269305	NM_001126112.2	191	cCt/ct	6/11	0.449026089786743	2	FACETS	0.173	0.133	0.22	0.087	0.066	0.11	SUBCLONAL	1	TRUE	0	0.449026089786743	2		603	566	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396221	396221	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	353	534	0	ENST00000262320.3:c.805C>T	p.Gln269Ter	p.Q269*	ENST00000262320	NM_003502.3	269	Cag/Tag	2/11	0.357200796513991	4	FACETS	0.996	0.956	1	0.996	0.956	1	CLONAL	4	TRUE	0	0.449026089786743	4		534	572	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1936885	1936885	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	41	454	1	ENST00000382891.5:c.1570A>G	p.Lys524Glu	p.K524E	ENST00000382891	NM_133335.3	524	Aaa/Gaa	7/22	0.243718943768647	2	FACETS	0.465	0.387	0.55	0.232	0.193	0.275	INDETERMINATE	1	TRUE	0	0.449026089786743	2		455	393	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117632	70117632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	356	533	1	ENST00000245479.2:c.100C>T	p.Pro34Ser	p.P34S	ENST00000245479	NM_000346.3	34	Ccc/Tcc	1/3	0.449026089786743	3	FACETS	0.99	0.947	1	0.99	0.947	1	CLONAL	3	TRUE	0	0.449026089786743	3		534	654	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778795	76778795	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	77	607	0	ENST00000373344.5:c.6784G>C	p.Glu2262Gln	p.E2262Q	ENST00000373344	NM_000489.3	2262	Gaa/Caa	31/35	0.314250022056871	4	FACETS	0.872	0.774	0.975	0.872	0.774	0.975	CLONAL	2	TRUE	2	0.449026089786743	4		607	285	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090909	5090909	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	45	383	0	ENST00000381652.3:c.3057C>G	p.Phe1019Leu	p.F1019L	ENST00000381652	NM_004972.3	1019	ttC/ttG	22/25	0.179483964021954	4	FACETS	0.931	0.797	1	0.931	0.797	1	INDETERMINATE	2	TRUE	2	0.449026089786743	4		383	156	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303214	15303214	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0067287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	196	524	0	ENST00000263388.2:c.314C>G	p.Ser105Ter	p.S105*	ENST00000263388	NM_000435.2	105	tCa/tGa	3/33	0.415046231332351	3	FACETS	0.938	0.874	1	0.938	0.874	1	CLONAL	2	TRUE	1	0.449026089786743	3		524	570	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251976	8251976	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	73	601	0	ENST00000335790.3:c.101G>T	p.Arg34Leu	p.R34L	ENST00000335790	NM_002315.2	34	cGc/cTc	2/4	0.43335092446003	3	FACETS	0.64	0.56	0.727	0.32	0.28	0.364	SUBCLONAL	1	TRUE	1	0.449026089786743	3		601	622	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0067288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	295	529	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.605425281360571	2	FACETS	0.927	0.888	0.965	0.927	0.888	0.965	CLONAL	2	TRUE	0	0.696340519086484	2		529	457	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657491	29657492	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0067288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	161	262	0	ENST00000356175.3:c.5726_5727del	p.Cys1909TyrfsTer5	p.C1909Yfs*5	ENST00000356175	NM_000267.3	1908	gaGTgt/gagt	38/57	0.605425281360571	2	FACETS	0.786	0.737	0.836	0.786	0.737	0.836	SUBCLONAL	2	TRUE	0	0.696340519086484	2		262	294	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664475	138664475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	15	212	0	ENST00000330315.3:c.1090G>A	p.Asp364Asn	p.D364N	ENST00000330315	NM_023067.3	364	Gac/Aac	1/1	1	2	FACETS	0.917	0.672	1	0.917	0.672	1	CLONAL	1	TRUE	1	0.15	2		212	218	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188320	10188320	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	29	337	0	ENST00000256474.2:c.463G>C	p.Val155Leu	p.V155L	ENST00000256474	NM_000551.3	155	Gtg/Ctg	2/3	0.185243193885622	1	FACETS	0.983	0.789	1	0.983	0.789	1	CLONAL	1	TRUE	0	0.15	1		337	364	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422404	47422404	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	36	420	0	ENST00000404338.3:c.472G>C	p.Asp158His	p.D158H	ENST00000404338	NM_004491.4	158	Gat/Cat	1/6	1	2	FACETS	0.958	0.787	1	0.958	0.787	1	CLONAL	1	TRUE	1	0.15	2		420	501	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594075	55594075	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1560418178	NA	P-0067290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	126	419	0	ENST00000288135.5:c.1861G>A	p.Ala621Thr	p.A621T	ENST00000288135	NM_000222.2	621	Gct/Act	12/21	1	2	FACETS	0.915	0.833	1	0.915	0.833	1	CLONAL	1	TRUE	1	0.533599493790784	2		419	516	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190834	11190834	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	129	332	0	ENST00000361445.4:c.5365G>T	p.Ala1789Ser	p.A1789S	ENST00000361445	NM_004958.3	1789	Gcc/Tcc	39/58	1	2	FACETS	0.793	0.721	0.868	0.793	0.721	0.868	SUBCLONAL	1	TRUE	1	0.533599493790784	2		332	610	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246245	41246245	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	45	436	0	ENST00000357654.3:c.1303G>A	p.Asp435Asn	p.D435N	ENST00000357654	NM_007294.3	435	Gat/Aat	10/23	0.281188170395799	3	FACETS	0.621	0.523	0.729	0.311	0.261	0.365	INDETERMINATE	1	TRUE	1	0.472642980953283	3		436	379	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982409	10982417	+	inframe_deletion	In_Frame_Del	DEL	GGCGCGGGC	GGCGCGGGC	-	novel	NA	P-0067291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	38	205	0	ENST00000327064.4:c.39_47del	p.Gly14_Gly16del	p.G14_G16del	ENST00000327064	NM_199141.1	11	GGCGCGGGC/-	1/16	0.477296223357077	3	FACETS	0.904	0.753	1	0.452	0.376	0.534	CLONAL	1	TRUE	1	0.472642980953283	3		205	220	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829812	76829826	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTTCCCCTCACCTG	ACTTCCCCTCACCTG	-	novel	NA	P-0067291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	111	185	0	ENST00000373344.5:c.6218-3_6229del		p.X2073_splice	ENST00000373344	NM_000489.3	2073		28/35	0.366506047160693	2	FACETS	1	0.961	1			1	CLONAL	3	TRUE	NA	0.472642980953283	2		185	152	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0067292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	124	450	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.332686707725949	2	FACETS	0.939	0.858	1	0.939	0.858	1	CLONAL	2	TRUE	0	0.3466169375669	2		450	381	SUCCESS
APC	324	MSKCC	GRCh37	5	112163677	112163677	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0067292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	110	258	0	ENST00000257430.4:c.1600A>T	p.Lys534Ter	p.K534*	ENST00000257430	NM_000038.5	534	Aaa/Taa	13/16	0.3466169375669	3	FACETS	0.874	0.798	0.952	0.874	0.798	0.952	CLONAL	3	TRUE	0	0.3466169375669	3		258	284	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89807250	89807252	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs397507553	NA	P-0067292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	104	292	0	ENST00000389301.3:c.3788_3790del	p.Phe1263del	p.F1263del	ENST00000389301	NM_000135.2	1263	tTCTcc/tcc	38/43	0.322710819339985	4	FACETS	0.995	0.898	1	0.663	0.598	0.731	CLONAL	2	TRUE	1	0.3466169375669	4		292	406	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178036	56178036	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	19	330	0	ENST00000399503.3:c.3009G>C	p.Lys1003Asn	p.K1003N	ENST00000399503	NM_005921.1	1003	aaG/aaC	14/20	0.3466169375669	3	FACETS	0.415	0.315	0.533	0.138	0.105	0.178	SUBCLONAL	1	TRUE	0	0.3466169375669	3		330	310	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601965	43601965	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161270866	NA	P-0067292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	118	369	0	ENST00000355710.3:c.1009G>A	p.Glu337Lys	p.E337K	ENST00000355710	NM_020975.4	337	Gag/Aag	5/20	0.3466169375669	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.3466169375669	3		369	344	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0067294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	68	351	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	1	2	FACETS	0.915	0.799	1	0.915	0.799	1	CLONAL	1	TRUE	1	0.325814349615627	2		351	456	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467362	66467362	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	70	470	0	ENST00000273854.3:c.907C>A	p.Gln303Lys	p.Q303K	ENST00000273854	NM_004439.5	303	Caa/Aaa	3/18	1	2	FACETS	0.997	0.873	1	0.997	0.873	1	CLONAL	1	TRUE	1	0.325814349615627	2		470	431	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187500	32187500	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs76408438	NA	P-0067294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	89	509	0	ENST00000375023.3:c.1379A>G	p.Asn460Ser	p.N460S	ENST00000375023	NM_004557.3	460	aAc/aGc	8/30	0.318855545292217	3	FACETS	1	0.953	1	0.569	0.506	0.637	CLONAL	1	TRUE	1	0.325814349615627	3		509	558	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652025	36652025	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067295-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	229	441	0	ENST00000244741.5:c.147G>A	p.Trp49Ter	p.W49*	ENST00000244741	NM_000389.4	49	tgG/tgA	2/3	0.842195237228625	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.842195237228625	1		441	305	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77937517	77937517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1159054700	NA	P-0067296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1426	90	403	0	ENST00000361507.4:c.1201C>T	p.His401Tyr	p.H401Y	ENST00000361507	NM_080491.2	401	Cac/Tac	4/10	0.575143394780923	10	FACETS	0.681	0.602	0.767			1	SUBCLONAL	1	TRUE	NA	0.575143394780923	10		403	1516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0067297-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	259	567	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.376117176399893	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.376117176399893	2		567	683	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0067297-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	63	466	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.96	0.835	1	0.96	0.835	1	CLONAL	1	TRUE	1	0.376117176399893	2		466	349	SUCCESS
APC	324	MSKCC	GRCh37	5	112175273	112175273	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123121	NA	P-0067297-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	108	360	0	ENST00000257430.4:c.3982C>T	p.Gln1328Ter	p.Q1328*	ENST00000257430	NM_000038.5	1328	Cag/Tag	16/16	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.376117176399893	2		360	533	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828962	72828962	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755878473	NA	P-0067297-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	90	409	0	ENST00000268489.5:c.7619C>T	p.Pro2540Leu	p.P2540L	ENST00000268489	NM_006885.3	2540	cCg/cTg	9/10	0.142462125761815	4	FACETS	0.97	0.861	1	0.485	0.43	0.543	INDETERMINATE	1	TRUE	2	0.376117176399893	4		409	679	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858642	57858642	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751408248	NA	P-0067297-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	235	336	0	ENST00000228682.2:c.380G>A	p.Gly127Asp	p.G127D	ENST00000228682	NM_005269.2	127	gGc/gAc	4/12	0.376117176399893	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.376117176399893	3		336	706	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098879	47098879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067297-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	52	383	0	ENST00000409792.3:c.6395G>A	p.Arg2132Gln	p.R2132Q	ENST00000409792	NM_014159.6	2132	cGg/cAg	15/21	0.342956117712166	3	FACETS	0.443	0.376	0.516	0.221	0.188	0.258	SUBCLONAL	1	TRUE	1	0.376117176399893	3		383	742	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270565	98270565	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067297-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	44	214	0	ENST00000331920.6:c.79C>G	p.Pro27Ala	p.P27A	ENST00000331920	NM_000264.3	27	Ccg/Gcg	1/24	0.315759216915368	4	FACETS	0.662	0.556	0.781	0.331	0.278	0.391	SUBCLONAL	1	TRUE	2	0.376117176399893	4		214	486	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63898399	63898399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067297-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	81	225	0	ENST00000398590.3:c.125C>T	p.Pro42Leu	p.P42L	ENST00000398590	NM_001177387.1	42	cCt/cTt	3/14	0.342956117712166	3	FACETS	1	0.948	1	0.565	0.499	0.634	CLONAL	1	TRUE	1	0.376117176399893	3		225	453	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619180	37619180	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	143	476	0	ENST00000447079.4:c.856C>T	p.Gln286Ter	p.Q286*	ENST00000447079	NM_015083.1	286	Cag/Tag	1/14	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.4927697260865	2		476	427	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37665979	37665979	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	78	315	0	ENST00000447079.4:c.2631T>G	p.Asp877Glu	p.D877E	ENST00000447079	NM_015083.1	877	gaT/gaG	7/14	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.4927697260865	2		315	288	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061112	38061201	+	inframe_deletion	In_Frame_Del	DEL	TCTCAGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCT	TCTCAGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCT	-	novel	NA	P-0067298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	82	418	0	ENST00000250448.2:c.788_877del	p.Gln263_Ser293delinsArg	p.Q263_S293delinsR	ENST00000250448	NM_004496.3	263	cAGAAGCGCTTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGGCGCCAAGGGCGGCCCTGAGAgc/cgc	2/2	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.4927697260865	2		418	286	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560191	29560191	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1555615091	NA	P-0067298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	115	377	0	ENST00000356175.3:c.3668T>G	p.Ile1223Arg	p.I1223R	ENST00000356175	NM_000267.3	1223	aTa/aGa	27/57	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.4927697260865	2		377	318	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024347	31024347	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	128	399	0	ENST00000375687.4:c.3832A>C	p.Asn1278His	p.N1278H	ENST00000375687	NM_015338.5	1278	Aat/Cat	13/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.4927697260865	2		399	376	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067301-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	30	317	0				ENST00000310581	NM_198253.2	-/1132			0.144171381840181	3	FACETS	1	0.883	1	0.562	0.456	0.679	INDETERMINATE	1	TRUE	1	0.31	3		317	199	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0067301-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	77	389	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.31	2		389	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0067302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	169	477	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.449102307424649	2		477	646	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	132	317	0				ENST00000310581	NM_198253.2	-/1132			0.393575999985526	3	FACETS	0.857	0.785	0.931	0.857	0.785	0.931	CLONAL	2	TRUE	1	0.449102307424649	3		317	420	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954210	48954210	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1354030520	NA	P-0067302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	54	210	0	ENST00000267163.4:c.1411C>T	p.Gln471Ter	p.Q471*	ENST00000267163	NM_000321.2	471	Caa/Taa	15/27	0.449102307424649	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.449102307424649	1		210	143	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882019	NA	P-0067302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	131	554	0	ENST00000269305.4:c.455dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	ccg/ccCg	5/11	1	2	FACETS	0.949	0.863	1	0.949	0.863	1	CLONAL	1	TRUE	1	0.449102307424649	2		554	615	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872380	45872380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	129	499	0	ENST00000391945.4:c.131C>T	p.Ser44Leu	p.S44L	ENST00000391945	NM_000400.3	44	tCa/tTa	3/23	1	2	FACETS	0.975	0.887	1	0.975	0.887	1	CLONAL	1	TRUE	1	0.449102307424649	2		499	589	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160464	99160481	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TACAGAGGTGGGTGCACC	TACAGAGGTGGGTGCACC	-	novel	NA	P-0067302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	121	401	0	ENST00000074304.5:c.943_949+11del		p.X315_splice	ENST00000074304	NM_001134224.1	315		11/26	0.154298126482123	5	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.449102307424649	5		401	723	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738737	43738748	+	inframe_deletion	In_Frame_Del	DEL	TCAGACATGACA	TCAGACATGACA	-	novel	NA	P-0067302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	110	481	0	ENST00000382044.4:c.2877_2888del	p.Asp959_Ser962del	p.D959_S962del	ENST00000382044	NM_001141980.1	959	gaTGTCATGTCTGAa/gaa	14/28	1	2	FACETS	0.905	0.817	0.999	0.905	0.817	0.999	CLONAL	1	TRUE	1	0.449102307424649	2		481	541	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433892	49433904	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTGAGGGACAG	GGCTGAGGGACAG	-	novel	NA	P-0067302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	154	565	0	ENST00000301067.7:c.7649_7661del	p.Pro2550LeufsTer29	p.P2550Lfs*29	ENST00000301067	NM_003482.3	2550	cCTGTCCCTCAGCCt/ct	31/54	1	2	FACETS	0.997	0.915	1	0.997	0.915	1	CLONAL	1	TRUE	1	0.449102307424649	2		565	688	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118522	17119544	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCACTGGTCACCACAAACTCGTACTTGCTGAGAGACTGGTCATCCTCACACCCCACAGGGTGGAGGGTGGAACGTGCGGCTGCGTGGACCTCCACGATGACAGCAAACTCTGTAACAACACAAGGCCCGTGGCTCCTCATCTCCCCCATGCTCCTCACCTCCCCTGCGCTAGCCCACCGTGGGCCCCACTCCGCTCATCCCAGGTCAGTGGGGAAGGCTGCTGGTGAAAAGACTGGCCCAAATCAATGCTTTGGTATTTAAAACCTTTCAGGTTATTCGTGAATAGTTAAGGGTTAACTTTTGCCTCAGTTAAACTAATAATTTATTATATTACAATAATCACAAAGTACTTTATATACATCAATTTACCTCTGGCTAAGCAGCCCTATGAGGGTGGTCTCACCATGACCCTATTCTACAGATGGGGAAACAGGCCTGGAGACGTTAAATAACCTGCTCGTAGTGGTAAGAATTTGAAGTCTGTTTGAAACCAGAGCCTGTGTTTCCAATGCTACCCGGAAAAAAGGCACTGCCTCGCAGGGAGTCAGGACCCAGCCTGGGTGCTGATTGGGGGCTCAGGGTAGCTCCACTCGGACCATGAGTCAGCAGCTGCTGGTCACCGCTGTGCTGGGGGAAGTCACTGATGAGCCTGGGGGGCTGATCCCTGGACATCCCCAAACCAAAAGACCAGGGGTTTGCTGAGCCCTGACCACACCAGTGAAGGCCGGGAAGACCTCGGGCACATGAGGTGAAGAAAAAGGCTGGAGGAGAGCAGAAGTCAGGACAGGGGAACAGTAGAAGAGTGAGGAGAGGATGGCAGGGCCCACAGAAGCAGGCAGCTCACACCCAGCATTCAGCAGGCCTCCATCTCATAGGCACCCAATCACCAGGACGACCAGGATCCTCCGGCCAGGGACACATCCTCCCACCCCACGATGGTGACCTGCAGCCCACTGACGACAGTCCCTGCCAGCCAACCTTCCCATCAGGTCCACTCACCCACCGCTACCTGTGTGAAGATAG	CCACTGGTCACCACAAACTCGTACTTGCTGAGAGACTGGTCATCCTCACACCCCACAGGGTGGAGGGTGGAACGTGCGGCTGCGTGGACCTCCACGATGACAGCAAACTCTGTAACAACACAAGGCCCGTGGCTCCTCATCTCCCCCATGCTCCTCACCTCCCCTGCGCTAGCCCACCGTGGGCCCCACTCCGCTCATCCCAGGTCAGTGGGGAAGGCTGCTGGTGAAAAGACTGGCCCAAATCAATGCTTTGGTATTTAAAACCTTTCAGGTTATTCGTGAATAGTTAAGGGTTAACTTTTGCCTCAGTTAAACTAATAATTTATTATATTACAATAATCACAAAGTACTTTATATACATCAATTTACCTCTGGCTAAGCAGCCCTATGAGGGTGGTCTCACCATGACCCTATTCTACAGATGGGGAAACAGGCCTGGAGACGTTAAATAACCTGCTCGTAGTGGTAAGAATTTGAAGTCTGTTTGAAACCAGAGCCTGTGTTTCCAATGCTACCCGGAAAAAAGGCACTGCCTCGCAGGGAGTCAGGACCCAGCCTGGGTGCTGATTGGGGGCTCAGGGTAGCTCCACTCGGACCATGAGTCAGCAGCTGCTGGTCACCGCTGTGCTGGGGGAAGTCACTGATGAGCCTGGGGGGCTGATCCCTGGACATCCCCAAACCAAAAGACCAGGGGTTTGCTGAGCCCTGACCACACCAGTGAAGGCCGGGAAGACCTCGGGCACATGAGGTGAAGAAAAAGGCTGGAGGAGAGCAGAAGTCAGGACAGGGGAACAGTAGAAGAGTGAGGAGAGGATGGCAGGGCCCACAGAAGCAGGCAGCTCACACCCAGCATTCAGCAGGCCTCCATCTCATAGGCACCCAATCACCAGGACGACCAGGATCCTCCGGCCAGGGACACATCCTCCCACCCCACGATGGTGACCTGCAGCCCACTGACGACAGTCCCTGCCAGCCAACCTTCCCATCAGGTCCACTCACCCACCGCTACCTGTGTGAAGATAG	-	novel	NA	P-0067302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	46	466	0	ENST00000285071.4:c.1300+150_1409del		p.X434_splice	ENST00000285071	NM_144997.5	434		12/14	1	2	FACETS	0.343	0.288	0.404	0.343	0.288	0.404	SUBCLONAL	1	TRUE	1	0.449102307424649	2		466	597	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690777	89690802	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	ATATCACTTTTAAACTTTTCTTTTAG	ATATCACTTTTAAACTTTTCTTTTAG	-	novel	NA	P-0067302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	49	266	0	ENST00000371953.3:c.210-26_210-1del		p.X70_splice	ENST00000371953	NM_000314.4	70			0.449102307424649	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	0	0.449102307424649	1		266	158	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817784	3817784	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	102	426	0	ENST00000262367.5:c.3187G>T	p.Glu1063Ter	p.E1063*	ENST00000262367	NM_004380.2	1063	Gaa/Taa	16/31	1	2	FACETS	0.979	0.88	1	0.979	0.88	1	CLONAL	1	TRUE	1	0.449102307424649	2		426	464	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176176011	176176011	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	75	398	0	ENST00000367669.3:c.104C>G	p.Pro35Arg	p.P35R	ENST00000367669	NM_022457.5	35	cCg/cGg	1/20	0.449102307424649	4	FACETS	0.612	0.535	0.695	0.204	0.178	0.232	SUBCLONAL	1	TRUE	1	0.449102307424649	4		398	791	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0067303-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	56	439	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.578198923280378	2		439	183	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40789994	40789994	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs746391800	NA	P-0067303-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	100	362	0	ENST00000373198.4:c.2737G>A	p.Glu913Lys	p.E913K	ENST00000373198	NM_133170.3	913	Gag/Aag	18/32	0.241904207036125	2	FACETS	0.716	0.643	0.794	0.358	0.321	0.397	INDETERMINATE	1	TRUE	0	0.578198923280378	2		362	483	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797299	135797303	+	frameshift_variant	Frame_Shift_Del	DEL	GCGAT	GCGAT	-	novel	NA	P-0067303-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	140	370	0	ENST00000298552.3:c.566_570del	p.His189ProfsTer27	p.H189Pfs*27	ENST00000298552	NM_001162426.1	189	cATCGC/c	7/23	0.578198923280378	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.578198923280378	1		370	335	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27093013	27093016	+	frameshift_variant	Frame_Shift_Del	DEL	AACA	AACA	-	novel	NA	P-0067303-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	153	408	0	ENST00000324856.7:c.2945_2948del	p.Asn982ThrfsTer56	p.N982Tfs*56	ENST00000324856	NM_006015.4	982	AACAac/ac	10/20	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.578198923280378	2		408	522	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981108	201981108	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067303-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	134	362	0	ENST00000359651.3:c.187C>T	p.Gln63Ter	p.Q63*	ENST00000359651		63	Cag/Tag	2/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.578198923280378	2		362	411	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067305-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	145	317	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.907	0.838	0.977	0.907	0.838	0.977	CLONAL	1	FALSE	1	0.855201364137855	2		317	374	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806089	1806089	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913479	NA	P-0067305-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	532	534	0	ENST00000260795.2:c.1108G>T	p.Gly370Cys	p.G370C	ENST00000260795		370	Ggc/Tgc	8/17	1	2	FACETS	0.997	0.976	1	1	0.998	1	CLONAL	2	FALSE	1	0.855201364137855	2		534	624	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107105	27107105	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067305-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	279	605	0	ENST00000324856.7:c.6716T>C	p.Leu2239Pro	p.L2239P	ENST00000324856	NM_006015.4	2239	cTt/cCt	20/20	1	2	FACETS	0.964	0.911	1	0.964	0.911	1	CLONAL	1	FALSE	1	0.855201364137855	2		605	677	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423223	47423223	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067305-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	329	585	0	ENST00000404338.3:c.1291G>C	p.Glu431Gln	p.E431Q	ENST00000404338	NM_004491.4	431	Gag/Cag	1/6	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.855201364137855	2		585	746	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913185	44913185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067305-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	233	483	0	ENST00000377967.4:c.860G>A	p.Trp287Ter	p.W287*	ENST00000377967	NM_021140.2	287	tGg/tAg	10/29	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.855201364137855	2		483	517	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196810	123196810	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067305-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	154	437	0	ENST00000218089.9:c.1701del	p.Phe567LeufsTer9	p.F567Lfs*9	ENST00000218089	NM_001042749.1	566	cTt/ct	18/35	1	2	FACETS	0.938	0.869	1	0.938	0.869	1	CLONAL	1	FALSE	1	0.855201364137855	2		437	384	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0067306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	42	439	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.677500766946381	2		439	123	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0067306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	115	305	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.677500766946381	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.677500766946381	1		305	204	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780068	NA	P-0067306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	104	555	0	ENST00000269305.4:c.472C>T	p.Arg158Cys	p.R158C	ENST00000269305	NM_001126112.2	158	Cgc/Tgc	5/11	1	2	FACETS	0.9	0.815	0.989	0.9	0.815	0.989	CLONAL	1	TRUE	1	0.677500766946381	2		555	341	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0067306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	34	466	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	1	2	FACETS	0.29	0.237	0.349	0.29	0.237	0.349	SUBCLONAL	1	TRUE	1	0.677500766946381	2		466	346	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265629	152265629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	115	359	0	ENST00000206249.3:c.1082C>T	p.Ala361Val	p.A361V	ENST00000206249	NM_000125.3	361	gCg/gTg	4/8	1	2	FACETS	0.981	0.894	1	0.981	0.894	1	CLONAL	1	TRUE	1	0.677500766946381	2		359	346	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056060	26056060	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	115	421	0	ENST00000343677.2:c.597G>C	p.Lys199Asn	p.K199N	ENST00000343677	NM_005319.3	199	aaG/aaC	1/1	1	2	FACETS	0.946	0.861	1	0.946	0.861	1	CLONAL	1	TRUE	1	0.677500766946381	2		421	359	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0067307-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	62	475	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.373414658453863	4	FACETS	1	0.912	1	0.356	0.308	0.407	CLONAL	1	TRUE	1	0.384601030376485	4		475	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578204	7578204	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520001	NA	P-0067307-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	36	460	0	ENST00000269305.4:c.645T>G	p.Ser215Arg	p.S215R	ENST00000269305	NM_001126112.2	215	agT/agG	6/11	0.312792684812384	1	FACETS	0.727	0.603	0.863	0.727	0.603	0.863	SUBCLONAL	1	TRUE	0	0.384601030376485	1		460	208	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670071	29670071	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1060500286	NA	P-0067307-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	59	364	0	ENST00000356175.3:c.7044G>A	p.Trp2348Ter	p.W2348*	ENST00000356175	NM_000267.3	2348	tgG/tgA	47/57	0.312792684812384	1	FACETS	0.921	0.8	1	0.921	0.8	1	CLONAL	1	TRUE	0	0.384601030376485	1		364	269	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0067309-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	65	166	1	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.354591618428481	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	2	TRUE	0	0.372014596440666	2		167	169	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221706	22221706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067309-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	54	387	0	ENST00000215832.6:c.25G>A	p.Ala9Thr	p.A9T	ENST00000215832	NM_002745.4	9	Gcg/Acg	1/9	0.339891015389453	3	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	1	0.372014596440666	3		387	156	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043438	180043438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373876329	NA	P-0067309-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	35	461	0	ENST00000261937.6:c.3148G>A	p.Val1050Met	p.V1050M	ENST00000261937	NM_182925.4	1050	Gtg/Atg	23/30	0.196522269909343	1	FACETS	0.794	0.657	0.943	0.794	0.657	0.943	INDETERMINATE	1	TRUE	0	0.372014596440666	1		461	193	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180678	32180678	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067309-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	22	332	0	ENST00000375023.3:c.2449A>G	p.Asn817Asp	p.N817D	ENST00000375023	NM_004557.3	817	Aat/Gat	16/30	0.374149191409137	3	FACETS	0.762	0.595	0.954	0.381	0.297	0.477	CLONAL	1	TRUE	1	0.372014596440666	3		332	184	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0067310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	44	305	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.394780076187558	1	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	0	0.394780076187558	1		305	172	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577508	7577508	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060501201	NA	P-0067310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	238	402	0	ENST00000269305.4:c.773A>G	p.Glu258Gly	p.E258G	ENST00000269305	NM_001126112.2	258	gAa/gGa	7/11	0.394780076187558	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	0	0.394780076187558	3		402	463	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157240	106157240	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	58	466	0	ENST00000380013.4:c.2141C>A	p.Ser714Ter	p.S714*	ENST00000380013	NM_001127208.2	714	tCa/tAa	3/11	0.355168701677699	3	FACETS	0.681	0.585	0.784	0.34	0.292	0.392	SUBCLONAL	1	TRUE	1	0.394780076187558	3		466	517	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260290	16260290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	57	555	0	ENST00000375759.3:c.7555C>T	p.Pro2519Ser	p.P2519S	ENST00000375759	NM_015001.2	2519	Ccc/Tcc	11/15	1	2	FACETS	0.496	0.425	0.573	0.496	0.425	0.573	SUBCLONAL	1	TRUE	1	0.394780076187558	2		555	582	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619114	37619114	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	267	558	0	ENST00000447079.4:c.793del	p.Ser265ValfsTer73	p.S265Vfs*73	ENST00000447079	NM_015083.1	264	Aaa/aa	1/14	0.384814865044181	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	0	0.394780076187558	3		558	525	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8501006	8501006	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	33	446	0	ENST00000356435.5:c.1876A>C	p.Ile626Leu	p.I626L	ENST00000356435		626	Att/Ctt	13/35	0.384876098738158	0	FACETS	0.314	0.256	0.379			1	SUBCLONAL	1	TRUE	0	0.394780076187558	0		446	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067311-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	385	512	0	ENST00000269305.4:c.166G>T	p.Glu56Ter	p.E56*	ENST00000269305	NM_001126112.2	56	Gaa/Taa	4/11	0.797859374929439	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.797859374929439	2		512	465	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878103	48878103	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067311-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	178	488	0	ENST00000267163.4:c.55G>T	p.Glu19Ter	p.E19*	ENST00000267163	NM_000321.2	19	Gaa/Taa	1/27	0.797859374929439	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.797859374929439	1		488	234	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938167	76938167	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067311-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	329	487	0	ENST00000373344.5:c.2581G>C	p.Asp861His	p.D861H	ENST00000373344	NM_000489.3	861	Gat/Cat	9/35	0.566947743682577	3	FACETS	0.927	0.886	0.969	0.927	0.886	0.969	CLONAL	2	TRUE	1	0.797859374929439	3		487	622	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578482	7578486	+	frameshift_variant	Frame_Shift_Del	DEL	TGGAA	TGGAA	-	novel	NA	P-0067312-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	201	574	0	ENST00000269305.4:c.444_448del	p.Ser149ThrfsTer30	p.S149Tfs*30	ENST00000269305	NM_001126112.2	148	gaTTCCAca/gaca	5/11	0.33217290631637	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.33217290631637	2		574	563	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274316	5274316	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067312-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	84	438	0	ENST00000357368.4:c.131G>T	p.Gly44Val	p.G44V	ENST00000357368	NM_002850.3	44	gGc/gTc	3/38	0.33217290631637	2	FACETS	0.984	0.872	1	0.492	0.436	0.552	CLONAL	1	TRUE	0	0.33217290631637	2		438	514	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076712	72076712	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067312-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	137	499	0	ENST00000357731.5:c.785A>C	p.Lys262Thr	p.K262T	ENST00000357731	NM_173808.2	262	aAg/aCg	5/7	0.324388298123428	3	FACETS	0.848	0.775	0.924	0.848	0.775	0.924	CLONAL	2	TRUE	1	0.33217290631637	3		499	567	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212252702	212252702	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067312-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	145	392	0	ENST00000342788.4:c.3151A>G	p.Ser1051Gly	p.S1051G	ENST00000342788	NM_005235.2	1051	Agc/Ggc	26/28	0.324388298123428	3	FACETS	0.983	0.902	1	0.983	0.902	1	CLONAL	2	TRUE	1	0.33217290631637	3		392	518	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864909	117864909	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067312-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	314	397	0	ENST00000297338.2:c.1200C>A	p.Asp400Glu	p.D400E	ENST00000297338	NM_006265.2	400	gaC/gaA	10/14	0.33217290631637	6	FACETS	0.966	0.916	1	0.966	0.916	1	CLONAL	4	TRUE	2	0.33217290631637	6		397	814	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0067313-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	17	171	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.645	0.492	0.816	0.645	0.492	0.816	SUBCLONAL	1	FALSE	1	0.703108669112632	2		171	75	SUCCESS
APC	324	MSKCC	GRCh37	5	112174835	112174835	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0067313-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	48	502	2	ENST00000257430.4:c.3544A>T	p.Lys1182Ter	p.K1182*	ENST00000257430	NM_000038.5	1182	Aaa/Taa	16/16	NA	2	FACETS	0.78	0.67	0.897			1	INDETERMINATE	1	FALSE	NA	0.703108669112632	2		504	175	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652308	206652308	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782430885	NA	P-0067313-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	153	493	3	ENST00000367120.3:c.1015G>A	p.Val339Met	p.V339M	ENST00000367120	NM_014002.3	339	Gtg/Atg	10/22	1	2	FACETS	0.938	0.865	1	0.938	0.865	1	CLONAL	1	FALSE	1	0.703108669112632	2		496	464	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432674	29432674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770027238	NA	P-0067313-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	104	400	0	ENST00000389048.3:c.3814G>A	p.Gly1272Arg	p.G1272R	ENST00000389048	NM_004304.4	1272	Ggg/Agg	25/29	0.580296070305258	1	FACETS	0.625	0.567	0.685	0.625	0.567	0.685	SUBCLONAL	1	FALSE	0	0.703108669112632	1		400	307	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972915	68972915	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs201372935	NA	P-0067313-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	28	332	3	ENST00000288368.4:c.1240G>A	p.Glu414Lys	p.E414K	ENST00000288368	NM_024870.2	414	Gaa/Aaa	11/40	0.191184380779841	4	FACETS	0.606	0.487	0.74			1	INDETERMINATE	1	FALSE	NA	0.703108669112632	4		335	224	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7590694	7590694	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0067313-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	146	583	0	ENST00000269305.4:c.-29+1G>T		p.X10_splice	ENST00000269305	NM_001126112.2	10			0.624425211470597	1	FACETS	0.852	0.791	0.914	0.852	0.791	0.914	CLONAL	1	FALSE	0	0.703108669112632	1		583	316	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727485	66727485	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067313-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	8	418	0	ENST00000307102.5:c.201C>A	p.Asp67Glu	p.D67E	ENST00000307102	NM_002755.3	67	gaC/gaA	2/11	1	2	FACETS	0.064	0.041	0.094	0.064	0.041	0.094	SUBCLONAL	1	FALSE	1	0.703108669112632	2		418	356	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750393	41750393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067313-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	99	486	2	ENST00000226382.2:c.235G>A	p.Ala79Thr	p.A79T	ENST00000226382	NM_003924.3	79	Gcc/Acc	1/3	1	2	FACETS	0.917	0.829	1	0.917	0.829	1	CLONAL	1	FALSE	1	0.703108669112632	2		488	307	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996806	100996806	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067313-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	62	426	1	ENST00000325455.5:c.1721C>T	p.Ala574Val	p.A574V	ENST00000325455	NM_001202474.3	574	gCa/gTa	2/8	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	FALSE	1	0.703108669112632	2		427	173	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0067314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	68	567	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.588	0.511	0.671	0.588	0.511	0.671	SUBCLONAL	1	TRUE	1	0.37	2		567	625	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	19	359	0	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	1	2	FACETS	0.187	0.141	0.241	0.187	0.141	0.241	SUBCLONAL	1	TRUE	1	0.37	2		359	550	SUCCESS
APC	324	MSKCC	GRCh37	5	112174658	112174658	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	61	377	0	ENST00000257430.4:c.3367C>T	p.Gln1123Ter	p.Q1123*	ENST00000257430	NM_000038.5	1123	Caa/Taa	16/16	1	2	FACETS	0.578	0.499	0.665	0.578	0.499	0.665	SUBCLONAL	1	TRUE	1	0.37	2		377	570	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604298	189604298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138832017	NA	P-0067314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	37	413	0	ENST00000264731.3:c.1465G>A	p.Ala489Thr	p.A489T	ENST00000264731	NM_003722.4	489	Gcc/Acc	11/14	1	2	FACETS	0.324	0.266	0.389	0.324	0.266	0.389	SUBCLONAL	1	TRUE	1	0.37	2		413	617	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50827554	50827555	+	missense_variant	Missense_Mutation	DNP	TT	TT	CG	novel	NA	P-0067314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	33	298	1	ENST00000398568.2:c.2439_2440delinsCG	p.Cys814Gly	p.C814G	ENST00000398568	NM_001042412.1	813	ttTTgt/ttCGgt	16/18	1	2	FACETS	0.387	0.315	0.469	0.387	0.315	0.469	SUBCLONAL	1	TRUE	1	0.37	2		299	461	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150921665	150921665	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	32	419	0	ENST00000271640.5:c.1335C>G	p.Phe445Leu	p.F445L	ENST00000271640	NM_001145415.1	445	ttC/ttG	11/22	1	2	FACETS	0.298	0.241	0.362	0.298	0.241	0.362	SUBCLONAL	1	TRUE	1	0.37	2		419	581	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0067315-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	65	490	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.802	0.698	0.914	0.802	0.698	0.914	CLONAL	1	TRUE	1	0.397051337872234	2		490	408	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs121913468	NA	P-0067315-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	168	345	0	ENST00000269571.5:c.2305G>C	p.Asp769His	p.D769H	ENST00000269571		769	Gac/Cac	19/27	0.386048241412335	3	FACETS	1	0.974	1			1	CLONAL	2	TRUE	NA	0.397051337872234	3		345	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0067315-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	77	381	0	ENST00000269305.4:c.375+1G>T		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.397051337872234	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.397051337872234	1		381	303	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508847	106508847	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067315-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	74	427	0	ENST00000359195.3:c.841C>G	p.Leu281Val	p.L281V	ENST00000359195	NM_002649.2	281	Ctg/Gtg	2/11	1	2	FACETS	0.84	0.738	0.948	0.84	0.738	0.948	CLONAL	1	TRUE	1	0.397051337872234	2		427	444	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840018	27840018	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067315-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	105	561	0	ENST00000328488.2:c.76G>A	p.Ala26Thr	p.A26T	ENST00000328488	NM_003533.2	26	Gct/Act	1/1	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.397051337872234	2		561	528	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389237	8389237	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067315-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	44	281	0	ENST00000356435.5:c.4381del	p.Ser1461GlnfsTer3	p.S1461Qfs*3	ENST00000356435		1461	Tca/ca	26/35	0.397051337872234	1	FACETS	0.879	0.746	1	0.879	0.746	1	CLONAL	1	TRUE	0	0.397051337872234	1		281	202	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578286	7578287	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0067316-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	488	312	0	ENST00000269305.4:c.562_563del	p.Leu188GlyfsTer20	p.L188Gfs*20	ENST00000269305	NM_001126112.2	188	CTg/g	6/11	0.750125179526272	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	0	0.750125179526272	3		312	593	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416854	121416854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555210473	NA	P-0067316-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	123	309	0	ENST00000257555.6:c.283G>A	p.Glu95Lys	p.E95K	ENST00000257555		95	Gag/Aag	1/10	0.750125179526272	3	FACETS	1	0.924	1	0.508	0.462	0.555	CLONAL	1	TRUE	1	0.750125179526272	3		309	444	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958571	175958571	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067316-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	85	361	0	ENST00000367669.3:c.1774A>C	p.Ile592Leu	p.I592L	ENST00000367669	NM_022457.5	592	Atc/Ctc	16/20	0.750125179526272	5	FACETS	0.799	0.707	0.897	0.2	0.176	0.225	SUBCLONAL	1	TRUE	1	0.750125179526272	5		361	603	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570354	87570354	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067316-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	140	397	0	ENST00000277120.3:c.2094C>G	p.Cys698Trp	p.C698W	ENST00000277120		698	tgC/tgG	17/19	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.750125179526272	2		397	364	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0067317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	46	270	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.22716797289418	2		270	373	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600330	10600330	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	48	394	0	ENST00000171111.5:c.1525G>T	p.Gly509Trp	p.G509W	ENST00000171111	NM_203500.1	509	Ggg/Tgg	4/6	0.22716797289418	1	FACETS	0.881	0.746	1	0.881	0.746	1	CLONAL	1	TRUE	0	0.22716797289418	1		394	425	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812179	212812179	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1575419937	NA	P-0067317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	65	332	0	ENST00000342788.4:c.397G>A	p.Glu133Lys	p.E133K	ENST00000342788	NM_005235.2	133	Gaa/Aaa	3/28	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.22716797289418	2		332	489	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2086919	2086919	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	57	464	0	ENST00000349721.2:c.2617G>T	p.Ala873Ser	p.A873S	ENST00000349721	NM_003070.3	873	Gcc/Tcc	18/34	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.22716797289418	2		464	461	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204864	NA	P-0067318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	70	295	0	ENST00000371953.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000371953	NM_000314.4	171	Cag/Tag	6/9	0.484932292402909	1	FACETS	0.893	0.789	1	0.893	0.789	1	CLONAL	1	TRUE	0	0.484932292402909	1		295	245	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242481	+	inframe_deletion	In_Frame_Del	DEL	AATTAAGAGAAGCAA	AATTAAGAGAAGCAA	-	rs121913425	NA	P-0067319-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	157	302	0	ENST00000275493.2:c.2237_2251del	p.Glu746_Thr751delinsAla	p.E746_T751delinsA	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAAca/gca	19/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		302	528	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306960	65306960	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067319-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	51	531	0	ENST00000342505.4:c.2617C>T	p.Arg873Cys	p.R873C	ENST00000342505	NM_002227.2	873	Cgc/Tgc	19/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		531	376	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503754	186503754	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067319-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	54	383	0	ENST00000323963.5:c.431A>C	p.Glu144Ala	p.E144A	ENST00000323963		144	gAa/gCa	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		383	419	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604629	43604629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067319-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	57	340	1	ENST00000355710.3:c.1214C>T	p.Pro405Leu	p.P405L	ENST00000355710	NM_020975.4	405	cCc/cTc	6/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		341	550	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849470	68849470	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	121	380	0	ENST00000261769.5:c.1373A>T	p.Asn458Ile	p.N458I	ENST00000261769	NM_004360.3	458	aAt/aTt	10/16	0.332120864580722	1	FACETS	0.991	0.898	1	0.991	0.898	1	CLONAL	1	TRUE	0	0.332120864580722	1		380	613	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591929	+	inframe_deletion	In_Frame_Del	DEL	CGCTTTTGTTTG	CGCTTTTGTTTG	-	novel	NA	P-0067321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	109	304	0	ENST00000342988.3:c.1081_1092del	p.Arg361_Leu364del	p.R361_L364del	ENST00000342988	NM_005359.5	361	CGCTTTTGTTTG/-	9/12	0.332120864580722	1	FACETS	0.934	0.841	1	0.934	0.841	1	CLONAL	1	TRUE	0	0.332120864580722	1		304	586	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026159	71026159	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	122	236	0	ENST00000318789.4:c.1463T>G	p.Leu488Arg	p.L488R	ENST00000318789	NM_032682.5	488	cTa/cGa	17/21	0.332120864580722	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.332120864580722	1		236	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876659675	NA	P-0067323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	361	385	0	ENST00000269305.4:c.764T>G	p.Ile255Ser	p.I255S	ENST00000269305	NM_001126112.2	255	aTc/aGc	7/11	0.753959482835737	2	FACETS	0.979	0.947	1	0.979	0.947	1	CLONAL	2	TRUE	0	0.753959482835737	2		385	489	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793431	242793431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376257658	NA	P-0067323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	192	429	0	ENST00000334409.5:c.646G>A	p.Val216Met	p.V216M	ENST00000334409	NM_005018.2	216	Gtg/Atg	5/5	0.753959482835737	3	FACETS	1	0.975	1	0.554	0.515	0.594	CLONAL	1	TRUE	1	0.753959482835737	3		429	633	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0067323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	952	315	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	0.753959482835737	7	FACETS	1	0.997	1			1	CLONAL	7	TRUE	NA	0.753959482835737	7		315	1020	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226574134	226574134	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	136	327	0	ENST00000366794.5:c.727G>T	p.Asp243Tyr	p.D243Y	ENST00000366794	NM_001618.3	243	Gac/Tac	6/23	1	2	FACETS	0.882	0.81	0.956	0.882	0.81	0.956	CLONAL	1	TRUE	1	0.753959482835737	2		327	409	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522076	157522076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376207220	NA	P-0067323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	209	544	0	ENST00000346085.5:c.4348G>A	p.Gly1450Ser	p.G1450S	ENST00000346085	NM_020732.3	1450	Ggc/Agc	18/20	0.154904458540439	6	FACETS	0.903	0.841	0.967			1	INDETERMINATE	2	TRUE	NA	0.753959482835737	6		544	770	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876659675	NA	P-0067323-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	8	385	0	ENST00000269305.4:c.764T>G	p.Ile255Ser	p.I255S	ENST00000269305	NM_001126112.2	255	aTc/aGc	7/11	1	2	FACETS	0.413	0.265	0.606	0.413	0.265	0.606	SUBCLONAL	1	TRUE	1	0.13	2		385	298	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793431	242793431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376257658	NA	P-0067323-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	10	429	0	ENST00000334409.5:c.646G>A	p.Val216Met	p.V216M	ENST00000334409	NM_005018.2	216	Gtg/Atg	5/5	1	2	FACETS	0.443	0.299	0.626	0.443	0.299	0.626	SUBCLONAL	1	TRUE	1	0.13	2		429	347	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0067323-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	21	315	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	1	2	FACETS	0.918	0.712	1	1	0.936	1	CLONAL	2	TRUE	1	0.13	2		315	176	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226574134	226574134	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067323-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	3	327	0	ENST00000366794.5:c.727G>T	p.Asp243Tyr	p.D243Y	ENST00000366794	NM_001618.3	243	Gac/Tac	6/23	1	2	FACETS	0.158	0.073	0.29	0.158	0.073	0.29	SUBCLONAL	1	TRUE	1	0.13	2		327	292	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	30	317	0				ENST00000310581	NM_198253.2	-/1132			0.3	2	FACETS	0.969	0.782	1			1	CLONAL	1	TRUE	NA	0.19	2		317	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0067324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	31	415	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.159210773735276	1	FACETS	0.642	0.519	0.782	0.642	0.519	0.782	SUBCLONAL	1	TRUE	0	0.19	1		415	460	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842018	3842018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	41	336	0	ENST00000262367.5:c.1294C>T	p.Pro432Ser	p.P432S	ENST00000262367	NM_004380.2	432	Cct/Tct	5/31	0.159210773735276	1	FACETS	0.84	0.7	0.996	0.84	0.7	0.996	CLONAL	1	TRUE	0	0.19	1		336	465	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453145	140453146	+	missense_variant	Missense_Mutation	DNP	AG	AG	GA	rs121913368	NA	P-0067324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	22	291	0	ENST00000288602.6:c.1789_1790delinsTC	p.Leu597Ser	p.L597S	ENST00000288602	NM_004333.4	597	CTa/TCa	15/18	1	2	FACETS	0.52	0.402	0.658	0.52	0.402	0.658	SUBCLONAL	1	TRUE	1	0.19	2		291	445	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306568	41306568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	44	317	0	ENST00000373198.4:c.1091G>A	p.Arg364Gln	p.R364Q	ENST00000373198	NM_133170.3	364	cGa/cAa	7/32	1	2	FACETS	0.957	0.803	1	0.957	0.803	1	CLONAL	1	TRUE	1	0.19	2		317	484	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041701	14041701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374978891	NA	P-0067324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	38	377	1	ENST00000311895.7:c.2248C>T	p.Arg750Cys	p.R750C	ENST00000311895	NM_005236.2	750	Cgc/Tgc	11/11	0.159210773735276	1	FACETS	0.67	0.553	0.801	0.67	0.553	0.801	SUBCLONAL	1	TRUE	0	0.19	1		378	540	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405915	49405915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866298036	NA	P-0067324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	34	348	0	ENST00000418115.1:c.223C>T	p.Pro75Ser	p.P75S	ENST00000418115	NM_001664.2	75	Cca/Tca	3/5	1	2	FACETS	0.836	0.683	1	0.836	0.683	1	CLONAL	1	TRUE	1	0.19	2		348	428	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577541	7577541	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	32	343	0	ENST00000269305.4:c.740A>C	p.Asn247Thr	p.N247T	ENST00000269305	NM_001126112.2	247	aAc/aCc	7/11	0.159210773735276	1	FACETS	0.661	0.536	0.803	0.661	0.536	0.803	SUBCLONAL	1	TRUE	0	0.19	1		343	461	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425470	49425470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	57	564	0	ENST00000301067.7:c.13018C>T	p.His4340Tyr	p.H4340Y	ENST00000301067	NM_003482.3	4340	Cat/Tat	39/54	0.159210773735276	1	FACETS	0.922	0.791	1	0.922	0.791	1	CLONAL	1	TRUE	0	0.19	1		564	589	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710637	40710637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1161104430	NA	P-0067324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	30	417	0	ENST00000373198.4:c.4214G>A	p.Gly1405Glu	p.G1405E	ENST00000373198	NM_133170.3	1405	gGa/gAa	31/32	1	2	FACETS	0.542	0.435	0.663	0.542	0.435	0.663	SUBCLONAL	1	TRUE	1	0.19	2		417	583	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344357	118344357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	33	404	0	ENST00000534358.1:c.2483C>T	p.Ser828Leu	p.S828L	ENST00000534358	NM_005933.3	828	tCa/tTa	3/36	0.159210773735276	1	FACETS	0.547	0.444	0.663	0.547	0.444	0.663	SUBCLONAL	1	TRUE	0	0.19	1		404	575	SUCCESS
APC	324	MSKCC	GRCh37	5	112179452	112179452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782312	NA	P-0067324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	40	425	0	ENST00000257430.4:c.8161C>T	p.Arg2721Cys	p.R2721C	ENST00000257430	NM_000038.5	2721	Cgc/Tgc	16/16	1	2	FACETS	0.638	0.529	0.76	0.638	0.529	0.76	SUBCLONAL	1	TRUE	1	0.19	2		425	660	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838350	156838350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745366033	NA	P-0067324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	99	511	0	ENST00000524377.1:c.628G>A	p.Asp210Asn	p.D210N	ENST00000524377	NM_002529.3	210	Gac/Aac	6/17	0.178277599661822	3	FACETS	0.823	0.735	0.917	0.823	0.735	0.917	CLONAL	2	TRUE	1	0.19	3		511	693	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630039	117630039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	30	318	0	ENST00000368508.3:c.6487C>T	p.Pro2163Ser	p.P2163S	ENST00000368508	NM_002944.2	2163	Cca/Tca	41/43	1	2	FACETS	0.616	0.495	0.753	0.616	0.495	0.753	SUBCLONAL	1	TRUE	1	0.19	2		318	513	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189084	32189084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149758111	NA	P-0067324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	36	427	0	ENST00000375023.3:c.470G>A	p.Arg157Gln	p.R157Q	ENST00000375023	NM_004557.3	157	cGg/cAg	4/30	1	2	FACETS	0.697	0.572	0.837	0.697	0.572	0.837	SUBCLONAL	1	TRUE	1	0.19	2		427	544	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100495	157100495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	31	242	0	ENST00000346085.5:c.1432G>A	p.Asp478Asn	p.D478N	ENST00000346085	NM_020732.3	478	Gac/Aac	1/20	1	2	FACETS	1	0.819	1	1	0.819	1	CLONAL	1	TRUE	1	0.19	2		242	323	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035043	37035043	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779029	NA	P-0067324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	97	387	0	ENST00000231790.2:c.5C>T	p.Ser2Leu	p.S2L	ENST00000231790	NM_000249.3	2	tCg/tTg	1/19	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.19	2		387	695	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866440	42866441	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0067324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	43	429	0	ENST00000398585.3:c.191_192delinsTT	p.Pro64Leu	p.P64L	ENST00000398585	NM_001135099.1	64	cCC/cTT	3/14	1	2	FACETS	0.689	0.575	0.815	0.689	0.575	0.815	SUBCLONAL	1	TRUE	1	0.19	2		429	657	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487140	56487140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	44	296	0	ENST00000267101.3:c.1286C>T	p.Ser429Leu	p.S429L	ENST00000267101	NM_001982.3	429	tCa/tTa	12/28	0.159210773735276	1	FACETS	0.973	0.817	1	0.973	0.817	1	CLONAL	1	TRUE	0	0.19	1		296	431	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81891882	81891882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	39	347	0	ENST00000359376.3:c.352G>A	p.Asp118Asn	p.D118N	ENST00000359376	NM_002661.3	118	Gat/Aat	4/33	0.159210773735276	1	FACETS	0.797	0.661	0.95	0.797	0.661	0.95	CLONAL	1	TRUE	0	0.19	1		347	466	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146567	55146567	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	27	364	0	ENST00000257290.5:c.2241A>T	p.Glu747Asp	p.E747D	ENST00000257290	NM_006206.4	747	gaA/gaT	16/23	1	2	FACETS	0.566	0.449	0.7	0.566	0.449	0.7	SUBCLONAL	1	TRUE	1	0.19	2		364	502	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276438	115276438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	31	347	0	ENST00000438362.2:c.890G>A	p.Gly297Glu	p.G297E	ENST00000438362	NM_001242891.1	297	gGa/gAa	9/20	0.178277599661822	3	FACETS	0.627	0.506	0.765	0.313	0.253	0.383	SUBCLONAL	1	TRUE	1	0.19	3		347	570	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8105977	8105977	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	39	393	0	ENST00000346208.3:c.797G>C	p.Cys266Ser	p.C266S	ENST00000346208		266	tGt/tCt	4/6	1	2	FACETS	0.834	0.691	0.994	0.834	0.691	0.994	CLONAL	1	TRUE	1	0.19	2		393	492	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343502	70343502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	22	187	0	ENST00000374080.3:c.1676C>T	p.Ser559Phe	p.S559F	ENST00000374080		559	tCt/tTt	12/45	1	1	FACETS	1	0.781	1	1	0.781	1	CLONAL	1	TRUE	0	0.19	1		187	209	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29444392	29444392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	90	416	1	ENST00000544604.2:c.928C>T	p.Pro310Ser	p.P310S	ENST00000544604	NM_001206998.1	310	Ccc/Tcc	7/9	1	2	FACETS	0.822	0.731	0.919	1	0.982	1	CLONAL	2	TRUE	1	0.19	2		417	576	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250050	53250051	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0067324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	35	172	0	ENST00000375401.3:c.198_199delinsTT	p.Pro67Ser	p.P67S	ENST00000375401	NM_004187.3	66	acCCcc/acTTcc	2/26	1	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.19	1		172	246	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542312	187542312	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	61	385	0	ENST00000441802.2:c.5428C>T	p.His1810Tyr	p.H1810Y	ENST00000441802	NM_005245.3	1810	Cac/Tac	10/27	1	2	FACETS	0.958	0.826	1	0.958	0.826	1	CLONAL	1	TRUE	1	0.19	2		385	670	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260595	10260595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	33	358	0	ENST00000340748.4:c.2267C>T	p.Thr756Ile	p.T756I	ENST00000340748		756	aCc/aTc	24/40	1	2	FACETS	0.742	0.604	0.898	0.742	0.604	0.898	SUBCLONAL	1	TRUE	1	0.19	2		358	468	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63700071	63700071	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	68	326	0	ENST00000279873.7:c.406A>T	p.Arg136Trp	p.R136W	ENST00000279873	NM_032199.2	136	Agg/Tgg	3/10	0.3	3	FACETS	1	0.953	1			1	CLONAL	1	TRUE	NA	0.19	3		326	647	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494148	140494150	+	missense_variant	Missense_Mutation	TNP	GGA	GGA	AGC	novel	NA	P-0067324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	59	467	0	ENST00000288602.6:c.1098_1100delinsGCT	p.Pro367Leu	p.P367L	ENST00000288602	NM_004333.4	366	gcTCCc/gcGCTc	8/18	1	2	FACETS	0.795	0.683	0.918	0.795	0.683	0.918	CLONAL	1	TRUE	1	0.19	2		467	781	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0067325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	167	321	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.411942522123063	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.419816124631243	3		321	468	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0067325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	297	530	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.204954375574251	5	FACETS	0.839	0.792	0.887	0.839	0.792	0.887	INDETERMINATE	3	TRUE	2	0.419816124631243	5		530	916	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0067325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	74	424	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.196125807884289	3	FACETS	0.767	0.679	0.86	0.767	0.679	0.86	INDETERMINATE	2	TRUE	1	0.419816124631243	3		424	278	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0067325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	208	529	4	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	0.310981433767737	4	FACETS	0.808	0.751	0.867	0.808	0.751	0.867	CLONAL	2	TRUE	2	0.419816124631243	4		533	871	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578238	7578255	+	inframe_deletion	In_Frame_Del	DEL	TCCACACGCAAATTTCCT	TCCACACGCAAATTTCCT	-	rs1567551704	NA	P-0067325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	283	331	0	ENST00000269305.4:c.594_611del	p.Gly199_Glu204del	p.G199_E204del	ENST00000269305	NM_001126112.2	198	gaAGGAAATTTGCGTGTGGAg/gag	6/11	0.419816124631243	2	FACETS	0.981	0.928	1	0.981	0.928	1	CLONAL	2	TRUE	0	0.419816124631243	2		331	687	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750945	128750945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	654	336	0	ENST00000377970.2:c.482C>T	p.Ser161Leu	p.S161L	ENST00000377970	NM_002467.4	161	tCa/tTa	2/3	0.419816124631243	6	FACETS	0.995	0.964	1	0.995	0.964	1	CLONAL	5	TRUE	1	0.419816124631243	6		336	1152	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241970	39241970	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	98	257	0	ENST00000402219.2:c.1876A>G	p.Thr626Ala	p.T626A	ENST00000402219	NM_005633.3	626	Aca/Gca	11/23	0.411942522123063	3	FACETS	0.962	0.86	1	0.481	0.43	0.535	CLONAL	1	TRUE	1	0.419816124631243	3		257	587	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411693	63411693	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	248	208	0	ENST00000330258.3:c.1474del	p.Arg492GlyfsTer49	p.R492Gfs*49	ENST00000330258	NM_152424.3	492	Agg/gg	2/2	0.268087451189301	2	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.419816124631243	2		208	473	SUCCESS
APC	324	MSKCC	GRCh37	5	112175787	112175788	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0067325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	201	316	1	ENST00000257430.4:c.4496_4497del	p.Gly1499ValfsTer14	p.G1499Vfs*14	ENST00000257430	NM_000038.5	1499	gGA/g	16/16	0.204954375574251	5	FACETS	0.885	0.821	0.951	0.59	0.547	0.634	INDETERMINATE	2	TRUE	2	0.419816124631243	5		317	882	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920377	114920377	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0067325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	111	243	1	ENST00000543371.1:c.1319-1G>A		p.X440_splice	ENST00000543371	NM_001198531.1	440			0.411942522123063	3	FACETS	1	0.916	1	0.509	0.459	0.563	CLONAL	1	TRUE	1	0.419816124631243	3		244	628	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0067326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	130	321	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.254105828040313	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	0	0.254105828040313	3		321	345	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788642	3788642	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	62	353	0	ENST00000262367.5:c.4312C>G	p.His1438Asp	p.H1438D	ENST00000262367	NM_004380.2	1438	Cat/Gat	26/31	0.239823158630589	4	FACETS	0.944	0.815	1	0.472	0.407	0.543	CLONAL	1	TRUE	2	0.254105828040313	4		353	648	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057848	27057848	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	129	544	0	ENST00000324856.7:c.1556C>T	p.Ser519Phe	p.S519F	ENST00000324856	NM_006015.4	519	tCc/tTc	3/20	0.187271234557571	4	FACETS	1	0.978	1	0.636	0.576	0.7	CLONAL	1	TRUE	2	0.254105828040313	4		544	1001	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204506578	204506578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	43	391	0	ENST00000367182.3:c.364C>T	p.Leu122Phe	p.L122F	ENST00000367182	NM_001278516.1	122	Ctc/Ttc	6/11	0.254105828040313	6	FACETS	0.65	0.542	0.771	0.13	0.108	0.155	SUBCLONAL	1	TRUE	1	0.254105828040313	6		391	785	SUCCESS
APC	324	MSKCC	GRCh37	5	112175358	112175358	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1554085480	NA	P-0067327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	143	391	0	ENST00000257430.4:c.4067C>G	p.Ser1356Ter	p.S1356*	ENST00000257430	NM_000038.5	1356	tCa/tGa	16/16	0.562551692196536	2	FACETS	0.941	0.882	1	0.941	0.882	1	CLONAL	2	TRUE	0	0.635627627948015	2		391	239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578260	7578260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204041	NA	P-0067327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	197	528	0	ENST00000269305.4:c.589G>A	p.Val197Met	p.V197M	ENST00000269305	NM_001126112.2	197	Gtg/Atg	6/11	0.528975771687944	2	FACETS	0.873	0.824	0.922	0.873	0.824	0.922	CLONAL	2	TRUE	0	0.635627627948015	2		528	355	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024354	31024354	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1327515633	NA	P-0067327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	457	448	0	ENST00000375687.4:c.3839T>C	p.Ile1280Thr	p.I1280T	ENST00000375687	NM_015338.5	1280	aTc/aCc	13/13	0.635627627948015	6	FACETS	0.996	0.965	1			1	CLONAL	5	TRUE	NA	0.635627627948015	6		448	656	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509384	106509384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388270746	NA	P-0067327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	154	472	0	ENST00000359195.3:c.1378C>T	p.Leu460Phe	p.L460F	ENST00000359195	NM_002649.2	460	Ctt/Ttt	2/11	0.549809289438824	3	FACETS	1	0.988	1	0.717	0.663	0.774	CLONAL	1	TRUE	1	0.635627627948015	3		472	445	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595381	141595382	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0067327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	72	538	0	ENST00000220592.5:c.51dup	p.Ile18HisfsTer11	p.I18Hfs*11	ENST00000220592	NM_012154.3	17	-/C	2/19	0.635627627948015	5	FACETS	0.475	0.414	0.542	0.095	0.082	0.109	SUBCLONAL	1	TRUE	0	0.635627627948015	5		538	931	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0067346-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	90	270	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.28240818761824	1	FACETS	0.826	0.742	0.913	0.826	0.742	0.913	INDETERMINATE	1	TRUE	0	0.546269028920108	1		270	290	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0067346-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	137	464	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.464198005983059	1	FACETS	0.887	0.815	0.961	0.887	0.815	0.961	CLONAL	1	TRUE	0	0.546269028920108	1		464	411	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347780	347780	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs754357905	NA	P-0067346-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	41	553	1	ENST00000262320.3:c.1726C>T	p.Arg576Ter	p.R576*	ENST00000262320	NM_003502.3	576	Cga/Tga	6/11	1	2	FACETS	0.339	0.282	0.402	0.339	0.282	0.402	SUBCLONAL	1	TRUE	1	0.546269028920108	2		554	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579419	7579431	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGGGCTGGTGC	AGGGGGCTGGTGC	-	novel	NA	P-0067346-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	196	637	0	ENST00000269305.4:c.256_268del	p.Ala86ProfsTer33	p.A86Pfs*33	ENST00000269305	NM_001126112.2	86	GCACCAGCCCCCTcc/cc	4/11	0.521905104498253	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.546269028920108	1		637	432	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0067347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	58	239	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.474983979102974	3	FACETS	1	0.933	1	1	0.933	1	CLONAL	2	TRUE	1	0.476082656196607	3		239	139	SUCCESS
APC	324	MSKCC	GRCh37	5	112175476	112175476	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	62	592	0	ENST00000257430.4:c.4188del	p.Phe1396LeufsTer19	p.F1396Lfs*19	ENST00000257430	NM_000038.5	1395	agT/ag	16/16	0.474983979102974	3	FACETS	0.796	0.69	0.91	0.398	0.345	0.455	CLONAL	1	TRUE	1	0.476082656196607	3		592	405	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707779	176707779	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	90	613	0	ENST00000439151.2:c.5836A>G	p.Ile1946Val	p.I1946V	ENST00000439151	NM_022455.4	1946	Att/Gtt	18/23	0.474983979102974	3	FACETS	0.99	0.882	1	0.495	0.441	0.552	CLONAL	1	TRUE	1	0.476082656196607	3		613	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577564	7577565	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	156	508	0	ENST00000269305.4:c.716dup	p.Asn239LysfsTer25	p.N239Kfs*25	ENST00000269305	NM_001126112.2	239	aac/aaAc	7/11	0.476082656196607	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.476082656196607	2		508	303	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933622	39933622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200141801	NA	P-0067347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	173	717	0	ENST00000378444.4:c.977C>T	p.Pro326Leu	p.P326L	ENST00000378444	NM_001123385.1	326	cCg/cTg	4/15	0.284087515033307	4	FACETS	0.894	0.827	0.963	0.894	0.827	0.963	INDETERMINATE	2	TRUE	2	0.476082656196607	4		717	600	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971306	13971306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs959752124	NA	P-0067347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	302	596	0	ENST00000405192.2:c.623G>A	p.Arg208His	p.R208H	ENST00000405192	NM_001163147.1	208	cGt/cAt	8/12	0.476082656196607	5	FACETS	1	0.959	1	1	0.959	1	CLONAL	3	TRUE	2	0.476082656196607	5		596	716	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102196226	102196226	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	45	477	0	ENST00000263464.3:c.883T>G	p.Cys295Gly	p.C295G	ENST00000263464	NM_001165.4	295	Tgt/Ggt	3/9	0.386207102976946	4	FACETS	0.933	0.789	1	0.467	0.394	0.546	CLONAL	1	TRUE	2	0.476082656196607	4		477	299	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272267	18272268	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0067347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	138	515	0	ENST00000222254.8:c.779dup	p.Pro261AlafsTer14	p.P261Afs*14	ENST00000222254	NM_005027.3	259	-/C	6/16	0.463704702277805	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.476082656196607	3		515	326	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175859	24175859	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs797045989	NA	P-0067347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	98	565	0	ENST00000263121.7:c.1087A>G	p.Lys363Glu	p.K363E	ENST00000263121	NM_003073.3	363	Aag/Gag	8/9	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.476082656196607	2		565	302	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92244459	92244459	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	29	557	0	ENST00000265734.4:c.976G>T	p.Ala326Ser	p.A326S	ENST00000265734	NM_001259.6	326	Gcc/Tcc	8/8	0.382321692580578	5	FACETS	0.366	0.293	0.449			1	SUBCLONAL	1	TRUE	NA	0.476082656196607	5		557	571	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106533	108106533	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	43	482	0	ENST00000278616.4:c.468G>C	p.Trp156Cys	p.W156C	ENST00000278616	NM_000051.3	156	tgG/tgC	5/63	0.386207102976946	4	FACETS	1	0.929	1	0.593	0.5	0.693	CLONAL	1	TRUE	2	0.476082656196607	4		482	225	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922234	100922235	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0067347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	38	474	0	ENST00000325455.5:c.2277_2278delinsTT	p.Met759_Val760delinsIleLeu	p.M759_V760delinsIL	ENST00000325455	NM_001202474.3	759	atGGtg/atTTtg	5/8	0.386207102976946	4	FACETS	0.962	0.801	1	0.481	0.4	0.57	CLONAL	1	TRUE	2	0.476082656196607	4		474	245	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs786201057	NA	P-0067348-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	352	520	0	ENST00000269305.4:c.374C>A	p.Thr125Lys	p.T125K	ENST00000269305	NM_001126112.2	125	aCg/aAg	4/11	0.785824197992406	2	FACETS	0.954	0.923	0.983	0.954	0.923	0.983	CLONAL	2	TRUE	0	0.800729602463462	2		520	461	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275747	41275747	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067348-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	211	502	0	ENST00000349496.5:c.1642C>T	p.Gln548Ter	p.Q548*	ENST00000349496	NM_001904.3	548	Cag/Tag	10/15	0.800729602463462	3	FACETS	1	0.954	1	0.515	0.48	0.551	CLONAL	1	TRUE	1	0.800729602463462	3		502	717	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0067349-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	118	530	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.42487633830702	1	FACETS	0.925	0.839	1	0.925	0.839	1	CLONAL	1	TRUE	0	0.42487633830702	1		530	473	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617452	43617452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067349-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	79	446	0	ENST00000355710.3:c.2789C>T	p.Thr930Met	p.T930M	ENST00000355710	NM_020975.4	930	aCg/aTg	16/20	1	2	FACETS	0.791	0.698	0.89	0.791	0.698	0.89	SUBCLONAL	1	TRUE	1	0.42487633830702	2		446	470	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371728	118371728	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067349-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	111	403	0	ENST00000534358.1:c.6185C>A	p.Thr2062Lys	p.T2062K	ENST00000534358	NM_005933.3	2062	aCa/aAa	25/36	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.42487633830702	2		403	475	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89176400	89176400	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067349-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	42	383	0	ENST00000336596.2:c.130T>G	p.Trp44Gly	p.W44G	ENST00000336596	NM_005233.5	44	Tgg/Ggg	2/17	0.145855880200127	2	FACETS	0.655	0.549	0.771	0.327	0.274	0.386	INDETERMINATE	1	TRUE	0	0.42487633830702	2		383	302	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128305429	128305429	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067349-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	107	383	0	ENST00000265960.3:c.867C>G	p.Phe289Leu	p.F289L	ENST00000265960	NM_001006617.1	289	ttC/ttG	7/12	1	2	FACETS	0.954	0.859	1	0.954	0.859	1	CLONAL	1	TRUE	1	0.42487633830702	2		383	528	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0067350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	207	789	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.516576152272615	2		790	556	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	50	518	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.539	0.459	0.627	0.539	0.459	0.627	SUBCLONAL	1	TRUE	1	0.516576152272615	2		518	359	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0067350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	25	177	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.813	0.652	0.992	0.813	0.652	0.992	CLONAL	1	TRUE	1	0.516576152272615	2		178	119	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646981	23646981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	25	527	2	ENST00000261584.4:c.886del	p.Met296Ter	p.M296*	ENST00000261584	NM_024675.3	296	Atg/tg	4/13	1	2	FACETS	0.745	0.595	0.911	0.745	0.595	0.911	CLONAL	1	TRUE	1	0.516576152272615	2		529	130	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0067350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	47	470	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.883	0.754	1	0.883	0.754	1	CLONAL	1	TRUE	1	0.516576152272615	2		470	206	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806633	1806633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56240927	NA	P-0067350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	94	646	0	ENST00000260795.2:c.1349C>T	p.Thr450Met	p.T450M	ENST00000260795		450	aCg/aTg	9/17	1	2	FACETS	0.786	0.703	0.874	0.786	0.703	0.874	SUBCLONAL	1	TRUE	1	0.516576152272615	2		646	463	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0067350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	28	545	4	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.673	0.544	0.817	0.673	0.544	0.817	SUBCLONAL	1	TRUE	1	0.516576152272615	2		549	161	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793211	139793212	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748531430	NA	P-0067350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	68	423	3	ENST00000247668.2:c.26dup	p.Gly10TrpfsTer70	p.G10Wfs*70	ENST00000247668	NM_021138.3	7	acc/aCcc	2/11	1	2	FACETS	0.784	0.686	0.887	0.784	0.686	0.887	SUBCLONAL	1	TRUE	1	0.516576152272615	2		426	336	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106917	27106917	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	115	701	0	ENST00000324856.7:c.6532del	p.Asp2178ThrfsTer22	p.D2178Tfs*22	ENST00000324856	NM_006015.4	2176	caG/ca	20/20	1	2	FACETS	0.976	0.885	1	0.976	0.885	1	CLONAL	1	TRUE	1	0.516576152272615	2		701	456	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934004	39934004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	99	608	1	ENST00000378444.4:c.595G>A	p.Ala199Thr	p.A199T	ENST00000378444	NM_001123385.1	199	Gcc/Acc	4/15	1	2	FACETS	0.973	0.875	1	0.973	0.875	1	CLONAL	1	TRUE	1	0.516576152272615	2		609	394	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488717	212488717	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1269407579	NA	P-0067350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	21	590	0	ENST00000342788.4:c.2132G>A	p.Arg711His	p.R711H	ENST00000342788	NM_005235.2	711	cGt/cAt	18/28	1	2	FACETS	0.343	0.265	0.434	0.343	0.265	0.434	SUBCLONAL	1	TRUE	1	0.516576152272615	2		590	237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578379	7578379	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060501209	NA	P-0067350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	26	681	0	ENST00000269305.4:c.551A>G	p.Asp184Gly	p.D184G	ENST00000269305	NM_001126112.2	184	gAt/gGt	5/11	1	2	FACETS	0.221	0.175	0.275	0.221	0.175	0.275	SUBCLONAL	1	TRUE	1	0.516576152272615	2		681	455	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591135	67591135	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	26	444	0	ENST00000274335.5:c.1728del	p.Arg577GlufsTer5	p.R577Efs*5	ENST00000274335		576	acG/ac	12/15	1	2	FACETS	0.977	0.791	1	0.977	0.791	1	CLONAL	1	TRUE	1	0.516576152272615	2		444	103	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942214	71942214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253875635	NA	P-0067350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	99	574	0	ENST00000298229.2:c.1478C>T	p.Thr493Met	p.T493M	ENST00000298229	NM_001567.3	493	aCg/aTg	12/28	1	2	FACETS	0.942	0.847	1	0.942	0.847	1	CLONAL	1	TRUE	1	0.516576152272615	2		574	407	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966987	25966987	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	61	580	0	ENST00000435504.4:c.2219C>T	p.Thr740Met	p.T740M	ENST00000435504		740	aCg/aTg	13/13	1	2	FACETS	0.689	0.597	0.786	0.689	0.597	0.786	SUBCLONAL	1	TRUE	1	0.516576152272615	2		580	343	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422041	47422041	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	135	615	0	ENST00000404338.3:c.109T>C	p.Cys37Arg	p.C37R	ENST00000404338	NM_004491.4	37	Tgt/Cgt	1/6	0.217050235658657	3	FACETS	0.779	0.715	0.846	0.779	0.715	0.846	INDETERMINATE	2	TRUE	1	0.516576152272615	3		615	422	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591058	67591058	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0067350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	40	422	0	ENST00000274335.5:c.1651A>T	p.Lys551Ter	p.K551*	ENST00000274335		551	Aag/Tag	12/15	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.516576152272615	2		422	119	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305239	39305239	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	90	459	0	ENST00000373001.3:c.1186C>G	p.Arg396Gly	p.R396G	ENST00000373001	NM_022157.3	396	Cga/Gga	7/7	1	2	FACETS	0.828	0.739	0.922	0.828	0.739	0.922	CLONAL	1	TRUE	1	0.516576152272615	2		459	421	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692776	89692777	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0067350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	27	282	0	ENST00000371953.3:c.263_264dup	p.Pro89IlefsTer11	p.P89Ifs*11	ENST00000371953	NM_000314.4	87	caa/caATa	5/9	0.516576152272615	2	FACETS	0.933	0.782	1	0.933	0.782	1	CLONAL	2	TRUE	0	0.516576152272615	2		282	56	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660532	67660532	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	60	448	0	ENST00000264010.4:c.1432G>A	p.Glu478Lys	p.E478K	ENST00000264010	NM_006565.3	478	Gag/Aag	8/12	1	2	FACETS	0.976	0.851	1	0.976	0.851	1	CLONAL	1	TRUE	1	0.516576152272615	2		448	238	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332583	65332583	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	35	481	0	ENST00000342505.4:c.956G>T	p.Gly319Val	p.G319V	ENST00000342505	NM_002227.2	319	gGg/gTg	7/25	1	2	FACETS	0.619	0.511	0.738	0.619	0.511	0.738	SUBCLONAL	1	TRUE	1	0.516576152272615	2		481	219	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61213538	61213538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs968303021	NA	P-0067350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	18	430	0	ENST00000301761.2:c.496C>T	p.Arg166Cys	p.R166C	ENST00000301761	NM_017841.2	166	Cgt/Tgt	4/4	1	2	FACETS	0.204	0.153	0.265	0.204	0.153	0.265	SUBCLONAL	1	TRUE	1	0.516576152272615	2		430	341	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95598891	95598891	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	37	413	0	ENST00000393063.1:c.268A>G	p.Ser90Gly	p.S90G	ENST00000393063	NM_030621.3	90	Agc/Ggc	4/28	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.516576152272615	2		413	134	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370830	55370831	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	69	600	0	ENST00000297316.4:c.134dup	p.Glu47ArgfsTer34	p.E47Rfs*34	ENST00000297316	NM_022454.3	44	-/A	1/2	1	2	FACETS	0.812	0.712	0.918	0.812	0.712	0.918	CLONAL	1	TRUE	1	0.516576152272615	2		600	329	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37882044	37882044	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	52	447	4	ENST00000269571.5:c.2810A>G	p.Lys937Arg	p.K937R	ENST00000269571		937	aAg/aGg	23/27	1	2	FACETS	0.606	0.519	0.701	0.606	0.519	0.701	SUBCLONAL	1	TRUE	1	0.516576152272615	2		451	332	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962854	2962854	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	92	494	0	ENST00000396946.4:c.2054G>A	p.Gly685Asp	p.G685D	ENST00000396946	NM_032415.4	685	gGc/gAc	16/25	1	2	FACETS	0.96	0.86	1	0.96	0.86	1	CLONAL	1	TRUE	1	0.516576152272615	2		494	371	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216467	2216467	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	58	661	0	ENST00000398665.3:c.2111T>C	p.Leu704Ser	p.L704S	ENST00000398665	NM_032482.2	704	tTg/tCg	20/28	0.217050235658657	3	FACETS	0.715	0.617	0.822	0.358	0.308	0.411	INDETERMINATE	1	TRUE	1	0.516576152272615	3		661	395	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874272	151874272	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	10	485	0	ENST00000262189.6:c.8266A>G	p.Ile2756Val	p.I2756V	ENST00000262189	NM_170606.2	2756	Atc/Gtc	38/59	1	2	FACETS	0.387	0.264	0.539	0.387	0.264	0.539	SUBCLONAL	1	TRUE	1	0.516576152272615	2		485	100	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129756	108129756	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	21	351	0	ENST00000278616.4:c.2420T>C	p.Leu807Ser	p.L807S	ENST00000278616	NM_000051.3	807	tTa/tCa	16/63	1	2	FACETS	0.753	0.589	0.937	0.753	0.589	0.937	CLONAL	1	TRUE	1	0.516576152272615	2		351	108	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422422	225422422	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	29	421	0	ENST00000264414.4:c.218T>C	p.Leu73Pro	p.L73P	ENST00000264414	NM_003590.4	73	cTc/cCc	2/16	1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.516576152272615	2		421	109	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882019	NA	P-0067352-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	271	754	0	ENST00000269305.4:c.455del	p.Pro152ArgfsTer18	p.P152Rfs*18	ENST00000269305	NM_001126112.2	152	cCg/cg	5/11	0.350252515562846	2	FACETS	0.956	0.902	1	0.956	0.902	1	CLONAL	2	TRUE	0	0.40158126857606	2		754	706	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265145	5265145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748255589	NA	P-0067352-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	103	736	0	ENST00000357368.4:c.442C>T	p.Arg148Trp	p.R148W	ENST00000357368	NM_002850.3	148	Cgg/Tgg	5/38	0.154805082277806	3	FACETS	0.819	0.733	0.911	0.273	0.244	0.304	INDETERMINATE	1	TRUE	0	0.40158126857606	3		736	752	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692917	89692917	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1085308046	NA	P-0067352-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	139	589	0	ENST00000371953.3:c.401T>C	p.Met134Thr	p.M134T	ENST00000371953	NM_000314.4	134	aTg/aCg	5/9	0.365265972486497	2	FACETS	0.776	0.712	0.842	0.776	0.712	0.842	SUBCLONAL	2	TRUE	0	0.40158126857606	2		589	446	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736248	243736248	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067352-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	187	512	0	ENST00000263826.5:c.799A>T	p.Ile267Phe	p.I267F	ENST00000263826	NM_005465.4	267	Att/Ttt	8/13	0.402302374678086	3	FACETS	0.94	0.873	1	0.94	0.873	1	CLONAL	2	TRUE	1	0.40158126857606	3		512	595	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272101	38272101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771078736	NA	P-0067352-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	109	603	0	ENST00000425967.3:c.2117G>A	p.Arg706Gln	p.R706Q	ENST00000425967	NM_001174067.1	706	cGg/cAg	16/19	0.107283264604727	6	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.40158126857606	6		603	713	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591103	67591104	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTAAACCAGACC	novel	NA	P-0067352-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	69	576	0	ENST00000274335.5:c.1700_1711dup	p.Lys567_Leu570dup	p.K567_L570dup	ENST00000274335		567	att/aTTAAACCAGACCtt	12/15	1	2	FACETS	0.676	0.59	0.769	0.676	0.59	0.769	SUBCLONAL	1	TRUE	1	0.40158126857606	2		576	508	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588950	67588951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGAG	novel	NA	P-0067352-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	89	588	0	ENST00000274335.5:c.1042_1045dup	p.Asp349AlafsTer16	p.D349Afs*16	ENST00000274335		347	-/CGAG	8/15	1	2	FACETS	0.961	0.856	1	0.961	0.856	1	CLONAL	1	TRUE	1	0.40158126857606	2		588	461	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0067353-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	62	475	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.999	0.866	1	0.999	0.866	1	CLONAL	1	TRUE	1	0.32	2		475	388	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390649	139390650	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs763016003	NA	P-0067353-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	23	790	1	ENST00000277541.6:c.7541_7542del	p.Pro2514ArgfsTer4	p.P2514Rfs*4	ENST00000277541	NM_017617.3	2514	cCT/c	34/34	1	2	FACETS	0.349	0.271	0.439	0.349	0.271	0.439	SUBCLONAL	1	TRUE	1	0.32	2		791	412	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95592924	95592924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755944755	NA	P-0067353-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	41	402	0	ENST00000393063.1:c.896C>T	p.Ser299Leu	p.S299L	ENST00000393063	NM_030621.3	299	tCg/tTg	8/28	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.32	2		402	201	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040908	47040908	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067353-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	82	787	0	ENST00000377604.3:c.1440del	p.Glu481ArgfsTer4	p.E481Rfs*4	ENST00000377604	NM_001204468.1	480	Ccc/cc	14/24	0.3	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.32	1		787	376	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	111	317	0				ENST00000310581	NM_198253.2	-/1132			0.785800886622846	3	FACETS	0.924	0.852	0.995	0.924	0.852	0.995	CLONAL	2	TRUE	1	0.785800886622846	3		317	213	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0067354-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	21953	848	0	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.785800886622846	71	FACETS	0.999	0.997	1	0.985	0.983	0.987	CLONAL	69	TRUE	1	0.785800886622846	71		848	22789	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720930	119720930	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067355-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	130	487	0	ENST00000316626.5:c.245T>G	p.Val82Gly	p.V82G	ENST00000316626		82	gTc/gGc	2/12	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.830505140471706	2		487	312	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437847	52437858	+	frameshift_variant	Frame_Shift_Del	DEL	TGACAGTTGCCC	TGACAGTTGCCC	G	novel	NA	P-0067355-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	120	595	0	ENST00000460680.1:c.1303_1314delinsC	p.Gly435ArgfsTer12	p.G435Rfs*12	ENST00000460680	NM_004656.3	435	GGGCAACTGTCA/C	13/17	0.830505140471706	1	FACETS	0.971	0.911	1	0.971	0.911	1	CLONAL	1	TRUE	0	0.830505140471706	1		595	174	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0067361-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	219	477	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		477	388	SUCCESS
APC	324	MSKCC	GRCh37	5	112175324	112175324	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1211642532	NA	P-0067361-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	197	272	0	ENST00000257430.4:c.4033G>T	p.Glu1345Ter	p.E1345*	ENST00000257430	NM_000038.5	1345	Gaa/Taa	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		272	307	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857047	9857047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568622613	NA	P-0067361-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	29	285	0	ENST00000330684.3:c.4354C>T	p.Arg1452Cys	p.R1452C	ENST00000330684	NM_001134407.1	1452	Cgc/Tgc	13/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		285	302	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285754	87285754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370304899	NA	P-0067361-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	38	356	1	ENST00000277120.3:c.91G>A	p.Ala31Thr	p.A31T	ENST00000277120		31	Gcc/Acc	2/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		357	326	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380283	25380283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913528	NA	P-0067361-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	117	264	1	ENST00000311936.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000311936	NM_004985.3	59	Gca/Aca	3/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		265	288	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150923507	150923507	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs376939142	NA	P-0067361-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	182	310	0	ENST00000271640.5:c.2154C>A	p.Phe718Leu	p.F718L	ENST00000271640	NM_001145415.1	718	ttC/ttA	13/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		310	478	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722351	176722351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067361-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	84	344	0	ENST00000439151.2:c.7982C>T	p.Thr2661Ile	p.T2661I	ENST00000439151	NM_022455.4	2661	aCt/aTt	23/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		344	426	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0067362-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	27	232	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.337362173587753	NA		232	148	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458348	12458350	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0067362-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	42	286	0	ENST00000287820.6:c.967_969del	p.Glu323del	p.E323del	ENST00000287820	NM_015869.4	322	cAGGag/cag	6/7	1	2	FACETS	0.958	0.805	1	0.958	0.805	1	CLONAL	1	TRUE	1	0.337362173587753	2		286	260	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0067362-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	83	232	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	0.139786987642919	6	FACETS	1	0.945	1	0.733	0.653	0.818	INDETERMINATE	2	TRUE	3	0.43586267497859	6		232	324	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589836	69589836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1390579117	NA	P-0067362-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	60	591	0	ENST00000168712.1:c.17C>T	p.Thr6Met	p.T6M	ENST00000168712	NM_002007.2	6	aCg/aTg	1/3	0.43586267497859	5	FACETS	0.911	0.786	1	0.228	0.196	0.262	CLONAL	1	TRUE	1	0.43586267497859	5		591	500	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350544	89350545	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0067362-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	64	219	0	ENST00000301030.4:c.2405_2406del	p.Leu802GlnfsTer7	p.L802Qfs*7	ENST00000301030	NM_001256183.1	802	cTC/c	9/13	NA	2	FACETS	0.825	0.729	0.924			1	INDETERMINATE	2	TRUE	NA	0.43586267497859	2		219	178	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986607	36986607	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067363-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	27	215	0	ENST00000354822.5:c.1082C>A	p.Ala361Glu	p.A361E	ENST00000354822	NM_001079668.2	361	gCg/gAg	3/3	1	2	FACETS	0.702	0.568	0.85	0.702	0.568	0.85	SUBCLONAL	1	TRUE	1	0.62	2		215	124	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0067364-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	17	477	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.726	0.541	0.948	0.726	0.541	0.948	CLONAL	1	TRUE	1	0.13	2		477	360	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067367-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	31	317	0				ENST00000310581	NM_198253.2	-/1132			0.225457661712231	6	FACETS	1	0.924	1	0.801	0.67	0.938	INDETERMINATE	2	TRUE	3	0.821585213852963	6		317	83	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155411	185155411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140970208	NA	P-0067367-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	52	372	0	ENST00000265026.3:c.652G>A	p.Ala218Thr	p.A218T	ENST00000265026	NM_004721.4	218	Gca/Aca	3/14	0.786901243342828	3	FACETS	0.735	0.632	0.845	0.367	0.316	0.423	SUBCLONAL	1	TRUE	1	0.821585213852963	3		372	243	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770558	40770558	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1473163818	NA	P-0067367-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	38	398	0	ENST00000373198.4:c.2824T>C	p.Ser942Pro	p.S942P	ENST00000373198	NM_133170.3	942	Tcc/Ccc	19/32	0.821585213852963	1	FACETS	0.599	0.513	0.688	0.599	0.513	0.688	SUBCLONAL	1	TRUE	0	0.821585213852963	1		398	91	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051596	30051596	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067367-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	52	315	0	ENST00000338641.4:c.530A>G	p.Tyr177Cys	p.Y177C	ENST00000338641	NM_000268.3	177	tAt/tGt	6/16	0.821585213852963	1	FACETS	0.981	0.888	1	0.981	0.888	1	CLONAL	1	TRUE	0	0.821585213852963	1		315	76	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15833960	15833960	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067367-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	14	71	0	ENST00000307771.7:c.718T>A	p.Tyr240Asn	p.Y240N	ENST00000307771	NM_005089.3	240	Tat/Aat	8/11	1	1	FACETS	0.956	0.774	1	0.956	0.774	1	CLONAL	1	TRUE	0	0.821585213852963	1		71	21	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25362737	25362737	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067367-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	37	264	0	ENST00000311936.3:c.559A>C	p.Ile187Leu	p.I187L	ENST00000311936	NM_004985.3	187	Att/Ctt	5/5	1	2	FACETS	0.901	0.765	1	0.901	0.765	1	CLONAL	1	TRUE	1	0.821585213852963	2		264	100	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2054673	2054673	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067367-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	43	380	0	ENST00000349721.2:c.1123A>G	p.Lys375Glu	p.K375E	ENST00000349721	NM_003070.3	375	Aaa/Gaa	6/34	0.182594393592743	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.821585213852963	0		380	119	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827364	72827364	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067367-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	107	413	0	ENST00000268489.5:c.9217C>A	p.Arg3073Ser	p.R3073S	ENST00000268489	NM_006885.3	3073	Cgt/Agt	9/10	0.776227416410561	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.821585213852963	2		413	123	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724136	61724136	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067367-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	72	370	0	ENST00000401558.2:c.766A>G	p.Asn256Asp	p.N256D	ENST00000401558	NM_003400.3	256	Aat/Gat	10/25	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.821585213852963	2		370	174	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272501	15272501	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367885841	NA	P-0067368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	36	465	0	ENST00000263388.2:c.5938G>A	p.Ala1980Thr	p.A1980T	ENST00000263388	NM_000435.2	1980	Gcc/Acc	33/33	1	2	FACETS	0.63	0.518	0.755	0.63	0.518	0.755	SUBCLONAL	1	TRUE	1	0.29	2		465	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578490	7578490	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	17	509	0	ENST00000269305.4:c.440T>A	p.Val147Asp	p.V147D	ENST00000269305	NM_001126112.2	147	gTt/gAt	5/11	1	2	FACETS	0.327	0.243	0.426	0.327	0.243	0.426	SUBCLONAL	1	TRUE	1	0.29	2		509	359	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278094	41278094	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	64	444	0	ENST00000349496.5:c.1970C>A	p.Ala657Asp	p.A657D	ENST00000349496	NM_001904.3	657	gCt/gAt	13/15	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.29	2		444	428	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490578	20490578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368121892	NA	P-0067368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	33	402	0	ENST00000346618.3:c.1315G>A	p.Gly439Arg	p.G439R	ENST00000346618	NM_001949.4	439	Ggg/Agg	7/7	1	2	FACETS	0.629	0.513	0.759	0.629	0.513	0.759	SUBCLONAL	1	TRUE	1	0.29	2		402	362	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024217	112024217	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1370673690	NA	P-0067368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	20	375	0	ENST00000368678.4:c.568C>T	p.Arg190Cys	p.R190C	ENST00000368678		190	Cgt/Tgt	7/13	1	2	FACETS	0.427	0.326	0.545	0.427	0.326	0.545	SUBCLONAL	1	TRUE	1	0.29	2		375	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0067369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	188	450	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.521861866631395	3	FACETS	0.911	0.86	0.962	0.911	0.86	0.962	CLONAL	3	TRUE	0	0.538764867445891	3		450	324	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0067369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	198	270	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.481502425172869	4	FACETS	0.881	0.834	0.926	0.881	0.834	0.926	CLONAL	4	TRUE	0	0.538764867445891	4		270	321	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10796780	10796780	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	109	362	0	ENST00000361367.2:c.2912A>C	p.Asp971Ala	p.D971A	ENST00000361367	NM_014633.3	971	gAt/gCt	23/25	0.443583901139405	3	FACETS	0.886	0.807	0.966	0.886	0.807	0.966	CLONAL	2	TRUE	1	0.538764867445891	3		362	290	SUCCESS
APC	324	MSKCC	GRCh37	5	112163677	112163677	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0067369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	101	258	0	ENST00000257430.4:c.1600A>T	p.Lys534Ter	p.K534*	ENST00000257430	NM_000038.5	534	Aaa/Taa	13/16	0.493847183852928	3	FACETS	0.901	0.819	0.986	0.901	0.819	0.986	CLONAL	2	TRUE	1	0.538764867445891	3		258	264	SUCCESS
APC	324	MSKCC	GRCh37	5	112176027	112176030	+	frameshift_variant	Frame_Shift_Del	DEL	TTAT	TTAT	-	novel	NA	P-0067369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	56	338	0	ENST00000257430.4:c.4738_4741del	p.Ile1580LeufsTer69	p.I1580Lfs*69	ENST00000257430	NM_000038.5	1579	aTTATt/at	16/16	0.493847183852928	3	FACETS	0.854	0.736	0.98	0.427	0.368	0.49	CLONAL	1	TRUE	1	0.538764867445891	3		338	309	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009265	69009268	+	missense_variant	Missense_Mutation	ONP	ATTC	ATTC	TTTT	novel	NA	P-0067369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	39	333	0	ENST00000288368.4:c.2382_2385delinsTTTT	p.Lys794Asn	p.K794N	ENST00000288368	NM_024870.2	794	aaATTC/aaTTTT	22/40	0.439202547952393	4	FACETS	0.628	0.521	0.745			1	SUBCLONAL	1	TRUE	NA	0.538764867445891	4		333	355	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209511	98209511	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200100952	NA	P-0067369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	29	316	0	ENST00000331920.6:c.4027G>A	p.Gly1343Arg	p.G1343R	ENST00000331920	NM_000264.3	1343	Ggg/Agg	23/24	0.493847183852928	3	FACETS	0.579	0.467	0.705	0.29	0.233	0.353	SUBCLONAL	1	TRUE	1	0.538764867445891	3		316	236	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306996	65306997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	117	373	5	ENST00000342505.4:c.2580dup	p.Pro861ThrfsTer4	p.P861Tfs*4	ENST00000342505	NM_002227.2	860	-/A	19/25	0.602758471760004	3	FACETS	0.907	0.821	0.997	0.454	0.41	0.499	CLONAL	1	TRUE	1	0.602758471760004	3		378	557	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296182	15296182	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519101	NA	P-0067371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	49	472	0	ENST00000263388.2:c.2182C>T	p.Arg728Cys	p.R728C	ENST00000263388	NM_000435.2	728	Cgc/Tgc	14/33	1	2	FACETS	0.167	0.14	0.195	0.167	0.14	0.195	SUBCLONAL	1	TRUE	1	0.84644558417166	2		472	695	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934133	39934133	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	293	171	0	ENST00000378444.4:c.466C>T	p.Gln156Ter	p.Q156*	ENST00000378444	NM_001123385.1	156	Caa/Taa	4/15	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.84644558417166	1		171	340	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375028	45375028	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	239	338	0	ENST00000262160.6:c.815C>T	p.Ala272Val	p.A272V	ENST00000262160	NM_005901.5	272	gCa/gTa	8/11	0.84644558417166	1	FACETS	0.975	0.934	1	0.975	0.934	1	CLONAL	1	TRUE	0	0.84644558417166	1		338	334	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99473477	99473477	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	110	303	0	ENST00000268035.6:c.2899C>G	p.Leu967Val	p.L967V	ENST00000268035	NM_000875.3	967	Ctg/Gtg	15/21	0.84644558417166	1	FACETS	0.426	0.386	0.467	0.426	0.386	0.467	SUBCLONAL	1	TRUE	0	0.84644558417166	1		303	352	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813097	76813097	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	219	170	0	ENST00000373344.5:c.6524T>A	p.Ile2175Asn	p.I2175N	ENST00000373344	NM_000489.3	2175	aTt/aAt	30/35	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.84644558417166	1		170	239	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572257	64572259	+	frameshift_variant	Frame_Shift_Del	DEL	TCT	TCT	C	novel	NA	P-0067371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	280	500	0	ENST00000312049.6:c.1380_1382delinsG	p.Glu461GlyfsTer69	p.E461Gfs*69	ENST00000312049	NM_130799.2	460	cgAGAg/cgGg	10/10	0.84644558417166	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.84644558417166	1		500	352	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946385	2946385	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067372-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	22	453	0	ENST00000396946.4:c.3352G>A	p.Ala1118Thr	p.A1118T	ENST00000396946	NM_032415.4	1118	Gcc/Acc	25/25	1	2	FACETS	0.506	0.392	0.64	0.506	0.392	0.64	SUBCLONAL	1	TRUE	1	0.24	2		453	362	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846074	68846074	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067372-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	23	400	0	ENST00000261769.5:c.1045G>T	p.Asp349Tyr	p.D349Y	ENST00000261769	NM_004360.3	349	Gac/Tac	8/16	1	2	FACETS	0.485	0.378	0.61	0.485	0.378	0.61	SUBCLONAL	1	TRUE	1	0.24	2		400	395	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894230	NA	P-0067373-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	46	389	0	ENST00000451590.1:c.35G>A	p.Gly12Asp	p.G12D	ENST00000451590	NM_001130442.1	12	gGc/gAc	2/5	0.282110232241555	3	FACETS	1	0.961	1	0.494	0.42	0.574	CLONAL	1	TRUE	0	0.3	3		389	238	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477807	140477807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs180177038	NA	P-0067373-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	61	313	0	ENST00000288602.6:c.1501G>A	p.Glu501Lys	p.E501K	ENST00000288602	NM_004333.4	501	Gaa/Aaa	12/18	0.3	5	FACETS	1	0.939	1	0.756	0.659	0.859	CLONAL	2	TRUE	2	0.3	5		313	260	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120360	94120360	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs749418654	NA	P-0067373-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	34	367	0	ENST00000369303.4:c.691C>T	p.Arg231Ter	p.R231*	ENST00000369303	NM_004440.3	231	Cga/Tga	3/17	0.3	1	FACETS	0.94	0.775	1	0.94	0.775	1	CLONAL	1	TRUE	0	0.3	1		367	205	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431638	6431638	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067373-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	31	179	0	ENST00000356142.4:c.191A>G	p.Tyr64Cys	p.Y64C	ENST00000356142	NM_018890.3	64	tAt/tGt	3/7	0.3	5	FACETS	1	0.836	1	0.68	0.557	0.813	CLONAL	2	TRUE	2	0.3	5		179	147	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401535	401535	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067373-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	55	382	0	ENST00000380956.4:c.857A>G	p.Asn286Ser	p.N286S	ENST00000380956	NM_001195286.1	286	aAc/aGc	7/9	0.3	4	FACETS	0.792	0.682	0.91	0.528	0.454	0.607	CLONAL	2	TRUE	1	0.3	4		382	301	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657354	29657354	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060500378	NA	P-0067373-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	32	345	0	ENST00000356175.3:c.5587T>C	p.Phe1863Leu	p.F1863L	ENST00000356175	NM_000267.3	1863	Ttt/Ctt	38/57	1	2	FACETS	1	0.819	1	1	0.819	1	CLONAL	1	TRUE	1	0.3	2		345	213	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21344815	21344815	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs148031742	NA	P-0067373-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	81	323	0	ENST00000215739.8:c.791+1G>A		p.X264_splice	ENST00000215739	NM_006767.3	264			0.3	1	FACETS	0.956	0.856	1	1	0.985	1	CLONAL	2	TRUE	0	0.3	1		323	240	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942532	17942538	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCGGT	GCGCGGT	-	novel	NA	P-0067373-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	57	292	0	ENST00000458235.1:c.2750_2756del	p.His917ArgfsTer52	p.H917Rfs*52	ENST00000458235	NM_000215.3	917	cACCGCGCg/cg	20/24	0.21542386896242	3	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	1	0.3	3		292	195	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560172	29560172	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067373-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	31	380	0	ENST00000356175.3:c.3649G>T	p.Asp1217Tyr	p.D1217Y	ENST00000356175	NM_000267.3	1217	Gat/Tat	27/57	1	2	FACETS	1	0.84	1	1	0.84	1	CLONAL	1	TRUE	1	0.3	2		380	200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0067374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	352	256	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.548250242874061	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.612400807915185	2		256	547	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061516	38061517	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGC	rs763371315	NA	P-0067374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	18	300	0	ENST00000250448.2:c.470_472dup	p.Gly157dup	p.G157dup	ENST00000250448	NM_004496.3	157	gac/gGCGac	2/2	1	2	FACETS	0.118	0.088	0.153	0.118	0.088	0.153	SUBCLONAL	1	TRUE	1	0.612400807915185	2		300	500	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969331	44969331	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	141	129	0	ENST00000377967.4:c.4013T>G	p.Val1338Gly	p.V1338G	ENST00000377967	NM_021140.2	1338	gTt/gGt	28/29	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.612400807915185	1		129	223	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180306	27180306	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	30	362	0	ENST00000380036.4:c.970G>T	p.Asp324Tyr	p.D324Y	ENST00000380036	NM_000459.3	324	Gat/Tat	7/23	0.529764430324645	1	FACETS	0.133	0.107	0.163	0.133	0.107	0.163	SUBCLONAL	1	TRUE	0	0.612400807915185	1		362	511	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830587	72830588	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	119	359	0	ENST00000268489.5:c.5993dup	p.Leu1998PhefsTer31	p.L1998Ffs*31	ENST00000268489	NM_006885.3	1998	tta/ttTa	9/10	0.196542190457239	1	FACETS	0.524	0.475	0.575	0.524	0.475	0.575	INDETERMINATE	1	TRUE	0	0.612400807915185	1		359	515	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066703	5066703	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	88	281	0	ENST00000381652.3:c.1240A>G	p.Lys414Glu	p.K414E	ENST00000381652	NM_004972.3	414	Aag/Gag	10/25	0.196542190457239	1	FACETS	0.707	0.634	0.782	0.707	0.634	0.782	INDETERMINATE	1	TRUE	0	0.612400807915185	1		281	282	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300922	137300922	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0067374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	123	310	0	ENST00000481739.1:c.567C>G	p.Tyr189Ter	p.Y189*	ENST00000481739	NM_002957.4	189	taC/taG	4/10	1	2	FACETS	0.636	0.576	0.698	0.636	0.576	0.698	SUBCLONAL	1	TRUE	1	0.612400807915185	2		310	632	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519985	NA	P-0067376-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	68	421	0	ENST00000269305.4:c.857A>G	p.Glu286Gly	p.E286G	ENST00000269305	NM_001126112.2	286	gAa/gGa	8/11	0.158497073893344	2	FACETS	0.907	0.793	1	0.907	0.793	1	CLONAL	2	TRUE	0	0.197839056342138	2		421	379	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667582	29667589	+	frameshift_variant	Frame_Shift_Del	DEL	GGTCAACT	GGTCAACT	-	novel	NA	P-0067376-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	99	331	0	ENST00000356175.3:c.6918_6925del	p.Glu2306AspfsTer10	p.E2306Dfs*10	ENST00000356175	NM_000267.3	2306	gaGGTCAACTtg/gatg	46/57	0.197839056342138	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.197839056342138	2		331	404	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0067378-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	279	314	4	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.420354215624911	3	FACETS	0.947	0.908	0.986			1	CLONAL	3	TRUE	NA	0.608146050416742	3		318	421	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508835	106508835	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067378-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	148	540	2	ENST00000359195.3:c.829C>T	p.Arg277Trp	p.R277W	ENST00000359195	NM_002649.2	277	Cgg/Tgg	2/11	1	2	FACETS	0.989	0.91	1	0.989	0.91	1	CLONAL	1	TRUE	1	0.608146050416742	2		542	492	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240285	41240285	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	9	272	0	ENST00000379561.5:c.65C>G	p.Ser22Trp	p.S22W	ENST00000379561	NM_002015.3	22	tCg/tGg	1/3	1	2	FACETS	0.117	0.076	0.168	0.117	0.076	0.168	SUBCLONAL	1	TRUE	1	0.409823734150485	2		272	377	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162722920	162722920	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	87	375	0	ENST00000367921.3:c.118C>T	p.Gln40Ter	p.Q40*	ENST00000367921	NM_006182.2	40	Cag/Tag	4/18	0.409823734150485	3	FACETS	0.958	0.85	1	0.479	0.425	0.537	CLONAL	1	TRUE	1	0.409823734150485	3		375	534	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023710	27023756	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCATGGGGGGAGGCGGCCCCTCCGCGGCCGGCGGGGGAACTCCCC	GGCCATGGGGGGAGGCGGCCCCTCCGCGGCCGGCGGGGGAACTCCCC	-	novel	NA	P-0067380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	79	332	0	ENST00000324856.7:c.816_862del	p.Met274HisfsTer110	p.M274Hfs*110	ENST00000324856	NM_006015.4	272	ggGGCCATGGGGGGAGGCGGCCCCTCCGCGGCCGGCGGGGGAACTCCCCag/ggag	1/20	0.409823734150485	1	FACETS	0.851	0.754	0.954	0.851	0.754	0.954	CLONAL	1	TRUE	0	0.409823734150485	1		332	360	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940297	49940297	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	115	421	0	ENST00000296474.3:c.746A>G	p.Tyr249Cys	p.Y249C	ENST00000296474	NM_002447.2	249	tAc/tGc	1/20	0.409823734150485	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.409823734150485	1		421	423	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430327	47430327	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs746605740	NA	P-0067380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	81	364	0	ENST00000377045.4:c.1602C>G	p.Ile534Met	p.I534M	ENST00000377045	NM_001654.4	534	atC/atG	15/16	1	2	FACETS	0.937	0.829	1	0.937	0.829	1	CLONAL	1	TRUE	1	0.409823734150485	2		364	422	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539105	187539105	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	116	378	0	ENST00000441802.2:c.8635A>C	p.Lys2879Gln	p.K2879Q	ENST00000441802	NM_005245.3	2879	Aag/Cag	10/27	0.409823734150485	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.409823734150485	1		378	368	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647067	23647067	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	94	423	0	ENST00000261584.4:c.800del	p.Pro267LeufsTer12	p.P267Lfs*12	ENST00000261584	NM_024675.3	267	cCt/ct	4/13	0.409823734150485	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.409823734150485	1		423	324	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163297	32163297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1239036035	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	87	449	2	ENST00000375023.3:c.5929G>A	p.Glu1977Lys	p.E1977K	ENST00000375023	NM_004557.3	1977	Gag/Aag	30/30	0.418223607159131	2	FACETS	0.805	0.714	0.901	0.402	0.357	0.451	CLONAL	1	TRUE	0	0.418223607159131	2		451	517	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762959	40762959	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs387906659	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	177	418	1	ENST00000392038.2:c.49G>A	p.Glu17Lys	p.E17K	ENST00000392038	NM_001626.4	17	Gaa/Aaa	3/14	0.418223607159131	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.418223607159131	3		419	499	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007768	45007768	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	97	370	0	ENST00000558401.1:c.215C>G	p.Ser72Ter	p.S72*	ENST00000558401	NM_004048.2	72	tCa/tGa	2/4	0.418223607159131	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.418223607159131	1		370	355	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813333	102813333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs539899150	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	212	432	2	ENST00000307046.8:c.356G>A	p.Arg119His	p.R119H	ENST00000307046	NM_001111285.1	119	cGc/cAc	3/4	0.418223607159131	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.418223607159131	3		434	531	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984723	72984723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879236303	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	108	426	0	ENST00000268489.5:c.2861C>T	p.Thr954Met	p.T954M	ENST00000268489	NM_006885.3	954	aCg/aTg	3/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.418223607159131	2		426	437	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025542	1025542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1023065435	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	102	443	0	ENST00000358495.3:c.833G>A	p.Arg278Gln	p.R278Q	ENST00000358495	NM_134424.2	278	cGa/cAa	9/12	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.418223607159131	2		443	419	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644448	18644448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751457593	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	73	288	0	ENST00000266497.5:c.2626C>T	p.Leu876Phe	p.L876F	ENST00000266497		876	Ctt/Ttt	18/31	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.418223607159131	2		288	323	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624965	9624965	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	66	370	0	ENST00000353224.5:c.12G>T	p.Lys4Asn	p.K4N	ENST00000353224	NM_177990.2	4	aaG/aaT	3/10	1	2	FACETS	0.945	0.826	1	0.945	0.826	1	CLONAL	1	TRUE	1	0.418223607159131	2		370	334	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3929850	3929850	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	85	353	0	ENST00000262367.5:c.68C>A	p.Ser23Ter	p.S23*	ENST00000262367	NM_004380.2	23	tCg/tAg	1/31	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.418223607159131	2		353	365	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753117	57753117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1185917187	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	96	443	0	ENST00000274289.3:c.899C>T	p.Pro300Leu	p.P300L	ENST00000274289	NM_006622.3	300	cCg/cTg	7/14	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.418223607159131	2		443	450	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293279	91293279	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	71	391	0	ENST00000355112.3:c.781C>A	p.His261Asn	p.H261N	ENST00000355112	NM_000057.2	261	Cat/Aat	3/22	0.418223607159131	1	FACETS	0.956	0.843	1	0.956	0.843	1	CLONAL	1	TRUE	0	0.418223607159131	1		391	281	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645448	67645448	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	120	455	0	ENST00000264010.4:c.713C>G	p.Ser238Ter	p.S238*	ENST00000264010	NM_006565.3	238	tCa/tGa	3/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.418223607159131	2		455	487	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411714	63411714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	98	472	0	ENST00000330258.3:c.1453G>A	p.Glu485Lys	p.E485K	ENST00000330258	NM_152424.3	485	Gag/Aag	2/2	0.135517253700259	0	FACETS	0.706	0.635	0.781			1	INDETERMINATE	1	TRUE	0	0.418223607159131	0		472	386	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281282	46281282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	91	343	0	ENST00000371998.3:c.4079C>T	p.Ser1360Leu	p.S1360L	ENST00000371998		1360	tCa/tTa	21/23	1	2	FACETS	0.961	0.857	1	0.961	0.857	1	CLONAL	1	TRUE	1	0.418223607159131	2		343	453	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133710889	133710889	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	77	312	0	ENST00000318560.5:c.56C>G	p.Ser19Trp	p.S19W	ENST00000318560	NM_005157.4	19	tCg/tGg	1/11	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.418223607159131	2		312	345	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869542	117869542	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	43	399	0	ENST00000297338.2:c.652G>C	p.Asp218His	p.D218H	ENST00000297338	NM_006265.2	218	Gat/Cat	6/14	1	2	FACETS	0.643	0.54	0.755	0.643	0.54	0.755	SUBCLONAL	1	TRUE	1	0.418223607159131	2		399	320	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510208	149510208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	103	408	0	ENST00000261799.4:c.1261G>A	p.Glu421Lys	p.E421K	ENST00000261799	NM_002609.3	421	Gag/Aag	9/23	0.135517253700259	0	FACETS	0.692	0.624	0.764			1	INDETERMINATE	1	TRUE	0	0.418223607159131	0		408	414	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524774	137524774	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	64	407	0	ENST00000367739.4:c.595C>T	p.Gln199Ter	p.Q199*	ENST00000367739	NM_000416.2	199	Cag/Tag	5/7	0.418223607159131	1	FACETS	0.887	0.775	1	0.887	0.775	1	CLONAL	1	TRUE	0	0.418223607159131	1		407	273	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856014	151856014	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	93	356	0	ENST00000262189.6:c.11604del	p.Lys3870ArgfsTer19	p.K3870Rfs*19	ENST00000262189	NM_170606.2	3868	agG/ag	44/59	1	2	FACETS	0.93	0.831	1	0.93	0.831	1	CLONAL	1	TRUE	1	0.418223607159131	2		356	478	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43773144	43773144	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	88	432	2	ENST00000382044.4:c.448G>C	p.Glu150Gln	p.E150Q	ENST00000382044	NM_001141980.1	150	Gag/Cag	5/28	0.418223607159131	1	FACETS	0.97	0.867	1	0.97	0.867	1	CLONAL	1	TRUE	0	0.418223607159131	1		434	343	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435150	56435150	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	115	518	0	ENST00000407977.2:c.1987C>T	p.Pro663Ser	p.P663S	ENST00000407977		663	Ccc/Tcc	9/10	0.418223607159131	2	FACETS	1	0.965	1	0.569	0.515	0.626	CLONAL	1	TRUE	0	0.418223607159131	2		518	483	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753972	57753972	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	89	321	1	ENST00000274289.3:c.652G>T	p.Glu218Ter	p.E218*	ENST00000274289	NM_006622.3	218	Gaa/Taa	5/14	1	2	FACETS	0.959	0.854	1	0.959	0.854	1	CLONAL	1	TRUE	1	0.418223607159131	2		322	444	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42788864	42788864	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	81	314	0	ENST00000575354.2:c.8C>A	p.Ser3Ter	p.S3*	ENST00000575354	NM_015125.3	3	tCg/tAg	1/20	0.418223607159131	3	FACETS	1	0.93	1	0.536	0.474	0.602	CLONAL	1	TRUE	1	0.418223607159131	3		314	437	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390362	118390362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	100	340	0	ENST00000534358.1:c.11176C>T	p.Leu3726Phe	p.L3726F	ENST00000534358	NM_005933.3	3726	Ctc/Ttc	32/36	0.403775147175589	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.418223607159131	1		340	370	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151181877	151181877	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	74	303	0	ENST00000262187.5:c.138G>C	p.Leu46Phe	p.L46F	ENST00000262187	NM_005614.3	46	ttG/ttC	3/8	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.418223607159131	2		303	347	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637390	176637390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	101	464	0	ENST00000439151.2:c.1990G>A	p.Glu664Lys	p.E664K	ENST00000439151	NM_022455.4	664	Gaa/Aaa	5/23	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.418223607159131	2		464	479	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981674	101981674	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	89	385	0	ENST00000282441.5:c.95G>T	p.Gly32Val	p.G32V	ENST00000282441	NM_001130145.2	32	gGa/gTa	1/9	0.403775147175589	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.418223607159131	1		385	273	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248008	59248008	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	111	486	1	ENST00000371222.2:c.735C>G	p.Ile245Met	p.I245M	ENST00000371222	NM_002228.3	245	atC/atG	1/1	1	2	FACETS	0.97	0.876	1	0.97	0.876	1	CLONAL	1	TRUE	1	0.418223607159131	2		487	547	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564534	41564534	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	91	407	1	ENST00000263253.7:c.3956G>C	p.Gly1319Ala	p.G1319A	ENST00000263253	NM_001429.3	1319	gGa/gCa	24/31	1	2	FACETS	0.879	0.783	0.98	0.879	0.783	0.98	CLONAL	1	TRUE	1	0.418223607159131	2		408	495	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89806408	89806408	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	102	345	0	ENST00000389301.3:c.3928G>C	p.Glu1310Gln	p.E1310Q	ENST00000389301	NM_000135.2	1310	Gag/Cag	39/43	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.418223607159131	2		345	401	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067207	37067207	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	84	362	1	ENST00000231790.2:c.1118G>C	p.Gly373Ala	p.G373A	ENST00000231790	NM_000249.3	373	gGa/gCa	12/19	0.418223607159131	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	0	0.418223607159131	1		363	313	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120796832	120796832	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	78	292	0	ENST00000257552.2:c.427G>C	p.Asp143His	p.D143H	ENST00000257552	NM_002442.3	143	Gac/Cac	7/15	0.418223607159131	3	FACETS	1	0.892	1	0.506	0.446	0.569	CLONAL	1	TRUE	1	0.418223607159131	3		292	446	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176448	142176448	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	47	266	0	ENST00000350721.4:c.7653G>A	p.Met2551Ile	p.M2551I	ENST00000350721	NM_001184.3	2551	atG/atA	45/47	0.210164079911711	4	FACETS	0.987	0.837	1	0.329	0.279	0.384	INDETERMINATE	1	TRUE	1	0.418223607159131	4		266	323	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243080	105243080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	80	433	2	ENST00000349310.3:c.203C>T	p.Pro68Leu	p.P68L	ENST00000349310	NM_001014432.1	68	cCc/cTc	5/15	1	2	FACETS	0.971	0.86	1	0.971	0.86	1	CLONAL	1	TRUE	1	0.418223607159131	2		435	394	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638104	176638104	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	86	434	0	ENST00000439151.2:c.2704G>C	p.Glu902Gln	p.E902Q	ENST00000439151	NM_022455.4	902	Gaa/Caa	5/23	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.418223607159131	2		434	393	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433256	49433256	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	96	463	0	ENST00000301067.7:c.8191C>T	p.Gln2731Ter	p.Q2731*	ENST00000301067	NM_003482.3	2731	Cag/Tag	32/54	1	2	FACETS	0.971	0.869	1	0.971	0.869	1	CLONAL	1	TRUE	1	0.418223607159131	2		463	473	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0067382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	212	214	0	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		214	235	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912165	29912165	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	10	166	0	ENST00000376809.5:c.886C>A	p.Leu296Met	p.L296M	ENST00000376809	NM_002116.7	296	Ctg/Atg	4/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		166	139	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942030	44942031	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0067382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	97	185	0	ENST00000377967.4:c.3283_3284del	p.Lys1095ValfsTer7	p.K1095Vfs*7	ENST00000377967	NM_021140.2	1094	AAa/a	22/29	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		185	127	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50820837	50820837	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	75	329	0	ENST00000398568.2:c.2012G>T	p.Gly671Val	p.G671V	ENST00000398568	NM_001042412.1	671	gGa/gTa	12/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		329	201	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146498	185146498	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	73	437	0	ENST00000265026.3:c.129del	p.Glu44ArgfsTer13	p.E44Rfs*13	ENST00000265026	NM_004721.4	43	ctC/ct	2/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		437	374	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835596	68835596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587783047	NA	P-0067383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	63	393	0	ENST00000261769.5:c.187C>T	p.Arg63Ter	p.R63*	ENST00000261769	NM_004360.3	63	Cga/Tga	3/16	0.434018313630579	1	FACETS	0.663	0.577	0.755	0.663	0.577	0.755	SUBCLONAL	1	TRUE	0	0.434018313630579	1		393	343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1131691035	NA	P-0067383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	122	517	0	ENST00000269305.4:c.592del	p.Glu198LysfsTer49	p.E198Kfs*49	ENST00000269305	NM_001126112.2	198	Gaa/aa	6/11	0.434018313630579	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.434018313630579	1		517	329	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458372	120458372	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	115	500	0	ENST00000256646.2:c.6973C>T	p.Gln2325Ter	p.Q2325*	ENST00000256646	NM_024408.3	2325	Cag/Tag	34/34	0.434018313630579	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.434018313630579	1		500	325	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6222674	6222697	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	TGCTGCTCTCCTTGTTGGCGTCCT	TGCTGCTCTCCTTGTTGGCGTCCT	A	novel	NA	P-0067383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	96	434	0	ENST00000252674.7:c.547-2_568delinsT		p.X183_splice	ENST00000252674	NM_005934.3	183		6/12	0.434018313630579	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.434018313630579	1		434	285	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0067384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	54	412	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.177650432269185	3	FACETS	0.762	0.654	0.878	0.508	0.436	0.586	SUBCLONAL	2	FALSE	0	0.244725248187126	3		412	325	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72834009	72834009	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	14	426	0	ENST00000268489.5:c.3884del	p.Val1295GlyfsTer50	p.V1295Gfs*50	ENST00000268489	NM_006885.3	1295	gTg/gg	8/10	0.185206638927627	3	FACETS	0.467	0.337	0.625	0.233	0.168	0.313	SUBCLONAL	1	FALSE	1	0.244725248187126	3		426	275	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203492	108203492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs138941496	NA	P-0067385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	62	334	0	ENST00000278616.4:c.7792C>T	p.Arg2598Ter	p.R2598*	ENST00000278616	NM_000051.3	2598	Cga/Tga	53/63	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.32	2		334	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0067385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	86	372	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	0.848	0.751	0.952	0.848	0.751	0.952	CLONAL	1	TRUE	1	0.32	2		372	634	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797987	42797987	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	45	661	0	ENST00000575354.2:c.4039A>C	p.Asn1347His	p.N1347H	ENST00000575354	NM_015125.3	1347	Aac/Cac	16/20	1	2	FACETS	0.484	0.406	0.57	0.484	0.406	0.57	SUBCLONAL	1	TRUE	1	0.32	2		661	581	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928087	+	inframe_deletion	In_Frame_Del	DEL	GAAGATTTG	GAAGATTTG	-	novel	NA	P-0067385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	79	417	0	ENST00000263967.3:c.1357_1365del	p.Glu453_Leu455del	p.E453_L455del	ENST00000263967	NM_006218.2	453	GAAGATTTG/-	8/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.32	2		417	408	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331643	8331643	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	69	435	0	ENST00000356435.5:c.5473G>C	p.Gly1825Arg	p.G1825R	ENST00000356435		1825	Ggc/Cgc	33/35	1	2	FACETS	0.746	0.65	0.85	0.746	0.65	0.85	SUBCLONAL	1	TRUE	1	0.32	2		435	578	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197364	27197364	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	86	393	0	ENST00000380036.4:c.1676del	p.Leu559GlnfsTer3	p.L559Qfs*3	ENST00000380036	NM_000459.3	559	cTa/ca	12/23	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.32	2		393	535	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	61	384	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.31	0.267	0.357	0.31	0.267	0.357	SUBCLONAL	1	TRUE	1	0.619959641415771	2		384	634	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0067386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	200	376	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	0.987	0.919	1	0.987	0.919	1	CLONAL	1	TRUE	1	0.619959641415771	2		376	654	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0067386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	186	256	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.619959641415771	2	FACETS	0.88	0.828	0.931	0.88	0.828	0.931	CLONAL	2	TRUE	0	0.619959641415771	2		256	341	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624242	89624243	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs121913290	NA	P-0067386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	176	130	0	ENST00000371953.3:c.17_18del	p.Lys6ArgfsTer4	p.K6Rfs*4	ENST00000371953	NM_000314.4	6	AAa/a	1/9	0.619959641415771	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	3	TRUE	0	0.619959641415771	3		130	247	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696461	47696461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	66	356	0	ENST00000347630.2:c.362G>A	p.Arg121Gln	p.R121Q	ENST00000347630	NM_001007230.1	121	cGg/cAg	6/11	1	2	FACETS	0.431	0.375	0.492	0.431	0.375	0.492	SUBCLONAL	1	TRUE	1	0.619959641415771	2		356	494	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56477612	56477612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757941835	NA	P-0067386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	196	311	0	ENST00000267101.3:c.160G>A	p.Glu54Lys	p.E54K	ENST00000267101	NM_001982.3	54	Gag/Aag	2/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.619959641415771	2		311	567	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317155	11317155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	63	389	0	ENST00000361445.4:c.339C>A	p.Asn113Lys	p.N113K	ENST00000361445	NM_004958.3	113	aaC/aaA	4/58	1	2	FACETS	0.332	0.286	0.381	0.332	0.286	0.381	SUBCLONAL	1	TRUE	1	0.619959641415771	2		389	613	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975633	26975633	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	224	331	0	ENST00000381527.3:c.1141C>A	p.His381Asn	p.H381N	ENST00000381527	NM_001260.1	381	Cac/Aac	12/13	NA	2	FACETS	0.96	0.897	1			1	INDETERMINATE	1	TRUE	NA	0.619959641415771	2		331	753	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274766	123274777	+	inframe_deletion	In_Frame_Del	DEL	CCCTATGCAGTA	CCCTATGCAGTA	-	novel	NA	P-0067386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	401	352	0	ENST00000358487.5:c.1141_1152del	p.Tyr381_Gly384del	p.Y381_G384del	ENST00000358487	NM_000141.4	381	TACTGCATAGGG/-	9/18	0.619959641415771	3	FACETS	1	0.972	1	0.681	0.651	0.71	CLONAL	2	TRUE	0	0.619959641415771	3		352	830	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252155	226252155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067388-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	44	194	0	ENST00000366813.1:c.103G>T	p.Gly35Trp	p.G35W	ENST00000366813		35	Ggg/Tgg	1/3	0.3	4	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	4		194	165	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0067389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	36	293	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.987	0.811	1	0.987	0.811	1	CLONAL	1	TRUE	1	0.16	2		293	456	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0067389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	13	267	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.367	0.26	0.498	0.367	0.26	0.498	SUBCLONAL	1	TRUE	1	0.16	2		267	443	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0067389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	32	308	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.808	0.655	0.981	0.808	0.655	0.981	CLONAL	1	TRUE	1	0.16	2		308	495	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0067389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	9	314	4	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.254	0.167	0.366	0.254	0.167	0.366	SUBCLONAL	1	TRUE	1	0.16	2		318	443	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0067389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	17	238	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.631	0.47	0.822	0.631	0.47	0.822	SUBCLONAL	1	TRUE	1	0.16	2		238	337	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0067389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	12	221	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.33	0.23	0.453	0.33	0.23	0.453	SUBCLONAL	1	TRUE	1	0.16	2		221	455	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0067389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	76	303	1	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	1	0.934	1	1	0.984	1	CLONAL	2	TRUE	1	0.16	2		304	435	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636762	176636763	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	39	295	0	ENST00000439151.2:c.1363dup	p.Met455AsnfsTer4	p.M455Nfs*4	ENST00000439151	NM_022455.4	454	-/A	5/23	1	2	FACETS	0.893	0.739	1	0.893	0.739	1	CLONAL	1	TRUE	1	0.16	2		295	546	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1039230	1039231	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCA	novel	NA	P-0067390-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	82	296	0	ENST00000358495.3:c.266_267insTGC	p.Thr89_Gln90insAla	p.T89_Q90insA	ENST00000358495	NM_134424.2	89	acg/acTGCg	4/12	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.549773732720249	2		296	288	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100070	27100070	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0067390-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	47	426	0	ENST00000324856.7:c.3867-1G>C		p.X1289_splice	ENST00000324856	NM_006015.4	1289			1	2	FACETS	0.803	0.685	0.929	0.803	0.685	0.929	CLONAL	1	TRUE	1	0.549773732720249	2		426	213	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0067391-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	228	389	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.802160021083767	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.802160021083767	1		389	322	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0067391-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	250	305	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.802160021083767	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.802160021083767	1		305	354	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092947	29092947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881688	NA	P-0067391-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	60	230	0	ENST00000328354.6:c.1037G>A	p.Arg346His	p.R346H	ENST00000328354	NM_007194.3	346	cGt/cAt	10/15	0.242327273640583	1	FACETS	0.56	0.493	0.629	0.56	0.493	0.629	INDETERMINATE	1	TRUE	0	0.802160021083767	1		230	160	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46603851	46603851	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067391-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	181	291	0	ENST00000263734.3:c.1208T>G	p.Leu403Arg	p.L403R	ENST00000263734	NM_001430.4	403	cTg/cGg	9/16	0.41661318532683	1	FACETS	0.732	0.686	0.779	0.732	0.686	0.779	INDETERMINATE	1	TRUE	0	0.802160021083767	1		291	369	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422317	47422317	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067391-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	205	366	0	ENST00000404338.3:c.385G>A	p.Glu129Lys	p.E129K	ENST00000404338	NM_004491.4	129	Gaa/Aaa	1/6	0.802160021083767	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.802160021083767	1		366	298	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486314	8486314	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067391-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	160	292	0	ENST00000356435.5:c.2503C>A	p.Gln835Lys	p.Q835K	ENST00000356435		835	Cag/Aag	17/35	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.802160021083767	2		292	352	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740467	58740467	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs773389405	NA	P-0067392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	14	294	0	ENST00000305921.3:c.1372C>T	p.Arg458Ter	p.R458*	ENST00000305921	NM_003620.3	458	Cga/Tga	6/6	1	2	FACETS	0.862	0.625	1	0.862	0.625	1	CLONAL	1	TRUE	1	0.17	2		294	191	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624949	9624949	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	16	326	0	ENST00000353224.5:c.28G>A	p.Glu10Lys	p.E10K	ENST00000353224	NM_177990.2	10	Gaa/Aaa	3/10	1	2	FACETS	0.826	0.611	1	0.826	0.611	1	CLONAL	1	TRUE	1	0.17	2		326	228	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570406	87570406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	14	300	0	ENST00000277120.3:c.2146G>A	p.Asp716Asn	p.D716N	ENST00000277120		716	Gac/Aac	17/19	1	2	FACETS	0.698	0.504	0.932	0.698	0.504	0.932	SUBCLONAL	1	TRUE	1	0.17	2		300	236	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486082	8486082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	14	301	0	ENST00000356435.5:c.2735C>T	p.Ser912Phe	p.S912F	ENST00000356435		912	tCc/tTc	17/35	1	2	FACETS	0.646	0.467	0.863	0.646	0.467	0.863	SUBCLONAL	1	TRUE	1	0.17	2		301	255	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224540	108224540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	15	313	0	ENST00000278616.4:c.8719C>T	p.Pro2907Ser	p.P2907S	ENST00000278616	NM_000051.3	2907	Cct/Tct	60/63	1	2	FACETS	0.611	0.446	0.809	0.611	0.446	0.809	SUBCLONAL	1	TRUE	1	0.17	2		313	289	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450048	32450048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444869026	NA	P-0067392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	12	268	0	ENST00000332351.3:c.764C>T	p.Ser255Leu	p.S255L	ENST00000332351	NM_024426.4	255	tCg/tTg	2/10	1	2	FACETS	0.669	0.47	0.913	0.669	0.47	0.913	SUBCLONAL	1	TRUE	1	0.17	2		268	211	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0067392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	11	261	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	1	2	FACETS	0.498	0.343	0.691	0.498	0.343	0.691	SUBCLONAL	1	TRUE	1	0.17	2		261	260	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057021	180057021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752512978	NA	P-0067392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	20	316	0	ENST00000261937.6:c.598G>A	p.Asp200Asn	p.D200N	ENST00000261937	NM_182925.4	200	Gat/Aat	5/30	1	2	FACETS	1	0.771	1	1	0.771	1	CLONAL	1	TRUE	1	0.17	2		316	234	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265308	152265308	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	12	247	0	ENST00000206249.3:c.761G>A	p.Gly254Glu	p.G254E	ENST00000206249	NM_000125.3	254	gGg/gAg	4/8	1	2	FACETS	0.713	0.501	0.973	0.713	0.501	0.973	CLONAL	1	TRUE	1	0.17	2		247	198	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508352	106508352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs890365557	NA	P-0067392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	13	278	0	ENST00000359195.3:c.346G>A	p.Val116Met	p.V116M	ENST00000359195	NM_002649.2	116	Gtg/Atg	2/11	0.13301791241323	3	FACETS	0.664	0.473	0.897	0.332	0.236	0.449	SUBCLONAL	1	TRUE	1	0.17	3		278	250	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244613	41244613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80356970	NA	P-0067392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	11	338	0	ENST00000357654.3:c.2935C>T	p.Arg979Cys	p.R979C	ENST00000357654	NM_007294.3	979	Cgt/Tgt	10/23	1	2	FACETS	0.608	0.42	0.841	0.608	0.42	0.841	SUBCLONAL	1	TRUE	1	0.17	2		338	213	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930115	68930115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	19	267	0	ENST00000288368.4:c.176C>T	p.Ser59Leu	p.S59L	ENST00000288368	NM_024870.2	59	tCa/tTa	2/40	1	2	FACETS	0.909	0.691	1	0.909	0.691	1	CLONAL	1	TRUE	1	0.17	2		267	246	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177896	56177896	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	16	330	0	ENST00000399503.3:c.2869C>T	p.Gln957Ter	p.Q957*	ENST00000399503	NM_005921.1	957	Caa/Taa	14/20	1	2	FACETS	0.705	0.521	0.925	0.705	0.521	0.925	CLONAL	1	TRUE	1	0.17	2		330	267	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662386	117662386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	11	338	0	ENST00000368508.3:c.4991C>T	p.Ser1664Phe	p.S1664F	ENST00000368508	NM_002944.2	1664	tCc/tTc	30/43	0.3	0	FACETS	0.562	0.389	0.778			1	SUBCLONAL	1	TRUE	0	0.17	0		338	191	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940078	31940079	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0067392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	22	309	0	ENST00000375333.2:c.221-1_221delinsAA		p.X74_splice	ENST00000375333	NM_032454.1	74		2/8	1	2	FACETS	1	0.823	1	1	0.823	1	CLONAL	1	TRUE	1	0.17	2		309	242	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40761074	40761074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs965617770	NA	P-0067392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	18	262	0	ENST00000392038.2:c.278C>T	p.Pro93Leu	p.P93L	ENST00000392038	NM_001626.4	93	cCa/cTa	4/14	1	2	FACETS	0.837	0.631	1	0.837	0.631	1	CLONAL	1	TRUE	1	0.17	2		262	253	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391432	139391433	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0067392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	12	289	0	ENST00000277541.6:c.6758_6759delinsTT	p.Pro2253Leu	p.P2253L	ENST00000277541	NM_017617.3	2253	cCC/cTT	34/34	1	2	FACETS	0.657	0.461	0.897	0.657	0.461	0.897	SUBCLONAL	1	TRUE	1	0.17	2		289	215	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420963	49420963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	13	227	0	ENST00000301067.7:c.14786C>T	p.Pro4929Leu	p.P4929L	ENST00000301067	NM_003482.3	4929	cCt/cTt	48/54	1	2	FACETS	0.686	0.489	0.925	0.686	0.489	0.925	SUBCLONAL	1	TRUE	1	0.17	2		227	223	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256622	16256622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	14	341	0	ENST00000375759.3:c.3887C>T	p.Pro1296Leu	p.P1296L	ENST00000375759	NM_015001.2	1296	cCc/cTc	11/15	0.0783258997429209	0	FACETS	0.563	0.406	0.751			1	INDETERMINATE	1	TRUE	0	0.17	0		341	243	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821920	72821920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	17	299	0	ENST00000268489.5:c.10255C>T	p.Pro3419Ser	p.P3419S	ENST00000268489	NM_006885.3	3419	Ccc/Tcc	10/10	1	2	FACETS	0.81	0.605	1	0.81	0.605	1	CLONAL	1	TRUE	1	0.17	2		299	247	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032249	26032249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	14	318	0	ENST00000244661.2:c.40G>A	p.Gly14Ser	p.G14S	ENST00000244661	NM_003537.3	14	Ggt/Agt	1/1	1	2	FACETS	0.698	0.504	0.932	0.698	0.504	0.932	SUBCLONAL	1	TRUE	1	0.17	2		318	236	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31495403	31495403	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	11	275	0	ENST00000344624.3:c.1745C>G	p.Thr582Arg	p.T582R	ENST00000344624		582	aCg/aGg	9/33	1	2	FACETS	0.619	0.428	0.857	0.619	0.428	0.857	SUBCLONAL	1	TRUE	1	0.17	2		275	209	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482417	56482417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	22	311	0	ENST00000267101.3:c.965C>T	p.Pro322Leu	p.P322L	ENST00000267101	NM_001982.3	322	cCt/cTt	8/28	1	2	FACETS	0.955	0.742	1	0.955	0.742	1	CLONAL	1	TRUE	1	0.17	2		311	271	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78938078	78938078	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	12	281	0	ENST00000306801.3:c.3956G>A	p.Gly1319Glu	p.G1319E	ENST00000306801	NM_020761.2	1319	gGa/gAa	34/34	1	2	FACETS	0.648	0.455	0.884	0.648	0.455	0.884	SUBCLONAL	1	TRUE	1	0.17	2		281	218	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435029	18435029	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	13	279	0	ENST00000266497.5:c.14G>C	p.Trp5Ser	p.W5S	ENST00000266497		5	tGg/tCg	1/31	1	2	FACETS	0.698	0.498	0.942	0.698	0.498	0.942	SUBCLONAL	1	TRUE	1	0.17	2		279	219	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553539	29553539	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1131691099	NA	P-0067392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	15	183	0	ENST00000356175.3:c.2088G>A	p.Trp696Ter	p.W696*	ENST00000356175	NM_000267.3	696	tgG/tgA	18/57	1	2	FACETS	1	0.822	1	1	0.822	1	CLONAL	1	TRUE	1	0.17	2		183	152	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206733	102206733	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	14	286	0	ENST00000263464.3:c.1361T>G	p.Leu454Arg	p.L454R	ENST00000263464	NM_001165.4	454	cTt/cGt	7/9	1	2	FACETS	0.858	0.621	1	0.858	0.621	1	CLONAL	1	TRUE	1	0.17	2		286	192	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082956	16082956	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	16	211	0	ENST00000281043.3:c.770A>G	p.Glu257Gly	p.E257G	ENST00000281043	NM_005378.4	257	gAg/gGg	2/3	1	2	FACETS	1	0.755	1	1	0.755	1	CLONAL	1	TRUE	1	0.17	2		211	185	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870364	155870364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	17	339	0	ENST00000368323.3:c.475C>T	p.Pro159Ser	p.P159S	ENST00000368323	NM_006912.5	159	Ccc/Tcc	6/6	0.0783258997429209	0	FACETS	0.593	0.442	0.772			1	INDETERMINATE	1	TRUE	0	0.17	0		339	280	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073998	8073999	+	missense_variant	Missense_Mutation	DNP	CT	CT	TG	novel	NA	P-0067392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	15	299	0	ENST00000377482.5:c.660_661delinsCA	p.Asp221Asn	p.D221N	ENST00000377482	NM_018948.3	220	gcAGat/gcCAat	4/4	1	2	FACETS	0.654	0.478	0.865	0.654	0.478	0.865	SUBCLONAL	1	TRUE	1	0.17	2		299	270	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966303	25966304	+	missense_variant	Missense_Mutation	DNP	AG	AG	GA	novel	NA	P-0067392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	18	322	0	ENST00000435504.4:c.2902_2903delinsTC	p.Leu968Ser	p.L968S	ENST00000435504		968	CTg/TCg	13/13	1	2	FACETS	0.746	0.561	0.963	0.746	0.561	0.963	CLONAL	1	TRUE	1	0.17	2		322	284	SUCCESS
EED	8726	MSKCC	GRCh37	11	85979574	85979574	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1301151502	NA	P-0067393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2	145	315	1	ENST00000263360.6:c.937C>T	p.Arg313Ter	p.R313*	ENST00000263360	NM_003797.3	313	Cga/Tga	9/12	0.973970641750675	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.988721077830655	1		316	147	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533140	63533140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	199	413	0	ENST00000307078.5:c.1754G>A	p.Gly585Asp	p.G585D	ENST00000307078	NM_004655.3	585	gGc/gAc	7/11	1	2	FACETS	0.943	0.885	1	0.943	0.885	1	CLONAL	1	TRUE	1	0.988721077830655	2		413	427	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467881	50467881	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	215	391	0	ENST00000331340.3:c.1116C>A	p.Asn372Lys	p.N372K	ENST00000331340	NM_006060.4	372	aaC/aaA	8/8	0.988721077830655	3	FACETS	1	0.975	1	0.541	0.506	0.576	CLONAL	1	TRUE	1	0.988721077830655	3		391	601	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840084	27840084	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	236	443	0	ENST00000328488.2:c.10A>T	p.Thr4Ser	p.T4S	ENST00000328488	NM_003533.2	4	Aca/Tca	1/1	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.988721077830655	2		443	427	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376250	225376250	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	108	314	0	ENST00000264414.4:c.704A>T	p.Lys235Met	p.K235M	ENST00000264414	NM_003590.4	235	aAg/aTg	6/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.988721077830655	2		314	204	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94067986	94067986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150543233	NA	P-0067394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	29	271	0	ENST00000369303.4:c.976G>A	p.Val326Ile	p.V326I	ENST00000369303	NM_004440.3	326	Gtt/Att	4/17	0.167122291618668	3	FACETS	1	0.923	1	0.665	0.536	0.811	CLONAL	1	TRUE	1	0.18	3		271	264	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180441	94180441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139461096	NA	P-0067394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	36	347	0	ENST00000323929.3:c.1727G>A	p.Arg576Gln	p.R576Q	ENST00000323929	NM_005591.3	576	cGa/cAa	15/20	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.18	2		347	325	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0067395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	115	382	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.23159608403928	3	FACETS	1	0.968	1	0.746	0.684	0.81	INDETERMINATE	2	TRUE	0	0.461432461346953	3		382	274	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564083	139564083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs574267042	NA	P-0067395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	53	350	0	ENST00000308874.7:c.223C>T	p.Arg75Cys	p.R75C	ENST00000308874		75	Cgc/Tgc	5/10	0.456307934219217	3	FACETS	1	0.886	1	0.518	0.445	0.596	CLONAL	1	TRUE	1	0.461432461346953	3		350	273	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920422	114920422	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	136	230	0	ENST00000543371.1:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000543371	NM_001198531.1	455	Cga/Tga	13/14	0.461432461346953	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.461432461346953	2		230	273	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956825	68956825	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs184081186	NA	P-0067395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	50	130	0	ENST00000288368.4:c.943G>A	p.Ala315Thr	p.A315T	ENST00000288368	NM_024870.2	315	Gct/Act	8/40	0.432363454786994	4	FACETS	1	0.923	1	0.376	0.321	0.435	CLONAL	1	TRUE	1	0.461432461346953	4		130	281	SUCCESS
APC	324	MSKCC	GRCh37	5	112175759	112175759	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1554085898	NA	P-0067395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	32	179	0	ENST00000257430.4:c.4468del	p.His1490IlefsTer17	p.H1490Ifs*17	ENST00000257430	NM_000038.5	1490	Cat/at	16/16	0.23159608403928	3	FACETS	0.575	0.468	0.695	0.192	0.156	0.232	INDETERMINATE	1	TRUE	0	0.461432461346953	3		179	297	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725055	89725055	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	29	56	0	ENST00000371953.3:c.1038C>A	p.Tyr346Ter	p.Y346*	ENST00000371953	NM_000314.4	346	taC/taA	9/9	0.461432461346953	2	FACETS	0.952	0.777	1	0.476	0.388	0.573	CLONAL	1	TRUE	0	0.461432461346953	2		56	132	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7590693	7590693	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0067395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	125	308	0	ENST00000269305.4:c.-29+2T>G		p.X10_splice	ENST00000269305	NM_001126112.2	10			0.461432461346953	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	0	0.461432461346953	2		308	268	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29678311	29679333	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAAAATAGCTACGAGTAGATTTTAAGTATTCTCACCACAAAAGATAAATATATGAGGTAACACATATGTTAATTTGCTTGATTTAGCCATTCTACAATGTAAACATTTTATTTATTTTTATTTTTCTTTATTAATTTTTTTTGAGACAGAGTCTTGCTCTGTCGCCCAGGCTGGAGTGCAGTAACACAATCTCGGCTCACTACAACCTCCGCCTCCTGGGTTCAAGCGATTCTCCTGCCTCATCCTCCCGAGTAGCTGGGATTACAGGCGCGTGCCACCATGCCCAGCTAATTTTTGTATTTTTGTAGAGATGGGGTTTCACCATGTTGGGCAAGCTGGTCTTGAACTCCTGACCTCAGGTGATCCGCCTGCCTCGGCCTCCCAAAGTGTTGGGATTACAGGCGTGAGCCACAGCGCCCAGCCAATGTAAACATATTTTAAAACATCATGTTGTACACCAAGCTTGCTCAACCCATGGCCTGCAGGCCGCACGCAGCCCAGGATGGCTTTGAATGCAGCCCAACACAAATTTGTAAACTTTCTTAAAACATTAAGTGATTTTTTGGGGTTTTTTTTTTTTTTTAAGCTCATCAACTGTAGTTAGTGTTAGTGTATTTTATATGTGGCCCAGTATATTCTTCTAATTCCAGTGTGGCCCAGGAAAGCTAAGAGATTGGACACCCCTGTTGCTATACCTTTTTATTTGTCAGCTTTTAAAAATTGCAGTACAGATCTTTTTGTTCAGCATTTGGTGAGTACCTACTATGTGCAAGATACTATGGCAAGAAAGTTGATAATTCCTAGGGATACACCAAGAGTTTGTATCCTAAAGCCCTTTAAAGTGCAATTTTAAAATTAATTGATTGCTGTTGTTAGGAAATAGGACAGCCACTTGGAAGGAGCAAACGATGGTTGTATTTGTCACCATATTAATTGATTTTTCTCTATTGTTTTCATCTTTCAGGACACTAAAGGAGACTCAGCCATGGTCCTCTCCCAAAGGTTCTGAAGGATACCTTGCAG	GAAAATAGCTACGAGTAGATTTTAAGTATTCTCACCACAAAAGATAAATATATGAGGTAACACATATGTTAATTTGCTTGATTTAGCCATTCTACAATGTAAACATTTTATTTATTTTTATTTTTCTTTATTAATTTTTTTTGAGACAGAGTCTTGCTCTGTCGCCCAGGCTGGAGTGCAGTAACACAATCTCGGCTCACTACAACCTCCGCCTCCTGGGTTCAAGCGATTCTCCTGCCTCATCCTCCCGAGTAGCTGGGATTACAGGCGCGTGCCACCATGCCCAGCTAATTTTTGTATTTTTGTAGAGATGGGGTTTCACCATGTTGGGCAAGCTGGTCTTGAACTCCTGACCTCAGGTGATCCGCCTGCCTCGGCCTCCCAAAGTGTTGGGATTACAGGCGTGAGCCACAGCGCCCAGCCAATGTAAACATATTTTAAAACATCATGTTGTACACCAAGCTTGCTCAACCCATGGCCTGCAGGCCGCACGCAGCCCAGGATGGCTTTGAATGCAGCCCAACACAAATTTGTAAACTTTCTTAAAACATTAAGTGATTTTTTGGGGTTTTTTTTTTTTTTTAAGCTCATCAACTGTAGTTAGTGTTAGTGTATTTTATATGTGGCCCAGTATATTCTTCTAATTCCAGTGTGGCCCAGGAAAGCTAAGAGATTGGACACCCCTGTTGCTATACCTTTTTATTTGTCAGCTTTTAAAAATTGCAGTACAGATCTTTTTGTTCAGCATTTGGTGAGTACCTACTATGTGCAAGATACTATGGCAAGAAAGTTGATAATTCCTAGGGATACACCAAGAGTTTGTATCCTAAAGCCCTTTAAAGTGCAATTTTAAAATTAATTGATTGCTGTTGTTAGGAAATAGGACAGCCACTTGGAAGGAGCAAACGATGGTTGTATTTGTCACCATATTAATTGATTTTTCTCTATTGTTTTCATCTTTCAGGACACTAAAGGAGACTCAGCCATGGTCCTCTCCCAAAGGTTCTGAAGGATACCTTGCAG	-	novel	NA	P-0067395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	125	0	0	ENST00000356175.3:c.7395-964_7453del		p.X2465_splice	ENST00000356175	NM_000267.3	2465		50/57	0.456307934219217	3	FACETS	1	0.987	1	1	0.993	1	CLONAL	4	TRUE	1	0.461432461346953	3		0	149	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0067396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	47	237	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.164622653392375	2	FACETS	0.92	0.782	1	0.92	0.782	1	CLONAL	2	TRUE	0	0.19	2		237	269	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574000	7574000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	46	314	0	ENST00000269305.4:c.1027G>T	p.Glu343Ter	p.E343*	ENST00000269305	NM_001126112.2	343	Gag/Tag	10/11	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.19	2		314	394	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988886	41988887	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	71	345	0	ENST00000219905.7:c.1680dup	p.Ser561Ter	p.S561*	ENST00000219905	NM_001164273.1	560	att/aTtt	3/24	1	2	FACETS	0.844	0.739	0.956	1	0.978	1	CLONAL	2	TRUE	1	0.19	2		345	443	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	153	317	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		317	317	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0067399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	125	292	2	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		294	291	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089463	27089463	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0067399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	104	473	0	ENST00000324856.7:c.2420-1G>A		p.X807_splice	ENST00000324856	NM_006015.4	807			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		473	480	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983087	201983088	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0067399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	55	445	0	ENST00000359651.3:c.937_938insTC	p.Gln313LeufsTer13	p.Q313Lfs*13	ENST00000359651		312	-/CT	7/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		445	344	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104352440	104352440	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	91	363	0	ENST00000369902.3:c.556C>T	p.Gln186Ter	p.Q186*	ENST00000369902	NM_016169.3	186	Cag/Tag	4/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		363	374	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039479	49039479	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1131690866	NA	P-0067399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	123	386	0	ENST00000267163.4:c.2465del	p.Pro822GlnfsTer4	p.P822Qfs*4	ENST00000267163	NM_000321.2	822	Cca/ca	23/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		386	264	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866359	37866359	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	155	406	0	ENST00000269571.5:c.664G>T	p.Gly222Cys	p.G222C	ENST00000269571		222	Ggt/Tgt	6/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		406	325	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866671	37866671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	229	489	0	ENST00000269571.5:c.838G>A	p.Glu280Lys	p.E280K	ENST00000269571		280	Gag/Aag	7/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		489	507	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0067399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	201	420	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		420	402	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026197	36026197	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	109	442	0	ENST00000358208.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000358208		267	Cgg/Tgg	7/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		442	363	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33290687	33290687	+	5_prime_UTR_variant	5'UTR	SNP	C	C	T	novel	NA	P-0067399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	77	322	0	ENST00000374542.5:c.-101G>A		p.*34*	ENST00000374542	NM_001141970.1	-/740		1/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		322	254	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009359	69009359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755479314	NA	P-0067399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	233	377	0	ENST00000288368.4:c.2476G>A	p.Asp826Asn	p.D826N	ENST00000288368	NM_024870.2	826	Gac/Aac	22/40	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		377	487	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964532	70964532	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	167	458	0	ENST00000276594.2:c.1496C>G	p.Thr499Arg	p.T499R	ENST00000276594	NM_024504.3	499	aCa/aGa	8/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		458	428	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2029101	2029101	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	111	532	0	ENST00000349721.2:c.79C>G	p.Leu27Val	p.L27V	ENST00000349721	NM_003070.3	27	Ctt/Gtt	2/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		532	382	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126692	5126692	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	88	362	0	ENST00000381652.3:c.3300G>A	p.Met1100Ile	p.M1100I	ENST00000381652	NM_004972.3	1100	atG/atA	25/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		362	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0067400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	88	477	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.143193108388798	5	FACETS	0.985	0.877	1	0.657	0.585	0.733	INDETERMINATE	2	TRUE	2	0.285325772379401	5		477	447	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100183	27100183	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1421112233	NA	P-0067400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	77	485	0	ENST00000324856.7:c.3979C>T	p.Gln1327Ter	p.Q1327*	ENST00000324856	NM_006015.4	1327	Cag/Tag	16/20	0.244351294787914	2	FACETS	1	0.965	1	0.628	0.553	0.707	CLONAL	1	TRUE	0	0.285325772379401	2		485	430	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21968234	21968234	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	93	367	0	ENST00000304494.5:c.465del	p.Asp156IlefsTer37	p.D156Ifs*37	ENST00000304494	NM_000077.4	155	ccC/cc	3/3	0.244351294787914	2	FACETS	0.891	0.798	0.987	0.891	0.798	0.987	CLONAL	2	TRUE	0	0.285325772379401	2		367	366	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600447	10600447	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	119	485	0	ENST00000171111.5:c.1408C>A	p.Arg470Ser	p.R470S	ENST00000171111	NM_203500.1	470	Cgt/Agt	4/6	0.244351294787914	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	0	0.285325772379401	2		485	403	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874791	151874791	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	49	400	0	ENST00000262189.6:c.7747G>T	p.Glu2583Ter	p.E2583*	ENST00000262189	NM_170606.2	2583	Gag/Tag	38/59	0.280579412510921	3	FACETS	0.919	0.78	1	0.46	0.39	0.536	CLONAL	1	TRUE	1	0.285325772379401	3		400	427	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434925	49434925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324674144	NA	P-0067400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	92	394	0	ENST00000301067.7:c.6628C>T	p.Pro2210Ser	p.P2210S	ENST00000301067	NM_003482.3	2210	Ccg/Tcg	31/54	0.280579412510921	3	FACETS	0.877	0.784	0.975	0.877	0.784	0.975	CLONAL	2	TRUE	1	0.285325772379401	3		394	420	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809248	243809248	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	92	417	0	ENST00000263826.5:c.376G>A	p.Asp126Asn	p.D126N	ENST00000263826	NM_005465.4	126	Gat/Aat	4/13	0.244351294787914	2	FACETS	0.951	0.853	1	0.951	0.853	1	CLONAL	2	TRUE	0	0.285325772379401	2		417	339	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181758	56181758	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0067400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	59	273	0	ENST00000399503.3:c.3983-1G>T		p.X1328_splice	ENST00000399503	NM_005921.1	1328			0.244351294787914	2	FACETS	1	0.97	1	0.749	0.65	0.855	CLONAL	1	TRUE	0	0.285325772379401	2		273	276	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381472	81381472	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	44	335	0	ENST00000222390.5:c.589C>A	p.Arg197Ser	p.R197S	ENST00000222390	NM_000601.4	197	Cgc/Agc	5/18	0.280579412510921	3	FACETS	1	0.842	1	0.501	0.421	0.588	CLONAL	1	TRUE	1	0.285325772379401	3		335	352	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446847	29446847	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	20	369	0	ENST00000544604.2:c.2678C>A	p.Pro893His	p.P893H	ENST00000544604	NM_001206998.1	893	cCt/cAt	8/9	0.246095250122515	5	FACETS	0.511	0.39	0.653	0.17	0.13	0.218	SUBCLONAL	1	TRUE	2	0.285325772379401	5		369	392	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573554	48573554	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	70	420	0	ENST00000342988.3:c.138G>T	p.Lys46Asn	p.K46N	ENST00000342988	NM_005359.5	46	aaG/aaT	2/12	0.251510301011981	2	FACETS	0.94	0.829	1	0.94	0.829	1	CLONAL	2	TRUE	0	0.285325772379401	2		420	261	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056758	102056758	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	55	256	0	ENST00000282441.5:c.698C>A	p.Pro233His	p.P233H	ENST00000282441	NM_001130145.2	233	cCt/cAt	4/9	0.23518829089224	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	2	TRUE	0	0.285325772379401	2		256	184	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966723	25966723	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	110	467	0	ENST00000435504.4:c.2483G>T	p.Arg828Ile	p.R828I	ENST00000435504		828	aGa/aTa	13/13	0.238303328492407	3	FACETS	0.972	0.879	1	0.648	0.586	0.713	CLONAL	2	TRUE	0	0.285325772379401	3		467	453	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77932738	77932738	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs368907942	NA	P-0067400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	45	395	0	ENST00000361507.4:c.1746G>T	p.Glu582Asp	p.E582D	ENST00000361507	NM_080491.2	582	gaG/gaT	8/10	0.285325772379401	5	FACETS	0.82	0.689	0.966	0.273	0.229	0.322	CLONAL	1	TRUE	2	0.285325772379401	5		395	549	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653110	29653110	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	51	462	0	ENST00000356175.3:c.5045G>T	p.Ser1682Ile	p.S1682I	ENST00000356175	NM_000267.3	1682	aGc/aTc	36/57	0.206442255495658	3	FACETS	0.839	0.713	0.976	0.419	0.356	0.488	CLONAL	1	TRUE	1	0.285325772379401	3		462	487	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47503931	47503931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1178793173	NA	P-0067400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	26	338	0	ENST00000404338.3:c.4486G>A	p.Glu1496Lys	p.E1496K	ENST00000404338	NM_004491.4	1496	Gaa/Aaa	6/6	0.251510301011981	2	FACETS	0.622	0.493	0.769	0.311	0.246	0.385	SUBCLONAL	1	TRUE	0	0.285325772379401	2		338	293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0067401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	142	661	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.273991393514684	2	FACETS	0.974	0.893	1	0.974	0.893	1	CLONAL	2	TRUE	0	0.273991393514684	2		661	532	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2115967	2115967	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs281875189	NA	P-0067401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	77	318	0	ENST00000349721.2:c.3602C>T	p.Ala1201Val	p.A1201V	ENST00000349721	NM_003070.3	1201	gCg/gTg	25/34	0.210974470047722	2	FACETS	1	0.976	1	0.728	0.643	0.819	CLONAL	1	TRUE	0	0.273991393514684	2		318	386	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917033	50917033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760638243	NA	P-0067401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	78	448	0	ENST00000440232.2:c.2285G>A	p.Arg762Gln	p.R762Q	ENST00000440232	NM_002691.3	762	cGa/cAa	19/27	0.152525990845907	4	FACETS	1	0.971	1	0.677	0.596	0.763	INDETERMINATE	1	TRUE	2	0.273991393514684	4		448	536	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155954	119155954	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	47	505	0	ENST00000264033.4:c.1619G>T	p.Arg540Leu	p.R540L	ENST00000264033	NM_005188.3	540	cGa/cTa	11/16	0.218379323265985	2	FACETS	0.661	0.558	0.775	0.331	0.279	0.388	SUBCLONAL	1	TRUE	0	0.273991393514684	2		505	519	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370864	55370864	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs757881222	NA	P-0067401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	157	373	2	ENST00000297316.4:c.166G>T	p.Ala56Ser	p.A56S	ENST00000297316	NM_022454.3	56	Gcc/Tcc	1/2	0.273991393514684	4	FACETS	0.886	0.821	0.952	0.886	0.821	0.952	CLONAL	4	TRUE	0	0.273991393514684	4		375	412	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197876	123197876	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	85	154	0	ENST00000218089.9:c.2000G>T	p.Arg667Leu	p.R667L	ENST00000218089	NM_001042749.1	667	cGg/cTg	20/35	0.273991393514684	2	FACETS	0.949	0.855	1			1	CLONAL	3	TRUE	NA	0.273991393514684	2		154	218	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446402	70446448	+	frameshift_variant	Frame_Shift_Del	DEL	TCAAGCGGAAGAATAACTCAACAACAACAAACAACAGTAAGCCTTCG	TCAAGCGGAAGAATAACTCAACAACAACAAACAACAGTAAGCCTTCG	-	novel	NA	P-0067402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	116	535	0	ENST00000373644.4:c.5345_5391del	p.Lys1782ThrfsTer7	p.K1782Tfs*7	ENST00000373644	NM_030625.2	1781	aTCAAGCGGAAGAATAACTCAACAACAACAAACAACAGTAAGCCTTCG/a	11/12	0.608674547972143	4	FACETS	0.924	0.834	1	0.462	0.417	0.51	CLONAL	1	TRUE	2	0.616730176787126	4		535	658	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265973	41266230	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCA	AACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCA	-	novel	NA	P-0067402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	78	290	0	ENST00000349496.5:c.14-43_228del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.616730176787126	4	FACETS	1	0.969	1	0.641	0.568	0.718	CLONAL	1	TRUE	2	0.616730176787126	4		290	319	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15365010	15365010	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	101	381	3	ENST00000263377.2:c.2111A>T	p.Glu704Val	p.E704V	ENST00000263377	NM_058243.2	704	gAg/gTg	11/20	0.560191805610146	4	FACETS	1	0.938	1	0.532	0.477	0.589	CLONAL	1	TRUE	2	0.616730176787126	4		384	498	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	133	524	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	1	2	FACETS	0.787	0.719	0.856	1	0.988	1	SUBCLONAL	2	TRUE	1	0.364446175513293	2		524	464	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456314	99456325	+	inframe_deletion	In_Frame_Del	DEL	GCGGCTCCAACA	GCGGCTCCAACA	-	novel	NA	P-0067403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	91	368	0	ENST00000268035.6:c.1633_1644del	p.Gly545_Ser548del	p.G545_S548del	ENST00000268035	NM_000875.3	544	tGCGGCTCCAACAgc/tgc	8/21	0.364446175513293	5	FACETS	0.798	0.711	0.89	0.798	0.711	0.89	SUBCLONAL	2	TRUE	3	0.364446175513293	5		368	484	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132793	152132793	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	30	321	0	ENST00000262189.6:c.79C>G	p.Pro27Ala	p.P27A	ENST00000262189	NM_170606.2	27	Ccg/Gcg	1/59	1	2	FACETS	0.722	0.585	0.875	0.722	0.585	0.875	SUBCLONAL	1	TRUE	1	0.364446175513293	2		321	228	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099560	157099560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1583024172	NA	P-0067403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	33	412	0	ENST00000346085.5:c.497C>T	p.Ala166Val	p.A166V	ENST00000346085	NM_020732.3	166	gCt/gTt	1/20	1	2	FACETS	0.73	0.598	0.877	0.73	0.598	0.877	SUBCLONAL	1	TRUE	1	0.364446175513293	2		412	248	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081691	143081691	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	37	404	0	ENST00000262992.4:c.1383C>A	p.Phe461Leu	p.F461L	ENST00000262992	NM_001101669.1	461	ttC/ttA	15/24	0.366039127897839	3	FACETS	0.902	0.748	1	0.451	0.374	0.537	CLONAL	1	TRUE	1	0.364446175513293	3		404	266	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981065	55981065	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	59	329	0	ENST00000263923.4:c.634A>G	p.Ile212Val	p.I212V	ENST00000263923	NM_002253.2	212	Att/Gtt	5/30	1	2	FACETS	0.848	0.742	0.958	1	0.977	1	CLONAL	2	TRUE	1	0.364446175513293	2		329	191	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152043	11152043	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755455174	NA	P-0067403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	70	442	0	ENST00000358026.2:c.4327C>T	p.Arg1443Trp	p.R1443W	ENST00000358026	NM_001128849.1	1443	Cgg/Tgg	31/36	0.366039127897839	3	FACETS	1	0.954	1	0.598	0.524	0.676	CLONAL	1	TRUE	1	0.364446175513293	3		442	380	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	36	428	0	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	1	2	FACETS	0.392	0.322	0.471	0.392	0.322	0.471	SUBCLONAL	1	TRUE	1	0.44	2		428	417	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863054	56863054	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1266824391	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	38	393	2	ENST00000519728.1:c.327del	p.Glu110LysfsTer15	p.E110Kfs*15	ENST00000519728	NM_002350.3	107	acA/ac	5/13	1	2	FACETS	0.468	0.387	0.558	0.468	0.387	0.558	SUBCLONAL	1	TRUE	1	0.44	2		395	369	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	32	478	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.475	0.387	0.575	0.475	0.387	0.575	SUBCLONAL	1	TRUE	1	0.44	2		478	306	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	37	518	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.418	0.345	0.5	0.418	0.345	0.5	SUBCLONAL	1	TRUE	1	0.44	2		518	402	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	78	398	0	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	1	2	FACETS	0.963	0.852	1	0.963	0.852	1	CLONAL	1	TRUE	1	0.44	2		398	368	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	38	437	0	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	0.404	0.334	0.482	0.404	0.334	0.482	SUBCLONAL	1	TRUE	1	0.44	2		437	428	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089123	37089125	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs63751247	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	97	341	0	ENST00000231790.2:c.1852_1854del	p.Lys618del	p.K618del	ENST00000231790	NM_000249.3	615	ctGAAg/ctg	16/19	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.44	2		341	401	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244223	5244223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199851847	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	45	433	0	ENST00000357368.4:c.1259G>A	p.Arg420His	p.R420H	ENST00000357368	NM_002850.3	420	cGc/cAc	11/38	1	2	FACETS	0.563	0.475	0.661	0.563	0.475	0.661	SUBCLONAL	1	TRUE	1	0.44	2		433	363	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	45	589	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.486	0.409	0.571	0.486	0.409	0.571	SUBCLONAL	1	TRUE	1	0.44	2		590	421	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155411	185155411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140970208	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	56	372	0	ENST00000265026.3:c.652G>A	p.Ala218Thr	p.A218T	ENST00000265026	NM_004721.4	218	Gca/Aca	3/14	1	2	FACETS	0.643	0.552	0.741	0.643	0.552	0.741	SUBCLONAL	1	TRUE	1	0.44	2		372	396	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	91	574	0	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.44	2		574	410	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	68	337	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.44	2		338	277	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	46	525	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.531	0.448	0.622	0.531	0.448	0.622	SUBCLONAL	1	TRUE	1	0.44	2		527	394	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042196	14042196	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	95	412	0	ENST00000311895.7:c.2747del	p.Lys916SerfsTer4	p.K916Sfs*4	ENST00000311895	NM_005236.2	915	Aaa/aa	11/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.44	2		412	391	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	25	462	1	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	1	2	FACETS	0.279	0.22	0.348	0.279	0.22	0.348	SUBCLONAL	1	TRUE	1	0.44	2		463	407	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121791	2121792	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs137854144	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	90	397	0	ENST00000219476.3:c.1959_1960del	p.Gly654LeufsTer2	p.G654Lfs*2	ENST00000219476	NM_000548.3	651	ccAGag/ccag	19/42	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.44	2		397	342	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216477	108216477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587782558	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	35	376	0	ENST00000278616.4:c.8432del	p.Lys2811SerfsTer46	p.K2811Sfs*46	ENST00000278616	NM_000051.3	2809	cAa/ca	58/63	1	2	FACETS	0.707	0.584	0.843	0.707	0.584	0.843	SUBCLONAL	1	TRUE	1	0.44	2		376	225	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357575	70357575	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	46	463	0	ENST00000374080.3:c.5827-1G>T		p.X1943_splice	ENST00000374080		1943			1	2	FACETS	0.5	0.422	0.587	0.5	0.422	0.587	SUBCLONAL	1	TRUE	1	0.44	2		463	418	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	43	386	2	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	0.182504924995863	0	FACETS	0.355	0.298	0.418			1	INDETERMINATE	1	TRUE	0	0.44	0		388	308	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	10	393	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.104	0.07	0.148	0.104	0.07	0.148	SUBCLONAL	1	TRUE	1	0.44	2		393	435	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742463	17742463	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	28	351	0	ENST00000250003.3:c.650del	p.Pro217ArgfsTer33	p.P217Rfs*33	ENST00000250003	NM_002478.4	215	ggC/gg	2/3	1	2	FACETS	0.386	0.308	0.474	0.386	0.308	0.474	SUBCLONAL	1	TRUE	1	0.44	2		351	330	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	21	206	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.612	0.475	0.768	0.612	0.475	0.768	SUBCLONAL	1	TRUE	1	0.44	2		206	156	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577138	7577138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780075	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	86	355	0	ENST00000269305.4:c.800G>A	p.Arg267Gln	p.R267Q	ENST00000269305	NM_001126112.2	267	cGg/cAg	8/11	0.146650630621896	3	FACETS	1	0.963	1	0.598	0.532	0.667	INDETERMINATE	1	TRUE	1	0.44	3		355	399	SUCCESS
APC	324	MSKCC	GRCh37	5	112173830	112173831	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	82	421	0	ENST00000257430.4:c.2544dup	p.Asp849ArgfsTer2	p.D849Rfs*2	ENST00000257430	NM_000038.5	847	gaa/gAaa	16/16	1	2	FACETS	0.978	0.868	1	0.978	0.868	1	CLONAL	1	TRUE	1	0.44	2		421	381	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	78	527	2	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	0.793	0.7	0.893	0.793	0.7	0.893	SUBCLONAL	1	TRUE	1	0.44	2		529	447	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921737	111921737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1170116948	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	79	321	0	ENST00000393256.3:c.526G>A	p.Glu176Lys	p.E176K	ENST00000393256	NM_006538.4	176	Gaa/Aaa	4/4	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.44	2		321	337	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	46	487	2	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	0.466	0.392	0.546	0.466	0.392	0.546	SUBCLONAL	1	TRUE	1	0.44	2		489	449	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602496	10602496	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750532889	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	133	421	0	ENST00000171111.5:c.1082C>T	p.Pro361Leu	p.P361L	ENST00000171111	NM_203500.1	361	cCg/cTg	3/6	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.44	2		421	476	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	109	319	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.44	2		325	357	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542110	187542110	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	49	487	1	ENST00000441802.2:c.5630del	p.Pro1877LeufsTer20	p.P1877Lfs*20	ENST00000441802	NM_005245.3	1877	cCt/ct	10/27	1	2	FACETS	0.528	0.448	0.616	0.528	0.448	0.616	SUBCLONAL	1	TRUE	1	0.44	2		488	422	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856617	111856617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1364785726	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	49	321	0	ENST00000341259.2:c.668C>T	p.Ala223Val	p.A223V	ENST00000341259	NM_005475.2	223	gCg/gTg	2/8	1	2	FACETS	0.669	0.569	0.778	0.669	0.569	0.778	SUBCLONAL	1	TRUE	1	0.44	2		321	333	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936518	49936518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867261592	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	57	516	0	ENST00000296474.3:c.1409G>A	p.Arg470His	p.R470H	ENST00000296474	NM_002447.2	470	cGt/cAt	2/20	1	2	FACETS	0.541	0.465	0.624	0.541	0.465	0.624	SUBCLONAL	1	TRUE	1	0.44	2		516	479	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656969	47656969	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779075	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	100	312	0	ENST00000233146.2:c.1165C>T	p.Arg389Ter	p.R389*	ENST00000233146	NM_000251.2	389	Cga/Tga	7/16	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.44	2		312	355	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149516607	149516607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148272095	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	112	362	1	ENST00000261799.4:c.4C>T	p.Arg2Trp	p.R2W	ENST00000261799	NM_002609.3	2	Cgg/Tgg	2/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.44	2		363	405	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67646013	67646014	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs1470210640	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	33	366	3	ENST00000264010.4:c.950_951del	p.Thr317ArgfsTer91	p.T317Rfs*91	ENST00000264010	NM_006565.3	314	aAC/a	4/12	1	2	FACETS	0.384	0.312	0.464	0.384	0.312	0.464	SUBCLONAL	1	TRUE	1	0.44	2		369	391	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	90	177	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.979	0.874	1	0.979	0.874	1	CLONAL	1	TRUE	1	0.44	2		178	418	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	55	625	0	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	0.511	0.438	0.592	0.511	0.438	0.592	SUBCLONAL	1	TRUE	1	0.44	2		625	489	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209593	98209593	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	41	410	1	ENST00000331920.6:c.3945del	p.Tyr1316ThrfsTer56	p.Y1316Tfs*56	ENST00000331920	NM_000264.3	1315	ccC/cc	23/24	1	2	FACETS	0.508	0.424	0.601	0.508	0.424	0.601	SUBCLONAL	1	TRUE	1	0.44	2		411	367	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652397	48652397	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	40	439	0	ENST00000376670.3:c.1073del	p.Pro358GlnfsTer74	p.P358Qfs*74	ENST00000376670	NM_002049.3	356	ggC/gg	6/6	1	2	FACETS	0.541	0.451	0.641	0.541	0.451	0.641	SUBCLONAL	1	TRUE	1	0.44	2		439	336	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717777	89717777	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs786204873	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	32	256	0	ENST00000371953.3:c.801+1G>A		p.X267_splice	ENST00000371953	NM_000314.4	267			1	2	FACETS	0.496	0.404	0.6	0.496	0.404	0.6	SUBCLONAL	1	TRUE	1	0.44	2		256	293	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27217701	27217701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772600804	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	82	310	0	ENST00000380036.4:c.3007C>T	p.Arg1003Cys	p.R1003C	ENST00000380036	NM_000459.3	1003	Cgc/Tgc	19/23	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.44	2		310	311	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989591	212989592	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1553563398	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	38	342	1	ENST00000342788.4:c.119_120del	p.Ser40Ter	p.S40*	ENST00000342788	NM_005235.2	40	tCT/t	2/28	1	2	FACETS	0.545	0.452	0.648	0.545	0.452	0.648	SUBCLONAL	1	TRUE	1	0.44	2		343	317	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11293546	11293546	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	36	314	0	ENST00000361445.4:c.2332-2A>G		p.X778_splice	ENST00000361445	NM_004958.3	778			1	2	FACETS	0.508	0.419	0.608	0.508	0.419	0.608	SUBCLONAL	1	TRUE	1	0.44	2		314	322	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303200	15303200	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775836288	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	94	447	0	ENST00000263388.2:c.328C>T	p.Arg110Cys	p.R110C	ENST00000263388	NM_000435.2	110	Cgt/Tgt	3/33	1	2	FACETS	0.989	0.885	1	0.989	0.885	1	CLONAL	1	TRUE	1	0.44	2		447	432	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515136	148515136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	37	393	1	ENST00000320356.2:c.1073G>A	p.Arg358His	p.R358H	ENST00000320356	NM_004456.4	358	cGc/cAc	10/20	1	2	FACETS	0.438	0.361	0.523	0.438	0.361	0.523	SUBCLONAL	1	TRUE	1	0.44	2		394	384	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445203	49445203	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	49	574	1	ENST00000301067.7:c.2263del	p.Arg755GlyfsTer175	p.R755Gfs*175	ENST00000301067	NM_003482.3	755	Cgg/gg	10/54	1	2	FACETS	0.409	0.346	0.479	0.409	0.346	0.479	SUBCLONAL	1	TRUE	1	0.44	2		575	544	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729609	41729609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	52	519	0	ENST00000242208.4:c.920G>A	p.Arg307Gln	p.R307Q	ENST00000242208	NM_002192.2	307	cGg/cAg	3/3	1	2	FACETS	0.567	0.484	0.658	0.567	0.484	0.658	SUBCLONAL	1	TRUE	1	0.44	2		519	417	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528284	157528284	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs749055122	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	48	487	0	ENST00000346085.5:c.6013del	p.Val2005TrpfsTer16	p.V2005Wfs*16	ENST00000346085	NM_020732.3	2003	aaG/aa	20/20	1	2	FACETS	0.488	0.413	0.571	0.488	0.413	0.571	SUBCLONAL	1	TRUE	1	0.44	2		487	447	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482363	56482363	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	103	390	0	ENST00000267101.3:c.911C>T	p.Ala304Val	p.A304V	ENST00000267101	NM_001982.3	304	gCc/gTc	8/28	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.44	2		390	446	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934426	39934426	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766556436	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	94	328	0	ENST00000378444.4:c.173C>T	p.Ala58Val	p.A58V	ENST00000378444	NM_001123385.1	58	gCg/gTg	4/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.44	2		328	362	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106162508	106162508	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	33	280	0	ENST00000380013.4:c.3426del	p.Asp1143MetfsTer9	p.D1143Mfs*9	ENST00000380013	NM_001127208.2	1141	gAa/ga	4/11	1	2	FACETS	0.543	0.444	0.654	0.543	0.444	0.654	SUBCLONAL	1	TRUE	1	0.44	2		280	276	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012710	36012710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1228673150	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	81	392	1	ENST00000358208.4:c.154G>A	p.Ala52Thr	p.A52T	ENST00000358208		52	Gcg/Acg	2/12	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.44	2		393	327	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246943	10246943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749413587	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	103	429	0	ENST00000340748.4:c.4462G>A	p.Ala1488Thr	p.A1488T	ENST00000340748		1488	Gca/Aca	37/40	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.44	2		429	414	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620140	21620140	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767021401	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	97	393	0	ENST00000382592.4:c.26C>T	p.Thr9Met	p.T9M	ENST00000382592	NM_014572.2	9	aCg/aTg	2/8	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.44	2		393	402	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276387	115276387	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779453730	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	111	350	0	ENST00000438362.2:c.941C>T	p.Thr314Ile	p.T314I	ENST00000438362	NM_001242891.1	314	aCc/aTc	9/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.44	2		350	411	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776208	135776208	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1564475110	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	119	388	0	ENST00000298552.3:c.2519C>T	p.Ser840Leu	p.S840L	ENST00000298552	NM_001162426.1	840	tCg/tTg	20/23	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.44	2		388	404	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955965	55955965	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754208569	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	42	358	0	ENST00000263923.4:c.3197G>A	p.Arg1066His	p.R1066H	ENST00000263923	NM_002253.2	1066	cGc/cAc	24/30	1	2	FACETS	0.57	0.477	0.672	0.57	0.477	0.672	SUBCLONAL	1	TRUE	1	0.44	2		358	335	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391949	139391949	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	58	445	0	ENST00000277541.6:c.6242T>C	p.Leu2081Pro	p.L2081P	ENST00000277541	NM_017617.3	2081	cTg/cCg	34/34	1	2	FACETS	0.62	0.534	0.713	0.62	0.534	0.713	SUBCLONAL	1	TRUE	1	0.44	2		445	425	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	52	276	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.872	0.749	1	0.872	0.749	1	CLONAL	1	TRUE	1	0.44	2		276	271	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490604	56490604	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373831196	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	94	409	0	ENST00000267101.3:c.2248C>T	p.Arg750Trp	p.R750W	ENST00000267101	NM_001982.3	750	Cgg/Tgg	19/28	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.44	2		409	398	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097624	11097625	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1165714406	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	47	421	0	ENST00000358026.2:c.810dup	p.Gly271ArgfsTer16	p.G271Rfs*16	ENST00000358026	NM_001128849.1	268	-/C	5/36	1	2	FACETS	0.522	0.441	0.611	0.522	0.441	0.611	SUBCLONAL	1	TRUE	1	0.44	2		421	409	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10796810	10796811	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1564972898	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	34	381	0	ENST00000361367.2:c.2949dup	p.Arg984ThrfsTer35	p.R984Tfs*35	ENST00000361367	NM_014633.3	981	cca/ccAa	23/25	1	2	FACETS	0.376	0.307	0.454	0.376	0.307	0.454	SUBCLONAL	1	TRUE	1	0.44	2		381	411	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273925	18273925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766254350	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	53	428	0	ENST00000222254.8:c.1258C>T	p.Arg420Trp	p.R420W	ENST00000222254	NM_005027.3	420	Cgg/Tgg	10/16	1	2	FACETS	0.579	0.495	0.671	0.579	0.495	0.671	SUBCLONAL	1	TRUE	1	0.44	2		428	416	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564558	86564558	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	37	471	0	ENST00000274376.6:c.290G>C	p.Gly97Ala	p.G97A	ENST00000274376	NM_002890.2	97	gGt/gCt	1/25	1	2	FACETS	0.388	0.319	0.464	0.388	0.319	0.464	SUBCLONAL	1	TRUE	1	0.44	2		471	434	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005395	42005395	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	59	441	0	ENST00000219905.7:c.3134del	p.Pro1045LeufsTer17	p.P1045Lfs*17	ENST00000219905	NM_001164273.1	1044	gCc/gc	9/24	1	2	FACETS	0.567	0.489	0.652	0.567	0.489	0.652	SUBCLONAL	1	TRUE	1	0.44	2		441	473	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104377163	104377163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1427876079	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	60	416	0	ENST00000369902.3:c.1274C>T	p.Ala425Val	p.A425V	ENST00000369902	NM_016169.3	425	gCg/gTg	10/12	1	2	FACETS	0.672	0.581	0.77	0.672	0.581	0.77	SUBCLONAL	1	TRUE	1	0.44	2		416	406	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631216	176631216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	139	453	0	ENST00000439151.2:c.1159G>A	p.Glu387Lys	p.E387K	ENST00000439151	NM_022455.4	387	Gaa/Aaa	4/23	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.44	2		453	542	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166455	118166456	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	95	463	0	ENST00000369448.3:c.969dup	p.His324AlafsTer2	p.H324Afs*2	ENST00000369448	NM_017709.3	322	atg/atGg	2/2	1	2	FACETS	0.979	0.877	1	0.979	0.877	1	CLONAL	1	TRUE	1	0.44	2		463	441	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540997	187540997	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367776554	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	50	512	0	ENST00000441802.2:c.6743C>T	p.Pro2248Leu	p.P2248L	ENST00000441802	NM_005245.3	2248	cCg/cTg	10/27	1	2	FACETS	0.474	0.403	0.553	0.474	0.403	0.553	SUBCLONAL	1	TRUE	1	0.44	2		512	479	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942192	71942192	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1006478277	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	100	430	0	ENST00000298229.2:c.1456C>T	p.Arg486Cys	p.R486C	ENST00000298229	NM_001567.3	486	Cgc/Tgc	12/28	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.44	2		430	424	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582126	52582126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	58	367	0	ENST00000394830.3:c.4702C>T	p.Arg1568Trp	p.R1568W	ENST00000394830	NM_018313.4	1568	Cgg/Tgg	30/30	1	2	FACETS	0.622	0.536	0.715	0.622	0.536	0.715	SUBCLONAL	1	TRUE	1	0.44	2		367	424	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137528098	137528098	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	30	273	0	ENST00000367739.4:c.200+2T>C		p.X67_splice	ENST00000367739	NM_000416.2	67			1	2	FACETS	0.524	0.424	0.637	0.524	0.424	0.637	SUBCLONAL	1	TRUE	1	0.44	2		273	260	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170804	11170804	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1306144699	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	83	392	0	ENST00000358026.2:c.4948C>T	p.Arg1650Ter	p.R1650*	ENST00000358026	NM_001128849.1	1650	Cga/Tga	35/36	1	2	FACETS	0.962	0.855	1	0.962	0.855	1	CLONAL	1	TRUE	1	0.44	2		392	392	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324092	31324092	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs151341248	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	19	186	0	ENST00000412585.2:c.471G>A	p.Trp157Ter	p.W157*	ENST00000412585	NM_005514.6	157	tgG/tgA	3/8	1	2	FACETS	0.499	0.381	0.636	0.499	0.381	0.636	SUBCLONAL	1	TRUE	1	0.44	2		186	173	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170754	11170754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1484835507	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	35	401	0	ENST00000358026.2:c.4898G>A	p.Arg1633Gln	p.R1633Q	ENST00000358026	NM_001128849.1	1633	cGg/cAg	35/36	1	2	FACETS	0.39	0.319	0.469	0.39	0.319	0.469	SUBCLONAL	1	TRUE	1	0.44	2		401	408	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864565	57864565	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs974867444	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	116	475	0	ENST00000228682.2:c.2042C>T	p.Pro681Leu	p.P681L	ENST00000228682	NM_005269.2	681	cCa/cTa	12/12	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.44	2		475	479	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430372	78430372	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	75	415	0	ENST00000370768.2:c.796A>G	p.Asn266Asp	p.N266D	ENST00000370768	NM_003902.3	266	Aat/Gat	10/20	1	2	FACETS	0.84	0.739	0.946	0.84	0.739	0.946	CLONAL	1	TRUE	1	0.44	2		415	406	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119666194	119666194	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	46	300	0	ENST00000316626.5:c.287G>A	p.Arg96Gln	p.R96Q	ENST00000316626		96	cGa/cAa	3/12	1	2	FACETS	0.777	0.659	0.906	0.777	0.659	0.906	CLONAL	1	TRUE	1	0.44	2		300	269	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685261	86685261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751563679	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	49	345	0	ENST00000274376.6:c.2977C>T	p.Arg993Cys	p.R993C	ENST00000274376	NM_002890.2	993	Cgt/Tgt	24/25	1	2	FACETS	0.635	0.539	0.738	0.635	0.539	0.738	SUBCLONAL	1	TRUE	1	0.44	2		345	351	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582301	119582301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759476802	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	51	412	0	ENST00000316626.5:c.1100G>A	p.Arg367Gln	p.R367Q	ENST00000316626		367	cGa/cAa	10/12	1	2	FACETS	0.599	0.511	0.695	0.599	0.511	0.695	SUBCLONAL	1	TRUE	1	0.44	2		412	387	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128848638	128848638	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1029412439	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	75	334	0	ENST00000249373.3:c.1303G>A	p.Gly435Arg	p.G435R	ENST00000249373	NM_005631.4	435	Ggg/Agg	7/12	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.44	2		334	331	SUCCESS
APC	324	MSKCC	GRCh37	5	112175430	112175430	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	69	394	0	ENST00000257430.4:c.4142del	p.Pro1381HisfsTer34	p.P1381Hfs*34	ENST00000257430	NM_000038.5	1380	aCc/ac	16/16	1	2	FACETS	0.802	0.702	0.909	0.802	0.702	0.909	CLONAL	1	TRUE	1	0.44	2		394	391	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245031	41245031	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	58	455	0	ENST00000357654.3:c.2517del	p.His839GlnfsTer7	p.H839Qfs*7	ENST00000357654	NM_007294.3	839	caC/ca	10/23	1	2	FACETS	0.587	0.505	0.676	0.587	0.505	0.676	SUBCLONAL	1	TRUE	1	0.44	2		455	449	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435307	110435307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1199525698	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	40	520	0	ENST00000375856.3:c.3094C>T	p.Pro1032Ser	p.P1032S	ENST00000375856	NM_003749.2	1032	Ccg/Tcg	1/2	1	2	FACETS	0.476	0.396	0.565	0.476	0.396	0.565	SUBCLONAL	1	TRUE	1	0.44	2		520	382	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250212	133250212	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	56	423	0	ENST00000320574.5:c.1308del	p.Val437TrpfsTer3	p.V437Wfs*3	ENST00000320574	NM_006231.2	436	ccC/cc	13/49	1	2	FACETS	0.692	0.595	0.796	0.692	0.595	0.796	SUBCLONAL	1	TRUE	1	0.44	2		423	368	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915785	112915785	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	59	383	0	ENST00000351677.2:c.1058T>C	p.Ile353Thr	p.I353T	ENST00000351677	NM_002834.3	353	aTt/aCt	9/16	1	2	FACETS	0.653	0.563	0.749	0.653	0.563	0.749	SUBCLONAL	1	TRUE	1	0.44	2		383	411	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151868359	151868359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1026459564	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	54	331	0	ENST00000262189.6:c.9443C>T	p.Ala3148Val	p.A3148V	ENST00000262189	NM_170606.2	3148	gCc/gTc	40/59	1	2	FACETS	0.625	0.535	0.722	0.625	0.535	0.722	SUBCLONAL	1	TRUE	1	0.44	2		331	393	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275228	41275228	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	60	408	0	ENST00000349496.5:c.1394T>C	p.Ile465Thr	p.I465T	ENST00000349496	NM_001904.3	465	aTc/aCc	9/15	1	2	FACETS	0.626	0.54	0.718	0.626	0.54	0.718	SUBCLONAL	1	TRUE	1	0.44	2		408	436	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231340	46231340	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	79	342	0	ENST00000334344.6:c.1180T>C	p.Tyr394His	p.Y394H	ENST00000334344	NM_152641.2	394	Tat/Cat	10/21	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.44	2		342	325	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941249	71941249	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769322084	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	68	562	0	ENST00000298229.2:c.1024C>T	p.Arg342Trp	p.R342W	ENST00000298229	NM_001567.3	342	Cgg/Tgg	9/28	1	2	FACETS	0.659	0.575	0.75	0.659	0.575	0.75	SUBCLONAL	1	TRUE	1	0.44	2		562	469	SUCCESS
REL	5966	MSKCC	GRCh37	2	61144114	61144114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	55	320	0	ENST00000295025.8:c.497C>T	p.Ala166Val	p.A166V	ENST00000295025	NM_002908.2	166	gCt/gTt	5/11	1	2	FACETS	0.779	0.67	0.896	0.779	0.67	0.896	SUBCLONAL	1	TRUE	1	0.44	2		320	321	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679638	33679638	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1322820152	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	47	449	0	ENST00000308377.4:c.2443A>G	p.Thr815Ala	p.T815A	ENST00000308377	NM_152270.3	815	Acc/Gcc	5/5	1	2	FACETS	0.503	0.425	0.588	0.503	0.425	0.588	SUBCLONAL	1	TRUE	1	0.44	2		449	425	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858180	40858180	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747602257	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	59	334	0	ENST00000428826.2:c.1684C>T	p.Arg562Cys	p.R562C	ENST00000428826		562	Cgc/Tgc	16/21	1	2	FACETS	0.646	0.558	0.742	0.646	0.558	0.742	SUBCLONAL	1	TRUE	1	0.44	2		334	415	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40447725	40447725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756814024	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	130	442	0	ENST00000345506.4:c.464C>T	p.Thr155Met	p.T155M	ENST00000345506	NM_003152.3	155	aCg/aTg	6/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.44	2		442	475	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082866	16082866	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	25	230	0	ENST00000281043.3:c.683del	p.Pro228GlnfsTer33	p.P228Qfs*33	ENST00000281043	NM_005378.4	227	gCc/gc	2/3	1	2	FACETS	0.563	0.446	0.695	0.563	0.446	0.695	SUBCLONAL	1	TRUE	1	0.44	2		230	202	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	188	789	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.885	0.826	0.945	1	0.993	1	CLONAL	2	TRUE	1	0.445364023991939	2		790	477	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	100	418	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.445364023991939	2		418	379	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	103	525	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.445364023991939	2		527	431	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	31	206	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.898	0.736	1	0.898	0.736	1	CLONAL	1	TRUE	1	0.445364023991939	2		206	155	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	104	526	0	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	1	2	FACETS	0.862	0.774	0.954	0.862	0.774	0.954	CLONAL	1	TRUE	1	0.445364023991939	2		526	542	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	83	544	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.859	0.762	0.962	0.859	0.762	0.962	CLONAL	1	TRUE	1	0.445364023991939	2		544	434	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	93	545	3	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.999	0.894	1	0.999	0.894	1	CLONAL	1	TRUE	1	0.445364023991939	2		548	418	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	106	390	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.445364023991939	2		392	410	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201874	152201874	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753014570	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	21	366	0	ENST00000206249.3:c.728G>A	p.Arg243His	p.R243H	ENST00000206249	NM_000125.3	243	cGt/cAt	3/8	1	2	FACETS	0.245	0.188	0.311	0.245	0.188	0.311	SUBCLONAL	1	TRUE	1	0.445364023991939	2		366	385	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	42	191	1	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	0.92	0.777	1	0.92	0.777	1	CLONAL	1	TRUE	1	0.445364023991939	2		192	205	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795103	242795104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768249210	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	77	524	1	ENST00000334409.5:c.105dup	p.Thr36HisfsTer70	p.T36Hfs*70	ENST00000334409	NM_005018.2	35	-/C	2/5	1	2	FACETS	0.758	0.668	0.855	0.758	0.668	0.855	SUBCLONAL	1	TRUE	1	0.445364023991939	2		525	456	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	88	383	2	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.445364023991939	2		385	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138729528	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	134	556	0	ENST00000269305.4:c.523C>T	p.Arg175Cys	p.R175C	ENST00000269305	NM_001126112.2	175	Cgc/Tgc	5/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.445364023991939	2		556	525	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032354	42032354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201349807	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	96	457	0	ENST00000219905.7:c.4538G>A	p.Arg1513His	p.R1513H	ENST00000219905	NM_001164273.1	1513	cGc/cAc	14/24	1	2	FACETS	0.998	0.894	1	0.998	0.894	1	CLONAL	1	TRUE	1	0.445364023991939	2		457	432	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370957	55370957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	79	398	0	ENST00000297316.4:c.259G>A	p.Ala87Thr	p.A87T	ENST00000297316	NM_022454.3	87	Gcg/Acg	1/2	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.445364023991939	2		398	312	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847275	68847277	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	103	415	0	ENST00000261769.5:c.1199_1201del	p.Asp400del	p.D400del	ENST00000261769	NM_004360.3	399	acTGAt/act	9/16	1	2	FACETS	0.962	0.865	1	0.962	0.865	1	CLONAL	1	TRUE	1	0.445364023991939	2		415	481	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246532	41246532	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357569	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	104	542	1	ENST00000357654.3:c.1016del	p.Lys339ArgfsTer2	p.K339Rfs*2	ENST00000357654	NM_007294.3	339	aAg/ag	10/23	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.445364023991939	2		543	451	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551951	150551952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs750805885	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	73	447	1	ENST00000369026.2:c.55dup	p.Ala19GlyfsTer91	p.A19Gfs*91	ENST00000369026	NM_021960.4	19	gcc/gGcc	1/3	1	2	FACETS	0.788	0.692	0.89	0.788	0.692	0.89	SUBCLONAL	1	TRUE	1	0.445364023991939	2		448	416	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277508	142277508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759350161	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	131	348	0	ENST00000350721.4:c.1843G>A	p.Ala615Thr	p.A615T	ENST00000350721	NM_001184.3	615	Gct/Act	8/47	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.445364023991939	2		348	460	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743987	41743987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1306116384	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	117	563	0	ENST00000301178.4:c.922C>T	p.Arg308Cys	p.R308C	ENST00000301178	NM_021913.4	308	Cgc/Tgc	7/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.445364023991939	2		563	472	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294664	1294665	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1060502990	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	84	446	1	ENST00000310581.5:c.336dup	p.Glu113ArgfsTer79	p.E113Rfs*79	ENST00000310581	NM_198253.2	112	-/C	2/16	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.445364023991939	2		447	367	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638326	117638326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752085591	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	98	423	0	ENST00000368508.3:c.6115C>T	p.Arg2039Cys	p.R2039C	ENST00000368508	NM_002944.2	2039	Cgt/Tgt	38/43	1	2	FACETS	0.969	0.869	1	0.969	0.869	1	CLONAL	1	TRUE	1	0.445364023991939	2		423	454	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224099	36224099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	64	361	0	ENST00000222270.7:c.6649C>T	p.Gln2217Ter	p.Q2217*	ENST00000222270	NM_014727.1	2217	Cag/Tag	28/37	1	2	FACETS	0.927	0.809	1	0.927	0.809	1	CLONAL	1	TRUE	1	0.445364023991939	2		361	310	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643536	38643536	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373477920	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	110	471	0	ENST00000299084.4:c.1006G>A	p.Val336Ile	p.V336I	ENST00000299084	NM_152594.2	336	Gta/Ata	7/7	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.445364023991939	2		471	485	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958189	2958189	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1211022340	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	79	379	0	ENST00000396946.4:c.2543G>A	p.Arg848His	p.R848H	ENST00000396946	NM_032415.4	848	cGc/cAc	19/25	1	2	FACETS	0.885	0.782	0.993	0.885	0.782	0.993	CLONAL	1	TRUE	1	0.445364023991939	2		379	401	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411772	63411772	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	90	289	0	ENST00000330258.3:c.1395del	p.Asn466IlefsTer75	p.N466Ifs*75	ENST00000330258	NM_152424.3	465	ccC/cc	2/2	1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.445364023991939	1		289	228	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429012	47429012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754787460	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	112	248	0	ENST00000377045.4:c.1375G>A	p.Gly459Arg	p.G459R	ENST00000377045	NM_001654.4	459	Ggg/Agg	13/16	1	1	FACETS	0.791	0.726	0.857	1	0.988	1	SUBCLONAL	2	TRUE	0	0.445364023991939	1		248	247	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553506	106553506	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	79	463	0	ENST00000369096.4:c.1471G>A	p.Ala491Thr	p.A491T	ENST00000369096	NM_001198.3	491	Gcg/Acg	5/7	1	2	FACETS	0.903	0.799	1	0.903	0.799	1	CLONAL	1	TRUE	1	0.445364023991939	2		463	393	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732969	30732969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893810	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	120	492	0	ENST00000295754.5:c.1582C>T	p.Arg528Cys	p.R528C	ENST00000295754	NM_003242.5	528	Cgt/Tgt	7/7	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.445364023991939	2		492	472	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1688567	1688568	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs746550458	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	88	437	3	ENST00000378625.1:c.757dup	p.Ala253GlyfsTer45	p.A253Gfs*45	ENST00000378625	NM_001198994.1	253	gcc/gGcc	6/14	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.445364023991939	2		440	376	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981465	63981465	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	109	556	0	ENST00000398590.3:c.1967C>A	p.Pro656His	p.P656H	ENST00000398590	NM_001177387.1	656	cCc/cAc	12/14	1	2	FACETS	0.884	0.796	0.976	0.884	0.796	0.976	CLONAL	1	TRUE	1	0.445364023991939	2		556	554	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969983	161969983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	100	356	0	ENST00000366898.1:c.986del	p.Gly329AlafsTer106	p.G329Afs*106	ENST00000366898	NM_004562.2	329	gGc/gc	9/12	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.445364023991939	2		356	355	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223789	53223789	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	94	266	0	ENST00000375401.3:c.3570T>G	p.Cys1190Trp	p.C1190W	ENST00000375401	NM_004187.3	1190	tgT/tgG	23/26	1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.445364023991939	1		266	241	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227878	55227878	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	98	395	0	ENST00000275493.2:c.1345G>T	p.Gly449Ter	p.G449*	ENST00000275493	NM_005228.3	449	Gga/Tga	12/28	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.445364023991939	2		395	415	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817509	39817509	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	86	465	0	ENST00000288319.7:c.54G>C	p.Leu18Phe	p.L18F	ENST00000288319	NM_182918.3	18	ttG/ttC	2/10	0.445364023991939	1	FACETS	0.839	0.748	0.934	0.839	0.748	0.934	CLONAL	1	TRUE	0	0.445364023991939	1		465	358	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209235	36209236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCTGCGT	novel	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	76	563	0	ENST00000222270.7:c.317_324dup	p.Pro109AlafsTer61	p.P109Afs*61	ENST00000222270	NM_014727.1	105	-/GGCTGCGT	1/37	1	2	FACETS	0.803	0.707	0.905	0.803	0.707	0.905	CLONAL	1	TRUE	1	0.445364023991939	2		563	425	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214359	55214359	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	111	399	0	ENST00000275493.2:c.485T>C	p.Ile162Thr	p.I162T	ENST00000275493	NM_005228.3	162	aTc/aCc	4/28	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.445364023991939	2		399	428	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991670	72991671	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	79	482	0	ENST00000268489.5:c.2374dup	p.Ala792GlyfsTer19	p.A792Gfs*19	ENST00000268489	NM_006885.3	792	gcc/gGcc	2/10	1	2	FACETS	0.896	0.792	1	0.896	0.792	1	CLONAL	1	TRUE	1	0.445364023991939	2		482	396	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544693	65544693	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	123	517	0	ENST00000358664.4:c.233del	p.Asn78ThrfsTer92	p.N78Tfs*92	ENST00000358664	NM_002382.4	78	aAc/ac	4/5	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.445364023991939	2		517	494	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970954	70970954	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	95	449	0	ENST00000276594.2:c.1307T>C	p.Leu436Pro	p.L436P	ENST00000276594	NM_024504.3	436	cTc/cCc	6/8	1	2	FACETS	0.997	0.893	1	0.997	0.893	1	CLONAL	1	TRUE	1	0.445364023991939	2		449	428	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80074641	80074641	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	97	325	0	ENST00000265081.6:c.2421G>A	p.Trp807Ter	p.W807*	ENST00000265081	NM_002439.4	807	tgG/tgA	17/24	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.445364023991939	2		325	379	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50773690	50773690	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	92	393	0	ENST00000307179.4:c.1236del	p.Lys412AsnfsTer12	p.K412Nfs*12	ENST00000307179		411	Aaa/aa	11/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.445364023991939	2		393	366	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527652	157527652	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	93	442	0	ENST00000346085.5:c.5381del	p.Lys1794ArgfsTer57	p.K1794Rfs*57	ENST00000346085	NM_020732.3	1793	Aaa/aa	20/20	1	2	FACETS	0.943	0.843	1	0.943	0.843	1	CLONAL	1	TRUE	1	0.445364023991939	2		442	443	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378284	225378286	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs770645060	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	93	320	0	ENST00000264414.4:c.609_611del	p.Glu203del	p.E203del	ENST00000264414	NM_003590.4	203	gaAGAt/gat	5/16	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.445364023991939	2		320	405	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42053984	42053984	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	84	412	0	ENST00000219905.7:c.7446A>G	p.Ile2482Met	p.I2482M	ENST00000219905	NM_001164273.1	2482	atA/atG	21/24	1	2	FACETS	0.943	0.838	1	0.943	0.838	1	CLONAL	1	TRUE	1	0.445364023991939	2		412	400	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917695	94917695	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	86	426	0	ENST00000536441.1:c.826A>G	p.Arg276Gly	p.R276G	ENST00000536441	NM_144665.3	276	Agg/Ggg	6/10	1	2	FACETS	0.928	0.826	1	0.928	0.826	1	CLONAL	1	TRUE	1	0.445364023991939	2		426	416	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799259	42799259	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1472447044	NA	P-0067405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	69	374	0	ENST00000575354.2:c.4746del	p.Pro1583LeufsTer37	p.P1583Lfs*37	ENST00000575354	NM_015125.3	1581	tcG/tc	20/20	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.445364023991939	2		374	275	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0067406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	338	477	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.586291767461437	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.586291767461437	2		477	502	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0067406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	14	314	4	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.148	0.106	0.198	0.148	0.106	0.198	SUBCLONAL	1	TRUE	1	0.586291767461437	2		318	323	SUCCESS
APC	324	MSKCC	GRCh37	5	112174502	112174502	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876659539	NA	P-0067406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	143	410	0	ENST00000257430.4:c.3211C>T	p.Gln1071Ter	p.Q1071*	ENST00000257430	NM_000038.5	1071	Caa/Taa	16/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.586291767461437	2		410	448	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435486	18435486	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	123	402	0	ENST00000266497.5:c.471G>T	p.Glu157Asp	p.E157D	ENST00000266497		157	gaG/gaT	1/31	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.586291767461437	2		402	389	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476364	88476364	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780933441	NA	P-0067406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	104	358	0	ENST00000360948.2:c.1768G>A	p.Glu590Lys	p.E590K	ENST00000360948	NM_001012338.2	590	Gag/Aag	15/19	1	2	FACETS	0.9	0.813	0.992	0.9	0.813	0.992	CLONAL	1	TRUE	1	0.586291767461437	2		358	394	SUCCESS
APC	324	MSKCC	GRCh37	5	112175206	112175206	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	115	414	0	ENST00000257430.4:c.3915del	p.Glu1306LysfsTer2	p.E1306Kfs*2	ENST00000257430	NM_000038.5	1305	gcA/gc	16/16	1	2	FACETS	0.962	0.873	1	0.962	0.873	1	CLONAL	1	TRUE	1	0.586291767461437	2		414	408	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911644	114911644	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0067406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	109	306	1	ENST00000543371.1:c.1161+1G>T		p.X387_splice	ENST00000543371	NM_001198531.1	387			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.586291767461437	2		307	328	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0067407-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	52	375	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.264133922967966	1	FACETS	0.97	0.838	1	0.97	0.838	1	CLONAL	1	TRUE	0	0.420945241718606	1		375	201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0067407-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	33	372	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.396827019123749	1	FACETS	0.884	0.732	1	0.884	0.732	1	CLONAL	1	TRUE	0	0.420945241718606	1		372	140	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040946	42040946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067407-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	37	474	0	ENST00000219905.7:c.5324G>T	p.Arg1775Ile	p.R1775I	ENST00000219905	NM_001164273.1	1775	aGa/aTa	16/24	0.184215646094579	0	FACETS	0.492	0.409	0.582			1	INDETERMINATE	1	TRUE	0	0.420945241718606	0		474	207	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112745407	112745407	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067407-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	52	274	0	ENST00000369452.4:c.725C>G	p.Thr242Arg	p.T242R	ENST00000369452	NM_007373.3	242	aCg/aGg	3/9	0.264133922967966	1	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	0	0.420945241718606	1		274	191	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163428	47163441	+	frameshift_variant	Frame_Shift_Del	DEL	ATTTCAAGAGAGTT	ATTTCAAGAGAGTT	-	novel	NA	P-0067407-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	45	408	0	ENST00000409792.3:c.2685_2698del	p.Thr896ArgfsTer15	p.T896Rfs*15	ENST00000409792	NM_014159.6	895	ctAACTCTCTTGAAATgc/ctgc	3/21	0.264133922967966	1	FACETS	0.771	0.655	0.896	0.771	0.655	0.896	SUBCLONAL	1	TRUE	0	0.420945241718606	1		408	219	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197819	123197819	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067407-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	22	140	0	ENST00000218089.9:c.1943A>G	p.Asn648Ser	p.N648S	ENST00000218089	NM_001042749.1	648	aAc/aGc	20/35	1	1	FACETS	0.581	0.455	0.724	0.581	0.455	0.724	SUBCLONAL	1	TRUE	0	0.420945241718606	1		140	142	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579378	7579378	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067408-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	462	463	0	ENST00000269305.4:c.309C>A	p.Tyr103Ter	p.Y103*	ENST00000269305	NM_001126112.2	103	taC/taA	4/11	0.894989357298762	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.902323177155007	2		463	507	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023019	150023019	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067408-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	378	371	0	ENST00000253339.5:c.244C>T	p.Arg82Ter	p.R82*	ENST00000253339		82	Cga/Tga	1/7	0.894989357298762	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.902323177155007	2		371	410	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861837	57861837	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs759838377	NA	P-0067408-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	193	449	1	ENST00000228682.2:c.1138C>T	p.Arg380Ter	p.R380*	ENST00000228682	NM_005269.2	380	Cga/Tga	10/12	0.898013355332625	3	FACETS	0.867	0.805	0.931	0.289	0.268	0.311	CLONAL	1	TRUE	0	0.902323177155007	3		450	716	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455188	29455188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1343280200	NA	P-0067408-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	343	411	1	ENST00000389048.3:c.2614G>A	p.Gly872Ser	p.G872S	ENST00000389048	NM_004304.4	872	Ggc/Agc	15/29	0.861735958442018	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.902323177155007	3		412	550	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29439402	29439402	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067408-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	363	377	0	ENST00000544604.2:c.617A>C	p.Gln206Pro	p.Q206P	ENST00000544604	NM_001206998.1	206	cAg/cCg	4/9	0.893649351919307	2	FACETS	0.991	0.969	1	0.991	0.969	1	CLONAL	2	TRUE	0	0.902323177155007	2		377	406	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146201	38146201	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067408-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	207	408	0	ENST00000317025.8:c.3305C>G	p.Pro1102Arg	p.P1102R	ENST00000317025	NM_023034.1	1102	cCa/cGa	19/24	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.902323177155007	2		408	450	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67624623	67624623	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067408-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	158	343	1	ENST00000272342.5:c.43A>G	p.Lys15Glu	p.K15E	ENST00000272342	NM_019002.3	15	Aaa/Gaa	1/6	0.861735958442018	3	FACETS	1	0.946	1	0.515	0.476	0.556	CLONAL	1	TRUE	1	0.902323177155007	3		344	493	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0067409-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	16	314	4	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.286	0.211	0.375	0.286	0.211	0.375	SUBCLONAL	1	TRUE	1	0.41	2		318	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0067409-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	23	494	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	1	2	FACETS	0.223	0.173	0.282	0.223	0.173	0.282	SUBCLONAL	1	TRUE	1	0.41	2		494	502	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067409-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	73	515	0	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	1	2	FACETS	0.716	0.628	0.811	0.716	0.628	0.811	SUBCLONAL	1	TRUE	1	0.41	2		515	497	SUCCESS
APC	324	MSKCC	GRCh37	5	112173374	112173374	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067409-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	23	471	0	ENST00000257430.4:c.2083C>T	p.Gln695Ter	p.Q695*	ENST00000257430	NM_000038.5	695	Cag/Tag	16/16	1	2	FACETS	0.275	0.214	0.346	0.275	0.214	0.346	SUBCLONAL	1	TRUE	1	0.41	2		471	408	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0067409-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	21	404	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.263	0.202	0.334	0.263	0.202	0.334	SUBCLONAL	1	TRUE	1	0.41	2		404	390	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	35	317	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		317	86	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099406	157099426	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAA	CAGCAGCAGCAGCAGCAGCAA	-	rs762617219	NA	P-0067410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	11	512	0	ENST00000346085.5:c.363_383del	p.Gln125_Gln131del	p.Q125_Q131del	ENST00000346085	NM_020732.3	115	CAGCAGCAGCAGCAGCAGCAA/-	1/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		512	212	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0067410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	74	613	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		613	207	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259649	89259649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	29	426	0	ENST00000336596.2:c.793G>A	p.Glu265Lys	p.E265K	ENST00000336596	NM_005233.5	265	Gaa/Aaa	3/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		426	338	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856345	45856345	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	47	377	0	ENST00000391945.4:c.1827C>G	p.Asp609Glu	p.D609E	ENST00000391945	NM_000400.3	609	gaC/gaG	19/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		377	168	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706940	117706940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	21	438	0	ENST00000368508.3:c.2210C>T	p.Ser737Leu	p.S737L	ENST00000368508	NM_002944.2	737	tCa/tTa	15/43	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		438	114	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939479	71939479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775305188	NA	P-0067410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	15	516	2	ENST00000298229.2:c.334G>A	p.Ala112Thr	p.A112T	ENST00000298229	NM_001567.3	112	Gcc/Acc	3/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		518	202	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859839	151859839	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	17	501	0	ENST00000262189.6:c.10823G>A	p.Arg3608Lys	p.R3608K	ENST00000262189	NM_170606.2	3608	aGa/aAa	43/59	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		501	159	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235887	108235887	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	38	443	0	ENST00000278616.4:c.8929G>T	p.Glu2977Ter	p.E2977*	ENST00000278616	NM_000051.3	2977	Gaa/Taa	62/63	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		443	124	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057916	27057916	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	14	465	0	ENST00000324856.7:c.1624C>T	p.Gln542Ter	p.Q542*	ENST00000324856	NM_006015.4	542	Cag/Tag	3/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		465	222	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061845	38061862	+	inframe_deletion	In_Frame_Del	DEL	CATGTAGGTGTTCATGGA	CATGTAGGTGTTCATGGA	-	novel	NA	P-0067410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	9	469	0	ENST00000250448.2:c.127_144del	p.Ser43_Met48del	p.S43_M48del	ENST00000250448	NM_004496.3	43	TCCATGAACACCTACATG/-	2/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		469	181	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923062	39923062	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	17	204	0	ENST00000378444.4:c.3646G>A	p.Glu1216Lys	p.E1216K	ENST00000378444	NM_001123385.1	1216	Gaa/Aaa	8/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		204	66	SUCCESS
APC	324	MSKCC	GRCh37	5	112179677	112179677	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	39	457	0	ENST00000257430.4:c.8386G>C	p.Asp2796His	p.D2796H	ENST00000257430	NM_000038.5	2796	Gat/Cat	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		457	158	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922825	44922826	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0067410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	32	208	0	ENST00000377967.4:c.1687_1688del	p.Pro563TrpfsTer17	p.P563Wfs*17	ENST00000377967	NM_021140.2	562	tgCCct/tgct	16/29	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		208	89	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051181	128051181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	80	417	0	ENST00000285398.2:c.142G>A	p.Glu48Lys	p.E48K	ENST00000285398	NM_000122.1	48	Gag/Aag	2/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		417	218	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43749805	43749805	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	46	469	1	ENST00000523873.1:c.658T>A	p.Leu220Ile	p.L220I	ENST00000523873		220	Tta/Ata	7/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		470	217	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828876	26828876	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	36	392	0	ENST00000381527.3:c.98G>C	p.Gly33Ala	p.G33A	ENST00000381527	NM_001260.1	33	gGt/gCt	1/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		392	202	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981112	201981112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	24	369	0	ENST00000359651.3:c.191C>T	p.Pro64Leu	p.P64L	ENST00000359651		64	cCc/cTc	2/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		369	185	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213932	36213932	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	10	472	0	ENST00000222270.7:c.2758T>C	p.Ser920Pro	p.S920P	ENST00000222270	NM_014727.1	920	Tca/Cca	6/37	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		472	171	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199810	108199810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	10	383	0	ENST00000278616.4:c.7152G>A	p.Met2384Ile	p.M2384I	ENST00000278616	NM_000051.3	2384	atG/atA	49/63	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		383	154	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259511	89259511	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	40	427	0	ENST00000336596.2:c.655G>C	p.Asp219His	p.D219H	ENST00000336596	NM_005233.5	219	Gac/Cac	3/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		427	381	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984795	72984795	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	49	382	0	ENST00000268489.5:c.2789T>A	p.Leu930Gln	p.L930Q	ENST00000268489	NM_006885.3	930	cTg/cAg	3/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		382	183	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267719	7267719	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	14	393	0	ENST00000302850.5:c.289G>C	p.Glu97Gln	p.E97Q	ENST00000302850	NM_000208.2	97	Gag/Cag	2/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		393	164	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415619	49415619	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	28	411	0	ENST00000301067.7:c.16558C>T	p.Gln5520Ter	p.Q5520*	ENST00000301067	NM_003482.3	5520	Cag/Tag	54/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		411	174	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95598909	95598909	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	27	360	0	ENST00000393063.1:c.250C>T	p.Gln84Ter	p.Q84*	ENST00000393063	NM_030621.3	84	Cag/Tag	4/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		360	164	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259138	89259138	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs369150999	NA	P-0067410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	25	424	0	ENST00000336596.2:c.282G>T	p.Lys94Asn	p.K94N	ENST00000336596	NM_005233.5	94	aaG/aaT	3/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		424	345	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349204	11349224	+	inframe_deletion	In_Frame_Del	DEL	CGCGGGGCACGGCCGCGGGCG	CGCGGGGCACGGCCGCGGGCG	-	rs757951209	NA	P-0067410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	13	416	0	ENST00000332029.2:c.112_132del	p.Arg38_Ala44del	p.R38_A44del	ENST00000332029	NM_003745.1	38	CGCCCGCGGCCGTGCCCCGCG/-	2/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		416	139	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259364	89259364	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	31	442	0	ENST00000336596.2:c.508G>C	p.Glu170Gln	p.E170Q	ENST00000336596	NM_005233.5	170	Gaa/Caa	3/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		442	427	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518254	103518254	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	31	382	0	ENST00000355739.4:c.2192T>G	p.Ile731Ser	p.I731S	ENST00000355739	NM_000123.3	731	aTt/aGt	9/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		382	174	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259232	89259232	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs982229155	NA	P-0067410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	24	432	0	ENST00000336596.2:c.376G>C	p.Glu126Gln	p.E126Q	ENST00000336596	NM_005233.5	126	Gag/Cag	3/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		432	313	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396286	396286	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	31	435	0	ENST00000262320.3:c.740G>A	p.Trp247Ter	p.W247*	ENST00000262320	NM_003502.3	247	tGg/tAg	2/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		435	143	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547849	41547849	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	12	349	0	ENST00000263253.7:c.2830G>A	p.Ala944Thr	p.A944T	ENST00000263253	NM_001429.3	944	Gct/Act	15/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		349	142	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941717	48941720	+	stop_gained	Nonsense_Mutation	ONP	CTTC	CTTC	TTTT	novel	NA	P-0067410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	25	310	0	ENST00000267163.4:c.1027_1030delinsTTTT	p.Leu343_Gln344delinsPheTer	p.L343_Q344delinsF*	ENST00000267163	NM_000321.2	343	CTTCag/TTTTag	10/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		310	96	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	113	789	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.285573468393669	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	2	TRUE	0	0.28	2		790	400	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	49	267	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.28	2		267	279	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	30	519	2	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.57	0.459	0.695	0.57	0.459	0.695	SUBCLONAL	1	TRUE	1	0.28	2		521	376	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	29	416	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.735	0.591	0.896	0.735	0.591	0.896	SUBCLONAL	1	TRUE	1	0.28	2		416	282	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	55	319	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.28	2		325	325	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67646013	67646014	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs1470210640	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	38	366	3	ENST00000264010.4:c.950_951del	p.Thr317ArgfsTer91	p.T317Rfs*91	ENST00000264010	NM_006565.3	314	aAC/a	4/12	1	2	FACETS	0.851	0.706	1	0.851	0.706	1	CLONAL	1	TRUE	1	0.28	2		369	319	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	56	545	3	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.28	2		548	331	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024505	16024505	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	51	401	0	ENST00000268712.3:c.1713del	p.Arg572GlufsTer18	p.R572Efs*18	ENST00000268712	NM_006311.3	571	ggG/gg	16/46	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.28	2		401	361	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	18	91	2	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	1	FACETS	1	0.806	1	1	0.806	1	CLONAL	1	TRUE	0	0.28	1		93	104	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308383	15308383	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	45	443	3	ENST00000263388.2:c.125del	p.Pro42LeufsTer194	p.P42Lfs*194	ENST00000263388	NM_000435.2	42	cCt/ct	2/33	1	2	FACETS	0.857	0.722	1	0.857	0.722	1	CLONAL	1	TRUE	1	0.28	2		446	375	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376626	8376626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772303653	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	32	326	0	ENST00000356435.5:c.4487G>A	p.Arg1496Gln	p.R1496Q	ENST00000356435		1496	cGa/cAa	27/35	1	2	FACETS	0.808	0.658	0.975	0.808	0.658	0.975	CLONAL	1	TRUE	1	0.28	2		326	283	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967566	26967566	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs369889152	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	43	365	0	ENST00000381527.3:c.709C>T	p.Arg237Ter	p.R237*	ENST00000381527	NM_001260.1	237	Cga/Tga	7/13	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.28	2		365	302	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100728	8100728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs771019738	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	28	436	5	ENST00000346208.3:c.708del	p.Ser237AlafsTer28	p.S237Afs*28	ENST00000346208		234	ttC/tt	3/6	1	2	FACETS	0.654	0.523	0.801	0.654	0.523	0.801	SUBCLONAL	1	TRUE	1	0.28	2		441	306	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223376	2223376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	46	467	0	ENST00000398665.3:c.3492del	p.Val1165CysfsTer8	p.V1165Cfs*8	ENST00000398665	NM_032482.2	1163	Ccc/cc	25/28	1	2	FACETS	0.876	0.74	1	0.876	0.74	1	CLONAL	1	TRUE	1	0.28	2		467	375	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764347	39764347	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	34	371	0	ENST00000288319.7:c.765del	p.Arg256GlyfsTer35	p.R256Gfs*35	ENST00000288319	NM_182918.3	255	ccC/cc	7/10	1	2	FACETS	0.662	0.541	0.797	0.662	0.541	0.797	SUBCLONAL	1	TRUE	1	0.28	2		371	367	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	51	418	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.28	2		418	333	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	38	414	1	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	0.887	0.736	1	0.887	0.736	1	CLONAL	1	TRUE	1	0.28	2		415	306	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	49	373	1	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.886	0.752	1	0.886	0.752	1	CLONAL	1	TRUE	1	0.28	2		374	395	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288710	15288710	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	27	322	0	ENST00000263388.2:c.4029del	p.Cys1344ValfsTer76	p.C1344Vfs*76	ENST00000263388	NM_000435.2	1343	ccC/cc	24/33	1	2	FACETS	0.936	0.75	1	0.936	0.75	1	CLONAL	1	TRUE	1	0.28	2		322	206	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781417	3781417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776549587	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	30	386	0	ENST00000262367.5:c.4948G>A	p.Val1650Ile	p.V1650I	ENST00000262367	NM_004380.2	1650	Gtc/Atc	30/31	1	2	FACETS	0.672	0.542	0.818	0.672	0.542	0.818	SUBCLONAL	1	TRUE	1	0.28	2		386	319	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119781	70119781	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1274036689	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	43	341	0	ENST00000245479.2:c.788del	p.Gly263AlafsTer16	p.G263Afs*16	ENST00000245479	NM_000346.3	261	gaG/ga	3/3	0.285573468393669	2	FACETS	1	0.943	1	0.64	0.54	0.749	CLONAL	1	TRUE	0	0.28	2		341	240	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	55	509	0	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	0.929	0.797	1	0.929	0.797	1	CLONAL	1	TRUE	1	0.28	2		509	423	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31025023	31025023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	53	411	0	ENST00000375687.4:c.4508C>T	p.Ser1503Leu	p.S1503L	ENST00000375687	NM_015338.5	1503	tCg/tTg	13/13	1	2	FACETS	0.999	0.855	1	0.999	0.855	1	CLONAL	1	TRUE	1	0.28	2		411	379	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729604	41729604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	30	444	0	ENST00000242208.4:c.925C>T	p.Arg309Trp	p.R309W	ENST00000242208	NM_002192.2	309	Cgg/Tgg	3/3	1	2	FACETS	0.611	0.492	0.744	0.611	0.492	0.744	SUBCLONAL	1	TRUE	1	0.28	2		444	351	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	62	342	4	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.28	2		346	429	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39629562	39629562	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	20	306	0	ENST00000262039.4:c.2260del	p.Thr754GlnfsTer7	p.T754Qfs*7	ENST00000262039	NM_002647.2	752	acA/ac	21/25	1	2	FACETS	0.533	0.408	0.679	0.533	0.408	0.679	SUBCLONAL	1	TRUE	1	0.28	2		306	268	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	38	397	2	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.848	0.704	1	0.848	0.704	1	CLONAL	1	TRUE	1	0.28	2		399	320	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348566	89348568	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs753054998	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	62	471	1	ENST00000301030.4:c.4382_4384del	p.Lys1461del	p.K1461del	ENST00000301030	NM_001256183.1	1461	aAGAga/aga	9/13	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.28	2		472	417	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626680	12626680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751232720	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	93	468	1	ENST00000251849.4:c.1609G>A	p.Val537Ile	p.V537I	ENST00000251849	NM_002880.3	537	Gta/Ata	15/17	1	2	FACETS	0.793	0.709	0.881	1	0.983	1	SUBCLONAL	2	TRUE	1	0.28	2		469	419	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372388	55372388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437921769	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	28	466	0	ENST00000297316.4:c.1078C>T	p.Arg360Cys	p.R360C	ENST00000297316	NM_022454.3	360	Cgc/Tgc	2/2	1	2	FACETS	0.69	0.552	0.845	0.69	0.552	0.845	SUBCLONAL	1	TRUE	1	0.28	2		466	290	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520087	106520087	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774448553	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	38	315	1	ENST00000359195.3:c.2515C>T	p.Arg839Cys	p.R839C	ENST00000359195	NM_002649.2	839	Cgc/Tgc	6/11	1	2	FACETS	0.998	0.829	1	0.998	0.829	1	CLONAL	1	TRUE	1	0.28	2		316	272	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450582	70450582	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150708897	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	42	375	2	ENST00000373644.4:c.5422G>A	p.Val1808Met	p.V1808M	ENST00000373644	NM_030625.2	1808	Gtg/Atg	12/12	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.28	2		377	287	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022499	12022499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200351280	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	57	488	0	ENST00000396373.4:c.605G>A	p.Arg202Gln	p.R202Q	ENST00000396373	NM_001987.4	202	cGg/cAg	5/8	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.28	2		488	374	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991949	72991949	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs753977275	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	41	497	4	ENST00000268489.5:c.2096del	p.Gly699AlafsTer125	p.G699Afs*125	ENST00000268489	NM_006885.3	699	gGc/gc	2/10	1	2	FACETS	0.957	0.801	1	0.957	0.801	1	CLONAL	1	TRUE	1	0.28	2		501	306	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222498	53222498	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782272528	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	51	206	0	ENST00000375401.3:c.4334G>A	p.Arg1445His	p.R1445H	ENST00000375401	NM_004187.3	1445	cGt/cAt	26/26	1	1	FACETS	1	0.892	1	1	0.978	1	CLONAL	2	TRUE	0	0.28	1		206	152	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752695	42752695	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1366176199	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	59	376	1	ENST00000222329.4:c.1569del	p.Leu525SerfsTer6	p.L525Sfs*6	ENST00000222329	NM_006494.2	523	ggG/gg	4/4	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.28	2		377	332	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883212	37883212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs566053951	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	54	385	0	ENST00000269571.5:c.3115G>A	p.Ala1039Thr	p.A1039T	ENST00000269571		1039	Gct/Act	25/27	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.28	2		385	326	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670255	134670255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1426484610	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	39	380	0	ENST00000398015.3:c.166C>T	p.Arg56Cys	p.R56C	ENST00000398015	NM_004441.4	56	Cgc/Tgc	3/16	0.3	1	FACETS	0.773	0.643	0.916	0.773	0.643	0.916	CLONAL	1	TRUE	0	0.28	1		380	310	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	44	422	0	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	0.988	0.833	1	0.988	0.833	1	CLONAL	1	TRUE	1	0.28	2		422	318	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927443	245927443	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	43	416	0	ENST00000388985.4:c.1085del	p.Phe362SerfsTer12	p.F362Sfs*12	ENST00000388985		362	tTc/tc	11/12	0.3	2	FACETS	0.817	0.685	0.962			1	CLONAL	1	TRUE	NA	0.28	2		416	376	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216189	36216189	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	49	581	0	ENST00000222270.7:c.3602del	p.Pro1201ArgfsTer154	p.P1201Rfs*154	ENST00000222270	NM_014727.1	1199	ggC/gg	11/37	1	2	FACETS	0.98	0.833	1	0.98	0.833	1	CLONAL	1	TRUE	1	0.28	2		581	357	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66779571	66779571	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773890369	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	50	346	1	ENST00000307102.5:c.901G>A	p.Gly301Arg	p.G301R	ENST00000307102	NM_002755.3	301	Gga/Aga	8/11	1	2	FACETS	0.96	0.817	1	0.96	0.817	1	CLONAL	1	TRUE	1	0.28	2		347	372	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660640	190660640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778185859	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	54	383	0	ENST00000441310.2:c.278G>A	p.Arg93His	p.R93H	ENST00000441310	NM_000534.4	93	cGt/cAt	3/13	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.28	2		383	373	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11227537	11227537	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	35	287	0	ENST00000361445.4:c.4291G>A	p.Gly1431Arg	p.G1431R	ENST00000361445	NM_004958.3	1431	Gga/Aga	29/58	1	2	FACETS	0.672	0.551	0.807	0.672	0.551	0.807	SUBCLONAL	1	TRUE	1	0.28	2		287	372	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522740	67522741	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	53	353	0	ENST00000274335.5:c.244dup	p.Ile82AsnfsTer24	p.I82Nfs*24	ENST00000274335		79	-/A	1/15	1	2	FACETS	0.961	0.822	1	0.961	0.822	1	CLONAL	1	TRUE	1	0.28	2		353	394	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395084	139395084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764798860	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	41	419	0	ENST00000277541.6:c.5854G>A	p.Ala1952Thr	p.A1952T	ENST00000277541	NM_017617.3	1952	Gca/Aca	31/34	1	2	FACETS	0.907	0.758	1	0.907	0.758	1	CLONAL	1	TRUE	1	0.28	2		419	323	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807542	1807542	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	47	426	0	ENST00000260795.2:c.1711C>T	p.Arg571Trp	p.R571W	ENST00000260795		571	Cgg/Tgg	12/17	1	2	FACETS	0.935	0.792	1	0.935	0.792	1	CLONAL	1	TRUE	1	0.28	2		426	359	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391407	139391407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780071276	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	39	445	1	ENST00000277541.6:c.6784G>A	p.Gly2262Ser	p.G2262S	ENST00000277541	NM_017617.3	2262	Ggc/Agc	34/34	1	2	FACETS	0.827	0.687	0.981	0.827	0.687	0.981	CLONAL	1	TRUE	1	0.28	2		446	337	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242701	98242701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs547776340	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	63	402	0	ENST00000331920.6:c.916G>A	p.Ala306Thr	p.A306T	ENST00000331920	NM_000264.3	306	Gcc/Acc	6/24	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.28	2		402	396	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880172	151880172	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	50	334	0	ENST00000262189.6:c.5152del	p.Arg1718GlyfsTer23	p.R1718Gfs*23	ENST00000262189	NM_170606.2	1718	Agg/gg	35/59	1	2	FACETS	0.989	0.843	1	0.989	0.843	1	CLONAL	1	TRUE	1	0.28	2		334	361	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986694	36986694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1228608392	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	13	342	0	ENST00000354822.5:c.995C>T	p.Ala332Val	p.A332V	ENST00000354822	NM_001079668.2	332	gCg/gTg	3/3	1	2	FACETS	0.44	0.314	0.594	0.44	0.314	0.594	SUBCLONAL	1	TRUE	1	0.28	2		342	211	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899182	78899182	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200660726	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	77	337	2	ENST00000306801.3:c.2821G>A	p.Ala941Thr	p.A941T	ENST00000306801	NM_020761.2	941	Gcg/Acg	24/34	0.285573468393669	2	FACETS	0.887	0.786	0.993	0.887	0.786	0.993	CLONAL	2	TRUE	0	0.28	2		339	310	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204984	128204984	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369637181	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	48	480	0	ENST00000341105.2:c.457G>A	p.Gly153Arg	p.G153R	ENST00000341105	NM_032638.4	153	Ggg/Agg	3/6	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.28	2		480	319	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93636565	93636565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	55	327	0	ENST00000375746.1:c.995C>T	p.Ala332Val	p.A332V	ENST00000375746	NM_001174167.1	332	gCa/gTa	8/14	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.28	2		327	323	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61305069	61305069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764188105	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	60	504	0	ENST00000341074.5:c.1057G>A	p.Glu353Lys	p.E353K	ENST00000341074	NM_002974.2	353	Gaa/Aaa	8/8	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.28	2		504	423	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202969	16202969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146447271	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	69	409	0	ENST00000375759.3:c.677G>A	p.Arg226Gln	p.R226Q	ENST00000375759	NM_015001.2	226	cGg/cAg	3/15	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.28	2		409	432	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174428	11174428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173643064	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	48	337	0	ENST00000361445.4:c.7247C>T	p.Ala2416Val	p.A2416V	ENST00000361445	NM_004958.3	2416	gCc/gTc	53/58	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.28	2		337	326	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919249	178919249	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	20	347	0	ENST00000263967.3:c.734A>G	p.Glu245Gly	p.E245G	ENST00000263967	NM_006218.2	245	gAa/gGa	4/21	1	2	FACETS	0.451	0.344	0.575	0.451	0.344	0.575	SUBCLONAL	1	TRUE	1	0.28	2		347	317	SUCCESS
AXL	558	MSKCC	GRCh37	19	41759584	41759584	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	40	371	0	ENST00000301178.4:c.2007A>G	p.Ile669Met	p.I669M	ENST00000301178	NM_021913.4	669	atA/atG	17/20	1	2	FACETS	0.848	0.707	1	0.848	0.707	1	CLONAL	1	TRUE	1	0.28	2		371	337	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686315	30686316	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	42	405	0	ENST00000295754.5:c.175dup	p.Ser59PhefsTer4	p.S59Ffs*4	ENST00000295754	NM_003242.5	57	-/T	2/7	1	2	FACETS	0.698	0.583	0.825	0.698	0.583	0.825	SUBCLONAL	1	TRUE	1	0.28	2		405	430	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513236	106513236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773788683	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	60	404	0	ENST00000359195.3:c.2140G>A	p.Ala714Thr	p.A714T	ENST00000359195	NM_002649.2	714	Gct/Act	4/11	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.28	2		404	386	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095658	178095658	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	53	423	0	ENST00000397062.3:c.1673G>A	p.Ser558Asn	p.S558N	ENST00000397062	NM_006164.4	558	aGc/aAc	5/5	1	2	FACETS	0.885	0.756	1	0.885	0.756	1	CLONAL	1	TRUE	1	0.28	2		423	428	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607649	43607649	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	72	644	0	ENST00000355710.3:c.1625A>T	p.Glu542Val	p.E542V	ENST00000355710	NM_020975.4	542	gAg/gTg	8/20	1	2	FACETS	0.997	0.873	1	0.997	0.873	1	CLONAL	1	TRUE	1	0.28	2		644	516	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40993264	40993265	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	60	320	0	ENST00000267868.3:c.93_94del	p.Cys31TrpfsTer33	p.C31Wfs*33	ENST00000267868	NM_002875.4	30	caGTgt/cagt	3/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.28	2		320	307	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635690	47635691	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	79	301	0	ENST00000233146.2:c.363dup	p.Lys122Ter	p.K122*	ENST00000233146	NM_000251.2	121	tat/taTt	2/16	0.285573468393669	2	FACETS	0.973	0.865	1	0.973	0.865	1	CLONAL	2	TRUE	0	0.28	2		301	290	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1735977	1735977	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	61	397	0	ENST00000378609.4:c.311C>T	p.Ala104Val	p.A104V	ENST00000378609	NM_002074.3	104	gCa/gTa	7/12	1	2	FACETS	0.993	0.859	1	0.993	0.859	1	CLONAL	1	TRUE	1	0.28	2		397	439	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032018	26032018	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	65	535	0	ENST00000244661.2:c.271A>T	p.Met91Leu	p.M91L	ENST00000244661	NM_003537.3	91	Atg/Ttg	1/1	1	2	FACETS	0.929	0.807	1	0.929	0.807	1	CLONAL	1	TRUE	1	0.28	2		535	500	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104672	193104672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1553278844	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	100	421	0	ENST00000367435.3:c.376C>T	p.Arg126Ter	p.R126*	ENST00000367435	NM_024529.4	126	Cga/Tga	5/17	0.245675289178864	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	1	0.28	3		421	363	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259176	89259176	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1365430715	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	36	391	0	ENST00000336596.2:c.320A>G	p.Asn107Ser	p.N107S	ENST00000336596	NM_005233.5	107	aAt/aGt	3/17	0.13023799163497	0	FACETS	0.541	0.446	0.648			1	INDETERMINATE	1	TRUE	0	0.28	0		391	342	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980362	7980362	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	45	411	0	ENST00000319144.4:c.1221G>T	p.Glu407Asp	p.E407D	ENST00000319144	NM_001139.2	407	gaG/gaT	9/15	1	2	FACETS	0.943	0.795	1	0.943	0.795	1	CLONAL	1	TRUE	1	0.28	2		411	341	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172203	99172203	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746024488	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	68	499	0	ENST00000074304.5:c.1769G>A	p.Cys590Tyr	p.C590Y	ENST00000074304	NM_001134224.1	590	tGt/tAt	17/26	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.28	2		499	429	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50751219	50751219	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	65	392	0	ENST00000307179.4:c.363del	p.Lys121AsnfsTer71	p.K121Nfs*71	ENST00000307179		120	Aaa/aa	5/20	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.28	2		392	421	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100184	30100184	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	43	336	0	ENST00000331968.5:c.1436C>A	p.Thr479Asn	p.T479N	ENST00000331968	NM_002742.2	479	aCt/aAt	10/18	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.28	2		336	267	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202711	128202711	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs387906632	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	42	420	0	ENST00000341105.2:c.1009C>T	p.Arg337Ter	p.R337*	ENST00000341105	NM_032638.4	337	Cga/Tga	4/6	1	2	FACETS	0.926	0.776	1	0.926	0.776	1	CLONAL	1	TRUE	1	0.28	2		420	324	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223956	36223956	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	46	458	1	ENST00000222270.7:c.6509del	p.Pro2170GlnfsTer6	p.P2170Qfs*6	ENST00000222270	NM_014727.1	2169	gCc/gc	28/37	1	2	FACETS	0.86	0.726	1	0.86	0.726	1	CLONAL	1	TRUE	1	0.28	2		459	382	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295970	1295970	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0067411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	39	495	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.817	0.679	0.97	0.817	0.679	0.97	CLONAL	1	TRUE	1	0.28	2		495	341	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	25	282	1	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	1	2	FACETS	0.716	0.563	0.891	0.716	0.563	0.891	SUBCLONAL	1	TRUE	1	0.17	2		283	411	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926888	112926888	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507546	NA	P-0067417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	35	291	0	ENST00000351677.2:c.1508G>T	p.Gly503Val	p.G503V	ENST00000351677	NM_002834.3	503	gGg/gTg	13/16	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.17	2		291	375	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61323006	61323006	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	28	361	0	ENST00000283752.5:c.1058G>T	p.Gly353Val	p.G353V	ENST00000283752	NM_006919.2	353	gGa/gTa	8/8	1	2	FACETS	0.692	0.552	0.852	0.692	0.552	0.852	SUBCLONAL	1	TRUE	1	0.17	2		361	476	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846147	68846147	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782359	NA	P-0067417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	31	255	0	ENST00000261769.5:c.1118C>G	p.Pro373Arg	p.P373R	ENST00000261769	NM_004360.3	373	cCg/cGg	8/16	1	2	FACETS	0.97	0.785	1	0.97	0.785	1	CLONAL	1	TRUE	1	0.17	2		255	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0067418-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	152	410	3	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.440570878318275	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	0	0.434126912738841	3		413	263	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250883	153250883	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067418-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	151	290	1	ENST00000281708.4:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000281708	NM_033632.3	393	Cga/Tga	8/12	0.440570878318275	3	FACETS	0.949	0.896	1	1	0.993	1	CLONAL	4	TRUE	1	0.434126912738841	3		291	223	SUCCESS
APC	324	MSKCC	GRCh37	5	112173590	112173590	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561575998	NA	P-0067418-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	77	355	0	ENST00000257430.4:c.2299C>T	p.Gln767Ter	p.Q767*	ENST00000257430	NM_000038.5	767	Cag/Tag	16/16	NA	2	FACETS	0.758	0.676	0.843			1	INDETERMINATE	2	TRUE	NA	0.434126912738841	2		355	234	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426729	49426730	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs576788910	NA	P-0067418-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	67	392	0	ENST00000301067.7:c.11756_11758dup	p.Gln3919dup	p.Q3919dup	ENST00000301067	NM_003482.3	3919	cta/cAGCta	39/54	0.427521376206458	3	FACETS	0.76	0.669	0.857	0.76	0.669	0.857	SUBCLONAL	2	TRUE	1	0.434126912738841	3		392	247	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068971	30068971	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067418-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	27	331	0	ENST00000331968.5:c.1958A>G	p.Glu653Gly	p.E653G	ENST00000331968	NM_002742.2	653	gAa/gGa	14/18	0.168926837547732	3	FACETS	1	0.813	1	0.505	0.406	0.614	INDETERMINATE	1	TRUE	1	0.434126912738841	3		331	150	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380358	14380360	+	inframe_deletion	In_Frame_Del	DEL	ACC	ACC	-	novel	NA	P-0067418-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	61	256	0	ENST00000256196.4:c.57_59del	p.Val20del	p.V20del	ENST00000256196		19	gtGGTc/gtc	1/6	0.440441293907207	4	FACETS	1	0.913	1	1	0.913	1	CLONAL	2	TRUE	2	0.434126912738841	4		256	192	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636548	73636548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067418-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	259	446	0	ENST00000377687.4:c.811C>T	p.Pro271Ser	p.P271S	ENST00000377687	NM_001730.3	271	Ccg/Tcg	2/4	0.434126912738841	7	FACETS	1	0.984	1	1	0.984	1	CLONAL	5	TRUE	2	0.434126912738841	7		446	459	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845268	42845268	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067418-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	106	293	0	ENST00000398585.3:c.994G>T	p.Ala332Ser	p.A332S	ENST00000398585	NM_001135099.1	332	Gcc/Tcc	9/14	0.440570878318275	4	FACETS	0.888	0.81	0.967	1	0.982	1	CLONAL	3	TRUE	2	0.434126912738841	4		293	263	SUCCESS
APC	324	MSKCC	GRCh37	5	112175509	112175515	+	frameshift_variant	Frame_Shift_Del	DEL	GAGTGAA	GAGTGAA	AT	novel	NA	P-0067418-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	79	368	0	ENST00000257430.4:c.4218_4224delinsAT	p.Glu1408MetfsTer13	p.E1408Mfs*13	ENST00000257430	NM_000038.5	1406	caGAGTGAA/caAT	16/16	NA	2	FACETS	0.774	0.692	0.86			1	INDETERMINATE	2	TRUE	NA	0.434126912738841	2		368	235	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0067419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	110	270	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.779456406733227	2		270	220	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0067419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	34	390	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.69619581880396	3	FACETS	0.836	0.694	0.99	0.418	0.347	0.495	CLONAL	1	TRUE	1	0.779456406733227	3		392	145	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0067419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	17	114	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	1	2	FACETS	0.969	0.758	1	0.969	0.758	1	CLONAL	1	TRUE	1	0.779456406733227	2		114	45	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0067419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	35	247	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.935	0.79	1	0.935	0.79	1	CLONAL	1	TRUE	1	0.779456406733227	2		247	96	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0067419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	90	253	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.931	0.84	1	0.931	0.84	1	CLONAL	1	TRUE	1	0.779456406733227	2		253	248	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089704	27089705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	103	480	0	ENST00000324856.7:c.2661dup	p.Gly888ArgfsTer48	p.G888Rfs*48	ENST00000324856	NM_006015.4	887	cca/ccAa	8/20	1	2	FACETS	0.958	0.87	1	0.958	0.87	1	CLONAL	1	TRUE	1	0.779456406733227	2		480	276	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610070	81610070	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	114	299	0	ENST00000298171.2:c.1670del	p.Leu557TrpfsTer4	p.L557Wfs*4	ENST00000298171	NM_000369.2	556	ccT/cc	10/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.779456406733227	2		299	272	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122579	108122581	+	inframe_deletion	In_Frame_Del	DEL	TTT	TTT	-	novel	NA	P-0067419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	68	252	0	ENST00000278616.4:c.1623_1625del	p.Cys541_Leu542delinsTrp	p.C541_L542delinsW	ENST00000278616	NM_000051.3	541	tgTTTg/tgg	11/63	0.751593111591393	1	FACETS	0.968	0.881	1	0.968	0.881	1	CLONAL	1	TRUE	0	0.779456406733227	1		252	110	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188315	10188315	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	43	168	0	ENST00000256474.2:c.458T>C	p.Leu153Pro	p.L153P	ENST00000256474	NM_000551.3	153	cTg/cCg	2/3	0.429732915626342	1	FACETS	0.878	0.745	1	0.878	0.745	1	CLONAL	1	TRUE	0	0.429732915626342	1		168	179	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161852	47161852	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	16	241	0	ENST00000409792.3:c.4274del	p.Lys1425ArgfsTer7	p.K1425Rfs*7	ENST00000409792	NM_014159.6	1425	aAg/ag	3/21	0.429732915626342	1	FACETS	0.225	0.166	0.295	0.225	0.166	0.295	SUBCLONAL	1	TRUE	0	0.429732915626342	1		241	260	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0067422-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	267	513	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.389614394948027	2	FACETS	0.852	0.807	0.897	0.852	0.807	0.897	CLONAL	2	TRUE	0	0.555932790715536	2		513	564	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964865	15964865	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067422-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	107	397	0	ENST00000268712.3:c.5731C>A	p.Pro1911Thr	p.P1911T	ENST00000268712	NM_006311.3	1911	Cca/Aca	37/46	0.56135108414839	1	FACETS	0.693	0.627	0.763	0.693	0.627	0.763	SUBCLONAL	1	TRUE	0	0.555932790715536	1		397	401	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756701	756701	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067422-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	91	420	0	ENST00000314574.4:c.127C>T	p.Pro43Ser	p.P43S	ENST00000314574	NM_005433.3	43	Ccg/Tcg	2/12	0.56135108414839	1	FACETS	0.559	0.499	0.622	0.559	0.499	0.622	SUBCLONAL	1	TRUE	0	0.555932790715536	1		420	423	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748439	162748439	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067422-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	83	437	0	ENST00000367921.3:c.2353C>G	p.Gln785Glu	p.Q785E	ENST00000367921	NM_006182.2	785	Caa/Gaa	17/18	0.56135108414839	1	FACETS	0.448	0.397	0.503	0.448	0.397	0.503	SUBCLONAL	1	TRUE	0	0.555932790715536	1		437	481	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918130	50918130	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555792834	NA	P-0067422-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	71	342	0	ENST00000440232.2:c.2447C>T	p.Ser816Phe	p.S816F	ENST00000440232	NM_002691.3	816	tCc/tTc	20/27	0.56135108414839	1	FACETS	0.551	0.484	0.621	0.551	0.484	0.621	SUBCLONAL	1	TRUE	0	0.555932790715536	1		342	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573996	7573997	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCTCTCGGAACATCTCGAAGC	novel	NA	P-0067422-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	125	323	0	ENST00000269305.4:c.1010_1030dup	p.Arg337_Glu343dup	p.R337_E343dup	ENST00000269305	NM_001126112.2	337	ctg/cGCTTCGAGATGTTCCGAGAGCtg	10/11	0.56135108414839	1	FACETS	0.746	0.681	0.814	0.746	0.681	0.814	SUBCLONAL	1	TRUE	0	0.555932790715536	1		323	435	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814707	139814707	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067422-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	75	397	0	ENST00000247668.2:c.700G>T	p.Glu234Ter	p.E234*	ENST00000247668	NM_021138.3	234	Gag/Tag	8/11	0.56135108414839	1	FACETS	0.546	0.481	0.614	0.546	0.481	0.614	SUBCLONAL	1	TRUE	0	0.555932790715536	1		397	357	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0067423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	50	321	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.580992586575669	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	1	0.581506138083848	3		321	95	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0067423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	57	298	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	1	2	FACETS	0.98	0.854	1	0.98	0.854	1	CLONAL	1	TRUE	1	0.581506138083848	2		298	200	SUCCESS
APC	324	MSKCC	GRCh37	5	112176027	112176030	+	frameshift_variant	Frame_Shift_Del	DEL	TTAT	TTAT	-	novel	NA	P-0067423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	33	338	0	ENST00000257430.4:c.4738_4741del	p.Ile1580LeufsTer69	p.I1580Lfs*69	ENST00000257430	NM_000038.5	1579	aTTATt/at	16/16	0.137857936081159	0	FACETS	0.374	0.31	0.443			1	INDETERMINATE	1	TRUE	0	0.581506138083848	0		338	127	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0067423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	31	390	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.175111696187667	3	FACETS	1	0.947	1	0.717	0.596	0.845	INDETERMINATE	1	TRUE	1	0.581506138083848	3		392	96	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120115	70120115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	54	329	0	ENST00000245479.2:c.1121del	p.Pro374ArgfsTer9	p.P374Rfs*9	ENST00000245479	NM_000346.3	373	Ccc/cc	3/3	0.175111696187667	3	FACETS	1	0.971	1	0.749	0.653	0.849	INDETERMINATE	1	TRUE	1	0.581506138083848	3		329	160	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117872	70117872	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	55	341	0	ENST00000245479.2:c.340G>C	p.Val114Leu	p.V114L	ENST00000245479	NM_000346.3	114	Gtg/Ctg	1/3	0.175111696187667	3	FACETS	1	0.932	1	0.563	0.487	0.642	INDETERMINATE	1	TRUE	1	0.581506138083848	3		341	217	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584725	48584725	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	49	330	0	ENST00000342988.3:c.803G>A	p.Trp268Ter	p.W268*	ENST00000342988	NM_005359.5	268	tGg/tAg	7/12	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.581506138083848	2		330	148	SUCCESS
APC	324	MSKCC	GRCh37	5	112173913	112173913	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	42	336	0	ENST00000257430.4:c.2624del	p.Lys875SerfsTer41	p.K875Sfs*41	ENST00000257430	NM_000038.5	874	tcA/tc	16/16	0.137857936081159	0	FACETS	0.388	0.329	0.45			1	INDETERMINATE	1	TRUE	0	0.581506138083848	0		336	156	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0067424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	18	270	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.241794942771869	4	FACETS	1	0.872	1	1	0.872	1	CLONAL	2	TRUE	2	0.241794942771869	4		270	76	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0067424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	11	239	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	1	0.799	1	1	0.799	1	CLONAL	1	TRUE	1	0.241794942771869	2		239	76	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592162	55592162	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143179681	NA	P-0067424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	10	239	0	ENST00000288135.5:c.1486G>A	p.Asp496Asn	p.D496N	ENST00000288135	NM_000222.2	496	Gat/Aat	9/21	0.109167441011852	0	FACETS	0.825	0.567	1			1	INDETERMINATE	1	TRUE	0	0.241794942771869	0		239	76	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10789359	10789359	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	10	249	0	ENST00000361367.2:c.1693C>A	p.Pro565Thr	p.P565T	ENST00000361367	NM_014633.3	565	Cca/Aca	14/25	1	2	FACETS	0.889	0.608	1	0.889	0.608	1	CLONAL	1	TRUE	1	0.241794942771869	2		249	93	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119962	70120010	+	frameshift_variant	Frame_Shift_Del	DEL	AGCAGCACCGCGGCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCA	AGCAGCACCGCGGCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCA	-	novel	NA	P-0067424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	60	256	0	ENST00000245479.2:c.971_1019del	p.Thr324ArgfsTer43	p.T324Rfs*43	ENST00000245479	NM_000346.3	322	AGCAGCACCGCGGCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAag/ag	3/3	0.241794942771869	4	FACETS	1	0.925	1	1	0.973	1	CLONAL	4	TRUE	1	0.241794942771869	4		256	145	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420562	49420562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	30	275	0	ENST00000301067.7:c.15187G>A	p.Ala5063Thr	p.A5063T	ENST00000301067	NM_003482.3	5063	Gcc/Acc	48/54	0.135871093167988	3	FACETS	0.986	0.807	1			1	INDETERMINATE	2	TRUE	NA	0.241794942771869	3		275	141	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607666	46607666	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	10	268	0	ENST00000263734.3:c.1855C>A	p.Pro619Thr	p.P619T	ENST00000263734	NM_001430.4	619	Ccg/Acg	12/16	0.241794942771869	4	FACETS	0.601	0.407	0.843	0.2	0.135	0.281	SUBCLONAL	1	TRUE	1	0.241794942771869	4		268	171	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	109	478	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.48	2		478	308	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	183	482	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.48	2		482	512	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	71	321	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.48	2		321	204	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	156	530	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.48	2		530	497	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1724709	1724709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778110947	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	32	237	0	ENST00000378609.4:c.472G>A	p.Val158Ile	p.V158I	ENST00000378609	NM_002074.3	158	Gtc/Atc	8/12	1	2	FACETS	0.261	0.212	0.318	0.261	0.212	0.318	SUBCLONAL	1	TRUE	1	0.48	2		237	510	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075382	8075382	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1311181353	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	129	256	1	ENST00000377482.5:c.188G>A	p.Arg63His	p.R63H	ENST00000377482	NM_018948.3	63	cGc/cAc	3/4	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.48	2		257	390	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781230	9781230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1255847906	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	155	248	0	ENST00000377346.4:c.1735G>A	p.Ala579Thr	p.A579T	ENST00000377346	NM_005026.3	579	Gcc/Acc	14/24	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.48	2		248	437	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199444	11199444	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1358692215	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	168	293	0	ENST00000361445.4:c.5047C>T	p.Arg1683Trp	p.R1683W	ENST00000361445	NM_004958.3	1683	Cgg/Tgg	36/58	1	2	FACETS	0.771	0.715	0.828	1	0.991	1	SUBCLONAL	2	TRUE	1	0.48	2		293	454	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100871	27100871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761500441	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	175	283	0	ENST00000324856.7:c.4153G>A	p.Glu1385Lys	p.E1385K	ENST00000324856	NM_006015.4	1385	Gaa/Aaa	18/20	1	2	FACETS	0.769	0.715	0.825	1	0.991	1	SUBCLONAL	2	TRUE	1	0.48	2		283	474	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39321417	39321417	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	113	292	0	ENST00000373001.3:c.604G>T	p.Asp202Tyr	p.D202Y	ENST00000373001	NM_022157.3	202	Gac/Tac	3/7	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.48	2		292	315	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363268	40363268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201425251	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	227	334	1	ENST00000397332.2:c.961C>T	p.Arg321Cys	p.R321C	ENST00000397332	NM_001033082.2	321	Cgc/Tgc	3/3	1	2	FACETS	0.811	0.762	0.862	1	0.993	1	CLONAL	2	TRUE	1	0.48	2		335	583	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804219	43804219	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	194	282	0	ENST00000372470.3:c.219G>T	p.Lys73Asn	p.K73N	ENST00000372470	NM_005373.2	73	aaG/aaT	3/12	1	2	FACETS	0.827	0.772	0.882	1	0.993	1	CLONAL	2	TRUE	1	0.48	2		282	489	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304242	65304242	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	20	276	0	ENST00000342505.4:c.2873T>G	p.Phe958Cys	p.F958C	ENST00000342505	NM_002227.2	958	tTt/tGt	21/25	1	2	FACETS	0.253	0.193	0.323	0.253	0.193	0.323	SUBCLONAL	1	TRUE	1	0.48	2		276	330	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65348982	65348982	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	66	292	0	ENST00000342505.4:c.183C>G	p.Cys61Trp	p.C61W	ENST00000342505	NM_002227.2	61	tgC/tgG	3/25	1	2	FACETS	0.507	0.441	0.579	0.507	0.441	0.579	SUBCLONAL	1	TRUE	1	0.48	2		292	542	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65349155	65349155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	26	273	0	ENST00000342505.4:c.10C>A	p.Leu4Ile	p.L4I	ENST00000342505	NM_002227.2	4	Cta/Ata	3/25	1	2	FACETS	0.287	0.227	0.356	0.287	0.227	0.356	SUBCLONAL	1	TRUE	1	0.48	2		273	377	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78420947	78420947	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	85	206	0	ENST00000370768.2:c.1773G>T	p.Lys591Asn	p.K591N	ENST00000370768	NM_003902.3	591	aaG/aaT	18/20	1	2	FACETS	0.839	0.757	0.923	1	0.984	1	CLONAL	2	TRUE	1	0.48	2		206	211	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78420973	78420973	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	15	271	0	ENST00000370768.2:c.1747A>G	p.Thr583Ala	p.T583A	ENST00000370768	NM_003902.3	583	Acc/Gcc	18/20	1	2	FACETS	0.213	0.155	0.283	0.213	0.155	0.283	SUBCLONAL	1	TRUE	1	0.48	2		271	293	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430375	78430375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569612114	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	76	293	0	ENST00000370768.2:c.793C>T	p.Arg265Trp	p.R265W	ENST00000370768	NM_003902.3	265	Cgg/Tgg	10/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.48	2		293	239	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166001	118166001	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147179158	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	210	341	0	ENST00000369448.3:c.511G>A	p.Asp171Asn	p.D171N	ENST00000369448	NM_017709.3	171	Gac/Aac	2/2	1	2	FACETS	0.806	0.754	0.858	1	0.993	1	CLONAL	2	TRUE	1	0.48	2		341	543	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150913857	150913857	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	49	195	0	ENST00000271640.5:c.500T>A	p.Phe167Tyr	p.F167Y	ENST00000271640	NM_001145415.1	167	tTc/tAc	5/22	1	2	FACETS	0.526	0.447	0.613	0.526	0.447	0.613	SUBCLONAL	1	TRUE	1	0.48	2		195	388	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150923356	150923356	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199613890	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	155	310	0	ENST00000271640.5:c.2003G>A	p.Arg668Gln	p.R668Q	ENST00000271640	NM_001145415.1	668	cGa/cAa	13/22	1	2	FACETS	0.767	0.71	0.826	1	0.99	1	SUBCLONAL	2	TRUE	1	0.48	2		310	421	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844768	156844768	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	53	428	0	ENST00000524377.1:c.1322A>C	p.Lys441Thr	p.K441T	ENST00000524377	NM_002529.3	441	aAa/aCa	11/17	1	2	FACETS	0.303	0.257	0.353	0.303	0.257	0.353	SUBCLONAL	1	TRUE	1	0.48	2		428	729	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849015	156849015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771421920	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	190	297	0	ENST00000524377.1:c.1907C>T	p.Ala636Val	p.A636V	ENST00000524377	NM_002529.3	636	gCg/gTg	15/17	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.48	2		297	539	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326623	161326623	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs386833414	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	152	198	0	ENST00000367975.2:c.398G>A	p.Arg133Gln	p.R133Q	ENST00000367975	NM_003001.3	133	cGa/cAa	5/6	1	2	FACETS	0.792	0.732	0.852	1	0.99	1	SUBCLONAL	2	TRUE	1	0.48	2		198	400	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724611	162724611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149507401	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	208	356	0	ENST00000367921.3:c.383G>A	p.Arg128His	p.R128H	ENST00000367921	NM_006182.2	128	cGc/cAc	5/18	1	2	FACETS	0.846	0.793	0.9	1	0.993	1	CLONAL	2	TRUE	1	0.48	2		356	512	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163313609	163313609	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	28	162	0	ENST00000271452.3:c.756G>T	p.Lys252Asn	p.K252N	ENST00000271452	NM_145697.2	252	aaG/aaT	10/14	1	2	FACETS	0.919	0.747	1	0.919	0.747	1	CLONAL	1	TRUE	1	0.48	2		162	127	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957464	175957465	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	55	264	0	ENST00000367669.3:c.1931dup	p.Asn644LysfsTer17	p.N644Kfs*17	ENST00000367669	NM_022457.5	644	aac/aaAc	17/20	1	2	FACETS	0.707	0.608	0.814	0.707	0.608	0.814	SUBCLONAL	1	TRUE	1	0.48	2		264	324	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176176072	176176072	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	104	260	0	ENST00000367669.3:c.43A>C	p.Ser15Arg	p.S15R	ENST00000367669	NM_022457.5	15	Agc/Cgc	1/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.48	2		260	318	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204501347	204501347	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	12	241	0	ENST00000367182.3:c.316C>A	p.Leu106Ile	p.L106I	ENST00000367182	NM_001278516.1	106	Ctt/Att	5/11	1	2	FACETS	0.22	0.154	0.301	0.22	0.154	0.301	SUBCLONAL	1	TRUE	1	0.48	2		241	227	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612807	228612807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	231	409	0	ENST00000366696.1:c.220G>A	p.Glu74Lys	p.E74K	ENST00000366696	NM_003493.2	74	Gag/Aag	1/1	1	2	FACETS	0.768	0.72	0.816	1	0.993	1	SUBCLONAL	2	TRUE	1	0.48	2		409	627	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231487101	231487101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143558208	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	83	231	0	ENST00000295050.7:c.502C>T	p.Arg168Cys	p.R168C	ENST00000295050	NM_032018.5	168	Cgc/Tgc	4/5	1	2	FACETS	0.636	0.562	0.714	0.636	0.562	0.714	SUBCLONAL	1	TRUE	1	0.48	2		231	544	SUCCESS
FH	2271	MSKCC	GRCh37	1	241661199	241661199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201115573	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	80	262	0	ENST00000366560.3:c.1462G>A	p.Glu488Lys	p.E488K	ENST00000366560	NM_000143.3	488	Gaa/Aaa	10/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.48	2		262	281	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680525	241680525	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	134	234	0	ENST00000366560.3:c.224C>A	p.Ser75Tyr	p.S75Y	ENST00000366560	NM_000143.3	75	tCt/tAt	2/10	1	2	FACETS	0.778	0.715	0.841	1	0.989	1	SUBCLONAL	2	TRUE	1	0.48	2		234	359	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670498	246670498	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	120	201	0	ENST00000388985.4:c.22A>C	p.Lys8Gln	p.K8Q	ENST00000388985		8	Aag/Cag	1/12	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.48	2		201	347	SUCCESS
RET	5979	MSKCC	GRCh37	10	43614982	43614982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	169	278	0	ENST00000355710.3:c.2396C>T	p.Pro799Leu	p.P799L	ENST00000355710	NM_020975.4	799	cCg/cTg	14/20	1	2	FACETS	0.844	0.785	0.904	1	0.992	1	CLONAL	2	TRUE	1	0.48	2		278	417	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333141	70333141	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	159	292	0	ENST00000373644.4:c.1046T>C	p.Phe349Ser	p.F349S	ENST00000373644	NM_030625.2	349	tTc/tCc	2/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.48	2		292	478	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692892	89692892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554898129	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	69	213	0	ENST00000371953.3:c.376G>A	p.Ala126Thr	p.A126T	ENST00000371953	NM_000314.4	126	Gct/Act	5/9	1	2	FACETS	0.952	0.853	1	1	0.984	1	CLONAL	2	TRUE	1	0.48	2		213	151	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276928	123276928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199757302	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	74	316	0	ENST00000358487.5:c.989G>A	p.Arg330Gln	p.R330Q	ENST00000358487	NM_000141.4	330	cGg/cAg	8/18	1	2	FACETS	0.665	0.583	0.751	0.665	0.583	0.751	SUBCLONAL	1	TRUE	1	0.48	2		316	464	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325170	123325170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371358242	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	154	307	0	ENST00000358487.5:c.158C>T	p.Ala53Val	p.A53V	ENST00000358487	NM_000141.4	53	gCg/gTg	3/18	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.48	2		307	633	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123353316	123353316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141724446	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	35	347	0	ENST00000358487.5:c.16C>T	p.Arg6Cys	p.R6C	ENST00000358487	NM_000141.4	6	Cgt/Tgt	2/18	1	2	FACETS	0.229	0.187	0.276	0.229	0.187	0.276	SUBCLONAL	1	TRUE	1	0.48	2		347	637	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10772960	10772960	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	128	178	0	ENST00000361367.2:c.1A>G	p.Met1?	p.M1?	ENST00000361367	NM_014633.3	1	Atg/Gtg	1/25	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.48	2		178	402	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10787957	10787957	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	47	233	0	ENST00000361367.2:c.1606C>T	p.Arg536Cys	p.R536C	ENST00000361367	NM_014633.3	536	Cgc/Tgc	13/25	1	2	FACETS	0.771	0.656	0.896	0.771	0.656	0.896	SUBCLONAL	1	TRUE	1	0.48	2		233	254	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	118	218	0	ENST00000256196.4:c.68G>C	p.Gly23Ala	p.G23A	ENST00000256196		23	gGc/gCc	1/6	1	2	FACETS	0.793	0.726	0.862	1	0.988	1	SUBCLONAL	2	TRUE	1	0.48	2		218	310	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47599004	47599004	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	55	291	0	ENST00000430070.2:c.596T>G	p.Phe199Cys	p.F199C	ENST00000430070	NM_018095.4	199	tTt/tGt	2/4	1	2	FACETS	0.424	0.363	0.492	0.424	0.363	0.492	SUBCLONAL	1	TRUE	1	0.48	2		291	540	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136996	64136996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	29	241	0	ENST00000334205.4:c.1507G>A	p.Glu503Lys	p.E503K	ENST00000334205	NM_003942.2	503	Gag/Aag	13/17	1	2	FACETS	0.272	0.218	0.334	0.272	0.218	0.334	SUBCLONAL	1	TRUE	1	0.48	2		241	444	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571819	64571819	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	40	240	0	ENST00000312049.6:c.1820G>A	p.Arg607His	p.R607H	ENST00000312049	NM_130799.2	607	cGc/cAc	10/10	1	2	FACETS	0.363	0.301	0.432	0.363	0.301	0.432	SUBCLONAL	1	TRUE	1	0.48	2		240	459	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462828	69462828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	194	319	0	ENST00000227507.2:c.641G>A	p.Gly214Asp	p.G214D	ENST00000227507	NM_053056.2	214	gGc/gAc	4/5	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.48	2		319	556	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939260	71939260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	13	321	0	ENST00000298229.2:c.209G>A	p.Arg70His	p.R70H	ENST00000298229	NM_001567.3	70	cGc/cAc	2/28	1	2	FACETS	0.102	0.072	0.139	0.102	0.072	0.139	SUBCLONAL	1	TRUE	1	0.48	2		321	532	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090300	77090300	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	67	259	0	ENST00000356341.3:c.425A>G	p.Tyr142Cys	p.Y142C	ENST00000356341	NM_002576.4	142	tAc/tGc	4/15	1	2	FACETS	0.666	0.581	0.758	0.666	0.581	0.758	SUBCLONAL	1	TRUE	1	0.48	2		259	419	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090363	77090363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	53	256	0	ENST00000356341.3:c.362C>T	p.Pro121Leu	p.P121L	ENST00000356341	NM_002576.4	121	cCg/cTg	4/15	1	2	FACETS	0.418	0.357	0.486	0.418	0.357	0.486	SUBCLONAL	1	TRUE	1	0.48	2		256	528	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94179032	94179032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148637964	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	30	237	0	ENST00000323929.3:c.1811G>A	p.Arg604His	p.R604H	ENST00000323929	NM_005591.3	604	cGt/cAt	16/20	1	2	FACETS	0.512	0.415	0.622	0.512	0.415	0.622	SUBCLONAL	1	TRUE	1	0.48	2		237	244	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94906474	94906474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1173588660	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	84	219	0	ENST00000536441.1:c.1424G>A	p.Arg475Gln	p.R475Q	ENST00000536441	NM_144665.3	475	cGa/cAa	10/10	1	2	FACETS	0.941	0.852	1	1	0.986	1	CLONAL	2	TRUE	1	0.48	2		219	186	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981826	101981826	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	40	275	0	ENST00000282441.5:c.247A>G	p.Thr83Ala	p.T83A	ENST00000282441	NM_001130145.2	83	Acc/Gcc	1/9	1	2	FACETS	0.372	0.309	0.442	0.372	0.309	0.442	SUBCLONAL	1	TRUE	1	0.48	2		275	448	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984950	101984950	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1017660144	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	106	194	0	ENST00000282441.5:c.397C>A	p.Gln133Lys	p.Q133K	ENST00000282441	NM_001130145.2	133	Cag/Aag	2/9	1	2	FACETS	0.873	0.797	0.95	1	0.988	1	CLONAL	2	TRUE	1	0.48	2		194	253	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102033200	102033200	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	218	290	0	ENST00000282441.5:c.586A>G	p.Thr196Ala	p.T196A	ENST00000282441	NM_001130145.2	196	Aca/Gca	3/9	1	2	FACETS	0.83	0.779	0.882	1	0.993	1	CLONAL	2	TRUE	1	0.48	2		290	547	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195901	102195901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	50	308	0	ENST00000263464.3:c.661G>A	p.Ala221Thr	p.A221T	ENST00000263464	NM_001165.4	221	Gct/Act	2/9	1	2	FACETS	0.448	0.38	0.522	0.448	0.38	0.522	SUBCLONAL	1	TRUE	1	0.48	2		308	465	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141873	108141873	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs538105098	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	81	227	0	ENST00000278616.4:c.2921C>T	p.Ser974Phe	p.S974F	ENST00000278616	NM_000051.3	974	tCc/tTc	19/63	0.275278798321476	0	FACETS	0.728	0.652	0.808			1	INDETERMINATE	1	TRUE	0	0.48	0		227	241	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143551	108143551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201780199	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	41	279	0	ENST00000278616.4:c.3256C>T	p.Arg1086Cys	p.R1086C	ENST00000278616	NM_000051.3	1086	Cgc/Tgc	22/63	0.275278798321476	0	FACETS	0.446	0.376	0.523			1	INDETERMINATE	1	TRUE	0	0.48	0		279	199	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180964	108180964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	99	234	0	ENST00000278616.4:c.5840C>T	p.Ser1947Phe	p.S1947F	ENST00000278616	NM_000051.3	1947	tCt/tTt	39/63	1	2	FACETS	0.946	0.863	1	1	0.988	1	CLONAL	2	TRUE	1	0.48	2		234	218	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343436	118343436	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	170	304	0	ENST00000534358.1:c.1562A>C	p.Asn521Thr	p.N521T	ENST00000534358	NM_005933.3	521	aAt/aCt	3/36	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.48	2		304	505	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360531	118360531	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs150800017	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	48	286	1	ENST00000534358.1:c.4504C>T	p.Arg1502Ter	p.R1502*	ENST00000534358	NM_005933.3	1502	Cga/Tga	12/36	1	2	FACETS	0.466	0.395	0.545	0.466	0.395	0.545	SUBCLONAL	1	TRUE	1	0.48	2		287	429	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103196	119103196	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	134	365	0	ENST00000264033.4:c.234G>T	p.Lys78Asn	p.K78N	ENST00000264033	NM_005188.3	78	aaG/aaT	2/16	1	2	FACETS	0.802	0.738	0.867	1	0.989	1	CLONAL	2	TRUE	1	0.48	2		365	348	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142450	119142450	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	24	295	0	ENST00000264033.4:c.449A>G	p.Asn150Ser	p.N150S	ENST00000264033	NM_005188.3	150	aAc/aGc	3/16	1	2	FACETS	0.347	0.272	0.433	0.347	0.272	0.433	SUBCLONAL	1	TRUE	1	0.48	2		295	288	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156203	119156203	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	79	311	0	ENST00000264033.4:c.1868C>A	p.Ser623Ter	p.S623*	ENST00000264033	NM_005188.3	623	tCa/tAa	11/16	1	2	FACETS	0.597	0.526	0.674	0.597	0.526	0.674	SUBCLONAL	1	TRUE	1	0.48	2		311	551	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402199	402199	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	48	299	0	ENST00000399788.2:c.4592A>G	p.Asp1531Gly	p.D1531G	ENST00000399788	NM_001042603.1	1531	gAc/gGc	27/28	1	2	FACETS	0.599	0.508	0.698	0.599	0.508	0.698	SUBCLONAL	1	TRUE	1	0.48	2		299	334	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416923	416923	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	193	372	0	ENST00000399788.2:c.3627A>C	p.Lys1209Asn	p.K1209N	ENST00000399788	NM_001042603.1	1209	aaA/aaC	23/28	1	2	FACETS	0.79	0.737	0.844	1	0.992	1	SUBCLONAL	2	TRUE	1	0.48	2		372	509	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385283	4385283	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	154	291	0	ENST00000261254.3:c.308C>T	p.Ala103Val	p.A103V	ENST00000261254	NM_001759.3	103	gCt/gTt	2/5	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.48	2		291	491	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398101	4398101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762849458	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	185	294	0	ENST00000261254.3:c.665C>T	p.Ser222Leu	p.S222L	ENST00000261254	NM_001759.3	222	tCg/tTg	4/5	1	2	FACETS	0.757	0.705	0.81	1	0.991	1	SUBCLONAL	2	TRUE	1	0.48	2		294	509	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870891	12870891	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	152	282	0	ENST00000228872.4:c.118G>T	p.Glu40Ter	p.E40*	ENST00000228872	NM_004064.3	40	Gag/Tag	1/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.48	2		282	490	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18496264	18496264	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	46	99	0	ENST00000266497.5:c.1399T>G	p.Phe467Val	p.F467V	ENST00000266497		467	Ttt/Gtt	9/31	1	2	FACETS	0.94	0.82	1	1	0.976	1	CLONAL	2	TRUE	1	0.48	2		99	102	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573894	18573894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759658584	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	58	246	0	ENST00000266497.5:c.2212C>T	p.Arg738Cys	p.R738C	ENST00000266497		738	Cgt/Tgt	15/31	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.48	2		246	173	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644403	18644403	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	81	236	0	ENST00000266497.5:c.2581A>C	p.Ile861Leu	p.I861L	ENST00000266497		861	Att/Ctt	18/31	1	2	FACETS	0.932	0.842	1	1	0.986	1	CLONAL	2	TRUE	1	0.48	2		236	181	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380184	25380184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	29	166	0	ENST00000311936.3:c.274G>A	p.Asp92Asn	p.D92N	ENST00000311936	NM_004985.3	92	Gat/Aat	3/5	1	2	FACETS	0.592	0.479	0.719	0.592	0.479	0.719	SUBCLONAL	1	TRUE	1	0.48	2		166	204	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46215240	46215240	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	15	160	0	ENST00000334344.6:c.675G>T	p.Trp225Cys	p.W225C	ENST00000334344	NM_152641.2	225	tgG/tgT	6/21	1	2	FACETS	0.573	0.424	0.748	0.573	0.424	0.748	SUBCLONAL	1	TRUE	1	0.48	2		160	109	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230589	46230589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	66	297	0	ENST00000334344.6:c.838G>A	p.Asp280Asn	p.D280N	ENST00000334344	NM_152641.2	280	Gat/Aat	8/21	1	2	FACETS	0.816	0.713	0.926	0.816	0.713	0.926	CLONAL	1	TRUE	1	0.48	2		297	337	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231437	46231437	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	25	295	0	ENST00000334344.6:c.1277C>T	p.Thr426Met	p.T426M	ENST00000334344	NM_152641.2	426	aCg/aTg	10/21	1	2	FACETS	0.358	0.282	0.445	0.358	0.282	0.445	SUBCLONAL	1	TRUE	1	0.48	2		295	291	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245659	46245659	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	92	353	0	ENST00000334344.6:c.3753G>T	p.Lys1251Asn	p.K1251N	ENST00000334344	NM_152641.2	1251	aaG/aaT	15/21	1	2	FACETS	0.764	0.681	0.851	0.764	0.681	0.851	SUBCLONAL	1	TRUE	1	0.48	2		353	502	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246581	46246581	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	33	287	0	ENST00000334344.6:c.4675G>T	p.Gly1559Ter	p.G1559*	ENST00000334344	NM_152641.2	1559	Gga/Tga	15/21	1	2	FACETS	0.288	0.234	0.349	0.288	0.234	0.349	SUBCLONAL	1	TRUE	1	0.48	2		287	478	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418678	49418678	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	187	253	0	ENST00000301067.7:c.15836A>G	p.Asp5279Gly	p.D5279G	ENST00000301067	NM_003482.3	5279	gAc/gGc	49/54	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.48	2		253	548	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420108	49420108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123729	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	74	284	0	ENST00000301067.7:c.15641G>A	p.Arg5214His	p.R5214H	ENST00000301067	NM_003482.3	5214	cGc/cAc	48/54	1	2	FACETS	0.543	0.476	0.615	0.543	0.476	0.615	SUBCLONAL	1	TRUE	1	0.48	2		284	568	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421682	49421682	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	198	278	0	ENST00000301067.7:c.14547C>A	p.Ser4849Arg	p.S4849R	ENST00000301067	NM_003482.3	4849	agC/agA	47/54	1	2	FACETS	0.777	0.725	0.829	1	0.992	1	SUBCLONAL	2	TRUE	1	0.48	2		278	531	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426495	49426495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	136	374	0	ENST00000301067.7:c.11993G>A	p.Gly3998Asp	p.G3998D	ENST00000301067	NM_003482.3	3998	gGc/gAc	39/54	1	2	FACETS	0.954	0.871	1	0.954	0.871	1	CLONAL	1	TRUE	1	0.48	2		374	594	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480597	50480597	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	191	317	0	ENST00000394963.4:c.467A>C	p.Lys156Thr	p.K156T	ENST00000394963	NM_003076.4	156	aAa/aCa	4/13	1	2	FACETS	0.801	0.747	0.855	1	0.992	1	CLONAL	2	TRUE	1	0.48	2		317	497	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478794	56478794	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	47	252	0	ENST00000267101.3:c.250A>G	p.Thr84Ala	p.T84A	ENST00000267101	NM_001982.3	84	Aca/Gca	3/28	1	2	FACETS	0.433	0.366	0.508	0.433	0.366	0.508	SUBCLONAL	1	TRUE	1	0.48	2		252	452	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860138	57860138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	178	244	0	ENST00000228682.2:c.878G>A	p.Arg293His	p.R293H	ENST00000228682	NM_005269.2	293	cGc/cAc	8/12	1	2	FACETS	0.786	0.731	0.841	1	0.991	1	SUBCLONAL	2	TRUE	1	0.48	2		244	472	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218339	69218339	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	77	275	0	ENST00000462284.1:c.431T>G	p.Leu144Arg	p.L144R	ENST00000462284	NM_002392.5	144	cTt/cGt	7/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.48	2		275	232	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856229	111856229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	20	249	0	ENST00000341259.2:c.280C>T	p.Arg94Cys	p.R94C	ENST00000341259	NM_005475.2	94	Cgt/Tgt	2/8	1	2	FACETS	0.22	0.168	0.281	0.22	0.168	0.281	SUBCLONAL	1	TRUE	1	0.48	2		249	379	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885140	111885140	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	187	299	0	ENST00000341259.2:c.1028C>A	p.Ser343Tyr	p.S343Y	ENST00000341259	NM_005475.2	343	tCt/tAt	6/8	1	2	FACETS	0.787	0.734	0.841	1	0.992	1	SUBCLONAL	2	TRUE	1	0.48	2		299	495	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118685	115118685	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	189	313	0	ENST00000257566.3:c.656T>G	p.Phe219Cys	p.F219C	ENST00000257566	NM_016569.3	219	tTt/tGt	2/8	1	2	FACETS	0.885	0.827	0.943	1	0.993	1	CLONAL	2	TRUE	1	0.48	2		313	445	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118806	115118806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754023417	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	82	356	0	ENST00000257566.3:c.535G>A	p.Glu179Lys	p.E179K	ENST00000257566	NM_016569.3	179	Gaa/Aaa	2/8	1	2	FACETS	0.69	0.61	0.775	0.69	0.61	0.775	SUBCLONAL	1	TRUE	1	0.48	2		356	495	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118850	115118850	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	52	344	0	ENST00000257566.3:c.491A>C	p.Lys164Thr	p.K164T	ENST00000257566	NM_016569.3	164	aAa/aCa	2/8	1	2	FACETS	0.51	0.435	0.592	0.51	0.435	0.592	SUBCLONAL	1	TRUE	1	0.48	2		344	425	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800918	120800918	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	199	307	0	ENST00000257552.2:c.330G>T	p.Lys110Asn	p.K110N	ENST00000257552	NM_002442.3	110	aaG/aaT	6/15	1	2	FACETS	0.758	0.707	0.809	1	0.992	1	SUBCLONAL	2	TRUE	1	0.48	2		307	547	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215787	133215787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762000608	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	39	296	0	ENST00000320574.5:c.5476C>T	p.Arg1826Trp	p.R1826W	ENST00000320574	NM_006231.2	1826	Cgg/Tgg	40/49	1	2	FACETS	0.32	0.265	0.382	0.32	0.265	0.382	SUBCLONAL	1	TRUE	1	0.48	2		296	508	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	170	300	0	ENST00000320574.5:c.1231G>C	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ctg	13/49	1	2	FACETS	0.798	0.741	0.855	1	0.991	1	SUBCLONAL	2	TRUE	1	0.48	2		300	444	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563008	21563008	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1027168412	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	150	303	0	ENST00000382592.4:c.911T>C	p.Phe304Ser	p.F304S	ENST00000382592	NM_014572.2	304	tTc/tCc	4/8	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.48	2		303	448	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29002020	29002020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs974445913	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	99	242	0	ENST00000282397.4:c.1145G>A	p.Arg382His	p.R382H	ENST00000282397	NM_002019.4	382	cGc/cAc	9/30	0.215187541964721	0	FACETS	0.708	0.64	0.778			1	INDETERMINATE	1	TRUE	0	0.48	0		242	303	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008075	29008075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1396825628	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	42	308	0	ENST00000282397.4:c.694G>A	p.Val232Ile	p.V232I	ENST00000282397	NM_002019.4	232	Gtc/Atc	6/30	0.215187541964721	0	FACETS	0.312	0.261	0.367			1	INDETERMINATE	1	TRUE	0	0.48	0		308	292	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906492	32906492	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	55	233	0	ENST00000380152.3:c.877G>T	p.Asp293Tyr	p.D293Y	ENST00000380152		293	Gat/Tat	10/27	0.215187541964721	0	FACETS	0.745	0.651	0.843			1	INDETERMINATE	1	TRUE	0	0.48	0		233	160	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912670	32912670	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398122776	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	35	295	0	ENST00000380152.3:c.4178C>T	p.Ala1393Val	p.A1393V	ENST00000380152		1393	gCg/gTg	11/27	0.215187541964721	0	FACETS	0.393	0.325	0.467			1	INDETERMINATE	1	TRUE	0	0.48	0		295	193	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953928	32953928	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	56	244	0	ENST00000380152.3:c.8995C>A	p.Leu2999Met	p.L2999M	ENST00000380152		2999	Ctg/Atg	23/27	0.215187541964721	0	FACETS	0.722	0.631	0.817			1	INDETERMINATE	1	TRUE	0	0.48	0		244	168	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972741	32972741	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	51	305	1	ENST00000380152.3:c.10091C>A	p.Ser3364Tyr	p.S3364Y	ENST00000380152		3364	tCt/tAt	27/27	0.215187541964721	0	FACETS	0.313	0.267	0.363			1	INDETERMINATE	1	TRUE	0	0.48	0		306	353	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134720	41134720	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	95	325	0	ENST00000379561.5:c.908G>T	p.Ser303Ile	p.S303I	ENST00000379561	NM_002015.3	303	aGc/aTc	2/3	1	2	FACETS	0.844	0.755	0.938	0.844	0.755	0.938	CLONAL	1	TRUE	1	0.48	2		325	469	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515036	103515036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775996769	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	168	305	2	ENST00000355739.4:c.1537G>A	p.Ala513Thr	p.A513T	ENST00000355739	NM_000123.3	513	Gca/Aca	8/15	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.48	2		307	477	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434967	110434967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	43	294	0	ENST00000375856.3:c.3434G>A	p.Arg1145His	p.R1145H	ENST00000375856	NM_003749.2	1145	cGc/cAc	1/2	1	2	FACETS	0.404	0.338	0.477	0.404	0.338	0.477	SUBCLONAL	1	TRUE	1	0.48	2		294	443	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436057	110436057	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1204032443	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	187	300	0	ENST00000375856.3:c.2344G>A	p.Asp782Asn	p.D782N	ENST00000375856	NM_003749.2	782	Gac/Aac	1/2	1	2	FACETS	0.87	0.812	0.928	1	0.993	1	CLONAL	2	TRUE	1	0.48	2		300	448	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436087	110436087	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	143	301	0	ENST00000375856.3:c.2314A>G	p.Ser772Gly	p.S772G	ENST00000375856	NM_003749.2	772	Agc/Ggc	1/2	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.48	2		301	432	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438264	110438264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	59	267	1	ENST00000375856.3:c.137G>A	p.Arg46His	p.R46H	ENST00000375856	NM_003749.2	46	cGc/cAc	1/2	1	2	FACETS	0.615	0.531	0.705	0.615	0.531	0.705	SUBCLONAL	1	TRUE	1	0.48	2		268	400	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100221	30100221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	62	207	0	ENST00000331968.5:c.1399C>T	p.Pro467Ser	p.P467S	ENST00000331968	NM_002742.2	467	Cct/Tct	10/18	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.48	2		207	217	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061634	38061634	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764371648	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	102	267	0	ENST00000250448.2:c.355C>T	p.Gln119Ter	p.Q119*	ENST00000250448	NM_004496.3	119	Cag/Tag	2/2	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.48	2		267	374	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422032	81422032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263008401	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	185	280	0	ENST00000298171.2:c.8C>T	p.Pro3Leu	p.P3L	ENST00000298171	NM_000369.2	3	cCg/cTg	1/10	1	2	FACETS	0.763	0.711	0.817	1	0.991	1	SUBCLONAL	2	TRUE	1	0.48	2		280	505	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554353	81554353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	18	244	0	ENST00000298171.2:c.373C>T	p.Leu125Phe	p.L125F	ENST00000298171	NM_000369.2	125	Ctc/Ttc	4/10	1	2	FACETS	0.245	0.184	0.317	0.245	0.184	0.317	SUBCLONAL	1	TRUE	1	0.48	2		244	306	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609510	81609510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	167	340	0	ENST00000298171.2:c.1108C>T	p.Leu370Phe	p.L370F	ENST00000298171	NM_000369.2	370	Ctc/Ttc	10/10	1	2	FACETS	0.775	0.719	0.832	1	0.991	1	SUBCLONAL	2	TRUE	1	0.48	2		340	449	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557556	95557556	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	130	295	0	ENST00000393063.1:c.5511G>T	p.Met1837Ile	p.M1837I	ENST00000393063	NM_030621.3	1837	atG/atT	26/28	1	2	FACETS	0.794	0.73	0.86	1	0.989	1	SUBCLONAL	2	TRUE	1	0.48	2		295	341	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562862	95562862	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	50	298	0	ENST00000393063.1:c.4395G>T	p.Lys1465Asn	p.K1465N	ENST00000393063	NM_030621.3	1465	aaG/aaT	24/28	1	2	FACETS	0.728	0.622	0.843	0.728	0.622	0.843	SUBCLONAL	1	TRUE	1	0.48	2		298	286	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572100	95572100	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	91	249	0	ENST00000393063.1:c.3008G>A	p.Arg1003Gln	p.R1003Q	ENST00000393063	NM_030621.3	1003	cGa/cAa	20/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.48	2		249	304	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239330	105239330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	58	353	0	ENST00000349310.3:c.1057G>A	p.Asp353Asn	p.D353N	ENST00000349310	NM_001014432.1	353	Gac/Aac	12/15	1	2	FACETS	0.459	0.394	0.529	0.459	0.394	0.529	SUBCLONAL	1	TRUE	1	0.48	2		353	527	SUCCESS
SCG5	6447	MSKCC	GRCh37	15	32935828	32935828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	106	291	0	ENST00000300175.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000300175	NM_001144757.1	12	gGc/gAc	2/6	1	2	FACETS	0.822	0.74	0.909	0.822	0.74	0.909	CLONAL	1	TRUE	1	0.48	2		291	537	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991274	41991274	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	35	273	0	ENST00000219905.7:c.2105G>T	p.Arg702Ile	p.R702I	ENST00000219905	NM_001164273.1	702	aGa/aTa	5/24	1	2	FACETS	0.688	0.569	0.819	0.688	0.569	0.819	SUBCLONAL	1	TRUE	1	0.48	2		273	212	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42050032	42050032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	61	186	0	ENST00000219905.7:c.7186C>T	p.Arg2396Ter	p.R2396*	ENST00000219905	NM_001164273.1	2396	Cga/Tga	19/24	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.48	2		186	184	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058856	42058856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	78	305	0	ENST00000219905.7:c.8576C>T	p.Ala2859Val	p.A2859V	ENST00000219905	NM_001164273.1	2859	gCt/gTt	24/24	1	2	FACETS	0.663	0.584	0.747	0.663	0.584	0.747	SUBCLONAL	1	TRUE	1	0.48	2		305	490	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059413	42059413	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	236	366	0	ENST00000219905.7:c.9133A>G	p.Thr3045Ala	p.T3045A	ENST00000219905	NM_001164273.1	3045	Aca/Gca	24/24	1	2	FACETS	0.833	0.784	0.884	1	0.994	1	CLONAL	2	TRUE	1	0.48	2		366	590	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50733634	50733634	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	72	324	0	ENST00000307179.4:c.193A>C	p.Lys65Gln	p.K65Q	ENST00000307179		65	Aaa/Caa	3/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.48	2		324	202	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50763967	50763967	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376852674	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	99	252	0	ENST00000307179.4:c.824G>A	p.Arg275Gln	p.R275Q	ENST00000307179		275	cGg/cAg	8/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.48	2		252	298	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996053	73996053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465926642	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	184	337	0	ENST00000318443.5:c.787G>A	p.Asp263Asn	p.D263N	ENST00000318443	NM_001024736.1	263	Gat/Aat	5/10	1	2	FACETS	0.828	0.772	0.885	1	0.992	1	CLONAL	2	TRUE	1	0.48	2		337	463	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996083	73996083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776686900	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	127	353	0	ENST00000318443.5:c.817G>A	p.Glu273Lys	p.E273K	ENST00000318443	NM_001024736.1	273	Gag/Aag	5/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.48	2		353	482	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669522	88669522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568926009	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	130	267	0	ENST00000360948.2:c.1376G>A	p.Arg459Gln	p.R459Q	ENST00000360948	NM_001012338.2	459	cGg/cAg	12/19	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.48	2		267	411	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670452	88670452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143617169	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	176	255	0	ENST00000360948.2:c.1234G>A	p.Glu412Lys	p.E412K	ENST00000360948	NM_001012338.2	412	Gaa/Aaa	11/19	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.48	2		255	501	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726711	88726711	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	155	286	1	ENST00000360948.2:c.333G>T	p.Lys111Asn	p.K111N	ENST00000360948	NM_001012338.2	111	aaG/aaT	4/19	1	2	FACETS	0.756	0.699	0.814	1	0.99	1	SUBCLONAL	2	TRUE	1	0.48	2		287	427	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312803	91312803	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	156	202	0	ENST00000355112.3:c.2542C>A	p.Leu848Ile	p.L848I	ENST00000355112	NM_000057.2	848	Ctc/Atc	12/22	1	2	FACETS	0.765	0.708	0.823	1	0.99	1	SUBCLONAL	2	TRUE	1	0.48	2		202	425	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250808	99250808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	173	277	0	ENST00000268035.6:c.112G>A	p.Asp38Asn	p.D38N	ENST00000268035	NM_000875.3	38	Gac/Aac	2/21	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.48	2		277	517	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99452016	99452016	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	185	294	0	ENST00000268035.6:c.1350C>A	p.Phe450Leu	p.F450L	ENST00000268035	NM_000875.3	450	ttC/ttA	6/21	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.48	2		294	540	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465555	99465555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753047347	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	174	331	0	ENST00000268035.6:c.2380C>T	p.Arg794Trp	p.R794W	ENST00000268035	NM_000875.3	794	Cgg/Tgg	11/21	1	2	FACETS	0.762	0.707	0.817	1	0.991	1	SUBCLONAL	2	TRUE	1	0.48	2		331	476	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478605	99478605	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	73	271	0	ENST00000268035.6:c.3247A>G	p.Thr1083Ala	p.T1083A	ENST00000268035	NM_000875.3	1083	Aca/Gca	17/21	1	2	FACETS	0.593	0.519	0.672	0.593	0.519	0.672	SUBCLONAL	1	TRUE	1	0.48	2		271	513	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343539	343539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755020386	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	28	306	0	ENST00000262320.3:c.2135G>A	p.Arg712Gln	p.R712Q	ENST00000262320	NM_003502.3	712	cGa/cAa	8/11	1	2	FACETS	0.222	0.177	0.274	0.222	0.177	0.274	SUBCLONAL	1	TRUE	1	0.48	2		306	525	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3929909	3929909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	137	213	0	ENST00000262367.5:c.9G>T	p.Glu3Asp	p.E3D	ENST00000262367	NM_004380.2	3	gaG/gaT	1/31	1	2	FACETS	0.818	0.754	0.883	1	0.99	1	CLONAL	2	TRUE	1	0.48	2		213	349	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857232	9857232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377337296	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	214	345	2	ENST00000330684.3:c.4169C>T	p.Ser1390Leu	p.S1390L	ENST00000330684	NM_001134407.1	1390	tCg/tTg	13/13	1	2	FACETS	0.767	0.718	0.817	1	0.992	1	SUBCLONAL	2	TRUE	1	0.48	2		347	581	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032105	10032105	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	124	289	0	ENST00000330684.3:c.718C>A	p.Leu240Met	p.L240M	ENST00000330684	NM_001134407.1	240	Ctg/Atg	3/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.48	2		289	418	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026086	14026086	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	111	281	0	ENST00000311895.7:c.1046C>A	p.Ala349Asp	p.A349D	ENST00000311895	NM_005236.2	349	gCc/gAc	6/11	1	2	FACETS	0.863	0.789	0.938	1	0.988	1	CLONAL	2	TRUE	1	0.48	2		281	268	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029408	14029408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368830992	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	67	303	0	ENST00000311895.7:c.1619C>T	p.Ser540Leu	p.S540L	ENST00000311895	NM_005236.2	540	tCg/tTg	8/11	1	2	FACETS	0.523	0.455	0.596	0.523	0.455	0.596	SUBCLONAL	1	TRUE	1	0.48	2		303	534	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029483	14029483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1455880995	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	198	296	0	ENST00000311895.7:c.1694C>T	p.Ala565Val	p.A565V	ENST00000311895	NM_005236.2	565	gCt/gTt	8/11	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.48	2		296	583	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825491	50825491	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1298625546	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	39	238	0	ENST00000398568.2:c.2122G>T	p.Asp708Tyr	p.D708Y	ENST00000398568	NM_001042412.1	708	Gat/Tat	14/18	1	2	FACETS	0.913	0.767	1	0.913	0.767	1	CLONAL	1	TRUE	1	0.48	2		238	178	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782323	56782323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144159027	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	180	245	0	ENST00000308159.5:c.164C>T	p.Thr55Met	p.T55M	ENST00000308159	NM_014669.4	55	aCg/aTg	2/22	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.48	2		245	534	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864581	56864581	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	173	247	2	ENST00000308159.5:c.1069A>G	p.Asn357Asp	p.N357D	ENST00000308159	NM_014669.4	357	Aac/Gac	10/22	1	2	FACETS	0.819	0.762	0.877	1	0.992	1	CLONAL	2	TRUE	1	0.48	2		249	440	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070546	67070546	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	92	303	0	ENST00000412916.2:c.170T>C	p.Phe57Ser	p.F57S	ENST00000412916		57	tTt/tCt	3/6	1	2	FACETS	0.786	0.701	0.875	0.786	0.701	0.875	SUBCLONAL	1	TRUE	1	0.48	2		303	488	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650719	67650719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1131691283	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	224	312	0	ENST00000264010.4:c.1024C>T	p.Arg342Cys	p.R342C	ENST00000264010	NM_006565.3	342	Cgt/Tgt	5/12	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.48	2		312	637	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654625	67654625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	152	269	0	ENST00000264010.4:c.1112G>A	p.Arg371His	p.R371H	ENST00000264010	NM_006565.3	371	cGc/cAc	6/12	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.48	2		269	461	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829616	72829616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745878919	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	100	237	0	ENST00000268489.5:c.6965G>A	p.Arg2322Gln	p.R2322Q	ENST00000268489	NM_006885.3	2322	cGa/cAa	9/10	1	2	FACETS	0.918	0.824	1	0.918	0.824	1	CLONAL	1	TRUE	1	0.48	2		237	454	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993158	72993158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1332687082	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	233	323	0	ENST00000268489.5:c.887C>T	p.Ser296Leu	p.S296L	ENST00000268489	NM_006885.3	296	tCg/tTg	2/10	1	2	FACETS	0.793	0.745	0.842	1	0.993	1	SUBCLONAL	2	TRUE	1	0.48	2		323	612	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993744	72993744	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs751847002	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	85	290	0	ENST00000268489.5:c.301A>G	p.Ser101Gly	p.S101G	ENST00000268489	NM_006885.3	101	Agc/Ggc	2/10	1	2	FACETS	0.794	0.705	0.888	0.794	0.705	0.888	SUBCLONAL	1	TRUE	1	0.48	2		290	446	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819655	81819655	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1248111391	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	181	277	0	ENST00000359376.3:c.61G>T	p.Ala21Ser	p.A21S	ENST00000359376	NM_002661.3	21	Gcc/Tcc	2/33	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.48	2		277	529	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953126	81953126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	31	275	0	ENST00000359376.3:c.2092G>A	p.Asp698Asn	p.D698N	ENST00000359376	NM_002661.3	698	Gac/Aac	20/33	1	2	FACETS	0.25	0.202	0.305	0.25	0.202	0.305	SUBCLONAL	1	TRUE	1	0.48	2		275	516	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965192	81965192	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	134	354	0	ENST00000359376.3:c.2672A>G	p.Asp891Gly	p.D891G	ENST00000359376	NM_002661.3	891	gAc/gGc	25/33	1	2	FACETS	0.976	0.891	1	0.976	0.891	1	CLONAL	1	TRUE	1	0.48	2		354	572	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544548	86544548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	64	298	0	ENST00000262426.4:c.373G>A	p.Asp125Asn	p.D125N	ENST00000262426	NM_001451.2	125	Gac/Aac	1/2	1	2	FACETS	0.606	0.526	0.692	0.606	0.526	0.692	SUBCLONAL	1	TRUE	1	0.48	2		298	440	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348415	89348415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780686131	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	242	383	0	ENST00000301030.4:c.4535G>A	p.Arg1512His	p.R1512H	ENST00000301030	NM_001256183.1	1512	cGc/cAc	9/13	1	2	FACETS	0.877	0.826	0.928	1	0.994	1	CLONAL	2	TRUE	1	0.48	2		383	575	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350710	89350710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138898373	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	121	299	0	ENST00000301030.4:c.2240C>T	p.Ser747Leu	p.S747L	ENST00000301030	NM_001256183.1	747	tCg/tTg	9/13	1	2	FACETS	0.778	0.712	0.845	1	0.987	1	SUBCLONAL	2	TRUE	1	0.48	2		299	324	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351024	89351024	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	150	316	0	ENST00000301030.4:c.1926G>T	p.Glu642Asp	p.E642D	ENST00000301030	NM_001256183.1	642	gaG/gaT	9/13	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.48	2		316	430	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	66	567	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.488	0.423	0.557	0.488	0.423	0.557	SUBCLONAL	1	TRUE	1	0.48	2		567	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	182	524	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.48	2		524	558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579580	7579580	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781866	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	27	276	0	ENST00000269305.4:c.107C>T	p.Pro36Leu	p.P36L	ENST00000269305	NM_001126112.2	36	cCg/cTg	4/11	1	2	FACETS	0.233	0.185	0.289	0.233	0.185	0.289	SUBCLONAL	1	TRUE	1	0.48	2		276	482	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984052	7984052	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	47	308	0	ENST00000319144.4:c.574G>A	p.Ala192Thr	p.A192T	ENST00000319144	NM_001139.2	192	Gcc/Acc	5/15	1	2	FACETS	0.389	0.328	0.457	0.389	0.328	0.457	SUBCLONAL	1	TRUE	1	0.48	2		308	503	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004612	16004612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	64	326	0	ENST00000268712.3:c.2642C>T	p.Ala881Val	p.A881V	ENST00000268712	NM_006311.3	881	gCc/gTc	20/46	1	2	FACETS	0.499	0.433	0.572	0.499	0.433	0.572	SUBCLONAL	1	TRUE	1	0.48	2		326	534	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119793	17119793	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143183215	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	162	274	0	ENST00000285071.4:c.1201C>T	p.Arg401Cys	p.R401C	ENST00000285071	NM_144997.5	401	Cgc/Tgc	11/14	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.48	2		274	463	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496915	29496915	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	35	167	0	ENST00000356175.3:c.486G>T	p.Gln162His	p.Q162H	ENST00000356175	NM_000267.3	162	caG/caT	5/57	1	2	FACETS	0.797	0.66	0.946	0.797	0.66	0.946	CLONAL	1	TRUE	1	0.48	2		167	183	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533316	29533316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1466678870	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	115	305	0	ENST00000356175.3:c.1319G>A	p.Arg440Gln	p.R440Q	ENST00000356175	NM_000267.3	440	cGa/cAa	12/57	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.48	2		305	377	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552231	29552231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	34	278	0	ENST00000356175.3:c.1964G>A	p.Gly655Glu	p.G655E	ENST00000356175	NM_000267.3	655	gGa/gAa	17/57	1	2	FACETS	0.611	0.502	0.731	0.611	0.502	0.731	SUBCLONAL	1	TRUE	1	0.48	2		278	232	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	10	372	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.219	0.148	0.308	0.219	0.148	0.308	SUBCLONAL	1	TRUE	1	0.48	2		372	190	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321607	30321607	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	18	226	0	ENST00000322652.5:c.1462G>T	p.Asp488Tyr	p.D488Y	ENST00000322652	NM_015355.2	488	Gat/Tat	13/16	1	2	FACETS	0.299	0.225	0.386	0.299	0.225	0.386	SUBCLONAL	1	TRUE	1	0.48	2		226	251	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321730	30321730	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	39	222	0	ENST00000322652.5:c.1585C>A	p.Leu529Ile	p.L529I	ENST00000322652	NM_015355.2	529	Ctt/Att	13/16	1	2	FACETS	0.713	0.596	0.841	0.713	0.596	0.841	SUBCLONAL	1	TRUE	1	0.48	2		222	228	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679749	33679749	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs199944678	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	192	346	0	ENST00000308377.4:c.2332C>T	p.Arg778Ter	p.R778*	ENST00000308377	NM_152270.3	778	Cga/Tga	5/5	1	2	FACETS	0.766	0.715	0.819	1	0.992	1	SUBCLONAL	2	TRUE	1	0.48	2		346	522	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679887	33679887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200734680	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	186	589	0	ENST00000308377.4:c.2194C>T	p.Arg732Cys	p.R732C	ENST00000308377	NM_152270.3	732	Cgc/Tgc	5/5	1	2	FACETS	0.781	0.728	0.836	1	0.992	1	SUBCLONAL	2	TRUE	1	0.48	2		589	496	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687382	37687382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	27	303	0	ENST00000447079.4:c.4286C>T	p.Ser1429Phe	p.S1429F	ENST00000447079	NM_015083.1	1429	tCt/tTt	14/14	1	2	FACETS	0.21	0.166	0.26	0.21	0.166	0.26	SUBCLONAL	1	TRUE	1	0.48	2		303	536	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38785098	38785098	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs982006343	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	202	315	0	ENST00000348513.6:c.1175A>G	p.Asn392Ser	p.N392S	ENST00000348513	NM_003079.4	392	aAc/aGc	11/11	1	2	FACETS	0.768	0.717	0.819	1	0.992	1	SUBCLONAL	2	TRUE	1	0.48	2		315	548	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40458277	40458277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	151	221	0	ENST00000345506.4:c.1492G>A	p.Val498Met	p.V498M	ENST00000345506	NM_003152.3	498	Gtg/Atg	14/20	1	2	FACETS	0.753	0.695	0.811	1	0.989	1	SUBCLONAL	2	TRUE	1	0.48	2		221	418	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752444	55752444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1422545682	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	65	257	0	ENST00000284073.2:c.902C>T	p.Ala301Val	p.A301V	ENST00000284073	NM_138962.2	301	gCg/gTg	12/14	1	2	FACETS	0.601	0.522	0.685	0.601	0.522	0.685	SUBCLONAL	1	TRUE	1	0.48	2		257	451	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752459	55752459	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773391520	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	169	255	0	ENST00000284073.2:c.917C>T	p.Pro306Leu	p.P306L	ENST00000284073	NM_138962.2	306	cCg/cTg	12/14	1	2	FACETS	0.769	0.714	0.825	1	0.991	1	SUBCLONAL	2	TRUE	1	0.48	2		255	458	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435533	56435533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369428576	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	29	325	0	ENST00000407977.2:c.1604C>T	p.Ser535Leu	p.S535L	ENST00000407977		535	tCg/tTg	9/10	1	2	FACETS	0.245	0.196	0.301	0.245	0.196	0.301	SUBCLONAL	1	TRUE	1	0.48	2		325	493	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439945	56439945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775028128	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	109	325	0	ENST00000407977.2:c.647C>T	p.Ser216Leu	p.S216L	ENST00000407977		216	tCg/tTg	6/10	1	2	FACETS	0.745	0.67	0.823	0.745	0.67	0.823	SUBCLONAL	1	TRUE	1	0.48	2		325	610	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740702	58740702	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	160	339	0	ENST00000305921.3:c.1607G>T	p.Arg536Met	p.R536M	ENST00000305921	NM_003620.3	536	aGg/aTg	6/6	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.48	2		339	490	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006796	62006796	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs559091155	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	188	371	0	ENST00000392795.3:c.592G>A	p.Glu198Lys	p.E198K	ENST00000392795	NM_001039933.1	198	Gag/Aag	5/6	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.48	2		371	555	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66518962	66518962	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	93	302	0	ENST00000358598.2:c.243G>T	p.Glu81Asp	p.E81D	ENST00000358598	NM_212471.2	81	gaG/gaT	3/11	1	2	FACETS	0.668	0.595	0.746	0.668	0.595	0.746	SUBCLONAL	1	TRUE	1	0.48	2		302	580	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39618810	39618810	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	23	208	0	ENST00000262039.4:c.2034A>C	p.Lys678Asn	p.K678N	ENST00000262039	NM_002647.2	678	aaA/aaC	18/25	1	2	FACETS	0.56	0.44	0.697	0.56	0.44	0.697	SUBCLONAL	1	TRUE	1	0.48	2		208	171	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637885	39637885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200000040	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	60	279	0	ENST00000262039.4:c.2302C>T	p.Arg768Trp	p.R768W	ENST00000262039	NM_002647.2	768	Cgg/Tgg	22/25	1	2	FACETS	0.839	0.728	0.957	0.839	0.728	0.957	CLONAL	1	TRUE	1	0.48	2		279	298	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375016	45375016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226662382	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	115	314	0	ENST00000262160.6:c.827C>T	p.Ser276Leu	p.S276L	ENST00000262160	NM_005901.5	276	tCg/tTg	8/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.48	2		314	322	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390363	56390363	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs902013273	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	107	258	1	ENST00000348428.3:c.1102G>A	p.Glu368Lys	p.E368K	ENST00000348428	NM_006785.3	368	Gaa/Aaa	10/17	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.48	2		259	346	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207002	1207002	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	186	294	0	ENST00000326873.7:c.90C>A	p.Asp30Glu	p.D30E	ENST00000326873	NM_000455.4	30	gaC/gaA	1/10	1	2	FACETS	0.761	0.709	0.815	1	0.991	1	SUBCLONAL	2	TRUE	1	0.48	2		294	509	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3113379	3113379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1170008066	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	205	292	0	ENST00000078429.4:c.373G>A	p.Glu125Lys	p.E125K	ENST00000078429	NM_002067.2	125	Gag/Aag	3/7	1	2	FACETS	0.806	0.754	0.859	1	0.993	1	CLONAL	2	TRUE	1	0.48	2		292	530	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244141	5244141	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	25	337	0	ENST00000357368.4:c.1341G>A	p.Trp447Ter	p.W447*	ENST00000357368	NM_002850.3	447	tgG/tgA	11/38	1	2	FACETS	0.213	0.168	0.266	0.213	0.168	0.266	SUBCLONAL	1	TRUE	1	0.48	2		337	488	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7141705	7141705	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs76077021	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	162	294	1	ENST00000302850.5:c.2665C>T	p.Arg889Trp	p.R889W	ENST00000302850	NM_000208.2	889	Cgg/Tgg	13/22	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.48	2		295	478	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142857	7142857	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	49	245	0	ENST00000302850.5:c.2512G>T	p.Ala838Ser	p.A838S	ENST00000302850	NM_000208.2	838	Gcc/Tcc	12/22	1	2	FACETS	0.372	0.315	0.435	0.372	0.315	0.435	SUBCLONAL	1	TRUE	1	0.48	2		245	549	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142922	7142922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1242001529	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	28	302	0	ENST00000302850.5:c.2447C>T	p.Thr816Met	p.T816M	ENST00000302850	NM_000208.2	816	aCg/aTg	12/22	1	2	FACETS	0.218	0.174	0.27	0.218	0.174	0.27	SUBCLONAL	1	TRUE	1	0.48	2		302	534	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166416	7166416	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	182	264	0	ENST00000302850.5:c.1611-1G>A		p.X537_splice	ENST00000302850	NM_000208.2	537			1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.48	2		264	533	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172413	7172413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764221583	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	141	268	0	ENST00000302850.5:c.1156G>A	p.Gly386Ser	p.G386S	ENST00000302850	NM_000208.2	386	Ggc/Agc	5/22	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.48	2		268	422	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184541	7184541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	62	307	0	ENST00000302850.5:c.760G>A	p.Ala254Thr	p.A254T	ENST00000302850	NM_000208.2	254	Gcc/Acc	3/22	1	2	FACETS	0.443	0.383	0.509	0.443	0.383	0.509	SUBCLONAL	1	TRUE	1	0.48	2		307	583	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100016	11100016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749059769	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	33	293	0	ENST00000358026.2:c.1142G>A	p.Arg381Gln	p.R381Q	ENST00000358026	NM_001128849.1	381	cGa/cAa	7/36	1	2	FACETS	0.244	0.198	0.296	0.244	0.198	0.296	SUBCLONAL	1	TRUE	1	0.48	2		293	564	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152197	11152197	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	132	273	0	ENST00000358026.2:c.4481T>C	p.Met1494Thr	p.M1494T	ENST00000358026	NM_001128849.1	1494	aTg/aCg	31/36	1	2	FACETS	0.995	0.907	1	0.995	0.907	1	CLONAL	1	TRUE	1	0.48	2		273	553	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054535	13054535	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	228	340	0	ENST00000316448.5:c.1062G>T	p.Glu354Asp	p.E354D	ENST00000316448	NM_004343.3	354	gaG/gaT	9/9	1	2	FACETS	0.851	0.8	0.903	1	0.994	1	CLONAL	2	TRUE	1	0.48	2		340	558	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303088	15303088	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	51	283	0	ENST00000263388.2:c.362A>G	p.Asp121Gly	p.D121G	ENST00000263388	NM_000435.2	121	gAt/gGt	4/33	1	2	FACETS	0.469	0.399	0.546	0.469	0.399	0.546	SUBCLONAL	1	TRUE	1	0.48	2		283	453	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215922	36215922	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	183	330	0	ENST00000222270.7:c.3462T>G	p.Phe1154Leu	p.F1154L	ENST00000222270	NM_014727.1	1154	ttT/ttG	10/37	1	2	FACETS	0.755	0.703	0.808	1	0.991	1	SUBCLONAL	2	TRUE	1	0.48	2		330	505	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40761099	40761099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393896368	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	172	317	0	ENST00000392038.2:c.253G>A	p.Glu85Lys	p.E85K	ENST00000392038	NM_001626.4	85	Gag/Aag	4/14	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.48	2		317	495	SUCCESS
AXL	558	MSKCC	GRCh37	19	41737126	41737126	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759570308	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	121	362	0	ENST00000301178.4:c.706C>T	p.Arg236Cys	p.R236C	ENST00000301178	NM_021913.4	236	Cgc/Tgc	6/20	1	2	FACETS	0.985	0.894	1	0.985	0.894	1	CLONAL	1	TRUE	1	0.48	2		362	512	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383618	42383618	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	129	293	0	ENST00000221972.3:c.393G>T	p.Arg131Ser	p.R131S	ENST00000221972	NM_021601.3	131	agG/agT	3/5	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.48	2		293	422	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793159	42793159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	164	534	0	ENST00000575354.2:c.1051C>T	p.Arg351Trp	p.R351W	ENST00000575354	NM_015125.3	351	Cgg/Tgg	7/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.48	2		534	521	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422152	47422152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	176	293	0	ENST00000404338.3:c.220C>T	p.Leu74Phe	p.L74F	ENST00000404338	NM_004491.4	74	Ctc/Ttc	1/6	1	2	FACETS	0.769	0.715	0.824	1	0.991	1	SUBCLONAL	2	TRUE	1	0.48	2		293	477	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918105	50918105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	45	388	0	ENST00000440232.2:c.2422C>T	p.Arg808Cys	p.R808C	ENST00000440232	NM_002691.3	808	Cgc/Tgc	20/27	1	2	FACETS	0.452	0.38	0.531	0.452	0.38	0.531	SUBCLONAL	1	TRUE	1	0.48	2		388	415	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469931	25469931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290621612	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	107	222	0	ENST00000264709.3:c.1111G>A	p.Glu371Lys	p.E371K	ENST00000264709	NM_175629.2	371	Gag/Aag	9/23	1	2	FACETS	0.802	0.722	0.886	0.802	0.722	0.886	CLONAL	1	TRUE	1	0.48	2		222	556	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470926	25470926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1203141216	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	185	338	0	ENST00000264709.3:c.835G>A	p.Asp279Asn	p.D279N	ENST00000264709	NM_175629.2	279	Gat/Aat	7/23	1	2	FACETS	0.78	0.727	0.835	1	0.992	1	SUBCLONAL	2	TRUE	1	0.48	2		338	494	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505360	25505360	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1363529598	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	76	217	0	ENST00000264709.3:c.398A>G	p.Glu133Gly	p.E133G	ENST00000264709	NM_175629.2	133	gAa/gGa	4/23	1	2	FACETS	0.685	0.603	0.773	0.685	0.603	0.773	SUBCLONAL	1	TRUE	1	0.48	2		217	462	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965611	25965611	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	86	305	0	ENST00000435504.4:c.3595C>A	p.Pro1199Thr	p.P1199T	ENST00000435504		1199	Ccc/Acc	13/13	1	2	FACETS	0.633	0.561	0.71	0.633	0.561	0.71	SUBCLONAL	1	TRUE	1	0.48	2		305	566	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982356	25982356	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	132	253	0	ENST00000435504.4:c.934C>T	p.Arg312Ter	p.R312*	ENST00000435504		312	Cga/Tga	9/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.48	2		253	415	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991662	25991662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	172	272	0	ENST00000435504.4:c.580C>A	p.Leu194Ile	p.L194I	ENST00000435504		194	Ctc/Atc	7/13	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.48	2		272	510	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443583	29443583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1462510005	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	103	263	0	ENST00000389048.3:c.3634C>T	p.Arg1212Cys	p.R1212C	ENST00000389048	NM_004304.4	1212	Cgc/Tgc	23/29	1	2	FACETS	0.705	0.632	0.782	0.705	0.632	0.782	SUBCLONAL	1	TRUE	1	0.48	2		263	609	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241093	39241093	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	73	300	0	ENST00000402219.2:c.1978C>T	p.Arg660Cys	p.R660C	ENST00000402219	NM_005633.3	660	Cgc/Tgc	12/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.48	2		300	209	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250031	39250031	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	36	283	0	ENST00000402219.2:c.1538C>T	p.Ala513Val	p.A513V	ENST00000402219	NM_005633.3	513	gCt/gTt	10/23	1	2	FACETS	0.633	0.524	0.753	0.633	0.524	0.753	SUBCLONAL	1	TRUE	1	0.48	2		283	237	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39251279	39251279	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	26	176	0	ENST00000402219.2:c.1075-1G>A		p.X359_splice	ENST00000402219	NM_005633.3	359			1	2	FACETS	0.699	0.56	0.855	0.699	0.56	0.855	SUBCLONAL	1	TRUE	1	0.48	2		176	155	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635558	47635558	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	89	199	1	ENST00000233146.2:c.230G>A	p.Ser77Asn	p.S77N	ENST00000233146	NM_000251.2	77	aGt/aAt	2/16	1	2	FACETS	0.792	0.715	0.872	1	0.984	1	SUBCLONAL	2	TRUE	1	0.48	2		200	234	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027713	48027713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781306	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	120	266	0	ENST00000234420.5:c.2591G>A	p.Gly864Glu	p.G864E	ENST00000234420	NM_000179.2	864	gGa/gAa	4/10	1	2	FACETS	0.903	0.83	0.976	1	0.99	1	CLONAL	2	TRUE	1	0.48	2		266	277	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033420	48033420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779285	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	96	292	0	ENST00000234420.5:c.3724C>T	p.Arg1242Cys	p.R1242C	ENST00000234420	NM_000179.2	1242	Cgt/Tgt	8/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.48	2		292	276	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149332	61149332	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	47	350	0	ENST00000295025.8:c.1522G>T	p.Glu508Ter	p.E508*	ENST00000295025	NM_002908.2	508	Gag/Tag	11/11	1	2	FACETS	0.486	0.411	0.569	0.486	0.411	0.569	SUBCLONAL	1	TRUE	1	0.48	2		350	403	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719233	61719233	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	85	287	0	ENST00000401558.2:c.1824G>A	p.Met608Ile	p.M608I	ENST00000401558	NM_003400.3	608	atG/atA	16/25	1	2	FACETS	0.773	0.696	0.853	1	0.982	1	SUBCLONAL	2	TRUE	1	0.48	2		287	229	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724120	61724120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781425578	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	91	389	0	ENST00000401558.2:c.782G>A	p.Arg261Gln	p.R261Q	ENST00000401558	NM_003400.3	261	cGa/cAa	10/25	1	2	FACETS	0.774	0.699	0.851	1	0.983	1	SUBCLONAL	2	TRUE	1	0.48	2		389	245	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67626735	67626735	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs923756234	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	68	182	0	ENST00000272342.5:c.406A>G	p.Ile136Val	p.I136V	ENST00000272342	NM_019002.3	136	Att/Gtt	3/6	1	2	FACETS	0.964	0.863	1	1	0.984	1	CLONAL	2	TRUE	1	0.48	2		182	147	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128036759	128036759	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs768687646	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	85	235	0	ENST00000285398.2:c.1720C>T	p.Arg574Ter	p.R574*	ENST00000285398	NM_000122.1	574	Cga/Tga	10/15	1	2	FACETS	0.973	0.867	1	0.973	0.867	1	CLONAL	1	TRUE	1	0.48	2		235	364	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128036890	128036890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	141	232	0	ENST00000285398.2:c.1589G>A	p.Arg530Gln	p.R530Q	ENST00000285398	NM_000122.1	530	cGa/cAa	10/15	1	2	FACETS	0.874	0.808	0.941	1	0.991	1	CLONAL	2	TRUE	1	0.48	2		232	336	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044465	128044465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374264195	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	182	264	0	ENST00000285398.2:c.1156G>A	p.Asp386Asn	p.D386N	ENST00000285398	NM_000122.1	386	Gac/Aac	8/15	1	2	FACETS	0.8	0.745	0.856	1	0.992	1	SUBCLONAL	2	TRUE	1	0.48	2		264	474	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050331	128050331	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755616510	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	95	295	0	ENST00000285398.2:c.326G>A	p.Arg109Gln	p.R109Q	ENST00000285398	NM_000122.1	109	cGa/cAa	3/15	1	2	FACETS	0.74	0.661	0.824	0.74	0.661	0.824	SUBCLONAL	1	TRUE	1	0.48	2		295	535	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095986	178095986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201871588	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	59	323	0	ENST00000397062.3:c.1345C>T	p.Arg449Cys	p.R449C	ENST00000397062	NM_006164.4	449	Cgc/Tgc	5/5	1	2	FACETS	0.513	0.442	0.59	0.513	0.442	0.59	SUBCLONAL	1	TRUE	1	0.48	2		323	479	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718969	190718969	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	29	216	0	ENST00000441310.2:c.971C>A	p.Ser324Tyr	p.S324Y	ENST00000441310	NM_000534.4	324	tCt/tAt	9/13	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.48	2		216	108	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257053	198257053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267599149	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	55	242	0	ENST00000335508.6:c.3889C>T	p.Arg1297Cys	p.R1297C	ENST00000335508	NM_012433.2	1297	Cgt/Tgt	25/25	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.48	2		242	196	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270084	198270084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777705664	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	46	332	0	ENST00000335508.6:c.1352G>A	p.Arg451Gln	p.R451Q	ENST00000335508	NM_012433.2	451	cGa/cAa	10/25	1	2	FACETS	0.522	0.441	0.611	0.522	0.441	0.611	SUBCLONAL	1	TRUE	1	0.48	2		332	367	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150030	202150030	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs931648756	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	216	289	0	ENST00000358485.4:c.1471C>T	p.Arg491Ter	p.R491*	ENST00000358485	NM_001080125.1	491	Cga/Tga	8/9	1	2	FACETS	0.78	0.73	0.83	1	0.993	1	SUBCLONAL	2	TRUE	1	0.48	2		289	577	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150039	202150039	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1368296717	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	78	288	0	ENST00000358485.4:c.1480C>T	p.Arg494Ter	p.R494*	ENST00000358485	NM_001080125.1	494	Cga/Tga	8/9	1	2	FACETS	0.588	0.517	0.663	0.588	0.517	0.663	SUBCLONAL	1	TRUE	1	0.48	2		288	553	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248672	212248672	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780519461	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	91	344	0	ENST00000342788.4:c.3595G>A	p.Glu1199Lys	p.E1199K	ENST00000342788	NM_005235.2	1199	Gag/Aag	28/28	1	2	FACETS	0.835	0.745	0.93	0.835	0.745	0.93	CLONAL	1	TRUE	1	0.48	2		344	454	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285282	212285282	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	14	295	0	ENST00000342788.4:c.3019C>A	p.Leu1007Ile	p.L1007I	ENST00000342788	NM_005235.2	1007	Ctc/Atc	25/28	1	2	FACETS	0.225	0.162	0.301	0.225	0.162	0.301	SUBCLONAL	1	TRUE	1	0.48	2		295	259	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295800	212295800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024245860	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	110	276	0	ENST00000342788.4:c.2513G>A	p.Arg838Gln	p.R838Q	ENST00000342788	NM_005235.2	838	cGa/cAa	21/28	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.48	2		276	325	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426728	212426728	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	186	331	0	ENST00000342788.4:c.2387C>A	p.Thr796Asn	p.T796N	ENST00000342788	NM_005235.2	796	aCt/aAt	20/28	1	2	FACETS	0.801	0.746	0.856	1	0.992	1	CLONAL	2	TRUE	1	0.48	2		331	484	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578338	212578338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	69	286	0	ENST00000342788.4:c.919G>A	p.Ala307Thr	p.A307T	ENST00000342788	NM_005235.2	307	Gcc/Acc	8/28	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.48	2		286	259	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339072	225339072	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	15	281	0	ENST00000264414.4:c.2197C>T	p.Arg733Ter	p.R733*	ENST00000264414	NM_003590.4	733	Cga/Tga	16/16	1	2	FACETS	0.302	0.221	0.399	0.302	0.221	0.399	SUBCLONAL	1	TRUE	1	0.48	2		281	207	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346690	225346690	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	77	232	0	ENST00000264414.4:c.1948T>C	p.Ser650Pro	p.S650P	ENST00000264414	NM_003590.4	650	Tca/Cca	14/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.48	2		232	226	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370819	225370819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199694647	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	66	272	0	ENST00000264414.4:c.1060C>T	p.Arg354Cys	p.R354C	ENST00000264414	NM_003590.4	354	Cgc/Tgc	8/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.48	2		272	228	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242800934	242800934	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	66	291	0	ENST00000334409.5:c.57G>A	p.Trp19Ter	p.W19*	ENST00000334409	NM_005018.2	19	tgG/tgA	1/5	1	2	FACETS	0.597	0.519	0.68	0.597	0.519	0.68	SUBCLONAL	1	TRUE	1	0.48	2		291	461	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561504	9561504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542553062	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	25	286	0	ENST00000353224.5:c.278C>T	p.Ser93Leu	p.S93L	ENST00000353224	NM_177990.2	93	tCg/tTg	4/10	1	2	FACETS	0.21	0.164	0.262	0.21	0.164	0.262	SUBCLONAL	1	TRUE	1	0.48	2		286	497	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021646	31021646	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1299423705	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	80	319	0	ENST00000375687.4:c.1645C>T	p.Arg549Cys	p.R549C	ENST00000375687	NM_015338.5	549	Cgt/Tgt	12/13	1	2	FACETS	0.629	0.555	0.708	0.629	0.555	0.708	SUBCLONAL	1	TRUE	1	0.48	2		319	530	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023108	31023108	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147895689	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	191	332	0	ENST00000375687.4:c.2593G>A	p.Glu865Lys	p.E865K	ENST00000375687	NM_015338.5	865	Gaa/Aaa	13/13	1	2	FACETS	0.762	0.711	0.815	1	0.992	1	SUBCLONAL	2	TRUE	1	0.48	2		332	522	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023598	31023598	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200702600	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	29	301	1	ENST00000375687.4:c.3083C>T	p.Ser1028Leu	p.S1028L	ENST00000375687	NM_015338.5	1028	tCg/tTg	13/13	1	2	FACETS	0.236	0.189	0.291	0.236	0.189	0.291	SUBCLONAL	1	TRUE	1	0.48	2		302	511	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012734	36012734	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	152	264	0	ENST00000358208.4:c.178G>A	p.Glu60Lys	p.E60K	ENST00000358208		60	Gag/Aag	2/12	1	2	FACETS	0.84	0.778	0.903	1	0.991	1	CLONAL	2	TRUE	1	0.48	2		264	377	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713383	40713383	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs773803715	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	87	352	0	ENST00000373198.4:c.4132C>T	p.Arg1378Ter	p.R1378*	ENST00000373198	NM_133170.3	1378	Cga/Tga	30/32	1	2	FACETS	0.588	0.521	0.66	0.588	0.521	0.66	SUBCLONAL	1	TRUE	1	0.48	2		352	616	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911144	40911144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776134993	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	86	211	0	ENST00000373198.4:c.2161C>T	p.Arg721Cys	p.R721C	ENST00000373198	NM_133170.3	721	Cgt/Tgt	13/32	1	2	FACETS	0.87	0.786	0.955	1	0.985	1	CLONAL	2	TRUE	1	0.48	2		211	206	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948513	54948513	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	20	251	0	ENST00000312783.6:c.805G>T	p.Glu269Ter	p.E269*	ENST00000312783	NM_198436.1	269	Gag/Tag	8/10	1	2	FACETS	0.276	0.211	0.352	0.276	0.211	0.352	SUBCLONAL	1	TRUE	1	0.48	2		251	302	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39774559	39774559	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1283544903	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	158	253	0	ENST00000288319.7:c.593C>T	p.Thr198Ile	p.T198I	ENST00000288319	NM_182918.3	198	aCt/aTt	5/10	1	2	FACETS	0.859	0.798	0.922	1	0.992	1	CLONAL	2	TRUE	1	0.48	2		253	383	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795352	39795352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372598575	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	27	286	0	ENST00000288319.7:c.368G>A	p.Arg123His	p.R123H	ENST00000288319	NM_182918.3	123	cGc/cAc	3/10	1	2	FACETS	0.218	0.172	0.269	0.218	0.172	0.269	SUBCLONAL	1	TRUE	1	0.48	2		286	517	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121015	29121015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121908701	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	33	258	0	ENST00000328354.6:c.542G>A	p.Arg181His	p.R181H	ENST00000328354	NM_007194.3	181	cGt/cAt	4/15	1	2	FACETS	0.595	0.488	0.715	0.595	0.488	0.715	SUBCLONAL	1	TRUE	1	0.48	2		258	231	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568612	41568612	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	19	316	0	ENST00000263253.7:c.4562A>G	p.Glu1521Gly	p.E1521G	ENST00000263253	NM_001429.3	1521	gAa/gGa	28/31	1	2	FACETS	0.24	0.182	0.308	0.24	0.182	0.308	SUBCLONAL	1	TRUE	1	0.48	2		316	330	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691878	30691878	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	162	311	0	ENST00000295754.5:c.380A>C	p.Lys127Thr	p.K127T	ENST00000295754	NM_003242.5	127	aAa/aCa	3/7	1	2	FACETS	0.783	0.726	0.841	1	0.991	1	SUBCLONAL	2	TRUE	1	0.48	2		311	431	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729969	30729969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200958264	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	218	287	1	ENST00000295754.5:c.1490G>A	p.Arg497Gln	p.R497Q	ENST00000295754	NM_003242.5	497	cGa/cAa	6/7	1	2	FACETS	0.812	0.762	0.864	1	0.993	1	CLONAL	2	TRUE	1	0.48	2		288	559	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37045944	37045944	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	68	294	0	ENST00000231790.2:c.359C>A	p.Ala120Asp	p.A120D	ENST00000231790	NM_000249.3	120	gCt/gAt	4/19	1	2	FACETS	0.859	0.752	0.972	0.859	0.752	0.972	CLONAL	1	TRUE	1	0.48	2		294	330	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277291	41277291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	69	319	0	ENST00000349496.5:c.1760G>A	p.Arg587Gln	p.R587Q	ENST00000349496	NM_001904.3	587	cGa/cAa	11/15	1	2	FACETS	0.694	0.607	0.788	0.694	0.607	0.788	SUBCLONAL	1	TRUE	1	0.48	2		319	414	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103660	47103660	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	26	312	0	ENST00000409792.3:c.6286G>T	p.Asp2096Tyr	p.D2096Y	ENST00000409792	NM_014159.6	2096	Gat/Tat	14/21	1	2	FACETS	0.213	0.168	0.265	0.213	0.168	0.265	SUBCLONAL	1	TRUE	1	0.48	2		312	509	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158180	47158180	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	24	233	2	ENST00000409792.3:c.4519G>T	p.Asp1507Tyr	p.D1507Y	ENST00000409792	NM_014159.6	1507	Gat/Tat	4/21	1	2	FACETS	0.397	0.312	0.494	0.397	0.312	0.494	SUBCLONAL	1	TRUE	1	0.48	2		235	252	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439913	52439913	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	172	254	0	ENST00000460680.1:c.799C>G	p.Gln267Glu	p.Q267E	ENST00000460680	NM_004656.3	267	Cag/Gag	10/17	1	2	FACETS	0.82	0.763	0.878	1	0.992	1	CLONAL	2	TRUE	1	0.48	2		254	437	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643542	52643542	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	113	279	0	ENST00000394830.3:c.2354T>A	p.Leu785His	p.L785H	ENST00000394830	NM_018313.4	785	cTt/cAt	17/30	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.48	2		279	382	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63983318	63983318	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs370385147	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	119	258	0	ENST00000398590.3:c.2683C>T	p.Arg895Ter	p.R895*	ENST00000398590	NM_001177387.1	895	Cga/Tga	13/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.48	2		258	388	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987049	69987049	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	166	340	0	ENST00000394351.3:c.110C>A	p.Ser37Tyr	p.S37Y	ENST00000394351	NM_000248.3	37	tCt/tAt	2/9	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.48	2		340	488	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72891539	72891539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755870786	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	71	279	0	ENST00000325599.8:c.223C>T	p.Arg75Cys	p.R75C	ENST00000325599	NM_018130.2	75	Cgc/Tgc	3/11	1	2	FACETS	0.652	0.57	0.739	0.652	0.57	0.739	SUBCLONAL	1	TRUE	1	0.48	2		279	454	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72893510	72893510	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	16	213	0	ENST00000325599.8:c.208G>T	p.Gly70Ter	p.G70*	ENST00000325599	NM_018130.2	70	Gga/Tga	2/11	1	2	FACETS	0.394	0.293	0.515	0.394	0.293	0.515	SUBCLONAL	1	TRUE	1	0.48	2		213	169	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114559	73114559	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	44	170	1	ENST00000356692.5:c.940A>G	p.Thr314Ala	p.T314A	ENST00000356692		314	Aca/Gca	9/9	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.48	2		171	148	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259251	89259251	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	57	292	0	ENST00000336596.2:c.395G>A	p.Gly132Glu	p.G132E	ENST00000336596	NM_005233.5	132	gGg/gAg	3/17	1	2	FACETS	0.759	0.655	0.87	0.759	0.655	0.87	SUBCLONAL	1	TRUE	1	0.48	2		292	313	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720928	119720928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	43	267	0	ENST00000316626.5:c.247G>A	p.Ala83Thr	p.A83T	ENST00000316626		83	Gcc/Acc	2/12	1	2	FACETS	0.509	0.427	0.599	0.509	0.427	0.599	SUBCLONAL	1	TRUE	1	0.48	2		267	352	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967264	134967264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748426868	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	75	355	0	ENST00000398015.3:c.2603G>A	p.Arg868Gln	p.R868Q	ENST00000398015	NM_004441.4	868	cGg/cAg	14/16	1	2	FACETS	0.571	0.501	0.646	0.571	0.501	0.646	SUBCLONAL	1	TRUE	1	0.48	2		355	547	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413638	138413638	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs375492591	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	88	313	0	ENST00000289153.2:c.1882C>T	p.Arg628Ter	p.R628*	ENST00000289153	NM_006219.2	628	Cga/Tga	12/22	1	2	FACETS	0.78	0.694	0.871	0.78	0.694	0.871	SUBCLONAL	1	TRUE	1	0.48	2		313	470	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453486	138453486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451809865	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	27	230	0	ENST00000289153.2:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000289153	NM_006219.2	321	cGa/cAa	5/22	1	2	FACETS	0.598	0.48	0.732	0.598	0.48	0.732	SUBCLONAL	1	TRUE	1	0.48	2		230	188	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461453	138461453	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	92	257	0	ENST00000289153.2:c.568G>T	p.Asp190Tyr	p.D190Y	ENST00000289153	NM_006219.2	190	Gat/Tat	3/22	1	2	FACETS	0.758	0.684	0.833	1	0.983	1	SUBCLONAL	2	TRUE	1	0.48	2		257	253	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178199	142178199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746049210	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	75	271	0	ENST00000350721.4:c.7219C>T	p.Arg2407Cys	p.R2407C	ENST00000350721	NM_001184.3	2407	Cgc/Tgc	43/47	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.48	2		271	251	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998141	169998141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1428010723	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	18	262	0	ENST00000295797.4:c.832C>T	p.Arg278Cys	p.R278C	ENST00000295797	NM_002740.5	278	Cgt/Tgt	9/18	1	2	FACETS	0.22	0.165	0.285	0.22	0.165	0.285	SUBCLONAL	1	TRUE	1	0.48	2		262	341	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178943780	178943780	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	77	222	0	ENST00000263967.3:c.2447T>G	p.Ile816Ser	p.I816S	ENST00000263967	NM_006218.2	816	aTt/aGt	17/21	1	2	FACETS	0.886	0.797	0.978	1	0.984	1	CLONAL	2	TRUE	1	0.48	2		222	181	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430231	181430231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	102	268	0	ENST00000325404.1:c.83C>T	p.Ala28Val	p.A28V	ENST00000325404	NM_003106.3	28	gCg/gTg	1/1	1	2	FACETS	0.964	0.867	1	0.964	0.867	1	CLONAL	1	TRUE	1	0.48	2		268	441	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183582	185183582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1272940392	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	64	287	0	ENST00000265026.3:c.1436C>T	p.Ala479Val	p.A479V	ENST00000265026	NM_004721.4	479	gCg/gTg	9/14	1	2	FACETS	0.644	0.56	0.735	0.644	0.56	0.735	SUBCLONAL	1	TRUE	1	0.48	2		287	414	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191451	185191451	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	93	335	0	ENST00000265026.3:c.2332G>T	p.Glu778Ter	p.E778*	ENST00000265026	NM_004721.4	778	Gaa/Taa	11/14	1	2	FACETS	0.733	0.653	0.817	0.733	0.653	0.817	SUBCLONAL	1	TRUE	1	0.48	2		335	529	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505347	186505347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	71	285	0	ENST00000323963.5:c.973C>T	p.Arg325Cys	p.R325C	ENST00000323963		325	Cgt/Tgt	9/11	1	2	FACETS	0.76	0.667	0.86	0.76	0.667	0.86	SUBCLONAL	1	TRUE	1	0.48	2		285	389	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186507027	186507027	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	128	236	0	ENST00000323963.5:c.1193A>G	p.Glu398Gly	p.E398G	ENST00000323963		398	gAg/gGg	11/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.48	2		236	379	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807650	1807650	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	136	301	0	ENST00000260795.2:c.1819T>C	p.Tyr607His	p.Y607H	ENST00000260795		607	Tac/Cac	12/17	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.48	2		301	474	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1941428	1941428	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	130	261	0	ENST00000382891.5:c.1804C>T	p.Arg602Trp	p.R602W	ENST00000382891	NM_133335.3	602	Cgg/Tgg	9/22	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.48	2		261	474	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1941494	1941494	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1253622631	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	143	232	0	ENST00000382891.5:c.1870A>C	p.Thr624Pro	p.T624P	ENST00000382891	NM_133335.3	624	Act/Cct	9/22	1	2	FACETS	0.77	0.71	0.831	1	0.989	1	SUBCLONAL	2	TRUE	1	0.48	2		232	387	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1978208	1978208	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	79	375	0	ENST00000382891.5:c.3628A>G	p.Thr1210Ala	p.T1210A	ENST00000382891	NM_133335.3	1210	Acg/Gcg	21/22	1	2	FACETS	0.564	0.496	0.636	0.564	0.496	0.636	SUBCLONAL	1	TRUE	1	0.48	2		375	584	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129918	55129918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501501	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	92	323	0	ENST00000257290.5:c.452G>A	p.Arg151His	p.R151H	ENST00000257290	NM_006206.4	151	cGc/cAc	4/23	1	2	FACETS	0.816	0.728	0.908	0.816	0.728	0.908	CLONAL	1	TRUE	1	0.48	2		323	470	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155192	55155192	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	24	360	0	ENST00000257290.5:c.2791A>G	p.Lys931Glu	p.K931E	ENST00000257290	NM_006206.4	931	Aaa/Gaa	21/23	1	2	FACETS	0.227	0.177	0.284	0.227	0.177	0.284	SUBCLONAL	1	TRUE	1	0.48	2		360	441	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564494	55564494	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	72	243	0	ENST00000288135.5:c.382G>T	p.Glu128Ter	p.E128*	ENST00000288135	NM_000222.2	128	Gaa/Taa	3/21	1	2	FACETS	0.629	0.551	0.713	0.629	0.551	0.713	SUBCLONAL	1	TRUE	1	0.48	2		243	477	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565870	55565870	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	125	225	0	ENST00000288135.5:c.694A>G	p.Thr232Ala	p.T232A	ENST00000288135	NM_000222.2	232	Acg/Gcg	4/21	1	2	FACETS	0.777	0.713	0.843	1	0.988	1	SUBCLONAL	2	TRUE	1	0.48	2		225	335	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593707	55593707	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	105	306	0	ENST00000288135.5:c.1773T>G	p.Phe591Leu	p.F591L	ENST00000288135	NM_000222.2	591	ttT/ttG	11/21	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.48	2		306	314	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961055	55961055	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1229432573	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	29	460	0	ENST00000263923.4:c.2885G>A	p.Arg962His	p.R962H	ENST00000263923	NM_002253.2	962	cGc/cAc	21/30	1	2	FACETS	0.261	0.209	0.32	0.261	0.209	0.32	SUBCLONAL	1	TRUE	1	0.48	2		460	463	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972903	55972903	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	21	211	0	ENST00000263923.4:c.1487A>C	p.Lys496Thr	p.K496T	ENST00000263923	NM_002253.2	496	aAa/aCa	11/30	1	2	FACETS	0.515	0.399	0.647	0.515	0.399	0.647	SUBCLONAL	1	TRUE	1	0.48	2		211	170	SUCCESS
REST	5978	MSKCC	GRCh37	4	57786019	57786019	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs869025312	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	17	236	0	ENST00000309042.7:c.965A>G	p.His322Arg	p.H322R	ENST00000309042	NM_005612.4	322	cAt/cGt	3/4	1	2	FACETS	0.367	0.275	0.476	0.367	0.275	0.476	SUBCLONAL	1	TRUE	1	0.48	2		236	193	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796749	57796750	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	122	345	0	ENST00000309042.7:c.1732dup	p.Ser578LysfsTer10	p.S578Kfs*10	ENST00000309042	NM_005612.4	575	-/A	4/4	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.48	2		345	365	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213873	66213873	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1383933498	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	88	308	0	ENST00000273854.3:c.2557C>T	p.Arg853Ter	p.R853*	ENST00000273854	NM_004439.5	853	Cga/Tga	15/18	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.48	2		308	260	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218804	66218804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759048340	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	11	259	0	ENST00000273854.3:c.2254G>A	p.Val752Met	p.V752M	ENST00000273854	NM_004439.5	752	Gtg/Atg	13/18	1	2	FACETS	0.345	0.239	0.474	0.345	0.239	0.474	SUBCLONAL	1	TRUE	1	0.48	2		259	133	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356133	66356133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1349813115	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	85	271	0	ENST00000273854.3:c.1364G>A	p.Arg455Gln	p.R455Q	ENST00000273854	NM_004439.5	455	cGg/cAg	5/18	1	2	FACETS	0.785	0.697	0.879	0.785	0.697	0.879	SUBCLONAL	1	TRUE	1	0.48	2		271	451	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467380	66467380	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	137	273	0	ENST00000273854.3:c.889G>T	p.Glu297Ter	p.E297*	ENST00000273854	NM_004439.5	297	Gag/Tag	3/18	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.48	2		273	412	SUCCESS
ALB	213	MSKCC	GRCh37	4	74275129	74275129	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	31	313	1	ENST00000295897.4:c.540C>A	p.Phe180Leu	p.F180L	ENST00000295897	NM_000477.5	180	ttC/ttA	5/15	1	2	FACETS	0.515	0.418	0.623	0.515	0.418	0.623	SUBCLONAL	1	TRUE	1	0.48	2		314	251	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84403390	84403390	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	95	283	0	ENST00000321945.7:c.95T>G	p.Phe32Cys	p.F32C	ENST00000321945	NM_139076.2	32	tTt/tGt	2/9	1	2	FACETS	0.773	0.7	0.849	1	0.984	1	SUBCLONAL	2	TRUE	1	0.48	2		283	256	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158212	106158212	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	170	332	0	ENST00000380013.4:c.3113A>C	p.Lys1038Thr	p.K1038T	ENST00000380013	NM_001127208.2	1038	aAg/aCg	3/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.48	2		332	512	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106182921	106182921	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	47	193	0	ENST00000380013.4:c.3960G>T	p.Glu1320Asp	p.E1320D	ENST00000380013	NM_001127208.2	1320	gaG/gaT	8/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.48	2		193	150	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193892	106193892	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1049545383	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	195	265	0	ENST00000380013.4:c.4354C>T	p.Arg1452Ter	p.R1452*	ENST00000380013	NM_001127208.2	1452	Cga/Tga	10/11	1	2	FACETS	0.789	0.736	0.842	1	0.992	1	SUBCLONAL	2	TRUE	1	0.48	2		265	515	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003277	143003277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369778611	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	123	232	1	ENST00000262992.4:c.2549C>T	p.Ser850Leu	p.S850L	ENST00000262992	NM_001101669.1	850	tCg/tTg	23/24	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.48	2		233	346	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130088	143130088	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1193204060	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	22	222	0	ENST00000262992.4:c.928A>G	p.Met310Val	p.M310V	ENST00000262992	NM_001101669.1	310	Atg/Gtg	11/24	1	2	FACETS	0.485	0.378	0.608	0.485	0.378	0.608	SUBCLONAL	1	TRUE	1	0.48	2		222	189	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332921	153332921	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	62	318	0	ENST00000281708.4:c.35G>T	p.Arg12Ile	p.R12I	ENST00000281708	NM_033632.3	12	aGa/aTa	2/12	1	2	FACETS	0.435	0.375	0.5	0.435	0.375	0.5	SUBCLONAL	1	TRUE	1	0.48	2		318	594	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509933	187509933	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	77	332	0	ENST00000441802.2:c.13580T>C	p.Phe4527Ser	p.F4527S	ENST00000441802	NM_005245.3	4527	tTc/tCc	27/27	1	2	FACETS	0.563	0.495	0.636	0.563	0.495	0.636	SUBCLONAL	1	TRUE	1	0.48	2		332	570	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525049	187525049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	129	295	0	ENST00000441802.2:c.10631C>T	p.Ala3544Val	p.A3544V	ENST00000441802	NM_005245.3	3544	gCg/gTg	19/27	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.48	2		295	384	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539570	187539570	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	20	334	0	ENST00000441802.2:c.8170C>A	p.Leu2724Ile	p.L2724I	ENST00000441802	NM_005245.3	2724	Ctc/Atc	10/27	1	2	FACETS	0.222	0.169	0.284	0.222	0.169	0.284	SUBCLONAL	1	TRUE	1	0.48	2		334	375	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539852	187539852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765674305	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	212	328	0	ENST00000441802.2:c.7888G>A	p.Asp2630Asn	p.D2630N	ENST00000441802	NM_005245.3	2630	Gac/Aac	10/27	1	2	FACETS	0.793	0.742	0.844	1	0.993	1	SUBCLONAL	2	TRUE	1	0.48	2		328	557	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542188	187542188	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1308584602	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	43	361	0	ENST00000441802.2:c.5552A>G	p.Asp1851Gly	p.D1851G	ENST00000441802	NM_005245.3	1851	gAc/gGc	10/27	1	2	FACETS	0.479	0.402	0.564	0.479	0.402	0.564	SUBCLONAL	1	TRUE	1	0.48	2		361	374	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228307	228307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762108779	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	35	122	0	ENST00000264932.6:c.629G>A	p.Arg210Gln	p.R210Q	ENST00000264932	NM_004168.2	210	cGa/cAa	6/15	1	2	FACETS	0.81	0.672	0.962	0.81	0.672	0.962	CLONAL	1	TRUE	1	0.48	2		122	180	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409433	31409433	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	87	283	0	ENST00000344624.3:c.3674T>C	p.Ile1225Thr	p.I1225T	ENST00000344624		1225	aTt/aCt	29/33	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.48	2		283	263	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31466354	31466354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376262500	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	130	269	0	ENST00000344624.3:c.2401C>T	p.Arg801Cys	p.R801C	ENST00000344624		801	Cgc/Tgc	16/33	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.48	2		269	395	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31521284	31521284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371022450	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	137	274	0	ENST00000344624.3:c.893G>A	p.Arg298Gln	p.R298Q	ENST00000344624		298	cGa/cAa	3/33	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.48	2		274	397	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861044	35861044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1327554053	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	156	242	0	ENST00000303115.3:c.173C>T	p.Ala58Val	p.A58V	ENST00000303115	NM_002185.3	58	gCt/gTt	2/8	1	2	FACETS	0.774	0.716	0.833	1	0.99	1	SUBCLONAL	2	TRUE	1	0.48	2		242	420	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871314	35871314	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs200751605	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	53	233	0	ENST00000303115.3:c.536C>T	p.Thr179Met	p.T179M	ENST00000303115	NM_002185.3	179	aCg/aTg	4/8	1	2	FACETS	0.821	0.706	0.945	0.821	0.706	0.945	CLONAL	1	TRUE	1	0.48	2		233	269	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459710	149459710	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	31	361	0	ENST00000286301.3:c.497G>T	p.Arg166Met	p.R166M	ENST00000286301	NM_005211.3	166	aGg/aTg	4/22	1	2	FACETS	0.241	0.194	0.294	0.241	0.194	0.294	SUBCLONAL	1	TRUE	1	0.48	2		361	537	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502704	149502704	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375978065	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	70	318	0	ENST00000261799.4:c.2084G>A	p.Arg695His	p.R695H	ENST00000261799	NM_002609.3	695	cGc/cAc	15/23	1	2	FACETS	0.59	0.516	0.671	0.59	0.516	0.671	SUBCLONAL	1	TRUE	1	0.48	2		318	494	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503888	149503888	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	141	269	0	ENST00000261799.4:c.1948T>C	p.Ser650Pro	p.S650P	ENST00000261799	NM_002609.3	650	Tcg/Ccg	14/23	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.48	2		269	419	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673772	176673772	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374330497	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	133	257	0	ENST00000439151.2:c.4472C>T	p.Ser1491Leu	p.S1491L	ENST00000439151	NM_022455.4	1491	tCg/tTg	10/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.48	2		257	452	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176700744	176700744	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886041218	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	132	242	0	ENST00000439151.2:c.5581C>T	p.Arg1861Ter	p.R1861*	ENST00000439151	NM_022455.4	1861	Cga/Tga	17/23	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.48	2		242	368	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707597	176707597	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	82	292	0	ENST00000439151.2:c.5654T>C	p.Phe1885Ser	p.F1885S	ENST00000439151	NM_022455.4	1885	tTc/tCc	18/23	1	2	FACETS	0.741	0.656	0.832	0.741	0.656	0.832	SUBCLONAL	1	TRUE	1	0.48	2		292	461	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721927	176721927	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	216	348	0	ENST00000439151.2:c.7558G>A	p.Ala2520Thr	p.A2520T	ENST00000439151	NM_022455.4	2520	Gca/Aca	23/23	1	2	FACETS	0.756	0.708	0.806	1	0.992	1	SUBCLONAL	2	TRUE	1	0.48	2		348	595	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030251	180030251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781063816	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	179	309	0	ENST00000261937.6:c.4033G>A	p.Glu1345Lys	p.E1345K	ENST00000261937	NM_182925.4	1345	Gag/Aag	30/30	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.48	2		309	517	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041170	180041170	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	210	372	0	ENST00000261937.6:c.3229C>T	p.Pro1077Ser	p.P1077S	ENST00000261937	NM_182925.4	1077	Ccc/Tcc	24/30	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.48	2		372	631	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048881	180048881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751002839	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	183	289	0	ENST00000261937.6:c.1681G>A	p.Glu561Lys	p.E561K	ENST00000261937	NM_182925.4	561	Gaa/Aaa	13/30	1	2	FACETS	0.776	0.723	0.831	1	0.991	1	SUBCLONAL	2	TRUE	1	0.48	2		289	491	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052971	180052971	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753074837	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	183	362	0	ENST00000261937.6:c.1319G>A	p.Arg440His	p.R440H	ENST00000261937	NM_182925.4	440	cGc/cAc	10/30	1	2	FACETS	0.766	0.713	0.82	1	0.991	1	SUBCLONAL	2	TRUE	1	0.48	2		362	498	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056400	180056400	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	79	262	0	ENST00000261937.6:c.844C>T	p.Arg282Ter	p.R282*	ENST00000261937	NM_182925.4	282	Cga/Tga	7/30	1	2	FACETS	0.673	0.594	0.758	0.673	0.594	0.758	SUBCLONAL	1	TRUE	1	0.48	2		262	489	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407576	407576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756602021	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	57	317	0	ENST00000380956.4:c.1334G>A	p.Arg445His	p.R445H	ENST00000380956	NM_001195286.1	445	cGc/cAc	9/9	1	2	FACETS	0.637	0.548	0.732	0.637	0.548	0.732	SUBCLONAL	1	TRUE	1	0.48	2		317	373	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488434	20488434	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	143	322	0	ENST00000346618.3:c.1090A>C	p.Asn364His	p.N364H	ENST00000346618	NM_001949.4	364	Aac/Cac	6/7	1	2	FACETS	0.818	0.756	0.882	1	0.99	1	CLONAL	2	TRUE	1	0.48	2		322	364	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020781	26020781	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1029963018	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	180	330	0	ENST00000357647.3:c.64G>A	p.Ala22Thr	p.A22T	ENST00000357647	NM_003529.2	22	Gcc/Acc	1/1	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.48	2		330	502	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021009	26021009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	201	389	1	ENST00000357647.3:c.292G>A	p.Glu98Lys	p.E98K	ENST00000357647	NM_003529.2	98	Gag/Aag	1/1	1	2	FACETS	0.777	0.726	0.829	1	0.992	1	SUBCLONAL	2	TRUE	1	0.48	2		390	539	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197068	26197068	+	stop_lost	Nonstop_Mutation	SNP	T	T	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	178	309	0	ENST00000356476.2:c.411A>C	p.Ter137TyrextTer?	p.*137Yext*?	ENST00000356476		137	taA/taC	1/1	1	2	FACETS	0.761	0.708	0.816	1	0.991	1	SUBCLONAL	2	TRUE	1	0.48	2		309	487	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671241	30671241	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763451532	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	211	318	1	ENST00000376406.3:c.5636G>A	p.Arg1879His	p.R1879H	ENST00000376406	NM_014641.2	1879	cGc/cAc	11/15	1	2	FACETS	0.789	0.739	0.841	1	0.993	1	SUBCLONAL	2	TRUE	1	0.48	2		319	557	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671951	30671951	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	143	342	0	ENST00000376406.3:c.5009T>C	p.Val1670Ala	p.V1670A	ENST00000376406	NM_014641.2	1670	gTc/gCc	10/15	1	2	FACETS	0.978	0.895	1	0.978	0.895	1	CLONAL	1	TRUE	1	0.48	2		342	609	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673437	30673437	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	180	350	0	ENST00000376406.3:c.3523G>T	p.Asp1175Tyr	p.D1175Y	ENST00000376406	NM_014641.2	1175	Gac/Tac	10/15	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.48	2		350	506	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31239616	31239616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	22	75	0	ENST00000376228.5:c.103G>A	p.Ala35Thr	p.A35T	ENST00000376228	NM_002117.5	35	Gcc/Acc	2/8	1	2	FACETS	0.751	0.605	0.906	1	0.934	1	CLONAL	2	TRUE	1	0.48	2		75	61	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183106	32183106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	28	323	0	ENST00000375023.3:c.1918T>C	p.Cys640Arg	p.C640R	ENST00000375023	NM_004557.3	640	Tgt/Cgt	12/30	1	2	FACETS	0.219	0.175	0.271	0.219	0.175	0.271	SUBCLONAL	1	TRUE	1	0.48	2		323	532	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185010	32185010	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	37	300	0	ENST00000375023.3:c.1658A>G	p.Asp553Gly	p.D553G	ENST00000375023	NM_004557.3	553	gAt/gGt	10/30	1	2	FACETS	0.275	0.226	0.33	0.275	0.226	0.33	SUBCLONAL	1	TRUE	1	0.48	2		300	560	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816544	32816544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376553490	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	106	334	0	ENST00000354258.4:c.1631G>A	p.Arg544His	p.R544H	ENST00000354258	NM_000593.5	544	cGc/cAc	7/11	1	2	FACETS	0.714	0.641	0.79	0.714	0.641	0.79	SUBCLONAL	1	TRUE	1	0.48	2		334	619	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821226	32821226	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	51	280	0	ENST00000354258.4:c.368G>T	p.Ser123Ile	p.S123I	ENST00000354258	NM_000593.5	123	aGc/aTc	1/11	1	2	FACETS	0.467	0.397	0.543	0.467	0.397	0.543	SUBCLONAL	1	TRUE	1	0.48	2		280	455	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36653571	36653571	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	154	226	0	ENST00000244741.5:c.489G>T	p.Lys163Asn	p.K163N	ENST00000244741	NM_000389.4	163	aaG/aaT	3/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.48	2		226	492	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140900	37140900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773910971	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	203	342	0	ENST00000373509.5:c.736G>A	p.Glu246Lys	p.E246K	ENST00000373509	NM_002648.3	246	Gaa/Aaa	5/6	1	2	FACETS	0.799	0.748	0.852	1	0.993	1	SUBCLONAL	2	TRUE	1	0.48	2		342	529	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112035560	112035560	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	139	258	0	ENST00000368678.4:c.334T>G	p.Leu112Val	p.L112V	ENST00000368678		112	Ttg/Gtg	4/13	1	2	FACETS	0.891	0.824	0.959	1	0.991	1	CLONAL	2	TRUE	1	0.48	2		258	325	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041180	112041180	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	76	326	0	ENST00000368678.4:c.75C>A	p.Ser25Arg	p.S25R	ENST00000368678		25	agC/agA	3/13	1	2	FACETS	0.546	0.479	0.618	0.546	0.479	0.618	SUBCLONAL	1	TRUE	1	0.48	2		326	580	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609950	117609950	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1304088293	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	108	264	0	ENST00000368508.3:c.6749T>C	p.Val2250Ala	p.V2250A	ENST00000368508	NM_002944.2	2250	gTg/gCg	43/43	0.3	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.48	1		264	279	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658458	117658458	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1240366975	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	73	334	0	ENST00000368508.3:c.5125G>T	p.Gly1709Cys	p.G1709C	ENST00000368508	NM_002944.2	1709	Ggt/Tgt	31/43	0.3	1	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	0	0.48	1		334	231	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674236	117674236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	157	293	0	ENST00000368508.3:c.4238G>A	p.Gly1413Glu	p.G1413E	ENST00000368508	NM_002944.2	1413	gGa/gAa	26/43	0.3	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.48	1		293	420	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677969	117677969	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	108	277	0	ENST00000368508.3:c.3964A>C	p.Asn1322His	p.N1322H	ENST00000368508	NM_002944.2	1322	Aac/Cac	25/43	0.3	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.48	1		277	282	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199772	138199772	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	95	293	0	ENST00000237289.4:c.1190C>A	p.Ser397Tyr	p.S397Y	ENST00000237289	NM_001270507.1	397	tCt/tAt	7/9	1	2	FACETS	0.795	0.71	0.884	0.795	0.71	0.884	SUBCLONAL	1	TRUE	1	0.48	2		293	498	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997689	149997689	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	25	291	0	ENST00000253339.5:c.2776+2T>C		p.X926_splice	ENST00000253339		926			1	2	FACETS	0.26	0.204	0.324	0.26	0.204	0.324	SUBCLONAL	1	TRUE	1	0.48	2		291	401	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001055	150001055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	12	286	0	ENST00000253339.5:c.2549G>A	p.Cys850Tyr	p.C850Y	ENST00000253339		850	tGc/tAc	4/7	1	2	FACETS	0.211	0.148	0.289	0.211	0.148	0.289	SUBCLONAL	1	TRUE	1	0.48	2		286	237	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222613	157222613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1296046545	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	37	319	0	ENST00000346085.5:c.1880C>T	p.Ala627Val	p.A627V	ENST00000346085	NM_020732.3	627	gCg/gTg	4/20	1	2	FACETS	0.254	0.209	0.305	0.254	0.209	0.305	SUBCLONAL	1	TRUE	1	0.48	2		319	607	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517412	157517412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138785718	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	68	222	0	ENST00000346085.5:c.3976C>T	p.Arg1326Cys	p.R1326C	ENST00000346085	NM_020732.3	1326	Cgc/Tgc	16/20	1	2	FACETS	0.576	0.502	0.656	0.576	0.502	0.656	SUBCLONAL	1	TRUE	1	0.48	2		222	492	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946387	2946387	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	176	270	0	ENST00000396946.4:c.3350A>G	p.Tyr1117Cys	p.Y1117C	ENST00000396946	NM_032415.4	1117	tAc/tGc	25/25	1	2	FACETS	0.789	0.733	0.845	1	0.991	1	SUBCLONAL	2	TRUE	1	0.48	2		270	465	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956956	2956956	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs750486472	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	31	237	0	ENST00000396946.4:c.2671C>T	p.Arg891Ter	p.R891*	ENST00000396946	NM_032415.4	891	Cga/Tga	20/25	1	2	FACETS	0.246	0.198	0.3	0.246	0.198	0.3	SUBCLONAL	1	TRUE	1	0.48	2		237	526	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985558	2985559	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	27	281	0	ENST00000396946.4:c.252dup	p.Gln85AlafsTer78	p.Q85Afs*78	ENST00000396946	NM_032415.4	84	-/G	4/25	1	2	FACETS	0.23	0.182	0.285	0.23	0.182	0.285	SUBCLONAL	1	TRUE	1	0.48	2		281	489	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273042	55273042	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	76	376	0	ENST00000275493.2:c.3365A>G	p.Asp1122Gly	p.D1122G	ENST00000275493	NM_005228.3	1122	gAc/gGc	28/28	1	2	FACETS	0.468	0.41	0.53	0.468	0.41	0.53	SUBCLONAL	1	TRUE	1	0.48	2		376	677	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346604	81346604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	63	261	0	ENST00000222390.5:c.1349C>T	p.Pro450Leu	p.P450L	ENST00000222390	NM_000601.4	450	cCc/cTc	11/18	1	2	FACETS	0.798	0.695	0.908	0.798	0.695	0.908	CLONAL	1	TRUE	1	0.48	2		261	329	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508253	106508253	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	183	296	0	ENST00000359195.3:c.247G>A	p.Val83Met	p.V83M	ENST00000359195	NM_002649.2	83	Gtg/Atg	2/11	1	2	FACETS	0.778	0.724	0.833	1	0.992	1	SUBCLONAL	2	TRUE	1	0.48	2		296	490	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526609	106526609	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	30	252	0	ENST00000359195.3:c.2902A>G	p.Ile968Val	p.I968V	ENST00000359195	NM_002649.2	968	Att/Gtt	10/11	1	2	FACETS	0.49	0.397	0.595	0.49	0.397	0.595	SUBCLONAL	1	TRUE	1	0.48	2		252	255	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526694	106526694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772274649	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	44	259	0	ENST00000359195.3:c.2987G>A	p.Gly996Glu	p.G996E	ENST00000359195	NM_002649.2	996	gGa/gAa	10/11	1	2	FACETS	0.481	0.404	0.566	0.481	0.404	0.566	SUBCLONAL	1	TRUE	1	0.48	2		259	381	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395430	116395430	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778445	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	95	285	0	ENST00000397752.3:c.1723C>A	p.Leu575Ile	p.L575I	ENST00000397752	NM_000245.2	575	Ctt/Att	6/21	1	2	FACETS	0.773	0.7	0.849	1	0.984	1	SUBCLONAL	2	TRUE	1	0.48	2		285	256	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124469334	124469334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	61	210	0	ENST00000357628.3:c.1568C>T	p.Ser523Leu	p.S523L	ENST00000357628	NM_015450.2	523	tCg/tTg	16/19	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.48	2		210	189	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124532413	124532413	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	41	244	0	ENST00000357628.3:c.31T>G	p.Tyr11Asp	p.Y11D	ENST00000357628	NM_015450.2	11	Tat/Gat	6/19	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.48	2		244	117	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843345	128843345	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1288405827	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	72	303	0	ENST00000249373.3:c.452G>A	p.Arg151Gln	p.R151Q	ENST00000249373	NM_005631.4	151	cGa/cAa	2/12	1	2	FACETS	0.599	0.524	0.679	0.599	0.524	0.679	SUBCLONAL	1	TRUE	1	0.48	2		303	501	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482836	140482836	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs575016745	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	174	338	0	ENST00000288602.6:c.1299A>C	p.Glu433Asp	p.E433D	ENST00000288602	NM_004333.4	433	gaA/gaC	10/18	1	2	FACETS	0.841	0.783	0.9	1	0.992	1	CLONAL	2	TRUE	1	0.48	2		338	431	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515021	148515021	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	151	289	0	ENST00000320356.2:c.1188G>T	p.Glu396Asp	p.E396D	ENST00000320356	NM_004456.4	396	gaG/gaT	10/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.48	2		289	425	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523590	148523590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	125	265	0	ENST00000320356.2:c.863G>A	p.Arg288Gln	p.R288Q	ENST00000320356	NM_004456.4	288	cGa/cAa	8/20	1	2	FACETS	0.768	0.704	0.834	1	0.988	1	SUBCLONAL	2	TRUE	1	0.48	2		265	339	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860557	151860557	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	82	361	0	ENST00000262189.6:c.10105A>G	p.Thr3369Ala	p.T3369A	ENST00000262189	NM_170606.2	3369	Aca/Gca	43/59	1	2	FACETS	0.568	0.501	0.639	0.568	0.501	0.639	SUBCLONAL	1	TRUE	1	0.48	2		361	602	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864332	151864332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1251668458	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	169	307	0	ENST00000262189.6:c.9649C>T	p.Arg3217Cys	p.R3217C	ENST00000262189	NM_170606.2	3217	Cgt/Tgt	42/59	1	2	FACETS	0.76	0.706	0.816	1	0.991	1	SUBCLONAL	2	TRUE	1	0.48	2		307	463	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879229	151879229	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763438739	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	57	323	0	ENST00000262189.6:c.5716C>T	p.Arg1906Ter	p.R1906*	ENST00000262189	NM_170606.2	1906	Cga/Tga	36/59	1	2	FACETS	0.49	0.421	0.565	0.49	0.421	0.565	SUBCLONAL	1	TRUE	1	0.48	2		323	485	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345765	152345765	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	132	232	0	ENST00000359321.1:c.805T>G	p.Phe269Val	p.F269V	ENST00000359321	NM_005431.1	269	Ttt/Gtt	3/3	1	2	FACETS	0.804	0.74	0.87	1	0.989	1	CLONAL	2	TRUE	1	0.48	2		232	342	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539027	23539027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751677679	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	32	565	0	ENST00000380871.4:c.412G>A	p.Glu138Lys	p.E138K	ENST00000380871	NM_006167.3	138	Gag/Aag	2/2	0.3	3	FACETS	0.275	0.222	0.335	0.092	0.074	0.112	SUBCLONAL	1	TRUE	0	0.48	3		565	601	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205193	38205193	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	21	274	0	ENST00000317025.8:c.497A>C	p.Glu166Ala	p.E166A	ENST00000317025	NM_023034.1	166	gAa/gCa	2/24	1	2	FACETS	0.227	0.174	0.288	0.227	0.174	0.288	SUBCLONAL	1	TRUE	1	0.48	2		274	386	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864534	56864534	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	43	277	0	ENST00000519728.1:c.497C>A	p.Ser166Tyr	p.S166Y	ENST00000519728	NM_002350.3	166	tCt/tAt	7/13	1	2	FACETS	0.725	0.612	0.849	0.725	0.612	0.849	SUBCLONAL	1	TRUE	1	0.48	2		277	247	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68984780	68984780	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	17	270	0	ENST00000288368.4:c.1544A>G	p.Lys515Arg	p.K515R	ENST00000288368	NM_024870.2	515	aAa/aGa	14/40	1	2	FACETS	0.349	0.261	0.453	0.349	0.261	0.453	SUBCLONAL	1	TRUE	1	0.48	2		270	203	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970976	70970976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1208665663	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	180	283	0	ENST00000276594.2:c.1285G>A	p.Asp429Asn	p.D429N	ENST00000276594	NM_024504.3	429	Gat/Aat	6/8	1	2	FACETS	0.791	0.736	0.847	1	0.992	1	SUBCLONAL	2	TRUE	1	0.48	2		283	474	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70971059	70971059	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	142	292	0	ENST00000276594.2:c.1202G>T	p.Arg401Ile	p.R401I	ENST00000276594	NM_024504.3	401	aGa/aTa	6/8	1	2	FACETS	0.766	0.706	0.828	1	0.989	1	SUBCLONAL	2	TRUE	1	0.48	2		292	386	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542196	141542196	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	204	302	0	ENST00000220592.5:c.2527G>T	p.Ala843Ser	p.A843S	ENST00000220592	NM_012154.3	843	Gcc/Tcc	19/19	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.48	2		302	570	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141557714	141557714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	182	272	0	ENST00000220592.5:c.1601G>A	p.Arg534His	p.R534H	ENST00000220592	NM_012154.3	534	cGc/cAc	13/19	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.48	2		272	544	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739743	145739743	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373178405	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	92	292	0	ENST00000428558.2:c.1708C>T	p.Arg570Trp	p.R570W	ENST00000428558	NM_004260.3	570	Cgg/Tgg	11/22	1	2	FACETS	0.83	0.741	0.924	0.83	0.741	0.924	CLONAL	1	TRUE	1	0.48	2		292	462	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2029228	2029228	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1165246987	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	155	323	0	ENST00000349721.2:c.206G>A	p.Gly69Asp	p.G69D	ENST00000349721	NM_003070.3	69	gGc/gAc	2/34	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.48	2		323	458	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2081937	2081937	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	156	288	0	ENST00000349721.2:c.2290A>G	p.Thr764Ala	p.T764A	ENST00000349721	NM_003070.3	764	Act/Gct	15/34	1	2	FACETS	0.81	0.751	0.871	1	0.991	1	CLONAL	2	TRUE	1	0.48	2		288	401	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2104068	2104068	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747313863	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	178	289	0	ENST00000349721.2:c.3191C>T	p.Ala1064Val	p.A1064V	ENST00000349721	NM_003070.3	1064	gCg/gTg	23/34	1	2	FACETS	0.769	0.716	0.824	1	0.991	1	SUBCLONAL	2	TRUE	1	0.48	2		289	482	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054752	5054752	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	83	271	0	ENST00000381652.3:c.804G>T	p.Glu268Asp	p.E268D	ENST00000381652	NM_004972.3	268	gaG/gaT	7/25	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.48	2		271	240	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457400	5457400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1480335907	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	147	267	0	ENST00000381577.3:c.374G>A	p.Arg125Gln	p.R125Q	ENST00000381577	NM_014143.3	125	cGa/cAa	3/7	1	2	FACETS	0.817	0.755	0.88	1	0.99	1	CLONAL	2	TRUE	1	0.48	2		267	375	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319965	8319965	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs141403124	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	159	223	0	ENST00000356435.5:c.5536G>A	p.Ala1846Thr	p.A1846T	ENST00000356435		1846	Gcg/Acg	34/35	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.48	2		223	478	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436666	8436666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	93	237	0	ENST00000356435.5:c.4012C>T	p.Pro1338Ser	p.P1338S	ENST00000356435		1338	Ccc/Tcc	24/35	1	2	FACETS	0.954	0.869	1	1	0.988	1	CLONAL	2	TRUE	1	0.48	2		237	203	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528597	8528597	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	109	247	0	ENST00000356435.5:c.535C>T	p.Arg179Ter	p.R179*	ENST00000356435		179	Cga/Tga	4/35	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.48	2		247	304	SUCCESS
MTAP	4507	MSKCC	GRCh37	9	21854751	21854751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200708704	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	30	299	1	ENST00000380172.4:c.572C>T	p.Ala191Val	p.A191V	ENST00000380172	NM_002451.3	191	gCg/gTg	6/8	1	2	FACETS	0.224	0.18	0.275	0.224	0.18	0.275	SUBCLONAL	1	TRUE	1	0.48	2		300	557	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21968228	21968228	+	stop_lost	Nonstop_Mutation	SNP	T	T	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	176	283	0	ENST00000304494.5:c.471A>T	p.Ter157CysextTer13	p.*157Cext*13	ENST00000304494	NM_000077.4	157	tgA/tgT	3/3	1	2	FACETS	0.799	0.743	0.855	1	0.992	1	SUBCLONAL	2	TRUE	1	0.48	2		283	459	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158089	27158089	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	163	339	0	ENST00000380036.4:c.313C>T	p.Arg105Ter	p.R105*	ENST00000380036	NM_000459.3	105	Cga/Tga	2/23	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.48	2		339	490	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27192520	27192520	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	54	264	0	ENST00000380036.4:c.1523A>C	p.Glu508Ala	p.E508A	ENST00000380036	NM_000459.3	508	gAa/gCa	11/23	1	2	FACETS	0.472	0.403	0.546	0.472	0.403	0.546	SUBCLONAL	1	TRUE	1	0.48	2		264	477	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020741	37020741	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	53	288	0	ENST00000358127.4:c.104A>G	p.Asp35Gly	p.D35G	ENST00000358127	NM_001280556.1	35	gAt/gGt	2/10	1	2	FACETS	0.436	0.372	0.507	0.436	0.372	0.507	SUBCLONAL	1	TRUE	1	0.48	2		288	506	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430560	80430560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	36	138	0	ENST00000286548.4:c.448G>A	p.Glu150Lys	p.E150K	ENST00000286548	NM_002072.3	150	Gaa/Aaa	3/7	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.48	2		138	110	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635251	87635251	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	161	245	0	ENST00000277120.3:c.2303A>C	p.Gln768Pro	p.Q768P	ENST00000277120		768	cAg/cCg	18/19	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.48	2		245	458	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93629441	93629441	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	160	224	0	ENST00000375746.1:c.875G>T	p.Arg292Ile	p.R292I	ENST00000375746	NM_001174167.1	292	aGa/aTa	7/14	1	2	FACETS	0.84	0.779	0.901	1	0.991	1	CLONAL	2	TRUE	1	0.48	2		224	397	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209478	98209478	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	191	294	0	ENST00000331920.6:c.4060T>G	p.Ser1354Ala	p.S1354A	ENST00000331920	NM_000264.3	1354	Tcc/Gcc	23/24	1	2	FACETS	0.847	0.791	0.903	1	0.993	1	CLONAL	2	TRUE	1	0.48	2		294	470	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128230352	128230352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530682321	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	57	300	0	ENST00000265960.3:c.1244C>T	p.Thr415Met	p.T415M	ENST00000265960	NM_001006617.1	415	aCg/aTg	10/12	1	2	FACETS	0.55	0.473	0.633	0.55	0.473	0.633	SUBCLONAL	1	TRUE	1	0.48	2		300	432	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137323827	137323827	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762302539	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	169	279	0	ENST00000481739.1:c.1120G>A	p.Val374Ile	p.V374I	ENST00000481739	NM_002957.4	374	Gtc/Atc	8/10	1	2	FACETS	0.8	0.743	0.858	1	0.991	1	SUBCLONAL	2	TRUE	1	0.48	2		279	440	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407515	139407515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762729988	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	165	251	0	ENST00000277541.6:c.2425G>A	p.Asp809Asn	p.D809N	ENST00000277541	NM_017617.3	809	Gac/Aac	15/34	1	2	FACETS	0.79	0.733	0.848	1	0.991	1	SUBCLONAL	2	TRUE	1	0.48	2		251	435	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15809068	15809068	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	184	250	0	ENST00000307771.7:c.53A>G	p.Tyr18Cys	p.Y18C	ENST00000307771	NM_005089.3	18	tAc/tGc	2/11	1	2	FACETS	0.786	0.732	0.84	1	0.992	1	SUBCLONAL	2	TRUE	1	0.48	2		250	488	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841213	15841213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765274095	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	104	339	0	ENST00000307771.7:c.1297C>T	p.Arg433Cys	p.R433C	ENST00000307771	NM_005089.3	433	Cgc/Tgc	11/11	1	2	FACETS	0.637	0.571	0.707	0.637	0.571	0.707	SUBCLONAL	1	TRUE	1	0.48	2		339	680	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931610	39931610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781373724	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	33	284	0	ENST00000378444.4:c.2989G>A	p.Ala997Thr	p.A997T	ENST00000378444	NM_001123385.1	997	Gca/Aca	4/15	1	2	FACETS	0.237	0.193	0.288	0.237	0.193	0.288	SUBCLONAL	1	TRUE	1	0.48	2		284	579	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932705	39932705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762605753	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	142	350	0	ENST00000378444.4:c.1894G>A	p.Gly632Ser	p.G632S	ENST00000378444	NM_001123385.1	632	Ggc/Agc	4/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.48	2		350	540	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969417	44969417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370298215	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	42	256	0	ENST00000377967.4:c.4099G>A	p.Gly1367Arg	p.G1367R	ENST00000377967	NM_021140.2	1367	Gga/Aga	28/29	1	2	FACETS	0.549	0.46	0.646	0.549	0.46	0.646	SUBCLONAL	1	TRUE	1	0.48	2		256	319	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045784	47045784	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	89	343	1	ENST00000377604.3:c.2665G>A	p.Glu889Lys	p.E889K	ENST00000377604	NM_001204468.1	889	Gag/Aag	23/24	1	2	FACETS	0.692	0.615	0.774	0.692	0.615	0.774	SUBCLONAL	1	TRUE	1	0.48	2		344	536	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222969	53222969	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	171	277	0	ENST00000375401.3:c.4103G>A	p.Gly1368Asp	p.G1368D	ENST00000375401	NM_004187.3	1368	gGc/gAc	24/26	1	2	FACETS	0.764	0.71	0.82	1	0.991	1	SUBCLONAL	2	TRUE	1	0.48	2		277	466	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53254028	53254028	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	158	276	0	ENST00000375401.3:c.44C>T	p.Pro15Leu	p.P15L	ENST00000375401	NM_004187.3	15	cCg/cTg	1/26	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.48	2		276	461	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413013	63413013	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1285996741	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	201	325	0	ENST00000330258.3:c.154C>G	p.Leu52Val	p.L52V	ENST00000330258	NM_152424.3	52	Ctg/Gtg	2/2	1	2	FACETS	0.853	0.798	0.908	1	0.993	1	CLONAL	2	TRUE	1	0.48	2		325	491	SUCCESS
AR	367	MSKCC	GRCh37	X	66765778	66765778	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	177	390	0	ENST00000374690.3:c.790C>T	p.Arg264Trp	p.R264W	ENST00000374690	NM_000044.3	264	Cgg/Tgg	1/8	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.48	2		390	530	SUCCESS
AR	367	MSKCC	GRCh37	X	66766331	66766331	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	100	141	0	ENST00000374690.3:c.1343G>A	p.Gly448Glu	p.G448E	ENST00000374690	NM_000044.3	448	gGa/gAa	1/8	1	2	FACETS	0.795	0.722	0.87	1	0.986	1	SUBCLONAL	2	TRUE	1	0.48	2		141	262	SUCCESS
AR	367	MSKCC	GRCh37	X	66942688	66942688	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	52	247	0	ENST00000374690.3:c.2469A>C	p.Lys823Asn	p.K823N	ENST00000374690	NM_000044.3	823	aaA/aaC	7/8	1	2	FACETS	0.623	0.532	0.721	0.623	0.532	0.721	SUBCLONAL	1	TRUE	1	0.48	2		247	348	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342672	70342672	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	117	257	0	ENST00000374080.3:c.1433A>G	p.Asp478Gly	p.D478G	ENST00000374080		478	gAc/gGc	10/45	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.48	2		257	456	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776380	76776380	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	43	290	0	ENST00000373344.5:c.7086G>T	p.Met2362Ile	p.M2362I	ENST00000373344	NM_000489.3	2362	atG/atT	34/35	0.275278798321476	0	FACETS	0.41	0.346	0.48			1	INDETERMINATE	1	TRUE	0	0.48	0		290	227	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872138	76872138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	60	213	0	ENST00000373344.5:c.5509G>A	p.Val1837Met	p.V1837M	ENST00000373344	NM_000489.3	1837	Gtg/Atg	22/35	0.275278798321476	0	FACETS	0.73	0.641	0.823			1	INDETERMINATE	1	TRUE	0	0.48	0		213	178	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937236	76937236	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	43	306	1	ENST00000373344.5:c.3512G>T	p.Arg1171Ile	p.R1171I	ENST00000373344	NM_000489.3	1171	aGa/aTa	9/35	0.275278798321476	0	FACETS	0.558	0.474	0.647			1	INDETERMINATE	1	TRUE	0	0.48	0		307	167	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938174	76938174	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	105	309	0	ENST00000373344.5:c.2574del	p.Gly859GlufsTer10	p.G859Efs*10	ENST00000373344	NM_000489.3	858	aaA/aa	9/35	0.275278798321476	0	FACETS	0.753	0.684	0.825			1	INDETERMINATE	1	TRUE	0	0.48	0		309	302	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938911	76938911	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	120	285	0	ENST00000373344.5:c.1837G>T	p.Asp613Tyr	p.D613Y	ENST00000373344	NM_000489.3	613	Gat/Tat	9/35	0.275278798321476	0	FACETS	0.828	0.758	0.899			1	INDETERMINATE	1	TRUE	0	0.48	0		285	314	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938967	76938967	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782774889	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	86	299	0	ENST00000373344.5:c.1781C>T	p.Ser594Phe	p.S594F	ENST00000373344	NM_000489.3	594	tCc/tTc	9/35	0.275278798321476	0	FACETS	0.824	0.743	0.908			1	INDETERMINATE	1	TRUE	0	0.48	0		299	226	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952157	76952157	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	56	231	0	ENST00000373344.5:c.278A>C	p.Asp93Ala	p.D93A	ENST00000373344	NM_000489.3	93	gAt/gCt	5/35	0.275278798321476	0	FACETS	0.867	0.762	0.974			1	INDETERMINATE	1	TRUE	0	0.48	0		231	140	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611788	100611788	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	53	214	0	ENST00000308731.7:c.1333G>T	p.Glu445Ter	p.E445*	ENST00000308731	NM_000061.2	445	Gaa/Taa	14/19	1	2	FACETS	0.686	0.588	0.792	0.686	0.588	0.792	SUBCLONAL	1	TRUE	1	0.48	2		214	322	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630266	100630266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368549990	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	48	279	0	ENST00000308731.7:c.7G>A	p.Ala3Thr	p.A3T	ENST00000308731	NM_000061.2	3	Gca/Aca	2/19	1	2	FACETS	0.485	0.411	0.567	0.485	0.411	0.567	SUBCLONAL	1	TRUE	1	0.48	2		279	412	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019669	123019669	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	131	290	0	ENST00000355640.3:c.157C>A	p.Leu53Ile	p.L53I	ENST00000355640		53	Ctt/Att	2/7	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.48	2		290	409	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019684	123019684	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	22	289	0	ENST00000355640.3:c.172G>T	p.Gly58Ter	p.G58*	ENST00000355640		58	Gga/Tga	2/7	1	2	FACETS	0.218	0.168	0.276	0.218	0.168	0.276	SUBCLONAL	1	TRUE	1	0.48	2		289	420	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176470	123176470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	69	237	0	ENST00000218089.9:c.437G>A	p.Arg146Gln	p.R146Q	ENST00000218089	NM_001042749.1	146	cGa/cAa	7/35	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.48	2		237	199	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190006	123190006	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs773224655	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	20	230	0	ENST00000218089.9:c.1225G>T	p.Asp409Tyr	p.D409Y	ENST00000218089	NM_001042749.1	409	Gat/Tat	14/35	1	2	FACETS	0.427	0.328	0.542	0.427	0.328	0.542	SUBCLONAL	1	TRUE	1	0.48	2		230	195	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190069	123190069	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	64	218	0	ENST00000218089.9:c.1288G>T	p.Glu430Ter	p.E430*	ENST00000218089	NM_001042749.1	430	Gaa/Taa	14/35	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.48	2		218	202	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205161	123205161	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	50	197	0	ENST00000218089.9:c.2521A>C	p.Asn841His	p.N841H	ENST00000218089	NM_001042749.1	841	Aat/Cat	25/35	1	2	FACETS	0.795	0.693	0.901	1	0.972	1	CLONAL	2	TRUE	1	0.48	2		197	131	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215251	123215251	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	48	185	0	ENST00000218089.9:c.2797G>T	p.Glu933Ter	p.E933*	ENST00000218089	NM_001042749.1	933	Gaa/Taa	28/35	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.48	2		185	147	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215311	123215311	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	61	229	0	ENST00000218089.9:c.2857C>T	p.Arg953Ter	p.R953*	ENST00000218089	NM_001042749.1	953	Cga/Tga	28/35	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.48	2		229	189	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480496	123480496	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	153	218	0	ENST00000371139.4:c.4G>T	p.Asp2Tyr	p.D2Y	ENST00000371139	NM_001114937.2	2	Gac/Tac	1/4	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.48	2		218	445	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251542	251542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200397144	NA	P-0067425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	24	192	0	ENST00000264932.6:c.1753C>T	p.Arg585Trp	p.R585W	ENST00000264932	NM_004168.2	585	Cgg/Tgg	13/15	1	2	FACETS	0.351	0.275	0.438	0.351	0.275	0.438	SUBCLONAL	1	TRUE	1	0.48	2		192	285	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374882	45374882	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs776149698	NA	P-0067435-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	46	404	0	ENST00000262160.6:c.961C>T	p.Arg321Ter	p.R321*	ENST00000262160	NM_005901.5	321	Cga/Tga	8/11	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	FALSE	1	0.279494259619898	2		404	309	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368252	45368252	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067435-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	26	499	0	ENST00000262160.6:c.1350C>G	p.Asp450Glu	p.D450E	ENST00000262160	NM_005901.5	450	gaC/gaG	11/11	1	2	FACETS	0.744	0.592	0.918	0.744	0.592	0.918	CLONAL	1	FALSE	1	0.279494259619898	2		499	250	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554453	63554453	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067435-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	119	723	0	ENST00000307078.5:c.286C>T	p.Arg96Ter	p.R96*	ENST00000307078	NM_004655.3	96	Cga/Tga	2/11	0.279494259619898	1	FACETS	0.915	0.841	0.989	1	0.992	1	CLONAL	3	FALSE	0	0.279494259619898	1		723	267	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843302	128843302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067435-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	34	574	0	ENST00000249373.3:c.409G>T	p.Asp137Tyr	p.D137Y	ENST00000249373	NM_005631.4	137	Gac/Tac	2/12	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	FALSE	1	0.279494259619898	2		574	210	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398286	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0067435-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	46	271	0	ENST00000311936.3:c.33_34delinsCT	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	11	gcTGgt/gcCTgt	2/5	0.145724624232166	4	FACETS	0.813	0.69	0.947	0.813	0.69	0.947	INDETERMINATE	2	FALSE	2	0.279494259619898	4		271	259	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482778	67482778	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067435-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	77	513	0	ENST00000327367.4:c.1182C>A	p.Cys394Ter	p.C394*	ENST00000327367	NM_005902.3	394	tgC/tgA	9/9	0.279494259619898	2	FACETS	0.987	0.877	1	0.987	0.877	1	CLONAL	2	FALSE	0	0.279494259619898	2		513	279	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448303	56448304	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0067435-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	104	607	0	ENST00000407977.2:c.342_343dup	p.Ala115GlyfsTer44	p.A115Gfs*44	ENST00000407977		115	gcc/gGGcc	3/10	0.279494259619898	1	FACETS	1	0.942	1	1	0.989	1	CLONAL	2	FALSE	0	0.279494259619898	1		607	304	SUCCESS
ATR	545	MSKCC	GRCh37	3	142218469	142218469	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067435-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	22	299	0	ENST00000350721.4:c.5380G>A	p.Asp1794Asn	p.D1794N	ENST00000350721	NM_001184.3	1794	Gat/Aat	31/47	1	2	FACETS	0.682	0.53	0.856	0.682	0.53	0.856	SUBCLONAL	1	FALSE	1	0.279494259619898	2		299	231	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778767	76778767	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067436-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	120	527	0	ENST00000373344.5:c.6812G>C	p.Arg2271Thr	p.R2271T	ENST00000373344	NM_000489.3	2271	aGa/aCa	31/35	0.661230294115037	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.661230294115037	1		527	234	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821467	32821467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067436-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	134	510	0	ENST00000354258.4:c.127C>T	p.Arg43Trp	p.R43W	ENST00000354258	NM_000593.5	43	Cgg/Tgg	1/11	1	2	FACETS	0.913	0.836	0.992	0.913	0.836	0.992	CLONAL	1	TRUE	1	0.661230294115037	2		510	444	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461166	120461166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200693165	NA	P-0067439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	53	439	1	ENST00000256646.2:c.5792G>A	p.Arg1931His	p.R1931H	ENST00000256646	NM_024408.3	1931	cGc/cAc	32/34	0.738447005281466	2	FACETS	0.456	0.391	0.526	0.228	0.195	0.263	SUBCLONAL	1	TRUE	0	0.738447005281466	2		440	315	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039230	49039230	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	258	381	0	ENST00000267163.4:c.2308C>T	p.Gln770Ter	p.Q770*	ENST00000267163	NM_000321.2	770	Cag/Tag	22/27	0.738447005281466	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.738447005281466	2		381	322	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562657	29562660	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs1064794276	NA	P-0067439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	244	423	0	ENST00000356175.3:c.3739_3742del	p.Phe1247IlefsTer18	p.F1247Ifs*18	ENST00000356175	NM_000267.3	1246	cTGTTt/ct	28/57	0.738447005281466	2	FACETS	0.955	0.915	0.994	0.955	0.915	0.994	CLONAL	2	TRUE	0	0.738447005281466	2		423	346	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796883	42796883	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	288	661	0	ENST00000575354.2:c.3347del	p.Pro1116GlnfsTer45	p.P1116Qfs*45	ENST00000575354	NM_015125.3	1114	gCc/gc	14/20	0.732241590418632	2	FACETS	0.907	0.87	0.943	0.907	0.87	0.943	CLONAL	2	TRUE	0	0.738447005281466	2		661	430	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128030517	128030517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	33	403	0	ENST00000285398.2:c.1751C>T	p.Thr584Met	p.T584M	ENST00000285398	NM_000122.1	584	aCg/aTg	11/15	0.738447005281466	2	FACETS	0.264	0.215	0.319	0.132	0.107	0.16	SUBCLONAL	1	TRUE	0	0.738447005281466	2		403	338	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090086	37090086	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63751310	NA	P-0067439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	263	412	0	ENST00000231790.2:c.1975C>T	p.Arg659Ter	p.R659*	ENST00000231790	NM_000249.3	659	Cga/Tga	17/19	0.738447005281466	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.738447005281466	2		412	347	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288573	33288573	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs202141130	NA	P-0067439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	303	465	0	ENST00000374542.5:c.979C>T	p.Arg327Ter	p.R327*	ENST00000374542	NM_001141970.1	327	Cga/Tga	3/8	0.738447005281466	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.738447005281466	2		465	399	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798734	135798734	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs118203390	NA	P-0067439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	231	426	1	ENST00000298552.3:c.508+1G>A		p.X170_splice	ENST00000298552	NM_001162426.1	170			0.738447005281466	2	FACETS	0.957	0.915	0.996	0.957	0.915	0.996	CLONAL	2	TRUE	0	0.738447005281466	2		427	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577605	7577631	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAACCTAGGAGATAACACAGGCCCAAG	CAACCTAGGAGATAACACAGGCCCAAG	-	novel	NA	P-0067439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	247	434	0	ENST00000269305.4:c.673-23_676del		p.X225_splice	ENST00000269305	NM_001126112.2	225		7/11	0.738447005281466	2	FACETS	0.981	0.941	1	0.981	0.941	1	CLONAL	2	TRUE	0	0.738447005281466	2		434	341	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361140	70361148	+	inframe_deletion	In_Frame_Del	DEL	CAACAGCAA	CAACAGCAA	-	novel	NA	P-0067439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	237	432	0	ENST00000374080.3:c.6339_6347del	p.Gln2113_Gln2115del	p.Q2113_Q2115del	ENST00000374080		2110	CAACAGCAA/-	43/45	0.691836517138425	2	FACETS	0.789	0.749	0.828			1	SUBCLONAL	2	TRUE	NA	0.738447005281466	2		432	407	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0067440-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	17	524	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		524	403	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs149840192	NA	P-0067440-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	41	883	2	ENST00000275493.2:c.866C>A	p.Ala289Asp	p.A289D	ENST00000275493	NM_005228.3	289	gCc/gAc	7/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		885	702	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696448	47696448	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067441-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	68	374	0	ENST00000347630.2:c.375T>G	p.Phe125Leu	p.F125L	ENST00000347630	NM_001007230.1	125	ttT/ttG	6/11	1	2	FACETS	0.778	0.679	0.886	0.778	0.679	0.886	SUBCLONAL	1	TRUE	1	0.358820943612901	2		374	487	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165717	185165717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067441-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	78	461	0	ENST00000265026.3:c.992C>T	p.Ser331Phe	p.S331F	ENST00000265026	NM_004721.4	331	tCt/tTt	5/14	0.358820943612901	1	FACETS	0.977	0.865	1	0.977	0.865	1	CLONAL	1	TRUE	0	0.358820943612901	1		461	365	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422986	12422986	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067441-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	52	460	0	ENST00000287820.6:c.476G>A	p.Cys159Tyr	p.C159Y	ENST00000287820	NM_015869.4	159	tGc/tAc	3/7	0.223844194000336	1	FACETS	0.674	0.576	0.78	0.674	0.576	0.78	SUBCLONAL	1	TRUE	0	0.358820943612901	1		460	353	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114607	73114607	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067441-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	37	408	0	ENST00000356692.5:c.988G>C	p.Asp330His	p.D330H	ENST00000356692		330	Gat/Cat	9/9	1	2	FACETS	0.576	0.476	0.688	0.576	0.476	0.688	SUBCLONAL	1	TRUE	1	0.358820943612901	2		408	358	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0067446-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	24	321	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		321	128	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0067446-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	45	530	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		530	310	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777893	NA	P-0067446-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	39	448	0	ENST00000361445.4:c.5930C>T	p.Thr1977Ile	p.T1977I	ENST00000361445	NM_004958.3	1977	aCa/aTa	43/58	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		448	293	SUCCESS
APC	324	MSKCC	GRCh37	5	112173785	112173785	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067446-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	14	435	0	ENST00000257430.4:c.2496del	p.Ser833AlafsTer9	p.S833Afs*9	ENST00000257430	NM_000038.5	832	Ccc/cc	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		435	248	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28631489	28631489	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067446-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	11	261	0	ENST00000241453.7:c.479T>G	p.Ile160Arg	p.I160R	ENST00000241453	NM_004119.2	160	aTa/aGa	4/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		261	178	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0067447-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	135	550	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	0.252657473424121	2	FACETS	0.879	0.801	0.96	0.879	0.801	0.96	CLONAL	2	TRUE	0	0.252657473424121	2		550	608	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307386	118307387	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0067447-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	13	186	0	ENST00000534358.1:c.165dup	p.Ser56LeufsTer91	p.S56Lfs*91	ENST00000534358	NM_005933.3	53	-/C	1/36	0.252657473424121	1	FACETS	0.789	0.568	1	0.789	0.568	1	CLONAL	1	TRUE	0	0.252657473424121	1		186	114	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43769866	43769866	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067447-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	68	384	1	ENST00000382044.4:c.880C>G	p.Leu294Val	p.L294V	ENST00000382044	NM_001141980.1	294	Ctg/Gtg	8/28	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.252657473424121	2		385	388	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677981	117677981	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067447-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	64	404	0	ENST00000368508.3:c.3952A>G	p.Thr1318Ala	p.T1318A	ENST00000368508	NM_002944.2	1318	Aca/Gca	25/43	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.252657473424121	2		404	431	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117959	70117959	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	16	522	0	ENST00000245479.2:c.427T>A	p.Trp143Arg	p.W143R	ENST00000245479	NM_000346.3	143	Tgg/Agg	1/3	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		522	255	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067454-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	26	317	0				ENST00000310581	NM_198253.2	-/1132			0.243019765565402	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		317	74	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0067454-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	102	485	1	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	0.899	0.819	0.98	0.899	0.819	0.98	CLONAL	1	TRUE	1	0.93	2		486	244	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0067454-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	78	519	2	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.69	0.616	0.768	0.69	0.616	0.768	SUBCLONAL	1	TRUE	1	0.93	2		521	243	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832122	72832122	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1410433669	NA	P-0067454-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	124	438	0	ENST00000268489.5:c.4459A>G	p.Ile1487Val	p.I1487V	ENST00000268489	NM_006885.3	1487	Ata/Gta	9/10	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.93	2		438	261	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15833849	15833849	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067454-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	44	92	0	ENST00000307771.7:c.607A>C	p.Lys203Gln	p.K203Q	ENST00000307771	NM_005089.3	203	Aag/Cag	8/11	1	1	FACETS	0.92	0.841	0.988	0.92	0.841	0.988	CLONAL	1	TRUE	0	0.93	1		92	55	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420610	49420610	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067454-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	112	544	0	ENST00000301067.7:c.15139G>C	p.Ala5047Pro	p.A5047P	ENST00000301067	NM_003482.3	5047	Gcc/Ccc	48/54	1	2	FACETS	0.952	0.873	1	0.952	0.873	1	CLONAL	1	TRUE	1	0.93	2		544	253	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156720	20156720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	96	344	0	ENST00000379607.5:c.37C>T	p.Arg13Cys	p.R13C	ENST00000379607	NM_001412.3	13	Cgc/Tgc	2/7	0.640685559448428	4	FACETS	0.857	0.767	0.953	0.429	0.383	0.477	CLONAL	1	TRUE	2	0.771904607050457	4		344	514	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258744	115258744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434596	NA	P-0067455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	234	371	0	ENST00000369535.4:c.38G>A	p.Gly13Asp	p.G13D	ENST00000369535	NM_002524.4	13	gGt/gAt	2/7	0.711303807902745	3	FACETS	0.917	0.867	0.967	0.917	0.867	0.967	CLONAL	2	TRUE	1	0.771904607050457	3		371	458	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519874	NA	P-0067455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	173	279	0	ENST00000356142.4:c.85C>A	p.Pro29Thr	p.P29T	ENST00000356142	NM_018890.3	29	Cct/Act	2/7	0.705356267917047	4	FACETS	0.937	0.872	1	0.624	0.581	0.668	CLONAL	2	TRUE	1	0.771904607050457	4		279	424	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710768	117710768	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	119	542	0	ENST00000368508.3:c.1504T>G	p.Phe502Val	p.F502V	ENST00000368508	NM_002944.2	502	Ttt/Gtt	12/43	0.621683595858465	3	FACETS	0.77	0.698	0.846	0.385	0.349	0.423	SUBCLONAL	1	TRUE	1	0.771904607050457	3		542	555	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546929	9546929	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1244914963	NA	P-0067455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	139	553	0	ENST00000353224.5:c.1093G>A	p.Gly365Ser	p.G365S	ENST00000353224	NM_177990.2	365	Ggc/Agc	5/10	0.339637934851057	6	FACETS	1	0.984	1	0.451	0.411	0.493	INDETERMINATE	1	TRUE	3	0.771904607050457	6		553	677	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517391	176517391	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	309	428	0	ENST00000292408.4:c.92A>G	p.Glu31Gly	p.E31G	ENST00000292408	NM_213647.1	31	gAg/gGg	3/18	0.771904607050457	3	FACETS	0.993	0.947	1	0.662	0.631	0.692	CLONAL	2	TRUE	0	0.771904607050457	3		428	559	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38641716	38641717	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	105	338	1	ENST00000299084.4:c.680dup	p.Asn227LysfsTer2	p.N227Kfs*2	ENST00000299084	NM_152594.2	226	caa/cAaa	6/7	0.771904607050457	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.771904607050457	1		339	155	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186501401	186501401	+	start_lost	Translation_Start_Site	SNP	T	T	G	novel	NA	P-0067455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	105	321	0	ENST00000323963.5:c.2T>G	p.Met1?	p.M1?	ENST00000323963		1	aTg/aGg	1/11	0.734985788660677	2	FACETS	0.883	0.802	0.967	0.442	0.401	0.484	CLONAL	1	TRUE	0	0.771904607050457	2		321	308	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56854489	56854489	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	236	418	0	ENST00000519728.1:c.71T>C	p.Val24Ala	p.V24A	ENST00000519728	NM_002350.3	24	gTa/gCa	2/13	0.771904607050457	6	FACETS	1	0.976	1	0.541	0.507	0.576	CLONAL	2	TRUE	2	0.771904607050457	6		418	719	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651201	45651201	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	136	514	0	ENST00000407780.3:c.824G>T	p.Trp275Leu	p.W275L	ENST00000407780	NM_001283052.1	275	tGg/tTg	5/7	0.771904607050457	3	FACETS	0.797	0.727	0.87	0.266	0.242	0.29	SUBCLONAL	1	TRUE	0	0.771904607050457	3		514	613	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864556	56864556	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	118	441	0	ENST00000308159.5:c.1044T>A	p.Phe348Leu	p.F348L	ENST00000308159	NM_014669.4	348	ttT/ttA	10/22	0.621683595858465	3	FACETS	0.952	0.865	1	0.476	0.432	0.522	CLONAL	1	TRUE	1	0.771904607050457	3		441	445	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0067456-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	108	439	0				ENST00000310581	NM_198253.2	-/1132			0.228885847406276	1	FACETS	1	0.971	1	1	0.971	1	INDETERMINATE	1	TRUE	0	0.422703192124683	1		439	341	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709505	176709505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067456-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	87	396	0	ENST00000439151.2:c.5932G>A	p.Glu1978Lys	p.E1978K	ENST00000439151	NM_022455.4	1978	Gaa/Aaa	19/23	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.422703192124683	2		396	297	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0067456-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	366	473	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.354661924814847	3	FACETS	0.888	0.848	0.929	0.888	0.848	0.929	CLONAL	3	TRUE	0	0.422703192124683	3		473	787	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521067	187521067	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067456-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	75	454	0	ENST00000441802.2:c.12088C>T	p.Pro4030Ser	p.P4030S	ENST00000441802	NM_005245.3	4030	Ccg/Tcg	22/27	0.422703192124683	3	FACETS	0.693	0.608	0.785	0.347	0.304	0.393	SUBCLONAL	1	TRUE	1	0.422703192124683	3		454	620	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175850	24175850	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067456-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	254	519	0	ENST00000263121.7:c.1078G>T	p.Glu360Ter	p.E360*	ENST00000263121	NM_003073.3	360	Gag/Tag	8/9	0.343179986237885	4	FACETS	1	0.988	1	0.794	0.747	0.842	CLONAL	2	TRUE	1	0.422703192124683	4		519	718	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444157	49444157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756805095	NA	P-0067456-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	63	576	0	ENST00000301067.7:c.3214G>A	p.Glu1072Lys	p.E1072K	ENST00000301067	NM_003482.3	1072	Gag/Aag	11/54	0.379111592704655	4	FACETS	0.484	0.417	0.556	0.242	0.208	0.278	SUBCLONAL	1	TRUE	2	0.422703192124683	4		576	877	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270437	10270437	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067456-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	44	587	0	ENST00000340748.4:c.1129G>A	p.Glu377Lys	p.E377K	ENST00000340748		377	Gag/Aag	16/40	0.180768127432272	5	FACETS	0.402	0.336	0.476	0.134	0.112	0.159	INDETERMINATE	1	TRUE	2	0.422703192124683	5		587	846	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1686045	1686045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067456-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	162	539	0	ENST00000378625.1:c.1216G>A	p.Glu406Lys	p.E406K	ENST00000378625	NM_001198994.1	406	Gag/Aag	10/14	0.17992427083945	3	FACETS	1	0.982	1	0.618	0.568	0.67	INDETERMINATE	1	TRUE	1	0.422703192124683	3		539	751	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652027	36652032	+	inframe_deletion	In_Frame_Del	DEL	ACTTCG	ACTTCG	-	novel	NA	P-0067456-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	416	557	0	ENST00000244741.5:c.153_158del	p.Asp52_Phe53del	p.D52_F53del	ENST00000244741	NM_000389.4	50	aACTTCGac/aac	2/3	0.320113742849774	4	FACETS	1	0.984	1	0.79	0.756	0.824	CLONAL	3	TRUE	0	0.422703192124683	4		557	886	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984175	201984379	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAAGAACAGAGGAGTTTAGGAAGTGTGAGTCAGGCTCAGCTTAGTCAGGCAGAGACCAGTGGGCATGGGTTACCTGGGGGTAACGCGGGCCAGGTGGGCGGGCTGGCAGCCTGGGGCCCATTTCCTGCCAAAGCACCTCTGACCATCCTTCTCTTCACCCAGGTACTACTACAAACGGGAGATCCTGGAACGGGTGGATGGCCGG	GAAGAACAGAGGAGTTTAGGAAGTGTGAGTCAGGCTCAGCTTAGTCAGGCAGAGACCAGTGGGCATGGGTTACCTGGGGGTAACGCGGGCCAGGTGGGCGGGCTGGCAGCCTGGGGCCCATTTCCTGCCAAAGCACCTCTGACCATCCTTCTCTTCACCCAGGTACTACTACAAACGGGAGATCCTGGAACGGGTGGATGGCCGG	-	novel	NA	P-0067456-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	252	77	0	ENST00000359651.3:c.1002-162_1044del		p.X334_splice	ENST00000359651		334		8/8	0.345327927639208	3	FACETS	1	0.987	1	1	0.996	1	CLONAL	5	TRUE	0	0.422703192124683	3		77	282	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842661	68842662	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0067457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	127	485	0	ENST00000261769.5:c.602dup	p.Val202CysfsTer7	p.V202Cfs*7	ENST00000261769	NM_004360.3	199	-/C	5/16	0.583665389845412	1	FACETS	0.506	0.464	0.549	0.506	0.464	0.549	SUBCLONAL	1	TRUE	0	0.839722564794413	1		485	347	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443586	52443586	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067458-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	70	464	0	ENST00000460680.1:c.106C>T	p.Gln36Ter	p.Q36*	ENST00000460680	NM_004656.3	36	Cag/Tag	3/17	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.2	2		464	555	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051600	30051618	+	frameshift_variant	Frame_Shift_Del	DEL	GATGACTCCGGAAATGTGG	GATGACTCCGGAAATGTGG	-	novel	NA	P-0067458-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	23	333	0	ENST00000338641.4:c.536_554del	p.Met179ArgfsTer24	p.M179Rfs*24	ENST00000338641	NM_000268.3	178	caGATGACTCCGGAAATGTGG/ca	6/16	1	2	FACETS	0.618	0.482	0.777	0.618	0.482	0.777	SUBCLONAL	1	TRUE	1	0.2	2		333	372	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054194	30054194	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067460-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	23	287	0	ENST00000338641.4:c.616G>T	p.Glu206Ter	p.E206*	ENST00000338641	NM_000268.3	206	Gaa/Taa	7/16	0.168113099354063	1	FACETS	0.801	0.625	1	0.801	0.625	1	CLONAL	1	TRUE	0	0.17	1		287	309	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441422	52441422	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067460-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	46	550	0	ENST00000460680.1:c.430del	p.His144MetfsTer43	p.H144Mfs*43	ENST00000460680	NM_004656.3	144	Cat/at	6/17	0.168113099354063	1	FACETS	0.931	0.784	1	0.931	0.784	1	CLONAL	1	TRUE	0	0.17	1		550	532	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412493	80412493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514698	NA	P-0067461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	24	456	0	ENST00000286548.4:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000286548	NM_002072.3	183	cGa/cAa	4/7	0.168474129995295	0	FACETS	0.435	0.342	0.54			1	INDETERMINATE	1	FALSE	0	0.32538363698941	0		456	229	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696689	47696689	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519972	NA	P-0067462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	101	495	0	ENST00000347630.2:c.259T>A	p.Tyr87Asn	p.Y87N	ENST00000347630	NM_001007230.1	87	Tac/Aac	5/11	1	2	FACETS	0.937	0.852	1	0.937	0.852	1	CLONAL	1	TRUE	1	0.855560497001381	2		495	252	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061191	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	125	586	0	ENST00000250448.2:c.798C>G	p.Phe266Leu	p.F266L	ENST00000250448	NM_004496.3	266	ttC/ttG	2/2	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.855560497001381	2		586	260	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40491388	40491388	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	25	484	0	ENST00000264657.5:c.412A>G	p.Thr138Ala	p.T138A	ENST00000264657	NM_139276.2	138	Acg/Gcg	5/24	1	2	FACETS	0.176	0.138	0.219	0.176	0.138	0.219	SUBCLONAL	1	TRUE	1	0.855560497001381	2		484	332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0067477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	29	389	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.618	0.496	0.757	0.618	0.496	0.757	SUBCLONAL	1	TRUE	1	0.24	2		389	391	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057936	27057937	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1415146710	NA	P-0067477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	39	408	0	ENST00000324856.7:c.1650dup	p.Tyr551LeufsTer72	p.Y551Lfs*72	ENST00000324856	NM_006015.4	548	-/C	3/20	1	2	FACETS	0.997	0.829	1	0.997	0.829	1	CLONAL	1	TRUE	1	0.24	2		408	326	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670621	30670621	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	27	352	0	ENST00000376406.3:c.5899G>T	p.Glu1967Ter	p.E1967*	ENST00000376406	NM_014641.2	1967	Gaa/Taa	13/15	1	2	FACETS	0.563	0.447	0.694	0.563	0.447	0.694	SUBCLONAL	1	TRUE	1	0.24	2		352	400	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562746	29562746	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs199474742	NA	P-0067477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	43	315	0	ENST00000356175.3:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000356175	NM_000267.3	1276	Cga/Tga	28/57	1	2	FACETS	0.993	0.833	1	0.993	0.833	1	CLONAL	1	TRUE	1	0.24	2		315	361	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497714	120497719	+	inframe_deletion	In_Frame_Del	DEL	TCGTTC	TCGTTC	-	novel	NA	P-0067477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	31	359	0	ENST00000256646.2:c.2163_2168del	p.Asn722_Glu723del	p.N722_E723del	ENST00000256646	NM_024408.3	721	gtGAACGAa/gta	13/34	1	2	FACETS	0.682	0.551	0.829	0.682	0.551	0.829	SUBCLONAL	1	TRUE	1	0.24	2		359	379	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975437	26975437	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	24	295	0	ENST00000381527.3:c.1063A>C	p.Lys355Gln	p.K355Q	ENST00000381527	NM_001260.1	355	Aaa/Caa	11/13	1	2	FACETS	0.615	0.483	0.768	0.615	0.483	0.768	SUBCLONAL	1	TRUE	1	0.24	2		295	325	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145740	11145740	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	19	357	0	ENST00000358026.2:c.4102G>T	p.Gly1368Cys	p.G1368C	ENST00000358026	NM_001128849.1	1368	Ggc/Tgc	29/36	1	2	FACETS	0.55	0.417	0.705	0.55	0.417	0.705	SUBCLONAL	1	TRUE	1	0.24	2		357	288	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61310400	61310400	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	15	81	0	ENST00000341074.5:c.217T>C	p.Tyr73His	p.Y73H	ENST00000341074	NM_002974.2	73	Tat/Cat	3/8	1	2	FACETS	1	0.832	1	1	0.832	1	CLONAL	1	TRUE	1	0.24	2		81	106	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619425	1619425	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	21	367	0	ENST00000344749.5:c.1216A>C	p.Ser406Arg	p.S406R	ENST00000344749	NM_001136139.2	406	Agc/Cgc	15/19	1	2	FACETS	0.519	0.4	0.659	0.519	0.4	0.659	SUBCLONAL	1	TRUE	1	0.24	2		367	337	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652045	36652045	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	30	408	0	ENST00000244741.5:c.167A>T	p.Glu56Val	p.E56V	ENST00000244741	NM_000389.4	56	gAg/gTg	2/3	1	2	FACETS	0.653	0.526	0.796	0.653	0.526	0.796	SUBCLONAL	1	TRUE	1	0.24	2		408	383	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76954106	76954106	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	16	86	0	ENST00000373344.5:c.145G>T	p.Gly49Cys	p.G49C	ENST00000373344	NM_000489.3	49	Ggt/Tgt	3/35	1	1	FACETS	0.986	0.737	1	0.986	0.737	1	CLONAL	1	TRUE	0	0.24	1		86	119	SUCCESS
AR	367	MSKCC	GRCh37	X	66863165	66863165	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	43	176	0	ENST00000374690.3:c.1684A>T	p.Ile562Phe	p.I562F	ENST00000374690	NM_000044.3	562	Atc/Ttc	2/8	1	1	FACETS	0.769	0.651	0.897	1	0.962	1	SUBCLONAL	2	TRUE	0	0.24	1		176	205	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974754	21974798	+	inframe_deletion	In_Frame_Del	DEL	CCCGACCCCGGGCCGCGGCCGTGGCCAGCCAGTCAGCCGAAGGCT	CCCGACCCCGGGCCGCGGCCGTGGCCAGCCAGTCAGCCGAAGGCT	-	novel	NA	P-0067477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	32	360	0	ENST00000304494.5:c.29_73del	p.Glu10_Arg24del	p.E10_R24del	ENST00000304494	NM_000077.4	10	gAGCCTTCGGCTGACTGGCTGGCCACGGCCGCGGCCCGGGGTCGGGta/gta	1/3	0.146832000499651	1	FACETS	0.899	0.733	1	0.899	0.733	1	CLONAL	1	TRUE	0	0.24	1		360	261	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913396	NA	P-0067479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	152	403	0	ENST00000349496.5:c.95A>T	p.Asp32Val	p.D32V	ENST00000349496	NM_001904.3	32	gAc/gTc	3/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.81	2		403	322	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295192	1295192	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0067479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	58	263	0				ENST00000310581	NM_198253.2	-/1132			0.127599749185618	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.81	0		263	153	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577512	7577512	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	8	355	0	ENST00000269305.4:c.769C>A	p.Leu257Met	p.L257M	ENST00000269305	NM_001126112.2	257	Ctg/Atg	7/11	1	2	FACETS	0.069	0.044	0.101	0.069	0.044	0.101	SUBCLONAL	1	TRUE	1	0.81	2		355	287	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525113	9525113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	71	321	0	ENST00000353224.5:c.1772C>T	p.Ala591Val	p.A591V	ENST00000353224	NM_177990.2	591	gCt/gTt	8/10	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.81	2		321	165	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0067480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	601	357	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.942448122801879	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.942448122801879	3		357	614	SUCCESS
ATR	545	MSKCC	GRCh37	3	142255043	142255043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	117	207	0	ENST00000350721.4:c.3726G>T	p.Arg1242Ser	p.R1242S	ENST00000350721	NM_001184.3	1242	agG/agT	20/47	0.942448122801879	3	FACETS	1	0.951	1	0.531	0.484	0.579	CLONAL	1	TRUE	1	0.942448122801879	3		207	344	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967809	18967809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	169	281	0	ENST00000262803.5:c.1948G>A	p.Val650Met	p.V650M	ENST00000262803	NM_002911.3	650	Gtg/Atg	14/24	0.942448122801879	2	FACETS	0.977	0.912	1	0.489	0.456	0.522	CLONAL	1	TRUE	0	0.942448122801879	2		281	367	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554364	141555290	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTCCCAGAAAGATGACGGGCTGCTGGAACACCGGCGGCCTGCGGAGAGGAGTGGCGTCAGGGGCCACGGTGAGACACGCCTGGACCTCTGACGCTAGTAGGTGCCACCATCACCTTTTGGAGGTGGTCAGTGTATCATGGTAATGCTTTTGAAAAGAATCCTTATCTTTTAACCGGAATACTAAAAACCCTGCAGATTAAATGACACAAGGTCTGAAATCTGCTTCAGAATAGCCACGGGTTGGGGGGCTTGGGTGGAGTGTACTCCAGACCAGATGGGCCAGGAGCTGACAGCTGTTGAGGCTGGGGCTCAGGCCCAGGCCCAGGAGGGCTCACCCTTCTACCCTCTACTCCCTCTGCAGCCACACCCACGCCAGGGTTTCTCACCGCCACCCTTAGCACCACCAATGCCTGGGGCCAGCTCGCTCTTTGTTGGGGTAGGGGGCTGTCCCCAGCATGGGCAGACGCTGAGAGGCCTCCACTCACTGGATGCCAGTAGCACTCCATCAAGCCTGACACCCCAACATGTCTCCAGACATGACCACGCGTCCCCTGGCAGCAAAACCACCCCATGGAGAACTTTCAGACCCTGAGTATATCCCAGTGGGGACTTCCCTGGGAGGCAGCACGCACAGGGGCAAGGACAGGCATGTGGGCCTCGGGCTCTCCGGGGAAAGGCGGAGGTGGTGACAGCACCTTCCTCCCGGGTTGAGAGTGCACCGCCGCACACCCCACCCAGCCTTGCTCGGCTGCTGCAGGCAACATCAGGAAGCATCAGAAGTGGCCGTTCTGCCAGCCCTGCCTGTTGGAAACCAGGTACATGAGGCCCTCGCCTCTGCTGCCCTCTCCCCGCATCCATTTCCCTGCATGCCTGTGACTCACTCTCCGCCCACATCCTCTCACTCCCATCGCCTGCCTTGCGGCAGA	GCTCCCAGAAAGATGACGGGCTGCTGGAACACCGGCGGCCTGCGGAGAGGAGTGGCGTCAGGGGCCACGGTGAGACACGCCTGGACCTCTGACGCTAGTAGGTGCCACCATCACCTTTTGGAGGTGGTCAGTGTATCATGGTAATGCTTTTGAAAAGAATCCTTATCTTTTAACCGGAATACTAAAAACCCTGCAGATTAAATGACACAAGGTCTGAAATCTGCTTCAGAATAGCCACGGGTTGGGGGGCTTGGGTGGAGTGTACTCCAGACCAGATGGGCCAGGAGCTGACAGCTGTTGAGGCTGGGGCTCAGGCCCAGGCCCAGGAGGGCTCACCCTTCTACCCTCTACTCCCTCTGCAGCCACACCCACGCCAGGGTTTCTCACCGCCACCCTTAGCACCACCAATGCCTGGGGCCAGCTCGCTCTTTGTTGGGGTAGGGGGCTGTCCCCAGCATGGGCAGACGCTGAGAGGCCTCCACTCACTGGATGCCAGTAGCACTCCATCAAGCCTGACACCCCAACATGTCTCCAGACATGACCACGCGTCCCCTGGCAGCAAAACCACCCCATGGAGAACTTTCAGACCCTGAGTATATCCCAGTGGGGACTTCCCTGGGAGGCAGCACGCACAGGGGCAAGGACAGGCATGTGGGCCTCGGGCTCTCCGGGGAAAGGCGGAGGTGGTGACAGCACCTTCCTCCCGGGTTGAGAGTGCACCGCCGCACACCCCACCCAGCCTTGCTCGGCTGCTGCAGGCAACATCAGGAAGCATCAGAAGTGGCCGTTCTGCCAGCCCTGCCTGTTGGAAACCAGGTACATGAGGCCCTCGCCTCTGCTGCCCTCTCCCCGCATCCATTTCCCTGCATGCCTGTGACTCACTCTCCGCCCACATCCTCTCACTCCCATCGCCTGCCTTGCGGCAGA	-	novel	NA	P-0067480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	102	274	0	ENST00000220592.5:c.1749-888_1787del		p.X583_splice	ENST00000220592	NM_012154.3	583		14/19	0.942448122801879	3	FACETS	0.647	0.581	0.717	0.324	0.29	0.359	SUBCLONAL	1	TRUE	1	0.942448122801879	3		274	492	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0067481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	93	314	4	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.916	0.821	1	0.916	0.821	1	CLONAL	1	TRUE	1	0.565702142546695	2		318	359	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0067481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	189	331	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.539635553486038	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.565702142546695	1		331	397	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573563	48573564	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs786203560	NA	P-0067481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	105	270	0	ENST00000342988.3:c.153dup	p.Asp52ArgfsTer2	p.D52Rfs*2	ENST00000342988	NM_005359.5	49	-/A	2/12	0.539635553486038	1	FACETS	0.785	0.711	0.862	0.785	0.711	0.862	SUBCLONAL	1	TRUE	0	0.565702142546695	1		270	339	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs377767347	NA	P-0067481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	14	301	0	ENST00000342988.3:c.1082G>T	p.Arg361Leu	p.R361L	ENST00000342988	NM_005359.5	361	cGc/cTc	9/12	0.539635553486038	1	FACETS	0.098	0.07	0.132	0.098	0.07	0.132	SUBCLONAL	1	TRUE	0	0.565702142546695	1		301	361	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184670	185184670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188669013	NA	P-0067481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	170	318	0	ENST00000265026.3:c.1562G>A	p.Arg521His	p.R521H	ENST00000265026	NM_004721.4	521	cGt/cAt	10/14	0.116971593438672	4	FACETS	0.926	0.858	0.996	0.926	0.858	0.996	INDETERMINATE	2	TRUE	2	0.565702142546695	4		318	508	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9928076	9928076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	128	241	0	ENST00000330684.3:c.1663G>A	p.Ala555Thr	p.A555T	ENST00000330684	NM_001134407.1	555	Gcc/Acc	8/13	1	2	FACETS	0.959	0.875	1	0.959	0.875	1	CLONAL	1	TRUE	1	0.565702142546695	2		241	472	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134251	11134251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218643327	NA	P-0067481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	120	280	0	ENST00000358026.2:c.2917C>T	p.Arg973Trp	p.R973W	ENST00000358026	NM_001128849.1	973	Cgg/Tgg	20/36	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.565702142546695	2		280	422	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250485	26250485	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	201	379	0	ENST00000446824.2:c.349C>T	p.Arg117Ter	p.R117*	ENST00000446824	NM_021018.2	117	Cga/Tga	1/1	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.565702142546695	2		379	674	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440739	56440739	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	338	325	0	ENST00000407977.2:c.479C>G	p.Pro160Arg	p.P160R	ENST00000407977		160	cCa/cGa	5/10	0.565702142546695	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.565702142546695	2		325	563	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56859039	56859039	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	79	221	0	ENST00000519728.1:c.165G>C	p.Arg55Ser	p.R55S	ENST00000519728	NM_002350.3	55	agG/agC	3/13	1	2	FACETS	0.763	0.676	0.856	0.763	0.676	0.856	SUBCLONAL	1	TRUE	1	0.565702142546695	2		221	366	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934573	NA	P-0067483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	147	287	0	ENST00000269305.4:c.722C>A	p.Ser241Tyr	p.S241Y	ENST00000269305	NM_001126112.2	241	tCc/tAc	7/11	0.328789923853656	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.345924472316045	2		287	383	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0067483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	129	319	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	0.191068373527993	5	FACETS	0.901	0.824	0.981	0.901	0.824	0.981	INDETERMINATE	3	TRUE	2	0.345924472316045	5		319	419	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928078	178928080	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs587776933	NA	P-0067483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	130	196	0	ENST00000263967.3:c.1359_1361del	p.Glu453del	p.E453del	ENST00000263967	NM_006218.2	452	ttAGAa/tta	8/21	0.191068373527993	5	FACETS	1	0.978	1	0.815	0.744	0.888	INDETERMINATE	2	TRUE	2	0.345924472316045	5		196	467	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	66	276	0	ENST00000256196.4:c.68G>T	p.Gly23Val	p.G23V	ENST00000256196		23	gGc/gTc	1/6	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.345924472316045	2		276	303	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47599489	47599489	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	92	401	0	ENST00000430070.2:c.111C>G	p.Phe37Leu	p.F37L	ENST00000430070	NM_018095.4	37	ttC/ttG	2/4	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.345924472316045	2		401	440	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965407	25965407	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	50	403	0	ENST00000435504.4:c.3799C>G	p.Gln1267Glu	p.Q1267E	ENST00000435504		1267	Cag/Gag	13/13	0.345924472316045	3	FACETS	0.627	0.532	0.731	0.313	0.266	0.366	SUBCLONAL	1	TRUE	1	0.345924472316045	3		403	541	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029065	14029065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1344869809	NA	P-0067483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	96	405	0	ENST00000311895.7:c.1276C>T	p.Leu426Phe	p.L426F	ENST00000311895	NM_005236.2	426	Ctt/Ttt	8/11	0.345924472316045	3	FACETS	1	0.974	1	0.646	0.577	0.718	CLONAL	1	TRUE	1	0.345924472316045	3		405	504	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0067484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	87	418	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.422284194337189	5	FACETS	1	0.921	1	0.349	0.309	0.392	CLONAL	1	TRUE	2	0.478375706011745	5		418	596	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0067484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	215	329	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.478375706011745	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.478375706011745	3		329	453	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	88	455	1	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.478375706011745	4	FACETS	1	0.894	1	0.336	0.298	0.376	CLONAL	1	TRUE	1	0.478375706011745	4		456	540	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994848	73994848	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910584858	NA	P-0067484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	10	62	0	ENST00000318443.5:c.332G>A	p.Arg111His	p.R111H	ENST00000318443	NM_001024736.1	111	cGc/cAc	3/10	0.46484359172109	3	FACETS	0.751	0.517	1	0.375	0.258	0.517	CLONAL	1	TRUE	1	0.478375706011745	3		62	69	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216306	2216306	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	61	374	0	ENST00000398665.3:c.1950C>G	p.Ser650Arg	p.S650R	ENST00000398665	NM_032482.2	650	agC/agG	20/28	0.271956031546516	4	FACETS	0.827	0.715	0.948	0.413	0.357	0.474	INDETERMINATE	1	TRUE	2	0.478375706011745	4		374	456	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853264	68853265	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	170	305	0	ENST00000261769.5:c.1648dup	p.Arg550LysfsTer5	p.R550Kfs*5	ENST00000261769	NM_004360.3	549	-/A	11/16	0.478375706011745	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	0	0.478375706011745	2		305	350	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109978	115110002	+	frameshift_variant	Frame_Shift_Del	DEL	TGGTGTTCAGATTGAGGAAGGGGTG	TGGTGTTCAGATTGAGGAAGGGGTG	-	novel	NA	P-0067484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	77	365	0	ENST00000257566.3:c.1876_1900del	p.His626CysfsTer255	p.H626Cfs*255	ENST00000257566	NM_016569.3	626	CACCCCTTCCTCAATCTGAACACCAtg/tg	8/8	0.449363659362411	3	FACETS	1	0.927	1	0.533	0.471	0.599	CLONAL	1	TRUE	1	0.478375706011745	3		365	374	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858435	27858435	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	120	486	0	ENST00000359303.2:c.136A>G	p.Thr46Ala	p.T46A	ENST00000359303	NM_003535.2	46	Acc/Gcc	1/1	0.478375706011745	4	FACETS	1	0.949	1	0.358	0.324	0.395	CLONAL	1	TRUE	1	0.478375706011745	4		486	690	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0067485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	89	496	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	0.483976507908819	3	FACETS	0.92	0.818	1	0.46	0.409	0.514	CLONAL	1	TRUE	1	0.493471605314984	3		496	489	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539540	187539540	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	61	289	0	ENST00000441802.2:c.8200C>A	p.Leu2734Ile	p.L2734I	ENST00000441802	NM_005245.3	2734	Ctt/Att	10/27	0.499820022211616	3	FACETS	0.824	0.714	0.942	0.412	0.357	0.471	CLONAL	1	TRUE	1	0.493471605314984	3		289	374	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665671	86665671	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	39	222	0	ENST00000274376.6:c.1652A>T	p.Glu551Val	p.E551V	ENST00000274376	NM_002890.2	551	gAa/gTa	12/25	0.499820022211616	4	FACETS	0.711	0.591	0.844	0.356	0.295	0.422	SUBCLONAL	1	TRUE	2	0.493471605314984	4		222	332	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748452	40748452	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs575460456	NA	P-0067486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	44	293	1	ENST00000392038.2:c.430C>T	p.Arg144Trp	p.R144W	ENST00000392038	NM_001626.4	144	Cgg/Tgg	5/14	0.783957232618919	4	FACETS	0.235	0.196	0.278	0.117	0.098	0.139	SUBCLONAL	1	TRUE	2	0.790075919587285	4		294	849	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267361	198267361	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754688962	NA	P-0067486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	239	369	0	ENST00000335508.6:c.1996A>G	p.Lys666Glu	p.K666E	ENST00000335508	NM_012433.2	666	Aag/Gag	14/25	0.790075919587285	3	FACETS	1	0.981	1	0.556	0.521	0.592	CLONAL	1	TRUE	1	0.790075919587285	3		369	759	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845222	128845222	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	426	327	0	ENST00000249373.3:c.717del	p.Val240SerfsTer62	p.V240Sfs*62	ENST00000249373	NM_005631.4	239	gCc/gc	3/12	0.783957232618919	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.790075919587285	4		327	954	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0067487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	13	305	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.478616570958027	4	FACETS	1	0.804	1			1	CLONAL	1	FALSE	NA	0.475127549830161	4		305	71	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691039	NA	P-0067487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	90	357	0	ENST00000269305.4:c.919+1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.475127549830161	11	FACETS	0.999	0.902	1			1	CLONAL	5	FALSE	NA	0.475127549830161	11		357	238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	66	321	0	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.475127549830161	11	FACETS	1	0.922	1			1	CLONAL	4	FALSE	NA	0.475127549830161	11		321	206	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519927	NA	P-0067487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	39	140	0	ENST00000263967.3:c.1625A>T	p.Glu542Val	p.E542V	ENST00000263967	NM_006218.2	542	gAa/gTa	10/21	0.475127549830161	9	FACETS	1	0.893	1	1	0.893	1	CLONAL	6	FALSE	3	0.475127549830161	9		140	71	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0067489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	219	638	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.539274461922312	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.539274461922312	2		638	402	SUCCESS
APC	324	MSKCC	GRCh37	5	112177620	112177620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	116	393	0	ENST00000257430.4:c.6329C>T	p.Ser2110Phe	p.S2110F	ENST00000257430	NM_000038.5	2110	tCc/tTc	16/16	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.539274461922312	NA		393	269	SUCCESS
APC	324	MSKCC	GRCh37	5	112174637	112174637	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	258	451	0	ENST00000257430.4:c.3346G>T	p.Gly1116Cys	p.G1116C	ENST00000257430	NM_000038.5	1116	Ggt/Tgt	16/16	0.539274461922312	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.539274461922312	2		451	426	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745553	162745553	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	261	408	0	ENST00000367921.3:c.1968C>A	p.Tyr656Ter	p.Y656*	ENST00000367921	NM_006182.2	656	taC/taA	15/18	0.539274461922312	4	FACETS	1	0.941	1	0.667	0.627	0.707	CLONAL	2	TRUE	1	0.539274461922312	4		408	745	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641402	23641402	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	125	456	0	ENST00000261584.4:c.2073C>A	p.Ser691Arg	p.S691R	ENST00000261584	NM_024675.3	691	agC/agA	5/13	0.539274461922312	3	FACETS	0.999	0.908	1	0.5	0.454	0.548	CLONAL	1	TRUE	1	0.539274461922312	3		456	589	SUCCESS
APC	324	MSKCC	GRCh37	5	112177696	112177696	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	214	435	0	ENST00000257430.4:c.6405C>G	p.Ile2135Met	p.I2135M	ENST00000257430	NM_000038.5	2135	atC/atG	16/16	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.539274461922312	NA		435	360	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952926	2952926	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	98	306	0	ENST00000396946.4:c.3014A>C	p.Lys1005Thr	p.K1005T	ENST00000396946	NM_032415.4	1005	aAg/aCg	22/25	0.539274461922312	5	FACETS	0.841	0.75	0.938			1	CLONAL	1	TRUE	NA	0.539274461922312	5		306	782	SUCCESS
APC	324	MSKCC	GRCh37	5	112177640	112177640	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587780546	NA	P-0067489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	161	395	0	ENST00000257430.4:c.6349C>G	p.Gln2117Glu	p.Q2117E	ENST00000257430	NM_000038.5	2117	Caa/Gaa	16/16	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.539274461922312	NA		395	314	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56862945	56862945	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	106	387	0	ENST00000308159.5:c.851G>T	p.Gly284Val	p.G284V	ENST00000308159	NM_014669.4	284	gGc/gTc	9/22	0.488179305652411	4	FACETS	0.93	0.835	1	0.465	0.417	0.515	CLONAL	1	TRUE	2	0.539274461922312	4		387	651	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295904	1295904	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0067489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	307	550	0				ENST00000310581	NM_198253.2	-/1132			0.500602907782316	5	FACETS	1	0.944	1	0.667	0.629	0.705	CLONAL	2	TRUE	2	0.539274461922312	5		550	1030	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0067490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	31	235	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.873	0.71	1	0.873	0.71	1	CLONAL	1	TRUE	1	0.275143843033914	2		235	258	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183724	10183724	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs869025616	NA	P-0067490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	31	404	0	ENST00000256474.2:c.193T>C	p.Ser65Pro	p.S65P	ENST00000256474	NM_000551.3	65	Tcg/Ccg	1/3	0.260123103425737	1	FACETS	0.532	0.431	0.647	0.532	0.431	0.647	SUBCLONAL	1	TRUE	0	0.275143843033914	1		404	365	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623222	52623223	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCGATGG	novel	NA	P-0067490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	46	424	0	ENST00000394830.3:c.2828_2829insCCATCGC	p.Leu943PhefsTer12	p.L943Ffs*12	ENST00000394830	NM_018313.4	943	tta/ttCCATCGCa	19/30	0.260123103425737	1	FACETS	0.712	0.601	0.834	0.712	0.601	0.834	SUBCLONAL	1	TRUE	0	0.275143843033914	1		424	405	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0067491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	84	329	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.9	0.803	1	0.9	0.803	1	CLONAL	1	TRUE	1	0.616386076921369	2		329	303	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0067491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	102	366	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.997	0.901	1	0.997	0.901	1	CLONAL	1	TRUE	1	0.616386076921369	2		366	332	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118751	115118752	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	154	534	0	ENST00000257566.3:c.589dup	p.Trp197LeufsTer30	p.W197Lfs*30	ENST00000257566	NM_016569.3	197	tgg/tTgg	2/8	0.616386076921369	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.616386076921369	1		534	308	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216340	2216340	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	27	524	0	ENST00000398665.3:c.1984T>C	p.Cys662Arg	p.C662R	ENST00000398665	NM_032482.2	662	Tgt/Cgt	20/28	1	2	FACETS	0.229	0.182	0.283	0.229	0.182	0.283	SUBCLONAL	1	TRUE	1	0.616386076921369	2		524	382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0067492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	255	661	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.291576919472878	3	FACETS	0.927	0.874	0.98	0.927	0.874	0.98	CLONAL	3	TRUE	0	0.341437704971787	3		661	629	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073971	8073971	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	172	452	1	ENST00000377482.5:c.688G>T	p.Gly230Ter	p.G230*	ENST00000377482	NM_018948.3	230	Gga/Tga	4/4	0.341437704971787	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.341437704971787	2		453	491	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820262	32820262	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	179	438	0	ENST00000354258.4:c.796T>C	p.Phe266Leu	p.F266L	ENST00000354258	NM_000593.5	266	Ttc/Ctc	2/11	0.151428807453694	5	FACETS	1	0.984	1	0.821	0.76	0.883	INDETERMINATE	2	TRUE	2	0.341437704971787	5		438	644	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149238674	149238674	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	165	462	0	ENST00000360632.3:c.1121T>C	p.Leu374Ser	p.L374S	ENST00000360632	NM_015472.4	374	tTg/tCg	7/7	0.198839367446231	4	FACETS	0.97	0.894	1	0.97	0.894	1	INDETERMINATE	2	TRUE	2	0.341437704971787	4		462	668	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610609	52610609	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	121	379	0	ENST00000394830.3:c.3564del	p.Glu1189LysfsTer4	p.E1189Kfs*4	ENST00000394830	NM_018313.4	1188	aaA/aa	23/30	0.341437704971787	2	FACETS	0.852	0.776	0.93	0.852	0.776	0.93	CLONAL	2	TRUE	0	0.341437704971787	2		379	416	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500562	99500562	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	112	587	0	ENST00000268035.6:c.3995G>C	p.Gly1332Ala	p.G1332A	ENST00000268035	NM_000875.3	1332	gGg/gCg	21/21	0.334561841431425	3	FACETS	1	0.968	1	0.591	0.532	0.653	CLONAL	1	TRUE	1	0.341437704971787	3		587	650	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186562	108186562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	204	385	0	ENST00000278616.4:c.6019G>A	p.Glu2007Lys	p.E2007K	ENST00000278616	NM_000051.3	2007	Gaa/Aaa	41/63	0.291576919472878	3	FACETS	0.986	0.924	1	0.986	0.924	1	CLONAL	3	TRUE	0	0.341437704971787	3		385	473	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0067495-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	178	377	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.570199144728525	4	FACETS	0.999	0.939	1	0.999	0.939	1	CLONAL	3	TRUE	1	0.570199144728525	4		377	327	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0067495-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	304	530	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.570199144728525	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.570199144728525	3		530	616	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0067495-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	252	709	0	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.570199144728525	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.570199144728525	2		709	430	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412095	63412095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852217	NA	P-0067495-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	332	292	0	ENST00000330258.3:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000330258	NM_152424.3	358	Cga/Tga	2/2	0.570199144728525	3	FACETS	0.878	0.85	0.905			1	CLONAL	4	TRUE	NA	0.570199144728525	3		292	426	SUCCESS
APC	324	MSKCC	GRCh37	5	112154979	112154980	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGAA	novel	NA	P-0067495-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	89	523	0	ENST00000257430.4:c.1251_1254dup	p.Thr419Ter	p.T419*	ENST00000257430	NM_000038.5	417	tgt/tgTGAAt	10/16	0.570199144728525	3	FACETS	0.824	0.733	0.92	0.412	0.366	0.46	CLONAL	1	TRUE	1	0.570199144728525	3		523	487	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222597	69222597	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067495-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	92	466	0	ENST00000462284.1:c.570C>A	p.His190Gln	p.H190Q	ENST00000462284	NM_002392.5	190	caC/caA	8/11	0.568342877903336	4	FACETS	0.976	0.87	1	0.325	0.29	0.363	CLONAL	1	TRUE	1	0.570199144728525	4		466	519	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145669	11145669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067495-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	134	595	0	ENST00000358026.2:c.4031C>T	p.Pro1344Leu	p.P1344L	ENST00000358026	NM_001128849.1	1344	cCc/cTc	29/36	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.570199144728525	2		595	406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0067496-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	359	661	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.585102798671277	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.577089088019659	1		661	646	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28601483	28601483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1430082772	NA	P-0067496-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	128	539	0	ENST00000253063.3:c.1168C>T	p.Arg390Cys	p.R390C	ENST00000253063	NM_031459.4	390	Cgc/Tgc	8/10	0.375537230923235	1	FACETS	0.527	0.479	0.577	0.527	0.479	0.577	SUBCLONAL	1	TRUE	0	0.577089088019659	1		539	599	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762067	43762067	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067496-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	212	454	0	ENST00000382044.4:c.1378C>T	p.Gln460Ter	p.Q460*	ENST00000382044	NM_001141980.1	460	Cag/Tag	11/28	0.585102798671277	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.577089088019659	1		454	445	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420186	88420186	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067496-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	257	495	0	ENST00000360948.2:c.2500T>C	p.Tyr834His	p.Y834H	ENST00000360948	NM_001012338.2	834	Tac/Cac	19/19	0.585102798671277	2	FACETS	1	0.993	1	0.692	0.652	0.732	CLONAL	1	TRUE	0	0.577089088019659	2		495	644	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272239	142272239	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067496-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	180	298	0	ENST00000350721.4:c.2635G>A	p.Ala879Thr	p.A879T	ENST00000350721	NM_001184.3	879	Gcc/Acc	13/47	0.15184012974436	3	FACETS	1	0.991	1	0.744	0.691	0.799	INDETERMINATE	1	TRUE	1	0.577089088019659	3		298	540	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367326	50367326	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067496-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	251	528	0	ENST00000331340.3:c.133C>A	p.Gln45Lys	p.Q45K	ENST00000331340	NM_006060.4	45	Caa/Aaa	3/8	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.577089088019659	2		528	647	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420842	49420877	+	inframe_deletion	In_Frame_Del	DEL	TTCAGGGGGCCGGGCACGGGGCTTGGGTCGGGCTGA	TTCAGGGGGCCGGGCACGGGGCTTGGGTCGGGCTGA	-	novel	NA	P-0067496-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	71	591	0	ENST00000301067.7:c.14872_14907del	p.Ser4958_Glu4969del	p.S4958_E4969del	ENST00000301067	NM_003482.3	4958	TCAGCCCGACCCAAGCCCCGTGCCCGGCCCCCTGAA/-	48/54	0.375537230923235	1	FACETS	0.285	0.248	0.324	0.285	0.248	0.324	SUBCLONAL	1	TRUE	0	0.577089088019659	1		591	615	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292490	15292490	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067496-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	135	614	0	ENST00000263388.2:c.2689G>C	p.Gly897Arg	p.G897R	ENST00000263388	NM_000435.2	897	Ggc/Cgc	17/33	0.502031166072871	3	FACETS	0.66	0.6	0.724	0.33	0.3	0.362	SUBCLONAL	1	TRUE	1	0.577089088019659	3		614	913	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638031	176638031	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067496-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	192	535	0	ENST00000439151.2:c.2631T>G	p.Ser877Arg	p.S877R	ENST00000439151	NM_022455.4	877	agT/agG	5/23	0.585102798671277	3	FACETS	0.948	0.878	1	0.316	0.292	0.341	CLONAL	1	TRUE	0	0.577089088019659	3		535	904	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752997	128752997	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067496-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	997	552	1	ENST00000377970.2:c.1158A>C	p.Lys386Asn	p.K386N	ENST00000377970	NM_002467.4	386	aaA/aaC	3/3	0.159387769353962	6	FACETS	1	0.996	1			1	INDETERMINATE	5	TRUE	NA	0.577089088019659	6		553	1399	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067497-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	65	317	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.783	0.682	0.891	0.783	0.682	0.891	SUBCLONAL	1	TRUE	1	0.436851683313412	2		317	380	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0067497-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	160	485	1	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.436851683313412	2		486	618	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0067497-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	70	414	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	1	2	FACETS	0.617	0.539	0.702	0.617	0.539	0.702	SUBCLONAL	1	TRUE	1	0.436851683313412	2		414	519	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80024721	80024721	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067497-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	28	336	0	ENST00000265081.6:c.1505C>G	p.Ser502Cys	p.S502C	ENST00000265081	NM_002439.4	502	tCt/tGt	10/24	1	2	FACETS	0.275	0.219	0.339	0.275	0.219	0.339	SUBCLONAL	1	TRUE	1	0.436851683313412	2		336	466	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181608	32181608	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067497-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	83	404	0	ENST00000375023.3:c.2177G>T	p.Cys726Phe	p.C726F	ENST00000375023	NM_004557.3	726	tGt/tTt	14/30	1	2	FACETS	0.706	0.625	0.793	0.706	0.625	0.793	SUBCLONAL	1	TRUE	1	0.436851683313412	2		404	538	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652043	36652044	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0067497-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	126	568	0	ENST00000244741.5:c.168_169dup	p.Thr57ArgfsTer92	p.T57Rfs*92	ENST00000244741	NM_000389.4	55	-/GA	2/3	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.436851683313412	2		568	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0067498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	67	369	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		369	471	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984479	7984479	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	65	263	0	ENST00000319144.4:c.379C>A	p.Pro127Thr	p.P127T	ENST00000319144	NM_001139.2	127	Ccc/Acc	3/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		263	374	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424428	49424444	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCACTTCCAAAGGCC	CCCCACTTCCAAAGGCC	GCCCTT	novel	NA	P-0067498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	46	326	2	ENST00000301067.7:c.13779_13795delinsAAGGGC	p.Ala4594ArgfsTer8	p.A4594Rfs*8	ENST00000301067	NM_003482.3	4593	ggGGCCTTTGGAAGTGGGGcg/ggAAGGGCcg	41/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		328	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0067499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	328	477	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.470221755989406	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.470221755989406	2		477	611	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0067499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	80	439	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.972	0.862	1	0.972	0.862	1	CLONAL	1	TRUE	1	0.470221755989406	2		439	350	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951166	48951166	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0067499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	68	262	0	ENST00000267163.4:c.1328C>G	p.Ser443Ter	p.S443*	ENST00000267163	NM_000321.2	443	tCa/tGa	13/27	0.470221755989406	1	FACETS	0.907	0.799	1	0.907	0.799	1	CLONAL	1	TRUE	0	0.470221755989406	1		262	244	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202210	108202210	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555124019	NA	P-0067499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	26	279	2	ENST00000278616.4:c.7555C>G	p.Leu2519Val	p.L2519V	ENST00000278616	NM_000051.3	2519	Ctt/Gtt	51/63	1	2	FACETS	0.321	0.254	0.397	0.321	0.254	0.397	SUBCLONAL	1	TRUE	1	0.470221755989406	2		281	345	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590370	67590370	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	102	291	0	ENST00000274335.5:c.1432C>A	p.Gln478Lys	p.Q478K	ENST00000274335		478	Caa/Aaa	11/15	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.470221755989406	2		291	420	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562747	29562747	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs137854556	NA	P-0067499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	230	346	0	ENST00000356175.3:c.3827G>C	p.Arg1276Pro	p.R1276P	ENST00000356175	NM_000267.3	1276	cGa/cCa	28/57	0.470221755989406	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.470221755989406	2		346	460	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0067500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	47	418	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.434103384457524	3	FACETS	0.784	0.673	0.903	0.784	0.673	0.903	CLONAL	2	TRUE	1	0.427835085806184	3		418	170	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0067500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	107	412	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.415158424995846	3	FACETS	1	0.959	1	0.728	0.663	0.794	CLONAL	2	TRUE	0	0.427835085806184	3		412	278	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581335	48581335	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	33	419	0	ENST00000342988.3:c.639del	p.Asn216ThrfsTer25	p.N216Tfs*25	ENST00000342988	NM_005359.5	213	aaC/aa	5/12	0.434103384457524	1	FACETS	0.625	0.514	0.748	0.625	0.514	0.748	SUBCLONAL	1	TRUE	0	0.427835085806184	1		419	194	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138729528	NA	P-0067511-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	27	632	0	ENST00000269305.4:c.523C>G	p.Arg175Gly	p.R175G	ENST00000269305	NM_001126112.2	175	Cgc/Ggc	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		632	175	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244223	5244223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199851847	NA	P-0067511-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	13	433	0	ENST00000357368.4:c.1259G>A	p.Arg420His	p.R420H	ENST00000357368	NM_002850.3	420	cGc/cAc	11/38	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		433	100	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	50	317	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.775298076718282	2		317	122	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658663	3658663	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	218	732	0	ENST00000294008.3:c.303A>T	p.Lys101Asn	p.K101N	ENST00000294008	NM_032444.2	101	aaA/aaT	2/15	0.69166415504509	2	FACETS	0.97	0.93	1	0.97	0.93	1	CLONAL	2	TRUE	0	0.775298076718282	2		732	290	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223164	36223164	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	96	849	0	ENST00000222270.7:c.5714A>G	p.Asp1905Gly	p.D1905G	ENST00000222270	NM_014727.1	1905	gAc/gGc	28/37	0.46478567204315	3	FACETS	0.929	0.834	1	0.464	0.417	0.514	INDETERMINATE	1	TRUE	1	0.775298076718282	3		849	370	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	72	317	0				ENST00000310581	NM_198253.2	-/1132			0.382439575285265	1	FACETS	0.901	0.793	1	0.901	0.793	1	CLONAL	1	FALSE	0	0.382439575285265	1		317	338	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0067513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	61	301	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.82	0.71	0.938	0.82	0.71	0.938	CLONAL	1	FALSE	1	0.382439575285265	2		301	389	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46124970	46124998	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	GTTCAGACAACTGTGCCTGTGTTTTACCA	GTTCAGACAACTGTGCCTGTGTTTTACCA	-	novel	NA	P-0067513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	38	398	0	ENST00000334344.6:c.187-29_187-1del		p.X63_splice	ENST00000334344	NM_152641.2	63			1	2	FACETS	0.669	0.555	0.795	0.669	0.555	0.795	SUBCLONAL	1	FALSE	1	0.382439575285265	2		398	297	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152864506	152864506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	56	296	0	ENST00000406277.2:c.22G>A	p.Gly8Arg	p.G8R	ENST00000406277	NM_152274.4	8	Ggg/Agg	2/7	1		FACETS		0.885	1				CLONAL	1	FALSE	1	0.382439575285265	2		296	285	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	115	317	0				ENST00000310581	NM_198253.2	-/1132			0.506189384975603	5	FACETS	0.909	0.832	0.988	0.909	0.832	0.988	CLONAL	3	TRUE	2	0.506189384975603	5		317	293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	181	548	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.497544588898472	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	1	0.506189384975603	3		548	432	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70411605	70411605	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs868611128	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	57	394	0	ENST00000373644.4:c.4279C>T	p.Arg1427Ter	p.R1427*	ENST00000373644	NM_030625.2	1427	Cga/Tga	5/12	1	2	FACETS	0.897	0.778	1	0.897	0.778	1	CLONAL	1	TRUE	1	0.506189384975603	2		394	251	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536625	120536625	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs202018032	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	79	518	0	ENST00000229340.5:c.467A>G	p.Asn156Ser	p.N156S	ENST00000229340	NM_006861.6	156	aAc/aGc	5/6	0.497544588898472	3	FACETS	0.912	0.806	1	0.456	0.403	0.513	CLONAL	1	TRUE	1	0.506189384975603	3		518	429	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042574	42042574	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	159	520	0	ENST00000219905.7:c.6769C>T	p.Pro2257Ser	p.P2257S	ENST00000219905	NM_001164273.1	2257	Cct/Tct	17/24	0.506189384975603	3	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	1	0.506189384975603	3		520	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579349	7579349	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	89	533	0	ENST00000269305.4:c.338T>C	p.Phe113Ser	p.F113S	ENST00000269305	NM_001126112.2	113	tTc/tCc	4/11	0.497544588898472	3	FACETS	1	0.946	1	0.549	0.49	0.612	CLONAL	1	TRUE	1	0.506189384975603	3		533	401	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37882068	37882068	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	71	439	0	ENST00000269571.5:c.2834C>T	p.Pro945Leu	p.P945L	ENST00000269571		945	cCc/cTc	23/27	0.497544588898472	3	FACETS	1	0.887	1	0.505	0.444	0.57	CLONAL	1	TRUE	1	0.506189384975603	3		439	348	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023508	31023508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	138	522	0	ENST00000375687.4:c.2993C>T	p.Ser998Phe	p.S998F	ENST00000375687	NM_015338.5	998	tCc/tTc	13/13	0.45534835900897	4	FACETS	0.982	0.902	1	0.982	0.902	1	CLONAL	2	TRUE	2	0.506189384975603	4		522	418	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485448	57485448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	74	449	0	ENST00000371085.3:c.1030G>A	p.Glu344Lys	p.E344K	ENST00000371085	NM_000516.4	344	Gag/Aag	12/13	0.45534835900897	4	FACETS	1	0.903	1	0.516	0.453	0.582	CLONAL	1	TRUE	2	0.506189384975603	4		449	427	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437777	52437777	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	91	455	0	ENST00000460680.1:c.1384C>T	p.Pro462Ser	p.P462S	ENST00000460680	NM_004656.3	462	Cct/Tct	13/17	0.506189384975603	2	FACETS	1	0.954	1	0.557	0.499	0.616	CLONAL	1	TRUE	0	0.506189384975603	2		455	323	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201758	66201758	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	74	459	0	ENST00000273854.3:c.2744G>A	p.Trp915Ter	p.W915*	ENST00000273854	NM_004439.5	915	tGg/tAg	16/18	0.497544588898472	3	FACETS	1	0.92	1	0.528	0.465	0.594	CLONAL	1	TRUE	1	0.506189384975603	3		459	347	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295230	1295230	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs796516131	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	42	406	0				ENST00000310581	NM_198253.2	-/1132			0.506189384975603	5	FACETS	0.939	0.787	1	0.313	0.262	0.369	CLONAL	1	TRUE	2	0.506189384975603	5		406	311	SUCCESS
APC	324	MSKCC	GRCh37	5	112175373	112175373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060503264	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	204	495	0	ENST00000257430.4:c.4082C>T	p.Pro1361Leu	p.P1361L	ENST00000257430	NM_000038.5	1361	cCc/cTc	16/16	0.506189384975603	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.506189384975603	3		495	312	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180939	32180939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	73	450	0	ENST00000375023.3:c.2411G>A	p.Gly804Glu	p.G804E	ENST00000375023	NM_004557.3	804	gGa/gAa	15/30	0.497544588898472	3	FACETS	1	0.951	1	0.577	0.509	0.649	CLONAL	1	TRUE	1	0.506189384975603	3		450	313	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184757	32184757	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	86	553	0	ENST00000375023.3:c.1826G>A	p.Gly609Glu	p.G609E	ENST00000375023	NM_004557.3	609	gGa/gAa	11/30	0.497544588898472	3	FACETS	1	0.942	1	0.544	0.485	0.608	CLONAL	1	TRUE	1	0.506189384975603	3		553	391	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683844	117683844	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200145587	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	109	471	0	ENST00000368508.3:c.3303G>A	p.Trp1101Ter	p.W1101*	ENST00000368508	NM_002944.2	1101	tgG/tgA	21/43	0.37585069859548	3	FACETS	0.974	0.889	1	0.974	0.889	1	CLONAL	2	TRUE	1	0.506189384975603	3		471	277	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856142	151856142	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	56	444	0	ENST00000262189.6:c.11476C>T	p.Gln3826Ter	p.Q3826*	ENST00000262189	NM_170606.2	3826	Caa/Taa	44/59	0.45534835900897	4	FACETS	0.852	0.733	0.982	0.426	0.366	0.491	CLONAL	1	TRUE	2	0.506189384975603	4		444	391	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123041	5123041	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1006182223	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	138	429	0	ENST00000381652.3:c.3097G>A	p.Val1033Met	p.V1033M	ENST00000381652	NM_004972.3	1033	Gtg/Atg	23/25	0.506189384975603	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.506189384975603	2		429	246	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	152	525	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.506189384975603	2	FACETS	0.978	0.911	1	0.978	0.911	1	CLONAL	2	TRUE	0	0.506189384975603	2		525	307	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27168576	27168576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753021890	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	139	389	0	ENST00000380036.4:c.448G>A	p.Glu150Lys	p.E150K	ENST00000380036	NM_000459.3	150	Gaa/Aaa	3/23	0.506189384975603	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.506189384975603	2		389	233	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391980	139391981	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	77	510	0	ENST00000277541.6:c.6210_6211delinsAA	p.Glu2071Lys	p.E2071K	ENST00000277541	NM_017617.3	2070	cgGGag/cgAAag	34/34	0.490281113096654	4	FACETS	1	0.943	1	0.372	0.328	0.418	CLONAL	1	TRUE	1	0.506189384975603	4		510	411	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412297	139412297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	250	523	0	ENST00000277541.6:c.1348G>A	p.Glu450Lys	p.E450K	ENST00000277541	NM_017617.3	450	Gag/Aag	8/34	0.490281113096654	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	1	0.506189384975603	4		523	471	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321324	1321324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	76	496	0	ENST00000400841.2:c.431G>A	p.Gly144Glu	p.G144E	ENST00000400841		144	gGg/gAg	4/6	0.471021177709519	2	FACETS	0.868	0.767	0.975			1	CLONAL	1	TRUE	NA	0.506189384975603	2		496	346	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468387	120468387	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	94	550	0	ENST00000256646.2:c.4052G>T	p.Cys1351Phe	p.C1351F	ENST00000256646	NM_024408.3	1351	tGt/tTt	25/34	0.506189384975603	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.506189384975603	1		550	239	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176104213	176104213	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	113	335	0	ENST00000367669.3:c.901G>T	p.Gly301Cys	p.G301C	ENST00000367669	NM_022457.5	301	Ggc/Tgc	8/20	0.506189384975603	5	FACETS	1	0.971	1	0.579	0.527	0.633	CLONAL	2	TRUE	1	0.506189384975603	5		335	339	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448425	49448425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763699658	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	167	566	0	ENST00000301067.7:c.286G>A	p.Val96Met	p.V96M	ENST00000301067	NM_003482.3	96	Gtg/Atg	3/54	0.497544588898472	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.506189384975603	3		566	389	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864537	57864537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750072514	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	147	624	0	ENST00000228682.2:c.2014G>A	p.Gly672Arg	p.G672R	ENST00000228682	NM_005269.2	672	Gga/Aga	12/12	0.497544588898472	3	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	1	0.506189384975603	3		624	360	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69230512	69230512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	53	292	0	ENST00000462284.1:c.901C>T	p.Pro301Ser	p.P301S	ENST00000462284	NM_002392.5	301	Cct/Tct	10/11	0.497544588898472	3	FACETS	1	0.943	1	0.594	0.512	0.68	CLONAL	1	TRUE	1	0.506189384975603	3		292	221	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986700	36986700	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	152	450	0	ENST00000354822.5:c.989C>G	p.Ala330Gly	p.A330G	ENST00000354822	NM_001079668.2	330	gCg/gGg	3/3	0.497544588898472	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.506189384975603	3		450	302	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029455	14029455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	96	530	0	ENST00000311895.7:c.1666C>T	p.Pro556Ser	p.P556S	ENST00000311895	NM_005236.2	556	Ccg/Tcg	8/11	0.497544588898472	3	FACETS	1	0.959	1	0.569	0.51	0.63	CLONAL	1	TRUE	1	0.506189384975603	3		530	418	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828677	72828677	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	81	546	0	ENST00000268489.5:c.7904G>A	p.Gly2635Glu	p.G2635E	ENST00000268489	NM_006885.3	2635	gGa/gAa	9/10	0.497544588898472	3	FACETS	1	0.939	1	0.545	0.483	0.61	CLONAL	1	TRUE	1	0.506189384975603	3		546	368	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979655	7979655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	58	410	0	ENST00000319144.4:c.1370C>T	p.Ser457Phe	p.S457F	ENST00000319144	NM_001139.2	457	tCc/tTc	11/15	0.497544588898472	3	FACETS	0.994	0.861	1	0.497	0.43	0.568	CLONAL	1	TRUE	1	0.506189384975603	3		410	289	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560218	29560218	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	81	457	0	ENST00000356175.3:c.3695C>T	p.Pro1232Leu	p.P1232L	ENST00000356175	NM_000267.3	1232	cCt/cTt	27/57	0.497544588898472	3	FACETS	1	0.951	1	0.566	0.503	0.634	CLONAL	1	TRUE	1	0.506189384975603	3		457	354	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29563015	29563015	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1349575030	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	58	417	0	ENST00000356175.3:c.3950T>C	p.Val1317Ala	p.V1317A	ENST00000356175	NM_000267.3	1317	gTt/gCt	29/57	0.497544588898472	3	FACETS	0.957	0.829	1	0.479	0.414	0.548	CLONAL	1	TRUE	1	0.506189384975603	3		417	300	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6213963	6213964	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	63	478	0	ENST00000252674.7:c.1393_1394delinsTT	p.Pro465Leu	p.P465L	ENST00000252674	NM_005934.3	465	CCg/TTg	9/12	0.497544588898472	3	FACETS	0.987	0.86	1	0.494	0.43	0.562	CLONAL	1	TRUE	1	0.506189384975603	3		478	316	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11022938	11022938	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	95	492	0	ENST00000327064.4:c.637G>A	p.Val213Met	p.V213M	ENST00000327064	NM_199141.1	213	Gtg/Atg	5/16	0.497544588898472	3	FACETS	1	0.974	1	0.639	0.574	0.708	CLONAL	1	TRUE	1	0.506189384975603	3		492	368	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952256	17952256	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1208932448	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	51	418	0	ENST00000458235.1:c.1084G>A	p.Glu362Lys	p.E362K	ENST00000458235	NM_000215.3	362	Gag/Aag	8/24	0.497544588898472	3	FACETS	0.842	0.72	0.974	0.421	0.36	0.487	CLONAL	1	TRUE	1	0.506189384975603	3		418	300	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797400	42797401	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	97	572	0	ENST00000575354.2:c.3762_3763delinsAA	p.Glu1255Lys	p.E1255K	ENST00000575354	NM_015125.3	1254	gaGGag/gaAAag	15/20	0.497544588898472	3	FACETS	1	0.956	1	0.562	0.504	0.623	CLONAL	1	TRUE	1	0.506189384975603	3		572	427	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424021	47424021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	83	528	0	ENST00000404338.3:c.2089C>T	p.Pro697Ser	p.P697S	ENST00000404338	NM_004491.4	697	Ccc/Tcc	1/6	0.497544588898472	3	FACETS	1	0.887	1	0.5	0.443	0.56	CLONAL	1	TRUE	1	0.506189384975603	3		528	411	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416694	29416695	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	69	570	0	ENST00000389048.3:c.4258_4259delinsAA	p.Gly1420Lys	p.G1420K	ENST00000389048	NM_004304.4	1420	GGg/AAg	29/29	0.497544588898472	3	FACETS	0.99	0.868	1	0.495	0.434	0.56	CLONAL	1	TRUE	1	0.506189384975603	3		570	345	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47613730	47613730	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	40	264	0	ENST00000263735.4:c.923T>G	p.Met308Arg	p.M308R	ENST00000263735	NM_002354.2	308	aTg/aGg	9/9	0.497544588898472	3	FACETS	1	0.865	1	0.516	0.433	0.605	CLONAL	1	TRUE	1	0.506189384975603	3		264	192	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225449691	225449691	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	51	312	0	ENST00000264414.4:c.36G>T	p.Lys12Asn	p.K12N	ENST00000264414	NM_003590.4	12	aaG/aaT	1/16	0.497544588898472	3	FACETS	0.956	0.82	1	0.478	0.41	0.552	CLONAL	1	TRUE	1	0.506189384975603	3		312	264	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980602	1980603	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	68	496	0	ENST00000382891.5:c.4064_4065delinsAA	p.Arg1355Gln	p.R1355Q	ENST00000382891	NM_133335.3	1355	cGG/cAA	22/22	1	2	FACETS	0.887	0.778	1	0.887	0.778	1	CLONAL	1	TRUE	1	0.506189384975603	2		496	303	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531031	187531036	+	inframe_deletion	In_Frame_Del	DEL	TTATCG	TTATCG	-	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	91	433	0	ENST00000441802.2:c.9987_9992del	p.Asp3330_Asn3331del	p.D3330_N3331del	ENST00000441802	NM_005245.3	3329	aaCGATAAt/aat	15/27	0.497544588898472	3	FACETS	1	0.958	1	0.573	0.512	0.637	CLONAL	1	TRUE	1	0.506189384975603	3		433	393	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531049	187531049	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	76	448	0	ENST00000441802.2:c.9974T>G	p.Val3325Gly	p.V3325G	ENST00000441802	NM_005245.3	3325	gTa/gGa	15/27	0.497544588898472	3	FACETS	0.965	0.851	1	0.482	0.425	0.543	CLONAL	1	TRUE	1	0.506189384975603	3		448	390	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638039	176638039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	231	531	0	ENST00000439151.2:c.2639G>A	p.Gly880Glu	p.G880E	ENST00000439151	NM_022455.4	880	gGa/gAa	5/23	0.506189384975603	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.506189384975603	3		531	356	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109319926	109319927	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	118	391	0	ENST00000436639.2:c.761_762delinsTT	p.Ser254Phe	p.S254F	ENST00000436639	NM_014454.2	254	tCC/tTT	5/10	0.37585069859548	3	FACETS	0.952	0.871	1	0.952	0.871	1	CLONAL	2	TRUE	1	0.506189384975603	3		391	307	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021731	69021731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	89	424	0	ENST00000288368.4:c.3019G>A	p.Asp1007Asn	p.D1007N	ENST00000288368	NM_024870.2	1007	Gat/Aat	25/40	0.497544588898472	3	FACETS	1	0.955	1	0.566	0.505	0.631	CLONAL	1	TRUE	1	0.506189384975603	3		424	389	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730325	133730325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	82	468	0	ENST00000318560.5:c.391C>T	p.Pro131Ser	p.P131S	ENST00000318560	NM_005157.4	131	Cct/Tct	3/11	0.490281113096654	4	FACETS	0.99	0.876	1	0.33	0.292	0.371	CLONAL	1	TRUE	1	0.506189384975603	4		468	493	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349197	70349197	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	136	266	0	ENST00000374080.3:c.3609C>G	p.Cys1203Trp	p.C1203W	ENST00000374080		1203	tgC/tgG	26/45	0.471021177709519	2	FACETS	0.923	0.871	0.973			1	CLONAL	3	TRUE	NA	0.506189384975603	2		266	194	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891190	101891190	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	84	299	0	ENST00000374994.4:c.151G>T	p.Asp51Tyr	p.D51Y	ENST00000374994	NM_004612.2	51	Gat/Tat	2/9	1	2	FACETS	1	0.89	1	1	0.985	1	CLONAL	2	TRUE	1	0.23802325556946	2		299	353	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678356	88678356	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	84	424	0	ENST00000360948.2:c.1180C>A	p.His394Asn	p.H394N	ENST00000360948	NM_001012338.2	394	Cac/Aac	9/19	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.23802325556946	2		424	473	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038475	180038475	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	81	364	0	ENST00000261937.6:c.3542A>T	p.Glu1181Val	p.E1181V	ENST00000261937	NM_182925.4	1181	gAa/gTa	27/30	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.23802325556946	2		364	473	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846107	68846118	+	inframe_deletion	In_Frame_Del	DEL	ACAGCTGTGATC	ACAGCTGTGATC	-	novel	NA	P-0067515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	107	388	0	ENST00000261769.5:c.1082_1093del	p.Ala361_Thr364del	p.A361_T364del	ENST00000261769	NM_004360.3	360	ACAGCTGTGATC/-	8/16	0.23802325556946	1	FACETS	0.945	0.854	1	1	0.988	1	CLONAL	2	TRUE	0	0.23802325556946	1		388	419	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400014	49400014	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866333389	NA	P-0067515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	85	352	0	ENST00000418115.1:c.323C>T	p.Pro108Leu	p.P108L	ENST00000418115	NM_001664.2	108	cCc/cTc	4/5	1	2	FACETS	0.773	0.686	0.865	1	0.98	1	SUBCLONAL	2	TRUE	1	0.23802325556946	2		352	462	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	360055	360055	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779951904	NA	P-0067515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	25	391	0	ENST00000262320.3:c.1034C>T	p.Pro345Leu	p.P345L	ENST00000262320	NM_003502.3	345	cCa/cTa	4/11	1	2	FACETS	0.444	0.349	0.554	0.444	0.349	0.554	SUBCLONAL	1	TRUE	1	0.23802325556946	2		391	473	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0067550-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	118	329	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.278530159228332	3	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	1	0.278530159228332	3		329	469	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3824629	3824629	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778882385	NA	P-0067550-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	52	476	0	ENST00000262367.5:c.2224C>T	p.Arg742Cys	p.R742C	ENST00000262367	NM_004380.2	742	Cgt/Tgt	12/31	1	2	FACETS	0.922	0.787	1	0.922	0.787	1	CLONAL	1	TRUE	1	0.278530159228332	2		476	405	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337298	89337298	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067550-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	57	294	0	ENST00000301030.4:c.7733T>C	p.Val2578Ala	p.V2578A	ENST00000301030	NM_001256183.1	2578	gTg/gCg	12/13	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.278530159228332	2		294	311	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650030	93650030	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0067550-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	32	372	0	ENST00000375746.1:c.1582-1G>C		p.X528_splice	ENST00000375746	NM_001174167.1	528			1	2	FACETS	0.723	0.588	0.874	0.723	0.588	0.874	SUBCLONAL	1	TRUE	1	0.278530159228332	2		372	318	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248889	133248889	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067550-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	63	489	0	ENST00000320574.5:c.1706T>C	p.Phe569Ser	p.F569S	ENST00000320574	NM_006231.2	569	tTc/tCc	16/49	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.278530159228332	2		489	441	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851382	63851382	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067550-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	67	532	0	ENST00000279873.7:c.2160G>C	p.Lys720Asn	p.K720N	ENST00000279873	NM_032199.2	720	aaG/aaC	10/10	1	2	FACETS	0.953	0.829	1	0.953	0.829	1	CLONAL	1	TRUE	1	0.278530159228332	2		532	505	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0067551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	21	270	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.942	0.728	1	0.942	0.728	1	CLONAL	1	TRUE	1	0.200741428243798	2		270	222	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0067551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	28	547	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.200741428243798	1	FACETS	0.954	0.765	1	0.954	0.765	1	CLONAL	1	TRUE	0	0.200741428243798	1		547	263	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0067551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	32	298	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	0.200741428243798	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.200741428243798	1		298	228	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577544	7577544	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587780074	NA	P-0067551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	53	423	0	ENST00000269305.4:c.737T>C	p.Met246Thr	p.M246T	ENST00000269305	NM_001126112.2	246	aTg/aCg	7/11	0.163650324930393	2	FACETS	0.957	0.822	1	0.957	0.822	1	CLONAL	2	TRUE	0	0.200741428243798	2		423	276	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969968	161969968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746215864	NA	P-0067551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	20	434	0	ENST00000366898.1:c.1001G>A	p.Arg334His	p.R334H	ENST00000366898	NM_004562.2	334	cGc/cAc	9/12	1	2	FACETS	0.8	0.613	1	0.8	0.613	1	CLONAL	1	TRUE	1	0.200741428243798	2		434	249	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29068964	29068964	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	14	368	0	ENST00000282397.4:c.17A>G	p.Asp6Gly	p.D6G	ENST00000282397	NM_002019.4	6	gAc/gGc	1/30	1	2	FACETS	0.519	0.374	0.693	0.519	0.374	0.693	SUBCLONAL	1	TRUE	1	0.200741428243798	2		368	269	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0067552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	152	533	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.543080504076378	2	FACETS	0.947	0.883	1	0.947	0.883	1	CLONAL	2	TRUE	0	0.540708081820784	2		533	297	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553300	106553300	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	90	578	0	ENST00000369096.4:c.1265G>T	p.Cys422Phe	p.C422F	ENST00000369096	NM_001198.3	422	tGt/tTt	5/7	0.543080504076378	2	FACETS	0.959	0.859	1	0.48	0.429	0.533	CLONAL	1	TRUE	0	0.540708081820784	2		578	347	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557930	187557930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs905514850	NA	P-0067552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	99	520	0	ENST00000441802.2:c.3781G>A	p.Asp1261Asn	p.D1261N	ENST00000441802	NM_005245.3	1261	Gac/Aac	5/27	0.543080504076378	2	FACETS	1	0.947	1	0.539	0.485	0.594	CLONAL	1	TRUE	0	0.540708081820784	2		520	340	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714194	43714194	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	93	600	0	ENST00000382044.4:c.3959C>G	p.Thr1320Arg	p.T1320R	ENST00000382044	NM_001141980.1	1320	aCa/aGa	19/28	1	2	FACETS	0.942	0.845	1	0.942	0.845	1	CLONAL	1	TRUE	1	0.540708081820784	2		600	365	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46725741	46725741	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	77	479	0	ENST00000371975.4:c.377T>A	p.Leu126Gln	p.L126Q	ENST00000371975	NM_003579.3	126	cTg/cAg	5/18	1	2	FACETS	0.946	0.839	1	0.946	0.839	1	CLONAL	1	TRUE	1	0.540708081820784	2		479	301	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206833	36207067	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CACTGAGCCGCTCGGAAAAGGACAAGCTCCCGGGCTTGGTCTGATCATCTAGTTTCTGCCGATGTCCTATTGTGGGGAGCAGGGAGGGGAGGGGATGGGGGGAGGGAAGGAGGGAGGGAAGAGATCAGAAAAAGTATTGTGGATTTCCTAAAACTGGGGCTTTTCTTGTCTTTCCCCTCTCTCTCCCCTCACCCCAACATAGACTCGCTAGAGATATGCCAGCTGAATTTGGGGC	CACTGAGCCGCTCGGAAAAGGACAAGCTCCCGGGCTTGGTCTGATCATCTAGTTTCTGCCGATGTCCTATTGTGGGGAGCAGGGAGGGGAGGGGATGGGGGGAGGGAAGGAGGGAGGGAAGAGATCAGAAAAAGTATTGTGGATTTCCTAAAACTGGGGCTTTTCTTGTCTTTCCCCTCTCTCTCCCCTCACCCCAACATAGACTCGCTAGAGATATGCCAGCTGAATTTGGGGC	-	novel	NA	P-0067552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	21	448	0	ENST00000300305.3:c.614-169_679del		p.X205_splice	ENST00000300305		205		6/8	NA	2	FACETS	0.215	0.165	0.273			1	INDETERMINATE	1	TRUE	NA	0.540708081820784	2		448	362	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691161	18691161	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	190	438	0	ENST00000266497.5:c.3272del	p.His1091LeufsTer24	p.H1091Lfs*24	ENST00000266497		1091	cAt/ct	23/31	0.313557296717776	4	FACETS	1	0.978	1			1	INDETERMINATE	2	TRUE	NA	0.540708081820784	4		438	486	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90960104	90960104	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	104	293	0	ENST00000265433.3:c.1862G>C	p.Gly621Ala	p.G621A	ENST00000265433	NM_002485.4	621	gGg/gCg	12/16	0.543080504076378	3	FACETS	1	0.969	1	0.592	0.533	0.652	CLONAL	1	TRUE	1	0.540708081820784	3		293	413	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253801	30253801	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	64	439	0	ENST00000307677.4:c.653T>C	p.Met218Thr	p.M218T	ENST00000307677	NM_138578.1	218	aTg/aCg	3/3	0.543080504076378	3	FACETS	0.808	0.704	0.921	0.404	0.352	0.461	CLONAL	1	TRUE	1	0.540708081820784	3		439	372	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989334	7989334	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	61	406	0	ENST00000319144.4:c.352G>A	p.Gly118Arg	p.G118R	ENST00000319144	NM_001139.2	118	Gga/Aga	2/15	0.543080504076378	2	FACETS	1	0.892	1	0.51	0.446	0.578	CLONAL	1	TRUE	0	0.540708081820784	2		406	221	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168975	11168975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329240441	NA	P-0067553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	18	382	0	ENST00000358026.2:c.4565C>T	p.Ser1522Leu	p.S1522L	ENST00000358026	NM_001128849.1	1522	tCg/tTg	32/36	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.206277280250164	2		382	136	SUCCESS
AR	367	MSKCC	GRCh37	X	66765695	66765695	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	11	334	0	ENST00000374690.3:c.707C>A	p.Ala236Asp	p.A236D	ENST00000374690	NM_000044.3	236	gCc/gAc	1/8	1	1	FACETS	1	0.77	1	1	0.77	1	CLONAL	1	TRUE	0	0.206277280250164	1		334	85	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	45	317	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.928	0.789	1	0.928	0.789	1	CLONAL	1	TRUE	1	0.459562848669695	2		317	211	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668681	52668681	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0067554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	104	407	0	ENST00000394830.3:c.1238C>G	p.Ser413Ter	p.S413*	ENST00000394830	NM_018313.4	413	tCa/tGa	12/30	0.459562848669695	1	FACETS	0.979	0.885	1	0.979	0.885	1	CLONAL	1	TRUE	0	0.459562848669695	1		407	356	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692793	89692793	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786204927	NA	P-0067554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	74	275	0	ENST00000371953.3:c.277C>G	p.His93Asp	p.H93D	ENST00000371953	NM_000314.4	93	Cat/Gat	5/9	0.459562848669695	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.459562848669695	1		275	206	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191490	10191497	+	frameshift_variant	Frame_Shift_Del	DEL	ATGCCTCC	ATGCCTCC	-	novel	NA	P-0067554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	102	426	0	ENST00000256474.2:c.484_491del	p.Cys162GlyfsTer9	p.C162Gfs*9	ENST00000256474	NM_000551.3	161	cgATGCCTCCag/cgag	3/3	0.459562848669695	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.459562848669695	1		426	316	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595922	43595922	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	106	448	0	ENST00000355710.3:c.89A>C	p.Tyr30Ser	p.Y30S	ENST00000355710	NM_020975.4	30	tAc/tCc	2/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.459562848669695	2		448	402	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40747931	40747931	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	108	566	0	ENST00000392038.2:c.487T>C	p.Phe163Leu	p.F163L	ENST00000392038	NM_001626.4	163	Ttt/Ctt	6/14	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.459562848669695	2		566	432	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374830	149374830	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	83	456	0	ENST00000360632.3:c.264C>G	p.His88Gln	p.H88Q	ENST00000360632	NM_015472.4	88	caC/caG	2/7	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.459562848669695	2		456	337	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326133	62326133	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	85	516	0	ENST00000360203.5:c.3149C>G	p.Pro1050Arg	p.P1050R	ENST00000360203	NM_001283009.1	1050	cCc/cGc	32/35	1	2	FACETS	0.946	0.842	1	0.946	0.842	1	CLONAL	1	TRUE	1	0.459562848669695	2		516	391	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067555-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	14	317	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		317	195	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067556-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	42	317	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.874	0.736	1	0.874	0.736	1	CLONAL	1	TRUE	1	0.395446592183021	2		317	243	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074281	30074281	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067556-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	105	490	0	ENST00000338641.4:c.1544del	p.Lys515SerfsTer7	p.K515Sfs*7	ENST00000338641	NM_000268.3	515	Aag/ag	14/16	0.395446592183021	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.395446592183021	1		490	386	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21340156	21340156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1327974340	NA	P-0067598-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	78	438	1	ENST00000215739.8:c.290G>A	p.Arg97Gln	p.R97Q	ENST00000215739	NM_006767.3	97	cGg/cAg	3/21	0.290382704212546	3	FACETS	0.754	0.666	0.848	0.503	0.444	0.565	SUBCLONAL	2	TRUE	0	0.290382704212546	3		439	408	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978462	2978462	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067598-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	20	393	0	ENST00000396946.4:c.868G>T	p.Gly290Trp	p.G290W	ENST00000396946	NM_032415.4	290	Ggg/Tgg	7/25	0.235753928491135	4	FACETS	0.512	0.391	0.654	0.256	0.195	0.327	SUBCLONAL	1	TRUE	2	0.290382704212546	4		393	347	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667561	29667561	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067598-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	99	447	0	ENST00000356175.3:c.6898del	p.Ala2300LeufsTer25	p.A2300Lfs*25	ENST00000356175	NM_000267.3	2299	gtG/gt	46/57	0.257905574324204	2	FACETS	0.932	0.839	1	0.932	0.839	1	CLONAL	2	TRUE	0	0.290382704212546	2		447	366	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0067600-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	55	270	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.729	0.626	0.841	0.729	0.626	0.841	SUBCLONAL	1	TRUE	1	0.385746974114921	2		270	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0067600-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	116	500	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	0.385746974114921	1	FACETS	0.918	0.831	1	0.918	0.831	1	CLONAL	1	TRUE	0	0.385746974114921	1		500	529	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575087	48575087	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067600-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	84	359	0	ENST00000342988.3:c.281T>G	p.Ile94Ser	p.I94S	ENST00000342988	NM_005359.5	94	aTc/aGc	3/12	0.385746974114921	1	FACETS	0.982	0.874	1	0.982	0.874	1	CLONAL	1	TRUE	0	0.385746974114921	1		359	358	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988452	41988455	+	frameshift_variant	Frame_Shift_Del	DEL	CAAA	CAAA	-	novel	NA	P-0067601-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	44	474	0	ENST00000219905.7:c.1246_1249del	p.Asn416ValfsTer7	p.N416Vfs*7	ENST00000219905	NM_001164273.1	415	tCAAAc/tc	3/24	0.90560578852578	1	FACETS	0.281	0.239	0.327	0.281	0.239	0.327	SUBCLONAL	1	TRUE	0	0.90560578852578	1		474	189	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288893	33288893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067601-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	193	452	0	ENST00000374542.5:c.659C>T	p.Ser220Phe	p.S220F	ENST00000374542	NM_001141970.1	220	tCc/tTc	3/8	0.90560578852578	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.90560578852578	1		452	230	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692997	89693016	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGAGACAAAAAGGTAAGTTA	AGAGACAAAAAGGTAAGTTA	-	novel	NA	P-0067601-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	65	381	0	ENST00000371953.3:c.481_492+8del		p.X161_splice	ENST00000371953	NM_000314.4	161		5/9	0.90560578852578	1	FACETS	0.982	0.915	1	0.982	0.915	1	CLONAL	1	TRUE	0	0.90560578852578	1		381	80	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55270209	55270209	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0067601-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	167	598	0	ENST00000275493.2:c.3163-1G>T		p.X1055_splice	ENST00000275493	NM_005228.3	1055			0.177935799840805	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.90560578852578	0		598	344	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572583	64572583	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067601-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	136	735	0	ENST00000312049.6:c.1273G>A	p.Glu425Lys	p.E425K	ENST00000312049	NM_130799.2	425	Gag/Aag	9/10	0.90560578852578	1	FACETS	0.567	0.525	0.609	0.567	0.525	0.609	SUBCLONAL	1	TRUE	0	0.90560578852578	1		735	290	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067602-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	38	317	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.788	0.664	0.921	0.788	0.664	0.921	CLONAL	1	TRUE	1	0.703850345128023	2		317	137	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602931	55602931	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067602-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	104	395	0	ENST00000288135.5:c.2641A>G	p.Lys881Glu	p.K881E	ENST00000288135	NM_000222.2	881	Aag/Gag	19/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.703850345128023	2		395	247	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345741	152345741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745877163	NA	P-0067602-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	99	419	0	ENST00000359321.1:c.829G>A	p.Val277Ile	p.V277I	ENST00000359321	NM_005431.1	277	Gtt/Att	3/3	0.690210247597647	3	FACETS	1	0.912	1	0.507	0.456	0.56	CLONAL	1	TRUE	1	0.703850345128023	3		419	375	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720659	89720659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067602-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	58	126	0	ENST00000371953.3:c.810G>A	p.Met270Ile	p.M270I	ENST00000371953	NM_000314.4	270	atG/atA	8/9	0.703850345128023	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.703850345128023	1		126	87	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0067604-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	145	450	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.40179541169585	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.40179541169585	1		450	459	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010560	48010560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067604-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	111	490	0	ENST00000234420.5:c.188C>T	p.Ser63Phe	p.S63F	ENST00000234420	NM_000179.2	63	tCc/tTc	1/10	0.178681386197189	5	FACETS	0.9	0.813	0.991	0.6	0.542	0.661	INDETERMINATE	2	TRUE	2	0.40179541169585	5		490	492	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0067604-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	78	516	0	ENST00000311936.3:c.180_181delinsAA	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggAAaa	3/5	1	2	FACETS	0.882	0.779	0.993	0.882	0.779	0.993	CLONAL	1	TRUE	1	0.40179541169585	2		516	440	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974783	21974786	+	frameshift_variant	Frame_Shift_Del	DEL	CAGT	CAGT	-	novel	NA	P-0067626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	54	377	0	ENST00000304494.5:c.41_44del	p.Asp14GlyfsTer11	p.D14Gfs*11	ENST00000304494	NM_000077.4	14	gACTGg/gg	1/3	0.274435235462225	1	FACETS	0.652	0.558	0.754	0.652	0.558	0.754	SUBCLONAL	1	TRUE	0	0.322498518260435	1		377	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577561	+	inframe_deletion	In_Frame_Del	DEL	CAGGAA	CAGGAA	-	novel	NA	P-0067626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	187	353	0	ENST00000269305.4:c.720_725del	p.Ser241_Cys242del	p.S241_C242del	ENST00000269305	NM_001126112.2	240	agTTCCTGc/agc	7/11	0.307756592523603	3	FACETS	1	0.986	1	0.83	0.772	0.889	CLONAL	2	TRUE	0	0.322498518260435	3		353	541	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899070	40899070	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	109	253	0	ENST00000373198.4:c.2200A>T	p.Thr734Ser	p.T734S	ENST00000373198	NM_133170.3	734	Acc/Tcc	14/32	NA	2	FACETS	0.904	0.819	0.992			1	INDETERMINATE	2	TRUE	NA	0.322498518260435	2		253	374	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005611	42005611	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	46	500	0	ENST00000219905.7:c.3347A>T	p.Glu1116Val	p.E1116V	ENST00000219905	NM_001164273.1	1116	gAg/gTg	9/24	0.287042864739429	3	FACETS	0.587	0.494	0.691	0.294	0.247	0.346	SUBCLONAL	1	TRUE	1	0.322498518260435	3		500	564	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273234	55273234	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	44	382	0	ENST00000275493.2:c.3557T>A	p.Ile1186Asn	p.I1186N	ENST00000275493	NM_005228.3	1186	aTc/aAc	28/28	1	2	FACETS	0.464	0.388	0.548	0.464	0.388	0.548	SUBCLONAL	1	TRUE	1	0.322498518260435	2		382	588	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045976	47045976	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	35	361	0	ENST00000377604.3:c.2771C>T	p.Thr924Ile	p.T924I	ENST00000377604	NM_001204468.1	924	aCc/aTc	24/24	0.219908151231094	3	FACETS	0.419	0.343	0.506			1	SUBCLONAL	1	TRUE	NA	0.322498518260435	3		361	601	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421295	12421295	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	42	398	0	ENST00000287820.6:c.175T>C	p.Ser59Pro	p.S59P	ENST00000287820	NM_015869.4	59	Tcc/Ccc	2/7	0.238932854443433	2	FACETS	0.504	0.42	0.597	0.252	0.21	0.299	SUBCLONAL	1	TRUE	0	0.322498518260435	2		398	517	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158508	106158508	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	36	330	0	ENST00000380013.4:c.3409G>A	p.Glu1137Lys	p.E1137K	ENST00000380013	NM_001127208.2	1137	Gag/Aag	3/11	1	2	FACETS	0.565	0.465	0.677	0.565	0.465	0.677	SUBCLONAL	1	TRUE	1	0.322498518260435	2		330	395	SUCCESS
ATM	472	MSKCC	GRCh37	11	108225545	108225545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1240328733	NA	P-0067626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	51	340	0	ENST00000278616.4:c.8794G>A	p.Glu2932Lys	p.E2932K	ENST00000278616	NM_000051.3	2932	Gag/Aag	61/63	1	2	FACETS	0.791	0.674	0.918	0.791	0.674	0.918	CLONAL	1	TRUE	1	0.322498518260435	2		340	400	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002882	69002882	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	25	336	0	ENST00000288368.4:c.2182A>G	p.Ser728Gly	p.S728G	ENST00000288368	NM_024870.2	728	Agc/Ggc	20/40	0.268256587904086	3	FACETS	0.364	0.286	0.454	0.121	0.095	0.152	SUBCLONAL	1	TRUE	0	0.322498518260435	3		336	495	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86667940	86667940	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067627-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	71	456	0	ENST00000274376.6:c.1704G>A	p.Trp568Ter	p.W568*	ENST00000274376	NM_002890.2	568	tgG/tgA	13/25	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.48749011368033	2		456	276	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061220	38061225	+	inframe_deletion	In_Frame_Del	DEL	CGTTCT	CGTTCT	-	novel	NA	P-0067627-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	155	560	0	ENST00000250448.2:c.764_769del	p.Glu255_Asn256del	p.E255_N256del	ENST00000250448	NM_004496.3	255	gAGAACGgc/ggc	2/2	0.241454839521254	6	FACETS	0.844	0.774	0.917			1	INDETERMINATE	2	TRUE	NA	0.48749011368033	6		560	744	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61729144	61729144	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067627-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	55	314	1	ENST00000401558.2:c.395T>A	p.Met132Lys	p.M132K	ENST00000401558	NM_003400.3	132	aTg/aAg	6/25	1	2	FACETS	0.973	0.842	1	0.973	0.842	1	CLONAL	1	TRUE	1	0.48749011368033	2		315	232	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0067628-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	25	314	4	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	0.863	0.68	1			1	INDETERMINATE	1	TRUE	NA	0.18	2		318	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0067628-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	88	529	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	0.879	0.781	0.984	1	0.983	1	CLONAL	2	TRUE	1	0.18	2		529	556	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741879	162741879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067628-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	69	429	0	ENST00000367921.3:c.1570G>A	p.Ala524Thr	p.A524T	ENST00000367921	NM_006182.2	524	Gct/Act	13/18	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.18	2		429	561	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784049	120784049	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067628-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	40	468	0	ENST00000257552.2:c.936C>A	p.Ser312Arg	p.S312R	ENST00000257552	NM_002442.3	312	agC/agA	13/15	1	2	FACETS	0.814	0.676	0.968	0.814	0.676	0.968	CLONAL	1	TRUE	1	0.18	2		468	546	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741934	162741934	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067628-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	35	424	0	ENST00000367921.3:c.1625C>A	p.Ala542Asp	p.A542D	ENST00000367921	NM_006182.2	542	gCc/gAc	13/18	1	2	FACETS	0.715	0.585	0.861	0.715	0.585	0.861	SUBCLONAL	1	TRUE	1	0.18	2		424	544	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0067629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	263	789	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.885	0.836	0.933	1	0.995	1	CLONAL	2	TRUE	1	0.500466702953264	2		790	594	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0067629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	13	395	11	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.118	0.083	0.161	0.118	0.083	0.161	SUBCLONAL	1	TRUE	1	0.500466702953264	2		406	440	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413010	49413010	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519952	NA	P-0067629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	90	261	0	ENST00000418115.1:c.13C>T	p.Arg5Trp	p.R5W	ENST00000418115	NM_001664.2	5	Cgg/Tgg	2/5	1	2	FACETS	0.831	0.741	0.925	0.831	0.741	0.925	CLONAL	1	TRUE	1	0.500466702953264	2		261	433	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	127	339	0	ENST00000324856.7:c.4555del	p.Gln1519ArgfsTer8	p.Q1519Rfs*8	ENST00000324856	NM_006015.4	1517	gCc/gc	18/20	1	2	FACETS	0.98	0.892	1	0.98	0.892	1	CLONAL	1	TRUE	1	0.500466702953264	2		339	518	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63760059	63760059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs963038555	NA	P-0067629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	103	255	0	ENST00000279873.7:c.712G>A	p.Glu238Lys	p.E238K	ENST00000279873	NM_032199.2	238	Gag/Aag	4/10	0.47471829950545	3	FACETS	0.984	0.884	1	0.492	0.442	0.545	CLONAL	1	TRUE	1	0.500466702953264	3		255	523	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	115	416	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	0.39318841652826	3	FACETS	1	0.966	1	0.573	0.519	0.63	CLONAL	1	TRUE	1	0.500466702953264	3		416	501	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390736	139390736	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	115	361	0	ENST00000277541.6:c.7455del	p.Ser2486ArgfsTer103	p.S2486Rfs*103	ENST00000277541	NM_017617.3	2485	ccC/cc	34/34	0.39318841652826	3	FACETS	0.856	0.772	0.945	0.428	0.386	0.473	CLONAL	1	TRUE	1	0.500466702953264	3		361	671	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249361	153249361	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	99	294	0	ENST00000281708.4:c.1417del	p.Arg473GlufsTer25	p.R473Efs*25	ENST00000281708	NM_033632.3	473	Aga/ga	9/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.500466702953264	2		294	357	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843236	128843237	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1248200595	NA	P-0067629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	66	319	0	ENST00000249373.3:c.349dup	p.Arg117ProfsTer19	p.R117Pfs*19	ENST00000249373	NM_005631.4	115	gcc/gCcc	2/12	1	2	FACETS	0.585	0.509	0.666	0.585	0.509	0.666	SUBCLONAL	1	TRUE	1	0.500466702953264	2		319	451	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953399	17953399	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	55	321	0	ENST00000458235.1:c.587del	p.Pro196GlnfsTer6	p.P196Qfs*6	ENST00000458235	NM_000215.3	196	cCa/ca	6/24	1	2	FACETS	0.479	0.41	0.554	0.479	0.41	0.554	SUBCLONAL	1	TRUE	1	0.500466702953264	2		321	459	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498235	498235	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	103	231	0	ENST00000399788.2:c.23del	p.Gly8AlafsTer58	p.G8Afs*58	ENST00000399788	NM_001042603.1	8	gGc/gc	1/28	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.500466702953264	2		231	376	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244278	153244278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	90	365	1	ENST00000281708.4:c.1879G>A	p.Val627Met	p.V627M	ENST00000281708	NM_033632.3	627	Gtg/Atg	12/12	1	2	FACETS	0.906	0.809	1	0.906	0.809	1	CLONAL	1	TRUE	1	0.500466702953264	2		366	397	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212055	5212055	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749770933	NA	P-0067629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	85	354	0	ENST00000357368.4:c.4976G>A	p.Arg1659His	p.R1659H	ENST00000357368	NM_002850.3	1659	cGc/cAc	32/38	1	2	FACETS	0.717	0.636	0.802	0.717	0.636	0.802	SUBCLONAL	1	TRUE	1	0.500466702953264	2		354	474	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910804	29910804	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0067629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	17	220	0	ENST00000376809.5:c.343+1G>A		p.X115_splice	ENST00000376809	NM_002116.7	115			1	2	FACETS	0.203	0.151	0.265	0.203	0.151	0.265	SUBCLONAL	1	TRUE	1	0.500466702953264	2		220	335	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1978338	1978338	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	127	312	0	ENST00000382891.5:c.3758T>G	p.Leu1253Arg	p.L1253R	ENST00000382891	NM_133335.3	1253	cTg/cGg	21/22	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.500466702953264	2		312	454	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216184	36216184	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	124	358	1	ENST00000222270.7:c.3596del	p.Gly1199AlafsTer156	p.G1199Afs*156	ENST00000222270	NM_014727.1	1198	Ggg/gg	11/37	1	2	FACETS	0.909	0.826	0.996	0.909	0.826	0.996	CLONAL	1	TRUE	1	0.500466702953264	2		359	545	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724419	117724419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	59	285	0	ENST00000368508.3:c.460G>A	p.Val154Met	p.V154M	ENST00000368508	NM_002944.2	154	Gtg/Atg	6/43	1	2	FACETS	0.679	0.588	0.778	0.679	0.588	0.778	SUBCLONAL	1	TRUE	1	0.500466702953264	2		285	347	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396310	396310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768412292	NA	P-0067629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	115	313	0	ENST00000262320.3:c.716C>T	p.Pro239Leu	p.P239L	ENST00000262320	NM_003502.3	239	cCg/cTg	2/11	1	2	FACETS	0.959	0.869	1	0.959	0.869	1	CLONAL	1	TRUE	1	0.500466702953264	2		313	479	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227753	53227753	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	69	317	0	ENST00000375401.3:c.2435T>A	p.Leu812Gln	p.L812Q	ENST00000375401	NM_004187.3	812	cTg/cAg	17/26	1	2	FACETS	0.724	0.634	0.82	0.724	0.634	0.82	SUBCLONAL	1	TRUE	1	0.500466702953264	2		317	381	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1327796	1327798	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs761286705	NA	P-0067629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	60	281	0	ENST00000400841.2:c.83_85del	p.Glu28del	p.E28del	ENST00000400841		28	gAAGga/gga	2/6	1	2	FACETS	0.697	0.604	0.797	0.697	0.604	0.797	SUBCLONAL	1	TRUE	1	0.500466702953264	2		281	344	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649649	206649649	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781992974	NA	P-0067629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	112	327	0	ENST00000367120.3:c.484C>T	p.Arg162Trp	p.R162W	ENST00000367120	NM_014002.3	162	Cgg/Tgg	6/22	1	2	FACETS	0.854	0.771	0.941	0.854	0.771	0.941	CLONAL	1	TRUE	1	0.500466702953264	2		327	524	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26971322	26971322	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	67	262	0	ENST00000381527.3:c.897del	p.Lys299AsnfsTer23	p.K299Nfs*23	ENST00000381527	NM_001260.1	298	gAa/ga	9/13	1	2	FACETS	0.974	0.855	1	0.974	0.855	1	CLONAL	1	TRUE	1	0.500466702953264	2		262	275	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291064	10291064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775139340	NA	P-0067629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	175	537	0	ENST00000340748.4:c.407G>A	p.Arg136His	p.R136H	ENST00000340748		136	cGc/cAc	4/40	1	2	FACETS	0.93	0.858	1	0.93	0.858	1	CLONAL	1	TRUE	1	0.500466702953264	2		537	752	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447220	187447220	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749366850	NA	P-0067629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	93	312	0	ENST00000232014.4:c.973C>T	p.Arg325Trp	p.R325W	ENST00000232014	NM_001130845.1	325	Cgg/Tgg	5/10	1	2	FACETS	0.852	0.762	0.948	0.852	0.762	0.948	CLONAL	1	TRUE	1	0.500466702953264	2		312	436	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618550	37618550	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1331274506	NA	P-0067629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	138	401	0	ENST00000447079.4:c.226A>G	p.Ile76Val	p.I76V	ENST00000447079	NM_015083.1	76	Atc/Gtc	1/14	1	2	FACETS	0.954	0.872	1	0.954	0.872	1	CLONAL	1	TRUE	1	0.500466702953264	2		401	578	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081604	143081604	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	94	346	0	ENST00000262992.4:c.1470C>A	p.Ser490Arg	p.S490R	ENST00000262992	NM_001101669.1	490	agC/agA	15/24	1	2	FACETS	0.91	0.814	1	0.91	0.814	1	CLONAL	1	TRUE	1	0.500466702953264	2		346	413	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275090	41275090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	137	342	0	ENST00000349496.5:c.1256G>A	p.Cys419Tyr	p.C419Y	ENST00000349496	NM_001904.3	419	tGt/tAt	9/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.500466702953264	2		342	460	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491355	2491355	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	95	368	0	ENST00000355716.4:c.398A>T	p.Asp133Val	p.D133V	ENST00000355716	NM_003820.2	133	gAc/gTc	4/8	1	2	FACETS	0.734	0.656	0.817	0.734	0.656	0.817	SUBCLONAL	1	TRUE	1	0.500466702953264	2		368	517	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445482	49445482	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	120	364	0	ENST00000301067.7:c.1984C>A	p.Leu662Met	p.L662M	ENST00000301067	NM_003482.3	662	Ctg/Atg	10/54	1	2	FACETS	0.888	0.805	0.975	0.888	0.805	0.975	CLONAL	1	TRUE	1	0.500466702953264	2		364	540	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11172953	11172953	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1413993125	NA	P-0067629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	106	274	0	ENST00000361445.4:c.7322G>A	p.Arg2441Gln	p.R2441Q	ENST00000361445	NM_004958.3	2441	cGa/cAa	54/58	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.500466702953264	2		274	420	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523311	9523311	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	94	290	0	ENST00000353224.5:c.1926del	p.Tyr643ThrfsTer21	p.Y643Tfs*21	ENST00000353224	NM_177990.2	642	ccC/cc	9/10	1	2	FACETS	0.907	0.812	1	0.907	0.812	1	CLONAL	1	TRUE	1	0.500466702953264	2		290	414	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193872	106193872	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1466911086	NA	P-0067629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	108	279	0	ENST00000380013.4:c.4334A>G	p.Gln1445Arg	p.Q1445R	ENST00000380013	NM_001127208.2	1445	cAg/cGg	10/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.500466702953264	2		279	391	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164401	36164464	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	CGCGGGGCCCAGCCGGGCCAGGCCTGGCGCCTCAGTAGGGCCTCCACACGGCCTCCTCCAGGCG	CGCGGGGCCCAGCCGGGCCAGGCCTGGCGCCTCAGTAGGGCCTCCACACGGCCTCCTCCAGGCG	-	novel	NA	P-0067629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	64	152	0	ENST00000300305.3:c.1411_*31del		p.*471*	ENST00000300305		471		8/8	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.500466702953264	2		152	209	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0067630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	36	366	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.22378738431988	3	FACETS	1	0.895	1	0.562	0.464	0.672	CLONAL	1	TRUE	1	0.22378738431988	3		366	318	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0067630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	19	270	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.716	0.545	0.917	0.716	0.545	0.917	CLONAL	1	TRUE	1	0.22378738431988	2		270	237	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280015	18280015	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	12	382	0	ENST00000222254.8:c.2098T>G	p.Ser700Ala	p.S700A	ENST00000222254	NM_005027.3	700	Tcg/Gcg	16/16	1	2	FACETS	0.556	0.391	0.758	0.556	0.391	0.758	SUBCLONAL	1	TRUE	1	0.22378738431988	2		382	193	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0067631-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	12	321	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.424	0.297	0.581	0.424	0.297	0.581	SUBCLONAL	1	TRUE	1	0.17	2		321	333	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0067631-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	25	502	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	0.609	0.479	0.759	0.609	0.479	0.759	SUBCLONAL	1	TRUE	1	0.17	2		502	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0067631-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	39	479	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			1	2	FACETS	0.752	0.622	0.898	0.752	0.622	0.898	SUBCLONAL	1	TRUE	1	0.17	2		479	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578488	7578488	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067632-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	117	571	0	ENST00000269305.4:c.442del	p.Asp148IlefsTer22	p.D148Ifs*22	ENST00000269305	NM_001126112.2	148	Gat/at	5/11	0.493949022446345	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.493949022446345	1		571	325	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578400	7578400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751477326	NA	P-0067632-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	11	524	0	ENST00000269305.4:c.530C>T	p.Pro177Leu	p.P177L	ENST00000269305	NM_001126112.2	177	cCc/cTc	5/11	0.493949022446345	1	FACETS	0.109	0.075	0.152	0.109	0.075	0.152	SUBCLONAL	1	TRUE	0	0.493949022446345	1		524	307	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427011	49427011	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067632-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	18	475	1	ENST00000301067.7:c.11477A>G	p.Gln3826Arg	p.Q3826R	ENST00000301067	NM_003482.3	3826	cAg/cGg	39/54	1	2	FACETS	0.202	0.152	0.262	0.202	0.152	0.262	SUBCLONAL	1	TRUE	1	0.493949022446345	2		476	360	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141546	11141546	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067632-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	67	500	0	ENST00000358026.2:c.3523G>C	p.Asp1175His	p.D1175H	ENST00000358026	NM_001128849.1	1175	Gac/Cac	25/36	0.375844548117249	1	FACETS	0.604	0.529	0.685	0.604	0.529	0.685	SUBCLONAL	1	TRUE	0	0.493949022446345	1		500	338	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485059	57485059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067632-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	72	460	0	ENST00000371085.3:c.893C>T	p.Ala298Val	p.A298V	ENST00000371085	NM_000516.4	298	gCt/gTt	11/13	1	2	FACETS	0.767	0.674	0.867	0.767	0.674	0.867	SUBCLONAL	1	TRUE	1	0.493949022446345	2		460	380	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399496	139399496	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1164530395	NA	P-0067632-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	19	568	0	ENST00000277541.6:c.4647C>A	p.Cys1549Ter	p.C1549*	ENST00000277541	NM_017617.3	1549	tgC/tgA	26/34	0.493949022446345	1	FACETS	0.169	0.128	0.218	0.169	0.128	0.218	SUBCLONAL	1	TRUE	0	0.493949022446345	1		568	342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0067633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	390	392	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.423983044223438	4	FACETS	0.966	0.93	1	0.966	0.93	1	CLONAL	4	TRUE	0	0.473796962757745	4		392	628	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0067633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	202	469	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.473796962757745	2	FACETS	0.919	0.861	0.977	0.919	0.861	0.977	CLONAL	2	TRUE	0	0.473796962757745	2		469	464	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0067633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	288	409	5	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	0.442298467808527	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	0	0.473796962757745	3		414	483	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575209	48575209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767326	NA	P-0067633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	149	286	0	ENST00000342988.3:c.403C>T	p.Arg135Ter	p.R135*	ENST00000342988	NM_005359.5	135	Cga/Tga	3/12	0.473796962757745	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.473796962757745	2		286	260	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917730	29917730	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	38	397	0	ENST00000389048.3:c.938A>C	p.Lys313Thr	p.K313T	ENST00000389048	NM_004304.4	313	aAg/aCg	3/29	0.473796962757745	2	FACETS	0.353	0.292	0.422	0.177	0.146	0.211	SUBCLONAL	1	TRUE	0	0.473796962757745	2		397	454	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939458	68939458	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs781218965	NA	P-0067633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	25	355	0	ENST00000288368.4:c.443A>C	p.Asn148Thr	p.N148T	ENST00000288368	NM_024870.2	148	aAc/aCc	5/40	0.473796962757745	7	FACETS	0.5	0.393	0.623	0.1	0.078	0.125	SUBCLONAL	1	TRUE	2	0.473796962757745	7		355	461	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194868	29194868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1174420112	NA	P-0067633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	39	482	0	ENST00000240100.2:c.860C>T	p.Ser287Leu	p.S287L	ENST00000240100	NM_001394.6	287	tCg/tTg	4/4	0.473796962757745	1	FACETS	0.279	0.231	0.333	0.279	0.231	0.333	SUBCLONAL	1	TRUE	0	0.473796962757745	1		482	450	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515300	31515300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	43	384	0	ENST00000344624.3:c.1085G>A	p.Arg362Lys	p.R362K	ENST00000344624		362	aGa/aAa	5/33	0.473796962757745	2	FACETS	0.39	0.326	0.46	0.195	0.163	0.23	SUBCLONAL	1	TRUE	0	0.473796962757745	2		384	466	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146715	185146716	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0067633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	164	471	0	ENST00000265026.3:c.347_348del	p.Ile116LysfsTer16	p.I116Kfs*16	ENST00000265026	NM_004721.4	116	ATa/a	2/14	0.204992164865724	3	FACETS	0.874	0.809	0.941	0.583	0.539	0.627	INDETERMINATE	2	TRUE	0	0.473796962757745	3		471	490	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0067634-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	107	321	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		321	199	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280804	41280804	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067634-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	207	459	0	ENST00000349496.5:c.2317C>T	p.Gln773Ter	p.Q773*	ENST00000349496	NM_001904.3	773	Cag/Tag	15/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		459	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587782289	NA	P-0067634-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	175	347	0	ENST00000269305.4:c.706T>G	p.Tyr236Asp	p.Y236D	ENST00000269305	NM_001126112.2	236	Tac/Gac	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		347	344	SUCCESS
APC	324	MSKCC	GRCh37	5	112174529	112174530	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	rs1060503327	NA	P-0067634-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	68	380	0	ENST00000257430.4:c.3241_3242del	p.Ser1081HisfsTer2	p.S1081Hfs*2	ENST00000257430	NM_000038.5	1080	GAg/g	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		380	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0067635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	88	515	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.341800597702267	1	FACETS	0.972	0.866	1	0.972	0.866	1	CLONAL	1	TRUE	0	0.341800597702267	1		515	439	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945059	38945059	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	32	446	0	ENST00000357387.3:c.4745A>T	p.Gln1582Leu	p.Q1582L	ENST00000357387	NM_152756.3	1582	cAa/cTa	35/38	0.341800597702267	1	FACETS	0.49	0.398	0.592	0.49	0.398	0.592	SUBCLONAL	1	TRUE	0	0.341800597702267	1		446	317	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	47	611	1	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.744	0.628	0.871	0.744	0.628	0.871	SUBCLONAL	1	TRUE	1	0.266150481148124	2		612	475	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468193	120468193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	38	355	0	ENST00000256646.2:c.4246G>A	p.Ala1416Thr	p.A1416T	ENST00000256646	NM_024408.3	1416	Gca/Aca	25/34	1	2	FACETS	0.652	0.539	0.778	0.652	0.539	0.778	SUBCLONAL	1	TRUE	1	0.266150481148124	2		355	438	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849047	156849047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142870382	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	30	306	0	ENST00000524377.1:c.1939G>A	p.Val647Met	p.V647M	ENST00000524377	NM_002529.3	647	Gtg/Atg	15/17	1	2	FACETS	0.59	0.476	0.72	0.59	0.476	0.72	SUBCLONAL	1	TRUE	1	0.266150481148124	2		306	382	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100286	8100286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241255776	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	38	335	0	ENST00000346208.3:c.260C>T	p.Pro87Leu	p.P87L	ENST00000346208		87	cCg/cTg	3/6	1	2	FACETS	0.845	0.7	1	0.845	0.7	1	CLONAL	1	TRUE	1	0.266150481148124	2		335	338	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518070	69518070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	23	252	0	ENST00000294312.3:c.295C>T	p.Arg99Trp	p.R99W	ENST00000294312	NM_005117.2	99	Cgg/Tgg	2/3	1	2	FACETS	0.6	0.468	0.752	0.6	0.468	0.752	SUBCLONAL	1	TRUE	1	0.266150481148124	2		252	288	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944716	71944716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750542712	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	36	322	0	ENST00000298229.2:c.2140G>A	p.Val714Ile	p.V714I	ENST00000298229	NM_001567.3	714	Gtc/Atc	19/28	1	2	FACETS	0.6	0.493	0.72	0.6	0.493	0.72	SUBCLONAL	1	TRUE	1	0.266150481148124	2		322	451	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118345013	118345013	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258907092	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	63	258	0	ENST00000534358.1:c.3139G>A	p.Asp1047Asn	p.D1047N	ENST00000534358	NM_005933.3	1047	Gac/Aac	3/36	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.266150481148124	2		258	430	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	35	250	2	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.741	0.608	0.889	0.741	0.608	0.889	SUBCLONAL	1	TRUE	1	0.266150481148124	2		252	355	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112893802	112893802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	26	248	0	ENST00000351677.2:c.691C>T	p.Arg231Ter	p.R231*	ENST00000351677	NM_002834.3	231	Cga/Tga	6/16	1	2	FACETS	0.537	0.425	0.665	0.537	0.425	0.665	SUBCLONAL	1	TRUE	1	0.266150481148124	2		248	364	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562463	21562463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	20	268	0	ENST00000382592.4:c.1456G>A	p.Ala486Thr	p.A486T	ENST00000382592	NM_014572.2	486	Gcc/Acc	4/8	0.184260949372281	3	FACETS	0.6	0.459	0.764	0.3	0.229	0.382	SUBCLONAL	1	TRUE	1	0.266150481148124	3		268	284	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514839	103514839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs577826260	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	73	357	0	ENST00000355739.4:c.1340C>T	p.Ala447Val	p.A447V	ENST00000355739	NM_000123.3	447	gCg/gTg	8/15	0.184260949372281	3	FACETS	1	0.971	1	0.694	0.609	0.785	CLONAL	1	TRUE	1	0.266150481148124	3		357	448	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220615	2220615	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	rs774508592	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	65	481	0	ENST00000326181.6:c.237del	p.Ile80SerfsTer48	p.I80Sfs*48	ENST00000326181	NM_032271.2	78	Ccc/cc	5/21	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.266150481148124	2		481	365	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642778	3642778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145353518	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	55	286	0	ENST00000294008.3:c.2249C>T	p.Thr750Met	p.T750M	ENST00000294008	NM_032444.2	750	aCg/aTg	11/15	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.266150481148124	2		286	408	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789591	3789591	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	45	270	0	ENST00000262367.5:c.4268del	p.Pro1423LeufsTer36	p.P1423Lfs*36	ENST00000262367	NM_004380.2	1423	cCt/ct	25/31	1	2	FACETS	0.751	0.632	0.883	0.751	0.632	0.883	SUBCLONAL	1	TRUE	1	0.266150481148124	2		270	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577111	7577111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	77	310	0	ENST00000269305.4:c.827C>T	p.Ala276Val	p.A276V	ENST00000269305	NM_001126112.2	276	gCc/gTc	8/11	0.253245897475813	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.266150481148124	1		310	399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	64	361	1	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	0.253245897475813	1	FACETS	0.979	0.85	1	0.979	0.85	1	CLONAL	1	TRUE	0	0.266150481148124	1		362	426	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032472	12032472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	52	213	0	ENST00000353533.5:c.908G>A	p.Gly303Asp	p.G303D	ENST00000353533	NM_003010.3	303	gGc/gAc	9/11	0.253245897475813	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.266150481148124	1		213	230	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	90	789	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.186491952227822	3	FACETS	0.797	0.71	0.889	0.531	0.473	0.593	SUBCLONAL	2	TRUE	0	0.266150481148124	3		790	481	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	67	371	0	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	0.186491952227822	3	FACETS	1	0.96	1	0.423	0.368	0.481	CLONAL	1	TRUE	0	0.266150481148124	3		371	450	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492776	56492776	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	73	303	0	ENST00000407977.2:c.163del	p.Met55TrpfsTer7	p.M55Wfs*7	ENST00000407977		55	Atg/tg	2/10	0.186491952227822	3	FACETS	0.847	0.745	0.955	0.565	0.497	0.637	CLONAL	2	TRUE	0	0.266150481148124	3		303	367	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119780	70119781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	38	304	0	ENST00000245479.2:c.788dup	p.Arg264GlnfsTer32	p.R264Qfs*32	ENST00000245479	NM_000346.3	261	gag/gaGg	3/3	0.186491952227822	3	FACETS	1	0.929	1	0.413	0.343	0.49	CLONAL	1	TRUE	0	0.266150481148124	3		304	261	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272237	15272237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs189252435	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	23	310	0	ENST00000263388.2:c.6202G>A	p.Gly2068Arg	p.G2068R	ENST00000263388	NM_000435.2	2068	Ggg/Agg	33/33	1	2	FACETS	0.561	0.438	0.704	0.561	0.438	0.704	SUBCLONAL	1	TRUE	1	0.266150481148124	2		310	308	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278100	18278100	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	77	298	0	ENST00000222254.8:c.1720C>T	p.Arg574Ter	p.R574*	ENST00000222254	NM_005027.3	574	Cga/Tga	13/16	1	2	FACETS	0.767	0.678	0.862	1	0.978	1	SUBCLONAL	2	TRUE	1	0.266150481148124	2		298	377	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258520	19258520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376625415	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	34	328	0	ENST00000162023.5:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000162023		127	cGa/cAa	8/13	1	2	FACETS	0.667	0.545	0.804	0.667	0.545	0.804	SUBCLONAL	1	TRUE	1	0.266150481148124	2		328	383	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	75	428	0	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.266150481148124	2		428	443	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	29	642	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.478	0.383	0.586	0.478	0.383	0.586	SUBCLONAL	1	TRUE	1	0.266150481148124	2		643	456	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797955	42797955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140554618	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	77	360	0	ENST00000575354.2:c.4007C>T	p.Pro1336Leu	p.P1336L	ENST00000575354	NM_015125.3	1336	cCg/cTg	16/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.266150481148124	2		360	417	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	17	123	2	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	0.912	0.687	1	0.912	0.687	1	CLONAL	1	TRUE	1	0.266150481148124	2		125	140	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868196	45868196	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	50	338	0	ENST00000391945.4:c.494G>T	p.Gly165Val	p.G165V	ENST00000391945	NM_000400.3	165	gGg/gTg	7/23	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.266150481148124	2		338	365	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991713	25991713	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs190136878	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	62	236	0	ENST00000435504.4:c.529A>C	p.Lys177Gln	p.K177Q	ENST00000435504		177	Aag/Cag	7/13	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.266150481148124	2		236	462	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39239433	39239433	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	39	246	0	ENST00000402219.2:c.2224del	p.Ile742LeufsTer24	p.I742Lfs*24	ENST00000402219	NM_005633.3	742	Att/tt	14/23	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.266150481148124	2		246	281	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639588	47639588	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63749897	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	57	302	0	ENST00000233146.2:c.687del	p.Ala230LeufsTer16	p.A230Lfs*16	ENST00000233146	NM_000251.2	227	agA/ag	4/16	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.266150481148124	2		302	409	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264413	46264413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375958201	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	49	329	0	ENST00000371998.3:c.1460G>A	p.Arg487His	p.R487H	ENST00000371998		487	cGt/cAt	11/23	0.184260949372281	3	FACETS	0.862	0.731	1	0.431	0.365	0.503	CLONAL	1	TRUE	1	0.266150481148124	3		329	484	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817412	39817412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200306085	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	52	346	0	ENST00000288319.7:c.151G>A	p.Val51Ile	p.V51I	ENST00000288319	NM_182918.3	51	Gtc/Atc	2/10	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.266150481148124	2		346	350	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665096	138665096	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs758370933	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	27	213	0	ENST00000330315.3:c.469C>G	p.Pro157Ala	p.P157A	ENST00000330315	NM_023067.3	157	Ccc/Gcc	1/1	1	2	FACETS	0.805	0.643	0.989	0.805	0.643	0.989	CLONAL	1	TRUE	1	0.266150481148124	2		213	252	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129987	55129987	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1207595829	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	33	330	2	ENST00000257290.5:c.521G>A	p.Ser174Asn	p.S174N	ENST00000257290	NM_006206.4	174	aGc/aAc	4/23	1	2	FACETS	0.566	0.461	0.685	0.566	0.461	0.685	SUBCLONAL	1	TRUE	1	0.266150481148124	2		332	438	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956194	55956194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs922679946	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	22	266	0	ENST00000263923.4:c.3121G>A	p.Val1041Met	p.V1041M	ENST00000263923	NM_002253.2	1041	Gtg/Atg	23/30	1	2	FACETS	0.453	0.351	0.572	0.453	0.351	0.572	SUBCLONAL	1	TRUE	1	0.266150481148124	2		266	365	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961827	55961827	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	19	221	0	ENST00000263923.4:c.2734C>T	p.Leu912Phe	p.L912F	ENST00000263923	NM_002253.2	912	Ctc/Ttc	20/30	1	2	FACETS	0.492	0.374	0.632	0.492	0.374	0.632	SUBCLONAL	1	TRUE	1	0.266150481148124	2		221	290	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645142	86645143	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	49	297	0	ENST00000274376.6:c.1217dup	p.Asn406LysfsTer12	p.N406Kfs*12	ENST00000274376	NM_002890.2	405	cca/ccAa	8/25	1	2	FACETS	0.916	0.778	1	0.916	0.778	1	CLONAL	1	TRUE	1	0.266150481148124	2		297	402	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047888	180047888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	28	385	0	ENST00000261937.6:c.2287G>A	p.Val763Met	p.V763M	ENST00000261937	NM_182925.4	763	Gtg/Atg	15/30	1	2	FACETS	0.555	0.444	0.682	0.555	0.444	0.682	SUBCLONAL	1	TRUE	1	0.266150481148124	2		385	379	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129329	152129329	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	25	282	0	ENST00000206249.3:c.287del	p.Gly96ValfsTer13	p.G96Vfs*13	ENST00000206249	NM_000125.3	94	ctG/ct	1/8	1	2	FACETS	0.604	0.476	0.75	0.604	0.476	0.75	SUBCLONAL	1	TRUE	1	0.266150481148124	2		282	311	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522454	157522454	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	44	360	0	ENST00000346085.5:c.4726C>T	p.Pro1576Ser	p.P1576S	ENST00000346085	NM_020732.3	1576	Ccg/Tcg	18/20	1	2	FACETS	0.843	0.709	0.992	0.843	0.709	0.992	CLONAL	1	TRUE	1	0.266150481148124	2		360	392	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	51	244	1	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	0.184260949372281	3	FACETS	1	0.945	1	0.62	0.529	0.719	CLONAL	1	TRUE	1	0.266150481148124	3		245	350	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346608	81346608	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1450812000	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	27	284	0	ENST00000222390.5:c.1345G>A	p.Gly449Arg	p.G449R	ENST00000222390	NM_000601.4	449	Gga/Aga	11/18	1	2	FACETS	0.648	0.516	0.798	0.648	0.516	0.798	SUBCLONAL	1	TRUE	1	0.266150481148124	2		284	313	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	103	418	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.992	0.895	1	1	0.988	1	CLONAL	2	TRUE	1	0.266150481148124	2		418	390	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863054	56863054	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1266824391	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	61	393	2	ENST00000519728.1:c.327del	p.Glu110LysfsTer15	p.E110Kfs*15	ENST00000519728	NM_002350.3	107	acA/ac	5/13	0.184260949372281	3	FACETS	1	0.934	1	0.567	0.49	0.65	CLONAL	1	TRUE	1	0.266150481148124	3		395	458	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956772	68956772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199819614	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	55	225	0	ENST00000288368.4:c.890G>A	p.Arg297His	p.R297H	ENST00000288368	NM_024870.2	297	cGt/cAt	8/40	0.184260949372281	3	FACETS	1	0.952	1	0.631	0.542	0.728	CLONAL	1	TRUE	1	0.266150481148124	3		225	371	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737820	145737820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs36023964	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	63	321	0	ENST00000428558.2:c.3010C>T	p.Arg1004Trp	p.R1004W	ENST00000428558	NM_004260.3	1004	Cgg/Tgg	18/22	0.266150481148124	5	FACETS	1	0.951	1	0.407	0.352	0.467	CLONAL	1	TRUE	2	0.266150481148124	5		321	542	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524967	8524967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	22	215	2	ENST00000356435.5:c.637G>A	p.Ala213Thr	p.A213T	ENST00000356435		213	Gcg/Acg	7/35	0.266150481148124	1	FACETS	0.517	0.401	0.652	0.517	0.401	0.652	SUBCLONAL	1	TRUE	0	0.266150481148124	1		217	277	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528710	8528710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768826930	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	37	328	0	ENST00000356435.5:c.422G>A	p.Arg141His	p.R141H	ENST00000356435		141	cGc/cAc	4/35	0.266150481148124	1	FACETS	0.697	0.576	0.831	0.697	0.576	0.831	SUBCLONAL	1	TRUE	0	0.266150481148124	1		328	346	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882049	36882050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs780753361	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	29	481	0	ENST00000358127.4:c.963dup	p.Ala322ArgfsTer19	p.A322Rfs*19	ENST00000358127	NM_001280556.1	321	-/C	8/10	1	2	FACETS	0.587	0.471	0.719	0.587	0.471	0.719	SUBCLONAL	1	TRUE	1	0.266150481148124	2		481	371	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570332	87570332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	42	357	0	ENST00000277120.3:c.2072G>A	p.Arg691His	p.R691H	ENST00000277120		691	cGc/cAc	17/19	1	2	FACETS	0.846	0.708	0.999	0.846	0.708	0.999	CLONAL	1	TRUE	1	0.266150481148124	2		357	373	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209627	98209627	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	32	323	0	ENST00000331920.6:c.3911G>T	p.Arg1304Met	p.R1304M	ENST00000331920	NM_000264.3	1304	aGg/aTg	23/24	1	2	FACETS	0.742	0.604	0.898	0.742	0.604	0.898	SUBCLONAL	1	TRUE	1	0.266150481148124	2		323	324	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15821896	15821896	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	56	294	0	ENST00000307771.7:c.294del	p.Lys98AsnfsTer10	p.K98Nfs*10	ENST00000307771	NM_005089.3	97	Aaa/aa	4/11	1	2	FACETS	0.983	0.845	1	0.983	0.845	1	CLONAL	1	TRUE	1	0.266150481148124	2		294	428	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044919	47044919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	48	372	1	ENST00000377604.3:c.2245C>T	p.Arg749Trp	p.R749W	ENST00000377604	NM_001204468.1	749	Cgg/Tgg	20/24	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.266150481148124	2		373	358	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551857	150551858	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	39	295	0	ENST00000369026.2:c.149dup	p.Gly51ArgfsTer59	p.G51Rfs*59	ENST00000369026	NM_021960.4	50	gga/ggGa	1/3	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.266150481148124	2		295	248	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652424	206652424	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	54	317	0	ENST00000367120.3:c.1135del	p.Leu379Ter	p.L379*	ENST00000367120	NM_014002.3	377	agC/ag	10/22	1	2	FACETS	0.933	0.799	1	0.933	0.799	1	CLONAL	1	TRUE	1	0.266150481148124	2		317	435	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456796	32456797	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	20	292	0	ENST00000332351.3:c.95dup	p.Val33SerfsTer19	p.V33Sfs*19	ENST00000332351	NM_024426.4	32	gga/ggGa	1/10	1	2	FACETS	0.462	0.353	0.59	0.462	0.353	0.59	SUBCLONAL	1	TRUE	1	0.266150481148124	2		292	325	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47594732	47594732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	68	360	0	ENST00000430070.2:c.1355C>T	p.Ala452Val	p.A452V	ENST00000430070	NM_018095.4	452	gCt/gTt	4/4	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.266150481148124	2		360	440	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518411	69518411	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	13	152	0	ENST00000294312.3:c.232+2T>G		p.X78_splice	ENST00000294312	NM_005117.2	78			1	2	FACETS	0.669	0.48	0.898	0.669	0.48	0.898	SUBCLONAL	1	TRUE	1	0.266150481148124	2		152	146	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998988	100998988	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	49	303	0	ENST00000325455.5:c.814G>C	p.Asp272His	p.D272H	ENST00000325455	NM_001202474.3	272	Gat/Cat	1/8	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.266150481148124	2		303	263	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376802	118376802	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782013311	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	51	357	0	ENST00000534358.1:c.10195C>T	p.Pro3399Ser	p.P3399S	ENST00000534358	NM_005933.3	3399	Cct/Tct	27/36	1	2	FACETS	0.91	0.775	1	0.91	0.775	1	CLONAL	1	TRUE	1	0.266150481148124	2		357	421	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858530	57858530	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	72	332	0	ENST00000228682.2:c.268G>T	p.Asp90Tyr	p.D90Y	ENST00000228682	NM_005269.2	90	Gat/Tat	4/12	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.266150481148124	2		332	421	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863230	57863230	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	33	278	0	ENST00000228682.2:c.1325C>A	p.Pro442His	p.P442H	ENST00000228682	NM_005269.2	442	cCt/cAt	11/12	1	2	FACETS	0.678	0.552	0.818	0.678	0.552	0.818	SUBCLONAL	1	TRUE	1	0.266150481148124	2		278	366	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133667	41133667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	80	258	0	ENST00000379561.5:c.1961C>T	p.Ser654Leu	p.S654L	ENST00000379561	NM_002015.3	654	tCa/tTa	2/3	0.184260949372281	3	FACETS	1	0.976	1	0.728	0.643	0.818	CLONAL	1	TRUE	1	0.266150481148124	3		258	468	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986623	36986623	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	25	267	1	ENST00000354822.5:c.1066C>T	p.Gln356Ter	p.Q356*	ENST00000354822	NM_001079668.2	356	Cag/Tag	3/3	1	2	FACETS	0.783	0.619	0.969	0.783	0.619	0.969	CLONAL	1	TRUE	1	0.266150481148124	2		268	240	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562840	95562840	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	55	313	0	ENST00000393063.1:c.4417del	p.Ser1473GlnfsTer17	p.S1473Qfs*17	ENST00000393063	NM_030621.3	1473	Tca/ca	24/28	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.266150481148124	2		313	378	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434731	99434731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	32	306	0	ENST00000268035.6:c.818G>A	p.Gly273Asp	p.G273D	ENST00000268035	NM_000875.3	273	gGc/gAc	3/21	1	2	FACETS	0.621	0.504	0.753	0.621	0.504	0.753	SUBCLONAL	1	TRUE	1	0.266150481148124	2		306	387	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50811839	50811839	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	58	204	0	ENST00000398568.2:c.1116G>A	p.Trp372Ter	p.W372*	ENST00000398568	NM_001042412.1	372	tgG/tgA	7/18	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.266150481148124	2		204	349	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828818	72828818	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	28	346	0	ENST00000268489.5:c.7763T>C	p.Leu2588Pro	p.L2588P	ENST00000268489	NM_006885.3	2588	cTg/cCg	9/10	1	2	FACETS	0.526	0.42	0.647	0.526	0.42	0.647	SUBCLONAL	1	TRUE	1	0.266150481148124	2		346	400	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830005	72830005	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	71	300	0	ENST00000268489.5:c.6576G>C	p.Trp2192Cys	p.W2192C	ENST00000268489	NM_006885.3	2192	tgG/tgC	9/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.266150481148124	2		300	379	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992134	72992134	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	73	351	0	ENST00000268489.5:c.1911del	p.Ser638ValfsTer22	p.S638Vfs*22	ENST00000268489	NM_006885.3	637	ggG/gg	2/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.266150481148124	2		351	393	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883689	37883689	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	75	382	0	ENST00000269571.5:c.3301C>A	p.Leu1101Ile	p.L1101I	ENST00000269571		1101	Ctc/Atc	26/27	0.256475430624525	3	FACETS	1	0.972	1	0.697	0.613	0.787	CLONAL	1	TRUE	1	0.266150481148124	3		382	458	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434933	56434933	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	125	359	0	ENST00000407977.2:c.2204T>C	p.Leu735Pro	p.L735P	ENST00000407977		735	cTg/cCg	9/10	0.186491952227822	3	FACETS	1	0.964	1	0.742	0.676	0.811	CLONAL	2	TRUE	0	0.266150481148124	3		359	478	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006591	62006591	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	34	267	0	ENST00000392795.3:c.688G>T	p.Glu230Ter	p.E230*	ENST00000392795	NM_001039933.1	230	Gag/Tag	6/6	0.186491952227822	3	FACETS	0.856	0.701	1	0.285	0.233	0.344	CLONAL	1	TRUE	0	0.266150481148124	3		267	338	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857643	78857644	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	30	310	0	ENST00000306801.3:c.1715dup	p.Leu572PhefsTer31	p.L572Ffs*31	ENST00000306801	NM_020761.2	571	-/T	16/34	0.186491952227822	3	FACETS	0.625	0.503	0.762	0.208	0.167	0.254	SUBCLONAL	1	TRUE	0	0.266150481148124	3		310	409	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604628	48604628	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	23	243	0	ENST00000342988.3:c.1450C>A	p.Leu484Met	p.L484M	ENST00000342988	NM_005359.5	484	Ctg/Atg	12/12	0.253245897475813	1	FACETS	0.457	0.356	0.573	0.457	0.356	0.573	SUBCLONAL	1	TRUE	0	0.266150481148124	1		243	328	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1206950	1206950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	63	224	0	ENST00000326873.7:c.38C>T	p.Thr13Met	p.T13M	ENST00000326873	NM_000455.4	13	aCg/aTg	1/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.266150481148124	2		224	321	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2214503	2214503	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	69	334	0	ENST00000398665.3:c.1831T>C	p.Trp611Arg	p.W611R	ENST00000398665	NM_032482.2	611	Tgg/Cgg	19/28	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.266150481148124	2		334	403	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123656	11123658	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	54	299	1	ENST00000358026.2:c.2314_2316del	p.Asn772del	p.N772del	ENST00000358026	NM_001128849.1	769	tACAac/tac	16/36	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.266150481148124	2		300	386	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141497	11141497	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	138	279	0	ENST00000358026.2:c.3474del	p.Leu1161SerfsTer3	p.L1161Sfs*3	ENST00000358026	NM_001128849.1	1158	gcT/gc	25/36	1	2	FACETS	0.912	0.84	0.986	1	0.993	1	CLONAL	3	TRUE	1	0.266150481148124	2		279	379	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968231	18968231	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	66	274	0	ENST00000262803.5:c.2071C>A	p.Leu691Met	p.L691M	ENST00000262803	NM_002911.3	691	Ctg/Atg	15/24	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.266150481148124	2		274	334	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213597	36213597	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	37	307	0	ENST00000222270.7:c.2699A>G	p.Asp900Gly	p.D900G	ENST00000222270	NM_014727.1	900	gAt/gGt	5/37	1	2	FACETS	0.638	0.526	0.763	0.638	0.526	0.763	SUBCLONAL	1	TRUE	1	0.266150481148124	2		307	436	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42384765	42384765	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	29	228	0	ENST00000221972.3:c.527T>C	p.Leu176Ser	p.L176S	ENST00000221972	NM_021601.3	176	tTg/tCg	4/5	1	2	FACETS	0.787	0.633	0.96	0.787	0.633	0.96	CLONAL	1	TRUE	1	0.266150481148124	2		228	277	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919705	50919705	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	61	374	0	ENST00000440232.2:c.2873T>C	p.Leu958Pro	p.L958P	ENST00000440232	NM_002691.3	958	cTg/cCg	23/27	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.266150481148124	2		374	394	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631087	67631087	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	42	331	0	ENST00000272342.5:c.1277del	p.Asn426IlefsTer13	p.N426Ifs*13	ENST00000272342	NM_019002.3	425	Aaa/aa	5/6	1	2	FACETS	0.874	0.732	1	0.874	0.732	1	CLONAL	1	TRUE	1	0.266150481148124	2		331	361	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634740	158634740	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs746369903	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	80	307	2	ENST00000263640.3:c.446T>A	p.Phe149Tyr	p.F149Y	ENST00000263640	NM_001105.4	149	tTt/tAt	5/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.266150481148124	2		309	439	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566715	212566715	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	81	331	0	ENST00000342788.4:c.1466A>C	p.Asp489Ala	p.D489A	ENST00000342788	NM_005235.2	489	gAc/gCc	12/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.266150481148124	2		331	445	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543629	9543629	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	67	244	0	ENST00000353224.5:c.1525A>G	p.Met509Val	p.M509V	ENST00000353224	NM_177990.2	509	Atg/Gtg	6/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.266150481148124	2		244	416	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281679	46281679	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1332677783	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	26	263	0	ENST00000371998.3:c.4126T>G	p.Phe1376Val	p.F1376V	ENST00000371998		1376	Ttt/Gtt	22/23	0.184260949372281	3	FACETS	0.562	0.445	0.696	0.281	0.222	0.348	SUBCLONAL	1	TRUE	1	0.266150481148124	3		263	394	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795428	39795428	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	30	327	0	ENST00000288319.7:c.292G>T	p.Asp98Tyr	p.D98Y	ENST00000288319	NM_182918.3	98	Gac/Tac	3/10	1	2	FACETS	0.618	0.498	0.753	0.618	0.498	0.753	SUBCLONAL	1	TRUE	1	0.266150481148124	2		327	365	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645748	12645749	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	27	313	0	ENST00000251849.4:c.720dup	p.Asn241Ter	p.N241*	ENST00000251849	NM_002880.3	240	-/T	7/17	1	2	FACETS	0.477	0.379	0.59	0.477	0.379	0.59	SUBCLONAL	1	TRUE	1	0.266150481148124	2		313	425	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732969	30732969	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	21	280	0	ENST00000295754.5:c.1582C>A	p.Arg528Ser	p.R528S	ENST00000295754	NM_003242.5	528	Cgt/Agt	7/7	1	2	FACETS	0.386	0.296	0.491	0.386	0.296	0.491	SUBCLONAL	1	TRUE	1	0.266150481148124	2		280	409	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442842	187442842	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	52	306	0	ENST00000232014.4:c.1864C>A	p.Leu622Ile	p.L622I	ENST00000232014	NM_001130845.1	622	Ctt/Att	9/10	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.266150481148124	2		306	364	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356185	66356185	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	33	332	0	ENST00000273854.3:c.1312A>G	p.Thr438Ala	p.T438A	ENST00000273854	NM_004439.5	438	Acc/Gcc	5/18	1	2	FACETS	0.596	0.485	0.721	0.596	0.485	0.721	SUBCLONAL	1	TRUE	1	0.266150481148124	2		332	416	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157120	106157120	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	45	315	0	ENST00000380013.4:c.2021A>G	p.Gln674Arg	p.Q674R	ENST00000380013	NM_001127208.2	674	cAg/cGg	3/11	1	2	FACETS	0.702	0.59	0.825	0.702	0.59	0.825	SUBCLONAL	1	TRUE	1	0.266150481148124	2		315	482	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539113	187539113	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	43	326	0	ENST00000441802.2:c.8627A>G	p.Asp2876Gly	p.D2876G	ENST00000441802	NM_005245.3	2876	gAc/gGc	10/27	1	2	FACETS	0.869	0.729	1	0.869	0.729	1	CLONAL	1	TRUE	1	0.266150481148124	2		326	372	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80024714	80024714	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	34	196	0	ENST00000265081.6:c.1498A>T	p.Ile500Phe	p.I500F	ENST00000265081	NM_002439.4	500	Att/Ttt	10/24	1	2	FACETS	0.628	0.513	0.757	0.628	0.513	0.757	SUBCLONAL	1	TRUE	1	0.266150481148124	2		196	407	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517817	176517817	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	28	338	0	ENST00000292408.4:c.427C>A	p.Pro143Thr	p.P143T	ENST00000292408	NM_213647.1	143	Ccc/Acc	4/18	1	2	FACETS	0.479	0.382	0.59	0.479	0.382	0.59	SUBCLONAL	1	TRUE	1	0.266150481148124	2		338	439	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286791	33286791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369424162	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	34	358	0	ENST00000374542.5:c.2146C>T	p.Arg716Trp	p.R716W	ENST00000374542	NM_001141970.1	716	Cgg/Tgg	7/8	1	2	FACETS	0.544	0.444	0.656	0.544	0.444	0.656	SUBCLONAL	1	TRUE	1	0.266150481148124	2		358	470	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969981	161969981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749768565	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	66	243	0	ENST00000366898.1:c.988G>A	p.Val330Met	p.V330M	ENST00000366898	NM_004562.2	330	Gtg/Atg	9/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.266150481148124	2		243	338	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982049	70982049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	60	278	0	ENST00000276594.2:c.47G>A	p.Cys16Tyr	p.C16Y	ENST00000276594	NM_024504.3	16	tGc/tAc	2/8	0.184260949372281	3	FACETS	0.772	0.669	0.882	0.772	0.669	0.882	SUBCLONAL	2	TRUE	1	0.266150481148124	3		278	331	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739380	145739380	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	54	276	2	ENST00000428558.2:c.1990C>A	p.Leu664Ile	p.L664I	ENST00000428558	NM_004260.3	664	Ctc/Atc	12/22	0.266150481148124	5	FACETS	1	0.948	1	0.417	0.356	0.483	CLONAL	1	TRUE	2	0.266150481148124	5		278	454	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2039871	2039871	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756891197	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	29	385	0	ENST00000349721.2:c.761C>T	p.Pro254Leu	p.P254L	ENST00000349721	NM_003070.3	254	cCg/cTg	4/34	0.266150481148124	1	FACETS	0.419	0.336	0.514	0.419	0.336	0.514	SUBCLONAL	1	TRUE	0	0.266150481148124	1		385	451	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80646014	80646014	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	29	204	0	ENST00000286548.4:c.136+2T>C		p.X46_splice	ENST00000286548	NM_002072.3	46			1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.266150481148124	2		204	181	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93636975	93636975	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	53	328	0	ENST00000375746.1:c.1025C>A	p.Pro342His	p.P342H	ENST00000375746	NM_001174167.1	342	cCc/cAc	9/14	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.266150481148124	2		328	378	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357469	70357469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	25	303	0	ENST00000374080.3:c.5810G>A	p.Gly1937Asp	p.G1937D	ENST00000374080		1937	gGt/gAt	40/45	1	2	FACETS	0.488	0.384	0.607	0.488	0.384	0.607	SUBCLONAL	1	TRUE	1	0.266150481148124	2		303	385	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0067653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	54	377	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.934	0.807	1	0.934	0.807	1	CLONAL	1	TRUE	1	0.49847465828751	2		377	232	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473722	67473722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs794727798	NA	P-0067653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	157	363	0	ENST00000327367.4:c.802C>T	p.Arg268Cys	p.R268C	ENST00000327367	NM_005902.3	268	Cgc/Tgc	6/9	0.49847465828751	2	FACETS	0.96	0.895	1	0.96	0.895	1	CLONAL	2	TRUE	0	0.49847465828751	2		363	328	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374882	45374882	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs776149698	NA	P-0067653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	132	404	0	ENST00000262160.6:c.961C>T	p.Arg321Ter	p.R321*	ENST00000262160	NM_005901.5	321	Cga/Tga	8/11	0.499094404545072	2	FACETS	0.963	0.892	1	0.963	0.892	1	CLONAL	2	TRUE	0	0.49847465828751	2		404	275	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570063	212570063	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746784831	NA	P-0067653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	22	324	0	ENST00000342788.4:c.1178G>A	p.Arg393Gln	p.R393Q	ENST00000342788	NM_005235.2	393	cGg/cAg	10/28	1	2	FACETS	0.291	0.226	0.367	0.291	0.226	0.367	SUBCLONAL	1	TRUE	1	0.49847465828751	2		324	303	SUCCESS
APC	324	MSKCC	GRCh37	5	112175322	112175322	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	209	359	0	ENST00000257430.4:c.4031C>A	p.Ser1344Ter	p.S1344*	ENST00000257430	NM_000038.5	1344	tCa/tAa	16/16	0.49847465828751	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.49847465828751	2		359	370	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205319	46205319	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	53	324	0	ENST00000334344.6:c.403C>T	p.Gln135Ter	p.Q135*	ENST00000334344	NM_152641.2	135	Caa/Taa	4/21	1	2	FACETS	0.868	0.748	0.997	0.868	0.748	0.997	CLONAL	1	TRUE	1	0.49847465828751	2		324	245	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554728	63554729	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0067653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	82	362	0	ENST00000307078.5:c.10dup	p.Ala4GlyfsTer16	p.A4Gfs*16	ENST00000307078	NM_004655.3	4	gct/gGct	2/11	1	2	FACETS	0.831	0.737	0.93	0.831	0.737	0.93	CLONAL	1	TRUE	1	0.49847465828751	2		362	396	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136988	11136988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	72	220	3	ENST00000358026.2:c.3181G>A	p.Glu1061Lys	p.E1061K	ENST00000358026	NM_001128849.1	1061	Gag/Aag	23/36	0.154118681199513	3	FACETS	1	0.945	1	0.564	0.497	0.635	INDETERMINATE	1	TRUE	1	0.49847465828751	3		223	320	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730061	41730061	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	81	360	0	ENST00000242208.4:c.468G>T	p.Trp156Cys	p.W156C	ENST00000242208	NM_002192.2	156	tgG/tgT	3/3	0.487691211755802	3	FACETS	0.881	0.779	0.989	0.44	0.389	0.495	CLONAL	1	TRUE	1	0.49847465828751	3		360	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0067655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	51	477	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		477	186	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488721	212488721	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	31	422	0	ENST00000342788.4:c.2128C>A	p.Leu710Ile	p.L710I	ENST00000342788	NM_005235.2	710	Ctt/Att	18/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		422	168	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	54	418	1	ENST00000257430.4:c.3919dup	p.Ile1307AsnfsTer8	p.I1307Nfs*8	ENST00000257430	NM_000038.5	1306	gaa/gAaa	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		419	176	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207672	102207672	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	18	408	0	ENST00000263464.3:c.1654C>G	p.Gln552Glu	p.Q552E	ENST00000263464	NM_001165.4	552	Caa/Gaa	9/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		408	116	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961712	41961712	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	33	479	0	ENST00000219905.7:c.620T>G	p.Val207Gly	p.V207G	ENST00000219905	NM_001164273.1	207	gTg/gGg	2/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		479	184	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099566	157099566	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1022306360	NA	P-0067655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	64	318	0	ENST00000346085.5:c.503G>C	p.Gly168Ala	p.G168A	ENST00000346085	NM_020732.3	168	gGc/gCc	1/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		318	291	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929243	32929243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398122578	NA	P-0067656-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	54	385	0	ENST00000380152.3:c.7253G>A	p.Arg2418Lys	p.R2418K	ENST00000380152		2418	aGa/aAa	14/27	0.139653353420921	0	FACETS	0.582	0.505	0.663			1	INDETERMINATE	1	TRUE	0	0.500649595464739	0		385	185	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031113	11031113	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067656-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	55	358	0	ENST00000327064.4:c.1198A>G	p.Met400Val	p.M400V	ENST00000327064	NM_199141.1	400	Atg/Gtg	11/16	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.500649595464739	2		358	217	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188269	10188269	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1559428164	NA	P-0067656-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	47	337	0	ENST00000256474.2:c.413del	p.Pro138HisfsTer21	p.P138Hfs*21	ENST00000256474	NM_000551.3	138	Cca/ca	2/3	0.500649595464739	1	FACETS	0.869	0.746	0.998	0.869	0.746	0.998	CLONAL	1	TRUE	0	0.500649595464739	1		337	162	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144838	47144838	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0067656-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	40	314	0	ENST00000409792.3:c.4915A>T	p.Lys1639Ter	p.K1639*	ENST00000409792	NM_014159.6	1639	Aaa/Taa	7/21	0.500649595464739	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.500649595464739	1		314	97	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239713	53239713	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067656-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	56	208	0	ENST00000375401.3:c.1629del	p.Glu543AspfsTer6	p.E543Dfs*6	ENST00000375401	NM_004187.3	543	gaA/ga	12/26	1	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.500649595464739	1		208	136	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0067657-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	64	418	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.190154512613099	4	FACETS	1	0.972	1	0.494	0.432	0.561	INDETERMINATE	1	TRUE	1	0.438933435732681	4		418	283	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067657-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	44	317	0				ENST00000310581	NM_198253.2	-/1132			0.217344661738022	4	FACETS	1	0.889	1	0.767	0.668	0.867	INDETERMINATE	3	TRUE	0	0.438933435732681	4		317	94	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254615	46254615	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0067657-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	54	260	0	ENST00000334344.6:c.4805A>T	p.Gln1602Leu	p.Q1602L	ENST00000334344	NM_152641.2	1602	cAa/cTa	16/21	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.438933435732681	2		260	227	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140165	50140165	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067658-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	51	657	0	ENST00000246792.3:c.260A>T	p.Gln87Leu	p.Q87L	ENST00000246792	NM_006270.3	87	cAg/cTg	3/6	1	2	FACETS	0.838	0.717	0.968	0.838	0.717	0.968	CLONAL	1	TRUE	1	0.434890283162216	2		657	280	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044892	47044892	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067658-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	49	398	0	ENST00000377604.3:c.2218G>T	p.Glu740Ter	p.E740*	ENST00000377604	NM_001204468.1	740	Gag/Tag	20/24	1	2	FACETS	0.788	0.672	0.914	0.788	0.672	0.914	CLONAL	1	TRUE	1	0.434890283162216	2		398	286	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211862	36211862	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067658-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	61	361	1	ENST00000222270.7:c.1613G>T	p.Arg538Leu	p.R538L	ENST00000222270	NM_014727.1	538	cGt/cTt	3/37	1	2	FACETS	0.998	0.869	1	0.998	0.869	1	CLONAL	1	TRUE	1	0.434890283162216	2		362	281	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335723	81335723	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067658-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	44	314	0	ENST00000222390.5:c.1637C>A	p.Ala546Asp	p.A546D	ENST00000222390	NM_000601.4	546	gCt/gAt	15/18	1	2	FACETS	0.739	0.623	0.864	0.739	0.623	0.864	SUBCLONAL	1	TRUE	1	0.434890283162216	2		314	274	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156718	20156719	+	missense_variant	Missense_Mutation	DNP	GC	GC	CG	novel	NA	P-0067658-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	40	281	0	ENST00000379607.5:c.38_39delinsCG	p.Arg13Pro	p.R13P	ENST00000379607	NM_001412.3	13	cGC/cCG	2/7	1	2	FACETS	0.601	0.501	0.711	0.601	0.501	0.711	SUBCLONAL	1	TRUE	1	0.434890283162216	2		281	306	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411913	63411914	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0067658-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	51	474	1	ENST00000330258.3:c.1253_1254delinsTT	p.Arg418Leu	p.R418L	ENST00000330258	NM_152424.3	418	cGG/cTT	2/2	1	2	FACETS	0.709	0.605	0.821	0.709	0.605	0.821	SUBCLONAL	1	TRUE	1	0.434890283162216	2		475	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0067659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	236	450	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.401101900858363	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.401101900858363	2		450	500	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0067659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	95	400	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.401101900858363	2		401	376	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939888	76939888	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0067659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	108	434	0	ENST00000373344.5:c.860T>G	p.Leu287Ter	p.L287*	ENST00000373344	NM_000489.3	287	tTa/tGa	9/35	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.401101900858363	2		434	448	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923606	39923606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777165878	NA	P-0067659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	98	368	0	ENST00000378444.4:c.3485G>A	p.Arg1162His	p.R1162H	ENST00000378444	NM_001123385.1	1162	cGc/cAc	7/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.401101900858363	2		368	400	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443599	52443601	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0067684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	18	386	0	ENST00000460680.1:c.91_93del	p.Glu31del	p.E31del	ENST00000460680	NM_004656.3	31	GAG/-	3/17	0.458101529563721	1	FACETS	0.331	0.25	0.426	0.331	0.25	0.426	SUBCLONAL	1	TRUE	0	0.458101529563721	1		386	183	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627205	12627205	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	12	335	0	ENST00000251849.4:c.1511A>C	p.Gln504Pro	p.Q504P	ENST00000251849	NM_002880.3	504	cAa/cCa	14/17	0.458101529563721	1	FACETS	0.211	0.148	0.289	0.211	0.148	0.289	SUBCLONAL	1	TRUE	0	0.458101529563721	1		335	191	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682186	37682187	+	missense_variant	Missense_Mutation	DNP	AA	AA	CC	novel	NA	P-0067684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	12	424	0	ENST00000447079.4:c.3377_3378delinsCC	p.Gln1126Pro	p.Q1126P	ENST00000447079	NM_015083.1	1126	cAA/cCC	13/14	1	2	FACETS	0.259	0.182	0.354	0.259	0.182	0.354	SUBCLONAL	1	TRUE	1	0.458101529563721	2		424	202	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417852	138417852	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	26	305	0	ENST00000289153.2:c.1667A>G	p.Asp556Gly	p.D556G	ENST00000289153	NM_006219.2	556	gAt/gGt	11/22	1	2	FACETS	0.696	0.557	0.853	0.696	0.557	0.853	SUBCLONAL	1	TRUE	1	0.458101529563721	2		305	163	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753062	42753063	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	rs1064794325	NA	P-0067684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	33	439	0	ENST00000222329.4:c.1201_1202del	p.Lys401GlufsTer10	p.K401Efs*10	ENST00000222329	NM_006494.2	401	AAg/g	4/4	1	2	FACETS	0.586	0.48	0.704	0.586	0.48	0.704	SUBCLONAL	1	TRUE	1	0.458101529563721	2		439	246	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437223	52437233	+	frameshift_variant	Frame_Shift_Del	DEL	CGTGGCTTCCA	CGTGGCTTCCA	-	novel	NA	P-0067684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	19	476	0	ENST00000460680.1:c.1811_1821del	p.Val604GlyfsTer35	p.V604Gfs*35	ENST00000460680	NM_004656.3	604	gTGGAAGCCACG/g	14/17	0.458101529563721	1	FACETS	0.447	0.342	0.568	0.447	0.342	0.568	SUBCLONAL	1	TRUE	0	0.458101529563721	1		476	143	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160217	22160217	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	30	415	0	ENST00000215832.6:c.414del	p.Lys138AsnfsTer47	p.K138Nfs*47	ENST00000215832	NM_002745.4	138	aaA/aa	3/9	0.357984281267763	1	FACETS	0.673	0.55	0.809	0.673	0.55	0.809	SUBCLONAL	1	TRUE	0	0.458101529563721	1		415	150	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183743	10183745	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	novel	NA	P-0067684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	21	419	0	ENST00000256474.2:c.214_216del	p.Ser72del	p.S72del	ENST00000256474	NM_000551.3	71	cCCTcc/ccc	1/3	0.458101529563721	1	FACETS	0.594	0.464	0.741	0.594	0.464	0.741	SUBCLONAL	1	TRUE	0	0.458101529563721	1		419	119	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0067685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	242	418	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.416997683889725	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.429573693104963	3		418	632	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0067686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	158	414	0	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	0.584044186413541	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.603775907745636	2		414	255	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952152	178952152	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	novel	NA	P-0067686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	33	365	0	ENST00000263967.3:c.3207A>G	p.Ter1069TrpextTer4	p.*1069Wext*4	ENST00000263967	NM_006218.2	1069	tgA/tgG	21/21	0.344617118458221	4	FACETS	0.596	0.487	0.718	0.298	0.243	0.359	INDETERMINATE	1	TRUE	2	0.603775907745636	4		365	294	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78811769	78811769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370002882	NA	P-0067686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	33	366	0	ENST00000306801.3:c.1184C>T	p.Thr395Met	p.T395M	ENST00000306801	NM_020761.2	395	aCg/aTg	10/34	0.575214602991208	3	FACETS	0.459	0.375	0.554	0.153	0.125	0.185	SUBCLONAL	1	TRUE	0	0.603775907745636	3		366	310	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466920	57466920	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	20	160	0	ENST00000371085.3:c.139G>C	p.Gly47Arg	p.G47R	ENST00000371085	NM_000516.4	47	Ggt/Cgt	1/13	0.277585917692272	5	FACETS	0.908	0.702	1	0.303	0.234	0.382	INDETERMINATE	1	TRUE	2	0.603775907745636	5		160	139	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973823	15973823	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs755471164	NA	P-0067686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	177	470	0	ENST00000268712.3:c.4169T>C	p.Phe1390Ser	p.F1390S	ENST00000268712	NM_006311.3	1390	tTt/tCt	31/46	0.584044186413541	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.603775907745636	2		470	279	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0067689-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	78	415	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.185206440597356	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	2	FALSE	0	0.191158599002301	2		415	388	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0067689-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	96	478	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.191158599002301	3	FACETS	0.978	0.879	1	1	0.981	1	CLONAL	3	FALSE	1	0.191158599002301	3		478	375	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347977	89347977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777649520	NA	P-0067689-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	36	552	0	ENST00000301030.4:c.4973C>T	p.Thr1658Ile	p.T1658I	ENST00000301030	NM_001256183.1	1658	aCt/aTt	9/13	0.169425877370124	3	FACETS	1	0.85	1	0.518	0.426	0.621	CLONAL	1	FALSE	1	0.191158599002301	3		552	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs878854073	NA	P-0067690-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	20	403	0	ENST00000269305.4:c.673-1G>A		p.X225_splice	ENST00000269305	NM_001126112.2	225			1	2	FACETS	0.662	0.505	0.848	0.662	0.505	0.848	SUBCLONAL	1	TRUE	1	0.11	2		403	549	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231793	36231794	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067690-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	38	483	0	ENST00000300305.3:c.590_591insA	p.Asp198GlyfsTer15	p.D198Gfs*15	ENST00000300305		197	gtg/gtAg	5/8	1	2	FACETS	0.92	0.758	1	0.92	0.758	1	CLONAL	1	TRUE	1	0.11	2		483	751	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745833	745833	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1386230265	NA	P-0067690-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	21	352	0	ENST00000314574.4:c.599A>G	p.Asp200Gly	p.D200G	ENST00000314574	NM_005433.3	200	gAt/gGt	6/12	1	2	FACETS	1	0.779	1	1	0.779	1	CLONAL	1	TRUE	1	0.11	2		352	377	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0067691-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	154	376	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.566826124226465	2		376	526	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070577	67070577	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067691-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	195	417	0	ENST00000412916.2:c.201G>T	p.Gln67His	p.Q67H	ENST00000412916		67	caG/caT	3/6	0.566826124226465	1	FACETS	0.957	0.894	1	0.957	0.894	1	CLONAL	1	TRUE	0	0.566826124226465	1		417	515	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0067691-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	109	293	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.566826124226465	2		293	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0067692-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	255	412	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.576735835797527	2	FACETS	0.868	0.826	0.91	0.868	0.826	0.91	CLONAL	2	TRUE	0	0.672188651824352	2		412	437	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0067692-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	158	405	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.288047087123519	4	FACETS	0.895	0.829	0.964	0.895	0.829	0.964	INDETERMINATE	2	TRUE	2	0.672188651824352	4		405	439	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268844	55269425	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACGGGCCATTCTAATAGCCTCAAAATCTCTGCACCAGGGGGATGAAAGAATGCATTTGCCAAGTCCTACAGACTCCAACTTCTACCGTGCCCTGATGGATGAAGAAGACATGGACGACGTGGTGGATGCCGACGAGTACCTCATCCCACAGCAGGGCTTCTTCAGCAGCCCCTCCACGTCACGGACTCCCCTCCTGAGCTCTCTGGTATGAAATCTCTGTCTCTCTCTCTCTCTCAAGCTGTGTCTACTCATTTGAACAAATTGAATTTTAGGGAAAATAACCATCTAGTGAAACTCACATGGATATGAAGTCAATTTTAACCAAATGGTAAAATCAAAATCAAAATAAATTAAGTGTATTAATTATTTTGTTGCATTGCAACAACTTGATTGTAAGCCTTTTAGGTCCACTATGGAATGTAATTAAATCAAAACTAAACCTAGTTGCTCTAAAACTAACGATTAAGACAAAAATTAAACACCTTCACAATATACCCTCCATGAGGCACACCACCTGCATTCAGGAAAAGTGGATGAGATGTGGTACAAGCATTCCATGGGCAACTTCTCTGTTTCTTTTTC	ACGGGCCATTCTAATAGCCTCAAAATCTCTGCACCAGGGGGATGAAAGAATGCATTTGCCAAGTCCTACAGACTCCAACTTCTACCGTGCCCTGATGGATGAAGAAGACATGGACGACGTGGTGGATGCCGACGAGTACCTCATCCCACAGCAGGGCTTCTTCAGCAGCCCCTCCACGTCACGGACTCCCCTCCTGAGCTCTCTGGTATGAAATCTCTGTCTCTCTCTCTCTCTCAAGCTGTGTCTACTCATTTGAACAAATTGAATTTTAGGGAAAATAACCATCTAGTGAAACTCACATGGATATGAAGTCAATTTTAACCAAATGGTAAAATCAAAATCAAAATAAATTAAGTGTATTAATTATTTTGTTGCATTGCAACAACTTGATTGTAAGCCTTTTAGGTCCACTATGGAATGTAATTAAATCAAAACTAAACCTAGTTGCTCTAAAACTAACGATTAAGACAAAAATTAAACACCTTCACAATATACCCTCCATGAGGCACACCACCTGCATTCAGGAAAAGTGGATGAGATGTGGTACAAGCATTCCATGGGCAACTTCTCTGTTTCTTTTTC	-	novel	NA	P-0067692-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	192	537	0	ENST00000275493.2:c.2947-36_3115-2del		p.X983_splice	ENST00000275493	NM_005228.3	983		25/28	0.288047087123519	4	FACETS	0.878	0.818	0.939	0.878	0.818	0.939	INDETERMINATE	2	TRUE	2	0.672188651824352	4		537	544	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47607029	47607029	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0067692-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	48	423	0	ENST00000263735.4:c.779C>G	p.Ser260Ter	p.S260*	ENST00000263735	NM_002354.2	260	tCa/tGa	7/9	0.605407057726787	2	FACETS	0.458	0.389	0.533	0.229	0.194	0.267	SUBCLONAL	1	TRUE	0	0.672188651824352	2		423	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs878854073	NA	P-0067709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	61	403	0	ENST00000269305.4:c.673-1G>A		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.138784531605389	2	FACETS	0.827	0.716	0.947	0.827	0.716	0.947	CLONAL	2	TRUE	0	0.18036427033984	2		403	409	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813446	32813447	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0067709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	34	418	0	ENST00000354258.4:c.2335_2336dup	p.Ile780LeufsTer80	p.I780Lfs*80	ENST00000354258	NM_000593.5	779	gct/gcGCt	11/11	0.153253136529832	3	FACETS	0.613	0.5	0.742	0.307	0.25	0.371	SUBCLONAL	1	TRUE	1	0.18036427033984	3		418	670	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264779	46264779	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	41	423	0	ENST00000371998.3:c.1649A>C	p.Asn550Thr	p.N550T	ENST00000371998		550	aAc/aCc	12/23	0.18036427033984	5	FACETS	0.734	0.609	0.873	0.245	0.203	0.291	SUBCLONAL	1	TRUE	2	0.18036427033984	5		423	787	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736232	243736232	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	41	366	0	ENST00000263826.5:c.815T>C	p.Leu272Pro	p.L272P	ENST00000263826	NM_005465.4	272	cTc/cCc	8/13	1	2	FACETS	0.848	0.706	1	0.848	0.706	1	CLONAL	1	TRUE	1	0.18036427033984	2		366	536	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0067710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	30	171	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.252243859716064	2		171	176	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782177	NA	P-0067710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	108	512	0	ENST00000269305.4:c.644G>T	p.Ser215Ile	p.S215I	ENST00000269305	NM_001126112.2	215	aGt/aTt	6/11	0.252243859716064	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.252243859716064	1		512	589	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860665	3860665	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	48	376	0	ENST00000262367.5:c.914A>C	p.Asn305Thr	p.N305T	ENST00000262367	NM_004380.2	305	aAc/aCc	3/31	1	2	FACETS	0.66	0.557	0.773	0.66	0.557	0.773	SUBCLONAL	1	TRUE	1	0.252243859716064	2		376	577	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475264	475264	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	53	334	0	ENST00000399788.2:c.373G>T	p.Ala125Ser	p.A125S	ENST00000399788	NM_001042603.1	125	Gcc/Tcc	4/28	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.252243859716064	2		334	389	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212252718	212252718	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0067710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	53	312	0	ENST00000342788.4:c.3136-1G>T		p.X1046_splice	ENST00000342788	NM_005235.2	1046			1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.252243859716064	2		312	362	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796343	57796346	+	frameshift_variant	Frame_Shift_Del	DEL	ATAT	ATAT	TTA	novel	NA	P-0067710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	80	467	0	ENST00000309042.7:c.1319_1322delinsTTA	p.Asn440IlefsTer9	p.N440Ifs*9	ENST00000309042	NM_005612.4	440	aATATt/aTTAt	4/4	0.252243859716064	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.252243859716064	1		467	505	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667633	29667633	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	52	278	0	ENST00000356175.3:c.6971del	p.Leu2324Ter	p.L2324*	ENST00000356175	NM_000267.3	2323	acT/ac	46/57	0.252243859716064	1	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	0	0.252243859716064	1		278	347	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	21	317	0				ENST00000310581	NM_198253.2	-/1132			0.273657605359613	0	FACETS	0.81	0.651	0.979			1	CLONAL	2	TRUE	0	0.316343453425325	0		317	56	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183785	10183785	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs5030828	NA	P-0067711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	49	599	0	ENST00000256474.2:c.254T>C	p.Leu85Pro	p.L85P	ENST00000256474	NM_000551.3	85	cTg/cCg	1/3	0.267445036832577	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	0	0.316343453425325	2		599	136	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807418	36807418	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	30	576	0	ENST00000373129.3:c.1246G>T	p.Asp416Tyr	p.D416Y	ENST00000373129	NM_032017.1	416	Gac/Tac	12/12	0.260522568330343	4	FACETS	0.771	0.628	0.928	0.514	0.419	0.619	CLONAL	2	TRUE	1	0.316343453425325	4		576	162	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0067712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	62	482	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.231440706234713	1	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	0	0.365312839699111	1		482	274	SUCCESS
APC	324	MSKCC	GRCh37	5	112175594	112175594	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0067712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	33	478	0	ENST00000257430.4:c.4303A>T	p.Arg1435Ter	p.R1435*	ENST00000257430	NM_000038.5	1435	Aga/Tga	16/16	0.231440706234713	1	FACETS	0.424	0.346	0.512	0.424	0.346	0.512	SUBCLONAL	1	TRUE	0	0.365312839699111	1		478	348	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245723	46245723	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	159	620	0	ENST00000334344.6:c.3817C>T	p.Arg1273Ter	p.R1273*	ENST00000334344	NM_152641.2	1273	Cga/Tga	15/21	0.365312839699111	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.365312839699111	2		620	416	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411923	116411923	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs34589476	NA	P-0067713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	95	492	0	ENST00000397752.3:c.2908C>T	p.Arg970Cys	p.R970C	ENST00000397752	NM_000245.2	970	Cgc/Tgc	14/21	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.290861369012696	2		492	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	94	520	0	ENST00000269305.4:c.404G>C	p.Cys135Ser	p.C135S	ENST00000269305	NM_001126112.2	135	tGc/tCc	5/11	0.290861369012696	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.290861369012696	1		520	529	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050852	49050852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1231557654	NA	P-0067713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	79	330	0	ENST00000267163.4:c.2536C>T	p.Gln846Ter	p.Q846*	ENST00000267163	NM_000321.2	846	Cag/Tag	25/27	0.290861369012696	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.290861369012696	1		330	365	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15840904	15840904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	14	117	0	ENST00000307771.7:c.988C>T	p.His330Tyr	p.H330Y	ENST00000307771	NM_005089.3	330	Cat/Tat	11/11	1	1	FACETS	0.571	0.415	0.758	0.571	0.415	0.758	SUBCLONAL	1	TRUE	0	0.290861369012696	1		117	144	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528086	29528086	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs864622107	NA	P-0067713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	21	143	0	ENST00000356175.3:c.1094C>G	p.Ser365Ter	p.S365*	ENST00000356175	NM_000267.3	365	tCa/tGa	10/57	0.290861369012696	1	FACETS	0.796	0.618	0.999	0.796	0.618	0.999	CLONAL	1	TRUE	0	0.290861369012696	1		143	155	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46602873	46602873	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	68	499	0	ENST00000263734.3:c.931G>T	p.Ala311Ser	p.A311S	ENST00000263734	NM_001430.4	311	Gca/Tca	8/16	1	2	FACETS	0.86	0.749	0.979	0.86	0.749	0.979	CLONAL	1	TRUE	1	0.290861369012696	2		499	544	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353866	40353866	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0067713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	30	455	0	ENST00000293328.3:c.2254G>T	p.Asp752Tyr	p.D752Y	ENST00000293328	NM_012448.3	752	Gac/Tac	19/19	0.290861369012696	2	FACETS	0.389	0.313	0.476	0.195	0.156	0.238	SUBCLONAL	1	TRUE	0	0.290861369012696	2		455	530	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400019	139400020	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	102	590	0	ENST00000277541.6:c.4328_4329insT	p.Leu1444AlafsTer35	p.L1444Afs*35	ENST00000277541	NM_017617.3	1443	ccg/ccTg	25/34	0.290861369012696	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.290861369012696	1		590	537	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265514	152265514	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	53	418	0	ENST00000206249.3:c.967G>C	p.Glu323Gln	p.E323Q	ENST00000206249	NM_000125.3	323	Gag/Cag	4/8	1	2	FACETS	0.767	0.655	0.89	0.767	0.655	0.89	SUBCLONAL	1	TRUE	1	0.290861369012696	2		418	475	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198141	185198141	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	96	513	0	ENST00000265026.3:c.2623G>C	p.Asp875His	p.D875H	ENST00000265026	NM_004721.4	875	Gat/Cat	13/14	0.184480256254032	3	FACETS	1	0.956	1	0.571	0.509	0.637	CLONAL	1	TRUE	1	0.290861369012696	3		513	662	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14016041	14016041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	67	357	0	ENST00000311895.7:c.361G>A	p.Asp121Asn	p.D121N	ENST00000311895	NM_005236.2	121	Gat/Aat	2/11	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.290861369012696	2		357	415	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124499123	124499123	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	32	318	0	ENST00000357628.3:c.590T>C	p.Leu197Ser	p.L197S	ENST00000357628	NM_015450.2	197	tTa/tCa	9/19	1	2	FACETS	0.738	0.601	0.892	0.738	0.601	0.892	SUBCLONAL	1	TRUE	1	0.290861369012696	2		318	298	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877442	28877442	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	80	381	1	ENST00000282397.4:c.3879C>A	p.Cys1293Ter	p.C1293*	ENST00000282397	NM_002019.4	1293	tgC/tgA	30/30	0.290861369012696	1	FACETS	0.981	0.867	1	0.981	0.867	1	CLONAL	1	TRUE	0	0.290861369012696	1		382	479	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709054	117709054	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	77	505	0	ENST00000368508.3:c.1903A>T	p.Asn635Tyr	p.N635Y	ENST00000368508	NM_002944.2	635	Aat/Tat	13/43	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.290861369012696	2		505	517	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0067714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	58	395	11	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		406	110	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346338	73346338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	72	164	0	ENST00000377767.4:c.1462G>A	p.Asp488Asn	p.D488N	ENST00000377767	NM_014953.3	488	Gat/Aat	10/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		164	182	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0067714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	42	471	0	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		471	201	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50784990	50784990	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs146125856	NA	P-0067714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	10	317	3	ENST00000307179.4:c.2327T>C	p.Leu776Pro	p.L776P	ENST00000307179		776	cTt/cCt	15/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		320	109	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0067714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	69	267	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		267	189	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398303	25398303	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1296330213	NA	P-0067714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	63	186	0	ENST00000311936.3:c.16C>A	p.Leu6Ile	p.L6I	ENST00000311936	NM_004985.3	6	Ctt/Att	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		186	178	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711882	89711882	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	35	164	0	ENST00000371953.3:c.500C>G	p.Thr167Ser	p.T167S	ENST00000371953	NM_000314.4	167	aCt/aGt	6/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		164	223	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573940	41573940	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	13	316	0	ENST00000263253.7:c.6225del	p.His2075GlnfsTer59	p.H2075Qfs*59	ENST00000263253	NM_001429.3	2075	caC/ca	31/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		316	207	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0067720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	115	476	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.272308379352418	1	FACETS	0.921	0.83	1	0.921	0.83	1	CLONAL	1	TRUE	0	0.272308379352418	1		476	792	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971124	21971125	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0067720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	92	358	0	ENST00000304494.5:c.233_234del	p.Leu78HisfsTer41	p.L78Hfs*41	ENST00000304494	NM_000077.4	78	cTC/c	2/3	0.272308379352418	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.272308379352418	1		358	532	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175857	24175859	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs875989800	NA	P-0067720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	74	330	0	ENST00000263121.7:c.1091_1093del	p.Lys364del	p.K364del	ENST00000263121	NM_003073.3	362	gAGAag/gag	8/9	0.272308379352418	1	FACETS	0.896	0.786	1	0.896	0.786	1	CLONAL	1	TRUE	0	0.272308379352418	1		330	524	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929412	44929415	+	frameshift_variant	Frame_Shift_Del	DEL	ACAA	ACAA	-	rs786205676	NA	P-0067720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	75	341	0	ENST00000377967.4:c.2515_2518del	p.Asn839ValfsTer27	p.N839Vfs*27	ENST00000377967	NM_021140.2	838	ACAAac/ac	17/29	0.272308379352418	1	FACETS	0.989	0.869	1	0.989	0.869	1	CLONAL	1	TRUE	0	0.272308379352418	1		341	481	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888172	112888172	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121918459	NA	P-0067720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	53	266	0	ENST00000351677.2:c.188A>G	p.Tyr63Cys	p.Y63C	ENST00000351677	NM_002834.3	63	tAt/tGt	3/16	0.272308379352418	1	FACETS	0.964	0.825	1	0.964	0.825	1	CLONAL	1	TRUE	0	0.272308379352418	1		266	349	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941843	71941843	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514511	NA	P-0067720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	82	315	0	ENST00000298229.2:c.1201C>T	p.Arg401Trp	p.R401W	ENST00000298229	NM_001567.3	401	Cgg/Tgg	11/28	0.272308379352418	1	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	0	0.272308379352418	1		315	510	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804188	46804190	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0067720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	85	312	0	ENST00000290295.7:c.817_819del	p.Lys273del	p.K273del	ENST00000290295	NM_006361.5	273	AAG/-	2/2	0.272308379352418	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.272308379352418	1		312	477	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155973	106155976	+	frameshift_variant	Frame_Shift_Del	DEL	GTGA	GTGA	-	novel	NA	P-0067720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	94	382	0	ENST00000380013.4:c.879_882del	p.Ser293ArgfsTer14	p.S293Rfs*14	ENST00000380013	NM_001127208.2	292	GTGAgt/gt	3/11	0.272308379352418	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.272308379352418	1		382	580	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867274	68867274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377489352	NA	P-0067720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	94	318	0	ENST00000261769.5:c.2521G>A	p.Glu841Lys	p.E841K	ENST00000261769	NM_004360.3	841	Gaa/Aaa	16/16	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.272308379352418	2		318	607	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690811	89690812	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0067720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	16	167	0	ENST00000371953.3:c.219_220del	p.Arg74ThrfsTer3	p.R74Tfs*3	ENST00000371953	NM_000314.4	73	gAA/g	4/9	0.272308379352418	1	FACETS	0.612	0.454	0.797	0.612	0.454	0.797	SUBCLONAL	1	TRUE	0	0.272308379352418	1		167	166	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63965648	63965652	+	frameshift_variant	Frame_Shift_Del	DEL	TTTCC	TTTCC	-	novel	NA	P-0067720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	83	314	0	ENST00000398590.3:c.559_563del	p.Ser187LeufsTer25	p.S187Lfs*25	ENST00000398590	NM_001177387.1	186	tTTTCC/t	6/14	0.272308379352418	1	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	0	0.272308379352418	1		314	523	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29440812	29440812	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	90	245	0	ENST00000544604.2:c.678C>G	p.Phe226Leu	p.F226L	ENST00000544604	NM_001206998.1	226	ttC/ttG	5/9	0.272308379352418	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.272308379352418	1		245	490	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150933149	150933150	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0067720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	100	287	0	ENST00000271640.5:c.2614_2615del	p.Ser872Ter	p.S872*	ENST00000271640	NM_001145415.1	871	GAg/g	16/22	0.272308379352418	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.272308379352418	1		287	541	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137481	202137482	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0067720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	85	332	0	ENST00000358485.4:c.710_711del	p.Tyr237Ter	p.Y237*	ENST00000358485	NM_001080125.1	237	TAt/t	4/9	0.272308379352418	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.272308379352418	1		332	495	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97879632	97879634	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0067720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	48	250	0	ENST00000289081.3:c.1035_1037del	p.Pro346del	p.P346del	ENST00000289081	NM_000136.2	345	tcTCCa/tca	11/15	0.272308379352418	1	FACETS	0.83	0.704	0.968	0.83	0.704	0.968	CLONAL	1	TRUE	0	0.272308379352418	1		250	367	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307152	65307154	+	inframe_deletion	In_Frame_Del	DEL	TAA	TAA	-	novel	NA	P-0067720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	68	338	2	ENST00000342505.4:c.2534_2536del	p.Ile845del	p.I845del	ENST00000342505	NM_002227.2	845	aTTAat/aat	18/25	0.272308379352418	1	FACETS	0.856	0.746	0.974	0.856	0.746	0.974	CLONAL	1	TRUE	0	0.272308379352418	1		340	504	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831402	89831402	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	109	350	1	ENST00000389301.3:c.2674del	p.Ser892ProfsTer29	p.S892Pfs*29	ENST00000389301	NM_000135.2	892	Tcc/cc	28/43	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.272308379352418	2		351	705	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480579	50480579	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	63	343	0	ENST00000394963.4:c.449T>A	p.Leu150His	p.L150H	ENST00000394963	NM_003076.4	150	cTc/cAc	4/13	1	2	FACETS	0.946	0.82	1	0.946	0.82	1	CLONAL	1	TRUE	1	0.272308379352418	2		343	489	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984450	7984452	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs749617913	NA	P-0067720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	78	286	0	ENST00000319144.4:c.406_408del	p.Glu136del	p.E136del	ENST00000319144	NM_001139.2	136	GAG/-	3/15	0.272308379352418	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.272308379352418	1		286	472	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982373	201982373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398134258	NA	P-0067724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	23	400	0	ENST00000359651.3:c.752G>A	p.Arg251Gln	p.R251Q	ENST00000359651		251	cGa/cAa	6/8	1	2	FACETS	0.827	0.644	1	0.827	0.644	1	CLONAL	1	TRUE	1	0.15	2		400	371	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290034	15290034	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258221482	NA	P-0067724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	25	546	0	ENST00000263388.2:c.3520C>T	p.Pro1174Ser	p.P1174S	ENST00000263388	NM_000435.2	1174	Ccc/Tcc	22/33	1	2	FACETS	0.857	0.675	1	0.857	0.675	1	CLONAL	1	TRUE	1	0.15	2		546	389	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294603	1294603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	17	547	0	ENST00000310581.5:c.398G>A	p.Gly133Glu	p.G133E	ENST00000310581	NM_198253.2	133	gGg/gAg	2/16	1	2	FACETS	0.685	0.51	0.893	0.685	0.51	0.893	SUBCLONAL	1	TRUE	1	0.15	2		547	331	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515276	149515276	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	21	493	0	ENST00000261799.4:c.206C>T	p.Pro69Leu	p.P69L	ENST00000261799	NM_002609.3	69	cCc/cTc	3/23	1	2	FACETS	0.729	0.561	0.926	0.729	0.561	0.926	CLONAL	1	TRUE	1	0.15	2		493	384	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244466	41244466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357049	NA	P-0067724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	21	447	1	ENST00000357654.3:c.3082C>T	p.Arg1028Cys	p.R1028C	ENST00000357654	NM_007294.3	1028	Cgt/Tgt	10/23	1	2	FACETS	0.78	0.6	0.99	0.78	0.6	0.99	CLONAL	1	TRUE	1	0.15	2		448	359	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866303	42866303	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	22	490	0	ENST00000398585.3:c.329C>T	p.Ser110Phe	p.S110F	ENST00000398585	NM_001135099.1	110	tCc/tTc	3/14	1	2	FACETS	0.833	0.645	1	0.833	0.645	1	CLONAL	1	TRUE	1	0.15	2		490	352	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155462	47155462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	16	362	0	ENST00000409792.3:c.4619C>T	p.Ser1540Phe	p.S1540F	ENST00000409792	NM_014159.6	1540	tCc/tTc	5/21	1	2	FACETS	0.773	0.571	1	0.773	0.571	1	CLONAL	1	TRUE	1	0.15	2		362	276	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342400	118342400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	18	318	0	ENST00000534358.1:c.526C>T	p.Arg176Cys	p.R176C	ENST00000534358	NM_005933.3	176	Cgt/Tgt	3/36	1	2	FACETS	0.822	0.619	1	0.822	0.619	1	CLONAL	1	TRUE	1	0.15	2		318	292	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166224	118166224	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	24	490	0	ENST00000369448.3:c.734T>C	p.Leu245Pro	p.L245P	ENST00000369448	NM_017709.3	245	cTc/cCc	2/2	1	2	FACETS	0.749	0.587	0.938	0.749	0.587	0.938	CLONAL	1	TRUE	1	0.15	2		490	427	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258744	115258745	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0067724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	9	296	0	ENST00000369535.4:c.37_38delinsAA	p.Gly13Asn	p.G13N	ENST00000369535	NM_002524.4	13	GGt/AAt	2/7	1	2	FACETS	0.415	0.274	0.596	0.415	0.274	0.596	SUBCLONAL	1	TRUE	1	0.15	2		296	289	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120034	70120034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1462690222	NA	P-0067724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	15	413	0	ENST00000245479.2:c.1036C>T	p.Pro346Ser	p.P346S	ENST00000245479	NM_000346.3	346	Ccg/Tcg	3/3	1	2	FACETS	0.81	0.592	1	0.81	0.592	1	CLONAL	1	TRUE	1	0.15	2		413	247	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560139	29560139	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0067724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	20	395	0	ENST00000356175.3:c.3616G>T	p.Glu1206Ter	p.E1206*	ENST00000356175	NM_000267.3	1206	Gag/Tag	27/57	1	2	FACETS	0.831	0.635	1	0.831	0.635	1	CLONAL	1	TRUE	1	0.15	2		395	321	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143460	108143460	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0067724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	24	386	0	ENST00000278616.4:c.3165T>A	p.Tyr1055Ter	p.Y1055*	ENST00000278616	NM_000051.3	1055	taT/taA	22/63	1	2	FACETS	1	0.808	1	1	0.808	1	CLONAL	1	TRUE	1	0.15	2		386	310	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426810	49426810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	29	572	0	ENST00000301067.7:c.11678C>T	p.Pro3893Leu	p.P3893L	ENST00000301067	NM_003482.3	3893	cCc/cTc	39/54	1	2	FACETS	0.867	0.695	1	0.867	0.695	1	CLONAL	1	TRUE	1	0.15	2		572	446	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668765	52668765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	27	368	0	ENST00000394830.3:c.1154C>T	p.Pro385Leu	p.P385L	ENST00000394830	NM_018313.4	385	cCt/cTt	12/30	1	2	FACETS	1	0.823	1	1	0.823	1	CLONAL	1	TRUE	1	0.15	2		368	347	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604227	189604227	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775037738	NA	P-0067724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	20	406	0	ENST00000264731.3:c.1394C>T	p.Pro465Leu	p.P465L	ENST00000264731	NM_003722.4	465	cCt/cTt	11/14	1	2	FACETS	0.923	0.706	1	0.923	0.706	1	CLONAL	1	TRUE	1	0.15	2		406	289	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578493	7578493	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1206165503	NA	P-0067725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	266	484	0	ENST00000269305.4:c.437G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tGg/tAg	5/11	0.74459271434192	1	FACETS	0.987	0.941	1	0.987	0.941	1	CLONAL	1	FALSE	0	0.754353780333079	1		484	445	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435926	56435926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759290047	NA	P-0067725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	56	609	0	ENST00000407977.2:c.1211G>A	p.Arg404His	p.R404H	ENST00000407977		404	cGc/cAc	9/10	0.230689134186793	2	FACETS	0.231	0.197	0.268	0.115	0.098	0.134	INDETERMINATE	1	FALSE	0	0.754353780333079	2		609	643	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900781	3900795	+	inframe_deletion	In_Frame_Del	DEL	CCCTTGAGCCTGGCC	CCCTTGAGCCTGGCC	-	novel	NA	P-0067725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	260	456	0	ENST00000262367.5:c.301_315del	p.Gly101_Gly105del	p.G101_G105del	ENST00000262367	NM_004380.2	101	GGCCAGGCTCAAGGG/-	2/31	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.754353780333079	2		456	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763098116	NA	P-0067726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	39	378	0	ENST00000269305.4:c.830G>A	p.Cys277Tyr	p.C277Y	ENST00000269305	NM_001126112.2	277	tGt/tAt	8/11	1	2	FACETS	0.548	0.454	0.654	0.548	0.454	0.654	SUBCLONAL	1	TRUE	1	0.253531181347919	2		378	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0067726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	90	548	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.253531181347919	2		548	649	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101468	27101468	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	48	295	0	ENST00000324856.7:c.4750C>T	p.Gln1584Ter	p.Q1584*	ENST00000324856	NM_006015.4	1584	Cag/Tag	18/20	1	2	FACETS	0.778	0.658	0.909	0.778	0.658	0.909	CLONAL	1	TRUE	1	0.253531181347919	2		295	487	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0067726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	97	466	0	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.253531181347919	2		466	718	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657051	215657051	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs758972589	NA	P-0067726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	23	273	0	ENST00000260947.4:c.334C>T	p.Arg112Ter	p.R112*	ENST00000260947	NM_000465.2	112	Cga/Tga	3/11	1	2	FACETS	0.619	0.483	0.776	0.619	0.483	0.776	SUBCLONAL	1	TRUE	1	0.253531181347919	2		273	293	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851765	134851765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	82	384	0	ENST00000398015.3:c.1171G>A	p.Val391Ile	p.V391I	ENST00000398015	NM_004441.4	391	Gtc/Atc	5/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.253531181347919	2		384	495	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057961	27057961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	39	384	0	ENST00000324856.7:c.1669C>T	p.Gln557Ter	p.Q557*	ENST00000324856	NM_006015.4	557	Cag/Tag	3/20	1	2	FACETS	0.455	0.376	0.544	0.455	0.376	0.544	SUBCLONAL	1	TRUE	1	0.253531181347919	2		384	676	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143176	30143176	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201290745	NA	P-0067726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	31	428	0	ENST00000389048.3:c.350C>T	p.Pro117Leu	p.P117L	ENST00000389048	NM_004304.4	117	cCg/cTg	1/29	1	2	FACETS	0.47	0.379	0.573	0.47	0.379	0.573	SUBCLONAL	1	TRUE	1	0.253531181347919	2		428	520	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992707	68992707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199541834	NA	P-0067726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	47	340	0	ENST00000288368.4:c.1672C>T	p.Pro558Ser	p.P558S	ENST00000288368	NM_024870.2	558	Ccc/Tcc	16/40	0.210506643585431	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.253531181347919	1		340	290	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246465	46246471	+	frameshift_variant	Frame_Shift_Del	DEL	AGGATAC	AGGATAC	-	novel	NA	P-0067726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	83	421	0	ENST00000334344.6:c.4559_4565del	p.Glu1520ValfsTer13	p.E1520Vfs*13	ENST00000334344	NM_152641.2	1520	gAGGATACt/gt	15/21	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.253531181347919	2		421	610	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212481	5212481	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776015928	NA	P-0067726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	35	391	0	ENST00000357368.4:c.4636G>A	p.Glu1546Lys	p.E1546K	ENST00000357368	NM_002850.3	1546	Gag/Aag	31/38	0.253531181347919	1	FACETS	0.513	0.42	0.617	0.513	0.42	0.617	SUBCLONAL	1	TRUE	0	0.253531181347919	1		391	470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs786202525	NA	P-0067728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	140	612	0	ENST00000269305.4:c.532del	p.His178ThrfsTer69	p.H178Tfs*69	ENST00000269305	NM_001126112.2	178	Cac/ac	5/11	0.235397562447613	2	FACETS	0.891	0.815	0.971	0.891	0.815	0.971	CLONAL	2	TRUE	0	0.261754089246321	2		612	600	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0067728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	94	304	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	1	0.966	1	1	0.988	1	CLONAL	2	TRUE	1	0.261754089246321	2		304	306	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612120	43612120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773256580	NA	P-0067728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	100	609	0	ENST00000355710.3:c.2225C>T	p.Thr742Met	p.T742M	ENST00000355710	NM_020975.4	742	aCg/aTg	12/20	0.201203569080587	2	FACETS	1	0.978	1	0.683	0.612	0.759	CLONAL	1	TRUE	0	0.261754089246321	2		609	559	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93657853	93657853	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	50	461	3	ENST00000375746.1:c.1879C>T	p.Arg627Cys	p.R627C	ENST00000375746	NM_001174167.1	627	Cgc/Tgc	14/14	1	2	FACETS	0.799	0.679	0.931	0.799	0.679	0.931	CLONAL	1	TRUE	1	0.261754089246321	2		464	478	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900995	114900995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	92	558	0	ENST00000543371.1:c.605C>T	p.Pro202Leu	p.P202L	ENST00000543371	NM_001198531.1	202	cCt/cTt	6/14	0.201203569080587	2	FACETS	1	0.973	1	0.65	0.579	0.725	CLONAL	1	TRUE	0	0.261754089246321	2		558	541	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs770248150	NA	P-0067728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	46	354	0	ENST00000311936.3:c.351A>C	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaC	4/5	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.261754089246321	2		354	266	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992725	68992725	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	19	466	0	ENST00000288368.4:c.1690T>C	p.Phe564Leu	p.F564L	ENST00000288368	NM_024870.2	564	Ttt/Ctt	16/40	1	2	FACETS	0.391	0.296	0.503	0.391	0.296	0.503	SUBCLONAL	1	TRUE	1	0.261754089246321	2		466	371	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0067729-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	74	475	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.335152291260966	3	FACETS	1	0.967	1	0.651	0.573	0.734	CLONAL	1	TRUE	1	0.335152291260966	3		475	396	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268555	46268556	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0067729-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	43	421	0	ENST00000371998.3:c.2943dup	p.Leu982AlafsTer7	p.L982Afs*7	ENST00000371998		981	atg/atGg	15/23	1	2	FACETS	0.555	0.465	0.656	0.555	0.465	0.656	SUBCLONAL	1	TRUE	1	0.335152291260966	2		421	462	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0067734-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	100	418	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.868317563824564	4	FACETS	1	0.96	1	0.376	0.339	0.416	CLONAL	1	TRUE	1	0.868317563824564	4		418	381	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067734-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	26	317	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.688	0.56	0.826	0.688	0.56	0.826	SUBCLONAL	1	TRUE	1	0.868317563824564	2		317	87	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437426	49437426	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067734-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	39	337	0	ENST00000301067.7:c.5459del	p.Ser1820CysfsTer32	p.S1820Cfs*32	ENST00000301067	NM_003482.3	1820	tCg/tg	23/54	1	2	FACETS	0.352	0.294	0.417	0.352	0.294	0.417	SUBCLONAL	1	TRUE	1	0.868317563824564	2		337	255	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715633	30715633	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067734-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	85	286	0	ENST00000295754.5:c.1291G>C	p.Glu431Gln	p.E431Q	ENST00000295754	NM_003242.5	431	Gaa/Caa	5/7	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.868317563824564	2		286	185	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538909	23538909	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs373263457	NA	P-0067735-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	113	327	0	ENST00000380871.4:c.530A>G	p.Tyr177Cys	p.Y177C	ENST00000380871	NM_006167.3	177	tAt/tGt	2/2	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.675617186980532	2		327	300	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948466	71948468	+	missense_variant	Missense_Mutation	TNP	GAC	GAC	TAT	novel	NA	P-0067735-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	20	349	0	ENST00000298229.2:c.3178_3180delinsTAT	p.Asp1060Tyr	p.D1060Y	ENST00000298229	NM_001567.3	1060	GAC/TAT	26/28	1	2	FACETS	0.218	0.167	0.279	0.218	0.167	0.279	SUBCLONAL	1	TRUE	1	0.675617186980532	2		349	271	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0067737-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	135	234	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	0.347023391743047	2	FACETS	0.797	0.731	0.864	0.797	0.731	0.864	SUBCLONAL	2	TRUE	0	0.421540852407058	2		234	402	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856442	111856442	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0067737-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	104	173	0	ENST00000341259.2:c.493A>G	p.Thr165Ala	p.T165A	ENST00000341259	NM_005475.2	165	Acc/Gcc	2/8	0.246833494728889	4	FACETS	0.761	0.685	0.84	0.761	0.685	0.84	INDETERMINATE	2	TRUE	2	0.421540852407058	4		173	461	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532522	63532522	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067737-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	57	212	0	ENST00000307078.5:c.2057C>G	p.Pro686Arg	p.P686R	ENST00000307078	NM_004655.3	686	cCt/cGt	8/11	0.357982947655908	3	FACETS	0.7	0.601	0.807	0.233	0.2	0.269	SUBCLONAL	1	TRUE	0	0.421540852407058	3		212	468	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	80	329	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.575457081159569	2		329	267	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	141	518	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.575457081159569	2		518	473	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	94	308	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.913	0.819	1	0.913	0.819	1	CLONAL	1	TRUE	1	0.575457081159569	2		308	358	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	133	320	1	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	1	2	FACETS	0.905	0.826	0.986	0.905	0.826	0.986	CLONAL	1	TRUE	1	0.575457081159569	2		321	511	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	31	117	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	1	0.575457081159569	2		117	105	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149793	202149794	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	97	377	0	ENST00000358485.4:c.1235_1236del	p.Lys412SerfsTer11	p.K412Sfs*11	ENST00000358485	NM_001080125.1	412	AAa/a	8/9	1	2	FACETS	0.914	0.821	1	0.914	0.821	1	CLONAL	1	TRUE	1	0.575457081159569	2		377	369	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	129	398	0	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.575457081159569	2		398	435	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226423	2226423	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	32	332	0	ENST00000398665.3:c.3907del	p.Ala1303LeufsTer24	p.A1303Lfs*24	ENST00000398665	NM_032482.2	1301	tcG/tc	27/28	1	2	FACETS	0.23	0.186	0.28	0.23	0.186	0.28	SUBCLONAL	1	TRUE	1	0.575457081159569	2		332	483	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290214	15290214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373181668	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	84	397	0	ENST00000263388.2:c.3421G>A	p.Val1141Met	p.V1141M	ENST00000263388	NM_000435.2	1141	Gtg/Atg	21/33	1	2	FACETS	0.539	0.477	0.605	0.539	0.477	0.605	SUBCLONAL	1	TRUE	1	0.575457081159569	2		397	542	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	93	234	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.575457081159569	2		234	306	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	65	547	1	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.429	0.373	0.491	0.429	0.373	0.491	SUBCLONAL	1	TRUE	1	0.575457081159569	2		548	526	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952142	178952142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253171657	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	66	221	0	ENST00000263967.3:c.3197C>T	p.Ala1066Val	p.A1066V	ENST00000263967	NM_006218.2	1066	gCa/gTa	21/21	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.575457081159569	2		221	229	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720712	89720712	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	13	105	0	ENST00000371953.3:c.867del	p.Val290Ter	p.V290*	ENST00000371953	NM_000314.4	288	gAa/ga	8/9	1	2	FACETS	0.717	0.524	0.94	0.717	0.524	0.94	CLONAL	1	TRUE	1	0.575457081159569	2		105	63	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	128	437	0	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	0.967	0.883	1	0.967	0.883	1	CLONAL	1	TRUE	1	0.575457081159569	2		437	460	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903745	41903746	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	135	369	2	ENST00000372991.4:c.811dup	p.Arg271ProfsTer53	p.R271Pfs*53	ENST00000372991	NM_001760.3	271	cgg/cCgg	5/5	1	2	FACETS	0.929	0.85	1	0.929	0.85	1	CLONAL	1	TRUE	1	0.575457081159569	2		371	505	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533760	63533760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764640447	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	153	367	0	ENST00000307078.5:c.1394G>A	p.Arg465His	p.R465H	ENST00000307078	NM_004655.3	465	cGc/cAc	6/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.575457081159569	2		367	481	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245720	46245720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	129	379	0	ENST00000334344.6:c.3814C>T	p.Arg1272Ter	p.R1272*	ENST00000334344	NM_152641.2	1272	Cga/Tga	15/21	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.575457081159569	2		379	428	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720928	176720928	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784209	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	161	286	0	ENST00000439151.2:c.6559C>T	p.Arg2187Ter	p.R2187*	ENST00000439151	NM_022455.4	2187	Cga/Tga	23/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.575457081159569	2		286	492	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089123	37089125	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs63751247	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	122	341	0	ENST00000231790.2:c.1852_1854del	p.Lys618del	p.K618del	ENST00000231790	NM_000249.3	615	ctGAAg/ctg	16/19	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.575457081159569	2		341	352	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916935	178916935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	76	268	0	ENST00000263967.3:c.322C>T	p.Arg108Cys	p.R108C	ENST00000263967	NM_006218.2	108	Cgt/Tgt	2/21	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.575457081159569	2		268	228	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	132	282	1	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	1	2	FACETS	0.946	0.864	1	0.946	0.864	1	CLONAL	1	TRUE	1	0.575457081159569	2		283	485	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741472	145741472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745874353	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	75	367	0	ENST00000428558.2:c.1031G>A	p.Arg344Gln	p.R344Q	ENST00000428558	NM_004260.3	344	cGg/cAg	5/22	0.575457081159569	3	FACETS	0.561	0.492	0.636	0.281	0.246	0.318	SUBCLONAL	1	TRUE	1	0.575457081159569	3		367	598	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859308	151859309	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	26	251	0	ENST00000262189.6:c.11353_11354del	p.Lys3785ValfsTer10	p.K3785Vfs*10	ENST00000262189	NM_170606.2	3785	AAg/g	43/59	1	2	FACETS	0.241	0.19	0.299	0.241	0.19	0.299	SUBCLONAL	1	TRUE	1	0.575457081159569	2		251	375	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025765	48025765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145959653	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	41	280	0	ENST00000234420.5:c.643G>A	p.Val215Ile	p.V215I	ENST00000234420	NM_000179.2	215	Gta/Ata	4/10	1	2	FACETS	0.532	0.445	0.626	0.532	0.445	0.626	SUBCLONAL	1	TRUE	1	0.575457081159569	2		280	268	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246826	10246826	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1292341520	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	128	315	0	ENST00000340748.4:c.4579G>A	p.Val1527Ile	p.V1527I	ENST00000340748		1527	Gtc/Atc	37/40	1	2	FACETS	0.925	0.844	1	0.925	0.844	1	CLONAL	1	TRUE	1	0.575457081159569	2		315	481	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574043	46574043	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1394833849	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	145	316	0	ENST00000263734.3:c.58C>T	p.Arg20Trp	p.R20W	ENST00000263734	NM_001430.4	20	Cgg/Tgg	2/16	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.575457081159569	2		316	494	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101666	27101666	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	169	356	0	ENST00000324856.7:c.4948C>T	p.Gln1650Ter	p.Q1650*	ENST00000324856	NM_006015.4	1650	Cag/Tag	18/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.575457081159569	2		356	509	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549014	21549014	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777319923	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	82	230	0	ENST00000382592.4:c.3262G>A	p.Val1088Met	p.V1088M	ENST00000382592	NM_014572.2	1088	Gtg/Atg	8/8	1	2	FACETS	0.913	0.813	1	0.913	0.813	1	CLONAL	1	TRUE	1	0.575457081159569	2		230	312	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964449	70964449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1247646437	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	245	319	0	ENST00000276594.2:c.1579G>A	p.Ala527Thr	p.A527T	ENST00000276594	NM_024504.3	527	Gca/Aca	8/8	0.575457081159569	3	FACETS	0.926	0.873	0.98	0.926	0.873	0.98	CLONAL	2	TRUE	1	0.575457081159569	3		319	592	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133748317	133748317	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	143	260	0	ENST00000318560.5:c.978C>A	p.Tyr326Ter	p.Y326*	ENST00000318560	NM_005157.4	326	taC/taA	6/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.575457081159569	2		260	453	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741917	40741917	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs886899893	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	117	343	0	ENST00000392038.2:c.1055A>G	p.Asn352Ser	p.N352S	ENST00000392038	NM_001626.4	352	aAc/aGc	11/14	1	2	FACETS	0.842	0.763	0.924	0.842	0.763	0.924	CLONAL	1	TRUE	1	0.575457081159569	2		343	483	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549179	21549179	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	120	346	0	ENST00000382592.4:c.3097C>A	p.Pro1033Thr	p.P1033T	ENST00000382592	NM_014572.2	1033	Cct/Act	8/8	1	2	FACETS	0.862	0.783	0.944	0.862	0.783	0.944	CLONAL	1	TRUE	1	0.575457081159569	2		346	484	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425196	49425199	+	frameshift_variant	Frame_Shift_Del	DEL	ACTG	ACTG	-	novel	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	144	350	0	ENST00000301067.7:c.13289_13292del	p.Ser4430Ter	p.S4430*	ENST00000301067	NM_003482.3	4430	tCAGTg/tg	39/54	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.575457081159569	2		350	479	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043366	180043366	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	106	329	0	ENST00000261937.6:c.3219+1G>A		p.X1073_splice	ENST00000261937	NM_182925.4	1073			1	2	FACETS	0.727	0.654	0.803	0.727	0.654	0.803	SUBCLONAL	1	TRUE	1	0.575457081159569	2		329	507	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2093688	2093688	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	53	248	0	ENST00000219066.1:c.589C>T	p.Gln197Ter	p.Q197*	ENST00000219066	NM_002528.5	197	Cag/Tag	4/6	1	2	FACETS	0.509	0.435	0.588	0.509	0.435	0.588	SUBCLONAL	1	TRUE	1	0.575457081159569	2		248	362	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1735914	1735914	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs150628410	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	152	298	0	ENST00000378609.4:c.374A>G	p.Asn125Ser	p.N125S	ENST00000378609	NM_002074.3	125	aAt/aGt	7/12	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.575457081159569	2		298	476	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471634	120471634	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	125	289	0	ENST00000256646.2:c.3857A>T	p.Asn1286Ile	p.N1286I	ENST00000256646	NM_024408.3	1286	aAt/aTt	23/34	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.575457081159569	2		289	430	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213468	36213468	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0067738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	128	344	0	ENST00000222270.7:c.2572-2A>G		p.X858_splice	ENST00000222270	NM_014727.1	858			1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.575457081159569	2		344	444	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693002	89693003	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0067743-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	84	408	0	ENST00000371953.3:c.491dup	p.Val166SerfsTer14	p.V166Sfs*14	ENST00000371953	NM_000314.4	162	-/A	5/9	0.794454716033661	3	FACETS	0.637	0.565	0.714	0.318	0.282	0.357	SUBCLONAL	1	TRUE	1	0.794454716033661	3		408	464	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022747	12022747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376242225	NA	P-0067743-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	186	683	1	ENST00000396373.4:c.853G>A	p.Val285Met	p.V285M	ENST00000396373	NM_001987.4	285	Gtg/Atg	5/8	0.794454716033661	3	FACETS	0.951	0.881	1	0.475	0.44	0.512	CLONAL	1	TRUE	1	0.794454716033661	3		684	688	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368218	45368218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0067743-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	162	475	0	ENST00000262160.6:c.1384C>T	p.Arg462Cys	p.R462C	ENST00000262160	NM_005901.5	462	Cgt/Tgt	11/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.794454716033661	2		475	389	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0067743-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	634	490	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	0.794454716033661	6	FACETS	0.958	0.934	0.981	0.958	0.934	0.981	CLONAL	5	TRUE	1	0.794454716033661	6		490	863	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996684	73996684	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067743-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	27	54	0	ENST00000318443.5:c.1240G>C	p.Ala414Pro	p.A414P	ENST00000318443	NM_001024736.1	414	Gcc/Ccc	6/10	0.794454716033661	2	FACETS	0.755	0.645	0.861	0.755	0.645	0.861	SUBCLONAL	2	TRUE	0	0.794454716033661	2		54	45	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001234	150001234	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067743-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	140	514	0	ENST00000253339.5:c.2370G>A	p.Met790Ile	p.M790I	ENST00000253339		790	atG/atA	4/7	0.794454716033661	3	FACETS	0.892	0.816	0.971	0.446	0.408	0.486	CLONAL	1	TRUE	1	0.794454716033661	3		514	552	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188211	10188249	+	inframe_deletion	In_Frame_Del	DEL	CTTCAGAGATGCAGGGACACACGATGGGCTTCTGGTTAA	CTTCAGAGATGCAGGGACACACGATGGGCTTCTGGTTAA	-	novel	NA	P-0067747-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	74	370	0	ENST00000256474.2:c.355_393del	p.Phe119_Asn131del	p.F119_N131del	ENST00000256474	NM_000551.3	118	ctCTTCAGAGATGCAGGGACACACGATGGGCTTCTGGTTAAc/ctc	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		370	380	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137522140	137522140	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067747-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	72	458	0	ENST00000367739.4:c.739C>A	p.Leu247Ile	p.L247I	ENST00000367739	NM_000416.2	247	Ctt/Att	6/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		458	517	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240806	53240806	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067747-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	112	259	0	ENST00000375401.3:c.1274T>G	p.Phe425Cys	p.F425C	ENST00000375401	NM_004187.3	425	tTc/tGc	10/26	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		259	344	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068453	16068453	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0067747-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	54	113	0	ENST00000268712.3:c.458A>C	p.His153Pro	p.H153P	ENST00000268712	NM_006311.3	153	cAt/cCt	5/46	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		113	164	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573988	7573988	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0067748-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	250	484	0	ENST00000269305.4:c.1039del	p.Ala347ProfsTer23	p.A347Pfs*23	ENST00000269305	NM_001126112.2	347	Gcc/cc	10/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		484	265	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061228	38061228	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067748-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	328	639	1	ENST00000250448.2:c.761del	p.Phe254SerfsTer67	p.F254Sfs*67	ENST00000250448	NM_004496.3	254	tTc/tc	2/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		640	989	SUCCESS
APC	324	MSKCC	GRCh37	5	112176740	112176740	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0067748-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	289	544	0	ENST00000257430.4:c.5453del	p.Asn1818IlefsTer45	p.N1818Ifs*45	ENST00000257430	NM_000038.5	1817	Aaa/aa	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		544	337	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095023	11095023	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0067748-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	293	657	2	ENST00000358026.2:c.196C>T	p.Gln66Ter	p.Q66*	ENST00000358026	NM_001128849.1	66	Cag/Tag	2/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		659	617	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099695	157099695	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0067748-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	138	331	0	ENST00000346085.5:c.632A>C	p.Gln211Pro	p.Q211P	ENST00000346085	NM_020732.3	211	cAg/cCg	1/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		331	307	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250047	53250047	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	73	230	0	ENST00000375401.3:c.202del	p.Arg68GlufsTer5	p.R68Efs*5	ENST00000375401	NM_004187.3	68	Cga/ga	2/26	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		230	128	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098795	47098795	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0067749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	87	542	0	ENST00000409792.3:c.6479del	p.Pro2160ArgfsTer88	p.P2160Rfs*88	ENST00000409792	NM_014159.6	2160	cCg/cg	15/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		542	201	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118541	17118541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471793185	NA	P-0067749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	78	527	0	ENST00000285071.4:c.1390G>A	p.Glu464Lys	p.E464K	ENST00000285071	NM_144997.5	464	Gag/Aag	12/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		527	249	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346792	89346792	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	57	515	0	ENST00000301030.4:c.6158C>G	p.Ala2053Gly	p.A2053G	ENST00000301030	NM_001256183.1	2053	gCg/gGg	9/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		515	214	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183756	10183772	+	frameshift_variant	Frame_Shift_Del	DEL	CTTCTGCAATCGCAGTC	CTTCTGCAATCGCAGTC	-	novel	NA	P-0067749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	77	503	0	ENST00000256474.2:c.226_242del	p.Phe76AlafsTer50	p.F76Afs*50	ENST00000256474	NM_000551.3	75	atCTTCTGCAATCGCAGTCcg/atcg	1/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		503	158	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0067822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	302	317	0				ENST00000310581	NM_198253.2	-/1132			0.838200411101552	5	FACETS	0.967	0.922	1	0.967	0.922	1	CLONAL	3	TRUE	2	0.83333533333793	5		317	562	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0067822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	580	396	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.838200411101552	3	FACETS	1	0.998	1	1	0.998	1	CLONAL	3	TRUE	0	0.83333533333793	3		396	595	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372780	81372780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752123971	NA	P-0067822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	36	402	0	ENST00000222390.5:c.754G>A	p.Asp252Asn	p.D252N	ENST00000222390	NM_000601.4	252	Gac/Aac	7/18	1	2	FACETS	0.248	0.204	0.297	0.248	0.204	0.297	SUBCLONAL	1	TRUE	1	0.83333533333793	2		402	349	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919281	48919281	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs587778870	NA	P-0067822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	272	352	0	ENST00000267163.4:c.446C>G	p.Ser149Ter	p.S149*	ENST00000267163	NM_000321.2	149	tCa/tGa	4/27	0.770096699528002	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	2	0.83333533333793	4		352	577	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38283744	38283744	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	198	527	0	ENST00000425967.3:c.734G>A	p.Ser245Asn	p.S245N	ENST00000425967	NM_001174067.1	245	aGc/aAc	7/19	0.838200411101552	2	FACETS	1	0.987	1	0.595	0.56	0.631	CLONAL	1	TRUE	0	0.83333533333793	2		527	399	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039186	49039186	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0067822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	311	356	0	ENST00000267163.4:c.2264T>C	p.Phe755Ser	p.F755S	ENST00000267163	NM_000321.2	755	tTc/tCc	22/27	0.770096699528002	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.83333533333793	4		356	640	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61705969	61705969	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0067822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	133	391	0	ENST00000401558.2:c.3202G>T	p.Glu1068Ter	p.E1068*	ENST00000401558	NM_003400.3	1068	Gaa/Taa	25/25	0.838200411101552	3	FACETS	0.914	0.835	0.995	0.457	0.417	0.498	CLONAL	1	TRUE	1	0.83333533333793	3		391	495	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522579	106522579	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0067822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	130	278	0	ENST00000359195.3:c.2556G>C	p.Glu852Asp	p.E852D	ENST00000359195	NM_002649.2	852	gaG/gaC	7/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.83333533333793	2		278	297	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391392	139391392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	235	662	0	ENST00000277541.6:c.6799G>A	p.Glu2267Lys	p.E2267K	ENST00000277541	NM_017617.3	2267	Gag/Aag	34/34	0.838200411101552	3	FACETS	1	0.981	1	0.559	0.523	0.595	CLONAL	1	TRUE	1	0.83333533333793	3		662	715	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0067823-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	116	392	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.292793096086503	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	0	0.321380295529333	1		392	503	SUCCESS
APC	324	MSKCC	GRCh37	5	112175378	112175378	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0067823-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	90	383	0	ENST00000257430.4:c.4087A>T	p.Lys1363Ter	p.K1363*	ENST00000257430	NM_000038.5	1363	Aaa/Taa	16/16	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	FALSE	1	0.321380295529333	2		383	546	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405884	70405884	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs748349829	NA	P-0067823-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	56	403	0	ENST00000373644.4:c.3398A>G	p.Asn1133Ser	p.N1133S	ENST00000373644	NM_030625.2	1133	aAt/aGt	4/12	1	2	FACETS	0.602	0.515	0.696	0.602	0.515	0.696	SUBCLONAL	1	FALSE	1	0.321380295529333	2		403	579	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920447	114920447	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0067823-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	90	334	0	ENST00000543371.1:c.1388G>T	p.Cys463Phe	p.C463F	ENST00000543371	NM_001198531.1	463	tGc/tTc	13/14	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.321380295529333	2		334	468	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045134	47045134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782351435	NA	P-0067823-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	79	511	0	ENST00000377604.3:c.2375G>A	p.Arg792Gln	p.R792Q	ENST00000377604	NM_001204468.1	792	cGg/cAg	21/24	1	2	FACETS	0.897	0.79	1	0.897	0.79	1	CLONAL	1	FALSE	1	0.321380295529333	2		511	548	SUCCESS
APC	324	MSKCC	GRCh37	5	112174983	112174986	+	frameshift_variant	Frame_Shift_Del	DEL	TCCA	TCCA	-	novel	NA	P-0067823-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	49	422	0	ENST00000257430.4:c.3696_3699del	p.His1232GlnfsTer32	p.H1232Qfs*32	ENST00000257430	NM_000038.5	1231	cTCCAt/ct	16/16	1	2	FACETS	0.58	0.491	0.678	0.58	0.491	0.678	SUBCLONAL	1	FALSE	1	0.321380295529333	2		422	526	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15967461	15967461	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0067823-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	103	355	0	ENST00000268712.3:c.5142G>C	p.Arg1714Ser	p.R1714S	ENST00000268712	NM_006311.3	1714	agG/agC	35/46	0.292793096086503	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	0	0.321380295529333	1		355	467	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599938	28599938	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148305939	NA	P-0067825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	41	726	0	ENST00000253063.3:c.820C>T	p.Arg274Trp	p.R274W	ENST00000253063	NM_031459.4	274	Cgg/Tgg	6/10	1	2	FACETS	0.84	0.699	0.997	0.84	0.699	0.997	CLONAL	1	TRUE	1	0.18244801881917	2		726	535	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0067825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	103	480	0	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	0.127260273176579	3	FACETS	0.866	0.776	0.963	0.866	0.776	0.963	CLONAL	2	TRUE	1	0.18244801881917	3		480	711	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431394	121431394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193922598	NA	P-0067825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	96	741	0	ENST00000257555.6:c.598C>T	p.Arg200Trp	p.R200W	ENST00000257555		200	Cgg/Tgg	3/10	0.127260273176579	3	FACETS	0.873	0.778	0.973	0.873	0.778	0.973	CLONAL	2	TRUE	1	0.18244801881917	3		741	658	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031776	11031776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776007903	NA	P-0067825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	84	912	0	ENST00000327064.4:c.1588G>A	p.Val530Met	p.V530M	ENST00000327064	NM_199141.1	530	Gtg/Atg	14/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.18244801881917	2		912	693	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280136	142280136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369434236	NA	P-0067825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	61	528	1	ENST00000350721.4:c.1298G>A	p.Arg433His	p.R433H	ENST00000350721	NM_001184.3	433	cGt/cAt	5/47	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.18244801881917	2		529	484	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303376	91303376	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1555419696	NA	P-0067825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	30	423	0	ENST00000355112.3:c.1088-1G>A		p.X363_splice	ENST00000355112	NM_000057.2	363			0.18244801881917	2	FACETS	0.747	0.602	0.913	0.374	0.301	0.457	CLONAL	1	TRUE	0	0.18244801881917	2		423	440	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579475	7579476	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	160	946	0	ENST00000269305.4:c.211_212insA	p.Pro71HisfsTer78	p.P71Hfs*78	ENST00000269305	NM_001126112.2	71	ccc/cAcc	4/11	0.16699830329821	3	FACETS	0.884	0.812	0.958	0.884	0.812	0.958	CLONAL	3	TRUE	0	0.18244801881917	3		946	722	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0067826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	207	400	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.840293938270261	2		401	481	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782329	NA	P-0067826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	233	441	0	ENST00000269305.4:c.746G>C	p.Arg249Thr	p.R249T	ENST00000269305	NM_001126112.2	249	aGg/aCg	7/11	NA	2	FACETS	0.948	0.891	1			1	INDETERMINATE	1	TRUE	NA	0.840293938270261	2		441	585	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938229	76938230	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0067826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	143	417	0	ENST00000373344.5:c.2518dup	p.Arg840LysfsTer9	p.R840Kfs*9	ENST00000373344	NM_000489.3	840	aga/aAga	9/35	0.343212482262025	1	FACETS	0.575	0.532	0.619	0.575	0.532	0.619	INDETERMINATE	1	TRUE	0	0.840293938270261	1		417	343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578509	7578509	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519978	NA	P-0067826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	336	515	0	ENST00000269305.4:c.421T>A	p.Cys141Ser	p.C141S	ENST00000269305	NM_001126112.2	141	Tgc/Agc	5/11	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.840293938270261	2		515	727	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606678	29606678	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs188859061	NA	P-0003823-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	48	420	0	ENST00000389048.3:c.1202G>A	p.Arg401Gln	p.R401Q	ENST00000389048	NM_004304.4	401	cGa/cAa	5/29	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.17	2		420	555	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718077	117718077	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0003823-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	36	356	0	ENST00000368508.3:c.779+1del		p.X260_splice	ENST00000368508	NM_002944.2	260			1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.17	2		356	393	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303023	15303023	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003823-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	49	559	0	ENST00000263388.2:c.427C>A	p.Leu143Ile	p.L143I	ENST00000263388	NM_000435.2	143	Ctc/Atc	4/33	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.17	2		559	559	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004226-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	127	446	0				ENST00000310581	NM_198253.2	-/1132			0.237646151553096	5	FACETS	0.982	0.896	1	0.655	0.597	0.714	INDETERMINATE	2	TRUE	2	0.50692435681901	5		446	449	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0004226-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	119	311	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.50692435681901	2		311	427	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645693	12645693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397516827	NA	P-0004226-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	205	539	0	ENST00000251849.4:c.776C>T	p.Ser259Phe	p.S259F	ENST00000251849	NM_002880.3	259	tCc/tTc	7/17	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.50692435681901	2		539	675	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230772	46230772	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004226-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	149	679	0	ENST00000334344.6:c.1021G>C	p.Glu341Gln	p.E341Q	ENST00000334344	NM_152641.2	341	Gag/Cag	8/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.50692435681901	2		679	518	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588849	69588849	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004226-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	174	298	0	ENST00000168712.1:c.387C>A	p.Phe129Leu	p.F129L	ENST00000168712	NM_002007.2	129	ttC/ttA	2/3	0.50692435681901	8	FACETS	0.806	0.741	0.873			1	CLONAL	2	TRUE	NA	0.50692435681901	8		298	1074	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467998	66467998	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004226-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	106	580	0	ENST00000273854.3:c.271G>A	p.Glu91Lys	p.E91K	ENST00000273854	NM_004439.5	91	Gaa/Aaa	3/18	1	2	FACETS	0.899	0.811	0.992	0.899	0.811	0.992	CLONAL	1	TRUE	1	0.50692435681901	2		580	465	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398262	25398262	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913538	NA	P-0004226-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	107	474	0	ENST00000311936.3:c.57G>C	p.Leu19Phe	p.L19F	ENST00000311936	NM_004985.3	19	ttG/ttC	2/5	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.50692435681901	2		474	413	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158626	26158626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772836222	NA	P-0004226-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	81	288	0	ENST00000289316.2:c.229G>A	p.Glu77Lys	p.E77K	ENST00000289316	NM_138720.2	77	Gag/Aag	1/2	0.329624504348727	1	FACETS	0.877	0.783	0.976	0.877	0.783	0.976	CLONAL	1	TRUE	0	0.50692435681901	1		288	272	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168983	11168983	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004226-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	154	286	0	ENST00000358026.2:c.4573G>C	p.Glu1525Gln	p.E1525Q	ENST00000358026	NM_001128849.1	1525	Gag/Cag	32/36	0.266258889657809	5	FACETS	0.981	0.903	1	0.654	0.602	0.708	INDETERMINATE	2	TRUE	2	0.50692435681901	5		286	545	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170834	11170834	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004226-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	195	345	0	ENST00000358026.2:c.4978G>A	p.Asp1660Asn	p.D1660N	ENST00000358026	NM_001128849.1	1660	Gac/Aac	35/36	0.266258889657809	5	FACETS	0.956	0.888	1	0.638	0.592	0.685	INDETERMINATE	2	TRUE	2	0.50692435681901	5		345	708	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170861	11170861	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1298648044	NA	P-0004226-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	194	337	0	ENST00000358026.2:c.5005G>A	p.Glu1669Lys	p.E1669K	ENST00000358026	NM_001128849.1	1669	Gag/Aag	35/36	0.266258889657809	5	FACETS	0.995	0.925	1	0.663	0.616	0.712	INDETERMINATE	2	TRUE	2	0.50692435681901	5		337	677	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	122	310	1	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	0.162527937589934	5	FACETS	1	0.934	1	1	0.993	1	CLONAL	7	FALSE	3	0.162527937589934	5		311	263	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	87	478	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.12327385064291	0	FACETS	0.924	0.838	1			1	CLONAL	5	FALSE	0	0.162527937589934	0		479	194	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	41	413	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.9	1	1	0.979	1	CLONAL	4	FALSE	1	0.162527937589934	2		413	118	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	50	383	0	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	0.162527937589934	5	FACETS	1	0.919	1	1	0.919	1	CLONAL	2	FALSE	3	0.162527937589934	5		383	341	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526152	189526152	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751300168	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	75	380	0	ENST00000264731.3:c.416C>T	p.Ala139Val	p.A139V	ENST00000264731	NM_003722.4	139	gCg/gTg	4/14	0.113497703814732	4	FACETS	0.787	0.689	0.892	0.787	0.689	0.892	SUBCLONAL	2	FALSE	2	0.162527937589934	4		380	682	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	150	476	0	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	1	0.971	1	1	0.994	1	CLONAL	5	FALSE	1	0.162527937589934	2		476	338	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	140	877	17	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	0.162527937589934	1	FACETS	0.959	0.887	1	1	0.994	1	CLONAL	5	FALSE	0	0.162527937589934	1		894	330	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258485	16258485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780910569	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	151	417	2	ENST00000375759.3:c.5750G>A	p.Arg1917His	p.R1917H	ENST00000375759	NM_015001.2	1917	cGc/cAc	11/15	0.162527937589934	5	FACETS	1	0.95	1	1	0.994	1	CLONAL	6	FALSE	3	0.162527937589934	5		419	373	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325881	65325881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	79	341	0	ENST00000342505.4:c.1241G>A	p.Arg414Gln	p.R414Q	ENST00000342505	NM_002227.2	414	cGg/cAg	9/25	1	2	FACETS	0.949	0.847	1	1	0.989	1	CLONAL	4	FALSE	1	0.162527937589934	2		341	256	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497847	25497847	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779859478	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	81	281	0	ENST00000264709.3:c.602G>A	p.Arg201His	p.R201H	ENST00000264709	NM_175629.2	201	cGc/cAc	6/23	1	2	FACETS	0.989	0.884	1	1	0.989	1	CLONAL	4	FALSE	1	0.162527937589934	2		281	252	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702211	47702211	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs63750657	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	71	266	0	ENST00000233146.2:c.1807G>T	p.Asp603Tyr	p.D603Y	ENST00000233146	NM_000251.2	603	Gat/Tat	12/16	1	2	FACETS	0.999	0.906	1	1	0.989	1	CLONAL	7	FALSE	1	0.162527937589934	2		266	125	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735422	204735422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	128	365	1	ENST00000302823.3:c.223C>T	p.Arg75Trp	p.R75W	ENST00000302823	NM_005214.4	75	Cgg/Tgg	2/4	1	2	FACETS	0.93	0.863	0.996	1	0.994	1	CLONAL	7	FALSE	1	0.162527937589934	2		366	242	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163278	47163278	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372092336	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	52	347	0	ENST00000409792.3:c.2848C>T	p.Arg950Cys	p.R950C	ENST00000409792	NM_014159.6	950	Cgt/Tgt	3/21	1	2	FACETS	0.964	0.836	1	1	0.983	1	CLONAL	4	FALSE	1	0.162527937589934	2		347	166	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030232	180030232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371358529	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	102	375	0	ENST00000261937.6:c.4052C>T	p.Pro1351Leu	p.P1351L	ENST00000261937	NM_182925.4	1351	cCg/cTg	30/30	0.12327385064291	0	FACETS	0.902	0.824	0.982			1	CLONAL	5	FALSE	0	0.162527937589934	0		375	233	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650071	93650071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1486347243	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	54	280	0	ENST00000375746.1:c.1622C>T	p.Pro541Leu	p.P541L	ENST00000375746	NM_001174167.1	541	cCg/cTg	12/14	0.162549384810443	0	FACETS	0.883	0.777	0.992			1	CLONAL	5	FALSE	0	0.162527937589934	0		280	126	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205534	61205534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140191819	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	90	289	0	ENST00000301761.2:c.319C>T	p.Arg107Cys	p.R107C	ENST00000301761	NM_017841.2	107	Cgc/Tgc	3/4	1	2	FACETS	1	0.907	1	1	0.991	1	CLONAL	5	FALSE	1	0.162527937589934	2		289	221	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133239	30133239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750160678	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	180	349	0	ENST00000263025.4:c.259C>T	p.Arg87Trp	p.R87W	ENST00000263025	NM_002746.2	87	Cgg/Tgg	2/9	0.162527937589934	1	FACETS	1	0.964	1	1	0.995	1	CLONAL	6	FALSE	0	0.162527937589934	1		349	328	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881117	37881117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542027040	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	159	360	0	ENST00000269571.5:c.2446C>T	p.Arg816Cys	p.R816C	ENST00000269571		816	Cgc/Tgc	20/27	0.162527937589934	8	FACETS	0.946	0.881	1	1	0.993	1	CLONAL	9	FALSE	4	0.162527937589934	8		360	342	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143000	7143000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369025474	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	150	350	0	ENST00000302850.5:c.2369C>T	p.Thr790Met	p.T790M	ENST00000302850	NM_000208.2	790	aCg/aTg	12/22	1	2	FACETS	0.927	0.861	0.993	1	0.994	1	CLONAL	6	FALSE	1	0.162527937589934	2		350	332	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429004	47429004	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780392848	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	136	148	0	ENST00000377045.4:c.1367G>A	p.Arg456Gln	p.R456Q	ENST00000377045	NM_001654.4	456	cGa/cAa	13/16	1	1	FACETS	1	0.983	1	1	0.994	1	CLONAL	10	FALSE	0	0.162527937589934	1		148	149	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223488	53223488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	86	171	0	ENST00000375401.3:c.3871C>T	p.Arg1291Cys	p.R1291C	ENST00000375401	NM_004187.3	1291	Cgc/Tgc	23/26	1	1	FACETS	1	0.972	1	1	0.991	1	CLONAL	10	FALSE	0	0.162527937589934	1		171	95	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53253966	53253966	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	113	167	0	ENST00000375401.3:c.106C>T	p.Pro36Ser	p.P36S	ENST00000375401	NM_004187.3	36	Ccc/Tcc	1/26	1	1	FACETS	0.96	0.929	0.984	1	0.993	1	CLONAL	11	FALSE	0	0.162527937589934	1		167	121	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130441	29130441	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	73	397	0	ENST00000328354.6:c.269del	p.Pro90LeufsTer20	p.P90Lfs*20	ENST00000328354	NM_007194.3	90	cCt/ct	2/15	0.162549384810443	0	FACETS	0.9	0.801	1			1	CLONAL	4	FALSE	0	0.162527937589934	0		397	209	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272337	15272337	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs771517374	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	149	654	4	ENST00000263388.2:c.6102del	p.Gly2035ValfsTer50	p.G2035Vfs*50	ENST00000263388	NM_000435.2	2034	ccC/cc	33/33	0.162527937589934	5	FACETS	1	0.963	1	1	0.994	1	CLONAL	6	FALSE	3	0.162527937589934	5		658	357	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514998	148515000	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs775039041	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	79	338	0	ENST00000320356.2:c.1209_1211del	p.Glu404del	p.E404del	ENST00000320356	NM_004456.4	403	gaAGAg/gag	10/20	1	2	FACETS	1	0.932	1	1	0.99	1	CLONAL	5	FALSE	1	0.162527937589934	2		338	186	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156288	106156289	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAC	rs924321610	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	64	428	0	ENST00000380013.4:c.1201_1203dup	p.Pro401dup	p.P401dup	ENST00000380013	NM_001127208.2	401	aca/aCACca	3/11	1	2	FACETS	0.947	0.833	1	1	0.986	1	CLONAL	4	FALSE	1	0.162527937589934	2		428	208	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817786	3817790	+	frameshift_variant	Frame_Shift_Del	DEL	TCCTC	TCCTC	-	novel	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	139	335	0	ENST00000262367.5:c.3181_3185del	p.Glu1061ArgfsTer4	p.E1061Rfs*4	ENST00000262367	NM_004380.2	1061	GAGGAa/a	16/31	0.162527937589934	5	FACETS	1	0.961	1	1	0.992	1	CLONAL	7	FALSE	1	0.162527937589934	5		335	288	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322767	30322768	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	62	206	0	ENST00000322652.5:c.1786dup	p.Thr596AsnfsTer6	p.T596Nfs*6	ENST00000322652	NM_015355.2	594	gaa/gAaa	14/16	0.162527937589934	5	FACETS	1	0.896	1	1	0.964	1	CLONAL	5	FALSE	1	0.162527937589934	5		206	186	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726544	41726544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs891614619	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	99	340	0	ENST00000301178.4:c.89C>T	p.Thr30Met	p.T30M	ENST00000301178	NM_021913.4	30	aCg/aTg	2/20	1	2	FACETS	1	0.946	1	1	0.992	1	CLONAL	5	FALSE	1	0.162527937589934	2		340	231	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885578	111885578	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs751470371	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	95	351	0	ENST00000341259.2:c.1355C>G	p.Ala452Gly	p.A452G	ENST00000341259	NM_005475.2	452	gCc/gGc	7/8	0.113497703814732	4	FACETS	1	0.952	1	1	0.988	1	CLONAL	4	FALSE	2	0.162527937589934	4		351	310	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444932	49444933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767415197	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	146	386	0	ENST00000301067.7:c.2533dup	p.Arg845ProfsTer3	p.R845Pfs*3	ENST00000301067	NM_003482.3	845	cgg/cCgg	10/54	0.113497703814732	4	FACETS	0.967	0.894	1	1	0.993	1	CLONAL	6	FALSE	2	0.162527937589934	4		386	360	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	83	376	6	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	1	2	FACETS	0.995	0.903	1	1	0.99	1	CLONAL	6	FALSE	1	0.162527937589934	2		382	171	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992720	68992721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs764112302	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	58	270	4	ENST00000288368.4:c.1693dup	p.Ser565PhefsTer3	p.S565Ffs*3	ENST00000288368	NM_024870.2	562	cgt/cgTt	16/40	1	2	FACETS	1	0.909	1	1	0.986	1	CLONAL	5	FALSE	1	0.162527937589934	2		274	138	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813902	50813902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1162538506	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	58	303	0	ENST00000398568.2:c.1456C>T	p.Arg486Cys	p.R486C	ENST00000398568	NM_001042412.1	486	Cgt/Tgt	8/18	0.162527937589934	1	FACETS	1	0.941	1	1	0.986	1	CLONAL	4	FALSE	0	0.162527937589934	1		303	147	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954180	32954180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45580035	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	47	315	0	ENST00000380152.3:c.9154C>T	p.Arg3052Trp	p.R3052W	ENST00000380152		3052	Cgg/Tgg	24/27	0.12327385064291	0	FACETS	0.802	0.69	0.919			1	CLONAL	4	FALSE	0	0.162527937589934	0		315	151	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845228	151845228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	110	344	0	ENST00000262189.6:c.13784G>A	p.Arg4595His	p.R4595H	ENST00000262189	NM_170606.2	4595	cGc/cAc	52/59	1	2	FACETS	1	0.955	1	1	0.992	1	CLONAL	5	FALSE	1	0.162527937589934	2		344	254	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971132	21971132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774633329	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	18	345	0	ENST00000304494.5:c.226G>A	p.Ala76Thr	p.A76T	ENST00000304494	NM_000077.4	76	Gcc/Acc	2/3	0.162549384810443	0	FACETS	0.914	0.69	1			1	CLONAL	1	FALSE	0	0.162527937589934	0		345	203	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522532	67522532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767837787	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	24	317	0	ENST00000274335.5:c.29C>T	p.Ala10Val	p.A10V	ENST00000274335		10	gCg/gTg	1/15	0.12327385064291	0	FACETS	1	0.898	1			1	CLONAL	1	FALSE	0	0.162527937589934	0		317	197	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399991	139399991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746144524	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	156	424	0	ENST00000277541.6:c.4357G>A	p.Glu1453Lys	p.E1453K	ENST00000277541	NM_017617.3	1453	Gag/Aag	25/34	0.113497703814732	4	FACETS	0.959	0.889	1	1	0.994	1	CLONAL	6	FALSE	2	0.162527937589934	4		424	388	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144146	11144146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	8	314	1	ENST00000358026.2:c.3727C>T	p.Arg1243Trp	p.R1243W	ENST00000358026	NM_001128849.1	1243	Cgg/Tgg	26/36	0.162527937589934	5	FACETS	0.307	0.196	0.451	0.153	0.098	0.226	SUBCLONAL	1	FALSE	3	0.162527937589934	5		315	399	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141426	11141426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	61	306	0	ENST00000358026.2:c.3403C>T	p.Arg1135Trp	p.R1135W	ENST00000358026	NM_001128849.1	1135	Cgg/Tgg	25/36	0.162527937589934	5	FACETS	0.857	0.743	0.98	1	0.959	1	CLONAL	3	FALSE	3	0.162527937589934	5		306	363	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781146	161781146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531247345	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	35	331	0	ENST00000366898.1:c.1259G>A	p.Arg420His	p.R420H	ENST00000366898	NM_004562.2	420	cGc/cAc	11/12	1	2	FACETS	1	0.86	1	1	0.966	1	CLONAL	2	FALSE	1	0.162527937589934	2		331	206	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50733660	50733661	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	54	239	1	ENST00000307179.4:c.226dup	p.Arg76LysfsTer3	p.R76Kfs*3	ENST00000307179		73	-/A	3/20	1	2	FACETS	0.929	0.814	1	1	0.985	1	CLONAL	5	FALSE	1	0.162527937589934	2		240	143	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	10	928	2	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	0.162527937589934	5	FACETS	0.379	0.255	0.536	0.189	0.127	0.268	SUBCLONAL	1	FALSE	3	0.162527937589934	5		930	404	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143994	11143994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	13	284	0	ENST00000358026.2:c.3575G>A	p.Arg1192His	p.R1192H	ENST00000358026	NM_001128849.1	1192	cGc/cAc	26/36	0.162527937589934	5	FACETS	0.433	0.308	0.588	0.217	0.154	0.294	SUBCLONAL	1	FALSE	3	0.162527937589934	5		284	459	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572201	64572201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301120298	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	146	335	0	ENST00000312049.6:c.1438C>T	p.Arg480Trp	p.R480W	ENST00000312049	NM_130799.2	480	Cgg/Tgg	10/10	1	2	FACETS	1	0.961	1	1	0.994	1	CLONAL	5	FALSE	1	0.162527937589934	2		335	340	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517693	187517693	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	10	232	0	ENST00000441802.2:c.13000+1G>A		p.X4334_splice	ENST00000441802	NM_005245.3	4334			1	2	FACETS	0.715	0.485	1	0.715	0.485	1	CLONAL	1	FALSE	1	0.162527937589934	2		232	172	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223050	5223050	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	24	396	1	ENST00000357368.4:c.2753C>T	p.Ala918Val	p.A918V	ENST00000357368	NM_002850.3	918	gCc/gTc	18/38	1	2	FACETS	0.941	0.738	1	0.941	0.738	1	CLONAL	1	FALSE	1	0.162527937589934	2		397	314	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187191	11187191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	10	281	0	ENST00000361445.4:c.6227G>A	p.Arg2076Gln	p.R2076Q	ENST00000361445	NM_004958.3	2076	cGa/cAa	45/58	1	2	FACETS	0.615	0.417	0.865	0.615	0.417	0.865	SUBCLONAL	1	FALSE	1	0.162527937589934	2		281	200	SUCCESS
ALB	213	MSKCC	GRCh37	4	74283258	74283258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs78575701	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	50	277	0	ENST00000295897.4:c.1300C>T	p.Arg434Cys	p.R434C	ENST00000295897	NM_000477.5	434	Cgt/Tgt	11/15	1	2	FACETS	1	0.932	1	1	0.985	1	CLONAL	6	FALSE	1	0.162527937589934	2		277	95	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143964	11143964	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	86	247	0	ENST00000358026.2:c.3547-2A>G		p.X1183_splice	ENST00000358026	NM_001128849.1	1183			0.162527937589934	5	FACETS	0.904	0.806	1	1	0.984	1	CLONAL	4	FALSE	3	0.162527937589934	5		247	364	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426222	49426223	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0004260-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	154	423	0	ENST00000301067.7:c.12265_12266del	p.Leu4089AlafsTer17	p.L4089Afs*17	ENST00000301067	NM_003482.3	4089	CTg/g	39/54	0.113497703814732	4	FACETS	1	0.961	1	1	0.994	1	CLONAL	6	FALSE	2	0.162527937589934	4		423	349	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0007764-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	170	624	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.802245347618168	2		624	415	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412110	63412110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852216	NA	P-0007764-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	505	304	0	ENST00000330258.3:c.1057C>T	p.Arg353Ter	p.R353*	ENST00000330258	NM_152424.3	353	Cga/Tga	2/2	0.802245347618168	2	FACETS	1	0.998	1			1	CLONAL	2	TRUE	NA	0.802245347618168	2		304	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0007764-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	456	458	0	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	0.802245347618168	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.802245347618168	2		458	507	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989691	15989691	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007764-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	488	557	0	ENST00000268712.3:c.3082C>T	p.Arg1028Ter	p.R1028*	ENST00000268712	NM_006311.3	1028	Cga/Tga	23/46	0.802245347618168	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.802245347618168	2		557	568	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs539507291	NA	P-0007764-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	309	593	0	ENST00000257555.6:c.862G>A	p.Gly288Arg	p.G288R	ENST00000257555		288	Ggg/Agg	4/10	0.802245347618168	3	FACETS	1	0.986	1	0.563	0.532	0.595	CLONAL	1	TRUE	1	0.802245347618168	3		593	958	SUCCESS
APC	324	MSKCC	GRCh37	5	112174231	112174232	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0007764-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	59	535	0	ENST00000257430.4:c.2943dup	p.Ser982LeufsTer3	p.S982Lfs*3	ENST00000257430	NM_000038.5	980	-/C	16/16	1	2	FACETS	0.787	0.689	0.889	0.787	0.689	0.889	SUBCLONAL	1	TRUE	1	0.802245347618168	2		535	187	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041245	29041245	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007764-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	92	497	0	ENST00000282397.4:c.183G>T	p.Trp61Cys	p.W61C	ENST00000282397	NM_002019.4	61	tgG/tgT	3/30	0.802245347618168	4	FACETS	0.57	0.506	0.638	0.19	0.168	0.213	SUBCLONAL	1	TRUE	1	0.802245347618168	4		497	725	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374772	118374772	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007764-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	74	552	0	ENST00000534358.1:c.8165G>T	p.Gly2722Val	p.G2722V	ENST00000534358	NM_005933.3	2722	gGt/gTt	27/36	0.34194159671288	6	FACETS	1	0.927	1	0.359	0.315	0.406	INDETERMINATE	1	TRUE	3	0.802245347618168	6		552	446	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0009738-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	23	133	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.883	0.691	1	0.883	0.691	1	CLONAL	1	TRUE	1	0.21	2		133	248	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867262	68867262	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009738-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	54	530	0	ENST00000261769.5:c.2509G>T	p.Gly837Ter	p.G837*	ENST00000261769	NM_004360.3	837	Gga/Tga	16/16	1	2	FACETS	0.985	0.842	1	0.985	0.842	1	CLONAL	1	TRUE	1	0.21	2		530	522	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783230	9783230	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009738-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	39	522	0	ENST00000377346.4:c.2474T>C	p.Ile825Thr	p.I825T	ENST00000377346	NM_005026.3	825	aTt/aCt	20/24	1	2	FACETS	0.703	0.582	0.839	0.703	0.582	0.839	SUBCLONAL	1	TRUE	1	0.21	2		522	528	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864928	117864928	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs896031371	NA	P-0009738-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	33	378	0	ENST00000297338.2:c.1181C>T	p.Thr394Ile	p.T394I	ENST00000297338	NM_006265.2	394	aCa/aTa	10/14	1	2	FACETS	0.677	0.551	0.82	0.677	0.551	0.82	SUBCLONAL	1	TRUE	1	0.21	2		378	464	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2110269	2110269	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009738-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	42	442	0	ENST00000349721.2:c.3308A>C	p.Glu1103Ala	p.E1103A	ENST00000349721	NM_003070.3	1103	gAa/gCa	24/34	1	2	FACETS	0.787	0.657	0.932	0.787	0.657	0.932	CLONAL	1	TRUE	1	0.21	2		442	508	SUCCESS
AR	367	MSKCC	GRCh37	X	66931421	66931421	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009738-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	55	633	0	ENST00000374690.3:c.2063C>T	p.Ala688Val	p.A688V	ENST00000374690	NM_000044.3	688	gCt/gTt	4/8	1	2	FACETS	0.977	0.836	1	0.977	0.836	1	CLONAL	1	TRUE	1	0.21	2		633	536	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444612	78444612	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	224	258	0	ENST00000370768.2:c.77G>T	p.Gly26Val	p.G26V	ENST00000370768	NM_003902.3	26	gGa/gTa	1/20	1	2	FACETS	0.9	0.84	0.961	0.9	0.84	0.961	CLONAL	1	TRUE	1	0.605038812765273	2		258	823	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972752	25972752	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1354885963	NA	P-0009931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	328	428	0	ENST00000435504.4:c.1673T>C	p.Leu558Pro	p.L558P	ENST00000435504		558	cTt/cCt	12/13	0.605038812765273	1	FACETS	0.971	0.922	1	0.971	0.922	1	CLONAL	1	TRUE	0	0.605038812765273	1		428	779	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478137	138478137	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	213	303	0	ENST00000289153.2:c.49A>T	p.Ile17Phe	p.I17F	ENST00000289153	NM_006219.2	17	Atc/Ttc	1/22	1	2	FACETS	0.856	0.797	0.916	0.856	0.797	0.916	CLONAL	1	TRUE	1	0.605038812765273	2		303	823	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912570	32912570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	329	672	0	ENST00000380152.3:c.4078G>A	p.Asp1360Asn	p.D1360N	ENST00000380152		1360	Gat/Aat	11/27	0.605038812765273	1	FACETS	0.954	0.906	1	0.954	0.906	1	CLONAL	1	TRUE	0	0.605038812765273	1		672	795	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164859	36164859	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	180	233	0	ENST00000300305.3:c.1016T>G	p.Leu339Arg	p.L339R	ENST00000300305		339	cTg/cGg	8/8	1	2	FACETS	0.933	0.864	1	0.933	0.864	1	CLONAL	1	TRUE	1	0.605038812765273	2		233	638	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105542	27105546	+	stop_gained	Nonsense_Mutation	ONP	AATAT	AATAT	CATAG	novel	NA	P-0009931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	294	403	0	ENST00000324856.7:c.5153_5157delinsCATAG	p.Glu1718_Tyr1719delinsAlaTer	p.E1718_Y1719delinsA*	ENST00000324856	NM_006015.4	1718	gAATAT/gCATAG	20/20	1	2	FACETS	0.859	0.808	0.91	0.859	0.808	0.91	CLONAL	1	TRUE	1	0.605038812765273	2		403	1132	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444612	78444612	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009931-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	141	258	0	ENST00000370768.2:c.77G>T	p.Gly26Val	p.G26V	ENST00000370768	NM_003902.3	26	gGa/gTa	1/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		258	556	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972752	25972752	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1354885963	NA	P-0009931-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	163	428	0	ENST00000435504.4:c.1673T>C	p.Leu558Pro	p.L558P	ENST00000435504		558	cTt/cCt	12/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		428	392	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478137	138478137	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009931-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	212	303	0	ENST00000289153.2:c.49A>T	p.Ile17Phe	p.I17F	ENST00000289153	NM_006219.2	17	Atc/Ttc	1/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		303	785	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912570	32912570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009931-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	243	672	0	ENST00000380152.3:c.4078G>A	p.Asp1360Asn	p.D1360N	ENST00000380152		1360	Gat/Aat	11/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		672	598	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164859	36164859	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009931-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	271	233	0	ENST00000300305.3:c.1016T>G	p.Leu339Arg	p.L339R	ENST00000300305		339	cTg/cGg	8/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		233	926	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105542	27105546	+	stop_gained	Nonsense_Mutation	ONP	AATAT	AATAT	CATAG	novel	NA	P-0009931-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	161	403	0	ENST00000324856.7:c.5153_5157delinsCATAG	p.Glu1718_Tyr1719delinsAlaTer	p.E1718_Y1719delinsA*	ENST00000324856	NM_006015.4	1718	gAATAT/gCATAG	20/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		403	586	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321706	30321706	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009931-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	197	903	0	ENST00000322652.5:c.1561A>C	p.Lys521Gln	p.K521Q	ENST00000322652	NM_015355.2	521	Aag/Cag	13/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		903	814	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955381	48955381	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs1258442224	NA	P-0009931-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	63	87	0	ENST00000267163.4:c.1499-2A>T		p.X500_splice	ENST00000267163	NM_000321.2	500			0.680920825866195	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.680920825866195	1		87	113	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444612	78444612	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009931-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	219	258	0	ENST00000370768.2:c.77G>T	p.Gly26Val	p.G26V	ENST00000370768	NM_003902.3	26	gGa/gTa	1/20	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.680920825866195	2		258	617	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972752	25972752	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1354885963	NA	P-0009931-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	168	428	0	ENST00000435504.4:c.1673T>C	p.Leu558Pro	p.L558P	ENST00000435504		558	cTt/cCt	12/13	0.608668016980896	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.680920825866195	1		428	302	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478137	138478137	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009931-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	162	303	0	ENST00000289153.2:c.49A>T	p.Ile17Phe	p.I17F	ENST00000289153	NM_006219.2	17	Atc/Ttc	1/22	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.680920825866195	2		303	452	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912570	32912570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009931-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	107	672	0	ENST00000380152.3:c.4078G>A	p.Asp1360Asn	p.D1360N	ENST00000380152		1360	Gat/Aat	11/27	0.680920825866195	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.680920825866195	1		672	190	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164859	36164859	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009931-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	231	233	0	ENST00000300305.3:c.1016T>G	p.Leu339Arg	p.L339R	ENST00000300305		339	cTg/cGg	8/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.680920825866195	2		233	616	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105542	27105546	+	stop_gained	Nonsense_Mutation	ONP	AATAT	AATAT	CATAG	novel	NA	P-0009931-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	146	403	0	ENST00000324856.7:c.5153_5157delinsCATAG	p.Glu1718_Tyr1719delinsAlaTer	p.E1718_Y1719delinsA*	ENST00000324856	NM_006015.4	1718	gAATAT/gCATAG	20/20	1	2	FACETS	0.966	0.889	1	0.966	0.889	1	CLONAL	1	TRUE	1	0.680920825866195	2		403	444	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1720709	1721731	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTGGAAAGAGAAAGCAAATCAAGACATCATGTAAACGCTCAGAAAGAAACATTGGGAATATGGATTGCTCAATGGTAGGGCTGCAGAGAACACAGCAGGCAAAGACCAGCAAGACTGTGCTCTGGTAAGAACAGAGGGCTGGGCCGGGTGCGGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCTGACGCGGGTGGATCACCTGAGATGGGGAGTTTGAGACCAGCCTGACCAACATAGAGAAACCCCATCTATACTAAAAATACAAAATTAGCTGGGCGTGGCGGCGTGCGCCTGTAATCCCAGCTACTCAAGAGGCTGAAGCAGGAGAACTGCTTGAAACCGGGAGGCGGCGGAGGCTGCGGTGAGCCAAGATTGCACCATTGCACCCCAGCCTGGGCAACAAGAGCAAAACTCCGTCTCAAAAAAAAAAAAAAAAGGGTGGGGGGATGGGGGAGGAACTACAGGGGACTGGGATGGGAGGGGATTTGCACTGGGGAGGCACACAAACACTGTGATCTTGGACACTGTGATTACTGTCCCCAAAGAGTAGAATTTATTCCAAAGGATAGTGAGAAAGTAGTCATCACTGACAGGTGTGCATGTTGCTGTAGCTGCCAGCCATCAGGGCTAATCTCATGGAGGAAGGAGGGAAGCGGGCTGACCAAGGCTGTGGTCAGGACTGCAGCAGAGCTCTGTCCAACCAACAGATACATCCTTCTAAGTCTCCTCACAAGGCCAGGGGCTGGAAACACTGCCTAGCCATCCGCGTGCTAAAGAGGAGGGCAGGTTCCCTGGTTAGCTGTGCCCCTGACCAGTAAGGCTCTGTAACCACTGGTGGCCTGAGTTATCTTACTGTCTTTCCCCTCCAGGATCCCAACCACTGCTCAGCTGTAGAGGTGGGAACGGGGACTGGCATACAACACCCTGTGAGTATCTGTGAGACAAGTGGTCAACACAGAGAAGTTTCCCATCGGGAGTTTTCTGTATCCCCATCTGTACATGAGGTTGTATAAGGAT	CTGGAAAGAGAAAGCAAATCAAGACATCATGTAAACGCTCAGAAAGAAACATTGGGAATATGGATTGCTCAATGGTAGGGCTGCAGAGAACACAGCAGGCAAAGACCAGCAAGACTGTGCTCTGGTAAGAACAGAGGGCTGGGCCGGGTGCGGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCTGACGCGGGTGGATCACCTGAGATGGGGAGTTTGAGACCAGCCTGACCAACATAGAGAAACCCCATCTATACTAAAAATACAAAATTAGCTGGGCGTGGCGGCGTGCGCCTGTAATCCCAGCTACTCAAGAGGCTGAAGCAGGAGAACTGCTTGAAACCGGGAGGCGGCGGAGGCTGCGGTGAGCCAAGATTGCACCATTGCACCCCAGCCTGGGCAACAAGAGCAAAACTCCGTCTCAAAAAAAAAAAAAAAAGGGTGGGGGGATGGGGGAGGAACTACAGGGGACTGGGATGGGAGGGGATTTGCACTGGGGAGGCACACAAACACTGTGATCTTGGACACTGTGATTACTGTCCCCAAAGAGTAGAATTTATTCCAAAGGATAGTGAGAAAGTAGTCATCACTGACAGGTGTGCATGTTGCTGTAGCTGCCAGCCATCAGGGCTAATCTCATGGAGGAAGGAGGGAAGCGGGCTGACCAAGGCTGTGGTCAGGACTGCAGCAGAGCTCTGTCCAACCAACAGATACATCCTTCTAAGTCTCCTCACAAGGCCAGGGGCTGGAAACACTGCCTAGCCATCCGCGTGCTAAAGAGGAGGGCAGGTTCCCTGGTTAGCTGTGCCCCTGACCAGTAAGGCTCTGTAACCACTGGTGGCCTGAGTTATCTTACTGTCTTTCCCCTCCAGGATCCCAACCACTGCTCAGCTGTAGAGGTGGGAACGGGGACTGGCATACAACACCCTGTGAGTATCTGTGAGACAAGTGGTCAACACAGAGAAGTTTCCCATCGGGAGTTTTCTGTATCCCCATCTGTACATGAGGTTGTATAAGGAT	-	novel	NA	P-0009931-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	188	420	0	ENST00000378609.4:c.699+103_700-1del		p.X233_splice	ENST00000378609	NM_002074.3	233			NA	2	FACETS	0.931	0.865	0.999			1	INDETERMINATE	1	TRUE	NA	0.680920825866195	2		420	593	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351431	89351446	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGGGACCCCTTGAG	GCGGGGACCCCTTGAG	-	novel	NA	P-0009931-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	168	765	1	ENST00000301030.4:c.1504_1519del	p.Leu502TrpfsTer3	p.L502Wfs*3	ENST00000301030	NM_001256183.1	502	CTCAAGGGGTCCCCGCtg/tg	9/13	0.680920825866195	1	FACETS	0.954	0.892	1	0.954	0.892	1	CLONAL	1	TRUE	0	0.680920825866195	1		766	341	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131411	202131411	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs777784105	NA	P-0012485-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	8	572	0	ENST00000358485.4:c.379C>T	p.Arg127Ter	p.R127*	ENST00000358485	NM_001080125.1	127	Cga/Tga	2/9	1	2	FACETS	0.31	0.198	0.456	0.31	0.198	0.456	SUBCLONAL	1	TRUE	1	0.13	2		572	397	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952076	178952076	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012485-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	9	537	0	ENST00000263967.3:c.3131A>C	p.Asn1044Thr	p.N1044T	ENST00000263967	NM_006218.2	1044	aAt/aCt	21/21	1	2	FACETS	0.371	0.244	0.534	0.371	0.244	0.534	SUBCLONAL	1	TRUE	1	0.13	2		537	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0013233-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	31	886	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	1	2	FACETS	0.59	0.475	0.72	0.59	0.475	0.72	SUBCLONAL	1	TRUE	1	0.15	2		886	701	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013233-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	31	732	0	ENST00000269305.4:c.313G>T	p.Gly105Cys	p.G105C	ENST00000269305	NM_001126112.2	105	Ggc/Tgc	4/11	1	2	FACETS	0.633	0.51	0.773	0.633	0.51	0.773	SUBCLONAL	1	TRUE	1	0.15	2		732	653	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0013233-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	37	741	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	1	2	FACETS	0.872	0.717	1	0.872	0.717	1	CLONAL	1	TRUE	1	0.15	2		741	566	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485953	8485953	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763256154	NA	P-0013233-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	32	197	0	ENST00000356435.5:c.2864C>T	p.Thr955Ile	p.T955I	ENST00000356435		955	aCc/aTc	17/35	1	2	FACETS	0.882	0.715	1	0.882	0.715	1	CLONAL	1	TRUE	1	0.15	2		197	484	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541548	29541549	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013233-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	19	33	0	ENST00000356175.3:c.1473dup	p.Leu492SerfsTer19	p.L492Sfs*19	ENST00000356175	NM_000267.3	491	tat/taTt	13/57	1	2	FACETS	0.802	0.613	1	1	0.919	1	CLONAL	2	TRUE	1	0.15	2		33	158	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124499058	124499058	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013233-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	27	70	0	ENST00000357628.3:c.655G>T	p.Asp219Tyr	p.D219Y	ENST00000357628	NM_015450.2	219	Gac/Tac	9/19	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.15	2		70	247	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101909985	101909985	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013233-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	35	90	0	ENST00000374994.4:c.1307del	p.Pro436HisfsTer6	p.P436Hfs*6	ENST00000374994	NM_004612.2	435	gaC/ga	8/9	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.15	2		90	351	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0013855-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	277	232	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.878119684906792	4	FACETS	0.951	0.901	1	0.951	0.901	1	CLONAL	2	TRUE	2	0.874616089225494	4		232	624	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0013855-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	195	597	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.878119684906792	4	FACETS	0.994	0.921	1	0.497	0.46	0.535	CLONAL	1	TRUE	2	0.874616089225494	4		597	841	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249092	55249092	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013855-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	213	603	0	ENST00000275493.2:c.2390G>C	p.Cys797Ser	p.C797S	ENST00000275493	NM_005228.3	797	tGc/tCc	20/28	0.878119684906792	4	FACETS	1	0.974	1	0.547	0.509	0.586	CLONAL	1	TRUE	2	0.874616089225494	4		603	835	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803613	1803613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778773	NA	P-0013855-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	197	639	0	ENST00000260795.2:c.791C>T	p.Thr264Met	p.T264M	ENST00000260795		264	aCg/aTg	6/17	0.878119684906792	4	FACETS	1	0.981	1	0.581	0.539	0.624	CLONAL	1	TRUE	2	0.874616089225494	4		639	727	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508644	106508644	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013855-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	151	526	0	ENST00000359195.3:c.638A>T	p.Lys213Met	p.K213M	ENST00000359195	NM_002649.2	213	aAg/aTg	2/11	0.878119684906792	4	FACETS	0.981	0.899	1	0.49	0.449	0.533	CLONAL	1	TRUE	2	0.874616089225494	4		526	660	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592144	55592144	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019864-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	111	278	0	ENST00000288135.5:c.1468G>C	p.Glu490Gln	p.E490Q	ENST00000288135	NM_000222.2	490	Gaa/Caa	9/21	1	2	FACETS	0.961	0.868	1	0.961	0.868	1	CLONAL	1	TRUE	1	0.464018760016311	2		278	498	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023101	1023101	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019864-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	146	332	0	ENST00000358495.3:c.1154C>A	p.Ser385Tyr	p.S385Y	ENST00000358495	NM_134424.2	385	tCt/tAt	11/12	1	2	FACETS	0.989	0.906	1	0.989	0.906	1	CLONAL	1	TRUE	1	0.464018760016311	2		332	636	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243525	46243533	+	inframe_deletion	In_Frame_Del	DEL	TGTTCCTGA	TGTTCCTGA	-	novel	NA	P-0019864-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	130	306	0	ENST00000334344.6:c.1881_1889del	p.Pro628_Val630del	p.P628_V630del	ENST00000334344	NM_152641.2	626	tcTGTTCCTGAt/tct	14/21	1	2	FACETS	0.985	0.897	1	0.985	0.897	1	CLONAL	1	TRUE	1	0.464018760016311	2		306	569	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873943	151873948	+	frameshift_variant	Frame_Shift_Del	DEL	TCCATC	TCCATC	CCATT	novel	NA	P-0019864-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	141	407	1	ENST00000262189.6:c.8590_8595delinsAATGG	p.Asp2864AsnfsTer42	p.D2864Nfs*42	ENST00000262189	NM_170606.2	2864	GATGGA/AATGG	38/59	0.334028507166247	3	FACETS	1	0.921	1	0.505	0.461	0.552	CLONAL	1	TRUE	1	0.464018760016311	3		408	741	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	67	446	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.986	0.865	1	0.986	0.865	1	CLONAL	1	TRUE	1	0.457393321580075	2		446	297	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0022366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	103	372	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.457393321580075	3	FACETS	0.9	0.807	0.998	0.45	0.403	0.499	CLONAL	1	TRUE	1	0.457393321580075	3		372	615	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121013	29121013	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786203973	NA	P-0022366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	87	351	0	ENST00000328354.6:c.544C>T	p.Pro182Ser	p.P182S	ENST00000328354	NM_007194.3	182	Cct/Tct	4/15	1	2	FACETS	0.829	0.737	0.926	0.829	0.737	0.926	CLONAL	1	TRUE	1	0.457393321580075	2		351	459	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717613	89717613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	88	286	0	ENST00000371953.3:c.638C>T	p.Pro213Leu	p.P213L	ENST00000371953	NM_000314.4	213	cCt/cTt	7/9	1	2	FACETS	0.948	0.845	1	0.948	0.845	1	CLONAL	1	TRUE	1	0.457393321580075	2		286	406	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923440	9923440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	97	424	0	ENST00000330684.3:c.1847C>T	p.Ser616Phe	p.S616F	ENST00000330684	NM_001134407.1	616	tCc/tTc	9/13	1	2	FACETS	0.86	0.77	0.955	0.86	0.77	0.955	CLONAL	1	TRUE	1	0.457393321580075	2		424	493	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346770	89346771	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0022366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	108	469	0	ENST00000301030.4:c.6179_6180delinsTT	p.Ser2060Phe	p.S2060F	ENST00000301030	NM_001256183.1	2060	tCC/tTT	9/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.457393321580075	2		469	408	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518553	69518554	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0022366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	68	410	0	ENST00000294312.3:c.91_92delinsAA	p.Gly31Lys	p.G31K	ENST00000294312	NM_005117.2	31	GGg/AAg	1/3	1	2	FACETS	0.898	0.787	1	0.898	0.787	1	CLONAL	1	TRUE	1	0.457393321580075	2		410	331	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425470	49425471	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0022366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	121	627	0	ENST00000301067.7:c.13017_13018delinsTT	p.His4340Tyr	p.H4340Y	ENST00000301067	NM_003482.3	4339	acCCat/acTTat	39/54	1	2	FACETS	0.941	0.854	1	0.941	0.854	1	CLONAL	1	TRUE	1	0.457393321580075	2		627	562	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410150	63410150	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1473629829	NA	P-0022366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	124	262	0	ENST00000330258.3:c.3017C>T	p.Ser1006Leu	p.S1006L	ENST00000330258	NM_152424.3	1006	tCa/tTa	2/2	1	1	FACETS	0.882	0.817	0.947	1	0.991	1	CLONAL	2	TRUE	0	0.457393321580075	1		262	237	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770576	40770576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	96	436	0	ENST00000373198.4:c.2806C>T	p.Arg936Ter	p.R936*	ENST00000373198	NM_133170.3	936	Cga/Tga	19/32	NA	2	FACETS	1	0.902	1			1	INDETERMINATE	1	TRUE	NA	0.457393321580075	2		436	417	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376665	8376665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753080783	NA	P-0022366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	105	399	0	ENST00000356435.5:c.4448C>T	p.Thr1483Met	p.T1483M	ENST00000356435		1483	aCg/aTg	27/35	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.457393321580075	2		399	435	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509660	106509660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757849968	NA	P-0022366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	117	456	0	ENST00000359195.3:c.1654C>T	p.Arg552Cys	p.R552C	ENST00000359195	NM_002649.2	552	Cgc/Tgc	2/11	0.457393321580075	3	FACETS	0.987	0.892	1	0.493	0.446	0.544	CLONAL	1	TRUE	1	0.457393321580075	3		456	637	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633421	8633421	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	101	381	0	ENST00000356435.5:c.248G>A	p.Arg83Lys	p.R83K	ENST00000356435		83	aGa/aAa	3/35	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.457393321580075	2		381	426	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420043	41420043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	119	494	0	ENST00000373198.4:c.278C>T	p.Pro93Leu	p.P93L	ENST00000373198	NM_133170.3	93	cCa/cTa	3/32	NA	2	FACETS	1	0.94	1			1	INDETERMINATE	1	TRUE	NA	0.457393321580075	2		494	497	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228783	36228783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	128	536	0	ENST00000222270.7:c.7682C>T	p.Pro2561Leu	p.P2561L	ENST00000222270	NM_014727.1	2561	cCc/cTc	35/37	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.457393321580075	2		536	531	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518079	176518080	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0022366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	110	504	0	ENST00000292408.4:c.577_578delinsAA	p.Gly193Lys	p.G193K	ENST00000292408	NM_213647.1	193	GGg/AAg	5/18	1	2	FACETS	0.986	0.89	1	0.986	0.89	1	CLONAL	1	TRUE	1	0.457393321580075	2		504	488	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860562	45860562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	75	485	0	ENST00000391945.4:c.1445C>T	p.Thr482Ile	p.T482I	ENST00000391945	NM_000400.3	482	aCc/aTc	15/23	1	2	FACETS	0.73	0.642	0.824	0.73	0.642	0.824	SUBCLONAL	1	TRUE	1	0.457393321580075	2		485	449	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540320	23540320	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	78	492	0	ENST00000380871.4:c.83C>T	p.Ser28Phe	p.S28F	ENST00000380871	NM_006167.3	28	tCc/tTc	1/2	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.457393321580075	2		492	338	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674159	117674159	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	105	366	0	ENST00000368508.3:c.4315T>A	p.Phe1439Ile	p.F1439I	ENST00000368508	NM_002944.2	1439	Ttt/Att	26/43	0.190394279195787	1	FACETS	0.864	0.78	0.952	0.864	0.78	0.952	INDETERMINATE	1	TRUE	0	0.457393321580075	1		366	410	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33687342	33687342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	111	409	0	ENST00000308377.4:c.1118G>A	p.Ser373Asn	p.S373N	ENST00000308377	NM_152270.3	373	aGt/aAt	3/5	0.457393321580075	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.457393321580075	1		409	366	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86545058	86545058	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	104	425	0	ENST00000262426.4:c.883C>T	p.Pro295Ser	p.P295S	ENST00000262426	NM_001451.2	295	Ccc/Tcc	1/2	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.457393321580075	2		425	410	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950433	68950433	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	140	396	0	ENST00000288368.4:c.745T>A	p.Cys249Ser	p.C249S	ENST00000288368	NM_024870.2	249	Tgt/Agt	7/40	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.457393321580075	2		396	453	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914938	32914938	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	119	432	0	ENST00000380152.3:c.6446T>A	p.Ile2149Asn	p.I2149N	ENST00000380152		2149	aTt/aAt	11/27	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.457393321580075	2		432	490	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581214	48581215	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0022366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	119	440	0	ENST00000342988.3:c.518_519delinsTT	p.Ser173Phe	p.S173F	ENST00000342988	NM_005359.5	173	tCC/tTT	5/12	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.457393321580075	2		440	473	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151866295	151866295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	93	309	0	ENST00000262189.6:c.9493C>T	p.Pro3165Ser	p.P3165S	ENST00000262189	NM_170606.2	3165	Cca/Tca	41/59	0.457393321580075	3	FACETS	1	0.904	1	0.507	0.452	0.565	CLONAL	1	TRUE	1	0.457393321580075	3		309	493	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235935	108235935	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770641163	NA	P-0022822-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	19	559	1	ENST00000278616.4:c.8977C>T	p.Arg2993Ter	p.R2993*	ENST00000278616	NM_000051.3	2993	Cga/Tga	62/63	1	2	FACETS	0.457	0.347	0.587	0.457	0.347	0.587	SUBCLONAL	1	FALSE	1	0.289474802076284	2		560	287	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436306	110436306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022822-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	52	749	4	ENST00000375856.3:c.2095G>A	p.Ala699Thr	p.A699T	ENST00000375856	NM_003749.2	699	Gcc/Acc	1/2	1	2	FACETS	0.474	0.402	0.553	0.474	0.402	0.553	SUBCLONAL	1	FALSE	1	0.289474802076284	2		753	758	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs869025608	NA	P-0022822-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	45	509	0	ENST00000307102.5:c.171G>T	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaT	2/11	1	2	FACETS	0.589	0.495	0.693	0.589	0.495	0.693	SUBCLONAL	1	FALSE	1	0.289474802076284	2		509	528	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436002	56436002	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1366537134	NA	P-0022822-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	130	730	0	ENST00000407977.2:c.1135C>T	p.Gln379Ter	p.Q379*	ENST00000407977		379	Cag/Tag	9/10	0.289474802076284	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	0	0.289474802076284	1		730	668	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289907	15289907	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265324934	NA	P-0022822-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	53	461	0	ENST00000263388.2:c.3647C>T	p.Ala1216Val	p.A1216V	ENST00000263388	NM_000435.2	1216	gCg/gTg	22/33	1	2	FACETS	0.494	0.42	0.575	0.494	0.42	0.575	SUBCLONAL	1	FALSE	1	0.289474802076284	2		461	741	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022822-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	18	469	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	0.527	0.397	0.679	0.527	0.397	0.679	SUBCLONAL	1	FALSE	1	0.289474802076284	2		469	236	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106709	27106709	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022822-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	71	666	0	ENST00000324856.7:c.6320G>A	p.Gly2107Asp	p.G2107D	ENST00000324856	NM_006015.4	2107	gGc/gAc	20/20	1	2	FACETS	0.678	0.591	0.771	0.678	0.591	0.771	SUBCLONAL	1	FALSE	1	0.289474802076284	2		666	724	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163456	108163456	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1565461434	NA	P-0022822-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	14	496	0	ENST00000278616.4:c.4547A>G	p.His1516Arg	p.H1516R	ENST00000278616	NM_000051.3	1516	cAt/cGt	30/63	1	2	FACETS	0.504	0.365	0.671	0.504	0.365	0.671	SUBCLONAL	1	FALSE	1	0.289474802076284	2		496	192	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779647	3779647	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022822-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	71	657	0	ENST00000262367.5:c.5401G>T	p.Val1801Leu	p.V1801L	ENST00000262367	NM_004380.2	1801	Gtg/Ttg	31/31	1	2	FACETS	0.756	0.66	0.86	0.756	0.66	0.86	SUBCLONAL	1	FALSE	1	0.289474802076284	2		657	649	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209201	36209201	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022822-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	65	708	2	ENST00000222270.7:c.281G>A	p.Gly94Glu	p.G94E	ENST00000222270	NM_014727.1	94	gGa/gAa	1/37	1	2	FACETS	0.803	0.697	0.919	0.803	0.697	0.919	CLONAL	1	FALSE	1	0.289474802076284	2		710	559	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451797	29451797	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022822-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	20	245	0	ENST00000389048.3:c.2768G>T	p.Gly923Val	p.G923V	ENST00000389048	NM_004304.4	923	gGg/gTg	16/29	1	2	FACETS	0.555	0.425	0.706	0.555	0.425	0.706	SUBCLONAL	1	FALSE	1	0.289474802076284	2		245	249	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873711	35873711	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022822-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	16	491	0	ENST00000303115.3:c.667A>C	p.Ser223Arg	p.S223R	ENST00000303115	NM_002185.3	223	Agt/Cgt	5/8	1	2	FACETS	0.509	0.377	0.667	0.509	0.377	0.667	SUBCLONAL	1	FALSE	1	0.289474802076284	2		491	217	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589634	67589634	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0022822-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	16	286	0	ENST00000274335.5:c.1397T>A	p.Leu466Ter	p.L466*	ENST00000274335		466	tTa/tAa	10/15	1	2	FACETS	0.666	0.495	0.868	0.666	0.495	0.868	SUBCLONAL	1	FALSE	1	0.289474802076284	2		286	166	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43749759	43749759	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022822-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	49	594	0	ENST00000523873.1:c.612T>G	p.Cys204Trp	p.C204W	ENST00000523873		204	tgT/tgG	7/8	1	2	FACETS	0.585	0.495	0.684	0.585	0.495	0.684	SUBCLONAL	1	FALSE	1	0.289474802076284	2		594	579	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13949320	13949320	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs756408088	NA	P-0022822-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	16	429	0	ENST00000405192.2:c.808A>G	p.Met270Val	p.M270V	ENST00000405192	NM_001163147.1	270	Atg/Gtg	9/12	1	2	FACETS	0.496	0.367	0.649	0.496	0.367	0.649	SUBCLONAL	1	FALSE	1	0.289474802076284	2		429	223	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242038	105242038	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023375-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	100	196	0	ENST00000349310.3:c.386C>T	p.Ser129Leu	p.S129L	ENST00000349310	NM_001014432.1	129	tCa/tTa	6/15	1	2	FACETS	0.955	0.857	1	0.955	0.857	1	CLONAL	1	TRUE	1	0.438177510886101	2		196	478	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457249	25457249	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs775365749	NA	P-0023375-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	51	148	0	ENST00000264709.3:c.2638A>G	p.Met880Val	p.M880V	ENST00000264709	NM_175629.2	880	Atg/Gtg	23/23	1	2	FACETS	0.446	0.379	0.52	0.446	0.379	0.52	SUBCLONAL	1	TRUE	1	0.438177510886101	2		148	522	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38981989	38981989	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023375-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	113	272	0	ENST00000357387.3:c.733C>T	p.Arg245Ter	p.R245*	ENST00000357387	NM_152756.3	245	Cga/Tga	8/38	0.438177510886101	3	FACETS	0.986	0.889	1	0.329	0.296	0.363	CLONAL	1	TRUE	0	0.438177510886101	3		272	638	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129719	30129719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1379935159	NA	P-0023375-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	135	195	0	ENST00000263025.4:c.494G>A	p.Arg165Gln	p.R165Q	ENST00000263025	NM_002746.2	165	cGa/cAa	3/9	0.380625831396928	3	FACETS	1	0.976	1	0.601	0.548	0.657	CLONAL	1	TRUE	1	0.438177510886101	3		195	625	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004919	16004919	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023375-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	50	178	0	ENST00000268712.3:c.2335A>T	p.Ser779Cys	p.S779C	ENST00000268712	NM_006311.3	779	Agt/Tgt	20/46	0.438177510886101	1	FACETS	0.407	0.346	0.474	0.407	0.346	0.474	SUBCLONAL	1	TRUE	0	0.438177510886101	1		178	438	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786466	135786481	+	frameshift_variant	Frame_Shift_Del	DEL	ATACCACAAACCATAG	ATACCACAAACCATAG	-	novel	NA	P-0023375-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	50	151	0	ENST00000298552.3:c.1049_1064del	p.Ser350Ter	p.S350*	ENST00000298552	NM_001162426.1	350	tCTATGGTTTGTGGTATg/tg	11/23	1	2	FACETS	0.445	0.377	0.519	0.445	0.377	0.519	SUBCLONAL	1	TRUE	1	0.438177510886101	2		151	513	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022685	31022685	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023375-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	38	201	0	ENST00000375687.4:c.2170del	p.Leu724Ter	p.L724*	ENST00000375687	NM_015338.5	724	Ctg/tg	13/13	1	2	FACETS	0.342	0.282	0.409	0.342	0.282	0.409	SUBCLONAL	1	TRUE	1	0.438177510886101	2		201	507	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216319	2216319	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023375-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	93	191	0	ENST00000398665.3:c.1963G>A	p.Glu655Lys	p.E655K	ENST00000398665	NM_032482.2	655	Gag/Aag	20/28	0.438177510886101	1	FACETS	0.913	0.819	1	0.913	0.819	1	CLONAL	1	TRUE	0	0.438177510886101	1		191	363	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903703	41903703	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	ACA	novel	NA	P-0023375-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	104	192	0	ENST00000372991.4:c.854delinsTGT	p.Thr285MetfsTer2	p.T285Mfs*2	ENST00000372991	NM_001760.3	285	aCa/aTGTa	5/5	1	2	FACETS	0.924	0.83	1	0.924	0.83	1	CLONAL	1	TRUE	1	0.438177510886101	2		192	514	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53253908	53253928	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCCCCGGGGCTTACCGCGGGT	GCCCCGGGGCTTACCGCGGGT	CCCCGGCCCCG	novel	NA	P-0023375-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	77	119	2	ENST00000375401.3:c.144_150+14delinsCGGGGCCGGGG		p.X48_splice	ENST00000375401	NM_004187.3	48		1/26	0.438177510886101	1	FACETS	0.943	0.837	1	0.943	0.837	1	CLONAL	1	TRUE	0	0.438177510886101	1		121	291	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097738	8097738	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024534-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	118	668	0	ENST00000346208.3:c.120G>C	p.Gln40His	p.Q40H	ENST00000346208		40	caG/caC	2/6	0.836747585513195	3	FACETS	0.839	0.761	0.92	0.419	0.38	0.46	CLONAL	1	TRUE	1	0.836747585513195	3		668	477	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857926	9857926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024534-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	129	599	2	ENST00000330684.3:c.3475C>T	p.Arg1159Cys	p.R1159C	ENST00000330684	NM_001134407.1	1159	Cgc/Tgc	13/13	0.45885155031234	3	FACETS	0.957	0.874	1			1	INDETERMINATE	1	TRUE	NA	0.836747585513195	3		601	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0024534-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	282	543	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.807000084515482	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.836747585513195	2		543	333	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78617593	78617593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024534-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	133	470	0	ENST00000306801.3:c.331G>A	p.Glu111Lys	p.E111K	ENST00000306801	NM_020761.2	111	Gag/Aag	3/34	0.659346249978319	3	FACETS	0.81	0.738	0.884	0.405	0.369	0.442	CLONAL	1	TRUE	1	0.836747585513195	3		470	557	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026357-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	110	446	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.925	0.839	1	0.925	0.839	1	CLONAL	1	TRUE	1	0.655223032423469	2		446	363	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476265	88476265	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026357-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	168	408	0	ENST00000360948.2:c.1867G>A	p.Gly623Arg	p.G623R	ENST00000360948	NM_001012338.2	623	Gga/Aga	15/19	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.655223032423469	2		408	467	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290241	15290241	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026357-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	215	557	0	ENST00000263388.2:c.3394del	p.Gln1132SerfsTer140	p.Q1132Sfs*140	ENST00000263388	NM_000435.2	1132	Cag/ag	21/33	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.655223032423469	2		557	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0026942-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	326	425	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.581715682145979	3	FACETS	0.961	0.926	0.996	0.961	0.926	0.996	CLONAL	3	TRUE	0	0.629723789207755	3		425	472	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0026942-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	8136	335	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.629723789207755	65	FACETS	1	0.998	1			1	CLONAL	64	TRUE	NA	0.629723789207755	65		335	8394	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14628978	14628978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026942-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	162	670	0	ENST00000254322.2:c.184G>A	p.Glu62Lys	p.E62K	ENST00000254322	NM_006145.1	62	Gag/Aag	1/3	0.592636342226683	3	FACETS	0.87	0.799	0.943	0.29	0.266	0.315	CLONAL	1	TRUE	0	0.629723789207755	3		670	778	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975444	13975444	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026942-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	63	494	0	ENST00000405192.2:c.443T>C	p.Leu148Pro	p.L148P	ENST00000405192	NM_001163147.1	148	cTg/cCg	7/12	0.629384018691057	4	FACETS	0.469	0.405	0.539	0.156	0.135	0.18	SUBCLONAL	1	TRUE	1	0.629723789207755	4		494	695	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953210	81953210	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026942-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	112	434	0	ENST00000359376.3:c.2176T>A	p.Tyr726Asn	p.Y726N	ENST00000359376	NM_002661.3	726	Tac/Aac	20/33	0.594354888735508	4	FACETS	0.923	0.832	1	0.231	0.208	0.255	CLONAL	1	TRUE	0	0.629723789207755	4		434	628	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251205	251205	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026942-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	87	189	0	ENST00000264932.6:c.1650G>C	p.Lys550Asn	p.K550N	ENST00000264932	NM_004168.2	550	aaG/aaC	12/15	0.629723789207755	6	FACETS	0.91	0.813	1			1	CLONAL	2	TRUE	NA	0.629723789207755	6		189	343	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348923	11348923	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026942-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	125	535	1	ENST00000332029.2:c.413A>G	p.Asp138Gly	p.D138G	ENST00000332029	NM_003745.1	138	gAt/gGt	2/2	0.602890305467599	4	FACETS	0.916	0.831	1	0.229	0.207	0.252	CLONAL	1	TRUE	0	0.629723789207755	4		536	706	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112425	115112425	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1443972149	NA	P-0026942-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	34	620	0	ENST00000257566.3:c.1315C>T	p.Pro439Ser	p.P439S	ENST00000257566	NM_016569.3	439	Ccc/Tcc	7/8	0.600887738814948	2	FACETS	0.277	0.226	0.334	0.138	0.113	0.167	SUBCLONAL	1	TRUE	0	0.629723789207755	2		620	390	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335661	81335661	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026942-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	105	413	0	ENST00000222390.5:c.1699G>C	p.Val567Leu	p.V567L	ENST00000222390	NM_000601.4	567	Gtt/Ctt	15/18	0.583785964610603	4	FACETS	0.983	0.883	1	0.328	0.294	0.363	CLONAL	1	TRUE	1	0.629723789207755	4		413	553	SUCCESS
APC	324	MSKCC	GRCh37	5	112179687	112179687	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026942-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	115	601	0	ENST00000257430.4:c.8396C>A	p.Ser2799Ter	p.S2799*	ENST00000257430	NM_000038.5	2799	tCa/tAa	16/16	1	2	FACETS	0.838	0.76	0.919	0.838	0.76	0.919	CLONAL	1	TRUE	1	0.629723789207755	2		601	436	SUCCESS
APC	324	MSKCC	GRCh37	5	112179638	112179639	+	missense_variant	Missense_Mutation	DNP	CC	CC	TG	novel	NA	P-0026942-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	104	560	0	ENST00000257430.4:c.8347_8348delinsTG	p.Pro2783Cys	p.P2783C	ENST00000257430	NM_000038.5	2783	CCt/TGt	16/16	1	2	FACETS	0.86	0.777	0.947	0.86	0.777	0.947	CLONAL	1	TRUE	1	0.629723789207755	2		560	384	SUCCESS
APC	324	MSKCC	GRCh37	5	112179776	112179776	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026942-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	110	523	0	ENST00000257430.4:c.8485C>G	p.Gln2829Glu	p.Q2829E	ENST00000257430	NM_000038.5	2829	Caa/Gaa	16/16	1	2	FACETS	0.987	0.896	1	0.987	0.896	1	CLONAL	1	TRUE	1	0.629723789207755	2		523	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576890	7576890	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028171-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	602	548	0	ENST00000269305.4:c.956del	p.Lys319ArgfsTer26	p.K319Rfs*26	ENST00000269305	NM_001126112.2	319	aAg/ag	9/11	0.929631787515148	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.929631787515148	2		548	630	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047489	49047505	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGACAGAATCTTAGTA	TTGACAGAATCTTAGTA	-	novel	NA	P-0028171-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	183	254	0	ENST00000267163.4:c.2490-6_2500del		p.X830_splice	ENST00000267163	NM_000321.2	830		24/27	0.929631787515148	2	FACETS	0.97	0.941	0.995	0.97	0.941	0.995	CLONAL	2	TRUE	0	0.929631787515148	2		254	203	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89865607	89865607	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028171-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	227	423	0	ENST00000389301.3:c.860A>G	p.Glu287Gly	p.E287G	ENST00000389301	NM_000135.2	287	gAg/gGg	10/43	0.929631787515148	2	FACETS	0.913	0.859	0.968	0.456	0.429	0.484	CLONAL	1	TRUE	0	0.929631787515148	2		423	535	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871916	45871916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028171-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	252	362	0	ENST00000391945.4:c.332C>T	p.Ser111Phe	p.S111F	ENST00000391945	NM_000400.3	111	tCc/tTc	5/23	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.929631787515148	2		362	492	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026066	48026066	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs63750491	NA	P-0028171-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	299	505	0	ENST00000234420.5:c.944C>G	p.Ser315Cys	p.S315C	ENST00000234420	NM_000179.2	315	tCt/tGt	4/10	0.929631787515148	2	FACETS	1	0.981	1	0.532	0.505	0.558	CLONAL	1	TRUE	0	0.929631787515148	2		505	605	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12393170	12393170	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028171-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	394	377	0	ENST00000287820.6:c.79C>T	p.Gln27Ter	p.Q27*	ENST00000287820	NM_015869.4	27	Caa/Taa	1/7	0.929631787515148	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.929631787515148	2		377	409	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643764	52643764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028171-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	194	414	0	ENST00000394830.3:c.2132G>A	p.Ser711Asn	p.S711N	ENST00000394830	NM_018313.4	711	aGt/aAt	17/30	0.929631787515148	2	FACETS	0.959	0.899	1	0.48	0.449	0.511	CLONAL	1	TRUE	0	0.929631787515148	2		414	435	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629397	187629397	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028171-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	242	502	0	ENST00000441802.2:c.1585C>A	p.Leu529Met	p.L529M	ENST00000441802	NM_005245.3	529	Ctg/Atg	2/27	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.929631787515148	2		502	473	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	896781	896781	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028171-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	203	381	0	ENST00000166345.3:c.260C>T	p.Pro87Leu	p.P87L	ENST00000166345	NM_004237.3	87	cCc/cTc	3/13	0.929631787515148	5	FACETS	1	0.942	1	0.255	0.236	0.275	CLONAL	1	TRUE	1	0.929631787515148	5		381	1026	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150921872	150921872	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1482999278	NA	P-0028171-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	247	445	0	ENST00000271640.5:c.1451G>A	p.Arg484Gln	p.R484Q	ENST00000271640	NM_001145415.1	484	cGg/cAg	12/22	0.913643649288082	4	FACETS	1	0.97	1	0.531	0.496	0.566	CLONAL	1	TRUE	2	0.929631787515148	4		445	966	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281552	49281554	+	missense_variant	Missense_Mutation	TNP	CCA	CCA	GCT	novel	NA	P-0028171-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	217	472	0	ENST00000282018.3:c.599_601delinsGCT	p.Thr200_Met201delinsSerLeu	p.T200_M201delinsSL	ENST00000282018	NM_020377.2	200	aCCAtg/aGCTtg	1/1	0.929631787515148	2	FACETS	0.979	0.921	1	0.489	0.46	0.519	CLONAL	1	TRUE	0	0.929631787515148	2		472	477	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442069	52442081	+	frameshift_variant	Frame_Shift_Del	DEL	GAGTTGCACAAGA	GAGTTGCACAAGA	-	novel	NA	P-0028707-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	228	561	0	ENST00000460680.1:c.268_280del	p.Ser90MetfsTer4	p.S90Mfs*4	ENST00000460680	NM_004656.3	90	TCTTGTGCAACTCat/at	5/17	0.723328946546416	1	FACETS	0.882	0.833	0.932	0.882	0.833	0.932	CLONAL	1	TRUE	0	0.723328946546416	1		561	456	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0028707-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	159	286	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.723328946546416	2		286	375	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0029532-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	152	232	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.179516065532802	3	FACETS	1	0.961	1	0.717	0.659	0.777	CLONAL	2	TRUE	0	0.29	3		232	558	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0029532-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	31	372	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.300259069393855	3	FACETS	0.394	0.317	0.481			1	SUBCLONAL	1	TRUE	NA	0.29	3		372	622	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0029532-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	119	486	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	0.222019261943405	2	FACETS	1	0.983	1	0.706	0.639	0.776	CLONAL	1	TRUE	0	0.29	2		486	581	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560493	65560493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029532-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	38	372	0	ENST00000358664.4:c.104G>T	p.Arg35Leu	p.R35L	ENST00000358664	NM_002382.4	35	cGt/cTt	3/5	1	2	FACETS	0.496	0.41	0.593	0.496	0.41	0.593	SUBCLONAL	1	TRUE	1	0.29	2		372	528	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165688	47165688	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029532-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	162	557	0	ENST00000409792.3:c.438A>T	p.Lys146Asn	p.K146N	ENST00000409792	NM_014159.6	146	aaA/aaT	3/21	0.222019261943405	2	FACETS	0.796	0.732	0.862	0.796	0.732	0.862	SUBCLONAL	2	TRUE	0	0.29	2		557	702	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017736	31017736	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368981019	NA	P-0029532-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	33	335	0	ENST00000375687.4:c.598G>A	p.Gly200Ser	p.G200S	ENST00000375687	NM_015338.5	200	Ggc/Agc	8/13	0.300259069393855	4	FACETS	0.453	0.368	0.55			1	SUBCLONAL	1	TRUE	NA	0.29	4		335	648	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163711	32163712	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029532-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	75	500	0	ENST00000375023.3:c.5514_5515insA	p.Pro1839ThrfsTer77	p.P1839Tfs*77	ENST00000375023	NM_004557.3	1838	-/A	30/30	0.235543311017206	4	FACETS	0.761	0.665	0.864	0.38	0.332	0.432	SUBCLONAL	1	TRUE	2	0.29	4		500	877	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151167739	151167739	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0029532-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	29	313	0	ENST00000262187.5:c.381-1G>A		p.X127_splice	ENST00000262187	NM_005614.3	127			NA	2	FACETS	0.442	0.354	0.542			1	INDETERMINATE	1	TRUE	NA	0.29	2		313	453	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031999	26031999	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1411351920	NA	P-0029532-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	105	653	0	ENST00000244661.2:c.290G>C	p.Cys97Ser	p.C97S	ENST00000244661	NM_003537.3	97	tGt/tCt	1/1	0.235543311017206	4	FACETS	0.907	0.811	1	0.453	0.405	0.505	CLONAL	1	TRUE	2	0.29	4		653	1030	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578189	7578189	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0031827-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	316	453	0	ENST00000269305.4:c.660T>G	p.Tyr220Ter	p.Y220*	ENST00000269305	NM_001126112.2	220	taT/taG	6/11	0.533407789297439	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.533407789297439	2		453	579	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759697	133759697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776289598	NA	P-0031827-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	254	474	0	ENST00000318560.5:c.2020C>T	p.Arg674Trp	p.R674W	ENST00000318560	NM_005157.4	674	Cgg/Tgg	11/11	0.533407789297439	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.533407789297439	2		474	469	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098898	47098898	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031827-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	335	483	0	ENST00000409792.3:c.6376G>T	p.Glu2126Ter	p.E2126*	ENST00000409792	NM_014159.6	2126	Gag/Tag	15/21	0.533407789297439	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.533407789297439	3		483	750	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163374	47163387	+	frameshift_variant	Frame_Shift_Del	DEL	AACTTTTTTTACTC	AACTTTTTTTACTC	-	novel	NA	P-0031827-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	106	447	0	ENST00000409792.3:c.2739_2752del	p.Lys913AsnfsTer17	p.K913Nfs*17	ENST00000409792	NM_014159.6	913	aaGAGTAAAAAAAGTTca/aaca	3/21	0.533407789297439	3	FACETS	0.8	0.719	0.887	0.4	0.359	0.444	SUBCLONAL	1	TRUE	1	0.533407789297439	3		447	629	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068292	30068292	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1274583081	NA	P-0031827-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	78	288	0	ENST00000331968.5:c.2107G>A	p.Val703Ile	p.V703I	ENST00000331968	NM_002742.2	703	Gtt/Att	15/18	0.533407789297439	3	FACETS	0.936	0.827	1	0.468	0.413	0.526	CLONAL	1	TRUE	1	0.533407789297439	3		288	396	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218413	133218413	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031827-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	119	429	0	ENST00000320574.5:c.5198A>T	p.Asn1733Ile	p.N1733I	ENST00000320574	NM_006231.2	1733	aAc/aTc	39/49	0.533407789297439	3	FACETS	1	0.921	1	0.509	0.461	0.559	CLONAL	1	TRUE	1	0.533407789297439	3		429	555	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0032151-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	448	405	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.539577895468308	3	FACETS	0.994	0.955	1	0.994	0.955	1	CLONAL	2	TRUE	1	0.728804878036445	3		405	844	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0032151-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	52	363	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	0.161	0.136	0.188	0.161	0.136	0.188	SUBCLONAL	1	TRUE	1	0.728804878036445	2		363	887	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119789	70119789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778047936	NA	P-0032151-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	47	331	0	ENST00000245479.2:c.791G>A	p.Arg264Lys	p.R264K	ENST00000245479	NM_000346.3	264	aGa/aAa	3/3	1	2	FACETS	0.222	0.187	0.261	0.222	0.187	0.261	SUBCLONAL	1	TRUE	1	0.728804878036445	2		331	581	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026604	6026604	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032151-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	46	329	0	ENST00000265849.7:c.1792C>G	p.Gln598Glu	p.Q598E	ENST00000265849	NM_000535.5	598	Cag/Gag	11/15	1	2	FACETS	0.179	0.15	0.211	0.179	0.15	0.211	SUBCLONAL	1	TRUE	1	0.728804878036445	2		329	704	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038773	47038773	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032151-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	42	400	0	ENST00000377604.3:c.782del	p.Gly261ValfsTer5	p.G261Vfs*5	ENST00000377604	NM_001204468.1	260	ctG/ct	9/24	0.728804878036445	1	FACETS	0.196	0.164	0.232	0.196	0.164	0.232	SUBCLONAL	1	TRUE	0	0.728804878036445	1		400	373	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510560	38510560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032151-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	39	292	0	ENST00000254066.5:c.814C>T	p.Arg272Trp	p.R272W	ENST00000254066	NM_000964.3	272	Cgg/Tgg	7/9	0.0999070455278674	4	FACETS	0.322	0.266	0.384	0.161	0.133	0.192	INDETERMINATE	1	TRUE	2	0.728804878036445	4		292	575	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163297	32163297	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032151-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	189	348	0	ENST00000375023.3:c.5929G>C	p.Glu1977Gln	p.E1977Q	ENST00000375023	NM_004557.3	1977	Gag/Cag	30/30	1	2	FACETS	0.689	0.638	0.741	0.689	0.638	0.741	SUBCLONAL	1	TRUE	1	0.728804878036445	2		348	753	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509433	106509433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747427177	NA	P-0032151-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	204	388	0	ENST00000359195.3:c.1427G>A	p.Arg476His	p.R476H	ENST00000359195	NM_002649.2	476	cGc/cAc	2/11	1	2	FACETS	0.793	0.738	0.849	0.793	0.738	0.849	SUBCLONAL	1	TRUE	1	0.728804878036445	2		388	706	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846206	128846206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761081288	NA	P-0032151-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	41	408	0	ENST00000249373.3:c.1136C>T	p.Ala379Val	p.A379V	ENST00000249373	NM_005631.4	379	gCg/gTg	5/12	1	2	FACETS	0.144	0.12	0.172	0.144	0.12	0.172	SUBCLONAL	1	TRUE	1	0.728804878036445	2		408	779	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166234	32166234	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032151-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	40	347	0	ENST00000375023.3:c.4720G>C	p.Glu1574Gln	p.E1574Q	ENST00000375023	NM_004557.3	1574	Gag/Cag	26/30	1	2	FACETS	0.159	0.131	0.189	0.159	0.131	0.189	SUBCLONAL	1	TRUE	1	0.728804878036445	2		347	692	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2208937	2208937	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032151-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	27	237	0	ENST00000398665.3:c.967G>A	p.Glu323Lys	p.E323K	ENST00000398665	NM_032482.2	323	Gaa/Aaa	12/28	1	2	FACETS	0.164	0.13	0.203	0.164	0.13	0.203	SUBCLONAL	1	TRUE	1	0.728804878036445	2		237	451	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526197	189526197	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032151-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	73	490	0	ENST00000264731.3:c.461C>T	p.Ser154Phe	p.S154F	ENST00000264731	NM_003722.4	154	tCc/tTc	4/14	1	2	FACETS	0.205	0.178	0.233	0.205	0.178	0.233	SUBCLONAL	1	TRUE	1	0.728804878036445	2		490	979	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847276	68847276	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032151-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	54	281	0	ENST00000261769.5:c.1198G>C	p.Asp400His	p.D400H	ENST00000261769	NM_004360.3	400	Gat/Cat	9/16	0.728804878036445	1	FACETS	0.245	0.209	0.283	0.245	0.209	0.283	SUBCLONAL	1	TRUE	0	0.728804878036445	1		281	385	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987077	36987077	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0032151-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	65	312	0	ENST00000354822.5:c.612C>G	p.Tyr204Ter	p.Y204*	ENST00000354822	NM_001079668.2	204	taC/taG	3/3	0.719891042292144	3	FACETS	0.34	0.294	0.39	0.17	0.147	0.195	SUBCLONAL	1	TRUE	1	0.728804878036445	3		312	715	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847333	68847333	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032151-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	43	311	0	ENST00000261769.5:c.1255G>C	p.Asp419His	p.D419H	ENST00000261769	NM_004360.3	419	Gat/Cat	9/16	0.728804878036445	1	FACETS	0.194	0.163	0.229	0.194	0.163	0.229	SUBCLONAL	1	TRUE	0	0.728804878036445	1		311	386	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866705	37866705	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032151-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	71	443	0	ENST00000269571.5:c.872T>G	p.Phe291Cys	p.F291C	ENST00000269571		291	tTc/tGc	7/27	0.0999070455278674	4	FACETS	0.392	0.341	0.447	0.196	0.17	0.224	INDETERMINATE	1	TRUE	2	0.728804878036445	4		443	859	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56412973	56412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032151-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	43	320	0	ENST00000348428.3:c.1987C>T	p.Leu663Phe	p.L663F	ENST00000348428	NM_006785.3	663	Ctt/Ttt	16/17	0.728804878036445	1	FACETS	0.191	0.16	0.225	0.191	0.16	0.225	SUBCLONAL	1	TRUE	0	0.728804878036445	1		320	393	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147555	47147555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032151-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	75	439	0	ENST00000409792.3:c.4771G>A	p.Ala1591Thr	p.A1591T	ENST00000409792	NM_014159.6	1591	Gct/Act	6/21	1	2	FACETS	0.239	0.209	0.272	0.239	0.209	0.272	SUBCLONAL	1	TRUE	1	0.728804878036445	2		439	860	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748267	43748267	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032151-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	59	382	0	ENST00000382044.4:c.2539G>A	p.Asp847Asn	p.D847N	ENST00000382044	NM_001141980.1	847	Gat/Aat	12/28	1	2	FACETS	0.22	0.189	0.255	0.22	0.189	0.255	SUBCLONAL	1	TRUE	1	0.728804878036445	2		382	735	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945414	71945414	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349004937	NA	P-0032151-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	39	398	0	ENST00000298229.2:c.2302G>A	p.Glu768Lys	p.E768K	ENST00000298229	NM_001567.3	768	Gag/Aag	20/28	0.728804878036445	1	FACETS	0.155	0.128	0.185	0.155	0.128	0.185	SUBCLONAL	1	TRUE	0	0.728804878036445	1		398	438	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217074	2217074	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032151-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	42	379	0	ENST00000398665.3:c.2529G>C	p.Glu843Asp	p.E843D	ENST00000398665	NM_032482.2	843	gaG/gaC	21/28	1	2	FACETS	0.205	0.171	0.243	0.205	0.171	0.243	SUBCLONAL	1	TRUE	1	0.728804878036445	2		379	562	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28607272	28607272	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1165980982	NA	P-0032151-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	133	357	0	ENST00000253063.3:c.1402C>G	p.Leu468Val	p.L468V	ENST00000253063	NM_031459.4	468	Ctg/Gtg	10/10	0.728804878036445	1	FACETS	0.604	0.554	0.655	0.604	0.554	0.655	SUBCLONAL	1	TRUE	0	0.728804878036445	1		357	384	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281635	49281635	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032151-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	49	389	0	ENST00000282018.3:c.682C>A	p.Leu228Met	p.L228M	ENST00000282018	NM_020377.2	228	Ctg/Atg	1/1	0.728804878036445	1	FACETS	0.18	0.152	0.211	0.18	0.152	0.211	SUBCLONAL	1	TRUE	0	0.728804878036445	1		389	474	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527589	41527589	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032151-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	38	371	0	ENST00000263253.7:c.1480C>G	p.Gln494Glu	p.Q494E	ENST00000263253	NM_001429.3	494	Cag/Gag	6/31	1	2	FACETS	0.148	0.122	0.178	0.148	0.122	0.178	SUBCLONAL	1	TRUE	1	0.728804878036445	2		371	705	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038856	47038857	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0032151-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	107	282	0	ENST00000377604.3:c.865_866del	p.Gln289GlyfsTer11	p.Q289Gfs*11	ENST00000377604	NM_001204468.1	288	tCA/t	9/24	0.728804878036445	1	FACETS	0.578	0.524	0.633	0.578	0.524	0.633	SUBCLONAL	1	TRUE	0	0.728804878036445	1		282	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0032332-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	246	429	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.792008219978615	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.792008219978615	1		429	331	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637584	52637584	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032332-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	222	401	0	ENST00000394830.3:c.2732C>G	p.Pro911Arg	p.P911R	ENST00000394830	NM_018313.4	911	cCa/cGa	18/30	0.753927826401553	1	FACETS	0.857	0.812	0.902	0.857	0.812	0.902	CLONAL	1	TRUE	0	0.792008219978615	1		401	395	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0032721-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	183	269	1	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.47454631160536	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.531147646628781	4		270	446	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578509	7578509	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519978	NA	P-0032721-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	255	473	0	ENST00000269305.4:c.421T>C	p.Cys141Arg	p.C141R	ENST00000269305	NM_001126112.2	141	Tgc/Cgc	5/11	0.532631231672955	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.531147646628781	2		473	462	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318754	163318755	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032721-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	296	333	0	ENST00000271452.3:c.1150dup	p.Arg384LysfsTer6	p.R384Kfs*6	ENST00000271452	NM_145697.2	382	gaa/gAaa	13/14	0.531147646628781	5	FACETS	0.833	0.788	0.879	0.5	0.473	0.528	CLONAL	3	TRUE	0	0.531147646628781	5		333	801	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213345	36213345	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032721-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	122	445	0	ENST00000222270.7:c.2542T>C	p.Ser848Pro	p.S848P	ENST00000222270	NM_014727.1	848	Tcg/Ccg	4/37	0.532631231672955	4	FACETS	0.916	0.828	1	0.458	0.414	0.504	CLONAL	1	TRUE	2	0.531147646628781	4		445	768	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228801	36228801	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032721-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	144	567	0	ENST00000222270.7:c.7700G>A	p.Arg2567His	p.R2567H	ENST00000222270	NM_014727.1	2567	cGt/cAt	35/37	0.532631231672955	4	FACETS	0.962	0.877	1	0.481	0.438	0.526	CLONAL	1	TRUE	2	0.531147646628781	4		567	863	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342860	87342860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032721-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	112	413	0	ENST00000277120.3:c.1145C>T	p.Pro382Leu	p.P382L	ENST00000277120		382	cCt/cTt	9/19	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.531147646628781	2		413	419	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609839	117609839	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032721-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	146	409	0	ENST00000368508.3:c.6860A>C	p.Lys2287Thr	p.K2287T	ENST00000368508	NM_002944.2	2287	aAg/aCg	43/43	0.532631231672955	3	FACETS	1	0.969	1	0.559	0.512	0.608	CLONAL	1	TRUE	1	0.531147646628781	3		409	622	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916546	39916546	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032721-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	106	399	0	ENST00000378444.4:c.4457A>C	p.Lys1486Thr	p.K1486T	ENST00000378444	NM_001123385.1	1486	aAg/aCg	11/15	0.470009246459621	3	FACETS	1	0.975	1	0.622	0.562	0.685	CLONAL	1	TRUE	1	0.531147646628781	3		399	406	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971043	55971043	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032721-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	97	388	2	ENST00000263923.4:c.1754A>G	p.Lys585Arg	p.K585R	ENST00000263923	NM_002253.2	585	aAg/aGg	13/30	0.531147646628781	5	FACETS	0.928	0.828	1	0.186	0.165	0.207	CLONAL	1	TRUE	0	0.531147646628781	5		390	707	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231302	46231302	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032721-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	132	392	0	ENST00000334344.6:c.1142T>G	p.Leu381Arg	p.L381R	ENST00000334344	NM_152641.2	381	cTt/cGt	10/21	0.532631231672955	3	FACETS	1	0.934	1	0.516	0.469	0.564	CLONAL	1	TRUE	1	0.531147646628781	3		392	610	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602729	55602729	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032721-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	106	342	0	ENST00000288135.5:c.2550T>G	p.Ser850Arg	p.S850R	ENST00000288135	NM_000222.2	850	agT/agG	18/21	0.531147646628781	5	FACETS	0.848	0.759	0.942	0.17	0.151	0.189	CLONAL	1	TRUE	0	0.531147646628781	5		342	846	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30733002	30733002	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032721-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	145	516	0	ENST00000295754.5:c.1615A>C	p.Ser539Arg	p.S539R	ENST00000295754	NM_003242.5	539	Agt/Cgt	7/7	0.532631231672955	4	FACETS	1	0.977	1	0.601	0.549	0.654	CLONAL	1	TRUE	2	0.531147646628781	4		516	696	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032991-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	275	446	0				ENST00000310581	NM_198253.2	-/1132			0.787248580287756	4	FACETS	0.874	0.833	0.915	0.874	0.833	0.915	CLONAL	3	TRUE	1	0.787248580287756	4		446	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764146326	NA	P-0032991-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	263	375	0	ENST00000269305.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000269305	NM_001126112.2	281	Gac/Aac	8/11	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.787248580287756	2		375	608	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051060	180051060	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs768956955	NA	P-0032991-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	253	335	0	ENST00000261937.6:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000261937	NM_182925.4	475	Cgg/Tgg	11/30	0.287483054709748	2	FACETS	0.807	0.771	0.844	0.807	0.771	0.844	INDETERMINATE	2	TRUE	0	0.787248580287756	2		335	398	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105841	27105842	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGAA	novel	NA	P-0032991-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	285	392	0	ENST00000324856.7:c.5453_5456dup	p.Asn1820GlufsTer3	p.N1820Efs*3	ENST00000324856	NM_006015.4	1818	cag/cAGAAag	20/20	0.316385401283865	4	FACETS	0.936	0.886	0.987	0.936	0.886	0.987	INDETERMINATE	2	TRUE	2	0.787248580287756	4		392	691	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438349	110438349	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032991-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	60	223	0	ENST00000375856.3:c.52C>T	p.Pro18Ser	p.P18S	ENST00000375856	NM_003749.2	18	Ccc/Tcc	1/2	0.285405198375774	6	FACETS	0.952	0.823	1	0.238	0.205	0.273	INDETERMINATE	1	TRUE	2	0.787248580287756	6		223	412	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24135751	24135751	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754395342	NA	P-0032991-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	100	339	0	ENST00000263121.7:c.238G>A	p.Gly80Arg	p.G80R	ENST00000263121	NM_003073.3	80	Gga/Aga	3/9	0.287483054709748	2	FACETS	0.596	0.536	0.66	0.298	0.268	0.33	INDETERMINATE	1	TRUE	0	0.787248580287756	2		339	426	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027213	49027214	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032991-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	226	255	0	ENST00000267163.4:c.1782dup	p.Pro595SerfsTer5	p.P595Sfs*5	ENST00000267163	NM_000321.2	594	ctt/cTtt	18/27	0.787248580287756	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.787248580287756	1		255	259	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633291	12633291	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032991-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	110	249	0	ENST00000251849.4:c.1109G>C	p.Gly370Ala	p.G370A	ENST00000251849	NM_002880.3	370	gGa/gCa	11/17	0.329352709775591	3	FACETS	0.815	0.736	0.897	0.272	0.245	0.299	INDETERMINATE	1	TRUE	0	0.787248580287756	3		249	478	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248444	212248444	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397514263	NA	P-0033580-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	72	442	0	ENST00000342788.4:c.3823C>T	p.Arg1275Trp	p.R1275W	ENST00000342788	NM_005235.2	1275	Cgg/Tgg	28/28	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.285545030902328	2		442	426	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196960	106196960	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033580-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	60	410	0	ENST00000380013.4:c.5293A>T	p.Asn1765Tyr	p.N1765Y	ENST00000380013	NM_001127208.2	1765	Aac/Tac	11/11	1	2	FACETS	0.98	0.846	1	0.98	0.846	1	CLONAL	1	TRUE	1	0.285545030902328	2		410	429	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390072	89390072	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121609-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	150	336	0	ENST00000336596.2:c.821G>T	p.Arg274Leu	p.R274L	ENST00000336596	NM_005233.5	274	cGa/cTa	4/17	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	NA	1	0.583399545060953	2		336	498	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0037675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	112	392	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.32	2		392	615	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0037675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	17	314	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	1	2	FACETS	0.186	0.138	0.244	0.186	0.138	0.244	SUBCLONAL	1	TRUE	1	0.32	2		314	570	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188296	32188296	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561687277	NA	P-0037675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	114	500	0	ENST00000375023.3:c.1045G>A	p.Gly349Ser	p.G349S	ENST00000375023	NM_004557.3	349	Ggc/Agc	6/30	1	2	FACETS	0.759	0.682	0.84	0.759	0.682	0.84	SUBCLONAL	1	TRUE	1	0.32	2		500	939	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267710	198267710	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	67	331	0	ENST00000335508.6:c.1769G>T	p.Arg590Ile	p.R590I	ENST00000335508	NM_012433.2	590	aGa/aTa	13/25	1	2	FACETS	0.657	0.571	0.751	0.657	0.571	0.751	SUBCLONAL	1	TRUE	1	0.32	2		331	637	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156740	20156740	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	138	252	0	ENST00000379607.5:c.17G>T	p.Gly6Val	p.G6V	ENST00000379607	NM_001412.3	6	gGt/gTt	2/7	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.32	2		252	619	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0037675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	98	492	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.32	2		492	549	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006662	62006662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	161	462	0	ENST00000392795.3:c.617C>A	p.Ala206Asp	p.A206D	ENST00000392795	NM_001039933.1	206	gCc/gAc	6/6	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.32	2		462	934	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115749	8115749	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	140	429	0	ENST00000346208.3:c.1095C>A	p.Asn365Lys	p.N365K	ENST00000346208		365	aaC/aaA	6/6	0.250178177073006	1	FACETS	0.992	0.905	1	0.992	0.905	1	CLONAL	1	TRUE	0	0.32	1		429	741	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024641	11024648	+	frameshift_variant	Frame_Shift_Del	DEL	TCATCATC	TCATCATC	-	novel	NA	P-0037675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	104	455	0	ENST00000327064.4:c.760_767del	p.Ile254GlyfsTer35	p.I254Gfs*35	ENST00000327064	NM_199141.1	253	aTCATCATC/a	6/16	1	2	FACETS	0.852	0.763	0.947	0.852	0.763	0.947	CLONAL	1	TRUE	1	0.32	2		455	763	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981806	70981806	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	106	400	0	ENST00000276594.2:c.290A>G	p.Lys97Arg	p.K97R	ENST00000276594	NM_024504.3	97	aAg/aGg	2/8	1	2	FACETS	0.795	0.712	0.883	0.795	0.712	0.883	SUBCLONAL	1	TRUE	1	0.32	2		400	833	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486218	8486218	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	130	394	0	ENST00000356435.5:c.2599C>A	p.Pro867Thr	p.P867T	ENST00000356435		867	Cca/Aca	17/35	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.32	2		394	702	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349608	70349608	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	115	494	0	ENST00000374080.3:c.3770G>T	p.Gly1257Val	p.G1257V	ENST00000374080		1257	gGc/gTc	27/45	1	2	FACETS	0.761	0.684	0.842	0.761	0.684	0.842	SUBCLONAL	1	TRUE	1	0.32	2		494	945	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178215	56178215	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1428148071	NA	P-0038833-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	75	497	0	ENST00000399503.3:c.3188C>G	p.Ser1063Cys	p.S1063C	ENST00000399503	NM_005921.1	1063	tCt/tGt	14/20	0.202149717826683	1	FACETS	0.56	0.49	0.635	0.56	0.49	0.635	SUBCLONAL	1	TRUE	0	0.323660148888723	1		497	694	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223049	1223634	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGACCGGTGGCGCAGCATGACTGTGGTGCCGTACTTGGAGGACCTGCACGGCGCGGACGAGGACGAGGACCTCTTCGACATCGAGGATGACATCATCTACACTCAGGACTTCACGGTGCCCGGTGAGTCTGGCGGGGGCCCCTGCCCGGCTCTGCTGACTCGGCCAGGATGTCCCACGGGAGCAGGGTGCCTGCCTGTCTGCAACAAGGACAGCTTCTGCCCTCTGGTGGCCAATCCCACGTCCCCAAAGCCTCCAGCCCACCTGCAGGCTGCCTCCGCCCTGCGGGCCGCTGGGACATGGCTGAAAGGTGTGGGGTCAGCGGGGGCACCAGCCCAGGCCTGTCTGGCCAGGAGGGTTCCTCAGGCGTCTCTCCGGGTGCTGCCCAGCCAGGCACCACCCACCGGCCTTGGCCTGAGTCCCAGCAGGAGCAGGCGGGGGAGCCCCAGGGTCGGGGGAGGGTAGGTGAGAGTCAGGGTGCAGGGTGGCCCCTCAGACAGCTGGCATGAGAGAGGGTCCAGTGGCCCTCCCTCCCGTCGTCCCTGAGGCCTGCCCGCTGGCCCTGATGCCGGCCGCCCTTCTTCCCT	AGGACCGGTGGCGCAGCATGACTGTGGTGCCGTACTTGGAGGACCTGCACGGCGCGGACGAGGACGAGGACCTCTTCGACATCGAGGATGACATCATCTACACTCAGGACTTCACGGTGCCCGGTGAGTCTGGCGGGGGCCCCTGCCCGGCTCTGCTGACTCGGCCAGGATGTCCCACGGGAGCAGGGTGCCTGCCTGTCTGCAACAAGGACAGCTTCTGCCCTCTGGTGGCCAATCCCACGTCCCCAAAGCCTCCAGCCCACCTGCAGGCTGCCTCCGCCCTGCGGGCCGCTGGGACATGGCTGAAAGGTGTGGGGTCAGCGGGGGCACCAGCCCAGGCCTGTCTGGCCAGGAGGGTTCCTCAGGCGTCTCTCCGGGTGCTGCCCAGCCAGGCACCACCCACCGGCCTTGGCCTGAGTCCCAGCAGGAGCAGGCGGGGGAGCCCCAGGGTCGGGGGAGGGTAGGTGAGAGTCAGGGTGCAGGGTGGCCCCTCAGACAGCTGGCATGAGAGAGGGTCCAGTGGCCCTCCCTCCCGTCGTCCCTGAGGCCTGCCCGCTGGCCCTGATGCCGGCCGCCCTTCTTCCCT	-	novel	NA	P-0038833-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	119	555	0	ENST00000326873.7:c.989_1108+466del		p.X330_splice	ENST00000326873	NM_000455.4	330		8/10	0.323660148888723	2	FACETS	1	0.978	1	0.635	0.575	0.698	CLONAL	1	TRUE	0	0.323660148888723	2		555	579	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611829	1611829	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038833-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	77	410	0	ENST00000344749.5:c.1833A>T	p.Lys611Asn	p.K611N	ENST00000344749	NM_001136139.2	611	aaA/aaT	19/19	0.323660148888723	2	FACETS	0.767	0.674	0.868	0.384	0.337	0.434	SUBCLONAL	1	TRUE	0	0.323660148888723	2		410	620	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600038	10600066	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGACGCCTAAAGGGCACCATGCAGAGAA	CAGACGCCTAAAGGGCACCATGCAGAGAA	-	novel	NA	P-0038833-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	210	459	0	ENST00000171111.5:c.1532-22_1538del		p.X511_splice	ENST00000171111	NM_203500.1	511		5/6	0.323660148888723	2	FACETS	0.957	0.893	1	0.957	0.893	1	CLONAL	2	TRUE	0	0.323660148888723	2		459	678	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266826	18266826	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038833-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	80	467	0	ENST00000222254.8:c.137G>T	p.Gly46Val	p.G46V	ENST00000222254	NM_005027.3	46	gGt/gTt	2/16	0.323660148888723	2	FACETS	0.739	0.65	0.834	0.369	0.325	0.417	SUBCLONAL	1	TRUE	0	0.323660148888723	2		467	669	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733240	40733240	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038833-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	57	530	0	ENST00000373198.4:c.3566C>A	p.Thr1189Lys	p.T1189K	ENST00000373198	NM_133170.3	1189	aCa/aAa	26/32	1	2	FACETS	0.496	0.425	0.574	0.496	0.425	0.574	SUBCLONAL	1	TRUE	1	0.323660148888723	2		530	710	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72897431	72897431	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038833-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	60	456	0	ENST00000325599.8:c.61G>C	p.Val21Leu	p.V21L	ENST00000325599	NM_018130.2	21	Gtg/Ctg	1/11	0.202149717826683	1	FACETS	0.486	0.418	0.56	0.486	0.418	0.56	SUBCLONAL	1	TRUE	0	0.323660148888723	1		456	639	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867505	35867505	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs764440449	NA	P-0038833-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	94	361	0	ENST00000303115.3:c.319A>G	p.Ile107Val	p.I107V	ENST00000303115	NM_002185.3	107	Ata/Gta	3/8	0.323660148888723	4	FACETS	1	0.916	1	0.517	0.46	0.579	CLONAL	1	TRUE	2	0.323660148888723	4		361	743	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86545001	86545001	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1489159316	NA	P-0038833-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	61	409	0	ENST00000262426.4:c.826G>A	p.Ala276Thr	p.A276T	ENST00000262426	NM_001451.2	276	Gcg/Acg	1/2	0.202149717826683	1	FACETS	0.521	0.449	0.6	0.521	0.449	0.6	SUBCLONAL	1	TRUE	0	0.323660148888723	1		409	606	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56801463	56801463	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0038833-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	42	381	0	ENST00000337432.4:c.965+2T>G		p.X322_splice	ENST00000337432	NM_058216.2	322			1	2	FACETS	0.478	0.398	0.566	0.478	0.398	0.566	SUBCLONAL	1	TRUE	1	0.323660148888723	2		381	543	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245610	46245610	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038833-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	75	531	0	ENST00000334344.6:c.3704C>G	p.Pro1235Arg	p.P1235R	ENST00000334344	NM_152641.2	1235	cCc/cGc	15/21	1	2	FACETS	0.646	0.566	0.733	0.646	0.566	0.733	SUBCLONAL	1	TRUE	1	0.323660148888723	2		531	717	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127390	55127390	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038833-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	68	500	0	ENST00000257290.5:c.178C>A	p.Pro60Thr	p.P60T	ENST00000257290	NM_006206.4	60	Ccc/Acc	3/23	0.202149717826683	1	FACETS	0.487	0.423	0.557	0.487	0.423	0.557	SUBCLONAL	1	TRUE	0	0.323660148888723	1		500	723	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0039237-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	112	492	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.609009890154592	5	FACETS	0.895	0.82	0.972			1	CLONAL	3	TRUE	NA	0.609009890154592	5		492	262	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577115	7577115	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039237-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	41	517	0	ENST00000269305.4:c.823T>G	p.Cys275Gly	p.C275G	ENST00000269305	NM_001126112.2	275	Tgt/Ggt	8/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.609009890154592	2		517	110	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391034	89391034	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039237-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	75	497	0	ENST00000336596.2:c.1100G>T	p.Gly367Val	p.G367V	ENST00000336596	NM_005233.5	367	gGg/gTg	5/17	0.195466239637279	3	FACETS	0.824	0.737	0.913	0.824	0.737	0.913	INDETERMINATE	2	TRUE	1	0.609009890154592	3		497	195	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266792	198266792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039237-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	49	405	0	ENST00000335508.6:c.2140G>A	p.Glu714Lys	p.E714K	ENST00000335508	NM_012433.2	714	Gaa/Aaa	15/25	0.61420723185229	4	FACETS	0.984	0.841	1	0.492	0.42	0.57	CLONAL	1	TRUE	2	0.609009890154592	4		405	263	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281758	49281758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777488065	NA	P-0039237-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	68	533	0	ENST00000282018.3:c.805G>A	p.Val269Ile	p.V269I	ENST00000282018	NM_020377.2	269	Gtc/Atc	1/1	0.61420723185229	2	FACETS	1	0.962	1	0.604	0.536	0.674	CLONAL	1	TRUE	0	0.609009890154592	2		533	185	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691027	NA	P-0039237-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	32	543	0	ENST00000269305.4:c.844del	p.Arg282GlyfsTer63	p.R282Gfs*63	ENST00000269305	NM_001126112.2	282	Cgg/gg	8/11	1	2	FACETS	0.991	0.825	1	0.991	0.825	1	CLONAL	1	TRUE	1	0.609009890154592	2		543	106	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101353	27101354	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCTT	novel	NA	P-0039237-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	67	497	0	ENST00000324856.7:c.4638_4641dup	p.His1548PhefsTer25	p.H1548Ffs*25	ENST00000324856	NM_006015.4	1545	-/CCTT	18/20	0.61420723185229	2	FACETS	0.974	0.883	1	0.974	0.883	1	CLONAL	2	TRUE	0	0.609009890154592	2		497	113	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117194	7117194	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039237-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	130	535	0	ENST00000302850.5:c.4022G>T	p.Gly1341Val	p.G1341V	ENST00000302850	NM_000208.2	1341	gGg/gTg	22/22	0.514486226454909	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.609009890154592	3		535	254	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382202	152382202	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039237-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	126	428	0	ENST00000206249.3:c.1312A>T	p.Met438Leu	p.M438L	ENST00000206249	NM_000125.3	438	Atg/Ttg	6/8	0.61420723185229	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.609009890154592	2		428	178	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141568617	141568617	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039237-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	125	485	0	ENST00000220592.5:c.845G>T	p.Cys282Phe	p.C282F	ENST00000220592	NM_012154.3	282	tGc/tTc	7/19	0.387364352341456	4	FACETS	0.878	0.823	0.931	0.878	0.823	0.931	CLONAL	4	TRUE	0	0.609009890154592	4		485	188	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970842	55970842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039237-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	70	524	0	ENST00000263923.4:c.1955G>T	p.Arg652Ile	p.R652I	ENST00000263923	NM_002253.2	652	aGa/aTa	13/30	0.61420723185229	3	FACETS	1	0.946	1	0.566	0.499	0.636	CLONAL	1	TRUE	1	0.609009890154592	3		524	265	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630356	67630356	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0039237-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	99	179	0	ENST00000272342.5:c.543-1G>T		p.X181_splice	ENST00000272342	NM_019002.3	181			0.421217476639307	6	FACETS	1	0.911	1	1	0.911	1	CLONAL	3	TRUE	3	0.609009890154592	6		179	240	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420192	88420192	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039237-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	103	505	0	ENST00000360948.2:c.2494C>A	p.Pro832Thr	p.P832T	ENST00000360948	NM_001012338.2	832	Cca/Aca	19/19	0.61420723185229	3	FACETS	0.931	0.85	1	0.931	0.85	1	CLONAL	2	TRUE	1	0.609009890154592	3		505	237	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31451639	31451639	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0039237-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	57	291	0	ENST00000344624.3:c.2682+1G>C		p.X894_splice	ENST00000344624		894			0.61420723185229	4	FACETS	0.932	0.805	1			1	CLONAL	1	TRUE	NA	0.609009890154592	4		291	323	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608947	100608947	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0039237-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	39	375	0	ENST00000308731.7:c.1661C>G	p.Ser554Ter	p.S554*	ENST00000308731	NM_000061.2	554	tCa/tGa	17/19	0.61420723185229	5	FACETS	1	0.894	1	0.365	0.305	0.43	CLONAL	1	TRUE	2	0.609009890154592	5		375	224	SUCCESS
AR	367	MSKCC	GRCh37	X	66765467	66765467	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039237-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	44	520	0	ENST00000374690.3:c.482del	p.Pro161HisfsTer14	p.P161Hfs*14	ENST00000374690	NM_000044.3	160	gCc/gc	1/8	1	2	FACETS	0.997	0.853	1	0.997	0.853	1	CLONAL	1	TRUE	1	0.609009890154592	2		520	145	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405948	49405948	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039705-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	253	307	0	ENST00000418115.1:c.190G>A	p.Glu64Lys	p.E64K	ENST00000418115	NM_001664.2	64	Gaa/Aaa	3/5	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.772790219500088	2		307	619	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916937	+	inframe_deletion	In_Frame_Del	DEL	GGCAACCGT	GGCAACCGT	-	novel	NA	P-0039705-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	429	296	0	ENST00000263967.3:c.317_325del	p.Gly106_Arg108del	p.G106_R108del	ENST00000263967	NM_006218.2	106	GGCAACCGT/-	2/21	0.760342765287682	2	FACETS	0.993	0.965	1	0.993	0.965	1	CLONAL	2	TRUE	0	0.772790219500088	2		296	559	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112497	115112497	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039705-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	297	369	0	ENST00000257566.3:c.1243C>A	p.His415Asn	p.H415N	ENST00000257566	NM_016569.3	415	Cac/Aac	7/8	0.772790219500088	3	FACETS	1	0.964	1	0.515	0.485	0.545	CLONAL	1	TRUE	1	0.772790219500088	3		369	1035	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945167	32945167	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs886040782	NA	P-0039705-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	247	277	0	ENST00000380152.3:c.8562del	p.Tyr2854Ter	p.Y2854*	ENST00000380152		2854	taT/ta	20/27	0.772790219500088	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.772790219500088	1		277	378	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214891	36214891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039705-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	201	351	0	ENST00000222270.7:c.3317G>T	p.Arg1106Leu	p.R1106L	ENST00000222270	NM_014727.1	1106	cGg/cTg	8/37	1	2	FACETS	0.963	0.9	1	0.963	0.9	1	CLONAL	1	TRUE	1	0.772790219500088	2		351	540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0040597-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	435	758	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.67870058523123	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.67870058523123	2		758	614	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88651917	88651917	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040597-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	130	379	0	ENST00000372037.3:c.264A>C	p.Glu88Asp	p.E88D	ENST00000372037	NM_004329.2	88	gaA/gaC	5/13	0.67870058523123	3	FACETS	1	0.976	1	0.595	0.544	0.648	CLONAL	1	TRUE	1	0.67870058523123	3		379	431	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061257	38061257	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040597-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	180	709	0	ENST00000250448.2:c.732G>A	p.Trp244Ter	p.W244*	ENST00000250448	NM_004496.3	244	tgG/tgA	2/2	0.67870058523123	3	FACETS	1	0.967	1	0.54	0.5	0.581	CLONAL	1	TRUE	1	0.67870058523123	3		709	658	SUCCESS
APC	324	MSKCC	GRCh37	5	112162944	112162944	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040597-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	257	456	0	ENST00000257430.4:c.1548+1del		p.K516fs	ENST00000257430	NM_000038.5	516	aaG/aa	12/16	0.67870058523123	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.67870058523123	2		456	358	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508137	106508137	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040597-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	150	614	0	ENST00000359195.3:c.131T>C	p.Leu44Pro	p.L44P	ENST00000359195	NM_002649.2	44	cTg/cCg	2/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.67870058523123	2		614	430	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189093	38189093	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040597-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	160	519	0	ENST00000317025.8:c.921A>T	p.Glu307Asp	p.E307D	ENST00000317025	NM_023034.1	307	gaA/gaT	5/24	0.67870058523123	1	FACETS	0.986	0.921	1	0.986	0.921	1	CLONAL	1	TRUE	0	0.67870058523123	1		519	316	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0041372-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	144	532	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.360893954684931	4	FACETS	0.938	0.868	1	0.704	0.651	0.758	CLONAL	3	TRUE	0	0.411314803090288	4		532	351	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0041372-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	18	539	0				ENST00000310581	NM_198253.2	-/1132			0.414957686608139	0	FACETS	0.526	0.402	0.666			1	SUBCLONAL	1	TRUE	0	0.411314803090288	0		539	98	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0041372-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	199	361	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.360893954684931	4	FACETS	1	0.97	1	0.792	0.743	0.841	CLONAL	3	TRUE	0	0.411314803090288	4		361	431	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041372-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	163	318	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	0.414957686608139	2	FACETS	0.872	0.817	0.927			1	CLONAL	3	TRUE	NA	0.411314803090288	2		318	303	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963940	2963941	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGA	novel	NA	P-0041372-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	28	822	0	ENST00000396946.4:c.1864_1866dup	p.Ser622dup	p.S622dup	ENST00000396946	NM_032415.4	622	-/TCC	15/25	1	2	FACETS	0.473	0.379	0.579	0.473	0.379	0.579	SUBCLONAL	1	TRUE	1	0.411314803090288	2		822	288	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534545	140534545	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041372-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	28	554	0	ENST00000288602.6:c.368C>G	p.Ser123Cys	p.S123C	ENST00000288602	NM_004333.4	123	tCt/tGt	3/18	0.414957686608139	3	FACETS	0.56	0.449	0.687	0.28	0.224	0.344	SUBCLONAL	1	TRUE	1	0.411314803090288	3		554	293	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2488158	2488158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1429446056	NA	P-0041372-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	61	677	0	ENST00000355716.4:c.55G>A	p.Asp19Asn	p.D19N	ENST00000355716	NM_003820.2	19	Gac/Aac	1/8	1	2	FACETS	0.634	0.548	0.727	0.634	0.548	0.727	SUBCLONAL	1	TRUE	1	0.411314803090288	2		677	468	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325861	65325861	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041372-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	56	795	0	ENST00000342505.4:c.1261C>T	p.His421Tyr	p.H421Y	ENST00000342505	NM_002227.2	421	Cat/Tat	9/25	0.350860698926111	3	FACETS	0.825	0.709	0.951	0.412	0.354	0.476	CLONAL	1	TRUE	1	0.411314803090288	3		795	398	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38632043	38632043	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041372-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	17	391	1	ENST00000299084.4:c.529C>T	p.Pro177Ser	p.P177S	ENST00000299084	NM_152594.2	177	Ccc/Tcc	5/7	0.412323982435779	3	FACETS	0.712	0.536	0.917	0.356	0.268	0.459	CLONAL	1	TRUE	1	0.411314803090288	3		392	140	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782077	66782077	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041372-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	32	471	0	ENST00000307102.5:c.1044G>C	p.Glu348Asp	p.E348D	ENST00000307102	NM_002755.3	348	gaG/gaC	10/11	0.412323982435779	3	FACETS	0.924	0.756	1	0.462	0.378	0.555	CLONAL	1	TRUE	1	0.411314803090288	3		471	203	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819756	81819756	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041372-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	33	690	0	ENST00000359376.3:c.162G>C	p.Trp54Cys	p.W54C	ENST00000359376	NM_002661.3	54	tgG/tgC	2/33	0.290832668647437	3	FACETS	0.636	0.52	0.767	0.318	0.26	0.384	SUBCLONAL	1	TRUE	1	0.411314803090288	3		690	304	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858452	89858452	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041372-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	26	701	0	ENST00000389301.3:c.1108G>C	p.Glu370Gln	p.E370Q	ENST00000389301	NM_000135.2	370	Gag/Cag	13/43	0.290832668647437	3	FACETS	0.462	0.366	0.572	0.231	0.183	0.286	SUBCLONAL	1	TRUE	1	0.411314803090288	3		701	330	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537076	41537076	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041372-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	34	442	0	ENST00000263253.7:c.1903G>C	p.Glu635Gln	p.E635Q	ENST00000263253	NM_001429.3	635	Gag/Cag	10/31	0.350860698926111	3	FACETS	0.834	0.686	0.998	0.417	0.343	0.499	CLONAL	1	TRUE	1	0.411314803090288	3		442	239	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217549	142217549	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041372-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	35	385	0	ENST00000350721.4:c.5448C>G	p.Ile1816Met	p.I1816M	ENST00000350721	NM_001184.3	1816	atC/atG	32/47	0.379032192966455	4	FACETS	1	0.883	1	0.546	0.451	0.651	CLONAL	1	TRUE	2	0.411314803090288	4		385	220	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925375	131925375	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041372-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	21	249	0	ENST00000265335.6:c.1298G>C	p.Arg433Thr	p.R433T	ENST00000265335		433	aGa/aCa	9/25	0.379032192966455	4	FACETS	0.98	0.762	1	0.49	0.381	0.615	CLONAL	1	TRUE	2	0.411314803090288	4		249	147	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017509	112017509	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041372-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	49	582	0	ENST00000368678.4:c.1004T>A	p.Ile335Asn	p.I335N	ENST00000368678		335	aTc/aAc	9/13	0.353288166957738	2	FACETS	0.745	0.634	0.865	0.372	0.317	0.433	SUBCLONAL	1	TRUE	0	0.411314803090288	2		582	320	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069594	69069601	+	frameshift_variant	Frame_Shift_Del	DEL	TGTTTCTG	TGTTTCTG	-	novel	NA	P-0041372-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	22	281	0	ENST00000288368.4:c.4271_4278del	p.Val1424GlyfsTer45	p.V1424Gfs*45	ENST00000288368	NM_024870.2	1423	aaTGTTTCTGtg/aatg	35/40	0.126586141121633	0	FACETS	0.589	0.464	0.728			1	INDETERMINATE	1	TRUE	0	0.411314803090288	0		281	107	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740776	145740776	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041372-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	130	838	0	ENST00000428558.2:c.1324G>A	p.Glu442Lys	p.E442K	ENST00000428558	NM_004260.3	442	Gag/Aag	7/22	0.385214650709315	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	2	0.411314803090288	4		838	394	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038521	47038521	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041372-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	64	321	0	ENST00000377604.3:c.683A>T	p.Lys228Ile	p.K228I	ENST00000377604	NM_001204468.1	228	aAa/aTa	8/24	0.414957686608139	2	FACETS	0.926	0.82	1			1	CLONAL	2	TRUE	NA	0.411314803090288	2		321	168	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133862	41133862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041372-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	86	740	0	ENST00000379561.5:c.1766G>A	p.Arg589Lys	p.R589K	ENST00000379561	NM_002015.3	589	aGa/aAa	2/3	0.414957686608139	4	FACETS	1	0.979	1	0.498	0.443	0.556	CLONAL	1	TRUE	1	0.411314803090288	4		740	395	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906618	32906618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041372-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	23	325	0	ENST00000380152.3:c.1003G>A	p.Glu335Lys	p.E335K	ENST00000380152		335	Gaa/Aaa	10/27	0.414957686608139	4	FACETS	0.849	0.666	1	0.283	0.222	0.353	CLONAL	1	TRUE	1	0.411314803090288	4		325	186	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544757	86544757	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041372-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	17	733	0	ENST00000262426.4:c.582G>A	p.Met194Ile	p.M194I	ENST00000262426	NM_001451.2	194	atG/atA	1/2	0.290832668647437	3	FACETS	0.443	0.331	0.575	0.221	0.165	0.288	SUBCLONAL	1	TRUE	1	0.411314803090288	3		733	225	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38785219	38785219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041372-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	128	599	0	ENST00000348513.6:c.1054G>A	p.Glu352Lys	p.E352K	ENST00000348513	NM_003079.4	352	Gag/Aag	11/11	0.414771615142113	3	FACETS	0.95	0.869	1	0.633	0.579	0.689	CLONAL	2	TRUE	0	0.411314803090288	3		599	395	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422077	47422077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041372-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	74	716	0	ENST00000404338.3:c.145G>A	p.Glu49Lys	p.E49K	ENST00000404338	NM_004491.4	49	Gag/Aag	1/6	0.382773223162738	4	FACETS	1	0.948	1			1	CLONAL	1	TRUE	NA	0.411314803090288	4		716	442	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326544	62326544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041372-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	46	837	0	ENST00000360203.5:c.3469C>T	p.Pro1157Ser	p.P1157S	ENST00000360203	NM_001283009.1	1157	Cct/Tct	33/35	0.175997911925069	1	FACETS	0.602	0.51	0.703	0.602	0.51	0.703	INDETERMINATE	1	TRUE	0	0.411314803090288	1		837	295	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175864	24175864	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041372-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	34	677	0	ENST00000263121.7:c.1092G>C	p.Lys364Asn	p.K364N	ENST00000263121	NM_003073.3	364	aaG/aaC	8/9	0.388057357587327	1	FACETS	0.608	0.501	0.727	0.608	0.501	0.727	SUBCLONAL	1	TRUE	0	0.411314803090288	1		677	216	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	893120	893120	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041372-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	24	508	0	ENST00000166345.3:c.7G>T	p.Glu3Ter	p.E3*	ENST00000166345	NM_004237.3	3	Gag/Tag	1/13	NA	2	FACETS	0.614	0.485	0.761			1	INDETERMINATE	1	TRUE	NA	0.411314803090288	2		508	190	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041409-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	123	936	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.896586139806458	2	FACETS	1	0.981	1	0.592	0.549	0.636	CLONAL	1	TRUE	0	0.894949568918481	2		936	232	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924280	11924280	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1294433193	NA	P-0041409-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	163	808	1	ENST00000353533.5:c.80del	p.Pro27ArgfsTer18	p.P27Rfs*18	ENST00000353533	NM_003010.3	26	tCc/tc	1/11	0.896586139806458	3	FACETS	0.911	0.84	0.983	0.455	0.42	0.492	CLONAL	1	TRUE	1	0.894949568918481	3		809	579	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968928	32968928	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041409-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	456	522	0	ENST00000380152.3:c.9359T>G	p.Ile3120Ser	p.I3120S	ENST00000380152		3120	aTt/aGt	25/27	0.894949568918481	8	FACETS	0.904	0.87	0.938	0.753	0.725	0.781	CLONAL	5	TRUE	2	0.894949568918481	8		522	831	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004792	16004792	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041409-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	117	560	0	ENST00000268712.3:c.2462C>A	p.Ser821Tyr	p.S821Y	ENST00000268712	NM_006311.3	821	tCt/tAt	20/46	0.896586139806458	3	FACETS	0.965	0.879	1	0.483	0.439	0.528	CLONAL	1	TRUE	1	0.894949568918481	3		560	392	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462152	120462152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1405408138	NA	P-0041409-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	72	606	0	ENST00000256646.2:c.5564C>T	p.Ser1855Phe	p.S1855F	ENST00000256646	NM_024408.3	1855	tCt/tTt	31/34	0.896586139806458	4	FACETS	0.659	0.577	0.746	0.22	0.192	0.249	SUBCLONAL	1	TRUE	1	0.894949568918481	4		606	463	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486203	8486203	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1191702282	NA	P-0041409-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	129	600	0	ENST00000356435.5:c.2614G>C	p.Glu872Gln	p.E872Q	ENST00000356435		872	Gag/Cag	17/35	0.896586139806458	3	FACETS	0.966	0.883	1	0.322	0.294	0.351	CLONAL	1	TRUE	0	0.894949568918481	3		600	432	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551496	150551496	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041409-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	114	651	0	ENST00000369026.2:c.511G>T	p.Glu171Ter	p.E171*	ENST00000369026	NM_021960.4	171	Gag/Tag	1/3	0.577205322102574	6	FACETS	1	0.975	1	0.312	0.282	0.344	CLONAL	1	TRUE	2	0.894949568918481	6		651	569	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671650	67671650	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041409-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	106	559	0	ENST00000264010.4:c.2059G>C	p.Glu687Gln	p.E687Q	ENST00000264010	NM_006565.3	687	Gaa/Caa	12/12	0.792680953444223	4	FACETS	0.891	0.802	0.984	0.445	0.401	0.492	CLONAL	1	TRUE	2	0.894949568918481	4		559	504	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508746	29508746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041409-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	110	426	0	ENST00000356175.3:c.673G>A	p.Glu225Lys	p.E225K	ENST00000356175	NM_000267.3	225	Gaa/Aaa	7/57	0.896586139806458	3	FACETS	1	0.949	1	0.533	0.484	0.583	CLONAL	1	TRUE	1	0.894949568918481	3		426	334	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866654	117866654	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041409-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	92	467	0	ENST00000297338.2:c.991G>C	p.Glu331Gln	p.E331Q	ENST00000297338	NM_006265.2	331	Gag/Cag	9/14	0.894949568918481	6	FACETS	0.9	0.801	1	0.225	0.2	0.252	CLONAL	1	TRUE	2	0.894949568918481	6		467	637	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490291	29490291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041409-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	72	457	0	ENST00000356175.3:c.376G>A	p.Glu126Lys	p.E126K	ENST00000356175	NM_000267.3	126	Gaa/Aaa	4/57	0.896586139806458	3	FACETS	0.82	0.724	0.921	0.41	0.362	0.461	CLONAL	1	TRUE	1	0.894949568918481	3		457	284	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575553	64575553	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041409-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	143	649	0	ENST00000312049.6:c.464C>G	p.Ser155Cys	p.S155C	ENST00000312049	NM_130799.2	155	tCc/tGc	3/10	NA	2	FACETS	1	0.934	1			1	INDETERMINATE	1	TRUE	NA	0.894949568918481	2		649	317	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs869320707	NA	P-0042203-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	105	592	0	ENST00000397752.3:c.3028+1G>T		p.X1010_splice	ENST00000397752	NM_000245.2	1010			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		592	384	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124503463	124503463	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042203-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	76	414	0	ENST00000357628.3:c.487G>T	p.Asp163Tyr	p.D163Y	ENST00000357628	NM_015450.2	163	Gac/Tac	8/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		414	377	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043121-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	21	446	0				ENST00000310581	NM_198253.2	-/1132			0.239493085885726	0	FACETS	1	0.82	1			1	CLONAL	1	TRUE	0	0.239493085885726	0		446	126	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0043121-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	80	338	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	NA	2	FACETS	0.872	0.773	0.978			1	INDETERMINATE	2	TRUE	NA	0.239493085885726	2		338	383	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918622	44918622	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043121-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	49	199	0	ENST00000377967.4:c.1105C>T	p.Gln369Ter	p.Q369*	ENST00000377967	NM_021140.2	369	Cag/Tag	12/29	1	1	FACETS	0.8	0.685	0.924	1	0.968	1	CLONAL	2	TRUE	0	0.239493085885726	1		199	225	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628266	187628266	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043121-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	97	469	1	ENST00000441802.2:c.2716C>T	p.Gln906Ter	p.Q906*	ENST00000441802	NM_005245.3	906	Cag/Tag	2/27	1	2	FACETS	0.758	0.678	0.843	1	0.982	1	SUBCLONAL	2	TRUE	1	0.239493085885726	2		470	534	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223356	2223356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1376643409	NA	P-0043121-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	68	486	0	ENST00000326181.6:c.968C>T	p.Ser323Leu	p.S323L	ENST00000326181	NM_032271.2	323	tCg/tTg	10/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.239493085885726	2		486	401	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799626	3799626	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0043121-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	29	197	0	ENST00000262367.5:c.3836+2T>G		p.X1279_splice	ENST00000262367	NM_004380.2	1279			1	2	FACETS	1	0.827	1	1	0.827	1	CLONAL	1	TRUE	1	0.239493085885726	2		197	236	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981763	201981779	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCAGACCAGGGCAGCC	CCCAGACCAGGGCAGCC	-	novel	NA	P-0043121-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	74	454	0	ENST00000359651.3:c.479-3_492del		p.X160_splice	ENST00000359651		160		4/8	1	2	FACETS	0.842	0.742	0.948	1	0.98	1	CLONAL	2	TRUE	1	0.239493085885726	2		454	367	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992795	72992795	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0043121-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	71	417	0	ENST00000268489.5:c.1250C>G	p.Ser417Ter	p.S417*	ENST00000268489	NM_006885.3	417	tCa/tGa	2/10	0.0634403963820147	4	FACETS	0.93	0.816	1	0.93	0.816	1	INDETERMINATE	2	TRUE	2	0.239493085885726	4		417	395	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551003	41551003	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043121-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	37	322	0	ENST00000263253.7:c.3147C>G	p.Phe1049Leu	p.F1049L	ENST00000263253	NM_001429.3	1049	ttC/ttG	17/31	0.239493085885726	1	FACETS	0.751	0.621	0.897	0.751	0.621	0.897	SUBCLONAL	1	TRUE	0	0.239493085885726	1		322	362	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947413	38947413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043121-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	52	421	0	ENST00000357387.3:c.4267G>A	p.Asp1423Asn	p.D1423N	ENST00000357387	NM_152756.3	1423	Gat/Aat	32/38	1	2	FACETS	0.737	0.627	0.858	0.737	0.627	0.858	SUBCLONAL	1	TRUE	1	0.239493085885726	2		421	589	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0045507-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	119	405	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.538907231353685	2		405	411	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983142	201983143	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0045507-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	120	303	0	ENST00000359651.3:c.994dup	p.Ala332GlyfsTer139	p.A332Gfs*139	ENST00000359651		331	cgg/cGgg	7/8	1	2	FACETS	0.909	0.825	0.996	0.909	0.825	0.996	CLONAL	1	TRUE	1	0.538907231353685	2		303	490	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260833	16260833	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045507-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	151	384	0	ENST00000375759.3:c.8098C>G	p.Leu2700Val	p.L2700V	ENST00000375759	NM_015001.2	2700	Ctt/Gtt	11/15	1	2	FACETS	0.883	0.81	0.958	0.883	0.81	0.958	CLONAL	1	TRUE	1	0.538907231353685	2		384	635	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261044	16261044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746961330	NA	P-0045507-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	124	321	0	ENST00000375759.3:c.8309C>T	p.Ser2770Leu	p.S2770L	ENST00000375759	NM_015001.2	2770	tCa/tTa	11/15	1	2	FACETS	0.909	0.827	0.995	0.909	0.827	0.995	CLONAL	1	TRUE	1	0.538907231353685	2		321	506	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56415066	56415066	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045507-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	97	154	0	ENST00000348428.3:c.2467G>C	p.Glu823Gln	p.E823Q	ENST00000348428	NM_006785.3	823	Gaa/Caa	17/17	0.538907231353685	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.538907231353685	1		154	258	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652048	36652049	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACCACTGGAGGGTG	novel	NA	P-0045507-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	117	372	0	ENST00000244741.5:c.173_186dup	p.Phe63HisfsTer90	p.F63Hfs*90	ENST00000244741	NM_000389.4	57	aca/acACCACTGGAGGGTGa	2/3	0.538907231353685	1	FACETS	0.766	0.696	0.839	0.766	0.696	0.839	SUBCLONAL	1	TRUE	0	0.538907231353685	1		372	414	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797301	135797307	+	frameshift_variant	Frame_Shift_Del	DEL	GATGAAA	GATGAAA	-	novel	NA	P-0045507-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	119	248	0	ENST00000298552.3:c.562_568del	p.Phe188AlafsTer20	p.F188Afs*20	ENST00000298552	NM_001162426.1	188	TTTCATCgc/gc	7/23	0.523171131570002	1	FACETS	0.891	0.813	0.972	0.891	0.813	0.972	CLONAL	1	TRUE	0	0.538907231353685	1		248	362	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105645	11105645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045507-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	102	231	0	ENST00000358026.2:c.1561C>T	p.Arg521Trp	p.R521W	ENST00000358026	NM_001128849.1	521	Cgg/Tgg	9/36	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.538907231353685	2		231	371	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713171	30713171	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045507-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	126	237	0	ENST00000295754.5:c.496C>T	p.Gln166Ter	p.Q166*	ENST00000295754	NM_003242.5	166	Caa/Taa	4/7	1	2	FACETS	0.886	0.806	0.969	0.886	0.806	0.969	CLONAL	1	TRUE	1	0.538907231353685	2		237	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0046165-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	42	591	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.225256563138255	1	FACETS	0.95	0.794	1	0.95	0.794	1	CLONAL	1	TRUE	0	0.19	1		591	421	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833925	44833925	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046165-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	23	124	0	ENST00000377967.4:c.349C>T	p.Gln117Ter	p.Q117*	ENST00000377967	NM_021140.2	117	Cag/Tag	4/29	1	1	FACETS	0.913	0.723	1	1	0.943	1	CLONAL	2	TRUE	0	0.19	1		124	120	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978662	70978662	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046165-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	66	482	0	ENST00000276594.2:c.991G>T	p.Ala331Ser	p.A331S	ENST00000276594	NM_024504.3	331	Gcc/Tcc	5/8	0.225256563138255	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.19	1		482	468	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144147	11144147	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064795161	NA	P-0046165-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	29	457	0	ENST00000358026.2:c.3728G>A	p.Arg1243Gln	p.R1243Q	ENST00000358026	NM_001128849.1	1243	cGg/cAg	26/36	1	2	FACETS	0.743	0.596	0.91	0.743	0.596	0.91	CLONAL	1	TRUE	1	0.19	2		457	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0046576-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	269	376	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.485116706070633	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.485116706070633	1		376	718	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225367705	225367705	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046576-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	30	261	0	ENST00000264414.4:c.1462A>T	p.Arg488Trp	p.R488W	ENST00000264414	NM_003590.4	488	Agg/Tgg	10/16	0.485116706070633	1	FACETS	0.52	0.423	0.628	0.52	0.423	0.628	SUBCLONAL	1	TRUE	0	0.485116706070633	1		261	180	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959195	2959195	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046576-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	534	379	0	ENST00000396946.4:c.2321A>C	p.Asp774Ala	p.D774A	ENST00000396946	NM_032415.4	774	gAc/gCc	18/25	0.485116706070633	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	1	0.485116706070633	3		379	1167	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593522	48593523	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0046888-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	86	518	1	ENST00000342988.3:c.1273_1274delinsTT	p.Ala425Phe	p.A425F	ENST00000342988	NM_005359.5	425	GCt/TTt	10/12	0.492958910129799	3	FACETS	1	0.972	1	0.424	0.379	0.471	CLONAL	1	TRUE	0	0.571922379791443	3		519	304	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047218-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	107	257	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	1	0.580589284343908	2		257	357	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610198	10610198	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047218-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	125	490	0	ENST00000171111.5:c.512G>T	p.Cys171Phe	p.C171F	ENST00000171111	NM_203500.1	171	tGc/tTc	2/6	0.580589284343908	1	FACETS	0.979	0.9	1	0.979	0.9	1	CLONAL	1	FALSE	0	0.580589284343908	1		490	312	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219336	1219336	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047218-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	110	415	0	ENST00000326873.7:c.388G>T	p.Glu130Ter	p.E130*	ENST00000326873	NM_000455.4	130	Gag/Tag	3/10	0.580589284343908	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	FALSE	0	0.580589284343908	1		415	263	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007131	62007131	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047218-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	21	436	0	ENST00000392795.3:c.551A>T	p.Lys184Met	p.K184M	ENST00000392795	NM_001039933.1	184	aAg/aTg	4/6	1	2	FACETS	0.195	0.15	0.248	0.195	0.15	0.248	SUBCLONAL	1	FALSE	1	0.580589284343908	2		436	371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781504	NA	P-0048462-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	404	576	0	ENST00000269305.4:c.314G>T	p.Gly105Val	p.G105V	ENST00000269305	NM_001126112.2	105	gGc/gTc	4/11	0.485315649818306	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	0	0.485315649818306	3		576	654	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439311	52439311	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs9848343	NA	P-0048462-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	213	469	0	ENST00000460680.1:c.932-1G>A		p.X311_splice	ENST00000460680	NM_004656.3	311			0.485315649818306	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.485315649818306	2		469	435	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980568	1980568	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs950025435	NA	P-0048462-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	245	536	0	ENST00000382891.5:c.4030G>A	p.Glu1344Lys	p.E1344K	ENST00000382891	NM_133335.3	1344	Gag/Aag	22/22	0.485315649818306	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.485315649818306	2		536	481	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149245644	149245644	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048462-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	88	426	0	ENST00000360632.3:c.884G>T	p.Ser295Ile	p.S295I	ENST00000360632	NM_015472.4	295	aGc/aTc	5/7	0.442962514201948	3	FACETS	0.885	0.787	0.99	0.443	0.393	0.495	CLONAL	1	TRUE	1	0.485315649818306	3		426	509	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0048660-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	107	257	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.396043158123121	2		257	471	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220594	1220595	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0048660-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	83	473	0	ENST00000326873.7:c.614_615del	p.Ala205GlyfsTer60	p.A205Gfs*60	ENST00000326873	NM_000455.4	204	ttCGcg/ttcg	5/10	0.396043158123121	1	FACETS	0.81	0.719	0.907	0.81	0.719	0.907	CLONAL	1	TRUE	0	0.396043158123121	1		473	415	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259184	36259184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048660-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	31	454	1	ENST00000300305.3:c.307C>T	p.Pro103Ser	p.P103S	ENST00000300305		103	Cct/Tct	3/8	1	2	FACETS	0.321	0.259	0.392	0.321	0.259	0.392	SUBCLONAL	1	TRUE	1	0.396043158123121	2		455	487	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0049443-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	29	311	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		311	389	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0050018-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	97	539	0				ENST00000310581	NM_198253.2	-/1132			0.822697984431684	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.822697984431684	1		539	127	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249017	55249018	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCA	rs1554350381	NA	P-0050018-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	154	546	0	ENST00000275493.2:c.2317_2319dup	p.His773dup	p.H773dup	ENST00000275493	NM_005228.3	773	ccc/ccCCAc	20/28	0.822697984431684	3	FACETS	0.836	0.768	0.907	0.418	0.384	0.454	CLONAL	1	TRUE	1	0.822697984431684	3		546	632	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865342	57865342	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145582008	NA	P-0050018-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	169	551	0	ENST00000228682.2:c.2819G>A	p.Arg940His	p.R940H	ENST00000228682	NM_005269.2	940	cGt/cAt	12/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.822697984431684	2		551	397	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591291	67591291	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050018-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	273	479	0	ENST00000274335.5:c.1789T>G	p.Trp597Gly	p.W597G	ENST00000274335		597	Tgg/Ggg	13/15	0.822697984431684	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.822697984431684	1		479	378	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717777	89717777	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs786204873	NA	P-0050018-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	153	343	0	ENST00000371953.3:c.801+1G>A		p.X267_splice	ENST00000371953	NM_000314.4	267			0.822697984431684	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.822697984431684	1		343	206	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874324	76874324	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050018-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	185	392	0	ENST00000373344.5:c.5398A>C	p.Met1800Leu	p.M1800L	ENST00000373344	NM_000489.3	1800	Atg/Ctg	21/35	1	2	FACETS	0.955	0.891	1	0.955	0.891	1	CLONAL	1	TRUE	1	0.822697984431684	2		392	471	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38981989	38981989	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050403-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	146	272	0	ENST00000357387.3:c.733C>T	p.Arg245Ter	p.R245*	ENST00000357387	NM_152756.3	245	Cga/Tga	8/38	0.616948928856084	3	FACETS	0.971	0.889	1	0.485	0.444	0.528	CLONAL	1	TRUE	1	0.616948928856084	3		272	638	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0050403-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	8353	325	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.616948928856084	25	FACETS	0.983	0.979	0.987			1	CLONAL	25	TRUE	NA	0.616948928856084	25		325	8919	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888210	112888210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121918464	NA	P-0050403-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	154	299	1	ENST00000351677.2:c.226G>A	p.Glu76Lys	p.E76K	ENST00000351677	NM_002834.3	76	Gag/Aag	3/16	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.616948928856084	2		300	490	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440904	56440904	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1458799446	NA	P-0050403-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	402	325	0	ENST00000407977.2:c.433C>T	p.Arg145Ter	p.R145*	ENST00000407977		145	Cga/Tga	4/10	0.616948928856084	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.616948928856084	2		325	645	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240375	98240375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1293146883	NA	P-0050403-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	163	321	0	ENST00000331920.6:c.1309G>A	p.Val437Ile	p.V437I	ENST00000331920	NM_000264.3	437	Gtc/Atc	9/24	0.612053339656042	4	FACETS	1	0.952	1	0.35	0.322	0.38	CLONAL	1	TRUE	1	0.616948928856084	4		321	813	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847399	68847399	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0050403-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	316	312	0	ENST00000261769.5:c.1320+1G>T		p.X440_splice	ENST00000261769	NM_004360.3	440			0.616948928856084	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.616948928856084	2		312	503	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918577	94918577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050403-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	152	294	0	ENST00000536441.1:c.605C>T	p.Ala202Val	p.A202V	ENST00000536441	NM_144665.3	202	gCt/gTt	5/10	1	2	FACETS	0.962	0.886	1	0.962	0.886	1	CLONAL	1	TRUE	1	0.616948928856084	2		294	512	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858298	27858298	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050403-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	229	493	0	ENST00000359303.2:c.273G>A	p.Met91Ile	p.M91I	ENST00000359303	NM_003535.2	91	atG/atA	1/1	0.616948928856084	3	FACETS	0.977	0.911	1	0.489	0.455	0.523	CLONAL	1	TRUE	1	0.616948928856084	3		493	994	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981363	68981363	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050403-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	93	182	0	ENST00000288368.4:c.1435A>T	p.Ile479Phe	p.I479F	ENST00000288368	NM_024870.2	479	Att/Ttt	12/40	0.616948928856084	3	FACETS	0.892	0.798	0.992	0.446	0.399	0.496	CLONAL	1	TRUE	1	0.616948928856084	3		182	442	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429761	78429761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050403-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	56	289	0	ENST00000370768.2:c.1027C>T	p.Leu343Phe	p.L343F	ENST00000370768	NM_003902.3	343	Ctt/Ttt	12/20	1	2	FACETS	0.343	0.294	0.397	0.343	0.294	0.397	SUBCLONAL	1	TRUE	1	0.616948928856084	2		289	529	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0051509-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	24	734	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.133345528089858	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		734	404	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431850	49431850	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051509-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	32	810	0	ENST00000301067.7:c.9289G>T	p.Glu3097Ter	p.E3097*	ENST00000301067	NM_003482.3	3097	Gag/Tag	34/54	0.235221182732202	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		810	554	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433575	49433575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051509-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	34	749	0	ENST00000301067.7:c.7978G>A	p.Glu2660Lys	p.E2660K	ENST00000301067	NM_003482.3	2660	Gaa/Aaa	31/54	0.235221182732202	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		749	597	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845343	151845345	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0051509-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	24	617	0	ENST00000262189.6:c.13667_13669del	p.His4556_Thr4557delinsPro	p.H4556_T4557delinsP	ENST00000262189	NM_170606.2	4556	cACAca/cca	52/59	0.133345528089858	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		617	446	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912660	NA	P-0051860-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	161	537	0	ENST00000269305.4:c.839G>T	p.Arg280Ile	p.R280I	ENST00000269305	NM_001126112.2	280	aGa/aTa	8/11	0.495446234559573	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.495446234559573	2		537	316	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913355	NA	P-0051860-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	121	357	0	ENST00000288602.6:c.1406G>T	p.Gly469Val	p.G469V	ENST00000288602	NM_004333.4	469	gGa/gTa	11/18	0.413118285925251	4	FACETS	0.939	0.856	1	0.939	0.856	1	CLONAL	2	TRUE	2	0.495446234559573	4		357	389	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691105	18691105	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051860-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	170	414	0	ENST00000266497.5:c.3216C>A	p.Phe1072Leu	p.F1072L	ENST00000266497		1072	ttC/ttA	23/31	0.311612144286831	5	FACETS	1	0.951	1			1	CLONAL	2	TRUE	NA	0.495446234559573	5		414	577	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484043	50484043	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051860-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	149	502	0	ENST00000394963.4:c.893A>T	p.Asp298Val	p.D298V	ENST00000394963	NM_003076.4	298	gAc/gTc	8/13	0.495446234559573	4	FACETS	0.92	0.846	0.995	0.92	0.846	0.995	CLONAL	2	TRUE	2	0.495446234559573	4		502	489	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274078	10274078	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051860-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	80	586	0	ENST00000330684.3:c.191C>A	p.Pro64His	p.P64H	ENST00000330684	NM_001134407.1	64	cCc/cAc	2/13	1	2	FACETS	0.997	0.885	1	0.997	0.885	1	CLONAL	1	TRUE	1	0.495446234559573	2		586	324	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219345	1219345	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051860-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	160	524	0	ENST00000326873.7:c.397G>C	p.Val133Leu	p.V133L	ENST00000326873	NM_000455.4	133	Gtg/Ctg	3/10	0.313962098290559	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	2	0.495446234559573	4		524	441	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230486796	230486796	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051860-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	267	487	0	ENST00000391860.1:c.457G>C	p.Ala153Pro	p.A153P	ENST00000391860	NM_001258311.1	153	Gcc/Ccc	3/7	0.495446234559573	8	FACETS	0.953	0.899	1	0.953	0.899	1	CLONAL	4	TRUE	4	0.495446234559573	8		487	703	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0052103-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	108	311	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.205080793955815	5	FACETS	1	0.944	1	1	0.944	1	CLONAL	3	TRUE	2	0.205080793955815	5		311	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0052103-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	99	542	0	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	0.204875437322953	3	FACETS	1	0.913	1			1	CLONAL	2	TRUE	NA	0.205080793955815	3		542	521	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748003	41748003	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052103-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	31	289	0	ENST00000226382.2:c.766G>T	p.Ala256Ser	p.A256S	ENST00000226382	NM_003924.3	256	Gca/Tca	3/3	1	2	FACETS	0.779	0.636	0.938	1	0.947	1	CLONAL	2	TRUE	1	0.205080793955815	2		289	194	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123353320	123353320	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052103-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	54	482	0	ENST00000358487.5:c.12G>C	p.Trp4Cys	p.W4C	ENST00000358487	NM_000141.4	4	tgG/tgC	2/18	0.205080793955815	3	FACETS	1	0.892	1	0.527	0.45	0.611	CLONAL	1	TRUE	1	0.205080793955815	3		482	551	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28971206	28971206	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0052103-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	27	337	0	ENST00000282397.4:c.1552-1G>C		p.X518_splice	ENST00000282397	NM_002019.4	518			0.205080793955815	3	FACETS	0.652	0.518	0.806	0.326	0.259	0.403	SUBCLONAL	1	TRUE	1	0.205080793955815	3		337	445	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40476785	40476785	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052103-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	67	513	0	ENST00000264657.5:c.1544C>G	p.Thr515Ser	p.T515S	ENST00000264657	NM_139276.2	515	aCc/aGc	17/24	0.205080793955815	3	FACETS	1	0.918	1	0.539	0.468	0.616	CLONAL	1	TRUE	1	0.205080793955815	3		513	668	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591241	67591467	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTCAGGTGGTTGACTCAAAAAGGTGTTCGGCAAAAGAAGTTGAACGAGTGGTTGGGCAATGAAAACACTGAAGAGTAAGTAGTTACTAAAGATGGTGATAGCAGAAGATTTTTCTCATTTTAGGAAAATGCATGACTTGCTTTGTTTTTAGAACAAGTGAGGAATTTTACTGAGTTTGGAACATCTTGTAGGAGAAAATGTATAAACTCAGTGCCATTATCCAGA	TTTTCAGGTGGTTGACTCAAAAAGGTGTTCGGCAAAAGAAGTTGAACGAGTGGTTGGGCAATGAAAACACTGAAGAGTAAGTAGTTACTAAAGATGGTGATAGCAGAAGATTTTTCTCATTTTAGGAAAATGCATGACTTGCTTTGTTTTTAGAACAAGTGAGGAATTTTACTGAGTTTGGAACATCTTGTAGGAGAAAATGTATAAACTCAGTGCCATTATCCAGA	-	novel	NA	P-0052103-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	37	493	0	ENST00000274335.5:c.1746-7_1814+151del		p.X582_splice	ENST00000274335		582		13/15	0.205080793955815	3	FACETS	0.67	0.551	0.803	0.335	0.275	0.402	SUBCLONAL	1	TRUE	1	0.205080793955815	3		493	594	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396746	139396746	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052214-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	239	476	0	ENST00000277541.6:c.5362G>C	p.Gly1788Arg	p.G1788R	ENST00000277541	NM_017617.3	1788	Ggc/Cgc	28/34	1	2	FACETS	0.979	0.923	1	0.979	0.923	1	CLONAL	1	TRUE	1	0.882572227606851	2		476	553	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390836	139390839	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	novel	NA	P-0052214-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	303	631	0	ENST00000277541.6:c.7352_7355del	p.Leu2451ArgfsTer25	p.L2451Rfs*25	ENST00000277541	NM_017617.3	2451	cTGGCg/cg	34/34	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.882572227606851	2		631	678	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913562	39913562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367859441	NA	P-0052214-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	261	440	1	ENST00000378444.4:c.4766G>A	p.Arg1589His	p.R1589H	ENST00000378444	NM_001123385.1	1589	cGc/cAc	13/15	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.882572227606851	2		441	585	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950021	44950022	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGAAGTCAATAGTACCCA	novel	NA	P-0052214-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	115	384	0	ENST00000377967.4:c.3793_3810dup	p.Lys1265_Met1270dup	p.K1265_M1270dup	ENST00000377967	NM_021140.2	1265	gtg/gTGAAGTCAATAGTACCCAtg	26/29	1	2	FACETS	0.595	0.54	0.653	0.595	0.54	0.653	SUBCLONAL	1	TRUE	1	0.882572227606851	2		384	438	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102136	27102136	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052214-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	275	508	0	ENST00000324856.7:c.5063del	p.Leu1688Ter	p.L1688*	ENST00000324856	NM_006015.4	1688	Tta/ta	19/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.882572227606851	2		508	603	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417443	139417444	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCTCCT	novel	NA	P-0052214-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	280	617	0	ENST00000277541.6:c.600_601insAGGAGGC	p.Ser201ArgfsTer57	p.S201Rfs*57	ENST00000277541	NM_017617.3	200	-/AGGAGGC	4/34	1	2	FACETS	0.882	0.834	0.932	0.882	0.834	0.932	CLONAL	1	TRUE	1	0.882572227606851	2		617	719	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933592	39933592	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052214-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	310	567	0	ENST00000378444.4:c.1007C>A	p.Ser336Ter	p.S336*	ENST00000378444	NM_001123385.1	336	tCg/tAg	4/15	1	2	FACETS	0.969	0.92	1	0.969	0.92	1	CLONAL	1	TRUE	1	0.882572227606851	2		567	725	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446855	49446855	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053191-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	104	422	0	ENST00000301067.7:c.955G>C	p.Ala319Pro	p.A319P	ENST00000301067	NM_003482.3	319	Gcg/Ccg	8/54	0.309371778856694	3	FACETS	0.83	0.742	0.924	0.415	0.371	0.462	CLONAL	1	TRUE	1	0.309371778856694	3		422	935	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967266	134967266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770160653	NA	P-0053191-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	88	476	0	ENST00000398015.3:c.2605C>T	p.Pro869Ser	p.P869S	ENST00000398015	NM_004441.4	869	Ccc/Tcc	14/16	1	2	FACETS	0.685	0.606	0.77	0.685	0.606	0.77	SUBCLONAL	1	TRUE	1	0.309371778856694	2		476	830	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082917	16082917	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053191-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	28	248	0	ENST00000281043.3:c.732del	p.Ser245AlafsTer16	p.S245Afs*16	ENST00000281043	NM_005378.4	244	aCc/ac	2/3	1	2	FACETS	0.575	0.459	0.707	0.575	0.459	0.707	SUBCLONAL	1	TRUE	1	0.254342005069954	2		248	383	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053430-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	116	446	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.912	0.835	0.991	0.912	0.835	0.991	CLONAL	1	TRUE	1	0.862313687047377	2		446	295	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0053430-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	91	372	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.862313687047377	3	FACETS	0.904	0.811	1	0.452	0.405	0.501	CLONAL	1	TRUE	1	0.862313687047377	3		372	334	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295258	1295258	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0053430-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	185	723	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.862313687047377	2		723	385	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246042	46246043	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0053430-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	101	170	0	ENST00000334344.6:c.4137_4138del	p.His1379GlnfsTer10	p.H1379Qfs*10	ENST00000334344	NM_152641.2	1379	cAT/c	15/21	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.862313687047377	2		170	229	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641048	117641048	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053430-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	113	146	0	ENST00000368508.3:c.5923A>C	p.Ile1975Leu	p.I1975L	ENST00000368508	NM_002944.2	1975	Atc/Ctc	36/43	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.862313687047377	2		146	260	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527280	187527280	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	206	339	0	ENST00000441802.2:c.10294G>T	p.Asp3432Tyr	p.D3432Y	ENST00000441802	NM_005245.3	3432	Gat/Tat	17/27	0.206489822147469	2	FACETS	0.998	0.929	1	0.998	0.929	1	CLONAL	2	TRUE	0	0.279651785394496	2		339	738	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873648	35873648	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	91	343	0	ENST00000303115.3:c.604G>C	p.Glu202Gln	p.E202Q	ENST00000303115	NM_002185.3	202	Gag/Cag	5/8	0.19351338918766	5	FACETS	1	0.932	1	0.357	0.316	0.401	CLONAL	1	TRUE	2	0.279651785394496	5		343	862	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112055	115112055	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201325654	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	214	458	0	ENST00000257566.3:c.1685C>T	p.Ala562Val	p.A562V	ENST00000257566	NM_016569.3	562	gCc/gTc	7/8	0.230186485612382	3	FACETS	1	0.985	1	0.79	0.737	0.845	CLONAL	2	TRUE	0	0.279651785394496	3		458	736	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120795681	120795681	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	212	274	0	ENST00000257552.2:c.472G>C	p.Glu158Gln	p.E158Q	ENST00000257552	NM_002442.3	158	Gag/Cag	8/15	0.230186485612382	3	FACETS	0.946	0.884	1	0.946	0.884	1	CLONAL	3	TRUE	0	0.279651785394496	3		274	609	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133748425	133748425	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	124	224	0	ENST00000318560.5:c.1085+1G>T		p.X362_splice	ENST00000318560	NM_005157.4	362			0.279651785394496	2	FACETS	0.977	0.89	1	0.977	0.89	1	CLONAL	2	TRUE	0	0.279651785394496	2		224	454	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271227	153271227	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	131	223	0	ENST00000281708.4:c.551G>T	p.Gly184Val	p.G184V	ENST00000281708	NM_033632.3	184	gGa/gTa	3/12	0.279651785394496	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.279651785394496	2		223	445	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068031	94068031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747304855	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	70	294	0	ENST00000369303.4:c.931G>A	p.Glu311Lys	p.E311K	ENST00000369303	NM_004440.3	311	Gaa/Aaa	4/17	1	2	FACETS	0.815	0.711	0.928	0.815	0.711	0.928	CLONAL	1	TRUE	1	0.279651785394496	2		294	614	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578281	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	273	457	0	ENST00000269305.4:c.568_569del	p.Pro190SerfsTer18	p.P190Sfs*18	ENST00000269305	NM_001126112.2	190	CCt/t	6/11	0.279651785394496	3	FACETS	0.862	0.811	0.913	0.862	0.811	0.913	CLONAL	3	TRUE	0	0.279651785394496	3		457	861	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934252	81934252	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	101	319	0	ENST00000359376.3:c.1229G>T	p.Ser410Ile	p.S410I	ENST00000359376	NM_002661.3	410	aGc/aTc	14/33	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.279651785394496	2		319	552	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821581	32821581	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	94	348	0	ENST00000354258.4:c.13C>G	p.Leu5Val	p.L5V	ENST00000354258	NM_000593.5	5	Ctc/Gtc	1/11	0.213129367892094	4	FACETS	1	0.98	1	0.743	0.662	0.828	CLONAL	1	TRUE	2	0.279651785394496	4		348	579	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250454	26250454	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	185	506	0	ENST00000446824.2:c.380T>A	p.Leu127His	p.L127H	ENST00000446824	NM_021018.2	127	cTc/cAc	1/1	0.213129367892094	4	FACETS	0.885	0.817	0.955	0.885	0.817	0.955	CLONAL	2	TRUE	2	0.279651785394496	4		506	957	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852109	128852109	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	199	397	0	ENST00000249373.3:c.2181G>T	p.Gln727His	p.Q727H	ENST00000249373	NM_005631.4	727	caG/caT	12/12	0.279651785394496	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.279651785394496	3		397	690	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125523659	125523659	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	157	251	0	ENST00000428830.2:c.1252G>C	p.Asp418His	p.D418H	ENST00000428830	NM_001114121.2	418	Gat/Cat	12/14	0.279651785394496	6	FACETS	1	0.97	1	0.373	0.342	0.406	CLONAL	2	TRUE	0	0.279651785394496	6		251	782	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348892	11348892	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs768393197	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	64	341	0	ENST00000332029.2:c.444C>G	p.Phe148Leu	p.F148L	ENST00000332029	NM_003745.1	148	ttC/ttG	2/2	1	2	FACETS	0.928	0.805	1	0.928	0.805	1	CLONAL	1	TRUE	1	0.279651785394496	2		341	493	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551266	29551266	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	245	367	0	ENST00000389048.3:c.1364G>T	p.Cys455Phe	p.C455F	ENST00000389048	NM_004304.4	455	tGt/tTt	6/29	0.23623098258897	3	FACETS	0.994	0.934	1	0.994	0.934	1	CLONAL	3	TRUE	0	0.279651785394496	3		367	670	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139562737	139562737	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	43	370	0	ENST00000308874.7:c.3G>A	p.Met1?	p.M1?	ENST00000308874		1	atG/atA	3/10	0.279651785394496	2	FACETS	0.513	0.428	0.606	0.256	0.214	0.303	SUBCLONAL	1	TRUE	0	0.279651785394496	2		370	600	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143044561	143044562	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	158	251	1	ENST00000262992.4:c.1900_1901delinsTT	p.Gly634Leu	p.G634L	ENST00000262992	NM_001101669.1	634	GGa/TTa	18/24	0.279651785394496	2	FACETS	0.989	0.911	1	0.989	0.911	1	CLONAL	2	TRUE	0	0.279651785394496	2		252	571	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32905105	32905105	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060502473	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	40	214	0	ENST00000380152.3:c.731A>G	p.Asp244Gly	p.D244G	ENST00000380152		244	gAt/gGt	9/27	1	2	FACETS	0.514	0.426	0.611	0.514	0.426	0.611	SUBCLONAL	1	TRUE	1	0.279651785394496	2		214	557	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61322920	61322920	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	57	198	1	ENST00000283752.5:c.1144C>A	p.Leu382Ile	p.L382I	ENST00000283752	NM_006919.2	382	Ctc/Atc	8/8	0.206489822147469	2	FACETS	1	0.954	1	0.629	0.543	0.722	CLONAL	1	TRUE	0	0.279651785394496	2		199	324	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677218	29677218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	180	281	0	ENST00000356175.3:c.7276G>A	p.Glu2426Lys	p.E2426K	ENST00000356175	NM_000267.3	2426	Gaa/Aaa	49/57	0.230186485612382	3	FACETS	1	0.985	1	0.828	0.767	0.889	CLONAL	2	TRUE	0	0.279651785394496	3		281	591	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863616	68863616	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	72	397	0	ENST00000261769.5:c.2355C>G	p.Asn785Lys	p.N785K	ENST00000261769	NM_004360.3	785	aaC/aaG	15/16	1	2	FACETS	0.694	0.606	0.79	0.694	0.606	0.79	SUBCLONAL	1	TRUE	1	0.279651785394496	2		397	742	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609765	117609765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	80	305	0	ENST00000368508.3:c.6934G>A	p.Asp2312Asn	p.D2312N	ENST00000368508	NM_002944.2	2312	Gac/Aac	43/43	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.279651785394496	2		305	571	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676219	29676219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	227	264	0	ENST00000356175.3:c.7208G>A	p.Arg2403Lys	p.R2403K	ENST00000356175	NM_000267.3	2403	aGa/aAa	48/57	0.230186485612382	3	FACETS	0.89	0.833	0.948	0.89	0.833	0.948	CLONAL	3	TRUE	0	0.279651785394496	3		264	693	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221257	5221257	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	252	365	0	ENST00000357368.4:c.3209A>T	p.Tyr1070Phe	p.Y1070F	ENST00000357368	NM_002850.3	1070	tAc/tTc	20/38	0.279651785394496	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	TRUE	0	0.279651785394496	3		365	658	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965914	90965914	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	142	264	0	ENST00000265433.3:c.1403G>T	p.Arg468Met	p.R468M	ENST00000265433	NM_002485.4	468	aGg/aTg	11/16	0.279651785394496	3	FACETS	0.885	0.809	0.964	0.885	0.809	0.964	CLONAL	2	TRUE	1	0.279651785394496	3		264	654	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936685	32936685	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	42	274	0	ENST00000380152.3:c.7831G>T	p.Asp2611Tyr	p.D2611Y	ENST00000380152		2611	Gat/Tat	17/27	1	2	FACETS	0.488	0.406	0.578	0.488	0.406	0.578	SUBCLONAL	1	TRUE	1	0.279651785394496	2		274	616	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282155	38282155	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	139	436	0	ENST00000425967.3:c.901G>T	p.Gly301Cys	p.G301C	ENST00000425967	NM_001174067.1	301	Ggt/Tgt	8/19	0.279651785394496	3	FACETS	1	0.977	1	0.614	0.558	0.672	CLONAL	1	TRUE	1	0.279651785394496	3		436	923	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140487354	140487354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	43	301	2	ENST00000288602.6:c.1171G>A	p.Asp391Asn	p.D391N	ENST00000288602	NM_004333.4	391	Gat/Aat	9/18	0.279651785394496	3	FACETS	0.416	0.347	0.494	0.208	0.173	0.247	SUBCLONAL	1	TRUE	1	0.279651785394496	3		303	842	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665749	29665749	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	168	233	0	ENST00000356175.3:c.6784G>A	p.Asp2262Asn	p.D2262N	ENST00000356175	NM_000267.3	2262	Gac/Aac	45/57	0.230186485612382	3	FACETS	1	0.982	1	0.802	0.742	0.865	CLONAL	2	TRUE	0	0.279651785394496	3		233	569	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874914	151874914	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	216	347	0	ENST00000262189.6:c.7624T>C	p.Ser2542Pro	p.S2542P	ENST00000262189	NM_170606.2	2542	Tca/Cca	38/59	0.279651785394496	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.279651785394496	3		347	782	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124503666	124503666	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	175	282	0	ENST00000357628.3:c.284G>T	p.Gly95Val	p.G95V	ENST00000357628	NM_015450.2	95	gGt/gTt	8/19	0.279651785394496	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.279651785394496	3		282	605	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143966	11143966	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	297	325	0	ENST00000358026.2:c.3547G>A	p.Asp1183Asn	p.D1183N	ENST00000358026	NM_001128849.1	1183	Gac/Aac	26/36	0.279651785394496	5	FACETS	1	0.987	1	0.686	0.648	0.725	CLONAL	3	TRUE	0	0.279651785394496	5		325	879	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774915	73774915	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs747143516	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	210	316	0	ENST00000254810.4:c.258G>C	p.Gln86His	p.Q86H	ENST00000254810	NM_005324.3	86	caG/caC	3/4	0.230186485612382	3	FACETS	0.854	0.797	0.913	0.854	0.797	0.913	CLONAL	3	TRUE	0	0.279651785394496	3		316	668	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217860	2217860	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	243	383	0	ENST00000398665.3:c.2634G>T	p.Lys878Asn	p.K878N	ENST00000398665	NM_032482.2	878	aaG/aaT	22/28	0.279651785394496	3	FACETS	0.965	0.907	1	0.965	0.907	1	CLONAL	3	TRUE	0	0.279651785394496	3		383	684	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17349152	17349152	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs201098090	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	93	342	0	ENST00000375499.3:c.716C>G	p.Ser239Cys	p.S239C	ENST00000375499	NM_003000.2	239	tCt/tGt	7/8	0.226099315604165	2	FACETS	1	0.961	1	0.585	0.522	0.653	CLONAL	1	TRUE	0	0.279651785394496	2		342	568	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250785	26250785	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	201	469	0	ENST00000446824.2:c.49C>A	p.Pro17Thr	p.P17T	ENST00000446824	NM_021018.2	17	Ccg/Acg	1/1	0.213129367892094	4	FACETS	0.958	0.888	1	0.958	0.888	1	CLONAL	2	TRUE	2	0.279651785394496	4		469	960	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684327	29684327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560262404	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	215	284	0	ENST00000356175.3:c.7847G>A	p.Arg2616Gln	p.R2616Q	ENST00000356175	NM_000267.3	2616	cGa/cAa	53/57	0.230186485612382	3	FACETS	0.867	0.81	0.925	0.867	0.81	0.925	CLONAL	3	TRUE	0	0.279651785394496	3		284	674	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805358	32805360	+	frameshift_variant	Frame_Shift_Del	DEL	GGC	GGC	AA	novel	NA	P-0054342-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	146	353	0	ENST00000374899.4:c.562_564delinsTT	p.Ala188PhefsTer62	p.A188Ffs*62	ENST00000374899	NM_018833.2	188	GCC/TT	3/12	0.213129367892094	4	FACETS	0.788	0.719	0.86	0.788	0.719	0.86	SUBCLONAL	2	TRUE	2	0.279651785394496	4		353	848	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	39	446	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.733	0.615	0.862	0.733	0.615	0.862	SUBCLONAL	1	TRUE	1	0.554100225167884	2		446	192	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0054640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	11	215	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.201	0.138	0.278	0.201	0.138	0.278	SUBCLONAL	1	TRUE	1	0.554100225167884	2		215	198	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0054640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	24	400	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.12482504957227	3	FACETS	0.376	0.295	0.47	0.188	0.147	0.235	INDETERMINATE	1	TRUE	1	0.554100225167884	3		400	294	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0054640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	144	405	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.429937417762334	2	FACETS	0.912	0.848	0.975	0.912	0.848	0.975	CLONAL	2	TRUE	0	0.554100225167884	2		405	285	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0054640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	44	394	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	0.12482504957227	3	FACETS	0.76	0.641	0.889	0.38	0.32	0.445	INDETERMINATE	1	TRUE	1	0.554100225167884	3		394	267	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711891	89711891	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660507	NA	P-0054640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	20	377	0	ENST00000371953.3:c.509G>T	p.Ser170Ile	p.S170I	ENST00000371953	NM_000314.4	170	aGt/aTt	6/9	0.12482504957227	3	FACETS	0.345	0.264	0.44	0.173	0.132	0.22	INDETERMINATE	1	TRUE	1	0.554100225167884	3		377	267	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918960	76918960	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	20	413	0	ENST00000373344.5:c.4031A>T	p.Lys1344Ile	p.K1344I	ENST00000373344	NM_000489.3	1344	aAa/aTa	12/35	1	2	FACETS	0.188	0.143	0.24	0.188	0.143	0.24	SUBCLONAL	1	TRUE	1	0.554100225167884	2		413	385	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0054640-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	54	215	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.101019363688795	4	FACETS	1	0.95	1	0.62	0.534	0.713	INDETERMINATE	1	FALSE	2	0.465486856663543	4		215	274	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0054640-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	51	400	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.349169756701902	3	FACETS	0.816	0.697	0.945	0.408	0.348	0.473	CLONAL	1	FALSE	1	0.465486856663543	3		400	331	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0054640-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	90	394	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	0.349169756701902	3	FACETS	1	0.973	1	0.646	0.577	0.718	CLONAL	1	FALSE	1	0.465486856663543	3		394	369	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711891	89711891	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660507	NA	P-0054640-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	43	377	0	ENST00000371953.3:c.509G>T	p.Ser170Ile	p.S170I	ENST00000371953	NM_000314.4	170	aGt/aTt	6/9	0.349169756701902	3	FACETS	0.616	0.516	0.725	0.308	0.258	0.363	SUBCLONAL	1	FALSE	1	0.465486856663543	3		377	370	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918960	76918960	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054640-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	48	413	0	ENST00000373344.5:c.4031A>T	p.Lys1344Ile	p.K1344I	ENST00000373344	NM_000489.3	1344	aAa/aTa	12/35	0.336418418083005	1	FACETS	0.47	0.398	0.547	0.47	0.398	0.547	SUBCLONAL	1	FALSE	0	0.465486856663543	1		413	337	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958842	55958842	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054640-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	63	551	0	ENST00000263923.4:c.3011A>T	p.His1004Leu	p.H1004L	ENST00000263923	NM_002253.2	1004	cAt/cTt	22/30	1	2	FACETS	0.815	0.71	0.928	0.815	0.71	0.928	CLONAL	1	FALSE	1	0.465486856663543	2		551	332	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0056460-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	148	389	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.94	0.866	1	0.94	0.866	1	CLONAL	1	TRUE	1	0.687677247491875	2		389	458	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0056460-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	147	404	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.687677247491875	1	FACETS	0.871	0.809	0.934	0.871	0.809	0.934	CLONAL	1	TRUE	0	0.687677247491875	1		404	322	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205045	123205045	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056460-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	85	113	0	ENST00000218089.9:c.2406del	p.Met803CysfsTer8	p.M803Cfs*8	ENST00000218089	NM_001042749.1	802	aTt/at	25/35	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.687677247491875	1		113	126	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836344	89836344	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056460-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	178	597	0	ENST00000389301.3:c.2405A>T	p.Asp802Val	p.D802V	ENST00000389301	NM_000135.2	802	gAt/gTt	26/43	1	2	FACETS	0.915	0.848	0.983	0.915	0.848	0.983	CLONAL	1	TRUE	1	0.687677247491875	2		597	566	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16001809	16001809	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056481-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	18	254	0	ENST00000268712.3:c.2692A>G	p.Met898Val	p.M898V	ENST00000268712	NM_006311.3	898	Atg/Gtg	21/46	1	2	FACETS	0.349	0.262	0.451	0.349	0.262	0.451	SUBCLONAL	1	TRUE	1	0.336392478807637	2		254	307	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242482	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAAC	AATTAAGAGAAGCAAC	T	novel	NA	P-0056481-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	38	290	0	ENST00000275493.2:c.2237_2252delinsT	p.Glu746_Thr751delinsVal	p.E746_T751delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACa/gTa	19/28	1	2	FACETS	0.664	0.551	0.791	0.664	0.551	0.791	SUBCLONAL	1	TRUE	1	0.336392478807637	2		290	340	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652117	36652117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs114149607	NA	P-0057072-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	39	0	0	ENST00000244741.5:c.239C>T	p.Thr80Met	p.T80M	ENST00000244741	NM_000389.4	80	aCg/aTg	2/3	1	2	FACETS	0.591	0.488	0.708	0.591	0.488	0.708	SUBCLONAL	1	TRUE	1	0.11	2		0	1199	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522696	176522696	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369266328	NA	P-0057072-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	28	0	0	ENST00000292408.4:c.1793G>A	p.Arg598Gln	p.R598Q	ENST00000292408	NM_213647.1	598	cGa/cAa	13/18	1	2	FACETS	0.456	0.362	0.564	0.456	0.362	0.564	SUBCLONAL	1	TRUE	1	0.11	2		0	1117	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374316	81374316	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057591-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	27	246	0	ENST00000222390.5:c.746G>T	p.Arg249Ile	p.R249I	ENST00000222390	NM_000601.4	249	aGa/aTa	6/18	0.300691215594464	4	FACETS	1	0.865	1	0.366	0.294	0.446	CLONAL	1	TRUE	1	0.439472789264391	4		246	161	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879337	151879337	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057591-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	35	507	1	ENST00000262189.6:c.5608C>T	p.Gln1870Ter	p.Q1870*	ENST00000262189	NM_170606.2	1870	Cag/Tag	36/59	NA	2	FACETS	0.838	0.694	0.996			1	INDETERMINATE	1	TRUE	NA	0.439472789264391	2		508	190	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878287	151878287	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057591-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	39	465	0	ENST00000262189.6:c.6658C>T	p.Gln2220Ter	p.Q2220*	ENST00000262189	NM_170606.2	2220	Cag/Tag	36/59	NA	2	FACETS	0.803	0.671	0.947			1	INDETERMINATE	1	TRUE	NA	0.439472789264391	2		465	221	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009251	69009251	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0057591-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	170	232	0	ENST00000288368.4:c.2369-1G>A		p.X790_splice	ENST00000288368	NM_024870.2	790			0.439472789264391	7	FACETS	1	0.974	1			1	CLONAL	5	TRUE	NA	0.439472789264391	7		232	304	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12647756	12647758	+	inframe_deletion	In_Frame_Del	DEL	TGC	TGC	-	novel	NA	P-0057591-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	78	266	0	ENST00000251849.4:c.622_624del	p.Ala208del	p.A208del	ENST00000251849	NM_002880.3	208	GCA/-	6/17	0.439472789264391	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.439472789264391	2		266	155	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16235929	16235929	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057591-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	62	290	0	ENST00000375759.3:c.995G>T	p.Arg332Leu	p.R332L	ENST00000375759	NM_015001.2	332	cGt/cTt	4/15	0.399866501349833	4	FACETS	1	0.895	1	1	0.895	1	CLONAL	2	TRUE	2	0.439472789264391	4		290	199	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009413	69009413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057591-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	181	361	0	ENST00000288368.4:c.2530G>A	p.Gly844Ser	p.G844S	ENST00000288368	NM_024870.2	844	Ggt/Agt	22/40	0.439472789264391	7	FACETS	0.926	0.873	0.979			1	CLONAL	6	TRUE	NA	0.439472789264391	7		361	311	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	59	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.203724783961449	4	FACETS	0.871	0.772	0.971	1	0.968	1	INDETERMINATE	3	TRUE	2	0.51423241035273	4		341	133	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0057825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	48	726	1	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	0.523329377223926	1	FACETS	0.889	0.793	0.981	1	0.978	1	CLONAL	2	TRUE	0	0.51423241035273	1		727	78	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575231	48575231	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs377767386	NA	P-0057825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	24	273	0	ENST00000342988.3:c.424+1G>A		p.X142_splice	ENST00000342988	NM_005359.5	142			0.523329377223926	1	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	0	0.51423241035273	1		273	62	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058036-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	170	446	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.788	0.727	0.85	0.788	0.727	0.85	SUBCLONAL	1	TRUE	1	0.678641323622469	2		446	636	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0058036-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	738	734	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.678641323622469	2		734	1071	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265115	46265115	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058036-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	346	444	0	ENST00000371998.3:c.1985C>G	p.Ser662Cys	p.S662C	ENST00000371998		662	tCt/tGt	12/23	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.678641323622469	2		444	1015	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358978	81358978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374484762	NA	P-0058036-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	291	331	0	ENST00000222390.5:c.983G>A	p.Arg328His	p.R328H	ENST00000222390	NM_000601.4	328	cGt/cAt	8/18	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.678641323622469	2		331	756	SUCCESS
FH	2271	MSKCC	GRCh37	1	241683007	241683007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058036-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	305	370	0	ENST00000366560.3:c.16C>T	p.Arg6Trp	p.R6W	ENST00000366560	NM_000143.3	6	Cgg/Tgg	1/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.678641323622469	2		370	878	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040640	47040640	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058036-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	261	190	0	ENST00000377604.3:c.1275G>A	p.Trp425Ter	p.W425*	ENST00000377604	NM_001204468.1	425	tgG/tgA	13/24	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.678641323622469	1		190	387	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082313	16082314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs780080562	NA	P-0058036-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	220	472	0	ENST00000281043.3:c.134dup	p.Glu47GlyfsTer8	p.E47Gfs*8	ENST00000281043	NM_005378.4	43	acc/aCcc	2/3	1	2	FACETS	0.654	0.608	0.701	0.654	0.608	0.701	SUBCLONAL	1	TRUE	1	0.678641323622469	2		472	992	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100115	157100115	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1015605215	NA	P-0058036-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	402	585	0	ENST00000346085.5:c.1052G>C	p.Gly351Ala	p.G351A	ENST00000346085	NM_020732.3	351	gGa/gCa	1/20	1	2	FACETS	0.91	0.865	0.955	0.91	0.865	0.955	CLONAL	1	TRUE	1	0.678641323622469	2		585	1302	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175942	176175942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs964768927	NA	P-0058036-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	308	423	0	ENST00000367669.3:c.173C>T	p.Ser58Leu	p.S58L	ENST00000367669	NM_022457.5	58	tCg/tTg	1/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.678641323622469	2		423	853	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184065	123184065	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058036-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	285	166	0	ENST00000218089.9:c.923G>T	p.Cys308Phe	p.C308F	ENST00000218089	NM_001042749.1	308	tGc/tTc	11/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.678641323622469	1		166	385	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923045	44923045	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058036-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	343	215	0	ENST00000377967.4:c.1906del	p.Leu636TyrfsTer55	p.L636Yfs*55	ENST00000377967	NM_021140.2	636	Cta/ta	16/29	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.678641323622469	1		215	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578195	7578197	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0059163-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	40	712	0	ENST00000269305.4:c.652_654del	p.Val218del	p.V218del	ENST00000269305	NM_001126112.2	218	GTG/-	6/11	0.266466168885126	2	FACETS	0.788	0.656	0.934	0.394	0.328	0.467	CLONAL	1	TRUE	0	0.266466168885126	2		712	381	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857044	9857044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201707833	NA	P-0059163-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	26	518	0	ENST00000330684.3:c.4357G>A	p.Val1453Met	p.V1453M	ENST00000330684	NM_001134407.1	1453	Gtg/Atg	13/13	0.266466168885126	4	FACETS	0.926	0.735	1	0.463	0.367	0.571	CLONAL	1	TRUE	2	0.266466168885126	4		518	267	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380577	31380577	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0059163-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	33	656	0	ENST00000328111.2:c.1066+1G>A		p.X356_splice	ENST00000328111	NM_006892.3	356			1	2	FACETS	0.866	0.708	1	0.866	0.708	1	CLONAL	1	TRUE	1	0.266466168885126	2		656	286	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604181	189604181	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0059163-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	30	570	0	ENST00000264731.3:c.1350-2A>T		p.X450_splice	ENST00000264731	NM_003722.4	450			0.266466168885126	2	FACETS	1	0.901	1	0.589	0.479	0.712	CLONAL	1	TRUE	0	0.266466168885126	2		570	191	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517945	8517946	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0059163-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	42	550	0	ENST00000356435.5:c.1445dup	p.Leu482PhefsTer25	p.L482Ffs*25	ENST00000356435		482	tta/ttTa	10/35	0.266466168885126	5	FACETS	1	0.89	1	0.361	0.302	0.427	CLONAL	1	TRUE	2	0.266466168885126	5		550	407	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8252045	8252045	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060472-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	62	677	0	ENST00000335790.3:c.32C>A	p.Pro11Gln	p.P11Q	ENST00000335790	NM_002315.2	11	cCg/cAg	2/4	1	2	FACETS	0.83	0.718	0.951	0.83	0.718	0.951	CLONAL	1	TRUE	1	0.294808743596949	2		677	507	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207657	102207657	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1308037938	NA	P-0060472-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	21	521	0	ENST00000263464.3:c.1639del	p.Gln547AsnfsTer21	p.Q547Nfs*21	ENST00000263464	NM_001165.4	547	Caa/aa	9/9	1	2	FACETS	0.353	0.271	0.448	0.353	0.271	0.448	SUBCLONAL	1	TRUE	1	0.294808743596949	2		521	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579431	7579431	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060472-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	55	752	0	ENST00000269305.4:c.256del	p.Ala86HisfsTer37	p.A86Hfs*37	ENST00000269305	NM_001126112.2	86	Gca/ca	4/11	1	2	FACETS	0.712	0.609	0.824	0.712	0.609	0.824	SUBCLONAL	1	TRUE	1	0.294808743596949	2		752	524	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221706	22221706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060472-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	46	547	0	ENST00000215832.6:c.25G>A	p.Ala9Thr	p.A9T	ENST00000215832	NM_002745.4	9	Gcg/Acg	1/9	0.294808743596949	5	FACETS	0.798	0.671	0.938	0.16	0.134	0.188	CLONAL	1	TRUE	0	0.294808743596949	5		547	564	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249465	153249465	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060472-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	46	594	0	ENST00000281708.4:c.1313C>A	p.Ser438Tyr	p.S438Y	ENST00000281708	NM_033632.3	438	tCt/tAt	9/12	1	2	FACETS	0.899	0.76	1	0.899	0.76	1	CLONAL	1	TRUE	1	0.294808743596949	2		594	347	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317551	1317551	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs757703756	NA	P-0060472-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	31	410	0	ENST00000400841.2:c.514A>G	p.Ile172Val	p.I172V	ENST00000400841		172	Ata/Gta	5/6	0.294808743596949	1	FACETS	0.687	0.558	0.832	0.687	0.558	0.832	SUBCLONAL	1	TRUE	0	0.294808743596949	1		410	261	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596051	43596051	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060472-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	48	615	0	ENST00000355710.3:c.218A>G	p.Tyr73Cys	p.Y73C	ENST00000355710	NM_020975.4	73	tAc/tGc	2/20	1	2	FACETS	0.724	0.612	0.846	0.724	0.612	0.846	SUBCLONAL	1	TRUE	1	0.294808743596949	2		615	450	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771496	112771496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761448239	NA	P-0060472-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	52	650	0	ENST00000369452.4:c.1669C>T	p.Pro557Ser	p.P557S	ENST00000369452	NM_007373.3	557	Cca/Tca	9/9	1	2	FACETS	0.764	0.651	0.887	0.764	0.651	0.887	SUBCLONAL	1	TRUE	1	0.294808743596949	2		650	462	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858635	57858635	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060472-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	53	659	0	ENST00000228682.2:c.373T>A	p.Ser125Thr	p.S125T	ENST00000228682	NM_005269.2	125	Tcc/Acc	4/12	1	2	FACETS	0.704	0.6	0.817	0.704	0.6	0.817	SUBCLONAL	1	TRUE	1	0.294808743596949	2		659	511	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934623	9934623	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs267604688	NA	P-0060472-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	45	531	0	ENST00000330684.3:c.1532C>A	p.Ser511Ter	p.S511*	ENST00000330684	NM_001134407.1	511	tCg/tAg	7/13	0.276048029564902	1	FACETS	0.707	0.596	0.83	0.707	0.596	0.83	SUBCLONAL	1	TRUE	0	0.294808743596949	1		531	368	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185105	99185105	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060472-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	38	519	0	ENST00000074304.5:c.2507A>T	p.Gln836Leu	p.Q836L	ENST00000074304	NM_001134224.1	836	cAg/cTg	23/26	1	2	FACETS	0.648	0.536	0.772	0.648	0.536	0.772	SUBCLONAL	1	TRUE	1	0.294808743596949	2		519	398	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566713	212566713	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060472-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	54	579	0	ENST00000342788.4:c.1468A>T	p.Asn490Tyr	p.N490Y	ENST00000342788	NM_005235.2	490	Aac/Tac	12/28	1	2	FACETS	0.864	0.74	0.999	0.864	0.74	0.999	CLONAL	1	TRUE	1	0.294808743596949	2		579	424	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430165	181430165	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060472-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	20	443	0	ENST00000325404.1:c.17A>C	p.Glu6Ala	p.E6A	ENST00000325404	NM_003106.3	6	gAg/gCg	1/1	0.184556955596918	3	FACETS	0.516	0.394	0.658	0.258	0.197	0.329	SUBCLONAL	1	TRUE	1	0.294808743596949	3		443	302	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528981	157528981	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060472-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	46	639	0	ENST00000346085.5:c.6706G>T	p.Ala2236Ser	p.A2236S	ENST00000346085	NM_020732.3	2236	Gca/Tca	20/20	0.276048029564902	1	FACETS	0.695	0.586	0.814	0.695	0.586	0.814	SUBCLONAL	1	TRUE	0	0.294808743596949	1		639	383	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494175	140494175	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060472-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	42	666	0	ENST00000288602.6:c.1073G>T	p.Gly358Val	p.G358V	ENST00000288602	NM_004333.4	358	gGg/gTg	8/18	1	2	FACETS	0.546	0.455	0.646	0.546	0.455	0.646	SUBCLONAL	1	TRUE	1	0.294808743596949	2		666	522	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841910	151841910	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060472-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	56	691	0	ENST00000262189.6:c.14231G>C	p.Gly4744Ala	p.G4744A	ENST00000262189	NM_170606.2	4744	gGa/gCa	55/59	1	2	FACETS	0.728	0.624	0.841	0.728	0.624	0.841	SUBCLONAL	1	TRUE	1	0.294808743596949	2		691	522	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0060555-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	111	498	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.119105317601089	4	FACETS	1	0.963	1			1	INDETERMINATE	3	FALSE	NA	0.202275481810133	4		498	392	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656914	45656914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060555-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	32	511	0	ENST00000407780.3:c.242G>A	p.Arg81Gln	p.R81Q	ENST00000407780	NM_001283052.1	81	cGg/cAg	3/7	1	2	FACETS	0.807	0.655	0.978	0.807	0.655	0.978	CLONAL	1	FALSE	1	0.202275481810133	2		511	392	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455091	50455091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1422790468	NA	P-0060748-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	43	349	0	ENST00000331340.3:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000331340	NM_006060.4	213	cGa/cAa	6/8	0.170295880809642	3	FACETS	0.438	0.365	0.519	0.146	0.121	0.173	INDETERMINATE	1	TRUE	0	0.293061589393204	3		349	769	SUCCESS
APC	324	MSKCC	GRCh37	5	112090679	112090679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1270741856	NA	P-0060748-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	35	232	0	ENST00000257430.4:c.92C>T	p.Ser31Phe	p.S31F	ENST00000257430	NM_000038.5	31	tCc/tTc	2/16	1	2	FACETS	0.449	0.367	0.541	0.449	0.367	0.541	SUBCLONAL	1	TRUE	1	0.293061589393204	2		232	532	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600386	10600386	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060748-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	212	468	0	ENST00000171111.5:c.1469A>G	p.Tyr490Cys	p.Y490C	ENST00000171111	NM_203500.1	490	tAc/tGc	4/6	0.218040328414928	2	FACETS	0.816	0.758	0.874	0.816	0.758	0.874	CLONAL	2	TRUE	0	0.293061589393204	2		468	887	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784619	43784619	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1323524336	NA	P-0060751-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	46	374	0	ENST00000382044.4:c.55C>T	p.Gln19Ter	p.Q19*	ENST00000382044	NM_001141980.1	19	Cag/Tag	2/28	0.250470577866269	1	FACETS	0.596	0.502	0.701	0.596	0.502	0.701	SUBCLONAL	1	TRUE	0	0.250470577866269	1		374	539	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045187	47045187	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060751-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	79	235	0	ENST00000377604.3:c.2428G>T	p.Glu810Ter	p.E810*	ENST00000377604	NM_001204468.1	810	Gag/Tag	21/24	1	1	FACETS	0.754	0.667	0.845	1	0.978	1	SUBCLONAL	2	TRUE	0	0.250470577866269	1		235	366	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101280	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCCCAGGGCCC	CCCCCCAGGGCCC	-	novel	NA	P-0060751-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	93	457	0	ENST00000324856.7:c.4551_4563del	p.Gln1519IlefsTer4	p.Q1519Ifs*4	ENST00000324856	NM_006015.4	1517	gCCCCCCAGGGCCCc/gc	18/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.250470577866269	2		457	573	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398280	25398281	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0060751-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	90	289	1	ENST00000311936.3:c.38_39delinsAA	p.Gly13Glu	p.G13E	ENST00000311936	NM_004985.3	13	gGC/gAA	2/5	0.250470577866269	4	FACETS	1	0.956	1	0.756	0.676	0.842	CLONAL	2	TRUE	1	0.250470577866269	4		290	396	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784630	43784630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060751-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	42	350	0	ENST00000382044.4:c.44C>T	p.Ser15Leu	p.S15L	ENST00000382044	NM_001141980.1	15	tCa/tTa	2/28	0.250470577866269	1	FACETS	0.546	0.456	0.647	0.546	0.456	0.647	SUBCLONAL	1	TRUE	0	0.250470577866269	1		350	537	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258511	19258511	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060751-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	52	455	0	ENST00000162023.5:c.389T>G	p.Leu130Arg	p.L130R	ENST00000162023		130	cTg/cGg	8/13	1	2	FACETS	0.665	0.566	0.775	0.665	0.566	0.775	SUBCLONAL	1	TRUE	1	0.250470577866269	2		455	624	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873654	37873654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219238007	NA	P-0061138-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	34	476	0	ENST00000269571.5:c.1819G>A	p.Asp607Asn	p.D607N	ENST00000269571		607	Gac/Aac	15/27	0.135417940804274	3	FACETS	0.952	0.777	1	0.476	0.388	0.576	CLONAL	1	TRUE	1	0.13	3		476	585	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321345	65321345	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061138-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	40	506	0	ENST00000342505.4:c.1495C>T	p.Gln499Ter	p.Q499*	ENST00000342505	NM_002227.2	499	Cag/Tag	11/25	1	2	FACETS	0.928	0.77	1	0.928	0.77	1	CLONAL	1	TRUE	1	0.13	2		506	663	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061010	38061010	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1407484362	NA	P-0061138-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	21	592	1	ENST00000250448.2:c.979G>A	p.Gly327Arg	p.G327R	ENST00000250448	NM_004496.3	327	Ggg/Agg	2/2	1	2	FACETS	0.844	0.649	1	0.844	0.649	1	CLONAL	1	TRUE	1	0.13	2		593	383	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835618	68835618	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061138-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	29	560	0	ENST00000261769.5:c.211del	p.Leu71SerfsTer12	p.L71Sfs*12	ENST00000261769	NM_004360.3	70	tCc/tc	3/16	0.135417940804274	1	FACETS	0.763	0.611	0.936	0.763	0.611	0.936	CLONAL	1	TRUE	0	0.13	1		560	547	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0061233-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	63	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.240523808420716	4	FACETS	0.833	0.725	0.95	0.833	0.725	0.95	CLONAL	2	TRUE	2	0.267676986360331	4		341	358	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602354	10602354	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061233-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	143	558	0	ENST00000171111.5:c.1224del	p.Met409Ter	p.M409*	ENST00000171111	NM_203500.1	408	ccC/cc	3/6	0.246191760023745	2	FACETS	0.999	0.915	1	0.999	0.915	1	CLONAL	2	TRUE	0	0.267676986360331	2		558	535	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007798	45007801	+	frameshift_variant	Frame_Shift_Del	DEL	TCTA	TCTA	-	novel	NA	P-0061233-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	109	427	0	ENST00000558401.1:c.248_251del	p.Tyr83SerfsTer19	p.Y83Sfs*19	ENST00000558401	NM_004048.2	82	tTCTAt/tt	2/4	0.245801815000939	2	FACETS	0.917	0.829	1	0.917	0.829	1	CLONAL	2	TRUE	0	0.267676986360331	2		427	444	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527931	157527931	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061233-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	138	539	0	ENST00000346085.5:c.5656G>T	p.Gly1886Trp	p.G1886W	ENST00000346085	NM_020732.3	1886	Ggg/Tgg	20/20	0.245801815000939	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.267676986360331	2		539	467	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576214	88576214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750565995	NA	P-0061233-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	96	375	0	ENST00000360948.2:c.1459G>A	p.Gly487Ser	p.G487S	ENST00000360948	NM_001012338.2	487	Ggc/Agc	13/19	0.240523808420716	4	FACETS	0.883	0.789	0.982	0.883	0.789	0.982	CLONAL	2	TRUE	2	0.267676986360331	4		375	515	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031965	10031965	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061233-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	48	433	0	ENST00000330684.3:c.858C>A	p.Tyr286Ter	p.Y286*	ENST00000330684	NM_001134407.1	286	taC/taA	3/13	0.267676986360331	3	FACETS	0.847	0.717	0.991	0.424	0.358	0.496	CLONAL	1	TRUE	1	0.267676986360331	3		433	480	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028759	42028759	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061233-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	136	474	1	ENST00000219905.7:c.4297C>T	p.Gln1433Ter	p.Q1433*	ENST00000219905	NM_001164273.1	1433	Cag/Tag	13/24	0.245801815000939	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.267676986360331	2		475	477	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040633	16040633	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0061233-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	31	266	0	ENST00000268712.3:c.1501A>T	p.Arg501Ter	p.R501*	ENST00000268712	NM_006311.3	501	Aga/Tga	14/46	0.267676986360331	3	FACETS	0.842	0.682	1	0.421	0.341	0.511	CLONAL	1	TRUE	1	0.267676986360331	3		266	312	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191135	2191135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061233-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	128	539	0	ENST00000398665.3:c.389C>T	p.Pro130Leu	p.P130L	ENST00000398665	NM_032482.2	130	cCc/cTc	5/28	0.246191760023745	2	FACETS	0.964	0.879	1	0.964	0.879	1	CLONAL	2	TRUE	0	0.267676986360331	2		539	496	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097056	11097056	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061233-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	136	520	0	ENST00000358026.2:c.547C>T	p.Gln183Ter	p.Q183*	ENST00000358026	NM_001128849.1	183	Cag/Tag	4/36	0.246191760023745	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	0	0.267676986360331	2		520	501	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0061430-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	75	516	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	0.696	0.611	0.786	0.696	0.611	0.786	SUBCLONAL	1	TRUE	1	0.445352161724694	2		516	484	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710987	114710987	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061430-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	43	232	0	ENST00000543371.1:c.211C>T	p.Arg71Cys	p.R71C	ENST00000543371	NM_001198531.1	71	Cgc/Tgc	2/14	0.348981266628574	3	FACETS	0.696	0.585	0.819	0.348	0.292	0.41	SUBCLONAL	1	TRUE	1	0.445352161724694	3		232	339	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101586	27101586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1420328983	NA	P-0061430-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	101	482	0	ENST00000324856.7:c.4868C>T	p.Ser1623Leu	p.S1623L	ENST00000324856	NM_006015.4	1623	tCg/tTg	18/20	0.258846994069322	3	FACETS	1	0.937	1	0.531	0.476	0.589	INDETERMINATE	1	TRUE	1	0.445352161724694	3		482	522	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727894	78727894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778029024	NA	P-0061430-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	115	360	0	ENST00000306801.3:c.739G>A	p.Glu247Lys	p.E247K	ENST00000306801	NM_020761.2	247	Gag/Aag	6/34	0.265678689169947	5	FACETS	1	0.98	1	0.446	0.402	0.492	INDETERMINATE	1	TRUE	2	0.445352161724694	5		360	644	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843721	156843721	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061430-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	178	516	0	ENST00000524377.1:c.1147T>A	p.Phe383Ile	p.F383I	ENST00000524377	NM_002529.3	383	Ttc/Atc	8/17	0.446319893727193	4	FACETS	0.755	0.697	0.815	0.503	0.465	0.544	SUBCLONAL	2	TRUE	1	0.445352161724694	4		516	765	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115693	108115693	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061430-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	136	343	0	ENST00000278616.4:c.841G>A	p.Glu281Lys	p.E281K	ENST00000278616	NM_000051.3	281	Gaa/Aaa	7/63	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.445352161724694	2		343	420	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934507	9934507	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061430-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	84	352	0	ENST00000330684.3:c.1648C>G	p.Leu550Val	p.L550V	ENST00000330684	NM_001134407.1	550	Cta/Gta	7/13	0.258846994069322	3	FACETS	0.889	0.787	0.997	0.444	0.393	0.499	INDETERMINATE	1	TRUE	1	0.445352161724694	3		352	519	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819651	81819651	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061430-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	122	380	0	ENST00000359376.3:c.57G>C	p.Lys19Asn	p.K19N	ENST00000359376	NM_002661.3	19	aaG/aaC	2/33	0.446319893727193	3	FACETS	1	0.913	1	0.504	0.457	0.555	CLONAL	1	TRUE	1	0.445352161724694	3		380	664	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105651	11105651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061430-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	79	325	0	ENST00000358026.2:c.1567G>A	p.Glu523Lys	p.E523K	ENST00000358026	NM_001128849.1	523	Gag/Aag	9/36	0.348981266628574	3	FACETS	0.757	0.667	0.854	0.379	0.333	0.427	SUBCLONAL	1	TRUE	1	0.445352161724694	3		325	573	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949977	44949978	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061430-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	140	347	0	ENST00000377967.4:c.3747dup	p.Lys1250Ter	p.K1250*	ENST00000377967	NM_021140.2	1249	tat/taTt	26/29	0.446319893727193	3	FACETS	1	0.983	1	0.659	0.603	0.718	CLONAL	1	TRUE	1	0.445352161724694	3		347	583	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966675	44966707	+	inframe_deletion	In_Frame_Del	DEL	TGAAGCAATGTCAGACATTGAGGGAAGCTCTCA	TGAAGCAATGTCAGACATTGAGGGAAGCTCTCA	-	novel	NA	P-0061430-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	207	369	0	ENST00000377967.4:c.3900_3932del	p.Lys1301_Ile1311del	p.K1301_I1311del	ENST00000377967	NM_021140.2	1300	cTGAAGCAATGTCAGACATTGAGGGAAGCTCTCAtt/ctt	27/29	0.446319893727193	3	FACETS	0.885	0.826	0.946	0.885	0.826	0.946	CLONAL	2	TRUE	1	0.445352161724694	3		369	642	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131229	202131229	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061430-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	70	395	0	ENST00000358485.4:c.197T>G	p.Leu66Arg	p.L66R	ENST00000358485	NM_001080125.1	66	cTt/cGt	2/9	0.215589479646271	4	FACETS	0.644	0.561	0.734	0.322	0.28	0.367	INDETERMINATE	1	TRUE	2	0.445352161724694	4		395	705	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983108	201983111	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	novel	NA	P-0061430-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	112	412	0	ENST00000359651.3:c.959_962del	p.Lys320ThrfsTer4	p.K320Tfs*4	ENST00000359651		319	aaAAAG/aa	7/8	0.397844306486497	3	FACETS	1	0.963	1	0.379	0.342	0.418	CLONAL	1	TRUE	0	0.445352161724694	3		412	541	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061305	38061316	+	inframe_deletion	In_Frame_Del	DEL	GAAGCAGTCATT	GAAGCAGTCATT	-	novel	NA	P-0061430-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	136	416	0	ENST00000250448.2:c.673_684del	p.Asn225_Phe228del	p.N225_F228del	ENST00000250448	NM_004496.3	225	AATGACTGCTTC/-	2/2	0.320547381522207	3	FACETS	1	0.983	1	0.441	0.402	0.481	CLONAL	1	TRUE	0	0.445352161724694	3		416	565	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141567225	141567225	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061430-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	62	358	0	ENST00000220592.5:c.989T>G	p.Val330Gly	p.V330G	ENST00000220592	NM_012154.3	330	gTc/gGc	8/19	0.326166050328804	5	FACETS	0.638	0.55	0.734	0.213	0.183	0.245	SUBCLONAL	1	TRUE	2	0.445352161724694	5		358	728	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230568	46230568	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061430-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	80	377	0	ENST00000334344.6:c.817C>A	p.Pro273Thr	p.P273T	ENST00000334344	NM_152641.2	273	Cct/Act	8/21	0.357521929238496	6	FACETS	0.844	0.742	0.954	0.211	0.185	0.239	CLONAL	1	TRUE	2	0.445352161724694	6		377	805	SUCCESS
ALK	238	MSKCC	GRCh37	2	29450495	29450495	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061430-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	86	444	0	ENST00000389048.3:c.2859A>C	p.Glu953Asp	p.E953D	ENST00000389048	NM_004304.4	953	gaA/gaC	17/29	0.258846994069322	3	FACETS	0.747	0.661	0.839	0.374	0.33	0.42	INDETERMINATE	1	TRUE	1	0.445352161724694	3		444	632	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023440	27023449	+	frameshift_variant	Frame_Shift_Del	DEL	AGCGCTGCAG	AGCGCTGCAG	-	novel	NA	P-0061430-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	35	314	0	ENST00000324856.7:c.550_559del	p.Leu184AlafsTer45	p.L184Afs*45	ENST00000324856	NM_006015.4	182	gcAGCGCTGCAG/gc	1/20	0.258846994069322	3	FACETS	0.63	0.518	0.755	0.315	0.259	0.378	INDETERMINATE	1	TRUE	1	0.445352161724694	3		314	305	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230486756	230486756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375905173	NA	P-0061430-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	66	355	1	ENST00000391860.1:c.497G>A	p.Arg166Gln	p.R166Q	ENST00000391860	NM_001258311.1	166	cGg/cAg	3/7	0.446319893727193	4	FACETS	0.692	0.601	0.791	0.231	0.2	0.264	SUBCLONAL	1	TRUE	1	0.445352161724694	4		356	619	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39294764	39294771	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CATACCTC	CATACCTC	ATT	novel	NA	P-0061430-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	79	293	0	ENST00000402219.2:c.211_213+5delinsAAT		p.X71_splice	ENST00000402219	NM_005633.3	71		2/23	0.258846994069322	3	FACETS	0.799	0.704	0.9	0.399	0.352	0.45	INDETERMINATE	1	TRUE	1	0.445352161724694	3		293	543	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165212	47165214	+	missense_variant	Missense_Mutation	TNP	GTT	GTT	ATG	novel	NA	P-0061430-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	42	385	0	ENST00000409792.3:c.912_914delinsCAT	p.Lys304_Thr305delinsAsnIle	p.K304_T305delinsNI	ENST00000409792	NM_014159.6	304	aaAACa/aaCATa	3/21	0.265678689169947	5	FACETS	0.396	0.329	0.47	0.132	0.109	0.157	INDETERMINATE	1	TRUE	2	0.445352161724694	5		385	795	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0061628-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	277	574	0	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.979944163901	8	FACETS	0.959	0.926	0.99	1	0.995	1	CLONAL	9	TRUE	1	0.4	8		574	353	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054191	30054223	+	inframe_deletion	In_Frame_Del	DEL	ATGGAATATCTGAAGATAGCTCAGGACCTGGAG	ATGGAATATCTGAAGATAGCTCAGGACCTGGAG	-	novel	NA	P-0062252-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	126	350	0	ENST00000338641.4:c.616_648del	p.Glu206_Met216del	p.E206_M216del	ENST00000338641	NM_000268.3	205	ATGGAATATCTGAAGATAGCTCAGGACCTGGAG/-	7/16	0.463884926693566	1	FACETS	0.979	0.894	1	0.979	0.894	1	CLONAL	1	TRUE	0	0.463884926693566	1		350	426	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062355-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	107	446	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.76	2		446	217	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119788	108119788	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs551872656	NA	P-0062355-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	177	320	0	ENST00000278616.4:c.1194T>A	p.Asp398Glu	p.D398E	ENST00000278616	NM_000051.3	398	gaT/gaA	9/63	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.76	2		320	360	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0062563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	54	372	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		372	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0063170-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	29	1497	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.220666290342645	3	FACETS	0.191	0.153	0.235			1	INDETERMINATE	1	TRUE	NA	0.53	3		1497	724	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0063170-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	13	257	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.13	0.092	0.176	0.13	0.092	0.176	SUBCLONAL	1	TRUE	1	0.53	2		257	378	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0063347-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	44	810	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.985	0.825	1	0.985	0.825	1	CLONAL	1	TRUE	1	0.14	2		810	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577041	7577041	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063347-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	38	579	0	ENST00000269305.4:c.897del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	299	ctG/ct	8/11	1	2	FACETS	0.73	0.601	0.874	0.73	0.601	0.874	SUBCLONAL	1	TRUE	1	0.14	2		579	744	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984782	11984782	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1164096095	NA	P-0063347-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	9	313	0	ENST00000353533.5:c.328C>T	p.Arg110Ter	p.R110*	ENST00000353533	NM_003010.3	110	Cga/Tga	3/11	1	2	FACETS	0.311	0.204	0.447	0.311	0.204	0.447	SUBCLONAL	1	TRUE	1	0.14	2		313	414	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045718	26045718	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063507-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	43	487	0	ENST00000540144.1:c.80G>T	p.Arg27Leu	p.R27L	ENST00000540144	NM_003531.2	27	cGt/cTt	1/1	0.838889449462584	3	FACETS	0.204	0.17	0.241	0.102	0.085	0.121	SUBCLONAL	1	TRUE	1	0.838889449462584	3		487	715	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0063790-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	30	157	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.268539369266493	9	FACETS	0.985	0.799	1	0.328	0.266	0.398	CLONAL	2	TRUE	3	0.268539369266493	9		157	220	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740376	58740376	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1064797099	NA	P-0063790-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	116	393	0	ENST00000305921.3:c.1281G>A	p.Trp427Ter	p.W427*	ENST00000305921	NM_003620.3	427	tgG/tgA	6/6	0.269532786723956	2	FACETS	1	0.977	1	1	0.993	1	CLONAL	5	TRUE	0	0.268539369266493	2		393	159	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0063790-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	39	167	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	0.268539369266493	5	FACETS	0.948	0.817	1	1	0.975	1	CLONAL	5	TRUE	3	0.268539369266493	5		167	86	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063806-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	28	324	0	ENST00000256196.4:c.68G>T	p.Gly23Val	p.G23V	ENST00000256196		23	gGc/gTc	1/6	1	2	FACETS	0.827	0.661	1	0.827	0.661	1	CLONAL	1	TRUE	1	0.16	2		324	423	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168509	56168509	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063882-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	51	409	0	ENST00000399503.3:c.1465C>T	p.Pro489Ser	p.P489S	ENST00000399503	NM_005921.1	489	Ccc/Tcc	8/20	0.254931300204615	3	FACETS	0.879	0.748	1	0.44	0.374	0.512	CLONAL	1	TRUE	1	0.254931300204615	3		409	513	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880175	151880175	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1277391709	NA	P-0063882-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	62	540	0	ENST00000262189.6:c.5149A>G	p.Lys1717Glu	p.K1717E	ENST00000262189	NM_170606.2	1717	Aaa/Gaa	35/59	0.254931300204615	3	FACETS	0.983	0.849	1	0.491	0.424	0.564	CLONAL	1	TRUE	1	0.254931300204615	3		540	558	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574580	41574580	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063953-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	43	548	0	ENST00000263253.7:c.6865G>T	p.Ala2289Ser	p.A2289S	ENST00000263253	NM_001429.3	2289	Gcc/Tcc	31/31	0.270704544484032	3	FACETS	1	0.941	1	0.63	0.531	0.737	CLONAL	1	TRUE	1	0.336700356715281	3		548	237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0063953-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	56	419	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.330503275226315	2	FACETS	0.807	0.702	0.919	0.807	0.702	0.919	CLONAL	2	TRUE	0	0.336700356715281	2		419	206	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468477	89468477	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063953-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	47	396	0	ENST00000336596.2:c.2011G>A	p.Ala671Thr	p.A671T	ENST00000336596	NM_005233.5	671	Gca/Aca	11/17	0.336608798126843	4	FACETS	0.998	0.854	1	0.998	0.854	1	CLONAL	2	TRUE	2	0.336700356715281	4		396	187	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933061	39933061	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs770014119	NA	P-0063953-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	32	516	0	ENST00000378444.4:c.1538G>T	p.Gly513Val	p.G513V	ENST00000378444	NM_001123385.1	513	gGg/gTg	4/15	0.22400757244065	4	FACETS	0.962	0.785	1	0.321	0.261	0.387	CLONAL	1	TRUE	1	0.336700356715281	4		516	264	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592135	55592135	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063953-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	26	376	0	ENST00000288135.5:c.1459G>A	p.Gly487Ser	p.G487S	ENST00000288135	NM_000222.2	487	Ggc/Agc	9/21	0.27673763971539	3	FACETS	0.889	0.709	1	0.444	0.354	0.547	CLONAL	1	TRUE	1	0.336700356715281	3		376	203	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176176113	176176113	+	frameshift_variant,start_lost	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063953-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	63	367	0	ENST00000367669.3:c.2del	p.Met1?	p.M1?	ENST00000367669	NM_022457.5	1	aTg/ag	1/20	0.270704544484032	3	FACETS	1	0.899	1	1	0.899	1	CLONAL	2	TRUE	1	0.336700356715281	3		367	213	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264324	30264324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063953-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	31	216	0	ENST00000322652.5:c.59C>T	p.Ser20Phe	p.S20F	ENST00000322652	NM_015355.2	20	tCc/tTc	1/16	0.240469091729733	4	FACETS	0.985	0.811	1	0.985	0.811	1	CLONAL	2	TRUE	2	0.336700356715281	4		216	125	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675174	30675174	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs150897053	NA	P-0063953-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	81	521	0	ENST00000376406.3:c.3071A>T	p.Glu1024Val	p.E1024V	ENST00000376406	NM_014641.2	1024	gAg/gTg	9/15	0.240469091729733	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	2	0.336700356715281	4		521	274	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906809	50906809	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063953-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	57	412	1	ENST00000440232.2:c.1197G>T	p.Gln399His	p.Q399H	ENST00000440232	NM_002691.3	399	caG/caT	10/27	0.240469091729733	4	FACETS	0.835	0.723	0.955	0.835	0.723	0.955	CLONAL	2	TRUE	2	0.336700356715281	4		413	271	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556169	29556169	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063953-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	17	166	0	ENST00000356175.3:c.2536G>T	p.Ala846Ser	p.A846S	ENST00000356175	NM_000267.3	846	Gcc/Tcc	21/57	0.240469091729733	4	FACETS	0.794	0.604	1	0.794	0.604	1	CLONAL	2	TRUE	2	0.336700356715281	4		166	85	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0063956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	525	320	0	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	0.778272451913052	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.778272451913052	3		320	899	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740522	58740522	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	513	412	0	ENST00000305921.3:c.1430del	p.Asn477IlefsTer6	p.N477Ifs*6	ENST00000305921	NM_003620.3	476	gAa/ga	6/6	0.534357420344704	4	FACETS	1	0.996	1	0.827	0.797	0.856	CLONAL	2	TRUE	1	0.778272451913052	4		412	945	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560464	95560464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	227	397	0	ENST00000393063.1:c.5125G>A	p.Asp1709Asn	p.D1709N	ENST00000393063	NM_030621.3	1709	Gat/Aat	25/28	1	2	FACETS	0.945	0.887	1	0.945	0.887	1	CLONAL	1	TRUE	1	0.778272451913052	2		397	617	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562495	95562495	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1566754840	NA	P-0063956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	280	405	0	ENST00000393063.1:c.4762del	p.Leu1588Ter	p.L1588*	ENST00000393063	NM_030621.3	1588	Ctg/tg	24/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.778272451913052	2		405	684	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0064012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	76	522	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	0.38172718274287	1	FACETS	0.522	0.459	0.589	0.522	0.459	0.589	SUBCLONAL	1	TRUE	0	0.454588625737255	1		522	495	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641513	47641513	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	107	336	0	ENST00000233146.2:c.898A>C	p.Met300Leu	p.M300L	ENST00000233146	NM_000251.2	300	Atg/Ctg	5/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.454588625737255	2		336	344	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288194	33288199	+	inframe_deletion	In_Frame_Del	DEL	GAGTGG	GAGTGG	-	novel	NA	P-0064012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	48	506	0	ENST00000374542.5:c.1209_1214del	p.His404_Ser405del	p.H404_S405del	ENST00000374542	NM_001141970.1	403	tcCCACTCt/tct	4/8	1	2	FACETS	0.384	0.324	0.45	0.384	0.324	0.45	SUBCLONAL	1	TRUE	1	0.454588625737255	2		506	550	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0064260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	62	246	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.73333152152714	3	FACETS	0.91	0.812	1	0.91	0.812	1	CLONAL	2	TRUE	1	0.73333152152714	3		246	127	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0064260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	71	307	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	0.73333152152714	2	FACETS	1	0.91	1	0.512	0.456	0.57	CLONAL	1	TRUE	0	0.73333152152714	2		307	189	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472548	88472548	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0064260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	141	587	0	ENST00000360948.2:c.2007C>G	p.Tyr669Ter	p.Y669*	ENST00000360948	NM_001012338.2	669	taC/taG	16/19	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.73333152152714	2		587	379	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641021	3641021	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	152	592	0	ENST00000294008.3:c.2618C>G	p.Ala873Gly	p.A873G	ENST00000294008	NM_032444.2	873	gCc/gGc	12/15	0.711082972713912	4	FACETS	1	0.928	1	0.507	0.464	0.551	CLONAL	1	TRUE	2	0.73333152152714	4		592	709	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031215	11031215	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	62	621	0	ENST00000327064.4:c.1300C>T	p.Leu434Phe	p.L434F	ENST00000327064	NM_199141.1	434	Ctc/Ttc	11/16	0.73333152152714	3	FACETS	0.402	0.347	0.461	0.201	0.173	0.231	SUBCLONAL	1	TRUE	1	0.73333152152714	3		621	575	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164370	47164370	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	33	251	0	ENST00000409792.3:c.1756C>A	p.His586Asn	p.H586N	ENST00000409792	NM_014159.6	586	Cat/Aat	3/21	1	2	FACETS	0.857	0.716	1	0.857	0.716	1	CLONAL	1	TRUE	1	0.73333152152714	2		251	105	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2191376	2191376	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764005673	NA	P-0064260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	295	517	0	ENST00000349721.2:c.4705G>A	p.Asp1569Asn	p.D1569N	ENST00000349721	NM_003070.3	1569	Gat/Aat	33/34	0.658061712683855	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.73333152152714	4		517	676	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0064302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	12	478	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.053	0.037	0.073	0.053	0.037	0.073	SUBCLONAL	1	TRUE	1	0.765230046229655	2		479	593	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0064302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	171	469	0	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.594	0.547	0.642	0.594	0.547	0.642	SUBCLONAL	1	TRUE	1	0.765230046229655	2		469	753	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0064302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	262	505	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.765230046229655	2		505	685	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175857	24175859	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs875989800	NA	P-0064302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	235	471	0	ENST00000263121.7:c.1091_1093del	p.Lys364del	p.K364del	ENST00000263121	NM_003073.3	362	gAGAag/gag	8/9	1	2	FACETS	0.966	0.907	1	0.966	0.907	1	CLONAL	1	TRUE	1	0.765230046229655	2		471	636	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0064302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	292	544	0	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.765230046229655	2		544	705	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835781	68835781	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060501215	NA	P-0064302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	277	313	0	ENST00000261769.5:c.377del	p.Pro126ArgfsTer89	p.P126Rfs*89	ENST00000261769	NM_004360.3	124	cgC/cg	3/16	1	2	FACETS	0.959	0.905	1	0.959	0.905	1	CLONAL	1	TRUE	1	0.765230046229655	2		313	755	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0064302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	351	460	2	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.765230046229655	2		462	855	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920173	76920173	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	206	188	0	ENST00000373344.5:c.3904del	p.Arg1302GlufsTer44	p.R1302Efs*44	ENST00000373344	NM_000489.3	1302	Aga/ga	11/35	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.765230046229655	1		188	295	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396886	139396886	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752754662	NA	P-0064302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	214	373	0	ENST00000277541.6:c.5222C>T	p.Ala1741Val	p.A1741V	ENST00000277541	NM_017617.3	1741	gCg/gTg	28/34	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.765230046229655	2		373	552	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223175	36223175	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	323	661	0	ENST00000222270.7:c.5730del	p.Arg1911AspfsTer23	p.R1911Dfs*23	ENST00000222270	NM_014727.1	1909	Ccc/cc	28/37	1	2	FACETS	0.998	0.946	1	0.998	0.946	1	CLONAL	1	TRUE	1	0.765230046229655	2		661	846	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428494	72428496	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0064302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	203	417	0	ENST00000477973.2:c.506_508del	p.Lys170del	p.K170del	ENST00000477973	NM_012234.5	170	AAG/-	2/4	0.765230046229655	2	FACETS	0.868	0.81	0.928	0.434	0.405	0.464	CLONAL	1	TRUE	0	0.765230046229655	2		417	611	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247295	153247295	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	293	567	0	ENST00000281708.4:c.1507G>A	p.Ala503Thr	p.A503T	ENST00000281708	NM_033632.3	503	Gca/Aca	10/12	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.765230046229655	2		567	751	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306559	163306559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781627921	NA	P-0064302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	172	280	0	ENST00000271452.3:c.356G>A	p.Arg119Gln	p.R119Q	ENST00000271452	NM_145697.2	119	cGg/cAg	6/14	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.765230046229655	2		280	398	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458044	120458045	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	273	509	0	ENST00000256646.2:c.7300dup	p.Ser2434PhefsTer2	p.S2434Ffs*2	ENST00000256646	NM_024408.3	2434	tct/tTct	34/34	1	2	FACETS	0.966	0.911	1	0.966	0.911	1	CLONAL	1	TRUE	1	0.765230046229655	2		509	739	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425941	49425941	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	305	613	0	ENST00000301067.7:c.12547C>T	p.Gln4183Ter	p.Q4183*	ENST00000301067	NM_003482.3	4183	Cag/Tag	39/54	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.765230046229655	2		613	759	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420193	49420193	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	288	536	0	ENST00000301067.7:c.15556del	p.His5186ThrfsTer57	p.H5186Tfs*57	ENST00000301067	NM_003482.3	5186	Cac/ac	48/54	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.765230046229655	2		536	741	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026924	71026987	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTCTACAAGAATTGCAGATTACAACTCTACGTGAGGCAAAAGGTGGAGTATCTACCTGACGAAA	GTCTACAAGAATTGCAGATTACAACTCTACGTGAGGCAAAAGGTGGAGTATCTACCTGACGAAA	-	novel	NA	P-0064302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	580	468	0	ENST00000318789.4:c.1340_1349-51del		p.X447_splice	ENST00000318789	NM_032682.5	447		15/21	0.765230046229655	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.765230046229655	2		468	704	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257121	19257121	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	158	338	0	ENST00000162023.5:c.842C>G	p.Ser281Trp	p.S281W	ENST00000162023		281	tCg/tGg	12/13	1	2	FACETS	0.945	0.875	1	0.945	0.875	1	CLONAL	1	TRUE	1	0.765230046229655	2		338	437	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970825	79970825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373961048	NA	P-0064302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	184	302	0	ENST00000265081.6:c.1051G>A	p.Asp351Asn	p.D351N	ENST00000265081	NM_002439.4	351	Gat/Aat	7/24	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.765230046229655	2		302	465	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752964	128752964	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	299	461	0	ENST00000377970.2:c.1125C>A	p.Asn375Lys	p.N375K	ENST00000377970	NM_002467.4	375	aaC/aaA	3/3	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.765230046229655	2		461	742	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0064302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	11	529	4	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	1	FACETS	0.08	0.055	0.111	0.08	0.055	0.111	SUBCLONAL	1	TRUE	0	0.765230046229655	1		533	223	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552710	226552710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	316	468	0	ENST00000366794.5:c.2651C>T	p.Ala884Val	p.A884V	ENST00000366794	NM_001618.3	884	gCg/gTg	19/23	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.765230046229655	2		468	711	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281574	15281574	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	245	439	0	ENST00000263388.2:c.4799G>A	p.Cys1600Tyr	p.C1600Y	ENST00000263388	NM_000435.2	1600	tGc/tAc	26/33	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.765230046229655	2		439	589	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0064302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	12	0	0	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	1	2	FACETS	0.043	0.03	0.06	0.043	0.03	0.06	SUBCLONAL	1	TRUE	1	0.765230046229655	2		0	724	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805786	46805786	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	34	590	1	ENST00000290295.7:c.170C>T	p.Ala57Val	p.A57V	ENST00000290295	NM_006361.5	57	gCg/gTg	1/2	1	2	FACETS	0.145	0.118	0.175	0.145	0.118	0.175	SUBCLONAL	1	TRUE	1	0.765230046229655	2		591	614	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583389	46583389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	285	406	0	ENST00000263734.3:c.317G>A	p.Gly106Asp	p.G106D	ENST00000263734	NM_001430.4	106	gGc/gAc	3/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.765230046229655	2		406	678	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29445371	29445371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1169381583	NA	P-0064302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	295	547	0	ENST00000544604.2:c.1202G>A	p.Arg401Gln	p.R401Q	ENST00000544604	NM_001206998.1	401	cGg/cAg	8/9	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.765230046229655	2		547	738	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70000969	70000969	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	27	326	0	ENST00000394351.3:c.570del	p.Thr192GlnfsTer20	p.T192Qfs*20	ENST00000394351	NM_000248.3	189	aTt/at	6/9	0.765230046229655	2	FACETS	0.152	0.121	0.189	0.076	0.06	0.095	SUBCLONAL	1	TRUE	0	0.765230046229655	2		326	463	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673127	30673127	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	77	577	0	ENST00000376406.3:c.3833T>A	p.Val1278Asp	p.V1278D	ENST00000376406	NM_014641.2	1278	gTc/gAc	10/15	1	2	FACETS	0.269	0.236	0.305	0.269	0.236	0.305	SUBCLONAL	1	TRUE	1	0.765230046229655	2		577	748	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805110	43805110	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	130	483	0	ENST00000372470.3:c.560T>C	p.Leu187Pro	p.L187P	ENST00000372470	NM_005373.2	187	cTg/cCg	4/12	1	2	FACETS	0.512	0.466	0.562	0.512	0.466	0.562	SUBCLONAL	1	TRUE	1	0.765230046229655	2		483	663	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105646	11105646	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs990869140	NA	P-0064302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	88	415	0	ENST00000358026.2:c.1562G>A	p.Arg521Gln	p.R521Q	ENST00000358026	NM_001128849.1	521	cGg/cAg	9/36	1	2	FACETS	0.366	0.325	0.411	0.366	0.325	0.411	SUBCLONAL	1	TRUE	1	0.765230046229655	2		415	628	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947865	178947865	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776932	NA	P-0064302-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	21	357	0	ENST00000263967.3:c.2740G>A	p.Gly914Arg	p.G914R	ENST00000263967	NM_006218.2	914	Gga/Aga	19/21	1	2	FACETS	0.485	0.372	0.616	0.485	0.372	0.616	SUBCLONAL	1	FALSE	1	0.211902843438088	2		357	409	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0064302-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	75	505	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	1	2	FACETS	0.989	0.872	1	1	0.983	1	CLONAL	2	FALSE	1	0.211902843438088	2		505	358	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175857	24175859	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs875989800	NA	P-0064302-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	32	471	0	ENST00000263121.7:c.1091_1093del	p.Lys364del	p.K364del	ENST00000263121	NM_003073.3	362	gAGAag/gag	8/9	0.155724609897155	0	FACETS	1	0.82	1			1	CLONAL	1	FALSE	0	0.211902843438088	0		471	237	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0064302-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	75	544	0	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	0.155724609897155	0	FACETS	0.979	0.867	1			1	CLONAL	2	FALSE	0	0.211902843438088	0		544	285	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272336	15272337	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs771517374	NA	P-0064302-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	31	501	1	ENST00000263388.2:c.6102dup	p.Gly2035ArgfsTer60	p.G2035Rfs*60	ENST00000263388	NM_000435.2	2034	-/C	33/33	0.155724609897155	0	FACETS	1	0.816	1			1	CLONAL	1	FALSE	0	0.211902843438088	0		502	230	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835781	68835781	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060501215	NA	P-0064302-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	82	313	0	ENST00000261769.5:c.377del	p.Pro126ArgfsTer89	p.P126Rfs*89	ENST00000261769	NM_004360.3	124	cgC/cg	3/16	0.155724609897155	0	FACETS	0.782	0.694	0.875			1	SUBCLONAL	2	FALSE	0	0.211902843438088	0		313	390	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0064302-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	81	460	2	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	0.155724609897155	0	FACETS	0.674	0.596	0.757			1	SUBCLONAL	2	FALSE	0	0.211902843438088	0		462	447	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920173	76920173	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064302-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	91	188	0	ENST00000373344.5:c.3904del	p.Arg1302GlufsTer44	p.R1302Efs*44	ENST00000373344	NM_000489.3	1302	Aga/ga	11/35	0.211902843438088	2	FACETS	0.942	0.852	1			1	CLONAL	4	FALSE	NA	0.211902843438088	2		188	228	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396886	139396886	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752754662	NA	P-0064302-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	14	373	0	ENST00000277541.6:c.5222C>T	p.Ala1741Val	p.A1741V	ENST00000277541	NM_017617.3	1741	gCg/gTg	28/34	0.155724609897155	0	FACETS	0.557	0.403	0.742			1	SUBCLONAL	1	FALSE	0	0.211902843438088	0		373	187	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223175	36223175	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064302-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	52	661	0	ENST00000222270.7:c.5730del	p.Arg1911AspfsTer23	p.R1911Dfs*23	ENST00000222270	NM_014727.1	1909	Ccc/cc	28/37	0.155724609897155	0	FACETS	0.727	0.624	0.838			1	SUBCLONAL	2	FALSE	0	0.211902843438088	0		661	266	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428494	72428496	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0064302-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	94	417	0	ENST00000477973.2:c.506_508del	p.Lys170del	p.K170del	ENST00000477973	NM_012234.5	170	AAG/-	2/4	0.211902843438088	1	FACETS	0.818	0.731	0.91	1	0.983	1	CLONAL	2	FALSE	0	0.211902843438088	1		417	485	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247295	153247295	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064302-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	131	567	0	ENST00000281708.4:c.1507G>A	p.Ala503Thr	p.A503T	ENST00000281708	NM_033632.3	503	Gca/Aca	10/12	0.108651665143629	4	FACETS	0.948	0.864	1	1	0.985	1	INDETERMINATE	3	FALSE	2	0.211902843438088	4		567	527	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306559	163306559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781627921	NA	P-0064302-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	71	280	0	ENST00000271452.3:c.356G>A	p.Arg119Gln	p.R119Q	ENST00000271452	NM_145697.2	119	cGg/cAg	6/14	0.172892562947867	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	0	0.211902843438088	1		280	401	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458044	120458045	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064302-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	75	509	0	ENST00000256646.2:c.7300dup	p.Ser2434PhefsTer2	p.S2434Ffs*2	ENST00000256646	NM_024408.3	2434	tct/tTct	34/34	0.172892562947867	1	FACETS	0.917	0.81	1	1	0.982	1	CLONAL	2	FALSE	0	0.211902843438088	1		509	345	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425941	49425941	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064302-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	57	613	0	ENST00000301067.7:c.12547C>T	p.Gln4183Ter	p.Q4183*	ENST00000301067	NM_003482.3	4183	Cag/Tag	39/54	0.108651665143629	4	FACETS	1	0.896	1	1	0.896	1	INDETERMINATE	2	FALSE	2	0.211902843438088	4		613	312	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420193	49420193	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064302-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	74	536	0	ENST00000301067.7:c.15556del	p.His5186ThrfsTer57	p.H5186Tfs*57	ENST00000301067	NM_003482.3	5186	Cac/ac	48/54	0.108651665143629	4	FACETS	1	0.958	1	1	0.958	1	INDETERMINATE	2	FALSE	2	0.211902843438088	4		536	352	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026924	71026987	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTCTACAAGAATTGCAGATTACAACTCTACGTGAGGCAAAAGGTGGAGTATCTACCTGACGAAA	GTCTACAAGAATTGCAGATTACAACTCTACGTGAGGCAAAAGGTGGAGTATCTACCTGACGAAA	-	novel	NA	P-0064302-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	263	468	0	ENST00000318789.4:c.1340_1349-51del		p.X447_splice	ENST00000318789	NM_032682.5	447		15/21	0.211902843438088	1	FACETS	0.994	0.941	1	1	0.996	1	CLONAL	4	FALSE	0	0.211902843438088	1		468	558	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257121	19257121	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064302-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	15	338	0	ENST00000162023.5:c.842C>G	p.Ser281Trp	p.S281W	ENST00000162023		281	tCg/tGg	12/13	0.155724609897155	0	FACETS	0.833	0.614	1			1	CLONAL	1	FALSE	0	0.211902843438088	0		338	134	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970825	79970825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373961048	NA	P-0064302-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	106	302	0	ENST00000265081.6:c.1051G>A	p.Asp351Asn	p.D351N	ENST00000265081	NM_002439.4	351	Gat/Aat	7/24	1	2	FACETS	0.892	0.807	0.98	1	0.99	1	CLONAL	3	FALSE	1	0.211902843438088	2		302	374	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752964	128752964	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064302-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	107	461	0	ENST00000377970.2:c.1125C>A	p.Asn375Lys	p.N375K	ENST00000377970	NM_002467.4	375	aaC/aaA	3/3	1	2	FACETS	1	0.964	1	1	0.989	1	CLONAL	2	FALSE	1	0.211902843438088	2		461	441	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0064432-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	39	486	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	0.284397967317196	1	FACETS	0.14	0.116	0.167	0.14	0.116	0.167	INDETERMINATE	1	TRUE	0	0.77112012415493	1		486	443	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0064432-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	37	486	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	0.284397967317196	1	FACETS	0.133	0.109	0.16	0.133	0.109	0.16	INDETERMINATE	1	TRUE	0	0.77112012415493	1		486	443	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0064432-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	163	459	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	0.291342567464774	3	FACETS	1	0.988	1	0.669	0.62	0.718	INDETERMINATE	1	TRUE	1	0.77112012415493	3		459	438	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599332	55599332	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519710	NA	P-0064432-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	849	379	0	ENST00000288135.5:c.2458G>T	p.Asp820Tyr	p.D820Y	ENST00000288135	NM_000222.2	820	Gat/Tat	17/21	0.77112012415493	6	FACETS	1	0.996	1			1	CLONAL	5	TRUE	NA	0.77112012415493	6		379	1060	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156719	20156719	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064432-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	155	321	0	ENST00000379607.5:c.38G>C	p.Arg13Pro	p.R13P	ENST00000379607	NM_001412.3	13	cGc/cCc	2/7	0.42920327179677	1	FACETS	0.698	0.648	0.748	0.698	0.648	0.748	INDETERMINATE	1	TRUE	0	0.77112012415493	1		321	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0064514-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	125	631	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	1	2	FACETS	0.952	0.864	1	1	0.989	1	CLONAL	2	TRUE	1	0.212044204471001	2		631	619	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0064521-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	262	530	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	0.152534444830342	5	FACETS	1	0.968	1			1	CLONAL	7	FALSE	NA	0.152534444830342	5		530	584	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913492	NA	P-0064521-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	118	234	0	ENST00000286548.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000286548	NM_002072.3	209	cAa/cTa	5/7	0.128240383024534	0	FACETS	1	0.92	1			1	CLONAL	5	FALSE	0	0.152534444830342	0		234	262	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023447	27023447	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064558-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	172	305	0	ENST00000324856.7:c.553C>T	p.Gln185Ter	p.Q185*	ENST00000324856	NM_006015.4	185	Cag/Tag	1/20	0.752912217747477	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.752912217747477	1		305	274	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1255456	1255456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374968697	NA	P-0064558-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	410	318	0	ENST00000310581.5:c.3103G>A	p.Val1035Ile	p.V1035I	ENST00000310581	NM_198253.2	1035	Gtc/Atc	14/16	0.752912217747477	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.752912217747477	3		318	749	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396490	396490	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064558-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	183	309	0	ENST00000262320.3:c.536del	p.Pro179LeufsTer63	p.P179Lfs*63	ENST00000262320	NM_003502.3	179	cCt/ct	2/11	0.752912217747477	1	FACETS	0.91	0.856	0.964	0.91	0.856	0.964	CLONAL	1	TRUE	0	0.752912217747477	1		309	333	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453138	+	protein_altering_variant	In_Frame_Del	DEL	TCACT	TCACT	CA	novel	NA	P-0064558-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	171	238	1	ENST00000288602.6:c.1797_1801delinsTG	p.Val600_Lys601delinsGlu	p.V600_K601delinsE	ENST00000288602	NM_004333.4	599	acAGTGAaa/acTGaa	15/18	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.752912217747477	2		239	442	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064701-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	29	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.171086493851024	3	FACETS	1	0.835	1	0.519	0.419	0.632	CLONAL	1	TRUE	1	0.2711006037016	3		341	234	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911442	32911443	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359365	NA	P-0064701-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	21	409	1	ENST00000380152.3:c.2957dup	p.Asn986LysfsTer2	p.N986Kfs*2	ENST00000380152		984	gaa/gAaa	11/27	0.171086493851024	3	FACETS	0.858	0.664	1	0.429	0.332	0.541	CLONAL	1	TRUE	1	0.2711006037016	3		410	205	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578462	7578468	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGGTG	GCGGGTG	-	novel	NA	P-0064701-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	78	891	0	ENST00000269305.4:c.462_468del	p.Thr155SerfsTer13	p.T155Sfs*13	ENST00000269305	NM_001126112.2	154	ggCACCCGC/gg	5/11	1	2	FACETS	0.91	0.8	1	0.91	0.8	1	CLONAL	1	TRUE	1	0.2711006037016	2		891	632	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41542792	41542792	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064701-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	23	596	0	ENST00000263253.7:c.2103G>C	p.Gln701His	p.Q701H	ENST00000263253	NM_001429.3	701	caG/caC	11/31	1	2	FACETS	0.381	0.296	0.48	0.381	0.296	0.48	SUBCLONAL	1	TRUE	1	0.2711006037016	2		596	445	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056054	26056054	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs762236209	NA	P-0064701-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	38	763	0	ENST00000343677.2:c.603G>C	p.Lys201Asn	p.K201N	ENST00000343677	NM_005319.3	201	aaG/aaC	1/1	1	2	FACETS	0.41	0.338	0.491	0.41	0.338	0.491	SUBCLONAL	1	TRUE	1	0.2711006037016	2		763	684	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894922	101894935	+	frameshift_variant	Frame_Shift_Del	DEL	CCAAATGAAGAGGA	CCAAATGAAGAGGA	-	novel	NA	P-0064701-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	23	571	0	ENST00000374994.4:c.477_490del	p.Asn160PhefsTer19	p.N160Ffs*19	ENST00000374994	NM_004612.2	159	CCAAATGAAGAGGAc/c	3/9	0.254755824880816	1	FACETS	0.323	0.251	0.407	0.323	0.251	0.407	SUBCLONAL	1	TRUE	0	0.2711006037016	1		571	454	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155404	47155404	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	74	404	0	ENST00000409792.3:c.4677G>C	p.Lys1559Asn	p.K1559N	ENST00000409792	NM_014159.6	1559	aaG/aaC	5/21	0.201813261290691	7	FACETS	1	0.938	1	1	0.938	1	CLONAL	5	FALSE	2	0.201813261290691	7		404	205	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155430	47155430	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	56	380	0	ENST00000409792.3:c.4651G>A	p.Asp1551Asn	p.D1551N	ENST00000409792	NM_014159.6	1551	Gat/Aat	5/21	0.201813261290691	7	FACETS	0.954	0.833	1	0.954	0.833	1	CLONAL	5	FALSE	2	0.201813261290691	7		380	175	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0064759-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	19	257	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.539	0.408	0.693	0.539	0.408	0.693	SUBCLONAL	1	TRUE	1	0.17	2		257	415	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971115	55971115	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064759-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	19	379	0	ENST00000263923.4:c.1682C>T	p.Pro561Leu	p.P561L	ENST00000263923	NM_002253.2	561	cCc/cTc	13/30	1	2	FACETS	0.609	0.461	0.783	0.609	0.461	0.783	SUBCLONAL	1	TRUE	1	0.17	2		379	367	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0064759-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	19	257	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.677	0.513	0.87	0.677	0.513	0.87	SUBCLONAL	1	TRUE	1	0.16	2		257	351	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169985715	169985715	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs567380681	NA	P-0064759-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	14	310	0	ENST00000295797.4:c.377G>T	p.Arg126Leu	p.R126L	ENST00000295797	NM_002740.5	126	cGt/cTt	5/18	1	2	FACETS	0.376	0.271	0.505	0.376	0.271	0.505	SUBCLONAL	1	TRUE	1	0.16	2		310	465	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431811	49431811	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773164595	NA	P-0064759-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	28	543	0	ENST00000301067.7:c.9328C>T	p.Arg3110Cys	p.R3110C	ENST00000301067	NM_003482.3	3110	Cgc/Tgc	34/54	1	2	FACETS	0.674	0.538	0.831	0.674	0.538	0.831	SUBCLONAL	1	TRUE	1	0.16	2		543	519	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025937	1025937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1391132880	NA	P-0064759-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	47	485	0	ENST00000358495.3:c.593C>T	p.Pro198Leu	p.P198L	ENST00000358495	NM_134424.2	198	cCg/cTg	8/12	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.16	2		485	506	SUCCESS
AXL	558	MSKCC	GRCh37	19	41759510	41759510	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064759-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	37	389	0	ENST00000301178.4:c.1935del	p.Thr646LeufsTer4	p.T646Lfs*4	ENST00000301178	NM_021913.4	645	Ccc/cc	17/20	1	2	FACETS	0.995	0.82	1	0.995	0.82	1	CLONAL	1	TRUE	1	0.16	2		389	465	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224548	108224548	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064759-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	37	402	0	ENST00000278616.4:c.8727A>T	p.Arg2909Ser	p.R2909S	ENST00000278616	NM_000051.3	2909	agA/agT	60/63	1	2	FACETS	0.905	0.745	1	0.905	0.745	1	CLONAL	1	TRUE	1	0.16	2		402	511	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150931661	150931661	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064759-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	32	324	0	ENST00000271640.5:c.2338G>C	p.Glu780Gln	p.E780Q	ENST00000271640	NM_001145415.1	780	Gag/Cag	15/22	0.217967105556618	4	FACETS	0.884	0.716	1			1	CLONAL	1	TRUE	NA	0.16	4		324	525	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872199	76872199	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0064759-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	17	249	0	ENST00000373344.5:c.5449-1G>A		p.X1817_splice	ENST00000373344	NM_000489.3	1817			1	2	FACETS	0.699	0.521	0.91	0.699	0.521	0.91	SUBCLONAL	1	TRUE	1	0.16	2		249	304	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0064759-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	45	257	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.236406984455656	2	FACETS	0.805	0.684	0.935	0.805	0.684	0.935	CLONAL	2	TRUE	0	0.27	2		257	207	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169985715	169985715	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs567380681	NA	P-0064759-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	48	310	0	ENST00000295797.4:c.377G>T	p.Arg126Leu	p.R126L	ENST00000295797	NM_002740.5	126	cGt/cTt	5/18	0.236406984455656	2	FACETS	1	0.864	1	0.509	0.432	0.594	CLONAL	1	TRUE	0	0.27	2		310	349	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025937	1025937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1391132880	NA	P-0064759-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	87	485	0	ENST00000358495.3:c.593C>T	p.Pro198Leu	p.P198L	ENST00000358495	NM_134424.2	198	cCg/cTg	8/12	0.236406984455656	2	FACETS	0.8	0.712	0.892	0.8	0.712	0.892	SUBCLONAL	2	TRUE	0	0.27	2		485	403	SUCCESS
AXL	558	MSKCC	GRCh37	19	41759510	41759510	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064759-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	69	389	0	ENST00000301178.4:c.1935del	p.Thr646LeufsTer4	p.T646Lfs*4	ENST00000301178	NM_021913.4	645	Ccc/cc	17/20	0.255262025019636	2	FACETS	0.897	0.789	1	0.897	0.789	1	CLONAL	2	TRUE	0	0.27	2		389	285	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224548	108224548	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064759-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	112	402	0	ENST00000278616.4:c.8727A>T	p.Arg2909Ser	p.R2909S	ENST00000278616	NM_000051.3	2909	agA/agT	60/63	0.239923526950711	3	FACETS	1	0.972	1	0.793	0.719	0.869	CLONAL	2	TRUE	0	0.27	3		402	396	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872199	76872199	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0064759-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	23	249	0	ENST00000373344.5:c.5449-1G>A		p.X1817_splice	ENST00000373344	NM_000489.3	1817			0.254676273389418	3	FACETS	0.741	0.579	0.927	0.37	0.289	0.464	CLONAL	1	TRUE	1	0.27	3		249	261	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29279923	29279923	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064759-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	24	351	0	ENST00000544604.2:c.169G>A	p.Glu57Lys	p.E57K	ENST00000544604	NM_001206998.1	57	Gag/Aag	1/9	0.255262025019636	2	FACETS	0.823	0.648	1	0.412	0.324	0.511	CLONAL	1	TRUE	0	0.27	2		351	216	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197548	106197548	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs370835195	NA	P-0064759-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	47	439	0	ENST00000380013.4:c.5881G>C	p.Glu1961Gln	p.E1961Q	ENST00000380013	NM_001127208.2	1961	Gag/Cag	11/11	0.236406984455656	2	FACETS	1	0.884	1	0.526	0.445	0.614	CLONAL	1	TRUE	0	0.27	2		439	331	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2077651	2077651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064759-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	29	404	0	ENST00000349721.2:c.2059G>A	p.Asp687Asn	p.D687N	ENST00000349721	NM_003070.3	687	Gat/Aat	14/34	0.236450630380858	2	FACETS	0.667	0.536	0.815	0.334	0.268	0.408	SUBCLONAL	1	TRUE	0	0.27	2		404	322	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874077	151874077	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064759-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	43	453	0	ENST00000262189.6:c.8461G>C	p.Glu2821Gln	p.E2821Q	ENST00000262189	NM_170606.2	2821	Gag/Cag	38/59	0.243449108217287	4	FACETS	0.859	0.719	1	0.429	0.359	0.507	CLONAL	1	TRUE	2	0.27	4		453	471	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138618	37138618	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs551680157	NA	P-0064759-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	48	459	0	ENST00000373509.5:c.152C>T	p.Ser51Leu	p.S51L	ENST00000373509	NM_002648.3	51	tCg/tTg	2/6	0.236406984455656	2	FACETS	1	0.928	1	0.581	0.494	0.676	CLONAL	1	TRUE	0	0.27	2		459	306	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0064759-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	45	492	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.171001256510383	3	FACETS	1	0.955	1	0.715	0.601	0.841	CLONAL	1	TRUE	1	0.15	3		492	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764146326	NA	P-0064759-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	37	503	0	ENST00000269305.4:c.841G>T	p.Asp281Tyr	p.D281Y	ENST00000269305	NM_001126112.2	281	Gac/Tac	8/11	1	2	FACETS	0.892	0.734	1	0.892	0.734	1	CLONAL	1	TRUE	1	0.15	2		503	553	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103157	119103157	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0064759-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	41	427	0	ENST00000264033.4:c.196-1G>T		p.X66_splice	ENST00000264033	NM_005188.3	66			1	2	FACETS	0.971	0.808	1	0.971	0.808	1	CLONAL	1	TRUE	1	0.15	2		427	563	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213956	2213957	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0064759-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	27	437	0	ENST00000398665.3:c.1773_1774del	p.Leu592ProfsTer74	p.L592Pfs*74	ENST00000398665	NM_032482.2	590	CGc/c	18/28	1	2	FACETS	0.804	0.639	0.993	0.804	0.639	0.993	CLONAL	1	TRUE	1	0.15	2		437	448	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111432	56111432	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064759-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	24	431	0	ENST00000399503.3:c.32C>T	p.Ser11Leu	p.S11L	ENST00000399503	NM_005921.1	11	tCg/tTg	1/20	1	2	FACETS	0.879	0.689	1	0.879	0.689	1	CLONAL	1	TRUE	1	0.15	2		431	364	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358952	81358952	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064759-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	24	395	0	ENST00000222390.5:c.1009C>A	p.His337Asn	p.H337N	ENST00000222390	NM_000601.4	337	Cat/Aat	8/18	1	2	FACETS	0.762	0.596	0.953	0.762	0.596	0.953	CLONAL	1	TRUE	1	0.15	2		395	420	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012438	29012438	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064759-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	38	453	0	ENST00000282397.4:c.433A>T	p.Ile145Phe	p.I145F	ENST00000282397	NM_002019.4	145	Att/Ttt	4/30	1	2	FACETS	0.938	0.775	1	0.938	0.775	1	CLONAL	1	TRUE	1	0.15	2		453	540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0064791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	391	1113	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.741100124053335	1	FACETS	0.994	0.96	1	0.994	0.96	1	CLONAL	1	FALSE	0	0.821683379454777	1		1113	564	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428478	72428478	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	297	520	0	ENST00000477973.2:c.526C>T	p.Gln176Ter	p.Q176*	ENST00000477973	NM_012234.5	176	Cag/Tag	2/4	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.821683379454777	2		520	674	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	244	721	4	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.86	0.805	0.917	0.86	0.805	0.917	CLONAL	1	TRUE	1	0.61	2		725	930	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	30	478	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.204	0.163	0.249	0.204	0.163	0.249	SUBCLONAL	1	TRUE	1	0.61	2		479	483	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	189	693	9	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	1	2	FACETS	0.932	0.865	1	0.932	0.865	1	CLONAL	1	TRUE	1	0.61	2		702	665	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	100	522	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.818	0.736	0.903	0.818	0.736	0.903	CLONAL	1	TRUE	1	0.61	2		522	401	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	165	860	9	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.74	0.681	0.801	0.74	0.681	0.801	SUBCLONAL	1	TRUE	1	0.61	2		869	731	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	295	877	17	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.61	2		894	837	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	294	928	2	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	1	2	FACETS	0.982	0.925	1	0.982	0.925	1	CLONAL	1	TRUE	1	0.61	2		930	982	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979514	7979514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141010860	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	177	699	1	ENST00000319144.4:c.1511C>T	p.Ala504Val	p.A504V	ENST00000319144	NM_001139.2	504	gCg/gTg	11/15	1	2	FACETS	0.911	0.843	0.981	0.911	0.843	0.981	CLONAL	1	TRUE	1	0.61	2		700	637	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088788	27088788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	196	835	0	ENST00000324856.7:c.2402del	p.Gly801ValfsTer32	p.G801Vfs*32	ENST00000324856	NM_006015.4	799	caG/ca	7/20	1	2	FACETS	0.878	0.815	0.943	0.878	0.815	0.943	CLONAL	1	TRUE	1	0.61	2		835	732	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100172	27100172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775802127	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	339	1032	0	ENST00000324856.7:c.3968G>A	p.Arg1323His	p.R1323H	ENST00000324856	NM_006015.4	1323	cGc/cAc	16/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.61	2		1032	1034	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937104	36937104	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	279	914	0	ENST00000361632.4:c.1215G>T	p.Glu405Asp	p.E405D	ENST00000361632		405	gaG/gaT	9/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.61	2		914	838	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849872	156849872	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370593942	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	223	758	2	ENST00000524377.1:c.2128G>A	p.Val710Met	p.V710M	ENST00000524377	NM_002529.3	710	Gtg/Atg	16/17	1	2	FACETS	0.972	0.908	1	0.972	0.908	1	CLONAL	1	TRUE	1	0.61	2		760	752	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163295896	163295896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748878165	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	106	535	0	ENST00000271452.3:c.55C>T	p.Arg19Cys	p.R19C	ENST00000271452	NM_145697.2	19	Cgc/Tgc	2/14	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.61	2		535	330	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717673	89717673	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770025422	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	161	665	0	ENST00000371953.3:c.698G>A	p.Arg233Gln	p.R233Q	ENST00000371953	NM_000314.4	233	cGa/cAa	7/9	1	2	FACETS	0.976	0.901	1	0.976	0.901	1	CLONAL	1	TRUE	1	0.61	2		665	541	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	103	941	2	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	1	2	FACETS	0.445	0.398	0.495	0.445	0.398	0.495	SUBCLONAL	1	TRUE	1	0.61	2		943	759	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432117	121432118	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776825	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	229	966	18	ENST00000257555.6:c.872dup	p.Gly292ArgfsTer25	p.G292Rfs*25	ENST00000257555		288	-/C	4/10	1	2	FACETS	0.876	0.818	0.936	0.876	0.818	0.936	CLONAL	1	TRUE	1	0.61	2		984	857	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680751	88680751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201252722	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	175	664	1	ENST00000360948.2:c.506G>A	p.Arg169His	p.R169H	ENST00000360948	NM_001012338.2	169	cGc/cAc	6/19	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.61	2		665	573	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652140	3652140	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759447034	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	235	841	1	ENST00000294008.3:c.929G>A	p.Arg310Gln	p.R310Q	ENST00000294008	NM_032444.2	310	cGa/cAa	4/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.61	2		842	736	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	174	764	1	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.854	0.789	0.921	0.854	0.789	0.921	CLONAL	1	TRUE	1	0.61	2		765	668	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099253	4099255	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs763469132	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	239	872	0	ENST00000262948.5:c.863_865del	p.Glu288del	p.E288del	ENST00000262948	NM_030662.3	288	gAAGga/gga	7/11	1	2	FACETS	0.976	0.914	1	0.976	0.914	1	CLONAL	1	TRUE	1	0.61	2		872	803	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296358	15296358	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	282	964	0	ENST00000263388.2:c.2084del	p.Pro695ArgfsTer165	p.P695Rfs*165	ENST00000263388	NM_000435.2	695	cCg/cg	13/33	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.61	2		964	895	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278091	18278091	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1165324884	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	217	782	0	ENST00000222254.8:c.1711C>T	p.Arg571Cys	p.R571C	ENST00000222254	NM_005027.3	571	Cgc/Tgc	13/16	1	2	FACETS	0.963	0.898	1	0.963	0.898	1	CLONAL	1	TRUE	1	0.61	2		782	739	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793223	42793223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775303325	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	263	1030	0	ENST00000575354.2:c.1115C>T	p.Ala372Val	p.A372V	ENST00000575354	NM_015125.3	372	gCg/gTg	7/20	1	2	FACETS	0.962	0.904	1	0.962	0.904	1	CLONAL	1	TRUE	1	0.61	2		1030	896	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424759	47424760	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	202	810	0	ENST00000404338.3:c.2834dup	p.Asn946GlufsTer11	p.N946Efs*11	ENST00000404338	NM_004491.4	943	gaa/gAaa	1/6	1	2	FACETS	0.859	0.798	0.922	0.859	0.798	0.922	CLONAL	1	TRUE	1	0.61	2		810	771	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918105	50918105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	193	763	0	ENST00000440232.2:c.2422C>T	p.Arg808Cys	p.R808C	ENST00000440232	NM_002691.3	808	Cgc/Tgc	20/27	1	2	FACETS	0.956	0.888	1	0.956	0.888	1	CLONAL	1	TRUE	1	0.61	2		763	662	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609593	46609593	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	223	962	0	ENST00000263734.3:c.2317C>A	p.Leu773Met	p.L773M	ENST00000263734	NM_001430.4	773	Ctg/Atg	15/16	1	2	FACETS	0.962	0.899	1	0.962	0.899	1	CLONAL	1	TRUE	1	0.61	2		962	760	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027807	48027807	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	153	645	0	ENST00000234420.5:c.2690del	p.Asn897IlefsTer9	p.N897Ifs*9	ENST00000234420	NM_000179.2	895	acA/ac	4/10	1	2	FACETS	0.952	0.876	1	0.952	0.876	1	CLONAL	1	TRUE	1	0.61	2		645	527	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794898	242794898	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138016578	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	227	861	0	ENST00000334409.5:c.311G>A	p.Arg104His	p.R104H	ENST00000334409	NM_005018.2	104	cGt/cAt	2/5	1	2	FACETS	0.954	0.892	1	0.954	0.892	1	CLONAL	1	TRUE	1	0.61	2		861	780	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026107	36026107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34881773	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	260	842	1	ENST00000358208.4:c.709G>A	p.Ala237Thr	p.A237T	ENST00000358208		237	Gcc/Acc	7/12	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.61	2		843	829	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564765	41564765	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	215	477	0	ENST00000263253.7:c.4066C>T	p.Arg1356Ter	p.R1356*	ENST00000263253	NM_001429.3	1356	Cga/Tga	25/31	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.61	2		477	703	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440372	52440372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	258	844	0	ENST00000460680.1:c.680G>A	p.Arg227His	p.R227H	ENST00000460680	NM_004656.3	227	cGc/cAc	9/17	1	2	FACETS	0.985	0.925	1	0.985	0.925	1	CLONAL	1	TRUE	1	0.61	2		844	859	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451364	187451364	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147478441	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	209	754	0	ENST00000232014.4:c.118C>T	p.Arg40Cys	p.R40C	ENST00000232014	NM_001130845.1	40	Cgt/Tgt	3/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.61	2		754	661	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964358	55964358	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	179	741	1	ENST00000263923.4:c.2455C>T	p.Arg819Ter	p.R819*	ENST00000263923	NM_002253.2	819	Cga/Tga	17/30	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.61	2		742	548	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630588	187630588	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	209	872	0	ENST00000441802.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000441802	NM_005245.3	132	Cga/Tga	2/27	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.61	2		872	637	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520201	176520201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368558499	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	248	953	0	ENST00000292408.4:c.1120G>A	p.Ala374Thr	p.A374T	ENST00000292408	NM_213647.1	374	Gcg/Acg	9/18	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.61	2		953	786	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057722	180057722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200878617	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	219	824	0	ENST00000261937.6:c.233C>T	p.Thr78Met	p.T78M	ENST00000261937	NM_182925.4	78	aCg/aTg	3/30	1	2	FACETS	0.96	0.896	1	0.96	0.896	1	CLONAL	1	TRUE	1	0.61	2		824	748	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527742	157527742	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	223	861	1	ENST00000346085.5:c.5471del	p.Gly1824ValfsTer27	p.G1824Vfs*27	ENST00000346085	NM_020732.3	1823	Ggg/gg	20/20	1	2	FACETS	0.898	0.838	0.96	0.898	0.838	0.96	CLONAL	1	TRUE	1	0.61	2		862	814	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984024	2984024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	206	784	0	ENST00000396946.4:c.506C>T	p.Thr169Met	p.T169M	ENST00000396946	NM_032415.4	169	aCg/aTg	5/25	1	2	FACETS	0.977	0.911	1	0.977	0.911	1	CLONAL	1	TRUE	1	0.61	2		784	691	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450267	50450267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	218	798	0	ENST00000331340.3:c.451G>A	p.Gly151Arg	p.G151R	ENST00000331340	NM_006060.4	151	Ggg/Agg	5/8	1	2	FACETS	0.995	0.93	1	0.995	0.93	1	CLONAL	1	TRUE	1	0.61	2		798	718	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	212	838	3	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.878	0.817	0.94	0.878	0.817	0.94	CLONAL	1	TRUE	1	0.61	2		841	792	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006006	22006006	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749530069	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	257	951	0	ENST00000276925.6:c.397C>T	p.Arg133Cys	p.R133C	ENST00000276925	NM_004936.3	133	Cgc/Tgc	2/2	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.61	2		951	813	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039372	47039372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	248	406	0	ENST00000377604.3:c.995G>A	p.Arg332His	p.R332H	ENST00000377604	NM_001204468.1	332	cGc/cAc	10/24	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.61	1		406	405	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040660	47040660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1477871550	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	224	400	0	ENST00000377604.3:c.1295C>T	p.Pro432Leu	p.P432L	ENST00000377604	NM_001204468.1	432	cCg/cTg	13/24	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.61	1		400	345	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651622	48651622	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557020433	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	300	496	0	ENST00000376670.3:c.788C>T	p.Thr263Met	p.T263M	ENST00000376670	NM_002049.3	263	aCg/aTg	5/6	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.61	1		496	472	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410102	63410102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761242587	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	255	526	0	ENST00000330258.3:c.3065G>A	p.Arg1022His	p.R1022H	ENST00000330258	NM_152424.3	1022	cGt/cAt	2/2	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.61	1		526	440	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206943203	206943203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1558602391	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	208	846	0	ENST00000423557.1:c.415G>A	p.Val139Met	p.V139M	ENST00000423557	NM_000572.2	139	Gtg/Atg	4/5	1	2	FACETS	0.935	0.871	1	0.935	0.871	1	CLONAL	1	TRUE	1	0.61	2		846	729	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57004348	57004348	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	G	G	A	rs767906014	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	223	896	0	ENST00000257254.3:c.131C>T	p.Thr44Met	p.T44M	ENST00000257254		44	aCg/aTg	1/2	1	2	FACETS	0.897	0.837	0.959	0.897	0.837	0.959	CLONAL	1	TRUE	1	0.61	2		896	815	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118353193	118353194	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	135	694	0	ENST00000534358.1:c.4074dup	p.Pro1359ThrfsTer12	p.P1359Tfs*12	ENST00000534358	NM_005933.3	1357	caa/cAaa	8/36	1	2	FACETS	0.829	0.757	0.903	0.829	0.757	0.903	CLONAL	1	TRUE	1	0.61	2		694	534	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373209	118373212	+	frameshift_variant	Frame_Shift_Del	DEL	CTTC	CTTC	-	novel	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	235	871	0	ENST00000534358.1:c.6605_6608del	p.Ser2202TyrfsTer10	p.S2202Yfs*10	ENST00000534358	NM_005933.3	2201	tCTTCc/tc	27/36	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.61	2		871	722	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425348	49425348	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	272	937	0	ENST00000301067.7:c.13140del	p.Asp4381ThrfsTer3	p.D4381Tfs*3	ENST00000301067	NM_003482.3	4380	ccA/cc	39/54	1	2	FACETS	0.992	0.933	1	0.992	0.933	1	CLONAL	1	TRUE	1	0.61	2		937	899	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574321	95574321	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	113	583	0	ENST00000393063.1:c.2546T>C	p.Leu849Pro	p.L849P	ENST00000393063	NM_030621.3	849	cTt/cCt	17/28	1	2	FACETS	0.829	0.751	0.91	0.829	0.751	0.91	CLONAL	1	TRUE	1	0.61	2		583	447	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51503060	51503060	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	177	678	1	ENST00000260433.2:c.1457del	p.Asn486ThrfsTer5	p.N486Tfs*5	ENST00000260433		486	aAc/ac	10/10	1	2	FACETS	0.966	0.894	1	0.966	0.894	1	CLONAL	1	TRUE	1	0.61	2		679	601	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16062159	16062159	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	174	778	0	ENST00000268712.3:c.647C>A	p.Pro216His	p.P216H	ENST00000268712	NM_006311.3	216	cCt/cAt	6/46	1	2	FACETS	0.897	0.829	0.967	0.897	0.829	0.967	CLONAL	1	TRUE	1	0.61	2		778	636	SUCCESS
YES1	7525	MSKCC	GRCh37	18	732958	732958	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	166	536	0	ENST00000314574.4:c.1299A>T	p.Lys433Asn	p.K433N	ENST00000314574	NM_005433.3	433	aaA/aaT	11/12	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.61	2		536	522	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229539	5229539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542345642	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	241	815	0	ENST00000357368.4:c.2312C>T	p.Pro771Leu	p.P771L	ENST00000357368	NM_002850.3	771	cCg/cTg	15/38	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.61	2		815	652	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134266	11134266	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064796254	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	173	771	0	ENST00000358026.2:c.2932C>T	p.Arg978Ter	p.R978*	ENST00000358026	NM_001128849.1	978	Cga/Tga	20/36	1	2	FACETS	0.814	0.751	0.879	0.814	0.751	0.879	CLONAL	1	TRUE	1	0.61	2		771	697	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273925	18273925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766254350	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	218	830	1	ENST00000222254.8:c.1258C>T	p.Arg420Trp	p.R420W	ENST00000222254	NM_005027.3	420	Cgg/Tgg	10/16	1	2	FACETS	0.884	0.824	0.945	0.884	0.824	0.945	CLONAL	1	TRUE	1	0.61	2		831	809	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705410	47705410	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	105	435	0	ENST00000233146.2:c.2211-1G>A		p.X737_splice	ENST00000233146	NM_000251.2	737			1	2	FACETS	0.887	0.802	0.977	0.887	0.802	0.977	CLONAL	1	TRUE	1	0.61	2		435	388	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027703	48027703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	156	573	0	ENST00000234420.5:c.2581G>A	p.Ala861Thr	p.A861T	ENST00000234420	NM_000179.2	861	Gct/Act	4/10	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.61	2		573	503	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321181	62321181	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756398600	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	237	898	0	ENST00000360203.5:c.2104C>T	p.Arg702Cys	p.R702C	ENST00000360203	NM_001283009.1	702	Cgc/Tgc	24/35	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.61	2		898	729	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42838074	42838074	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140790362	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	161	648	0	ENST00000398585.3:c.1585G>A	p.Gly529Ser	p.G529S	ENST00000398585	NM_001135099.1	529	Ggc/Agc	14/14	1	2	FACETS	0.92	0.848	0.994	0.92	0.848	0.994	CLONAL	1	TRUE	1	0.61	2		648	574	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446062	29446062	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	35	764	0	ENST00000544604.2:c.1893G>T	p.Glu631Asp	p.E631D	ENST00000544604	NM_001206998.1	631	gaG/gaT	8/9	1	2	FACETS	0.172	0.14	0.208	0.172	0.14	0.208	SUBCLONAL	1	TRUE	1	0.61	2		764	666	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20486976	20486976	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	164	559	0	ENST00000346618.3:c.941C>T	p.Thr314Ile	p.T314I	ENST00000346618	NM_001949.4	314	aCt/aTt	5/7	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.61	2		559	496	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913196	44913196	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773995635	NA	P-0064947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	120	304	0	ENST00000377967.4:c.871G>A	p.Gly291Arg	p.G291R	ENST00000377967	NM_021140.2	291	Gga/Aga	10/29	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.61	1		304	196	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0065006-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	381	383	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.782929027689898	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	0	0.79294036633669	3		384	445	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415901	49415902	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0065006-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	201	452	0	ENST00000301067.7:c.16445_16446del	p.Val5482GlyfsTer7	p.V5482Gfs*7	ENST00000301067	NM_003482.3	5482	gTG/g	53/54	0.741104949435665	3	FACETS	1	0.991	1	0.694	0.649	0.74	CLONAL	1	TRUE	1	0.79294036633669	3		452	510	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549319	187549319	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065006-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	13	399	0	ENST00000441802.2:c.4799C>G	p.Ser1600Trp	p.S1600W	ENST00000441802	NM_005245.3	1600	tCg/tGg	9/27	0.79294036633669	1	FACETS	0.099	0.07	0.134	0.099	0.07	0.134	SUBCLONAL	1	TRUE	0	0.79294036633669	1		399	200	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426022	49426022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1131691768	NA	P-0065006-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	233	544	0	ENST00000301067.7:c.12466C>T	p.Gln4156Ter	p.Q4156*	ENST00000301067	NM_003482.3	4156	Caa/Taa	39/54	0.741104949435665	3	FACETS	0.763	0.718	0.808	0.763	0.718	0.808	SUBCLONAL	2	TRUE	1	0.79294036633669	3		544	538	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155353	99155353	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0065006-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	119	306	0	ENST00000074304.5:c.580-1G>C		p.X194_splice	ENST00000074304	NM_001134224.1	194			1	2	FACETS	0.754	0.687	0.824	0.754	0.687	0.824	SUBCLONAL	1	TRUE	1	0.79294036633669	2		306	398	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32191698	32191698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065006-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	330	489	0	ENST00000375023.3:c.8C>T	p.Pro3Leu	p.P3L	ENST00000375023	NM_004557.3	3	cCc/cTc	1/30	0.769999608554577	2	FACETS	0.998	0.967	1	0.998	0.967	1	CLONAL	2	TRUE	0	0.79294036633669	2		489	417	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100328	157100328	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065006-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	134	287	0	ENST00000346085.5:c.1265T>A	p.Leu422Gln	p.L422Q	ENST00000346085	NM_020732.3	422	cTg/cAg	1/20	0.79294036633669	2	FACETS	1	0.989	1	0.695	0.647	0.743	CLONAL	1	TRUE	0	0.79294036633669	2		287	243	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223565	55223565	+	protein_altering_variant	In_Frame_Ins	INS	G	G	CCTA	novel	NA	P-0065006-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	79	406	0	ENST00000275493.2:c.932delinsCCTA	p.Cys311delinsSerTyr	p.C311delinsSY	ENST00000275493	NM_005228.3	311	tGt/tCCTAt	8/28	0.365681937632235	2	FACETS	0.304	0.267	0.343	0.152	0.133	0.172	INDETERMINATE	1	TRUE	0	0.79294036633669	2		406	656	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200490	67200492	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs745334788	NA	P-0065006-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	37	540	0	ENST00000312629.5:c.686_688del	p.Phe229del	p.F229del	ENST00000312629	NM_003952.2	228	acCTTc/acc	8/15	0.72610975224377	3	FACETS	0.213	0.175	0.256	0.107	0.087	0.128	SUBCLONAL	1	TRUE	1	0.79294036633669	3		540	611	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	15	654	0	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	1	2	FACETS	0.109	0.079	0.146	0.109	0.079	0.146	SUBCLONAL	1	TRUE	1	0.41	2		654	670	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855817	45855817	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	137	627	0	ENST00000391945.4:c.1993G>T	p.Gly665Cys	p.G665C	ENST00000391945	NM_000400.3	665	Ggt/Tgt	21/23	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.41	2		627	667	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769112	112769123	+	inframe_deletion	In_Frame_Del	DEL	CAAATGAAATTG	CAAATGAAATTG	-	novel	NA	P-0065038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	67	370	0	ENST00000369452.4:c.1393_1404del	p.Asn465_Ala468del	p.N465_A468del	ENST00000369452	NM_007373.3	464	cCAAATGAAATTGca/cca	7/9	1	2	FACETS	0.695	0.606	0.792	0.695	0.606	0.792	SUBCLONAL	1	TRUE	1	0.41	2		370	470	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0065056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	52	539	0				ENST00000310581	NM_198253.2	-/1132			0.321383497825525	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.372652837795627	1		539	189	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0065056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	68	734	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.992	0.868	1	0.992	0.868	1	CLONAL	1	TRUE	1	0.372652837795627	2		734	368	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087458	27087458	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	142	640	0	ENST00000324856.7:c.2032C>T	p.Gln678Ter	p.Q678*	ENST00000324856	NM_006015.4	678	Cag/Tag	5/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.372652837795627	2		640	554	SUCCESS
AR	367	MSKCC	GRCh37	X	66766207	66766207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	56	692	0	ENST00000374690.3:c.1219C>T	p.Arg407Cys	p.R407C	ENST00000374690	NM_000044.3	407	Cgc/Tgc	1/8	0.372652837795627	1	FACETS	0.689	0.593	0.793	0.689	0.593	0.793	SUBCLONAL	1	TRUE	0	0.372652837795627	1		692	355	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950082	44950082	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0065056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	96	394	0	ENST00000377967.4:c.3851C>G	p.Ser1284Ter	p.S1284*	ENST00000377967	NM_021140.2	1284	tCa/tGa	26/29	0.372652837795627	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.372652837795627	1		394	311	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37092133	37092133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs864622445	NA	P-0065056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	107	404	0	ENST00000231790.2:c.2260G>A	p.Glu754Lys	p.E754K	ENST00000231790	NM_000249.3	754	Gag/Aag	19/19	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.372652837795627	2		404	414	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556722	41556722	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	105	520	0	ENST00000263253.7:c.3667C>T	p.Gln1223Ter	p.Q1223*	ENST00000263253	NM_001429.3	1223	Caa/Taa	20/31	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.372652837795627	2		520	455	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551958	150551958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs932863734	NA	P-0065056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	49	655	0	ENST00000369026.2:c.49G>A	p.Gly17Arg	p.G17R	ENST00000369026	NM_021960.4	17	Ggg/Agg	1/3	1	2	FACETS	0.524	0.444	0.612	0.524	0.444	0.612	SUBCLONAL	1	TRUE	1	0.372652837795627	2		655	502	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491357	2491357	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	84	734	0	ENST00000355716.4:c.400C>G	p.His134Asp	p.H134D	ENST00000355716	NM_003820.2	134	Cac/Gac	4/8	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.372652837795627	2		734	391	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650171	206650171	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0065056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	100	709	0	ENST00000367120.3:c.691A>T	p.Lys231Ter	p.K231*	ENST00000367120	NM_014002.3	231	Aag/Tag	7/22	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.372652837795627	2		709	452	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884106	37884106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	131	751	0	ENST00000269571.5:c.3577A>G	p.Asn1193Asp	p.N1193D	ENST00000269571		1193	Aac/Gac	27/27	1	2	FACETS	0.751	0.686	0.818	1	0.987	1	SUBCLONAL	2	TRUE	1	0.372652837795627	2		751	468	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007708	62007708	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	80	592	0	ENST00000392795.3:c.159C>G	p.Phe53Leu	p.F53L	ENST00000392795	NM_001039933.1	53	ttC/ttG	3/6	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.372652837795627	2		592	368	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101890	11101891	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0065056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	101	714	0	ENST00000358026.2:c.1312dup	p.Ala438GlyfsTer17	p.A438Gfs*17	ENST00000358026	NM_001128849.1	437	aag/aaGg	8/36	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.372652837795627	2		714	403	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976431	25976432	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTCTTTCCATGGCTCCACTTTTTTCTCCTTCTCAATCTC	novel	NA	P-0065056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	56	348	0	ENST00000435504.4:c.1075_1113dup	p.Glu359_Glu371dup	p.E359_E371dup	ENST00000435504		359	-/GAGATTGAGAAGGAGAAAAAAGTGGAGCCATGGAAAGAA	11/13	1	2	FACETS	0.678	0.582	0.783	0.678	0.582	0.783	SUBCLONAL	1	TRUE	1	0.372652837795627	2		348	443	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982359	25982359	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	111	354	0	ENST00000435504.4:c.931G>T	p.Asp311Tyr	p.D311Y	ENST00000435504		311	Gat/Tat	9/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.372652837795627	2		354	406	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434245	12434245	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	111	382	0	ENST00000287820.6:c.613C>G	p.His205Asp	p.H205D	ENST00000287820	NM_015869.4	205	Cat/Gat	4/7	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.372652837795627	2		382	498	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201669	66201669	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	109	466	0	ENST00000273854.3:c.2833C>G	p.Leu945Val	p.L945V	ENST00000273854	NM_004439.5	945	Ctg/Gtg	16/18	1	2	FACETS	0.774	0.701	0.849	1	0.985	1	SUBCLONAL	2	TRUE	1	0.372652837795627	2		466	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	305	545	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.217774916175355	4	FACETS	1	0.986	1	1	0.996	1	CLONAL	6	TRUE	0	0.217774916175355	4		546	528	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145543	61145543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767519747	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	143	358	0	ENST00000295025.8:c.655C>T	p.Arg219Cys	p.R219C	ENST00000295025	NM_002908.2	219	Cgt/Tgt	7/11	0.197755633337668	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.217774916175355	3		358	611	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852158	128852158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141955434	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	196	580	0	ENST00000249373.3:c.2230C>T	p.Pro744Ser	p.P744S	ENST00000249373	NM_005631.4	744	Cct/Tct	12/12	0.214313446146001	4	FACETS	0.963	0.898	1	1	0.993	1	CLONAL	4	TRUE	2	0.217774916175355	4		580	569	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134988	41134988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	131	383	0	ENST00000379561.5:c.640C>T	p.Arg214Cys	p.R214C	ENST00000379561	NM_002015.3	214	Cgt/Tgt	2/3	1	2	FACETS	1	0.979	1	1	0.992	1	CLONAL	2	TRUE	1	0.217774916175355	2		383	486	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003314	143003314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1451831325	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	121	269	0	ENST00000262992.4:c.2512C>T	p.Arg838Cys	p.R838C	ENST00000262992	NM_001101669.1	838	Cgt/Tgt	23/24	1	2	FACETS	0.938	0.855	1	1	0.992	1	CLONAL	3	TRUE	1	0.217774916175355	2		269	395	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956553	93956553	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1035177735	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	126	400	0	ENST00000369303.4:c.2683C>T	p.Arg895Ter	p.R895*	ENST00000369303	NM_004440.3	895	Cga/Tga	15/17	0.181891844608064	4	FACETS	0.86	0.782	0.942	0.86	0.782	0.942	CLONAL	3	TRUE	1	0.217774916175355	4		400	546	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240319	5240319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773233463	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	114	419	0	ENST00000357368.4:c.1595G>A	p.Arg532Gln	p.R532Q	ENST00000357368	NM_002850.3	532	cGg/cAg	12/38	1	2	FACETS	0.994	0.905	1	1	0.991	1	CLONAL	3	TRUE	1	0.217774916175355	2		419	351	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127759	47127759	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	153	408	0	ENST00000409792.3:c.5323G>T	p.Gly1775Trp	p.G1775W	ENST00000409792	NM_014159.6	1775	Ggg/Tgg	11/21	0.139281650466256	5	FACETS	0.963	0.884	1	0.963	0.884	1	CLONAL	3	TRUE	2	0.217774916175355	5		408	645	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	70	417	0				ENST00000310581	NM_198253.2	-/1132			0.0658481003975639	3	FACETS	0.846	0.745	0.952	1	0.965	1	INDETERMINATE	3	TRUE	1	0.217774916175355	3		417	281	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508167	106508167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	157	471	0	ENST00000359195.3:c.161C>T	p.Pro54Leu	p.P54L	ENST00000359195	NM_002649.2	54	cCc/cTc	2/11	0.214313446146001	4	FACETS	1	0.975	1	1	0.991	1	CLONAL	3	TRUE	2	0.217774916175355	4		471	514	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939191	36939191	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	206	618	0	ENST00000361632.4:c.518C>T	p.Ser173Phe	p.S173F	ENST00000361632		173	tCc/tTc	5/16	0.197755633337668	3	FACETS	0.914	0.854	0.975	1	0.994	1	CLONAL	4	TRUE	1	0.217774916175355	3		618	574	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405962	49405962	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	199	399	0	ENST00000418115.1:c.176A>G	p.Asp59Gly	p.D59G	ENST00000418115	NM_001664.2	59	gAc/gGc	3/5	0.139281650466256	5	FACETS	0.913	0.853	0.974	1	0.992	1	CLONAL	5	TRUE	2	0.217774916175355	5		399	531	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633420	3633420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766110479	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	125	575	0	ENST00000294008.3:c.4831G>A	p.Glu1611Lys	p.E1611K	ENST00000294008	NM_032444.2	1611	Gag/Aag	14/15	1	2	FACETS	1	0.973	1	1	0.991	1	CLONAL	2	TRUE	1	0.217774916175355	2		575	486	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444311	50444311	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778251001	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	222	458	0	ENST00000331340.3:c.241G>A	p.Asp81Asn	p.D81N	ENST00000331340	NM_006060.4	81	Gat/Aat	4/8	0.214313446146001	4	FACETS	1	0.957	1	1	0.995	1	CLONAL	4	TRUE	2	0.217774916175355	4		458	605	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584806	48584806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370176106	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	162	451	0	ENST00000342988.3:c.884C>T	p.Pro295Leu	p.P295L	ENST00000342988	NM_005359.5	295	cCg/cTg	7/12	1	2	FACETS	1	0.978	1	1	0.993	1	CLONAL	2	TRUE	1	0.217774916175355	2		451	635	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644711	134644711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	169	457	0	ENST00000398015.3:c.112C>T	p.Pro38Ser	p.P38S	ENST00000398015	NM_004441.4	38	Cct/Tct	2/16	NA	2	FACETS	0.987	0.914	1			1	INDETERMINATE	3	TRUE	NA	0.217774916175355	2		457	524	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437443	110437443	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753666571	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	96	397	0	ENST00000375856.3:c.958C>T	p.Pro320Ser	p.P320S	ENST00000375856	NM_003749.2	320	Ccc/Tcc	1/2	1	2	FACETS	0.84	0.755	0.928	1	0.989	1	CLONAL	3	TRUE	1	0.217774916175355	2		397	350	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442998	49442998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375144626	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	107	462	0	ENST00000301067.7:c.3910C>T	p.Arg1304Cys	p.R1304C	ENST00000301067	NM_003482.3	1304	Cgc/Tgc	12/54	1	2	FACETS	1	0.914	1	1	0.988	1	CLONAL	2	TRUE	1	0.217774916175355	2		462	484	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112494	115112494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	137	547	0	ENST00000257566.3:c.1246C>T	p.Leu416Phe	p.L416F	ENST00000257566	NM_016569.3	416	Ctt/Ttt	7/8	0.214669508909928	1	FACETS	1	0.979	1	1	0.992	1	CLONAL	2	TRUE	0	0.217774916175355	1		547	461	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187546	32187546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	179	565	0	ENST00000375023.3:c.1333C>T	p.Pro445Ser	p.P445S	ENST00000375023	NM_004557.3	445	Ccc/Tcc	8/30	0.181891844608064	4	FACETS	0.974	0.901	1	0.974	0.901	1	CLONAL	3	TRUE	1	0.217774916175355	4		565	685	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844780	156844780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	166	652	0	ENST00000524377.1:c.1334G>A	p.Arg445Lys	p.R445K	ENST00000524377	NM_002529.3	445	aGa/aAa	11/17	0.197755633337668	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.217774916175355	3		652	716	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490459	20490459	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	232	484	0	ENST00000346618.3:c.1196C>T	p.Pro399Leu	p.P399L	ENST00000346618	NM_001949.4	399	cCt/cTt	7/7	0.190625038106124	4	FACETS	1	0.982	1	1	0.993	1	CLONAL	4	TRUE	1	0.217774916175355	4		484	585	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760671	59760671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	197	329	0	ENST00000259008.2:c.3736C>T	p.Pro1246Ser	p.P1246S	ENST00000259008	NM_032043.2	1246	Cct/Tct	20/20	0.139281650466256	5	FACETS	1	0.939	1	1	0.989	1	CLONAL	4	TRUE	2	0.217774916175355	5		329	595	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213090	39213090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	137	576	0	ENST00000402219.2:c.3877C>T	p.Pro1293Ser	p.P1293S	ENST00000402219	NM_005633.3	1293	Cct/Tct	23/23	0.197755633337668	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.217774916175355	3		576	620	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467864	50467864	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	187	500	0	ENST00000331340.3:c.1099G>A	p.Asp367Asn	p.D367N	ENST00000331340	NM_006060.4	367	Gac/Aac	8/8	0.214313446146001	4	FACETS	1	0.978	1	1	0.994	1	CLONAL	4	TRUE	2	0.217774916175355	4		500	469	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573905	41573905	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	148	594	0	ENST00000263253.7:c.6190C>T	p.Pro2064Ser	p.P2064S	ENST00000263253	NM_001429.3	2064	Ccc/Tcc	31/31	1	2	FACETS	0.93	0.856	1	1	0.993	1	CLONAL	3	TRUE	1	0.217774916175355	2		594	487	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859461	151859461	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	249	545	0	ENST00000262189.6:c.11201C>T	p.Pro3734Leu	p.P3734L	ENST00000262189	NM_170606.2	3734	cCt/cTt	43/59	0.214313446146001	4	FACETS	1	0.959	1	1	0.995	1	CLONAL	4	TRUE	2	0.217774916175355	4		545	679	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268218	153268218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	145	349	0	ENST00000281708.4:c.590C>T	p.Thr197Ile	p.T197I	ENST00000281708	NM_033632.3	197	aCt/aTt	4/12	1	2	FACETS	1	0.974	1	1	0.992	1	CLONAL	2	TRUE	1	0.217774916175355	2		349	576	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10785223	10785223	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	212	457	0	ENST00000361367.2:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000361367	NM_014633.3	331	Caa/Taa	9/25	0.213392279964915	3	FACETS	1	0.979	1	1	0.993	1	CLONAL	3	TRUE	1	0.217774916175355	3		457	646	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637900	39637900	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	131	383	0	ENST00000262039.4:c.2317C>T	p.Leu773Phe	p.L773F	ENST00000262039	NM_002647.2	773	Ctt/Ttt	22/25	1	2	FACETS	1	0.979	1	1	0.992	1	CLONAL	2	TRUE	1	0.217774916175355	2		383	484	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394334	162394334	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	215	325	0	ENST00000366898.1:c.734G>A	p.Arg245Lys	p.R245K	ENST00000366898	NM_004562.2	245	aGg/aAg	6/12	0.181891844608064	4	FACETS	0.93	0.873	0.988	1	0.993	1	CLONAL	5	TRUE	1	0.217774916175355	4		325	517	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46597018	46597018	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	103	372	0	ENST00000263734.3:c.832T>A	p.Tyr278Asn	p.Y278N	ENST00000263734	NM_001430.4	278	Tat/Aat	7/16	0.197755633337668	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.217774916175355	3		372	434	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373793	118373793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	204	510	0	ENST00000534358.1:c.7186C>T	p.Pro2396Ser	p.P2396S	ENST00000534358	NM_005933.3	2396	Cca/Tca	27/36	0.213392279964915	3	FACETS	0.888	0.829	0.948	1	0.993	1	CLONAL	4	TRUE	1	0.217774916175355	3		510	585	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115272914	115272914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	225	425	0	ENST00000438362.2:c.1459C>T	p.Pro487Ser	p.P487S	ENST00000438362	NM_001242891.1	487	Cct/Tct	12/20	0.197755633337668	3	FACETS	0.941	0.882	1	1	0.994	1	CLONAL	4	TRUE	1	0.217774916175355	3		425	609	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608107	28608107	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	134	458	0	ENST00000241453.7:c.1859C>T	p.Ala620Val	p.A620V	ENST00000241453	NM_004119.2	620	gCt/gTt	15/24	0.217774916175355	1	FACETS	1	0.978	1	1	0.992	1	CLONAL	2	TRUE	0	0.217774916175355	1		458	456	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740328	46740328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	222	452	0	ENST00000371975.4:c.1808C>T	p.Ala603Val	p.A603V	ENST00000371975	NM_003579.3	603	gCc/gTc	16/18	0.197755633337668	3	FACETS	0.93	0.871	0.989	1	0.994	1	CLONAL	4	TRUE	1	0.217774916175355	3		452	608	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11293520	11293520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	172	398	0	ENST00000361445.4:c.2356C>T	p.Pro786Ser	p.P786S	ENST00000361445	NM_004958.3	786	Cca/Tca	15/58	0.0658481003975639	3	FACETS	0.98	0.906	1	1	0.99	1	INDETERMINATE	3	TRUE	1	0.217774916175355	3		398	596	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	256507	256508	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	100	355	0	ENST00000264932.6:c.1967_1968delinsTT	p.Thr656Ile	p.T656I	ENST00000264932	NM_004168.2	656	aCC/aTT	15/15	0.0658481003975639	3	FACETS	1	0.969	1	1	0.969	1	INDETERMINATE	2	TRUE	1	0.217774916175355	3		355	424	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229650	98229651	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	273	482	0	ENST00000331920.6:c.2307_2308delinsTT	p.Arg770Ter	p.R770*	ENST00000331920	NM_000264.3	769	acCCga/acTTga	15/24	NA	2	FACETS	1	0.956	1			1	INDETERMINATE	5	TRUE	NA	0.217774916175355	2		482	499	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732958	74732959	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	144	481	0	ENST00000359995.5:c.284_285delinsTT	p.Pro95Leu	p.P95L	ENST00000359995	NM_001195427.1	95	cCC/cTT	1/3	0.139281650466256	5	FACETS	0.891	0.819	0.967	1	0.978	1	CLONAL	4	TRUE	2	0.217774916175355	5		481	492	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30302595	30302595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3	24	14	0	ENST00000322652.5:c.686C>T	p.Ser229Phe	p.S229F	ENST00000322652	NM_015355.2	229	tCc/tTc	7/16	0.139281650466256	5	FACETS	0.985	0.891	1	1	0.97	1	CLONAL	11	TRUE	2	0.217774916175355	5		14	27	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99491841	99491841	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	108	420	0	ENST00000268035.6:c.3626C>T	p.Ala1209Val	p.A1209V	ENST00000268035	NM_000875.3	1209	gCc/gTc	20/21	0.214669508909928	1	FACETS	1	0.917	1	1	0.989	1	CLONAL	2	TRUE	0	0.217774916175355	1		420	435	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842331	68842331	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs973519600	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	118	363	0	ENST00000261769.5:c.392C>T	p.Ser131Phe	p.S131F	ENST00000261769	NM_004360.3	131	tCc/tTc	4/16	1	2	FACETS	1	0.971	1	1	0.99	1	CLONAL	2	TRUE	1	0.217774916175355	2		363	462	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922625	56922625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	165	477	0	ENST00000519728.1:c.1495G>A	p.Asp499Asn	p.D499N	ENST00000519728	NM_002350.3	499	Gat/Aat	13/13	1	2	FACETS	0.896	0.827	0.966	1	0.994	1	CLONAL	3	TRUE	1	0.217774916175355	2		477	564	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0065174-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	126	269	1	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.36998627069207	4	FACETS	0.862	0.793	0.933	0.862	0.793	0.933	CLONAL	3	TRUE	1	0.464951000465967	4		270	307	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0065174-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	83	262	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.402838031766724	3	FACETS	0.756	0.675	0.841	0.756	0.675	0.841	SUBCLONAL	2	TRUE	1	0.464951000465967	3		262	291	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0065174-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	174	481	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.371695159430118	3	FACETS	1	0.975	1	0.732	0.682	0.783	CLONAL	2	TRUE	0	0.464951000465967	3		481	420	SUCCESS
APC	324	MSKCC	GRCh37	5	112175438	112175439	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0065174-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	60	520	0	ENST00000257430.4:c.4147_4148del	p.Met1383ValfsTer2	p.M1383Vfs*2	ENST00000257430	NM_000038.5	1383	ATg/g	16/16	0.402838031766724	3	FACETS	0.672	0.58	0.772	0.336	0.29	0.386	SUBCLONAL	1	TRUE	1	0.464951000465967	3		520	473	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028805	47028805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065174-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	222	283	6	ENST00000377604.3:c.109C>T	p.Arg37Trp	p.R37W	ENST00000377604	NM_001204468.1	37	Cgg/Tgg	3/24	0.447269983076333	2	FACETS	0.907	0.862	0.95			1	CLONAL	3	TRUE	NA	0.464951000465967	2		289	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577544	7577544	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587780074	NA	P-0065174-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	149	516	0	ENST00000269305.4:c.737T>G	p.Met246Arg	p.M246R	ENST00000269305	NM_001126112.2	246	aTg/aGg	7/11	0.402838031766724	3	FACETS	0.839	0.772	0.907	0.839	0.772	0.907	CLONAL	2	TRUE	1	0.464951000465967	3		516	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578178	7578178	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065174-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	99	640	0	ENST00000269305.4:c.671A>T	p.Glu224Val	p.E224V	ENST00000269305	NM_001126112.2	224	gAg/gTg	6/11	0.402838031766724	3	FACETS	0.961	0.861	1	0.481	0.43	0.534	CLONAL	1	TRUE	1	0.464951000465967	3		640	546	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154769	2154769	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1457247306	NA	P-0065245-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	170	456	0	ENST00000434045.2:c.452C>T	p.Ser151Leu	p.S151L	ENST00000434045	NM_001127598.1	151	tCg/tTg	4/5	0.207379119311195	3	FACETS	0.94	0.867	1	0.94	0.867	1	CLONAL	2	FALSE	1	0.3	3		456	693	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0065256-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	113	582	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.305020960053937	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.305020960053937	3		582	394	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061313	38061313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1204900727	NA	P-0065256-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	133	517	0	ENST00000250448.2:c.676G>A	p.Asp226Asn	p.D226N	ENST00000250448	NM_004496.3	226	Gac/Aac	2/2	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.305020960053937	2		517	807	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50782647	50782647	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065256-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	88	495	0	ENST00000307179.4:c.2159C>A	p.Pro720Gln	p.P720Q	ENST00000307179		720	cCa/cAa	14/20	1	2	FACETS	0.855	0.758	0.959	0.855	0.758	0.959	CLONAL	1	TRUE	1	0.305020960053937	2		495	675	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188317	32188317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144492578	NA	P-0065257-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	108	534	0	ENST00000375023.3:c.1024G>A	p.Val342Met	p.V342M	ENST00000375023	NM_004557.3	342	Gtg/Atg	6/30	0.392150666847985	5	FACETS	0.76	0.68	0.844	0.19	0.17	0.211	SUBCLONAL	1	TRUE	1	0.416054891600372	5		534	1110	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602290	10602290	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065257-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	172	419	1	ENST00000171111.5:c.1288G>T	p.Gly430Cys	p.G430C	ENST00000171111	NM_203500.1	430	Ggc/Tgc	3/6	0.296882157222052	2	FACETS	1	0.989	1	0.719	0.665	0.774	CLONAL	1	TRUE	0	0.416054891600372	2		420	575	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207064	1207065	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1131690917	NA	P-0065257-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	163	438	0	ENST00000326873.7:c.157dup	p.Asp53GlyfsTer110	p.D53Gfs*110	ENST00000326873	NM_000455.4	51	atg/atGg	1/10	0.296882157222052	2	FACETS	1	0.987	1	0.686	0.633	0.741	CLONAL	1	TRUE	0	0.416054891600372	2		438	571	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243778409	243778409	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065257-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	56	317	0	ENST00000263826.5:c.616C>T	p.Pro206Ser	p.P206S	ENST00000263826	NM_005465.4	206	Ccc/Tcc	6/13	0.416054891600372	6	FACETS	0.614	0.525	0.712	0.154	0.131	0.178	SUBCLONAL	1	TRUE	2	0.416054891600372	6		317	803	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843540	3843540	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065257-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	184	373	0	ENST00000262367.5:c.1063del	p.Gln355SerfsTer34	p.Q355Sfs*34	ENST00000262367	NM_004380.2	355	Cag/ag	4/31	0.305986084062231	4	FACETS	0.775	0.717	0.836	0.775	0.717	0.836	SUBCLONAL	2	TRUE	2	0.416054891600372	4		373	808	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998985	11998985	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065261-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	153	340	0	ENST00000353533.5:c.487C>T	p.Gln163Ter	p.Q163*	ENST00000353533	NM_003010.3	163	Cag/Tag	4/11	0.712965551865848	1	FACETS	0.952	0.889	1	0.952	0.889	1	CLONAL	1	TRUE	0	0.712965551865848	1		340	290	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266821	198266821	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065261-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	167	332	0	ENST00000335508.6:c.2111T>A	p.Ile704Asn	p.I704N	ENST00000335508	NM_012433.2	704	aTc/aAc	15/25	1	2	FACETS	0.962	0.891	1	0.962	0.891	1	CLONAL	1	TRUE	1	0.712965551865848	2		332	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs878854073	NA	P-0065261-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	149	359	0	ENST00000269305.4:c.673-1G>A		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.712965551865848	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.712965551865848	1		359	251	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186711	11186711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065261-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	166	419	0	ENST00000361445.4:c.6494C>T	p.Ser2165Phe	p.S2165F	ENST00000361445	NM_004958.3	2165	tCc/tTc	46/58	0.202439554996667	3	FACETS	1	0.929	1	0.336	0.309	0.363	INDETERMINATE	1	TRUE	0	0.712965551865848	3		419	627	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945081	31945081	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065261-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	360	470	0	ENST00000340398.3:c.20C>G	p.Thr7Ser	p.T7S	ENST00000340398	NM_001013699.2	7	aCt/aGt	1/1	0.493859598546037	3	FACETS	0.945	0.903	0.987	0.945	0.903	0.987	CLONAL	2	TRUE	1	0.712965551865848	3		470	725	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21337354	21337354	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065261-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	180	370	0	ENST00000215739.8:c.239T>C	p.Ile80Thr	p.I80T	ENST00000215739	NM_006767.3	80	aTt/aCt	2/21	0.712965551865848	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.712965551865848	1		370	294	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40859995	40859995	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065261-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	153	359	0	ENST00000428826.2:c.1641C>G	p.Phe547Leu	p.F547L	ENST00000428826		547	ttC/ttG	15/21	1	2	FACETS	0.858	0.791	0.928	0.858	0.791	0.928	CLONAL	1	TRUE	1	0.712965551865848	2		359	500	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631970	67631970	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065261-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	158	457	0	ENST00000272342.5:c.2156A>G	p.Glu719Gly	p.E719G	ENST00000272342	NM_019002.3	719	gAg/gGg	5/6	1	2	FACETS	0.872	0.805	0.942	0.872	0.805	0.942	CLONAL	1	TRUE	1	0.712965551865848	2		457	508	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047040	128047040	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757474477	NA	P-0065261-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	42	432	0	ENST00000285398.2:c.695C>T	p.Thr232Ile	p.T232I	ENST00000285398	NM_000122.1	232	aCt/aTt	6/15	1	2	FACETS	0.245	0.205	0.291	0.245	0.205	0.291	SUBCLONAL	1	TRUE	1	0.712965551865848	2		432	480	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187215	38187215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763425861	NA	P-0065261-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	240	499	0	ENST00000317025.8:c.1262G>A	p.Arg421Gln	p.R421Q	ENST00000317025	NM_023034.1	421	cGa/cAa	6/24	0.704748863776191	2	FACETS	1	0.966	1	0.52	0.489	0.552	CLONAL	1	TRUE	0	0.712965551865848	2		499	647	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578213	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs864309495	NA	P-0065277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	186	641	0	ENST00000269305.4:c.636del	p.Arg213AspfsTer34	p.R213Dfs*34	ENST00000269305	NM_001126112.2	212	ttT/tt	6/11	0.37560399275796	3	FACETS	1	0.987	1	0.81	0.758	0.862	CLONAL	2	TRUE	0	0.464863905443163	3		641	406	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29497003	29497003	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397514641	NA	P-0065277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	105	232	0	ENST00000356175.3:c.574C>T	p.Arg192Ter	p.R192*	ENST00000356175	NM_000267.3	192	Cga/Tga	5/57	0.469834838966476	2	FACETS	0.937	0.856	1	0.937	0.856	1	CLONAL	2	TRUE	0	0.464863905443163	2		232	241	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618627	37618661	+	frameshift_variant	Frame_Shift_Del	DEL	ATCAGATCGGAGCGACCGCCTGCACAAACATCGTC	ATCAGATCGGAGCGACCGCCTGCACAAACATCGTC	-	novel	NA	P-0065277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	545	653	0	ENST00000447079.4:c.304_338del	p.Ser102ProfsTer13	p.S102Pfs*13	ENST00000447079	NM_015083.1	101	ggATCAGATCGGAGCGACCGCCTGCACAAACATCGTCac/ggac	1/14	0.464863905443163	6	FACETS	1	0.983	1			1	CLONAL	6	TRUE	NA	0.464863905443163	6		653	744	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50731346	50731346	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	206	292	0	ENST00000307179.4:c.76G>C	p.Val26Leu	p.V26L	ENST00000307179		26	Gtt/Ctt	2/20	0.464863905443163	7	FACETS	1	0.973	1			1	CLONAL	4	TRUE	NA	0.464863905443163	7		292	450	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	201	539	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		539	376	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	302	418	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		418	363	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	244	455	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		455	541	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39321393	39321393	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	245	271	0	ENST00000373001.3:c.628A>G	p.Lys210Glu	p.K210E	ENST00000373001	NM_022157.3	210	Aaa/Gaa	3/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		271	559	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428607	78428607	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	155	256	0	ENST00000370768.2:c.1192A>G	p.Thr398Ala	p.T398A	ENST00000370768	NM_003902.3	398	Acc/Gcc	14/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		256	350	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844401	156844401	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	423	569	0	ENST00000524377.1:c.1234G>T	p.Asp412Tyr	p.D412Y	ENST00000524377	NM_002529.3	412	Gac/Tac	10/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		569	948	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724604	162724604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	334	365	2	ENST00000367921.3:c.376G>A	p.Gly126Ser	p.G126S	ENST00000367921	NM_006182.2	126	Ggc/Agc	5/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		367	712	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652384	206652384	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	282	388	0	ENST00000367120.3:c.1091G>A	p.Ser364Asn	p.S364N	ENST00000367120	NM_014002.3	364	aGc/aAc	10/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		388	607	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243668561	243668561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	274	263	0	ENST00000263826.5:c.1430G>A	p.Gly477Glu	p.G477E	ENST00000263826	NM_005465.4	477	gGa/gAa	13/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		263	538	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021968	246021969	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	181	279	0	ENST00000388985.4:c.905_906delinsAA	p.Trp302Ter	p.W302*	ENST00000388985		302	tGG/tAA	10/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		279	466	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076800	102076800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768834182	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	115	361	0	ENST00000282441.5:c.979C>T	p.Arg327Trp	p.R327W	ENST00000282441	NM_001130145.2	327	Cgg/Tgg	5/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		361	442	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188226	108188226	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	157	239	0	ENST00000278616.4:c.6325T>C	p.Trp2109Arg	p.W2109R	ENST00000278616	NM_000051.3	2109	Tgg/Cgg	43/63	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		239	313	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202172	108202172	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1555123920	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	48	220	0	ENST00000278616.4:c.7517G>A	p.Arg2506Lys	p.R2506K	ENST00000278616	NM_000051.3	2506	aGa/aAa	51/63	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		220	182	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373911	118373912	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	124	367	0	ENST00000534358.1:c.7304_7305delinsTT	p.Ser2435Phe	p.S2435F	ENST00000534358	NM_005933.3	2435	tCC/tTT	27/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		367	476	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18576963	18576963	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778117246	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	224	311	0	ENST00000266497.5:c.2371C>T	p.Arg791Cys	p.R791C	ENST00000266497		791	Cgt/Tgt	16/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		311	537	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434505	49434505	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	302	480	0	ENST00000301067.7:c.7048C>T	p.Gln2350Ter	p.Q2350*	ENST00000301067	NM_003482.3	2350	Cag/Tag	31/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		480	483	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864778	57864778	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	168	459	0	ENST00000228682.2:c.2255C>G	p.Pro752Arg	p.P752R	ENST00000228682	NM_005269.2	752	cCt/cGt	12/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		459	525	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69229735	69229736	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	80	257	0	ENST00000462284.1:c.811_812delinsAA	p.Gly271Lys	p.G271K	ENST00000462284	NM_002392.5	271	GGa/AAa	9/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		257	287	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636025	28636025	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	225	279	0	ENST00000241453.7:c.347C>T	p.Pro116Leu	p.P116L	ENST00000241453	NM_004119.2	116	cCa/cTa	3/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		279	555	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518663	103518663	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1251846599	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	190	240	0	ENST00000355739.4:c.2251A>G	p.Lys751Glu	p.K751E	ENST00000355739	NM_000123.3	751	Aaa/Gaa	10/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		240	429	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459909	99459909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	213	298	1	ENST00000268035.6:c.2005C>T	p.Pro669Ser	p.P669S	ENST00000268035	NM_000875.3	669	Ccc/Tcc	10/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		299	497	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779484	3779484	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	333	483	0	ENST00000262367.5:c.5564T>G	p.Ile1855Ser	p.I1855S	ENST00000262367	NM_004380.2	1855	aTc/aGc	31/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		483	783	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923469	9923469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775819322	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	250	333	0	ENST00000330684.3:c.1818G>A	p.Trp606Ter	p.W606*	ENST00000330684	NM_001134407.1	606	tgG/tgA	9/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		333	528	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650716	67650716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780911615	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	292	287	0	ENST00000264010.4:c.1021C>T	p.Arg341Cys	p.R341C	ENST00000264010	NM_006565.3	341	Cgt/Tgt	5/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		287	688	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	294	352	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		352	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	321	457	0	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		457	746	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40860060	40860060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	284	298	1	ENST00000428826.2:c.1576C>T	p.His526Tyr	p.H526Y	ENST00000428826		526	Cac/Tac	15/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		299	548	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41197709	41197709	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	315	445	0	ENST00000357654.3:c.5578C>T	p.His1860Tyr	p.H1860Y	ENST00000357654	NM_007294.3	1860	Cac/Tac	23/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		445	713	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438161	56438161	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	263	374	0	ENST00000407977.2:c.832G>A	p.Glu278Lys	p.E278K	ENST00000407977		278	Gag/Aag	7/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		374	578	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581195	48581195	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	251	276	0	ENST00000342988.3:c.499G>T	p.Glu167Ter	p.E167*	ENST00000342988	NM_005359.5	167	Gag/Tag	5/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		276	557	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272174	15272174	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1422446947	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	253	414	0	ENST00000263388.2:c.6265C>T	p.Pro2089Ser	p.P2089S	ENST00000263388	NM_000435.2	2089	Ccg/Tcg	33/33	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		414	536	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292580	15292580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867505691	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	257	404	0	ENST00000263388.2:c.2599G>A	p.Gly867Ser	p.G867S	ENST00000263388	NM_000435.2	867	Ggc/Agc	17/33	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		404	568	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905494	50905494	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	598	451	0	ENST00000440232.2:c.622C>T	p.Pro208Ser	p.P208S	ENST00000440232	NM_002691.3	208	Ccg/Tcg	6/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		451	666	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905495	50905495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774030917	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	282	451	0	ENST00000440232.2:c.623C>T	p.Pro208Leu	p.P208L	ENST00000440232	NM_002691.3	208	cCg/cTg	6/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		451	670	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251650	212251650	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	347	445	0	ENST00000342788.4:c.3409C>G	p.Pro1137Ala	p.P1137A	ENST00000342788	NM_005235.2	1137	Cca/Gca	27/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		445	728	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566773	212566773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	275	344	0	ENST00000342788.4:c.1408C>T	p.His470Tyr	p.H470Y	ENST00000342788	NM_005235.2	470	Cat/Tat	12/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		344	591	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419876	41419876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	293	416	0	ENST00000373198.4:c.445G>A	p.Ala149Thr	p.A149T	ENST00000373198	NM_133170.3	149	Gca/Aca	3/32	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		416	598	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866465	42866465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	314	420	0	ENST00000398585.3:c.167G>A	p.Gly56Glu	p.G56E	ENST00000398585	NM_001135099.1	56	gGa/gAa	3/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		420	562	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21348460	21348460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763950976	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	306	511	0	ENST00000215739.8:c.1517C>T	p.Pro506Leu	p.P506L	ENST00000215739	NM_006767.3	506	cCg/cTg	14/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		511	626	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29083886	29083886	+	stop_lost	Nonstop_Mutation	SNP	C	C	A	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	88	129	0	ENST00000328354.6:c.1631G>T	p.Ter544LeuextTer48	p.*544Lext*48	ENST00000328354	NM_007194.3	544	tGa/tTa	15/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		129	104	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498390	89498390	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1240798724	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	197	257	0	ENST00000336596.2:c.2362A>G	p.Ile788Val	p.I788V	ENST00000336596	NM_005233.5	788	Atc/Gtc	14/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		257	477	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447775	187447775	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779270221	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	299	383	0	ENST00000232014.4:c.418C>T	p.Arg140Cys	p.R140C	ENST00000232014	NM_001130845.1	140	Cgt/Tgt	5/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		383	670	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608664	189608665	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	204	287	0	ENST00000264731.3:c.1739_1740delinsTT	p.Ser580Phe	p.S580F	ENST00000264731	NM_003722.4	580	tCC/tTT	13/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		287	483	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612028	189612028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs900140738	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	252	361	0	ENST00000264731.3:c.1780C>T	p.Arg594Ter	p.R594*	ENST00000264731	NM_003722.4	594	Cga/Tga	14/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		361	609	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139724	55139724	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	247	329	0	ENST00000257290.5:c.1385G>A	p.Trp462Ter	p.W462*	ENST00000257290	NM_006206.4	462	tGg/tAg	10/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		329	527	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141007	55141007	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	240	296	0	ENST00000257290.5:c.1654-1G>A		p.X552_splice	ENST00000257290	NM_006206.4	552			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		296	483	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31939883	31939883	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs149278445	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	690	390	0	ENST00000375333.2:c.110A>G	p.Asn37Ser	p.N37S	ENST00000375333	NM_032454.1	37	aAc/aGc	1/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		390	972	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816580	32816580	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	719	386	0	ENST00000354258.4:c.1595del	p.Val532GlyfsTer23	p.V532Gfs*23	ENST00000354258	NM_000593.5	532	gTg/gg	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		386	1121	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964415	93964415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867402067	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	498	273	0	ENST00000369303.4:c.2482G>A	p.Glu828Lys	p.E828K	ENST00000369303	NM_004440.3	828	Gaa/Aaa	14/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		273	1289	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536166	106536166	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	458	384	0	ENST00000369096.4:c.133G>A	p.Asp45Asn	p.D45N	ENST00000369096	NM_001198.3	45	Gat/Aat	2/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		384	991	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536182	106536182	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	259	360	0	ENST00000369096.4:c.149C>G	p.Thr50Arg	p.T50R	ENST00000369096	NM_001198.3	50	aCa/aGa	2/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		360	997	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511320	157511320	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	266	351	1	ENST00000346085.5:c.3838G>A	p.Asp1280Asn	p.D1280N	ENST00000346085	NM_020732.3	1280	Gac/Aac	15/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		352	314	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468158	50468158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	280	381	0	ENST00000331340.3:c.1393G>A	p.Glu465Lys	p.E465K	ENST00000331340	NM_006060.4	465	Gaa/Aaa	8/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		381	607	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381541	81381541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	223	268	0	ENST00000222390.5:c.520G>A	p.Glu174Lys	p.E174K	ENST00000222390	NM_000601.4	174	Gaa/Aaa	5/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		268	476	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520027	106520027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370034420	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	215	242	0	ENST00000359195.3:c.2455G>A	p.Asp819Asn	p.D819N	ENST00000359195	NM_002649.2	819	Gat/Aat	6/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		242	435	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370868	55370868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757855527	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	242	411	0	ENST00000297316.4:c.170G>A	p.Gly57Glu	p.G57E	ENST00000297316	NM_022454.3	57	gGg/gAg	1/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		411	1106	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050711	69050711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	206	233	0	ENST00000288368.4:c.4046C>T	p.Ser1349Phe	p.S1349F	ENST00000288368	NM_024870.2	1349	tCc/tTc	33/40	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		233	585	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211359	98211359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751826546	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	255	360	0	ENST00000331920.6:c.3796C>T	p.His1266Tyr	p.H1266Y	ENST00000331920	NM_000264.3	1266	Cac/Tac	22/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		360	296	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391586	139391586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	260	375	0	ENST00000277541.6:c.6605C>T	p.Ser2202Phe	p.S2202F	ENST00000277541	NM_017617.3	2202	tCc/tTc	34/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		375	861	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239751	53239751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	296	206	0	ENST00000375401.3:c.1591C>T	p.Pro531Ser	p.P531S	ENST00000375401	NM_004187.3	531	Ccg/Tcg	12/26	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		206	326	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065336-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	128	446	0				ENST00000310581	NM_198253.2	-/1132			0.26310999760892	3	FACETS	0.905	0.834	0.978	1	0.98	1	CLONAL	4	TRUE	0	0.26310999760892	3		446	304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0065336-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	346	1113	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.26310999760892	3	FACETS	0.929	0.888	0.969	1	0.996	1	CLONAL	5	TRUE	0	0.26310999760892	3		1113	641	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057751	27057751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065336-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	229	581	0	ENST00000324856.7:c.1459C>T	p.Gln487Ter	p.Q487*	ENST00000324856	NM_006015.4	487	Cag/Tag	3/20	0.26310999760892	3	FACETS	0.996	0.934	1	1	0.993	1	CLONAL	3	TRUE	1	0.26310999760892	3		581	659	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916825	48916825	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065336-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	257	329	0	ENST00000267163.4:c.355G>T	p.Glu119Ter	p.E119*	ENST00000267163	NM_000321.2	119	Gag/Tag	3/27	0.26310999760892	5	FACETS	1	0.985	1	1	0.993	1	CLONAL	6	TRUE	0	0.26310999760892	5		329	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0065337-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	134	586	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.289495773299415	2	FACETS	0.936	0.856	1	0.936	0.856	1	CLONAL	2	TRUE	0	0.310648165561716	2		586	461	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341138	8341138	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065337-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	86	457	0	ENST00000356435.5:c.5078G>T	p.Gly1693Val	p.G1693V	ENST00000356435		1693	gGa/gTa	30/35	0.273159752315358	2	FACETS	0.75	0.669	0.836	0.75	0.669	0.836	SUBCLONAL	2	TRUE	0	0.310648165561716	2		457	369	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794779	120794779	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768324684	NA	P-0065337-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	38	457	0	ENST00000257552.2:c.578C>T	p.Thr193Met	p.T193M	ENST00000257552	NM_002442.3	193	aCg/aTg	9/15	0.294538841379006	4	FACETS	0.564	0.465	0.674	0.282	0.232	0.337	SUBCLONAL	1	TRUE	2	0.310648165561716	4		457	569	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250996	10250996	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs776723837	NA	P-0065337-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	32	389	0	ENST00000340748.4:c.3484G>C	p.Asp1162His	p.D1162H	ENST00000340748		1162	Gac/Cac	32/40	0.310648165561716	1	FACETS	0.496	0.403	0.6	0.496	0.403	0.6	SUBCLONAL	1	TRUE	0	0.310648165561716	1		389	351	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867694	45867694	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065337-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	129	546	0	ENST00000391945.4:c.706G>T	p.Ala236Ser	p.A236S	ENST00000391945	NM_000400.3	236	Gcc/Tcc	8/23	0.310648165561716	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.310648165561716	2		546	383	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506356	120506356	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065337-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	123	521	0	ENST00000256646.2:c.1756G>T	p.Asp586Tyr	p.D586Y	ENST00000256646	NM_024408.3	586	Gat/Tat	11/34	0.248048570998418	3	FACETS	1	0.984	1	0.73	0.661	0.801	CLONAL	1	TRUE	1	0.310648165561716	3		521	627	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917745	29917745	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065337-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	155	459	0	ENST00000389048.3:c.923G>T	p.Gly308Val	p.G308V	ENST00000389048	NM_004304.4	308	gGg/gTg	3/29	0.22352398906878	4	FACETS	0.853	0.786	0.922	1	0.984	1	CLONAL	3	TRUE	2	0.310648165561716	4		459	511	SUCCESS
ATR	545	MSKCC	GRCh37	3	142232350	142232350	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065337-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	166	380	0	ENST00000350721.4:c.4634A>T	p.Gln1545Leu	p.Q1545L	ENST00000350721	NM_001184.3	1545	cAg/cTg	26/47	0.278846169685636	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.310648165561716	4		380	583	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438605	49438605	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065337-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	40	517	0	ENST00000301067.7:c.4885del	p.Ser1629LeufsTer93	p.S1629Lfs*93	ENST00000301067	NM_003482.3	1629	Tct/ct	19/54	0.294538841379006	4	FACETS	0.693	0.576	0.824	0.347	0.288	0.412	SUBCLONAL	1	TRUE	2	0.310648165561716	4		517	487	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457845	69457845	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065337-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	55	420	0	ENST00000227507.2:c.245T>C	p.Met82Thr	p.M82T	ENST00000227507	NM_053056.2	82	aTg/aCg	2/5	0.305408961589791	3	FACETS	1	0.943	1	0.6	0.516	0.691	CLONAL	1	TRUE	1	0.310648165561716	3		420	341	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944401	40944401	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065337-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	141	464	0	ENST00000373198.4:c.2101T>A	p.Tyr701Asn	p.Y701N	ENST00000373198	NM_133170.3	701	Tac/Aac	12/32	0.310648165561716	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.310648165561716	2		464	401	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0065350-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	106	366	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.365566348285177	5	FACETS	0.968	0.866	1	0.323	0.288	0.359	CLONAL	1	TRUE	2	0.365566348285177	5		366	928	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579533	7579533	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065350-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	253	584	0	ENST00000269305.4:c.154C>T	p.Gln52Ter	p.Q52*	ENST00000269305	NM_001126112.2	52	Caa/Taa	4/11	0.365566348285177	2	FACETS	0.976	0.918	1	0.976	0.918	1	CLONAL	2	TRUE	0	0.365566348285177	2		584	709	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724422	162724422	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0065350-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	122	413	0	ENST00000367921.3:c.194C>G	p.Ser65Ter	p.S65*	ENST00000367921	NM_006182.2	65	tCa/tGa	5/18	0.365566348285177	5	FACETS	1	0.966	1	0.384	0.347	0.424	CLONAL	1	TRUE	2	0.365566348285177	5		413	897	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0065492-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	258	539	0				ENST00000310581	NM_198253.2	-/1132			0.438102660035041	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	1	0.438102660035041	4		539	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0065492-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	278	523	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.438102660035041	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	3	TRUE	0	0.438102660035041	3		523	513	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780677	56780677	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060502588	NA	P-0065492-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	137	325	0	ENST00000337432.4:c.692C>G	p.Ser231Ter	p.S231*	ENST00000337432	NM_058216.2	231	tCa/tGa	4/9	0.43459679844744	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.438102660035041	3		325	353	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100312	27100312	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065492-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	292	595	0	ENST00000324856.7:c.4024C>T	p.Gln1342Ter	p.Q1342*	ENST00000324856	NM_006015.4	1342	Cag/Tag	17/20	0.438102660035041	5	FACETS	0.951	0.9	1	0.951	0.9	1	CLONAL	3	TRUE	2	0.438102660035041	5		595	774	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488281	56488281	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065492-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	230	490	0	ENST00000267101.3:c.1800C>G	p.Ile600Met	p.I600M	ENST00000267101	NM_001982.3	600	atC/atG	15/28	0.386927834783735	4	FACETS	0.948	0.892	1			1	CLONAL	3	TRUE	NA	0.438102660035041	4		490	531	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023168	27023168	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065492-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	179	450	0	ENST00000324856.7:c.275del	p.Gly92AlafsTer9	p.G92Afs*9	ENST00000324856	NM_006015.4	92	Ggc/gc	1/20	0.438102660035041	5	FACETS	0.95	0.878	1	0.633	0.585	0.683	CLONAL	2	TRUE	2	0.438102660035041	5		450	713	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061493	38061493	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065492-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	186	479	0	ENST00000250448.2:c.496del	p.Tyr166ThrfsTer28	p.Y166Tfs*28	ENST00000250448	NM_004496.3	166	Tac/ac	2/2	0.39733071688774	4	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	2	0.438102660035041	4		479	602	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240833	53240833	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065492-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	82	406	0	ENST00000375401.3:c.1247T>C	p.Val416Ala	p.V416A	ENST00000375401	NM_004187.3	416	gTg/gCg	10/26	0.356102440761444	4	FACETS	1	0.941	1			1	CLONAL	1	TRUE	NA	0.438102660035041	4		406	488	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134370	30134370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065492-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	86	363	0	ENST00000263025.4:c.161G>A	p.Gly54Asp	p.G54D	ENST00000263025	NM_002746.2	54	gGc/gAc	1/9	0.295550897887823	4	FACETS	1	0.97	1	0.636	0.565	0.711	CLONAL	1	TRUE	2	0.438102660035041	4		363	444	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392065	81392065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1467541182	NA	P-0065492-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	101	280	0	ENST00000222390.5:c.212C>T	p.Ala71Val	p.A71V	ENST00000222390	NM_000601.4	71	gCt/gTt	2/18	0.39733071688774	4	FACETS	0.931	0.84	1	0.931	0.84	1	CLONAL	2	TRUE	2	0.438102660035041	4		280	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0065498-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	494	572	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.588579597997763	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.594249990952108	2		572	824	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967264	134967264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748426868	NA	P-0065498-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	212	537	0	ENST00000398015.3:c.2603G>A	p.Arg868Gln	p.R868Q	ENST00000398015	NM_004441.4	868	cGg/cAg	14/16	0.588579597997763	2	FACETS	1	0.959	1	0.519	0.484	0.555	CLONAL	1	TRUE	0	0.594249990952108	2		537	687	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508589	106508589	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1257245065	NA	P-0065498-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	214	407	0	ENST00000359195.3:c.583C>A	p.Leu195Ile	p.L195I	ENST00000359195	NM_002649.2	195	Ctc/Atc	2/11	0.285471183985871	2	FACETS	1	0.991	1	0.678	0.636	0.721	INDETERMINATE	1	TRUE	0	0.594249990952108	2		407	531	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47679339	47679339	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065498-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	304	367	0	ENST00000347630.2:c.868G>A	p.Glu290Lys	p.E290K	ENST00000347630	NM_001007230.1	290	Gag/Aag	10/11	0.336984848264434	5	FACETS	0.946	0.898	0.994			1	INDETERMINATE	3	TRUE	NA	0.594249990952108	5		367	682	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158464	26158464	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs916752202	NA	P-0065498-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	106	464	0	ENST00000289316.2:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000289316	NM_138720.2	23	Cag/Tag	1/2	0.295395658168421	3	FACETS	0.59	0.529	0.655	0.295	0.264	0.328	INDETERMINATE	1	TRUE	1	0.594249990952108	3		464	784	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233280	46233280	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0065498-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	209	377	0	ENST00000334344.6:c.1498+1G>T		p.X500_splice	ENST00000334344	NM_152641.2	500			0.580909631819004	2	FACETS	0.897	0.847	0.947	0.897	0.847	0.947	CLONAL	2	TRUE	0	0.594249990952108	2		377	392	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29422382	29422382	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs786203307	NA	P-0065498-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	228	264	0	ENST00000356175.3:c.55G>T	p.Glu19Ter	p.E19*	ENST00000356175	NM_000267.3	19	Gag/Tag	1/57	0.588579597997763	2	FACETS	0.974	0.924	1	0.974	0.924	1	CLONAL	2	TRUE	0	0.594249990952108	2		264	394	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146530	185146530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065498-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	290	453	0	ENST00000265026.3:c.161C>T	p.Thr54Ile	p.T54I	ENST00000265026	NM_004721.4	54	aCa/aTa	2/14	0.53851285081618	2	FACETS	0.946	0.902	0.989	0.946	0.902	0.989	CLONAL	2	TRUE	0	0.594249990952108	2		453	516	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984990	101984990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065498-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	33	244	0	ENST00000282441.5:c.437G>A	p.Gly146Glu	p.G146E	ENST00000282441	NM_001130145.2	146	gGa/gAa	2/9	0.285471183985871	2	FACETS	0.4	0.326	0.481	0.2	0.163	0.241	INDETERMINATE	1	TRUE	0	0.594249990952108	2		244	278	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0065499-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	153	375	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.386438951949151	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.386438951949151	2		375	348	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0065499-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	476	407	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.386438951949151	9	FACETS	1	0.989	1			1	CLONAL	5	TRUE	NA	0.386438951949151	9		407	1071	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375142	31375142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537913125	NA	P-0065499-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	220	498	0	ENST00000328111.2:c.539C>T	p.Thr180Met	p.T180M	ENST00000328111	NM_006892.3	180	aCg/aTg	6/23	0.386438951949151	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.386438951949151	3		498	641	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844722	156844722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs986498490	NA	P-0065499-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	194	551	0	ENST00000524377.1:c.1276G>A	p.Val426Ile	p.V426I	ENST00000524377	NM_002529.3	426	Gtc/Atc	11/17	0.306617957206788	4	FACETS	0.943	0.875	1	0.943	0.875	1	CLONAL	2	TRUE	2	0.386438951949151	4		551	738	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918306	44918306	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs777683511	NA	P-0065499-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	110	128	0	ENST00000377967.4:c.931A>G	p.Ile311Val	p.I311V	ENST00000377967	NM_021140.2	311	Att/Gtt	11/29	0.386438951949151	2	FACETS	0.883	0.813	0.952			1	CLONAL	3	TRUE	NA	0.386438951949151	2		128	215	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032057	26032057	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561919033	NA	P-0065499-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	86	489	0	ENST00000244661.2:c.232G>A	p.Asp78Asn	p.D78N	ENST00000244661	NM_003537.3	78	Gac/Aac	1/1	0.306617957206788	4	FACETS	0.894	0.791	1	0.447	0.395	0.503	CLONAL	1	TRUE	2	0.386438951949151	4		489	690	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769112	112769112	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065499-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	51	305	0	ENST00000369452.4:c.1391C>G	p.Pro464Arg	p.P464R	ENST00000369452	NM_007373.3	464	cCa/cGa	7/9	0.386438951949151	2	FACETS	0.812	0.694	0.941	0.406	0.347	0.471	CLONAL	1	TRUE	0	0.386438951949151	2		305	325	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372073	45372079	+	protein_altering_variant	In_Frame_Del	DEL	ATCTCTG	ATCTCTG	TACA	novel	NA	P-0065499-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	20	333	0	ENST00000262160.6:c.1090_1096delinsTGTA	p.Gln364_Tyr366delinsCysAsn	p.Q364_Y366delinsCN	ENST00000262160	NM_005901.5	364	CAGAGATat/TGTAat	9/11	0.386438951949151	2	FACETS	0.263	0.2	0.336	0.131	0.1	0.168	SUBCLONAL	1	TRUE	0	0.386438951949151	2		333	394	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934200	48934204	+	frameshift_variant	Frame_Shift_Del	DEL	ATGCT	ATGCT	-	novel	NA	P-0065500-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	187	320	0	ENST00000267163.4:c.658_662del	p.Leu220CysfsTer3	p.L220Cfs*3	ENST00000267163	NM_000321.2	219	ATGCTa/a	7/27	0.849530047661297	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.849530047661297	1		320	250	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264730	11264730	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065500-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	208	421	0	ENST00000361445.4:c.3832G>C	p.Asp1278His	p.D1278H	ENST00000361445	NM_004958.3	1278	Gat/Cat	26/58	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.849530047661297	2		421	452	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380343	14380344	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGCCGCCCC	novel	NA	P-0065607-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	92	333	0	ENST00000256196.4:c.65_73dup	p.Gly22_Gly24dup	p.G22_G24dup	ENST00000256196		22	gtg/gGGGGCGGCGtg	1/6	0.294196334806836	3	FACETS	1	0.967	1	0.792	0.712	0.874	CLONAL	2	TRUE	0	0.3	3		333	297	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866690	37866690	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065607-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	69	444	0	ENST00000269571.5:c.857A>G	p.Glu286Gly	p.E286G	ENST00000269571		286	gAg/gGg	7/27	1	2	FACETS	0.989	0.864	1	0.989	0.864	1	CLONAL	1	TRUE	1	0.3	2		444	465	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380343	14380344	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGCCGCCCC	novel	NA	P-0065607-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	128	333	0	ENST00000256196.4:c.65_73dup	p.Gly22_Gly24dup	p.G22_G24dup	ENST00000256196		22	gtg/gGGGGCGGCGtg	1/6	0.547938533856032	3	FACETS	1	0.929	1	0.673	0.62	0.726	CLONAL	2	TRUE	0	0.547938533856032	3		333	295	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982787	90982792	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TAAAAA	TAAAAA	-	novel	NA	P-0065615-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	193	438	0	ENST00000265433.3:c.703-7_703-2del		p.X235_splice	ENST00000265433	NM_002485.4	235			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		438	1092	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669462	241669485	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAAATTCCTGAAAAGAAAAGAAAA	TAAATTCCTGAAAAGAAAAGAAAA	-	novel	NA	P-0065670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	57	220	0	ENST00000366560.3:c.739-17_745del		p.X247_splice	ENST00000366560	NM_000143.3	247		6/10	0.261308623803806	3	FACETS	1	0.911	1	0.538	0.464	0.618	CLONAL	1	TRUE	1	0.357734738332161	3		220	349	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188179	108188180	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0065670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	56	317	0	ENST00000278616.4:c.6279_6280insAT	p.Glu2094MetfsTer3	p.E2094Mfs*3	ENST00000278616	NM_000051.3	2093	cct/ccTAt	43/63	0.357734738332161	1	FACETS	0.949	0.82	1	0.949	0.82	1	CLONAL	1	TRUE	0	0.357734738332161	1		317	271	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143334	30143334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	55	524	0	ENST00000389048.3:c.192C>A	p.Phe64Leu	p.F64L	ENST00000389048	NM_004304.4	64	ttC/ttA	1/29	1	2	FACETS	0.456	0.39	0.529	0.456	0.39	0.529	SUBCLONAL	1	TRUE	1	0.357734738332161	2		524	674	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47600671	47600672	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0065670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	59	415	0	ENST00000263735.4:c.147_148dup	p.Ser50PhefsTer20	p.S50Ffs*20	ENST00000263735	NM_002354.2	49	act/acTTt	2/9	1	2	FACETS	0.833	0.719	0.956	0.833	0.719	0.956	CLONAL	1	TRUE	1	0.357734738332161	2		415	396	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0065693-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	98	311	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.275490305390897	3	FACETS	0.985	0.885	1	0.985	0.885	1	CLONAL	2	TRUE	1	0.275490305390897	3		311	411	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129945	69129945	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748812788	NA	P-0065693-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	115	461	0	ENST00000288368.4:c.4699C>T	p.Arg1567Trp	p.R1567W	ENST00000288368	NM_024870.2	1567	Cgg/Tgg	38/40	0.244452261028273	3	FACETS	0.965	0.874	1	0.965	0.874	1	CLONAL	2	TRUE	1	0.275490305390897	3		461	492	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515297	31515297	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065693-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	43	451	0	ENST00000344624.3:c.1088C>G	p.Ala363Gly	p.A363G	ENST00000344624		363	gCt/gGt	5/33	1	2	FACETS	0.708	0.593	0.835	0.708	0.593	0.835	SUBCLONAL	1	TRUE	1	0.275490305390897	2		451	441	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065696-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	94	446	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.751463526407929	2		446	244	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0065696-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	165	418	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.889	0.823	0.957	0.889	0.823	0.957	CLONAL	1	TRUE	1	0.751463526407929	2		418	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0065696-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	422	512	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.738874226109635	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.751463526407929	2		512	538	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0065696-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	12	516	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	0.094	0.066	0.13	0.094	0.066	0.13	SUBCLONAL	1	TRUE	1	0.751463526407929	2		516	338	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971189	21971189	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065696-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	162	412	0	ENST00000304494.5:c.169G>T	p.Ala57Ser	p.A57S	ENST00000304494	NM_000077.4	57	Gcc/Tcc	2/3	1	2	FACETS	0.923	0.855	0.994	0.923	0.855	0.994	CLONAL	1	TRUE	1	0.751463526407929	2		412	467	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916851	48916851	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0065696-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	135	286	0	ENST00000267163.4:c.380+1G>T		p.X127_splice	ENST00000267163	NM_000321.2	127			1	2	FACETS	0.896	0.823	0.971	0.896	0.823	0.971	CLONAL	1	TRUE	1	0.751463526407929	2		286	401	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918709	44918709	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065696-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	162	302	0	ENST00000377967.4:c.1192C>T	p.Gln398Ter	p.Q398*	ENST00000377967	NM_021140.2	398	Cag/Tag	12/29	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.751463526407929	2		302	387	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975459	13975459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80157564	NA	P-0065696-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	161	447	0	ENST00000405192.2:c.428C>T	p.Thr143Met	p.T143M	ENST00000405192	NM_001163147.1	143	aCg/aTg	7/12	1	2	FACETS	0.921	0.853	0.992	0.921	0.853	0.992	CLONAL	1	TRUE	1	0.751463526407929	2		447	465	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031565	11031565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065696-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	198	568	0	ENST00000327064.4:c.1480G>A	p.Glu494Lys	p.E494K	ENST00000327064	NM_199141.1	494	Gaa/Aaa	13/16	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.751463526407929	2		568	521	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033932	49033932	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065696-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	176	332	0	ENST00000267163.4:c.2069A>G	p.Asn690Ser	p.N690S	ENST00000267163	NM_000321.2	690	aAt/aGt	20/27	1	2	FACETS	0.922	0.856	0.989	0.922	0.856	0.989	CLONAL	1	TRUE	1	0.751463526407929	2		332	508	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3794896	3794896	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065696-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	132	295	0	ENST00000262367.5:c.3981G>C	p.Lys1327Asn	p.K1327N	ENST00000262367	NM_004380.2	1327	aaG/aaC	23/31	0.460336106697937	1	FACETS	0.611	0.561	0.662	0.611	0.561	0.662	SUBCLONAL	1	TRUE	0	0.751463526407929	1		295	359	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10789515	10789515	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065696-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	188	469	1	ENST00000361367.2:c.1849C>T	p.Gln617Ter	p.Q617*	ENST00000361367	NM_014633.3	617	Cag/Tag	14/25	0.307409581570121	1	FACETS	0.659	0.615	0.704	0.659	0.615	0.704	INDETERMINATE	1	TRUE	0	0.751463526407929	1		470	474	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0065700-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	53	269	1	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.817	0.699	0.946	0.817	0.699	0.946	CLONAL	1	TRUE	1	0.33	2		270	393	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779451	3779451	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065700-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	185	585	0	ENST00000262367.5:c.5597G>T	p.Arg1866Leu	p.R1866L	ENST00000262367	NM_004380.2	1866	cGc/cTc	31/31	0.3	3	FACETS	1	0.944	1	0.515	0.474	0.558	CLONAL	1	TRUE	1	0.33	3		585	1268	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933181	39933181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065700-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	101	528	0	ENST00000378444.4:c.1418G>A	p.Ser473Asn	p.S473N	ENST00000378444	NM_001123385.1	473	aGt/aAt	4/15	1	2	FACETS	0.676	0.604	0.754	0.676	0.604	0.754	SUBCLONAL	1	TRUE	1	0.33	2		528	905	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061319	38061319	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065700-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	61	517	0	ENST00000250448.2:c.670T>C	p.Phe224Leu	p.F224L	ENST00000250448	NM_004496.3	224	Ttc/Ctc	2/2	1	2	FACETS	0.453	0.389	0.522	0.453	0.389	0.522	SUBCLONAL	1	TRUE	1	0.33	2		517	817	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0065701-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	133	492	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.472328099600699	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.472328099600699	2		492	236	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0065701-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	224	624	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.472328099600699	2	FACETS	0.984	0.927	1	0.984	0.927	1	CLONAL	2	TRUE	0	0.472328099600699	2		624	482	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250883	153250883	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065701-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	26	328	0	ENST00000281708.4:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000281708	NM_033632.3	393	Cga/Tga	8/12	1	2	FACETS	0.917	0.739	1	0.917	0.739	1	CLONAL	1	TRUE	1	0.472328099600699	2		328	120	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412110	63412110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852216	NA	P-0065701-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	139	304	0	ENST00000330258.3:c.1057C>T	p.Arg353Ter	p.R353*	ENST00000330258	NM_152424.3	353	Cga/Tga	2/2	1	1	FACETS	0.767	0.711	0.823	1	0.99	1	SUBCLONAL	2	TRUE	0	0.472328099600699	1		304	293	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998898	11998898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065701-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	36	319	0	ENST00000353533.5:c.400C>T	p.Arg134Trp	p.R134W	ENST00000353533	NM_003010.3	134	Cgg/Tgg	4/11	1	2	FACETS	0.971	0.81	1	0.971	0.81	1	CLONAL	1	TRUE	1	0.472328099600699	2		319	157	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032541	12032541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267604739	NA	P-0065701-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	52	365	0	ENST00000353533.5:c.977C>T	p.Pro326Leu	p.P326L	ENST00000353533	NM_003010.3	326	cCg/cTg	9/11	1	2	FACETS	0.902	0.776	1	0.902	0.776	1	CLONAL	1	TRUE	1	0.472328099600699	2		365	244	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117872	70117872	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065701-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	309	549	0	ENST00000245479.2:c.340G>C	p.Val114Leu	p.V114L	ENST00000245479	NM_000346.3	114	Gtg/Ctg	1/3	0.472328099600699	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.472328099600699	2		549	573	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158117	27158117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760573137	NA	P-0065701-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	105	538	0	ENST00000380036.4:c.341G>A	p.Arg114Gln	p.R114Q	ENST00000380036	NM_000459.3	114	cGa/cAa	2/23	1	2	FACETS	0.93	0.838	1	0.93	0.838	1	CLONAL	1	TRUE	1	0.472328099600699	2		538	478	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247377	153247379	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	novel	NA	P-0065701-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	109	476	0	ENST00000281708.4:c.1423_1425del	p.Val475del	p.V475del	ENST00000281708	NM_033632.3	475	GTT/-	10/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.472328099600699	2		476	420	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139023	50139023	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065701-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	100	532	0	ENST00000246792.3:c.540C>A	p.Asp180Glu	p.D180E	ENST00000246792	NM_006270.3	180	gaC/gaA	5/6	1	2	FACETS	0.774	0.694	0.859	0.774	0.694	0.859	SUBCLONAL	1	TRUE	1	0.472328099600699	2		532	547	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161411	2161411	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065701-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	123	518	0	ENST00000434045.2:c.116G>A	p.Arg39His	p.R39H	ENST00000434045	NM_001127598.1	39	cGc/cAc	2/5	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.472328099600699	2		518	490	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576754	67576754	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0065701-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	66	297	0	ENST00000274335.5:c.837-1G>T		p.X279_splice	ENST00000274335		279			0.472328099600699	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	2	TRUE	0	0.472328099600699	2		297	136	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0065704-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	98	436	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.0774080043104468	4	FACETS	1	0.945	1	1	0.945	1	INDETERMINATE	2	TRUE	2	0.206308717621749	4		436	527	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971366	13971366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568607536	NA	P-0065704-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	66	342	0	ENST00000405192.2:c.563G>A	p.Arg188His	p.R188H	ENST00000405192	NM_001163147.1	188	cGc/cAc	8/12	0.0774080043104468	4	FACETS	1	0.969	1	0.709	0.616	0.81	INDETERMINATE	1	TRUE	2	0.206308717621749	4		342	544	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271456	26271456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1325544768	NA	P-0065704-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	38	674	0	ENST00000305910.3:c.157C>T	p.Arg53Cys	p.R53C	ENST00000305910	NM_003534.2	53	Cgc/Tgc	1/1	0.160964040236894	3	FACETS	0.669	0.552	0.801	0.335	0.276	0.401	SUBCLONAL	1	TRUE	1	0.206308717621749	3		674	607	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0065728-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	316	782	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.230971067455996	2	FACETS	0.869	0.823	0.916	1	0.993	1	CLONAL	3	TRUE	0	0.271396307728639	2		782	893	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0065728-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	157	642	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.271396307728639	1	FACETS	0.762	0.7	0.826	1	0.989	1	SUBCLONAL	2	TRUE	0	0.271396307728639	1		642	656	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0065728-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	31	434	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	1	2	FACETS	0.431	0.348	0.526	0.431	0.348	0.526	SUBCLONAL	1	TRUE	1	0.271396307728639	2		434	530	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427369	49427369	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1565779294	NA	P-0065728-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	86	680	0	ENST00000301067.7:c.11119C>T	p.Arg3707Ter	p.R3707*	ENST00000301067	NM_003482.3	3707	Cga/Tga	39/54	1	2	FACETS	0.907	0.802	1	0.907	0.802	1	CLONAL	1	TRUE	1	0.271396307728639	2		680	699	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066809	77066809	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065728-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	37	540	0	ENST00000356341.3:c.676G>A	p.Glu226Lys	p.E226K	ENST00000356341	NM_002576.4	226	Gaa/Aaa	7/15	1	2	FACETS	0.542	0.446	0.649	0.542	0.446	0.649	SUBCLONAL	1	TRUE	1	0.271396307728639	2		540	503	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907309	32907309	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065728-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	15	0	0	ENST00000380152.3:c.1695del	p.Thr566ProfsTer7	p.T566Pfs*7	ENST00000380152		565	gCc/gc	10/27	0.257409211645767	0	FACETS	0.268	0.195	0.355			1	SUBCLONAL	1	TRUE	0	0.271396307728639	0		0	301	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003528	42003528	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065728-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	49	383	0	ENST00000219905.7:c.3065C>G	p.Thr1022Arg	p.T1022R	ENST00000219905	NM_001164273.1	1022	aCa/aGa	8/24	0.271396307728639	1	FACETS	0.806	0.685	0.939	0.806	0.685	0.939	CLONAL	1	TRUE	0	0.271396307728639	1		383	387	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936847	78936847	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065728-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	193	607	0	ENST00000306801.3:c.3929A>T	p.His1310Leu	p.H1310L	ENST00000306801	NM_020761.2	1310	cAc/cTc	33/34	0.133749387673488	3	FACETS	1	0.971	1	1	0.971	1	INDETERMINATE	2	TRUE	1	0.271396307728639	3		607	743	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602293	10602313	+	inframe_deletion	In_Frame_Del	DEL	CGACGGCATAGATGTGGCCAT	CGACGGCATAGATGTGGCCAT	-	novel	NA	P-0065728-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	140	741	0	ENST00000171111.5:c.1265_1285del	p.Asp422_Val428del	p.D422_V428del	ENST00000171111	NM_203500.1	422	gATGGCCACATCTATGCCGTCGgc/ggc	3/6	0.133749387673488	3	FACETS	1	0.977	1	0.614	0.559	0.672	INDETERMINATE	1	TRUE	1	0.271396307728639	3		741	954	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1962783	1962783	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065728-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	82	558	0	ENST00000382891.5:c.3277G>T	p.Val1093Phe	p.V1093F	ENST00000382891	NM_133335.3	1093	Gtt/Ttt	18/22	0.271396307728639	1	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	0	0.271396307728639	1		558	507	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196343	106196343	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065728-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	88	643	0	ENST00000380013.4:c.4676C>G	p.Ser1559Cys	p.S1559C	ENST00000380013	NM_001127208.2	1559	tCt/tGt	11/11	0.271396307728639	1	FACETS	0.999	0.887	1	0.999	0.887	1	CLONAL	1	TRUE	0	0.271396307728639	1		643	561	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910617	29910617	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065728-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	133	1055	0	ENST00000376809.5:c.157G>C	p.Asp53His	p.D53H	ENST00000376809	NM_002116.7	53	Gac/Cac	2/8	1	2	FACETS	0.937	0.85	1	0.937	0.85	1	CLONAL	1	TRUE	1	0.271396307728639	2		1055	1046	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687370	117687370	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs535778217	NA	P-0065728-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	28	352	0	ENST00000368508.3:c.2681G>T	p.Arg894Leu	p.R894L	ENST00000368508	NM_002944.2	894	cGg/cTg	18/43	0.271396307728639	0	FACETS	0.363	0.29	0.447			1	SUBCLONAL	1	TRUE	0	0.271396307728639	0		352	414	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484177	8484177	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065728-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	32	453	0	ENST00000356435.5:c.3355A>T	p.Asn1119Tyr	p.N1119Y	ENST00000356435		1119	Aac/Tac	19/35	0.230971067455996	2	FACETS	0.458	0.371	0.557	0.229	0.185	0.279	SUBCLONAL	1	TRUE	0	0.271396307728639	2		453	515	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0065743-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	19	104	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.539	0.408	0.696	0.539	0.408	0.696	SUBCLONAL	1	TRUE	1	0.12	2		104	587	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653805	89653805	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659443	NA	P-0065743-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	8	44	0	ENST00000371953.3:c.103A>G	p.Met35Val	p.M35V	ENST00000371953	NM_000314.4	35	Atg/Gtg	2/9	1	2	FACETS	0.369	0.237	0.543	0.369	0.237	0.543	SUBCLONAL	1	TRUE	1	0.12	2		44	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0065754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	266	545	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.519968879814404	5	FACETS	0.958	0.919	0.996	0.958	0.919	0.996	CLONAL	5	TRUE	0	0.519968879814404	5		546	380	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425600	47425600	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	80	364	0	ENST00000404338.3:c.3669del	p.Arg1224GlyfsTer28	p.R1224Gfs*28	ENST00000404338	NM_004491.4	1223	aGg/ag	1/6	0.45382802532965	3	FACETS	1	0.966	1	0.774	0.7	0.848	CLONAL	2	TRUE	0	0.519968879814404	3		364	167	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231774	36231774	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1569061768	NA	P-0065754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	8	698	0	ENST00000300305.3:c.610C>T	p.Arg204Ter	p.R204*	ENST00000300305		204	Cga/Tga	5/8	0.496675979313179	2	FACETS	0.079	0.05	0.116	0.039	0.025	0.058	SUBCLONAL	1	TRUE	0	0.519968879814404	2		698	390	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670441	134670441	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	11	513	0	ENST00000398015.3:c.352G>C	p.Asp118His	p.D118H	ENST00000398015	NM_004441.4	118	Gac/Cac	3/16	0.295643741331853	5	FACETS	0.352	0.243	0.487	0.117	0.081	0.163	INDETERMINATE	1	TRUE	2	0.519968879814404	5		513	214	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839869	27839869	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs758539201	NA	P-0065754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	196	788	0	ENST00000328488.2:c.225C>G	p.Ile75Met	p.I75M	ENST00000328488	NM_003533.2	75	atC/atG	1/1	0.519968879814404	6	FACETS	1	0.984	1	0.597	0.555	0.64	CLONAL	2	TRUE	2	0.519968879814404	6		788	644	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324681	31324681	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137854653	NA	P-0065754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	20	219	0	ENST00000412585.2:c.127G>A	p.Glu43Lys	p.E43K	ENST00000412585	NM_005514.6	43	Gag/Aag	2/8	0.519968879814404	6	FACETS	0.83	0.638	1	0.208	0.159	0.264	CLONAL	1	TRUE	2	0.519968879814404	6		219	189	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432773	49432773	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0065795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	41	500	0	ENST00000301067.7:c.8367-1G>C		p.X2789_splice	ENST00000301067	NM_003482.3	2789			1	2	FACETS	0.496	0.413	0.588	0.496	0.413	0.588	SUBCLONAL	1	TRUE	1	0.378459394766125	2		500	437	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950346	17950346	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	34	566	0	ENST00000458235.1:c.1381G>C	p.Gly461Arg	p.G461R	ENST00000458235	NM_000215.3	461	Ggg/Cgg	10/24	1	2	FACETS	0.443	0.362	0.534	0.443	0.362	0.534	SUBCLONAL	1	TRUE	1	0.378459394766125	2		566	406	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115119828	115120850	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCAATGCTATTACAAAAAAAAAATCAGTGATTTTAAATGACTATTACAGGATCTTCTCTTCCAGGCAGGTTTTGGTCAGGCAAGGACCTTTAAACATTATGTAAAATATGGTTGATAATATTCACACATTAAAAAAAAGGTGTGTGTCTCCTCACTGGCTCCTTAAGTCTGCAAACATAATCTTAAATTATGCAAAATTGCCTGCTGAACTCGCCCTTGGGTTACAGACACGTGAAGTAGTGTGGGCAAACAAACCAAAATGCCCTTCGATTTCTCTCTGACCAGGGCAGCAGCAGGCCCCTTTAGACCCAGAGGCTAGACTGGAGGGCAGAAAGGGCCGGGGAATGGTGTCAGGCCTCCCAATACCCACACAAAAGGAAAGGGCTTTAAGTTTTTCTCTCTGAGAACAAAATAAAACAGACAACACAACATCAACAAAGAAATAAGGATGTTCCAGGAGGGTTTGAAGAGTGAGTTTCTTGCAGTAGAGTGCCTTTTTTTTTTTTCTTTCCTGCTCCCTGCAGGGATGTCTGTGCTCCACTGAAAAATTCTGTCTGTTCGGGAGGGAACCCAGGATGCAGACCAAATGCAAGACCCATGCAGATGCCCAGGTAAGCTGAAATTTCCTGCCACCGGGGCAGGGCCTGGAAGTCTGTGCATACATTTCTAGGGGAACTAACTTTTCGTCCAAGCCGTAATAACCGACCAACCGACTGTTCTGGGAGCAGAGAAATAAAGGGAGGAAAAAACTCTCCAACAGCTTAGGGGAGGAGGCCCCCACTGCTTACCTTCCCGACTTGGTAATGACCATCTCGGTGCCCCGCTTGTGAAACTGATCCCAAAGTTCTTTAGCCTCCAGGTGCACCTTGGGGTCGTCCTCCACCTCTTCTTCGGGCTCCATGGTCTTCAAAGGCCTCAGATGCGCCTGGGGCCCCAGGGAGGAGAACGGGATGCCGGTCTCGGCCGCCCCCACCAATTGATCCATGATCGGCTTGGCCAGGGCGCCCGGCAGCGAGAGCGCC	TTCAATGCTATTACAAAAAAAAAATCAGTGATTTTAAATGACTATTACAGGATCTTCTCTTCCAGGCAGGTTTTGGTCAGGCAAGGACCTTTAAACATTATGTAAAATATGGTTGATAATATTCACACATTAAAAAAAAGGTGTGTGTCTCCTCACTGGCTCCTTAAGTCTGCAAACATAATCTTAAATTATGCAAAATTGCCTGCTGAACTCGCCCTTGGGTTACAGACACGTGAAGTAGTGTGGGCAAACAAACCAAAATGCCCTTCGATTTCTCTCTGACCAGGGCAGCAGCAGGCCCCTTTAGACCCAGAGGCTAGACTGGAGGGCAGAAAGGGCCGGGGAATGGTGTCAGGCCTCCCAATACCCACACAAAAGGAAAGGGCTTTAAGTTTTTCTCTCTGAGAACAAAATAAAACAGACAACACAACATCAACAAAGAAATAAGGATGTTCCAGGAGGGTTTGAAGAGTGAGTTTCTTGCAGTAGAGTGCCTTTTTTTTTTTTCTTTCCTGCTCCCTGCAGGGATGTCTGTGCTCCACTGAAAAATTCTGTCTGTTCGGGAGGGAACCCAGGATGCAGACCAAATGCAAGACCCATGCAGATGCCCAGGTAAGCTGAAATTTCCTGCCACCGGGGCAGGGCCTGGAAGTCTGTGCATACATTTCTAGGGGAACTAACTTTTCGTCCAAGCCGTAATAACCGACCAACCGACTGTTCTGGGAGCAGAGAAATAAAGGGAGGAAAAAACTCTCCAACAGCTTAGGGGAGGAGGCCCCCACTGCTTACCTTCCCGACTTGGTAATGACCATCTCGGTGCCCCGCTTGTGAAACTGATCCCAAAGTTCTTTAGCCTCCAGGTGCACCTTGGGGTCGTCCTCCACCTCTTCTTCGGGCTCCATGGTCTTCAAAGGCCTCAGATGCGCCTGGGGCCCCAGGGAGGAGAACGGGATGCCGGTCTCGGCCGCCCCCACCAATTGATCCATGATCGGCTTGGCCAGGGCGCCCGGCAGCGAGAGCGCC	-	novel	NA	P-0065795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1	84	0	0	ENST00000257566.3:c.157_389+790del		p.X53_splice	ENST00000257566	NM_016569.3	53		1/8	1	2	FACETS	1	0.989	1	1	0.991	1	CLONAL	5	TRUE	1	0.378459394766125	2		0	85	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560445	95560445	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1269643869	NA	P-0065795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	43	460	0	ENST00000393063.1:c.5144T>G	p.Leu1715Arg	p.L1715R	ENST00000393063	NM_030621.3	1715	cTc/cGc	25/28	1	2	FACETS	0.537	0.45	0.634	0.537	0.45	0.634	SUBCLONAL	1	TRUE	1	0.378459394766125	2		460	423	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710880	117710881	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0065795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	23	511	0	ENST00000368508.3:c.1391_1392delinsAA	p.Ala464Glu	p.A464E	ENST00000368508	NM_002944.2	464	gCC/gAA	12/43	1	2	FACETS	0.315	0.245	0.396	0.315	0.245	0.396	SUBCLONAL	1	TRUE	1	0.378459394766125	2		511	386	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0065818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	30	269	1	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.993	0.808	1	1	0.958	1	CLONAL	2	TRUE	1	0.158104268240245	2		270	191	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0065818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	85	372	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.158104268240245	2	FACETS	1	0.908	1	1	0.98	1	CLONAL	3	TRUE	0	0.158104268240245	2		372	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0065818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	101	343	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.913	0.816	1	1	0.986	1	CLONAL	2	TRUE	1	0.158104268240245	2		343	700	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291020	15291020	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	69	628	1	ENST00000263388.2:c.3190G>A	p.Glu1064Lys	p.E1064K	ENST00000263388	NM_000435.2	1064	Gaa/Aaa	20/33	1	2	FACETS	0.954	0.829	1	0.954	0.829	1	CLONAL	1	TRUE	1	0.158104268240245	2		629	915	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265085	198265085	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	123	457	0	ENST00000335508.6:c.2792A>G	p.Gln931Arg	p.Q931R	ENST00000335508	NM_012433.2	931	cAg/cGg	19/25	1	2	FACETS	0.862	0.781	0.946	1	0.991	1	CLONAL	3	TRUE	1	0.158104268240245	2		457	602	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723585	49723585	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1351426382	NA	P-0065818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	14	44	0	ENST00000449682.2:c.1057G>C	p.Glu353Gln	p.E353Q	ENST00000449682	NM_020998.3	353	Gag/Cag	9/18	1	2	FACETS	1	0.831	1	1	0.938	1	CLONAL	3	TRUE	1	0.158104268240245	2		44	51	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163205	47163205	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	63	485	0	ENST00000409792.3:c.2921G>C	p.Arg974Thr	p.R974T	ENST00000409792	NM_014159.6	974	aGa/aCa	3/21	1	2	FACETS	0.872	0.756	0.997	1	0.976	1	CLONAL	2	TRUE	1	0.158104268240245	2		485	457	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831322	89831322	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	48	597	0	ENST00000389301.3:c.2754G>C	p.Glu918Asp	p.E918D	ENST00000389301	NM_000135.2	918	gaG/gaC	28/43	1	2	FACETS	0.692	0.583	0.812	0.692	0.583	0.812	SUBCLONAL	1	TRUE	1	0.158104268240245	2		597	878	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741872	145741872	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs776528292	NA	P-0065818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	53	615	0	ENST00000428558.2:c.631G>C	p.Asp211His	p.D211H	ENST00000428558	NM_004260.3	211	Gat/Cat	5/22	1	2	FACETS	0.731	0.621	0.852	0.731	0.621	0.852	SUBCLONAL	1	TRUE	1	0.158104268240245	2		615	917	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533547	63533547	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750084404	NA	P-0065859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	178	475	0	ENST00000307078.5:c.1607C>T	p.Thr536Met	p.T536M	ENST00000307078	NM_004655.3	536	aCg/aTg	6/11	0.746792570931297	4	FACETS	1	0.951	1	0.347	0.32	0.374	CLONAL	1	TRUE	1	0.746792570931297	4		475	801	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47643559	47643559	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs753075410	NA	P-0065859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	108	345	0	ENST00000233146.2:c.1067T>G	p.Ile356Arg	p.I356R	ENST00000233146	NM_000251.2	356	aTa/aGa	6/16	0.746792570931297	3	FACETS	1	0.922	1	0.511	0.462	0.561	CLONAL	1	TRUE	1	0.746792570931297	3		345	389	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533547	63533547	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750084404	NA	P-0065859-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	166	475	0	ENST00000307078.5:c.1607C>T	p.Thr536Met	p.T536M	ENST00000307078	NM_004655.3	536	aCg/aTg	6/11	0.712606865275037	4	FACETS	1	0.939	1	0.341	0.314	0.37	CLONAL	1	TRUE	1	0.712606865275037	4		475	779	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47643559	47643559	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs753075410	NA	P-0065859-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	94	345	0	ENST00000233146.2:c.1067T>G	p.Ile356Arg	p.I356R	ENST00000233146	NM_000251.2	356	aTa/aGa	6/16	0.712606865275037	3	FACETS	0.932	0.835	1	0.466	0.417	0.517	CLONAL	1	TRUE	1	0.712606865275037	3		345	384	SUCCESS
EED	8726	MSKCC	GRCh37	11	85956344	85956344	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065859-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	21	385	0	ENST00000263360.6:c.73A>T	p.Ser25Cys	p.S25C	ENST00000263360	NM_003797.3	25	Agt/Tgt	1/12	1	2	FACETS	0.145	0.111	0.184	0.145	0.111	0.184	SUBCLONAL	1	TRUE	1	0.712606865275037	2		385	407	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589794	28589794	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065859-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	25	422	0	ENST00000241453.7:c.2586A>T	p.Glu862Asp	p.E862D	ENST00000241453	NM_004119.2	862	gaA/gaT	21/24	1	2	FACETS	0.207	0.163	0.258	0.207	0.163	0.258	SUBCLONAL	1	TRUE	1	0.712606865275037	2		422	339	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	172	446	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		446	496	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0065870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	357	516	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		516	842	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509358	46509358	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764723132	NA	P-0065870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	107	487	0	ENST00000262741.5:c.1373C>T	p.Ser458Leu	p.S458L	ENST00000262741	NM_003629.3	458	tCg/tTg	10/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		487	453	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51504696	51504696	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	224	426	1	ENST00000260433.2:c.1084G>T	p.Glu362Ter	p.E362*	ENST00000260433		362	Gag/Tag	9/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		427	919	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128069	30128069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	115	602	0	ENST00000263025.4:c.1060G>A	p.Asp354Asn	p.D354N	ENST00000263025	NM_002746.2	354	Gac/Aac	8/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		602	888	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828666	72828666	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1267854671	NA	P-0065870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	80	546	0	ENST00000268489.5:c.7915C>G	p.Gln2639Glu	p.Q2639E	ENST00000268489	NM_006885.3	2639	Cag/Gag	9/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		546	910	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965223	81965223	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	107	465	0	ENST00000359376.3:c.2703G>C	p.Gln901His	p.Q901H	ENST00000359376	NM_002661.3	901	caG/caC	25/33	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		465	802	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61305326	61305326	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	36	46	0	ENST00000341074.5:c.800del	p.Met267ArgfsTer9	p.M267Rfs*9	ENST00000341074	NM_002974.2	267	aTg/ag	8/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		46	88	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6217990	6217990	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	45	580	0	ENST00000252674.7:c.1173C>G	p.Phe391Leu	p.F391L	ENST00000252674	NM_005934.3	391	ttC/ttG	7/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		580	696	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881473	111881473	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	113	542	0	ENST00000393256.3:c.151G>A	p.Glu51Lys	p.E51K	ENST00000393256	NM_006538.4	51	Gaa/Aaa	2/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		542	821	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295171	1295171	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0065870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	259	527	1				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		528	603	SUCCESS
APC	324	MSKCC	GRCh37	5	112174864	112174864	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	180	457	0	ENST00000257430.4:c.3573G>C	p.Gln1191His	p.Q1191H	ENST00000257430	NM_000038.5	1191	caG/caC	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		457	764	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165239	32165239	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	291	642	0	ENST00000375023.3:c.4889C>G	p.Thr1630Ser	p.T1630S	ENST00000375023	NM_004557.3	1630	aCc/aGc	27/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		642	762	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859891	151859891	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	152	522	0	ENST00000262189.6:c.10771C>T	p.Gln3591Ter	p.Q3591*	ENST00000262189	NM_170606.2	3591	Cag/Tag	43/59	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		522	1005	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396916	139396916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761345476	NA	P-0065870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	342	417	0	ENST00000277541.6:c.5192C>T	p.Pro1731Leu	p.P1731L	ENST00000277541	NM_017617.3	1731	cCg/cTg	28/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		417	455	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1685559	1685559	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773021672	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	136	511	0	ENST00000378625.1:c.1467G>A	p.Met489Ile	p.M489I	ENST00000378625	NM_001198994.1	489	atG/atA	12/14	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.403291998118702	2		511	643	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935363	36935363	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	108	458	0	ENST00000361632.4:c.1364G>A	p.Trp455Ter	p.W455*	ENST00000361632		455	tGg/tAg	10/16	1	2	FACETS	0.874	0.786	0.966	0.874	0.786	0.966	CLONAL	1	TRUE	1	0.403291998118702	2		458	613	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429310	78429310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	101	360	0	ENST00000370768.2:c.1132G>A	p.Glu378Lys	p.E378K	ENST00000370768	NM_003902.3	378	Gaa/Aaa	13/20	1	2	FACETS	0.853	0.764	0.947	0.853	0.764	0.947	CLONAL	1	TRUE	1	0.403291998118702	2		360	587	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261341	115261341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	129	363	0	ENST00000438362.2:c.2380C>T	p.Pro794Ser	p.P794S	ENST00000438362	NM_001242891.1	794	Cct/Tct	19/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.403291998118702	2		363	578	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150934619	150934619	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148408413	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	58	131	0	ENST00000271640.5:c.3143G>A	p.Arg1048Gln	p.R1048Q	ENST00000271640	NM_001145415.1	1048	cGa/cAa	17/22	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.403291998118702	2		131	273	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843671	156843671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	156	618	0	ENST00000524377.1:c.1097C>T	p.Pro366Leu	p.P366L	ENST00000524377	NM_002529.3	366	cCc/cTc	8/17	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.403291998118702	2		618	770	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226573222	226573222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	148	306	0	ENST00000366794.5:c.994G>A	p.Glu332Lys	p.E332K	ENST00000366794	NM_001618.3	332	Gag/Aag	7/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.403291998118702	2		306	628	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608383	43608383	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	158	666	0	ENST00000355710.3:c.1731C>A	p.Asp577Glu	p.D577E	ENST00000355710	NM_020975.4	577	gaC/gaA	9/20	1	2	FACETS	0.85	0.779	0.924	0.85	0.779	0.924	CLONAL	1	TRUE	1	0.403291998118702	2		666	922	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003427	57003427	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	122	497	0	ENST00000257254.3:c.1052G>A	p.Ser351Asn	p.S351N	ENST00000257254		351	aGc/aAc	1/2	1	2	FACETS	0.868	0.786	0.955	0.868	0.786	0.955	CLONAL	1	TRUE	1	0.403291998118702	2		497	697	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936058	71936059	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	47	320	0	ENST00000298229.2:c.30_31delinsAA	p.Gly11Arg	p.G11R	ENST00000298229	NM_001567.3	10	ccGGgg/ccAAgg	1/28	1	2	FACETS	0.832	0.707	0.969	0.832	0.707	0.969	CLONAL	1	TRUE	1	0.403291998118702	2		320	280	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066823	77066823	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	128	448	0	ENST00000356341.3:c.662C>T	p.Pro221Leu	p.P221L	ENST00000356341	NM_002576.4	221	cCc/cTc	7/15	1	2	FACETS	0.895	0.813	0.982	0.895	0.813	0.982	CLONAL	1	TRUE	1	0.403291998118702	2		448	709	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165714	108165715	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	97	303	0	ENST00000278616.4:c.4837_4838delinsAA	p.Gly1613Lys	p.G1613K	ENST00000278616	NM_000051.3	1613	GGa/AAa	32/63	1	2	FACETS	0.978	0.875	1	0.978	0.875	1	CLONAL	1	TRUE	1	0.403291998118702	2		303	492	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218009	108218009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	82	289	0	ENST00000278616.4:c.8588G>A	p.Gly2863Asp	p.G2863D	ENST00000278616	NM_000051.3	2863	gGt/gAt	59/63	1	2	FACETS	0.941	0.834	1	0.941	0.834	1	CLONAL	1	TRUE	1	0.403291998118702	2		289	432	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022745	12022745	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	165	570	0	ENST00000396373.4:c.851C>T	p.Ser284Phe	p.S284F	ENST00000396373	NM_001987.4	284	tCc/tTc	5/8	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.403291998118702	2		570	747	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415911	49415911	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	135	459	0	ENST00000301067.7:c.16436C>G	p.Pro5479Arg	p.P5479R	ENST00000301067	NM_003482.3	5479	cCt/cGt	53/54	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.403291998118702	2		459	651	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427027	49427028	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	81	535	1	ENST00000301067.7:c.11460_11461delinsTT	p.Gln3821Ter	p.Q3821*	ENST00000301067	NM_003482.3	3820	ccCCag/ccTTag	39/54	1	2	FACETS	0.705	0.622	0.793	0.705	0.622	0.793	SUBCLONAL	1	TRUE	1	0.403291998118702	2		536	570	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446475	49446476	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	103	503	0	ENST00000301067.7:c.1129_1130delinsTT	p.Pro377Phe	p.P377F	ENST00000301067	NM_003482.3	377	CCt/TTt	9/54	1	2	FACETS	0.839	0.752	0.93	0.839	0.752	0.93	CLONAL	1	TRUE	1	0.403291998118702	2		503	609	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117384	115117384	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1312058352	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	102	444	0	ENST00000257566.3:c.790C>T	p.Pro264Ser	p.P264S	ENST00000257566	NM_016569.3	264	Cct/Tct	4/8	1	2	FACETS	0.891	0.799	0.988	0.891	0.799	0.988	CLONAL	1	TRUE	1	0.403291998118702	2		444	568	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562732	21562732	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	103	538	0	ENST00000382592.4:c.1187T>C	p.Phe396Ser	p.F396S	ENST00000382592	NM_014572.2	396	tTc/tCc	4/8	0.403291998118702	1	FACETS	0.904	0.814	0.999	0.904	0.814	0.999	CLONAL	1	TRUE	0	0.403291998118702	1		538	451	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954153	32954153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	102	350	0	ENST00000380152.3:c.9127G>A	p.Glu3043Lys	p.E3043K	ENST00000380152		3043	Gaa/Aaa	24/27	0.403291998118702	1	FACETS	0.899	0.809	0.994	0.899	0.809	0.994	CLONAL	1	TRUE	0	0.403291998118702	1		350	449	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039389	49039394	+	frameshift_variant	Frame_Shift_Ins	INS	TTTCCT	TTTCCT	CCCTTAC	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	121	435	0	ENST00000267163.4:c.2374_2379delinsCCCTTAC	p.Phe792ProfsTer23	p.F792Pfs*23	ENST00000267163	NM_000321.2	792	TTTCCT/CCCTTAC	23/27	0.403291998118702	1	FACETS	0.843	0.765	0.926	0.843	0.765	0.926	CLONAL	1	TRUE	0	0.403291998118702	1		435	568	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423535	88423535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	138	398	0	ENST00000360948.2:c.2300G>A	p.Gly767Glu	p.G767E	ENST00000360948	NM_001012338.2	767	gGa/gAa	18/19	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.403291998118702	2		398	594	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303979	91303979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1302320494	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	112	387	0	ENST00000355112.3:c.1376C>T	p.Pro459Leu	p.P459L	ENST00000355112	NM_000057.2	459	cCc/cTc	7/22	1	2	FACETS	0.887	0.8	0.98	0.887	0.8	0.98	CLONAL	1	TRUE	1	0.403291998118702	2		387	626	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577537	7577538	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	108	416	0	ENST00000269305.4:c.743_744delinsAA	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGG/cAA	7/11	0.37103547749767	1	FACETS	0.938	0.847	1	0.938	0.847	1	CLONAL	1	TRUE	0	0.403291998118702	1		416	456	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353869	40353869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	114	409	0	ENST00000293328.3:c.2251C>T	p.Leu751Phe	p.L751F	ENST00000293328	NM_012448.3	751	Ctt/Ttt	19/19	NA	2	FACETS	0.973	0.879	1			1	INDETERMINATE	1	TRUE	NA	0.403291998118702	2		409	581	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61310397	61310397	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	76	139	0	ENST00000341074.5:c.220C>T	p.His74Tyr	p.H74Y	ENST00000341074	NM_002974.2	74	Cat/Tat	3/8	0.393652823326116	3	FACETS	1	0.908	1	1	0.908	1	CLONAL	2	TRUE	1	0.403291998118702	3		139	222	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211732	36211732	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	126	512	0	ENST00000222270.7:c.1483C>T	p.Pro495Ser	p.P495S	ENST00000222270	NM_014727.1	495	Ccc/Tcc	3/37	1	2	FACETS	0.923	0.837	1	0.923	0.837	1	CLONAL	1	TRUE	1	0.403291998118702	2		512	677	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212179	36212180	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	58	299	0	ENST00000222270.7:c.1930_1931delinsTT	p.Pro644Phe	p.P644F	ENST00000222270	NM_014727.1	644	CCc/TTc	3/37	1	2	FACETS	0.885	0.765	1	0.885	0.765	1	CLONAL	1	TRUE	1	0.403291998118702	2		299	325	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867492	45867492	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	130	635	0	ENST00000391945.4:c.815+1G>A		p.X272_splice	ENST00000391945	NM_000400.3	272			1	2	FACETS	0.969	0.881	1	0.969	0.881	1	CLONAL	1	TRUE	1	0.403291998118702	2		635	665	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523009	25523009	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs772542252	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	113	395	0	ENST00000264709.3:c.176C>T	p.Pro59Leu	p.P59L	ENST00000264709	NM_175629.2	59	cCg/cTg	3/23	1	2	FACETS	0.887	0.8	0.978	0.887	0.8	0.978	CLONAL	1	TRUE	1	0.403291998118702	2		395	632	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967325	25967326	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	141	487	0	ENST00000435504.4:c.1880_1881delinsTT	p.Ser627Phe	p.S627F	ENST00000435504		627	tCC/tTT	13/13	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.403291998118702	2		487	664	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976506	25976506	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	96	313	0	ENST00000435504.4:c.1039G>A	p.Glu347Lys	p.E347K	ENST00000435504		347	Gag/Aag	11/13	1	2	FACETS	0.97	0.868	1	0.97	0.868	1	CLONAL	1	TRUE	1	0.403291998118702	2		313	491	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224083	39224083	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	80	223	0	ENST00000402219.2:c.3061C>T	p.Pro1021Ser	p.P1021S	ENST00000402219	NM_005633.3	1021	Cct/Tct	19/23	1	2	FACETS	0.916	0.81	1	0.916	0.81	1	CLONAL	1	TRUE	1	0.403291998118702	2		223	433	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546872	9546872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	125	476	0	ENST00000353224.5:c.1150C>T	p.His384Tyr	p.H384Y	ENST00000353224	NM_177990.2	384	Cat/Tat	5/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.403291998118702	2		476	576	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574301	41574303	+	missense_variant	Missense_Mutation	TNP	GGA	GGA	ATG	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	105	543	0	ENST00000263253.7:c.6586_6588delinsATG	p.Gly2196Met	p.G2196M	ENST00000263253	NM_001429.3	2196	GGA/ATG	31/31	1	2	FACETS	0.739	0.662	0.82	0.739	0.662	0.82	SUBCLONAL	1	TRUE	1	0.403291998118702	2		543	705	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911635	134911635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458439882	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	250	428	1	ENST00000398015.3:c.2100G>A	p.Met700Ile	p.M700I	ENST00000398015	NM_004441.4	700	atG/atA	11/16	0.393652823326116	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.403291998118702	3		429	674	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374983	138374984	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	62	307	0	ENST00000289153.2:c.3075_3075+1delinsAA		p.X1025_splice	ENST00000289153	NM_006219.2	1025		21/22	0.393652823326116	3	FACETS	0.733	0.634	0.84	0.367	0.317	0.42	SUBCLONAL	1	TRUE	1	0.403291998118702	3		307	504	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456729	138456729	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	76	245	0	ENST00000289153.2:c.622-1G>A		p.X208_splice	ENST00000289153	NM_006219.2	208			0.393652823326116	3	FACETS	0.953	0.839	1	0.477	0.419	0.538	CLONAL	1	TRUE	1	0.403291998118702	3		245	475	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598054	55598054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	117	314	0	ENST00000288135.5:c.2251G>A	p.Asp751Asn	p.D751N	ENST00000288135	NM_000222.2	751	Gat/Aat	16/21	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.403291998118702	2		314	546	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604689	55604689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	134	344	0	ENST00000288135.5:c.2897C>T	p.Ser966Phe	p.S966F	ENST00000288135	NM_000222.2	966	tCc/tTc	21/21	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.403291998118702	2		344	643	SUCCESS
ALB	213	MSKCC	GRCh37	4	74279203	74279203	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	119	423	0	ENST00000295897.4:c.910G>A	p.Glu304Lys	p.E304K	ENST00000295897	NM_000477.5	304	Gaa/Aaa	8/15	1	2	FACETS	0.946	0.856	1	0.946	0.856	1	CLONAL	1	TRUE	1	0.403291998118702	2		423	624	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557999	187557999	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	121	422	0	ENST00000441802.2:c.3712G>T	p.Glu1238Ter	p.E1238*	ENST00000441802	NM_005245.3	1238	Gaa/Taa	5/27	1	2	FACETS	0.933	0.845	1	0.933	0.845	1	CLONAL	1	TRUE	1	0.403291998118702	2		422	643	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015636	112015636	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	126	456	1	ENST00000368678.4:c.1206G>T	p.Lys402Asn	p.K402N	ENST00000368678		402	aaG/aaT	11/13	1	2	FACETS	0.957	0.868	1	0.957	0.868	1	CLONAL	1	TRUE	1	0.403291998118702	2		457	653	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638377	117638377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	106	401	0	ENST00000368508.3:c.6064C>T	p.Gln2022Ter	p.Q2022*	ENST00000368508	NM_002944.2	2022	Caa/Taa	38/43	1	2	FACETS	0.853	0.767	0.945	0.853	0.767	0.945	CLONAL	1	TRUE	1	0.403291998118702	2		401	616	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641110	117641110	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752657920	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	115	439	0	ENST00000368508.3:c.5861G>A	p.Gly1954Glu	p.G1954E	ENST00000368508	NM_002944.2	1954	gGa/gAa	36/43	1	2	FACETS	0.774	0.697	0.854	0.774	0.697	0.854	SUBCLONAL	1	TRUE	1	0.403291998118702	2		439	737	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959079	2959079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542412710	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	131	408	1	ENST00000396946.4:c.2437G>A	p.Glu813Lys	p.E813K	ENST00000396946	NM_032415.4	813	Gag/Aag	18/25	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.403291998118702	2		409	649	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729363	41729363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	122	407	0	ENST00000242208.4:c.1166C>T	p.Ser389Leu	p.S389L	ENST00000242208	NM_002192.2	389	tCg/tTg	3/3	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.403291998118702	2		407	599	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508793	106508793	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370152741	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	127	466	0	ENST00000359195.3:c.787G>A	p.Glu263Lys	p.E263K	ENST00000359195	NM_002649.2	263	Gaa/Aaa	2/11	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.403291998118702	2		466	621	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275843	38275843	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781608303	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	140	413	1	ENST00000425967.3:c.1426C>T	p.Arg476Trp	p.R476W	ENST00000425967	NM_001174067.1	476	Cgg/Tgg	11/19	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.403291998118702	2		414	613	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931844	68931844	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765407651	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	101	356	0	ENST00000288368.4:c.274G>A	p.Glu92Lys	p.E92K	ENST00000288368	NM_024870.2	92	Gaa/Aaa	3/40	1	2	FACETS	0.874	0.783	0.97	0.874	0.783	0.97	CLONAL	1	TRUE	1	0.403291998118702	2		356	573	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375972	8375972	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	127	369	0	ENST00000356435.5:c.4625A>G	p.Asn1542Ser	p.N1542S	ENST00000356435		1542	aAc/aGc	28/35	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.403291998118702	2		369	619	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471048	8471048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	86	336	0	ENST00000356435.5:c.3451C>T	p.Arg1151Cys	p.R1151C	ENST00000356435		1151	Cgc/Tgc	20/35	1	2	FACETS	0.879	0.781	0.984	0.879	0.781	0.984	CLONAL	1	TRUE	1	0.403291998118702	2		336	485	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250260	110250260	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	86	501	0	ENST00000374672.4:c.415A>G	p.Ser139Gly	p.S139G	ENST00000374672	NM_004235.4	139	Agc/Ggc	3/5	1	2	FACETS	0.781	0.692	0.875	0.781	0.692	0.875	SUBCLONAL	1	TRUE	1	0.403291998118702	2		501	546	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396850	139396851	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	114	391	0	ENST00000277541.6:c.5257_5258delinsAA	p.Gly1753Lys	p.G1753K	ENST00000277541	NM_017617.3	1753	GGg/AAg	28/34	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.403291998118702	2		391	541	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413166	139413166	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	106	507	0	ENST00000277541.6:c.976G>T	p.Gly326Cys	p.G326C	ENST00000277541	NM_017617.3	326	Ggc/Tgc	6/34	1	2	FACETS	0.789	0.708	0.875	0.789	0.708	0.875	SUBCLONAL	1	TRUE	1	0.403291998118702	2		507	666	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422716	47422716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1413219188	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	116	392	0	ENST00000377045.4:c.188G>A	p.Arg63Gln	p.R63Q	ENST00000377045	NM_001654.4	63	cGa/cAa	3/16	1	2	FACETS	0.895	0.808	0.986	0.895	0.808	0.986	CLONAL	1	TRUE	1	0.403291998118702	2		392	643	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426424	47426424	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs919593802	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	154	571	0	ENST00000377045.4:c.767G>A	p.Gly256Glu	p.G256E	ENST00000377045	NM_001654.4	256	gGg/gAg	9/16	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.403291998118702	2		571	758	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430329	47430329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	95	426	0	ENST00000377045.4:c.1604C>T	p.Ser535Phe	p.S535F	ENST00000377045	NM_001654.4	535	tCc/tTc	15/16	1	2	FACETS	0.809	0.722	0.902	0.809	0.722	0.902	CLONAL	1	TRUE	1	0.403291998118702	2		426	582	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76764088	76764088	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557034949	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	122	360	1	ENST00000373344.5:c.7220G>A	p.Arg2407Gln	p.R2407Q	ENST00000373344	NM_000489.3	2407	cGa/cAa	35/35	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.403291998118702	2		361	590	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76949344	76949344	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	88	316	0	ENST00000373344.5:c.453A>C	p.Lys151Asn	p.K151N	ENST00000373344	NM_000489.3	151	aaA/aaC	6/35	1	2	FACETS	0.889	0.79	0.993	0.889	0.79	0.993	CLONAL	1	TRUE	1	0.403291998118702	2		316	491	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196797	123196797	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	95	329	0	ENST00000218089.9:c.1684A>C	p.Lys562Gln	p.K562Q	ENST00000218089	NM_001042749.1	562	Aaa/Caa	18/35	1	2	FACETS	0.992	0.887	1	0.992	0.887	1	CLONAL	1	TRUE	1	0.403291998118702	2		329	475	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696449	47696449	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	65	459	0	ENST00000347630.2:c.374T>G	p.Phe125Cys	p.F125C	ENST00000347630	NM_001007230.1	125	tTt/tGt	6/11	0.201319981637479	3	FACETS	1	0.905	1	0.527	0.457	0.603	CLONAL	1	TRUE	1	0.229183479678407	3		459	600	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432669	49432669	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1190017036	NA	P-0065910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	58	551	0	ENST00000301067.7:c.8470A>G	p.Thr2824Ala	p.T2824A	ENST00000301067	NM_003482.3	2824	Aca/Gca	34/54	1	2	FACETS	0.684	0.587	0.791	0.684	0.587	0.791	SUBCLONAL	1	TRUE	1	0.229183479678407	2		551	740	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907402	32907430	+	frameshift_variant	Frame_Shift_Del	DEL	ATGAAACATCTTATAAAGGAAAAAAAATA	ATGAAACATCTTATAAAGGAAAAAAAATA	-	novel	NA	P-0065910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	56	426	0	ENST00000380152.3:c.1787_1815del	p.Asp596AlafsTer10	p.D596Afs*10	ENST00000380152		596	gATGAAACATCTTATAAAGGAAAAAAAATA/g	10/27	0.201319981637479	3	FACETS	0.887	0.765	1	0.887	0.765	1	CLONAL	2	TRUE	1	0.229183479678407	3		426	307	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955539	90955539	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	88	332	0	ENST00000265433.3:c.2126T>C	p.Ile709Thr	p.I709T	ENST00000265433	NM_002485.4	709	aTa/aCa	14/16	0.229362043621703	4	FACETS	1	0.964	1	0.797	0.71	0.887	CLONAL	2	TRUE	1	0.229183479678407	4		332	395	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120478175	120478175	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	40	474	0	ENST00000256646.2:c.3575A>G	p.Gln1192Arg	p.Q1192R	ENST00000256646	NM_024408.3	1192	cAg/cGg	22/34	0.201319981637479	3	FACETS	0.593	0.492	0.707	0.297	0.246	0.354	SUBCLONAL	1	TRUE	1	0.229183479678407	3		474	656	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735551	204735558	+	frameshift_variant	Frame_Shift_Del	DEL	GGACTGAG	GGACTGAG	-	novel	NA	P-0065910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	46	463	0	ENST00000302823.3:c.354_361del	p.Leu119HisfsTer32	p.L119Hfs*32	ENST00000302823	NM_005214.4	118	GGACTGAGg/g	2/4	1	2	FACETS	0.549	0.461	0.647	0.549	0.461	0.647	SUBCLONAL	1	TRUE	1	0.229183479678407	2		463	731	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268434	198268434	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	33	348	0	ENST00000335508.6:c.1594T>C	p.Phe532Leu	p.F532L	ENST00000335508	NM_012433.2	532	Ttt/Ctt	12/25	1	2	FACETS	0.722	0.588	0.872	0.722	0.588	0.872	SUBCLONAL	1	TRUE	1	0.229183479678407	2		348	399	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0065911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	17	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.621	0.463	0.809	0.621	0.463	0.809	SUBCLONAL	1	TRUE	1	0.18	2		341	304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577587	7577587	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	23	392	0	ENST00000269305.4:c.694A>T	p.Ile232Phe	p.I232F	ENST00000269305	NM_001126112.2	232	Atc/Ttc	7/11	1	2	FACETS	0.957	0.748	1	0.957	0.748	1	CLONAL	1	TRUE	1	0.18	2		392	267	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032565	12032565	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	11	313	0	ENST00000353533.5:c.1003del	p.Glu335AsnfsTer28	p.E335Nfs*28	ENST00000353533	NM_003010.3	334	aGg/ag	9/11	1	2	FACETS	0.568	0.392	0.787	0.568	0.392	0.787	SUBCLONAL	1	TRUE	1	0.18	2		313	215	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954192	48954192	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065919-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4	60	158	0	ENST00000267163.4:c.1393G>T	p.Glu465Ter	p.E465*	ENST00000267163	NM_000321.2	465	Gaa/Taa	15/27	0.88620617241106	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.88620617241106	2		158	64	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112326	115112326	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065919-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	220	458	0	ENST00000257566.3:c.1414G>T	p.Ala472Ser	p.A472S	ENST00000257566	NM_016569.3	472	Gcg/Tcg	7/8	0.88620617241106	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.88620617241106	3		458	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577157	7577157	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0065919-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	395	417	0	ENST00000269305.4:c.783-2A>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.88620617241106	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.88620617241106	3		417	408	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165603	118165603	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065919-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	333	546	0	ENST00000369448.3:c.113G>T	p.Arg38Leu	p.R38L	ENST00000369448	NM_017709.3	38	cGa/cTa	2/2	0.626025852616127	4	FACETS	0.872	0.836	0.907	0.872	0.836	0.907	CLONAL	3	TRUE	1	0.88620617241106	4		546	542	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606731	43606731	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1588871155	NA	P-0065919-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	133	592	0	ENST00000355710.3:c.1340C>A	p.Ala447Asp	p.A447D	ENST00000355710	NM_020975.4	447	gCc/gAc	7/20	NA	2	FACETS	0.95	0.876	1			1	INDETERMINATE	1	TRUE	NA	0.88620617241106	2		592	316	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943716	71943716	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065919-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	187	511	0	ENST00000298229.2:c.1759G>T	p.Asp587Tyr	p.D587Y	ENST00000298229	NM_001567.3	587	Gac/Tac	15/28	0.88620617241106	3	FACETS	1	0.951	1	0.514	0.478	0.552	CLONAL	1	TRUE	1	0.88620617241106	3		511	592	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420282	88420282	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065919-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	341	502	0	ENST00000360948.2:c.2404G>T	p.Val802Phe	p.V802F	ENST00000360948	NM_001012338.2	802	Gtc/Ttc	19/19	0.88620617241106	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.88620617241106	3		502	511	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46266508	46266511	+	frameshift_variant	Frame_Shift_Del	DEL	TCAA	TCAA	-	novel	NA	P-0065919-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	74	406	2	ENST00000371998.3:c.2493_2496del	p.Phe831LeufsTer8	p.F831Lfs*8	ENST00000371998		831	ttTCAA/tt	13/23	0.88620617241106	3	FACETS	0.867	0.785	0.948	0.867	0.785	0.948	CLONAL	2	TRUE	1	0.88620617241106	3		408	139	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045756	143045756	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065919-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	99	376	0	ENST00000262992.4:c.1878C>G	p.Ile626Met	p.I626M	ENST00000262992	NM_001101669.1	626	atC/atG	17/24	0.88620617241106	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.88620617241106	1		376	107	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686805	117686806	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0065919-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	46	454	0	ENST00000368508.3:c.2911_2912delinsAT	p.Gly971Ile	p.G971I	ENST00000368508	NM_002944.2	971	GGt/ATt	19/43	0.43417054459638	3	FACETS	0.71	0.605	0.823	0.237	0.201	0.275	INDETERMINATE	1	TRUE	0	0.88620617241106	3		454	211	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952136	76952136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs782377443	NA	P-0065919-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	65	357	0	ENST00000373344.5:c.299A>G	p.Asp100Gly	p.D100G	ENST00000373344	NM_000489.3	100	gAt/gGt	5/35	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.88620617241106	NA		357	166	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034356	123034356	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065919-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	62	357	1	ENST00000355640.3:c.1114del	p.Gln372LysfsTer21	p.Q372Kfs*21	ENST00000355640		371	ttC/tt	6/7	0.695986632803211	3	FACETS	1	0.946	1			1	CLONAL	1	TRUE	NA	0.88620617241106	3		358	178	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577137	7577137	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	147	468	0	ENST00000269305.4:c.801del	p.Asn268ThrfsTer77	p.N268Tfs*77	ENST00000269305	NM_001126112.2	267	cgG/cg	8/11	0.408225700093542	1	FACETS	0.999	0.916	1	0.999	0.916	1	CLONAL	1	TRUE	0	0.408225700093542	1		468	574	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544691	86544691	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	135	559	0	ENST00000262426.4:c.516C>A	p.Phe172Leu	p.F172L	ENST00000262426	NM_001451.2	172	ttC/ttA	1/2	1	2	FACETS	0.928	0.844	1	0.928	0.844	1	CLONAL	1	TRUE	1	0.408225700093542	2		559	713	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0065943-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	205	328	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.863532554527781	2		328	468	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741694	17741694	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065943-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	321	411	0	ENST00000250003.3:c.365T>G	p.Leu122Arg	p.L122R	ENST00000250003	NM_002478.4	122	cTg/cGg	1/3	0.39652318721003	3	FACETS	0.865	0.826	0.905	0.865	0.826	0.905	INDETERMINATE	2	TRUE	1	0.863532554527781	3		411	615	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729601	41729601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065943-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	112	484	0	ENST00000242208.4:c.928C>T	p.Arg310Trp	p.R310W	ENST00000242208	NM_002192.2	310	Cgg/Tgg	3/3	1	2	FACETS	0.419	0.377	0.463	0.419	0.377	0.463	SUBCLONAL	1	TRUE	1	0.863532554527781	2		484	619	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178619	56178619	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065943-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	62	421	0	ENST00000399503.3:c.3592T>C	p.Ser1198Pro	p.S1198P	ENST00000399503	NM_005921.1	1198	Tct/Cct	14/20	1	2	FACETS	0.234	0.202	0.269	0.234	0.202	0.269	SUBCLONAL	1	TRUE	1	0.863532554527781	2		421	613	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0065945-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	14	311	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.53741226426338	1	FACETS	0.289	0.21	0.382	0.289	0.21	0.382	SUBCLONAL	1	TRUE	0	0.53741226426338	1		311	132	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578214	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs864309495	NA	P-0065945-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	456	590	0	ENST00000269305.4:c.635_636del	p.Phe212SerfsTer3	p.F212Sfs*3	ENST00000269305	NM_001126112.2	212	tTT/t	6/11	0.53741226426338	3	FACETS	0.989	0.955	1	0.989	0.955	1	CLONAL	3	TRUE	0	0.53741226426338	3		590	726	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240072	41240073	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0065945-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	100	292	1	ENST00000379561.5:c.277_278delinsAT	p.Ala93Met	p.A93M	ENST00000379561	NM_002015.3	93	GCg/ATg	1/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.53741226426338	2		293	307	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744053	39744053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	114	362	0	ENST00000361337.2:c.1681G>A	p.Glu561Lys	p.E561K	ENST00000361337	NM_003286.2	561	Gag/Aag	16/21	1	2	FACETS	0.873	0.79	0.961	0.873	0.79	0.961	CLONAL	1	TRUE	1	0.50703503342195	2		362	515	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040901	42040901	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	189	430	0	ENST00000219905.7:c.5279C>A	p.Pro1760His	p.P1760H	ENST00000219905	NM_001164273.1	1760	cCt/cAt	16/24	1	2	FACETS	0.972	0.9	1	0.972	0.9	1	CLONAL	1	TRUE	1	0.50703503342195	2		430	767	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578161	7578178	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGTTGCAAACCAGACCT	CAGTTGCAAACCAGACCT	-	novel	NA	P-0065973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	155	400	0	ENST00000269305.4:c.671_672+16del		p.X224_splice	ENST00000269305	NM_001126112.2	224		6/11	0.50703503342195	1	FACETS	0.937	0.865	1	0.937	0.865	1	CLONAL	1	TRUE	0	0.50703503342195	1		400	487	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418394	139418394	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755775484	NA	P-0065973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	150	476	0	ENST00000277541.6:c.178C>T	p.Pro60Ser	p.P60S	ENST00000277541	NM_017617.3	60	Ccc/Tcc	3/34	0.50703503342195	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.50703503342195	1		476	412	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040965	47040965	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	88	475	0	ENST00000377604.3:c.1495G>T	p.Ala499Ser	p.A499S	ENST00000377604	NM_001204468.1	499	Gcc/Tcc	14/24	0.535755194584683	2	FACETS	0.743	0.663	0.827	0.371	0.331	0.414	SUBCLONAL	1	TRUE	0	0.628486677295039	2		475	377	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092815	27092831	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCCATATTCCATGGG	CCCCCATATTCCATGGG	-	novel	NA	P-0065975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	212	336	0	ENST00000324856.7:c.2836_2852del	p.Pro946TrpfsTer55	p.P946Wfs*55	ENST00000324856	NM_006015.4	946	CCCCCATATTCCATGGGt/t	9/20	0.522152211975495	4	FACETS	1	0.989	1	0.816	0.767	0.864	CLONAL	2	TRUE	1	0.628486677295039	4		336	449	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736460	85736487	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTACTTGATGTTCGACAAGAAATTTC	TTCTACTTGATGTTCGACAAGAAATTTC	-	novel	NA	P-0065975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	237	383	0	ENST00000370580.1:c.160_187del	p.Glu54LysfsTer7	p.E54Kfs*7	ENST00000370580	NM_003921.4	54	GAAATTTCTTGTCGAACATCAAGTAGAAaa/aa	2/3	0.522152211975495	4	FACETS	1	0.99	1	0.829	0.783	0.875	CLONAL	2	TRUE	1	0.628486677295039	4		383	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577562	7577563	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0065975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	193	324	0	ENST00000269305.4:c.718_719del	p.Ser240PhefsTer23	p.S240Ffs*23	ENST00000269305	NM_001126112.2	240	AGt/t	7/11	0.532049487379014	2	FACETS	0.858	0.808	0.907	0.858	0.808	0.907	CLONAL	2	TRUE	0	0.628486677295039	2		324	358	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41247883	41247883	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs774284145	NA	P-0065975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	134	292	0	ENST00000357654.3:c.650G>C	p.Ser217Thr	p.S217T	ENST00000357654	NM_007294.3	217	aGt/aCt	9/23	0.532049487379014	2	FACETS	0.781	0.724	0.838	0.781	0.724	0.838	SUBCLONAL	2	TRUE	0	0.628486677295039	2		292	273	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52676062	52676062	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0065975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	219	257	0	ENST00000394830.3:c.996-1G>A		p.X332_splice	ENST00000394830	NM_018313.4	332			0.508055420218293	4	FACETS	0.927	0.887	0.966	0.927	0.887	0.966	CLONAL	4	TRUE	0	0.628486677295039	4		257	306	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	19	215	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.145	0.109	0.187	0.145	0.109	0.187	SUBCLONAL	1	TRUE	1	0.521565883587946	2		215	503	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	250	501	0	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.521565883587946	2		501	939	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	48	405	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	0.204	0.172	0.24	0.204	0.172	0.24	SUBCLONAL	1	TRUE	1	0.521565883587946	2		405	902	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11168277	11168277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	83	277	0	ENST00000361445.4:c.7595C>T	p.Ala2532Val	p.A2532V	ENST00000361445	NM_004958.3	2532	gCg/gTg	57/58	1	2	FACETS	0.482	0.425	0.543	0.482	0.425	0.543	SUBCLONAL	1	TRUE	1	0.521565883587946	2		277	660	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217225	11217225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	99	308	0	ENST00000361445.4:c.4453G>A	p.Glu1485Lys	p.E1485K	ENST00000361445	NM_004958.3	1485	Gag/Aag	30/58	1	2	FACETS	0.491	0.438	0.548	0.491	0.438	0.548	SUBCLONAL	1	TRUE	1	0.521565883587946	2		308	773	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551952	150551952	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	110	372	2	ENST00000369026.2:c.55del	p.Ala19ProfsTer30	p.A19Pfs*30	ENST00000369026	NM_021960.4	19	Gcc/cc	1/3	0.521565883587946	3	FACETS	0.549	0.493	0.61	0.275	0.246	0.305	SUBCLONAL	1	TRUE	1	0.521565883587946	3		374	968	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717714	89717714	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167662	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	77	239	0	ENST00000371953.3:c.740del	p.Leu247TyrfsTer9	p.L247Yfs*9	ENST00000371953	NM_000314.4	247	Tta/ta	7/9	1	2	FACETS	0.548	0.482	0.619	0.548	0.482	0.619	SUBCLONAL	1	TRUE	1	0.521565883587946	2		239	539	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725042	89725042	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1085308041	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	60	207	0	ENST00000371953.3:c.1027-2A>G		p.X343_splice	ENST00000371953	NM_000314.4	343			1	2	FACETS	0.535	0.462	0.614	0.535	0.462	0.614	SUBCLONAL	1	TRUE	1	0.521565883587946	2		207	430	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944489	71944489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375770720	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	129	393	0	ENST00000298229.2:c.2045G>A	p.Arg682Gln	p.R682Q	ENST00000298229	NM_001567.3	682	cGg/cAg	18/28	1	2	FACETS	0.565	0.512	0.621	0.565	0.512	0.621	SUBCLONAL	1	TRUE	1	0.521565883587946	2		393	875	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121531	108121531	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779815	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	114	344	0	ENST00000278616.4:c.1339C>T	p.Arg447Ter	p.R447*	ENST00000278616	NM_000051.3	447	Cga/Tga	10/63	1	2	FACETS	0.522	0.47	0.578	0.522	0.47	0.578	SUBCLONAL	1	TRUE	1	0.521565883587946	2		344	837	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434367	121434367	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	41	415	0	ENST00000257555.6:c.1136del	p.Pro379LeufsTer5	p.P379Lfs*5	ENST00000257555		377	ctC/ct	6/10	1	2	FACETS	0.192	0.159	0.229	0.192	0.159	0.229	SUBCLONAL	1	TRUE	1	0.521565883587946	2		415	818	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641778	23641778	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144617793	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	69	232	0	ENST00000261584.4:c.1697G>A	p.Arg566His	p.R566H	ENST00000261584	NM_024675.3	566	cGt/cAt	5/13	1	2	FACETS	0.44	0.383	0.502	0.44	0.383	0.502	SUBCLONAL	1	TRUE	1	0.521565883587946	2		232	601	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17124931	17124931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372304384	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	120	422	1	ENST00000285071.4:c.791C>T	p.Ala264Val	p.A264V	ENST00000285071	NM_144997.5	264	gCg/gTg	8/14	1	2	FACETS	0.526	0.475	0.581	0.526	0.475	0.581	SUBCLONAL	1	TRUE	1	0.521565883587946	2		423	874	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	101	332	2	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	0.454	0.405	0.505	0.454	0.405	0.505	SUBCLONAL	1	TRUE	1	0.521565883587946	2		334	854	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400688	56400688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140664950	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	110	270	0	ENST00000348428.3:c.1282G>A	p.Val428Ile	p.V428I	ENST00000348428	NM_006785.3	428	Gtt/Att	11/17	1	2	FACETS	0.585	0.526	0.648	0.585	0.526	0.648	SUBCLONAL	1	TRUE	1	0.521565883587946	2		270	721	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619849	1619849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758087547	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	92	385	0	ENST00000344749.5:c.1097C>T	p.Thr366Met	p.T366M	ENST00000344749	NM_001136139.2	366	aCg/aTg	14/19	1	2	FACETS	0.428	0.379	0.479	0.428	0.379	0.479	SUBCLONAL	1	TRUE	1	0.521565883587946	2		385	825	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622415	1622415	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	58	249	0	ENST00000344749.5:c.550-1G>T		p.X184_splice	ENST00000344749	NM_001136139.2	184			1	2	FACETS	0.433	0.372	0.499	0.433	0.372	0.499	SUBCLONAL	1	TRUE	1	0.521565883587946	2		249	514	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457192	25457192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771922296	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	125	344	0	ENST00000264709.3:c.2695C>T	p.Arg899Cys	p.R899C	ENST00000264709	NM_175629.2	899	Cgc/Tgc	23/23	1	2	FACETS	0.555	0.502	0.611	0.555	0.502	0.611	SUBCLONAL	1	TRUE	1	0.521565883587946	2		344	863	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143052	30143052	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1244823020	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	109	531	0	ENST00000389048.3:c.474del	p.Glu160ArgfsTer26	p.E160Rfs*26	ENST00000389048	NM_004304.4	158	ccC/cc	1/29	1	2	FACETS	0.425	0.381	0.472	0.425	0.381	0.472	SUBCLONAL	1	TRUE	1	0.521565883587946	2		531	983	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172272	99172272	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs374507988	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	121	416	0	ENST00000074304.5:c.1837+1G>A		p.X613_splice	ENST00000074304	NM_001134224.1	613			1	2	FACETS	0.498	0.449	0.549	0.498	0.449	0.549	SUBCLONAL	1	TRUE	1	0.521565883587946	2		416	932	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415537	152415537	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519714	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	101	358	0	ENST00000206249.3:c.1387T>C	p.Ser463Pro	p.S463P	ENST00000206249	NM_000125.3	463	Tcc/Ccc	7/8	1	2	FACETS	0.51	0.456	0.568	0.51	0.456	0.568	SUBCLONAL	1	TRUE	1	0.521565883587946	2		358	759	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400023	139400023	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	134	443	1	ENST00000277541.6:c.4325del	p.Pro1442ArgfsTer3	p.P1442Rfs*3	ENST00000277541	NM_017617.3	1442	cCg/cg	25/34	1	2	FACETS	0.567	0.514	0.622	0.567	0.514	0.622	SUBCLONAL	1	TRUE	1	0.521565883587946	2		444	907	SUCCESS
AR	367	MSKCC	GRCh37	X	66937403	66937403	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886039558	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	112	323	0	ENST00000374690.3:c.2257C>T	p.Arg753Ter	p.R753*	ENST00000374690	NM_000044.3	753	Cga/Tga	5/8	1	2	FACETS	0.584	0.526	0.646	0.584	0.526	0.646	SUBCLONAL	1	TRUE	1	0.521565883587946	2		323	735	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097653	27097665	+	frameshift_variant	Frame_Shift_Del	DEL	ATGTGGGCACATC	ATGTGGGCACATC	-	novel	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	127	350	0	ENST00000324856.7:c.3243_3255del	p.Asn1081LysfsTer8	p.N1081Kfs*8	ENST00000324856	NM_006015.4	1081	aATGTGGGCACATCa/aa	12/20	1	2	FACETS	0.558	0.505	0.614	0.558	0.505	0.614	SUBCLONAL	1	TRUE	1	0.521565883587946	2		350	873	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091457	193091457	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	97	382	0	ENST00000367435.3:c.127T>C	p.Trp43Arg	p.W43R	ENST00000367435	NM_024529.4	43	Tgg/Cgg	1/17	0.521565883587946	3	FACETS	0.509	0.453	0.569	0.255	0.226	0.285	SUBCLONAL	1	TRUE	1	0.521565883587946	3		382	921	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920669	100920669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	63	243	0	ENST00000325455.5:c.2479C>T	p.Leu827Phe	p.L827F	ENST00000325455	NM_001202474.3	827	Ctt/Ttt	6/8	1	2	FACETS	0.568	0.493	0.65	0.568	0.493	0.65	SUBCLONAL	1	TRUE	1	0.521565883587946	2		243	425	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444505	49444505	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1565815073	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	127	434	0	ENST00000301067.7:c.2866del	p.Glu956SerfsTer2	p.E956Sfs*2	ENST00000301067	NM_003482.3	956	Gag/ag	11/54	1	2	FACETS	0.545	0.493	0.599	0.545	0.493	0.599	SUBCLONAL	1	TRUE	1	0.521565883587946	2		434	894	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43773181	43773181	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	99	346	0	ENST00000382044.4:c.411G>T	p.Glu137Asp	p.E137D	ENST00000382044	NM_001141980.1	137	gaG/gaT	5/28	1	2	FACETS	0.484	0.432	0.54	0.484	0.432	0.54	SUBCLONAL	1	TRUE	1	0.521565883587946	2		346	784	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2090008	2090008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139309757	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	110	443	0	ENST00000219066.1:c.856G>A	p.Gly286Ser	p.G286S	ENST00000219066	NM_002528.5	286	Ggc/Agc	6/6	1	2	FACETS	0.51	0.458	0.565	0.51	0.458	0.565	SUBCLONAL	1	TRUE	1	0.521565883587946	2		443	827	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829874	72829875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	114	360	0	ENST00000268489.5:c.6706dup	p.Gln2236ProfsTer35	p.Q2236Pfs*35	ENST00000268489	NM_006885.3	2236	cag/cCag	9/10	1	2	FACETS	0.518	0.466	0.573	0.518	0.466	0.573	SUBCLONAL	1	TRUE	1	0.521565883587946	2		360	844	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211623	5211623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1234272445	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	52	334	0	ENST00000357368.4:c.5212G>A	p.Ala1738Thr	p.A1738T	ENST00000357368	NM_002850.3	1738	Gcc/Acc	33/38	1	2	FACETS	0.288	0.244	0.336	0.288	0.244	0.336	SUBCLONAL	1	TRUE	1	0.521565883587946	2		334	693	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054639	13054639	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	137	431	0	ENST00000316448.5:c.1166A>C	p.Glu389Ala	p.E389A	ENST00000316448	NM_004343.3	389	gAg/gCg	9/9	1	2	FACETS	0.588	0.534	0.644	0.588	0.534	0.644	SUBCLONAL	1	TRUE	1	0.521565883587946	2		431	894	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662517	227662517	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	118	468	0	ENST00000305123.5:c.938del	p.Pro313ArgfsTer35	p.P313Rfs*35	ENST00000305123	NM_005544.2	313	cCg/cg	1/2	1	2	FACETS	0.502	0.452	0.554	0.502	0.452	0.554	SUBCLONAL	1	TRUE	1	0.521565883587946	2		468	902	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29445314	29445314	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	122	430	0	ENST00000544604.2:c.1145C>A	p.Pro382His	p.P382H	ENST00000544604	NM_001206998.1	382	cCt/cAt	8/9	1	2	FACETS	0.516	0.466	0.569	0.516	0.466	0.569	SUBCLONAL	1	TRUE	1	0.521565883587946	2		430	906	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759799	133759799	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	119	357	0	ENST00000318560.5:c.2122A>G	p.Ser708Gly	p.S708G	ENST00000318560	NM_005157.4	708	Agc/Ggc	11/11	1	2	FACETS	0.629	0.568	0.694	0.629	0.568	0.694	SUBCLONAL	1	TRUE	1	0.521565883587946	2		357	725	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393409	139393409	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	109	407	0	ENST00000277541.6:c.6122T>C	p.Val2041Ala	p.V2041A	ENST00000277541	NM_017617.3	2041	gTg/gCg	33/34	1	2	FACETS	0.483	0.433	0.536	0.483	0.433	0.536	SUBCLONAL	1	TRUE	1	0.521565883587946	2		407	866	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0065988-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	118	389	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.308981762320119	3	FACETS	0.793	0.718	0.872	0.793	0.718	0.872	SUBCLONAL	2	TRUE	1	0.307635251656818	3		389	558	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161420	185161420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065988-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	64	230	0	ENST00000265026.3:c.847C>T	p.Pro283Ser	p.P283S	ENST00000265026	NM_004721.4	283	Cct/Tct	4/14	0.171207630129878	2	FACETS	1	0.961	1	0.64	0.558	0.728	INDETERMINATE	1	TRUE	0	0.307635251656818	2		230	325	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0065988-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	107	334	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.171207630129878	2	FACETS	1	0.983	1	0.75	0.676	0.827	INDETERMINATE	1	TRUE	0	0.307635251656818	2		334	464	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058013	27058013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065988-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	66	390	0	ENST00000324856.7:c.1721C>T	p.Ser574Phe	p.S574F	ENST00000324856	NM_006015.4	574	tCc/tTc	3/20	0.208418101817502	3	FACETS	0.831	0.721	0.949	0.415	0.36	0.475	CLONAL	1	TRUE	1	0.307635251656818	3		390	596	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602430	10602430	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065988-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	162	453	0	ENST00000171111.5:c.1148C>A	p.Ser383Ter	p.S383*	ENST00000171111	NM_203500.1	383	tCg/tAg	3/6	0.202342951925839	3	FACETS	1	0.946	1	0.689	0.635	0.744	CLONAL	2	TRUE	0	0.307635251656818	3		453	588	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524927	8524927	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065988-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	28	210	0	ENST00000356435.5:c.677G>C	p.Arg226Thr	p.R226T	ENST00000356435		226	aGa/aCa	7/35	0.308981762320119	1	FACETS	0.697	0.56	0.851	0.697	0.56	0.851	SUBCLONAL	1	TRUE	0	0.307635251656818	1		210	221	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401513	401513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065988-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	98	417	0	ENST00000380956.4:c.835G>T	p.Gly279Ter	p.G279*	ENST00000380956	NM_001195286.1	279	Gga/Tga	7/9	0.242163907051488	3	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.307635251656818	3		417	545	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31239525	31239525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs281860368	NA	P-0065988-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	93	462	0	ENST00000376228.5:c.194C>T	p.Ala65Val	p.A65V	ENST00000376228	NM_002117.5	65	gCg/gTg	2/8	0.184122611228036	2	FACETS	0.991	0.883	1	0.496	0.441	0.553	INDETERMINATE	1	TRUE	0	0.307635251656818	2		462	610	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883138	37883139	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0065988-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	50	378	0	ENST00000269571.5:c.3046dup	p.Asp1016GlyfsTer6	p.D1016Gfs*6	ENST00000269571		1014	atg/atGg	25/27	0.166929383083953	4	FACETS	0.88	0.747	1	0.44	0.373	0.513	INDETERMINATE	1	TRUE	2	0.307635251656818	4		378	483	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259473	55259473	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065988-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	76	300	0	ENST00000275493.2:c.2531T>A	p.Leu844Gln	p.L844Q	ENST00000275493	NM_005228.3	844	cTg/cAg	21/28	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.307635251656818	2		300	464	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544075	18544078	+	frameshift_variant	Frame_Shift_Del	DEL	GGTG	GGTG	TGT	novel	NA	P-0065988-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	48	289	0	ENST00000266497.5:c.1892_1895delinsTGT	p.Gly631ValfsTer5	p.G631Vfs*5	ENST00000266497		631	gGGTGg/gTGTg	13/31	0.187021424036413	1	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	0	0.307635251656818	1		289	247	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292756	62292756	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065988-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	122	414	0	ENST00000360203.5:c.208C>A	p.Arg70Ser	p.R70S	ENST00000360203	NM_001283009.1	70	Cgc/Agc	3/35	0.308981762320119	3	FACETS	0.821	0.745	0.901	0.821	0.745	0.901	CLONAL	2	TRUE	1	0.307635251656818	3		414	557	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248629	59248629	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065988-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	36	380	0	ENST00000371222.2:c.114G>T	p.Met38Ile	p.M38I	ENST00000371222	NM_002228.3	38	atG/atT	1/1	NA	2	FACETS	0.399	0.327	0.48			1	INDETERMINATE	1	TRUE	NA	0.307635251656818	2		380	587	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243900	53243900	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065988-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	34	373	0	ENST00000375401.3:c.1093G>A	p.Val365Ile	p.V365I	ENST00000375401	NM_004187.3	365	Gtc/Atc	8/26	1	2	FACETS	0.509	0.416	0.614	0.509	0.416	0.614	SUBCLONAL	1	TRUE	1	0.307635251656818	2		373	434	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857716	78857716	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065988-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	43	447	0	ENST00000306801.3:c.1786G>A	p.Val596Met	p.V596M	ENST00000306801	NM_020761.2	596	Gtg/Atg	16/34	0.166929383083953	4	FACETS	0.686	0.573	0.811	0.343	0.286	0.406	INDETERMINATE	1	TRUE	2	0.307635251656818	4		447	533	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023606	1023606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065988-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	27	246	0	ENST00000358495.3:c.958G>A	p.Glu320Lys	p.E320K	ENST00000358495	NM_134424.2	320	Gaa/Aaa	10/12	0.308981762320119	3	FACETS	0.473	0.376	0.585	0.237	0.188	0.293	SUBCLONAL	1	TRUE	1	0.307635251656818	3		246	428	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530082	212530082	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065988-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	67	367	0	ENST00000342788.4:c.1837del	p.Glu613SerfsTer40	p.E613Sfs*40	ENST00000342788	NM_005235.2	613	Gag/ag	15/28	NA	2	FACETS	1	0.93	1			1	INDETERMINATE	1	TRUE	NA	0.307635251656818	2		367	396	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938311	76938311	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065988-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	19	334	0	ENST00000373344.5:c.2437G>T	p.Glu813Ter	p.E813*	ENST00000373344	NM_000489.3	813	Gag/Tag	9/35	1	2	FACETS	0.329	0.249	0.424	0.329	0.249	0.424	SUBCLONAL	1	TRUE	1	0.307635251656818	2		334	375	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0065988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	53	389	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.599	0.51	0.697	0.599	0.51	0.697	SUBCLONAL	1	FALSE	1	0.282528186202126	2		389	626	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161420	185161420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	31	230	0	ENST00000265026.3:c.847C>T	p.Pro283Ser	p.P283S	ENST00000265026	NM_004721.4	283	Cct/Tct	4/14	0.282528186202126	1	FACETS	0.41	0.331	0.499	0.41	0.331	0.499	SUBCLONAL	1	FALSE	0	0.282528186202126	1		230	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0065988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	81	334	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			1	2	FACETS	0.985	0.869	1	0.985	0.869	1	CLONAL	1	FALSE	1	0.282528186202126	2		334	582	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058013	27058013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	50	390	0	ENST00000324856.7:c.1721C>T	p.Ser574Phe	p.S574F	ENST00000324856	NM_006015.4	574	tCc/tTc	3/20	1	2	FACETS	0.591	0.501	0.69	0.591	0.501	0.69	SUBCLONAL	1	FALSE	1	0.282528186202126	2		390	599	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845583	128845583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764495218	NA	P-0065988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	29	427	0	ENST00000249373.3:c.880G>A	p.Val294Ile	p.V294I	ENST00000249373	NM_005631.4	294	Gtc/Atc	4/12	1	2	FACETS	0.438	0.351	0.537	0.438	0.351	0.537	SUBCLONAL	1	FALSE	1	0.282528186202126	2		427	469	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602430	10602430	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	46	453	0	ENST00000171111.5:c.1148C>A	p.Ser383Ter	p.S383*	ENST00000171111	NM_203500.1	383	tCg/tAg	3/6	1	2	FACETS	0.604	0.508	0.71	0.604	0.508	0.71	SUBCLONAL	1	FALSE	1	0.282528186202126	2		453	539	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524927	8524927	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	34	210	0	ENST00000356435.5:c.677G>C	p.Arg226Thr	p.R226T	ENST00000356435		226	aGa/aCa	7/35	0.282528186202126	1	FACETS	0.492	0.402	0.593	0.492	0.402	0.593	SUBCLONAL	1	FALSE	0	0.282528186202126	1		210	420	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401513	401513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	24	417	0	ENST00000380956.4:c.835G>T	p.Gly279Ter	p.G279*	ENST00000380956	NM_001195286.1	279	Gga/Tga	7/9	1	2	FACETS	0.364	0.284	0.456	0.364	0.284	0.456	SUBCLONAL	1	FALSE	1	0.282528186202126	2		417	467	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31239525	31239525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs281860368	NA	P-0065988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	33	462	0	ENST00000376228.5:c.194C>T	p.Ala65Val	p.A65V	ENST00000376228	NM_002117.5	65	gCg/gTg	2/8	1	2	FACETS	0.438	0.356	0.531	0.438	0.356	0.531	SUBCLONAL	1	FALSE	1	0.282528186202126	2		462	533	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883138	37883139	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0065988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	25	378	0	ENST00000269571.5:c.3046dup	p.Asp1016GlyfsTer6	p.D1016Gfs*6	ENST00000269571		1014	atg/atGg	25/27	1	2	FACETS	0.37	0.291	0.462	0.37	0.291	0.462	SUBCLONAL	1	FALSE	1	0.282528186202126	2		378	478	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259473	55259473	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	44	300	0	ENST00000275493.2:c.2531T>A	p.Leu844Gln	p.L844Q	ENST00000275493	NM_005228.3	844	cTg/cAg	21/28	1	2	FACETS	0.589	0.493	0.695	0.589	0.493	0.695	SUBCLONAL	1	FALSE	1	0.282528186202126	2		300	529	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544075	18544078	+	frameshift_variant	Frame_Shift_Del	DEL	GGTG	GGTG	TGT	novel	NA	P-0065988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	45	289	0	ENST00000266497.5:c.1892_1895delinsTGT	p.Gly631ValfsTer5	p.G631Vfs*5	ENST00000266497		631	gGGTGg/gTGTg	13/31	0.0607211555628635	3	FACETS	0.797	0.67	0.937	0.399	0.335	0.469	INDETERMINATE	1	FALSE	1	0.282528186202126	3		289	456	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292756	62292756	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	40	414	0	ENST00000360203.5:c.208C>A	p.Arg70Ser	p.R70S	ENST00000360203	NM_001283009.1	70	Cgc/Agc	3/35	1	2	FACETS	0.522	0.433	0.622	0.522	0.433	0.622	SUBCLONAL	1	FALSE	1	0.282528186202126	2		414	542	SUCCESS
ATM	472	MSKCC	GRCh37	11	108126976	108126978	+	missense_variant	Missense_Mutation	TNP	GTC	GTC	TTT	novel	NA	P-0065988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	33	285	0	ENST00000278616.4:c.2159_2161delinsTTT	p.Arg720_Leu721delinsLeuPhe	p.R720_L721delinsLF	ENST00000278616	NM_000051.3	720	cGTCtt/cTTTtt	14/63	1	2	FACETS	0.365	0.296	0.443	0.365	0.296	0.443	SUBCLONAL	1	FALSE	1	0.282528186202126	2		285	640	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	143	797	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.310137373013655	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.510786543596418	1		797	363	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	152	287	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.510786543596418	2		287	425	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	33	405	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	0.232	0.188	0.281	0.232	0.188	0.281	SUBCLONAL	1	TRUE	1	0.510786543596418	2		405	557	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	81	305	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	0.503317391333076	3	FACETS	0.915	0.81	1	0.458	0.405	0.514	CLONAL	1	TRUE	1	0.510786543596418	3		305	435	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519922	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	342	441	0	ENST00000397062.3:c.235G>A	p.Glu79Lys	p.E79K	ENST00000397062	NM_006164.4	79	Gag/Aag	2/5	0.510786543596418	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.510786543596418	2		441	589	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	37	109	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.503317391333076	3	FACETS	1	0.952	1	0.705	0.593	0.824	CLONAL	1	TRUE	1	0.510786543596418	3		109	129	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	70	419	0	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	0.496	0.432	0.564	0.496	0.432	0.564	SUBCLONAL	1	TRUE	1	0.510786543596418	2		419	553	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	85	477	0	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.951	0.847	1	0.951	0.847	1	CLONAL	1	TRUE	1	0.510786543596418	2		477	350	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011144	12011144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	15	356	0	ENST00000353533.5:c.551C>T	p.Ser184Leu	p.S184L	ENST00000353533	NM_003010.3	184	tCg/tTg	5/11	0.503317391333076	3	FACETS	0.155	0.113	0.207	0.078	0.056	0.104	SUBCLONAL	1	TRUE	1	0.510786543596418	3		356	475	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720744	89720744	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167674	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	12	90	0	ENST00000371953.3:c.895G>T	p.Glu299Ter	p.E299*	ENST00000371953	NM_000314.4	299	Gaa/Taa	8/9	0.503317391333076	3	FACETS	0.819	0.586	1	0.41	0.293	0.547	CLONAL	1	TRUE	1	0.510786543596418	3		90	72	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007443	62007443	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	100	472	0	ENST00000392795.3:c.424C>T	p.Arg142Ter	p.R142*	ENST00000392795	NM_001039933.1	142	Cga/Tga	3/6	0.503317391333076	3	FACETS	0.772	0.69	0.858	0.386	0.345	0.429	SUBCLONAL	1	TRUE	1	0.510786543596418	3		472	637	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149799	202149799	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	127	486	0	ENST00000358485.4:c.1245del	p.Phe415LeufsTer26	p.F415Lfs*26	ENST00000358485	NM_001080125.1	414	Ttt/tt	8/9	0.510786543596418	2	FACETS	0.923	0.84	1	0.461	0.42	0.505	CLONAL	1	TRUE	0	0.510786543596418	2		486	539	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568865	212568866	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	113	331	0	ENST00000342788.4:c.1252dup	p.Ser418PhefsTer2	p.S418Ffs*2	ENST00000342788	NM_005235.2	418	tct/tTct	11/28	0.510786543596418	2	FACETS	0.975	0.883	1	0.487	0.441	0.536	CLONAL	1	TRUE	0	0.510786543596418	2		331	454	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725507	117725507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775119219	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	36	323	0	ENST00000368508.3:c.374C>T	p.Ser125Phe	p.S125F	ENST00000368508	NM_002944.2	125	tCt/tTt	5/43	1	2	FACETS	0.392	0.322	0.469	0.392	0.322	0.469	SUBCLONAL	1	TRUE	1	0.510786543596418	2		323	360	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519505	137519506	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs780346130	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	115	443	4	ENST00000367739.4:c.1132_1133del	p.Ser378PhefsTer6	p.S378Ffs*6	ENST00000367739	NM_000416.2	378	AGt/t	7/7	1	2	FACETS	0.816	0.737	0.898	0.816	0.737	0.898	CLONAL	1	TRUE	1	0.510786543596418	2		447	552	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454670	99454670	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs780247189	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	96	371	0	ENST00000268035.6:c.1589C>T	p.Ala530Val	p.A530V	ENST00000268035	NM_000875.3	530	gCa/gTa	7/21	1	2	FACETS	0.872	0.782	0.967	0.872	0.782	0.967	CLONAL	1	TRUE	1	0.510786543596418	2		371	431	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262102	10262102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	69	448	0	ENST00000340748.4:c.2189G>A	p.Arg730His	p.R730H	ENST00000340748		730	cGc/cAc	23/40	1	2	FACETS	0.436	0.38	0.498	0.436	0.38	0.498	SUBCLONAL	1	TRUE	1	0.510786543596418	2		448	619	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943380	71943380	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1394942069	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	52	433	0	ENST00000298229.2:c.1712G>A	p.Arg571Gln	p.R571Q	ENST00000298229	NM_001567.3	571	cGg/cAg	14/28	0.510786543596418	2	FACETS	0.388	0.33	0.451	0.194	0.165	0.226	SUBCLONAL	1	TRUE	0	0.510786543596418	2		433	525	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991716	72991718	+	inframe_deletion	In_Frame_Del	DEL	CCG	CCG	-	rs761186383	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	51	459	2	ENST00000268489.5:c.2327_2329del	p.Ala776del	p.A776del	ENST00000268489	NM_006885.3	776	gCGGtg/gtg	2/10	1	2	FACETS	0.377	0.32	0.439	0.377	0.32	0.439	SUBCLONAL	1	TRUE	1	0.510786543596418	2		461	530	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205089	128205089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	53	567	2	ENST00000341105.2:c.352G>A	p.Val118Met	p.V118M	ENST00000341105	NM_032638.4	118	Gtg/Atg	3/6	1	2	FACETS	0.375	0.32	0.436	0.375	0.32	0.436	SUBCLONAL	1	TRUE	1	0.510786543596418	2		569	553	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214871	36214871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	38	405	1	ENST00000222270.7:c.3302del	p.Pro1101LeufsTer81	p.P1101Lfs*81	ENST00000222270	NM_014727.1	1099	ggC/gg	8/37	1	2	FACETS	0.348	0.288	0.416	0.348	0.288	0.416	SUBCLONAL	1	TRUE	1	0.510786543596418	2		406	427	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944121	71944123	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	43	487	0	ENST00000298229.2:c.1960_1962del	p.Glu654del	p.E654del	ENST00000298229	NM_001567.3	652	GAG/-	17/28	0.510786543596418	2	FACETS	0.342	0.285	0.404	0.171	0.142	0.202	SUBCLONAL	1	TRUE	0	0.510786543596418	2		487	493	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139440210	139440210	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	130	624	0	ENST00000277541.6:c.29G>A	p.Cys10Tyr	p.C10Y	ENST00000277541	NM_017617.3	10	tGc/tAc	1/34	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.510786543596418	2		624	469	SUCCESS
BTK	695	MSKCC	GRCh37	X	100629549	100629549	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	107	386	1	ENST00000308731.7:c.215del	p.Asn72IlefsTer49	p.N72Ifs*49	ENST00000308731	NM_000061.2	72	aAt/at	3/19	0.310137373013655	1	FACETS	0.66	0.595	0.728	0.66	0.595	0.728	SUBCLONAL	1	TRUE	0	0.510786543596418	1		387	473	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660879	227660879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756434990	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	91	541	0	ENST00000305123.5:c.2576C>T	p.Thr859Met	p.T859M	ENST00000305123	NM_005544.2	859	aCg/aTg	1/2	0.510786543596418	2	FACETS	0.838	0.749	0.933	0.419	0.374	0.467	CLONAL	1	TRUE	0	0.510786543596418	2		541	425	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930154	68930154	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	41	334	1	ENST00000288368.4:c.213+2T>C		p.X71_splice	ENST00000288368	NM_024870.2	71			0.504320147467428	4	FACETS	0.337	0.28	0.401	0.084	0.07	0.101	SUBCLONAL	1	TRUE	0	0.510786543596418	4		335	719	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435129	110435129	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	45	497	3	ENST00000375856.3:c.3272del	p.Pro1091ArgfsTer15	p.P1091Rfs*15	ENST00000375856	NM_003749.2	1091	cCg/cg	1/2	1	2	FACETS	0.384	0.323	0.452	0.384	0.323	0.452	SUBCLONAL	1	TRUE	1	0.510786543596418	2		500	459	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088658	27088659	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	122	381	0	ENST00000324856.7:c.2272dup	p.Gln758ProfsTer59	p.Q758Pfs*59	ENST00000324856	NM_006015.4	756	aac/aaCc	7/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.510786543596418	2		381	432	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214714	36214714	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	36	439	0	ENST00000222270.7:c.3145del	p.Ala1049ArgfsTer133	p.A1049Rfs*133	ENST00000222270	NM_014727.1	1047	cGg/cg	8/37	1	2	FACETS	0.396	0.326	0.474	0.396	0.326	0.474	SUBCLONAL	1	TRUE	1	0.510786543596418	2		439	356	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211549	36211549	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	20	319	0	ENST00000222270.7:c.1304del	p.Pro435GlnfsTer40	p.P435Qfs*40	ENST00000222270	NM_014727.1	434	Ccc/cc	3/37	1	2	FACETS	0.282	0.215	0.359	0.282	0.215	0.359	SUBCLONAL	1	TRUE	1	0.510786543596418	2		319	278	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270105	66270105	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	109	347	0	ENST00000273854.3:c.1777C>A	p.Leu593Ile	p.L593I	ENST00000273854	NM_004439.5	593	Ctc/Atc	8/18	1	2	FACETS	0.878	0.793	0.968	0.878	0.793	0.968	CLONAL	1	TRUE	1	0.510786543596418	2		347	486	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347873	128347873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	85	390	0	ENST00000265960.3:c.632G>A	p.Cys211Tyr	p.C211Y	ENST00000265960	NM_001006617.1	211	tGc/tAc	5/12	1	2	FACETS	0.792	0.704	0.886	0.792	0.704	0.886	SUBCLONAL	1	TRUE	1	0.510786543596418	2		390	420	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251712	212251712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	97	533	0	ENST00000342788.4:c.3347C>T	p.Ala1116Val	p.A1116V	ENST00000342788	NM_005235.2	1116	gCa/gTa	27/28	0.510786543596418	2	FACETS	0.692	0.618	0.769	0.346	0.309	0.385	SUBCLONAL	1	TRUE	0	0.510786543596418	2		533	549	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075278	16075278	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	120	353	0	ENST00000268712.3:c.274T>C	p.Phe92Leu	p.F92L	ENST00000268712	NM_006311.3	92	Ttt/Ctt	4/46	0.503317391333076	3	FACETS	0.864	0.781	0.951	0.432	0.39	0.476	CLONAL	1	TRUE	1	0.510786543596418	3		353	683	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47599086	47599086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148905856	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	151	449	0	ENST00000430070.2:c.514C>T	p.Arg172Trp	p.R172W	ENST00000430070	NM_018095.4	172	Cgg/Tgg	2/4	0.510786543596418	2	FACETS	1	0.94	1	0.514	0.472	0.558	CLONAL	1	TRUE	0	0.510786543596418	2		449	575	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508785	148508785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	52	361	0	ENST00000320356.2:c.1879G>A	p.Ala627Thr	p.A627T	ENST00000320356	NM_004456.4	627	Gca/Aca	16/20	1	2	FACETS	0.406	0.346	0.473	0.406	0.346	0.473	SUBCLONAL	1	TRUE	1	0.510786543596418	2		361	501	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150915445	150915445	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	134	368	0	ENST00000271640.5:c.791T>C	p.Val264Ala	p.V264A	ENST00000271640	NM_001145415.1	264	gTg/gCg	7/22	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.510786543596418	2		368	461	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196903	108196903	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	58	368	0	ENST00000278616.4:c.6926T>C	p.Leu2309Pro	p.L2309P	ENST00000278616	NM_000051.3	2309	cTg/cCg	47/63	0.510786543596418	2	FACETS	0.439	0.378	0.506	0.22	0.188	0.253	SUBCLONAL	1	TRUE	0	0.510786543596418	2		368	517	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950285	38950285	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	35	414	0	ENST00000357387.3:c.3665del	p.Thr1222LysfsTer8	p.T1222Kfs*8	ENST00000357387	NM_152756.3	1222	aCa/aa	31/38	1	2	FACETS	0.252	0.206	0.304	0.252	0.206	0.304	SUBCLONAL	1	TRUE	1	0.510786543596418	2		414	544	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319439	11319439	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs368184120	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	91	472	0	ENST00000361445.4:c.28A>G	p.Thr10Ala	p.T10A	ENST00000361445	NM_004958.3	10	Acc/Gcc	2/58	1	2	FACETS	0.631	0.561	0.705	0.631	0.561	0.705	SUBCLONAL	1	TRUE	1	0.510786543596418	2		472	565	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857449	68857449	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	174	412	0	ENST00000261769.5:c.2084G>C	p.Cys695Ser	p.C695S	ENST00000261769	NM_004360.3	695	tGt/tCt	13/16	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.510786543596418	2		412	500	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940225	49940225	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	54	501	0	ENST00000296474.3:c.818C>A	p.Pro273His	p.P273H	ENST00000296474	NM_002447.2	273	cCt/cAt	1/20	1	2	FACETS	0.367	0.313	0.426	0.367	0.313	0.426	SUBCLONAL	1	TRUE	1	0.510786543596418	2		501	576	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214717	133214717	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	39	382	0	ENST00000320574.5:c.5561C>T	p.Ala1854Val	p.A1854V	ENST00000320574	NM_006231.2	1854	gCt/gTt	41/49	1	2	FACETS	0.293	0.242	0.349	0.293	0.242	0.349	SUBCLONAL	1	TRUE	1	0.510786543596418	2		382	522	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005566	42005566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	161	491	0	ENST00000219905.7:c.3302G>A	p.Arg1101Lys	p.R1101K	ENST00000219905	NM_001164273.1	1101	aGg/aAg	9/24	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.510786543596418	2		491	625	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561129	9561129	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	52	464	0	ENST00000353224.5:c.653A>C	p.Glu218Ala	p.E218A	ENST00000353224	NM_177990.2	218	gAg/gCg	4/10	0.503317391333076	3	FACETS	0.438	0.372	0.51	0.219	0.186	0.255	SUBCLONAL	1	TRUE	1	0.510786543596418	3		464	584	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544975	86544975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370401697	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	51	420	0	ENST00000262426.4:c.800C>T	p.Ala267Val	p.A267V	ENST00000262426	NM_001451.2	267	gCg/gTg	1/2	1	2	FACETS	0.558	0.476	0.647	0.558	0.476	0.647	SUBCLONAL	1	TRUE	1	0.510786543596418	2		420	358	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230893	53230893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	113	405	0	ENST00000375401.3:c.1900C>T	p.Arg634Cys	p.R634C	ENST00000375401	NM_004187.3	634	Cgc/Tgc	14/26	0.310137373013655	1	FACETS	0.716	0.648	0.787	0.716	0.648	0.787	SUBCLONAL	1	TRUE	0	0.510786543596418	1		405	460	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510654	38510654	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	101	429	0	ENST00000254066.5:c.908G>A	p.Gly303Asp	p.G303D	ENST00000254066	NM_000964.3	303	gGc/gAc	7/9	0.503317391333076	3	FACETS	0.899	0.806	0.998	0.45	0.403	0.499	CLONAL	1	TRUE	1	0.510786543596418	3		429	552	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156848967	156848967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	43	499	0	ENST00000524377.1:c.1859G>A	p.Gly620Asp	p.G620D	ENST00000524377	NM_002529.3	620	gGc/gAc	15/17	1	2	FACETS	0.335	0.28	0.396	0.335	0.28	0.396	SUBCLONAL	1	TRUE	1	0.510786543596418	2		499	502	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525515	137525515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	99	350	0	ENST00000367739.4:c.500G>A	p.Cys167Tyr	p.C167Y	ENST00000367739	NM_000416.2	167	tGt/tAt	4/7	1	2	FACETS	0.834	0.748	0.924	0.834	0.748	0.924	CLONAL	1	TRUE	1	0.510786543596418	2		350	465	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046764	42046764	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	134	362	1	ENST00000219905.7:c.7138C>T	p.Pro2380Ser	p.P2380S	ENST00000219905	NM_001164273.1	2380	Ccg/Tcg	18/24	1	2	FACETS	0.885	0.807	0.966	0.885	0.807	0.966	CLONAL	1	TRUE	1	0.510786543596418	2		363	593	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139227	37139227	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767784431	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	97	452	0	ENST00000373509.5:c.571del	p.Ala191ArgfsTer83	p.A191Rfs*83	ENST00000373509	NM_002648.3	189	tcG/tc	4/6	1	2	FACETS	0.808	0.724	0.897	0.808	0.724	0.897	CLONAL	1	TRUE	1	0.510786543596418	2		452	470	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383209	42383209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	159	510	0	ENST00000221972.3:c.233del	p.Pro78LeufsTer14	p.P78Lfs*14	ENST00000221972	NM_021601.3	77	Ccc/cc	2/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.510786543596418	2		510	540	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064724	80064724	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs763245421	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	40	400	0	ENST00000265081.6:c.2155A>T	p.Ile719Phe	p.I719F	ENST00000265081	NM_002439.4	719	Att/Ttt	15/24	1	2	FACETS	0.401	0.333	0.475	0.401	0.333	0.475	SUBCLONAL	1	TRUE	1	0.510786543596418	2		400	391	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114799783	114799783	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	85	209	0	ENST00000543371.1:c.451-1G>A		p.X151_splice	ENST00000543371	NM_001198531.1	151			0.503317391333076	3	FACETS	1	0.942	1	0.545	0.485	0.609	CLONAL	1	TRUE	1	0.510786543596418	3		209	383	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975474	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	122	503	0	ENST00000405192.2:c.413_414insA	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	ccc/ccAc	7/12	1	2	FACETS	0.928	0.843	1	0.928	0.843	1	CLONAL	1	TRUE	1	0.510786543596418	2		503	515	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0065990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	33	311	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.247571468968174	2		311	180	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519975	NA	P-0065990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	57	497	0	ENST00000269305.4:c.403T>C	p.Cys135Arg	p.C135R	ENST00000269305	NM_001126112.2	135	Tgc/Cgc	5/11	0.247571468968174	1	FACETS	0.989	0.851	1	0.989	0.851	1	CLONAL	1	TRUE	0	0.247571468968174	1		497	408	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591806	48591806	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	31	443	0	ENST00000342988.3:c.969G>A	p.Trp323Ter	p.W323*	ENST00000342988	NM_005359.5	323	tgG/tgA	9/12	0.229537140056985	1	FACETS	0.975	0.794	1	0.975	0.794	1	CLONAL	1	TRUE	0	0.247571468968174	1		443	225	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438248	56438249	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTAA	novel	NA	P-0065990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	32	454	0	ENST00000407977.2:c.744_745insTTAC	p.Gln249LeufsTer11	p.Q249Lfs*11	ENST00000407977		248	-/TTAC	7/10	0.229537140056985	1	FACETS	0.676	0.55	0.818	0.676	0.55	0.818	SUBCLONAL	1	TRUE	0	0.247571468968174	1		454	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0065991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	214	380	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.486206680614283	2	FACETS	0.961	0.904	1	0.961	0.904	1	CLONAL	2	TRUE	0	0.486206680614283	2		380	458	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094450	27094450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779484265	NA	P-0065991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	30	477	1	ENST00000324856.7:c.3158G>A	p.Arg1053His	p.R1053H	ENST00000324856	NM_006015.4	1053	cGc/cAc	11/20	0.168063897867823	3	FACETS	0.293	0.236	0.359	0.147	0.118	0.18	INDETERMINATE	1	TRUE	1	0.486206680614283	3		478	523	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216188	36216188	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs756135109	NA	P-0065991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	190	554	0	ENST00000222270.7:c.3596G>T	p.Gly1199Val	p.G1199V	ENST00000222270	NM_014727.1	1199	gGc/gTc	11/37	0.13403947302107	6	FACETS	1	0.964	1	0.709	0.657	0.762	INDETERMINATE	2	TRUE	3	0.486206680614283	6		554	725	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0065994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	156	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.446867349606355	4	FACETS	0.958	0.891	1	0.958	0.891	1	CLONAL	3	TRUE	1	0.473423169833235	4		341	338	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0065994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	54	254	1	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.473423169833235	2		255	190	SUCCESS
APC	324	MSKCC	GRCh37	5	112174096	112174096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs137854575	NA	P-0065994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	89	478	0	ENST00000257430.4:c.2805C>A	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	taC/taA	16/16	1	2	FACETS	0.913	0.814	1	0.913	0.814	1	CLONAL	1	TRUE	1	0.473423169833235	2		478	412	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0065994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	158	389	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	0.473423169833235	2	FACETS	0.954	0.887	1	0.954	0.887	1	CLONAL	2	TRUE	0	0.473423169833235	2		389	350	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482760	67482761	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0065994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	73	361	0	ENST00000327367.4:c.1166_1167del	p.Val389AspfsTer8	p.V389Dfs*8	ENST00000327367	NM_005902.3	388	acTGtg/actg	9/9	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.473423169833235	2		361	303	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932171	39932171	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555918056	NA	P-0065994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	172	281	1	ENST00000378444.4:c.2428C>T	p.Arg810Ter	p.R810*	ENST00000378444	NM_001123385.1	810	Cga/Tga	4/15	0.473423169833235	2	FACETS	0.859	0.81	0.907			1	CLONAL	3	TRUE	NA	0.473423169833235	2		282	282	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979317	93979317	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs267601170	NA	P-0065994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	127	431	0	ENST00000369303.4:c.1511A>T	p.Asn504Ile	p.N504I	ENST00000369303	NM_004440.3	504	aAt/aTt	7/17	0.301226760786194	2	FACETS	0.874	0.804	0.945	0.874	0.804	0.945	CLONAL	2	TRUE	0	0.473423169833235	2		431	307	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275240	41275240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	46	522	0	ENST00000349496.5:c.1406G>A	p.Arg469His	p.R469H	ENST00000349496	NM_001904.3	469	cGt/cAt	9/15	1	2	FACETS	0.45	0.379	0.528	0.45	0.379	0.528	SUBCLONAL	1	TRUE	1	0.473423169833235	2		522	432	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358653	67358659	+	frameshift_variant	Frame_Shift_Del	DEL	CCATCAC	CCATCAC	-	novel	NA	P-0065994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	68	472	0	ENST00000327367.4:c.162_168del	p.Ile55ArgfsTer59	p.I55Rfs*59	ENST00000327367	NM_005902.3	54	gCCATCACc/gc	1/9	1	2	FACETS	0.964	0.846	1	0.964	0.846	1	CLONAL	1	TRUE	1	0.473423169833235	2		472	298	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516852	187516852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776855582	NA	P-0065994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	99	429	0	ENST00000441802.2:c.13129G>A	p.Asp4377Asn	p.D4377N	ENST00000441802	NM_005245.3	4377	Gat/Aat	26/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.473423169833235	2		429	318	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500456	99500456	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	31	605	1	ENST00000268035.6:c.3889C>G	p.Pro1297Ala	p.P1297A	ENST00000268035	NM_000875.3	1297	Cca/Gca	21/21	1	2	FACETS	0.363	0.293	0.441	0.363	0.293	0.441	SUBCLONAL	1	TRUE	1	0.473423169833235	2		606	361	SUCCESS
APC	324	MSKCC	GRCh37	5	112175573	112175573	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	116	568	0	ENST00000257430.4:c.4282G>T	p.Gly1428Ter	p.G1428*	ENST00000257430	NM_000038.5	1428	Gga/Tga	16/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.473423169833235	2		568	384	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0065995-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	121	810	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.198435416894968	5	FACETS	0.86	0.783	0.941	0.86	0.783	0.941	CLONAL	3	TRUE	2	0.314278860637793	5		810	439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0065995-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	171	574	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.290577948638417	2	FACETS	0.997	0.923	1	0.997	0.923	1	CLONAL	2	TRUE	0	0.314278860637793	2		574	546	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523665	148523665	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065995-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	51	374	0	ENST00000320356.2:c.788A>G	p.Asn263Ser	p.N263S	ENST00000320356	NM_004456.4	263	aAc/aGc	8/20	1	2	FACETS	0.996	0.851	1	0.996	0.851	1	CLONAL	1	TRUE	1	0.314278860637793	2		374	326	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023148	27023162	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCGGAGCCGGCA	GCGGCGGAGCCGGCA	CCGCCGCC	novel	NA	P-0065995-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	88	451	1	ENST00000324856.7:c.254_268delinsCCGCCGCC	p.Gly85AlafsTer14	p.G85Afs*14	ENST00000324856	NM_006015.4	85	gGCGGCGGAGCCGGCAgc/gCCGCCGCCgc	1/20	0.314278860637793	3	FACETS	1	0.979	1	0.74	0.659	0.826	CLONAL	1	TRUE	1	0.314278860637793	3		452	438	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	91	446	0				ENST00000310581	NM_198253.2	-/1132			0.621605174532774	3	FACETS	1	0.975	1	0.644	0.579	0.712	CLONAL	1	TRUE	1	0.621605174532774	3		446	298	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653796	89653798	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs1554893765	NA	P-0065996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	76	438	0	ENST00000371953.3:c.97_99del	p.Ile33del	p.I33del	ENST00000371953	NM_000314.4	32	ATT/-	2/9	0.602472864864408	2	FACETS	0.899	0.817	0.979	0.899	0.817	0.979	CLONAL	2	TRUE	0	0.621605174532774	2		438	136	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926872	112926872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507541	NA	P-0065996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	28	852	2	ENST00000351677.2:c.1492C>T	p.Arg498Trp	p.R498W	ENST00000351677	NM_002834.3	498	Cgg/Tgg	13/16	1	2	FACETS	0.25	0.199	0.307	0.25	0.199	0.307	SUBCLONAL	1	TRUE	1	0.621605174532774	2		854	361	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289986	15289986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377099118	NA	P-0065996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	146	1456	3	ENST00000263388.2:c.3568C>T	p.Arg1190Cys	p.R1190C	ENST00000263388	NM_000435.2	1190	Cgc/Tgc	22/33	0.613363057166636	3	FACETS	0.856	0.783	0.933	0.428	0.391	0.467	CLONAL	1	TRUE	1	0.621605174532774	3		1459	719	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586056	29586057	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0065996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	85	417	1	ENST00000356175.3:c.4276_4277del	p.Gln1426GlufsTer19	p.Q1426Efs*19	ENST00000356175	NM_000267.3	1426	CAg/g	32/57	0.621605174532774	3	FACETS	0.905	0.835	0.973	0.905	0.835	0.973	CLONAL	3	TRUE	0	0.621605174532774	3		418	132	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230561649	230561649	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0065996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	142	1255	1				ENST00000391860	NM_001258311.1	-/409			1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.621605174532774	2		1256	343	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719814	52719814	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	141	947	0	ENST00000322088.6:c.1026G>T	p.Lys342Asn	p.K342N	ENST00000322088	NM_014225.5	342	aaG/aaT	9/15	0.613363057166636	3	FACETS	1	0.941	1	0.518	0.474	0.564	CLONAL	1	TRUE	1	0.621605174532774	3		947	574	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934874	NA	P-0065997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	105	488	0	ENST00000269305.4:c.451C>A	p.Pro151Thr	p.P151T	ENST00000269305	NM_001126112.2	151	Ccc/Acc	5/11	0.268544644097475	4	FACETS	0.996	0.903	1	1	0.984	1	CLONAL	3	TRUE	2	0.268544644097475	4		488	332	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742679	39742679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	49	425	0	ENST00000361337.2:c.1522C>T	p.Arg508Cys	p.R508C	ENST00000361337	NM_003286.2	508	Cgt/Tgt	15/21	0.145898659003985	5	FACETS	1	0.961	1			1	INDETERMINATE	1	TRUE	NA	0.268544644097475	5		425	350	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30102089	30102089	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	13	333	0	ENST00000331968.5:c.1378A>C	p.Ser460Arg	p.S460R	ENST00000331968	NM_002742.2	460	Agc/Cgc	9/18	0.25714083007871	2	FACETS	0.733	0.527	0.982	0.367	0.263	0.491	CLONAL	1	TRUE	0	0.268544644097475	2		333	132	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097790	27097790	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	71	481	0	ENST00000324856.7:c.3379C>T	p.Gln1127Ter	p.Q1127*	ENST00000324856	NM_006015.4	1127	Cag/Tag	12/20	0.268544644097475	8	FACETS	1	0.945	1			1	CLONAL	2	TRUE	NA	0.268544644097475	8		481	418	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032525	12032525	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	23	243	0	ENST00000353533.5:c.961del	p.Val321Ter	p.V321*	ENST00000353533	NM_003010.3	321	Gtg/tg	9/11	0.151108770260928	0	FACETS	1	0.896	1			1	INDETERMINATE	1	TRUE	0	0.268544644097475	0		243	102	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342693	87342693	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	30	385	0	ENST00000277120.3:c.978G>T	p.Glu326Asp	p.E326D	ENST00000277120		326	gaG/gaT	9/19	0.242128817032295	1	FACETS	0.875	0.71	1	0.875	0.71	1	CLONAL	1	TRUE	0	0.268544644097475	1		385	221	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264281	30264281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	35	234	0	ENST00000322652.5:c.16C>T	p.His6Tyr	p.H6Y	ENST00000322652	NM_015355.2	6	Cac/Tac	1/16	0.251614936998302	4	FACETS	1	0.884	1	0.54	0.449	0.639	CLONAL	2	TRUE	0	0.268544644097475	4		234	153	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226566850	226566850	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	26	389	0	ENST00000366794.5:c.1738G>C	p.Glu580Gln	p.E580Q	ENST00000366794	NM_001618.3	580	Gaa/Caa	12/23	0.268544644097475	4	FACETS	0.787	0.624	0.973	0.394	0.312	0.487	CLONAL	1	TRUE	2	0.268544644097475	4		389	312	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066012-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	118	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.939	1	1	0.99	1	CLONAL	2	FALSE	1	0.232269128845142	2		341	486	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230492905	230492905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs534656022	NA	P-0066012-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	184	715	0	ENST00000391860.1:c.149C>T	p.Thr50Met	p.T50M	ENST00000391860	NM_001258311.1	50	aCg/aTg	2/7	0.232269128845142	0	FACETS	1	0.948	1			1	CLONAL	2	FALSE	0	0.232269128845142	0		715	593	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440757	56440757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774211426	NA	P-0066012-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	222	727	0	ENST00000407977.2:c.461C>T	p.Pro154Leu	p.P154L	ENST00000407977		154	cCg/cTg	5/10	1	2	FACETS	1	0.978	1	1	0.995	1	CLONAL	2	FALSE	1	0.232269128845142	2		727	860	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586262	48586262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658694	NA	P-0066012-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	101	443	0	ENST00000342988.3:c.931C>T	p.Gln311Ter	p.Q311*	ENST00000342988	NM_005359.5	311	Cag/Tag	8/12	0.232269128845142	0	FACETS	0.951	0.859	1			1	CLONAL	2	FALSE	0	0.232269128845142	0		443	351	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817414	39817414	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542019196	NA	P-0066012-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	118	671	0	ENST00000288319.7:c.149G>A	p.Arg50His	p.R50H	ENST00000288319	NM_182918.3	50	cGc/cAc	2/10	0.232269128845142	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	0	0.232269128845142	1		671	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576856	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066012-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	219	703	0	ENST00000269305.4:c.990_991insA	p.Gln331ThrfsTer6	p.Q331Tfs*6	ENST00000269305	NM_001126112.2	330	-/A	9/11	0.232269128845142	0	FACETS	0.76	0.711	0.81			1	SUBCLONAL	3	FALSE	0	0.232269128845142	0		703	635	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262382	46262382	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0066012-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	159	568	0	ENST00000371998.3:c.964+2T>C		p.X322_splice	ENST00000371998		322			1	2	FACETS	1	0.967	1	1	0.992	1	CLONAL	2	FALSE	1	0.232269128845142	2		568	624	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973799	131973799	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066012-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	133	474	0	ENST00000265335.6:c.3502G>C	p.Asp1168His	p.D1168H	ENST00000265335		1168	Gat/Cat	23/25	1	2	FACETS	0.986	0.899	1	1	0.99	1	CLONAL	2	FALSE	1	0.232269128845142	2		474	581	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	180	710	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.597	0.552	0.643	0.597	0.552	0.643	SUBCLONAL	1	TRUE	1	0.868070799066635	2		713	695	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	127	582	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.525	0.478	0.575	0.525	0.478	0.575	SUBCLONAL	1	TRUE	1	0.868070799066635	2		582	557	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	62	435	0	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	0.205	0.177	0.236	0.205	0.177	0.236	SUBCLONAL	1	TRUE	1	0.868070799066635	2		435	696	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	138	455	4	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.501	0.457	0.547	0.501	0.457	0.547	SUBCLONAL	1	TRUE	1	0.868070799066635	2		459	635	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	90	501	0	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.335	0.297	0.375	0.335	0.297	0.375	SUBCLONAL	1	TRUE	1	0.868070799066635	2		501	619	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	141	455	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.552	0.505	0.602	0.552	0.505	0.602	SUBCLONAL	1	TRUE	1	0.868070799066635	2		455	588	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101401	27101402	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	58	255	0	ENST00000324856.7:c.4689dup	p.Met1564HisfsTer8	p.M1564Hfs*8	ENST00000324856	NM_006015.4	1561	-/C	18/20	1	2	FACETS	0.431	0.373	0.494	0.431	0.373	0.494	SUBCLONAL	1	TRUE	1	0.868070799066635	2		255	310	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263974	104263974	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776579	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	90	334	0	ENST00000369902.3:c.71del	p.Pro24ArgfsTer72	p.P24Rfs*72	ENST00000369902	NM_016169.3	22	gCc/gc	1/12	1	2	FACETS	0.525	0.469	0.584	0.525	0.469	0.584	SUBCLONAL	1	TRUE	1	0.868070799066635	2		334	395	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900984	114900984	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778855667	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	160	500	0	ENST00000543371.1:c.598del	p.Leu200SerfsTer25	p.L200Sfs*25	ENST00000543371	NM_001198531.1	198	caC/ca	6/14	1	2	FACETS	0.537	0.494	0.582	0.537	0.494	0.582	SUBCLONAL	1	TRUE	1	0.868070799066635	2		500	686	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	23	335	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	0.22	0.172	0.275	0.22	0.172	0.275	SUBCLONAL	1	TRUE	1	0.868070799066635	2		335	241	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495715	56495715	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	86	445	0	ENST00000267101.3:c.3910del	p.His1304MetfsTer7	p.H1304Mfs*7	ENST00000267101	NM_001982.3	1302	gCc/gc	28/28	1	2	FACETS	0.388	0.344	0.435	0.388	0.344	0.435	SUBCLONAL	1	TRUE	1	0.868070799066635	2		445	511	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112884105	112884105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	85	215	0	ENST00000351677.2:c.40G>A	p.Val14Met	p.V14M	ENST00000351677	NM_002834.3	14	Gtg/Atg	2/16	1	2	FACETS	0.519	0.462	0.58	0.519	0.462	0.58	SUBCLONAL	1	TRUE	1	0.868070799066635	2		215	377	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800902	120800903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748469666	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	113	397	1	ENST00000257552.2:c.345dup	p.Leu116AlafsTer15	p.L116Afs*15	ENST00000257552	NM_002442.3	115	-/G	6/15	1	2	FACETS	0.439	0.396	0.484	0.439	0.396	0.484	SUBCLONAL	1	TRUE	1	0.868070799066635	2		398	593	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913837	32913837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359507	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	84	328	2	ENST00000380152.3:c.5351del	p.Asn1784ThrfsTer7	p.N1784Tfs*7	ENST00000380152		1782	cAa/ca	11/27	1	2	FACETS	0.508	0.451	0.568	0.508	0.451	0.568	SUBCLONAL	1	TRUE	1	0.868070799066635	2		330	381	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43733757	43733757	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	115	312	0	ENST00000382044.4:c.3065del	p.Asn1022MetfsTer20	p.N1022Mfs*20	ENST00000382044	NM_001141980.1	1022	aAt/at	15/28	1	2	FACETS	0.535	0.484	0.588	0.535	0.484	0.588	SUBCLONAL	1	TRUE	1	0.868070799066635	2		312	495	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1023835002	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	42	619	0	ENST00000558401.1:c.1A>G	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Gtg	1/4	1	2	FACETS	0.172	0.143	0.204	0.172	0.143	0.204	SUBCLONAL	1	TRUE	1	0.868070799066635	2		619	562	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	112	449	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	1	2	FACETS	0.465	0.419	0.513	0.465	0.419	0.513	SUBCLONAL	1	TRUE	1	0.868070799066635	2		449	555	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007619	45007619	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs111482205	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	60	402	0	ENST00000558401.1:c.68-2A>G		p.X23_splice	ENST00000558401	NM_004048.2	23			1	2	FACETS	0.266	0.229	0.306	0.266	0.229	0.306	SUBCLONAL	1	TRUE	1	0.868070799066635	2		402	520	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727483	66727483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504317	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	111	399	0	ENST00000307102.5:c.199G>A	p.Asp67Asn	p.D67N	ENST00000307102	NM_002755.3	67	Gac/Aac	2/11	1	2	FACETS	0.421	0.379	0.465	0.421	0.379	0.465	SUBCLONAL	1	TRUE	1	0.868070799066635	2		399	608	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858356	9858356	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	112	452	0	ENST00000330684.3:c.3045G>T	p.Lys1015Asn	p.K1015N	ENST00000330684	NM_001134407.1	1015	aaG/aaT	13/13	1	2	FACETS	0.46	0.415	0.507	0.46	0.415	0.507	SUBCLONAL	1	TRUE	1	0.868070799066635	2		452	561	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646981	23646981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	69	444	2	ENST00000261584.4:c.886del	p.Met296Ter	p.M296*	ENST00000261584	NM_024675.3	296	Atg/tg	4/13	1	2	FACETS	0.259	0.225	0.295	0.259	0.225	0.295	SUBCLONAL	1	TRUE	1	0.868070799066635	2		446	614	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	61	563	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.193	0.166	0.222	0.193	0.166	0.222	SUBCLONAL	1	TRUE	1	0.868070799066635	2		563	729	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855967	68855967	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	165	450	0	ENST00000261769.5:c.1779del	p.Ile594TyrfsTer19	p.I594Yfs*19	ENST00000261769	NM_004360.3	592	gCc/gc	12/16	1	2	FACETS	0.657	0.606	0.709	0.657	0.606	0.709	SUBCLONAL	1	TRUE	1	0.868070799066635	2		450	579	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	127	424	0	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	1	2	FACETS	0.495	0.45	0.542	0.495	0.45	0.542	SUBCLONAL	1	TRUE	1	0.868070799066635	2		424	591	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214594	5214594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768496731	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	142	502	0	ENST00000357368.4:c.4472C>T	p.Thr1491Met	p.T1491M	ENST00000357368	NM_002850.3	1491	aCg/aTg	29/38	1	2	FACETS	0.529	0.483	0.576	0.529	0.483	0.576	SUBCLONAL	1	TRUE	1	0.868070799066635	2		502	619	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	127	855	2	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	0.863399366628745	3	FACETS	0.43	0.389	0.473	0.215	0.194	0.237	SUBCLONAL	1	TRUE	1	0.868070799066635	3		857	976	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47503775	47503775	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	433	468	1	ENST00000404338.3:c.4335del	p.Gly1446AlafsTer353	p.G1446Afs*353	ENST00000404338	NM_004491.4	1444	Ccc/cc	6/6	0.863399366628745	3	FACETS	0.792	0.759	0.825	0.792	0.759	0.825	SUBCLONAL	2	TRUE	1	0.868070799066635	3		469	903	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812260	212812260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751175543	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	95	404	1	ENST00000342788.4:c.316C>T	p.Arg106Cys	p.R106C	ENST00000342788	NM_005235.2	106	Cgt/Tgt	3/28	1	2	FACETS	0.468	0.418	0.52	0.468	0.418	0.52	SUBCLONAL	1	TRUE	1	0.868070799066635	2		405	468	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019143	31019144	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	130	382	0	ENST00000375687.4:c.742dup	p.Glu248GlyfsTer6	p.E248Gfs*6	ENST00000375687	NM_015338.5	246	-/G	9/13	1	2	FACETS	0.485	0.441	0.531	0.485	0.441	0.531	SUBCLONAL	1	TRUE	1	0.868070799066635	2		382	618	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39772519	39772519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	134	447	1	ENST00000288319.7:c.722C>T	p.Thr241Met	p.T241M	ENST00000288319	NM_182918.3	241	aCg/aTg	6/10	1	2	FACETS	0.522	0.475	0.57	0.522	0.475	0.57	SUBCLONAL	1	TRUE	1	0.868070799066635	2		448	592	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574223	41574223	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1419903766	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	87	543	0	ENST00000263253.7:c.6508A>G	p.Met2170Val	p.M2170V	ENST00000263253	NM_001429.3	2170	Atg/Gtg	31/31	1	2	FACETS	0.302	0.267	0.339	0.302	0.267	0.339	SUBCLONAL	1	TRUE	1	0.868070799066635	2		543	664	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	175	419	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	0.440739369453234	2	FACETS	0.615	0.568	0.663	0.307	0.284	0.332	INDETERMINATE	1	TRUE	0	0.868070799066635	2		419	656	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37045935	37045935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750781	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	238	383	0	ENST00000231790.2:c.350C>T	p.Thr117Met	p.T117M	ENST00000231790	NM_000249.3	117	aCg/aTg	4/19	0.440739369453234	2	FACETS	1	0.952	1	0.506	0.477	0.535	INDETERMINATE	1	TRUE	0	0.868070799066635	2		383	542	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	295	377	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.440739369453234	2	FACETS	1	0.971	1	0.517	0.491	0.544	INDETERMINATE	1	TRUE	0	0.868070799066635	2		377	657	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165968	47165968	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	46	440	0	ENST00000409792.3:c.158G>T	p.Arg53Leu	p.R53L	ENST00000409792	NM_014159.6	53	cGa/cTa	3/21	0.440739369453234	2	FACETS	0.172	0.145	0.203	0.086	0.072	0.102	INDETERMINATE	1	TRUE	0	0.868070799066635	2		440	615	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	49	446	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.245	0.207	0.286	0.245	0.207	0.286	SUBCLONAL	1	TRUE	1	0.868070799066635	2		446	461	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916957	178916957	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200018596	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	80	324	0	ENST00000263967.3:c.344G>T	p.Arg115Leu	p.R115L	ENST00000263967	NM_006218.2	115	cGa/cTa	2/21	1	2	FACETS	0.476	0.422	0.534	0.476	0.422	0.534	SUBCLONAL	1	TRUE	1	0.868070799066635	2		324	387	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	54	400	0	ENST00000263967.3:c.3012G>T	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atT	21/21	1	2	FACETS	0.241	0.205	0.279	0.241	0.205	0.279	SUBCLONAL	1	TRUE	1	0.868070799066635	2		400	517	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467373	66467373	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	112	428	0	ENST00000273854.3:c.896del	p.Asn299MetfsTer123	p.N299Mfs*123	ENST00000273854	NM_004439.5	299	aAt/at	3/18	1	2	FACETS	0.447	0.403	0.493	0.447	0.403	0.493	SUBCLONAL	1	TRUE	1	0.868070799066635	2		428	577	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518767	176518767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755103491	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	155	481	2	ENST00000292408.4:c.685G>A	p.Ala229Thr	p.A229T	ENST00000292408	NM_213647.1	229	Gct/Act	6/18	1	2	FACETS	0.561	0.515	0.608	0.561	0.515	0.608	SUBCLONAL	1	TRUE	1	0.868070799066635	2		483	637	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609902	117609902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781588795	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	114	368	0	ENST00000368508.3:c.6797C>T	p.Thr2266Met	p.T2266M	ENST00000368508	NM_002944.2	2266	aCg/aTg	43/43	1	2	FACETS	0.501	0.453	0.552	0.501	0.453	0.552	SUBCLONAL	1	TRUE	1	0.868070799066635	2		368	524	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469779	157469779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749077422	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	60	462	0	ENST00000346085.5:c.2573C>T	p.Ala858Val	p.A858V	ENST00000346085	NM_020732.3	858	gCg/gTg	9/20	1	2	FACETS	0.218	0.187	0.251	0.218	0.187	0.251	SUBCLONAL	1	TRUE	1	0.868070799066635	2		462	635	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962914	2962914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147823569	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	96	372	0	ENST00000396946.4:c.1994C>T	p.Ser665Leu	p.S665L	ENST00000396946	NM_032415.4	665	tCg/tTg	16/25	1	2	FACETS	0.451	0.404	0.502	0.451	0.404	0.502	SUBCLONAL	1	TRUE	1	0.868070799066635	2		372	490	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	66	405	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	0.225	0.195	0.258	0.225	0.195	0.258	SUBCLONAL	1	TRUE	1	0.868070799066635	2		405	676	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012245	152012245	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	100	419	0	ENST00000262189.6:c.568C>T	p.Arg190Ter	p.R190*	ENST00000262189	NM_170606.2	190	Cga/Tga	4/59	1	2	FACETS	0.479	0.43	0.531	0.479	0.43	0.531	SUBCLONAL	1	TRUE	1	0.868070799066635	2		419	481	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	114	656	1	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	0.444	0.401	0.49	0.444	0.401	0.49	SUBCLONAL	1	TRUE	1	0.868070799066635	2		657	591	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759623	133759623	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	139	536	0	ENST00000318560.5:c.1950del	p.Leu651TrpfsTer43	p.L651Wfs*43	ENST00000318560	NM_005157.4	649	aCc/ac	11/11	1	2	FACETS	0.528	0.482	0.575	0.528	0.482	0.575	SUBCLONAL	1	TRUE	1	0.868070799066635	2		536	607	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300040	137300040	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	61	356	0	ENST00000481739.1:c.331del	p.Leu111TrpfsTer57	p.L111Wfs*57	ENST00000481739	NM_002957.4	109	Ccc/cc	3/10	1	2	FACETS	0.314	0.271	0.36	0.314	0.271	0.36	SUBCLONAL	1	TRUE	1	0.868070799066635	2		356	448	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321355	1321355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	111	428	0	ENST00000400841.2:c.400G>A	p.Val134Met	p.V134M	ENST00000400841		134	Gtg/Atg	4/6	1	2	FACETS	0.431	0.388	0.476	0.431	0.388	0.476	SUBCLONAL	1	TRUE	1	0.868070799066635	2		428	593	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910372	29910372	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs41548119	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	141	803	0	ENST00000376809.5:c.46del	p.Ala16ProfsTer4	p.A16Pfs*4	ENST00000376809	NM_002116.7	14	tcG/tc	1/8	1	2	FACETS	0.316	0.287	0.346	0.316	0.287	0.346	SUBCLONAL	1	TRUE	1	0.868070799066635	2		803	1029	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799299	42799300	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1158987717	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	17	166	0	ENST00000575354.2:c.4790dup	p.Pro1598ThrfsTer16	p.P1598Tfs*16	ENST00000575354	NM_015125.3	1595	tcc/tCcc	20/20	0.863399366628745	3	FACETS	0.208	0.155	0.271	0.104	0.077	0.136	SUBCLONAL	1	TRUE	1	0.868070799066635	3		166	270	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1696761	1696761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201229178	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	148	412	0	ENST00000378625.1:c.85G>A	p.Asp29Asn	p.D29N	ENST00000378625	NM_001198994.1	29	Gat/Aat	2/14	1	2	FACETS	0.568	0.521	0.617	0.568	0.521	0.617	SUBCLONAL	1	TRUE	1	0.868070799066635	2		412	600	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150933381	150933382	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	80	441	0	ENST00000271640.5:c.2849dup	p.Asp951ArgfsTer39	p.D951Rfs*39	ENST00000271640	NM_001145415.1	948	cac/caCc	16/22	1	2	FACETS	0.321	0.282	0.362	0.321	0.282	0.362	SUBCLONAL	1	TRUE	1	0.868070799066635	2		441	575	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711287	114711287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	116	341	0	ENST00000543371.1:c.302C>T	p.Pro101Leu	p.P101L	ENST00000543371	NM_001198531.1	101	cCc/cTc	3/14	1	2	FACETS	0.644	0.585	0.705	0.644	0.585	0.705	SUBCLONAL	1	TRUE	1	0.868070799066635	2		341	415	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741529	17741529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781111019	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	134	421	0	ENST00000250003.3:c.200C>T	p.Ala67Val	p.A67V	ENST00000250003	NM_002478.4	67	gCg/gTg	1/3	1	2	FACETS	0.691	0.632	0.751	0.691	0.632	0.751	SUBCLONAL	1	TRUE	1	0.868070799066635	2		421	447	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205262	61205262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	123	400	0	ENST00000301761.2:c.202G>A	p.Ala68Thr	p.A68T	ENST00000301761	NM_017841.2	68	Gcc/Acc	2/4	1	2	FACETS	0.522	0.474	0.572	0.522	0.474	0.572	SUBCLONAL	1	TRUE	1	0.868070799066635	2		400	543	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307290	118307291	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	35	193	0	ENST00000534358.1:c.69dup	p.Arg24AlafsTer123	p.R24Afs*123	ENST00000534358	NM_005933.3	21	-/G	1/36	1	2	FACETS	0.395	0.327	0.471	0.395	0.327	0.471	SUBCLONAL	1	TRUE	1	0.868070799066635	2		193	204	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944877	31944877	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	83	286	0	ENST00000340398.3:c.224C>T	p.Ala75Val	p.A75V	ENST00000340398	NM_001013699.2	75	gCg/gTg	1/1	1	2	FACETS	0.477	0.423	0.534	0.477	0.423	0.534	SUBCLONAL	1	TRUE	1	0.868070799066635	2		286	401	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856076	111856076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757743643	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	125	447	0	ENST00000341259.2:c.127C>T	p.Arg43Cys	p.R43C	ENST00000341259	NM_005475.2	43	Cgc/Tgc	2/8	1	2	FACETS	0.544	0.495	0.596	0.544	0.495	0.596	SUBCLONAL	1	TRUE	1	0.868070799066635	2		447	529	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103498619	103498619	+	frameshift_variant,start_lost	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	113	389	0	ENST00000355739.4:c.7del	p.Val3?	p.V3?	ENST00000355739	NM_000123.3	1	atG/at	1/15	1	2	FACETS	0.507	0.459	0.559	0.507	0.459	0.559	SUBCLONAL	1	TRUE	1	0.868070799066635	2		389	513	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566126	95566126	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	39	300	1	ENST00000393063.1:c.4197del	p.Asp1400MetfsTer3	p.D1400Mfs*3	ENST00000393063	NM_030621.3	1399	aaA/aa	23/28	1	2	FACETS	0.195	0.161	0.232	0.195	0.161	0.232	SUBCLONAL	1	TRUE	1	0.868070799066635	2		301	461	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991307	41991308	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	106	361	0	ENST00000219905.7:c.2140_2141dup	p.Leu714PhefsTer2	p.L714Ffs*2	ENST00000219905	NM_001164273.1	713	gat/gaTTt	5/24	1	2	FACETS	0.5	0.451	0.553	0.5	0.451	0.553	SUBCLONAL	1	TRUE	1	0.868070799066635	2		361	488	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51503148	51503148	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs72552260	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	155	410	0	ENST00000260433.2:c.1369C>T	p.Arg457Ter	p.R457*	ENST00000260433		457	Cga/Tga	10/10	1	2	FACETS	0.572	0.526	0.621	0.572	0.526	0.621	SUBCLONAL	1	TRUE	1	0.868070799066635	2		410	624	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349706	15349706	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767464916	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	144	555	0	ENST00000263377.2:c.3868C>T	p.Arg1290Cys	p.R1290C	ENST00000263377	NM_058243.2	1290	Cgc/Tgc	19/20	1	2	FACETS	0.514	0.47	0.559	0.514	0.47	0.559	SUBCLONAL	1	TRUE	1	0.868070799066635	2		555	646	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424760	47424760	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	134	492	3	ENST00000404338.3:c.2834del	p.Lys945ArgfsTer3	p.K945Rfs*3	ENST00000404338	NM_004491.4	943	gAa/ga	1/6	0.863399366628745	3	FACETS	0.471	0.428	0.518	0.236	0.214	0.259	SUBCLONAL	1	TRUE	1	0.868070799066635	3		495	939	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36014555	36014555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772219397	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	118	412	0	ENST00000358208.4:c.328C>T	p.Arg110Trp	p.R110W	ENST00000358208		110	Cgg/Tgg	3/12	1	2	FACETS	0.557	0.505	0.611	0.557	0.505	0.611	SUBCLONAL	1	TRUE	1	0.868070799066635	2		412	488	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37622745	37622745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138762569	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	110	400	0	ENST00000249071.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000249071	NM_002872.4	183	Cgg/Tgg	6/7	1	2	FACETS	0.462	0.417	0.511	0.462	0.417	0.511	SUBCLONAL	1	TRUE	1	0.868070799066635	2		400	548	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748151	41748151	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587776626	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	109	378	0	ENST00000226382.2:c.618del	p.Ser207AlafsTer102	p.S207Afs*102	ENST00000226382	NM_003924.3	206	ccC/cc	3/3	1	2	FACETS	0.545	0.492	0.6	0.545	0.492	0.6	SUBCLONAL	1	TRUE	1	0.868070799066635	2		378	461	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356317	66356317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs965251708	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	144	449	0	ENST00000273854.3:c.1180G>A	p.Ala394Thr	p.A394T	ENST00000273854	NM_004439.5	394	Gca/Aca	5/18	1	2	FACETS	0.525	0.48	0.572	0.525	0.48	0.572	SUBCLONAL	1	TRUE	1	0.868070799066635	2		449	632	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196270	106196270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs906127830	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	86	477	0	ENST00000380013.4:c.4603C>T	p.Pro1535Ser	p.P1535S	ENST00000380013	NM_001127208.2	1535	Cca/Tca	11/11	1	2	FACETS	0.285	0.252	0.32	0.285	0.252	0.32	SUBCLONAL	1	TRUE	1	0.868070799066635	2		477	696	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045834	143045834	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	124	393	0	ENST00000262992.4:c.1800G>C	p.Gln600His	p.Q600H	ENST00000262992	NM_001101669.1	600	caG/caC	17/24	1	2	FACETS	0.532	0.483	0.583	0.532	0.483	0.583	SUBCLONAL	1	TRUE	1	0.868070799066635	2		393	537	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144258384	144258385	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	85	398	0	ENST00000262995.4:c.49_50dup	p.Glu18ArgfsTer5	p.E18Rfs*5	ENST00000262995	NM_207123.2	15	tcc/tCCcc	1/11	1	2	FACETS	0.451	0.401	0.505	0.451	0.401	0.505	SUBCLONAL	1	TRUE	1	0.868070799066635	2		398	434	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873742	35873742	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	58	345	0	ENST00000303115.3:c.698A>G	p.Asn233Ser	p.N233S	ENST00000303115	NM_002185.3	233	aAt/aGt	5/8	1	2	FACETS	0.255	0.219	0.294	0.255	0.219	0.294	SUBCLONAL	1	TRUE	1	0.868070799066635	2		345	525	SUCCESS
APC	324	MSKCC	GRCh37	5	112173719	112173719	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs564269909	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	133	405	0	ENST00000257430.4:c.2428A>G	p.Arg810Gly	p.R810G	ENST00000257430	NM_000038.5	810	Agg/Ggg	16/16	1	2	FACETS	0.499	0.454	0.546	0.499	0.454	0.546	SUBCLONAL	1	TRUE	1	0.868070799066635	2		405	614	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670626	30670626	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	111	489	0	ENST00000376406.3:c.5894del	p.Pro1965ArgfsTer6	p.P1965Rfs*6	ENST00000376406	NM_014641.2	1965	cCg/cg	13/15	1	2	FACETS	0.422	0.38	0.466	0.422	0.38	0.466	SUBCLONAL	1	TRUE	1	0.868070799066635	2		489	606	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6439774	6439774	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	132	361	0	ENST00000356142.4:c.300C>A	p.Cys100Ter	p.C100*	ENST00000356142	NM_018890.3	100	tgC/tgA	5/7	1	2	FACETS	0.504	0.458	0.551	0.504	0.458	0.551	SUBCLONAL	1	TRUE	1	0.868070799066635	2		361	604	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29197635	29197635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	160	436	0	ENST00000240100.2:c.559G>A	p.Gly187Arg	p.G187R	ENST00000240100	NM_001394.6	187	Ggg/Agg	2/4	1	2	FACETS	0.579	0.532	0.627	0.579	0.532	0.627	SUBCLONAL	1	TRUE	1	0.868070799066635	2		436	637	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982034	70982034	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1339967021	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	78	466	0	ENST00000276594.2:c.62G>C	p.Ser21Thr	p.S21T	ENST00000276594	NM_024504.3	21	aGc/aCc	2/8	1	2	FACETS	0.342	0.301	0.386	0.342	0.301	0.386	SUBCLONAL	1	TRUE	1	0.868070799066635	2		466	525	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27183516	27183516	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	123	410	0	ENST00000380036.4:c.1090G>T	p.Gly364Cys	p.G364C	ENST00000380036	NM_000459.3	364	Ggt/Tgt	8/23	1	2	FACETS	0.489	0.443	0.536	0.489	0.443	0.536	SUBCLONAL	1	TRUE	1	0.868070799066635	2		410	580	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908843	101908843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	31	399	0	ENST00000374994.4:c.1207G>A	p.Ala403Thr	p.A403T	ENST00000374994	NM_004612.2	403	Gca/Aca	7/9	1	2	FACETS	0.126	0.101	0.154	0.126	0.101	0.154	SUBCLONAL	1	TRUE	1	0.868070799066635	2		399	568	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787785	135787785	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	107	345	0	ENST00000298552.3:c.797C>A	p.Pro266His	p.P266H	ENST00000298552	NM_001162426.1	266	cCc/cAc	9/23	1	2	FACETS	0.5	0.45	0.552	0.5	0.45	0.552	SUBCLONAL	1	TRUE	1	0.868070799066635	2		345	493	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	16	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.424	0.312	0.559	0.424	0.312	0.559	SUBCLONAL	1	TRUE	1	0.15	2		341	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0066014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	53	537	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.3	3	FACETS	0.904	0.769	1			1	CLONAL	1	TRUE	NA	0.15	3		537	840	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764146326	NA	P-0066014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	46	375	0	ENST00000269305.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000269305	NM_001126112.2	281	Gac/Aac	8/11	0.3	3	FACETS	0.803	0.674	0.946			1	CLONAL	1	TRUE	NA	0.15	3		375	821	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106873	27106873	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	44	0	0	ENST00000324856.7:c.6484G>A	p.Val2162Met	p.V2162M	ENST00000324856	NM_006015.4	2162	Gtg/Atg	20/20	1	2	FACETS	0.53	0.443	0.628	0.53	0.443	0.628	SUBCLONAL	1	TRUE	1	0.15	2		0	1106	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0066017-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	62	269	1	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.297169142781595	14	FACETS	1	0.951	1	0.223	0.192	0.255	CLONAL	2	FALSE	3	0.297169142781595	14		270	474	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937028	48937028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066017-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	104	371	0	ENST00000267163.4:c.796C>T	p.Gln266Ter	p.Q266*	ENST00000267163	NM_000321.2	266	Caa/Taa	8/27	0.277823371943389	3	FACETS	0.87	0.789	0.953	0.87	0.789	0.953	CLONAL	3	FALSE	0	0.297169142781595	3		371	308	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0066017-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	118	383	0	ENST00000269305.4:c.375+1del		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.241723762241515	4	FACETS	0.991	0.898	1	0.991	0.898	1	CLONAL	2	FALSE	2	0.297169142781595	4		383	520	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332910	153332910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066017-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	57	397	0	ENST00000281708.4:c.46G>A	p.Gly16Arg	p.G16R	ENST00000281708	NM_033632.3	16	Gga/Aga	2/12	0.273169578418594	1	FACETS	0.981	0.846	1	0.981	0.846	1	CLONAL	1	FALSE	0	0.297169142781595	1		397	333	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104353441	104353441	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066017-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	117	420	0	ENST00000369902.3:c.646G>T	p.Gly216Trp	p.G216W	ENST00000369902	NM_016169.3	216	Ggg/Tgg	5/12	0.28628206810115	2	FACETS	0.913	0.83	1	0.913	0.83	1	CLONAL	2	FALSE	0	0.297169142781595	2		420	431	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156613	2156613	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066017-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	111	453	0	ENST00000434045.2:c.309C>A	p.Asp103Glu	p.D103E	ENST00000434045	NM_001127598.1	103	gaC/gaA	3/5	0.297169142781595	2	FACETS	0.92	0.834	1	0.92	0.834	1	CLONAL	2	FALSE	0	0.297169142781595	2		453	406	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917602	94917602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066017-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	44	430	0	ENST00000536441.1:c.919C>T	p.His307Tyr	p.H307Y	ENST00000536441	NM_144665.3	307	Cat/Tat	6/10	0.28628206810115	2	FACETS	0.879	0.74	1	0.439	0.37	0.516	CLONAL	1	FALSE	0	0.297169142781595	2		430	337	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211823	36211823	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066017-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	525	501	0	ENST00000222270.7:c.1574G>T	p.Arg525Leu	p.R525L	ENST00000222270	NM_014727.1	525	cGg/cTg	3/37	0.297169142781595	9	FACETS	0.938	0.905	0.97	1	0.99	1	CLONAL	8	FALSE	2	0.297169142781595	9		501	961	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771195	161771195	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs961239925	NA	P-0066017-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	76	343	0	ENST00000366898.1:c.1334G>A	p.Trp445Ter	p.W445*	ENST00000366898	NM_004562.2	445	tGg/tAg	12/12	0.291043934846663	3	FACETS	1	0.972	1	0.694	0.612	0.783	CLONAL	1	FALSE	1	0.297169142781595	3		343	423	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696425	47696425	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519967	NA	P-0066027-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	119	417	0	ENST00000347630.2:c.398T>G	p.Phe133Cys	p.F133C	ENST00000347630	NM_001007230.1	133	tTc/tGc	6/11	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.589438461230204	2		417	403	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975414	13975414	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066027-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	64	432	0	ENST00000405192.2:c.473del	p.Thr158AsnfsTer97	p.T158Nfs*97	ENST00000405192	NM_001163147.1	158	aCa/aa	7/12	1	2	FACETS	0.285	0.246	0.328	0.285	0.246	0.328	SUBCLONAL	1	TRUE	1	0.589438461230204	2		432	761	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436408	52436408	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	174	525	0	ENST00000460680.1:c.2086del	p.Ile696SerfsTer40	p.I696Sfs*40	ENST00000460680	NM_004656.3	696	Atc/tc	17/17	0.378982652630467	2	FACETS	0.996	0.926	1	0.996	0.926	1	CLONAL	2	TRUE	0	0.378982652630467	2		525	461	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497681	125497681	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0066031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	86	450	0	ENST00000428830.2:c.245T>A	p.Leu82Ter	p.L82*	ENST00000428830	NM_001114121.2	82	tTa/tAa	3/14	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.378982652630467	2		450	430	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264490	30264490	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	53	400	0	ENST00000322652.5:c.225A>C	p.Lys75Asn	p.K75N	ENST00000322652	NM_015355.2	75	aaA/aaC	1/16	1	2	FACETS	0.869	0.745	1	0.869	0.745	1	CLONAL	1	TRUE	1	0.378982652630467	2		400	322	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188277	10188278	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1553619976	NA	P-0066031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	176	380	0	ENST00000256474.2:c.422dup	p.Asn141LysfsTer3	p.N141Kfs*3	ENST00000256474	NM_000551.3	140	-/A	2/3	0.378982652630467	2	FACETS	0.994	0.925	1	0.994	0.925	1	CLONAL	2	TRUE	0	0.378982652630467	2		380	467	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535377	66535381	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGG	CAGGG	A	novel	NA	P-0066031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	63	492	0	ENST00000273854.3:c.80_84delinsT	p.Ser27LeufsTer34	p.S27Lfs*34	ENST00000273854	NM_004439.5	27	tCCCTG/tT	1/18	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.378982652630467	2		492	309	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183823	10183823	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	26	388	0	ENST00000256474.2:c.292T>A	p.Tyr98Asn	p.Y98N	ENST00000256474	NM_000551.3	98	Tac/Aac	1/3	0.189491597565543	1	FACETS	0.576	0.456	0.715	0.576	0.456	0.715	SUBCLONAL	1	TRUE	0	0.189491597565543	1		388	431	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007644	45007648	+	frameshift_variant	Frame_Shift_Del	DEL	TCACG	TCACG	-	novel	NA	P-0066032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	44	358	0	ENST00000558401.1:c.94_98del	p.Arg32SerfsTer23	p.R32Sfs*23	ENST00000558401	NM_004048.2	31	TCACGt/t	2/4	0.189491597565543	1	FACETS	0.932	0.782	1	0.932	0.782	1	CLONAL	1	TRUE	0	0.189491597565543	1		358	451	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	50	446	0				ENST00000310581	NM_198253.2	-/1132			0.242554452838078	3	FACETS	1	0.962	1	0.718	0.615	0.829	CLONAL	1	TRUE	1	0.33153721720424	3		446	245	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0066033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	132	343	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.0760205354614016	3	FACETS	0.869	0.799	0.941			1	INDETERMINATE	3	TRUE	NA	0.33153721720424	3		343	356	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0066033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	154	157	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.33153721720424	5	FACETS	0.904	0.833	0.977	0.904	0.833	0.977	CLONAL	3	TRUE	2	0.33153721720424	5		157	513	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382201	152382201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781324888	NA	P-0066033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	148	354	0	ENST00000206249.3:c.1311G>A	p.Met437Ile	p.M437I	ENST00000206249	NM_000125.3	437	atG/atA	6/8	0.33153721720424	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.33153721720424	2		354	418	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670357	134670357	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369940994	NA	P-0066033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	177	390	0	ENST00000398015.3:c.268C>T	p.Arg90Cys	p.R90C	ENST00000398015	NM_004441.4	90	Cgc/Tgc	3/16	0.322889817399912	4	FACETS	0.86	0.798	0.924	1	0.987	1	CLONAL	3	TRUE	2	0.33153721720424	4		390	551	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741429	145741429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	227	538	0	ENST00000428558.2:c.1074G>A	p.Met358Ile	p.M358I	ENST00000428558	NM_004260.3	358	atG/atA	5/22	0.33153721720424	5	FACETS	0.867	0.81	0.926	0.867	0.81	0.926	CLONAL	3	TRUE	2	0.33153721720424	5		538	788	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225674	26225674	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	207	597	0	ENST00000360408.1:c.292G>A	p.Glu98Lys	p.E98K	ENST00000360408	NM_003532.2	98	Gag/Aag	1/1	0.33153721720424	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.33153721720424	2		597	565	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740830	145740830	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765611938	NA	P-0066033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	170	445	0	ENST00000428558.2:c.1270G>A	p.Asp424Asn	p.D424N	ENST00000428558	NM_004260.3	424	Gac/Aac	7/22	0.33153721720424	5	FACETS	1	0.977	1	0.769	0.709	0.83	CLONAL	2	TRUE	2	0.33153721720424	5		445	666	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846158	68846158	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	130	349	0	ENST00000261769.5:c.1129C>A	p.Pro377Thr	p.P377T	ENST00000261769	NM_004360.3	377	Ccc/Acc	8/16	0.33153721720424	5	FACETS	0.839	0.762	0.919			1	CLONAL	2	TRUE	NA	0.33153721720424	5		349	700	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124362	2124362	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	45	395	0	ENST00000219476.3:c.2517G>T	p.Met839Ile	p.M839I	ENST00000219476	NM_000548.3	839	atG/atT	22/42	1	2	FACETS	0.765	0.645	0.896	0.765	0.645	0.896	SUBCLONAL	1	TRUE	1	0.33153721720424	2		395	355	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471707	120471707	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	165	429	0	ENST00000256646.2:c.3784G>A	p.Glu1262Lys	p.E1262K	ENST00000256646	NM_024408.3	1262	Gag/Aag	23/34	0.3140584249207	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.33153721720424	3		429	499	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855995	68855995	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	157	407	0	ENST00000261769.5:c.1803C>G	p.Phe601Leu	p.F601L	ENST00000261769	NM_004360.3	601	ttC/ttG	12/16	0.33153721720424	5	FACETS	0.959	0.881	1			1	CLONAL	2	TRUE	NA	0.33153721720424	5		407	739	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134238	41134238	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	77	396	0	ENST00000379561.5:c.1390G>C	p.Glu464Gln	p.E464Q	ENST00000379561	NM_002015.3	464	Gag/Cag	2/3	0.33153721720424	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.33153721720424	1		396	329	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652055	36652072	+	inframe_deletion	In_Frame_Del	DEL	GGAGGGTGACTTCGCCTG	GGAGGGTGACTTCGCCTG	-	novel	NA	P-0066033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	127	500	0	ENST00000244741.5:c.181_198del	p.Gly61_Glu66del	p.G61_E66del	ENST00000244741	NM_000389.4	59	ctGGAGGGTGACTTCGCCTGg/ctg	2/3	0.33153721720424	2	FACETS	0.932	0.852	1	0.932	0.852	1	CLONAL	2	TRUE	0	0.33153721720424	2		500	411	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359353	118359353	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	78	337	0	ENST00000534358.1:c.4357G>T	p.Glu1453Ter	p.E1453*	ENST00000534358	NM_005933.3	1453	Gag/Tag	11/36	0.3140584249207	3	FACETS	1	0.931	1	0.541	0.476	0.61	CLONAL	1	TRUE	1	0.33153721720424	3		337	507	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554960	187554960	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	78	361	0	ENST00000441802.2:c.4201C>G	p.His1401Asp	p.H1401D	ENST00000441802	NM_005245.3	1401	Cac/Gac	7/27	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.33153721720424	2		361	459	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980404	201980423	+	frameshift_variant	Frame_Shift_Del	DEL	CCCAGATGTCATTGGAGGGT	CCCAGATGTCATTGGAGGGT	-	novel	NA	P-0066033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	176	441	1	ENST00000359651.3:c.140_159del	p.Pro47HisfsTer38	p.P47Hfs*38	ENST00000359651		47	cCCCAGATGTCATTGGAGGGT/c	1/8	0.225211128025331	3	FACETS	0.84	0.781	0.901	0.84	0.781	0.901	CLONAL	3	TRUE	0	0.33153721720424	3		442	491	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069357	30069357	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	133	428	0	ENST00000338641.4:c.1222G>T	p.Glu408Ter	p.E408*	ENST00000338641	NM_000268.3	408	Gaa/Taa	12/16	0.33153721720424	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.33153721720424	2		428	374	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs869320707	NA	P-0066035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	167	592	0	ENST00000397752.3:c.3028+1G>T		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.2872709278346	2	FACETS	0.804	0.741	0.87	0.804	0.741	0.87	CLONAL	2	TRUE	0	0.2872709278346	2		592	723	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783674	50783674	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	153	347	0	ENST00000398568.2:c.65A>T	p.Tyr22Phe	p.Y22F	ENST00000398568	NM_001042412.1	22	tAc/tTc	3/18	0.2872709278346	3	FACETS	0.973	0.894	1	0.973	0.894	1	CLONAL	2	TRUE	1	0.2872709278346	3		347	626	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564765	41564765	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	42	477	0	ENST00000263253.7:c.4066C>T	p.Arg1356Ter	p.R1356*	ENST00000263253	NM_001429.3	1356	Cga/Tga	25/31	1	2	FACETS	0.395	0.329	0.469	0.395	0.329	0.469	SUBCLONAL	1	TRUE	1	0.342129759054837	2		477	621	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021440	42021440	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	112	504	0	ENST00000219905.7:c.3736C>T	p.Arg1246Ter	p.R1246*	ENST00000219905	NM_001164273.1	1246	Cga/Tga	11/24	1	2	FACETS	0.956	0.861	1	0.956	0.861	1	CLONAL	1	TRUE	1	0.342129759054837	2		504	685	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55260505	55260505	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs987884612	NA	P-0066036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	68	358	0	ENST00000275493.2:c.2672A>G	p.Tyr891Cys	p.Y891C	ENST00000275493	NM_005228.3	891	tAt/tGt	22/28	1	2	FACETS	0.795	0.693	0.905	0.795	0.693	0.905	CLONAL	1	TRUE	1	0.342129759054837	2		358	500	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023467	27023467	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	96	503	0	ENST00000324856.7:c.574del	p.Leu192TrpfsTer40	p.L192Wfs*40	ENST00000324856	NM_006015.4	191	ggC/gg	1/20	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.342129759054837	2		503	538	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572918	41572921	+	frameshift_variant	Frame_Shift_Del	DEL	ATCC	ATCC	-	novel	NA	P-0066036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	137	571	0	ENST00000263253.7:c.5204_5207del	p.Ile1735SerfsTer26	p.I1735Sfs*26	ENST00000263253	NM_001429.3	1735	ATCCag/ag	31/31	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.342129759054837	2		571	733	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50816378	50816378	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0066037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	168	368	0	ENST00000398568.2:c.1817+1G>A		p.X606_splice	ENST00000398568	NM_001042412.1	606			0.800698950222929	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.800698950222929	1		368	251	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943993	71943994	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAGC	novel	NA	P-0066037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	146	547	1	ENST00000298229.2:c.1928_1931dup	p.His644GlnfsTer10	p.H644Qfs*10	ENST00000298229	NM_001567.3	642	-/AAGC	16/28	0.203929843524992	3	FACETS	0.939	0.861	1	0.469	0.43	0.51	INDETERMINATE	1	TRUE	1	0.800698950222929	3		548	544	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0066038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	227	232	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.251188608975526	5	FACETS	1	0.972	1	1	0.972	1	CLONAL	4	TRUE	1	0.251188608975526	5		232	586	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028689	12028689	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0066038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	31	291	0	ENST00000353533.5:c.891+1G>A		p.X297_splice	ENST00000353533	NM_003010.3	297			0.199282784653747	1	FACETS	0.534	0.432	0.65	0.534	0.432	0.65	SUBCLONAL	1	TRUE	0	0.251188608975526	1		291	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576911	7576923	+	frameshift_variant	Frame_Shift_Del	DEL	GTGTTGTTGGGCA	GTGTTGTTGGGCA	-	novel	NA	P-0066038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	71	415	0	ENST00000269305.4:c.923_935del	p.Leu308ProfsTer33	p.L308Pfs*33	ENST00000269305	NM_001126112.2	308	cTGCCCAACAACACc/cc	9/11	0.199282784653747	1	FACETS	0.787	0.687	0.895	0.787	0.687	0.895	SUBCLONAL	1	TRUE	0	0.251188608975526	1		415	628	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0066046-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	46	721	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.608	0.511	0.716	0.608	0.511	0.716	SUBCLONAL	1	TRUE	1	0.24	2		721	630	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176330	24176330	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1057517825	NA	P-0066046-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	42	544	0	ENST00000263121.7:c.1121G>A	p.Arg374Gln	p.R374Q	ENST00000263121	NM_003073.3	374	cGg/cAg	9/9	1	2	FACETS	0.711	0.594	0.842	0.711	0.594	0.842	SUBCLONAL	1	TRUE	1	0.24	2		544	492	SUCCESS
APC	324	MSKCC	GRCh37	5	112175749	112175756	+	frameshift_variant	Frame_Shift_Del	DEL	TACTTTAT	TACTTTAT	-	novel	NA	P-0066046-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	87	735	0	ENST00000257430.4:c.4461_4468del	p.Leu1488PhefsTer23	p.L1488Ffs*23	ENST00000257430	NM_000038.5	1486	gaTACTTTATta/gata	16/16	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.24	2		735	722	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910849	114910849	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066046-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	55	723	0	ENST00000543371.1:c.968C>A	p.Ser323Ter	p.S323*	ENST00000543371	NM_001198531.1	323	tCg/tAg	9/14	1	2	FACETS	0.645	0.55	0.748	0.645	0.55	0.748	SUBCLONAL	1	TRUE	1	0.24	2		723	711	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236193	108236193	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066046-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	97	756	0	ENST00000278616.4:c.9129A>C	p.Lys3043Asn	p.K3043N	ENST00000278616	NM_000051.3	3043	aaA/aaC	63/63	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.24	2		756	701	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89842215	89842215	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs777736014	NA	P-0066046-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	58	678	0	ENST00000389301.3:c.1835A>G	p.Lys612Arg	p.K612R	ENST00000389301	NM_000135.2	612	aAa/aGa	21/43	1	2	FACETS	0.761	0.653	0.879	0.761	0.653	0.879	SUBCLONAL	1	TRUE	1	0.24	2		678	635	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38978749	38978749	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066046-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	34	466	0	ENST00000357387.3:c.757A>G	p.Ile253Val	p.I253V	ENST00000357387	NM_152756.3	253	Att/Gtt	9/38	1	2	FACETS	0.77	0.63	0.927	0.77	0.63	0.927	CLONAL	1	TRUE	1	0.24	2		466	368	SUCCESS
APC	324	MSKCC	GRCh37	5	112175033	112175033	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066046-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	50	644	0	ENST00000257430.4:c.3742A>C	p.Thr1248Pro	p.T1248P	ENST00000257430	NM_000038.5	1248	Act/Cct	16/16	1	2	FACETS	0.726	0.615	0.847	0.726	0.615	0.847	SUBCLONAL	1	TRUE	1	0.24	2		644	574	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266583	142266585	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	rs779715723	NA	P-0066081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	30	339	0	ENST00000350721.4:c.3339_3341del	p.Ile1114del	p.I1114del	ENST00000350721	NM_001184.3	1113	atCATa/ata	16/47	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.16	2		339	331	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436431	52436453	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGCATGCCTGCGAAGAGGTAGAG	AGCATGCCTGCGAAGAGGTAGAG	-	novel	NA	P-0066081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	22	345	0	ENST00000460680.1:c.2057-16_2063del		p.X686_splice	ENST00000460680	NM_004656.3	686		17/17	1	2	FACETS	0.932	0.723	1	0.932	0.723	1	CLONAL	1	TRUE	1	0.16	2		345	295	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971032	21971038	+	frameshift_variant	Frame_Shift_Del	DEL	GCATCGC	GCATCGC	-	novel	NA	P-0066085-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	198	593	0	ENST00000304494.5:c.320_326del	p.Arg107ProfsTer37	p.R107Pfs*37	ENST00000304494	NM_000077.4	107	cGCGATGCc/cc	2/3	0.789922891880698	1	FACETS	0.879	0.83	0.927	0.879	0.83	0.927	CLONAL	1	TRUE	0	0.789922891880698	1		593	345	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1747287	1747287	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs754777749	NA	P-0066085-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	259	524	0	ENST00000378609.4:c.111C>G	p.Ile37Met	p.I37M	ENST00000378609	NM_002074.3	37	atC/atG	5/12	0.789922891880698	1	FACETS	0.994	0.95	1	0.994	0.95	1	CLONAL	1	TRUE	0	0.789922891880698	1		524	399	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15821902	15821903	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0066085-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	207	234	0	ENST00000307771.7:c.295_296del	p.Arg99AlafsTer45	p.R99Afs*45	ENST00000307771	NM_005089.3	99	CGg/g	4/11	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.789922891880698	1		234	279	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719737	61719737	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066087-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	73	487	1	ENST00000401558.2:c.1531G>A	p.Glu511Lys	p.E511K	ENST00000401558	NM_003400.3	511	Gag/Aag	14/25	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.82185306101365	2		488	174	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874365	151874365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746319127	NA	P-0066087-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	71	521	0	ENST00000262189.6:c.8173G>A	p.Glu2725Lys	p.E2725K	ENST00000262189	NM_170606.2	2725	Gag/Aag	38/59	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.82185306101365	2		521	171	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578538	7578538	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066087-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	179	559	0	ENST00000269305.4:c.392del	p.Asn131ThrfsTer39	p.N131Tfs*39	ENST00000269305	NM_001126112.2	131	aAc/ac	5/11	0.82185306101365	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.82185306101365	1		559	244	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295960	1295960	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0066087-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	188	765	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.82185306101365	2		765	423	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121792	2121792	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066087-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	159	598	0	ENST00000219476.3:c.1954G>C	p.Glu652Gln	p.E652Q	ENST00000219476	NM_000548.3	652	Gag/Cag	19/42	0.188945219029127	1	FACETS	0.71	0.663	0.758	0.71	0.663	0.758	INDETERMINATE	1	TRUE	0	0.82185306101365	1		598	321	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76812990	76812990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066087-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	47	451	0	ENST00000373344.5:c.6631G>A	p.Glu2211Lys	p.E2211K	ENST00000373344	NM_000489.3	2211	Gag/Aag	30/35	0.386431465118789	1	FACETS	0.468	0.403	0.536	0.468	0.403	0.536	INDETERMINATE	1	TRUE	0	0.82185306101365	1		451	144	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968988	15968988	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066087-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	111	466	0	ENST00000268712.3:c.4762C>T	p.Gln1588Ter	p.Q1588*	ENST00000268712	NM_006311.3	1588	Cag/Tag	33/46	0.82185306101365	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.82185306101365	1		466	140	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305377	65305377	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066087-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	135	617	0	ENST00000342505.4:c.2751C>A	p.Asn917Lys	p.N917K	ENST00000342505	NM_002227.2	917	aaC/aaA	20/25	0.386431465118789	1	FACETS	0.725	0.673	0.777	0.725	0.673	0.777	INDETERMINATE	1	TRUE	0	0.82185306101365	1		617	267	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679433	29679433	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1555536380	NA	P-0066087-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	87	387	0	ENST00000356175.3:c.7552+1G>T		p.X2518_splice	ENST00000356175	NM_000267.3	2518			0.82185306101365	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.82185306101365	1		387	124	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111532	8111532	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066087-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	188	498	0	ENST00000346208.3:c.1018G>A	p.Ala340Thr	p.A340T	ENST00000346208		340	Gcc/Acc	5/6	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.82185306101365	2		498	439	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933207	100933210	+	frameshift_variant	Frame_Shift_Del	DEL	GAAA	GAAA	-	novel	NA	P-0066087-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	72	459	0	ENST00000325455.5:c.2180_2183del	p.Leu727GlnfsTer2	p.L727Qfs*2	ENST00000325455	NM_001202474.3	727	cTTTCa/ca	4/8	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.82185306101365	2		459	166	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251126	99251126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066087-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	47	526	0	ENST00000268035.6:c.430G>A	p.Glu144Lys	p.E144K	ENST00000268035	NM_000875.3	144	Gag/Aag	2/21	0.458895762911769	1	FACETS	0.292	0.248	0.339	0.292	0.248	0.339	INDETERMINATE	1	TRUE	0	0.82185306101365	1		526	231	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135804195	135804195	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066087-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	82	586	0	ENST00000298552.3:c.65G>T	p.Arg22Leu	p.R22L	ENST00000298552	NM_001162426.1	22	cGg/cTg	3/23	1	2	FACETS	0.51	0.453	0.571	0.51	0.453	0.571	SUBCLONAL	1	TRUE	1	0.82185306101365	2		586	391	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717733	89717733	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066087-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	69	387	0	ENST00000371953.3:c.758T>G	p.Ile253Ser	p.I253S	ENST00000371953	NM_000314.4	253	aTc/aGc	7/9	0.82185306101365	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.82185306101365	1		387	95	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626879	14626879	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066087-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	185	626	0	ENST00000254322.2:c.896G>C	p.Gly299Ala	p.G299A	ENST00000254322	NM_006145.1	299	gGa/gCa	3/3	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.82185306101365	2		626	450	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275878	38275878	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066087-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	191	575	0	ENST00000425967.3:c.1391C>G	p.Ser464Cys	p.S464C	ENST00000425967	NM_001174067.1	464	tCc/tGc	11/19	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.82185306101365	2		575	425	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556865	29556865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066087-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	16	281	2	ENST00000356175.3:c.2863G>A	p.Asp955Asn	p.D955N	ENST00000356175	NM_000267.3	955	Gat/Aat	22/57	0.82185306101365	1	FACETS	0.314	0.237	0.401	0.314	0.237	0.401	SUBCLONAL	1	TRUE	0	0.82185306101365	1		283	73	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624440	140624440	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066087-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	130	432	0	ENST00000288602.6:c.64G>T	p.Asp22Tyr	p.D22Y	ENST00000288602	NM_004333.4	22	Gac/Tac	1/18	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.82185306101365	2		432	297	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353986	15353986	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066087-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	80	212	0	ENST00000263377.2:c.2894C>G	p.Ser965Cys	p.S965C	ENST00000263377	NM_058243.2	965	tCt/tGt	14/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.82185306101365	2		212	169	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150913879	150913879	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066087-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	80	377	0	ENST00000271640.5:c.522G>C	p.Lys174Asn	p.K174N	ENST00000271640	NM_001145415.1	174	aaG/aaC	5/22	0.600385423812444	4	FACETS	1	0.961	1	0.394	0.35	0.44	CLONAL	1	TRUE	1	0.82185306101365	4		377	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578476	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTGCCGGGCGG	GGGTGCCGGGCGG	-	rs876659215	NA	P-0066088-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	202	761	0	ENST00000269305.4:c.454_466del	p.Pro152AlafsTer14	p.P152Afs*14	ENST00000269305	NM_001126112.2	152	CCGCCCGGCACCCgc/gc	5/11	0.329436849702307	2	FACETS	0.989	0.922	1	0.989	0.922	1	CLONAL	2	TRUE	0	0.339339206479466	2		761	602	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953355	17953355	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs56269787	NA	P-0066088-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	77	405	0	ENST00000458235.1:c.631A>G	p.Arg211Gly	p.R211G	ENST00000458235	NM_000215.3	211	Agg/Ggg	6/24	0.226712300113787	5	FACETS	1	0.931	1	0.363	0.318	0.411	CLONAL	1	TRUE	2	0.339339206479466	5		405	629	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226503	41226504	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0066088-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	183	460	0	ENST00000357654.3:c.4519_4520del	p.Arg1507ValfsTer13	p.R1507Vfs*13	ENST00000357654	NM_007294.3	1507	AGg/g	14/23	0.329436849702307	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.339339206479466	2		460	520	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644769	67644769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066088-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	191	480	0	ENST00000264010.4:c.34G>A	p.Glu12Lys	p.E12K	ENST00000264010	NM_006565.3	12	Gag/Aag	3/12	0.339339206479466	3	FACETS	0.981	0.911	1	0.981	0.911	1	CLONAL	2	TRUE	1	0.339339206479466	3		480	671	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852092	128852092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066088-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	70	434	0	ENST00000249373.3:c.2164G>A	p.Gly722Arg	p.G722R	ENST00000249373	NM_005631.4	722	Ggg/Agg	12/12	0.339339206479466	5	FACETS	0.867	0.755	0.988	0.289	0.251	0.33	CLONAL	1	TRUE	2	0.339339206479466	5		434	718	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	63	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.362316576225854	2		341	318	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643747	38643747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748390368	NA	P-0066112-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	26	420	0	ENST00000299084.4:c.1217C>T	p.Ala406Val	p.A406V	ENST00000299084	NM_152594.2	406	gCc/gTc	7/7	1	2	FACETS	0.734	0.58	0.911	0.734	0.58	0.911	CLONAL	1	TRUE	1	0.14	2		420	506	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396221	396221	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs140151215	NA	P-0066113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	176	458	0	ENST00000262320.3:c.805C>G	p.Gln269Glu	p.Q269E	ENST00000262320	NM_003502.3	269	Cag/Gag	2/11	0.836103653028679	1	FACETS	0.965	0.919	1	0.965	0.919	1	CLONAL	1	TRUE	0	0.855336970237591	1		458	244	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508470	106508470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1463222028	NA	P-0066113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	119	387	0	ENST00000359195.3:c.464C>T	p.Thr155Met	p.T155M	ENST00000359195	NM_002649.2	155	aCg/aTg	2/11	1	2	FACETS	0.983	0.903	1	0.983	0.903	1	CLONAL	1	TRUE	1	0.855336970237591	2		387	283	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829811	76829811	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	125	326	0	ENST00000373344.5:c.6230G>A	p.Trp2077Ter	p.W2077*	ENST00000373344	NM_000489.3	2077	tGg/tAg	28/35	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.855336970237591	2		326	248	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711882	89711882	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	175	349	0	ENST00000371953.3:c.500del	p.Thr167IlefsTer16	p.T167Ifs*16	ENST00000371953	NM_000314.4	167	aCt/at	6/9	0.855336970237591	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.855336970237591	1		349	228	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256530	+	missense_variant	Missense_Mutation	DNP	TG	TG	CT	rs1057519834	NA	P-0066114-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	8	402	0	ENST00000369535.4:c.181_182delinsAG	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	CAa/AGa	3/7	1	2	FACETS	0.275	0.176	0.404	0.275	0.176	0.404	SUBCLONAL	1	TRUE	1	0.15	2		402	388	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251854	212251854	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775252191	NA	P-0066114-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	27	390	0	ENST00000342788.4:c.3205G>A	p.Gly1069Arg	p.G1069R	ENST00000342788	NM_005235.2	1069	Gga/Aga	27/28	1	2	FACETS	0.778	0.618	0.961	0.778	0.618	0.961	CLONAL	1	TRUE	1	0.15	2		390	463	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066600	94066600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355103404	NA	P-0066114-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	38	494	0	ENST00000369303.4:c.1159G>A	p.Gly387Arg	p.G387R	ENST00000369303	NM_004440.3	387	Gga/Aga	5/17	1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.15	2		494	496	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663580	117663580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1417876029	NA	P-0066114-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	22	308	0	ENST00000368508.3:c.4652G>A	p.Gly1551Glu	p.G1551E	ENST00000368508	NM_002944.2	1551	gGa/gAa	28/43	1	2	FACETS	0.836	0.647	1	0.836	0.647	1	CLONAL	1	TRUE	1	0.15	2		308	351	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636826	8636826	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1353675904	NA	P-0066114-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	28	406	0	ENST00000356435.5:c.83G>A	p.Arg28Gln	p.R28Q	ENST00000356435		28	cGa/cAa	2/35	1	2	FACETS	0.841	0.671	1	0.841	0.671	1	CLONAL	1	TRUE	1	0.15	2		406	444	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945141	32945141	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066114-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	23	348	0	ENST00000380152.3:c.8536G>A	p.Glu2846Lys	p.E2846K	ENST00000380152		2846	Gag/Aag	20/27	1	2	FACETS	0.918	0.716	1	0.918	0.716	1	CLONAL	1	TRUE	1	0.15	2		348	334	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753819	42753819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066114-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	45	564	0	ENST00000222329.4:c.445C>T	p.Pro149Ser	p.P149S	ENST00000222329	NM_006494.2	149	Ccc/Tcc	4/4	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.15	2		564	544	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111995761	111995762	+	missense_variant	Missense_Mutation	DNP	AC	AC	CT	novel	NA	P-0066114-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	30	368	1	ENST00000368678.4:c.1336_1337delinsAG	p.Val446Arg	p.V446R	ENST00000368678		446	GTg/AGg	12/13	1	2	FACETS	0.873	0.703	1	0.873	0.703	1	CLONAL	1	TRUE	1	0.15	2		369	458	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652353	48652353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1340713003	NA	P-0066115-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	75	290	0	ENST00000376670.3:c.1024G>A	p.Gly342Ser	p.G342S	ENST00000376670	NM_002049.3	342	Ggt/Agt	6/6	1	1	FACETS	0.846	0.754	0.942	1	0.982	1	CLONAL	2	FALSE	0	0.332877953927473	1		290	222	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215925	36215926	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0066115-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	68	469	0	ENST00000222270.7:c.3467dup	p.Asn1156LysfsTer21	p.N1156Kfs*21	ENST00000222270	NM_014727.1	1155	-/A	10/37	1	2	FACETS	0.812	0.708	0.925	0.812	0.708	0.925	CLONAL	1	FALSE	1	0.332877953927473	2		469	503	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057653	27057653	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066115-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	70	453	0	ENST00000324856.7:c.1361del	p.Tyr454LeufsTer165	p.Y454Lfs*165	ENST00000324856	NM_006015.4	454	tAt/tt	3/20	0.263880493838402	1	FACETS	0.831	0.727	0.942	0.831	0.727	0.942	CLONAL	1	FALSE	0	0.332877953927473	1		453	422	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066116-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	72	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.365194517744973	3	FACETS	0.754	0.672	0.838	0.754	0.672	0.838	INDETERMINATE	2	TRUE	1	0.666294228004429	3		341	191	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0066116-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	268	642	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.641966628842525	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.666294228004429	2		642	392	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0066116-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	82	407	3	ENST00000257430.4:c.3919dup	p.Ile1307AsnfsTer8	p.I1307Nfs*8	ENST00000257430	NM_000038.5	1306	gaa/gAaa	16/16	1	2	FACETS	0.82	0.731	0.914	0.82	0.731	0.914	CLONAL	1	TRUE	1	0.666294228004429	2		410	300	SUCCESS
APC	324	MSKCC	GRCh37	5	112175261	112175261	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066116-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	98	439	0	ENST00000257430.4:c.3971del	p.Pro1324GlnfsTer91	p.P1324Qfs*91	ENST00000257430	NM_000038.5	1324	Cca/ca	16/16	1	2	FACETS	0.943	0.851	1	0.943	0.851	1	CLONAL	1	TRUE	1	0.666294228004429	2		439	312	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920436	114920436	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066116-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	182	343	0	ENST00000543371.1:c.1377G>T	p.Trp459Cys	p.W459C	ENST00000543371	NM_001198531.1	459	tgG/tgT	13/14	0.623848894683461	2	FACETS	0.932	0.881	0.982	0.932	0.881	0.982	CLONAL	2	TRUE	0	0.666294228004429	2		343	293	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035190	30035192	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs1555987732	NA	P-0066117-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	90	387	0	ENST00000338641.4:c.357_359del	p.Phe119del	p.F119del	ENST00000338641	NM_000268.3	118	TTC/-	3/16	0.679254209469551	1	FACETS	0.931	0.847	1	0.931	0.847	1	CLONAL	1	TRUE	0	0.679254209469551	1		387	188	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934574	NA	P-0066118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	24	427	0	ENST00000269305.4:c.844C>G	p.Arg282Gly	p.R282G	ENST00000269305	NM_001126112.2	282	Cgg/Ggg	8/11	0.159951414388667	3	FACETS	0.262	0.205	0.328	0.131	0.102	0.164	INDETERMINATE	1	TRUE	1	0.77	3		427	329	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883587	37883587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	136	385	0	ENST00000269571.5:c.3199G>A	p.Glu1067Lys	p.E1067K	ENST00000269571		1067	Gaa/Aaa	26/27	0.3	19	FACETS	0.837	0.759	0.918			1	INDETERMINATE	3	TRUE	NA	0.77	19		385	1062	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37876053	37876053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	301	324	0	ENST00000269571.5:c.1912G>A	p.Asp638Asn	p.D638N	ENST00000269571		638	Gat/Aat	16/27	0.3	19	FACETS	0.927	0.874	0.981			1	INDETERMINATE	6	TRUE	NA	0.77	19		324	1061	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0066118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	17	476	0	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	0.159	0.119	0.208	0.159	0.119	0.208	SUBCLONAL	1	TRUE	1	0.77	2		476	277	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934574	NA	P-0066118-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	50	427	0	ENST00000269305.4:c.844C>G	p.Arg282Gly	p.R282G	ENST00000269305	NM_001126112.2	282	Cgg/Ggg	8/11	0.210063855395541	3	FACETS	0.804	0.687	0.932	0.536	0.458	0.622	CLONAL	2	FALSE	0	0.22942616931655	3		427	302	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883587	37883587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066118-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1381	249	385	0	ENST00000269571.5:c.3199G>A	p.Glu1067Lys	p.E1067K	ENST00000269571		1067	Gaa/Aaa	26/27	0.22942616931655	60	FACETS	1	0.947	1			1	CLONAL	10	FALSE	NA	0.22942616931655	60		385	1630	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37876053	37876053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066118-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	675	324	0	ENST00000269571.5:c.1912G>A	p.Asp638Asn	p.D638N	ENST00000269571		638	Gat/Aat	16/27	0.22942616931655	60	FACETS	0.991	0.954	1			1	CLONAL	24	FALSE	NA	0.22942616931655	60		324	1894	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0066119-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	110	545	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.655674905962734	1	FACETS	0.982	0.903	1	0.982	0.903	1	CLONAL	1	TRUE	0	0.676995153345377	1		546	219	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066119-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	79	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.868	0.773	0.967	0.868	0.773	0.967	CLONAL	1	TRUE	1	0.676995153345377	2		341	269	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0066119-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	235	418	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	0.660056275653155	2	FACETS	0.897	0.853	0.94	0.897	0.853	0.94	CLONAL	2	TRUE	0	0.676995153345377	2		418	387	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2115581	2115581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45471596	NA	P-0066119-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	146	370	0	ENST00000219476.3:c.1661C>T	p.Ser554Leu	p.S554L	ENST00000219476	NM_000548.3	554	tCg/tTg	16/42	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.676995153345377	2		370	347	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119857	70119857	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066119-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	108	418	0	ENST00000245479.2:c.859G>T	p.Glu287Ter	p.E287*	ENST00000245479	NM_000346.3	287	Gag/Tag	3/3	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.676995153345377	2		418	304	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066119-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	92	333	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.676995153345377	1	FACETS	0.977	0.892	1	0.977	0.892	1	CLONAL	1	TRUE	0	0.676995153345377	1		333	184	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945780	17945780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1009464631	NA	P-0066119-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	32	515	0	ENST00000458235.1:c.2080G>A	p.Glu694Lys	p.E694K	ENST00000458235	NM_000215.3	694	Gag/Aag	16/24	1	2	FACETS	0.263	0.213	0.318	0.263	0.213	0.318	SUBCLONAL	1	TRUE	1	0.676995153345377	2		515	360	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508614	106508614	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377001952	NA	P-0066119-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	104	376	0	ENST00000359195.3:c.608C>T	p.Thr203Met	p.T203M	ENST00000359195	NM_002649.2	203	aCg/aTg	2/11	1	2	FACETS	0.969	0.879	1	0.969	0.879	1	CLONAL	1	TRUE	1	0.676995153345377	2		376	317	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937947	36937948	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0066119-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	100	541	0	ENST00000361632.4:c.888dup	p.Leu297AlafsTer116	p.L297Afs*116	ENST00000361632		296	-/G	7/16	1	2	FACETS	0.821	0.74	0.905	0.821	0.74	0.905	CLONAL	1	TRUE	1	0.676995153345377	2		541	360	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841283	15841283	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066119-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	165	312	0	ENST00000307771.7:c.1367A>G	p.Gln456Arg	p.Q456R	ENST00000307771	NM_005089.3	456	cAa/cGa	11/11	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.676995153345377	1		312	250	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0066135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	224	582	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.707487749472285	2		582	502	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118704	115118706	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0066135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	195	653	0	ENST00000257566.3:c.635_637del	p.Asn212del	p.N212del	ENST00000257566	NM_016569.3	212	aACAtt/att	2/8	1	2	FACETS	0.899	0.837	0.963	0.899	0.837	0.963	CLONAL	1	TRUE	1	0.707487749472285	2		653	613	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221666	36221666	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1568379151	NA	P-0066135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	216	675	0	ENST00000222270.7:c.5335C>T	p.Arg1779Ter	p.R1779*	ENST00000222270	NM_014727.1	1779	Cga/Tga	26/37	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.707487749472285	2		675	564	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112542	115112543	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0066135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	198	630	0	ENST00000257566.3:c.1197dup	p.Ser400ValfsTer7	p.S400Vfs*7	ENST00000257566	NM_016569.3	399	-/G	7/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.707487749472285	2		630	519	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070561	67070561	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	203	527	0	ENST00000412916.2:c.185C>A	p.Thr62Asn	p.T62N	ENST00000412916		62	aCc/aAc	3/6	0.707487749472285	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.707487749472285	1		527	335	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845669	68845669	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	174	579	0	ENST00000261769.5:c.915del	p.Ser306AlafsTer50	p.S306Afs*50	ENST00000261769	NM_004360.3	305	ctC/ct	7/16	0.707487749472285	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.707487749472285	1		579	316	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0066136-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	42	246	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.266630998803826	5	FACETS	0.809	0.675	0.959	0.202	0.168	0.24	CLONAL	1	TRUE	1	0.266630998803826	5		246	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578476	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTGCCGGGCGG	GGGTGCCGGGCGG	-	rs876659215	NA	P-0066136-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	78	761	0	ENST00000269305.4:c.454_466del	p.Pro152AlafsTer14	p.P152Afs*14	ENST00000269305	NM_001126112.2	152	CCGCCCGGCACCCgc/gc	5/11	0.266630998803826	1	FACETS	0.802	0.705	0.907	0.802	0.705	0.907	CLONAL	1	TRUE	0	0.266630998803826	1		761	632	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21346071	21346071	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370315661	NA	P-0066136-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	31	692	2	ENST00000215739.8:c.946G>A	p.Val316Met	p.V316M	ENST00000215739	NM_006767.3	316	Gtg/Atg	9/21	1	2	FACETS	0.413	0.333	0.504	0.413	0.333	0.504	SUBCLONAL	1	TRUE	1	0.266630998803826	2		694	563	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21336680	21336681	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs587777613	NA	P-0066136-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	47	688	3	ENST00000215739.8:c.27dup	p.Gln10AlafsTer24	p.Q10Afs*24	ENST00000215739	NM_006767.3	7	acg/acGg	1/21	1	2	FACETS	0.745	0.629	0.873	0.745	0.629	0.873	SUBCLONAL	1	TRUE	1	0.266630998803826	2		691	473	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391197	139391197	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066136-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	103	803	1	ENST00000277541.6:c.6994C>A	p.Pro2332Thr	p.P2332T	ENST00000277541	NM_017617.3	2332	Cca/Aca	34/34	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.266630998803826	2		804	580	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	115	481	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.551915976161673	2		481	370	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	47	324	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.283	0.239	0.333	0.283	0.239	0.333	SUBCLONAL	1	TRUE	1	0.551915976161673	2		324	601	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	155	501	0	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.939	0.864	1	0.939	0.864	1	CLONAL	1	TRUE	1	0.551915976161673	2		501	598	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272337	15272337	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs771517374	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	145	654	4	ENST00000263388.2:c.6102del	p.Gly2035ValfsTer50	p.G2035Vfs*50	ENST00000263388	NM_000435.2	2034	ccC/cc	33/33	1	2	FACETS	0.778	0.712	0.848	0.778	0.712	0.848	SUBCLONAL	1	TRUE	1	0.551915976161673	2		658	675	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	27	529	4	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	2	FACETS	0.272	0.216	0.335	0.272	0.216	0.335	SUBCLONAL	1	TRUE	1	0.551915976161673	2		533	360	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	57	656	1	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	0.292	0.25	0.338	0.292	0.25	0.338	SUBCLONAL	1	TRUE	1	0.551915976161673	2		657	707	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	147	539	3	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.812	0.744	0.883	0.812	0.744	0.883	CLONAL	1	TRUE	1	0.551915976161673	2		542	656	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	94	358	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.787	0.704	0.874	0.787	0.704	0.874	SUBCLONAL	1	TRUE	1	0.551915976161673	2		358	433	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764347	39764347	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	36	474	1	ENST00000288319.7:c.765del	p.Arg256GlyfsTer35	p.R256Gfs*35	ENST00000288319	NM_182918.3	255	ccC/cc	7/10	1	2	FACETS	0.197	0.161	0.237	0.197	0.161	0.237	SUBCLONAL	1	TRUE	1	0.551915976161673	2		475	663	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729892	41729892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762543780	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	32	450	0	ENST00000242208.4:c.637G>A	p.Ala213Thr	p.A213T	ENST00000242208	NM_002192.2	213	Gct/Act	3/3	1	2	FACETS	0.202	0.163	0.246	0.202	0.163	0.246	SUBCLONAL	1	TRUE	1	0.551915976161673	2		450	575	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	46	596	0	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.223	0.187	0.263	0.223	0.187	0.263	SUBCLONAL	1	TRUE	1	0.551915976161673	2		596	748	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928226	178928226	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519872	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	21	497	0	ENST00000263967.3:c.1412C>T	p.Pro471Leu	p.P471L	ENST00000263967	NM_006218.2	471	cCa/cTa	9/21	1	2	FACETS	0.192	0.147	0.245	0.192	0.147	0.245	SUBCLONAL	1	TRUE	1	0.551915976161673	2		497	396	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905055	50905055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	121	434	2	ENST00000440232.2:c.342del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	113	Ggg/gg	4/27	1	2	FACETS	0.806	0.731	0.884	0.806	0.731	0.884	CLONAL	1	TRUE	1	0.551915976161673	2		436	544	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982776	7982776	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	163	540	0	ENST00000319144.4:c.1009T>C	p.Cys337Arg	p.C337R	ENST00000319144	NM_001139.2	337	Tgc/Cgc	8/15	1	2	FACETS	0.948	0.874	1	0.948	0.874	1	CLONAL	1	TRUE	1	0.551915976161673	2		540	623	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246393	53246393	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	150	535	0	ENST00000375401.3:c.589del	p.Leu197TyrfsTer37	p.L197Yfs*37	ENST00000375401	NM_004187.3	197	Cta/ta	5/26	1	2	FACETS	0.782	0.716	0.851	0.782	0.716	0.851	SUBCLONAL	1	TRUE	1	0.551915976161673	2		535	695	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647182	23647182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	90	566	0	ENST00000261584.4:c.685C>T	p.Pro229Ser	p.P229S	ENST00000261584	NM_024675.3	229	Cca/Tca	4/13	1	2	FACETS	0.728	0.649	0.811	0.728	0.649	0.811	SUBCLONAL	1	TRUE	1	0.551915976161673	2		566	448	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733223	74733223	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	96	484	0	ENST00000359995.5:c.20del	p.Pro7LeufsTer7	p.P7Lfs*7	ENST00000359995	NM_001195427.1	7	cCt/ct	1/3	1	2	FACETS	0.771	0.691	0.856	0.771	0.691	0.856	SUBCLONAL	1	TRUE	1	0.551915976161673	2		484	451	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350772	89350775	+	frameshift_variant	Frame_Shift_Del	DEL	TTTG	TTTG	-	rs886039734	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	9	425	0	ENST00000301030.4:c.2175_2178del	p.Asn725LysfsTer23	p.N725Kfs*23	ENST00000301030	NM_001256183.1	725	aaCAAA/aa	9/13	1	2	FACETS	0.082	0.053	0.118	0.082	0.053	0.118	SUBCLONAL	1	TRUE	1	0.551915976161673	2		425	400	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435199	49435199	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	100	447	0	ENST00000301067.7:c.6354del	p.Ala2119LeufsTer25	p.A2119Lfs*25	ENST00000301067	NM_003482.3	2118	ccC/cc	31/54	1	2	FACETS	0.859	0.772	0.95	0.859	0.772	0.95	CLONAL	1	TRUE	1	0.551915976161673	2		447	422	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916932	178916932	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	14	425	0	ENST00000263967.3:c.319A>T	p.Asn107Tyr	p.N107Y	ENST00000263967	NM_006218.2	107	Aac/Tac	2/21	1	2	FACETS	0.121	0.087	0.163	0.121	0.087	0.163	SUBCLONAL	1	TRUE	1	0.551915976161673	2		425	419	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916894	178916894	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	12	462	0	ENST00000263967.3:c.285del	p.Gln96AsnfsTer4	p.Q96Nfs*4	ENST00000263967	NM_006218.2	94	cTt/ct	2/21	1	2	FACETS	0.102	0.071	0.141	0.102	0.071	0.141	SUBCLONAL	1	TRUE	1	0.551915976161673	2		462	426	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589586	67589588	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	novel	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	19	356	0	ENST00000274335.5:c.1350_1352del	p.His450_Glu451delinsGln	p.H450_E451delinsQ	ENST00000274335		450	cATGaa/caa	10/15	1	2	FACETS	0.238	0.181	0.306	0.238	0.181	0.306	SUBCLONAL	1	TRUE	1	0.551915976161673	2		356	289	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515115	31515115	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	113	489	0	ENST00000344624.3:c.1270A>G	p.Ser424Gly	p.S424G	ENST00000344624		424	Agt/Ggt	5/33	1	2	FACETS	0.792	0.716	0.872	0.792	0.716	0.872	SUBCLONAL	1	TRUE	1	0.551915976161673	2		489	517	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883987	37883987	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758365405	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	202	659	3	ENST00000269571.5:c.3458G>A	p.Arg1153Gln	p.R1153Q	ENST00000269571		1153	cGa/cAa	27/27	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.551915976161673	2		662	692	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1978406	1978406	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	170	462	0	ENST00000382891.5:c.3826G>A	p.Gly1276Arg	p.G1276R	ENST00000382891	NM_133335.3	1276	Ggg/Agg	21/22	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.551915976161673	2		462	549	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2966396	2966396	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	130	423	0	ENST00000396946.4:c.1784G>T	p.Gly595Val	p.G595V	ENST00000396946	NM_032415.4	595	gGg/gTg	14/25	1	2	FACETS	0.85	0.775	0.929	0.85	0.775	0.929	CLONAL	1	TRUE	1	0.551915976161673	2		423	554	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149375036	149375036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	160	539	0	ENST00000360632.3:c.58G>A	p.Val20Ile	p.V20I	ENST00000360632	NM_015472.4	20	Gtc/Atc	2/7	1	2	FACETS	0.808	0.742	0.876	0.808	0.742	0.876	CLONAL	1	TRUE	1	0.551915976161673	2		539	718	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141589	202141589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	51	479	0	ENST00000358485.4:c.877G>A	p.Gly293Arg	p.G293R	ENST00000358485	NM_001080125.1	293	Gga/Aga	7/9	1	2	FACETS	0.319	0.27	0.372	0.319	0.27	0.372	SUBCLONAL	1	TRUE	1	0.551915976161673	2		479	580	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720806	89720820	+	inframe_deletion	In_Frame_Del	DEL	TTTAACAAAAAATGA	TTTAACAAAAAATGA	-	novel	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	108	147	0	ENST00000371953.3:c.958_972del	p.Thr321_Leu325del	p.T321_L325del	ENST00000371953	NM_000314.4	319	acTTTAACAAAAAATGAt/act	8/9	0.551915976161673	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.551915976161673	2		147	159	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260450	16260450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs539910371	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	170	601	0	ENST00000375759.3:c.7715C>T	p.Pro2572Leu	p.P2572L	ENST00000375759	NM_015001.2	2572	cCg/cTg	11/15	1	2	FACETS	0.798	0.735	0.863	0.798	0.735	0.863	SUBCLONAL	1	TRUE	1	0.551915976161673	2		601	772	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474025	29474025	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	151	510	0	ENST00000389048.3:c.2150A>G	p.Glu717Gly	p.E717G	ENST00000389048	NM_004304.4	717	gAg/gGg	12/29	1	2	FACETS	0.935	0.859	1	0.935	0.859	1	CLONAL	1	TRUE	1	0.551915976161673	2		510	585	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16062139	16062139	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138433631	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	34	436	1	ENST00000268712.3:c.667G>A	p.Val223Met	p.V223M	ENST00000268712	NM_006311.3	223	Gtg/Atg	6/46	1	2	FACETS	0.202	0.165	0.245	0.202	0.165	0.245	SUBCLONAL	1	TRUE	1	0.551915976161673	2		437	609	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085683	16085685	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	rs777089361	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	161	503	0	ENST00000281043.3:c.865_867del	p.Ser289del	p.S289del	ENST00000281043	NM_005378.4	287	TCC/-	3/3	1	2	FACETS	0.961	0.886	1	0.961	0.886	1	CLONAL	1	TRUE	1	0.551915976161673	2		503	607	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428198	47428198	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	66	505	0	ENST00000377045.4:c.1158G>T	p.Glu386Asp	p.E386D	ENST00000377045	NM_001654.4	386	gaG/gaT	11/16	1	2	FACETS	0.381	0.33	0.436	0.381	0.33	0.436	SUBCLONAL	1	TRUE	1	0.551915976161673	2		505	628	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101837	11101837	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	163	512	0	ENST00000358026.2:c.1257G>T	p.Glu419Asp	p.E419D	ENST00000358026	NM_001128849.1	419	gaG/gaT	8/36	1	2	FACETS	0.835	0.769	0.905	0.835	0.769	0.905	CLONAL	1	TRUE	1	0.551915976161673	2		512	707	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007149	152007149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	108	420	0	ENST00000262189.6:c.751G>A	p.Ala251Thr	p.A251T	ENST00000262189	NM_170606.2	251	Gct/Act	6/59	1	2	FACETS	0.786	0.709	0.867	0.786	0.709	0.867	SUBCLONAL	1	TRUE	1	0.551915976161673	2		420	498	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528471	157528471	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	35	555	0	ENST00000346085.5:c.6196C>A	p.Pro2066Thr	p.P2066T	ENST00000346085	NM_020732.3	2066	Ccc/Acc	20/20	1	2	FACETS	0.204	0.166	0.246	0.204	0.166	0.246	SUBCLONAL	1	TRUE	1	0.551915976161673	2		555	623	SUCCESS
SCG5	6447	MSKCC	GRCh37	15	32935963	32935963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567248964	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	162	495	0	ENST00000300175.4:c.170G>A	p.Arg57Gln	p.R57Q	ENST00000300175	NM_001144757.1	57	cGa/cAa	2/6	1	2	FACETS	0.942	0.868	1	0.942	0.868	1	CLONAL	1	TRUE	1	0.551915976161673	2		495	623	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940589	71940589	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	211	574	0	ENST00000298229.2:c.743del	p.Leu248CysfsTer14	p.L248Cfs*14	ENST00000298229	NM_001567.3	247	cTt/ct	6/28	1	2	FACETS	0.988	0.92	1	0.988	0.92	1	CLONAL	1	TRUE	1	0.551915976161673	2		574	774	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797916	42797916	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	175	720	1	ENST00000575354.2:c.3968A>G	p.Glu1323Gly	p.E1323G	ENST00000575354	NM_015125.3	1323	gAg/gGg	16/20	1	2	FACETS	0.944	0.872	1	0.944	0.872	1	CLONAL	1	TRUE	1	0.551915976161673	2		721	672	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271969	15271969	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	155	536	0	ENST00000263388.2:c.6470T>C	p.Val2157Ala	p.V2157A	ENST00000263388	NM_000435.2	2157	gTa/gCa	33/33	1	2	FACETS	0.869	0.799	0.943	0.869	0.799	0.943	CLONAL	1	TRUE	1	0.551915976161673	2		536	646	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429316	78429316	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	157	474	0	ENST00000370768.2:c.1126C>G	p.Leu376Val	p.L376V	ENST00000370768	NM_003902.3	376	Cta/Gta	13/20	1	2	FACETS	0.991	0.913	1	0.991	0.913	1	CLONAL	1	TRUE	1	0.551915976161673	2		474	574	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0066138-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	70	284	0	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	0.247156040201324	2	FACETS	0.84	0.74	0.945	0.84	0.74	0.945	CLONAL	2	TRUE	0	0.293537710635286	2		284	284	SUCCESS
APC	324	MSKCC	GRCh37	5	112111363	112111363	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066138-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	36	318	0	ENST00000257430.4:c.460G>C	p.Glu154Gln	p.E154Q	ENST00000257430	NM_000038.5	154	Gaa/Caa	5/16	1	2	FACETS	0.705	0.581	0.843	0.705	0.581	0.843	SUBCLONAL	1	TRUE	1	0.293537710635286	2		318	348	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211608	46211608	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066138-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	45	395	1	ENST00000334344.6:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000334344	NM_152641.2	192	Caa/Taa	5/21	0.170326607305459	3	FACETS	0.59	0.495	0.695	0.295	0.247	0.348	INDETERMINATE	1	TRUE	1	0.293537710635286	3		396	596	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411884	116411893	+	intron_variant	Intron	DEL	TCTTTCTCTC	TCTTTCTCTC	-	novel	NA	P-0066138-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	187	528	0	ENST00000397752.3:c.2888-18_2888-9del		p.*963*	ENST00000397752	NM_000245.2	-/1390			0.247156040201324	2	FACETS	0.785	0.726	0.845	0.785	0.726	0.845	SUBCLONAL	2	TRUE	0	0.293537710635286	2		528	812	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056039	26056039	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs61742488	NA	P-0066138-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	75	535	0	ENST00000343677.2:c.618G>C	p.Lys206Asn	p.K206N	ENST00000343677	NM_005319.3	206	aaG/aaC	1/1	1	2	FACETS	0.72	0.63	0.816	0.72	0.63	0.816	SUBCLONAL	1	TRUE	1	0.293537710635286	2		535	710	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302794	15302794	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066138-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	36	621	0	ENST00000263388.2:c.656del	p.Thr219IlefsTer17	p.T219Ifs*17	ENST00000263388	NM_000435.2	219	aCt/at	4/33	0.293537710635286	1	FACETS	0.408	0.335	0.49	0.408	0.335	0.49	SUBCLONAL	1	TRUE	0	0.293537710635286	1		621	513	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821965	72821965	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150064087	NA	P-0066138-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	92	524	0	ENST00000268489.5:c.10210C>T	p.Pro3404Ser	p.P3404S	ENST00000268489	NM_006885.3	3404	Ccc/Tcc	10/10	0.293537710635286	1	FACETS	0.983	0.876	1	0.983	0.876	1	CLONAL	1	TRUE	0	0.293537710635286	1		524	544	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50773822	50773822	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066138-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	52	508	0	ENST00000307179.4:c.1363C>G	p.Leu455Val	p.L455V	ENST00000307179		455	Ctc/Gtc	11/20	0.293537710635286	1	FACETS	0.476	0.405	0.555	0.476	0.405	0.555	SUBCLONAL	1	TRUE	0	0.293537710635286	1		508	635	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275414	115275414	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066138-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	39	457	0	ENST00000438362.2:c.999C>G	p.Ile333Met	p.I333M	ENST00000438362	NM_001242891.1	333	atC/atG	10/20	0.293537710635286	1	FACETS	0.442	0.366	0.527	0.442	0.366	0.527	SUBCLONAL	1	TRUE	0	0.293537710635286	1		457	513	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	71	446	0				ENST00000310581	NM_198253.2	-/1132			0.337259429857158	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.337259429857158	1		446	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934573	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	167	543	0	ENST00000269305.4:c.722C>A	p.Ser241Tyr	p.S241Y	ENST00000269305	NM_001126112.2	241	tCc/tAc	7/11	0.285708707633812	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.337259429857158	1		543	575	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716344	18716344	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778895247	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	101	523	0	ENST00000266497.5:c.3691G>A	p.Glu1231Lys	p.E1231K	ENST00000266497		1231	Gaa/Aaa	26/31	0.337259429857158	1	FACETS	0.866	0.776	0.961	0.866	0.776	0.961	CLONAL	1	TRUE	0	0.337259429857158	1		523	575	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424958105	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	56	580	0	ENST00000334344.6:c.940C>T	p.Arg314Cys	p.R314C	ENST00000334344	NM_152641.2	314	Cgt/Tgt	8/21	1	2	FACETS	0.514	0.44	0.595	0.514	0.44	0.595	SUBCLONAL	1	TRUE	1	0.337259429857158	2		580	646	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514563	41514563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	98	508	0	ENST00000373198.4:c.98C>T	p.Ser33Phe	p.S33F	ENST00000373198	NM_133170.3	33	tCc/tTc	2/32	1	2	FACETS	0.901	0.805	1	0.901	0.805	1	CLONAL	1	TRUE	1	0.337259429857158	2		508	645	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976476	25976476	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	102	471	0	ENST00000435504.4:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000435504		357	Cga/Tga	11/13	1	2	FACETS	0.968	0.867	1	0.968	0.867	1	CLONAL	1	TRUE	1	0.337259429857158	2		471	625	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606667	29606667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs4363989	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	125	540	0	ENST00000389048.3:c.1213G>A	p.Glu405Lys	p.E405K	ENST00000389048	NM_004304.4	405	Gaa/Aaa	5/29	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.337259429857158	2		540	689	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729949	41729949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1165688714	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	116	666	0	ENST00000242208.4:c.580G>A	p.Glu194Lys	p.E194K	ENST00000242208	NM_002192.2	194	Gaa/Aaa	3/3	1	2	FACETS	0.981	0.885	1	0.981	0.885	1	CLONAL	1	TRUE	1	0.337259429857158	2		666	701	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243472	46243472	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	128	524	0	ENST00000334344.6:c.1825C>T	p.Gln609Ter	p.Q609*	ENST00000334344	NM_152641.2	609	Cag/Tag	14/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.337259429857158	2		524	629	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008200	29008200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1014160326	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	123	592	0	ENST00000282397.4:c.671G>A	p.Arg224Gln	p.R224Q	ENST00000282397	NM_002019.4	224	cGa/cAa	5/30	0.337259429857158	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.337259429857158	1		592	602	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956965	2956965	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142828146	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	88	536	2	ENST00000396946.4:c.2662C>T	p.Arg888Cys	p.R888C	ENST00000396946	NM_032415.4	888	Cgt/Tgt	20/25	1	2	FACETS	0.908	0.806	1	0.908	0.806	1	CLONAL	1	TRUE	1	0.337259429857158	2		538	575	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980912	40980912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	132	607	0	ENST00000373198.4:c.1574C>T	p.Ala525Val	p.A525V	ENST00000373198	NM_133170.3	525	gCt/gTt	10/32	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.337259429857158	2		607	694	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115252203	115252203	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	130	447	0	ENST00000369535.4:c.437C>T	p.Ala146Val	p.A146V	ENST00000369535	NM_002524.4	146	gCc/gTc	4/7	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.337259429857158	2		447	714	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426121	47426121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519786	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	256	329	0	ENST00000377045.4:c.641C>T	p.Ser214Phe	p.S214F	ENST00000377045	NM_001654.4	214	tCc/tTc	7/16	0.329738986001458	2	FACETS	1	0.974	1			1	CLONAL	3	TRUE	NA	0.337259429857158	2		329	486	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713470	40713470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318044562	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	102	598	0	ENST00000373198.4:c.4045C>T	p.Arg1349Cys	p.R1349C	ENST00000373198	NM_133170.3	1349	Cgt/Tgt	30/32	1	2	FACETS	0.882	0.789	0.98	0.882	0.789	0.98	CLONAL	1	TRUE	1	0.337259429857158	2		598	686	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971077	21971077	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	122	599	1	ENST00000304494.5:c.281T>A	p.Leu94Gln	p.L94Q	ENST00000304494	NM_000077.4	94	cTg/cAg	2/3	0.337259429857158	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.337259429857158	1		600	484	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246459	10246459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	123	509	0	ENST00000340748.4:c.4678C>T	p.Pro1560Ser	p.P1560S	ENST00000340748		1560	Cct/Tct	38/40	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.337259429857158	2		509	632	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981881	70981881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	96	721	0	ENST00000276594.2:c.215G>A	p.Arg72Gln	p.R72Q	ENST00000276594	NM_024504.3	72	cGg/cAg	2/8	1	2	FACETS	0.914	0.815	1	0.914	0.815	1	CLONAL	1	TRUE	1	0.337259429857158	2		721	623	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527925	157527925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377877762	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	95	716	0	ENST00000346085.5:c.5650C>T	p.Arg1884Trp	p.R1884W	ENST00000346085	NM_020732.3	1884	Cgg/Tgg	20/20	1	2	FACETS	0.808	0.72	0.902	0.808	0.72	0.902	CLONAL	1	TRUE	1	0.337259429857158	2		716	697	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638804	176638804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1021852466	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	159	548	0	ENST00000439151.2:c.3404C>T	p.Pro1135Leu	p.P1135L	ENST00000439151	NM_022455.4	1135	cCa/cTa	5/23	0.337259429857158	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.337259429857158	1		548	705	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041112	112041112	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	94	671	0	ENST00000368678.4:c.143C>T	p.Pro48Leu	p.P48L	ENST00000368678		48	cCc/cTc	3/13	1	2	FACETS	0.769	0.684	0.859	0.769	0.684	0.859	SUBCLONAL	1	TRUE	1	0.337259429857158	2		671	725	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505512	157505512	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	86	537	0	ENST00000346085.5:c.3493G>A	p.Glu1165Lys	p.E1165K	ENST00000346085	NM_020732.3	1165	Gaa/Aaa	13/20	1	2	FACETS	0.835	0.739	0.937	0.835	0.739	0.937	CLONAL	1	TRUE	1	0.337259429857158	2		537	611	SUCCESS
REST	5978	MSKCC	GRCh37	4	57797467	57797467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs114282228	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	166	735	0	ENST00000309042.7:c.2443C>T	p.Pro815Ser	p.P815S	ENST00000309042	NM_005612.4	815	Cct/Tct	4/4	0.337259429857158	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.337259429857158	1		735	690	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566448	139566448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs960621872	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	129	495	0	ENST00000308874.7:c.707C>T	p.Pro236Leu	p.P236L	ENST00000308874		236	cCc/cTc	9/10	1	2	FACETS	0.789	0.719	0.86	1	0.987	1	SUBCLONAL	2	TRUE	1	0.337259429857158	2		495	485	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539651	187539651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1330099752	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	154	529	0	ENST00000441802.2:c.8089G>A	p.Glu2697Lys	p.E2697K	ENST00000441802	NM_005245.3	2697	Gaa/Aaa	10/27	0.337259429857158	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.337259429857158	1		529	611	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745120	41745120	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1177926109	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	150	596	0	ENST00000301178.4:c.1186G>A	p.Asp396Asn	p.D396N	ENST00000301178	NM_021913.4	396	Gac/Aac	9/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.337259429857158	2		596	680	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25990476	25990476	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	123	495	0	ENST00000435504.4:c.751C>T	p.Gln251Ter	p.Q251*	ENST00000435504		251	Cag/Tag	8/13	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.337259429857158	2		495	554	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483922	88483922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	58	543	0	ENST00000360948.2:c.1648G>A	p.Gly550Arg	p.G550R	ENST00000360948	NM_001012338.2	550	Gga/Aga	14/19	1	2	FACETS	0.588	0.505	0.678	0.588	0.505	0.678	SUBCLONAL	1	TRUE	1	0.337259429857158	2		543	585	SUCCESS
BLM	641	MSKCC	GRCh37	15	91337532	91337532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	119	425	0	ENST00000355112.3:c.3155C>T	p.Pro1052Leu	p.P1052L	ENST00000355112	NM_000057.2	1052	cCt/cTt	16/22	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.337259429857158	2		425	614	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939522	71939522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528612645	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	147	728	2	ENST00000298229.2:c.377C>T	p.Pro126Leu	p.P126L	ENST00000298229	NM_001567.3	126	cCg/cTg	3/28	0.337259429857158	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.337259429857158	1		730	586	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41554431	41554431	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	157	466	2	ENST00000263253.7:c.3517C>T	p.Gln1173Ter	p.Q1173*	ENST00000263253	NM_001429.3	1173	Cag/Tag	19/31	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.337259429857158	2		468	755	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115272974	115272974	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	142	590	0	ENST00000438362.2:c.1399C>T	p.His467Tyr	p.H467Y	ENST00000438362	NM_001242891.1	467	Cat/Tat	12/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.337259429857158	2		590	781	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676262	29676262	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060500385	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	28	427	0	ENST00000356175.3:c.7251C>G	p.Tyr2417Ter	p.Y2417*	ENST00000356175	NM_000267.3	2417	taC/taG	48/57	0.285708707633812	1	FACETS	0.256	0.204	0.316	0.256	0.204	0.316	SUBCLONAL	1	TRUE	0	0.337259429857158	1		427	539	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27192537	27192537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	238	533	0	ENST00000380036.4:c.1540G>A	p.Glu514Lys	p.E514K	ENST00000380036	NM_000459.3	514	Gaa/Aaa	11/23	0.337259429857158	1	FACETS	0.833	0.782	0.886	1	0.994	1	CLONAL	2	TRUE	0	0.337259429857158	1		533	704	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130406	29130406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876659833	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	60	613	0	ENST00000328354.6:c.304G>A	p.Gly102Arg	p.G102R	ENST00000328354	NM_007194.3	102	Gga/Aga	2/15	1	2	FACETS	0.45	0.387	0.519	0.45	0.387	0.519	SUBCLONAL	1	TRUE	1	0.337259429857158	2		613	791	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348686	118348686	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	123	385	0	ENST00000534358.1:c.3339G>C	p.Lys1113Asn	p.K1113N	ENST00000534358	NM_005933.3	1113	aaG/aaC	5/36	0.337259429857158	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.337259429857158	1		385	580	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152074	11152074	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	97	614	0	ENST00000358026.2:c.4358C>A	p.Ser1453Tyr	p.S1453Y	ENST00000358026	NM_001128849.1	1453	tCc/tAc	31/36	1	2	FACETS	0.771	0.687	0.86	0.771	0.687	0.86	SUBCLONAL	1	TRUE	1	0.337259429857158	2		614	746	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223174	36223175	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	68	800	1	ENST00000222270.7:c.5724_5725delinsAT	p.Pro1909Ser	p.P1909S	ENST00000222270	NM_014727.1	1908	gcTCcc/gcATcc	28/37	1	2	FACETS	0.533	0.463	0.609	0.533	0.463	0.609	SUBCLONAL	1	TRUE	1	0.337259429857158	2		801	757	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662992	227662992	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1446029674	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	79	562	0	ENST00000305123.5:c.463C>A	p.Pro155Thr	p.P155T	ENST00000305123	NM_005544.2	155	Ccc/Acc	1/2	1	2	FACETS	0.789	0.694	0.89	0.789	0.694	0.89	SUBCLONAL	1	TRUE	1	0.337259429857158	2		562	594	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664881	29664881	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	84	490	0	ENST00000356175.3:c.6624G>A	p.Trp2208Ter	p.W2208*	ENST00000356175	NM_000267.3	2208	tgG/tgA	43/57	0.285708707633812	1	FACETS	0.732	0.647	0.822	0.732	0.647	0.822	SUBCLONAL	1	TRUE	0	0.337259429857158	1		490	566	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879159	151879159	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	148	684	0	ENST00000262189.6:c.5786T>C	p.Leu1929Ser	p.L1929S	ENST00000262189	NM_170606.2	1929	tTa/tCa	36/59	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.337259429857158	2		684	750	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794872	242794872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200323895	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	104	624	0	ENST00000334409.5:c.337G>A	p.Ala113Thr	p.A113T	ENST00000334409	NM_005018.2	113	Gcc/Acc	2/5	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.337259429857158	2		624	614	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2047378	2047378	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	26	417	0	ENST00000349721.2:c.940C>A	p.Gln314Lys	p.Q314K	ENST00000349721	NM_003070.3	314	Cag/Aag	5/34	NA	2	FACETS	0.414	0.328	0.514			1	INDETERMINATE	1	TRUE	NA	0.337259429857158	2		417	372	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210836	2210836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	94	544	0	ENST00000398665.3:c.1333G>A	p.Ala445Thr	p.A445T	ENST00000398665	NM_032482.2	445	Gcg/Acg	14/28	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.337259429857158	2		544	552	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677896	117677896	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	90	490	0	ENST00000368508.3:c.4037A>G	p.Asn1346Ser	p.N1346S	ENST00000368508	NM_002944.2	1346	aAc/aGc	25/43	1	2	FACETS	0.853	0.757	0.954	0.853	0.757	0.954	CLONAL	1	TRUE	1	0.337259429857158	2		490	626	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005885	69005885	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	108	499	0	ENST00000288368.4:c.2296G>A	p.Glu766Lys	p.E766K	ENST00000288368	NM_024870.2	766	Gaa/Aaa	21/40	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.337259429857158	2		499	562	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037406	12037406	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066142-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	229	916	2	ENST00000396373.4:c.1037A>G	p.Tyr346Cys	p.Y346C	ENST00000396373	NM_001987.4	346	tAt/tGt	6/8	0.362198971453562	4	FACETS	0.959	0.897	1	0.959	0.897	1	CLONAL	2	TRUE	2	0.49554153095175	4		918	721	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920050	1920050	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066142-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	174	829	0	ENST00000382891.5:c.1110G>C	p.Leu370Phe	p.L370F	ENST00000382891	NM_133335.3	370	ttG/ttC	5/22	0.311446552977379	5	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.49554153095175	5		829	864	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491300	2491300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066142-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	107	853	0	ENST00000355716.4:c.343G>A	p.Glu115Lys	p.E115K	ENST00000355716	NM_003820.2	115	Gag/Aag	4/8	0.495595830137893	3	FACETS	0.865	0.777	0.957	0.432	0.388	0.479	CLONAL	1	TRUE	1	0.49554153095175	3		853	623	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562958	29562958	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs878853890	NA	P-0066142-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	233	494	0	ENST00000356175.3:c.3897del	p.Lys1299AsnfsTer10	p.K1299Nfs*10	ENST00000356175	NM_000267.3	1298	cAa/ca	29/57	0.348656123898815	4	FACETS	0.953	0.907	0.997	0.953	0.907	0.997	CLONAL	4	TRUE	0	0.49554153095175	4		494	369	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920300	1920300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066142-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	185	672	0	ENST00000382891.5:c.1360G>A	p.Gly454Arg	p.G454R	ENST00000382891	NM_133335.3	454	Gga/Aga	5/22	0.311446552977379	5	FACETS	0.881	0.815	0.948			1	CLONAL	2	TRUE	NA	0.49554153095175	5		672	739	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10789674	10789674	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	179	477	2	ENST00000361367.2:c.1926T>G	p.Asn642Lys	p.N642K	ENST00000361367	NM_014633.3	642	aaT/aaG	15/25	1	2	FACETS	0.958	0.888	1	0.958	0.888	1	CLONAL	1	TRUE	1	0.643523111444271	2		479	581	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129152	2129152	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057522974	NA	P-0066143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	34	635	0	ENST00000219476.3:c.3086T>C	p.Met1029Thr	p.M1029T	ENST00000219476	NM_000548.3	1029	aTg/aCg	27/42	0.616768328197015	1	FACETS	0.121	0.099	0.147	0.121	0.099	0.147	SUBCLONAL	1	TRUE	0	0.643523111444271	1		635	590	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0066145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	34	167	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.270638421968341	2		167	205	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486049	29486050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0066145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	86	351	0	ENST00000356175.3:c.233dup	p.Asn78LysfsTer29	p.N78Kfs*29	ENST00000356175	NM_000267.3	76	gaa/gAaa	3/57	0.270638421968341	2	FACETS	0.924	0.824	1	0.924	0.824	1	CLONAL	2	TRUE	0	0.270638421968341	2		351	344	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584575	52584575	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	101	638	0	ENST00000394830.3:c.4438C>T	p.Gln1480Ter	p.Q1480*	ENST00000394830	NM_018313.4	1480	Cag/Tag	29/30	0.570933082492831	1	FACETS	0.961	0.873	1	0.961	0.873	1	CLONAL	1	TRUE	0	0.570933082492831	1		638	263	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058663	47058664	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0066146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	27	560	0	ENST00000409792.3:c.7614_7615del	p.His2538GlnfsTer7	p.H2538Qfs*7	ENST00000409792	NM_014159.6	2538	caCAaa/caaa	21/21	1	2	FACETS	0.364	0.29	0.447	0.364	0.29	0.447	SUBCLONAL	1	TRUE	1	0.570933082492831	2		560	260	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183763	10183763	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs869025621	NA	P-0066146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	103	559	0	ENST00000256474.2:c.232A>C	p.Asn78His	p.N78H	ENST00000256474	NM_000551.3	78	Aat/Cat	1/3	1	2	FACETS	0.805	0.737	0.875	1	0.987	1	CLONAL	2	TRUE	1	0.570933082492831	2		559	224	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53241047	53241767	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGCCTGCTCAAAGCCAAAGGCTTCTGGGGGCCGCTTACACTCCTGAAACCCAAAGGAGAACATGTCACCAAAACAGAGGCAAAGAGGTGAAGAATCCTCCCAAGTGGAACTGGAATATAAGGGGTAGGGAGGGAGAAGAGCCCTAGGTCTGCACTCAAGGCCCCTGAGGCAGGCCTTACTTTACAGCTGTACCTTTTGCTCTTACCACTTCGGCTTAGTCTTTTCATTCCCCATCATGCTTTTGCTCAGTTCCTCCCTACTGAAATGTCCTTTTCCACTTTCTTTCATTGGTTCCTCAAAACTCAATTCCAGTCTCACAACTTCCAGGGAGTCATCTCATGCTCTTTTCTTCCTTTAGGACTTTATCTAAATGGCTCTGACTTTAATATGCTATCCTGTGTTCTTCTGCCACCATTTTTCCTCTCTAGCTAAAATGTGATTCTTTTTTTTTTTTTTTTTGAGACGGAGTCTTGCTCTGTCACCCAGACTGGAGTGCAGGGTCACAATCTCAACTCACTGCAACCTCCGCCTCCCAGGTTCAAGCGATTCTCCTGCCTCAGCTTCCCGAGTAGCTGGGATTACAGGTGCCCGCCACCACGCCCAGCTAATTTTTGTATTTTTAGTAGAGATGGGGTTTCACCATGTTGGCCAGGCTGGTCTCAAACTCCTGACCCTGTGATCCGCCCGCCTTGGCCTCCCAAGTGCTGGGATTACAGGCGTG	AGCCTGCTCAAAGCCAAAGGCTTCTGGGGGCCGCTTACACTCCTGAAACCCAAAGGAGAACATGTCACCAAAACAGAGGCAAAGAGGTGAAGAATCCTCCCAAGTGGAACTGGAATATAAGGGGTAGGGAGGGAGAAGAGCCCTAGGTCTGCACTCAAGGCCCCTGAGGCAGGCCTTACTTTACAGCTGTACCTTTTGCTCTTACCACTTCGGCTTAGTCTTTTCATTCCCCATCATGCTTTTGCTCAGTTCCTCCCTACTGAAATGTCCTTTTCCACTTTCTTTCATTGGTTCCTCAAAACTCAATTCCAGTCTCACAACTTCCAGGGAGTCATCTCATGCTCTTTTCTTCCTTTAGGACTTTATCTAAATGGCTCTGACTTTAATATGCTATCCTGTGTTCTTCTGCCACCATTTTTCCTCTCTAGCTAAAATGTGATTCTTTTTTTTTTTTTTTTTGAGACGGAGTCTTGCTCTGTCACCCAGACTGGAGTGCAGGGTCACAATCTCAACTCACTGCAACCTCCGCCTCCCAGGTTCAAGCGATTCTCCTGCCTCAGCTTCCCGAGTAGCTGGGATTACAGGTGCCCGCCACCACGCCCAGCTAATTTTTGTATTTTTAGTAGAGATGGGGTTTCACCATGTTGGCCAGGCTGGTCTCAAACTCCTGACCCTGTGATCCGCCCGCCTTGGCCTCCCAAGTGCTGGGATTACAGGCGTG	-	novel	NA	P-0066146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	40	320	0	ENST00000375401.3:c.1123-679_1164del		p.X375_splice	ENST00000375401	NM_004187.3	375		9/26	1	1	FACETS	0.575	0.485	0.673	0.575	0.485	0.673	SUBCLONAL	1	TRUE	0	0.570933082492831	1		320	174	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18943175	18943198	+	inframe_deletion	In_Frame_Del	DEL	GGCCCGGGCGGTGGCGGCGCGGGA	GGCCCGGGCGGTGGCGGCGCGGGA	-	rs768202667	NA	P-0066146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	93	360	0	ENST00000262803.5:c.168_191del	p.Gly57_Gly64del	p.G57_G64del	ENST00000262803	NM_002911.3	53	GGCCCGGGCGGTGGCGGCGCGGGA/-	1/24	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.570933082492831	2		360	261	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721463	49721467	+	frameshift_variant,stop_lost	Frame_Shift_Del	DEL	AACCC	AACCC	-	novel	NA	P-0066146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	76	376	0	ENST00000449682.2:c.2172_2176del	p.Ter726ProfsTer?	p.*726Pfs*?	ENST00000449682	NM_020998.3	724	ctGGGTTag/ctag	18/18	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.570933082492831	2		376	200	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	54	446	0				ENST00000310581	NM_198253.2	-/1132			0.148022204579948	0	FACETS	0.364	0.315	0.415			1	INDETERMINATE	1	TRUE	0	0.6	0		446	198	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981098	201981098	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	86	576	0	ENST00000359651.3:c.177G>A	p.Trp59Ter	p.W59*	ENST00000359651		59	tgG/tgA	2/8	1	2	FACETS	0.579	0.514	0.648	0.579	0.514	0.648	SUBCLONAL	1	TRUE	1	0.6	2		576	495	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0066150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	48	533	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	0.253951987617465	4	FACETS	0.756	0.65	0.869	0.756	0.65	0.869	INDETERMINATE	2	FALSE	2	0.579420713400021	4		533	173	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1023835002	NA	P-0066160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	786	619	0	ENST00000558401.1:c.1A>G	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Gtg	1/4	0.777386161381237	5	FACETS	0.911	0.888	0.934	1	0.997	1	CLONAL	4	TRUE	2	0.777386161381237	5		619	1202	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56852643	56852643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs966758586	NA	P-0066160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	323	523	2	ENST00000308159.5:c.557C>T	p.Ala186Val	p.A186V	ENST00000308159	NM_014669.4	186	gCg/gTg	6/22	0.777386161381237	2	FACETS	1	0.979	1	0.529	0.502	0.557	CLONAL	1	TRUE	0	0.777386161381237	2		525	785	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864023	97864023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881729	NA	P-0066160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	248	568	0	ENST00000289081.3:c.1643G>A	p.Arg548Gln	p.R548Q	ENST00000289081	NM_000136.2	548	cGa/cAa	15/15	1	2	FACETS	0.982	0.924	1	0.982	0.924	1	CLONAL	1	TRUE	1	0.777386161381237	2		568	650	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967008	18967008	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	260	582	0	ENST00000262803.5:c.1723C>T	p.Gln575Ter	p.Q575*	ENST00000262803	NM_002911.3	575	Cag/Tag	13/24	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.777386161381237	2		582	649	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949126	44949132	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTATT	GGCTATT	-	novel	NA	P-0066160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	245	548	0	ENST00000377967.4:c.3691_3697del	p.Ile1231GlyfsTer32	p.I1231Gfs*32	ENST00000377967	NM_021140.2	1229	caGGCTATT/ca	25/29	0.777386161381237	1	FACETS	0.963	0.917	1	0.963	0.917	1	CLONAL	1	TRUE	0	0.777386161381237	1		548	400	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	158	721	4	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.908	0.836	0.983	0.908	0.836	0.983	CLONAL	1	TRUE	1	0.566575243042367	2		725	614	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957419	1957419	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	128	683	1	ENST00000382891.5:c.2523del		p.X841_splice	ENST00000382891	NM_133335.3	841			1	2	FACETS	0.893	0.814	0.975	0.893	0.814	0.975	CLONAL	1	TRUE	1	0.566575243042367	2		684	506	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675571	86675571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1561325048	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	94	453	0	ENST00000274376.6:c.2513del	p.Asn838MetfsTer4	p.N838Mfs*4	ENST00000274376	NM_002890.2	836	gAa/ga	19/25	1	2	FACETS	0.798	0.714	0.885	0.798	0.714	0.885	SUBCLONAL	1	TRUE	1	0.566575243042367	2		453	416	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	166	690	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.885	0.816	0.957	0.885	0.816	0.957	CLONAL	1	TRUE	1	0.566575243042367	2		690	662	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	174	760	5	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.895	0.827	0.966	0.895	0.827	0.966	CLONAL	1	TRUE	1	0.566575243042367	2		765	686	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	42	529	4	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	2	FACETS	0.501	0.42	0.59	0.501	0.42	0.59	SUBCLONAL	1	TRUE	1	0.566575243042367	2		533	296	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	77	335	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.566575243042367	2		335	249	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	211	855	2	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.566575243042367	2		857	744	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	145	832	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.254744882792845	3	FACETS	1	0.961	1			1	INDETERMINATE	1	TRUE	NA	0.566575243042367	3		832	605	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	215	806	4	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.566575243042367	2		810	708	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	155	782	3	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.566575243042367	2		785	546	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	183	821	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.566575243042367	2		821	630	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs767894241	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	127	668	2	ENST00000358127.4:c.76dup	p.Val26GlyfsTer49	p.V26Gfs*49	ENST00000358127	NM_001280556.1	26	gtt/gGtt	2/10	1	2	FACETS	0.798	0.726	0.873	0.798	0.726	0.873	SUBCLONAL	1	TRUE	1	0.566575243042367	2		670	562	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103389	2103389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45482691	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	115	534	0	ENST00000219476.3:c.272C>T	p.Pro91Leu	p.P91L	ENST00000219476	NM_000548.3	91	cCg/cTg	4/42	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.566575243042367	2		534	403	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266134	41266136	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs587776850	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	182	618	0	ENST00000349496.5:c.133_135del	p.Ser45del	p.S45del	ENST00000349496	NM_001904.3	44	cCTTct/cct	3/15	0.553572743856458	2	FACETS	0.922	0.853	0.992	0.461	0.426	0.496	CLONAL	1	TRUE	0	0.566575243042367	2		618	697	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931452	131931452	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507178	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	226	618	17	ENST00000265335.6:c.2165del	p.Lys722ArgfsTer14	p.K722Rfs*14	ENST00000265335		719	ctA/ct	13/25	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.566575243042367	2		635	685	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	204	752	15	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.566575243042367	2		767	715	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270530	98270530	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs751977093	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	58	506	0	ENST00000331920.6:c.114del	p.Leu39CysfsTer41	p.L39Cfs*41	ENST00000331920	NM_000264.3	38	ggG/gg	1/24	1	2	FACETS	0.638	0.551	0.731	0.638	0.551	0.731	SUBCLONAL	1	TRUE	1	0.566575243042367	2		506	321	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029445	16029446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	179	574	7	ENST00000268712.3:c.1584dup	p.Glu529ArgfsTer7	p.E529Rfs*7	ENST00000268712	NM_006311.3	528	-/A	15/46	1	2	FACETS	0.959	0.887	1	0.959	0.887	1	CLONAL	1	TRUE	1	0.566575243042367	2		581	659	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103754	47103755	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	rs749901643	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	166	708	0	ENST00000409792.3:c.6190_6191dup	p.Asp2064GlufsTer84	p.D2064Efs*84	ENST00000409792	NM_014159.6	2064	gac/gaGAc	14/21	1	2	FACETS	0.823	0.758	0.891	0.823	0.758	0.891	CLONAL	1	TRUE	1	0.566575243042367	2		708	712	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856187	111856187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs73428142	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	160	708	0	ENST00000341259.2:c.238C>T	p.Arg80Cys	p.R80C	ENST00000341259	NM_005475.2	80	Cgc/Tgc	2/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.566575243042367	2		708	522	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193731	106193731	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1011713319	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	172	572	0	ENST00000380013.4:c.4193T>C	p.Leu1398Pro	p.L1398P	ENST00000380013	NM_001127208.2	1398	cTc/cCc	10/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.566575243042367	2		572	547	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279524	1279524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774381540	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	148	665	0	ENST00000310581.5:c.2012G>A	p.Arg671Gln	p.R671Q	ENST00000310581	NM_198253.2	671	cGg/cAg	5/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.566575243042367	2		665	460	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912075	50912077	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs398122386	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	180	735	0	ENST00000440232.2:c.1812_1814del	p.Ser605del	p.S605del	ENST00000440232	NM_002691.3	603	ttCTCc/ttc	15/27	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.566575243042367	2		735	545	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183297	56183297	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	181	596	1	ENST00000399503.3:c.4207G>T	p.Gly1403Ter	p.G1403*	ENST00000399503	NM_005921.1	1403	Gga/Tga	18/20	1	2	FACETS	0.984	0.912	1	0.984	0.912	1	CLONAL	1	TRUE	1	0.566575243042367	2		597	649	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371776	118371776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555045451	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	200	659	0	ENST00000534358.1:c.6233G>A	p.Arg2078His	p.R2078H	ENST00000534358	NM_005933.3	2078	cGt/cAt	25/36	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.566575243042367	2		659	681	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434005	49434005	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	161	809	0	ENST00000301067.7:c.7548del	p.Asn2517IlefsTer26	p.N2517Ifs*26	ENST00000301067	NM_003482.3	2516	ccC/cc	31/54	0.254744882792845	3	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.566575243042367	3		809	590	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874287	155874287	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs869025194	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	205	691	0	ENST00000368323.3:c.244T>C	p.Phe82Leu	p.F82L	ENST00000368323	NM_006912.5	82	Ttt/Ctt	5/6	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.566575243042367	2		691	716	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446892	187446892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	233	797	0	ENST00000232014.4:c.1301G>A	p.Ser434Asn	p.S434N	ENST00000232014	NM_001130845.1	434	aGc/aAc	5/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.566575243042367	2		797	687	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872969	136872969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767830104	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	195	743	0	ENST00000241393.3:c.529G>A	p.Val177Ile	p.V177I	ENST00000241393	NM_003467.2	177	Gtc/Atc	2/2	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.566575243042367	2		743	684	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132814	152132815	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	55	534	0	ENST00000262189.6:c.57dup	p.Glu20ArgfsTer39	p.E20Rfs*39	ENST00000262189	NM_170606.2	19	-/C	1/59	1	2	FACETS	0.428	0.366	0.494	0.428	0.366	0.494	SUBCLONAL	1	TRUE	1	0.566575243042367	2		534	454	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588086	67588086	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	131	428	0	ENST00000274335.5:c.917-1G>A		p.X306_splice	ENST00000274335		306			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.566575243042367	2		428	443	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900423	3900423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	194	712	0	ENST00000262367.5:c.673C>T	p.Pro225Ser	p.P225S	ENST00000262367	NM_004380.2	225	Ccg/Tcg	2/31	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.566575243042367	2		712	663	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460475	149460476	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs753211296	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	155	848	2	ENST00000286301.3:c.161dup	p.Ser55IlefsTer9	p.S55Ifs*9	ENST00000286301	NM_005211.3	54	cca/ccCa	3/22	1	2	FACETS	0.846	0.777	0.917	0.846	0.777	0.917	CLONAL	1	TRUE	1	0.566575243042367	2		850	647	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371742	118371742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	177	576	0	ENST00000534358.1:c.6199C>T	p.Arg2067Cys	p.R2067C	ENST00000534358	NM_005933.3	2067	Cgc/Tgc	25/36	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.566575243042367	2		576	618	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144152	11144152	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	171	738	0	ENST00000358026.2:c.3733G>A	p.Ala1245Thr	p.A1245T	ENST00000358026	NM_001128849.1	1245	Gcc/Acc	26/36	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.566575243042367	2		738	575	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77934490	77934490	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	161	640	0	ENST00000361507.4:c.1535del	p.Pro512LeufsTer19	p.P512Lfs*19	ENST00000361507	NM_080491.2	512	cCt/ct	6/10	1	2	FACETS	0.884	0.814	0.957	0.884	0.814	0.957	CLONAL	1	TRUE	1	0.566575243042367	2		640	643	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61306485	61306485	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	113	488	0	ENST00000341074.5:c.702A>G	p.Ile234Met	p.I234M	ENST00000341074	NM_002974.2	234	atA/atG	7/8	1	2	FACETS	0.879	0.796	0.965	0.879	0.796	0.965	CLONAL	1	TRUE	1	0.566575243042367	2		488	454	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184149	56184150	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	183	565	0	ENST00000399503.3:c.4359dup	p.His1454ThrfsTer10	p.H1454Tfs*10	ENST00000399503	NM_005921.1	1452	gaa/gAaa	19/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.566575243042367	2		565	618	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428251	33428251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150134822	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	137	699	1	ENST00000345365.6:c.872G>A	p.Arg291His	p.R291H	ENST00000345365	NM_002878.3	291	cGc/cAc	9/10	1	2	FACETS	0.93	0.851	1	0.93	0.851	1	CLONAL	1	TRUE	1	0.566575243042367	2		700	520	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317523	1317523	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs766414150	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	137	551	0	ENST00000400841.2:c.542A>G	p.Tyr181Cys	p.Y181C	ENST00000400841		181	tAc/tGc	5/6	1	2	FACETS	0.95	0.869	1	0.95	0.869	1	CLONAL	1	TRUE	1	0.566575243042367	2		551	509	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38788578	38788578	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	151	544	0	ENST00000348513.6:c.583C>G	p.Arg195Gly	p.R195G	ENST00000348513	NM_003079.4	195	Cgt/Ggt	8/11	1	2	FACETS	0.948	0.872	1	0.948	0.872	1	CLONAL	1	TRUE	1	0.566575243042367	2		544	562	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639902	3639902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1233559596	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	129	741	0	ENST00000294008.3:c.3737G>A	p.Ser1246Asn	p.S1246N	ENST00000294008	NM_032444.2	1246	aGc/aAc	12/15	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.566575243042367	2		741	444	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265451	152265453	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs748961781	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	187	593	0	ENST00000206249.3:c.909_911del	p.Lys303del	p.K303del	ENST00000206249	NM_000125.3	302	AAG/-	4/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.566575243042367	2		593	599	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587482	29587482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs546073780	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	56	554	0	ENST00000356175.3:c.4463G>A	p.Arg1488His	p.R1488H	ENST00000356175	NM_000267.3	1488	cGt/cAt	33/57	1	2	FACETS	0.35	0.3	0.406	0.35	0.3	0.406	SUBCLONAL	1	TRUE	1	0.566575243042367	2		554	564	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230459314	230459314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs578048672	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	202	744	0	ENST00000391860.1:c.1087G>A	p.Ala363Thr	p.A363T	ENST00000391860	NM_001258311.1	363	Gcc/Acc	7/7	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.566575243042367	2		744	627	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864846	57864846	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	101	805	0	ENST00000228682.2:c.2323C>T	p.Pro775Ser	p.P775S	ENST00000228682	NM_005269.2	775	Ccc/Tcc	12/12	1	2	FACETS	0.538	0.481	0.598	0.538	0.481	0.598	SUBCLONAL	1	TRUE	1	0.566575243042367	2		805	663	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073292	8073292	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	169	612	0	ENST00000377482.5:c.1367T>C	p.Leu456Ser	p.L456S	ENST00000377482	NM_018948.3	456	tTa/tCa	4/4	1	2	FACETS	0.948	0.876	1	0.948	0.876	1	CLONAL	1	TRUE	1	0.566575243042367	2		612	629	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2029140	2029140	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374826893	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	166	839	2	ENST00000349721.2:c.118G>A	p.Val40Ile	p.V40I	ENST00000349721	NM_003070.3	40	Gtc/Atc	2/34	1	2	FACETS	0.972	0.897	1	0.972	0.897	1	CLONAL	1	TRUE	1	0.566575243042367	2		841	603	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12043882	12043882	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	151	595	0	ENST00000396373.4:c.1264del	p.Thr422ProfsTer6	p.T422Pfs*6	ENST00000396373	NM_001987.4	421	Aaa/aa	8/8	1	2	FACETS	0.893	0.82	0.969	0.893	0.82	0.969	CLONAL	1	TRUE	1	0.566575243042367	2		595	597	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183582	185183582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1272940392	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	168	567	0	ENST00000265026.3:c.1436C>T	p.Ala479Val	p.A479V	ENST00000265026	NM_004721.4	479	gCg/gTg	9/14	1	2	FACETS	0.995	0.919	1	0.995	0.919	1	CLONAL	1	TRUE	1	0.566575243042367	2		567	596	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436608	110436608	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	129	754	0	ENST00000375856.3:c.1793A>G	p.Tyr598Cys	p.Y598C	ENST00000375856	NM_003749.2	598	tAc/tGc	1/2	1	2	FACETS	0.884	0.806	0.966	0.884	0.806	0.966	CLONAL	1	TRUE	1	0.566575243042367	2		754	515	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591118	67591123	+	inframe_deletion	In_Frame_Del	DEL	ATCCAG	ATCCAG	-	novel	NA	P-0066161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	210	548	0	ENST00000274335.5:c.1711_1716del	p.Ile571_Gln572del	p.I571_Q572del	ENST00000274335		571	ATCCAG/-	12/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.566575243042367	2		548	693	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0066162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	411	782	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		782	696	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0066162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	141	539	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		539	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0066162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	357	744	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		745	722	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436662	110436662	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1172028943	NA	P-0066162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	93	818	0	ENST00000375856.3:c.1739C>T	p.Thr580Met	p.T580M	ENST00000375856	NM_003749.2	580	aCg/aTg	1/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		818	630	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443805	49443805	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1350491800	NA	P-0066162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	123	871	0	ENST00000301067.7:c.3566G>A	p.Arg1189His	p.R1189H	ENST00000301067	NM_003482.3	1189	cGt/cAt	11/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		871	860	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023202	27023202	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	59	723	0	ENST00000324856.7:c.308C>A	p.Ser103Ter	p.S103*	ENST00000324856	NM_006015.4	103	tCg/tAg	1/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.180191041699018	2		723	512	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392870	118392870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	92	867	0	ENST00000534358.1:c.11902C>T	p.Arg3968Trp	p.R3968W	ENST00000534358	NM_005933.3	3968	Cgg/Tgg	36/36	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.180191041699018	2		867	756	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573983	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AG	novel	NA	P-0066164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	96	826	0	ENST00000269305.4:c.1044_1045delinsCT	p.Leu348_Glu349delinsPheTer	p.L348_E349delinsF*	ENST00000269305	NM_001126112.2	348	ttGGaa/ttCTaa	10/11	1	2	FACETS	0.795	0.709	0.887	1	0.982	1	SUBCLONAL	2	TRUE	1	0.180191041699018	2		826	670	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266825	18266825	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	83	873	0	ENST00000222254.8:c.136G>A	p.Gly46Ser	p.G46S	ENST00000222254	NM_005027.3	46	Ggt/Agt	2/16	0.159384300020641	3	FACETS	1	0.976	1	0.733	0.647	0.825	CLONAL	1	TRUE	1	0.180191041699018	3		873	685	SUCCESS
AR	367	MSKCC	GRCh37	X	66766399	66766399	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	11	135	0	ENST00000374690.3:c.1411G>C	p.Gly471Arg	p.G471R	ENST00000374690	NM_000044.3	471	Ggc/Cgc	1/8	1	1	FACETS	1	0.761	1	1	0.761	1	CLONAL	1	TRUE	0	0.180191041699018	1		135	100	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0066165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	237	797	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		797	601	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0066165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	819	405	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		405	993	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0066165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	90	731	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		731	347	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	32	936	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		936	661	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	51	936	0	ENST00000206249.3:c.1610A>G	p.Tyr537Cys	p.Y537C	ENST00000206249	NM_000125.3	537	tAt/tGt	8/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		936	661	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28931588	NA	P-0066165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	111	839	0	ENST00000349496.5:c.94G>C	p.Asp32His	p.D32H	ENST00000349496	NM_001904.3	32	Gac/Cac	3/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		839	350	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107147	27107148	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0066165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	257	971	0	ENST00000324856.7:c.6759_6760del	p.Tyr2254ArgfsTer23	p.Y2254Rfs*23	ENST00000324856	NM_006015.4	2253	cTG/c	20/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		971	722	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050906	49050906	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	86	494	0	ENST00000267163.4:c.2590del	p.Glu864LysfsTer9	p.E864Kfs*9	ENST00000267163	NM_000321.2	864	Gaa/aa	25/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		494	276	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63810687	63810687	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	154	669	0	ENST00000279873.7:c.774C>A	p.Cys258Ter	p.C258*	ENST00000279873	NM_032199.2	258	tgC/tgA	5/10	1	2	FACETS	0.922	0.853	0.992	0.922	0.853	0.992	CLONAL	1	TRUE	1	0.803309390480218	2		669	416	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514698	103514698	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	307	850	0	ENST00000355739.4:c.1199A>C	p.Asp400Ala	p.D400A	ENST00000355739	NM_000123.3	400	gAt/gCt	8/15	1	2	FACETS	0.963	0.912	1	0.963	0.912	1	CLONAL	1	TRUE	1	0.803309390480218	2		850	794	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343520	70343520	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	241	374	0	ENST00000374080.3:c.1694T>C	p.Ile565Thr	p.I565T	ENST00000374080		565	aTt/aCt	12/45	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.803309390480218	1		374	304	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519896	NA	P-0066167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	254	858	2	ENST00000281708.4:c.1514G>A	p.Arg505His	p.R505H	ENST00000281708	NM_033632.3	505	cGc/cAc	10/12	0.243247148658409	3	FACETS	1	0.989	1	0.617	0.58	0.655	INDETERMINATE	1	TRUE	1	0.798805617372085	3		860	721	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578528	7578528	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	341	1016	0	ENST00000269305.4:c.402T>G	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	ttT/ttG	5/11	0.798805617372085	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.798805617372085	1		1016	480	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138197249	138197249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777456133	NA	P-0066167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	252	968	1	ENST00000237289.4:c.751G>A	p.Gly251Ser	p.G251S	ENST00000237289	NM_001270507.1	251	Ggc/Agc	5/9	1	2	FACETS	0.995	0.938	1	0.995	0.938	1	CLONAL	1	TRUE	1	0.798805617372085	2		969	634	SUCCESS
APC	324	MSKCC	GRCh37	5	112151191	112151191	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0066167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	139	420	0	ENST00000257430.4:c.835-1G>A		p.X279_splice	ENST00000257430	NM_000038.5	279			1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.798805617372085	2		420	266	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89874746	89874746	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	262	757	0	ENST00000389301.3:c.552T>A	p.His184Gln	p.H184Q	ENST00000389301	NM_000135.2	184	caT/caA	6/43	1	2	FACETS	0.995	0.939	1	0.995	0.939	1	CLONAL	1	TRUE	1	0.798805617372085	2		757	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0066168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	184	1113	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.465676255009258	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.465676255009258	1		1113	597	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0066168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	196	810	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.38319293985813	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.465676255009258	1		810	637	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096994	11096994	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	162	960	0	ENST00000358026.2:c.485T>C	p.Leu162Ser	p.L162S	ENST00000358026	NM_001128849.1	162	tTg/tCg	4/36	0.465676255009258	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.465676255009258	1		960	505	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859527	151859527	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	200	1011	0	ENST00000262189.6:c.11135del	p.Pro3712LeufsTer7	p.P3712Lfs*7	ENST00000262189	NM_170606.2	3712	cCt/ct	43/59	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.465676255009258	2		1011	840	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202220	108202220	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	63	324	0	ENST00000278616.4:c.7565A>C	p.Gln2522Pro	p.Q2522P	ENST00000278616	NM_000051.3	2522	cAa/cCa	51/63	0.273710088968961	1	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	0	0.273710088968961	1		324	384	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187253	38187254	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	88	399	0	ENST00000317025.8:c.1223dup	p.Ser409GlufsTer9	p.S409Efs*9	ENST00000317025	NM_023034.1	408	aag/aaAg	6/24	1	2	FACETS	0.955	0.847	1	0.955	0.847	1	CLONAL	1	TRUE	1	0.273710088968961	2		399	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0066176-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	232	545	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.201489399990126	3	FACETS	0.931	0.882	0.98	1	0.996	1	CLONAL	6	FALSE	1	0.218801609626181	3		546	421	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0066176-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	149	473	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.177818033527165	3	FACETS	1	0.974	1	1	0.99	1	CLONAL	3	FALSE	1	0.218801609626181	3		473	446	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750546	41750546	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066176-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	117	570	0	ENST00000226382.2:c.82T>C	p.Ser28Pro	p.S28P	ENST00000226382	NM_003924.3	28	Tca/Cca	1/3	0.0997566737340474	4	FACETS	0.999	0.907	1	1	0.985	1	INDETERMINATE	3	FALSE	2	0.218801609626181	4		570	435	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180889	108180891	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CTT	CTT	-	rs866749094	NA	P-0066176-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	24	215	0	ENST00000278616.4:c.5769_5771del	p.Ser1924del	p.S1924del	ENST00000278616	NM_000051.3	1922	cCTTct/cct	39/63	0.201489399990126	3	FACETS	1	0.845	1	0.546	0.43	0.678	CLONAL	1	FALSE	1	0.218801609626181	3		215	223	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875905	76875907	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0066176-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	118	88	0	ENST00000373344.5:c.5228_5230del	p.Arg1743del	p.R1743del	ENST00000373344	NM_000489.3	1743	aGGAtt/att	20/35	0.150210908792453	2	FACETS	1	0.953	1			1	CLONAL	5	FALSE	NA	0.218801609626181	2		88	208	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0066176-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	262	545	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.533053457702729	3	FACETS	1	0.988	1	1	0.996	1	CLONAL	3	FALSE	1	0.533053457702729	3		546	382	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0066176-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	227	473	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.198532600754702	4	FACETS	1	0.989	1	0.817	0.768	0.866	INDETERMINATE	2	FALSE	1	0.533053457702729	4		473	533	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750546	41750546	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066176-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	222	570	0	ENST00000226382.2:c.82T>C	p.Ser28Pro	p.S28P	ENST00000226382	NM_003924.3	28	Tca/Cca	1/3	0.41785407287652	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	FALSE	2	0.533053457702729	4		570	592	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180889	108180891	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CTT	CTT	-	rs866749094	NA	P-0066176-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	12	215	0	ENST00000278616.4:c.5769_5771del	p.Ser1924del	p.S1924del	ENST00000278616	NM_000051.3	1922	cCTTct/cct	39/63	0.533053457702729	2	FACETS	0.157	0.11	0.215	0.078	0.055	0.108	SUBCLONAL	1	FALSE	0	0.533053457702729	2		215	287	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875905	76875907	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0066176-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	211	88	0	ENST00000373344.5:c.5228_5230del	p.Arg1743del	p.R1743del	ENST00000373344	NM_000489.3	1743	aGGAtt/att	20/35	0.352102946694601	2	FACETS	1	0.992	1			1	CLONAL	2	FALSE	NA	0.533053457702729	2		88	321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0066177-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	273	498	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.421813176005425	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.424825081293897	2		498	560	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0066177-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	145	473	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.424825081293897	2		473	537	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520465	176520465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61737768	NA	P-0066177-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	66	635	0	ENST00000292408.4:c.1310G>A	p.Arg437His	p.R437H	ENST00000292408	NM_213647.1	437	cGt/cAt	10/18	0.256972805366872	1	FACETS	0.48	0.417	0.548	0.48	0.417	0.548	SUBCLONAL	1	TRUE	0	0.424825081293897	1		635	510	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76812977	76812977	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0066177-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	116	245	0	ENST00000373344.5:c.6644T>A	p.Leu2215Ter	p.L2215*	ENST00000373344	NM_000489.3	2215	tTa/tAa	30/35	0.0870306358335913	5	FACETS	0.929	0.842	1			1	INDETERMINATE	2	TRUE	NA	0.424825081293897	5		245	481	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26928013	26928013	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066177-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	104	219	0	ENST00000381527.3:c.452A>G	p.Asp151Gly	p.D151G	ENST00000381527	NM_001260.1	151	gAt/gGt	4/13	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.424825081293897	2		219	445	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969941	161969941	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529808032	NA	P-0066178-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	60	453	0	ENST00000366898.1:c.1028C>T	p.Pro343Leu	p.P343L	ENST00000366898	NM_004562.2	343	cCg/cTg	9/12	0.267839705638687	1	FACETS	0.96	0.83	1	0.96	0.83	1	CLONAL	1	TRUE	0	0.277569996270205	1		453	388	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0066178-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	99	311	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.277569996270205	4	FACETS	0.986	0.885	1	0.986	0.885	1	CLONAL	2	TRUE	2	0.277569996270205	4		311	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577157	7577157	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1060501207	NA	P-0066178-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	86	479	0	ENST00000269305.4:c.783-2A>G		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.267839705638687	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.277569996270205	1		479	393	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	895004	895004	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066178-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	69	393	0	ENST00000166345.3:c.195T>G	p.Phe65Leu	p.F65L	ENST00000166345	NM_004237.3	65	ttT/ttG	2/13	0.272757691837261	3	FACETS	1	0.893	1	0.514	0.448	0.585	CLONAL	1	TRUE	1	0.277569996270205	3		393	551	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420211	49420211	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066178-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	170	590	0	ENST00000301067.7:c.15538G>T	p.Val5180Leu	p.V5180L	ENST00000301067	NM_003482.3	5180	Gtg/Ttg	48/54	0.277569996270205	2	FACETS	0.961	0.888	1	0.961	0.888	1	CLONAL	2	TRUE	0	0.277569996270205	2		590	637	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58725305	58725330	+	frameshift_variant	Frame_Shift_Del	DEL	ACCAGACACAAGTGTCCACACTCTTG	ACCAGACACAAGTGTCCACACTCTTG	-	novel	NA	P-0066178-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	51	495	0	ENST00000305921.3:c.882_907del	p.Asp295SerfsTer11	p.D295Sfs*11	ENST00000305921	NM_003620.3	293	gaACCAGACACAAGTGTCCACACTCTTGac/gaac	4/6	0.277569996270205	3	FACETS	0.685	0.581	0.799	0.342	0.29	0.4	SUBCLONAL	1	TRUE	1	0.277569996270205	3		495	611	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1735964	1735974	+	frameshift_variant	Frame_Shift_Del	DEL	AGAAGGGGCAT	AGAAGGGGCAT	-	novel	NA	P-0066178-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	95	513	0	ENST00000378609.4:c.314_324del	p.Tyr105TrpfsTer11	p.Y105Wfs*11	ENST00000378609	NM_002074.3	105	tATGCCCCTTCT/t	7/12	0.267839705638687	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.277569996270205	1		513	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578502	7578502	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066179-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	38	663	0	ENST00000269305.4:c.428T>C	p.Val143Ala	p.V143A	ENST00000269305	NM_001126112.2	143	gTg/gCg	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		663	579	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127293	55127293	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066179-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	38	476	1	ENST00000257290.5:c.81A>T	p.Leu27Phe	p.L27F	ENST00000257290	NM_006206.4	27	ttA/ttT	3/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		477	472	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	24	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.652	0.511	0.813	0.652	0.511	0.813	SUBCLONAL	1	TRUE	1	0.243071907033374	2		341	303	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0066180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	42	591	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	0.775	0.647	0.916	0.775	0.647	0.916	CLONAL	1	TRUE	1	0.243071907033374	2		591	446	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617579	100617579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	44	464	0	ENST00000308731.7:c.490G>A	p.Gly164Ser	p.G164S	ENST00000308731	NM_000061.2	164	Ggc/Agc	6/19	1	2	FACETS	0.696	0.584	0.821	0.696	0.584	0.821	SUBCLONAL	1	TRUE	1	0.243071907033374	2		464	520	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66524021	66524025	+	frameshift_variant	Frame_Shift_Del	DEL	TTAGT	TTAGT	C	novel	NA	P-0066180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	75	354	0	ENST00000358598.2:c.749_753delinsC	p.Leu250ProfsTer6	p.L250Pfs*6	ENST00000358598	NM_212471.2	250	cTTAGT/cC	8/11	0.179104240620525	2	FACETS	0.751	0.661	0.846	0.751	0.661	0.846	SUBCLONAL	2	TRUE	0	0.243071907033374	2		354	411	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0066181-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	163	481	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.787246492369451	1	FACETS	0.958	0.903	1	0.958	0.903	1	CLONAL	1	TRUE	0	0.787246492369451	1		481	262	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0066181-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	202	455	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.94	0.878	1	0.94	0.878	1	CLONAL	1	TRUE	1	0.787246492369451	2		455	546	SUCCESS
AXL	558	MSKCC	GRCh37	19	41759511	41759511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066181-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	236	512	0	ENST00000301178.4:c.1934C>T	p.Pro645Leu	p.P645L	ENST00000301178	NM_021913.4	645	cCc/cTc	17/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.787246492369451	2		512	599	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636843	2636843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066181-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	246	522	0	ENST00000342085.4:c.1292C>T	p.Ser431Phe	p.S431F	ENST00000342085	NM_002613.4	431	tCc/tTc	11/14	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.787246492369451	2		522	624	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	67	446	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.815	0.715	0.922	0.815	0.715	0.922	CLONAL	1	TRUE	1	0.553281290759148	2		446	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0066182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	161	537	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.976	0.9	1	0.976	0.9	1	CLONAL	1	TRUE	1	0.553281290759148	2		537	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0066182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	171	627	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.553281290759148	2		627	610	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971029	21971029	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519852	NA	P-0066182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	279	601	0	ENST00000304494.5:c.329G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tGg/tAg	2/3	0.54560831334661	2	FACETS	0.993	0.945	1	0.993	0.945	1	CLONAL	2	TRUE	0	0.553281290759148	2		601	508	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149917	202149917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	121	608	0	ENST00000358485.4:c.1358C>T	p.Pro453Leu	p.P453L	ENST00000358485	NM_001080125.1	453	cCg/cTg	8/9	1	2	FACETS	0.885	0.804	0.97	0.885	0.804	0.97	CLONAL	1	TRUE	1	0.553281290759148	2		608	494	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324471	31324471	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs41559613	NA	P-0066182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	139	404	0	ENST00000412585.2:c.337G>T	p.Glu113Ter	p.E113*	ENST00000412585	NM_005514.6	113	Gag/Tag	2/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.553281290759148	2		404	384	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543629	148543629	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	88	443	0	ENST00000320356.2:c.179G>A	p.Trp60Ter	p.W60*	ENST00000320356	NM_004456.4	60	tGg/tAg	3/20	0.553281290759148	1	FACETS	0.738	0.66	0.818	0.738	0.66	0.818	SUBCLONAL	1	TRUE	0	0.553281290759148	1		443	312	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0066183-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	24	492	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.684	0.537	0.852	0.684	0.537	0.852	SUBCLONAL	1	TRUE	1	0.27	2		492	260	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066183-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	48	621	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	1	2	FACETS	0.766	0.648	0.896	0.766	0.648	0.896	SUBCLONAL	1	TRUE	1	0.27	2		621	464	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218483	1218483	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs775595174	NA	P-0066183-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	43	536	0	ENST00000326873.7:c.358G>T	p.Glu120Ter	p.E120*	ENST00000326873	NM_000455.4	120	Gaa/Taa	2/10	0.3	3	FACETS	0.766	0.641	0.904			1	CLONAL	1	TRUE	NA	0.27	3		536	472	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142977	30142978	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0066183-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	33	683	0	ENST00000389048.3:c.548_549delinsTT	p.Gly183Val	p.G183V	ENST00000389048	NM_004304.4	183	gGG/gTT	1/29	1	2	FACETS	0.469	0.381	0.569	0.469	0.381	0.569	SUBCLONAL	1	TRUE	1	0.27	2		683	521	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93953258	93953259	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0066183-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	15	371	0	ENST00000369303.4:c.2883-1_2883delinsTT		p.X961_splice	ENST00000369303	NM_004440.3	961		17/17	1	2	FACETS	0.799	0.589	1	0.799	0.589	1	CLONAL	1	TRUE	1	0.27	2		371	139	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43738993	43738993	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066183-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	65	635	0	ENST00000523873.1:c.10C>A	p.Leu4Met	p.L4M	ENST00000523873		4	Ctg/Atg	1/8	1	2	FACETS	0.743	0.644	0.851	0.743	0.644	0.851	SUBCLONAL	1	TRUE	1	0.27	2		635	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0066184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	429	498	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.829110704421393	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.829110704421393	2		498	509	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0066184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	187	473	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.829110704421393	2		473	433	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023783	27023783	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	110	639	0	ENST00000324856.7:c.889C>T	p.Gln297Ter	p.Q297*	ENST00000324856	NM_006015.4	297	Caa/Taa	1/20	1	2	FACETS	0.767	0.697	0.84	0.767	0.697	0.84	SUBCLONAL	1	TRUE	1	0.829110704421393	2		639	346	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814221	76814222	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0066184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	127	210	0	ENST00000373344.5:c.6422dup	p.Ser2142IlefsTer3	p.S2142Ifs*3	ENST00000373344	NM_000489.3	2141	cca/ccCa	29/35	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.829110704421393	1		210	155	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0066189-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	29	181	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.15009306513888	6	FACETS	1	0.879	1			1	CLONAL	2	TRUE	NA	0.15009306513888	6		181	223	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0066189-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	36	133	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.15009306513888	6	FACETS	1	0.845	1			1	CLONAL	3	TRUE	NA	0.15009306513888	6		133	204	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0066189-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	115	492	1	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.15009306513888	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	3	TRUE	1	0.15009306513888	4		493	529	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846080	68846080	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555515726	NA	P-0066189-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	67	521	0	ENST00000261769.5:c.1051C>T	p.Gln351Ter	p.Q351*	ENST00000261769	NM_004360.3	351	Caa/Taa	8/16	0.15009306513888	2	FACETS	0.918	0.8	1	0.918	0.8	1	CLONAL	2	TRUE	0	0.15009306513888	2		521	486	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750454	57750454	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066189-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	30	534	0	ENST00000274289.3:c.2014C>T	p.Arg672Ter	p.R672*	ENST00000274289	NM_006622.3	672	Cga/Tga	14/14	0.15009306513888	3	FACETS	0.999	0.805	1	0.5	0.402	0.61	CLONAL	1	TRUE	1	0.15009306513888	3		534	430	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426712	121426712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066189-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	41	665	0	ENST00000257555.6:c.403G>A	p.Asp135Asn	p.D135N	ENST00000257555		135	Gat/Aat	2/10	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.15009306513888	2		665	515	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439427	220439427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066189-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	27	606	0	ENST00000243786.2:c.280G>A	p.Glu94Lys	p.E94K	ENST00000243786	NM_002191.3	94	Gag/Aag	2/2	1	2	FACETS	0.833	0.662	1	0.833	0.662	1	CLONAL	1	TRUE	1	0.15009306513888	2		606	432	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851993	128851993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1200280970	NA	P-0066189-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	37	696	0	ENST00000249373.3:c.2065C>T	p.Pro689Ser	p.P689S	ENST00000249373	NM_005631.4	689	Cct/Tct	12/12	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.15009306513888	2		696	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0066189-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	39	620	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.15009306513888	2		620	446	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178943776	178943776	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066189-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	36	334	0	ENST00000263967.3:c.2443C>G	p.Gln815Glu	p.Q815E	ENST00000263967	NM_006218.2	815	Caa/Gaa	17/21	0.15009306513888	6	FACETS	0.776	0.638	0.93			1	CLONAL	2	TRUE	NA	0.15009306513888	6		334	402	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159066	143159066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066189-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	23	292	0	ENST00000262992.4:c.787C>T	p.His263Tyr	p.H263Y	ENST00000262992	NM_001101669.1	263	Cat/Tat	10/24	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.15009306513888	2		292	212	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562854	95562854	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs753582860	NA	P-0066189-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	19	504	0	ENST00000393063.1:c.4403C>G	p.Ser1468Cys	p.S1468C	ENST00000393063	NM_030621.3	1468	tCt/tGt	24/28	1	2	FACETS	0.728	0.552	0.935	0.728	0.552	0.935	CLONAL	1	TRUE	1	0.15009306513888	2		504	348	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014290	70014290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066189-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	33	554	0	ENST00000394351.3:c.1151C>T	p.Ser384Phe	p.S384F	ENST00000394351	NM_000248.3	384	tCt/tTt	9/9	1	2	FACETS	0.881	0.717	1	0.881	0.717	1	CLONAL	1	TRUE	1	0.15009306513888	2		554	499	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351259	89351259	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066189-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	66	628	0	ENST00000301030.4:c.1691C>G	p.Ser564Cys	p.S564C	ENST00000301030	NM_001256183.1	564	tCt/tGt	9/13	0.15009306513888	2	FACETS	0.903	0.785	1	0.903	0.785	1	CLONAL	2	TRUE	0	0.15009306513888	2		628	487	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647254	23647254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066189-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	42	511	1	ENST00000261584.4:c.613G>A	p.Glu205Lys	p.E205K	ENST00000261584	NM_024675.3	205	Gaa/Aaa	4/13	0.121798227711656	3	FACETS	0.84	0.703	0.991	0.84	0.703	0.991	CLONAL	2	TRUE	1	0.15009306513888	3		512	358	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812155	212812155	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066190-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	50	390	0	ENST00000342788.4:c.421G>T	p.Glu141Ter	p.E141*	ENST00000342788	NM_005235.2	141	Gaa/Taa	3/28	0.366910605384993	4	FACETS	0.747	0.637	0.866			1	INDETERMINATE	1	FALSE	NA	0.708508375488365	4		390	323	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249370	153249370	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066190-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	325	494	0	ENST00000281708.4:c.1408C>A	p.His470Asn	p.H470N	ENST00000281708	NM_033632.3	470	Cat/Aat	9/12	0.711157622297204	4	FACETS	0.935	0.905	0.964	0.935	0.905	0.964	CLONAL	4	FALSE	0	0.708508375488365	4		494	419	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858253	27858376	+	frameshift_variant	Frame_Shift_Del	DEL	TTCAAAGAGACCCACCAGATAGGCCTCGCACGCCTCTTGCAGCGCCATCACCGCCGAGCTCTGGAAACGAAGGTCGGTTTTGAAATCCTGCGCGATTTCTCGCACCAGGCGCTGAAATGGCAGT	TTCAAAGAGACCCACCAGATAGGCCTCGCACGCCTCTTGCAGCGCCATCACCGCCGAGCTCTGGAAACGAAGGTCGGTTTTGAAATCCTGCGCGATTTCTCGCACCAGGCGCTGAAATGGCAGT	-	novel	NA	P-0066190-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1523	367	694	0	ENST00000359303.2:c.195_318del	p.Leu66ThrfsTer?	p.L66Tfs*?	ENST00000359303	NM_003535.2	65	aaACTGCCATTTCAGCGCCTGGTGCGAGAAATCGCGCAGGATTTCAAAACCGACCTTCGTTTCCAGAGCTCGGCGGTGATGGCGCTGCAAGAGGCGTGCGAGGCCTATCTGGTGGGTCTCTTTGAA/aa	1/1	0.708508375488365	15	FACETS	1	0.963	1			1	CLONAL	3	FALSE	NA	0.708508375488365	15		694	1890	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141015	55141029	+	inframe_deletion	In_Frame_Del	DEL	GGTATGAAATTCGCT	GGTATGAAATTCGCT	-	novel	NA	P-0066190-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	560	451	0	ENST00000257290.5:c.1663_1677del	p.Tyr555_Trp559del	p.Y555_W559del	ENST00000257290	NM_006206.4	554	aGGTATGAAATTCGCTgg/agg	12/23	0.708508375488365	7	FACETS	0.964	0.945	0.982			1	CLONAL	7	FALSE	NA	0.708508375488365	7		451	649	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937852	76937852	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066190-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	423	480	0	ENST00000373344.5:c.2896del	p.Glu966ArgfsTer4	p.E966Rfs*4	ENST00000373344	NM_000489.3	966	Gag/ag	9/35	0.490316989124319	5	FACETS	0.953	0.92	0.985			1	CLONAL	4	FALSE	NA	0.708508375488365	5		480	646	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878060	48878075	+	frameshift_variant	Frame_Shift_Del	DEL	AACCCCCCGAAAAACG	AACCCCCCGAAAAACG	TTT	novel	NA	P-0066190-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	303	613	3	ENST00000267163.4:c.12_27delinsTTT	p.Lys4AsnfsTer57	p.K4Nfs*57	ENST00000267163	NM_000321.2	4	aaAACCCCCCGAAAAACG/aaTTT	1/27	0.591597805028769	5	FACETS	0.931	0.892	0.968	0.744	0.713	0.775	CLONAL	4	FALSE	0	0.708508375488365	5		616	474	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0066191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	261	797	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.648587495174674	2		797	690	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0066191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	60	157	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.648587495174674	2		157	183	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0066191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	234	224	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.648587495174674	2		224	714	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221995	1221995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201090	NA	P-0066191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	175	545	0	ENST00000326873.7:c.910C>T	p.Arg304Trp	p.R304W	ENST00000326873	NM_000455.4	304	Cgg/Tgg	7/10	1	2	FACETS	0.992	0.92	1	0.992	0.92	1	CLONAL	1	TRUE	1	0.648587495174674	2		545	544	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717696	89717696	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1554825207	NA	P-0066191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	107	106	0	ENST00000371953.3:c.721T>G	p.Phe241Val	p.F241V	ENST00000371953	NM_000314.4	241	Ttt/Gtt	7/9	0.195373697270487	2	FACETS	0.853	0.771	0.937	0.426	0.385	0.469	INDETERMINATE	1	TRUE	0	0.648587495174674	2		106	387	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056352	27056352	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1557591264	NA	P-0066191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	183	571	3	ENST00000324856.7:c.1348C>T	p.Gln450Ter	p.Q450*	ENST00000324856	NM_006015.4	450	Cag/Tag	2/20	1	2	FACETS	0.889	0.824	0.955	0.889	0.824	0.955	CLONAL	1	TRUE	1	0.648587495174674	2		574	635	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692892	89692892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554898129	NA	P-0066191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	82	49	0	ENST00000371953.3:c.376G>A	p.Ala126Thr	p.A126T	ENST00000371953	NM_000314.4	126	Gct/Act	5/9	0.195373697270487	2	FACETS	1	0.979	1	0.687	0.621	0.754	INDETERMINATE	1	TRUE	0	0.648587495174674	2		49	184	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106148	27106149	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0066191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	87	438	0	ENST00000324856.7:c.5759_5760del	p.Ser1920AsnfsTer8	p.S1920Nfs*8	ENST00000324856	NM_006015.4	1920	aGC/a	20/20	1	2	FACETS	0.354	0.313	0.398	0.354	0.313	0.398	SUBCLONAL	1	TRUE	1	0.648587495174674	2		438	757	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41905029	41905029	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs147099303	NA	P-0066191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	262	392	0	ENST00000372991.4:c.518A>G	p.Asp173Gly	p.D173G	ENST00000372991	NM_001760.3	173	gAc/gGc	3/5	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.648587495174674	2		392	795	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	19	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.813	0.616	1	0.813	0.616	1	CLONAL	1	TRUE	1	0.14	2		341	334	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974697	+	inframe_deletion	In_Frame_Del	DEL	GTA	GTA	-	novel	NA	P-0066193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	15	524	0	ENST00000304494.5:c.130_132del	p.Tyr44del	p.Y44del	ENST00000304494	NM_000077.4	44	TAC/-	1/3	1	2	FACETS	0.503	0.366	0.668	0.503	0.366	0.668	SUBCLONAL	1	TRUE	1	0.14	2		524	426	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217869	7217870	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	27	473	0	ENST00000380728.2:c.141dup	p.Gln48ThrfsTer49	p.Q48Tfs*49	ENST00000380728		47	-/A	3/11	1	2	FACETS	0.901	0.716	1	0.901	0.716	1	CLONAL	1	TRUE	1	0.14	2		473	428	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954204	48954204	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	17	145	0	ENST00000267163.4:c.1405T>A	p.Ser469Thr	p.S469T	ENST00000267163	NM_000321.2	469	Tcc/Acc	15/27	1	2	FACETS	0.916	0.684	1	0.916	0.684	1	CLONAL	1	TRUE	1	0.14	2		145	265	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0066194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	195	530	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	0.93	0.867	0.996	0.93	0.867	0.996	CLONAL	1	TRUE	1	0.721483208465998	2		530	581	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0066194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	188	591	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.721483208465998	2		591	471	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0066194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	77	652	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	0.721483208465998	1	FACETS	0.467	0.414	0.523	0.467	0.414	0.523	SUBCLONAL	1	TRUE	0	0.721483208465998	1		652	292	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385170	41385171	+	missense_variant	Missense_Mutation	DNP	TT	TT	GG	novel	NA	P-0066195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	10	519	0	ENST00000373198.4:c.790_791delinsCC	p.Lys264Pro	p.K264P	ENST00000373198	NM_133170.3	264	AAg/CCg	6/32	NA	2	FACETS	0.329	0.225	0.458			1	INDETERMINATE	1	TRUE	NA	0.626579448628799	2		519	97	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579347	+	frameshift_variant	Frame_Shift_Del	DEL	GTGCAAGTCACAGACTTGGCTGTCCCAGAATGCAA	GTGCAAGTCACAGACTTGGCTGTCCCAGAATGCAA	TTGCAC	novel	NA	P-0066195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	44	539	1	ENST00000269305.4:c.340_374delinsGTGCAA	p.Leu114ValfsTer25	p.L114Vfs*25	ENST00000269305	NM_001126112.2	114	TTGCATTCTGGGACAGCCAAGTCTGTGACTTGCACg/GTGCAAg	4/11	0.626579448628799	2	FACETS	0.989	0.878	1	0.989	0.878	1	CLONAL	2	TRUE	0	0.626579448628799	2		540	71	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	142	446	0				ENST00000310581	NM_198253.2	-/1132			0.502332269289919	6	FACETS	1	0.977	1	0.776	0.716	0.838	INDETERMINATE	2	TRUE	3	0.852022465464404	6		446	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0066197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	284	616	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	NA	2	FACETS	0.98	0.951	1			1	INDETERMINATE	2	TRUE	NA	0.852022465464404	2		616	340	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690805	89690805	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	58	66	0	ENST00000371953.3:c.212G>A	p.Cys71Tyr	p.C71Y	ENST00000371953	NM_000314.4	71	tGt/tAt	4/9	0.848703688737313	2	FACETS	0.873	0.801	0.938	0.873	0.801	0.938	CLONAL	2	TRUE	0	0.852022465464404	2		66	78	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11301683	11301683	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	118	564	0	ENST00000361445.4:c.1468G>T	p.Ala490Ser	p.A490S	ENST00000361445	NM_004958.3	490	Gct/Tct	10/58	0.549289362150251	4	FACETS	1	0.966	1	0.377	0.343	0.414	CLONAL	1	TRUE	1	0.852022465464404	4		564	453	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162459	47162459	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	231	380	0	ENST00000409792.3:c.3667C>A	p.Gln1223Lys	p.Q1223K	ENST00000409792	NM_014159.6	1223	Caa/Aaa	3/21	0.852022465464404	4	FACETS	1	0.956	1			1	CLONAL	2	TRUE	NA	0.852022465464404	4		380	494	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131205	55131205	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1442	5641	495	0	ENST00000257290.5:c.748C>A	p.Pro250Thr	p.P250T	ENST00000257290	NM_006206.4	250	Cct/Act	5/23	0.852022465464404	54	FACETS	1	0.996	1	0.832	0.826	0.839	CLONAL	43	TRUE	2	0.852022465464404	54		495	7083	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182928	123182929	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	CC	novel	NA	P-0066197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	158	70	0	ENST00000218089.9:c.893_893+1inv		p.X298_splice	ENST00000218089	NM_001042749.1	298		10/35	0.852022465464404	4	FACETS	1	0.988	1			1	CLONAL	4	TRUE	NA	0.852022465464404	4		70	167	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0066199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	155	372	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.319491749817905	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.334112804709038	2		372	439	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0066199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	96	539	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.334112804709038	2		539	553	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775164	73775164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867543814	NA	P-0066199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	152	961	0	ENST00000254810.4:c.92C>T	p.Pro31Leu	p.P31L	ENST00000254810	NM_005324.3	31	cCc/cTc	2/4	1	2	FACETS	0.885	0.808	0.965	0.885	0.808	0.965	CLONAL	1	TRUE	1	0.334112804709038	2		961	1028	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057848	27057848	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	159	799	0	ENST00000324856.7:c.1556C>T	p.Ser519Phe	p.S519F	ENST00000324856	NM_006015.4	519	tCc/tTc	3/20	1	2	FACETS	0.982	0.9	1	0.982	0.9	1	CLONAL	1	TRUE	1	0.334112804709038	2		799	969	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916138	9916138	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	100	624	0	ENST00000330684.3:c.2151G>T	p.Leu717Phe	p.L717F	ENST00000330684	NM_001134407.1	717	ttG/ttT	10/13	1	2	FACETS	0.87	0.778	0.968	0.87	0.778	0.968	CLONAL	1	TRUE	1	0.334112804709038	2		624	688	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178533	32178533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	96	654	0	ENST00000375023.3:c.2861G>A	p.Cys954Tyr	p.C954Y	ENST00000375023	NM_004557.3	954	tGc/tAc	18/30	0.257791825272412	3	FACETS	0.827	0.736	0.924	0.413	0.368	0.462	CLONAL	1	TRUE	1	0.334112804709038	3		654	811	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0066200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	162	257	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.437435740112267	5	FACETS	1	0.983	1	0.791	0.735	0.847	INDETERMINATE	2	TRUE	2	0.757791303490711	5		257	385	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196879	108196880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs773570504	NA	P-0066200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	117	514	0	ENST00000278616.4:c.6908dup	p.Glu2304GlyfsTer69	p.E2304Gfs*69	ENST00000278616	NM_000051.3	2301	gca/gcAa	47/63	0.757791303490711	3	FACETS	1	0.952	1	0.536	0.488	0.587	CLONAL	1	TRUE	1	0.757791303490711	3		514	397	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56402551	56402551	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	167	315	1	ENST00000348428.3:c.1593A>T	p.Glu531Asp	p.E531D	ENST00000348428	NM_006785.3	531	gaA/gaT	13/17	0.757791303490711	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.757791303490711	2		316	220	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748110	41748110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	118	442	2	ENST00000226382.2:c.659C>T	p.Pro220Leu	p.P220L	ENST00000226382	NM_003924.3	220	cCg/cTg	3/3	0.671232141423852	4	FACETS	1	0.955	1	0.544	0.493	0.597	CLONAL	1	TRUE	2	0.757791303490711	4		444	503	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971205	21971213	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACCTGCCA	GACCTGCCA	-	novel	NA	P-0066200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	106	647	0	ENST00000304494.5:c.151-6_153del		p.X51_splice	ENST00000304494	NM_000077.4	51		2/3	0.752938039191785	3	FACETS	0.989	0.912	1	0.989	0.912	1	CLONAL	2	TRUE	1	0.757791303490711	3		647	195	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913237	NA	P-0066201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	430	505	0	ENST00000369535.4:c.35G>C	p.Gly12Ala	p.G12A	ENST00000369535	NM_002524.4	12	gGt/gCt	2/7	0.368820497953029	4	FACETS	0.876	0.844	0.908			1	INDETERMINATE	3	TRUE	NA	0.83687925430576	4		505	718	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784100	9784100	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	239	590	0	ENST00000377346.4:c.2668G>A	p.Gly890Ser	p.G890S	ENST00000377346	NM_005026.3	890	Ggc/Agc	21/24	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.544303790633468	2		590	654	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233322	69233322	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1476086953	NA	P-0066202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	13	523	0	ENST00000462284.1:c.1187A>G	p.Glu396Gly	p.E396G	ENST00000462284	NM_002392.5	396	gAa/gGa	11/11	1	2	FACETS	0.227	0.162	0.307	0.227	0.162	0.307	SUBCLONAL	1	TRUE	1	0.544303790633468	2		523	210	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0066203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	33	820	0	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	0.213240718027051	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	FALSE	0	0.244157786815565	1		820	185	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0066203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	9	400	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.199521196022182	3	FACETS	0.719	0.479	1	0.36	0.239	0.511	CLONAL	1	FALSE	1	0.244157786815565	3		400	115	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247295	153247295	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	23	567	0	ENST00000281708.4:c.1507G>A	p.Ala503Thr	p.A503T	ENST00000281708	NM_033632.3	503	Gca/Aca	10/12	1	2	FACETS	0.805	0.63	1	0.805	0.63	1	CLONAL	1	FALSE	1	0.244157786815565	2		567	234	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0066203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	10	134	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	0.677	0.461	0.945	0.677	0.461	0.945	SUBCLONAL	1	FALSE	1	0.244157786815565	2		134	121	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022535	12022535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159947	NA	P-0066203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	26	871	0	ENST00000396373.4:c.641C>T	p.Pro214Leu	p.P214L	ENST00000396373	NM_001987.4	214	cCg/cTg	5/8	0.244157786815565	4	FACETS	0.957	0.76	1	0.478	0.38	0.591	CLONAL	1	FALSE	2	0.244157786815565	4		871	277	SUCCESS
APC	324	MSKCC	GRCh37	5	112174587	112174587	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	22	421	0	ENST00000257430.4:c.3298del	p.Ser1100LeufsTer26	p.S1100Lfs*26	ENST00000257430	NM_000038.5	1099	gTt/gt	16/16	1	2	FACETS	1	0.832	1	1	0.832	1	CLONAL	1	FALSE	1	0.244157786815565	2		421	167	SUCCESS
AR	367	MSKCC	GRCh37	X	66765883	66765883	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1213709903	NA	P-0066204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	113	412	0	ENST00000374690.3:c.895G>A	p.Ala299Thr	p.A299T	ENST00000374690	NM_000044.3	299	Gca/Aca	1/8	1	1	FACETS	0.772	0.721	0.821	1	0.99	1	SUBCLONAL	2	TRUE	0	0.604355235869785	1		412	169	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599359	55599359	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0066204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	159	524	0	ENST00000288135.5:c.2484+1G>A		p.X828_splice	ENST00000288135	NM_000222.2	828			0.160656076123046	6	FACETS	0.927	0.859	0.996	0.927	0.859	0.996	INDETERMINATE	3	TRUE	3	0.604355235869785	6		524	418	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441529	6441529	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	132	347	0	ENST00000356142.4:c.376A>G	p.Asn126Asp	p.N126D	ENST00000356142	NM_018890.3	126	Aac/Gac	6/7	0.428088553978586	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	2	0.604355235869785	4		347	331	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974677	21974698	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CTGGATCGGCCTCCGACCGTAA	CTGGATCGGCCTCCGACCGTAA	-	novel	NA	P-0066204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	84	709	0	ENST00000304494.5:c.129_150del	p.Ser43ArgfsTer3	p.S43Rfs*3	ENST00000304494	NM_000077.4	43	agTTACGGTCGGAGGCCGATCCAG/ag	1/3	0.604355235869785	1	FACETS	0.995	0.899	1	0.995	0.899	1	CLONAL	1	TRUE	0	0.604355235869785	1		709	195	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	47	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.25	2		341	359	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0066207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	85	642	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.238535982775828	1	FACETS	0.829	0.732	0.932	0.829	0.732	0.932	CLONAL	1	TRUE	0	0.25	1		642	718	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448310	56448310	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567880628	NA	P-0066207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	91	658	0	ENST00000407977.2:c.337C>T	p.Arg113Ter	p.R113*	ENST00000407977		113	Cga/Tga	3/10	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.25	2		658	723	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328402	137328402	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	77	656	0	ENST00000481739.1:c.1331A>T	p.Asp444Val	p.D444V	ENST00000481739	NM_002957.4	444	gAc/gTc	10/10	1	2	FACETS	0.862	0.756	0.975	0.862	0.756	0.975	CLONAL	1	TRUE	1	0.25	2		656	715	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971137	21971146	+	frameshift_variant	Frame_Shift_Del	DEL	TCGGCGCAGT	TCGGCGCAGT	-	novel	NA	P-0066207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	73	675	0	ENST00000304494.5:c.212_221del	p.Asn71ThrfsTer72	p.N71Tfs*72	ENST00000304494	NM_000077.4	71	aACTGCGCCGAc/ac	2/3	1	2	FACETS	0.894	0.782	1	0.894	0.782	1	CLONAL	1	TRUE	1	0.25	2		675	653	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	67	446	0				ENST00000310581	NM_198253.2	-/1132			0.378684110742789	5	FACETS	1	0.973	1	0.493	0.431	0.56	CLONAL	1	TRUE	2	0.378684110742789	5		446	375	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052719	42052719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	80	281	0	ENST00000219905.7:c.7390C>T	p.Leu2464Phe	p.L2464F	ENST00000219905	NM_001164273.1	2464	Ctt/Ttt	20/24	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.378684110742789	2		281	414	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801025	1801025	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140087676	NA	P-0066213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	60	429	0	ENST00000260795.2:c.154G>A	p.Gly52Ser	p.G52S	ENST00000260795		52	Ggc/Agc	2/17	0.366036530838288	3	FACETS	0.845	0.73	0.97	0.423	0.365	0.485	CLONAL	1	TRUE	1	0.378684110742789	3		429	446	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651943	36651944	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGGCCCAG	novel	NA	P-0066213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	156	406	0	ENST00000244741.5:c.66_73dup	p.Val25AlafsTer9	p.V25Afs*9	ENST00000244741	NM_000389.4	22	ttc/ttCGGCCCAGc	2/3	0.378684110742789	3	FACETS	0.897	0.827	0.97	0.897	0.827	0.97	CLONAL	2	TRUE	1	0.378684110742789	3		406	546	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058383	42058383	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	94	408	0	ENST00000219905.7:c.8103C>G	p.Ile2701Met	p.I2701M	ENST00000219905	NM_001164273.1	2701	atC/atG	24/24	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.378684110742789	2		408	456	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42057093	42057093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1303212719	NA	P-0066213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	75	343	0	ENST00000219905.7:c.7754C>T	p.Ser2585Leu	p.S2585L	ENST00000219905	NM_001164273.1	2585	tCa/tTa	23/24	1	2	FACETS	0.98	0.864	1	0.98	0.864	1	CLONAL	1	TRUE	1	0.378684110742789	2		343	404	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42053942	42053942	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	56	304	0	ENST00000219905.7:c.7404C>A	p.Phe2468Leu	p.F2468L	ENST00000219905	NM_001164273.1	2468	ttC/ttA	21/24	1	2	FACETS	0.838	0.721	0.964	0.838	0.721	0.964	CLONAL	1	TRUE	1	0.378684110742789	2		304	353	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058606	42058606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	68	354	0	ENST00000219905.7:c.8326C>T	p.His2776Tyr	p.H2776Y	ENST00000219905	NM_001164273.1	2776	Cat/Tat	24/24	1	2	FACETS	0.798	0.696	0.907	0.798	0.696	0.907	CLONAL	1	TRUE	1	0.378684110742789	2		354	450	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218045	108218045	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782451	NA	P-0066214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	82	355	0	ENST00000278616.4:c.8624A>G	p.Asn2875Ser	p.N2875S	ENST00000278616	NM_000051.3	2875	aAt/aGt	59/63	0.730072550006449	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.730072550006449	2		355	105	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910883	114910883	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1477809102	NA	P-0066214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	67	393	1	ENST00000543371.1:c.1001+1G>A		p.X334_splice	ENST00000543371	NM_001198531.1	334			1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.730072550006449	2		394	170	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700262	117700262	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	77	341	0	ENST00000368508.3:c.2557C>G	p.Gln853Glu	p.Q853E	ENST00000368508	NM_002944.2	853	Caa/Gaa	17/43	0.730072550006449	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.730072550006449	2		341	95	SUCCESS
APC	324	MSKCC	GRCh37	5	112174886	112174886	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0066214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	89	442	0	ENST00000257430.4:c.3595A>T	p.Lys1199Ter	p.K1199*	ENST00000257430	NM_000038.5	1199	Aag/Tag	16/16	0.730072550006449	2	FACETS	0.968	0.9	1	0.968	0.9	1	CLONAL	2	TRUE	0	0.730072550006449	2		442	126	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919700	96919700	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	51	409	0	ENST00000258439.3:c.563T>A	p.Ile188Asn	p.I188N	ENST00000258439	NM_001193304.2	188	aTc/aAc	4/4	1	2	FACETS	0.957	0.832	1	0.957	0.832	1	CLONAL	1	TRUE	1	0.730072550006449	2		409	146	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831095	72831095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	33	458	0	ENST00000268489.5:c.5486C>T	p.Pro1829Leu	p.P1829L	ENST00000268489	NM_006885.3	1829	cCa/cTa	9/10	1	2	FACETS	0.66	0.547	0.783	0.66	0.547	0.783	SUBCLONAL	1	TRUE	1	0.730072550006449	2		458	137	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609084	43609084	+	protein_altering_variant	In_Frame_Ins	INS	G	G	CCTA	novel	NA	P-0066214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	57	660	0	ENST00000355710.3:c.1840delinsCCTA	p.Glu614delinsProLys	p.E614delinsPK	ENST00000355710	NM_020975.4	614	Gag/CCTAag	10/20	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.730072550006449	2		660	151	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0066215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	110	473	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		473	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0066215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	57	524	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		524	488	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0066216-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	150	257	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.602228077736632	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.628520360878516	2		257	234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0066216-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	173	490	0	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	0.628520360878516	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.628520360878516	1		490	335	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519938	NA	P-0066216-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	102	381	0	ENST00000263967.3:c.1034A>T	p.Asn345Ile	p.N345I	ENST00000263967	NM_006218.2	345	aAt/aTt	5/21	0.244921592372779	1	FACETS	0.897	0.818	0.979	0.897	0.818	0.979	INDETERMINATE	1	TRUE	0	0.628520360878516	1		381	248	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602445	10602445	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066216-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	160	609	0	ENST00000171111.5:c.1133del	p.Gly378AlafsTer22	p.G378Afs*22	ENST00000171111	NM_203500.1	378	gGc/gc	3/6	0.628520360878516	1	FACETS	0.891	0.827	0.955	0.891	0.827	0.955	CLONAL	1	TRUE	0	0.628520360878516	1		609	392	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291025	11291054	+	inframe_deletion	In_Frame_Del	DEL	GGCATCCCGGGACTGGTCTATCATGCCAAT	GGCATCCCGGGACTGGTCTATCATGCCAAT	-	novel	NA	P-0066216-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	47	446	0	ENST00000361445.4:c.2707_2736del	p.Ile903_Ala912del	p.I903_A912del	ENST00000361445	NM_004958.3	903	ATTGGCATGATAGACCAGTCCCGGGATGCC/-	18/58	0.327082726196565	1	FACETS	0.286	0.242	0.335	0.286	0.242	0.335	INDETERMINATE	1	TRUE	0	0.628520360878516	1		446	358	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178190	56178206	+	frameshift_variant	Frame_Shift_Del	DEL	AGTAACATACACAGGCC	AGTAACATACACAGGCC	GGCG	novel	NA	P-0066216-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	152	554	1	ENST00000399503.3:c.3163_3179delinsGGCG	p.Ser1055GlyfsTer23	p.S1055Gfs*23	ENST00000399503	NM_005921.1	1055	AGTAACATACACAGGCCa/GGCGa	14/20	0.628520360878516	1	FACETS	0.889	0.824	0.956	0.889	0.824	0.956	CLONAL	1	TRUE	0	0.628520360878516	1		555	373	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0066217-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	47	246	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.237625712296701	4	FACETS	1	0.911	1	1	0.911	1	CLONAL	2	TRUE	2	0.390290684079471	4		246	155	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0066217-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	74	758	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.937	1	1	0.985	1	CLONAL	2	TRUE	1	0.390290684079471	2		758	178	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945314	54945314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066217-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	18	190	0	ENST00000312783.6:c.1112G>A	p.Arg371Lys	p.R371K	ENST00000312783	NM_198436.1	371	aGg/aAg	10/10	1	2	FACETS	0.756	0.588	0.94	1	0.918	1	CLONAL	2	TRUE	1	0.390290684079471	2		190	61	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0066218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	61	157	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.718858226602469	2	FACETS	0.879	0.799	0.955	0.879	0.799	0.955	CLONAL	2	TRUE	0	0.74600447626633	2		157	93	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0066218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	249	638	0	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.710965384487462	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.74600447626633	2		638	293	SUCCESS
APC	324	MSKCC	GRCh37	5	112175162	112175162	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561588104	NA	P-0066218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	28	427	0	ENST00000257430.4:c.3871C>T	p.Gln1291Ter	p.Q1291*	ENST00000257430	NM_000038.5	1291	Cag/Tag	16/16	0.690790919919998	3	FACETS	0.799	0.649	0.964	0.399	0.324	0.482	CLONAL	1	TRUE	1	0.74600447626633	3		427	129	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0066218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	76	307	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.690790919919998	3	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	1	0.74600447626633	3		307	134	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61720070	61720070	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	23	382	0	ENST00000401558.2:c.1364A>C	p.Lys455Thr	p.K455T	ENST00000401558	NM_003400.3	455	aAg/aCg	13/25	0.690790919919998	3	FACETS	0.77	0.61	0.947	0.385	0.305	0.474	CLONAL	1	TRUE	1	0.74600447626633	3		382	110	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076781	72076781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767198961	NA	P-0066218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	64	463	1	ENST00000357731.5:c.716G>A	p.Arg239His	p.R239H	ENST00000357731	NM_173808.2	239	cGc/cAc	5/7	0.690790919919998	3	FACETS	0.788	0.688	0.894	0.394	0.344	0.447	SUBCLONAL	1	TRUE	1	0.74600447626633	3		464	299	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274290	5274290	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368676720	NA	P-0066218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	126	508	1	ENST00000357368.4:c.157G>A	p.Val53Met	p.V53M	ENST00000357368	NM_002850.3	53	Gtg/Atg	3/38	0.74600447626633	3	FACETS	0.983	0.912	1	0.983	0.912	1	CLONAL	2	TRUE	1	0.74600447626633	3		509	236	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511145	148511145	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	86	508	0	ENST00000320356.2:c.1757A>T	p.Asp586Val	p.D586V	ENST00000320356	NM_004456.4	586	gAc/gTc	15/20	0.74600447626633	3	FACETS	1	0.916	1	0.343	0.306	0.381	CLONAL	1	TRUE	0	0.74600447626633	3		508	308	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88672062	88672062	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	13	112	0	ENST00000372037.3:c.596T>G	p.Phe199Cys	p.F199C	ENST00000372037	NM_004329.2	199	tTt/tGt	8/13	0.684067109121452	2	FACETS	1	0.897	1	0.697	0.54	0.852	CLONAL	1	TRUE	0	0.74600447626633	2		112	25	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213852	2213852	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	83	599	0	ENST00000398665.3:c.1664G>A	p.Gly555Asp	p.G555D	ENST00000398665	NM_032482.2	555	gGt/gAt	18/28	0.74600447626633	3	FACETS	1	0.952	1	0.558	0.498	0.619	CLONAL	1	TRUE	1	0.74600447626633	3		599	274	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592124	67592124	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	47	407	0	ENST00000274335.5:c.1940T>C	p.Leu647Pro	p.L647P	ENST00000274335		647	cTt/cCt	14/15	0.690790919919998	3	FACETS	0.848	0.724	0.981	0.424	0.362	0.491	CLONAL	1	TRUE	1	0.74600447626633	3		407	204	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360583	70360583	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	126	647	0	ENST00000374080.3:c.6143T>C	p.Leu2048Pro	p.L2048P	ENST00000374080		2048	cTa/cCa	42/45	0.583986762629532	2	FACETS	0.96	0.88	1	0.48	0.44	0.521	CLONAL	1	TRUE	0	0.74600447626633	2		647	352	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598933	28598933	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	103	645	0	ENST00000253063.3:c.493T>G	p.Leu165Val	p.L165V	ENST00000253063	NM_031459.4	165	Ttg/Gtg	4/10	0.690790919919998	3	FACETS	0.985	0.889	1	0.492	0.444	0.543	CLONAL	1	TRUE	1	0.74600447626633	3		645	385	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857876	9857876	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	66	589	0	ENST00000330684.3:c.3525A>C	p.Glu1175Asp	p.E1175D	ENST00000330684	NM_001134407.1	1175	gaA/gaC	13/13	0.712956441755892	3	FACETS	0.945	0.83	1	0.315	0.276	0.356	CLONAL	1	TRUE	0	0.74600447626633	3		589	257	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874270	151874271	+	missense_variant	Missense_Mutation	DNP	GA	GA	AC	novel	NA	P-0066218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	30	455	1	ENST00000262189.6:c.8267_8268delinsGT	p.Ile2756Ser	p.I2756S	ENST00000262189	NM_170606.2	2756	aTC/aGT	38/59	0.646904060462171	3	FACETS	0.722	0.589	0.868	0.241	0.196	0.29	SUBCLONAL	1	TRUE	0	0.74600447626633	3		456	153	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576923	7576955	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAA	AGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAA	-	novel	NA	P-0066221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	146	612	0	ENST00000269305.4:c.920-29_923del		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	0.390569744403694	1	FACETS	0.796	0.727	0.867	0.796	0.727	0.867	SUBCLONAL	1	TRUE	0	0.390569744403694	1		612	756	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052717	42052734	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCTTACTCGAGTAAGTG	TTCTTACTCGAGTAAGTG	-	novel	NA	P-0066221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	99	437	0	ENST00000219905.7:c.7392_7398+11del		p.X2464_splice	ENST00000219905	NM_001164273.1	2464		20/24	1	2	FACETS	0.798	0.714	0.888	0.798	0.714	0.888	SUBCLONAL	1	TRUE	1	0.390569744403694	2		437	635	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244034	41244034	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs397509079	NA	P-0066221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	383	526	0	ENST00000357654.3:c.3514G>T	p.Glu1172Ter	p.E1172*	ENST00000357654	NM_007294.3	1172	Gaa/Taa	10/23	0.364900755590148	2	FACETS	0.905	0.861	0.95	0.905	0.861	0.95	CLONAL	2	TRUE	0	0.390569744403694	2		526	1083	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2189794	2189820	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTAGGTGGCTTGCCCCTGCCCAGAGG	GGTAGGTGGCTTGCCCCTGCCCAGAGG	-	novel	NA	P-0066221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	86	591	0	ENST00000398665.3:c.264+2_264+28del		p.X88_splice	ENST00000398665	NM_032482.2	88		4/28	1	2	FACETS	0.66	0.584	0.742	0.66	0.584	0.742	SUBCLONAL	1	TRUE	1	0.390569744403694	2		591	667	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130086	143130086	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	108	392	0	ENST00000262992.4:c.930G>T	p.Met310Ile	p.M310I	ENST00000262992	NM_001101669.1	310	atG/atT	11/24	0.390569744403694	1	FACETS	0.881	0.794	0.972	0.881	0.794	0.972	CLONAL	1	TRUE	0	0.390569744403694	1		392	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0066222-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	52	733	0	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.2	2		733	438	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142001	108142001	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749471737	NA	P-0066222-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	27	521	0	ENST00000278616.4:c.2945G>A	p.Arg982His	p.R982H	ENST00000278616	NM_000051.3	982	cGt/cAt	20/63	1	2	FACETS	0.722	0.574	0.891	0.722	0.574	0.891	SUBCLONAL	1	TRUE	1	0.2	2		521	374	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932203	39932203	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs769227489	NA	P-0066222-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	31	738	0	ENST00000378444.4:c.2396A>G	p.Lys799Arg	p.K799R	ENST00000378444	NM_001123385.1	799	aAa/aGa	4/15	1	2	FACETS	0.698	0.564	0.85	0.698	0.564	0.85	SUBCLONAL	1	TRUE	1	0.2	2		738	444	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508727	29508727	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0066222-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	29	561	0	ENST00000356175.3:c.655-1G>C		p.X219_splice	ENST00000356175	NM_000267.3	219			1	2	FACETS	0.98	0.788	1	0.98	0.788	1	CLONAL	1	TRUE	1	0.2	2		561	296	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40498634	40498634	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066222-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	30	542	0	ENST00000264657.5:c.226A>G	p.Asn76Asp	p.N76D	ENST00000264657	NM_139276.2	76	Aat/Gat	3/24	1	2	FACETS	0.843	0.68	1	0.843	0.68	1	CLONAL	1	TRUE	1	0.2	2		542	356	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202123018	202123018	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066222-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	36	666	0	ENST00000358485.4:c.64T>G	p.Phe22Val	p.F22V	ENST00000358485	NM_001080125.1	22	Ttt/Gtt	1/9	0.138395545902744	3	FACETS	0.567	0.465	0.683	0.189	0.155	0.228	SUBCLONAL	1	TRUE	0	0.2	3		666	698	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778455	3778455	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066223-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	17	822	0	ENST00000262367.5:c.6593T>A	p.Leu2198Gln	p.L2198Q	ENST00000262367	NM_004380.2	2198	cTg/cAg	31/31	0.479718244592203	3	FACETS	0.327	0.244	0.426	0.164	0.122	0.213	SUBCLONAL	1	TRUE	1	0.507027703171733	3		822	257	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099858	157099858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066223-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	40	599	0	ENST00000346085.5:c.795G>A	p.Met265Ile	p.M265I	ENST00000346085	NM_020732.3	265	atG/atA	1/20	0.305175737424369	3	FACETS	0.895	0.75	1	0.298	0.25	0.351	CLONAL	1	TRUE	0	0.507027703171733	3		599	221	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11803080	11803080	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066223-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	28	441	0	ENST00000396373.4:c.19C>T	p.Gln7Ter	p.Q7*	ENST00000396373	NM_001987.4	7	Cag/Tag	1/8	0.507027703171733	4	FACETS	0.393	0.313	0.483	0.196	0.156	0.242	SUBCLONAL	1	TRUE	2	0.507027703171733	4		441	424	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316030	14316030	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066223-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	25	292	1	ENST00000256196.4:c.395A>G	p.Asp132Gly	p.D132G	ENST00000256196		132	gAt/gGt	4/6	1	2	FACETS	0.829	0.664	1	0.829	0.664	1	CLONAL	1	TRUE	1	0.507027703171733	2		293	119	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518414	69518414	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs1325706402	NA	P-0066223-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	11	305	0	ENST00000294312.3:c.231C>G	p.His77Gln	p.H77Q	ENST00000294312	NM_005117.2	77	caC/caG	1/3	0.503029720710226	4	FACETS	1	0.741	1	0.352	0.248	0.474	CLONAL	1	TRUE	1	0.507027703171733	4		305	62	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098594	11098594	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066223-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	14	700	0	ENST00000358026.2:c.1112A>C	p.Glu371Ala	p.E371A	ENST00000358026	NM_001128849.1	371	gAg/gCg	6/36	1	2	FACETS	0.242	0.175	0.324	0.242	0.175	0.324	SUBCLONAL	1	TRUE	1	0.507027703171733	2		700	228	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798854	42798862	+	inframe_deletion	In_Frame_Del	DEL	CAGCTCTTT	CAGCTCTTT	-	novel	NA	P-0066223-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	23	742	0	ENST00000575354.2:c.4429_4437del	p.Leu1477_Gln1479del	p.L1477_Q1479del	ENST00000575354	NM_015125.3	1476	CAGCTCTTT/-	19/20	0.454708155868909	4	FACETS	0.375	0.292	0.471	0.094	0.073	0.118	SUBCLONAL	1	TRUE	0	0.507027703171733	4		742	365	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967912	93967912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066223-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	29	523	0	ENST00000369303.4:c.2015C>T	p.Thr672Ile	p.T672I	ENST00000369303	NM_004440.3	672	aCa/aTa	11/17	0.507027703171733	4	FACETS	0.759	0.613	0.924	0.253	0.204	0.308	CLONAL	1	TRUE	1	0.507027703171733	4		523	227	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031735	69031746	+	inframe_deletion	In_Frame_Del	DEL	CATCTTTTCAGC	CATCTTTTCAGC	-	novel	NA	P-0066223-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	26	497	0	ENST00000288368.4:c.3492_3503del	p.His1164_Ser1167del	p.H1164_S1167del	ENST00000288368	NM_024870.2	1164	CATCTTTTCAGC/-	28/40	0.487929756562046	5	FACETS	0.528	0.418	0.654	0.132	0.104	0.164	SUBCLONAL	1	TRUE	1	0.507027703171733	5		497	342	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0066224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	35	344	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	0.6989157852099	2	FACETS	0.682	0.568	0.806	0.341	0.284	0.403	SUBCLONAL	1	TRUE	0	0.702505988623492	2		344	146	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0066224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	207	642	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.691511213419283	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.702505988623492	1		642	350	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94169002	94169002	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1591640825	NA	P-0066224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	62	350	0	ENST00000323929.3:c.1990C>G	p.Gln664Glu	p.Q664E	ENST00000323929	NM_005591.3	664	Caa/Gaa	18/20	0.159196992703046	2	FACETS	0.729	0.638	0.826	0.365	0.319	0.413	INDETERMINATE	1	TRUE	0	0.702505988623492	2		350	242	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81902846	81902846	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1219414299	NA	P-0066224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	100	429	0	ENST00000359376.3:c.507C>G	p.Ile169Met	p.I169M	ENST00000359376	NM_002661.3	169	atC/atG	6/33	0.702505988623492	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.702505988623492	1		429	184	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31237856	31237856	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	70	564	0	ENST00000376228.5:c.902C>G	p.Ser301Cys	p.S301C	ENST00000376228	NM_002117.5	301	tCt/tGt	5/8	0.702505988623492	3	FACETS	0.395	0.344	0.45	0.197	0.172	0.225	SUBCLONAL	1	TRUE	1	0.702505988623492	3		564	682	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	234	721	4	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.988	0.922	1	0.988	0.922	1	CLONAL	1	TRUE	1	0.49	2		725	967	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	64	710	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.234	0.201	0.269	0.234	0.201	0.269	SUBCLONAL	1	TRUE	1	0.49	2		713	1118	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	276	782	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.49	2		782	992	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	213	505	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.49	2		505	828	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	204	442	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.49	2		442	782	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	255	642	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.49	2		642	996	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	227	652	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	1	2	FACETS	0.944	0.88	1	0.944	0.88	1	CLONAL	1	TRUE	1	0.49	2		652	981	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101259	27101259	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	273	659	0	ENST00000324856.7:c.4541del	p.Thr1514ArgfsTer13	p.T1514Rfs*13	ENST00000324856	NM_006015.4	1514	aCg/ag	18/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.49	2		659	1010	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279528	123279528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1159063118	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	220	594	0	ENST00000358487.5:c.904G>A	p.Gly302Arg	p.G302R	ENST00000358487	NM_000141.4	302	Ggg/Agg	7/18	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.49	2		594	833	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307393	118307394	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1555138552	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	92	307	1	ENST00000534358.1:c.173dup	p.Ala59GlyfsTer88	p.A59Gfs*88	ENST00000534358	NM_005933.3	56	tcc/tCcc	1/36	1	2	FACETS	0.801	0.715	0.892	0.801	0.715	0.892	CLONAL	1	TRUE	1	0.49	2		308	469	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006380	12006380	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	193	509	0	ENST00000396373.4:c.349del	p.Leu117PhefsTer5	p.L117Ffs*5	ENST00000396373	NM_001987.4	116	ctC/ct	4/8	1	2	FACETS	0.991	0.919	1	0.991	0.919	1	CLONAL	1	TRUE	1	0.49	2		509	795	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218357	133218357	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1335665224	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	187	503	0	ENST00000320574.5:c.5254G>A	p.Asp1752Asn	p.D1752N	ENST00000320574	NM_006231.2	1752	Gac/Aac	39/49	1	2	FACETS	0.987	0.914	1	0.987	0.914	1	CLONAL	1	TRUE	1	0.49	2		503	773	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249349	133249349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780556141	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	263	597	0	ENST00000320574.5:c.1550C>T	p.Pro517Leu	p.P517L	ENST00000320574	NM_006231.2	517	cCc/cTc	15/49	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.49	2		597	936	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912770	32912771	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs80359439	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	29	452	0	ENST00000380152.3:c.4284dup	p.Gln1429SerfsTer9	p.Q1429Sfs*9	ENST00000380152		1426	-/T	11/27	1	2	FACETS	0.264	0.211	0.324	0.264	0.211	0.324	SUBCLONAL	1	TRUE	1	0.49	2		452	449	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913436	32913436	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	125	450	0	ENST00000380152.3:c.4948del	p.Ser1650ValfsTer20	p.S1650Vfs*20	ENST00000380152		1648	gcA/gc	11/27	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.49	2		450	453	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122297	2122297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45517215	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	178	612	0	ENST00000219476.3:c.2153G>A	p.Arg718His	p.R718H	ENST00000219476	NM_000548.3	718	cGc/cAc	20/42	1	2	FACETS	0.836	0.771	0.904	0.836	0.771	0.904	CLONAL	1	TRUE	1	0.49	2		612	869	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136771	2136771	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886051796	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	272	643	0	ENST00000219476.3:c.4888G>A	p.Val1630Met	p.V1630M	ENST00000219476	NM_000548.3	1630	Gtg/Atg	38/42	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.49	2		643	1054	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038692	14038692	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs760553358	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	124	365	0	ENST00000311895.7:c.2017G>A	p.Gly673Ser	p.G673S	ENST00000311895	NM_005236.2	673	Ggt/Agt	10/11	1	2	FACETS	0.964	0.876	1	0.964	0.876	1	CLONAL	1	TRUE	1	0.49	2		365	525	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992078	72992078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	227	644	0	ENST00000268489.5:c.1967G>A	p.Gly656Asp	p.G656D	ENST00000268489	NM_006885.3	656	gGc/gAc	2/10	1	2	FACETS	0.994	0.927	1	0.994	0.927	1	CLONAL	1	TRUE	1	0.49	2		644	932	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993516	72993516	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772845316	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	267	653	0	ENST00000268489.5:c.529G>A	p.Ala177Thr	p.A177T	ENST00000268489	NM_006885.3	177	Gcg/Acg	2/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.49	2		653	1016	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346226	89346226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	147	707	0	ENST00000301030.4:c.6724G>A	p.Ala2242Thr	p.A2242T	ENST00000301030	NM_001256183.1	2242	Gcg/Acg	9/13	1	2	FACETS	0.609	0.555	0.665	0.609	0.555	0.665	SUBCLONAL	1	TRUE	1	0.49	2		707	986	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579346	7579348	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs764486868	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	225	576	0	ENST00000269305.4:c.339_341del	p.Phe113del	p.F113del	ENST00000269305	NM_001126112.2	113	ttCTTg/ttg	4/11	1	2	FACETS	0.958	0.892	1	0.958	0.892	1	CLONAL	1	TRUE	1	0.49	2		576	959	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657517	29657517	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs876658854	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	25	382	0	ENST00000356175.3:c.5749+1G>T		p.X1917_splice	ENST00000356175	NM_000267.3	1917			1	2	FACETS	0.258	0.203	0.322	0.258	0.203	0.322	SUBCLONAL	1	TRUE	1	0.49	2		382	395	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308382	15308383	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs749829137	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	175	626	0	ENST00000263388.2:c.125dup	p.Cys43LeufsTer32	p.C43Lfs*32	ENST00000263388	NM_000435.2	42	cct/ccCt	2/33	1	2	FACETS	0.732	0.674	0.793	0.732	0.674	0.793	SUBCLONAL	1	TRUE	1	0.49	2		626	976	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967090	18967091	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	96	508	0	ENST00000262803.5:c.1814_1815dup	p.Leu606SerfsTer3	p.L606Sfs*3	ENST00000262803	NM_002911.3	602	gca/gcAGa	13/24	1	2	FACETS	0.518	0.461	0.578	0.518	0.461	0.578	SUBCLONAL	1	TRUE	1	0.49	2		508	757	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223640	36223640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	297	801	0	ENST00000222270.7:c.6190G>A	p.Val2064Met	p.V2064M	ENST00000222270	NM_014727.1	2064	Gtg/Atg	28/37	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.49	2		801	1187	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229346	36229346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1452431678	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	278	633	0	ENST00000222270.7:c.8036G>A	p.Arg2679His	p.R2679H	ENST00000222270	NM_014727.1	2679	cGc/cAc	37/37	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.49	2		633	1040	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457204	25457204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762126968	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	247	605	0	ENST00000264709.3:c.2683G>A	p.Val895Met	p.V895M	ENST00000264709	NM_175629.2	895	Gtg/Atg	23/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.49	2		605	899	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25462033	25462033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	192	527	0	ENST00000264709.3:c.2374C>T	p.Arg792Cys	p.R792C	ENST00000264709	NM_175629.2	792	Cgc/Tgc	20/23	1	2	FACETS	0.935	0.866	1	0.935	0.866	1	CLONAL	1	TRUE	1	0.49	2		527	838	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67626692	67626692	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1298232483	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	59	326	0	ENST00000272342.5:c.369del	p.Lys123AsnfsTer46	p.K123Nfs*46	ENST00000272342	NM_019002.3	121	agA/ag	3/6	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.49	2		326	228	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378265	225378266	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	89	389	0	ENST00000264414.4:c.629dup	p.Leu210PhefsTer20	p.L210Ffs*20	ENST00000264414	NM_003590.4	210	ttg/ttTg	5/16	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.49	2		389	358	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663054	227663054	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	206	567	0	ENST00000305123.5:c.401del	p.Gly134AlafsTer16	p.G134Afs*16	ENST00000305123	NM_005544.2	134	gGc/gc	1/2	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.49	2		567	810	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714430	40714430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777325904	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	219	572	0	ENST00000373198.4:c.3967G>A	p.Val1323Ile	p.V1323I	ENST00000373198	NM_133170.3	1323	Gtc/Atc	29/32	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.49	2		572	884	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42843768	42843768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745742232	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	172	513	0	ENST00000398585.3:c.1151C>T	p.Ala384Val	p.A384V	ENST00000398585	NM_001135099.1	384	gCg/gTg	10/14	1	2	FACETS	0.959	0.885	1	0.959	0.885	1	CLONAL	1	TRUE	1	0.49	2		513	732	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	230	579	0	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	1	2	FACETS	0.943	0.879	1	0.943	0.879	1	CLONAL	1	TRUE	1	0.49	2		579	996	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437542	52437542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772037576	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	243	632	0	ENST00000460680.1:c.1619G>A	p.Arg540His	p.R540H	ENST00000460680	NM_004656.3	540	cGt/cAt	13/17	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.49	2		632	957	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269009	142269009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369913351	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	43	407	0	ENST00000350721.4:c.2941G>A	p.Val981Ile	p.V981I	ENST00000350721	NM_001184.3	981	Gtt/Att	14/47	1	2	FACETS	0.326	0.272	0.386	0.326	0.272	0.386	SUBCLONAL	1	TRUE	1	0.49	2		407	538	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573449	55573449	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	122	409	0	ENST00000288135.5:c.1111A>G	p.Ile371Val	p.I371V	ENST00000288135	NM_000222.2	371	Atc/Gtc	6/21	1	2	FACETS	0.976	0.887	1	0.976	0.887	1	CLONAL	1	TRUE	1	0.49	2		409	510	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197255	106197255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1222260506	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	237	537	0	ENST00000380013.4:c.5588C>T	p.Ala1863Val	p.A1863V	ENST00000380013	NM_001127208.2	1863	gCc/gTc	11/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.49	2		537	808	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247172	153247173	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	142	390	0	ENST00000281708.4:c.1629_1630del	p.Arg543SerfsTer7	p.R543Sfs*7	ENST00000281708	NM_033632.3	543	agAGtc/agtc	10/12	1	2	FACETS	0.961	0.879	1	0.961	0.879	1	CLONAL	1	TRUE	1	0.49	2		390	603	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516959	187516959	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	173	397	0	ENST00000441802.2:c.13022C>A	p.Pro4341His	p.P4341H	ENST00000441802	NM_005245.3	4341	cCc/cAc	26/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.49	2		397	615	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279431	1279431	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754809046	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	200	529	0	ENST00000310581.5:c.2105C>T	p.Pro702Leu	p.P702L	ENST00000310581	NM_198253.2	702	cCg/cTg	5/16	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.49	2		529	811	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39002763	39002763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1303852277	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	132	396	0	ENST00000357387.3:c.266G>A	p.Arg89Gln	p.R89Q	ENST00000357387	NM_152756.3	89	cGg/cAg	5/38	1	2	FACETS	0.964	0.879	1	0.964	0.879	1	CLONAL	1	TRUE	1	0.49	2		396	559	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589603	67589603	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	58	344	0	ENST00000274335.5:c.1366T>A	p.Phe456Ile	p.F456I	ENST00000274335		456	Ttt/Att	10/15	1	2	FACETS	0.877	0.76	1	0.877	0.76	1	CLONAL	1	TRUE	1	0.49	2		344	270	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672317	86672317	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	188	468	0	ENST00000274376.6:c.2119C>T	p.Arg707Cys	p.R707C	ENST00000274376	NM_002890.2	707	Cgt/Tgt	16/25	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.49	2		468	671	SUCCESS
APC	324	MSKCC	GRCh37	5	112177263	112177263	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	189	543	0	ENST00000257430.4:c.5972A>G	p.Glu1991Gly	p.E1991G	ENST00000257430	NM_000038.5	1991	gAg/gGg	16/16	1	2	FACETS	0.981	0.909	1	0.981	0.909	1	CLONAL	1	TRUE	1	0.49	2		543	786	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323362	31323363	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748204482	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	107	456	0	ENST00000412585.2:c.626dup	p.Thr211AspfsTer10	p.T211Dfs*10	ENST00000412585	NM_005514.6	209	cca/ccCa	4/8	0.493368281319347	1	FACETS	0.665	0.599	0.734	0.665	0.599	0.734	SUBCLONAL	1	TRUE	0	0.49	1		456	496	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185023	32185023	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	191	599	0	ENST00000375023.3:c.1645G>C	p.Glu549Gln	p.E549Q	ENST00000375023	NM_004557.3	549	Gag/Cag	10/30	0.493368281319347	1	FACETS	0.918	0.853	0.985	0.918	0.853	0.985	CLONAL	1	TRUE	0	0.49	1		599	641	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282205	38282205	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	246	621	0	ENST00000425967.3:c.851A>G	p.His284Arg	p.H284R	ENST00000425967	NM_001174067.1	284	cAc/cGc	8/19	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.49	2		621	967	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128206867	128206867	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1357329809	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	183	442	0	ENST00000265960.3:c.1356A>G	p.Ile452Met	p.I452M	ENST00000265960	NM_001006617.1	452	atA/atG	11/12	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.49	2		442	670	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391409	139391409	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	253	662	0	ENST00000277541.6:c.6782del	p.Gly2261AlafsTer34	p.G2261Afs*34	ENST00000277541	NM_017617.3	2261	gGc/gc	34/34	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.49	2		662	1009	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932816	39932816	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	254	722	0	ENST00000378444.4:c.1783A>G	p.Ile595Val	p.I595V	ENST00000378444	NM_001123385.1	595	Att/Gtt	4/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.49	2		722	995	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650391	48650391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200509606	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	245	729	1	ENST00000376670.3:c.361G>A	p.Val121Met	p.V121M	ENST00000376670	NM_002049.3	121	Gtg/Atg	3/6	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.49	2		730	947	SUCCESS
AR	367	MSKCC	GRCh37	X	66765207	66765207	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	113	397	0	ENST00000374690.3:c.219G>T	p.Gln73His	p.Q73H	ENST00000374690	NM_000044.3	73	caG/caT	1/8	1	2	FACETS	0.756	0.682	0.834	0.756	0.682	0.834	SUBCLONAL	1	TRUE	1	0.49	2		397	610	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0066226-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	22	257	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.827	0.641	1	0.827	0.641	1	CLONAL	1	TRUE	1	0.177359448177188	2		257	300	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678541	88678541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145157285	NA	P-0066226-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	41	678	0	ENST00000360948.2:c.995C>T	p.Thr332Met	p.T332M	ENST00000360948	NM_001012338.2	332	aCg/aTg	9/19	1	2	FACETS	0.945	0.787	1	0.945	0.787	1	CLONAL	1	TRUE	1	0.177359448177188	2		678	489	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15822322	15822322	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0066226-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	36	106	0	ENST00000307771.7:c.399+2T>C		p.X133_splice	ENST00000307771	NM_005089.3	133			1	1	FACETS	0.934	0.776	1	1	0.963	1	CLONAL	2	TRUE	0	0.177359448177188	1		106	198	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589782	69589782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs906608234	NA	P-0066226-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	56	1017	0	ENST00000168712.1:c.71C>T	p.Ala24Val	p.A24V	ENST00000168712	NM_002007.2	24	gCg/gTg	1/3	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.177359448177188	2		1017	594	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60795970	60795970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066226-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	36	556	0	ENST00000333681.4:c.608G>A	p.Gly203Asp	p.G203D	ENST00000333681		203	gGc/gAc	3/3	1	2	FACETS	0.978	0.805	1	0.978	0.805	1	CLONAL	1	TRUE	1	0.177359448177188	2		556	415	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0066227-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	72	492	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.21783409657162	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.29	1		492	371	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500838	8500838	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066227-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	100	759	0	ENST00000356435.5:c.2044G>A	p.Glu682Lys	p.E682K	ENST00000356435		682	Gaa/Aaa	13/35	0.21783409657162	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.29	1		759	555	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347729	347729	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs754163738	NA	P-0066227-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	36	769	0	ENST00000262320.3:c.1777G>T	p.Ala593Ser	p.A593S	ENST00000262320	NM_003502.3	593	Gcc/Tcc	6/11	0.0548554107936612	3	FACETS	0.512	0.42	0.616			1	INDETERMINATE	1	TRUE	NA	0.29	3		769	555	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109813	115109813	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066227-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	74	907	0	ENST00000257566.3:c.2065G>T	p.Gly689Cys	p.G689C	ENST00000257566	NM_016569.3	689	Ggc/Tgc	8/8	0.21783409657162	1	FACETS	0.989	0.87	1	0.989	0.87	1	CLONAL	1	TRUE	0	0.29	1		907	441	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557489	21557489	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1170530046	NA	P-0066227-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	57	834	0	ENST00000382592.4:c.2356G>T	p.Gly786Cys	p.G786C	ENST00000382592	NM_014572.2	786	Ggc/Tgc	5/8	0.21783409657162	1	FACETS	0.662	0.568	0.763	0.662	0.568	0.763	SUBCLONAL	1	TRUE	0	0.29	1		834	508	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879262	151879262	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs144021585	NA	P-0066227-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	37	682	0	ENST00000262189.6:c.5683A>G	p.Met1895Val	p.M1895V	ENST00000262189	NM_170606.2	1895	Atg/Gtg	36/59	1	2	FACETS	0.477	0.392	0.572	0.477	0.392	0.572	SUBCLONAL	1	TRUE	1	0.29	2		682	535	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937674	17937674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265005806	NA	P-0066227-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	43	780	0	ENST00000458235.1:c.3253C>T	p.Arg1085Trp	p.R1085W	ENST00000458235	NM_000215.3	1085	Cgg/Tgg	24/24	0.27453683658591	1	FACETS	0.591	0.495	0.697	0.591	0.495	0.697	SUBCLONAL	1	TRUE	0	0.29	1		780	429	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564657	139564657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066227-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	32	815	0	ENST00000308874.7:c.446C>T	p.Pro149Leu	p.P149L	ENST00000308874		149	cCc/cTc	7/10	0.21783409657162	1	FACETS	0.473	0.384	0.574	0.473	0.384	0.574	SUBCLONAL	1	TRUE	0	0.29	1		815	399	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612867	228612867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066227-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	48	1173	0	ENST00000366696.1:c.160C>T	p.Arg54Cys	p.R54C	ENST00000366696	NM_003493.2	54	Cgc/Tgc	1/1	0.298122970012327	3	FACETS	0.438	0.369	0.514	0.219	0.184	0.257	SUBCLONAL	1	TRUE	1	0.29	3		1173	866	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246490634	246490634	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066227-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	114	495	0	ENST00000388985.4:c.400A>T	p.Asn134Tyr	p.N134Y	ENST00000388985		134	Aac/Tac	5/12	0.298122970012327	3	FACETS	0.891	0.806	0.98	0.891	0.806	0.98	CLONAL	2	TRUE	1	0.29	3		495	505	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868320	56868320	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066227-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	37	747	0	ENST00000308159.5:c.1703G>C	p.Arg568Pro	p.R568P	ENST00000308159	NM_014669.4	568	cGc/cCc	15/22	0.300457338459532	1	FACETS	0.472	0.389	0.565	0.472	0.389	0.565	SUBCLONAL	1	TRUE	0	0.29	1		747	462	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760785	59760785	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066227-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	70	586	0	ENST00000259008.2:c.3622G>T	p.Asp1208Tyr	p.D1208Y	ENST00000259008	NM_032043.2	1208	Gac/Tac	20/20	1	2	FACETS	0.952	0.832	1	0.952	0.832	1	CLONAL	1	TRUE	1	0.29	2		586	507	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561069	9561069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066227-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	67	705	2	ENST00000353224.5:c.713G>A	p.Arg238Lys	p.R238K	ENST00000353224	NM_177990.2	238	aGa/aAa	4/10	0.27453683658591	1	FACETS	0.806	0.702	0.919	0.806	0.702	0.919	CLONAL	1	TRUE	0	0.29	1		707	490	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31020719	31020719	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066227-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	22	635	0	ENST00000375687.4:c.1016A>T	p.Gln339Leu	p.Q339L	ENST00000375687	NM_015338.5	339	cAg/cTg	11/13	0.27453683658591	1	FACETS	0.33	0.255	0.417	0.33	0.255	0.417	SUBCLONAL	1	TRUE	0	0.29	1		635	393	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446745	29446745	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066227-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	34	879	0	ENST00000544604.2:c.2576G>T	p.Arg859Leu	p.R859L	ENST00000544604	NM_001206998.1	859	cGa/cTa	8/9	0.21783409657162	1	FACETS	0.48	0.392	0.578	0.48	0.392	0.578	SUBCLONAL	1	TRUE	0	0.29	1		879	418	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573987	41573987	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066227-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	43	858	0	ENST00000263253.7:c.6272A>T	p.Lys2091Met	p.K2091M	ENST00000263253	NM_001429.3	2091	aAg/aTg	31/31	0.21783409657162	1	FACETS	0.517	0.433	0.611	0.517	0.433	0.611	SUBCLONAL	1	TRUE	0	0.29	1		858	490	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480458	89480458	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066227-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	45	640	0	ENST00000336596.2:c.2295C>G	p.Phe765Leu	p.F765L	ENST00000336596	NM_005233.5	765	ttC/ttG	13/17	0.21783409657162	1	FACETS	0.491	0.413	0.579	0.491	0.413	0.579	SUBCLONAL	1	TRUE	0	0.29	1		640	540	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729986	41729986	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066227-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	82	880	0	ENST00000242208.4:c.543C>A	p.His181Gln	p.H181Q	ENST00000242208	NM_002192.2	181	caC/caA	3/3	1	2	FACETS	0.881	0.777	0.992	0.881	0.777	0.992	CLONAL	1	TRUE	1	0.29	2		880	642	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381468	81381468	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066227-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	48	605	0	ENST00000222390.5:c.593A>T	p.Tyr198Phe	p.Y198F	ENST00000222390	NM_000601.4	198	tAc/tTc	5/18	1	2	FACETS	0.546	0.461	0.64	0.546	0.461	0.64	SUBCLONAL	1	TRUE	1	0.29	2		605	606	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2123869	2123869	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066227-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	38	803	0	ENST00000349721.2:c.3913G>T	p.Gly1305Trp	p.G1305W	ENST00000349721	NM_003070.3	1305	Ggg/Tgg	27/34	0.21783409657162	1	FACETS	0.403	0.332	0.482	0.403	0.332	0.482	SUBCLONAL	1	TRUE	0	0.29	1		803	556	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0066228-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	53	133	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.551783436797929	3	FACETS	0.898	0.772	1	0.449	0.386	0.517	CLONAL	1	TRUE	1	0.551783436797929	3		133	273	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879277	151879277	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs956673837	NA	P-0066228-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	170	673	0	ENST00000262189.6:c.5668C>T	p.Arg1890Ter	p.R1890*	ENST00000262189	NM_170606.2	1890	Cga/Tga	36/59	0.551783436797929	1	FACETS	0.981	0.911	1	0.981	0.911	1	CLONAL	1	TRUE	0	0.551783436797929	1		673	455	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032069	26032069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066228-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	240	873	1	ENST00000244661.2:c.220G>A	p.Glu74Lys	p.E74K	ENST00000244661	NM_003537.3	74	Gaa/Aaa	1/1	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.551783436797929	2		874	794	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233207	46233207	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066228-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	179	554	0	ENST00000334344.6:c.1426C>T	p.Gln476Ter	p.Q476*	ENST00000334344	NM_152641.2	476	Caa/Taa	11/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.551783436797929	2		554	582	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950783	38950783	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066228-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	113	381	0	ENST00000357387.3:c.3167C>G	p.Ser1056Cys	p.S1056C	ENST00000357387	NM_152756.3	1056	tCt/tGt	31/38	1	2	FACETS	0.999	0.906	1	0.999	0.906	1	CLONAL	1	TRUE	1	0.551783436797929	2		381	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0066230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	157	424	0	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	0.659339200244004	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.659339200244004	1		424	314	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589619	67589620	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0066230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	63	271	0	ENST00000274335.5:c.1384_1385del	p.Glu462IlefsTer2	p.E462Ifs*2	ENST00000274335		461	cGA/c	10/15	0.659339200244004	1	FACETS	0.928	0.827	1	0.928	0.827	1	CLONAL	1	TRUE	0	0.659339200244004	1		271	138	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405612	139405612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	16	290	1	ENST00000277541.6:c.2579G>A	p.Gly860Asp	p.G860D	ENST00000277541	NM_017617.3	860	gGc/gAc	16/34	0.659339200244004	1	FACETS	0.128	0.094	0.168	0.128	0.094	0.168	SUBCLONAL	1	TRUE	0	0.659339200244004	1		291	255	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424515	47424516	+	stop_gained	Nonsense_Mutation	DNP	CA	CA	TT	novel	NA	P-0066230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	93	384	0	ENST00000404338.3:c.2583_2584delinsTT	p.Lys862Ter	p.K862*	ENST00000404338	NM_004491.4	861	gcCAaa/gcTTaa	1/6	0.659339200244004	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.659339200244004	1		384	187	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2060924	2060924	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	158	440	0	ENST00000349721.2:c.1630G>C	p.Val544Leu	p.V544L	ENST00000349721	NM_003070.3	544	Gtt/Ctt	9/34	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.659339200244004	2		440	443	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0066234-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	4991	216	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	0.861143034153579	80	FACETS	1	0.998	1	1	0.998	1	CLONAL	79	TRUE	1	0.861143034153579	80		216	5070	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020724	26020724	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1426138687	NA	P-0066234-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	32	370	0	ENST00000357647.3:c.7C>T	p.Arg3Cys	p.R3C	ENST00000357647	NM_003529.2	3	Cgc/Tgc	1/1	0.693917267892505	5	FACETS	0.624	0.508	0.753	0.208	0.169	0.251	SUBCLONAL	1	TRUE	2	0.861143034153579	5		370	273	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546126	29546126	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066234-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	194	302	0	ENST00000356175.3:c.1632del	p.Ala545GlnfsTer11	p.A545Qfs*11	ENST00000356175	NM_000267.3	544	gAa/ga	14/57	0.849341302138184	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	4	TRUE	0	0.861143034153579	4		302	209	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267399	198267399	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066234-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	42	312	0	ENST00000335508.6:c.1958A>G	p.Lys653Arg	p.K653R	ENST00000335508	NM_012433.2	653	aAa/aGa	14/25	0.859435608747668	4	FACETS	0.646	0.542	0.76	0.215	0.18	0.254	SUBCLONAL	1	TRUE	1	0.861143034153579	4		312	281	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752817	57752817	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066234-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	46	214	1	ENST00000274289.3:c.1111C>A	p.Leu371Ile	p.L371I	ENST00000274289	NM_006622.3	371	Ctt/Att	8/14	0.41622392544891	6	FACETS	1	0.953	1	0.221	0.188	0.257	INDETERMINATE	1	TRUE	0	0.861143034153579	6		215	219	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0066235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	38	308	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	0.619	0.512	0.739	0.619	0.512	0.739	SUBCLONAL	1	TRUE	1	0.3	2		308	409	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981823	201981824	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	57	378	0	ENST00000359651.3:c.535dup	p.Tyr179LeufsTer17	p.Y179Lfs*17	ENST00000359651		178	-/T	4/8	0.0874169523357911	3	FACETS	0.895	0.777	1	0.895	0.777	1	INDETERMINATE	2	TRUE	1	0.3	3		378	244	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061339	38061339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	51	339	0	ENST00000250448.2:c.650C>T	p.Ser217Phe	p.S217F	ENST00000250448	NM_004496.3	217	tCc/tTc	2/2	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.3	2		339	324	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089562	27089562	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	39	369	0	ENST00000324856.7:c.2518del	p.Gln840LysfsTer19	p.Q840Kfs*19	ENST00000324856	NM_006015.4	840	Caa/aa	8/20	0.0874169523357911	3	FACETS	0.849	0.706	1	0.425	0.353	0.505	INDETERMINATE	1	TRUE	1	0.3	3		369	352	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729960	30729962	+	frameshift_variant	Frame_Shift_Del	DEL	ATC	ATC	GT	novel	NA	P-0066235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	41	243	0	ENST00000295754.5:c.1481_1483delinsGT	p.Asp494GlyfsTer24	p.D494Gfs*24	ENST00000295754	NM_003242.5	494	gATCga/gGTga	6/7	0.223780331221209	6	FACETS	0.707	0.587	0.839	0.177	0.146	0.21	SUBCLONAL	1	TRUE	2	0.3	6		243	619	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0066236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	39	358	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.566	0.468	0.677	0.566	0.468	0.677	SUBCLONAL	1	TRUE	1	0.18	2		358	765	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835931	151835932	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0066236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	39	344	0	ENST00000262189.6:c.14592_14593del	p.Gly4865ThrfsTer20	p.G4865Tfs*20	ENST00000262189	NM_170606.2	4864	agAGga/agga	58/59	1	2	FACETS	0.588	0.486	0.703	0.588	0.486	0.703	SUBCLONAL	1	TRUE	1	0.18	2		344	737	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7293887	7293887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1171697715	NA	P-0066236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	50	543	0	ENST00000302850.5:c.16C>T	p.Arg6Trp	p.R6W	ENST00000302850	NM_000208.2	6	Cgg/Tgg	1/22	1	2	FACETS	0.705	0.597	0.825	0.705	0.597	0.825	SUBCLONAL	1	TRUE	1	0.18	2		543	788	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188174	11188174	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066237-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	114	364	0	ENST00000361445.4:c.5920T>C	p.Tyr1974His	p.Y1974H	ENST00000361445	NM_004958.3	1974	Tac/Cac	43/58	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.43	2		364	503	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	133	446	0				ENST00000310581	NM_198253.2	-/1132			0.4351684246133	4	FACETS	1	0.945	1	1	0.945	1	CLONAL	3	TRUE	1	0.532959141507325	4		446	250	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882005	NA	P-0066238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	283	395	0	ENST00000269305.4:c.713G>C	p.Cys238Ser	p.C238S	ENST00000269305	NM_001126112.2	238	tGt/tCt	7/11	0.2280653734381	4	FACETS	1	0.991	1			1	INDETERMINATE	3	TRUE	NA	0.532959141507325	4		395	468	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750924	128750924	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	149	411	0	ENST00000377970.2:c.461C>T	p.Ser154Leu	p.S154L	ENST00000377970	NM_002467.4	154	tCg/tTg	2/3	0.532959141507325	3	FACETS	0.899	0.831	0.968	0.899	0.831	0.968	CLONAL	2	TRUE	1	0.532959141507325	3		411	394	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212018	142212018	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	87	387	0	ENST00000350721.4:c.6034G>C	p.Glu2012Gln	p.E2012Q	ENST00000350721	NM_001184.3	2012	Gaa/Caa	35/47	0.532959141507325	3	FACETS	1	0.94	1	0.541	0.482	0.603	CLONAL	1	TRUE	1	0.532959141507325	3		387	382	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217651	7217651	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	232	424	0	ENST00000380728.2:c.276del	p.Val93PhefsTer16	p.V93Ffs*16	ENST00000380728		92	aaA/aa	4/11	0.2280653734381	4	FACETS	1	0.962	1			1	INDETERMINATE	3	TRUE	NA	0.532959141507325	4		424	436	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231410	46231410	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0066238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	184	384	0	ENST00000334344.6:c.1250C>G	p.Ser417Ter	p.S417*	ENST00000334344	NM_152641.2	417	tCa/tGa	10/21	0.532959141507325	4	FACETS	0.986	0.917	1	0.986	0.917	1	CLONAL	2	TRUE	2	0.532959141507325	4		384	537	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497572	125497572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768467449	NA	P-0066238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	66	377	0	ENST00000428830.2:c.136G>A	p.Val46Ile	p.V46I	ENST00000428830	NM_001114121.2	46	Gta/Ata	3/14	0.532959141507325	3	FACETS	0.769	0.67	0.875	0.384	0.335	0.438	SUBCLONAL	1	TRUE	1	0.532959141507325	3		377	408	SUCCESS
APC	324	MSKCC	GRCh37	5	112175941	112175941	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	103	416	0	ENST00000257430.4:c.4650G>C	p.Glu1550Asp	p.E1550D	ENST00000257430	NM_000038.5	1550	gaG/gaC	16/16	1	2	FACETS	0.95	0.856	1	0.95	0.856	1	CLONAL	1	TRUE	1	0.532959141507325	2		416	407	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372765	81372765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	194	375	0	ENST00000222390.5:c.769G>A	p.Asp257Asn	p.D257N	ENST00000222390	NM_000601.4	257	Gat/Aat	7/18	0.532959141507325	3	FACETS	0.968	0.905	1	0.968	0.905	1	CLONAL	2	TRUE	1	0.532959141507325	3		375	476	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239889	41239889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1290398156	NA	P-0066238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	75	389	0	ENST00000379561.5:c.461C>T	p.Ser154Leu	p.S154L	ENST00000379561	NM_002015.3	154	tCg/tTg	1/3	0.47089164580523	3	FACETS	1	0.895	1	0.508	0.448	0.571	CLONAL	1	TRUE	1	0.532959141507325	3		389	351	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950681	38950681	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	89	377	0	ENST00000357387.3:c.3269C>A	p.Ser1090Tyr	p.S1090Y	ENST00000357387	NM_152756.3	1090	tCt/tAt	31/38	NA	2	FACETS	0.903	0.806	1			1	INDETERMINATE	1	TRUE	NA	0.532959141507325	2		377	370	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566456	41566456	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	141	377	0	ENST00000263253.7:c.4333G>C	p.Asp1445His	p.D1445H	ENST00000263253	NM_001429.3	1445	Gat/Cat	27/31	0.47089164580523	3	FACETS	0.825	0.76	0.893	0.825	0.76	0.893	CLONAL	2	TRUE	1	0.532959141507325	3		377	406	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564739	41564739	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	184	437	0	ENST00000263253.7:c.4040G>C	p.Gly1347Ala	p.G1347A	ENST00000263253	NM_001429.3	1347	gGa/gCa	25/31	0.47089164580523	3	FACETS	0.922	0.86	0.986	0.922	0.86	0.986	CLONAL	2	TRUE	1	0.532959141507325	3		437	474	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564595	41564595	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	199	424	0	ENST00000263253.7:c.4017G>C	p.Met1339Ile	p.M1339I	ENST00000263253	NM_001429.3	1339	atG/atC	24/31	0.47089164580523	3	FACETS	0.981	0.918	1	0.981	0.918	1	CLONAL	2	TRUE	1	0.532959141507325	3		424	482	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142066	108142066	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	68	383	0	ENST00000278616.4:c.3010A>T	p.Ser1004Cys	p.S1004C	ENST00000278616	NM_000051.3	1004	Agc/Tgc	20/63	0.532959141507325	3	FACETS	0.757	0.661	0.86	0.378	0.33	0.43	SUBCLONAL	1	TRUE	1	0.532959141507325	3		383	427	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231127	46231127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	153	351	0	ENST00000334344.6:c.1047C>G	p.Phe349Leu	p.F349L	ENST00000334344	NM_152641.2	349	ttC/ttG	9/21	0.532959141507325	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.532959141507325	4		351	392	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	63	721	4	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.846	0.73	0.972	0.846	0.73	0.972	CLONAL	1	TRUE	1	0.19	2		725	784	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	139	710	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.894	0.814	0.978	1	0.989	1	CLONAL	2	TRUE	1	0.19	2		713	818	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	19	94	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.837	0.637	1	0.837	0.637	1	CLONAL	1	TRUE	1	0.19	2		94	239	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	55	338	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.19	2		338	572	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	90	478	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.19	2		479	726	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	107	324	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.19	2		324	781	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835781	68835781	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060501215	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	78	313	0	ENST00000261769.5:c.377del	p.Pro126ArgfsTer89	p.P126Rfs*89	ENST00000261769	NM_004360.3	124	cgC/cg	3/16	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.19	2		313	792	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817720	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	50	274	0	ENST00000262367.5:c.3250dup	p.Ile1084AsnfsTer3	p.I1084Nfs*3	ENST00000262367	NM_004380.2	1084	atc/aAtc		1	2	FACETS	0.795	0.673	0.929	0.795	0.673	0.929	CLONAL	1	TRUE	1	0.19	2		274	662	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	112	501	0	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.871	0.784	0.962	1	0.987	1	CLONAL	2	TRUE	1	0.19	2		501	677	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289907	15289907	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265324934	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	70	461	0	ENST00000263388.2:c.3647C>T	p.Ala1216Val	p.A1216V	ENST00000263388	NM_000435.2	1216	gCg/gTg	22/33	1	2	FACETS	0.9	0.783	1	0.9	0.783	1	CLONAL	1	TRUE	1	0.19	2		461	819	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	39	279	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.643	0.532	0.768	0.643	0.532	0.768	SUBCLONAL	1	TRUE	1	0.19	2		279	638	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	55	782	3	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.805	0.688	0.934	0.805	0.688	0.934	CLONAL	1	TRUE	1	0.19	2		785	719	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276316	15276316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372834264	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	55	317	0	ENST00000263388.2:c.5678G>A	p.Arg1893Gln	p.R1893Q	ENST00000263388	NM_000435.2	1893	cGa/cAa	31/33	1	2	FACETS	0.943	0.806	1	0.943	0.806	1	CLONAL	1	TRUE	1	0.19	2		317	614	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259092	89259092	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	58	276	0	ENST00000336596.2:c.236A>C	p.Asn79Thr	p.N79T	ENST00000336596	NM_005233.5	79	aAc/aCc	3/17	1	2	FACETS	0.887	0.761	1	0.887	0.761	1	CLONAL	1	TRUE	1	0.19	2		276	688	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	54	358	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	1	2	FACETS	0.731	0.623	0.849	0.731	0.623	0.849	SUBCLONAL	1	TRUE	1	0.19	2		358	778	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740376	145740376	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35407712	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	51	390	0	ENST00000428558.2:c.1564C>T	p.Arg522Cys	p.R522C	ENST00000428558	NM_004260.3	522	Cgc/Tgc	9/22	1	2	FACETS	0.706	0.599	0.825	0.706	0.599	0.825	SUBCLONAL	1	TRUE	1	0.19	2		390	760	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542109	187542110	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1560943587	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	59	350	2	ENST00000441802.2:c.5630dup	p.Val1878CysfsTer8	p.V1878Cfs*8	ENST00000441802	NM_005245.3	1877	cct/ccCt	10/27	1	2	FACETS	0.79	0.678	0.912	0.79	0.678	0.912	CLONAL	1	TRUE	1	0.19	2		352	786	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	37	249	2	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	1	2	FACETS	0.792	0.652	0.948	0.792	0.652	0.948	CLONAL	1	TRUE	1	0.19	2		251	492	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932085	39932085	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	52	396	1	ENST00000378444.4:c.2514del	p.Lys839SerfsTer17	p.K839Sfs*17	ENST00000378444	NM_001123385.1	838	ccC/cc	4/15	1	2	FACETS	0.74	0.628	0.862	0.74	0.628	0.862	SUBCLONAL	1	TRUE	1	0.19	2		397	740	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721164	176721165	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1562308992	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	45	331	0	ENST00000439151.2:c.6801dup	p.Ala2268SerfsTer13	p.A2268Sfs*13	ENST00000439151	NM_022455.4	2265	-/A	23/23	1	2	FACETS	0.712	0.597	0.84	0.712	0.597	0.84	SUBCLONAL	1	TRUE	1	0.19	2		331	665	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638917	176638917	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749199217	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	64	326	0	ENST00000439151.2:c.3517C>T	p.Arg1173Cys	p.R1173C	ENST00000439151	NM_022455.4	1173	Cgc/Tgc	5/23	1	2	FACETS	0.83	0.717	0.952	0.83	0.717	0.952	CLONAL	1	TRUE	1	0.19	2		326	812	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370958	55370958	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	31	294	2	ENST00000297316.4:c.260C>T	p.Ala87Val	p.A87V	ENST00000297316	NM_022454.3	87	gCg/gTg	1/2	1	2	FACETS	0.547	0.441	0.667	0.547	0.441	0.667	SUBCLONAL	1	TRUE	1	0.19	2		296	597	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935669	15935669	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	65	338	0	ENST00000268712.3:c.7264C>T	p.Arg2422Ter	p.R2422*	ENST00000268712	NM_006311.3	2422	Cga/Tga	46/46	1	2	FACETS	0.92	0.796	1	0.92	0.796	1	CLONAL	1	TRUE	1	0.19	2		338	744	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138382756	138382756	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	43	241	1	ENST00000289153.2:c.2788del	p.Thr930LeufsTer62	p.T930Lfs*62	ENST00000289153	NM_006219.2	930	Act/ct	19/22	1	2	FACETS	0.804	0.672	0.951	0.804	0.672	0.951	CLONAL	1	TRUE	1	0.19	2		242	563	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360612	70360617	+	inframe_deletion	In_Frame_Del	DEL	CAGCAA	CAGCAA	-	rs753370104	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	52	384	0	ENST00000374080.3:c.6183_6188del	p.Gln2075_Gln2076del	p.Q2075_Q2076del	ENST00000374080		2058	CAGCAA/-	42/45	1	2	FACETS	0.656	0.556	0.765	0.656	0.556	0.765	SUBCLONAL	1	TRUE	1	0.19	2		384	835	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030224	180030224	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761089407	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	65	352	0	ENST00000261937.6:c.4060C>T	p.Arg1354Cys	p.R1354C	ENST00000261937	NM_182925.4	1354	Cgc/Tgc	30/30	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.19	2		352	669	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962888	2962888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1016457945	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	45	329	0	ENST00000396946.4:c.2020G>A	p.Asp674Asn	p.D674N	ENST00000396946	NM_032415.4	674	Gac/Aac	16/25	1	2	FACETS	0.885	0.744	1	0.885	0.744	1	CLONAL	1	TRUE	1	0.19	2		329	535	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865761	57865761	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	55	389	0	ENST00000228682.2:c.3243del	p.Asn1082ThrfsTer7	p.N1082Tfs*7	ENST00000228682	NM_005269.2	1080	Ccc/cc	12/12	1	2	FACETS	0.784	0.67	0.91	0.784	0.67	0.91	CLONAL	1	TRUE	1	0.19	2		389	738	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982767	7982767	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	55	349	0	ENST00000319144.4:c.1018del	p.Leu340SerfsTer12	p.L340Sfs*12	ENST00000319144	NM_001139.2	340	Ctc/tc	8/15	1	2	FACETS	0.925	0.791	1	0.925	0.791	1	CLONAL	1	TRUE	1	0.19	2		349	626	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214806	36214806	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	51	257	0	ENST00000222270.7:c.3232C>T	p.Arg1078Cys	p.R1078C	ENST00000222270	NM_014727.1	1078	Cgc/Tgc	8/37	1	2	FACETS	0.955	0.812	1	0.955	0.812	1	CLONAL	1	TRUE	1	0.19	2		257	562	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286255	66286255	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	40	260	1	ENST00000273854.3:c.1431del	p.Ile480LeufsTer21	p.I480Lfs*21	ENST00000273854	NM_004439.5	477	aaA/aa	6/18	1	2	FACETS	0.688	0.571	0.819	0.688	0.571	0.819	SUBCLONAL	1	TRUE	1	0.19	2		261	612	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244440	41244440	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80357841	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	56	300	0	ENST00000357654.3:c.3108del	p.Phe1036LeufsTer12	p.F1036Lfs*12	ENST00000357654	NM_007294.3	1036	ttT/tt	10/23	1	2	FACETS	0.843	0.721	0.977	0.843	0.721	0.977	CLONAL	1	TRUE	1	0.19	2		300	699	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610154	10610154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	57	351	0	ENST00000171111.5:c.556G>A	p.Gly186Ser	p.G186S	ENST00000171111	NM_203500.1	186	Ggc/Agc	2/6	1	2	FACETS	0.813	0.696	0.941	0.813	0.696	0.941	CLONAL	1	TRUE	1	0.19	2		351	738	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564503	55564503	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1044091916	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	45	256	0	ENST00000288135.5:c.391G>A	p.Asp131Asn	p.D131N	ENST00000288135	NM_000222.2	131	Gac/Aac	3/21	1	2	FACETS	0.754	0.633	0.889	0.754	0.633	0.889	SUBCLONAL	1	TRUE	1	0.19	2		256	628	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31493322	31493322	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	41	267	0	ENST00000344624.3:c.1834del	p.Leu612Ter	p.L612*	ENST00000344624		612	Ctg/tg	10/33	1	2	FACETS	0.679	0.564	0.806	0.679	0.564	0.806	SUBCLONAL	1	TRUE	1	0.19	2		267	636	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524364	176524364	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759042869	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	40	331	0	ENST00000292408.4:c.2225C>T	p.Ala742Val	p.A742V	ENST00000292408	NM_213647.1	742	gCg/gTg	17/18	1	2	FACETS	0.679	0.563	0.809	0.679	0.563	0.809	SUBCLONAL	1	TRUE	1	0.19	2		331	620	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891121	112891121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507521	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	66	310	0	ENST00000351677.2:c.455G>A	p.Arg152His	p.R152H	ENST00000351677	NM_002834.3	152	cGc/cAc	4/16	1	2	FACETS	0.775	0.671	0.888	0.775	0.671	0.888	SUBCLONAL	1	TRUE	1	0.19	2		310	897	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223996	36223997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs747928028	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	56	370	0	ENST00000222270.7:c.6552dup	p.Lys2185GlnfsTer25	p.K2185Qfs*25	ENST00000222270	NM_014727.1	2182	-/C	28/37	1	2	FACETS	0.777	0.664	0.9	0.777	0.664	0.9	SUBCLONAL	1	TRUE	1	0.19	2		370	759	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434973	110434973	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	56	398	0	ENST00000375856.3:c.3428del	p.Gly1143AlafsTer116	p.G1143Afs*116	ENST00000375856	NM_003749.2	1143	gGc/gc	1/2	1	2	FACETS	0.828	0.708	0.959	0.828	0.708	0.959	CLONAL	1	TRUE	1	0.19	2		398	712	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446988	187446988	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139744042	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	78	379	0	ENST00000232014.4:c.1205G>A	p.Arg402His	p.R402H	ENST00000232014	NM_001130845.1	402	cGc/cAc	5/10	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.19	2		379	783	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32890650	32890650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358762	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	52	202	0	ENST00000380152.3:c.53G>A	p.Arg18His	p.R18H	ENST00000380152		18	cGc/cAc	2/27	1	2	FACETS	0.817	0.694	0.952	0.817	0.694	0.952	CLONAL	1	TRUE	1	0.19	2		202	670	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878445	151878445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748645400	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	74	326	0	ENST00000262189.6:c.6500G>A	p.Arg2167Gln	p.R2167Q	ENST00000262189	NM_170606.2	2167	cGg/cAg	36/59	1	2	FACETS	0.96	0.84	1	0.96	0.84	1	CLONAL	1	TRUE	1	0.19	2		326	811	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181358	185181359	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1560126178	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	32	230	0	ENST00000265026.3:c.1305dup	p.His436ThrfsTer3	p.H436Tfs*3	ENST00000265026	NM_004721.4	433	-/A	8/14	1	2	FACETS	0.59	0.478	0.717	0.59	0.478	0.717	SUBCLONAL	1	TRUE	1	0.19	2		230	571	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620377	43620377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	60	293	0	ENST00000355710.3:c.2986C>T	p.Pro996Ser	p.P996S	ENST00000355710	NM_020975.4	996	Ccg/Tcg	18/20	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.19	2		293	625	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739435	145739440	+	inframe_deletion	In_Frame_Del	DEL	TGTGGC	TGTGGC	-	rs781471399	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	76	374	0	ENST00000428558.2:c.1930_1935del	p.Ala644_Thr645del	p.A644_T645del	ENST00000428558	NM_004260.3	644	GCCACA/-	12/22	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.19	2		374	693	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416542	29416542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201759867	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	54	423	0	ENST00000389048.3:c.4411G>A	p.Val1471Met	p.V1471M	ENST00000389048	NM_004304.4	1471	Gtg/Atg	29/29	1	2	FACETS	0.769	0.656	0.894	0.769	0.656	0.894	SUBCLONAL	1	TRUE	1	0.19	2		423	739	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	41	280	3	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.589	0.489	0.7	0.589	0.489	0.7	SUBCLONAL	1	TRUE	1	0.19	2		283	733	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662784	117662784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	56	279	0	ENST00000368508.3:c.4681G>A	p.Val1561Met	p.V1561M	ENST00000368508	NM_002944.2	1561	Gtg/Atg	29/43	1	2	FACETS	0.982	0.841	1	0.982	0.841	1	CLONAL	1	TRUE	1	0.19	2		279	600	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142103	108142103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	52	267	0	ENST00000278616.4:c.3047G>A	p.Gly1016Glu	p.G1016E	ENST00000278616	NM_000051.3	1016	gGa/gAa	20/63	1	2	FACETS	0.78	0.663	0.909	0.78	0.663	0.909	CLONAL	1	TRUE	1	0.19	2		267	702	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775649	9775649	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	75	330	0	ENST00000377346.4:c.195del	p.Glu66ArgfsTer44	p.E66Rfs*44	ENST00000377346	NM_005026.3	64	ggC/gg	4/24	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.19	2		330	628	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402531	20402531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	27	302	0	ENST00000346618.3:c.68C>T	p.Ala23Val	p.A23V	ENST00000346618	NM_001949.4	23	gCt/gTt	1/7	1	2	FACETS	0.538	0.427	0.666	0.538	0.427	0.666	SUBCLONAL	1	TRUE	1	0.19	2		302	528	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609713	28609713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	70	302	0	ENST00000241453.7:c.1516G>A	p.Ala506Thr	p.A506T	ENST00000241453	NM_004119.2	506	Gcc/Acc	12/24	1	2	FACETS	0.932	0.811	1	0.932	0.811	1	CLONAL	1	TRUE	1	0.19	2		302	791	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850347	128850347	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	47	306	0	ENST00000249373.3:c.1610G>A	p.Trp537Ter	p.W537*	ENST00000249373	NM_005631.4	537	tGg/tAg	9/12	1	2	FACETS	0.925	0.78	1	0.925	0.78	1	CLONAL	1	TRUE	1	0.19	2		306	535	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437750	52437750	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs946145283	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	56	326	0	ENST00000460680.1:c.1411G>A	p.Ala471Thr	p.A471T	ENST00000460680	NM_004656.3	471	Gct/Act	13/17	1	2	FACETS	0.868	0.743	1	0.868	0.743	1	CLONAL	1	TRUE	1	0.19	2		326	679	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849283	89849283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763908621	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	37	233	0	ENST00000389301.3:c.1610C>T	p.Ala537Val	p.A537V	ENST00000389301	NM_000135.2	537	gCt/gTt	17/43	1	2	FACETS	0.748	0.616	0.896	0.748	0.616	0.896	SUBCLONAL	1	TRUE	1	0.19	2		233	521	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549243	21549243	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	63	417	0	ENST00000382592.4:c.3033G>A	p.Trp1011Ter	p.W1011*	ENST00000382592	NM_014572.2	1011	tgG/tgA	8/8	1	2	FACETS	0.877	0.757	1	0.877	0.757	1	CLONAL	1	TRUE	1	0.19	2		417	756	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860096	57860096	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	58	334	0	ENST00000228682.2:c.836T>G	p.Leu279Arg	p.L279R	ENST00000228682	NM_005269.2	279	cTg/cGg	8/12	1	2	FACETS	0.906	0.777	1	0.906	0.777	1	CLONAL	1	TRUE	1	0.19	2		334	674	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169518	11169518	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	52	274	0	ENST00000358026.2:c.4684A>G	p.Met1562Val	p.M1562V	ENST00000358026	NM_001128849.1	1562	Atg/Gtg	33/36	1	2	FACETS	0.887	0.755	1	0.887	0.755	1	CLONAL	1	TRUE	1	0.19	2		274	617	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007454	62007454	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	59	364	0	ENST00000392795.3:c.413G>C	p.Gly138Ala	p.G138A	ENST00000392795	NM_001039933.1	138	gGc/gCc	3/6	1	2	FACETS	0.907	0.779	1	0.907	0.779	1	CLONAL	1	TRUE	1	0.19	2		364	685	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437938	110437938	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	19	185	0	ENST00000375856.3:c.463C>G	p.Pro155Ala	p.P155A	ENST00000375856	NM_003749.2	155	Ccc/Gcc	1/2	1	2	FACETS	0.752	0.571	0.964	0.752	0.571	0.964	CLONAL	1	TRUE	1	0.19	2		185	266	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214727	36214728	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	37	328	0	ENST00000222270.7:c.3159dup	p.Pro1054AlafsTer34	p.P1054Afs*34	ENST00000222270	NM_014727.1	1051	-/G	8/37	1	2	FACETS	0.748	0.616	0.896	0.748	0.616	0.896	SUBCLONAL	1	TRUE	1	0.19	2		328	521	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446275	29446275	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	48	332	1	ENST00000544604.2:c.2111del	p.Gly704AlafsTer69	p.G704Afs*69	ENST00000544604	NM_001206998.1	702	aaG/aa	8/9	1	2	FACETS	0.871	0.736	1	0.871	0.736	1	CLONAL	1	TRUE	1	0.19	2		333	580	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782056	9782056	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	40	378	1	ENST00000377346.4:c.2079G>T	p.Lys693Asn	p.K693N	ENST00000377346	NM_005026.3	693	aaG/aaT	17/24	1	2	FACETS	0.644	0.534	0.767	0.644	0.534	0.767	SUBCLONAL	1	TRUE	1	0.19	2		379	654	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259532	16259532	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	52	362	0	ENST00000375759.3:c.6797A>G	p.Asp2266Gly	p.D2266G	ENST00000375759	NM_015001.2	2266	gAt/gGt	11/15	1	2	FACETS	0.76	0.646	0.886	0.76	0.646	0.886	SUBCLONAL	1	TRUE	1	0.19	2		362	720	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142885	30142886	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	57	382	0	ENST00000389048.3:c.640dup	p.Arg214ProfsTer12	p.R214Pfs*12	ENST00000389048	NM_004304.4	214	cgc/cCgc	1/29	1	2	FACETS	0.89	0.763	1	0.89	0.763	1	CLONAL	1	TRUE	1	0.19	2		382	674	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106931	27106931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	61	395	0	ENST00000324856.7:c.6542C>T	p.Ala2181Val	p.A2181V	ENST00000324856	NM_006015.4	2181	gCa/gTa	20/20	1	2	FACETS	0.802	0.69	0.923	0.802	0.69	0.923	CLONAL	1	TRUE	1	0.19	2		395	801	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101011	41101011	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	50	374	0	ENST00000373198.4:c.1345C>A	p.Leu449Met	p.L449M	ENST00000373198	NM_133170.3	449	Ctg/Atg	8/32	1	2	FACETS	0.917	0.778	1	0.917	0.778	1	CLONAL	1	TRUE	1	0.19	2		374	574	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451161	70451161	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	42	342	1	ENST00000373644.4:c.6005del	p.Leu2002TrpfsTer18	p.L2002Wfs*18	ENST00000373644	NM_030625.2	2001	Ttt/tt	12/12	1	2	FACETS	0.621	0.517	0.737	0.621	0.517	0.737	SUBCLONAL	1	TRUE	1	0.19	2		343	712	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096720	178096720	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	47	228	0	ENST00000397062.3:c.611del	p.Asn204MetfsTer17	p.N204Mfs*17	ENST00000397062	NM_006164.4	204	aAt/at	5/5	1	2	FACETS	0.724	0.61	0.851	0.724	0.61	0.851	SUBCLONAL	1	TRUE	1	0.19	2		228	683	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650057	206650057	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	51	306	0	ENST00000367120.3:c.577C>T	p.Pro193Ser	p.P193S	ENST00000367120	NM_014002.3	193	Ccc/Tcc	7/22	1	2	FACETS	0.828	0.703	0.966	0.828	0.703	0.966	CLONAL	1	TRUE	1	0.19	2		306	648	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339581	339581	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	43	257	0	ENST00000262320.3:c.2321G>A	p.Gly774Asp	p.G774D	ENST00000262320	NM_003502.3	774	gGc/gAc	10/11	1	2	FACETS	0.924	0.773	1	0.924	0.773	1	CLONAL	1	TRUE	1	0.19	2		257	490	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326904	62326905	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	50	381	0	ENST00000360203.5:c.3730_3731dup	p.Gln1245AlafsTer120	p.Q1245Afs*120	ENST00000360203	NM_001283009.1	1241	-/TG	34/35	1	2	FACETS	0.742	0.629	0.868	0.742	0.629	0.868	SUBCLONAL	1	TRUE	1	0.19	2		381	709	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988317	41988317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs548777775	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	40	285	0	ENST00000219905.7:c.1109C>T	p.Pro370Leu	p.P370L	ENST00000219905	NM_001164273.1	370	cCg/cTg	3/24	1	2	FACETS	0.651	0.539	0.775	0.651	0.539	0.775	SUBCLONAL	1	TRUE	1	0.19	2		285	647	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139103	50139111	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GGGGGACCT	GGGGGACCT	-	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	35	143	0	ENST00000246792.3:c.454-2_460del		p.X152_splice	ENST00000246792	NM_006270.3	152		5/6	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.19	2		143	354	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056091	26056091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200043061	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	59	365	1	ENST00000343677.2:c.566C>T	p.Ala189Val	p.A189V	ENST00000343677	NM_005319.3	189	gCt/gTt	1/1	1	2	FACETS	0.804	0.691	0.929	0.804	0.691	0.929	CLONAL	1	TRUE	1	0.19	2		366	772	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753822	42753822	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	61	432	0	ENST00000222329.4:c.442A>G	p.Thr148Ala	p.T148A	ENST00000222329	NM_006494.2	148	Acg/Gcg	4/4	1	2	FACETS	0.92	0.793	1	0.92	0.793	1	CLONAL	1	TRUE	1	0.19	2		432	698	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295686	1295686	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	68	433	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.19	2		433	606	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267542	7267542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750269551	NA	P-0066239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	53	286	0	ENST00000302850.5:c.466G>A	p.Ala156Thr	p.A156T	ENST00000302850	NM_000208.2	156	Gcc/Acc	2/22	1	2	FACETS	0.775	0.659	0.902	0.775	0.659	0.902	CLONAL	1	TRUE	1	0.19	2		286	720	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589830	69589830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066240-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	43	830	0	ENST00000168712.1:c.23C>T	p.Ala8Val	p.A8V	ENST00000168712	NM_002007.2	8	gCg/gTg	1/3	0.330086575861466	2	FACETS	0.189	0.157	0.224	0.094	0.078	0.112	INDETERMINATE	1	TRUE	0	0.596256151691279	2		830	764	SUCCESS
APC	324	MSKCC	GRCh37	5	112174096	112174096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs137854575	NA	P-0066240-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	123	478	0	ENST00000257430.4:c.2805C>A	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	taC/taA	16/16	0.357426548445172	1	FACETS	0.526	0.477	0.576	0.526	0.477	0.576	INDETERMINATE	1	TRUE	0	0.596256151691279	1		478	551	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911645	114911645	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0066240-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	199	355	0	ENST00000543371.1:c.1161+2T>C		p.X387_splice	ENST00000543371	NM_001198531.1	387			0.30990552458719	2	FACETS	1	0.991	1	0.688	0.644	0.733	INDETERMINATE	1	TRUE	0	0.596256151691279	2		355	485	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109663	115109663	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770230836	NA	P-0066240-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	85	486	0	ENST00000257566.3:c.2215C>T	p.Arg739Cys	p.R739C	ENST00000257566	NM_016569.3	739	Cgc/Tgc	8/8	0.289651802433136	2	FACETS	0.518	0.459	0.582	0.259	0.229	0.291	INDETERMINATE	1	TRUE	0	0.596256151691279	2		486	550	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47602388	47602388	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066240-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	91	356	0	ENST00000263735.4:c.441A>C	p.Glu147Asp	p.E147D	ENST00000263735	NM_002354.2	147	gaA/gaC	4/9	1	2	FACETS	0.609	0.543	0.68	0.609	0.543	0.68	SUBCLONAL	1	TRUE	1	0.596256151691279	2		356	501	SUCCESS
APC	324	MSKCC	GRCh37	5	112175240	112175240	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066240-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	183	528	0	ENST00000257430.4:c.3949del	p.Glu1317LysfsTer4	p.E1317Kfs*4	ENST00000257430	NM_000038.5	1317	Gaa/aa	16/16	0.357426548445172	1	FACETS	0.767	0.712	0.823	0.767	0.712	0.823	INDETERMINATE	1	TRUE	0	0.596256151691279	1		528	562	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591153	67591153	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0066242-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	26	442	0	ENST00000274335.5:c.1745+1G>T		p.X582_splice	ENST00000274335		582			1	2	FACETS	0.224	0.176	0.278	0.224	0.176	0.278	SUBCLONAL	1	TRUE	1	0.413699672998096	2		442	562	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120667	115120667	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066242-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	92	553	0	ENST00000257566.3:c.339G>A	p.Trp113Ter	p.W113*	ENST00000257566	NM_016569.3	113	tgG/tgA	1/8	1	2	FACETS	0.404	0.357	0.453	0.404	0.357	0.453	SUBCLONAL	1	TRUE	1	0.413699672998096	2		553	1102	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748442	162748442	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066243-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	225	530	0	ENST00000367921.3:c.2356G>C	p.Glu786Gln	p.E786Q	ENST00000367921	NM_006182.2	786	Gaa/Caa	17/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		530	878	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646801	23646802	+	frameshift_variant	Frame_Shift_Ins	INS	TT	TT	AAA	novel	NA	P-0066243-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	202	477	0	ENST00000261584.4:c.1065_1066delinsTTT	p.Leu355PhefsTer6	p.L355Ffs*6	ENST00000261584	NM_024675.3	355	ttAAaa/ttTTTaa	4/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		477	802	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249380	110249380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066243-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	230	510	0	ENST00000374672.4:c.1193G>A	p.Cys398Tyr	p.C398Y	ENST00000374672	NM_004235.4	398	tGt/tAt	4/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		510	956	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0066244-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	207	539	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.742624958231753	2		539	514	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0066244-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	198	303	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.961	0.897	1	0.961	0.897	1	CLONAL	1	TRUE	1	0.742624958231753	2		303	555	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383671	84383671	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066244-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	282	490	0	ENST00000321945.7:c.1181T>C	p.Ile394Thr	p.I394T	ENST00000321945	NM_139076.2	394	aTt/aCt	9/9	1	2	FACETS	0.974	0.919	1	0.974	0.919	1	CLONAL	1	TRUE	1	0.742624958231753	2		490	780	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0066245-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	183	401	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		401	532	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2111885	2111885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45517154	NA	P-0066245-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	413	402	1	ENST00000219476.3:c.1133C>T	p.Pro378Leu	p.P378L	ENST00000219476	NM_000548.3	378	cCg/cTg	12/42	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		403	855	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750638	128750638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066245-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	202	462	0	ENST00000377970.2:c.175G>A	p.Ala59Thr	p.A59T	ENST00000377970	NM_002467.4	59	Gcg/Acg	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		462	1128	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803534	43803535	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0066245-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	183	509	0	ENST00000372470.3:c.15_16delinsAA	p.Leu6Ile	p.L6I	ENST00000372470	NM_005373.2	5	gcCCtc/gcAAtc	1/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		509	900	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910334	29910334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066245-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	282	475	0	ENST00000376809.5:c.4G>T	p.Ala2Ser	p.A2S	ENST00000376809	NM_002116.7	2	Gcc/Tcc	1/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		475	784	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066539	94066539	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066245-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	203	471	0	ENST00000369303.4:c.1220C>G	p.Ala407Gly	p.A407G	ENST00000369303	NM_004440.3	407	gCc/gGc	5/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		471	838	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900732	32900732	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066246-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	86	364	0	ENST00000380152.3:c.613A>G	p.Ser205Gly	p.S205G	ENST00000380152		205	Agt/Ggt	7/27	0.353780446137706	3	FACETS	0.805	0.712	0.904	0.402	0.356	0.452	CLONAL	1	TRUE	1	0.353241594389803	3		364	712	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418406	139418406	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1348892740	NA	P-0066247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	140	492	0	ENST00000277541.6:c.166C>T	p.Arg56Ter	p.R56*	ENST00000277541	NM_017617.3	56	Cga/Tga	3/34	0.228229616807981	4	FACETS	1	0.975	1	0.4	0.364	0.438	CLONAL	1	TRUE	1	0.364067729254746	4		492	874	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047698	180047698	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	149	620	0	ENST00000261937.6:c.2317A>C	p.Ser773Arg	p.S773R	ENST00000261937	NM_182925.4	773	Agc/Cgc	16/30	0.364067729254746	1	FACETS	0.973	0.891	1	0.973	0.891	1	CLONAL	1	TRUE	0	0.364067729254746	1		620	688	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128230380	128230380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	109	399	0	ENST00000265960.3:c.1216G>A	p.Gly406Arg	p.G406R	ENST00000265960	NM_001006617.1	406	Gga/Aga	10/12	0.228229616807981	4	FACETS	1	0.899	1	0.334	0.299	0.37	CLONAL	1	TRUE	1	0.364067729254746	4		399	816	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0066248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	20	269	1	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.316	0.242	0.403	0.316	0.242	0.403	SUBCLONAL	1	TRUE	1	0.453769571890716	2		270	279	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835596	68835596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587783047	NA	P-0066248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	159	457	0	ENST00000261769.5:c.187C>T	p.Arg63Ter	p.R63*	ENST00000261769	NM_004360.3	63	Cga/Tga	3/16	0.445707246235374	1	FACETS	0.88	0.81	0.952	0.88	0.81	0.952	CLONAL	1	TRUE	0	0.453769571890716	1		457	616	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555526101	NA	P-0066248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	59	478	0	ENST00000269305.4:c.497C>G	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tGa	5/11	0.445707246235374	1	FACETS	0.263	0.226	0.305	0.263	0.226	0.305	SUBCLONAL	1	TRUE	0	0.453769571890716	1		478	763	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021828	71021828	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0066248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	139	305	0	ENST00000318789.4:c.1531-1G>C		p.X511_splice	ENST00000318789	NM_032682.5	511			1	2	FACETS	0.904	0.824	0.986	0.904	0.824	0.986	CLONAL	1	TRUE	1	0.453769571890716	2		305	678	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501213	140501213	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	47	256	0	ENST00000288602.6:c.859G>C	p.Asp287His	p.D287H	ENST00000288602	NM_004333.4	287	Gat/Cat	6/18	1	2	FACETS	0.524	0.443	0.613	0.524	0.443	0.613	SUBCLONAL	1	TRUE	1	0.453769571890716	2		256	395	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070315	37070315	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs730881741	NA	P-0066248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	181	403	0	ENST00000231790.2:c.1450G>T	p.Asp484Tyr	p.D484Y	ENST00000231790	NM_000249.3	484	Gat/Tat	13/19	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.453769571890716	2		403	775	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333096	70333096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	200	381	0	ENST00000373644.4:c.1001C>T	p.Ser334Leu	p.S334L	ENST00000373644	NM_030625.2	334	tCa/tTa	2/12	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.453769571890716	2		381	803	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668677	52668677	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	57	292	0	ENST00000394830.3:c.1242G>C	p.Lys414Asn	p.K414N	ENST00000394830	NM_018313.4	414	aaG/aaC	12/30	0.118474613181924	4	FACETS	0.527	0.451	0.61	0.264	0.225	0.305	INDETERMINATE	1	TRUE	2	0.453769571890716	4		292	693	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668799	52668799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	49	332	0	ENST00000394830.3:c.1120G>A	p.Glu374Lys	p.E374K	ENST00000394830	NM_018313.4	374	Gaa/Aaa	12/30	0.118474613181924	4	FACETS	0.455	0.384	0.533	0.228	0.192	0.267	INDETERMINATE	1	TRUE	2	0.453769571890716	4		332	690	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668805	52668805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	44	326	0	ENST00000394830.3:c.1114G>A	p.Glu372Lys	p.E372K	ENST00000394830	NM_018313.4	372	Gaa/Aaa	12/30	0.118474613181924	4	FACETS	0.412	0.345	0.487	0.206	0.172	0.244	INDETERMINATE	1	TRUE	2	0.453769571890716	4		326	684	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467493	66467493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1208833706	NA	P-0066248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	176	409	0	ENST00000273854.3:c.776C>T	p.Ser259Leu	p.S259L	ENST00000273854	NM_004439.5	259	tCa/tTa	3/18	1	2	FACETS	0.947	0.874	1	0.947	0.874	1	CLONAL	1	TRUE	1	0.453769571890716	2		409	819	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066249-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	233	446	0				ENST00000310581	NM_198253.2	-/1132			0.381914958087257	3	FACETS	0.919	0.859	0.979	0.919	0.859	0.979	CLONAL	2	TRUE	1	0.381914958087257	3		446	791	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0066249-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	449	726	1	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	0.366362869526018	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.381914958087257	2		727	1128	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066249-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	183	574	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	1	2	FACETS	0.987	0.911	1	0.987	0.911	1	CLONAL	1	TRUE	1	0.381914958087257	2		574	971	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867469	35867469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs191585195	NA	P-0066249-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	125	380	0	ENST00000303115.3:c.283G>A	p.Glu95Lys	p.E95K	ENST00000303115	NM_002185.3	95	Gag/Aag	3/8	0.381914958087257	3	FACETS	0.966	0.875	1	0.483	0.437	0.532	CLONAL	1	TRUE	1	0.381914958087257	3		380	807	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094465	27094473	+	inframe_deletion	In_Frame_Del	DEL	TGAAGGAGA	TGAAGGAGA	-	novel	NA	P-0066249-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	159	628	1	ENST00000324856.7:c.3174_3182del	p.Lys1059_Ile1061del	p.K1059_I1061del	ENST00000324856	NM_006015.4	1058	gTGAAGGAGAtt/gtt	11/20	1	2	FACETS	0.897	0.822	0.976	0.897	0.822	0.976	CLONAL	1	TRUE	1	0.381914958087257	2		629	928	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652021	36652021	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066249-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	195	730	0	ENST00000244741.5:c.143del	p.Arg48HisfsTer100	p.R48Hfs*100	ENST00000244741	NM_000389.4	48	cGa/ca	2/3	1	2	FACETS	0.99	0.916	1	0.99	0.916	1	CLONAL	1	TRUE	1	0.381914958087257	2		730	1031	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066249-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	159	446	0				ENST00000310581	NM_198253.2	-/1132			0.425973467774541	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.425973467774541	3		446	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578509	7578509	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519978	NA	P-0066249-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	20	473	0	ENST00000269305.4:c.421T>C	p.Cys141Arg	p.C141R	ENST00000269305	NM_001126112.2	141	Tgc/Cgc	5/11	0.425973467774541	2	FACETS	0.157	0.119	0.202	0.079	0.059	0.101	SUBCLONAL	1	TRUE	0	0.425973467774541	2		473	598	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0066249-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	265	726	1	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	0.425973467774541	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.425973467774541	2		727	601	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066249-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	115	574	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	1	2	FACETS	0.987	0.893	1	0.987	0.893	1	CLONAL	1	TRUE	1	0.425973467774541	2		574	547	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487277	56487277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035001455	NA	P-0066249-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	24	318	0	ENST00000267101.3:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000267101	NM_001982.3	475	Cgg/Tgg	12/28	1	2	FACETS	0.231	0.181	0.29	0.231	0.181	0.29	SUBCLONAL	1	TRUE	1	0.425973467774541	2		318	487	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867469	35867469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs191585195	NA	P-0066249-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	106	380	0	ENST00000303115.3:c.283G>A	p.Glu95Lys	p.E95K	ENST00000303115	NM_002185.3	95	Gag/Aag	3/8	0.425973467774541	3	FACETS	1	0.939	1	0.531	0.478	0.588	CLONAL	1	TRUE	1	0.425973467774541	3		380	568	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164769	36164769	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755073984	NA	P-0066249-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	63	501	0	ENST00000300305.3:c.1106C>T	p.Ser369Leu	p.S369L	ENST00000300305		369	tCg/tTg	8/8	0.196958723818183	3	FACETS	0.499	0.431	0.573	0.166	0.143	0.191	INDETERMINATE	1	TRUE	0	0.425973467774541	3		501	719	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094465	27094473	+	inframe_deletion	In_Frame_Del	DEL	TGAAGGAGA	TGAAGGAGA	-	novel	NA	P-0066249-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	143	628	1	ENST00000324856.7:c.3174_3182del	p.Lys1059_Ile1061del	p.K1059_I1061del	ENST00000324856	NM_006015.4	1058	gTGAAGGAGAtt/gtt	11/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.425973467774541	2		629	574	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652021	36652021	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066249-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	233	730	0	ENST00000244741.5:c.143del	p.Arg48HisfsTer100	p.R48Hfs*100	ENST00000244741	NM_000389.4	48	cGa/ca	2/3	0.173110894105053	3	FACETS	0.971	0.911	1	0.971	0.911	1	INDETERMINATE	2	TRUE	1	0.425973467774541	3		730	683	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	157	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.595461826229146	2		341	519	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577113	7577113	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555525279	NA	P-0066254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	221	391	0	ENST00000269305.4:c.825T>G	p.Cys275Trp	p.C275W	ENST00000269305	NM_001126112.2	275	tgT/tgG	8/11	0.595461826229146	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.595461826229146	1		391	459	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974695	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691187	NA	P-0066254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	222	423	0	ENST00000304494.5:c.132del	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	taC/ta	1/3	0.595461826229146	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.595461826229146	1		423	491	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111882	56111882	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	169	340	0	ENST00000399503.3:c.482G>C	p.Gly161Ala	p.G161A	ENST00000399503	NM_005921.1	161	gGt/gCt	1/20	1	2	FACETS	0.999	0.924	1	0.999	0.924	1	CLONAL	1	TRUE	1	0.595461826229146	2		340	568	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130305	11130305	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	23	374	0	ENST00000358026.2:c.2545del	p.Arg849GlyfsTer9	p.R849Gfs*9	ENST00000358026	NM_001128849.1	848	ctC/ct	18/36	0.595461826229146	1	FACETS	0.126	0.098	0.159	0.126	0.098	0.159	SUBCLONAL	1	TRUE	0	0.595461826229146	1		374	429	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672303	30672303	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs752865436	NA	P-0066255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	131	648	0	ENST00000376406.3:c.4657T>A	p.Ser1553Thr	p.S1553T	ENST00000376406	NM_014641.2	1553	Tct/Act	10/15	1	2	FACETS	0.765	0.696	0.839	0.765	0.696	0.839	SUBCLONAL	1	TRUE	1	0.487606682716551	2		648	702	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0066256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	313	550	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.475420613649697	4	FACETS	0.953	0.901	1	0.953	0.901	1	CLONAL	2	TRUE	2	0.552442431965455	4		550	923	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577529	7577529	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	387	492	0	ENST00000269305.4:c.752del	p.Ile251ThrfsTer94	p.I251Tfs*94	ENST00000269305	NM_001126112.2	251	aTc/ac	7/11	0.552442431965455	3	FACETS	0.954	0.918	0.989	0.954	0.918	0.989	CLONAL	3	TRUE	0	0.552442431965455	3		492	625	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097856	8097856	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	257	558	0	ENST00000346208.3:c.238C>G	p.His80Asp	p.H80D	ENST00000346208		80	Cac/Gac	2/6	0.552442431965455	5	FACETS	0.988	0.928	1	0.494	0.464	0.525	CLONAL	2	TRUE	1	0.552442431965455	5		558	861	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0066257-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	17	311	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.643	0.478	0.84	0.643	0.478	0.84	SUBCLONAL	1	TRUE	1	0.11	2		311	481	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578195	7578197	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0066257-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	29	712	0	ENST00000269305.4:c.652_654del	p.Val218del	p.V218del	ENST00000269305	NM_001126112.2	218	GTG/-	6/11	1	2	FACETS	0.816	0.653	1	0.816	0.653	1	CLONAL	1	TRUE	1	0.11	2		712	646	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593485	48593485	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066257-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	39	296	0	ENST00000342988.3:c.1236C>A	p.Tyr412Ter	p.Y412*	ENST00000342988	NM_005359.5	412	taC/taA	10/12	1	2	FACETS	0.978	0.808	1	0.978	0.808	1	CLONAL	1	TRUE	1	0.11	2		296	725	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262559	16262559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066257-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	30	329	0	ENST00000375759.3:c.9824G>A	p.Ser3275Asn	p.S3275N	ENST00000375759	NM_015001.2	3275	aGt/aAt	11/15	1	2	FACETS	0.99	0.796	1	0.99	0.796	1	CLONAL	1	TRUE	1	0.11	2		329	551	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851156	151851156	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066257-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	70	339	0	ENST00000262189.6:c.12215del	p.Pro4072GlnfsTer11	p.P4072Qfs*11	ENST00000262189	NM_170606.2	4072	cCa/ca	48/59	1	2	FACETS	0.948	0.827	1	1	0.98	1	CLONAL	2	TRUE	1	0.11	2		339	671	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0066258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	40	257	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.212133975570302	3	FACETS	0.954	0.802	1	0.954	0.802	1	CLONAL	2	FALSE	1	0.230203018009181	3		257	203	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577520	7577520	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1330865474	NA	P-0066258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	145	328	0	ENST00000269305.4:c.761T>G	p.Ile254Ser	p.I254S	ENST00000269305	NM_001126112.2	254	aTc/aGc	7/11	0.0558930952553358	3	FACETS	1	0.979	1			1	INDETERMINATE	2	FALSE	NA	0.230203018009181	3		328	578	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0066258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	317	470	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.209091950718089	3	FACETS	0.896	0.849	0.944	1	0.99	1	CLONAL	4	FALSE	0	0.230203018009181	3		470	857	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057658	27057658	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	139	410	0	ENST00000324856.7:c.1366C>T	p.Gln456Ter	p.Q456*	ENST00000324856	NM_006015.4	456	Caa/Taa	3/20	0.155724058163992	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	FALSE	0	0.230203018009181	2		410	576	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0066270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	162	232	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.83842410432716	2		232	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0066270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	304	688	0	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	0.822103654812612	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.83842410432716	1		688	419	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477184	67477184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1320208623	NA	P-0066270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	38	613	0	ENST00000327367.4:c.991G>A	p.Val331Ile	p.V331I	ENST00000327367	NM_005902.3	331	Gtc/Atc	7/9	0.2901808785351	1	FACETS	0.101	0.083	0.121	0.101	0.083	0.121	INDETERMINATE	1	TRUE	0	0.83842410432716	1		613	523	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312684	30312684	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	187	441	0	ENST00000262643.3:c.665C>A	p.Ser222Ter	p.S222*	ENST00000262643	NM_001238.2	222	tCa/tAa	8/12	0.243097180211507	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.83842410432716	0		441	356	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552869	106552869	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	283	671	0	ENST00000369096.4:c.834G>T	p.Lys278Asn	p.K278N	ENST00000369096	NM_001198.3	278	aaG/aaT	5/7	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.83842410432716	2		671	673	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636297	87636297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	221	600	0	ENST00000277120.3:c.2462C>T	p.Thr821Ile	p.T821I	ENST00000277120		821	aCc/aTc	19/19	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.83842410432716	2		600	494	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0066271-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	51	436	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.262490725640206	3	FACETS	0.583	0.495	0.679	0.291	0.247	0.34	SUBCLONAL	1	TRUE	1	0.375885694947121	3		436	553	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392092	118392092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066271-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	52	528	0	ENST00000534358.1:c.11603C>T	p.Ser3868Phe	p.S3868F	ENST00000534358	NM_005933.3	3868	tCc/tTc	35/36	1	2	FACETS	0.487	0.414	0.567	0.487	0.414	0.567	SUBCLONAL	1	TRUE	1	0.375885694947121	2		528	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0066272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	137	621	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	0.231971458936212	2	FACETS	0.808	0.74	0.88	0.808	0.74	0.88	CLONAL	2	TRUE	0	0.332912931382288	2		621	509	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499579	18499579	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	93	489	0	ENST00000266497.5:c.1434G>C	p.Leu478Phe	p.L478F	ENST00000266497		478	ttG/ttC	10/31	0.314564449404136	3	FACETS	1	0.963	1	0.595	0.53	0.663	CLONAL	1	TRUE	1	0.332912931382288	3		489	548	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812319	212812319	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	184	549	0	ENST00000342788.4:c.257A>T	p.Tyr86Phe	p.Y86F	ENST00000342788	NM_005235.2	86	tAc/tTc	3/28	0.120686615217069	3	FACETS	1	0.966	1	0.713	0.661	0.766	INDETERMINATE	2	TRUE	0	0.332912931382288	3		549	603	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670732	134670732	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	119	714	0	ENST00000398015.3:c.643A>G	p.Ser215Gly	p.S215G	ENST00000398015	NM_004441.4	215	Agc/Ggc	3/16	0.332912931382288	4	FACETS	1	0.972	1	0.301	0.271	0.332	CLONAL	1	TRUE	0	0.332912931382288	4		714	792	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55963854	55963854	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	556	451	0	ENST00000263923.4:c.2589G>T	p.Arg863Ser	p.R863S	ENST00000263923	NM_002253.2	863	agG/agT	18/30	0.332912931382288	9	FACETS	0.969	0.938	1			1	CLONAL	8	TRUE	NA	0.332912931382288	9		451	933	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288633	198288633	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	39	516	0	ENST00000335508.6:c.94G>T	p.Gly32Cys	p.G32C	ENST00000335508	NM_012433.2	32	Ggc/Tgc	2/25	0.120686615217069	3	FACETS	0.446	0.369	0.532	0.149	0.123	0.178	INDETERMINATE	1	TRUE	0	0.332912931382288	3		516	613	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641418	47641418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs563410947	NA	P-0066272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	64	359	0	ENST00000233146.2:c.803C>T	p.Ser268Leu	p.S268L	ENST00000233146	NM_000251.2	268	tCa/tTa	5/16	0.182866747449874	4	FACETS	1	0.897	1	0.52	0.451	0.594	INDETERMINATE	1	TRUE	2	0.332912931382288	4		359	493	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406141	70406141	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	77	590	0	ENST00000373644.4:c.3655A>G	p.Ile1219Val	p.I1219V	ENST00000373644	NM_030625.2	1219	Ata/Gta	4/12	1	2	FACETS	0.807	0.71	0.912	0.807	0.71	0.912	CLONAL	1	TRUE	1	0.332912931382288	2		590	573	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47595304	47595305	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0066272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	35	528	0	ENST00000430070.2:c.782_783del	p.Lys261ArgfsTer18	p.K261Rfs*18	ENST00000430070	NM_018095.4	261	aAA/a	4/4	0.332912931382288	3	FACETS	0.377	0.308	0.455	0.189	0.154	0.228	SUBCLONAL	1	TRUE	1	0.332912931382288	3		528	650	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443922	18443922	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	33	436	0	ENST00000266497.5:c.895C>T	p.Gln299Ter	p.Q299*	ENST00000266497		299	Caa/Taa	3/31	0.314564449404136	3	FACETS	0.466	0.379	0.565	0.233	0.189	0.283	SUBCLONAL	1	TRUE	1	0.332912931382288	3		436	496	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508881	106508881	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	TT	novel	NA	P-0066272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	89	653	0	ENST00000359195.3:c.875delinsTT	p.Trp292PhefsTer37	p.W292Ffs*37	ENST00000359195	NM_002649.2	292	tGg/tTTg	2/11	0.332912931382288	3	FACETS	0.803	0.711	0.901	0.401	0.355	0.451	CLONAL	1	TRUE	1	0.332912931382288	3		653	777	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0066272-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	349	621	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	0.529943961256338	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.528575950405847	2		621	591	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499579	18499579	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066272-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	141	489	0	ENST00000266497.5:c.1434G>C	p.Leu478Phe	p.L478F	ENST00000266497		478	ttG/ttC	10/31	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.528575950405847	2		489	509	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812319	212812319	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066272-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	294	549	0	ENST00000342788.4:c.257A>T	p.Tyr86Phe	p.Y86F	ENST00000342788	NM_005235.2	86	tAc/tTc	3/28	0.453813480522442	3	FACETS	0.992	0.94	1	0.992	0.94	1	CLONAL	2	TRUE	1	0.528575950405847	3		549	709	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670732	134670732	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066272-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	219	714	0	ENST00000398015.3:c.643A>G	p.Ser215Gly	p.S215G	ENST00000398015	NM_004441.4	215	Agc/Ggc	3/16	0.529943961256338	5	FACETS	1	0.986	1	0.249	0.231	0.268	CLONAL	1	TRUE	0	0.528575950405847	5		714	1193	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55963854	55963854	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066272-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	114	451	0	ENST00000263923.4:c.2589G>T	p.Arg863Ser	p.R863S	ENST00000263923	NM_002253.2	863	agG/agT	18/30	1	2	FACETS	0.95	0.861	1	0.95	0.861	1	CLONAL	1	TRUE	1	0.528575950405847	2		451	454	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288633	198288633	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066272-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	137	516	0	ENST00000335508.6:c.94G>T	p.Gly32Cys	p.G32C	ENST00000335508	NM_012433.2	32	Ggc/Tgc	2/25	0.453813480522442	3	FACETS	1	0.924	1	0.507	0.462	0.554	CLONAL	1	TRUE	1	0.528575950405847	3		516	646	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641418	47641418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs563410947	NA	P-0066272-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	99	359	0	ENST00000233146.2:c.803C>T	p.Ser268Leu	p.S268L	ENST00000233146	NM_000251.2	268	tCa/tTa	5/16	0.529943961256338	3	FACETS	1	0.902	1	0.503	0.451	0.557	CLONAL	1	TRUE	1	0.528575950405847	3		359	471	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406141	70406141	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066272-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	158	590	0	ENST00000373644.4:c.3655A>G	p.Ile1219Val	p.I1219V	ENST00000373644	NM_030625.2	1219	Ata/Gta	4/12	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.528575950405847	2		590	575	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	39	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.748	0.622	0.887	0.748	0.622	0.887	SUBCLONAL	1	TRUE	1	0.32	2		341	326	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0066273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	68	442	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.706	0.614	0.805	0.706	0.614	0.805	SUBCLONAL	1	TRUE	1	0.32	2		442	602	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098519	108098519	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs876658520	NA	P-0066273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	26	178	0	ENST00000278616.4:c.89T>G	p.Phe30Cys	p.F30C	ENST00000278616	NM_000051.3	30	tTt/tGt	3/63	1	2	FACETS	0.412	0.326	0.511	0.412	0.326	0.511	SUBCLONAL	1	TRUE	1	0.32	2		178	394	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163485	108163485	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748898098	NA	P-0066273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	29	230	0	ENST00000278616.4:c.4576C>T	p.Pro1526Ser	p.P1526S	ENST00000278616	NM_000051.3	1526	Ccc/Tcc	30/63	1	2	FACETS	0.493	0.395	0.603	0.493	0.395	0.603	SUBCLONAL	1	TRUE	1	0.32	2		230	368	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045796	180045796	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	36	582	0	ENST00000261937.6:c.2975C>A	p.Ala992Glu	p.A992E	ENST00000261937	NM_182925.4	992	gCg/gAg	21/30	1	2	FACETS	0.381	0.312	0.458	0.381	0.312	0.458	SUBCLONAL	1	TRUE	1	0.32	2		582	591	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979000	7979000	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	33	540	0	ENST00000319144.4:c.1567A>G	p.Ser523Gly	p.S523G	ENST00000319144	NM_001139.2	523	Agt/Ggt	12/15	1	2	FACETS	0.324	0.263	0.394	0.324	0.263	0.394	SUBCLONAL	1	TRUE	1	0.32	2		540	636	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760914	133760914	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	43	465	0	ENST00000318560.5:c.3237C>A	p.Asn1079Lys	p.N1079K	ENST00000318560	NM_005157.4	1079	aaC/aaA	11/11	1	2	FACETS	0.431	0.36	0.51	0.431	0.36	0.51	SUBCLONAL	1	TRUE	1	0.32	2		465	624	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317878	8317878	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151311972	NA	P-0066274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	150	451	0	ENST00000356435.5:c.5735C>T	p.Thr1912Met	p.T1912M	ENST00000356435		1912	aCg/aTg	35/35	0.593822942259737	3	FACETS	0.99	0.919	1	0.99	0.919	1	CLONAL	2	TRUE	1	0.593822942259737	3		451	331	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696638	47696638	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	70	425	0	ENST00000347630.2:c.310T>A	p.Phe104Ile	p.F104I	ENST00000347630	NM_001007230.1	104	Ttc/Atc	5/11	0.593822942259737	3	FACETS	0.881	0.773	0.996	0.441	0.386	0.498	CLONAL	1	TRUE	1	0.593822942259737	3		425	347	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936072	44936082	+	splice_donor_variant,intron_variant	Splice_Site	DEL	GTGAGTCTGAA	GTGAGTCTGAA	-	novel	NA	P-0066274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	12	158	0	ENST00000377967.4:c.2832+1_2832+11del		p.X944_splice	ENST00000377967	NM_021140.2	944			1	1	FACETS	0.418	0.299	0.557	0.418	0.299	0.557	SUBCLONAL	1	TRUE	0	0.593822942259737	1		158	68	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121321	29121321	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs757340619	NA	P-0066274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	48	442	0	ENST00000328354.6:c.354C>A	p.Asp118Glu	p.D118E	ENST00000328354	NM_007194.3	118	gaC/gaA	3/15	1	2	FACETS	0.703	0.6	0.813	0.703	0.6	0.813	SUBCLONAL	1	TRUE	1	0.593822942259737	2		442	230	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	137	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.645612643024998	2	FACETS	0.94	0.882	0.997	0.94	0.882	0.997	CLONAL	2	TRUE	0	0.677668456774433	2		341	215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577144	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs879253942	NA	P-0066275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	403	524	0	ENST00000269305.4:c.794T>C	p.Leu265Pro	p.L265P	ENST00000269305	NM_001126112.2	265	cTg/cCg	8/11	0.676914527270527	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.677668456774433	2		524	539	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51507431	51507431	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs754344873	NA	P-0066275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	244	425	0	ENST00000260433.2:c.859-2A>G		p.X287_splice	ENST00000260433		287			0.676914527270527	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.677668456774433	3		425	478	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561063	9561063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	205	594	0	ENST00000353224.5:c.719C>T	p.Ala240Val	p.A240V	ENST00000353224	NM_177990.2	240	gCa/gTa	4/10	0.676914527270527	3	FACETS	1	0.961	1	0.524	0.487	0.562	CLONAL	1	TRUE	1	0.677668456774433	3		594	773	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390180	89390180	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1273	177	530	0	ENST00000336596.2:c.929A>C	p.Tyr310Ser	p.Y310S	ENST00000336596	NM_005233.5	310	tAc/tCc	4/17	0.677668456774433	8	FACETS	1	0.965	1			1	CLONAL	1	TRUE	NA	0.677668456774433	8		530	1450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0066278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	214	463	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.431907786088666	2	FACETS	0.946	0.887	1	0.946	0.887	1	CLONAL	2	TRUE	0	0.431907786088666	2		463	524	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543635	29543635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201449759	NA	P-0066278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	125	460	0	ENST00000389048.3:c.1528C>T	p.Arg510Trp	p.R510W	ENST00000389048	NM_004304.4	510	Cgg/Tgg	7/29	0.338143424225574	3	FACETS	0.997	0.904	1	0.498	0.452	0.548	CLONAL	1	TRUE	1	0.431907786088666	3		460	706	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458740	120458740	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	245	569	0	ENST00000256646.2:c.6605C>G	p.Ser2202Cys	p.S2202C	ENST00000256646	NM_024408.3	2202	tCt/tGt	34/34	0.208098318810605	4	FACETS	0.94	0.881	1	0.627	0.587	0.668	INDETERMINATE	2	TRUE	1	0.431907786088666	4		569	864	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28601385	28601385	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	110	515	0	ENST00000253063.3:c.1070C>G	p.Pro357Arg	p.P357R	ENST00000253063	NM_031459.4	357	cCt/cGt	8/10	0.424426982088258	2	FACETS	0.878	0.791	0.97	0.439	0.395	0.485	CLONAL	1	TRUE	0	0.431907786088666	2		515	580	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266236	198266236	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	44	362	0	ENST00000335508.6:c.2384G>C	p.Cys795Ser	p.C795S	ENST00000335508	NM_012433.2	795	tGt/tCt	17/25	0.379382632269673	3	FACETS	0.942	0.796	1	0.471	0.398	0.551	CLONAL	1	TRUE	1	0.431907786088666	3		362	263	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620389	43620389	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	38	433	0	ENST00000355710.3:c.2998G>T	p.Asp1000Tyr	p.D1000Y	ENST00000355710	NM_020975.4	1000	Gac/Tac	18/20	0.208098318810605	4	FACETS	0.366	0.302	0.439	0.122	0.1	0.147	INDETERMINATE	1	TRUE	1	0.431907786088666	4		433	688	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447887	49447887	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	228	467	0	ENST00000301067.7:c.547C>G	p.Pro183Ala	p.P183A	ENST00000301067	NM_003482.3	183	Cct/Gct	5/54	0.424426982088258	2	FACETS	0.899	0.844	0.955	0.899	0.844	0.955	CLONAL	2	TRUE	0	0.431907786088666	2		467	587	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458161	120458161	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0066278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	267	573	0	ENST00000256646.2:c.7184C>G	p.Ser2395Ter	p.S2395*	ENST00000256646	NM_024408.3	2395	tCa/tGa	34/34	0.208098318810605	4	FACETS	1	0.981	1	0.73	0.687	0.774	INDETERMINATE	2	TRUE	1	0.431907786088666	4		573	808	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950666	38950666	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	71	459	0	ENST00000357387.3:c.3284A>G	p.Lys1095Arg	p.K1095R	ENST00000357387	NM_152756.3	1095	aAg/aGg	31/38	0.39113671536952	3	FACETS	1	0.909	1	0.522	0.458	0.59	CLONAL	1	TRUE	1	0.431907786088666	3		459	383	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893324	32893324	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	17	433	0	ENST00000380152.3:c.178A>C	p.Asn60His	p.N60H	ENST00000380152		60	Aac/Cac	3/27	1	2	FACETS	0.266	0.198	0.347	0.266	0.198	0.347	SUBCLONAL	1	TRUE	1	0.431907786088666	2		433	296	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43772051	43772084	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCATACCAGTATTAGCATCCACATCAGACAGCCT	TCATACCAGTATTAGCATCCACATCAGACAGCCT	ATATGTTTATATGGTTA	novel	NA	P-0066278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	49	431	0	ENST00000382044.4:c.631_658+6delinsTAACCATATAAACATAT		p.X211_splice	ENST00000382044	NM_001141980.1	211		6/28	0.42353883509061	2	FACETS	0.683	0.581	0.795	0.342	0.29	0.398	SUBCLONAL	1	TRUE	0	0.431907786088666	2		431	332	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0066280-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	42	426	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	0.311922183325181	3	FACETS	0.96	0.831	1	0.96	0.831	1	INDETERMINATE	2	TRUE	1	0.606679421869485	3		426	94	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94201032	94201032	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs570102851	NA	P-0066280-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	64	361	0	ENST00000323929.3:c.1045C>T	p.Arg349Trp	p.R349W	ENST00000323929	NM_005591.3	349	Cgg/Tgg	10/20	0.311922183325181	3	FACETS	0.996	0.889	1	0.996	0.889	1	INDETERMINATE	2	TRUE	1	0.606679421869485	3		361	138	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	179	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.442885380099157	4	FACETS	0.931	0.865	0.999	0.931	0.865	0.999	CLONAL	2	TRUE	2	0.576017372746857	4		341	526	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0066281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	227	721	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.542351677308182	3	FACETS	0.847	0.795	0.9	0.847	0.795	0.9	CLONAL	2	TRUE	1	0.576017372746857	3		721	599	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274877	41274877	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	127	385	0	ENST00000349496.5:c.1127G>A	p.Arg376His	p.R376H	ENST00000349496	NM_001904.3	376	cGt/cAt	8/15	0.575421519629776	3	FACETS	0.827	0.75	0.907	0.413	0.375	0.454	CLONAL	1	TRUE	1	0.576017372746857	3		385	687	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416698	29416698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56181542	NA	P-0066281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	117	429	0	ENST00000389048.3:c.4255G>A	p.Glu1419Lys	p.E1419K	ENST00000389048	NM_004304.4	1419	Gag/Aag	29/29	0.575421519629776	3	FACETS	0.888	0.803	0.977	0.444	0.401	0.489	CLONAL	1	TRUE	1	0.576017372746857	3		429	589	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029193	26029193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	125	351	0	ENST00000435504.4:c.157C>T	p.Leu53Phe	p.L53F	ENST00000435504		53	Ctt/Ttt	4/13	0.575421519629776	3	FACETS	0.981	0.891	1	0.49	0.445	0.537	CLONAL	1	TRUE	1	0.576017372746857	3		351	570	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114917829	114917829	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0066281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	156	277	0	ENST00000543371.1:c.1318+1G>T		p.X440_splice	ENST00000543371	NM_001198531.1	440			0.542351677308182	3	FACETS	0.804	0.743	0.866	0.804	0.743	0.866	CLONAL	2	TRUE	1	0.576017372746857	3		277	434	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705439	43705439	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	275	424	0	ENST00000382044.4:c.5183del	p.Pro1728LeufsTer82	p.P1728Lfs*82	ENST00000382044	NM_001141980.1	1728	cCt/ct	24/28	0.575421519629776	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.576017372746857	3		424	589	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0066282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	48	215	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.782	0.666	0.907	1	0.966	1	CLONAL	2	TRUE	1	0.23	2		215	267	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115820	8115820	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	32	559	0	ENST00000346208.3:c.1166G>T	p.Ser389Ile	p.S389I	ENST00000346208		389	aGc/aTc	6/6	1	2	FACETS	0.595	0.482	0.722	0.595	0.482	0.722	SUBCLONAL	1	TRUE	1	0.23	2		559	468	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435691	18435691	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	38	377	0	ENST00000266497.5:c.676G>T	p.Glu226Ter	p.E226*	ENST00000266497		226	Gag/Tag	1/31	1	2	FACETS	0.972	0.806	1	0.972	0.806	1	CLONAL	1	TRUE	1	0.23	2		377	340	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900741	3900741	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	57	548	0	ENST00000262367.5:c.355G>T	p.Gly119Cys	p.G119C	ENST00000262367	NM_004380.2	119	Ggc/Tgc	2/31	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.23	2		548	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0066282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	45	556	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	1	2	FACETS	0.826	0.694	0.971	0.826	0.694	0.971	CLONAL	1	TRUE	1	0.23	2		556	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579592	7579592	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0066282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	38	521	0	ENST00000269305.4:c.97-2A>T		p.X33_splice	ENST00000269305	NM_001126112.2	33			1	2	FACETS	0.733	0.606	0.874	0.733	0.606	0.874	SUBCLONAL	1	TRUE	1	0.23	2		521	451	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602688	10602690	+	missense_variant	Missense_Mutation	TNP	CAG	CAG	AAA	novel	NA	P-0066282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	39	612	0	ENST00000171111.5:c.888_890delinsTTT	p.Cys297Phe	p.C297F	ENST00000171111	NM_203500.1	296	cgCTGc/cgTTTc	3/6	1	2	FACETS	0.771	0.639	0.917	0.771	0.639	0.917	CLONAL	1	TRUE	1	0.23	2		612	440	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46714226	46714226	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	56	495	0	ENST00000371975.4:c.46G>A	p.Glu16Lys	p.E16K	ENST00000371975	NM_003579.3	16	Gaa/Aaa	2/18	1	2	FACETS	0.986	0.846	1	0.986	0.846	1	CLONAL	1	TRUE	1	0.23	2		495	494	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243801035	243801035	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	46	356	0	ENST00000263826.5:c.439G>T	p.Asp147Tyr	p.D147Y	ENST00000263826	NM_005465.4	147	Gat/Tat	5/13	0.177950793764216	3	FACETS	1	0.951	1	0.67	0.566	0.783	CLONAL	1	TRUE	1	0.23	3		356	333	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937518	32937518	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs730881582	NA	P-0066282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	36	499	0	ENST00000380152.3:c.8179G>T	p.Ala2727Ser	p.A2727S	ENST00000380152		2727	Gct/Tct	18/27	1	2	FACETS	0.771	0.634	0.924	0.771	0.634	0.924	CLONAL	1	TRUE	1	0.23	2		499	406	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023781	31023781	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	56	579	0	ENST00000375687.4:c.3266C>G	p.Pro1089Arg	p.P1089R	ENST00000375687	NM_015338.5	1089	cCa/cGa	13/13	1	2	FACETS	0.897	0.769	1	0.897	0.769	1	CLONAL	1	TRUE	1	0.23	2		579	543	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0066285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	78	257	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.193262843299302	4	FACETS	0.947	0.835	1	0.947	0.835	1	CLONAL	2	TRUE	2	0.214086087418702	4		257	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1567548223	NA	P-0066285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	164	469	0	ENST00000269305.4:c.797del	p.Gly266AspfsTer79	p.G266Dfs*79	ENST00000269305	NM_001126112.2	266	gGa/ga	8/11	0.214086087418702	5	FACETS	0.988	0.91	1	0.741	0.682	0.802	CLONAL	3	TRUE	1	0.214086087418702	5		469	683	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0066285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	56	396	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.174873176337652	2	FACETS	1	0.913	1	0.545	0.467	0.629	CLONAL	1	TRUE	0	0.214086087418702	2		396	480	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39708780	39708780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	33	298	0	ENST00000361337.2:c.391G>A	p.Glu131Lys	p.E131K	ENST00000361337	NM_003286.2	131	Gag/Aag	6/21	0.214086087418702	7	FACETS	0.932	0.758	1	0.186	0.151	0.226	CLONAL	1	TRUE	2	0.214086087418702	7		298	508	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	112	446	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		446	501	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	382	446	0				ENST00000310581	NM_198253.2	-/1132			0.926737991873664	2	FACETS	0.995	0.977	1	0.995	0.977	1	CLONAL	2	TRUE	0	0.93179182591458	2		446	412	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004277	29004277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370686484	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	227	385	0	ENST00000282397.4:c.1016G>A	p.Arg339Gln	p.R339Q	ENST00000282397	NM_002019.4	339	cGa/cAa	8/30	0.164731361305876	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93179182591458	0		385	504	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	622	455	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.93179182591458	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.93179182591458	2		455	660	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	417	396	0				ENST00000310581	NM_198253.2	-/1132			0.926737991873664	2	FACETS	0.99	0.973	1	0.99	0.973	1	CLONAL	2	TRUE	0	0.93179182591458	2		396	452	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812182	212812182	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	124	430	0	ENST00000342788.4:c.394C>T	p.Gln132Ter	p.Q132*	ENST00000342788	NM_005235.2	132	Caa/Taa	3/28	0.641958057292048	1	FACETS	0.349	0.319	0.381	0.349	0.319	0.381	SUBCLONAL	1	TRUE	0	0.93179182591458	1		430	407	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956220	55956220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190050670	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	284	409	0	ENST00000263923.4:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000263923	NM_002253.2	1032	cGa/cAa	23/30	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.93179182591458	2		409	590	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467699	50467699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	364	576	0	ENST00000331340.3:c.934G>A	p.Asp312Asn	p.D312N	ENST00000331340	NM_006060.4	312	Gac/Aac	8/8	0.577680960256159	1	FACETS	0.69	0.662	0.717	0.69	0.662	0.717	SUBCLONAL	1	TRUE	0	0.93179182591458	1		576	605	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574004	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	349	490	1	ENST00000269305.4:c.1023_1024delinsTT	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	341	ttCCga/ttTTga	10/11	0.472886046043146	1	FACETS	0.707	0.679	0.735	0.707	0.679	0.735	INDETERMINATE	1	TRUE	0	0.93179182591458	1		491	566	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274277	5274277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1327116960	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	188	498	0	ENST00000357368.4:c.170C>T	p.Thr57Met	p.T57M	ENST00000357368	NM_002850.3	57	aCg/aTg	3/38	0.472465495252051	1	FACETS	0.316	0.292	0.339	0.316	0.292	0.339	INDETERMINATE	1	TRUE	0	0.93179182591458	1		498	683	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755511	39755511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	452	584	0	ENST00000288319.7:c.1254G>A	p.Met418Ile	p.M418I	ENST00000288319	NM_182918.3	418	atG/atA	10/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.93179182591458	2		584	896	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892177	9892177	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555488097	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	199	572	0	ENST00000330684.3:c.2313G>A	p.Trp771Ter	p.W771*	ENST00000330684	NM_001134407.1	771	tgG/tgA	11/13	0.641958057292048	1	FACETS	0.401	0.374	0.429	0.401	0.374	0.429	SUBCLONAL	1	TRUE	0	0.93179182591458	1		572	569	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988838	41988838	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	311	501	0	ENST00000219905.7:c.1630C>T	p.Pro544Ser	p.P544S	ENST00000219905	NM_001164273.1	544	Ccc/Tcc	3/24	0.577680960256159	1	FACETS	0.661	0.632	0.691	0.661	0.632	0.691	SUBCLONAL	1	TRUE	0	0.93179182591458	1		501	539	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923281	26923281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	274	418	0	ENST00000381527.3:c.277G>A	p.Val93Met	p.V93M	ENST00000381527	NM_001260.1	93	Gtg/Atg	3/13	0.164731361305876	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93179182591458	0		418	552	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561090	9561090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	461	477	0	ENST00000353224.5:c.692C>T	p.Ser231Leu	p.S231L	ENST00000353224	NM_177990.2	231	tCa/tTa	4/10	0.482850145794623	3	FACETS	0.913	0.88	0.946	0.913	0.88	0.946	INDETERMINATE	2	TRUE	1	0.93179182591458	3		477	794	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713479	40713479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	497	550	0	ENST00000373198.4:c.4036G>A	p.Asp1346Asn	p.D1346N	ENST00000373198	NM_133170.3	1346	Gat/Aat	30/32	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.93179182591458	2		550	885	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170325	32170325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	404	549	0	ENST00000375023.3:c.3283C>T	p.His1095Tyr	p.H1095Y	ENST00000375023	NM_004557.3	1095	Cac/Tac	21/30	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.93179182591458	2		549	816	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129903	69129903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752113779	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	300	563	0	ENST00000288368.4:c.4657G>A	p.Gly1553Arg	p.G1553R	ENST00000288368	NM_024870.2	1553	Gga/Aga	38/40	1	2	FACETS	0.851	0.805	0.896	0.851	0.805	0.896	CLONAL	1	TRUE	1	0.93179182591458	2		563	757	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	185	454	0	ENST00000269305.4:c.775del	p.Asp259ThrfsTer86	p.D259Tfs*86	ENST00000269305	NM_001126112.2	259	Gac/ac	7/11	0.472886046043146	1	FACETS	0.368	0.341	0.395	0.368	0.341	0.395	INDETERMINATE	1	TRUE	0	0.93179182591458	1		454	577	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99136609	99136609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	141	448	0	ENST00000074304.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000074304	NM_001134224.1	33	tCt/tTt	3/26	0.466120661325132	1	FACETS	0.325	0.298	0.353	0.325	0.298	0.353	INDETERMINATE	1	TRUE	0	0.93179182591458	1		448	497	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635614	47635614	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1443234544	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	352	377	0	ENST00000233146.2:c.286C>T	p.Arg96Cys	p.R96C	ENST00000233146	NM_000251.2	96	Cgt/Tgt	2/16	0.466120661325132	1	FACETS	0.697	0.669	0.725	0.697	0.669	0.725	INDETERMINATE	1	TRUE	0	0.93179182591458	1		377	579	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944364	40944364	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	307	448	0	ENST00000373198.4:c.2138G>A	p.Gly713Glu	p.G713E	ENST00000373198	NM_133170.3	713	gGa/gAa	12/32	1	2	FACETS	0.89	0.844	0.937	0.89	0.844	0.937	CLONAL	1	TRUE	1	0.93179182591458	2		448	740	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022763	31022763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218506765	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	354	587	0	ENST00000375687.4:c.2248C>T	p.Pro750Ser	p.P750S	ENST00000375687	NM_015338.5	750	Ccc/Tcc	13/13	0.482850145794623	3	FACETS	1	0.988	1	0.564	0.535	0.593	INDETERMINATE	1	TRUE	1	0.93179182591458	3		587	988	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155815	106155815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	330	529	0	ENST00000380013.4:c.716C>T	p.Ser239Phe	p.S239F	ENST00000380013	NM_001127208.2	239	tCc/tTc	3/11	1	2	FACETS	0.952	0.906	0.999	0.952	0.906	0.999	CLONAL	1	TRUE	1	0.93179182591458	2		529	744	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686838	117686838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868806134	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	126	432	0	ENST00000368508.3:c.2879G>A	p.Gly960Glu	p.G960E	ENST00000368508	NM_002944.2	960	gGa/gAa	19/43	0.604266358895183	1	FACETS	0.33	0.301	0.36	0.33	0.301	0.36	SUBCLONAL	1	TRUE	0	0.93179182591458	1		432	438	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794647	42794647	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761218687	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	181	560	0	ENST00000575354.2:c.1727C>T	p.Pro576Leu	p.P576L	ENST00000575354	NM_015125.3	576	cCt/cTt	10/20	0.472465495252051	1	FACETS	0.37	0.343	0.397	0.37	0.343	0.397	INDETERMINATE	1	TRUE	0	0.93179182591458	1		560	561	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390207	89390207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	367	487	0	ENST00000336596.2:c.956C>T	p.Ser319Phe	p.S319F	ENST00000336596	NM_005233.5	319	tCc/tTc	4/17	NA	2	FACETS	0.929	0.886	0.973			1	INDETERMINATE	1	TRUE	NA	0.93179182591458	2		487	848	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857512	9857512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1431125566	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	291	577	0	ENST00000330684.3:c.3889G>A	p.Asp1297Asn	p.D1297N	ENST00000330684	NM_001134407.1	1297	Gac/Aac	13/13	0.641958057292048	1	FACETS	0.654	0.624	0.684	0.654	0.624	0.684	SUBCLONAL	1	TRUE	0	0.93179182591458	1		577	510	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687256	117687256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	138	419	0	ENST00000368508.3:c.2795C>T	p.Ser932Phe	p.S932F	ENST00000368508	NM_002944.2	932	tCc/tTc	18/43	0.604266358895183	1	FACETS	0.351	0.321	0.381	0.351	0.321	0.381	SUBCLONAL	1	TRUE	0	0.93179182591458	1		419	451	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931823	28931823	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	299	489	0	ENST00000282397.4:c.2117-1G>A		p.X706_splice	ENST00000282397	NM_002019.4	706			0.164731361305876	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93179182591458	0		489	604	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46588067	46588067	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776254639	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	179	603	0	ENST00000263734.3:c.617C>T	p.Pro206Leu	p.P206L	ENST00000263734	NM_001430.4	206	cCt/cTt	6/16	0.466120661325132	1	FACETS	0.309	0.286	0.333	0.309	0.286	0.333	INDETERMINATE	1	TRUE	0	0.93179182591458	1		603	664	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336678	81336679	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	TT	TT	AA	novel	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	137	347	1	ENST00000222390.5:c.1543_1544inv	p.Asn515Phe	p.N515F	ENST00000222390	NM_000601.4	515	AAt/TTt	14/18	0.472465495252051	1	FACETS	0.374	0.343	0.406	0.374	0.343	0.406	INDETERMINATE	1	TRUE	0	0.93179182591458	1		348	420	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571573	95571573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	133	437	0	ENST00000393063.1:c.3104C>T	p.Pro1035Leu	p.P1035L	ENST00000393063	NM_030621.3	1035	cCa/cTa	21/28	0.472465495252051	1	FACETS	0.31	0.283	0.338	0.31	0.283	0.338	INDETERMINATE	1	TRUE	0	0.93179182591458	1		437	492	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043463	180043464	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	453	511	0	ENST00000261937.6:c.3122_3123delinsAA	p.Arg1041Gln	p.R1041Q	ENST00000261937	NM_182925.4	1041	cGG/cAA	23/30	0.926737991873664	2	FACETS	0.978	0.961	0.994	0.978	0.961	0.994	CLONAL	2	TRUE	0	0.93179182591458	2		511	497	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873482	136873482	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	156	491	0	ENST00000241393.3:c.16A>G	p.Ile6Val	p.I6V	ENST00000241393	NM_003467.2	6	Ata/Gta	2/2	0.466120661325132	1	FACETS	0.345	0.318	0.373	0.345	0.318	0.373	INDETERMINATE	1	TRUE	0	0.93179182591458	1		491	518	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085891	16085891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772736778	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	151	514	0	ENST00000281043.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000281043	NM_005378.4	356	cCa/cTa	3/3	0.466120661325132	1	FACETS	0.305	0.28	0.331	0.305	0.28	0.331	INDETERMINATE	1	TRUE	0	0.93179182591458	1		514	568	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528063	157528063	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772262995	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	394	657	0	ENST00000346085.5:c.5788C>T	p.Pro1930Ser	p.P1930S	ENST00000346085	NM_020732.3	1930	Cct/Tct	20/20	0.604266358895183	1	FACETS	0.75	0.723	0.777	0.75	0.723	0.777	SUBCLONAL	1	TRUE	0	0.93179182591458	1		657	602	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164240	47164240	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	148	510	0	ENST00000409792.3:c.1886del	p.Lys629SerfsTer2	p.K629Sfs*2	ENST00000409792	NM_014159.6	629	aAg/ag	3/21	0.5091232341732	3	FACETS	0.516	0.471	0.563	0.172	0.157	0.188	INDETERMINATE	1	TRUE	0	0.93179182591458	3		510	903	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610606	81610606	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1000765116	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	394	536	0	ENST00000298171.2:c.2204T>C	p.Met735Thr	p.M735T	ENST00000298171	NM_000369.2	735	aTg/aCg	10/10	0.472465495252051	1	FACETS	0.712	0.686	0.739	0.712	0.686	0.739	INDETERMINATE	1	TRUE	0	0.93179182591458	1		536	634	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026987	71026987	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1430321888	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	600	570	0	ENST00000318789.4:c.1340T>C	p.Ile447Thr	p.I447T	ENST00000318789	NM_032682.5	447	aTt/aCt	15/21	0.169465669356812	5	FACETS	1	0.992	1			1	INDETERMINATE	3	TRUE	NA	0.93179182591458	5		570	965	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456481	99456481	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	181	529	0	ENST00000268035.6:c.1798G>A	p.Glu600Lys	p.E600K	ENST00000268035	NM_000875.3	600	Gag/Aag	8/21	0.577680960256159	1	FACETS	0.404	0.375	0.433	0.404	0.375	0.433	SUBCLONAL	1	TRUE	0	0.93179182591458	1		529	514	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755599	39755599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	426	571	0	ENST00000288319.7:c.1166A>G	p.Lys389Arg	p.K389R	ENST00000288319	NM_182918.3	389	aAg/aGg	10/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.93179182591458	2		571	890	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652113	36652113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1379336902	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	434	623	0	ENST00000244741.5:c.235C>T	p.Pro79Ser	p.P79S	ENST00000244741	NM_000389.4	79	Ccc/Tcc	2/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.93179182591458	2		623	913	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852448	42852448	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	406	515	0	ENST00000398585.3:c.638G>A	p.Trp213Ter	p.W213*	ENST00000398585	NM_001135099.1	213	tGg/tAg	6/14	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.93179182591458	2		515	855	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572191	64572192	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	423	588	0	ENST00000312049.6:c.1447_1448delinsTT	p.Pro483Leu	p.P483L	ENST00000312049	NM_130799.2	483	CCa/TTa	10/10	0.472465495252051	1	FACETS	0.674	0.649	0.7	0.674	0.649	0.7	INDETERMINATE	1	TRUE	0	0.93179182591458	1		588	719	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61323120	61323120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	365	539	0	ENST00000283752.5:c.944C>T	p.Ser315Leu	p.S315L	ENST00000283752	NM_006919.2	315	tCa/tTa	8/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.93179182591458	2		539	728	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828162	50828162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	322	451	0	ENST00000398568.2:c.2500C>T	p.Pro834Ser	p.P834S	ENST00000398568	NM_001042412.1	834	Cca/Tca	17/18	0.472465495252051	1	FACETS	0.67	0.641	0.699	0.67	0.641	0.699	INDETERMINATE	1	TRUE	0	0.93179182591458	1		451	551	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261334	115261334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	670	438	0	ENST00000438362.2:c.2387C>T	p.Pro796Leu	p.P796L	ENST00000438362	NM_001242891.1	796	cCt/cTt	19/20	0.93179182591458	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.93179182591458	2		438	702	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0066288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	319	498	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.676006961394246	1	FACETS	0.903	0.867	0.939	0.903	0.867	0.939	CLONAL	1	FALSE	0	0.830778031687913	1		498	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1131691023	NA	P-0066288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	53	677	0	ENST00000269305.4:c.470T>C	p.Val157Ala	p.V157A	ENST00000269305	NM_001126112.2	157	gTc/gCc	5/11	0.676006961394246	1	FACETS	0.151	0.129	0.176	0.151	0.129	0.176	SUBCLONAL	1	FALSE	0	0.830778031687913	1		677	493	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913409	NA	P-0066288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	273	521	0	ENST00000349496.5:c.134C>G	p.Ser45Cys	p.S45C	ENST00000349496	NM_001904.3	45	tCt/tGt	3/15	0.830778031687913	3	FACETS	1	0.947	1			1	CLONAL	1	FALSE	NA	0.830778031687913	3		521	923	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003535	57003535	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	C	C	T	rs760732461	NA	P-0066288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	282	693	0	ENST00000257254.3:c.944G>A	p.Arg315His	p.R315H	ENST00000257254		315	cGc/cAc	1/2	0.123480692372672	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.830778031687913	0		693	634	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556256	29556256	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	196	559	1	ENST00000356175.3:c.2623G>T	p.Gly875Cys	p.G875C	ENST00000356175	NM_000267.3	875	Ggt/Tgt	21/57	0.614290033541569	1	FACETS	0.63	0.59	0.67	0.63	0.59	0.67	SUBCLONAL	1	FALSE	0	0.830778031687913	1		560	438	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670050	86670050	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	171	361	0	ENST00000274376.6:c.1847G>A	p.Cys616Tyr	p.C616Y	ENST00000274376	NM_002890.2	616	tGt/tAt	14/25	0.830778031687913	1	FACETS	0.963	0.913	1	0.963	0.913	1	CLONAL	1	FALSE	0	0.830778031687913	1		361	250	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325656	87325656	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1564102617	NA	P-0066288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	225	470	0	ENST00000277120.3:c.533A>G	p.Asn178Ser	p.N178S	ENST00000277120		178	aAt/aGt	6/19	0.574761105312858	3	FACETS	1	0.991	1	0.664	0.623	0.706	CLONAL	1	FALSE	1	0.830778031687913	3		470	577	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0066288-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	257	643	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.40916013511892	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.40916013511892	2		643	575	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78704367	78704367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780768526	NA	P-0066288-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	142	561	0	ENST00000306801.3:c.515C>T	p.Thr172Met	p.T172M	ENST00000306801	NM_020761.2	172	aCg/aTg	5/34	0.350427901260476	2	FACETS	0.834	0.768	0.902	0.834	0.768	0.902	CLONAL	2	TRUE	0	0.40916013511892	2		561	416	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045648	26045648	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066288-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	118	627	0	ENST00000540144.1:c.10A>G	p.Thr4Ala	p.T4A	ENST00000540144	NM_003531.2	4	Acg/Gcg	1/1	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.40916013511892	2		627	540	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	81	446	0				ENST00000310581	NM_198253.2	-/1132			0.322898183553364	4	FACETS	1	0.978	1	0.749	0.663	0.84	CLONAL	1	TRUE	2	0.347877997268984	4		446	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0066293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	271	433	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.296478910710341	4	FACETS	1	0.974	1	0.788	0.745	0.832	CLONAL	3	TRUE	0	0.347877997268984	4		433	666	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106024	27106024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369894428	NA	P-0066293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	207	583	0	ENST00000324856.7:c.5635C>T	p.Arg1879Trp	p.R1879W	ENST00000324856	NM_006015.4	1879	Cgg/Tgg	20/20	0.347877997268984	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	1	0.347877997268984	3		583	683	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597380	52597380	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	42	436	0	ENST00000394830.3:c.3930G>T	p.Glu1310Asp	p.E1310D	ENST00000394830	NM_018313.4	1310	gaG/gaT	25/30	0.230917834370455	3	FACETS	0.524	0.437	0.621	0.262	0.218	0.311	SUBCLONAL	1	TRUE	1	0.347877997268984	3		436	541	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65569055	65569055	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0066293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	43	337	0	ENST00000358664.4:c.3G>A	p.Met1?	p.M1?	ENST00000358664	NM_002382.4	1	atG/atA	1/5	0.29038980686974	3	FACETS	0.694	0.582	0.819	0.347	0.291	0.41	SUBCLONAL	1	TRUE	1	0.347877997268984	3		337	418	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146610	185146610	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	234	448	0	ENST00000265026.3:c.241G>C	p.Glu81Gln	p.E81Q	ENST00000265026	NM_004721.4	81	Gag/Cag	2/14	0.347877997268984	5	FACETS	0.953	0.893	1	0.953	0.893	1	CLONAL	3	TRUE	2	0.347877997268984	5		448	716	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12043924	12043924	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	59	397	0	ENST00000396373.4:c.1303G>C	p.Glu435Gln	p.E435Q	ENST00000396373	NM_001987.4	435	Gag/Cag	8/8	0.347877997268984	4	FACETS	0.671	0.577	0.775	0.336	0.288	0.388	SUBCLONAL	1	TRUE	2	0.347877997268984	4		397	681	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105872	27105872	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0066293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	184	454	0	ENST00000324856.7:c.5483C>G	p.Ser1828Ter	p.S1828*	ENST00000324856	NM_006015.4	1828	tCa/tGa	20/20	0.347877997268984	3	FACETS	0.928	0.86	0.998	0.928	0.86	0.998	CLONAL	2	TRUE	1	0.347877997268984	3		454	669	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41558754	41558754	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	70	279	0	ENST00000263253.7:c.3699G>T	p.Lys1233Asn	p.K1233N	ENST00000263253	NM_001429.3	1233	aaG/aaT	21/31	0.347877997268984	3	FACETS	0.958	0.837	1	0.479	0.418	0.544	CLONAL	1	TRUE	1	0.347877997268984	3		279	493	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991631	72991631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751779532	NA	P-0066293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	59	527	0	ENST00000268489.5:c.2414G>A	p.Arg805Gln	p.R805Q	ENST00000268489	NM_006885.3	805	cGg/cAg	2/10	0.177728604108339	5	FACETS	0.823	0.708	0.949	0.274	0.236	0.317	INDETERMINATE	1	TRUE	2	0.347877997268984	5		527	627	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442533	49442533	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	69	412	0	ENST00000301067.7:c.4040C>G	p.Ser1347Cys	p.S1347C	ENST00000301067	NM_003482.3	1347	tCt/tGt	13/54	0.322898183553364	4	FACETS	0.881	0.767	1	0.44	0.383	0.502	CLONAL	1	TRUE	2	0.347877997268984	4		412	607	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061577	38061578	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATGA	novel	NA	P-0066293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	48	437	0	ENST00000250448.2:c.411_412insTCAT	p.Met138SerfsTer90	p.M138Sfs*90	ENST00000250448	NM_004496.3	137	-/TCAT	2/2	0.29038980686974	3	FACETS	0.624	0.528	0.731	0.312	0.264	0.366	SUBCLONAL	1	TRUE	1	0.347877997268984	3		437	519	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135777005	135777005	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	185	317	0	ENST00000298552.3:c.2473G>T	p.Glu825Ter	p.E825*	ENST00000298552	NM_001162426.1	825	Gag/Tag	19/23	0.246238297047055	3	FACETS	0.853	0.795	0.912	0.853	0.795	0.912	CLONAL	3	TRUE	0	0.347877997268984	3		317	488	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023006	31023006	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777338946	NA	P-0066293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	134	479	0	ENST00000375687.4:c.2491C>T	p.Leu831Phe	p.L831F	ENST00000375687	NM_015338.5	831	Ctt/Ttt	13/13	0.347877997268984	3	FACETS	1	0.974	1	0.595	0.541	0.652	CLONAL	1	TRUE	1	0.347877997268984	3		479	760	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246490622	246490622	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755188670	NA	P-0066293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	43	372	0	ENST00000388985.4:c.412G>A	p.Glu138Lys	p.E138K	ENST00000388985		138	Gaa/Aaa	5/12	0.347877997268984	4	FACETS	0.516	0.431	0.611			1	SUBCLONAL	1	TRUE	NA	0.347877997268984	4		372	646	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572203	64572203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	97	542	1	ENST00000312049.6:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000312049	NM_130799.2	479	cGg/cAg	10/10	0.142570380155013	4	FACETS	1	0.961	1	0.584	0.521	0.65	INDETERMINATE	1	TRUE	2	0.347877997268984	4		543	644	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445458	49445458	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	86	596	0	ENST00000301067.7:c.2008C>T	p.Pro670Ser	p.P670S	ENST00000301067	NM_003482.3	670	Ccc/Tcc	10/54	0.322898183553364	4	FACETS	0.841	0.744	0.946	0.421	0.372	0.473	CLONAL	1	TRUE	2	0.347877997268984	4		596	792	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730114	41730114	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	84	446	0	ENST00000242208.4:c.415G>C	p.Glu139Gln	p.E139Q	ENST00000242208	NM_002192.2	139	Gag/Cag	3/3	0.22048397690668	5	FACETS	1	0.945	1	0.373	0.329	0.42	CLONAL	1	TRUE	2	0.347877997268984	5		446	657	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536160	41536160	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	60	356	0	ENST00000263253.7:c.1777C>A	p.Pro593Thr	p.P593T	ENST00000263253	NM_001429.3	593	Cct/Act	9/31	0.347877997268984	3	FACETS	0.803	0.693	0.923	0.402	0.346	0.462	CLONAL	1	TRUE	1	0.347877997268984	3		356	504	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023799	31023799	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs746598633	NA	P-0066293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	110	502	0	ENST00000375687.4:c.3284C>G	p.Ser1095Cys	p.S1095C	ENST00000375687	NM_015338.5	1095	tCc/tGc	13/13	0.347877997268984	3	FACETS	1	0.946	1	0.54	0.485	0.597	CLONAL	1	TRUE	1	0.347877997268984	3		502	688	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024488	31024488	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	124	462	0	ENST00000375687.4:c.3973C>A	p.Leu1325Ile	p.L1325I	ENST00000375687	NM_015338.5	1325	Ctt/Att	13/13	0.347877997268984	3	FACETS	1	0.982	1	0.682	0.618	0.748	CLONAL	1	TRUE	1	0.347877997268984	3		462	614	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578175	7578175	+	splice_donor_variant	Splice_Site	SNP	A	A	T	rs1555525703	NA	P-0066295-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	321	494	0	ENST00000269305.4:c.672+2T>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		494	542	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645904	67645904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266478000	NA	P-0066295-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	294	462	0	ENST00000264010.4:c.832C>T	p.Arg278Cys	p.R278C	ENST00000264010	NM_006565.3	278	Cgt/Tgt	4/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		462	460	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211387	36211387	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066295-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	126	484	0	ENST00000222270.7:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000222270	NM_014727.1	380	Gag/Cag	3/37	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		484	707	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023222	33023222	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066295-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	174	506	0	ENST00000300177.4:c.331C>A	p.Arg111Ser	p.R111S	ENST00000300177	NM_001191322.1	111	Cgc/Agc	2/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		506	525	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39613853	39613853	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066295-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	129	431	0	ENST00000262039.4:c.1771A>T	p.Ile591Phe	p.I591F	ENST00000262039	NM_002647.2	591	Atc/Ttc	16/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		431	296	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038826	47038826	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066295-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	267	383	0	ENST00000377604.3:c.835del	p.Gln279ArgfsTer29	p.Q279Rfs*29	ENST00000377604	NM_001204468.1	278	gCc/gc	9/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		383	692	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524307	148524307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066295-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	149	421	0	ENST00000320356.2:c.677C>T	p.Ala226Val	p.A226V	ENST00000320356	NM_004456.4	226	gCc/gTc	7/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		421	444	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639929	93639929	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066295-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	134	410	0	ENST00000375746.1:c.1258G>A	p.Glu420Lys	p.E420K	ENST00000375746	NM_001174167.1	420	Gaa/Aaa	10/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		410	599	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099136	157099136	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	89	409	0	ENST00000346085.5:c.73C>G	p.Leu25Val	p.L25V	ENST00000346085	NM_020732.3	25	Ctc/Gtc	1/20	0.480175613463529	6	FACETS	0.912	0.808	1			1	CLONAL	1	TRUE	NA	0.480175613463529	6		409	797	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936768	78936768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs987417975	NA	P-0066301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	123	589	0	ENST00000306801.3:c.3850G>A	p.Gly1284Arg	p.G1284R	ENST00000306801	NM_020761.2	1284	Gga/Aga	33/34	0.461699955267492	3	FACETS	0.879	0.795	0.966	0.293	0.265	0.322	CLONAL	1	TRUE	0	0.480175613463529	3		589	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578515	7578516	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCCAGTTGGCAAAACATCTTGTTGAG	novel	NA	P-0066301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	261	518	0	ENST00000269305.4:c.388_414dup	p.Leu130_Ala138dup	p.L130_A138dup	ENST00000269305	NM_001126112.2	130	-/CTCAACAAGATGTTTTGCCAACTGGCC	5/11	0.461699955267492	3	FACETS	0.842	0.791	0.893	0.561	0.527	0.595	CLONAL	2	TRUE	0	0.480175613463529	3		518	801	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445178	49445178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771291128	NA	P-0066301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	162	702	0	ENST00000301067.7:c.2288C>T	p.Pro763Leu	p.P763L	ENST00000301067	NM_003482.3	763	cCg/cTg	10/54	0.302683472706336	5	FACETS	1	0.978	1	0.397	0.364	0.432	CLONAL	1	TRUE	2	0.480175613463529	5		702	975	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679174	88679174	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	107	452	0	ENST00000360948.2:c.863A>C	p.Asn288Thr	p.N288T	ENST00000360948	NM_001012338.2	288	aAc/aCc	8/19	0.447472020239955	3	FACETS	0.999	0.899	1	0.5	0.449	0.553	CLONAL	1	TRUE	1	0.480175613463529	3		452	553	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36989325	36989325	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs372925758	NA	P-0066301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	31	465	0	ENST00000354822.5:c.10G>T	p.Gly4Ter	p.G4*	ENST00000354822	NM_001079668.2	4	Gga/Tga	1/3	0.432095383506816	3	FACETS	0.275	0.222	0.336			1	SUBCLONAL	1	TRUE	NA	0.480175613463529	3		465	582	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862879	9862879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	94	428	0	ENST00000330684.3:c.2424G>A	p.Met808Ile	p.M808I	ENST00000330684	NM_001134407.1	808	atG/atA	12/13	NA	2	FACETS	0.824	0.737	0.917			1	INDETERMINATE	1	TRUE	NA	0.480175613463529	2		428	475	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69012074	69012074	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	39	318	0	ENST00000288368.4:c.2711A>C	p.Lys904Thr	p.K904T	ENST00000288368	NM_024870.2	904	aAa/aCa	23/40	0.483316422143124	5	FACETS	0.653	0.541	0.777	0.163	0.135	0.195	SUBCLONAL	1	TRUE	1	0.480175613463529	5		318	428	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	29	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.483	0.388	0.592	0.483	0.388	0.592	SUBCLONAL	1	TRUE	1	0.32	2		341	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs747342068	NA	P-0066304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	59	412	0	ENST00000269305.4:c.394A>C	p.Lys132Gln	p.K132Q	ENST00000269305	NM_001126112.2	132	Aag/Cag	5/11	1	2	FACETS	0.496	0.426	0.573	0.496	0.426	0.573	SUBCLONAL	1	TRUE	1	0.32	2		412	743	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959067	2959067	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376539147	NA	P-0066304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	53	404	0	ENST00000396946.4:c.2449G>A	p.Ala817Thr	p.A817T	ENST00000396946	NM_032415.4	817	Gcg/Acg	18/25	1	2	FACETS	0.533	0.454	0.619	0.533	0.454	0.619	SUBCLONAL	1	TRUE	1	0.32	2		404	622	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066305-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	133	446	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.959	0.881	1	0.959	0.881	1	CLONAL	1	TRUE	1	0.743436573837907	2		446	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066305-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	441	252	0	ENST00000269305.4:c.380C>A	p.Ser127Tyr	p.S127Y	ENST00000269305	NM_001126112.2	127	tCc/tAc	5/11	0.716076360349698	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.743436573837907	2		252	581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0066306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	379	630	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.646971065223138	2	FACETS	0.988	0.951	1	0.988	0.951	1	CLONAL	2	TRUE	0	0.646971065223138	2		630	593	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087944	27087944	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0066306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	127	443	0	ENST00000324856.7:c.2231C>G	p.Ser744Ter	p.S744*	ENST00000324856	NM_006015.4	744	tCa/tGa	6/20	0.646971065223138	3	FACETS	0.973	0.886	1	0.487	0.443	0.532	CLONAL	1	TRUE	1	0.646971065223138	3		443	534	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913381	NA	P-0066306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	343	461	0	ENST00000304494.5:c.322G>T	p.Asp108Tyr	p.D108Y	ENST00000304494	NM_000077.4	108	Gat/Tat	2/3	0.646971065223138	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.646971065223138	2		461	526	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379426	225379426	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	128	358	0	ENST00000264414.4:c.442C>T	p.Arg148Ter	p.R148*	ENST00000264414	NM_003590.4	148	Cga/Tga	4/16	0.241194597759546	4	FACETS	0.91	0.835	0.987	0.91	0.835	0.987	INDETERMINATE	2	TRUE	2	0.646971065223138	4		358	358	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610499	10610499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs541663797	NA	P-0066306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	302	446	0	ENST00000171111.5:c.211C>T	p.Arg71Trp	p.R71W	ENST00000171111	NM_203500.1	71	Cgg/Tgg	2/6	0.646971065223138	2	FACETS	0.993	0.952	1	0.993	0.952	1	CLONAL	2	TRUE	0	0.646971065223138	2		446	470	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763447	41763447	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	323	489	0	ENST00000301178.4:c.2246C>T	p.Pro749Leu	p.P749L	ENST00000301178	NM_021913.4	749	cCa/cTa	19/20	0.646971065223138	4	FACETS	0.958	0.909	1	0.958	0.909	1	CLONAL	2	TRUE	2	0.646971065223138	4		489	858	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241084	39241084	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730881024	NA	P-0066306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	197	320	0	ENST00000402219.2:c.1987A>G	p.Ile663Val	p.I663V	ENST00000402219	NM_005633.3	663	Ata/Gta	12/23	0.644601827295433	4	FACETS	0.987	0.922	1	0.987	0.922	1	CLONAL	2	TRUE	2	0.646971065223138	4		320	508	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464953	120464953	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	124	415	0	ENST00000256646.2:c.5119G>T	p.Gly1707Cys	p.G1707C	ENST00000256646	NM_024408.3	1707	Ggc/Tgc	28/34	0.646971065223138	3	FACETS	0.919	0.835	1	0.46	0.417	0.504	CLONAL	1	TRUE	1	0.646971065223138	3		415	552	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533378	29533378	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs878853865	NA	P-0066306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	132	394	0	ENST00000356175.3:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000356175	NM_000267.3	461	Cga/Tga	12/57	0.424861605359718	4	FACETS	1	0.957	1	0.543	0.494	0.594	CLONAL	1	TRUE	2	0.646971065223138	4		394	619	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250440	26250440	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	186	571	0	ENST00000446824.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000446824	NM_021018.2	132	Cgc/Ggc	1/1	0.646971065223138	3	FACETS	0.948	0.877	1	0.316	0.292	0.341	CLONAL	1	TRUE	0	0.646971065223138	3		571	803	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005299	29005299	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	253	325	0	ENST00000282397.4:c.962C>G	p.Ser321Cys	p.S321C	ENST00000282397	NM_002019.4	321	tCt/tGt	7/30	0.625652855045125	3	FACETS	0.948	0.908	0.986	0.948	0.908	0.986	CLONAL	3	TRUE	0	0.646971065223138	3		325	364	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177993	56177993	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	284	474	0	ENST00000399503.3:c.2966C>A	p.Ser989Tyr	p.S989Y	ENST00000399503	NM_005921.1	989	tCt/tAt	14/20	0.570876157580908	3	FACETS	1	0.988	1	0.743	0.708	0.779	CLONAL	2	TRUE	0	0.646971065223138	3		474	521	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105598	11105598	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	327	460	0	ENST00000358026.2:c.1515del	p.Thr506ArgfsTer107	p.T506Rfs*107	ENST00000358026	NM_001128849.1	505	gCc/gc	9/36	0.646971065223138	2	FACETS	0.966	0.927	1	0.966	0.927	1	CLONAL	2	TRUE	0	0.646971065223138	2		460	523	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326518	161326518	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	107	126	0	ENST00000367975.2:c.293C>G	p.Ser98Cys	p.S98C	ENST00000367975	NM_003001.3	98	tCt/tGt	5/6	0.646971065223138	5	FACETS	1	0.972	1	0.779	0.709	0.849	CLONAL	2	TRUE	2	0.646971065223138	5		126	279	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456895	149456895	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	348	532	0	ENST00000286301.3:c.833G>C	p.Cys278Ser	p.C278S	ENST00000286301	NM_005211.3	278	tGc/tCc	6/22	0.646971065223138	2	FACETS	0.973	0.934	1	0.973	0.934	1	CLONAL	2	TRUE	0	0.646971065223138	2		532	553	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390219	89390219	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	211	389	0	ENST00000336596.2:c.968C>A	p.Thr323Asn	p.T323N	ENST00000336596	NM_005233.5	323	aCc/aAc	4/17	0.501936159023836	4	FACETS	0.921	0.862	0.982	0.921	0.862	0.982	CLONAL	2	TRUE	2	0.646971065223138	4		389	583	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937973	36937973	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	334	626	0	ENST00000361632.4:c.863A>T	p.Glu288Val	p.E288V	ENST00000361632		288	gAg/gTg	7/16	0.646971065223138	3	FACETS	0.99	0.944	1	0.99	0.944	1	CLONAL	2	TRUE	1	0.646971065223138	3		626	690	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212154	5212154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	47	558	0	ENST00000357368.4:c.4877C>T	p.Ser1626Phe	p.S1626F	ENST00000357368	NM_002850.3	1626	tCc/tTc	32/38	0.646971065223138	2	FACETS	0.317	0.268	0.372	0.159	0.134	0.186	SUBCLONAL	1	TRUE	0	0.646971065223138	2		558	458	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212140	5212140	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1455190303	NA	P-0066306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	48	560	0	ENST00000357368.4:c.4891A>G	p.Met1631Val	p.M1631V	ENST00000357368	NM_002850.3	1631	Atg/Gtg	32/38	0.646971065223138	2	FACETS	0.319	0.27	0.373	0.16	0.135	0.187	SUBCLONAL	1	TRUE	0	0.646971065223138	2		560	465	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10794131	10794131	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	25	393	0	ENST00000361367.2:c.2509G>C	p.Glu837Gln	p.E837Q	ENST00000361367	NM_014633.3	837	Gaa/Caa	20/25	0.588670592973958	2	FACETS	0.2	0.157	0.249	0.1	0.078	0.125	SUBCLONAL	1	TRUE	0	0.646971065223138	2		393	387	SUCCESS
ATM	472	MSKCC	GRCh37	11	108127063	108127063	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	25	267	0	ENST00000278616.4:c.2246C>G	p.Ala749Gly	p.A749G	ENST00000278616	NM_000051.3	749	gCc/gGc	14/63	0.557487980729848	3	FACETS	0.304	0.24	0.379	0.152	0.12	0.19	SUBCLONAL	1	TRUE	1	0.646971065223138	3		267	336	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432237	49432237	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	324	588	0	ENST00000301067.7:c.8902C>G	p.Pro2968Ala	p.P2968A	ENST00000301067	NM_003482.3	2968	Ccg/Gcg	34/54	0.646971065223138	3	FACETS	0.885	0.841	0.929	0.885	0.841	0.929	CLONAL	2	TRUE	1	0.646971065223138	3		588	749	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827897	170827897	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	181	243	0	ENST00000296930.5:c.637G>C	p.Asp213His	p.D213H	ENST00000296930	NM_002520.6	213	Gac/Cac	8/11	0.646971065223138	2	FACETS	0.945	0.893	0.997	0.945	0.893	0.997	CLONAL	2	TRUE	0	0.646971065223138	2		243	296	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012416	152012416	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	94	393	0	ENST00000262189.6:c.397C>A	p.Leu133Ile	p.L133I	ENST00000262189	NM_170606.2	133	Ctc/Atc	4/59	0.241194597759546	4	FACETS	1	0.917	1	0.515	0.46	0.572	INDETERMINATE	1	TRUE	2	0.646971065223138	4		393	465	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46255786	46255786	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	126	323	0	ENST00000371998.3:c.398A>T	p.Asn133Ile	p.N133I	ENST00000371998		133	aAc/aTc	6/23	0.555944579866693	4	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.646971065223138	4		323	443	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225338987	225338987	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs766471279	NA	P-0066306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	161	334	0	ENST00000264414.4:c.2282G>T	p.Arg761Leu	p.R761L	ENST00000264414	NM_003590.4	761	cGc/cTc	16/16	0.241194597759546	4	FACETS	1	0.932	1	1	0.932	1	INDETERMINATE	2	TRUE	2	0.646971065223138	4		334	408	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444943	49444996	+	inframe_deletion	In_Frame_Del	DEL	GCATGGCTCCTCAGACTGGGGGGACAGGTGTGATTCCTCAGGTTGGGGGGACAA	GCATGGCTCCTCAGACTGGGGGGACAGGTGTGATTCCTCAGGTTGGGGGGACAA	-	rs1565816363	NA	P-0066306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	224	529	0	ENST00000301067.7:c.2470_2523del	p.Gln827_Pro844del	p.Q827_P844del	ENST00000301067	NM_003482.3	824	TTGTCCCCCCAACCTGAGGAATCACACCTGTCCCCCCAGTCTGAGGAGCCATGC/-	10/54	0.646971065223138	3	FACETS	1	0.99	1	0.657	0.615	0.701	CLONAL	1	TRUE	1	0.646971065223138	3		529	697	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502708	149502708	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	341	444	0	ENST00000261799.4:c.2080C>A	p.His694Asn	p.H694N	ENST00000261799	NM_002609.3	694	Cac/Aac	15/23	0.646971065223138	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.646971065223138	2		444	496	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880998	37880998	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs144434331	NA	P-0066307-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	24	483	0	ENST00000269571.5:c.2327G>T	p.Gly776Val	p.G776V	ENST00000269571		776	gGt/gTt	20/27	1	2	FACETS	0.201	0.156	0.253	0.201	0.156	0.253	SUBCLONAL	1	TRUE	1	0.20470855597636	2		483	1166	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988262	36988262	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066307-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	135	423	0	ENST00000354822.5:c.391C>T	p.Gln131Ter	p.Q131*	ENST00000354822	NM_001079668.2	131	Cag/Tag	2/3	1	2	FACETS	0.928	0.844	1	1	0.99	1	CLONAL	2	TRUE	1	0.20470855597636	2		423	711	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986975	36986975	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066307-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	115	380	0	ENST00000354822.5:c.714G>C	p.Trp238Cys	p.W238C	ENST00000354822	NM_001079668.2	238	tgG/tgC	3/3	1	2	FACETS	0.87	0.785	0.959	1	0.987	1	CLONAL	2	TRUE	1	0.20470855597636	2		380	646	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874287	155874290	+	protein_altering_variant	In_Frame_Del	DEL	ACTC	ACTC	T	novel	NA	P-0066307-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	85	329	0	ENST00000368323.3:c.241_244delinsA	p.Glu81_Phe82delinsIle	p.E81_F82delinsI	ENST00000368323	NM_006912.5	81	GAGTtt/Att	5/6	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.20470855597636	2		329	706	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	50	446	0				ENST00000310581	NM_198253.2	-/1132			0.362276224178017	6	FACETS	0.872	0.745	1	0.581	0.497	0.673	CLONAL	2	TRUE	3	0.362276224178017	6		446	273	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935669	15935669	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	97	338	0	ENST00000268712.3:c.7264C>T	p.Arg2422Ter	p.R2422*	ENST00000268712	NM_006311.3	2422	Cga/Tga	46/46	0.292275539394445	4	FACETS	1	0.972	1	0.633	0.566	0.705	CLONAL	1	TRUE	2	0.362276224178017	4		338	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	313	252	0	ENST00000269305.4:c.380C>A	p.Ser127Tyr	p.S127Y	ENST00000269305	NM_001126112.2	127	tCc/tAc	5/11	0.362276224178017	5	FACETS	1	0.986	1			1	CLONAL	4	TRUE	NA	0.362276224178017	5		252	611	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955550	48955550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913304	NA	P-0066310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	81	228	0	ENST00000267163.4:c.1666C>T	p.Arg556Ter	p.R556*	ENST00000267163	NM_000321.2	556	Cga/Tga	17/27	0.19262972397472	4	FACETS	0.823	0.73	0.921			1	INDETERMINATE	2	TRUE	NA	0.362276224178017	4		228	370	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906786	50906786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778843530	NA	P-0066310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	141	165	0	ENST00000440232.2:c.1174G>A	p.Val392Met	p.V392M	ENST00000440232	NM_002691.3	392	Gtg/Atg	10/27	0.210393842502367	4	FACETS	0.852	0.784	0.922	0.639	0.588	0.691	INDETERMINATE	3	TRUE	0	0.362276224178017	4		165	415	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227854	55227854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1166858113	NA	P-0066310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	91	223	0	ENST00000275493.2:c.1321G>A	p.Val441Ile	p.V441I	ENST00000275493	NM_005228.3	441	Gtc/Atc	12/28	0.376283879891713	4	FACETS	0.827	0.738	0.919	0.827	0.738	0.919	CLONAL	2	TRUE	2	0.362276224178017	4		223	414	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557762	21557762	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1172808550	NA	P-0066310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	121	250	0	ENST00000382592.4:c.2083G>A	p.Ala695Thr	p.A695T	ENST00000382592	NM_014572.2	695	Gcc/Acc	5/8	0.292275539394445	4	FACETS	0.826	0.749	0.906	0.826	0.749	0.906	CLONAL	2	TRUE	2	0.362276224178017	4		250	551	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553478	29553478	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781807	NA	P-0066310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	115	370	1	ENST00000356175.3:c.2033del	p.Pro678ArgfsTer10	p.P678Rfs*10	ENST00000356175	NM_000267.3	676	aCc/ac	18/57	0.292275539394445	4	FACETS	0.802	0.726	0.883	0.802	0.726	0.883	CLONAL	2	TRUE	2	0.362276224178017	4		371	539	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981832	63981832	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	177	361	1	ENST00000398590.3:c.2340del	p.Thr781ProfsTer11	p.T781Pfs*11	ENST00000398590	NM_001177387.1	778	ggC/gg	12/14	0.372146591428421	2	FACETS	0.999	0.929	1	0.999	0.929	1	CLONAL	2	TRUE	0	0.362276224178017	2		362	489	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280263	142280263	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	97	225	0	ENST00000350721.4:c.1171T>C	p.Tyr391His	p.Y391H	ENST00000350721	NM_001184.3	391	Tac/Cac	5/47	0.376283879891713	4	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	2	0.362276224178017	4		225	351	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2110313	2110313	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	131	306	0	ENST00000349721.2:c.3352C>T	p.Gln1118Ter	p.Q1118*	ENST00000349721	NM_003070.3	1118	Cag/Tag	24/34	0.189969860130881	4	FACETS	1	0.932	1	1	0.932	1	INDETERMINATE	2	TRUE	2	0.362276224178017	4		306	481	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123260399	123260399	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	51	226	0	ENST00000358487.5:c.1502T>C	p.Val501Ala	p.V501A	ENST00000358487	NM_000141.4	501	gTg/gCg	11/18	0.352654532924955	2	FACETS	0.706	0.601	0.82	0.353	0.3	0.41	SUBCLONAL	1	TRUE	0	0.362276224178017	2		226	399	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942855	44942855	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0066310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	100	101	0	ENST00000377967.4:c.3433+2T>C		p.X1145_splice	ENST00000377967	NM_021140.2	1145			0.19262972397472	2	FACETS	0.979	0.899	1			1	INDETERMINATE	3	TRUE	NA	0.362276224178017	2		101	188	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325831	30325831	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	122	290	0	ENST00000322652.5:c.2029G>T	p.Ala677Ser	p.A677S	ENST00000322652	NM_015355.2	677	Gct/Tct	16/16	0.292275539394445	4	FACETS	0.989	0.9	1	0.989	0.9	1	CLONAL	2	TRUE	2	0.362276224178017	4		290	464	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55597557	55597557	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	43	260	0	ENST00000288135.5:c.2205G>T	p.Lys735Asn	p.K735N	ENST00000288135	NM_000222.2	735	aaG/aaT	15/21	0.352654532924955	2	FACETS	0.873	0.735	1	0.436	0.367	0.512	CLONAL	1	TRUE	0	0.362276224178017	2		260	272	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759964	133759964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1394145426	NA	P-0066310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	142	149	0	ENST00000318560.5:c.2287C>T	p.Pro763Ser	p.P763S	ENST00000318560	NM_005157.4	763	Cct/Tct	11/11	0.362276224178017	5	FACETS	0.871	0.8	0.944			1	CLONAL	3	TRUE	NA	0.362276224178017	5		149	463	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527578	41527578	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	87	291	0	ENST00000263253.7:c.1469A>C	p.Asn490Thr	p.N490T	ENST00000263253	NM_001429.3	490	aAc/aCc	6/31	0.274478373176644	3	FACETS	1	0.966	1	0.41	0.364	0.459	CLONAL	1	TRUE	0	0.362276224178017	3		291	461	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090024	37090024	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1352164825	NA	P-0066310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	153	253	0	ENST00000231790.2:c.1913G>T	p.Gly638Val	p.G638V	ENST00000231790	NM_000249.3	638	gGa/gTa	17/19	0.373149471721636	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.362276224178017	2		253	374	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226553713	226553713	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	57	195	0	ENST00000366794.5:c.2447A>C	p.Lys816Thr	p.K816T	ENST00000366794	NM_001618.3	816	aAg/aCg	18/23	0.189969860130881	4	FACETS	0.974	0.838	1	0.487	0.419	0.561	INDETERMINATE	1	TRUE	2	0.362276224178017	4		195	440	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416428	49416428	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	73	258	0	ENST00000301067.7:c.16283G>A	p.Gly5428Asp	p.G5428D	ENST00000301067	NM_003482.3	5428	gGc/gAc	51/54	0.175543995814588	3	FACETS	1	0.915	1	0.527	0.462	0.596	INDETERMINATE	1	TRUE	1	0.362276224178017	3		258	452	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819228	3819229	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	91	219	0	ENST00000262367.5:c.3006dup	p.Ala1003SerfsTer5	p.A1003Sfs*5	ENST00000262367	NM_004380.2	1002	-/A	15/31	0.180228937044959	5	FACETS	0.953	0.851	1			1	INDETERMINATE	2	TRUE	NA	0.362276224178017	5		219	407	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124510996	124510996	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	63	144	0	ENST00000357628.3:c.224del	p.Asn75MetfsTer10	p.N75Mfs*10	ENST00000357628	NM_015450.2	75	aAt/at	7/19	0.128677877554148	4	FACETS	0.837	0.731	0.95	0.837	0.731	0.95	INDETERMINATE	2	TRUE	2	0.362276224178017	4		144	283	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0066311-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	141	624	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.95	0.875	1	1	0.993	1	CLONAL	4	TRUE	1	0.190797148999519	2		624	389	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0066311-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	242	810	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.190797148999519	8	FACETS	0.961	0.913	1	1	0.995	1	CLONAL	10	TRUE	2	0.190797148999519	8		810	415	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151625	55151625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571523023	NA	P-0066311-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	79	315	0	ENST00000257290.5:c.2411G>A	p.Arg804Gln	p.R804Q	ENST00000257290	NM_006206.4	804	cGa/cAa	17/23	1	2	FACETS	0.958	0.858	1	1	0.989	1	CLONAL	4	TRUE	1	0.190797148999519	2		315	216	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0066311-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	69	317	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	1	0.935	1	1	0.988	1	CLONAL	4	TRUE	1	0.190797148999519	2		317	169	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325170	123325170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371358242	NA	P-0066311-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	148	458	0	ENST00000358487.5:c.158C>T	p.Ala53Val	p.A53V	ENST00000358487	NM_000141.4	53	gCg/gTg	3/18	1	2	FACETS	1	0.929	1	1	0.994	1	CLONAL	4	TRUE	1	0.190797148999519	2		458	386	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588877	69588877	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1179344852	NA	P-0066311-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	70	441	0	ENST00000168712.1:c.359C>T	p.Pro120Leu	p.P120L	ENST00000168712	NM_002007.2	120	cCc/cTc	2/3	1	2	FACETS	0.913	0.81	1	1	0.987	1	CLONAL	4	TRUE	1	0.190797148999519	2		441	201	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265565	152265565	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066311-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	120	424	0	ENST00000206249.3:c.1018G>T	p.Ala340Ser	p.A340S	ENST00000206249	NM_000125.3	340	Gct/Tct	4/8	0.190797148999519	7	FACETS	1	0.946	1	0.704	0.64	0.77	CLONAL	4	TRUE	1	0.190797148999519	7		424	440	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556254	29556254	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066311-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	134	443	0	ENST00000356175.3:c.2621A>C	p.Lys874Thr	p.K874T	ENST00000356175	NM_000267.3	874	aAg/aCg	21/57	1	2	FACETS	0.927	0.857	0.998	1	0.994	1	CLONAL	5	TRUE	1	0.190797148999519	2		443	303	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533011	63533012	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCTCA	novel	NA	P-0066311-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	141	444	0	ENST00000307078.5:c.1878_1882dup	p.Arg628LeufsTer63	p.R628Lfs*63	ENST00000307078	NM_004655.3	628	cgg/cTGAGCgg	7/11	1	2	FACETS	0.941	0.872	1	1	0.994	1	CLONAL	5	TRUE	1	0.190797148999519	2		444	314	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97869460	97869460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066311-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	156	468	1	ENST00000289081.3:c.1421G>A	p.Gly474Asp	p.G474D	ENST00000289081	NM_000136.2	474	gGc/gAc	14/15	1	2	FACETS	1	0.963	1	1	0.994	1	CLONAL	4	TRUE	1	0.190797148999519	2		469	385	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298090	15298090	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066311-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	97	470	0	ENST00000263388.2:c.1666C>A	p.His556Asn	p.H556N	ENST00000263388	NM_000435.2	556	Cat/Aat	11/33	1	2	FACETS	1	0.956	1	1	0.991	1	CLONAL	4	TRUE	1	0.190797148999519	2		470	234	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964905	25964907	+	inframe_deletion	In_Frame_Del	DEL	ACG	ACG	-	novel	NA	P-0066311-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	131	417	0	ENST00000435504.4:c.4299_4301del	p.Val1434del	p.V1434del	ENST00000435504		1433	gtCGTt/gtt	13/13	1	2	FACETS	1	0.931	1	1	0.993	1	CLONAL	4	TRUE	1	0.190797148999519	2		417	339	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052720	42052720	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066311-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	72	337	0	ENST00000219905.7:c.7391T>A	p.Leu2464His	p.L2464H	ENST00000219905	NM_001164273.1	2464	cTt/cAt	20/24	1	2	FACETS	1	0.954	1	1	0.987	1	CLONAL	3	TRUE	1	0.190797148999519	2		337	219	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0066312-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	30	413	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		413	385	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005006	150005006	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066312-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	58	474	0	ENST00000253339.5:c.1219C>T	p.Gln407Ter	p.Q407*	ENST00000253339		407	Cag/Tag	3/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		474	478	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470569	25470569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066312-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	50	432	0	ENST00000264709.3:c.905G>A	p.Gly302Asp	p.G302D	ENST00000264709	NM_175629.2	302	gGc/gAc	8/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		432	446	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004976	150004976	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs748618436	NA	P-0066312-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	54	490	0	ENST00000253339.5:c.1249C>G	p.His417Asp	p.H417D	ENST00000253339		417	Cat/Gat	3/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		490	439	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6213182	6213182	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0066312-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	21	403	0	ENST00000252674.7:c.1552-1G>A		p.X518_splice	ENST00000252674	NM_005934.3	518			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		403	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0066324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	123	545	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		546	368	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924333	112924333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	105	422	0	ENST00000351677.2:c.1279G>A	p.Gly427Ser	p.G427S	ENST00000351677	NM_002834.3	427	Ggc/Agc	11/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		422	498	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0066324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	104	418	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		418	376	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554662	63554662	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	299	511	0	ENST00000307078.5:c.77T>C	p.Val26Ala	p.V26A	ENST00000307078	NM_004655.3	26	gTg/gCg	2/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		511	654	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509914	187509914	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	56	444	0	ENST00000441802.2:c.13599G>C	p.Glu4533Asp	p.E4533D	ENST00000441802	NM_005245.3	4533	gaG/gaC	27/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		444	595	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510177	187510177	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	55	457	0	ENST00000441802.2:c.13336G>A	p.Asp4446Asn	p.D4446N	ENST00000441802	NM_005245.3	4446	Gat/Aat	27/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		457	633	SUCCESS
APC	324	MSKCC	GRCh37	5	112175133	112175133	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0066324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	100	378	0	ENST00000257430.4:c.3842C>G	p.Ser1281Ter	p.S1281*	ENST00000257430	NM_000038.5	1281	tCa/tGa	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		378	416	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965672	90965672	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0066324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	37	344	0	ENST00000265433.3:c.1645A>T	p.Lys549Ter	p.K549*	ENST00000265433	NM_002485.4	549	Aaa/Taa	11/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		344	340	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226081	53226081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556837428	NA	P-0066324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	146	422	0	ENST00000375401.3:c.2768G>A	p.Arg923Gln	p.R923Q	ENST00000375401	NM_004187.3	923	cGg/cAg	19/26	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		422	508	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	64	446	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.908	0.794	1	0.908	0.794	1	CLONAL	1	TRUE	1	0.494377643989939	2		446	285	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0066325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	17	498	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.116	0.085	0.152	0.116	0.085	0.152	SUBCLONAL	1	TRUE	1	0.494377643989939	2		498	595	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926885	112926885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507544	NA	P-0066325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	112	385	0	ENST00000351677.2:c.1505C>T	p.Ser502Leu	p.S502L	ENST00000351677	NM_002834.3	502	tCa/tTa	13/16	1	2	FACETS	0.927	0.838	1	0.927	0.838	1	CLONAL	1	TRUE	1	0.494377643989939	2		385	489	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821930	59821930	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs200313471	NA	P-0066325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	104	326	0	ENST00000259008.2:c.2120G>T	p.Arg707Leu	p.R707L	ENST00000259008	NM_032043.2	707	cGt/cTt	15/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.494377643989939	2		326	366	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560097	29560097	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	78	409	0	ENST00000356175.3:c.3574G>T	p.Glu1192Ter	p.E1192*	ENST00000356175	NM_000267.3	1192	Gaa/Taa	27/57	1	2	FACETS	0.524	0.461	0.592	0.524	0.461	0.592	SUBCLONAL	1	TRUE	1	0.494377643989939	2		409	602	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045920	180045920	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	98	480	0	ENST00000261937.6:c.2851G>A	p.Glu951Lys	p.E951K	ENST00000261937	NM_182925.4	951	Gag/Aag	21/30	1	2	FACETS	0.979	0.879	1	0.979	0.879	1	CLONAL	1	TRUE	1	0.494377643989939	2		480	405	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157627	106157635	+	frameshift_variant	Frame_Shift_Del	DEL	AGAATAAAG	AGAATAAAG	CGAAT	novel	NA	P-0066326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	134	331	0	ENST00000380013.4:c.2528_2536delinsCGAAT	p.Glu843AlafsTer29	p.E843Afs*29	ENST00000380013	NM_001127208.2	843	gAGAATAAAGaa/gCGAATaa	3/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.429941403014212	2		331	586	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	220	797	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.699130968827798	2		797	589	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	125	478	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.818	0.746	0.893	0.818	0.746	0.893	CLONAL	1	TRUE	1	0.699130968827798	2		479	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	38	1113	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.133	0.109	0.16	0.133	0.109	0.16	SUBCLONAL	1	TRUE	1	0.699130968827798	2		1113	815	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	53	498	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.208	0.177	0.242	0.208	0.177	0.242	SUBCLONAL	1	TRUE	1	0.699130968827798	2		498	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	33	555	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	1	2	FACETS	0.113	0.091	0.138	0.113	0.091	0.138	SUBCLONAL	1	TRUE	1	0.699130968827798	2		555	835	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	225	324	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.942	0.882	1	0.942	0.882	1	CLONAL	1	TRUE	1	0.699130968827798	2		324	683	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	255	760	5	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.997	0.937	1	0.997	0.937	1	CLONAL	1	TRUE	1	0.699130968827798	2		765	732	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	310	535	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.699130968827798	2	FACETS	1	0.968	1	0.516	0.488	0.544	CLONAL	1	TRUE	0	0.699130968827798	2		535	860	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	185	455	4	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.764	0.707	0.822	0.764	0.707	0.822	SUBCLONAL	1	TRUE	1	0.699130968827798	2		459	693	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960080	134960080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1042786	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	50	489	1	ENST00000398015.3:c.2437G>A	p.Val813Ile	p.V813I	ENST00000398015	NM_004441.4	813	Gtc/Atc	13/16	1	2	FACETS	0.21	0.178	0.246	0.21	0.178	0.246	SUBCLONAL	1	TRUE	1	0.699130968827798	2		490	681	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	268	501	0	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.942	0.886	0.998	0.942	0.886	0.998	CLONAL	1	TRUE	1	0.699130968827798	2		501	814	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	209	298	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.699130968827798	2	FACETS	0.952	0.906	0.997	0.952	0.906	0.997	CLONAL	2	TRUE	0	0.699130968827798	2		298	314	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	247	563	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.892	0.837	0.949	0.892	0.837	0.949	CLONAL	1	TRUE	1	0.699130968827798	2		563	792	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39772519	39772519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	258	447	1	ENST00000288319.7:c.722C>T	p.Thr241Met	p.T241M	ENST00000288319	NM_182918.3	241	aCg/aTg	6/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.699130968827798	2		448	604	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783245	9783245	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756497515	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	167	453	0	ENST00000377346.4:c.2489G>A	p.Arg830His	p.R830H	ENST00000377346	NM_005026.3	830	cGt/cAt	20/24	1	2	FACETS	0.679	0.625	0.734	0.679	0.625	0.734	SUBCLONAL	1	TRUE	1	0.699130968827798	2		453	704	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087548	27087548	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	332	582	0	ENST00000324856.7:c.2122C>T	p.Gln708Ter	p.Q708*	ENST00000324856	NM_006015.4	708	Cag/Tag	5/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.699130968827798	2		582	844	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106100	27106100	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	186	580	0	ENST00000324856.7:c.5715del	p.Lys1905AsnfsTer18	p.K1905Nfs*18	ENST00000324856	NM_006015.4	1904	gAa/ga	20/20	1	2	FACETS	0.707	0.654	0.761	0.707	0.654	0.761	SUBCLONAL	1	TRUE	1	0.699130968827798	2		580	753	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317715	163317715	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199764107	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	21	370	0	ENST00000271452.3:c.1111C>T	p.Arg371Cys	p.R371C	ENST00000271452	NM_145697.2	371	Cgc/Tgc	12/14	1	2	FACETS	0.241	0.186	0.305	0.241	0.186	0.305	SUBCLONAL	1	TRUE	1	0.699130968827798	2		370	249	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850705	63850705	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs201178069	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	116	471	0	ENST00000279873.7:c.1489del	p.Ile497Ter	p.I497*	ENST00000279873	NM_032199.2	495	Aaa/aa	10/10	0.699130968827798	2	FACETS	0.498	0.45	0.55	0.249	0.225	0.275	SUBCLONAL	1	TRUE	0	0.699130968827798	2		471	666	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457820	69457822	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	97	351	0	ENST00000227507.2:c.227_229del	p.Glu76del	p.E76del	ENST00000227507	NM_053056.2	74	GAG/-	2/5	1	2	FACETS	0.607	0.544	0.674	0.607	0.544	0.674	SUBCLONAL	1	TRUE	1	0.699130968827798	2		351	457	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633481	69633481	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	118	391	0	ENST00000334134.2:c.220+1G>A		p.X74_splice	ENST00000334134	NM_005247.2	74			1	2	FACETS	0.562	0.508	0.618	0.562	0.508	0.618	SUBCLONAL	1	TRUE	1	0.699130968827798	2		391	601	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633607	69633607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	35	393	1	ENST00000334134.2:c.95G>A	p.Arg32His	p.R32H	ENST00000334134	NM_005247.2	32	cGt/cAt	1/3	1	2	FACETS	0.19	0.155	0.23	0.19	0.155	0.23	SUBCLONAL	1	TRUE	1	0.699130968827798	2		394	526	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	261	542	1	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.699130968827798	2		543	709	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	92	291	0	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	0.874	0.786	0.966	0.874	0.786	0.966	CLONAL	1	TRUE	1	0.699130968827798	2		291	301	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981861	101981863	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	254	519	0	ENST00000282441.5:c.286_288del	p.Phe96del	p.F96del	ENST00000282441	NM_001130145.2	94	tcCTTc/tcc	1/9	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.699130968827798	2		519	660	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158382	108158382	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781785	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	152	366	0	ENST00000278616.4:c.4049C>T	p.Thr1350Met	p.T1350M	ENST00000278616	NM_000051.3	1350	aCg/aTg	27/63	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.699130968827798	2		366	352	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398279	25398279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894365	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	12	330	0	ENST00000311936.3:c.40G>A	p.Val14Ile	p.V14I	ENST00000311936	NM_004985.3	14	Gta/Ata	2/5	0.163749632302133	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.699130968827798	0		330	256	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444729	49444729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199724002	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	296	591	0	ENST00000301067.7:c.2737G>A	p.Glu913Lys	p.E913K	ENST00000301067	NM_003482.3	913	Gag/Aag	10/54	1	2	FACETS	0.978	0.924	1	0.978	0.924	1	CLONAL	1	TRUE	1	0.699130968827798	2		591	866	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478816	56478816	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	232	437	0	ENST00000267101.3:c.272T>C	p.Met91Thr	p.M91T	ENST00000267101	NM_001982.3	91	aTg/aCg	3/28	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.699130968827798	2		437	633	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	222	464	5	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.825	0.77	0.881	0.825	0.77	0.881	CLONAL	1	TRUE	1	0.699130968827798	2		469	770	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435978	110435978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762132376	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	178	569	0	ENST00000375856.3:c.2423G>A	p.Arg808His	p.R808H	ENST00000375856	NM_003749.2	808	cGc/cAc	1/2	1	2	FACETS	0.752	0.696	0.811	0.752	0.696	0.811	SUBCLONAL	1	TRUE	1	0.699130968827798	2		569	677	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005368	42005368	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	216	496	0	ENST00000219905.7:c.3104C>A	p.Pro1035His	p.P1035H	ENST00000219905	NM_001164273.1	1035	cCt/cAt	9/24	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.699130968827798	2		496	608	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828024	72828024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200701402	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	201	539	1	ENST00000268489.5:c.8557G>A	p.Ala2853Thr	p.A2853T	ENST00000268489	NM_006885.3	2853	Gca/Aca	9/10	1	2	FACETS	0.768	0.713	0.824	0.768	0.713	0.824	SUBCLONAL	1	TRUE	1	0.699130968827798	2		540	749	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830902	72830903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	232	606	0	ENST00000268489.5:c.5677_5678dup	p.Asp1894GlyfsTer21	p.D1894Gfs*21	ENST00000268489	NM_006885.3	1893	agg/agAGg	9/10	1	2	FACETS	0.758	0.708	0.81	0.758	0.708	0.81	SUBCLONAL	1	TRUE	1	0.699130968827798	2		606	875	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991949	72991949	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs753977275	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	59	467	0	ENST00000268489.5:c.2096del	p.Gly699AlafsTer125	p.G699Afs*125	ENST00000268489	NM_006885.3	699	gGc/gc	2/10	1	2	FACETS	0.24	0.206	0.278	0.24	0.206	0.278	SUBCLONAL	1	TRUE	1	0.699130968827798	2		467	702	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs878854073	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	195	432	0	ENST00000269305.4:c.673-1G>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			1	2	FACETS	0.97	0.904	1	0.97	0.904	1	CLONAL	1	TRUE	1	0.699130968827798	2		432	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	53	622	0	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	1	2	FACETS	0.187	0.158	0.218	0.187	0.158	0.218	SUBCLONAL	1	TRUE	1	0.699130968827798	2		622	812	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78617590	78617590	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	182	459	0	ENST00000306801.3:c.328T>C	p.Tyr110His	p.Y110H	ENST00000306801	NM_020761.2	110	Tac/Cac	3/34	1	2	FACETS	0.677	0.626	0.73	0.677	0.626	0.73	SUBCLONAL	1	TRUE	1	0.699130968827798	2		459	769	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368233	45368233	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	40	416	0	ENST00000262160.6:c.1369G>A	p.Gly457Arg	p.G457R	ENST00000262160	NM_005901.5	457	Gga/Aga	11/11	0.699130968827798	2	FACETS	0.233	0.193	0.277	0.116	0.096	0.139	SUBCLONAL	1	TRUE	0	0.699130968827798	2		416	492	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244243	5244243	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1390768500	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	59	545	0	ENST00000357368.4:c.1239del	p.Ser414AlafsTer30	p.S414Afs*30	ENST00000357368	NM_002850.3	413	ccC/cc	11/38	1	2	FACETS	0.228	0.196	0.264	0.228	0.196	0.264	SUBCLONAL	1	TRUE	1	0.699130968827798	2		545	739	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265139	5265139	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	50	595	0	ENST00000357368.4:c.448C>T	p.Arg150Trp	p.R150W	ENST00000357368	NM_002850.3	150	Cgg/Tgg	5/38	1	2	FACETS	0.183	0.155	0.215	0.183	0.155	0.215	SUBCLONAL	1	TRUE	1	0.699130968827798	2		595	780	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353815	15353815	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780028668	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	115	213	0	ENST00000263377.2:c.3065C>T	p.Pro1022Leu	p.P1022L	ENST00000263377	NM_058243.2	1022	cCg/cTg	14/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.699130968827798	2		213	309	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266717	18266717	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765334654	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	274	495	0	ENST00000222254.8:c.28C>T	p.Arg10Cys	p.R10C	ENST00000222254	NM_005027.3	10	Cgc/Tgc	2/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.699130968827798	2		495	720	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469530	25469530	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755744291	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	52	437	0	ENST00000264709.3:c.1238del	p.Gly413AlafsTer238	p.G413Afs*238	ENST00000264709	NM_175629.2	413	gGc/gc	10/23	1	2	FACETS	0.298	0.254	0.347	0.298	0.254	0.347	SUBCLONAL	1	TRUE	1	0.699130968827798	2		437	499	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416646	29416646	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544926207	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	301	542	0	ENST00000389048.3:c.4307G>A	p.Arg1436His	p.R1436H	ENST00000389048	NM_004304.4	1436	cGc/cAc	29/29	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.699130968827798	2		542	786	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098815	178098815	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	224	488	0	ENST00000397062.3:c.230A>G	p.Asp77Gly	p.D77G	ENST00000397062	NM_006164.4	77	gAt/gGt	2/5	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.699130968827798	2		488	605	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384650	31384651	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs756395138	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	214	534	3	ENST00000328111.2:c.1359dup	p.Leu454AlafsTer11	p.L454Afs*11	ENST00000328111	NM_006892.3	451	gag/gaGg	13/23	1	2	FACETS	0.885	0.826	0.945	0.885	0.826	0.945	CLONAL	1	TRUE	1	0.699130968827798	2		537	692	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261555	142261555	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	24	352	0	ENST00000350721.4:c.3402del	p.Phe1134LeufsTer6	p.F1134Lfs*6	ENST00000350721	NM_001184.3	1134	ttT/tt	17/47	1	2	FACETS	0.218	0.171	0.272	0.218	0.171	0.272	SUBCLONAL	1	TRUE	1	0.699130968827798	2		352	315	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916726	178916726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772110575	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	120	378	0	ENST00000263967.3:c.113G>A	p.Arg38His	p.R38H	ENST00000263967	NM_006218.2	38	cGt/cAt	2/21	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.699130968827798	2		378	325	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952142	178952142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253171657	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	132	394	0	ENST00000263967.3:c.3197C>T	p.Ala1066Val	p.A1066V	ENST00000263967	NM_006218.2	1066	gCa/gTa	21/21	1	2	FACETS	0.981	0.9	1	0.981	0.9	1	CLONAL	1	TRUE	1	0.699130968827798	2		394	385	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201756	66201756	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	220	471	0	ENST00000273854.3:c.2746C>T	p.Gln916Ter	p.Q916*	ENST00000273854	NM_004439.5	916	Cag/Tag	16/18	1	2	FACETS	0.997	0.934	1	0.997	0.934	1	CLONAL	1	TRUE	1	0.699130968827798	2		471	631	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007332	143007332	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	105	324	0	ENST00000262992.4:c.2452del	p.Arg818GlufsTer4	p.R818Efs*4	ENST00000262992	NM_001101669.1	818	Aga/ga	22/24	1	2	FACETS	0.801	0.724	0.881	0.801	0.724	0.881	CLONAL	1	TRUE	1	0.699130968827798	2		324	375	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518900	187518900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745695748	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	181	395	0	ENST00000441802.2:c.12304G>A	p.Gly4102Arg	p.G4102R	ENST00000441802	NM_005245.3	4102	Gga/Aga	24/27	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.699130968827798	2		395	513	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967280	38967280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770728330	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	108	420	0	ENST00000357387.3:c.1201C>T	p.Arg401Cys	p.R401C	ENST00000357387	NM_152756.3	401	Cgt/Tgt	14/38	1	2	FACETS	0.739	0.668	0.813	0.739	0.668	0.813	SUBCLONAL	1	TRUE	1	0.699130968827798	2		420	418	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675268	176675269	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	251	517	1	ENST00000439151.2:c.4591dup	p.Met1531AsnfsTer4	p.M1531Nfs*4	ENST00000439151	NM_022455.4	1528	-/A	11/23	1	2	FACETS	0.963	0.904	1	0.963	0.904	1	CLONAL	1	TRUE	1	0.699130968827798	2		518	746	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803455	32803455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148976382	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	196	489	2	ENST00000374899.4:c.704G>A	p.Arg235His	p.R235H	ENST00000374899	NM_018833.2	235	cGc/cAc	4/12	1	2	FACETS	0.863	0.802	0.925	0.863	0.802	0.925	CLONAL	1	TRUE	1	0.699130968827798	2		491	650	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527705	157527705	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	274	492	0	ENST00000346085.5:c.5430G>T	p.Gln1810His	p.Q1810H	ENST00000346085	NM_020732.3	1810	caG/caT	20/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.699130968827798	2		492	740	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559317	141559317	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	44	494	0	ENST00000220592.5:c.1484C>T	p.Ala495Val	p.A495V	ENST00000220592	NM_012154.3	495	gCg/gTg	12/19	0.118742815212219	3	FACETS	0.212	0.177	0.251	0.106	0.088	0.126	INDETERMINATE	1	TRUE	1	0.699130968827798	3		494	802	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97873817	97873817	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	203	589	5	ENST00000289081.3:c.1257del	p.Thr420ArgfsTer27	p.T420Rfs*27	ENST00000289081	NM_000136.2	419	ccC/cc	13/15	1	2	FACETS	0.724	0.673	0.777	0.724	0.673	0.777	SUBCLONAL	1	TRUE	1	0.699130968827798	2		594	802	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900180	101900180	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1554700593	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	125	390	0	ENST00000374994.4:c.614T>C	p.Ile205Thr	p.I205T	ENST00000374994	NM_004612.2	205	aTt/aCt	4/9	1	2	FACETS	0.666	0.605	0.729	0.666	0.605	0.729	SUBCLONAL	1	TRUE	1	0.699130968827798	2		390	537	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760024	133760024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	168	464	2	ENST00000318560.5:c.2352del	p.Arg785GlyfsTer3	p.R785Gfs*3	ENST00000318560	NM_005157.4	783	Ccc/cc	11/11	1	2	FACETS	0.885	0.819	0.953	0.885	0.819	0.953	CLONAL	1	TRUE	1	0.699130968827798	2		466	543	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391880	139391880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	39	597	0	ENST00000277541.6:c.6311G>A	p.Arg2104His	p.R2104H	ENST00000277541	NM_017617.3	2104	cGc/cAc	34/34	1	2	FACETS	0.144	0.119	0.172	0.144	0.119	0.172	SUBCLONAL	1	TRUE	1	0.699130968827798	2		597	775	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139818391	139818393	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1004692565	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	215	432	0	ENST00000247668.2:c.1230_1232del	p.Phe411del	p.F411del	ENST00000247668	NM_021138.3	409	cTCTtc/ctc	10/11	1	2	FACETS	0.969	0.906	1	0.969	0.906	1	CLONAL	1	TRUE	1	0.699130968827798	2		432	635	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422384	47422384	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	135	415	0	ENST00000377045.4:c.23del	p.Pro8LeufsTer26	p.P8Lfs*26	ENST00000377045	NM_001654.4	6	ggC/gg	2/16	1	2	FACETS	0.679	0.619	0.74	0.679	0.619	0.74	SUBCLONAL	1	TRUE	1	0.699130968827798	2		415	569	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250047	53250047	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	219	446	0	ENST00000375401.3:c.202C>T	p.Arg68Ter	p.R68*	ENST00000375401	NM_004187.3	68	Cga/Tga	2/26	1	2	FACETS	0.967	0.904	1	0.967	0.904	1	CLONAL	1	TRUE	1	0.699130968827798	2		446	648	SUCCESS
AR	367	MSKCC	GRCh37	X	66766339	66766350	+	inframe_deletion	In_Frame_Del	DEL	GGTGGTGGTGGG	GGTGGTGGTGGG	-	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	136	432	0	ENST00000374690.3:c.1359_1370del	p.Gly470_Gly473del	p.G470_G473del	ENST00000374690	NM_000044.3	451	GGTGGTGGTGGG/-	1/8	1	2	FACETS	0.823	0.753	0.894	0.823	0.753	0.894	CLONAL	1	TRUE	1	0.699130968827798	2		432	473	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366908	40366908	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	198	552	0	ENST00000397332.2:c.289G>A	p.Gly97Arg	p.G97R	ENST00000397332	NM_001033082.2	97	Ggg/Agg	2/3	1	2	FACETS	0.933	0.869	0.998	0.933	0.869	0.998	CLONAL	1	TRUE	1	0.699130968827798	2		552	607	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944361	206944361	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	256	515	1	ENST00000423557.1:c.269A>G	p.Tyr90Cys	p.Y90C	ENST00000423557	NM_000572.2	90	tAc/tGc	3/5	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.699130968827798	2		516	685	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578182	226578182	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	258	514	0	ENST00000366794.5:c.546G>T	p.Lys182Asn	p.K182N	ENST00000366794	NM_001618.3	182	aaG/aaT	4/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.699130968827798	2		514	700	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198433	108198433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	145	358	0	ENST00000278616.4:c.7037C>T	p.Ala2346Val	p.A2346V	ENST00000278616	NM_000051.3	2346	gCa/gTa	48/63	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.699130968827798	2		358	361	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212552	133212552	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	167	465	0	ENST00000320574.5:c.5737T>A	p.Phe1913Ile	p.F1913I	ENST00000320574	NM_006231.2	1913	Ttt/Att	42/49	1	2	FACETS	0.783	0.723	0.845	0.783	0.723	0.845	SUBCLONAL	1	TRUE	1	0.699130968827798	2		465	610	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947621	48947621	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	71	280	0	ENST00000267163.4:c.1208A>G	p.Tyr403Cys	p.Y403C	ENST00000267163	NM_000321.2	403	tAt/tGt	12/27	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.699130968827798	2		280	177	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514485	103514485	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	142	487	0	ENST00000355739.4:c.986T>C	p.Leu329Pro	p.L329P	ENST00000355739	NM_000123.3	329	cTg/cCg	8/15	1	2	FACETS	0.668	0.611	0.728	0.668	0.611	0.728	SUBCLONAL	1	TRUE	1	0.699130968827798	2		487	608	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51504536	51504536	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	51	421	0	ENST00000260433.2:c.1244T>A	p.Leu415His	p.L415H	ENST00000260433		415	cTt/cAt	9/10	1	2	FACETS	0.24	0.204	0.281	0.24	0.204	0.281	SUBCLONAL	1	TRUE	1	0.699130968827798	2		421	607	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900612	3900612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	51	518	0	ENST00000262367.5:c.484G>A	p.Ala162Thr	p.A162T	ENST00000262367	NM_004380.2	162	Gcg/Acg	2/31	1	2	FACETS	0.197	0.167	0.231	0.197	0.167	0.231	SUBCLONAL	1	TRUE	1	0.699130968827798	2		518	740	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348560	89348563	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	226	548	1	ENST00000301030.4:c.4387_4390del	p.Glu1463AsnfsTer67	p.E1463Nfs*67	ENST00000301030	NM_001256183.1	1463	GAGAaa/aa	9/13	1	2	FACETS	0.883	0.826	0.942	0.883	0.826	0.942	CLONAL	1	TRUE	1	0.699130968827798	2		549	732	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989382	7989382	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	274	534	0	ENST00000319144.4:c.304T>C	p.Tyr102His	p.Y102H	ENST00000319144	NM_001139.2	102	Tac/Cac	2/15	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.699130968827798	2		534	601	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042386	16042386	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	59	351	0	ENST00000268712.3:c.1288G>A	p.Val430Met	p.V430M	ENST00000268712	NM_006311.3	430	Gtg/Atg	12/46	1	2	FACETS	0.819	0.716	0.928	0.819	0.716	0.928	CLONAL	1	TRUE	1	0.699130968827798	2		351	206	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78931528	78931528	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	149	431	0	ENST00000306801.3:c.3475C>T	p.Gln1159Ter	p.Q1159*	ENST00000306801	NM_020761.2	1159	Cag/Tag	29/34	1	2	FACETS	0.679	0.622	0.737	0.679	0.622	0.737	SUBCLONAL	1	TRUE	1	0.699130968827798	2		431	628	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873283	136873283	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	310	508	0	ENST00000241393.3:c.215T>C	p.Met72Thr	p.M72T	ENST00000241393	NM_003467.2	72	aTg/aCg	2/2	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.699130968827798	2		508	788	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306755	41306755	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	37	441	0	ENST00000373198.4:c.904del	p.Ala302ProfsTer21	p.A302Pfs*21	ENST00000373198	NM_133170.3	302	Gcc/cc	7/32	1	2	FACETS	0.156	0.128	0.187	0.156	0.128	0.187	SUBCLONAL	1	TRUE	1	0.699130968827798	2		441	679	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57474001	57474001	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	70	378	0	ENST00000371085.3:c.218G>A	p.Gly73Asp	p.G73D	ENST00000371085	NM_000516.4	73	gGc/gAc	3/13	1	2	FACETS	0.268	0.233	0.306	0.268	0.233	0.306	SUBCLONAL	1	TRUE	1	0.699130968827798	2		378	748	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852503	42852503	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	208	482	0	ENST00000398585.3:c.583C>A	p.Leu195Ile	p.L195I	ENST00000398585	NM_001135099.1	195	Ctt/Att	6/14	1	2	FACETS	0.951	0.887	1	0.951	0.887	1	CLONAL	1	TRUE	1	0.699130968827798	2		482	626	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446537	29446537	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	201	515	1	ENST00000544604.2:c.2372del	p.Gly791AlafsTer14	p.G791Afs*14	ENST00000544604	NM_001206998.1	790	Ggg/gg	8/9	1	2	FACETS	0.991	0.925	1	0.991	0.925	1	CLONAL	1	TRUE	1	0.699130968827798	2		516	580	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691809	30691809	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	50	528	1	ENST00000295754.5:c.311C>A	p.Pro104His	p.P104H	ENST00000295754	NM_003242.5	104	cCc/cAc	3/7	1	2	FACETS	0.259	0.219	0.302	0.259	0.219	0.302	SUBCLONAL	1	TRUE	1	0.699130968827798	2		529	553	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138382752	138382752	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	158	337	0	ENST00000289153.2:c.2792G>A	p.Gly931Asp	p.G931D	ENST00000289153	NM_006219.2	931	gGc/gAc	19/22	1	2	FACETS	0.96	0.887	1	0.96	0.887	1	CLONAL	1	TRUE	1	0.699130968827798	2		337	471	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185200210	185200210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762865838	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	132	442	1	ENST00000265026.3:c.2867G>A	p.Arg956Lys	p.R956K	ENST00000265026	NM_004721.4	956	aGg/aAg	14/14	1	2	FACETS	0.702	0.64	0.766	0.702	0.64	0.766	SUBCLONAL	1	TRUE	1	0.699130968827798	2		443	538	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467704	66467704	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	192	453	1	ENST00000273854.3:c.565G>T	p.Gly189Cys	p.G189C	ENST00000273854	NM_004439.5	189	Ggt/Tgt	3/18	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.699130968827798	2		454	506	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157089	106157089	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	298	543	0	ENST00000380013.4:c.1993del	p.Thr665GlnfsTer35	p.T665Qfs*35	ENST00000380013	NM_001127208.2	664	Aaa/aa	3/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.699130968827798	2		543	776	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144361498	144361499	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1182019563	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	60	531	0	ENST00000262995.4:c.1554dup	p.Val519ArgfsTer3	p.V519Rfs*3	ENST00000262995	NM_207123.2	516	-/C	6/11	1	2	FACETS	0.21	0.18	0.242	0.21	0.18	0.242	SUBCLONAL	1	TRUE	1	0.699130968827798	2		531	818	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180401	32180401	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	251	542	0	ENST00000375023.3:c.2530C>A	p.Leu844Met	p.L844M	ENST00000375023	NM_004557.3	844	Ctg/Atg	17/30	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.699130968827798	2		542	696	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771219	161771219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149953814	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	36	420	0	ENST00000366898.1:c.1310C>T	p.Pro437Leu	p.P437L	ENST00000366898	NM_004562.2	437	cCg/cTg	12/12	1	2	FACETS	0.175	0.144	0.211	0.175	0.144	0.211	SUBCLONAL	1	TRUE	1	0.699130968827798	2		420	587	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124481113	124481113	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	60	387	0	ENST00000357628.3:c.1283del	p.Asn428IlefsTer7	p.N428Ifs*7	ENST00000357628	NM_015450.2	428	aAt/at	14/19	1	2	FACETS	0.718	0.626	0.816	0.718	0.626	0.816	SUBCLONAL	1	TRUE	1	0.699130968827798	2		387	239	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145736911	145736911	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1341756990	NA	P-0066327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	238	520	0	ENST00000428558.2:c.3530A>G	p.Tyr1177Cys	p.Y1177C	ENST00000428558	NM_004260.3	1177	tAc/tGc	22/22	0.118742815212219	3	FACETS	1	0.991	1	0.674	0.632	0.716	INDETERMINATE	1	TRUE	1	0.699130968827798	3		520	682	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574030	7574030	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	179	434	0	ENST00000269305.4:c.997del	p.Arg333ValfsTer12	p.R333Vfs*12	ENST00000269305	NM_001126112.2	333	Cgt/gt	10/11	0.415357499581703	2	FACETS	0.971	0.905	1	0.971	0.905	1	CLONAL	2	TRUE	0	0.415357499581703	2		434	444	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779284	3779284	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1035114591	NA	P-0066328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	95	490	0	ENST00000262367.5:c.5764C>G	p.Pro1922Ala	p.P1922A	ENST00000262367	NM_004380.2	1922	Ccc/Gcc	31/31	0.398486076238886	3	FACETS	1	0.934	1	0.531	0.474	0.591	CLONAL	1	TRUE	1	0.415357499581703	3		490	520	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39212986	39212986	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	84	450	0	ENST00000402219.2:c.3981G>T	p.Leu1327Phe	p.L1327F	ENST00000402219	NM_005633.3	1327	ttG/ttT	23/23	0.388052523918997	3	FACETS	0.818	0.724	0.919	0.409	0.362	0.46	CLONAL	1	TRUE	1	0.415357499581703	3		450	597	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807987	1807987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1297767255	NA	P-0066328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	240	730	0	ENST00000260795.2:c.1963C>T	p.Arg655Trp	p.R655W	ENST00000260795		655	Cgg/Tgg	14/17	0.279991945975565	3	FACETS	0.847	0.799	0.896	0.847	0.799	0.896	CLONAL	3	TRUE	0	0.415357499581703	3		730	549	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6038900	6038900	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	71	350	0	ENST00000265849.7:c.544G>C	p.Ala182Pro	p.A182P	ENST00000265849	NM_000535.5	182	Gcc/Ccc	6/15	1	2	FACETS	0.95	0.834	1	0.95	0.834	1	CLONAL	1	TRUE	1	0.415357499581703	2		350	360	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540133	23540134	+	missense_variant	Missense_Mutation	DNP	CA	CA	TG	novel	NA	P-0066328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	55	339	0	ENST00000380871.4:c.269_270inv	p.Leu90Pro	p.L90P	ENST00000380871	NM_006167.3	90	cTG/cCA	1/2	0.384004792648706	1	FACETS	0.916	0.793	1	0.916	0.793	1	CLONAL	1	TRUE	0	0.415357499581703	1		339	229	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066329-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	62	446	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.927	0.812	1	0.927	0.812	1	CLONAL	1	TRUE	1	0.610942725939534	2		446	219	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916614	178916614	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0066329-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	237	274	0	ENST00000263967.3:c.1A>G	p.Met1?	p.M1?	ENST00000263967	NM_006218.2	1	Atg/Gtg	2/21	0.269429125983987	4	FACETS	1	0.989	1	0.8	0.754	0.845	INDETERMINATE	2	TRUE	1	0.610942725939534	4		274	521	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939842	76939842	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066329-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	55	194	0	ENST00000373344.5:c.906T>G	p.Ser302Arg	p.S302R	ENST00000373344	NM_000489.3	302	agT/agG	9/35	1	1	FACETS	0.528	0.456	0.604	0.528	0.456	0.604	SUBCLONAL	1	TRUE	0	0.610942725939534	1		194	237	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0066330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	186	257	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.372113263974761	2	FACETS	0.824	0.773	0.876	0.824	0.773	0.876	CLONAL	2	TRUE	0	0.589126380884056	2		257	383	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0066330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	126	246	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.212127863049186	1	FACETS	0.888	0.814	0.963	0.888	0.814	0.963	INDETERMINATE	1	TRUE	0	0.589126380884056	1		246	340	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0066330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	186	404	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.589126380884056	1	FACETS	0.893	0.832	0.955	0.893	0.832	0.955	CLONAL	1	TRUE	0	0.589126380884056	1		404	499	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11019872	11019872	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	31	504	0	ENST00000327064.4:c.547T>G	p.Phe183Val	p.F183V	ENST00000327064	NM_199141.1	183	Ttc/Gtc	4/16	0.25901842350312	0	FACETS	0.087	0.07	0.106			1	INDETERMINATE	1	TRUE	0	0.589126380884056	0		504	497	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10783587	10783587	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	27	336	0	ENST00000361367.2:c.835T>G	p.Phe279Val	p.F279V	ENST00000361367	NM_014633.3	279	Ttt/Gtt	7/25	1	2	FACETS	0.23	0.182	0.284	0.23	0.182	0.284	SUBCLONAL	1	TRUE	1	0.589126380884056	2		336	399	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148516746	148516746	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	40	416	0	ENST00000320356.2:c.941A>G	p.Lys314Arg	p.K314R	ENST00000320356	NM_004456.4	314	aAg/aGg	9/20	0.298530072261729	1	FACETS	0.177	0.147	0.211	0.177	0.147	0.211	INDETERMINATE	1	TRUE	0	0.589126380884056	1		416	540	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411729	63411729	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	231	274	0	ENST00000330258.3:c.1438G>T	p.Glu480Ter	p.E480*	ENST00000330258	NM_152424.3	480	Gag/Tag	2/2	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.589126380884056	1		274	410	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424472	47424472	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	83	266	0	ENST00000377045.4:c.392A>C	p.Lys131Thr	p.K131T	ENST00000377045	NM_001654.4	131	aAg/aCg	5/16	1	1	FACETS	0.522	0.463	0.583	0.522	0.463	0.583	SUBCLONAL	1	TRUE	0	0.589126380884056	1		266	381	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573563	48573564	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAAA	novel	NA	P-0066330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	78	431	0	ENST00000342988.3:c.150_153dup	p.Asp52LysfsTer3	p.D52Kfs*3	ENST00000342988	NM_005359.5	49	-/AAAA	2/12	0.589126380884056	1	FACETS	0.578	0.513	0.648	0.578	0.513	0.648	SUBCLONAL	1	TRUE	0	0.589126380884056	1		431	323	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066331-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	49	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.610033542264887	2		341	160	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0066331-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	140	389	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.610033542264887	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.610033542264887	1		389	294	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881041	37881042	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0066331-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	151	545	1	ENST00000269571.5:c.2372_2373dup	p.Ser792HisfsTer7	p.S792Hfs*7	ENST00000269571		790	-/AC	20/27	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.610033542264887	2		546	480	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717724	89717735	+	frameshift_variant	Frame_Shift_Del	DEL	GTGGTGATATCA	GTGGTGATATCA	TACCTGTG	novel	NA	P-0066340-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	45	240	0	ENST00000371953.3:c.749_760delinsTACCTGTG	p.Cys250LeufsTer5	p.C250Lfs*5	ENST00000371953	NM_000314.4	250	tGTGGTGATATCAaa/tTACCTGTGaa	7/9	1	2	FACETS	0.769	0.662	0.881	0.769	0.662	0.881	SUBCLONAL	1	TRUE	1	0.899911179836518	2		240	130	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198284	138198284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066340-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	28	292	0	ENST00000237289.4:c.877G>A	p.Asp293Asn	p.D293N	ENST00000237289	NM_001270507.1	293	Gat/Aat	6/9	0.163207846046291	3	FACETS	0.571	0.462	0.693	0.286	0.231	0.347	INDETERMINATE	1	TRUE	1	0.899911179836518	3		292	158	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0066341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	41	133	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.333072742064847	3	FACETS	0.875	0.745	1	0.875	0.745	1	CLONAL	2	TRUE	1	0.439636853492173	3		133	130	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0066341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	212	348	1	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			0.392166667451087	3	FACETS	0.852	0.795	0.911	0.852	0.795	0.911	CLONAL	2	TRUE	1	0.439636853492173	3		349	690	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	51	446	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.330586940846308	2		446	265	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0066342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	45	492	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.330586940846308	2		492	206	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171607	36171607	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1569008655	NA	P-0066342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	100	361	0	ENST00000300305.3:c.958C>T	p.Arg320Ter	p.R320*	ENST00000300305		320	Cga/Tga	7/8	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.330586940846308	2		361	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0066342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	112	389	0	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	0.330523286256498	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	2	TRUE	0	0.330586940846308	2		389	336	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651906	36651906	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	40	448	0	ENST00000244741.5:c.28C>T	p.Gln10Ter	p.Q10*	ENST00000244741	NM_000389.4	10	Cag/Tag	2/3	1	2	FACETS	0.605	0.503	0.718	0.605	0.503	0.718	SUBCLONAL	1	TRUE	1	0.330586940846308	2		448	400	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557447	21557447	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	118	455	0	ENST00000382592.4:c.2398G>A	p.Asp800Asn	p.D800N	ENST00000382592	NM_014572.2	800	Gat/Aat	5/8	0.330586940846308	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.330586940846308	1		455	440	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340168	116340168	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	59	391	0	ENST00000397752.3:c.1030G>C	p.Gly344Arg	p.G344R	ENST00000397752	NM_000245.2	344	Ggg/Cgg	2/21	1	2	FACETS	0.85	0.733	0.976	0.85	0.733	0.976	CLONAL	1	TRUE	1	0.330586940846308	2		391	420	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384833	17384914	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTGAGGCTGCGGCAGGCGCTGGGTGCCCTGGGGTCCCCTGGGGCCCGGGGAGCATCGCACTGAGGCCTCTGCTTCCCTGCA	GGTGAGGCTGCGGCAGGCGCTGGGTGCCCTGGGGTCCCCTGGGGCCCGGGGAGCATCGCACTGAGGCCTCTGCTTCCCTGCA	-	novel	NA	P-0066342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	64	458	0	ENST00000359435.4:c.465+1_466-1del		p.X155_splice	ENST00000359435	NM_001033549.1	155		4/9	1	2	FACETS	0.77	0.668	0.88	0.77	0.668	0.88	SUBCLONAL	1	TRUE	1	0.330586940846308	2		458	503	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615720	1615722	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs1568334096	NA	P-0066342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	26	490	0	ENST00000344749.5:c.1549_1551del	p.Glu517del	p.E517del	ENST00000344749	NM_001136139.2	517	GAG/-	17/19	1	2	FACETS	0.322	0.254	0.4	0.322	0.254	0.4	SUBCLONAL	1	TRUE	1	0.330586940846308	2		490	488	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944586	40944586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066343-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	52	336	0	ENST00000373198.4:c.1916C>T	p.Ala639Val	p.A639V	ENST00000373198	NM_133170.3	639	gCa/gTa	12/32	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.202851229298672	2		336	491	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183752	10183752	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs5030803	NA	P-0066343-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	34	319	0	ENST00000256474.2:c.221T>A	p.Val74Asp	p.V74D	ENST00000256474	NM_000551.3	74	gTc/gAc	1/3	0.202851229298672	1	FACETS	1	0.82	1	1	0.82	1	CLONAL	1	TRUE	0	0.202851229298672	1		319	301	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295168	1295169	+	upstream_gene_variant	5'Flank	DNP	CG	CG	TC	novel	NA	P-0066343-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	29	329	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.937	0.754	1	0.937	0.754	1	CLONAL	1	TRUE	1	0.202851229298672	2		329	305	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0066344-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	559	688	0	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	0.68389396388967	2	FACETS	0.932	0.904	0.959	0.932	0.904	0.959	CLONAL	2	TRUE	0	0.709750119897268	2		688	845	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941730	48941742	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTATAGACAGGTA	CTATAGACAGGTA	-	novel	NA	P-0066344-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	196	187	0	ENST00000267163.4:c.1040_1049+3del		p.X347_splice	ENST00000267163	NM_000321.2	347		10/27	0.687858252735071	2	FACETS	0.897	0.85	0.942	0.897	0.85	0.942	CLONAL	2	TRUE	0	0.709750119897268	2		187	308	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485439	57485439	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs3205253	NA	P-0066344-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	274	315	0	ENST00000371085.3:c.1021A>G	p.Ile341Val	p.I341V	ENST00000371085	NM_000516.4	341	Att/Gtt	12/13	1	2	FACETS	0.98	0.924	1	0.98	0.924	1	CLONAL	1	TRUE	1	0.709750119897268	2		315	788	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0066345-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	417	232	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.489106267046655	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.489106267046655	3		232	652	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203436	NA	P-0066345-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	253	570	0	ENST00000269305.4:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269305	NM_001126112.2	163	Tac/Cac	5/11	0.489106267046655	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.489106267046655	1		570	663	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724542	162724542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1041487062	NA	P-0066345-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	357	577	0	ENST00000367921.3:c.314G>A	p.Arg105His	p.R105H	ENST00000367921	NM_006182.2	105	cGc/cAc	5/18	0.421201639744309	3	FACETS	0.937	0.891	0.985	0.937	0.891	0.985	CLONAL	2	TRUE	1	0.489106267046655	3		577	969	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053520	37053520	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750085	NA	P-0066345-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	26	443	0	ENST00000231790.2:c.607G>A	p.Asp203Asn	p.D203N	ENST00000231790	NM_000249.3	203	Gat/Aat	8/19	0.449262775348634	2	FACETS	0.261	0.206	0.324	0.131	0.103	0.162	SUBCLONAL	1	TRUE	0	0.489106267046655	2		443	407	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877861	151877861	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066345-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	136	589	0	ENST00000262189.6:c.7084T>G	p.Ser2362Ala	p.S2362A	ENST00000262189	NM_170606.2	2362	Tca/Gca	36/59	0.489106267046655	3	FACETS	0.835	0.759	0.914	0.278	0.253	0.305	CLONAL	1	TRUE	0	0.489106267046655	3		589	829	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0066346-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	287	744	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.350900218968789	2	FACETS	1	0.964	1	1	0.995	1	CLONAL	3	TRUE	0	0.350900218968789	2		745	537	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0066346-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	136	310	0	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	0.140015710402312	3	FACETS	0.982	0.899	1	0.982	0.899	1	INDETERMINATE	2	TRUE	1	0.350900218968789	3		310	464	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0066346-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	152	289	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.350900218968789	6	FACETS	1	0.967	1			1	CLONAL	4	TRUE	NA	0.350900218968789	6		289	344	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206903	162206903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756064095	NA	P-0066346-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	81	427	0	ENST00000366898.1:c.772G>A	p.Val258Met	p.V258M	ENST00000366898	NM_004562.2	258	Gtg/Atg	7/12	0.350900218968789	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.350900218968789	1		427	334	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141427	11141427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066346-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	155	331	0	ENST00000358026.2:c.3404G>A	p.Arg1135Gln	p.R1135Q	ENST00000358026	NM_001128849.1	1135	cGg/cAg	25/36	0.350900218968789	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.350900218968789	2		331	386	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468157	50468157	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066346-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	23	429	0	ENST00000331340.3:c.1392C>A	p.Cys464Ter	p.C464*	ENST00000331340	NM_006060.4	464	tgC/tgA	8/8	0.140015710402312	3	FACETS	0.344	0.267	0.433	0.172	0.133	0.217	INDETERMINATE	1	TRUE	1	0.350900218968789	3		429	448	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247203	153247203	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066346-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	94	369	0	ENST00000281708.4:c.1599T>G	p.Cys533Trp	p.C533W	ENST00000281708	NM_033632.3	533	tgT/tgG	10/12	0.180325465896773	1	FACETS	1	0.973	1	1	0.973	1	INDETERMINATE	1	TRUE	0	0.350900218968789	1		369	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0066347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	398	820	0	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	0.500926308404505	2	FACETS	0.988	0.946	1	0.988	0.946	1	CLONAL	2	TRUE	0	0.500926308404505	2		820	804	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175481	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0066347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	128	436	0	ENST00000257430.4:c.4192_4193del	p.Arg1399PhefsTer9	p.R1399Ffs*9	ENST00000257430	NM_000038.5	1397	GAg/g	16/16	0.500926308404505	1	FACETS	0.927	0.848	1	0.927	0.848	1	CLONAL	1	TRUE	0	0.500926308404505	1		436	413	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982338	201982339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0066347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	239	525	0	ENST00000359651.3:c.719_720dup	p.Lys241ProfsTer14	p.K241Pfs*14	ENST00000359651		239	-/CC	6/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.500926308404505	2		525	849	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589607	67589609	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0066348-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	38	263	0	ENST00000274335.5:c.1372_1374del	p.Glu458del	p.E458del	ENST00000274335		457	cAAGaa/caa	10/15	0.73290864497616	1	FACETS	0.608	0.517	0.704	0.608	0.517	0.704	SUBCLONAL	1	TRUE	0	0.73290864497616	1		263	108	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692902	89692902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909218	NA	P-0066348-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	79	311	0	ENST00000371953.3:c.386G>A	p.Gly129Glu	p.G129E	ENST00000371953	NM_000314.4	129	gGa/gAa	5/9	0.73290864497616	1	FACETS	0.99	0.903	1	0.99	0.903	1	CLONAL	1	TRUE	0	0.73290864497616	1		311	138	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821636	72821638	+	inframe_deletion	In_Frame_Del	DEL	ACT	ACT	-	rs1283843849	NA	P-0066348-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	10	306	3	ENST00000268489.5:c.10537_10539del	p.Ser3513del	p.S3513del	ENST00000268489	NM_006885.3	3513	AGT/-	10/10	0.73290864497616	1	FACETS	0.096	0.064	0.135	0.096	0.064	0.135	SUBCLONAL	1	TRUE	0	0.73290864497616	1		309	181	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624305	89624305	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066348-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	28	296	0	ENST00000371953.3:c.79T>G	p.Tyr27Asp	p.Y27D	ENST00000371953	NM_000314.4	27	Tat/Gat	1/9	0.73290864497616	1	FACETS	0.184	0.147	0.226	0.184	0.147	0.226	SUBCLONAL	1	TRUE	0	0.73290864497616	1		296	263	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943343	71943343	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066348-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	70	531	0	ENST00000298229.2:c.1675A>T	p.Asn559Tyr	p.N559Y	ENST00000298229	NM_001567.3	559	Aat/Tat	14/28	0.73290864497616	1	FACETS	0.209	0.182	0.238	0.209	0.182	0.238	SUBCLONAL	1	TRUE	0	0.73290864497616	1		531	580	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578260	7578260	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786204041	NA	P-0066350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	439	496	0	ENST00000269305.4:c.589G>C	p.Val197Leu	p.V197L	ENST00000269305	NM_001126112.2	197	Gtg/Ctg	6/11	NA	2	FACETS	0.967	0.934	0.998			1	INDETERMINATE	2	TRUE	NA	0.688041307767168	2		496	660	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060568	38060613	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	AGCTAGGAAGTGTTTAGGACGGGTCTGGAATACACACCTTGGTAGT	AGCTAGGAAGTGTTTAGGACGGGTCTGGAATACACACCTTGGTAGT	-	novel	NA	P-0066350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	245	588	0	ENST00000250448.2:c.1376_*2del		p.*459*	ENST00000250448	NM_004496.3	459		2/2	0.111188437863893	3	FACETS	1	0.99	1	0.64	0.6	0.68	INDETERMINATE	1	TRUE	1	0.688041307767168	3		588	748	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163714	47163714	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	131	374	0	ENST00000409792.3:c.2412G>T	p.Leu804Phe	p.L804F	ENST00000409792	NM_014159.6	804	ttG/ttT	3/21	1	2	FACETS	0.803	0.734	0.875	0.803	0.734	0.875	CLONAL	1	TRUE	1	0.688041307767168	2		374	474	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845593	128845593	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	40	432	0	ENST00000249373.3:c.890C>G	p.Ala297Gly	p.A297G	ENST00000249373	NM_005631.4	297	gCa/gGa	4/12	0.688041307767168	3	FACETS	0.225	0.186	0.268	0.112	0.093	0.134	SUBCLONAL	1	TRUE	1	0.688041307767168	3		432	696	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220424	98220424	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs779388970	NA	P-0066350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	52	358	0	ENST00000331920.6:c.3039C>A	p.Tyr1013Ter	p.Y1013*	ENST00000331920	NM_000264.3	1013	taC/taA	18/24	0.111188437863893	3	FACETS	0.396	0.337	0.461	0.198	0.168	0.231	INDETERMINATE	1	TRUE	1	0.688041307767168	3		358	513	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696441	47696441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066360-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	144	483	0	ENST00000347630.2:c.382G>A	p.Gly128Ser	p.G128S	ENST00000347630	NM_001007230.1	128	Ggc/Agc	6/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.372082002325951	2		483	669	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865651	57865651	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066360-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	162	624	0	ENST00000228682.2:c.3128A>G	p.Asp1043Gly	p.D1043G	ENST00000228682	NM_005269.2	1043	gAc/gGc	12/12	1	2	FACETS	0.946	0.868	1	0.946	0.868	1	CLONAL	1	TRUE	1	0.372082002325951	2		624	920	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678565	88678565	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066360-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	144	514	0	ENST00000360948.2:c.971T>C	p.Val324Ala	p.V324A	ENST00000360948	NM_001012338.2	324	gTg/gCg	9/19	1	2	FACETS	0.965	0.881	1	0.965	0.881	1	CLONAL	1	TRUE	1	0.372082002325951	2		514	802	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609638	81609638	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200182253	NA	P-0066360-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	165	509	0	ENST00000298171.2:c.1236G>A	p.Met412Ile	p.M412I	ENST00000298171	NM_000369.2	412	atG/atA	10/10	0.372082002325951	1	FACETS	0.964	0.887	1	0.964	0.887	1	CLONAL	1	TRUE	0	0.372082002325951	1		509	749	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124469382	124469382	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066360-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	54	212	0	ENST00000357628.3:c.1520C>G	p.Ser507Cys	p.S507C	ENST00000357628	NM_015450.2	507	tCt/tGt	16/19	0.372082002325951	3	FACETS	0.856	0.742	0.977	0.856	0.742	0.977	CLONAL	2	TRUE	1	0.372082002325951	3		212	201	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324922	31324922	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066360-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	154	572	0	ENST00000412585.2:c.14C>G	p.Ala5Gly	p.A5G	ENST00000412585	NM_005514.6	5	gCg/gGg	1/8	0.372082002325951	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.372082002325951	1		572	612	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916872	178916872	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066360-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	57	418	0	ENST00000263967.3:c.259A>G	p.Arg87Gly	p.R87G	ENST00000263967	NM_006218.2	87	Aga/Gga	2/21	0.372082002325951	3	FACETS	0.822	0.707	0.947	0.411	0.353	0.474	CLONAL	1	TRUE	1	0.372082002325951	3		418	442	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435943	116435943	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066360-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	137	550	0	ENST00000397752.3:c.3938A>G	p.Tyr1313Cys	p.Y1313C	ENST00000397752	NM_000245.2	1313	tAt/tGt	21/21	0.372082002325951	3	FACETS	1	0.93	1	0.513	0.467	0.562	CLONAL	1	TRUE	1	0.372082002325951	3		550	851	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591922	48591945	+	inframe_deletion	In_Frame_Del	DEL	TTTGTTTGGGTCAACTCTCCAATG	TTTGTTTGGGTCAACTCTCCAATG	-	novel	NA	P-0066360-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	94	462	0	ENST00000342988.3:c.1086_1109del	p.Cys363_Val370del	p.C363_V370del	ENST00000342988	NM_005359.5	362	tTTTGTTTGGGTCAACTCTCCAATGtc/ttc	9/12	0.372082002325951	1	FACETS	0.77	0.687	0.858	0.77	0.687	0.858	SUBCLONAL	1	TRUE	0	0.372082002325951	1		462	534	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578425	7578436	+	frameshift_variant	Frame_Shift_Del	DEL	TGTGCTGTGACT	TGTGCTGTGACT	CA	novel	NA	P-0066360-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	175	616	2	ENST00000269305.4:c.494_505delinsTG	p.Gln165LeufsTer2	p.Q165Lfs*2	ENST00000269305	NM_001126112.2	165	cAGTCACAGCACAtg/cTGtg	5/11	0.372082002325951	1	FACETS	0.958	0.884	1	0.958	0.884	1	CLONAL	1	TRUE	0	0.372082002325951	1		618	799	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73340154	73340154	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066360-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	51	332	0	ENST00000377767.4:c.1926C>G	p.Asp642Glu	p.D642E	ENST00000377767	NM_014953.3	642	gaC/gaG	15/21	1	2	FACETS	0.843	0.721	0.977	0.843	0.721	0.977	CLONAL	1	TRUE	1	0.372082002325951	2		332	325	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31238906	31238906	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs41543517	NA	P-0066360-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	71	225	0	ENST00000376228.5:c.563G>C	p.Cys188Ser	p.C188S	ENST00000376228	NM_002117.5	188	tGc/tCc	3/8	0.372082002325951	1	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	0	0.372082002325951	1		225	302	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912157	50912157	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066360-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	144	501	0	ENST00000440232.2:c.1891G>T	p.Gly631Cys	p.G631C	ENST00000440232	NM_002691.3	631	Ggc/Tgc	15/27	0.372082002325951	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.372082002325951	1		501	572	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374421	81374421	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066360-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	146	352	0	ENST00000222390.5:c.641G>T	p.Cys214Phe	p.C214F	ENST00000222390	NM_000601.4	214	tGc/tTc	6/18	0.372082002325951	3	FACETS	0.968	0.89	1	0.968	0.89	1	CLONAL	2	TRUE	1	0.372082002325951	3		352	481	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197749	66197749	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066360-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	274	377	0	ENST00000273854.3:c.2950G>T	p.Glu984Ter	p.E984*	ENST00000273854	NM_004439.5	984	Gag/Tag	17/18	0.372082002325951	3	FACETS	0.966	0.915	1	0.966	0.915	1	CLONAL	3	TRUE	0	0.372082002325951	3		377	603	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38196127	38196127	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0066360-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	62	363	0	ENST00000317025.8:c.676-2A>G		p.X226_splice	ENST00000317025	NM_023034.1	226			1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.372082002325951	2		363	318	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873733	35873736	+	stop_gained	Nonsense_Mutation	ONP	CGTC	CGTC	AGTG	novel	NA	P-0066360-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	91	397	0	ENST00000216797.5:c.115_118delinsCACT	p.Asp39_Glu40delinsHisTer	p.D39_E40delinsH*	ENST00000216797	NM_020529.2	39	GACGag/CACTag	1/6	0.372082002325951	1	FACETS	0.962	0.859	1	0.962	0.859	1	CLONAL	1	TRUE	0	0.372082002325951	1		397	414	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	211	721	4	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.699534706952086	2		725	575	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	346	710	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.893	0.857	0.928	1	0.997	1	CLONAL	2	TRUE	1	0.699534706952086	2		713	554	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	187	478	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.955	0.906	1	1	0.994	1	CLONAL	2	TRUE	1	0.699534706952086	2		479	280	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	196	372	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.699534706952086	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.699534706952086	3		372	367	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318754	163318755	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	75	333	0	ENST00000271452.3:c.1150dup	p.Arg384LysfsTer6	p.R384Kfs*6	ENST00000271452	NM_145697.2	382	gaa/gAaa	13/14	0.699534706952086	4	FACETS	0.99	0.873	1	0.33	0.291	0.372	CLONAL	1	TRUE	1	0.699534706952086	4		333	368	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	132	422	2	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	1	2	FACETS	0.822	0.752	0.895	0.822	0.752	0.895	CLONAL	1	TRUE	1	0.699534706952086	2		424	459	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	158	324	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.978	0.904	1	0.978	0.904	1	CLONAL	1	TRUE	1	0.699534706952086	2		324	462	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	189	760	5	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.993	0.925	1	0.993	0.925	1	CLONAL	1	TRUE	1	0.699534706952086	2		765	544	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691872	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs79375991	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	227	425	7	ENST00000295754.5:c.383del	p.Lys128SerfsTer35	p.K128Sfs*35	ENST00000295754	NM_003242.5	125	gAa/ga	3/7	1	2	FACETS	0.836	0.793	0.879	1	0.995	1	CLONAL	2	TRUE	1	0.699534706952086	2		432	388	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522532	67522532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767837787	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	123	317	0	ENST00000274335.5:c.29C>T	p.Ala10Val	p.A10V	ENST00000274335		10	gCg/gTg	1/15	1	2	FACETS	0.956	0.874	1	0.956	0.874	1	CLONAL	1	TRUE	1	0.699534706952086	2		317	368	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780232	9780232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761356083	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	149	499	0	ENST00000377346.4:c.1402G>A	p.Ala468Thr	p.A468T	ENST00000377346	NM_005026.3	468	Gcc/Acc	11/24	1	2	FACETS	0.984	0.907	1	0.984	0.907	1	CLONAL	1	TRUE	1	0.699534706952086	2		499	433	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649922	88649922	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786201038	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	67	227	0	ENST00000372037.3:c.176del	p.Leu59Ter	p.L59*	ENST00000372037	NM_004329.2	57	ccT/cc	4/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.699534706952086	2		227	156	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659631	88659632	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	98	325	0	ENST00000372037.3:c.419dup	p.Val141CysfsTer8	p.V141Cfs*8	ENST00000372037	NM_004329.2	138	-/C	6/13	1	2	FACETS	0.898	0.811	0.988	0.898	0.811	0.988	CLONAL	1	TRUE	1	0.699534706952086	2		325	312	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	183	514	0	ENST00000227507.2:c.859C>T	p.Pro287Ser	p.P287S	ENST00000227507	NM_053056.2	287	Ccc/Tcc	5/5	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.699534706952086	2		514	501	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216477	108216477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587782558	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	49	217	0	ENST00000278616.4:c.8432del	p.Lys2811SerfsTer46	p.K2811Sfs*46	ENST00000278616	NM_000051.3	2809	cAa/ca	58/63	1	2	FACETS	0.865	0.746	0.99	0.865	0.746	0.99	CLONAL	1	TRUE	1	0.699534706952086	2		217	162	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870846	12870846	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	155	399	0	ENST00000228872.4:c.73A>T	p.Lys25Ter	p.K25*	ENST00000228872	NM_004064.3	25	Aag/Tag	1/3	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.699534706952086	2		399	408	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	174	832	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.983	0.912	1	0.983	0.912	1	CLONAL	1	TRUE	1	0.699534706952086	2		832	506	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438316	110438317	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	rs532810290	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	76	343	0	ENST00000375856.3:c.82_84dup	p.Asn28dup	p.N28dup	ENST00000375856	NM_003749.2	28	-/AAC	1/2	1	2	FACETS	0.612	0.54	0.688	0.612	0.54	0.688	SUBCLONAL	1	TRUE	1	0.699534706952086	2		343	355	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993737	72993737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776936617	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	174	565	1	ENST00000268489.5:c.308G>A	p.Arg103His	p.R103H	ENST00000268489	NM_006885.3	103	cGc/cAc	2/10	1	2	FACETS	0.888	0.823	0.956	0.888	0.823	0.956	CLONAL	1	TRUE	1	0.699534706952086	2		566	560	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979514	7979514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141010860	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	147	699	1	ENST00000319144.4:c.1511C>T	p.Ala504Val	p.A504V	ENST00000319144	NM_001139.2	504	gCg/gTg	11/15	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.699534706952086	2		700	415	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883773	37883774	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs766671083	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	171	502	0	ENST00000269571.5:c.3391dup	p.Leu1131ProfsTer8	p.L1131Pfs*8	ENST00000269571		1129	gcc/gCcc	26/27	1	2	FACETS	0.922	0.855	0.992	0.922	0.855	0.992	CLONAL	1	TRUE	1	0.699534706952086	2		502	530	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	198	806	4	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.699534706952086	2		810	521	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867522	78867522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770546124	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	220	448	2	ENST00000306801.3:c.2258C>T	p.Ala753Val	p.A753V	ENST00000306801	NM_020761.2	753	gCg/gTg	20/34	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.699534706952086	2		450	517	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212149	5212149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1377011238	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	161	502	0	ENST00000357368.4:c.4882C>T	p.Arg1628Cys	p.R1628C	ENST00000357368	NM_002850.3	1628	Cgc/Tgc	32/38	1	2	FACETS	0.977	0.904	1	0.977	0.904	1	CLONAL	1	TRUE	1	0.699534706952086	2		502	471	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291061	10291061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377146699	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	302	751	0	ENST00000340748.4:c.410C>T	p.Thr137Met	p.T137M	ENST00000340748		137	aCg/aTg	4/40	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.699534706952086	2		751	850	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031524	11031524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754546102	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	192	554	0	ENST00000327064.4:c.1439C>T	p.Thr480Met	p.T480M	ENST00000327064	NM_199141.1	480	aCg/aTg	13/16	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.699534706952086	2		554	534	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298032	15298032	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371176740	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	152	485	0	ENST00000263388.2:c.1724C>T	p.Thr575Met	p.T575M	ENST00000263388	NM_000435.2	575	aCg/aTg	11/33	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.699534706952086	2		485	401	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792423	33792423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	140	365	0	ENST00000498907.2:c.898C>T	p.Arg300Cys	p.R300C	ENST00000498907	NM_004364.3	300	Cgc/Tgc	1/1	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.699534706952086	2		365	375	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210868	36210868	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376781845	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	170	548	0	ENST00000222270.7:c.619C>T	p.Arg207Trp	p.R207W	ENST00000222270	NM_014727.1	207	Cgg/Tgg	3/37	1	2	FACETS	0.912	0.844	0.981	0.912	0.844	0.981	CLONAL	1	TRUE	1	0.699534706952086	2		548	533	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725130	47725130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	66	461	0	ENST00000449228.1:c.614C>A	p.Pro205His	p.P205H	ENST00000449228	NM_001127240.2	205	cCt/cAt	4/4	1	2	FACETS	0.405	0.352	0.462	0.405	0.352	0.462	SUBCLONAL	1	TRUE	1	0.699534706952086	2		461	466	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182508	99182508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	151	392	1	ENST00000074304.5:c.2311C>T	p.Arg771Trp	p.R771W	ENST00000074304	NM_001134224.1	771	Cgg/Tgg	22/26	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.699534706952086	2		393	405	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150022	202150022	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	159	414	0	ENST00000358485.4:c.1463T>C	p.Leu488Pro	p.L488P	ENST00000358485	NM_001080125.1	488	cTg/cCg	8/9	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.699534706952086	2		414	421	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	191	488	0	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.699534706952086	2		488	544	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795103	242795104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768249210	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	104	490	3	ENST00000334409.5:c.105dup	p.Thr36HisfsTer70	p.T36Hfs*70	ENST00000334409	NM_005018.2	35	-/C	2/5	1	2	FACETS	0.611	0.549	0.675	0.611	0.549	0.675	SUBCLONAL	1	TRUE	1	0.699534706952086	2		493	487	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670843	134670843	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	125	435	0	ENST00000398015.3:c.754C>T	p.Arg252Ter	p.R252*	ENST00000398015	NM_004441.4	252	Cga/Tga	3/16	1	2	FACETS	0.933	0.853	1	0.933	0.853	1	CLONAL	1	TRUE	1	0.699534706952086	2		435	383	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266651	142266651	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	71	389	0	ENST00000350721.4:c.3273del	p.Phe1091LeufsTer28	p.F1091Lfs*28	ENST00000350721	NM_001184.3	1091	ttT/tt	16/47	1	2	FACETS	0.819	0.724	0.918	0.819	0.724	0.918	CLONAL	1	TRUE	1	0.699534706952086	2		389	248	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557909	187557909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564430066	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	212	453	0	ENST00000441802.2:c.3802C>T	p.Arg1268Trp	p.R1268W	ENST00000441802	NM_005245.3	1268	Cgg/Tgg	5/27	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.699534706952086	2		453	575	SUCCESS
APC	324	MSKCC	GRCh37	5	112174604	112174604	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768454793	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	127	435	0	ENST00000257430.4:c.3313C>T	p.Arg1105Trp	p.R1105W	ENST00000257430	NM_000038.5	1105	Cgg/Tgg	16/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.699534706952086	2		435	339	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504305	149504305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780819031	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	100	397	0	ENST00000261799.4:c.1897G>A	p.Val633Ile	p.V633I	ENST00000261799	NM_002609.3	633	Gtc/Atc	13/23	1	2	FACETS	0.979	0.887	1	0.979	0.887	1	CLONAL	1	TRUE	1	0.699534706952086	2		397	292	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32191658	32191659	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGCAGCAGC	rs35795312	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	81	492	0	ENST00000375023.3:c.39_47dup	p.Leu14_Leu16dup	p.L14_L16dup	ENST00000375023	NM_004557.3	14	cta/ctGCTGCTGCTa	1/30	1	2	FACETS	0.458	0.404	0.515	0.458	0.404	0.515	SUBCLONAL	1	TRUE	1	0.699534706952086	2		492	506	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	143	511	0	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	0.84	0.771	0.911	0.84	0.771	0.911	CLONAL	1	TRUE	1	0.699534706952086	2		511	487	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222591	157222591	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	161	479	2	ENST00000346085.5:c.1862del	p.Pro621ArgfsTer47	p.P621Rfs*47	ENST00000346085	NM_020732.3	620	Ccc/cc	4/20	1	2	FACETS	0.928	0.858	1	0.928	0.858	1	CLONAL	1	TRUE	1	0.699534706952086	2		481	496	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510805	157510806	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1289067120	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	168	436	0	ENST00000346085.5:c.3586dup	p.Gln1196ProfsTer14	p.Q1196Pfs*14	ENST00000346085	NM_020732.3	1194	acc/aCcc	14/20	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.699534706952086	2		436	480	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527817	157527817	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	158	485	1	ENST00000346085.5:c.5547del	p.Leu1850Ter	p.L1850*	ENST00000346085	NM_020732.3	1848	Ccc/cc	20/20	1	2	FACETS	0.931	0.86	1	0.931	0.86	1	CLONAL	1	TRUE	1	0.699534706952086	2		486	485	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508152	106508152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1446853033	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	134	397	0	ENST00000359195.3:c.146G>A	p.Arg49His	p.R49H	ENST00000359195	NM_002649.2	49	cGc/cAc	2/11	0.699534706952086	3	FACETS	0.942	0.86	1	0.471	0.43	0.514	CLONAL	1	TRUE	1	0.699534706952086	3		397	549	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508508	106508508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	32	352	0	ENST00000359195.3:c.502G>A	p.Val168Met	p.V168M	ENST00000359195	NM_002649.2	168	Gtg/Atg	2/11	0.699534706952086	3	FACETS	0.264	0.214	0.321	0.132	0.107	0.161	SUBCLONAL	1	TRUE	1	0.699534706952086	3		352	468	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873887	151873887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761131667	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	281	420	0	ENST00000262189.6:c.8651G>A	p.Arg2884Gln	p.R2884Q	ENST00000262189	NM_170606.2	2884	cGa/cAa	38/59	0.699534706952086	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.699534706952086	3		420	523	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012386	152012386	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	97	385	6	ENST00000262189.6:c.427del	p.Ser143ValfsTer3	p.S143Vfs*3	ENST00000262189	NM_170606.2	143	Agt/gt	4/59	0.699534706952086	3	FACETS	0.857	0.768	0.95	0.428	0.384	0.475	CLONAL	1	TRUE	1	0.699534706952086	3		391	437	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372206	55372206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	123	469	0	ENST00000297316.4:c.896C>T	p.Ala299Val	p.A299V	ENST00000297316	NM_022454.3	299	gCg/gTg	2/2	0.699534706952086	3	FACETS	0.894	0.812	0.979	0.447	0.406	0.49	CLONAL	1	TRUE	1	0.699534706952086	3		469	531	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982040	70982040	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113166129	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	130	462	1	ENST00000276594.2:c.56C>T	p.Pro19Leu	p.P19L	ENST00000276594	NM_024504.3	19	cCg/cTg	2/8	0.699534706952086	3	FACETS	0.931	0.848	1	0.465	0.424	0.509	CLONAL	1	TRUE	1	0.699534706952086	3		463	539	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1684347	1684348	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCTCCT	rs71578334	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	96	426	0	ENST00000378625.1:c.1766_1771dup	p.Glu589_Glu590dup	p.E589_E590dup	ENST00000378625	NM_001198994.1	589	ggc/gAGGAGGgc	14/14	1	2	FACETS	0.597	0.534	0.663	0.597	0.534	0.663	SUBCLONAL	1	TRUE	1	0.699534706952086	2		426	460	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589686	69589686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756925670	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	211	691	0	ENST00000168712.1:c.167C>T	p.Ala56Val	p.A56V	ENST00000168712	NM_002007.2	56	gCg/gTg	1/3	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.699534706952086	2		691	528	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998792	100998792	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1340917879	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	171	447	0	ENST00000325455.5:c.1010G>A	p.Ser337Asn	p.S337N	ENST00000325455	NM_001202474.3	337	aGc/aAc	1/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.699534706952086	2		447	397	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432555	49432555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	161	462	0	ENST00000301067.7:c.8584C>T	p.Pro2862Ser	p.P2862S	ENST00000301067	NM_003482.3	2862	Cca/Tca	34/54	1	2	FACETS	0.955	0.883	1	0.955	0.883	1	CLONAL	1	TRUE	1	0.699534706952086	2		462	482	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95595827	95595827	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555375788	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	85	278	0	ENST00000393063.1:c.716A>G	p.Asp239Gly	p.D239G	ENST00000393063	NM_030621.3	239	gAc/gGc	7/28	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.699534706952086	2		278	241	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105236701	105236703	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs1412281689	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	163	394	0	ENST00000349310.3:c.1418_1420del	p.Ser473del	p.S473del	ENST00000349310	NM_001014432.1	473	tCCTac/tac	15/15	1	2	FACETS	0.878	0.811	0.946	0.878	0.811	0.946	CLONAL	1	TRUE	1	0.699534706952086	2		394	531	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459333	99459333	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	153	330	0	ENST00000268035.6:c.1969C>A	p.Leu657Ile	p.L657I	ENST00000268035	NM_000875.3	657	Ctt/Att	9/21	1	2	FACETS	0.992	0.916	1	0.992	0.916	1	CLONAL	1	TRUE	1	0.699534706952086	2		330	441	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121554	2121554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774895427	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	167	458	0	ENST00000219476.3:c.1883G>A	p.Arg628His	p.R628H	ENST00000219476	NM_000548.3	628	cGc/cAc	18/42	1	2	FACETS	0.984	0.912	1	0.984	0.912	1	CLONAL	1	TRUE	1	0.699534706952086	2		458	485	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832404	72832404	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	147	456	0	ENST00000268489.5:c.4177G>A	p.Val1393Met	p.V1393M	ENST00000268489	NM_006885.3	1393	Gtg/Atg	9/10	1	2	FACETS	0.926	0.852	1	0.926	0.852	1	CLONAL	1	TRUE	1	0.699534706952086	2		456	454	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56432347	56432347	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	103	241	0	ENST00000407977.2:c.2309G>A	p.Gly770Asp	p.G770D	ENST00000407977		770	gGc/gAc	10/10	1	2	FACETS	0.895	0.81	0.983	0.895	0.81	0.983	CLONAL	1	TRUE	1	0.699534706952086	2		241	329	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211495	36211495	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	77	265	1	ENST00000222270.7:c.1249del	p.Leu417SerfsTer58	p.L417Sfs*58	ENST00000222270	NM_014727.1	416	Ccc/cc	3/37	1	2	FACETS	0.957	0.854	1	0.957	0.854	1	CLONAL	1	TRUE	1	0.699534706952086	2		266	230	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221621	36221621	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	186	494	0	ENST00000222270.7:c.5290T>C	p.Tyr1764His	p.Y1764H	ENST00000222270	NM_014727.1	1764	Tac/Cac	26/37	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.699534706952086	2		494	504	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905945	50905945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781682472	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	151	506	1	ENST00000440232.2:c.917G>A	p.Arg306His	p.R306H	ENST00000440232	NM_002691.3	306	cGc/cAc	8/27	1	2	FACETS	0.951	0.877	1	0.951	0.877	1	CLONAL	1	TRUE	1	0.699534706952086	2		507	454	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31025073	31025073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146743741	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	196	427	1	ENST00000375687.4:c.4558G>A	p.Gly1520Ser	p.G1520S	ENST00000375687	NM_015338.5	1520	Ggt/Agt	13/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.699534706952086	2		428	484	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919213	178919213	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	83	298	0	ENST00000263967.3:c.698T>C	p.Leu233Ser	p.L233S	ENST00000263967	NM_006218.2	233	tTg/tCg	4/21	1	2	FACETS	0.92	0.823	1	0.92	0.823	1	CLONAL	1	TRUE	1	0.699534706952086	2		298	258	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430476	181430476	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	24	486	0	ENST00000325404.1:c.328T>A	p.Tyr110Asn	p.Y110N	ENST00000325404	NM_003106.3	110	Tac/Aac	1/1	1	2	FACETS	0.154	0.12	0.193	0.154	0.12	0.193	SUBCLONAL	1	TRUE	1	0.699534706952086	2		486	447	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156639	106156639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746523679	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	143	468	0	ENST00000380013.4:c.1540C>T	p.His514Tyr	p.H514Y	ENST00000380013	NM_001127208.2	514	Cat/Tat	3/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.699534706952086	2		468	387	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183307	56183307	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	152	394	2	ENST00000399503.3:c.4217A>G	p.Gln1406Arg	p.Q1406R	ENST00000399503	NM_005921.1	1406	cAg/cGg	18/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.699534706952086	2		396	390	SUCCESS
APC	324	MSKCC	GRCh37	5	112173825	112173825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776878597	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	124	379	0	ENST00000257430.4:c.2534G>A	p.Arg845His	p.R845H	ENST00000257430	NM_000038.5	845	cGt/cAt	16/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.699534706952086	2		379	338	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370714	55370714	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1429058725	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	140	398	0	ENST00000297316.4:c.16G>A	p.Ala6Thr	p.A6T	ENST00000297316	NM_022454.3	6	Gcg/Acg	1/2	0.699534706952086	3	FACETS	1	0.959	1	0.538	0.493	0.585	CLONAL	1	TRUE	1	0.699534706952086	3		398	502	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005911	69005912	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	106	339	0	ENST00000288368.4:c.2327dup	p.Gly777TrpfsTer3	p.G777Wfs*3	ENST00000288368	NM_024870.2	774	-/C	21/40	0.699534706952086	3	FACETS	0.969	0.875	1	0.485	0.437	0.534	CLONAL	1	TRUE	1	0.699534706952086	3		339	422	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69143567	69143567	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	103	300	0	ENST00000288368.4:c.4776del		p.X1592_splice	ENST00000288368	NM_024870.2	1592			0.699534706952086	3	FACETS	0.889	0.8	0.982	0.445	0.4	0.491	CLONAL	1	TRUE	1	0.699534706952086	3		300	447	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868968	117868968	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	109	255	0	ENST00000297338.2:c.731A>G	p.Asp244Gly	p.D244G	ENST00000297338	NM_006265.2	244	gAt/gGt	7/14	0.699534706952086	3	FACETS	0.987	0.893	1	0.494	0.446	0.543	CLONAL	1	TRUE	1	0.699534706952086	3		255	426	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730407	133730407	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	148	335	0	ENST00000318560.5:c.473C>A	p.Pro158His	p.P158H	ENST00000318560	NM_005157.4	158	cCt/cAt	3/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.699534706952086	2		335	378	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0066364-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	107	269	1	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.668770900128564	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.668770900128564	3		270	193	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879229	151879229	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763438739	NA	P-0066364-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	258	628	0	ENST00000262189.6:c.5716C>T	p.Arg1906Ter	p.R1906*	ENST00000262189	NM_170606.2	1906	Cga/Tga	36/59	0.668770900128564	3	FACETS	0.91	0.86	0.959	0.91	0.86	0.959	CLONAL	2	TRUE	1	0.668770900128564	3		628	566	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297919	15297919	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1442385919	NA	P-0066364-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	163	557	0	ENST00000263388.2:c.1837A>G	p.Thr613Ala	p.T613A	ENST00000263388	NM_000435.2	613	Aca/Gca	11/33	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.668770900128564	2		557	449	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913396	NA	P-0066366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	167	474	0	ENST00000349496.5:c.95A>G	p.Asp32Gly	p.D32G	ENST00000349496	NM_001904.3	32	gAc/gGc	3/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.717228762038063	2		474	443	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78435612	78435612	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs868301311	NA	P-0066366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	75	339	2	ENST00000370768.2:c.208G>T	p.Gly70Ter	p.G70*	ENST00000370768	NM_003902.3	70	Gga/Tga	2/20	1	2	FACETS	0.854	0.759	0.953	0.854	0.759	0.953	CLONAL	1	TRUE	1	0.717228762038063	2		341	245	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399129	139399129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745901158	NA	P-0066366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	52	366	0	ENST00000277541.6:c.5014C>T	p.Arg1672Cys	p.R1672C	ENST00000277541	NM_017617.3	1672	Cgc/Tgc	26/34	1	2	FACETS	0.452	0.386	0.522	0.452	0.386	0.522	SUBCLONAL	1	TRUE	1	0.717228762038063	2		366	321	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217197	66217197	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	123	431	0	ENST00000273854.3:c.2418C>G	p.Ile806Met	p.I806M	ENST00000273854	NM_004439.5	806	atC/atG	14/18	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.717228762038063	2		431	338	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654712	29654712	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	307	443	0	ENST00000356175.3:c.5401C>T	p.Gln1801Ter	p.Q1801*	ENST00000356175	NM_000267.3	1801	Cag/Tag	37/57	0.638738938780518	5	FACETS	1	0.974	1			1	CLONAL	2	TRUE	NA	0.717228762038063	5		443	848	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574154	41574154	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs757934635	NA	P-0066366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	179	480	0	ENST00000263253.7:c.6439C>G	p.Gln2147Glu	p.Q2147E	ENST00000263253	NM_001429.3	2147	Cag/Gag	31/31	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.717228762038063	2		480	452	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195419	102195419	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	29	438	0	ENST00000263464.3:c.179T>C	p.Val60Ala	p.V60A	ENST00000263464	NM_001165.4	60	gTg/gCg	2/9	0.717228762038063	3	FACETS	0.211	0.169	0.26	0.106	0.084	0.13	SUBCLONAL	1	TRUE	1	0.717228762038063	3		438	520	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063334	67063334	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	85	370	0	ENST00000412916.2:c.24G>C	p.Gln8His	p.Q8H	ENST00000412916		8	caG/caC	1/6	0.244197854450134	3	FACETS	1	0.969	1	0.61	0.547	0.676	INDETERMINATE	1	TRUE	1	0.717228762038063	3		370	264	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013738	12013738	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	180	346	0	ENST00000353533.5:c.680A>T	p.His227Leu	p.H227L	ENST00000353533	NM_003010.3	227	cAc/cTc	6/11	0.690883567439175	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.717228762038063	2		346	233	SUCCESS
PHF6	84295	MSKCC	GRCh37	X	133547868	133547868	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	118	407	0	ENST00000332070.3:c.601C>A	p.His201Asn	p.H201N	ENST00000332070	NM_032458.2	201	Cac/Aac	7/10	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.717228762038063	2		407	317	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556437	29556465	+	frameshift_variant	Frame_Shift_Del	DEL	ACAAATTGAAGAATACCATCAGCAAGTTT	ACAAATTGAAGAATACCATCAGCAAGTTT	-	novel	NA	P-0066366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	336	404	0	ENST00000356175.3:c.2804_2832del	p.Asn935IlefsTer2	p.N935Ifs*2	ENST00000356175	NM_000267.3	935	aACAAATTGAAGAATACCATCAGCAAGTTT/a	21/57	0.638738938780518	5	FACETS	0.938	0.895	0.982			1	CLONAL	3	TRUE	NA	0.717228762038063	5		404	691	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250668	26250668	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	376	572	0	ENST00000446824.2:c.166C>T	p.Gln56Ter	p.Q56*	ENST00000446824	NM_021018.2	56	Cag/Tag	1/1	0.713788530579834	4	FACETS	1	0.994	1	0.61	0.583	0.636	CLONAL	2	TRUE	0	0.717228762038063	4		572	738	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22408252	22408252	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	104	385	0	ENST00000344548.3:c.143G>T	p.Gly48Val	p.G48V	ENST00000344548	NM_001039802.1	48	gGa/gTa	4/7	1	2	FACETS	0.868	0.786	0.953	0.868	0.786	0.953	CLONAL	1	TRUE	1	0.717228762038063	2		385	334	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2029030	2029030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1187602827	NA	P-0066366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	155	529	0	ENST00000349721.2:c.8C>T	p.Thr3Met	p.T3M	ENST00000349721	NM_003070.3	3	aCg/aTg	2/34	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.717228762038063	2		529	388	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483979	212483979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066366-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	93	350	0	ENST00000342788.4:c.2224G>A	p.Glu742Lys	p.E742K	ENST00000342788	NM_005235.2	742	Gaa/Aaa	19/28	0.387815085161533	3	FACETS	1	0.975	1	0.631	0.569	0.696	INDETERMINATE	1	TRUE	1	0.717228762038063	3		350	279	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696449	47696449	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	174	459	0	ENST00000347630.2:c.374T>G	p.Phe125Cys	p.F125C	ENST00000347630	NM_001007230.1	125	tTt/tGt	6/11	1	2	FACETS	0.901	0.832	0.973	1	0.992	1	CLONAL	2	TRUE	1	0.27194470126755	2		459	710	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858913	243858913	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs866698621	NA	P-0066382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	92	297	0	ENST00000263826.5:c.152T>G	p.Leu51Arg	p.L51R	ENST00000263826	NM_005465.4	51	cTc/cGc	2/13	1	2	FACETS	0.813	0.727	0.904	1	0.983	1	CLONAL	2	TRUE	1	0.27194470126755	2		297	416	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244466	41244466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357049	NA	P-0066382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	95	372	0	ENST00000357654.3:c.3082C>T	p.Arg1028Cys	p.R1028C	ENST00000357654	NM_007294.3	1028	Cgt/Tgt	10/23	1	2	FACETS	0.83	0.743	0.921	1	0.984	1	CLONAL	2	TRUE	1	0.27194470126755	2		372	421	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307418	118307418	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	80	240	0	ENST00000534358.1:c.191C>G	p.Ala64Gly	p.A64G	ENST00000534358	NM_005933.3	64	gCg/gGg	1/36	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.27194470126755	2		240	403	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495648	72495648	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0066382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	168	309	0	ENST00000477973.2:c.424A>T	p.Arg142Ter	p.R142*	ENST00000477973	NM_012234.5	142	Aga/Tga	1/4	1	2	FACETS	0.929	0.857	1	1	0.992	1	CLONAL	2	TRUE	1	0.27194470126755	2		309	665	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450340	50450340	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	212	494	0	ENST00000331340.3:c.524G>T	p.Cys175Phe	p.C175F	ENST00000331340	NM_006060.4	175	tGc/tTc	5/8	0.27194470126755	3	FACETS	0.981	0.917	1	1	0.992	1	CLONAL	3	TRUE	1	0.27194470126755	3		494	602	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	9	269	1	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.61	0.404	0.871	0.61	0.404	0.871	SUBCLONAL	1	TRUE	1	0.18	2		270	164	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	45	731	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.18	2		731	464	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294664	1294664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	27	543	0	ENST00000310581.5:c.337G>A	p.Glu113Lys	p.E113K	ENST00000310581	NM_198253.2	113	Gag/Aag	2/16	1	2	FACETS	0.633	0.503	0.782	0.633	0.503	0.782	SUBCLONAL	1	TRUE	1	0.18	2		543	474	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835629	68835629	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658932	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	80	468	0	ENST00000261769.5:c.220C>T	p.Arg74Ter	p.R74*	ENST00000261769	NM_004360.3	74	Cga/Tga	3/16	0.3	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.18	1		468	763	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745476	162745476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471671366	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	42	426	0	ENST00000367921.3:c.1891C>T	p.Arg631Trp	p.R631W	ENST00000367921	NM_006182.2	631	Cgg/Tgg	15/18	0.187173617840059	3	FACETS	0.965	0.805	1	0.483	0.402	0.572	CLONAL	1	TRUE	1	0.18	3		426	527	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021828	71021828	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	35	411	0	ENST00000318789.4:c.1531-1G>A		p.X511_splice	ENST00000318789	NM_032682.5	511			1	2	FACETS	0.819	0.671	0.985	0.819	0.671	0.985	CLONAL	1	TRUE	1	0.18	2		411	475	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641083	93641083	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	25	354	0	ENST00000375746.1:c.1429C>G	p.Gln477Glu	p.Q477E	ENST00000375746	NM_001174167.1	477	Cag/Gag	11/14	0.3	1	FACETS	0.563	0.443	0.702	0.563	0.443	0.702	SUBCLONAL	1	TRUE	0	0.18	1		354	449	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38064160	38064160	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	64	710	0	ENST00000250448.2:c.18G>C	p.Lys6Asn	p.K6N	ENST00000250448	NM_004496.3	6	aaG/aaC	1/2	1	2	FACETS	0.934	0.808	1	0.934	0.808	1	CLONAL	1	TRUE	1	0.18	2		710	761	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802635	135802635	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203343	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	47	420	0	ENST00000298552.3:c.163C>T	p.Gln55Ter	p.Q55*	ENST00000298552	NM_001162426.1	55	Cag/Tag	4/23	1	2	FACETS	0.705	0.593	0.828	0.705	0.593	0.828	SUBCLONAL	1	TRUE	1	0.18	2		420	741	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489526	40489526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	65	487	0	ENST00000264657.5:c.724G>A	p.Asp242Asn	p.D242N	ENST00000264657	NM_139276.2	242	Gac/Aac	8/24	1	2	FACETS	0.98	0.849	1	0.98	0.849	1	CLONAL	1	TRUE	1	0.18	2		487	737	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258542	16258542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs946117307	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	81	618	0	ENST00000375759.3:c.5807G>A	p.Arg1936Gln	p.R1936Q	ENST00000375759	NM_015001.2	1936	cGa/cAa	11/15	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.18	2		618	831	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127539	55127539	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	41	411	0	ENST00000257290.5:c.327G>C	p.Glu109Asp	p.E109D	ENST00000257290	NM_006206.4	109	gaG/gaC	3/23	0.3	1	FACETS	0.74	0.616	0.879	0.74	0.616	0.879	SUBCLONAL	1	TRUE	0	0.18	1		411	560	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512419	149512419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs942220808	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	56	548	0	ENST00000261799.4:c.1021G>A	p.Glu341Lys	p.E341K	ENST00000261799	NM_002609.3	341	Gag/Aag	7/23	1	2	FACETS	0.91	0.778	1	0.91	0.778	1	CLONAL	1	TRUE	1	0.18	2		548	684	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62303953	62303953	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	51	434	0	ENST00000360203.5:c.744C>G	p.Ile248Met	p.I248M	ENST00000360203	NM_001283009.1	248	atC/atG	9/35	1	2	FACETS	0.847	0.719	0.988	0.847	0.719	0.988	CLONAL	1	TRUE	1	0.18	2		434	669	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526209	189526209	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767384779	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	56	579	0	ENST00000264731.3:c.473C>T	p.Ala158Val	p.A158V	ENST00000264731	NM_003722.4	158	gCt/gTt	4/14	1	2	FACETS	0.835	0.714	0.968	0.835	0.714	0.968	CLONAL	1	TRUE	1	0.18	2		579	745	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489537	56489537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	56	461	0	ENST00000267101.3:c.2002G>A	p.Gly668Arg	p.G668R	ENST00000267101	NM_001982.3	668	Ggg/Agg	17/28	1	2	FACETS	0.738	0.631	0.856	0.738	0.631	0.856	SUBCLONAL	1	TRUE	1	0.18	2		461	843	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524393	176524393	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	41	510	0	ENST00000292408.4:c.2254G>A	p.Glu752Lys	p.E752K	ENST00000292408	NM_213647.1	752	Gag/Aag	17/18	1	2	FACETS	0.661	0.549	0.786	0.661	0.549	0.786	SUBCLONAL	1	TRUE	1	0.18	2		510	689	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52729226	52729226	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	53	487	0	ENST00000322088.6:c.1762C>G	p.Leu588Val	p.L588V	ENST00000322088	NM_014225.5	588	Ctc/Gtc	15/15	1	2	FACETS	0.853	0.727	0.993	0.853	0.727	0.993	CLONAL	1	TRUE	1	0.18	2		487	690	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118830	115118853	+	inframe_deletion	In_Frame_Del	DEL	TCCACCGAGAATTGTGAAATTTAT	TCCACCGAGAATTGTGAAATTTAT	-	novel	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	40	486	0	ENST00000257566.3:c.488_511del	p.Tyr163_Met171delinsLeu	p.Y163_M171delinsL	ENST00000257566	NM_016569.3	163	tATAAATTTCACAATTCTCGGTGGAtg/ttg	2/8	1	2	FACETS	0.832	0.691	0.99	0.832	0.691	0.99	CLONAL	1	TRUE	1	0.18	2		486	534	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149450094	149450094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	69	472	0	ENST00000286301.3:c.1123G>A	p.Glu375Lys	p.E375K	ENST00000286301	NM_005211.3	375	Gag/Aag	8/22	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.18	2		472	656	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2039549	2039549	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	53	509	0	ENST00000349721.2:c.439C>T	p.Gln147Ter	p.Q147*	ENST00000349721	NM_003070.3	147	Cag/Tag	4/34	NA	2	FACETS	0.776	0.66	0.903			1	INDETERMINATE	1	TRUE	NA	0.18	2		509	759	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112280	115112281	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	31	494	0	ENST00000257566.3:c.1458_1459dup	p.Asp487GlyfsTer146	p.D487Gfs*146	ENST00000257566	NM_016569.3	487	gac/gGGac	7/8	1	2	FACETS	0.696	0.562	0.848	0.696	0.562	0.848	SUBCLONAL	1	TRUE	1	0.18	2		494	495	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78931424	78931424	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	51	481	0	ENST00000306801.3:c.3371G>A	p.Gly1124Glu	p.G1124E	ENST00000306801	NM_020761.2	1124	gGa/gAa	29/34	1	2	FACETS	0.901	0.765	1	0.901	0.765	1	CLONAL	1	TRUE	1	0.18	2		481	629	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582876	95582876	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	30	419	0	ENST00000393063.1:c.1666C>G	p.Pro556Ala	p.P556A	ENST00000393063	NM_030621.3	556	Ccc/Gcc	11/28	1	2	FACETS	0.797	0.642	0.974	0.797	0.642	0.974	CLONAL	1	TRUE	1	0.18	2		419	418	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10800428	10800428	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	44	461	0	ENST00000361367.2:c.3298G>C	p.Glu1100Gln	p.E1100Q	ENST00000361367	NM_014633.3	1100	Gag/Cag	25/25	1	2	FACETS	0.795	0.666	0.939	0.795	0.666	0.939	CLONAL	1	TRUE	1	0.18	2		461	615	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2097727	2097727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1421779919	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	33	405	0	ENST00000219066.1:c.122G>A	p.Arg41Lys	p.R41K	ENST00000219066	NM_002528.5	41	aGa/aAa	1/6	1	2	FACETS	0.652	0.53	0.791	0.652	0.53	0.791	SUBCLONAL	1	TRUE	1	0.18	2		405	562	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628575	90628575	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs774623780	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	42	501	0	ENST00000330062.3:c.1012G>T	p.Asp338Tyr	p.D338Y	ENST00000330062	NM_002168.2	338	Gat/Tat	8/11	0.3	1	FACETS	0.708	0.59	0.839	0.708	0.59	0.839	SUBCLONAL	1	TRUE	0	0.18	1		501	600	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660831	227660831	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	50	601	0	ENST00000305123.5:c.2624G>T	p.Arg875Leu	p.R875L	ENST00000305123	NM_005544.2	875	cGa/cTa	1/2	0.3	1	FACETS	0.67	0.567	0.784	0.67	0.567	0.784	SUBCLONAL	1	TRUE	0	0.18	1		601	754	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817754	3817754	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	55	385	0	ENST00000262367.5:c.3217C>G	p.Gln1073Glu	p.Q1073E	ENST00000262367	NM_004380.2	1073	Cag/Gag	16/31	1	2	FACETS	0.895	0.764	1	0.895	0.764	1	CLONAL	1	TRUE	1	0.18	2		385	683	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258538	16258538	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	80	625	0	ENST00000375759.3:c.5803G>C	p.Glu1935Gln	p.E1935Q	ENST00000375759	NM_015001.2	1935	Gag/Cag	11/15	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.18	2		625	828	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958595	175958595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	36	400	0	ENST00000367669.3:c.1750G>A	p.Asp584Asn	p.D584N	ENST00000367669	NM_022457.5	584	Gat/Aat	16/20	0.187173617840059	3	FACETS	1	0.864	1	0.53	0.436	0.636	CLONAL	1	TRUE	1	0.18	3		400	411	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858539	27858539	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	53	556	0	ENST00000359303.2:c.32C>G	p.Ser11Cys	p.S11C	ENST00000359303	NM_003535.2	11	tCt/tGt	1/1	1	2	FACETS	0.741	0.63	0.863	0.741	0.63	0.863	SUBCLONAL	1	TRUE	1	0.18	2		556	795	SUCCESS
APC	324	MSKCC	GRCh37	5	112179541	112179541	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs767530768	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	38	428	0	ENST00000257430.4:c.8250G>C	p.Glu2750Asp	p.E2750D	ENST00000257430	NM_000038.5	2750	gaG/gaC	16/16	1	2	FACETS	0.843	0.696	1	0.843	0.696	1	CLONAL	1	TRUE	1	0.18	2		428	501	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287544	33287544	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	77	512	0	ENST00000374542.5:c.1553C>T	p.Ser518Leu	p.S518L	ENST00000374542	NM_001141970.1	518	tCa/tTa	6/8	1	2	FACETS	0.871	0.763	0.988	0.871	0.763	0.988	CLONAL	1	TRUE	1	0.18	2		512	982	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124682	108124682	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	36	417	0	ENST00000278616.4:c.2040C>G	p.Phe680Leu	p.F680L	ENST00000278616	NM_000051.3	680	ttC/ttG	13/63	1	2	FACETS	0.803	0.66	0.964	0.803	0.66	0.964	CLONAL	1	TRUE	1	0.18	2		417	498	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937230	76937230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910849788	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	16	406	0	ENST00000373344.5:c.3518C>T	p.Ser1173Leu	p.S1173L	ENST00000373344	NM_000489.3	1173	tCa/tTa	9/35	1	2	FACETS	0.561	0.414	0.737	0.561	0.414	0.737	SUBCLONAL	1	TRUE	1	0.18	2		406	317	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362480	118362480	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	36	388	0	ENST00000534358.1:c.4841C>G	p.Ser1614Cys	p.S1614C	ENST00000534358	NM_005933.3	1614	tCt/tGt	15/36	1	2	FACETS	0.828	0.68	0.994	0.828	0.68	0.994	CLONAL	1	TRUE	1	0.18	2		388	483	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21630765	21630765	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	29	361	0	ENST00000421138.2:c.839C>G	p.Ser280Cys	p.S280C	ENST00000421138		280	tCt/tGt	8/16	0.3	1	FACETS	0.808	0.649	0.988	0.808	0.649	0.988	CLONAL	1	TRUE	0	0.18	1		361	363	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188235	10188236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0066384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	96	260	0	ENST00000256474.2:c.378_379insA	p.Gly127ArgfsTer5	p.G127Rfs*5	ENST00000256474	NM_000551.3	126	-/A	2/3	0.38804871363171	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	0	0.38804871363171	1		260	393	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441196	52441201	+	inframe_deletion	In_Frame_Del	DEL	CAATGG	CAATGG	-	novel	NA	P-0066384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	82	341	0	ENST00000460680.1:c.569_574del	p.Pro190_Asp192delinsHis	p.P190_D192delinsH	ENST00000460680	NM_004656.3	190	cCCATTGac/cac	7/17	0.38804871363171	1	FACETS	0.908	0.806	1	0.908	0.806	1	CLONAL	1	TRUE	0	0.38804871363171	1		341	375	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221697	22221702	+	inframe_deletion	In_Frame_Del	DEL	CCGGGC	CCGGGC	-	novel	NA	P-0066384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	69	358	0	ENST00000215832.6:c.29_34del	p.Gly10_Pro11del	p.G10_P11del	ENST00000215832	NM_002745.4	10	gGCCCGGag/gag	1/9	1	2	FACETS	0.969	0.849	1	0.969	0.849	1	CLONAL	1	TRUE	1	0.38804871363171	2		358	367	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164514	47164514	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	44	319	0	ENST00000409792.3:c.1612G>T	p.Gly538Ter	p.G538*	ENST00000409792	NM_014159.6	538	Gga/Tga	3/21	0.38804871363171	1	FACETS	0.556	0.468	0.652	0.556	0.468	0.652	SUBCLONAL	1	TRUE	0	0.38804871363171	1		319	329	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143044484	143044484	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	35	227	0	ENST00000262992.4:c.1978G>A	p.Gly660Arg	p.G660R	ENST00000262992	NM_001101669.1	660	Ggg/Agg	18/24	0.204203692229958	1	FACETS	0.442	0.363	0.53	0.442	0.363	0.53	INDETERMINATE	1	TRUE	0	0.38804871363171	1		227	329	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255466	16255466	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	73	353	0	ENST00000375759.3:c.2731T>C	p.Ser911Pro	p.S911P	ENST00000375759	NM_015001.2	911	Tct/Cct	11/15	0.204203692229958	1	FACETS	0.528	0.462	0.599	0.528	0.462	0.599	INDETERMINATE	1	TRUE	0	0.38804871363171	1		353	574	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0066387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	304	591	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.6131305653136	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	0	0.632741000364581	3		591	410	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949629	151949629	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0066387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	50	350	0	ENST00000262189.6:c.1469+2T>G		p.X490_splice	ENST00000262189	NM_170606.2	490			0.163597771681374	2	FACETS	0.538	0.459	0.623	0.269	0.229	0.312	INDETERMINATE	1	TRUE	0	0.632741000364581	2		350	294	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139640	202139645	+	inframe_deletion	In_Frame_Del	DEL	CTCGGA	CTCGGA	-	novel	NA	P-0066387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	50	439	0	ENST00000358485.4:c.804_809del	p.Asp269_Ser270del	p.D269_S270del	ENST00000358485	NM_001080125.1	267	atCTCGGAc/atc	6/9	0.212248811942676	3	FACETS	0.549	0.467	0.638	0.274	0.233	0.319	INDETERMINATE	1	TRUE	1	0.632741000364581	3		439	379	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624780	9624780	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	65	386	0	ENST00000353224.5:c.197C>A	p.Pro66His	p.P66H	ENST00000353224	NM_177990.2	66	cCt/cAt	3/10	0.646972222373426	3	FACETS	0.966	0.846	1	0.322	0.282	0.365	CLONAL	1	TRUE	0	0.632741000364581	3		386	280	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2104102	2104102	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	38	414	0	ENST00000349721.2:c.3225G>C	p.Met1075Ile	p.M1075I	ENST00000349721	NM_003070.3	1075	atG/atC	23/34	0.597754232317824	4	FACETS	0.373	0.308	0.446	0.124	0.102	0.149	SUBCLONAL	1	TRUE	1	0.632741000364581	4		414	526	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258894	16258894	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	271	547	3	ENST00000375759.3:c.6164del	p.Pro2055LeufsTer9	p.P2055Lfs*9	ENST00000375759	NM_015001.2	2053	aaC/aa	11/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.529240860526875	2		550	970	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	137	721	4	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.589	0.535	0.645	0.589	0.535	0.645	SUBCLONAL	1	TRUE	1	0.529240860526875	2		725	879	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	243	710	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.991	0.927	1	0.991	0.927	1	CLONAL	1	TRUE	1	0.529240860526875	2		713	927	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	203	412	7	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.529240860526875	2		419	725	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	266	478	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.767	0.724	0.811	1	0.994	1	SUBCLONAL	2	TRUE	1	0.529240860526875	2		479	655	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	122	372	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.529240860526875	2		372	433	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	152	481	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.943	0.866	1	0.943	0.866	1	CLONAL	1	TRUE	1	0.529240860526875	2		481	609	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	187	464	5	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.904	0.836	0.973	0.904	0.836	0.973	CLONAL	1	TRUE	1	0.529240860526875	2		469	782	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	195	279	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.529240860526875	1	FACETS	0.975	0.909	1	0.975	0.909	1	CLONAL	1	TRUE	0	0.529240860526875	1		279	556	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198389	138198389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751123351	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	192	392	0	ENST00000237289.4:c.982G>A	p.Ala328Thr	p.A328T	ENST00000237289	NM_001270507.1	328	Gca/Aca	6/9	1	2	FACETS	0.975	0.905	1	0.975	0.905	1	CLONAL	1	TRUE	1	0.529240860526875	2		392	744	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	242	436	0	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.529240860526875	2		436	881	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	184	422	5	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.979	0.907	1	0.979	0.907	1	CLONAL	1	TRUE	1	0.529240860526875	2		427	710	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678783	52678784	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	102	217	0	ENST00000394830.3:c.835dup	p.Ile279AsnfsTer8	p.I279Nfs*8	ENST00000394830	NM_018313.4	279	ata/aAta	9/30	1	2	FACETS	0.94	0.847	1	0.94	0.847	1	CLONAL	1	TRUE	1	0.529240860526875	2		217	410	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822563	72822564	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	rs376311468	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	115	525	0	ENST00000268489.5:c.9609_9611dup	p.Gln3204dup	p.Q3204dup	ENST00000268489	NM_006885.3	3204	caa/caGCAa	10/10	1	2	FACETS	0.519	0.467	0.573	0.519	0.467	0.573	SUBCLONAL	1	TRUE	1	0.529240860526875	2		525	838	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	116	531	0	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	0.509	0.458	0.562	0.509	0.458	0.562	SUBCLONAL	1	TRUE	1	0.529240860526875	2		531	862	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006026	22006026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1256288325	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	247	522	0	ENST00000276925.6:c.377G>A	p.Arg126His	p.R126H	ENST00000276925	NM_004936.3	126	cGc/cAc	2/2	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.529240860526875	2		522	876	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489571	56489571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	234	440	0	ENST00000267101.3:c.2036G>A	p.Arg679Gln	p.R679Q	ENST00000267101	NM_001982.3	679	cGa/cAa	17/28	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.529240860526875	2		440	879	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155778	106155779	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs759055581	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	197	449	0	ENST00000380013.4:c.685dup	p.Thr229AsnfsTer25	p.T229Nfs*25	ENST00000380013	NM_001127208.2	227	gaa/gAaa	3/11	1	2	FACETS	0.838	0.777	0.902	0.838	0.777	0.902	CLONAL	1	TRUE	1	0.529240860526875	2		449	888	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740809	58740809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs765769406	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	272	493	0	ENST00000305921.3:c.1714C>T	p.Arg572Ter	p.R572*	ENST00000305921	NM_003620.3	572	Cga/Tga	6/6	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.529240860526875	2		493	940	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656840	45656840	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	163	510	0	ENST00000407780.3:c.316del	p.Gln106ArgfsTer11	p.Q106Rfs*11	ENST00000407780	NM_001283052.1	106	Cag/ag	3/7	1	2	FACETS	0.707	0.649	0.768	0.707	0.649	0.768	SUBCLONAL	1	TRUE	1	0.529240860526875	2		510	871	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123616	108123616	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	60	253	0	ENST00000278616.4:c.1880del	p.Phe627SerfsTer22	p.F627Sfs*22	ENST00000278616	NM_000051.3	625	aaT/aa	12/63	1	2	FACETS	0.869	0.756	0.989	0.869	0.756	0.989	CLONAL	1	TRUE	1	0.529240860526875	2		253	261	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099403	157099426	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAGCAA	CAGCAGCAGCAGCAGCAGCAGCAA	-	rs770869529	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	71	506	0	ENST00000346085.5:c.369_392del	p.Gln124_Gln131del	p.Q124_Q131del	ENST00000346085	NM_020732.3	114	CAGCAGCAGCAGCAGCAGCAGCAA/-	1/20	1	2	FACETS	0.316	0.275	0.361	0.316	0.275	0.361	SUBCLONAL	1	TRUE	1	0.529240860526875	2		506	848	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133806	55133806	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs77524207	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	132	400	0	ENST00000257290.5:c.1019G>A	p.Arg340Gln	p.R340Q	ENST00000257290	NM_006206.4	340	cGg/cAg	7/23	1	2	FACETS	0.644	0.585	0.706	0.644	0.585	0.706	SUBCLONAL	1	TRUE	1	0.529240860526875	2		400	775	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216189	36216189	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	209	497	3	ENST00000222270.7:c.3602del	p.Pro1201ArgfsTer154	p.P1201Rfs*154	ENST00000222270	NM_014727.1	1199	ggC/gg	11/37	1	2	FACETS	0.922	0.857	0.988	0.922	0.857	0.988	CLONAL	1	TRUE	1	0.529240860526875	2		500	857	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346613	89346613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370535812	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	59	476	0	ENST00000301030.4:c.6337G>A	p.Gly2113Ser	p.G2113S	ENST00000301030	NM_001256183.1	2113	Ggc/Agc	9/13	1	2	FACETS	0.304	0.261	0.351	0.304	0.261	0.351	SUBCLONAL	1	TRUE	1	0.529240860526875	2		476	734	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222520	39222520	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	154	363	0	ENST00000402219.2:c.3090del	p.Lys1030AsnfsTer6	p.K1030Nfs*6	ENST00000402219	NM_005633.3	1030	aaA/aa	20/23	1	2	FACETS	0.964	0.886	1	0.964	0.886	1	CLONAL	1	TRUE	1	0.529240860526875	2		363	604	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346972	89346972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1251064433	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	177	440	0	ENST00000301030.4:c.5978G>A	p.Arg1993His	p.R1993H	ENST00000301030	NM_001256183.1	1993	cGt/cAt	9/13	1	2	FACETS	0.919	0.849	0.991	0.919	0.849	0.991	CLONAL	1	TRUE	1	0.529240860526875	2		440	728	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124202	2124202	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs796053511	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	212	429	0	ENST00000219476.3:c.2357G>A	p.Arg786His	p.R786H	ENST00000219476	NM_000548.3	786	cGc/cAc	22/42	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.529240860526875	2		429	735	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111145	193111146	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	rs760591174	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	32	417	0	ENST00000367435.3:c.687_688dup	p.Val230GlufsTer28	p.V230Efs*28	ENST00000367435	NM_024529.4	226	-/AG	7/17	1	2	FACETS	0.257	0.208	0.313	0.257	0.208	0.313	SUBCLONAL	1	TRUE	1	0.529240860526875	2		417	470	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420934	49420934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs569620684	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	202	411	0	ENST00000301067.7:c.14815G>A	p.Glu4939Lys	p.E4939K	ENST00000301067	NM_003482.3	4939	Gaa/Aaa	48/54	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.529240860526875	2		411	726	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119974	70120026	+	frameshift_variant	Frame_Shift_Del	DEL	GCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAGGCGCCGCC	GCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAGGCGCCGCC	-	novel	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	157	443	0	ENST00000245479.2:c.984_1036del	p.Ser330AlafsTer230	p.S330Afs*230	ENST00000245479	NM_000346.3	326	GCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAGGCGCCGCCg/g	3/3	1	2	FACETS	0.906	0.833	0.982	0.906	0.833	0.982	CLONAL	1	TRUE	1	0.529240860526875	2		443	655	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485879	8485879	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	186	499	0	ENST00000356435.5:c.2938A>G	p.Thr980Ala	p.T980A	ENST00000356435		980	Aca/Gca	17/35	1	2	FACETS	0.85	0.786	0.916	0.85	0.786	0.916	CLONAL	1	TRUE	1	0.529240860526875	2		499	827	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882974	89882974	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748624754	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	37	401	0	ENST00000389301.3:c.50del	p.Gly17AlafsTer27	p.G17Afs*27	ENST00000389301	NM_000135.2	17	gGc/gc	1/43	1	2	FACETS	0.244	0.2	0.293	0.244	0.2	0.293	SUBCLONAL	1	TRUE	1	0.529240860526875	2		401	573	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433721	49433721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374000532	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	44	475	0	ENST00000301067.7:c.7832G>A	p.Arg2611His	p.R2611H	ENST00000301067	NM_003482.3	2611	cGc/cAc	31/54	1	2	FACETS	0.194	0.161	0.229	0.194	0.161	0.229	SUBCLONAL	1	TRUE	1	0.529240860526875	2		475	859	SUCCESS
MTAP	4507	MSKCC	GRCh37	9	21854745	21854745	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	196	417	0	ENST00000380172.4:c.571del	p.Ala191ArgfsTer6	p.A191Rfs*6	ENST00000380172	NM_002451.3	189	tGg/tg	6/8	1	2	FACETS	0.877	0.813	0.943	0.877	0.813	0.943	CLONAL	1	TRUE	1	0.529240860526875	2		417	845	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435700	56435701	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	173	440	0	ENST00000407977.2:c.1436_1437del	p.Val479GlyfsTer25	p.V479Gfs*25	ENST00000407977		479	gTG/g	9/10	1	2	FACETS	0.878	0.809	0.948	0.878	0.809	0.948	CLONAL	1	TRUE	1	0.529240860526875	2		440	745	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311682	15311684	+	inframe_deletion	In_Frame_Del	DEL	CGG	CGG	-	rs894374843	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	171	581	12	ENST00000263388.2:c.33_35del	p.Arg13del	p.R13del	ENST00000263388	NM_000435.2	11	cgCCGt/cgt	1/33	1	2	FACETS	0.77	0.709	0.834	0.77	0.709	0.834	SUBCLONAL	1	TRUE	1	0.529240860526875	2		593	839	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335809	73335809	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144010862	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	148	319	0	ENST00000377767.4:c.2486G>A	p.Arg829His	p.R829H	ENST00000377767	NM_014953.3	829	cGt/cAt	18/21	1	2	FACETS	0.966	0.886	1	0.966	0.886	1	CLONAL	1	TRUE	1	0.529240860526875	2		319	579	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084127	47084127	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	241	499	0	ENST00000409792.3:c.7162del	p.Thr2388ProfsTer23	p.T2388Pfs*23	ENST00000409792	NM_014159.6	2388	Acc/cc	17/21	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.529240860526875	2		499	887	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366311	15366311	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	229	401	0	ENST00000263377.2:c.1844A>C	p.Lys615Thr	p.K615T	ENST00000263377	NM_058243.2	615	aAg/aCg	10/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.529240860526875	2		401	765	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591091	67591091	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768613622	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	114	340	0	ENST00000274335.5:c.1684C>T	p.Arg562Cys	p.R562C	ENST00000274335		562	Cgt/Tgt	12/15	1	2	FACETS	0.804	0.727	0.885	0.804	0.727	0.885	CLONAL	1	TRUE	1	0.529240860526875	2		340	536	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284927	15284927	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	234	439	0	ENST00000263388.2:c.4688C>A	p.Pro1563His	p.P1563H	ENST00000263388	NM_000435.2	1563	cCt/cAt	25/33	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.529240860526875	2		439	749	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121515	108121516	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTTCTAC	novel	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	186	360	0	ENST00000278616.4:c.1325_1331dup	p.Gln445SerfsTer44	p.Q445Sfs*44	ENST00000278616	NM_000051.3	441	-/CTTCTAC	10/63	1	2	FACETS	0.848	0.784	0.914	0.848	0.784	0.914	CLONAL	1	TRUE	1	0.529240860526875	2		360	829	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381487	81381487	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	44	371	0	ENST00000222390.5:c.574A>G	p.Ser192Gly	p.S192G	ENST00000222390	NM_000601.4	192	Agc/Ggc	5/18	1	2	FACETS	0.23	0.192	0.273	0.23	0.192	0.273	SUBCLONAL	1	TRUE	1	0.529240860526875	2		371	722	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675311	241675311	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	115	411	0	ENST00000366560.3:c.511A>G	p.Ser171Gly	p.S171G	ENST00000366560	NM_000143.3	171	Agc/Ggc	4/10	1	2	FACETS	0.915	0.829	1	0.915	0.829	1	CLONAL	1	TRUE	1	0.529240860526875	2		411	475	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229424	36229424	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	218	468	0	ENST00000222270.7:c.8114G>C	p.Cys2705Ser	p.C2705S	ENST00000222270	NM_014727.1	2705	tGt/tCt	37/37	1	2	FACETS	0.94	0.876	1	0.94	0.876	1	CLONAL	1	TRUE	1	0.529240860526875	2		468	876	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63973901	63973901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157063173	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	266	463	0	ENST00000398590.3:c.1262C>T	p.Thr421Met	p.T421M	ENST00000398590	NM_001177387.1	421	aCg/aTg	9/14	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.529240860526875	2		463	897	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437052	110437054	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	novel	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	86	434	0	ENST00000375856.3:c.1347_1349del	p.Ser452del	p.S452del	ENST00000375856	NM_003749.2	449	tcGTCc/tcc	1/2	1	2	FACETS	0.518	0.459	0.582	0.518	0.459	0.582	SUBCLONAL	1	TRUE	1	0.529240860526875	2		434	627	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912169	127912169	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	157	341	0	ENST00000373547.4:c.701G>A	p.Cys234Tyr	p.C234Y	ENST00000373547	NM_002721.4	234	tGc/tAc	7/7	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.529240860526875	2		341	580	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	364653	364653	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	183	406	0	ENST00000262320.3:c.909del	p.Tyr304IlefsTer110	p.Y304Ifs*110	ENST00000262320	NM_003502.3	303	ccC/cc	3/11	1	2	FACETS	0.988	0.915	1	0.988	0.915	1	CLONAL	1	TRUE	1	0.529240860526875	2		406	700	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1685605	1685605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	73	409	1	ENST00000378625.1:c.1421C>T	p.Ala474Val	p.A474V	ENST00000378625	NM_001198994.1	474	gCc/gTc	12/14	1	2	FACETS	0.342	0.298	0.389	0.342	0.298	0.389	SUBCLONAL	1	TRUE	1	0.529240860526875	2		410	807	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350222	89350222	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs763212052	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	202	460	0	ENST00000301030.4:c.2728A>G	p.Arg910Gly	p.R910G	ENST00000301030	NM_001256183.1	910	Agg/Ggg	9/13	1	2	FACETS	0.895	0.831	0.961	0.895	0.831	0.961	CLONAL	1	TRUE	1	0.529240860526875	2		460	853	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349887	89349889	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0066394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	222	481	1	ENST00000301030.4:c.3061_3063del	p.Glu1021del	p.E1021del	ENST00000301030	NM_001256183.1	1021	GAG/-	9/13	1	2	FACETS	0.976	0.91	1	0.976	0.91	1	CLONAL	1	TRUE	1	0.529240860526875	2		482	860	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830866	72830870	+	frameshift_variant	Frame_Shift_Del	DEL	CGGAC	CGGAC	-	novel	NA	P-0066395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	158	681	0	ENST00000268489.5:c.5711_5715del	p.Gly1904GlufsTer23	p.G1904Efs*23	ENST00000268489	NM_006885.3	1904	gGTCCG/g	9/10	1	2	FACETS	0.895	0.822	0.972	0.895	0.822	0.972	CLONAL	1	TRUE	1	0.46078909220234	2		681	766	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344435	118344435	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377416766	NA	P-0066395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	145	550	0	ENST00000534358.1:c.2561C>T	p.Ala854Val	p.A854V	ENST00000534358	NM_005933.3	854	gCc/gTc	3/36	1	2	FACETS	0.893	0.816	0.973	0.893	0.816	0.973	CLONAL	1	TRUE	1	0.46078909220234	2		550	705	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942794	44942794	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	108	235	0	ENST00000377967.4:c.3375del	p.Ile1126TyrfsTer4	p.I1126Yfs*4	ENST00000377967	NM_021140.2	1125	aCc/ac	23/29	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.46078909220234	1		235	277	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752396	57752396	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	111	360	0	ENST00000274289.3:c.1177G>C	p.Glu393Gln	p.E393Q	ENST00000274289	NM_006622.3	393	Gaa/Caa	9/14	1	2	FACETS	0.952	0.86	1	0.952	0.86	1	CLONAL	1	TRUE	1	0.46078909220234	2		360	506	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997811	149997811	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1481274477	NA	P-0066396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	33	434	1	ENST00000253339.5:c.2656C>T	p.Arg886Ter	p.R886*	ENST00000253339		886	Cga/Tga	5/7	0.680479457668714	2	FACETS	0.278	0.227	0.336	0.139	0.113	0.168	SUBCLONAL	1	TRUE	0	0.671835246581126	2		435	353	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39690082	39690082	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1246537609	NA	P-0066396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	375	493	0	ENST00000361337.2:c.107A>G	p.Lys36Arg	p.K36R	ENST00000361337	NM_003286.2	36	aAa/aGa	3/21	0.680479457668714	4	FACETS	1	0.984	1			1	CLONAL	2	TRUE	NA	0.671835246581126	4		493	875	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266928	41266928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	110	487	0	ENST00000349496.5:c.599G>A	p.Arg200His	p.R200H	ENST00000349496	NM_001904.3	200	cGt/cAt	5/15	0.680479457668714	4	FACETS	0.525	0.47	0.583			1	SUBCLONAL	1	TRUE	NA	0.671835246581126	4		487	1043	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1268641	1268641	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755183437	NA	P-0066396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	20	466	0	ENST00000310581.5:c.2576G>A	p.Arg859Gln	p.R859Q	ENST00000310581	NM_198253.2	859	cGg/cAg	9/16	NA	2	FACETS	0.203	0.155	0.259			1	INDETERMINATE	1	TRUE	NA	0.671835246581126	2		466	293	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937590	76937590	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	85	370	0	ENST00000373344.5:c.3158C>T	p.Thr1053Ile	p.T1053I	ENST00000373344	NM_000489.3	1053	aCt/aTt	9/35	0.671835246581126	6	FACETS	0.6	0.529	0.676			1	SUBCLONAL	1	TRUE	NA	0.671835246581126	6		370	989	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066397-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	84	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.248315629637801	3	FACETS	0.877	0.787	0.97	0.877	0.787	0.97	INDETERMINATE	2	TRUE	1	0.490632774227365	3		341	243	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0066397-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	106	104	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.490632774227365	2	FACETS	0.948	0.868	1	0.948	0.868	1	CLONAL	2	TRUE	0	0.490632774227365	2		104	228	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934574	NA	P-0066397-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	281	427	0	ENST00000269305.4:c.844C>G	p.Arg282Gly	p.R282G	ENST00000269305	NM_001126112.2	282	Cgg/Ggg	8/11	0.490632774227365	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.490632774227365	2		427	528	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925316	114925317	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs745872748	NA	P-0066397-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	173	353	7	ENST00000543371.1:c.1403dup	p.Cys469ValfsTer8	p.C469Vfs*8	ENST00000543371	NM_001198531.1	465	aga/agAa	14/14	0.490632774227365	3	FACETS	0.884	0.82	0.949	0.884	0.82	0.949	CLONAL	2	TRUE	1	0.490632774227365	3		360	497	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054540	42054541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0066397-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	155	327	3	ENST00000219905.7:c.7731dup	p.Asp2578ArgfsTer45	p.D2578Rfs*45	ENST00000219905	NM_001164273.1	2575	aga/agAa	22/24	0.490632774227365	2	FACETS	0.972	0.905	1	0.972	0.905	1	CLONAL	2	TRUE	0	0.490632774227365	2		330	325	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591110	67591110	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066397-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	93	374	1	ENST00000274335.5:c.1703C>G	p.Pro568Arg	p.P568R	ENST00000274335		568	cCa/cGa	12/15	0.490632774227365	2	FACETS	1	0.941	1	0.535	0.48	0.593	CLONAL	1	TRUE	0	0.490632774227365	2		375	354	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265810	41266364	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATG	TCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATG	-	novel	NA	P-0066397-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	95	62	0	ENST00000349496.5:c.14-204_242-78del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.482272901466383	4	FACETS	1	0.947	1	1	0.99	1	CLONAL	4	TRUE	2	0.490632774227365	4		62	141	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278091	41278091	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066397-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	231	513	1	ENST00000349496.5:c.1967C>A	p.Ala656Asp	p.A656D	ENST00000349496	NM_001904.3	656	gCt/gAt	13/15	0.482272901466383	4	FACETS	0.946	0.885	1	0.946	0.885	1	CLONAL	2	TRUE	2	0.490632774227365	4		514	742	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0066398-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	37	583	0	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	0.2214062846518	0	FACETS	0.286	0.236	0.34			1	INDETERMINATE	1	TRUE	0	0.498219026822765	0		583	261	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183725	10183725	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs5030826	NA	P-0066398-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	62	542	0	ENST00000256474.2:c.194C>A	p.Ser65Ter	p.S65*	ENST00000256474	NM_000551.3	65	tCg/tAg	1/3	0.498219026822765	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.498219026822765	1		542	153	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818286	43818286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066398-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	25	587	0	ENST00000372470.3:c.1751C>T	p.Ser584Phe	p.S584F	ENST00000372470	NM_005373.2	584	tCc/tTc	12/12	1	2	FACETS	0.293	0.231	0.365	0.293	0.231	0.365	SUBCLONAL	1	TRUE	1	0.498219026822765	2		587	342	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52692274	52692278	+	frameshift_variant	Frame_Shift_Del	DEL	CTACA	CTACA	-	novel	NA	P-0066398-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	35	443	0	ENST00000394830.3:c.582_586del	p.Val195TyrfsTer9	p.V195Yfs*9	ENST00000394830	NM_018313.4	194	gtTGTAGct/gtct	6/30	0.498219026822765	1	FACETS	0.776	0.647	0.914	0.776	0.647	0.914	CLONAL	1	TRUE	0	0.498219026822765	1		443	136	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426307	47426314	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GATGGTGA	GATGGTGA	-	novel	NA	P-0066398-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	49	310	0	ENST00000377045.4:c.725_727+5del		p.X242_splice	ENST00000377045	NM_001654.4	242		8/16	1	1	FACETS	0.754	0.647	0.867	0.754	0.647	0.867	SUBCLONAL	1	TRUE	0	0.498219026822765	1		310	196	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066398-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	432	446	0				ENST00000310581	NM_198253.2	-/1132			0.868537071761435	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.868537071761435	3		446	701	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952459	38952459	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs147397604	NA	P-0066398-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	239	499	0	ENST00000357387.3:c.2966A>G	p.Asn989Ser	p.N989S	ENST00000357387	NM_152756.3	989	aAc/aGc	30/38	0.868537071761435	3	FACETS	0.978	0.916	1	0.489	0.458	0.521	CLONAL	1	TRUE	1	0.868537071761435	3		499	807	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0066399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	360	694	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.653898617707072	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.666211977317268	2		694	515	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984398	201984398	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	370	505	0	ENST00000359651.3:c.1063G>C	p.Gly355Arg	p.G355R	ENST00000359651		355	Ggc/Cgc	8/8	0.653898617707072	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.666211977317268	2		505	523	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1042212	1042212	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	293	489	0	ENST00000358495.3:c.13G>C	p.Glu5Gln	p.E5Q	ENST00000358495	NM_134424.2	5	Gag/Cag	2/12	0.666211977317268	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.666211977317268	3		489	566	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016175	31016176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0066399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	285	474	0	ENST00000375687.4:c.422dup	p.Ser142GlufsTer112	p.S142Efs*112	ENST00000375687	NM_015338.5	141	cag/cAag	6/13	0.653898617707072	2	FACETS	0.983	0.942	1	0.983	0.942	1	CLONAL	2	TRUE	0	0.666211977317268	2		474	435	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990436	81990436	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	274	510	0	ENST00000359376.3:c.3707G>T	p.Ser1236Ile	p.S1236I	ENST00000359376	NM_002661.3	1236	aGt/aTt	32/33	0.666211977317268	3	FACETS	0.954	0.904	1	0.954	0.904	1	CLONAL	2	TRUE	1	0.666211977317268	3		510	575	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964145	28964145	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	206	510	0	ENST00000282397.4:c.1757A>G	p.Asp586Gly	p.D586G	ENST00000282397	NM_002019.4	586	gAc/gGc	13/30	0.666211977317268	2	FACETS	0.963	0.915	1	0.963	0.915	1	CLONAL	2	TRUE	0	0.666211977317268	2		510	321	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	146	446	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.923	0.847	1	0.923	0.847	1	CLONAL	1	TRUE	1	0.571793007230432	2		446	553	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0066400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	34	133	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.589	0.485	0.703	0.589	0.485	0.703	SUBCLONAL	1	TRUE	1	0.571793007230432	2		133	202	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057874	27057874	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	60	556	0	ENST00000324856.7:c.1582C>T	p.Gln528Ter	p.Q528*	ENST00000324856	NM_006015.4	528	Cag/Tag	3/20	1	2	FACETS	0.19	0.163	0.22	0.19	0.163	0.22	SUBCLONAL	1	TRUE	1	0.571793007230432	2		556	1103	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347610	118347610	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs782451966	NA	P-0066400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	72	460	0	ENST00000534358.1:c.3247C>T	p.Arg1083Ter	p.R1083*	ENST00000534358	NM_005933.3	1083	Cga/Tga	4/36	0.571810612331871	1	FACETS	0.273	0.238	0.31	0.273	0.238	0.31	SUBCLONAL	1	TRUE	0	0.571793007230432	1		460	659	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820792	3820792	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057520589	NA	P-0066400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	59	543	0	ENST00000262367.5:c.2659C>T	p.Gln887Ter	p.Q887*	ENST00000262367	NM_004380.2	887	Cag/Tag	14/31	1	2	FACETS	0.2	0.171	0.232	0.2	0.171	0.232	SUBCLONAL	1	TRUE	1	0.571793007230432	2		543	1030	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592283	29592283	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	28	306	0	ENST00000356175.3:c.4698G>C	p.Leu1566Phe	p.L1566F	ENST00000356175	NM_000267.3	1566	ttG/ttC	35/57	1	2	FACETS	0.238	0.19	0.293	0.238	0.19	0.293	SUBCLONAL	1	TRUE	1	0.571793007230432	2		306	412	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556657	41556657	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	293	448	0	ENST00000263253.7:c.3602G>T	p.Cys1201Phe	p.C1201F	ENST00000263253	NM_001429.3	1201	tGt/tTt	20/31	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.571793007230432	2		448	867	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591145	67591153	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TACTTGATG	TACTTGATG	-	novel	NA	P-0066400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	18	386	0	ENST00000274335.5:c.1740_1745+3del		p.X580_splice	ENST00000274335		580		12/15	1	2	FACETS	0.107	0.08	0.14	0.107	0.08	0.14	SUBCLONAL	1	TRUE	1	0.571793007230432	2		386	587	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10785358	10785358	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869312709	NA	P-0066400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	76	412	0	ENST00000361367.2:c.1126G>A	p.Glu376Lys	p.E376K	ENST00000361367	NM_014633.3	376	Gaa/Aaa	9/25	1	2	FACETS	0.508	0.447	0.574	0.508	0.447	0.574	SUBCLONAL	1	TRUE	1	0.571793007230432	2		412	523	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655489	67655489	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	416	379	0	ENST00000264010.4:c.1352A>G	p.Asp451Gly	p.D451G	ENST00000264010	NM_006565.3	451	gAt/gGt	7/12	0.571810612331871	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.571793007230432	2		379	635	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806088	1806089	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0066400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	277	470	0	ENST00000260795.2:c.1107_1108delinsTT	p.Gly370Cys	p.G370C	ENST00000260795		369	gcGGgc/gcTTgc	8/17	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.571793007230432	2		470	864	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404579	8404579	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	113	389	0	ENST00000356435.5:c.4168A>T	p.Ile1390Phe	p.I1390F	ENST00000356435		1390	Atc/Ttc	25/35	0.571810612331871	2	FACETS	0.859	0.778	0.944	0.43	0.389	0.472	CLONAL	1	TRUE	0	0.571793007230432	2		389	460	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900216	101900216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	172	425	0	ENST00000374994.4:c.650G>A	p.Gly217Glu	p.G217E	ENST00000374994	NM_004612.2	217	gGa/gAa	4/9	0.571793007230432	2	FACETS	0.956	0.884	1	0.478	0.442	0.516	CLONAL	1	TRUE	0	0.571793007230432	2		425	629	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44733232	44733233	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0066400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	145	313	0	ENST00000377967.4:c.225+1dup		p.K75fs	ENST00000377967	NM_021140.2	75	aag/aaGg	2/29	0.265047445659808	1	FACETS	0.583	0.534	0.635	0.583	0.534	0.635	INDETERMINATE	1	TRUE	0	0.571793007230432	1		313	621	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123199724	123199724	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0066400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	90	284	0	ENST00000218089.9:c.2026-2A>G		p.X676_splice	ENST00000218089	NM_001042749.1	676			0.265047445659808	1	FACETS	0.903	0.814	0.994	0.903	0.814	0.994	INDETERMINATE	1	TRUE	0	0.571793007230432	1		284	249	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0066401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	159	498	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.391562808422713	1	FACETS	0.976	0.898	1	0.976	0.898	1	CLONAL	1	TRUE	0	0.391562808422713	1		498	669	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266889	18266889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781740870	NA	P-0066401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	112	429	0	ENST00000222254.8:c.200G>A	p.Arg67Gln	p.R67Q	ENST00000222254	NM_005027.3	67	cGa/cAa	2/16	1	2	FACETS	0.965	0.87	1	0.965	0.87	1	CLONAL	1	TRUE	1	0.391562808422713	2		429	593	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110803	2110803	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	173	464	0	ENST00000219476.3:c.1108C>T	p.Gln370Ter	p.Q370*	ENST00000219476	NM_000548.3	370	Cag/Tag	11/42	0.391562808422713	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.391562808422713	1		464	564	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39239471	39239471	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	57	251	0	ENST00000402219.2:c.2186G>T	p.Trp729Leu	p.W729L	ENST00000402219	NM_005633.3	729	tGg/tTg	14/23	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.391562808422713	2		251	257	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10800638	10800638	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	87	329	0	ENST00000361367.2:c.3508G>C	p.Asp1170His	p.D1170H	ENST00000361367	NM_014633.3	1170	Gat/Cat	25/25	1	2	FACETS	0.846	0.751	0.947	0.846	0.751	0.947	CLONAL	1	TRUE	1	0.391562808422713	2		329	525	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390469	118390469	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	77	484	0	ENST00000534358.1:c.11283G>C	p.Leu3761Phe	p.L3761F	ENST00000534358	NM_005933.3	3761	ttG/ttC	32/36	0.391562808422713	1	FACETS	0.479	0.421	0.542	0.479	0.421	0.542	SUBCLONAL	1	TRUE	0	0.391562808422713	1		484	660	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86546569	86546569	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	157	487	0	ENST00000262426.4:c.1018G>A	p.Asp340Asn	p.D340N	ENST00000262426	NM_001451.2	340	Gac/Aac	2/2	0.391562808422713	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.391562808422713	1		487	617	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645741	215645741	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	101	435	0	ENST00000260947.4:c.857T>A	p.Ile286Lys	p.I286K	ENST00000260947	NM_000465.2	286	aTa/aAa	4/11	1	2	FACETS	0.994	0.892	1	0.994	0.892	1	CLONAL	1	TRUE	1	0.391562808422713	2		435	519	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866070	37866399	+	splice_donor_variant,splice_acceptor_variant,inframe_deletion,intron_variant	Splice_Site	DEL	CCCCTGTTCTCCGATGTGTAAGGGCTCCCGCTGCTGGGGAGAGAGTTCTGAGGATTGTCAGAGCCGTGAGTCTCAGGGAGGCCTGGAGTCAGGGAAGGGGAGGGCTGGGGCCGGGTGGAATGCAGGTGTCATACAGGTGACATGGGAGGGGTGGGATAACAGGCTTGGGATGTCTCCCCTGGGCCAGGTAGTCTCCCTAGAAGGTGATGCTGATGAGGGTCTGGTGCCCAGGGCGCCACTCAGCCCTCATCCTGCCCTTTGCCCAACAGTGACGCGCACTGTCTGTGCCGGTGGCTGTGCCCGCTGCAAGGGGCCACTGCCCACTGACTG	CCCCTGTTCTCCGATGTGTAAGGGCTCCCGCTGCTGGGGAGAGAGTTCTGAGGATTGTCAGAGCCGTGAGTCTCAGGGAGGCCTGGAGTCAGGGAAGGGGAGGGCTGGGGCCGGGTGGAATGCAGGTGTCATACAGGTGACATGGGAGGGGTGGGATAACAGGCTTGGGATGTCTCCCCTGGGCCAGGTAGTCTCCCTAGAAGGTGATGCTGATGAGGGTCTGGTGCCCAGGGCGCCACTCAGCCCTCATCCTGCCCTTTGCCCAACAGTGACGCGCACTGTCTGTGCCGGTGGCTGTGCCCGCTGCAAGGGGCCACTGCCCACTGACTG	-	novel	NA	P-0066401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	161	497	0	ENST00000269571.5:c.580_705del		p.X194_splice	ENST00000269571		194	caCCCCTGTTCTCCGATGTGTAAGGGCTCCCGCTGCTGGGGAGAGAGTTCTGAGGATTGTCAGAGCCGTGAGTCTCAGGGAGGCCTGGAGTCAGGGAAGGGGAGGGCTGGGGCCGGGTGGAATGCAGGTGTCATACAGGTGACATGGGAGGGGTGGGATAACAGGCTTGGGATGTCTCCCCTGGGCCAGGTAGTCTCCCTAGAAGGTGATGCTGATGAGGGTCTGGTGCCCAGGGCGCCACTCAGCCCTCATCCTGCCCTTTGCCCAACAGTGACGCGCACTGTCTGTGCCGGTGGCTGTGCCCGCTGCAAGGGGCCACTGCCCACTGACTGc/cac	5-6/27	0.391562808422713	4	FACETS	0.971	0.889	1	0.324	0.296	0.353	CLONAL	1	TRUE	1	0.391562808422713	4		497	1178	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0066402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	55	325	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.540129854444186	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.587690368346722	1		325	123	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647757	2647757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201983709	NA	P-0066402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	96	405	0	ENST00000342085.4:c.1660G>A	p.Ala554Thr	p.A554T	ENST00000342085	NM_002613.4	554	Gct/Act	14/14	0.168648872554716	2	FACETS	0.999	0.9	1	0.5	0.45	0.551	INDETERMINATE	1	TRUE	0	0.587690368346722	2		405	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579340	7579340	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	148	484	0	ENST00000269305.4:c.347del	p.Ser116LeufsTer7	p.S116Lfs*7	ENST00000269305	NM_001126112.2	116	tCt/tt	4/11	0.529842626313283	2	FACETS	0.947	0.885	1	0.947	0.885	1	CLONAL	2	TRUE	0	0.587690368346722	2		484	266	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372128	55372128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	86	505	0	ENST00000297316.4:c.818G>A	p.Arg273Gln	p.R273Q	ENST00000297316	NM_022454.3	273	cGa/cAa	2/2	0.358886554903649	3	FACETS	1	0.979	1	0.709	0.636	0.785	CLONAL	1	TRUE	1	0.587690368346722	3		505	267	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244191	5244191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237664443	NA	P-0066402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	54	515	0	ENST00000357368.4:c.1291C>T	p.Arg431Trp	p.R431W	ENST00000357368	NM_002850.3	431	Cgg/Tgg	11/38	1	2	FACETS	0.593	0.509	0.683	0.593	0.509	0.683	SUBCLONAL	1	TRUE	1	0.587690368346722	2		515	310	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852483	63852484	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0066402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	53	430	0	ENST00000279873.7:c.3263dup	p.Asn1088LysfsTer73	p.N1088Kfs*73	ENST00000279873	NM_032199.2	1087	-/A	10/10	0.272064527094791	1	FACETS	0.363	0.311	0.42	0.363	0.311	0.42	INDETERMINATE	1	TRUE	0	0.587690368346722	1		430	351	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636656	73636656	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	624	574	0	ENST00000377687.4:c.919T>A	p.Ser307Thr	p.S307T	ENST00000377687	NM_001730.3	307	Tca/Aca	2/4	0.556377573802491	5	FACETS	1	0.993	1	1	0.993	1	CLONAL	4	TRUE	1	0.587690368346722	5		574	933	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223798	53223798	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	117	258	0	ENST00000375401.3:c.3561C>G	p.Ile1187Met	p.I1187M	ENST00000375401	NM_004187.3	1187	atC/atG	23/26	1	1	FACETS	0.777	0.725	0.826	1	0.99	1	SUBCLONAL	2	TRUE	0	0.587690368346722	1		258	181	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577265	64577265	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555166469	NA	P-0066402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	36	466	0	ENST00000312049.6:c.317A>G	p.Tyr106Cys	p.Y106C	ENST00000312049	NM_130799.2	106	tAt/tGt	2/10	0.178634393373368	5	FACETS	0.599	0.493	0.717			1	INDETERMINATE	1	TRUE	NA	0.587690368346722	5		466	385	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073637	8073637	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	57	590	0	ENST00000377482.5:c.1022A>G	p.Tyr341Cys	p.Y341C	ENST00000377482	NM_018948.3	341	tAc/tGc	4/4	1	2	FACETS	0.674	0.58	0.775	0.674	0.58	0.775	SUBCLONAL	1	TRUE	1	0.422079677693171	2		590	401	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11308073	11308073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749298128	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	65	529	0	ENST00000361445.4:c.919G>A	p.Gly307Arg	p.G307R	ENST00000361445	NM_004958.3	307	Gga/Aga	7/58	1	2	FACETS	0.751	0.654	0.856	0.751	0.654	0.856	SUBCLONAL	1	TRUE	1	0.422079677693171	2		529	410	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258894	16258894	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	86	547	3	ENST00000375759.3:c.6164del	p.Pro2055LeufsTer9	p.P2055Lfs*9	ENST00000375759	NM_015001.2	2053	aaC/aa	11/15	1	2	FACETS	0.886	0.787	0.991	0.886	0.787	0.991	CLONAL	1	TRUE	1	0.422079677693171	2		550	460	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057924	27057924	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	79	562	0	ENST00000324856.7:c.1636del	p.Gln546ArgfsTer73	p.Q546Rfs*73	ENST00000324856	NM_006015.4	544	caC/ca	3/20	1	2	FACETS	0.77	0.679	0.867	0.77	0.679	0.867	SUBCLONAL	1	TRUE	1	0.422079677693171	2		562	486	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	100	721	4	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.987	0.886	1	0.987	0.886	1	CLONAL	1	TRUE	1	0.422079677693171	2		725	480	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933539	36933539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148104401	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	99	638	0	ENST00000361632.4:c.1748G>A	p.Arg583His	p.R583H	ENST00000361632		583	cGt/cAt	13/16	1	2	FACETS	0.994	0.892	1	0.994	0.892	1	CLONAL	1	TRUE	1	0.422079677693171	2		638	472	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36940986	36940986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs923298829	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	79	434	0	ENST00000361632.4:c.353G>A	p.Arg118His	p.R118H	ENST00000361632		118	cGc/cAc	3/16	1	2	FACETS	0.915	0.809	1	0.915	0.809	1	CLONAL	1	TRUE	1	0.422079677693171	2		434	409	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692958	89692958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660321	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	38	392	0	ENST00000371953.3:c.442G>A	p.Ala148Thr	p.A148T	ENST00000371953	NM_000314.4	148	Gca/Aca	5/9	1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	1	0.422079677693171	2		392	178	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948208	71948209	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs749079348	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	54	549	0	ENST00000298229.2:c.2927dup	p.Pro977ThrfsTer7	p.P977Tfs*7	ENST00000298229	NM_001567.3	974	gcc/gCcc	26/28	1	2	FACETS	0.641	0.549	0.741	0.641	0.549	0.741	SUBCLONAL	1	TRUE	1	0.422079677693171	2		549	399	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	25	351	2	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.517	0.409	0.64	0.517	0.409	0.64	SUBCLONAL	1	TRUE	1	0.422079677693171	2		353	229	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244905	46244905	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	89	592	0	ENST00000334344.6:c.2999C>A	p.Pro1000His	p.P1000H	ENST00000334344	NM_152641.2	1000	cCt/cAt	15/21	1	2	FACETS	0.88	0.784	0.983	0.88	0.784	0.983	CLONAL	1	TRUE	1	0.422079677693171	2		592	479	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420606	49420606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886041404	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	94	519	0	ENST00000301067.7:c.15143G>A	p.Arg5048His	p.R5048H	ENST00000301067	NM_003482.3	5048	cGt/cAt	48/54	1	2	FACETS	0.981	0.877	1	0.981	0.877	1	CLONAL	1	TRUE	1	0.422079677693171	2		519	454	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435078	49435078	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	53	516	0	ENST00000301067.7:c.6475C>T	p.Leu2159Phe	p.L2159F	ENST00000301067	NM_003482.3	2159	Ctc/Ttc	31/54	1	2	FACETS	0.663	0.567	0.767	0.663	0.567	0.767	SUBCLONAL	1	TRUE	1	0.422079677693171	2		516	379	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	71	470	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.902	0.792	1	0.902	0.792	1	CLONAL	1	TRUE	1	0.422079677693171	2		470	373	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	75	471	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	1	2	FACETS	0.834	0.734	0.941	0.834	0.734	0.941	CLONAL	1	TRUE	1	0.422079677693171	2		471	426	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557837	21557837	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	71	485	1	ENST00000382592.4:c.2008A>G	p.Lys670Glu	p.K670E	ENST00000382592	NM_014572.2	670	Aag/Gag	5/8	1	2	FACETS	0.924	0.812	1	0.924	0.812	1	CLONAL	1	TRUE	1	0.422079677693171	2		486	364	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004277	29004277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370686484	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	87	385	0	ENST00000282397.4:c.1016G>A	p.Arg339Gln	p.R339Q	ENST00000282397	NM_002019.4	339	cGa/cAa	8/30	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.422079677693171	2		385	361	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058861	42058861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749267770	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	74	515	0	ENST00000219905.7:c.8581C>T	p.Arg2861Trp	p.R2861W	ENST00000219905	NM_001164273.1	2861	Cgg/Tgg	24/24	1	2	FACETS	0.801	0.704	0.904	0.801	0.704	0.904	CLONAL	1	TRUE	1	0.422079677693171	2		515	438	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658481	3658481	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140876043	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	85	469	0	ENST00000294008.3:c.485C>T	p.Thr162Met	p.T162M	ENST00000294008	NM_032444.2	162	aCg/aTg	2/15	1	2	FACETS	0.848	0.752	0.949	0.848	0.752	0.949	CLONAL	1	TRUE	1	0.422079677693171	2		469	475	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822586	72822586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	63	563	1	ENST00000268489.5:c.9589del	p.Gln3197SerfsTer44	p.Q3197Sfs*44	ENST00000268489	NM_006885.3	3197	Cag/ag	10/10	1	2	FACETS	0.737	0.64	0.842	0.737	0.64	0.842	SUBCLONAL	1	TRUE	1	0.422079677693171	2		564	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	80	1497	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	1	2	FACETS	0.8	0.706	0.899	0.8	0.706	0.899	SUBCLONAL	1	TRUE	1	0.422079677693171	2		1497	474	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	68	460	1	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	0.742	0.648	0.844	0.742	0.648	0.844	SUBCLONAL	1	TRUE	1	0.422079677693171	2		461	434	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661917	29661917	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	46	443	0	ENST00000356175.3:c.5815del	p.Cys1939AlafsTer19	p.C1939Afs*19	ENST00000356175	NM_000267.3	1937	cgT/cg	39/57	1	2	FACETS	0.781	0.662	0.911	0.781	0.662	0.911	CLONAL	1	TRUE	1	0.422079677693171	2		443	279	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	85	473	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.422079677693171	2		473	386	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	177	710	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.881	0.819	0.944	1	0.992	1	CLONAL	2	TRUE	1	0.422079677693171	2		713	476	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	45	594	3	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.472	0.397	0.555	0.472	0.397	0.555	SUBCLONAL	1	TRUE	1	0.422079677693171	2		597	452	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66522016	66522016	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1568698504	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	50	420	0	ENST00000358598.2:c.671G>A	p.Trp224Ter	p.W224*	ENST00000358598	NM_212471.2	224	tGg/tAg	7/11	1	2	FACETS	0.716	0.61	0.831	0.716	0.61	0.831	SUBCLONAL	1	TRUE	1	0.422079677693171	2		420	331	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584827	48584827	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	66	385	0	ENST00000342988.3:c.904+1G>A		p.X302_splice	ENST00000342988	NM_005359.5	302			0.342537116681572	1	FACETS	0.857	0.751	0.969	0.857	0.751	0.969	CLONAL	1	TRUE	0	0.422079677693171	1		385	288	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	31	94	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.948	0.777	1	0.948	0.777	1	CLONAL	1	TRUE	1	0.422079677693171	2		94	155	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610561	10610561	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766652922	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	59	547	0	ENST00000171111.5:c.149G>A	p.Arg50His	p.R50H	ENST00000171111	NM_203500.1	50	cGc/cAc	2/6	1	2	FACETS	0.708	0.611	0.812	0.708	0.611	0.812	SUBCLONAL	1	TRUE	1	0.422079677693171	2		547	395	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285030	15285030	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	60	471	0	ENST00000263388.2:c.4585G>A	p.Ala1529Thr	p.A1529T	ENST00000263388	NM_000435.2	1529	Gcc/Acc	25/33	1	2	FACETS	0.752	0.651	0.861	0.752	0.651	0.861	SUBCLONAL	1	TRUE	1	0.422079677693171	2		471	378	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	150	621	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.781	0.72	0.844	1	0.989	1	SUBCLONAL	2	TRUE	1	0.422079677693171	2		622	455	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	53	338	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.646	0.552	0.747	0.646	0.552	0.747	SUBCLONAL	1	TRUE	1	0.422079677693171	2		338	389	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607487	46607487	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	53	554	2	ENST00000263734.3:c.1681del	p.Gln561SerfsTer7	p.Q561Sfs*7	ENST00000263734	NM_001430.4	559	aCc/ac	12/16	1	2	FACETS	0.584	0.499	0.677	0.584	0.499	0.677	SUBCLONAL	1	TRUE	1	0.422079677693171	2		556	430	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010482	48010482	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1558644995	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	57	431	0	ENST00000234420.5:c.114del	p.Ala40ProfsTer41	p.A40Pfs*41	ENST00000234420	NM_000179.2	37	gCc/gc	1/10	1	2	FACETS	0.736	0.634	0.846	0.736	0.634	0.846	SUBCLONAL	1	TRUE	1	0.422079677693171	2		431	367	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682810	190682810	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	17	233	0	ENST00000441310.2:c.492del	p.Lys164AsnfsTer6	p.K164Nfs*6	ENST00000441310	NM_000534.4	162	gcA/gc	5/13	1	2	FACETS	0.526	0.395	0.68	0.526	0.395	0.68	SUBCLONAL	1	TRUE	1	0.422079677693171	2		233	153	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662847	227662847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	60	456	0	ENST00000305123.5:c.608C>T	p.Ala203Val	p.A203V	ENST00000305123	NM_005544.2	203	gCc/gTc	1/2	1	2	FACETS	0.709	0.613	0.813	0.709	0.613	0.813	SUBCLONAL	1	TRUE	1	0.422079677693171	2		456	401	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46277813	46277813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758545305	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	66	423	0	ENST00000371998.3:c.3611C>T	p.Ala1204Val	p.A1204V	ENST00000371998		1204	gCg/gTg	19/23	1	2	FACETS	0.959	0.839	1	0.959	0.839	1	CLONAL	1	TRUE	1	0.422079677693171	2		423	326	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164557	36164557	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	72	400	0	ENST00000300305.3:c.1318G>A	p.Ala440Thr	p.A440T	ENST00000300305		440	Gcg/Acg	8/8	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.422079677693171	2		400	331	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252947	36252947	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	59	497	0	ENST00000300305.3:c.415A>G	p.Asn139Asp	p.N139D	ENST00000300305		139	Aac/Gac	4/8	1	2	FACETS	0.734	0.634	0.842	0.734	0.634	0.842	SUBCLONAL	1	TRUE	1	0.422079677693171	2		497	381	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	52	310	1	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	0.635	0.542	0.736	0.635	0.542	0.736	SUBCLONAL	1	TRUE	1	0.422079677693171	2		311	388	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633207	12633207	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs730880382	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	88	386	0	ENST00000251849.4:c.1193G>T	p.Arg398Leu	p.R398L	ENST00000251849	NM_002880.3	398	cGc/cTc	11/17	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.422079677693171	2		386	411	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499363	89499363	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1317589623	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	87	461	0	ENST00000336596.2:c.2538del	p.Met847TrpfsTer10	p.M847Wfs*10	ENST00000336596	NM_005233.5	845	Ccc/cc	15/17	1	2	FACETS	0.982	0.874	1	0.982	0.874	1	CLONAL	1	TRUE	1	0.422079677693171	2		461	420	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911580	134911580	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766084445	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	73	486	0	ENST00000398015.3:c.2045G>A	p.Arg682His	p.R682H	ENST00000398015	NM_004441.4	682	cGc/cAc	11/16	1	2	FACETS	0.818	0.718	0.924	0.818	0.718	0.924	CLONAL	1	TRUE	1	0.422079677693171	2		486	423	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403528	138403528	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749977364	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	65	409	0	ENST00000289153.2:c.2254C>T	p.Arg752Trp	p.R752W	ENST00000289153	NM_006219.2	752	Cgg/Tgg	15/22	1	2	FACETS	0.917	0.8	1	0.917	0.8	1	CLONAL	1	TRUE	1	0.422079677693171	2		409	336	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	79	415	3	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	1	2	FACETS	0.885	0.782	0.994	0.885	0.782	0.994	CLONAL	1	TRUE	1	0.422079677693171	2		418	423	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920141	1920141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1211896693	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	58	540	0	ENST00000382891.5:c.1201C>T	p.Arg401Trp	p.R401W	ENST00000382891	NM_133335.3	401	Cgg/Tgg	5/22	1	2	FACETS	0.751	0.648	0.862	0.751	0.648	0.862	SUBCLONAL	1	TRUE	1	0.422079677693171	2		540	366	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1941428	1941428	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	48	387	0	ENST00000382891.5:c.1804C>T	p.Arg602Trp	p.R602W	ENST00000382891	NM_133335.3	602	Cgg/Tgg	9/22	1	2	FACETS	0.637	0.54	0.743	0.637	0.54	0.743	SUBCLONAL	1	TRUE	1	0.422079677693171	2		387	357	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957419	1957419	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	46	683	1	ENST00000382891.5:c.2523del		p.X841_splice	ENST00000382891	NM_133335.3	841			1	2	FACETS	0.625	0.528	0.731	0.625	0.528	0.731	SUBCLONAL	1	TRUE	1	0.422079677693171	2		684	349	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535351	66535351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs963468479	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	52	450	0	ENST00000273854.3:c.110G>A	p.Arg37Gln	p.R37Q	ENST00000273854	NM_004439.5	37	cGg/cAg	1/18	0.177414425153586	3	FACETS	0.853	0.729	0.987	0.426	0.364	0.494	INDETERMINATE	1	TRUE	1	0.422079677693171	3		450	350	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245474	153245474	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	50	446	0	ENST00000281708.4:c.1717T>C	p.Cys573Arg	p.C573R	ENST00000281708	NM_033632.3	573	Tgc/Cgc	11/12	0.177414425153586	3	FACETS	0.935	0.798	1	0.467	0.399	0.542	INDETERMINATE	1	TRUE	1	0.422079677693171	3		446	307	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38942984	38942984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs77464125	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	52	331	0	ENST00000357387.3:c.5003C>T	p.Pro1668Leu	p.P1668L	ENST00000357387	NM_152756.3	1668	cCg/cTg	37/38	1	2	FACETS	0.85	0.728	0.981	0.85	0.728	0.981	CLONAL	1	TRUE	1	0.422079677693171	2		331	290	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	46	412	7	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.645	0.545	0.754	0.645	0.545	0.754	SUBCLONAL	1	TRUE	1	0.422079677693171	2		419	338	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	69	478	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.856	0.76	0.955	1	0.981	1	CLONAL	2	TRUE	1	0.422079677693171	2		479	191	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675571	86675571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1561325048	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	14	453	0	ENST00000274376.6:c.2513del	p.Asn838MetfsTer4	p.N838Mfs*4	ENST00000274376	NM_002890.2	836	gAa/ga	19/25	0.422079677693171	1	FACETS	0.646	0.475	0.845	0.646	0.475	0.845	SUBCLONAL	1	TRUE	0	0.422079677693171	1		453	81	SUCCESS
APC	324	MSKCC	GRCh37	5	112175430	112175430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660713	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	21	479	0	ENST00000257430.4:c.4139C>T	p.Thr1380Ile	p.T1380I	ENST00000257430	NM_000038.5	1380	aCc/aTc	16/16	1	2	FACETS	0.288	0.222	0.366	0.288	0.222	0.366	SUBCLONAL	1	TRUE	1	0.422079677693171	2		479	345	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	40	469	0	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.485	0.403	0.575	0.485	0.403	0.575	SUBCLONAL	1	TRUE	1	0.422079677693171	2		469	391	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721713	176721713	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	67	551	0	ENST00000439151.2:c.7349del	p.Asn2450IlefsTer6	p.N2450Ifs*6	ENST00000439151	NM_022455.4	2448	tcA/tc	23/23	1	2	FACETS	0.72	0.628	0.819	0.72	0.628	0.819	SUBCLONAL	1	TRUE	1	0.422079677693171	2		551	441	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129337	152129338	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	57	442	0	ENST00000206249.3:c.296dup	p.Leu100ThrfsTer57	p.L100Tfs*57	ENST00000206249	NM_000125.3	97	ttc/ttCc	1/8	1	2	FACETS	0.752	0.648	0.865	0.752	0.648	0.865	SUBCLONAL	1	TRUE	1	0.422079677693171	2		442	359	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415519	152415519	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	55	434	0	ENST00000206249.3:c.1370-1G>T		p.X457_splice	ENST00000206249	NM_000125.3	457			1	2	FACETS	0.718	0.617	0.828	0.718	0.617	0.828	SUBCLONAL	1	TRUE	1	0.422079677693171	2		434	363	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100172	157100172	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1235492881	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	62	434	2	ENST00000346085.5:c.1114del	p.Arg372GlyfsTer7	p.R372Gfs*7	ENST00000346085	NM_020732.3	370	tCc/tc	1/20	1	2	FACETS	0.773	0.671	0.883	0.773	0.671	0.883	SUBCLONAL	1	TRUE	1	0.422079677693171	2		436	380	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043349	6043349	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781716	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	12	96	1	ENST00000265849.7:c.325del	p.Glu109LysfsTer3	p.E109Kfs*3	ENST00000265849	NM_000535.5	109	Gaa/aa	4/15	1	2	FACETS	0.72	0.514	0.964	0.72	0.514	0.964	CLONAL	1	TRUE	1	0.422079677693171	2		97	79	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729691	41729691	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	72	559	0	ENST00000242208.4:c.838G>T	p.Gly280Ter	p.G280*	ENST00000242208	NM_002192.2	280	Gga/Tga	3/3	1	2	FACETS	0.765	0.671	0.866	0.765	0.671	0.866	SUBCLONAL	1	TRUE	1	0.422079677693171	2		559	446	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482927	140482927	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	55	670	3	ENST00000288602.6:c.1208del	p.Pro403LeufsTer8	p.P403Lfs*8	ENST00000288602	NM_004333.4	403	cCt/ct	10/18	1	2	FACETS	0.656	0.563	0.758	0.656	0.563	0.758	SUBCLONAL	1	TRUE	1	0.422079677693171	2		673	397	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371633	55371633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs931390946	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	50	390	0	ENST00000297316.4:c.323C>T	p.Ala108Val	p.A108V	ENST00000297316	NM_022454.3	108	gCg/gTg	2/2	0.422079677693171	3	FACETS	0.769	0.655	0.894	0.385	0.327	0.447	SUBCLONAL	1	TRUE	1	0.422079677693171	3		390	373	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372056	55372056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	71	469	0	ENST00000297316.4:c.746G>A	p.Gly249Asp	p.G249D	ENST00000297316	NM_022454.3	249	gGc/gAc	2/2	0.422079677693171	3	FACETS	0.851	0.744	0.965	0.425	0.372	0.483	CLONAL	1	TRUE	1	0.422079677693171	3		469	479	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570254	87570254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747525829	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	69	498	1	ENST00000277120.3:c.1994C>T	p.Thr665Met	p.T665M	ENST00000277120		665	aCg/aTg	17/19	1	2	FACETS	0.886	0.776	1	0.886	0.776	1	CLONAL	1	TRUE	1	0.422079677693171	2		499	369	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242736	98242736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878853859	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	68	470	0	ENST00000331920.6:c.881G>A	p.Arg294His	p.R294H	ENST00000331920	NM_000264.3	294	cGc/cAc	6/24	1	2	FACETS	0.788	0.688	0.895	0.788	0.688	0.895	SUBCLONAL	1	TRUE	1	0.422079677693171	2		470	409	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759752	133759752	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1332380683	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	51	440	0	ENST00000318560.5:c.2075C>T	p.Thr692Met	p.T692M	ENST00000318560	NM_005157.4	692	aCg/aTg	11/11	1	2	FACETS	0.707	0.603	0.819	0.707	0.603	0.819	SUBCLONAL	1	TRUE	1	0.422079677693171	2		440	342	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418405	139418405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1286309175	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	72	451	0	ENST00000277541.6:c.167G>A	p.Arg56Gln	p.R56Q	ENST00000277541	NM_017617.3	56	cGa/cAa	3/34	1	2	FACETS	0.98	0.862	1	0.98	0.862	1	CLONAL	1	TRUE	1	0.422079677693171	2		451	348	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1720522	1720522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1198479789	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	90	539	0	ENST00000378609.4:c.886G>A	p.Val296Ile	p.V296I	ENST00000378609	NM_002074.3	296	Gtc/Atc	10/12	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.422079677693171	2		539	417	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489240	2489240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	63	439	0	ENST00000355716.4:c.145G>A	p.Val49Met	p.V49M	ENST00000355716	NM_003820.2	49	Gtg/Atg	2/8	1	2	FACETS	0.834	0.725	0.951	0.834	0.725	0.951	CLONAL	1	TRUE	1	0.422079677693171	2		439	358	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106924	27106924	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	84	569	0	ENST00000324856.7:c.6535A>T	p.Ser2179Cys	p.S2179C	ENST00000324856	NM_006015.4	2179	Agc/Tgc	20/20	1	2	FACETS	0.885	0.785	0.99	0.885	0.785	0.99	CLONAL	1	TRUE	1	0.422079677693171	2		569	450	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313217	65313217	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	77	468	0	ENST00000342505.4:c.1897C>A	p.Leu633Met	p.L633M	ENST00000342505	NM_002227.2	633	Ctg/Atg	13/25	1	2	FACETS	0.96	0.848	1	0.96	0.848	1	CLONAL	1	TRUE	1	0.422079677693171	2		468	380	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176118182	176118182	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	24	210	0	ENST00000367669.3:c.791T>G	p.Leu264Arg	p.L264R	ENST00000367669	NM_022457.5	264	cTt/cGt	6/20	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.422079677693171	2		210	81	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610141	43610141	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	82	619	0	ENST00000355710.3:c.2093A>G	p.Asp698Gly	p.D698G	ENST00000355710	NM_020975.4	698	gAc/gGc	11/20	1	2	FACETS	0.82	0.725	0.92	0.82	0.725	0.92	CLONAL	1	TRUE	1	0.422079677693171	2		619	474	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88676901	88676901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	38	245	0	ENST00000372037.3:c.686C>T	p.Thr229Ile	p.T229I	ENST00000372037	NM_004329.2	229	aCt/aTt	9/13	1	2	FACETS	0.919	0.768	1	0.919	0.768	1	CLONAL	1	TRUE	1	0.422079677693171	2		245	196	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248622	8248622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	63	579	0	ENST00000335790.3:c.265G>A	p.Ala89Thr	p.A89T	ENST00000335790	NM_002315.2	89	Gct/Act	3/4	1	2	FACETS	0.712	0.618	0.814	0.712	0.618	0.814	SUBCLONAL	1	TRUE	1	0.422079677693171	2		579	419	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69458736	69458736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	62	439	0	ENST00000227507.2:c.551C>T	p.Thr184Ile	p.T184I	ENST00000227507	NM_053056.2	184	aCc/aTc	3/5	1	2	FACETS	0.823	0.715	0.939	0.823	0.715	0.939	CLONAL	1	TRUE	1	0.422079677693171	2		439	357	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344510	118344510	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	79	589	0	ENST00000534358.1:c.2636A>C	p.Glu879Ala	p.E879A	ENST00000534358	NM_005933.3	879	gAg/gCg	3/36	1	2	FACETS	0.834	0.736	0.938	0.834	0.736	0.938	CLONAL	1	TRUE	1	0.422079677693171	2		589	449	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514003	125514003	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	64	414	0	ENST00000428830.2:c.941A>G	p.Tyr314Cys	p.Y314C	ENST00000428830	NM_001114121.2	314	tAc/tGc	10/14	1	2	FACETS	0.838	0.729	0.954	0.838	0.729	0.954	CLONAL	1	TRUE	1	0.422079677693171	2		414	362	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112340	115112340	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	64	464	0	ENST00000257566.3:c.1400T>C	p.Val467Ala	p.V467A	ENST00000257566	NM_016569.3	467	gTg/gCg	7/8	1	2	FACETS	0.933	0.814	1	0.933	0.814	1	CLONAL	1	TRUE	1	0.422079677693171	2		464	325	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619966	21619966	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1389686342	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	62	577	0	ENST00000382592.4:c.200C>T	p.Thr67Ile	p.T67I	ENST00000382592	NM_014572.2	67	aCc/aTc	2/8	1	2	FACETS	0.682	0.59	0.78	0.682	0.59	0.78	SUBCLONAL	1	TRUE	1	0.422079677693171	2		577	431	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914398	32914398	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	16	391	0	ENST00000380152.3:c.5906T>C	p.Val1969Ala	p.V1969A	ENST00000380152		1969	gTc/gCc	11/27	0.292519126258263	0	FACETS	0.348	0.259	0.451			1	SUBCLONAL	1	TRUE	0	0.422079677693171	0		391	126	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050912	49050912	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	50	392	0	ENST00000267163.4:c.2596A>G	p.Ser866Gly	p.S866G	ENST00000267163	NM_000321.2	866	Agc/Ggc	25/27	1	2	FACETS	0.811	0.693	0.94	0.811	0.693	0.94	CLONAL	1	TRUE	1	0.422079677693171	2		392	292	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335929	73335929	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141022568	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	65	447	0	ENST00000377767.4:c.2366G>A	p.Arg789Gln	p.R789Q	ENST00000377767	NM_014953.3	789	cGg/cAg	18/21	1	2	FACETS	0.851	0.742	0.968	0.851	0.742	0.968	CLONAL	1	TRUE	1	0.422079677693171	2		447	362	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636753	73636753	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	83	597	0	ENST00000377687.4:c.1016A>C	p.His339Pro	p.H339P	ENST00000377687	NM_001730.3	339	cAc/cCc	2/4	1	2	FACETS	0.866	0.768	0.971	0.866	0.768	0.971	CLONAL	1	TRUE	1	0.422079677693171	2		597	454	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437319	110437319	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	22	270	0	ENST00000375856.3:c.1082T>C	p.Val361Ala	p.V361A	ENST00000375856	NM_003749.2	361	gTg/gCg	1/2	1	2	FACETS	0.444	0.345	0.558	0.444	0.345	0.558	SUBCLONAL	1	TRUE	1	0.422079677693171	2		270	235	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30047530	30047531	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	21	277	0	ENST00000331968.5:c.2470dup	p.Met824AsnfsTer9	p.M824Nfs*9	ENST00000331968	NM_002742.2	824	atg/aAtg	17/18	1	2	FACETS	0.913	0.714	1	0.913	0.714	1	CLONAL	1	TRUE	1	0.422079677693171	2		277	109	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30099949	30099949	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	66	480	0	ENST00000331968.5:c.1671C>G	p.His557Gln	p.H557Q	ENST00000331968	NM_002742.2	557	caC/caG	10/18	1	2	FACETS	0.825	0.72	0.938	0.825	0.72	0.938	CLONAL	1	TRUE	1	0.422079677693171	2		480	379	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988253	36988253	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	59	431	0	ENST00000354822.5:c.400A>G	p.Met134Val	p.M134V	ENST00000354822	NM_001079668.2	134	Atg/Gtg	2/3	1	2	FACETS	0.726	0.627	0.833	0.726	0.627	0.833	SUBCLONAL	1	TRUE	1	0.422079677693171	2		431	385	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988393	36988393	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	75	433	0	ENST00000354822.5:c.260C>G	p.Ala87Gly	p.A87G	ENST00000354822	NM_001079668.2	87	gCc/gGc	2/3	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.422079677693171	2		433	345	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50782073	50782073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1388007452	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	42	342	0	ENST00000307179.4:c.1966G>A	p.Ala656Thr	p.A656T	ENST00000307179		656	Gcc/Acc	13/20	1	2	FACETS	0.706	0.592	0.83	0.706	0.592	0.83	SUBCLONAL	1	TRUE	1	0.422079677693171	2		342	282	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631953	90631953	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	74	470	0	ENST00000330062.3:c.400A>C	p.Ser134Arg	p.S134R	ENST00000330062	NM_002168.2	134	Agt/Cgt	4/11	1	2	FACETS	0.899	0.791	1	0.899	0.791	1	CLONAL	1	TRUE	1	0.422079677693171	2		470	390	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127668	2127668	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	97	633	0	ENST00000219476.3:c.2907C>A	p.Ser969Arg	p.S969R	ENST00000219476	NM_000548.3	969	agC/agA	26/42	1	2	FACETS	0.964	0.863	1	0.964	0.863	1	CLONAL	1	TRUE	1	0.422079677693171	2		633	477	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273928	10273928	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	70	502	0	ENST00000330684.3:c.341A>T	p.Asp114Val	p.D114V	ENST00000330684	NM_001134407.1	114	gAt/gTt	2/13	1	2	FACETS	0.911	0.799	1	0.911	0.799	1	CLONAL	1	TRUE	1	0.422079677693171	2		502	364	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029567	14029567	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	67	457	0	ENST00000311895.7:c.1778T>A	p.Ile593Asn	p.I593N	ENST00000311895	NM_005236.2	593	aTt/aAt	8/11	1	2	FACETS	0.904	0.791	1	0.904	0.791	1	CLONAL	1	TRUE	1	0.422079677693171	2		457	351	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822534	72822534	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs750996016	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	63	616	0	ENST00000268489.5:c.9641C>A	p.Pro3214Gln	p.P3214Q	ENST00000268489	NM_006885.3	3214	cCa/cAa	10/10	1	2	FACETS	0.682	0.591	0.779	0.682	0.591	0.779	SUBCLONAL	1	TRUE	1	0.422079677693171	2		616	438	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829421	72829421	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	69	470	0	ENST00000268489.5:c.7160C>A	p.Pro2387His	p.P2387H	ENST00000268489	NM_006885.3	2387	cCc/cAc	9/10	1	2	FACETS	0.83	0.726	0.941	0.83	0.726	0.941	CLONAL	1	TRUE	1	0.422079677693171	2		470	394	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831531	72831531	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs552751209	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	66	529	0	ENST00000268489.5:c.5050C>T	p.Pro1684Ser	p.P1684S	ENST00000268489	NM_006885.3	1684	Ccc/Tcc	9/10	1	2	FACETS	0.719	0.626	0.819	0.719	0.626	0.819	SUBCLONAL	1	TRUE	1	0.422079677693171	2		529	435	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7218338	7218338	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1166742047	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	66	409	0	ENST00000380728.2:c.34A>G	p.Asn12Asp	p.N12D	ENST00000380728		12	Aac/Gac	2/11	1	2	FACETS	0.871	0.761	0.989	0.871	0.761	0.989	CLONAL	1	TRUE	1	0.422079677693171	2		409	359	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995296	15995296	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	81	532	0	ENST00000268712.3:c.2897C>T	p.Ala966Val	p.A966V	ENST00000268712	NM_006311.3	966	gCa/gTa	22/46	1	2	FACETS	0.907	0.803	1	0.907	0.803	1	CLONAL	1	TRUE	1	0.422079677693171	2		532	423	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670154	29670154	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1555535455	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	24	204	0	ENST00000356175.3:c.7126+1G>A		p.X2376_splice	ENST00000356175	NM_000267.3	2376			1	2	FACETS	0.693	0.549	0.857	0.693	0.549	0.857	SUBCLONAL	1	TRUE	1	0.422079677693171	2		204	164	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435974	56435974	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	72	662	0	ENST00000407977.2:c.1163A>G	p.His388Arg	p.H388R	ENST00000407977		388	cAc/cGc	9/10	1	2	FACETS	0.77	0.675	0.872	0.77	0.675	0.872	SUBCLONAL	1	TRUE	1	0.422079677693171	2		662	443	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533809	63533809	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	79	582	0	ENST00000307078.5:c.1345A>G	p.Thr449Ala	p.T449A	ENST00000307078	NM_004655.3	449	Acc/Gcc	6/11	1	2	FACETS	0.98	0.867	1	0.98	0.867	1	CLONAL	1	TRUE	1	0.422079677693171	2		582	382	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226854	2226854	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	80	591	0	ENST00000398665.3:c.4337del	p.Pro1446ArgfsTer72	p.P1446Rfs*72	ENST00000398665	NM_032482.2	1445	gCc/gc	27/28	1	2	FACETS	0.974	0.863	1	0.974	0.863	1	CLONAL	1	TRUE	1	0.422079677693171	2		591	389	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954254	17954254	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	64	499	0	ENST00000458235.1:c.355G>T	p.Gly119Trp	p.G119W	ENST00000458235	NM_000215.3	119	Ggg/Tgg	4/24	1	2	FACETS	0.822	0.715	0.936	0.822	0.715	0.936	CLONAL	1	TRUE	1	0.422079677693171	2		499	369	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917113	50917113	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	77	488	0	ENST00000440232.2:c.2365C>T	p.Pro789Ser	p.P789S	ENST00000440232	NM_002691.3	789	Ccc/Tcc	19/27	1	2	FACETS	0.924	0.815	1	0.924	0.815	1	CLONAL	1	TRUE	1	0.422079677693171	2		488	395	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085729	16085729	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140581169	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	66	417	0	ENST00000281043.3:c.905G>A	p.Arg302His	p.R302H	ENST00000281043	NM_005378.4	302	cGt/cAt	3/3	1	2	FACETS	0.866	0.756	0.984	0.866	0.756	0.984	CLONAL	1	TRUE	1	0.422079677693171	2		417	361	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39294852	39294854	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	21	306	0	ENST00000402219.2:c.128_130del	p.Asp43del	p.D43del	ENST00000402219	NM_005633.3	43	gATGct/gct	2/23	1	2	FACETS	0.413	0.319	0.522	0.413	0.319	0.522	SUBCLONAL	1	TRUE	1	0.422079677693171	2		306	241	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149908	99149908	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	72	500	0	ENST00000074304.5:c.220A>G	p.Thr74Ala	p.T74A	ENST00000074304	NM_001134224.1	74	Acc/Gcc	5/26	1	2	FACETS	0.781	0.685	0.884	0.781	0.685	0.884	SUBCLONAL	1	TRUE	1	0.422079677693171	2		500	437	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530181	212530181	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	59	481	0	ENST00000342788.4:c.1738T>C	p.Cys580Arg	p.C580R	ENST00000342788	NM_005235.2	580	Tgc/Cgc	15/28	1	2	FACETS	0.803	0.695	0.92	0.803	0.695	0.92	CLONAL	1	TRUE	1	0.422079677693171	2		481	348	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645984	215645984	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1559425604	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	37	460	2	ENST00000260947.4:c.614del	p.Lys205SerfsTer7	p.K205Sfs*7	ENST00000260947	NM_000465.2	205	aAg/ag	4/11	1	2	FACETS	0.564	0.466	0.672	0.564	0.466	0.672	SUBCLONAL	1	TRUE	1	0.422079677693171	2		462	311	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662830	227662830	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	43	480	0	ENST00000305123.5:c.625A>T	p.Met209Leu	p.M209L	ENST00000305123	NM_005544.2	209	Atg/Ttg	1/2	1	2	FACETS	0.479	0.401	0.566	0.479	0.401	0.566	SUBCLONAL	1	TRUE	1	0.422079677693171	2		480	425	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39772494	39772494	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	70	495	0	ENST00000288319.7:c.745+2T>C		p.X249_splice	ENST00000288319	NM_182918.3	249			1	2	FACETS	0.871	0.763	0.985	0.871	0.763	0.985	CLONAL	1	TRUE	1	0.422079677693171	2		495	381	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29445488	29445488	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	74	467	0	ENST00000544604.2:c.1319A>G	p.Tyr440Cys	p.Y440C	ENST00000544604	NM_001206998.1	440	tAc/tGc	8/9	1	2	FACETS	0.868	0.764	0.979	0.868	0.764	0.979	CLONAL	1	TRUE	1	0.422079677693171	2		467	404	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650809	12650809	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	44	339	0	ENST00000251849.4:c.346A>G	p.Thr116Ala	p.T116A	ENST00000251849	NM_002880.3	116	Act/Gct	4/17	1	2	FACETS	0.906	0.767	1	0.906	0.767	1	CLONAL	1	TRUE	1	0.422079677693171	2		339	230	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713742	30713742	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs727504292	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	88	595	0	ENST00000295754.5:c.1067G>C	p.Arg356Pro	p.R356P	ENST00000295754	NM_003242.5	356	cGg/cCg	4/7	1	2	FACETS	0.889	0.791	0.993	0.889	0.791	0.993	CLONAL	1	TRUE	1	0.422079677693171	2		595	469	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164744	47164744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	69	471	0	ENST00000409792.3:c.1382C>T	p.Ser461Leu	p.S461L	ENST00000409792	NM_014159.6	461	tCa/tTa	3/21	1	2	FACETS	0.867	0.759	0.982	0.867	0.759	0.982	CLONAL	1	TRUE	1	0.422079677693171	2		471	377	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63982044	63982044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	64	532	2	ENST00000398590.3:c.2546G>A	p.Ser849Asn	p.S849N	ENST00000398590	NM_001177387.1	849	aGc/aAc	12/14	1	2	FACETS	0.776	0.675	0.884	0.776	0.675	0.884	SUBCLONAL	1	TRUE	1	0.422079677693171	2		534	391	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448623	89448623	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	73	430	0	ENST00000336596.2:c.1587T>A	p.Ser529Arg	p.S529R	ENST00000336596	NM_005233.5	529	agT/agA	7/17	1	2	FACETS	0.846	0.743	0.955	0.846	0.743	0.955	CLONAL	1	TRUE	1	0.422079677693171	2		430	409	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968244	134968244	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	84	508	1	ENST00000398015.3:c.2757G>A	p.Trp919Ter	p.W919*	ENST00000398015	NM_004441.4	919	tgG/tgA	15/16	1	2	FACETS	0.865	0.767	0.969	0.865	0.767	0.969	CLONAL	1	TRUE	1	0.422079677693171	2		509	460	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430219	181430219	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	54	369	0	ENST00000325404.1:c.71A>G	p.Asn24Ser	p.N24S	ENST00000325404	NM_003106.3	24	aAc/aGc	1/1	1	2	FACETS	0.755	0.648	0.871	0.755	0.648	0.871	SUBCLONAL	1	TRUE	1	0.422079677693171	2		369	339	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129961	55129961	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	73	552	0	ENST00000257290.5:c.499del	p.Val167TrpfsTer18	p.V167Wfs*18	ENST00000257290	NM_006206.4	165	gaG/ga	4/23	1	2	FACETS	0.762	0.669	0.862	0.762	0.669	0.862	SUBCLONAL	1	TRUE	1	0.422079677693171	2		552	454	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592208	55592208	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	28	289	0	ENST00000288135.5:c.1532A>G	p.Asn511Ser	p.N511S	ENST00000288135	NM_000222.2	511	aAc/aGc	9/21	1	2	FACETS	0.702	0.566	0.855	0.702	0.566	0.855	SUBCLONAL	1	TRUE	1	0.422079677693171	2		289	189	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230795	66230795	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	27	453	0	ENST00000273854.3:c.2176A>T	p.Ser726Cys	p.S726C	ENST00000273854	NM_004439.5	726	Agt/Tgt	12/18	0.177414425153586	3	FACETS	1	0.902	1	0.601	0.485	0.728	INDETERMINATE	1	TRUE	1	0.422079677693171	3		453	129	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114321	143114321	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	55	350	0	ENST00000262992.4:c.1100G>T	p.Gly367Val	p.G367V	ENST00000262992	NM_001101669.1	367	gGa/gTa	13/24	0.177414425153586	3	FACETS	0.999	0.86	1	0.499	0.43	0.575	INDETERMINATE	1	TRUE	1	0.422079677693171	3		350	316	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144258385	144258385	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755581817	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	58	393	1	ENST00000262995.4:c.50del	p.Pro17ArgfsTer5	p.P17Rfs*5	ENST00000262995	NM_207123.2	15	tCc/tc	1/11	0.177414425153586	3	FACETS	0.94	0.812	1	0.47	0.406	0.54	INDETERMINATE	1	TRUE	1	0.422079677693171	3		394	354	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524627	187524627	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	58	401	0	ENST00000441802.2:c.11053T>C	p.Ser3685Pro	p.S3685P	ENST00000441802	NM_005245.3	3685	Tcc/Ccc	19/27	1	2	FACETS	0.723	0.624	0.831	0.723	0.624	0.831	SUBCLONAL	1	TRUE	1	0.422079677693171	2		401	380	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183300	56183300	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	68	402	0	ENST00000399503.3:c.4210G>T	p.Glu1404Ter	p.E1404*	ENST00000399503	NM_005921.1	1404	Gag/Tag	18/20	1	2	FACETS	0.824	0.72	0.935	0.824	0.72	0.935	CLONAL	1	TRUE	1	0.422079677693171	2		402	391	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393220	393220	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	81	487	0	ENST00000380956.4:c.68A>G	p.Lys23Arg	p.K23R	ENST00000380956	NM_001195286.1	23	aAg/aGg	2/9	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.422079677693171	2		487	355	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225607	26225607	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	78	650	0	ENST00000360408.1:c.225A>G	p.Ile75Met	p.I75M	ENST00000360408	NM_003532.2	75	atA/atG	1/1	1	2	FACETS	0.868	0.766	0.976	0.868	0.766	0.976	CLONAL	1	TRUE	1	0.422079677693171	2		650	426	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839795	27839795	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	65	733	0	ENST00000328488.2:c.299A>G	p.Tyr100Cys	p.Y100C	ENST00000328488	NM_003533.2	100	tAc/tGc	1/1	1	2	FACETS	0.667	0.579	0.761	0.667	0.579	0.761	SUBCLONAL	1	TRUE	1	0.422079677693171	2		733	462	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31238181	31238181	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	19	57	0	ENST00000376228.5:c.701C>A	p.Pro234His	p.P234H	ENST00000376228	NM_002117.5	234	cCt/cAt	4/8	1	2	FACETS	1	0.818	1	1	0.946	1	CLONAL	2	TRUE	1	0.422079677693171	2		57	44	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816427	32816427	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	71	492	0	ENST00000354258.4:c.1746+2T>C		p.X582_splice	ENST00000354258	NM_000593.5	582			1	2	FACETS	0.837	0.734	0.947	0.837	0.734	0.947	CLONAL	1	TRUE	1	0.422079677693171	2		492	402	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821054	32821055	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	52	593	0	ENST00000354258.4:c.539dup	p.Ala181SerfsTer7	p.A181Sfs*7	ENST00000354258	NM_000593.5	180	gga/ggGa	1/11	1	2	FACETS	0.638	0.545	0.74	0.638	0.545	0.74	SUBCLONAL	1	TRUE	1	0.422079677693171	2		593	386	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117650589	117650589	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1007896648	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	21	484	0	ENST00000368508.3:c.5269G>A	p.Gly1757Ser	p.G1757S	ENST00000368508	NM_002944.2	1757	Ggc/Agc	32/43	NA	2	FACETS	0.465	0.359	0.587			1	INDETERMINATE	1	TRUE	NA	0.422079677693171	2		484	214	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683773	117683773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	36	410	0	ENST00000368508.3:c.3374C>T	p.Ala1125Val	p.A1125V	ENST00000368508	NM_002944.2	1125	gCc/gTc	21/43	NA	2	FACETS	0.634	0.524	0.756			1	INDETERMINATE	1	TRUE	NA	0.422079677693171	2		410	269	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157488259	157488259	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	87	460	0	ENST00000346085.5:c.2965C>A	p.Leu989Met	p.L989M	ENST00000346085	NM_020732.3	989	Ctg/Atg	10/20	1	2	FACETS	0.989	0.88	1	0.989	0.88	1	CLONAL	1	TRUE	1	0.422079677693171	2		460	417	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468143	50468143	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	58	537	0	ENST00000331340.3:c.1378A>G	p.Lys460Glu	p.K460E	ENST00000331340	NM_006060.4	460	Aag/Gag	8/8	1	2	FACETS	0.727	0.627	0.835	0.727	0.627	0.835	SUBCLONAL	1	TRUE	1	0.422079677693171	2		537	378	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524649	106524649	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	47	376	0	ENST00000359195.3:c.2810T>C	p.Val937Ala	p.V937A	ENST00000359195	NM_002649.2	937	gTg/gCg	9/11	1	2	FACETS	0.801	0.68	0.932	0.801	0.68	0.932	CLONAL	1	TRUE	1	0.422079677693171	2		376	278	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845547	151845547	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	82	594	0	ENST00000262189.6:c.13465A>G	p.Ile4489Val	p.I4489V	ENST00000262189	NM_170606.2	4489	Att/Gtt	52/59	1	2	FACETS	0.986	0.875	1	0.986	0.875	1	CLONAL	1	TRUE	1	0.422079677693171	2		594	394	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845621	151845621	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	79	510	0	ENST00000262189.6:c.13391T>A	p.Phe4464Tyr	p.F4464Y	ENST00000262189	NM_170606.2	4464	tTc/tAc	52/59	1	2	FACETS	0.948	0.838	1	0.948	0.838	1	CLONAL	1	TRUE	1	0.422079677693171	2		510	395	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860340	151860340	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	66	511	0	ENST00000262189.6:c.10322T>A	p.Ile3441Lys	p.I3441K	ENST00000262189	NM_170606.2	3441	aTa/aAa	43/59	1	2	FACETS	0.745	0.649	0.848	0.745	0.649	0.848	SUBCLONAL	1	TRUE	1	0.422079677693171	2		511	420	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538844	23538844	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	56	467	0	ENST00000380871.4:c.595del	p.Ala199ProfsTer2	p.A199Pfs*2	ENST00000380871	NM_006167.3	199	Gcc/cc	2/2	0.422079677693171	3	FACETS	0.756	0.649	0.872	0.378	0.324	0.436	SUBCLONAL	1	TRUE	1	0.422079677693171	3		467	425	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38153425	38153425	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757704368	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	79	426	0	ENST00000317025.8:c.2804C>T	p.Pro935Leu	p.P935L	ENST00000317025	NM_023034.1	935	cCg/cTg	16/24	0.422079677693171	3	FACETS	0.99	0.874	1	0.495	0.437	0.557	CLONAL	1	TRUE	1	0.422079677693171	3		426	458	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187111	38187111	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs979464720	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	55	458	0	ENST00000317025.8:c.1366A>G	p.Thr456Ala	p.T456A	ENST00000317025	NM_023034.1	456	Aca/Gca	6/24	0.422079677693171	3	FACETS	0.67	0.574	0.775	0.335	0.287	0.388	SUBCLONAL	1	TRUE	1	0.422079677693171	3		458	471	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050747	69050747	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	12	194	0	ENST00000288368.4:c.4082T>C	p.Val1361Ala	p.V1361A	ENST00000288368	NM_024870.2	1361	gTt/gCt	33/40	0.422079677693171	3	FACETS	0.943	0.675	1	0.472	0.337	0.63	CLONAL	1	TRUE	1	0.422079677693171	3		194	73	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74858968	74858968	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	20	222	0	ENST00000284811.8:c.236A>G	p.Tyr79Cys	p.Y79C	ENST00000284811		79	tAc/tGc	4/4	0.422079677693171	3	FACETS	0.66	0.508	0.835	0.33	0.254	0.418	SUBCLONAL	1	TRUE	1	0.422079677693171	3		222	174	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436686	8436686	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	32	329	0	ENST00000356435.5:c.3992T>G	p.Met1331Arg	p.M1331R	ENST00000356435		1331	aTg/aGg	24/35	1	2	FACETS	0.908	0.746	1	0.908	0.746	1	CLONAL	1	TRUE	1	0.422079677693171	2		329	167	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738288	133738288	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	76	543	0	ENST00000318560.5:c.688C>T	p.Pro230Ser	p.P230S	ENST00000318560	NM_005157.4	230	Ccc/Tcc	4/11	1	2	FACETS	0.785	0.691	0.885	0.785	0.691	0.885	SUBCLONAL	1	TRUE	1	0.422079677693171	2		543	459	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15833988	15833988	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	46	287	0	ENST00000307771.7:c.746A>G	p.Asn249Ser	p.N249S	ENST00000307771	NM_005089.3	249	aAc/aGc	8/11	0.365407167875169	1	FACETS	0.796	0.678	0.924	0.796	0.678	0.924	CLONAL	1	TRUE	0	0.422079677693171	1		287	216	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945221	44945221	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	22	263	0	ENST00000377967.4:c.3548del	p.Asn1184IlefsTer3	p.N1184Ifs*3	ENST00000377967	NM_021140.2	1182	gAa/ga	24/29	0.365407167875169	1	FACETS	0.741	0.584	0.917	0.741	0.584	0.917	CLONAL	1	TRUE	0	0.422079677693171	1		263	111	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350030	70350030	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	21	504	0	ENST00000374080.3:c.4013A>G	p.Asn1338Ser	p.N1338S	ENST00000374080		1338	aAc/aGc	28/45	0.365407167875169	1	FACETS	0.243	0.187	0.309	0.243	0.187	0.309	SUBCLONAL	1	TRUE	0	0.422079677693171	1		504	323	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913517	NA	P-0066404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	261	460	0	ENST00000288135.5:c.1676T>A	p.Val559Asp	p.V559D	ENST00000288135	NM_000222.2	559	gTt/gAt	11/21	1	2	FACETS	0.963	0.909	1	0.963	0.909	1	CLONAL	1	TRUE	1	0.830986498500351	2		460	652	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0066410-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	39	492	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.579	0.482	0.687	0.579	0.482	0.687	SUBCLONAL	1	TRUE	1	0.45190825799276	2		492	298	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207162	1207162	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs137853076	NA	P-0066410-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	57	442	0	ENST00000326873.7:c.250A>T	p.Lys84Ter	p.K84*	ENST00000326873	NM_000455.4	84	Aag/Tag	1/10	0.273502156822073	1	FACETS	0.445	0.382	0.513	0.445	0.382	0.513	SUBCLONAL	1	TRUE	0	0.45190825799276	1		442	439	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630476	90630476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066410-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	53	487	0	ENST00000330062.3:c.835G>A	p.Asp279Asn	p.D279N	ENST00000330062	NM_002168.2	279	Gac/Aac	7/11	1	2	FACETS	0.474	0.404	0.55	0.474	0.404	0.55	SUBCLONAL	1	TRUE	1	0.45190825799276	2		487	495	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224493	108224493	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs748192003	NA	P-0066410-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	33	352	0	ENST00000278616.4:c.8672G>T	p.Gly2891Val	p.G2891V	ENST00000278616	NM_000051.3	2891	gGt/gTt	60/63	1	2	FACETS	0.425	0.346	0.513	0.425	0.346	0.513	SUBCLONAL	1	TRUE	1	0.45190825799276	2		352	344	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0066410-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	54	391	1	ENST00000265081.6:c.1141A>T	p.Lys381Ter	p.K381*	ENST00000265081	NM_002439.4	381	Aaa/Taa	7/24	1	2	FACETS	0.666	0.571	0.768	0.666	0.571	0.768	SUBCLONAL	1	TRUE	1	0.45190825799276	2		392	359	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1331478	1331478	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066410-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	57	378	0	ENST00000400841.2:c.50G>T	p.Gly17Val	p.G17V	ENST00000400841		17	gGc/gTc	1/6	1	2	FACETS	0.573	0.493	0.661	0.573	0.493	0.661	SUBCLONAL	1	TRUE	1	0.45190825799276	2		378	440	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971004	55971004	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066410-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	76	416	0	ENST00000263923.4:c.1793T>G	p.Leu598Trp	p.L598W	ENST00000263923	NM_002253.2	598	tTg/tGg	13/30	1	2	FACETS	0.702	0.618	0.793	0.702	0.618	0.793	SUBCLONAL	1	TRUE	1	0.45190825799276	2		416	479	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930934	39930934	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066410-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	22	300	0	ENST00000378444.4:c.3007T>A	p.Leu1003Ile	p.L1003I	ENST00000378444	NM_001123385.1	1003	Tta/Ata	5/15	1	2	FACETS	0.453	0.352	0.569	0.453	0.352	0.569	SUBCLONAL	1	TRUE	1	0.45190825799276	2		300	215	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18439817	18439817	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066410-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	27	344	0	ENST00000266497.5:c.715C>A	p.Gln239Lys	p.Q239K	ENST00000266497		239	Caa/Aaa	2/31	0.252055099590507	1	FACETS	0.374	0.299	0.46	0.374	0.299	0.46	INDETERMINATE	1	TRUE	0	0.45190825799276	1		344	247	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357585	70357585	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066410-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	69	530	1	ENST00000374080.3:c.5836C>A	p.Pro1946Thr	p.P1946T	ENST00000374080		1946	Cct/Act	41/45	1	2	FACETS	0.55	0.48	0.626	0.55	0.48	0.626	SUBCLONAL	1	TRUE	1	0.45190825799276	2		531	555	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69012079	69012079	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0066410-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	115	287	0	ENST00000288368.4:c.2715+1G>C		p.X905_splice	ENST00000288368	NM_024870.2	905			0.45190825799276	3	FACETS	0.891	0.812	0.973	0.891	0.812	0.973	CLONAL	2	TRUE	1	0.45190825799276	3		287	350	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0066412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	56	215	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.898	0.776	1	0.898	0.776	1	CLONAL	1	TRUE	1	0.46	2		215	271	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453153	140453153	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913337	NA	P-0066412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	73	294	1	ENST00000288602.6:c.1782T>A	p.Asp594Glu	p.D594E	ENST00000288602	NM_004333.4	594	gaT/gaA	15/18	1	2	FACETS	0.953	0.84	1	0.953	0.84	1	CLONAL	1	TRUE	1	0.46	2		295	333	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916535	39916574	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CATCACAAATCTTGTTCTCTAAGCAGTACAGGACCACTTC	CATCACAAATCTTGTTCTCTAAGCAGTACAGGACCACTTC	-	novel	NA	P-0066412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	82	383	0	ENST00000378444.4:c.4429_4468del	p.Glu1477Ter	p.E1477*	ENST00000378444	NM_001123385.1	1477	GAAGTGGTCCTGTACTGCTTAGAGAACAAGATTTGTGATGta/ta	11/15	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.46	2		383	329	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971209	21971209	+	splice_acceptor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0066412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	150	384	0	ENST00000304494.5:c.151-2del		p.X51_splice	ENST00000304494	NM_000077.4	51			0.455732657750306	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.46	2		384	317	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061007	38061022	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCGGGGGCCGGCGC	GCCCGGGGGCCGGCGC	-	novel	NA	P-0066413-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	278	476	0	ENST00000250448.2:c.967_982del	p.Ala323ProfsTer22	p.A323Pfs*22	ENST00000250448	NM_004496.3	323	GCGCCGGCCCCCGGGCcc/cc	2/2	0.777561401682183	3	FACETS	1	0.979	1	0.543	0.511	0.576	CLONAL	1	TRUE	1	0.777561401682183	3		476	914	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115897	8115898	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066413-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	268	484	0	ENST00000346208.3:c.1244dup	p.Met415IlefsTer92	p.M415Ifs*92	ENST00000346208		415	atg/aTtg	6/6	0.777561401682183	3	FACETS	1	0.956	1	0.51	0.479	0.542	CLONAL	1	TRUE	1	0.777561401682183	3		484	938	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518094	69518094	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066413-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	206	378	0	ENST00000294312.3:c.271G>C	p.Ala91Pro	p.A91P	ENST00000294312	NM_005117.2	91	Gcc/Ccc	2/3	0.10803363653548	5	FACETS	0.849	0.791	0.908			1	INDETERMINATE	2	TRUE	NA	0.777561401682183	5		378	676	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0066415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	219	523	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	0.860074746201129	3	FACETS	0.92	0.888	0.949	0.92	0.888	0.949	CLONAL	3	TRUE	0	0.860074746201129	3		523	264	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519985	NA	P-0066415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	298	620	0	ENST00000269305.4:c.857A>G	p.Glu286Gly	p.E286G	ENST00000269305	NM_001126112.2	286	gAa/gGa	8/11	0.736895132342737	3	FACETS	0.915	0.888	0.941	0.915	0.888	0.941	CLONAL	3	TRUE	0	0.860074746201129	3		620	361	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797890	45797890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146044717	NA	P-0066415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	40	645	0	ENST00000450313.1:c.881G>A	p.Arg294His	p.R294H	ENST00000450313	NM_012222.2	294	cGc/cAc	10/16	0.5512164695989	4	FACETS	0.331	0.275	0.394	0.11	0.091	0.132	SUBCLONAL	1	TRUE	1	0.860074746201129	4		645	522	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123788	11123788	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1064795105	NA	P-0066415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	28	438	0	ENST00000358026.2:c.2438C>T	p.Ser813Leu	p.S813L	ENST00000358026	NM_001128849.1	813	tCa/tTa	16/36	0.619030383180125	4	FACETS	0.314	0.25	0.386	0.157	0.125	0.193	SUBCLONAL	1	TRUE	2	0.860074746201129	4		438	386	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925319	114925319	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	169	440	0	ENST00000543371.1:c.1397A>C	p.Lys466Thr	p.K466T	ENST00000543371	NM_001198531.1	466	aAa/aCa	14/14	0.5512164695989	4	FACETS	0.889	0.838	0.939	0.889	0.838	0.939	CLONAL	3	TRUE	1	0.860074746201129	4		440	274	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86545140	86545140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	90	615	0	ENST00000262426.4:c.965C>T	p.Pro322Leu	p.P322L	ENST00000262426	NM_001451.2	322	cCa/cTa	1/2	0.860074746201129	4	FACETS	0.788	0.702	0.879	0.394	0.351	0.44	SUBCLONAL	1	TRUE	2	0.860074746201129	4		615	494	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572101	95572101	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1060503605	NA	P-0066415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	43	449	0	ENST00000393063.1:c.3007C>T	p.Arg1003Ter	p.R1003*	ENST00000393063	NM_030621.3	1003	Cga/Tga	20/28	0.79295821466541	2	FACETS	0.585	0.497	0.679	0.292	0.248	0.34	SUBCLONAL	1	TRUE	0	0.860074746201129	2		449	171	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52676007	52676007	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	162	375	0	ENST00000394830.3:c.1050A>C	p.Gln350His	p.Q350H	ENST00000394830	NM_018313.4	350	caA/caC	11/30	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.48	2		375	611	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839700	27839700	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	223	618	0	ENST00000328488.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000328488	NM_003533.2	132	Cga/Tga	1/1	1	2	FACETS	0.837	0.779	0.898	0.837	0.779	0.898	CLONAL	1	TRUE	1	0.48	2		618	1110	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0066417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	22	364	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	1	2	FACETS	0.122	0.094	0.154	0.122	0.094	0.154	SUBCLONAL	1	TRUE	1	0.768065064905446	2		364	471	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032069	10032069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868215122	NA	P-0066417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	227	517	0	ENST00000330684.3:c.754G>A	p.Asp252Asn	p.D252N	ENST00000330684	NM_001134407.1	252	Gat/Aat	3/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.768065064905446	2		517	567	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827922	40827922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	243	551	0	ENST00000373198.4:c.2506G>A	p.Asp836Asn	p.D836N	ENST00000373198	NM_133170.3	836	Gat/Aat	17/32	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.768065064905446	2		551	629	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256530	+	missense_variant	Missense_Mutation	DNP	TG	TG	CT	rs1057519834	NA	P-0066417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	213	402	0	ENST00000369535.4:c.181_182delinsAG	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	CAa/AGa	3/7	1	2	FACETS	0.966	0.905	1	0.966	0.905	1	CLONAL	1	TRUE	1	0.768065064905446	2		402	574	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991913	72991913	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	272	597	0	ENST00000268489.5:c.2132C>G	p.Pro711Arg	p.P711R	ENST00000268489	NM_006885.3	711	cCc/cGc	2/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.768065064905446	2		597	694	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509270	106509270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	58	482	0	ENST00000359195.3:c.1264G>A	p.Asp422Asn	p.D422N	ENST00000359195	NM_002649.2	422	Gac/Aac	2/11	1	2	FACETS	0.262	0.225	0.302	0.262	0.225	0.302	SUBCLONAL	1	TRUE	1	0.768065064905446	2		482	577	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247238	153247239	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0066417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	230	516	0	ENST00000281708.4:c.1563dup	p.Met522TyrfsTer10	p.M522Yfs*10	ENST00000281708	NM_033632.3	521	-/T	10/12	1	2	FACETS	0.921	0.864	0.98	0.921	0.864	0.98	CLONAL	1	TRUE	1	0.768065064905446	2		516	650	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312918	30312918	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	267	577	0	ENST00000262643.3:c.721T>A	p.Leu241Ile	p.L241I	ENST00000262643	NM_001238.2	241	Tta/Ata	9/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.768065064905446	2		577	669	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245383	153245383	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	190	501	0	ENST00000281708.4:c.1808T>A	p.Val603Asp	p.V603D	ENST00000281708	NM_033632.3	603	gTt/gAt	11/12	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.768065064905446	2		501	478	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914145	32914145	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	155	526	0	ENST00000380152.3:c.5653T>A	p.Cys1885Ser	p.C1885S	ENST00000380152		1885	Tgc/Agc	11/27	1	2	FACETS	0.919	0.85	0.991	0.919	0.85	0.991	CLONAL	1	TRUE	1	0.768065064905446	2		526	439	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714708	52714708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	194	545	0	ENST00000322088.6:c.466C>T	p.Pro156Ser	p.P156S	ENST00000322088	NM_014225.5	156	Ccc/Tcc	4/15	1	2	FACETS	0.876	0.815	0.937	0.876	0.815	0.937	CLONAL	1	TRUE	1	0.768065064905446	2		545	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	341	450	0	ENST00000269305.4:c.398T>A	p.Met133Lys	p.M133K	ENST00000269305	NM_001126112.2	133	aTg/aAg	5/11	0.719022653629868	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.719022653629868	1		450	549	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692811	89692811	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	59	173	0	ENST00000371953.3:c.295G>T	p.Glu99Ter	p.E99*	ENST00000371953	NM_000314.4	99	Gaa/Taa	5/9	0.719022653629868	1	FACETS	0.767	0.679	0.857	0.767	0.679	0.857	SUBCLONAL	1	TRUE	0	0.719022653629868	1		173	137	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124503451	124503451	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	42	392	0	ENST00000357628.3:c.499C>G	p.Gln167Glu	p.Q167E	ENST00000357628	NM_015450.2	167	Cag/Gag	8/19	1	2	FACETS	0.174	0.145	0.207	0.174	0.145	0.207	SUBCLONAL	1	TRUE	1	0.719022653629868	2		392	671	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988301	41988301	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1281012102	NA	P-0066419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	274	421	0	ENST00000219905.7:c.1093T>A	p.Ser365Thr	p.S365T	ENST00000219905	NM_001164273.1	365	Tcc/Acc	3/24	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.719022653629868	2		421	760	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0066420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	522	579	1	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.793267019755716	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.79296948448821	2		580	626	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620387	43620387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748288493	NA	P-0066420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	286	525	2	ENST00000355710.3:c.2996C>T	p.Ala999Val	p.A999V	ENST00000355710	NM_020975.4	999	gCg/gTg	18/20	0.791658135620941	4	FACETS	0.941	0.883	1	0.471	0.441	0.501	CLONAL	1	TRUE	2	0.79296948448821	4		527	1374	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38178602	38178602	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9358	577	390	0	ENST00000317025.8:c.1797C>G	p.Ile599Met	p.I599M	ENST00000317025	NM_023034.1	599	atC/atG	8/24	0.79296948448821	55	FACETS	1	0.985	1			1	CLONAL	3	TRUE	NA	0.79296948448821	55		390	9935	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150923227	150923227	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	293	536	0	ENST00000271640.5:c.1874T>G	p.Val625Gly	p.V625G	ENST00000271640	NM_001145415.1	625	gTt/gGt	13/22	0.702366878015327	6	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.79296948448821	6		536	1307	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054525	42054525	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	164	402	0	ENST00000219905.7:c.7709C>A	p.Pro2570His	p.P2570H	ENST00000219905	NM_001164273.1	2570	cCt/cAt	22/24	0.793267019755716	3	FACETS	1	0.977	1	0.381	0.352	0.411	CLONAL	1	TRUE	0	0.79296948448821	3		402	505	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0066424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	156	539	0				ENST00000310581	NM_198253.2	-/1132			0.328107795098667	3	FACETS	0.938	0.866	1	0.938	0.866	1	CLONAL	2	TRUE	1	0.441555927266603	3		539	460	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374245	138374245	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	173	354	0	ENST00000289153.2:c.3199G>T	p.Asp1067Tyr	p.D1067Y	ENST00000289153	NM_006219.2	1067	Gac/Tac	22/22	0.441555927266603	3	FACETS	1	0.985	1	0.638	0.588	0.689	CLONAL	1	TRUE	1	0.441555927266603	3		354	750	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259079	89259079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267599943	NA	P-0066424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	89	388	0	ENST00000336596.2:c.223G>A	p.Asp75Asn	p.D75N	ENST00000336596	NM_005233.5	75	Gac/Aac	3/17	0.441555927266603	3	FACETS	0.63	0.558	0.707	0.315	0.279	0.354	SUBCLONAL	1	TRUE	1	0.441555927266603	3		388	781	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597429	52597429	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	279	435	0	ENST00000394830.3:c.3881del	p.Leu1294Ter	p.L1294*	ENST00000394830	NM_018313.4	1294	tTa/ta	25/30	0.308505773748621	3	FACETS	1	0.978	1	0.71	0.671	0.75	CLONAL	2	TRUE	0	0.441555927266603	3		435	724	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781851	9781851	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746943903	NA	P-0066425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	41	347	0	ENST00000377346.4:c.1988G>A	p.Arg663His	p.R663H	ENST00000377346	NM_005026.3	663	cGc/cAc	16/24	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.22	2		347	366	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108221	209108221	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	41	413	0	ENST00000345146.2:c.628A>C	p.Ser210Arg	p.S210R	ENST00000345146	NM_005896.2	210	Agc/Cgc	6/10	1	2	FACETS	0.809	0.674	0.958	0.809	0.674	0.958	CLONAL	1	TRUE	1	0.22	2		413	461	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120791	115120791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	57	482	0	ENST00000257566.3:c.215C>T	p.Ala72Val	p.A72V	ENST00000257566	NM_016569.3	72	gCc/gTc	1/8	1	2	FACETS	0.978	0.839	1	0.978	0.839	1	CLONAL	1	TRUE	1	0.22	2		482	530	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1795770	1795770	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	78	744	0	ENST00000260795.2:c.109G>C	p.Glu37Gln	p.E37Q	ENST00000260795		37	Gaa/Caa	1/17	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.22	2		744	609	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066428-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	56	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.861	0.75	0.978	0.861	0.75	0.978	CLONAL	1	TRUE	1	0.684364031369551	2		341	190	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0066428-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	8	928	2	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	0.684364031369551	1	FACETS	0.039	0.025	0.058	0.039	0.025	0.058	SUBCLONAL	1	TRUE	0	0.684364031369551	1		930	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs864622237	NA	P-0066428-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	203	368	0	ENST00000269305.4:c.700T>C	p.Tyr234His	p.Y234H	ENST00000269305	NM_001126112.2	234	Tac/Cac	7/11	0.684364031369551	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.684364031369551	1		368	331	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591826	48591826	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs281875324	NA	P-0066428-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	85	443	0	ENST00000342988.3:c.989A>C	p.Glu330Ala	p.E330A	ENST00000342988	NM_005359.5	330	gAa/gCa	9/12	0.684364031369551	1	FACETS	0.996	0.908	1	0.996	0.908	1	CLONAL	1	TRUE	0	0.684364031369551	1		443	164	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436072	56436082	+	frameshift_variant	Frame_Shift_Del	DEL	AGCAGGGAGGT	AGCAGGGAGGT	-	novel	NA	P-0066428-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	204	544	0	ENST00000407977.2:c.1055_1065del	p.His352ArgfsTer87	p.H352Rfs*87	ENST00000407977		352	cACCTCCCTGCT/c	9/10	0.684364031369551	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.684364031369551	1		544	387	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866579	117866579	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066428-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	86	395	0	ENST00000297338.2:c.1066C>G	p.Pro356Ala	p.P356A	ENST00000297338	NM_006265.2	356	Ccc/Gcc	9/14	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.684364031369551	2		395	231	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974792	21974792	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs141798398	NA	P-0066429-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	134	630	1	ENST00000304494.5:c.35C>A	p.Ser12Ter	p.S12*	ENST00000304494	NM_000077.4	12	tCg/tAg	1/3	0.207647188133035	1	FACETS	0.864	0.792	0.94	1	0.992	1	CLONAL	3	TRUE	0	0.207647188133035	1		631	446	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0066431-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	265	436	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.255447066508617	6	FACETS	1	0.96	1	1	0.992	1	CLONAL	5	TRUE	2	0.255447066508617	6		436	615	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353763	68353763	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066431-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	25	328	0	ENST00000487270.1:c.598A>T	p.Ile200Phe	p.I200F	ENST00000487270	NM_133509.3	200	Atc/Ttc	7/11	0.255447066508617	6	FACETS	0.745	0.587	0.927	0.186	0.146	0.232	CLONAL	1	TRUE	2	0.255447066508617	6		328	397	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038546	47038561	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TGGCGTGCCCAAGTCA	TGGCGTGCCCAAGTCA	-	novel	NA	P-0066431-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	89	591	0	ENST00000377604.3:c.708_723del	p.Cys236TrpfsTer25	p.C236Wfs*25	ENST00000377604	NM_001204468.1	236	tgTGGCGTGCCCAAGTCA/tg	8/24	0.186224616594026	3	FACETS	0.929	0.828	1	0.929	0.828	1	CLONAL	2	TRUE	1	0.255447066508617	3		591	423	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0066431-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	347	436	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.313210463061878	7	FACETS	1	0.96	1	1	0.96	1	CLONAL	5	TRUE	2	0.313210463061878	7		436	783	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353763	68353763	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066431-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	43	328	0	ENST00000487270.1:c.598A>T	p.Ile200Phe	p.I200F	ENST00000487270	NM_133509.3	200	Atc/Ttc	7/11	0.313210463061878	7	FACETS	0.824	0.689	0.975	0.165	0.137	0.195	CLONAL	1	TRUE	2	0.313210463061878	7		328	594	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038546	47038561	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TGGCGTGCCCAAGTCA	TGGCGTGCCCAAGTCA	-	novel	NA	P-0066431-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	126	591	0	ENST00000377604.3:c.708_723del	p.Cys236TrpfsTer25	p.C236Wfs*25	ENST00000377604	NM_001204468.1	236	tgTGGCGTGCCCAAGTCA/tg	8/24	0.281428407344137	3	FACETS	0.799	0.726	0.876	0.799	0.726	0.876	SUBCLONAL	2	TRUE	1	0.313210463061878	3		591	582	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2115830	2115830	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066431-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	45	454	0	ENST00000349721.2:c.3465G>T	p.Gln1155His	p.Q1155H	ENST00000349721	NM_003070.3	1155	caG/caT	25/34	1	2	FACETS	0.578	0.486	0.68	0.578	0.486	0.68	SUBCLONAL	1	TRUE	1	0.313210463061878	2		454	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0066432-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	221	545	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.551941971015124	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.551941971015124	1		546	461	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555353	106555353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066432-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	58	355	0	ENST00000369096.4:c.2470G>A	p.Asp824Asn	p.D824N	ENST00000369096	NM_001198.3	824	Gat/Aat	7/7	1	2	FACETS	0.457	0.393	0.526	0.457	0.393	0.526	SUBCLONAL	1	TRUE	1	0.551941971015124	2		355	460	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73633589	73633589	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066432-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	223	257	1	ENST00000377687.4:c.124G>C	p.Asp42His	p.D42H	ENST00000377687	NM_001730.3	42	Gac/Cac	1/4	0.279011029672637	2	FACETS	0.937	0.886	0.989	0.937	0.886	0.989	INDETERMINATE	2	TRUE	0	0.551941971015124	2		258	431	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361138	66361138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066432-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	76	351	0	ENST00000273854.3:c.1034G>A	p.Arg345Lys	p.R345K	ENST00000273854	NM_004439.5	345	aGa/aAa	4/18	0.499311475117216	1	FACETS	0.523	0.462	0.589	0.523	0.462	0.589	SUBCLONAL	1	TRUE	0	0.551941971015124	1		351	381	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780169	9780169	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0066432-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	55	533	0	ENST00000377346.4:c.1340-1G>C		p.X447_splice	ENST00000377346	NM_005026.3	447			1	2	FACETS	0.331	0.283	0.384	0.331	0.283	0.384	SUBCLONAL	1	TRUE	1	0.551941971015124	2		533	602	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984347	201984347	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066432-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	43	435	0	ENST00000359651.3:c.1014del	p.Lys338AsnfsTer109	p.K338Nfs*109	ENST00000359651		338	Aaa/aa	8/8	0.170489233391054	3	FACETS	0.266	0.222	0.316	0.133	0.111	0.158	INDETERMINATE	1	TRUE	1	0.551941971015124	3		435	747	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73633532	73633532	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066432-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	270	305	1	ENST00000377687.4:c.67G>A	p.Asp23Asn	p.D23N	ENST00000377687	NM_001730.3	23	Gac/Aac	1/4	0.279011029672637	2	FACETS	0.965	0.917	1	0.965	0.917	1	INDETERMINATE	2	TRUE	0	0.551941971015124	2		306	507	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112201	115112215	+	inframe_deletion	In_Frame_Del	DEL	GAAGAACTGTTGGCC	GAAGAACTGTTGGCC	-	novel	NA	P-0066432-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	48	444	0	ENST00000257566.3:c.1525_1539del	p.Gly509_Phe513del	p.G509_F513del	ENST00000257566	NM_016569.3	509	GGCCAACAGTTCTTC/-	7/8	0.106705498861235	3	FACETS	0.389	0.328	0.455	0.194	0.164	0.228	INDETERMINATE	1	TRUE	1	0.551941971015124	3		444	571	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73633715	73633715	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066432-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	243	274	3	ENST00000377687.4:c.250G>C	p.Asp84His	p.D84H	ENST00000377687	NM_001730.3	84	Gac/Cac	1/4	0.279011029672637	2	FACETS	0.961	0.911	1	0.961	0.911	1	INDETERMINATE	2	TRUE	0	0.551941971015124	2		277	458	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210435	2210435	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs866975812	NA	P-0066432-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	176	416	0	ENST00000398665.3:c.1042G>T	p.Glu348Ter	p.E348*	ENST00000398665	NM_032482.2	348	Gag/Tag	13/28	0.551941971015124	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.551941971015124	1		416	441	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73633503	73633503	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066432-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	270	300	1	ENST00000377687.4:c.38G>T	p.Gly13Val	p.G13V	ENST00000377687	NM_001730.3	13	gGa/gTa	1/4	0.279011029672637	2	FACETS	0.988	0.94	1	0.988	0.94	1	INDETERMINATE	2	TRUE	0	0.551941971015124	2		301	495	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0066433-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	126	473	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.928	0.849	1	0.928	0.849	1	CLONAL	1	TRUE	1	0.708939857838651	2		473	383	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589578	67589583	+	inframe_deletion	In_Frame_Del	DEL	AAAATT	AAAATT	-	novel	NA	P-0066433-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	57	248	0	ENST00000274335.5:c.1342_1347del	p.Lys448_Leu449del	p.K448_L449del	ENST00000274335		447	aaAAAATTa/aaa	10/15	1	2	FACETS	0.999	0.876	1	0.999	0.876	1	CLONAL	1	TRUE	1	0.708939857838651	2		248	161	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578242	7578242	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882003	NA	P-0066433-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	393	530	1	ENST00000269305.4:c.607G>T	p.Val203Leu	p.V203L	ENST00000269305	NM_001126112.2	203	Gtg/Ttg	6/11	0.708939857838651	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.708939857838651	2		531	552	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217553	142217554	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0066433-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	65	340	0	ENST00000350721.4:c.5443_5444del	p.Asp1815TyrfsTer6	p.D1815Yfs*6	ENST00000350721	NM_001184.3	1815	GAt/t	32/47	1	2	FACETS	0.697	0.611	0.788	0.697	0.611	0.788	SUBCLONAL	1	TRUE	1	0.708939857838651	2		340	263	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508535	106508535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066434-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	38	341	0	ENST00000359195.3:c.529C>T	p.Arg177Cys	p.R177C	ENST00000359195	NM_002649.2	177	Cgc/Tgc	2/11	1	2	FACETS	0.752	0.621	0.897	0.752	0.621	0.897	SUBCLONAL	1	TRUE	1	0.229840634821441	2		341	440	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574025	7574025	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066434-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	87	349	0	ENST00000269305.4:c.1002del	p.Arg335ValfsTer10	p.R335Vfs*10	ENST00000269305	NM_001126112.2	334	ggG/gg	10/11	1	2	FACETS	0.756	0.671	0.845	1	0.979	1	SUBCLONAL	2	TRUE	1	0.229840634821441	2		349	501	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936951	48936951	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066434-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	42	274	0	ENST00000267163.4:c.721del	p.Thr241GlnfsTer23	p.T241Qfs*23	ENST00000267163	NM_000321.2	240	aAa/aa	8/27	1	2	FACETS	0.932	0.78	1	0.932	0.78	1	CLONAL	1	TRUE	1	0.229840634821441	2		274	392	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0066452-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	198	320	0	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.718813383559861	2		320	494	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51535088	51535088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150890833	NA	P-0066452-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	131	289	0	ENST00000260433.2:c.22C>T	p.Pro8Ser	p.P8S	ENST00000260433		8	Ccg/Tcg	2/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.718813383559861	2		289	348	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	114	797	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.39	2		797	465	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	83	492	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.39	2		492	385	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1688567	1688568	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs746550458	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	26	383	1	ENST00000378625.1:c.757dup	p.Ala253GlyfsTer45	p.A253Gfs*45	ENST00000378625	NM_001198994.1	253	gcc/gGcc	6/14	1	2	FACETS	0.296	0.233	0.367	0.296	0.233	0.367	SUBCLONAL	1	TRUE	1	0.39	2		384	451	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	18	529	4	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	2	FACETS	0.407	0.307	0.524	0.407	0.307	0.524	SUBCLONAL	1	TRUE	1	0.39	2		533	227	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	130	806	4	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.988	0.898	1	0.988	0.898	1	CLONAL	1	TRUE	1	0.39	2		810	675	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188071	11188071	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	119	440	0	ENST00000361445.4:c.6023A>G	p.Gln2008Arg	p.Q2008R	ENST00000361445	NM_004958.3	2008	cAg/cGg	43/58	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.39	2		440	602	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023571	27023571	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	65	389	0	ENST00000324856.7:c.680del	p.Pro227ArgfsTer5	p.P227Rfs*5	ENST00000324856	NM_006015.4	226	gCc/gc	1/20	1	2	FACETS	0.921	0.803	1	0.921	0.803	1	CLONAL	1	TRUE	1	0.39	2		389	362	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057988	27057988	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	141	519	0	ENST00000324856.7:c.1696C>T	p.Gln566Ter	p.Q566*	ENST00000324856	NM_006015.4	566	Cag/Tag	3/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.39	2		519	584	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313286	65313286	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	99	430	0	ENST00000342505.4:c.1828G>T	p.Gly610Ter	p.G610*	ENST00000342505	NM_002227.2	610	Gga/Tga	13/25	1	2	FACETS	0.99	0.887	1	0.99	0.887	1	CLONAL	1	TRUE	1	0.39	2		430	513	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325840	65325840	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	117	412	0	ENST00000342505.4:c.1282G>C	p.Ala428Pro	p.A428P	ENST00000342505	NM_002227.2	428	Gcc/Ccc	9/25	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.39	2		412	593	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339110	65339111	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	93	475	2	ENST00000342505.4:c.425dup	p.Ile143AspfsTer9	p.I143Dfs*9	ENST00000342505	NM_002227.2	142	aag/aaAg	5/25	1	2	FACETS	0.795	0.708	0.887	0.795	0.708	0.887	SUBCLONAL	1	TRUE	1	0.39	2		477	600	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483245	120483245	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61755044	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	85	402	0	ENST00000256646.2:c.3116C>T	p.Thr1039Met	p.T1039M	ENST00000256646	NM_024408.3	1039	aCg/aTg	19/34	1	2	FACETS	0.891	0.791	0.998	0.891	0.791	0.998	CLONAL	1	TRUE	1	0.39	2		402	489	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652423	206652423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140533827	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	85	404	0	ENST00000367120.3:c.1130G>A	p.Ser377Asn	p.S377N	ENST00000367120	NM_014002.3	377	aGc/aAc	10/22	1	2	FACETS	0.78	0.691	0.875	0.78	0.691	0.875	SUBCLONAL	1	TRUE	1	0.39	2		404	559	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653844	89653844	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	68	251	0	ENST00000371953.3:c.142A>T	p.Asn48Tyr	p.N48Y	ENST00000371953	NM_000314.4	48	Aac/Tac	2/9	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.39	2		251	329	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711928	89711928	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554900593	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	74	252	0	ENST00000371953.3:c.548del	p.Lys183ArgfsTer16	p.K183Rfs*16	ENST00000371953	NM_000314.4	182	ttA/tt	6/9	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.39	2		252	369	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466019	69466019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	127	423	0	ENST00000227507.2:c.857C>A	p.Thr286Lys	p.T286K	ENST00000227507	NM_053056.2	286	aCa/aAa	5/5	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.39	2		423	528	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433060	49433060	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1251778848	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	101	457	0	ENST00000301067.7:c.8311C>T	p.Arg2771Ter	p.R2771*	ENST00000301067	NM_003482.3	2771	Cga/Tga	33/54	1	2	FACETS	0.972	0.872	1	0.972	0.872	1	CLONAL	1	TRUE	1	0.39	2		457	533	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856565	111856565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1386743022	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	22	382	0	ENST00000341259.2:c.616G>A	p.Ala206Thr	p.A206T	ENST00000341259	NM_005475.2	206	Gcc/Acc	2/8	1	2	FACETS	0.291	0.225	0.368	0.291	0.225	0.368	SUBCLONAL	1	TRUE	1	0.39	2		382	388	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907421	32907421	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359306	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	95	308	5	ENST00000380152.3:c.1813del	p.Ile605TyrfsTer9	p.I605Yfs*9	ENST00000380152		602	ggA/gg	10/27	1	2	FACETS	0.948	0.847	1	0.948	0.847	1	CLONAL	1	TRUE	1	0.39	2		313	514	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614595	38614595	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	60	217	0	ENST00000299084.4:c.361G>T	p.Glu121Ter	p.E121*	ENST00000299084	NM_152594.2	121	Gag/Tag	3/7	1	2	FACETS	0.999	0.867	1	0.999	0.867	1	CLONAL	1	TRUE	1	0.39	2		217	308	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465378	99465378	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	81	292	0	ENST00000268035.6:c.2203C>T	p.Pro735Ser	p.P735S	ENST00000268035	NM_000875.3	735	Cct/Tct	11/21	1	2	FACETS	0.982	0.87	1	0.982	0.87	1	CLONAL	1	TRUE	1	0.39	2		292	423	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500510	99500510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144738779	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	67	485	0	ENST00000268035.6:c.3943C>T	p.Pro1315Ser	p.P1315S	ENST00000268035	NM_000875.3	1315	Cca/Tca	21/21	1	2	FACETS	0.71	0.618	0.809	0.71	0.618	0.809	SUBCLONAL	1	TRUE	1	0.39	2		485	484	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786703	3786703	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587783497	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	101	443	0	ENST00000262367.5:c.4508A>G	p.Tyr1503Cys	p.Y1503C	ENST00000262367	NM_004380.2	1503	tAc/tGc	27/31	1	2	FACETS	0.879	0.788	0.976	0.879	0.788	0.976	CLONAL	1	TRUE	1	0.39	2		443	589	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	121	527	0	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	1	2	FACETS	0.993	0.899	1	0.993	0.899	1	CLONAL	1	TRUE	1	0.39	2		527	625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	88	509	0	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	1	2	FACETS	0.764	0.678	0.855	0.764	0.678	0.855	SUBCLONAL	1	TRUE	1	0.39	2		509	591	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	82	782	3	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.85	0.751	0.954	0.85	0.751	0.954	CLONAL	1	TRUE	1	0.39	2		785	495	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687471	37687472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs760014508	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	82	463	2	ENST00000447079.4:c.4382dup	p.Thr1463AsnfsTer50	p.T1463Nfs*50	ENST00000447079	NM_015083.1	1459	tgg/tGgg	14/14	1	2	FACETS	0.739	0.653	0.831	0.739	0.653	0.831	SUBCLONAL	1	TRUE	1	0.39	2		465	569	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354436	40354436	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	126	514	1	ENST00000293328.3:c.2159del	p.Gly720AlafsTer46	p.G720Afs*46	ENST00000293328	NM_012448.3	720	gGc/gc	18/19	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.39	2		515	643	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475061	40475063	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	16	392	0	ENST00000264657.5:c.1847_1849del	p.Glu616del	p.E616del	ENST00000264657	NM_139276.2	616	gAAGga/gga	20/24	1	2	FACETS	0.143	0.105	0.189	0.143	0.105	0.189	SUBCLONAL	1	TRUE	1	0.39	2		392	573	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40856671	40856671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	76	260	0	ENST00000428826.2:c.1966G>A	p.Gly656Arg	p.G656R	ENST00000428826		656	Gga/Aga	18/21	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.39	2		260	369	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740623	58740624	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs763475304	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	99	429	0	ENST00000305921.3:c.1535dup	p.Asn512LysfsTer16	p.N512Kfs*16	ENST00000305921	NM_003620.3	510	caa/cAaa	6/6	1	2	FACETS	0.888	0.794	0.986	0.888	0.794	0.986	CLONAL	1	TRUE	1	0.39	2		429	572	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291083	10291084	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755889652	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	172	725	2	ENST00000340748.4:c.387dup	p.Lys130GlnfsTer19	p.K130Qfs*19	ENST00000340748		129	-/C	4/40	1	2	FACETS	0.813	0.747	0.882	0.813	0.747	0.882	CLONAL	1	TRUE	1	0.39	2		727	1085	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214713	36214714	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	54	389	1	ENST00000222270.7:c.3145dup	p.Ala1049GlyfsTer39	p.A1049Gfs*39	ENST00000222270	NM_014727.1	1047	cgg/cGgg	8/37	1	2	FACETS	0.667	0.571	0.772	0.667	0.571	0.772	SUBCLONAL	1	TRUE	1	0.39	2		390	415	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799063	42799065	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs751580245	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	86	379	0	ENST00000575354.2:c.4550_4552del	p.Lys1517del	p.K1517del	ENST00000575354	NM_015125.3	1516	cAGAag/cag	20/20	1	2	FACETS	0.946	0.841	1	0.946	0.841	1	CLONAL	1	TRUE	1	0.39	2		379	466	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905980	50905980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775232133	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	95	455	0	ENST00000440232.2:c.952G>A	p.Glu318Lys	p.E318K	ENST00000440232	NM_002691.3	318	Gag/Aag	8/27	1	2	FACETS	0.924	0.826	1	0.924	0.826	1	CLONAL	1	TRUE	1	0.39	2		455	527	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523021	25523021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457666600	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	111	395	0	ENST00000264709.3:c.164G>A	p.Arg55His	p.R55H	ENST00000264709	NM_175629.2	55	cGc/cAc	3/23	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.39	2		395	534	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098894	178098895	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	78	379	0	ENST00000397062.3:c.150dup	p.Gln51ThrfsTer5	p.Q51Tfs*5	ENST00000397062	NM_006164.4	50	-/A	2/5	1	2	FACETS	0.786	0.692	0.886	0.786	0.692	0.886	SUBCLONAL	1	TRUE	1	0.39	2		379	509	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661401	227661401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1379358223	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	102	497	0	ENST00000305123.5:c.2054G>A	p.Ser685Asn	p.S685N	ENST00000305123	NM_005544.2	685	aGc/aAc	1/2	1	2	FACETS	0.983	0.882	1	0.983	0.882	1	CLONAL	1	TRUE	1	0.39	2		497	532	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37045891	37045891	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	96	301	0	ENST00000231790.2:c.307-1G>T		p.X103_splice	ENST00000231790	NM_000249.3	103			1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.39	2		301	461	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913400	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	109	380	0	ENST00000349496.5:c.98C>A	p.Ser33Tyr	p.S33Y	ENST00000349496	NM_001904.3	33	tCt/tAt	3/15	1	2	FACETS	0.941	0.847	1	0.941	0.847	1	CLONAL	1	TRUE	1	0.39	2		380	594	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274739	142274740	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	37	251	1	ENST00000350721.4:c.2319_2320dup	p.Ile774LysfsTer6	p.I774Kfs*6	ENST00000350721	NM_001184.3	774	ata/aAAta	10/47	1	2	FACETS	0.497	0.41	0.594	0.497	0.41	0.594	SUBCLONAL	1	TRUE	1	0.39	2		252	382	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920127	1920127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	121	485	0	ENST00000382891.5:c.1187C>T	p.Pro396Leu	p.P396L	ENST00000382891	NM_133335.3	396	cCc/cTc	5/22	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.39	2		485	566	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247214	153247214	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	120	377	0	ENST00000281708.4:c.1588A>T	p.Thr530Ser	p.T530S	ENST00000281708	NM_033632.3	530	Act/Tct	10/12	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.39	2		377	545	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294451	1294451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773758089	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	94	478	0	ENST00000310581.5:c.550G>A	p.Ala184Thr	p.A184T	ENST00000310581	NM_198253.2	184	Gcc/Acc	2/16	1	2	FACETS	0.938	0.837	1	0.938	0.837	1	CLONAL	1	TRUE	1	0.39	2		478	514	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637121	176637122	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1299932363	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	125	431	0	ENST00000439151.2:c.1727dup	p.Asn576LysfsTer8	p.N576Kfs*8	ENST00000439151	NM_022455.4	574	gga/ggAa	5/23	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.39	2		431	598	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638456	176638456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750354456	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	130	440	0	ENST00000439151.2:c.3056G>A	p.Arg1019His	p.R1019H	ENST00000439151	NM_022455.4	1019	cGc/cAc	5/23	1	2	FACETS	0.985	0.895	1	0.985	0.895	1	CLONAL	1	TRUE	1	0.39	2		440	677	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176662910	176662911	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	71	333	0	ENST00000439151.2:c.3891dup	p.Gln1298ThrfsTer16	p.Q1298Tfs*16	ENST00000439151	NM_022455.4	1295	-/A	6/23	1	2	FACETS	0.922	0.809	1	0.922	0.809	1	CLONAL	1	TRUE	1	0.39	2		333	395	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401777	401777	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	98	428	0	ENST00000380956.4:c.1099G>T	p.Glu367Ter	p.E367*	ENST00000380956	NM_001195286.1	367	Gag/Tag	7/9	1	2	FACETS	0.982	0.879	1	0.982	0.879	1	CLONAL	1	TRUE	1	0.39	2		428	512	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522190	157522190	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	105	488	1	ENST00000346085.5:c.4466del	p.Pro1489LeufsTer5	p.P1489Lfs*5	ENST00000346085	NM_020732.3	1488	Ccc/cc	18/20	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.39	2		489	532	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527741	157527742	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	107	436	0	ENST00000346085.5:c.5471dup	p.Asp1825Ter	p.D1825*	ENST00000346085	NM_020732.3	1822	-/G	20/20	1	2	FACETS	0.902	0.811	0.999	0.902	0.811	0.999	CLONAL	1	TRUE	1	0.39	2		436	608	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372092	55372093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	59	465	0	ENST00000297316.4:c.788dup	p.Glu264GlyfsTer101	p.E264Gfs*101	ENST00000297316	NM_022454.3	261	ggc/ggCc	2/2	1	2	FACETS	0.747	0.645	0.858	0.747	0.645	0.858	SUBCLONAL	1	TRUE	1	0.39	2		465	405	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955596	90955596	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	51	255	0	ENST00000265433.3:c.2071-2A>G		p.X691_splice	ENST00000265433	NM_002485.4	691			1	2	FACETS	0.749	0.64	0.869	0.749	0.64	0.869	SUBCLONAL	1	TRUE	1	0.39	2		255	349	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970951	21970951	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	84	481	1	ENST00000304494.5:c.407del	p.Gly136AlafsTer10	p.G136Afs*10	ENST00000304494	NM_000077.4	136	gGc/gc	2/3	1	2	FACETS	0.874	0.774	0.98	0.874	0.774	0.98	CLONAL	1	TRUE	1	0.39	2		482	493	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867574	101867574	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1264167074	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	16	170	0	ENST00000374994.4:c.91del	p.Ala31ArgfsTer19	p.A31Rfs*19	ENST00000374994	NM_004612.2	29	ccG/cc	1/9	1	2	FACETS	0.494	0.367	0.645	0.494	0.367	0.645	SUBCLONAL	1	TRUE	1	0.39	2		170	166	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424734	47424734	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	86	442	0	ENST00000377045.4:c.547del	p.Gln183ArgfsTer109	p.Q183Rfs*109	ENST00000377045	NM_001654.4	181	aCc/ac	6/16	1	2	FACETS	0.831	0.737	0.931	0.831	0.737	0.931	CLONAL	1	TRUE	1	0.39	2		442	531	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223796	53223796	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	96	451	0	ENST00000375401.3:c.3563G>C	p.Cys1188Ser	p.C1188S	ENST00000375401	NM_004187.3	1188	tGt/tCt	23/26	1	2	FACETS	0.797	0.711	0.888	0.797	0.711	0.888	SUBCLONAL	1	TRUE	1	0.39	2		451	618	SUCCESS
AR	367	MSKCC	GRCh37	X	66942786	66942786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs9332971	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	54	314	0	ENST00000374690.3:c.2567G>A	p.Arg856His	p.R856H	ENST00000374690	NM_000044.3	856	cGc/cAc	7/8	1	2	FACETS	0.733	0.628	0.846	0.733	0.628	0.846	SUBCLONAL	1	TRUE	1	0.39	2		314	378	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199469672	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	21	267	0	ENST00000374080.3:c.131G>T	p.Gly44Val	p.G44V	ENST00000374080		44	gGt/gTt	2/45	1	2	FACETS	0.238	0.183	0.303	0.238	0.183	0.303	SUBCLONAL	1	TRUE	1	0.39	2		267	452	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256463	16256463	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1445836153	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	129	477	0	ENST00000375759.3:c.3728G>A	p.Arg1243Gln	p.R1243Q	ENST00000375759	NM_015001.2	1243	cGg/cAg	11/15	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.39	2		477	649	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932175	36932175	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	78	467	0	ENST00000361632.4:c.2294G>T	p.Gly765Val	p.G765V	ENST00000361632		765	gGg/gTg	16/16	1	2	FACETS	0.743	0.654	0.839	0.743	0.654	0.839	SUBCLONAL	1	TRUE	1	0.39	2		467	538	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429826	78429826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	108	397	0	ENST00000370768.2:c.962G>A	p.Arg321Lys	p.R321K	ENST00000370768	NM_003902.3	321	aGg/aAg	12/20	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.39	2		397	528	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433311	78433311	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	58	276	0	ENST00000370768.2:c.290G>T	p.Ser97Ile	p.S97I	ENST00000370768	NM_003902.3	97	aGc/aTc	4/20	1	2	FACETS	0.918	0.794	1	0.918	0.794	1	CLONAL	1	TRUE	1	0.39	2		276	324	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695712	117695712	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	60	328	0	ENST00000369458.3:c.724+1G>A		p.X242_splice	ENST00000369458	NM_024626.3	242			1	2	FACETS	0.777	0.672	0.89	0.777	0.672	0.89	SUBCLONAL	1	TRUE	1	0.39	2		328	396	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480011	120480012	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1557812162	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	99	408	0	ENST00000256646.2:c.3415dup	p.Leu1139ProfsTer9	p.L1139Pfs*9	ENST00000256646	NM_024408.3	1139	ctg/cCtg	21/34	1	2	FACETS	0.953	0.853	1	0.953	0.853	1	CLONAL	1	TRUE	1	0.39	2		408	533	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510850	120510850	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	70	312	0	ENST00000256646.2:c.1114C>A	p.Leu372Met	p.L372M	ENST00000256646	NM_024408.3	372	Ctg/Atg	7/34	1	2	FACETS	0.909	0.796	1	0.909	0.796	1	CLONAL	1	TRUE	1	0.39	2		312	395	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163307819	163307819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	76	258	0	ENST00000271452.3:c.445G>A	p.Ala149Thr	p.A149T	ENST00000271452	NM_145697.2	149	Gcg/Acg	7/14	1	2	FACETS	0.997	0.879	1	0.997	0.879	1	CLONAL	1	TRUE	1	0.39	2		258	391	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218928	193218928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	84	332	0	ENST00000367435.3:c.1486G>A	p.Val496Ile	p.V496I	ENST00000367435	NM_024529.4	496	Gta/Ata	16/17	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.39	2		332	334	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652291	206652291	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	93	448	0	ENST00000367120.3:c.998C>T	p.Ala333Val	p.A333V	ENST00000367120	NM_014002.3	333	gCc/gTc	10/22	1	2	FACETS	0.921	0.821	1	0.921	0.821	1	CLONAL	1	TRUE	1	0.39	2		448	518	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230461153	230461153	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	46	318	1	ENST00000391860.1:c.937A>G	p.Ile313Val	p.I313V	ENST00000391860	NM_001258311.1	313	Atc/Gtc	6/7	1	2	FACETS	0.614	0.518	0.72	0.614	0.518	0.72	SUBCLONAL	1	TRUE	1	0.39	2		319	384	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103496	77103496	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	109	413	0	ENST00000356341.3:c.70A>T	p.Ile24Phe	p.I24F	ENST00000356341	NM_002576.4	24	Att/Ttt	2/15	1	2	FACETS	0.922	0.83	1	0.922	0.83	1	CLONAL	1	TRUE	1	0.39	2		413	606	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917640	94917640	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	81	409	0	ENST00000536441.1:c.881A>G	p.Lys294Arg	p.K294R	ENST00000536441	NM_144665.3	294	aAg/aGg	6/10	1	2	FACETS	0.846	0.748	0.951	0.846	0.748	0.951	CLONAL	1	TRUE	1	0.39	2		409	491	SUCCESS
ATM	472	MSKCC	GRCh37	11	108100041	108100041	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881370	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	81	232	1	ENST00000278616.4:c.322G>A	p.Ala108Thr	p.A108T	ENST00000278616	NM_000051.3	108	Gca/Aca	4/63	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.39	2		233	396	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196150	108196150	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1555119144	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	84	312	0	ENST00000278616.4:c.6686T>A	p.Val2229Asp	p.V2229D	ENST00000278616	NM_000051.3	2229	gTc/gAc	46/63	1	2	FACETS	0.972	0.863	1	0.972	0.863	1	CLONAL	1	TRUE	1	0.39	2		312	443	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552639	18552639	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	83	385	0	ENST00000266497.5:c.2050T>C	p.Cys684Arg	p.C684R	ENST00000266497		684	Tgc/Cgc	14/31	1	2	FACETS	0.876	0.775	0.983	0.876	0.775	0.983	CLONAL	1	TRUE	1	0.39	2		385	486	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434026	49434026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	111	440	0	ENST00000301067.7:c.7527G>T	p.Lys2509Asn	p.K2509N	ENST00000301067	NM_003482.3	2509	aaG/aaT	31/54	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.39	2		440	489	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437175	49437175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368134008	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	45	389	0	ENST00000301067.7:c.5504G>A	p.Arg1835His	p.R1835H	ENST00000301067	NM_003482.3	1835	cGt/cAt	24/54	1	2	FACETS	0.483	0.406	0.568	0.483	0.406	0.568	SUBCLONAL	1	TRUE	1	0.39	2		389	478	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493993	56493993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	96	421	0	ENST00000267101.3:c.3165G>A	p.Met1055Ile	p.M1055I	ENST00000267101	NM_001982.3	1055	atG/atA	26/28	1	2	FACETS	0.885	0.791	0.985	0.885	0.791	0.985	CLONAL	1	TRUE	1	0.39	2		421	556	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495145	56495145	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	76	405	0	ENST00000267101.3:c.3502G>T	p.Gly1168Cys	p.G1168C	ENST00000267101	NM_001982.3	1168	Ggt/Tgt	27/28	1	2	FACETS	0.769	0.676	0.868	0.769	0.676	0.868	SUBCLONAL	1	TRUE	1	0.39	2		405	507	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885861	111885861	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	109	478	0	ENST00000341259.2:c.1483G>T	p.Glu495Ter	p.E495*	ENST00000341259	NM_005475.2	495	Gag/Tag	8/8	1	2	FACETS	0.947	0.853	1	0.947	0.853	1	CLONAL	1	TRUE	1	0.39	2		478	590	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32905163	32905163	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	71	286	0	ENST00000380152.3:c.789T>A	p.Ser263Arg	p.S263R	ENST00000380152		263	agT/agA	9/27	1	2	FACETS	0.924	0.811	1	0.924	0.811	1	CLONAL	1	TRUE	1	0.39	2		286	394	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73348127	73348127	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	70	299	0	ENST00000377767.4:c.1058G>A	p.Trp353Ter	p.W353*	ENST00000377767	NM_014953.3	353	tGg/tAg	7/21	1	2	FACETS	0.994	0.872	1	0.994	0.872	1	CLONAL	1	TRUE	1	0.39	2		299	361	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435136	110435136	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	99	480	0	ENST00000375856.3:c.3265del	p.Ala1089ProfsTer17	p.A1089Pfs*17	ENST00000375856	NM_003749.2	1089	Gcc/cc	1/2	1	2	FACETS	0.994	0.89	1	0.994	0.89	1	CLONAL	1	TRUE	1	0.39	2		480	511	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133066	30133066	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	52	280	0	ENST00000331968.5:c.536-1G>T		p.X179_splice	ENST00000331968	NM_002742.2	179			1	2	FACETS	0.753	0.644	0.872	0.753	0.644	0.872	SUBCLONAL	1	TRUE	1	0.39	2		280	354	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679217	88679217	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	71	360	0	ENST00000360948.2:c.820A>T	p.Thr274Ser	p.T274S	ENST00000360948	NM_001012338.2	274	Acg/Tcg	8/19	1	2	FACETS	0.788	0.69	0.893	0.788	0.69	0.893	SUBCLONAL	1	TRUE	1	0.39	2		360	462	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842447	68842447	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	102	419	0	ENST00000261769.5:c.508C>A	p.Pro170Thr	p.P170T	ENST00000261769	NM_004360.3	170	Cca/Aca	4/16	1	2	FACETS	0.932	0.836	1	0.932	0.836	1	CLONAL	1	TRUE	1	0.39	2		419	561	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822702	72822702	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	93	436	0	ENST00000268489.5:c.9473C>T	p.Thr3158Ile	p.T3158I	ENST00000268489	NM_006885.3	3158	aCt/aTt	10/10	1	2	FACETS	0.873	0.779	0.974	0.873	0.779	0.974	CLONAL	1	TRUE	1	0.39	2		436	546	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89842212	89842212	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	112	361	0	ENST00000389301.3:c.1838T>C	p.Ile613Thr	p.I613T	ENST00000389301	NM_000135.2	613	aTc/aCc	21/43	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.39	2		361	511	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040716	16040716	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	82	221	0	ENST00000268712.3:c.1418A>G	p.Asp473Gly	p.D473G	ENST00000268712	NM_006311.3	473	gAt/gGt	14/46	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.39	2		221	353	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665143	29665143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555534961	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	68	296	0	ENST00000356175.3:c.6742C>T	p.Arg2248Cys	p.R2248C	ENST00000356175	NM_000267.3	2248	Cgt/Tgt	44/57	1	2	FACETS	0.92	0.805	1	0.92	0.805	1	CLONAL	1	TRUE	1	0.39	2		296	379	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40447670	40447670	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	88	423	0	ENST00000345506.4:c.409A>G	p.Met137Val	p.M137V	ENST00000345506	NM_003152.3	137	Atg/Gtg	6/20	1	2	FACETS	0.844	0.749	0.944	0.844	0.749	0.944	CLONAL	1	TRUE	1	0.39	2		423	535	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40457669	40457669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	66	345	0	ENST00000345506.4:c.1422G>T	p.Gln474His	p.Q474H	ENST00000345506	NM_003152.3	474	caG/caT	13/20	1	2	FACETS	0.808	0.704	0.92	0.808	0.704	0.92	CLONAL	1	TRUE	1	0.39	2		345	419	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245792	41245792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357153	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	112	385	0	ENST00000357654.3:c.1756C>T	p.Pro586Ser	p.P586S	ENST00000357654	NM_007294.3	586	Cct/Tct	10/23	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.39	2		385	539	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699390	47699390	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	99	345	0	ENST00000347630.2:c.118A>G	p.Asn40Asp	p.N40D	ENST00000347630	NM_001007230.1	40	Aac/Gac	4/11	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.39	2		345	467	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533081	63533081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763417360	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	109	352	0	ENST00000307078.5:c.1813G>A	p.Ala605Thr	p.A605T	ENST00000307078	NM_004655.3	605	Gcc/Acc	7/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.39	2		352	479	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217037	2217037	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	102	452	0	ENST00000398665.3:c.2492G>T	p.Arg831Leu	p.R831L	ENST00000398665	NM_032482.2	831	cGg/cTg	21/28	1	2	FACETS	0.967	0.868	1	0.967	0.868	1	CLONAL	1	TRUE	1	0.39	2		452	541	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267417	7267417	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	83	386	0	ENST00000302850.5:c.591del	p.Ala198ProfsTer84	p.A198Pfs*84	ENST00000302850	NM_000208.2	197	ccC/cc	2/22	1	2	FACETS	0.881	0.78	0.989	0.881	0.78	0.989	CLONAL	1	TRUE	1	0.39	2		386	483	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265374	10265374	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	122	475	0	ENST00000340748.4:c.1672G>A	p.Val558Met	p.V558M	ENST00000340748		558	Gtg/Atg	20/40	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.39	2		475	580	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097631	11097631	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	103	431	0	ENST00000358026.2:c.811G>C	p.Gly271Arg	p.G271R	ENST00000358026	NM_001128849.1	271	Ggg/Cgg	5/36	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.39	2		431	495	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375400	15375400	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	30	464	0	ENST00000263377.2:c.1027G>T	p.Ala343Ser	p.A343S	ENST00000263377	NM_058243.2	343	Gca/Tca	6/20	1	2	FACETS	0.263	0.211	0.323	0.263	0.211	0.323	SUBCLONAL	1	TRUE	1	0.39	2		464	584	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942575	17942575	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	53	285	0	ENST00000458235.1:c.2713C>A	p.Leu905Met	p.L905M	ENST00000458235	NM_000215.3	905	Ctg/Atg	20/24	1	2	FACETS	0.882	0.757	1	0.882	0.757	1	CLONAL	1	TRUE	1	0.39	2		285	308	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424352	47424352	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	118	466	0	ENST00000404338.3:c.2420A>G	p.Gln807Arg	p.Q807R	ENST00000404338	NM_004491.4	807	cAa/cGa	1/6	1	2	FACETS	0.979	0.886	1	0.979	0.886	1	CLONAL	1	TRUE	1	0.39	2		466	618	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754932	29754932	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	91	392	0	ENST00000389048.3:c.1003A>G	p.Ser335Gly	p.S335G	ENST00000389048	NM_004304.4	335	Agt/Ggt	4/29	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.39	2		392	463	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128030499	128030499	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	86	323	0	ENST00000285398.2:c.1769T>C	p.Met590Thr	p.M590T	ENST00000285398	NM_000122.1	590	aTg/aCg	11/15	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.39	2		323	422	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095796	178095796	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	96	407	0	ENST00000397062.3:c.1535A>G	p.Gln512Arg	p.Q512R	ENST00000397062	NM_006164.4	512	cAg/cGg	5/5	1	2	FACETS	0.882	0.788	0.982	0.882	0.788	0.982	CLONAL	1	TRUE	1	0.39	2		407	558	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738262	190738262	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	94	297	0	ENST00000441310.2:c.2514G>T	p.Met838Ile	p.M838I	ENST00000441310	NM_000534.4	838	atG/atT	12/13	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.39	2		297	471	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267291	198267291	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	78	344	0	ENST00000335508.6:c.2066T>A	p.Ile689Asn	p.I689N	ENST00000335508	NM_012433.2	689	aTc/aAc	14/25	1	2	FACETS	0.891	0.786	1	0.891	0.786	1	CLONAL	1	TRUE	1	0.39	2		344	449	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661920	227661920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769456251	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	80	451	0	ENST00000305123.5:c.1535C>T	p.Ala512Val	p.A512V	ENST00000305123	NM_005544.2	512	gCc/gTc	1/2	1	2	FACETS	0.862	0.761	0.969	0.862	0.761	0.969	CLONAL	1	TRUE	1	0.39	2		451	476	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561481	9561481	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	88	416	0	ENST00000353224.5:c.301A>G	p.Arg101Gly	p.R101G	ENST00000353224	NM_177990.2	101	Agg/Ggg	4/10	1	2	FACETS	0.876	0.779	0.98	0.876	0.779	0.98	CLONAL	1	TRUE	1	0.39	2		416	515	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979352	40979352	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	88	365	0	ENST00000373198.4:c.1781A>G	p.Tyr594Cys	p.Y594C	ENST00000373198	NM_133170.3	594	tAc/tGc	11/32	0.127090687816318	0	FACETS	0.561	0.498	0.627			1	INDETERMINATE	1	TRUE	0	0.39	0		365	491	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164497	36164497	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	68	375	0	ENST00000300305.3:c.1378A>G	p.Ser460Gly	p.S460G	ENST00000300305		460	Agc/Ggc	8/8	1	2	FACETS	0.937	0.82	1	0.937	0.82	1	CLONAL	1	TRUE	1	0.39	2		375	372	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21304072	21304072	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	93	339	0	ENST00000354336.3:c.851G>A	p.Gly284Glu	p.G284E	ENST00000354336	NM_005207.3	284	gGg/gAg	3/3	1	2	FACETS	0.958	0.855	1	0.958	0.855	1	CLONAL	1	TRUE	1	0.39	2		339	498	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513659	41513659	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	140	458	0	ENST00000263253.7:c.563C>A	p.Pro188His	p.P188H	ENST00000263253	NM_001429.3	188	cCt/cAt	2/31	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.39	2		458	635	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573960	41573960	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	128	431	0	ENST00000263253.7:c.6245C>T	p.Ala2082Val	p.A2082V	ENST00000263253	NM_001429.3	2082	gCt/gTt	31/31	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.39	2		431	529	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713930	30713930	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	69	419	0	ENST00000295754.5:c.1254+1G>A		p.X418_splice	ENST00000295754	NM_003242.5	418			1	2	FACETS	0.718	0.626	0.816	0.718	0.626	0.816	SUBCLONAL	1	TRUE	1	0.39	2		419	493	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439911	52439911	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	100	328	0	ENST00000460680.1:c.801G>T	p.Gln267His	p.Q267H	ENST00000460680	NM_004656.3	267	caG/caT	10/17	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.39	2		328	512	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199879	128199879	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1161135105	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	78	479	0	ENST00000341105.2:c.1426G>A	p.Val476Met	p.V476M	ENST00000341105	NM_032638.4	476	Gtg/Atg	6/6	1	2	FACETS	0.752	0.662	0.848	0.752	0.662	0.848	SUBCLONAL	1	TRUE	1	0.39	2		479	532	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968191	134968191	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	67	384	0	ENST00000398015.3:c.2704C>A	p.Leu902Met	p.L902M	ENST00000398015	NM_004441.4	902	Ctg/Atg	15/16	1	2	FACETS	0.872	0.761	0.991	0.872	0.761	0.991	CLONAL	1	TRUE	1	0.39	2		384	394	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045842	143045842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	81	370	0	ENST00000262992.4:c.1792G>T	p.Ala598Ser	p.A598S	ENST00000262992	NM_001101669.1	598	Gcc/Tcc	17/24	1	2	FACETS	0.927	0.82	1	0.927	0.82	1	CLONAL	1	TRUE	1	0.39	2		370	448	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519169	187519169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751396320	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	84	329	1	ENST00000441802.2:c.12214G>A	p.Gly4072Arg	p.G4072R	ENST00000441802	NM_005245.3	4072	Gga/Aga	23/27	1	2	FACETS	0.874	0.774	0.98	0.874	0.774	0.98	CLONAL	1	TRUE	1	0.39	2		330	493	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224539	224539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	51	217	0	ENST00000264932.6:c.215C>T	p.Ala72Val	p.A72V	ENST00000264932	NM_004168.2	72	gCa/gTa	3/15	1	2	FACETS	0.927	0.794	1	0.927	0.794	1	CLONAL	1	TRUE	1	0.39	2		217	282	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233597	233597	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060503713	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	47	193	0	ENST00000264932.6:c.901T>C	p.Tyr301His	p.Y301H	ENST00000264932	NM_004168.2	301	Tat/Cat	8/15	1	2	FACETS	0.972	0.827	1	0.972	0.827	1	CLONAL	1	TRUE	1	0.39	2		193	248	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295500	1295500	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	83	490	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.9	0.797	1	0.9	0.797	1	CLONAL	1	TRUE	1	0.39	2		491	473	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295506	1295506	+	upstream_gene_variant	5'Flank	SNP	A	A	G	rs900271807	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	90	484	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.997	0.888	1	0.997	0.888	1	CLONAL	1	TRUE	1	0.39	2		484	463	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752895	57752895	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	81	390	0	ENST00000274289.3:c.1033T>C	p.Ser345Pro	p.S345P	ENST00000274289	NM_006622.3	345	Tct/Cct	8/14	1	2	FACETS	0.784	0.692	0.882	0.784	0.692	0.882	SUBCLONAL	1	TRUE	1	0.39	2		390	530	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753321	57753321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	97	397	0	ENST00000274289.3:c.803G>A	p.Cys268Tyr	p.C268Y	ENST00000274289	NM_006622.3	268	tGt/tAt	6/14	1	2	FACETS	0.832	0.743	0.926	0.832	0.743	0.926	CLONAL	1	TRUE	1	0.39	2		397	598	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149452949	149452949	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	73	368	0	ENST00000286301.3:c.997G>T	p.Gly333Cys	p.G333C	ENST00000286301	NM_005211.3	333	Ggt/Tgt	7/22	1	2	FACETS	0.752	0.659	0.851	0.752	0.659	0.851	SUBCLONAL	1	TRUE	1	0.39	2		368	498	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168961	32168961	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs776583688	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	96	533	0	ENST00000375023.3:c.4072A>G	p.Thr1358Ala	p.T1358A	ENST00000375023	NM_004557.3	1358	Acc/Gcc	22/30	1	2	FACETS	0.952	0.851	1	0.952	0.851	1	CLONAL	1	TRUE	1	0.39	2		533	517	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169926	32169926	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	94	386	0	ENST00000375023.3:c.3682C>T	p.Gln1228Ter	p.Q1228*	ENST00000375023	NM_004557.3	1228	Cag/Tag	21/30	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.39	2		386	474	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184845	32184845	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	103	424	0	ENST00000375023.3:c.1739-1G>T		p.X580_splice	ENST00000375023	NM_004557.3	580			1	2	FACETS	0.815	0.73	0.905	0.815	0.73	0.905	CLONAL	1	TRUE	1	0.39	2		424	648	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652191	36652191	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	54	381	0	ENST00000244741.5:c.313A>G	p.Thr105Ala	p.T105A	ENST00000244741	NM_000389.4	105	Aca/Gca	2/3	1	2	FACETS	0.627	0.536	0.725	0.627	0.536	0.725	SUBCLONAL	1	TRUE	1	0.39	2		381	442	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683740	162683740	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	75	406	0	ENST00000366898.1:c.229G>T	p.Gly77Cys	p.G77C	ENST00000366898	NM_004562.2	77	Ggt/Tgt	3/12	1	2	FACETS	0.795	0.698	0.898	0.795	0.698	0.898	SUBCLONAL	1	TRUE	1	0.39	2		406	484	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397801	116397801	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	68	328	0	ENST00000397752.3:c.2075T>A	p.Ile692Asn	p.I692N	ENST00000397752	NM_000245.2	692	aTt/aAt	8/21	1	2	FACETS	0.807	0.705	0.917	0.807	0.705	0.917	CLONAL	1	TRUE	1	0.39	2		328	432	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843303	128843303	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	89	430	0	ENST00000249373.3:c.410A>T	p.Asp137Val	p.D137V	ENST00000249373	NM_005631.4	137	gAc/gTc	2/12	1	2	FACETS	0.883	0.785	0.987	0.883	0.785	0.987	CLONAL	1	TRUE	1	0.39	2		430	517	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345945	152345945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780202744	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	105	396	0	ENST00000359321.1:c.625C>T	p.Pro209Ser	p.P209S	ENST00000359321	NM_005431.1	209	Cct/Tct	3/3	1	2	FACETS	0.884	0.794	0.98	0.884	0.794	0.98	CLONAL	1	TRUE	1	0.39	2		396	609	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38184349	38184349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	100	321	0	ENST00000317025.8:c.1607G>A	p.Ser536Asn	p.S536N	ENST00000317025	NM_023034.1	536	aGt/aAt	7/24	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.39	2		321	487	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117861237	117861237	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	73	269	0	ENST00000297338.2:c.1652A>G	p.Gln551Arg	p.Q551R	ENST00000297338	NM_006265.2	551	cAg/cGg	13/14	1	2	FACETS	0.893	0.785	1	0.893	0.785	1	CLONAL	1	TRUE	1	0.39	2		269	419	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566064	141566064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	43	374	0	ENST00000220592.5:c.1200G>A	p.Met400Ile	p.M400I	ENST00000220592	NM_012154.3	400	atG/atA	10/19	1	2	FACETS	0.444	0.371	0.524	0.444	0.371	0.524	SUBCLONAL	1	TRUE	1	0.39	2		374	497	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2081923	2081923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	105	390	0	ENST00000349721.2:c.2276C>T	p.Thr759Ile	p.T759I	ENST00000349721	NM_003070.3	759	aCc/aTc	15/34	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.39	2		390	478	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484278	8484278	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	79	361	0	ENST00000356435.5:c.3254T>C	p.Leu1085Pro	p.L1085P	ENST00000356435		1085	cTg/cCg	19/35	1	2	FACETS	0.871	0.769	0.98	0.871	0.769	0.98	CLONAL	1	TRUE	1	0.39	2		361	465	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285776	87285776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	110	460	1	ENST00000277120.3:c.113G>A	p.Cys38Tyr	p.C38Y	ENST00000277120		38	tGc/tAc	2/19	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.39	2		461	501	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97869552	97869552	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	80	408	1	ENST00000289081.3:c.1330-1G>T		p.X444_splice	ENST00000289081	NM_000136.2	444			1	2	FACETS	0.918	0.811	1	0.918	0.811	1	CLONAL	1	TRUE	1	0.39	2		409	447	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221984	98221984	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	97	419	0	ENST00000331920.6:c.2785A>G	p.Asn929Asp	p.N929D	ENST00000331920	NM_000264.3	929	Aac/Gac	17/24	1	2	FACETS	0.94	0.841	1	0.94	0.841	1	CLONAL	1	TRUE	1	0.39	2		419	529	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232214	98232214	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	24	297	0	ENST00000331920.6:c.1729-1G>T		p.X577_splice	ENST00000331920	NM_000264.3	577			1	2	FACETS	0.273	0.213	0.342	0.273	0.213	0.342	SUBCLONAL	1	TRUE	1	0.39	2		297	451	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137313542	137313542	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	95	473	0	ENST00000481739.1:c.801C>G	p.Asn267Lys	p.N267K	ENST00000481739	NM_002957.4	267	aaC/aaG	6/10	1	2	FACETS	0.878	0.784	0.978	0.878	0.784	0.978	CLONAL	1	TRUE	1	0.39	2		473	555	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410135	63410135	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	88	447	1	ENST00000330258.3:c.3032G>T	p.Arg1011Met	p.R1011M	ENST00000330258	NM_152424.3	1011	aGg/aTg	2/2	1	2	FACETS	0.84	0.746	0.94	0.84	0.746	0.94	CLONAL	1	TRUE	1	0.39	2		448	537	SUCCESS
AR	367	MSKCC	GRCh37	X	66943679	66943679	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	76	319	0	ENST00000374690.3:c.2759A>G	p.Gln920Arg	p.Q920R	ENST00000374690	NM_000044.3	920	cAg/cGg	8/8	1	2	FACETS	0.955	0.842	1	0.955	0.842	1	CLONAL	1	TRUE	1	0.39	2		319	408	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347849	70347849	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	75	420	0	ENST00000374080.3:c.3088G>A	p.Ala1030Thr	p.A1030T	ENST00000374080		1030	Gca/Aca	22/45	1	2	FACETS	0.682	0.598	0.772	0.682	0.598	0.772	SUBCLONAL	1	TRUE	1	0.39	2		420	564	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190048	123190048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	56	265	0	ENST00000218089.9:c.1267C>T	p.Pro423Ser	p.P423S	ENST00000218089	NM_001042749.1	423	Cca/Tca	14/35	1	2	FACETS	0.828	0.713	0.952	0.828	0.713	0.952	CLONAL	1	TRUE	1	0.39	2		265	347	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196756	123196756	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	52	294	0	ENST00000218089.9:c.1643T>C	p.Leu548Pro	p.L548P	ENST00000218089	NM_001042749.1	548	cTt/cCt	18/35	1	2	FACETS	0.907	0.777	1	0.907	0.777	1	CLONAL	1	TRUE	1	0.39	2		294	294	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2039786	2039786	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066453-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	112	636	0	ENST00000349721.2:c.676C>T	p.Gln226Ter	p.Q226*	ENST00000349721	NM_003070.3	226	Cag/Tag	4/34	1	2	FACETS	0.878	0.791	0.97	0.878	0.791	0.97	CLONAL	1	TRUE	1	0.39	2		636	654	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0066454-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	99	591	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.439868282185006	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.439868282185006	1		591	278	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0066454-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	41	353	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	0.755	0.633	0.888	0.755	0.633	0.888	SUBCLONAL	1	TRUE	1	0.439868282185006	2		353	247	SUCCESS
APC	324	MSKCC	GRCh37	5	112175539	112175539	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066454-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	79	383	0	ENST00000257430.4:c.4248del	p.Ile1417LeufsTer2	p.I1417Lfs*2	ENST00000257430	NM_000038.5	1416	ggC/gg	16/16	1	2	FACETS	0.863	0.763	0.97	0.863	0.763	0.97	CLONAL	1	TRUE	1	0.439868282185006	2		383	416	SUCCESS
APC	324	MSKCC	GRCh37	5	112173803	112173803	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0066454-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	57	322	0	ENST00000257430.4:c.2512A>T	p.Arg838Ter	p.R838*	ENST00000257430	NM_000038.5	838	Aga/Tga	16/16	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.439868282185006	2		322	240	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609993	81609993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139892516	NA	P-0066454-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	19	480	0	ENST00000298171.2:c.1591C>T	p.Arg531Trp	p.R531W	ENST00000298171	NM_000369.2	531	Cgg/Tgg	10/10	0.378996987761437	1	FACETS	0.208	0.157	0.267	0.208	0.157	0.267	SUBCLONAL	1	TRUE	0	0.439868282185006	1		480	324	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1691321	1691321	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1233142145	NA	P-0066454-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	96	380	0	ENST00000378625.1:c.284C>A	p.Ala95Glu	p.A95E	ENST00000378625	NM_001198994.1	95	gCa/gAa	4/14	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.439868282185006	2		380	352	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609732	28609732	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066454-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	57	380	0	ENST00000241453.7:c.1497T>A	p.Ser499Arg	p.S499R	ENST00000241453	NM_004119.2	499	agT/agA	12/24	0.180753602702528	6	FACETS	0.972	0.835	1	0.324	0.278	0.374	INDETERMINATE	1	TRUE	3	0.439868282185006	6		380	501	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585362	29585363	+	inframe_insertion,splice_region_variant	In_Frame_Ins	INS	-	-	TGGTTAGCC	novel	NA	P-0066454-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	71	289	0	ENST00000356175.3:c.4112_4120dup	p.Ser1373_Gln1374insLeuValSer	p.S1373_Q1374insLVS	ENST00000356175	NM_000267.3	1371	gtg/gTGGTTAGCCtg	31/57	0.392467961718577	3	FACETS	1	0.954	1	0.59	0.518	0.665	CLONAL	1	TRUE	1	0.439868282185006	3		289	334	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559777	29559777	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066454-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	94	365	0	ENST00000356175.3:c.3374C>G	p.Ala1125Gly	p.A1125G	ENST00000356175	NM_000267.3	1125	gCg/gGg	26/57	0.392467961718577	3	FACETS	1	0.92	1	0.518	0.463	0.577	CLONAL	1	TRUE	1	0.439868282185006	3		365	503	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890187	76890187	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066454-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	40	291	0	ENST00000373344.5:c.4707G>C	p.Gln1569His	p.Q1569H	ENST00000373344	NM_000489.3	1569	caG/caC	17/35	0.439868282185006	1	FACETS	0.839	0.708	0.981	0.839	0.708	0.981	CLONAL	1	TRUE	0	0.439868282185006	1		291	169	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982993	201982993	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066454-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	84	383	0	ENST00000359651.3:c.842A>G	p.Asp281Gly	p.D281G	ENST00000359651		281	gAc/gGc	7/8	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.439868282185006	2		383	359	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628014	187628014	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066454-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	69	387	0	ENST00000441802.2:c.2968G>C	p.Asp990His	p.D990H	ENST00000441802	NM_005245.3	990	Gac/Cac	2/27	0.439868282185006	1	FACETS	0.952	0.839	1	0.952	0.839	1	CLONAL	1	TRUE	0	0.439868282185006	1		387	257	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0066455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	125	630	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.222609135909742	2	FACETS	0.79	0.717	0.866	0.79	0.717	0.866	SUBCLONAL	2	TRUE	0	0.27	2		630	586	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286219	66286219	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	77	378	0	ENST00000273854.3:c.1467G>A	p.Trp489Ter	p.W489*	ENST00000273854	NM_004439.5	489	tgG/tgA	6/18	0.295991930062482	1	FACETS	0.821	0.721	0.928	0.821	0.721	0.928	CLONAL	1	TRUE	0	0.27	1		378	601	SUCCESS
APC	324	MSKCC	GRCh37	5	112175162	112175162	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	135	421	0	ENST00000257430.4:c.3871del	p.Gln1291ArgfsTer14	p.Q1291Rfs*14	ENST00000257430	NM_000038.5	1291	Cag/ag	16/16	1	2	FACETS	0.806	0.735	0.881	1	0.988	1	CLONAL	2	TRUE	1	0.27	2		421	620	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0066456-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	54	288	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.207428986045654	2		288	517	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044850	47044850	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066456-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	71	194	0	ENST00000377604.3:c.2176C>T	p.Arg726Ter	p.R726*	ENST00000377604	NM_001204468.1	726	Cga/Tga	20/24	1	1	FACETS	0.872	0.766	0.984	1	0.98	1	CLONAL	2	TRUE	0	0.207428986045654	1		194	352	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099864	27099864	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0066456-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	45	312	0	ENST00000324856.7:c.3743C>G	p.Ser1248Ter	p.S1248*	ENST00000324856	NM_006015.4	1248	tCa/tGa	15/20	0.207428986045654	1	FACETS	0.787	0.662	0.926	0.787	0.662	0.926	CLONAL	1	TRUE	0	0.207428986045654	1		312	494	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981470	201981470	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0066456-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	118	278	0	ENST00000359651.3:c.386-2A>T		p.X129_splice	ENST00000359651		129			0.151966445600047	2	FACETS	0.837	0.76	0.917	1	0.978	1	CLONAL	3	TRUE	0	0.207428986045654	2		278	453	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420606	49420606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886041404	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	217	519	0	ENST00000301067.7:c.15143G>A	p.Arg5048His	p.R5048H	ENST00000301067	NM_003482.3	5048	cGt/cAt	48/54	1	2	FACETS	0.979	0.918	1	0.979	0.918	1	CLONAL	1	TRUE	1	0.758707609227675	2		519	584	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	398	710	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.909	0.878	0.939	1	0.997	1	CLONAL	2	TRUE	1	0.758707609227675	2		713	577	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	131	478	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.79	0.723	0.86	0.79	0.723	0.86	SUBCLONAL	1	TRUE	1	0.758707609227675	2		479	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	244	498	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.758707609227675	2		498	600	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	183	455	4	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.955	0.889	1	0.955	0.889	1	CLONAL	1	TRUE	1	0.758707609227675	2		459	505	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	155	480	7	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.778	0.717	0.841	0.778	0.717	0.841	SUBCLONAL	1	TRUE	1	0.758707609227675	2		487	525	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	105	298	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.92	0.835	1	0.92	0.835	1	CLONAL	1	TRUE	1	0.758707609227675	2		298	301	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	214	877	17	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.758707609227675	2		894	559	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	52	529	4	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	2	FACETS	0.529	0.454	0.61	0.529	0.454	0.61	SUBCLONAL	1	TRUE	1	0.758707609227675	2		533	259	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	186	405	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	0.869	0.808	0.932	0.869	0.808	0.932	CLONAL	1	TRUE	1	0.758707609227675	2		405	564	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	129	782	3	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.795	0.726	0.865	0.795	0.726	0.865	SUBCLONAL	1	TRUE	1	0.758707609227675	2		785	428	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778917	9778917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774975013	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	209	497	0	ENST00000377346.4:c.1186G>A	p.Ala396Thr	p.A396T	ENST00000377346	NM_005026.3	396	Gcc/Acc	9/24	1	2	FACETS	0.906	0.847	0.967	0.906	0.847	0.967	CLONAL	1	TRUE	1	0.758707609227675	2		497	608	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	157	415	1	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	0.821	0.758	0.887	0.821	0.758	0.887	CLONAL	1	TRUE	1	0.758707609227675	2		416	504	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	219	396	0	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	1	2	FACETS	0.997	0.935	1	0.997	0.935	1	CLONAL	1	TRUE	1	0.758707609227675	2		396	579	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307280	65307283	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	202	352	0	ENST00000342505.4:c.2405_2408del	p.Lys802ArgfsTer11	p.K802Rfs*11	ENST00000342505	NM_002227.2	802	aAAGAg/ag	18/25	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.758707609227675	2		352	501	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692929	89692929	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1554898159	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	159	344	1	ENST00000371953.3:c.413A>G	p.Tyr138Cys	p.Y138C	ENST00000371953	NM_000314.4	138	tAt/tGt	5/9	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.758707609227675	2		345	417	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133242038	133242038	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	213	372	1	ENST00000320574.5:c.2320-2A>G		p.X774_splice	ENST00000320574	NM_006231.2	774			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.758707609227675	2		373	529	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914617	32914617	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359561	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	130	437	0	ENST00000380152.3:c.6129del	p.Gly2044AlafsTer7	p.G2044Afs*7	ENST00000380152		2042	cAa/ca	11/27	1	2	FACETS	0.941	0.864	1	0.941	0.864	1	CLONAL	1	TRUE	1	0.758707609227675	2		437	364	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955465	48955465	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	125	308	0	ENST00000267163.4:c.1585del	p.Tyr529ThrfsTer3	p.Y529Tfs*3	ENST00000267163	NM_000321.2	527	gaT/ga	17/27	1	2	FACETS	0.963	0.883	1	0.963	0.883	1	CLONAL	1	TRUE	1	0.758707609227675	2		308	342	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	142	328	0	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.758707609227675	2		328	370	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654642	67654642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	236	330	0	ENST00000264010.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000264010	NM_006565.3	377	Cgt/Tgt	6/12	0.758707609227675	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.758707609227675	1		330	363	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17120457	17120457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767714543	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	219	392	0	ENST00000285071.4:c.1102G>A	p.Val368Ile	p.V368I	ENST00000285071	NM_144997.5	368	Gtt/Att	10/14	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.758707609227675	2		392	551	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262139	10262139	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	236	457	3	ENST00000340748.4:c.2152del	p.Met718CysfsTer59	p.M718Cfs*59	ENST00000340748		718	Atg/tg	23/40	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.758707609227675	2		460	613	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289895	15289895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370233852	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	251	642	0	ENST00000263388.2:c.3659G>A	p.Arg1220Gln	p.R1220Q	ENST00000263388	NM_000435.2	1220	cGg/cAg	22/33	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.758707609227675	2		642	647	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257144	19257144	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	102	282	0	ENST00000162023.5:c.819del	p.Thr274ProfsTer?	p.T274Pfs*?	ENST00000162023		273	ccC/cc	12/13	1	2	FACETS	0.82	0.741	0.901	0.82	0.741	0.901	CLONAL	1	TRUE	1	0.758707609227675	2		282	328	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085789	16085789	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	222	416	0	ENST00000281043.3:c.965G>A	p.Arg322Gln	p.R322Q	ENST00000281043	NM_005378.4	322	cGa/cAa	3/3	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.758707609227675	2		416	525	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262616	39262616	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779162761	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	127	317	0	ENST00000402219.2:c.890C>T	p.Ser297Leu	p.S297L	ENST00000402219	NM_005633.3	297	tCg/tTg	7/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.758707609227675	2		317	296	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627979	37627979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780585104	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	146	410	0	ENST00000249071.6:c.281G>A	p.Arg94His	p.R94H	ENST00000249071	NM_002872.4	94	cGc/cAc	4/7	1	2	FACETS	0.752	0.69	0.815	0.752	0.69	0.815	SUBCLONAL	1	TRUE	1	0.758707609227675	2		410	512	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935635	49935635	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	159	410	0	ENST00000296474.3:c.1729del	p.His577ThrfsTer5	p.H577Tfs*5	ENST00000296474	NM_002447.2	577	Cac/ac	5/20	1	2	FACETS	0.83	0.766	0.895	0.83	0.766	0.895	CLONAL	1	TRUE	1	0.758707609227675	2		410	505	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	152	350	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.997	0.922	1	0.997	0.922	1	CLONAL	1	TRUE	1	0.758707609227675	2		350	402	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921555	178921555	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	93	274	0	ENST00000263967.3:c.1037T>A	p.Val346Glu	p.V346E	ENST00000263967	NM_006218.2	346	gTa/gAa	5/21	1	2	FACETS	0.898	0.81	0.989	0.898	0.81	0.989	CLONAL	1	TRUE	1	0.758707609227675	2		274	273	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874147	151874148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs747256476	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	113	413	4	ENST00000262189.6:c.8390dup	p.Glu2798GlyfsTer11	p.E2798Gfs*11	ENST00000262189	NM_170606.2	2797	aag/aaAg	38/59	1	2	FACETS	0.649	0.587	0.713	0.649	0.587	0.713	SUBCLONAL	1	TRUE	1	0.758707609227675	2		417	459	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566347	141566347	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	180	390	0	ENST00000220592.5:c.1065del	p.Lys355AsnfsTer2	p.K355Nfs*2	ENST00000220592	NM_012154.3	355	aaA/aa	9/19	1	2	FACETS	0.914	0.85	0.98	0.914	0.85	0.98	CLONAL	1	TRUE	1	0.758707609227675	2		390	519	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944336	76944336	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	127	282	0	ENST00000373344.5:c.569C>A	p.Pro190His	p.P190H	ENST00000373344	NM_000489.3	190	cCt/cAt	7/35	1	2	FACETS	0.951	0.872	1	0.951	0.872	1	CLONAL	1	TRUE	1	0.758707609227675	2		282	352	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150935101	150935103	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs750285110	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	194	360	0	ENST00000271640.5:c.3199_3201del	p.Pro1067del	p.P1067del	ENST00000271640	NM_001145415.1	1066	tCTCct/tct	18/22	0.672776947814596	3	FACETS	0.995	0.924	1	0.497	0.462	0.534	CLONAL	1	TRUE	1	0.758707609227675	3		360	709	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911618	114911618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	185	367	0	ENST00000543371.1:c.1136C>T	p.Ala379Val	p.A379V	ENST00000543371	NM_001198531.1	379	gCc/gTc	10/14	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.758707609227675	2		367	467	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129132	64129132	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	221	471	0	ENST00000334205.4:c.670C>A	p.Leu224Met	p.L224M	ENST00000334205	NM_003942.2	224	Ctg/Atg	7/17	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.758707609227675	2		471	523	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390689	118390689	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	180	317	0	ENST00000534358.1:c.11339T>C	p.Met3780Thr	p.M3780T	ENST00000534358	NM_005933.3	3780	aTg/aCg	33/36	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.758707609227675	2		317	456	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446004	49446004	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	293	566	0	ENST00000301067.7:c.1462C>T	p.Pro488Ser	p.P488S	ENST00000301067	NM_003482.3	488	Ccg/Tcg	10/54	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.758707609227675	2		566	725	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2105463	2105463	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs982250014	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	149	346	0	ENST00000219476.3:c.542T>C	p.Val181Ala	p.V181A	ENST00000219476	NM_000548.3	181	gTg/gCg	6/42	1	2	FACETS	0.893	0.823	0.964	0.893	0.823	0.964	CLONAL	1	TRUE	1	0.758707609227675	2		346	440	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823856	3823856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369853866	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	235	423	0	ENST00000262367.5:c.2359G>A	p.Ala787Thr	p.A787T	ENST00000262367	NM_004380.2	787	Gcg/Acg	13/31	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.758707609227675	2		423	579	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211634	5211634	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	193	356	0	ENST00000357368.4:c.5201A>G	p.Asp1734Gly	p.D1734G	ENST00000357368	NM_002850.3	1734	gAc/gGc	33/38	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.758707609227675	2		356	499	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610673	10610673	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	174	434	0	ENST00000171111.5:c.37T>C	p.Cys13Arg	p.C13R	ENST00000171111	NM_203500.1	13	Tgc/Cgc	2/6	1	2	FACETS	0.864	0.801	0.928	0.864	0.801	0.928	CLONAL	1	TRUE	1	0.758707609227675	2		434	531	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568903	212568903	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	126	318	0	ENST00000342788.4:c.1215G>T	p.Gln405His	p.Q405H	ENST00000342788	NM_005235.2	405	caG/caT	11/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.758707609227675	2		318	289	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36024649	36024649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	194	431	0	ENST00000358208.4:c.638G>A	p.Gly213Asp	p.G213D	ENST00000358208		213	gGc/gAc	6/12	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.758707609227675	2		431	506	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21343925	21343925	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	173	355	0	ENST00000215739.8:c.605T>C	p.Met202Thr	p.M202T	ENST00000215739	NM_006767.3	202	aTg/aCg	7/21	1	2	FACETS	0.956	0.888	1	0.956	0.888	1	CLONAL	1	TRUE	1	0.758707609227675	2		355	477	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157213	106157213	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	220	414	0	ENST00000380013.4:c.2114A>G	p.Gln705Arg	p.Q705R	ENST00000380013	NM_001127208.2	705	cAa/cGa	3/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.758707609227675	2		414	555	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271255	26271255	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs756096962	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	262	594	0	ENST00000305910.3:c.358A>G	p.Ile120Val	p.I120V	ENST00000305910	NM_003534.2	120	Atc/Gtc	1/1	1	2	FACETS	0.966	0.91	1	0.966	0.91	1	CLONAL	1	TRUE	1	0.758707609227675	2		594	715	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671771	30671771	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	232	529	0	ENST00000376406.3:c.5189C>A	p.Pro1730His	p.P1730H	ENST00000376406	NM_014641.2	1730	cCt/cAt	10/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.758707609227675	2		529	593	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38186954	38186954	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780197286	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	189	331	0	ENST00000317025.8:c.1523C>T	p.Ala508Val	p.A508V	ENST00000317025	NM_023034.1	508	gCt/gTt	6/24	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.758707609227675	2		331	488	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549376	5549376	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	198	400	0	ENST00000397747.3:c.403G>T	p.Glu135Ter	p.E135*	ENST00000397747	NM_025239.3	135	Gaa/Taa	4/7	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.758707609227675	2		400	487	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649598	48649598	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	210	419	0	ENST00000376670.3:c.82C>T	p.Pro28Ser	p.P28S	ENST00000376670	NM_002049.3	28	Cca/Tca	2/6	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.758707609227675	2		419	464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0066459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	108	343	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		343	465	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0066459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	22	413	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		413	240	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755478	133755478	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355584861	NA	P-0066459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	90	444	0	ENST00000318560.5:c.1447C>T	p.Arg483Trp	p.R483W	ENST00000318560	NM_005157.4	483	Cgg/Tgg	9/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		444	511	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532456	63532456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780123	NA	P-0066459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	115	482	0	ENST00000307078.5:c.2123C>T	p.Ser708Leu	p.S708L	ENST00000307078	NM_004655.3	708	tCg/tTg	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		482	655	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603007	48603007	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0066459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	35	330	0	ENST00000342988.3:c.1309-1G>C		p.X437_splice	ENST00000342988	NM_005359.5	437			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		330	399	SUCCESS
APC	324	MSKCC	GRCh37	5	112174001	112174002	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1554084403	NA	P-0066459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	66	516	0	ENST00000257430.4:c.2711_2712del	p.Arg904LysfsTer7	p.R904Kfs*7	ENST00000257430	NM_000038.5	904	AGa/a	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		516	441	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	41	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		341	200	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900983	114900984	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0066459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	80	541	0	ENST00000543371.1:c.598dup	p.Leu200ProfsTer10	p.L200Pfs*10	ENST00000543371	NM_001198531.1	198	cac/caCc	6/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		541	565	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591853	48591853	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	15	550	0	ENST00000342988.3:c.1016T>G	p.Phe339Cys	p.F339C	ENST00000342988	NM_005359.5	339	tTt/tGt	9/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		550	268	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	108	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.209151079870792	7	FACETS	0.92	0.835	1	1	0.968	1	CLONAL	5	FALSE	3	0.209151079870792	7		341	342	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220652	1220653	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	129	402	0	ENST00000326873.7:c.672dup	p.Ala225CysfsTer41	p.A225Cfs*41	ENST00000326873	NM_000455.4	224	att/aTtt	5/10	0.209151079870792	2	FACETS	1	0.952	1	1	0.991	1	CLONAL	4	FALSE	0	0.209151079870792	2		402	295	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375978	8375978	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556078617	NA	P-0066461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	51	349	0	ENST00000356435.5:c.4619C>T	p.Thr1540Ile	p.T1540I	ENST00000356435		1540	aCc/aTc	28/35	0.142761814999968	3	FACETS	1	0.964	1	0.499	0.425	0.579	CLONAL	1	FALSE	0	0.209151079870792	3		349	360	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120783979	120783979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112244011	NA	P-0066461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	124	423	0	ENST00000257552.2:c.1006G>A	p.Ala336Thr	p.A336T	ENST00000257552	NM_002442.3	336	Gcc/Acc	13/15	0.209151079870792	3	FACETS	1	0.969	1	1	0.989	1	CLONAL	3	FALSE	1	0.209151079870792	3		423	386	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411786	63411786	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	38	497	0	ENST00000330258.3:c.1381C>A	p.Gln461Lys	p.Q461K	ENST00000330258	NM_152424.3	461	Caa/Aaa	2/2	0.142761814999968	3	FACETS	1	0.928	1	0.413	0.342	0.491	CLONAL	1	FALSE	0	0.209151079870792	3		497	324	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649045	37649045	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	92	372	0	ENST00000447079.4:c.2150G>A	p.Ser717Asn	p.S717N	ENST00000447079	NM_015083.1	717	aGc/aAc	4/14	0.209151079870792	6	FACETS	0.965	0.862	1	0.965	0.862	1	CLONAL	3	FALSE	3	0.209151079870792	6		372	431	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009137	27009151	+	inframe_deletion	In_Frame_Del	DEL	GGCCCCTCCCGGCGG	GGCCCCTCCCGGCGG	-	rs929685736	NA	P-0066461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	23	274	0	ENST00000335756.4:c.82_96del	p.Arg28_Ser32del	p.R28_S32del	ENST00000335756	NM_001809.3	25	GGCCCCTCCCGGCGG/-	1/5	0.209151079870792	5	FACETS	1	0.864	1	0.576	0.45	0.72	CLONAL	1	FALSE	3	0.209151079870792	5		274	251	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434455	110434455	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	61	339	0	ENST00000375856.3:c.3946C>T	p.Pro1316Ser	p.P1316S	ENST00000375856	NM_003749.2	1316	Cct/Tct	1/2	0.209151079870792	3	FACETS	1	0.889	1	1	0.889	1	CLONAL	2	FALSE	1	0.209151079870792	3		339	314	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205715	108205715	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28942103	NA	P-0066461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	110	334	0	ENST00000278616.4:c.8030A>G	p.Tyr2677Cys	p.Y2677C	ENST00000278616	NM_000051.3	2677	tAt/tGt	55/63	0.209151079870792	2	FACETS	0.96	0.877	1	1	0.989	1	CLONAL	4	FALSE	0	0.209151079870792	2		334	274	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492870	8492870	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	32	322	0	ENST00000356435.5:c.2459C>A	p.Thr820Asn	p.T820N	ENST00000356435		820	aCt/aAt	16/35	0.142761814999968	3	FACETS	1	0.92	1	0.419	0.341	0.506	CLONAL	1	FALSE	0	0.209151079870792	3		322	269	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602622	10602629	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGGCAT	CAGGGCAT	-	novel	NA	P-0066461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	123	430	0	ENST00000171111.5:c.949_956del	p.Met317ProfsTer30	p.M317Pfs*30	ENST00000171111	NM_203500.1	317	ATGCCCTGc/c	3/6	0.209151079870792	2	FACETS	0.875	0.802	0.95	1	0.989	1	CLONAL	4	FALSE	0	0.209151079870792	2		430	336	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242481	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAA	AATTAAGAGAAGCAA	TTC	rs727503016	NA	P-0066462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	9	371	2	ENST00000275493.2:c.2237_2251delinsTTC	p.Glu746_Thr751delinsValPro	p.E746_T751delinsVP	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAAca/gTTCca	19/28	1	2	FACETS	0.311	0.205	0.448	0.311	0.205	0.448	SUBCLONAL	1	TRUE	1	0.13	2		373	445	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0066464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	24	269	1	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.729	0.572	0.908	0.729	0.572	0.908	CLONAL	1	FALSE	1	0.237008360939904	2		270	278	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0066464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	70	298	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.215484223036967	2	FACETS	0.837	0.734	0.946	0.837	0.734	0.946	CLONAL	2	FALSE	0	0.237008360939904	2		298	353	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	162	476	0	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	0.213115557321584	2	FACETS	0.993	0.914	1	0.993	0.914	1	CLONAL	2	FALSE	0	0.237008360939904	2		476	688	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845621	63845622	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0066464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	63	478	0	ENST00000279873.7:c.1365dup	p.Glu456ArgfsTer31	p.E456Rfs*31	ENST00000279873	NM_032199.2	454	gaa/gAaa	9/10	1	2	FACETS	0.738	0.638	0.848	0.738	0.638	0.848	SUBCLONAL	1	FALSE	1	0.237008360939904	2		478	720	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370827	55370828	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0066464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	44	421	0	ENST00000297316.4:c.131_132dup	p.Lys45Ter	p.K45*	ENST00000297316	NM_022454.3	43	-/GT	1/2	1	2	FACETS	0.993	0.835	1	0.993	0.835	1	CLONAL	1	FALSE	1	0.237008360939904	2		421	374	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714434	40714434	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1195276406	NA	P-0066464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	47	442	0	ENST00000373198.4:c.3963G>T	p.Glu1321Asp	p.E1321D	ENST00000373198	NM_133170.3	1321	gaG/gaT	29/32	0.237008360939904	1	FACETS	0.537	0.452	0.631	0.537	0.452	0.631	SUBCLONAL	1	FALSE	0	0.237008360939904	1		442	651	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374838	149374838	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	26	377	0	ENST00000360632.3:c.256C>T	p.Arg86Cys	p.R86C	ENST00000360632	NM_015472.4	86	Cgc/Tgc	2/7	1	2	FACETS	0.647	0.513	0.801	0.647	0.513	0.801	SUBCLONAL	1	FALSE	1	0.237008360939904	2		377	339	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180497	56180497	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1194707690	NA	P-0066464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	38	329	0	ENST00000399503.3:c.3826T>G	p.Tyr1276Asp	p.Y1276D	ENST00000399503	NM_005921.1	1276	Tat/Gat	16/20	1	2	FACETS	0.751	0.621	0.896	0.751	0.621	0.896	SUBCLONAL	1	FALSE	1	0.237008360939904	2		329	427	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411119	63411122	+	frameshift_variant	Frame_Shift_Del	DEL	GAGG	GAGG	-	novel	NA	P-0066464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	36	449	0	ENST00000330258.3:c.2045_2048del	p.Thr682LysfsTer36	p.T682Kfs*36	ENST00000330258	NM_152424.3	682	aCCTCa/aa	2/2	1	2	FACETS	0.557	0.457	0.67	0.557	0.457	0.67	SUBCLONAL	1	FALSE	1	0.237008360939904	2		449	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0066465-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	113	361	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.43175844213077	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.43175844213077	1		361	340	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557837	187557837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs184443677	NA	P-0066465-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	57	430	0	ENST00000441802.2:c.3874G>A	p.Glu1292Lys	p.E1292K	ENST00000441802	NM_005245.3	1292	Gaa/Aaa	5/27	1	2	FACETS	0.672	0.578	0.773	0.672	0.578	0.773	SUBCLONAL	1	TRUE	1	0.43175844213077	2		430	393	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201008	108201008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881383	NA	P-0066465-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	73	340	0	ENST00000278616.4:c.7375C>T	p.Arg2459Cys	p.R2459C	ENST00000278616	NM_000051.3	2459	Cgt/Tgt	50/63	0.105863364478916	0	FACETS	0.572	0.504	0.644			1	INDETERMINATE	1	TRUE	0	0.43175844213077	0		340	336	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664690	138664690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1382669559	NA	P-0066465-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	54	252	0	ENST00000330315.3:c.875C>T	p.Pro292Leu	p.P292L	ENST00000330315	NM_023067.3	292	cCg/cTg	1/1	0.148481227421457	4	FACETS	1	0.918	1	0.551	0.473	0.635	INDETERMINATE	1	TRUE	2	0.43175844213077	4		252	325	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023936	31023936	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066465-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	79	416	0	ENST00000375687.4:c.3421G>C	p.Asp1141His	p.D1141H	ENST00000375687	NM_015338.5	1141	Gac/Cac	13/13	0.370811376595336	3	FACETS	0.732	0.644	0.826			1	SUBCLONAL	1	TRUE	NA	0.43175844213077	3		416	608	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135077	11135077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066465-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	121	330	0	ENST00000358026.2:c.3044G>A	p.Gly1015Asp	p.G1015D	ENST00000358026	NM_001128849.1	1015	gGc/gAc	21/36	0.43175844213077	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.43175844213077	1		330	300	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216405	36216413	+	inframe_deletion	In_Frame_Del	DEL	ACCCATTCC	ACCCATTCC	-	novel	NA	P-0066465-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	47	412	0	ENST00000222270.7:c.3676_3684del	p.His1226_Phe1228del	p.H1226_F1228del	ENST00000222270	NM_014727.1	1223	gACCCATTCCac/gac	12/37	1	2	FACETS	0.544	0.46	0.637	0.544	0.46	0.637	SUBCLONAL	1	TRUE	1	0.43175844213077	2		412	400	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867557	101867588	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCGGCGGCGCTGCTCCCGGGGGCGACGGGTGA	GCGGCGGCGCTGCTCCCGGGGGCGACGGGTGA	-	novel	NA	P-0066465-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	18	222	0	ENST00000374994.4:c.80_97+14del		p.X27_splice	ENST00000374994	NM_004612.2	27		1/9	0.43175844213077	1	FACETS	0.617	0.471	0.783	0.617	0.471	0.783	SUBCLONAL	1	TRUE	0	0.43175844213077	1		222	106	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246451	46246452	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0066465-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	145	409	0	ENST00000334344.6:c.4546_4547del	p.Lys1516GlufsTer7	p.K1516Efs*7	ENST00000334344	NM_152641.2	1515	gtAAag/gtag	15/21	0.194537218249643	4	FACETS	0.854	0.783	0.928	0.854	0.783	0.928	INDETERMINATE	2	TRUE	2	0.43175844213077	4		409	563	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0066466-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	27	269	1	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.218239730919761	3	FACETS	0.97	0.774	1	0.485	0.387	0.596	CLONAL	1	TRUE	1	0.230847362861704	3		270	269	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0066466-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	105	343	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.219890313405619	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	2	TRUE	0	0.230847362861704	2		343	443	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247295	153247295	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066466-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	140	567	0	ENST00000281708.4:c.1507G>A	p.Ala503Thr	p.A503T	ENST00000281708	NM_033632.3	503	Gca/Aca	10/12	0.218239730919761	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.230847362861704	3		567	631	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555687605	NA	P-0066466-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	126	410	0	ENST00000342988.3:c.1610A>G	p.Asp537Gly	p.D537G	ENST00000342988	NM_005359.5	537	gAc/gGc	12/12	0.219890313405619	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	0	0.230847362861704	2		410	524	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066466-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	68	453	0	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	0.218239730919761	3	FACETS	1	0.903	1	0.523	0.455	0.597	CLONAL	1	TRUE	1	0.230847362861704	3		453	628	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814142	76814142	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066466-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	83	263	0	ENST00000373344.5:c.6502C>T	p.Gln2168Ter	p.Q2168*	ENST00000373344	NM_000489.3	2168	Cag/Tag	29/35	0.190836606840838	4	FACETS	0.97	0.86	1	0.97	0.86	1	CLONAL	2	TRUE	2	0.230847362861704	4		263	456	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0066466-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	134	297	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	0.230847362861704	3	FACETS	0.988	0.905	1	0.988	0.905	1	CLONAL	3	TRUE	0	0.230847362861704	3		297	437	SUCCESS
APC	324	MSKCC	GRCh37	5	112173952	112173953	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0066466-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	45	389	0	ENST00000257430.4:c.2661_2662del	p.Ala888GlnfsTer23	p.A888Qfs*23	ENST00000257430	NM_000038.5	887	atTGcc/atcc	16/16	0.218239730919761	3	FACETS	0.821	0.689	0.966	0.41	0.344	0.483	CLONAL	1	TRUE	1	0.230847362861704	3		389	530	SUCCESS
APC	324	MSKCC	GRCh37	5	112175760	112175761	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTTTG	novel	NA	P-0066466-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	98	435	0	ENST00000257430.4:c.4470_4474dup	p.Ala1492ValfsTer17	p.A1492Vfs*17	ENST00000257430	NM_000038.5	1490	cat/caTTTTGt	16/16	0.218239730919761	3	FACETS	0.822	0.735	0.914	0.822	0.735	0.914	CLONAL	2	TRUE	1	0.230847362861704	3		435	576	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685311	89685311	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786204922	NA	P-0066467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	114	230	0	ENST00000371953.3:c.206A>G	p.Asn69Ser	p.N69S	ENST00000371953	NM_000314.4	69	aAt/aGt	3/9	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.779500779535267	2		230	282	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163877	47163878	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0066467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	146	426	0	ENST00000409792.3:c.2248_2249del	p.Glu750ThrfsTer9	p.E750Tfs*9	ENST00000409792	NM_014159.6	750	GAa/a	3/21	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.779500779535267	2		426	371	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593660	55593661	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTCCTTATGATCACAAATGGGAGTTTCCCAGAAACAGGCTGAGTT	novel	NA	P-0066467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	83	357	0	ENST00000288135.5:c.1729_1773dup	p.Pro577_Phe591dup	p.P577_F591dup	ENST00000288135	NM_000222.2	577	ctt/cTTCCTTATGATCACAAATGGGAGTTTCCCAGAAACAGGCTGAGTTtt	11/21	1	2	FACETS	0.475	0.421	0.533	0.475	0.421	0.533	SUBCLONAL	1	TRUE	1	0.779500779535267	2		357	448	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604764	48604765	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs377767376	NA	P-0066468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	38	513	0	ENST00000342988.3:c.1587dup	p.His530ThrfsTer47	p.H530Tfs*47	ENST00000342988	NM_005359.5	529	tta/ttAa	12/12	0.194725518081005	1	FACETS	0.829	0.686	0.989	0.829	0.686	0.989	CLONAL	1	TRUE	0	0.194725518081005	1		513	425	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437603	56437603	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	59	499	0	ENST00000407977.2:c.859del	p.Val287SerfsTer132	p.V287Sfs*132	ENST00000407977		287	Gtc/tc	8/10	0.179689775151532	2	FACETS	1	0.961	1	0.675	0.582	0.776	CLONAL	1	TRUE	0	0.194725518081005	2		499	449	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916567	39916568	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0066468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	22	421	0	ENST00000378444.4:c.4435dup	p.Val1479GlyfsTer11	p.V1479Gfs*11	ENST00000378444	NM_001123385.1	1479	gtc/gGtc	11/15	1	2	FACETS	0.647	0.501	0.817	0.647	0.501	0.817	SUBCLONAL	1	TRUE	1	0.194725518081005	2		421	349	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0066469-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	78	582	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.417826038168532	2		582	311	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0066469-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	252	505	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	0.417826038168532	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.417826038168532	2		505	528	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066469-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	188	476	0	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	0.417826038168532	2	FACETS	0.974	0.91	1	0.974	0.91	1	CLONAL	2	TRUE	0	0.417826038168532	2		476	462	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720877	89720877	+	splice_donor_variant	Splice_Site	SNP	T	T	G	rs1114167624	NA	P-0066469-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	11	180	0	ENST00000371953.3:c.1026+2T>G		p.X342_splice	ENST00000371953	NM_000314.4	342			0.417826038168532	1	FACETS	0.28	0.193	0.386	0.28	0.193	0.386	SUBCLONAL	1	TRUE	0	0.417826038168532	1		180	149	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650595	67650651	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCATTAACTGTGCCCTTGATCTTGCTCTTCCTGTTACTCCATCCTTTCTCTAGGTAC	TCATTAACTGTGCCCTTGATCTTGCTCTTCCTGTTACTCCATCCTTTCTCTAGGTAC	-	novel	NA	P-0066469-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	140	214	0	ENST00000264010.4:c.953-51_958del		p.X318_splice	ENST00000264010	NM_006565.3	318		5/12	1	2	FACETS	0.785	0.721	0.85	1	0.989	1	SUBCLONAL	2	TRUE	1	0.417826038168532	2		214	427	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845507	63845507	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066469-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	80	435	0	ENST00000279873.7:c.1249del	p.Leu417CysfsTer62	p.L417Cfs*62	ENST00000279873	NM_032199.2	416	Ccc/cc	9/10	0.417826038168532	2	FACETS	0.936	0.829	1	0.468	0.414	0.526	CLONAL	1	TRUE	0	0.417826038168532	2		435	409	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0066471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	21	262	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.89	0.694	1	0.89	0.694	1	CLONAL	1	TRUE	1	0.374524284845126	2		262	126	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0066471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	20	442	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.366428663771885	4	FACETS	0.385	0.294	0.493	0.096	0.073	0.124	SUBCLONAL	1	TRUE	0	0.374524284845126	4		442	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0066471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	223	758	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.366428663771885	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	4	TRUE	0	0.374524284845126	4		758	401	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710676	114710676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	53	358	0	ENST00000543371.1:c.161C>T	p.Thr54Met	p.T54M	ENST00000543371	NM_001198531.1	54	aCg/aTg	1/14	0.374524284845126	3	FACETS	1	0.953	1	0.634	0.545	0.729	CLONAL	1	TRUE	1	0.374524284845126	3		358	265	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141587	202141587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771150445	NA	P-0066471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	9	377	0	ENST00000358485.4:c.875G>A	p.Arg292Gln	p.R292Q	ENST00000358485	NM_001080125.1	292	cGg/cAg	7/9	0.374524284845126	3	FACETS	0.228	0.15	0.328	0.076	0.05	0.11	SUBCLONAL	1	TRUE	0	0.374524284845126	3		377	250	SUCCESS
APC	324	MSKCC	GRCh37	5	112116587	112116587	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	22	334	0	ENST00000257430.4:c.636del	p.Lys212AsnfsTer7	p.K212Nfs*7	ENST00000257430	NM_000038.5	211	gAa/ga	6/16	1	2	FACETS	0.778	0.609	0.97	0.778	0.609	0.97	CLONAL	1	TRUE	1	0.374524284845126	2		334	151	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247246	153247246	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	70	414	0	ENST00000281708.4:c.1556A>G	p.Tyr519Cys	p.Y519C	ENST00000281708	NM_033632.3	519	tAt/tGt	10/12	0.352794131720337	4	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	2	0.374524284845126	4		414	239	SUCCESS
AR	367	MSKCC	GRCh37	X	66941695	66941695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768366293	NA	P-0066471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	62	387	0	ENST00000374690.3:c.2339G>A	p.Arg780Gln	p.R780Q	ENST00000374690	NM_000044.3	780	cGg/cAg	6/8	0.374524284845126	4	FACETS	0.846	0.738	0.961	0.564	0.492	0.641	CLONAL	2	TRUE	1	0.374524284845126	4		387	269	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0066472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	146	455	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.289560752766169	3	FACETS	0.796	0.733	0.861	0.796	0.733	0.861	INDETERMINATE	2	TRUE	1	0.522193014778287	3		455	443	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714415	40714415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765339833	NA	P-0066472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	303	401	2	ENST00000373198.4:c.3982G>A	p.Asp1328Asn	p.D1328N	ENST00000373198	NM_133170.3	1328	Gac/Aac	29/32	0.366051127269064	6	FACETS	0.899	0.854	0.944	0.899	0.854	0.944	CLONAL	4	TRUE	2	0.522193014778287	6		403	660	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409949	63409950	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0066472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	132	486	0	ENST00000330258.3:c.3217_3218delinsTT	p.Pro1073Leu	p.P1073L	ENST00000330258	NM_152424.3	1073	CCa/TTa	2/2	0.242166012629318	3	FACETS	1	0.986	1	0.715	0.654	0.778	INDETERMINATE	1	TRUE	1	0.522193014778287	3		486	446	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0066476-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	32	254	1	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.17	2		255	313	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925688	114925688	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066476-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	61	371	0	ENST00000543371.1:c.1766C>G	p.Thr589Ser	p.T589S	ENST00000543371	NM_001198531.1	589	aCc/aGc	14/14	0.132313352429434	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.17	1		371	585	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0066476-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	116	390	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	0.802	0.722	0.886	1	0.985	1	CLONAL	2	TRUE	1	0.17	2		390	851	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627187	86627187	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066476-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	48	336	0	ENST00000274376.6:c.562A>G	p.Arg188Gly	p.R188G	ENST00000274376	NM_002890.2	188	Aga/Gga	2/25	1	2	FACETS	0.821	0.693	0.963	0.821	0.693	0.963	CLONAL	1	TRUE	1	0.17	2		336	688	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609930	117609930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144393305	NA	P-0066476-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	26	301	0	ENST00000368508.3:c.6769G>A	p.Asp2257Asn	p.D2257N	ENST00000368508	NM_002944.2	2257	Gac/Aac	43/43	0.132313352429434	1	FACETS	0.568	0.449	0.705	0.568	0.449	0.705	SUBCLONAL	1	TRUE	0	0.17	1		301	493	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22161972	22161972	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066476-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	50	307	0	ENST00000215832.6:c.283A>C	p.Ile95Leu	p.I95L	ENST00000215832	NM_002745.4	95	Atc/Ctc	2/9	1	2	FACETS	0.937	0.794	1	0.937	0.794	1	CLONAL	1	TRUE	1	0.17	2		307	628	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47108587	47108587	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066476-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	28	213	0	ENST00000409792.3:c.6082A>C	p.Lys2028Gln	p.K2028Q	ENST00000409792	NM_014159.6	2028	Aaa/Caa	13/21	1	2	FACETS	0.676	0.54	0.833	0.676	0.54	0.833	SUBCLONAL	1	TRUE	1	0.17	2		213	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587781702	NA	P-0066477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	581	361	0	ENST00000269305.4:c.920-1G>C		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.936454556470552	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.936454556470552	1		361	651	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430477	181430477	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	223	335	0	ENST00000325404.1:c.329A>G	p.Tyr110Cys	p.Y110C	ENST00000325404	NM_003106.3	110	tAc/tGc	1/1	0.548357126193317	1	FACETS	0.298	0.278	0.319	0.298	0.278	0.319	INDETERMINATE	1	TRUE	0	0.936454556470552	1		335	849	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946306	81946306	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	558	240	0	ENST00000359376.3:c.2039A>T	p.Tyr680Phe	p.Y680F	ENST00000359376	NM_002661.3	680	tAt/tTt	19/33	0.936454556470552	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.936454556470552	1		240	614	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052951	180052951	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	554	331	0	ENST00000261937.6:c.1339del	p.Ala447ProfsTer46	p.A447Pfs*46	ENST00000261937	NM_182925.4	447	Gcc/cc	10/30	0.936454556470552	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.936454556470552	1		331	625	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39576600	39576600	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0066477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	261	231	0	ENST00000262039.4:c.892-2A>C		p.X298_splice	ENST00000262039	NM_002647.2	298			1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.936454556470552	2		231	554	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401637	401637	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs775326241	NA	P-0066477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	442	384	0	ENST00000380956.4:c.959C>A	p.Ala320Asp	p.A320D	ENST00000380956	NM_001195286.1	320	gCc/gAc	7/9	0.321374700805925	1	FACETS	0.483	0.462	0.504	0.483	0.462	0.504	INDETERMINATE	1	TRUE	0	0.936454556470552	1		384	1039	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783847	50783847	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	431	310	0	ENST00000398568.2:c.238G>T	p.Ala80Ser	p.A80S	ENST00000398568	NM_001042412.1	80	Gca/Tca	3/18	0.936454556470552	1	FACETS	0.999	0.978	1	0.999	0.978	1	CLONAL	1	TRUE	0	0.936454556470552	1		310	490	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446793	49446793	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	509	354	0	ENST00000301067.7:c.1017del	p.Trp339CysfsTer63	p.W339Cfs*63	ENST00000301067	NM_003482.3	339	tgG/tg	8/54	1	2	FACETS	0.906	0.87	0.942	0.906	0.87	0.942	CLONAL	1	TRUE	1	0.936454556470552	2		354	1200	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805694	32805694	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	418	242	1	ENST00000374899.4:c.317A>T	p.Tyr106Phe	p.Y106F	ENST00000374899	NM_018833.2	106	tAc/tTc	2/12	0.396302028581708	1	FACETS	0.525	0.503	0.548	0.525	0.503	0.548	INDETERMINATE	1	TRUE	0	0.936454556470552	1		243	904	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39638012	39638012	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	403	220	0	ENST00000262039.4:c.2429del	p.Arg810GlnfsTer6	p.R810Qfs*6	ENST00000262039	NM_002647.2	810	cGa/ca	22/25	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.936454556470552	2		220	830	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134885807	134885807	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	200	308	1	ENST00000398015.3:c.1718C>A	p.Ala573Asp	p.A573D	ENST00000398015	NM_004441.4	573	gCt/gAt	9/16	0.548357126193317	1	FACETS	0.272	0.252	0.292	0.272	0.252	0.292	INDETERMINATE	1	TRUE	0	0.936454556470552	1		309	836	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61306866	61306866	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0066477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	374	273	0	ENST00000341074.5:c.612+2T>G		p.X204_splice	ENST00000341074	NM_002974.2	204			NA	2	FACETS	1	0.956	1			1	INDETERMINATE	1	TRUE	NA	0.936454556470552	2		273	798	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411081	63411081	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1249641553	NA	P-0066477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	472	195	0	ENST00000330258.3:c.2086A>T	p.Arg696Trp	p.R696W	ENST00000330258	NM_152424.3	696	Agg/Tgg	2/2	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.936454556470552	1		195	507	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981680	101981680	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	437	287	0	ENST00000282441.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000282441	NM_001130145.2	34	gGg/gTg	1/9	0.385059672656335	1	FACETS	0.673	0.648	0.697	0.673	0.648	0.697	INDETERMINATE	1	TRUE	0	0.936454556470552	1		287	738	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444996	49445020	+	frameshift_variant	Frame_Shift_Del	DEL	AGCATGGCTCCTCAGGCACAGGAGA	AGCATGGCTCCTCAGGCACAGGAGA	CGCAT	novel	NA	P-0066477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	479	363	1	ENST00000301067.7:c.2446_2470delinsATGCG	p.Ser816MetfsTer7	p.S816Mfs*7	ENST00000301067	NM_003482.3	816	TCTCCTGTGCCTGAGGAGCCATGCTtg/ATGCGtg	10/54	1	2	FACETS	0.877	0.84	0.913	0.877	0.84	0.913	CLONAL	1	TRUE	1	0.936454556470552	2		364	1167	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	201	539	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.733443660451735	2		539	444	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	195	455	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.733443660451735	2		455	532	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258815	16258815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	295	501	0	ENST00000375759.3:c.6080C>T	p.Ser2027Phe	p.S2027F	ENST00000375759	NM_015001.2	2027	tCc/tTc	11/15	1	2	FACETS	0.986	0.932	1	0.986	0.932	1	CLONAL	1	TRUE	1	0.733443660451735	2		501	816	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259453	16259453	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1291646884	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	276	488	0	ENST00000375759.3:c.6718C>T	p.Pro2240Ser	p.P2240S	ENST00000375759	NM_015001.2	2240	Cct/Tct	11/15	1	2	FACETS	0.959	0.904	1	0.959	0.904	1	CLONAL	1	TRUE	1	0.733443660451735	2		488	785	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846343	156846343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	175	422	0	ENST00000524377.1:c.1784G>A	p.Gly595Glu	p.G595E	ENST00000524377	NM_002529.3	595	gGg/gAg	14/17	0.733443660451735	4	FACETS	0.89	0.82	0.964	0.297	0.273	0.322	CLONAL	1	TRUE	1	0.733443660451735	4		422	929	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243859016	243859016	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs397514606	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	301	305	0	ENST00000263826.5:c.49G>A	p.Glu17Lys	p.E17K	ENST00000263826	NM_005465.4	17	Gaa/Aaa	2/13	0.733443660451735	4	FACETS	0.984	0.942	1	0.984	0.942	1	CLONAL	3	TRUE	1	0.733443660451735	4		305	482	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32438063	32438063	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762688982	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	180	340	0	ENST00000332351.3:c.974C>T	p.Ser325Leu	p.S325L	ENST00000332351	NM_024426.4	325	tCa/tTa	5/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.733443660451735	2		340	467	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715647	18715647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	155	334	0	ENST00000266497.5:c.3478G>A	p.Glu1160Lys	p.E1160K	ENST00000266497		1160	Gaa/Aaa	25/31	1	2	FACETS	0.927	0.856	0.999	0.927	0.856	0.999	CLONAL	1	TRUE	1	0.733443660451735	2		334	456	SUCCESS
BLM	641	MSKCC	GRCh37	15	91290720	91290720	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs139282091	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	130	261	0	ENST00000355112.3:c.98C>T	p.Ser33Leu	p.S33L	ENST00000355112	NM_000057.2	33	tCa/tTa	2/22	1	2	FACETS	0.923	0.846	1	0.923	0.846	1	CLONAL	1	TRUE	1	0.733443660451735	2		261	384	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291043	10291043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	379	771	0	ENST00000340748.4:c.428C>T	p.Ser143Phe	p.S143F	ENST00000340748		143	tCc/tTc	4/40	1	2	FACETS	0.969	0.921	1	0.969	0.921	1	CLONAL	1	TRUE	1	0.733443660451735	2		771	1067	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286791	212286791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	139	339	0	ENST00000342788.4:c.2905G>A	p.Glu969Lys	p.E969K	ENST00000342788	NM_005235.2	969	Gaa/Aaa	24/28	1	2	FACETS	0.877	0.806	0.951	0.877	0.806	0.951	CLONAL	1	TRUE	1	0.733443660451735	2		339	432	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212289012	212289012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	133	296	0	ENST00000342788.4:c.2734G>A	p.Glu912Lys	p.E912K	ENST00000342788	NM_005235.2	912	Gaa/Aaa	23/28	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.733443660451735	2		296	362	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632279	215632279	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	168	384	0	ENST00000260947.4:c.1495C>T	p.His499Tyr	p.H499Y	ENST00000260947	NM_000465.2	499	Cac/Tac	6/11	1	2	FACETS	0.895	0.829	0.963	0.895	0.829	0.963	CLONAL	1	TRUE	1	0.733443660451735	2		384	512	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40828006	40828006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	199	398	0	ENST00000373198.4:c.2422G>A	p.Glu808Lys	p.E808K	ENST00000373198	NM_133170.3	808	Gag/Aag	17/32	1	2	FACETS	0.91	0.849	0.974	0.91	0.849	0.974	CLONAL	1	TRUE	1	0.733443660451735	2		398	596	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	180	396	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.733443660451735	2		396	429	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686895	117686895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	140	291	0	ENST00000368508.3:c.2822C>T	p.Ser941Phe	p.S941F	ENST00000368508	NM_002944.2	941	tCc/tTc	19/43	1	2	FACETS	0.846	0.777	0.918	0.846	0.777	0.918	CLONAL	1	TRUE	1	0.733443660451735	2		291	451	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	336	364	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.678697989109577	3	FACETS	0.905	0.874	0.936	0.905	0.874	0.936	CLONAL	3	TRUE	0	0.733443660451735	3		364	461	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509081	106509081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187257485	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	205	423	0	ENST00000359195.3:c.1075C>T	p.Arg359Cys	p.R359C	ENST00000359195	NM_002649.2	359	Cgc/Tgc	2/11	1	2	FACETS	0.863	0.804	0.923	0.863	0.804	0.923	CLONAL	1	TRUE	1	0.733443660451735	2		423	648	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69032512	69032512	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	149	298	0	ENST00000288368.4:c.3586G>A	p.Gly1196Arg	p.G1196R	ENST00000288368	NM_024870.2	1196	Gga/Aga	29/40	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.733443660451735	2		298	404	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058566	69058566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866534903	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	120	308	0	ENST00000288368.4:c.4210C>T	p.His1404Tyr	p.H1404Y	ENST00000288368	NM_024870.2	1404	Cat/Tat	34/40	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.733443660451735	2		308	321	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980487	70980487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	232	441	0	ENST00000276594.2:c.890G>A	p.Gly297Glu	p.G297E	ENST00000276594	NM_024504.3	297	gGa/gAa	4/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.733443660451735	2		441	621	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115871	8115871	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	246	446	0	ENST00000346208.3:c.1217T>G	p.Ile406Ser	p.I406S	ENST00000346208		406	aTc/aGc	6/6	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.733443660451735	2		446	658	SUCCESS
EED	8726	MSKCC	GRCh37	11	85968564	85968564	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	145	259	0	ENST00000263360.6:c.560T>C	p.Val187Ala	p.V187A	ENST00000263360	NM_003797.3	187	gTt/gCt	6/12	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.733443660451735	2		259	395	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435429	110435429	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776062794	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	263	418	0	ENST00000375856.3:c.2972C>T	p.Pro991Leu	p.P991L	ENST00000375856	NM_003749.2	991	cCg/cTg	1/2	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.733443660451735	2		418	660	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572535	95572535	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852978	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	178	352	0	ENST00000393063.1:c.2830C>T	p.Arg944Ter	p.R944*	ENST00000393063	NM_030621.3	944	Cga/Tga	19/28	1	2	FACETS	0.977	0.908	1	0.977	0.908	1	CLONAL	1	TRUE	1	0.733443660451735	2		352	497	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293055	91293055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	221	398	0	ENST00000355112.3:c.557C>T	p.Ser186Leu	p.S186L	ENST00000355112	NM_000057.2	186	tCa/tTa	3/22	1	2	FACETS	0.963	0.901	1	0.963	0.901	1	CLONAL	1	TRUE	1	0.733443660451735	2		398	626	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041785	14041785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	216	390	0	ENST00000311895.7:c.2332G>A	p.Glu778Lys	p.E778K	ENST00000311895	NM_005236.2	778	Gag/Aag	11/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.733443660451735	2		390	575	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783712	50783713	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	200	369	0	ENST00000398568.2:c.106_107del	p.Gln36LysfsTer4	p.Q36Kfs*4	ENST00000398568	NM_001042412.1	35	ACa/a	3/18	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.733443660451735	2		369	519	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679823	33679824	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	187	418	1	ENST00000308377.4:c.2257_2258delinsAT	p.Ser753Ile	p.S753I	ENST00000308377	NM_152270.3	753	TCa/ATa	5/5	1	2	FACETS	0.896	0.833	0.961	0.896	0.833	0.961	CLONAL	1	TRUE	1	0.733443660451735	2		419	569	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36217204	36217204	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	176	371	0	ENST00000222270.7:c.3953G>A	p.Trp1318Ter	p.W1318*	ENST00000222270	NM_014727.1	1318	tGg/tAg	14/37	1	2	FACETS	0.89	0.826	0.957	0.89	0.826	0.957	CLONAL	1	TRUE	1	0.733443660451735	2		371	539	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181483	38181483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	250	406	0	ENST00000396334.3:c.496C>T	p.Pro166Ser	p.P166S	ENST00000396334	NM_002468.4	166	Ccc/Tcc	2/5	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.733443660451735	2		406	674	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515642	31515642	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173905095	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	205	296	0	ENST00000344624.3:c.977C>T	p.Pro326Leu	p.P326L	ENST00000344624		326	cCt/cTt	4/33	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.733443660451735	2		296	507	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947448	38947448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	178	352	0	ENST00000357387.3:c.4232C>T	p.Ser1411Phe	p.S1411F	ENST00000357387	NM_152756.3	1411	tCc/tTc	32/38	1	2	FACETS	0.957	0.89	1	0.957	0.89	1	CLONAL	1	TRUE	1	0.733443660451735	2		352	507	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642504	117642504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	248	498	0	ENST00000368508.3:c.5695C>T	p.Leu1899Phe	p.L1899F	ENST00000368508	NM_002944.2	1899	Ctt/Ttt	35/43	1	2	FACETS	0.919	0.863	0.976	0.919	0.863	0.976	CLONAL	1	TRUE	1	0.733443660451735	2		498	736	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647417	117647417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	219	399	0	ENST00000368508.3:c.5527G>A	p.Gly1843Arg	p.G1843R	ENST00000368508	NM_002944.2	1843	Gga/Aga	33/43	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.733443660451735	2		399	553	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434449	140434449	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	178	283	0	ENST00000288602.6:c.2249C>T	p.Ser750Phe	p.S750F	ENST00000288602	NM_004333.4	750	tCt/tTt	18/18	1	2	FACETS	0.981	0.912	1	0.981	0.912	1	CLONAL	1	TRUE	1	0.733443660451735	2		283	495	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	85	446	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.876070689694469	2		446	192	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929214	44929214	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	141	333	0	ENST00000377967.4:c.2314T>G	p.Leu772Val	p.L772V	ENST00000377967	NM_021140.2	772	Tta/Gta	17/29	1	2	FACETS	0.922	0.852	0.994	0.922	0.852	0.994	CLONAL	1	TRUE	1	0.876070689694469	2		333	349	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69458623	69458623	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	134	305	0	ENST00000227507.2:c.438C>A	p.Asn146Lys	p.N146K	ENST00000227507	NM_053056.2	146	aaC/aaA	3/5	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.876070689694469	2		305	302	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350625	15350625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35676845	NA	P-0066480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	13	424	0	ENST00000263377.2:c.3290G>A	p.Arg1097His	p.R1097H	ENST00000263377	NM_058243.2	1097	cGt/cAt	16/20	0.653035311320653	1	FACETS	0.131	0.093	0.178	0.131	0.093	0.178	SUBCLONAL	1	TRUE	0	0.653035311320653	1		424	204	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322774	30322774	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	64	291	0	ENST00000322652.5:c.1787C>A	p.Thr596Asn	p.T596N	ENST00000322652	NM_015355.2	596	aCc/aAc	14/16	1	2	FACETS	0.951	0.838	1	0.951	0.838	1	CLONAL	1	TRUE	1	0.653035311320653	2		291	206	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665360	138665360	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	47	403	0	ENST00000330315.3:c.205G>C	p.Glu69Gln	p.E69Q	ENST00000330315	NM_023067.3	69	Gag/Cag	1/1	1	2	FACETS	0.554	0.471	0.644	0.554	0.471	0.644	SUBCLONAL	1	TRUE	1	0.653035311320653	2		403	260	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165587	118165587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751161016	NA	P-0066480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	91	516	0	ENST00000369448.3:c.97G>A	p.Val33Ile	p.V33I	ENST00000369448	NM_017709.3	33	Gta/Ata	2/2	0.653035311320653	1	FACETS	0.973	0.885	1	0.973	0.885	1	CLONAL	1	TRUE	0	0.653035311320653	1		516	193	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555525585	NA	P-0066481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	79	279	0	ENST00000269305.4:c.673-2A>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.53332201839726	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.531156483745306	1		279	209	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122997	7122997	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867075117	NA	P-0066481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	101	306	0	ENST00000302850.5:c.3262C>T	p.Arg1088Cys	p.R1088C	ENST00000302850	NM_000208.2	1088	Cgc/Tgc	18/22	0.53332201839726	4	FACETS	1	0.964	1	0.388	0.348	0.43	CLONAL	1	TRUE	1	0.531156483745306	4		306	500	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839688	42839688	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	78	362	0	ENST00000398585.3:c.1551C>A	p.Phe517Leu	p.F517L	ENST00000398585	NM_001135099.1	517	ttC/ttA	13/14	0.53332201839726	3	FACETS	0.742	0.654	0.836	0.247	0.218	0.279	SUBCLONAL	1	TRUE	0	0.531156483745306	3		362	501	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565929	55565929	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	140	203	0	ENST00000288135.5:c.753T>G	p.Ser251Arg	p.S251R	ENST00000288135	NM_000222.2	251	agT/agG	4/21	0.53332201839726	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.531156483745306	2		203	245	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207761	29207761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	113	307	2	ENST00000240100.2:c.35G>A	p.Cys12Tyr	p.C12Y	ENST00000240100	NM_001394.6	12	tGc/tAc	1/4	0.53332201839726	4	FACETS	0.925	0.842	1	0.463	0.421	0.506	CLONAL	2	TRUE	0	0.531156483745306	4		309	352	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019750	123019750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	184	316	0	ENST00000355640.3:c.238G>T	p.Val80Phe	p.V80F	ENST00000355640		80	Gtt/Ttt	2/7	0.307427126007607	5	FACETS	1	0.983	1	0.786	0.731	0.842	INDETERMINATE	2	TRUE	2	0.531156483745306	5		316	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0066482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	240	537	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.699176516209794	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.699176516209794	2		537	341	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0066482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	58	287	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.699176516209794	2		287	144	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777092	9777092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146796121	NA	P-0066482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	20	519	0	ENST00000377346.4:c.856C>T	p.Arg286Trp	p.R286W	ENST00000377346	NM_005026.3	286	Cgg/Tgg	7/24	0.699866816348307	2	FACETS	0.204	0.155	0.26	0.102	0.077	0.13	SUBCLONAL	1	TRUE	0	0.699176516209794	2		519	281	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612346	1612346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769011342	NA	P-0066482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	121	437	0	ENST00000344749.5:c.1673G>A	p.Arg558His	p.R558H	ENST00000344749	NM_001136139.2	558	cGc/cAc	18/19	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.699176516209794	2		437	323	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589579	67589593	+	inframe_deletion	In_Frame_Del	DEL	AAATTACATGAATAT	AAATTACATGAATAT	-	novel	NA	P-0066482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	56	260	0	ENST00000274335.5:c.1344_1358del	p.Lys448_Tyr452del	p.K448_Y452del	ENST00000274335		448	AAATTACATGAATAT/-	10/15	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.699176516209794	2		260	159	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0066492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	23	1497	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1497	272	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0066492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	10	902	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		902	244	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89340796	89341429	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACAGCCCCTGGGGCCTGTGCTGTGAAAGCCCTCGATGTGGCAGCCCTGGGGTGCCTGAGAGCAGCAGGTGGAGCCCAGCAGTTTAAACAGAAAATAATGCCAGCGCTGACACCCGTGAGAGGTAGGTAGGGGCAGGTGCTCCAACTGCATGGACAAGTGTTACGGAGGGACTGAGCTGCTGAGGCCCAGCCCAGTGGCCTGAGGGCCTTGCCCGTGCGGGGAGCTGTCTGCTGTCTGCTGCAGCCTTCTTGGCTCCTTTCTGAGGCTCGCCCAAGGCTAGAGGCATGCAAAGGACTCTGTAGCCCCTGCAAGGTGCTGAGCACCCGGGAAGCTCCTGGTCAAAGTGCAGAATCTATCAAGGGGAGGGGAGGCGGGCAGGGTGCAGGCACTTGGACTCATGGGCCTGGCATGCAGACGGGCCCTACCTGGCTCTCCAGGGGCATGTTGTAGACCTCGGAGTCCAGCAGCATCGTGCAGGCGCTGAATGGCACTGCCTGGTTGGCGATGGTCCTGGCCGCCCGGCAGTGAACCCGCAGAATCTCCTGCTCACAGGATACGATCAGCTTCTCCTGAAGGAGGAGAGGAGTAGAGTGAGCTGGGACACAGCCACGCTCCAGGCCCCACTGTCAACAC	GACAGCCCCTGGGGCCTGTGCTGTGAAAGCCCTCGATGTGGCAGCCCTGGGGTGCCTGAGAGCAGCAGGTGGAGCCCAGCAGTTTAAACAGAAAATAATGCCAGCGCTGACACCCGTGAGAGGTAGGTAGGGGCAGGTGCTCCAACTGCATGGACAAGTGTTACGGAGGGACTGAGCTGCTGAGGCCCAGCCCAGTGGCCTGAGGGCCTTGCCCGTGCGGGGAGCTGTCTGCTGTCTGCTGCAGCCTTCTTGGCTCCTTTCTGAGGCTCGCCCAAGGCTAGAGGCATGCAAAGGACTCTGTAGCCCCTGCAAGGTGCTGAGCACCCGGGAAGCTCCTGGTCAAAGTGCAGAATCTATCAAGGGGAGGGGAGGCGGGCAGGGTGCAGGCACTTGGACTCATGGGCCTGGCATGCAGACGGGCCCTACCTGGCTCTCCAGGGGCATGTTGTAGACCTCGGAGTCCAGCAGCATCGTGCAGGCGCTGAATGGCACTGCCTGGTTGGCGATGGTCCTGGCCGCCCGGCAGTGAACCCGCAGAATCTCCTGCTCACAGGATACGATCAGCTTCTCCTGAAGGAGGAGAGGAGTAGAGTGAGCTGGGACACAGCCACGCTCCAGGCCCCACTGTCAACAC	-	novel	NA	P-0066492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	17	2	0	ENST00000301030.4:c.7570-64_7713+426del		p.X2524_splice	ENST00000301030	NM_001256183.1	2524		11/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		2	40	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007635	45007635	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	51	464	1	ENST00000558401.1:c.82C>T	p.Gln28Ter	p.Q28*	ENST00000558401	NM_004048.2	28	Cag/Tag	2/4	0.858548605674087	1	FACETS	0.186	0.158	0.216	0.186	0.158	0.216	SUBCLONAL	1	TRUE	0	0.858548605674087	1		465	365	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007643	45007643	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	205	471	0	ENST00000558401.1:c.90C>A	p.Tyr30Ter	p.Y30*	ENST00000558401	NM_004048.2	30	taC/taA	2/4	0.858548605674087	1	FACETS	0.747	0.705	0.788	0.747	0.705	0.788	SUBCLONAL	1	TRUE	0	0.858548605674087	1		471	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0066494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	294	401	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.858548605674087	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.858548605674087	1		401	373	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268195	153268195	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	277	488	1	ENST00000281708.4:c.613A>G	p.Thr205Ala	p.T205A	ENST00000281708	NM_033632.3	205	Aca/Gca	4/12	1	2	FACETS	0.95	0.898	1	0.95	0.898	1	CLONAL	1	TRUE	1	0.858548605674087	2		489	679	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955548	90955548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	85	360	0	ENST00000265433.3:c.2117C>T	p.Ser706Leu	p.S706L	ENST00000265433	NM_002485.4	706	tCa/tTa	14/16	1	2	FACETS	0.633	0.565	0.704	0.633	0.565	0.704	SUBCLONAL	1	TRUE	1	0.858548605674087	2		360	313	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636213	87636213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs988042143	NA	P-0066494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	286	564	1	ENST00000277120.3:c.2378C>T	p.Thr793Met	p.T793M	ENST00000277120		793	aCg/aTg	19/19	1	2	FACETS	0.991	0.939	1	0.991	0.939	1	CLONAL	1	TRUE	1	0.858548605674087	2		565	672	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104353775	104353775	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	331	527	0	ENST00000369902.3:c.709G>T	p.Asp237Tyr	p.D237Y	ENST00000369902	NM_016169.3	237	Gac/Tac	6/12	0.858548605674087	1	FACETS	0.996	0.962	1	0.996	0.962	1	CLONAL	1	TRUE	0	0.858548605674087	1		527	442	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10785709	10785709	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	194	528	0	ENST00000361367.2:c.1245G>T	p.Trp415Cys	p.W415C	ENST00000361367	NM_014633.3	415	tgG/tgT	10/25	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.858548605674087	2		528	447	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562660	21562660	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	241	616	0	ENST00000382592.4:c.1259G>T	p.Gly420Val	p.G420V	ENST00000382592	NM_014572.2	420	gGc/gTc	4/8	NA	2	FACETS	0.952	0.896	1			1	INDETERMINATE	1	TRUE	NA	0.858548605674087	2		616	590	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16022790	16022790	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	151	422	0	ENST00000268712.3:c.1862A>C	p.Glu621Ala	p.E621A	ENST00000268712	NM_006311.3	621	gAg/gCg	17/46	0.858548605674087	1	FACETS	0.999	0.949	1	0.999	0.949	1	CLONAL	1	TRUE	0	0.858548605674087	1		422	201	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369218	40369218	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	346	500	0	ENST00000293328.3:c.1340A>G	p.Gln447Arg	p.Q447R	ENST00000293328	NM_012448.3	447	cAg/cGg	11/19	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.858548605674087	2		500	804	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533683	63533683	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	356	596	0	ENST00000307078.5:c.1471G>T	p.Ala491Ser	p.A491S	ENST00000307078	NM_004655.3	491	Gcc/Tcc	6/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.858548605674087	2		596	815	SUCCESS
REST	5978	MSKCC	GRCh37	4	57798181	57798181	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	203	449	0	ENST00000309042.7:c.3157G>T	p.Val1053Phe	p.V1053F	ENST00000309042	NM_005612.4	1053	Gtc/Ttc	4/4	1	2	FACETS	0.927	0.868	0.988	0.927	0.868	0.988	CLONAL	1	TRUE	1	0.858548605674087	2		449	510	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295629	1295629	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0066494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	1478	671	1				ENST00000310581	NM_198253.2	-/1132			0.621622458849704	6	FACETS	0.927	0.911	0.942	0.927	0.911	0.942	CLONAL	5	TRUE	1	0.858548605674087	6		672	2019	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969185	93969185	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	268	477	0	ENST00000369303.4:c.1811del	p.Gly604AlafsTer25	p.G604Afs*25	ENST00000369303	NM_004440.3	604	gGc/gc	10/17	1	2	FACETS	0.965	0.912	1	0.965	0.912	1	CLONAL	1	TRUE	1	0.858548605674087	2		477	647	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710919	117710919	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	304	505	0	ENST00000368508.3:c.1353G>T	p.Glu451Asp	p.E451D	ENST00000368508	NM_002944.2	451	gaG/gaT	12/43	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.858548605674087	2		505	701	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0066495-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	189	582	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.215780478036093	2	FACETS	0.766	0.712	0.822	0.766	0.712	0.822	INDETERMINATE	2	TRUE	0	0.406443692703797	2		582	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764146326	NA	P-0066500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	235	375	0	ENST00000269305.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000269305	NM_001126112.2	281	Gac/Aac	8/11	0.439759297049737	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.450894745413355	2		375	472	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067850	30067850	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	72	353	0	ENST00000338641.4:c.1035G>T	p.Met345Ile	p.M345I	ENST00000338641	NM_000268.3	345	atG/atT	11/16	0.439759297049737	2	FACETS	0.674	0.59	0.763	0.337	0.295	0.382	SUBCLONAL	1	TRUE	0	0.450894745413355	2		353	474	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413010	49413010	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519952	NA	P-0066501-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	84	405	0	ENST00000418115.1:c.13C>T	p.Arg5Trp	p.R5W	ENST00000418115	NM_001664.2	5	Cgg/Tgg	2/5	0.149891181816321	2	FACETS	0.89	0.786	1	0.89	0.786	1	CLONAL	2	TRUE	0	0.149891181816321	2		405	630	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197397	27197397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771377363	NA	P-0066501-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	55	434	0	ENST00000380036.4:c.1709C>T	p.Ser570Leu	p.S570L	ENST00000380036	NM_000459.3	570	tCg/tTg	12/23	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.149891181816321	2		434	610	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980519	70980519	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066501-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	61	510	0	ENST00000276594.2:c.858A>C	p.Lys286Asn	p.K286N	ENST00000276594	NM_024504.3	286	aaA/aaC	4/8	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.149891181816321	2		510	661	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777954	27777954	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066501-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	65	639	1	ENST00000369163.2:c.103G>T	p.Gly35Cys	p.G35C	ENST00000369163	NM_003536.2	35	Ggt/Tgt	1/1	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.149891181816321	2		640	779	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118897	70118897	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066501-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	58	571	0	ENST00000245479.2:c.469G>T	p.Glu157Ter	p.E157*	ENST00000245479	NM_000346.3	157	Gag/Tag	2/3	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.149891181816321	2		571	711	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230907	66230907	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066501-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	33	416	0	ENST00000273854.3:c.2064A>C	p.Glu688Asp	p.E688D	ENST00000273854	NM_004439.5	688	gaA/gaC	12/18	1	2	FACETS	0.912	0.742	1	0.912	0.742	1	CLONAL	1	TRUE	1	0.149891181816321	2		416	483	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229250	36229250	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066501-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	71	616	0	ENST00000222270.7:c.7940C>G	p.Ala2647Gly	p.A2647G	ENST00000222270	NM_014727.1	2647	gCc/gGc	37/37	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.149891181816321	2		616	921	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994325	21994326	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0066501-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	43	395	0	ENST00000579755.1:c.5_6del	p.Val2AlafsTer60	p.V2Afs*60	ENST00000579755		2	gTG/g	1/3	1				0.94	1				CLONAL	1	TRUE	1	0.149891181816321	2		395	448	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110684	8110684	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs141907099	NA	P-0066501-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	59	484	0	ENST00000585124.1:c.208C>T	p.Arg70Trp	p.R70W	ENST00000585124	NM_004217.3	70	Cgg/Tgg	5/9	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.149891181816321	2		484	594	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0066502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	13	257	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.288	0.205	0.391	0.288	0.205	0.391	SUBCLONAL	1	TRUE	1	0.249947747556778	2		257	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0066502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	9	345	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	1	2	FACETS	0.16	0.105	0.231	0.16	0.105	0.231	SUBCLONAL	1	TRUE	1	0.249947747556778	2		345	449	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0066502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	22	257	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.492	0.381	0.621	0.492	0.381	0.621	SUBCLONAL	1	TRUE	1	0.249947747556778	2		257	358	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0066502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	72	298	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.249947747556778	3	FACETS	0.864	0.759	0.976	0.864	0.759	0.976	CLONAL	2	TRUE	1	0.249947747556778	3		298	375	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913351	NA	P-0066502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	27	318	0	ENST00000288602.6:c.1397G>C	p.Gly466Ala	p.G466A	ENST00000288602	NM_004333.4	466	gGa/gCa	11/18	1	2	FACETS	0.558	0.444	0.689	0.558	0.444	0.689	SUBCLONAL	1	TRUE	1	0.249947747556778	2		318	387	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952049	178952049	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242945375	NA	P-0066502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	47	367	0	ENST00000263967.3:c.3104C>T	p.Ala1035Val	p.A1035V	ENST00000263967	NM_006218.2	1035	gCt/gTt	21/21	1	2	FACETS	0.816	0.689	0.955	0.816	0.689	0.955	CLONAL	1	TRUE	1	0.249947747556778	2		367	461	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102906	71102906	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs564508875	NA	P-0066503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	53	362	0	ENST00000318789.4:c.301A>G	p.Met101Val	p.M101V	ENST00000318789	NM_032682.5	101	Atg/Gtg	8/21	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.190584210894179	2		362	500	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931644	39931644	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0066505-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	26	384	1	ENST00000378444.4:c.2955T>A	p.Tyr985Ter	p.Y985*	ENST00000378444	NM_001123385.1	985	taT/taA	4/15	1	2	FACETS	0.176	0.139	0.219	0.176	0.139	0.219	SUBCLONAL	1	TRUE	1	0.572558265208995	2		385	516	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678341	88678341	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	158	409	0	ENST00000360948.2:c.1195C>A	p.Pro399Thr	p.P399T	ENST00000360948	NM_001012338.2	399	Ccc/Acc	9/19	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.899888205018902	2		409	342	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593573	55593606	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCCCACAGAAACCCATGTATGAAGTACAGTGGA	TCCCCACAGAAACCCATGTATGAAGTACAGTGGA	-	novel	NA	P-0066506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	204	488	0	ENST00000288135.5:c.1648-9_1672del		p.X550_splice	ENST00000288135	NM_000222.2	550		11/21	0.138731450306665	4	FACETS	0.886	0.83	0.943	0.886	0.83	0.943	INDETERMINATE	2	TRUE	2	0.899888205018902	4		488	486	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0066514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	57	544	2	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.29	2		546	356	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	13	330	0	ENST00000335508.6:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000335508	NM_012433.2	902	Gaa/Aaa	18/25	1	2	FACETS	0.402	0.287	0.543	0.402	0.287	0.543	SUBCLONAL	1	TRUE	1	0.29	2		330	223	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491397	18491397	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1242525432	NA	P-0066514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	44	338	0	ENST00000266497.5:c.1310T>C	p.Ile437Thr	p.I437T	ENST00000266497		437	aTa/aCa	8/31	NA	2	FACETS	0.882	0.742	1			1	INDETERMINATE	1	TRUE	NA	0.29	2		338	344	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273953	10273953	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555491453	NA	P-0066514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	25	508	0	ENST00000330684.3:c.316C>T	p.Gln106Ter	p.Q106*	ENST00000330684	NM_001134407.1	106	Cag/Tag	2/13	0.231599207212001	0	FACETS	0.949	0.759	1			1	CLONAL	1	TRUE	0	0.29	0		508	129	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739042	46739044	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	rs773026168	NA	P-0066514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	22	429	0	ENST00000371975.4:c.1393_1395del	p.Asp465del	p.D465del	ENST00000371975	NM_003579.3	464	tATGat/tat	13/18	1	2	FACETS	0.646	0.502	0.811	0.646	0.502	0.811	SUBCLONAL	1	TRUE	1	0.29	2		429	235	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0066515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	26	486	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.673	0.532	0.837	0.673	0.532	0.837	SUBCLONAL	1	TRUE	1	0.13	2		486	594	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653802	89653802	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	22	396	0	ENST00000371953.3:c.100G>C	p.Ala34Pro	p.A34P	ENST00000371953	NM_000314.4	34	Gct/Cct	2/9	1	2	FACETS	1	0.783	1	1	0.783	1	CLONAL	1	TRUE	1	0.13	2		396	335	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653798	89653803	+	frameshift_variant	Frame_Shift_Ins	INS	TATTGC	TATTGC	ATATTGG	novel	NA	P-0066515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	22	401	0	ENST00000371953.3:c.96_101delinsATATTGG	p.Ile33TyrfsTer11	p.I33Yfs*11	ENST00000371953	NM_000314.4	32	atTATTGCt/atATATTGGt	2/9	1	2	FACETS	1	0.783	1	1	0.783	1	CLONAL	1	TRUE	1	0.13	2		401	335	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904855	101904855	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066529-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	51	261	0	ENST00000374994.4:c.843T>G	p.Asp281Glu	p.D281E	ENST00000374994	NM_004612.2	281	gaT/gaG	5/9	1	2	FACETS	0.991	0.842	1	0.991	0.842	1	CLONAL	1	TRUE	1	0.18	2		261	572	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850717	63850717	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs139520430	NA	P-0066529-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	37	381	0	ENST00000279873.7:c.1495G>C	p.Gly499Arg	p.G499R	ENST00000279873	NM_032199.2	499	Ggg/Cgg	10/10	1	2	FACETS	0.558	0.458	0.67	0.558	0.458	0.67	SUBCLONAL	1	TRUE	1	0.18	2		381	737	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675071	40675071	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	72	282	0	ENST00000249776.8:c.35T>G	p.Val12Gly	p.V12G	ENST00000249776	NM_033286.3	12	gTt/gGt	1/9	0.390594186572384	3	FACETS	1	0.935	1	0.549	0.482	0.619	CLONAL	1	TRUE	1	0.466385993752249	3		282	347	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573430	48573430	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	22	277	0	ENST00000342988.3:c.14C>G	p.Ser5Cys	p.S5C	ENST00000342988	NM_005359.5	5	tCt/tGt	2/12	0.252156009569385	1	FACETS	0.629	0.495	0.779	0.629	0.495	0.779	INDETERMINATE	1	TRUE	0	0.466385993752249	1		277	115	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830603	72830603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	38	287	0	ENST00000268489.5:c.5978C>T	p.Ser1993Phe	p.S1993F	ENST00000268489	NM_006885.3	1993	tCc/tTc	9/10	1	2	FACETS	0.881	0.737	1	0.881	0.737	1	CLONAL	1	TRUE	1	0.466385993752249	2		287	185	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0066530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	44	810	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.466385993752249	2	FACETS	0.934	0.793	1	0.467	0.396	0.544	CLONAL	1	TRUE	0	0.466385993752249	2		810	202	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99806194	99806194	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	17	134	0	ENST00000280892.6:c.478G>C	p.Glu160Gln	p.E160Q	ENST00000280892	NM_001130678.1	160	Gaa/Caa	6/7	0.209138774125972	4	FACETS	1	0.84	1	0.383	0.291	0.489	INDETERMINATE	1	TRUE	1	0.466385993752249	4		134	93	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504356	186504356	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	37	142	0	ENST00000323963.5:c.693T>A	p.Asp231Glu	p.D231E	ENST00000323963		231	gaT/gaA	7/11	0.209138774125972	4	FACETS	0.891	0.762	1	0.891	0.762	1	INDETERMINATE	3	TRUE	1	0.466385993752249	4		142	87	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0066531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	53	710	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.148	0.125	0.172	0.148	0.125	0.172	SUBCLONAL	1	TRUE	1	0.750747359311688	2		713	957	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0066531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	119	501	0	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.405	0.366	0.447	0.405	0.366	0.447	SUBCLONAL	1	TRUE	1	0.750747359311688	2		501	782	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0066531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	317	436	0	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	1	2	FACETS	0.998	0.946	1	0.998	0.946	1	CLONAL	1	TRUE	1	0.750747359311688	2		436	846	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692922	89692922	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201044	NA	P-0066531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	411	372	0	ENST00000371953.3:c.406T>C	p.Cys136Arg	p.C136R	ENST00000371953	NM_000314.4	136	Tgt/Cgt	5/9	0.750747359311688	2	FACETS	0.966	0.935	0.995	0.966	0.935	0.995	CLONAL	2	TRUE	0	0.750747359311688	2		372	567	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	18	383	0	ENST00000397062.3:c.246A>T	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaT	2/5	1	2	FACETS	0.066	0.049	0.087	0.066	0.049	0.087	SUBCLONAL	1	TRUE	1	0.750747359311688	2		383	722	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023769	27023769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	86	332	2	ENST00000324856.7:c.879del	p.Thr294ProfsTer69	p.T294Pfs*69	ENST00000324856	NM_006015.4	292	aCc/ac	1/20	1	2	FACETS	0.371	0.328	0.416	0.371	0.328	0.416	SUBCLONAL	1	TRUE	1	0.750747359311688	2		334	618	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057976	27057976	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	301	403	0	ENST00000324856.7:c.1684C>T	p.Gln562Ter	p.Q562*	ENST00000324856	NM_006015.4	562	Cag/Tag	3/20	1	2	FACETS	0.979	0.926	1	0.979	0.926	1	CLONAL	1	TRUE	1	0.750747359311688	2		403	819	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	276	399	0	ENST00000227507.2:c.859C>G	p.Pro287Ala	p.P287A	ENST00000227507	NM_053056.2	287	Ccc/Gcc	5/5	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.750747359311688	2		399	715	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	142	365	0	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	1	2	FACETS	0.703	0.644	0.764	0.703	0.644	0.764	SUBCLONAL	1	TRUE	1	0.750747359311688	2		365	538	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61729435	61729435	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	54	268	0	ENST00000401558.2:c.312del	p.Lys104AsnfsTer17	p.K104Nfs*17	ENST00000401558	NM_003400.3	104	aaA/aa	5/25	1	2	FACETS	0.251	0.214	0.292	0.251	0.214	0.292	SUBCLONAL	1	TRUE	1	0.750747359311688	2		268	572	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266112	41266112	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913228	NA	P-0066531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	250	340	0	ENST00000349496.5:c.109T>C	p.Ser37Pro	p.S37P	ENST00000349496	NM_001904.3	37	Tct/Cct	3/15	1	2	FACETS	0.9	0.846	0.956	0.9	0.846	0.956	CLONAL	1	TRUE	1	0.750747359311688	2		340	740	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551951	150551952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs750805885	NA	P-0066531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	61	332	1	ENST00000369026.2:c.55dup	p.Ala19GlyfsTer91	p.A19Gfs*91	ENST00000369026	NM_021960.4	19	gcc/gGcc	1/3	1	2	FACETS	0.234	0.201	0.269	0.234	0.201	0.269	SUBCLONAL	1	TRUE	1	0.750747359311688	2		333	695	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589223	67589225	+	inframe_deletion	In_Frame_Del	DEL	TAA	TAA	-	novel	NA	P-0066531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	18	309	0	ENST00000274335.5:c.1214_1216del	p.Ile405del	p.I405del	ENST00000274335		404	tTAAta/tta	9/15	1	2	FACETS	0.081	0.06	0.106	0.081	0.06	0.106	SUBCLONAL	1	TRUE	1	0.750747359311688	2		309	590	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157488275	157488275	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377351099	NA	P-0066531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	63	379	0	ENST00000346085.5:c.2981C>T	p.Ala994Val	p.A994V	ENST00000346085	NM_020732.3	994	gCg/gTg	10/20	1	2	FACETS	0.263	0.227	0.302	0.263	0.227	0.302	SUBCLONAL	1	TRUE	1	0.750747359311688	2		379	638	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982463	25982463	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	287	313	0	ENST00000435504.4:c.827C>T	p.Ser276Phe	p.S276F	ENST00000435504		276	tCc/tTc	9/13	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.750747359311688	2		313	644	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196093	138196093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1405321250	NA	P-0066531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	89	389	0	ENST00000237289.4:c.407G>A	p.Arg136His	p.R136H	ENST00000237289	NM_001270507.1	136	cGc/cAc	3/9	1	2	FACETS	0.278	0.246	0.312	0.278	0.246	0.312	SUBCLONAL	1	TRUE	1	0.750747359311688	2		389	853	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672814	86672816	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	novel	NA	P-0066531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	61	347	0	ENST00000274376.6:c.2307_2309del	p.Leu770del	p.L770del	ENST00000274376	NM_002890.2	767	tcGTTg/tcg	17/25	1	2	FACETS	0.224	0.193	0.258	0.224	0.193	0.258	SUBCLONAL	1	TRUE	1	0.750747359311688	2		347	725	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352533	89352533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771447879	NA	P-0066531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	232	357	0	ENST00000301030.4:c.806C>T	p.Thr269Met	p.T269M	ENST00000301030	NM_001256183.1	269	aCg/aTg	8/13	1	2	FACETS	0.914	0.857	0.973	0.914	0.857	0.973	CLONAL	1	TRUE	1	0.750747359311688	2		357	676	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522796	67522796	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	91	408	0	ENST00000274335.5:c.293C>T	p.Ala98Val	p.A98V	ENST00000274335		98	gCa/gTa	1/15	1	2	FACETS	0.322	0.285	0.361	0.322	0.285	0.361	SUBCLONAL	1	TRUE	1	0.750747359311688	2		408	753	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094463	27094464	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0066531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	82	348	0	ENST00000324856.7:c.3173_3174del	p.Val1058GlufsTer46	p.V1058Efs*46	ENST00000324856	NM_006015.4	1057	tcTGtg/tctg	11/20	1	2	FACETS	0.304	0.267	0.343	0.304	0.267	0.343	SUBCLONAL	1	TRUE	1	0.750747359311688	2		348	719	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422637	47422637	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	258	352	0	ENST00000404338.3:c.705C>A	p.Asn235Lys	p.N235K	ENST00000404338	NM_004491.4	235	aaC/aaA	1/6	1	2	FACETS	0.986	0.929	1	0.986	0.929	1	CLONAL	1	TRUE	1	0.750747359311688	2		352	697	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6222401	6222412	+	inframe_deletion	In_Frame_Del	DEL	GGGGTGGGGGTG	GGGGTGGGGGTG	-	rs753690040	NA	P-0066531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	118	278	0	ENST00000252674.7:c.830_841del	p.Pro277_Pro280del	p.P277_P280del	ENST00000252674	NM_005934.3	277	cCACCCCCACCCCgg/cgg	6/12	1	2	FACETS	0.558	0.505	0.614	0.558	0.505	0.614	SUBCLONAL	1	TRUE	1	0.750747359311688	2		278	563	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218888	36218888	+	splice_donor_variant	Splice_Site	SNP	T	T	G	rs1599685443	NA	P-0066531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	297	445	0	ENST00000222270.7:c.4497+2T>G		p.X1499_splice	ENST00000222270	NM_014727.1	1499			1	2	FACETS	0.966	0.913	1	0.966	0.913	1	CLONAL	1	TRUE	1	0.750747359311688	2		445	819	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888856	76888856	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	68	303	0	ENST00000373344.5:c.4973C>T	p.Thr1658Ile	p.T1658I	ENST00000373344	NM_000489.3	1658	aCt/aTt	19/35	1	2	FACETS	0.322	0.28	0.367	0.322	0.28	0.367	SUBCLONAL	1	TRUE	1	0.750747359311688	2		303	563	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850620	63850620	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0066531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	242	318	0	ENST00000279873.7:c.1399-1G>C		p.X467_splice	ENST00000279873	NM_032199.2	467			1	2	FACETS	0.93	0.874	0.988	0.93	0.874	0.988	CLONAL	1	TRUE	1	0.750747359311688	2		318	693	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148904	119148904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	67	334	1	ENST00000264033.4:c.1124G>A	p.Gly375Asp	p.G375D	ENST00000264033	NM_005188.3	375	gGc/gAc	8/16	1	2	FACETS	0.287	0.249	0.329	0.287	0.249	0.329	SUBCLONAL	1	TRUE	1	0.750747359311688	2		335	621	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943669	71943669	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0066531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	76	335	0	ENST00000298229.2:c.1713-1G>A		p.X571_splice	ENST00000298229	NM_001567.3	571			1	2	FACETS	0.264	0.231	0.299	0.264	0.231	0.299	SUBCLONAL	1	TRUE	1	0.750747359311688	2		335	768	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423570	47423571	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0066531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	304	381	0	ENST00000404338.3:c.1641_1642del	p.Ile548SerfsTer21	p.I548Sfs*21	ENST00000404338	NM_004491.4	546	aaACac/aaac	1/6	1	2	FACETS	0.99	0.937	1	0.99	0.937	1	CLONAL	1	TRUE	1	0.750747359311688	2		381	818	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945184	44945184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	107	297	0	ENST00000377967.4:c.3508C>T	p.Pro1170Ser	p.P1170S	ENST00000377967	NM_021140.2	1170	Cct/Tct	24/29	1	2	FACETS	0.506	0.455	0.56	0.506	0.455	0.56	SUBCLONAL	1	TRUE	1	0.750747359311688	2		297	563	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442863	187442863	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	82	364	0	ENST00000232014.4:c.1843G>C	p.Ala615Pro	p.A615P	ENST00000232014	NM_001130845.1	615	Gcc/Ccc	9/10	1	2	FACETS	0.333	0.293	0.375	0.333	0.293	0.375	SUBCLONAL	1	TRUE	1	0.750747359311688	2		364	656	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264162	46264162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	47	361	0	ENST00000371998.3:c.1209G>A	p.Met403Ile	p.M403I	ENST00000371998		403	atG/atA	11/23	1	2	FACETS	0.171	0.144	0.202	0.171	0.144	0.202	SUBCLONAL	1	TRUE	1	0.750747359311688	2		361	731	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200150	138200150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	94	400	0	ENST00000237289.4:c.1568C>T	p.Ala523Val	p.A523V	ENST00000237289	NM_001270507.1	523	gCc/gTc	7/9	1	2	FACETS	0.316	0.28	0.353	0.316	0.28	0.353	SUBCLONAL	1	TRUE	1	0.750747359311688	2		400	793	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	36	446	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.781	0.647	0.927	0.781	0.647	0.927	CLONAL	1	TRUE	1	0.43093837797023	2		446	214	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	112	433	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.43093837797023	2		433	512	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	47	133	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.996	0.85	1	0.996	0.85	1	CLONAL	1	TRUE	1	0.43093837797023	2		133	219	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	116	499	0	ENST00000269571.5:c.829G>C	p.Asp277His	p.D277H	ENST00000269571		277	Gac/Cac	7/27	1	2	FACETS	0.972	0.879	1	0.972	0.879	1	CLONAL	1	TRUE	1	0.43093837797023	2		499	554	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868193	37868193	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	24	369	0	ENST00000269571.5:c.914C>G	p.Ser305Cys	p.S305C	ENST00000269571		305	tCt/tGt	8/27	1	2	FACETS	0.286	0.224	0.358	0.286	0.224	0.358	SUBCLONAL	1	TRUE	1	0.43093837797023	2		369	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793881	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	121	435	0	ENST00000269305.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGg/gAg	8/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.43093837797023	2		435	510	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844229	68844229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	97	275	0	ENST00000261769.5:c.817G>A	p.Glu273Lys	p.E273K	ENST00000261769	NM_004360.3	273	Gaa/Aaa	6/16	0.43093837797023	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.43093837797023	1		275	286	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788651	3788651	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	80	316	0	ENST00000262367.5:c.4303G>T	p.Asp1435Tyr	p.D1435Y	ENST00000262367	NM_004380.2	1435	Gat/Tat	26/31	0.43093837797023	1	FACETS	0.998	0.888	1	0.998	0.888	1	CLONAL	1	TRUE	0	0.43093837797023	1		316	292	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032566	47032566	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	94	370	0	ENST00000377604.3:c.472G>T	p.Glu158Ter	p.E158*	ENST00000377604	NM_001204468.1	158	Gag/Tag	5/24	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.43093837797023	2		370	369	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842331	68842331	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	74	339	0	ENST00000261769.5:c.392C>A	p.Ser131Tyr	p.S131Y	ENST00000261769	NM_004360.3	131	tCc/tAc	4/16	0.43093837797023	1	FACETS	0.913	0.808	1	0.913	0.808	1	CLONAL	1	TRUE	0	0.43093837797023	1		339	295	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041704	42041704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	124	462	0	ENST00000219905.7:c.5899C>T	p.Gln1967Ter	p.Q1967*	ENST00000219905	NM_001164273.1	1967	Cag/Tag	17/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.43093837797023	2		462	496	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981202	201981202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750329636	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	138	422	0	ENST00000359651.3:c.281G>A	p.Arg94Gln	p.R94Q	ENST00000359651		94	cGa/cAa	2/8	0.43093837797023	3	FACETS	1	0.981	1	0.635	0.58	0.693	CLONAL	1	TRUE	1	0.43093837797023	3		422	613	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547972	41547972	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	118	377	0	ENST00000263253.7:c.2953G>C	p.Asp985His	p.D985H	ENST00000263253	NM_001429.3	985	Gat/Cat	15/31	0.43093837797023	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.43093837797023	1		377	332	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233099	69233099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1221150148	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	97	435	0	ENST00000462284.1:c.964C>T	p.Pro322Ser	p.P322S	ENST00000462284	NM_002392.5	322	Cca/Tca	11/11	1	2	FACETS	0.913	0.817	1	0.913	0.817	1	CLONAL	1	TRUE	1	0.43093837797023	2		435	493	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265115	46265115	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	116	444	0	ENST00000371998.3:c.1985C>G	p.Ser662Cys	p.S662C	ENST00000371998		662	tCt/tGt	12/23	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.43093837797023	2		444	511	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265715	10265715	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	106	375	0	ENST00000340748.4:c.1462C>G	p.Leu488Val	p.L488V	ENST00000340748		488	Ctg/Gtg	19/40	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.43093837797023	2		375	444	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844205	68844205	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs876659503	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	101	325	0	ENST00000261769.5:c.793G>T	p.Glu265Ter	p.E265*	ENST00000261769	NM_004360.3	265	Gag/Tag	6/16	0.43093837797023	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.43093837797023	1		325	320	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564792	41564792	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	119	422	0	ENST00000263253.7:c.4093G>A	p.Glu1365Lys	p.E1365K	ENST00000263253	NM_001429.3	1365	Gaa/Aaa	25/31	0.43093837797023	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.43093837797023	1		422	370	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196324	106196324	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	31	485	0	ENST00000380013.4:c.4657C>G	p.Gln1553Glu	p.Q1553E	ENST00000380013	NM_001127208.2	1553	Cag/Gag	11/11	1	2	FACETS	0.247	0.199	0.302	0.247	0.199	0.302	SUBCLONAL	1	TRUE	1	0.43093837797023	2		485	582	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858180	9858180	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867432846	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	101	422	0	ENST00000330684.3:c.3221C>T	p.Pro1074Leu	p.P1074L	ENST00000330684	NM_001134407.1	1074	cCt/cTt	13/13	0.43093837797023	1	FACETS	0.915	0.824	1	0.915	0.824	1	CLONAL	1	TRUE	0	0.43093837797023	1		422	402	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371947	55371947	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	27	454	0	ENST00000297316.4:c.637C>G	p.Pro213Ala	p.P213A	ENST00000297316	NM_022454.3	213	Ccg/Gcg	2/2	1	2	FACETS	0.345	0.274	0.426	0.345	0.274	0.426	SUBCLONAL	1	TRUE	1	0.43093837797023	2		454	363	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4094460	4094460	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	72	316	0	ENST00000262948.5:c.1083G>C	p.Lys361Asn	p.K361N	ENST00000262948	NM_030662.3	361	aaG/aaC	10/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.43093837797023	2		316	287	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432447	49432447	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	103	492	0	ENST00000301067.7:c.8692C>G	p.Gln2898Glu	p.Q2898E	ENST00000301067	NM_003482.3	2898	Cag/Gag	34/54	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.43093837797023	2		492	445	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43771713	43771713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	114	345	0	ENST00000382044.4:c.670G>A	p.Glu224Lys	p.E224K	ENST00000382044	NM_001141980.1	224	Gaa/Aaa	7/28	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.43093837797023	2		345	479	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707967	47707967	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	99	356	0	ENST00000233146.2:c.2591A>T	p.Asp864Val	p.D864V	ENST00000233146	NM_000251.2	864	gAt/gTt	15/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.43093837797023	2		356	382	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883728	37883728	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	39	571	0	ENST00000269571.5:c.3340G>T	p.Glu1114Ter	p.E1114*	ENST00000269571		1114	Gag/Tag	26/27	1	2	FACETS	0.371	0.307	0.442	0.371	0.307	0.442	SUBCLONAL	1	TRUE	1	0.43093837797023	2		571	488	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041776	42041776	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	138	449	0	ENST00000219905.7:c.5971A>G	p.Lys1991Glu	p.K1991E	ENST00000219905	NM_001164273.1	1991	Aag/Gag	17/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.43093837797023	2		449	532	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131951694	131951694	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	20	268	0	ENST00000265335.6:c.3037-1G>C		p.X1013_splice	ENST00000265335		1013			1	2	FACETS	0.236	0.18	0.302	0.236	0.18	0.302	SUBCLONAL	1	TRUE	1	0.43093837797023	2		268	393	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268887	55268887	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	30	496	0	ENST00000275493.2:c.2953G>C	p.Glu985Gln	p.E985Q	ENST00000275493	NM_005228.3	985	Gaa/Caa	25/28	1	2	FACETS	0.248	0.199	0.304	0.248	0.199	0.304	SUBCLONAL	1	TRUE	1	0.43093837797023	2		496	561	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881446	37881446	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747974836	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	27	432	0	ENST00000269571.5:c.2638G>C	p.Asp880His	p.D880H	ENST00000269571		880	Gat/Cat	21/27	1	2	FACETS	0.267	0.211	0.33	0.267	0.211	0.33	SUBCLONAL	1	TRUE	1	0.43093837797023	2		432	470	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041390	42041390	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1428651067	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	153	486	0	ENST00000219905.7:c.5585C>G	p.Ser1862Cys	p.S1862C	ENST00000219905	NM_001164273.1	1862	tCt/tGt	17/24	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.43093837797023	2		486	567	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652162	36652163	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	106	444	0	ENST00000244741.5:c.285dup	p.Gly96TrpfsTer33	p.G96Wfs*33	ENST00000244741	NM_000389.4	95	cct/ccTt	2/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.43093837797023	2		444	402	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199797	108199797	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	117	308	0	ENST00000278616.4:c.7139G>C	p.Arg2380Thr	p.R2380T	ENST00000278616	NM_000051.3	2380	aGa/aCa	49/63	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.43093837797023	2		308	459	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139102	50139102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1039650903	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	81	153	0	ENST00000246792.3:c.461G>A	p.Arg154Gln	p.R154Q	ENST00000246792	NM_006270.3	154	cGa/cAa	5/6	0.43093837797023	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	1	0.43093837797023	3		153	207	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954350	48954350	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	98	271	0	ENST00000267163.4:c.1471C>G	p.Leu491Val	p.L491V	ENST00000267163	NM_000321.2	491	Ctt/Gtt	16/27	0.43093837797023	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.43093837797023	1		271	312	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842501	68843523	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGGATTTGGCAGAGAAGTACCAAGGAGAGAAAGGGAAAAGACCCAGTGTTGGGATCCTTCTTTACTAATTCTTTTTCTTTCATTTTGTCTTCAGATCAAATCCAACAAAGACAAAGAAGGCAAGGTTTTCTACAGCATCACTGGCCAAGGAGCTGACACACCCCCTGTTGGTGTCTTTATTATTGAAAGAGAAACAGGATGGCTGAAGGTGACAGAGCCTCTGGATAGAGAACGCATTGCCACATACACTGTAAGTATCTCTTAGAAGCTTGTTGACACCGGGGTAACATCCACCCAGGATTTTTTGGTCAACCCATGCTGGATCCGCAGATCAGAGGCTCTGAACACATGAGGAGCTTAACTTGACACCTCTTGACCTGTTGCTAAGGAGAAGTGATGGGAGAACGTGGGACAGTTTGGGGTTGTTAATTTTTCTCCTTGTCAGGAAGAAAGGAAGGAGAATCCGCATGCATCCTCATACAACCAGGACAAATTTAGACCCAAGATGTCAACCTGTTCTTGGGGCTGGAAGTCCCTGACCTAAAGGAACAGGACAGTGATGATATAAGGGAGCAAAACCCATTTCTTGGGCTTGGCAGCAGCAAGAGCTTAGGAAAACCAAGAGGTCTTTTTTTTTTTTTTTTGAGATAGGGTTTCACTCTGTCACCCAGGCTGGAACCACAACCTCCACTTCCCGGGTTCAAGTGATTCTCCTGCTTCAACCTCCCGAGTAGCTGGATTATAGGCAGCTGCCATCATGCCCAGCTAATTTTTTGCGTTTTTATTAGAGATGAGGTTTTACCATGTTGGCCAGAGTGGTCTCAAACTCCTGACCTCAGGCGATTCACCCTACTTGGCCTCCCAAAGTGCTGGGATTACAGGAGGGAGCCACTGCACCCGGCCTACAAGAGGTCATTTGTTTTTGTTTTGGATTTTTGTTTTTTTGAGACCGAGTCTACCTGTGTCACTCAAGCTGGAATGCAGTGGTACAATCTTAGCTCACTGCAGCCTGGACCTTCTGG	AGGGATTTGGCAGAGAAGTACCAAGGAGAGAAAGGGAAAAGACCCAGTGTTGGGATCCTTCTTTACTAATTCTTTTTCTTTCATTTTGTCTTCAGATCAAATCCAACAAAGACAAAGAAGGCAAGGTTTTCTACAGCATCACTGGCCAAGGAGCTGACACACCCCCTGTTGGTGTCTTTATTATTGAAAGAGAAACAGGATGGCTGAAGGTGACAGAGCCTCTGGATAGAGAACGCATTGCCACATACACTGTAAGTATCTCTTAGAAGCTTGTTGACACCGGGGTAACATCCACCCAGGATTTTTTGGTCAACCCATGCTGGATCCGCAGATCAGAGGCTCTGAACACATGAGGAGCTTAACTTGACACCTCTTGACCTGTTGCTAAGGAGAAGTGATGGGAGAACGTGGGACAGTTTGGGGTTGTTAATTTTTCTCCTTGTCAGGAAGAAAGGAAGGAGAATCCGCATGCATCCTCATACAACCAGGACAAATTTAGACCCAAGATGTCAACCTGTTCTTGGGGCTGGAAGTCCCTGACCTAAAGGAACAGGACAGTGATGATATAAGGGAGCAAAACCCATTTCTTGGGCTTGGCAGCAGCAAGAGCTTAGGAAAACCAAGAGGTCTTTTTTTTTTTTTTTTGAGATAGGGTTTCACTCTGTCACCCAGGCTGGAACCACAACCTCCACTTCCCGGGTTCAAGTGATTCTCCTGCTTCAACCTCCCGAGTAGCTGGATTATAGGCAGCTGCCATCATGCCCAGCTAATTTTTTGCGTTTTTATTAGAGATGAGGTTTTACCATGTTGGCCAGAGTGGTCTCAAACTCCTGACCTCAGGCGATTCACCCTACTTGGCCTCCCAAAGTGCTGGGATTACAGGAGGGAGCCACTGCACCCGGCCTACAAGAGGTCATTTGTTTTTGTTTTGGATTTTTGTTTTTTTGAGACCGAGTCTACCTGTGTCACTCAAGCTGGAATGCAGTGGTACAATCTTAGCTCACTGCAGCCTGGACCTTCTGG	-	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	57	430	0	ENST00000261769.5:c.531+31_688-577del		p.X177_splice	ENST00000261769	NM_004360.3	177		5/16	0.43093837797023	1	FACETS	0.647	0.558	0.742	0.647	0.558	0.742	SUBCLONAL	1	TRUE	0	0.43093837797023	1		430	321	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76931749	76931749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	106	347	0	ENST00000373344.5:c.3781G>A	p.Asp1261Asn	p.D1261N	ENST00000373344	NM_000489.3	1261	Gat/Aat	10/35	0.43093837797023	3	FACETS	1	0.942	1	0.534	0.48	0.591	CLONAL	1	TRUE	1	0.43093837797023	3		347	560	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781821	9781821	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	66	340	0	ENST00000377346.4:c.1958C>G	p.Ser653Cys	p.S653C	ENST00000377346	NM_005026.3	653	tCc/tGc	16/24	0.310854677515214	1	FACETS	0.928	0.815	1	0.928	0.815	1	CLONAL	1	TRUE	0	0.43093837797023	1		340	259	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878087	48878100	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCGCTGCCGCCG	CGCCGCTGCCGCCG	-	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	75	451	0	ENST00000267163.4:c.41_54del	p.Ala14GlyfsTer12	p.A14Gfs*12	ENST00000267163	NM_000321.2	13	gcCGCCGCTGCCGCCGcg/gccg	1/27	0.43093837797023	1	FACETS	0.851	0.752	0.955	0.851	0.752	0.955	CLONAL	1	TRUE	0	0.43093837797023	1		451	321	SUCCESS
AR	367	MSKCC	GRCh37	X	66766006	66766006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	112	452	0	ENST00000374690.3:c.1018G>A	p.Glu340Lys	p.E340K	ENST00000374690	NM_000044.3	340	Gaa/Aaa	1/8	0.43093837797023	3	FACETS	1	0.968	1	0.587	0.53	0.647	CLONAL	1	TRUE	1	0.43093837797023	3		452	538	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90970960	90970960	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	111	338	0	ENST00000265433.3:c.1117G>A	p.Asp373Asn	p.D373N	ENST00000265433	NM_002485.4	373	Gat/Aat	9/16	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.43093837797023	2		338	470	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14026302	14026302	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	66	206	0	ENST00000405192.2:c.142C>T	p.Gln48Ter	p.Q48*	ENST00000405192	NM_001163147.1	48	Caa/Taa	4/12	1	2	FACETS	0.972	0.851	1	0.972	0.851	1	CLONAL	1	TRUE	1	0.43093837797023	2		206	315	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434506	121434506	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	90	439	0	ENST00000257555.6:c.1270C>G	p.Pro424Ala	p.P424A	ENST00000257555		424	Cct/Gct	6/10	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.43093837797023	2		439	415	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631815	67631815	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	93	385	0	ENST00000272342.5:c.2001G>C	p.Glu667Asp	p.E667D	ENST00000272342	NM_019002.3	667	gaG/gaC	5/6	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.43093837797023	2		385	423	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139055	50139055	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	179	322	0	ENST00000246792.3:c.508G>C	p.Glu170Gln	p.E170Q	ENST00000246792	NM_006270.3	170	Gag/Cag	5/6	0.43093837797023	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.43093837797023	3		322	423	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677839	58677839	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	91	415	0	ENST00000305921.3:c.64G>C	p.Glu22Gln	p.E22Q	ENST00000305921	NM_003620.3	22	Gag/Cag	1/6	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.43093837797023	2		415	396	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041381	42041381	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	151	474	0	ENST00000219905.7:c.5576C>A	p.Ser1859Tyr	p.S1859Y	ENST00000219905	NM_001164273.1	1859	tCt/tAt	17/24	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.43093837797023	2		474	555	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331688	8331688	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	113	328	0	ENST00000356435.5:c.5428G>C	p.Glu1810Gln	p.E1810Q	ENST00000356435		1810	Gag/Cag	33/35	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.43093837797023	2		328	468	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0066533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	44	181	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.739283150849918	2	FACETS	0.876	0.753	1	0.438	0.376	0.503	CLONAL	1	TRUE	0	0.772487350099448	2		181	130	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971184	21971184	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs201208890	NA	P-0066533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	45	504	0	ENST00000579755.1:c.217A>C	p.Ser73Arg	p.S73R	ENST00000579755		73	Agt/Cgt	2/3	0.713597437910492	0	FACETS		NA	1			1	NA	1	TRUE	0	0.772487350099448	0		504	117	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076862	41076862	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs750249800	NA	P-0066533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	43	328	0	ENST00000373198.4:c.1558G>A	p.Glu520Lys	p.E520K	ENST00000373198	NM_133170.3	520	Gag/Aag	9/32	0.174690173443337	3	FACETS	0.536	0.451	0.629			1	INDETERMINATE	1	TRUE	NA	0.772487350099448	3		328	288	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493621	56493621	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1343971705	NA	P-0066533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	77	518	0	ENST00000267101.3:c.2938-1G>T		p.X980_splice	ENST00000267101	NM_001982.3	980			0.772487350099448	3	FACETS	0.555	0.488	0.626	0.277	0.244	0.313	SUBCLONAL	1	TRUE	1	0.772487350099448	3		518	498	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255375	16255375	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	138	527	0	ENST00000375759.3:c.2640G>C	p.Leu880Phe	p.L880F	ENST00000375759	NM_015001.2	880	ttG/ttC	11/15	1	2	FACETS	0.893	0.821	0.967	0.893	0.821	0.967	CLONAL	1	TRUE	1	0.772487350099448	2		527	400	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951847	2951847	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868687398	NA	P-0066533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	95	448	0	ENST00000396946.4:c.3103G>A	p.Glu1035Lys	p.E1035K	ENST00000396946	NM_032415.4	1035	Gaa/Aaa	23/25	0.548666429451747	4	FACETS	0.89	0.795	0.989			1	CLONAL	1	TRUE	NA	0.772487350099448	4		448	490	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575080	48575080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	95	359	0	ENST00000342988.3:c.274C>T	p.His92Tyr	p.H92Y	ENST00000342988	NM_005359.5	92	Cat/Tat	3/12	0.73517053295842	1	FACETS	0.883	0.811	0.954	0.883	0.811	0.954	CLONAL	1	TRUE	0	0.772487350099448	1		359	171	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542357	187542357	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs769432838	NA	P-0066533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	24	558	0	ENST00000441802.2:c.5383C>T	p.Arg1795Ter	p.R1795*	ENST00000441802	NM_005245.3	1795	Cga/Tga	10/27	1	2	FACETS	0.165	0.129	0.206	0.165	0.129	0.206	SUBCLONAL	1	TRUE	1	0.772487350099448	2		558	377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs587781702	NA	P-0066533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	243	555	0	ENST00000269305.4:c.920-1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.739283150849918	2	FACETS	0.904	0.865	0.941	0.904	0.865	0.941	CLONAL	2	TRUE	0	0.772487350099448	2		555	348	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307256	118307256	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	58	217	0	ENST00000534358.1:c.29C>G	p.Pro10Arg	p.P10R	ENST00000534358	NM_005933.3	10	cCc/cGc	1/36	1	2	FACETS	0.894	0.784	1	0.894	0.784	1	CLONAL	1	TRUE	1	0.772487350099448	2		217	168	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354506	91354506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779179608	NA	P-0066533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	127	479	0	ENST00000355112.3:c.3946G>A	p.Asp1316Asn	p.D1316N	ENST00000355112	NM_000057.2	1316	Gac/Aac	21/22	0.174690173443337	3	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.772487350099448	3		479	329	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260219	19260219	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	132	481	0	ENST00000162023.5:c.74A>C	p.Lys25Thr	p.K25T	ENST00000162023		25	aAg/aCg	7/13	0.716462972090453	3	FACETS	1	0.963	1	0.547	0.501	0.595	CLONAL	1	TRUE	1	0.772487350099448	3		481	433	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739717	41739717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	89	544	0	ENST00000242208.4:c.256G>A	p.Ala86Thr	p.A86T	ENST00000242208	NM_002192.2	86	Gcg/Acg	2/3	0.772487350099448	4	FACETS	0.853	0.759	0.952	0.426	0.379	0.476	CLONAL	1	TRUE	2	0.772487350099448	4		544	479	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958589	175958589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	86	352	0	ENST00000367669.3:c.1756C>T	p.Arg586Cys	p.R586C	ENST00000367669	NM_022457.5	586	Cgt/Tgt	16/20	0.738377629723756	3	FACETS	0.916	0.818	1	0.458	0.409	0.51	CLONAL	1	TRUE	1	0.772487350099448	3		352	337	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74859040	74859041	+	protein_altering_variant	In_Frame_Ins	INS	-	-	GAG	novel	NA	P-0066533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	74	251	0	ENST00000284811.8:c.163_164insCTC	p.Asn55delinsThrHis	p.N55delinsTH	ENST00000284811		55	aac/aCTCac	4/4	0.772487350099448	3	FACETS	1	0.895	1	0.337	0.298	0.377	CLONAL	1	TRUE	0	0.772487350099448	3		251	263	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007737	45007744	+	frameshift_variant	Frame_Shift_Del	DEL	AATGGAGA	AATGGAGA	-	novel	NA	P-0066533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	132	489	0	ENST00000558401.1:c.184_191del	p.Asn62GlufsTer3	p.N62Efs*3	ENST00000558401	NM_004048.2	62	AATGGAGAg/g	2/4	1	2	FACETS	0.921	0.846	0.998	0.921	0.846	0.998	CLONAL	1	TRUE	1	0.772487350099448	2		489	371	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38949905	38949905	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1384004906	NA	P-0066533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	117	440	0	ENST00000357387.3:c.4045G>A	p.Glu1349Lys	p.E1349K	ENST00000357387	NM_152756.3	1349	Gaa/Aaa	31/38	0.739789043824017	4	FACETS	0.967	0.876	1			1	CLONAL	1	TRUE	NA	0.772487350099448	4		440	555	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099872	157099872	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	30	415	1	ENST00000346085.5:c.809C>A	p.Ser270Tyr	p.S270Y	ENST00000346085	NM_020732.3	270	tCc/tAc	1/20	1	2	FACETS	0.301	0.243	0.366	0.301	0.243	0.366	SUBCLONAL	1	TRUE	1	0.772487350099448	2		416	258	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954317	48954317	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	27	269	0	ENST00000267163.4:c.1438A>T	p.Asn480Tyr	p.N480Y	ENST00000267163	NM_000321.2	480	Aac/Tac	16/27	0.730882541063675	4	FACETS	0.309	0.245	0.382	0.077	0.061	0.096	SUBCLONAL	1	TRUE	0	0.772487350099448	4		269	401	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309580	30309580	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	148	534	0	ENST00000307677.4:c.442G>T	p.Gly148Trp	p.G148W	ENST00000307677	NM_138578.1	148	Ggg/Tgg	2/3	0.738377629723756	3	FACETS	0.989	0.909	1	0.495	0.454	0.536	CLONAL	1	TRUE	1	0.772487350099448	3		534	537	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670119	86670119	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0066533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	76	273	0	ENST00000274376.6:c.1916C>G	p.Ser639Ter	p.S639*	ENST00000274376	NM_002890.2	639	tCa/tGa	14/25	0.648429829147415	1	FACETS	0.951	0.868	1	0.951	0.868	1	CLONAL	1	TRUE	0	0.772487350099448	1		273	127	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929178	32929178	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	81	390	0	ENST00000380152.3:c.7188G>C	p.Leu2396Phe	p.L2396F	ENST00000380152		2396	ttG/ttC	14/27	0.730882541063675	4	FACETS	0.771	0.682	0.867	0.193	0.17	0.217	SUBCLONAL	1	TRUE	0	0.772487350099448	4		390	482	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0066535-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	76	376	0	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	1	2	FACETS	0.845	0.742	0.957	0.845	0.742	0.957	CLONAL	1	TRUE	1	0.29	2		376	620	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0066535-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	79	310	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.923	0.813	1	0.923	0.813	1	CLONAL	1	TRUE	1	0.29	2		310	590	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421555	32421555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066535-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	61	397	0	ENST00000332351.3:c.1037C>T	p.Thr346Met	p.T346M	ENST00000332351	NM_024426.4	346	aCg/aTg	6/10	1	2	FACETS	0.797	0.688	0.915	0.797	0.688	0.915	CLONAL	1	TRUE	1	0.29	2		397	528	SUCCESS
APC	324	MSKCC	GRCh37	5	112175322	112175322	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066535-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	139	351	0	ENST00000257430.4:c.4031C>A	p.Ser1344Ter	p.S1344*	ENST00000257430	NM_000038.5	1344	tCa/tAa	16/16	0.287000161519504	2	FACETS	0.864	0.79	0.94	0.864	0.79	0.94	CLONAL	2	TRUE	0	0.29	2		351	555	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509348	46509348	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066535-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	83	326	0	ENST00000262741.5:c.1383A>C	p.Arg461Ser	p.R461S	ENST00000262741	NM_003629.3	461	agA/agC	10/10	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.29	2		326	567	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426606	49426611	+	inframe_deletion	In_Frame_Del	DEL	TGTTGC	TGTTGC	-	rs748029700	NA	P-0066535-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	109	591	0	ENST00000301067.7:c.11877_11882del	p.Gln3964_Gln3965del	p.Q3964_Q3965del	ENST00000301067	NM_003482.3	3959	caGCAACAa/caa	39/54	1	2	FACETS	0.864	0.775	0.958	0.864	0.775	0.958	CLONAL	1	TRUE	1	0.29	2		591	870	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40460307	40460307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1220900989	NA	P-0066535-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	65	354	0	ENST00000345506.4:c.2018G>A	p.Arg673His	p.R673H	ENST00000345506	NM_003152.3	673	cGc/cAc	17/20	1	2	FACETS	0.717	0.622	0.821	0.717	0.622	0.821	SUBCLONAL	1	TRUE	1	0.29	2		354	625	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176337	24176337	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066535-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	66	237	0	ENST00000263121.7:c.1128G>T	p.Arg376Ser	p.R376S	ENST00000263121	NM_003073.3	376	agG/agT	9/9	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.29	2		237	402	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29279846	29279847	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCC	rs958418836	NA	P-0066535-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	16	117	0	ENST00000544604.2:c.107_109dup	p.Pro36dup	p.P36dup	ENST00000544604	NM_001206998.1	36	ctg/ctGCCg	1/9	1	2	FACETS	0.613	0.455	0.8	0.613	0.455	0.8	SUBCLONAL	1	TRUE	1	0.29	2		117	180	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0066536-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	65	215	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.460801286480887	3	FACETS	1	0.934	1	0.555	0.484	0.63	CLONAL	1	TRUE	1	0.460560358957809	3		215	313	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517201	NA	P-0066536-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	37	237	0	ENST00000263967.3:c.1637A>C	p.Gln546Pro	p.Q546P	ENST00000263967	NM_006218.2	546	cAg/cCg	10/21	0.449812994466697	3	FACETS	0.772	0.64	0.918	0.257	0.213	0.306	CLONAL	1	TRUE	0	0.460560358957809	3		237	256	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433745	149433745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537011691	NA	P-0066536-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	123	375	0	ENST00000286301.3:c.2806G>A	p.Gly936Ser	p.G936S	ENST00000286301	NM_005211.3	936	Ggc/Agc	22/22	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.460560358957809	2		375	534	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119050	70119050	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066536-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	341	441	1	ENST00000245479.2:c.622C>T	p.Gln208Ter	p.Q208*	ENST00000245479	NM_000346.3	208	Cag/Tag	2/3	0.460801286480887	4	FACETS	0.916	0.872	0.961	0.916	0.872	0.961	CLONAL	3	TRUE	1	0.460560358957809	4		442	787	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029193	26029195	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0066536-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	139	279	0	ENST00000435504.4:c.155_157del	p.Pro52del	p.P52del	ENST00000435504		52	cCTCtt/ctt	4/13	0.460801286480887	3	FACETS	0.91	0.837	0.985	0.91	0.837	0.985	CLONAL	2	TRUE	1	0.460560358957809	3		279	408	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812259	212812259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs991337964	NA	P-0066536-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	61	360	0	ENST00000342788.4:c.317G>A	p.Arg106His	p.R106H	ENST00000342788	NM_005235.2	106	cGt/cAt	3/28	0.460801286480887	3	FACETS	0.797	0.69	0.912	0.398	0.345	0.456	CLONAL	1	TRUE	1	0.460560358957809	3		360	409	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031708	36031708	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066536-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	275	507	0	ENST00000358208.4:c.1537G>A	p.Glu513Lys	p.E513K	ENST00000358208		513	Gag/Aag	12/12	0.460801286480887	4	FACETS	1	0.975	1	0.708	0.667	0.75	CLONAL	2	TRUE	1	0.460560358957809	4		507	821	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415669	152415669	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066536-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	136	385	0	ENST00000206249.3:c.1519C>A	p.Leu507Ile	p.L507I	ENST00000206249	NM_000125.3	507	Ctc/Atc	7/8	0.460801286480887	3	FACETS	1	0.941	1	0.521	0.475	0.57	CLONAL	1	TRUE	1	0.460560358957809	3		385	697	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008497	70008497	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066536-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	146	356	0	ENST00000394351.3:c.784C>A	p.Gln262Lys	p.Q262K	ENST00000394351	NM_000248.3	262	Caa/Aaa	8/9	0.453817479614194	2	FACETS	1	0.929	1	0.508	0.465	0.553	CLONAL	1	TRUE	0	0.460560358957809	2		356	624	SUCCESS
APC	324	MSKCC	GRCh37	5	112173846	112173846	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0066536-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	90	362	0	ENST00000257430.4:c.2555T>A	p.Leu852Ter	p.L852*	ENST00000257430	NM_000038.5	852	tTg/tAg	16/16	1	2	FACETS	0.857	0.764	0.955	0.857	0.764	0.955	CLONAL	1	TRUE	1	0.460560358957809	2		362	456	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117750	70117750	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066536-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	147	482	0	ENST00000245479.2:c.218T>G	p.Ile73Ser	p.I73S	ENST00000245479	NM_000346.3	73	aTc/aGc	1/3	0.460801286480887	4	FACETS	1	0.951	1	0.353	0.322	0.386	CLONAL	1	TRUE	1	0.460560358957809	4		482	880	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411144	63411144	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066536-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	40	196	0	ENST00000330258.3:c.2023C>T	p.Gln675Ter	p.Q675*	ENST00000330258	NM_152424.3	675	Cag/Tag	2/2	0.39324987435685	2	FACETS	0.463	0.385	0.549			1	SUBCLONAL	1	TRUE	NA	0.460560358957809	2		196	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0066537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	188	402	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.360970391103731	2	FACETS	0.976	0.91	1	0.976	0.91	1	CLONAL	2	TRUE	0	0.399723444752857	2		402	482	SUCCESS
BLM	641	MSKCC	GRCh37	15	91333930	91333930	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	169	341	0	ENST00000355112.3:c.2875C>G	p.Arg959Gly	p.R959G	ENST00000355112	NM_000057.2	959	Cga/Gga	15/22	0.313784044252367	5	FACETS	1	0.953	1	0.697	0.643	0.752	CLONAL	2	TRUE	2	0.399723444752857	5		341	647	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	90	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.484476935150429	3	FACETS	0.907	0.807	1	0.453	0.403	0.506	CLONAL	1	TRUE	1	0.484476935150429	3		341	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0066538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	272	463	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.484476935150429	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.484476935150429	2		463	486	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577265	64577265	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555166469	NA	P-0066538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	347	466	0	ENST00000312049.6:c.317A>G	p.Tyr106Cys	p.Y106C	ENST00000312049	NM_130799.2	106	tAt/tGt	2/10	0.438444796423341	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	1	0.484476935150429	4		466	678	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6222401	6222412	+	inframe_deletion	In_Frame_Del	DEL	GGGGTGGGGGTG	GGGGTGGGGGTG	-	rs753690040	NA	P-0066538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	12	278	0	ENST00000252674.7:c.830_841del	p.Pro277_Pro280del	p.P277_P280del	ENST00000252674	NM_005934.3	277	cCACCCCCACCCCgg/cgg	6/12	1	2	FACETS	0.211	0.148	0.288	0.211	0.148	0.288	SUBCLONAL	1	TRUE	1	0.484476935150429	2		278	235	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739882	41739882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	154	351	0	ENST00000242208.4:c.91G>A	p.Ala31Thr	p.A31T	ENST00000242208	NM_002192.2	31	Gcg/Acg	2/3	0.303332154312744	4	FACETS	0.832	0.766	0.901	0.832	0.766	0.901	CLONAL	2	TRUE	2	0.484476935150429	4		351	567	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349250	11349250	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	60	396	0	ENST00000332029.2:c.86C>T	p.Ser29Phe	p.S29F	ENST00000332029	NM_003745.1	29	tCc/tTc	2/2	0.251794637354729	1	FACETS	0.565	0.49	0.646	0.565	0.49	0.646	INDETERMINATE	1	TRUE	0	0.484476935150429	1		396	332	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447621	187447621	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778230721	NA	P-0066538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	50	523	0	ENST00000232014.4:c.572C>T	p.Pro191Leu	p.P191L	ENST00000232014	NM_001130845.1	191	cCg/cTg	5/10	0.247113665825346	4	FACETS	0.417	0.353	0.488	0.208	0.176	0.244	INDETERMINATE	1	TRUE	2	0.484476935150429	4		523	735	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11150198	11150198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769555654	NA	P-0066538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	72	304	0	ENST00000358026.2:c.4235G>A	p.Arg1412His	p.R1412H	ENST00000358026	NM_001128849.1	1412	cGt/cAt	30/36	1	2	FACETS	0.649	0.569	0.735	0.649	0.569	0.735	SUBCLONAL	1	TRUE	1	0.484476935150429	2		304	458	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215617260	215617260	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	51	307	0	ENST00000260947.4:c.1588C>A	p.Pro530Thr	p.P530T	ENST00000260947	NM_000465.2	530	Cct/Act	7/11	0.481081627997832	3	FACETS	0.598	0.509	0.696	0.299	0.254	0.348	SUBCLONAL	1	TRUE	1	0.484476935150429	3		307	437	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73649883	73649884	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	24	331	0	ENST00000377687.4:c.1234dup	p.Trp412LeufsTer8	p.W412Lfs*8	ENST00000377687	NM_001730.3	411	-/T	4/4	0.484476935150429	2	FACETS	0.241	0.188	0.302	0.121	0.094	0.151	SUBCLONAL	1	TRUE	0	0.484476935150429	2		331	411	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792088	42792088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	36	394	1	ENST00000575354.2:c.892C>T	p.Arg298Trp	p.R298W	ENST00000575354	NM_015125.3	298	Cgg/Tgg	6/20	0.237034100675918	5	FACETS	0.431	0.353	0.518	0.144	0.117	0.173	INDETERMINATE	1	TRUE	2	0.484476935150429	5		395	596	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443910	18443910	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	119	256	0	ENST00000266497.5:c.883G>C	p.Asp295His	p.D295H	ENST00000266497		295	Gat/Cat	3/31	0.579373466457328	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.579373466457328	1		256	225	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100610	67100610	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	137	303	0	ENST00000412916.2:c.308T>G	p.Leu103Arg	p.L103R	ENST00000412916		103	cTg/cGg	4/6	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.579373466457328	2		303	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0066539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	156	375	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.20135052936205	3	FACETS	1	0.985	1	0.433	0.398	0.468	INDETERMINATE	1	TRUE	0	0.579373466457328	3		375	535	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191805	123191805	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	113	255	0	ENST00000218089.9:c.1400del	p.Phe467SerfsTer3	p.F467Sfs*3	ENST00000218089	NM_001042749.1	465	gTt/gt	15/35	0.579373466457328	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.579373466457328	1		255	256	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31238972	31238972	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	12	32	0	ENST00000376228.5:c.497T>A	p.Ile166Asn	p.I166N	ENST00000376228	NM_002117.5	166	aTc/aAc	3/8	0.109350107318953	5	FACETS	0.79	0.573	1	0.527	0.382	0.692	INDETERMINATE	2	TRUE	2	0.579373466457328	5		32	49	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273500	38273500	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	131	373	0	ENST00000425967.3:c.1835T>A	p.Leu612Gln	p.L612Q	ENST00000425967	NM_001174067.1	612	cTg/cAg	14/19	0.188192508416112	2	FACETS	1	0.949	1	0.526	0.481	0.572	INDETERMINATE	1	TRUE	0	0.579373466457328	2		373	430	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236087	108236087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781894	NA	P-0066576-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	315	476	4	ENST00000278616.4:c.9023G>A	p.Arg3008His	p.R3008H	ENST00000278616	NM_000051.3	3008	cGt/cAt	63/63	0.835930602966419	1	FACETS	0.966	0.93	1	0.966	0.93	1	CLONAL	1	TRUE	0	0.835930602966419	1		480	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0066585-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	327	447	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.310076180372951	2	FACETS	0.958	0.906	1	0.958	0.906	1	CLONAL	2	TRUE	0	0.325803044396086	2		447	1048	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543797	212543797	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs756983861	NA	P-0066585-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	105	372	0	ENST00000342788.4:c.1602G>C	p.Glu534Asp	p.E534D	ENST00000342788	NM_005235.2	534	gaG/gaC	13/28	1	2	FACETS	0.822	0.736	0.913	0.822	0.736	0.913	CLONAL	1	TRUE	1	0.325803044396086	2		372	784	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112025307	112025307	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0066585-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	370	251	0	ENST00000368678.4:c.444-2A>G		p.X148_splice	ENST00000368678		148			0.226885322684193	4	FACETS	0.988	0.944	1			1	CLONAL	4	TRUE	NA	0.325803044396086	4		251	762	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404549	139405264	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTGTCTGGTGGGGAGCCCCAGCACCCACAGGCTGCGTCACACCCGTCTCCTGTGCTTGGGGTCTCTCTCCCCACCTGCTCCTGTCCTCAAGCTCCAGGGCAGGGGGCAGCTTTGCAGGCTTCACAGACCGAGCAGGGGAGGAGAGACAGTTCTTGCCTCTGCCTGCCAGGTGATGCCAGCAAGACCCCCGGCTTCTGCCAACCTCAACCTCTGTGAAGCAGGGCTGGGAGGCCTGAGAGCCCTGGCCTGCAGCGGGGCCCGATGAGCCAGGCGGGAGTGCAGGCCGGGCCCGAGCCATCCTCGGCTCAGTGAAGAGCCGTGGGAGGGGCTCTCGTGACTCTTCCGCGAAGTGCAGGGAGGAGCAAGCCGGCTCTGGGGCCCTCCTGAACCACCCTGGCCATCCCTCAGCACATCCCCCACACCTGACCCAACCCTCCCCGGCCACACTCCGGCCTCCCTGGGTGCTTATGGCCAGCACCATGCGCACCAACCCTGCCCGGGGGAACTGAGGCCTGAGAGCTTCCTGGAGGAGGCCAGAGCCGCGGGGCTACTCACTGGGCCGGCAGTCGTCGATGTCGGTCTCGCAGTTGCGCCCACTGTAGCCGGCCTGGCAGTGGCAGCGGTAGCCGCCGTGGGTGTTCTGGCAGGATGCGCCGTGCCGGCACGGGCTCAGAACGCACTCGTTGATGTCGACCTCACAGGTCTGCCCTGCGGG	GGTGTCTGGTGGGGAGCCCCAGCACCCACAGGCTGCGTCACACCCGTCTCCTGTGCTTGGGGTCTCTCTCCCCACCTGCTCCTGTCCTCAAGCTCCAGGGCAGGGGGCAGCTTTGCAGGCTTCACAGACCGAGCAGGGGAGGAGAGACAGTTCTTGCCTCTGCCTGCCAGGTGATGCCAGCAAGACCCCCGGCTTCTGCCAACCTCAACCTCTGTGAAGCAGGGCTGGGAGGCCTGAGAGCCCTGGCCTGCAGCGGGGCCCGATGAGCCAGGCGGGAGTGCAGGCCGGGCCCGAGCCATCCTCGGCTCAGTGAAGAGCCGTGGGAGGGGCTCTCGTGACTCTTCCGCGAAGTGCAGGGAGGAGCAAGCCGGCTCTGGGGCCCTCCTGAACCACCCTGGCCATCCCTCAGCACATCCCCCACACCTGACCCAACCCTCCCCGGCCACACTCCGGCCTCCCTGGGTGCTTATGGCCAGCACCATGCGCACCAACCCTGCCCGGGGGAACTGAGGCCTGAGAGCTTCCTGGAGGAGGCCAGAGCCGCGGGGCTACTCACTGGGCCGGCAGTCGTCGATGTCGGTCTCGCAGTTGCGCCCACTGTAGCCGGCCTGGCAGTGGCAGCGGTAGCCGCCGTGGGTGTTCTGGCAGGATGCGCCGTGCCGGCACGGGCTCAGAACGCACTCGTTGATGTCGACCTCACAGGTCTGCCCTGCGGG	-	novel	NA	P-0066585-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	38	79	0	ENST00000277541.6:c.2588-7_2741-136del		p.X863_splice	ENST00000277541	NM_017617.3	863		17/34	0.319811069937111	3	FACETS	1	0.918	1	0.59	0.491	0.698	CLONAL	1	TRUE	1	0.325803044396086	3		79	230	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0066606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	101	486	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.277912183114649	2		486	583	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499706	8499706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	86	488	0	ENST00000356435.5:c.2263G>A	p.Glu755Lys	p.E755K	ENST00000356435		755	Gaa/Aaa	14/35	0.269947577743926	1	FACETS	0.943	0.836	1	0.943	0.836	1	CLONAL	1	TRUE	0	0.277912183114649	1		488	565	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453135	140453136	+	missense_variant	Missense_Mutation	DNP	CA	CA	TT	rs121913377	NA	P-0066606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	100	355	0	ENST00000288602.6:c.1799_1800delinsAA	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTG/gAA	15/18	0.277912183114649	2	FACETS	0.847	0.761	0.936	0.847	0.761	0.936	CLONAL	2	TRUE	0	0.277912183114649	2		355	425	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031690	69031690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371787029	NA	P-0066606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	70	434	0	ENST00000288368.4:c.3445C>T	p.Arg1149Cys	p.R1149C	ENST00000288368	NM_024870.2	1149	Cgc/Tgc	28/40	0.277912183114649	3	FACETS	0.922	0.804	1	0.461	0.402	0.525	CLONAL	1	TRUE	1	0.277912183114649	3		434	622	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041623	42041623	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	112	567	0	ENST00000219905.7:c.5818C>T	p.Gln1940Ter	p.Q1940*	ENST00000219905	NM_001164273.1	1940	Cag/Tag	17/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.277912183114649	2		567	666	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056238	27056238	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	85	501	1	ENST00000324856.7:c.1234C>T	p.Gln412Ter	p.Q412*	ENST00000324856	NM_006015.4	412	Cag/Tag	2/20	1	2	FACETS	0.904	0.799	1	0.904	0.799	1	CLONAL	1	TRUE	1	0.277912183114649	2		502	677	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189585700	189585700	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	49	433	0	ENST00000264731.3:c.961A>T	p.Ile321Phe	p.I321F	ENST00000264731	NM_003722.4	321	Att/Ttt	7/14	1	2	FACETS	0.681	0.577	0.795	0.681	0.577	0.795	SUBCLONAL	1	TRUE	1	0.277912183114649	2		433	518	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973116	25973116	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	93	474	0	ENST00000435504.4:c.1309C>T	p.Gln437Ter	p.Q437*	ENST00000435504		437	Caa/Taa	12/13	1	2	FACETS	0.97	0.863	1	0.97	0.863	1	CLONAL	1	TRUE	1	0.277912183114649	2		474	690	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447512	12447512	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	80	502	0	ENST00000287820.6:c.751A>C	p.Ile251Leu	p.I251L	ENST00000287820	NM_015869.4	251	Ata/Cta	5/7	1	2	FACETS	0.898	0.791	1	0.898	0.791	1	CLONAL	1	TRUE	1	0.277912183114649	2		502	641	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0066608-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	352	416	0	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.844595635424888	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.87005951353571	2		416	402	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0066608-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	200	473	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.825	0.77	0.881	0.825	0.77	0.881	CLONAL	1	TRUE	1	0.87005951353571	2		473	557	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937611	76937615	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTT	CTTTT	-	novel	NA	P-0066608-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	166	111	0	ENST00000373344.5:c.3133_3137del	p.Lys1045Ter	p.K1045*	ENST00000373344	NM_000489.3	1045	AAAAGt/t	9/35	1	1	FACETS	0.962	0.916	1	0.962	0.916	1	CLONAL	1	TRUE	0	0.87005951353571	1		111	224	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577098	7577099	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTCCC	novel	NA	P-0066609-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	148	595	0	ENST00000269305.4:c.835_839dup	p.Asp281GlyfsTer66	p.D281Gfs*66	ENST00000269305	NM_001126112.2	280	aga/agGGGAGa	8/11	0.216640410732314	2	FACETS	0.861	0.791	0.933	1	0.984	1	CLONAL	3	TRUE	0	0.216640410732314	2		595	529	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0066610-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	107	248	2	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.194912225663546	2	FACETS	0.893	0.802	0.988	0.893	0.802	0.988	CLONAL	2	TRUE	0	0.194912225663546	2		250	615	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0066610-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	157	630	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.18586849161785	2	FACETS	0.932	0.854	1	0.932	0.854	1	CLONAL	2	TRUE	0	0.194912225663546	2		630	864	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917794	29917794	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201750304	NA	P-0066610-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	113	505	14	ENST00000389048.3:c.874C>T	p.Arg292Cys	p.R292C	ENST00000389048	NM_004304.4	292	Cgc/Tgc	3/29	0.0730397372070672	4	FACETS	1	0.937	1	1	0.937	1	INDETERMINATE	2	TRUE	2	0.194912225663546	4		519	658	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526547	66526547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066610-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	75	526	2	ENST00000358598.2:c.1103G>A	p.Arg368Gln	p.R368Q	ENST00000358598	NM_212471.2	368	cGa/cAa	11/11	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.194912225663546	2		528	680	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495242	212495242	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066610-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	36	455	0	ENST00000342788.4:c.2024T>A	p.Val675Asp	p.V675D	ENST00000342788	NM_005235.2	675	gTt/gAt	17/28	0.0730397372070672	4	FACETS	0.659	0.54	0.793	0.329	0.27	0.397	INDETERMINATE	1	TRUE	2	0.194912225663546	4		455	670	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270156	66270156	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs142184664	NA	P-0066610-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	34	511	0	ENST00000273854.3:c.1726G>T	p.Ala576Ser	p.A576S	ENST00000273854	NM_004439.5	576	Gct/Tct	8/18	1	2	FACETS	0.565	0.46	0.683	0.565	0.46	0.683	SUBCLONAL	1	TRUE	1	0.194912225663546	2		511	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0066611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	387	389	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.795886103703476	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.795886103703476	1		389	501	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523142	176523142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778323767	NA	P-0066611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	323	644	0	ENST00000292408.4:c.1906G>A	p.Gly636Ser	p.G636S	ENST00000292408	NM_213647.1	636	Ggc/Agc	14/18	0.789578331062266	3	FACETS	1	0.981	1	0.36	0.34	0.38	CLONAL	1	TRUE	0	0.795886103703476	3		644	1052	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21351565	21351565	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	44	525	0	ENST00000215739.8:c.2451del	p.Leu818TrpfsTer4	p.L818Wfs*4	ENST00000215739	NM_006767.3	817	ctG/ct	21/21	0.795886103703476	1	FACETS	0.156	0.13	0.184	0.156	0.13	0.184	SUBCLONAL	1	TRUE	0	0.795886103703476	1		525	427	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21351542	21351542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776893978	NA	P-0066611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	43	534	0	ENST00000215739.8:c.2428C>T	p.Arg810Trp	p.R810W	ENST00000215739	NM_006767.3	810	Cgg/Tgg	21/21	0.795886103703476	1	FACETS	0.151	0.126	0.178	0.151	0.126	0.178	SUBCLONAL	1	TRUE	0	0.795886103703476	1		534	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0066616-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	71	545	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.506537906495372	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	4	TRUE	0	0.504348961771484	4		546	100	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206942060	206942060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066616-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	21	446	0	ENST00000423557.1:c.458G>A	p.Gly153Asp	p.G153D	ENST00000423557	NM_000572.2	153	gGc/gAc	5/5	0.420904348182583	5	FACETS	0.881	0.695	1			1	CLONAL	2	TRUE	NA	0.504348961771484	5		446	83	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206942038	206942038	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066616-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	18	439	0	ENST00000423557.1:c.480G>C	p.Glu160Asp	p.E160D	ENST00000423557	NM_000572.2	160	gaG/gaC	5/5	0.420904348182583	5	FACETS	0.814	0.628	1			1	CLONAL	2	TRUE	NA	0.504348961771484	5		439	77	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41228504	41228504	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs80358063	NA	P-0066616-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	16	309	0	ENST00000357654.3:c.4484+1G>A		p.X1495_splice	ENST00000357654	NM_007294.3	1495			0.506537906495372	1	FACETS	0.765	0.609	0.92	1	0.924	1	CLONAL	2	TRUE	0	0.504348961771484	1		309	31	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271287	18271287	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200357667	NA	P-0066616-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	36	534	0	ENST00000222254.8:c.329C>T	p.Thr110Ile	p.T110I	ENST00000222254	NM_005027.3	110	aCa/aTa	3/16	0.504348961771484	6	FACETS	0.913	0.762	1	0.457	0.381	0.539	CLONAL	2	TRUE	2	0.504348961771484	6		534	157	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670734	86670734	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0066616-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	23	225	0	ENST00000274376.6:c.2011+1G>C		p.X671_splice	ENST00000274376	NM_002890.2	671			0.506537906495372	2	FACETS	1	0.839	1	1	0.839	1	CLONAL	2	TRUE	0	0.504348961771484	2		225	45	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005265	150005302	+	frameshift_variant	Frame_Shift_Del	DEL	AATGCCTCTCTGTCCTTGATTAGGAGGATTCATGGGGG	AATGCCTCTCTGTCCTTGATTAGGAGGATTCATGGGGG	-	novel	NA	P-0066616-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	47	528	0	ENST00000253339.5:c.923_960del	p.Ser308Ter	p.S308*	ENST00000253339		308	tCCCCCATGAATCCTCCTAATCAAGGACAGAGAGGCATT/t	3/7	0.506537906495372	5	FACETS	0.909	0.815	0.999	1	0.954	1	CLONAL	5	TRUE	1	0.504348961771484	5		528	72	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859600	151859600	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066616-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	30	607	0	ENST00000262189.6:c.11062G>T	p.Asp3688Tyr	p.D3688Y	ENST00000262189	NM_170606.2	3688	Gat/Tat	43/59	0.504348961771484	5	FACETS	1	0.923	1	0.81	0.673	0.954	CLONAL	2	TRUE	2	0.504348961771484	5		607	86	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0066617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	267	758	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.361497790025943	2	FACETS	0.757	0.713	0.801	0.757	0.713	0.801	SUBCLONAL	2	TRUE	0	0.484710280946765	2		758	728	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061291	38061291	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	66	563	1	ENST00000250448.2:c.698G>A	p.Arg233His	p.R233H	ENST00000250448	NM_004496.3	233	cGc/cAc	2/2	0.463867214949388	2	FACETS	0.503	0.437	0.575	0.252	0.218	0.288	SUBCLONAL	1	TRUE	0	0.484710280946765	2		564	541	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805160	43805160	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs913913702	NA	P-0066617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	94	608	0	ENST00000372470.3:c.610T>C	p.Ser204Pro	p.S204P	ENST00000372470	NM_005373.2	204	Tct/Cct	4/12	0.397434679918476	3	FACETS	0.675	0.6	0.754	0.225	0.2	0.252	SUBCLONAL	1	TRUE	0	0.484710280946765	3		608	714	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830445	72830445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	76	240	0	ENST00000268489.5:c.6136C>T	p.Pro2046Ser	p.P2046S	ENST00000268489	NM_006885.3	2046	Ccc/Tcc	9/10	0.484710280946765	1	FACETS	0.935	0.832	1	0.935	0.832	1	CLONAL	1	TRUE	0	0.484710280946765	1		240	254	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805142	43805158	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAGGCCTCACTCAGC	CAGAGGCCTCACTCAGC	-	novel	NA	P-0066617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	88	581	0	ENST00000372470.3:c.593_609del	p.Gln198LeufsTer26	p.Q198Lfs*26	ENST00000372470	NM_005373.2	198	CAGAGGCCTCACTCAGCc/c	4/12	0.397434679918476	3	FACETS	0.621	0.549	0.696	0.207	0.183	0.232	SUBCLONAL	1	TRUE	0	0.484710280946765	3		581	727	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46715772	46715772	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	117	423	0	ENST00000371975.4:c.191G>C	p.Cys64Ser	p.C64S	ENST00000371975	NM_003579.3	64	tGt/tCt	3/18	0.397434679918476	3	FACETS	1	0.957	1	0.366	0.331	0.403	CLONAL	1	TRUE	0	0.484710280946765	3		423	546	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350006	15350006	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	129	523	0	ENST00000263377.2:c.3646A>C	p.Thr1216Pro	p.T1216P	ENST00000263377	NM_058243.2	1216	Aca/Cca	18/20	0.367827616150861	5	FACETS	1	0.969	1	0.386	0.35	0.424	CLONAL	1	TRUE	2	0.484710280946765	5		523	793	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439911	52439911	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1553645511	NA	P-0066617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	57	444	0	ENST00000460680.1:c.801G>C	p.Gln267His	p.Q267H	ENST00000460680	NM_004656.3	267	caG/caC	10/17	0.205248074452467	3	FACETS	0.494	0.424	0.571	0.165	0.141	0.191	INDETERMINATE	1	TRUE	0	0.484710280946765	3		444	591	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428433	72428433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	29	506	0	ENST00000477973.2:c.571G>A	p.Val191Ile	p.V191I	ENST00000477973	NM_012234.5	191	Gtt/Att	2/4	0.205248074452467	3	FACETS	0.426	0.342	0.521	0.142	0.114	0.174	INDETERMINATE	1	TRUE	0	0.484710280946765	3		506	349	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541895	187541895	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	204	554	0	ENST00000441802.2:c.5845G>C	p.Glu1949Gln	p.E1949Q	ENST00000441802	NM_005245.3	1949	Gag/Cag	10/27	0.470745468910876	3	FACETS	1	0.991	1	0.499	0.464	0.534	CLONAL	1	TRUE	0	0.484710280946765	3		554	699	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955174	17955174	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	275	501	0	ENST00000458235.1:c.53T>G	p.Leu18Arg	p.L18R	ENST00000458235	NM_000215.3	18	cTc/cGc	2/24	0.367827616150861	5	FACETS	0.993	0.933	1	0.662	0.622	0.703	CLONAL	2	TRUE	2	0.484710280946765	5		501	987	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152112	11152112	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	90	563	0	ENST00000358026.2:c.4396G>T	p.Asp1466Tyr	p.D1466Y	ENST00000358026	NM_001128849.1	1466	Gac/Tac	31/36	0.484710280946765	3	FACETS	0.548	0.485	0.615	0.274	0.242	0.308	SUBCLONAL	1	TRUE	1	0.484710280946765	3		563	842	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0066619-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	84	708	2	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.3370084204116	2		710	360	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0066619-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	154	757	4	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.338637192526887	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.3370084204116	3		761	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577505	7577505	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs745425759	NA	P-0066619-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	129	631	3	ENST00000269305.4:c.776A>T	p.Asp259Val	p.D259V	ENST00000269305	NM_001126112.2	259	gAc/gTc	7/11	0.282906909725428	3	FACETS	1	0.958	1			1	CLONAL	2	TRUE	NA	0.3370084204116	3		634	415	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575096	48575096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555685159	NA	P-0066619-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	67	646	4	ENST00000342988.3:c.290G>A	p.Arg97His	p.R97H	ENST00000342988	NM_005359.5	97	cGt/cAt	3/12	0.301726119659053	2	FACETS	0.777	0.683	0.876	0.777	0.683	0.876	SUBCLONAL	2	TRUE	0	0.3370084204116	2		650	256	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712823	43712823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28903077	NA	P-0066619-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	147	843	1	ENST00000382044.4:c.4361G>A	p.Arg1454Gln	p.R1454Q	ENST00000382044	NM_001141980.1	1454	cGa/cAa	21/28	0.27084983185791	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.3370084204116	3		844	463	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43699735	43699735	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137879443	NA	P-0066619-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	138	776	4	ENST00000382044.4:c.5780C>T	p.Thr1927Met	p.T1927M	ENST00000382044	NM_001141980.1	1927	aCg/aTg	28/28	0.27084983185791	3	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	1	0.3370084204116	3		780	465	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs770248150	NA	P-0066619-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	77	609	2	ENST00000311936.3:c.351A>T	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaT	4/5	0.338637192526887	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.3370084204116	3		611	226	SUCCESS
ALB	213	MSKCC	GRCh37	4	74282070	74282070	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs370819889	NA	P-0066619-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	47	489	1	ENST00000295897.4:c.1289C>T	p.Ala430Val	p.A430V	ENST00000295897	NM_000477.5	430	gCg/gTg	10/15	0.338637192526887	3	FACETS	0.976	0.838	1	0.976	0.838	1	CLONAL	2	TRUE	1	0.3370084204116	3		490	167	SUCCESS
APC	324	MSKCC	GRCh37	5	112175560	112175561	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCAGATAG	novel	NA	P-0066619-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	41	767	6	ENST00000257430.4:c.4272_4279dup	p.Pro1427GlnfsTer49	p.P1427Qfs*49	ENST00000257430	NM_000038.5	1423	-/CCAGATAG	16/16	0.338637192526887	3	FACETS	0.589	0.49	0.698	0.294	0.245	0.349	SUBCLONAL	1	TRUE	1	0.3370084204116	3		773	483	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029105	14029105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066619-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	79	629	3	ENST00000311895.7:c.1316C>T	p.Thr439Ile	p.T439I	ENST00000311895	NM_005236.2	439	aCc/aTc	8/11	0.284241007176985	4	FACETS	0.885	0.784	0.992	0.885	0.784	0.992	CLONAL	2	TRUE	2	0.3370084204116	4		632	354	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80057384	80057384	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066619-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	38	638	0	ENST00000265081.6:c.1783G>C	p.Asp595His	p.D595H	ENST00000265081	NM_002439.4	595	Gat/Cat	13/24	1	2	FACETS	0.744	0.618	0.884	0.744	0.618	0.884	SUBCLONAL	1	TRUE	1	0.3370084204116	2		638	303	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258986	153258986	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066619-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	39	613	1	ENST00000281708.4:c.829C>T	p.Gln277Ter	p.Q277*	ENST00000281708	NM_033632.3	277	Caa/Taa	5/12	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.3370084204116	2		614	189	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0066620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	197	481	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.48243125017257	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.48243125017257	1		481	448	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0066620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	75	215	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.328813592699918	1	FACETS	0.794	0.703	0.891	0.794	0.703	0.891	SUBCLONAL	1	TRUE	0	0.48243125017257	1		215	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0066620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	182	744	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.48243125017257	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.48243125017257	1		745	513	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245265	53245265	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1569278482	NA	P-0066620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	170	301	0	ENST00000375401.3:c.772C>T	p.Arg258Trp	p.R258W	ENST00000375401	NM_004187.3	258	Cgg/Tgg	6/26	1	1	FACETS	0.825	0.773	0.877	1	0.992	1	CLONAL	2	TRUE	0	0.48243125017257	1		301	324	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444306	50444306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1265571297	NA	P-0066620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	78	589	0	ENST00000331340.3:c.236C>T	p.Ala79Val	p.A79V	ENST00000331340	NM_006060.4	79	gCg/gTg	4/8	0.259402527304256	3	FACETS	0.479	0.42	0.543	0.239	0.21	0.272	INDETERMINATE	1	TRUE	1	0.48243125017257	3		589	838	SUCCESS
APC	324	MSKCC	GRCh37	5	112175475	112175475	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	241	574	0	ENST00000257430.4:c.4184del	p.Ser1395IlefsTer20	p.S1395Ifs*20	ENST00000257430	NM_000038.5	1395	aGt/at	16/16	0.48243125017257	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.48243125017257	1		574	533	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197595	27197595	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	68	375	0	ENST00000380036.4:c.1907A>T	p.Asp636Val	p.D636V	ENST00000380036	NM_000459.3	636	gAc/gTc	12/23	0.328813592699918	1	FACETS	0.553	0.483	0.627	0.553	0.483	0.627	SUBCLONAL	1	TRUE	0	0.48243125017257	1		375	387	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200200	138200200	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	201	691	0	ENST00000237289.4:c.1618T>G	p.Phe540Val	p.F540V	ENST00000237289	NM_001270507.1	540	Ttc/Gtc	7/9	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.48243125017257	2		691	755	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027493	48027493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749918474	NA	P-0066620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	130	548	0	ENST00000234420.5:c.2371C>T	p.Arg791Cys	p.R791C	ENST00000234420	NM_000179.2	791	Cgt/Tgt	4/10	1	2	FACETS	0.931	0.848	1	0.931	0.848	1	CLONAL	1	TRUE	1	0.48243125017257	2		548	579	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792404	33793160	+	frameshift_variant	Frame_Shift_Del	DEL	CGCTGCTTGGCCTTGTCGCGGCTCTTGCGCACCGCGATGTTGTTGCGCTCGCGCCGCACCCGGTACTCGTTGCTGTTCTTGTCCACCGACTTCTTGGCCTTGCCCGCGCCGCTGCCGCCACTCGCGCGGAGGTCGGGGTGCGCGGCGCCCAGCCCCTTGAGCGCGCTGCCAGGGCCCGGCAGGCCGGCGGCACCGAGCGCGGGCGCGGGGTGCGGGCTGGGCACGGGCGTGGGCGGCGGCGTGGGGTGACCGGGCTGCAGGTGCATGGTGGTCTGGCCGCAGTGCGCGATCTGGAACTGCAGGTGCGGGGCGGCCAGGTGCGCGGGCGGCGGGTGCGGGTGCGGGTGCGAGGGCGGCGGCGGCGGCGGCGGCTGGTAAGGGAAGAGGCCGGCCAGCGCCAGCTGCTTGGCTTCATCCTCCTCGCGGGGCTCCTGCTTGATCACCAGCGGCCGCAGCGCCGGCGCCCCGACGCGCTCGTACAGGGGCTCCAGCCTGCCGTCCAGGTAGCCGGCGGCCGCGCAGCCGTAGCCGGGCGGGGGCCCGTGCGCTCCCCCGGGCATGACGGCGCCGCCGGGGCCCGCGGGCGCGCCCGGGTAGTCAAAGTCGCCGCCGCCGCCGCCGCCCGTGGGGCCCACGGCCGCCTTGGCCTTCTCCTGCTGCCGGCTGTGCTGGAACAGGTCGGCCAGGAACTCGTCGTTGAAGGCGGCCGGGTCGATGTAGGCGCTGATGTCGATGGACGTCTCGTGCTCGCAGATGC	CGCTGCTTGGCCTTGTCGCGGCTCTTGCGCACCGCGATGTTGTTGCGCTCGCGCCGCACCCGGTACTCGTTGCTGTTCTTGTCCACCGACTTCTTGGCCTTGCCCGCGCCGCTGCCGCCACTCGCGCGGAGGTCGGGGTGCGCGGCGCCCAGCCCCTTGAGCGCGCTGCCAGGGCCCGGCAGGCCGGCGGCACCGAGCGCGGGCGCGGGGTGCGGGCTGGGCACGGGCGTGGGCGGCGGCGTGGGGTGACCGGGCTGCAGGTGCATGGTGGTCTGGCCGCAGTGCGCGATCTGGAACTGCAGGTGCGGGGCGGCCAGGTGCGCGGGCGGCGGGTGCGGGTGCGGGTGCGAGGGCGGCGGCGGCGGCGGCGGCTGGTAAGGGAAGAGGCCGGCCAGCGCCAGCTGCTTGGCTTCATCCTCCTCGCGGGGCTCCTGCTTGATCACCAGCGGCCGCAGCGCCGGCGCCCCGACGCGCTCGTACAGGGGCTCCAGCCTGCCGTCCAGGTAGCCGGCGGCCGCGCAGCCGTAGCCGGGCGGGGGCCCGTGCGCTCCCCCGGGCATGACGGCGCCGCCGGGGCCCGCGGGCGCGCCCGGGTAGTCAAAGTCGCCGCCGCCGCCGCCGCCCGTGGGGCCCACGGCCGCCTTGGCCTTCTCCTGCTGCCGGCTGTGCTGGAACAGGTCGGCCAGGAACTCGTCGTTGAAGGCGGCCGGGTCGATGTAGGCGCTGATGTCGATGGACGTCTCGTGCTCGCAGATGC	-	novel	NA	P-0066620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	131	561	0	ENST00000498907.2:c.161_917del	p.Gly54AlafsTer12	p.G54Afs*12	ENST00000498907	NM_004364.3	54	gGCATCTGCGAGCACGAGACGTCCATCGACATCAGCGCCTACATCGACCCGGCCGCCTTCAACGACGAGTTCCTGGCCGACCTGTTCCAGCACAGCCGGCAGCAGGAGAAGGCCAAGGCGGCCGTGGGCCCCACGGGCGGCGGCGGCGGCGGCGACTTTGACTACCCGGGCGCGCCCGCGGGCCCCGGCGGCGCCGTCATGCCCGGGGGAGCGCACGGGCCCCCGCCCGGCTACGGCTGCGCGGCCGCCGGCTACCTGGACGGCAGGCTGGAGCCCCTGTACGAGCGCGTCGGGGCGCCGGCGCTGCGGCCGCTGGTGATCAAGCAGGAGCCCCGCGAGGAGGATGAAGCCAAGCAGCTGGCGCTGGCCGGCCTCTTCCCTTACCAGCCGCCGCCGCCGCCGCCGCCCTCGCACCCGCACCCGCACCCGCCGCCCGCGCACCTGGCCGCCCCGCACCTGCAGTTCCAGATCGCGCACTGCGGCCAGACCACCATGCACCTGCAGCCCGGTCACCCCACGCCGCCGCCCACGCCCGTGCCCAGCCCGCACCCCGCGCCCGCGCTCGGTGCCGCCGGCCTGCCGGGCCCTGGCAGCGCGCTCAAGGGGCTGGGCGCCGCGCACCCCGACCTCCGCGCGAGTGGCGGCAGCGGCGCGGGCAAGGCCAAGAAGTCGGTGGACAAGAACAGCAACGAGTACCGGGTGCGGCGCGAGCGCAACAACATCGCGGTGCGCAAGAGCCGCGACAAGGCCAAGCAGCGc/gc	1/1	0.328813592699918	1	FACETS	0.794	0.724	0.866	0.794	0.724	0.866	SUBCLONAL	1	TRUE	0	0.48243125017257	1		561	519	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670462	246670462	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	160	489	0	ENST00000388985.4:c.58G>T	p.Ala20Ser	p.A20S	ENST00000388985		20	Gcc/Tcc	1/12	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.48243125017257	2		489	631	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057053	180057053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369974304	NA	P-0066620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	179	672	0	ENST00000261937.6:c.566G>A	p.Arg189Gln	p.R189Q	ENST00000261937	NM_182925.4	189	cGg/cAg	5/30	0.48243125017257	2	FACETS	1	0.94	1	0.51	0.471	0.55	CLONAL	1	TRUE	0	0.48243125017257	2		672	728	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575228	48575228	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	72	337	0	ENST00000342988.3:c.423del	p.Ile141MetfsTer6	p.I141Mfs*6	ENST00000342988	NM_005359.5	141	aTt/at	3/12	0.48243125017257	1	FACETS	0.956	0.847	1	0.956	0.847	1	CLONAL	1	TRUE	0	0.48243125017257	1		337	237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0066621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	203	464	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.502585219910877	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.501168964669129	2		464	356	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479325	50479325	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	87	390	0	ENST00000394963.4:c.173A>C	p.Tyr58Ser	p.Y58S	ENST00000394963	NM_003076.4	58	tAt/tCt	1/13	0.502585219910877	2	FACETS	1	0.956	1	0.565	0.506	0.628	CLONAL	1	TRUE	0	0.501168964669129	2		390	307	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117737454	117737454	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	57	280	0	ENST00000368508.3:c.195C>G	p.Asn65Lys	p.N65K	ENST00000368508	NM_002944.2	65	aaC/aaG	3/43	0.502585219910877	2	FACETS	1	0.947	1	0.586	0.511	0.665	CLONAL	1	TRUE	0	0.501168964669129	2		280	194	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866296	42866310	+	inframe_deletion	In_Frame_Del	DEL	TGTCCCGGATGGGGA	TGTCCCGGATGGGGA	-	novel	NA	P-0066621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	108	541	0	ENST00000398585.3:c.322_336del	p.Ser108_Thr112del	p.S108_T112del	ENST00000398585	NM_001135099.1	108	TCCCCATCCGGGACA/-	3/14	0.502585219910877	2	FACETS	1	0.906	1	0.501	0.453	0.552	CLONAL	1	TRUE	0	0.501168964669129	2		541	430	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937758	76937758	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	29	513	0	ENST00000373344.5:c.2990A>T	p.Asp997Val	p.D997V	ENST00000373344	NM_000489.3	997	gAc/gTc	9/35	0.502585219910877	3	FACETS	0.433	0.348	0.53	0.217	0.174	0.265	SUBCLONAL	1	TRUE	1	0.501168964669129	3		513	334	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	23	348	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.417	0.324	0.526	0.417	0.324	0.526	SUBCLONAL	1	TRUE	1	0.22	2		348	501	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134988	41134988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	50	383	0	ENST00000379561.5:c.640C>T	p.Arg214Cys	p.R214C	ENST00000379561	NM_002015.3	214	Cgt/Tgt	2/3	1	2	FACETS	0.969	0.823	1	0.969	0.823	1	CLONAL	1	TRUE	1	0.22	2		383	469	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692782	89692782	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	41	277	0	ENST00000371953.3:c.266C>A	p.Pro89His	p.P89H	ENST00000371953	NM_000314.4	89	cCt/cAt	5/9	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.22	2		277	304	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	91	487	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	0.819	0.73	0.914	1	0.982	1	CLONAL	2	TRUE	1	0.22	2		487	505	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	9	104	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.221	0.145	0.318	0.221	0.145	0.318	SUBCLONAL	1	TRUE	1	0.22	2		104	371	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	67	442	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.22	2		442	595	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660469	67660469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	40	364	0	ENST00000264010.4:c.1369C>T	p.Arg457Ter	p.R457*	ENST00000264010	NM_006565.3	457	Cga/Tga	8/12	1	2	FACETS	0.697	0.578	0.829	0.697	0.578	0.829	SUBCLONAL	1	TRUE	1	0.22	2		364	522	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518519	204518519	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	70	553	0	ENST00000367182.3:c.1182C>A	p.Phe394Leu	p.F394L	ENST00000367182	NM_001278516.1	394	ttC/ttA	11/11	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.22	2		553	604	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	109	413	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	0.919	0.828	1	1	0.987	1	CLONAL	2	TRUE	1	0.22	2		413	539	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509723	106509723	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	28	467	0	ENST00000359195.3:c.1717G>T	p.Glu573Ter	p.E573*	ENST00000359195	NM_002649.2	573	Gaa/Taa	2/11	1	2	FACETS	0.488	0.389	0.601	0.488	0.389	0.601	SUBCLONAL	1	TRUE	1	0.22	2		467	522	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625251	69625251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782147248	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	69	605	0	ENST00000334134.2:c.542G>A	p.Arg181His	p.R181H	ENST00000334134	NM_005247.2	181	cGc/cAc	3/3	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.22	2		605	589	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418997	116418997	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200754673	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	42	367	0	ENST00000397752.3:c.3508C>T	p.Arg1170Ter	p.R1170*	ENST00000397752	NM_000245.2	1170	Cga/Tga	17/21	1	2	FACETS	0.87	0.727	1	0.87	0.727	1	CLONAL	1	TRUE	1	0.22	2		367	439	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	41	344	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.948	0.791	1	0.948	0.791	1	CLONAL	1	TRUE	1	0.22	2		344	393	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919244	48919244	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913296	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	15	296	0	ENST00000267163.4:c.409G>T	p.Glu137Ter	p.E137*	ENST00000267163	NM_000321.2	137	Gaa/Taa	4/27	1	2	FACETS	0.467	0.341	0.619	0.467	0.341	0.619	SUBCLONAL	1	TRUE	1	0.22	2		296	292	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951156	48951156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060503078	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	40	301	0	ENST00000267163.4:c.1318G>A	p.Glu440Lys	p.E440K	ENST00000267163	NM_000321.2	440	Gaa/Aaa	13/27	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.22	2		301	273	SUCCESS
APC	324	MSKCC	GRCh37	5	112178211	112178211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs901983934	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	50	489	0	ENST00000257430.4:c.6920C>T	p.Ser2307Leu	p.S2307L	ENST00000257430	NM_000038.5	2307	tCg/tTg	16/16	1	2	FACETS	0.791	0.67	0.923	0.791	0.67	0.923	CLONAL	1	TRUE	1	0.22	2		489	575	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249457	153249457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	29	451	0	ENST00000281708.4:c.1321C>T	p.Arg441Trp	p.R441W	ENST00000281708	NM_033632.3	441	Cgg/Tgg	9/12	1	2	FACETS	0.577	0.462	0.708	0.577	0.462	0.708	SUBCLONAL	1	TRUE	1	0.22	2		451	457	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951085	17951085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	48	442	0	ENST00000458235.1:c.1208G>A	p.Arg403His	p.R403H	ENST00000458235	NM_000215.3	403	cGc/cAc	9/24	1	2	FACETS	0.783	0.662	0.917	0.783	0.662	0.917	CLONAL	1	TRUE	1	0.22	2		442	557	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162904	47162904	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs757432733	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	38	407	0	ENST00000409792.3:c.3222G>T	p.Lys1074Asn	p.K1074N	ENST00000409792	NM_014159.6	1074	aaG/aaT	3/21	1	2	FACETS	0.643	0.531	0.769	0.643	0.531	0.769	SUBCLONAL	1	TRUE	1	0.22	2		407	537	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672842	86672842	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	57	422	0	ENST00000274376.6:c.2329G>T	p.Glu777Ter	p.E777*	ENST00000274376	NM_002890.2	777	Gaa/Taa	17/25	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.22	2		422	452	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375016	45375016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226662382	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	55	468	0	ENST00000262160.6:c.827C>T	p.Ser276Leu	p.S276L	ENST00000262160	NM_005901.5	276	tCg/tTg	8/11	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.22	2		468	486	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829617	72829617	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	29	485	0	ENST00000268489.5:c.6964C>T	p.Arg2322Ter	p.R2322*	ENST00000268489	NM_006885.3	2322	Cga/Tga	9/10	1	2	FACETS	0.475	0.38	0.583	0.475	0.38	0.583	SUBCLONAL	1	TRUE	1	0.22	2		485	555	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743948	41743948	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751738506	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	47	643	0	ENST00000301178.4:c.883C>T	p.Arg295Trp	p.R295W	ENST00000301178	NM_021913.4	295	Cgg/Tgg	7/20	1	2	FACETS	0.643	0.541	0.755	0.643	0.541	0.755	SUBCLONAL	1	TRUE	1	0.22	2		643	665	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652336	206652336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149219314	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	45	593	0	ENST00000367120.3:c.1043G>A	p.Arg348Gln	p.R348Q	ENST00000367120	NM_014002.3	348	cGa/cAa	10/22	1	2	FACETS	0.554	0.464	0.653	0.554	0.464	0.653	SUBCLONAL	1	TRUE	1	0.22	2		593	739	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103525652	103525652	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	34	381	0	ENST00000355739.4:c.2923G>T	p.Glu975Ter	p.E975*	ENST00000355739	NM_000123.3	975	Gaa/Taa	14/15	1	2	FACETS	0.622	0.507	0.751	0.622	0.507	0.751	SUBCLONAL	1	TRUE	1	0.22	2		381	497	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871986	45871986	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs748842373	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	28	360	0	ENST00000391945.4:c.262C>T	p.Arg88Ter	p.R88*	ENST00000391945	NM_000400.3	88	Cga/Tga	5/23	1	2	FACETS	0.552	0.441	0.68	0.552	0.441	0.68	SUBCLONAL	1	TRUE	1	0.22	2		360	461	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761219	59761219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs575998972	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	37	526	0	ENST00000259008.2:c.3188C>T	p.Ser1063Leu	p.S1063L	ENST00000259008	NM_032043.2	1063	tCg/tTg	20/20	1	2	FACETS	0.647	0.533	0.775	0.647	0.533	0.775	SUBCLONAL	1	TRUE	1	0.22	2		526	520	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606678	29606678	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs188859061	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	45	420	0	ENST00000389048.3:c.1202G>A	p.Arg401Gln	p.R401Q	ENST00000389048	NM_004304.4	401	cGa/cAa	5/29	1	2	FACETS	0.685	0.575	0.807	0.685	0.575	0.807	SUBCLONAL	1	TRUE	1	0.22	2		420	597	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678001	117678001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs62430836	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	69	450	0	ENST00000368508.3:c.3932G>A	p.Arg1311Gln	p.R1311Q	ENST00000368508	NM_002944.2	1311	cGa/cAa	25/43	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.22	2		450	516	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651136	206651136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553385811	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	58	580	0	ENST00000367120.3:c.746C>T	p.Ala249Val	p.A249V	ENST00000367120	NM_014002.3	249	gCc/gTc	8/22	1	2	FACETS	0.837	0.719	0.966	0.837	0.719	0.966	CLONAL	1	TRUE	1	0.22	2		580	630	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453494	138453494	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1291010707	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	43	353	0	ENST00000289153.2:c.954G>T	p.Lys318Asn	p.K318N	ENST00000289153	NM_006219.2	318	aaG/aaT	5/22	1	2	FACETS	0.944	0.791	1	0.944	0.791	1	CLONAL	1	TRUE	1	0.22	2		353	414	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217654	7217654	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	67	443	0	ENST00000380728.2:c.273G>T	p.Lys91Asn	p.K91N	ENST00000380728		91	aaG/aaT	4/11	1	2	FACETS	0.962	0.836	1	0.962	0.836	1	CLONAL	1	TRUE	1	0.22	2		443	633	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753027	57753027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1192733931	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	33	490	0	ENST00000274289.3:c.989G>A	p.Arg330Gln	p.R330Q	ENST00000274289	NM_006622.3	330	cGa/cAa	7/14	1	2	FACETS	0.523	0.425	0.634	0.523	0.425	0.634	SUBCLONAL	1	TRUE	1	0.22	2		490	574	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926518	59926518	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1330277587	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	28	336	0	ENST00000259008.2:c.479G>T	p.Arg160Ile	p.R160I	ENST00000259008	NM_032043.2	160	aGa/aTa	5/20	1	2	FACETS	0.663	0.53	0.815	0.663	0.53	0.815	SUBCLONAL	1	TRUE	1	0.22	2		336	384	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142844	7142844	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1135401738	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	35	537	0	ENST00000302850.5:c.2525C>T	p.Ala842Val	p.A842V	ENST00000302850	NM_000208.2	842	gCg/gTg	12/22	1	2	FACETS	0.497	0.406	0.6	0.497	0.406	0.6	SUBCLONAL	1	TRUE	1	0.22	2		537	640	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938212	76938212	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	23	444	0	ENST00000373344.5:c.2536G>T	p.Asp846Tyr	p.D846Y	ENST00000373344	NM_000489.3	846	Gat/Tat	9/35	1	2	FACETS	0.466	0.362	0.586	0.466	0.362	0.586	SUBCLONAL	1	TRUE	1	0.22	2		444	449	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098664	2098664	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	58	469	0	ENST00000219476.3:c.48G>T	p.Lys16Asn	p.K16N	ENST00000219476	NM_000548.3	16	aaG/aaT	2/42	1	2	FACETS	0.785	0.673	0.906	0.785	0.673	0.906	CLONAL	1	TRUE	1	0.22	2		469	672	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026848	71026848	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	47	412	0	ENST00000318789.4:c.1374T>G	p.Phe458Leu	p.F458L	ENST00000318789	NM_032682.5	458	ttT/ttG	16/21	1	2	FACETS	0.905	0.764	1	0.905	0.764	1	CLONAL	1	TRUE	1	0.22	2		412	472	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853187	68853187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373605261	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	34	411	0	ENST00000261769.5:c.1570C>T	p.Arg524Trp	p.R524W	ENST00000261769	NM_004360.3	524	Cgg/Tgg	11/16	1	2	FACETS	0.527	0.429	0.637	0.527	0.429	0.637	SUBCLONAL	1	TRUE	1	0.22	2		411	587	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915264	32915264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881549	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	33	481	0	ENST00000380152.3:c.6772G>A	p.Glu2258Lys	p.E2258K	ENST00000380152		2258	Gaa/Aaa	11/27	1	2	FACETS	0.704	0.573	0.852	0.704	0.573	0.852	SUBCLONAL	1	TRUE	1	0.22	2		481	426	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38996934	38996934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762282621	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	23	393	0	ENST00000357387.3:c.443G>A	p.Arg148Gln	p.R148Q	ENST00000357387	NM_152756.3	148	cGa/cAa	6/38	1	2	FACETS	0.49	0.381	0.616	0.49	0.381	0.616	SUBCLONAL	1	TRUE	1	0.22	2		393	427	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342580	118342580	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	40	488	0	ENST00000534358.1:c.706A>G	p.Thr236Ala	p.T236A	ENST00000534358	NM_005933.3	236	Aca/Gca	3/36	1	2	FACETS	0.631	0.524	0.751	0.631	0.524	0.751	SUBCLONAL	1	TRUE	1	0.22	2		488	576	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739629	41739629	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	37	381	0	ENST00000242208.4:c.344A>G	p.Glu115Gly	p.E115G	ENST00000242208	NM_002192.2	115	gAa/gGa	2/3	1	2	FACETS	0.86	0.71	1	0.86	0.71	1	CLONAL	1	TRUE	1	0.22	2		381	391	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144336729	144336729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1363184155	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	31	340	0	ENST00000262995.4:c.172C>T	p.Arg58Cys	p.R58C	ENST00000262995	NM_207123.2	58	Cgt/Tgt	2/11	1	2	FACETS	0.801	0.648	0.973	0.801	0.648	0.973	CLONAL	1	TRUE	1	0.22	2		340	352	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544981	86544981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	41	472	0	ENST00000262426.4:c.806C>T	p.Ala269Val	p.A269V	ENST00000262426	NM_001451.2	269	gCc/gTc	1/2	1	2	FACETS	0.89	0.742	1	0.89	0.742	1	CLONAL	1	TRUE	1	0.22	2		472	419	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424279	47424279	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	46	467	0	ENST00000404338.3:c.2347C>T	p.Arg783Ter	p.R783*	ENST00000404338	NM_004491.4	783	Cga/Tga	1/6	1	2	FACETS	0.698	0.587	0.821	0.698	0.587	0.821	SUBCLONAL	1	TRUE	1	0.22	2		467	599	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47502632	47502632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1189080194	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	50	365	0	ENST00000404338.3:c.4108G>A	p.Glu1370Lys	p.E1370K	ENST00000404338	NM_004491.4	1370	Gaa/Aaa	5/6	1	2	FACETS	0.937	0.796	1	0.937	0.796	1	CLONAL	1	TRUE	1	0.22	2		365	485	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342687	70342687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	66	504	0	ENST00000374080.3:c.1448G>A	p.Arg483Gln	p.R483Q	ENST00000374080		483	cGa/cAa	10/45	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.22	2		504	557	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288609	33288609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	93	449	0	ENST00000374542.5:c.943G>A	p.Asp315Asn	p.D315N	ENST00000374542	NM_001141970.1	315	Gat/Aat	3/8	1	2	FACETS	0.766	0.683	0.854	1	0.981	1	SUBCLONAL	2	TRUE	1	0.22	2		449	552	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432650	49432650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1271513534	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	78	593	1	ENST00000301067.7:c.8489G>A	p.Arg2830Gln	p.R2830Q	ENST00000301067	NM_003482.3	2830	cGa/cAa	34/54	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.22	2		594	701	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423781	47423781	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	57	547	0	ENST00000404338.3:c.1849C>T	p.Arg617Ter	p.R617*	ENST00000404338	NM_004491.4	617	Cga/Tga	1/6	1	2	FACETS	0.851	0.73	0.983	0.851	0.73	0.983	CLONAL	1	TRUE	1	0.22	2		547	609	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440958	56440958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369636118	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	54	489	0	ENST00000407977.2:c.379C>T	p.Arg127Trp	p.R127W	ENST00000407977		127	Cgg/Tgg	4/10	1	2	FACETS	0.797	0.68	0.925	0.797	0.68	0.925	CLONAL	1	TRUE	1	0.22	2		489	616	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25459873	25459873	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	29	393	0	ENST00000264709.3:c.2410C>T	p.Pro804Ser	p.P804S	ENST00000264709	NM_175629.2	804	Ccg/Tcg	21/23	1	2	FACETS	0.545	0.436	0.668	0.545	0.436	0.668	SUBCLONAL	1	TRUE	1	0.22	2		393	484	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074109	8074109	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	50	481	0	ENST00000377482.5:c.550G>T	p.Glu184Ter	p.E184*	ENST00000377482	NM_018948.3	184	Gaa/Taa	4/4	1	2	FACETS	0.709	0.601	0.829	0.709	0.601	0.829	SUBCLONAL	1	TRUE	1	0.22	2		481	641	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27183496	27183496	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	30	418	1	ENST00000380036.4:c.1070A>C	p.Asp357Ala	p.D357A	ENST00000380036	NM_000459.3	357	gAt/gCt	8/23	1	2	FACETS	0.563	0.453	0.689	0.563	0.453	0.689	SUBCLONAL	1	TRUE	1	0.22	2		419	484	SUCCESS
APC	324	MSKCC	GRCh37	5	112174218	112174218	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	32	497	0	ENST00000257430.4:c.2927G>T	p.Arg976Ile	p.R976I	ENST00000257430	NM_000038.5	976	aGa/aTa	16/16	1	2	FACETS	0.655	0.531	0.795	0.655	0.531	0.795	SUBCLONAL	1	TRUE	1	0.22	2		497	444	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295832	1295832	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	77	742	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.22	2		742	658	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594177	55594177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	54	393	0	ENST00000288135.5:c.1880C>T	p.Pro627Leu	p.P627L	ENST00000288135	NM_000222.2	627	cCg/cTg	13/21	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.22	2		393	455	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217500	142217500	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	17	387	0	ENST00000350721.4:c.5497C>A	p.Pro1833Thr	p.P1833T	ENST00000350721	NM_001184.3	1833	Cct/Act	32/47	1	2	FACETS	0.471	0.351	0.614	0.471	0.351	0.614	SUBCLONAL	1	TRUE	1	0.22	2		387	328	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715763	18715763	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	48	492	0	ENST00000266497.5:c.3594G>T	p.Leu1198Phe	p.L1198F	ENST00000266497		1198	ttG/ttT	25/31	1	2	FACETS	0.802	0.678	0.939	0.802	0.678	0.939	CLONAL	1	TRUE	1	0.22	2		492	544	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40498712	40498712	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	42	396	0	ENST00000264657.5:c.148G>T	p.Glu50Ter	p.E50*	ENST00000264657	NM_139276.2	50	Gaa/Taa	3/24	1	2	FACETS	0.692	0.577	0.819	0.692	0.577	0.819	SUBCLONAL	1	TRUE	1	0.22	2		396	552	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954202	32954202	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	30	448	0	ENST00000380152.3:c.9176A>C	p.Lys3059Thr	p.K3059T	ENST00000380152		3059	aAa/aCa	24/27	1	2	FACETS	0.588	0.473	0.718	0.588	0.473	0.718	SUBCLONAL	1	TRUE	1	0.22	2		448	464	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074298	8074299	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	50	576	0	ENST00000377482.5:c.359_360dup	p.Asn121Ter	p.N121*	ENST00000377482	NM_018948.3	120	-/TG	4/4	1	2	FACETS	0.668	0.566	0.781	0.668	0.566	0.781	SUBCLONAL	1	TRUE	1	0.22	2		576	680	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427368	49427368	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778477	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	67	514	0	ENST00000301067.7:c.11120G>A	p.Arg3707Gln	p.R3707Q	ENST00000301067	NM_003482.3	3707	cGa/cAa	39/54	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.22	2		514	535	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967185	93967185	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	24	317	0	ENST00000369303.4:c.2167C>A	p.Leu723Ile	p.L723I	ENST00000369303	NM_004440.3	723	Ctc/Atc	12/17	1	2	FACETS	0.68	0.533	0.848	0.68	0.533	0.848	SUBCLONAL	1	TRUE	1	0.22	2		317	321	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463291	25463291	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs766854284	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	39	577	0	ENST00000264709.3:c.2202C>A	p.Phe734Leu	p.F734L	ENST00000264709	NM_175629.2	734	ttC/ttA	19/23	1	2	FACETS	0.659	0.546	0.786	0.659	0.546	0.786	SUBCLONAL	1	TRUE	1	0.22	2		577	538	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950705	38950705	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	31	459	0	ENST00000357387.3:c.3245A>C	p.Lys1082Thr	p.K1082T	ENST00000357387	NM_152756.3	1082	aAa/aCa	31/38	1	2	FACETS	0.606	0.49	0.738	0.606	0.49	0.738	SUBCLONAL	1	TRUE	1	0.22	2		459	465	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681163	86681163	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	44	370	0	ENST00000274376.6:c.2804A>C	p.Lys935Thr	p.K935T	ENST00000274376	NM_002890.2	935	aAa/aCa	22/25	1	2	FACETS	0.971	0.816	1	0.971	0.816	1	CLONAL	1	TRUE	1	0.22	2		370	412	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782195	56782195	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	60	384	0	ENST00000308159.5:c.36A>C	p.Gln12His	p.Q12H	ENST00000308159	NM_014669.4	12	caA/caC	2/22	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.22	2		384	464	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513436	41513436	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	56	530	0	ENST00000263253.7:c.341del	p.Gly114AspfsTer2	p.G114Dfs*2	ENST00000263253	NM_001429.3	114	Gga/ga	2/31	1	2	FACETS	0.901	0.772	1	0.901	0.772	1	CLONAL	1	TRUE	1	0.22	2		530	565	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041751	29041751	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	29	283	0	ENST00000282397.4:c.68C>A	p.Ser23Tyr	p.S23Y	ENST00000282397	NM_002019.4	23	tCt/tAt	2/30	1	2	FACETS	0.745	0.598	0.911	0.745	0.598	0.911	CLONAL	1	TRUE	1	0.22	2		283	354	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514232	69514232	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	110	467	0	ENST00000294312.3:c.449A>C	p.Gln150Pro	p.Q150P	ENST00000294312	NM_005117.2	150	cAg/cCg	3/3	1	2	FACETS	0.804	0.724	0.888	1	0.985	1	CLONAL	2	TRUE	1	0.22	2		467	622	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050872	13050872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	40	423	0	ENST00000316448.5:c.403G>A	p.Asp135Asn	p.D135N	ENST00000316448	NM_004343.3	135	Gac/Aac	4/9	1	2	FACETS	0.639	0.53	0.761	0.639	0.53	0.761	SUBCLONAL	1	TRUE	1	0.22	2		423	569	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721190	61721190	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	33	353	0	ENST00000401558.2:c.1084G>T	p.Glu362Ter	p.E362*	ENST00000401558	NM_003400.3	362	Gaa/Taa	12/25	1	2	FACETS	0.613	0.499	0.743	0.613	0.499	0.743	SUBCLONAL	1	TRUE	1	0.22	2		353	489	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549458	187549458	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748147223	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	40	543	0	ENST00000441802.2:c.4660G>A	p.Asp1554Asn	p.D1554N	ENST00000441802	NM_005245.3	1554	Gac/Aac	9/27	1	2	FACETS	0.541	0.448	0.645	0.541	0.448	0.645	SUBCLONAL	1	TRUE	1	0.22	2		543	672	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56867286	56867286	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	26	456	0	ENST00000308159.5:c.1505T>C	p.Leu502Pro	p.L502P	ENST00000308159	NM_014669.4	502	cTt/cCt	13/22	1	2	FACETS	0.455	0.36	0.566	0.455	0.36	0.566	SUBCLONAL	1	TRUE	1	0.22	2		456	519	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184764	32184764	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	43	583	0	ENST00000375023.3:c.1819C>A	p.Leu607Ile	p.L607I	ENST00000375023	NM_004557.3	607	Ctt/Att	11/30	1	2	FACETS	0.591	0.494	0.7	0.591	0.494	0.7	SUBCLONAL	1	TRUE	1	0.22	2		583	661	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636974	176636974	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	80	489	0	ENST00000439151.2:c.1574G>T	p.Arg525Leu	p.R525L	ENST00000439151	NM_022455.4	525	cGg/cTg	5/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.22	2		489	604	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1296331	1296331	+	upstream_gene_variant	5'Flank	SNP	A	A	G	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	28	432	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.481	0.384	0.593	0.481	0.384	0.593	SUBCLONAL	1	TRUE	1	0.22	2		432	529	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724416	112724416	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs767508015	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	72	500	0	ENST00000369452.4:c.300G>T	p.Glu100Asp	p.E100D	ENST00000369452	NM_007373.3	100	gaG/gaT	2/9	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.22	2		500	509	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229294	123229294	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	35	360	0	ENST00000218089.9:c.3778G>T	p.Glu1260Ter	p.E1260*	ENST00000218089	NM_001042749.1	1260	Gaa/Taa	34/35	1	2	FACETS	0.684	0.56	0.823	0.684	0.56	0.823	SUBCLONAL	1	TRUE	1	0.22	2		360	465	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950346	15950346	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	79	513	0	ENST00000268712.3:c.6598A>C	p.Asn2200His	p.N2200H	ENST00000268712	NM_006311.3	2200	Aat/Cat	42/46	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.22	2		513	604	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231689	66231689	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	46	369	0	ENST00000273854.3:c.2011G>T	p.Glu671Ter	p.E671*	ENST00000273854	NM_004439.5	671	Gaa/Taa	11/18	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.22	2		369	339	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280597	115280597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	36	340	0	ENST00000438362.2:c.434G>A	p.Arg145Gln	p.R145Q	ENST00000438362	NM_001242891.1	145	cGa/cAa	4/20	1	2	FACETS	0.695	0.571	0.834	0.695	0.571	0.834	SUBCLONAL	1	TRUE	1	0.22	2		340	471	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352517	73352517	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	24	368	0	ENST00000377767.4:c.388G>A	p.Glu130Lys	p.E130K	ENST00000377767	NM_014953.3	130	Gaa/Aaa	3/21	1	2	FACETS	0.55	0.43	0.687	0.55	0.43	0.687	SUBCLONAL	1	TRUE	1	0.22	2		368	397	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848019	151848019	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	50	375	0	ENST00000262189.6:c.12740C>A	p.Ser4247Ter	p.S4247*	ENST00000262189	NM_170606.2	4247	tCa/tAa	51/59	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.22	2		375	409	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670692	134670692	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	31	496	0	ENST00000398015.3:c.603A>C	p.Gln201His	p.Q201H	ENST00000398015	NM_004441.4	201	caA/caC	3/16	1	2	FACETS	0.524	0.423	0.639	0.524	0.423	0.639	SUBCLONAL	1	TRUE	1	0.22	2		496	538	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64288887	64288887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	47	361	0	ENST00000370651.3:c.283G>A	p.Glu95Lys	p.E95K	ENST00000370651	NM_003463.4	95	Gaa/Aaa	4/6	1	2	FACETS	0.917	0.774	1	0.917	0.774	1	CLONAL	1	TRUE	1	0.22	2		361	466	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100016	11100016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749059769	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	67	484	0	ENST00000358026.2:c.1142G>A	p.Arg381Gln	p.R381Q	ENST00000358026	NM_001128849.1	381	cGa/cAa	7/36	1	2	FACETS	0.967	0.84	1	0.967	0.84	1	CLONAL	1	TRUE	1	0.22	2		484	630	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215783	133215783	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763031537	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	30	428	0	ENST00000320574.5:c.5480C>T	p.Ser1827Leu	p.S1827L	ENST00000320574	NM_006231.2	1827	tCg/tTg	40/49	1	2	FACETS	0.563	0.453	0.689	0.563	0.453	0.689	SUBCLONAL	1	TRUE	1	0.22	2		428	484	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975445	26975446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	31	481	0	ENST00000381527.3:c.1076dup	p.Leu359PhefsTer7	p.L359Ffs*7	ENST00000381527	NM_001260.1	357	-/T	11/13	1	2	FACETS	0.534	0.431	0.651	0.534	0.431	0.651	SUBCLONAL	1	TRUE	1	0.22	2		481	528	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213248	39213248	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	47	522	0	ENST00000402219.2:c.3719A>C	p.Lys1240Thr	p.K1240T	ENST00000402219	NM_005633.3	1240	aAa/aCa	23/23	1	2	FACETS	0.66	0.556	0.776	0.66	0.556	0.776	SUBCLONAL	1	TRUE	1	0.22	2		522	647	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398116	4398116	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1012989280	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	67	434	0	ENST00000261254.3:c.680C>T	p.Ala227Val	p.A227V	ENST00000261254	NM_001759.3	227	gCc/gTc	4/5	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.22	2		434	485	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275709	41275709	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	132	503	0	ENST00000349496.5:c.1604G>A	p.Arg535Gln	p.R535Q	ENST00000349496	NM_001904.3	535	cGa/cAa	10/15	1	2	FACETS	1	0.917	1	1	0.99	1	CLONAL	2	TRUE	1	0.22	2		503	596	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876980	151876980	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	72	486	0	ENST00000262189.6:c.7381G>T	p.Asp2461Tyr	p.D2461Y	ENST00000262189	NM_170606.2	2461	Gat/Tat	37/59	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.22	2		486	568	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410495	63410495	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	64	646	0	ENST00000330258.3:c.2672G>T	p.Arg891Met	p.R891M	ENST00000330258	NM_152424.3	891	aGg/aTg	2/2	1	2	FACETS	0.938	0.813	1	0.938	0.813	1	CLONAL	1	TRUE	1	0.22	2		646	620	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957767	1957767	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	49	487	0	ENST00000382891.5:c.2733G>T	p.Met911Ile	p.M911I	ENST00000382891	NM_133335.3	911	atG/atT	15/22	1	2	FACETS	0.833	0.705	0.973	0.833	0.705	0.973	CLONAL	1	TRUE	1	0.22	2		487	535	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856077	68856077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	42	506	0	ENST00000261769.5:c.1885G>A	p.Glu629Lys	p.E629K	ENST00000261769	NM_004360.3	629	Gaa/Aaa	12/16	1	2	FACETS	0.635	0.529	0.753	0.635	0.529	0.753	SUBCLONAL	1	TRUE	1	0.22	2		506	601	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252163	226252163	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	31	245	0	ENST00000366813.1:c.111G>T	p.Lys37Asn	p.K37N	ENST00000366813		37	aaG/aaT	1/3	1	2	FACETS	0.752	0.608	0.914	0.752	0.608	0.914	CLONAL	1	TRUE	1	0.22	2		245	375	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0066623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	221	232	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		232	507	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967215	134967215	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	132	800	0	ENST00000398015.3:c.2554G>T	p.Ala852Ser	p.A852S	ENST00000398015	NM_004441.4	852	Gct/Tct	14/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		800	454	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907632	111907632	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	31	568	0	ENST00000393256.3:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000393256	NM_006538.4	136	Cag/Tag	3/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		568	362	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495299	212495299	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	22	653	0	ENST00000342788.4:c.1967G>T	p.Gly656Val	p.G656V	ENST00000342788	NM_005235.2	656	gGa/gTa	17/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		653	311	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956705	93956705	+	splice_acceptor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0066623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	26	549	0	ENST00000369303.4:c.2533-2del		p.X845_splice	ENST00000369303	NM_004440.3	845			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		549	302	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0066624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	22	269	1	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.406	0.315	0.512	0.406	0.315	0.512	SUBCLONAL	1	TRUE	1	0.380295568910076	2		270	285	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0066624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	199	343	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.370574545870968	2	FACETS	0.916	0.855	0.979	0.916	0.855	0.979	CLONAL	2	TRUE	0	0.380295568910076	2		343	571	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0066624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	89	479	0	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	1	2	FACETS	0.764	0.678	0.855	0.764	0.678	0.855	SUBCLONAL	1	TRUE	1	0.380295568910076	2		479	613	SUCCESS
APC	324	MSKCC	GRCh37	5	112174835	112174835	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0066624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	111	433	0	ENST00000257430.4:c.3544A>T	p.Lys1182Ter	p.K1182*	ENST00000257430	NM_000038.5	1182	Aaa/Taa	16/16	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.380295568910076	2		433	574	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022925	31022925	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	222	553	0	ENST00000375687.4:c.2410G>T	p.Gly804Ter	p.G804*	ENST00000375687	NM_015338.5	804	Gga/Tga	13/13	0.380295568910076	5	FACETS	0.824	0.767	0.884	0.55	0.511	0.59	CLONAL	2	TRUE	2	0.380295568910076	5		553	1112	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987156	69987156	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	85	455	0	ENST00000394351.3:c.217A>G	p.Ser73Gly	p.S73G	ENST00000394351	NM_000248.3	73	Agc/Ggc	2/9	1	2	FACETS	0.703	0.622	0.79	0.703	0.622	0.79	SUBCLONAL	1	TRUE	1	0.380295568910076	2		455	636	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492752	56492752	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	97	464	0	ENST00000407977.2:c.187C>G	p.Leu63Val	p.L63V	ENST00000407977		63	Ctc/Gtc	2/10	0.380295568910076	3	FACETS	0.717	0.638	0.801	0.358	0.319	0.401	SUBCLONAL	1	TRUE	1	0.380295568910076	3		464	847	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528146	29528146	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	192	396	0	ENST00000356175.3:c.1154G>T	p.Arg385Leu	p.R385L	ENST00000356175	NM_000267.3	385	cGt/cTt	10/57	0.380295568910076	3	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	1	0.380295568910076	3		396	595	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0066625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	53	269	1	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.507190134635183	2		270	207	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0066625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	195	287	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.507190134635183	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.507190134635183	3		287	430	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100462	8100462	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	171	724	0	ENST00000346208.3:c.436G>T	p.Ala146Ser	p.A146S	ENST00000346208		146	Gcc/Tcc	3/6	1	2	FACETS	0.944	0.871	1	0.944	0.871	1	CLONAL	1	TRUE	1	0.507190134635183	2		724	714	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068451	16068451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	14	131	0	ENST00000268712.3:c.460G>A	p.Glu154Lys	p.E154K	ENST00000268712	NM_006311.3	154	Gaa/Aaa	5/46	1	2	FACETS	0.361	0.262	0.479	0.361	0.262	0.479	SUBCLONAL	1	TRUE	1	0.507190134635183	2		131	153	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054612	13054612	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs201971744	NA	P-0066625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	180	690	0	ENST00000316448.5:c.1139A>G	p.Glu380Gly	p.E380G	ENST00000316448	NM_004343.3	380	gAg/gGg	9/9	1	2	FACETS	0.94	0.869	1	0.94	0.869	1	CLONAL	1	TRUE	1	0.507190134635183	2		690	755	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951994	178951994	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	126	497	0	ENST00000263967.3:c.3049G>C	p.Asp1017His	p.D1017H	ENST00000263967	NM_006218.2	1017	Gat/Cat	21/21	1	2	FACETS	0.982	0.894	1	0.982	0.894	1	CLONAL	1	TRUE	1	0.507190134635183	2		497	506	SUCCESS
REST	5978	MSKCC	GRCh37	4	57797599	57797599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	146	657	2	ENST00000309042.7:c.2575G>A	p.Asp859Asn	p.D859N	ENST00000309042	NM_005612.4	859	Gat/Aat	4/4	1	2	FACETS	0.918	0.841	0.999	0.918	0.841	0.999	CLONAL	1	TRUE	1	0.507190134635183	2		659	627	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836762	151836762	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	24	417	0	ENST00000262189.6:c.14458C>T	p.Gln4820Ter	p.Q4820*	ENST00000262189	NM_170606.2	4820	Cag/Tag	56/59	0.507190134635183	1	FACETS	0.188	0.147	0.235	0.188	0.147	0.235	SUBCLONAL	1	TRUE	0	0.507190134635183	1		417	376	SUCCESS
AR	367	MSKCC	GRCh37	X	66765842	66765842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	174	759	0	ENST00000374690.3:c.854C>A	p.Ala285Asp	p.A285D	ENST00000374690	NM_000044.3	285	gCc/gAc	1/8	1	2	FACETS	0.923	0.852	0.997	0.923	0.852	0.997	CLONAL	1	TRUE	1	0.507190134635183	2		759	743	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937439	76937439	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	109	572	0	ENST00000373344.5:c.3309G>T	p.Lys1103Asn	p.K1103N	ENST00000373344	NM_000489.3	1103	aaG/aaT	9/35	0.316037337896041	1	FACETS	0.753	0.681	0.828	0.753	0.681	0.828	SUBCLONAL	1	TRUE	0	0.507190134635183	1		572	426	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807523	36807523	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	141	509	1	ENST00000373129.3:c.1141C>G	p.Gln381Glu	p.Q381E	ENST00000373129	NM_032017.1	381	Cag/Gag	12/12	1	2	FACETS	0.924	0.845	1	0.924	0.845	1	CLONAL	1	TRUE	1	0.507190134635183	2		510	602	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231488637	231488637	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs371202002	NA	P-0066625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	149	506	0	ENST00000295050.7:c.1000A>G	p.Arg334Gly	p.R334G	ENST00000295050	NM_032018.5	334	Aga/Gga	5/5	0.507190134635183	3	FACETS	1	0.967	1	0.555	0.508	0.603	CLONAL	1	TRUE	1	0.507190134635183	3		506	664	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118353175	118353175	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	114	476	0	ENST00000534358.1:c.4051C>T	p.Pro1351Ser	p.P1351S	ENST00000534358	NM_005933.3	1351	Cca/Tca	8/36	1	2	FACETS	0.904	0.818	0.994	0.904	0.818	0.994	CLONAL	1	TRUE	1	0.507190134635183	2		476	497	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880836	28880836	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	165	615	0	ENST00000282397.4:c.3794C>G	p.Pro1265Arg	p.P1265R	ENST00000282397	NM_002019.4	1265	cCc/cGc	29/30	1	2	FACETS	0.893	0.821	0.966	0.893	0.821	0.966	CLONAL	1	TRUE	1	0.507190134635183	2		615	729	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965626	25965626	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	296	592	0	ENST00000435504.4:c.3580A>G	p.Thr1194Ala	p.T1194A	ENST00000435504		1194	Aca/Gca	13/13	0.507190134635183	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.507190134635183	2		592	580	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561257	9561257	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	165	604	0	ENST00000353224.5:c.525G>T	p.Met175Ile	p.M175I	ENST00000353224	NM_177990.2	175	atG/atT	4/10	0.507190134635183	3	FACETS	1	0.955	1	0.528	0.486	0.573	CLONAL	1	TRUE	1	0.507190134635183	3		604	772	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37059022	37059022	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	150	481	0	ENST00000231790.2:c.816G>C	p.Leu272Phe	p.L272F	ENST00000231790	NM_000249.3	272	ttG/ttC	10/19	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.507190134635183	2		481	547	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158343	106158343	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	32	588	0	ENST00000380013.4:c.3244G>C	p.Glu1082Gln	p.E1082Q	ENST00000380013	NM_001127208.2	1082	Gag/Cag	3/11	1	2	FACETS	0.221	0.179	0.269	0.221	0.179	0.269	SUBCLONAL	1	TRUE	1	0.507190134635183	2		588	571	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124467361	124467361	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0066625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	125	405	0	ENST00000357628.3:c.1595-2A>T		p.X532_splice	ENST00000357628	NM_015450.2	532			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.507190134635183	2		405	463	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124503404	124503404	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	88	384	0	ENST00000357628.3:c.546G>T	p.Lys182Asn	p.K182N	ENST00000357628	NM_015450.2	182	aaG/aaT	8/19	1	2	FACETS	0.98	0.876	1	0.98	0.876	1	CLONAL	1	TRUE	1	0.507190134635183	2		384	354	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045871	47045871	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1556782770	NA	P-0066625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	219	748	0	ENST00000377604.3:c.2668-2A>G		p.X890_splice	ENST00000377604	NM_001204468.1	890			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.507190134635183	2		748	820	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412436	63412436	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	186	733	0	ENST00000330258.3:c.731A>T	p.Glu244Val	p.E244V	ENST00000330258	NM_152424.3	244	gAa/gTa	2/2	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.507190134635183	2		733	713	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0066626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	696	345	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.530600719466915	5	FACETS	0.995	0.972	1	0.995	0.972	1	CLONAL	5	TRUE	0	0.54155178357473	5		345	936	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0066626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	20	442	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.547684589481254	5	FACETS	0.149	0.113	0.192	0.05	0.037	0.064	SUBCLONAL	1	TRUE	2	0.54155178357473	5		442	896	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828552	72828552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	269	543	0	ENST00000268489.5:c.8029G>A	p.Glu2677Lys	p.E2677K	ENST00000268489	NM_006885.3	2677	Gag/Aag	9/10	0.223372204863899	2	FACETS	0.775	0.732	0.818	0.775	0.732	0.818	INDETERMINATE	2	TRUE	0	0.54155178357473	2		543	641	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643524	38643524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758102077	NA	P-0066626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	58	516	0	ENST00000299084.4:c.994C>T	p.Arg332Cys	p.R332C	ENST00000299084	NM_152594.2	332	Cgt/Tgt	7/7	0.547684589481254	3	FACETS	0.394	0.338	0.455	0.131	0.112	0.152	SUBCLONAL	1	TRUE	0	0.54155178357473	3		516	691	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190804	106190804	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	267	429	0	ENST00000380013.4:c.4082G>A	p.Gly1361Asp	p.G1361D	ENST00000380013	NM_001127208.2	1361	gGt/gAt	9/11	0.547684589481254	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.54155178357473	2		429	491	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32971078	32971078	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	178	435	0	ENST00000380152.3:c.9545A>T	p.His3182Leu	p.H3182L	ENST00000380152		3182	cAt/cTt	26/27	0.235445815739426	5	FACETS	1	0.983	1	0.796	0.74	0.853	INDETERMINATE	2	TRUE	2	0.54155178357473	5		435	499	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122680	108122680	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0066626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	296	494	0	ENST00000278616.4:c.1724C>G	p.Ser575Ter	p.S575*	ENST00000278616	NM_000051.3	575	tCa/tGa	11/63	0.547684589481254	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	0	0.54155178357473	3		494	440	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439862	220439863	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0066626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	432	628	0	ENST00000243786.2:c.717dup	p.Pro240AlafsTer114	p.P240Afs*114	ENST00000243786	NM_002191.3	239	tgg/tGgg	2/2	0.547684589481254	3	FACETS	0.927	0.893	0.961	0.927	0.893	0.961	CLONAL	3	TRUE	0	0.54155178357473	3		628	729	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032058	10032058	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	37	477	0	ENST00000330684.3:c.765del	p.Trp255Ter	p.W255*	ENST00000330684	NM_001134407.1	255	tgG/tg	3/13	NA	2	FACETS	0.234	0.192	0.281			1	INDETERMINATE	1	TRUE	NA	0.54155178357473	2		477	584	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426790	49426811	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGCTGTAAAGAGCCCATGGG	GCTGCTGTAAAGAGCCCATGGG	-	novel	NA	P-0066629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	32	503	0	ENST00000301067.7:c.11677_11698del	p.Pro3893PhefsTer79	p.P3893Ffs*79	ENST00000301067	NM_003482.3	3893	CCCATGGGCTCTTTACAGCAGCtt/tt	39/54	0.126017929467077	3	FACETS	0.277	0.224	0.337	0.139	0.112	0.169	INDETERMINATE	1	TRUE	1	0.503587014915234	3		503	574	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046680	42046681	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	136	440	0	ENST00000219905.7:c.7056dup	p.Glu2353Ter	p.E2353*	ENST00000219905	NM_001164273.1	2352	att/aTtt	18/24	1	2	FACETS	0.968	0.884	1	0.968	0.884	1	CLONAL	1	TRUE	1	0.503587014915234	2		440	558	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061109	38061112	+	frameshift_variant	Frame_Shift_Del	DEL	GGCT	GGCT	CG	novel	NA	P-0066629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	9	429	0	ENST00000250448.2:c.877_880delinsCG	p.Ser293ArgfsTer9	p.S293Rfs*9	ENST00000250448	NM_004496.3	293	AGCCgc/CGgc	2/2	0.359608669794584	1	FACETS	0.082	0.053	0.118	0.082	0.053	0.118	SUBCLONAL	1	TRUE	0	0.503587014915234	1		429	327	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0066630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	104	539	0				ENST00000310581	NM_198253.2	-/1132			0.460818768321563	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.460818768321563	1		539	287	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0066630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	155	455	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.188637810240134	5	FACETS	0.883	0.811	0.958			1	INDETERMINATE	2	TRUE	NA	0.460818768321563	5		455	644	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920412	134920412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746798014	NA	P-0066630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	128	445	0	ENST00000398015.3:c.2227C>T	p.Arg743Trp	p.R743W	ENST00000398015	NM_004441.4	743	Cgg/Tgg	12/16	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.460818768321563	2		445	544	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444289	50444289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	76	532	0	ENST00000331340.3:c.219G>A	p.Met73Ile	p.M73I	ENST00000331340	NM_006060.4	73	atG/atA	4/8	0.279083683222994	1	FACETS	0.447	0.392	0.506	0.447	0.392	0.506	SUBCLONAL	1	TRUE	0	0.460818768321563	1		532	568	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128206814	128206814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	133	337	0	ENST00000265960.3:c.1409C>T	p.Ser470Leu	p.S470L	ENST00000265960	NM_001006617.1	470	tCg/tTg	11/12	0.460818768321563	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.460818768321563	1		337	416	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212522507	212522507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	69	426	0	ENST00000342788.4:c.1918G>A	p.Gly640Ser	p.G640S	ENST00000342788	NM_005235.2	640	Ggc/Agc	16/28	0.23816072713589	1	FACETS	0.453	0.395	0.515	0.453	0.395	0.515	INDETERMINATE	1	TRUE	0	0.460818768321563	1		426	509	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509175	106509175	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	77	501	0	ENST00000359195.3:c.1169G>A	p.Gly390Glu	p.G390E	ENST00000359195	NM_002649.2	390	gGg/gAg	2/11	1	2	FACETS	0.543	0.477	0.615	0.543	0.477	0.615	SUBCLONAL	1	TRUE	1	0.460818768321563	2		501	615	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673388	30673388	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	166	617	0	ENST00000376406.3:c.3572A>G	p.Lys1191Arg	p.K1191R	ENST00000376406	NM_014641.2	1191	aAa/aGa	10/15	1	2	FACETS	0.933	0.859	1	0.933	0.859	1	CLONAL	1	TRUE	1	0.460818768321563	2		617	772	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141561	11141561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	146	445	0	ENST00000358026.2:c.3538C>T	p.Pro1180Ser	p.P1180S	ENST00000358026	NM_001128849.1	1180	Cct/Tct	25/36	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.460818768321563	2		445	627	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540746	187540746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	145	474	0	ENST00000441802.2:c.6994C>T	p.His2332Tyr	p.H2332Y	ENST00000441802	NM_005245.3	2332	Cat/Tat	10/27	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.460818768321563	2		474	616	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737509	204737509	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs758600786	NA	P-0066630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	74	428	0	ENST00000302823.3:c.646C>T	p.Gln216Ter	p.Q216*	ENST00000302823	NM_005214.4	216	Cag/Tag	4/4	0.23816072713589	1	FACETS	0.516	0.453	0.584	0.516	0.453	0.584	INDETERMINATE	1	TRUE	0	0.460818768321563	1		428	479	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279353	38279354	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0066630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	135	449	0	ENST00000425967.3:c.1135_1136delinsAT	p.Gly379Ile	p.G379I	ENST00000425967	NM_001174067.1	379	GGa/ATa	9/19	1	2	FACETS	0.88	0.801	0.962	0.88	0.801	0.962	CLONAL	1	TRUE	1	0.460818768321563	2		449	666	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306634	41306634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1238580448	NA	P-0066630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	107	357	0	ENST00000373198.4:c.1025C>T	p.Ser342Phe	p.S342F	ENST00000373198	NM_133170.3	342	tCt/tTt	7/32	0.182226043544668	3	FACETS	1	0.971	1	0.605	0.546	0.668	INDETERMINATE	1	TRUE	1	0.460818768321563	3		357	472	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117233	7117234	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0066630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	128	488	0	ENST00000302850.5:c.3982_3983delinsAT	p.Pro1328Ile	p.P1328I	ENST00000302850	NM_000208.2	1328	CCc/ATc	22/22	1	2	FACETS	0.855	0.776	0.937	0.855	0.776	0.937	CLONAL	1	TRUE	1	0.460818768321563	2		488	650	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849141	156849141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1419179271	NA	P-0066630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	75	437	0	ENST00000524377.1:c.2033C>T	p.Thr678Ile	p.T678I	ENST00000524377	NM_002529.3	678	aCc/aTc	15/17	0.182226043544668	3	FACETS	0.557	0.488	0.632	0.279	0.244	0.316	INDETERMINATE	1	TRUE	1	0.460818768321563	3		437	719	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860328	151860328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	131	450	0	ENST00000262189.6:c.10334G>A	p.Arg3445Lys	p.R3445K	ENST00000262189	NM_170606.2	3445	aGg/aAg	43/59	0.279083683222994	1	FACETS	0.777	0.708	0.849	0.777	0.708	0.849	SUBCLONAL	1	TRUE	0	0.460818768321563	1		450	563	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914696	39914696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	102	341	0	ENST00000378444.4:c.4666C>T	p.Pro1556Ser	p.P1556S	ENST00000378444	NM_001123385.1	1556	Ccc/Tcc	12/15	1	2	FACETS	0.93	0.836	1	0.93	0.836	1	CLONAL	1	TRUE	1	0.460818768321563	2		341	476	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024589	14024589	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	97	353	0	ENST00000311895.7:c.815C>T	p.Pro272Leu	p.P272L	ENST00000311895	NM_005236.2	272	cCt/cTt	5/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.460818768321563	2		353	378	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066632-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	121	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.842089169227788	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	0	0.842089169227788	3		341	135	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0066632-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	186	248	2	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.795815584910831	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.842089169227788	2		250	217	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003344	42003344	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066632-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	289	297	5	ENST00000219905.7:c.2881G>T	p.Glu961Ter	p.E961*	ENST00000219905	NM_001164273.1	961	Gaa/Taa	8/24	0.810415349297241	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.842089169227788	2		302	338	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31407020	31407020	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066632-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	162	241	2	ENST00000344624.3:c.3887G>A	p.Arg1296Gln	p.R1296Q	ENST00000344624		1296	cGa/cAa	31/33	0.489995046094529	3	FACETS	0.862	0.806	0.919	0.862	0.806	0.919	INDETERMINATE	2	TRUE	1	0.842089169227788	3		243	317	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578544	7578545	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0066632-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	367	262	3	ENST00000269305.4:c.385dup	p.Ala129GlyfsTer20	p.A129Gfs*20	ENST00000269305	NM_001126112.2	129	gcc/gGcc	5/11	0.798124191949815	2	FACETS	0.921	0.893	0.948	0.921	0.893	0.948	CLONAL	2	TRUE	0	0.842089169227788	2		265	473	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938672	76938681	+	frameshift_variant	Frame_Shift_Del	DEL	TGATAGTTTT	TGATAGTTTT	-	novel	NA	P-0066632-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	38	271	5	ENST00000373344.5:c.2067_2076del	p.Lys690PhefsTer3	p.K690Ffs*3	ENST00000373344	NM_000489.3	689	caAAAACTATCA/ca	9/35	0.314476849976226	5	FACETS	1	0.931	1	0.408	0.342	0.479	INDETERMINATE	1	TRUE	2	0.842089169227788	5		276	167	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295591	1295591	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0066632-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	149	269	0				ENST00000310581	NM_198253.2	-/1132			0.716838806932588	4	FACETS	0.96	0.879	1	0.48	0.439	0.522	CLONAL	1	TRUE	2	0.842089169227788	4		269	679	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045858	26045858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	34	608	0	ENST00000540144.1:c.220G>A	p.Glu74Lys	p.E74K	ENST00000540144	NM_003531.2	74	Gaa/Aaa	1/1	1	2	FACETS	0.455	0.371	0.549	0.455	0.371	0.549	SUBCLONAL	1	TRUE	1	0.311993638185694	2		608	479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0066634-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	218	744	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.677159088442219	1	FACETS	0.888	0.84	0.935	0.888	0.84	0.935	CLONAL	1	TRUE	0	0.772744417960343	1		745	390	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206857	162206857	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs373750972	NA	P-0066634-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	255	585	0	ENST00000366898.1:c.818A>G	p.Asn273Ser	p.N273S	ENST00000366898	NM_004562.2	273	aAt/aGt	7/12	1	2	FACETS	0.985	0.928	1	0.985	0.928	1	CLONAL	1	TRUE	1	0.772744417960343	2		585	670	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066644-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	176	446	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.942	0.878	1	0.942	0.878	1	CLONAL	1	TRUE	1	0.916248583084048	2		446	408	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993339	72993339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368995910	NA	P-0066644-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	115	552	0	ENST00000268489.5:c.706G>A	p.Val236Met	p.V236M	ENST00000268489	NM_006885.3	236	Gtg/Atg	2/10	1	2	FACETS	0.329	0.296	0.363	0.329	0.296	0.363	SUBCLONAL	1	TRUE	1	0.916248583084048	2		552	764	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0066645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	135	456	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.600180924035972	2		456	415	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971717	18971717	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	200	1377	0	ENST00000262803.5:c.2383C>G	p.Pro795Ala	p.P795A	ENST00000262803	NM_002911.3	795	Ccc/Gcc	17/24	1	2	FACETS	0.993	0.924	1	0.993	0.924	1	CLONAL	1	TRUE	1	0.600180924035972	2		1377	671	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0066646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	24	325	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.878	0.689	1	0.878	0.689	1	CLONAL	1	TRUE	1	0.172998804833004	2		325	316	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888189	112888189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507511	NA	P-0066646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	71	499	0	ENST00000351677.2:c.205G>A	p.Glu69Lys	p.E69K	ENST00000351677	NM_002834.3	69	Gag/Aag	3/16	1	2	FACETS	0.87	0.761	0.986	1	0.979	1	CLONAL	2	TRUE	1	0.172998804833004	2		499	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0066646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	85	485	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	1	2	FACETS	0.977	0.866	1	1	0.984	1	CLONAL	2	TRUE	1	0.172998804833004	2		485	503	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188188	32188188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370312303	NA	P-0066646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	70	660	0	ENST00000375023.3:c.1153C>T	p.Arg385Cys	p.R385C	ENST00000375023	NM_004557.3	385	Cgc/Tgc	6/30	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.172998804833004	2		660	649	SUCCESS
APC	324	MSKCC	GRCh37	5	112177149	112177149	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	31	558	0	ENST00000257430.4:c.5858A>G	p.Asn1953Ser	p.N1953S	ENST00000257430	NM_000038.5	1953	aAt/aGt	16/16	1	2	FACETS	0.851	0.688	1	0.851	0.688	1	CLONAL	1	TRUE	1	0.172998804833004	2		558	421	SUCCESS
APC	324	MSKCC	GRCh37	5	112177137	112177137	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	31	575	0	ENST00000257430.4:c.5849del	p.Lys1950SerfsTer20	p.K1950Sfs*20	ENST00000257430	NM_000038.5	1949	gAa/ga	16/16	1	2	FACETS	0.826	0.668	1	0.826	0.668	1	CLONAL	1	TRUE	1	0.172998804833004	2		575	434	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938931	178938933	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	novel	NA	P-0066646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	48	213	0	ENST00000263967.3:c.2175_2177del	p.Asp725del	p.D725del	ENST00000263967	NM_006218.2	725	GAT/-	14/21	0.172998804833004	3	FACETS	0.962	0.823	1	1	0.962	1	CLONAL	3	TRUE	1	0.172998804833004	3		213	209	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431556	6431556	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	51	305	0	ENST00000356142.4:c.109T>G	p.Phe37Val	p.F37V	ENST00000356142	NM_018890.3	37	Ttt/Gtt	3/7	1	2	FACETS	0.812	0.693	0.942	1	0.968	1	CLONAL	2	TRUE	1	0.172998804833004	2		305	363	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0066651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	106	441	3	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	1	2	FACETS	0.976	0.876	1	0.976	0.876	1	CLONAL	1	TRUE	1	0.310255890252173	2		444	700	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888075	81888075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780140339	NA	P-0066651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	65	525	0	ENST00000359376.3:c.220C>T	p.Arg74Cys	p.R74C	ENST00000359376	NM_002661.3	74	Cgc/Tgc	3/33	1	2	FACETS	0.803	0.697	0.917	0.803	0.697	0.917	CLONAL	1	TRUE	1	0.310255890252173	2		525	522	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929516	81929516	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs760949449	NA	P-0066651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	65	657	0	ENST00000359376.3:c.1177G>T	p.Ala393Ser	p.A393S	ENST00000359376	NM_002661.3	393	Gcc/Tcc	13/33	1	2	FACETS	0.599	0.518	0.686	0.599	0.518	0.686	SUBCLONAL	1	TRUE	1	0.310255890252173	2		657	700	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs985033810	NA	P-0066651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	102	488	2	ENST00000269305.4:c.731G>T	p.Gly244Val	p.G244V	ENST00000269305	NM_001126112.2	244	gGc/gTc	7/11	0.190908741432012	2	FACETS	1	0.943	1	0.54	0.484	0.599	CLONAL	1	TRUE	0	0.310255890252173	2		490	609	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082359	16082359	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	85	687	2	ENST00000281043.3:c.173C>T	p.Thr58Met	p.T58M	ENST00000281043	NM_005378.4	58	aCg/aTg	2/3	0.305485876093451	1	FACETS	0.86	0.762	0.965	0.86	0.762	0.965	CLONAL	1	TRUE	0	0.310255890252173	1		689	538	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69143594	69143594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	47	462	0	ENST00000288368.4:c.4802C>T	p.Pro1601Leu	p.P1601L	ENST00000288368	NM_024870.2	1601	cCc/cTc	40/40	1	2	FACETS	0.542	0.457	0.636	0.542	0.457	0.636	SUBCLONAL	1	TRUE	1	0.310255890252173	2		462	559	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166590	118166590	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	45	648	0	ENST00000369448.3:c.1100A>G	p.Asn367Ser	p.N367S	ENST00000369448	NM_017709.3	367	aAc/aGc	2/2	1	2	FACETS	0.445	0.373	0.525	0.445	0.373	0.525	SUBCLONAL	1	TRUE	1	0.310255890252173	2		648	652	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211644	46211645	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	108	452	0	ENST00000334344.6:c.612dup	p.Ala205CysfsTer2	p.A205Cfs*2	ENST00000334344	NM_152641.2	204	ctt/cTtt	5/21	0.217481064840863	2	FACETS	1	0.98	1	0.684	0.616	0.755	CLONAL	1	TRUE	0	0.310255890252173	2		452	509	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439522	220439522	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	110	758	0	ENST00000243786.2:c.375G>T	p.Gln125His	p.Q125H	ENST00000243786	NM_002191.3	125	caG/caT	2/2	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.310255890252173	2		758	696	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546909	9546909	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	169	695	0	ENST00000353224.5:c.1113C>A	p.His371Gln	p.H371Q	ENST00000353224	NM_177990.2	371	caC/caA	5/10	0.155271663246489	5	FACETS	0.926	0.852	1	0.617	0.568	0.669	INDETERMINATE	2	TRUE	2	0.310255890252173	5		695	862	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171654	36171654	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	144	594	0	ENST00000300305.3:c.911C>T	p.Pro304Leu	p.P304L	ENST00000300305		304	cCt/cTt	7/8	0.305485876093451	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.310255890252173	1		594	770	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070903	30070903	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	91	580	0	ENST00000338641.4:c.1420del	p.Glu474ArgfsTer11	p.E474Rfs*11	ENST00000338641	NM_000268.3	473	ctG/ct	13/16	0.160367928084851	2	FACETS	1	0.945	1	0.549	0.489	0.613	INDETERMINATE	1	TRUE	0	0.310255890252173	2		580	534	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149290651	149290651	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	191	444	0	ENST00000360632.3:c.568G>T	p.Val190Leu	p.V190L	ENST00000360632	NM_015472.4	190	Gtg/Ttg	3/7	0.282708031852597	3	FACETS	1	0.985	1	0.808	0.751	0.865	CLONAL	2	TRUE	0	0.310255890252173	3		444	587	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92404138	92404138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1374316336	NA	P-0066651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	61	562	0	ENST00000265734.4:c.241G>A	p.Asp81Asn	p.D81N	ENST00000265734	NM_001259.6	81	Gat/Aat	3/8	0.310255890252173	5	FACETS	0.569	0.489	0.657			1	SUBCLONAL	1	TRUE	NA	0.310255890252173	5		562	1012	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357638	70357638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	33	372	0	ENST00000374080.3:c.5889G>A	p.Met1963Ile	p.M1963I	ENST00000374080		1963	atG/atA	41/45	1	1	FACETS	0.58	0.473	0.699	0.58	0.473	0.699	SUBCLONAL	1	TRUE	0	0.310255890252173	1		372	310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0066654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	71	532	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.275158262398465	1	FACETS	0.978	0.857	1	0.978	0.857	1	CLONAL	1	TRUE	0	0.275158262398465	1		532	455	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	67	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.275158262398465	2		341	416	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584320	52584532	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTATTTTAATTGTATAAGAAAAAGGGGTGTTTATTGTATGATATACTATGCTAACAGCAGTAAGACAGCTTTGAGGAAGCATGTATTTCACAAAGGCTTATTTAGAAGGAATCTTACCTGCCAGTGTCTGATCCCACTTGCTAATGCTGTTGGACTCCGCACTGAGTCCTTCAATGTATTTCAGGTAGGCCTCTGAGTGAAGAAGCCGCTGGG	TTATTTTAATTGTATAAGAAAAAGGGGTGTTTATTGTATGATATACTATGCTAACAGCAGTAAGACAGCTTTGAGGAAGCATGTATTTCACAAAGGCTTATTTAGAAGGAATCTTACCTGCCAGTGTCTGATCCCACTTGCTAATGCTGTTGGACTCCGCACTGAGTCCTTCAATGTATTTCAGGTAGGCCTCTGAGTGAAGAAGCCGCTGGG	-	novel	NA	P-0066654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	45	120	0	ENST00000394830.3:c.4481_4576+117del		p.X1494_splice	ENST00000394830	NM_018313.4	1494		29/30	0.275158262398465	1	FACETS	0.931	0.81	1	1	0.98	1	CLONAL	3	TRUE	0	0.275158262398465	1		120	101	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643828	38643828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779454951	NA	P-0066654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	66	519	0	ENST00000299084.4:c.1298G>A	p.Cys433Tyr	p.C433Y	ENST00000299084	NM_152594.2	433	tGt/tAt	7/7	1	2	FACETS	0.848	0.736	0.968	0.848	0.736	0.968	CLONAL	1	TRUE	1	0.275158262398465	2		519	566	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713865	30713865	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	68	641	0	ENST00000295754.5:c.1190A>T	p.Asp397Val	p.D397V	ENST00000295754	NM_003242.5	397	gAc/gTc	4/7	0.275158262398465	1	FACETS	0.714	0.621	0.814	0.714	0.621	0.814	SUBCLONAL	1	TRUE	0	0.275158262398465	1		641	597	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028804	47028804	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	40	238	0	ENST00000377604.3:c.108C>A	p.Tyr36Ter	p.Y36*	ENST00000377604	NM_001204468.1	36	taC/taA	3/24	1	1	FACETS	1	0.852	1	1	0.97	1	CLONAL	2	TRUE	0	0.229485511966744	1		238	153	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411856	116411882	+	intron_variant	Intron	DEL	CCATGATAGCCGTCTTTAACAAGCTCT	CCATGATAGCCGTCTTTAACAAGCTCT	-	novel	NA	P-0066655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	104	536	0	ENST00000397752.3:c.2888-47_2888-21del		p.*963*	ENST00000397752	NM_000245.2	-/1390			0.229485511966744	3	FACETS	1	0.922	1	1	0.922	1	CLONAL	3	TRUE	0	0.229485511966744	3		536	330	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101756	71101756	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0066665-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	150	408	1	ENST00000318789.4:c.442A>T	p.Lys148Ter	p.K148*	ENST00000318789	NM_032682.5	148	Aaa/Taa	9/21	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.488115929647706	2		409	548	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41201182	41201182	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066665-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	88	444	0	ENST00000357654.3:c.5362G>A	p.Gly1788Ser	p.G1788S	ENST00000357654	NM_007294.3	1788	Ggt/Agt	21/23	1	2	FACETS	0.879	0.784	0.98	0.879	0.784	0.98	CLONAL	1	TRUE	1	0.488115929647706	2		444	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0066666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	500	512	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.643478201204802	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	0	0.643478201204802	3		512	669	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007152	152007152	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	191	368	0	ENST00000262189.6:c.748T>C	p.Trp250Arg	p.W250R	ENST00000262189	NM_170606.2	250	Tgg/Cgg	6/59	0.607233088367557	3	FACETS	1	0.983	1	0.593	0.55	0.636	CLONAL	1	TRUE	1	0.643478201204802	3		368	662	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0066667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	49	539	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.225686481139874	2		539	375	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0066667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	76	353	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.225686481139874	2		353	613	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325158	123325158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56226109	NA	P-0066667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	77	450	0	ENST00000358487.5:c.170C>T	p.Ser57Leu	p.S57L	ENST00000358487	NM_000141.4	57	tCg/tTg	3/18	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.225686481139874	2		450	646	SUCCESS
APC	324	MSKCC	GRCh37	5	112175876	112175876	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085992	NA	P-0066667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	105	416	0	ENST00000257430.4:c.4585C>T	p.Gln1529Ter	p.Q1529*	ENST00000257430	NM_000038.5	1529	Cag/Tag	16/16	0.211500312058304	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.225686481139874	1		416	704	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298003	15298003	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752404540	NA	P-0066667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	57	429	0	ENST00000263388.2:c.1753G>A	p.Glu585Lys	p.E585K	ENST00000263388	NM_000435.2	585	Gaa/Aaa	11/33	1	2	FACETS	0.853	0.732	0.986	0.853	0.732	0.986	CLONAL	1	TRUE	1	0.225686481139874	2		429	592	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980844	40980844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	52	462	0	ENST00000373198.4:c.1642G>A	p.Glu548Lys	p.E548K	ENST00000373198	NM_133170.3	548	Gaa/Aaa	10/32	1	2	FACETS	0.747	0.635	0.87	0.747	0.635	0.87	SUBCLONAL	1	TRUE	1	0.225686481139874	2		462	617	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546607	9546607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	99	445	0	ENST00000353224.5:c.1415G>A	p.Gly472Glu	p.G472E	ENST00000353224	NM_177990.2	472	gGg/gAg	5/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.225686481139874	2		445	666	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468182	50468182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	51	440	0	ENST00000331340.3:c.1417G>A	p.Asp473Asn	p.D473N	ENST00000331340	NM_006060.4	473	Gat/Aat	8/8	1	2	FACETS	0.828	0.703	0.964	0.828	0.703	0.964	CLONAL	1	TRUE	1	0.225686481139874	2		440	546	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511068	148511068	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	60	315	0	ENST00000320356.2:c.1834C>T	p.Gln612Ter	p.Q612*	ENST00000320356	NM_004456.4	612	Cag/Tag	15/20	1	2	FACETS	0.922	0.794	1	0.922	0.794	1	CLONAL	1	TRUE	1	0.225686481139874	2		315	577	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857788	9857788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs918332999	NA	P-0066667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	86	459	0	ENST00000330684.3:c.3613G>A	p.Glu1205Lys	p.E1205K	ENST00000330684	NM_001134407.1	1205	Gag/Aag	13/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.225686481139874	2		459	652	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023105	33023105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	62	407	0	ENST00000300177.4:c.214G>A	p.Glu72Lys	p.E72K	ENST00000300177	NM_001191322.1	72	Gag/Aag	2/2	1	2	FACETS	0.951	0.821	1	0.951	0.821	1	CLONAL	1	TRUE	1	0.225686481139874	2		407	578	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882055	36882055	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773593708	NA	P-0066667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	70	446	0	ENST00000358127.4:c.958C>T	p.Pro320Ser	p.P320S	ENST00000358127	NM_001280556.1	320	Ccc/Tcc	8/10	0.225686481139874	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.225686481139874	1		446	483	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227019	2227019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	47	391	0	ENST00000398665.3:c.4499C>T	p.Ser1500Phe	p.S1500F	ENST00000398665	NM_032482.2	1500	tCt/tTt	27/28	1	2	FACETS	0.803	0.677	0.941	0.803	0.677	0.941	CLONAL	1	TRUE	1	0.225686481139874	2		391	519	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403593	138403593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768628634	NA	P-0066667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	87	377	0	ENST00000289153.2:c.2189C>T	p.Ala730Val	p.A730V	ENST00000289153	NM_006219.2	730	gCc/gTc	15/22	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.225686481139874	2		377	613	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156721	20156721	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	55	169	0	ENST00000379607.5:c.36A>C	p.Arg12Ser	p.R12S	ENST00000379607	NM_001412.3	12	agA/agC	2/7	1	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.225686481139874	1		169	327	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808338	1808338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	69	643	0	ENST00000260795.2:c.2096C>T	p.Pro699Leu	p.P699L	ENST00000260795		699	cCt/cTt	15/17	NA	2	FACETS	0.929	0.809	1			1	INDETERMINATE	1	TRUE	NA	0.225686481139874	2		643	658	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718096	117718096	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	62	363	0	ENST00000368508.3:c.761T>C	p.Leu254Ser	p.L254S	ENST00000368508	NM_002944.2	254	tTa/tCa	7/43	0.225686481139874	1	FACETS	0.987	0.854	1	0.987	0.854	1	CLONAL	1	TRUE	0	0.225686481139874	1		363	494	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50810099	50810099	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	61	359	0	ENST00000398568.2:c.923C>G	p.Thr308Arg	p.T308R	ENST00000398568	NM_001042412.1	308	aCg/aGg	6/18	0.225686481139874	1	FACETS	0.82	0.707	0.942	0.82	0.707	0.942	CLONAL	1	TRUE	0	0.225686481139874	1		359	585	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392035	81392035	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	56	315	0	ENST00000222390.5:c.242C>T	p.Pro81Leu	p.P81L	ENST00000222390	NM_000601.4	81	cCa/cTa	2/18	1	2	FACETS	0.928	0.795	1	0.928	0.795	1	CLONAL	1	TRUE	1	0.225686481139874	2		315	535	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218448	36218449	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0066667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	48	423	0	ENST00000222270.7:c.4227_4228delinsTT	p.Gln1410Ter	p.Q1410*	ENST00000222270	NM_014727.1	1409	ctCCag/ctTTag	16/37	1	2	FACETS	0.861	0.728	1	0.861	0.728	1	CLONAL	1	TRUE	1	0.225686481139874	2		423	494	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047138	77047138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	87	453	0	ENST00000356341.3:c.1406C>T	p.Pro469Leu	p.P469L	ENST00000356341	NM_002576.4	469	cCt/cTt	13/15	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.225686481139874	2		453	746	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178079	142178079	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	70	365	0	ENST00000350721.4:c.7339C>T	p.Pro2447Ser	p.P2447S	ENST00000350721	NM_001184.3	2447	Cct/Tct	43/47	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.225686481139874	2		365	602	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631954	67631954	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	78	496	0	ENST00000272342.5:c.2140A>G	p.Lys714Glu	p.K714E	ENST00000272342	NM_019002.3	714	Aag/Gag	5/6	1	2	FACETS	0.952	0.836	1	0.952	0.836	1	CLONAL	1	TRUE	1	0.225686481139874	2		496	726	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981996	70981996	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755804388	NA	P-0066667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	63	420	0	ENST00000276594.2:c.100C>T	p.Pro34Ser	p.P34S	ENST00000276594	NM_024504.3	34	Ccg/Tcg	2/8	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.225686481139874	2		420	481	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782621	9782621	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1310527452	NA	P-0066667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	55	352	0	ENST00000377346.4:c.2383C>T	p.Gln795Ter	p.Q795*	ENST00000377346	NM_005026.3	795	Cag/Tag	19/24	1	2	FACETS	0.932	0.798	1	0.932	0.798	1	CLONAL	1	TRUE	1	0.225686481139874	2		352	523	SUCCESS
REST	5978	MSKCC	GRCh37	4	57797783	57797783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	69	404	0	ENST00000309042.7:c.2759C>T	p.Ser920Leu	p.S920L	ENST00000309042	NM_005612.4	920	tCa/tTa	4/4	1	2	FACETS	0.895	0.779	1	0.895	0.779	1	CLONAL	1	TRUE	1	0.225686481139874	2		404	683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0066668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	145	429	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	1	2	FACETS	0.967	0.887	1	0.967	0.887	1	CLONAL	1	TRUE	1	0.552274341955906	2		429	543	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0066668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	111	325	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.552274341955906	2		325	400	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0066668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	176	721	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.552274341955906	2		721	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0066668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	134	336	0	ENST00000269305.4:c.994-1G>T		p.X332_splice	ENST00000269305	NM_001126112.2	332			1	2	FACETS	0.98	0.896	1	0.98	0.896	1	CLONAL	1	TRUE	1	0.552274341955906	2		336	495	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100108	157100132	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGCAGGAGGCGGCGGCGGCGGCG	GCAGCAGGAGGCGGCGGCGGCGGCG	-	novel	NA	P-0066668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	125	486	0	ENST00000346085.5:c.1047_1071del	p.Ala350MetfsTer11	p.A350Mfs*11	ENST00000346085	NM_020732.3	349	GCAGCAGGAGGCGGCGGCGGCGGCGgc/gc	1/20	1	2	FACETS	0.872	0.793	0.954	0.872	0.793	0.954	CLONAL	1	TRUE	1	0.552274341955906	2		486	519	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119734	70119736	+	frameshift_variant	Frame_Shift_Del	DEL	CAG	CAG	T	novel	NA	P-0066668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	128	288	0	ENST00000245479.2:c.736_738delinsT	p.Gln246SerfsTer5	p.Q246Sfs*5	ENST00000245479	NM_000346.3	246	CAG/T	3/3	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.552274341955906	2		288	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0066669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	212	820	0	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	0.267364367525876	3	FACETS	0.944	0.886	1	0.944	0.886	1	CLONAL	3	FALSE	0	0.353748855398648	3		820	498	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0066669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	208	215	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.353748855398648	7	FACETS	1	0.98	1	0.907	0.855	0.96	CLONAL	5	FALSE	1	0.353748855398648	7		215	407	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552630	18552630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200787716	NA	P-0066669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	287	402	0	ENST00000266497.5:c.2041C>T	p.Arg681Cys	p.R681C	ENST00000266497		681	Cgc/Tgc	14/31	0.353748855398648	5	FACETS	0.925	0.881	0.969			1	CLONAL	5	FALSE	NA	0.353748855398648	5		402	537	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125296	7125296	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs777937157	NA	P-0066669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	43	551	0	ENST00000302850.5:c.3256G>A	p.Val1086Met	p.V1086M	ENST00000302850	NM_000208.2	1086	Gtg/Atg	17/22	0.233423640847401	5	FACETS	0.74	0.619	0.874	0.247	0.206	0.292	SUBCLONAL	1	FALSE	2	0.353748855398648	5		551	503	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744942	39744942	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	94	443	0	ENST00000361337.2:c.1732C>T	p.Gln578Ter	p.Q578*	ENST00000361337	NM_003286.2	578	Cag/Tag	17/21	0.300339099370256	4	FACETS	0.799	0.715	0.888	0.799	0.715	0.888	SUBCLONAL	2	FALSE	2	0.353748855398648	4		443	450	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120419	70120420	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0066669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	68	512	0	ENST00000245479.2:c.1425dup	p.Met476HisfsTer102	p.M476Hfs*102	ENST00000245479	NM_000346.3	474	cgc/cgCc	3/3	0.267364367525876	3	FACETS	1	0.885	1	0.338	0.295	0.385	CLONAL	1	FALSE	0	0.353748855398648	3		512	446	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718249	117718249	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs564942341	NA	P-0066669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	75	420	0	ENST00000368508.3:c.608T>C	p.Ile203Thr	p.I203T	ENST00000368508	NM_002944.2	203	aTt/aCt	7/43	0.125723735925642	4	FACETS	1	0.975	1	0.728	0.642	0.821	INDETERMINATE	1	FALSE	2	0.353748855398648	4		420	394	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162475136	162475136	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	26	400	0	ENST00000366898.1:c.605C>A	p.Pro202His	p.P202H	ENST00000366898	NM_004562.2	202	cCt/cAt	5/12	0.300339099370256	4	FACETS	0.466	0.368	0.578	0.233	0.184	0.289	SUBCLONAL	1	FALSE	2	0.353748855398648	4		400	427	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0066670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	78	535	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.174142303383457	2		535	716	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0066670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	138	439	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.174142303383457	2	FACETS	0.969	0.882	1	0.969	0.882	1	CLONAL	2	TRUE	0	0.174142303383457	2		439	818	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232135	98232135	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	105	376	0	ENST00000331920.6:c.1807C>T	p.Arg603Cys	p.R603C	ENST00000331920	NM_000264.3	603	Cgc/Tgc	13/24	0.15857601042023	3	FACETS	0.977	0.876	1	0.977	0.876	1	CLONAL	2	TRUE	1	0.174142303383457	3		376	671	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847399	68847399	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0066670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	78	379	0	ENST00000261769.5:c.1320+1G>A		p.X440_splice	ENST00000261769	NM_004360.3	440			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.174142303383457	2		379	654	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124532330	124532330	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1554434730	NA	P-0066670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	43	246	0	ENST00000357628.3:c.114C>G	p.Ser38Arg	p.S38R	ENST00000357628	NM_015450.2	38	agC/agG	6/19	0.174142303383457	3	FACETS	1	0.886	1	0.538	0.45	0.636	CLONAL	1	TRUE	1	0.174142303383457	3		246	499	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651493	52651493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	63	366	0	ENST00000394830.3:c.1603G>A	p.Glu535Lys	p.E535K	ENST00000394830	NM_018313.4	535	Gag/Aag	15/30	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.174142303383457	2		366	664	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856025	68856025	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	71	472	0	ENST00000261769.5:c.1833del	p.Ile612Ter	p.I612*	ENST00000261769	NM_004360.3	611	gtC/gt	12/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.174142303383457	2		472	684	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680680	30680680	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs934431987	NA	P-0066670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	61	473	0	ENST00000376406.3:c.1039A>G	p.Met347Val	p.M347V	ENST00000376406	NM_014641.2	347	Atg/Gtg	5/15	1	2	FACETS	0.978	0.843	1	0.978	0.843	1	CLONAL	1	TRUE	1	0.174142303383457	2		473	716	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020245	123020245	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	111	391	0	ENST00000355640.3:c.733A>T	p.Ser245Cys	p.S245C	ENST00000355640		245	Agt/Tgt	2/7	0.174142303383457	8	FACETS	0.968	0.869	1	0.323	0.289	0.358	CLONAL	2	TRUE	2	0.174142303383457	8		391	1002	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0066679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	78	539	0				ENST00000310581	NM_198253.2	-/1132			0.460682153589435	1	FACETS	0.843	0.75	0.939	0.843	0.75	0.939	CLONAL	1	TRUE	0	0.522136127143015	1		539	262	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776220	135776220	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs118203706	NA	P-0066679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	125	371	0	ENST00000298552.3:c.2507C>G	p.Ser836Ter	p.S836*	ENST00000298552	NM_001162426.1	836	tCa/tGa	20/23	0.522136127143015	1	FACETS	0.926	0.847	1	0.926	0.847	1	CLONAL	1	TRUE	0	0.522136127143015	1		371	382	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105238746	105238746	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749544983	NA	P-0066679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	140	325	0	ENST00000349310.3:c.1216C>T	p.Arg406Cys	p.R406C	ENST00000349310	NM_001014432.1	406	Cgc/Tgc	13/15	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.522136127143015	2		325	462	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438048	438048	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	152	322	0	ENST00000399788.2:c.1921C>G	p.Leu641Val	p.L641V	ENST00000399788	NM_001042603.1	641	Ctc/Gtc	14/28	1	2	FACETS	0.901	0.827	0.978	0.901	0.827	0.978	CLONAL	1	TRUE	1	0.522136127143015	2		322	646	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458253	12458253	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	152	291	0	ENST00000287820.6:c.870C>G	p.Ile290Met	p.I290M	ENST00000287820	NM_015869.4	290	atC/atG	6/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.522136127143015	2		291	501	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59793381	59793381	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3014	2617	233	0	ENST00000259008.2:c.2423G>C	p.Arg808Thr	p.R808T	ENST00000259008	NM_032043.2	808	aGa/aCa	17/20	0.522136127143015	32	FACETS	0.983	0.966	1			1	CLONAL	16	TRUE	NA	0.522136127143015	32		233	5631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0066681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	134	545	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.248200593569686	2	FACETS	0.875	0.798	0.956	0.875	0.798	0.956	CLONAL	2	TRUE	0	0.248200593569686	2		546	617	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657089	215657089	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876659369	NA	P-0066681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	40	360	0	ENST00000260947.4:c.296G>A	p.Arg99Lys	p.R99K	ENST00000260947	NM_000465.2	99	aGa/aAa	3/11	0.170206860836467	1	FACETS	0.575	0.477	0.684	0.575	0.477	0.684	SUBCLONAL	1	TRUE	0	0.248200593569686	1		360	491	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37863279	37863279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	60	470	2	ENST00000269571.5:c.110C>T	p.Ala37Val	p.A37V	ENST00000269571		37	gCc/gTc	2/27	0.248200593569686	7	FACETS	0.685	0.588	0.791	0.114	0.098	0.132	SUBCLONAL	1	TRUE	1	0.248200593569686	7		472	1144	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	386	710	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.699227139998938	2	FACETS	0.937	0.903	0.97	0.937	0.903	0.97	CLONAL	2	TRUE	0	0.699227139998938	2		713	589	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	173	621	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.811	0.75	0.874	0.811	0.75	0.874	CLONAL	1	TRUE	1	0.699227139998938	2		622	610	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	173	478	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.972	0.902	1	0.972	0.902	1	CLONAL	1	TRUE	1	0.699227139998938	2		479	509	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675571	86675571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1561325048	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	89	453	0	ENST00000274376.6:c.2513del	p.Asn838MetfsTer4	p.N838Mfs*4	ENST00000274376	NM_002890.2	836	gAa/ga	19/25	1	2	FACETS	0.608	0.542	0.677	0.608	0.542	0.677	SUBCLONAL	1	TRUE	1	0.699227139998938	2		453	419	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	27	389	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.143	0.113	0.177	0.143	0.113	0.177	SUBCLONAL	1	TRUE	1	0.699227139998938	2		389	540	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231488893	231488894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs567805129	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	154	420	0	ENST00000295050.7:c.1263dup	p.Ile422TyrfsTer11	p.I422Yfs*11	ENST00000295050	NM_032018.5	419	aat/aaTt	5/5	1	2	FACETS	0.888	0.819	0.96	0.888	0.819	0.96	CLONAL	1	TRUE	1	0.699227139998938	2		420	496	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	35	481	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.25	0.205	0.301	0.25	0.205	0.301	SUBCLONAL	1	TRUE	1	0.699227139998938	2		481	400	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272336	15272337	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs771517374	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	34	501	1	ENST00000263388.2:c.6102dup	p.Gly2035ArgfsTer60	p.G2035Rfs*60	ENST00000263388	NM_000435.2	2034	-/C	33/33	1	2	FACETS	0.215	0.175	0.26	0.215	0.175	0.26	SUBCLONAL	1	TRUE	1	0.699227139998938	2		502	452	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	144	442	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.766	0.702	0.831	0.766	0.702	0.831	SUBCLONAL	1	TRUE	1	0.699227139998938	2		442	538	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1688567	1688568	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs746550458	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	127	383	1	ENST00000378625.1:c.757dup	p.Ala253GlyfsTer45	p.A253Gfs*45	ENST00000378625	NM_001198994.1	253	gcc/gGcc	6/14	1	2	FACETS	0.934	0.855	1	0.934	0.855	1	CLONAL	1	TRUE	1	0.699227139998938	2		384	389	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2492119	2492119	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	46	466	0	ENST00000355716.4:c.517A>G	p.Asn173Asp	p.N173D	ENST00000355716	NM_003820.2	173	Aat/Gat	5/8	1	2	FACETS	0.322	0.271	0.377	0.322	0.271	0.377	SUBCLONAL	1	TRUE	1	0.699227139998938	2		466	409	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429978	78429978	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	192	384	0	ENST00000370768.2:c.901del	p.Ile301TyrfsTer22	p.I301Yfs*22	ENST00000370768	NM_003902.3	301	Ata/ta	11/20	1	2	FACETS	0.969	0.902	1	0.969	0.902	1	CLONAL	1	TRUE	1	0.699227139998938	2		384	567	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957465	175957465	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	133	412	0	ENST00000367669.3:c.1931del	p.Asn644ThrfsTer3	p.N644Tfs*3	ENST00000367669	NM_022457.5	644	aAc/ac	17/20	1	2	FACETS	0.803	0.734	0.874	0.803	0.734	0.874	CLONAL	1	TRUE	1	0.699227139998938	2		412	474	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	169	693	9	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	1	2	FACETS	0.909	0.841	0.978	0.909	0.841	0.978	CLONAL	1	TRUE	1	0.699227139998938	2		702	532	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	136	382	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.922	0.846	1	0.922	0.846	1	CLONAL	1	TRUE	1	0.699227139998938	2		387	422	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47594883	47594883	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs756343868	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	180	589	0	ENST00000430070.2:c.1204del	p.Glu402ArgfsTer27	p.E402Rfs*27	ENST00000430070	NM_018095.4	402	Gag/ag	4/4	1	2	FACETS	0.948	0.88	1	0.948	0.88	1	CLONAL	1	TRUE	1	0.699227139998938	2		589	543	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589560	69589560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745670123	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	59	739	1	ENST00000168712.1:c.293C>T	p.Ala98Val	p.A98V	ENST00000168712	NM_002007.2	98	gCg/gTg	1/3	1	2	FACETS	0.318	0.273	0.366	0.318	0.273	0.366	SUBCLONAL	1	TRUE	1	0.699227139998938	2		740	531	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944732	71944732	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	48	517	0	ENST00000298229.2:c.2160del	p.Val721CysfsTer37	p.V721Cfs*37	ENST00000298229	NM_001567.3	719	tCc/tc	19/28	1	2	FACETS	0.277	0.234	0.325	0.277	0.234	0.325	SUBCLONAL	1	TRUE	1	0.699227139998938	2		517	495	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945008	31945008	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	58	566	1	ENST00000340398.3:c.93del	p.Ser32LeufsTer5	p.S32Lfs*5	ENST00000340398	NM_001013699.2	31	ccC/cc	1/1	1	2	FACETS	0.281	0.241	0.325	0.281	0.241	0.325	SUBCLONAL	1	TRUE	1	0.699227139998938	2		567	590	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424427	49424427	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs577303074	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	60	422	1	ENST00000301067.7:c.13796C>T	p.Ala4599Val	p.A4599V	ENST00000301067	NM_003482.3	4599	gCg/gTg	41/54	1	2	FACETS	0.398	0.344	0.457	0.398	0.344	0.457	SUBCLONAL	1	TRUE	1	0.699227139998938	2		423	431	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	37	455	4	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.235	0.194	0.282	0.235	0.194	0.282	SUBCLONAL	1	TRUE	1	0.699227139998938	2		459	450	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120535059	120535059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	180	455	0	ENST00000229340.5:c.596G>A	p.Arg199His	p.R199H	ENST00000229340	NM_006861.6	199	cGc/cAc	6/6	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.699227139998938	2		455	500	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	134	484	5	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.81	0.741	0.882	0.81	0.741	0.882	CLONAL	1	TRUE	1	0.699227139998938	2		489	473	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562286	21562286	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755582869	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	166	568	0	ENST00000382592.4:c.1633C>T	p.Arg545Cys	p.R545C	ENST00000382592	NM_014572.2	545	Cgt/Tgt	4/8	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.699227139998938	2		568	467	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562888	21562888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759368766	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	116	481	1	ENST00000382592.4:c.1031C>T	p.Pro344Leu	p.P344L	ENST00000382592	NM_014572.2	344	cCg/cTg	4/8	1	2	FACETS	0.796	0.723	0.871	0.796	0.723	0.871	SUBCLONAL	1	TRUE	1	0.699227139998938	2		482	417	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972625	32972626	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1328254546	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	172	408	0	ENST00000380152.3:c.9981dup	p.Phe3328IlefsTer3	p.F3328Ifs*3	ENST00000380152		3325	-/A	27/27	1	2	FACETS	0.904	0.838	0.973	0.904	0.838	0.973	CLONAL	1	TRUE	1	0.699227139998938	2		408	544	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435306	110435306	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	110	571	0	ENST00000375856.3:c.3095C>A	p.Pro1032Gln	p.P1032Q	ENST00000375856	NM_003749.2	1032	cCg/cAg	1/2	1	2	FACETS	0.753	0.681	0.827	0.753	0.681	0.827	SUBCLONAL	1	TRUE	1	0.699227139998938	2		571	418	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241276	105241276	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	69	478	0	ENST00000349310.3:c.632C>T	p.Thr211Ile	p.T211I	ENST00000349310	NM_001014432.1	211	aCa/aTa	8/15	0.339698330582699	3	FACETS	0.566	0.494	0.643	0.283	0.247	0.322	INDETERMINATE	1	TRUE	1	0.699227139998938	3		478	471	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712535	43712535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756376679	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	221	474	0	ENST00000382044.4:c.4649C>T	p.Thr1550Met	p.T1550M	ENST00000382044	NM_001141980.1	1550	aCg/aTg	21/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.699227139998938	2		474	551	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457294	67457294	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1085307496	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	197	680	0	ENST00000327367.4:c.268C>T	p.Arg90Cys	p.R90C	ENST00000327367	NM_005902.3	90	Cgc/Tgc	2/9	1	2	FACETS	0.918	0.855	0.982	0.918	0.855	0.982	CLONAL	1	TRUE	1	0.699227139998938	2		680	614	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817720	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	144	274	0	ENST00000262367.5:c.3250dup	p.Ile1084AsnfsTer3	p.I1084Nfs*3	ENST00000262367	NM_004380.2	1084	atc/aAtc		1	2	FACETS	0.804	0.738	0.873	0.804	0.738	0.873	CLONAL	1	TRUE	1	0.699227139998938	2		274	512	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828768	3828768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	95	478	0	ENST00000262367.5:c.1874G>A	p.Arg625His	p.R625H	ENST00000262367	NM_004380.2	625	cGc/cAc	9/31	1	2	FACETS	0.461	0.411	0.514	0.461	0.411	0.514	SUBCLONAL	1	TRUE	1	0.699227139998938	2		478	589	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578371	7578371	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	178	524	0	ENST00000269305.4:c.559G>T	p.Gly187Cys	p.G187C	ENST00000269305	NM_001126112.2	187	Ggt/Tgt	5/11	1	2	FACETS	0.964	0.895	1	0.964	0.895	1	CLONAL	1	TRUE	1	0.699227139998938	2		524	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	190	482	0	ENST00000269305.4:c.379T>C	p.Ser127Pro	p.S127P	ENST00000269305	NM_001126112.2	127	Tcc/Ccc	5/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.699227139998938	2		482	517	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16022738	16022738	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	145	347	2	ENST00000268712.3:c.1914del	p.Gly639ValfsTer2	p.G639Vfs*2	ENST00000268712	NM_006311.3	638	aaA/aa	17/46	1	2	FACETS	0.807	0.741	0.875	0.807	0.741	0.875	CLONAL	1	TRUE	1	0.699227139998938	2		349	514	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552144	29552144	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	47	385	0	ENST00000356175.3:c.1882del	p.Tyr628ThrfsTer3	p.Y628Tfs*3	ENST00000356175	NM_000267.3	626	cTt/ct	17/57	1	2	FACETS	0.308	0.26	0.361	0.308	0.26	0.361	SUBCLONAL	1	TRUE	1	0.699227139998938	2		385	436	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870631	40870631	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs751414770	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	128	372	0	ENST00000428826.2:c.772C>T	p.Arg258Ter	p.R258*	ENST00000428826		258	Cga/Tga	9/21	1	2	FACETS	0.939	0.859	1	0.939	0.859	1	CLONAL	1	TRUE	1	0.699227139998938	2		372	390	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368203	45368203	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	69	387	0	ENST00000262160.6:c.1399T>C	p.Ser467Pro	p.S467P	ENST00000262160	NM_005901.5	467	Tca/Cca	11/11	0.189517242411481	1	FACETS	0.295	0.258	0.335	0.295	0.258	0.335	INDETERMINATE	1	TRUE	0	0.699227139998938	1		387	435	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212257	5212257	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs571743236	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	59	493	0	ENST00000357368.4:c.4774G>A	p.Gly1592Ser	p.G1592S	ENST00000357368	NM_002850.3	1592	Ggt/Agt	32/38	1	2	FACETS	0.378	0.325	0.434	0.378	0.325	0.434	SUBCLONAL	1	TRUE	1	0.699227139998938	2		493	447	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271870	15271870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528151296	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	166	593	0	ENST00000263388.2:c.6569C>T	p.Ala2190Val	p.A2190V	ENST00000263388	NM_000435.2	2190	gCg/gTg	33/33	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.699227139998938	2		593	430	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285086	15285086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	151	497	0	ENST00000263388.2:c.4529G>A	p.Arg1510His	p.R1510H	ENST00000263388	NM_000435.2	1510	cGc/cAc	25/33	1	2	FACETS	0.982	0.906	1	0.982	0.906	1	CLONAL	1	TRUE	1	0.699227139998938	2		497	440	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216184	36216184	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	153	577	2	ENST00000222270.7:c.3596del	p.Gly1199AlafsTer156	p.G1199Afs*156	ENST00000222270	NM_014727.1	1198	Ggg/gg	11/37	1	2	FACETS	0.943	0.87	1	0.943	0.87	1	CLONAL	1	TRUE	1	0.699227139998938	2		579	464	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795609	42795609	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	206	706	1	ENST00000575354.2:c.2694del	p.Ala900ProfsTer24	p.A900Pfs*24	ENST00000575354	NM_015125.3	897	Ccc/cc	10/20	1	2	FACETS	0.977	0.912	1	0.977	0.912	1	CLONAL	1	TRUE	1	0.699227139998938	2		707	603	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796882	42796883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761345552	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	148	582	3	ENST00000575354.2:c.3347dup	p.Ser1117LysfsTer34	p.S1117Kfs*34	ENST00000575354	NM_015125.3	1114	gcc/gCcc	14/20	1	2	FACETS	0.788	0.724	0.855	0.788	0.724	0.855	SUBCLONAL	1	TRUE	1	0.699227139998938	2		585	537	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523087	25523087	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746009417	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	144	437	0	ENST00000264709.3:c.98G>A	p.Arg33His	p.R33H	ENST00000264709	NM_175629.2	33	cGt/cAt	3/23	1	2	FACETS	0.974	0.897	1	0.974	0.897	1	CLONAL	1	TRUE	1	0.699227139998938	2		437	423	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213242	39213243	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1558454973	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	82	578	0	ENST00000402219.2:c.3724dup	p.Ser1242LysfsTer2	p.S1242Kfs*2	ENST00000402219	NM_005633.3	1242	agt/aAgt	23/23	1	2	FACETS	0.438	0.386	0.492	0.438	0.386	0.492	SUBCLONAL	1	TRUE	1	0.699227139998938	2		578	536	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030877	36030877	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751005087	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	159	415	1	ENST00000358208.4:c.1156G>A	p.Val386Ile	p.V386I	ENST00000358208		386	Gtc/Atc	10/12	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.699227139998938	2		416	415	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206814	36206814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150042294	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	170	465	1	ENST00000300305.3:c.698G>A	p.Arg233His	p.R233H	ENST00000300305		233	cGc/cAc	6/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.699227139998938	2		466	445	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655236	45655236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140894768	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	154	392	1	ENST00000407780.3:c.616G>A	p.Ala206Thr	p.A206T	ENST00000407780	NM_001283052.1	206	Gca/Aca	4/7	1	2	FACETS	0.992	0.916	1	0.992	0.916	1	CLONAL	1	TRUE	1	0.699227139998938	2		393	444	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691872	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs79375991	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	314	425	7	ENST00000295754.5:c.383del	p.Lys128SerfsTer35	p.K128Sfs*35	ENST00000295754	NM_003242.5	125	gAa/ga	3/7	1	2	FACETS	0.849	0.812	0.885	1	0.996	1	CLONAL	2	TRUE	1	0.699227139998938	2		432	529	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165283	47165283	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	188	465	0	ENST00000409792.3:c.843del	p.Glu282LysfsTer19	p.E282Kfs*19	ENST00000409792	NM_014159.6	281	aaA/aa	3/21	1	2	FACETS	0.884	0.822	0.949	0.884	0.822	0.949	CLONAL	1	TRUE	1	0.699227139998938	2		465	608	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960080	134960080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1042786	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	145	489	1	ENST00000398015.3:c.2437G>A	p.Val813Ile	p.V813I	ENST00000398015	NM_004441.4	813	Gtc/Atc	13/16	NA	2	FACETS	0.892	0.82	0.966			1	INDETERMINATE	1	TRUE	NA	0.699227139998938	2		490	465	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	129	522	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.813	0.742	0.886	0.813	0.742	0.886	CLONAL	1	TRUE	1	0.699227139998938	2		522	454	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	132	454	1	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	0.579	0.527	0.634	0.579	0.527	0.634	SUBCLONAL	1	TRUE	1	0.699227139998938	2		455	652	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187558039	187558039	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	39	377	0	ENST00000441802.2:c.3672del	p.Lys1225AsnfsTer9	p.K1225Nfs*9	ENST00000441802	NM_005245.3	1224	ccC/cc	5/27	1	2	FACETS	0.214	0.177	0.255	0.214	0.177	0.255	SUBCLONAL	1	TRUE	1	0.699227139998938	2		377	522	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945092	38945092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769767383	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	162	411	0	ENST00000357387.3:c.4712C>T	p.Ser1571Leu	p.S1571L	ENST00000357387	NM_152756.3	1571	tCg/tTg	35/38	1	2	FACETS	0.934	0.864	1	0.934	0.864	1	CLONAL	1	TRUE	1	0.699227139998938	2		411	496	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588981	67588981	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	28	405	0	ENST00000274335.5:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000274335		358	Cga/Tga	8/15	1	2	FACETS	0.161	0.128	0.199	0.161	0.128	0.199	SUBCLONAL	1	TRUE	1	0.699227139998938	2		405	496	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944382	131944382	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs748536322	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	156	331	1	ENST00000265335.6:c.2801del	p.Asn934IlefsTer6	p.N934Ifs*6	ENST00000265335		932	Aaa/aa	17/25	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.699227139998938	2		332	417	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	138	468	0	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	1	2	FACETS	0.942	0.865	1	0.942	0.865	1	CLONAL	1	TRUE	1	0.699227139998938	2		468	419	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393180	393180	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1403333371	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	66	396	0	ENST00000380956.4:c.28G>A	p.Gly10Arg	p.G10R	ENST00000380956	NM_001195286.1	10	Gga/Aga	2/9	1	2	FACETS	0.489	0.426	0.556	0.489	0.426	0.556	SUBCLONAL	1	TRUE	1	0.699227139998938	2		396	386	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170135	32170135	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542331250	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	171	514	0	ENST00000375023.3:c.3473G>A	p.Arg1158Gln	p.R1158Q	ENST00000375023	NM_004557.3	1158	cGa/cAa	21/30	0.29411716925444	1	FACETS	0.776	0.722	0.83	0.776	0.722	0.83	INDETERMINATE	1	TRUE	0	0.699227139998938	1		514	410	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288785	33288785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765273333	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	66	445	0	ENST00000374542.5:c.767G>A	p.Arg256His	p.R256H	ENST00000374542	NM_001141970.1	256	cGc/cAc	3/8	1	2	FACETS	0.405	0.352	0.462	0.405	0.352	0.462	SUBCLONAL	1	TRUE	1	0.699227139998938	2		445	466	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553602	106553602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1562174876	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	179	522	0	ENST00000369096.4:c.1567G>A	p.Ala523Thr	p.A523T	ENST00000369096	NM_001198.3	523	Gcc/Acc	5/7	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.699227139998938	2		522	502	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	65	441	3	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	1	2	FACETS	0.41	0.357	0.468	0.41	0.357	0.468	SUBCLONAL	1	TRUE	1	0.699227139998938	2		444	453	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741409	145741409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs549497811	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	185	588	0	ENST00000428558.2:c.1094G>A	p.Arg365Gln	p.R365Q	ENST00000428558	NM_004260.3	365	cGg/cAg	5/22	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.699227139998938	2		588	506	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319934	8319934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764537367	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	71	386	0	ENST00000356435.5:c.5567C>T	p.Thr1856Met	p.T1856M	ENST00000356435		1856	aCg/aTg	34/35	0.460005123468456	3	FACETS	0.497	0.434	0.564	0.248	0.217	0.282	SUBCLONAL	1	TRUE	1	0.699227139998938	3		386	552	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786002	135786002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769331772	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	158	490	0	ENST00000298552.3:c.1219G>A	p.Val407Met	p.V407M	ENST00000298552	NM_001162426.1	407	Gtg/Atg	12/23	1	2	FACETS	0.97	0.896	1	0.97	0.896	1	CLONAL	1	TRUE	1	0.699227139998938	2		490	466	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934301	39934302	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	155	219	0	ENST00000378444.4:c.297_298del	p.Lys100ArgfsTer85	p.K100Rfs*85	ENST00000378444	NM_001123385.1	99	gaGAaa/gaaa	4/15	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.699227139998938	1		219	233	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228288	53228288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1569264240	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	131	225	0	ENST00000375401.3:c.2114G>A	p.Arg705His	p.R705H	ENST00000375401	NM_004187.3	705	cGc/cAc	15/26	1	1	FACETS	0.975	0.905	1	0.975	0.905	1	CLONAL	1	TRUE	0	0.699227139998938	1		225	250	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023043	27023043	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	18	356	0	ENST00000324856.7:c.149T>C	p.Met50Thr	p.M50T	ENST00000324856	NM_006015.4	50	aTg/aCg	1/20	1	2	FACETS	0.19	0.143	0.246	0.19	0.143	0.246	SUBCLONAL	1	TRUE	1	0.699227139998938	2		356	271	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944712	206944712	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	191	319	0	ENST00000423557.1:c.214G>A	p.Glu72Lys	p.E72K	ENST00000423557	NM_000572.2	72	Gag/Aag	2/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.699227139998938	2		319	495	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115779	8115779	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	39	466	1	ENST00000346208.3:c.1125C>A	p.Cys375Ter	p.C375*	ENST00000346208		375	tgC/tgA	6/6	1	2	FACETS	0.201	0.166	0.241	0.201	0.166	0.241	SUBCLONAL	1	TRUE	1	0.699227139998938	2		467	554	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10795708	10795710	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs968571283	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	49	449	0	ENST00000361367.2:c.2880_2882del	p.Arg962del	p.R962del	ENST00000361367	NM_014633.3	959	aaGAGg/aag	22/25	1	2	FACETS	0.248	0.209	0.29	0.248	0.209	0.29	SUBCLONAL	1	TRUE	1	0.699227139998938	2		449	566	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433584	49433584	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	175	538	0	ENST00000301067.7:c.7969G>A	p.Ala2657Thr	p.A2657T	ENST00000301067	NM_003482.3	2657	Gcg/Acg	31/54	1	2	FACETS	0.972	0.902	1	0.972	0.902	1	CLONAL	1	TRUE	1	0.699227139998938	2		538	515	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123875328	123875328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	44	299	0	ENST00000330479.4:c.284G>A	p.Arg95Gln	p.R95Q	ENST00000330479	NM_020382.3	95	cGa/cAa	3/9	1	2	FACETS	0.314	0.263	0.369	0.314	0.263	0.369	SUBCLONAL	1	TRUE	1	0.699227139998938	2		299	401	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953749	48953749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1312442837	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	45	207	0	ENST00000267163.4:c.1352G>A	p.Arg451His	p.R451H	ENST00000267163	NM_000321.2	451	cGc/cAc	14/27	1	2	FACETS	0.402	0.339	0.471	0.402	0.339	0.471	SUBCLONAL	1	TRUE	1	0.699227139998938	2		207	320	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434939	110434941	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	rs1262166340	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	75	503	0	ENST00000375856.3:c.3460_3462del	p.Ser1154del	p.S1154del	ENST00000375856	NM_003749.2	1154	TCC/-	1/2	1	2	FACETS	0.424	0.372	0.479	0.424	0.372	0.479	SUBCLONAL	1	TRUE	1	0.699227139998938	2		503	506	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108024	30108024	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	30	333	0	ENST00000331968.5:c.783G>T	p.Lys261Asn	p.K261N	ENST00000331968	NM_002742.2	261	aaG/aaT	5/18	1	2	FACETS	0.211	0.17	0.258	0.211	0.17	0.258	SUBCLONAL	1	TRUE	1	0.699227139998938	2		333	406	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239378	105239378	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1247419183	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	201	605	0	ENST00000349310.3:c.1009G>A	p.Val337Met	p.V337M	ENST00000349310	NM_001014432.1	337	Gtg/Atg	12/15	0.339698330582699	3	FACETS	1	0.989	1	0.652	0.608	0.697	INDETERMINATE	1	TRUE	1	0.699227139998938	3		605	595	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465644	99465644	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	175	419	0	ENST00000268035.6:c.2470del	p.Arg824GlyfsTer15	p.R824Gfs*15	ENST00000268035	NM_000875.3	823	gcA/gc	11/21	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.699227139998938	2		419	431	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639077	3639077	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	151	506	1	ENST00000294008.3:c.4562C>A	p.Pro1521His	p.P1521H	ENST00000294008	NM_032444.2	1521	cCt/cAt	12/15	1	2	FACETS	0.931	0.858	1	0.931	0.858	1	CLONAL	1	TRUE	1	0.699227139998938	2		507	464	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032192	10032193	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	23	447	0	ENST00000330684.3:c.630dup	p.Glu211Ter	p.E211*	ENST00000330684	NM_001134407.1	210	-/T	3/13	1	2	FACETS	0.166	0.129	0.209	0.166	0.129	0.209	SUBCLONAL	1	TRUE	1	0.699227139998938	2		447	396	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041990	14041990	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	197	459	0	ENST00000311895.7:c.2537C>A	p.Pro846His	p.P846H	ENST00000311895	NM_005236.2	846	cCt/cAt	11/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.699227139998938	2		459	494	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38793825	38793825	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	189	381	0	ENST00000348513.6:c.157-1G>T		p.X53_splice	ENST00000348513	NM_003079.4	53			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.699227139998938	2		381	502	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40880880	40880880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754966338	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	109	358	0	ENST00000428826.2:c.80G>A	p.Arg27Gln	p.R27Q	ENST00000428826		27	cGa/cAa	3/21	1	2	FACETS	0.49	0.441	0.542	0.49	0.441	0.542	SUBCLONAL	1	TRUE	1	0.699227139998938	2		358	636	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41201139	41201139	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	105	390	0	ENST00000357654.3:c.5405C>T	p.Thr1802Ile	p.T1802I	ENST00000357654	NM_007294.3	1802	aCa/aTa	21/23	1	2	FACETS	0.712	0.642	0.785	0.712	0.642	0.785	SUBCLONAL	1	TRUE	1	0.699227139998938	2		390	422	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554152	63554153	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	376	533	0	ENST00000307078.5:c.586_587del	p.Tyr196ProfsTer16	p.Y196Pfs*16	ENST00000307078	NM_004655.3	196	TAc/c	2/11	0.699227139998938	2	FACETS	0.99	0.956	1	0.99	0.956	1	CLONAL	2	TRUE	0	0.699227139998938	2		533	543	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223105	1223105	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	164	537	0	ENST00000326873.7:c.1042G>T	p.Asp348Tyr	p.D348Y	ENST00000326873	NM_000455.4	348	Gac/Tac	8/10	1	2	FACETS	0.99	0.916	1	0.99	0.916	1	CLONAL	1	TRUE	1	0.699227139998938	2		537	474	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6230694	6230694	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	184	481	0	ENST00000252674.7:c.307G>A	p.Asp103Asn	p.D103N	ENST00000252674	NM_005934.3	103	Gac/Aac	4/12	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.699227139998938	2		481	496	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101925	11101925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	172	458	0	ENST00000358026.2:c.1345G>A	p.Glu449Lys	p.E449K	ENST00000358026	NM_001128849.1	449	Gag/Aag	8/36	1	2	FACETS	0.99	0.918	1	0.99	0.918	1	CLONAL	1	TRUE	1	0.699227139998938	2		458	497	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289857	15289857	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	156	565	0	ENST00000263388.2:c.3697C>A	p.Leu1233Ile	p.L1233I	ENST00000263388	NM_000435.2	1233	Ctt/Att	22/33	1	2	FACETS	0.885	0.817	0.956	0.885	0.817	0.956	CLONAL	1	TRUE	1	0.699227139998938	2		565	504	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300164	15300164	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	159	501	0	ENST00000263388.2:c.1112T>C	p.Val371Ala	p.V371A	ENST00000263388	NM_000435.2	371	gTg/gCg	7/33	1	2	FACETS	0.89	0.822	0.96	0.89	0.822	0.96	CLONAL	1	TRUE	1	0.699227139998938	2		501	511	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218396	36218396	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	151	485	0	ENST00000222270.7:c.4175C>A	p.Pro1392Gln	p.P1392Q	ENST00000222270	NM_014727.1	1392	cCg/cAg	16/37	1	2	FACETS	0.917	0.845	0.991	0.917	0.845	0.991	CLONAL	1	TRUE	1	0.699227139998938	2		485	471	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383119	42383119	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	35	381	0	ENST00000221972.3:c.139G>T	p.Gly47Trp	p.G47W	ENST00000221972	NM_021601.3	47	Ggg/Tgg	2/5	1	2	FACETS	0.277	0.227	0.333	0.277	0.227	0.333	SUBCLONAL	1	TRUE	1	0.699227139998938	2		381	361	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912885	50912885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1363178844	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	141	370	0	ENST00000440232.2:c.2116G>A	p.Ala706Thr	p.A706T	ENST00000440232	NM_002691.3	706	Gcc/Acc	17/27	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.699227139998938	2		370	382	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724335	52724335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	49	489	0	ENST00000322088.6:c.1467G>A	p.Met489Ile	p.M489I	ENST00000322088	NM_014225.5	489	atG/atA	12/15	1	2	FACETS	0.285	0.241	0.333	0.285	0.241	0.333	SUBCLONAL	1	TRUE	1	0.699227139998938	2		489	492	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29444422	29444422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	335	444	2	ENST00000544604.2:c.958G>A	p.Val320Met	p.V320M	ENST00000544604	NM_001206998.1	320	Gtg/Atg	7/9	0.487954902280209	2	FACETS	0.884	0.848	0.919	0.884	0.848	0.919	CLONAL	2	TRUE	0	0.699227139998938	2		446	542	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035147	37035147	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63751012	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	128	330	0	ENST00000231790.2:c.109G>T	p.Glu37Ter	p.E37*	ENST00000231790	NM_000249.3	37	Gag/Tag	1/19	1	2	FACETS	0.932	0.853	1	0.932	0.853	1	CLONAL	1	TRUE	1	0.699227139998938	2		330	393	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805468	1805470	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	36	441	0	ENST00000260795.2:c.982_984del	p.Asn328del	p.N328del	ENST00000260795		327	cACAac/cac	7/17	1	2	FACETS	0.254	0.208	0.304	0.254	0.208	0.304	SUBCLONAL	1	TRUE	1	0.699227139998938	2		441	406	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294267	1294267	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	140	517	0	ENST00000310581.5:c.734A>G	p.Glu245Gly	p.E245G	ENST00000310581	NM_198253.2	245	gAg/gGg	2/16	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.699227139998938	2		517	398	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950592	38950592	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	108	462	0	ENST00000357387.3:c.3358T>A	p.Leu1120Ile	p.L1120I	ENST00000357387	NM_152756.3	1120	Tta/Ata	31/38	1	2	FACETS	0.666	0.601	0.734	0.666	0.601	0.734	SUBCLONAL	1	TRUE	1	0.699227139998938	2		462	464	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032281	26032281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	40	436	0	ENST00000244661.2:c.8G>A	p.Arg3His	p.R3H	ENST00000244661	NM_003537.3	3	cGt/cAt	1/1	1	2	FACETS	0.271	0.225	0.322	0.271	0.225	0.322	SUBCLONAL	1	TRUE	1	0.699227139998938	2		436	422	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225771	26225771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	183	587	1	ENST00000360408.1:c.389G>A	p.Arg130His	p.R130H	ENST00000360408	NM_003532.2	130	cGc/cAc	1/1	1	2	FACETS	0.886	0.822	0.951	0.886	0.822	0.951	CLONAL	1	TRUE	1	0.699227139998938	2		588	591	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910684	29910684	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	40	804	0	ENST00000376809.5:c.224G>T	p.Trp75Leu	p.W75L	ENST00000376809	NM_002116.7	75	tGg/tTg	2/8	1	2	FACETS	0.166	0.137	0.198	0.166	0.137	0.198	SUBCLONAL	1	TRUE	1	0.699227139998938	2		804	691	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805994	32805994	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	151	460	0	ENST00000374899.4:c.17T>C	p.Leu6Pro	p.L6P	ENST00000374899	NM_018833.2	6	cTg/cCg	2/12	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.699227139998938	2		460	407	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157470078	157470078	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554226159	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	170	467	0	ENST00000346085.5:c.2872C>T	p.Gln958Ter	p.Q958*	ENST00000346085	NM_020732.3	958	Caa/Taa	9/20	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.699227139998938	2		467	484	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622264	162622264	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	38	427	0	ENST00000366898.1:c.433A>C	p.Ser145Arg	p.S145R	ENST00000366898	NM_004562.2	145	Agc/Cgc	4/12	1	2	FACETS	0.23	0.19	0.275	0.23	0.19	0.275	SUBCLONAL	1	TRUE	1	0.699227139998938	2		427	472	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277082	38277082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1271245426	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	121	418	2	ENST00000425967.3:c.1346C>T	p.Ala449Val	p.A449V	ENST00000425967	NM_001174067.1	449	gCc/gTc	10/19	1	2	FACETS	0.967	0.883	1	0.967	0.883	1	CLONAL	1	TRUE	1	0.699227139998938	2		420	358	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223559	53223559	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	138	222	0	ENST00000375401.3:c.3800G>A	p.Arg1267Lys	p.R1267K	ENST00000375401	NM_004187.3	1267	aGa/aAa	23/26	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.699227139998938	1		222	193	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	128	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.985	0.901	1	0.985	0.901	1	CLONAL	1	TRUE	1	0.626333920086882	2		341	415	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0066683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	87	721	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.331779999968106	1	FACETS	0.368	0.327	0.413	0.368	0.327	0.413	INDETERMINATE	1	TRUE	0	0.626333920086882	1		721	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0066683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	123	490	0	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	0.621768804279636	1	FACETS	0.899	0.826	0.974	0.899	0.826	0.974	CLONAL	1	TRUE	0	0.626333920086882	1		490	300	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0066683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	146	353	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.331779999968106	1	FACETS	0.854	0.789	0.92	0.854	0.789	0.92	INDETERMINATE	1	TRUE	0	0.626333920086882	1		353	375	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247168	153247168	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1560758208	NA	P-0066683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	203	313	0	ENST00000281708.4:c.1634A>G	p.Tyr545Cys	p.Y545C	ENST00000281708	NM_033632.3	545	tAt/tGt	10/12	0.626333920086882	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.626333920086882	1		313	364	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576370	67576370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540361957	NA	P-0066683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	109	296	0	ENST00000274335.5:c.649G>A	p.Glu217Lys	p.E217K	ENST00000274335		217	Gaa/Aaa	5/15	0.626333920086882	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.626333920086882	1		296	237	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890137	76890137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	20	164	0	ENST00000373344.5:c.4757C>T	p.Pro1586Leu	p.P1586L	ENST00000373344	NM_000489.3	1586	cCa/cTa	17/35	1	1	FACETS	0.212	0.162	0.269	0.212	0.162	0.269	SUBCLONAL	1	TRUE	0	0.626333920086882	1		164	207	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675960	30675960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775696423	NA	P-0066683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	176	422	0	ENST00000376406.3:c.2396C>T	p.Pro799Leu	p.P799L	ENST00000376406	NM_014641.2	799	cCa/cTa	8/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.626333920086882	2		422	529	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056604	26056605	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0066683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	59	410	1	ENST00000343677.2:c.52_53delinsTT	p.Ala18Phe	p.A18F	ENST00000343677	NM_005319.3	18	GCc/TTc	1/1	1	2	FACETS	0.472	0.407	0.542	0.472	0.407	0.542	SUBCLONAL	1	TRUE	1	0.626333920086882	2		411	399	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092741	27092741	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	112	383	0	ENST00000324856.7:c.2762G>A	p.Gly921Glu	p.G921E	ENST00000324856	NM_006015.4	921	gGg/gAg	9/20	1	2	FACETS	0.852	0.772	0.935	0.852	0.772	0.935	CLONAL	1	TRUE	1	0.626333920086882	2		383	420	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350929	89350929	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0066683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	80	338	0	ENST00000301030.4:c.2021T>A	p.Leu674Ter	p.L674*	ENST00000301030	NM_001256183.1	674	tTa/tAa	9/13	0.216585858398601	1	FACETS	0.399	0.352	0.448	0.399	0.352	0.448	INDETERMINATE	1	TRUE	0	0.626333920086882	1		338	440	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412045	116412045	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0066689-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	160	355	0	ENST00000397752.3:c.3028+2T>A		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.258706823435161	2	FACETS	0.877	0.806	0.951	0.877	0.806	0.951	CLONAL	2	TRUE	0	0.258706823435161	2		355	705	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579349	7579349	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066689-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	68	335	0	ENST00000269305.4:c.338del	p.Phe113SerfsTer10	p.F113Sfs*10	ENST00000269305	NM_001126112.2	113	tTc/tc	4/11	0.242825997372214	1	FACETS	0.867	0.755	0.987	0.867	0.755	0.987	CLONAL	1	TRUE	0	0.258706823435161	1		335	528	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425014	47425014	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066689-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	70	351	0	ENST00000404338.3:c.3082A>G	p.Asn1028Asp	p.N1028D	ENST00000404338	NM_004491.4	1028	Aat/Gat	1/6	1	2	FACETS	0.822	0.717	0.937	0.822	0.717	0.937	CLONAL	1	TRUE	1	0.258706823435161	2		351	658	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480553	123480553	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066689-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	72	350	0	ENST00000371139.4:c.61C>A	p.Leu21Ile	p.L21I	ENST00000371139	NM_001114937.2	21	Ctt/Att	1/4	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.258706823435161	2		350	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0066691-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	182	452	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.576416223554032	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.654717339990137	1		452	362	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340407	8340407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201651279	NA	P-0066691-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	191	509	0	ENST00000356435.5:c.5189G>A	p.Arg1730Gln	p.R1730Q	ENST00000356435		1730	cGg/cAg	31/35	1	2	FACETS	0.9	0.836	0.966	0.9	0.836	0.966	CLONAL	1	TRUE	1	0.654717339990137	2		509	648	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857275	9857275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426934537	NA	P-0066691-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	55	565	0	ENST00000330684.3:c.4126C>T	p.Arg1376Cys	p.R1376C	ENST00000330684	NM_001134407.1	1376	Cgc/Tgc	13/13	1	2	FACETS	0.233	0.198	0.27	0.233	0.198	0.27	SUBCLONAL	1	TRUE	1	0.654717339990137	2		565	722	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26046009	26046009	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066691-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	37	536	0	ENST00000540144.1:c.371A>G	p.Asp124Gly	p.D124G	ENST00000540144	NM_003531.2	124	gAt/gGt	1/1	1	2	FACETS	0.179	0.147	0.215	0.179	0.147	0.215	SUBCLONAL	1	TRUE	1	0.654717339990137	2		536	631	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859942	151859942	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066691-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	215	579	0	ENST00000262189.6:c.10720del	p.Ser3574LeufsTer3	p.S3574Lfs*3	ENST00000262189	NM_170606.2	3574	Tct/ct	43/59	0.604745154215357	1	FACETS	0.92	0.865	0.976	0.92	0.865	0.976	CLONAL	1	TRUE	0	0.654717339990137	1		579	480	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143175	24143175	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066691-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	193	600	0	ENST00000263121.7:c.407C>G	p.Pro136Arg	p.P136R	ENST00000263121	NM_003073.3	136	cCc/cGc	4/9	1	2	FACETS	0.94	0.874	1	0.94	0.874	1	CLONAL	1	TRUE	1	0.654717339990137	2		600	627	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16052779	16052779	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066691-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	140	187	0	ENST00000268712.3:c.895G>A	p.Ala299Thr	p.A299T	ENST00000268712	NM_006311.3	299	Gca/Aca	9/46	0.185804831512442	1	FACETS	0.777	0.717	0.84	0.777	0.717	0.84	INDETERMINATE	1	TRUE	0	0.654717339990137	1		187	370	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0066692-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	22	257	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.794	1	1	0.794	1	CLONAL	1	TRUE	1	0.18	2		257	239	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0066692-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	27	418	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	TRUE	1	0.18	2		418	280	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578415	7578415	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066692-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	18	521	0	ENST00000269305.4:c.515T>A	p.Val172Asp	p.V172D	ENST00000269305	NM_001126112.2	172	gTt/gAt	5/11	0.147546736064546	1	FACETS	0.609	0.458	0.787	0.609	0.458	0.787	SUBCLONAL	1	TRUE	0	0.18	1		521	299	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591903	48591903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066692-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	32	468	0	ENST00000342988.3:c.1066C>T	p.Pro356Ser	p.P356S	ENST00000342988	NM_005359.5	356	Cct/Tct	9/12	1	2	FACETS	1	0.821	1	1	0.821	1	CLONAL	1	TRUE	1	0.18	2		468	352	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513200	106513200	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066692-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	25	383	0	ENST00000359195.3:c.2104G>C	p.Glu702Gln	p.E702Q	ENST00000359195	NM_002649.2	702	Gag/Cag	4/11	0.147546736064546	3	FACETS	0.94	0.742	1	0.47	0.371	0.584	CLONAL	1	TRUE	1	0.18	3		383	322	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513316	106513316	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066692-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	17	358	0	ENST00000359195.3:c.2220G>T	p.Glu740Asp	p.E740D	ENST00000359195	NM_002649.2	740	gaG/gaT	4/11	0.147546736064546	3	FACETS	0.741	0.553	0.964	0.37	0.276	0.482	CLONAL	1	TRUE	1	0.18	3		358	278	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033189	69033189	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs769657897	NA	P-0066692-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	23	366	0	ENST00000288368.4:c.3629G>T	p.Cys1210Phe	p.C1210F	ENST00000288368	NM_024870.2	1210	tGt/tTt	30/40	1	2	FACETS	0.858	0.669	1	0.858	0.669	1	CLONAL	1	TRUE	1	0.18	2		366	298	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633264	12633264	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066692-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	24	348	0	ENST00000251849.4:c.1136T>G	p.Val379Gly	p.V379G	ENST00000251849	NM_002880.3	379	gTt/gGt	11/17	1	2	FACETS	0.984	0.773	1	0.984	0.773	1	CLONAL	1	TRUE	1	0.18	2		348	271	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412735	63412736	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066692-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	18	444	0	ENST00000330258.3:c.431dup	p.Thr145AspfsTer13	p.T145Dfs*13	ENST00000330258	NM_152424.3	144	aag/aaAg	2/2	0.147546736064546	1	FACETS	0.705	0.532	0.91	0.705	0.532	0.91	CLONAL	1	TRUE	0	0.18	1		444	258	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0066693-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	155	382	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.386945038050746	2	FACETS	0.933	0.865	1	0.933	0.865	1	CLONAL	2	TRUE	0	0.437262610586199	2		382	380	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480495	57480495	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1422801076	NA	P-0066693-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1192	100	345	0	ENST00000371085.3:c.490G>A	p.Glu164Lys	p.E164K	ENST00000371085	NM_000516.4	164	Gaa/Aaa	6/13	0.437262610586199	11	FACETS	1	0.926	1	0.096	0.085	0.107	CLONAL	1	TRUE	0	0.437262610586199	11		345	1292	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412530	63412530	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066693-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	61	477	0	ENST00000330258.3:c.637C>T	p.Gln213Ter	p.Q213*	ENST00000330258	NM_152424.3	213	Cag/Tag	2/2	0.300036467293836	5	FACETS	0.901	0.778	1	0.3	0.259	0.345	CLONAL	1	TRUE	2	0.437262610586199	5		477	513	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456855	32456855	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066693-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	73	357	0	ENST00000332351.3:c.37G>A	p.Ala13Thr	p.A13T	ENST00000332351	NM_024426.4	13	Gcg/Acg	1/10	0.431453168263086	3	FACETS	1	0.933	1	0.545	0.48	0.615	CLONAL	1	TRUE	1	0.437262610586199	3		357	373	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433282	49433282	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1355857425	NA	P-0066693-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	118	438	0	ENST00000301067.7:c.8165C>G	p.Ala2722Gly	p.A2722G	ENST00000301067	NM_003482.3	2722	gCt/gGt	32/54	0.437262610586199	6	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.437262610586199	6		438	743	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144359634	144359634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748539714	NA	P-0066693-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	102	494	0	ENST00000262995.4:c.1076C>T	p.Thr359Met	p.T359M	ENST00000262995	NM_207123.2	359	aCg/aTg	4/11	0.400705012970939	4	FACETS	1	0.944	1	0.541	0.484	0.601	CLONAL	1	TRUE	2	0.437262610586199	4		494	620	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	69	351	2	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.38781195341583	2		353	353	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	242	710	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.93	0.874	0.987	1	0.995	1	CLONAL	2	TRUE	1	0.38781195341583	2		713	671	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607487	46607487	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	112	554	2	ENST00000263734.3:c.1681del	p.Gln561SerfsTer7	p.Q561Sfs*7	ENST00000263734	NM_001430.4	559	aCc/ac	12/16	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.38781195341583	2		556	566	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	102	310	1	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.38781195341583	2		311	505	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	77	412	7	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.877	0.772	0.988	0.877	0.772	0.988	CLONAL	1	TRUE	1	0.38781195341583	2		419	453	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411576	63411576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	100	278	0	ENST00000330258.3:c.1591C>T	p.Arg531Ter	p.R531*	ENST00000330258	NM_152424.3	531	Cga/Tga	2/2	1	1	FACETS	0.825	0.75	0.901	1	0.986	1	CLONAL	2	TRUE	0	0.38781195341583	1		278	252	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	93	382	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.38781195341583	2		387	416	SUCCESS
MAD2L2	10459	MSKCC	GRCh37	1	11736105	11736105	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	64	400	1	ENST00000235310.3:c.425del	p.Pro142GlnfsTer45	p.P142Qfs*45	ENST00000235310		142	cCa/ca	8/11	1	2	FACETS	0.716	0.621	0.818	0.716	0.621	0.818	SUBCLONAL	1	TRUE	1	0.38781195341583	2		401	461	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262680	16262680	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	26	448	1	ENST00000375759.3:c.9950del	p.Pro3317ArgfsTer83	p.P3317Rfs*83	ENST00000375759	NM_015001.2	3315	caC/ca	11/15	1	2	FACETS	0.281	0.222	0.349	0.281	0.222	0.349	SUBCLONAL	1	TRUE	1	0.38781195341583	2		449	477	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150936218	150936218	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs111660370	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	103	483	0	ENST00000271640.5:c.3669+1G>A		p.X1223_splice	ENST00000271640	NM_001145415.1	1223			1	2	FACETS	0.869	0.78	0.964	0.869	0.78	0.964	CLONAL	1	TRUE	1	0.38781195341583	2		483	611	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843643	156843643	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	96	613	0	ENST00000524377.1:c.1069G>A	p.Gly357Ser	p.G357S	ENST00000524377	NM_002529.3	357	Ggc/Agc	8/17	1	2	FACETS	0.867	0.774	0.965	0.867	0.774	0.965	CLONAL	1	TRUE	1	0.38781195341583	2		613	571	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740216	162740216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775098890	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	108	543	1	ENST00000367921.3:c.1418G>A	p.Arg473His	p.R473H	ENST00000367921	NM_006182.2	473	cGc/cAc	12/18	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.38781195341583	2		544	541	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	114	501	0	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.38781195341583	2		501	574	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188136	108188136	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1800060	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	65	260	0	ENST00000278616.4:c.6235G>A	p.Val2079Ile	p.V2079I	ENST00000278616	NM_000051.3	2079	Gtc/Atc	43/63	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.38781195341583	2		260	292	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298725	46298725	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	64	247	0	ENST00000334344.6:c.5372A>G	p.Lys1791Arg	p.K1791R	ENST00000334344	NM_152641.2	1791	aAg/aGg	21/21	0.38781195341583	3	FACETS	1	0.914	1	0.533	0.463	0.607	CLONAL	1	TRUE	1	0.38781195341583	3		247	370	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420913	49420913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756017412	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	91	554	0	ENST00000301067.7:c.14836G>A	p.Val4946Ile	p.V4946I	ENST00000301067	NM_003482.3	4946	Gtc/Atc	48/54	0.38781195341583	3	FACETS	0.818	0.727	0.915	0.409	0.363	0.458	CLONAL	1	TRUE	1	0.38781195341583	3		554	685	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434247	49434247	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	118	566	0	ENST00000301067.7:c.7306del	p.Cys2436AlafsTer49	p.C2436Afs*49	ENST00000301067	NM_003482.3	2436	Tgc/gc	31/54	0.38781195341583	3	FACETS	1	0.921	1	0.511	0.461	0.563	CLONAL	1	TRUE	1	0.38781195341583	3		566	711	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480010	50480010	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	105	475	0	ENST00000394963.4:c.249del	p.Asn84ThrfsTer79	p.N84Tfs*79	ENST00000394963	NM_003076.4	82	Ggg/gg	2/13	0.38781195341583	3	FACETS	0.966	0.867	1	0.483	0.433	0.536	CLONAL	1	TRUE	1	0.38781195341583	3		475	669	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	76	351	5	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	1	2	FACETS	0.935	0.824	1	0.935	0.824	1	CLONAL	1	TRUE	1	0.38781195341583	2		356	419	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058342	42058342	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201470885	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	92	478	0	ENST00000219905.7:c.8062G>A	p.Val2688Ile	p.V2688I	ENST00000219905	NM_001164273.1	2688	Gtc/Atc	24/24	1	2	FACETS	0.966	0.862	1	0.966	0.862	1	CLONAL	1	TRUE	1	0.38781195341583	2		478	491	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	73	480	7	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.871	0.765	0.985	0.871	0.765	0.985	CLONAL	1	TRUE	1	0.38781195341583	2		487	432	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465391	99465391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912429	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	95	423	0	ENST00000268035.6:c.2216G>A	p.Arg739Gln	p.R739Q	ENST00000268035	NM_000875.3	739	cGg/cAg	11/21	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.38781195341583	2		423	477	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828208	50828208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	105	506	0	ENST00000398568.2:c.2546G>A	p.Gly849Asp	p.G849D	ENST00000398568	NM_001042412.1	849	gGc/gAc	17/18	1	2	FACETS	0.945	0.849	1	0.945	0.849	1	CLONAL	1	TRUE	1	0.38781195341583	2		506	573	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132613	67132613	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	29	329	0	ENST00000412916.2:c.496G>A	p.Ala166Thr	p.A166T	ENST00000412916		166	Gca/Aca	6/6	1	2	FACETS	0.36	0.288	0.441	0.36	0.288	0.441	SUBCLONAL	1	TRUE	1	0.38781195341583	2		329	416	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821959	72821960	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762108866	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	88	524	2	ENST00000268489.5:c.10215dup	p.Gly3406ArgfsTer25	p.G3406Rfs*25	ENST00000268489	NM_006885.3	3405	-/C	10/10	1	2	FACETS	0.906	0.805	1	0.906	0.805	1	CLONAL	1	TRUE	1	0.38781195341583	2		526	501	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	126	580	0	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.38781195341583	2		580	631	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	83	500	5	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	0.897	0.795	1	0.897	0.795	1	CLONAL	1	TRUE	1	0.38781195341583	2		505	477	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099208	4099208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	97	382	0	ENST00000262948.5:c.910C>T	p.Pro304Ser	p.P304S	ENST00000262948	NM_030662.3	304	Ccc/Tcc	7/11	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.38781195341583	2		382	454	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4123862	4123862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	90	348	0	ENST00000262948.5:c.11G>A	p.Arg4Gln	p.R4Q	ENST00000262948	NM_030662.3	4	cGg/cAg	1/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.38781195341583	2		348	381	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240271	5240271	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	78	501	0	ENST00000357368.4:c.1643del	p.Pro548ArgfsTer37	p.P548Rfs*37	ENST00000357368	NM_002850.3	548	cCg/cg	12/38	1	2	FACETS	0.938	0.828	1	0.938	0.828	1	CLONAL	1	TRUE	1	0.38781195341583	2		501	429	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311681	15311682	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGGCGG	rs894374843	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	31	668	0	ENST00000263388.2:c.30_35dup	p.Arg12_Arg13dup	p.R12_R13dup	ENST00000263388	NM_000435.2	12	cgt/cgCCGCCGt	1/33	1	2	FACETS	0.32	0.258	0.39	0.32	0.258	0.39	SUBCLONAL	1	TRUE	1	0.38781195341583	2		668	500	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731468	47731468	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1284528511	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	88	491	2	ENST00000449228.1:c.324del	p.Phe109SerfsTer120	p.F109Sfs*120	ENST00000449228	NM_001127240.2	108	ggG/gg	2/4	1	2	FACETS	0.957	0.852	1	0.957	0.852	1	CLONAL	1	TRUE	1	0.38781195341583	2		493	474	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	88	587	2	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	1	2	FACETS	0.864	0.768	0.967	0.864	0.768	0.967	CLONAL	1	TRUE	1	0.38781195341583	2		589	525	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497908	25497908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1247178186	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	83	381	0	ENST00000264709.3:c.541C>T	p.Arg181Cys	p.R181C	ENST00000264709	NM_175629.2	181	Cgt/Tgt	6/23	1	2	FACETS	0.986	0.875	1	0.986	0.875	1	CLONAL	1	TRUE	1	0.38781195341583	2		381	434	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523072	25523072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369618387	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	118	508	0	ENST00000264709.3:c.113G>A	p.Arg38His	p.R38H	ENST00000264709	NM_175629.2	38	cGc/cAc	3/23	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.38781195341583	2		508	516	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	91	860	9	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.723	0.643	0.809	0.723	0.643	0.809	SUBCLONAL	1	TRUE	1	0.38781195341583	2		869	649	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141605	202141605	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	54	453	0	ENST00000358485.4:c.893T>C	p.Ile298Thr	p.I298T	ENST00000358485	NM_001080125.1	298	aTc/aCc	7/9	1	2	FACETS	0.538	0.459	0.623	0.538	0.459	0.623	SUBCLONAL	1	TRUE	1	0.38781195341583	2		453	518	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736166	204736166	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	95	456	0	ENST00000302823.3:c.529del	p.Tyr177IlefsTer10	p.Y177Ifs*10	ENST00000302823	NM_005214.4	175	Ttt/tt	3/4	1	2	FACETS	0.933	0.834	1	0.933	0.834	1	CLONAL	1	TRUE	1	0.38781195341583	2		456	525	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422842	12422842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	84	336	0	ENST00000287820.6:c.332C>T	p.Ala111Val	p.A111V	ENST00000287820	NM_015869.4	111	gCa/gTa	3/7	0.371608188717123	2	FACETS	1	0.917	1	0.519	0.461	0.581	CLONAL	1	TRUE	0	0.38781195341583	2		336	417	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976873	55976873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750983015	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	89	415	1	ENST00000263923.4:c.1039C>T	p.Arg347Cys	p.R347C	ENST00000263923	NM_002253.2	347	Cgt/Tgt	8/30	1	2	FACETS	0.964	0.858	1	0.964	0.858	1	CLONAL	1	TRUE	1	0.38781195341583	2		416	476	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1266595	1266595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	95	457	0	ENST00000310581.5:c.2638G>A	p.Ala880Thr	p.A880T	ENST00000310581	NM_198253.2	880	Gcg/Acg	10/16	1	2	FACETS	0.961	0.858	1	0.961	0.858	1	CLONAL	1	TRUE	1	0.38781195341583	2		457	510	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970916	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	59	334	0	ENST00000265081.6:c.1147_1148del	p.Lys383GlyfsTer20	p.K383Gfs*20	ENST00000265081	NM_002439.4	381	AAa/a	7/24	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.38781195341583	2		334	272	SUCCESS
APC	324	MSKCC	GRCh37	5	112173260	112173261	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs863225322	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	46	303	0	ENST00000257430.4:c.1974_1975del	p.Asn659GlnfsTer14	p.N659Qfs*14	ENST00000257430	NM_000038.5	657	AGa/a	16/16	1	2	FACETS	0.919	0.78	1	0.919	0.78	1	CLONAL	1	TRUE	1	0.38781195341583	2		303	258	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	79	404	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.994	0.879	1	0.994	0.879	1	CLONAL	1	TRUE	1	0.38781195341583	2		404	410	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058747	180058748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755445139	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	109	515	1	ENST00000261937.6:c.89dup	p.Thr31AspfsTer15	p.T31Dfs*15	ENST00000261937	NM_182925.4	30	ccg/ccCg	2/30	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.38781195341583	2		516	535	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910405	29910405	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	102	548	0	ENST00000376809.5:c.73+2T>C		p.X25_splice	ENST00000376809	NM_002116.7	25			1	2	FACETS	0.934	0.838	1	0.934	0.838	1	CLONAL	1	TRUE	1	0.38781195341583	2		548	563	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286937	33286937	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	47	539	0	ENST00000374542.5:c.2000C>A	p.Pro667His	p.P667H	ENST00000374542	NM_001141970.1	667	cCc/cAc	7/8	1	2	FACETS	0.385	0.324	0.452	0.385	0.324	0.452	SUBCLONAL	1	TRUE	1	0.38781195341583	2		539	630	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005485	150005485	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	37	532	0	ENST00000253339.5:c.740C>A	p.Pro247His	p.P247H	ENST00000253339		247	cCt/cAt	3/7	1	2	FACETS	0.335	0.275	0.402	0.335	0.275	0.402	SUBCLONAL	1	TRUE	1	0.38781195341583	2		532	570	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420067	152420067	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141662120	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	84	360	0	ENST00000206249.3:c.1754C>T	p.Thr585Met	p.T585M	ENST00000206249	NM_000125.3	585	aCg/aTg	8/8	1	2	FACETS	0.98	0.87	1	0.98	0.87	1	CLONAL	1	TRUE	1	0.38781195341583	2		360	442	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952980	2952980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376039195	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	90	443	0	ENST00000396946.4:c.2960C>T	p.Thr987Met	p.T987M	ENST00000396946	NM_032415.4	987	aCg/aTg	22/25	1	2	FACETS	0.969	0.863	1	0.969	0.863	1	CLONAL	1	TRUE	1	0.38781195341583	2		443	479	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6045646	6045646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	17	71	0	ENST00000265849.7:c.40G>A	p.Ala14Thr	p.A14T	ENST00000265849	NM_000535.5	14	Gcc/Acc	2/15	1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	1	0.38781195341583	2		71	76	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468081	50468081	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	103	544	0	ENST00000331340.3:c.1316G>T	p.Arg439Leu	p.R439L	ENST00000331340	NM_006060.4	439	cGc/cTc	8/8	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.38781195341583	2		544	513	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403116	116403116	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45440991	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	84	334	0	ENST00000397752.3:c.2377C>T	p.Arg793Cys	p.R793C	ENST00000397752	NM_000245.2	793	Cgc/Tgc	11/21	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.38781195341583	2		334	376	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372093	55372093	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	32	517	3	ENST00000297316.4:c.788del	p.Pro263ArgfsTer124	p.P263Rfs*124	ENST00000297316	NM_022454.3	261	ggC/gg	2/2	1	2	FACETS	0.309	0.25	0.376	0.309	0.25	0.376	SUBCLONAL	1	TRUE	1	0.38781195341583	2		520	534	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900359	101900359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	48	282	0	ENST00000374994.4:c.793G>A	p.Ala265Thr	p.A265T	ENST00000374994	NM_004612.2	265	Gca/Aca	4/9	0.38781195341583	3	FACETS	0.921	0.782	1	0.46	0.391	0.536	CLONAL	1	TRUE	1	0.38781195341583	3		282	321	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405231	139405231	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762050048	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	180	442	0	ENST00000277541.6:c.2614G>A	p.Glu872Lys	p.E872K	ENST00000277541	NM_017617.3	872	Gag/Aag	17/34	0.38781195341583	3	FACETS	1	0.933	1	1	0.933	1	CLONAL	2	TRUE	1	0.38781195341583	3		442	551	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807409	36807409	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	110	432	0	ENST00000373129.3:c.1255C>T	p.Pro419Ser	p.P419S	ENST00000373129	NM_032017.1	419	Ccc/Tcc	12/12	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.38781195341583	2		432	510	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796204	45796204	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1454804175	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	98	424	0	ENST00000450313.1:c.1502A>G	p.Gln501Arg	p.Q501R	ENST00000450313	NM_012222.2	501	cAg/cGg	15/16	1	2	FACETS	0.97	0.868	1	0.97	0.868	1	CLONAL	1	TRUE	1	0.38781195341583	2		424	521	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739364	46739364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	89	484	0	ENST00000371975.4:c.1555G>A	p.Val519Met	p.V519M	ENST00000371975	NM_003579.3	519	Gtg/Atg	14/18	1	2	FACETS	0.916	0.815	1	0.916	0.815	1	CLONAL	1	TRUE	1	0.38781195341583	2		484	501	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332695	65332695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	87	385	0	ENST00000342505.4:c.844G>A	p.Gly282Ser	p.G282S	ENST00000342505	NM_002227.2	282	Ggt/Agt	7/25	1	2	FACETS	0.847	0.751	0.948	0.847	0.751	0.948	CLONAL	1	TRUE	1	0.38781195341583	2		385	530	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335016	65335016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	87	383	0	ENST00000342505.4:c.625C>T	p.Pro209Ser	p.P209S	ENST00000342505	NM_002227.2	209	Cca/Tca	6/25	1	2	FACETS	0.921	0.819	1	0.921	0.819	1	CLONAL	1	TRUE	1	0.38781195341583	2		383	487	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012405	176012405	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	77	297	0	ENST00000367669.3:c.1531-2A>G		p.X511_splice	ENST00000367669	NM_022457.5	511			1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.38781195341583	2		297	374	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279539	123279539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	98	519	0	ENST00000358487.5:c.893G>A	p.Gly298Asp	p.G298D	ENST00000358487	NM_000141.4	298	gGc/gAc	7/18	1	2	FACETS	0.946	0.847	1	0.946	0.847	1	CLONAL	1	TRUE	1	0.38781195341583	2		519	534	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432327	49432327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	126	597	0	ENST00000301067.7:c.8812C>T	p.Pro2938Ser	p.P2938S	ENST00000301067	NM_003482.3	2938	Ccg/Tcg	34/54	0.38781195341583	3	FACETS	1	0.961	1	0.556	0.504	0.61	CLONAL	1	TRUE	1	0.38781195341583	3		597	698	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880906	28880906	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	37	467	1	ENST00000282397.4:c.3724T>C	p.Tyr1242His	p.Y1242H	ENST00000282397	NM_002019.4	1242	Tac/Cac	29/30	1	2	FACETS	0.387	0.319	0.464	0.387	0.319	0.464	SUBCLONAL	1	TRUE	1	0.38781195341583	2		468	493	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436077	110436077	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	102	528	0	ENST00000375856.3:c.2324T>C	p.Val775Ala	p.V775A	ENST00000375856	NM_003749.2	775	gTc/gCc	1/2	1	2	FACETS	0.98	0.879	1	0.98	0.879	1	CLONAL	1	TRUE	1	0.38781195341583	2		528	537	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021429	42021429	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1474272053	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	99	430	0	ENST00000219905.7:c.3725G>A	p.Arg1242Gln	p.R1242Q	ENST00000219905	NM_001164273.1	1242	cGa/cAa	11/24	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.38781195341583	2		430	470	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690585	88690585	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	39	359	0	ENST00000360948.2:c.445A>G	p.Thr149Ala	p.T149A	ENST00000360948	NM_001012338.2	149	Acg/Gcg	5/19	1	2	FACETS	0.406	0.336	0.484	0.406	0.336	0.484	SUBCLONAL	1	TRUE	1	0.38781195341583	2		359	495	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99451979	99451979	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	27	483	0	ENST00000268035.6:c.1313A>G	p.Asn438Ser	p.N438S	ENST00000268035	NM_000875.3	438	aAc/aGc	6/21	1	2	FACETS	0.261	0.207	0.323	0.261	0.207	0.323	SUBCLONAL	1	TRUE	1	0.38781195341583	2		483	533	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348867	11348867	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	69	460	0	ENST00000332029.2:c.469G>C	p.Ala157Pro	p.A157P	ENST00000332029	NM_003745.1	157	Gcg/Ccg	2/2	1	2	FACETS	0.962	0.842	1	0.962	0.842	1	CLONAL	1	TRUE	1	0.38781195341583	2		460	370	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029454	14029454	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	57	544	0	ENST00000311895.7:c.1665T>A	p.His555Gln	p.H555Q	ENST00000311895	NM_005236.2	555	caT/caA	8/11	1	2	FACETS	0.463	0.397	0.535	0.463	0.397	0.535	SUBCLONAL	1	TRUE	1	0.38781195341583	2		544	635	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81979788	81979788	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	101	463	0	ENST00000359376.3:c.3490T>C	p.Ser1164Pro	p.S1164P	ENST00000359376	NM_002661.3	1164	Tcc/Ccc	31/33	1	2	FACETS	0.961	0.862	1	0.961	0.862	1	CLONAL	1	TRUE	1	0.38781195341583	2		463	542	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38787109	38787109	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	85	470	0	ENST00000348513.6:c.884A>G	p.Gln295Arg	p.Q295R	ENST00000348513	NM_003079.4	295	cAg/cGg	10/11	1	2	FACETS	0.915	0.812	1	0.915	0.812	1	CLONAL	1	TRUE	1	0.38781195341583	2		470	479	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554077	63554077	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	131	576	0	ENST00000307078.5:c.662T>C	p.Val221Ala	p.V221A	ENST00000307078	NM_004655.3	221	gTg/gCg	2/11	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.38781195341583	2		576	646	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39638015	39638015	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	88	333	0	ENST00000262039.4:c.2432G>A	p.Arg811Lys	p.R811K	ENST00000262039	NM_002647.2	811	aGg/aAg	22/25	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.38781195341583	2		333	408	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56338922	56338922	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1159016094	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	61	355	0	ENST00000348428.3:c.51del	p.Thr18ArgfsTer55	p.T18Rfs*55	ENST00000348428	NM_006785.3	16	gCc/gc	1/17	1	2	FACETS	0.974	0.846	1	0.974	0.846	1	CLONAL	1	TRUE	1	0.38781195341583	2		355	323	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6262304	6262305	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	113	444	0	ENST00000252674.7:c.210dup	p.Tyr71LeufsTer101	p.Y71Lfs*101	ENST00000252674	NM_005934.3	70	-/C	3/12	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.38781195341583	2		444	551	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267613	7267613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	80	500	0	ENST00000302850.5:c.395G>A	p.Gly132Asp	p.G132D	ENST00000302850	NM_000208.2	132	gGc/gAc	2/22	1	2	FACETS	0.786	0.693	0.885	0.786	0.693	0.885	SUBCLONAL	1	TRUE	1	0.38781195341583	2		500	525	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281154	15281154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	105	482	0	ENST00000263388.2:c.5102C>T	p.Ala1701Val	p.A1701V	ENST00000263388	NM_000435.2	1701	gCg/gTg	27/33	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.38781195341583	2		482	531	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40761069	40761069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374073998	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	75	379	0	ENST00000392038.2:c.283G>A	p.Glu95Lys	p.E95K	ENST00000392038	NM_001626.4	95	Gag/Aag	4/14	1	2	FACETS	0.891	0.784	1	0.891	0.784	1	CLONAL	1	TRUE	1	0.38781195341583	2		379	434	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140174	50140174	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	96	438	0	ENST00000246792.3:c.251C>T	p.Thr84Ile	p.T84I	ENST00000246792	NM_006270.3	84	aCc/aTc	3/6	1	2	FACETS	0.919	0.821	1	0.919	0.821	1	CLONAL	1	TRUE	1	0.38781195341583	2		438	539	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52693381	52693382	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	95	454	0	ENST00000322088.6:c.36dup	p.Ile13HisfsTer11	p.I13Hfs*11	ENST00000322088	NM_014225.5	11	tac/taCc	1/15	1	2	FACETS	0.988	0.883	1	0.988	0.883	1	CLONAL	1	TRUE	1	0.38781195341583	2		454	496	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467451	25467451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	126	511	0	ENST00000264709.3:c.1625G>A	p.Gly542Glu	p.G542E	ENST00000264709	NM_175629.2	542	gGg/gAg	14/23	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.38781195341583	2		511	576	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635627	47635627	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	55	254	0	ENST00000233146.2:c.299T>C	p.Val100Ala	p.V100A	ENST00000233146	NM_000251.2	100	gTt/gCt	2/16	1	2	FACETS	0.992	0.855	1	0.992	0.855	1	CLONAL	1	TRUE	1	0.38781195341583	2		254	286	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101106	41101106	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	88	472	0	ENST00000373198.4:c.1250G>A	p.Cys417Tyr	p.C417Y	ENST00000373198	NM_133170.3	417	tGc/tAc	8/32	1	2	FACETS	0.883	0.785	0.987	0.883	0.785	0.987	CLONAL	1	TRUE	1	0.38781195341583	2		472	514	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945332	54945332	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	64	261	0	ENST00000312783.6:c.1094A>G	p.Lys365Arg	p.K365R	ENST00000312783	NM_198436.1	365	aAg/aGg	10/10	1	2	FACETS	0.988	0.861	1	0.988	0.861	1	CLONAL	1	TRUE	1	0.38781195341583	2		261	334	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29445423	29445423	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	103	581	0	ENST00000544604.2:c.1254C>A	p.Ser418Arg	p.S418R	ENST00000544604	NM_001206998.1	418	agC/agA	8/9	1	2	FACETS	0.952	0.854	1	0.952	0.854	1	CLONAL	1	TRUE	1	0.38781195341583	2		581	558	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49724992	49724992	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	105	343	0	ENST00000449682.2:c.352A>G	p.Lys118Glu	p.K118E	ENST00000449682	NM_020998.3	118	Aaa/Gaa	3/18	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.38781195341583	2		343	441	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39003674	39003674	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	50	316	0	ENST00000357387.3:c.246G>T	p.Glu82Asp	p.E82D	ENST00000357387	NM_152756.3	82	gaG/gaT	4/38	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.38781195341583	2		316	250	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751200	57751200	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	82	406	0	ENST00000274289.3:c.1667del	p.Phe556SerfsTer14	p.F556Sfs*14	ENST00000274289	NM_006622.3	556	tTc/tc	12/14	1	2	FACETS	0.883	0.781	0.991	0.883	0.781	0.991	CLONAL	1	TRUE	1	0.38781195341583	2		406	479	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755750	57755750	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115808605	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	80	475	0	ENST00000274289.3:c.37G>A	p.Ala13Thr	p.A13T	ENST00000274289	NM_006622.3	13	Gcc/Acc	1/14	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.38781195341583	2		475	387	SUCCESS
APC	324	MSKCC	GRCh37	5	112177462	112177462	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	74	425	0	ENST00000257430.4:c.6171G>T	p.Lys2057Asn	p.K2057N	ENST00000257430	NM_000038.5	2057	aaG/aaT	16/16	1	2	FACETS	0.964	0.848	1	0.964	0.848	1	CLONAL	1	TRUE	1	0.38781195341583	2		425	396	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31238990	31238990	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs72558148	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	13	242	0	ENST00000376228.5:c.479C>T	p.Ala160Val	p.A160V	ENST00000376228	NM_002117.5	160	gCg/gTg	3/8	1	2	FACETS	0.279	0.199	0.377	0.279	0.199	0.377	SUBCLONAL	1	TRUE	1	0.38781195341583	2		242	240	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324691	31324753	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGCCGGGACACGGAGGTGTAGAAATACCTCATGGAGTGGGAGCCTGGGGGTGAGGAGGGGCT	GGGCCGGGACACGGAGGTGTAGAAATACCTCATGGAGTGGGAGCCTGGGGGTGAGGAGGGGCT	-	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	23	346	0	ENST00000412585.2:c.74-19_117del		p.X25_splice	ENST00000412585	NM_005514.6	25		2/8	1	2	FACETS	0.31	0.241	0.389	0.31	0.241	0.389	SUBCLONAL	1	TRUE	1	0.38781195341583	2		346	383	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120573	94120573	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	36	366	0	ENST00000369303.4:c.478C>A	p.Leu160Ile	p.L160I	ENST00000369303	NM_004440.3	160	Ctt/Att	3/17	1	2	FACETS	0.406	0.334	0.488	0.406	0.334	0.488	SUBCLONAL	1	TRUE	1	0.38781195341583	2		366	457	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265476	152265476	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	83	409	0	ENST00000206249.3:c.929T>C	p.Leu310Pro	p.L310P	ENST00000206249	NM_000125.3	310	cTg/cCg	4/8	1	2	FACETS	0.903	0.8	1	0.903	0.8	1	CLONAL	1	TRUE	1	0.38781195341583	2		409	474	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978462	2978462	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1331618139	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	74	365	0	ENST00000396946.4:c.868G>A	p.Gly290Arg	p.G290R	ENST00000396946	NM_032415.4	290	Ggg/Agg	7/25	1	2	FACETS	0.94	0.827	1	0.94	0.827	1	CLONAL	1	TRUE	1	0.38781195341583	2		365	406	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851492	128851492	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	54	441	0	ENST00000249373.3:c.1817A>G	p.Asp606Gly	p.D606G	ENST00000249373	NM_005631.4	606	gAc/gGc	11/12	1	2	FACETS	0.527	0.45	0.612	0.527	0.45	0.612	SUBCLONAL	1	TRUE	1	0.38781195341583	2		441	528	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460508	8460508	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs368896994	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	93	473	0	ENST00000356435.5:c.3778A>G	p.Ile1260Val	p.I1260V	ENST00000356435		1260	Atc/Gtc	22/35	0.38781195341583	3	FACETS	0.91	0.81	1	0.455	0.405	0.509	CLONAL	1	TRUE	1	0.38781195341583	3		473	629	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920537	127920537	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	58	253	0	ENST00000373547.4:c.362A>G	p.Gln121Arg	p.Q121R	ENST00000373547	NM_002721.4	121	cAg/cGg	4/7	0.38781195341583	3	FACETS	1	0.873	1	0.506	0.437	0.58	CLONAL	1	TRUE	1	0.38781195341583	3		253	353	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650780	48650780	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	145	317	1	ENST00000376670.3:c.649A>G	p.Arg217Gly	p.R217G	ENST00000376670	NM_002049.3	217	Agg/Ggg	4/6	1	1	FACETS	0.988	0.918	1	1	0.992	1	CLONAL	2	TRUE	0	0.38781195341583	1		318	305	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412582	63412582	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066694-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	41	244	0	ENST00000330258.3:c.585G>T	p.Lys195Asn	p.K195N	ENST00000330258	NM_152424.3	195	aaG/aaT	2/2	1	1	FACETS	0.699	0.586	0.821	0.699	0.586	0.821	SUBCLONAL	1	TRUE	0	0.38781195341583	1		244	244	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256530	+	missense_variant	Missense_Mutation	DNP	TG	TG	AT	novel	NA	P-0066695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	31	484	1	ENST00000369535.4:c.181_182delinsAT	p.Gln61Ile	p.Q61I	ENST00000369535	NM_002524.4	61	CAa/ATa	3/7	0.163527553107752	2	FACETS	1	0.837	1	0.518	0.419	0.63	CLONAL	1	TRUE	0	0.166129201512579	2		485	360	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031966	10031966	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	52	579	0	ENST00000330684.3:c.857A>G	p.Tyr286Cys	p.Y286C	ENST00000330684	NM_001134407.1	286	tAc/tGc	3/13	0.166129201512579	2	FACETS	1	0.961	1	0.715	0.609	0.829	CLONAL	1	TRUE	0	0.166129201512579	2		579	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0066695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	32	495	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	1	2	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	1	0.166129201512579	2		495	364	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412884	49412884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	10	516	0	ENST00000418115.1:c.139G>A	p.Glu47Lys	p.E47K	ENST00000418115	NM_001664.2	47	Gag/Aag	2/5	1	2	FACETS	0.268	0.18	0.379	0.268	0.18	0.379	SUBCLONAL	1	TRUE	1	0.166129201512579	2		516	450	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517914	8517914	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	23	448	0	ENST00000356435.5:c.1477C>A	p.Leu493Met	p.L493M	ENST00000356435		493	Ctg/Atg	10/35	0.166129201512579	2	FACETS	0.719	0.56	0.904	0.36	0.28	0.452	CLONAL	1	TRUE	0	0.166129201512579	2		448	385	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150936218	150936218	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0066695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	108	534	0	ENST00000271640.5:c.3669+1G>T		p.X1223_splice	ENST00000271640	NM_001145415.1	1223			0.166129201512579	3	FACETS	0.872	0.786	0.964	1	0.977	1	CLONAL	3	TRUE	1	0.166129201512579	3		534	538	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251853	8251853	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	34	586	0	ENST00000335790.3:c.224G>T	p.Arg75Leu	p.R75L	ENST00000335790	NM_002315.2	75	cGa/cTa	2/4	1	2	FACETS	0.952	0.778	1	0.952	0.778	1	CLONAL	1	TRUE	1	0.166129201512579	2		586	430	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514299	69514299	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	58	542	0	ENST00000294312.3:c.382C>T	p.Pro128Ser	p.P128S	ENST00000294312	NM_005117.2	128	Cca/Tca	3/3	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.166129201512579	2		542	476	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658324	18658324	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	19	499	0	ENST00000266497.5:c.3129G>T	p.Lys1043Asn	p.K1043N	ENST00000266497		1043	aaG/aaT	22/31	1	2	FACETS	0.722	0.547	0.927	0.722	0.547	0.927	CLONAL	1	TRUE	1	0.166129201512579	2		499	317	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853924	59853924	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0066695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	21	409	0	ENST00000259008.2:c.1936-1G>T		p.X646_splice	ENST00000259008	NM_032043.2	646			1	2	FACETS	0.761	0.586	0.966	0.761	0.586	0.966	CLONAL	1	TRUE	1	0.166129201512579	2		409	332	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031281	36031281	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	47	443	0	ENST00000358208.4:c.1400C>G	p.Pro467Arg	p.P467R	ENST00000358208		467	cCt/cGt	11/12	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.166129201512579	2		443	406	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155024	55155024	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	73	562	0	ENST00000257290.5:c.2733T>A	p.Ser911Arg	p.S911R	ENST00000257290	NM_006206.4	911	agT/agA	20/23	1	2	FACETS	0.976	0.857	1	1	0.982	1	CLONAL	2	TRUE	1	0.166129201512579	2		562	450	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412224	63412224	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	64	639	0	ENST00000330258.3:c.943G>C	p.Asp315His	p.D315H	ENST00000330258	NM_152424.3	315	Gat/Cat	2/2	1	2	FACETS	0.766	0.664	0.876	1	0.972	1	SUBCLONAL	2	TRUE	1	0.166129201512579	2		639	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579865	7579868	+	frameshift_variant	Frame_Shift_Del	DEL	CTGA	CTGA	-	novel	NA	P-0066696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	405	354	0	ENST00000269305.4:c.45_48del	p.Ser15ArgfsTer28	p.S15Rfs*28	ENST00000269305	NM_001126112.2	15	agTCAG/ag	2/11	0.656124529167862	4	FACETS	0.934	0.917	0.949	1	0.997	1	CLONAL	5	FALSE	0	0.648218954751518	4		354	441	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927483	178927483	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	104	256	0	ENST00000263967.3:c.1246A>G	p.Lys416Glu	p.K416E	ENST00000263967	NM_006218.2	416	Aaa/Gaa	7/21	0.333649289195243	6	FACETS	0.867	0.781	0.956	0.289	0.26	0.319	INDETERMINATE	2	FALSE	0	0.648218954751518	6		256	425	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245033	133245033	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	51	442	0	ENST00000320574.5:c.2082G>C	p.Lys694Asn	p.K694N	ENST00000320574	NM_006231.2	694	aaG/aaC	19/49	NA	2	FACETS	0.426	0.363	0.495			1	INDETERMINATE	1	FALSE	NA	0.648218954751518	2		442	369	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547021	9547021	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	93	402	0	ENST00000353224.5:c.1001A>T	p.Asp334Val	p.D334V	ENST00000353224	NM_177990.2	334	gAt/gTt	5/10	0.468587335282096	6	FACETS	1	0.956	1	0.191	0.169	0.213	CLONAL	1	FALSE	0	0.648218954751518	6		402	576	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27173268	27173268	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	159	398	0	ENST00000380036.4:c.809G>C	p.Gly270Ala	p.G270A	ENST00000380036	NM_000459.3	270	gGa/gCa	6/23	0.656124529167862	5	FACETS	0.75	0.69	0.812	0.375	0.345	0.406	SUBCLONAL	2	FALSE	1	0.648218954751518	5		398	645	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0066697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	54	418	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.464	0.398	0.536	0.464	0.398	0.536	SUBCLONAL	1	TRUE	1	0.680305155346593	2		418	342	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0066697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	33	104	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.404	0.331	0.486	0.404	0.331	0.486	SUBCLONAL	1	TRUE	1	0.680305155346593	2		104	240	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339230	70339230	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs199469667	NA	P-0066697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	15	287	0	ENST00000374080.3:c.107T>G	p.Leu36Arg	p.L36R	ENST00000374080		36	cTg/cGg	2/45	1	2	FACETS	0.107	0.077	0.142	0.107	0.077	0.142	SUBCLONAL	1	TRUE	1	0.680305155346593	2		287	413	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101006	27101006	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	78	401	0	ENST00000324856.7:c.4288C>T	p.Gln1430Ter	p.Q1430*	ENST00000324856	NM_006015.4	1430	Cag/Tag	18/20	1	2	FACETS	0.551	0.487	0.62	0.551	0.487	0.62	SUBCLONAL	1	TRUE	1	0.680305155346593	2		401	416	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696462	47696462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	178	498	0	ENST00000347630.2:c.361C>T	p.Arg121Trp	p.R121W	ENST00000347630	NM_001007230.1	121	Cgg/Tgg	6/11	0.390631874461831	2	FACETS	1	0.95	1	0.514	0.477	0.552	INDETERMINATE	1	TRUE	0	0.680305155346593	2		498	509	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720857	89720857	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	20	205	0	ENST00000371953.3:c.1008C>A	p.Tyr336Ter	p.Y336*	ENST00000371953	NM_000314.4	336	taC/taA	8/9	1	2	FACETS	0.414	0.319	0.522	0.414	0.319	0.522	SUBCLONAL	1	TRUE	1	0.680305155346593	2		205	142	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423976	47423977	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0066697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	94	474	0	ENST00000404338.3:c.2048_2049del	p.Glu683ValfsTer8	p.E683Vfs*8	ENST00000404338	NM_004491.4	682	AGa/a	1/6	1	2	FACETS	0.481	0.428	0.536	0.481	0.428	0.536	SUBCLONAL	1	TRUE	1	0.680305155346593	2		474	575	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466300	120466300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761870508	NA	P-0066698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	49	381	1	ENST00000256646.2:c.4819C>T	p.Arg1607Cys	p.R1607C	ENST00000256646	NM_024408.3	1607	Cgc/Tgc	26/34	0.412734174797683	4	FACETS	0.497	0.42	0.582			1	SUBCLONAL	1	TRUE	NA	0.410515485498512	4		382	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0066698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	176	387	0	ENST00000269305.4:c.838A>T	p.Arg280Ter	p.R280*	ENST00000269305	NM_001126112.2	280	Aga/Tga	8/11	0.365102104410779	2	FACETS	0.888	0.825	0.952	0.888	0.825	0.952	CLONAL	2	TRUE	0	0.410515485498512	2		387	483	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609055	43609055	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	141	492	0	ENST00000355710.3:c.1811C>G	p.Ala604Gly	p.A604G	ENST00000355710	NM_020975.4	604	gCt/gGt	10/20	0.333878817877973	4	FACETS	1	0.982	1	0.649	0.591	0.708	CLONAL	1	TRUE	2	0.410515485498512	4		492	747	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341350	89341350	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	36	259	0	ENST00000301030.4:c.7585T>C	p.Ser2529Pro	p.S2529P	ENST00000301030	NM_001256183.1	2529	Tcc/Ccc	11/13	0.15380986256955	5	FACETS	0.869	0.717	1			1	INDETERMINATE	1	TRUE	NA	0.410515485498512	5		259	326	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622398	1622398	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0066698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	55	311	0	ENST00000344749.5:c.566C>G	p.Ser189Ter	p.S189*	ENST00000344749	NM_001136139.2	189	tCa/tGa	9/19	0.384685946975016	2	FACETS	0.805	0.692	0.926	0.402	0.346	0.463	CLONAL	1	TRUE	0	0.410515485498512	2		311	333	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223964	36223964	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769681222	NA	P-0066698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	48	495	0	ENST00000222270.7:c.6514G>A	p.Val2172Ile	p.V2172I	ENST00000222270	NM_014727.1	2172	Gtc/Atc	28/37	0.410515485498512	5	FACETS	0.453	0.381	0.532			1	SUBCLONAL	1	TRUE	NA	0.410515485498512	5		495	835	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	893180	893180	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	30	289	0	ENST00000166345.3:c.67G>C	p.Val23Leu	p.V23L	ENST00000166345	NM_004237.3	23	Gtg/Ctg	1/13	0.412734174797683	3	FACETS	0.354	0.285	0.434	0.177	0.142	0.217	SUBCLONAL	1	TRUE	1	0.410515485498512	3		289	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578537	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs879254214	NA	P-0066701-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	115	466	1	ENST00000269305.4:c.393_395del	p.Asn131del	p.N131del	ENST00000269305	NM_001126112.2	131	aaCAAg/aag	5/11	0.191228075390333	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.265046083230628	1		467	604	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28979946	28979946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764045713	NA	P-0066701-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	77	334	0	ENST00000282397.4:c.1522C>T	p.Arg508Cys	p.R508C	ENST00000282397	NM_002019.4	508	Cgc/Tgc	11/30	0.155956219533722	4	FACETS	0.97	0.851	1	0.485	0.425	0.549	INDETERMINATE	1	TRUE	2	0.265046083230628	4		334	758	SUCCESS
APC	324	MSKCC	GRCh37	5	112175349	112175350	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0066701-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	104	376	0	ENST00000257430.4:c.4058_4059del	p.Glu1353ValfsTer21	p.E1353Vfs*21	ENST00000257430	NM_000038.5	1353	gAA/g	16/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.265046083230628	2		376	643	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501288	140501288	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507470	NA	P-0066701-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	151	231	0	ENST00000288602.6:c.784C>A	p.Gln262Lys	p.Q262K	ENST00000288602	NM_004333.4	262	Caa/Aaa	6/18	0.17850487271685	3	FACETS	0.982	0.901	1	0.982	0.901	1	CLONAL	2	TRUE	1	0.265046083230628	3		231	657	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216482	2216482	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs372258317	NA	P-0066701-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	44	434	0	ENST00000398665.3:c.2126C>G	p.Pro709Arg	p.P709R	ENST00000398665	NM_032482.2	709	cCg/cGg	20/28	0.17850487271685	3	FACETS	0.596	0.499	0.704	0.298	0.249	0.352	SUBCLONAL	1	TRUE	1	0.265046083230628	3		434	631	SUCCESS
APC	324	MSKCC	GRCh37	5	112170660	112170660	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0066701-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	55	275	0	ENST00000257430.4:c.1756A>T	p.Lys586Ter	p.K586*	ENST00000257430	NM_000038.5	586	Aaa/Taa	15/16	1	2	FACETS	0.686	0.586	0.795	0.686	0.586	0.795	SUBCLONAL	1	TRUE	1	0.265046083230628	2		275	605	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974985	18974985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1349791107	NA	P-0066701-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	32	388	1	ENST00000262803.5:c.2782C>T	p.Arg928Cys	p.R928C	ENST00000262803	NM_002911.3	928	Cgc/Tgc	20/24	0.178507833111462	2	FACETS	0.456	0.37	0.555	0.228	0.185	0.278	SUBCLONAL	1	TRUE	0	0.265046083230628	2		389	529	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181956	38181956	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066701-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	43	488	0	ENST00000396334.3:c.580C>A	p.Gln194Lys	p.Q194K	ENST00000396334	NM_002468.4	194	Caa/Aaa	3/5	1	2	FACETS	0.469	0.391	0.555	0.469	0.391	0.555	SUBCLONAL	1	TRUE	1	0.265046083230628	2		488	692	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920451	114920451	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0066701-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	112	370	0	ENST00000543371.1:c.1391+1G>C		p.X464_splice	ENST00000543371	NM_001198531.1	464			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.265046083230628	2		370	626	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819694	81819694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770382676	NA	P-0066702-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	76	469	0	ENST00000359376.3:c.100C>T	p.Arg34Cys	p.R34C	ENST00000359376	NM_002661.3	34	Cgc/Tgc	2/33	0.389845668168525	3	FACETS	0.707	0.62	0.8	0.353	0.31	0.4	SUBCLONAL	1	TRUE	1	0.438561338187993	3		469	598	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916948	178916950	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0066702-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	86	375	0	ENST00000263967.3:c.337_339del	p.Leu113del	p.L113del	ENST00000263967	NM_006218.2	112	aTCCtc/atc	2/21	0.164287293261613	3	FACETS	1	0.921	1	0.684	0.616	0.754	INDETERMINATE	2	TRUE	0	0.438561338187993	3		375	233	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963907	2963907	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066702-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	117	538	0	ENST00000396946.4:c.1900G>C	p.Glu634Gln	p.E634Q	ENST00000396946	NM_032415.4	634	Gag/Cag	15/25	0.392523615803666	2	FACETS	0.963	0.872	1	0.482	0.436	0.53	CLONAL	1	TRUE	0	0.438561338187993	2		538	554	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43700176	43700176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066702-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	90	346	0	ENST00000382044.4:c.5711C>T	p.Ser1904Phe	p.S1904F	ENST00000382044	NM_001141980.1	1904	tCt/tTt	27/28	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.438561338187993	2		346	391	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124487019	124487019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066702-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	35	325	0	ENST00000357628.3:c.983G>A	p.Arg328Lys	p.R328K	ENST00000357628	NM_015450.2	328	aGa/aAa	12/19	1	2	FACETS	0.836	0.692	0.993	0.836	0.692	0.993	CLONAL	1	TRUE	1	0.438561338187993	2		325	191	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163865	47163865	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0066702-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	45	482	0	ENST00000409792.3:c.2261C>G	p.Ser754Ter	p.S754*	ENST00000409792	NM_014159.6	754	tCa/tGa	3/21	0.41353111507826	2	FACETS	0.834	0.707	0.972	0.417	0.353	0.486	CLONAL	1	TRUE	0	0.438561338187993	2		482	246	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578282	+	inframe_deletion	In_Frame_Del	DEL	TGCTGAGGAGGG	TGCTGAGGAGGG	-	novel	NA	P-0066702-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	122	576	0	ENST00000269305.4:c.567_578del	p.Pro190_His193del	p.P190_H193del	ENST00000269305	NM_001126112.2	189	gcCCCTCCTCAGCAt/gct	6/11	0.438561338187993	1	FACETS	0.987	0.899	1	0.987	0.899	1	CLONAL	1	TRUE	0	0.438561338187993	1		576	440	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478785	56478785	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	87	272	0	ENST00000267101.3:c.241C>G	p.Arg81Gly	p.R81G	ENST00000267101	NM_001982.3	81	Cga/Gga	3/28	0.530831470769079	3	FACETS	1	0.956	1	0.57	0.509	0.634	CLONAL	1	TRUE	1	0.555563151903935	3		272	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0066703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	179	886	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.555563151903935	2	FACETS	0.863	0.821	0.902	1	0.992	1	CLONAL	3	TRUE	0	0.555563151903935	2		886	249	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175996729	175996729	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs769472624	NA	P-0066703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	67	381	0	ENST00000367669.3:c.1708C>A	p.His570Asn	p.H570N	ENST00000367669	NM_022457.5	570	Cat/Aat	15/20	0.50683620943345	4	FACETS	1	0.915	1	0.53	0.463	0.601	CLONAL	1	TRUE	2	0.555563151903935	4		381	354	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413574	32413574	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	88	288	0	ENST00000332351.3:c.1376A>T	p.Lys459Met	p.K459M	ENST00000332351	NM_024426.4	459	aAg/aTg	9/10	0.530831470769079	3	FACETS	1	0.978	1	0.686	0.615	0.76	CLONAL	1	TRUE	1	0.555563151903935	3		288	295	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505096	149505096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	97	415	0	ENST00000261799.4:c.1719C>G	p.Ser573Arg	p.S573R	ENST00000261799	NM_002609.3	573	agC/agG	12/23	0.530831470769079	3	FACETS	1	0.965	1	0.586	0.526	0.648	CLONAL	1	TRUE	1	0.555563151903935	3		415	381	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950442	68950442	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1233335178	NA	P-0066703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	64	300	0	ENST00000288368.4:c.754T>G	p.Leu252Val	p.L252V	ENST00000288368	NM_024870.2	252	Tta/Gta	7/40	0.555563151903935	3	FACETS	1	0.908	1	0.524	0.458	0.594	CLONAL	1	TRUE	1	0.555563151903935	3		300	281	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	61	446	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.218806722677613	2		446	466	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860517	151860517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772864510	NA	P-0066704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	71	519	0	ENST00000262189.6:c.10145G>A	p.Arg3382Gln	p.R3382Q	ENST00000262189	NM_170606.2	3382	cGg/cAg	43/59	0.17929792279158	3	FACETS	0.94	0.819	1	0.47	0.409	0.535	CLONAL	1	TRUE	1	0.218806722677613	3		519	766	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409089	4409089	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777848359	NA	P-0066705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	83	436	0	ENST00000261254.3:c.784C>T	p.Arg262Cys	p.R262C	ENST00000261254	NM_001759.3	262	Cgt/Tgt	5/5	1	2	FACETS	0.836	0.738	0.94	0.836	0.738	0.94	CLONAL	1	TRUE	1	0.333825836015775	2		436	595	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578509	7578510	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGTCTT	novel	NA	P-0066705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	84	485	0	ENST00000269305.4:c.415_420dup	p.Lys139_Thr140dup	p.K139_T140dup	ENST00000269305	NM_001126112.2	139	-/AAGACC	5/11	0.294215767927841	1	FACETS	0.817	0.724	0.917	0.817	0.724	0.917	CLONAL	1	TRUE	0	0.333825836015775	1		485	513	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564174	139564174	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs767145762	NA	P-0066705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	65	371	0	ENST00000308874.7:c.313+1G>A		p.X105_splice	ENST00000308874		105			0.280404390507785	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.333825836015775	1		371	307	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554955	106554963	+	inframe_deletion	In_Frame_Del	DEL	AGTGCCACA	AGTGCCACA	-	novel	NA	P-0066705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	71	527	0	ENST00000369096.4:c.2074_2082del	p.Cys692_Lys694del	p.C692_K694del	ENST00000369096	NM_001198.3	691	cAGTGCCACAag/cag	7/7	1	2	FACETS	0.732	0.639	0.832	0.732	0.639	0.832	SUBCLONAL	1	TRUE	1	0.333825836015775	2		527	581	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131253	202131254	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0066705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	69	363	0	ENST00000358485.4:c.222_223del	p.Asp74GlufsTer2	p.D74Efs*2	ENST00000358485	NM_001080125.1	74	gAC/g	2/9	1	2	FACETS	0.774	0.675	0.881	0.774	0.675	0.881	SUBCLONAL	1	TRUE	1	0.333825836015775	2		363	534	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416364	29416364	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs141242925	NA	P-0066705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	76	490	0	ENST00000389048.3:c.4589G>T	p.Arg1530Met	p.R1530M	ENST00000389048	NM_004304.4	1530	aGg/aTg	29/29	1	2	FACETS	0.789	0.693	0.892	0.789	0.693	0.892	SUBCLONAL	1	TRUE	1	0.333825836015775	2		490	577	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245405	41245405	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	97	219	0	ENST00000357654.3:c.2143del	p.Thr715ProfsTer21	p.T715Pfs*21	ENST00000357654	NM_007294.3	715	Acc/cc	10/23	0.21132028299442	3	FACETS	1	0.974	1	0.432	0.386	0.481	CLONAL	1	TRUE	0	0.333825836015775	3		219	523	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112919970	112919970	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	33	173	0	ENST00000351677.2:c.1185C>A	p.Asp395Glu	p.D395E	ENST00000351677	NM_002834.3	395	gaC/gaA	10/16	0.280404390507785	1	FACETS	0.713	0.584	0.856	0.713	0.584	0.856	SUBCLONAL	1	TRUE	0	0.333825836015775	1		173	231	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969405	44969405	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	252	196	0	ENST00000377967.4:c.4087C>T	p.Arg1363Ter	p.R1363*	ENST00000377967	NM_021140.2	1363	Cga/Tga	28/29	0.638345634192915	2	FACETS	1	0.987	1			1	CLONAL	2	TRUE	NA	0.667562288033814	2		196	352	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514831	44514831	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	328	473	0	ENST00000291552.4:c.416C>T	p.Pro139Leu	p.P139L	ENST00000291552	NM_006758.2	139	cCg/cTg	6/8	0.667562288033814	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.667562288033814	2		473	451	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610087	10610087	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	304	497	0	ENST00000171111.5:c.623A>T	p.Tyr208Phe	p.Y208F	ENST00000171111	NM_203500.1	208	tAc/tTc	2/6	0.639979817382715	4	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	2	0.667562288033814	4		497	757	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44515820	44515820	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	226	358	0	ENST00000291552.4:c.233A>G	p.Tyr78Cys	p.Y78C	ENST00000291552	NM_006758.2	78	tAt/tGt	4/8	0.667562288033814	2	FACETS	0.993	0.947	1	0.993	0.947	1	CLONAL	2	TRUE	0	0.667562288033814	2		358	341	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31448708	31448708	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	215	363	0	ENST00000344624.3:c.2828A>T	p.Asn943Ile	p.N943I	ENST00000344624		943	aAc/aTc	20/33	0.639979817382715	4	FACETS	0.87	0.814	0.928	0.87	0.814	0.928	CLONAL	2	TRUE	2	0.667562288033814	4		363	617	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573225	64573226	+	stop_gained	Nonsense_Mutation	DNP	TC	TC	CA	novel	NA	P-0066732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	302	493	1	ENST00000312049.6:c.1066_1067delinsTG	p.Glu356Ter	p.E356*	ENST00000312049	NM_130799.2	356	GAa/TGa	8/10	0.667562288033814	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.667562288033814	2		494	449	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375951	118375951	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	77	552	0	ENST00000534358.1:c.9344C>G	p.Pro3115Arg	p.P3115R	ENST00000534358	NM_005933.3	3115	cCc/cGc	27/36	0.667562288033814	2	FACETS	0.444	0.39	0.501	0.222	0.195	0.251	SUBCLONAL	1	TRUE	0	0.667562288033814	2		552	520	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287607	33287607	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	309	445	0	ENST00000374542.5:c.1490del	p.Met497SerfsTer31	p.M497Sfs*31	ENST00000374542	NM_001141970.1	497	aTg/ag	6/8	0.667562288033814	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.667562288033814	2		445	462	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115435	115115437	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	rs1319662056	NA	P-0066733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	103	383	0	ENST00000257566.3:c.889_891del	p.Asn297del	p.N297del	ENST00000257566	NM_016569.3	297	AAC/-	5/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.456480702784805	2		383	371	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711875	89711875	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587782603	NA	P-0066733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	86	330	0	ENST00000371953.3:c.493G>A	p.Gly165Arg	p.G165R	ENST00000371953	NM_000314.4	165	Gga/Aga	6/9	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.456480702784805	2		330	352	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417861	138417861	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	167	322	0	ENST00000289153.2:c.1658A>G	p.Asn553Ser	p.N553S	ENST00000289153	NM_006219.2	553	aAt/aGt	11/22	0.425523381910565	3	FACETS	0.958	0.888	1	0.958	0.888	1	CLONAL	2	TRUE	1	0.456480702784805	3		322	469	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331979	81331979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763933267	NA	P-0066733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	78	372	0	ENST00000222390.5:c.2105G>A	p.Arg702His	p.R702H	ENST00000222390	NM_000601.4	702	cGt/cAt	18/18	1	2	FACETS	0.944	0.835	1	0.944	0.835	1	CLONAL	1	TRUE	1	0.456480702784805	2		372	362	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449874	29449874	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	157	604	0	ENST00000389048.3:c.2981A>G	p.Glu994Gly	p.E994G	ENST00000389048	NM_004304.4	994	gAa/gGa	18/29	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.456480702784805	2		604	577	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436673	52436673	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	130	525	1	ENST00000460680.1:c.2001G>T	p.Arg667Ser	p.R667S	ENST00000460680	NM_004656.3	667	agG/agT	16/17	0.417091258987522	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.456480702784805	1		526	436	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0066734-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	124	533	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	1	2	FACETS	0.923	0.841	1	0.923	0.841	1	CLONAL	1	TRUE	1	0.572672456236115	2		533	469	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0066735-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	35	582	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.160398517606386	3	FACETS	0.804	0.659	0.967	0.402	0.329	0.484	CLONAL	1	TRUE	1	0.23	3		582	422	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746132	162746132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1374086542	NA	P-0066735-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	63	397	0	ENST00000367921.3:c.2255G>A	p.Arg752His	p.R752H	ENST00000367921	NM_006182.2	752	cGc/cAc	16/18	0.126930601691317	3	FACETS	0.77	0.665	0.885	0.385	0.332	0.443	INDETERMINATE	1	TRUE	1	0.23	3		397	793	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0066735-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	130	498	0	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.298405981441424	1	FACETS	0.78	0.71	0.854	1	0.987	1	SUBCLONAL	2	TRUE	0	0.23	1		498	641	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858237	27858238	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs763163035	NA	P-0066735-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	63	624	0	ENST00000359303.2:c.333_334del	p.Ala112TyrfsTer11	p.A112Yfs*11	ENST00000359303	NM_003535.2	111	tgTGct/tgct	1/1	0.291413400784771	3	FACETS	0.718	0.619	0.825	0.239	0.206	0.275	SUBCLONAL	1	TRUE	0	0.23	3		624	851	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047220	180047220	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066735-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	46	492	0	ENST00000261937.6:c.2495C>G	p.Ser832Cys	p.S832C	ENST00000261937	NM_182925.4	832	tCc/tGc	17/30	0.291413400784771	3	FACETS	0.701	0.59	0.825	0.234	0.196	0.275	SUBCLONAL	1	TRUE	0	0.23	3		492	636	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524976	8524976	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066735-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	128	347	0	ENST00000356435.5:c.628A>T	p.Thr210Ser	p.T210S	ENST00000356435		210	Acc/Tcc	7/35	0.126930601691317	3	FACETS	1	0.954	1	1	0.954	1	INDETERMINATE	2	TRUE	1	0.23	3		347	576	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532672	46532672	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1397949671	NA	P-0066735-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	38	399	0	ENST00000262741.5:c.406C>G	p.Leu136Val	p.L136V	ENST00000262741	NM_003629.3	136	Ctc/Gtc	4/10	1	2	FACETS	0.763	0.631	0.91	0.763	0.631	0.91	CLONAL	1	TRUE	1	0.23	2		399	433	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73112886	73112886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066735-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	48	333	0	ENST00000356692.5:c.482G>A	p.Ser161Asn	p.S161N	ENST00000356692		161	aGc/aAc	6/9	0.2015757344138	2	FACETS	1	0.942	1	0.619	0.526	0.721	CLONAL	1	TRUE	0	0.23	2		333	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577155	7577155	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	225	483	0	ENST00000269305.4:c.783del	p.Ser261ArgfsTer84	p.S261Rfs*84	ENST00000269305	NM_001126112.2	261	agT/ag	8/11	0.516978319005231	2	FACETS	0.843	0.795	0.892	0.843	0.795	0.892	CLONAL	2	TRUE	0	0.563020033970543	2		483	474	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265353	152265353	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	99	528	0	ENST00000206249.3:c.806G>T	p.Arg269Leu	p.R269L	ENST00000206249	NM_000125.3	269	cGc/cTc	4/8	1	2	FACETS	0.845	0.76	0.935	0.845	0.76	0.935	CLONAL	1	TRUE	1	0.563020033970543	2		528	416	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502361	186502361	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	116	545	0	ENST00000323963.5:c.84G>T	p.Trp28Cys	p.W28C	ENST00000323963		28	tgG/tgT	3/11	0.563020033970543	4	FACETS	0.833	0.751	0.92	0.278	0.25	0.307	CLONAL	1	TRUE	1	0.563020033970543	4		545	773	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098965	178098967	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0066736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	94	518	0	ENST00000397062.3:c.78_80del	p.Gln26_Asp27delinsHis	p.Q26_D27delinsH	ENST00000397062	NM_006164.4	26	caAGAt/cat	2/5	1	2	FACETS	0.82	0.735	0.91	0.82	0.735	0.91	CLONAL	1	TRUE	1	0.563020033970543	2		518	407	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533775	63533775	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1032366089	NA	P-0066736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	153	695	0	ENST00000307078.5:c.1379A>G	p.Tyr460Cys	p.Y460C	ENST00000307078	NM_004655.3	460	tAt/tGt	6/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.563020033970543	2		695	513	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721270	176721270	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	161	614	0	ENST00000439151.2:c.6901G>T	p.Gly2301Trp	p.G2301W	ENST00000439151	NM_022455.4	2301	Ggg/Tgg	23/23	0.550740311221079	1	FACETS	0.974	0.903	1	0.974	0.903	1	CLONAL	1	TRUE	0	0.563020033970543	1		614	422	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331642	8331642	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	86	510	0	ENST00000356435.5:c.5474G>T	p.Gly1825Val	p.G1825V	ENST00000356435		1825	gGc/gTc	33/35	0.490543692271017	0	FACETS	0.513	0.461	0.568			1	SUBCLONAL	1	TRUE	0	0.563020033970543	0		510	260	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577586	7577586	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587781589	NA	P-0066737-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	90	326	0	ENST00000269305.4:c.695T>G	p.Ile232Ser	p.I232S	ENST00000269305	NM_001126112.2	232	aTc/aGc	7/11	0.253305751503194	0	FACETS	0.809	0.741	0.876			1	CLONAL	4	FALSE	0	0.253305751503194	0		326	164	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685268	89685268	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs1085308043	NA	P-0066737-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	105	245	0	ENST00000371953.3:c.165-2A>T		p.X55_splice	ENST00000371953	NM_000314.4	55			0.253305751503194	0	FACETS	0.789	0.735	0.84			1	SUBCLONAL	5	FALSE	0	0.253305751503194	0		245	157	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206761	27206761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376225163	NA	P-0066737-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	96	357	0	ENST00000380036.4:c.2546G>A	p.Arg849Gln	p.R849Q	ENST00000380036	NM_000459.3	849	cGg/cAg	15/23	1	2	FACETS	0.899	0.812	0.989	1	0.99	1	CLONAL	3	FALSE	1	0.253305751503194	2		357	281	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878982	151878982	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066737-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	140	468	0	ENST00000262189.6:c.5963C>G	p.Pro1988Arg	p.P1988R	ENST00000262189	NM_170606.2	1988	cCt/cGt	36/59	0.23422806614684	2	FACETS	0.894	0.828	0.961	1	0.991	1	CLONAL	4	FALSE	0	0.253305751503194	2		468	309	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0066738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	345	550	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.7063497418038	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	FALSE	1	0.7063497418038	3		550	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0066738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	431	498	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.7063497418038	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	FALSE	0	0.7063497418038	2		498	549	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136825	55136825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1324781921	NA	P-0066738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	209	283	0	ENST00000257290.5:c.1147C>T	p.Arg383Cys	p.R383C	ENST00000257290	NM_006206.4	383	Cgt/Tgt	8/23	0.7063497418038	3	FACETS	0.998	0.942	1	0.998	0.942	1	CLONAL	2	FALSE	1	0.7063497418038	3		283	401	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410115	63410115	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	65	558	0	ENST00000330258.3:c.3052C>T	p.Pro1018Ser	p.P1018S	ENST00000330258	NM_152424.3	1018	Cct/Tct	2/2	0.566811599746665	2	FACETS	0.308	0.267	0.353	0.154	0.133	0.177	SUBCLONAL	1	FALSE	0	0.7063497418038	2		558	597	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921774	111921780	+	frameshift_variant	Frame_Shift_Del	DEL	GTTACAT	GTTACAT	-	novel	NA	P-0066738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	271	359	0	ENST00000393256.3:c.563_569del	p.Arg188LeufsTer52	p.R188Lfs*52	ENST00000393256	NM_006538.4	188	cGTTACATt/ct	4/4	0.594525638957036	4	FACETS	0.968	0.915	1	0.968	0.915	1	CLONAL	2	FALSE	2	0.7063497418038	4		359	676	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249476	153249476	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	336	357	0	ENST00000281708.4:c.1302del	p.Ile435LeufsTer63	p.I435Lfs*63	ENST00000281708	NM_033632.3	434	atC/at	9/12	0.7063497418038	3	FACETS	0.995	0.95	1	0.995	0.95	1	CLONAL	2	FALSE	1	0.7063497418038	3		357	647	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0066739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	115	343	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.270837642349585	2		343	684	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845518	128845518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748004767	NA	P-0066739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	55	396	0	ENST00000249373.3:c.815C>T	p.Ala272Val	p.A272V	ENST00000249373	NM_005631.4	272	gCg/gTg	4/12	1	2	FACETS	0.596	0.509	0.691	0.596	0.509	0.691	SUBCLONAL	1	TRUE	1	0.270837642349585	2		396	682	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50916702	50916702	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	61	376	0	ENST00000440232.2:c.2174G>A	p.Arg725His	p.R725H	ENST00000440232	NM_002691.3	725	cGt/cAt	18/27	1	2	FACETS	0.591	0.509	0.681	0.591	0.509	0.681	SUBCLONAL	1	TRUE	1	0.270837642349585	2		376	762	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943982	71943982	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	42	475	0	ENST00000298229.2:c.1915C>G	p.Leu639Val	p.L639V	ENST00000298229	NM_001567.3	639	Ctg/Gtg	16/28	0.270837642349585	1	FACETS	0.322	0.268	0.383	0.322	0.268	0.383	SUBCLONAL	1	TRUE	0	0.270837642349585	1		475	833	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403585	138403585	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	44	321	0	ENST00000289153.2:c.2197T>G	p.Leu733Val	p.L733V	ENST00000289153	NM_006219.2	733	Tta/Gta	15/22	1	2	FACETS	0.454	0.379	0.537	0.454	0.379	0.537	SUBCLONAL	1	TRUE	1	0.270837642349585	2		321	716	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637750	52637750	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0066744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	95	262	0	ENST00000394830.3:c.2568-2A>G		p.X856_splice	ENST00000394830	NM_018313.4	856			0.549421523410289	1	FACETS	0.82	0.739	0.904	0.82	0.739	0.904	CLONAL	1	TRUE	0	0.549421523410289	1		262	306	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640809	3640809	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	155	548	0	ENST00000294008.3:c.2830C>G	p.Pro944Ala	p.P944A	ENST00000294008	NM_032444.2	944	Cct/Gct	12/15	1	2	FACETS	0.907	0.834	0.983	0.907	0.834	0.983	CLONAL	1	TRUE	1	0.549421523410289	2		548	622	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183854	10183854	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	138	371	0	ENST00000256474.2:c.323del	p.Arg108ProfsTer51	p.R108Pfs*51	ENST00000256474	NM_000551.3	108	cGc/cc	1/3	0.549421523410289	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.549421523410289	1		371	359	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10266579	10266579	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	33	478	0	ENST00000340748.4:c.1394G>T	p.Trp465Leu	p.W465L	ENST00000340748		465	tGg/tTg	18/40	1	2	FACETS	0.191	0.155	0.232	0.191	0.155	0.232	SUBCLONAL	1	TRUE	1	0.549421523410289	2		478	630	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0066745-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	316	345	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.498758409915831	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.498758409915831	1		345	862	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848547	151848547	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066745-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	108	476	0	ENST00000262189.6:c.12646G>T	p.Asp4216Tyr	p.D4216Y	ENST00000262189	NM_170606.2	4216	Gat/Tat	50/59	0.225820097193678	1	FACETS	0.809	0.731	0.889	0.809	0.731	0.889	INDETERMINATE	1	TRUE	0	0.498758409915831	1		476	402	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638422	176638422	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066745-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	359	569	0	ENST00000439151.2:c.3022T>A	p.Ser1008Thr	p.S1008T	ENST00000439151	NM_022455.4	1008	Tct/Act	5/23	0.315124081305927	2	FACETS	0.805	0.766	0.845	0.805	0.766	0.845	CLONAL	2	TRUE	0	0.498758409915831	2		569	894	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161990430	161990430	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066745-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	75	504	0	ENST00000366898.1:c.890T>G	p.Leu297Trp	p.L297W	ENST00000366898	NM_004562.2	297	tTg/tGg	8/12	0.392951561983547	1	FACETS	0.842	0.747	0.942	0.842	0.747	0.942	CLONAL	1	TRUE	0	0.498758409915831	1		504	268	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0066746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	74	257	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.198758928702452	5	FACETS	0.791	0.693	0.897			1	SUBCLONAL	2	FALSE	NA	0.198758928702452	5		257	611	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0066746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	211	389	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.200442556688233	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	4	FALSE	0	0.198758928702452	4		389	578	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165701	185165701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	132	492	0	ENST00000265026.3:c.976C>T	p.Arg326Trp	p.R326W	ENST00000265026	NM_004721.4	326	Cgg/Tgg	5/14	0.0864891842889532	3	FACETS	0.866	0.79	0.946	1	0.981	1	INDETERMINATE	3	FALSE	1	0.198758928702452	3		492	562	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936057	71936058	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs878853122	NA	P-0066746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	47	370	0	ENST00000298229.2:c.35dup	p.Ala13ArgfsTer62	p.A13Rfs*62	ENST00000298229	NM_001567.3	10	ccg/ccGg	1/28	1	2	FACETS	1	0.88	1	1	0.974	1	CLONAL	2	FALSE	1	0.198758928702452	2		370	228	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869480	102869481	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0066746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	24	528	0	ENST00000307046.8:c.159_160dup	p.Cys54SerfsTer50	p.C54Sfs*50	ENST00000307046	NM_001111285.1	54	tgc/tCTgc	2/4	0.200442556688233	1	FACETS	0.498	0.389	0.623	0.498	0.389	0.623	SUBCLONAL	1	FALSE	0	0.198758928702452	1		528	437	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524481	187524482	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0066746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	66	610	0	ENST00000441802.2:c.11197_11198dup	p.Phe3734TyrfsTer26	p.F3734Yfs*26	ENST00000441802	NM_005245.3	3733	gta/gtGTa	19/27	0.200442556688233	0	FACETS	0.749	0.654	0.851			1	SUBCLONAL	2	FALSE	0	0.198758928702452	0		610	355	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278212	142278212	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	86	430	0	ENST00000350721.4:c.1613A>T	p.Asp538Val	p.D538V	ENST00000350721	NM_001184.3	538	gAt/gTt	7/47	0.0864891842889532	3	FACETS	0.849	0.753	0.952	0.849	0.753	0.952	INDETERMINATE	2	FALSE	1	0.198758928702452	3		430	560	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033273	69033273	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	70	498	0	ENST00000288368.4:c.3713A>C	p.Lys1238Thr	p.K1238T	ENST00000288368	NM_024870.2	1238	aAa/aCa	30/40	0.200442556688233	0	FACETS	1	0.949	1			1	CLONAL	1	FALSE	0	0.198758928702452	0		498	482	SUCCESS
APC	324	MSKCC	GRCh37	5	112177366	112177367	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0066746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	66	552	0	ENST00000257430.4:c.6080_6081dup	p.Ser2029ValfsTer16	p.S2029Vfs*16	ENST00000257430	NM_000038.5	2025	-/TC	16/16	0.200442556688233	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	0	0.198758928702452	1		552	488	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959034	28959036	+	missense_variant	Missense_Mutation	TNP	GTA	GTA	TTT	novel	NA	P-0066746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	86	543	0	ENST00000282397.4:c.2102_2104delinsAAA	p.Ile701_Gln702delinsLysLys	p.I701_Q702delinsKK	ENST00000282397	NM_002019.4	701	aTACaa/aAAAaa	14/30	0.200442556688233	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	0	0.198758928702452	1		543	598	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0066747-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	57	545	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.197585118460325	3	FACETS	0.593	0.508	0.685	0.198	0.169	0.229	INDETERMINATE	1	TRUE	0	0.380058487944378	3		546	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0066747-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	231	560	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.197585118460325	3	FACETS	1	0.986	1	0.784	0.736	0.833	INDETERMINATE	2	TRUE	0	0.380058487944378	3		560	615	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525060	157525060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1215965074	NA	P-0066747-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	147	505	0	ENST00000346085.5:c.4955C>T	p.Thr1652Met	p.T1652M	ENST00000346085	NM_020732.3	1652	aCg/aTg	19/20	0.385666009432487	4	FACETS	1	0.96	1			1	CLONAL	1	TRUE	NA	0.380058487944378	4		505	978	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0066747-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	60	480	0	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	0.287599158638562	5	FACETS	0.489	0.42	0.565	0.163	0.14	0.189	SUBCLONAL	1	TRUE	2	0.380058487944378	5		480	1014	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8339047	8339047	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066747-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	21	438	1	ENST00000356435.5:c.5254G>T	p.Glu1752Ter	p.E1752*	ENST00000356435		1752	Gag/Tag	32/35	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.380058487944378	NA		439	420	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2115637	2115637	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs45517190	NA	P-0066747-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	122	491	0	ENST00000219476.3:c.1716+1G>A		p.X572_splice	ENST00000219476	NM_000548.3	572			0.116860187514087	4	FACETS	1	0.984	1	0.73	0.661	0.801	INDETERMINATE	1	TRUE	2	0.380058487944378	4		491	607	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245261	46245261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066747-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	249	538	0	ENST00000334344.6:c.3355C>T	p.Gln1119Ter	p.Q1119*	ENST00000334344	NM_152641.2	1119	Cag/Tag	15/21	0.318733436565386	5	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.380058487944378	5		538	880	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426209	49426210	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGC	novel	NA	P-0066747-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	141	769	0	ENST00000301067.7:c.12276_12278dup	p.Pro4094dup	p.P4094dup	ENST00000301067	NM_003482.3	4094	cca/ccGCCa	39/54	0.385666009432487	3	FACETS	1	0.974	1			1	CLONAL	1	TRUE	NA	0.380058487944378	3		769	752	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101227	4101227	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066747-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	94	631	0	ENST00000262948.5:c.580G>A	p.Asp194Asn	p.D194N	ENST00000262948	NM_030662.3	194	Gat/Aat	5/11	0.177933130016942	3	FACETS	1	0.96	1	0.578	0.516	0.644	INDETERMINATE	1	TRUE	1	0.380058487944378	3		631	509	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733340	40733340	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066747-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	36	471	0	ENST00000373198.4:c.3466C>T	p.His1156Tyr	p.H1156Y	ENST00000373198	NM_133170.3	1156	Cac/Tac	26/32	0.385666009432487	1	FACETS	0.344	0.283	0.413	0.344	0.283	0.413	SUBCLONAL	1	TRUE	0	0.380058487944378	1		471	446	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0066748-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	41	1497	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	1	2	FACETS	0.16	0.132	0.19	0.16	0.132	0.19	SUBCLONAL	1	TRUE	1	0.82	2		1497	626	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0066748-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	19	257	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.101	0.076	0.131	0.101	0.076	0.131	SUBCLONAL	1	TRUE	1	0.82	2		257	457	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231488893	231488894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs567805129	NA	P-0066748-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	65	420	0	ENST00000295050.7:c.1263dup	p.Ile422TyrfsTer11	p.I422Yfs*11	ENST00000295050	NM_032018.5	419	aat/aaTt	5/5	1	2	FACETS	0.315	0.273	0.36	0.315	0.273	0.36	SUBCLONAL	1	TRUE	1	0.82	2		420	504	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	111	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.339843166477059	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.339843166477059	1		341	498	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0066749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	282	372	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.339843166477059	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.339843166477059	2		372	750	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591892	48591892	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	140	580	0	ENST00000342988.3:c.1055G>T	p.Gly352Val	p.G352V	ENST00000342988	NM_005359.5	352	gGa/gTa	9/12	0.339843166477059	1	FACETS	0.943	0.86	1	0.943	0.86	1	CLONAL	1	TRUE	0	0.339843166477059	1		580	725	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217240	11217240	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148486930	NA	P-0066749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	126	535	0	ENST00000361445.4:c.4438C>T	p.Arg1480Cys	p.R1480C	ENST00000361445	NM_004958.3	1480	Cgc/Tgc	30/58	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.339843166477059	2		535	718	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178941944	178941944	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	97	430	0	ENST00000263967.3:c.2263C>G	p.Leu755Val	p.L755V	ENST00000263967	NM_006218.2	755	Cta/Gta	15/21	1	2	FACETS	0.817	0.728	0.911	0.817	0.728	0.911	CLONAL	1	TRUE	1	0.339843166477059	2		430	699	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969941	161969941	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529808032	NA	P-0066749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	95	453	0	ENST00000366898.1:c.1028C>T	p.Pro343Leu	p.P343L	ENST00000366898	NM_004562.2	343	cCg/cTg	9/12	1	2	FACETS	0.984	0.879	1	0.984	0.879	1	CLONAL	1	TRUE	1	0.339843166477059	2		453	568	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597539	28597539	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	65	544	0	ENST00000241453.7:c.2366T>A	p.Leu789His	p.L789H	ENST00000241453	NM_004119.2	789	cTt/cAt	19/24	0.324948878574529	3	FACETS	0.526	0.455	0.603	0.263	0.227	0.302	SUBCLONAL	1	TRUE	1	0.339843166477059	3		544	851	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807800	1807800	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	161	728	1	ENST00000260795.2:c.1859C>A	p.Ala620Asp	p.A620D	ENST00000260795		620	gCc/gAc	13/17	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.339843166477059	2		729	897	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066750-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	20	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.334	0.255	0.427	0.334	0.255	0.427	SUBCLONAL	1	TRUE	1	0.32	2		341	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555526268	NA	P-0066750-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	80	454	0	ENST00000269305.4:c.406C>G	p.Gln136Glu	p.Q136E	ENST00000269305	NM_001126112.2	136	Caa/Gaa	5/11	0.212567536563548	1	FACETS	0.627	0.552	0.708	0.627	0.552	0.708	SUBCLONAL	1	TRUE	0	0.32	1		454	670	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371799	55371820	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCCGCGCTGGGCCCCGAG	GGCGGCCGCGCTGGGCCCCGAG	-	novel	NA	P-0066750-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	58	402	1	ENST00000297316.4:c.499_520del	p.Leu167TrpfsTer213	p.L167Wfs*213	ENST00000297316	NM_022454.3	163	caGGCGGCCGCGCTGGGCCCCGAG/ca	2/2	0.3	3	FACETS	0.662	0.568	0.765			1	SUBCLONAL	1	TRUE	NA	0.32	3		403	635	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99136536	99136536	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781317145	NA	P-0066750-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	65	392	0	ENST00000074304.5:c.25C>T	p.Arg9Cys	p.R9C	ENST00000074304	NM_001134224.1	9	Cgc/Tgc	3/26	1	2	FACETS	0.703	0.61	0.804	0.703	0.61	0.804	SUBCLONAL	1	TRUE	1	0.32	2		392	578	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	365	582	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.58162783243304	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.58162783243304	3		582	712	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	143	425	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.966	0.886	1	0.966	0.886	1	CLONAL	1	TRUE	1	0.58162783243304	2		425	509	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519886	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	203	392	0	ENST00000349496.5:c.97T>C	p.Ser33Pro	p.S33P	ENST00000349496	NM_001904.3	33	Tct/Cct	3/15	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.58162783243304	2		392	688	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	223	690	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.58162783243304	2		690	709	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727454	66727454	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519909	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	193	383	0	ENST00000307102.5:c.170A>C	p.Lys57Thr	p.K57T	ENST00000307102	NM_002755.3	57	aAg/aCg	2/11	1	2	FACETS	0.992	0.922	1	0.992	0.922	1	CLONAL	1	TRUE	1	0.58162783243304	2		383	669	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604754	48604754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	207	394	0	ENST00000342988.3:c.1576G>A	p.Glu526Lys	p.E526K	ENST00000342988	NM_005359.5	526	Gaa/Aaa	12/12	0.58162783243304	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.58162783243304	1		394	440	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453132	140453132	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913365	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	286	334	0	ENST00000288602.6:c.1803A>C	p.Lys601Asn	p.K601N	ENST00000288602	NM_004333.4	601	aaA/aaC	15/18	0.58162783243304	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.58162783243304	2		334	478	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130699	29130699	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	198	367	0	ENST00000328354.6:c.11A>G	p.Glu4Gly	p.E4G	ENST00000328354	NM_007194.3	4	gAg/gGg	2/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.58162783243304	2		367	655	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662181	227662181	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	259	507	0	ENST00000305123.5:c.1274T>C	p.Phe425Ser	p.F425S	ENST00000305123	NM_005544.2	425	tTc/tCc	1/2	0.278942751941701	3	FACETS	0.814	0.767	0.862	0.814	0.767	0.862	INDETERMINATE	2	TRUE	1	0.58162783243304	3		507	706	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716287	52716287	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1468288521	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	171	485	0	ENST00000322088.6:c.731T>C	p.Val244Ala	p.V244A	ENST00000322088	NM_014225.5	244	gTg/gCg	6/15	1	2	FACETS	0.945	0.874	1	0.945	0.874	1	CLONAL	1	TRUE	1	0.58162783243304	2		485	622	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910791	29910791	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs41541814	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	211	589	0	ENST00000376809.5:c.331C>T	p.Gln111Ter	p.Q111*	ENST00000376809	NM_002116.7	111	Cag/Tag	2/8	0.58162783243304	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.58162783243304	1		589	484	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100991	27100991	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	142	393	0	ENST00000324856.7:c.4273C>T	p.Gln1425Ter	p.Q1425*	ENST00000324856	NM_006015.4	1425	Caa/Taa	18/20	1	2	FACETS	0.996	0.914	1	0.996	0.914	1	CLONAL	1	TRUE	1	0.58162783243304	2		393	490	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438330	110438330	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	131	324	0	ENST00000375856.3:c.71A>G	p.Asn24Ser	p.N24S	ENST00000375856	NM_003749.2	24	aAc/aGc	1/2	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.58162783243304	2		324	422	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713724	30713724	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	210	535	0	ENST00000295754.5:c.1049T>C	p.Leu350Pro	p.L350P	ENST00000295754	NM_003242.5	350	cTg/cCg	4/7	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.58162783243304	2		535	672	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50790795	50790795	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	161	283	0	ENST00000307179.4:c.3041T>G	p.Phe1014Cys	p.F1014C	ENST00000307179		1014	tTt/tGt	19/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.58162783243304	2		283	457	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434019	49434019	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	176	505	0	ENST00000301067.7:c.7534A>G	p.Ser2512Gly	p.S2512G	ENST00000301067	NM_003482.3	2512	Agt/Ggt	31/54	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.58162783243304	2		505	591	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972631	32972631	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	52	375	0	ENST00000380152.3:c.9981A>C	p.Lys3327Asn	p.K3327N	ENST00000380152		3327	aaA/aaC	27/27	1	2	FACETS	0.296	0.251	0.344	0.296	0.251	0.344	SUBCLONAL	1	TRUE	1	0.58162783243304	2		375	605	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38971985	38971985	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	104	283	0	ENST00000357387.3:c.966A>C	p.Glu322Asp	p.E322D	ENST00000357387	NM_152756.3	322	gaA/gaC	11/38	1	2	FACETS	0.956	0.864	1	0.956	0.864	1	CLONAL	1	TRUE	1	0.58162783243304	2		283	374	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10794714	10794714	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	164	333	0	ENST00000361367.2:c.2621T>C	p.Leu874Pro	p.L874P	ENST00000361367	NM_014633.3	874	cTt/cCt	21/25	1	2	FACETS	0.921	0.85	0.996	0.921	0.85	0.996	CLONAL	1	TRUE	1	0.58162783243304	2		333	612	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392145	81392145	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	145	332	0	ENST00000222390.5:c.132A>C	p.Lys44Asn	p.K44N	ENST00000222390	NM_000601.4	44	aaA/aaC	2/18	0.58162783243304	2	FACETS	1	0.964	1	0.543	0.499	0.588	CLONAL	1	TRUE	0	0.58162783243304	2		332	459	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845509	128845509	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	332	439	0	ENST00000249373.3:c.806A>G	p.Tyr269Cys	p.Y269C	ENST00000249373	NM_005631.4	269	tAc/tGc	4/12	0.58162783243304	2	FACETS	0.982	0.94	1	0.982	0.94	1	CLONAL	2	TRUE	0	0.58162783243304	2		439	581	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052620	42052620	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	281	409	0	ENST00000219905.7:c.7291A>G	p.Asn2431Asp	p.N2431D	ENST00000219905	NM_001164273.1	2431	Aat/Gat	20/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.58162783243304	2		409	897	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144336880	144336880	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	147	316	0	ENST00000262995.4:c.323T>G	p.Val108Gly	p.V108G	ENST00000262995	NM_207123.2	108	gTt/gGt	2/11	1	2	FACETS	0.987	0.907	1	0.987	0.907	1	CLONAL	1	TRUE	1	0.58162783243304	2		316	512	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571969	64571969	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	190	480	0	ENST00000312049.6:c.1670A>C	p.Lys557Thr	p.K557T	ENST00000312049	NM_130799.2	557	aAg/aCg	10/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.58162783243304	2		480	601	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965675	25965675	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	228	437	0	ENST00000435504.4:c.3531A>C	p.Lys1177Asn	p.K1177N	ENST00000435504		1177	aaA/aaC	13/13	0.278942751941701	3	FACETS	1	0.988	1	0.62	0.579	0.662	INDETERMINATE	1	TRUE	1	0.58162783243304	3		437	816	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474724	138474724	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	262	333	0	ENST00000289153.2:c.269A>G	p.Glu90Gly	p.E90G	ENST00000289153	NM_006219.2	90	gAg/gGg	2/22	0.58162783243304	3	FACETS	0.984	0.93	1	0.984	0.93	1	CLONAL	2	TRUE	1	0.58162783243304	3		333	591	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786088	3786088	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	203	417	0	ENST00000262367.5:c.4677A>C	p.Glu1559Asp	p.E1559D	ENST00000262367	NM_004380.2	1559	gaA/gaC	28/31	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.58162783243304	2		417	671	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541648	187541648	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	280	461	0	ENST00000441802.2:c.6092T>G	p.Val2031Gly	p.V2031G	ENST00000441802	NM_005245.3	2031	gTt/gGt	10/27	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.58162783243304	2		461	852	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46277843	46277843	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	90	365	0	ENST00000371998.3:c.3641T>C	p.Val1214Ala	p.V1214A	ENST00000371998		1214	gTg/gCg	19/23	0.278942751941701	3	FACETS	0.523	0.463	0.586	0.261	0.231	0.293	INDETERMINATE	1	TRUE	1	0.58162783243304	3		365	764	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552960	106552960	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	240	520	0	ENST00000369096.4:c.925T>G	p.Phe309Val	p.F309V	ENST00000369096	NM_001198.3	309	Ttt/Gtt	5/7	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.58162783243304	2		520	782	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747092	40747092	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	212	333	0	ENST00000373198.4:c.2990A>G	p.Glu997Gly	p.E997G	ENST00000373198	NM_133170.3	997	gAg/gGg	22/32	0.278942751941701	3	FACETS	0.806	0.754	0.859	0.806	0.754	0.859	INDETERMINATE	2	TRUE	1	0.58162783243304	3		333	584	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149452942	149452942	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	198	427	0	ENST00000286301.3:c.1004A>C	p.Asn335Thr	p.N335T	ENST00000286301	NM_005211.3	335	aAc/aCc	7/22	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.58162783243304	2		427	632	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796730	57796730	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	168	447	0	ENST00000309042.7:c.1706A>C	p.Lys569Thr	p.K569T	ENST00000309042	NM_005612.4	569	aAa/aCa	4/4	1	2	FACETS	0.862	0.795	0.932	0.862	0.795	0.932	CLONAL	1	TRUE	1	0.58162783243304	2		447	670	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77930334	77930334	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1864299321	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	185	450	0	ENST00000361507.4:c.2015A>G	p.Lys672Arg	p.K672R	ENST00000361507	NM_080491.2	672	aAg/aGg	10/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.58162783243304	2		450	590	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005883	69005883	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs879245533	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	93	325	0	ENST00000288368.4:c.2294A>C	p.Gln765Pro	p.Q765P	ENST00000288368	NM_024870.2	765	cAa/cCa	21/40	1	2	FACETS	0.727	0.65	0.808	0.727	0.65	0.808	SUBCLONAL	1	TRUE	1	0.58162783243304	2		325	440	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707857	43707857	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	270	457	0	ENST00000382044.4:c.5024T>G	p.Leu1675Arg	p.L1675R	ENST00000382044	NM_001141980.1	1675	cTt/cGt	23/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.58162783243304	2		457	842	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948746	55948746	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	133	311	0	ENST00000263923.4:c.3719A>G	p.Glu1240Gly	p.E1240G	ENST00000263923	NM_002253.2	1240	gAa/gGa	28/30	1	2	FACETS	0.977	0.894	1	0.977	0.894	1	CLONAL	1	TRUE	1	0.58162783243304	2		311	468	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47491314	47491314	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	168	341	0	ENST00000404338.3:c.3897del	p.Phe1299LeufsTer16	p.F1299Lfs*16	ENST00000404338	NM_004491.4	1299	Ttt/tt	3/6	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.58162783243304	2		341	524	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217010	2217010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	192	482	0	ENST00000398665.3:c.2465G>A	p.Ser822Asn	p.S822N	ENST00000398665	NM_032482.2	822	aGc/aAc	21/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.58162783243304	2		482	589	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805943	46805943	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	112	387	0	ENST00000290295.7:c.13A>C	p.Asn5His	p.N5H	ENST00000290295	NM_006361.5	5	Aat/Cat	1/2	1	2	FACETS	0.9	0.815	0.988	0.9	0.815	0.988	CLONAL	1	TRUE	1	0.58162783243304	2		387	428	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999006	100999006	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	133	487	0	ENST00000325455.5:c.796G>T	p.Ala266Ser	p.A266S	ENST00000325455	NM_001202474.3	266	Gcc/Tcc	1/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.58162783243304	2		487	424	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422697	47422697	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	189	403	0	ENST00000404338.3:c.765A>C	p.Lys255Asn	p.K255N	ENST00000404338	NM_004491.4	255	aaA/aaC	1/6	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.58162783243304	2		403	574	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589627	69589627	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1250882382	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	198	782	0	ENST00000168712.1:c.226T>C	p.Tyr76His	p.Y76H	ENST00000168712	NM_002007.2	76	Tac/Cac	1/3	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.58162783243304	2		782	631	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372079	55372079	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	133	537	0	ENST00000297316.4:c.769T>C	p.Ser257Pro	p.S257P	ENST00000297316	NM_022454.3	257	Tcg/Ccg	2/2	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.58162783243304	2		537	404	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915698	112915698	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	223	408	0	ENST00000351677.2:c.971A>C	p.Lys324Thr	p.K324T	ENST00000351677	NM_002834.3	324	aAa/aCa	9/16	1	2	FACETS	0.987	0.922	1	0.987	0.922	1	CLONAL	1	TRUE	1	0.58162783243304	2		408	777	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149566	202149566	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	270	457	0	ENST00000358485.4:c.1007T>G	p.Leu336Arg	p.L336R	ENST00000358485	NM_001080125.1	336	cTt/cGt	8/9	0.58162783243304	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.58162783243304	1		457	523	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066757-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	53	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.933	0.796	1	0.933	0.796	1	CLONAL	1	TRUE	1	0.235756526345849	2		341	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0066757-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	132	563	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.213119871679469	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.235756526345849	1		563	790	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066757-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	74	422	2	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	1	2	FACETS	0.799	0.698	0.907	0.799	0.698	0.907	CLONAL	1	TRUE	1	0.235756526345849	2		424	786	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163587	32163587	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1191585262	NA	P-0066757-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	130	498	0	ENST00000375023.3:c.5639G>C	p.Arg1880Pro	p.R1880P	ENST00000375023	NM_004557.3	1880	cGg/cCg	30/30	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.235756526345849	2		498	859	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890149	76890150	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066757-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	59	396	0	ENST00000373344.5:c.4744dup	p.Thr1582AsnfsTer19	p.T1582Nfs*19	ENST00000373344	NM_000489.3	1582	aca/aAca	17/35	1	2	FACETS	0.831	0.715	0.958	0.831	0.715	0.958	CLONAL	1	TRUE	1	0.235756526345849	2		396	602	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795008	242795008	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066757-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	95	620	0	ENST00000334409.5:c.201G>T	p.Trp67Cys	p.W67C	ENST00000334409	NM_005018.2	67	tgG/tgT	2/5	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.235756526345849	2		620	770	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491070	120491070	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557817079	NA	P-0066759-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	206	536	0	ENST00000256646.2:c.2719G>A	p.Asp907Asn	p.D907N	ENST00000256646	NM_024408.3	907	Gac/Aac	17/34	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.47	2		536	664	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0066760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	44	537	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.145	0.121	0.172	0.145	0.121	0.172	SUBCLONAL	1	TRUE	1	0.819006606006089	2		537	739	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0066761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	65	287	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.239583389030734	4	FACETS	1	0.943	1	0.761	0.666	0.863	CLONAL	2	FALSE	1	0.238063652271839	4		287	296	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708999	117708999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34203286	NA	P-0066761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	25	489	0	ENST00000368508.3:c.1958C>T	p.Ser653Phe	p.S653F	ENST00000368508	NM_002944.2	653	tCt/tTt	13/43	0.239583389030734	0	FACETS	0.576	0.455	0.714			1	SUBCLONAL	1	FALSE	0	0.238063652271839	0		489	278	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045541	47045541	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	39	698	0	ENST00000377604.3:c.2508G>T	p.Arg836Ser	p.R836S	ENST00000377604	NM_001204468.1	836	agG/agT	22/24	NA	2	FACETS	0.738	0.612	0.879			1	INDETERMINATE	1	FALSE	NA	0.238063652271839	2		698	444	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066762-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	119	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.308419251289888	3	FACETS	0.928	0.843	1	0.928	0.843	1	CLONAL	2	TRUE	1	0.344973002156767	3		341	436	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523747	41523747	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066762-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	174	443	0	ENST00000263253.7:c.1163G>T	p.Cys388Phe	p.C388F	ENST00000263253	NM_001429.3	388	tGc/tTc	4/31	0.295664074095014	2	FACETS	0.936	0.867	1	0.936	0.867	1	CLONAL	2	TRUE	0	0.344973002156767	2		443	539	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0066762-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	51	254	1	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.344973002156767	2		255	273	SUCCESS
APC	324	MSKCC	GRCh37	5	112164646	112164646	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066762-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	150	315	0	ENST00000257430.4:c.1720G>T	p.Glu574Ter	p.E574*	ENST00000257430	NM_000038.5	574	Gaa/Taa	14/16	0.295664074095014	2	FACETS	0.836	0.769	0.906	0.836	0.769	0.906	CLONAL	2	TRUE	0	0.344973002156767	2		315	520	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841252	15841252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1569074760	NA	P-0066762-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	276	627	0	ENST00000307771.7:c.1336C>T	p.Arg446Trp	p.R446W	ENST00000307771	NM_005089.3	446	Cgg/Tgg	11/11	0.158830812033953	5	FACETS	0.863	0.812	0.915	0.863	0.812	0.915	INDETERMINATE	3	TRUE	2	0.344973002156767	5		627	938	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10786176	10786176	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066762-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	84	421	0	ENST00000361367.2:c.1495A>G	p.Thr499Ala	p.T499A	ENST00000361367	NM_014633.3	499	Acg/Gcg	12/25	1	2	FACETS	0.867	0.767	0.973	0.867	0.767	0.973	CLONAL	1	TRUE	1	0.344973002156767	2		421	562	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3824695	3824695	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0066762-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	69	450	0	ENST00000262367.5:c.2159-1G>A		p.X720_splice	ENST00000262367	NM_004380.2	720			1	2	FACETS	0.897	0.784	1	0.897	0.784	1	CLONAL	1	TRUE	1	0.344973002156767	2		450	446	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051204	13051204	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066762-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	86	525	0	ENST00000316448.5:c.640T>C	p.Ser214Pro	p.S214P	ENST00000316448	NM_004343.3	214	Tca/Cca	5/9	0.308419251289888	3	FACETS	0.847	0.75	0.952	0.424	0.375	0.476	CLONAL	1	TRUE	1	0.344973002156767	3		525	690	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231707	36232376	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTATACCAGCCTGGAGGGTGTACCAGCCTGGAGGGTGTACCAGCCCCAAGTGGATGCACTTACTTCGAGGTTCTCGGGGCCCATCCACTGTGATTTTGATGGCTCTGTGGTAGGTGGCGACTTGCGGTGGGTTTGTGAAGACAGTGATGGTCAGAGTGAAGCTTTTCCCTGTGGGGACACGATAGAGAACAAAACAGAATGAGGTTGGTGGCCTGAACATATCTGTTGAATAACCAATCATTAATTTATGCTGTCCAGCCCTTCAGCACAAGTTACCAGTTTTGACAACACTCCCGGAATTTTGGCTTTGCTTCAATTCTGGAATACACACCTATGATAGTTGCCTAAGTGTAACACTTCACATAGTTATATGGCTTTAATGTAATCATCAATAAACAATACAAGATCAAGAAAGATTAGAATTTATTTTCTGTTAAGTCAGGATTTCCGGAAACCATAGAGTCAGATTGGCAGCTCTCCACTTCTGGTTCCCAACTTCCCTGCTCCCATCTTTCCCAATTATTTATAATTCAGGGCAAATAAGAGTAGAAGAAACCATATCCATCTTTCTCTTCTTACTTTGTACCTTTGAAGATCAGGAAAGATAGAATTTCTAAGTTTGAAAACAGGCTAAATTAGAATCATTCTGTCTATATTTTTAAAAGACGA	AGTATACCAGCCTGGAGGGTGTACCAGCCTGGAGGGTGTACCAGCCCCAAGTGGATGCACTTACTTCGAGGTTCTCGGGGCCCATCCACTGTGATTTTGATGGCTCTGTGGTAGGTGGCGACTTGCGGTGGGTTTGTGAAGACAGTGATGGTCAGAGTGAAGCTTTTCCCTGTGGGGACACGATAGAGAACAAAACAGAATGAGGTTGGTGGCCTGAACATATCTGTTGAATAACCAATCATTAATTTATGCTGTCCAGCCCTTCAGCACAAGTTACCAGTTTTGACAACACTCCCGGAATTTTGGCTTTGCTTCAATTCTGGAATACACACCTATGATAGTTGCCTAAGTGTAACACTTCACATAGTTATATGGCTTTAATGTAATCATCAATAAACAATACAAGATCAAGAAAGATTAGAATTTATTTTCTGTTAAGTCAGGATTTCCGGAAACCATAGAGTCAGATTGGCAGCTCTCCACTTCTGGTTCCCAACTTCCCTGCTCCCATCTTTCCCAATTATTTATAATTCAGGGCAAATAAGAGTAGAAGAAACCATATCCATCTTTCTCTTCTTACTTTGTACCTTTGAAGATCAGGAAAGATAGAATTTCTAAGTTTGAAAACAGGCTAAATTAGAATCATTCTGTCTATATTTTTAAAAGACGA	-	novel	NA	P-0066762-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	34	580	0	ENST00000300305.3:c.509-501_613+64del		p.X170_splice	ENST00000300305		170		5/8	1	2	FACETS	0.315	0.256	0.381	0.315	0.256	0.381	SUBCLONAL	1	TRUE	1	0.344973002156767	2		580	626	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281913	142281913	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066762-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	29	411	0	ENST00000350721.4:c.331G>T	p.Ala111Ser	p.A111S	ENST00000350721	NM_001184.3	111	Gca/Tca	4/47	1	2	FACETS	0.368	0.295	0.451	0.368	0.295	0.451	SUBCLONAL	1	TRUE	1	0.344973002156767	2		411	457	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0066763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	45	269	1	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.511978480016683	4	FACETS	0.846	0.715	0.991	0.282	0.238	0.331	CLONAL	1	TRUE	1	0.511978480016683	4		270	314	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204864	NA	P-0066763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	90	307	0	ENST00000371953.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000371953	NM_000314.4	171	Cag/Tag	6/9	1	2	FACETS	0.833	0.743	0.928	0.833	0.743	0.928	CLONAL	1	TRUE	1	0.511978480016683	2		307	422	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799627	3799627	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs200782888	NA	P-0066763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	67	221	0	ENST00000262367.5:c.3836+1G>A		p.X1279_splice	ENST00000262367	NM_004380.2	1279			1	2	FACETS	0.85	0.745	0.962	0.85	0.745	0.962	CLONAL	1	TRUE	1	0.511978480016683	2		221	308	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122373	17122373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375352888	NA	P-0066763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	202	436	0	ENST00000285071.4:c.1022G>A	p.Arg341Gln	p.R341Q	ENST00000285071	NM_144997.5	341	cGg/cAg	9/14	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.511978480016683	2		436	750	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0066763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	151	481	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.903	0.828	0.981	0.903	0.828	0.981	CLONAL	1	TRUE	1	0.511978480016683	2		481	653	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089661	27089662	+	missense_variant	Missense_Mutation	DNP	GC	GC	CT	novel	NA	P-0066763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	221	668	1	ENST00000324856.7:c.2617_2618delinsCT	p.Ala873Leu	p.A873L	ENST00000324856	NM_006015.4	873	GCc/CTc	8/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.511978480016683	2		669	855	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948526	71948526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756352122	NA	P-0066763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	254	660	0	ENST00000298229.2:c.3238C>T	p.Arg1080Cys	p.R1080C	ENST00000298229	NM_001567.3	1080	Cgt/Tgt	26/28	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.511978480016683	2		660	878	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0066766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	182	318	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.570228051650227	2		318	545	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0066766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	158	442	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.570228051650227	2		442	493	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0066766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	161	902	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.570228051650227	2		902	486	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717609	89717609	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs876661024	NA	P-0066766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	11	228	0	ENST00000371953.3:c.635-1G>A		p.X212_splice	ENST00000371953	NM_000314.4	212			0.570228051650227	1	FACETS	0.096	0.066	0.133	0.096	0.066	0.133	SUBCLONAL	1	FALSE	0	0.570228051650227	1		228	288	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218009	108218009	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786201911	NA	P-0066766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	105	303	0	ENST00000278616.4:c.8588G>T	p.Gly2863Val	p.G2863V	ENST00000278616	NM_000051.3	2863	gGt/gTt	59/63	0.570228051650227	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	0	0.570228051650227	1		303	224	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0066766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	115	311	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.570228051650227	2		311	384	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241460	105241460	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs983007851	NA	P-0066766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	203	338	0	ENST00000349310.3:c.520C>T	p.Arg174Cys	p.R174C	ENST00000349310	NM_001014432.1	174	Cgc/Tgc	7/15	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.570228051650227	2		338	560	SUCCESS
APC	324	MSKCC	GRCh37	5	112173345	112173346	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	A	novel	NA	P-0066766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	125	336	0	ENST00000257430.4:c.2054_2055delinsA	p.Trp685Ter	p.W685*	ENST00000257430	NM_000038.5	685	tGG/tA	16/16	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.570228051650227	2		336	398	SUCCESS
APC	324	MSKCC	GRCh37	5	112176027	112176027	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066768-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	35	456	0	ENST00000257430.4:c.4737del	p.Ile1580PhefsTer70	p.I1580Ffs*70	ENST00000257430	NM_000038.5	1579	aTt/at	16/16	0.54455391687367	1	FACETS	0.288	0.236	0.345	0.288	0.236	0.345	SUBCLONAL	1	TRUE	0	0.54455391687367	1		456	325	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696644	47696644	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519964	NA	P-0066768-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	123	431	0	ENST00000347630.2:c.304T>G	p.Phe102Val	p.F102V	ENST00000347630	NM_001007230.1	102	Ttc/Gtc	5/11	1	2	FACETS	0.986	0.898	1	0.986	0.898	1	CLONAL	1	TRUE	1	0.54455391687367	2		431	458	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999243	100999243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066768-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	11	368	0	ENST00000325455.5:c.559C>T	p.Arg187Trp	p.R187W	ENST00000325455	NM_001202474.3	187	Cgg/Tgg	1/8	1	2	FACETS	0.184	0.127	0.256	0.184	0.127	0.256	SUBCLONAL	1	TRUE	1	0.54455391687367	2		368	219	SUCCESS
APC	324	MSKCC	GRCh37	5	112175770	112175770	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066768-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	22	483	0	ENST00000257430.4:c.4480del	p.Glu1494LysfsTer13	p.E1494Kfs*13	ENST00000257430	NM_000038.5	1493	acG/ac	16/16	0.54455391687367	1	FACETS	0.178	0.137	0.224	0.178	0.137	0.224	SUBCLONAL	1	TRUE	0	0.54455391687367	1		483	331	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014084	14014084	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066768-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	68	337	0	ENST00000311895.7:c.62A>G	p.Gln21Arg	p.Q21R	ENST00000311895	NM_005236.2	21	cAg/cGg	1/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.54455391687367	2		337	203	SUCCESS
APC	324	MSKCC	GRCh37	5	112176548	112176549	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0066768-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	17	467	0	ENST00000257430.4:c.5258dup	p.Ser1754IlefsTer15	p.S1754Ifs*15	ENST00000257430	NM_000038.5	1753	gca/gCca	16/16	0.54455391687367	1	FACETS	0.149	0.111	0.195	0.149	0.111	0.195	SUBCLONAL	1	TRUE	0	0.54455391687367	1		467	304	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690821	89690821	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0066769-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	40	216	0	ENST00000371953.3:c.228T>A	p.Tyr76Ter	p.Y76*	ENST00000371953	NM_000314.4	76	taT/taA	4/9	0.279369467545032	1	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	0	0.279369467545032	1		216	223	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874160	155874160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066769-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	60	318	0	ENST00000368323.3:c.371C>T	p.Thr124Ile	p.T124I	ENST00000368323	NM_006912.5	124	aCt/aTt	5/6	1	2	FACETS	0.727	0.626	0.836	0.727	0.626	0.836	SUBCLONAL	1	TRUE	1	0.279369467545032	2		318	591	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066775-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	56	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.19	2		341	426	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0066775-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	17	254	1	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.552	0.412	0.72	0.552	0.412	0.72	SUBCLONAL	1	TRUE	1	0.19	2		255	324	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939259	71939259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771645618	NA	P-0066775-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	31	596	0	ENST00000298229.2:c.208C>T	p.Arg70Cys	p.R70C	ENST00000298229	NM_001567.3	70	Cgc/Tgc	2/28	1	2	FACETS	0.587	0.474	0.716	0.587	0.474	0.716	SUBCLONAL	1	TRUE	1	0.19	2		596	556	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828461	72828461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139821312	NA	P-0066775-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	68	530	0	ENST00000268489.5:c.8120C>T	p.Ala2707Val	p.A2707V	ENST00000268489	NM_006885.3	2707	gCg/gTg	9/10	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.19	2		530	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0066775-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	73	820	0	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.19	2		820	683	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930087	68930087	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066775-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	12	356	0	ENST00000288368.4:c.148T>G	p.Leu50Val	p.L50V	ENST00000288368	NM_024870.2	50	Tta/Gta	2/40	1	2	FACETS	0.24	0.168	0.33	0.24	0.168	0.33	SUBCLONAL	1	TRUE	1	0.19	2		356	526	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126334	5126334	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066775-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	24	314	0	ENST00000381652.3:c.3179A>G	p.Glu1060Gly	p.E1060G	ENST00000381652	NM_004972.3	1060	gAa/gGa	24/25	1	2	FACETS	0.555	0.434	0.695	0.555	0.434	0.695	SUBCLONAL	1	TRUE	1	0.19	2		314	455	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389399	8389399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066775-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	24	325	0	ENST00000356435.5:c.4219G>A	p.Gly1407Arg	p.G1407R	ENST00000356435		1407	Gga/Aga	26/35	1	2	FACETS	0.558	0.436	0.698	0.558	0.436	0.698	SUBCLONAL	1	TRUE	1	0.19	2		325	453	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0066777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	291	582	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.565068910514302	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.667733798869043	4		582	709	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056346	180056346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs186187161	NA	P-0066777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	130	501	2	ENST00000261937.6:c.898G>A	p.Val300Ile	p.V300I	ENST00000261937	NM_182925.4	300	Gtc/Atc	7/30	1	2	FACETS	0.897	0.82	0.976	0.897	0.82	0.976	CLONAL	1	TRUE	1	0.667733798869043	2		503	434	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0066777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	245	257	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.667733798869043	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.667733798869043	2		257	346	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2115961	2115961	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	169	398	0	ENST00000349721.2:c.3596T>C	p.Ile1199Thr	p.I1199T	ENST00000349721	NM_003070.3	1199	aTc/aCc	25/34	1	2	FACETS	0.948	0.877	1	0.948	0.877	1	CLONAL	1	TRUE	1	0.667733798869043	2		398	534	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432830	432830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	38	438	0	ENST00000399788.2:c.2086C>T	p.Arg696Trp	p.R696W	ENST00000399788	NM_001042603.1	696	Cgg/Tgg	15/28	0.667733798869043	2	FACETS	0.197	0.162	0.236	0.099	0.081	0.118	SUBCLONAL	1	TRUE	0	0.667733798869043	2		438	577	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804274	43804274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1215318596	NA	P-0066778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	116	492	1	ENST00000372470.3:c.274G>A	p.Val92Met	p.V92M	ENST00000372470	NM_005373.2	92	Gtg/Atg	3/12	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.357305698842079	2		493	630	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518940	187518940	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs940602352	NA	P-0066778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	87	379	0	ENST00000441802.2:c.12264G>T	p.Gln4088His	p.Q4088H	ENST00000441802	NM_005245.3	4088	caG/caT	24/27	1	2	FACETS	0.949	0.843	1	0.949	0.843	1	CLONAL	1	TRUE	1	0.357305698842079	2		379	513	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61324647	61324647	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0066778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	76	277	0	ENST00000283752.5:c.470-1G>T		p.X157_splice	ENST00000283752	NM_006919.2	157			0.357305698842079	3	FACETS	1	0.911	1	0.521	0.458	0.588	CLONAL	1	TRUE	1	0.357305698842079	3		277	481	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0066779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	105	425	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.574237852942403	1	FACETS	0.947	0.863	1	0.947	0.863	1	CLONAL	1	TRUE	0	0.582142011283651	1		425	270	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0066779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	96	431	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.582142011283651	2		431	320	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174418	11174418	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	116	364	0	ENST00000361445.4:c.7257A>T	p.Glu2419Asp	p.E2419D	ENST00000361445	NM_004958.3	2419	gaA/gaT	53/58	0.574237852942403	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.582142011283651	1		364	260	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0066779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	44	215	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.874	0.744	1	0.874	0.744	1	CLONAL	1	TRUE	1	0.582142011283651	2		215	173	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416680	121416680	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	67	488	0	ENST00000257555.6:c.109C>G	p.Leu37Val	p.L37V	ENST00000257555		37	Ctc/Gtc	1/10	1	2	FACETS	0.765	0.67	0.865	0.765	0.67	0.865	SUBCLONAL	1	TRUE	1	0.582142011283651	2		488	301	SUCCESS
APC	324	MSKCC	GRCh37	5	112175539	112175540	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATTAT	novel	NA	P-0066779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	105	469	0	ENST00000257430.4:c.4250_4254dup	p.Ser1419LeufsTer2	p.S1419Lfs*2	ENST00000257430	NM_000038.5	1416	-/ATTAT	16/16	1	2	FACETS	0.741	0.667	0.818	0.741	0.667	0.818	SUBCLONAL	1	TRUE	1	0.582142011283651	2		469	487	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383673	15383673	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	23	477	0	ENST00000263377.2:c.238G>T	p.Ala80Ser	p.A80S	ENST00000263377	NM_058243.2	80	Gca/Tca	2/20	0.57178234677245	2	FACETS	0.179	0.139	0.226	0.09	0.069	0.113	SUBCLONAL	1	TRUE	0	0.582142011283651	2		477	441	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0066780-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	74	413	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.452	0.395	0.512	0.452	0.395	0.512	SUBCLONAL	1	TRUE	1	0.545289921169709	2		413	601	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717719	89717720	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs780264945	NA	P-0066780-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	139	203	0	ENST00000371953.3:c.750_751del	p.Cys250TrpfsTer2	p.C250Wfs*2	ENST00000371953	NM_000314.4	248	ccTGtg/cctg	7/9	0.531333210504182	1	FACETS	0.934	0.859	1	0.934	0.859	1	CLONAL	1	TRUE	0	0.545289921169709	1		203	397	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385153	41385153	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776806194	NA	P-0066780-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	27	305	0	ENST00000373198.4:c.808C>T	p.Arg270Cys	p.R270C	ENST00000373198	NM_133170.3	270	Cgc/Tgc	6/32	1	2	FACETS	0.193	0.153	0.239	0.193	0.153	0.239	SUBCLONAL	1	TRUE	1	0.545289921169709	2		305	513	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0066780-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	109	246	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.871	0.787	0.959	0.871	0.787	0.959	CLONAL	1	TRUE	1	0.545289921169709	2		246	459	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948770	55948770	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368229220	NA	P-0066780-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	125	263	0	ENST00000263923.4:c.3695G>A	p.Arg1232Gln	p.R1232Q	ENST00000263923	NM_002253.2	1232	cGg/cAg	28/30	1	2	FACETS	0.841	0.765	0.921	0.841	0.765	0.921	CLONAL	1	TRUE	1	0.545289921169709	2		263	545	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0066780-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	371	318	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	0.524059671358687	2	FACETS	0.957	0.916	0.998	0.957	0.916	0.998	CLONAL	2	TRUE	0	0.545289921169709	2		318	711	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522414	176522414	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066780-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	301	366	0	ENST00000292408.4:c.1603A>G	p.Asn535Asp	p.N535D	ENST00000292408	NM_213647.1	535	Aac/Gac	12/18	0.524059671358687	2	FACETS	0.909	0.865	0.954	0.909	0.865	0.954	CLONAL	2	TRUE	0	0.545289921169709	2		366	607	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522551	176522551	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774571806	NA	P-0066780-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	300	457	2	ENST00000292408.4:c.1648G>A	p.Val550Met	p.V550M	ENST00000292408	NM_213647.1	550	Gtg/Atg	13/18	0.524059671358687	2	FACETS	0.926	0.881	0.971	0.926	0.881	0.971	CLONAL	2	TRUE	0	0.545289921169709	2		459	594	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405827	157405827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373508866	NA	P-0066780-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	169	411	0	ENST00000346085.5:c.2069C>T	p.Thr690Met	p.T690M	ENST00000346085	NM_020732.3	690	aCg/aTg	6/20	1	2	FACETS	0.898	0.828	0.971	0.898	0.828	0.971	CLONAL	1	TRUE	1	0.545289921169709	2		411	690	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737819	145737819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750261857	NA	P-0066780-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	160	459	0	ENST00000428558.2:c.3011G>A	p.Arg1004Gln	p.R1004Q	ENST00000428558	NM_004260.3	1004	cGg/cAg	18/22	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.545289921169709	2		459	587	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390962	139390962	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560981171	NA	P-0066780-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	164	516	0	ENST00000277541.6:c.7229C>T	p.Pro2410Leu	p.P2410L	ENST00000277541	NM_017617.3	2410	cCg/cTg	34/34	1	2	FACETS	0.857	0.789	0.928	0.857	0.789	0.928	CLONAL	1	TRUE	1	0.545289921169709	2		516	702	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461957	120461957	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066780-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	147	353	0	ENST00000256646.2:c.5759C>G	p.Ala1920Gly	p.A1920G	ENST00000256646	NM_024408.3	1920	gCt/gGt	31/34	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.545289921169709	2		353	522	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713835	30713835	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066780-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	188	493	1	ENST00000295754.5:c.1160T>C	p.Val387Ala	p.V387A	ENST00000295754	NM_003242.5	387	gTg/gCg	4/7	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.545289921169709	2		494	668	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430305	181430305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066780-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	82	231	0	ENST00000325404.1:c.157C>T	p.Arg53Cys	p.R53C	ENST00000325404	NM_003106.3	53	Cgc/Tgc	1/1	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.545289921169709	2		231	289	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401726	401726	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066780-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	110	518	0	ENST00000380956.4:c.1048C>A	p.Leu350Met	p.L350M	ENST00000380956	NM_001195286.1	350	Ctg/Atg	7/9	1	2	FACETS	0.502	0.451	0.556	0.502	0.451	0.556	SUBCLONAL	1	TRUE	1	0.545289921169709	2		518	804	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578530	7578530	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs267605077	NA	P-0066781-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	35	404	1	ENST00000269305.4:c.400T>C	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	Ttt/Ctt	5/11	1	2	FACETS	0.281	0.229	0.34	0.281	0.229	0.34	SUBCLONAL	1	TRUE	1	0.238487414262263	2		405	1043	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574006	7574006	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066781-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	72	311	0	ENST00000269305.4:c.1021T>G	p.Phe341Val	p.F341V	ENST00000269305	NM_001126112.2	341	Ttc/Gtc	10/11	1	2	FACETS	0.666	0.581	0.759	0.666	0.581	0.759	SUBCLONAL	1	TRUE	1	0.238487414262263	2		311	906	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0066782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	275	157	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.576045582170841	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	4	TRUE	0	0.572540323353978	4		157	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0066782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	381	555	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.528919709273497	3	FACETS	0.966	0.93	1	0.966	0.93	1	CLONAL	3	TRUE	0	0.572540323353978	3		555	591	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640329	3640329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752187463	NA	P-0066782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	293	390	1	ENST00000294008.3:c.3310C>T	p.Arg1104Trp	p.R1104W	ENST00000294008	NM_032444.2	1104	Cgg/Tgg	12/15	0.572540323353978	9	FACETS	1	0.964	1	0.296	0.278	0.315	CLONAL	2	TRUE	2	0.572540323353978	9		391	1482	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181784	56181785	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0066782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	193	259	0	ENST00000399503.3:c.4011dup	p.Tyr1338IlefsTer11	p.Y1338Ifs*11	ENST00000399503	NM_005921.1	1336	-/A	17/20	0.576045582170841	3	FACETS	0.994	0.931	1			1	CLONAL	2	TRUE	NA	0.572540323353978	3		259	436	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438196	110438196	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	199	357	0	ENST00000375856.3:c.205C>T	p.Gln69Ter	p.Q69*	ENST00000375856	NM_003749.2	69	Caa/Taa	1/2	NA	2	FACETS	0.917	0.864	0.97			1	INDETERMINATE	2	TRUE	NA	0.572540323353978	2		357	379	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181846	56181847	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0066782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	86	273	0	ENST00000399503.3:c.4071_4072del	p.Ser1358ValfsTer4	p.S1358Vfs*4	ENST00000399503	NM_005921.1	1357	cTT/c	17/20	0.576045582170841	3	FACETS	0.909	0.809	1			1	CLONAL	1	TRUE	NA	0.572540323353978	3		273	425	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859435	151859435	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0066782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	465	460	0	ENST00000262189.6:c.11227A>T	p.Lys3743Ter	p.K3743*	ENST00000262189	NM_170606.2	3743	Aag/Tag	43/59	0.572540323353978	6	FACETS	0.897	0.861	0.933	0.897	0.861	0.933	CLONAL	4	TRUE	2	0.572540323353978	6		460	971	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137273	64137273	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	270	428	0	ENST00000334205.4:c.1707del	p.Cys570AlafsTer32	p.C570Afs*32	ENST00000334205	NM_003942.2	569	Ccc/cc	14/17	0.572540323353978	5	FACETS	1	0.989	1	0.801	0.755	0.847	CLONAL	2	TRUE	2	0.572540323353978	5		428	730	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057520005	NA	P-0066783-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	184	528	0	ENST00000269305.4:c.820G>C	p.Val274Leu	p.V274L	ENST00000269305	NM_001126112.2	274	Gtt/Ctt	8/11	0.437477338355532	1	FACETS	0.938	0.869	1	0.938	0.869	1	CLONAL	1	TRUE	0	0.460944885019011	1		528	655	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134829	41134829	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066783-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	88	475	0	ENST00000379561.5:c.799C>T	p.Arg267Ter	p.R267*	ENST00000379561	NM_002015.3	267	Cga/Tga	2/3	0.437477338355532	1	FACETS	0.459	0.407	0.515	0.459	0.407	0.515	SUBCLONAL	1	TRUE	0	0.460944885019011	1		475	640	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868586	37868586	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066783-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	104	449	0	ENST00000269571.5:c.1033C>G	p.Leu345Val	p.L345V	ENST00000269571		345	Ctg/Gtg	9/27	1	2	FACETS	0.607	0.544	0.675	0.607	0.544	0.675	SUBCLONAL	1	TRUE	1	0.460944885019011	2		449	743	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211894	123211894	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066783-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	29	573	0	ENST00000218089.9:c.2761C>G	p.Leu921Val	p.L921V	ENST00000218089	NM_001042749.1	921	Ctc/Gtc	27/35	0.361351354892027	0	FACETS	0.217	0.174	0.265			1	SUBCLONAL	1	TRUE	0	0.460944885019011	0		573	313	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505389	157505394	+	frameshift_variant	Frame_Shift_Del	DEL	GAGCTG	GAGCTG	CAGCT	novel	NA	P-0066783-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	115	369	0	ENST00000346085.5:c.3370_3375delinsCAGCT	p.Glu1124GlnfsTer6	p.E1124Qfs*6	ENST00000346085	NM_020732.3	1124	GAGCTG/CAGCT	13/20	0.255011579109242	1	FACETS	0.684	0.619	0.754	0.684	0.619	0.754	INDETERMINATE	1	TRUE	0	0.460944885019011	1		369	561	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755744	57755744	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	163	402	0	ENST00000274289.3:c.43A>C	p.Thr15Pro	p.T15P	ENST00000274289	NM_006622.3	15	Acc/Ccc	1/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		402	685	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0066848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	222	591	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.539832930717605	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.544642217307717	1		591	557	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085839	16085839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372079635	NA	P-0066848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	216	450	0	ENST00000281043.3:c.1015G>A	p.Val339Met	p.V339M	ENST00000281043	NM_005378.4	339	Gtg/Atg	3/3	0.544642217307717	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.544642217307717	1		450	501	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745214	41745214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750029623	NA	P-0066848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	162	308	0	ENST00000301178.4:c.1280G>A	p.Arg427His	p.R427H	ENST00000301178	NM_021913.4	427	cGc/cAc	9/20	0.544642217307717	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.544642217307717	1		308	365	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630724	67630724	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	129	372	0	ENST00000272342.5:c.910G>C	p.Ala304Pro	p.A304P	ENST00000272342	NM_019002.3	304	Gct/Cct	5/6	1	2	FACETS	0.8	0.728	0.876	0.8	0.728	0.876	SUBCLONAL	1	TRUE	1	0.544642217307717	2		372	592	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10264991	10264991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753503985	NA	P-0066848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	206	369	0	ENST00000340748.4:c.1949G>A	p.Arg650His	p.R650H	ENST00000340748		650	cGc/cAc	21/40	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.544642217307717	2		369	696	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956685	93956685	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	153	309	0	ENST00000369303.4:c.2551G>C	p.Glu851Gln	p.E851Q	ENST00000369303	NM_004440.3	851	Gaa/Caa	15/17	1	2	FACETS	0.964	0.886	1	0.964	0.886	1	CLONAL	1	TRUE	1	0.544642217307717	2		309	583	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	75	341	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.198193415985362	5	FACETS	1	0.959	1	0.808	0.712	0.911	CLONAL	2	TRUE	2	0.198193415985362	5		341	405	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377241	118377241	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782228819	NA	P-0066850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	54	678	1	ENST00000534358.1:c.10634G>A	p.Arg3545Gln	p.R3545Q	ENST00000534358	NM_005933.3	3545	cGg/cAg	27/36	0.185052098935308	3	FACETS	0.859	0.733	0.998	0.43	0.366	0.499	CLONAL	1	TRUE	1	0.198193415985362	3		679	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0066850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	108	383	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.185127808661737	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	0	0.198193415985362	2		384	511	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575671	48575671	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0066850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	26	232	0	ENST00000342988.3:c.431C>G	p.Ser144Ter	p.S144*	ENST00000342988	NM_005359.5	144	tCa/tGa	4/12	0.198193415985362	1	FACETS	0.889	0.706	1	0.889	0.706	1	CLONAL	1	TRUE	0	0.198193415985362	1		232	266	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0066850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	115	782	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.198193415985362	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.198193415985362	2		782	498	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344360	118344360	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0066850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	48	628	0	ENST00000534358.1:c.2486C>G	p.Ser829Ter	p.S829*	ENST00000534358	NM_005933.3	829	tCa/tGa	3/36	0.185052098935308	3	FACETS	0.832	0.702	0.975	0.416	0.351	0.488	CLONAL	1	TRUE	1	0.198193415985362	3		628	640	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344629	118344629	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	138	596	0	ENST00000534358.1:c.2755G>T	p.Glu919Ter	p.E919*	ENST00000534358	NM_005933.3	919	Gaa/Taa	3/36	0.185052098935308	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.198193415985362	3		596	686	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439904	56439904	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0066850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	122	560	0	ENST00000407977.2:c.687+1G>A		p.X229_splice	ENST00000407977		229			0.185127808661737	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.198193415985362	2		560	563	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0066851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	113	314	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	1	2	FACETS	0.897	0.813	0.983	0.897	0.813	0.983	CLONAL	1	TRUE	1	0.61619320761806	2		314	409	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0066851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	193	554	2	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.942	0.875	1	0.942	0.875	1	CLONAL	1	TRUE	1	0.61619320761806	2		556	665	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0066851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	135	400	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.61619320761806	2		400	382	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913273	NA	P-0066851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	43	242	0	ENST00000263967.3:c.1624G>C	p.Glu542Gln	p.E542Q	ENST00000263967	NM_006218.2	542	Gaa/Caa	10/21	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.61619320761806	2		242	130	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411576	63411576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	403	278	0	ENST00000330258.3:c.1591C>T	p.Arg531Ter	p.R531*	ENST00000330258	NM_152424.3	531	Cga/Tga	2/2	0.61619320761806	3	FACETS	0.895	0.855	0.935	0.895	0.855	0.935	CLONAL	2	TRUE	1	0.61619320761806	3		278	956	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0066851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	234	416	0	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.61619320761806	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.61619320761806	1		416	436	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941014	71941014	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202155977	NA	P-0066851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	209	635	0	ENST00000298229.2:c.890C>T	p.Pro297Leu	p.P297L	ENST00000298229	NM_001567.3	297	cCg/cTg	8/28	1	2	FACETS	0.917	0.854	0.981	0.917	0.854	0.981	CLONAL	1	TRUE	1	0.61619320761806	2		635	740	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120255	70120256	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	204	563	0	ENST00000245479.2:c.1258dup	p.Tyr420LeufsTer158	p.Y420Lfs*158	ENST00000245479	NM_000346.3	419	-/T	3/3	0.306214035741138	3	FACETS	1	0.98	1	0.57	0.53	0.611	INDETERMINATE	1	TRUE	1	0.61619320761806	3		563	760	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	37	355	0	ENST00000311936.3:c.437C>A	p.Ala146Glu	p.A146E	ENST00000311936	NM_004985.3	146	gCa/gAa	4/5	1	2	FACETS	0.946	0.796	1	0.946	0.796	1	CLONAL	1	TRUE	1	0.61619320761806	2		355	127	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117872	70117872	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	275	494	0	ENST00000245479.2:c.340G>T	p.Val114Leu	p.V114L	ENST00000245479	NM_000346.3	114	Gtg/Ttg	1/3	0.306214035741138	3	FACETS	0.815	0.77	0.862	0.815	0.77	0.862	INDETERMINATE	2	TRUE	1	0.61619320761806	3		494	716	SUCCESS
APC	324	MSKCC	GRCh37	5	112173775	112173775	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	128	473	0	ENST00000257430.4:c.2484del	p.Thr829GlnfsTer13	p.T829Qfs*13	ENST00000257430	NM_000038.5	828	acT/ac	16/16	1	2	FACETS	0.999	0.913	1	0.999	0.913	1	CLONAL	1	TRUE	1	0.61619320761806	2		473	416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0066852-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	360	343	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.732136944682073	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.732136944682073	2		343	473	SUCCESS
APC	324	MSKCC	GRCh37	5	112174878	112174878	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066852-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	100	397	0	ENST00000257430.4:c.3587C>A	p.Ser1196Ter	p.S1196*	ENST00000257430	NM_000038.5	1196	tCa/tAa	16/16	0.722193248735026	2	FACETS	0.911	0.847	0.971	0.911	0.847	0.971	CLONAL	2	TRUE	0	0.732136944682073	2		397	150	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643791	38643791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752958999	NA	P-0066852-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	80	350	0	ENST00000299084.4:c.1261G>A	p.Val421Ile	p.V421I	ENST00000299084	NM_152594.2	421	Gtc/Atc	7/7	1	2	FACETS	0.95	0.85	1	0.95	0.85	1	CLONAL	1	TRUE	1	0.732136944682073	2		350	230	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675615	30675616	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0066852-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	147	454	0	ENST00000376406.3:c.2740_2741delinsTT	p.Ala914Leu	p.A914L	ENST00000376406	NM_014641.2	914	GCa/TTa	8/15	0.732136944682073	6	FACETS	0.837	0.768	0.909			1	CLONAL	2	TRUE	NA	0.732136944682073	6		454	591	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275633	41275633	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066852-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	132	350	0	ENST00000349496.5:c.1528A>C	p.Thr510Pro	p.T510P	ENST00000349496	NM_001904.3	510	Act/Cct	10/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.732136944682073	2		350	289	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046738	42046738	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs933034569	NA	P-0066852-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	84	356	1	ENST00000219905.7:c.7112C>T	p.Ala2371Val	p.A2371V	ENST00000219905	NM_001164273.1	2371	gCg/gTg	18/24	1	2	FACETS	0.929	0.833	1	0.929	0.833	1	CLONAL	1	TRUE	1	0.732136944682073	2		357	247	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0066853-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	17	345	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	1	2	FACETS	0.138	0.103	0.182	0.138	0.103	0.182	SUBCLONAL	1	TRUE	1	0.447181682545986	2		345	549	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293551	1293551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	165	496	0	ENST00000310581.5:c.1450G>A	p.Glu484Lys	p.E484K	ENST00000310581	NM_198253.2	484	Gaa/Aaa	2/16	1	2	FACETS	0.917	0.846	0.992	0.917	0.846	0.992	CLONAL	1	TRUE	1	0.55166042456351	2		496	652	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	166	481	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	1	2	FACETS	0.894	0.824	0.967	0.894	0.824	0.967	CLONAL	1	TRUE	1	0.55166042456351	2		481	673	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	285	469	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.55166042456351	3	FACETS	0.923	0.873	0.974	0.923	0.873	0.974	CLONAL	2	TRUE	1	0.55166042456351	3		469	714	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076902	41076902	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	137	402	0	ENST00000373198.4:c.1518G>A	p.Trp506Ter	p.W506*	ENST00000373198	NM_133170.3	506	tgG/tgA	9/32	1	2	FACETS	0.898	0.821	0.979	0.898	0.821	0.979	CLONAL	1	TRUE	1	0.55166042456351	2		402	553	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566827	212566827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202247795	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	192	562	0	ENST00000342788.4:c.1354G>A	p.Glu452Lys	p.E452K	ENST00000342788	NM_005235.2	452	Gaa/Aaa	12/28	1	2	FACETS	0.961	0.892	1	0.961	0.892	1	CLONAL	1	TRUE	1	0.55166042456351	2		562	724	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254614	1254614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201330213	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	156	457	0	ENST00000310581.5:c.3164C>T	p.Ser1055Leu	p.S1055L	ENST00000310581	NM_198253.2	1055	tCg/tTg	15/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.55166042456351	2		457	524	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139929	50139929	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374650566	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	166	488	0	ENST00000246792.3:c.400G>A	p.Asp134Asn	p.D134N	ENST00000246792	NM_006270.3	134	Gac/Aac	4/6	1	2	FACETS	0.975	0.9	1	0.975	0.9	1	CLONAL	1	TRUE	1	0.55166042456351	2		488	617	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032408	10032408	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	183	475	0	ENST00000330684.3:c.415G>A	p.Asp139Asn	p.D139N	ENST00000330684	NM_001134407.1	139	Gat/Aat	3/13	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.55166042456351	2		475	658	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007752	45007753	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	204	551	0	ENST00000558401.1:c.204dup	p.Val69SerfsTer21	p.V69Sfs*21	ENST00000558401	NM_004048.2	67	gaa/gAaa	2/4	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.55166042456351	2		551	594	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129904	69129904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	212	565	0	ENST00000288368.4:c.4658G>A	p.Gly1553Glu	p.G1553E	ENST00000288368	NM_024870.2	1553	gGa/gAa	38/40	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.55166042456351	2		565	753	SUCCESS
YES1	7525	MSKCC	GRCh37	18	732954	732954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	151	489	0	ENST00000314574.4:c.1303C>T	p.Pro435Ser	p.P435S	ENST00000314574	NM_005433.3	435	Cca/Tca	11/12	1	2	FACETS	0.957	0.879	1	0.957	0.879	1	CLONAL	1	TRUE	1	0.55166042456351	2		489	572	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720929	176720929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1471211571	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	238	570	0	ENST00000439151.2:c.6560G>A	p.Arg2187Gln	p.R2187Q	ENST00000439151	NM_022455.4	2187	cGa/cAa	23/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.55166042456351	2		570	805	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	129	539	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.55166042456351	2		539	464	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650812	93650812	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	174	462	0	ENST00000375746.1:c.1738G>A	p.Glu580Lys	p.E580K	ENST00000375746	NM_001174167.1	580	Gaa/Aaa	13/14	1	2	FACETS	0.997	0.922	1	0.997	0.922	1	CLONAL	1	TRUE	1	0.55166042456351	2		462	633	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286836	33286836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	713	676	0	ENST00000374542.5:c.2101C>T	p.Pro701Ser	p.P701S	ENST00000374542	NM_001141970.1	701	Cct/Tct	7/8	0.55166042456351	3	FACETS	0.972	0.945	0.998	0.972	0.945	0.998	CLONAL	3	TRUE	0	0.55166042456351	3		676	1131	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372262	55372262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	177	579	0	ENST00000297316.4:c.952C>T	p.Gln318Ter	p.Q318*	ENST00000297316	NM_022454.3	318	Cag/Tag	2/2	1	2	FACETS	0.901	0.833	0.972	0.901	0.833	0.972	CLONAL	1	TRUE	1	0.55166042456351	2		579	712	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189936	66189936	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	145	425	0	ENST00000273854.3:c.3010G>A	p.Asp1004Asn	p.D1004N	ENST00000273854	NM_004439.5	1004	Gat/Aat	18/18	1	2	FACETS	0.984	0.903	1	0.984	0.903	1	CLONAL	1	TRUE	1	0.55166042456351	2		425	534	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39763623	39763623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	163	454	0	ENST00000288319.7:c.829C>T	p.Pro277Ser	p.P277S	ENST00000288319	NM_182918.3	277	Cct/Tct	8/10	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.55166042456351	2		454	581	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917770	29917770	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	207	521	0	ENST00000389048.3:c.898C>T	p.Gln300Ter	p.Q300*	ENST00000389048	NM_004304.4	300	Cag/Tag	3/29	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.55166042456351	2		521	683	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178651	32178651	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	411	570	0	ENST00000375023.3:c.2743T>A	p.Phe915Ile	p.F915I	ENST00000375023	NM_004557.3	915	Ttc/Atc	18/30	0.55166042456351	3	FACETS	1	0.976	1	0.687	0.657	0.718	CLONAL	2	TRUE	0	0.55166042456351	3		570	922	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344188	118344188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	232	702	0	ENST00000534358.1:c.2314C>T	p.Pro772Ser	p.P772S	ENST00000534358	NM_005933.3	772	Ccc/Tcc	3/36	0.55166042456351	1	FACETS	0.897	0.841	0.954	0.897	0.841	0.954	CLONAL	1	TRUE	0	0.55166042456351	1		702	679	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571920	64571920	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	225	527	0	ENST00000312049.6:c.1719C>G	p.Ser573Arg	p.S573R	ENST00000312049	NM_130799.2	573	agC/agG	10/10	0.55166042456351	1	FACETS	0.981	0.92	1	0.981	0.92	1	CLONAL	1	TRUE	0	0.55166042456351	1		527	602	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557380	21557380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	202	484	0	ENST00000382592.4:c.2465C>T	p.Ser822Phe	p.S822F	ENST00000382592	NM_014572.2	822	tCc/tTc	5/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.55166042456351	2		484	676	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098437	11098437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555755005	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	183	541	0	ENST00000358026.2:c.955C>T	p.Pro319Ser	p.P319S	ENST00000358026	NM_001128849.1	319	Cca/Tca	6/36	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.55166042456351	2		541	624	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690697	33690697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1908571803	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	210	583	0	ENST00000308377.4:c.130G>A	p.Glu44Lys	p.E44K	ENST00000308377	NM_152270.3	44	Gag/Aag	2/5	1	2	FACETS	0.913	0.849	0.979	0.913	0.849	0.979	CLONAL	1	TRUE	1	0.55166042456351	2		583	834	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118354938	118354938	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	214	468	0	ENST00000534358.1:c.4127C>T	p.Thr1376Ile	p.T1376I	ENST00000534358	NM_005933.3	1376	aCt/aTt	9/36	0.55166042456351	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.55166042456351	1		468	530	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059187	42059187	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	264	693	0	ENST00000219905.7:c.8907G>A	p.Met2969Ile	p.M2969I	ENST00000219905	NM_001164273.1	2969	atG/atA	24/24	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.55166042456351	2		693	945	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976925	18976925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	208	553	0	ENST00000262803.5:c.3310G>A	p.Glu1104Lys	p.E1104K	ENST00000262803	NM_002911.3	1104	Gag/Aag	23/24	1	2	FACETS	0.992	0.924	1	0.992	0.924	1	CLONAL	1	TRUE	1	0.55166042456351	2		553	760	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991280	41991280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	150	466	0	ENST00000219905.7:c.2111C>T	p.Ser704Phe	p.S704F	ENST00000219905	NM_001164273.1	704	tCc/tTc	5/24	1	2	FACETS	0.975	0.895	1	0.975	0.895	1	CLONAL	1	TRUE	1	0.55166042456351	2		466	558	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50790794	50790794	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	232	382	0	ENST00000307179.4:c.3040T>C	p.Phe1014Leu	p.F1014L	ENST00000307179		1014	Ttt/Ctt	19/20	0.458093978859307	3	FACETS	0.92	0.865	0.976			1	CLONAL	2	TRUE	NA	0.55166042456351	3		382	583	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2218093	2218093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	172	529	0	ENST00000326181.6:c.155C>T	p.Thr52Ile	p.T52I	ENST00000326181	NM_032271.2	52	aCc/aTc	4/21	1	2	FACETS	0.913	0.843	0.986	0.913	0.843	0.986	CLONAL	1	TRUE	1	0.55166042456351	2		529	683	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456360	32456360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	170	573	0	ENST00000332351.3:c.532G>A	p.Gly178Arg	p.G178R	ENST00000332351	NM_024426.4	178	Ggg/Agg	1/10	0.543063227514519	3	FACETS	1	0.936	1	0.509	0.469	0.551	CLONAL	1	TRUE	1	0.55166042456351	3		573	772	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690501	33690501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	229	561	0	ENST00000308377.4:c.326C>T	p.Ser109Phe	p.S109F	ENST00000308377	NM_152270.3	109	tCt/tTt	2/5	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.55166042456351	2		561	763	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622141	1622141	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	218	597	0	ENST00000344749.5:c.734C>T	p.Ser245Phe	p.S245F	ENST00000344749	NM_001136139.2	245	tCc/tTc	10/19	0.474638187043252	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.55166042456351	1		597	571	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449799	149449799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	191	637	0	ENST00000286301.3:c.1265C>T	p.Ser422Phe	p.S422F	ENST00000286301	NM_005211.3	422	tCt/tTt	9/22	1	2	FACETS	0.909	0.842	0.977	0.909	0.842	0.977	CLONAL	1	TRUE	1	0.55166042456351	2		637	762	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455527	189455528	+	splice_acceptor_variant	Splice_Site	DNP	AG	AG	TA	novel	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	99	399	0	ENST00000264731.3:c.63-2_63-1delinsTA		p.X21_splice	ENST00000264731	NM_003722.4	21			0.181209297772676	3	FACETS	0.958	0.859	1	0.479	0.429	0.531	INDETERMINATE	1	TRUE	1	0.55166042456351	3		399	478	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729149	66729149	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	894	592	0	ENST00000307102.5:c.357T>A	p.His119Gln	p.H119Q	ENST00000307102	NM_002755.3	119	caT/caA	3/11	0.549409410096187	5	FACETS	0.992	0.966	1	0.992	0.966	1	CLONAL	4	TRUE	1	0.55166042456351	5		592	1493	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380065	116380065	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	420	552	0	ENST00000397752.3:c.1454C>T	p.Pro485Leu	p.P485L	ENST00000397752	NM_000245.2	485	cCa/cTa	4/21	0.55166042456351	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.55166042456351	3		552	937	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426253	49426253	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	163	563	0	ENST00000301067.7:c.12235C>A	p.Gln4079Lys	p.Q4079K	ENST00000301067	NM_003482.3	4079	Caa/Aaa	39/54	1	2	FACETS	0.784	0.721	0.849	0.784	0.721	0.849	SUBCLONAL	1	TRUE	1	0.55166042456351	2		563	754	SUCCESS
APC	324	MSKCC	GRCh37	5	112175271	112175272	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0066859-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	50	369	0	ENST00000257430.4:c.3982_3983del	p.Gln1328AlafsTer3	p.Q1328Afs*3	ENST00000257430	NM_000038.5	1327	tCA/t	16/16	0.207302724774534	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	0	0.207302724774534	1		369	394	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911561	114911561	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066859-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	44	385	0	ENST00000543371.1:c.1079A>C	p.Tyr360Ser	p.Y360S	ENST00000543371	NM_001198531.1	360	tAt/tCt	10/14	1	2	FACETS	0.967	0.812	1	0.967	0.812	1	CLONAL	1	TRUE	1	0.207302724774534	2		385	439	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381471	81381471	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558400297	NA	P-0066859-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	24	301	0	ENST00000222390.5:c.590G>A	p.Arg197His	p.R197H	ENST00000222390	NM_000601.4	197	cGc/cAc	5/18	1	2	FACETS	0.897	0.706	1	0.897	0.706	1	CLONAL	1	TRUE	1	0.207302724774534	2		301	258	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577499	7577500	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066859-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	83	375	0	ENST00000269305.4:c.781dup	p.Ser261LysfsTer3	p.S261Kfs*3	ENST00000269305	NM_001126112.2	261	agt/aAgt	7/11	1	2	FACETS	0.766	0.677	0.86	1	0.979	1	SUBCLONAL	2	TRUE	1	0.207302724774534	2		375	523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0066860-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	62	361	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	1	2	FACETS	0.86	0.741	0.988	0.86	0.741	0.988	CLONAL	1	TRUE	1	0.196796514255873	2		361	733	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50483706	50483706	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066860-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	54	374	0	ENST00000394963.4:c.811C>T	p.Gln271Ter	p.Q271*	ENST00000394963	NM_003076.4	271	Cag/Tag	7/13	1	2	FACETS	0.963	0.822	1	0.963	0.822	1	CLONAL	1	TRUE	1	0.196796514255873	2		374	570	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	153	582	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.660382980456001	2		582	461	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	75	215	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.805	0.714	0.902	0.805	0.714	0.902	CLONAL	1	TRUE	1	0.660382980456001	2		215	282	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2492096	2492097	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs772088410	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	130	461	0	ENST00000355716.4:c.500dup	p.Thr169AspfsTer65	p.T169Dfs*65	ENST00000355716	NM_003820.2	165	tgc/tgCc	5/8	1	2	FACETS	0.589	0.535	0.645	0.589	0.535	0.645	SUBCLONAL	1	TRUE	1	0.660382980456001	2		461	669	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057936	27057937	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1415146710	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	256	525	0	ENST00000324856.7:c.1650dup	p.Tyr551LeufsTer72	p.Y551Lfs*72	ENST00000324856	NM_006015.4	548	-/C	3/20	1	2	FACETS	0.872	0.818	0.927	0.872	0.818	0.927	CLONAL	1	TRUE	1	0.660382980456001	2		525	889	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	353	324	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.757	0.723	0.791	1	0.996	1	SUBCLONAL	2	TRUE	1	0.660382980456001	2		324	706	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	66	760	5	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.22	0.19	0.252	0.22	0.19	0.252	SUBCLONAL	1	TRUE	1	0.660382980456001	2		765	910	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685304	89685305	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1060500113	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	103	186	0	ENST00000371953.3:c.200dup	p.Tyr68IlefsTer6	p.Y68Ifs*6	ENST00000371953	NM_000314.4	67	ata/aTta	3/9	0.652751694011705	2	FACETS	0.923	0.855	0.989	0.923	0.855	0.989	CLONAL	2	TRUE	0	0.660382980456001	2		186	169	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	570	535	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.652751694011705	2	FACETS	0.985	0.956	1	0.985	0.956	1	CLONAL	2	TRUE	0	0.660382980456001	2		535	876	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114817	108114817	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786204543	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	100	347	1	ENST00000278616.4:c.640del	p.Ser214ProfsTer16	p.S214Pfs*16	ENST00000278616	NM_000051.3	212	Ttt/tt	6/63	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.660382980456001	2		348	294	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206609	108206609	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs762154857	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	151	417	0	ENST00000278616.4:c.8189A>G	p.Gln2730Arg	p.Q2730R	ENST00000278616	NM_000051.3	2730	cAg/cGg	56/63	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.660382980456001	2		417	440	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444987	49444987	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	158	520	0	ENST00000301067.7:c.2479del	p.Gln827AsnfsTer103	p.Q827Nfs*103	ENST00000301067	NM_003482.3	827	Caa/aa	10/54	1	2	FACETS	0.592	0.543	0.644	0.592	0.543	0.644	SUBCLONAL	1	TRUE	1	0.660382980456001	2		520	808	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222592	69222592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555187172	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	115	379	0	ENST00000462284.1:c.565C>T	p.Arg189Cys	p.R189C	ENST00000462284	NM_002392.5	189	Cgc/Tgc	8/11	1	2	FACETS	0.762	0.691	0.836	0.762	0.691	0.836	SUBCLONAL	1	TRUE	1	0.660382980456001	2		379	457	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112272	115112272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544562535	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	34	430	0	ENST00000257566.3:c.1468G>A	p.Ala490Thr	p.A490T	ENST00000257566	NM_016569.3	490	Gcc/Acc	7/8	1	2	FACETS	0.187	0.152	0.226	0.187	0.152	0.226	SUBCLONAL	1	TRUE	1	0.660382980456001	2		430	552	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436504	110436504	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760629200	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	46	607	0	ENST00000375856.3:c.1897G>A	p.Gly633Arg	p.G633R	ENST00000375856	NM_003749.2	633	Gga/Aga	1/2	1	2	FACETS	0.175	0.146	0.206	0.175	0.146	0.206	SUBCLONAL	1	TRUE	1	0.660382980456001	2		607	798	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	140	435	0	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	0.768	0.703	0.836	0.768	0.703	0.836	SUBCLONAL	1	TRUE	1	0.660382980456001	2		435	552	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347057	347057	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs773888441	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	110	383	0	ENST00000262320.3:c.1954G>A	p.Gly652Arg	p.G652R	ENST00000262320	NM_003502.3	652	Ggg/Agg	7/11	1	2	FACETS	0.609	0.549	0.672	0.609	0.549	0.672	SUBCLONAL	1	TRUE	1	0.660382980456001	2		383	547	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645069	67645069	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	188	434	0	ENST00000264010.4:c.334G>T	p.Glu112Ter	p.E112*	ENST00000264010	NM_006565.3	112	Gaa/Taa	3/12	1	2	FACETS	0.917	0.852	0.984	0.917	0.852	0.984	CLONAL	1	TRUE	1	0.660382980456001	2		434	621	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291473	10291473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61750053	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	82	359	0	ENST00000340748.4:c.206G>A	p.Arg69His	p.R69H	ENST00000340748		69	cGt/cAt	3/40	1	2	FACETS	0.66	0.586	0.739	0.66	0.586	0.739	SUBCLONAL	1	TRUE	1	0.660382980456001	2		359	376	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303876	30303876	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	207	453	0	ENST00000262643.3:c.116del	p.Leu39CysfsTer36	p.L39Cfs*36	ENST00000262643	NM_001238.2	38	Ttt/tt	4/12	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.660382980456001	2		453	624	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794374	242794374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763027752	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	230	440	0	ENST00000334409.5:c.568G>A	p.Val190Ile	p.V190I	ENST00000334409	NM_005018.2	190	Gtc/Atc	3/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.660382980456001	2		440	652	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	211	405	0	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	1	2	FACETS	0.968	0.904	1	0.968	0.904	1	CLONAL	1	TRUE	1	0.660382980456001	2		405	660	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427721	72427721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1382885623	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	179	472	0	ENST00000477973.2:c.769G>A	p.Val257Ile	p.V257I	ENST00000477973	NM_012234.5	257	Gtc/Atc	4/4	1	2	FACETS	0.706	0.652	0.762	0.706	0.652	0.762	SUBCLONAL	1	TRUE	1	0.660382980456001	2		472	768	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519145	187519145	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	160	400	0	ENST00000441802.2:c.12238G>T	p.Gly4080Ter	p.G4080*	ENST00000441802	NM_005245.3	4080	Gga/Tga	23/27	1	2	FACETS	0.923	0.852	0.996	0.923	0.852	0.996	CLONAL	1	TRUE	1	0.660382980456001	2		400	525	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6045627	6045627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs10254120	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	50	139	0	ENST00000265849.7:c.59G>A	p.Arg20Gln	p.R20Q	ENST00000265849	NM_000535.5	20	cGg/cAg	2/15	1	2	FACETS	0.823	0.709	0.944	0.823	0.709	0.944	CLONAL	1	TRUE	1	0.660382980456001	2		139	184	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	111	477	3	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	1	2	FACETS	0.459	0.413	0.508	0.459	0.413	0.508	SUBCLONAL	1	TRUE	1	0.660382980456001	2		480	732	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354666	70354666	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs727503868	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	224	418	0	ENST00000374080.3:c.4831C>T	p.Arg1611Cys	p.R1611C	ENST00000374080		1611	Cgt/Tgt	35/45	1	2	FACETS	0.955	0.894	1	0.955	0.894	1	CLONAL	1	TRUE	1	0.660382980456001	2		418	710	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057933	27057934	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	315	550	0	ENST00000324856.7:c.1642_1643dup	p.Gln548HisfsTer72	p.Q548Hfs*72	ENST00000324856	NM_006015.4	547	-/CA	3/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.660382980456001	2		550	920	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707914	43707914	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1327359362	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	266	512	0	ENST00000382044.4:c.4967G>A	p.Arg1656Gln	p.R1656Q	ENST00000382044	NM_001141980.1	1656	cGa/cAa	23/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.660382980456001	2		512	766	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183347	56183347	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	159	347	0	ENST00000399503.3:c.4257G>T	p.Glu1419Asp	p.E1419D	ENST00000399503	NM_005921.1	1419	gaG/gaT	18/20	1	2	FACETS	0.971	0.897	1	0.971	0.897	1	CLONAL	1	TRUE	1	0.660382980456001	2		347	496	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553723	106553723	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	287	467	1	ENST00000369096.4:c.1688C>A	p.Pro563His	p.P563H	ENST00000369096	NM_001198.3	563	cCc/cAc	5/7	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.660382980456001	2		468	820	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528636	8528636	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1332170873	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	148	415	0	ENST00000356435.5:c.496G>A	p.Val166Met	p.V166M	ENST00000356435		166	Gtg/Atg	4/35	1	2	FACETS	0.869	0.798	0.941	0.869	0.798	0.941	CLONAL	1	TRUE	1	0.660382980456001	2		415	516	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912295	97912296	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1057519366	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	217	411	0	ENST00000289081.3:c.595dup	p.Leu199ProfsTer12	p.L199Pfs*12	ENST00000289081	NM_000136.2	199	ctg/cCtg	7/15	1	2	FACETS	0.993	0.928	1	0.993	0.928	1	CLONAL	1	TRUE	1	0.660382980456001	2		411	662	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229578	98229578	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	164	409	0	ENST00000331920.6:c.2380C>T	p.Gln794Ter	p.Q794*	ENST00000331920	NM_000264.3	794	Caa/Taa	15/24	1	2	FACETS	0.955	0.883	1	0.955	0.883	1	CLONAL	1	TRUE	1	0.660382980456001	2		409	520	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937503	76937503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	90	488	0	ENST00000373344.5:c.3245G>A	p.Ser1082Asn	p.S1082N	ENST00000373344	NM_000489.3	1082	aGt/aAt	9/35	1	2	FACETS	0.846	0.759	0.938	0.846	0.759	0.938	CLONAL	1	TRUE	1	0.660382980456001	2		488	322	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0066862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	41	269	1	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.3678923125327	3	FACETS	0.949	0.807	1	0.949	0.807	1	CLONAL	2	TRUE	1	0.3678923125327	3		270	139	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89791020	89791020	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	57	273	0	ENST00000336032.3:c.407G>A	p.Gly136Glu	p.G136E	ENST00000336032	NM_006813.2	136	gGa/gAa	1/2	0.3678923125327	3	FACETS	0.826	0.711	0.952	0.413	0.355	0.476	CLONAL	1	TRUE	1	0.3678923125327	3		273	444	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972440	81972440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs891516801	NA	P-0066862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	87	440	0	ENST00000359376.3:c.3233G>A	p.Arg1078Gln	p.R1078Q	ENST00000359376	NM_002661.3	1078	cGa/cAa	29/33	0.3678923125327	3	FACETS	1	0.887	1	0.5	0.443	0.56	CLONAL	1	TRUE	1	0.3678923125327	3		440	560	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831831	72831831	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	86	476	0	ENST00000268489.5:c.4750C>T	p.Gln1584Ter	p.Q1584*	ENST00000268489	NM_006885.3	1584	Cag/Tag	9/10	0.3678923125327	4	FACETS	0.891	0.788	1	0.445	0.394	0.501	CLONAL	1	TRUE	2	0.3678923125327	4		476	718	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198262833	198262833	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	31	301	0	ENST00000335508.6:c.3142G>A	p.Glu1048Lys	p.E1048K	ENST00000335508	NM_012433.2	1048	Gaa/Aaa	22/25	0.30974502097097	3	FACETS	0.75	0.609	0.908	0.25	0.203	0.303	CLONAL	1	TRUE	0	0.3678923125327	3		301	266	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579406	7579406	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0066862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	230	511	0	ENST00000269305.4:c.281C>G	p.Ser94Ter	p.S94*	ENST00000269305	NM_001126112.2	94	tCa/tGa	4/11	0.358156960596052	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.3678923125327	2		511	597	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845816	72845816	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs199992763	NA	P-0066862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	86	471	0	ENST00000268489.5:c.3651C>G	p.Ile1217Met	p.I1217M	ENST00000268489	NM_006885.3	1217	atC/atG	6/10	0.3678923125327	4	FACETS	0.97	0.859	1	0.485	0.429	0.545	CLONAL	1	TRUE	2	0.3678923125327	4		471	659	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998273	100998273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	66	335	0	ENST00000325455.5:c.1529C>T	p.Ala510Val	p.A510V	ENST00000325455	NM_001202474.3	510	gCg/gTg	1/8	0.3678923125327	3	FACETS	1	0.942	1	0.573	0.499	0.651	CLONAL	1	TRUE	1	0.3678923125327	3		335	371	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845580	151845580	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1287135873	NA	P-0066862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	101	456	0	ENST00000262189.6:c.13432C>T	p.Arg4478Ter	p.R4478*	ENST00000262189	NM_170606.2	4478	Cga/Tga	52/59	0.22811140147689	5	FACETS	1	0.972	1	0.421	0.377	0.469	CLONAL	1	TRUE	2	0.3678923125327	5		456	674	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687120	37687120	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1158026447	NA	P-0066862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	104	407	0	ENST00000447079.4:c.4024G>C	p.Asp1342His	p.D1342H	ENST00000447079	NM_015083.1	1342	Gat/Cat	14/14	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.3678923125327	NA		407	590	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282725	1282725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	42	361	0	ENST00000310581.5:c.1588C>T	p.Pro530Ser	p.P530S	ENST00000310581	NM_198253.2	530	Ccg/Tcg	3/16	0.3678923125327	4	FACETS	0.454	0.378	0.539	0.227	0.189	0.27	SUBCLONAL	1	TRUE	2	0.3678923125327	4		361	688	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178130	56178130	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	64	423	0	ENST00000399503.3:c.3103G>C	p.Glu1035Gln	p.E1035Q	ENST00000399503	NM_005921.1	1035	Gaa/Caa	14/20	0.3678923125327	3	FACETS	0.805	0.698	0.92	0.402	0.349	0.46	CLONAL	1	TRUE	1	0.3678923125327	3		423	512	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230486829	230486829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	57	376	0	ENST00000391860.1:c.424G>A	p.Glu142Lys	p.E142K	ENST00000391860	NM_001258311.1	142	Gaa/Aaa	3/7	0.3678923125327	3	FACETS	0.774	0.665	0.892	0.387	0.332	0.446	SUBCLONAL	1	TRUE	1	0.3678923125327	3		376	474	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50763829	50763829	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0066862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	45	283	0	ENST00000307179.4:c.687-1G>C		p.X229_splice	ENST00000307179		229			0.3678923125327	3	FACETS	0.83	0.7	0.973	0.415	0.35	0.487	CLONAL	1	TRUE	1	0.3678923125327	3		283	349	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290978	15290978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	62	438	0	ENST00000263388.2:c.3232G>A	p.Gly1078Ser	p.G1078S	ENST00000263388	NM_000435.2	1078	Ggt/Agt	20/33	0.3678923125327	3	FACETS	0.675	0.583	0.775	0.338	0.291	0.388	SUBCLONAL	1	TRUE	1	0.3678923125327	3		438	591	SUCCESS
REST	5978	MSKCC	GRCh37	4	57797771	57797771	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	53	403	0	ENST00000309042.7:c.2747C>G	p.Ser916Cys	p.S916C	ENST00000309042	NM_005612.4	916	tCt/tGt	4/4	0.191148794905194	5	FACETS	0.877	0.748	1	0.292	0.249	0.339	INDETERMINATE	1	TRUE	2	0.3678923125327	5		403	510	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289211	33289211	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	61	379	0	ENST00000374542.5:c.341C>T	p.Ser114Phe	p.S114F	ENST00000374542	NM_001141970.1	114	tCt/tTt	3/8	0.358156960596052	2	FACETS	0.691	0.597	0.793	0.345	0.298	0.397	SUBCLONAL	1	TRUE	0	0.3678923125327	2		379	480	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646726	23646726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555461435	NA	P-0066862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	29	384	0	ENST00000261584.4:c.1141C>T	p.Leu381Phe	p.L381F	ENST00000261584	NM_024675.3	381	Ctt/Ttt	4/13	0.349333499010698	4	FACETS	0.407	0.326	0.5	0.136	0.108	0.167	SUBCLONAL	1	TRUE	1	0.3678923125327	4		384	530	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570272	95570272	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	25	379	0	ENST00000393063.1:c.3461G>A	p.Arg1154Lys	p.R1154K	ENST00000393063	NM_030621.3	1154	aGa/aAa	22/28	0.3678923125327	3	FACETS	0.37	0.291	0.461	0.185	0.145	0.231	SUBCLONAL	1	TRUE	1	0.3678923125327	3		379	435	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858405	27858405	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	175	515	0	ENST00000359303.2:c.166C>G	p.Gln56Glu	p.Q56E	ENST00000359303	NM_003535.2	56	Cag/Gag	1/1	0.3678923125327	9	FACETS	0.885	0.813	0.96	0.253	0.232	0.275	CLONAL	2	TRUE	2	0.3678923125327	9		515	1230	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11297985	11297985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1412858508	NA	P-0066862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	96	382	1	ENST00000361445.4:c.2123G>A	p.Arg708Gln	p.R708Q	ENST00000361445	NM_004958.3	708	cGg/cAg	13/58	0.3678923125327	3	FACETS	1	0.934	1	0.532	0.475	0.592	CLONAL	1	TRUE	1	0.3678923125327	3		383	581	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665418	182665418	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	19	255	0	ENST00000292782.4:c.523C>G	p.Leu175Val	p.L175V	ENST00000292782	NM_020640.2	175	Cta/Gta	5/7	0.3678923125327	3	FACETS	0.741	0.566	0.944	0.371	0.283	0.472	CLONAL	1	TRUE	1	0.3678923125327	3		255	165	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519801	29519801	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	40	386	0	ENST00000389048.3:c.1770G>C	p.Leu590Phe	p.L590F	ENST00000389048	NM_004304.4	590	ttG/ttC	9/29	0.3678923125327	3	FACETS	0.447	0.371	0.532	0.223	0.185	0.266	SUBCLONAL	1	TRUE	1	0.3678923125327	3		386	576	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260041	16260041	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	213	491	0	ENST00000375759.3:c.7306C>T	p.Gln2436Ter	p.Q2436*	ENST00000375759	NM_015001.2	2436	Cag/Tag	11/15	0.3678923125327	3	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	1	0.3678923125327	3		491	685	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385378	4385378	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	89	410	0	ENST00000261254.3:c.403G>T	p.Glu135Ter	p.E135*	ENST00000261254	NM_001759.3	135	Gag/Tag	2/5	0.3678923125327	3	FACETS	0.938	0.832	1	0.469	0.416	0.525	CLONAL	1	TRUE	1	0.3678923125327	3		410	611	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347281	89347281	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1327231451	NA	P-0066862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	49	439	0	ENST00000301030.4:c.5669C>T	p.Pro1890Leu	p.P1890L	ENST00000301030	NM_001256183.1	1890	cCt/cTt	9/13	0.3678923125327	3	FACETS	0.54	0.457	0.632	0.27	0.228	0.316	SUBCLONAL	1	TRUE	1	0.3678923125327	3		439	584	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687112	37687112	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	94	402	0	ENST00000447079.4:c.4016G>T	p.Gly1339Val	p.G1339V	ENST00000447079	NM_015083.1	1339	gGa/gTa	14/14	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.3678923125327	NA		402	583	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879296	56879296	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	51	315	0	ENST00000519728.1:c.813G>T	p.Lys271Asn	p.K271N	ENST00000519728	NM_002350.3	271	aaG/aaT	9/13	0.188106981628004	5	FACETS	0.754	0.64	0.878			1	INDETERMINATE	1	TRUE	NA	0.3678923125327	5		315	571	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573760	41573760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753072432	NA	P-0066862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	55	483	0	ENST00000263253.7:c.6045G>A	p.Met2015Ile	p.M2015I	ENST00000263253	NM_001429.3	2015	atG/atA	31/31	0.3678923125327	3	FACETS	0.538	0.459	0.624	0.269	0.229	0.312	SUBCLONAL	1	TRUE	1	0.3678923125327	3		483	658	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873688	35873688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	29	284	0	ENST00000216797.5:c.163G>A	p.Glu55Lys	p.E55K	ENST00000216797	NM_020529.2	55	Gag/Aag	1/6	0.3678923125327	5	FACETS	0.447	0.358	0.549	0.149	0.119	0.183	SUBCLONAL	1	TRUE	2	0.3678923125327	5		284	547	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727466	88727466	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	61	423	0	ENST00000360948.2:c.313C>A	p.Leu105Ile	p.L105I	ENST00000360948	NM_001012338.2	105	Ctt/Att	3/19	0.312148548618823	4	FACETS	0.768	0.662	0.882	0.256	0.22	0.294	SUBCLONAL	1	TRUE	1	0.3678923125327	4		423	591	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658361	117658361	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	21	421	0	ENST00000368508.3:c.5222C>A	p.Ser1741Ter	p.S1741*	ENST00000368508	NM_002944.2	1741	tCa/tAa	31/43	0.3678923125327	5	FACETS	0.509	0.392	0.646	0.17	0.13	0.216	SUBCLONAL	1	TRUE	2	0.3678923125327	5		421	348	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0066932-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	12	269	1	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.824	1	1	0.824	1	CLONAL	1	TRUE	1	0.16	2		270	119	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131411	202131411	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs777784105	NA	P-0066932-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	11	572	0	ENST00000358485.4:c.379C>T	p.Arg127Ter	p.R127*	ENST00000358485	NM_001080125.1	127	Cga/Tga	2/9	0.150101348010108	1	FACETS	0.325	0.223	0.453	0.325	0.223	0.453	SUBCLONAL	1	TRUE	0	0.16	1		572	389	SUCCESS
PHF6	84295	MSKCC	GRCh37	X	133547563	133547563	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066932-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	21	266	0	ENST00000332070.3:c.461C>T	p.Ser154Leu	p.S154L	ENST00000332070	NM_032458.2	154	tCa/tTa	6/10	1	2	FACETS	0.911	0.703	1	0.911	0.703	1	CLONAL	1	TRUE	1	0.16	2		266	288	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066983-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	36	446	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.595	0.493	0.708	0.595	0.493	0.708	SUBCLONAL	1	TRUE	1	0.532718425588912	2		446	227	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409092	4409092	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1199884235	NA	P-0066983-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	66	554	0	ENST00000261254.3:c.787C>T	p.Gln263Ter	p.Q263*	ENST00000261254	NM_001759.3	263	Cag/Tag	5/5	1	2	FACETS	0.427	0.371	0.488	0.427	0.371	0.488	SUBCLONAL	1	TRUE	1	0.532718425588912	2		554	580	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917681	178917681	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066983-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	57	342	0	ENST00000263967.3:c.556G>A	p.Asp186Asn	p.D186N	ENST00000263967	NM_006218.2	186	Gat/Aat	3/21	1	2	FACETS	0.65	0.561	0.747	0.65	0.561	0.747	SUBCLONAL	1	TRUE	1	0.532718425588912	2		342	329	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123627	11123627	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066983-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	55	459	0	ENST00000358026.2:c.2277C>G	p.Ile759Met	p.I759M	ENST00000358026	NM_001128849.1	759	atC/atG	16/36	0.532718425588912	3	FACETS	0.476	0.407	0.552	0.238	0.203	0.276	SUBCLONAL	1	TRUE	1	0.532718425588912	3		459	549	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0066984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	69	797	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.216525758161531	2		797	543	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0066984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	124	418	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.216525758161531	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.216525758161531	2		418	497	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0066984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	39	348	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.681	0.564	0.812	0.681	0.564	0.812	SUBCLONAL	1	TRUE	1	0.216525758161531	2		348	529	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372518	55372518	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	56	504	0	ENST00000297316.4:c.1208G>T	p.Ser403Ile	p.S403I	ENST00000297316	NM_022454.3	403	aGc/aTc	2/2	1	2	FACETS	0.956	0.819	1	0.956	0.819	1	CLONAL	1	TRUE	1	0.216525758161531	2		504	541	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685286	89685286	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	45	360	0	ENST00000371953.3:c.181C>A	p.His61Asn	p.H61N	ENST00000371953	NM_000314.4	61	Cat/Aat	3/9	1	2	FACETS	0.875	0.736	1	0.875	0.736	1	CLONAL	1	TRUE	1	0.216525758161531	2		360	475	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	38	390	0	ENST00000256196.4:c.68G>A	p.Gly23Asp	p.G23D	ENST00000256196		23	gGc/gAc	1/6	1	2	FACETS	0.902	0.747	1	0.902	0.747	1	CLONAL	1	TRUE	1	0.216525758161531	2		390	389	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813307	102813307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764732420	NA	P-0066987-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	106	533	0	ENST00000307046.8:c.382G>A	p.Asp128Asn	p.D128N	ENST00000307046	NM_001111285.1	128	Gac/Aac	3/4	0.510256578641361	3	FACETS	1	0.959	1	0.562	0.506	0.62	CLONAL	1	TRUE	1	0.510256578641361	3		533	464	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499362	89499363	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0066987-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	138	618	0	ENST00000336596.2:c.2538dup	p.Met847HisfsTer26	p.M847Hfs*26	ENST00000336596	NM_005233.5	844	-/C	15/17	0.510256578641361	3	FACETS	1	0.979	1	0.616	0.563	0.671	CLONAL	1	TRUE	1	0.510256578641361	3		618	551	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905944	50905944	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755457889	NA	P-0066987-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	214	645	0	ENST00000440232.2:c.916C>T	p.Arg306Cys	p.R306C	ENST00000440232	NM_002691.3	306	Cgc/Tgc	8/27	0.47291158144364	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.510256578641361	4		645	555	SUCCESS
APC	324	MSKCC	GRCh37	5	112173561	112173561	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066987-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	298	618	0	ENST00000257430.4:c.2274del	p.Ala759ProfsTer2	p.A759Pfs*2	ENST00000257430	NM_000038.5	757	cAa/ca	16/16	0.510256578641361	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	0	0.510256578641361	3		618	471	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575148	64575148	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1565647197	NA	P-0066988-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	260	745	0	ENST00000312049.6:c.659G>A	p.Trp220Ter	p.W220*	ENST00000312049	NM_130799.2	220	tGg/tAg	4/10	0.598041335405077	2	FACETS	0.991	0.945	1	0.991	0.945	1	CLONAL	2	TRUE	0	0.608671633577292	2		745	431	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288363	33288363	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066988-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	25	694	0	ENST00000374542.5:c.1045G>T	p.Asp349Tyr	p.D349Y	ENST00000374542	NM_001141970.1	349	Gac/Tac	4/8	0.598041335405077	2	FACETS	0.166	0.13	0.207	0.083	0.065	0.104	SUBCLONAL	1	TRUE	0	0.608671633577292	2		694	496	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286878	33286885	+	frameshift_variant	Frame_Shift_Del	DEL	CCACCCTC	CCACCCTC	-	novel	NA	P-0066988-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	232	763	0	ENST00000374542.5:c.2052_2059del	p.Arg685LeufsTer53	p.R685Lfs*53	ENST00000374542	NM_001141970.1	684	acGAGGGTGGac/acac	7/8	0.598041335405077	2	FACETS	0.794	0.75	0.839	0.794	0.75	0.839	SUBCLONAL	2	TRUE	0	0.608671633577292	2		763	480	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922909	44922910	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0066988-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	24	313	0	ENST00000377967.4:c.1771_1772del	p.Ile591PhefsTer5	p.I591Ffs*5	ENST00000377967	NM_021140.2	590	acTAtt/actt	16/29	0.582260766585029	2	FACETS	0.248	0.194	0.31			1	SUBCLONAL	1	TRUE	NA	0.608671633577292	2		313	318	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0066989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	157	532	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.593195102305207	1	FACETS	0.942	0.875	1	0.942	0.875	1	CLONAL	1	TRUE	0	0.630582461180046	1		532	362	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0066989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	103	262	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.315422192213605	1	FACETS	0.844	0.768	0.922	0.844	0.768	0.922	INDETERMINATE	1	TRUE	0	0.630582461180046	1		262	265	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745587	162745587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751660319	NA	P-0066989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	157	519	1	ENST00000367921.3:c.2002C>T	p.Arg668Cys	p.R668C	ENST00000367921	NM_006182.2	668	Cgc/Tgc	15/18	1	2	FACETS	0.98	0.904	1	0.98	0.904	1	CLONAL	1	TRUE	1	0.630582461180046	2		520	508	SUCCESS
APC	324	MSKCC	GRCh37	5	112128207	112128207	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	56	406	0	ENST00000257430.4:c.712del	p.Gln238LysfsTer55	p.Q238Kfs*55	ENST00000257430	NM_000038.5	237	tCc/tc	7/16	0.315422192213605	1	FACETS	0.332	0.286	0.383	0.332	0.286	0.383	INDETERMINATE	1	TRUE	0	0.630582461180046	1		406	366	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910798	114910798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs951950988	NA	P-0066989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	200	543	0	ENST00000543371.1:c.917C>T	p.Thr306Met	p.T306M	ENST00000543371	NM_001198531.1	306	aCg/aTg	9/14	1	2	FACETS	0.963	0.896	1	0.963	0.896	1	CLONAL	1	TRUE	1	0.630582461180046	2		543	659	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639093	3639093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775915651	NA	P-0066989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	142	494	0	ENST00000294008.3:c.4546G>A	p.Gly1516Arg	p.G1516R	ENST00000294008	NM_032444.2	1516	Ggg/Agg	12/15	0.612749184281302	2	FACETS	0.912	0.836	0.989	0.456	0.418	0.495	CLONAL	1	TRUE	0	0.630582461180046	2		494	494	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712574	52712574	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	161	395	0	ENST00000394830.3:c.178T>G	p.Tyr60Asp	p.Y60D	ENST00000394830	NM_018313.4	60	Tat/Gat	3/30	1	2	FACETS	0.934	0.861	1	0.934	0.861	1	CLONAL	1	TRUE	1	0.630582461180046	2		395	547	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56872928	56872928	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	112	464	0	ENST00000308159.5:c.2083T>A	p.Leu695Met	p.L695M	ENST00000308159	NM_014669.4	695	Ttg/Atg	19/22	0.60978584962678	2	FACETS	0.723	0.654	0.796	0.362	0.327	0.398	SUBCLONAL	1	TRUE	0	0.630582461180046	2		464	491	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978467	2978467	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0066989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	107	309	0	ENST00000396946.4:c.865-2A>T		p.X289_splice	ENST00000396946	NM_032415.4	289			0.630582461180046	3	FACETS	1	0.928	1	0.517	0.466	0.569	CLONAL	1	TRUE	1	0.630582461180046	3		309	432	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0066990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	23	425	0	ENST00000304494.5:c.151-1G>A		p.X51_splice	ENST00000304494	NM_000077.4	51			0.541095500314191	1	FACETS	0.156	0.121	0.196	0.156	0.121	0.196	SUBCLONAL	1	TRUE	0	0.541095500314191	1		425	398	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665655	86665655	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	88	315	0	ENST00000274376.6:c.1636C>T	p.Gln546Ter	p.Q546*	ENST00000274376	NM_002890.2	546	Cag/Tag	12/25	1	2	FACETS	0.847	0.756	0.943	0.847	0.756	0.943	CLONAL	1	TRUE	1	0.541095500314191	2		315	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573988	7573988	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	133	431	0	ENST00000269305.4:c.1039G>A	p.Ala347Thr	p.A347T	ENST00000269305	NM_001126112.2	347	Gcc/Acc	10/11	0.541095500314191	1	FACETS	0.881	0.808	0.956	0.881	0.808	0.956	CLONAL	1	TRUE	0	0.541095500314191	1		431	407	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000904-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	30	663	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.789	0.635	0.965	0.789	0.635	0.965	CLONAL	1	TRUE	1	0.16	2		663	475	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29090061	29090061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540635787	NA	P-0000904-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	16	92	0	ENST00000328354.6:c.1420C>T	p.Arg474Cys	p.R474C	ENST00000328354	NM_007194.3	474	Cgt/Tgt	13/15	1	2	FACETS	0.769	0.574	0.998	1	0.9	1	CLONAL	2	TRUE	1	0.16	2		92	130	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004226-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	98	663	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		663	274	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158626	26158626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772836222	NA	P-0004226-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	125	203	0	ENST00000289316.2:c.229G>A	p.Glu77Lys	p.E77K	ENST00000289316	NM_138720.2	77	Gag/Aag	1/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		203	276	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0004226-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	69	303	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		303	157	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588849	69588849	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004226-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	174	404	0	ENST00000168712.1:c.387C>A	p.Phe129Leu	p.F129L	ENST00000168712	NM_002007.2	129	ttC/ttA	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		404	570	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398262	25398262	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913538	NA	P-0004226-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	72	338	0	ENST00000311936.3:c.57G>C	p.Leu19Phe	p.L19F	ENST00000311936	NM_004985.3	19	ttG/ttC	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		338	148	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230772	46230772	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004226-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	70	480	0	ENST00000334344.6:c.1021G>C	p.Glu341Gln	p.E341Q	ENST00000334344	NM_152641.2	341	Gag/Cag	8/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		480	191	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168983	11168983	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004226-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	26	427	0	ENST00000358026.2:c.4573G>C	p.Glu1525Gln	p.E1525Q	ENST00000358026	NM_001128849.1	1525	Gag/Cag	32/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		427	409	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170834	11170834	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004226-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	34	493	0	ENST00000358026.2:c.4978G>A	p.Asp1660Asn	p.D1660N	ENST00000358026	NM_001128849.1	1660	Gac/Aac	35/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		493	433	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170861	11170861	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1298648044	NA	P-0004226-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	27	457	0	ENST00000358026.2:c.5005G>A	p.Glu1669Lys	p.E1669K	ENST00000358026	NM_001128849.1	1669	Gag/Aag	35/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		457	410	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645693	12645693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397516827	NA	P-0004226-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	191	550	0	ENST00000251849.4:c.776C>T	p.Ser259Phe	p.S259F	ENST00000251849	NM_002880.3	259	tCc/tTc	7/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		550	443	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004226-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	140	663	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		663	333	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158626	26158626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772836222	NA	P-0004226-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	99	203	0	ENST00000289316.2:c.229G>A	p.Glu77Lys	p.E77K	ENST00000289316	NM_138720.2	77	Gag/Aag	1/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		203	223	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0004226-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	103	303	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		303	237	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588849	69588849	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004226-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	199	404	0	ENST00000168712.1:c.387C>A	p.Phe129Leu	p.F129L	ENST00000168712	NM_002007.2	129	ttC/ttA	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		404	809	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398262	25398262	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913538	NA	P-0004226-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	107	338	0	ENST00000311936.3:c.57G>C	p.Leu19Phe	p.L19F	ENST00000311936	NM_004985.3	19	ttG/ttC	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		338	240	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230772	46230772	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004226-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	146	480	0	ENST00000334344.6:c.1021G>C	p.Glu341Gln	p.E341Q	ENST00000334344	NM_152641.2	341	Gag/Cag	8/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		480	293	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168983	11168983	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004226-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	76	427	0	ENST00000358026.2:c.4573G>C	p.Glu1525Gln	p.E1525Q	ENST00000358026	NM_001128849.1	1525	Gag/Cag	32/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		427	441	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170834	11170834	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004226-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	92	493	0	ENST00000358026.2:c.4978G>A	p.Asp1660Asn	p.D1660N	ENST00000358026	NM_001128849.1	1660	Gac/Aac	35/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		493	503	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170861	11170861	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1298648044	NA	P-0004226-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	87	457	0	ENST00000358026.2:c.5005G>A	p.Glu1669Lys	p.E1669K	ENST00000358026	NM_001128849.1	1669	Gag/Aag	35/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		457	481	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645693	12645693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397516827	NA	P-0004226-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	240	550	0	ENST00000251849.4:c.776C>T	p.Ser259Phe	p.S259F	ENST00000251849	NM_002880.3	259	tCc/tTc	7/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		550	548	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135804253	135804253	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004226-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	34	580	0	ENST00000298552.3:c.7C>T	p.Gln3Ter	p.Q3*	ENST00000298552	NM_001162426.1	3	Caa/Taa	3/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		580	360	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0005813-T10-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	10	438	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		438	23	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0006660-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	76	602	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.21	2		602	505	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0006660-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	13	132	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.452	0.322	0.611	0.452	0.322	0.611	SUBCLONAL	1	TRUE	1	0.21	2		132	274	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717615	89717615	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909227	NA	P-0006660-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	72	271	0	ENST00000371953.3:c.640C>T	p.Gln214Ter	p.Q214*	ENST00000371953	NM_000314.4	214	Cag/Tag	7/9	1	2	FACETS	0.857	0.753	0.969	1	0.979	1	CLONAL	2	TRUE	1	0.21	2		271	400	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038623	14038623	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006660-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	56	237	0	ENST00000311895.7:c.1948G>C	p.Asp650His	p.D650H	ENST00000311895	NM_005236.2	650	Gat/Cat	10/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.21	2		237	404	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856106	151856106	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs772980746	NA	P-0006660-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	58	363	0	ENST00000262189.6:c.11512C>G	p.Pro3838Ala	p.P3838A	ENST00000262189	NM_170606.2	3838	Cca/Gca	44/59	1	2	FACETS	0.986	0.848	1	0.986	0.848	1	CLONAL	1	TRUE	1	0.21	2		363	560	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215341	123215341	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006660-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	37	223	0	ENST00000218089.9:c.2887C>T	p.Gln963Ter	p.Q963*	ENST00000218089	NM_001042749.1	963	Cag/Tag	28/35	1	2	FACETS	0.998	0.825	1	0.998	0.825	1	CLONAL	1	TRUE	1	0.21	2		223	353	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020808	26020808	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs377197123	NA	P-0006660-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	85	722	0	ENST00000357647.3:c.91C>G	p.Pro31Ala	p.P31A	ENST00000357647	NM_003529.2	31	Ccg/Gcg	1/1	0.193683641024531	3	FACETS	1	0.926	1	0.533	0.47	0.6	CLONAL	1	TRUE	1	0.21	3		722	839	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56882287	56882287	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006660-T09-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	45	357	0	ENST00000519728.1:c.985G>A	p.Asp329Asn	p.D329N	ENST00000519728	NM_002350.3	329	Gat/Aat	10/13	1	2	FACETS	0.763	0.64	0.898	0.763	0.64	0.898	SUBCLONAL	1	TRUE	1	0.21	2		357	562	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436504	110436504	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760629200	NA	P-0006687-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	40	704	0	ENST00000375856.3:c.1897G>A	p.Gly633Arg	p.G633R	ENST00000375856	NM_003749.2	633	Gga/Aga	1/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		704	426	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343507	343507	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567261095	NA	P-0006687-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	48	485	0	ENST00000262320.3:c.2167C>T	p.Arg723Ter	p.R723*	ENST00000262320	NM_003502.3	723	Cga/Tga	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		485	254	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836642	89836642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747723074	NA	P-0006687-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	119	549	0	ENST00000389301.3:c.2248G>A	p.Val750Met	p.V750M	ENST00000389301	NM_000135.2	750	Gtg/Atg	25/43	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		549	277	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0006687-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	107	519	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		519	240	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942605	17942605	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006687-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	40	432	0	ENST00000458235.1:c.2683C>T	p.Arg895Cys	p.R895C	ENST00000458235	NM_000215.3	895	Cgc/Tgc	20/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		432	226	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266016	41266403	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	In_Frame_Del	DEL	GCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAAT	GCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAAT	-	novel	NA	P-0006687-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	61	479	0	ENST00000349496.5:c.18_242-37del		p.A5_D81del	ENST00000349496	NM_001904.3	5		3/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		479	235	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508490	106508490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006687-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	43	565	0	ENST00000359195.3:c.484G>A	p.Val162Ile	p.V162I	ENST00000359195	NM_002649.2	162	Gtc/Atc	2/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		565	358	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0008424-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	70	118	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.535297808359917	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.535297808359917	1		118	170	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760819	133760819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769953778	NA	P-0008424-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	158	368	0	ENST00000318560.5:c.3142G>A	p.Glu1048Lys	p.E1048K	ENST00000318560	NM_005157.4	1048	Gag/Aag	11/11	1	2	FACETS	0.82	0.753	0.89	0.82	0.753	0.89	CLONAL	1	TRUE	1	0.535297808359917	2		368	720	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772229	68772230	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCTGCCA	novel	NA	P-0008424-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	181	337	0	ENST00000261769.5:c.84_91dup	p.Gly31AlafsTer28	p.G31Afs*28	ENST00000261769	NM_004360.3	26	-/CCCTGCCA	2/16	0.535297808359917	1	FACETS	0.962	0.894	1	0.962	0.894	1	CLONAL	1	TRUE	0	0.535297808359917	1		337	515	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373658	118373658	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008424-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	276	446	0	ENST00000534358.1:c.7051A>T	p.Ile2351Phe	p.I2351F	ENST00000534358	NM_005933.3	2351	Atc/Ttc	27/36	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.535297808359917	2		446	973	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0008885-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	492	372	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.657244077811451	2	FACETS	0.988	0.957	1	0.988	0.957	1	CLONAL	2	TRUE	0	0.678509222100248	2		372	734	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775907	9775907	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008885-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	142	396	0	ENST00000377346.4:c.371G>A	p.Gly124Asp	p.G124D	ENST00000377346	NM_005026.3	124	gGc/gAc	5/24	1	2	FACETS	0.868	0.797	0.942	0.868	0.797	0.942	CLONAL	1	TRUE	1	0.678509222100248	2		396	482	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25362828	25362828	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs104894362	NA	P-0008885-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	539	279	0	ENST00000311936.3:c.468C>G	p.Phe156Leu	p.F156L	ENST00000311936	NM_004985.3	156	ttC/ttG	5/5	0.496670987306601	4	FACETS	0.986	0.953	1	0.986	0.953	1	CLONAL	3	TRUE	1	0.678509222100248	4		279	902	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371708	225371708	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009420-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	28	413	0	ENST00000264414.4:c.896T>G	p.Met299Arg	p.M299R	ENST00000264414	NM_003590.4	299	aTg/aGg	7/16	1	2	FACETS	0.721	0.578	0.884	0.721	0.578	0.884	SUBCLONAL	1	TRUE	1	0.257882883465245	2		413	301	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645968	67645968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009420-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	24	511	0	ENST00000264010.4:c.896G>A	p.Cys299Tyr	p.C299Y	ENST00000264010	NM_006565.3	299	tGt/tAt	4/12	1	2	FACETS	0.449	0.351	0.561	0.449	0.351	0.561	SUBCLONAL	1	TRUE	1	0.257882883465245	2		511	415	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216476	108216477	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587782558	NA	P-0009420-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	25	322	0	ENST00000278616.4:c.8432dup	p.Ser2812ValfsTer3	p.S2812Vfs*3	ENST00000278616	NM_000051.3	2809	caa/cAaa	58/63	0.21396683991499	1	FACETS	0.778	0.617	0.962	0.778	0.617	0.962	CLONAL	1	TRUE	0	0.257882883465245	1		322	217	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190742011	190742011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377603311	NA	P-0009420-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	46	392	0	ENST00000441310.2:c.2648G>A	p.Arg883His	p.R883H	ENST00000441310	NM_000534.4	883	cGt/cAt	13/13	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.257882883465245	2		392	306	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420269	88420269	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009420-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	27	607	0	ENST00000360948.2:c.2417G>T	p.Cys806Phe	p.C806F	ENST00000360948	NM_001012338.2	806	tGc/tTc	19/19	1	2	FACETS	0.511	0.406	0.631	0.511	0.406	0.631	SUBCLONAL	1	TRUE	1	0.257882883465245	2		607	410	SUCCESS
APC	324	MSKCC	GRCh37	5	112175784	112175784	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009420-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	44	567	0	ENST00000257430.4:c.4493A>T	p.Asp1498Val	p.D1498V	ENST00000257430	NM_000038.5	1498	gAt/gTt	16/16	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.257882883465245	2		567	336	SUCCESS
APC	324	MSKCC	GRCh37	5	112175783	112175783	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009420-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	43	566	0	ENST00000257430.4:c.4492del	p.Asp1498MetfsTer9	p.D1498Mfs*9	ENST00000257430	NM_000038.5	1498	Gat/at	16/16	1	2	FACETS	0.99	0.831	1	0.99	0.831	1	CLONAL	1	TRUE	1	0.257882883465245	2		566	337	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913514	NA	P-0010949-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	42	178	0	ENST00000288135.5:c.2466T>G	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaG	17/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		178	87	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593583	55593603	+	protein_altering_variant	In_Frame_Del	DEL	AACCCATGTATGAAGTACAGT	AACCCATGTATGAAGTACAGT	TAC	novel	NA	P-0010949-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	70	0	0	ENST00000288135.5:c.1649_1669delinsTAC	p.Lys550_Trp557delinsIleArg	p.K550_W557delinsIR	ENST00000288135	NM_000222.2	550	aAACCCATGTATGAAGTACAGTgg/aTACgg	11/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		0	140	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598110	55598110	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010949-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	144	259	0	ENST00000288135.5:c.2307G>C	p.Leu769Phe	p.L769F	ENST00000288135	NM_000222.2	769	ttG/ttC	16/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		259	359	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0012428-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	344	312	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.615822102789891	3	FACETS	0.914	0.87	0.959	0.914	0.87	0.959	CLONAL	2	TRUE	1	0.615822102789891	3		312	799	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570432	95570433	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs886037700	NA	P-0012428-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	363	276	0	ENST00000393063.1:c.3300dup	p.Ser1101IlefsTer3	p.S1101Ifs*3	ENST00000393063	NM_030621.3	1100	-/A	22/28	0.615822102789891	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.615822102789891	3		276	760	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032254	26032254	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012428-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	294	521	0	ENST00000244661.2:c.35C>T	p.Thr12Ile	p.T12I	ENST00000244661	NM_003537.3	12	aCc/aTc	1/1	0.106311366207469	4	FACETS	0.832	0.785	0.88	0.832	0.785	0.88	INDETERMINATE	2	TRUE	2	0.615822102789891	4		521	927	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0014569-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	54	575	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.15	2		575	706	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0014569-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	191	438	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.3	4	FACETS	0.889	0.823	0.957	1	0.982	1	CLONAL	4	TRUE	1	0.15	4		438	824	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284979	15284979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774475688	NA	P-0014569-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	38	365	0	ENST00000263388.2:c.4636C>T	p.Arg1546Cys	p.R1546C	ENST00000263388	NM_000435.2	1546	Cgc/Tgc	25/33	1	2	FACETS	0.897	0.74	1	0.897	0.74	1	CLONAL	1	TRUE	1	0.15	2		365	565	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009359	69009359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755479314	NA	P-0014569-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	38	358	0	ENST00000288368.4:c.2476G>A	p.Asp826Asn	p.D826N	ENST00000288368	NM_024870.2	826	Gac/Aac	22/40	1	2	FACETS	0.877	0.723	1	0.877	0.723	1	CLONAL	1	TRUE	1	0.15	2		358	578	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459688	40459688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780900178	NA	P-0014569-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	55	496	0	ENST00000345506.4:c.1853G>A	p.Arg618His	p.R618H	ENST00000345506	NM_003152.3	618	cGc/cAc	16/20	1	2	FACETS	0.929	0.793	1	0.929	0.793	1	CLONAL	1	TRUE	1	0.15	2		496	789	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797429	45797429	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151316420	NA	P-0014569-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	53	525	0	ENST00000450313.1:c.1090C>T	p.Arg364Cys	p.R364C	ENST00000450313	NM_012222.2	364	Cgc/Tgc	12/16	0.105672940519821	3	FACETS	0.984	0.837	1	0.492	0.418	0.573	CLONAL	1	TRUE	1	0.15	3		525	772	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040983	47040983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556779506	NA	P-0014569-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	34	501	0	ENST00000377604.3:c.1513C>T	p.Pro505Ser	p.P505S	ENST00000377604	NM_001204468.1	505	Cct/Tct	14/24	1	2	FACETS	0.667	0.543	0.807	0.667	0.543	0.807	SUBCLONAL	1	TRUE	1	0.15	2		501	680	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242478	+	protein_altering_variant	In_Frame_Del	DEL	GGAATTAAGAGAAG	GGAATTAAGAGAAG	AAATC	novel	NA	P-0014569-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	178	370	0	ENST00000275493.2:c.2235_2248delinsAAATC	p.Glu746_Ala750delinsAsnPro	p.E746_A750delinsNP	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGca/aaAAATCca	19/28	0.3	4	FACETS	1	0.927	1	1	0.987	1	CLONAL	4	TRUE	1	0.15	4		370	681	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954326	48954326	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	C	C	TG	novel	NA	P-0014569-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	54	266	0	ENST00000267163.4:c.1447delinsTG	p.His483Ter	p.H483*	ENST00000267163	NM_000321.2	483	Cat/TGat	16/27	0.123387421400812	3	FACETS	1	0.914	1	0.729	0.625	0.841	CLONAL	2	TRUE	0	0.15	3		266	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0016618-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	44	594	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.272803935320721	6	FACETS	1	0.929	1	0.3	0.252	0.354	CLONAL	1	FALSE	2	0.272803935320721	6		594	415	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880257	37880257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016618-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	46	593	0	ENST00000269571.5:c.2301C>G	p.Ile767Met	p.I767M	ENST00000269571		767	atC/atG	19/27	0.256434262695427	5	FACETS	1	0.957	1	0.477	0.403	0.558	CLONAL	1	FALSE	2	0.272803935320721	5		593	332	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263956	104263956	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016618-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	24	515	1	ENST00000369902.3:c.47C>T	p.Pro16Leu	p.P16L	ENST00000369902	NM_016169.3	16	cCg/cTg	1/12	0.272803935320721	5	FACETS	0.715	0.56	0.893	0.357	0.28	0.447	SUBCLONAL	1	FALSE	3	0.272803935320721	5		516	347	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016618-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	24	482	0	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	0.192212198805631	1	FACETS	0.553	0.434	0.689	0.553	0.434	0.689	SUBCLONAL	1	FALSE	0	0.272803935320721	1		482	275	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968852	15968852	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016618-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	38	571	0	ENST00000268712.3:c.4898G>C	p.Arg1633Thr	p.R1633T	ENST00000268712	NM_006311.3	1633	aGa/aCa	33/46	0.25827664011612	0	FACETS	0.564	0.467	0.672			1	SUBCLONAL	1	FALSE	0	0.272803935320721	0		571	359	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2164199	2164199	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016618-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	37	509	0	ENST00000398665.3:c.16G>C	p.Glu6Gln	p.E6Q	ENST00000398665	NM_032482.2	6	Gag/Cag	1/28	0.272803935320721	3	FACETS	0.788	0.651	0.942			1	CLONAL	1	FALSE	NA	0.272803935320721	3		509	391	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974761	21974816	+	frameshift_variant	Frame_Shift_Del	DEL	CCGGGCCGCGGCCGTGGCCAGCCAGTCAGCCGAAGGCTCCATGCTGCTCCCCGCCG	CCGGGCCGCGGCCGTGGCCAGCCAGTCAGCCGAAGGCTCCATGCTGCTCCCCGCCG	-	novel	NA	P-0016618-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	88	706	0	ENST00000304494.5:c.11_66del	p.Ala4GlyfsTer21	p.A4Gfs*21	ENST00000304494	NM_000077.4	4	gCGGCGGGGAGCAGCATGGAGCCTTCGGCTGACTGGCTGGCCACGGCCGCGGCCCGG/g	1/3	0.202664030044088	0	FACETS	0.762	0.682	0.845			1	SUBCLONAL	2	FALSE	0	0.272803935320721	0		706	308	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942711	44942712	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0016618-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	14	372	0	ENST00000377967.4:c.3293dup	p.Leu1098PhefsTer5	p.L1098Ffs*5	ENST00000377967	NM_021140.2	1097	-/T	23/29	0.272803935320721	1	FACETS	0.441	0.319	0.588	0.441	0.319	0.588	SUBCLONAL	1	FALSE	0	0.272803935320721	1		372	201	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913396	NA	P-0017591-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	89	343	0	ENST00000349496.5:c.95A>G	p.Asp32Gly	p.D32G	ENST00000349496	NM_001904.3	32	gAc/gGc	3/15	0.327834591062531	3	FACETS	0.715	0.634	0.802	0.358	0.317	0.401	SUBCLONAL	1	TRUE	1	0.439845837553968	3		343	690	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582133	95582133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752424727	NA	P-0017591-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	39	348	0	ENST00000393063.1:c.1778C>T	p.Ser593Leu	p.S593L	ENST00000393063	NM_030621.3	593	tCg/tTg	12/28	0.439845837553968	2	FACETS	0.303	0.251	0.362	0.152	0.125	0.181	SUBCLONAL	1	TRUE	0	0.439845837553968	2		348	585	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401616	401616	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017591-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	37	406	0	ENST00000380956.4:c.938G>A	p.Arg313Lys	p.R313K	ENST00000380956	NM_001195286.1	313	aGg/aAg	7/9	0.280151419842485	3	FACETS	0.334	0.275	0.401	0.167	0.137	0.201	SUBCLONAL	1	TRUE	1	0.439845837553968	3		406	614	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018462-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	47	324	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	1	2	FACETS	0.818	0.691	0.957	0.818	0.691	0.957	CLONAL	1	FALSE	1	0.260067789217601	2		324	442	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0018462-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	24	250	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.403	0.315	0.505	0.403	0.315	0.505	SUBCLONAL	1	FALSE	1	0.260067789217601	2		250	458	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248120	110248120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018462-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	42	225	1	ENST00000374672.4:c.1352C>T	p.Thr451Met	p.T451M	ENST00000374672	NM_004235.4	451	aCg/aTg	5/5	1	2	FACETS	0.767	0.641	0.907	0.767	0.641	0.907	CLONAL	1	FALSE	1	0.260067789217601	2		226	421	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221243	1221243	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1057520606	NA	P-0018462-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	105	234	1	ENST00000326873.7:c.766G>T	p.Glu256Ter	p.E256*	ENST00000326873	NM_000455.4	256	Gaa/Taa	6/10	1	2	FACETS	0.792	0.712	0.875	1	0.984	1	SUBCLONAL	2	FALSE	1	0.260067789217601	2		235	510	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943776	9943776	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018462-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	57	290	0	ENST00000330684.3:c.1165G>T	p.Val389Leu	p.V389L	ENST00000330684	NM_001134407.1	389	Gtg/Ttg	5/13	1	2	FACETS	0.861	0.74	0.994	0.861	0.74	0.994	CLONAL	1	FALSE	1	0.260067789217601	2		290	509	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39251221	39251221	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018462-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	35	193	0	ENST00000402219.2:c.1132A>T	p.Thr378Ser	p.T378S	ENST00000402219	NM_005633.3	378	Aca/Tca	9/23	1	2	FACETS	0.979	0.806	1	0.979	0.806	1	CLONAL	1	FALSE	1	0.260067789217601	2		193	275	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582150	189582150	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs576751351	NA	P-0018462-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	65	267	0	ENST00000264731.3:c.709G>A	p.Val237Ile	p.V237I	ENST00000264731	NM_003722.4	237	Gtc/Atc	5/14	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	FALSE	1	0.260067789217601	2		267	449	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748369	162748369	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0018462-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	99	247	0	ENST00000367921.3:c.2284-1G>T		p.X762_splice	ENST00000367921	NM_006182.2	762			0.219958001680657	3	FACETS	0.965	0.866	1	0.965	0.866	1	CLONAL	2	FALSE	1	0.260067789217601	3		247	446	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858829	78858829	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018462-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	47	320	0	ENST00000306801.3:c.1864G>T	p.Ala622Ser	p.A622S	ENST00000306801	NM_020761.2	622	Gcc/Tcc	17/34	1	2	FACETS	0.71	0.599	0.832	0.71	0.599	0.832	SUBCLONAL	1	FALSE	1	0.260067789217601	2		320	509	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245298	53245298	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018462-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	50	160	0	ENST00000375401.3:c.739G>T	p.Gly247Cys	p.G247C	ENST00000375401	NM_004187.3	247	Ggc/Tgc	6/26	1	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	0	0.260067789217601	1		160	265	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143324208	143324208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0018462-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	33	157	0	ENST00000262992.4:c.256-1G>A		p.X86_splice	ENST00000262992	NM_001101669.1	86			1	2	FACETS	0.872	0.713	1	0.872	0.713	1	CLONAL	1	FALSE	1	0.260067789217601	2		157	291	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050409	176050409	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018462-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	45	216	0	ENST00000367669.3:c.1156G>C	p.Ala386Pro	p.A386P	ENST00000367669	NM_022457.5	386	Gca/Cca	11/20	0.219958001680657	3	FACETS	1	0.931	1	0.598	0.504	0.7	CLONAL	1	FALSE	1	0.260067789217601	3		216	327	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18762488	18762488	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018462-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	45	200	0	ENST00000266497.5:c.3984G>T	p.Lys1328Asn	p.K1328N	ENST00000266497		1328	aaG/aaT	29/31	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	FALSE	1	0.260067789217601	2		200	337	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132973	30132973	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018462-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	51	260	0	ENST00000331968.5:c.628A>T	p.Thr210Ser	p.T210S	ENST00000331968	NM_002742.2	210	Act/Tct	4/18	1	2	FACETS	0.851	0.724	0.99	0.851	0.724	0.99	CLONAL	1	FALSE	1	0.260067789217601	2		260	461	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191156	2191156	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018462-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	70	298	1	ENST00000398665.3:c.410G>T	p.Gly137Val	p.G137V	ENST00000398665	NM_032482.2	137	gGg/gTg	5/28	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	FALSE	1	0.260067789217601	2		299	521	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134252	11134252	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018462-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	44	252	0	ENST00000358026.2:c.2918G>C	p.Arg973Pro	p.R973P	ENST00000358026	NM_001128849.1	973	cGg/cCg	20/36	1	2	FACETS	0.736	0.617	0.866	0.736	0.617	0.866	SUBCLONAL	1	FALSE	1	0.260067789217601	2		252	460	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79968563	79968564	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0018462-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	56	206	1	ENST00000265081.6:c.913_914delinsTT	p.Gly305Leu	p.G305L	ENST00000265081	NM_002439.4	305	GGa/TTa	6/24	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	FALSE	1	0.260067789217601	2		207	426	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956778	68956778	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018462-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	85	196	0	ENST00000288368.4:c.896G>T	p.Arg299Leu	p.R299L	ENST00000288368	NM_024870.2	299	cGg/cTg	8/40	0.219958001680657	3	FACETS	0.89	0.791	0.995	0.89	0.791	0.995	CLONAL	2	FALSE	1	0.260067789217601	3		196	415	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229478	98229478	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018462-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	49	329	0	ENST00000331920.6:c.2480G>T	p.Ser827Ile	p.S827I	ENST00000331920	NM_000264.3	827	aGt/aTt	15/24	1	2	FACETS	0.772	0.654	0.902	0.772	0.654	0.902	CLONAL	1	FALSE	1	0.260067789217601	2		329	488	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018514-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	152	286	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.860697137231407	4	FACETS	0.816	0.755	0.878	0.816	0.755	0.878	CLONAL	2	TRUE	2	0.896028573073296	4		286	394	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0018514-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	101	268	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.870142742181935	4	FACETS	0.915	0.822	1	0.305	0.274	0.338	CLONAL	1	TRUE	1	0.896028573073296	4		268	467	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216560	2216560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777525091	NA	P-0018514-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	136	536	0	ENST00000398665.3:c.2204C>T	p.Thr735Met	p.T735M	ENST00000398665	NM_032482.2	735	aCg/aTg	20/28	0.896028573073296	3	FACETS	0.951	0.872	1	0.476	0.436	0.517	CLONAL	1	TRUE	1	0.896028573073296	3		536	462	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0018514-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	508	365	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	0.870142742181935	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	1	0.896028573073296	4		365	667	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030475	47030475	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782595848	NA	P-0018514-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	141	377	0	ENST00000377604.3:c.250C>T	p.Arg84Trp	p.R84W	ENST00000377604	NM_001204468.1	84	Cgg/Tgg	4/24	0.734272760476931	5	FACETS	1	0.945	1	0.349	0.318	0.381	CLONAL	1	TRUE	2	0.896028573073296	5		377	705	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88676897	88676897	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782682	NA	P-0018514-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	233	203	0	ENST00000372037.3:c.682C>T	p.Arg228Ter	p.R228*	ENST00000372037	NM_004329.2	228	Cga/Tga	9/13	0.896028573073296	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.896028573073296	3		203	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018514-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	500	365	0	ENST00000269305.4:c.775del	p.Asp259ThrfsTer86	p.D259Tfs*86	ENST00000269305	NM_001126112.2	259	Gac/ac	7/11	0.896028573073296	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	4	TRUE	0	0.896028573073296	4		365	523	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281013	49281013	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018514-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	150	381	0	ENST00000282018.3:c.60T>A	p.Asn20Lys	p.N20K	ENST00000282018	NM_020377.2	20	aaT/aaA	1/1	0.896028573073296	7	FACETS	1	0.941	1	0.208	0.189	0.227	CLONAL	1	TRUE	2	0.896028573073296	7		381	1043	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50733602	50733602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763929433	NA	P-0018514-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	222	336	0	ENST00000307179.4:c.161G>A	p.Arg54His	p.R54H	ENST00000307179		54	cGt/cAt	3/20	0.766429732215262	4	FACETS	0.973	0.916	1	0.973	0.916	1	CLONAL	2	TRUE	2	0.896028573073296	4		336	483	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019982-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	49	543	0	ENST00000322088.6:c.548G>T	p.Arg183Leu	p.R183L	ENST00000322088	NM_014225.5	183	cGg/cTg	5/15	1	2	FACETS	0.402	0.339	0.47	0.402	0.339	0.47	SUBCLONAL	1	TRUE	1	0.371352868240704	2		543	657	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339164	116339165	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019982-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	41	354	0	ENST00000397752.3:c.27dup	p.Gly10TrpfsTer18	p.G10Wfs*18	ENST00000397752	NM_000245.2	9	cct/ccTt	2/21	0.197434325838475	3	FACETS	0.391	0.325	0.465	0.196	0.162	0.233	INDETERMINATE	1	TRUE	1	0.371352868240704	3		354	669	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0019982-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	111	361	0	ENST00000397752.3:c.3028+1G>C		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.197434325838475	3	FACETS	0.967	0.87	1	0.484	0.435	0.535	INDETERMINATE	1	TRUE	1	0.371352868240704	3		361	733	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220494	123220494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019982-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	37	383	0	ENST00000218089.9:c.3151G>A	p.Gly1051Ser	p.G1051S	ENST00000218089	NM_001042749.1	1051	Ggt/Agt	30/35	1	2	FACETS	0.371	0.305	0.445	0.371	0.305	0.445	SUBCLONAL	1	TRUE	1	0.371352868240704	2		383	537	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922293	100922293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149186732	NA	P-0021229-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	245	264	0	ENST00000325455.5:c.2219G>A	p.Arg740Gln	p.R740Q	ENST00000325455	NM_001202474.3	740	cGa/cAa	5/8	0.916221026251068	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.916221026251068	1		264	289	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29115386	29115386	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021668-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	86	256	0	ENST00000328354.6:c.680G>A	p.Gly227Glu	p.G227E	ENST00000328354	NM_007194.3	227	gGa/gAa	5/15	0.581905877947869	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.581905877947869	1		256	204	SUCCESS
APC	324	MSKCC	GRCh37	5	112163662	112163662	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1428025300	NA	P-0021668-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	53	324	0	ENST00000257430.4:c.1585C>T	p.Leu529Phe	p.L529F	ENST00000257430	NM_000038.5	529	Ctt/Ttt	13/16	0.352736478557951	3	FACETS	0.556	0.475	0.644	0.278	0.237	0.322	SUBCLONAL	1	TRUE	1	0.581905877947869	3		324	423	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059188	27059194	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTCTC	GGGTCTC	-	novel	NA	P-0021868-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	472	336	0	ENST00000324856.7:c.1825_1831del	p.Gly609ArgfsTer8	p.G609Rfs*8	ENST00000324856	NM_006015.4	609	GGGTCTCag/ag	4/20	0.82363879652107	2	FACETS	0.983	0.959	1	0.983	0.959	1	CLONAL	2	TRUE	0	0.82363879652107	2		336	583	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0022117-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	520	502	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.783010681903597	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.783010681903597	2		502	592	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856394	111856394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1194532448	NA	P-0022117-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	379	610	0	ENST00000341259.2:c.445C>T	p.Arg149Cys	p.R149C	ENST00000341259	NM_005475.2	149	Cgc/Tgc	2/8	0.473687510689721	6	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	3	0.783010681903597	6		610	778	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281855	49281855	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022117-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	345	526	0	ENST00000282018.3:c.902A>C	p.Asn301Thr	p.N301T	ENST00000282018	NM_020377.2	301	aAt/aCt	1/1	0.751163493555562	3	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.783010681903597	3		526	568	SUCCESS
SCG5	6447	MSKCC	GRCh37	15	32976764	32976764	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1265762656	NA	P-0022117-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	315	403	0	ENST00000300175.4:c.383A>G	p.Asp128Gly	p.D128G	ENST00000300175	NM_001144757.1	128	gAt/gGt	4/6	0.580159845999238	4	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	2	0.783010681903597	4		403	706	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37882824	37882824	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs761891977	NA	P-0022117-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1289	218	532	0	ENST00000269571.5:c.2882T>C	p.Ile961Thr	p.I961T	ENST00000269571		961	aTt/aCt	24/27	0.783010681903597	8	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.783010681903597	8		532	1507	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0023610-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	86	170	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.487199838642105	2	FACETS	1	0.98	1	0.726	0.653	0.802	CLONAL	1	TRUE	0	0.487199838642105	2		170	243	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120196	70120196	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023610-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	265	885	0	ENST00000245479.2:c.1198G>C	p.Glu400Gln	p.E400Q	ENST00000245479	NM_000346.3	400	Gag/Cag	3/3	0.487199838642105	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.487199838642105	1		885	795	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989661	68989661	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023610-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	120	441	0	ENST00000288368.4:c.1599G>A	p.Met533Ile	p.M533I	ENST00000288368	NM_024870.2	533	atG/atA	15/40	0.487199838642105	2	FACETS	0.659	0.595	0.726	0.329	0.297	0.363	SUBCLONAL	1	TRUE	0	0.487199838642105	2		441	748	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553614	29553614	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023610-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	48	511	0	ENST00000356175.3:c.2163T>G	p.Cys721Trp	p.C721W	ENST00000356175	NM_000267.3	721	tgT/tgG	18/57	0.442201314700111	2	FACETS	0.351	0.296	0.411	0.175	0.148	0.206	SUBCLONAL	1	TRUE	0	0.487199838642105	2		511	562	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144810	11144810	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023610-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	388	708	0	ENST00000358026.2:c.3886del	p.Val1296CysfsTer10	p.V1296Cfs*10	ENST00000358026	NM_001128849.1	1295	gaG/ga	28/36	0.448666969667104	2	FACETS	0.934	0.892	0.975	0.934	0.892	0.975	CLONAL	2	TRUE	0	0.487199838642105	2		708	853	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719772	61719772	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023610-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	114	233	0	ENST00000401558.2:c.1496G>T	p.Trp499Leu	p.W499L	ENST00000401558	NM_003400.3	499	tGg/tTg	14/25	0.418962471119232	3	FACETS	1	0.947	1	0.357	0.323	0.394	CLONAL	1	TRUE	0	0.487199838642105	3		233	543	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748113	41748113	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023610-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	112	568	0	ENST00000226382.2:c.656G>T	p.Ser219Ile	p.S219I	ENST00000226382	NM_003924.3	219	aGc/aTc	3/3	0.487199838642105	2	FACETS	0.723	0.651	0.798	0.361	0.325	0.399	SUBCLONAL	1	TRUE	0	0.487199838642105	2		568	636	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127794	47127794	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0026481-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	23	267	0	ENST00000409792.3:c.5288C>G	p.Ser1763Ter	p.S1763*	ENST00000409792	NM_014159.6	1763	tCa/tGa	11/21	0.309534106443503	4	FACETS	1	0.917	1	0.695	0.548	0.861	CLONAL	1	FALSE	2	0.309534106443503	4		267	140	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591894	48591906	+	protein_altering_variant	In_Frame_Del	DEL	TACGTGGACCCTT	TACGTGGACCCTT	GGAGTAA	novel	NA	P-0026481-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	17	268	1	ENST00000342988.3:c.1057_1069delinsGGAGTAA	p.Tyr353_Ser357delinsGlyValThr	p.Y353_S357delinsGVT	ENST00000342988	NM_005359.5	353	TACGTGGACCCTTct/GGAGTAAct	9/12	0.30686824906735	2	FACETS	0.82	0.629	1	0.82	0.629	1	CLONAL	2	FALSE	0	0.309534106443503	2		269	67	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249278	10249278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026481-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	52	211	0	ENST00000340748.4:c.3904G>A	p.Gly1302Ser	p.G1302S	ENST00000340748		1302	Ggt/Agt	34/40	0.309534106443503	4	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	FALSE	2	0.309534106443503	4		211	197	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582093	189582093	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026481-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	52	261	0	ENST00000264731.3:c.652C>A	p.Pro218Thr	p.P218T	ENST00000264731	NM_003722.4	218	Cca/Aca	5/14	0.309534106443503	9	FACETS	1	0.948	1	0.414	0.355	0.477	CLONAL	2	FALSE	3	0.309534106443503	9		261	282	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591906	48591906	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026481-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	16	253	0	ENST00000342988.3:c.1069T>A	p.Ser357Thr	p.S357T	ENST00000342988	NM_005359.5	357	Tct/Act	9/12	0.30686824906735	2	FACETS	0.795	0.604	1	0.795	0.604	1	CLONAL	2	FALSE	0	0.309534106443503	2		253	65	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207162	1207162	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs137853076	NA	P-0026561-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	37	529	0	ENST00000326873.7:c.250A>T	p.Lys84Ter	p.K84*	ENST00000326873	NM_000455.4	84	Aag/Tag	1/10	0.3	2	FACETS	0.408	0.335	0.49			1	SUBCLONAL	1	TRUE	NA	0.25	2		529	725	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0026561-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	49	606	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	1	2	FACETS	0.557	0.47	0.652	0.557	0.47	0.652	SUBCLONAL	1	TRUE	1	0.25	2		606	704	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683976	29683976	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0026561-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	27	423	0	ENST00000356175.3:c.7676-2A>G		p.X2559_splice	ENST00000356175	NM_000267.3	2559			1	2	FACETS	0.514	0.409	0.635	0.514	0.409	0.635	SUBCLONAL	1	TRUE	1	0.25	2		423	420	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472631	88472631	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026561-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	39	527	0	ENST00000360948.2:c.1924G>T	p.Gly642Ter	p.G642*	ENST00000360948	NM_001012338.2	642	Gga/Tga	16/19	1	2	FACETS	0.583	0.483	0.695	0.583	0.483	0.695	SUBCLONAL	1	TRUE	1	0.25	2		527	535	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864517	57864517	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026561-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	52	606	0	ENST00000228682.2:c.1994C>A	p.Thr665Asn	p.T665N	ENST00000228682	NM_005269.2	665	aCc/aAc	12/12	0.116114902428171	3	FACETS	0.627	0.533	0.731	0.314	0.266	0.366	INDETERMINATE	1	TRUE	1	0.25	3		606	746	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830868	156830868	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026561-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	51	631	0	ENST00000524377.1:c.142C>G	p.Leu48Val	p.L48V	ENST00000524377	NM_002529.3	48	Ctg/Gtg	1/17	1	2	FACETS	0.642	0.544	0.748	0.642	0.544	0.748	SUBCLONAL	1	TRUE	1	0.25	2		631	636	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52677334	52677345	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCTGCAGCCA	TGGCTGCAGCCA	CGGCG	novel	NA	P-0026561-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	37	478	1	ENST00000394830.3:c.914_925delinsCGCCG	p.Leu305SerfsTer4	p.L305Sfs*4	ENST00000394830	NM_018313.4	305	tTGGCTGCAGCCAga/tCGCCGga	10/30	1	2	FACETS	0.571	0.47	0.685	0.571	0.47	0.685	SUBCLONAL	1	TRUE	1	0.25	2		479	518	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692817	89692819	+	inframe_deletion	In_Frame_Del	DEL	ATC	ATC	-	novel	NA	P-0027054-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	238	175	0	ENST00000371953.3:c.302_304del	p.Ile101del	p.I101del	ENST00000371953	NM_000314.4	101	ATC/-	5/9	0.865385151006026	2	FACETS	0.974	0.944	1	0.974	0.944	1	CLONAL	2	TRUE	0	0.879089977346873	2		175	278	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141872	108141872	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027054-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	194	346	0	ENST00000278616.4:c.2920T>C	p.Ser974Pro	p.S974P	ENST00000278616	NM_000051.3	974	Tcc/Ccc	19/63	0.865385151006026	2	FACETS	0.929	0.869	0.99	0.465	0.434	0.495	CLONAL	1	TRUE	0	0.879089977346873	2		346	475	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923159	48923159	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027054-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	202	74	0	ENST00000267163.4:c.607+1del		p.G203fs	ENST00000267163	NM_000321.2	203	Ggg/gg	6/27	0.865385151006026	2	FACETS	0.901	0.865	0.934	0.901	0.865	0.934	CLONAL	2	TRUE	0	0.879089977346873	2		74	255	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578541	7578541	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027054-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	607	734	0	ENST00000269305.4:c.389T>A	p.Leu130His	p.L130H	ENST00000269305	NM_001126112.2	130	cTc/cAc	5/11	0.865385151006026	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.879089977346873	2		734	678	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185570	27185570	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027054-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	606	620	0	ENST00000380036.4:c.1270T>A	p.Cys424Ser	p.C424S	ENST00000380036	NM_000459.3	424	Tgc/Agc	9/23	0.865813246910745	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.879089977346873	2		620	675	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875981	76875984	+	frameshift_variant	Frame_Shift_Del	DEL	ACAA	ACAA	-	novel	NA	P-0027054-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	206	281	0	ENST00000373344.5:c.5151_5154del	p.Cys1718MetfsTer6	p.C1718Mfs*6	ENST00000373344	NM_000489.3	1717	gtTTGT/gt	20/35	0.863783747419619	1	FACETS	0.903	0.861	0.942	0.903	0.861	0.942	CLONAL	1	TRUE	0	0.879089977346873	1		281	291	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028352-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	279	902	0	ENST00000269305.4:c.313G>T	p.Gly105Cys	p.G105C	ENST00000269305	NM_001126112.2	105	Ggc/Tgc	4/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		902	824	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455091	50455091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1422790468	NA	P-0028352-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	83	498	0	ENST00000331340.3:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000331340	NM_006060.4	213	cGa/cAa	6/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		498	647	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs730881677	NA	P-0028352-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	326	678	0	ENST00000304494.5:c.151-1G>T		p.X51_splice	ENST00000304494	NM_000077.4	51			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		678	751	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436143	51436143	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028352-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	210	543	0	ENST00000262662.1:c.103A>T	p.Asn35Tyr	p.N35Y	ENST00000262662		35	Aat/Tat	3/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		543	637	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515104	103515104	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028352-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	105	715	0	ENST00000355739.4:c.1605G>T	p.Lys535Asn	p.K535N	ENST00000355739	NM_000123.3	535	aaG/aaT	8/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		715	654	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2194557	2194557	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028352-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	95	634	0	ENST00000398665.3:c.632A>T	p.Lys211Ile	p.K211I	ENST00000398665	NM_032482.2	211	aAa/aTa	7/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		634	612	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081587	143081587	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028352-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	231	653	0	ENST00000262992.4:c.1487G>A	p.Ser496Asn	p.S496N	ENST00000262992	NM_001101669.1	496	aGt/aAt	15/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		653	798	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410154	139410154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028352-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	99	720	0	ENST00000277541.6:c.1684C>T	p.His562Tyr	p.H562Y	ENST00000277541	NM_017617.3	562	Cac/Tac	11/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		720	461	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922722	44922722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1340911940	NA	P-0028352-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	105	692	0	ENST00000377967.4:c.1583C>T	p.Thr528Ile	p.T528I	ENST00000377967	NM_021140.2	528	aCa/aTa	16/29	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		692	539	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533390	29533390	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0028352-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	181	613	0	ENST00000356175.3:c.1392+1G>T		p.X464_splice	ENST00000356175	NM_000267.3	464			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		613	640	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0029064-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	168	240	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.540930461428436	1	FACETS	0.906	0.84	0.975	0.906	0.84	0.975	CLONAL	1	TRUE	0	0.540930461428436	1		240	500	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0029064-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	62	134	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.540930461428436	1	FACETS	0.871	0.766	0.981	0.871	0.766	0.981	CLONAL	1	TRUE	0	0.540930461428436	1		134	192	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699369	47699369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029064-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	74	444	0	ENST00000347630.2:c.139G>A	p.Glu47Lys	p.E47K	ENST00000347630	NM_001007230.1	47	Gaa/Aaa	4/11	0.393038538082852	1	FACETS	0.36	0.316	0.408	0.36	0.316	0.408	SUBCLONAL	1	TRUE	0	0.540930461428436	1		444	554	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844241	68844241	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029064-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	158	377	0	ENST00000261769.5:c.830del	p.Pro277GlnfsTer5	p.P277Qfs*5	ENST00000261769	NM_004360.3	277	Cca/ca	6/16	0.540930461428436	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.540930461428436	1		377	367	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254863	16254863	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029064-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	99	545	1	ENST00000375759.3:c.2128G>C	p.Glu710Gln	p.E710Q	ENST00000375759	NM_015001.2	710	Gag/Cag	11/15	0.540930461428436	1	FACETS	0.497	0.445	0.552	0.497	0.445	0.552	SUBCLONAL	1	TRUE	0	0.540930461428436	1		546	537	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787747	135787747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1467020958	NA	P-0029064-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	72	434	0	ENST00000298552.3:c.835C>T	p.His279Tyr	p.H279Y	ENST00000298552	NM_001162426.1	279	Cac/Tac	9/23	0.393038538082852	1	FACETS	0.382	0.334	0.433	0.382	0.334	0.433	SUBCLONAL	1	TRUE	0	0.540930461428436	1		434	509	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961471	54961471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029064-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	122	349	0	ENST00000312783.6:c.161C>T	p.Ser54Phe	p.S54F	ENST00000312783	NM_198436.1	54	tCc/tTc	4/10	0.540930461428436	4	FACETS	0.726	0.655	0.8			1	SUBCLONAL	1	TRUE	NA	0.540930461428436	4		349	958	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427369	49427369	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1565779294	NA	P-0029064-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	82	735	0	ENST00000301067.7:c.11119C>T	p.Arg3707Ter	p.R3707*	ENST00000301067	NM_003482.3	3707	Cga/Tga	39/54	1	2	FACETS	0.477	0.42	0.537	0.477	0.42	0.537	SUBCLONAL	1	TRUE	1	0.540930461428436	2		735	636	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257995	16257995	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1176124993	NA	P-0029064-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	118	649	2	ENST00000375759.3:c.5260G>A	p.Asp1754Asn	p.D1754N	ENST00000375759	NM_015001.2	1754	Gac/Aac	11/15	0.540930461428436	1	FACETS	0.596	0.54	0.655	0.596	0.54	0.655	SUBCLONAL	1	TRUE	0	0.540930461428436	1		651	534	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058045	27058045	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029064-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	106	617	0	ENST00000324856.7:c.1753C>T	p.Gln585Ter	p.Q585*	ENST00000324856	NM_006015.4	585	Cag/Tag	3/20	0.540930461428436	1	FACETS	0.489	0.439	0.541	0.489	0.439	0.541	SUBCLONAL	1	TRUE	0	0.540930461428436	1		617	585	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433784	49433784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760007799	NA	P-0029064-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	105	625	0	ENST00000301067.7:c.7769C>T	p.Ser2590Leu	p.S2590L	ENST00000301067	NM_003482.3	2590	tCg/tTg	31/54	1	2	FACETS	0.535	0.48	0.595	0.535	0.48	0.595	SUBCLONAL	1	TRUE	1	0.540930461428436	2		625	725	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257344	16257344	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029064-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	107	529	0	ENST00000375759.3:c.4609G>C	p.Glu1537Gln	p.E1537Q	ENST00000375759	NM_015001.2	1537	Gaa/Caa	11/15	0.540930461428436	1	FACETS	0.559	0.504	0.618	0.559	0.504	0.618	SUBCLONAL	1	TRUE	0	0.540930461428436	1		529	516	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40879737	40879737	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029064-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	69	386	0	ENST00000428826.2:c.162G>T	p.Gln54His	p.Q54H	ENST00000428826		54	caG/caT	4/21	0.393038538082852	1	FACETS	0.366	0.319	0.417	0.366	0.319	0.417	SUBCLONAL	1	TRUE	0	0.540930461428436	1		386	508	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039363	47039363	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029064-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	149	664	0	ENST00000377604.3:c.986C>A	p.Ser329Tyr	p.S329Y	ENST00000377604	NM_001204468.1	329	tCc/tAc	10/24	0.393038538082852	1	FACETS	0.695	0.638	0.755	0.695	0.638	0.755	SUBCLONAL	1	TRUE	0	0.540930461428436	1		664	578	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972664	76972667	+	missense_variant	Missense_Mutation	ONP	GATG	GATG	AATA	novel	NA	P-0029064-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	82	341	0	ENST00000373344.5:c.74_77delinsTATT	p.Ser25_Ser26delinsLeuLeu	p.S25_S26delinsLL	ENST00000373344	NM_000489.3	25	tCATCa/tTATTa	2/35	0.393038538082852	1	FACETS	0.446	0.394	0.501	0.446	0.394	0.501	SUBCLONAL	1	TRUE	0	0.540930461428436	1		341	496	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258619	16258619	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029064-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	102	723	0	ENST00000375759.3:c.5884G>A	p.Glu1962Lys	p.E1962K	ENST00000375759	NM_015001.2	1962	Gaa/Aaa	11/15	0.540930461428436	1	FACETS	0.483	0.433	0.536	0.483	0.433	0.536	SUBCLONAL	1	TRUE	0	0.540930461428436	1		723	570	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259055	153259055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029064-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	105	409	0	ENST00000281708.4:c.760G>A	p.Asp254Asn	p.D254N	ENST00000281708	NM_033632.3	254	Gat/Aat	5/12	0.27294518621578	1	FACETS	0.426	0.382	0.473	0.426	0.382	0.473	INDETERMINATE	1	TRUE	0	0.540930461428436	1		409	665	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271294	26271294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029064-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	265	712	0	ENST00000305910.3:c.319G>A	p.Asp107Asn	p.D107N	ENST00000305910	NM_003534.2	107	Gat/Aat	1/1	0.540930461428436	4	FACETS	1	0.971	1	0.356	0.332	0.38	CLONAL	1	TRUE	1	0.540930461428436	4		712	1415	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258277	16258277	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029064-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	92	630	0	ENST00000375759.3:c.5542G>C	p.Asp1848His	p.D1848H	ENST00000375759	NM_015001.2	1848	Gac/Cac	11/15	0.540930461428436	1	FACETS	0.427	0.38	0.477	0.427	0.38	0.477	SUBCLONAL	1	TRUE	0	0.540930461428436	1		630	581	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258628	16258628	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029064-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	107	720	0	ENST00000375759.3:c.5893G>T	p.Glu1965Ter	p.E1965*	ENST00000375759	NM_015001.2	1965	Gag/Tag	11/15	0.540930461428436	1	FACETS	0.514	0.462	0.568	0.514	0.462	0.568	SUBCLONAL	1	TRUE	0	0.540930461428436	1		720	562	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258670	16258670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029064-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	108	761	0	ENST00000375759.3:c.5935G>A	p.Glu1979Lys	p.E1979K	ENST00000375759	NM_015001.2	1979	Gag/Aag	11/15	0.540930461428436	1	FACETS	0.473	0.425	0.523	0.473	0.425	0.523	SUBCLONAL	1	TRUE	0	0.540930461428436	1		761	616	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749990	162749990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029064-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	106	563	1	ENST00000367921.3:c.2522C>T	p.Ser841Leu	p.S841L	ENST00000367921	NM_006182.2	841	tCa/tTa	18/18	0.480004046135867	4	FACETS	0.522	0.466	0.581	0.174	0.155	0.194	SUBCLONAL	1	TRUE	1	0.540930461428436	4		564	1158	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163309214	163309214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029064-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	88	445	0	ENST00000271452.3:c.553G>A	p.Asp185Asn	p.D185N	ENST00000271452	NM_145697.2	185	Gat/Aat	8/14	0.480004046135867	4	FACETS	0.472	0.417	0.531	0.157	0.139	0.177	SUBCLONAL	1	TRUE	1	0.540930461428436	4		445	1062	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807344	3807344	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029064-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	69	433	0	ENST00000262367.5:c.3643G>A	p.Gly1215Arg	p.G1215R	ENST00000262367	NM_004380.2	1215	Ggg/Agg	19/31	1	2	FACETS	0.451	0.393	0.513	0.451	0.393	0.513	SUBCLONAL	1	TRUE	1	0.540930461428436	2		433	566	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679981	33679981	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029064-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	112	502	0	ENST00000308377.4:c.2100C>G	p.Ile700Met	p.I700M	ENST00000308377	NM_152270.3	700	atC/atG	5/5	0.393038538082852	1	FACETS	0.452	0.407	0.5	0.452	0.407	0.5	SUBCLONAL	1	TRUE	0	0.540930461428436	1		502	668	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696704	47696704	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029064-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	90	419	0	ENST00000347630.2:c.244G>C	p.Asp82His	p.D82H	ENST00000347630	NM_001007230.1	82	Gat/Cat	5/11	0.393038538082852	1	FACETS	0.407	0.361	0.455	0.407	0.361	0.455	SUBCLONAL	1	TRUE	0	0.540930461428436	1		419	597	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11114020	11114020	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029064-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	65	503	0	ENST00000358026.2:c.1948G>C	p.Glu650Gln	p.E650Q	ENST00000358026	NM_001128849.1	650	Gaa/Caa	13/36	0.471443428138242	1	FACETS	0.389	0.338	0.444	0.389	0.338	0.444	SUBCLONAL	1	TRUE	0	0.540930461428436	1		503	451	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226889	142226889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029064-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	90	439	0	ENST00000350721.4:c.4915G>A	p.Asp1639Asn	p.D1639N	ENST00000350721	NM_001184.3	1639	Gat/Aat	28/47	0.540930461428436	1	FACETS	0.414	0.368	0.464	0.414	0.368	0.464	SUBCLONAL	1	TRUE	0	0.540930461428436	1		439	586	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155204	106155204	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029064-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	114	516	0	ENST00000380013.4:c.105G>C	p.Gln35His	p.Q35H	ENST00000380013	NM_001127208.2	35	caG/caC	3/11	0.27294518621578	1	FACETS	0.452	0.407	0.499	0.452	0.407	0.499	INDETERMINATE	1	TRUE	0	0.540930461428436	1		516	681	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696652	176696652	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1384505425	NA	P-0029064-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	82	518	0	ENST00000439151.2:c.5353G>C	p.Asp1785His	p.D1785H	ENST00000439151	NM_022455.4	1785	Gat/Cat	16/23	0.393038538082852	1	FACETS	0.355	0.313	0.4	0.355	0.313	0.4	SUBCLONAL	1	TRUE	0	0.540930461428436	1		518	623	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176700699	176700699	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029064-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	83	446	0	ENST00000439151.2:c.5536G>T	p.Glu1846Ter	p.E1846*	ENST00000439151	NM_022455.4	1846	Gag/Tag	17/23	0.393038538082852	1	FACETS	0.371	0.327	0.417	0.371	0.327	0.417	SUBCLONAL	1	TRUE	0	0.540930461428436	1		446	604	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858279	27858279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029064-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1806	140	718	0	ENST00000359303.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000359303	NM_003535.2	98	Gag/Aag	1/1	0.540930461428436	4	FACETS	0.41	0.371	0.451	0.137	0.123	0.151	SUBCLONAL	1	TRUE	1	0.540930461428436	4		718	1946	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0029944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	392	355	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.305849986409511	6	FACETS	0.967	0.928	1			1	CLONAL	6	TRUE	NA	0.305849986409511	6		355	712	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298100	11298100	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	74	495	0	ENST00000361445.4:c.2008G>A	p.Asp670Asn	p.D670N	ENST00000361445	NM_004958.3	670	Gac/Aac	13/58	1	2	FACETS	0.738	0.646	0.837	0.738	0.646	0.837	SUBCLONAL	1	TRUE	1	0.305849986409511	2		495	656	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251992	8251992	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	138	493	1	ENST00000335790.3:c.85C>A	p.Arg29Ser	p.R29S	ENST00000335790	NM_002315.2	29	Cgc/Agc	2/4	0.165252624011613	4	FACETS	1	0.986	1	0.737	0.67	0.806	INDETERMINATE	1	TRUE	2	0.305849986409511	4		494	800	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514302	69514302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	132	451	0	ENST00000294312.3:c.379C>A	p.Arg127Ser	p.R127S	ENST00000294312	NM_005117.2	127	Cgc/Agc	3/3	0.165252624011613	4	FACETS	1	0.986	1	0.744	0.676	0.816	INDETERMINATE	1	TRUE	2	0.305849986409511	4		451	757	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962529	100962529	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	108	395	0	ENST00000325455.5:c.1868G>T	p.Arg623Leu	p.R623L	ENST00000325455	NM_001202474.3	623	cGc/cTc	3/8	0.165252624011613	4	FACETS	0.809	0.728	0.894	0.809	0.728	0.894	INDETERMINATE	2	TRUE	2	0.305849986409511	4		395	570	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424087	49424087	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	232	343	0	ENST00000301067.7:c.13975C>G	p.Arg4659Gly	p.R4659G	ENST00000301067	NM_003482.3	4659	Cgg/Ggg	42/54	0.305849986409511	3	FACETS	0.901	0.845	0.958	0.901	0.845	0.958	CLONAL	3	TRUE	0	0.305849986409511	3		343	647	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431709	49431709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752428122	NA	P-0029944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	72	538	0	ENST00000301067.7:c.9430G>A	p.Ala3144Thr	p.A3144T	ENST00000301067	NM_003482.3	3144	Gca/Aca	34/54	0.305849986409511	3	FACETS	0.657	0.573	0.748	0.219	0.191	0.25	SUBCLONAL	1	TRUE	0	0.305849986409511	3		538	826	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240208	41240208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755011775	NA	P-0029944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	34	301	0	ENST00000379561.5:c.142G>A	p.Ala48Thr	p.A48T	ENST00000379561	NM_002015.3	48	Gcg/Acg	1/3	1	2	FACETS	0.449	0.366	0.542	0.449	0.366	0.542	SUBCLONAL	1	TRUE	1	0.305849986409511	2		301	495	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435766	110435766	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs549588978	NA	P-0029944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	82	441	0	ENST00000375856.3:c.2635G>C	p.Gly879Arg	p.G879R	ENST00000375856	NM_003749.2	879	Ggc/Cgc	1/2	1	2	FACETS	0.968	0.855	1	0.968	0.855	1	CLONAL	1	TRUE	1	0.305849986409511	2		441	554	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000362	42000363	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0029944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	173	422	0	ENST00000219905.7:c.2381_2382insTT	p.Trp795TyrfsTer23	p.W795Yfs*23	ENST00000219905	NM_001164273.1	794	gga/ggTTa	7/24	0.296451454296591	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	0	0.305849986409511	2		422	556	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66735666	66735666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	45	344	0	ENST00000307102.5:c.487G>A	p.Glu163Lys	p.E163K	ENST00000307102	NM_002755.3	163	Gaa/Aaa	4/11	0.296451454296591	2	FACETS	0.54	0.453	0.636	0.27	0.226	0.318	SUBCLONAL	1	TRUE	0	0.305849986409511	2		344	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577125	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0029944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	119	460	0	ENST00000269305.4:c.813_814delinsTT	p.Glu271_Val272delinsAspLeu	p.E271_V272delinsDL	ENST00000269305	NM_001126112.2	271	gaGGtg/gaTTtg	8/11	0.199779530362764	2	FACETS	1	0.97	1	0.59	0.534	0.65	CLONAL	1	TRUE	0	0.305849986409511	2		460	659	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15952254	15952254	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	146	488	2	ENST00000268712.3:c.6441C>A	p.Tyr2147Ter	p.Y2147*	ENST00000268712	NM_006311.3	2147	taC/taA	41/46	0.199779530362764	2	FACETS	1	0.987	1	0.72	0.659	0.784	CLONAL	1	TRUE	0	0.305849986409511	2		490	663	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38787131	38787131	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	79	502	0	ENST00000348513.6:c.862G>A	p.Glu288Lys	p.E288K	ENST00000348513	NM_003079.4	288	Gag/Aag	10/11	0.305849986409511	4	FACETS	0.856	0.752	0.968	0.285	0.25	0.323	CLONAL	1	TRUE	1	0.305849986409511	4		502	788	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223205	41223205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502355	NA	P-0029944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	85	498	0	ENST00000357654.3:c.4726G>A	p.Glu1576Lys	p.E1576K	ENST00000357654	NM_007294.3	1576	Gaa/Aaa	15/23	0.305849986409511	4	FACETS	0.811	0.716	0.914	0.27	0.238	0.305	CLONAL	1	TRUE	1	0.305849986409511	4		498	895	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244945	41244945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	65	492	0	ENST00000357654.3:c.2603C>T	p.Ser868Leu	p.S868L	ENST00000357654	NM_007294.3	868	tCa/tTa	10/23	0.305849986409511	4	FACETS	0.606	0.524	0.695	0.202	0.174	0.232	SUBCLONAL	1	TRUE	1	0.305849986409511	4		492	916	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244957	41244957	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357003	NA	P-0029944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	71	486	0	ENST00000357654.3:c.2591C>T	p.Ser864Leu	p.S864L	ENST00000357654	NM_007294.3	864	tCa/tTa	10/23	0.305849986409511	4	FACETS	0.684	0.596	0.78	0.228	0.198	0.26	SUBCLONAL	1	TRUE	1	0.305849986409511	4		486	886	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425482	47425482	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	270	540	0	ENST00000404338.3:c.3550G>T	p.Gly1184Trp	p.G1184W	ENST00000404338	NM_004491.4	1184	Ggg/Tgg	1/6	0.272614861944672	3	FACETS	1	0.989	1	0.802	0.755	0.85	CLONAL	2	TRUE	0	0.305849986409511	3		540	846	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607794	46607794	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	80	524	0	ENST00000263734.3:c.1983C>G	p.Phe661Leu	p.F661L	ENST00000263734	NM_001430.4	661	ttC/ttG	12/16	0.305849986409511	3	FACETS	0.736	0.646	0.831	0.368	0.323	0.416	SUBCLONAL	1	TRUE	1	0.305849986409511	3		524	820	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561324	9561324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	87	527	0	ENST00000353224.5:c.458G>A	p.Gly153Glu	p.G153E	ENST00000353224	NM_177990.2	153	gGa/gAa	4/10	0.305849986409511	1	FACETS	0.753	0.667	0.845	0.753	0.667	0.845	SUBCLONAL	1	TRUE	0	0.305849986409511	1		527	640	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376719	31376719	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	142	400	0	ENST00000328111.2:c.714G>T	p.Trp238Cys	p.W238C	ENST00000328111	NM_006892.3	238	tgG/tgT	7/23	0.226979214604751	4	FACETS	1	0.986	1	0.723	0.659	0.79	CLONAL	1	TRUE	2	0.305849986409511	4		400	839	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101188	41101188	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	176	449	0	ENST00000373198.4:c.1168C>A	p.Pro390Thr	p.P390T	ENST00000373198	NM_133170.3	390	Cca/Aca	8/32	1	2	FACETS	0.78	0.72	0.842	1	0.99	1	SUBCLONAL	2	TRUE	1	0.305849986409511	2		449	738	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101197	41101197	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	109	427	0	ENST00000373198.4:c.1159G>T	p.Val387Leu	p.V387L	ENST00000373198	NM_133170.3	387	Gta/Tta	8/32	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.305849986409511	2		427	707	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670721	134670721	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	141	467	0	ENST00000398015.3:c.632C>A	p.Thr211Lys	p.T211K	ENST00000398015	NM_004441.4	211	aCa/aAa	3/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.305849986409511	2		467	717	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188406	142188406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910993590	NA	P-0029944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	49	390	0	ENST00000350721.4:c.6325C>T	p.Arg2109Cys	p.R2109C	ENST00000350721	NM_001184.3	2109	Cgc/Tgc	38/47	1	2	FACETS	0.659	0.559	0.77	0.659	0.559	0.77	SUBCLONAL	1	TRUE	1	0.305849986409511	2		390	486	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517454	176517461	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTGCGT	CTGTGCGT	-	novel	NA	P-0029944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	93	448	0	ENST00000292408.4:c.161_168del	p.Arg54LeufsTer5	p.R54Lfs*5	ENST00000292408	NM_213647.1	52	cCTGTGCGT/c	3/18	0.284227366361789	3	FACETS	1	0.939	1			1	CLONAL	1	TRUE	NA	0.305849986409511	3		448	648	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562124	176562124	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	71	524	0	ENST00000439151.2:c.20T>G	p.Leu7Arg	p.L7R	ENST00000439151	NM_022455.4	7	cTa/cGa	2/23	0.284227366361789	3	FACETS	0.571	0.497	0.651			1	SUBCLONAL	1	TRUE	NA	0.305849986409511	3		524	938	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124532326	124532326	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	83	307	0	ENST00000357628.3:c.118G>A	p.Gly40Arg	p.G40R	ENST00000357628	NM_015450.2	40	Gga/Aga	6/19	1	2	FACETS	0.803	0.715	0.896	1	0.981	1	CLONAL	2	TRUE	1	0.305849986409511	2		307	338	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341782	8341782	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	49	532	0	ENST00000356435.5:c.4858G>C	p.Val1620Leu	p.V1620L	ENST00000356435		1620	Gtg/Ctg	29/35	0.235254978719035	1	FACETS	0.467	0.395	0.547	0.467	0.395	0.547	SUBCLONAL	1	TRUE	0	0.305849986409511	1		532	581	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912263	97912263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	50	372	0	ENST00000289081.3:c.628G>A	p.Glu210Lys	p.E210K	ENST00000289081	NM_000136.2	210	Gaa/Aaa	7/15	NA	2	FACETS	0.631	0.536	0.736			1	INDETERMINATE	1	TRUE	NA	0.305849986409511	2		372	518	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0031344-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	147	1407	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.481784589286379	2		1407	591	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0031344-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	206	460	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.481784589286379	2		460	837	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170217	32170217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031344-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	430	485	0	ENST00000375023.3:c.3391C>T	p.Pro1131Ser	p.P1131S	ENST00000375023	NM_004557.3	1131	Cct/Tct	21/30	0.481784589286379	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.481784589286379	3		485	1066	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375964	8375964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144763077	NA	P-0031344-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	207	425	0	ENST00000356435.5:c.4633G>A	p.Asp1545Asn	p.D1545N	ENST00000356435		1545	Gat/Aat	28/35	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.481784589286379	2		425	754	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317572	1317572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031344-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	110	175	0	ENST00000400841.2:c.493G>A	p.Glu165Lys	p.E165K	ENST00000400841		165	Gaa/Aaa	5/6	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.481784589286379	2		175	341	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467675	50467675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759124417	NA	P-0031344-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	157	424	0	ENST00000331340.3:c.910G>A	p.Glu304Lys	p.E304K	ENST00000331340	NM_006060.4	304	Gaa/Aaa	8/8	1	2	FACETS	0.895	0.822	0.972	0.895	0.822	0.972	CLONAL	1	TRUE	1	0.481784589286379	2		424	728	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0031344-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	165	372	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.481784589286379	2		372	655	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844404	156844404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199826686	NA	P-0031344-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	280	747	1	ENST00000524377.1:c.1237G>A	p.Glu413Lys	p.E413K	ENST00000524377	NM_002529.3	413	Gaa/Aaa	10/17	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.481784589286379	2		748	1161	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873232	71873232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031344-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	214	470	0	ENST00000357731.5:c.962G>A	p.Gly321Glu	p.G321E	ENST00000357731	NM_173808.2	321	gGa/gAa	7/7	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.481784589286379	2		470	817	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853095	151853095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031344-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	148	452	0	ENST00000262189.6:c.11860C>T	p.Gln3954Ter	p.Q3954*	ENST00000262189	NM_170606.2	3954	Cag/Tag	46/59	1	2	FACETS	0.835	0.764	0.909	0.835	0.764	0.909	CLONAL	1	TRUE	1	0.481784589286379	2		452	736	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583923	46583923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031344-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	198	469	0	ENST00000263734.3:c.430C>T	p.Arg144Cys	p.R144C	ENST00000263734	NM_001430.4	144	Cgt/Tgt	4/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.481784589286379	2		469	732	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552770	226552770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031344-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	204	505	0	ENST00000366794.5:c.2591C>T	p.Ser864Phe	p.S864F	ENST00000366794	NM_001618.3	864	tCc/tTc	19/23	1	2	FACETS	0.946	0.878	1	0.946	0.878	1	CLONAL	1	TRUE	1	0.481784589286379	2		505	895	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498522	89498522	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031344-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	168	378	0	ENST00000336596.2:c.2494G>A	p.Asp832Asn	p.D832N	ENST00000336596	NM_005233.5	832	Gat/Aat	14/17	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.481784589286379	2		378	672	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204636	108204636	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781994	NA	P-0031344-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	102	324	0	ENST00000278616.4:c.7951C>T	p.Gln2651Ter	p.Q2651*	ENST00000278616	NM_000051.3	2651	Cag/Tag	54/63	1	2	FACETS	0.859	0.772	0.951	0.859	0.772	0.951	CLONAL	1	TRUE	1	0.481784589286379	2		324	493	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10796782	10796782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031344-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	178	403	0	ENST00000361367.2:c.2914G>A	p.Asp972Asn	p.D972N	ENST00000361367	NM_014633.3	972	Gat/Aat	23/25	1	2	FACETS	0.992	0.916	1	0.992	0.916	1	CLONAL	1	TRUE	1	0.481784589286379	2		403	745	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250853	99250853	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031344-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	204	484	0	ENST00000268035.6:c.157A>C	p.Thr53Pro	p.T53P	ENST00000268035	NM_000875.3	53	Acg/Ccg	2/21	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.481784589286379	2		484	834	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096966	11096966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031344-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	221	447	0	ENST00000358026.2:c.457C>T	p.Pro153Ser	p.P153S	ENST00000358026	NM_001128849.1	153	Ccg/Tcg	4/36	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.481784589286379	2		447	781	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211144	36211144	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031344-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	198	529	0	ENST00000222270.7:c.895G>A	p.Gly299Ser	p.G299S	ENST00000222270	NM_014727.1	299	Ggt/Agt	3/37	1	2	FACETS	0.834	0.773	0.899	0.834	0.773	0.899	CLONAL	1	TRUE	1	0.481784589286379	2		529	985	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222405	39222406	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0031344-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	189	390	0	ENST00000402219.2:c.3204_3205delinsTT	p.Pro1069Ser	p.P1069S	ENST00000402219	NM_005633.3	1068	atCCct/atTTct	20/23	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.481784589286379	2		390	779	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683752	162683752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031344-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	218	449	0	ENST00000366898.1:c.217C>T	p.Pro73Ser	p.P73S	ENST00000366898	NM_004562.2	73	Ccg/Tcg	3/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.481784589286379	2		449	796	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395479	116395480	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0031344-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	164	357	1	ENST00000397752.3:c.1772_1773delinsAA	p.Arg591Gln	p.R591Q	ENST00000397752	NM_000245.2	591	cGG/cAA	6/21	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.481784589286379	2		358	655	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907759	76907759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031344-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	190	399	0	ENST00000373344.5:c.4402G>A	p.Asp1468Asn	p.D1468N	ENST00000373344	NM_000489.3	1468	Gat/Aat	15/35	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.481784589286379	2		399	695	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631171	176631171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031642-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	294	540	0	ENST00000439151.2:c.1114C>T	p.Pro372Ser	p.P372S	ENST00000439151	NM_022455.4	372	Cct/Tct	4/23	1	2	FACETS	0.982	0.927	1	0.982	0.927	1	CLONAL	1	TRUE	1	0.686918010028952	2		540	872	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022105	5022105	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1183427218	NA	P-0031642-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	137	404	0	ENST00000381652.3:c.118C>T	p.Gln40Ter	p.Q40*	ENST00000381652	NM_004972.3	40	Cag/Tag	3/25	0.686918010028952	1	FACETS	0.974	0.904	1	0.974	0.904	1	CLONAL	1	TRUE	0	0.686918010028952	1		404	269	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11308150	11308150	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs757384321	NA	P-0031642-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	200	449	0	ENST00000361445.4:c.842G>A	p.Arg281His	p.R281H	ENST00000361445	NM_004958.3	281	cGt/cAt	7/58	0.686918010028952	3	FACETS	0.923	0.856	0.991	0.461	0.428	0.496	CLONAL	1	TRUE	1	0.686918010028952	3		449	848	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874964	151874965	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	GCCTAGGCATATCTACAGAT	novel	NA	P-0031642-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	241	427	0	ENST00000262189.6:c.7554_7573dup	p.Pro2525HisfsTer3	p.P2525Hfs*3	ENST00000262189	NM_170606.2	2525	cct/cATCTGTAGATATGCCTAGGCct	38/59	0.686918010028952	2	FACETS	1	0.96	1	0.514	0.483	0.547	CLONAL	1	TRUE	0	0.686918010028952	2		427	682	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694644	176694644	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031642-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	218	524	0	ENST00000439151.2:c.5228G>T	p.Trp1743Leu	p.W1743L	ENST00000439151	NM_022455.4	1743	tGg/tTg	15/23	1	2	FACETS	0.95	0.888	1	0.95	0.888	1	CLONAL	1	TRUE	1	0.686918010028952	2		524	668	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627397	14627397	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031642-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	327	663	0	ENST00000254322.2:c.673G>C	p.Asp225His	p.D225H	ENST00000254322	NM_006145.1	225	Gac/Cac	2/3	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.686918010028952	2		663	939	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511714	46511714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031642-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	102	364	0	ENST00000262741.5:c.1063G>A	p.Glu355Lys	p.E355K	ENST00000262741	NM_003629.3	355	Gag/Aag	9/10	0.686918010028952	3	FACETS	0.98	0.883	1	0.49	0.441	0.541	CLONAL	1	TRUE	1	0.686918010028952	3		364	407	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0035156-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	55	410	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.213050314641112	4	FACETS	0.766	0.658	0.885	0.766	0.658	0.885	SUBCLONAL	2	TRUE	2	0.217971040399501	4		410	401	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587781845	NA	P-0035156-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	78	628	0	ENST00000269305.4:c.511G>T	p.Glu171Ter	p.E171*	ENST00000269305	NM_001126112.2	171	Gag/Tag	5/11	1	2	FACETS	0.786	0.694	0.885	1	0.978	1	SUBCLONAL	2	TRUE	1	0.217971040399501	2		628	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578420	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AG	novel	NA	P-0035156-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	81	396	0	ENST00000269305.4:c.510_511delinsCT	p.Glu171Ter	p.E171*	ENST00000269305	NM_001126112.2	170	acGGag/acCTag	5/11	1	2	FACETS	0.804	0.711	0.903	1	0.98	1	CLONAL	2	TRUE	1	0.217971040399501	2		396	462	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513346	44513346	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035156-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	69	254	0	ENST00000291552.4:c.589T>G	p.Ser197Ala	p.S197A	ENST00000291552	NM_006758.2	197	Tcc/Gcc	8/8	1	2	FACETS	0.915	0.802	1	1	0.98	1	CLONAL	2	TRUE	1	0.217971040399501	2		254	346	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856024	45856024	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035156-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	23	282	0	ENST00000391945.4:c.1882A>T	p.Thr628Ser	p.T628S	ENST00000391945	NM_000400.3	628	Aca/Tca	20/23	0.217971040399501	4	FACETS	0.583	0.453	0.733	0.194	0.151	0.245	SUBCLONAL	1	TRUE	1	0.217971040399501	4		282	441	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486220	99486220	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1238271705	NA	P-0035156-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	25	291	1	ENST00000268035.6:c.3526G>A	p.Val1176Met	p.V1176M	ENST00000268035	NM_000875.3	1176	Gtg/Atg	19/21	1	2	FACETS	0.699	0.551	0.869	0.699	0.551	0.869	SUBCLONAL	1	TRUE	1	0.217971040399501	2		292	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0035466-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	143	425	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.193246895710041	2	FACETS	1	0.985	1	0.693	0.633	0.757	CLONAL	1	TRUE	0	0.27	2		425	764	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962930	2962930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349831751	NA	P-0035466-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	66	534	0	ENST00000396946.4:c.1978C>T	p.Arg660Trp	p.R660W	ENST00000396946	NM_032415.4	660	Cgg/Tgg	16/25	0.3	6	FACETS	0.802	0.694	0.919	0.2	0.173	0.23	CLONAL	1	TRUE	2	0.27	6		534	939	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641180	3641180	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035466-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	229	597	0	ENST00000294008.3:c.2459G>C	p.Arg820Thr	p.R820T	ENST00000294008	NM_032444.2	820	aGg/aCg	12/15	0.3	6	FACETS	0.839	0.782	0.898	0.839	0.782	0.898	CLONAL	3	TRUE	3	0.27	6		597	1038	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022653	36022653	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035466-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	117	484	0	ENST00000358208.4:c.526C>G	p.Leu176Val	p.L176V	ENST00000358208		176	Ctc/Gtc	5/12	0.174148947848405	4	FACETS	1	0.983	1	0.735	0.663	0.811	CLONAL	1	TRUE	2	0.27	4		484	749	SUCCESS
SCG5	6447	MSKCC	GRCh37	15	32935938	32935938	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035466-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	58	525	0	ENST00000300175.4:c.145G>C	p.Glu49Gln	p.E49Q	ENST00000300175	NM_001144757.1	49	Gag/Cag	2/6	0.191924003843662	2	FACETS	0.742	0.637	0.856	0.371	0.318	0.428	SUBCLONAL	1	TRUE	0	0.27	2		525	579	SUCCESS
PHF6	84295	MSKCC	GRCh37	X	133511718	133511718	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035466-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	30	174	0	ENST00000332070.3:c.71G>A	p.Arg24Lys	p.R24K	ENST00000332070	NM_032458.2	24	aGa/aAa	2/10	0.3	2	FACETS	1	0.852	1			1	CLONAL	1	TRUE	NA	0.27	2		174	210	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242477	+	inframe_deletion	In_Frame_Del	DEL	TTAAGAGAA	TTAAGAGAA	-	novel	NA	P-0035466-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	78	419	0	ENST00000275493.2:c.2239_2247del	p.Leu747_Glu749del	p.L747_E749del	ENST00000275493	NM_005228.3	747	TTAAGAGAA/-	19/28	0.3				0.965	1				CLONAL	1	TRUE	2	0.27	6		419	696	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0036265-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	96	353	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.049867987029715	3	FACETS	1	0.975	1	0.665	0.594	0.74	INDETERMINATE	1	TRUE	1	0.29	3		353	570	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67637153	67637153	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036265-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	41	393	0	ENST00000272342.5:c.2764C>T	p.Pro922Ser	p.P922S	ENST00000272342	NM_019002.3	922	Ccc/Tcc	6/6	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.29	2		393	227	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630459	187630459	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037275-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	15	441	0	ENST00000441802.2:c.523G>T	p.Asp175Tyr	p.D175Y	ENST00000441802	NM_005245.3	175	Gat/Tat	2/27	1	2	FACETS	0.996	0.729	1	0.996	0.729	1	CLONAL	1	TRUE	1	0.12	2		441	251	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473653	67473653	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037275-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	26	384	0	ENST00000327367.4:c.733G>T	p.Gly245Trp	p.G245W	ENST00000327367	NM_005902.3	245	Ggg/Tgg	6/9	1	2	FACETS	0.957	0.757	1	0.957	0.757	1	CLONAL	1	TRUE	1	0.12	2		384	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0039277-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	136	868	0	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.176783228543456	2	FACETS	0.832	0.756	0.912	0.832	0.756	0.912	CLONAL	2	TRUE	0	0.176783228543456	2		868	925	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076812	72076812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039277-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	46	622	0	ENST00000357731.5:c.685G>A	p.Glu229Lys	p.E229K	ENST00000357731	NM_173808.2	229	Gaa/Aaa	5/7	1	2	FACETS	0.753	0.633	0.887	0.753	0.633	0.887	SUBCLONAL	1	TRUE	1	0.176783228543456	2		622	691	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919214	48919214	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0039277-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	36	143	0	ENST00000267163.4:c.381-2A>T		p.X127_splice	ENST00000267163	NM_000321.2	127			0.176783228543456	2	FACETS	0.956	0.8	1	1	0.951	1	CLONAL	3	TRUE	0	0.176783228543456	2		143	142	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242701	98242701	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039277-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	97	734	0	ENST00000331920.6:c.916G>T	p.Ala306Ser	p.A306S	ENST00000331920	NM_000264.3	306	Gcc/Tcc	6/24	0.156205532864397	3	FACETS	1	0.978	1	0.71	0.632	0.793	CLONAL	1	TRUE	1	0.176783228543456	3		734	841	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508424	106508424	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039277-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	51	667	0	ENST00000359195.3:c.418C>G	p.Arg140Gly	p.R140G	ENST00000359195	NM_002649.2	140	Cgg/Ggg	2/11	1	2	FACETS	0.854	0.724	0.996	0.854	0.724	0.996	CLONAL	1	TRUE	1	0.176783228543456	2		667	676	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996746	100996746	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039277-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	37	544	0	ENST00000325455.5:c.1781C>A	p.Ala594Glu	p.A594E	ENST00000325455	NM_001202474.3	594	gCa/gAa	2/8	1	2	FACETS	0.694	0.571	0.832	0.694	0.571	0.832	SUBCLONAL	1	TRUE	1	0.176783228543456	2		544	603	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36989309	36989309	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039277-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	59	765	0	ENST00000354822.5:c.26C>A	p.Ala9Glu	p.A9E	ENST00000354822	NM_001079668.2	9	gCg/gAg	1/3	1	2	FACETS	0.977	0.84	1	0.977	0.84	1	CLONAL	1	TRUE	1	0.176783228543456	2		765	683	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304171	91304171	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039277-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	143	545	0	ENST00000355112.3:c.1568A>G	p.Asn523Ser	p.N523S	ENST00000355112	NM_000057.2	523	aAt/aGt	7/22	0.156205532864397	3	FACETS	0.852	0.778	0.929	1	0.982	1	CLONAL	3	TRUE	1	0.176783228543456	3		545	689	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032222	10032222	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039277-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	46	695	1	ENST00000330684.3:c.601C>A	p.Gln201Lys	p.Q201K	ENST00000330684	NM_001134407.1	201	Cag/Aag	3/13	1	2	FACETS	0.736	0.618	0.867	0.736	0.618	0.867	SUBCLONAL	1	TRUE	1	0.176783228543456	2		696	707	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160440	99160440	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039277-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	42	750	0	ENST00000074304.5:c.919G>C	p.Glu307Gln	p.E307Q	ENST00000074304	NM_001134224.1	307	Gag/Cag	11/26	1	2	FACETS	0.606	0.504	0.72	0.606	0.504	0.72	SUBCLONAL	1	TRUE	1	0.176783228543456	2		750	784	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098973	178098973	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039277-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	60	466	0	ENST00000397062.3:c.72G>T	p.Trp24Cys	p.W24C	ENST00000397062	NM_006164.4	24	tgG/tgT	2/5	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.176783228543456	2		466	454	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12647738	12647738	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039277-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	46	536	0	ENST00000251849.4:c.642G>T	p.Met214Ile	p.M214I	ENST00000251849	NM_002880.3	214	atG/atT	6/17	1	2	FACETS	0.808	0.679	0.951	0.808	0.679	0.951	CLONAL	1	TRUE	1	0.176783228543456	2		536	644	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164788	106164788	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039277-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	36	617	0	ENST00000380013.4:c.3656A>T	p.His1219Leu	p.H1219L	ENST00000380013	NM_001127208.2	1219	cAc/cTc	6/11	1	2	FACETS	0.715	0.586	0.859	0.715	0.586	0.859	SUBCLONAL	1	TRUE	1	0.176783228543456	2		617	570	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982054	38982054	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039277-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	31	515	0	ENST00000357387.3:c.668T>C	p.Ile223Thr	p.I223T	ENST00000357387	NM_152756.3	223	aTa/aCa	8/38	1	2	FACETS	0.57	0.46	0.696	0.57	0.46	0.696	SUBCLONAL	1	TRUE	1	0.176783228543456	2		515	615	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437236	110437236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1245478155	NA	P-0039277-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	28	272	0	ENST00000375856.3:c.1165C>T	p.Pro389Ser	p.P389S	ENST00000375856	NM_003749.2	389	Ccc/Tcc	1/2	0.176783228543456	2	FACETS	1	0.842	1	0.53	0.424	0.65	CLONAL	1	TRUE	0	0.176783228543456	2		272	299	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0039410-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	46	1407	0				ENST00000310581	NM_198253.2	-/1132			0.708007842019119	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	1	0.692173092690916	3		1407	80	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0039410-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	18	353	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.156100963015799	3	FACETS	1	0.882	1	0.409	0.319	0.507	INDETERMINATE	1	TRUE	0	0.692173092690916	3		353	57	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0039410-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	118	532	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.692173092690916	6	FACETS	1	0.967	1			1	CLONAL	5	TRUE	NA	0.692173092690916	6		532	157	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971187	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0039410-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	33	849	1	ENST00000304494.5:c.171_172delinsTT	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	57	gcCCga/gcTTga	2/3	0.708007842019119	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.692173092690916	2		850	41	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222727	5222727	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746980740	NA	P-0039410-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	17	464	0	ENST00000357368.4:c.3076C>T	p.Arg1026Cys	p.R1026C	ENST00000357368	NM_002850.3	1026	Cgc/Tgc	18/38	0.271645705923176	3	FACETS	0.906	0.693	1	0.302	0.231	0.382	INDETERMINATE	1	TRUE	0	0.692173092690916	3		464	73	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477813	140477813	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs180177037	NA	P-0039410-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	110	289	0	ENST00000288602.6:c.1495A>G	p.Lys499Glu	p.K499E	ENST00000288602	NM_004333.4	499	Aaa/Gaa	12/18	0.692173092690916	6	FACETS	0.987	0.913	1			1	CLONAL	4	TRUE	NA	0.692173092690916	6		289	192	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956771	68956771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774302685	NA	P-0039410-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	79	286	0	ENST00000288368.4:c.889C>T	p.Arg297Cys	p.R297C	ENST00000288368	NM_024870.2	297	Cgt/Tgt	8/40	0.403296879524375	5	FACETS	1	0.941	1	1	0.941	1	INDETERMINATE	3	TRUE	2	0.692173092690916	5		286	148	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504382	149504382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039410-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	10	358	0	ENST00000261799.4:c.1820G>A	p.Gly607Asp	p.G607D	ENST00000261799	NM_002609.3	607	gGc/gAc	13/23	0.228423805473402	2	FACETS	0.722	0.507	0.971	0.361	0.253	0.486	INDETERMINATE	1	TRUE	0	0.692173092690916	2		358	40	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677912	117677912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765109582	NA	P-0039410-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	23	328	0	ENST00000368508.3:c.4021G>A	p.Ala1341Thr	p.A1341T	ENST00000368508	NM_002944.2	1341	Gct/Act	25/43	0.55592759688602	1	FACETS	0.69	0.559	0.828	0.69	0.559	0.828	SUBCLONAL	1	TRUE	0	0.692173092690916	1		328	63	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870265	44870265	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0039410-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	20	235	0	ENST00000377967.4:c.443+1G>C		p.X148_splice	ENST00000377967	NM_021140.2	148			0.708007842019119	3	FACETS	1	0.793	1	0.505	0.396	0.625	CLONAL	1	TRUE	1	0.692173092690916	3		235	77	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs267605076	NA	P-0040965-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	301	192	0	ENST00000269305.4:c.672G>T	p.Glu224Asp	p.E224D	ENST00000269305	NM_001126112.2	224	gaG/gaT	6/11	0.47862753629535	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.478704087805811	2		192	613	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750596	41750596	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040965-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	146	434	0	ENST00000226382.2:c.32C>T	p.Ser11Phe	p.S11F	ENST00000226382	NM_003924.3	11	tCc/tTc	1/3	0.47862753629535	3	FACETS	1	0.977	1	0.595	0.545	0.648	CLONAL	1	TRUE	1	0.478704087805811	3		434	635	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372161	55372161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200451706	NA	P-0040965-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	524	655	0	ENST00000297316.4:c.851C>T	p.Pro284Leu	p.P284L	ENST00000297316	NM_022454.3	284	cCg/cTg	2/2	0.478704087805811	7	FACETS	0.981	0.939	1	0.589	0.563	0.614	CLONAL	3	TRUE	2	0.478704087805811	7		655	1634	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0041296-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	217	443	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.567064785799825	2		443	671	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160488	108160488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730881369	NA	P-0041296-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	230	445	0	ENST00000278616.4:c.4396C>T	p.Arg1466Ter	p.R1466*	ENST00000278616	NM_000051.3	1466	Cga/Tga	29/63	0.567064785799825	1	FACETS	0.923	0.865	0.981	0.923	0.865	0.981	CLONAL	1	TRUE	0	0.567064785799825	1		445	630	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589599	67589604	+	inframe_deletion	In_Frame_Del	DEL	TCAGTT	TCAGTT	-	novel	NA	P-0041296-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	211	390	0	ENST00000274335.5:c.1365_1370del	p.Phe456_Gln457del	p.F456_Q457del	ENST00000274335		454	acTCAGTTt/act	10/15	1	2	FACETS	0.927	0.863	0.993	0.927	0.863	0.993	CLONAL	1	TRUE	1	0.567064785799825	2		390	803	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339565	116339565	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs779093896	NA	P-0041296-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	241	571	0	ENST00000397752.3:c.427C>T	p.Arg143Ter	p.R143*	ENST00000397752	NM_000245.2	143	Cga/Tga	2/21	1	2	FACETS	0.936	0.876	0.998	0.936	0.876	0.998	CLONAL	1	TRUE	1	0.567064785799825	2		571	908	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692827	89692836	+	frameshift_variant	Frame_Shift_Del	DEL	TTTGTGAAGA	TTTGTGAAGA	-	novel	NA	P-0041296-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	127	153	0	ENST00000371953.3:c.312_321del	p.Cys105LeufsTer5	p.C105Lfs*5	ENST00000371953	NM_000314.4	104	tTTTGTGAAGAt/tt	5/9	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.567064785799825	2		153	353	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375375	15375375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146695616	NA	P-0041296-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	196	681	0	ENST00000263377.2:c.1052C>T	p.Ser351Leu	p.S351L	ENST00000263377	NM_058243.2	351	tCg/tTg	6/20	1	2	FACETS	0.901	0.836	0.968	0.901	0.836	0.968	CLONAL	1	TRUE	1	0.567064785799825	2		681	767	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923143	48923163	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTTTTATTAGCTAAAGGTAA	ATTTTTATTAGCTAAAGGTAA	-	novel	NA	P-0041296-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	203	268	0	ENST00000267163.4:c.591_607+4del		p.X197_splice	ENST00000267163	NM_000321.2	197		6/27	0.567064785799825	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.567064785799825	1		268	439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1064795203	NA	P-0041659-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	364	532	0	ENST00000269305.4:c.532C>G	p.His178Asp	p.H178D	ENST00000269305	NM_001126112.2	178	Cac/Gac	5/11	0.812233231556388	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.812233231556388	2		532	440	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589623	67589634	+	inframe_deletion	In_Frame_Del	DEL	ATATGATAGATT	ATATGATAGATT	-	novel	NA	P-0041659-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	40	331	0	ENST00000274335.5:c.1392_1403del	p.Asp464_Tyr467del	p.D464_Y467del	ENST00000274335		462	gaATATGATAGATTa/gaa	10/15	0.784204512052611	4	FACETS	0.265	0.219	0.316	0.088	0.073	0.106	SUBCLONAL	1	TRUE	1	0.812233231556388	4		331	674	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0041715-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	39	461	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.205675392763856	3	FACETS	0.831	0.689	0.989	0.416	0.344	0.495	CLONAL	1	FALSE	1	0.239333592595773	3		461	439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0041715-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	116	442	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.190896481110213	2	FACETS	0.76	0.686	0.837	0.76	0.686	0.837	SUBCLONAL	2	FALSE	0	0.239333592595773	2		442	638	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0041715-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	122	432	1	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.239333592595773	3	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	FALSE	1	0.239333592595773	3		433	541	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691191	18691191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774205366	NA	P-0041715-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	154	588	0	ENST00000266497.5:c.3302G>A	p.Arg1101His	p.R1101H	ENST00000266497		1101	cGt/cAt	23/31	0.239333592595773	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	FALSE	1	0.239333592595773	3		588	606	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0041715-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	111	840	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	0.205675392763856	3	FACETS	1	0.98	1	0.688	0.618	0.761	CLONAL	1	FALSE	1	0.239333592595773	3		840	755	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653437	206653437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782340929	NA	P-0041715-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	59	742	1	ENST00000367120.3:c.1321C>T	p.Arg441Trp	p.R441W	ENST00000367120	NM_014002.3	441	Cgg/Tgg	12/22	1	2	FACETS	0.799	0.687	0.921	0.799	0.687	0.921	CLONAL	1	FALSE	1	0.239333592595773	2		743	617	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853328	68853328	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786202290	NA	P-0041715-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	44	633	0	ENST00000261769.5:c.1711G>A	p.Gly571Ser	p.G571S	ENST00000261769	NM_004360.3	571	Ggt/Agt	11/16	1	2	FACETS	0.625	0.524	0.738	0.625	0.524	0.738	SUBCLONAL	1	FALSE	1	0.239333592595773	2		633	588	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844722	156844722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs986498490	NA	P-0041715-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	72	1055	0	ENST00000524377.1:c.1276G>A	p.Val426Ile	p.V426I	ENST00000524377	NM_002529.3	426	Gtc/Atc	11/17	1	2	FACETS	0.652	0.568	0.743	0.652	0.568	0.743	SUBCLONAL	1	FALSE	1	0.239333592595773	2		1055	923	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223053	5223053	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041715-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	70	1053	0	ENST00000357368.4:c.2750C>A	p.Ala917Glu	p.A917E	ENST00000357368	NM_002850.3	917	gCa/gAa	18/38	1	2	FACETS	0.767	0.667	0.874	0.767	0.667	0.874	SUBCLONAL	1	FALSE	1	0.239333592595773	2		1053	763	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0041905-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	398	472	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.767277114318817	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.768269232765865	2		472	483	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260707	16260707	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041905-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	205	472	0	ENST00000375759.3:c.7972G>T	p.Val2658Leu	p.V2658L	ENST00000375759	NM_015001.2	2658	Gtg/Ttg	11/15	1	2	FACETS	0.953	0.891	1	0.953	0.891	1	CLONAL	1	TRUE	1	0.768269232765865	2		472	560	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789684	3789684	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041905-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	121	300	0	ENST00000262367.5:c.4175G>A	p.Arg1392Gln	p.R1392Q	ENST00000262367	NM_004380.2	1392	cGa/cAa	25/31	0.768269232765865	5	FACETS	0.796	0.719	0.877	0.265	0.239	0.293	SUBCLONAL	1	TRUE	2	0.768269232765865	5		300	852	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660472	67660472	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041905-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	256	269	0	ENST00000264010.4:c.1372A>G	p.Lys458Glu	p.K458E	ENST00000264010	NM_006565.3	458	Aag/Gag	8/12	0.666839274129156	4	FACETS	0.943	0.889	0.997	0.943	0.889	0.997	CLONAL	2	TRUE	2	0.768269232765865	4		269	625	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836985	89836985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs539161141	NA	P-0041905-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	114	338	0	ENST00000389301.3:c.2209G>A	p.Ala737Thr	p.A737T	ENST00000389301	NM_000135.2	737	Gct/Act	24/43	0.666839274129156	4	FACETS	0.856	0.773	0.944	0.428	0.386	0.472	CLONAL	1	TRUE	2	0.768269232765865	4		338	613	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56402502	56402502	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0041905-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	108	239	0	ENST00000348428.3:c.1544T>A	p.Leu515Ter	p.L515*	ENST00000348428	NM_006785.3	515	tTa/tAa	13/17	0.768269232765865	1	FACETS	0.931	0.862	0.999	0.931	0.862	0.999	CLONAL	1	TRUE	0	0.768269232765865	1		239	186	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940449	29940449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375097381	NA	P-0041905-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	85	232	0	ENST00000389048.3:c.782G>A	p.Arg261Gln	p.R261Q	ENST00000389048	NM_004304.4	261	cGa/cAa	2/29	0.768269232765865	3	FACETS	0.906	0.808	1	0.453	0.404	0.505	CLONAL	1	TRUE	1	0.768269232765865	3		232	338	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231825	36231825	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041905-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	360	423	0	ENST00000300305.3:c.559G>T	p.Ala187Ser	p.A187S	ENST00000300305		187	Gcc/Tcc	5/8	0.501319207687473	4	FACETS	0.985	0.939	1	0.985	0.939	1	CLONAL	2	TRUE	2	0.768269232765865	4		423	841	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610695	52610695	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041905-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	223	298	0	ENST00000394830.3:c.3478C>T	p.Arg1160Ter	p.R1160*	ENST00000394830	NM_018313.4	1160	Cga/Tga	23/30	0.768269232765865	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.768269232765865	2		298	280	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462360	89462360	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041905-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	25	293	0	ENST00000336596.2:c.1832A>T	p.Glu611Val	p.E611V	ENST00000336596	NM_005233.5	611	gAg/gTg	10/17	0.768269232765865	3	FACETS	0.211	0.166	0.263			1	SUBCLONAL	1	TRUE	NA	0.768269232765865	3		293	427	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468391	89468391	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041905-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	167	294	0	ENST00000336596.2:c.1925T>G	p.Leu642Arg	p.L642R	ENST00000336596	NM_005233.5	642	cTt/cGt	11/17	0.768269232765865	3	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.768269232765865	3		294	463	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280085	66280085	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041905-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	140	322	0	ENST00000273854.3:c.1604T>A	p.Val535Asp	p.V535D	ENST00000273854	NM_004439.5	535	gTt/gAt	7/18	0.767277114318817	2	FACETS	0.895	0.824	0.969	0.448	0.412	0.485	CLONAL	1	TRUE	0	0.768269232765865	2		322	407	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840582	36840582	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042293-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	36	485	0	ENST00000358127.4:c.1151C>G	p.Ala384Gly	p.A384G	ENST00000358127	NM_001280556.1	384	gCc/gGc	10/10	0.676219240899687	1	FACETS	0.176	0.145	0.212	0.176	0.145	0.212	SUBCLONAL	1	TRUE	0	0.676219240899687	1		485	400	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988128	85988128	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042748-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	106	288	0	ENST00000263360.6:c.1073A>G	p.Tyr358Cys	p.Y358C	ENST00000263360	NM_003797.3	358	tAc/tGc	10/12	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.572084172849393	2		288	358	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875985	76875985	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042748-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	65	181	0	ENST00000373344.5:c.5150T>G	p.Val1717Gly	p.V1717G	ENST00000373344	NM_000489.3	1717	gTt/gGt	20/35	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.572084172849393	2		181	226	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720677	89720677	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	18	144	0	ENST00000371953.3:c.828T>G	p.Asn276Lys	p.N276K	ENST00000371953	NM_000314.4	276	aaT/aaG	8/9	0.542873582186042	2	FACETS	0.873	0.699	1	0.873	0.699	1	CLONAL	2	TRUE	0	0.542873582186042	2		144	38	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435291	18435291	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	282	678	0	ENST00000266497.5:c.276A>C	p.Lys92Asn	p.K92N	ENST00000266497		92	aaA/aaC	1/31	0.495035471787395	4	FACETS	0.941	0.887	0.996	0.941	0.887	0.996	CLONAL	2	TRUE	2	0.542873582186042	4		678	852	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378658	25378658	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	107	395	0	ENST00000311936.3:c.340G>C	p.Val114Leu	p.V114L	ENST00000311936	NM_004985.3	114	Gta/Cta	4/5	0.495035471787395	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.542873582186042	4		395	268	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058379	42058379	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	111	629	0	ENST00000219905.7:c.8099G>T	p.Arg2700Ile	p.R2700I	ENST00000219905	NM_001164273.1	2700	aGa/aTa	24/24	0.542873582186042	3	FACETS	0.633	0.569	0.702	0.317	0.284	0.351	SUBCLONAL	1	TRUE	1	0.542873582186042	3		629	821	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801794	3801794	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	184	653	0	ENST00000262367.5:c.3712G>T	p.Glu1238Ter	p.E1238*	ENST00000262367	NM_004380.2	1238	Gag/Tag	20/31	0.542873582186042	3	FACETS	1	0.968	1	0.543	0.502	0.586	CLONAL	1	TRUE	1	0.542873582186042	3		653	793	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0044333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	361	768	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.542873582186042	2	FACETS	0.957	0.915	0.998	0.957	0.915	0.998	CLONAL	2	TRUE	0	0.542873582186042	2		768	695	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436185	56436185	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0044333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	301	618	0	ENST00000407977.2:c.953-1G>C		p.X318_splice	ENST00000407977		318			0.542873582186042	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.542873582186042	2		618	506	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945592	54945592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	130	408	0	ENST00000312783.6:c.978G>T	p.Lys326Asn	p.K326N	ENST00000312783	NM_198436.1	326	aaG/aaT	9/10	0.27122528272844	5	FACETS	0.928	0.848	1	0.619	0.565	0.675	INDETERMINATE	2	TRUE	2	0.542873582186042	5		408	468	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713901	30713901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	380	788	0	ENST00000295754.5:c.1226C>T	p.Ser409Phe	p.S409F	ENST00000295754	NM_003242.5	409	tCt/tTt	4/7	0.542873582186042	2	FACETS	0.98	0.939	1	0.98	0.939	1	CLONAL	2	TRUE	0	0.542873582186042	2		788	714	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139834	55139834	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746574289	NA	P-0044333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	350	675	0	ENST00000257290.5:c.1495G>A	p.Val499Met	p.V499M	ENST00000257290	NM_006206.4	499	Gtg/Atg	10/23	0.538818546067358	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.542873582186042	2		675	632	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665655	86665655	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	60	304	0	ENST00000274376.6:c.1636C>T	p.Gln546Ter	p.Q546*	ENST00000274376	NM_002890.2	546	Cag/Tag	12/25	0.542873582186042	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	0	0.542873582186042	2		304	104	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157495219	157495219	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554229937	NA	P-0044333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	714	721	0	ENST00000346085.5:c.3103G>T	p.Glu1035Ter	p.E1035*	ENST00000346085	NM_020732.3	1035	Gaa/Taa	11/20	0.542873582186042	6	FACETS	1	0.976	1	1	0.976	1	CLONAL	4	TRUE	2	0.542873582186042	6		721	1360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587781845	NA	P-0046285-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	204	628	0	ENST00000269305.4:c.511G>T	p.Glu171Ter	p.E171*	ENST00000269305	NM_001126112.2	171	Gag/Tag	5/11	0.760271570795419	3	FACETS	0.901	0.837	0.967	0.451	0.418	0.484	CLONAL	1	TRUE	1	0.760271570795419	3		628	822	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0046285-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	312	332	0	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			0.745875881739102	2	FACETS	0.979	0.945	1	0.979	0.945	1	CLONAL	2	TRUE	0	0.760271570795419	2		332	419	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230492731	230492731	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046285-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	255	547	0	ENST00000391860.1:c.323G>T	p.Ser108Ile	p.S108I	ENST00000391860	NM_001258311.1	108	aGc/aTc	2/7	0.656386865226741	3	FACETS	0.908	0.86	0.955	0.908	0.86	0.955	CLONAL	2	TRUE	1	0.760271570795419	3		547	510	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499632	18499632	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs764573135	NA	P-0046285-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	228	543	0	ENST00000266497.5:c.1487T>C	p.Val496Ala	p.V496A	ENST00000266497		496	gTc/gCc	10/31	0.302184520180958	4	FACETS	1	0.991	1	0.341	0.318	0.364	INDETERMINATE	1	TRUE	0	0.760271570795419	4		543	774	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578277	7578284	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGGGGC	GGAGGGGC	-	novel	NA	P-0046285-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	471	702	0	ENST00000269305.4:c.565_572del	p.Ala189SerfsTer17	p.A189Sfs*17	ENST00000269305	NM_001126112.2	189	GCCCCTCCt/t	6/11	0.760271570795419	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.760271570795419	3		702	844	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136170	11136170	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046285-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	311	486	0	ENST00000358026.2:c.3155del	p.Phe1052SerfsTer54	p.F1052Sfs*54	ENST00000358026	NM_001128849.1	1052	Ttc/tc	22/36	0.760271570795419	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.760271570795419	2		486	386	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146538	185146538	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046285-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	414	569	0	ENST00000265026.3:c.169A>C	p.Ile57Leu	p.I57L	ENST00000265026	NM_004721.4	57	Atc/Ctc	2/14	0.760271570795419	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.760271570795419	4		569	918	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057874	27057874	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046794-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	544	630	0	ENST00000324856.7:c.1582C>T	p.Gln528Ter	p.Q528*	ENST00000324856	NM_006015.4	528	Cag/Tag	3/20	0.499943356915382	3	FACETS	0.945	0.913	0.976			1	CLONAL	3	TRUE	NA	0.499943356915382	3		630	960	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604634	43604634	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046794-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	146	531	0	ENST00000355710.3:c.1219A>C	p.Thr407Pro	p.T407P	ENST00000355710	NM_020975.4	407	Acc/Ccc	6/20	0.499943356915382	1	FACETS	0.973	0.896	1	0.973	0.896	1	CLONAL	1	TRUE	0	0.499943356915382	1		531	450	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604641	43604641	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046794-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	149	518	0	ENST00000355710.3:c.1226C>A	p.Ser409Tyr	p.S409Y	ENST00000355710	NM_020975.4	409	tCc/tAc	6/20	0.499943356915382	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.499943356915382	1		518	446	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615014	43615014	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764784013	NA	P-0046794-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	169	534	0	ENST00000355710.3:c.2428G>A	p.Gly810Ser	p.G810S	ENST00000355710	NM_020975.4	810	Ggc/Agc	14/20	0.499943356915382	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.499943356915382	1		534	466	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236215	108236215	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046794-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	182	487	0	ENST00000278616.4:c.9151G>A	p.Gly3051Arg	p.G3051R	ENST00000278616	NM_000051.3	3051	Gga/Aga	63/63	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.499943356915382	2		487	631	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555263	106555263	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046794-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	151	488	0	ENST00000369096.4:c.2380T>C	p.Ser794Pro	p.S794P	ENST00000369096	NM_001198.3	794	Tca/Cca	7/7	0.499943356915382	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.499943356915382	1		488	439	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0046823-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	56	170	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.505325751485837	2	FACETS	0.839	0.726	0.961	0.42	0.363	0.481	CLONAL	1	TRUE	0	0.511307237328485	2		170	261	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0046823-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4595	178	438	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.511307237328485	46	FACETS	0.893	0.818	0.973	0.042	0.038	0.046	CLONAL	2	TRUE	3	0.511307237328485	46		438	4773	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203553	108203553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046823-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	35	463	0	ENST00000278616.4:c.7853G>A	p.Arg2618Lys	p.R2618K	ENST00000278616	NM_000051.3	2618	aGa/aAa	53/63	0.515136872508322	3	FACETS	0.33	0.27	0.398	0.11	0.09	0.133	SUBCLONAL	1	TRUE	0	0.511307237328485	3		463	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0046823-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	415	520	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	0.486135197972418	4	FACETS	0.994	0.96	1	0.994	0.96	1	CLONAL	4	TRUE	0	0.511307237328485	4		520	617	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242484	55242507	+	inframe_deletion	In_Frame_Del	DEL	TCTCCGAAAGCCAACAAGGAAATC	TCTCCGAAAGCCAACAAGGAAATC	-	rs121913463	NA	P-0046823-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	3075	419	0	ENST00000275493.2:c.2254_2277del	p.Ser752_Ile759del	p.S752_I759del	ENST00000275493	NM_005228.3	752	TCTCCGAAAGCCAACAAGGAAATC/-	19/28	0.511307237328485	46	FACETS	1	0.993	1	0.978	0.97	0.986	CLONAL	42	TRUE	3	0.511307237328485	46		419	3503	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267361	198267361	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754688962	NA	P-0046823-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	133	550	0	ENST00000335508.6:c.1996A>G	p.Lys666Glu	p.K666E	ENST00000335508	NM_012433.2	666	Aag/Gag	14/25	0.515136872508322	3	FACETS	1	0.948	1	0.352	0.321	0.385	CLONAL	1	TRUE	0	0.511307237328485	3		550	618	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133761003	133761003	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1021481710	NA	P-0046823-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	99	520	0	ENST00000318560.5:c.3326C>T	p.Ala1109Val	p.A1109V	ENST00000318560	NM_005157.4	1109	gCg/gTg	11/11	0.458121647364933	2	FACETS	1	0.945	1	0.536	0.483	0.592	CLONAL	1	TRUE	0	0.511307237328485	2		520	361	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539390	187539390	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046823-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	47	581	0	ENST00000441802.2:c.8350C>G	p.Gln2784Glu	p.Q2784E	ENST00000441802	NM_005245.3	2784	Caa/Gaa	10/27	0.515136872508322	1	FACETS	0.346	0.293	0.405	0.346	0.293	0.405	SUBCLONAL	1	TRUE	0	0.511307237328485	1		581	395	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115252190	115252190	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046823-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	75	396	0	ENST00000369535.4:c.450G>C	p.Gln150His	p.Q150H	ENST00000369535	NM_002524.4	150	caG/caC	4/7	0.505325751485837	2	FACETS	0.946	0.837	1	0.473	0.418	0.531	CLONAL	1	TRUE	0	0.511307237328485	2		396	310	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203529	108203529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046823-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	33	431	0	ENST00000278616.4:c.7829G>A	p.Arg2610Lys	p.R2610K	ENST00000278616	NM_000051.3	2610	aGa/aAa	53/63	0.515136872508322	3	FACETS	0.348	0.283	0.421	0.116	0.094	0.141	SUBCLONAL	1	TRUE	0	0.511307237328485	3		431	466	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204687	108204687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046823-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	34	349	0	ENST00000278616.4:c.8002G>A	p.Glu2668Lys	p.E2668K	ENST00000278616	NM_000051.3	2668	Gaa/Aaa	54/63	0.515136872508322	3	FACETS	0.394	0.322	0.475	0.131	0.107	0.159	SUBCLONAL	1	TRUE	0	0.511307237328485	3		349	424	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392030	118392030	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046823-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	70	518	0	ENST00000534358.1:c.11541C>G	p.Phe3847Leu	p.F3847L	ENST00000534358	NM_005933.3	3847	ttC/ttG	35/36	0.515136872508322		FACETS		0.564	0.735				SUBCLONAL	1	TRUE	0	0.511307237328485	3		518	532	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346858	91346858	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046823-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	79	459	0	ENST00000355112.3:c.3466G>C	p.Asp1156His	p.D1156H	ENST00000355112	NM_000057.2	1156	Gat/Cat	18/22	0.498487493005117	2	FACETS	0.939	0.833	1	0.47	0.416	0.526	CLONAL	1	TRUE	0	0.511307237328485	2		459	329	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670115	29670115	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046823-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	31	424	0	ENST00000356175.3:c.7088C>G	p.Ser2363Cys	p.S2363C	ENST00000356175	NM_000267.3	2363	tCt/tGt	47/57	0.486135197972418	4	FACETS	0.414	0.334	0.504	0.103	0.083	0.126	SUBCLONAL	1	TRUE	0	0.511307237328485	4		424	443	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1266609	1266609	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046823-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	59	523	0	ENST00000310581.5:c.2624C>G	p.Pro875Arg	p.P875R	ENST00000310581	NM_198253.2	875	cCt/cGt	10/16	0.511307237328485	5	FACETS	0.61	0.525	0.704	0.122	0.105	0.141	SUBCLONAL	1	TRUE	0	0.511307237328485	5		523	668	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38946579	38946579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046823-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	82	331	0	ENST00000357387.3:c.4390G>A	p.Asp1464Asn	p.D1464N	ENST00000357387	NM_152756.3	1464	Gat/Aat	33/38	0.457027393146221	3	FACETS	1	0.891	1	0.502	0.445	0.563	CLONAL	1	TRUE	1	0.511307237328485	3		331	401	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204495484	204495489	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCAGGT	TCAGGT	A	novel	NA	P-0046823-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	68	416	0	ENST00000367182.3:c.79-4_80delinsA		p.X27_splice	ENST00000367182	NM_001278516.1	27		3/11	0.471556893167055	5	FACETS	0.953	0.831	1	0.318	0.277	0.362	CLONAL	1	TRUE	2	0.511307237328485	5		416	493	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0048888-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	328	286	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.438524463462598	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	0	0.438524463462598	3		286	591	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65569055	65569055	+	start_lost	Translation_Start_Site	SNP	C	C	A	novel	NA	P-0048888-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	222	350	0	ENST00000358664.4:c.3G>T	p.Met1?	p.M1?	ENST00000358664	NM_002382.4	1	atG/atT	1/5	0.437796376297166	2	FACETS	0.999	0.939	1	0.999	0.939	1	CLONAL	2	TRUE	0	0.438524463462598	2		350	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572966	7572990	+	frameshift_variant	Frame_Shift_Del	DEL	TTTATGGCGGGAGGTAGACTGACCC	TTTATGGCGGGAGGTAGACTGACCC	-	novel	NA	P-0048888-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	254	437	0	ENST00000269305.4:c.1119_1143del	p.Gly374AsnfsTer40	p.G374Nfs*40	ENST00000269305	NM_001126112.2	373	aaGGGTCAGTCTACCTCCCGCCATAAA/aa	11/11	0.438524463462598	2	FACETS	0.922	0.87	0.976	0.922	0.87	0.976	CLONAL	2	TRUE	0	0.438524463462598	2		437	628	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971191	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCGC	GGGCGC	A	novel	NA	P-0048888-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	281	516	0	ENST00000304494.5:c.167_172delinsT	p.Ser56MetfsTer62	p.S56Mfs*62	ENST00000304494	NM_000077.4	56	aGCGCCCga/aTga	2/3	0.438524463462598	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.438524463462598	2		516	629	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913517	NA	P-0049621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	257	421	0	ENST00000288135.5:c.1676T>A	p.Val559Asp	p.V559D	ENST00000288135	NM_000222.2	559	gTt/gAt	11/21	1	2	FACETS	0.941	0.89	0.992	1	0.995	1	CLONAL	2	TRUE	1	0.48520450108899	2		421	563	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513750	41513753	+	frameshift_variant	Frame_Shift_Del	DEL	ACTG	ACTG	-	novel	NA	P-0049621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	42	594	1	ENST00000263253.7:c.659_662del	p.Thr220SerfsTer16	p.T220Sfs*16	ENST00000263253	NM_001429.3	218	ttACTG/tt	2/31	1	2	FACETS	0.239	0.199	0.284	0.239	0.199	0.284	SUBCLONAL	1	TRUE	1	0.48520450108899	2		595	724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0050859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	32	425	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		425	216	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260606	16260606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200512596	NA	P-0050859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	45	530	0	ENST00000375759.3:c.7871G>A	p.Arg2624Gln	p.R2624Q	ENST00000375759	NM_015001.2	2624	cGg/cAg	11/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		530	207	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2084147	2084147	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	10	358	0	ENST00000349721.2:c.2477T>G	p.Leu826Arg	p.L826R	ENST00000349721	NM_003070.3	826	cTc/cGc	17/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		358	163	SUCCESS
APC	324	MSKCC	GRCh37	5	112175279	112175284	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CCTAGA	CCTAGA	TAGG	novel	NA	P-0050859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	30	446	1	ENST00000257430.4:c.3988_3993delinsTAGG	p.Pro1330Ter	p.P1330*	ENST00000257430	NM_000038.5	1330	CCTAGA/TAGG	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		447	192	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977949	134977949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56186270	NA	P-0051005-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	72	428	0	ENST00000398015.3:c.2942C>T	p.Thr981Met	p.T981M	ENST00000398015	NM_004441.4	981	aCg/aTg	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		428	362	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432435	49432435	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051005-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	125	531	0	ENST00000301067.7:c.8704C>T	p.Gln2902Ter	p.Q2902*	ENST00000301067	NM_003482.3	2902	Cag/Tag	34/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		531	480	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456650	138456650	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs750830394	NA	P-0051005-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	36	356	0	ENST00000289153.2:c.700A>G	p.Ile234Val	p.I234V	ENST00000289153	NM_006219.2	234	Att/Gtt	4/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		356	275	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457823	69457823	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051005-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	66	377	0	ENST00000227507.2:c.223G>T	p.Glu75Ter	p.E75*	ENST00000227507	NM_053056.2	75	Gag/Tag	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		377	382	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432335	49432335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051005-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	134	520	0	ENST00000301067.7:c.8804C>T	p.Ser2935Leu	p.S2935L	ENST00000301067	NM_003482.3	2935	tCa/tTa	34/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		520	473	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432354	49432354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051005-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	127	518	0	ENST00000301067.7:c.8785C>T	p.Leu2929Phe	p.L2929F	ENST00000301067	NM_003482.3	2929	Ctt/Ttt	34/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		518	472	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432359	49432359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051005-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	125	543	0	ENST00000301067.7:c.8780C>T	p.Ser2927Leu	p.S2927L	ENST00000301067	NM_003482.3	2927	tCa/tTa	34/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		543	473	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432703	49432704	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCTG	novel	NA	P-0051005-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	54	494	0	ENST00000301067.7:c.8431_8435dup	p.Gln2812HisfsTer41	p.Q2812Hfs*41	ENST00000301067	NM_003482.3	2812	cag/caCAGCAg	34/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		494	516	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346386	89346387	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0051005-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	40	424	0	ENST00000301030.4:c.6562_6563dup	p.Ala2189ArgfsTer30	p.A2189Rfs*30	ENST00000301030	NM_001256183.1	2188	ccg/ccCCg	9/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		424	382	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1627360	1627360	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051005-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	62	392	0	ENST00000344749.5:c.364C>G	p.Gln122Glu	p.Q122E	ENST00000344749	NM_001136139.2	122	Cag/Gag	6/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		392	335	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141568662	141568662	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051005-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	30	451	0	ENST00000220592.5:c.800T>A	p.Val267Glu	p.V267E	ENST00000220592	NM_012154.3	267	gTg/gAg	7/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		451	477	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977949	134977949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56186270	NA	P-0051005-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	306	428	0	ENST00000398015.3:c.2942C>T	p.Thr981Met	p.T981M	ENST00000398015	NM_004441.4	981	aCg/aTg	16/16	0.361532942343444	3	FACETS	0.877	0.83	0.925	0.877	0.83	0.925	CLONAL	2	TRUE	1	0.535456989932428	3		428	826	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432435	49432435	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051005-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	446	531	0	ENST00000301067.7:c.8704C>T	p.Gln2902Ter	p.Q2902*	ENST00000301067	NM_003482.3	2902	Cag/Tag	34/54	0.303839076403348	2	FACETS	0.863	0.827	0.899	0.863	0.827	0.899	INDETERMINATE	2	TRUE	0	0.535456989932428	2		531	965	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456650	138456650	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs750830394	NA	P-0051005-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	92	356	0	ENST00000289153.2:c.700A>G	p.Ile234Val	p.I234V	ENST00000289153	NM_006219.2	234	Att/Gtt	4/22	0.361532942343444	3	FACETS	1	0.942	1	0.54	0.483	0.601	CLONAL	1	TRUE	1	0.535456989932428	3		356	403	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457823	69457823	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051005-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	242	377	0	ENST00000227507.2:c.223G>T	p.Glu75Ter	p.E75*	ENST00000227507	NM_053056.2	75	Gag/Tag	2/5	0.399922962322593	3	FACETS	1	0.992	1	0.714	0.668	0.76	CLONAL	1	TRUE	1	0.535456989932428	3		377	803	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432335	49432335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051005-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	431	520	0	ENST00000301067.7:c.8804C>T	p.Ser2935Leu	p.S2935L	ENST00000301067	NM_003482.3	2935	tCa/tTa	34/54	0.303839076403348	2	FACETS	0.854	0.817	0.89	0.854	0.817	0.89	INDETERMINATE	2	TRUE	0	0.535456989932428	2		520	943	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432354	49432354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051005-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	450	518	0	ENST00000301067.7:c.8785C>T	p.Leu2929Phe	p.L2929F	ENST00000301067	NM_003482.3	2929	Ctt/Ttt	34/54	0.303839076403348	2	FACETS	0.872	0.836	0.908	0.872	0.836	0.908	INDETERMINATE	2	TRUE	0	0.535456989932428	2		518	964	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432359	49432359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051005-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	465	543	0	ENST00000301067.7:c.8780C>T	p.Ser2927Leu	p.S2927L	ENST00000301067	NM_003482.3	2927	tCa/tTa	34/54	0.303839076403348	2	FACETS	0.883	0.848	0.919	0.883	0.848	0.919	INDETERMINATE	2	TRUE	0	0.535456989932428	2		543	983	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432703	49432704	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCTG	novel	NA	P-0051005-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	159	494	0	ENST00000301067.7:c.8431_8435dup	p.Gln2812HisfsTer41	p.Q2812Hfs*41	ENST00000301067	NM_003482.3	2812	cag/caCAGCAg	34/54	0.303839076403348	2	FACETS	0.602	0.551	0.655	0.301	0.275	0.328	INDETERMINATE	1	TRUE	0	0.535456989932428	2		494	987	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346386	89346387	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0051005-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	146	424	0	ENST00000301030.4:c.6562_6563dup	p.Ala2189ArgfsTer30	p.A2189Rfs*30	ENST00000301030	NM_001256183.1	2188	ccg/ccCCg	9/13	0.365034937970956	1	FACETS	0.559	0.511	0.609	0.559	0.511	0.609	SUBCLONAL	1	TRUE	0	0.535456989932428	1		424	714	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1627360	1627360	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051005-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	253	392	0	ENST00000344749.5:c.364C>G	p.Gln122Glu	p.Q122E	ENST00000344749	NM_001136139.2	122	Cag/Gag	6/19	0.539788196184658	2	FACETS	1	0.992	1	0.683	0.642	0.724	CLONAL	1	TRUE	0	0.535456989932428	2		392	692	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141568662	141568662	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051005-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	148	451	0	ENST00000220592.5:c.800T>A	p.Val267Glu	p.V267E	ENST00000220592	NM_012154.3	267	gTg/gAg	7/19	0.539788196184658	4	FACETS	0.773	0.705	0.845	0.193	0.176	0.212	SUBCLONAL	1	TRUE	0	0.535456989932428	4		451	1098	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780851	9780851	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777389	NA	P-0051005-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	64	573	0	ENST00000377346.4:c.1573G>A	p.Glu525Lys	p.E525K	ENST00000377346	NM_005026.3	525	Gag/Aag	13/24	0.399922962322593	3	FACETS	0.326	0.281	0.375	0.163	0.14	0.188	SUBCLONAL	1	TRUE	1	0.535456989932428	3		573	930	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115952	8115953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0051634-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	150	500	0	ENST00000346208.3:c.1299_1300dup	p.His434ProfsTer42	p.H434Pfs*42	ENST00000346208		433	cac/caCCc	6/6	0.754125998242421	3	FACETS	1	0.984	1	0.633	0.584	0.683	CLONAL	1	TRUE	1	0.754125998242421	3		500	433	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195298	102195368	+	frameshift_variant	Frame_Shift_Del	DEL	TTTGAACTGAAATACGACTTGTCATGTGAACTGTACCGAATGTCTACGTATTCCACTTTTCCTGCTGGGGT	TTTGAACTGAAATACGACTTGTCATGTGAACTGTACCGAATGTCTACGTATTCCACTTTTCCTGCTGGGGT	-	novel	NA	P-0051634-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	102	379	0	ENST00000263464.3:c.59_129del	p.Phe20SerfsTer19	p.F20Sfs*19	ENST00000263464	NM_001165.4	20	TTTGAACTGAAATACGACTTGTCATGTGAACTGTACCGAATGTCTACGTATTCCACTTTTCCTGCTGGGGTt/t	2/9	0.754125998242421	2	FACETS	0.97	0.88	1	0.485	0.44	0.531	CLONAL	1	TRUE	0	0.754125998242421	2		379	279	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224493	108224493	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs748192003	NA	P-0051634-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	242	300	0	ENST00000278616.4:c.8672G>A	p.Gly2891Asp	p.G2891D	ENST00000278616	NM_000051.3	2891	gGt/gAt	60/63	0.754125998242421	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.754125998242421	2		300	298	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155011	55155011	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1560491697	NA	P-0051634-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	92	446	0	ENST00000257290.5:c.2720A>G	p.Asn907Ser	p.N907S	ENST00000257290	NM_006206.4	907	aAt/aGt	20/23	0.74328211686869	4	FACETS	1	0.938	1	0.357	0.319	0.397	CLONAL	1	TRUE	1	0.754125998242421	4		446	400	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155038	55155038	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1403858596	NA	P-0051634-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	85	486	1	ENST00000257290.5:c.2747C>A	p.Ala916Asp	p.A916D	ENST00000257290	NM_006206.4	916	gCc/gAc	20/23	0.74328211686869	4	FACETS	0.899	0.798	1	0.3	0.266	0.335	CLONAL	1	TRUE	1	0.754125998242421	4		487	440	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332821	152332821	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051634-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	120	356	0	ENST00000206249.3:c.1127T>C	p.Val376Ala	p.V376A	ENST00000206249	NM_000125.3	376	gTc/gCc	5/8	0.754125998242421	4	FACETS	0.881	0.797	0.968	0.22	0.199	0.242	CLONAL	1	TRUE	0	0.754125998242421	4		356	634	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0052316-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	148	602	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.834	0.764	0.907	1	0.99	1	CLONAL	2	FALSE	1	0.275858798118783	2		602	643	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0052316-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	80	786	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.273984557998174	1	FACETS	0.871	0.768	0.982	0.871	0.768	0.982	CLONAL	1	FALSE	0	0.275858798118783	1		786	574	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691039	NA	P-0052316-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	120	788	0	ENST00000269305.4:c.919+1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.275858798118783	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	0	0.275858798118783	1		788	645	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573991	7573991	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567542019	NA	P-0052316-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	53	643	0	ENST00000269305.4:c.1036G>T	p.Glu346Ter	p.E346*	ENST00000269305	NM_001126112.2	346	Gag/Tag	10/11	0.275858798118783	1	FACETS	0.66	0.563	0.766	0.66	0.563	0.766	SUBCLONAL	1	FALSE	0	0.275858798118783	1		643	502	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880827	28880827	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368266056	NA	P-0052316-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	105	671	0	ENST00000282397.4:c.3803C>T	p.Ser1268Leu	p.S1268L	ENST00000282397	NM_002019.4	1268	tCg/tTg	29/30	0.275858798118783	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	0	0.275858798118783	1		671	494	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442065	52442065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052316-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	113	661	0	ENST00000460680.1:c.284C>T	p.Ala95Val	p.A95V	ENST00000460680	NM_004656.3	95	gCc/gTc	5/17	0.238770283796684	0	FACETS	1	0.974	1			1	CLONAL	1	FALSE	0	0.275858798118783	0		661	485	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225449726	225449726	+	frameshift_variant,start_lost	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052316-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	45	480	0	ENST00000264414.4:c.1del	p.Met1?	p.M1?	ENST00000264414	NM_003590.4	1	Atg/tg	1/16	0.275858798118783	1	FACETS	0.681	0.573	0.8	0.681	0.573	0.8	SUBCLONAL	1	FALSE	0	0.275858798118783	1		480	413	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776176	135776176	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054353-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	323	402	0	ENST00000298552.3:c.2551C>T	p.Gln851Ter	p.Q851*	ENST00000298552	NM_001162426.1	851	Cag/Tag	20/23	0.818404198174356	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.818404198174356	1		402	446	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528225	157528225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786205584	NA	P-0054353-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	329	537	0	ENST00000346085.5:c.5950G>A	p.Glu1984Lys	p.E1984K	ENST00000346085	NM_020732.3	1984	Gag/Aag	20/20	1	2	FACETS	0.831	0.787	0.875	0.831	0.787	0.875	CLONAL	1	TRUE	1	0.818404198174356	2		537	968	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226551692	226551692	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054353-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	41	419	0	ENST00000366794.5:c.2738G>C	p.Gly913Ala	p.G913A	ENST00000366794	NM_001618.3	913	gGa/gCa	20/23	1	2	FACETS	0.123	0.102	0.147	0.123	0.102	0.147	SUBCLONAL	1	TRUE	1	0.818404198174356	2		419	814	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246474	10246474	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054353-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	53	493	0	ENST00000340748.4:c.4663C>G	p.Arg1555Gly	p.R1555G	ENST00000340748		1555	Cgc/Ggc	38/40	1	2	FACETS	0.162	0.137	0.189	0.162	0.137	0.189	SUBCLONAL	1	TRUE	1	0.818404198174356	2		493	800	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218948	193218948	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054532-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	106	378	0	ENST00000367435.3:c.1506C>A	p.His502Gln	p.H502Q	ENST00000367435	NM_024529.4	502	caC/caA	16/17	0.581838969364803	3	FACETS	0.964	0.868	1	0.482	0.434	0.532	CLONAL	1	TRUE	1	0.581838969364803	3		378	488	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005555	42005570	+	frameshift_variant	Frame_Shift_Del	DEL	GCATTTTCAGAGGAAG	GCATTTTCAGAGGAAG	-	novel	NA	P-0054532-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	394	531	0	ENST00000219905.7:c.3293_3308del	p.His1098LeufsTer30	p.H1098Lfs*30	ENST00000219905	NM_001164273.1	1097	aaGCATTTTCAGAGGAAG/aa	9/24	0.581838969364803	3	FACETS	0.997	0.953	1	0.997	0.953	1	CLONAL	2	TRUE	1	0.581838969364803	3		531	877	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577111	7577111	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786202082	NA	P-0054532-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	378	501	0	ENST00000269305.4:c.827C>A	p.Ala276Asp	p.A276D	ENST00000269305	NM_001126112.2	276	gCc/gAc	8/11	0.57108172561839	2	FACETS	0.993	0.954	1	0.993	0.954	1	CLONAL	2	TRUE	0	0.581838969364803	2		501	654	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682381	37682381	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054532-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	177	541	0	ENST00000447079.4:c.3572C>T	p.Ser1191Leu	p.S1191L	ENST00000447079	NM_015083.1	1191	tCa/tTa	13/14	0.581838969364803	3	FACETS	0.944	0.871	1	0.472	0.435	0.51	CLONAL	1	TRUE	1	0.581838969364803	3		541	832	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116194	209116194	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054532-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	300	347	0	ENST00000345146.2:c.82G>C	p.Glu28Gln	p.E28Q	ENST00000345146	NM_005896.2	28	Gag/Cag	3/10	0.2746129511969	4	FACETS	1	0.976	1	0.703	0.666	0.742	INDETERMINATE	2	TRUE	1	0.581838969364803	4		347	773	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940142	31940142	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054532-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	236	605	0	ENST00000375333.2:c.284C>G	p.Ser95Cys	p.S95C	ENST00000375333	NM_032454.1	95	tCt/tGt	2/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.581838969364803	2		605	784	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971220	13971220	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054532-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	778	452	0	ENST00000405192.2:c.709G>C	p.Glu237Gln	p.E237Q	ENST00000405192	NM_001163147.1	237	Gaa/Caa	8/12	0.581838969364803	6	FACETS	0.923	0.898	0.947	1	0.996	1	CLONAL	5	TRUE	2	0.581838969364803	6		452	1254	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913381	NA	P-0054532-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	324	523	0	ENST00000304494.5:c.322G>A	p.Asp108Asn	p.D108N	ENST00000304494	NM_000077.4	108	Gat/Aat	2/3	0.581563597447898	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.581838969364803	2		523	557	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894830	101894830	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054532-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	340	446	0	ENST00000374994.4:c.383C>G	p.Ala128Gly	p.A128G	ENST00000374994	NM_004612.2	128	gCt/gGt	3/9	0.581838969364803	2	FACETS	0.952	0.911	0.993	0.952	0.911	0.993	CLONAL	2	TRUE	0	0.581838969364803	2		446	614	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894866	101894866	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054532-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	327	478	0	ENST00000374994.4:c.419C>A	p.Ser140Ter	p.S140*	ENST00000374994	NM_004612.2	140	tCa/tAa	3/9	0.581838969364803	2	FACETS	0.927	0.886	0.969	0.927	0.886	0.969	CLONAL	2	TRUE	0	0.581838969364803	2		478	606	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426126	47426126	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054532-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	180	546	0	ENST00000377045.4:c.646C>G	p.Pro216Ala	p.P216A	ENST00000377045	NM_001654.4	216	Ccc/Gcc	7/16	0.17747652754228	6	FACETS	0.755	0.696	0.815			1	INDETERMINATE	2	TRUE	NA	0.581838969364803	6		546	887	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224579	53224579	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054532-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	144	446	0	ENST00000375401.3:c.3134A>G	p.Tyr1045Cys	p.Y1045C	ENST00000375401	NM_004187.3	1045	tAc/tGc	21/26	NA	2	FACETS	0.8	0.732	0.87			1	INDETERMINATE	1	TRUE	NA	0.581838969364803	2		446	619	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0055502-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	19	410	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.626	0.473	0.806	0.626	0.473	0.806	SUBCLONAL	1	TRUE	1	0.12	2		410	506	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259439	55259439	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs397517126	NA	P-0055502-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	11	0	0	ENST00000275493.2:c.2497T>G	p.Leu833Val	p.L833V	ENST00000275493	NM_005228.3	833	Ttg/Gtg	21/28	1	2	FACETS	0.401	0.276	0.559	0.401	0.276	0.559	SUBCLONAL	1	TRUE	1	0.12	2		0	457	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056361-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	42	663	0				ENST00000310581	NM_198253.2	-/1132			0.256847897704549	1	FACETS	0.914	0.766	1	0.914	0.766	1	CLONAL	1	FALSE	0	0.256847897704549	1		663	312	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31448657	31448657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757002340	NA	P-0056361-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	23	300	0	ENST00000344624.3:c.2879C>T	p.Ser960Leu	p.S960L	ENST00000344624		960	tCg/tTg	20/33	0.256847897704549	1	FACETS	0.805	0.631	1	0.805	0.631	1	CLONAL	1	FALSE	0	0.256847897704549	1		300	194	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192609	94192610	+	missense_variant	Missense_Mutation	DNP	GA	GA	AG	novel	NA	P-0056361-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	15	311	0	ENST00000323929.3:c.1464_1465delinsCT	p.His489Tyr	p.H489Y	ENST00000323929	NM_005591.3	488	cgTCat/cgCTat	13/20	1	2	FACETS	0.573	0.419	0.756	0.573	0.419	0.756	SUBCLONAL	1	FALSE	1	0.256847897704549	2		311	204	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0056860-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	106	444	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.762452992251497	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	0	0.759364032231576	3		444	121	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483979	212483979	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056860-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	54	417	0	ENST00000342788.4:c.2224G>C	p.Glu742Gln	p.E742Q	ENST00000342788	NM_005235.2	742	Gaa/Caa	19/28	0.750129869424319	4	FACETS	1	0.87	1	0.336	0.29	0.386	CLONAL	1	TRUE	1	0.759364032231576	4		417	248	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027127	49027127	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0056860-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	85	352	0	ENST00000267163.4:c.1696-2A>T		p.X566_splice	ENST00000267163	NM_000321.2	566			0.762452992251497	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	4	TRUE	0	0.759364032231576	4		352	96	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602408	28602408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056860-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	138	451	0	ENST00000241453.7:c.1960G>A	p.Glu654Lys	p.E654K	ENST00000241453	NM_004119.2	654	Gaa/Aaa	16/24	0.762452992251497	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	4	TRUE	0	0.759364032231576	4		451	150	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636196	28636196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056860-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	168	491	1	ENST00000241453.7:c.176C>T	p.Ser59Phe	p.S59F	ENST00000241453	NM_004119.2	59	tCc/tTc	3/24	0.762452992251497	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	4	TRUE	0	0.759364032231576	4		492	175	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690810	89690810	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1488857080	NA	P-0056860-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	81	297	1	ENST00000371953.3:c.217G>T	p.Glu73Ter	p.E73*	ENST00000371953	NM_000314.4	73	Gaa/Taa	4/9	0.762452992251497	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.759364032231576	2		298	95	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15840928	15840928	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056860-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	39	162	0	ENST00000307771.7:c.1012G>C	p.Glu338Gln	p.E338Q	ENST00000307771	NM_005089.3	338	Gaa/Caa	11/11	0.762452992251497	2	FACETS	0.842	0.744	0.934			1	CLONAL	2	TRUE	NA	0.759364032231576	2		162	61	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841331	15841331	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056860-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	39	273	0	ENST00000307771.7:c.1415G>C	p.Arg472Thr	p.R472T	ENST00000307771	NM_005089.3	472	aGa/aCa	11/11	0.762452992251497	2	FACETS	1	0.965	1			1	CLONAL	1	TRUE	NA	0.759364032231576	2		273	71	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058732	42058732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056860-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	30	527	0	ENST00000219905.7:c.8452G>A	p.Asp2818Asn	p.D2818N	ENST00000219905	NM_001164273.1	2818	Gat/Aat	24/24	0.762452992251497	2	FACETS	0.888	0.737	1	0.444	0.368	0.524	CLONAL	1	TRUE	0	0.759364032231576	2		527	89	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95573958	95573958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1256068472	NA	P-0056860-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	29	370	0	ENST00000393063.1:c.2791G>A	p.Val931Ile	p.V931I	ENST00000393063	NM_030621.3	931	Gtt/Att	18/28	0.762452992251497	4	FACETS	0.824	0.669	0.997	0.275	0.223	0.333	CLONAL	1	TRUE	1	0.759364032231576	4		370	163	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057811	27057811	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057071-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	217	403	0	ENST00000324856.7:c.1519C>T	p.Gln507Ter	p.Q507*	ENST00000324856	NM_006015.4	507	Caa/Taa	3/20	0.65211967589283	2	FACETS	1	0.977	1	0.547	0.512	0.583	CLONAL	1	TRUE	0	0.648695996856317	2		403	611	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478638	57478638	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057071-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	205	384	0	ENST00000371085.3:c.310G>A	p.Glu104Lys	p.E104K	ENST00000371085	NM_000516.4	104	Gaa/Aaa	4/13	0.648695996856317	6	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.648695996856317	6		384	1124	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0057732-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	135	575	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.358697874022755	4	FACETS	1	0.975	1	0.602	0.547	0.66	CLONAL	1	TRUE	2	0.355739471383467	4		575	854	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0057732-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	302	171	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.358697874022755	4	FACETS	0.898	0.849	0.948	1	0.993	1	CLONAL	3	TRUE	2	0.355739471383467	4		171	854	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0057732-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	179	410	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.355739471383467	7	FACETS	0.879	0.81	0.952	0.352	0.324	0.381	CLONAL	2	TRUE	2	0.355739471383467	7		410	1081	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106543511	106543511	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057732-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	108	430	0	ENST00000369096.4:c.313G>T	p.Glu105Ter	p.E105*	ENST00000369096	NM_001198.3	105	Gaa/Taa	3/7	0.355272903944567	4	FACETS	1	0.942	1	0.537	0.481	0.595	CLONAL	1	TRUE	2	0.355739471383467	4		430	767	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609905	81609906	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0057732-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	68	561	0	ENST00000298171.2:c.1504_1505del	p.Val502LeufsTer60	p.V502Lfs*60	ENST00000298171	NM_000369.2	501	acTGtc/actc	10/10	0.296464528004102	3	FACETS	0.632	0.549	0.721	0.211	0.183	0.241	SUBCLONAL	1	TRUE	0	0.355739471383467	3		561	713	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306583	41306583	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057732-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	73	444	2	ENST00000373198.4:c.1076G>T	p.Arg359Leu	p.R359L	ENST00000373198	NM_133170.3	359	cGa/cTa	7/32	0.358697874022755	3	FACETS	0.738	0.645	0.838	0.246	0.215	0.28	SUBCLONAL	1	TRUE	0	0.355739471383467	3		446	655	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503789	186503789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781218973	NA	P-0057732-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	87	421	0	ENST00000323963.5:c.466G>A	p.Val156Ile	p.V156I	ENST00000323963		156	Gtt/Att	5/11	0.357298303066889	4	FACETS	0.774	0.684	0.87	0.193	0.171	0.218	SUBCLONAL	1	TRUE	0	0.355739471383467	4		421	857	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651578	48651578	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0057732-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	106	525	0	ENST00000376670.3:c.745-1G>T		p.X249_splice	ENST00000376670	NM_002049.3	249			1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.355739471383467	2		525	591	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432664	29432664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113994087	NA	P-0058122-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	57	333	0	ENST00000389048.3:c.3824G>A	p.Arg1275Gln	p.R1275Q	ENST00000389048	NM_004304.4	1275	cGa/cAa	25/29	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.36	2		333	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0058861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4	19	622	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.598687956634245	2	FACETS	0.92	0.802	1	1	0.949	1	CLONAL	3	TRUE	0	0.598687956634245	2		622	23	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0058861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	14	532	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.546782511520088	4	FACETS	1	0.88	1	0.692	0.516	0.89	CLONAL	1	TRUE	2	0.598687956634245	4		532	54	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0058861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	19	461	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.598687956634245	1	FACETS	0.824	0.695	0.936	1	0.949	1	CLONAL	2	TRUE	0	0.598687956634245	1		461	27	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272207	15272207	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1051094199	NA	P-0058861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	32	329	0	ENST00000263388.2:c.6232C>T	p.Arg2078Trp	p.R2078W	ENST00000263388	NM_000435.2	2078	Cgg/Tgg	33/33	0.29025294743241	3	FACETS	0.926	0.807	1	1	0.96	1	INDETERMINATE	3	TRUE	1	0.598687956634245	3		329	50	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398625	116398625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45587940	NA	P-0058861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	29	277	0	ENST00000397752.3:c.2215C>T	p.Arg739Cys	p.R739C	ENST00000397752	NM_000245.2	739	Cgt/Tgt	9/21	0.546782511520088	4	FACETS	0.86	0.726	0.996	1	0.94	1	CLONAL	3	TRUE	2	0.598687956634245	4		277	60	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042420	42042421	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0058861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	26	352	0	ENST00000219905.7:c.6616_6617del	p.Lys2206AspfsTer17	p.K2206Dfs*17	ENST00000219905	NM_001164273.1	2205	acAAag/acag	17/24	1	2	FACETS	0.804	0.671	0.938	1	0.953	1	CLONAL	2	TRUE	1	0.598687956634245	2		352	54	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379350	225379350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	105	384	0	ENST00000264414.4:c.518G>A	p.Arg173Gln	p.R173Q	ENST00000264414	NM_003590.4	173	cGg/cAg	4/16	1	2	FACETS	0.991	0.894	1	0.991	0.894	1	CLONAL	1	TRUE	1	0.488232601827888	2		384	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577579	7577579	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0059173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	328	458	0	ENST00000269305.4:c.702C>G	p.Tyr234Ter	p.Y234*	ENST00000269305	NM_001126112.2	234	taC/taG	7/11	0.443049310510014	2	FACETS	0.826	0.785	0.869	0.826	0.785	0.869	CLONAL	2	TRUE	0	0.488232601827888	2		458	813	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631362	117631362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150262256	NA	P-0059173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	166	407	0	ENST00000368508.3:c.6316G>A	p.Ala2106Thr	p.A2106T	ENST00000368508	NM_002944.2	2106	Gcc/Acc	40/43	1	2	FACETS	0.963	0.887	1	0.963	0.887	1	CLONAL	1	TRUE	1	0.488232601827888	2		407	706	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	101	663	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.357368773578513	2		663	428	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0059406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	130	532	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.245291601129768	2	FACETS	1	0.986	1	0.736	0.672	0.803	CLONAL	1	TRUE	0	0.357368773578513	2		532	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	232	811	0	ENST00000269305.4:c.853G>C	p.Glu285Gln	p.E285Q	ENST00000269305	NM_001126112.2	285	Gag/Cag	8/11	0.291208326124022	2	FACETS	0.861	0.806	0.918	0.861	0.806	0.918	CLONAL	2	TRUE	0	0.357368773578513	2		811	754	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139792	55139792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1354231704	NA	P-0059406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	182	792	0	ENST00000257290.5:c.1453G>A	p.Glu485Lys	p.E485K	ENST00000257290	NM_006206.4	485	Gag/Aag	10/23	0.272523366203383	2	FACETS	0.816	0.757	0.877	0.816	0.757	0.877	CLONAL	2	TRUE	0	0.357368773578513	2		792	624	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28600619	28600619	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	78	741	0	ENST00000253063.3:c.970G>A	p.Glu324Lys	p.E324K	ENST00000253063	NM_031459.4	324	Gag/Aag	7/10	0.257717859045642	3	FACETS	0.766	0.673	0.866	0.383	0.336	0.433	SUBCLONAL	1	TRUE	1	0.357368773578513	3		741	672	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233129	69233129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773519801	NA	P-0059406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	79	756	0	ENST00000462284.1:c.994C>T	p.Arg332Cys	p.R332C	ENST00000462284	NM_002392.5	332	Cgt/Tgt	11/11	0.267281506234321	3	FACETS	0.699	0.614	0.79	0.349	0.307	0.395	SUBCLONAL	1	TRUE	1	0.357368773578513	3		756	746	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129430	2129430	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs45517289	NA	P-0059406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	166	776	0	ENST00000219476.3:c.3284+1G>A		p.X1095_splice	ENST00000219476	NM_000548.3	1095			0.279464652121325	2	FACETS	0.909	0.841	0.979	0.909	0.841	0.979	CLONAL	2	TRUE	0	0.357368773578513	2		776	511	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262902	46262902	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	153	553	0	ENST00000371998.3:c.1075G>A	p.Asp359Asn	p.D359N	ENST00000371998		359	Gat/Aat	10/23	0.16808728538876	4	FACETS	0.812	0.744	0.882	0.812	0.744	0.882	INDETERMINATE	2	TRUE	2	0.357368773578513	4		553	716	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038212	30038212	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	160	600	0	ENST00000338641.4:c.385G>T	p.Glu129Ter	p.E129*	ENST00000338641	NM_000268.3	129	Gaa/Taa	4/16	0.279464652121325	2	FACETS	0.842	0.777	0.909	0.842	0.777	0.909	CLONAL	2	TRUE	0	0.357368773578513	2		600	532	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158466	26158466	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	106	768	0	ENST00000289316.2:c.69G>C	p.Gln23His	p.Q23H	ENST00000289316	NM_138720.2	23	caG/caC	1/2	1	2	FACETS	0.737	0.66	0.818	0.737	0.66	0.818	SUBCLONAL	1	TRUE	1	0.357368773578513	2		768	805	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059481-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	217	663	0				ENST00000310581	NM_198253.2	-/1132			0.636558617194455	6	FACETS	0.804	0.748	0.862	0.402	0.374	0.431	CLONAL	2	TRUE	2	0.636558617194455	6		663	964	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0059481-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	647	463	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.617473597495746	4	FACETS	1	0.985	1	1	0.998	1	CLONAL	4	TRUE	2	0.636558617194455	4		463	824	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131895051	131895051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370769989	NA	P-0059481-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	241	241	0	ENST00000265335.6:c.205G>A	p.Asp69Asn	p.D69N	ENST00000265335		69	Gat/Aat	2/25	0.605885631861202	3	FACETS	0.919	0.878	0.959	0.919	0.878	0.959	CLONAL	3	TRUE	0	0.636558617194455	3		241	362	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731065	162731065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747307320	NA	P-0059481-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	205	516	0	ENST00000367921.3:c.920G>A	p.Arg307His	p.R307H	ENST00000367921	NM_006182.2	307	cGc/cAc	9/18	0.636558617194455	6	FACETS	1	0.982	1	0.237	0.219	0.256	CLONAL	1	TRUE	1	0.636558617194455	6		516	1236	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881513	48881513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059481-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	377	365	0	ENST00000267163.4:c.235G>T	p.Glu79Ter	p.E79*	ENST00000267163	NM_000321.2	79	Gag/Tag	2/27	0.633039743461539	3	FACETS	0.999	0.966	1	0.999	0.966	1	CLONAL	3	TRUE	0	0.636558617194455	3		365	521	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858570	9858570	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064797025	NA	P-0059481-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	207	521	0	ENST00000330684.3:c.2831C>T	p.Ser944Leu	p.S944L	ENST00000330684	NM_001134407.1	944	tCa/tTa	13/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.636558617194455	2		521	580	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797351	135797351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777484049	NA	P-0059481-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	126	431	0	ENST00000298552.3:c.518C>T	p.Ala173Val	p.A173V	ENST00000298552	NM_001162426.1	173	gCg/gTg	7/23	0.636558617194455	3	FACETS	0.802	0.727	0.879	0.267	0.242	0.293	CLONAL	1	TRUE	0	0.636558617194455	3		431	651	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68758616	68758616	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059481-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	165	511	0	ENST00000487270.1:c.772C>G	p.Gln258Glu	p.Q258E	ENST00000487270	NM_133509.3	258	Cag/Gag	8/11	0.168320935138114	2	FACETS	0.971	0.897	1	0.485	0.448	0.523	INDETERMINATE	1	TRUE	0	0.636558617194455	2		511	534	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68758652	68758652	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059481-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	170	505	0	ENST00000487270.1:c.808C>T	p.Gln270Ter	p.Q270*	ENST00000487270	NM_133509.3	270	Cag/Tag	8/11	0.168320935138114	2	FACETS	0.929	0.859	1	0.464	0.429	0.501	INDETERMINATE	1	TRUE	0	0.636558617194455	2		505	575	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554240	63554240	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059481-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	221	619	0	ENST00000307078.5:c.499G>T	p.Asp167Tyr	p.D167Y	ENST00000307078	NM_004655.3	167	Gat/Tat	2/11	0.636558617194455	4	FACETS	0.989	0.919	1	0.494	0.459	0.531	CLONAL	1	TRUE	2	0.636558617194455	4		619	1149	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285243	212285243	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059481-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	106	397	0	ENST00000342788.4:c.3058G>C	p.Glu1020Gln	p.E1020Q	ENST00000342788	NM_005235.2	1020	Gag/Cag	25/28	0.636558617194455	3	FACETS	0.894	0.805	0.987	0.447	0.402	0.494	CLONAL	1	TRUE	1	0.636558617194455	3		397	491	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713612	30713612	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55751315	NA	P-0059481-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	194	584	0	ENST00000295754.5:c.937C>T	p.Arg313Trp	p.R313W	ENST00000295754	NM_003242.5	313	Cgg/Tgg	4/7	0.636558617194455	4	FACETS	0.946	0.875	1	0.473	0.437	0.511	CLONAL	1	TRUE	2	0.636558617194455	4		584	1054	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220488	123220488	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059481-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	112	421	0	ENST00000218089.9:c.3145C>A	p.Leu1049Ile	p.L1049I	ENST00000218089	NM_001042749.1	1049	Cta/Ata	30/35	0.636558617194455	3	FACETS	0.808	0.729	0.891	0.404	0.364	0.446	CLONAL	1	TRUE	1	0.636558617194455	3		421	574	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0059836-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	418	514	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	0.506091298329483	4	FACETS	0.84	0.809	0.87	0.84	0.809	0.87	INDETERMINATE	3	TRUE	1	0.934163719144856	4		514	687	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777841	3777841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059836-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	247	560	0	ENST00000262367.5:c.7207C>T	p.Pro2403Ser	p.P2403S	ENST00000262367	NM_004380.2	2403	Ccc/Tcc	31/31	1	2	FACETS	0.923	0.871	0.976	0.923	0.871	0.976	CLONAL	1	TRUE	1	0.934163719144856	2		560	573	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059937-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	31	491	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.795	0.644	0.966	0.795	0.644	0.966	CLONAL	1	TRUE	1	0.23	2		491	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0059937-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	47	622	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.176924825648892	1	FACETS	0.8	0.676	0.937	0.8	0.676	0.937	CLONAL	1	TRUE	0	0.23	1		622	452	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246614	46246614	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059937-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	36	322	0	ENST00000334344.6:c.4708A>G	p.Ile1570Val	p.I1570V	ENST00000334344	NM_152641.2	1570	Ata/Gta	15/21	1	2	FACETS	0.72	0.592	0.863	0.72	0.592	0.863	SUBCLONAL	1	TRUE	1	0.23	2		322	435	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575174	48575174	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059937-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	37	267	0	ENST00000342988.3:c.368del	p.Cys123LeufsTer6	p.C123Lfs*6	ENST00000342988	NM_005359.5	123	tGt/tt	3/12	0.176924825648892	1	FACETS	0.802	0.663	0.957	0.802	0.663	0.957	CLONAL	1	TRUE	0	0.23	1		267	355	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145704	11145704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059937-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	40	417	0	ENST00000358026.2:c.4066C>T	p.Arg1356Trp	p.R1356W	ENST00000358026	NM_001128849.1	1356	Cgg/Tgg	29/36	1	2	FACETS	0.716	0.594	0.851	0.716	0.594	0.851	SUBCLONAL	1	TRUE	1	0.23	2		417	486	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945150	44945150	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059937-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	38	298	0	ENST00000377967.4:c.3474del	p.Asn1158LysfsTer20	p.N1158Kfs*20	ENST00000377967	NM_021140.2	1158	aaT/aa	24/29	1	2	FACETS	0.789	0.652	0.941	0.789	0.652	0.941	CLONAL	1	TRUE	1	0.23	2		298	419	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054664	5054664	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060272-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	133	374	0	ENST00000381652.3:c.716A>C	p.Gln239Pro	p.Q239P	ENST00000381652	NM_004972.3	239	cAa/cCa	7/25	0.153515672825916	3	FACETS	0.817	0.755	0.88	0.817	0.755	0.88	INDETERMINATE	2	TRUE	1	0.740832674347756	3		374	301	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355053	73355053	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060272-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	137	317	0	ENST00000377767.4:c.317A>G	p.Tyr106Cys	p.Y106C	ENST00000377767	NM_014953.3	106	tAt/tGt	2/21	0.740832674347756	2	FACETS	1	0.98	1	0.591	0.546	0.636	CLONAL	1	TRUE	0	0.740832674347756	2		317	313	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947596	48947596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1566196458	NA	P-0060558-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	11	219	0	ENST00000267163.4:c.1183C>T	p.Gln395Ter	p.Q395*	ENST00000267163	NM_000321.2	395	Caa/Taa	12/27	1	2	FACETS	0.181	0.125	0.249	0.181	0.125	0.249	SUBCLONAL	1	TRUE	1	0.85222312785554	2		219	143	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713155	30713155	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060558-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	19	382	0	ENST00000295754.5:c.480G>C	p.Leu160Phe	p.L160F	ENST00000295754	NM_003242.5	160	ttG/ttC	4/7	1	2	FACETS	0.15	0.114	0.193	0.15	0.114	0.193	SUBCLONAL	1	TRUE	1	0.85222312785554	2		382	297	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982688	90982688	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060558-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	107	323	0	ENST00000265433.3:c.800del	p.Gly267GlufsTer9	p.G267Efs*9	ENST00000265433	NM_002485.4	267	gGa/ga	7/16	0.85222312785554	1	FACETS	0.895	0.834	0.953	0.895	0.834	0.953	CLONAL	1	TRUE	0	0.85222312785554	1		323	161	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060604-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	5	663	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.35	0.198	0.562	0.35	0.198	0.562	SUBCLONAL	1	TRUE	1	0.221358719602092	2		663	129	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527502	29527503	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0060604-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	15	416	0	ENST00000356175.3:c.952_953del	p.Glu318LysfsTer11	p.E318Kfs*11	ENST00000356175	NM_000267.3	317	acAGaa/acaa	9/57	1	2	FACETS	0.729	0.534	0.96	0.729	0.534	0.96	CLONAL	1	TRUE	1	0.221358719602092	2		416	186	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684021	29684022	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0060604-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	26	370	0	ENST00000356175.3:c.7722dup	p.Val2575SerfsTer5	p.V2575Sfs*5	ENST00000356175	NM_000267.3	2573	-/A	52/57	1	2	FACETS	1	0.842	1	1	0.842	1	CLONAL	1	TRUE	1	0.221358719602092	2		370	220	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0060728-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	219	477	3	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.675	0.628	0.723	0.675	0.628	0.723	SUBCLONAL	1	TRUE	1	0.667331741993676	2		480	973	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950005	44950005	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060728-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	278	206	1	ENST00000377967.4:c.3774G>A	p.Trp1258Ter	p.W1258*	ENST00000377967	NM_021140.2	1258	tgG/tgA	26/29	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.667331741993676	1		207	396	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50818289	50818289	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060728-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	239	365	0	ENST00000398568.2:c.1867G>T	p.Glu623Ter	p.E623*	ENST00000398568	NM_001042412.1	623	Gaa/Taa	11/18	0.667331741993676	1	FACETS	0.92	0.868	0.972	0.92	0.868	0.972	CLONAL	1	TRUE	0	0.667331741993676	1		365	519	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070611	67070611	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060728-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	308	437	0	ENST00000412916.2:c.235C>T	p.Gln79Ter	p.Q79*	ENST00000412916		79	Caa/Taa	3/6	0.667331741993676	1	FACETS	0.975	0.928	1	0.975	0.928	1	CLONAL	1	TRUE	0	0.667331741993676	1		437	631	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144361452	144361452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060728-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	344	522	0	ENST00000262995.4:c.1502C>T	p.Pro501Leu	p.P501L	ENST00000262995	NM_207123.2	501	cCa/cTa	6/11	0.110911568866012	3	FACETS	1	0.994	1	0.683	0.647	0.719	INDETERMINATE	1	TRUE	1	0.667331741993676	3		522	1007	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157256642	157256642	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060728-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	306	419	0	ENST00000346085.5:c.1969C>G	p.Leu657Val	p.L657V	ENST00000346085	NM_020732.3	657	Ctg/Gtg	5/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.667331741993676	2		419	912	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0061080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	244	286	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.552283305781837	2	FACETS	0.909	0.864	0.953	0.909	0.864	0.953	CLONAL	2	TRUE	0	0.645235035944224	2		286	416	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0061080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	172	525	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	1	2	FACETS	0.919	0.851	0.99	0.919	0.851	0.99	CLONAL	1	TRUE	1	0.645235035944224	2		525	580	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412110	63412110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852216	NA	P-0061080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	197	629	0	ENST00000330258.3:c.1057C>T	p.Arg353Ter	p.R353*	ENST00000330258	NM_152424.3	353	Cga/Tga	2/2	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.645235035944224	2		629	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578418	7578418	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	247	588	0	ENST00000269305.4:c.512A>G	p.Glu171Gly	p.E171G	ENST00000269305	NM_001126112.2	171	gAg/gGg	5/11	0.645235035944224	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.645235035944224	1		588	440	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453468	40453468	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866679330	NA	P-0061080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	196	487	0	ENST00000345506.4:c.1165C>T	p.Arg389Cys	p.R389C	ENST00000345506	NM_003152.3	389	Cgc/Tgc	10/20	1	2	FACETS	0.986	0.918	1	0.986	0.918	1	CLONAL	1	TRUE	1	0.645235035944224	2		487	616	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584540	48584541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0061080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	222	472	0	ENST00000342988.3:c.714dup	p.Gln239AlafsTer25	p.Q239Afs*25	ENST00000342988	NM_005359.5	238	ttg/ttGg	6/12	0.645235035944224	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.645235035944224	1		472	431	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933335	39933335	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	231	588	0	ENST00000378444.4:c.1264A>T	p.Ser422Cys	p.S422C	ENST00000378444	NM_001123385.1	422	Agc/Tgc	4/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.645235035944224	2		588	671	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171638	36171639	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0061080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	229	471	0	ENST00000300305.3:c.926dup	p.Met310HisfsTer290	p.M310Hfs*290	ENST00000300305		309	ggc/ggGc	7/8	0.645235035944224	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.645235035944224	1		471	462	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971107	21971108	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0061080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	198	517	0	ENST00000304494.5:c.250_251delinsTT	p.Asp84Phe	p.D84F	ENST00000304494	NM_000077.4	84	GAc/TTc	2/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.645235035944224	2		517	517	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346066	152346066	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	154	521	0	ENST00000359321.1:c.504A>C	p.Leu168Phe	p.L168F	ENST00000359321	NM_005431.1	168	ttA/ttC	3/3	1	2	FACETS	0.873	0.803	0.944	0.873	0.803	0.944	CLONAL	1	TRUE	1	0.645235035944224	2		521	547	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0061409-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	36	410	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		410	453	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589663	67589663	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs587777709	NA	P-0061518-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	12	302	0	ENST00000274335.5:c.1425+1G>C		p.X475_splice	ENST00000274335		475			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		302	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587782272	NA	P-0061518-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	19	405	0	ENST00000269305.4:c.994-1G>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		405	378	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061628-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	6	663	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.621	1	1	0.621	1	CLONAL	1	TRUE	1	0.35	2		663	34	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0061628-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	420	627	0	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.303202067713879	56	FACETS	1	0.982	1	0.968	0.947	0.987	CLONAL	52	TRUE	2	0.35	56		627	480	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239504	123239504	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061628-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	10	515	0	ENST00000358487.5:c.2333A>C	p.Gln778Pro	p.Q778P	ENST00000358487	NM_000141.4	778	cAg/cCg	18/18	0.303202067713879	1	FACETS	0.982	0.684	1	0.982	0.684	1	CLONAL	1	TRUE	0	0.35	1		515	48	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	119	355	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.608205622715093	2		355	341	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244243	5244243	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1390768500	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	127	411	0	ENST00000357368.4:c.1239del	p.Ser414AlafsTer30	p.S414Afs*30	ENST00000357368	NM_002850.3	413	ccC/cc	11/38	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.608205622715093	2		411	371	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	96	261	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.999	0.9	1	0.999	0.9	1	CLONAL	1	TRUE	1	0.608205622715093	2		264	316	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	141	434	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.608205622715093	2		434	403	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	31	387	1	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.25	0.202	0.304	0.25	0.202	0.304	SUBCLONAL	1	TRUE	1	0.608205622715093	2		388	408	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	138	460	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.608205622715093	2		463	410	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370236	40370236	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs761761205	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	109	394	7	ENST00000293328.3:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000293328	NM_012448.3	368	Cag/ag	9/19	1	2	FACETS	0.791	0.715	0.871	0.791	0.715	0.871	SUBCLONAL	1	TRUE	1	0.608205622715093	2		401	453	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	143	563	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.608205622715093	2		563	454	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	202	450	2	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.608205622715093	2		452	650	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	120	429	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.608205622715093	2		429	375	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	116	415	0	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	0.608205622715093	3	FACETS	1	0.932	1	0.517	0.468	0.568	CLONAL	1	TRUE	1	0.608205622715093	3		415	481	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784362	9784363	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	77	367	0	ENST00000377346.4:c.2751dup	p.Asn918GlufsTer31	p.N918Efs*31	ENST00000377346	NM_005026.3	916	ctg/ctGg	22/24	1	2	FACETS	0.604	0.533	0.68	0.604	0.533	0.68	SUBCLONAL	1	TRUE	1	0.608205622715093	2		367	419	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258917	16258917	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	210	461	0	ENST00000375759.3:c.6182A>G	p.Glu2061Gly	p.E2061G	ENST00000375759	NM_015001.2	2061	gAa/gGa	11/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.608205622715093	2		461	582	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	109	397	0	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.608205622715093	2		397	345	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057925	27057925	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	193	414	0	ENST00000324856.7:c.1633C>A	p.Pro545Thr	p.P545T	ENST00000324856	NM_006015.4	545	Ccc/Acc	3/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.608205622715093	2		414	546	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101067	27101068	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	116	400	0	ENST00000324856.7:c.4354dup	p.Gln1452ProfsTer39	p.Q1452Pfs*39	ENST00000324856	NM_006015.4	1450	ggc/ggCc	18/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.608205622715093	2		400	358	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363600	40363600	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs201943505	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	32	407	0	ENST00000397332.2:c.629C>A	p.Ser210Tyr	p.S210Y	ENST00000397332	NM_001033082.2	210	tCt/tAt	3/3	1	2	FACETS	0.259	0.21	0.315	0.259	0.21	0.315	SUBCLONAL	1	TRUE	1	0.608205622715093	2		407	406	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	157	405	3	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.608205622715093	2		408	515	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015344	176015344	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	18	246	0	ENST00000367669.3:c.1394A>G	p.Asn465Ser	p.N465S	ENST00000367669	NM_022457.5	465	aAt/aGt	12/20	0.608205622715093	3	FACETS	0.274	0.206	0.354	0.137	0.103	0.177	SUBCLONAL	1	TRUE	1	0.608205622715093	3		246	282	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218952	193218952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	94	346	0	ENST00000367435.3:c.1510C>T	p.Arg504Cys	p.R504C	ENST00000367435	NM_024529.4	504	Cgt/Tgt	16/17	0.608205622715093	3	FACETS	0.873	0.78	0.97	0.436	0.39	0.485	CLONAL	1	TRUE	1	0.608205622715093	3		346	462	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653795	206653795	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1572248443	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	87	356	0	ENST00000367120.3:c.1346T>G	p.Val449Gly	p.V449G	ENST00000367120	NM_014002.3	449	gTg/gGg	13/22	0.608205622715093	3	FACETS	0.763	0.678	0.853	0.381	0.339	0.427	SUBCLONAL	1	TRUE	1	0.608205622715093	3		356	489	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252102	226252102	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	32	54	0	ENST00000366813.1:c.50C>A	p.Pro17His	p.P17H	ENST00000366813		17	cCc/cAc	1/3	0.608205622715093	3	FACETS	1	0.904	1	0.572	0.473	0.678	CLONAL	1	TRUE	1	0.608205622715093	3		54	120	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653830	89653830	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	149	236	0	ENST00000371953.3:c.129del	p.Gly44AlafsTer10	p.G44Afs*10	ENST00000371953	NM_000314.4	43	gAa/ga	2/9	0.608205622715093	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.608205622715093	2		236	216	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112760244	112760244	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	30	280	0	ENST00000369452.4:c.913A>G	p.Lys305Glu	p.K305E	ENST00000369452	NM_007373.3	305	Aaa/Gaa	4/9	0.608205622715093	2	FACETS	0.312	0.252	0.38	0.156	0.126	0.19	SUBCLONAL	1	TRUE	0	0.608205622715093	2		280	316	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154242	2154242	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755455183	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	109	449	0	ENST00000434045.2:c.686del	p.Pro229GlnfsTer27	p.P229Qfs*27	ENST00000434045	NM_001127598.1	229	cCa/ca	5/5	1	2	FACETS	0.883	0.799	0.97	0.883	0.799	0.97	CLONAL	1	TRUE	1	0.608205622715093	2		449	406	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8252045	8252045	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	124	458	0	ENST00000335790.3:c.32C>A	p.Pro11Gln	p.P11Q	ENST00000335790	NM_002315.2	11	cCg/cAg	2/4	1	2	FACETS	0.95	0.867	1	0.95	0.867	1	CLONAL	1	TRUE	1	0.608205622715093	2		458	429	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466029	69466030	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTGCGG	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	127	427	0	ENST00000227507.2:c.869_874dup	p.Val290_Arg291dup	p.V290_R291dup	ENST00000227507	NM_053056.2	290	-/GTGCGG	5/5	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.608205622715093	2		427	397	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945376	71945376	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	149	385	0	ENST00000298229.2:c.2264C>A	p.Ala755Asp	p.A755D	ENST00000298229	NM_001567.3	755	gCc/gAc	20/28	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.608205622715093	2		385	445	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999195	100999195	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	80	491	0	ENST00000325455.5:c.607C>A	p.Pro203Thr	p.P203T	ENST00000325455	NM_001202474.3	203	Cct/Act	1/8	1	2	FACETS	0.656	0.581	0.736	0.656	0.581	0.736	SUBCLONAL	1	TRUE	1	0.608205622715093	2		491	401	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148919	119148919	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1377506801	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	27	301	0	ENST00000264033.4:c.1139T>C	p.Leu380Pro	p.L380P	ENST00000264033	NM_005188.3	380	cTa/cCa	8/16	1	2	FACETS	0.287	0.229	0.354	0.287	0.229	0.354	SUBCLONAL	1	TRUE	1	0.608205622715093	2		301	309	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243876	46243876	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs746164328	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	57	377	0	ENST00000334344.6:c.1970A>G	p.Asn657Ser	p.N657S	ENST00000334344	NM_152641.2	657	aAc/aGc	15/21	1	2	FACETS	0.39	0.335	0.451	0.39	0.335	0.451	SUBCLONAL	1	TRUE	1	0.608205622715093	2		377	480	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245552	46245552	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	27	354	0	ENST00000334344.6:c.3646A>G	p.Thr1216Ala	p.T1216A	ENST00000334344	NM_152641.2	1216	Acg/Gcg	15/21	1	2	FACETS	0.212	0.168	0.262	0.212	0.168	0.262	SUBCLONAL	1	TRUE	1	0.608205622715093	2		354	419	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864516	57864516	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	97	477	0	ENST00000228682.2:c.1993A>G	p.Thr665Ala	p.T665A	ENST00000228682	NM_005269.2	665	Acc/Gcc	12/12	1	2	FACETS	0.747	0.67	0.828	0.747	0.67	0.828	SUBCLONAL	1	TRUE	1	0.608205622715093	2		477	427	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864814	57864814	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	94	463	0	ENST00000228682.2:c.2291A>G	p.Asn764Ser	p.N764S	ENST00000228682	NM_005269.2	764	aAc/aGc	12/12	1	2	FACETS	0.636	0.568	0.708	0.636	0.568	0.708	SUBCLONAL	1	TRUE	1	0.608205622715093	2		463	486	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109971	115109971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	133	379	0	ENST00000257566.3:c.1907C>T	p.Pro636Leu	p.P636L	ENST00000257566	NM_016569.3	636	cCg/cTg	8/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.608205622715093	2		379	363	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536740	120536740	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	108	435	0	ENST00000229340.5:c.353-1G>A		p.X118_splice	ENST00000229340	NM_006861.6	118			1	2	FACETS	0.796	0.719	0.877	0.796	0.719	0.877	SUBCLONAL	1	TRUE	1	0.608205622715093	2		435	446	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563282	21563282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756335536	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	90	468	0	ENST00000382592.4:c.637G>A	p.Asp213Asn	p.D213N	ENST00000382592	NM_014572.2	213	Gac/Aac	4/8	1	2	FACETS	0.691	0.617	0.77	0.691	0.617	0.77	SUBCLONAL	1	TRUE	1	0.608205622715093	2		468	428	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619969	21619969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	37	425	0	ENST00000382592.4:c.197C>T	p.Ala66Val	p.A66V	ENST00000382592	NM_014572.2	66	gCc/gTc	2/8	1	2	FACETS	0.218	0.179	0.262	0.218	0.179	0.262	SUBCLONAL	1	TRUE	1	0.608205622715093	2		425	558	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005296	29005296	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	71	278	0	ENST00000282397.4:c.965T>C	p.Val322Ala	p.V322A	ENST00000282397	NM_002019.4	322	gTt/gCt	7/30	1	2	FACETS	0.714	0.628	0.805	0.714	0.628	0.805	SUBCLONAL	1	TRUE	1	0.608205622715093	2		278	327	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060912	38060912	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	17	425	0	ENST00000250448.2:c.1077del	p.Ile360Ter	p.I360*	ENST00000250448	NM_004496.3	359	ccC/cc	2/2	1	2	FACETS	0.152	0.113	0.199	0.152	0.113	0.199	SUBCLONAL	1	TRUE	1	0.608205622715093	2		425	367	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779100	3779100	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	90	458	1	ENST00000262367.5:c.5948del	p.Pro1983GlnfsTer16	p.P1983Qfs*16	ENST00000262367	NM_004380.2	1983	cCa/ca	31/31	1	2	FACETS	0.763	0.681	0.848	0.763	0.681	0.848	SUBCLONAL	1	TRUE	1	0.608205622715093	2		459	388	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819207	3819207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	144	354	0	ENST00000262367.5:c.3028C>T	p.Pro1010Ser	p.P1010S	ENST00000262367	NM_004380.2	1010	Cct/Tct	15/31	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.608205622715093	2		354	409	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819242	3819242	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	59	354	0	ENST00000262367.5:c.2993A>G	p.Lys998Arg	p.K998R	ENST00000262367	NM_004380.2	998	aAg/aGg	15/31	1	2	FACETS	0.442	0.381	0.508	0.442	0.381	0.508	SUBCLONAL	1	TRUE	1	0.608205622715093	2		354	439	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862739	9862739	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	74	330	0	ENST00000330684.3:c.2564A>G	p.Asp855Gly	p.D855G	ENST00000330684	NM_001134407.1	855	gAc/gGc	12/13	1	2	FACETS	0.651	0.573	0.733	0.651	0.573	0.733	SUBCLONAL	1	TRUE	1	0.608205622715093	2		330	374	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654678	67654678	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	130	347	0	ENST00000264010.4:c.1165A>G	p.Arg389Gly	p.R389G	ENST00000264010	NM_006565.3	389	Agg/Ggg	6/12	1	2	FACETS	0.99	0.905	1	0.99	0.905	1	CLONAL	1	TRUE	1	0.608205622715093	2		347	432	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663350	67663351	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	164	350	0	ENST00000264010.4:c.1756dup	p.Glu586GlyfsTer10	p.E586Gfs*10	ENST00000264010	NM_006565.3	584	gag/gaGg	10/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.608205622715093	2		350	488	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822340	72822340	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754562944	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	136	461	0	ENST00000268489.5:c.9835A>G	p.Met3279Val	p.M3279V	ENST00000268489	NM_006885.3	3279	Atg/Gtg	10/10	1	2	FACETS	0.816	0.746	0.889	0.816	0.746	0.889	CLONAL	1	TRUE	1	0.608205622715093	2		461	548	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830234	72830234	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	98	419	2	ENST00000268489.5:c.6347del	p.Pro2116ArgfsTer60	p.P2116Rfs*60	ENST00000268489	NM_006885.3	2116	cCg/cg	9/10	1	2	FACETS	0.82	0.737	0.907	0.82	0.737	0.907	CLONAL	1	TRUE	1	0.608205622715093	2		421	393	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953241	81953241	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1195957943	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	141	358	0	ENST00000359376.3:c.2211del	p.Glu738SerfsTer12	p.E738Sfs*12	ENST00000359376	NM_002661.3	736	aCc/ac	20/33	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.608205622715093	2		358	433	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972491	81972493	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	rs749338323	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	144	347	0	ENST00000359376.3:c.3291_3293del	p.Asn1097del	p.N1097del	ENST00000359376	NM_002661.3	1095	gACAac/gac	29/33	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.608205622715093	2		347	409	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346157	89346158	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs878855327	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	120	441	2	ENST00000301030.4:c.6792dup	p.Ala2265ArgfsTer8	p.A2265Rfs*8	ENST00000301030	NM_001256183.1	2264	-/C	9/13	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.608205622715093	2		443	374	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877344	89877344	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	135	380	0	ENST00000389301.3:c.419A>C	p.Glu140Ala	p.E140A	ENST00000389301	NM_000135.2	140	gAg/gCg	4/43	1	2	FACETS	0.947	0.867	1	0.947	0.867	1	CLONAL	1	TRUE	1	0.608205622715093	2		380	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579839	7579839	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	104	367	0	ENST00000269305.4:c.74T>G	p.Leu25Arg	p.L25R	ENST00000269305	NM_001126112.2	25	cTa/cGa	2/11	1	2	FACETS	0.828	0.747	0.913	0.828	0.747	0.913	CLONAL	1	TRUE	1	0.608205622715093	2		367	413	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533258	29533258	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	106	372	0	ENST00000356175.3:c.1261T>C	p.Ser421Pro	p.S421P	ENST00000356175	NM_000267.3	421	Tcc/Ccc	12/57	1	2	FACETS	0.719	0.647	0.794	0.719	0.647	0.794	SUBCLONAL	1	TRUE	1	0.608205622715093	2		372	485	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619243	37619243	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs748346154	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	53	398	0	ENST00000447079.4:c.919A>G	p.Arg307Gly	p.R307G	ENST00000447079	NM_015083.1	307	Agg/Ggg	1/14	1	2	FACETS	0.346	0.295	0.402	0.346	0.295	0.402	SUBCLONAL	1	TRUE	1	0.608205622715093	2		398	504	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533796	63533796	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	24	413	0	ENST00000307078.5:c.1358A>G	p.Gln453Arg	p.Q453R	ENST00000307078	NM_004655.3	453	cAg/cGg	6/11	1	2	FACETS	0.191	0.149	0.239	0.191	0.149	0.239	SUBCLONAL	1	TRUE	1	0.608205622715093	2		413	413	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796038	78796038	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	139	375	0	ENST00000306801.3:c.928G>A	p.Gly310Ser	p.G310S	ENST00000306801	NM_020761.2	310	Ggt/Agt	8/34	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.608205622715093	2		375	421	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39537707	39537707	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	36	304	0	ENST00000262039.4:c.241T>C	p.Phe81Leu	p.F81L	ENST00000262039	NM_002647.2	81	Ttt/Ctt	2/25	1	2	FACETS	0.312	0.257	0.374	0.312	0.257	0.374	SUBCLONAL	1	TRUE	1	0.608205622715093	2		304	379	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581257	48581257	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	56	365	0	ENST00000342988.3:c.561T>A	p.Ser187Arg	p.S187R	ENST00000342988	NM_005359.5	187	agT/agA	5/12	1	2	FACETS	0.396	0.34	0.457	0.396	0.34	0.457	SUBCLONAL	1	TRUE	1	0.608205622715093	2		365	465	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223375	2223376	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	43	430	0	ENST00000398665.3:c.3492dup	p.Val1165ArgfsTer28	p.V1165Rfs*28	ENST00000398665	NM_032482.2	1162	-/C	25/28	1	2	FACETS	0.353	0.295	0.416	0.353	0.295	0.416	SUBCLONAL	1	TRUE	1	0.608205622715093	2		430	401	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5207991	5207991	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs749395911	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	93	451	0	ENST00000357368.4:c.5720A>G	p.Asp1907Gly	p.D1907G	ENST00000357368	NM_002850.3	1907	gAc/gGc	37/38	1	2	FACETS	0.716	0.64	0.796	0.716	0.64	0.796	SUBCLONAL	1	TRUE	1	0.608205622715093	2		451	427	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221206	5221206	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200191658	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	139	435	2	ENST00000357368.4:c.3260C>T	p.Thr1087Met	p.T1087M	ENST00000357368	NM_002850.3	1087	aCg/aTg	20/38	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.608205622715093	2		437	449	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349649	15349649	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs755041038	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	40	434	0	ENST00000263377.2:c.3925A>G	p.Thr1309Ala	p.T1309A	ENST00000263377	NM_058243.2	1309	Acc/Gcc	19/20	1	2	FACETS	0.33	0.274	0.391	0.33	0.274	0.391	SUBCLONAL	1	TRUE	1	0.608205622715093	2		434	399	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228837	36228837	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	25	488	0	ENST00000222270.7:c.7736T>C	p.Val2579Ala	p.V2579A	ENST00000222270	NM_014727.1	2579	gTc/gCc	35/37	1	2	FACETS	0.173	0.136	0.217	0.173	0.136	0.217	SUBCLONAL	1	TRUE	1	0.608205622715093	2		488	474	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40743944	40743944	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	60	456	0	ENST00000392038.2:c.763T>C	p.Tyr255His	p.Y255H	ENST00000392038	NM_001626.4	255	Tat/Cat	9/14	1	2	FACETS	0.454	0.392	0.521	0.454	0.392	0.521	SUBCLONAL	1	TRUE	1	0.608205622715093	2		456	435	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798975	42798975	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	144	457	0	ENST00000575354.2:c.4460-1G>A		p.X1487_splice	ENST00000575354	NM_015125.3	1487			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.608205622715093	2		457	418	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918194	50918194	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	36	424	0	ENST00000440232.2:c.2515del	p.Leu839SerfsTer49	p.L839Sfs*49	ENST00000440232	NM_002691.3	837	tgC/tg	20/27	1	2	FACETS	0.354	0.292	0.424	0.354	0.292	0.424	SUBCLONAL	1	TRUE	1	0.608205622715093	2		424	334	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	87	384	3	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	0.878	0.784	0.975	0.878	0.784	0.975	CLONAL	1	TRUE	1	0.608205622715093	2		387	326	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965559	25965559	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	131	389	0	ENST00000435504.4:c.3647G>A	p.Ser1216Asn	p.S1216N	ENST00000435504		1216	aGc/aAc	13/13	1	2	FACETS	0.856	0.782	0.934	0.856	0.782	0.934	CLONAL	1	TRUE	1	0.608205622715093	2		389	503	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149157	61149157	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	81	453	0	ENST00000295025.8:c.1347A>G	p.Ile449Met	p.I449M	ENST00000295025	NM_002908.2	449	atA/atG	11/11	1	2	FACETS	0.587	0.519	0.659	0.587	0.519	0.659	SUBCLONAL	1	TRUE	1	0.608205622715093	2		453	454	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61712986	61712986	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	95	365	0	ENST00000401558.2:c.2425A>G	p.Asn809Asp	p.N809D	ENST00000401558	NM_003400.3	809	Aac/Gac	20/25	1	2	FACETS	0.791	0.709	0.877	0.791	0.709	0.877	SUBCLONAL	1	TRUE	1	0.608205622715093	2		365	395	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630934	67630934	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	62	340	0	ENST00000272342.5:c.1120T>C	p.Phe374Leu	p.F374L	ENST00000272342	NM_019002.3	374	Ttt/Ctt	5/6	1	2	FACETS	0.666	0.58	0.759	0.666	0.58	0.759	SUBCLONAL	1	TRUE	1	0.608205622715093	2		340	306	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285265	198285265	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1234164862	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	34	288	0	ENST00000335508.6:c.302A>G	p.Tyr101Cys	p.Y101C	ENST00000335508	NM_012433.2	101	tAt/tGt	4/25	1	2	FACETS	0.325	0.266	0.391	0.325	0.266	0.391	SUBCLONAL	1	TRUE	1	0.608205622715093	2		288	344	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537079	41537079	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	43	335	0	ENST00000263253.7:c.1906A>G	p.Lys636Glu	p.K636E	ENST00000263253	NM_001429.3	636	Aaa/Gaa	10/31	1	2	FACETS	0.304	0.254	0.359	0.304	0.254	0.359	SUBCLONAL	1	TRUE	1	0.608205622715093	2		335	465	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067176	37067178	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	rs876660192	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	115	329	0	ENST00000231790.2:c.1091_1093del	p.Thr364del	p.T364del	ENST00000231790	NM_000249.3	363	ACA/-	12/19	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.608205622715093	2		329	373	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1962783	1962783	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1440755101	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	123	361	0	ENST00000382891.5:c.3277G>A	p.Val1093Ile	p.V1093I	ENST00000382891	NM_133335.3	1093	Gtt/Att	18/22	1	2	FACETS	0.965	0.88	1	0.965	0.88	1	CLONAL	1	TRUE	1	0.608205622715093	2		361	419	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114277	143114277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs76891221	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	113	292	0	ENST00000262992.4:c.1144C>T	p.Arg382Trp	p.R382W	ENST00000262992	NM_001101669.1	382	Cgg/Tgg	13/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.608205622715093	2		292	327	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235399	235399	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	53	326	0	ENST00000264932.6:c.1205T>C	p.Val402Ala	p.V402A	ENST00000264932	NM_004168.2	402	gTc/gCc	9/15	1	2	FACETS	0.494	0.423	0.571	0.494	0.423	0.571	SUBCLONAL	1	TRUE	1	0.608205622715093	2		326	353	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254603	1254603	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	55	340	0	ENST00000310581.5:c.3175A>G	p.Lys1059Glu	p.K1059E	ENST00000310581	NM_198253.2	1059	Aag/Gag	15/16	1	2	FACETS	0.63	0.543	0.724	0.63	0.543	0.724	SUBCLONAL	1	TRUE	1	0.608205622715093	2		340	287	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593252	67593253	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	113	328	0	ENST00000274335.5:c.1999_2000dup	p.Lys668Ter	p.K668*	ENST00000274335		666	-/GT	15/15	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.608205622715093	2		328	365	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435812	149435812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1265832673	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	59	386	0	ENST00000286301.3:c.2412G>A	p.Met804Ile	p.M804I	ENST00000286301	NM_005211.3	804	atG/atA	18/22	1	2	FACETS	0.484	0.418	0.555	0.484	0.418	0.555	SUBCLONAL	1	TRUE	1	0.608205622715093	2		386	401	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562912	176562912	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	127	360	0	ENST00000439151.2:c.808C>T	p.Gln270Ter	p.Q270*	ENST00000439151	NM_022455.4	270	Caa/Taa	2/23	1	2	FACETS	0.829	0.755	0.905	0.829	0.755	0.905	CLONAL	1	TRUE	1	0.608205622715093	2		360	504	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176618906	176618906	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1232661858	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	107	296	0	ENST00000439151.2:c.949A>G	p.Thr317Ala	p.T317A	ENST00000439151	NM_022455.4	317	Acg/Gcg	3/23	1	2	FACETS	0.803	0.725	0.885	0.803	0.725	0.885	CLONAL	1	TRUE	1	0.608205622715093	2		296	438	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911279	29911279	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199474571	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	28	393	0	ENST00000376809.5:c.578G>A	p.Arg193His	p.R193H	ENST00000376809	NM_002116.7	193	cGc/cAc	3/8	1	2	FACETS	0.254	0.203	0.313	0.254	0.203	0.313	SUBCLONAL	1	TRUE	1	0.608205622715093	2		393	362	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323307	31323307	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	29	312	0	ENST00000412585.2:c.682T>C	p.Trp228Arg	p.W228R	ENST00000412585	NM_005514.6	228	Tgg/Cgg	4/8	1	2	FACETS	0.313	0.251	0.382	0.313	0.251	0.382	SUBCLONAL	1	TRUE	1	0.608205622715093	2		312	305	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983042	111983042	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	86	375	2	ENST00000368678.4:c.1505del	p.Lys502ArgfsTer53	p.K502Rfs*53	ENST00000368678		502	aAg/ag	13/13	1	2	FACETS	0.586	0.52	0.655	0.586	0.52	0.655	SUBCLONAL	1	TRUE	1	0.608205622715093	2		377	483	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196027	138196027	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	137	398	0	ENST00000237289.4:c.341G>A	p.Gly114Asp	p.G114D	ENST00000237289	NM_001270507.1	114	gGc/gAc	3/9	1	2	FACETS	0.967	0.886	1	0.967	0.886	1	CLONAL	1	TRUE	1	0.608205622715093	2		398	466	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157256646	157256646	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	125	311	0	ENST00000346085.5:c.1977del	p.Gly660GlufsTer8	p.G660Efs*8	ENST00000346085	NM_020732.3	658	gCc/gc	5/20	1	2	FACETS	0.873	0.795	0.953	0.873	0.795	0.953	CLONAL	1	TRUE	1	0.608205622715093	2		311	471	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527398	157527398	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	147	342	1	ENST00000346085.5:c.5127del	p.Ala1710HisfsTer56	p.A1710Hfs*56	ENST00000346085	NM_020732.3	1708	cAa/ca	20/20	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.608205622715093	2		343	473	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946388	2946388	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	142	401	0	ENST00000396946.4:c.3349T>C	p.Tyr1117His	p.Y1117H	ENST00000396946	NM_032415.4	1117	Tac/Cac	25/25	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.608205622715093	2		401	376	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985503	2985503	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	86	348	0	ENST00000396946.4:c.308A>G	p.Tyr103Cys	p.Y103C	ENST00000396946	NM_032415.4	103	tAc/tGc	4/25	1	2	FACETS	0.677	0.602	0.756	0.677	0.602	0.756	SUBCLONAL	1	TRUE	1	0.608205622715093	2		348	418	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508728	148508728	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs267601395	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	80	277	0	ENST00000320356.2:c.1936T>C	p.Tyr646His	p.Y646H	ENST00000320356	NM_004456.4	646	Tac/Cac	16/20	0.608205622715093	3	FACETS	0.735	0.649	0.826	0.367	0.324	0.413	SUBCLONAL	1	TRUE	1	0.608205622715093	3		277	467	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917642	151917643	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	45	202	0	ENST00000262189.6:c.3677_3678del	p.Glu1226AlafsTer6	p.E1226Afs*6	ENST00000262189	NM_170606.2	1226	gAG/g	23/59	0.608205622715093	3	FACETS	0.835	0.709	0.973	0.418	0.354	0.487	CLONAL	1	TRUE	1	0.608205622715093	3		202	231	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551450	141551450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	154	336	3	ENST00000220592.5:c.1847G>A	p.Gly616Asp	p.G616D	ENST00000220592	NM_012154.3	616	gGc/gAc	15/19	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.608205622715093	2		339	423	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759406	133759406	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1371645607	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	119	317	0	ENST00000318560.5:c.1729C>T	p.Arg577Ter	p.R577*	ENST00000318560	NM_005157.4	577	Cga/Tga	11/11	1	2	FACETS	0.991	0.902	1	0.991	0.902	1	CLONAL	1	TRUE	1	0.608205622715093	2		317	395	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300039	137300040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755912201	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	95	328	3	ENST00000481739.1:c.331dup	p.Leu111ProfsTer70	p.L111Pfs*70	ENST00000481739	NM_002957.4	108	-/C	3/10	1	2	FACETS	0.885	0.795	0.979	0.885	0.795	0.979	CLONAL	1	TRUE	1	0.608205622715093	2		331	353	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417337	139417337	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	53	396	0	ENST00000277541.6:c.707del	p.Thr236ArgfsTer41	p.T236Rfs*41	ENST00000277541	NM_017617.3	236	aCg/ag	4/34	1	2	FACETS	0.522	0.447	0.603	0.522	0.447	0.603	SUBCLONAL	1	TRUE	1	0.608205622715093	2		396	334	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937693	44937693	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	30	248	0	ENST00000377967.4:c.2881A>G	p.Thr961Ala	p.T961A	ENST00000377967	NM_021140.2	961	Aca/Gca	19/29	1	2	FACETS	0.321	0.259	0.391	0.321	0.259	0.391	SUBCLONAL	1	TRUE	1	0.608205622715093	2		248	307	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	53	378	1	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	1	2	FACETS	0.438	0.374	0.507	0.438	0.374	0.507	SUBCLONAL	1	TRUE	1	0.608205622715093	2		379	398	SUCCESS
AR	367	MSKCC	GRCh37	X	66942672	66942672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	84	275	0	ENST00000374690.3:c.2453C>T	p.Pro818Leu	p.P818L	ENST00000374690	NM_000044.3	818	cCa/cTa	7/8	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.608205622715093	2		275	267	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938230	76938230	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	116	362	5	ENST00000373344.5:c.2518del	p.Arg840GlufsTer29	p.R840Efs*29	ENST00000373344	NM_000489.3	840	Aga/ga	9/35	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.608205622715093	2		367	351	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860012	152860012	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	92	359	0	ENST00000406277.2:c.416C>T	p.Pro139Leu	p.P139L	ENST00000406277	NM_152274.4	139	cCa/cTa	5/7	1		FACETS		0.726	0.9				CLONAL	1	TRUE	1	0.608205622715093	2		359	373	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061909-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	25	663	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		663	413	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0061909-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	70	786	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		786	620	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024721	14024721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1340754747	NA	P-0061909-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	9	0	0	ENST00000311895.7:c.947C>T	p.Thr316Met	p.T316M	ENST00000311895	NM_005236.2	316	aCg/aTg	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		0	231	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0061909-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	34	481	0	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		481	669	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883123	37883123	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061909-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	45	370	0	ENST00000269571.5:c.3026T>C	p.Leu1009Pro	p.L1009P	ENST00000269571		1009	cTg/cCg	25/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		370	543	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120022	70120022	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061909-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	37	368	0	ENST00000245479.2:c.1024C>G	p.Pro342Ala	p.P342A	ENST00000245479	NM_000346.3	342	Ccg/Gcg	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		368	466	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44919303	44919312	+	frameshift_variant	Frame_Shift_Del	DEL	AATAAAACTA	AATAAAACTA	-	novel	NA	P-0061909-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	16	130	0	ENST00000377967.4:c.1234_1243del	p.Lys412TyrfsTer24	p.K412Yfs*24	ENST00000377967	NM_021140.2	411	AATAAAACTAaa/aa	13/29	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		130	197	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922996	44922997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061909-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	39	373	0	ENST00000377967.4:c.1859dup	p.Asn620LysfsTer19	p.N620Kfs*19	ENST00000377967	NM_021140.2	619	-/A	16/29	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		373	668	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830159	72830159	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1216714586	NA	P-0061909-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	49	408	0	ENST00000268489.5:c.6422T>C	p.Leu2141Pro	p.L2141P	ENST00000268489	NM_006885.3	2141	cTc/cCc	9/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		408	687	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879240	151879240	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061909-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	39	427	0	ENST00000262189.6:c.5705T>C	p.Val1902Ala	p.V1902A	ENST00000262189	NM_170606.2	1902	gTt/gCt	36/59	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		427	627	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875645	35875645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201449880	NA	P-0062001-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	11	0	0	ENST00000303115.3:c.832G>A	p.Asp278Asn	p.D278N	ENST00000303115	NM_002185.3	278	Gat/Aat	7/8	0.271261917085667	3	FACETS	0.335	0.231	0.465	0.167	0.115	0.233	SUBCLONAL	1	TRUE	1	0.27361723165098	3		0	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0062001-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	167	988	1	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.261484202043365	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.27361723165098	2		989	554	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457269	89457269	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062001-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	4	0	0	ENST00000336596.2:c.1750G>A	p.Gly584Ser	p.G584S	ENST00000336596	NM_005233.5	584	Ggc/Agc	9/17	0.23892415926987	2	FACETS	0.271	0.142	0.457	0.135	0.071	0.229	SUBCLONAL	1	TRUE	0	0.27361723165098	2		0	108	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431662	6431662	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062001-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	18	300	0	ENST00000356142.4:c.215A>G	p.Tyr72Cys	p.Y72C	ENST00000356142	NM_018890.3	72	tAt/tGt	3/7	0.199493467039612	4	FACETS	0.846	0.64	1	0.423	0.32	0.544	CLONAL	1	TRUE	2	0.27361723165098	4		300	198	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242482	55242506	+	protein_altering_variant	In_Frame_Del	DEL	CATCTCCGAAAGCCAACAAGGAAAT	CATCTCCGAAAGCCAACAAGGAAAT	G	novel	NA	P-0062001-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	74	401	0	ENST00000275493.2:c.2252_2276delinsG	p.Thr751_Ile759delinsSer	p.T751_I759delinsS	ENST00000275493	NM_005228.3	751	aCATCTCCGAAAGCCAACAAGGAAATc/aGc	19/28	0.199493467039612	4	FACETS	0.876	0.771	0.988	0.876	0.771	0.988	CLONAL	2	TRUE	2	0.27361723165098	4		401	393	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0062116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	185	286	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.731258217033047	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	TRUE	0	0.733787062650099	3		286	225	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220443	1220443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202466	NA	P-0062116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	828	749	0	ENST00000326873.7:c.536C>T	p.Pro179Leu	p.P179L	ENST00000326873	NM_000455.4	179	cCg/cTg	4/10	0.719287358862097	2	FACETS	0.978	0.956	0.999	0.978	0.956	0.999	CLONAL	2	TRUE	0	0.733787062650099	2		749	1154	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0062116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1185	369	607	1	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	0.731258217033047	3	FACETS	0.885	0.837	0.933	0.295	0.279	0.311	CLONAL	1	TRUE	0	0.733787062650099	3		608	1554	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793010	33793010	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs974386262	NA	P-0062116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	237	419	1	ENST00000498907.2:c.311G>A	p.Gly104Asp	p.G104D	ENST00000498907	NM_004364.3	104	gGc/gAc	1/1	0.733787062650099	3	FACETS	1	0.957	1	0.515	0.482	0.55	CLONAL	1	TRUE	1	0.733787062650099	3		420	857	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214871	36214871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	300	627	4	ENST00000222270.7:c.3302del	p.Pro1101LeufsTer81	p.P1101Lfs*81	ENST00000222270	NM_014727.1	1099	ggC/gg	8/37	0.733787062650099	3	FACETS	0.849	0.798	0.901	0.424	0.399	0.451	CLONAL	1	TRUE	1	0.733787062650099	3		631	1317	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076931	41076932	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0062116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	185	446	0	ENST00000373198.4:c.1488dup	p.Pro497AlafsTer3	p.P497Afs*3	ENST00000373198	NM_133170.3	496	-/G	9/32	0.712030085090855	3	FACETS	0.885	0.819	0.953	0.442	0.409	0.477	CLONAL	1	TRUE	1	0.733787062650099	3		446	779	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730075	41730075	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	600	562	0	ENST00000242208.4:c.454C>A	p.Arg152Ser	p.R152S	ENST00000242208	NM_002192.2	152	Cgt/Agt	3/3	0.733787062650099	3	FACETS	0.899	0.868	0.931	0.899	0.868	0.931	CLONAL	2	TRUE	1	0.733787062650099	3		562	1243	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413565	32413565	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	431	505	0	ENST00000332351.3:c.1385G>T	p.Arg462Leu	p.R462L	ENST00000332351	NM_024426.4	462	cGg/cTg	9/10	0.712030085090855	3	FACETS	0.923	0.885	0.961	0.923	0.885	0.961	CLONAL	2	TRUE	1	0.733787062650099	3		505	870	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0062116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	814	710	4	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	0.712030085090855	3	FACETS	0.917	0.889	0.944	0.917	0.889	0.944	CLONAL	2	TRUE	1	0.733787062650099	3		714	1654	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536133	106536133	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs923684599	NA	P-0062116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	402	586	0	ENST00000369096.4:c.100A>G	p.Lys34Glu	p.K34E	ENST00000369096	NM_001198.3	34	Aag/Gag	2/7	1	2	FACETS	0.964	0.918	1	0.964	0.918	1	CLONAL	1	TRUE	1	0.733787062650099	2		586	1137	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600479	10600479	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	984	661	0	ENST00000171111.5:c.1376G>T	p.Arg459Leu	p.R459L	ENST00000171111	NM_203500.1	459	cGa/cTa	4/6	0.719287358862097	2	FACETS	0.98	0.959	0.999	0.98	0.959	0.999	CLONAL	2	TRUE	0	0.733787062650099	2		661	1369	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595651	55595651	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	45	351	0	ENST00000288135.5:c.2141+1del		p.C714fs	ENST00000288135	NM_000222.2	714	tGc/tc	14/21	1	2	FACETS	0.943	0.812	1	0.943	0.812	1	CLONAL	1	TRUE	1	0.733787062650099	2		351	130	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599928	10599928	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs752854170	NA	P-0062116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	919	564	0	ENST00000171111.5:c.1648A>G	p.Met550Val	p.M550V	ENST00000171111	NM_203500.1	550	Atg/Gtg	5/6	0.719287358862097	2	FACETS	0.95	0.929	0.97	0.95	0.929	0.97	CLONAL	2	TRUE	0	0.733787062650099	2		564	1319	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097625	11097625	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	425	595	1	ENST00000358026.2:c.810del	p.Met272CysfsTer31	p.M272Cfs*31	ENST00000358026	NM_001128849.1	269	Ccc/cc	5/36	0.719287358862097	2	FACETS	1	0.976	1	0.517	0.493	0.541	CLONAL	1	TRUE	0	0.733787062650099	2		596	1121	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609003	43609003	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0062116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	379	762	0	ENST00000355710.3:c.1763del		p.X588_splice	ENST00000355710	NM_020975.4	588			1	2	FACETS	0.913	0.868	0.959	0.913	0.868	0.959	CLONAL	1	TRUE	1	0.733787062650099	2		762	1131	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534232	534232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	290	553	0	ENST00000451590.1:c.91G>A	p.Glu31Lys	p.E31K	ENST00000451590	NM_001130442.1	31	Gaa/Aaa	2/5	0.712030085090855	3	FACETS	0.813	0.763	0.864	0.406	0.381	0.432	CLONAL	1	TRUE	1	0.733787062650099	3		553	1329	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17120438	17120438	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	323	532	0	ENST00000285071.4:c.1121T>A	p.Val374Glu	p.V374E	ENST00000285071	NM_144997.5	374	gTg/gAg	10/14	1	2	FACETS	0.947	0.896	0.998	0.947	0.896	0.998	CLONAL	1	TRUE	1	0.733787062650099	2		532	930	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713805	30713805	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	882	757	0	ENST00000295754.5:c.1130A>C	p.His377Pro	p.H377P	ENST00000295754	NM_003242.5	377	cAc/cCc	4/7	0.733787062650099	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.733787062650099	2		757	1201	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067126	37067126	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs267607815	NA	P-0062116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	307	239	0	ENST00000231790.2:c.1039-2A>T		p.X347_splice	ENST00000231790	NM_000249.3	347			0.733787062650099	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.733787062650099	2		239	375	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958847	55958847	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	203	473	0	ENST00000263923.4:c.3006G>T	p.Leu1002Phe	p.L1002F	ENST00000263923	NM_002253.2	1002	ttG/ttT	22/30	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.733787062650099	2		473	540	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230747	66230747	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	52	427	0	ENST00000273854.3:c.2224G>T	p.Val742Leu	p.V742L	ENST00000273854	NM_004439.5	742	Gtg/Ttg	12/18	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.733787062650099	2		427	118	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532801	187532801	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	315	544	0	ENST00000441802.2:c.9592T>G	p.Ser3198Ala	p.S3198A	ENST00000441802	NM_005245.3	3198	Tct/Gct	14/27	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.733787062650099	2		544	834	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950785	79950785	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1480047980	NA	P-0062116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	252	375	0	ENST00000265081.6:c.237+2T>C		p.X79_splice	ENST00000265081	NM_002439.4	79			1	2	FACETS	0.946	0.889	1	0.946	0.889	1	CLONAL	1	TRUE	1	0.733787062650099	2		375	726	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915007	131915007	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1554097755	NA	P-0062116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	63	339	0	ENST00000265335.6:c.366-2A>G		p.X122_splice	ENST00000265335		122			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.733787062650099	2		339	139	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030365	180030366	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0062116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	355	674	1	ENST00000261937.6:c.3918_3919delinsTT	p.Ala1307Ser	p.A1307S	ENST00000261937	NM_182925.4	1306	gtGGct/gtTTct	30/30	1	2	FACETS	0.839	0.795	0.884	0.839	0.795	0.884	CLONAL	1	TRUE	1	0.733787062650099	2		675	1153	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515223	106515223	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	361	508	1	ENST00000359195.3:c.2366C>A	p.Pro789His	p.P789H	ENST00000359195	NM_002649.2	789	cCt/cAt	5/11	0.712030085090855	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.733787062650099	3		509	658	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124532410	124532411	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	rs1462186598	NA	P-0062116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	58	333	0	ENST00000357628.3:c.33_34del	p.Leu14GlufsTer4	p.L14Efs*4	ENST00000357628	NM_015450.2	11	taTAca/taca	6/19	0.712030085090855	3	FACETS	0.878	0.78	0.978	0.878	0.78	0.978	CLONAL	2	TRUE	1	0.733787062650099	3		333	123	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152373161	152373161	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	347	482	0	ENST00000359321.1:c.4T>A	p.Cys2Ser	p.C2S	ENST00000359321	NM_005431.1	2	Tgt/Agt	1/3	0.712030085090855	3	FACETS	0.927	0.877	0.979	0.464	0.438	0.49	CLONAL	1	TRUE	1	0.733787062650099	3		482	1394	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90971032	90971032	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	389	446	0	ENST00000265433.3:c.1045G>C	p.Asp349His	p.D349H	ENST00000265433	NM_002485.4	349	Gat/Cat	9/16	0.712030085090855	3	FACETS	0.979	0.938	1	0.979	0.938	1	CLONAL	2	TRUE	1	0.733787062650099	3		446	740	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141569616	141569616	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	298	563	0	ENST00000220592.5:c.668C>T	p.Ala223Val	p.A223V	ENST00000220592	NM_012154.3	223	gCg/gTg	6/19	0.712030085090855	3	FACETS	0.965	0.909	1	0.483	0.454	0.512	CLONAL	1	TRUE	1	0.733787062650099	3		563	1150	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248122	110248122	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	298	521	0	ENST00000374672.4:c.1350C>A	p.His450Gln	p.H450Q	ENST00000374672	NM_004235.4	450	caC/caA	5/5	0.692058852539423	3	FACETS	0.92	0.866	0.975	0.46	0.433	0.488	CLONAL	1	TRUE	1	0.733787062650099	3		521	1207	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18943156	18943157	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	A	novel	NA	P-0062116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	150	372	2	ENST00000262803.5:c.138_139delinsA	p.Gly49AlafsTer45	p.G49Afs*45	ENST00000262803	NM_002911.3	46	acGCcc/acAcc	1/24	0.733787062650099	3	FACETS	0.521	0.475	0.569	0.261	0.237	0.285	SUBCLONAL	1	TRUE	1	0.733787062650099	3		374	1072	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs267605076	NA	P-0062122-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	39	192	0	ENST00000269305.4:c.672G>T	p.Glu224Asp	p.E224D	ENST00000269305	NM_001126112.2	224	gaG/gaT	6/11	1	2	FACETS	0.632	0.522	0.755	0.632	0.522	0.755	SUBCLONAL	1	TRUE	1	0.18	2		192	686	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0062122-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	51	243	0	ENST00000288602.6:c.1397G>T	p.Gly466Val	p.G466V	ENST00000288602	NM_004333.4	466	gGa/gTa	11/18	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.18	2		243	447	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52693404	52693404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062122-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	52	201	0	ENST00000322088.6:c.55G>A	p.Glu19Lys	p.E19K	ENST00000322088	NM_014225.5	19	Gaa/Aaa	1/15	1	2	FACETS	0.916	0.779	1	0.916	0.779	1	CLONAL	1	TRUE	1	0.18	2		201	631	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602293	10602293	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062122-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	43	220	0	ENST00000171111.5:c.1285G>T	p.Gly429Cys	p.G429C	ENST00000171111	NM_203500.1	429	Ggc/Tgc	3/6	1	2	FACETS	0.718	0.6	0.85	0.718	0.6	0.85	SUBCLONAL	1	TRUE	1	0.18	2		220	665	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191101	2191101	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062122-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	49	174	0	ENST00000398665.3:c.355G>T	p.Val119Leu	p.V119L	ENST00000398665	NM_032482.2	119	Gtg/Ttg	5/28	1	2	FACETS	0.804	0.68	0.941	0.804	0.68	0.941	CLONAL	1	TRUE	1	0.18	2		174	677	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225360594	225360594	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062122-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	31	125	0	ENST00000264414.4:c.1797G>T	p.Met599Ile	p.M599I	ENST00000264414	NM_003590.4	599	atG/atT	13/16	1	2	FACETS	0.685	0.553	0.835	0.685	0.553	0.835	SUBCLONAL	1	TRUE	1	0.18	2		125	503	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798129	45798129	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062122-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	98	207	0	ENST00000450313.1:c.722G>T	p.Arg241Leu	p.R241L	ENST00000450313	NM_012222.2	241	cGg/cTg	9/16	0.129046804082133	3	FACETS	1	0.98	1	0.74	0.66	0.826	CLONAL	1	TRUE	1	0.18	3		207	802	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425401	49425401	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062122-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	59	210	0	ENST00000301067.7:c.13087G>T	p.Ala4363Ser	p.A4363S	ENST00000301067	NM_003482.3	4363	Gcc/Tcc	39/54	1	2	FACETS	0.885	0.76	1	0.885	0.76	1	CLONAL	1	TRUE	1	0.18	2		210	741	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240228	41240228	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1279773350	NA	P-0062122-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	23	106	0	ENST00000379561.5:c.122G>T	p.Ser41Ile	p.S41I	ENST00000379561	NM_002015.3	41	aGc/aTc	1/3	1	2	FACETS	0.565	0.44	0.711	0.565	0.44	0.711	SUBCLONAL	1	TRUE	1	0.18	2		106	452	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662284	67662284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062122-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	36	164	0	ENST00000264010.4:c.1530G>A	p.Met510Ile	p.M510I	ENST00000264010	NM_006565.3	510	atG/atA	9/12	1	2	FACETS	0.678	0.556	0.815	0.678	0.556	0.815	SUBCLONAL	1	TRUE	1	0.18	2		164	590	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613140	52613140	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062122-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	42	180	0	ENST00000394830.3:c.3388G>C	p.Asp1130His	p.D1130H	ENST00000394830	NM_018313.4	1130	Gac/Cac	22/30	1	2	FACETS	0.758	0.631	0.898	0.758	0.631	0.898	SUBCLONAL	1	TRUE	1	0.18	2		180	616	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048674	180048674	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062122-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	49	191	0	ENST00000261937.6:c.1888G>T	p.Gly630Trp	p.G630W	ENST00000261937	NM_182925.4	630	Ggg/Tgg	13/30	1	2	FACETS	0.774	0.655	0.907	0.774	0.655	0.907	CLONAL	1	TRUE	1	0.18	2		191	703	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90994961	90994961	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062122-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	34	103	0	ENST00000265433.3:c.160G>T	p.Val54Leu	p.V54L	ENST00000265433	NM_002485.4	54	Gta/Tta	2/16	1	2	FACETS	0.893	0.73	1	0.893	0.73	1	CLONAL	1	TRUE	1	0.18	2		103	423	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429027	47429028	+	missense_variant	Missense_Mutation	DNP	GA	GA	AG	novel	NA	P-0062122-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	48	211	0	ENST00000377045.4:c.1390_1391delinsAG	p.Glu464Arg	p.E464R	ENST00000377045	NM_001654.4	464	GAg/AGg	13/16	1	2	FACETS	0.86	0.726	1	0.86	0.726	1	CLONAL	1	TRUE	1	0.18	2		211	620	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410786	63410786	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062122-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	34	198	0	ENST00000330258.3:c.2381C>T	p.Ser794Leu	p.S794L	ENST00000330258	NM_152424.3	794	tCa/tTa	2/2	1	2	FACETS	0.586	0.477	0.708	0.586	0.477	0.708	SUBCLONAL	1	TRUE	1	0.18	2		198	645	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	105	663	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.861	0.774	0.954	0.861	0.774	0.954	CLONAL	1	TRUE	1	0.434539733712171	2		663	561	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	108	476	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.572	0.513	0.635	0.572	0.513	0.635	SUBCLONAL	1	TRUE	1	0.434539733712171	2		476	869	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	33	502	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	0.166	0.134	0.202	0.166	0.134	0.202	SUBCLONAL	1	TRUE	1	0.434539733712171	2		502	916	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788618	3788618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398124146	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	19	389	0	ENST00000262367.5:c.4336C>T	p.Arg1446Cys	p.R1446C	ENST00000262367	NM_004380.2	1446	Cgc/Tgc	26/31	1	2	FACETS	0.139	0.104	0.179	0.139	0.104	0.179	SUBCLONAL	1	TRUE	1	0.434539733712171	2		389	631	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151270	202151270	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	125	367	0	ENST00000358485.4:c.1570C>T	p.Gln524Ter	p.Q524*	ENST00000358485	NM_001080125.1	524	Cag/Tag	9/9	0.434539733712171	1	FACETS	0.99	0.902	1	0.99	0.902	1	CLONAL	1	TRUE	0	0.434539733712171	1		367	455	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575671	48575671	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	19	270	0	ENST00000342988.3:c.431C>G	p.Ser144Ter	p.S144*	ENST00000342988	NM_005359.5	144	tCa/tGa	4/12	1	2	FACETS	0.595	0.455	0.756	0.595	0.455	0.756	SUBCLONAL	1	TRUE	1	0.434539733712171	2		270	147	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982743	7982743	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764382022	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	65	496	0	ENST00000319144.4:c.1042G>C	p.Glu348Gln	p.E348Q	ENST00000319144	NM_001139.2	348	Gag/Cag	8/15	1	2	FACETS	0.387	0.335	0.444	0.387	0.335	0.444	SUBCLONAL	1	TRUE	1	0.434539733712171	2		496	773	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663346	227663346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024227751	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	61	493	0	ENST00000305123.5:c.109G>A	p.Glu37Lys	p.E37K	ENST00000305123	NM_005544.2	37	Gag/Aag	1/2	0.434539733712171	1	FACETS	0.321	0.277	0.37	0.321	0.277	0.37	SUBCLONAL	1	TRUE	0	0.434539733712171	1		493	684	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	234	549	0	ENST00000269571.5:c.829G>T	p.Asp277Tyr	p.D277Y	ENST00000269571		277	Gac/Tac	7/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.434539733712171	2		549	975	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807902	3807902	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	48	510	0	ENST00000262367.5:c.3517C>T	p.Arg1173Ter	p.R1173*	ENST00000262367	NM_004380.2	1173	Cga/Tga	18/31	1	2	FACETS	0.311	0.262	0.365	0.311	0.262	0.365	SUBCLONAL	1	TRUE	1	0.434539733712171	2		510	710	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37863341	37863341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	73	572	0	ENST00000269571.5:c.172G>A	p.Gly58Arg	p.G58R	ENST00000269571		58	Gga/Aga	2/27	1	2	FACETS	0.311	0.27	0.354	0.311	0.27	0.354	SUBCLONAL	1	TRUE	1	0.434539733712171	2		572	1082	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272519	21272519	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	184	633	0	ENST00000354336.3:c.297C>G	p.Ile99Met	p.I99M	ENST00000354336	NM_005207.3	99	atC/atG	1/3	1	2	FACETS	0.832	0.767	0.899	0.832	0.767	0.899	CLONAL	1	TRUE	1	0.434539733712171	2		633	1018	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17947999	17947999	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	102	403	0	ENST00000458235.1:c.1725G>C	p.Leu575Phe	p.L575F	ENST00000458235	NM_000215.3	575	ttG/ttC	13/24	1	2	FACETS	0.541	0.483	0.602	0.541	0.483	0.602	SUBCLONAL	1	TRUE	1	0.434539733712171	2		403	868	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619799	1619799	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs535113552	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	50	588	0	ENST00000344749.5:c.1147G>A	p.Asp383Asn	p.D383N	ENST00000344749	NM_001136139.2	383	Gac/Aac	14/19	1	2	FACETS	0.245	0.206	0.287	0.245	0.206	0.287	SUBCLONAL	1	TRUE	1	0.434539733712171	2		588	941	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527778	157527778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	184	521	0	ENST00000346085.5:c.5503G>A	p.Glu1835Lys	p.E1835K	ENST00000346085	NM_020732.3	1835	Gag/Aag	20/20	0.285272940938118	1	FACETS	0.875	0.809	0.942	0.875	0.809	0.942	CLONAL	1	TRUE	0	0.434539733712171	1		521	758	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176336	24176336	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	82	354	0	ENST00000263121.7:c.1127G>C	p.Arg376Thr	p.R376T	ENST00000263121	NM_003073.3	376	aGg/aCg	9/9	1	2	FACETS	0.541	0.476	0.61	0.541	0.476	0.61	SUBCLONAL	1	TRUE	1	0.434539733712171	2		354	698	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218357	133218357	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1335665224	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	123	495	0	ENST00000320574.5:c.5254G>A	p.Asp1752Asn	p.D1752N	ENST00000320574	NM_006231.2	1752	Gac/Aac	39/49	0.208833252964634	3	FACETS	0.712	0.643	0.785	0.237	0.214	0.262	INDETERMINATE	1	TRUE	0	0.434539733712171	3		495	968	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422098	81422098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	56	542	0	ENST00000298171.2:c.74C>T	p.Ser25Leu	p.S25L	ENST00000298171	NM_000369.2	25	tCg/tTg	1/10	1	2	FACETS	0.29	0.248	0.337	0.29	0.248	0.337	SUBCLONAL	1	TRUE	1	0.434539733712171	2		542	888	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105967	27105967	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	69	620	0	ENST00000324856.7:c.5578G>T	p.Glu1860Ter	p.E1860*	ENST00000324856	NM_006015.4	1860	Gag/Tag	20/20	1	2	FACETS	0.306	0.265	0.35	0.306	0.265	0.35	SUBCLONAL	1	TRUE	1	0.434539733712171	2		620	1038	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179180	123179180	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	27	141	0	ENST00000218089.9:c.629C>G	p.Ser210Ter	p.S210*	ENST00000218089	NM_001042749.1	210	tCa/tGa	8/35	1	1	FACETS	0.608	0.489	0.741	0.608	0.489	0.741	SUBCLONAL	1	TRUE	0	0.434539733712171	1		141	160	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818189	32818189	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777683307	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	64	516	0	ENST00000354258.4:c.1336G>A	p.Glu446Lys	p.E446K	ENST00000354258	NM_000593.5	446	Gaa/Aaa	5/11	0.285272940938118	1	FACETS	0.301	0.26	0.346	0.301	0.26	0.346	SUBCLONAL	1	TRUE	0	0.434539733712171	1		516	766	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922749	44922749	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	72	248	0	ENST00000377967.4:c.1610C>G	p.Ser537Ter	p.S537*	ENST00000377967	NM_021140.2	537	tCa/tGa	16/29	1	1	FACETS	0.583	0.511	0.66	0.583	0.511	0.66	SUBCLONAL	1	TRUE	0	0.434539733712171	1		248	445	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429415	47429415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs969755578	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	197	215	0	ENST00000377045.4:c.1543C>T	p.Arg515Cys	p.R515C	ENST00000377045	NM_001654.4	515	Cgt/Tgt	14/16	1	1	FACETS	0.885	0.832	0.938	1	0.994	1	CLONAL	2	TRUE	0	0.434539733712171	1		215	401	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981533	201981534	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	36	440	0	ENST00000359651.3:c.449dup	p.Gln151ProfsTer10	p.Q151Pfs*10	ENST00000359651		149	-/T	3/8	1	2	FACETS	0.239	0.195	0.288	0.239	0.195	0.288	SUBCLONAL	1	TRUE	1	0.434539733712171	2		440	694	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10772978	10772978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	60	380	0	ENST00000361367.2:c.19G>A	p.Glu7Lys	p.E7K	ENST00000361367	NM_014633.3	7	Gag/Aag	1/25	0.180223814441908	0	FACETS	0.26	0.223	0.299			1	INDETERMINATE	1	TRUE	0	0.434539733712171	0		380	601	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244141	46244141	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	61	467	0	ENST00000334344.6:c.2235G>C	p.Gln745His	p.Q745H	ENST00000334344	NM_152641.2	745	caG/caC	15/21	0.107601118793775	4	FACETS	0.661	0.57	0.76	0.331	0.285	0.38	INDETERMINATE	1	TRUE	2	0.434539733712171	4		467	609	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448443	49448443	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	90	558	0	ENST00000301067.7:c.268G>C	p.Asp90His	p.D90H	ENST00000301067	NM_003482.3	90	Gat/Cat	3/54	0.107601118793775	4	FACETS	0.552	0.488	0.62	0.276	0.244	0.31	INDETERMINATE	1	TRUE	2	0.434539733712171	4		558	1077	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495513	56495513	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	72	541	0	ENST00000267101.3:c.3703C>G	p.Leu1235Val	p.L1235V	ENST00000267101	NM_001982.3	1235	Ctg/Gtg	28/28	0.107601118793775	4	FACETS	0.419	0.365	0.478	0.21	0.182	0.239	INDETERMINATE	1	TRUE	2	0.434539733712171	4		541	1134	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50733678	50733678	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	15	304	0	ENST00000307179.4:c.237C>G	p.Phe79Leu	p.F79L	ENST00000307179		79	ttC/ttG	3/20	1	2	FACETS	0.266	0.194	0.352	0.266	0.194	0.352	SUBCLONAL	1	TRUE	1	0.434539733712171	2		304	260	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807323	3807323	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	43	387	0	ENST00000262367.5:c.3664C>T	p.Pro1222Ser	p.P1222S	ENST00000262367	NM_004380.2	1222	Cct/Tct	19/31	1	2	FACETS	0.33	0.276	0.391	0.33	0.276	0.391	SUBCLONAL	1	TRUE	1	0.434539733712171	2		387	599	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	71	432	0	ENST00000356175.3:c.1318C>G	p.Arg440Gly	p.R440G	ENST00000356175	NM_000267.3	440	Cga/Gga	12/57	1	2	FACETS	0.639	0.559	0.726	0.639	0.559	0.726	SUBCLONAL	1	TRUE	1	0.434539733712171	2		432	511	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627277	37627277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	55	493	0	ENST00000447079.4:c.1192G>A	p.Glu398Lys	p.E398K	ENST00000447079	NM_015083.1	398	Gaa/Aaa	2/14	1	2	FACETS	0.389	0.332	0.451	0.389	0.332	0.451	SUBCLONAL	1	TRUE	1	0.434539733712171	2		493	651	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251535	10251535	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	59	537	0	ENST00000340748.4:c.3397G>C	p.Glu1133Gln	p.E1133Q	ENST00000340748		1133	Gag/Cag	31/40	1	2	FACETS	0.256	0.219	0.297	0.256	0.219	0.297	SUBCLONAL	1	TRUE	1	0.434539733712171	2		537	1060	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132445	11132445	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	189	627	0	ENST00000358026.2:c.2661G>C	p.Lys887Asn	p.K887N	ENST00000358026	NM_001128849.1	887	aaG/aaC	19/36	1	2	FACETS	0.805	0.744	0.87	0.805	0.744	0.87	CLONAL	1	TRUE	1	0.434539733712171	2		627	1080	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229034	36229034	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	74	552	0	ENST00000222270.7:c.7814C>T	p.Ser2605Phe	p.S2605F	ENST00000222270	NM_014727.1	2605	tCt/tTt	36/37	1	2	FACETS	0.337	0.294	0.384	0.337	0.294	0.384	SUBCLONAL	1	TRUE	1	0.434539733712171	2		552	1011	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47503587	47503587	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	124	381	0	ENST00000404338.3:c.4143-1G>A		p.X1381_splice	ENST00000404338	NM_004491.4	1381			1	2	FACETS	0.867	0.786	0.952	0.867	0.786	0.952	CLONAL	1	TRUE	1	0.434539733712171	2		381	658	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919590	96919590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	53	434	0	ENST00000258439.3:c.673G>A	p.Glu225Lys	p.E225K	ENST00000258439	NM_001193304.2	225	Gag/Aag	4/4	0.125630688686333	3	FACETS	0.404	0.344	0.47	0.202	0.172	0.235	INDETERMINATE	1	TRUE	1	0.434539733712171	3		434	735	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881692	111881692	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	246	428	0	ENST00000393256.3:c.370T>C	p.Phe124Leu	p.F124L	ENST00000393256	NM_006538.4	124	Ttc/Ctc	2/4	0.434539733712171	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.434539733712171	1		428	733	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564603	41564604	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	37	458	1	ENST00000263253.7:c.4025_4025+1delinsTT		p.X1342_splice	ENST00000263253	NM_001429.3	1342		24/31	1	2	FACETS	0.321	0.264	0.385	0.321	0.264	0.385	SUBCLONAL	1	TRUE	1	0.434539733712171	2		459	530	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637660	52637660	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1370481342	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	77	383	0	ENST00000394830.3:c.2656C>T	p.Leu886Phe	p.L886F	ENST00000394830	NM_018313.4	886	Ctt/Ttt	18/30	0.107601118793775	4	FACETS	0.82	0.727	0.918	0.82	0.727	0.918	INDETERMINATE	2	TRUE	2	0.434539733712171	4		383	310	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683400	182683400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	56	325	0	ENST00000292782.4:c.145G>A	p.Glu49Lys	p.E49K	ENST00000292782	NM_020640.2	49	Gaa/Aaa	2/7	0.107601118793775	4	FACETS	1	0.964	1	0.692	0.598	0.793	INDETERMINATE	1	TRUE	2	0.434539733712171	4		325	267	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953898	131953898	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	22	330	0	ENST00000265335.6:c.3301G>T	p.Glu1101Ter	p.E1101*	ENST00000265335		1101	Gag/Tag	21/25	1	2	FACETS	0.44	0.342	0.553	0.44	0.342	0.553	SUBCLONAL	1	TRUE	1	0.434539733712171	2		330	230	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750330	133750330	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062311-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	78	454	0	ENST00000318560.5:c.1161G>C	p.Leu387Phe	p.L387F	ENST00000318560	NM_005157.4	387	ttG/ttC	7/11	0.434539733712171	1	FACETS	0.4	0.351	0.452	0.4	0.351	0.452	SUBCLONAL	1	TRUE	0	0.434539733712171	1		454	703	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062513-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	281	663	0				ENST00000310581	NM_198253.2	-/1132			0.254130355171659	5	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	2	0.254130355171659	5		663	937	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0062513-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	290	476	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.254130355171659	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.254130355171659	3		476	1033	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0062513-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	226	504	4	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.254130355171659	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.254130355171659	2		508	724	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170814959	170814959	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062513-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	35	149	0	ENST00000296930.5:c.7G>C	p.Asp3His	p.D3H	ENST00000296930	NM_002520.6	3	Gat/Cat	1/11	1	2	FACETS	1	0.842	1	1	0.842	1	CLONAL	1	TRUE	1	0.254130355171659	2		149	269	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120642	115120642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062513-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	134	603	0	ENST00000257566.3:c.364G>A	p.Glu122Lys	p.E122K	ENST00000257566	NM_016569.3	122	Gag/Aag	1/8	0.254130355171659	3	FACETS	1	0.972	1	0.588	0.534	0.646	CLONAL	1	TRUE	1	0.254130355171659	3		603	1010	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513314	106513314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559655430	NA	P-0062513-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	88	426	0	ENST00000359195.3:c.2218G>A	p.Glu740Lys	p.E740K	ENST00000359195	NM_002649.2	740	Gag/Aag	4/11	0.254130355171659	3	FACETS	0.981	0.868	1	0.49	0.434	0.551	CLONAL	1	TRUE	1	0.254130355171659	3		426	796	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374702	118374702	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587783680	NA	P-0062513-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	140	520	0	ENST00000534358.1:c.8095C>T	p.Arg2699Ter	p.R2699*	ENST00000534358	NM_005933.3	2699	Cga/Tga	27/36	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.254130355171659	2		520	913	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240320	5240320	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1456886552	NA	P-0062513-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	82	529	0	ENST00000357368.4:c.1594C>T	p.Arg532Trp	p.R532W	ENST00000357368	NM_002850.3	532	Cgg/Tgg	12/38	0.180796452764837	4	FACETS	0.836	0.735	0.945	0.418	0.367	0.473	CLONAL	1	TRUE	2	0.254130355171659	4		529	968	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912855	32912855	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062513-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	64	419	0	ENST00000380152.3:c.4363G>C	p.Glu1455Gln	p.E1455Q	ENST00000380152		1455	Gaa/Caa	11/27	0.232748971640292	4	FACETS	1	0.894	1	0.519	0.449	0.594	CLONAL	1	TRUE	2	0.254130355171659	4		419	609	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134033	41134033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062513-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	291	590	0	ENST00000379561.5:c.1595C>T	p.Ser532Phe	p.S532F	ENST00000379561	NM_002015.3	532	tCt/tTt	2/3	0.232748971640292	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.254130355171659	4		590	1233	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037880	49037880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062513-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	65	302	0	ENST00000267163.4:c.2120C>T	p.Ser707Phe	p.S707F	ENST00000267163	NM_000321.2	707	tCc/tTc	21/27	0.254130355171659	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	2	TRUE	0	0.254130355171659	2		302	248	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964739	15964739	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062513-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	106	411	0	ENST00000268712.3:c.5857C>G	p.Gln1953Glu	p.Q1953E	ENST00000268712	NM_006311.3	1953	Caa/Gaa	37/46	0.254130355171659	2	FACETS	1	0.976	1	0.65	0.583	0.72	CLONAL	1	TRUE	0	0.254130355171659	2		411	642	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965107	15965107	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062513-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	155	557	0	ENST00000268712.3:c.5489C>G	p.Ser1830Cys	p.S1830C	ENST00000268712	NM_006311.3	1830	tCt/tGt	37/46	0.254130355171659	2	FACETS	1	0.982	1	0.631	0.577	0.688	CLONAL	1	TRUE	0	0.254130355171659	2		557	966	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980635	1980635	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	novel	NA	P-0062513-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	71	480	0	ENST00000382891.5:c.4097A>G	p.Ter1366TrpextTer64	p.*1366Wext*64	ENST00000382891	NM_133335.3	1366	tAg/tGg	22/22	0.232748971640292	4	FACETS	0.567	0.492	0.647	0.283	0.246	0.324	SUBCLONAL	1	TRUE	2	0.254130355171659	4		480	1237	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266583	142266585	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	rs779715723	NA	P-0062552-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	33	396	0	ENST00000350721.4:c.3339_3341del	p.Ile1114del	p.I1114del	ENST00000350721	NM_001184.3	1113	atCATa/ata	16/47	0.283546536661996	3	FACETS	0.89	0.728	1	0.445	0.364	0.536	CLONAL	1	TRUE	1	0.307669978165838	3		396	278	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367548	40367548	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062552-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	170	789	0	ENST00000397332.2:c.13G>C	p.Ala5Pro	p.A5P	ENST00000397332	NM_001033082.2	5	Gct/Cct	1/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.307669978165838	2		789	973	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0062609-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	92	269	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		269	413	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845622	63845622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062609-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	94	401	0	ENST00000279873.7:c.1365del	p.Glu456LysfsTer23	p.E456Kfs*23	ENST00000279873	NM_032199.2	454	gAa/ga	9/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		401	638	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214093	108214095	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	novel	NA	P-0062609-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	119	341	0	ENST00000278616.4:c.8416_8418del	p.Met2806del	p.M2806del	ENST00000278616	NM_000051.3	2805	ATG/-	57/63	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		341	526	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991971	72991972	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGAA	novel	NA	P-0062609-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	52	384	0	ENST00000268489.5:c.2073_2074insTTCA	p.Glu692PhefsTer42	p.E692Ffs*42	ENST00000268489	NM_006885.3	691	-/TTCA	2/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		384	534	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233196	69233196	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1237701932	NA	P-0062664-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	281	686	1	ENST00000462284.1:c.1061A>G	p.Glu354Gly	p.E354G	ENST00000462284	NM_002392.5	354	gAa/gGa	11/11	0.473292259042106	3	FACETS	0.99	0.935	1	0.99	0.935	1	CLONAL	2	TRUE	1	0.473292259042106	3		687	742	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026112	71026112	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs797045585	NA	P-0063060-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	21	397	0	ENST00000318789.4:c.1510C>G	p.Arg504Gly	p.R504G	ENST00000318789	NM_032682.5	504	Cgc/Ggc	17/21	1	2	FACETS	0.358	0.275	0.455	0.358	0.275	0.455	SUBCLONAL	1	FALSE	1	0.306542009621077	2		397	383	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0063122-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	76	491	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.298528457459234	3	FACETS	0.755	0.666	0.849	0.755	0.666	0.849	SUBCLONAL	2	TRUE	1	0.32	3		491	365	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0063122-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	123	631	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.273855482347947	2	FACETS	0.793	0.721	0.867	0.793	0.721	0.867	SUBCLONAL	2	TRUE	0	0.32	2		631	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576853	7576853	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs11575996	NA	P-0063122-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	180	838	0	ENST00000269305.4:c.993G>T	p.Gln331His	p.Q331H	ENST00000269305	NM_001126112.2	331	caG/caT	9/11	0.24419864827655	2	FACETS	0.857	0.794	0.923	0.857	0.794	0.923	CLONAL	2	TRUE	0	0.32	2		838	656	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135303	30135303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1174219763	NA	P-0063122-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	62	543	1	ENST00000331968.5:c.515G>A	p.Arg172His	p.R172H	ENST00000331968	NM_002742.2	172	cGt/cAt	3/18	0.298528457459234	3	FACETS	0.71	0.613	0.816	0.355	0.306	0.408	SUBCLONAL	1	TRUE	1	0.32	3		544	633	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679887	33679887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200734680	NA	P-0063122-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	202	802	0	ENST00000308377.4:c.2194C>T	p.Arg732Cys	p.R732C	ENST00000308377	NM_152270.3	732	Cgc/Tgc	5/5	0.298528457459234	3	FACETS	0.915	0.85	0.982	0.915	0.85	0.982	CLONAL	2	TRUE	1	0.32	3		802	800	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929487	44929487	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063241-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	33	624	0	ENST00000377967.4:c.2587C>T	p.Gln863Ter	p.Q863*	ENST00000377967	NM_021140.2	863	Cag/Tag	17/29	1	2	FACETS	0.98	0.802	1	0.98	0.802	1	CLONAL	1	FALSE	1	0.242134351854586	2		624	278	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405971	49405971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063241-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	34	547	0	ENST00000418115.1:c.167C>T	p.Ala56Val	p.A56V	ENST00000418115	NM_001664.2	56	gCt/gTt	3/5	1	2	FACETS	0.851	0.697	1	0.851	0.697	1	CLONAL	1	FALSE	1	0.242134351854586	2		547	330	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651437	52651438	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063241-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	16	582	0	ENST00000394830.3:c.1658dup	p.Asp554GlyfsTer4	p.D554Gfs*4	ENST00000394830	NM_018313.4	553	aag/aaAg	15/30	1	2	FACETS	0.811	0.602	1	0.811	0.602	1	CLONAL	1	FALSE	1	0.242134351854586	2		582	163	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2058415	2058417	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0063241-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	23	569	0	ENST00000349721.2:c.1477_1479del	p.Lys493del	p.K493del	ENST00000349721	NM_003070.3	491	cAGAag/cag	8/34	0.170134297554677	1	FACETS	0.58	0.453	0.727	0.58	0.453	0.727	SUBCLONAL	1	FALSE	0	0.242134351854586	1		569	288	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0063364-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	247	394	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		394	662	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0063364-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	283	416	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		416	728	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440844	52440844	+	splice_donor_variant	Splice_Site	DEL	C	C	-	rs1064795667	NA	P-0063364-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	511	356	0	ENST00000460680.1:c.659+1del		p.X220_splice	ENST00000460680	NM_004656.3	220			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		356	672	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346723	89346723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768819121	NA	P-0063489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	69	504	0	ENST00000301030.4:c.6227C>T	p.Pro2076Leu	p.P2076L	ENST00000301030	NM_001256183.1	2076	cCg/cTg	9/13	0.376964931867549	3	FACETS	1	0.94	1	0.563	0.493	0.638	CLONAL	1	TRUE	1	0.379582650613724	3		504	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577576	7577577	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	118	333	0	ENST00000269305.4:c.704dup	p.Asn235LysfsTer5	p.N235Kfs*5	ENST00000269305	NM_001126112.2	235	aac/aaAc	7/11	0.379582650613724	2	FACETS	0.971	0.888	1	0.971	0.888	1	CLONAL	2	TRUE	0	0.379582650613724	2		333	320	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498423	89498423	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1203973847	NA	P-0063489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	70	378	0	ENST00000336596.2:c.2395C>G	p.Arg799Gly	p.R799G	ENST00000336596	NM_005233.5	799	Cgc/Ggc	14/17	0.376964931867549	3	FACETS	1	0.922	1	0.536	0.47	0.608	CLONAL	1	TRUE	1	0.379582650613724	3		378	409	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796781	135796781	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	383	649	0	ENST00000298552.3:c.706G>T	p.Gly236Ter	p.G236*	ENST00000298552	NM_001162426.1	236	Gga/Tga	8/23	0.654897915960668	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.653659780173128	2		649	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577065	7577065	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs372613518	NA	P-0063720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	615	1015	0	ENST00000269305.4:c.873G>C	p.Lys291Asn	p.K291N	ENST00000269305	NM_001126112.2	291	aaG/aaC	8/11	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.653659780173128	2		1015	898	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287419	33287419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	704	1099	0	ENST00000374542.5:c.1678G>T	p.Glu560Ter	p.E560*	ENST00000374542	NM_001141970.1	560	Gaa/Taa	6/8	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.653659780173128	2		1099	957	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0063730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	116	355	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		355	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0063730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	159	417	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		417	568	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393421	139393421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	186	309	0	ENST00000277541.6:c.6110C>T	p.Ala2037Val	p.A2037V	ENST00000277541	NM_017617.3	2037	gCc/gTc	33/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		309	796	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936978	48936978	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	113	484	0	ENST00000267163.4:c.746C>A	p.Ser249Ter	p.S249*	ENST00000267163	NM_000321.2	249	tCa/tAa	8/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		484	437	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867706	45867706	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	96	414	0	ENST00000391945.4:c.694G>T	p.Val232Phe	p.V232F	ENST00000391945	NM_000400.3	232	Gtc/Ttc	8/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		414	869	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828224	50828224	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	140	456	0	ENST00000398568.2:c.2562G>T	p.Gln854His	p.Q854H	ENST00000398568	NM_001042412.1	854	caG/caT	17/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		456	667	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170834	99170834	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	198	573	0	ENST00000074304.5:c.1463C>T	p.Pro488Leu	p.P488L	ENST00000074304	NM_001134224.1	488	cCc/cTc	16/26	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		573	782	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172057	32172057	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	285	450	0	ENST00000375023.3:c.2975G>C	p.Cys992Ser	p.C992S	ENST00000375023	NM_004557.3	992	tGt/tCt	19/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		450	1036	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14028641	14028641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	65	408	0	ENST00000405192.2:c.37G>A	p.Val13Ile	p.V13I	ENST00000405192	NM_001163147.1	13	Gtc/Atc	2/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		408	455	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845222	151845222	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1217182001	NA	P-0063730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	165	588	0	ENST00000262189.6:c.13790G>T	p.Arg4597Leu	p.R4597L	ENST00000262189	NM_170606.2	4597	cGc/cTc	52/59	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		588	831	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0063738-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4	41	332	0	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			1	2	FACETS	0.939	0.879	0.983	1	0.982	1	CLONAL	3	TRUE	1	0.646650446831404	2		332	45	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921430	39921430	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063738-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	207	438	0	ENST00000378444.4:c.4390del	p.Glu1464ArgfsTer20	p.E1464Rfs*20	ENST00000378444	NM_001123385.1	1464	Gag/ag	10/15	1	2	FACETS	0.903	0.841	0.966	0.903	0.841	0.966	CLONAL	1	TRUE	1	0.646650446831404	2		438	709	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0063880-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	32	286	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.924	0.752	1	0.924	0.752	1	CLONAL	1	TRUE	1	0.231602886286031	2		286	299	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0063880-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	145	624	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.231602886286031	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.231602886286031	1		624	852	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0063880-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	44	295	1	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.229246001312111	1	FACETS	0.672	0.563	0.792	0.672	0.563	0.792	SUBCLONAL	1	TRUE	0	0.231602886286031	1		296	500	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362446	40362447	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1202978138	NA	P-0063880-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	49	393	1	ENST00000293328.3:c.1749dup	p.His584ThrfsTer8	p.H584Tfs*8	ENST00000293328	NM_012448.3	583	-/A	14/19	1	2	FACETS	0.534	0.451	0.625	0.534	0.451	0.625	SUBCLONAL	1	TRUE	1	0.231602886286031	2		394	793	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994397	25994397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757065305	NA	P-0063880-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	60	395	0	ENST00000435504.4:c.416C>T	p.Ser139Phe	p.S139F	ENST00000435504		139	tCc/tTc	6/13	0.229246001312111	1	FACETS	0.557	0.479	0.643	0.557	0.479	0.643	SUBCLONAL	1	TRUE	0	0.231602886286031	1		395	822	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428199	49428201	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0063880-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	129	584	0	ENST00000301067.7:c.10499_10501del	p.Gly3500del	p.G3500del	ENST00000301067	NM_003482.3	3500	gGAGtg/gtg	37/54	1	2	FACETS	0.96	0.869	1	0.96	0.869	1	CLONAL	1	TRUE	1	0.231602886286031	2		584	1160	SUCCESS
REST	5978	MSKCC	GRCh37	4	57797899	57797899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063880-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	36	401	0	ENST00000309042.7:c.2875C>T	p.Leu959Phe	p.L959F	ENST00000309042	NM_005612.4	959	Ctc/Ttc	4/4	0.231602886286031	1	FACETS	0.448	0.367	0.539	0.448	0.367	0.539	SUBCLONAL	1	TRUE	0	0.231602886286031	1		401	614	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624274	89624274	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs587782187	NA	P-0063942-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	91	198	0	ENST00000371953.3:c.48T>G	p.Tyr16Ter	p.Y16*	ENST00000371953	NM_000314.4	16	taT/taG	1/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		198	286	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445748	49445748	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063942-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	234	722	0	ENST00000301067.7:c.1718C>G	p.Ser573Cys	p.S573C	ENST00000301067	NM_003482.3	573	tCt/tGt	10/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		722	949	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003787	45003787	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063942-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	159	443	0	ENST00000558401.1:c.43del	p.Leu15PhefsTer29	p.L15Ffs*29	ENST00000558401	NM_004048.2	15	Ctt/tt	1/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		443	561	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220452	1220452	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730881974	NA	P-0063942-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	186	544	2	ENST00000326873.7:c.545T>C	p.Leu182Pro	p.L182P	ENST00000326873	NM_000455.4	182	cTg/cCg	4/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		546	578	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213914	2213914	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063942-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	199	545	0	ENST00000398665.3:c.1726C>T	p.Gln576Ter	p.Q576*	ENST00000398665	NM_032482.2	576	Cag/Tag	18/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		545	622	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600434	10600450	+	frameshift_variant	Frame_Shift_Del	DEL	GCATAAAGGAGACGATT	GCATAAAGGAGACGATT	-	novel	NA	P-0063942-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	174	584	0	ENST00000171111.5:c.1405_1421del	p.Asn469ArgfsTer5	p.N469Rfs*5	ENST00000171111	NM_203500.1	469	AATCGTCTCCTTTATGCc/c	4/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		584	644	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660706	227660706	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063942-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	86	603	0	ENST00000305123.5:c.2749A>T	p.Ser917Cys	p.S917C	ENST00000305123	NM_005544.2	917	Agc/Tgc	1/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		603	682	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054254	30054254	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1555994854	NA	P-0063942-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	123	394	0	ENST00000338641.4:c.675+1G>A		p.X225_splice	ENST00000338641	NM_000268.3	225			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		394	467	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527622	41527622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063942-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	154	387	0	ENST00000263253.7:c.1513C>T	p.Pro505Ser	p.P505S	ENST00000263253	NM_001429.3	505	Ccc/Tcc	6/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		387	533	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120695	94120695	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063942-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	147	432	0	ENST00000369303.4:c.356G>T	p.Cys119Phe	p.C119F	ENST00000369303	NM_004440.3	119	tGc/tTc	3/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		432	491	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484363	8484363	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063942-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	159	309	0	ENST00000356435.5:c.3169G>T	p.Gly1057Trp	p.G1057W	ENST00000356435		1057	Ggg/Tgg	19/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		309	448	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0063944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	29	80	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.231642060997544	3	FACETS	1	0.928	1	0.447	0.363	0.539	CLONAL	1	TRUE	0	0.324636213940757	3		80	155	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0063944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	21	498	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.367	0.282	0.465	0.367	0.282	0.465	SUBCLONAL	1	TRUE	1	0.324636213940757	2		499	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	67	349	0	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.324636213940757	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.324636213940757	1		349	321	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0063944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	485	360	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.324636213940757	12	FACETS	0.987	0.956	1	0.987	0.956	1	CLONAL	11	TRUE	1	0.324636213940757	12		360	722	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557315	29557315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	29	292	0	ENST00000356175.3:c.3028C>T	p.Gln1010Ter	p.Q1010*	ENST00000356175	NM_000267.3	1010	Caa/Taa	23/57	0.317481185651704	2	FACETS	0.839	0.678	1	0.419	0.339	0.51	CLONAL	1	TRUE	0	0.324636213940757	2		292	213	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720917	176720917	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	43	380	0	ENST00000439151.2:c.6548G>A	p.Cys2183Tyr	p.C2183Y	ENST00000439151	NM_022455.4	2183	tGt/tAt	23/23	1	2	FACETS	0.659	0.552	0.777	0.659	0.552	0.777	SUBCLONAL	1	TRUE	1	0.324636213940757	2		380	402	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5466784	5466784	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	67	403	0	ENST00000381577.3:c.805G>A	p.Val269Met	p.V269M	ENST00000381577	NM_014143.3	269	Gtg/Atg	6/7	0.324636213940757	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.324636213940757	1		403	287	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039817	47039817	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0063944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	49	146	0	ENST00000377604.3:c.1162del		p.X388_splice	ENST00000377604	NM_001204468.1	388			0.324636213940757	2	FACETS	1	0.952	1			1	CLONAL	2	TRUE	NA	0.324636213940757	2		146	124	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076781	72076781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767198961	NA	P-0063951-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	229	498	0	ENST00000357731.5:c.716G>A	p.Arg239His	p.R239H	ENST00000357731	NM_173808.2	239	cGc/cAc	5/7	NA	2	FACETS	0.742	0.694	0.792			1	INDETERMINATE	1	TRUE	NA	0.805695569044045	2		498	766	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942093	81942093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs926237449	NA	P-0063951-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	253	455	0	ENST00000359376.3:c.1630G>A	p.Glu544Lys	p.E544K	ENST00000359376	NM_002661.3	544	Gag/Aag	17/33	0.704580132139191	3	FACETS	1	0.983	1	0.563	0.529	0.598	CLONAL	1	TRUE	1	0.805695569044045	3		455	782	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577497	7577497	+	splice_donor_variant	Splice_Site	SNP	A	A	C	rs876659076	NA	P-0063951-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	461	418	0	ENST00000269305.4:c.782+2T>G		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.807621882658648	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.805695569044045	2		418	542	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619113	37619113	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063951-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7894	483	551	0	ENST00000447079.4:c.789G>T	p.Lys263Asn	p.K263N	ENST00000447079	NM_015083.1	263	aaG/aaT	1/14	0.805695569044045	27	FACETS	0.792	0.751	0.835			1	SUBCLONAL	2	TRUE	NA	0.805695569044045	27		551	8377	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222281	39222281	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572955351	NA	P-0063951-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	38	327	0	ENST00000402219.2:c.3329C>T	p.Ser1110Leu	p.S1110L	ENST00000402219	NM_005633.3	1110	tCg/tTg	20/23	0.807621882658648	3	FACETS	0.193	0.159	0.232	0.097	0.079	0.116	SUBCLONAL	1	TRUE	1	0.805695569044045	3		327	685	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525925	148525925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063951-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	132	334	0	ENST00000320356.2:c.532C>T	p.Leu178Phe	p.L178F	ENST00000320356	NM_004456.4	178	Ctt/Ttt	6/20	0.807621882658648	3	FACETS	0.756	0.689	0.827	0.378	0.344	0.414	SUBCLONAL	1	TRUE	1	0.805695569044045	3		334	608	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772299	68772321	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGCGTCCTGGGCAGAGGTGAGGG	CGCGTCCTGGGCAGAGGTGAGGG	-	novel	NA	P-0063952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	236	532	0	ENST00000261769.5:c.152_163+11del		p.X51_splice	ENST00000261769	NM_004360.3	51		2/16	0.594174297047027	1	FACETS	0.92	0.865	0.976	0.92	0.865	0.976	CLONAL	1	TRUE	0	0.594174297047027	1		532	607	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063356	67063356	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	277	477	0	ENST00000412916.2:c.46G>T	p.Glu16Ter	p.E16*	ENST00000412916		16	Gag/Tag	1/6	0.594174297047027	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.594174297047027	1		477	590	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119208	3119208	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	317	606	0	ENST00000078429.4:c.740G>T	p.Arg247Leu	p.R247L	ENST00000078429	NM_002067.2	247	cGg/cTg	6/7	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.594174297047027	2		606	948	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729701	41729701	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063963-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	52	419	0	ENST00000242208.4:c.828A>T	p.Glu276Asp	p.E276D	ENST00000242208	NM_002192.2	276	gaA/gaT	3/3	1	2	FACETS	0.762	0.651	0.883	0.762	0.651	0.883	SUBCLONAL	1	TRUE	1	0.361024057579768	2		419	378	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	87	286	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.136536495511459	3	FACETS	1	0.895	1	0.67	0.597	0.748	INDETERMINATE	2	TRUE	0	0.235921669713132	3		286	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs786201057	NA	P-0064074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	142	355	0	ENST00000269305.4:c.374C>A	p.Thr125Lys	p.T125K	ENST00000269305	NM_001126112.2	125	aCg/aAg	4/11	0.136536495511459	3	FACETS	0.984	0.899	1	0.656	0.599	0.715	INDETERMINATE	2	TRUE	0	0.235921669713132	3		355	684	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139151	37139151	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	79	436	0	ENST00000373509.5:c.491T>A	p.Leu164His	p.L164H	ENST00000373509	NM_002648.3	164	cTc/cAc	4/6	0.18889529395393	2	FACETS	0.851	0.748	0.962	0.425	0.374	0.481	CLONAL	1	TRUE	0	0.235921669713132	2		436	787	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31495424	31495424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561252258	NA	P-0064092-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	212	351	2	ENST00000344624.3:c.1724G>A	p.Arg575Gln	p.R575Q	ENST00000344624		575	cGg/cAg	9/33	1	2	FACETS	0.964	0.903	1	0.964	0.903	1	CLONAL	1	TRUE	1	0.843019909922197	2		353	522	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753099	57753099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064092-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	313	441	2	ENST00000274289.3:c.917C>T	p.Pro306Leu	p.P306L	ENST00000274289	NM_006622.3	306	cCt/cTt	7/14	1	2	FACETS	0.984	0.933	1	0.984	0.933	1	CLONAL	1	TRUE	1	0.843019909922197	2		443	755	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777867	27777867	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064092-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	431	585	0	ENST00000369163.2:c.16C>T	p.Gln6Ter	p.Q6*	ENST00000369163	NM_003536.2	6	Cag/Tag	1/1	1	2	FACETS	0.966	0.923	1	0.966	0.923	1	CLONAL	1	TRUE	1	0.843019909922197	2		585	1059	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288324	33288324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749468991	NA	P-0064092-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	450	559	0	ENST00000374542.5:c.1084C>T	p.Arg362Trp	p.R362W	ENST00000374542	NM_001141970.1	362	Cgg/Tgg	4/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.843019909922197	2		559	1034	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15840914	15840914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064092-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	42	196	0	ENST00000307771.7:c.998G>A	p.Arg333Lys	p.R333K	ENST00000307771	NM_005089.3	333	aGa/aAa	11/11	1	2	FACETS	0.33	0.276	0.389	0.33	0.276	0.389	SUBCLONAL	1	TRUE	1	0.843019909922197	2		196	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0064173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	79	425	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.535	0.469	0.606	0.535	0.469	0.606	SUBCLONAL	1	TRUE	1	0.312976716170472	2		425	944	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0064173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	33	467	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	1	2	FACETS	0.199	0.161	0.242	0.199	0.161	0.242	SUBCLONAL	1	TRUE	1	0.312976716170472	2		467	1061	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923059	39923059	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	67	568	0	ENST00000378444.4:c.3649C>T	p.Arg1217Ter	p.R1217*	ENST00000378444	NM_001123385.1	1217	Cga/Tga	8/15	1	2	FACETS	0.441	0.382	0.506	0.441	0.382	0.506	SUBCLONAL	1	TRUE	1	0.312976716170472	2		568	970	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176338	24176338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	129	350	0	ENST00000263121.7:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000263121	NM_003073.3	377	Cgt/Tgt	9/9	0.312976716170472	3	FACETS	1	0.982	1	0.672	0.61	0.737	CLONAL	1	TRUE	1	0.312976716170472	3		350	709	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246557	46246557	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161560614	NA	P-0064173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	64	533	0	ENST00000334344.6:c.4651G>A	p.Ala1551Thr	p.A1551T	ENST00000334344	NM_152641.2	1551	Gca/Aca	15/21	1	2	FACETS	0.478	0.413	0.549	0.478	0.413	0.549	SUBCLONAL	1	TRUE	1	0.312976716170472	2		533	856	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438166	110438166	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	66	478	0	ENST00000375856.3:c.235G>A	p.Glu79Lys	p.E79K	ENST00000375856	NM_003749.2	79	Gag/Aag	1/2	1	2	FACETS	0.511	0.443	0.586	0.511	0.443	0.586	SUBCLONAL	1	TRUE	1	0.312976716170472	2		478	825	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238987	5238987	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	66	641	0	ENST00000357368.4:c.1792T>C	p.Ser598Pro	p.S598P	ENST00000357368	NM_002850.3	598	Tcg/Ccg	13/38	1	2	FACETS	0.439	0.38	0.504	0.439	0.38	0.504	SUBCLONAL	1	TRUE	1	0.312976716170472	2		641	960	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105646	27105652	+	frameshift_variant	Frame_Shift_Del	DEL	GTGTCTA	GTGTCTA	-	novel	NA	P-0064173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	141	651	0	ENST00000324856.7:c.5259_5265del	p.Ser1754GlnfsTer14	p.S1754Qfs*14	ENST00000324856	NM_006015.4	1753	GTGTCTAgt/gt	20/20	1	2	FACETS	0.786	0.714	0.861	0.786	0.714	0.861	SUBCLONAL	1	TRUE	1	0.312976716170472	2		651	1147	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770606	40770606	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	90	473	0	ENST00000373198.4:c.2776G>T	p.Ala926Ser	p.A926S	ENST00000373198	NM_133170.3	926	Gcc/Tcc	19/32	1	2	FACETS	0.676	0.599	0.758	0.676	0.599	0.758	SUBCLONAL	1	TRUE	1	0.312976716170472	2		473	851	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064189-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	51	663	0				ENST00000310581	NM_198253.2	-/1132			0.213044823885396	4	FACETS	1	0.964	1	0.744	0.636	0.861	CLONAL	1	TRUE	2	0.278222965031889	4		663	315	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0064189-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	136	554	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	1	0.974	1	1	0.992	1	CLONAL	2	TRUE	1	0.278222965031889	2		554	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0064189-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	176	589	0	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	0.233859196968576	3	FACETS	1	0.984	1	0.818	0.758	0.88	CLONAL	2	TRUE	0	0.278222965031889	3		589	587	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665360	138665360	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906920	NA	P-0064189-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	78	475	0	ENST00000330315.3:c.205G>A	p.Glu69Lys	p.E69K	ENST00000330315	NM_023067.3	69	Gag/Aag	1/1	0.278222965031889	5	FACETS	0.883	0.779	0.994	0.589	0.519	0.663	CLONAL	2	TRUE	2	0.278222965031889	5		475	450	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519130	187519130	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064189-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	86	379	0	ENST00000441802.2:c.12253C>T	p.Gln4085Ter	p.Q4085*	ENST00000441802	NM_005245.3	4085	Cag/Tag	23/27	0.237366228360387	3	FACETS	0.821	0.73	0.917	0.821	0.73	0.917	CLONAL	2	TRUE	1	0.278222965031889	3		379	429	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330648	65330648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064189-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	48	431	0	ENST00000342505.4:c.998C>T	p.Ser333Phe	p.S333F	ENST00000342505	NM_002227.2	333	tCt/tTt	8/25	0.237366228360387	3	FACETS	0.737	0.623	0.863	0.369	0.311	0.432	SUBCLONAL	1	TRUE	1	0.278222965031889	3		431	533	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592630	28592630	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064189-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	86	497	0	ENST00000241453.7:c.2515G>C	p.Asp839His	p.D839H	ENST00000241453	NM_004119.2	839	Gat/Cat	20/24	0.213044823885396	4	FACETS	1	0.978	1	0.747	0.662	0.837	CLONAL	1	TRUE	2	0.278222965031889	4		497	529	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718672	190718672	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773928881	NA	P-0064189-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	48	231	0	ENST00000441310.2:c.830G>A	p.Arg277Gln	p.R277Q	ENST00000441310	NM_000534.4	277	cGa/cAa	8/13	0.113114727313602	5	FACETS	1	0.943	1	0.417	0.353	0.487	INDETERMINATE	1	TRUE	2	0.278222965031889	5		231	391	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629737	187629737	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0064189-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	42	502	0	ENST00000441802.2:c.1245C>G	p.Tyr415Ter	p.Y415*	ENST00000441802	NM_005245.3	415	taC/taG	2/27	0.237366228360387	3	FACETS	0.605	0.505	0.718	0.303	0.252	0.359	SUBCLONAL	1	TRUE	1	0.278222965031889	3		502	568	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960163	151960163	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064189-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	27	226	0	ENST00000262189.6:c.1237T>A	p.Tyr413Asn	p.Y413N	ENST00000262189	NM_170606.2	413	Tat/Aat	9/59	0.117720350178291	4	FACETS	1	0.875	1	0.566	0.453	0.694	INDETERMINATE	1	TRUE	2	0.278222965031889	4		226	219	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913517	NA	P-0064201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	19	382	0	ENST00000288135.5:c.1676T>C	p.Val559Ala	p.V559A	ENST00000288135	NM_000222.2	559	gTt/gCt	11/21	0.226062780305477	2	FACETS	0.226	0.17	0.291	0.113	0.085	0.146	SUBCLONAL	1	FALSE	0	0.3	2		382	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs967461896	NA	P-0064317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	81	1189	0	ENST00000269305.4:c.526T>G	p.Cys176Gly	p.C176G	ENST00000269305	NM_001126112.2	176	Tgc/Ggc	5/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.233231805686516	2		1189	563	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129473	64129473	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	36	1048	0	ENST00000334205.4:c.905A>T	p.Gln302Leu	p.Q302L	ENST00000334205	NM_003942.2	302	cAg/cTg	8/17	1	2	FACETS	0.647	0.532	0.777	0.647	0.532	0.777	SUBCLONAL	1	TRUE	1	0.233231805686516	2		1048	477	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243942	41243942	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	32	305	1	ENST00000357654.3:c.3606C>A	p.Tyr1202Ter	p.Y1202*	ENST00000357654	NM_007294.3	1202	taC/taA	10/23	0.233231805686516	5	FACETS	0.773	0.627	0.939			1	CLONAL	1	TRUE	NA	0.233231805686516	5		306	479	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069344	30069345	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0064358-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	235	518	0	ENST00000338641.4:c.1211_1212del	p.Glu404GlyfsTer2	p.E404Gfs*2	ENST00000338641	NM_000268.3	403	gcAGag/gcag	12/16	0.806201491604497	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.806201491604497	1		518	320	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0064359-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	309	497	0	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	0.918807553015422	1	FACETS	0.983	0.955	1	0.983	0.955	1	CLONAL	1	TRUE	0	0.918807553015422	1		497	370	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932867	39932867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747939351	NA	P-0064359-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	333	693	0	ENST00000378444.4:c.1732G>A	p.Ala578Thr	p.A578T	ENST00000378444	NM_001123385.1	578	Gca/Aca	4/15	1	2	FACETS	0.928	0.882	0.974	0.928	0.882	0.974	CLONAL	1	TRUE	1	0.918807553015422	2		693	781	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813358	102813358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064359-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	295	566	0	ENST00000307046.8:c.331C>T	p.Pro111Ser	p.P111S	ENST00000307046	NM_001111285.1	111	Ccc/Tcc	3/4	1	2	FACETS	0.976	0.926	1	0.976	0.926	1	CLONAL	1	TRUE	1	0.918807553015422	2		566	658	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207162	1207162	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs137853076	NA	P-0064371-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	94	529	0	ENST00000326873.7:c.250A>T	p.Lys84Ter	p.K84*	ENST00000326873	NM_000455.4	84	Aag/Tag	1/10	0.574729922725723	1	FACETS	0.796	0.717	0.877	0.796	0.717	0.877	SUBCLONAL	1	TRUE	0	0.574729922725723	1		529	293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0064371-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	128	692	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.44597081188746	2	FACETS	1	0.988	1	0.742	0.684	0.802	CLONAL	1	TRUE	0	0.574729922725723	2		692	300	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163325125	163325125	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064371-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	47	331	0	ENST00000271452.3:c.1261G>A	p.Glu421Lys	p.E421K	ENST00000271452	NM_145697.2	421	Gaa/Aaa	14/14	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.574729922725723	2		331	161	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599973	10599974	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0064371-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	107	540	0	ENST00000171111.5:c.1602_1603delinsTT	p.Glu535Ter	p.E535*	ENST00000171111	NM_203500.1	534	gtGGag/gtTTag	5/6	0.574729922725723	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.574729922725723	1		540	250	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519925	29519925	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0064371-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	20	421	0	ENST00000389048.3:c.1648-2A>T		p.X550_splice	ENST00000389048	NM_004304.4	550			0.257441551854054	1	FACETS	0.299	0.23	0.378	0.299	0.23	0.378	INDETERMINATE	1	TRUE	0	0.574729922725723	1		421	166	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755717	39755717	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064371-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	20	492	0	ENST00000288319.7:c.1048C>A	p.Arg350Ser	p.R350S	ENST00000288319	NM_182918.3	350	Cgc/Agc	10/10	1	2	FACETS	0.262	0.2	0.334	0.262	0.2	0.334	SUBCLONAL	1	TRUE	1	0.574729922725723	2		492	266	SUCCESS
ATR	545	MSKCC	GRCh37	3	142168413	142168413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1314855850	NA	P-0064371-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	84	351	0	ENST00000350721.4:c.7793G>A	p.Arg2598Gln	p.R2598Q	ENST00000350721	NM_001184.3	2598	cGa/cAa	47/47	0.29545875637573	0	FACETS	0.471	0.421	0.522			1	INDETERMINATE	1	TRUE	0	0.574729922725723	0		351	264	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937831	76937831	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064371-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	52	504	1	ENST00000373344.5:c.2917C>A	p.Gln973Lys	p.Q973K	ENST00000373344	NM_000489.3	973	Cag/Aag	9/35	0.574729922725723	1	FACETS	0.561	0.482	0.644	0.561	0.482	0.644	SUBCLONAL	1	TRUE	0	0.574729922725723	1		505	230	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587781525	NA	P-0064390-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	91	528	0	ENST00000269305.4:c.842A>T	p.Asp281Val	p.D281V	ENST00000269305	NM_001126112.2	281	gAc/gTc	8/11	0.201391546374403	3	FACETS	1	0.98	1			1	CLONAL	1	FALSE	NA	0.312376335734989	3		528	455	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156507	106156507	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064390-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	71	552	0	ENST00000380013.4:c.1408T>C	p.Cys470Arg	p.C470R	ENST00000380013	NM_001127208.2	470	Tgc/Cgc	3/11	0.263686966446521	4	FACETS	1	0.967	1	0.667	0.584	0.756	CLONAL	1	FALSE	2	0.312376335734989	4		552	447	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878517	151878517	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064390-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	30	533	0	ENST00000262189.6:c.6428A>C	p.Asp2143Ala	p.D2143A	ENST00000262189	NM_170606.2	2143	gAt/gCt	36/59	0.263686966446521	4	FACETS	0.573	0.461	0.7	0.286	0.23	0.35	SUBCLONAL	1	FALSE	2	0.312376335734989	4		533	440	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750803	57750803	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064390-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	24	438	0	ENST00000274289.3:c.1801T>C	p.Tyr601His	p.Y601H	ENST00000274289	NM_006622.3	601	Tac/Cac	13/14	0.263686966446521	4	FACETS	0.573	0.449	0.716	0.286	0.224	0.358	SUBCLONAL	1	FALSE	2	0.312376335734989	4		438	352	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0064407-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	11	507	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	1	2	FACETS	0.097	0.067	0.136	0.097	0.067	0.136	SUBCLONAL	1	TRUE	1	0.42427228821102	2		507	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578441	7578441	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1567553246	NA	P-0064407-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	55	648	0	ENST00000269305.4:c.489C>G	p.Tyr163Ter	p.Y163*	ENST00000269305	NM_001126112.2	163	taC/taG	5/11	1	2	FACETS	0.292	0.248	0.339	0.292	0.248	0.339	SUBCLONAL	1	TRUE	1	0.42427228821102	2		648	889	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0064420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	165	430	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		430	356	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060853	38060859	+	frameshift_variant	Frame_Shift_Del	DEL	AAGCCGT	AAGCCGT	-	novel	NA	P-0064420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	191	478	0	ENST00000250448.2:c.1130_1136del	p.His377ArgfsTer10	p.H377Rfs*10	ENST00000250448	NM_004496.3	377	cACGGCTTg/cg	2/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		478	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0064501-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	11	622	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.856	0.6	1	0.856	0.6	1	CLONAL	1	TRUE	1	0.329374112346968	2		622	78	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064501-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	16	286	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.329374112346968	4	FACETS	1	0.878	1	0.666	0.499	0.858	CLONAL	1	TRUE	2	0.329374112346968	4		286	97	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577184	64577184	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555166357	NA	P-0064501-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	21	526	1	ENST00000312049.6:c.398A>G	p.Tyr133Cys	p.Y133C	ENST00000312049	NM_130799.2	133	tAc/tGc	2/10	1	2	FACETS	0.973	0.759	1	0.973	0.759	1	CLONAL	1	TRUE	1	0.329374112346968	2		527	131	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440928	56440928	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064501-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	20	531	0	ENST00000407977.2:c.409G>T	p.Val137Phe	p.V137F	ENST00000407977		137	Gtc/Ttc	4/10	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.329374112346968	2		531	97	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593590	55593607	+	inframe_deletion	In_Frame_Del	DEL	GTATGAAGTACAGTGGAA	GTATGAAGTACAGTGGAA	-	novel	NA	P-0064507-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	327	441	0	ENST00000288135.5:c.1657_1674del	p.Tyr553_Lys558del	p.Y553_K558del	ENST00000288135	NM_000222.2	552	atGTATGAAGTACAGTGGAAg/atg	11/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		441	372	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544642	65544642	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064507-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	233	600	0	ENST00000358664.4:c.284T>G	p.Leu95Arg	p.L95R	ENST00000358664	NM_002382.4	95	cTg/cGg	4/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		600	256	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821604	72821618	+	inframe_deletion	In_Frame_Del	DEL	CCGCCGCCGCCGCCA	CCGCCGCCGCCGCCA	-	rs771374165	NA	P-0064507-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	94	425	0	ENST00000268489.5:c.10557_10571del	p.Gly3523_Gly3527del	p.G3523_G3527del	ENST00000268489	NM_006885.3	3519	ggTGGCGGCGGCGGCGGc/ggc	10/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		425	244	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243795	41243795	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs397509098	NA	P-0064507-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	149	571	0	ENST00000357654.3:c.3753T>A	p.Cys1251Ter	p.C1251*	ENST00000357654	NM_007294.3	1251	tgT/tgA	10/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		571	569	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679680	33679680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	333	597	0	ENST00000308377.4:c.2401G>A	p.Asp801Asn	p.D801N	ENST00000308377	NM_152270.3	801	Gat/Aat	5/5	1	2	FACETS	0.989	0.942	1	0.989	0.942	1	CLONAL	1	TRUE	1	0.948134065599319	2		597	710	SUCCESS
REST	5978	MSKCC	GRCh37	4	57776827	57776827	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	276	542	0	ENST00000309042.7:c.23A>C	p.Gln8Pro	p.Q8P	ENST00000309042	NM_005612.4	8	cAg/cCg	2/4	1	2	FACETS	0.95	0.9	1	0.95	0.9	1	CLONAL	1	TRUE	1	0.948134065599319	2		542	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0064546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	128	575	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.567495579285295	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.567495579285295	1		575	317	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0064546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	292	431	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.47636891253927	6	FACETS	0.957	0.91	1			1	CLONAL	4	TRUE	NA	0.567495579285295	6		431	574	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305274	39305274	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	52	517	0	ENST00000373001.3:c.1151C>G	p.Ser384Cys	p.S384C	ENST00000373001	NM_022157.3	384	tCc/tGc	7/7	1	2	FACETS	0.352	0.299	0.409	0.352	0.299	0.409	SUBCLONAL	1	TRUE	1	0.567495579285295	2		517	521	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994398	25995197	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGACGACGATACTAGGGAAAAAAAAGTGACAATAAAAGATTTTTGTTAACAGAGATACCAAGCACCATTCCTTCCCCAATCATATGCTGCTACCTGGAGTAAGAACTATGACCAAACACTTTTGGGAACGATGTACTTTTTGGAGTTTTACTGCAAACAGCCTCCCTTTTCAGTTTTTTTCCTCAGAAAGTTCTAATGAAGGATGATAGGATAGGGAAGGGATGAGTGTTAGTATTCATTACTTTTCATTTATTACTTTTTCAATAGAATTGACTGAAGAATGACTCATCAAATCAGATAAAACTTAGGAAAGATTCTAGGGCCTTTAAGACAGTATCTATGGTCTCACAGTAAATCTAATGACAACACGATACAGTGGAAGGGCCTTGGGTTGGCAGTTTAAAATAAAGACATTAAGGCCATTCGACCTCAAAACTCTACCACAGTTTTAATCCTTACATTCCTTCATCCTTTAAATCAACAGTTACAGGCTTACCAACGTGAGAGGGCATTTTAAGATGTCTCTAATGGAAGCAATTTGAATTTGCATAAGATGTAACCACTCTCTACTTCATCACTAGCTGTTTTATATTGCCTGGCAGAGTTTAGCCAGATCTGAGTGGGTCTTATGCGAACAAGGGTTCTTTAAGAATCTATACCTCTTAAACAGCAAGTAGATATTTATGTTCTATAAAATTAAACAATATGTGAGTAGTGTTTACGATAAATACAGAAATTGCTGATTCAGTACCCTTATTAAAAAAAAATTATAATCACTACTGCTAGTGATGACTCTTGA	AGGACGACGATACTAGGGAAAAAAAAGTGACAATAAAAGATTTTTGTTAACAGAGATACCAAGCACCATTCCTTCCCCAATCATATGCTGCTACCTGGAGTAAGAACTATGACCAAACACTTTTGGGAACGATGTACTTTTTGGAGTTTTACTGCAAACAGCCTCCCTTTTCAGTTTTTTTCCTCAGAAAGTTCTAATGAAGGATGATAGGATAGGGAAGGGATGAGTGTTAGTATTCATTACTTTTCATTTATTACTTTTTCAATAGAATTGACTGAAGAATGACTCATCAAATCAGATAAAACTTAGGAAAGATTCTAGGGCCTTTAAGACAGTATCTATGGTCTCACAGTAAATCTAATGACAACACGATACAGTGGAAGGGCCTTGGGTTGGCAGTTTAAAATAAAGACATTAAGGCCATTCGACCTCAAAACTCTACCACAGTTTTAATCCTTACATTCCTTCATCCTTTAAATCAACAGTTACAGGCTTACCAACGTGAGAGGGCATTTTAAGATGTCTCTAATGGAAGCAATTTGAATTTGCATAAGATGTAACCACTCTCTACTTCATCACTAGCTGTTTTATATTGCCTGGCAGAGTTTAGCCAGATCTGAGTGGGTCTTATGCGAACAAGGGTTCTTTAAGAATCTATACCTCTTAAACAGCAAGTAGATATTTATGTTCTATAAAATTAAACAATATGTGAGTAGTGTTTACGATAAATACAGAAATTGCTGATTCAGTACCCTTATTAAAAAAAAATTATAATCACTACTGCTAGTGATGACTCTTGA	-	novel	NA	P-0064546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	79	469	0	ENST00000435504.4:c.404-788_415del		p.X135_splice	ENST00000435504		135		6/13	0.567495579285295	1	FACETS	0.785	0.7	0.874	0.785	0.7	0.874	SUBCLONAL	1	TRUE	0	0.567495579285295	1		469	254	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652129	36652129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34916193	NA	P-0064630-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	404	705	0	ENST00000244741.5:c.251G>A	p.Arg84Gln	p.R84Q	ENST00000244741	NM_000389.4	84	cGa/cAa	2/3	0.79413128399296	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	4	TRUE	0	0.79413128399296	4		705	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577025	7577025	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0064630-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	286	720	0	ENST00000269305.4:c.913A>T	p.Lys305Ter	p.K305*	ENST00000269305	NM_001126112.2	305	Aag/Tag	8/11	0.724814329357588	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	4	TRUE	0	0.79413128399296	4		720	322	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441780	49441780	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555195442	NA	P-0064630-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	243	521	0	ENST00000301067.7:c.4204C>T	p.Gln1402Ter	p.Q1402*	ENST00000301067	NM_003482.3	1402	Cag/Tag	14/54	0.79413128399296	7	FACETS	1	0.956	1			1	CLONAL	3	TRUE	NA	0.79413128399296	7		521	598	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961526	54961526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1211313151	NA	P-0064630-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	41	476	0	ENST00000312783.6:c.106C>T	p.Pro36Ser	p.P36S	ENST00000312783	NM_198436.1	36	Cca/Tca	4/10	0.373373661185675	4	FACETS	0.657	0.55	0.774	0.164	0.137	0.194	INDETERMINATE	1	TRUE	0	0.79413128399296	4		476	282	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255775	16255775	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064630-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	63	618	0	ENST00000375759.3:c.3040G>T	p.Val1014Leu	p.V1014L	ENST00000375759	NM_015001.2	1014	Gtg/Ttg	11/15	0.694702091799751	3	FACETS	0.803	0.701	0.911			1	CLONAL	1	TRUE	NA	0.79413128399296	3		618	276	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416398	49416398	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064630-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	348	599	0	ENST00000301067.7:c.16313G>T	p.Arg5438Leu	p.R5438L	ENST00000301067	NM_003482.3	5438	cGg/cTg	51/54	0.79413128399296	7	FACETS	0.929	0.887	0.971			1	CLONAL	4	TRUE	NA	0.79413128399296	7		599	704	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132978	30132978	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064630-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	204	504	0	ENST00000331968.5:c.623C>A	p.Ser208Tyr	p.S208Y	ENST00000331968	NM_002742.2	208	tCc/tAc	4/18	0.765214833308103	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.79413128399296	2		504	249	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17124850	17124850	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0064630-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	137	629	0	ENST00000285071.4:c.871+1G>T		p.X291_splice	ENST00000285071	NM_144997.5	291			0.773919205453717	2	FACETS	1	0.987	1	0.656	0.61	0.702	CLONAL	1	TRUE	0	0.79413128399296	2		629	263	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121166	11121166	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064630-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	224	595	0	ENST00000358026.2:c.2233C>T	p.Gln745Ter	p.Q745*	ENST00000358026	NM_001128849.1	745	Cag/Tag	15/36	0.79413128399296	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.79413128399296	2		595	273	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008487	70008487	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064630-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	192	497	0	ENST00000394351.3:c.774A>T	p.Gln258His	p.Q258H	ENST00000394351	NM_000248.3	258	caA/caT	8/9	0.79413128399296	2	FACETS	0.999	0.959	1	0.999	0.959	1	CLONAL	2	TRUE	0	0.79413128399296	2		497	242	SUCCESS
ALB	213	MSKCC	GRCh37	4	74274318	74274318	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1250260879	NA	P-0064630-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	22	425	0	ENST00000295897.4:c.282del	p.Phe94LeufsTer47	p.F94Lfs*47	ENST00000295897	NM_000477.5	93	cTt/ct	4/15	0.472834705890788	3	FACETS	0.355	0.276	0.446	0.118	0.092	0.149	INDETERMINATE	1	TRUE	0	0.79413128399296	3		425	218	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955163	93955163	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064630-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	29	312	0	ENST00000369303.4:c.2735G>T	p.Ser912Ile	p.S912I	ENST00000369303	NM_004440.3	912	aGc/aTc	16/17	0.561936556661605	5	FACETS	0.613	0.494	0.748	0.204	0.164	0.25	SUBCLONAL	1	TRUE	2	0.79413128399296	5		312	261	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480506	123480506	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064630-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	69	301	0	ENST00000371139.4:c.14C>A	p.Ala5Asp	p.A5D	ENST00000371139	NM_001114937.2	5	gCt/gAt	1/4	0.680496297728525	2	FACETS	1	0.953	1			1	CLONAL	1	TRUE	NA	0.79413128399296	2		301	155	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61305221	61305221	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	CG	novel	NA	P-0064630-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	24	404	0	ENST00000341074.5:c.905delinsCG	p.Met302ThrfsTer26	p.M302Tfs*26	ENST00000341074	NM_002974.2	302	aTg/aCGg	8/8	0.389942612788759	6	FACETS	0.734	0.579	0.912	0.245	0.193	0.304	INDETERMINATE	1	TRUE	3	0.79413128399296	6		404	213	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	104	663	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.881	0.798	0.968	0.881	0.798	0.968	CLONAL	1	TRUE	1	0.694098986685129	2		663	340	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121909229	NA	P-0064637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	163	347	0	ENST00000371953.3:c.389G>C	p.Arg130Pro	p.R130P	ENST00000371953	NM_000314.4	130	cGa/cCa	5/9	1	2	FACETS	0.964	0.892	1	0.964	0.892	1	CLONAL	1	TRUE	1	0.694098986685129	2		347	487	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692809	89692826	+	inframe_deletion	In_Frame_Del	DEL	TAGAACTTATCAAACCCT	TAGAACTTATCAAACCCT	-	novel	NA	P-0064637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	99	180	0	ENST00000371953.3:c.294_311del	p.Glu99_Phe104del	p.E99_F104del	ENST00000371953	NM_000314.4	98	cTAGAACTTATCAAACCCTtt/ctt	5/9	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.694098986685129	2		180	282	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719423	190719423	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	205	512	0	ENST00000441310.2:c.1425A>G	p.Ile475Met	p.I475M	ENST00000441310	NM_000534.4	475	atA/atG	9/13	0.437573921393389	1	FACETS	0.779	0.73	0.829	0.779	0.73	0.829	SUBCLONAL	1	TRUE	0	0.694098986685129	1		512	495	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155703	56155704	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0064637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	149	420	0	ENST00000399503.3:c.795_796del	p.Glu265AspfsTer35	p.E265Dfs*35	ENST00000399503	NM_005921.1	265	gaATct/gact	3/20	0.390091760647673	1	FACETS	0.512	0.471	0.556	0.512	0.471	0.556	INDETERMINATE	1	TRUE	0	0.694098986685129	1		420	547	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0064657-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	101	525	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.313796124202747	2		525	540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0064657-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	169	501	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	NA	2	FACETS	0.901	0.832	0.971			1	INDETERMINATE	2	TRUE	NA	0.313796124202747	2		501	598	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692805	89692805	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204928	NA	P-0064657-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	21	226	0	ENST00000371953.3:c.289C>T	p.Gln97Ter	p.Q97*	ENST00000371953	NM_000314.4	97	Cag/Tag	5/9	0.313796124202747	1	FACETS	0.513	0.396	0.648	0.513	0.396	0.648	SUBCLONAL	1	TRUE	0	0.313796124202747	1		226	220	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335825	73335825	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064657-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	46	426	0	ENST00000377767.4:c.2470G>T	p.Ala824Ser	p.A824S	ENST00000377767	NM_014953.3	824	Gct/Tct	18/21	1	2	FACETS	0.644	0.543	0.756	0.644	0.543	0.756	SUBCLONAL	1	TRUE	1	0.313796124202747	2		426	455	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30302702	30302702	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064657-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	15	195	0	ENST00000322652.5:c.793A>G	p.Met265Val	p.M265V	ENST00000322652	NM_015355.2	265	Atg/Gtg	7/16	0.189005739911148	2	FACETS	0.429	0.314	0.567	0.214	0.157	0.284	SUBCLONAL	1	TRUE	0	0.313796124202747	2		195	223	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162954	47162954	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064657-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	58	499	0	ENST00000409792.3:c.3172G>T	p.Asp1058Tyr	p.D1058Y	ENST00000409792	NM_014159.6	1058	Gat/Tat	3/21	0.313796124202747	1	FACETS	0.656	0.565	0.756	0.656	0.565	0.756	SUBCLONAL	1	TRUE	0	0.313796124202747	1		499	475	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542225	187542225	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064657-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	43	579	0	ENST00000441802.2:c.5515G>T	p.Glu1839Ter	p.E1839*	ENST00000441802	NM_005245.3	1839	Gaa/Taa	10/27	1	2	FACETS	0.51	0.427	0.603	0.51	0.427	0.603	SUBCLONAL	1	TRUE	1	0.313796124202747	2		579	537	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045137	47045137	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064657-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	84	648	0	ENST00000377604.3:c.2378del	p.Arg793GlnfsTer9	p.R793Qfs*9	ENST00000377604	NM_001204468.1	793	cGa/ca	21/24	1	2	FACETS	0.97	0.858	1	0.97	0.858	1	CLONAL	1	TRUE	1	0.313796124202747	2		648	552	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	262	286	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.661777496069187	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.686204371026935	2		286	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0064683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	172	463	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.686204371026935	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.686204371026935	1		463	311	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617634	100617634	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1555978891	NA	P-0064683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	146	220	0	ENST00000308731.7:c.435C>A	p.Cys145Ter	p.C145*	ENST00000308731	NM_000061.2	145	tgC/tgA	6/19	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.686204371026935	1		220	196	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932195	36932205	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGCCCAGCA	GCTGCCCAGCA	-	novel	NA	P-0064683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	157	669	0	ENST00000361632.4:c.2264_2274del	p.Leu755ProfsTer13	p.L755Pfs*13	ENST00000361632		755	cTGCTGGGCAGC/c	16/16	1	2	FACETS	0.93	0.858	1	0.93	0.858	1	CLONAL	1	TRUE	1	0.686204371026935	2		669	492	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311647	15311872	+	coding_sequence_variant,5_prime_UTR_variant	Frame_Shift_Del	DEL	CGGGTGGCGGTGGCGGTGGCGGCGACATCGGGCGACGGCGGCGGCGGCGGCCACGGGCCCCCGGCCCCATGGCGGCCGGCCGCGACCCTCCCCTCCTCCCTCCTTCCCTGGGCTCCGGGCGCGTCCCGGGCCAGCCTCCGCGCCGCCAACTTCGCCGAAGTGAGGCGGCCGGGCCGCCCCGCCCCCAGCCCTCGAAGGCTCGCCCCGCCCCGGGGCCGGCCCAGCG	CGGGTGGCGGTGGCGGTGGCGGCGACATCGGGCGACGGCGGCGGCGGCGGCCACGGGCCCCCGGCCCCATGGCGGCCGGCCGCGACCCTCCCCTCCTCCCTCCTTCCCTGGGCTCCGGGCGCGTCCCGGGCCAGCCTCCGCGCCGCCAACTTCGCCGAAGTGAGGCGGCCGGGCCGCCCCGCCCCCAGCCCTCGAAGGCTCGCCCCGCCCCGGGGCCGGCCCAGCG	-	novel	NA	P-0064683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	100	766	0				ENST00000263388	NM_000435.2	?-24/2321		1/33	1	2	FACETS	0.586	0.526	0.65	0.586	0.526	0.65	SUBCLONAL	1	TRUE	1	0.686204371026935	2		766	497	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449478	31449523	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGATTCATTCCAAAATTTAAATGATGACTTGGATGAGTCATGGC	CAGGATTCATTCCAAAATTTAAATGATGACTTGGATGAGTCATGGC	-	novel	NA	P-0064683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	136	364	0	ENST00000344624.3:c.2686_2731del	p.Ala896IlefsTer35	p.A896Ifs*35	ENST00000344624		896	GCCATGACTCATCCAAGTCATCATTTAAATTTTGGAATGAATCCTGat/at	19/33	1	2	FACETS	0.969	0.89	1	0.969	0.89	1	CLONAL	1	TRUE	1	0.686204371026935	2		364	409	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742841	145742841	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	404	533	0	ENST00000428558.2:c.170G>A	p.Gly57Asp	p.G57D	ENST00000428558	NM_004260.3	57	gGc/gAc	3/22	0.686204371026935	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.686204371026935	3		533	506	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293567	137293567	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	36	693	0	ENST00000481739.1:c.118G>C	p.Gly40Arg	p.G40R	ENST00000481739	NM_002957.4	40	Ggc/Cgc	2/10	1	2	FACETS	0.221	0.182	0.266	0.221	0.182	0.266	SUBCLONAL	1	TRUE	1	0.686204371026935	2		693	474	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426121	47426121	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064711-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	79	380	0	ENST00000377045.4:c.641C>A	p.Ser214Tyr	p.S214Y	ENST00000377045	NM_001654.4	214	tCc/tAc	7/16	1	2	FACETS	0.828	0.728	0.936	0.828	0.728	0.936	CLONAL	1	TRUE	1	0.26	2		380	734	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92300830	92300830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064711-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	39	247	0	ENST00000265734.4:c.557G>A	p.Arg186Lys	p.R186K	ENST00000265734	NM_001259.6	186	aGa/aAa	5/8	1	2	FACETS	0.482	0.398	0.575	0.482	0.398	0.575	SUBCLONAL	1	TRUE	1	0.26	2		247	623	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0064711-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	138	175	0	ENST00000311936.3:c.34_35delinsTT	p.Gly12Phe	p.G12F	ENST00000311936	NM_004985.3	12	GGt/TTt	2/5	0.3	3	FACETS	0.998	0.912	1			1	CLONAL	2	TRUE	NA	0.26	3		175	601	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5055766	5055766	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064711-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	63	252	0	ENST00000381652.3:c.1034A>G	p.His345Arg	p.H345R	ENST00000381652	NM_004972.3	345	cAt/cGt	8/25	0.243216506293044	1	FACETS	0.88	0.763	1	0.88	0.763	1	CLONAL	1	TRUE	0	0.26	1		252	479	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76953101	76953101	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064711-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	50	172	0	ENST00000373344.5:c.212C>A	p.Ser71Tyr	p.S71Y	ENST00000373344	NM_000489.3	71	tCc/tAc	4/35	1	2	FACETS	0.901	0.766	1	0.901	0.766	1	CLONAL	1	TRUE	1	0.26	2		172	427	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288973	11288973	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064711-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	50	285	0	ENST00000361445.4:c.2782G>C	p.Asp928His	p.D928H	ENST00000361445	NM_004958.3	928	Gac/Cac	19/58	1	2	FACETS	0.554	0.469	0.648	0.554	0.469	0.648	SUBCLONAL	1	TRUE	1	0.26	2		285	694	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021450	42021451	+	frameshift_variant	Frame_Shift_Ins	INS	AG	AG	GAT	novel	NA	P-0064711-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	86	288	0	ENST00000219905.7:c.3746_3747delinsGAT	p.Glu1249GlyfsTer2	p.E1249Gfs*2	ENST00000219905	NM_001164273.1	1249	gAG/gGAT	11/24	0.243216506293044	1	FACETS	0.877	0.777	0.985	0.877	0.777	0.985	CLONAL	1	TRUE	0	0.26	1		288	656	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0064712-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	162	491	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.487991671242929	3	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	1	0.487991671242929	3		491	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863224683	NA	P-0064712-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	316	467	0	ENST00000269305.4:c.388C>G	p.Leu130Val	p.L130V	ENST00000269305	NM_001126112.2	130	Ctc/Gtc	5/11	0.487991671242929	2	FACETS	0.981	0.934	1	0.981	0.934	1	CLONAL	2	TRUE	0	0.487991671242929	2		467	660	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974763	21974763	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064712-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	160	515	0	ENST00000304494.5:c.64del	p.Arg22GlyfsTer4	p.R22Gfs*4	ENST00000304494	NM_000077.4	22	Cgg/gg	1/3	1	2	FACETS	0.902	0.829	0.978	0.902	0.829	0.978	CLONAL	1	TRUE	1	0.487991671242929	2		515	727	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0064773-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	265	491	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.293041498590347	3	FACETS	1	0.991	1	1	0.991	1	INDETERMINATE	2	TRUE	1	0.547831714027465	3		491	515	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0064773-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	220	463	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.547831714027465	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.547831714027465	1		463	558	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100298	27100299	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0064773-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	283	548	2	ENST00000324856.7:c.4012dup	p.Ser1338PhefsTer107	p.S1338Ffs*107	ENST00000324856	NM_006015.4	1337	gat/gaTt	17/20	0.274715652595565	1	FACETS	0.856	0.807	0.907	0.856	0.807	0.907	INDETERMINATE	1	TRUE	0	0.547831714027465	1		550	876	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438210	49438210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1361870384	NA	P-0064773-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	228	439	0	ENST00000301067.7:c.5059C>T	p.Arg1687Cys	p.R1687C	ENST00000301067	NM_003482.3	1687	Cgc/Tgc	20/54	0.311857874784307	1	FACETS	0.852	0.798	0.908	0.852	0.798	0.908	INDETERMINATE	1	TRUE	0	0.547831714027465	1		439	709	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064789-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	105	663	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.978	0.891	1	0.978	0.891	1	CLONAL	1	TRUE	1	0.792393375553868	2		663	271	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0064789-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	153	533	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.951	0.88	1	0.951	0.88	1	CLONAL	1	TRUE	1	0.792393375553868	2		533	406	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967268	38967268	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	36	220	0	ENST00000357387.3:c.1213T>G	p.Leu405Val	p.L405V	ENST00000357387	NM_152756.3	405	Tta/Gta	14/38	1	2	FACETS	0.695	0.572	0.832	0.695	0.572	0.832	SUBCLONAL	1	TRUE	1	0.283698449263712	2		220	365	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0064830-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	81	432	1	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.213441430577027	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	2	0.274000589639619	4		433	326	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0064830-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	95	535	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.274000589639619	2	FACETS	0.945	0.848	1	0.945	0.848	1	CLONAL	2	TRUE	0	0.274000589639619	2		535	367	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs11575997	NA	P-0064830-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	190	659	0	ENST00000269305.4:c.993+1G>T		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.274000589639619	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.274000589639619	2		659	608	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636650	73636650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064830-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	199	669	0	ENST00000377687.4:c.913C>T	p.Pro305Ser	p.P305S	ENST00000377687	NM_001730.3	305	Cca/Tca	2/4	0.218791286615272	5	FACETS	0.995	0.921	1	0.663	0.614	0.714	CLONAL	2	TRUE	2	0.274000589639619	5		669	1030	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479822	67479822	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064830-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	97	587	0	ENST00000327367.4:c.1129G>C	p.Val377Leu	p.V377L	ENST00000327367	NM_005902.3	377	Gtc/Ctc	8/9	0.274000589639619	2	FACETS	1	0.965	1	0.597	0.533	0.665	CLONAL	1	TRUE	0	0.274000589639619	2		587	593	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976533	7976533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780420901	NA	P-0064830-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	156	437	0	ENST00000319144.4:c.1859C>T	p.Pro620Leu	p.P620L	ENST00000319144	NM_001139.2	620	cCg/cTg	14/15	0.274000589639619	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.274000589639619	2		437	551	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714390	40714391	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0064830-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	278	575	0	ENST00000373198.4:c.4005_4006dup	p.Phe1336TyrfsTer16	p.F1336Yfs*16	ENST00000373198	NM_133170.3	1336	ttc/tATtc	29/32	0.274000589639619	2	FACETS	0.915	0.864	0.967	1	0.993	1	CLONAL	3	TRUE	0	0.274000589639619	2		575	739	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522609	67522610	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0064830-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	144	539	0	ENST00000274335.5:c.108dup	p.Val38SerfsTer7	p.V38Sfs*7	ENST00000274335		36	tcc/tCcc	1/15	0.274000589639619	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.274000589639619	2		539	506	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222761	53222761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064830-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	68	699	0	ENST00000375401.3:c.4175C>T	p.Pro1392Leu	p.P1392L	ENST00000375401	NM_004187.3	1392	cCt/cTt	25/26	1	2	FACETS	0.854	0.744	0.974	0.854	0.744	0.974	CLONAL	1	TRUE	1	0.274000589639619	2		699	581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0064832-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	168	432	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.470305178074177	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	3	TRUE	0	0.489957132676576	3		432	275	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186812	108186812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064832-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	124	483	0	ENST00000278616.4:c.6170C>T	p.Ser2057Leu	p.S2057L	ENST00000278616	NM_000051.3	2057	tCa/tTa	42/63	0.428766019553636	4	FACETS	0.979	0.895	1	0.979	0.895	1	CLONAL	2	TRUE	2	0.489957132676576	4		483	385	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0064832-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	196	244	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.489957132676576	6	FACETS	0.903	0.851	0.953	1	0.985	1	CLONAL	5	TRUE	2	0.489957132676576	6		244	351	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572237	64572237	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064832-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	109	713	0	ENST00000312049.6:c.1402G>T	p.Glu468Ter	p.E468*	ENST00000312049	NM_130799.2	468	Gag/Tag	10/10	0.428766019553636	4	FACETS	0.861	0.78	0.945	0.861	0.78	0.945	CLONAL	2	TRUE	2	0.489957132676576	4		713	385	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933420	100933420	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064832-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	110	397	0	ENST00000325455.5:c.1970C>A	p.Pro657Gln	p.P657Q	ENST00000325455	NM_001202474.3	657	cCa/cAa	4/8	0.428766019553636	4	FACETS	0.911	0.827	0.999	0.911	0.827	0.999	CLONAL	2	TRUE	2	0.489957132676576	4		397	367	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464354	464354	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064832-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	106	416	0	ENST00000399788.2:c.840A>T	p.Arg280Ser	p.R280S	ENST00000399788	NM_001042603.1	280	agA/agT	7/28	0.489957132676576	6	FACETS	0.891	0.802	0.983	0.445	0.401	0.492	CLONAL	2	TRUE	2	0.489957132676576	6		416	481	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929084	32929084	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064832-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	34	387	0	ENST00000380152.3:c.7094A>C	p.His2365Pro	p.H2365P	ENST00000380152		2365	cAt/cCt	14/27	0.465911720302123	3	FACETS	0.697	0.572	0.835	0.348	0.286	0.418	SUBCLONAL	1	TRUE	1	0.489957132676576	3		387	248	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544742	65544742	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064832-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	95	403	0	ENST00000358664.4:c.184C>T	p.Gln62Ter	p.Q62*	ENST00000358664	NM_002382.4	62	Caa/Taa	4/5	0.47950866998524	2	FACETS	0.95	0.866	1	0.95	0.866	1	CLONAL	2	TRUE	0	0.489957132676576	2		403	204	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602776	55602776	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0064832-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	104	341	0	ENST00000288135.5:c.2596+1G>T		p.X866_splice	ENST00000288135	NM_000222.2	866			0.489957132676576	3	FACETS	1	0.925	1	1	0.925	1	CLONAL	2	TRUE	1	0.489957132676576	3		341	260	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973942	55973943	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0064832-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	115	481	0	ENST00000263923.4:c.1373_1374delinsAT	p.Trp458Tyr	p.W458Y	ENST00000263923	NM_002253.2	458	tGG/tAT	10/30	0.489957132676576	3	FACETS	0.91	0.831	0.992	0.91	0.831	0.992	CLONAL	2	TRUE	1	0.489957132676576	3		481	321	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319909	8319909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064832-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	93	439	0	ENST00000356435.5:c.5592G>T	p.Met1864Ile	p.M1864I	ENST00000356435		1864	atG/atT	34/35	0.48819914145074	2	FACETS	0.836	0.758	0.916	0.836	0.758	0.916	CLONAL	2	TRUE	0	0.489957132676576	2		439	227	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0064834-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	69	1407	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.841044268847966	2		1407	144	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711929	89711929	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1554900594	NA	P-0064834-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	40	1060	0	ENST00000371953.3:c.547A>T	p.Lys183Ter	p.K183*	ENST00000371953	NM_000314.4	183	Aag/Tag	6/9	0.841044268847966	1	FACETS	0.427	0.363	0.496	0.427	0.363	0.496	SUBCLONAL	1	TRUE	0	0.841044268847966	1		1060	129	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0064834-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	267	1562	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.841044268847966	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.841044268847966	2		1562	304	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805519	46805520	+	stop_gained	Nonsense_Mutation	DNP	AC	AC	TA	novel	NA	P-0064834-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	186	1701	0	ENST00000290295.7:c.436_437delinsTA	p.Val146Ter	p.V146*	ENST00000290295	NM_006361.5	146	GTg/TAg	1/2	0.841044268847966	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.841044268847966	2		1701	207	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224554	36224554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751409145	NA	P-0064834-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	17	1808	0	ENST00000222270.7:c.7016G>A	p.Arg2339Gln	p.R2339Q	ENST00000222270	NM_014727.1	2339	cGg/cAg	29/37	1	2	FACETS	0.155	0.116	0.203	0.155	0.116	0.203	SUBCLONAL	1	TRUE	1	0.841044268847966	2		1808	260	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0064839-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	106	491	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.147885238482675	5	FACETS	1	0.967	1	0.778	0.702	0.858	INDETERMINATE	2	TRUE	2	0.287610628967509	5		491	452	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216546	108216546	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs529296539	NA	P-0064839-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	79	234	0	ENST00000278616.4:c.8495G>T	p.Arg2832Leu	p.R2832L	ENST00000278616	NM_000051.3	2832	cGt/cTt	58/63	0.287610628967509	2	FACETS	0.95	0.845	1	0.95	0.845	1	CLONAL	2	TRUE	0	0.287610628967509	2		234	289	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7119557	7119557	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064839-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	148	272	0	ENST00000302850.5:c.3697G>T	p.Ala1233Ser	p.A1233S	ENST00000302850	NM_000208.2	1233	Gca/Tca	21/22	0.214155184144772	2	FACETS	1	0.987	1	0.727	0.665	0.791	CLONAL	1	TRUE	0	0.287610628967509	2		272	708	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670806	134670806	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064839-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	186	315	0	ENST00000398015.3:c.717C>A	p.Tyr239Ter	p.Y239*	ENST00000398015	NM_004441.4	239	taC/taA	3/16	0.214155184144772	2	FACETS	0.858	0.794	0.924	0.858	0.794	0.924	CLONAL	2	TRUE	0	0.287610628967509	2		315	754	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684051	29684051	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064842-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	93	377	1	ENST00000356175.3:c.7749del	p.Leu2584TrpfsTer19	p.L2584Wfs*19	ENST00000356175	NM_000267.3	2583	ctC/ct	52/57	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		378	518	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851458	63851458	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064843-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	63	489	0	ENST00000279873.7:c.2236G>T	p.Val746Phe	p.V746F	ENST00000279873	NM_032199.2	746	Gtc/Ttc	10/10	0.24988494606294	0	FACETS	0.278	0.241	0.319			1	INDETERMINATE	1	TRUE	0	0.468947492728962	0		489	513	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480336	89480336	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064843-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	68	326	0	ENST00000336596.2:c.2173G>A	p.Gly725Arg	p.G725R	ENST00000336596	NM_005233.5	725	Ggg/Agg	13/17	0.26686211468883	1	FACETS	0.433	0.377	0.493	0.433	0.377	0.493	INDETERMINATE	1	TRUE	0	0.468947492728962	1		326	513	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801796	3801796	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064843-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	159	399	0	ENST00000262367.5:c.3710G>T	p.Cys1237Phe	p.C1237F	ENST00000262367	NM_004380.2	1237	tGt/tTt	20/31	0.26686211468883	1	FACETS	0.944	0.87	1	0.944	0.87	1	INDETERMINATE	1	TRUE	0	0.468947492728962	1		399	550	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0064904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	113	491	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.612786216905371	2		491	318	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0064904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	147	622	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.612786216905371	1	FACETS	0.935	0.865	1	0.935	0.865	1	CLONAL	1	TRUE	0	0.612786216905371	1		622	356	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858914	89858914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150290184	NA	P-0064904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	121	479	0	ENST00000389301.3:c.1048C>T	p.Arg350Trp	p.R350W	ENST00000389301	NM_000135.2	350	Cgg/Tgg	12/43	0.612786216905371	3	FACETS	0.918	0.832	1	0.459	0.416	0.504	CLONAL	1	TRUE	1	0.612786216905371	3		479	562	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958113	54958113	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	124	458	0	ENST00000312783.6:c.494T>G	p.Phe165Cys	p.F165C	ENST00000312783	NM_198436.1	165	tTt/tGt	6/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.612786216905371	2		458	370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0064924-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	411	624	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.710071311157319	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.700694760890518	2		624	521	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955496	48955496	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064924-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	175	269	0	ENST00000267163.4:c.1612del	p.Ala538GlnfsTer5	p.A538Qfs*5	ENST00000267163	NM_000321.2	538	Gca/ca	17/27	0.710071311157319	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.700694760890518	1		269	241	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930130	68930130	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064924-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	22	373	0	ENST00000288368.4:c.191A>C	p.Asn64Thr	p.N64T	ENST00000288368	NM_024870.2	64	aAt/aCt	2/40	0.710071311157319	2	FACETS	0.171	0.132	0.216	0.086	0.066	0.108	SUBCLONAL	1	TRUE	0	0.700694760890518	2		373	367	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929041	32929041	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs80358930	NA	P-0064924-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	206	375	0	ENST00000380152.3:c.7051G>C	p.Ala2351Pro	p.A2351P	ENST00000380152		2351	Gca/Cca	14/27	0.710071311157319	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.700694760890518	1		375	287	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437169	121437169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1204330040	NA	P-0064924-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	581	629	1	ENST00000257555.6:c.1600G>A	p.Ala534Thr	p.A534T	ENST00000257555		534	Gcc/Acc	8/10	0.0898164561381828	5	FACETS	1	0.994	1			1	INDETERMINATE	3	TRUE	NA	0.700694760890518	5		630	1021	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203436	NA	P-0064934-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	64	758	0	ENST00000269305.4:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269305	NM_001126112.2	163	Tac/Cac	5/11	0.240585948691491	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.240585948691491	1		758	428	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602583	10602583	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064934-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	55	716	0	ENST00000171111.5:c.995del	p.Gly332AlafsTer68	p.G332Afs*68	ENST00000171111	NM_203500.1	332	gGc/gc	3/6	0.240585948691491	1	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	0	0.240585948691491	1		716	393	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248497	212248497	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064934-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	35	689	0	ENST00000342788.4:c.3770A>T	p.Asp1257Val	p.D1257V	ENST00000342788	NM_005235.2	1257	gAc/gTc	28/28	1	2	FACETS	0.564	0.461	0.679	0.564	0.461	0.679	SUBCLONAL	1	TRUE	1	0.240585948691491	2		689	516	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161862	47161862	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064934-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	69	553	0	ENST00000409792.3:c.4264C>T	p.Gln1422Ter	p.Q1422*	ENST00000409792	NM_014159.6	1422	Cag/Tag	3/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.240585948691491	2		553	466	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868277	37868297	+	inframe_deletion	In_Frame_Del	DEL	AGTGCAGCAAGCCCTGTGCCC	AGTGCAGCAAGCCCTGTGCCC	-	novel	NA	P-0064934-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	111	706	0	ENST00000269571.5:c.998_1018del	p.Lys333_Ala339del	p.K333_A339del	ENST00000269571		333	aAGTGCAGCAAGCCCTGTGCCCga/aga	8/27	0.240585948691491	5	FACETS	1	0.961	1			1	CLONAL	2	TRUE	NA	0.240585948691491	5		706	555	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221947	1221947	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0064934-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	58	534	0	ENST00000326873.7:c.863-1G>C		p.X288_splice	ENST00000326873	NM_000455.4	288			0.240585948691491	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.240585948691491	1		534	321	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95584074	95584074	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064934-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	61	427	0	ENST00000393063.1:c.1394G>C	p.Gly465Ala	p.G465A	ENST00000393063	NM_030621.3	465	gGc/gCc	10/28	0.108658587978118	3	FACETS	0.856	0.743	0.977	0.856	0.743	0.977	INDETERMINATE	2	TRUE	1	0.240585948691491	3		427	332	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145596	11145596	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064934-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	65	581	0	ENST00000358026.2:c.3958G>T	p.Asp1320Tyr	p.D1320Y	ENST00000358026	NM_001128849.1	1320	Gac/Tac	29/36	0.240585948691491	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.240585948691491	1		581	335	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753453	42753453	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064934-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	62	877	0	ENST00000222329.4:c.811A>T	p.Thr271Ser	p.T271S	ENST00000222329	NM_006494.2	271	Acg/Tcg	4/4	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.240585948691491	2		877	421	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147503	47147503	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064934-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	37	757	0	ENST00000409792.3:c.4823C>T	p.Ala1608Val	p.A1608V	ENST00000409792	NM_014159.6	1608	gCc/gTc	6/21	1	2	FACETS	0.528	0.435	0.634	0.528	0.435	0.634	SUBCLONAL	1	TRUE	1	0.240585948691491	2		757	582	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796970	57796970	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064934-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	71	866	0	ENST00000309042.7:c.1946A>T	p.Asp649Val	p.D649V	ENST00000309042	NM_005612.4	649	gAc/gTc	4/4	0.240585948691491	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.240585948691491	1		866	439	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	204	663	0				ENST00000310581	NM_198253.2	-/1132			0.378206816369208	3	FACETS	0.962	0.897	1	0.962	0.897	1	CLONAL	2	TRUE	1	0.37920876313624	3		663	665	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106063	8106063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	143	399	0	ENST00000346208.3:c.883G>A	p.Gly295Arg	p.G295R	ENST00000346208		295	Gga/Aga	4/6	1	2	FACETS	0.957	0.873	1	0.957	0.873	1	CLONAL	1	TRUE	1	0.37920876313624	2		399	788	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115840	8115840	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	136	445	0	ENST00000346208.3:c.1186C>T	p.Leu396Phe	p.L396F	ENST00000346208		396	Ctc/Ttc	6/6	1	2	FACETS	0.867	0.789	0.95	0.867	0.789	0.95	CLONAL	1	TRUE	1	0.37920876313624	2		445	827	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443940	18443940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866374517	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	171	274	0	ENST00000266497.5:c.913C>T	p.Pro305Ser	p.P305S	ENST00000266497		305	Cca/Tca	3/31	0.376612644780846	4	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	2	0.37920876313624	4		274	607	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727481	88727481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	425	408	0	ENST00000360948.2:c.298G>A	p.Glu100Lys	p.E100K	ENST00000360948	NM_001012338.2	100	Gag/Aag	3/19	0.37920876313624	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	1	0.37920876313624	4		408	986	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134365	2134366	+	missense_variant	Missense_Mutation	DNP	CC	CC	GT	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	345	574	0	ENST00000219476.3:c.4142_4143delinsGT	p.Pro1381Arg	p.P1381R	ENST00000219476	NM_000548.3	1381	cCC/cGT	34/42	0.378206816369208	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.37920876313624	3		574	1010	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807367	3807367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	205	234	0	ENST00000262367.5:c.3620C>T	p.Ser1207Phe	p.S1207F	ENST00000262367	NM_004380.2	1207	tCc/tTc	19/31	0.378206816369208	3	FACETS	0.97	0.904	1	0.97	0.904	1	CLONAL	2	TRUE	1	0.37920876313624	3		234	663	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826577	50826577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	189	238	0	ENST00000398568.2:c.2302C>T	p.Pro768Ser	p.P768S	ENST00000398568	NM_001042412.1	768	Cct/Tct	15/18	0.37920876313624	3	FACETS	0.975	0.906	1	0.975	0.906	1	CLONAL	2	TRUE	1	0.37920876313624	3		238	608	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644985	67644985	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	373	415	0	ENST00000264010.4:c.250C>T	p.Pro84Ser	p.P84S	ENST00000264010	NM_006565.3	84	Cca/Tca	3/12	0.37920876313624	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.37920876313624	3		415	1128	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	583	682	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.37920876313624	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.37920876313624	3		682	1161	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579878	7579878	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1482497533	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	401	374	0	ENST00000269305.4:c.35C>T	p.Pro12Leu	p.P12L	ENST00000269305	NM_001126112.2	12	cCc/cTc	2/11	0.37920876313624	3	FACETS	0.962	0.92	1	0.962	0.92	1	CLONAL	3	TRUE	0	0.37920876313624	3		374	872	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592318	29592318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	292	230	0	ENST00000356175.3:c.4733C>T	p.Ser1578Phe	p.S1578F	ENST00000356175	NM_000267.3	1578	tCc/tTc	35/57	0.37920876313624	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	3	TRUE	0	0.37920876313624	3		230	609	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763235	59763235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761639530	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	383	286	0	ENST00000259008.2:c.2867C>T	p.Ser956Leu	p.S956L	ENST00000259008	NM_032043.2	956	tCa/tTa	19/20	0.37920876313624	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	0	0.37920876313624	3		286	771	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223320	2223320	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1174739572	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	166	427	0	ENST00000398665.3:c.3431C>T	p.Ser1144Leu	p.S1144L	ENST00000398665	NM_032482.2	1144	tCg/tTg	25/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.37920876313624	2		427	765	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085942	16085942	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	247	379	1	ENST00000281043.3:c.1118G>A	p.Arg373Gln	p.R373Q	ENST00000281043	NM_005378.4	373	cGa/cAa	3/3	0.376612644780846	4	FACETS	0.918	0.859	0.978	0.918	0.859	0.978	CLONAL	2	TRUE	2	0.37920876313624	4		380	979	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812335	212812335	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	204	333	0	ENST00000342788.4:c.241C>T	p.Arg81Ter	p.R81*	ENST00000342788	NM_005235.2	81	Cga/Tga	3/28	0.376612644780846	4	FACETS	0.896	0.833	0.962	0.896	0.833	0.962	CLONAL	2	TRUE	2	0.37920876313624	4		333	828	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624780	9624780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	254	311	0	ENST00000353224.5:c.197C>T	p.Pro66Leu	p.P66L	ENST00000353224	NM_177990.2	66	cCt/cTt	3/10	0.214110913612895	5	FACETS	1	0.983	1	0.752	0.705	0.801	INDETERMINATE	2	TRUE	2	0.37920876313624	5		311	931	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790024	40790024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437230315	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	243	376	0	ENST00000373198.4:c.2707G>A	p.Gly903Ser	p.G903S	ENST00000373198	NM_133170.3	903	Ggc/Agc	18/32	0.214110913612895	5	FACETS	1	0.968	1	0.704	0.658	0.751	INDETERMINATE	2	TRUE	2	0.37920876313624	5		376	952	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827922	40827922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	263	365	0	ENST00000373198.4:c.2506G>A	p.Asp836Asn	p.D836N	ENST00000373198	NM_133170.3	836	Gat/Aat	17/32	0.214110913612895	5	FACETS	1	0.98	1	0.735	0.689	0.782	INDETERMINATE	2	TRUE	2	0.37920876313624	5		365	987	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980726	40980726	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	236	352	0	ENST00000373198.4:c.1760C>T	p.Ser587Leu	p.S587L	ENST00000373198	NM_133170.3	587	tCa/tTa	10/32	0.214110913612895	5	FACETS	1	0.954	1	0.684	0.639	0.731	INDETERMINATE	2	TRUE	2	0.37920876313624	5		352	951	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101176	41101176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370385649	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	255	493	0	ENST00000373198.4:c.1180G>A	p.Glu394Lys	p.E394K	ENST00000373198	NM_133170.3	394	Gaa/Aaa	8/32	0.214110913612895	5	FACETS	1	0.977	1	0.725	0.679	0.772	INDETERMINATE	2	TRUE	2	0.37920876313624	5		493	970	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169988293	169988293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	126	309	0	ENST00000295797.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000295797	NM_002740.5	179	Cat/Tat	6/18	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.37920876313624	2		309	644	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532867	187532867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762890230	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	268	320	1	ENST00000441802.2:c.9526G>A	p.Glu3176Lys	p.E3176K	ENST00000441802	NM_005245.3	3176	Gaa/Aaa	14/27	0.37823074715005	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.37920876313624	2		321	648	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873660	35873660	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs201559094	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	102	352	0	ENST00000303115.3:c.616C>T	p.Arg206Ter	p.R206*	ENST00000303115	NM_002185.3	206	Cga/Tga	5/8	0.378206816369208	3	FACETS	0.865	0.774	0.962	0.432	0.387	0.481	CLONAL	1	TRUE	1	0.37920876313624	3		352	740	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80040380	80040380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	101	234	0	ENST00000265081.6:c.1709C>T	p.Ser570Leu	p.S570L	ENST00000265081	NM_002439.4	570	tCa/tTa	12/24	1	2	FACETS	0.941	0.844	1	0.941	0.844	1	CLONAL	1	TRUE	1	0.37920876313624	2		234	566	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80160639	80160639	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	103	345	0	ENST00000265081.6:c.3008C>T	p.Ser1003Phe	p.S1003F	ENST00000265081	NM_002439.4	1003	tCc/tTc	22/24	1	2	FACETS	0.895	0.803	0.993	0.895	0.803	0.993	CLONAL	1	TRUE	1	0.37920876313624	2		345	607	SUCCESS
APC	324	MSKCC	GRCh37	5	112154789	112154789	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs556566281	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	114	353	0	ENST00000257430.4:c.1060C>T	p.Pro354Ser	p.P354S	ENST00000257430	NM_000038.5	354	Cct/Tct	10/16	1	2	FACETS	0.919	0.829	1	0.919	0.829	1	CLONAL	1	TRUE	1	0.37920876313624	2		353	654	SUCCESS
APC	324	MSKCC	GRCh37	5	112179425	112179425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs76933416	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	169	426	0	ENST00000257430.4:c.8134C>T	p.Pro2712Ser	p.P2712S	ENST00000257430	NM_000038.5	2712	Ccc/Tcc	16/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.37920876313624	2		426	807	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120501	94120501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760168204	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	108	358	0	ENST00000369303.4:c.550C>T	p.Leu184Phe	p.L184F	ENST00000369303	NM_004440.3	184	Ctt/Ttt	3/17	1	2	FACETS	0.929	0.836	1	0.929	0.836	1	CLONAL	1	TRUE	1	0.37920876313624	2		358	613	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521992	157521992	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554235619	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	161	520	0	ENST00000346085.5:c.4264C>T	p.Gln1422Ter	p.Q1422*	ENST00000346085	NM_020732.3	1422	Cag/Tag	18/20	1	2	FACETS	0.974	0.893	1	0.974	0.893	1	CLONAL	1	TRUE	1	0.37920876313624	2		520	872	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729504	41729504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	157	447	0	ENST00000242208.4:c.1025C>T	p.Pro342Leu	p.P342L	ENST00000242208	NM_002192.2	342	cCc/cTc	3/3	0.37920876313624	4	FACETS	1	0.954	1	0.355	0.325	0.387	CLONAL	1	TRUE	1	0.37920876313624	4		447	1072	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729907	41729907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	313	382	0	ENST00000242208.4:c.622G>A	p.Glu208Lys	p.E208K	ENST00000242208	NM_002192.2	208	Gaa/Aaa	3/3	0.37920876313624	4	FACETS	0.86	0.814	0.907	0.86	0.814	0.907	CLONAL	3	TRUE	1	0.37920876313624	4		382	882	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220247	55220247	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	289	338	0	ENST00000275493.2:c.637A>G	p.Ile213Val	p.I213V	ENST00000275493	NM_005228.3	213	Atc/Gtc	6/28	0.37920876313624	5	FACETS	0.93	0.878	0.983	0.93	0.878	0.983	CLONAL	3	TRUE	2	0.37920876313624	5		338	857	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481408	140481408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867748453	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	300	256	0	ENST00000288602.6:c.1400C>T	p.Ser467Leu	p.S467L	ENST00000288602	NM_004333.4	467	tCa/tTa	11/18	0.37920876313624	5	FACETS	1	0.957	1	1	0.957	1	CLONAL	3	TRUE	2	0.37920876313624	5		256	816	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934283	68934283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773476490	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	193	257	0	ENST00000288368.4:c.349C>T	p.Arg117Cys	p.R117C	ENST00000288368	NM_024870.2	117	Cgt/Tgt	4/40	0.37920876313624	2	FACETS	0.93	0.867	0.995	0.93	0.867	0.995	CLONAL	2	TRUE	0	0.37920876313624	2		257	547	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650317	48650317	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	381	460	0	ENST00000376670.3:c.287G>A	p.Trp96Ter	p.W96*	ENST00000376670	NM_002049.3	96	tGg/tAg	3/6	0.37823074715005	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.37920876313624	2		460	943	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1685758	1685758	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	155	434	0	ENST00000378625.1:c.1343T>G	p.Leu448Arg	p.L448R	ENST00000378625	NM_001198994.1	448	cTg/cGg	11/14	0.37920876313624	5	FACETS	0.979	0.894	1	0.245	0.223	0.268	CLONAL	1	TRUE	1	0.37920876313624	5		434	1310	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948317	71948317	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	205	554	0	ENST00000298229.2:c.3029C>T	p.Pro1010Leu	p.P1010L	ENST00000298229	NM_001567.3	1010	cCa/cTa	26/28	0.37920876313624	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.37920876313624	1		554	778	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118391587	118391587	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	136	282	0	ENST00000534358.1:c.11500G>C	p.Val3834Leu	p.V3834L	ENST00000534358	NM_005933.3	3834	Gtt/Ctt	34/36	0.37920876313624	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.37920876313624	1		282	468	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148875	119148876	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	CA	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	111	280	0	ENST00000264033.4:c.1096-1_1096delinsCA		p.X366_splice	ENST00000264033	NM_005188.3	366		8/16	0.37920876313624	1	FACETS	0.951	0.859	1	0.951	0.859	1	CLONAL	1	TRUE	0	0.37920876313624	1		280	499	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341219	341220	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	112	320	1	ENST00000262320.3:c.2264_2265delinsTT	p.Ala755Val	p.A755V	ENST00000262320	NM_003502.3	755	gCC/gTT	9/11	0.378206816369208	3	FACETS	0.942	0.848	1	0.471	0.424	0.521	CLONAL	1	TRUE	1	0.37920876313624	3		321	746	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512402	38512403	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	263	386	0	ENST00000254066.5:c.1313_1314delinsTT	p.Ala438Val	p.A438V	ENST00000254066	NM_000964.3	438	gCC/gTT	9/9	0.37920876313624	3	FACETS	0.897	0.848	0.947	0.897	0.848	0.947	CLONAL	3	TRUE	0	0.37920876313624	3		386	613	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732922	74732923	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	530	438	0	ENST00000359995.5:c.320_321delinsTT	p.Pro107Leu	p.P107L	ENST00000359995	NM_001195427.1	107	cCC/cTT	1/3	0.37920876313624	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.37920876313624	3		438	1036	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390462	56390462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	219	316	0	ENST00000348428.3:c.1201C>T	p.Leu401Phe	p.L401F	ENST00000348428	NM_006785.3	401	Ctt/Ttt	10/17	0.37920876313624	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.37920876313624	2		316	567	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61305062	61305062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	306	382	0	ENST00000341074.5:c.1064C>T	p.Ser355Leu	p.S355L	ENST00000341074	NM_002974.2	355	tCa/tTa	8/8	0.37920876313624	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.37920876313624	2		382	754	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619335	1619336	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	201	584	1	ENST00000344749.5:c.1305_1306delinsAA	p.Gly436Ser	p.G436S	ENST00000344749	NM_001136139.2	435	ctGGgc/ctAAgc	15/19	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.37920876313624	2		585	991	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271687	15271687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	860	462	0	ENST00000263388.2:c.6752C>T	p.Ser2251Phe	p.S2251F	ENST00000263388	NM_000435.2	2251	tCc/tTc	33/33	0.37920876313624	5	FACETS	0.903	0.878	0.928	1	0.996	1	CLONAL	5	TRUE	1	0.37920876313624	5		462	1576	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271815	15271816	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	811	554	0	ENST00000263388.2:c.6623_6624delinsTT	p.Pro2208Leu	p.P2208L	ENST00000263388	NM_000435.2	2208	cCC/cTT	33/33	0.37920876313624	5	FACETS	1	0.992	1	1	0.992	1	CLONAL	4	TRUE	1	0.37920876313624	5		554	1586	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355317	15355317	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	330	261	0	ENST00000263377.2:c.2306C>T	p.Pro769Leu	p.P769L	ENST00000263377	NM_058243.2	769	cCt/cTt	13/20	0.37920876313624	5	FACETS	1	0.966	1	1	0.966	1	CLONAL	4	TRUE	1	0.37920876313624	5		261	672	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376296	225376296	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	188	247	0	ENST00000264414.4:c.658G>A	p.Glu220Lys	p.E220K	ENST00000264414	NM_003590.4	220	Gaa/Aaa	6/16	0.376612644780846	4	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	2	0.37920876313624	4		247	675	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660262	227660262	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	296	483	0	ENST00000305123.5:c.3193G>A	p.Gly1065Arg	p.G1065R	ENST00000305123	NM_005544.2	1065	Gga/Aga	1/2	0.376612644780846	4	FACETS	0.969	0.912	1	0.969	0.912	1	CLONAL	2	TRUE	2	0.37920876313624	4		483	1111	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29445671	29445671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	309	453	0	ENST00000544604.2:c.1502C>T	p.Pro501Leu	p.P501L	ENST00000544604	NM_001206998.1	501	cCg/cTg	8/9	0.376612644780846	4	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	2	0.37920876313624	4		453	1111	SUCCESS
ALB	213	MSKCC	GRCh37	4	74279161	74279161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	263	346	0	ENST00000295897.4:c.868G>A	p.Glu290Lys	p.E290K	ENST00000295897	NM_000477.5	290	Gaa/Aaa	8/15	0.37823074715005	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.37920876313624	2		346	693	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520738	176520738	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	113	287	0	ENST00000292408.4:c.1481C>G	p.Pro494Arg	p.P494R	ENST00000292408	NM_213647.1	494	cCt/cGt	11/18	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.37920876313624	2		287	506	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673133	30673133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	171	361	0	ENST00000376406.3:c.3827C>T	p.Ser1276Phe	p.S1276F	ENST00000376406	NM_014641.2	1276	tCc/tTc	10/15	0.368688342993753	3	FACETS	1	0.983	1	0.627	0.577	0.679	CLONAL	1	TRUE	1	0.37920876313624	3		361	855	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967956	93967956	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	122	318	0	ENST00000369303.4:c.1971A>T	p.Lys657Asn	p.K657N	ENST00000369303	NM_004440.3	657	aaA/aaT	11/17	1	2	FACETS	0.976	0.884	1	0.976	0.884	1	CLONAL	1	TRUE	1	0.37920876313624	2		318	659	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332073	81332074	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	91	284	0	ENST00000222390.5:c.2011-1_2011delinsAA		p.X671_splice	ENST00000222390	NM_000601.4	671		18/18	0.37920876313624	3	FACETS	0.958	0.852	1	0.479	0.426	0.536	CLONAL	1	TRUE	1	0.37920876313624	3		284	596	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397762	116397762	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	865	330	0	ENST00000397752.3:c.2036G>T	p.Gly679Val	p.G679V	ENST00000397752	NM_000245.2	679	gGa/gTa	8/21	0.37920876313624	10	FACETS	0.968	0.943	0.994			1	CLONAL	8	TRUE	NA	0.37920876313624	10		330	1482	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27109634	27109634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564028920	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	89	226	0	ENST00000380036.4:c.46C>T	p.Leu16Phe	p.L16F	ENST00000380036	NM_000459.3	16	Ctt/Ttt	1/23	0.37920876313624	1	FACETS	0.908	0.81	1	0.908	0.81	1	CLONAL	1	TRUE	0	0.37920876313624	1		226	419	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615609	100615609	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0064935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	254	352	0	ENST00000308731.7:c.723T>A	p.Tyr241Ter	p.Y241*	ENST00000308731	NM_000061.2	241	taT/taA	8/19	0.37823074715005	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.37920876313624	2		352	664	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0064937-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	109	355	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		355	406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0064937-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	143	363	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		363	625	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40860102	40860102	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0064937-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	119	268	0	ENST00000428826.2:c.1535-1G>T		p.X512_splice	ENST00000428826		512			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		268	601	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600505	10600505	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064937-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	206	392	0	ENST00000171111.5:c.1350G>T	p.Trp450Cys	p.W450C	ENST00000171111	NM_203500.1	450	tgG/tgT	4/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		392	681	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027133	49027133	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0064937-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	98	154	0	ENST00000267163.4:c.1700C>G	p.Ser567Ter	p.S567*	ENST00000267163	NM_000321.2	567	tCa/tGa	18/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		154	394	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332453	153332453	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0064937-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	47	261	0	ENST00000281708.4:c.501+2T>A		p.X167_splice	ENST00000281708	NM_033632.3	167			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		261	510	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43806069	43806069	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064937-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	108	290	0	ENST00000372470.3:c.865C>A	p.Leu289Met	p.L289M	ENST00000372470	NM_005373.2	289	Ctg/Atg	6/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		290	534	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844719	156844719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064937-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	268	502	0	ENST00000524377.1:c.1273G>A	p.Ala425Thr	p.A425T	ENST00000524377	NM_002529.3	425	Gcc/Acc	11/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		502	1129	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495334	56495334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064937-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	84	375	0	ENST00000267101.3:c.3524G>T	p.Gly1175Val	p.G1175V	ENST00000267101	NM_001982.3	1175	gGc/gTc	28/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		375	831	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30095732	30095732	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064937-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	40	174	0	ENST00000331968.5:c.1756G>A	p.Asp586Asn	p.D586N	ENST00000331968	NM_002742.2	586	Gat/Aat	12/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		174	391	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474102	29474102	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs370435082	NA	P-0064937-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	190	371	0	ENST00000389048.3:c.2073C>A	p.Ser691Arg	p.S691R	ENST00000389048	NM_004304.4	691	agC/agA	12/29	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		371	626	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730081	41730082	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0064937-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	107	348	1	ENST00000242208.4:c.447_448delinsTT	p.Val150Leu	p.V150L	ENST00000242208	NM_002192.2	149	gtGGtg/gtTTtg	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		349	904	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341716	8341716	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064937-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	87	310	0	ENST00000356435.5:c.4924A>T	p.Thr1642Ser	p.T1642S	ENST00000356435		1642	Aca/Tca	29/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		310	628	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349551	70349551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064937-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	55	365	0	ENST00000374080.3:c.3713C>T	p.Ser1238Leu	p.S1238L	ENST00000374080		1238	tCa/tTa	27/45	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		365	653	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064938-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	52	663	0				ENST00000310581	NM_198253.2	-/1132			0.829524566913279	3	FACETS	0.811	0.715	0.908	0.811	0.715	0.908	CLONAL	2	FALSE	1	0.822091253085309	3		663	110	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0064938-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	141	389	0	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	0.515167467238393	5	FACETS	1	0.976	1			1	CLONAL	3	FALSE	NA	0.822091253085309	5		389	234	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0064938-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	27	198	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	0.548031577101372	6	FACETS	0.905	0.725	1	0.302	0.241	0.369	CLONAL	1	FALSE	3	0.822091253085309	6		198	192	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064938-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	78	309	0	ENST00000335508.6:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000335508	NM_012433.2	902	Gaa/Aaa	18/25	1	2	FACETS	0.891	0.797	0.987	0.891	0.797	0.987	CLONAL	1	FALSE	1	0.822091253085309	2		309	213	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950110	44950110	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0064938-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	171	117	0	ENST00000377967.4:c.3878+1G>C		p.X1293_splice	ENST00000377967	NM_021140.2	1293			0.829524566913279	2	FACETS	1	0.982	1			1	CLONAL	2	FALSE	NA	0.822091253085309	2		117	201	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982400	201982401	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0064938-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	376	410	0	ENST00000359651.3:c.782_783dup	p.Glu262SerfsTer33	p.E262Sfs*33	ENST00000359651		260	tgt/tgTCt	6/8	0.822091253085309	7	FACETS	0.984	0.948	1			1	CLONAL	5	FALSE	NA	0.822091253085309	7		410	568	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093383	30093383	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064938-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	39	239	0	ENST00000331968.5:c.1880T>A	p.Leu627His	p.L627H	ENST00000331968	NM_002742.2	627	cTt/cAt	13/18	0.688428177996246	3	FACETS	0.598	0.499	0.705	0.299	0.249	0.353	SUBCLONAL	1	FALSE	1	0.822091253085309	3		239	224	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50774065	50774065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064938-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	113	413	0	ENST00000307179.4:c.1606G>A	p.Glu536Lys	p.E536K	ENST00000307179		536	Gaa/Aaa	11/20	0.387601239048608	4	FACETS	1	0.979	1	0.639	0.58	0.7	INDETERMINATE	1	FALSE	2	0.822091253085309	4		413	392	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924817	49924817	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064938-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	174	420	0	ENST00000296474.3:c.4126G>C	p.Glu1376Gln	p.E1376Q	ENST00000296474	NM_002447.2	1376	Gaa/Caa	20/20	0.746542175831907	6	FACETS	0.912	0.85	0.975	0.912	0.85	0.975	CLONAL	3	FALSE	3	0.822091253085309	6		420	409	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	250	663	0				ENST00000310581	NM_198253.2	-/1132			0.67781861550312	4	FACETS	0.975	0.928	1	0.975	0.928	1	CLONAL	3	TRUE	1	0.67781861550312	4		663	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0064939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	203	566	1	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.67781861550312	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.67781861550312	1		567	385	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872195	45872195	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	158	484	0	ENST00000391945.4:c.239T>C	p.Ile80Thr	p.I80T	ENST00000391945	NM_000400.3	80	aTt/aCt	4/23	1	2	FACETS	0.921	0.85	0.994	0.921	0.85	0.994	CLONAL	1	TRUE	1	0.67781861550312	2		484	506	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481696	56481696	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	312	455	0	ENST00000267101.3:c.731T>C	p.Phe244Ser	p.F244S	ENST00000267101	NM_001982.3	244	tTt/tCt	6/28	0.636137250596433	2	FACETS	0.957	0.918	0.995	0.957	0.918	0.995	CLONAL	2	TRUE	0	0.67781861550312	2		455	481	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047494	49047495	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	novel	NA	P-0064939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	242	234	0	ENST00000267163.4:c.2490-1_2490del		p.X830_splice	ENST00000267163	NM_000321.2	830			0.67781861550312	2	FACETS	0.957	0.913	1	0.957	0.913	1	CLONAL	2	TRUE	0	0.67781861550312	2		234	373	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128268597	128268597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	153	313	0	ENST00000265960.3:c.1058G>A	p.Arg353His	p.R353H	ENST00000265960	NM_001006617.1	353	cGc/cAc	8/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.67781861550312	2		313	382	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847271	68847274	+	frameshift_variant	Frame_Shift_Del	DEL	TGAC	TGAC	-	novel	NA	P-0064939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	174	432	0	ENST00000261769.5:c.1196_1199del	p.Thr399MetfsTer17	p.T399Mfs*17	ENST00000261769	NM_004360.3	398	gTGACt/gt	9/16	0.67781861550312	1	FACETS	0.995	0.933	1	0.995	0.933	1	CLONAL	1	TRUE	0	0.67781861550312	1		432	341	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821668	72821668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	260	479	0	ENST00000268489.5:c.10507C>T	p.His3503Tyr	p.H3503Y	ENST00000268489	NM_006885.3	3503	Cac/Tac	10/10	0.67781861550312	9	FACETS	1	0.962	1			1	CLONAL	2	TRUE	NA	0.67781861550312	9		479	1244	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828513	72828513	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1623	394	507	0	ENST00000268489.5:c.8068C>G	p.Gln2690Glu	p.Q2690E	ENST00000268489	NM_006885.3	2690	Cag/Gag	9/10	0.67781861550312	9	FACETS	0.972	0.92	1			1	CLONAL	2	TRUE	NA	0.67781861550312	9		507	2017	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719053	52719053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	173	397	0	ENST00000322088.6:c.829G>A	p.Glu277Lys	p.E277K	ENST00000322088	NM_014225.5	277	Gag/Aag	7/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.67781861550312	2		397	482	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000070	30000071	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	137	359	0	ENST00000338641.4:c.83_84insA	p.Met29HisfsTer20	p.M29Hfs*20	ENST00000338641	NM_000268.3	28	acc/acAc	1/16	0.67781861550312	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.67781861550312	1		359	257	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0064944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	354	682	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.611834036194639	2	FACETS	0.999	0.96	1	0.999	0.96	1	CLONAL	2	TRUE	0	0.611834036194639	2		682	579	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0064944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	384	520	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.58947192697535	5	FACETS	1	0.966	1	1	0.966	1	CLONAL	3	TRUE	2	0.611834036194639	5		520	793	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706977	117706977	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764959275	NA	P-0064944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	131	537	0	ENST00000368508.3:c.2173G>A	p.Asp725Asn	p.D725N	ENST00000368508	NM_002944.2	725	Gac/Aac	15/43	0.611834036194639	3	FACETS	0.908	0.826	0.993	0.454	0.413	0.497	CLONAL	1	TRUE	1	0.611834036194639	3		537	616	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259441	55259442	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0064944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	388	467	1	ENST00000275493.2:c.2499_2500delinsTT	p.Leu833_Val834delinsPheLeu	p.L833_V834delinsFL	ENST00000275493	NM_005228.3	833	ttGGtg/ttTTtg	21/28	0.58947192697535	5	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	2	0.611834036194639	5		468	783	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969072	93969072	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	107	509	0	ENST00000369303.4:c.1924G>T	p.Gly642Ter	p.G642*	ENST00000369303	NM_004440.3	642	Gga/Tga	10/17	0.611834036194639	3	FACETS	0.857	0.772	0.947	0.428	0.386	0.474	CLONAL	1	TRUE	1	0.611834036194639	3		509	533	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371842	55371842	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267607082	NA	P-0064944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	111	640	2	ENST00000297316.4:c.532G>A	p.Gly178Ser	p.G178S	ENST00000297316	NM_022454.3	178	Ggc/Agc	2/2	0.611834036194639	3	FACETS	0.963	0.87	1	0.482	0.435	0.53	CLONAL	1	TRUE	1	0.611834036194639	3		642	492	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65349140	65349140	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	231	519	0	ENST00000342505.4:c.25G>T	p.Asp9Tyr	p.D9Y	ENST00000342505	NM_002227.2	9	Gac/Tac	3/25	0.611834036194639	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.611834036194639	3		519	487	SUCCESS
CBL	867	MSKCC	GRCh37	11	119077263	119077263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1028757126	NA	P-0064944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1437	156	924	0	ENST00000264033.4:c.136C>T	p.His46Tyr	p.H46Y	ENST00000264033	NM_005188.3	46	Cac/Tac	1/16	0.611834036194639	7	FACETS	0.81	0.739	0.885	0.162	0.147	0.177	CLONAL	1	TRUE	2	0.611834036194639	7		924	1593	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435153	18435153	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	131	555	0	ENST00000266497.5:c.138G>C	p.Glu46Asp	p.E46D	ENST00000266497		46	gaG/gaC	1/31	0.611834036194639	2	FACETS	1	0.964	1	0.548	0.502	0.595	CLONAL	1	TRUE	0	0.611834036194639	2		555	391	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495067	56495067	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1451	206	742	0	ENST00000267101.3:c.3424C>G	p.Pro1142Ala	p.P1142A	ENST00000267101	NM_001982.3	1142	Cct/Gct	27/28	0.611834036194639	8	FACETS	1	0.978	1	0.192	0.177	0.208	CLONAL	1	TRUE	2	0.611834036194639	8		742	1657	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63973769	63973769	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	134	556	0	ENST00000398590.3:c.1130G>T	p.Gly377Val	p.G377V	ENST00000398590	NM_001177387.1	377	gGt/gTt	9/14	0.611834036194639	3	FACETS	0.917	0.835	1	0.458	0.417	0.501	CLONAL	1	TRUE	1	0.611834036194639	3		556	624	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538248	187538248	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs752588652	NA	P-0064944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	124	513	0	ENST00000441802.2:c.8986A>G	p.Ile2996Val	p.I2996V	ENST00000441802	NM_005245.3	2996	Atc/Gtc	11/27	0.524991941876226	3	FACETS	1	0.964	1	0.558	0.508	0.611	CLONAL	1	TRUE	1	0.611834036194639	3		513	474	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545627	106545628	+	missense_variant	Missense_Mutation	DNP	TG	TG	CT	novel	NA	P-0064944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	261	576	1	ENST00000359195.3:c.3104_3105delinsCT	p.Leu1035Pro	p.L1035P	ENST00000359195	NM_002649.2	1035	cTG/cCT	11/11	0.57415957270443	4	FACETS	0.95	0.894	1	0.95	0.894	1	CLONAL	2	TRUE	2	0.611834036194639	4		577	724	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128848609	128848610	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs754335556	NA	P-0064944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	114	535	0	ENST00000249373.3:c.1276_1277del	p.Leu426ValfsTer13	p.L426Vfs*13	ENST00000249373	NM_005631.4	425	aCT/a	7/12	0.57415957270443	4	FACETS	0.839	0.756	0.927	0.419	0.378	0.464	CLONAL	1	TRUE	2	0.611834036194639	4		535	716	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0064946-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	169	171	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.611821339338348	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.600074559276117	1		171	385	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0064946-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	78	527	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.563	0.496	0.634	0.563	0.496	0.634	SUBCLONAL	1	TRUE	1	0.600074559276117	2		527	462	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657652	37657652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064946-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	69	422	0	ENST00000447079.4:c.2569C>T	p.His857Tyr	p.H857Y	ENST00000447079	NM_015083.1	857	Cat/Tat	6/14	0.611821339338348	1	FACETS	0.958	0.855	1	0.958	0.855	1	CLONAL	1	TRUE	0	0.600074559276117	1		422	168	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729666	41729666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064946-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	147	662	0	ENST00000242208.4:c.863C>T	p.Ser288Leu	p.S288L	ENST00000242208	NM_002192.2	288	tCg/tTg	3/3	0.348036951593846	1	FACETS	0.884	0.816	0.953	0.884	0.816	0.953	INDETERMINATE	1	TRUE	0	0.600074559276117	1		662	388	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070558	67070558	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064946-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	179	436	0	ENST00000412916.2:c.182G>A	p.Gly61Glu	p.G61E	ENST00000412916		61	gGa/gAa	3/6	0.579582056383729	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.600074559276117	1		436	375	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850861	63850861	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064946-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	76	572	0	ENST00000279873.7:c.1639C>G	p.Leu547Val	p.L547V	ENST00000279873	NM_032199.2	547	Ctg/Gtg	10/10	1	2	FACETS	0.424	0.372	0.479	0.424	0.372	0.479	SUBCLONAL	1	TRUE	1	0.600074559276117	2		572	598	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43700244	43700244	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064951-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	44	521	0	ENST00000382044.4:c.5643G>C	p.Leu1881Phe	p.L1881F	ENST00000382044	NM_001141980.1	1881	ttG/ttC	27/28	0.171890018105813	3	FACETS	0.846	0.712	0.993	0.423	0.356	0.497	INDETERMINATE	1	TRUE	1	0.362559069674112	3		521	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0064955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	206	988	1	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.405856766605401	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.405856766605401	1		989	790	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711879	89711879	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	33	489	0	ENST00000371953.3:c.497T>G	p.Val166Gly	p.V166G	ENST00000371953	NM_000314.4	166	gTa/gGa	6/9	1	2	FACETS	0.372	0.303	0.45	0.372	0.303	0.45	SUBCLONAL	1	TRUE	1	0.405856766605401	2		489	437	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003849	57003849	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	164	910	0	ENST00000257254.3:c.630T>G	p.Phe210Leu	p.F210L	ENST00000257254		210	ttT/ttG	1/2	1	2	FACETS	0.934	0.858	1	0.934	0.858	1	CLONAL	1	TRUE	1	0.405856766605401	2		910	865	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608478	28608478	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	64	696	1	ENST00000241453.7:c.1664T>G	p.Ile555Ser	p.I555S	ENST00000241453	NM_004119.2	555	aTt/aGt	13/24	1	2	FACETS	0.463	0.4	0.531	0.463	0.4	0.531	SUBCLONAL	1	TRUE	1	0.405856766605401	2		697	681	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371795	45371795	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	90	714	0	ENST00000262160.6:c.1196A>G	p.Asn399Ser	p.N399S	ENST00000262160	NM_005901.5	399	aAt/aGt	10/11	1	2	FACETS	0.691	0.613	0.773	0.691	0.613	0.773	SUBCLONAL	1	TRUE	1	0.405856766605401	2		714	642	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566017	141566017	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	53	713	0	ENST00000220592.5:c.1247C>A	p.Pro416His	p.P416H	ENST00000220592	NM_012154.3	416	cCc/cAc	10/19	0.381556747672216	3	FACETS	0.353	0.299	0.411	0.176	0.149	0.206	SUBCLONAL	1	TRUE	1	0.405856766605401	3		713	891	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0064999-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	193	533	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.557048443450054	2		533	547	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428674	49428674	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064999-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	158	722	0	ENST00000301067.7:c.10276A>C	p.Lys3426Gln	p.K3426Q	ENST00000301067	NM_003482.3	3426	Aag/Cag	35/54	0.557048443450054	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.557048443450054	1		722	396	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679643	33679643	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064999-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	199	714	0	ENST00000308377.4:c.2438T>C	p.Val813Ala	p.V813A	ENST00000308377	NM_152270.3	813	gTc/gCc	5/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.557048443450054	2		714	632	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0065025-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	170	403	1	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		404	348	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200963	108200963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065025-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	143	436	0	ENST00000278616.4:c.7330G>A	p.Glu2444Lys	p.E2444K	ENST00000278616	NM_000051.3	2444	Gag/Aag	50/63	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		436	315	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843333	128843333	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065025-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	113	619	0	ENST00000249373.3:c.440G>C	p.Cys147Ser	p.C147S	ENST00000249373	NM_005631.4	147	tGc/tCc	2/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		619	454	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61324175	61324175	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065025-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	185	542	0	ENST00000283752.5:c.658C>T	p.His220Tyr	p.H220Y	ENST00000283752	NM_006919.2	220	Cat/Tat	7/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		542	461	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221092	5221092	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065025-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	225	677	0	ENST00000357368.4:c.3374del	p.Lys1125SerfsTer33	p.K1125Sfs*33	ENST00000357368	NM_002850.3	1125	aAg/ag	20/38	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		677	473	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300189	15300189	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065025-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	251	558	0	ENST00000263388.2:c.1087G>T	p.Asp363Tyr	p.D363Y	ENST00000263388	NM_000435.2	363	Gat/Tat	7/33	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		558	519	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212564	36212564	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065025-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	141	705	0	ENST00000222270.7:c.2315T>A	p.Leu772Gln	p.L772Q	ENST00000222270	NM_014727.1	772	cTg/cAg	3/37	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		705	921	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425188	47425194	+	frameshift_variant	Frame_Shift_Del	DEL	GACTATG	GACTATG	-	novel	NA	P-0065025-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	327	587	0	ENST00000404338.3:c.3256_3262del	p.Asp1086LeufsTer8	p.D1086Lfs*8	ENST00000404338	NM_004491.4	1086	GACTATGct/ct	1/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		587	576	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940133	49940133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065025-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	152	672	0	ENST00000296474.3:c.910C>T	p.Pro304Ser	p.P304S	ENST00000296474	NM_002447.2	304	Cca/Tca	1/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		672	769	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63965840	63965840	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065025-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	206	456	0	ENST00000398590.3:c.749G>C	p.Arg250Thr	p.R250T	ENST00000398590	NM_001177387.1	250	aGa/aCa	6/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		456	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0065027-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	159	386	0	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	0.282045948395044	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	3	TRUE	0	0.3	3		386	382	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795794	42795794	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065027-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	128	525	0	ENST00000575354.2:c.2786del	p.Pro929LeufsTer17	p.P929Lfs*17	ENST00000575354	NM_015125.3	928	gCc/gc	11/20	0.254018764868716	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.3	3		525	464	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526302	189526302	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866938979	NA	P-0065027-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	75	509	0	ENST00000264731.3:c.566C>T	p.Ser189Leu	p.S189L	ENST00000264731	NM_003722.4	189	tCg/tTg	4/14	0.3	3	FACETS	1	0.907	1	0.52	0.456	0.588	CLONAL	1	TRUE	1	0.3	3		509	553	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133009	30133009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760058972	NA	P-0065027-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	121	413	0	ENST00000331968.5:c.592G>A	p.Gly198Ser	p.G198S	ENST00000331968	NM_002742.2	198	Ggt/Agt	4/18	0.197922087008496	4	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	2	0.3	4		413	496	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057736	27057736	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065027-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	117	485	0	ENST00000324856.7:c.1444C>T	p.Gln482Ter	p.Q482*	ENST00000324856	NM_006015.4	482	Cag/Tag	3/20	0.209171975469091	2	FACETS	0.778	0.705	0.855	0.778	0.705	0.855	SUBCLONAL	2	TRUE	0	0.3	2		485	501	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141551	11141551	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065027-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	120	426	0	ENST00000358026.2:c.3528C>A	p.Ser1176Arg	p.S1176R	ENST00000358026	NM_001128849.1	1176	agC/agA	25/36	0.254018764868716	3	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	1	0.3	3		426	435	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065031-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	116	663	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.714	0.65	0.78	0.714	0.65	0.78	SUBCLONAL	1	TRUE	1	0.878752469826112	2		663	370	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0065031-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	194	476	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.229676562628474	4	FACETS	1	0.969	1	0.539	0.5	0.58	INDETERMINATE	1	TRUE	2	0.878752469826112	4		476	769	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0065031-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	202	501	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.869573822770809	2	FACETS	0.894	0.837	0.953	0.447	0.418	0.477	CLONAL	1	TRUE	0	0.878752469826112	2		501	514	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0065031-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	34	303	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.200784631397587	3	FACETS	0.891	0.743	1	0.446	0.371	0.525	INDETERMINATE	1	TRUE	1	0.878752469826112	3		303	125	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520000	NA	P-0065031-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	322	565	0	ENST00000269305.4:c.452C>A	p.Pro151His	p.P151H	ENST00000269305	NM_001126112.2	151	cCc/cAc	5/11	0.869573822770809	2	FACETS	1	0.991	1	0.583	0.556	0.611	CLONAL	1	TRUE	0	0.878752469826112	2		565	628	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953760	48953760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913302	NA	P-0065031-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	38	167	0	ENST00000267163.4:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000267163	NM_000321.2	455	Cga/Tga	14/27	0.878752469826112	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.878752469826112	1		167	46	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777933	3777933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1048314482	NA	P-0065031-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	218	692	0	ENST00000262367.5:c.7115C>T	p.Ser2372Leu	p.S2372L	ENST00000262367	NM_004380.2	2372	tCg/tTg	31/31	0.240697356733841	2	FACETS	0.708	0.661	0.756	0.354	0.33	0.378	INDETERMINATE	1	TRUE	0	0.878752469826112	2		692	701	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477853	140477853	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs180177036	NA	P-0065031-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	43	375	0	ENST00000288602.6:c.1455G>C	p.Leu485Phe	p.L485F	ENST00000288602	NM_004333.4	485	ttG/ttC	12/18	0.136859221259069	4	FACETS	1	0.852	1	0.502	0.426	0.584	INDETERMINATE	1	TRUE	2	0.878752469826112	4		375	183	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498472	89498472	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065031-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	60	440	0	ENST00000336596.2:c.2446del	p.Glu816ArgfsTer2	p.E816Rfs*2	ENST00000336596	NM_005233.5	815	tGg/tg	14/17	1	2	FACETS	0.581	0.507	0.66	0.581	0.507	0.66	SUBCLONAL	1	TRUE	1	0.878752469826112	2		440	235	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945109	44945109	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0065031-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	71	150	0	ENST00000377967.4:c.3434-1G>A		p.X1145_splice	ENST00000377967	NM_021140.2	1145			0.420477286830041	2	FACETS	1	0.972	1			1	INDETERMINATE	2	TRUE	NA	0.878752469826112	2		150	78	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786795	3786795	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065031-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	179	403	0	ENST00000262367.5:c.4416G>T	p.Trp1472Cys	p.W1472C	ENST00000262367	NM_004380.2	1472	tgG/tgT	27/31	0.240697356733841	2	FACETS	1	0.99	1	0.647	0.609	0.684	INDETERMINATE	1	TRUE	0	0.878752469826112	2		403	315	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752940	42752940	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065031-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	281	634	0	ENST00000222329.4:c.1324G>C	p.Asp442His	p.D442H	ENST00000222329	NM_006494.2	442	Gac/Cac	4/4	0.229676562628474	4	FACETS	0.952	0.902	1	0.952	0.902	1	INDETERMINATE	2	TRUE	2	0.878752469826112	4		634	631	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813099	76813099	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065031-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	11	152	0	ENST00000373344.5:c.6522G>C	p.Lys2174Asn	p.K2174N	ENST00000373344	NM_000489.3	2174	aaG/aaC	30/35	0.420477286830041	2	FACETS	0.302	0.211	0.411			1	INDETERMINATE	1	TRUE	NA	0.878752469826112	2		152	83	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0065032-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	381	363	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.349950632078763	3	FACETS	1	0.991	1	0.76	0.726	0.795	CLONAL	2	TRUE	0	0.482224843504774	3		363	860	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430515	181430515	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065032-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	225	354	0	ENST00000325404.1:c.367G>A	p.Asp123Asn	p.D123N	ENST00000325404	NM_003106.3	123	Gat/Aat	1/1	0.277689755655907	5	FACETS	0.893	0.833	0.956	0.596	0.555	0.637	INDETERMINATE	2	TRUE	2	0.482224843504774	5		354	900	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435288	110435288	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065032-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	140	432	0	ENST00000375856.3:c.3113C>T	p.Pro1038Leu	p.P1038L	ENST00000375856	NM_003749.2	1038	cCg/cTg	1/2	0.420963852666048	4	FACETS	0.772	0.701	0.846	0.257	0.233	0.282	SUBCLONAL	1	TRUE	1	0.482224843504774	4		432	1115	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476286	88476286	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065032-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	100	296	0	ENST00000360948.2:c.1846G>T	p.Val616Phe	p.V616F	ENST00000360948	NM_001012338.2	616	Gtc/Ttc	15/19	1	2	FACETS	0.739	0.662	0.821	0.739	0.662	0.821	SUBCLONAL	1	TRUE	1	0.482224843504774	2		296	561	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150921660	150921660	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065032-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	277	307	0	ENST00000271640.5:c.1330C>T	p.Gln444Ter	p.Q444*	ENST00000271640	NM_001145415.1	444	Cag/Tag	11/22	0.33526205198699	3	FACETS	0.877	0.827	0.928	0.877	0.827	0.928	CLONAL	2	TRUE	1	0.482224843504774	3		307	813	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	459820	459820	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065032-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	89	296	0	ENST00000399788.2:c.1275G>T	p.Lys425Asn	p.K425N	ENST00000399788	NM_001042603.1	425	aaG/aaT	10/28	0.482224843504774	4	FACETS	0.642	0.568	0.721	0.214	0.189	0.241	SUBCLONAL	1	TRUE	1	0.482224843504774	4		296	852	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858489	9858489	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065032-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	118	322	0	ENST00000330684.3:c.2912A>G	p.Gln971Arg	p.Q971R	ENST00000330684	NM_001134407.1	971	cAg/cGg	13/13	0.349950632078763	3	FACETS	0.859	0.776	0.947	0.286	0.258	0.316	CLONAL	1	TRUE	0	0.482224843504774	3		322	707	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653214	29653214	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0065032-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	368	334	0	ENST00000356175.3:c.5149A>T	p.Lys1717Ter	p.K1717*	ENST00000356175	NM_000267.3	1717	Aag/Tag	36/57	0.482224843504774	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.482224843504774	3		334	931	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29445216	29445217	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0065032-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	220	368	1	ENST00000544604.2:c.1047_1048delinsTT	p.Glu350Ter	p.E350*	ENST00000544604	NM_001206998.1	349	gtGGag/gtTTag	8/9	0.36333679924544	2	FACETS	1	0.991	1	0.687	0.642	0.733	CLONAL	1	TRUE	0	0.482224843504774	2		369	664	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436415	52436415	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065032-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	249	330	0	ENST00000460680.1:c.2079G>T	p.Glu693Asp	p.E693D	ENST00000460680	NM_004656.3	693	gaG/gaT	17/17	0.457072835091761	3	FACETS	0.903	0.848	0.958	0.903	0.848	0.958	CLONAL	2	TRUE	1	0.482224843504774	3		330	710	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204938	128204938	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065032-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	219	353	0	ENST00000341105.2:c.503C>G	p.Ser168Cys	p.S168C	ENST00000341105	NM_032638.4	168	tCc/tGc	3/6	0.457072835091761	3	FACETS	1	0.991	1	0.727	0.678	0.777	CLONAL	1	TRUE	1	0.482224843504774	3		353	775	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182681702	182681702	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065032-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	192	233	0	ENST00000292782.4:c.356A>T	p.Lys119Ile	p.K119I	ENST00000292782	NM_020640.2	119	aAa/aTa	3/7	0.277689755655907	5	FACETS	0.965	0.896	1	0.643	0.597	0.691	INDETERMINATE	2	TRUE	2	0.482224843504774	5		233	711	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505338	186505338	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065032-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	216	278	0	ENST00000323963.5:c.964G>T	p.Gly322Trp	p.G322W	ENST00000323963		322	Ggg/Tgg	9/11	0.277689755655907	5	FACETS	0.99	0.923	1	0.66	0.615	0.706	INDETERMINATE	2	TRUE	2	0.482224843504774	5		278	780	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673405	30673405	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065032-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1290	393	445	0	ENST00000376406.3:c.3555G>T	p.Gln1185His	p.Q1185H	ENST00000376406	NM_014641.2	1185	caG/caT	10/15	0.482224843504774	5	FACETS	0.835	0.791	0.879	0.556	0.527	0.586	CLONAL	2	TRUE	2	0.482224843504774	5		445	1683	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964481	93964481	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065032-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	227	282	0	ENST00000369303.4:c.2416G>T	p.Glu806Ter	p.E806*	ENST00000369303	NM_004440.3	806	Gaa/Taa	14/17	0.321653262184457	3	FACETS	1	0.961	1	0.687	0.645	0.729	CLONAL	2	TRUE	0	0.482224843504774	3		282	567	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964515	93964515	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0065032-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	174	210	0	ENST00000369303.4:c.2383-1G>T		p.X795_splice	ENST00000369303	NM_004440.3	795			0.321653262184457	3	FACETS	1	0.934	1	0.669	0.623	0.717	CLONAL	2	TRUE	0	0.482224843504774	3		210	446	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976731	90976731	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1280333137	NA	P-0065032-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	113	218	0	ENST00000265433.3:c.901G>C	p.Gly301Arg	p.G301R	ENST00000265433	NM_002485.4	301	Ggt/Cgt	8/16	0.33276476882997	4	FACETS	0.817	0.741	0.897	0.817	0.741	0.897	CLONAL	2	TRUE	2	0.482224843504774	4		218	425	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760526	133760526	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065032-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	132	322	0	ENST00000318560.5:c.2849A>T	p.Gln950Leu	p.Q950L	ENST00000318560	NM_005157.4	950	cAg/cTg	11/11	0.482224843504774	4	FACETS	0.816	0.739	0.896	0.204	0.184	0.224	CLONAL	1	TRUE	0	0.482224843504774	4		322	995	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426661	47426661	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065032-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	122	371	0	ENST00000377045.4:c.906C>A	p.Tyr302Ter	p.Y302*	ENST00000377045	NM_001654.4	302	taC/taA	10/16	NA	2	FACETS	0.705	0.638	0.775			1	INDETERMINATE	1	TRUE	NA	0.482224843504774	2		371	718	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939018	76939022	+	frameshift_variant	Frame_Shift_Del	DEL	TTTGA	TTTGA	-	novel	NA	P-0065032-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	147	290	0	ENST00000373344.5:c.1726_1730del	p.Ser576AsnfsTer4	p.S576Nfs*4	ENST00000373344	NM_000489.3	576	TCAAAa/a	9/35	0.138025868226312	3	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.482224843504774	3		290	521	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32903612	32903612	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507873	NA	P-0065035-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	23	235	0	ENST00000380152.3:c.664C>T	p.Pro222Ser	p.P222S	ENST00000380152		222	Cct/Tct	8/27	1	2	FACETS	0.877	0.688	1	0.877	0.688	1	CLONAL	1	TRUE	1	0.277600352766962	2		235	189	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097665	27097665	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0065035-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	89	502	0	ENST00000324856.7:c.3254C>G	p.Ser1085Ter	p.S1085*	ENST00000324856	NM_006015.4	1085	tCa/tGa	12/20	0.277600352766962	1	FACETS	0.884	0.784	0.989	0.884	0.784	0.989	CLONAL	1	TRUE	0	0.277600352766962	1		502	625	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984368	201984368	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065035-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	103	446	0	ENST00000359651.3:c.1033G>C	p.Val345Leu	p.V345L	ENST00000359651		345	Gtg/Ctg	8/8	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.277600352766962	2		446	620	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041376	47041376	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065035-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	90	569	0	ENST00000377604.3:c.1720T>G	p.Tyr574Asp	p.Y574D	ENST00000377604	NM_001204468.1	574	Tac/Gac	16/24	1	2	FACETS	0.921	0.817	1	0.921	0.817	1	CLONAL	1	TRUE	1	0.277600352766962	2		569	704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	118	510	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.242319202054705	1	FACETS	0.894	0.806	0.988	0.894	0.806	0.988	CLONAL	1	TRUE	0	0.248056099007432	1		510	932	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0065076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	171	355	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.248056099007432	2	FACETS	0.912	0.841	0.986	0.912	0.841	0.986	CLONAL	2	TRUE	0	0.248056099007432	2		355	756	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77961420	77961420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747769924	NA	P-0065076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	54	348	0	ENST00000361507.4:c.403G>A	p.Gly135Ser	p.G135S	ENST00000361507	NM_080491.2	135	Ggt/Agt	3/10	1	2	FACETS	0.455	0.387	0.53	0.455	0.387	0.53	SUBCLONAL	1	TRUE	1	0.248056099007432	2		348	956	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517937	187517937	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	165	493	0	ENST00000441802.2:c.12757C>G	p.Pro4253Ala	p.P4253A	ENST00000441802	NM_005245.3	4253	Cct/Gct	25/27	0.243334589699588	3	FACETS	1	0.98	1	0.609	0.558	0.663	CLONAL	1	TRUE	1	0.248056099007432	3		493	1227	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31472174	31472174	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	222	351	0	ENST00000344624.3:c.2237G>T	p.Gly746Val	p.G746V	ENST00000344624		746	gGg/gTg	14/33	0.248056099007432	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.248056099007432	3		351	975	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959335	38959335	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0065076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	82	301	0	ENST00000357387.3:c.2140A>T	p.Arg714Ter	p.R714*	ENST00000357387	NM_152756.3	714	Aga/Tga	22/38	0.248056099007432	3	FACETS	0.86	0.757	0.971	0.43	0.378	0.486	CLONAL	1	TRUE	1	0.248056099007432	3		301	864	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637795	176637795	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	117	410	0	ENST00000439151.2:c.2395G>T	p.Val799Phe	p.V799F	ENST00000439151	NM_022455.4	799	Gtt/Ttt	5/23	1	2	FACETS	0.93	0.837	1	0.93	0.837	1	CLONAL	1	TRUE	1	0.248056099007432	2		410	1014	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509514	106509514	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	146	430	0	ENST00000359195.3:c.1508C>A	p.Thr503Lys	p.T503K	ENST00000359195	NM_002649.2	503	aCg/aAg	2/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.248056099007432	2		430	1057	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255388	16255388	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	182	471	0	ENST00000375759.3:c.2653G>C	p.Glu885Gln	p.E885Q	ENST00000375759	NM_015001.2	885	Gag/Cag	11/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.564656790110785	2		471	604	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193181537	193181539	+	inframe_deletion	In_Frame_Del	DEL	ATC	ATC	-	novel	NA	P-0065080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	23	375	0	ENST00000367435.3:c.1086_1088del	p.Ile364del	p.I364del	ENST00000367435	NM_024529.4	362	ATC/-	13/17	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.564656790110785	2		375	76	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741510	17741510	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs767856910	NA	P-0065080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	523	490	0	ENST00000250003.3:c.181G>C	p.Glu61Gln	p.E61Q	ENST00000250003	NM_002478.4	61	Gag/Cag	1/3	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.564656790110785	2		490	1723	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003536	57003536	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	G	G	C	rs137997556	NA	P-0065080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1401	512	546	0	ENST00000257254.3:c.943C>G	p.Arg315Gly	p.R315G	ENST00000257254		315	Cgc/Ggc	1/2	1	2	FACETS	0.948	0.906	0.991	0.948	0.906	0.991	CLONAL	1	TRUE	1	0.564656790110785	2		546	1913	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941459	71941459	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	457	548	0	ENST00000298229.2:c.1144G>C	p.Glu382Gln	p.E382Q	ENST00000298229	NM_001567.3	382	Gag/Cag	10/28	0.564656790110785	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.564656790110785	1		548	1142	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434348	121434348	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	395	470	0	ENST00000257555.6:c.1112C>T	p.Ser371Leu	p.S371L	ENST00000257555		371	tCa/tTa	6/10	1	2	FACETS	0.969	0.92	1	0.969	0.92	1	CLONAL	1	TRUE	1	0.564656790110785	2		470	1444	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202290	133202290	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1290	516	489	0	ENST00000320574.5:c.6598G>C	p.Glu2200Gln	p.E2200Q	ENST00000320574	NM_006231.2	2200	Gag/Cag	47/49	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.564656790110785	2		489	1806	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937001	48937005	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAA	CAGAA	-	rs1566192530	NA	P-0065080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	74	334	0	ENST00000267163.4:c.772_776del	p.Asn258GlufsTer11	p.N258Efs*11	ENST00000267163	NM_000321.2	257	CAGAAc/c	8/27	0.564656790110785	1	FACETS	0.918	0.818	1	0.918	0.818	1	CLONAL	1	TRUE	0	0.564656790110785	1		334	205	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121829	2121829	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs991714565	NA	P-0065080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1489	411	485	0	ENST00000219476.3:c.1991C>T	p.Ser664Phe	p.S664F	ENST00000219476	NM_000548.3	664	tCt/tTt	19/42	0.564656790110785	3	FACETS	0.983	0.932	1	0.491	0.466	0.517	CLONAL	1	TRUE	1	0.564656790110785	3		485	1900	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519986	NA	P-0065080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	423	472	0	ENST00000269305.4:c.809T>G	p.Phe270Cys	p.F270C	ENST00000269305	NM_001126112.2	270	tTt/tGt	8/11	0.564656790110785	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.564656790110785	1		472	948	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011149	12011149	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	14	328	0	ENST00000353533.5:c.556G>C	p.Asp186His	p.D186H	ENST00000353533	NM_003010.3	186	Gat/Cat	5/11	0.564656790110785	1	FACETS	0.809	0.609	1	0.809	0.609	1	CLONAL	1	TRUE	0	0.564656790110785	1		328	44	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011197	12011197	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	18	283	0	ENST00000353533.5:c.604G>C	p.Glu202Gln	p.E202Q	ENST00000353533	NM_003010.3	202	Gaa/Caa	5/11	0.564656790110785	1	FACETS	0.995	0.786	1	0.995	0.786	1	CLONAL	1	TRUE	0	0.564656790110785	1		283	46	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6227114	6227114	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0065080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	469	446	0	ENST00000252674.7:c.421-1G>C		p.X141_splice	ENST00000252674	NM_005934.3	141			1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.564656790110785	2		446	1534	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223013	36223013	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1714	739	653	0	ENST00000222270.7:c.5642C>G	p.Ser1881Cys	p.S1881C	ENST00000222270	NM_014727.1	1881	tCc/tGc	27/37	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.564656790110785	2		653	2453	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389228	31389228	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	331	362	0	ENST00000328111.2:c.2141T>G	p.Leu714Arg	p.L714R	ENST00000328111	NM_006892.3	714	cTg/cGg	19/23	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.564656790110785	2		362	989	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46266471	46266471	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0065080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	22	412	0	ENST00000371998.3:c.2456C>G	p.Ser819Ter	p.S819*	ENST00000371998		819	tCa/tGa	13/23	1	2	FACETS	0.634	0.498	0.786	0.634	0.498	0.786	SUBCLONAL	1	TRUE	1	0.564656790110785	2		412	123	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504433	186504433	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	16	323	0	ENST00000323963.5:c.770A>G	p.Glu257Gly	p.E257G	ENST00000323963		257	gAg/gGg	7/11	0.532379676359409	4	FACETS	0.629	0.468	0.818	0.314	0.234	0.409	SUBCLONAL	1	TRUE	2	0.564656790110785	4		323	141	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146495	55146495	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	39	365	0	ENST00000257290.5:c.2169A>C	p.Leu723Phe	p.L723F	ENST00000257290	NM_006206.4	723	ttA/ttC	16/23	0.564656790110785	3	FACETS	0.813	0.68	0.958	0.406	0.34	0.479	CLONAL	1	TRUE	1	0.564656790110785	3		365	218	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971001	55971001	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	426	398	1	ENST00000263923.4:c.1796C>A	p.Pro599His	p.P599H	ENST00000263923	NM_002253.2	599	cCc/cAc	13/30	0.564656790110785	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.564656790110785	3		399	910	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144359469	144359469	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	81	417	0	ENST00000262995.4:c.911C>T	p.Ser304Phe	p.S304F	ENST00000262995	NM_207123.2	304	tCt/tTt	4/11	0.564656790110785	1	FACETS	0.919	0.824	1	0.919	0.824	1	CLONAL	1	TRUE	0	0.564656790110785	1		417	224	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144359510	144359510	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	120	429	1	ENST00000262995.4:c.952C>T	p.Gln318Ter	p.Q318*	ENST00000262995	NM_207123.2	318	Cag/Tag	4/11	0.564656790110785	1	FACETS	0.965	0.884	1	0.965	0.884	1	CLONAL	1	TRUE	0	0.564656790110785	1		430	316	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538277	187538277	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	23	388	0	ENST00000441802.2:c.8957G>T	p.Arg2986Met	p.R2986M	ENST00000441802	NM_005245.3	2986	aGg/aTg	11/27	0.564656790110785	1	FACETS	0.65	0.518	0.794	0.65	0.518	0.794	SUBCLONAL	1	TRUE	0	0.564656790110785	1		388	90	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80037344	80037344	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	22	308	0	ENST00000265081.6:c.1631del	p.Asn544IlefsTer11	p.N544Ifs*11	ENST00000265081	NM_002439.4	544	Aat/at	11/24	1	2	FACETS	0.847	0.671	1	0.847	0.671	1	CLONAL	1	TRUE	1	0.564656790110785	2		308	92	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971130	13971130	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs541367225	NA	P-0065080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	256	406	0	ENST00000405192.2:c.799T>G	p.Ser267Ala	p.S267A	ENST00000405192	NM_001163147.1	267	Tca/Gca	8/12	0.564656790110785	3	FACETS	1	0.984	1	0.572	0.535	0.609	CLONAL	1	TRUE	1	0.564656790110785	3		406	1017	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760036	133760036	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs770760322	NA	P-0065080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	356	443	0	ENST00000318560.5:c.2359G>T	p.Val787Leu	p.V787L	ENST00000318560	NM_005157.4	787	Gtg/Ttg	11/11	1	2	FACETS	0.986	0.934	1	0.986	0.934	1	CLONAL	1	TRUE	1	0.564656790110785	2		443	1279	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399257	139399257	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1264	470	498	0	ENST00000277541.6:c.4886del	p.His1629ProfsTer20	p.H1629Pfs*20	ENST00000277541	NM_017617.3	1629	cAc/cc	26/34	1	2	FACETS	0.96	0.915	1	0.96	0.915	1	CLONAL	1	TRUE	1	0.564656790110785	2		498	1734	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412204	139412204	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1448146225	NA	P-0065081-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	106	450	0	ENST00000277541.6:c.1441G>A	p.Gly481Ser	p.G481S	ENST00000277541	NM_017617.3	481	Ggc/Agc	8/34	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.31	2		450	590	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86648999	86648999	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs975191415	NA	P-0065081-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	49	215	0	ENST00000274376.6:c.1279C>T	p.Arg427Ter	p.R427*	ENST00000274376	NM_002890.2	427	Cga/Tga	9/25	0.303284819783964	1	FACETS	0.873	0.744	1	0.873	0.744	1	CLONAL	1	TRUE	0	0.31	1		215	306	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679216	88679216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs187007070	NA	P-0065081-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	166	402	0	ENST00000360948.2:c.821C>T	p.Thr274Met	p.T274M	ENST00000360948	NM_001012338.2	274	aCg/aTg	8/19	0.303284819783964	2	FACETS	0.961	0.888	1	0.961	0.888	1	CLONAL	2	TRUE	0	0.31	2		402	557	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098956	178098956	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065081-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	135	361	0	ENST00000397062.3:c.89T>G	p.Leu30Arg	p.L30R	ENST00000397062	NM_006164.4	30	cTt/cGt	2/5	0.303284819783964	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.31	1		361	598	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1952883	1952883	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065081-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	112	426	0	ENST00000382891.5:c.1966A>G	p.Lys656Glu	p.K656E	ENST00000382891	NM_133335.3	656	Aaa/Gaa	10/22	0.303284819783964	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.31	1		426	578	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372780	81372780	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065081-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	74	349	0	ENST00000222390.5:c.754G>T	p.Asp252Tyr	p.D252Y	ENST00000222390	NM_000601.4	252	Gac/Tac	7/18	1	2	FACETS	0.915	0.802	1	0.915	0.802	1	CLONAL	1	TRUE	1	0.31	2		349	522	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937565	17937565	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065081-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	93	427	0	ENST00000458235.1:c.3362T>C	p.Leu1121Pro	p.L1121P	ENST00000458235	NM_000215.3	1121	cTg/cCg	24/24	1	2	FACETS	0.954	0.849	1	0.954	0.849	1	CLONAL	1	TRUE	1	0.31	2		427	629	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144390287	144390287	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065081-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	148	400	0	ENST00000262995.4:c.2120G>A	p.Trp707Ter	p.W707*	ENST00000262995	NM_207123.2	707	tGg/tAg	11/11	0.303284819783964	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.31	1		400	626	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849975	151849975	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065081-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	107	478	0	ENST00000262189.6:c.12341A>G	p.Glu4114Gly	p.E4114G	ENST00000262189	NM_170606.2	4114	gAg/gGg	49/59	1	2	FACETS	0.916	0.821	1	0.916	0.821	1	CLONAL	1	TRUE	1	0.31	2		478	754	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934574	NA	P-0065097-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	164	289	0	ENST00000269305.4:c.844C>G	p.Arg282Gly	p.R282G	ENST00000269305	NM_001126112.2	282	Cgg/Ggg	8/11	0.237887778274506	3	FACETS	1	0.945	1	1	0.945	1	CLONAL	3	TRUE	0	0.237887778274506	3		289	501	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864218	57864218	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065097-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	79	474	3	ENST00000228682.2:c.1700del	p.Pro567LeufsTer46	p.P567Lfs*46	ENST00000228682	NM_005269.2	565	ttC/tt	12/12	0.237887778274506	3	FACETS	1	0.961	1	0.612	0.539	0.691	CLONAL	1	TRUE	1	0.237887778274506	3		477	607	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035300	42035301	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0065097-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	129	351	0	ENST00000219905.7:c.5142_5143del	p.Ser1715IlefsTer13	p.S1715Ifs*13	ENST00000219905	NM_001164273.1	1714	acTTca/acca	15/24	0.237887778274506	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.237887778274506	2		351	449	SUCCESS
ALK	238	MSKCC	GRCh37	2	29430037	29430037	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065097-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	38	255	0	ENST00000389048.3:c.3938G>A	p.Trp1313Ter	p.W1313*	ENST00000389048	NM_004304.4	1313	tGg/tAg	26/29	0.219351912615105	4	FACETS	0.885	0.732	1	0.442	0.366	0.528	CLONAL	1	TRUE	2	0.237887778274506	4		255	447	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14028665	14028665	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065097-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	35	207	0	ENST00000405192.2:c.13T>A	p.Tyr5Asn	p.Y5N	ENST00000405192	NM_001163147.1	5	Tat/Aat	2/12	1	2	FACETS	0.873	0.717	1	0.873	0.717	1	CLONAL	1	TRUE	1	0.237887778274506	2		207	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0065098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	69	171	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	1	2	FACETS	0.821	0.716	0.933	0.821	0.716	0.933	CLONAL	1	TRUE	1	0.341140613496651	2		171	493	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0065098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	16	80	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.727	0.542	0.943	0.727	0.542	0.943	CLONAL	1	TRUE	1	0.341140613496651	2		80	129	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0065098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	19	112	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	0.379	0.287	0.486	0.379	0.287	0.486	SUBCLONAL	1	TRUE	1	0.341140613496651	2		112	294	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248998	55248999	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCAGCG	rs727504263	NA	P-0065098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	123	208	0	ENST00000275493.2:c.2300_2308dup	p.Ala767_Val769dup	p.A767_V769dup	ENST00000275493	NM_005228.3	767	atg/aTGGCCAGCGtg	20/28	0.334815536376782	3	FACETS	0.874	0.795	0.956	0.874	0.795	0.956	CLONAL	2	TRUE	1	0.341140613496651	3		208	483	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065115-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	534	663	0				ENST00000310581	NM_198253.2	-/1132			0.46364660839787	4	FACETS	1	0.979	1	0.762	0.737	0.788	CLONAL	3	TRUE	0	0.630100999271134	4		663	906	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0065115-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	511	463	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.630100999271134	2	FACETS	0.981	0.948	1	0.981	0.948	1	CLONAL	2	TRUE	0	0.630100999271134	2		463	827	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941720	48941720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065115-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	75	245	0	ENST00000267163.4:c.1030C>T	p.Gln344Ter	p.Q344*	ENST00000267163	NM_000321.2	344	Cag/Tag	10/27	0.630100999271134	2	FACETS	0.815	0.738	0.893	0.815	0.738	0.893	CLONAL	2	TRUE	0	0.630100999271134	2		245	146	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216590	108216590	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065115-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	182	421	0	ENST00000278616.4:c.8539G>C	p.Glu2847Gln	p.E2847Q	ENST00000278616	NM_000051.3	2847	Gag/Cag	58/63	1	2	FACETS	0.977	0.907	1	0.977	0.907	1	CLONAL	1	TRUE	1	0.630100999271134	2		421	591	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383227	31383227	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148132847	NA	P-0065115-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	248	584	1	ENST00000328111.2:c.1139G>A	p.Arg380Gln	p.R380Q	ENST00000328111	NM_006892.3	380	cGa/cAa	11/23	1	2	FACETS	0.917	0.86	0.976	0.917	0.86	0.976	CLONAL	1	TRUE	1	0.630100999271134	2		585	858	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213594	36213594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201585209	NA	P-0065115-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	114	646	0	ENST00000222270.7:c.2696G>A	p.Arg899Gln	p.R899Q	ENST00000222270	NM_014727.1	899	cGg/cAg	5/37	1	2	FACETS	0.378	0.34	0.419	0.378	0.34	0.419	SUBCLONAL	1	TRUE	1	0.630100999271134	2		646	957	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860081	57860081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065115-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	284	637	0	ENST00000228682.2:c.821G>A	p.Gly274Asp	p.G274D	ENST00000228682	NM_005269.2	274	gGc/gAc	8/12	1	2	FACETS	0.985	0.928	1	0.985	0.928	1	CLONAL	1	TRUE	1	0.630100999271134	2		637	915	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984018	7984018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065115-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	579	631	0	ENST00000319144.4:c.608C>T	p.Ser203Phe	p.S203F	ENST00000319144	NM_001139.2	203	tCc/tTc	5/15	0.630100999271134	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.630100999271134	2		631	914	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512323	38512323	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065115-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	244	498	0	ENST00000254066.5:c.1234G>A	p.Glu412Lys	p.E412K	ENST00000254066	NM_000964.3	412	Gaa/Aaa	9/9	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.630100999271134	2		498	703	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271758	18271758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065115-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	127	708	0	ENST00000222254.8:c.445G>A	p.Glu149Lys	p.E149K	ENST00000222254	NM_005027.3	149	Gag/Aag	4/16	0.390355597631412	1	FACETS	0.347	0.314	0.382	0.347	0.314	0.382	SUBCLONAL	1	TRUE	0	0.630100999271134	1		708	795	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531892	41531892	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065115-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	158	403	0	ENST00000263253.7:c.1604C>A	p.Ser535Ter	p.S535*	ENST00000263253	NM_001429.3	535	tCa/tAa	7/31	0.630100999271134	1	FACETS	0.909	0.844	0.975	0.909	0.844	0.975	CLONAL	1	TRUE	0	0.630100999271134	1		403	378	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176662925	176662925	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065115-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	186	473	0	ENST00000439151.2:c.3900G>C	p.Lys1300Asn	p.K1300N	ENST00000439151	NM_022455.4	1300	aaG/aaC	6/23	1	2	FACETS	0.948	0.88	1	0.948	0.88	1	CLONAL	1	TRUE	1	0.630100999271134	2		473	623	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374308	15374308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182685268	NA	P-0065115-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	125	549	0	ENST00000263377.2:c.1264G>A	p.Val422Ile	p.V422I	ENST00000263377	NM_058243.2	422	Gtc/Atc	7/20	0.390355597631412	1	FACETS	0.354	0.321	0.39	0.354	0.321	0.39	SUBCLONAL	1	TRUE	0	0.630100999271134	1		549	767	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0065117-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	9	286	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.085	0.055	0.122	0.085	0.055	0.122	SUBCLONAL	1	TRUE	1	0.686199603821552	2		286	310	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0065117-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	18	355	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.169	0.127	0.218	0.169	0.127	0.218	SUBCLONAL	1	TRUE	1	0.686199603821552	2		355	311	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0065117-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	94	299	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.996	0.899	1	0.996	0.899	1	CLONAL	1	TRUE	1	0.686199603821552	2		299	275	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591085	67591085	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519839	NA	P-0065117-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	10	511	0	ENST00000274335.5:c.1678G>T	p.Asp560Tyr	p.D560Y	ENST00000274335		560	Gac/Tac	12/15	1	2	FACETS	0.072	0.048	0.102	0.072	0.048	0.102	SUBCLONAL	1	TRUE	1	0.686199603821552	2		511	406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28934873	NA	P-0065117-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	12	621	0	ENST00000269305.4:c.398T>C	p.Met133Thr	p.M133T	ENST00000269305	NM_001126112.2	133	aTg/aCg	5/11	0.686199603821552	1	FACETS	0.051	0.035	0.071	0.051	0.035	0.071	SUBCLONAL	1	TRUE	0	0.686199603821552	1		621	447	SUCCESS
APC	324	MSKCC	GRCh37	5	112175328	112175328	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065117-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	234	505	0	ENST00000257430.4:c.4037C>A	p.Ser1346Ter	p.S1346*	ENST00000257430	NM_000038.5	1346	tCa/tAa	16/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.686199603821552	2		505	623	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121604	2121604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746677177	NA	P-0065117-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	222	626	0	ENST00000219476.3:c.1933G>A	p.Val645Ile	p.V645I	ENST00000219476	NM_000548.3	645	Gtc/Atc	18/42	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.686199603821552	2		626	606	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326591	161326591	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065117-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	37	273	0	ENST00000367975.2:c.366C>A	p.Phe122Leu	p.F122L	ENST00000367975	NM_003001.3	122	ttC/ttA	5/6	1	2	FACETS	0.366	0.302	0.436	0.366	0.302	0.436	SUBCLONAL	1	TRUE	1	0.686199603821552	2		273	295	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989634	15989634	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065117-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	24	506	0	ENST00000268712.3:c.3139G>T	p.Glu1047Ter	p.E1047*	ENST00000268712	NM_006311.3	1047	Gaa/Taa	23/46	0.686199603821552	1	FACETS	0.101	0.078	0.127	0.101	0.078	0.127	SUBCLONAL	1	TRUE	0	0.686199603821552	1		506	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0065129-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	71	575	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.19	2		575	717	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262239	115262239	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065129-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	38	282	0	ENST00000438362.2:c.2315G>T	p.Arg772Leu	p.R772L	ENST00000438362	NM_001242891.1	772	cGc/cTc	18/20	1	2	FACETS	0.606	0.5	0.725	0.606	0.5	0.725	SUBCLONAL	1	TRUE	1	0.19	2		282	660	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617433	43617433	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065129-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	64	377	0	ENST00000355710.3:c.2770T>A	p.Phe924Ile	p.F924I	ENST00000355710	NM_020975.4	924	Ttt/Att	16/20	1	2	FACETS	0.899	0.778	1	0.899	0.778	1	CLONAL	1	TRUE	1	0.19	2		377	749	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828540	72828540	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0065129-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	57	429	0	ENST00000268489.5:c.8041A>T	p.Lys2681Ter	p.K2681*	ENST00000268489	NM_006885.3	2681	Aag/Tag	9/10	0.141087243806749	3	FACETS	0.819	0.701	0.949	0.41	0.35	0.475	CLONAL	1	TRUE	1	0.19	3		429	802	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249399	153249399	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065129-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	46	369	0	ENST00000281708.4:c.1379A>T	p.His460Leu	p.H460L	ENST00000281708	NM_033632.3	460	cAt/cTt	9/12	1	2	FACETS	0.914	0.769	1	0.914	0.769	1	CLONAL	1	TRUE	1	0.19	2		369	530	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926900	112926900	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs886039463	NA	P-0065133-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	51	235	0	ENST00000351677.2:c.1520C>A	p.Thr507Lys	p.T507K	ENST00000351677	NM_002834.3	507	aCa/aAa	13/16	0.3	4	FACETS	0.968	0.83	1	0.323	0.276	0.373	INDETERMINATE	1	TRUE	1	0.69	4		235	258	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0065133-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	54	236	0	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	1	2	FACETS	0.921	0.801	1	0.921	0.801	1	CLONAL	1	TRUE	1	0.69	2		236	170	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926900	112926900	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs886039463	NA	P-0065133-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	200	235	0	ENST00000351677.2:c.1520C>A	p.Thr507Lys	p.T507K	ENST00000351677	NM_002834.3	507	aCa/aAa	13/16	0.590700786329852	3	FACETS	1	0.975	1	0.553	0.513	0.594	CLONAL	1	TRUE	1	0.590700786329852	3		235	793	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0065133-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	249	236	0	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.590700786329852	2		236	643	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0065140-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	175	601	2	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.846	0.784	0.909	0.846	0.784	0.909	CLONAL	1	TRUE	1	0.775132425651157	2		603	534	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0065140-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	175	286	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.775132425651157	3	FACETS	0.905	0.848	0.962	0.905	0.848	0.962	CLONAL	2	TRUE	1	0.775132425651157	3		286	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0065140-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	476	575	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.775132425651157	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.775132425651157	2		575	600	SUCCESS
APC	324	MSKCC	GRCh37	5	112173995	112173995	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065140-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	140	501	0	ENST00000257430.4:c.2704G>T	p.Glu902Ter	p.E902*	ENST00000257430	NM_000038.5	902	Gaa/Taa	16/16	1	2	FACETS	0.86	0.791	0.931	0.86	0.791	0.931	CLONAL	1	TRUE	1	0.775132425651157	2		501	420	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448526	49448526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371342351	NA	P-0065140-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	588	613	0	ENST00000301067.7:c.185C>T	p.Pro62Leu	p.P62L	ENST00000301067	NM_003482.3	62	cCg/cTg	3/54	0.775132425651157	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.775132425651157	3		613	1040	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7590687	7590720	+	splice_donor_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	GAGCTTACCCAATCCAGGGAAGCGTGTCACCGTC	GAGCTTACCCAATCCAGGGAAGCGTGTCACCGTC	-	novel	NA	P-0065169-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	204	519	0	ENST00000269305.4:c.-54_-29+8del		p.X18_splice	ENST00000269305	NM_001126112.2	18		1/11	0.837593402241099	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.837593402241099	1		519	279	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0065177-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	52	665	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.642366374243308	3	FACETS	0.239	0.202	0.279	0.119	0.101	0.14	SUBCLONAL	1	TRUE	1	0.638922380514727	3		665	900	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631839	90631839	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519906	NA	P-0065177-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	455	763	0	ENST00000330062.3:c.514A>T	p.Arg172Trp	p.R172W	ENST00000330062	NM_002168.2	172	Agg/Tgg	4/11	0.642366374243308	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.638922380514727	3		763	917	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0065177-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	321	469	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.642366374243308	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.638922380514727	2		469	496	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678783	52678784	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065177-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	190	312	0	ENST00000394830.3:c.835dup	p.Ile279AsnfsTer8	p.I279Nfs*8	ENST00000394830	NM_018313.4	279	ata/aAta	9/30	0.642366374243308	2	FACETS	0.915	0.864	0.965	0.915	0.864	0.965	CLONAL	2	TRUE	0	0.638922380514727	2		312	325	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023715	27023716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0065177-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	328	672	0	ENST00000324856.7:c.827dup	p.Gly277ArgfsTer123	p.G277Rfs*123	ENST00000324856	NM_006015.4	274	atg/atGg	1/20	0.642366374243308	2	FACETS	0.881	0.842	0.919	0.881	0.842	0.919	CLONAL	2	TRUE	0	0.638922380514727	2		672	583	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0065209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	24	361	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.555871422880214	4	FACETS	0.299	0.233	0.374	0.1	0.077	0.125	SUBCLONAL	1	TRUE	1	0.555836432862126	4		361	450	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004628	150004628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	187	598	0	ENST00000253339.5:c.1597C>T	p.Pro533Ser	p.P533S	ENST00000253339		533	Cct/Tct	3/7	0.549700928545367	2	FACETS	1	0.951	1	0.516	0.479	0.555	CLONAL	1	TRUE	0	0.555836432862126	2		598	652	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361136	66361136	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	109	441	0	ENST00000273854.3:c.1036G>T	p.Glu346Ter	p.E346*	ENST00000273854	NM_004439.5	346	Gag/Tag	4/18	0.555871422880214	3	FACETS	0.844	0.76	0.932	0.422	0.38	0.466	CLONAL	1	TRUE	1	0.555836432862126	3		441	594	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575169	48575169	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	191	404	0	ENST00000342988.3:c.366del	p.Lys122AsnfsTer7	p.K122Nfs*7	ENST00000342988	NM_005359.5	121	ttA/tt	3/12	0.549700928545367	2	FACETS	0.987	0.93	1	0.987	0.93	1	CLONAL	2	TRUE	0	0.555836432862126	2		404	348	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946060	13946060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	108	346	0	ENST00000405192.2:c.1036G>A	p.Glu346Lys	p.E346K	ENST00000405192	NM_001163147.1	346	Gaa/Aaa	10/12	0.555836432862126	7	FACETS	1	0.924	1	0.173	0.155	0.192	CLONAL	1	TRUE	1	0.555836432862126	7		346	895	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021535	31021535	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs757832294	NA	P-0065209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	158	563	0	ENST00000375687.4:c.1534C>T	p.Gln512Ter	p.Q512*	ENST00000375687	NM_015338.5	512	Cag/Tag	12/13	0.362649275969728	5	FACETS	1	0.969	1	0.373	0.341	0.406	CLONAL	1	TRUE	2	0.555836432862126	5		563	932	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0065209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	269	318	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.555871422880214	4	FACETS	0.949	0.901	0.997	0.949	0.901	0.997	CLONAL	3	TRUE	1	0.555836432862126	4		318	529	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124503463	124503463	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	223	441	0	ENST00000357628.3:c.487G>T	p.Asp163Tyr	p.D163Y	ENST00000357628	NM_015450.2	163	Gac/Tac	8/19	0.555871422880214	3	FACETS	0.884	0.829	0.94	0.884	0.829	0.94	CLONAL	2	TRUE	1	0.555836432862126	3		441	580	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203580	108203580	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs767670019	NA	P-0065209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	247	422	0	ENST00000278616.4:c.7880A>G	p.Tyr2627Cys	p.Y2627C	ENST00000278616	NM_000051.3	2627	tAt/tGt	53/63	0.555836432862126	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.555836432862126	2		422	425	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140454002	140454002	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057517915	NA	P-0065209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	191	344	0	ENST00000288602.6:c.1726G>T	p.Asp576Tyr	p.D576Y	ENST00000288602	NM_004333.4	576	Gac/Tac	14/18	0.543881930603873	4	FACETS	1	0.987	1	0.808	0.756	0.861	CLONAL	2	TRUE	1	0.555836432862126	4		344	441	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497654	125497654	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	223	424	0	ENST00000428830.2:c.218A>G	p.His73Arg	p.H73R	ENST00000428830	NM_001114121.2	73	cAc/cGc	3/14	0.555836432862126	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.555836432862126	2		424	378	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431976	49431976	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	493	659	0	ENST00000301067.7:c.9163C>T	p.Pro3055Ser	p.P3055S	ENST00000301067	NM_003482.3	3055	Cct/Tct	34/54	0.555836432862126	6	FACETS	0.969	0.928	1			1	CLONAL	3	TRUE	NA	0.555836432862126	6		659	1289	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784078	120784078	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	346	617	0	ENST00000257552.2:c.907C>A	p.Arg303Ser	p.R303S	ENST00000257552	NM_002442.3	303	Cgc/Agc	13/15	0.549700928545367	2	FACETS	0.983	0.941	1	0.983	0.941	1	CLONAL	2	TRUE	0	0.555836432862126	2		617	633	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28886144	28886144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	82	265	0	ENST00000282397.4:c.3478G>A	p.Ala1160Thr	p.A1160T	ENST00000282397	NM_002019.4	1160	Gca/Aca	26/30	1	2	FACETS	0.86	0.765	0.961	0.86	0.765	0.961	CLONAL	1	TRUE	1	0.555836432862126	2		265	343	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435893	110435893	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	198	530	0	ENST00000375856.3:c.2508G>T	p.Glu836Asp	p.E836D	ENST00000375856	NM_003749.2	836	gaG/gaT	1/2	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.555836432862126	2		530	565	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724721	43724721	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	300	496	0	ENST00000382044.4:c.3346G>T	p.Gly1116Trp	p.G1116W	ENST00000382044	NM_001141980.1	1116	Ggg/Tgg	17/28	0.549700928545367	2	FACETS	0.937	0.892	0.982	0.937	0.892	0.982	CLONAL	2	TRUE	0	0.555836432862126	2		496	576	SUCCESS
BLM	641	MSKCC	GRCh37	15	91308574	91308574	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	241	435	0	ENST00000355112.3:c.2123G>T	p.Gly708Val	p.G708V	ENST00000355112	NM_000057.2	708	gGg/gTg	9/22	0.549700928545367	2	FACETS	0.999	0.948	1	0.999	0.948	1	CLONAL	2	TRUE	0	0.555836432862126	2		435	434	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641121	3641121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759271070	NA	P-0065209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	170	517	0	ENST00000294008.3:c.2518G>A	p.Glu840Lys	p.E840K	ENST00000294008	NM_032444.2	840	Gaa/Aaa	12/15	0.525291881194005	4	FACETS	1	0.947	1	0.346	0.318	0.375	CLONAL	1	TRUE	1	0.555836432862126	4		517	917	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029255	14029255	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	469	539	0	ENST00000311895.7:c.1466A>G	p.Lys489Arg	p.K489R	ENST00000311895	NM_005236.2	489	aAa/aGa	8/11	0.38946930322392	5	FACETS	0.899	0.865	0.932	1	0.995	1	CLONAL	4	TRUE	2	0.555836432862126	5		539	861	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50820771	50820771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	77	353	0	ENST00000398568.2:c.1946G>A	p.Gly649Glu	p.G649E	ENST00000398568	NM_001042412.1	649	gGa/gAa	12/18	0.555871422880214	3	FACETS	0.823	0.726	0.927	0.412	0.363	0.464	CLONAL	1	TRUE	1	0.555836432862126	3		353	430	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992548	72992548	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	149	476	0	ENST00000268489.5:c.1497G>T	p.Leu499Phe	p.L499F	ENST00000268489	NM_006885.3	499	ttG/ttT	2/10	0.555871422880214	3	FACETS	1	0.926	1	0.506	0.463	0.55	CLONAL	1	TRUE	1	0.555836432862126	3		476	677	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556157	29556158	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0065209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	58	165	0	ENST00000356175.3:c.2524_2525delinsCT	p.Gly842Leu	p.G842L	ENST00000356175	NM_000267.3	842	GGc/CTc	21/57	0.555871422880214	4	FACETS	1	0.951	1	0.608	0.527	0.694	CLONAL	1	TRUE	2	0.555836432862126	4		165	267	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928264	178928264	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1004909638	NA	P-0065209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	245	392	0	ENST00000263967.3:c.1450G>T	p.Val484Leu	p.V484L	ENST00000263967	NM_006218.2	484	Gta/Tta	9/21	0.555871422880214	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.555836432862126	3		392	531	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295847	1295847	+	upstream_gene_variant	5'Flank	SNP	C	C	T	rs1049319082	NA	P-0065209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1359	330	638	0				ENST00000310581	NM_198253.2	-/1132			0.555836432862126	7	FACETS	0.84	0.791	0.89	0.336	0.316	0.356	CLONAL	2	TRUE	2	0.555836432862126	7		638	1689	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876427	35876427	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	224	538	0	ENST00000303115.3:c.1219A>T	p.Ser407Cys	p.S407C	ENST00000303115	NM_002185.3	407	Agc/Tgc	8/8	0.555871422880214	5	FACETS	0.782	0.729	0.837	0.391	0.364	0.419	SUBCLONAL	2	TRUE	1	0.555836432862126	5		538	945	SUCCESS
APC	324	MSKCC	GRCh37	5	112174793	112174793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	135	477	0	ENST00000257430.4:c.3502G>A	p.Glu1168Lys	p.E1168K	ENST00000257430	NM_000038.5	1168	Gaa/Aaa	16/16	0.552701740613437	2	FACETS	1	0.93	1	0.509	0.466	0.554	CLONAL	1	TRUE	0	0.555836432862126	2		477	477	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480156	20480156	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	110	379	0	ENST00000346618.3:c.473G>A	p.Arg158Lys	p.R158K	ENST00000346618	NM_001949.4	158	aGa/aAa	2/7	0.555871422880214	3	FACETS	1	0.908	1	0.503	0.454	0.554	CLONAL	1	TRUE	1	0.555836432862126	3		379	503	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839921	27839921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	217	681	0	ENST00000328488.2:c.173C>T	p.Ser58Leu	p.S58L	ENST00000328488	NM_003533.2	58	tCg/tTg	1/1	0.555871422880214	3	FACETS	1	0.934	1	0.502	0.467	0.539	CLONAL	1	TRUE	1	0.555836432862126	3		681	993	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843391	128843391	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	125	457	0	ENST00000249373.3:c.498C>A	p.Phe166Leu	p.F166L	ENST00000249373	NM_005631.4	166	ttC/ttA	2/12	0.555871422880214	3	FACETS	0.808	0.733	0.888	0.404	0.366	0.444	CLONAL	1	TRUE	1	0.555836432862126	3		457	711	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0065220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	206	557	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		557	696	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099026	27099026	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	194	529	0	ENST00000324856.7:c.3442C>T	p.Gln1148Ter	p.Q1148*	ENST00000324856	NM_006015.4	1148	Cag/Tag	13/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		529	712	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0065220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	74	509	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		509	670	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097621	27097622	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	197	480	0	ENST00000324856.7:c.3216dup	p.Trp1073MetfsTer32	p.W1073Mfs*32	ENST00000324856	NM_006015.4	1070	-/A	12/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		480	756	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0065220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	166	444	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		444	580	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524927	187524927	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	170	513	0	ENST00000441802.2:c.10753C>T	p.Gln3585Ter	p.Q3585*	ENST00000441802	NM_005245.3	3585	Cag/Tag	19/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		513	675	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094404	27094404	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1296513906	NA	P-0065220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	197	529	0	ENST00000324856.7:c.3112A>G	p.Met1038Val	p.M1038V	ENST00000324856	NM_006015.4	1038	Atg/Gtg	11/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		529	721	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243776987	243776987	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	38	361	0	ENST00000263826.5:c.682G>A	p.Val228Ile	p.V228I	ENST00000263826	NM_005465.4	228	Gtt/Att	7/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		361	414	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63537641	63537641	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	343	434	0	ENST00000307078.5:c.991A>C	p.Lys331Gln	p.K331Q	ENST00000307078	NM_004655.3	331	Aaa/Caa	4/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		434	617	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0065238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	280	622	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.446244749306262	2		622	949	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975459	13975459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80157564	NA	P-0065238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	193	513	0	ENST00000405192.2:c.428C>T	p.Thr143Met	p.T143M	ENST00000405192	NM_001163147.1	143	aCg/aTg	7/12	0.446244749306262	3	FACETS	1	0.951	1	0.519	0.479	0.559	CLONAL	1	TRUE	1	0.446244749306262	3		513	1020	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0065238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	144	482	8	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.987	0.903	1	0.987	0.903	1	CLONAL	1	TRUE	1	0.446244749306262	2		490	654	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0065238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	109	537	3	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.602	0.54	0.667	0.602	0.54	0.667	SUBCLONAL	1	TRUE	1	0.446244749306262	2		540	812	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0065238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	201	639	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.95	0.881	1	0.95	0.881	1	CLONAL	1	TRUE	1	0.446244749306262	2		639	948	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	152	563	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.845	0.774	0.92	0.845	0.774	0.92	CLONAL	1	TRUE	1	0.446244749306262	2		563	806	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0065238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	181	475	0	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.446244749306262	2		475	776	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	218	645	3	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.446244749306262	2		648	946	SUCCESS
APC	324	MSKCC	GRCh37	5	112175166	112175166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371113837	NA	P-0065238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	129	478	0	ENST00000257430.4:c.3875C>T	p.Thr1292Met	p.T1292M	ENST00000257430	NM_000038.5	1292	aCg/aTg	16/16	1	2	FACETS	0.895	0.813	0.98	0.895	0.813	0.98	CLONAL	1	TRUE	1	0.446244749306262	2		478	646	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245024	133245024	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs752846614	NA	P-0065238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	207	636	3	ENST00000320574.5:c.2091del	p.Leu698CysfsTer94	p.L698Cfs*94	ENST00000320574	NM_006231.2	697	ccC/cc	19/49	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.446244749306262	2		639	865	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231107	53231107	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	135	498	2	ENST00000375401.3:c.1795del	p.Arg599ValfsTer60	p.R599Vfs*60	ENST00000375401	NM_004187.3	599	Cgt/gt	13/26	1	2	FACETS	0.81	0.737	0.887	0.81	0.737	0.887	CLONAL	1	TRUE	1	0.446244749306262	2		500	747	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266128	198266128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	68	362	0	ENST00000335508.6:c.2492G>A	p.Arg831Gln	p.R831Q	ENST00000335508	NM_012433.2	831	cGa/cAa	17/25	1	2	FACETS	0.924	0.809	1	0.924	0.809	1	CLONAL	1	TRUE	1	0.446244749306262	2		362	330	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798840	42798840	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	208	535	1	ENST00000575354.2:c.4412G>A	p.Arg1471Gln	p.R1471Q	ENST00000575354	NM_015125.3	1471	cGg/cAg	19/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.446244749306262	2		536	772	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602863	10602863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	227	591	0	ENST00000171111.5:c.715G>A	p.Val239Met	p.V239M	ENST00000171111	NM_203500.1	239	Gtg/Atg	3/6	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.446244749306262	2		591	940	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711990	89711990	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	236	329	0	ENST00000371953.3:c.609del	p.Pro204GlnfsTer17	p.P204Qfs*17	ENST00000371953	NM_000314.4	203	aTt/at	6/9	0.446244749306262	3	FACETS	0.969	0.918	1	0.969	0.918	1	CLONAL	3	TRUE	0	0.446244749306262	3		329	445	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659847	227659847	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	92	265	0	ENST00000305123.5:c.3608del	p.Pro1203HisfsTer24	p.P1203Hfs*24	ENST00000305123	NM_005544.2	1203	cCa/ca	1/2	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.446244749306262	2		265	395	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553478	29553478	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781807	NA	P-0065238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	179	534	4	ENST00000356175.3:c.2033del	p.Pro678ArgfsTer10	p.P678Rfs*10	ENST00000356175	NM_000267.3	676	aCc/ac	18/57	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.446244749306262	2		538	769	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610320	10610320	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	206	679	0	ENST00000171111.5:c.390del	p.Lys131ArgfsTer26	p.K131Rfs*26	ENST00000171111	NM_203500.1	130	ccC/cc	2/6	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.446244749306262	2		679	881	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845609	72845609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs190630040	NA	P-0065238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	205	569	0	ENST00000268489.5:c.3731C>T	p.Thr1244Met	p.T1244M	ENST00000268489	NM_006885.3	1244	aCg/aTg	7/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.446244749306262	2		569	839	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115272985	115272985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536073175	NA	P-0065238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	109	480	0	ENST00000438362.2:c.1388C>T	p.Thr463Met	p.T463M	ENST00000438362	NM_001242891.1	463	aCg/aTg	12/20	1	2	FACETS	0.827	0.744	0.913	0.827	0.744	0.913	CLONAL	1	TRUE	1	0.446244749306262	2		480	591	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600498	43600498	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1264337497	NA	P-0065238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	214	624	0	ENST00000355710.3:c.724G>A	p.Val242Met	p.V242M	ENST00000355710	NM_020975.4	242	Gtg/Atg	4/20	0.446244749306262	3	FACETS	1	0.974	1	0.551	0.512	0.592	CLONAL	1	TRUE	1	0.446244749306262	3		624	1064	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77937650	77937650	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	179	411	0	ENST00000361507.4:c.1068del	p.Lys357SerfsTer70	p.K357Sfs*70	ENST00000361507	NM_080491.2	356	ccC/cc	4/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.446244749306262	2		411	620	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3113466	3113466	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	169	547	0	ENST00000078429.4:c.460T>C	p.Ser154Pro	p.S154P	ENST00000078429	NM_002067.2	154	Tcc/Ccc	3/7	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.446244749306262	2		547	632	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6270729	6270729	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	241	611	0	ENST00000252674.7:c.54A>T	p.Gln18His	p.Q18H	ENST00000252674	NM_005934.3	18	caA/caT	2/12	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.446244749306262	2		611	945	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221763	36221763	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	159	581	0	ENST00000222270.7:c.5433del	p.Ser1812GlnfsTer83	p.S1812Qfs*83	ENST00000222270	NM_014727.1	1811	tCc/tc	26/37	1	2	FACETS	0.987	0.907	1	0.987	0.907	1	CLONAL	1	TRUE	1	0.446244749306262	2		581	722	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229268	36229268	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	240	713	0	ENST00000222270.7:c.7958A>G	p.His2653Arg	p.H2653R	ENST00000222270	NM_014727.1	2653	cAc/cGc	37/37	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.446244749306262	2		713	990	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47503656	47503656	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	210	552	0	ENST00000404338.3:c.4211T>G	p.Leu1404Trp	p.L1404W	ENST00000404338	NM_004491.4	1404	tTg/tGg	6/6	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.446244749306262	2		552	826	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588971	67588972	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	83	414	0	ENST00000274335.5:c.1067dup	p.Leu356PhefsTer8	p.L356Ffs*8	ENST00000274335		354	-/T	8/15	1	2	FACETS	0.875	0.776	0.98	0.875	0.776	0.98	CLONAL	1	TRUE	1	0.446244749306262	2		414	425	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589609	67589610	+	protein_altering_variant	In_Frame_Ins	INS	-	-	CAAAAA	novel	NA	P-0065238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	37	252	0	ENST00000274335.5:c.1372_1373insCAAAAA	p.Glu458delinsAlaLysLys	p.E458delinsAKK	ENST00000274335		458	gaa/gCAAAAAaa	10/15	1	2	FACETS	0.568	0.47	0.676	0.568	0.47	0.676	SUBCLONAL	1	TRUE	1	0.446244749306262	2		252	292	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729263	41729265	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0065238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	119	389	0	ENST00000242208.4:c.1264_1266del	p.Glu422del	p.E422del	ENST00000242208	NM_002192.2	422	GAG/-	3/3	0.446244749306262	3	FACETS	0.924	0.835	1	0.462	0.417	0.509	CLONAL	1	TRUE	1	0.446244749306262	3		389	706	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878844	151878844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	154	569	0	ENST00000262189.6:c.6101C>T	p.Ala2034Val	p.A2034V	ENST00000262189	NM_170606.2	2034	gCa/gTa	36/59	0.446244749306262	3	FACETS	0.929	0.85	1	0.464	0.425	0.506	CLONAL	1	TRUE	1	0.446244749306262	3		569	909	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372375	55372376	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0065238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	214	610	0	ENST00000297316.4:c.1069dup	p.Glu357GlyfsTer8	p.E357Gfs*8	ENST00000297316	NM_022454.3	355	-/G	2/2	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.446244749306262	2		610	856	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430617	80430617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	14	70	0	ENST00000286548.4:c.391G>A	p.Ala131Thr	p.A131T	ENST00000286548	NM_002072.3	131	Gca/Aca	3/7	1	2	FACETS	0.794	0.585	1	0.794	0.585	1	CLONAL	1	TRUE	1	0.446244749306262	2		70	79	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0065239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	170	442	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.622828071382653	2	FACETS	0.993	0.938	1	0.993	0.938	1	CLONAL	2	TRUE	0	0.631421103780002	2		442	271	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947865	178947865	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776932	NA	P-0065239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	109	446	0	ENST00000263967.3:c.2740G>A	p.Gly914Arg	p.G914R	ENST00000263967	NM_006218.2	914	Gga/Aga	19/21	0.622828071382653	2	FACETS	0.904	0.836	0.97	0.904	0.836	0.97	CLONAL	2	TRUE	0	0.631421103780002	2		446	191	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487277	56487277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035001455	NA	P-0065239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	19	442	0	ENST00000267101.3:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000267101	NM_001982.3	475	Cgg/Tgg	12/28	0.513049531179996	2	FACETS	0.183	0.138	0.235	0.091	0.069	0.118	SUBCLONAL	1	TRUE	0	0.631421103780002	2		442	329	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610422	10610422	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	189	619	0	ENST00000171111.5:c.288C>G	p.His96Gln	p.H96Q	ENST00000171111	NM_203500.1	96	caC/caG	2/6	0.548150140000841	2	FACETS	0.886	0.835	0.936	0.886	0.835	0.936	CLONAL	2	TRUE	0	0.631421103780002	2		619	338	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639900	3639900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs978074181	NA	P-0065239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	19	572	0	ENST00000294008.3:c.3739G>A	p.Glu1247Lys	p.E1247K	ENST00000294008	NM_032444.2	1247	Gag/Aag	12/15	0.513049531179996	2	FACETS	0.196	0.148	0.252	0.098	0.074	0.126	SUBCLONAL	1	TRUE	0	0.631421103780002	2		572	307	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670789	134670789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368276671	NA	P-0065239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	187	592	0	ENST00000398015.3:c.700G>A	p.Val234Met	p.V234M	ENST00000398015	NM_004441.4	234	Gtg/Atg	3/16	0.622828071382653	2	FACETS	0.906	0.854	0.957	0.906	0.854	0.957	CLONAL	2	TRUE	0	0.631421103780002	2		592	327	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683508	29683508	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0065239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	13	424	0	ENST00000356175.3:c.7583C>G	p.Ser2528Ter	p.S2528*	ENST00000356175	NM_000267.3	2528	tCa/tGa	51/57	0.622828071382653	2	FACETS	0.239	0.171	0.322	0.12	0.085	0.161	SUBCLONAL	1	TRUE	0	0.631421103780002	2		424	172	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215532	5215532	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	163	584	0	ENST00000357368.4:c.4171C>G	p.Leu1391Val	p.L1391V	ENST00000357368	NM_002850.3	1391	Ctc/Gtc	27/38	0.548150140000841	2	FACETS	0.827	0.774	0.88	0.827	0.774	0.88	CLONAL	2	TRUE	0	0.631421103780002	2		584	312	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753282	42753282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	62	716	0	ENST00000222329.4:c.982C>T	p.Pro328Ser	p.P328S	ENST00000222329	NM_006494.2	328	Ccc/Tcc	4/4	0.177179604496821	6	FACETS	0.924	0.8	1	0.308	0.266	0.353	INDETERMINATE	1	TRUE	3	0.631421103780002	6		716	481	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0065240-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	84	557	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.345002914328175	2		557	454	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971137	21971137	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065240-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	73	547	0	ENST00000304494.5:c.221A>T	p.Asp74Val	p.D74V	ENST00000304494	NM_000077.4	74	gAc/gTc	2/3	0.345002914328175	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.345002914328175	1		547	334	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729529	41729529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138538132	NA	P-0065240-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	105	593	0	ENST00000242208.4:c.1000G>A	p.Gly334Ser	p.G334S	ENST00000242208	NM_002192.2	334	Ggc/Agc	3/3	0.208771237376508	3	FACETS	0.809	0.729	0.893	0.809	0.729	0.893	CLONAL	2	TRUE	1	0.345002914328175	3		593	441	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TC	novel	NA	P-0065240-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	50	415	0	ENST00000311936.3:c.180_181inv	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggGAaa	3/5	0.321935031522074	1	FACETS	0.655	0.558	0.762	0.655	0.558	0.762	SUBCLONAL	1	TRUE	0	0.345002914328175	1		415	366	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112942518	112942518	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065240-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	68	341	0	ENST00000351677.2:c.1732A>G	p.Arg578Gly	p.R578G	ENST00000351677	NM_002834.3	578	Aga/Gga	15/16	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.345002914328175	2		341	373	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119827	70119828	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065242-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	41	422	0	ENST00000245479.2:c.830dup	p.Leu278AlafsTer18	p.L278Afs*18	ENST00000245479	NM_000346.3	277	gag/gAag	3/3	1	2	FACETS	0.419	0.349	0.498	0.419	0.349	0.498	SUBCLONAL	1	TRUE	1	0.403867388028116	2		422	484	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508804	29508804	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs1060500274	NA	P-0065258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	79	306	0	ENST00000356175.3:c.730+1G>C		p.X244_splice	ENST00000356175	NM_000267.3	244			1	2	FACETS	0.774	0.691	0.86	0.774	0.691	0.86	SUBCLONAL	1	TRUE	1	0.850656850659127	2		306	240	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117639417	117639417	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0065258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	104	360	0	ENST00000368508.3:c.5941-2A>G		p.X1981_splice	ENST00000368508	NM_002944.2	1981			0.850656850659127	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.850656850659127	1		360	137	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008941	152008973	+	protein_altering_variant	In_Frame_Del	DEL	TTCATCCCACAGTTTACCAGCTTGATCATCTGA	TTCATCCCACAGTTTACCAGCTTGATCATCTGA	CCC	novel	NA	P-0065258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	57	389	1	ENST00000262189.6:c.649_681delinsGGG	p.Ser217_Glu227delinsGly	p.S217_E227delinsG	ENST00000262189	NM_170606.2	217	TCAGATGATCAAGCTGGTAAACTGTGGGATGAA/GGG	5/59	0.387690656897709	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.850656850659127	0		390	160	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1688018	1688027	+	missense_variant	Missense_Mutation	ONP	TTTCTTTTCC	TTTCTTTTCC	ATGATCGTCT	novel	NA	P-0065258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	79	521	0	ENST00000378625.1:c.849_858delinsAGACGATCAT	p.Glu284_Lys286delinsAspAspHis	p.E284_K286delinsDDH	ENST00000378625	NM_001198994.1	283	gtGGAAAAGAAA/gtAGACGATCAT	7/14	1	2	FACETS	0.609	0.541	0.681	0.609	0.541	0.681	SUBCLONAL	1	TRUE	1	0.850656850659127	2		521	305	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0065329-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	37	473	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.164349755865403	2		473	332	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618616	37618616	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065329-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	26	614	0	ENST00000447079.4:c.292G>C	p.Glu98Gln	p.E98Q	ENST00000447079	NM_015083.1	98	Gaa/Caa	1/14	1	2	FACETS	0.673	0.532	0.835	0.673	0.532	0.835	SUBCLONAL	1	TRUE	1	0.164349755865403	2		614	470	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0065337-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	384	429	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	0.311206652090513	1	FACETS	1	0.989	1	1	0.997	1	CLONAL	2	TRUE	0	0.311206652090513	1		429	931	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882025	NA	P-0065337-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	304	581	0	ENST00000269305.4:c.646G>T	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ttg	6/11	0.21611419501424	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.311206652090513	4		581	1191	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065337-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	237	483	0	ENST00000269305.4:c.772del	p.Glu258LysfsTer87	p.E258Kfs*87	ENST00000269305	NM_001126112.2	258	Gaa/aa	7/11	0.21611419501424	4	FACETS	0.944	0.881	1	0.944	0.881	1	CLONAL	2	TRUE	2	0.311206652090513	4		483	1058	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089547	27089547	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065337-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	359	590	0	ENST00000324856.7:c.2503A>T	p.Met835Leu	p.M835L	ENST00000324856	NM_006015.4	835	Atg/Ttg	8/20	0.311206652090513	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.311206652090513	2		590	1037	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405193	70405193	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065337-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	288	544	0	ENST00000373644.4:c.2707G>T	p.Ala903Ser	p.A903S	ENST00000373644	NM_030625.2	903	Gcc/Tcc	4/12	0.311206652090513	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.311206652090513	2		544	838	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437370	121437370	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065337-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	111	601	0	ENST00000257555.6:c.1708C>T	p.Gln570Ter	p.Q570*	ENST00000257555		570	Cag/Tag	9/10	0.311206652090513	3	FACETS	0.878	0.788	0.973	0.439	0.394	0.487	CLONAL	1	TRUE	1	0.311206652090513	3		601	939	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135376	30135376	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065337-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	149	412	0	ENST00000331968.5:c.442G>T	p.Ala148Ser	p.A148S	ENST00000331968	NM_002742.2	148	Gct/Tct	3/18	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.311206652090513	2		412	722	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003500	42003500	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065337-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	238	472	0	ENST00000219905.7:c.3037A>G	p.Thr1013Ala	p.T1013A	ENST00000219905	NM_001164273.1	1013	Aca/Gca	8/24	0.183712891027015	3	FACETS	0.905	0.846	0.967	0.905	0.846	0.967	INDETERMINATE	2	TRUE	1	0.311206652090513	3		472	976	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888167	81888167	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065337-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	85	493	0	ENST00000359376.3:c.312C>A	p.Phe104Leu	p.F104L	ENST00000359376	NM_002661.3	104	ttC/ttA	3/33	0.311206652090513	2	FACETS	0.653	0.577	0.736	0.327	0.288	0.368	SUBCLONAL	1	TRUE	0	0.311206652090513	2		493	836	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858025	40858025	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065337-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	228	454	0	ENST00000428826.2:c.1839G>C	p.Lys613Asn	p.K613N	ENST00000428826		613	aaG/aaC	16/21	0.21611419501424	4	FACETS	0.955	0.89	1	0.955	0.89	1	CLONAL	2	TRUE	2	0.311206652090513	4		454	1006	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574691	41574691	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065337-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	306	598	0	ENST00000263253.7:c.6976A>G	p.Ser2326Gly	p.S2326G	ENST00000263253	NM_001429.3	2326	Agt/Ggt	31/31	0.299513411653437	3	FACETS	0.994	0.937	1	0.994	0.937	1	CLONAL	2	TRUE	1	0.311206652090513	3		598	1143	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968528	55968528	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0065337-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	131	360	0	ENST00000263923.4:c.2134+1G>A		p.X712_splice	ENST00000263923	NM_002253.2	712			0.311206652090513	5	FACETS	1	0.983	1	0.346	0.314	0.381	CLONAL	1	TRUE	1	0.311206652090513	5		360	891	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630457	187630457	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065337-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	353	586	0	ENST00000441802.2:c.525T>A	p.Asp175Glu	p.D175E	ENST00000441802	NM_005245.3	175	gaT/gaA	2/27	0.311206652090513	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.311206652090513	2		586	989	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753099	57753099	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065337-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	329	542	0	ENST00000274289.3:c.917C>A	p.Pro306His	p.P306H	ENST00000274289	NM_006622.3	306	cCt/cAt	7/14	0.311206652090513	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.311206652090513	2		542	890	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671868	30671868	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065337-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	153	604	0	ENST00000376406.3:c.5092C>A	p.Pro1698Thr	p.P1698T	ENST00000376406	NM_014641.2	1698	Cct/Act	10/15	0.311206652090513	3	FACETS	1	0.972	1	0.575	0.525	0.627	CLONAL	1	TRUE	1	0.311206652090513	3		604	988	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157470060	157470060	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs746676470	NA	P-0065337-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	158	589	0	ENST00000346085.5:c.2854G>T	p.Ala952Ser	p.A952S	ENST00000346085	NM_020732.3	952	Gct/Tct	9/20	0.311206652090513	3	FACETS	1	0.972	1	0.571	0.523	0.622	CLONAL	1	TRUE	1	0.311206652090513	3		589	1027	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727849	41727874	+	frameshift_variant	Frame_Shift_Del	DEL	GAGCTGCCAAGCTCAGGGACCCCCAG	GAGCTGCCAAGCTCAGGGACCCCCAG	ACTCTGGCTTCAACCTACTCA	novel	NA	P-0065337-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	303	516	2	ENST00000301178.4:c.474_499delinsACTCTGGCTTCAACCTACTCA	p.Ser159LeufsTer49	p.S159Lfs*49	ENST00000301178	NM_021913.4	158	ctGAGCTGCCAAGCTCAGGGACCCCCAGag/ctACTCTGGCTTCAACCTACTCAag	4/20	0.311206652090513	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.311206652090513	2		518	837	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0065340-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	521	617	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.545917990673819	3	FACETS	0.961	0.93	0.991	0.961	0.93	0.991	CLONAL	3	FALSE	0	0.569299002854129	3		618	816	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0065340-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	212	476	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.569129773052651	2	FACETS	1	0.988	1	0.623	0.582	0.664	CLONAL	1	FALSE	0	0.569299002854129	2		476	598	SUCCESS
APC	324	MSKCC	GRCh37	5	112175907	112175907	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0065340-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	104	621	0	ENST00000257430.4:c.4616C>G	p.Ser1539Ter	p.S1539*	ENST00000257430	NM_000038.5	1539	tCa/tGa	16/16	0.569129773052651	2	FACETS	0.586	0.525	0.649	0.293	0.262	0.325	SUBCLONAL	1	FALSE	0	0.569299002854129	2		621	624	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950220	38950220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065340-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	44	562	0	ENST00000357387.3:c.3730G>A	p.Asp1244Asn	p.D1244N	ENST00000357387	NM_152756.3	1244	Gat/Aat	31/38	0.502856633244185	4	FACETS	0.28	0.234	0.331	0.14	0.117	0.166	SUBCLONAL	1	FALSE	2	0.569299002854129	4		562	867	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404833	70404833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376078561	NA	P-0065340-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	94	476	0	ENST00000373644.4:c.2347G>A	p.Gly783Ser	p.G783S	ENST00000373644	NM_030625.2	783	Ggc/Agc	4/12	0.553365989683494	4	FACETS	0.715	0.636	0.799	0.238	0.212	0.267	SUBCLONAL	1	FALSE	1	0.569299002854129	4		476	725	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52663053	52663053	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0065340-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	41	320	0	ENST00000394830.3:c.1302-2A>G		p.X434_splice	ENST00000394830	NM_018313.4	434			0.569299002854129	2	FACETS	0.447	0.374	0.528	0.224	0.187	0.264	SUBCLONAL	1	FALSE	0	0.569299002854129	2		320	322	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87338580	87338580	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065340-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	232	477	0	ENST00000277120.3:c.676C>G	p.Pro226Ala	p.P226A	ENST00000277120		226	Cct/Gct	7/19	0.339315743415448	3	FACETS	0.887	0.834	0.942	0.592	0.556	0.628	INDETERMINATE	2	FALSE	0	0.569299002854129	3		477	590	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307177	65307177	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065340-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	97	653	0	ENST00000342505.4:c.2511C>G	p.Phe837Leu	p.F837L	ENST00000342505	NM_002227.2	837	ttC/ttG	18/25	0.545452396236002	4	FACETS	0.576	0.513	0.644	0.288	0.256	0.322	SUBCLONAL	1	FALSE	2	0.569299002854129	4		653	928	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503923	149503923	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065340-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	242	552	0	ENST00000261799.4:c.1913C>T	p.Ser638Phe	p.S638F	ENST00000261799	NM_002609.3	638	tCc/tTc	14/23	0.502856633244185	4	FACETS	0.937	0.879	0.996	0.937	0.879	0.996	CLONAL	2	FALSE	2	0.569299002854129	4		552	712	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981611	63981611	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065340-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	352	708	0	ENST00000398590.3:c.2113A>C	p.Lys705Gln	p.K705Q	ENST00000398590	NM_001177387.1	705	Aag/Cag	12/14	0.339315743415448	3	FACETS	1	0.986	1	0.719	0.686	0.753	INDETERMINATE	2	FALSE	0	0.569299002854129	3		708	736	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933516	36933516	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs769348066	NA	P-0065340-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	385	782	0	ENST00000361632.4:c.1771G>C	p.Glu591Gln	p.E591Q	ENST00000361632		591	Gag/Cag	13/16	NA	2	FACETS	0.965	0.925	1			1	INDETERMINATE	2	FALSE	NA	0.569299002854129	2		782	701	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0065341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	112	488	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.313060182659038	2		488	575	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069315	30069315	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	94	600	0	ENST00000338641.4:c.1180G>T	p.Glu394Ter	p.E394*	ENST00000338641	NM_000268.3	394	Gag/Tag	12/16	0.298876221541181	1	FACETS	0.949	0.847	1	0.949	0.847	1	CLONAL	1	TRUE	0	0.313060182659038	1		600	534	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545939	41545939	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	113	553	0	ENST00000263253.7:c.2554C>T	p.Gln852Ter	p.Q852*	ENST00000263253	NM_001429.3	852	Cag/Tag	14/31	0.298876221541181	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	0	0.313060182659038	1		553	608	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56866264	56866264	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1374778377	NA	P-0065341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	116	441	2	ENST00000308159.5:c.1309C>G	p.Leu437Val	p.L437V	ENST00000308159	NM_014669.4	437	Ctc/Gtc	12/22	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.313060182659038	2		443	575	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245192	46245192	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	116	611	0	ENST00000334344.6:c.3286C>T	p.Gln1096Ter	p.Q1096*	ENST00000334344	NM_152641.2	1096	Cag/Tag	15/21	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.313060182659038	2		611	699	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371818	55371818	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	192	555	0	ENST00000297316.4:c.508G>A	p.Glu170Lys	p.E170K	ENST00000297316	NM_022454.3	170	Gag/Aag	2/2	0.313060182659038	3	FACETS	0.973	0.903	1	0.973	0.903	1	CLONAL	2	TRUE	1	0.313060182659038	3		555	729	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749386	43749386	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	81	419	0	ENST00000382044.4:c.1420G>T	p.Glu474Ter	p.E474*	ENST00000382044	NM_001141980.1	474	Gaa/Taa	12/28	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.313060182659038	2		419	465	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161744	56161744	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1406908752	NA	P-0065341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	80	456	0	ENST00000399503.3:c.1241G>A	p.Arg414His	p.R414H	ENST00000399503	NM_005921.1	414	cGc/cAc	6/20	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.313060182659038	2		456	466	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069345	30069345	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	90	584	0	ENST00000338641.4:c.1210G>C	p.Glu404Gln	p.E404Q	ENST00000338641	NM_000268.3	404	Gag/Cag	12/16	0.298876221541181	1	FACETS	0.942	0.838	1	0.942	0.838	1	CLONAL	1	TRUE	0	0.313060182659038	1		584	515	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249413	110249413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	131	632	0	ENST00000374672.4:c.1160C>T	p.Ser387Leu	p.S387L	ENST00000374672	NM_004235.4	387	tCg/tTg	4/5	0.313060182659038	2	FACETS	1	0.936	1	0.52	0.472	0.57	CLONAL	1	TRUE	0	0.313060182659038	2		632	805	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26927925	26927925	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	65	493	0	ENST00000381527.3:c.364C>T	p.Gln122Ter	p.Q122*	ENST00000381527	NM_001260.1	122	Cag/Tag	4/13	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.313060182659038	2		493	409	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0065341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	244	432	1	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.313060182659038	5	FACETS	1	0.977	1	1	0.977	1	CLONAL	4	TRUE	1	0.313060182659038	5		433	538	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484433	57484433	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	121	492	0	ENST00000371085.3:c.614C>G	p.Ser205Cys	p.S205C	ENST00000371085	NM_000516.4	205	tCt/tGt	8/13	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.313060182659038	2		492	691	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258802	16258802	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	118	650	0	ENST00000375759.3:c.6067G>T	p.Val2023Leu	p.V2023L	ENST00000375759	NM_015001.2	2023	Gtg/Ttg	11/15	0.313060182659038	1	FACETS	0.975	0.882	1	0.975	0.882	1	CLONAL	1	TRUE	0	0.313060182659038	1		650	652	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342889	118342889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	98	557	0	ENST00000534358.1:c.1015C>T	p.Pro339Ser	p.P339S	ENST00000534358	NM_005933.3	339	Cca/Tca	3/36	0.313060182659038	3	FACETS	0.911	0.812	1	0.455	0.406	0.508	CLONAL	1	TRUE	1	0.313060182659038	3		557	795	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343051	118343051	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	84	554	0	ENST00000534358.1:c.1177C>G	p.Gln393Glu	p.Q393E	ENST00000534358	NM_005933.3	393	Cag/Gag	3/36	0.313060182659038	3	FACETS	0.797	0.703	0.897	0.398	0.351	0.449	SUBCLONAL	1	TRUE	1	0.313060182659038	3		554	779	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646704	23646704	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	95	476	0	ENST00000261584.4:c.1163C>T	p.Pro388Leu	p.P388L	ENST00000261584	NM_024675.3	388	cCt/cTt	4/13	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.313060182659038	2		476	572	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926554	59926554	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	75	434	0	ENST00000259008.2:c.443G>C	p.Arg148Thr	p.R148T	ENST00000259008	NM_032043.2	148	aGa/aCa	5/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.313060182659038	2		434	342	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100954	41100954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1463467204	NA	P-0065341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	91	550	0	ENST00000373198.4:c.1402G>A	p.Glu468Lys	p.E468K	ENST00000373198	NM_133170.3	468	Gag/Aag	8/32	1	2	FACETS	0.89	0.791	0.996	0.89	0.791	0.996	CLONAL	1	TRUE	1	0.313060182659038	2		550	653	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356385	66356385	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	104	563	0	ENST00000273854.3:c.1112C>A	p.Thr371Asn	p.T371N	ENST00000273854	NM_004439.5	371	aCt/aAt	5/18	1	2	FACETS	0.875	0.784	0.973	0.875	0.784	0.973	CLONAL	1	TRUE	1	0.313060182659038	2		563	759	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518873	187518873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	92	411	0	ENST00000441802.2:c.12331G>T	p.Ala4111Ser	p.A4111S	ENST00000441802	NM_005245.3	4111	Gcc/Tcc	24/27	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.313060182659038	2		411	573	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295759	1295759	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0065341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	155	714	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.313060182659038	2		714	800	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858287	27858287	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	170	668	0	ENST00000359303.2:c.284A>T	p.Glu95Val	p.E95V	ENST00000359303	NM_003535.2	95	gAg/gTg	1/1	0.313060182659038	4	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.313060182659038	4		668	1057	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124481048	124481048	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs797045169	NA	P-0065341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	37	316	0	ENST00000357628.3:c.1348G>T	p.Glu450Ter	p.E450*	ENST00000357628	NM_015450.2	450	Gaa/Taa	14/19	0.313060182659038	4	FACETS	1	0.873	1	0.356	0.294	0.424	CLONAL	1	TRUE	1	0.313060182659038	4		316	291	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124503533	124503533	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1419371633	NA	P-0065341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	277	426	0	ENST00000357628.3:c.417G>C	p.Trp139Cys	p.W139C	ENST00000357628	NM_015450.2	139	tgG/tgC	8/19	0.313060182659038	4	FACETS	0.935	0.881	0.99	0.935	0.881	0.99	CLONAL	3	TRUE	1	0.313060182659038	4		426	828	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065356-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	87	663	0				ENST00000310581	NM_198253.2	-/1132			0.250158250963687	1	FACETS	0.537	0.485	0.59	0.537	0.485	0.59	INDETERMINATE	1	TRUE	0	0.85945177437643	1		663	215	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722761	49722761	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs62262682	NA	P-0065356-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	20	30	2	ENST00000449682.2:c.1478G>T	p.Arg493Leu	p.R493L	ENST00000449682	NM_020998.3	493	cGt/cTt	13/18	0.41564377719697	1	FACETS	0.492	0.392	0.597	0.492	0.392	0.597	INDETERMINATE	1	TRUE	0	0.85945177437643	1		32	54	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912056	50912056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065356-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	101	667	0	ENST00000440232.2:c.1790C>T	p.Pro597Leu	p.P597L	ENST00000440232	NM_002691.3	597	cCc/cTc	15/27	0.271375328591351	3	FACETS	0.596	0.534	0.661	0.199	0.178	0.221	INDETERMINATE	1	TRUE	0	0.85945177437643	3		667	564	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065357-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	81	663	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.841	0.753	0.93	0.841	0.753	0.93	CLONAL	1	TRUE	1	0.852800709140075	2		663	226	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788618	3788618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398124146	NA	P-0065357-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	9	389	0	ENST00000262367.5:c.4336C>T	p.Arg1446Cys	p.R1446C	ENST00000262367	NM_004380.2	1446	Cgc/Tgc	26/31	1	2	FACETS	0.049	0.032	0.072	0.049	0.032	0.072	SUBCLONAL	1	TRUE	1	0.852800709140075	2		389	427	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969882	81969882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065357-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	204	460	0	ENST00000359376.3:c.2951G>A	p.Arg984His	p.R984H	ENST00000359376	NM_002661.3	984	cGc/cAc	27/33	1	2	FACETS	0.906	0.848	0.966	0.906	0.848	0.966	CLONAL	1	TRUE	1	0.852800709140075	2		460	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587782272	NA	P-0065374-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	294	405	0	ENST00000269305.4:c.994-1G>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		405	323	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289265	33289265	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065375-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	256	452	0	ENST00000374542.5:c.287del	p.His96ProfsTer48	p.H96Pfs*48	ENST00000374542	NM_001141970.1	96	cAc/cc	3/8	0.616567572015491	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	FALSE	0	0.616567572015491	2		452	398	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0065380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	158	80	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.689156131793328	4	FACETS	0.942	0.873	1	0.942	0.873	1	CLONAL	2	TRUE	2	0.689156131793328	4		80	411	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786117	3786117	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	197	389	0	ENST00000262367.5:c.4648G>C	p.Glu1550Gln	p.E1550Q	ENST00000262367	NM_004380.2	1550	Gaa/Caa	28/31	0.152984737204517	3	FACETS	1	0.992	1	0.739	0.69	0.789	INDETERMINATE	1	TRUE	1	0.689156131793328	3		389	520	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17941394	17941394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	173	509	0	ENST00000458235.1:c.3014C>T	p.Ser1005Phe	p.S1005F	ENST00000458235	NM_000215.3	1005	tCt/tTt	22/24	0.152984737204517	3	FACETS	1	0.987	1	0.659	0.611	0.708	INDETERMINATE	1	TRUE	1	0.689156131793328	3		509	512	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576178	88576178	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368708129	NA	P-0065380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	103	469	1	ENST00000360948.2:c.1495G>A	p.Asp499Asn	p.D499N	ENST00000360948	NM_001012338.2	499	Gac/Aac	13/19	0.689156131793328	1	FACETS	0.626	0.567	0.687	0.626	0.567	0.687	SUBCLONAL	1	TRUE	0	0.689156131793328	1		470	313	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396516	30396516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs537554301	NA	P-0065380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	101	380	0	ENST00000331968.5:c.203C>T	p.Ser68Leu	p.S68L	ENST00000331968	NM_002742.2	68	tCg/tTg	1/18	0.538635124387437	1	FACETS	0.616	0.557	0.676	0.616	0.557	0.676	SUBCLONAL	1	TRUE	0	0.689156131793328	1		380	312	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324471	31324471	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs41559613	NA	P-0065380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	334	348	0	ENST00000412585.2:c.337G>T	p.Glu113Ter	p.E113*	ENST00000412585	NM_005514.6	113	Gag/Tag	2/8	0.617567898484028	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.689156131793328	2		348	466	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295176	1295176	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1475402448	NA	P-0065380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	83	441	0				ENST00000310581	NM_198253.2	-/1132			0.689156131793328	3	FACETS	0.683	0.605	0.766	0.342	0.302	0.383	SUBCLONAL	1	TRUE	1	0.689156131793328	3		441	474	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180845	106180845	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1053483975	NA	P-0065380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	146	364	0	ENST00000380013.4:c.3873G>T	p.Trp1291Cys	p.W1291C	ENST00000380013	NM_001127208.2	1291	tgG/tgT	7/11	1	2	FACETS	0.872	0.801	0.944	0.872	0.801	0.944	CLONAL	1	TRUE	1	0.689156131793328	2		364	486	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546342	46546342	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	213	422	0	ENST00000262741.5:c.187G>T	p.Ala63Ser	p.A63S	ENST00000262741	NM_003629.3	63	Gca/Tca	2/10	1	2	FACETS	0.98	0.916	1	0.98	0.916	1	CLONAL	1	TRUE	1	0.689156131793328	2		422	631	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195739	102195739	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	202	450	0	ENST00000263464.3:c.499A>T	p.Asn167Tyr	p.N167Y	ENST00000263464	NM_001165.4	167	Aat/Tat	2/9	0.689156131793328	3	FACETS	0.95	0.882	1			1	CLONAL	1	TRUE	NA	0.689156131793328	3		450	830	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4388056	4388056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	143	471	0	ENST00000261254.3:c.542C>T	p.Ala181Val	p.A181V	ENST00000261254	NM_001759.3	181	gCt/gTt	3/5	0.152984737204517	3	FACETS	1	0.983	1	0.63	0.579	0.682	INDETERMINATE	1	TRUE	1	0.689156131793328	3		471	443	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454579	99454579	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	164	402	0	ENST00000268035.6:c.1498A>T	p.Thr500Ser	p.T500S	ENST00000268035	NM_000875.3	500	Acg/Tcg	7/21	1	2	FACETS	0.933	0.863	1	0.933	0.863	1	CLONAL	1	TRUE	1	0.689156131793328	2		402	510	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119707	70119707	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	186	438	0	ENST00000245479.2:c.709C>A	p.Pro237Thr	p.P237T	ENST00000245479	NM_000346.3	237	Cca/Aca	3/3	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.689156131793328	2		438	400	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136250	202136250	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	178	421	0	ENST00000358485.4:c.494A>C	p.Tyr165Ser	p.Y165S	ENST00000358485	NM_001080125.1	165	tAt/tCt	3/9	0.689156131793328	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.689156131793328	1		421	316	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537214	41537215	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TA	novel	NA	P-0065380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	173	321	0	ENST00000263253.7:c.2041_2042delinsTA	p.Gly681Ter	p.G681*	ENST00000263253	NM_001429.3	681	GGa/TAa	10/31	1	2	FACETS	0.89	0.824	0.958	0.89	0.824	0.958	CLONAL	1	TRUE	1	0.689156131793328	2		321	564	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691773	30691783	+	frameshift_variant	Frame_Shift_Del	DEL	ACGAGAACATA	ACGAGAACATA	-	novel	NA	P-0065380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	275	466	0	ENST00000295754.5:c.277_287del	p.Glu93ThrfsTer7	p.E93Tfs*7	ENST00000295754	NM_003242.5	92	gACGAGAACATA/g	3/7	0.689156131793328	2	FACETS	0.837	0.797	0.875	0.837	0.797	0.875	CLONAL	2	TRUE	0	0.689156131793328	2		466	477	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665150	138665150	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	251	390	0	ENST00000330315.3:c.415G>T	p.Glu139Ter	p.E139*	ENST00000330315	NM_023067.3	139	Gag/Tag	1/1	0.689156131793328	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.689156131793328	4		390	546	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535458	187535458	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	175	361	0	ENST00000441802.2:c.9116G>C	p.Gly3039Ala	p.G3039A	ENST00000441802	NM_005245.3	3039	gGa/gCa	12/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.689156131793328	2		361	453	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527299	137527299	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1800563	NA	P-0065380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	356	367	0	ENST00000367739.4:c.347C>A	p.Ser116Ter	p.S116*	ENST00000367739	NM_000416.2	116	tCa/tAa	3/7	0.667569487807048	2	FACETS	0.941	0.905	0.976	0.941	0.905	0.976	CLONAL	2	TRUE	0	0.689156131793328	2		367	549	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94908669	94908669	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	CTA	novel	NA	P-0065380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	153	355	0	ENST00000536441.1:c.1385delinsTAG	p.Ser462LeufsTer11	p.S462Lfs*11	ENST00000536441	NM_144665.3	462	tCa/tTAGa	9/10	1	2	FACETS	0.857	0.789	0.927	0.857	0.789	0.927	CLONAL	1	TRUE	1	0.689156131793328	2		355	518	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469672	NA	P-0065382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	119	335	0	ENST00000374080.3:c.131G>A	p.Gly44Asp	p.G44D	ENST00000374080		44	gGt/gAt	2/45	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.470674545882395	2		335	470	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490535	56490535	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	90	393	0	ENST00000267101.3:c.2179G>A	p.Val727Met	p.V727M	ENST00000267101	NM_001982.3	727	Gtg/Atg	19/28	1	2	FACETS	0.747	0.665	0.834	0.747	0.665	0.834	SUBCLONAL	1	TRUE	1	0.470674545882395	2		393	512	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0065383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	91	286	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.458998455099167	2		286	305	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612974	228612974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756810829	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	150	582	1	ENST00000366696.1:c.53G>A	p.Arg18His	p.R18H	ENST00000366696	NM_003493.2	18	cGc/cAc	1/1	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.497966442744728	2		583	559	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	80	610	4	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.571	0.503	0.643	0.571	0.503	0.643	SUBCLONAL	1	TRUE	1	0.497966442744728	2		614	563	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	137	261	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.497966442744728	2		264	378	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	88	460	1	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	0.856	0.763	0.954	0.856	0.763	0.954	CLONAL	1	TRUE	1	0.497966442744728	2		461	413	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	154	294	2	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.94	0.875	1	1	0.992	1	CLONAL	2	TRUE	1	0.497966442744728	2		296	329	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	79	477	3	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.642	0.566	0.723	0.642	0.566	0.723	SUBCLONAL	1	TRUE	1	0.497966442744728	2		480	494	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661663	227661664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761880048	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	98	459	1	ENST00000305123.5:c.1791dup	p.His598AlafsTer13	p.H598Afs*13	ENST00000305123	NM_005544.2	597	-/G	1/2	1	2	FACETS	0.881	0.79	0.976	0.881	0.79	0.976	CLONAL	1	TRUE	1	0.497966442744728	2		460	447	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	28	645	3	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.215	0.171	0.266	0.215	0.171	0.266	SUBCLONAL	1	TRUE	1	0.497966442744728	2		648	522	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736510	85736511	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs387906351	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	103	337	2	ENST00000370580.1:c.136dup	p.Ile46AsnfsTer4	p.I46Nfs*4	ENST00000370580	NM_003921.4	46	ata/aAta	2/3	1	2	FACETS	0.841	0.756	0.93	0.841	0.756	0.93	CLONAL	1	TRUE	1	0.497966442744728	2		339	492	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100727	8100728	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs771019738	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	72	443	1	ENST00000346208.3:c.708dup	p.Ser237GlnfsTer66	p.S237Qfs*66	ENST00000346208		234	ttc/ttCc	3/6	0.497966442744728	1	FACETS	0.754	0.665	0.848	0.754	0.665	0.848	SUBCLONAL	1	TRUE	0	0.497966442744728	1		444	288	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692981	89692982	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	71	303	0	ENST00000371953.3:c.469dup	p.Glu157GlyfsTer23	p.E157Gfs*23	ENST00000371953	NM_000314.4	155	-/G	5/9	0.497966442744728	1	FACETS	0.846	0.748	0.95	0.846	0.748	0.95	CLONAL	1	TRUE	0	0.497966442744728	1		303	253	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10794117	10794117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs949336975	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	147	372	2	ENST00000361367.2:c.2495G>A	p.Arg832His	p.R832H	ENST00000361367	NM_014633.3	832	cGc/cAc	20/25	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.497966442744728	2		374	535	SUCCESS
ATM	472	MSKCC	GRCh37	11	108168092	108168092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	63	289	0	ENST00000278616.4:c.4988G>A	p.Gly1663Asp	p.G1663D	ENST00000278616	NM_000051.3	1663	gGt/gAt	33/63	0.497966442744728	3	FACETS	0.932	0.811	1	0.466	0.405	0.531	CLONAL	1	TRUE	1	0.497966442744728	3		289	339	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216477	108216477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587782558	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	97	242	0	ENST00000278616.4:c.8432del	p.Lys2811SerfsTer46	p.K2811Sfs*46	ENST00000278616	NM_000051.3	2809	cAa/ca	58/63	0.497966442744728	3	FACETS	0.997	0.905	1	0.997	0.905	1	CLONAL	2	TRUE	1	0.497966442744728	3		242	244	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478928	56478928	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	107	381	0	ENST00000267101.3:c.384C>A	p.Ser128Arg	p.S128R	ENST00000267101	NM_001982.3	128	agC/agA	3/28	1	2	FACETS	0.918	0.828	1	0.918	0.828	1	CLONAL	1	TRUE	1	0.497966442744728	2		381	468	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914613	32914613	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1160083526	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	95	386	0	ENST00000380152.3:c.6121T>A	p.Ser2041Thr	p.S2041T	ENST00000380152		2041	Tcc/Acc	11/27	1	2	FACETS	0.961	0.862	1	0.961	0.862	1	CLONAL	1	TRUE	1	0.497966442744728	2		386	397	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396233	396234	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769619638	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	118	411	0	ENST00000262320.3:c.792dup	p.Gly265ArgfsTer20	p.G265Rfs*20	ENST00000262320	NM_003502.3	264	-/C	2/11	1	2	FACETS	0.967	0.877	1	0.967	0.877	1	CLONAL	1	TRUE	1	0.497966442744728	2		411	490	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396998	396999	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	102	372	0	ENST00000262320.3:c.27dup	p.Asp11GlyfsTer18	p.D11Gfs*18	ENST00000262320	NM_003502.3	9	-/C	2/11	1	2	FACETS	0.881	0.792	0.974	0.881	0.792	0.974	CLONAL	1	TRUE	1	0.497966442744728	2		372	465	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779646	3779646	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	102	486	0	ENST00000262367.5:c.5402T>C	p.Val1801Ala	p.V1801A	ENST00000262367	NM_004380.2	1801	gTg/gCg	31/31	1	2	FACETS	0.848	0.762	0.939	0.848	0.762	0.939	CLONAL	1	TRUE	1	0.497966442744728	2		486	483	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641386	23641386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567218116	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	105	417	0	ENST00000261584.4:c.2089G>A	p.Gly697Ser	p.G697S	ENST00000261584	NM_024675.3	697	Ggc/Agc	5/13	1	2	FACETS	0.903	0.813	0.997	0.903	0.813	0.997	CLONAL	1	TRUE	1	0.497966442744728	2		417	467	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991586	72991586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768340392	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	122	419	0	ENST00000268489.5:c.2459G>A	p.Arg820His	p.R820H	ENST00000268489	NM_006885.3	820	cGc/cAc	2/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.497966442744728	2		419	443	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993013	72993014	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	116	480	0	ENST00000268489.5:c.1031dup	p.Asn344LysfsTer13	p.N344Kfs*13	ENST00000268489	NM_006885.3	344	aac/aaAc	2/10	1	2	FACETS	0.881	0.797	0.968	0.881	0.797	0.968	CLONAL	1	TRUE	1	0.497966442744728	2		480	529	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556292	29556292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1251621684	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	91	387	0	ENST00000356175.3:c.2659G>A	p.Ala887Thr	p.A887T	ENST00000356175	NM_000267.3	887	Gca/Aca	21/57	1	2	FACETS	0.883	0.789	0.982	0.883	0.789	0.982	CLONAL	1	TRUE	1	0.497966442744728	2		387	414	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884217	37884218	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768092215	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	102	410	1	ENST00000269571.5:c.3694dup	p.Ala1232GlyfsTer45	p.A1232Gfs*45	ENST00000269571		1230	cgg/cGgg	27/27	1	2	FACETS	0.942	0.848	1	0.942	0.848	1	CLONAL	1	TRUE	1	0.497966442744728	2		411	435	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512401	38512402	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs745553450	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	71	329	1	ENST00000254066.5:c.1319dup	p.Pro441AlafsTer5	p.P441Afs*5	ENST00000254066	NM_000964.3	438	gcc/gCcc	9/9	1	2	FACETS	0.862	0.758	0.972	0.862	0.758	0.972	CLONAL	1	TRUE	1	0.497966442744728	2		330	331	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244044	41244045	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs397507216	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	114	407	0	ENST00000357654.3:c.3503dup	p.Asn1168LysfsTer2	p.N1168Kfs*2	ENST00000357654	NM_007294.3	1168	aat/aaAt	10/23	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.497966442744728	2		407	453	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734176	58734177	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	94	345	0	ENST00000305921.3:c.1238dup	p.Cys414MetfsTer20	p.C414Mfs*20	ENST00000305921	NM_003620.3	412	tcc/tCcc	5/6	1	2	FACETS	0.996	0.893	1	0.996	0.893	1	CLONAL	1	TRUE	1	0.497966442744728	2		345	379	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533938	63533939	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	198	413	0	ENST00000307078.5:c.1214_1215dup	p.Gly406ArgfsTer53	p.G406Rfs*53	ENST00000307078	NM_004655.3	405	-/AG	6/11	1	2	FACETS	0.872	0.817	0.928	1	0.993	1	CLONAL	2	TRUE	1	0.497966442744728	2		413	456	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245995	5245996	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	93	469	0	ENST00000357368.4:c.779dup	p.Asn261GlnfsTer30	p.N261Qfs*30	ENST00000357368	NM_002850.3	260	ggc/ggGc	10/38	1	2	FACETS	0.823	0.735	0.915	0.823	0.735	0.915	CLONAL	1	TRUE	1	0.497966442744728	2		469	454	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134252	11134252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	97	313	0	ENST00000358026.2:c.2918G>A	p.Arg973Gln	p.R973Q	ENST00000358026	NM_001128849.1	973	cGg/cAg	20/36	1	2	FACETS	0.943	0.847	1	0.943	0.847	1	CLONAL	1	TRUE	1	0.497966442744728	2		313	413	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272237	15272238	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	86	428	1	ENST00000263388.2:c.6201dup	p.Gly2068ArgfsTer27	p.G2068Rfs*27	ENST00000263388	NM_000435.2	2067	-/C	33/33	1	2	FACETS	0.921	0.821	1	0.921	0.821	1	CLONAL	1	TRUE	1	0.497966442744728	2		429	375	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350626	15350626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1234699192	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	99	393	0	ENST00000263377.2:c.3289C>T	p.Arg1097Cys	p.R1097C	ENST00000263377	NM_058243.2	1097	Cgt/Tgt	16/20	1	2	FACETS	0.984	0.885	1	0.984	0.885	1	CLONAL	1	TRUE	1	0.497966442744728	2		393	404	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210932	36210932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	109	532	0	ENST00000222270.7:c.683C>T	p.Ala228Val	p.A228V	ENST00000222270	NM_014727.1	228	gCa/gTa	3/37	1	2	FACETS	0.96	0.867	1	0.96	0.867	1	CLONAL	1	TRUE	1	0.497966442744728	2		532	456	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422660	47422660	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	31	363	0	ENST00000404338.3:c.728T>C	p.Leu243Ser	p.L243S	ENST00000404338	NM_004491.4	243	tTa/tCa	1/6	1	2	FACETS	0.264	0.213	0.322	0.264	0.213	0.322	SUBCLONAL	1	TRUE	1	0.497966442744728	2		363	471	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424759	47424760	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	142	432	1	ENST00000404338.3:c.2834dup	p.Asn946GlufsTer11	p.N946Efs*11	ENST00000404338	NM_004491.4	943	gaa/gAaa	1/6	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.497966442744728	2		433	541	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605215	46605215	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1407435090	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	81	350	0	ENST00000263734.3:c.1432A>T	p.Ser478Cys	p.S478C	ENST00000263734	NM_001430.4	478	Agc/Tgc	10/16	1	2	FACETS	0.911	0.809	1	0.911	0.809	1	CLONAL	1	TRUE	1	0.497966442744728	2		350	357	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378265	225378266	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	80	267	0	ENST00000264414.4:c.629dup	p.Leu210PhefsTer20	p.L210Ffs*20	ENST00000264414	NM_003590.4	210	ttg/ttTg	5/16	1	2	FACETS	0.913	0.81	1	0.913	0.81	1	CLONAL	1	TRUE	1	0.497966442744728	2		267	352	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422542	225422542	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	74	231	0	ENST00000264414.4:c.98T>C	p.Ile33Thr	p.I33T	ENST00000264414	NM_003590.4	33	aTt/aCt	2/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.497966442744728	2		231	266	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221709	22221717	+	inframe_deletion	In_Frame_Del	DEL	CCGCCGCCG	CCGCCGCCG	-	rs751880548	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	52	268	0	ENST00000215832.6:c.14_22del	p.Ala5_Ala7del	p.A5_A7del	ENST00000215832	NM_002745.4	5	gCGGCGGCGGgc/ggc	1/9	1	2	FACETS	0.9	0.775	1	0.9	0.775	1	CLONAL	1	TRUE	1	0.497966442744728	2		268	232	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69998250	69998250	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	46	343	0	ENST00000394351.3:c.494del	p.Pro165HisfsTer17	p.P165Hfs*17	ENST00000394351	NM_000248.3	164	Ccc/cc	5/9	1	2	FACETS	0.403	0.34	0.474	0.403	0.34	0.474	SUBCLONAL	1	TRUE	1	0.497966442744728	2		343	458	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851793	134851793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	115	494	0	ENST00000398015.3:c.1199C>T	p.Thr400Ile	p.T400I	ENST00000398015	NM_004441.4	400	aCc/aTc	5/16	1	2	FACETS	0.966	0.875	1	0.966	0.875	1	CLONAL	1	TRUE	1	0.497966442744728	2		494	478	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665096	138665096	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs758370933	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	75	340	0	ENST00000330315.3:c.469C>G	p.Pro157Ala	p.P157A	ENST00000330315	NM_023067.3	157	Ccc/Gcc	1/1	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.497966442744728	2		340	237	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144359669	144359671	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	119	370	0	ENST00000262995.4:c.1114_1116del	p.Ser372del	p.S372del	ENST00000262995	NM_207123.2	371	AGT/-	4/11	1	2	FACETS	0.994	0.902	1	0.994	0.902	1	CLONAL	1	TRUE	1	0.497966442744728	2		370	481	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945616	38945619	+	frameshift_variant	Frame_Shift_Del	DEL	AGTT	AGTT	-	rs1390116297	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	68	319	0	ENST00000357387.3:c.4607_4610del	p.Gln1536ArgfsTer27	p.Q1536Rfs*27	ENST00000357387	NM_152756.3	1536	cAACTg/cg	34/38	1	2	FACETS	0.748	0.655	0.848	0.748	0.655	0.848	SUBCLONAL	1	TRUE	1	0.497966442744728	2		319	365	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722311	176722311	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs747099587	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	118	452	0	ENST00000439151.2:c.7942T>A	p.Ser2648Thr	p.S2648T	ENST00000439151	NM_022455.4	2648	Tct/Act	23/23	1	2	FACETS	0.954	0.865	1	0.954	0.865	1	CLONAL	1	TRUE	1	0.497966442744728	2		452	497	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032108	26032108	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	152	535	0	ENST00000244661.2:c.181T>A	p.Leu61Met	p.L61M	ENST00000244661	NM_003537.3	61	Ttg/Atg	1/1	1	2	FACETS	0.986	0.905	1	0.986	0.905	1	CLONAL	1	TRUE	1	0.497966442744728	2		535	619	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6031624	6031624	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	94	145	0	ENST00000265849.7:c.968T>G	p.Leu323Arg	p.L323R	ENST00000265849	NM_000535.5	323	cTt/cGt	9/15	0.307314143640324	4	FACETS	1	0.974	1	0.816	0.74	0.894	CLONAL	2	TRUE	1	0.497966442744728	4		145	231	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	83	364	0	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	0.307314143640324	4	FACETS	0.875	0.773	0.983	0.292	0.257	0.328	CLONAL	1	TRUE	1	0.497966442744728	4		364	571	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846173	151846173	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	145	406	0	ENST00000262189.6:c.12839A>G	p.Tyr4280Cys	p.Y4280C	ENST00000262189	NM_170606.2	4280	tAc/tGc	52/59	0.40186975194491	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.497966442744728	1		406	408	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	88	389	0	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	NA	2	FACETS	0.752	0.669	0.84			1	INDETERMINATE	1	TRUE	NA	0.497966442744728	2		389	470	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145743006	145743006	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	68	411	0	ENST00000428558.2:c.98C>A	p.Ala33Glu	p.A33E	ENST00000428558	NM_004260.3	33	gCg/gAg	2/22	NA	2	FACETS	0.853	0.748	0.965			1	INDETERMINATE	1	TRUE	NA	0.497966442744728	2		411	320	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404588	8404588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	75	280	0	ENST00000356435.5:c.4159G>A	p.Ala1387Thr	p.A1387T	ENST00000356435		1387	Gcg/Acg	25/35	1	2	FACETS	0.978	0.865	1	0.978	0.865	1	CLONAL	1	TRUE	1	0.497966442744728	2		280	308	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890149	76890150	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	75	293	0	ENST00000373344.5:c.4744dup	p.Thr1582AsnfsTer19	p.T1582Nfs*19	ENST00000373344	NM_000489.3	1582	aca/aAca	17/35	1	2	FACETS	0.837	0.738	0.941	0.837	0.738	0.941	CLONAL	1	TRUE	1	0.497966442744728	2		293	360	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0065384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	28	248	1	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	2	FACETS	0.543	0.437	0.663	0.543	0.437	0.663	SUBCLONAL	1	TRUE	1	0.497966442744728	2		249	207	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0065385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	379	501	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.755150189715239	2	FACETS	0.993	0.962	1	0.993	0.962	1	CLONAL	2	TRUE	0	0.766436115677337	2		501	498	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608662	189608662	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0065385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	267	317	0	ENST00000264731.3:c.1737C>G	p.Tyr579Ter	p.Y579*	ENST00000264731	NM_003722.4	579	taC/taG	13/14	0.754968398332181	3	FACETS	1	0.97	1	0.683	0.65	0.716	CLONAL	2	TRUE	0	0.766436115677337	3		317	470	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777894	NA	P-0065386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	70	380	0	ENST00000361445.4:c.6644C>T	p.Ser2215Phe	p.S2215F	ENST00000361445	NM_004958.3	2215	tCt/tTt	47/58	0.573604471266238	1	FACETS	0.781	0.691	0.874	0.781	0.691	0.874	SUBCLONAL	1	TRUE	0	0.573604471266238	1		380	223	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223069	5223069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs906063149	NA	P-0065386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	105	611	0	ENST00000357368.4:c.2734G>A	p.Gly912Ser	p.G912S	ENST00000357368	NM_002850.3	912	Ggc/Agc	18/38	1	2	FACETS	0.598	0.537	0.663	0.598	0.537	0.663	SUBCLONAL	1	TRUE	1	0.573604471266238	2		611	612	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295193	1295194	+	upstream_gene_variant	5'Flank	INS	-	-	CGGAAAGGAAGGGGAGGGGCTGGGAGGGCC	novel	NA	P-0065386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	22	424	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.278	0.215	0.35	0.278	0.215	0.35	SUBCLONAL	1	TRUE	1	0.573604471266238	2		424	276	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211175	36211175	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	395	506	0	ENST00000222270.7:c.926C>T	p.Ser309Leu	p.S309L	ENST00000222270	NM_014727.1	309	tCa/tTa	3/37	0.500405940125784	6	FACETS	1	0.988	1	1	0.988	1	CLONAL	4	TRUE	2	0.500405940125784	6		506	734	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211267	36211267	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	462	572	0	ENST00000222270.7:c.1018C>A	p.Pro340Thr	p.P340T	ENST00000222270	NM_014727.1	340	Ccc/Acc	3/37	0.500405940125784	6	FACETS	1	0.981	1	1	0.981	1	CLONAL	4	TRUE	2	0.500405940125784	6		572	895	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211996	36211996	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	490	599	0	ENST00000222270.7:c.1747C>G	p.Pro583Ala	p.P583A	ENST00000222270	NM_014727.1	583	Cca/Gca	3/37	0.500405940125784	6	FACETS	1	0.993	1	1	0.993	1	CLONAL	4	TRUE	2	0.500405940125784	6		599	874	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218943	36219848	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTGCCAGCTCTCCTGGGGAAGCTGGCTCTTCTCATCCTGTTAACCCACTCCCCAGCTGCTAGAATCTGCGTTCGGCTGGTTCGACGCCCACGACCCCAAGTACTGGCGACGGAGTACCCGGCTGCCAAAGTGAGCAAGGCTGGGTAGCAGAAGGGAAGCCGGGGAGTGAGGGCAAGGCCAGGGCATGCAGGGGCCACGCTGGGCTGAGAAGAGATGAGCAGAGGTAGGGTCTGGAGCAGAGCTGGAGAGGAGGGTGGTGGAACCCAGGTGAGATTCCCTGGTGGTTCTAGACTAGCAAAGCTTTGTTTCTGCTTTGTGCAGGGGAATGCTGGGGACAAAGCAGTGAGCGAATCAGATTGGGCTCTGCTTAAAGAGCTCATTGTGGAGCCGGGCAGGCACTGAAGACCCAGATGGTCAGGGCAGTGATGGAGAATACCAGGGGGCGGTGGGGGCCCGGAGGGGTACCTGCTGGAGCCGAGGTGTCAGGGAAGGCTTCCTGAAAGAGATGGCATTGGAGCAGAGCTGGGGAGGAAGAGTATTGCAGGCATGAGGAGCAGCATTTCGTATGTCCAAGCTGGCACAAGAGGGCCTGGCTTATTTGGTGGACTGAGAGAAATTCCACATAGAGAGGGAGTAGCGGGTGTCATGGCGAGTTCAGGCTGGTTTGTGGATGGGCCCCCGTTCAGCTGCCCTTGTTGGGCACATCAGCTGCTAACCCTGCCTGTCCACAGCGGAGTCCTTCCCAATGCGGTGTTGCCCCCATCCCTGGATCATGTCTATGCGCAGTGGAGACAGCAGGAACCAGAGACCCCAGAATCAGGGCAGCCTCCAGGGGATCCCTCAGCAGGTACTGGGAAGTGGGGGTCCAGAAGCCAGGGCCCTGTGTTGGTGGCCTGGCTCCGGGT	CCTGCCAGCTCTCCTGGGGAAGCTGGCTCTTCTCATCCTGTTAACCCACTCCCCAGCTGCTAGAATCTGCGTTCGGCTGGTTCGACGCCCACGACCCCAAGTACTGGCGACGGAGTACCCGGCTGCCAAAGTGAGCAAGGCTGGGTAGCAGAAGGGAAGCCGGGGAGTGAGGGCAAGGCCAGGGCATGCAGGGGCCACGCTGGGCTGAGAAGAGATGAGCAGAGGTAGGGTCTGGAGCAGAGCTGGAGAGGAGGGTGGTGGAACCCAGGTGAGATTCCCTGGTGGTTCTAGACTAGCAAAGCTTTGTTTCTGCTTTGTGCAGGGGAATGCTGGGGACAAAGCAGTGAGCGAATCAGATTGGGCTCTGCTTAAAGAGCTCATTGTGGAGCCGGGCAGGCACTGAAGACCCAGATGGTCAGGGCAGTGATGGAGAATACCAGGGGGCGGTGGGGGCCCGGAGGGGTACCTGCTGGAGCCGAGGTGTCAGGGAAGGCTTCCTGAAAGAGATGGCATTGGAGCAGAGCTGGGGAGGAAGAGTATTGCAGGCATGAGGAGCAGCATTTCGTATGTCCAAGCTGGCACAAGAGGGCCTGGCTTATTTGGTGGACTGAGAGAAATTCCACATAGAGAGGGAGTAGCGGGTGTCATGGCGAGTTCAGGCTGGTTTGTGGATGGGCCCCCGTTCAGCTGCCCTTGTTGGGCACATCAGCTGCTAACCCTGCCTGTCCACAGCGGAGTCCTTCCCAATGCGGTGTTGCCCCCATCCCTGGATCATGTCTATGCGCAGTGGAGACAGCAGGAACCAGAGACCCCAGAATCAGGGCAGCCTCCAGGGGATCCCTCAGCAGGTACTGGGAAGTGGGGGTCCAGAAGCCAGGGCCCTGTGTTGGTGGCCTGGCTCCGGGT	-	novel	NA	P-0065387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	372	563	0	ENST00000222270.7:c.4498-52_4688-34del		p.X1500_splice	ENST00000222270	NM_014727.1	1500		19-20/37	0.500405940125784	6	FACETS	0.99	0.947	1	0.99	0.947	1	CLONAL	4	TRUE	2	0.500405940125784	6		563	751	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0065388-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	44	466	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.781	0.654	0.922	0.781	0.654	0.922	CLONAL	1	TRUE	1	0.19	2		466	593	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0065388-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	44	425	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.8	0.67	0.944	0.8	0.67	0.944	CLONAL	1	TRUE	1	0.19	2		425	579	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21344772	21344772	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065388-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	42	407	0	ENST00000215739.8:c.749A>C	p.Lys250Thr	p.K250T	ENST00000215739	NM_006767.3	250	aAa/aCa	8/21	1	2	FACETS	0.877	0.732	1	0.877	0.732	1	CLONAL	1	TRUE	1	0.19	2		407	504	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0065388-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	51	308	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.19	2		308	473	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	66	418	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.683	0.597	0.774	0.683	0.597	0.774	SUBCLONAL	1	TRUE	1	0.594862325750914	2		418	325	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	108	431	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.854	0.772	0.94	0.854	0.772	0.94	CLONAL	1	TRUE	1	0.594862325750914	2		431	425	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027958	48027958	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1558666905	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	119	438	0	ENST00000234420.5:c.2836G>T	p.Glu946Ter	p.E946*	ENST00000234420	NM_000179.2	946	Gaa/Taa	4/10	1	2	FACETS	0.87	0.79	0.953	0.87	0.79	0.953	CLONAL	1	TRUE	1	0.594862325750914	2		438	460	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732866	44732866	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	102	203	0	ENST00000377967.4:c.69G>T	p.Lys23Asn	p.K23N	ENST00000377967	NM_021140.2	23	aaG/aaT	1/29	1	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.594862325750914	1		203	190	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604668	48604668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	35	429	0	ENST00000342988.3:c.1490G>A	p.Arg497His	p.R497H	ENST00000342988	NM_005359.5	497	cGc/cAc	12/12	1	2	FACETS	0.237	0.194	0.286	0.237	0.194	0.286	SUBCLONAL	1	TRUE	1	0.594862325750914	2		429	496	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339110	65339110	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs747560156	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	144	444	0	ENST00000342505.4:c.426G>T	p.Lys142Asn	p.K142N	ENST00000342505	NM_002227.2	142	aaG/aaT	5/25	1	2	FACETS	0.946	0.868	1	0.946	0.868	1	CLONAL	1	TRUE	1	0.594862325750914	2		444	512	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400905	72400905	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	118	388	1	ENST00000357731.5:c.266C>A	p.Pro89His	p.P89H	ENST00000357731	NM_173808.2	89	cCt/cAt	2/7	1	2	FACETS	0.902	0.819	0.987	0.902	0.819	0.987	CLONAL	1	TRUE	1	0.594862325750914	2		389	440	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165520	118165520	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	154	459	0	ENST00000369448.3:c.30T>A	p.Asp10Glu	p.D10E	ENST00000369448	NM_017709.3	10	gaT/gaA	2/2	1	2	FACETS	0.872	0.801	0.945	0.872	0.801	0.945	CLONAL	1	TRUE	1	0.594862325750914	2		459	594	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150919401	150919401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377752861	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	126	416	0	ENST00000271640.5:c.1180C>T	p.Arg394Trp	p.R394W	ENST00000271640	NM_001145415.1	394	Cgg/Tgg	10/22	1	2	FACETS	0.849	0.773	0.928	0.849	0.773	0.928	CLONAL	1	TRUE	1	0.594862325750914	2		416	499	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956150	175956150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374830292	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	72	311	0	ENST00000367669.3:c.2062G>A	p.Asp688Asn	p.D688N	ENST00000367669	NM_022457.5	688	Gac/Aac	18/20	1	2	FACETS	0.893	0.789	1	0.893	0.789	1	CLONAL	1	TRUE	1	0.594862325750914	2		311	271	SUCCESS
FH	2271	MSKCC	GRCh37	1	241676991	241676991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	68	314	0	ENST00000366560.3:c.290G>A	p.Gly97Asp	p.G97D	ENST00000366560	NM_000143.3	97	gGc/gAc	3/10	1	2	FACETS	0.733	0.643	0.829	0.733	0.643	0.829	SUBCLONAL	1	TRUE	1	0.594862325750914	2		314	312	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716138	243716138	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	65	321	0	ENST00000263826.5:c.1056G>T	p.Glu352Asp	p.E352D	ENST00000263826	NM_005465.4	352	gaG/gaT	10/13	1	2	FACETS	0.828	0.725	0.936	0.828	0.725	0.936	CLONAL	1	TRUE	1	0.594862325750914	2		321	264	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333442	70333442	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	115	458	0	ENST00000373644.4:c.1347G>T	p.Trp449Cys	p.W449C	ENST00000373644	NM_030625.2	449	tgG/tgT	2/12	1	2	FACETS	0.83	0.752	0.911	0.83	0.752	0.911	CLONAL	1	TRUE	1	0.594862325750914	2		458	466	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426835	70426835	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	109	379	0	ENST00000373644.4:c.4495C>A	p.Leu1499Ile	p.L1499I	ENST00000373644	NM_030625.2	1499	Ctt/Att	7/12	1	2	FACETS	0.82	0.741	0.902	0.82	0.741	0.902	CLONAL	1	TRUE	1	0.594862325750914	2		379	447	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685310	89685310	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	64	239	0	ENST00000371953.3:c.205A>C	p.Asn69His	p.N69H	ENST00000371953	NM_000314.4	69	Aat/Cat	3/9	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.594862325750914	2		239	184	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724261	112724261	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	116	431	0	ENST00000369452.4:c.145G>T	p.Asp49Tyr	p.D49Y	ENST00000369452	NM_007373.3	49	Gat/Tat	2/9	1	2	FACETS	0.794	0.72	0.872	0.794	0.72	0.872	SUBCLONAL	1	TRUE	1	0.594862325750914	2		431	491	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10794758	10794758	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	96	354	0	ENST00000361367.2:c.2665C>A	p.Leu889Ile	p.L889I	ENST00000361367	NM_014633.3	889	Ctt/Att	21/25	1	2	FACETS	0.801	0.718	0.887	0.801	0.718	0.887	CLONAL	1	TRUE	1	0.594862325750914	2		354	403	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132779	64132779	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776640922	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	129	514	0	ENST00000334205.4:c.913G>A	p.Asp305Asn	p.D305N	ENST00000334205	NM_003942.2	305	Gat/Aat	9/17	1	2	FACETS	0.909	0.83	0.992	0.909	0.83	0.992	CLONAL	1	TRUE	1	0.594862325750914	2		514	477	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94209538	94209538	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	63	274	0	ENST00000323929.3:c.576G>A	p.Met192Ile	p.M192I	ENST00000323929	NM_005591.3	192	atG/atA	7/20	1	2	FACETS	0.851	0.744	0.963	0.851	0.744	0.963	CLONAL	1	TRUE	1	0.594862325750914	2		274	249	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219165	94219165	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782472	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	86	379	0	ENST00000323929.3:c.239G>T	p.Arg80Ile	p.R80I	ENST00000323929	NM_005591.3	80	aGa/aTa	4/20	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.594862325750914	2		379	286	SUCCESS
ATM	472	MSKCC	GRCh37	11	108159816	108159816	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	13	97	0	ENST00000278616.4:c.4222C>A	p.Leu1408Ile	p.L1408I	ENST00000278616	NM_000051.3	1408	Ctt/Att	28/63	1	2	FACETS	0.857	0.631	1	0.857	0.631	1	CLONAL	1	TRUE	1	0.594862325750914	2		97	51	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374253	118374253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	48	553	0	ENST00000534358.1:c.7646C>T	p.Ser2549Phe	p.S2549F	ENST00000534358	NM_005933.3	2549	tCc/tTc	27/36	1	2	FACETS	0.301	0.254	0.352	0.301	0.254	0.352	SUBCLONAL	1	TRUE	1	0.594862325750914	2		553	537	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404855	404855	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	129	370	0	ENST00000399788.2:c.4339G>T	p.Glu1447Ter	p.E1447*	ENST00000399788	NM_001042603.1	1447	Gaa/Taa	26/28	0.517295070128011	3	FACETS	0.893	0.812	0.978	0.447	0.406	0.489	CLONAL	1	TRUE	1	0.594862325750914	3		370	630	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435481	18435481	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	119	372	0	ENST00000266497.5:c.466C>A	p.Leu156Ile	p.L156I	ENST00000266497		156	Cta/Ata	1/31	0.517295070128011	3	FACETS	1	0.986	1	0.733	0.669	0.799	CLONAL	1	TRUE	1	0.594862325750914	3		372	354	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491384	18491384	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	69	306	0	ENST00000266497.5:c.1297G>T	p.Glu433Ter	p.E433*	ENST00000266497		433	Gaa/Taa	8/31	0.517295070128011	3	FACETS	1	0.882	1	0.502	0.441	0.566	CLONAL	1	TRUE	1	0.594862325750914	3		306	300	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636366	21636366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561515655	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	78	363	2	ENST00000421138.2:c.644G>A	p.Arg215Gln	p.R215Q	ENST00000421138		215	cGa/cAa	7/16	0.517295070128011	3	FACETS	0.855	0.755	0.961	0.427	0.377	0.481	CLONAL	1	TRUE	1	0.594862325750914	3		365	398	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	96	361	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.517295070128011	3	FACETS	0.799	0.723	0.877	0.799	0.723	0.877	SUBCLONAL	2	TRUE	1	0.594862325750914	3		361	262	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425854	49425854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760279999	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	104	528	0	ENST00000301067.7:c.12634C>T	p.Arg4212Trp	p.R4212W	ENST00000301067	NM_003482.3	4212	Cgg/Tgg	39/54	0.517295070128011	3	FACETS	0.777	0.697	0.861	0.388	0.348	0.431	SUBCLONAL	1	TRUE	1	0.594862325750914	3		528	584	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864433	57864433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs538595523	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	113	566	0	ENST00000228682.2:c.1910G>A	p.Arg637Gln	p.R637Q	ENST00000228682	NM_005269.2	637	cGg/cAg	12/12	0.517295070128011	3	FACETS	0.837	0.755	0.923	0.418	0.377	0.462	CLONAL	1	TRUE	1	0.594862325750914	3		566	589	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212572	133212572	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	98	417	0	ENST00000320574.5:c.5717C>A	p.Ser1906Tyr	p.S1906Y	ENST00000320574	NM_006231.2	1906	tCt/tAt	42/49	0.517295070128011	3	FACETS	0.921	0.826	1	0.461	0.413	0.511	CLONAL	1	TRUE	1	0.594862325750914	3		417	464	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248859	133248859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149296223	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	138	473	0	ENST00000320574.5:c.1736G>A	p.Arg579His	p.R579H	ENST00000320574	NM_006231.2	579	cGc/cAc	16/49	0.517295070128011	3	FACETS	0.871	0.794	0.951	0.436	0.397	0.476	CLONAL	1	TRUE	1	0.594862325750914	3		473	691	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249842	133249842	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	224	415	0	ENST00000320574.5:c.1381T>C	p.Ser461Pro	p.S461P	ENST00000320574	NM_006231.2	461	Tca/Cca	14/49	0.517295070128011	3	FACETS	0.936	0.88	0.992	0.936	0.88	0.992	CLONAL	2	TRUE	1	0.594862325750914	3		415	522	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555686	21555686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194403560	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	130	492	0	ENST00000382592.4:c.2584C>T	p.Arg862Trp	p.R862W	ENST00000382592	NM_014572.2	862	Cgg/Tgg	6/8	1	2	FACETS	0.883	0.806	0.963	0.883	0.806	0.963	CLONAL	1	TRUE	1	0.594862325750914	2		492	495	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608510	28608510	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	88	432	0	ENST00000241453.7:c.1632C>A	p.Phe544Leu	p.F544L	ENST00000241453	NM_004119.2	544	ttC/ttA	13/24	1	2	FACETS	0.751	0.67	0.837	0.751	0.67	0.837	SUBCLONAL	1	TRUE	1	0.594862325750914	2		432	394	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893637	28893637	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	112	333	0	ENST00000282397.4:c.3209C>A	p.Ser1070Tyr	p.S1070Y	ENST00000282397	NM_002019.4	1070	tCt/tAt	24/30	1	2	FACETS	0.932	0.845	1	0.932	0.845	1	CLONAL	1	TRUE	1	0.594862325750914	2		333	404	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913531	32913531	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555284041	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	72	446	0	ENST00000380152.3:c.5039C>A	p.Ser1680Tyr	p.S1680Y	ENST00000380152		1680	tCt/tAt	11/27	1	2	FACETS	0.731	0.644	0.824	0.731	0.644	0.824	SUBCLONAL	1	TRUE	1	0.594862325750914	2		446	331	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913852	32913852	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	60	417	0	ENST00000380152.3:c.5360T>G	p.Phe1787Cys	p.F1787C	ENST00000380152		1787	tTt/tGt	11/27	1	2	FACETS	0.791	0.689	0.9	0.791	0.689	0.9	SUBCLONAL	1	TRUE	1	0.594862325750914	2		417	255	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923137	48923137	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	50	225	0	ENST00000267163.4:c.585G>T	p.Trp195Cys	p.W195C	ENST00000267163	NM_000321.2	195	tgG/tgT	6/27	1	2	FACETS	0.894	0.77	1	0.894	0.77	1	CLONAL	1	TRUE	1	0.594862325750914	2		225	188	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934182	48934182	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1267000381	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	62	296	0	ENST00000267163.4:c.637G>A	p.Val213Met	p.V213M	ENST00000267163	NM_000321.2	213	Gtg/Atg	7/27	1	2	FACETS	0.902	0.79	1	0.902	0.79	1	CLONAL	1	TRUE	1	0.594862325750914	2		296	231	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955517	48955517	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	57	312	0	ENST00000267163.4:c.1633G>T	p.Glu545Ter	p.E545*	ENST00000267163	NM_000321.2	545	Gaa/Taa	17/27	1	2	FACETS	0.837	0.727	0.954	0.837	0.727	0.954	CLONAL	1	TRUE	1	0.594862325750914	2		312	229	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606090	81606090	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	151	463	0	ENST00000298171.2:c.760G>T	p.Ala254Ser	p.A254S	ENST00000298171	NM_000369.2	254	Gca/Tca	9/10	1	2	FACETS	0.954	0.878	1	0.954	0.878	1	CLONAL	1	TRUE	1	0.594862325750914	2		463	532	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95592973	95592973	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	55	292	0	ENST00000393063.1:c.847G>T	p.Asp283Tyr	p.D283Y	ENST00000393063	NM_030621.3	283	Gat/Tat	8/28	1	2	FACETS	0.777	0.672	0.889	0.777	0.672	0.889	SUBCLONAL	1	TRUE	1	0.594862325750914	2		292	238	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38631949	38631949	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	64	348	0	ENST00000299084.4:c.435G>T	p.Glu145Asp	p.E145D	ENST00000299084	NM_152594.2	145	gaG/gaT	5/7	1	2	FACETS	0.771	0.674	0.874	0.771	0.674	0.874	SUBCLONAL	1	TRUE	1	0.594862325750914	2		348	279	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708548	43708548	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	150	506	0	ENST00000382044.4:c.4748G>T	p.Arg1583Ile	p.R1583I	ENST00000382044	NM_001141980.1	1583	aGa/aTa	22/28	1	2	FACETS	0.944	0.868	1	0.944	0.868	1	CLONAL	1	TRUE	1	0.594862325750914	2		506	534	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784496	43784496	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	101	425	0	ENST00000382044.4:c.178G>T	p.Glu60Ter	p.E60*	ENST00000382044	NM_001141980.1	60	Gaa/Taa	2/28	1	2	FACETS	0.83	0.747	0.917	0.83	0.747	0.917	CLONAL	1	TRUE	1	0.594862325750914	2		425	409	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799249	88799249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774269690	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	123	431	0	ENST00000360948.2:c.136C>T	p.Arg46Trp	p.R46W	ENST00000360948	NM_001012338.2	46	Cgg/Tgg	2/19	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.594862325750914	2		431	402	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916206	9916206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	112	384	0	ENST00000330684.3:c.2083C>T	p.Arg695Trp	p.R695W	ENST00000330684	NM_001134407.1	695	Cgg/Tgg	10/13	1	2	FACETS	0.773	0.699	0.851	0.773	0.699	0.851	SUBCLONAL	1	TRUE	1	0.594862325750914	2		384	487	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032064	10032064	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	101	463	0	ENST00000330684.3:c.759C>A	p.Phe253Leu	p.F253L	ENST00000330684	NM_001134407.1	253	ttC/ttA	3/13	1	2	FACETS	0.82	0.738	0.906	0.82	0.738	0.906	CLONAL	1	TRUE	1	0.594862325750914	2		463	414	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965122	81965122	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	139	430	0	ENST00000359376.3:c.2602A>C	p.Asn868His	p.N868H	ENST00000359376	NM_002661.3	868	Aac/Cac	25/33	1	2	FACETS	0.924	0.846	1	0.924	0.846	1	CLONAL	1	TRUE	1	0.594862325750914	2		430	506	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544565	86544565	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	125	587	0	ENST00000262426.4:c.390C>A	p.Phe130Leu	p.F130L	ENST00000262426	NM_001451.2	130	ttC/ttA	1/2	1	2	FACETS	0.924	0.842	1	0.924	0.842	1	CLONAL	1	TRUE	1	0.594862325750914	2		587	455	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592269	29592269	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	13	289	0	ENST00000356175.3:c.4684G>T	p.Glu1562Ter	p.E1562*	ENST00000356175	NM_000267.3	1562	Gaa/Taa	35/57	1	2	FACETS	0.204	0.145	0.276	0.204	0.145	0.276	SUBCLONAL	1	TRUE	1	0.594862325750914	2		289	214	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740436	58740436	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs769061997	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	128	384	0	ENST00000305921.3:c.1341G>T	p.Glu447Asp	p.E447D	ENST00000305921	NM_003620.3	447	gaG/gaT	6/6	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.594862325750914	2		384	423	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885920	59885920	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	112	391	0	ENST00000259008.2:c.826C>A	p.Leu276Ile	p.L276I	ENST00000259008	NM_032043.2	276	Ctt/Att	7/20	1	2	FACETS	0.914	0.828	1	0.914	0.828	1	CLONAL	1	TRUE	1	0.594862325750914	2		391	412	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926543	59926543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	49	346	0	ENST00000259008.2:c.454G>T	p.Asp152Tyr	p.D152Y	ENST00000259008	NM_032043.2	152	Gat/Tat	5/20	1	2	FACETS	0.723	0.618	0.834	0.723	0.618	0.834	SUBCLONAL	1	TRUE	1	0.594862325750914	2		346	228	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39647380	39647380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1306170227	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	106	385	0	ENST00000262039.4:c.2552C>T	p.Ser851Leu	p.S851L	ENST00000262039	NM_002647.2	851	tCg/tTg	24/25	1	2	FACETS	0.806	0.727	0.889	0.806	0.727	0.889	CLONAL	1	TRUE	1	0.594862325750914	2		385	442	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61322903	61322903	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	52	247	0	ENST00000283752.5:c.1161C>A	p.Phe387Leu	p.F387L	ENST00000283752	NM_006919.2	387	ttC/ttA	8/8	1	2	FACETS	0.791	0.681	0.908	0.791	0.681	0.908	CLONAL	1	TRUE	1	0.594862325750914	2		247	221	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4102411	4102411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs751317148	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	139	450	0	ENST00000262948.5:c.491G>T	p.Arg164Met	p.R164M	ENST00000262948	NM_030662.3	164	aGg/aTg	4/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.594862325750914	2		450	436	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10259683	10259683	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	63	292	0	ENST00000340748.4:c.2549A>G	p.Asp850Gly	p.D850G	ENST00000340748		850	gAt/gGt	26/40	1	2	FACETS	0.728	0.635	0.827	0.728	0.635	0.827	SUBCLONAL	1	TRUE	1	0.594862325750914	2		292	291	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383356	42383356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782043875	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	127	454	0	ENST00000221972.3:c.376C>T	p.Arg126Cys	p.R126C	ENST00000221972	NM_021601.3	126	Cgc/Tgc	2/5	1	2	FACETS	0.947	0.864	1	0.947	0.864	1	CLONAL	1	TRUE	1	0.594862325750914	2		454	451	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723453	52723453	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	112	334	0	ENST00000322088.6:c.1314C>A	p.Phe438Leu	p.F438L	ENST00000322088	NM_014225.5	438	ttC/ttA	11/15	1	2	FACETS	0.937	0.849	1	0.937	0.849	1	CLONAL	1	TRUE	1	0.594862325750914	2		334	402	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142991	30142991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs62129830	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	139	611	0	ENST00000389048.3:c.535C>T	p.Arg179Cys	p.R179C	ENST00000389048	NM_004304.4	179	Cgc/Tgc	1/29	1	2	FACETS	0.96	0.88	1	0.96	0.88	1	CLONAL	1	TRUE	1	0.594862325750914	2		611	487	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143196	30143196	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	117	521	0	ENST00000389048.3:c.330G>T	p.Trp110Cys	p.W110C	ENST00000389048	NM_004304.4	110	tgG/tgT	1/29	1	2	FACETS	0.941	0.855	1	0.941	0.855	1	CLONAL	1	TRUE	1	0.594862325750914	2		521	418	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631339	67631339	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	17	372	0	ENST00000272342.5:c.1525G>T	p.Asp509Tyr	p.D509Y	ENST00000272342	NM_019002.3	509	Gat/Tat	5/6	1	2	FACETS	0.282	0.21	0.365	0.282	0.21	0.365	SUBCLONAL	1	TRUE	1	0.594862325750914	2		372	203	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631576	67631576	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	73	487	0	ENST00000272342.5:c.1762G>T	p.Glu588Ter	p.E588*	ENST00000272342	NM_019002.3	588	Gaa/Taa	5/6	1	2	FACETS	0.99	0.877	1	0.99	0.877	1	CLONAL	1	TRUE	1	0.594862325750914	2		487	248	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248427	212248427	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	67	492	0	ENST00000342788.4:c.3840G>T	p.Glu1280Asp	p.E1280D	ENST00000342788	NM_005235.2	1280	gaG/gaT	28/28	1	2	FACETS	0.431	0.375	0.491	0.431	0.375	0.491	SUBCLONAL	1	TRUE	1	0.594862325750914	2		492	523	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426627	212426627	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	83	420	0	ENST00000342788.4:c.2487+1G>A		p.X829_splice	ENST00000342788	NM_005235.2	829			1	2	FACETS	0.762	0.678	0.852	0.762	0.678	0.852	SUBCLONAL	1	TRUE	1	0.594862325750914	2		420	366	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488657	212488657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374970657	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	39	431	0	ENST00000342788.4:c.2192C>T	p.Thr731Met	p.T731M	ENST00000342788	NM_005235.2	731	aCg/aTg	18/28	1	2	FACETS	0.297	0.246	0.354	0.297	0.246	0.354	SUBCLONAL	1	TRUE	1	0.594862325750914	2		431	441	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812293	212812293	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569995088	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	77	426	0	ENST00000342788.4:c.283C>T	p.Arg95Cys	p.R95C	ENST00000342788	NM_005235.2	95	Cgt/Tgt	3/28	1	2	FACETS	0.717	0.634	0.805	0.717	0.634	0.805	SUBCLONAL	1	TRUE	1	0.594862325750914	2		426	361	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645660	215645660	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs202118376	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	85	458	0	ENST00000260947.4:c.938C>A	p.Ser313Tyr	p.S313Y	ENST00000260947	NM_000465.2	313	tCt/tAt	4/11	1	2	FACETS	0.843	0.752	0.939	0.843	0.752	0.939	CLONAL	1	TRUE	1	0.594862325750914	2		458	339	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646149	215646149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881412	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	81	383	0	ENST00000260947.4:c.449G>A	p.Arg150Gln	p.R150Q	ENST00000260947	NM_000465.2	150	cGa/cAa	4/11	1	2	FACETS	0.776	0.689	0.868	0.776	0.689	0.868	SUBCLONAL	1	TRUE	1	0.594862325750914	2		383	351	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437278	220437278	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	85	502	0	ENST00000243786.2:c.182G>T	p.Arg61Ile	p.R61I	ENST00000243786	NM_002191.3	61	aGa/aTa	1/2	1	2	FACETS	0.584	0.518	0.655	0.584	0.518	0.655	SUBCLONAL	1	TRUE	1	0.594862325750914	2		502	489	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376146	225376146	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	45	335	0	ENST00000264414.4:c.808T>C	p.Ser270Pro	p.S270P	ENST00000264414	NM_003590.4	270	Tcc/Ccc	6/16	1	2	FACETS	0.638	0.541	0.744	0.638	0.541	0.744	SUBCLONAL	1	TRUE	1	0.594862325750914	2		335	237	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911144	40911144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776134993	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	53	250	0	ENST00000373198.4:c.2161C>T	p.Arg721Cys	p.R721C	ENST00000373198	NM_133170.3	721	Cgt/Tgt	13/32	1	2	FACETS	0.865	0.748	0.99	0.865	0.748	0.99	CLONAL	1	TRUE	1	0.594862325750914	2		250	206	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419913	41419913	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	133	519	0	ENST00000373198.4:c.408G>A	p.Trp136Ter	p.W136*	ENST00000373198	NM_133170.3	136	tgG/tgA	3/32	1	2	FACETS	0.827	0.754	0.902	0.827	0.754	0.902	CLONAL	1	TRUE	1	0.594862325750914	2		519	541	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764365	39764365	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	99	334	0	ENST00000288319.7:c.747T>A	p.Asp249Glu	p.D249E	ENST00000288319	NM_182918.3	249	gaT/gaA	7/10	1	2	FACETS	0.789	0.709	0.873	0.789	0.709	0.873	SUBCLONAL	1	TRUE	1	0.594862325750914	2		334	422	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775467	39775467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1048054600	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	138	512	0	ENST00000288319.7:c.553G>A	p.Ala185Thr	p.A185T	ENST00000288319	NM_182918.3	185	Gcc/Acc	4/10	1	2	FACETS	0.889	0.813	0.967	0.889	0.813	0.967	CLONAL	1	TRUE	1	0.594862325750914	2		512	522	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182637	38182637	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs748659894	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	57	405	0	ENST00000396334.3:c.790C>T	p.Arg264Ter	p.R264*	ENST00000396334	NM_002468.4	264	Cga/Tga	5/5	1	2	FACETS	0.429	0.368	0.494	0.429	0.368	0.494	SUBCLONAL	1	TRUE	1	0.594862325750914	2		405	447	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266847	41266847	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	128	482	0	ENST00000349496.5:c.518T>C	p.Val173Ala	p.V173A	ENST00000349496	NM_001904.3	173	gTt/gCt	5/15	1	2	FACETS	0.934	0.852	1	0.934	0.852	1	CLONAL	1	TRUE	1	0.594862325750914	2		482	461	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277291	41277291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	114	398	0	ENST00000349496.5:c.1760G>A	p.Arg587Gln	p.R587Q	ENST00000349496	NM_001904.3	587	cGa/cAa	11/15	1	2	FACETS	0.885	0.803	0.971	0.885	0.803	0.971	CLONAL	1	TRUE	1	0.594862325750914	2		398	433	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69988316	69988316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747126448	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	108	337	0	ENST00000394351.3:c.329G>A	p.Arg110Gln	p.R110Q	ENST00000394351	NM_000248.3	110	cGa/cAa	3/9	1	2	FACETS	0.897	0.811	0.986	0.897	0.811	0.986	CLONAL	1	TRUE	1	0.594862325750914	2		337	405	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014163	70014163	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868519483	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	43	492	0	ENST00000394351.3:c.1024G>A	p.Asp342Asn	p.D342N	ENST00000394351	NM_000248.3	342	Gat/Aat	9/9	1	2	FACETS	0.273	0.228	0.323	0.273	0.228	0.323	SUBCLONAL	1	TRUE	1	0.594862325750914	2		492	530	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873100	134873100	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	108	442	0	ENST00000398015.3:c.1404G>T	p.Glu468Asp	p.E468D	ENST00000398015	NM_004441.4	468	gaG/gaT	6/16	1	2	FACETS	0.938	0.849	1	0.938	0.849	1	CLONAL	1	TRUE	1	0.594862325750914	2		442	387	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138383891	138383891	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	118	320	1	ENST00000289153.2:c.2659G>T	p.Glu887Ter	p.E887*	ENST00000289153	NM_006219.2	887	Gaa/Taa	18/22	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.594862325750914	2		321	362	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474618	138474618	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	61	342	0	ENST00000289153.2:c.375A>C	p.Lys125Asn	p.K125N	ENST00000289153	NM_006219.2	125	aaA/aaC	2/22	1	2	FACETS	0.865	0.756	0.981	0.865	0.756	0.981	CLONAL	1	TRUE	1	0.594862325750914	2		342	237	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587113	189587113	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs148052765	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	86	298	0	ENST00000264731.3:c.1130C>T	p.Pro377Leu	p.P377L	ENST00000264731	NM_003722.4	377	cCg/cTg	9/14	1	2	FACETS	0.836	0.746	0.93	0.836	0.746	0.93	CLONAL	1	TRUE	1	0.594862325750914	2		298	346	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920289	1920289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146822227	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	144	479	0	ENST00000382891.5:c.1349G>A	p.Arg450Gln	p.R450Q	ENST00000382891	NM_133335.3	450	cGa/cAa	5/22	1	2	FACETS	0.955	0.877	1	0.955	0.877	1	CLONAL	1	TRUE	1	0.594862325750914	2		479	507	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129833	55129833	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	76	385	0	ENST00000257290.5:c.368-1G>T		p.X123_splice	ENST00000257290	NM_006206.4	123			1	2	FACETS	0.722	0.637	0.811	0.722	0.637	0.811	SUBCLONAL	1	TRUE	1	0.594862325750914	2		385	354	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561767	55561767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780349712	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	147	404	0	ENST00000288135.5:c.157G>A	p.Glu53Lys	p.E53K	ENST00000288135	NM_000222.2	53	Gag/Aag	2/21	1	2	FACETS	0.985	0.905	1	0.985	0.905	1	CLONAL	1	TRUE	1	0.594862325750914	2		404	502	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955584	55955584	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	62	337	0	ENST00000263923.4:c.3361G>T	p.Glu1121Ter	p.E1121*	ENST00000263923	NM_002253.2	1121	Gaa/Taa	25/30	1	2	FACETS	0.755	0.659	0.858	0.755	0.659	0.858	SUBCLONAL	1	TRUE	1	0.594862325750914	2		337	276	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970930	55970930	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	112	430	0	ENST00000263923.4:c.1867G>T	p.Asp623Tyr	p.D623Y	ENST00000263923	NM_002253.2	623	Gac/Tac	13/30	1	2	FACETS	0.934	0.847	1	0.934	0.847	1	CLONAL	1	TRUE	1	0.594862325750914	2		430	403	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972973	55972973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	25	369	0	ENST00000263923.4:c.1417G>A	p.Ala473Thr	p.A473T	ENST00000263923	NM_002253.2	473	Gct/Act	11/30	1	2	FACETS	0.35	0.277	0.434	0.35	0.277	0.434	SUBCLONAL	1	TRUE	1	0.594862325750914	2		369	240	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981172	55981172	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	54	360	0	ENST00000263923.4:c.527G>T	p.Arg176Ile	p.R176I	ENST00000263923	NM_002253.2	176	aGa/aTa	5/30	1	2	FACETS	0.701	0.604	0.805	0.701	0.604	0.805	SUBCLONAL	1	TRUE	1	0.594862325750914	2		360	259	SUCCESS
REST	5978	MSKCC	GRCh37	4	57798251	57798251	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	23	403	0	ENST00000309042.7:c.3227G>A	p.Ser1076Asn	p.S1076N	ENST00000309042	NM_005612.4	1076	aGc/aAc	4/4	1	2	FACETS	0.227	0.177	0.286	0.227	0.177	0.286	SUBCLONAL	1	TRUE	1	0.594862325750914	2		403	340	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155280	106155280	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	26	487	0	ENST00000380013.4:c.181T>G	p.Tyr61Asp	p.Y61D	ENST00000380013	NM_001127208.2	61	Tat/Gat	3/11	1	2	FACETS	0.179	0.141	0.223	0.179	0.141	0.223	SUBCLONAL	1	TRUE	1	0.594862325750914	2		487	488	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130163	143130163	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	50	298	0	ENST00000262992.4:c.853G>T	p.Glu285Ter	p.E285*	ENST00000262992	NM_001101669.1	285	Gaa/Taa	11/24	1	2	FACETS	0.812	0.698	0.934	0.812	0.698	0.934	CLONAL	1	TRUE	1	0.594862325750914	2		298	207	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259070	153259070	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	50	369	0	ENST00000281708.4:c.745A>G	p.Lys249Glu	p.K249E	ENST00000281708	NM_033632.3	249	Aaa/Gaa	5/12	1	2	FACETS	0.609	0.52	0.705	0.609	0.52	0.705	SUBCLONAL	1	TRUE	1	0.594862325750914	2		369	276	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268137	153268137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752114536	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	133	409	0	ENST00000281708.4:c.671G>A	p.Arg224Gln	p.R224Q	ENST00000281708	NM_033632.3	224	cGa/cAa	4/12	1	2	FACETS	0.804	0.734	0.878	0.804	0.734	0.878	CLONAL	1	TRUE	1	0.594862325750914	2		409	556	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530381	187530381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753202486	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	153	499	0	ENST00000441802.2:c.10162G>A	p.Val3388Ile	p.V3388I	ENST00000441802	NM_005245.3	3388	Gtc/Atc	16/27	1	2	FACETS	0.875	0.804	0.948	0.875	0.804	0.948	CLONAL	1	TRUE	1	0.594862325750914	2		499	588	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861051	35861051	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	72	390	0	ENST00000303115.3:c.180G>T	p.Glu60Asp	p.E60D	ENST00000303115	NM_002185.3	60	gaG/gaT	2/8	0.517295070128011	3	FACETS	0.594	0.519	0.674	0.297	0.259	0.337	SUBCLONAL	1	TRUE	1	0.594862325750914	3		390	529	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751901	57751901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148954251	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	136	415	0	ENST00000274289.3:c.1336C>T	p.Arg446Trp	p.R446W	ENST00000274289	NM_006622.3	446	Cgg/Tgg	10/14	1	2	FACETS	0.918	0.84	0.999	0.918	0.84	0.999	CLONAL	1	TRUE	1	0.594862325750914	2		415	498	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589618	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519838	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	37	282	0	ENST00000274335.5:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000274335		461	Cga/Tga	10/15	1	2	FACETS	0.622	0.518	0.736	0.622	0.518	0.736	SUBCLONAL	1	TRUE	1	0.594862325750914	2		282	200	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590466	67590466	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	97	331	0	ENST00000274335.5:c.1528G>T	p.Glu510Ter	p.E510*	ENST00000274335		510	Gaa/Taa	11/15	1	2	FACETS	0.929	0.836	1	0.929	0.836	1	CLONAL	1	TRUE	1	0.594862325750914	2		331	351	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	89	535	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.783	0.699	0.872	0.783	0.699	0.872	SUBCLONAL	1	TRUE	1	0.594862325750914	2		535	382	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	116	466	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	1	2	FACETS	0.926	0.841	1	0.926	0.841	1	CLONAL	1	TRUE	1	0.594862325750914	2		466	421	SUCCESS
APC	324	MSKCC	GRCh37	5	112176176	112176176	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	164	492	0	ENST00000257430.4:c.4885C>T	p.His1629Tyr	p.H1629Y	ENST00000257430	NM_000038.5	1629	Cat/Tat	16/16	1	2	FACETS	0.911	0.841	0.985	0.911	0.841	0.985	CLONAL	1	TRUE	1	0.594862325750914	2		492	605	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058733	180058733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751762446	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	105	453	0	ENST00000261937.6:c.104C>T	p.Thr35Met	p.T35M	ENST00000261937	NM_182925.4	35	aCg/aTg	2/30	1	2	FACETS	0.817	0.737	0.901	0.817	0.737	0.901	CLONAL	1	TRUE	1	0.594862325750914	2		453	432	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401631	401631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	140	618	0	ENST00000380956.4:c.953G>T	p.Trp318Leu	p.W318L	ENST00000380956	NM_001195286.1	318	tGg/tTg	7/9	1	2	FACETS	0.93	0.852	1	0.93	0.852	1	CLONAL	1	TRUE	1	0.594862325750914	2		618	506	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911075	29911075	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	40	347	0	ENST00000376809.5:c.374G>C	p.Cys125Ser	p.C125S	ENST00000376809	NM_002116.7	125	tGc/tCc	3/8	1	2	FACETS	0.523	0.437	0.617	0.523	0.437	0.617	SUBCLONAL	1	TRUE	1	0.594862325750914	2		347	257	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800513	32800513	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	141	537	0	ENST00000374899.4:c.1034T>G	p.Phe345Cys	p.F345C	ENST00000374899	NM_018833.2	345	tTt/tGt	6/12	1	2	FACETS	0.813	0.744	0.885	0.813	0.744	0.885	CLONAL	1	TRUE	1	0.594862325750914	2		537	583	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715868	117715868	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	67	307	0	ENST00000368508.3:c.890G>T	p.Arg297Ile	p.R297I	ENST00000368508	NM_002944.2	297	aGa/aTa	9/43	1	2	FACETS	0.822	0.722	0.928	0.822	0.722	0.928	CLONAL	1	TRUE	1	0.594862325750914	2		307	274	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163911	152163911	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	101	378	0	ENST00000206249.3:c.632G>T	p.Arg211Ile	p.R211I	ENST00000206249	NM_000125.3	211	aGa/aTa	2/8	1	2	FACETS	0.884	0.797	0.976	0.884	0.797	0.976	CLONAL	1	TRUE	1	0.594862325750914	2		378	384	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265321	152265321	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	78	382	0	ENST00000206249.3:c.774C>A	p.Asp258Glu	p.D258E	ENST00000206249	NM_000125.3	258	gaC/gaA	4/8	1	2	FACETS	0.703	0.622	0.789	0.703	0.622	0.789	SUBCLONAL	1	TRUE	1	0.594862325750914	2		382	373	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958193	2958193	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	38	432	3	ENST00000396946.4:c.2539C>T	p.Gln847Ter	p.Q847*	ENST00000396946	NM_032415.4	847	Cag/Tag	19/25	1	2	FACETS	0.307	0.254	0.367	0.307	0.254	0.367	SUBCLONAL	1	TRUE	1	0.594862325750914	2		435	416	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381529	81381529	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	87	395	0	ENST00000222390.5:c.532C>T	p.Arg178Ter	p.R178*	ENST00000222390	NM_000601.4	178	Cga/Tga	5/18	1	2	FACETS	0.752	0.67	0.838	0.752	0.67	0.838	SUBCLONAL	1	TRUE	1	0.594862325750914	2		395	389	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92404119	92404119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761377867	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	20	401	0	ENST00000265734.4:c.260G>A	p.Arg87Gln	p.R87Q	ENST00000265734	NM_001259.6	87	cGa/cAa	3/8	1	2	FACETS	0.177	0.135	0.227	0.177	0.135	0.227	SUBCLONAL	1	TRUE	1	0.594862325750914	2		401	379	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124482883	124482883	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1459987627	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	54	321	0	ENST00000357628.3:c.1141C>A	p.His381Asn	p.H381N	ENST00000357628	NM_015450.2	381	Cat/Aat	13/19	1	2	FACETS	0.971	0.843	1	0.971	0.843	1	CLONAL	1	TRUE	1	0.594862325750914	2		321	187	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931826	68931826	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs759461290	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	85	389	0	ENST00000288368.4:c.256G>T	p.Glu86Ter	p.E86*	ENST00000288368	NM_024870.2	86	Gaa/Taa	3/40	1	2	FACETS	0.928	0.829	1	0.928	0.829	1	CLONAL	1	TRUE	1	0.594862325750914	2		389	308	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934328	68934328	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	73	297	0	ENST00000288368.4:c.394T>A	p.Leu132Ile	p.L132I	ENST00000288368	NM_024870.2	132	Tta/Ata	4/40	1	2	FACETS	0.841	0.742	0.944	0.841	0.742	0.944	CLONAL	1	TRUE	1	0.594862325750914	2		297	292	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965728	90965728	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs920311188	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	15	375	1	ENST00000265433.3:c.1589C>A	p.Ser530Tyr	p.S530Y	ENST00000265433	NM_002485.4	530	tCt/tAt	11/16	1	2	FACETS	0.171	0.124	0.227	0.171	0.124	0.227	SUBCLONAL	1	TRUE	1	0.594862325750914	2		376	295	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457333	5457333	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	139	448	0	ENST00000381577.3:c.307G>T	p.Asp103Tyr	p.D103Y	ENST00000381577	NM_014143.3	103	Gat/Tat	3/7	1	2	FACETS	0.927	0.849	1	0.927	0.849	1	CLONAL	1	TRUE	1	0.594862325750914	2		448	504	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97934320	97934320	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	62	243	0	ENST00000289081.3:c.455A>C	p.Asn152Thr	p.N152T	ENST00000289081	NM_000136.2	152	aAt/aCt	5/15	1	2	FACETS	0.872	0.763	0.988	0.872	0.763	0.988	CLONAL	1	TRUE	1	0.594862325750914	2		243	239	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649733	48649733	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	43	245	0	ENST00000376670.3:c.217C>A	p.Pro73Thr	p.P73T	ENST00000376670	NM_002049.3	73	Cca/Aca	2/6	1	1	FACETS	0.464	0.392	0.542	0.464	0.392	0.542	SUBCLONAL	1	TRUE	0	0.594862325750914	1		245	219	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650601	48650601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140561920	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	150	329	0	ENST00000376670.3:c.571C>T	p.Arg191Cys	p.R191C	ENST00000376670	NM_002049.3	191	Cgt/Tgt	3/6	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.594862325750914	1		329	289	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410201	63410201	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	121	295	0	ENST00000330258.3:c.2966A>G	p.Tyr989Cys	p.Y989C	ENST00000330258	NM_152424.3	989	tAt/tGt	2/2	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.594862325750914	1		295	209	SUCCESS
AR	367	MSKCC	GRCh37	X	66905884	66905884	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	60	187	0	ENST00000374690.3:c.1801G>T	p.Asp601Tyr	p.D601Y	ENST00000374690	NM_000044.3	601	Gat/Tat	3/8	1	1	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	0	0.594862325750914	1		187	141	SUCCESS
AR	367	MSKCC	GRCh37	X	66937433	66937433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	112	227	0	ENST00000374690.3:c.2287C>T	p.Leu763Phe	p.L763F	ENST00000374690	NM_000044.3	763	Ctc/Ttc	5/8	1	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.594862325750914	1		227	220	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0065390-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	30	602	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		602	117	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916861	178916861	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1560137208	NA	P-0065390-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	53	387	0	ENST00000263967.3:c.248T>C	p.Phe83Ser	p.F83S	ENST00000263967	NM_006218.2	83	tTt/tCt	2/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		387	200	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604801	48604802	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065390-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	43	437	0	ENST00000342988.3:c.1624dup	p.Thr542AsnfsTer35	p.T542Nfs*35	ENST00000342988	NM_005359.5	541	-/A	12/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		437	96	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19261526	19261526	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065390-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	37	363	0	ENST00000162023.5:c.19C>T	p.Gln7Ter	p.Q7*	ENST00000162023		7	Cag/Tag	6/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		363	115	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577157	7577157	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0065410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	292	453	0	ENST00000269305.4:c.783-2A>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		453	461	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953089	2953089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	400	578	0	ENST00000396946.4:c.2851G>A	p.Glu951Lys	p.E951K	ENST00000396946	NM_032415.4	951	Gag/Aag	22/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		578	977	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646225	215646225	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	37	286	0	ENST00000260947.4:c.373G>C	p.Glu125Gln	p.E125Q	ENST00000260947	NM_000465.2	125	Gaa/Caa	4/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		286	241	SUCCESS
AR	367	MSKCC	GRCh37	X	66943551	66943551	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	249	452	0	ENST00000374690.3:c.2631C>A	p.Phe877Leu	p.F877L	ENST00000374690	NM_000044.3	877	ttC/ttA	8/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		452	751	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754651	41754651	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	181	556	0	ENST00000301178.4:c.1637A>T	p.Glu546Val	p.E546V	ENST00000301178	NM_021913.4	546	gAg/gTg	14/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		556	848	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925492	114925492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs534110993	NA	P-0065410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	167	482	2	ENST00000543371.1:c.1570G>A	p.Asp524Asn	p.D524N	ENST00000543371	NM_001198531.1	524	Gac/Aac	14/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		484	616	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50816365	50816365	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0065410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	162	366	0	ENST00000398568.2:c.1805C>G	p.Ser602Ter	p.S602*	ENST00000398568	NM_001042412.1	602	tCa/tGa	10/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		366	274	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204513697	204513697	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	192	415	0	ENST00000367182.3:c.707A>G	p.Asp236Gly	p.D236G	ENST00000367182	NM_001278516.1	236	gAt/gGt	9/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		415	355	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622032	43622032	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	161	424	0	ENST00000355710.3:c.3049G>C	p.Asp1017His	p.D1017H	ENST00000355710	NM_020975.4	1017	Gac/Cac	19/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		424	900	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472183	472183	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	389	415	0	ENST00000399788.2:c.618G>T	p.Glu206Asp	p.E206D	ENST00000399788	NM_001042603.1	206	gaG/gaT	5/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		415	916	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49419998	49419999	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0065410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	486	523	0	ENST00000301067.7:c.15750_15751delinsTT	p.Glu5251Ter	p.E5251*	ENST00000301067	NM_003482.3	5250	ctGGag/ctTTag	48/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		523	1134	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070610	67070610	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	341	443	0	ENST00000412916.2:c.234del	p.Gln79LysfsTer10	p.Q79Kfs*10	ENST00000412916		78	cgA/cg	3/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		443	585	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027997	48027997	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	276	498	0	ENST00000234420.5:c.2875C>A	p.Arg959Ser	p.R959S	ENST00000234420	NM_000179.2	959	Cgc/Agc	4/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		498	811	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646206	215646206	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	47	304	0	ENST00000260947.4:c.392G>C	p.Ser131Thr	p.S131T	ENST00000260947	NM_000465.2	131	aGt/aCt	4/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		304	280	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589543	67589543	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	38	217	0	ENST00000274335.5:c.1306G>T	p.Val436Phe	p.V436F	ENST00000274335		436	Gtt/Ttt	10/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		217	64	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671579	30671579	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	192	568	0	ENST00000376406.3:c.5381C>T	p.Ala1794Val	p.A1794V	ENST00000376406	NM_014641.2	1794	gCa/gTa	10/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		568	923	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192529	138192529	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	205	477	0	ENST00000237289.4:c.165G>C	p.Gln55His	p.Q55H	ENST00000237289	NM_001270507.1	55	caG/caC	2/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		477	861	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624365	140624365	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0065410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	305	421	0	ENST00000288602.6:c.138+1G>T		p.X46_splice	ENST00000288602	NM_004333.4	46			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		421	816	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945101	151945102	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0065410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	56	347	0	ENST00000262189.6:c.2417_2418delinsAA	p.Ser806Ter	p.S806*	ENST00000262189	NM_170606.2	806	tCC/tAA	14/59	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		347	366	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889121	76889121	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	120	329	0	ENST00000373344.5:c.4889C>A	p.Thr1630Asn	p.T1630N	ENST00000373344	NM_000489.3	1630	aCt/aAt	18/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		329	328	SUCCESS
BTK	695	MSKCC	GRCh37	X	100629540	100629540	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	130	356	0	ENST00000308731.7:c.224C>T	p.Pro75Leu	p.P75L	ENST00000308731	NM_000061.2	75	cCa/cTa	3/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		356	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0065412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	338	616	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.901153686705517	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.901153686705517	1		616	412	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788617	3788617	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	240	496	0	ENST00000262367.5:c.4337G>C	p.Arg1446Pro	p.R1446P	ENST00000262367	NM_004380.2	1446	cGc/cCc	26/31	1	2	FACETS	0.898	0.845	0.952	0.898	0.845	0.952	CLONAL	1	TRUE	1	0.901153686705517	2		496	593	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163313637	163313637	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	129	300	0	ENST00000271452.3:c.784G>T	p.Val262Phe	p.V262F	ENST00000271452	NM_145697.2	262	Gtc/Ttc	10/14	1	2	FACETS	0.772	0.707	0.838	0.772	0.707	0.838	SUBCLONAL	1	TRUE	1	0.901153686705517	2		300	371	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954326	48954326	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1131690910	NA	P-0065412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	152	281	0	ENST00000267163.4:c.1447del	p.His483IlefsTer12	p.H483Ifs*12	ENST00000267163	NM_000321.2	483	Cat/at	16/27	0.901153686705517	1	FACETS	0.981	0.937	1	0.981	0.937	1	CLONAL	1	TRUE	0	0.901153686705517	1		281	189	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51504536	51504536	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	281	522	0	ENST00000260433.2:c.1244T>G	p.Leu415Arg	p.L415R	ENST00000260433		415	cTt/cGt	9/10	1	2	FACETS	0.959	0.908	1	0.959	0.908	1	CLONAL	1	TRUE	1	0.901153686705517	2		522	650	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561244	9561244	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	310	590	0	ENST00000353224.5:c.538G>T	p.Ala180Ser	p.A180S	ENST00000353224	NM_177990.2	180	Gcc/Tcc	4/10	1	2	FACETS	0.968	0.919	1	0.968	0.919	1	CLONAL	1	TRUE	1	0.901153686705517	2		590	711	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413069	63413069	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768534964	NA	P-0065412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	334	711	0	ENST00000330258.3:c.98C>A	p.Ala33Glu	p.A33E	ENST00000330258	NM_152424.3	33	gCa/gAa	2/2	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.901153686705517	2		711	734	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099056	27099056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065413-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	43	783	0	ENST00000324856.7:c.3472G>A	p.Gly1158Arg	p.G1158R	ENST00000324856	NM_006015.4	1158	Gga/Aga	13/20	0.377160023783013	4	FACETS	0.283	0.236	0.335	0.142	0.118	0.168	INDETERMINATE	1	TRUE	2	0.842983236702811	4		783	664	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0065414-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	448	414	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.782344411271076	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.782344411271076	2		414	546	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0065414-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	227	508	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.992	0.931	1	0.992	0.931	1	CLONAL	1	TRUE	1	0.782344411271076	2		508	585	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872103	76872104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065414-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	130	273	0	ENST00000373344.5:c.5543dup	p.Tyr1849ValfsTer12	p.Y1849Vfs*12	ENST00000373344	NM_000489.3	1848	cag/caAg	22/35	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.782344411271076	2		273	280	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0065415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	44	525	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.771	0.647	0.908	0.771	0.647	0.908	CLONAL	1	TRUE	1	0.260478253576585	2		525	438	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	34	415	0	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.581	0.475	0.702	0.581	0.475	0.702	SUBCLONAL	1	TRUE	1	0.260478253576585	2		415	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579584	7579585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0065415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	51	718	0	ENST00000269305.4:c.102dup	p.Pro36AlafsTer7	p.P36Afs*7	ENST00000269305	NM_001126112.2	34	-/C	4/11	1	2	FACETS	0.625	0.53	0.728	0.625	0.53	0.728	SUBCLONAL	1	TRUE	1	0.260478253576585	2		718	627	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059214	47059214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141852778	NA	P-0065415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	66	602	0	ENST00000409792.3:c.7447G>A	p.Val2483Ile	p.V2483I	ENST00000409792	NM_014159.6	2483	Gtc/Atc	20/21	1	2	FACETS	0.835	0.725	0.954	0.835	0.725	0.954	CLONAL	1	TRUE	1	0.260478253576585	2		602	607	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0065415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	31	491	3	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	1	2	FACETS	0.633	0.512	0.77	0.633	0.512	0.77	SUBCLONAL	1	TRUE	1	0.260478253576585	2		494	376	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690846	89690846	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	18	191	0	ENST00000371953.3:c.253G>T	p.Val85Phe	p.V85F	ENST00000371953	NM_000314.4	85	Gtt/Ttt	4/9	1	2	FACETS	0.49	0.369	0.633	0.49	0.369	0.633	SUBCLONAL	1	TRUE	1	0.260478253576585	2		191	282	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202909	16202909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs975826717	NA	P-0065415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	39	753	0	ENST00000375759.3:c.617G>A	p.Arg206His	p.R206H	ENST00000375759	NM_015001.2	206	cGc/cAc	3/15	1	2	FACETS	0.513	0.424	0.612	0.513	0.424	0.612	SUBCLONAL	1	TRUE	1	0.260478253576585	2		753	584	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099026	27099026	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	125	529	0	ENST00000324856.7:c.3442C>T	p.Gln1148Ter	p.Q1148*	ENST00000324856	NM_006015.4	1148	Cag/Tag	13/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.260478253576585	2		529	671	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466003	69466038	+	inframe_deletion	In_Frame_Del	DEL	GTGGACCTGGCTTGCACACCCACCGACGTGCGGGAC	GTGGACCTGGCTTGCACACCCACCGACGTGCGGGAC	-	novel	NA	P-0065415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	127	813	0	ENST00000227507.2:c.847_882del	p.Leu283_Asp294del	p.L283_D294del	ENST00000227507	NM_053056.2	281	GTGGACCTGGCTTGCACACCCACCGACGTGCGGGAC/-	5/5	1	2	FACETS	0.851	0.774	0.932	1	0.988	1	CLONAL	2	TRUE	1	0.260478253576585	2		813	573	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338671	70338671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	65	550	0	ENST00000374080.3:c.67G>T	p.Asp23Tyr	p.D23Y	ENST00000374080		23	Gat/Tat	1/45	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.260478253576585	2		550	450	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922328	178922328	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	40	281	0	ENST00000263967.3:c.1097C>G	p.Pro366Arg	p.P366R	ENST00000263967	NM_006218.2	366	cCc/cGc	6/21	1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.260478253576585	2		281	304	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996755	100996757	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0065415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	48	517	0	ENST00000325455.5:c.1770_1772del	p.Phe591del	p.F591del	ENST00000325455	NM_001202474.3	590	ttCTTt/ttt	2/8	0.260478253576585	2	FACETS	0.698	0.59	0.817	0.349	0.295	0.409	SUBCLONAL	1	TRUE	0	0.260478253576585	2		517	528	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918920	76918921	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	44	484	2	ENST00000373344.5:c.4070dup	p.Thr1358AspfsTer4	p.T1358Dfs*4	ENST00000373344	NM_000489.3	1357	aag/aaAg	12/35	1	2	FACETS	0.598	0.501	0.706	0.598	0.501	0.706	SUBCLONAL	1	TRUE	1	0.260478253576585	2		486	565	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562747	29562747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137854556	NA	P-0065415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	31	498	0	ENST00000356175.3:c.3827G>A	p.Arg1276Gln	p.R1276Q	ENST00000356175	NM_000267.3	1276	cGa/cAa	28/57	1	2	FACETS	0.453	0.365	0.552	0.453	0.365	0.552	SUBCLONAL	1	TRUE	1	0.260478253576585	2		498	526	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253376	226253376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	24	301	0	ENST00000366813.1:c.148C>T	p.Arg50Cys	p.R50C	ENST00000366813		50	Cgt/Tgt	2/3	1	2	FACETS	0.562	0.441	0.702	0.562	0.441	0.702	SUBCLONAL	1	TRUE	1	0.260478253576585	2		301	328	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782283	56782283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770006120	NA	P-0065415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	41	601	0	ENST00000308159.5:c.124C>T	p.Arg42Cys	p.R42C	ENST00000308159	NM_014669.4	42	Cgc/Tgc	2/22	1	2	FACETS	0.595	0.495	0.706	0.595	0.495	0.706	SUBCLONAL	1	TRUE	1	0.260478253576585	2		601	529	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280803	41280803	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	43	659	0	ENST00000349496.5:c.2316T>A	p.Asn772Lys	p.N772K	ENST00000349496	NM_001904.3	772	aaT/aaA	15/15	1	2	FACETS	0.54	0.451	0.639	0.54	0.451	0.639	SUBCLONAL	1	TRUE	1	0.260478253576585	2		659	611	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934318	49934318	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	55	763	0	ENST00000296474.3:c.2189G>T	p.Ser730Ile	p.S730I	ENST00000296474	NM_002447.2	730	aGt/aTt	8/20	1	2	FACETS	0.667	0.57	0.773	0.667	0.57	0.773	SUBCLONAL	1	TRUE	1	0.260478253576585	2		763	633	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922321	178922321	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	43	282	0	ENST00000263967.3:c.1090G>C	p.Gly364Arg	p.G364R	ENST00000263967	NM_006218.2	364	Gga/Cga	6/21	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.260478253576585	2		282	308	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470594	25470594	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs755769867	NA	P-0065416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	230	423	0	ENST00000264709.3:c.880G>T	p.Glu294Ter	p.E294*	ENST00000264709	NM_175629.2	294	Gag/Tag	8/23	0.846765133528973	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.846765133528973	1		423	237	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843239	128843239	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1188326206	NA	P-0065416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	272	444	0	ENST00000249373.3:c.346C>T	p.Pro116Ser	p.P116S	ENST00000249373	NM_005631.4	116	Ccc/Tcc	2/12	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.846765133528973	2		444	505	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	86	663	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.977	0.875	1	0.977	0.875	1	CLONAL	1	TRUE	1	0.633571519555952	2		663	278	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624301	89624301	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	194	519	0	ENST00000371953.3:c.75G>C	p.Leu25Phe	p.L25F	ENST00000371953	NM_000314.4	25	ttG/ttC	1/9	0.633571519555952	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.633571519555952	1		519	370	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439609	51439610	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	224	545	0	ENST00000262662.1:c.175dup	p.Arg59LysfsTer4	p.R59Kfs*4	ENST00000262662		58	-/A	4/4	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.633571519555952	2		545	670	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331968	81331968	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	205	550	0	ENST00000222390.5:c.2116T>A	p.Phe706Ile	p.F706I	ENST00000222390	NM_000601.4	706	Ttt/Att	18/18	0.633571519555952	3	FACETS	1	0.981	1	0.573	0.533	0.614	CLONAL	1	TRUE	1	0.633571519555952	3		550	744	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0065418-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	60	442	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.19	2		442	579	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390791	139390791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375025242	NA	P-0065418-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	86	848	0	ENST00000277541.6:c.7400C>T	p.Ser2467Leu	p.S2467L	ENST00000277541	NM_017617.3	2467	tCg/tTg	34/34	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.19	2		848	870	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912471	32912471	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065418-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	48	428	0	ENST00000380152.3:c.3979G>C	p.Ala1327Pro	p.A1327P	ENST00000380152		1327	Gcc/Ccc	11/27	0.194541204289818	3	FACETS	0.944	0.797	1	0.472	0.398	0.553	CLONAL	1	TRUE	1	0.19	3		428	586	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936102	49936103	+	missense_variant	Missense_Mutation	DNP	TG	TG	CC	novel	NA	P-0065418-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	64	849	0	ENST00000296474.3:c.1567_1568delinsGG	p.Gln523Gly	p.Q523G	ENST00000296474	NM_002447.2	523	CAa/GGa	4/20	1	2	FACETS	0.781	0.674	0.896	0.781	0.674	0.896	SUBCLONAL	1	TRUE	1	0.19	2		849	863	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0065419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	57	432	1	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.185803305730065	2	FACETS	1	0.967	1	0.724	0.625	0.831	CLONAL	1	FALSE	0	0.24452351741281	2		433	322	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0065419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	43	535	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.67	0.56	0.792	0.67	0.56	0.792	SUBCLONAL	1	FALSE	1	0.24452351741281	2		535	525	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39647351	39647351	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0065419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	49	399	0	ENST00000262039.4:c.2524-1G>T		p.X842_splice	ENST00000262039	NM_002647.2	842			1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	FALSE	1	0.24452351741281	2		399	367	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546122	29546122	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs894292181	NA	P-0065419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	27	471	0	ENST00000356175.3:c.1627C>T	p.Gln543Ter	p.Q543*	ENST00000356175	NM_000267.3	543	Cag/Tag	14/57	0.168739297653934	1	FACETS	0.426	0.338	0.527	0.426	0.338	0.527	SUBCLONAL	1	FALSE	0	0.24452351741281	1		471	455	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600481	43600481	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	40	665	0	ENST00000355710.3:c.707A>C	p.Lys236Thr	p.K236T	ENST00000355710	NM_020975.4	236	aAg/aCg	4/20	0.168739297653934	1	FACETS	0.603	0.501	0.717	0.603	0.501	0.717	SUBCLONAL	1	FALSE	0	0.24452351741281	1		665	476	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794714	120794714	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	103	550	0	ENST00000257552.2:c.643G>T	p.Gly215Cys	p.G215C	ENST00000257552	NM_002442.3	215	Ggc/Tgc	9/15	0.185803305730065	2	FACETS	0.984	0.887	1	0.984	0.887	1	CLONAL	2	FALSE	0	0.24452351741281	2		550	428	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51504611	51504611	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	32	551	0	ENST00000260433.2:c.1169A>C	p.Lys390Thr	p.K390T	ENST00000260433		390	aAg/aCg	9/10	0.122827007336251	0	FACETS	0.422	0.342	0.512			1	INDETERMINATE	1	FALSE	0	0.24452351741281	0		551	469	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576217	88576217	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs752483865	NA	P-0065419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	33	543	0	ENST00000360948.2:c.1456C>A	p.His486Asn	p.H486N	ENST00000360948	NM_001012338.2	486	Cac/Aac	13/19	0.122827007336251	0	FACETS	0.482	0.392	0.583			1	INDETERMINATE	1	FALSE	0	0.24452351741281	0		543	423	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980345	7980345	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	40	661	0	ENST00000319144.4:c.1238del	p.Leu413CysfsTer2	p.L413Cfs*2	ENST00000319144	NM_001139.2	413	tTg/tg	9/15	0.168739297653934	1	FACETS	0.569	0.472	0.676	0.569	0.472	0.676	SUBCLONAL	1	FALSE	0	0.24452351741281	1		661	505	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653193	29653193	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	42	606	0	ENST00000356175.3:c.5129del	p.Leu1710TrpfsTer3	p.L1710Wfs*3	ENST00000356175	NM_000267.3	1710	Ttg/tg	36/57	0.168739297653934	1	FACETS	0.62	0.518	0.734	0.62	0.518	0.734	SUBCLONAL	1	FALSE	0	0.24452351741281	1		606	486	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095867	29095867	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs750984976	NA	P-0065419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	50	417	0	ENST00000328354.6:c.967A>G	p.Thr323Ala	p.T323A	ENST00000328354	NM_007194.3	323	Acc/Gcc	9/15	0.122827007336251	0	FACETS	0.776	0.66	0.903			1	INDETERMINATE	1	FALSE	0	0.24452351741281	0		417	398	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673467	30673467	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	46	664	0	ENST00000376406.3:c.3493G>A	p.Ala1165Thr	p.A1165T	ENST00000376406	NM_014641.2	1165	Gcc/Acc	10/15	0.238563885004418	4	FACETS	0.708	0.595	0.834	0.236	0.198	0.278	SUBCLONAL	1	FALSE	1	0.24452351741281	4		664	661	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465532	8465532	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	31	467	0	ENST00000356435.5:c.3648C>G	p.Asn1216Lys	p.N1216K	ENST00000356435		1216	aaC/aaG	21/35	0.150366851674074	2	FACETS	0.535	0.432	0.652	0.267	0.216	0.326	SUBCLONAL	1	FALSE	0	0.24452351741281	2		467	474	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	58	663	0				ENST00000310581	NM_198253.2	-/1132			0.363602004391724	4	FACETS	0.776	0.673	0.886	0.776	0.673	0.886	SUBCLONAL	2	TRUE	2	0.394908463077915	4		663	264	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0065420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	181	602	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.343400363343824	5	FACETS	0.978	0.917	1	0.978	0.917	1	CLONAL	4	TRUE	1	0.394908463077915	5		602	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0065420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	216	754	0	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	0.384386420069912	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.394908463077915	2		754	543	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910349	29910349	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	248	845	2	ENST00000376809.5:c.19C>T	p.Arg7Ter	p.R7*	ENST00000376809	NM_002116.7	7	Cga/Tga	1/8	0.394908463077915	3	FACETS	0.955	0.903	1	0.955	0.903	1	CLONAL	3	TRUE	0	0.394908463077915	3		847	525	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450105	32450105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1190263054	NA	P-0065420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	107	694	0	ENST00000332351.3:c.707C>T	p.Ala236Val	p.A236V	ENST00000332351	NM_024426.4	236	gCg/gTg	2/10	0.351927646377344	2	FACETS	1	0.959	1	0.561	0.506	0.619	CLONAL	1	TRUE	0	0.394908463077915	2		694	483	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325123	123325123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371714070	NA	P-0065420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	96	702	2	ENST00000358487.5:c.205G>A	p.Val69Met	p.V69M	ENST00000358487	NM_000141.4	69	Gtg/Atg	3/18	0.394914566221381	3	FACETS	0.933	0.833	1	0.466	0.416	0.52	CLONAL	1	TRUE	1	0.394908463077915	3		704	624	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012397	176012397	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	22	465	0	ENST00000367669.3:c.1537G>T	p.Glu513Ter	p.E513*	ENST00000367669	NM_022457.5	513	Gag/Tag	14/20	0.394908463077915	5	FACETS	0.56	0.434	0.706	0.14	0.108	0.177	SUBCLONAL	1	TRUE	1	0.394908463077915	5		465	317	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929263	32929263	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1566241084	NA	P-0065420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	14	398	0	ENST00000380152.3:c.7274del	p.Asn2425IlefsTer42	p.N2425Ifs*42	ENST00000380152		2425	Aat/at	14/27	1	2	FACETS	0.379	0.274	0.505	0.379	0.274	0.505	SUBCLONAL	1	TRUE	1	0.394908463077915	2		398	187	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441990	40441990	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	82	638	0	ENST00000345506.4:c.235G>C	p.Asp79His	p.D79H	ENST00000345506	NM_003152.3	79	Gat/Cat	4/20	0.394021839681627	3	FACETS	0.906	0.8	1	0.453	0.4	0.509	CLONAL	1	TRUE	1	0.394908463077915	3		638	549	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248666	212248666	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	74	663	0	ENST00000342788.4:c.3601G>C	p.Glu1201Gln	p.E1201Q	ENST00000342788	NM_005235.2	1201	Gag/Cag	28/28	0.384386420069912	2	FACETS	0.884	0.777	0.998	0.442	0.388	0.499	CLONAL	1	TRUE	0	0.394908463077915	2		663	424	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795108	242795108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	51	746	0	ENST00000334409.5:c.101C>T	p.Pro34Leu	p.P34L	ENST00000334409	NM_005018.2	34	cCc/cTc	2/5	0.384386420069912	2	FACETS	0.529	0.45	0.616	0.265	0.225	0.308	SUBCLONAL	1	TRUE	0	0.394908463077915	2		746	488	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446171	187446171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	40	621	0	ENST00000232014.4:c.1517C>T	p.Ser506Phe	p.S506F	ENST00000232014	NM_001130845.1	506	tCt/tTt	6/10	0.343400363343824	5	FACETS	0.493	0.409	0.588	0.123	0.102	0.147	SUBCLONAL	1	TRUE	1	0.394908463077915	5		621	654	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582020	189582020	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0065420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	293	623	0	ENST00000264731.3:c.580-1G>C		p.X194_splice	ENST00000264731	NM_003722.4	194			0.343400363343824	5	FACETS	0.926	0.879	0.973	0.926	0.879	0.973	CLONAL	4	TRUE	1	0.394908463077915	5		623	638	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280049	66280049	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	26	536	0	ENST00000273854.3:c.1640G>T	p.Gly547Val	p.G547V	ENST00000273854	NM_004439.5	547	gGc/gTc	7/18	0.386788655793536	2	FACETS	0.316	0.25	0.392	0.158	0.125	0.196	SUBCLONAL	1	TRUE	0	0.394908463077915	2		536	417	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2039663	2039663	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	59	754	0	ENST00000349721.2:c.553C>T	p.Gln185Ter	p.Q185*	ENST00000349721	NM_003070.3	185	Cag/Tag	4/34	0.394914566221381	4	FACETS	0.569	0.489	0.657	0.142	0.122	0.165	SUBCLONAL	1	TRUE	0	0.394908463077915	4		754	732	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753886	133753886	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	200	536	0	ENST00000318560.5:c.1355T>A	p.Leu452Gln	p.L452Q	ENST00000318560	NM_005157.4	452	cTa/cAa	8/11	0.328664485076515	5	FACETS	1	0.986	1	0.817	0.761	0.875	CLONAL	2	TRUE	2	0.394908463077915	5		536	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs786201057	NA	P-0065427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	334	728	0	ENST00000269305.4:c.374C>G	p.Thr125Arg	p.T125R	ENST00000269305	NM_001126112.2	125	aCg/aGg	4/11	0.245273933881551	4	FACETS	0.88	0.836	0.924			1	CLONAL	4	TRUE	NA	0.299249170170485	4		728	824	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56171051	56171051	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs775970017	NA	P-0065427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	98	768	0	ENST00000399503.3:c.1879A>G	p.Ile627Val	p.I627V	ENST00000399503	NM_005921.1	627	Atc/Gtc	10/20	0.299249170170485	7	FACETS	0.972	0.865	1	0.194	0.173	0.218	CLONAL	1	TRUE	2	0.299249170170485	7		768	1178	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523720	176523720	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	136	865	1	ENST00000292408.4:c.2131C>A	p.Pro711Thr	p.P711T	ENST00000292408	NM_213647.1	711	Ccc/Acc	16/18	0.299249170170485	5	FACETS	1	0.957	1	0.365	0.331	0.401	CLONAL	1	TRUE	2	0.299249170170485	5		866	1202	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0065438-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	31	491	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.17	2		491	324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579547	7579547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567557016	NA	P-0065438-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	38	586	0	ENST00000269305.4:c.140del	p.Pro47ArgfsTer76	p.P47Rfs*76	ENST00000269305	NM_001126112.2	47	cCg/cg	4/11	1	2	FACETS	0.675	0.557	0.808	0.675	0.557	0.808	SUBCLONAL	1	TRUE	1	0.17	2		586	662	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281148	142281148	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065438-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	40	535	0	ENST00000350721.4:c.1096C>A	p.Gln366Lys	p.Q366K	ENST00000350721	NM_001184.3	366	Caa/Aaa	4/47	1	2	FACETS	0.778	0.645	0.926	0.778	0.645	0.926	CLONAL	1	TRUE	1	0.17	2		535	605	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0065439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	421	557	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.625422452373631	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.62594550499452	2		557	619	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10797077	10797077	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1019586922	NA	P-0065439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	155	448	0	ENST00000361367.2:c.2992G>A	p.Glu998Lys	p.E998K	ENST00000361367	NM_014633.3	998	Gaa/Aaa	24/25	0.625422452373631	3	FACETS	1	0.955	1	0.529	0.486	0.573	CLONAL	1	TRUE	1	0.62594550499452	3		448	615	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359382	118359382	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	108	563	0	ENST00000534358.1:c.4386G>C	p.Glu1462Asp	p.E1462D	ENST00000534358	NM_005933.3	1462	gaG/gaC	11/36	0.625422452373631	3	FACETS	0.547	0.49	0.607	0.273	0.245	0.304	SUBCLONAL	1	TRUE	1	0.62594550499452	3		563	829	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657029	47657029	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs151244108	NA	P-0065439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	153	449	0	ENST00000233146.2:c.1225C>T	p.Gln409Ter	p.Q409*	ENST00000233146	NM_000251.2	409	Cag/Tag	7/16	0.625422452373631	4	FACETS	1	0.933	1	0.511	0.468	0.556	CLONAL	1	TRUE	2	0.62594550499452	4		449	778	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021628	31021628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	171	599	0	ENST00000375687.4:c.1627G>A	p.Glu543Lys	p.E543K	ENST00000375687	NM_015338.5	543	Gaa/Aaa	12/13	0.625422452373631	5	FACETS	0.969	0.89	1	0.323	0.296	0.351	CLONAL	1	TRUE	2	0.62594550499452	5		599	1093	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022844	31022844	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	182	569	0	ENST00000375687.4:c.2329G>C	p.Glu777Gln	p.E777Q	ENST00000375687	NM_015338.5	777	Gag/Cag	13/13	0.625422452373631	5	FACETS	1	0.952	1	0.349	0.321	0.377	CLONAL	1	TRUE	2	0.62594550499452	5		569	1078	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664463	138664463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	91	260	0	ENST00000330315.3:c.1102G>A	p.Gly368Ser	p.G368S	ENST00000330315	NM_023067.3	368	Ggc/Agc	1/1	0.49026990318436	5	FACETS	1	0.961	1	0.391	0.348	0.436	CLONAL	1	TRUE	2	0.62594550499452	5		260	481	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242931	142242931	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	196	526	0	ENST00000350721.4:c.4056G>C	p.Leu1352Phe	p.L1352F	ENST00000350721	NM_001184.3	1352	ttG/ttC	22/47	0.49026990318436	5	FACETS	1	0.984	1	0.407	0.377	0.439	CLONAL	1	TRUE	2	0.62594550499452	5		526	994	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591118	67591126	+	inframe_deletion	In_Frame_Del	DEL	ATCCAGCTG	ATCCAGCTG	-	novel	NA	P-0065439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	337	434	0	ENST00000274335.5:c.1712_1720del	p.Ile571_Leu573del	p.I571_L573del	ENST00000274335		571	ATCCAGCTG/-	12/15	0.625422452373631	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.62594550499452	2		434	509	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129270	152129270	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	97	484	0	ENST00000206249.3:c.223C>T	p.Gln75Ter	p.Q75*	ENST00000206249	NM_000125.3	75	Cag/Tag	1/8	0.533484185918584	4	FACETS	0.811	0.725	0.904	0.406	0.362	0.452	CLONAL	1	TRUE	2	0.62594550499452	4		484	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0065441-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	50	472	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	1	2	FACETS	0.805	0.682	0.94	0.805	0.682	0.94	CLONAL	1	TRUE	1	0.2	2		472	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0065442-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	781	573	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.553369707549846	4	FACETS	0.97	0.951	0.987			1	CLONAL	4	TRUE	NA	0.735941220979588	4		573	950	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0065442-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	129	358	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.894	0.819	0.972	0.894	0.819	0.972	CLONAL	1	TRUE	1	0.735941220979588	2		358	392	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521481	8521481	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760428875	NA	P-0065442-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	238	390	0	ENST00000356435.5:c.757G>A	p.Val253Ile	p.V253I	ENST00000356435		253	Gtt/Att	9/35	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.735941220979588	2		390	633	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0065443-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	166	622	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.410981331596282	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.410981331596282	1		622	554	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488249	56488249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065443-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	154	508	0	ENST00000267101.3:c.1768C>T	p.Pro590Ser	p.P590S	ENST00000267101	NM_001982.3	590	Ccc/Tcc	15/28	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.410981331596282	2		508	682	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478788	56478788	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065443-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	120	375	0	ENST00000267101.3:c.244G>C	p.Glu82Gln	p.E82Q	ENST00000267101	NM_001982.3	82	Gaa/Caa	3/28	1	2	FACETS	0.956	0.865	1	0.956	0.865	1	CLONAL	1	TRUE	1	0.410981331596282	2		375	611	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943362	71943362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065443-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	130	531	0	ENST00000298229.2:c.1694G>A	p.Gly565Glu	p.G565E	ENST00000298229	NM_001567.3	565	gGa/gAa	14/28	0.410981331596282	1	FACETS	0.76	0.691	0.833	0.76	0.691	0.833	SUBCLONAL	1	TRUE	0	0.410981331596282	1		531	661	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422570	47422570	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065443-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	242	518	0	ENST00000404338.3:c.638C>A	p.Ala213Glu	p.A213E	ENST00000404338	NM_004491.4	213	gCa/gAa	1/6	0.252564153418929	3	FACETS	0.904	0.848	0.962	0.904	0.848	0.962	CLONAL	2	TRUE	1	0.410981331596282	3		518	785	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248124	110248124	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	138	532	0	ENST00000374672.4:c.1348C>T	p.His450Tyr	p.H450Y	ENST00000374672	NM_004235.4	450	Cac/Tac	5/5	0.242777576273608	3	FACETS	0.876	0.799	0.957	0.876	0.799	0.957	CLONAL	2	TRUE	1	0.2645350157024	3		532	674	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065445-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	83	663	0				ENST00000310581	NM_198253.2	-/1132			0.264921369768471	3	FACETS	1	0.914	1	0.515	0.459	0.574	INDETERMINATE	1	TRUE	1	0.675748558109338	3		663	319	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652025	36652025	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065445-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	537	663	0	ENST00000244741.5:c.147G>A	p.Trp49Ter	p.W49*	ENST00000244741	NM_000389.4	49	tgG/tgA	2/3	0.655455985486153	3	FACETS	0.879	0.853	0.905	0.879	0.853	0.905	CLONAL	3	TRUE	0	0.675748558109338	3		663	806	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392080	81392080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065445-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	104	514	0	ENST00000222390.5:c.197C>T	p.Thr66Ile	p.T66I	ENST00000222390	NM_000601.4	66	aCt/aTt	2/18	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.675748558109338	2		514	304	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652125	36652135	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCGAGGCCG	CGGCGAGGCCG	-	novel	NA	P-0065445-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	94	646	0	ENST00000244741.5:c.247_257del	p.Arg83GlyfsTer2	p.R83Gfs*2	ENST00000244741	NM_000389.4	83	CGGCGAGGCCGg/g	2/3	0.655455985486153	3	FACETS	0.469	0.417	0.525	0.156	0.139	0.175	SUBCLONAL	1	TRUE	0	0.675748558109338	3		646	793	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422443	47422443	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065446-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	104	453	0	ENST00000404338.3:c.511A>G	p.Asn171Asp	p.N171D	ENST00000404338	NM_004491.4	171	Aat/Gat	1/6	1	2	FACETS	1	0.904	1	1	0.988	1	CLONAL	2	FALSE	1	0.204515625708952	2		453	506	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346889	70346889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065446-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	102	463	0	ENST00000374080.3:c.2756C>T	p.Thr919Ile	p.T919I	ENST00000374080		919	aCt/aTt	20/45	0.204515625708952	0	FACETS	0.855	0.781	0.931			1	CLONAL	4	FALSE	0	0.204515625708952	0		463	232	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0065449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	301	355	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.3	6	FACETS	0.945	0.895	0.995			1	CLONAL	7	TRUE	NA	0.16	6		355	751	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115733	108115733	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1370428326	NA	P-0065449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	69	373	0	ENST00000278616.4:c.881G>T	p.Gly294Val	p.G294V	ENST00000278616	NM_000051.3	294	gGa/gTa	7/63	1	2	FACETS	0.805	0.702	0.915	1	0.976	1	CLONAL	2	TRUE	1	0.16	2		373	536	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46715707	46715707	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	34	384	0	ENST00000371975.4:c.126G>T	p.Gln42His	p.Q42H	ENST00000371975	NM_003579.3	42	caG/caT	3/18	1	2	FACETS	0.675	0.55	0.816	0.675	0.55	0.816	SUBCLONAL	1	TRUE	1	0.16	2		384	630	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16047011	16047011	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0065449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	24	305	0	ENST00000268712.3:c.1083-1G>C		p.X361_splice	ENST00000268712	NM_006311.3	361			1	2	FACETS	0.626	0.49	0.784	0.626	0.49	0.784	SUBCLONAL	1	TRUE	1	0.16	2		305	479	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871591	37871591	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	46	517	0	ENST00000269571.5:c.1201G>C	p.Glu401Gln	p.E401Q	ENST00000269571		401	Gag/Cag	10/27	1	2	FACETS	0.746	0.626	0.878	0.746	0.626	0.878	SUBCLONAL	1	TRUE	1	0.16	2		517	771	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1650243	1650243	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	86	460	0	ENST00000344749.5:c.5A>G	p.Asn2Ser	p.N2S	ENST00000344749	NM_001136139.2	2	aAc/aGc	2/19	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.16	2		460	760	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6222355	6222355	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	32	408	0	ENST00000252674.7:c.887G>T	p.Ser296Ile	p.S296I	ENST00000252674	NM_005934.3	296	aGc/aTc	6/12	1	2	FACETS	0.705	0.571	0.858	0.705	0.571	0.858	SUBCLONAL	1	TRUE	1	0.16	2		408	567	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290911	15290911	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs189545202	NA	P-0065449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	42	513	0	ENST00000263388.2:c.3299G>T	p.Arg1100Leu	p.R1100L	ENST00000263388	NM_000435.2	1100	cGt/cTt	20/33	1	2	FACETS	0.753	0.627	0.894	0.753	0.627	0.894	SUBCLONAL	1	TRUE	1	0.16	2		513	697	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872914	136872914	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	46	621	0	ENST00000241393.3:c.584G>T	p.Trp195Leu	p.W195L	ENST00000241393	NM_003467.2	195	tGg/tTg	2/2	1	2	FACETS	0.68	0.57	0.801	0.68	0.57	0.801	SUBCLONAL	1	TRUE	1	0.16	2		621	846	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69032463	69032463	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs778599632	NA	P-0065449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	67	422	0	ENST00000288368.4:c.3537G>T	p.Gln1179His	p.Q1179H	ENST00000288368	NM_024870.2	1179	caG/caT	29/40	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.16	2		422	670	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057926	27057928	+	frameshift_variant	Frame_Shift_Del	DEL	CCC	CCC	TT	novel	NA	P-0065449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	68	531	0	ENST00000324856.7:c.1634_1636delinsTT	p.Pro545LeufsTer74	p.P545Lfs*74	ENST00000324856	NM_006015.4	545	cCCCag/cTTag	3/20	1	2	FACETS	0.995	0.864	1	0.995	0.864	1	CLONAL	1	TRUE	1	0.16	2		531	854	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866681	37866681	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065450-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	206	534	0	ENST00000269571.5:c.848C>G	p.Pro283Arg	p.P283R	ENST00000269571		283	cCc/cGc	7/27	0.294043260634879	4	FACETS	0.84	0.781	0.9	0.84	0.781	0.9	CLONAL	2	TRUE	2	0.469236947500522	4		534	768	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55963919	55963919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41469552	NA	P-0065451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	43	402	0	ENST00000263923.4:c.2524C>T	p.Arg842Cys	p.R842C	ENST00000263923	NM_002253.2	842	Cgt/Tgt	18/30	0.265810707994299	5	FACETS	0.879	0.748	1	0.586	0.499	0.679	INDETERMINATE	2	FALSE	2	0.564772030467779	5		402	160	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs760043106	NA	P-0065451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	90	725	0	ENST00000269305.4:c.584T>G	p.Ile195Ser	p.I195S	ENST00000269305	NM_001126112.2	195	aTc/aGc	6/11	0.559706997846644	2	FACETS	0.834	0.759	0.91	0.834	0.759	0.91	CLONAL	2	FALSE	0	0.564772030467779	2		725	191	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959366	26959366	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1418353379	NA	P-0065451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	98	426	0	ENST00000381527.3:c.533G>A	p.Arg178Gln	p.R178Q	ENST00000381527	NM_001260.1	178	cGa/cAa	6/13	0.497159790948154	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	3	FALSE	1	0.564772030467779	4		426	171	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0065452-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	119	502	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.35751170495691	2	FACETS	0.773	0.704	0.843	0.773	0.704	0.843	SUBCLONAL	2	TRUE	0	0.404201190843009	2		502	381	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604750	48604750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065452-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	142	539	0	ENST00000342988.3:c.1572G>T	p.Trp524Cys	p.W524C	ENST00000342988	NM_005359.5	524	tgG/tgT	12/12	0.404201190843009	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.404201190843009	1		539	425	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335007	65335007	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065452-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	131	410	0	ENST00000342505.4:c.634C>G	p.Pro212Ala	p.P212A	ENST00000342505	NM_002227.2	212	Ccc/Gcc	6/25	0.274230773608126	3	FACETS	1	0.986	1	0.745	0.679	0.813	CLONAL	1	TRUE	1	0.404201190843009	3		410	523	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298765	46298765	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065452-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	26	421	0	ENST00000334344.6:c.5412del	p.Asn1804LysfsTer35	p.N1804Kfs*35	ENST00000334344	NM_152641.2	1804	aaC/aa	21/21	0.356323379626859	3	FACETS	0.385	0.304	0.477	0.192	0.152	0.239	SUBCLONAL	1	TRUE	1	0.404201190843009	3		421	402	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858260	59858260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28997571	NA	P-0065452-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	117	432	0	ENST00000259008.2:c.1735C>T	p.Arg579Cys	p.R579C	ENST00000259008	NM_032043.2	579	Cgt/Tgt	12/20	0.404201190843009	3	FACETS	0.897	0.816	0.98	0.897	0.816	0.98	CLONAL	2	TRUE	1	0.404201190843009	3		432	388	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	279	663	0				ENST00000310581	NM_198253.2	-/1132			0.528739414297128	5	FACETS	0.91	0.864	0.956	0.91	0.864	0.956	CLONAL	3	TRUE	2	0.807275406977887	5		663	560	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101176	41101176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370385649	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	290	493	0	ENST00000373198.4:c.1180G>A	p.Glu394Lys	p.E394K	ENST00000373198	NM_133170.3	394	Gaa/Aaa	8/32	0.702297127712427	3	FACETS	1	0.992	1	0.638	0.603	0.674	CLONAL	1	TRUE	1	0.807275406977887	3		493	790	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	500	394	0	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	0.75581071078011	4	FACETS	0.888	0.858	0.918			1	CLONAL	3	TRUE	NA	0.807275406977887	4		394	840	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374253	118374253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	390	553	0	ENST00000534358.1:c.7646C>T	p.Ser2549Phe	p.S2549F	ENST00000534358	NM_005933.3	2549	tCc/tTc	27/36	0.485829476154381	2	FACETS	0.797	0.768	0.826	0.797	0.768	0.826	SUBCLONAL	2	TRUE	0	0.807275406977887	2		553	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs530941076	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	641	559	0	ENST00000269305.4:c.658T>A	p.Tyr220Asn	p.Y220N	ENST00000269305	NM_001126112.2	220	Tat/Aat	6/11	0.777366694107283	3	FACETS	0.969	0.95	0.987	0.969	0.95	0.987	CLONAL	3	TRUE	0	0.807275406977887	3		559	767	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733217	40733217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	410	466	0	ENST00000373198.4:c.3589G>A	p.Glu1197Lys	p.E1197K	ENST00000373198	NM_133170.3	1197	Gaa/Aaa	26/32	0.702297127712427	3	FACETS	0.906	0.869	0.943	0.906	0.869	0.943	CLONAL	2	TRUE	1	0.807275406977887	3		466	787	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709162	117709162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867987684	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	211	426	0	ENST00000368508.3:c.1795G>A	p.Glu599Lys	p.E599K	ENST00000368508	NM_002944.2	599	Gaa/Aaa	13/43	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.807275406977887	2		426	489	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106162522	106162522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	289	181	0	ENST00000380013.4:c.3436C>T	p.Pro1146Ser	p.P1146S	ENST00000380013	NM_001127208.2	1146	Cct/Tct	4/11	0.777366694107283	3	FACETS	0.968	0.939	0.995	0.968	0.939	0.995	CLONAL	3	TRUE	0	0.807275406977887	3		181	346	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087961	27087961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	588	440	0	ENST00000324856.7:c.2248C>T	p.Arg750Ter	p.R750*	ENST00000324856	NM_006015.4	750	Cga/Tga	6/20	0.736798852174942	4	FACETS	0.992	0.963	1	0.992	0.963	1	CLONAL	3	TRUE	1	0.807275406977887	4		440	885	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	220	283	0	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	NA	2	FACETS	0.946	0.908	0.982			1	INDETERMINATE	2	TRUE	NA	0.807275406977887	2		283	288	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134458	30134458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1044163469	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	113	435	0	ENST00000263025.4:c.73C>T	p.Pro25Ser	p.P25S	ENST00000263025	NM_002746.2	25	Ccg/Tcg	1/9	0.311963752381946	4	FACETS	0.988	0.893	1	0.494	0.446	0.544	INDETERMINATE	1	TRUE	2	0.807275406977887	4		435	512	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873648	35873648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867618621	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	381	394	0	ENST00000303115.3:c.604G>A	p.Glu202Lys	p.E202K	ENST00000303115	NM_002185.3	202	Gag/Aag	5/8	0.372694632996189	5	FACETS	0.841	0.803	0.879	0.841	0.803	0.879	INDETERMINATE	3	TRUE	2	0.807275406977887	5		394	827	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099412	157099426	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAA	CAGCAGCAGCAGCAA	-	rs774668010	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	100	647	0	ENST00000346085.5:c.363_377del	p.Gln127_Gln131del	p.Q127_Q131del	ENST00000346085	NM_020732.3	117	CAGCAGCAGCAGCAA/-	1/20	1	2	FACETS	0.402	0.36	0.447	0.402	0.36	0.447	SUBCLONAL	1	TRUE	1	0.807275406977887	2		647	616	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432368	432368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1362895739	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	163	141	0	ENST00000399788.2:c.2155C>T	p.Arg719Cys	p.R719C	ENST00000399788	NM_001042603.1	719	Cgc/Tgc	16/28	0.807275406977887	2	FACETS	0.99	0.947	1	0.99	0.947	1	CLONAL	2	TRUE	0	0.807275406977887	2		141	204	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350155	81350155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758567520	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	309	193	0	ENST00000222390.5:c.1177C>T	p.Arg393Cys	p.R393C	ENST00000222390	NM_000601.4	393	Cgt/Tgt	10/18	0.806102787986305	5	FACETS	0.983	0.938	1	0.983	0.938	1	CLONAL	3	TRUE	2	0.807275406977887	5		193	574	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687561	37687561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	519	434	0	ENST00000447079.4:c.4465C>T	p.Pro1489Ser	p.P1489S	ENST00000447079	NM_015083.1	1489	Cct/Tct	14/14	0.502295709618894	4	FACETS	0.919	0.889	0.949	0.919	0.889	0.949	CLONAL	3	TRUE	1	0.807275406977887	4		434	843	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188995	32188995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753307747	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	450	660	1	ENST00000375023.3:c.559G>A	p.Glu187Lys	p.E187K	ENST00000375023	NM_004557.3	187	Gag/Aag	4/30	0.807275406977887	5	FACETS	0.886	0.845	0.927	0.591	0.563	0.618	CLONAL	2	TRUE	2	0.807275406977887	5		661	1391	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086209	16086209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	481	429	0	ENST00000281043.3:c.1385G>A	p.Arg462Gln	p.R462Q	ENST00000281043	NM_005378.4	462	cGg/cAg	3/3	0.436148145945355	5	FACETS	0.93	0.895	0.966	0.93	0.895	0.966	INDETERMINATE	3	TRUE	2	0.807275406977887	5		429	944	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244973	123244973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	401	555	0	ENST00000358487.5:c.2131G>A	p.Glu711Lys	p.E711K	ENST00000358487	NM_000141.4	711	Gaa/Aaa	16/18	0.311963752381946	4	FACETS	1	0.987	1	1	0.987	1	INDETERMINATE	2	TRUE	2	0.807275406977887	4		555	837	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518073	8518073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1480778931	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	183	456	0	ENST00000356435.5:c.1318G>A	p.Glu440Lys	p.E440K	ENST00000356435		440	Gaa/Aaa	10/35	0.254518486947959	1	FACETS	0.604	0.563	0.645	0.604	0.563	0.645	INDETERMINATE	1	TRUE	0	0.807275406977887	1		456	448	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858369	9858369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1163766811	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	340	519	0	ENST00000330684.3:c.3032G>A	p.Arg1011Gln	p.R1011Q	ENST00000330684	NM_001134407.1	1011	cGg/cAg	13/13	0.311963752381946	4	FACETS	1	0.964	1	1	0.964	1	INDETERMINATE	2	TRUE	2	0.807275406977887	4		519	750	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381528	81381528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776090604	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	431	377	0	ENST00000222390.5:c.533G>A	p.Arg178Gln	p.R178Q	ENST00000222390	NM_000601.4	178	cGa/cAa	5/18	0.806102787986305	5	FACETS	0.94	0.903	0.978	0.94	0.903	0.978	CLONAL	3	TRUE	2	0.807275406977887	5		377	837	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233630	233630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	156	121	0	ENST00000264932.6:c.934C>T	p.Arg312Cys	p.R312C	ENST00000264932	NM_004168.2	312	Cgt/Tgt	8/15	0.528739414297128	5	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	TRUE	2	0.807275406977887	5		121	269	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893644	28893644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	248	356	0	ENST00000282397.4:c.3202C>T	p.Pro1068Ser	p.P1068S	ENST00000282397	NM_002019.4	1068	Cct/Tct	24/30	0.767607606978338	2	FACETS	0.893	0.857	0.928	0.893	0.857	0.928	CLONAL	2	TRUE	0	0.807275406977887	2		356	344	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560226	29560226	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555615109	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	208	378	0	ENST00000356175.3:c.3703C>T	p.Gln1235Ter	p.Q1235*	ENST00000356175	NM_000267.3	1235	Cag/Tag	27/57	0.75581071078011	4	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.807275406977887	4		378	802	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61306990	61306990	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746310287	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	319	351	0	ENST00000341074.5:c.490C>T	p.Pro164Ser	p.P164S	ENST00000341074	NM_002974.2	164	Cct/Tct	6/8	0.807275406977887	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.807275406977887	2		351	385	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280072	18280072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	134	541	0	ENST00000222254.8:c.2155C>T	p.Pro719Ser	p.P719S	ENST00000222254	NM_005027.3	719	Ccg/Tcg	16/16	0.618215836579753	4	FACETS	0.929	0.846	1	0.31	0.282	0.339	CLONAL	1	TRUE	1	0.807275406977887	4		541	646	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073796	8073796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	681	481	0	ENST00000377482.5:c.863C>T	p.Pro288Leu	p.P288L	ENST00000377482	NM_018948.3	288	cCc/cTc	4/4	0.736798852174942	4	FACETS	0.951	0.924	0.977	0.951	0.924	0.977	CLONAL	3	TRUE	1	0.807275406977887	4		481	1069	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089586	27089586	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	737	670	0	ENST00000324856.7:c.2542C>T	p.Pro848Ser	p.P848S	ENST00000324856	NM_006015.4	848	Cca/Tca	8/20	0.736798852174942	4	FACETS	0.962	0.937	0.988	0.962	0.937	0.988	CLONAL	3	TRUE	1	0.807275406977887	4		670	1143	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837954	156837954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	533	630	0	ENST00000524377.1:c.487G>A	p.Glu163Lys	p.E163K	ENST00000524377	NM_002529.3	163	Gag/Aag	5/17	0.807275406977887	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.807275406977887	3		630	890	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981783	201981783	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	442	519	0	ENST00000359651.3:c.494T>C	p.Phe165Ser	p.F165S	ENST00000359651		165	tTt/tCt	4/8	0.807275406977887	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.807275406977887	3		519	726	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114905817	114905817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	372	408	0	ENST00000543371.1:c.836C>T	p.Pro279Leu	p.P279L	ENST00000543371	NM_001198531.1	279	cCc/cTc	8/14	0.311963752381946	4	FACETS	1	0.987	1	1	0.987	1	INDETERMINATE	2	TRUE	2	0.807275406977887	4		408	769	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123353316	123353316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141724446	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	312	548	0	ENST00000358487.5:c.16C>T	p.Arg6Cys	p.R6C	ENST00000358487	NM_000141.4	6	Cgt/Tgt	2/18	0.311963752381946	4	FACETS	0.845	0.8	0.89	0.845	0.8	0.89	INDETERMINATE	2	TRUE	2	0.807275406977887	4		548	827	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10797129	10797129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	274	300	0	ENST00000361367.2:c.3044C>T	p.Ser1015Leu	p.S1015L	ENST00000361367	NM_014633.3	1015	tCa/tTa	24/25	0.261005826703691	5	FACETS	1	0.987	1	0.764	0.722	0.806	INDETERMINATE	2	TRUE	2	0.807275406977887	5		300	655	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420672	49420673	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	490	629	1	ENST00000301067.7:c.15076_15077delinsTT	p.Pro5026Leu	p.P5026L	ENST00000301067	NM_003482.3	5026	CCg/TTg	48/54	0.807275406977887	2	FACETS	0.977	0.953	1	0.977	0.953	1	CLONAL	2	TRUE	0	0.807275406977887	2		630	621	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133236014	133236014	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	490	592	0	ENST00000320574.5:c.3142G>T	p.Glu1048Ter	p.E1048*	ENST00000320574	NM_006231.2	1048	Gag/Tag	26/49	0.807275406977887	3	FACETS	0.924	0.89	0.958			1	CLONAL	2	TRUE	NA	0.807275406977887	3		592	922	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560301	95560301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	363	389	0	ENST00000393063.1:c.5288C>T	p.Pro1763Leu	p.P1763L	ENST00000393063	NM_030621.3	1763	cCt/cTt	25/28	0.704492169667794	3	FACETS	0.921	0.882	0.961	0.921	0.882	0.961	CLONAL	2	TRUE	1	0.807275406977887	3		389	685	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50810162	50810162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	220	331	0	ENST00000398568.2:c.986C>T	p.Ser329Phe	p.S329F	ENST00000398568	NM_001042412.1	329	tCc/tTc	6/18	0.265989966191486	3	FACETS	0.812	0.765	0.86	0.541	0.51	0.573	INDETERMINATE	2	TRUE	0	0.807275406977887	3		331	471	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33430502	33430502	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1216040595	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	227	586	0	ENST00000345365.6:c.638C>T	p.Ser213Phe	p.S213F	ENST00000345365	NM_002878.3	213	tCc/tTc	7/10	0.502295709618894	4	FACETS	1	0.973	1	0.362	0.337	0.387	CLONAL	1	TRUE	1	0.807275406977887	4		586	937	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280072	18280073	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	136	546	0	ENST00000222254.8:c.2155_2156delinsTT	p.Pro719Leu	p.P719L	ENST00000222254	NM_005027.3	719	CCg/TTg	16/16	0.618215836579753	4	FACETS	0.943	0.859	1	0.314	0.286	0.344	CLONAL	1	TRUE	1	0.807275406977887	4		546	646	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425420	47425420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	257	494	0	ENST00000404338.3:c.3488C>T	p.Thr1163Ile	p.T1163I	ENST00000404338	NM_004491.4	1163	aCc/aTc	1/6	0.678290512621507	3	FACETS	1	0.976	1	0.538	0.505	0.571	CLONAL	1	TRUE	1	0.807275406977887	3		494	831	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022280	26022280	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	321	429	0	ENST00000435504.4:c.377G>C	p.Gly126Ala	p.G126A	ENST00000435504		126	gGa/gCa	5/13	0.436148145945355	5	FACETS	0.983	0.932	1	0.656	0.621	0.691	INDETERMINATE	2	TRUE	2	0.807275406977887	5		429	894	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248530	212248530	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1225136962	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	540	558	0	ENST00000342788.4:c.3737G>A	p.Ser1246Asn	p.S1246N	ENST00000342788	NM_005235.2	1246	aGc/aAc	28/28	0.372694632996189	5	FACETS	0.921	0.887	0.954	0.921	0.887	0.954	INDETERMINATE	3	TRUE	2	0.807275406977887	5		558	1071	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793310	242793311	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	305	611	0	ENST00000334409.5:c.766_767delinsAA	p.Gly256Lys	p.G256K	ENST00000334409	NM_005018.2	256	GGa/AAa	5/5	0.372694632996189	5	FACETS	0.946	0.894	0.999	0.631	0.596	0.666	INDETERMINATE	2	TRUE	2	0.807275406977887	5		611	883	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306548	41306548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	201	421	0	ENST00000373198.4:c.1111G>A	p.Gly371Arg	p.G371R	ENST00000373198	NM_133170.3	371	Gga/Aga	7/32	0.702297127712427	3	FACETS	1	0.967	1	0.532	0.495	0.57	CLONAL	1	TRUE	1	0.807275406977887	3		421	657	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171630	36171630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	430	461	0	ENST00000300305.3:c.935C>T	p.Thr312Ile	p.T312I	ENST00000300305		312	aCc/aTc	7/8	0.231297339940154	6	FACETS	0.993	0.951	1	0.993	0.951	1	INDETERMINATE	3	TRUE	3	0.807275406977887	6		461	935	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165194	47165194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	383	280	0	ENST00000409792.3:c.932C>T	p.Ser311Phe	p.S311F	ENST00000409792	NM_014159.6	311	tCc/tTc	3/21	0.516404574193689	4	FACETS	1	0.993	1	0.779	0.746	0.812	CLONAL	2	TRUE	1	0.807275406977887	4		280	734	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457269	89457270	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	308	281	0	ENST00000336596.2:c.1750_1751delinsAA	p.Gly584Asn	p.G584N	ENST00000336596	NM_005233.5	584	GGc/AAc	9/17	0.4498969165325	3	FACETS	1	0.994	1	0.808	0.777	0.838	INDETERMINATE	2	TRUE	0	0.807275406977887	3		281	442	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540722	187540722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	730	532	0	ENST00000441802.2:c.7018G>A	p.Gly2340Ser	p.G2340S	ENST00000441802	NM_005245.3	2340	Ggc/Agc	10/27	0.777366694107283	3	FACETS	0.986	0.969	1	0.986	0.969	1	CLONAL	3	TRUE	0	0.807275406977887	3		532	858	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515619	31515619	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	243	334	0	ENST00000344624.3:c.1000C>T	p.Pro334Ser	p.P334S	ENST00000344624		334	Cct/Tct	4/33	0.372694632996189	5	FACETS	1	0.976	1	0.713	0.671	0.756	INDETERMINATE	2	TRUE	2	0.807275406977887	5		334	622	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672167	30672167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	425	728	0	ENST00000376406.3:c.4793G>A	p.Arg1598Lys	p.R1598K	ENST00000376406	NM_014641.2	1598	aGg/aAg	10/15	0.807275406977887	5	FACETS	0.769	0.732	0.807	0.513	0.488	0.538	SUBCLONAL	2	TRUE	2	0.807275406977887	5		728	1513	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170157	32170157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1216758886	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	359	600	0	ENST00000375023.3:c.3451G>A	p.Gly1151Ser	p.G1151S	ENST00000375023	NM_004557.3	1151	Ggc/Agc	21/30	0.807275406977887	5	FACETS	0.755	0.715	0.796	0.503	0.477	0.531	SUBCLONAL	2	TRUE	2	0.807275406977887	5		600	1302	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553798	106553798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	218	469	0	ENST00000369096.4:c.1763C>T	p.Ser588Phe	p.S588F	ENST00000369096	NM_001198.3	588	tCc/tTc	5/7	1	2	FACETS	0.93	0.871	0.989	0.93	0.871	0.989	CLONAL	1	TRUE	1	0.807275406977887	2		469	581	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381511	81381511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	332	406	0	ENST00000222390.5:c.550G>A	p.Glu184Lys	p.E184K	ENST00000222390	NM_000601.4	184	Gaa/Aaa	5/18	0.806102787986305	5	FACETS	0.992	0.94	1	0.661	0.627	0.696	CLONAL	2	TRUE	2	0.807275406977887	5		406	917	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124482883	124482883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	160	245	0	ENST00000357628.3:c.1141C>T	p.His381Tyr	p.H381Y	ENST00000357628	NM_015450.2	381	Cat/Tat	13/19	0.806102787986305	5	FACETS	0.816	0.753	0.881	0.544	0.502	0.588	CLONAL	2	TRUE	2	0.807275406977887	5		245	537	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849988	151849988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	367	486	0	ENST00000262189.6:c.12328C>T	p.Pro4110Ser	p.P4110S	ENST00000262189	NM_170606.2	4110	Cct/Tct	49/59	0.806102787986305	5	FACETS	0.966	0.919	1	0.644	0.612	0.677	CLONAL	2	TRUE	2	0.807275406977887	5		486	1040	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152373132	152373133	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	368	431	0	ENST00000359321.1:c.32_33delinsAA	p.Gly11Glu	p.G11E	ENST00000359321	NM_005431.1	11	gGG/gAA	1/3	0.806102787986305	5	FACETS	0.918	0.878	0.958	0.918	0.878	0.958	CLONAL	3	TRUE	2	0.807275406977887	5		431	732	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275762	38275762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	136	557	0	ENST00000425967.3:c.1507G>A	p.Glu503Lys	p.E503K	ENST00000425967	NM_001174067.1	503	Gag/Aag	11/19	0.227051898042773	2	FACETS	0.616	0.563	0.671	0.308	0.281	0.336	INDETERMINATE	1	TRUE	0	0.807275406977887	2		557	547	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376015	8376015	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764257459	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	160	435	0	ENST00000356435.5:c.4582C>T	p.Pro1528Ser	p.P1528S	ENST00000356435		1528	Cct/Tct	28/35	0.254518486947959	1	FACETS	0.558	0.517	0.599	0.558	0.517	0.599	INDETERMINATE	1	TRUE	0	0.807275406977887	1		435	424	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197528	27197528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	185	452	0	ENST00000380036.4:c.1840C>T	p.Arg614Ter	p.R614*	ENST00000380036	NM_000459.3	614	Cga/Tga	12/23	0.254518486947959	1	FACETS	0.546	0.508	0.584	0.546	0.508	0.584	INDETERMINATE	1	TRUE	0	0.807275406977887	1		452	501	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563549	87563549	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	374	424	0	ENST00000277120.3:c.1937G>A	p.Arg646Lys	p.R646K	ENST00000277120		646	aGg/aAg	16/19	0.266676131268351	5	FACETS	1	0.992	1	0.669	0.643	0.695	INDETERMINATE	3	TRUE	0	0.807275406977887	5		424	612	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128322021	128322021	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	154	470	0	ENST00000265960.3:c.739C>T	p.Pro247Ser	p.P247S	ENST00000265960	NM_001006617.1	247	Ccg/Tcg	6/12	0.807275406977887	3	FACETS	0.743	0.681	0.807	0.371	0.34	0.404	SUBCLONAL	1	TRUE	1	0.807275406977887	3		470	721	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401369	139401370	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0065455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	507	501	0	ENST00000277541.6:c.3699_3700delinsTT	p.Arg1234Trp	p.R1234W	ENST00000277541	NM_017617.3	1233	tcCCgg/tcTTgg	23/34	0.807275406977887	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.807275406977887	3		501	824	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0065458-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	162	491	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.308827361303043	1	FACETS	0.87	0.807	0.934	0.87	0.807	0.934	INDETERMINATE	1	TRUE	0	0.610321551676296	1		491	424	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0065458-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	163	322	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	0.610321551676296	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.610321551676296	1		322	358	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0065458-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	278	504	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.510731102958169	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.610321551676296	1		504	595	SUCCESS
APC	324	MSKCC	GRCh37	5	112175524	112175524	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065458-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	513	559	0	ENST00000257430.4:c.4233del	p.Ser1411ArgfsTer4	p.S1411Rfs*4	ENST00000257430	NM_000038.5	1411	agT/ag	16/16	0.372525790904627	3	FACETS	1	0.986	1	0.7	0.673	0.726	CLONAL	2	TRUE	0	0.610321551676296	3		559	1045	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039405	47039405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065458-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	37	339	0	ENST00000377604.3:c.1028G>A	p.Arg343His	p.R343H	ENST00000377604	NM_001204468.1	343	cGc/cAc	10/24	0.390383602864804	2	FACETS	0.236	0.194	0.283			1	SUBCLONAL	1	TRUE	NA	0.610321551676296	2		339	513	SUCCESS
APC	324	MSKCC	GRCh37	5	112175351	112175351	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065458-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	159	489	0	ENST00000257430.4:c.4063del	p.Ser1355LeufsTer60	p.S1355Lfs*60	ENST00000257430	NM_000038.5	1354	Ttt/tt	16/16	0.372525790904627	3	FACETS	0.726	0.665	0.789	0.242	0.221	0.263	SUBCLONAL	1	TRUE	0	0.610321551676296	3		489	937	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477184	67477184	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1320208623	NA	P-0065458-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	424	643	0	ENST00000327367.4:c.991G>T	p.Val331Phe	p.V331F	ENST00000327367	NM_005902.3	331	Gtc/Ttc	7/9	0.547062855796643	2	FACETS	0.929	0.893	0.964	0.929	0.893	0.964	CLONAL	2	TRUE	0	0.610321551676296	2		643	748	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903715	114903724	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCGTATTA	CCCCGTATTA	-	novel	NA	P-0065458-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	175	497	0	ENST00000543371.1:c.722_731del	p.Pro241HisfsTer7	p.P241Hfs*7	ENST00000543371	NM_001198531.1	240	tCCCCGTATTAc/tc	7/14	1	2	FACETS	0.807	0.745	0.87	0.807	0.745	0.87	CLONAL	1	TRUE	1	0.610321551676296	2		497	711	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218033	108218033	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555139547	NA	P-0065458-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	127	399	0	ENST00000278616.4:c.8612G>C	p.Arg2871Thr	p.R2871T	ENST00000278616	NM_000051.3	2871	aGa/aCa	59/63	0.610321551676296	1	FACETS	0.893	0.82	0.966	0.893	0.82	0.966	CLONAL	1	TRUE	0	0.610321551676296	1		399	324	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517929	8517929	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065458-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	35	476	0	ENST00000356435.5:c.1462T>A	p.Tyr488Asn	p.Y488N	ENST00000356435		488	Tat/Aat	10/35	0.237573575372118	1	FACETS	0.121	0.098	0.146	0.121	0.098	0.146	INDETERMINATE	1	TRUE	0	0.610321551676296	1		476	660	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0065461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	56	491	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.93	0.801	1	0.93	0.801	1	CLONAL	1	TRUE	1	0.351951954597731	2		491	342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	G	rs1131691039	NA	P-0065461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	156	485	0	ENST00000269305.4:c.919+1G>C		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.342363749574735	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.351951954597731	1		485	715	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0065462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	129	622	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.285329431904771	2		622	846	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508514	106508514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1406220505	NA	P-0065462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	85	520	0	ENST00000359195.3:c.508G>A	p.Asp170Asn	p.D170N	ENST00000359195	NM_002649.2	170	Gac/Aac	2/11	0.20330847522478	3	FACETS	1	0.926	1	0.531	0.47	0.597	CLONAL	1	TRUE	1	0.285329431904771	3		520	641	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502386	186502386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs953593626	NA	P-0065462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	49	454	0	ENST00000323963.5:c.109G>A	p.Asp37Asn	p.D37N	ENST00000323963		37	Gat/Aat	3/11	0.25617710464755	4	FACETS	0.539	0.455	0.632	0.27	0.227	0.316	SUBCLONAL	1	TRUE	2	0.285329431904771	4		454	819	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409060	4409060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781695497	NA	P-0065462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	67	493	0	ENST00000261254.3:c.755C>T	p.Ala252Val	p.A252V	ENST00000261254	NM_001759.3	252	gCg/gTg	5/5	1	2	FACETS	0.708	0.615	0.809	0.708	0.615	0.809	SUBCLONAL	1	TRUE	1	0.285329431904771	2		493	663	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602422	10602422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373063629	NA	P-0065462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	53	778	0	ENST00000171111.5:c.1156G>A	p.Gly386Ser	p.G386S	ENST00000171111	NM_203500.1	386	Ggc/Agc	3/6	0.172693528874125	2	FACETS	0.509	0.433	0.592	0.254	0.216	0.296	SUBCLONAL	1	TRUE	0	0.285329431904771	2		778	730	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044595	47044595	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	110	444	0	ENST00000377604.3:c.2092G>T	p.Glu698Ter	p.E698*	ENST00000377604	NM_001204468.1	698	Gag/Tag	18/24	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.351222649174409	1		444	367	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115728	8115728	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	113	547	1	ENST00000346208.3:c.1074G>T	p.Lys358Asn	p.K358N	ENST00000346208		358	aaG/aaT	6/6	1	2	FACETS	0.972	0.876	1	0.972	0.876	1	CLONAL	1	TRUE	1	0.351222649174409	2		548	662	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579394	7579394	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	106	828	0	ENST00000269305.4:c.293del	p.Pro98LeufsTer25	p.P98Lfs*25	ENST00000269305	NM_001126112.2	98	cCt/ct	4/11	0.331766363557636	1	FACETS	0.812	0.729	0.899	0.812	0.729	0.899	CLONAL	1	TRUE	0	0.351222649174409	1		828	613	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602289	10602290	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0065463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	97	825	0	ENST00000171111.5:c.1288_1289delinsTT	p.Gly430Phe	p.G430F	ENST00000171111	NM_203500.1	430	GGc/TTc	3/6	0.351222649174409	1	FACETS	0.799	0.714	0.889	0.799	0.714	0.889	SUBCLONAL	1	TRUE	0	0.351222649174409	1		825	570	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251632	212251632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	105	767	0	ENST00000342788.4:c.3427G>A	p.Gly1143Arg	p.G1143R	ENST00000342788	NM_005235.2	1143	Gga/Aga	27/28	0.319978683404294	2	FACETS	0.796	0.713	0.884	0.398	0.356	0.442	SUBCLONAL	1	TRUE	0	0.351222649174409	2		767	751	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868350	45868350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765679315	NA	P-0065463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	90	759	1	ENST00000391945.4:c.427C>T	p.Arg143Trp	p.R143W	ENST00000391945	NM_000400.3	143	Cgg/Tgg	6/23	1	2	FACETS	0.787	0.699	0.881	0.787	0.699	0.881	SUBCLONAL	1	TRUE	1	0.351222649174409	2		760	651	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020560	69020560	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	65	428	0	ENST00000288368.4:c.2932G>T	p.Glu978Ter	p.E978*	ENST00000288368	NM_024870.2	978	Gag/Tag	24/40	1	2	FACETS	0.791	0.687	0.903	0.791	0.687	0.903	CLONAL	1	TRUE	1	0.351222649174409	2		428	468	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119929	70119929	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	97	876	0	ENST00000245479.2:c.931G>T	p.Gly311Cys	p.G311C	ENST00000245479	NM_000346.3	311	Ggc/Tgc	3/3	1	2	FACETS	0.966	0.863	1	0.966	0.863	1	CLONAL	1	TRUE	1	0.351222649174409	2		876	572	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971155	21971155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501260	NA	P-0065463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	48	850	0	ENST00000304494.5:c.203C>T	p.Ala68Val	p.A68V	ENST00000304494	NM_000077.4	68	gCg/gTg	2/3	0.326048969867059	0	FACETS	0.395	0.334	0.462			1	SUBCLONAL	1	TRUE	0	0.351222649174409	0		850	449	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410703	32410703	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	94	613	0	ENST00000332351.3:c.1455del	p.Trp486GlyfsTer14	p.W486Gfs*14	ENST00000332351	NM_024426.4	485	cgG/cg	10/10	0.351222649174409	1	FACETS	0.834	0.744	0.929	0.834	0.744	0.929	CLONAL	1	TRUE	0	0.351222649174409	1		613	529	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858986	57858986	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	109	733	0	ENST00000228682.2:c.482G>T	p.Arg161Leu	p.R161L	ENST00000228682	NM_005269.2	161	cGg/cTg	5/12	1	2	FACETS	0.956	0.86	1	0.956	0.86	1	CLONAL	1	TRUE	1	0.351222649174409	2		733	649	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060859	38060859	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	120	888	0	ENST00000250448.2:c.1130A>T	p.His377Leu	p.H377L	ENST00000250448	NM_004496.3	377	cAc/cTc	2/2	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.351222649174409	2		888	662	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061544	38061544	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	90	741	0	ENST00000250448.2:c.445G>T	p.Gly149Cys	p.G149C	ENST00000250448	NM_004496.3	149	Ggc/Tgc	2/2	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.351222649174409	2		741	461	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554392	63554392	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	117	688	0	ENST00000307078.5:c.347G>T	p.Gly116Val	p.G116V	ENST00000307078	NM_004655.3	116	gGa/gTa	2/11	1	2	FACETS	0.915	0.826	1	0.915	0.826	1	CLONAL	1	TRUE	1	0.351222649174409	2		688	728	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6227107	6227108	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0065463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	98	703	0	ENST00000252674.7:c.426_427delinsTT	p.Met142_Val143delinsIleLeu	p.M142_V143delinsIL	ENST00000252674	NM_005934.3	142	atGGta/atTTta	5/12	0.351222649174409	1	FACETS	0.89	0.797	0.988	0.89	0.797	0.988	CLONAL	1	TRUE	0	0.351222649174409	1		703	517	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096029	11096091	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGCCATGCTGGGATGGGGCCCCCGCCCAGCCCCATGGACCAGCACTCCCAAGGTACAGAACT	GGGCCATGCTGGGATGGGGCCCCCGCCCAGCCCCATGGACCAGCACTCCCAAGGTACAGAACT	-	novel	NA	P-0065463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	101	723	0	ENST00000358026.2:c.304_355+11del		p.X102_splice	ENST00000358026	NM_001128849.1	102		3/36	0.351222649174409	1	FACETS	0.867	0.777	0.961	0.867	0.777	0.961	CLONAL	1	TRUE	0	0.351222649174409	1		723	547	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213294	36213294	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746188688	NA	P-0065463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	89	695	3	ENST00000222270.7:c.2491G>A	p.Gly831Arg	p.G831R	ENST00000222270	NM_014727.1	831	Ggg/Agg	4/37	1	2	FACETS	0.835	0.741	0.935	0.835	0.741	0.935	CLONAL	1	TRUE	1	0.351222649174409	2		698	607	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017177	31017177	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	82	528	0	ENST00000375687.4:c.508C>G	p.Pro170Ala	p.P170A	ENST00000375687	NM_015338.5	170	Cct/Gct	7/13	0.270374835941958	1	FACETS	0.728	0.643	0.818	0.728	0.643	0.818	SUBCLONAL	1	TRUE	0	0.351222649174409	1		528	529	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790059	40790059	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	55	666	0	ENST00000373198.4:c.2672C>A	p.Ala891Asp	p.A891D	ENST00000373198	NM_133170.3	891	gCt/gAt	18/32	0.270374835941958	1	FACETS	0.419	0.358	0.486	0.419	0.358	0.486	SUBCLONAL	1	TRUE	0	0.351222649174409	1		666	616	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037160	71037160	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	106	631	0	ENST00000318789.4:c.1131A>T	p.Lys377Asn	p.K377N	ENST00000318789	NM_032682.5	377	aaA/aaT	14/21	0.351222649174409	1	FACETS	0.824	0.74	0.912	0.824	0.74	0.912	CLONAL	1	TRUE	0	0.351222649174409	1		631	604	SUCCESS
ATR	545	MSKCC	GRCh37	3	142257459	142257459	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	91	390	0	ENST00000350721.4:c.3590A>T	p.Asp1197Val	p.D1197V	ENST00000350721	NM_001184.3	1197	gAc/gTc	19/47	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.351222649174409	2		390	509	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584523	189584524	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0065463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	92	600	0	ENST00000264731.3:c.819_820delinsAA	p.Gln274Lys	p.Q274K	ENST00000264731	NM_003722.4	273	gcCCag/gcAAag	6/14	1	2	FACETS	0.919	0.818	1	0.919	0.818	1	CLONAL	1	TRUE	1	0.351222649174409	2		600	570	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139711	55139711	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	85	553	0	ENST00000257290.5:c.1372A>T	p.Asn458Tyr	p.N458Y	ENST00000257290	NM_006206.4	458	Aat/Tat	10/23	1	2	FACETS	0.945	0.838	1	0.945	0.838	1	CLONAL	1	TRUE	1	0.351222649174409	2		553	512	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948202	55948203	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0065463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	59	324	0	ENST00000263923.4:c.3768_3769delinsAA	p.Asn1256_Gln1257delinsLysLys	p.N1256_Q1257delinsKK	ENST00000263923	NM_002253.2	1256	aaCCag/aaAAag	29/30	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.351222649174409	2		324	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0065464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	135	617	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.249437122450688	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.249437122450688	1		618	896	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770613	40770613	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	90	470	0	ENST00000373198.4:c.2769G>A	p.Trp923Ter	p.W923*	ENST00000373198	NM_133170.3	923	tgG/tgA	19/32	1	2	FACETS	0.883	0.783	0.991	0.883	0.783	0.991	CLONAL	1	TRUE	1	0.249437122450688	2		470	817	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1720491	1720491	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0065464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	106	512	0	ENST00000378609.4:c.916+1G>A		p.X306_splice	ENST00000378609	NM_002074.3	306			1	2	FACETS	0.985	0.882	1	0.985	0.882	1	CLONAL	1	TRUE	1	0.249437122450688	2		512	863	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022477	12022477	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	136	788	0	ENST00000396373.4:c.583G>T	p.Asp195Tyr	p.D195Y	ENST00000396373	NM_001987.4	195	Gac/Tac	5/8	0.249437122450688	1	FACETS	0.877	0.796	0.963	0.877	0.796	0.963	CLONAL	1	TRUE	0	0.249437122450688	1		788	1088	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374354	15374354	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	119	485	0	ENST00000263377.2:c.1218A>C	p.Lys406Asn	p.K406N	ENST00000263377	NM_058243.2	406	aaA/aaC	7/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.249437122450688	2		485	899	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62303943	62303943	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	228	468	0	ENST00000360203.5:c.734C>G	p.Thr245Arg	p.T245R	ENST00000360203	NM_001283009.1	245	aCa/aGa	9/35	0.165983910297259	3	FACETS	1	0.952	1			1	CLONAL	2	TRUE	NA	0.249437122450688	3		468	1002	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572427	41572427	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	147	619	0	ENST00000263253.7:c.4956G>T	p.Met1652Ile	p.M1652I	ENST00000263253	NM_001429.3	1652	atG/atT	30/31	0.16186542790286	4	FACETS	1	0.958	1			1	CLONAL	1	TRUE	NA	0.249437122450688	4		619	1355	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725581	117725581	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	100	399	0	ENST00000368508.3:c.300C>A	p.Asp100Glu	p.D100E	ENST00000368508	NM_002944.2	100	gaC/gaA	5/43	0.198683842712413	4	FACETS	1	0.953	1	0.562	0.501	0.627	CLONAL	1	TRUE	2	0.249437122450688	4		399	891	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065466-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	51	663	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		663	368	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931672	39931672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065466-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	121	511	0	ENST00000378444.4:c.2927G>A	p.Arg976Gln	p.R976Q	ENST00000378444	NM_001123385.1	976	cGa/cAa	4/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		511	632	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690831	89690831	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs786204925	NA	P-0065466-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	48	301	0	ENST00000371953.3:c.238A>T	p.Lys80Ter	p.K80*	ENST00000371953	NM_000314.4	80	Aaa/Taa	4/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		301	189	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578525	7578525	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519976	NA	P-0065467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	159	619	0	ENST00000269305.4:c.405C>G	p.Cys135Trp	p.C135W	ENST00000269305	NM_001126112.2	135	tgC/tgG	5/11	0.24942744419604	2	FACETS	1	0.982	1	0.627	0.575	0.68	CLONAL	1	TRUE	0	0.341963163472893	2		619	742	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42840381	42840381	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs943194436	NA	P-0065467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	163	540	0	ENST00000398585.3:c.1367T>G	p.Leu456Arg	p.L456R	ENST00000398585	NM_001135099.1	456	cTg/cGg	12/14	0.0929976833170532	3	FACETS	1	0.978	1	0.594	0.545	0.646	INDETERMINATE	1	TRUE	1	0.341963163472893	3		540	939	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0065469-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	99	355	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		355	332	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282209	38282209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065469-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	76	545	0	ENST00000425967.3:c.847C>T	p.Pro283Ser	p.P283S	ENST00000425967	NM_001174067.1	283	Cct/Tct	8/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		545	471	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852635	63852635	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065469-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	251	441	0	ENST00000279873.7:c.3413A>T	p.Gln1138Leu	p.Q1138L	ENST00000279873	NM_032199.2	1138	cAg/cTg	10/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		441	736	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10787960	10787960	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065469-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	80	242	0	ENST00000361367.2:c.1609C>G	p.Leu537Val	p.L537V	ENST00000361367	NM_014633.3	537	Cta/Gta	13/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		242	231	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610218	10610219	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0065469-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	222	478	0	ENST00000171111.5:c.491_492del	p.Ile164ArgfsTer9	p.I164Rfs*9	ENST00000171111	NM_203500.1	164	aTC/a	2/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		478	471	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101913	11101913	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065469-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	42	448	0	ENST00000358026.2:c.1333C>T	p.Gln445Ter	p.Q445*	ENST00000358026	NM_001128849.1	445	Cag/Tag	8/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		448	459	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101920	11101921	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0065469-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	41	444	0	ENST00000358026.2:c.1344_1345dup	p.Glu449AlafsTer53	p.E449Afs*53	ENST00000358026	NM_001128849.1	447	ctg/ctGCg	8/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		444	452	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739060	40739060	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065469-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	185	439	0	ENST00000373198.4:c.3224C>A	p.Pro1075His	p.P1075H	ENST00000373198	NM_133170.3	1075	cCc/cAc	24/32	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		439	578	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876307	35876307	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065469-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	169	475	0	ENST00000303115.3:c.1099C>A	p.Leu367Ile	p.L367I	ENST00000303115	NM_002185.3	367	Ctc/Atc	8/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		475	557	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6036966	6036966	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754164213	NA	P-0065469-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	126	318	0	ENST00000265849.7:c.794A>G	p.Asn265Ser	p.N265S	ENST00000265849	NM_000535.5	265	aAt/aGt	7/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		318	422	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124475334	124475334	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065469-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	113	286	0	ENST00000357628.3:c.1504G>A	p.Gly502Arg	p.G502R	ENST00000357628	NM_015450.2	502	Gga/Aga	15/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		286	238	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202983	27202983	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065469-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	203	443	0	ENST00000380036.4:c.2075C>A	p.Ala692Asp	p.A692D	ENST00000380036	NM_000459.3	692	gCc/gAc	13/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		443	532	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123837	46123837	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0065469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	91	500	0	ENST00000334344.6:c.103A>T	p.Lys35Ter	p.K35*	ENST00000334344	NM_152641.2	35	Aaa/Taa	2/21	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.381237299726557	2		500	431	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0065469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	64	434	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	0.744	0.646	0.85	0.744	0.646	0.85	SUBCLONAL	1	TRUE	1	0.381237299726557	2		434	451	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206757	36206757	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	95	517	0	ENST00000300305.3:c.755C>T	p.Ser252Phe	p.S252F	ENST00000300305		252	tCc/tTc	6/8	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.381237299726557	2		517	484	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245234	46245234	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	93	598	0	ENST00000334344.6:c.3328G>T	p.Gly1110Ter	p.G1110*	ENST00000334344	NM_152641.2	1110	Gga/Tga	15/21	1	2	FACETS	0.903	0.806	1	0.903	0.806	1	CLONAL	1	TRUE	1	0.381237299726557	2		598	540	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0065470-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	93	1407	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1407	231	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0065470-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	186	575	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		575	299	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5055687	5055687	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1338813094	NA	P-0065470-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	69	209	0	ENST00000381652.3:c.955G>A	p.Asp319Asn	p.D319N	ENST00000381652	NM_004972.3	319	Gat/Aat	8/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		209	187	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256584	115256584	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065470-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	86	244	0	ENST00000369535.4:c.127del	p.Gln43LysfsTer4	p.Q43Kfs*4	ENST00000369535	NM_002524.4	43	Caa/aa	3/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		244	217	SUCCESS
REL	5966	MSKCC	GRCh37	2	61121638	61121638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	26	432	0	ENST00000295025.8:c.260G>A	p.Gly87Asp	p.G87D	ENST00000295025	NM_002908.2	87	gGc/gAc	3/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		432	103	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30668380	30668380	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	116	504	0	ENST00000376406.3:c.6132G>T	p.Gln2044His	p.Q2044H	ENST00000376406	NM_014641.2	2044	caG/caT	15/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		504	363	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	94	663	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		663	309	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120502	70120502	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774375417	NA	P-0065472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	72	483	0	ENST00000245479.2:c.1504G>A	p.Val502Ile	p.V502I	ENST00000245479	NM_000346.3	502	Gtc/Atc	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		483	503	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629838	187629838	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	164	496	0	ENST00000441802.2:c.1144C>A	p.Pro382Thr	p.P382T	ENST00000441802	NM_005245.3	382	Ccc/Acc	2/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		496	501	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931622	39931622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	151	454	0	ENST00000378444.4:c.2977C>T	p.Arg993Trp	p.R993W	ENST00000378444	NM_001123385.1	993	Cgg/Tgg	4/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		454	455	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020808	26020808	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs377197123	NA	P-0065473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	40	722	0	ENST00000357647.3:c.91C>G	p.Pro31Ala	p.P31A	ENST00000357647	NM_003529.2	31	Ccg/Gcg	1/1	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		722	649	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216590	108216590	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	33	421	0	ENST00000278616.4:c.8539G>C	p.Glu2847Gln	p.E2847Q	ENST00000278616	NM_000051.3	2847	Gag/Cag	58/63	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		421	400	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0065473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	17	325	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		325	271	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120527	70120527	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0065473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	43	539	0	ENST00000245479.2:c.1529G>C	p.Ter510SerextTer49	p.*510Sext*49	ENST00000245479	NM_000346.3	510	tGa/tCa	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		539	458	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0065473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	49	478	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		478	522	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937611	17937611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	35	502	0	ENST00000458235.1:c.3316G>A	p.Glu1106Lys	p.E1106K	ENST00000458235	NM_000215.3	1106	Gag/Aag	24/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		502	469	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641177	117641177	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773843792	NA	P-0065473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	28	617	0	ENST00000368508.3:c.5794G>A	p.Glu1932Lys	p.E1932K	ENST00000368508	NM_002944.2	1932	Gag/Aag	36/43	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		617	487	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063717	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0065473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	38	367	0	ENST00000412916.2:c.165+1G>T		p.X55_splice	ENST00000412916		55			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		367	299	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753795	42753795	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1433054936	NA	P-0065473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	47	601	0	ENST00000222329.4:c.469G>A	p.Glu157Lys	p.E157K	ENST00000222329	NM_006494.2	157	Gag/Aag	4/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		601	585	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196110	108196110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1482691031	NA	P-0065473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	23	424	0	ENST00000278616.4:c.6646G>A	p.Asp2216Asn	p.D2216N	ENST00000278616	NM_000051.3	2216	Gat/Aat	46/63	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		424	348	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846050	68846072	+	frameshift_variant	Frame_Shift_Del	DEL	TATACCCTGGTGGTTCAAGCTGC	TATACCCTGGTGGTTCAAGCTGC	-	novel	NA	P-0065473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	42	505	0	ENST00000261769.5:c.1022_1044del	p.Tyr341Ter	p.Y341*	ENST00000261769	NM_004360.3	341	TATACCCTGGTGGTTCAAGCTGCt/t	8/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		505	390	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231488	5231488	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200172769	NA	P-0065473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	22	472	0	ENST00000357368.4:c.1988C>T	p.Ser663Leu	p.S663L	ENST00000357368	NM_002850.3	663	tCa/tTa	14/38	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		472	384	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976582	55976582	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	34	409	0	ENST00000263923.4:c.1243C>G	p.Leu415Val	p.L415V	ENST00000263923	NM_002253.2	415	Ctg/Gtg	9/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		409	399	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0065479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	35	491	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		491	429	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0065479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	63	602	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		602	612	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0065479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	48	443	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		443	559	SUCCESS
REL	5966	MSKCC	GRCh37	2	61121638	61121638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	27	432	0	ENST00000295025.8:c.260G>A	p.Gly87Asp	p.G87D	ENST00000295025	NM_002908.2	87	gGc/gAc	3/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		432	534	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692849	89692849	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554898097	NA	P-0065479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	8	126	0	ENST00000371953.3:c.333G>A	p.Trp111Ter	p.W111*	ENST00000371953	NM_000314.4	111	tgG/tgA	5/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		126	157	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466019	69466019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	49	562	0	ENST00000227507.2:c.857C>T	p.Thr286Ile	p.T286I	ENST00000227507	NM_053056.2	286	aCa/aTa	5/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		562	567	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661897	227661897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs544750977	NA	P-0065479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	29	599	0	ENST00000305123.5:c.1558C>T	p.Arg520Trp	p.R520W	ENST00000305123	NM_005544.2	520	Cgg/Tgg	1/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		599	570	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521525	46521525	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	35	415	2	ENST00000262741.5:c.883del	p.Met295Ter	p.M295*	ENST00000262741	NM_003629.3	295	Atg/tg	7/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		417	646	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061154	38061154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	31	532	0	ENST00000250448.2:c.835G>A	p.Gly279Arg	p.G279R	ENST00000250448	NM_004496.3	279	Ggg/Agg	2/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		532	531	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828912	72828913	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0065479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	84	558	0	ENST00000268489.5:c.7668_7669del	p.Gln2557GlufsTer21	p.Q2557Efs*21	ENST00000268489	NM_006885.3	2556	gcGCag/gcag	9/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		558	786	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508267	38508267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754292583	NA	P-0065479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	28	478	0	ENST00000254066.5:c.575G>A	p.Arg192His	p.R192H	ENST00000254066	NM_000964.3	192	cGc/cAc	5/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		478	537	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058013	27058013	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	79	562	0	ENST00000324856.7:c.1723del	p.Gln575SerfsTer44	p.Q575Sfs*44	ENST00000324856	NM_006015.4	574	tCc/tc	3/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		562	724	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723363	49723363	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs894395300	NA	P-0065479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	22	328	0	ENST00000449682.2:c.1180G>A	p.Gly394Ser	p.G394S	ENST00000449682	NM_020998.3	394	Ggc/Agc	10/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		328	357	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0065480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	40	463	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		463	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0065480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	190	490	0	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		490	605	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059194	27059194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	82	288	0	ENST00000324856.7:c.1831C>T	p.Gln611Ter	p.Q611*	ENST00000324856	NM_006015.4	611	Cag/Tag	4/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		288	491	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741919	17741919	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	30	322	0	ENST00000250003.3:c.590C>G	p.Ser197Cys	p.S197C	ENST00000250003	NM_002478.4	197	tCc/tGc	1/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		322	288	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111855996	111855996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779622961	NA	P-0065480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	52	395	0	ENST00000341259.2:c.47C>T	p.Ser16Leu	p.S16L	ENST00000341259	NM_005475.2	16	tCa/tTa	2/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		395	399	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982143	201982143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	111	453	1	ENST00000359651.3:c.667G>A	p.Asp223Asn	p.D223N	ENST00000359651		223	Gat/Aat	5/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		454	585	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772254	68772254	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	48	346	0	ENST00000261769.5:c.103G>T	p.Glu35Ter	p.E35*	ENST00000261769	NM_004360.3	35	Gag/Tag	2/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		346	410	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5286082	5286082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200430287	NA	P-0065480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	53	411	0	ENST00000357368.4:c.70G>A	p.Val24Ile	p.V24I	ENST00000357368	NM_002850.3	24	Gtt/Att	2/38	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		411	536	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56873485	56873485	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	38	355	0	ENST00000308159.5:c.2189G>A	p.Arg730Lys	p.R730K	ENST00000308159	NM_014669.4	730	aGa/aAa	20/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		355	484	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733240	74733240	+	start_lost	Translation_Start_Site	SNP	C	C	G	novel	NA	P-0065480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	36	367	0	ENST00000359995.5:c.3G>C	p.Met1?	p.M1?	ENST00000359995	NM_001195427.1	1	atG/atC	1/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		367	473	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1253881	1253881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	106	402	0	ENST00000310581.5:c.3361C>T	p.Pro1121Ser	p.P1121S	ENST00000310581	NM_198253.2	1121	Ccg/Tcg	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		402	709	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096580	178096580	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	35	462	0	ENST00000397062.3:c.751G>C	p.Glu251Gln	p.E251Q	ENST00000397062	NM_006164.4	251	Gag/Cag	5/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		462	594	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914653	32914653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	37	432	0	ENST00000380152.3:c.6161C>T	p.Ala2054Val	p.A2054V	ENST00000380152		2054	gCt/gTt	11/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		432	437	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115693	108115693	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	69	327	0	ENST00000278616.4:c.841G>C	p.Glu281Gln	p.E281Q	ENST00000278616	NM_000051.3	281	Gaa/Caa	7/63	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		327	433	SUCCESS
SCG5	6447	MSKCC	GRCh37	15	32976847	32976847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	47	343	0	ENST00000300175.4:c.466G>A	p.Asp156Asn	p.D156N	ENST00000300175	NM_001144757.1	156	Gac/Aac	4/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		343	474	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054425	42054425	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	106	357	0	ENST00000219905.7:c.7609G>C	p.Glu2537Gln	p.E2537Q	ENST00000219905	NM_001164273.1	2537	Gag/Cag	22/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		357	497	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245819	41245819	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs397508903	NA	P-0065480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	185	345	0	ENST00000357654.3:c.1729G>C	p.Glu577Gln	p.E577Q	ENST00000357654	NM_007294.3	577	Gaa/Caa	10/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		345	531	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62297368	62297368	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	50	313	0	ENST00000360203.5:c.550G>C	p.Glu184Gln	p.E184Q	ENST00000360203	NM_001283009.1	184	Gag/Cag	7/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		313	498	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598088	52598088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	50	355	0	ENST00000394830.3:c.3778G>A	p.Asp1260Asn	p.D1260N	ENST00000394830	NM_018313.4	1260	Gat/Aat	24/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		355	611	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242942	142242942	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	51	376	0	ENST00000350721.4:c.4045C>G	p.Gln1349Glu	p.Q1349E	ENST00000350721	NM_001184.3	1349	Caa/Gaa	22/47	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		376	718	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435856	149435856	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	38	386	0	ENST00000286301.3:c.2368C>G	p.His790Asp	p.H790D	ENST00000286301	NM_005211.3	790	Cat/Gat	18/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		386	411	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109321771	109321771	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs749261620	NA	P-0065480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	29	357	0	ENST00000436639.2:c.652C>G	p.Gln218Glu	p.Q218E	ENST00000436639	NM_014454.2	218	Caa/Gaa	4/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		357	533	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0065481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	144	602	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		602	695	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771344	68771372	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGGCGCTGCTGCTGCTGCTGCAGGTACCC	CGGCGCTGCTGCTGCTGCTGCAGGTACCC	-	novel	NA	P-0065481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	65	279	0	ENST00000261769.5:c.29_48+9del		p.X10_splice	ENST00000261769	NM_004360.3	10		1/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		279	298	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119634961	119634961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	136	453	0	ENST00000316626.5:c.538C>T	p.Arg180Trp	p.R180W	ENST00000316626		180	Cgg/Tgg	5/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		453	691	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	35	477	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		477	688	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	106	486	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		486	712	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0065482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	223	384	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		384	472	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0065482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	66	358	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		358	398	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0065482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	17	455	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		455	410	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0065482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	159	528	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		528	672	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857307	68857307	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs971882211	NA	P-0065482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	31	402	0	ENST00000261769.5:c.1942G>T	p.Glu648Ter	p.E648*	ENST00000261769	NM_004360.3	648	Gaa/Taa	13/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		402	522	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347143	347143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367788267	NA	P-0065482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	31	457	0	ENST00000262320.3:c.1868C>T	p.Ser623Leu	p.S623L	ENST00000262320	NM_003502.3	623	tCg/tTg	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		457	541	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21347167	21347167	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747430075	NA	P-0065482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	109	615	0	ENST00000215739.8:c.1234C>T	p.Arg412Cys	p.R412C	ENST00000215739	NM_006767.3	412	Cgc/Tgc	11/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		615	624	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654694	67654694	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	114	493	0	ENST00000264010.4:c.1181T>C	p.Leu394Pro	p.L394P	ENST00000264010	NM_006565.3	394	cTg/cCg	6/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		493	614	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0065483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	138	532	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		532	553	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	83	663	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		663	280	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0065484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	270	371	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		371	420	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100375	27100375	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	192	477	0	ENST00000324856.7:c.4087C>T	p.Gln1363Ter	p.Q1363*	ENST00000324856	NM_006015.4	1363	Caa/Taa	17/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		477	519	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699350	18699350	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	129	371	0	ENST00000266497.5:c.3451A>G	p.Thr1151Ala	p.T1151A	ENST00000266497		1151	Aca/Gca	24/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		371	423	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873409	136873409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs923351521	NA	P-0065484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	53	415	0	ENST00000241393.3:c.89G>A	p.Arg30His	p.R30H	ENST00000241393	NM_003467.2	30	cGt/cAt	2/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		415	482	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651983	36651984	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0065484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	458	460	0	ENST00000244741.5:c.106dup	p.Ala36GlyfsTer12	p.A36Gfs*12	ENST00000244741	NM_000389.4	35	-/G	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		460	658	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054635	13054635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	205	472	0	ENST00000316448.5:c.1162G>A	p.Asp388Asn	p.D388N	ENST00000316448	NM_004343.3	388	Gat/Aat	9/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		472	646	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349290	89349290	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	366	500	0	ENST00000301030.4:c.3660G>T	p.Arg1220Ser	p.R1220S	ENST00000301030	NM_001256183.1	1220	agG/agT	9/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		500	815	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243563	41243563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876659467	NA	P-0065484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	200	495	0	ENST00000357654.3:c.3985G>A	p.Glu1329Lys	p.E1329K	ENST00000357654	NM_007294.3	1329	Gaa/Aaa	10/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		495	612	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39567840	39567840	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	81	282	0	ENST00000262039.4:c.596G>C	p.Arg199Thr	p.R199T	ENST00000262039	NM_002647.2	199	aGa/aCa	5/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		282	304	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982575	10982575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764822141	NA	P-0065484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	147	430	0	ENST00000327064.4:c.197C>T	p.Ser66Leu	p.S66L	ENST00000327064	NM_199141.1	66	tCg/tTg	1/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		430	436	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0065485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	9	285	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		285	433	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803669	1803669	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769692611	NA	P-0065485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	44	449	0	ENST00000260795.2:c.847C>A	p.Pro283Thr	p.P283T	ENST00000260795		283	Ccc/Acc	6/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		449	552	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593609	55593611	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	rs121913685	NA	P-0065486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	246	323	0	ENST00000288135.5:c.1679_1681del	p.Val560del	p.V560del	ENST00000288135	NM_000222.2	559	GTT/-	11/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		323	587	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456284	32456284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	58	359	0	ENST00000332351.3:c.608C>T	p.Pro203Leu	p.P203L	ENST00000332351	NM_024426.4	203	cCc/cTc	1/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		359	438	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860152	151860152	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	88	492	0	ENST00000262189.6:c.10510A>T	p.Thr3504Ser	p.T3504S	ENST00000262189	NM_170606.2	3504	Act/Tct	43/59	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		492	696	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs530941076	NA	P-0065494-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	110	622	0	ENST00000269305.4:c.658T>C	p.Tyr220His	p.Y220H	ENST00000269305	NM_001126112.2	220	Tat/Cat	6/11	0.52460198812826	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.52460198812826	1		622	224	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871287	35871287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149161098	NA	P-0065494-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	105	434	0	ENST00000303115.3:c.509G>A	p.Arg170His	p.R170H	ENST00000303115	NM_002185.3	170	cGc/cAc	4/8	0.303837735287461	4	FACETS	0.911	0.825	1	0.911	0.825	1	INDETERMINATE	2	TRUE	2	0.52460198812826	4		434	335	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695863	117695863	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065494-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	98	512	0	ENST00000369458.3:c.574T>C	p.Ser192Pro	p.S192P	ENST00000369458	NM_024626.3	192	Tcg/Ccg	4/6	0.16808972632148	5	FACETS	1	0.957	1	0.739	0.668	0.813	INDETERMINATE	2	TRUE	2	0.52460198812826	5		512	301	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750519	41750519	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065494-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	69	528	0	ENST00000226382.2:c.109A>G	p.Ser37Gly	p.S37G	ENST00000226382	NM_003924.3	37	Agc/Ggc	1/3	0.412004750584097	3	FACETS	0.794	0.704	0.889	0.794	0.704	0.889	SUBCLONAL	2	TRUE	1	0.52460198812826	3		528	209	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573102	41573102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065494-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	41	709	0	ENST00000263253.7:c.5387G>A	p.Cys1796Tyr	p.C1796Y	ENST00000263253	NM_001429.3	1796	tGc/tAc	31/31	1	2	FACETS	0.704	0.592	0.826	0.704	0.592	0.826	SUBCLONAL	1	TRUE	1	0.52460198812826	2		709	222	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038527	47038527	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065494-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	133	533	0	ENST00000377604.3:c.689G>T	p.Arg230Leu	p.R230L	ENST00000377604	NM_001204468.1	230	cGa/cTa	8/24	0.520304171326311	4	FACETS	0.842	0.777	0.908	0.842	0.777	0.908	CLONAL	3	TRUE	1	0.52460198812826	4		533	306	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123700	46123700	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065494-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	31	587	0	ENST00000334344.6:c.81C>G	p.His27Gln	p.H27Q	ENST00000334344	NM_152641.2	27	caC/caG	1/21	0.489549492909928	2	FACETS	0.542	0.441	0.654	0.271	0.22	0.327	SUBCLONAL	1	TRUE	0	0.52460198812826	2		587	218	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0065525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	113	491	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.25138216487025	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.19	3		491	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882025	NA	P-0065525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	131	616	0	ENST00000269305.4:c.646G>C	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ctg	6/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.19	2		616	1078	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884908	134884908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202034365	NA	P-0065525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	34	483	0	ENST00000398015.3:c.1684G>A	p.Val562Ile	p.V562I	ENST00000398015	NM_004441.4	562	Gtc/Atc	8/16	0.197988174650262	1	FACETS	0.5	0.407	0.605	0.5	0.407	0.605	SUBCLONAL	1	TRUE	0	0.19	1		483	648	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366135	15366137	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0065525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	53	443	0	ENST00000263377.2:c.2018_2020del	p.Ser673del	p.S673del	ENST00000263377	NM_058243.2	673	tCCTgt/tgt	10/20	1	2	FACETS	0.723	0.615	0.841	0.723	0.615	0.841	SUBCLONAL	1	TRUE	1	0.19	2		443	772	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940889	49940889	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	84	728	0	ENST00000296474.3:c.154G>C	p.Gly52Arg	p.G52R	ENST00000296474	NM_002447.2	52	Gga/Cga	1/20	1	2	FACETS	0.722	0.635	0.815	0.722	0.635	0.815	SUBCLONAL	1	TRUE	1	0.19	2		728	1225	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0065526-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	553	636	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.591538528453197	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.591538528453197	2		636	893	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103525620	103525620	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149859074	NA	P-0065526-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	129	322	0	ENST00000355739.4:c.2891G>A	p.Arg964Gln	p.R964Q	ENST00000355739	NM_000123.3	964	cGg/cAg	14/15	0.591538528453197	3	FACETS	0.83	0.754	0.91	0.415	0.377	0.455	CLONAL	1	TRUE	1	0.591538528453197	3		322	681	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33680364	33680364	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065526-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	29	64	0	ENST00000308377.4:c.1913A>C	p.Asn638Thr	p.N638T	ENST00000308377	NM_152270.3	638	aAc/aCc	4/5	0.344631491735127	2	FACETS	1	0.923	1	0.613	0.508	0.723	INDETERMINATE	1	TRUE	0	0.591538528453197	2		64	80	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435736	56435949	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGGAGTCACTGGCTGGCCCATCTGCCAGGTACCCACTGCGTTCTGTGCAATAGCTTTCTCCAGATCCACTGCTGTCAGGGGGCCTGGCCCGGCGTAGGGGCACTGGGCAAGCAGCAGGGTGCTGTGAGGTGGATTGGAGGTGGCTCAGTCCCCAGCCTTGTGCATAGGGGTGCTGGGCTCCTGCCAGGCGCTGCTGCTCTCCTGGAGCCCGG	GCTGGAGTCACTGGCTGGCCCATCTGCCAGGTACCCACTGCGTTCTGTGCAATAGCTTTCTCCAGATCCACTGCTGTCAGGGGGCCTGGCCCGGCGTAGGGGCACTGGGCAAGCAGCAGGGTGCTGTGAGGTGGATTGGAGGTGGCTCAGTCCCCAGCCTTGTGCATAGGGGTGCTGGGCTCCTGCCAGGCGCTGCTGCTCTCCTGGAGCCCGG	-	novel	NA	P-0065526-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	256	471	0	ENST00000407977.2:c.1188_1401del	p.Arg397GlnfsTer34	p.R397Qfs*34	ENST00000407977		396	ccCCGGGCTCCAGGAGAGCAGCAGCGCCTGGCAGGAGCCCAGCACCCCTATGCACAAGGCTGGGGACTGAGCCACCTCCAATCCACCTCACAGCACCCTGCTGCTTGCCCAGTGCCCCTACGCCGGGCCAGGCCCCCTGACAGCAGTGGATCTGGAGAAAGCTATTGCACAGAACGCAGTGGGTACCTGGCAGATGGGCCAGCCAGTGACTCCAGC/cc	9/10	0.591538528453197	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.591538528453197	1		471	586	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31401666	31401666	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065526-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	100	249	0	ENST00000344624.3:c.3998A>T	p.Asn1333Ile	p.N1333I	ENST00000344624		1333	aAt/aTt	33/33	0.50232786894736	4	FACETS	0.903	0.808	1	0.451	0.404	0.502	CLONAL	1	TRUE	2	0.591538528453197	4		249	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0065527-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	490	597	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.664266493990503	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.661983538241183	2		597	672	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0065527-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	604	410	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.572868535268033	6	FACETS	0.992	0.96	1	0.992	0.96	1	CLONAL	4	TRUE	2	0.661983538241183	6		410	1069	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231345	5231345	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765642813	NA	P-0065527-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	235	614	2	ENST00000357368.4:c.2131G>A	p.Val711Met	p.V711M	ENST00000357368	NM_002850.3	711	Gtg/Atg	14/38	0.664266493990503	3	FACETS	1	0.976	1	0.363	0.339	0.388	CLONAL	1	TRUE	0	0.661983538241183	3		616	868	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56401599	56401600	+	missense_variant	Missense_Mutation	DNP	GT	GT	TG	novel	NA	P-0065527-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	170	430	0	ENST00000348428.3:c.1461_1462delinsTG	p.Phe488Val	p.F488V	ENST00000348428	NM_006785.3	487	gtGTtt/gtTGtt	12/17	0.664266493990503	2	FACETS	1	0.942	1	0.51	0.472	0.548	CLONAL	1	TRUE	0	0.661983538241183	2		430	504	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719571	61719571	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065527-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	159	304	0	ENST00000401558.2:c.1612G>C	p.Ala538Pro	p.A538P	ENST00000401558	NM_003400.3	538	Gct/Cct	15/25	0.664266493990503	4	FACETS	1	0.957	1			1	CLONAL	1	TRUE	NA	0.661983538241183	4		304	750	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31493367	31493367	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065527-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	176	391	0	ENST00000344624.3:c.1789C>A	p.His597Asn	p.H597N	ENST00000344624		597	Cac/Aac	10/33	0.664266493990503	3	FACETS	1	0.944	1	0.342	0.316	0.369	CLONAL	1	TRUE	0	0.661983538241183	3		391	690	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0065528-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	22	1407	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.791	1	1	0.791	1	CLONAL	1	TRUE	1	0.18	2		1407	240	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374244	138374244	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065528-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	10	419	0	ENST00000289153.2:c.3200A>T	p.Asp1067Val	p.D1067V	ENST00000289153	NM_006219.2	1067	gAc/gTc	22/22	1	2	FACETS	0.222	0.149	0.315	0.222	0.149	0.315	SUBCLONAL	1	TRUE	1	0.18	2		419	500	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0065529-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	74	441	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.23	2		441	625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0065529-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	121	414	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.3	3	FACETS	0.856	0.775	0.942	0.856	0.775	0.942	CLONAL	2	TRUE	1	0.23	3		414	685	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21336680	21336681	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs587777613	NA	P-0065529-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	99	552	1	ENST00000215739.8:c.27dup	p.Gln10AlafsTer24	p.Q10Afs*24	ENST00000215739	NM_006767.3	7	acg/acGg	1/21	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.23	2		553	789	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267194	41267194	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065529-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	80	515	0	ENST00000349496.5:c.778C>T	p.His260Tyr	p.H260Y	ENST00000349496	NM_001904.3	260	Cac/Tac	6/15	1	2	FACETS	0.98	0.862	1	0.98	0.862	1	CLONAL	1	TRUE	1	0.23	2		515	710	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117861249	117861249	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065529-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	38	351	0	ENST00000297338.2:c.1640del	p.Gly547AlafsTer65	p.G547Afs*65	ENST00000297338	NM_006265.2	547	gGc/gc	13/14	1	2	FACETS	0.52	0.429	0.623	0.52	0.429	0.623	SUBCLONAL	1	TRUE	1	0.23	2		351	635	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	103	663	0				ENST00000310581	NM_198253.2	-/1132			0.150916042685269	0	FACETS	0.921	0.83	1			1	INDETERMINATE	1	TRUE	0	0.343740508471315	0		663	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	23	543	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	1	2	FACETS	0.161	0.125	0.204	0.161	0.125	0.204	SUBCLONAL	1	TRUE	1	0.343740508471315	2		543	829	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671462	30671462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	256	608	0	ENST00000376406.3:c.5498C>T	p.Ser1833Phe	p.S1833F	ENST00000376406	NM_014641.2	1833	tCc/tTc	10/15	0.27003669738222	4	FACETS	0.917	0.859	0.978	0.612	0.572	0.652	CLONAL	2	TRUE	1	0.343740508471315	4		608	1091	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525065	9525065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1225133285	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	136	531	0	ENST00000353224.5:c.1820C>T	p.Pro607Leu	p.P607L	ENST00000353224	NM_177990.2	607	cCc/cTc	8/10	1	2	FACETS	0.774	0.708	0.843	1	0.988	1	SUBCLONAL	2	TRUE	1	0.343740508471315	2		531	511	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239868	41239868	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	151	380	1	ENST00000379561.5:c.482G>A	p.Gly161Asp	p.G161D	ENST00000379561	NM_002015.3	161	gGc/gAc	1/3	1	2	FACETS	0.755	0.693	0.819	1	0.988	1	SUBCLONAL	2	TRUE	1	0.343740508471315	2		381	582	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380017	116380017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752842662	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	173	392	0	ENST00000397752.3:c.1406G>A	p.Arg469Gln	p.R469Q	ENST00000397752	NM_000245.2	469	cGa/cAa	4/21	1	2	FACETS	0.862	0.798	0.928	1	0.992	1	CLONAL	2	TRUE	1	0.343740508471315	2		392	584	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007741	45007742	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	267	463	0	ENST00000558401.1:c.194_195del	p.Arg65AsnfsTer2	p.R65Nfs*2	ENST00000558401	NM_004048.2	63	gGA/g	2/4	1	2	FACETS	0.964	0.907	1	1	0.995	1	CLONAL	2	TRUE	1	0.343740508471315	2		463	806	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307276	65307277	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	85	424	0	ENST00000342505.4:c.2411_2412del	p.Arg804IlefsTer3	p.R804Ifs*3	ENST00000342505	NM_002227.2	804	aGA/a	18/25	1	2	FACETS	0.79	0.699	0.887	0.79	0.699	0.887	SUBCLONAL	1	TRUE	1	0.343740508471315	2		424	626	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185619	27185619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217204389	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	160	437	0	ENST00000380036.4:c.1319C>T	p.Ser440Phe	p.S440F	ENST00000380036	NM_000459.3	440	tCt/tTt	9/23	1	2	FACETS	0.801	0.738	0.866	1	0.99	1	CLONAL	2	TRUE	1	0.343740508471315	2		437	581	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748129	41748129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776131193	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	27	363	0	ENST00000226382.2:c.640G>A	p.Gly214Ser	p.G214S	ENST00000226382	NM_003924.3	214	Ggc/Agc	3/3	1	2	FACETS	0.317	0.252	0.393	0.317	0.252	0.393	SUBCLONAL	1	TRUE	1	0.343740508471315	2		363	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577544	7577544	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587780074	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	52	387	0	ENST00000269305.4:c.737T>G	p.Met246Arg	p.M246R	ENST00000269305	NM_001126112.2	246	aTg/aGg	7/11	1	2	FACETS	0.421	0.358	0.491	0.421	0.358	0.491	SUBCLONAL	1	TRUE	1	0.343740508471315	2		387	718	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827616	72827617	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	116	414	0	ENST00000268489.5:c.8964_8965del	p.Arg2988SerfsTer32	p.R2988Sfs*32	ENST00000268489	NM_006885.3	2988	agAGtc/agtc	9/10	1	2	FACETS	0.935	0.843	1	0.935	0.843	1	CLONAL	1	TRUE	1	0.343740508471315	2		414	722	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758775	41758775	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374737642	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	175	515	0	ENST00000301178.4:c.1829G>A	p.Arg610Gln	p.R610Q	ENST00000301178	NM_021913.4	610	cGa/cAa	16/20	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.343740508471315	2		515	686	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561532	9561532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755247878	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	111	424	0	ENST00000353224.5:c.250G>A	p.Gly84Ser	p.G84S	ENST00000353224	NM_177990.2	84	Ggc/Agc	4/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.343740508471315	2		424	531	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198260870	198260870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	55	397	0	ENST00000335508.6:c.3449C>T	p.Ser1150Leu	p.S1150L	ENST00000335508	NM_012433.2	1150	tCg/tTg	23/25	0.343740508471315	2	FACETS	0.608	0.521	0.704	0.304	0.26	0.352	SUBCLONAL	1	TRUE	0	0.343740508471315	2		397	526	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346113	89346114	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs1555525296	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	115	347	0	ENST00000301030.4:c.6836_6837del	p.Val2279GlyfsTer16	p.V2279Gfs*16	ENST00000301030	NM_001256183.1	2279	gTG/g	9/13	1	2	FACETS	0.822	0.747	0.9	1	0.987	1	CLONAL	2	TRUE	1	0.343740508471315	2		347	407	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209285	133209285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500834	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	203	548	0	ENST00000320574.5:c.6101C>T	p.Ser2034Phe	p.S2034F	ENST00000320574	NM_006231.2	2034	tCc/tTc	44/49	1	2	FACETS	0.85	0.791	0.91	1	0.993	1	CLONAL	2	TRUE	1	0.343740508471315	2		548	695	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042025	42042025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199971244	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	175	482	0	ENST00000219905.7:c.6220C>T	p.Arg2074Cys	p.R2074C	ENST00000219905	NM_001164273.1	2074	Cgt/Tgt	17/24	1	2	FACETS	0.803	0.743	0.865	1	0.991	1	CLONAL	2	TRUE	1	0.343740508471315	2		482	634	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155902	106155902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	181	491	0	ENST00000380013.4:c.803C>T	p.Ser268Leu	p.S268L	ENST00000380013	NM_001127208.2	268	tCg/tTg	3/11	1	2	FACETS	0.76	0.703	0.818	1	0.99	1	SUBCLONAL	2	TRUE	1	0.343740508471315	2		491	693	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057017	180057017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	191	552	0	ENST00000261937.6:c.602C>T	p.Ala201Val	p.A201V	ENST00000261937	NM_182925.4	201	gCc/gTc	5/30	0.150916042685269	0	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	0	0.343740508471315	0		552	684	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546050	29546050	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	196	453	0	ENST00000356175.3:c.1555C>T	p.Gln519Ter	p.Q519*	ENST00000356175	NM_000267.3	519	Caa/Taa	14/57	1	2	FACETS	0.823	0.765	0.883	1	0.992	1	CLONAL	2	TRUE	1	0.343740508471315	2		453	693	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101487	27101487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	171	522	0	ENST00000324856.7:c.4769C>T	p.Pro1590Leu	p.P1590L	ENST00000324856	NM_006015.4	1590	cCc/cTc	18/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.343740508471315	2		522	736	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653222	206653222	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	131	554	0	ENST00000367120.3:c.1193A>G	p.Asp398Gly	p.D398G	ENST00000367120	NM_014002.3	398	gAc/gGc	11/22	0.264284827369405	4	FACETS	1	0.91	1	0.335	0.303	0.368	CLONAL	1	TRUE	1	0.343740508471315	4		554	1020	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230561466	230561466	+	5_prime_UTR_variant	5'UTR	SNP	G	G	A	novel	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	184	590	0	ENST00000391860.1:c.-137C>T		p.*46*	ENST00000391860	NM_001258311.1	-/409		1/7	0.264284827369405	4	FACETS	0.841	0.777	0.908	0.561	0.518	0.605	CLONAL	2	TRUE	1	0.343740508471315	4		590	855	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63662009	63662009	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	207	463	0	ENST00000279873.7:c.113T>A	p.Leu38His	p.L38H	ENST00000279873	NM_032199.2	38	cTt/cAt	2/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.343740508471315	2		463	886	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719920	18719920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	74	304	0	ENST00000266497.5:c.3817G>A	p.Asp1273Asn	p.D1273N	ENST00000266497		1273	Gat/Aat	27/31	0.343740508471315	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.343740508471315	1		304	286	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515360	103515360	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	41	474	0	ENST00000355739.4:c.1861C>T	p.Gln621Ter	p.Q621*	ENST00000355739	NM_000123.3	621	Cag/Tag	8/15	1	2	FACETS	0.355	0.295	0.422	0.355	0.295	0.422	SUBCLONAL	1	TRUE	1	0.343740508471315	2		474	672	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95599740	95599740	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778227	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	181	421	0	ENST00000393063.1:c.56C>T	p.Pro19Leu	p.P19L	ENST00000393063	NM_030621.3	19	cCt/cTt	3/28	1	2	FACETS	0.758	0.701	0.816	1	0.99	1	SUBCLONAL	2	TRUE	1	0.343740508471315	2		421	695	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354486	91354486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	197	524	0	ENST00000355112.3:c.3926G>A	p.Arg1309Lys	p.R1309K	ENST00000355112	NM_000057.2	1309	aGa/aAa	21/22	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.343740508471315	2		524	781	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858439	9858439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	143	434	0	ENST00000330684.3:c.2962C>T	p.Leu988Phe	p.L988F	ENST00000330684	NM_001134407.1	988	Ctc/Ttc	13/13	0.343740508471315	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.343740508471315	1		434	563	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352054	89352055	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	196	477	0	ENST00000301030.4:c.895_896del	p.Ser299LeufsTer49	p.S299Lfs*49	ENST00000301030	NM_001256183.1	299	AGc/c	9/13	1	2	FACETS	0.83	0.771	0.89	1	0.992	1	CLONAL	2	TRUE	1	0.343740508471315	2		477	687	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59793372	59793374	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	109	318	0	ENST00000259008.2:c.2430_2432del	p.Leu811del	p.L811del	ENST00000259008	NM_032043.2	810	ctTCTa/cta	17/20	1	2	FACETS	0.919	0.834	1	1	0.988	1	CLONAL	2	TRUE	1	0.343740508471315	2		318	345	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56367694	56367694	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	117	362	0	ENST00000348428.3:c.520G>T	p.Glu174Ter	p.E174*	ENST00000348428	NM_006785.3	174	Gag/Tag	4/17	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.343740508471315	2		362	478	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403536	138403537	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	189	397	0	ENST00000289153.2:c.2245_2246del	p.Ser749CysfsTer8	p.S749Cfs*8	ENST00000289153	NM_006219.2	749	AGt/t	15/22	1	2	FACETS	0.76	0.705	0.818	1	0.991	1	SUBCLONAL	2	TRUE	1	0.343740508471315	2		397	723	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201741	66201741	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	150	441	0	ENST00000273854.3:c.2761A>T	p.Ser921Cys	p.S921C	ENST00000273854	NM_004439.5	921	Agc/Tgc	16/18	0.150916042685269	0	FACETS	1	0.937	1			1	INDETERMINATE	1	TRUE	0	0.343740508471315	0		441	560	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99806092	99806092	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	57	239	0	ENST00000280892.6:c.580G>C	p.Glu194Gln	p.E194Q	ENST00000280892	NM_001130678.1	194	Gaa/Caa	6/7	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.343740508471315	2		239	278	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915118	131915118	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	115	305	0	ENST00000265335.6:c.475C>T	p.Gln159Ter	p.Q159*	ENST00000265335		159	Caa/Taa	4/25	1	2	FACETS	0.8	0.727	0.877	1	0.986	1	SUBCLONAL	2	TRUE	1	0.343740508471315	2		305	418	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168698	32168698	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	176	532	0	ENST00000375023.3:c.4225C>G	p.Leu1409Val	p.L1409V	ENST00000375023	NM_004557.3	1409	Ctc/Gtc	23/30	0.27003669738222	4	FACETS	0.783	0.721	0.847	0.522	0.481	0.565	SUBCLONAL	2	TRUE	1	0.343740508471315	4		532	879	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372544	55372544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773818791	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	133	425	0	ENST00000297316.4:c.1234C>T	p.Pro412Ser	p.P412S	ENST00000297316	NM_022454.3	412	Cct/Tct	2/2	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.343740508471315	2		425	616	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2029224	2029224	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	157	510	0	ENST00000349721.2:c.202G>A	p.Glu68Lys	p.E68K	ENST00000349721	NM_003070.3	68	Gaa/Aaa	2/34	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.343740508471315	2		510	611	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	286	663	0				ENST00000310581	NM_198253.2	-/1132			0.551984655187532	2	FACETS	0.799	0.768	0.828	0.799	0.768	0.828	SUBCLONAL	2	TRUE	0	0.899661337759773	2		663	398	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0065532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	495	532	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.306138324551912	4	FACETS	0.987	0.958	1	0.74	0.718	0.762	INDETERMINATE	3	TRUE	0	0.899661337759773	4		532	706	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624913	9624913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	512	463	0	ENST00000353224.5:c.64C>T	p.His22Tyr	p.H22Y	ENST00000353224	NM_177990.2	22	Cat/Tat	3/10	0.214979834903235	4	FACETS	0.995	0.957	1	0.995	0.957	1	INDETERMINATE	2	TRUE	2	0.899661337759773	4		463	1086	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483910	212483910	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	286	353	0	ENST00000342788.4:c.2293T>C	p.Phe765Leu	p.F765L	ENST00000342788	NM_005235.2	765	Ttc/Ctc	19/28	0.295053883480443	3	FACETS	0.844	0.803	0.885	0.844	0.803	0.885	INDETERMINATE	2	TRUE	1	0.899661337759773	3		353	546	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876498	59876498	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501758	NA	P-0065532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	326	416	0	ENST00000259008.2:c.1303C>T	p.His435Tyr	p.H435Y	ENST00000259008	NM_032043.2	435	Cat/Tat	9/20	0.295053883480443	3	FACETS	1	0.995	1	0.711	0.676	0.746	INDETERMINATE	1	TRUE	1	0.899661337759773	3		416	739	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969164	93969164	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	384	408	0	ENST00000369303.4:c.1832C>T	p.Pro611Leu	p.P611L	ENST00000369303	NM_004440.3	611	cCt/cTt	10/17	0.195831828297835	3	FACETS	0.801	0.766	0.835	0.801	0.766	0.835	INDETERMINATE	2	TRUE	1	0.899661337759773	3		408	773	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27172614	27172614	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	439	411	0	ENST00000380036.4:c.629G>T	p.Arg210Ile	p.R210I	ENST00000380036	NM_000459.3	210	aGa/aTa	5/23	0.899661337759773	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.899661337759773	1		411	494	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156742	20156742	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0065532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	273	289	0	ENST00000379607.5:c.17-2A>C		p.X6_splice	ENST00000379607	NM_001412.3	6			0.342241816765412	1	FACETS	0.636	0.604	0.668	0.636	0.604	0.668	INDETERMINATE	1	TRUE	0	0.899661337759773	1		289	525	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0065533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	705	575	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.527962060570604	4	FACETS	1	0.996	1	1	0.996	1	CLONAL	4	TRUE	0	0.526487811059286	4		575	933	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730876	40730876	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372862828	NA	P-0065533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	461	527	3	ENST00000373198.4:c.3659G>A	p.Arg1220Gln	p.R1220Q	ENST00000373198	NM_133170.3	1220	cGg/cAg	27/32	0.443192616453816	6	FACETS	0.918	0.881	0.955	0.918	0.881	0.955	CLONAL	4	TRUE	2	0.526487811059286	6		530	979	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10273407	10273407	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	146	400	0	ENST00000340748.4:c.896C>T	p.Pro299Leu	p.P299L	ENST00000340748		299	cCc/cTc	12/40	0.527962060570604	2	FACETS	1	0.976	1	0.581	0.534	0.63	CLONAL	1	TRUE	0	0.526487811059286	2		400	477	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112131	115112131	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772620679	NA	P-0065533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	68	675	2	ENST00000257566.3:c.1609G>A	p.Ala537Thr	p.A537T	ENST00000257566	NM_016569.3	537	Gct/Act	7/8	0.350994382578937	5	FACETS	0.557	0.483	0.637	0.186	0.161	0.213	SUBCLONAL	1	TRUE	2	0.526487811059286	5		677	830	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316080	11316080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	242	498	1	ENST00000361445.4:c.674C>T	p.Pro225Leu	p.P225L	ENST00000361445	NM_004958.3	225	cCg/cTg	5/58	0.386895538654459	3	FACETS	0.974	0.917	1	0.974	0.917	1	CLONAL	2	TRUE	1	0.526487811059286	3		499	596	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77051784	77051784	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	188	482	0	ENST00000356341.3:c.1023G>T	p.Trp341Cys	p.W341C	ENST00000356341	NM_002576.4	341	tgG/tgT	11/15	0.386895538654459	3	FACETS	1	0.99	1	0.714	0.663	0.766	CLONAL	1	TRUE	1	0.526487811059286	3		482	632	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221577	2221577	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	90	503	0	ENST00000326181.6:c.446C>A	p.Thr149Lys	p.T149K	ENST00000326181	NM_032271.2	149	aCg/aAg	7/21	0.527962060570604	2	FACETS	0.688	0.612	0.768	0.344	0.306	0.384	SUBCLONAL	1	TRUE	0	0.526487811059286	2		503	497	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738964	145738975	+	inframe_deletion	In_Frame_Del	DEL	CTGGGACCCAGG	CTGGGACCCAGG	-	novel	NA	P-0065533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	109	717	0	ENST00000428558.2:c.2180_2191del	p.Ala727_Pro730del	p.A727_P730del	ENST00000428558	NM_004260.3	727	gCCTGGGTCCCAGgg/ggg	13/22	0.526487811059286	6	FACETS	0.66	0.591	0.734			1	SUBCLONAL	1	TRUE	NA	0.526487811059286	6		717	1288	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0065534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	124	355	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.939	0.852	1	0.939	0.852	1	CLONAL	1	TRUE	1	0.431002172855769	2		355	613	SUCCESS
APC	324	MSKCC	GRCh37	5	112155042	112155042	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0065534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	138	364	0	ENST00000257430.4:c.1312+1G>T		p.X438_splice	ENST00000257430	NM_000038.5	438			0.431002172855769	1	FACETS	0.917	0.838	0.998	0.917	0.838	0.998	CLONAL	1	TRUE	0	0.431002172855769	1		364	548	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059284	27059284	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0065534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	141	351	0	ENST00000324856.7:c.1920+1G>A		p.X640_splice	ENST00000324856	NM_006015.4	640			1	2	FACETS	0.929	0.848	1	0.929	0.848	1	CLONAL	1	TRUE	1	0.431002172855769	2		351	704	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560491	65560491	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	197	375	0	ENST00000358664.4:c.106A>T	p.Arg36Trp	p.R36W	ENST00000358664	NM_002382.4	36	Agg/Tgg	3/5	0.431002172855769	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.431002172855769	1		375	653	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913119	44913119	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	133	341	0	ENST00000377967.4:c.794A>T	p.Lys265Met	p.K265M	ENST00000377967	NM_021140.2	265	aAg/aTg	10/29	1	2	FACETS	0.948	0.863	1	0.948	0.863	1	CLONAL	1	TRUE	1	0.431002172855769	2		341	651	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604790	48604790	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1568211615	NA	P-0065534-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	78	460	0	ENST00000342988.3:c.1612G>T	p.Glu538Ter	p.E538*	ENST00000342988	NM_005359.5	538	Gaa/Taa	12/12	0.222264838764454	4	FACETS	0.898	0.801	0.998	0.898	0.801	0.998	CLONAL	3	FALSE	1	0.316475040656415	4		460	241	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28929495	NA	P-0065534-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	128	429	0	ENST00000275493.2:c.2155G>T	p.Gly719Cys	p.G719C	ENST00000275493	NM_005228.3	719	Ggc/Tgc	18/28	0.316475040656415	5	FACETS	1	0.958	1	1	0.987	1	CLONAL	4	FALSE	2	0.316475040656415	5		429	282	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0065534-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	178	426	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.316475040656415	5	FACETS	1	0.957	1	1	0.99	1	CLONAL	4	FALSE	2	0.316475040656415	5		426	402	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432033	49432033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065534-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	109	513	0	ENST00000301067.7:c.9106C>T	p.Pro3036Ser	p.P3036S	ENST00000301067	NM_003482.3	3036	Ccc/Tcc	34/54	0.316475040656415	6	FACETS	0.858	0.776	0.944	0.858	0.776	0.944	CLONAL	3	FALSE	3	0.316475040656415	6		513	437	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124469350	124469350	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065534-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	14	262	0	ENST00000357628.3:c.1552C>G	p.Leu518Val	p.L518V	ENST00000357628	NM_015450.2	518	Ctg/Gtg	16/19	0.316475040656415	5	FACETS	1	0.881	1	0.725	0.532	0.951	CLONAL	1	FALSE	3	0.316475040656415	5		262	90	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650539	48650539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065534-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	55	590	0	ENST00000376670.3:c.509G>A	p.Ser170Asn	p.S170N	ENST00000376670	NM_002049.3	170	aGt/aAt	3/6	0.252788828884362	5	FACETS	1	0.966	1	0.488	0.419	0.563	CLONAL	1	FALSE	2	0.316475040656415	5		590	350	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065535-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	41	663	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		663	165	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0065535-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	287	473	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		473	416	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921172	50921172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1445817375	NA	P-0065535-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	131	442	0	ENST00000440232.2:c.3292C>T	p.Arg1098Cys	p.R1098C	ENST00000440232	NM_002691.3	1098	Cgc/Tgc	27/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		442	385	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111502	8111503	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0065536-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	244	442	0	ENST00000346208.3:c.990dup	p.Asn331GlufsTer21	p.N331Efs*21	ENST00000346208		330	agg/aGgg	5/6	0.584704973474976	3	FACETS	0.801	0.753	0.85	0.801	0.753	0.85	CLONAL	2	TRUE	1	0.607022108583549	3		442	654	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681031	37681031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143648695	NA	P-0065536-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	112	413	0	ENST00000447079.4:c.3200G>A	p.Arg1067Gln	p.R1067Q	ENST00000447079	NM_015083.1	1067	cGa/cAa	12/14	0.607022108583549	4	FACETS	1	0.946	1	0.536	0.484	0.591	CLONAL	1	TRUE	2	0.607022108583549	4		413	553	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101257	27101269	+	frameshift_variant	Frame_Shift_Del	DEL	CACGGGCTCTGCC	CACGGGCTCTGCC	-	novel	NA	P-0065536-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	182	480	0	ENST00000324856.7:c.4540_4552del	p.Thr1514ProfsTer9	p.T1514Pfs*9	ENST00000324856	NM_006015.4	1513	agCACGGGCTCTGCC/ag	18/20	0.606850594353772	3	FACETS	0.915	0.855	0.977	0.915	0.855	0.977	CLONAL	2	TRUE	1	0.607022108583549	3		480	427	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172317	7172317	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065536-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	93	381	0	ENST00000302850.5:c.1252G>C	p.Glu418Gln	p.E418Q	ENST00000302850	NM_000208.2	418	Gag/Cag	5/22	0.598291345584565	3	FACETS	1	0.896	1	0.501	0.448	0.556	CLONAL	1	TRUE	1	0.607022108583549	3		381	399	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660649	190660649	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs139414606	NA	P-0065536-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	130	431	0	ENST00000441310.2:c.287C>G	p.Ala96Gly	p.A96G	ENST00000441310	NM_000534.4	96	gCc/gGc	3/13	0.537213660178024	4	FACETS	1	0.969	1	0.381	0.347	0.417	CLONAL	1	TRUE	1	0.607022108583549	4		431	602	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021009	26021009	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065536-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	143	621	0	ENST00000357647.3:c.292G>C	p.Glu98Gln	p.E98Q	ENST00000357647	NM_003529.2	98	Gag/Cag	1/1	0.607022108583549	3	FACETS	1	0.95	1	0.527	0.482	0.573	CLONAL	1	TRUE	1	0.607022108583549	3		621	583	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686345	117686345	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065536-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	191	329	0	ENST00000368508.3:c.2996C>A	p.Ser999Tyr	p.S999Y	ENST00000368508	NM_002944.2	999	tCt/tAt	20/43	0.598291345584565	3	FACETS	0.949	0.889	1	0.949	0.889	1	CLONAL	2	TRUE	1	0.607022108583549	3		329	432	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239514	123239514	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	268	410	0	ENST00000358487.5:c.2323C>A	p.Pro775Thr	p.P775T	ENST00000358487	NM_000141.4	775	Cct/Act	18/18	0.415917146819573	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.415917146819573	2		410	608	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226563	1226563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	187	367	0	ENST00000326873.7:c.1219G>A	p.Glu407Lys	p.E407K	ENST00000326873	NM_000455.4	407	Gag/Aag	9/10	0.380057656032858	2	FACETS	0.931	0.868	0.995	0.931	0.868	0.995	CLONAL	2	TRUE	0	0.415917146819573	2		367	483	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713510	30713517	+	frameshift_variant	Frame_Shift_Del	DEL	TTTCCCTA	TTTCCCTA	-	novel	NA	P-0065537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	261	412	0	ENST00000295754.5:c.836_843del	p.Phe279Ter	p.F279*	ENST00000295754	NM_003242.5	279	TTTCCCTAt/t	4/7	0.415917146819573	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.415917146819573	2		412	617	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821615	72821638	+	inframe_deletion	In_Frame_Del	DEL	GCCACCGCCGCCGCCGCCGCCACT	GCCACCGCCGCCGCCGCCGCCACT	-	rs750348888	NA	P-0065537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	68	482	2	ENST00000268489.5:c.10537_10560del	p.Ser3513_Gly3520del	p.S3513_G3520del	ENST00000268489	NM_006885.3	3513	AGTGGCGGCGGCGGCGGCGGTGGC/-	10/10	0.415917146819573	3	FACETS	0.729	0.635	0.83	0.364	0.317	0.415	SUBCLONAL	1	TRUE	1	0.415917146819573	3		484	542	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484858	57485003	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTTTGTGGAGTGACCGCCCACCCCCTGCGCTTGCCCAGGAGGCCCTGGTCTGCACTGTTTATAGAGAAGAACCCCGTGCAAGCATTCCAGACCCCTGGCCGAAAGCGCGCTTCTCCCAAGCATTCACACGGCCTCCCTTCTTGT	AGGTTTGTGGAGTGACCGCCCACCCCCTGCGCTTGCCCAGGAGGCCCTGGTCTGCACTGTTTATAGAGAAGAACCCCGTGCAAGCATTCCAGACCCCTGGCCGAAAGCGCGCTTCTCCCAAGCATTCACACGGCCTCCCTTCTTGT	-	novel	NA	P-0065538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	25	415	0	ENST00000371085.3:c.839+1_840-1del		p.X280_splice	ENST00000371085	NM_000516.4	280		10/13	0.444061584811929	6	FACETS	0.461	0.363	0.575			1	SUBCLONAL	1	TRUE	NA	0.444061584811929	6		415	461	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198269	185198269	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	62	403	0	ENST00000265026.3:c.2751G>C	p.Lys917Asn	p.K917N	ENST00000265026	NM_004721.4	917	aaG/aaC	13/14	0.426364515684853	3	FACETS	0.992	0.862	1	0.496	0.431	0.566	CLONAL	1	TRUE	1	0.444061584811929	3		403	344	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307953	11307957	+	frameshift_variant	Frame_Shift_Del	DEL	TCCCA	TCCCA	CCCC	novel	NA	P-0065538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	47	455	1	ENST00000361445.4:c.1035_1039delinsGGGG	p.Phe345LeufsTer21	p.F345Lfs*21	ENST00000361445	NM_004958.3	345	ttTGGGAcc/ttGGGGcc	7/58	1	2	FACETS	0.897	0.764	1	0.897	0.764	1	CLONAL	1	TRUE	1	0.444061584811929	2		456	236	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578509	7578509	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519978	NA	P-0065539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	323	400	0	ENST00000269305.4:c.421T>C	p.Cys141Arg	p.C141R	ENST00000269305	NM_001126112.2	141	Tgc/Cgc	5/11	0.60893398232033	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.616444272303917	3		400	409	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458729	120458729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	96	453	0	ENST00000256646.2:c.6616G>A	p.Glu2206Lys	p.E2206K	ENST00000256646	NM_024408.3	2206	Gaa/Aaa	34/34	0.616444272303917	3	FACETS	1	0.926	1	0.52	0.466	0.576	CLONAL	1	TRUE	1	0.616444272303917	3		453	392	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631594	90631594	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	192	453	0	ENST00000330062.3:c.675C>G	p.Asp225Glu	p.D225E	ENST00000330062	NM_002168.2	225	gaC/gaG	5/11	0.616444272303917	2	FACETS	0.995	0.942	1	0.995	0.942	1	CLONAL	2	TRUE	0	0.616444272303917	2		453	313	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944254	81944259	+	inframe_deletion	In_Frame_Del	DEL	CCTGCG	CCTGCG	-	novel	NA	P-0065539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	49	347	0	ENST00000359376.3:c.1864_1869del	p.Leu622_Arg623del	p.L622_R623del	ENST00000359376	NM_002661.3	621	caCCTGCGc/cac	18/33	0.562253021663833	4	FACETS	0.776	0.661	0.902	0.388	0.33	0.451	CLONAL	1	TRUE	2	0.616444272303917	4		347	331	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544234	86544234	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770701846	NA	P-0065539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	147	499	0	ENST00000262426.4:c.59G>A	p.Gly20Glu	p.G20E	ENST00000262426	NM_001451.2	20	gGg/gAg	1/2	0.562253021663833	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	2	0.616444272303917	4		499	368	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961240	15961240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	219	354	0	ENST00000268712.3:c.6149C>T	p.Thr2050Ile	p.T2050I	ENST00000268712	NM_006311.3	2050	aCa/aTa	39/46	0.60893398232033	3	FACETS	0.93	0.886	0.974	0.93	0.886	0.974	CLONAL	3	TRUE	0	0.616444272303917	3		354	333	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530078	63530078	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0065539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	75	308	0	ENST00000307078.5:c.2357T>A	p.Leu786Ter	p.L786*	ENST00000307078	NM_004655.3	786	tTg/tAg	10/11	0.616444272303917	4	FACETS	0.84	0.739	0.949	0.21	0.184	0.238	CLONAL	1	TRUE	0	0.616444272303917	4		308	468	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502621	149502621	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	67	341	0	ENST00000261799.4:c.2167G>A	p.Gly723Arg	p.G723R	ENST00000261799	NM_002609.3	723	Ggg/Agg	15/23	0.616444272303917	2	FACETS	0.788	0.691	0.889	0.394	0.345	0.445	SUBCLONAL	1	TRUE	0	0.616444272303917	2		341	276	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940216	31940216	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	219	461	0	ENST00000375333.2:c.358C>T	p.Pro120Ser	p.P120S	ENST00000375333	NM_032454.1	120	Ccg/Tcg	2/8	0.616444272303917	3	FACETS	0.995	0.937	1	0.995	0.937	1	CLONAL	2	TRUE	1	0.616444272303917	3		461	467	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410450	139410455	+	inframe_deletion	In_Frame_Del	DEL	GTGTAA	GTGTAA	-	novel	NA	P-0065539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	62	364	0	ENST00000277541.6:c.1647_1652del	p.Tyr550_Thr551del	p.Y550_T551del	ENST00000277541	NM_017617.3	549	acTTACACc/acc	10/34	0.616444272303917	2	FACETS	0.919	0.805	1	0.459	0.402	0.519	CLONAL	1	TRUE	0	0.616444272303917	2		364	219	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0065540-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	13	286	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.426	0.302	0.578	0.426	0.302	0.578	SUBCLONAL	1	TRUE	1	0.14	2		286	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0065540-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	38	575	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.899	0.742	1	0.899	0.742	1	CLONAL	1	TRUE	1	0.14	2		575	604	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0065540-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	25	371	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	1	2	FACETS	0.882	0.694	1	0.882	0.694	1	CLONAL	1	TRUE	1	0.14	2		371	405	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0065541-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	60	295	1	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		296	491	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0065541-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	108	243	0	ENST00000288602.6:c.1397G>T	p.Gly466Val	p.G466V	ENST00000288602	NM_004333.4	466	gGa/gTa	11/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		243	414	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426881	70426881	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065541-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	70	332	0	ENST00000373644.4:c.4541T>A	p.Val1514Glu	p.V1514E	ENST00000373644	NM_030625.2	1514	gTg/gAg	7/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		332	563	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161789	47161789	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065541-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	63	373	0	ENST00000409792.3:c.4337G>T	p.Gly1446Val	p.G1446V	ENST00000409792	NM_014159.6	1446	gGg/gTg	3/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		373	517	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039340	47039345	+	frameshift_variant	Frame_Shift_Ins	INS	ACCCTA	ACCCTA	CCCCCTTT	novel	NA	P-0065541-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	80	419	0	ENST00000377604.3:c.963_968delinsCCCCCTTT	p.Tyr323LeufsTer13	p.Y323Lfs*13	ENST00000377604	NM_001204468.1	321	gcACCCTAc/gcCCCCCTTTc	10/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		419	463	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852107	63852107	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	46	539	0	ENST00000279873.7:c.2885T>C	p.Met962Thr	p.M962T	ENST00000279873	NM_032199.2	962	aTg/aCg	10/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		539	630	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124723	108124723	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	73	346	0	ENST00000278616.4:c.2081T>C	p.Leu694Pro	p.L694P	ENST00000278616	NM_000051.3	694	cTt/cCt	13/63	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		346	576	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411998	116412044	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ATGGTTTCAAATGAATCTGTAGACTACCGAGCTACTTTTCCAGAAGG	ATGGTTTCAAATGAATCTGTAGACTACCGAGCTACTTTTCCAGAAGG	C	novel	NA	P-0065541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	113	465	0	ENST00000397752.3:c.2983_3028+1delinsC		p.X995_splice	ENST00000397752	NM_000245.2	995		14/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		465	814	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0065542-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	333	397	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.306498952789819	4	FACETS	0.967	0.92	1	0.967	0.92	1	CLONAL	4	TRUE	0	0.306498952789819	4		397	734	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627182	37627182	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0065542-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	238	264	0	ENST00000447079.4:c.1097C>G	p.Ser366Ter	p.S366*	ENST00000447079	NM_015083.1	366	tCa/tGa	2/14	0.306498952789819	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	3	TRUE	0	0.306498952789819	3		264	581	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602727	10602727	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065542-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	197	464	0	ENST00000171111.5:c.851A>T	p.Gln284Leu	p.Q284L	ENST00000171111	NM_203500.1	284	cAg/cTg	3/6	0.306498952789819	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.306498952789819	2		464	577	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205319	61205319	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065542-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	75	275	0	ENST00000301761.2:c.259A>T	p.Ser87Cys	p.S87C	ENST00000301761	NM_017841.2	87	Agt/Tgt	2/4	0.254538813837759	3	FACETS	0.999	0.877	1	0.499	0.438	0.565	CLONAL	1	TRUE	1	0.306498952789819	3		275	565	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892316	9892316	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065542-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	114	374	0	ENST00000330684.3:c.2174T>C	p.Leu725Pro	p.L725P	ENST00000330684	NM_001134407.1	725	cTg/cCg	11/13	0.284349513509676	3	FACETS	0.753	0.68	0.829	0.753	0.68	0.829	SUBCLONAL	2	TRUE	1	0.306498952789819	3		374	570	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872852	136872853	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0065542-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	142	431	0	ENST00000241393.3:c.645_646delinsAA	p.Leu216Met	p.L216M	ENST00000241393	NM_003467.2	215	atCCtg/atAAtg	2/2	0.251840802525062	4	FACETS	0.788	0.719	0.861	0.788	0.719	0.861	SUBCLONAL	2	TRUE	2	0.306498952789819	4		431	768	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031761	36031761	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065542-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	90	485	0	ENST00000358208.4:c.1590C>A	p.Tyr530Ter	p.Y530*	ENST00000358208		530	taC/taA	12/12	0.254538813837759	3	FACETS	0.995	0.883	1	0.497	0.441	0.557	CLONAL	1	TRUE	1	0.306498952789819	3		485	681	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31429638	31429638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065542-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	34	235	0	ENST00000344624.3:c.3160G>A	p.Glu1054Lys	p.E1054K	ENST00000344624		1054	Gag/Aag	24/33	0.213167839268756	5	FACETS	0.513	0.418	0.621	0.171	0.139	0.207	SUBCLONAL	1	TRUE	2	0.306498952789819	5		235	631	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86668013	86668013	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0065542-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	138	236	0	ENST00000274376.6:c.1776+1G>T		p.X592_splice	ENST00000274376	NM_002890.2	592			0.306498952789819	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.306498952789819	2		236	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0065543-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	240	622	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.292686960014213	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.26	2		622	779	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0065543-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	407	554	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.302141103441576	3	FACETS	1	0.985	1	1	0.996	1	CLONAL	4	TRUE	0	0.26	3		554	835	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089686	27089686	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0065543-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	292	430	0	ENST00000324856.7:c.2642C>G	p.Ser881Ter	p.S881*	ENST00000324856	NM_006015.4	881	tCa/tGa	8/20	0.302141103441576	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	3	TRUE	0	0.26	3		430	837	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290969	15290969	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065543-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	137	462	0	ENST00000263388.2:c.3241T>A	p.Cys1081Ser	p.C1081S	ENST00000263388	NM_000435.2	1081	Tgt/Agt	20/33	0.198936193615342	3	FACETS	1	0.98	1	0.644	0.585	0.705	CLONAL	1	TRUE	1	0.26	3		462	925	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578340	212578340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1448870993	NA	P-0065543-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	131	288	0	ENST00000342788.4:c.917G>A	p.Arg306His	p.R306H	ENST00000342788	NM_005235.2	306	cGt/cAt	8/28	0.286838101150222	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.26	4		288	521	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960138	134960138	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065543-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	241	348	0	ENST00000398015.3:c.2495A>G	p.Asp832Gly	p.D832G	ENST00000398015	NM_004441.4	832	gAt/gGt	13/16	0.290633099476835	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	TRUE	0	0.26	3		348	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0065544-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	186	463	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.660550901182189	2		463	512	SUCCESS
APC	324	MSKCC	GRCh37	5	112174784	112174784	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0065544-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	159	442	0	ENST00000257430.4:c.3493A>T	p.Lys1165Ter	p.K1165*	ENST00000257430	NM_000038.5	1165	Aaa/Taa	16/16	0.660550901182189	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.660550901182189	1		442	307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579469	7579469	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065544-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	242	542	0	ENST00000269305.4:c.218del	p.Val73GlyfsTer50	p.V73Gfs*50	ENST00000269305	NM_001126112.2	73	gTg/gg	4/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.660550901182189	2		542	677	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40990972	40990972	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065544-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	141	355	0	ENST00000267868.3:c.16C>T	p.Gln6Ter	p.Q6*	ENST00000267868	NM_002875.4	6	Cag/Tag	2/10	1	2	FACETS	0.928	0.852	1	0.928	0.852	1	CLONAL	1	TRUE	1	0.660550901182189	2		355	460	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830351	72830351	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065544-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	175	542	0	ENST00000268489.5:c.6230C>G	p.Ala2077Gly	p.A2077G	ENST00000268489	NM_006885.3	2077	gCa/gGa	9/10	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.660550901182189	2		542	510	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910456	32910456	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28897712	NA	P-0065545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	85	179	0	ENST00000380152.3:c.1964C>G	p.Pro655Arg	p.P655R	ENST00000380152		655	cCa/cGa	11/27	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.346782675324356	2		179	423	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	77	276	0	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.346782675324356	2		276	433	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692895	89692895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781255	NA	P-0065545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	62	189	0	ENST00000371953.3:c.379G>A	p.Gly127Arg	p.G127R	ENST00000371953	NM_000314.4	127	Gga/Aga	5/9	0.346782675324356	1	FACETS	0.985	0.858	1	0.985	0.858	1	CLONAL	1	TRUE	0	0.346782675324356	1		189	300	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946767	71946767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	127	469	0	ENST00000298229.2:c.2708C>T	p.Pro903Leu	p.P903L	ENST00000298229	NM_001567.3	903	cCc/cTc	24/28	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.346782675324356	2		469	651	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486070	29486070	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs746824139	NA	P-0065545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	62	151	0	ENST00000356175.3:c.247C>T	p.Gln83Ter	p.Q83*	ENST00000356175	NM_000267.3	83	Cag/Tag	3/57	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.346782675324356	2		151	337	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112091	115112091	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	94	449	0	ENST00000257566.3:c.1649C>G	p.Ser550Cys	p.S550C	ENST00000257566	NM_016569.3	550	tCc/tGc	7/8	0.346782675324356	1	FACETS	0.865	0.772	0.963	0.865	0.772	0.963	CLONAL	1	TRUE	0	0.346782675324356	1		449	518	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42026719	42026719	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0065545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	50	224	0	ENST00000219905.7:c.3844-1G>C		p.X1282_splice	ENST00000219905	NM_001164273.1	1282			1	2	FACETS	0.723	0.615	0.841	0.723	0.615	0.841	SUBCLONAL	1	TRUE	1	0.346782675324356	2		224	399	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656520	3656520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	98	362	0	ENST00000294008.3:c.715G>A	p.Glu239Lys	p.E239K	ENST00000294008	NM_032444.2	239	Gaa/Aaa	3/15	1	2	FACETS	0.953	0.852	1	0.953	0.852	1	CLONAL	1	TRUE	1	0.346782675324356	2		362	593	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33689991	33689991	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	97	376	1	ENST00000308377.4:c.836A>G	p.Tyr279Cys	p.Y279C	ENST00000308377	NM_152270.3	279	tAc/tGc	2/5	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.346782675324356	2		377	541	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628656	187628656	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	65	439	0	ENST00000441802.2:c.2326A>T	p.Ile776Phe	p.I776F	ENST00000441802	NM_005245.3	776	Att/Ttt	2/27	1	2	FACETS	0.57	0.493	0.652	0.57	0.493	0.652	SUBCLONAL	1	TRUE	1	0.346782675324356	2		439	658	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939555	68939555	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	49	163	0	ENST00000288368.4:c.540G>T	p.Leu180Phe	p.L180F	ENST00000288368	NM_024870.2	180	ttG/ttT	5/40	1	2	FACETS	0.891	0.759	1	0.891	0.759	1	CLONAL	1	TRUE	1	0.346782675324356	2		163	317	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	20	1407	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.714	0.547	0.91	0.714	0.547	0.91	CLONAL	1	TRUE	1	0.2	2		1407	280	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	33	209	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	0.862	0.702	1	0.862	0.702	1	CLONAL	1	TRUE	1	0.2	2		209	383	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	38	525	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.81	0.67	0.967	0.81	0.67	0.967	CLONAL	1	TRUE	1	0.2	2		525	469	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	29	436	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.621	0.498	0.762	0.621	0.498	0.762	SUBCLONAL	1	TRUE	1	0.2	2		436	467	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253974	133253974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61732929	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	54	259	0	ENST00000320574.5:c.776G>A	p.Arg259His	p.R259H	ENST00000320574	NM_006231.2	259	cGc/cAc	8/49	1	2	FACETS	0.978	0.836	1	0.978	0.836	1	CLONAL	1	TRUE	1	0.2	2		259	552	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255799	16255799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs115566585	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	56	392	0	ENST00000375759.3:c.3064G>A	p.Val1022Met	p.V1022M	ENST00000375759	NM_015001.2	1022	Gtg/Atg	11/15	1	2	FACETS	0.71	0.607	0.823	0.71	0.607	0.823	SUBCLONAL	1	TRUE	1	0.2	2		392	789	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	71	557	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.2	2		557	694	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	18	206	0	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	0.575	0.433	0.744	0.575	0.433	0.744	SUBCLONAL	1	TRUE	1	0.2	2		206	313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	51	557	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	0.703	0.597	0.821	0.703	0.597	0.821	SUBCLONAL	1	TRUE	1	0.2	2		557	725	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	68	301	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.2	2		301	630	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	54	352	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.964	0.824	1	0.964	0.824	1	CLONAL	1	TRUE	1	0.2	2		352	560	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638491	176638491	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784096	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	53	336	1	ENST00000439151.2:c.3091C>T	p.Arg1031Ter	p.R1031*	ENST00000439151	NM_022455.4	1031	Cga/Tga	5/23	1	2	FACETS	0.72	0.613	0.838	0.72	0.613	0.838	SUBCLONAL	1	TRUE	1	0.2	2		337	736	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333863	70333863	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs750883311	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	40	353	0	ENST00000373644.4:c.1768C>T	p.Arg590Ter	p.R590*	ENST00000373644	NM_030625.2	590	Cga/Tga	2/12	1	2	FACETS	0.585	0.485	0.697	0.585	0.485	0.697	SUBCLONAL	1	TRUE	1	0.2	2		353	684	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005534	150005534	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	59	304	0	ENST00000253339.5:c.691G>A	p.Gly231Arg	p.G231R	ENST00000253339		231	Gga/Aga	3/7	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.2	2		304	559	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637555	52637555	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	34	282	0	ENST00000394830.3:c.2761C>T	p.Arg921Ter	p.R921*	ENST00000394830	NM_018313.4	921	Cga/Tga	18/30	1	2	FACETS	0.769	0.628	0.928	0.769	0.628	0.928	CLONAL	1	TRUE	1	0.2	2		282	442	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822585	72822586	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs764626362	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	42	360	0	ENST00000268489.5:c.9589dup	p.Gln3197ProfsTer42	p.Q3197Pfs*42	ENST00000268489	NM_006885.3	3197	cag/cCag	10/10	1	2	FACETS	0.54	0.449	0.641	0.54	0.449	0.641	SUBCLONAL	1	TRUE	1	0.2	2		360	778	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692799	89692799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	22	160	0	ENST00000371953.3:c.283C>T	p.Pro95Ser	p.P95S	ENST00000371953	NM_000314.4	95	Cca/Tca	5/9	1	2	FACETS	0.898	0.698	1	0.898	0.698	1	CLONAL	1	TRUE	1	0.2	2		160	245	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40738973	40738973	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	26	231	0	ENST00000373198.4:c.3311G>T	p.Ser1104Ile	p.S1104I	ENST00000373198	NM_133170.3	1104	aGt/aTt	24/32	1	2	FACETS	0.56	0.443	0.695	0.56	0.443	0.695	SUBCLONAL	1	TRUE	1	0.2	2		231	464	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044500	12044500	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367662793	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	52	236	0	ENST00000353533.5:c.1123G>A	p.Val375Ile	p.V375I	ENST00000353533	NM_003010.3	375	Gtt/Att	11/11	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.2	2		236	462	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522274	157522274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567836947	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	51	375	0	ENST00000346085.5:c.4546G>A	p.Val1516Ile	p.V1516I	ENST00000346085	NM_020732.3	1516	Gtc/Atc	18/20	1	2	FACETS	0.889	0.755	1	0.889	0.755	1	CLONAL	1	TRUE	1	0.2	2		375	574	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792593	33792593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	18	237	0	ENST00000498907.2:c.728C>T	p.Ala243Val	p.A243V	ENST00000498907	NM_004364.3	243	gCc/gTc	1/1	1	2	FACETS	0.552	0.415	0.714	0.552	0.415	0.714	SUBCLONAL	1	TRUE	1	0.2	2		237	326	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102918	71102918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148369068	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	56	275	0	ENST00000318789.4:c.289G>A	p.Val97Met	p.V97M	ENST00000318789	NM_032682.5	97	Gtg/Atg	8/21	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.2	2		275	480	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850620	63850620	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	34	248	0	ENST00000279873.7:c.1399-1G>T		p.X467_splice	ENST00000279873	NM_032199.2	467			1	2	FACETS	0.746	0.609	0.9	0.746	0.609	0.9	SUBCLONAL	1	TRUE	1	0.2	2		248	456	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300040	137300040	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	45	266	1	ENST00000481739.1:c.331del	p.Leu111TrpfsTer57	p.L111Wfs*57	ENST00000481739	NM_002957.4	109	Ccc/cc	3/10	1	2	FACETS	0.879	0.739	1	0.879	0.739	1	CLONAL	1	TRUE	1	0.2	2		267	512	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216189	36216189	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	67	417	1	ENST00000222270.7:c.3602del	p.Pro1201ArgfsTer154	p.P1201Rfs*154	ENST00000222270	NM_014727.1	1199	ggC/gg	11/37	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.2	2		418	632	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806242	1806242	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	45	292	0	ENST00000260795.2:c.1261C>T	p.Arg421Ter	p.R421*	ENST00000260795		421	Cga/Tga	8/17	1	2	FACETS	0.841	0.707	0.99	0.841	0.707	0.99	CLONAL	1	TRUE	1	0.2	2		292	535	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940369	13940369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373175151	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	33	224	0	ENST00000405192.2:c.1137G>A	p.Met379Ile	p.M379I	ENST00000405192	NM_001163147.1	379	atG/atA	11/12	1	2	FACETS	0.84	0.684	1	0.84	0.684	1	CLONAL	1	TRUE	1	0.2	2		224	393	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661726	227661726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760281604	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	41	369	0	ENST00000305123.5:c.1729G>A	p.Val577Met	p.V577M	ENST00000305123	NM_005544.2	577	Gtg/Atg	1/2	1	2	FACETS	0.801	0.667	0.95	0.801	0.667	0.95	CLONAL	1	TRUE	1	0.2	2		369	512	SUCCESS
APC	324	MSKCC	GRCh37	5	112179452	112179452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782312	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	62	319	0	ENST00000257430.4:c.8161C>T	p.Arg2721Cys	p.R2721C	ENST00000257430	NM_000038.5	2721	Cgc/Tgc	16/16	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.2	2		319	607	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056317	27056317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776238347	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	51	296	0	ENST00000324856.7:c.1313C>T	p.Ala438Val	p.A438V	ENST00000324856	NM_006015.4	438	gCg/gTg	2/20	1	2	FACETS	0.881	0.748	1	0.881	0.748	1	CLONAL	1	TRUE	1	0.2	2		296	579	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858561	57858561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763470494	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	49	350	0	ENST00000228682.2:c.299G>A	p.Arg100His	p.R100H	ENST00000228682	NM_005269.2	100	cGc/cAc	4/12	1	2	FACETS	0.799	0.676	0.935	0.799	0.676	0.935	CLONAL	1	TRUE	1	0.2	2		350	613	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607453	46607453	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150597114	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	54	360	0	ENST00000263734.3:c.1642G>A	p.Glu548Lys	p.E548K	ENST00000263734	NM_001430.4	548	Gag/Aag	12/16	1	2	FACETS	0.89	0.759	1	0.89	0.759	1	CLONAL	1	TRUE	1	0.2	2		360	607	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753419	42753419	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	42	406	0	ENST00000222329.4:c.845C>T	p.Thr282Met	p.T282M	ENST00000222329	NM_006494.2	282	aCg/aTg	4/4	1	2	FACETS	0.579	0.482	0.687	0.579	0.482	0.687	SUBCLONAL	1	TRUE	1	0.2	2		406	726	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927426	245927426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138010213	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	35	251	0	ENST00000388985.4:c.1102G>A	p.Val368Ile	p.V368I	ENST00000388985		368	Gtc/Atc	11/12	1	2	FACETS	0.613	0.501	0.739	0.613	0.501	0.739	SUBCLONAL	1	TRUE	1	0.2	2		251	571	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199321	16199321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	50	326	1	ENST00000375759.3:c.94G>A	p.Val32Met	p.V32M	ENST00000375759	NM_015001.2	32	Gtg/Atg	2/15	1	2	FACETS	0.817	0.692	0.954	0.817	0.692	0.954	CLONAL	1	TRUE	1	0.2	2		327	612	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191024	2191024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1449424439	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	58	325	0	ENST00000398665.3:c.278C>T	p.Thr93Met	p.T93M	ENST00000398665	NM_032482.2	93	aCg/aTg	5/28	1	2	FACETS	0.967	0.83	1	0.967	0.83	1	CLONAL	1	TRUE	1	0.2	2		325	600	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466378	120466378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779822957	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	67	353	0	ENST00000256646.2:c.4741C>T	p.Arg1581Trp	p.R1581W	ENST00000256646	NM_024408.3	1581	Cgg/Tgg	26/34	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.2	2		353	599	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294414	1294414	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779999492	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	46	451	0	ENST00000310581.5:c.587G>A	p.Arg196His	p.R196H	ENST00000310581	NM_198253.2	196	cGt/cAt	2/16	1	2	FACETS	0.67	0.563	0.788	0.67	0.563	0.788	SUBCLONAL	1	TRUE	1	0.2	2		451	687	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853887	59853887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786203170	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	47	267	0	ENST00000259008.2:c.1972C>T	p.Arg658Trp	p.R658W	ENST00000259008	NM_032043.2	658	Cgg/Tgg	14/20	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.2	2		267	439	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21344765	21344765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869320686	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	54	288	0	ENST00000215739.8:c.742G>A	p.Gly248Arg	p.G248R	ENST00000215739	NM_006767.3	248	Gga/Aga	8/21	1	2	FACETS	0.936	0.799	1	0.936	0.799	1	CLONAL	1	TRUE	1	0.2	2		288	577	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215884	98215884	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1344231723	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	42	215	1	ENST00000331920.6:c.3325G>A	p.Gly1109Ser	p.G1109S	ENST00000331920	NM_000264.3	1109	Ggc/Agc	20/24	1	2	FACETS	0.828	0.691	0.981	0.828	0.691	0.981	CLONAL	1	TRUE	1	0.2	2		216	507	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423781	47423781	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	48	362	0	ENST00000404338.3:c.1849C>T	p.Arg617Ter	p.R617*	ENST00000404338	NM_004491.4	617	Cga/Tga	1/6	1	2	FACETS	0.862	0.728	1	0.862	0.728	1	CLONAL	1	TRUE	1	0.2	2		362	557	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2039765	2039767	+	inframe_deletion	In_Frame_Del	DEL	CAG	CAG	-	novel	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	43	422	0	ENST00000349721.2:c.663_665del	p.Gln238del	p.Q238del	ENST00000349721	NM_003070.3	219	CAG/-	4/34	1	2	FACETS	0.579	0.483	0.686	0.579	0.483	0.686	SUBCLONAL	1	TRUE	1	0.2	2		422	743	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120508138	120508138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1557824894	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	47	289	0	ENST00000256646.2:c.1619C>T	p.Pro540Leu	p.P540L	ENST00000256646	NM_024408.3	540	cCg/cTg	10/34	1	2	FACETS	0.806	0.68	0.946	0.806	0.68	0.946	CLONAL	1	TRUE	1	0.2	2		289	583	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100432	8100432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	57	437	0	ENST00000346208.3:c.406G>A	p.Ala136Thr	p.A136T	ENST00000346208		136	Gcc/Acc	3/6	1	2	FACETS	0.865	0.741	1	0.865	0.741	1	CLONAL	1	TRUE	1	0.2	2		437	659	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597933	43597933	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	39	361	0	ENST00000355710.3:c.481A>G	p.Lys161Glu	p.K161E	ENST00000355710	NM_020975.4	161	Aag/Gag	3/20	1	2	FACETS	0.608	0.503	0.726	0.608	0.503	0.726	SUBCLONAL	1	TRUE	1	0.2	2		361	641	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57004194	57004194	+	stop_gained,NMD_transcript_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	56	419	0	ENST00000257254.3:c.285G>A	p.Trp95Ter	p.W95*	ENST00000257254		95	tgG/tgA	1/2	1	2	FACETS	0.921	0.789	1	0.921	0.789	1	CLONAL	1	TRUE	1	0.2	2		419	608	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575147	64575147	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886039414	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	57	397	0	ENST00000312049.6:c.660G>A	p.Trp220Ter	p.W220*	ENST00000312049	NM_130799.2	220	tgG/tgA	4/10	1	2	FACETS	0.976	0.837	1	0.976	0.837	1	CLONAL	1	TRUE	1	0.2	2		397	584	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944761	31944761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	24	115	0	ENST00000340398.3:c.340G>A	p.Ala114Thr	p.A114T	ENST00000340398	NM_001013699.2	114	Gct/Act	1/1	1	2	FACETS	0.996	0.784	1	0.996	0.784	1	CLONAL	1	TRUE	1	0.2	2		115	241	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205259	46205259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1028736703	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	35	229	0	ENST00000334344.6:c.343C>T	p.Pro115Ser	p.P115S	ENST00000334344	NM_152641.2	115	Cca/Tca	4/21	1	2	FACETS	0.882	0.723	1	0.882	0.723	1	CLONAL	1	TRUE	1	0.2	2		229	397	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996121	73996121	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	64	420	0	ENST00000318443.5:c.855G>A	p.Trp285Ter	p.W285*	ENST00000318443	NM_001024736.1	285	tgG/tgA	5/10	1	2	FACETS	0.885	0.766	1	0.885	0.766	1	CLONAL	1	TRUE	1	0.2	2		420	723	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679154	88679154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	35	277	0	ENST00000360948.2:c.883G>A	p.Ala295Thr	p.A295T	ENST00000360948	NM_001012338.2	295	Gcc/Acc	8/19	1	2	FACETS	0.761	0.623	0.915	0.761	0.623	0.915	CLONAL	1	TRUE	1	0.2	2		277	460	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226182	2226182	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	69	443	0	ENST00000326181.6:c.1878+1G>A		p.X626_splice	ENST00000326181	NM_032271.2	626			1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.2	2		443	689	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297933	15297933	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778350156	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	47	384	0	ENST00000263388.2:c.1823G>A	p.Cys608Tyr	p.C608Y	ENST00000263388	NM_000435.2	608	tGc/tAc	11/33	1	2	FACETS	0.777	0.655	0.912	0.777	0.655	0.912	CLONAL	1	TRUE	1	0.2	2		384	605	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387665	17387665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201104012	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	42	337	0	ENST00000359435.4:c.733G>A	p.Val245Ile	p.V245I	ENST00000359435	NM_001033549.1	245	Gtt/Att	8/9	1	2	FACETS	0.742	0.619	0.879	0.742	0.619	0.879	SUBCLONAL	1	TRUE	1	0.2	2		337	566	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277956	18277956	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	42	255	0	ENST00000222254.8:c.1576G>T	p.Glu526Ter	p.E526*	ENST00000222254	NM_005027.3	526	Gag/Tag	13/16	1	2	FACETS	0.82	0.685	0.971	0.82	0.685	0.971	CLONAL	1	TRUE	1	0.2	2		255	512	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223676	36223676	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	57	421	0	ENST00000222270.7:c.6226C>T	p.Gln2076Ter	p.Q2076*	ENST00000222270	NM_014727.1	2076	Cag/Tag	28/37	1	2	FACETS	0.856	0.733	0.99	0.856	0.733	0.99	CLONAL	1	TRUE	1	0.2	2		421	666	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024942	31024942	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	61	365	0	ENST00000375687.4:c.4427A>G	p.His1476Arg	p.H1476R	ENST00000375687	NM_015338.5	1476	cAc/cGc	13/13	1	2	FACETS	0.838	0.722	0.965	0.838	0.722	0.965	CLONAL	1	TRUE	1	0.2	2		365	728	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735432	40735432	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	37	308	0	ENST00000373198.4:c.3441G>T	p.Gln1147His	p.Q1147H	ENST00000373198	NM_133170.3	1147	caG/caT	25/32	1	2	FACETS	0.746	0.614	0.893	0.746	0.614	0.893	SUBCLONAL	1	TRUE	1	0.2	2		308	496	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433419	138433419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219115228	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	26	251	0	ENST00000289153.2:c.1193C>T	p.Ala398Val	p.A398V	ENST00000289153	NM_006219.2	398	gCt/gTt	7/22	1	2	FACETS	0.765	0.606	0.946	0.765	0.606	0.946	CLONAL	1	TRUE	1	0.2	2		251	340	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1953917	1953917	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	53	326	0	ENST00000382891.5:c.2096G>A	p.Arg699Gln	p.R699Q	ENST00000382891	NM_133335.3	699	cGg/cAg	11/22	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.2	2		326	523	SUCCESS
APC	324	MSKCC	GRCh37	5	112154813	112154813	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	49	322	0	ENST00000257430.4:c.1084G>T	p.Gly362Cys	p.G362C	ENST00000257430	NM_000038.5	362	Ggc/Tgc	10/16	1	2	FACETS	0.867	0.734	1	0.867	0.734	1	CLONAL	1	TRUE	1	0.2	2		322	565	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176719150	176719150	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784199	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	55	270	0	ENST00000439151.2:c.6454C>T	p.Arg2152Ter	p.R2152*	ENST00000439151	NM_022455.4	2152	Cga/Tga	22/23	1	2	FACETS	0.841	0.719	0.975	0.841	0.719	0.975	CLONAL	1	TRUE	1	0.2	2		270	654	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662401	117662401	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	38	343	0	ENST00000368508.3:c.4976C>A	p.Pro1659Gln	p.P1659Q	ENST00000368508	NM_002944.2	1659	cCa/cAa	30/43	1	2	FACETS	0.76	0.628	0.908	0.76	0.628	0.908	CLONAL	1	TRUE	1	0.2	2		343	500	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522037	157522037	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1376702390	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	62	423	0	ENST00000346085.5:c.4309C>T	p.Gln1437Ter	p.Q1437*	ENST00000346085	NM_020732.3	1437	Cag/Tag	18/20	1	2	FACETS	0.964	0.832	1	0.964	0.832	1	CLONAL	1	TRUE	1	0.2	2		423	643	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2966411	2966411	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	42	241	0	ENST00000396946.4:c.1769A>G	p.Asp590Gly	p.D590G	ENST00000396946	NM_032415.4	590	gAc/gGc	14/25	1	2	FACETS	0.873	0.729	1	0.873	0.729	1	CLONAL	1	TRUE	1	0.2	2		241	481	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845390	151845390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754423379	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	82	371	0	ENST00000262189.6:c.13622G>A	p.Arg4541Gln	p.R4541Q	ENST00000262189	NM_170606.2	4541	cGa/cAa	52/59	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.2	2		371	677	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938584	76938584	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	41	257	0	ENST00000373344.5:c.2164T>C	p.Ser722Pro	p.S722P	ENST00000373344	NM_000489.3	722	Tca/Cca	9/35	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.2	2		257	383	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589169	67589169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766524768	NA	P-0065547-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	77	317	0	ENST00000274335.5:c.1157G>A	p.Arg386Gln	p.R386Q	ENST00000274335		386	cGa/cAa	9/15	0.457268058422146	2	FACETS	0.52	0.461	0.584	0.26	0.23	0.292	INDETERMINATE	1	TRUE	0	0.899367878049973	2		317	329	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625584	1625584	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065547-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	99	433	0	ENST00000344749.5:c.490G>C	p.Gly164Arg	p.G164R	ENST00000344749	NM_001136139.2	164	Ggc/Cgc	7/19	0.467335165071523	3	FACETS	0.508	0.454	0.566	0.254	0.227	0.283	INDETERMINATE	1	TRUE	1	0.899367878049973	3		433	628	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795540	42795540	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065547-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	247	508	0	ENST00000575354.2:c.2620G>C	p.Gly874Arg	p.G874R	ENST00000575354	NM_015125.3	874	Ggc/Cgc	10/20	0.467335165071523	3	FACETS	1	0.982	1	0.556	0.522	0.591	INDETERMINATE	1	TRUE	1	0.899367878049973	3		508	716	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632255	215632255	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065547-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	98	337	0	ENST00000260947.4:c.1519G>C	p.Val507Leu	p.V507L	ENST00000260947	NM_000465.2	507	Gtg/Ctg	6/11	0.527784473227219	1	FACETS	0.325	0.292	0.359	0.325	0.292	0.359	INDETERMINATE	1	TRUE	0	0.899367878049973	1		337	369	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0065548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	31	533	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.225	0.181	0.274	0.225	0.181	0.274	SUBCLONAL	1	TRUE	1	0.460914694603912	2		533	599	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	111	324	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	1	2	FACETS	0.731	0.658	0.808	0.731	0.658	0.808	SUBCLONAL	1	TRUE	1	0.460914694603912	2		324	659	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396523	139396523	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0065548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	38	455	0	ENST00000277541.6:c.5402C>G	p.Ser1801Ter	p.S1801*	ENST00000277541	NM_017617.3	1801	tCa/tGa	29/34	0.250604509810576	3	FACETS	0.277	0.228	0.332	0.138	0.114	0.166	INDETERMINATE	1	TRUE	1	0.460914694603912	3		455	733	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724469	112724469	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0065548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	37	378	0	ENST00000369452.4:c.353C>G	p.Ser118Ter	p.S118*	ENST00000369452	NM_007373.3	118	tCa/tGa	2/9	1	2	FACETS	0.25	0.206	0.301	0.25	0.206	0.301	SUBCLONAL	1	TRUE	1	0.460914694603912	2		378	641	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14300941	14300941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	16	146	0	ENST00000256196.4:c.557C>T	p.Ser186Leu	p.S186L	ENST00000256196		186	tCa/tTa	6/6	1	2	FACETS	0.231	0.17	0.303	0.231	0.17	0.303	SUBCLONAL	1	TRUE	1	0.460914694603912	2		146	301	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634831	158634832	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0065548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	41	403	0	ENST00000263640.3:c.354_355del	p.Asn119PhefsTer31	p.N119Ffs*31	ENST00000263640	NM_001105.4	118	caGAat/caat	5/11	1	2	FACETS	0.262	0.217	0.312	0.262	0.217	0.312	SUBCLONAL	1	TRUE	1	0.460914694603912	2		403	679	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713408	30713408	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	154	438	0	ENST00000295754.5:c.733G>T	p.Glu245Ter	p.E245*	ENST00000295754	NM_003242.5	245	Gag/Tag	4/7	0.460914694603912	1	FACETS	0.825	0.758	0.895	0.825	0.758	0.895	CLONAL	1	TRUE	0	0.460914694603912	1		438	623	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937863	76937863	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782545048	NA	P-0065548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	82	311	0	ENST00000373344.5:c.2885C>T	p.Ser962Phe	p.S962F	ENST00000373344	NM_000489.3	962	tCt/tTt	9/35	1	2	FACETS	0.511	0.451	0.576	0.511	0.451	0.576	SUBCLONAL	1	TRUE	1	0.460914694603912	2		311	696	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0065549-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	26	286	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.915	0.73	1	0.915	0.73	1	CLONAL	1	TRUE	1	0.29	2		286	196	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0065549-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	37	430	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.299636896151596	1	FACETS	0.902	0.748	1	0.902	0.748	1	CLONAL	1	TRUE	0	0.29	1		430	242	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003485	57003485	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	C	C	T	rs764929700	NA	P-0065549-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	55	520	0	ENST00000257254.3:c.994G>A	p.Ala332Thr	p.A332T	ENST00000257254		332	Gca/Aca	1/2	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.29	2		520	375	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073670	8073670	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065549-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	49	425	0	ENST00000377482.5:c.989C>G	p.Ser330Trp	p.S330W	ENST00000377482	NM_018948.3	330	tCg/tGg	4/4	0.299636896151596	1	FACETS	0.993	0.846	1	0.993	0.846	1	CLONAL	1	TRUE	0	0.29	1		425	291	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134428	2134428	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065549-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	60	530	0	ENST00000219476.3:c.4205G>C	p.Gly1402Ala	p.G1402A	ENST00000219476	NM_000548.3	1402	gGg/gCg	34/42	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.29	2		530	353	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0065550-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	52	170	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.943	0.808	1	0.943	0.808	1	CLONAL	1	TRUE	1	0.367715661398933	2		170	300	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640008	3640008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202032197	NA	P-0065550-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	81	490	0	ENST00000294008.3:c.3631G>A	p.Glu1211Lys	p.E1211K	ENST00000294008	NM_032444.2	1211	Gaa/Aaa	12/15	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.367715661398933	2		490	433	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176176059	176176059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065550-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	66	485	0	ENST00000367669.3:c.56C>T	p.Ser19Leu	p.S19L	ENST00000367669	NM_022457.5	19	tCg/tTg	1/20	0.35303513704439	3	FACETS	0.9	0.783	1	0.45	0.391	0.513	CLONAL	1	TRUE	1	0.367715661398933	3		485	472	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	50	663	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.45	0.383	0.524	0.45	0.383	0.524	SUBCLONAL	1	TRUE	1	0.556818233685736	2		663	399	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423413	116423413	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913247	NA	P-0065551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	168	452	0	ENST00000397752.3:c.3688T>C	p.Tyr1230His	p.Y1230H	ENST00000397752	NM_000245.2	1230	Tat/Cat	19/21	0.556818233685736	3	FACETS	1	0.947	1	0.518	0.477	0.561	CLONAL	1	TRUE	1	0.556818233685736	3		452	744	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141992	108141992	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1565425094	NA	P-0065551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	144	448	0	ENST00000278616.4:c.2936T>C	p.Leu979Ser	p.L979S	ENST00000278616	NM_000051.3	979	tTg/tCg	20/63	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.556818233685736	2		448	468	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366462	118366462	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	214	491	0	ENST00000534358.1:c.5411A>C	p.Asn1804Thr	p.N1804T	ENST00000534358	NM_005933.3	1804	aAt/aCt	19/36	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.556818233685736	2		491	658	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097628	11097628	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	216	672	0	ENST00000358026.2:c.808C>A	p.Pro270Thr	p.P270T	ENST00000358026	NM_001128849.1	270	Ccc/Acc	5/36	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.556818233685736	2		672	742	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927476	178927476	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	121	378	0	ENST00000263967.3:c.1239G>C	p.Lys413Asn	p.K413N	ENST00000263967	NM_006218.2	413	aaG/aaC	7/21	1	2	FACETS	0.925	0.841	1	0.925	0.841	1	CLONAL	1	TRUE	1	0.556818233685736	2		378	470	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753954	133753954	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	130	385	0	ENST00000318560.5:c.1423del	p.Cys475ValfsTer45	p.C475Vfs*45	ENST00000318560	NM_005157.4	475	Tgt/gt	8/11	1	2	FACETS	0.844	0.769	0.923	0.844	0.769	0.923	CLONAL	1	TRUE	1	0.556818233685736	2		385	553	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0065552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	34	286	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.170972491876073	3	FACETS	1	0.939	1	0.701	0.573	0.846	CLONAL	1	TRUE	1	0.11	3		286	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0065552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	33	425	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.83	1	1	0.83	1	CLONAL	1	TRUE	1	0.11	2		425	587	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604764	48604765	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs377767376	NA	P-0065552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	30	461	0	ENST00000342988.3:c.1587dup	p.His530ThrfsTer47	p.H530Tfs*47	ENST00000342988	NM_005359.5	529	tta/ttAa	12/12	1	2	FACETS	0.909	0.731	1	0.909	0.731	1	CLONAL	1	TRUE	1	0.11	2		461	600	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127294	55127294	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	32	437	0	ENST00000257290.5:c.82C>G	p.Pro28Ala	p.P28A	ENST00000257290	NM_006206.4	28	Ccc/Gcc	3/23	0.126935608057052	3	FACETS	1	0.902	1	0.595	0.482	0.723	CLONAL	1	TRUE	1	0.11	3		437	516	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0065553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	142	434	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.503913483601127	3	FACETS	0.878	0.809	0.947	0.878	0.809	0.947	CLONAL	2	TRUE	1	0.546428896951008	3		434	377	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722761	49722761	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs62262682	NA	P-0065553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	14	30	2	ENST00000449682.2:c.1478G>T	p.Arg493Leu	p.R493L	ENST00000449682	NM_020998.3	493	cGt/cTt	13/18	0.44082086171718	5	FACETS	1	0.862	1	0.613	0.466	0.771	CLONAL	2	TRUE	1	0.546428896951008	5		32	38	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918761	32918761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1239798218	NA	P-0065553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	47	316	0	ENST00000380152.3:c.6908C>T	p.Ser2303Phe	p.S2303F	ENST00000380152		2303	tCc/tTc	12/27	0.411858629164282	4	FACETS	1	0.962	1	0.723	0.619	0.834	CLONAL	1	TRUE	2	0.546428896951008	4		316	184	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937446	178937446	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	33	210	0	ENST00000263967.3:c.1834C>T	p.Arg612Ter	p.R612*	ENST00000263967	NM_006218.2	612	Cga/Tga	12/21	0.532898362350141	4	FACETS	0.785	0.643	0.942	0.262	0.214	0.314	CLONAL	1	TRUE	1	0.546428896951008	4		210	238	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795129	242795129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	124	544	0	ENST00000334409.5:c.80C>T	p.Ser27Phe	p.S27F	ENST00000334409	NM_005018.2	27	tCc/tTc	2/5	0.503913483601127	3	FACETS	1	0.929	1	0.513	0.466	0.563	CLONAL	1	TRUE	1	0.546428896951008	3		544	563	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244982	123244982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	121	585	0	ENST00000358487.5:c.2122C>T	p.Pro708Ser	p.P708S	ENST00000358487	NM_000141.4	708	Ccc/Tcc	16/18	1	2	FACETS	0.765	0.693	0.84	0.765	0.693	0.84	SUBCLONAL	1	TRUE	1	0.546428896951008	2		585	579	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525838	148525838	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554498830	NA	P-0065553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	149	368	0	ENST00000320356.2:c.619C>T	p.Arg207Ter	p.R207*	ENST00000320356	NM_004456.4	207	Cga/Tga	6/20	0.546428896951008	6	FACETS	0.82	0.751	0.892	0.41	0.375	0.446	CLONAL	2	TRUE	2	0.546428896951008	6		368	696	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713470	40713470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318044562	NA	P-0065553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	191	533	0	ENST00000373198.4:c.4045C>T	p.Arg1349Cys	p.R1349C	ENST00000373198	NM_133170.3	1349	Cgt/Tgt	30/32	0.0833194984292176	4	FACETS	0.886	0.824	0.95	0.886	0.824	0.95	INDETERMINATE	2	TRUE	2	0.546428896951008	4		533	610	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709529	176709529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777258117	NA	P-0065553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	150	387	0	ENST00000439151.2:c.5956C>T	p.Arg1986Cys	p.R1986C	ENST00000439151	NM_022455.4	1986	Cgc/Tgc	19/23	0.489618233292816	5	FACETS	1	0.932	1	0.675	0.622	0.731	CLONAL	2	TRUE	2	0.546428896951008	5		387	493	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0065553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	208	402	0				ENST00000310581	NM_198253.2	-/1132			0.528995319710926	5	FACETS	0.97	0.91	1	0.97	0.91	1	CLONAL	3	TRUE	2	0.546428896951008	5		402	476	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40468827	40468827	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	193	377	0	ENST00000264657.5:c.2237C>T	p.Pro746Leu	p.P746L	ENST00000264657	NM_139276.2	746	cCc/cTc	23/24	0.51300770650667	3	FACETS	0.804	0.749	0.861	0.804	0.749	0.861	CLONAL	2	TRUE	1	0.546428896951008	3		377	559	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626635	100626635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	196	229	0	ENST00000308731.7:c.295C>T	p.Pro99Ser	p.P99S	ENST00000308731	NM_000061.2	99	Cct/Tct	4/19	0.327280147135389	2	FACETS	0.906	0.866	0.944			1	INDETERMINATE	3	TRUE	NA	0.546428896951008	2		229	264	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777867	3777867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	268	649	0	ENST00000262367.5:c.7181C>T	p.Ser2394Phe	p.S2394F	ENST00000262367	NM_004380.2	2394	tCc/tTc	31/31	0.103085319283128	6	FACETS	0.903	0.851	0.956	0.903	0.851	0.956	INDETERMINATE	3	TRUE	3	0.546428896951008	6		649	758	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298084	15298084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs75068032	NA	P-0065553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	208	530	0	ENST00000263388.2:c.1672C>T	p.Arg558Cys	p.R558C	ENST00000263388	NM_000435.2	558	Cgc/Tgc	11/33	0.475605243408846	5	FACETS	0.969	0.903	1	0.646	0.602	0.691	CLONAL	2	TRUE	2	0.546428896951008	5		530	715	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022385	12022385	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	327	589	0	ENST00000396373.4:c.491C>T	p.Pro164Leu	p.P164L	ENST00000396373	NM_001987.4	164	cCa/cTa	5/8	0.546428896951008	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.546428896951008	3		589	734	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56866276	56866276	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	189	467	0	ENST00000308159.5:c.1321C>T	p.Gln441Ter	p.Q441*	ENST00000308159	NM_014669.4	441	Cag/Tag	12/22	0.336092123270551	4	FACETS	0.836	0.776	0.897	0.836	0.776	0.897	CLONAL	2	TRUE	2	0.546428896951008	4		467	640	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934257	81934257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	143	435	0	ENST00000359376.3:c.1234G>A	p.Glu412Lys	p.E412K	ENST00000359376	NM_002661.3	412	Gag/Aag	14/33	0.103085319283128	6	FACETS	1	0.946	1	0.694	0.636	0.754	INDETERMINATE	2	TRUE	3	0.546428896951008	6		435	526	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350088	89350089	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0065553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	195	626	0	ENST00000301030.4:c.2861_2862delinsTT	p.Ala954Val	p.A954V	ENST00000301030	NM_001256183.1	954	gCC/gTT	9/13	0.103085319283128	6	FACETS	0.962	0.893	1	0.642	0.595	0.69	INDETERMINATE	2	TRUE	3	0.546428896951008	6		626	776	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553655	29553665	+	frameshift_variant	Frame_Shift_Del	DEL	ATAACACATTC	ATAACACATTC	-	novel	NA	P-0065553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	105	536	0	ENST00000356175.3:c.2206_2216del	p.Asn736GlyfsTer28	p.N736Gfs*28	ENST00000356175	NM_000267.3	735	tATAACACATTC/t	18/57	0.51300770650667	3	FACETS	0.85	0.763	0.941	0.425	0.381	0.471	CLONAL	1	TRUE	1	0.546428896951008	3		536	576	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576032	29576033	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0065553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	165	480	0	ENST00000356175.3:c.4005_4006delinsTT	p.Gln1336Ter	p.Q1336*	ENST00000356175	NM_000267.3	1335	aaCCag/aaTTag	30/57	0.51300770650667	3	FACETS	0.816	0.756	0.878	0.816	0.756	0.878	CLONAL	2	TRUE	1	0.546428896951008	3		480	471	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627982	37627982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	125	562	0	ENST00000447079.4:c.1897C>T	p.Pro633Ser	p.P633S	ENST00000447079	NM_015083.1	633	Cca/Tca	2/14	0.51300770650667	3	FACETS	0.892	0.809	0.979	0.446	0.404	0.49	CLONAL	1	TRUE	1	0.546428896951008	3		562	653	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030293	11030293	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	259	509	0	ENST00000327064.4:c.1043T>G	p.Leu348Arg	p.L348R	ENST00000327064	NM_199141.1	348	cTg/cGg	9/16	0.489618233292816	5	FACETS	1	0.972	1	0.706	0.663	0.749	CLONAL	2	TRUE	2	0.546428896951008	5		509	815	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376253	225376255	+	stop_gained	Nonsense_Mutation	TNP	ATA	ATA	GAT	novel	NA	P-0065553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	26	360	0	ENST00000264414.4:c.699_701delinsATC	p.Tyr233_Ile234delinsTer	p.Y233_I234delins*	ENST00000264414	NM_003590.4	233	taTATa/taATCa	6/16	0.503913483601127	3	FACETS	0.566	0.451	0.697	0.283	0.225	0.349	SUBCLONAL	1	TRUE	1	0.546428896951008	3		360	214	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662440	227662440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781722234	NA	P-0065553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	252	597	0	ENST00000305123.5:c.1015C>T	p.Pro339Ser	p.P339S	ENST00000305123	NM_005544.2	339	Cca/Tca	1/2	0.503913483601127	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.546428896951008	3		597	574	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101160	41101160	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866048434	NA	P-0065553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	241	543	0	ENST00000373198.4:c.1196G>A	p.Arg399Lys	p.R399K	ENST00000373198	NM_133170.3	399	aGa/aAa	8/32	0.0833194984292176	4	FACETS	1	0.942	1	1	0.942	1	INDETERMINATE	2	TRUE	2	0.546428896951008	4		543	680	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626435	12626435	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	173	531	0	ENST00000251849.4:c.1714A>G	p.Lys572Glu	p.K572E	ENST00000251849	NM_002880.3	572	Aag/Gag	16/17	0.546428896951008	5	FACETS	1	0.982	1	0.407	0.375	0.441	CLONAL	1	TRUE	2	0.546428896951008	5		531	943	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627249	12627249	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1553610155	NA	P-0065553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	336	408	0	ENST00000251849.4:c.1467G>T	p.Leu489Phe	p.L489F	ENST00000251849	NM_002880.3	489	ttG/ttT	14/17	0.546428896951008	5	FACETS	0.907	0.867	0.946	1	0.993	1	CLONAL	4	TRUE	2	0.546428896951008	5		408	617	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156580	106156580	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	88	525	0	ENST00000380013.4:c.1481G>A	p.Gly494Glu	p.G494E	ENST00000380013	NM_001127208.2	494	gGg/gAg	3/11	1	2	FACETS	0.734	0.653	0.819	0.734	0.653	0.819	SUBCLONAL	1	TRUE	1	0.546428896951008	2		525	439	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867520	35867520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	104	375	1	ENST00000303115.3:c.334G>A	p.Gly112Arg	p.G112R	ENST00000303115	NM_002185.3	112	Gga/Aga	3/8	0.528995319710926	5	FACETS	1	0.956	1	0.728	0.66	0.799	CLONAL	2	TRUE	2	0.546428896951008	5		376	317	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555225	106555225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780985666	NA	P-0065553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	117	473	0	ENST00000369096.4:c.2342G>A	p.Gly781Glu	p.G781E	ENST00000369096	NM_001198.3	781	gGg/gAg	7/7	0.546428896951008	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.546428896951008	1		473	302	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704565	117704565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200615700	NA	P-0065553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	58	431	0	ENST00000368508.3:c.2411C>T	p.Thr804Ile	p.T804I	ENST00000368508	NM_002944.2	804	aCc/aTc	16/43	0.546428896951008	1	FACETS	0.714	0.622	0.812	0.714	0.622	0.812	SUBCLONAL	1	TRUE	0	0.546428896951008	1		431	216	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753001	128753001	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	265	546	0	ENST00000377970.2:c.1162A>C	p.Ser388Arg	p.S388R	ENST00000377970	NM_002467.4	388	Agc/Cgc	3/3	0.411858629164282	4	FACETS	0.964	0.907	1	0.964	0.907	1	CLONAL	2	TRUE	2	0.546428896951008	4		546	778	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0065554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	156	425	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.257410364947266	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	FALSE	1	0.257694014308827	3		425	585	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246027152	246027152	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065555-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	61	591	0	ENST00000388985.4:c.850A>G	p.Lys284Glu	p.K284E	ENST00000388985		284	Aag/Gag	9/12	0.56878887512693	4	FACETS	0.619	0.534	0.711	0.155	0.133	0.178	SUBCLONAL	1	TRUE	0	0.569405942163991	4		591	543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579359	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0065555-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	623	836	0	ENST00000269305.4:c.327_328dup	p.Arg110ProfsTer14	p.R110Pfs*14	ENST00000269305	NM_001126112.2	110	cgt/cCCgt	4/11	0.569405942163991	5	FACETS	0.955	0.931	0.978	0.955	0.931	0.978	CLONAL	5	TRUE	0	0.569405942163991	5		836	850	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978493	70978493	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065555-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	201	670	0	ENST00000276594.2:c.1160A>T	p.Lys387Met	p.K387M	ENST00000276594	NM_024504.3	387	aAg/aTg	5/8	0.504306487896851	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	2	0.569405942163991	4		670	523	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0065557-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	23	286	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.385	0.299	0.484	0.385	0.299	0.484	SUBCLONAL	1	TRUE	1	0.29	2		286	412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	rs886039483	NA	P-0065557-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	88	459	0	ENST00000269305.4:c.376T>A	p.Tyr126Asn	p.Y126N	ENST00000269305	NM_001126112.2	126	Tac/Aac	5/11	1	2	FACETS	0.819	0.725	0.919	0.819	0.725	0.919	CLONAL	1	TRUE	1	0.29	2		459	741	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044895	47044895	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065557-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	98	639	0	ENST00000377604.3:c.2221G>T	p.Glu741Ter	p.E741*	ENST00000377604	NM_001204468.1	741	Gag/Tag	20/24	1	2	FACETS	0.692	0.616	0.774	0.692	0.616	0.774	SUBCLONAL	1	TRUE	1	0.29	2		639	976	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245455	153245455	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065558-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	221	400	0	ENST00000281708.4:c.1736G>T	p.Gly579Val	p.G579V	ENST00000281708	NM_033632.3	579	gGg/gTg	11/12	0.301679581975881	3	FACETS	0.936	0.878	0.995	0.936	0.878	0.995	CLONAL	3	TRUE	0	0.319641199911832	3		400	571	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0065558-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	214	446	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	0.286974286147051	3	FACETS	0.936	0.877	0.996	0.936	0.877	0.996	CLONAL	3	TRUE	0	0.319641199911832	3		446	553	SUCCESS
APC	324	MSKCC	GRCh37	5	112175350	112175351	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065558-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	178	463	0	ENST00000257430.4:c.4063dup	p.Ser1355PhefsTer20	p.S1355Ffs*20	ENST00000257430	NM_000038.5	1353	-/T	16/16	0.319641199911832	2	FACETS	0.967	0.896	1	0.967	0.896	1	CLONAL	2	TRUE	0	0.319641199911832	2		463	576	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982134	201982135	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065558-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	196	633	0	ENST00000359651.3:c.659dup	p.Asp220GlufsTer4	p.D220Efs*4	ENST00000359651		220	gat/gAat	5/8	0.319641199911832	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.319641199911832	3		633	628	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113379	209113379	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065559-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	40	330	0	ENST00000345146.2:c.128A>G	p.Asp43Gly	p.D43G	ENST00000345146	NM_005896.2	43	gAt/gGt	4/10	0.12175504001187	4	FACETS	0.287	0.237	0.342	0.096	0.079	0.114	INDETERMINATE	1	TRUE	1	0.805208571679665	4		330	626	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597604	28597604	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065559-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	67	344	0	ENST00000241453.7:c.2301A>T	p.Glu767Asp	p.E767D	ENST00000241453	NM_004119.2	767	gaA/gaT	19/24	1	2	FACETS	0.353	0.308	0.403	0.353	0.308	0.403	SUBCLONAL	1	TRUE	1	0.805208571679665	2		344	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0065561-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	135	617	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.185253482224189	3	FACETS	0.999	0.914	1	0.999	0.914	1	CLONAL	3	FALSE	0	0.201944864973502	3		618	491	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190860	106190860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs577810844	NA	P-0065561-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	47	406	3	ENST00000380013.4:c.4138C>T	p.His1380Tyr	p.H1380Y	ENST00000380013	NM_001127208.2	1380	Cat/Tat	9/11	0.201944864973502	5	FACETS	1	0.918	1	0.571	0.482	0.67	CLONAL	1	FALSE	3	0.201944864973502	5		409	531	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411886	116411901	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TTTCTCTCTGTTTTAA	TTTCTCTCTGTTTTAA	-	novel	NA	P-0065561-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	407	622	0	ENST00000397752.3:c.2888-17_2888-2del		p.X963_splice	ENST00000397752	NM_000245.2	963			0.201944864973502	8	FACETS	1	0.977	1	0.903	0.864	0.943	CLONAL	7	FALSE	0	0.201944864973502	8		622	896	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045189	47045189	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065561-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	109	585	0	ENST00000377604.3:c.2430G>T	p.Glu810Asp	p.E810D	ENST00000377604	NM_001204468.1	810	gaG/gaT	21/24	0.0901050749938292	4	FACETS	0.86	0.776	0.948	1	0.977	1	INDETERMINATE	3	FALSE	2	0.201944864973502	4		585	503	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244231	46244232	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0065561-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	72	565	0	ENST00000334344.6:c.2330_2331del	p.Thr777SerfsTer63	p.T777Sfs*63	ENST00000334344	NM_152641.2	775	ttACac/ttac	15/21	0.201944864973502	6	FACETS	0.823	0.72	0.935	0.549	0.48	0.624	CLONAL	2	FALSE	3	0.201944864973502	6		565	608	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433905	149433905	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065561-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	100	439	0	ENST00000286301.3:c.2743C>A	p.Gln915Lys	p.Q915K	ENST00000286301	NM_005211.3	915	Caa/Aaa	21/22	0.201944864973502	5	FACETS	0.862	0.773	0.956	1	0.975	1	CLONAL	3	FALSE	3	0.201944864973502	5		439	499	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302436	15302436	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065561-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	144	716	0	ENST00000263388.2:c.835C>T	p.Gln279Ter	p.Q279*	ENST00000263388	NM_000435.2	279	Cag/Tag	6/33	NA	2	FACETS	1	0.959	1			1	INDETERMINATE	3	FALSE	NA	0.201944864973502	2		716	446	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481887	56481887	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065561-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	113	533	0	ENST00000267101.3:c.815T>C	p.Leu272Pro	p.L272P	ENST00000267101	NM_001982.3	272	cTg/cCg	7/28	0.201944864973502	6	FACETS	0.874	0.789	0.964	0.874	0.789	0.964	CLONAL	3	FALSE	3	0.201944864973502	6		533	599	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230540	46230543	+	frameshift_variant	Frame_Shift_Del	DEL	ATGG	ATGG	-	novel	NA	P-0065561-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	116	413	0	ENST00000334344.6:c.791_794del	p.Trp264PhefsTer27	p.W264Ffs*27	ENST00000334344	NM_152641.2	263	gaATGG/ga	8/21	0.201944864973502	6	FACETS	0.871	0.787	0.96	0.871	0.787	0.96	CLONAL	3	FALSE	3	0.201944864973502	6		413	617	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372495	118372495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065561-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	153	537	0	ENST00000534358.1:c.6428C>T	p.Ser2143Leu	p.S2143L	ENST00000534358	NM_005933.3	2143	tCa/tTa	26/36	0.201944864973502	5	FACETS	0.905	0.83	0.984	1	0.985	1	CLONAL	3	FALSE	3	0.201944864973502	5		537	727	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864807	57864807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065561-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	133	674	0	ENST00000228682.2:c.2284G>A	p.Gly762Ser	p.G762S	ENST00000228682	NM_005269.2	762	Ggc/Agc	12/12	0.201944864973502	6	FACETS	0.884	0.805	0.968	0.884	0.805	0.968	CLONAL	3	FALSE	3	0.201944864973502	6		674	697	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919939	50919939	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065561-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	37	559	0	ENST00000440232.2:c.3026G>T	p.Arg1009Leu	p.R1009L	ENST00000440232	NM_002691.3	1009	cGc/cTc	24/27	0.201944864973502	3	FACETS	1	0.858	1	0.523	0.431	0.625	CLONAL	1	FALSE	1	0.201944864973502	3		559	386	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448574	89448574	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065561-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	51	470	0	ENST00000336596.2:c.1538C>T	p.Thr513Ile	p.T513I	ENST00000336596	NM_005233.5	513	aCa/aTa	7/17	0.0901050749938292	4	FACETS	1	0.922	1	0.568	0.483	0.662	INDETERMINATE	1	FALSE	2	0.201944864973502	4		470	534	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512401	149512401	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065561-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	116	679	0	ENST00000261799.4:c.1039A>T	p.Thr347Ser	p.T347S	ENST00000261799	NM_002609.3	347	Act/Tct	7/23	0.201944864973502	5	FACETS	0.885	0.8	0.973	1	0.98	1	CLONAL	3	FALSE	3	0.201944864973502	5		679	564	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975483	13975483	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065561-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	117	487	0	ENST00000405192.2:c.404C>G	p.Ser135Cys	p.S135C	ENST00000405192	NM_001163147.1	135	tCc/tGc	7/12	0.0901050749938292	4	FACETS	1	0.973	1	1	0.973	1	INDETERMINATE	2	FALSE	2	0.201944864973502	4		487	575	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0065562-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	43	217	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		217	176	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061264	38061264	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065562-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	63	418	0	ENST00000250448.2:c.725C>G	p.Ser242Cys	p.S242C	ENST00000250448	NM_004496.3	242	tCc/tGc	2/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		418	237	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061261	38061261	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065562-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	66	413	0	ENST00000250448.2:c.728A>C	p.Tyr243Ser	p.Y243S	ENST00000250448	NM_004496.3	243	tAc/tCc	2/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		413	237	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692920	89692921	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs398123323	NA	P-0065562-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	38	315	0	ENST00000371953.3:c.405dup	p.Cys136MetfsTer44	p.C136Mfs*44	ENST00000371953	NM_000314.4	135	ata/atAa	5/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		315	130	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437617	52437618	+	missense_variant	Missense_Mutation	DNP	TT	TT	GG	novel	NA	P-0065562-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	18	424	1	ENST00000460680.1:c.1543_1544delinsCC	p.Asn515Pro	p.N515P	ENST00000460680	NM_004656.3	515	AAc/CCc	13/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		425	224	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627359	14627359	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065562-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	23	407	0	ENST00000254322.2:c.711del	p.Phe237LeufsTer3	p.F237Lfs*3	ENST00000254322	NM_006145.1	237	ttT/tt	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		407	237	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0065563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	52	532	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.313949614177414	2		532	292	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239940	53239940	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	60	323	0	ENST00000375401.3:c.1501T>C	p.Trp501Arg	p.W501R	ENST00000375401	NM_004187.3	501	Tgg/Cgg	11/26	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.313949614177414	2		323	315	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510790	120510790	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	49	379	0	ENST00000256646.2:c.1174A>T	p.Thr392Ser	p.T392S	ENST00000256646	NM_024408.3	392	Acc/Tcc	7/34	1	2	FACETS	0.703	0.596	0.82	0.703	0.596	0.82	SUBCLONAL	1	TRUE	1	0.313949614177414	2		379	444	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214329	55214329	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs551591429	NA	P-0065563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	69	342	0	ENST00000275493.2:c.455A>G	p.Asn152Ser	p.N152S	ENST00000275493	NM_005228.3	152	aAc/aGc	4/28	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.313949614177414	2		342	428	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346553	81346553	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	76	302	0	ENST00000222390.5:c.1400C>G	p.Ser467Cys	p.S467C	ENST00000222390	NM_000601.4	467	tCt/tGt	11/18	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.313949614177414	2		302	386	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739467	145739467	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758743745	NA	P-0065563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	43	443	0	ENST00000428558.2:c.1903C>T	p.His635Tyr	p.H635Y	ENST00000428558	NM_004260.3	635	Cac/Tac	12/22	1	2	FACETS	0.761	0.638	0.896	0.761	0.638	0.896	SUBCLONAL	1	TRUE	1	0.313949614177414	2		443	360	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863382	57863382	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	154	498	0	ENST00000228682.2:c.1477T>A	p.Ser493Thr	p.S493T	ENST00000228682	NM_005269.2	493	Tcc/Acc	11/12	0.701639353588835	4	FACETS	1	0.966	1	0.549	0.504	0.596	CLONAL	1	TRUE	2	0.701639353588835	4		498	680	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	176	601	2	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.981	0.905	1	0.981	0.905	1	CLONAL	1	TRUE	1	0.46	2		603	780	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120031	70120031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	140	339	0	ENST00000245479.2:c.1037del	p.Pro346ArgfsTer37	p.P346Rfs*37	ENST00000245479	NM_000346.3	345	Ccc/cc	3/3	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.46	2		339	552	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	113	261	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.763	0.688	0.842	0.763	0.688	0.842	SUBCLONAL	1	TRUE	1	0.46	2		264	644	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	136	294	2	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.46	2		296	529	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	52	455	0	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.315	0.267	0.367	0.315	0.267	0.367	SUBCLONAL	1	TRUE	1	0.46	2		455	718	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	56	369	5	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	1	2	FACETS	0.373	0.319	0.432	0.373	0.319	0.432	SUBCLONAL	1	TRUE	1	0.46	2		374	653	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027676	48027678	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs587782858	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	136	333	0	ENST00000234420.5:c.2561_2563del	p.Lys854del	p.K854del	ENST00000234420	NM_000179.2	852	AAG/-	4/10	1	2	FACETS	0.883	0.804	0.964	0.883	0.804	0.964	CLONAL	1	TRUE	1	0.46	2		333	670	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905061	50905061	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	120	333	0	ENST00000440232.2:c.347del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	115	Ccc/cc	4/27	1	2	FACETS	0.928	0.841	1	0.928	0.841	1	CLONAL	1	TRUE	1	0.46	2		333	562	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	147	477	3	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.885	0.81	0.964	0.885	0.81	0.964	CLONAL	1	TRUE	1	0.46	2		480	722	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	113	240	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.931	0.841	1	0.931	0.841	1	CLONAL	1	TRUE	1	0.46	2		240	528	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888847	76888847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	145	301	0	ENST00000373344.5:c.4982G>A	p.Arg1661His	p.R1661H	ENST00000373344	NM_000489.3	1661	cGt/cAt	19/35	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.46	2		301	597	SUCCESS
ATM	472	MSKCC	GRCh37	11	108168020	108168020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752459491	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	34	230	0	ENST00000278616.4:c.4916C>T	p.Pro1639Leu	p.P1639L	ENST00000278616	NM_000051.3	1639	cCg/cTg	33/63	1	2	FACETS	0.318	0.259	0.384	0.318	0.259	0.384	SUBCLONAL	1	TRUE	1	0.46	2		230	465	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	104	299	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.46	2		299	446	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220336	5220336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754772522	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	123	355	0	ENST00000357368.4:c.3484C>T	p.Arg1162Cys	p.R1162C	ENST00000357368	NM_002850.3	1162	Cgc/Tgc	21/38	1	2	FACETS	0.937	0.85	1	0.937	0.85	1	CLONAL	1	TRUE	1	0.46	2		355	571	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247373	153247373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	160	332	0	ENST00000281708.4:c.1429G>A	p.Gly477Ser	p.G477S	ENST00000281708	NM_033632.3	477	Ggt/Agt	10/12	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.46	2		332	688	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	46	393	0	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.273	0.229	0.322	0.273	0.229	0.322	SUBCLONAL	1	TRUE	1	0.46	2		393	732	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	143	329	5	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.46	2		334	601	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245449	153245449	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	159	299	0	ENST00000281708.4:c.1742A>C	p.Gln581Pro	p.Q581P	ENST00000281708	NM_033632.3	581	cAg/cCg	11/12	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.46	2		299	672	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198027	185198027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184685567	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	148	307	0	ENST00000265026.3:c.2509C>T	p.Arg837Cys	p.R837C	ENST00000265026	NM_004721.4	837	Cgc/Tgc	13/14	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.46	2		307	611	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504056	123504056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1362460627	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	88	213	0	ENST00000371139.4:c.232C>T	p.Arg78Trp	p.R78W	ENST00000371139	NM_001114937.2	78	Cgg/Tgg	3/4	1	2	FACETS	0.915	0.816	1	0.915	0.816	1	CLONAL	1	TRUE	1	0.46	2		213	418	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735467	40735467	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776642212	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	122	357	0	ENST00000373198.4:c.3406C>T	p.Arg1136Cys	p.R1136C	ENST00000373198	NM_133170.3	1136	Cgt/Tgt	25/32	1	2	FACETS	0.824	0.746	0.905	0.824	0.746	0.905	CLONAL	1	TRUE	1	0.46	2		357	644	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557725	21557725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs915063122	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	44	389	0	ENST00000382592.4:c.2120G>A	p.Arg707Gln	p.R707Q	ENST00000382592	NM_014572.2	707	cGg/cAg	5/8	1	2	FACETS	0.265	0.222	0.314	0.265	0.222	0.314	SUBCLONAL	1	TRUE	1	0.46	2		389	721	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615538	43615538	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	135	424	0	ENST00000355710.3:c.2617C>T	p.Arg873Trp	p.R873W	ENST00000355710	NM_020975.4	873	Cgg/Tgg	15/20	1	2	FACETS	0.872	0.794	0.953	0.872	0.794	0.953	CLONAL	1	TRUE	1	0.46	2		424	673	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156936	106156936	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs763386429	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	141	411	0	ENST00000380013.4:c.1842del	p.Leu615SerfsTer24	p.L615Sfs*24	ENST00000380013	NM_001127208.2	613	Ggg/gg	3/11	1	2	FACETS	0.8	0.73	0.874	0.8	0.73	0.874	SUBCLONAL	1	TRUE	1	0.46	2		411	766	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733232	74733232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	51	374	0	ENST00000359995.5:c.11G>A	p.Gly4Asp	p.G4D	ENST00000359995	NM_001195427.1	4	gGc/gAc	1/3	1	2	FACETS	0.365	0.31	0.426	0.365	0.31	0.426	SUBCLONAL	1	TRUE	1	0.46	2		374	607	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501350	140501350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906660	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	109	217	0	ENST00000288602.6:c.722C>T	p.Thr241Met	p.T241M	ENST00000288602	NM_004333.4	241	aCg/aTg	6/18	1	2	FACETS	0.975	0.88	1	0.975	0.88	1	CLONAL	1	TRUE	1	0.46	2		217	486	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222582	157222582	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	156	451	0	ENST00000346085.5:c.1849C>T	p.Gln617Ter	p.Q617*	ENST00000346085	NM_020732.3	617	Cag/Tag	4/20	1	2	FACETS	0.91	0.835	0.989	0.91	0.835	0.989	CLONAL	1	TRUE	1	0.46	2		451	745	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222339	2222339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771191963	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	151	456	0	ENST00000326181.6:c.623G>A	p.Arg208Gln	p.R208Q	ENST00000326181	NM_032271.2	208	cGa/cAa	8/21	1	2	FACETS	0.992	0.909	1	0.992	0.909	1	CLONAL	1	TRUE	1	0.46	2		456	662	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661395	227661396	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	rs138975702	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	112	457	1	ENST00000305123.5:c.2057_2059dup	p.Ser686dup	p.S686dup	ENST00000305123	NM_005544.2	686	aac/aGCAac	1/2	1	2	FACETS	0.712	0.641	0.787	0.712	0.641	0.787	SUBCLONAL	1	TRUE	1	0.46	2		458	684	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099468	157099470	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	rs1429292576	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	156	451	0	ENST00000346085.5:c.413_415del	p.Asn138del	p.N138del	ENST00000346085	NM_020732.3	135	tcCAAc/tcc	1/20	1	2	FACETS	0.854	0.783	0.928	0.854	0.783	0.928	CLONAL	1	TRUE	1	0.46	2		451	794	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924316	112924316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1420362815	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	167	316	0	ENST00000351677.2:c.1262G>A	p.Arg421Gln	p.R421Q	ENST00000351677	NM_002834.3	421	cGg/cAg	11/16	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.46	2		316	675	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	55	388	3	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.327	0.279	0.38	0.327	0.279	0.38	SUBCLONAL	1	TRUE	1	0.46	2		391	731	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533790	63533790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	158	419	0	ENST00000307078.5:c.1364C>T	p.Pro455Leu	p.P455L	ENST00000307078	NM_004655.3	455	cCa/cTa	6/11	1	2	FACETS	0.954	0.876	1	0.954	0.876	1	CLONAL	1	TRUE	1	0.46	2		419	720	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933823	39933823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727503826	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	153	456	0	ENST00000378444.4:c.776C>T	p.Ser259Leu	p.S259L	ENST00000378444	NM_001123385.1	259	tCg/tTg	4/15	1	2	FACETS	0.973	0.892	1	0.973	0.892	1	CLONAL	1	TRUE	1	0.46	2		456	684	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	188	487	0	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.46	2		487	810	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862139	68862139	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	159	355	0	ENST00000261769.5:c.2231del	p.Pro744GlnfsTer26	p.P744Qfs*26	ENST00000261769	NM_004360.3	743	Ccc/cc	14/16	1	2	FACETS	0.989	0.909	1	0.989	0.909	1	CLONAL	1	TRUE	1	0.46	2		355	699	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202925	27202925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749958421	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	160	361	0	ENST00000380036.4:c.2017C>T	p.Arg673Cys	p.R673C	ENST00000380036	NM_000459.3	673	Cgt/Tgt	13/23	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.46	2		361	625	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	157	448	0	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	1	2	FACETS	0.836	0.766	0.908	0.836	0.766	0.908	CLONAL	1	TRUE	1	0.46	2		448	817	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050315	37050315	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs63751101	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	140	256	1	ENST00000231790.2:c.469del	p.Tyr157ThrfsTer3	p.Y157Tfs*3	ENST00000231790	NM_000249.3	155	cTt/ct	6/19	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.46	2		257	607	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031979	10031979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	145	362	0	ENST00000330684.3:c.844G>A	p.Asp282Asn	p.D282N	ENST00000330684	NM_001134407.1	282	Gat/Aat	3/13	1	2	FACETS	0.93	0.85	1	0.93	0.85	1	CLONAL	1	TRUE	1	0.46	2		362	678	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760598	133760598	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	165	486	0	ENST00000318560.5:c.2925del	p.Ile976SerfsTer93	p.I976Sfs*93	ENST00000318560	NM_005157.4	974	aCc/ac	11/11	1	2	FACETS	0.935	0.86	1	0.935	0.86	1	CLONAL	1	TRUE	1	0.46	2		486	767	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1977050	1977050	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	58	333	0	ENST00000382891.5:c.3544G>A	p.Asp1182Asn	p.D1182N	ENST00000382891	NM_133335.3	1182	Gat/Aat	20/22	1	2	FACETS	0.4	0.343	0.462	0.4	0.343	0.462	SUBCLONAL	1	TRUE	1	0.46	2		333	630	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992720	68992721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs764112302	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	103	305	5	ENST00000288368.4:c.1693dup	p.Ser565PhefsTer3	p.S565Ffs*3	ENST00000288368	NM_024870.2	562	cgt/cgTt	16/40	1	2	FACETS	0.763	0.684	0.846	0.763	0.684	0.846	SUBCLONAL	1	TRUE	1	0.46	2		310	587	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778282	3778282	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	130	456	0	ENST00000262367.5:c.6766del	p.Leu2256SerfsTer46	p.L2256Sfs*46	ENST00000262367	NM_004380.2	2256	Ctc/tc	31/31	1	2	FACETS	0.75	0.68	0.822	0.75	0.68	0.822	SUBCLONAL	1	TRUE	1	0.46	2		456	754	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397217	397217	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753427028	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	191	403	0	ENST00000380956.4:c.602G>A	p.Arg201His	p.R201H	ENST00000380956	NM_001195286.1	201	cGc/cAc	5/9	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.46	2		403	732	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444933	49444933	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767415197	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	39	444	0	ENST00000301067.7:c.2533del	p.Arg845GlyfsTer85	p.R845Gfs*85	ENST00000301067	NM_003482.3	845	Cgg/gg	10/54	1	2	FACETS	0.231	0.191	0.276	0.231	0.191	0.276	SUBCLONAL	1	TRUE	1	0.46	2		444	734	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647143	2647143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	131	271	0	ENST00000342085.4:c.1421G>A	p.Arg474Gln	p.R474Q	ENST00000342085	NM_002613.4	474	cGa/cAa	13/14	1	2	FACETS	0.957	0.872	1	0.957	0.872	1	CLONAL	1	TRUE	1	0.46	2		271	595	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214714	36214714	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	123	350	0	ENST00000222270.7:c.3145del	p.Ala1049ArgfsTer133	p.A1049Rfs*133	ENST00000222270	NM_014727.1	1047	cGg/cg	8/37	1	2	FACETS	0.983	0.893	1	0.983	0.893	1	CLONAL	1	TRUE	1	0.46	2		350	544	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257889	19257889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1482048547	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	183	478	0	ENST00000162023.5:c.497G>A	p.Arg166His	p.R166H	ENST00000162023		166	cGc/cAc	9/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.46	2		478	742	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632770	23632770	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs180177131	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	32	268	0	ENST00000261584.4:c.3026del	p.Pro1009LeufsTer6	p.P1009Lfs*6	ENST00000261584	NM_024675.3	1009	cCt/ct	10/13	1	2	FACETS	0.238	0.192	0.29	0.238	0.192	0.29	SUBCLONAL	1	TRUE	1	0.46	2		268	585	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80063767	80063769	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs758193305	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	106	249	0	ENST00000265081.6:c.1917_1919del	p.Phe639del	p.F639del	ENST00000265081	NM_002439.4	638	TTC/-	14/24	1	2	FACETS	0.989	0.891	1	0.989	0.891	1	CLONAL	1	TRUE	1	0.46	2		249	466	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106543608	106543608	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	37	246	0	ENST00000369096.4:c.410G>T	p.Arg137Met	p.R137M	ENST00000369096	NM_001198.3	137	aGg/aTg	3/7	1	2	FACETS	0.295	0.243	0.354	0.295	0.243	0.354	SUBCLONAL	1	TRUE	1	0.46	2		246	545	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467833	66467834	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	51	351	0	ENST00000273854.3:c.435dup	p.Thr146AspfsTer3	p.T146Dfs*3	ENST00000273854	NM_004439.5	145	-/G	3/18	1	2	FACETS	0.359	0.304	0.419	0.359	0.304	0.419	SUBCLONAL	1	TRUE	1	0.46	2		351	618	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353818	15353819	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	32	182	1	ENST00000263377.2:c.3061dup	p.His1021ProfsTer72	p.H1021Pfs*72	ENST00000263377	NM_058243.2	1021	cat/cCat	14/20	1	2	FACETS	0.485	0.395	0.586	0.485	0.395	0.586	SUBCLONAL	1	TRUE	1	0.46	2		183	287	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217650	7217653	+	frameshift_variant	Frame_Shift_Del	DEL	CTTT	CTTT	-	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	106	378	0	ENST00000380728.2:c.274_277del	p.Lys92PhefsTer16	p.K92Ffs*16	ENST00000380728		92	AAAGtt/tt	4/11	1	2	FACETS	0.692	0.621	0.767	0.692	0.621	0.767	SUBCLONAL	1	TRUE	1	0.46	2		378	666	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969968	161969968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746215864	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	119	284	0	ENST00000366898.1:c.1001G>A	p.Arg334His	p.R334H	ENST00000366898	NM_004562.2	334	cGc/cAc	9/12	1	2	FACETS	0.96	0.87	1	0.96	0.87	1	CLONAL	1	TRUE	1	0.46	2		284	539	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191097	185191097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200211552	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	165	421	0	ENST00000265026.3:c.1978G>A	p.Gly660Arg	p.G660R	ENST00000265026	NM_004721.4	660	Gga/Aga	11/14	1	2	FACETS	0.909	0.836	0.985	0.909	0.836	0.985	CLONAL	1	TRUE	1	0.46	2		421	789	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37680973	37680973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764290780	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	73	331	0	ENST00000447079.4:c.3142C>T	p.Arg1048Ter	p.R1048*	ENST00000447079	NM_015083.1	1048	Cga/Tga	12/14	1	2	FACETS	0.435	0.38	0.494	0.435	0.38	0.494	SUBCLONAL	1	TRUE	1	0.46	2		331	730	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307690	11307690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	130	289	0	ENST00000361445.4:c.1217C>T	p.Ala406Val	p.A406V	ENST00000361445	NM_004958.3	406	gCc/gTc	8/58	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.46	2		289	528	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165857	118165857	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1476955055	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	183	410	0	ENST00000369448.3:c.367G>A	p.Gly123Ser	p.G123S	ENST00000369448	NM_017709.3	123	Ggt/Agt	2/2	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.46	2		410	775	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150933591	150933591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149404089	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	42	343	1	ENST00000271640.5:c.3053G>A	p.Arg1018Gln	p.R1018Q	ENST00000271640	NM_001145415.1	1018	cGa/cAa	16/22	1	2	FACETS	0.295	0.246	0.35	0.295	0.246	0.35	SUBCLONAL	1	TRUE	1	0.46	2		344	619	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451018	70451018	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	156	464	0	ENST00000373644.4:c.5858C>T	p.Ala1953Val	p.A1953V	ENST00000373644	NM_030625.2	1953	gCc/gTc	12/12	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.46	2		464	673	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10785426	10785426	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	36	294	0	ENST00000361367.2:c.1194G>T	p.Lys398Asn	p.K398N	ENST00000361367	NM_014633.3	398	aaG/aaT	9/25	1	2	FACETS	0.261	0.214	0.314	0.261	0.214	0.314	SUBCLONAL	1	TRUE	1	0.46	2		294	600	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111958580	111958580	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	40	225	0	ENST00000375549.3:c.53-1G>A		p.X18_splice	ENST00000375549	NM_003002.3	18			1	2	FACETS	0.392	0.325	0.465	0.392	0.325	0.465	SUBCLONAL	1	TRUE	1	0.46	2		225	444	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447922	49447922	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1362887681	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	121	364	2	ENST00000301067.7:c.512G>A	p.Arg171His	p.R171H	ENST00000301067	NM_003482.3	171	cGc/cAc	5/54	1	2	FACETS	0.865	0.784	0.951	0.865	0.784	0.951	CLONAL	1	TRUE	1	0.46	2		366	608	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636296	73636296	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	49	403	0	ENST00000377687.4:c.559C>A	p.Pro187Thr	p.P187T	ENST00000377687	NM_001730.3	187	Cct/Act	2/4	1	2	FACETS	0.252	0.212	0.295	0.252	0.212	0.295	SUBCLONAL	1	TRUE	1	0.46	2		403	847	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994634	73994634	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	38	464	0	ENST00000318443.5:c.118G>A	p.Ala40Thr	p.A40T	ENST00000318443	NM_001024736.1	40	Gca/Aca	3/10	1	2	FACETS	0.228	0.188	0.274	0.228	0.188	0.274	SUBCLONAL	1	TRUE	1	0.46	2		464	724	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500394	99500394	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	63	437	0	ENST00000268035.6:c.3827A>C	p.Glu1276Ala	p.E1276A	ENST00000268035	NM_000875.3	1276	gAg/gCg	21/21	1	2	FACETS	0.384	0.331	0.441	0.384	0.331	0.441	SUBCLONAL	1	TRUE	1	0.46	2		437	714	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226366	2226366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	183	444	0	ENST00000326181.6:c.1979C>T	p.Ala660Val	p.A660V	ENST00000326181	NM_032271.2	660	gCt/gTt	20/21	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.46	2		444	755	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984852	72984852	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	131	354	0	ENST00000268489.5:c.2732T>A	p.Ile911Asn	p.I911N	ENST00000268489	NM_006885.3	911	aTc/aAc	3/10	1	2	FACETS	0.943	0.859	1	0.943	0.859	1	CLONAL	1	TRUE	1	0.46	2		354	604	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372091	45372091	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	63	294	0	ENST00000262160.6:c.1078C>A	p.Pro360Thr	p.P360T	ENST00000262160	NM_005901.5	360	Ccc/Acc	9/11	1	2	FACETS	0.38	0.328	0.437	0.38	0.328	0.437	SUBCLONAL	1	TRUE	1	0.46	2		294	721	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593462	48593462	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1179609154	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	62	365	0	ENST00000342988.3:c.1213C>T	p.His405Tyr	p.H405Y	ENST00000342988	NM_005359.5	405	Cac/Tac	10/12	1	2	FACETS	0.383	0.331	0.441	0.383	0.331	0.441	SUBCLONAL	1	TRUE	1	0.46	2		365	703	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096931	11096931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502073	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	76	431	0	ENST00000358026.2:c.422C>T	p.Ser141Leu	p.S141L	ENST00000358026	NM_001128849.1	141	tCg/tTg	4/36	1	2	FACETS	0.476	0.417	0.54	0.476	0.417	0.54	SUBCLONAL	1	TRUE	1	0.46	2		431	694	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626894	14626894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772131060	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	199	406	0	ENST00000254322.2:c.881G>A	p.Arg294Gln	p.R294Q	ENST00000254322	NM_006145.1	294	cGg/cAg	3/3	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.46	2		406	833	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376437	15376437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202093296	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	124	347	0	ENST00000263377.2:c.577G>A	p.Val193Ile	p.V193I	ENST00000263377	NM_058243.2	193	Gtt/Att	5/20	1	2	FACETS	0.968	0.879	1	0.968	0.879	1	CLONAL	1	TRUE	1	0.46	2		347	557	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422062	47422062	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774121374	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	192	380	0	ENST00000404338.3:c.130C>T	p.Arg44Cys	p.R44C	ENST00000404338	NM_004491.4	44	Cgc/Tgc	1/6	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.46	2		380	734	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905131	50905131	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	150	395	0	ENST00000440232.2:c.413G>A	p.Cys138Tyr	p.C138Y	ENST00000440232	NM_002691.3	138	tGc/tAc	4/27	1	2	FACETS	0.913	0.837	0.994	0.913	0.837	0.994	CLONAL	1	TRUE	1	0.46	2		395	714	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265223	46265223	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	140	362	0	ENST00000371998.3:c.2093T>C	p.Val698Ala	p.V698A	ENST00000371998		698	gTa/gCa	12/23	1	2	FACETS	0.861	0.785	0.94	0.861	0.785	0.94	CLONAL	1	TRUE	1	0.46	2		362	707	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626659	12626659	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	154	440	0	ENST00000251849.4:c.1630G>T	p.Gly544Trp	p.G544W	ENST00000251849	NM_002880.3	544	Ggg/Tgg	15/17	1	2	FACETS	0.883	0.81	0.96	0.883	0.81	0.96	CLONAL	1	TRUE	1	0.46	2		440	758	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612242	189612242	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	146	357	0	ENST00000264731.3:c.1994T>C	p.Met665Thr	p.M665T	ENST00000264731	NM_003722.4	665	aTg/aCg	14/14	1	2	FACETS	0.977	0.894	1	0.977	0.894	1	CLONAL	1	TRUE	1	0.46	2		357	650	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803222	1803222	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	173	453	0	ENST00000260795.2:c.574G>T	p.Gly192Cys	p.G192C	ENST00000260795		192	Ggc/Tgc	4/17	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.46	2		453	682	SUCCESS
ALB	213	MSKCC	GRCh37	4	74285257	74285257	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	61	285	0	ENST00000295897.4:c.1686G>T	p.Lys562Asn	p.K562N	ENST00000295897	NM_000477.5	562	aaG/aaT	13/15	1	2	FACETS	0.507	0.438	0.582	0.507	0.438	0.582	SUBCLONAL	1	TRUE	1	0.46	2		285	523	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143181643	143181643	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	42	242	0	ENST00000262992.4:c.688+2T>C		p.X230_splice	ENST00000262992	NM_001101669.1	230			1	2	FACETS	0.359	0.3	0.426	0.359	0.3	0.426	SUBCLONAL	1	TRUE	1	0.46	2		242	508	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930596	131930597	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	105	203	0	ENST00000265335.6:c.1832_1833del	p.Ile611LysfsTer2	p.I611Kfs*2	ENST00000265335		610	cAT/c	12/25	1	2	FACETS	0.959	0.864	1	0.959	0.864	1	CLONAL	1	TRUE	1	0.46	2		203	476	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638326	176638326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750009132	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	183	418	0	ENST00000439151.2:c.2926G>A	p.Ala976Thr	p.A976T	ENST00000439151	NM_022455.4	976	Gcc/Acc	5/23	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.46	2		418	789	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672914	30672914	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778836256	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	228	585	0	ENST00000376406.3:c.4046G>A	p.Arg1349Gln	p.R1349Q	ENST00000376406	NM_014641.2	1349	cGg/cAg	10/15	1	2	FACETS	0.962	0.897	1	0.962	0.897	1	CLONAL	1	TRUE	1	0.46	2		585	1030	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805601	32805601	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	166	412	0	ENST00000374899.4:c.410T>C	p.Leu137Ser	p.L137S	ENST00000374899	NM_018833.2	137	tTg/tCg	2/12	1	2	FACETS	0.929	0.855	1	0.929	0.855	1	CLONAL	1	TRUE	1	0.46	2		412	777	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124503576	124503576	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	133	343	1	ENST00000357628.3:c.374T>C	p.Phe125Ser	p.F125S	ENST00000357628	NM_015450.2	125	tTc/tCc	8/19	1	2	FACETS	0.912	0.831	0.997	0.912	0.831	0.997	CLONAL	1	TRUE	1	0.46	2		344	634	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197387	27197387	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	145	335	0	ENST00000380036.4:c.1699T>C	p.Phe567Leu	p.F567L	ENST00000380036	NM_000459.3	567	Ttt/Ctt	12/23	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.46	2		335	619	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030517	47030517	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	145	404	0	ENST00000377604.3:c.292C>T	p.Arg98Ter	p.R98*	ENST00000377604	NM_001204468.1	98	Cga/Tga	4/24	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.46	2		404	584	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123025168	123025168	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0065565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	250	431	0	ENST00000355640.3:c.1056+2T>C		p.X352_splice	ENST00000355640		352			1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.46	2		431	913	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0065574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	166	410	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.426379560517474	6	FACETS	0.857	0.787	0.929	0.428	0.393	0.465	CLONAL	2	TRUE	2	0.426379560517474	6		410	842	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260223	19260223	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767499551	NA	P-0065574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	56	420	0	ENST00000162023.5:c.70C>T	p.Arg24Trp	p.R24W	ENST00000162023		24	Cgg/Tgg	7/13	0.149283677528752	4	FACETS	0.678	0.58	0.784	0.339	0.29	0.392	INDETERMINATE	1	TRUE	2	0.426379560517474	4		420	553	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190825	32190825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779661107	NA	P-0065574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	95	453	0	ENST00000375023.3:c.112G>A	p.Gly38Arg	p.G38R	ENST00000375023	NM_004557.3	38	Gga/Aga	2/30	0.426379560517474	3	FACETS	0.945	0.843	1	0.473	0.421	0.527	CLONAL	1	TRUE	1	0.426379560517474	3		453	572	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39575950	39575950	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	35	341	0	ENST00000262039.4:c.883C>A	p.Gln295Lys	p.Q295K	ENST00000262039	NM_002647.2	295	Cag/Aag	8/25	1	2	FACETS	0.39	0.319	0.469	0.39	0.319	0.469	SUBCLONAL	1	TRUE	1	0.426379560517474	2		341	421	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628058	187628058	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	43	458	0	ENST00000441802.2:c.2924A>G	p.Asp975Gly	p.D975G	ENST00000441802	NM_005245.3	975	gAt/gGt	2/27	0.426379560517474	3	FACETS	0.321	0.268	0.381	0.161	0.134	0.191	SUBCLONAL	1	TRUE	1	0.426379560517474	3		458	762	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958196	2958196	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1190416265	NA	P-0065574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	125	395	0	ENST00000396946.4:c.2536C>A	p.Leu846Met	p.L846M	ENST00000396946	NM_032415.4	846	Ctg/Atg	19/25	0.426379560517474	7	FACETS	0.844	0.764	0.927	0.337	0.305	0.371	CLONAL	2	TRUE	2	0.426379560517474	7		395	718	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972904	55972906	+	frameshift_variant	Frame_Shift_Del	DEL	TAT	TAT	AA	novel	NA	P-0065574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	31	331	0	ENST00000263923.4:c.1484_1486delinsTT	p.Asn495IlefsTer12	p.N495Ifs*12	ENST00000263923	NM_002253.2	495	aATAaa/aTTaa	11/30	0.426379560517474	3	FACETS	0.355	0.286	0.433	0.177	0.143	0.217	SUBCLONAL	1	TRUE	1	0.426379560517474	3		331	497	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0065575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	16	80	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.15840274316254	3	FACETS	1	0.818	1	0.568	0.421	0.742	CLONAL	1	TRUE	1	0.15840274316254	3		80	192	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0065575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	51	472	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	1	2	FACETS	0.931	0.794	1	1	0.973	1	CLONAL	2	TRUE	1	0.15840274316254	2		472	346	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129169	64129169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746466314	NA	P-0065575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	14	439	0	ENST00000334205.4:c.707C>T	p.Ser236Leu	p.S236L	ENST00000334205	NM_003942.2	236	tCg/tTg	7/17	0.15840274316254	3	FACETS	0.548	0.395	0.735	0.183	0.131	0.245	SUBCLONAL	1	TRUE	0	0.15840274316254	3		439	348	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175916374	175916374	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	17	203	0	ENST00000367669.3:c.2135A>G	p.Glu712Gly	p.E712G	ENST00000367669	NM_022457.5	712	gAg/gGg	19/20	1	2	FACETS	1	0.754	1	1	0.754	1	CLONAL	1	TRUE	1	0.15840274316254	2		203	213	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57004016	57004016	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	55	453	0	ENST00000257254.3:c.463G>T	p.Val155Leu	p.V155L	ENST00000257254		155	Gtg/Ttg	1/2	0.15840274316254	3	FACETS	0.986	0.847	1	0.657	0.564	0.758	CLONAL	2	TRUE	0	0.15840274316254	3		453	380	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201002	108201002	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1591160295	NA	P-0065575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	16	322	0	ENST00000278616.4:c.7369G>T	p.Glu2457Ter	p.E2457*	ENST00000278616	NM_000051.3	2457	Gag/Tag	50/63	1	2	FACETS	0.662	0.489	0.87	0.662	0.489	0.87	SUBCLONAL	1	TRUE	1	0.15840274316254	2		322	305	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001895	29001895	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	46	275	0	ENST00000282397.4:c.1270G>T	p.Val424Phe	p.V424F	ENST00000282397	NM_002019.4	424	Gtc/Ttc	9/30	1	2	FACETS	1	0.897	1	1	0.974	1	CLONAL	2	TRUE	1	0.15840274316254	2		275	270	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954250	32954250	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	34	329	0	ENST00000380152.3:c.9224T>A	p.Ile3075Lys	p.I3075K	ENST00000380152		3075	aTa/aAa	24/27	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.15840274316254	2		329	339	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992118	72992118	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	26	463	0	ENST00000268489.5:c.1927C>G	p.Pro643Ala	p.P643A	ENST00000268489	NM_006885.3	643	Ccc/Gcc	2/10	0.13361308781467	1	FACETS	0.81	0.642	1	0.81	0.642	1	CLONAL	1	TRUE	0	0.15840274316254	1		463	373	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943351	17943351	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1428917753	NA	P-0065575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	26	300	0	ENST00000458235.1:c.2657A>G	p.Tyr886Cys	p.Y886C	ENST00000458235	NM_000215.3	886	tAt/tGt	19/24	1	2	FACETS	0.922	0.731	1	0.922	0.731	1	CLONAL	1	TRUE	1	0.15840274316254	2		300	356	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978890	25978919	+	inframe_deletion	In_Frame_Del	DEL	CTGAGAGTCTTTCCTTCCAGCCTTGGGCTG	CTGAGAGTCTTTCCTTCCAGCCTTGGGCTG	-	novel	NA	P-0065575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	16	239	0	ENST00000435504.4:c.1004_1033del	p.Ala335_Ser344del	p.A335_S344del	ENST00000435504		335	gCAGCCCAAGGCTGGAAGGAAAGACTCTCAGaa/gaa	10/13	1	2	FACETS	0.89	0.659	1	0.89	0.659	1	CLONAL	1	TRUE	1	0.15840274316254	2		239	227	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99180080	99180080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	23	342	0	ENST00000074304.5:c.2023G>A	p.Asp675Asn	p.D675N	ENST00000074304	NM_001134224.1	675	Gac/Aac	19/26	0.15840274316254	3	FACETS	0.986	0.769	1	0.493	0.384	0.618	CLONAL	1	TRUE	1	0.15840274316254	3		342	318	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130426	29130426	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs750596499	NA	P-0065575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	50	356	0	ENST00000328354.6:c.284G>C	p.Arg95Pro	p.R95P	ENST00000328354	NM_007194.3	95	cGa/cCa	2/15	1	2	FACETS	0.77	0.655	0.896	1	0.965	1	SUBCLONAL	2	TRUE	1	0.15840274316254	2		356	410	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147582	47147582	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	27	423	1	ENST00000409792.3:c.4744G>T	p.Glu1582Ter	p.E1582*	ENST00000409792	NM_014159.6	1582	Gag/Tag	6/21	1	2	FACETS	1	0.817	1	1	0.817	1	CLONAL	1	TRUE	1	0.15840274316254	2		424	332	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199891	128199891	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	21	423	0	ENST00000341105.2:c.1414C>G	p.Pro472Ala	p.P472A	ENST00000341105	NM_032638.4	472	Ccg/Gcg	6/6	0.15840274316254	3	FACETS	0.786	0.605	0.998	0.393	0.302	0.499	CLONAL	1	TRUE	1	0.15840274316254	3		423	364	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261538	142261538	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	28	274	0	ENST00000350721.4:c.3419G>T	p.Ser1140Ile	p.S1140I	ENST00000350721	NM_001184.3	1140	aGc/aTc	17/47	0.15840274316254	3	FACETS	1	0.899	1	0.606	0.485	0.743	CLONAL	1	TRUE	1	0.15840274316254	3		274	315	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144361236	144361236	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	45	334	0	ENST00000262995.4:c.1286T>G	p.Val429Gly	p.V429G	ENST00000262995	NM_207123.2	429	gTc/gGc	6/11	1	2	FACETS	0.778	0.656	0.913	1	0.962	1	CLONAL	2	TRUE	1	0.15840274316254	2		334	365	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295706	1295706	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0065575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	51	489	0				ENST00000310581	NM_198253.2	-/1132			0.15840274316254	4	FACETS	0.792	0.674	0.921	0.792	0.674	0.921	CLONAL	2	TRUE	2	0.15840274316254	4		489	471	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953601	38953601	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	48	265	0	ENST00000357387.3:c.2752G>T	p.Glu918Ter	p.E918*	ENST00000357387	NM_152756.3	918	Gaa/Taa	28/38	0.15840274316254	4	FACETS	1	0.901	1	1	0.901	1	CLONAL	2	TRUE	2	0.15840274316254	4		265	325	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335606	81335606	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	59	273	0	ENST00000222390.5:c.1754C>A	p.Ala585Asp	p.A585D	ENST00000222390	NM_000601.4	585	gCc/gAc	15/18	0.15840274316254	4	FACETS	0.896	0.776	1	1	0.963	1	CLONAL	3	TRUE	2	0.15840274316254	4		273	321	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874692	151874692	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	22	428	0	ENST00000262189.6:c.7846C>A	p.Pro2616Thr	p.P2616T	ENST00000262189	NM_170606.2	2616	Cct/Act	38/59	1	2	FACETS	0.689	0.533	0.871	0.689	0.533	0.871	SUBCLONAL	1	TRUE	1	0.15840274316254	2		428	403	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759407	133759407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749127690	NA	P-0065575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	35	352	0	ENST00000318560.5:c.1730G>A	p.Arg577Gln	p.R577Q	ENST00000318560	NM_005157.4	577	cGa/cAa	11/11	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.15840274316254	2		352	306	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619275	23619275	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224786	NA	P-0065576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	369	348	0	ENST00000261584.4:c.3260G>A	p.Ser1087Asn	p.S1087N	ENST00000261584	NM_024675.3	1087	aGc/aAc	12/13	0.653653874765023	2	FACETS	0.871	0.849	0.892	1	0.997	1	CLONAL	3	TRUE	0	0.652053926498168	2		348	433	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829228	72829228	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	220	462	0	ENST00000268489.5:c.7353G>T	p.Lys2451Asn	p.K2451N	ENST00000268489	NM_006885.3	2451	aaG/aaT	9/10	0.653653874765023	3	FACETS	1	0.991	1	0.47	0.44	0.501	CLONAL	1	TRUE	0	0.652053926498168	3		462	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577581	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0065576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	461	374	0	ENST00000269305.4:c.700_701del	p.Tyr234GlnfsTer5	p.Y234Qfs*5	ENST00000269305	NM_001126112.2	234	TAc/c	7/11	0.653653874765023	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.652053926498168	3		374	548	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738236	145738236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377343487	NA	P-0065576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	248	527	0	ENST00000428558.2:c.2749G>A	p.Glu917Lys	p.E917K	ENST00000428558	NM_004260.3	917	Gag/Aag	16/22	0.652053926498168	6	FACETS	1	0.992	1	0.356	0.332	0.38	CLONAL	1	TRUE	2	0.652053926498168	6		527	1232	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738720	145738720	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	277	649	1	ENST00000428558.2:c.2344G>C	p.Asp782His	p.D782H	ENST00000428558	NM_004260.3	782	Gat/Cat	15/22	0.652053926498168	6	FACETS	1	0.993	1	0.361	0.338	0.385	CLONAL	1	TRUE	2	0.652053926498168	6		650	1356	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2060822	2060822	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	93	396	0	ENST00000349721.2:c.1528G>C	p.Asp510His	p.D510H	ENST00000349721	NM_003070.3	510	Gat/Cat	9/34	0.653653874765023	3	FACETS	0.643	0.573	0.718	0.214	0.191	0.24	SUBCLONAL	1	TRUE	0	0.652053926498168	3		396	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0065577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	438	449	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.462939490800673	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	TRUE	0	0.462939490800673	3		451	763	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641433	18641433	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	94	407	0	ENST00000266497.5:c.2432A>C	p.Lys811Thr	p.K811T	ENST00000266497		811	aAg/aCg	17/31	0.395143676032088	4	FACETS	0.928	0.827	1	0.464	0.413	0.518	CLONAL	1	TRUE	2	0.462939490800673	4		407	640	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720262	43720262	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	151	393	0	ENST00000382044.4:c.3780del	p.Asp1261MetfsTer10	p.D1261Mfs*10	ENST00000382044	NM_001141980.1	1260	acA/ac	18/28	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.462939490800673	2		393	587	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624888	9624888	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	107	457	0	ENST00000353224.5:c.89A>G	p.Gln30Arg	p.Q30R	ENST00000353224	NM_177990.2	30	cAg/cGg	3/10	1	2	FACETS	0.887	0.799	0.98	0.887	0.799	0.98	CLONAL	1	TRUE	1	0.462939490800673	2		457	521	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30946592	30946594	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs752094508	NA	P-0065577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	100	282	1	ENST00000375687.4:c.25_27del	p.Lys9del	p.K9del	ENST00000375687	NM_015338.5	5	cAGAag/cag	1/13	0.462939490800673	10	FACETS	1	0.931	1			1	CLONAL	1	TRUE	NA	0.462939490800673	10		283	1162	SUCCESS
APC	324	MSKCC	GRCh37	5	112175098	112175098	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	118	391	0	ENST00000257430.4:c.3807del	p.Cys1270ValfsTer18	p.C1270Vfs*18	ENST00000257430	NM_000038.5	1269	atA/at	16/16	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.462939490800673	2		391	500	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946073	13946073	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	97	334	0	ENST00000405192.2:c.1023A>T	p.Lys341Asn	p.K341N	ENST00000405192	NM_001163147.1	341	aaA/aaT	10/12	0.394378185842215	5	FACETS	1	0.919	1	0.346	0.308	0.385	CLONAL	1	TRUE	2	0.462939490800673	5		334	685	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065578-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	55	663	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.757	0.653	0.869	0.757	0.653	0.869	SUBCLONAL	1	TRUE	1	0.526265989890159	2		663	276	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692980	89692980	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060500126	NA	P-0065578-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	281	365	0	ENST00000371953.3:c.464A>G	p.Tyr155Cys	p.Y155C	ENST00000371953	NM_000314.4	155	tAt/tGt	5/9	0.526265989890159	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.526265989890159	2		365	521	SUCCESS
ALB	213	MSKCC	GRCh37	4	74276041	74276041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267600248	NA	P-0065578-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	137	338	0	ENST00000295897.4:c.628C>T	p.Arg210Trp	p.R210W	ENST00000295897	NM_000477.5	210	Cgg/Tgg	6/15	1	2	FACETS	0.99	0.905	1	0.99	0.905	1	CLONAL	1	TRUE	1	0.526265989890159	2		338	526	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115267879	115267879	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065578-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	137	412	0	ENST00000438362.2:c.1854C>A	p.Asn618Lys	p.N618K	ENST00000438362	NM_001242891.1	618	aaC/aaA	15/20	1	2	FACETS	0.888	0.811	0.969	0.888	0.811	0.969	CLONAL	1	TRUE	1	0.526265989890159	2		412	586	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796762	135796763	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065578-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	132	362	0	ENST00000298552.3:c.724_725insA	p.Leu242HisfsTer13	p.L242Hfs*13	ENST00000298552	NM_001162426.1	242	ctg/cAtg	8/23	0.526265989890159	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.526265989890159	1		362	358	SUCCESS
AR	367	MSKCC	GRCh37	X	66766412	66766412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200390780	NA	P-0065579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	21	164	0	ENST00000374690.3:c.1424C>T	p.Ala475Val	p.A475V	ENST00000374690	NM_000044.3	475	gCg/gTg	1/8	1	1	FACETS	0.127	0.098	0.16	0.127	0.098	0.16	SUBCLONAL	1	TRUE	0	0.852534888676993	1		164	223	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065580-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	50	663	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		663	408	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123080	5123080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065580-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	31	339	0	ENST00000381652.3:c.3136G>A	p.Glu1046Lys	p.E1046K	ENST00000381652	NM_004972.3	1046	Gaa/Aaa	23/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		339	563	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50784095	50784095	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065580-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	95	401	0	ENST00000398568.2:c.486C>A	p.Phe162Leu	p.F162L	ENST00000398568	NM_001042412.1	162	ttC/ttA	3/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		401	587	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348664	89348664	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065580-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	97	437	0	ENST00000301030.4:c.4286A>G	p.Asp1429Gly	p.D1429G	ENST00000301030	NM_001256183.1	1429	gAt/gGt	9/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		437	596	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553255	41553255	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065580-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	76	429	0	ENST00000263253.7:c.3344G>A	p.Trp1115Ter	p.W1115*	ENST00000263253	NM_001429.3	1115	tGg/tAg	18/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		429	585	SUCCESS
ALB	213	MSKCC	GRCh37	4	74283261	74283261	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065580-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	117	343	0	ENST00000295897.4:c.1303T>C	p.Tyr435His	p.Y435H	ENST00000295897	NM_000477.5	435	Tac/Cac	11/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		343	604	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652158	36652159	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0065580-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	371	507	0	ENST00000244741.5:c.282dup	p.Pro95AlafsTer34	p.P95Afs*34	ENST00000244741	NM_000389.4	94	cgg/cGgg	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		507	848	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201802	152201802	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065580-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	126	337	0	ENST00000206249.3:c.656A>G	p.Tyr219Cys	p.Y219C	ENST00000206249	NM_000125.3	219	tAt/tGt	3/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		337	609	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0065581-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	58	355	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.92	0.795	1	0.92	0.795	1	CLONAL	1	TRUE	1	0.371752277834404	2		355	339	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073921	8073922	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0065581-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	77	459	0	ENST00000377482.5:c.737_738insCT	p.Leu246PhefsTer2	p.L246Ffs*2	ENST00000377482	NM_018948.3	246	tta/ttCTa	4/4	0.371752277834404	1	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	0	0.371752277834404	1		459	336	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150923080	150923080	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065581-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	89	403	0	ENST00000271640.5:c.1727A>T	p.His576Leu	p.H576L	ENST00000271640	NM_001145415.1	576	cAt/cTt	13/22	0.351525573008932	2	FACETS	1	0.93	1	0.53	0.472	0.591	CLONAL	1	TRUE	0	0.371752277834404	2		403	452	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838409	156838409	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065581-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	137	528	0	ENST00000524377.1:c.687del	p.Thr230GlnfsTer9	p.T230Qfs*9	ENST00000524377	NM_002529.3	229	ctC/ct	6/17	0.351525573008932	2	FACETS	0.828	0.759	0.899	0.828	0.759	0.899	CLONAL	2	TRUE	0	0.371752277834404	2		528	445	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945014	31945014	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065581-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	101	555	0	ENST00000340398.3:c.87C>A	p.Ser29Arg	p.S29R	ENST00000340398	NM_001013699.2	29	agC/agA	1/1	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.371752277834404	2		555	509	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811772	102811772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065581-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	83	501	0	ENST00000307046.8:c.412C>T	p.Pro138Ser	p.P138S	ENST00000307046	NM_001111285.1	138	Cca/Tca	4/4	1	2	FACETS	0.932	0.826	1	0.932	0.826	1	CLONAL	1	TRUE	1	0.371752277834404	2		501	479	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679418	29679419	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065581-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	72	335	0	ENST00000356175.3:c.7539dup	p.Lys2514Ter	p.K2514*	ENST00000356175	NM_000267.3	2513	act/acTt	50/57	1	2	FACETS	0.936	0.821	1	0.936	0.821	1	CLONAL	1	TRUE	1	0.371752277834404	2		335	414	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966100	25966100	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1559497961	NA	P-0065581-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	60	455	0	ENST00000435504.4:c.3106C>T	p.Leu1036Phe	p.L1036F	ENST00000435504		1036	Ctt/Ttt	13/13	1	2	FACETS	0.705	0.608	0.809	0.705	0.608	0.809	SUBCLONAL	1	TRUE	1	0.371752277834404	2		455	458	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202752	128202752	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1442352352	NA	P-0065581-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	75	435	0	ENST00000341105.2:c.968A>G	p.His323Arg	p.H323R	ENST00000341105	NM_032638.4	323	cAc/cGc	4/6	0.216730420587451	1	FACETS	0.797	0.702	0.899	0.797	0.702	0.899	INDETERMINATE	1	TRUE	0	0.371752277834404	1		435	412	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372008	55372008	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065581-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	54	492	0	ENST00000297316.4:c.698A>C	p.Asp233Ala	p.D233A	ENST00000297316	NM_022454.3	233	gAc/gCc	2/2	0.360449129751346	3	FACETS	0.893	0.765	1	0.446	0.382	0.516	CLONAL	1	TRUE	1	0.371752277834404	3		492	386	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028828	47028828	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0065581-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	72	445	0	ENST00000377604.3:c.132T>G	p.Tyr44Ter	p.Y44*	ENST00000377604	NM_001204468.1	44	taT/taG	3/24	1	2	FACETS	0.942	0.827	1	0.942	0.827	1	CLONAL	1	TRUE	1	0.371752277834404	2		445	411	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053022	180053023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750808726	NA	P-0065588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	211	550	2	ENST00000261937.6:c.1267dup	p.Gln423ProfsTer4	p.Q423Pfs*4	ENST00000261937	NM_182925.4	423	cag/cCag	10/30	0.898136233357556	3	FACETS	0.785	0.73	0.842	0.393	0.365	0.421	SUBCLONAL	1	TRUE	1	0.898136233357556	3		552	867	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016647	12016648	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0065588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	201	356	0	ENST00000353533.5:c.783_784del	p.Asp263CysfsTer4	p.D263Cfs*4	ENST00000353533	NM_003010.3	261	acAAga/acga	7/11	0.879739702215469	1	FACETS	0.893	0.853	0.932	0.893	0.853	0.932	CLONAL	1	TRUE	0	0.898136233357556	1		356	276	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061348	38061348	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	141	451	0	ENST00000250448.2:c.641G>T	p.Trp214Leu	p.W214L	ENST00000250448	NM_004496.3	214	tGg/tTg	2/2	0.898136233357556	3	FACETS	0.678	0.619	0.74	0.339	0.309	0.37	SUBCLONAL	1	TRUE	1	0.898136233357556	3		451	671	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226197	53226197	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	222	348	0	ENST00000375401.3:c.2652G>T	p.Gln884His	p.Q884H	ENST00000375401	NM_004187.3	884	caG/caT	19/26	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.898136233357556	2		348	487	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053022	180053023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750808726	NA	P-0065588-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	197	550	2	ENST00000261937.6:c.1267dup	p.Gln423ProfsTer4	p.Q423Pfs*4	ENST00000261937	NM_182925.4	423	cag/cCag	10/30	0.827113246466713	3	FACETS	0.778	0.721	0.836	0.389	0.36	0.418	SUBCLONAL	1	TRUE	1	0.832550741524507	3		552	862	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016647	12016648	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0065588-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	181	356	0	ENST00000353533.5:c.783_784del	p.Asp263CysfsTer4	p.D263Cfs*4	ENST00000353533	NM_003010.3	261	acAAga/acga	7/11	0.832550741524507	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.832550741524507	1		356	246	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061348	38061348	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065588-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	126	451	0	ENST00000250448.2:c.641G>T	p.Trp214Leu	p.W214L	ENST00000250448	NM_004496.3	214	tGg/tTg	2/2	0.827113246466713	3	FACETS	0.591	0.536	0.65	0.296	0.268	0.325	SUBCLONAL	1	TRUE	1	0.832550741524507	3		451	725	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226197	53226197	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065588-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	186	348	0	ENST00000375401.3:c.2652G>T	p.Gln884His	p.Q884H	ENST00000375401	NM_004187.3	884	caG/caT	19/26	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.832550741524507	2		348	410	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1749278	1749279	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0065589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	55	343	0	ENST00000378609.4:c.93_94del	p.Gln32AspfsTer46	p.Q32Dfs*46	ENST00000378609	NM_002074.3	31	tcTCag/tcag	4/12	1	2	FACETS	0.848	0.726	0.981	1	0.972	1	CLONAL	2	TRUE	1	0.13	2		343	499	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621900	1621900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780652877	NA	P-0065589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	35	637	0	ENST00000344749.5:c.892G>A	p.Gly298Arg	p.G298R	ENST00000344749	NM_001136139.2	298	Gga/Aga	11/19	1	2	FACETS	0.932	0.762	1	0.932	0.762	1	CLONAL	1	TRUE	1	0.13	2		637	578	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739583	41739583	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0065589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	10	177	0	ENST00000242208.4:c.388+2T>C		p.X130_splice	ENST00000242208	NM_002192.2	130			1	2	FACETS	0.874	0.593	1	0.874	0.593	1	CLONAL	1	TRUE	1	0.13	2		177	176	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	197	690	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.395646807922	2		691	739	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952086	178952086	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	129	502	0	ENST00000263967.3:c.3141T>A	p.His1047Gln	p.H1047Q	ENST00000263967	NM_006218.2	1047	caT/caA	21/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.395646807922	2		502	528	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370236	40370236	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs761761205	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	79	394	7	ENST00000293328.3:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000293328	NM_012448.3	368	Cag/ag	9/19	1	2	FACETS	0.844	0.745	0.95	0.844	0.745	0.95	CLONAL	1	TRUE	1	0.395646807922	2		401	473	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	106	381	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.395646807922	2		381	525	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	143	352	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.395646807922	2		352	482	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151289	202151290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	107	361	0	ENST00000358485.4:c.1596dup	p.Leu533ThrfsTer6	p.L533Tfs*6	ENST00000358485	NM_001080125.1	530	aga/agAa	9/9	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.395646807922	2		361	441	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278901	1278901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772441504	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	133	575	0	ENST00000310581.5:c.2141C>T	p.Thr714Met	p.T714M	ENST00000310581	NM_198253.2	714	aCg/aTg	6/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.395646807922	2		575	586	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518112	8518112	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs533774328	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	109	551	0	ENST00000356435.5:c.1279C>T	p.Arg427Ter	p.R427*	ENST00000356435		427	Cga/Tga	10/35	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.395646807922	2		551	498	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	69	394	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.395646807922	2		394	313	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661663	227661664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761880048	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	106	459	1	ENST00000305123.5:c.1791dup	p.His598AlafsTer13	p.H598Afs*13	ENST00000305123	NM_005544.2	597	-/G	1/2	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.395646807922	2		460	486	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100302	157100302	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1417035592	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	76	355	0	ENST00000346085.5:c.1243del	p.Ala415ProfsTer15	p.A415Pfs*15	ENST00000346085	NM_020732.3	413	tcG/tc	1/20	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.395646807922	2		355	344	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067242	37067242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750760	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	125	436	0	ENST00000231790.2:c.1153C>T	p.Arg385Cys	p.R385C	ENST00000231790	NM_000249.3	385	Cgt/Tgt	12/19	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.395646807922	2		436	474	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786734	3786734	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	105	515	0	ENST00000262367.5:c.4477del	p.Ile1493TyrfsTer57	p.I1493Yfs*57	ENST00000262367	NM_004380.2	1493	Ata/ta	27/31	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.395646807922	2		515	513	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	95	639	2	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.821	0.732	0.915	0.821	0.732	0.915	CLONAL	1	TRUE	1	0.395646807922	2		641	585	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424178	49424178	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs886040960	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	52	354	0	ENST00000301067.7:c.13884del	p.Thr4629ProfsTer11	p.T4629Pfs*11	ENST00000301067	NM_003482.3	4628	ccC/cc	42/54	1	2	FACETS	0.811	0.694	0.938	0.811	0.694	0.938	CLONAL	1	TRUE	1	0.395646807922	2		354	324	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55960967	55960967	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	85	355	0	ENST00000263923.4:c.2971+2T>C		p.X991_splice	ENST00000263923	NM_002253.2	991			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.395646807922	2		355	327	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698135	47698135	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63750737	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	50	161	0	ENST00000233146.2:c.1697del	p.Asn566IlefsTer24	p.N566Ifs*24	ENST00000233146	NM_000251.2	565	Aaa/aa	11/16	0.395646807922	2	FACETS	1	0.961	1	0.687	0.592	0.788	CLONAL	1	TRUE	0	0.395646807922	2		161	184	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	163	386	20	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	1	2	FACETS	1	0.976	1	1	0.993	1	CLONAL	2	TRUE	1	0.395646807922	2		406	372	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56862947	56862947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	103	502	0	ENST00000308159.5:c.853G>A	p.Gly285Arg	p.G285R	ENST00000308159	NM_014669.4	285	Ggg/Agg	9/22	1	2	FACETS	0.947	0.85	1	0.947	0.85	1	CLONAL	1	TRUE	1	0.395646807922	2		502	550	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279578	1279578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs890242322	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	110	523	1	ENST00000310581.5:c.1958G>A	p.Arg653His	p.R653H	ENST00000310581	NM_198253.2	653	cGt/cAt	5/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.395646807922	2		524	439	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47685288	47685288	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	78	316	0	ENST00000347630.2:c.662G>A	p.Arg221His	p.R221H	ENST00000347630	NM_001007230.1	221	cGt/cAt	8/11	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.395646807922	2		316	353	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271253	1271253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778051907	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	100	426	0	ENST00000310581.5:c.2449G>A	p.Ala817Thr	p.A817T	ENST00000310581	NM_198253.2	817	Gcc/Acc	8/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.395646807922	2		426	397	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250398	10250398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1010743136	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	132	623	1	ENST00000340748.4:c.3854G>A	p.Arg1285His	p.R1285H	ENST00000340748		1285	cGc/cAc	33/40	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.395646807922	2		624	564	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605204	46605204	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1459319402	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	87	417	3	ENST00000263734.3:c.1421G>C	p.Ser474Thr	p.S474T	ENST00000263734	NM_001430.4	474	aGc/aCc	10/16	0.395646807922	2	FACETS	1	0.946	1	0.551	0.491	0.615	CLONAL	1	TRUE	0	0.395646807922	2		420	399	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197435	106197435	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	121	502	2	ENST00000380013.4:c.5772del	p.Ala1925ProfsTer25	p.A1925Pfs*25	ENST00000380013	NM_001127208.2	1923	gAa/ga	11/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.395646807922	2		504	496	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647972	3647972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138799572	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	117	531	0	ENST00000294008.3:c.1192C>T	p.Arg398Trp	p.R398W	ENST00000294008	NM_032444.2	398	Cgg/Tgg	6/15	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.395646807922	2		531	551	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288765	33288765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761608312	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	128	582	0	ENST00000374542.5:c.787C>T	p.Arg263Cys	p.R263C	ENST00000374542	NM_001141970.1	263	Cgc/Tgc	3/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.395646807922	2		582	567	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279304	18279304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761752973	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	111	517	0	ENST00000222254.8:c.1756G>A	p.Ala586Thr	p.A586T	ENST00000222254	NM_005027.3	586	Gcc/Acc	14/16	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.395646807922	2		517	516	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094668	2094668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766136810	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	113	519	0	ENST00000219066.1:c.512C>T	p.Thr171Met	p.T171M	ENST00000219066	NM_002528.5	171	aCg/aTg	3/6	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.395646807922	2		519	469	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923021	44923021	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747505929	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	149	541	0	ENST00000377967.4:c.1882G>A	p.Ala628Thr	p.A628T	ENST00000377967	NM_021140.2	628	Gca/Aca	16/29	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.395646807922	2		541	582	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135650	64135650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	125	590	0	ENST00000334205.4:c.1118C>T	p.Ala373Val	p.A373V	ENST00000334205	NM_003942.2	373	gCg/gTg	10/17	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.395646807922	2		590	583	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	157	563	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.395646807922	2		563	573	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21345981	21345981	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773016962	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	129	649	0	ENST00000215739.8:c.856G>A	p.Gly286Arg	p.G286R	ENST00000215739	NM_006767.3	286	Ggg/Agg	9/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.395646807922	2		649	526	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1690639	1690640	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs766419075	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	123	501	0	ENST00000378625.1:c.475_476del	p.Gln159AlafsTer138	p.Q159Afs*138	ENST00000378625	NM_001198994.1	159	CAg/g	5/14	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.395646807922	2		501	544	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601958	43601958	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	154	661	0	ENST00000355710.3:c.1002G>T	p.Trp334Cys	p.W334C	ENST00000355710	NM_020975.4	334	tgG/tgT	5/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.395646807922	2		661	570	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47595150	47595150	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760663862	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	147	579	0	ENST00000430070.2:c.937C>T	p.Arg313Cys	p.R313C	ENST00000430070	NM_018095.4	313	Cgc/Tgc	4/4	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.395646807922	2		579	557	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94963993	94963993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	90	426	0	ENST00000536441.1:c.32C>T	p.Ala11Val	p.A11V	ENST00000536441	NM_144665.3	11	gCc/gTc	1/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.395646807922	2		426	334	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115709	108115709	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1591504622	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	61	271	0	ENST00000278616.4:c.857A>G	p.Gln286Arg	p.Q286R	ENST00000278616	NM_000051.3	286	cAa/cGa	7/63	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.395646807922	2		271	254	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120785287	120785287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138291229	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	127	550	0	ENST00000257552.2:c.821C>T	p.Ala274Val	p.A274V	ENST00000257552	NM_002442.3	274	gCg/gTg	12/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.395646807922	2		550	538	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21553830	21553830	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	83	397	0	ENST00000382592.4:c.2772G>T	p.Lys924Asn	p.K924N	ENST00000382592	NM_014572.2	924	aaG/aaT	7/8	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.395646807922	2		397	397	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50790810	50790810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	72	244	0	ENST00000307179.4:c.3056G>A	p.Arg1019Lys	p.R1019K	ENST00000307179		1019	aGg/aAg	19/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.395646807922	2		244	311	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832732	3832732	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	125	514	0	ENST00000262367.5:c.1526C>A	p.Pro509Gln	p.P509Q	ENST00000262367	NM_004380.2	509	cCa/cAa	6/31	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.395646807922	2		514	569	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661945	29661945	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854552	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	115	429	0	ENST00000356175.3:c.5839C>T	p.Arg1947Ter	p.R1947*	ENST00000356175	NM_000267.3	1947	Cga/Tga	39/57	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.395646807922	2		429	475	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690124	33690124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760685634	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	121	505	0	ENST00000308377.4:c.703G>A	p.Val235Ile	p.V235I	ENST00000308377	NM_152270.3	235	Gtc/Atc	2/5	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.395646807922	2		505	525	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105514	11105514	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	128	485	0	ENST00000358026.2:c.1430A>C	p.Asn477Thr	p.N477T	ENST00000358026	NM_001128849.1	477	aAt/aCt	9/36	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.395646807922	2		485	539	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290024	15290024	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	148	710	0	ENST00000263388.2:c.3530T>C	p.Leu1177Pro	p.L1177P	ENST00000263388	NM_000435.2	1177	cTa/cCa	22/33	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.395646807922	2		710	644	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867083	45867083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1203996233	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	145	603	0	ENST00000391945.4:c.1036G>A	p.Val346Met	p.V346M	ENST00000391945	NM_000400.3	346	Gtg/Atg	11/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.395646807922	2		603	529	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422505	47422505	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1568467157	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	124	576	0	ENST00000404338.3:c.578del	p.Lys193SerfsTer3	p.K193Sfs*3	ENST00000404338	NM_004491.4	191	acA/ac	1/6	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.395646807922	2		576	587	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419969	41419969	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	121	645	0	ENST00000373198.4:c.352G>T	p.Gly118Trp	p.G118W	ENST00000373198	NM_133170.3	118	Ggg/Tgg	3/32	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.395646807922	2		645	534	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21349215	21349217	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs746246349	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	128	635	0	ENST00000215739.8:c.1843_1845del	p.Lys615del	p.K615del	ENST00000215739	NM_006767.3	614	atGAAg/atg	16/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.395646807922	2		635	529	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191422	185191422	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	128	609	0	ENST00000265026.3:c.2306del	p.Asn769ThrfsTer55	p.N769Tfs*55	ENST00000265026	NM_004721.4	768	gAa/ga	11/14	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.395646807922	2		609	496	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526286	31526286	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	137	585	0	ENST00000344624.3:c.754C>T	p.Arg252Ter	p.R252*	ENST00000344624		252	Cga/Tga	2/33	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.395646807922	2		585	543	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80024685	80024685	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs76249824	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	39	197	0	ENST00000265081.6:c.1469C>A	p.Ser490Tyr	p.S490Y	ENST00000265081	NM_002439.4	490	tCt/tAt	10/24	1	2	FACETS	0.832	0.695	0.982	0.832	0.695	0.982	CLONAL	1	TRUE	1	0.395646807922	2		197	237	SUCCESS
APC	324	MSKCC	GRCh37	5	112179234	112179234	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	93	512	0	ENST00000257430.4:c.7943C>T	p.Ala2648Val	p.A2648V	ENST00000257430	NM_000038.5	2648	gCa/gTa	16/16	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.395646807922	2		512	432	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199888	138199888	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	144	713	1	ENST00000237289.4:c.1309del	p.Ala437ProfsTer40	p.A437Pfs*40	ENST00000237289	NM_001270507.1	436	Ggg/gg	7/9	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.395646807922	2		714	618	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336622	81336622	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	83	314	0	ENST00000222390.5:c.1600C>T	p.Gln534Ter	p.Q534*	ENST00000222390	NM_000601.4	534	Cag/Tag	14/18	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.395646807922	2		314	334	SUCCESS
AR	367	MSKCC	GRCh37	X	66766114	66766114	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065589-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	93	638	0	ENST00000374690.3:c.1130del	p.Pro377LeufsTer102	p.P377Lfs*102	ENST00000374690	NM_000044.3	376	Ccc/cc	1/8	1	2	FACETS	0.948	0.846	1	0.948	0.846	1	CLONAL	1	TRUE	1	0.395646807922	2		638	496	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	151	601	2	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.47611411763809	2		603	621	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	136	482	8	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.9	0.82	0.982	0.9	0.82	0.982	CLONAL	1	TRUE	1	0.47611411763809	2		490	635	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	218	261	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.862	0.809	0.916	1	0.994	1	CLONAL	2	TRUE	1	0.47611411763809	2		264	531	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	81	349	1	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	0.23949082369225	2	FACETS	0.828	0.733	0.928	0.414	0.366	0.464	INDETERMINATE	1	TRUE	0	0.47611411763809	2		350	411	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024683	11024683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	139	480	0	ENST00000327064.4:c.800G>A	p.Arg267His	p.R267H	ENST00000327064	NM_199141.1	267	cGc/cAc	6/16	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.47611411763809	2		480	575	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	55	369	5	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	1	2	FACETS	0.394	0.336	0.456	0.394	0.336	0.456	SUBCLONAL	1	TRUE	1	0.47611411763809	2		374	587	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	160	450	2	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.888	0.815	0.963	0.888	0.815	0.963	CLONAL	1	TRUE	1	0.47611411763809	2		452	757	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	88	477	3	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.601	0.533	0.674	0.601	0.533	0.674	SUBCLONAL	1	TRUE	1	0.47611411763809	2		480	615	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294261	11294261	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	141	427	0	ENST00000361445.4:c.2270T>C	p.Leu757Pro	p.L757P	ENST00000361445	NM_004958.3	757	cTg/cCg	14/58	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.47611411763809	2		427	571	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599234	28599234	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	71	561	0	ENST00000253063.3:c.685del	p.Gln229ArgfsTer18	p.Q229Rfs*18	ENST00000253063	NM_031459.4	227	gCc/gc	5/10	1	2	FACETS	0.439	0.382	0.499	0.439	0.382	0.499	SUBCLONAL	1	TRUE	1	0.47611411763809	2		561	680	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78426110	78426110	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	143	490	0	ENST00000370768.2:c.1415C>A	p.Pro472His	p.P472H	ENST00000370768	NM_003902.3	472	cCt/cAt	15/20	1	2	FACETS	0.93	0.85	1	0.93	0.85	1	CLONAL	1	TRUE	1	0.47611411763809	2		490	646	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699428	117699428	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	58	390	0	ENST00000369458.3:c.213G>A	p.Trp71Ter	p.W71*	ENST00000369458	NM_024626.3	71	tgG/tgA	3/6	1	2	FACETS	0.42	0.361	0.485	0.42	0.361	0.485	SUBCLONAL	1	TRUE	1	0.47611411763809	2		390	580	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462933	120462933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1450649026	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	144	514	0	ENST00000256646.2:c.5398C>T	p.Arg1800Cys	p.R1800C	ENST00000256646	NM_024408.3	1800	Cgt/Tgt	30/34	1	2	FACETS	0.995	0.911	1	0.995	0.911	1	CLONAL	1	TRUE	1	0.47611411763809	2		514	608	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465372	120465372	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1230304595	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	136	531	0	ENST00000256646.2:c.4889G>A	p.Arg1630His	p.R1630H	ENST00000256646	NM_024408.3	1630	cGc/cAc	27/34	1	2	FACETS	0.923	0.842	1	0.923	0.842	1	CLONAL	1	TRUE	1	0.47611411763809	2		531	619	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980293	201980293	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	146	433	0	ENST00000359651.3:c.33del	p.Phe11LeufsTer32	p.F11Lfs*32	ENST00000359651		10	aTt/at	1/8	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.47611411763809	2		433	563	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615146	43615146	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	49	510	0	ENST00000355710.3:c.2560T>A	p.Phe854Ile	p.F854I	ENST00000355710	NM_020975.4	854	Ttt/Att	14/20	1	2	FACETS	0.353	0.298	0.413	0.353	0.298	0.413	SUBCLONAL	1	TRUE	1	0.47611411763809	2		510	583	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724426	112724426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	154	438	0	ENST00000369452.4:c.310C>T	p.Arg104Cys	p.R104C	ENST00000369452	NM_007373.3	104	Cgt/Tgt	2/9	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.47611411763809	2		438	601	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135692	64135692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368450242	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	136	478	0	ENST00000334205.4:c.1160G>A	p.Arg387Gln	p.R387Q	ENST00000334205	NM_003942.2	387	cGg/cAg	10/17	1	2	FACETS	0.904	0.824	0.987	0.904	0.824	0.987	CLONAL	1	TRUE	1	0.47611411763809	2		478	632	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77070009	77070009	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	44	481	0	ENST00000356341.3:c.531G>T	p.Glu177Asp	p.E177D	ENST00000356341	NM_002576.4	177	gaG/gaT	6/15	1	2	FACETS	0.282	0.235	0.333	0.282	0.235	0.333	SUBCLONAL	1	TRUE	1	0.47611411763809	2		481	656	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114817	108114817	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786204543	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	97	348	0	ENST00000278616.4:c.640del	p.Ser214ProfsTer16	p.S214Pfs*16	ENST00000278616	NM_000051.3	212	Ttt/tt	6/63	1	2	FACETS	0.833	0.746	0.925	0.833	0.746	0.925	CLONAL	1	TRUE	1	0.47611411763809	2		348	489	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1039243	1039243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	38	447	0	ENST00000358495.3:c.254C>T	p.Ala85Val	p.A85V	ENST00000358495	NM_134424.2	85	gCa/gTa	4/12	1	2	FACETS	0.276	0.227	0.33	0.276	0.227	0.33	SUBCLONAL	1	TRUE	1	0.47611411763809	2		447	579	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380283	25380283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913528	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	68	565	0	ENST00000311936.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000311936	NM_004985.3	59	Gca/Aca	3/5	1	2	FACETS	0.546	0.476	0.622	0.546	0.476	0.622	SUBCLONAL	1	TRUE	1	0.47611411763809	2		565	523	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230555	46230556	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	79	416	0	ENST00000334344.6:c.805_806del	p.Leu269IlefsTer10	p.L269Ifs*10	ENST00000334344	NM_152641.2	268	tcTTta/tcta	8/21	1	2	FACETS	0.541	0.476	0.611	0.541	0.476	0.611	SUBCLONAL	1	TRUE	1	0.47611411763809	2		416	613	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856391	111856391	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	136	480	0	ENST00000341259.2:c.442C>T	p.Arg148Cys	p.R148C	ENST00000341259	NM_005475.2	148	Cgc/Tgc	2/8	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.47611411763809	2		480	533	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856434	111856434	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs776317487	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	129	505	2	ENST00000341259.2:c.489del	p.Thr165ProfsTer32	p.T165Pfs*32	ENST00000341259	NM_005475.2	162	gCc/gc	2/8	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.47611411763809	2		507	533	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112212	115112212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	135	545	0	ENST00000257566.3:c.1528C>T	p.Gln510Ter	p.Q510*	ENST00000257566	NM_016569.3	510	Caa/Taa	7/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.47611411763809	2		545	505	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434170	121434170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757068809	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	148	592	0	ENST00000257555.6:c.1061C>T	p.Thr354Met	p.T354M	ENST00000257555		354	aCg/aTg	5/10	1	2	FACETS	0.848	0.776	0.924	0.848	0.776	0.924	CLONAL	1	TRUE	1	0.47611411763809	2		592	733	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030479	49030479	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	105	292	0	ENST00000267163.4:c.1959del	p.Val654CysfsTer4	p.V654Cfs*4	ENST00000267163	NM_000321.2	652	Aaa/aa	19/27	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.47611411763809	2		292	431	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436791	110436793	+	inframe_deletion	In_Frame_Del	DEL	CCG	CCG	-	rs769193882	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	113	527	7	ENST00000375856.3:c.1608_1610del	p.Gly537del	p.G537del	ENST00000375856	NM_003749.2	536	ggCGGt/ggt	1/2	1	2	FACETS	0.805	0.726	0.887	0.805	0.726	0.887	CLONAL	1	TRUE	1	0.47611411763809	2		534	590	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738680	43738681	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	68	451	0	ENST00000382044.4:c.2944dup	p.Ala982GlyfsTer7	p.A982Gfs*7	ENST00000382044	NM_001141980.1	982	gct/gGct	14/28	1	2	FACETS	0.459	0.399	0.524	0.459	0.399	0.524	SUBCLONAL	1	TRUE	1	0.47611411763809	2		451	622	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354356	354356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781736051	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	112	410	0	ENST00000262320.3:c.1202G>A	p.Arg401His	p.R401H	ENST00000262320	NM_003502.3	401	cGc/cAc	5/11	1	2	FACETS	0.907	0.819	0.998	0.907	0.819	0.998	CLONAL	1	TRUE	1	0.47611411763809	2		410	519	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134569	2134569	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs397514939	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	66	631	0	ENST00000219476.3:c.4351del	p.Arg1451AlafsTer25	p.R1451Afs*25	ENST00000219476	NM_000548.3	1449	tCc/tc	34/42	1	2	FACETS	0.405	0.351	0.463	0.405	0.351	0.463	SUBCLONAL	1	TRUE	1	0.47611411763809	2		631	685	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858152	9858152	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764204930	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	120	484	0	ENST00000330684.3:c.3249G>T	p.Lys1083Asn	p.K1083N	ENST00000330684	NM_001134407.1	1083	aaG/aaT	13/13	1	2	FACETS	0.877	0.794	0.963	0.877	0.794	0.963	CLONAL	1	TRUE	1	0.47611411763809	2		484	575	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923497	9923497	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	73	381	0	ENST00000330684.3:c.1790C>A	p.Pro597His	p.P597H	ENST00000330684	NM_001134407.1	597	cCt/cAt	9/13	1	2	FACETS	0.678	0.595	0.767	0.678	0.595	0.767	SUBCLONAL	1	TRUE	1	0.47611411763809	2		381	452	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842662	68842662	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	158	451	2	ENST00000261769.5:c.602del	p.Pro201LeufsTer14	p.P201Lfs*14	ENST00000261769	NM_004360.3	200	Ccc/cc	5/16	1	2	FACETS	0.985	0.905	1	0.985	0.905	1	CLONAL	1	TRUE	1	0.47611411763809	2		453	674	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969978	81969978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755551138	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	105	443	0	ENST00000359376.3:c.3047C>T	p.Thr1016Met	p.T1016M	ENST00000359376	NM_002661.3	1016	aCg/aTg	27/33	1	2	FACETS	0.865	0.778	0.956	0.865	0.778	0.956	CLONAL	1	TRUE	1	0.47611411763809	2		443	510	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544554	86544554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	138	507	0	ENST00000262426.4:c.379G>A	p.Ala127Thr	p.A127T	ENST00000262426	NM_001451.2	127	Gcc/Acc	1/2	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.47611411763809	2		507	541	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349702	89349702	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	137	400	0	ENST00000301030.4:c.3248G>T	p.Gly1083Val	p.G1083V	ENST00000301030	NM_001256183.1	1083	gGg/gTg	9/13	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.47611411763809	2		400	529	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89806459	89806459	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1015729981	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	73	411	0	ENST00000389301.3:c.3877G>A	p.Glu1293Lys	p.E1293K	ENST00000389301	NM_000135.2	1293	Gag/Aag	39/43	1	2	FACETS	0.514	0.449	0.583	0.514	0.449	0.583	SUBCLONAL	1	TRUE	1	0.47611411763809	2		411	597	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	120	304	0	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	0.979	0.888	1	0.979	0.888	1	CLONAL	1	TRUE	1	0.47611411763809	2		304	515	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526546	66526546	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs387906692	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	91	429	0	ENST00000358598.2:c.1102C>T	p.Arg368Ter	p.R368*	ENST00000358598	NM_212471.2	368	Cga/Tga	11/11	1	2	FACETS	0.602	0.535	0.673	0.602	0.535	0.673	SUBCLONAL	1	TRUE	1	0.47611411763809	2		429	635	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732279	74732279	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	143	513	0	ENST00000359995.5:c.630del	p.Lys211SerfsTer21	p.K211Sfs*21	ENST00000359995	NM_001195427.1	210	ccC/cc	2/3	1	2	FACETS	0.907	0.829	0.989	0.907	0.829	0.989	CLONAL	1	TRUE	1	0.47611411763809	2		513	662	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78931483	78931483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766868607	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	66	431	0	ENST00000306801.3:c.3430G>A	p.Val1144Met	p.V1144M	ENST00000306801	NM_020761.2	1144	Gtg/Atg	29/34	1	2	FACETS	0.527	0.458	0.602	0.527	0.458	0.602	SUBCLONAL	1	TRUE	1	0.47611411763809	2		431	526	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619172	1619172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374199541	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	98	628	0	ENST00000344749.5:c.1388C>T	p.Ala463Val	p.A463V	ENST00000344749	NM_001136139.2	463	gCg/gTg	16/19	1	2	FACETS	0.566	0.505	0.631	0.566	0.505	0.631	SUBCLONAL	1	TRUE	1	0.47611411763809	2		628	727	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191072	2191072	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	74	498	1	ENST00000398665.3:c.326A>G	p.His109Arg	p.H109R	ENST00000398665	NM_032482.2	109	cAt/cGt	5/28	1	2	FACETS	0.51	0.446	0.578	0.51	0.446	0.578	SUBCLONAL	1	TRUE	1	0.47611411763809	2		499	610	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226899	2226899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762029066	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	137	603	0	ENST00000398665.3:c.4379C>T	p.Thr1460Met	p.T1460M	ENST00000398665	NM_032482.2	1460	aCg/aTg	27/28	1	2	FACETS	0.931	0.85	1	0.931	0.85	1	CLONAL	1	TRUE	1	0.47611411763809	2		603	618	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4090658	4090658	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs565860695	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	114	383	0	ENST00000262948.5:c.1141G>A	p.Gly381Ser	p.G381S	ENST00000262948	NM_030662.3	381	Ggc/Agc	11/11	1	2	FACETS	0.916	0.828	1	0.916	0.828	1	CLONAL	1	TRUE	1	0.47611411763809	2		383	523	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231539	5231539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760884281	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	57	441	0	ENST00000357368.4:c.1937C>T	p.Thr646Met	p.T646M	ENST00000357368	NM_002850.3	646	aCg/aTg	14/38	1	2	FACETS	0.507	0.436	0.585	0.507	0.436	0.585	SUBCLONAL	1	TRUE	1	0.47611411763809	2		441	472	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184585	7184585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	136	421	0	ENST00000302850.5:c.716G>A	p.Cys239Tyr	p.C239Y	ENST00000302850	NM_000208.2	239	tGc/tAc	3/22	1	2	FACETS	0.967	0.882	1	0.967	0.882	1	CLONAL	1	TRUE	1	0.47611411763809	2		421	591	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265645	10265645	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	45	480	0	ENST00000340748.4:c.1532T>G	p.Ile511Ser	p.I511S	ENST00000340748		511	aTt/aGt	19/40	1	2	FACETS	0.325	0.273	0.384	0.325	0.273	0.384	SUBCLONAL	1	TRUE	1	0.47611411763809	2		480	581	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298120	15298120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376606994	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	98	464	1	ENST00000263388.2:c.1636G>A	p.Val546Met	p.V546M	ENST00000263388	NM_000435.2	546	Gtg/Atg	11/33	1	2	FACETS	0.854	0.765	0.948	0.854	0.765	0.948	CLONAL	1	TRUE	1	0.47611411763809	2		465	482	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953860	17953860	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746488415	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	122	606	0	ENST00000458235.1:c.542C>T	p.Pro181Leu	p.P181L	ENST00000458235	NM_000215.3	181	cCg/cTg	5/24	1	2	FACETS	0.795	0.72	0.873	0.795	0.72	0.873	SUBCLONAL	1	TRUE	1	0.47611411763809	2		606	645	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36208928	36208928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	39	235	0	ENST00000222270.7:c.8C>T	p.Ala3Val	p.A3V	ENST00000222270	NM_014727.1	3	gCg/gTg	1/37	1	2	FACETS	0.596	0.496	0.705	0.596	0.496	0.705	SUBCLONAL	1	TRUE	1	0.47611411763809	2		235	275	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224087	36224087	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	121	415	1	ENST00000222270.7:c.6641del	p.Pro2214GlnfsTer2	p.P2214Qfs*2	ENST00000222270	NM_014727.1	2213	Ccc/cc	28/37	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.47611411763809	2		416	463	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752695	42752695	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1366176199	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	147	481	0	ENST00000222329.4:c.1569del	p.Leu525SerfsTer6	p.L525Sfs*6	ENST00000222329	NM_006494.2	523	ggG/gg	4/4	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.47611411763809	2		481	585	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793444	42793444	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	164	493	0	ENST00000575354.2:c.1246C>G	p.Pro416Ala	p.P416A	ENST00000575354	NM_015125.3	416	Ccc/Gcc	8/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.47611411763809	2		493	643	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	165	496	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.47611411763809	2		496	629	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660592	190660595	+	frameshift_variant	Frame_Shift_Del	DEL	AAAT	AAAT	-	rs773464464	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	104	360	0	ENST00000441310.2:c.235_238del	p.Asn79ValfsTer8	p.N79Vfs*8	ENST00000441310	NM_000534.4	77	aAAATa/aa	3/13	1	2	FACETS	0.762	0.684	0.845	0.762	0.684	0.845	SUBCLONAL	1	TRUE	1	0.47611411763809	2		360	573	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537950	212537950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	56	383	0	ENST00000342788.4:c.1655G>A	p.Cys552Tyr	p.C552Y	ENST00000342788	NM_005235.2	552	tGt/tAt	14/28	NA	2	FACETS	0.477	0.409	0.551			1	INDETERMINATE	1	TRUE	NA	0.47611411763809	2		383	493	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215609818	215609818	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	98	307	0	ENST00000260947.4:c.1876A>G	p.Asn626Asp	p.N626D	ENST00000260947	NM_000465.2	626	Aat/Gat	9/11	1	2	FACETS	0.936	0.84	1	0.936	0.84	1	CLONAL	1	TRUE	1	0.47611411763809	2		307	440	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645490	215645490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781596	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	139	465	0	ENST00000260947.4:c.1108C>T	p.Arg370Cys	p.R370C	ENST00000260947	NM_000465.2	370	Cgt/Tgt	4/11	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.47611411763809	2		465	580	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375061	31375061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147421711	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	145	475	0	ENST00000328111.2:c.458C>T	p.Ser153Leu	p.S153L	ENST00000328111	NM_006892.3	153	tCg/tTg	6/23	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.47611411763809	2		475	598	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730832	40730832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs914506046	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	157	508	0	ENST00000373198.4:c.3703C>T	p.Arg1235Cys	p.R1235C	ENST00000373198	NM_133170.3	1235	Cgc/Tgc	27/32	0.290025377701752	1	FACETS	0.88	0.81	0.952	0.88	0.81	0.952	CLONAL	1	TRUE	0	0.47611411763809	1		508	571	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41818336	41818336	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	69	548	0	ENST00000373198.4:c.38T>C	p.Leu13Pro	p.L13P	ENST00000373198	NM_133170.3	13	cTg/cCg	1/32	0.290025377701752	1	FACETS	0.392	0.341	0.446	0.392	0.341	0.446	SUBCLONAL	1	TRUE	0	0.47611411763809	1		548	564	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259202	36259202	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	101	495	0	ENST00000300305.3:c.289T>G	p.Phe97Val	p.F97V	ENST00000300305		97	Ttc/Gtc	3/8	1	2	FACETS	0.692	0.62	0.769	0.692	0.62	0.769	SUBCLONAL	1	TRUE	1	0.47611411763809	2		495	613	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	123	465	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.84	0.762	0.922	0.84	0.762	0.922	CLONAL	1	TRUE	1	0.47611411763809	2		466	615	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30730003	30730003	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	122	378	0	ENST00000295754.5:c.1524G>T	p.Gln508His	p.Q508H	ENST00000295754	NM_003242.5	508	caG/caT	6/7	1	2	FACETS	0.944	0.857	1	0.944	0.857	1	CLONAL	1	TRUE	1	0.47611411763809	2		378	543	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067255	37067255	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	118	456	0	ENST00000231790.2:c.1168del	p.Glu390AsnfsTer11	p.E390Nfs*11	ENST00000231790	NM_000249.3	389	cGg/cg	12/19	1	2	FACETS	0.843	0.763	0.927	0.843	0.763	0.927	CLONAL	1	TRUE	1	0.47611411763809	2		456	588	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142975	47142975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1478147351	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	111	302	0	ENST00000409792.3:c.4988C>T	p.Thr1663Met	p.T1663M	ENST00000409792	NM_014159.6	1663	aCg/aTg	8/21	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.47611411763809	2		302	463	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165510	47165510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	182	599	0	ENST00000409792.3:c.616G>A	p.Ala206Thr	p.A206T	ENST00000409792	NM_014159.6	206	Gca/Aca	3/21	1	2	FACETS	0.963	0.89	1	0.963	0.89	1	CLONAL	1	TRUE	1	0.47611411763809	2		599	794	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72842110	72842110	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	123	307	0	ENST00000325599.8:c.1138G>A	p.Asp380Asn	p.D380N	ENST00000325599	NM_018130.2	380	Gat/Aat	10/11	1	2	FACETS	0.966	0.877	1	0.966	0.877	1	CLONAL	1	TRUE	1	0.47611411763809	2		307	535	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204984	128204984	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369637181	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	128	532	0	ENST00000341105.2:c.457G>A	p.Gly153Arg	p.G153R	ENST00000341105	NM_032638.4	153	Ggg/Agg	3/6	1	2	FACETS	0.992	0.903	1	0.992	0.903	1	CLONAL	1	TRUE	1	0.47611411763809	2		532	542	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920520	134920520	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	98	412	0	ENST00000398015.3:c.2335A>G	p.Thr779Ala	p.T779A	ENST00000398015	NM_004441.4	779	Acc/Gcc	12/16	1	2	FACETS	0.822	0.736	0.912	0.822	0.736	0.912	CLONAL	1	TRUE	1	0.47611411763809	2		412	501	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413668	138413668	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	66	400	0	ENST00000289153.2:c.1852T>C	p.Tyr618His	p.Y618H	ENST00000289153	NM_006219.2	618	Tac/Cac	12/22	1	2	FACETS	0.485	0.421	0.554	0.485	0.421	0.554	SUBCLONAL	1	TRUE	1	0.47611411763809	2		400	572	SUCCESS
ATR	545	MSKCC	GRCh37	3	142224123	142224123	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	135	385	0	ENST00000350721.4:c.5054A>G	p.Glu1685Gly	p.E1685G	ENST00000350721	NM_001184.3	1685	gAa/gGa	29/47	1	2	FACETS	0.933	0.851	1	0.933	0.851	1	CLONAL	1	TRUE	1	0.47611411763809	2		385	608	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612286	189612286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	122	420	0	ENST00000264731.3:c.2038G>A	p.Glu680Lys	p.E680K	ENST00000264731	NM_003722.4	680	Gag/Aag	14/14	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.47611411763809	2		420	495	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796354	57796355	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	135	410	0	ENST00000309042.7:c.1336dup	p.Thr446AsnfsTer18	p.T446Nfs*18	ENST00000309042	NM_005612.4	444	gaa/gAaa	4/4	1	2	FACETS	0.937	0.855	1	0.937	0.855	1	CLONAL	1	TRUE	1	0.47611411763809	2		410	605	SUCCESS
REST	5978	MSKCC	GRCh37	4	57797468	57797469	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	136	565	0	ENST00000309042.7:c.2447_2448del	p.Leu816ProfsTer4	p.L816Pfs*4	ENST00000309042	NM_005612.4	815	cCT/c	4/4	1	2	FACETS	0.87	0.793	0.95	0.87	0.793	0.95	CLONAL	1	TRUE	1	0.47611411763809	2		565	657	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201749	66201749	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	122	442	0	ENST00000273854.3:c.2753A>G	p.Glu918Gly	p.E918G	ENST00000273854	NM_004439.5	918	gAg/gGg	16/18	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.47611411763809	2		442	502	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196213	106196213	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs370735654	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	148	410	1	ENST00000380013.4:c.4546C>T	p.Arg1516Ter	p.R1516*	ENST00000380013	NM_001127208.2	1516	Cga/Tga	11/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.47611411763809	2		411	600	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143043305	143043305	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	44	317	0	ENST00000262992.4:c.2111T>C	p.Val704Ala	p.V704A	ENST00000262992	NM_001101669.1	704	gTg/gCg	19/24	1	2	FACETS	0.44	0.369	0.518	0.44	0.369	0.518	SUBCLONAL	1	TRUE	1	0.47611411763809	2		317	420	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295674	1295674	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	142	601	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.981	0.897	1	0.981	0.897	1	CLONAL	1	TRUE	1	0.47611411763809	2		601	608	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950345	38950345	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	116	440	0	ENST00000357387.3:c.3605G>T	p.Arg1202Met	p.R1202M	ENST00000357387	NM_152756.3	1202	aGg/aTg	31/38	1	2	FACETS	0.85	0.769	0.936	0.85	0.769	0.936	CLONAL	1	TRUE	1	0.47611411763809	2		440	573	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950733	79950733	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	117	397	2	ENST00000265081.6:c.191del	p.Pro64GlnfsTer16	p.P64Qfs*16	ENST00000265081	NM_002439.4	63	Ccc/cc	1/24	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.47611411763809	2		399	441	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	139	438	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.92	0.84	1	0.92	0.84	1	CLONAL	1	TRUE	1	0.47611411763809	2		439	635	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176700669	176700671	+	splice_acceptor_variant,intron_variant	Splice_Site	TNP	ATA	ATA	CTG	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	50	364	0	ENST00000439151.2:c.5510-4_5510-2delinsCTG		p.X1837_splice	ENST00000439151	NM_022455.4	1837			1	2	FACETS	0.399	0.338	0.465	0.399	0.338	0.465	SUBCLONAL	1	TRUE	1	0.47611411763809	2		364	527	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681090	30681090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61754764	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	215	420	0	ENST00000376406.3:c.629C>T	p.Pro210Leu	p.P210L	ENST00000376406	NM_014641.2	210	cCg/cTg	5/15	0.23949082369225	2	FACETS	0.842	0.79	0.896	0.842	0.79	0.896	INDETERMINATE	2	TRUE	0	0.47611411763809	2		420	536	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813469	32813469	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	51	421	0	ENST00000354258.4:c.2314A>C	p.Ile772Leu	p.I772L	ENST00000354258	NM_000593.5	772	Atc/Ctc	11/11	0.23949082369225	2	FACETS	0.369	0.313	0.43	0.184	0.156	0.215	INDETERMINATE	1	TRUE	0	0.47611411763809	2		421	581	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967888	93967888	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	49	350	0	ENST00000369303.4:c.2039del	p.Leu680CysfsTer29	p.L680Cfs*29	ENST00000369303	NM_004440.3	680	tTg/tg	11/17	1	2	FACETS	0.404	0.342	0.472	0.404	0.342	0.472	SUBCLONAL	1	TRUE	1	0.47611411763809	2		350	510	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528051	157528051	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554237658	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	158	527	0	ENST00000346085.5:c.5776C>T	p.Arg1926Ter	p.R1926*	ENST00000346085	NM_020732.3	1926	Cga/Tga	20/20	1	2	FACETS	0.948	0.871	1	0.948	0.871	1	CLONAL	1	TRUE	1	0.47611411763809	2		527	700	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850945	128850945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762491039	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	93	393	0	ENST00000249373.3:c.1792G>A	p.Gly598Arg	p.G598R	ENST00000249373	NM_005631.4	598	Ggg/Agg	10/12	1	2	FACETS	0.844	0.754	0.939	0.844	0.754	0.939	CLONAL	1	TRUE	1	0.47611411763809	2		393	463	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012386	152012386	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	106	381	0	ENST00000262189.6:c.427del	p.Ser143ValfsTer3	p.S143Vfs*3	ENST00000262189	NM_170606.2	143	Agt/gt	4/59	1	2	FACETS	0.816	0.734	0.902	0.816	0.734	0.902	CLONAL	1	TRUE	1	0.47611411763809	2		381	546	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194608	29194608	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs552819707	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	135	522	0	ENST00000240100.2:c.1120G>A	p.Val374Met	p.V374M	ENST00000240100	NM_001394.6	374	Gtg/Atg	4/4	1	2	FACETS	0.953	0.869	1	0.953	0.869	1	CLONAL	1	TRUE	1	0.47611411763809	2		522	595	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741992	145741992	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775651175	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	141	524	1	ENST00000428558.2:c.511C>T	p.Arg171Trp	p.R171W	ENST00000428558	NM_004260.3	171	Cgg/Tgg	5/22	1	2	FACETS	0.875	0.799	0.954	0.875	0.799	0.954	CLONAL	1	TRUE	1	0.47611411763809	2		525	677	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128322020	128322020	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	225	388	0	ENST00000265960.3:c.740del	p.Pro247ArgfsTer27	p.P247Rfs*27	ENST00000265960	NM_001006617.1	247	cCg/cg	6/12	0.47611411763809	3	FACETS	0.884	0.828	0.941	0.884	0.828	0.941	CLONAL	2	TRUE	1	0.47611411763809	3		388	662	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293721	137293721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	106	431	0	ENST00000481739.1:c.272G>A	p.Ser91Asn	p.S91N	ENST00000481739	NM_002957.4	91	aGc/aAc	2/10	0.47611411763809	3	FACETS	0.984	0.885	1	0.492	0.442	0.545	CLONAL	1	TRUE	1	0.47611411763809	3		431	560	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222477	53222477	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	129	278	0	ENST00000375401.3:c.4355del	p.Gly1452AlafsTer26	p.G1452Afs*26	ENST00000375401	NM_004187.3	1452	gGc/gc	26/26	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.47611411763809	1		278	287	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0065598-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	22	597	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.166831192367849	1	FACETS	0.757	0.587	0.956	0.757	0.587	0.956	CLONAL	1	TRUE	0	0.16	1		597	334	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0065598-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	27	379	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.166831192367849	1	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	0	0.16	1		379	261	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335863	73335863	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065598-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	25	285	0	ENST00000377767.4:c.2432C>T	p.Ala811Val	p.A811V	ENST00000377767	NM_014953.3	811	gCa/gTa	18/21	1	2	FACETS	0.974	0.768	1	0.974	0.768	1	CLONAL	1	TRUE	1	0.16	2		285	321	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866386	37866386	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065598-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	30	509	0	ENST00000269571.5:c.691C>G	p.Leu231Val	p.L231V	ENST00000269571		231	Ctg/Gtg	6/27	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.16	2		509	325	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0065598-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	112	597	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.678822953115603	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.678822953115603	1		597	195	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0065598-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	29	379	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.11136808538696	4	FACETS	0.815	0.674	0.965	0.815	0.674	0.965	INDETERMINATE	2	TRUE	2	0.678822953115603	4		379	88	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866386	37866386	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065598-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	124	509	0	ENST00000269571.5:c.691C>G	p.Leu231Val	p.L231V	ENST00000269571		231	Ctg/Gtg	6/27	0.610211653583176	3	FACETS	1	0.97	1	0.572	0.521	0.624	CLONAL	1	TRUE	1	0.678822953115603	3		509	428	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0065599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	23	344	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	1	2	FACETS	0.779	0.609	0.974	0.779	0.609	0.974	CLONAL	1	TRUE	1	0.24	2		344	246	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953040	2953040	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141751925	NA	P-0065599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	70	299	0	ENST00000396946.4:c.2900G>A	p.Arg967His	p.R967H	ENST00000396946	NM_032415.4	967	cGc/cAc	22/25	1	2	FACETS	0.953	0.838	1	1	0.981	1	CLONAL	2	TRUE	1	0.24	2		299	306	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420760	49420761	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AT	novel	NA	P-0065599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	24	350	1	ENST00000301067.7:c.14988_14989delinsAT	p.Gln4997Ter	p.Q4997*	ENST00000301067	NM_003482.3	4996	atCCag/atATag	48/54	0.156808624646718	3	FACETS	0.713	0.56	0.89	0.357	0.28	0.445	SUBCLONAL	1	TRUE	1	0.24	3		351	314	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178941873	178941873	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	19	161	0	ENST00000263967.3:c.2192A>G	p.Gln731Arg	p.Q731R	ENST00000263967	NM_006218.2	731	cAg/cGg	15/21	1	2	FACETS	0.646	0.491	0.828	0.646	0.491	0.828	SUBCLONAL	1	TRUE	1	0.24	2		161	245	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420760	49420760	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	22	351	0	ENST00000301067.7:c.14989C>T	p.Gln4997Ter	p.Q4997*	ENST00000301067	NM_003482.3	4997	Cag/Tag	48/54	0.156808624646718	3	FACETS	0.656	0.509	0.827	0.328	0.254	0.414	SUBCLONAL	1	TRUE	1	0.24	3		351	313	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81960768	81960768	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	74	539	0	ENST00000359376.3:c.2499G>T	p.Glu833Asp	p.E833D	ENST00000359376	NM_002661.3	833	gaG/gaT	23/33	1	2	FACETS	0.372	0.325	0.424	0.372	0.325	0.424	SUBCLONAL	1	TRUE	1	0.44266378259564	2		539	898	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	253	601	2	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.44266378259564	2		603	1059	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	124	663	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.741	0.671	0.815	0.741	0.671	0.815	SUBCLONAL	1	TRUE	1	0.44266378259564	2		663	756	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	161	607	1	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	0.268584667926638	3	FACETS	0.673	0.615	0.734	0.337	0.307	0.367	SUBCLONAL	1	TRUE	1	0.44266378259564	3		608	1320	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	224	554	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	0.911	0.848	0.977	0.911	0.848	0.977	CLONAL	1	TRUE	1	0.44266378259564	2		554	1111	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778944	9778944	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	142	591	0	ENST00000377346.4:c.1213C>A	p.Arg405Ser	p.R405S	ENST00000377346	NM_005026.3	405	Cgc/Agc	9/24	1	2	FACETS	0.572	0.52	0.627	0.572	0.52	0.627	SUBCLONAL	1	TRUE	1	0.44266378259564	2		591	1121	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782604	9782604	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	104	404	0	ENST00000377346.4:c.2366T>G	p.Leu789Arg	p.L789R	ENST00000377346	NM_005026.3	789	cTg/cGg	19/24	1	2	FACETS	0.581	0.52	0.646	0.581	0.52	0.646	SUBCLONAL	1	TRUE	1	0.44266378259564	2		404	809	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199368	11199368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761298829	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	55	436	0	ENST00000361445.4:c.5123C>T	p.Ala1708Val	p.A1708V	ENST00000361445	NM_004958.3	1708	gCc/gTc	36/58	1	2	FACETS	0.318	0.271	0.37	0.318	0.271	0.37	SUBCLONAL	1	TRUE	1	0.44266378259564	2		436	781	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316110	11316110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	124	537	0	ENST00000361445.4:c.644C>T	p.Ala215Val	p.A215V	ENST00000361445	NM_004958.3	215	gCc/gTc	5/58	1	2	FACETS	0.498	0.449	0.549	0.498	0.449	0.549	SUBCLONAL	1	TRUE	1	0.44266378259564	2		537	1126	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36823877	36823877	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373166224	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	104	448	0	ENST00000373129.3:c.305C>T	p.Thr102Met	p.T102M	ENST00000373129	NM_032017.1	102	aCg/aTg	5/12	1	2	FACETS	0.555	0.497	0.618	0.555	0.497	0.618	SUBCLONAL	1	TRUE	1	0.44266378259564	2		448	846	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46733197	46733197	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754817150	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	122	476	1	ENST00000371975.4:c.958C>T	p.Arg320Trp	p.R320W	ENST00000371975	NM_003579.3	320	Cgg/Tgg	9/18	1	2	FACETS	0.533	0.481	0.588	0.533	0.481	0.588	SUBCLONAL	1	TRUE	1	0.44266378259564	2		477	1034	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46736442	46736442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	92	463	0	ENST00000371975.4:c.1154C>T	p.Thr385Ile	p.T385I	ENST00000371975	NM_003579.3	385	aCc/aTc	10/18	1	2	FACETS	0.473	0.419	0.53	0.473	0.419	0.53	SUBCLONAL	1	TRUE	1	0.44266378259564	2		463	879	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248461	59248461	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1185	101	677	0	ENST00000371222.2:c.282del	p.Thr95ProfsTer9	p.T95Pfs*9	ENST00000371222	NM_002228.3	94	ccC/cc	1/1	1	2	FACETS	0.355	0.316	0.397	0.355	0.316	0.397	SUBCLONAL	1	TRUE	1	0.44266378259564	2		677	1286	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78435634	78435635	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	20	383	0	ENST00000370768.2:c.185dup	p.Gln63ThrfsTer14	p.Q63Tfs*14	ENST00000370768	NM_003902.3	62	gga/ggGa	2/20	1	2	FACETS	0.286	0.218	0.365	0.286	0.218	0.365	SUBCLONAL	1	TRUE	1	0.44266378259564	2		383	316	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165599	118165599	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779398843	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	230	601	0	ENST00000369448.3:c.109G>A	p.Gly37Arg	p.G37R	ENST00000369448	NM_017709.3	37	Gga/Aga	2/2	1	2	FACETS	0.929	0.866	0.995	0.929	0.866	0.995	CLONAL	1	TRUE	1	0.44266378259564	2		601	1118	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150935128	150935128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761722681	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	65	493	0	ENST00000271640.5:c.3224G>A	p.Arg1075His	p.R1075H	ENST00000271640	NM_001145415.1	1075	cGc/cAc	18/22	1	2	FACETS	0.324	0.28	0.372	0.324	0.28	0.372	SUBCLONAL	1	TRUE	1	0.44266378259564	2		493	906	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745623	162745623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs572243397	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	127	507	0	ENST00000367921.3:c.2038C>T	p.Arg680Cys	p.R680C	ENST00000367921	NM_006182.2	680	Cgc/Tgc	15/18	1	2	FACETS	0.564	0.51	0.621	0.564	0.51	0.621	SUBCLONAL	1	TRUE	1	0.44266378259564	2		507	1017	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615093	43615093	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	119	650	0	ENST00000355710.3:c.2507G>T	p.Ser836Ile	p.S836I	ENST00000355710	NM_020975.4	836	aGc/aTc	14/20	1	2	FACETS	0.472	0.424	0.522	0.472	0.424	0.522	SUBCLONAL	1	TRUE	1	0.44266378259564	2		650	1140	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619164	43619164	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	160	629	0	ENST00000355710.3:c.2849del	p.Asn950ThrfsTer15	p.N950Tfs*15	ENST00000355710	NM_020975.4	949	ggA/gg	17/20	1	2	FACETS	0.657	0.601	0.715	0.657	0.601	0.715	SUBCLONAL	1	TRUE	1	0.44266378259564	2		629	1101	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405652	70405652	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	74	455	0	ENST00000373644.4:c.3171del	p.Lys1057AsnfsTer25	p.K1057Nfs*25	ENST00000373644	NM_030625.2	1056	Aaa/aa	4/12	1	2	FACETS	0.434	0.379	0.493	0.434	0.379	0.493	SUBCLONAL	1	TRUE	1	0.44266378259564	2		455	771	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	42	153	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.44266378259564	2		153	153	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	60	285	0	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	0.526	0.454	0.605	0.526	0.454	0.605	SUBCLONAL	1	TRUE	1	0.44266378259564	2		285	515	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998981	100998981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1321866717	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	95	576	1	ENST00000325455.5:c.821G>A	p.Arg274His	p.R274H	ENST00000325455	NM_001202474.3	274	cGc/cAc	1/8	1	2	FACETS	0.418	0.371	0.468	0.418	0.371	0.468	SUBCLONAL	1	TRUE	1	0.44266378259564	2		577	1028	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102033222	102033222	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	87	530	0	ENST00000282441.5:c.608G>T	p.Arg203Met	p.R203M	ENST00000282441	NM_001130145.2	203	aGg/aTg	3/9	1	2	FACETS	0.396	0.349	0.446	0.396	0.349	0.446	SUBCLONAL	1	TRUE	1	0.44266378259564	2		530	993	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216623	108216623	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs749193688	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	56	474	0	ENST00000278616.4:c.8572A>G	p.Thr2858Ala	p.T2858A	ENST00000278616	NM_000051.3	2858	Act/Gct	58/63	1	2	FACETS	0.645	0.555	0.744	0.645	0.555	0.744	SUBCLONAL	1	TRUE	1	0.44266378259564	2		474	392	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236200	108236200	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555152041	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	95	560	0	ENST00000278616.4:c.9136A>G	p.Ser3046Gly	p.S3046G	ENST00000278616	NM_000051.3	3046	Agc/Ggc	63/63	1	2	FACETS	0.483	0.429	0.54	0.483	0.429	0.54	SUBCLONAL	1	TRUE	1	0.44266378259564	2		560	889	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348807	118348807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555038090	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	119	492	0	ENST00000534358.1:c.3460C>T	p.Arg1154Trp	p.R1154W	ENST00000534358	NM_005933.3	1154	Cgg/Tgg	5/36	1	2	FACETS	0.534	0.481	0.591	0.534	0.481	0.591	SUBCLONAL	1	TRUE	1	0.44266378259564	2		492	1006	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499631	18499631	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	75	484	0	ENST00000266497.5:c.1486G>A	p.Val496Ile	p.V496I	ENST00000266497		496	Gtc/Atc	10/31	1	2	FACETS	0.422	0.369	0.479	0.422	0.369	0.479	SUBCLONAL	1	TRUE	1	0.44266378259564	2		484	803	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	114	446	1	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.735	0.662	0.811	0.735	0.662	0.811	SUBCLONAL	1	TRUE	1	0.44266378259564	2		447	701	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422640	49422640	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	100	545	0	ENST00000301067.7:c.14353A>G	p.Met4785Val	p.M4785V	ENST00000301067	NM_003482.3	4785	Atg/Gtg	45/54	0.268584667926638	3	FACETS	0.456	0.406	0.51	0.228	0.203	0.255	SUBCLONAL	1	TRUE	1	0.44266378259564	3		545	1210	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	338	515	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	0.268584667926638	3	FACETS	0.895	0.848	0.943	0.895	0.848	0.943	CLONAL	2	TRUE	1	0.44266378259564	3		515	1042	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	103	567	3	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	0.268584667926638	3	FACETS	0.479	0.427	0.535	0.24	0.213	0.268	SUBCLONAL	1	TRUE	1	0.44266378259564	3		570	1186	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888199	112888199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918454	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	160	480	0	ENST00000351677.2:c.215C>T	p.Ala72Val	p.A72V	ENST00000351677	NM_002834.3	72	gCc/gTc	3/16	0.268584667926638	3	FACETS	0.966	0.886	1	0.483	0.443	0.525	CLONAL	1	TRUE	1	0.44266378259564	3		480	914	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915716	112915716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	214	505	0	ENST00000351677.2:c.989C>T	p.Thr330Ile	p.T330I	ENST00000351677	NM_002834.3	330	aCa/aTa	9/16	0.268584667926638	3	FACETS	1	0.984	1	0.601	0.558	0.645	CLONAL	1	TRUE	1	0.44266378259564	3		505	983	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112259	115112259	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1208681777	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	92	585	0	ENST00000257566.3:c.1481C>T	p.Ala494Val	p.A494V	ENST00000257566	NM_016569.3	494	gCc/gTc	7/8	0.268584667926638	3	FACETS	0.446	0.395	0.501	0.223	0.197	0.251	SUBCLONAL	1	TRUE	1	0.44266378259564	3		585	1139	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907216	32907216	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	53	531	0	ENST00000380152.3:c.1601A>T	p.Glu534Val	p.E534V	ENST00000380152		534	gAa/gTa	10/27	1	2	FACETS	0.433	0.369	0.503	0.433	0.369	0.503	SUBCLONAL	1	TRUE	1	0.44266378259564	2		531	553	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911073	32911074	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359335	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	48	440	1	ENST00000380152.3:c.2588dup	p.Asn863LysfsTer18	p.N863Kfs*18	ENST00000380152		861	caa/cAaa	11/27	1	2	FACETS	0.563	0.477	0.657	0.563	0.477	0.657	SUBCLONAL	1	TRUE	1	0.44266378259564	2		441	385	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878058	48878058	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1226865525	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	116	501	0	ENST00000267163.4:c.13del	p.Thr5ProfsTer60	p.T5Pfs*60	ENST00000267163	NM_000321.2	4	Aaa/aa	1/27	1	2	FACETS	0.53	0.477	0.586	0.53	0.477	0.586	SUBCLONAL	1	TRUE	1	0.44266378259564	2		501	989	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281036	49281036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	86	470	0	ENST00000282018.3:c.83G>A	p.Ser28Asn	p.S28N	ENST00000282018	NM_020377.2	28	aGc/aAc	1/1	1	2	FACETS	0.546	0.482	0.613	0.546	0.482	0.613	SUBCLONAL	1	TRUE	1	0.44266378259564	2		470	712	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42002990	42002990	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	80	507	0	ENST00000219905.7:c.2527G>T	p.Gly843Cys	p.G843C	ENST00000219905	NM_001164273.1	843	Ggt/Tgt	8/24	1	2	FACETS	0.456	0.401	0.516	0.456	0.401	0.516	SUBCLONAL	1	TRUE	1	0.44266378259564	2		507	792	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007896	45007897	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	124	464	0	ENST00000558401.1:c.346+1dup		p.W115fs	ENST00000558401	NM_004048.2	115	tgg/tGgg	2/4	1	2	FACETS	0.624	0.564	0.687	0.624	0.564	0.687	SUBCLONAL	1	TRUE	1	0.44266378259564	2		464	898	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50733661	50733661	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1567603601	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	70	370	0	ENST00000307179.4:c.226del	p.Arg76AspfsTer36	p.R76Dfs*36	ENST00000307179		74	Aaa/aa	3/20	1	2	FACETS	0.508	0.443	0.579	0.508	0.443	0.579	SUBCLONAL	1	TRUE	1	0.44266378259564	2		370	622	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	111	482	8	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.575	0.516	0.637	0.575	0.516	0.637	SUBCLONAL	1	TRUE	1	0.44266378259564	2		490	872	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658460	3658460	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776018346	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	139	462	0	ENST00000294008.3:c.506C>T	p.Ser169Leu	p.S169L	ENST00000294008	NM_032444.2	169	tCg/tTg	2/15	1	2	FACETS	0.658	0.598	0.72	0.658	0.598	0.72	SUBCLONAL	1	TRUE	1	0.44266378259564	2		462	955	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781450	3781450	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs770154926	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	87	526	0	ENST00000262367.5:c.4915G>T	p.Ala1639Ser	p.A1639S	ENST00000262367	NM_004380.2	1639	Gct/Tct	30/31	1	2	FACETS	0.416	0.368	0.469	0.416	0.368	0.469	SUBCLONAL	1	TRUE	1	0.44266378259564	2		526	944	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348842	11348842	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	111	489	0	ENST00000332029.2:c.494del	p.Pro165ArgfsTer40	p.P165Rfs*40	ENST00000332029	NM_003745.1	165	cCg/cg	2/2	1	2	FACETS	0.574	0.515	0.636	0.574	0.515	0.636	SUBCLONAL	1	TRUE	1	0.44266378259564	2		489	874	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867343	68867343	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142927667	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	102	516	0	ENST00000261769.5:c.2590G>A	p.Glu864Lys	p.E864K	ENST00000261769	NM_004360.3	864	Gaa/Aaa	16/16	1	2	FACETS	0.418	0.373	0.467	0.418	0.373	0.467	SUBCLONAL	1	TRUE	1	0.44266378259564	2		516	1102	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89865629	89865629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1010833101	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	105	538	0	ENST00000389301.3:c.838G>A	p.Ala280Thr	p.A280T	ENST00000389301	NM_000135.2	280	Gct/Act	10/43	1	2	FACETS	0.472	0.422	0.526	0.472	0.422	0.526	SUBCLONAL	1	TRUE	1	0.44266378259564	2		538	1005	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	111	509	3	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.462	0.414	0.513	0.462	0.414	0.513	SUBCLONAL	1	TRUE	1	0.44266378259564	2		512	1086	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546031	29546031	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	64	436	0	ENST00000356175.3:c.1539del	p.Lys513AsnfsTer13	p.K513Nfs*13	ENST00000356175	NM_000267.3	512	agA/ag	14/57	1	2	FACETS	0.318	0.274	0.366	0.318	0.274	0.366	SUBCLONAL	1	TRUE	1	0.44266378259564	2		436	909	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679411	33679411	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	82	503	0	ENST00000308377.4:c.2670del	p.Lys890AsnfsTer27	p.K890Nfs*27	ENST00000308377	NM_152270.3	890	aaA/aa	5/5	1	2	FACETS	0.399	0.351	0.451	0.399	0.351	0.451	SUBCLONAL	1	TRUE	1	0.44266378259564	2		503	928	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33689905	33689905	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	114	533	0	ENST00000308377.4:c.922C>T	p.Leu308Phe	p.L308F	ENST00000308377	NM_152270.3	308	Ctc/Ttc	2/5	1	2	FACETS	0.47	0.422	0.521	0.47	0.422	0.521	SUBCLONAL	1	TRUE	1	0.44266378259564	2		533	1096	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686901	37686901	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	74	397	1	ENST00000447079.4:c.3810del	p.Gly1271AspfsTer23	p.G1271Dfs*23	ENST00000447079	NM_015083.1	1269	Ccc/cc	14/14	1	2	FACETS	0.407	0.356	0.463	0.407	0.356	0.463	SUBCLONAL	1	TRUE	1	0.44266378259564	2		398	821	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866710	37866710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258412021	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	51	546	0	ENST00000269571.5:c.877G>A	p.Ala293Thr	p.A293T	ENST00000269571		293	Gcc/Acc	7/27	1	2	FACETS	0.199	0.168	0.233	0.199	0.168	0.233	SUBCLONAL	1	TRUE	1	0.44266378259564	2		546	1160	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369263	40369264	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	96	574	0	ENST00000293328.3:c.1294dup	p.Ala432GlyfsTer14	p.A432Gfs*14	ENST00000293328	NM_012448.3	432	gca/gGca	11/19	1	2	FACETS	0.43	0.382	0.481	0.43	0.382	0.481	SUBCLONAL	1	TRUE	1	0.44266378259564	2		574	1009	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435135	56435135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746854614	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	182	683	0	ENST00000407977.2:c.2002C>T	p.Arg668Trp	p.R668W	ENST00000407977		668	Cgg/Tgg	9/10	1	2	FACETS	0.605	0.557	0.656	0.605	0.557	0.656	SUBCLONAL	1	TRUE	1	0.44266378259564	2		683	1359	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1229	131	910	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.435	0.393	0.479	0.435	0.393	0.479	SUBCLONAL	1	TRUE	1	0.44266378259564	2		916	1360	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119910	70119910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1297203260	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	129	563	1	ENST00000245479.2:c.916del	p.Val306CysfsTer77	p.V306Cfs*77	ENST00000245479	NM_000346.3	304	ccG/cc	3/3	1	2	FACETS	0.58	0.525	0.638	0.58	0.525	0.638	SUBCLONAL	1	TRUE	1	0.44266378259564	2		564	1005	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120031	70120031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	76	339	0	ENST00000245479.2:c.1037del	p.Pro346ArgfsTer37	p.P346Rfs*37	ENST00000245479	NM_000346.3	345	Ccc/cc	3/3	1	2	FACETS	0.412	0.36	0.467	0.412	0.36	0.467	SUBCLONAL	1	TRUE	1	0.44266378259564	2		339	834	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120115	70120115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	104	526	0	ENST00000245479.2:c.1121del	p.Pro374ArgfsTer9	p.P374Rfs*9	ENST00000245479	NM_000346.3	373	Ccc/cc	3/3	1	2	FACETS	0.519	0.464	0.578	0.519	0.464	0.578	SUBCLONAL	1	TRUE	1	0.44266378259564	2		526	905	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733223	74733223	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	153	506	0	ENST00000359995.5:c.20del	p.Pro7LeufsTer7	p.P7Lfs*7	ENST00000359995	NM_001195427.1	7	cCt/ct	1/3	1	2	FACETS	0.647	0.591	0.706	0.647	0.591	0.706	SUBCLONAL	1	TRUE	1	0.44266378259564	2		506	1069	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78811790	78811790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780423020	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	76	398	0	ENST00000306801.3:c.1205C>T	p.Ala402Val	p.A402V	ENST00000306801	NM_020761.2	402	gCg/gTg	10/34	1	2	FACETS	0.44	0.385	0.499	0.44	0.385	0.499	SUBCLONAL	1	TRUE	1	0.44266378259564	2		398	781	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609314	39609314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766344105	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	75	381	0	ENST00000262039.4:c.1616G>A	p.Arg539His	p.R539H	ENST00000262039	NM_002647.2	539	cGt/cAt	15/25	1	2	FACETS	0.501	0.438	0.568	0.501	0.438	0.568	SUBCLONAL	1	TRUE	1	0.44266378259564	2		381	677	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223046	1223046	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	113	636	0	ENST00000326873.7:c.983C>T	p.Thr328Ile	p.T328I	ENST00000326873	NM_000455.4	328	aCc/aTc	8/10	1	2	FACETS	0.444	0.398	0.493	0.444	0.398	0.493	SUBCLONAL	1	TRUE	1	0.44266378259564	2		636	1150	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244243	5244243	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1390768500	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	66	411	0	ENST00000357368.4:c.1239del	p.Ser414AlafsTer30	p.S414Afs*30	ENST00000357368	NM_002850.3	413	ccC/cc	11/38	1	2	FACETS	0.26	0.224	0.298	0.26	0.224	0.298	SUBCLONAL	1	TRUE	1	0.44266378259564	2		411	1149	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602637	10602637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777523734	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	108	627	0	ENST00000171111.5:c.941C>T	p.Thr314Met	p.T314M	ENST00000171111	NM_203500.1	314	aCg/aTg	3/6	1	2	FACETS	0.392	0.351	0.437	0.392	0.351	0.437	SUBCLONAL	1	TRUE	1	0.44266378259564	2		627	1244	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627730	14627730	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1252	120	698	0	ENST00000254322.2:c.340A>T	p.Thr114Ser	p.T114S	ENST00000254322	NM_006145.1	114	Acc/Tcc	2/3	1	2	FACETS	0.395	0.355	0.437	0.395	0.355	0.437	SUBCLONAL	1	TRUE	1	0.44266378259564	2		698	1372	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272347	15272347	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779314594	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	142	619	0	ENST00000263388.2:c.6092G>A	p.Arg2031His	p.R2031H	ENST00000263388	NM_000435.2	2031	cGc/cAc	33/33	1	2	FACETS	0.522	0.474	0.572	0.522	0.474	0.572	SUBCLONAL	1	TRUE	1	0.44266378259564	2		619	1230	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950364	17950364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	114	546	0	ENST00000458235.1:c.1363G>A	p.Ala455Thr	p.A455T	ENST00000458235	NM_000215.3	455	Gca/Aca	10/24	1	2	FACETS	0.483	0.433	0.535	0.483	0.433	0.535	SUBCLONAL	1	TRUE	1	0.44266378259564	2		546	1067	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18964065	18964065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	102	522	0	ENST00000262803.5:c.1062G>A	p.Met354Ile	p.M354I	ENST00000262803	NM_002911.3	354	atG/atA	8/24	1	2	FACETS	0.452	0.403	0.504	0.452	0.403	0.504	SUBCLONAL	1	TRUE	1	0.44266378259564	2		522	1020	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209011	36209011	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	40	176	1	ENST00000222270.7:c.95del	p.Gly32AlafsTer14	p.G32Afs*14	ENST00000222270	NM_014727.1	31	Ggg/gg	1/37	1	2	FACETS	0.492	0.41	0.584	0.492	0.41	0.584	SUBCLONAL	1	TRUE	1	0.44266378259564	2		177	367	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1313	158	690	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.485	0.443	0.53	0.485	0.443	0.53	SUBCLONAL	1	TRUE	1	0.44266378259564	2		691	1471	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794734	42794735	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	142	598	0	ENST00000575354.2:c.1817_1818del	p.Val606GlyfsTer83	p.V606Gfs*83	ENST00000575354	NM_015125.3	605	aGT/a	10/20	1	2	FACETS	0.615	0.559	0.673	0.615	0.559	0.673	SUBCLONAL	1	TRUE	1	0.44266378259564	2		598	1044	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796976	42796976	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	165	680	0	ENST00000575354.2:c.3437del	p.Pro1146GlnfsTer15	p.P1146Qfs*15	ENST00000575354	NM_015125.3	1145	aCc/ac	14/20	1	2	FACETS	0.553	0.506	0.602	0.553	0.506	0.602	SUBCLONAL	1	TRUE	1	0.44266378259564	2		680	1348	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906837	50906837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778135510	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	167	462	0	ENST00000440232.2:c.1225C>T	p.Arg409Trp	p.R409W	ENST00000440232	NM_002691.3	409	Cgg/Tgg	10/27	1	2	FACETS	0.948	0.872	1	0.948	0.872	1	CLONAL	1	TRUE	1	0.44266378259564	2		462	796	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471024	25471024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	85	601	0	ENST00000264709.3:c.737C>T	p.Ala246Val	p.A246V	ENST00000264709	NM_175629.2	246	gCt/gTt	7/23	0.44266378259564	2	FACETS	0.351	0.309	0.397	0.176	0.154	0.199	SUBCLONAL	1	TRUE	0	0.44266378259564	2		601	1093	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	147	310	0	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	0.44266378259564	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	0	0.44266378259564	2		310	326	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635656	47635656	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	275	386	0	ENST00000233146.2:c.328A>T	p.Lys110Ter	p.K110*	ENST00000233146	NM_000251.2	110	Aag/Tag	2/16	0.44266378259564	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.44266378259564	2		386	612	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	141	610	4	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	0.44266378259564	2	FACETS	0.604	0.55	0.662	0.302	0.275	0.331	SUBCLONAL	1	TRUE	0	0.44266378259564	2		614	1054	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033678	48033678	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	39	449	0	ENST00000234420.5:c.3889A>G	p.Ser1297Gly	p.S1297G	ENST00000234420	NM_000179.2	1297	Agc/Ggc	9/10	0.44266378259564	2	FACETS	0.373	0.309	0.445	0.187	0.154	0.223	SUBCLONAL	1	TRUE	0	0.44266378259564	2		449	472	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103827	209103827	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	66	466	0	ENST00000345146.2:c.1122G>T	p.Lys374Asn	p.K374N	ENST00000345146	NM_005896.2	374	aaG/aaT	9/10	1	2	FACETS	0.386	0.334	0.442	0.386	0.334	0.442	SUBCLONAL	1	TRUE	1	0.44266378259564	2		466	773	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368388	225368388	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1366667901	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	40	350	0	ENST00000264414.4:c.1358del	p.Asn453ThrfsTer2	p.N453Tfs*2	ENST00000264414	NM_003590.4	453	aAc/ac	9/16	1	2	FACETS	0.446	0.371	0.53	0.446	0.371	0.53	SUBCLONAL	1	TRUE	1	0.44266378259564	2		350	405	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400338	225400338	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	63	385	0	ENST00000264414.4:c.285T>A	p.Asn95Lys	p.N95K	ENST00000264414	NM_003590.4	95	aaT/aaA	3/16	1	2	FACETS	0.464	0.401	0.532	0.464	0.401	0.532	SUBCLONAL	1	TRUE	1	0.44266378259564	2		385	614	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022236	31022236	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	37	441	1	ENST00000375687.4:c.1721T>G	p.Ile574Ser	p.I574S	ENST00000375687	NM_015338.5	574	aTt/aGt	13/13	1	2	FACETS	0.239	0.196	0.287	0.239	0.196	0.287	SUBCLONAL	1	TRUE	1	0.44266378259564	2		442	700	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024224	31024224	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	121	577	0	ENST00000375687.4:c.3709T>A	p.Ser1237Thr	p.S1237T	ENST00000375687	NM_015338.5	1237	Tcc/Acc	13/13	1	2	FACETS	0.536	0.484	0.592	0.536	0.484	0.592	SUBCLONAL	1	TRUE	1	0.44266378259564	2		577	1019	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739002	40739003	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	114	454	0	ENST00000373198.4:c.3281dup	p.Glu1095GlyfsTer23	p.E1095Gfs*23	ENST00000373198	NM_133170.3	1094	ccg/ccCg	24/32	1	2	FACETS	0.575	0.517	0.637	0.575	0.517	0.637	SUBCLONAL	1	TRUE	1	0.44266378259564	2		454	895	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790165	40790165	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	133	502	0	ENST00000373198.4:c.2566del	p.Glu856SerfsTer22	p.E856Sfs*22	ENST00000373198	NM_133170.3	856	Gag/ag	18/32	1	2	FACETS	0.585	0.53	0.643	0.585	0.53	0.643	SUBCLONAL	1	TRUE	1	0.44266378259564	2		502	1027	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306628	41306628	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	82	499	0	ENST00000373198.4:c.1031A>G	p.Asn344Ser	p.N344S	ENST00000373198	NM_133170.3	344	aAc/aGc	7/32	1	2	FACETS	0.457	0.403	0.516	0.457	0.403	0.516	SUBCLONAL	1	TRUE	1	0.44266378259564	2		499	810	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961553	54961553	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750077869	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	105	523	0	ENST00000312783.6:c.79G>A	p.Val27Met	p.V27M	ENST00000312783	NM_198436.1	27	Gtg/Atg	4/10	1	2	FACETS	0.613	0.549	0.681	0.613	0.549	0.681	SUBCLONAL	1	TRUE	1	0.44266378259564	2		523	774	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326159	62326159	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs115303435	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	143	529	0	ENST00000360203.5:c.3175G>A	p.Ala1059Thr	p.A1059T	ENST00000360203	NM_001283009.1	1059	Gcc/Acc	32/35	1	2	FACETS	0.655	0.596	0.716	0.655	0.596	0.716	SUBCLONAL	1	TRUE	1	0.44266378259564	2		529	987	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164875	36164875	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	116	604	0	ENST00000300305.3:c.1000C>T	p.Arg334Cys	p.R334C	ENST00000300305		334	Cgc/Tgc	8/8	1	2	FACETS	0.421	0.378	0.467	0.421	0.378	0.467	SUBCLONAL	1	TRUE	1	0.44266378259564	2		604	1245	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715678	30715678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039551	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	94	480	0	ENST00000295754.5:c.1336G>A	p.Asp446Asn	p.D446N	ENST00000295754	NM_003242.5	446	Gat/Aat	5/7	1	2	FACETS	0.475	0.422	0.532	0.475	0.422	0.532	SUBCLONAL	1	TRUE	1	0.44266378259564	2		480	894	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37061949	37061949	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	81	457	0	ENST00000231790.2:c.1033A>G	p.Thr345Ala	p.T345A	ENST00000231790	NM_000249.3	345	Acc/Gcc	11/19	1	2	FACETS	0.37	0.325	0.418	0.37	0.325	0.418	SUBCLONAL	1	TRUE	1	0.44266378259564	2		457	990	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164508	47164508	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs201756643	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	85	491	0	ENST00000409792.3:c.1618C>T	p.Arg540Ter	p.R540*	ENST00000409792	NM_014159.6	540	Cga/Tga	3/21	1	2	FACETS	0.566	0.5	0.636	0.566	0.5	0.636	SUBCLONAL	1	TRUE	1	0.44266378259564	2		491	679	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620657	52620657	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	96	475	0	ENST00000394830.3:c.3096del	p.Phe1032LeufsTer102	p.F1032Lfs*102	ENST00000394830	NM_018313.4	1032	ttT/tt	21/30	1	2	FACETS	0.532	0.473	0.594	0.532	0.473	0.594	SUBCLONAL	1	TRUE	1	0.44266378259564	2		475	816	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662971	52662971	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755190183	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	78	452	0	ENST00000394830.3:c.1382G>A	p.Arg461His	p.R461H	ENST00000394830	NM_018313.4	461	cGc/cAc	13/30	1	2	FACETS	0.515	0.452	0.583	0.515	0.452	0.583	SUBCLONAL	1	TRUE	1	0.44266378259564	2		452	684	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027035	71027035	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1440023751	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	126	629	0	ENST00000318789.4:c.1292C>T	p.Thr431Met	p.T431M	ENST00000318789	NM_032682.5	431	aCg/aTg	15/21	1	2	FACETS	0.472	0.426	0.521	0.472	0.426	0.521	SUBCLONAL	1	TRUE	1	0.44266378259564	2		629	1205	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498433	89498433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369423490	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	78	483	0	ENST00000336596.2:c.2405C>T	p.Thr802Met	p.T802M	ENST00000336596	NM_005233.5	802	aCg/aTg	14/17	1	2	FACETS	0.451	0.396	0.511	0.451	0.396	0.511	SUBCLONAL	1	TRUE	1	0.44266378259564	2		483	781	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665338	138665338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	62	552	0	ENST00000330315.3:c.227C>T	p.Thr76Met	p.T76M	ENST00000330315	NM_023067.3	76	aCg/aTg	1/1	1	2	FACETS	0.275	0.236	0.317	0.275	0.236	0.317	SUBCLONAL	1	TRUE	1	0.44266378259564	2		552	1020	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217557	142217557	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1268253442	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	45	416	1	ENST00000350721.4:c.5440del	p.Arg1814GlufsTer10	p.R1814Efs*10	ENST00000350721	NM_001184.3	1814	Aga/ga	32/47	1	2	FACETS	0.391	0.328	0.46	0.391	0.328	0.46	SUBCLONAL	1	TRUE	1	0.44266378259564	2		417	520	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430519	181430519	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	94	547	0	ENST00000325404.1:c.371A>G	p.Lys124Arg	p.K124R	ENST00000325404	NM_003106.3	124	aAg/aGg	1/1	1	2	FACETS	0.406	0.36	0.455	0.406	0.36	0.455	SUBCLONAL	1	TRUE	1	0.44266378259564	2		547	1047	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1962801	1962801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772470710	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	94	511	0	ENST00000382891.5:c.3295G>A	p.Glu1099Lys	p.E1099K	ENST00000382891	NM_133335.3	1099	Gag/Aag	18/22	1	2	FACETS	0.436	0.387	0.489	0.436	0.387	0.489	SUBCLONAL	1	TRUE	1	0.44266378259564	2		511	974	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1977081	1977081	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs947581121	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	125	521	0	ENST00000382891.5:c.3575G>A	p.Arg1192Gln	p.R1192Q	ENST00000382891	NM_133335.3	1192	cGg/cAg	20/22	1	2	FACETS	0.555	0.501	0.612	0.555	0.501	0.612	SUBCLONAL	1	TRUE	1	0.44266378259564	2		521	1018	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748144	41748144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	84	442	0	ENST00000226382.2:c.625G>A	p.Gly209Arg	p.G209R	ENST00000226382	NM_003924.3	209	Ggg/Agg	3/3	1	2	FACETS	0.433	0.381	0.488	0.433	0.381	0.488	SUBCLONAL	1	TRUE	1	0.44266378259564	2		442	877	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748254	41748254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1560465736	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	198	446	1	ENST00000226382.2:c.515C>T	p.Ser172Leu	p.S172L	ENST00000226382	NM_003924.3	172	tCg/tTg	3/3	1	2	FACETS	0.949	0.879	1	0.949	0.879	1	CLONAL	1	TRUE	1	0.44266378259564	2		447	943	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067013	143067013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	62	396	0	ENST00000262992.4:c.1700C>T	p.Ala567Val	p.A567V	ENST00000262992	NM_001101669.1	567	gCc/gTc	16/24	1	2	FACETS	0.431	0.372	0.495	0.431	0.372	0.495	SUBCLONAL	1	TRUE	1	0.44266378259564	2		396	650	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	30	424	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	0.517	0.418	0.629	0.517	0.418	0.629	SUBCLONAL	1	TRUE	1	0.44266378259564	2		424	262	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293485	1293485	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs758250185	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	79	554	0	ENST00000310581.5:c.1516C>T	p.Gln506Ter	p.Q506*	ENST00000310581	NM_198253.2	506	Cag/Tag	2/16	1	2	FACETS	0.356	0.312	0.404	0.356	0.312	0.404	SUBCLONAL	1	TRUE	1	0.44266378259564	2		554	1002	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160585	56160585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	124	530	0	ENST00000399503.3:c.862del	p.Arg288GlufsTer24	p.R288Efs*24	ENST00000399503	NM_005921.1	287	Ccc/cc	4/20	1	2	FACETS	0.54	0.487	0.595	0.54	0.487	0.595	SUBCLONAL	1	TRUE	1	0.44266378259564	2		530	1038	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178577	56178579	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs750747779	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	84	465	1	ENST00000399503.3:c.3560_3562del	p.Glu1187del	p.E1187del	ENST00000399503	NM_005921.1	1184	GAA/-	14/20	1	2	FACETS	0.439	0.387	0.495	0.439	0.387	0.495	SUBCLONAL	1	TRUE	1	0.44266378259564	2		466	865	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522741	67522741	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	87	455	0	ENST00000274335.5:c.244del	p.Ile82SerfsTer32	p.I82Sfs*32	ENST00000274335		80	Aaa/aa	1/15	1	2	FACETS	0.402	0.355	0.453	0.402	0.355	0.453	SUBCLONAL	1	TRUE	1	0.44266378259564	2		455	977	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	118	261	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.803	0.726	0.884	0.803	0.726	0.884	CLONAL	1	TRUE	1	0.44266378259564	2		264	664	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	214	570	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	1	2	FACETS	0.941	0.875	1	0.941	0.875	1	CLONAL	1	TRUE	1	0.44266378259564	2		570	1027	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497245	149497245	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	71	493	0	ENST00000261799.4:c.3073del	p.Leu1025CysfsTer20	p.L1025Cfs*20	ENST00000261799	NM_002609.3	1025	Ctg/tg	22/23	1	2	FACETS	0.364	0.317	0.415	0.364	0.317	0.415	SUBCLONAL	1	TRUE	1	0.44266378259564	2		493	881	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562321	176562321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	93	597	0	ENST00000439151.2:c.217C>T	p.Arg73Trp	p.R73W	ENST00000439151	NM_022455.4	73	Cgg/Tgg	2/23	1	2	FACETS	0.442	0.392	0.496	0.442	0.392	0.496	SUBCLONAL	1	TRUE	1	0.44266378259564	2		597	950	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910707	29910707	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199474417	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	78	624	0	ENST00000376809.5:c.247T>C	p.Tyr83His	p.Y83H	ENST00000376809	NM_002116.7	83	Tat/Cat	2/8	0.241992326848162	2	FACETS	0.284	0.249	0.323	0.142	0.124	0.162	INDETERMINATE	1	TRUE	0	0.44266378259564	2		624	1239	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31239029	31239029	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	58	328	0	ENST00000376228.5:c.440A>G	p.Tyr147Cys	p.Y147C	ENST00000376228	NM_002117.5	147	tAc/tGc	3/8	0.241992326848162	2	FACETS	0.413	0.355	0.477	0.207	0.177	0.239	INDETERMINATE	1	TRUE	0	0.44266378259564	2		328	634	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31239116	31239117	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	rs769608795	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	78	441	0	ENST00000376228.5:c.352_353del	p.Thr118ProfsTer20	p.T118Pfs*20	ENST00000376228	NM_002117.5	118	ACc/c	3/8	0.241992326848162	2	FACETS	0.386	0.339	0.438	0.193	0.169	0.219	INDETERMINATE	1	TRUE	0	0.44266378259564	2		441	912	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31239458	31239460	+	missense_variant	Missense_Mutation	TNP	CTC	CTC	GTT	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1307	94	704	0	ENST00000376228.5:c.259_261delinsAAC	p.Glu87Asn	p.E87N	ENST00000376228	NM_002117.5	87	GAG/AAC	2/8	0.241992326848162	2	FACETS	0.303	0.268	0.34	0.152	0.134	0.171	INDETERMINATE	1	TRUE	0	0.44266378259564	2		704	1401	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	74	349	1	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	0.241992326848162	2	FACETS	0.44	0.384	0.5	0.22	0.192	0.25	INDETERMINATE	1	TRUE	0	0.44266378259564	2		350	760	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805355	32805355	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	102	533	0	ENST00000374899.4:c.567del	p.Phe189LeufsTer61	p.F189Lfs*61	ENST00000374899	NM_018833.2	189	ttT/tt	3/12	0.241992326848162	2	FACETS	0.47	0.419	0.524	0.235	0.209	0.262	INDETERMINATE	1	TRUE	0	0.44266378259564	2		533	981	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37141815	37141815	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	102	524	0	ENST00000373509.5:c.890A>G	p.Gln297Arg	p.Q297R	ENST00000373509	NM_002648.3	297	cAg/cGg	6/6	0.241992326848162	2	FACETS	0.455	0.406	0.507	0.227	0.203	0.254	INDETERMINATE	1	TRUE	0	0.44266378259564	2		524	1013	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982095	93982095	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779416238	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	70	490	0	ENST00000369303.4:c.1370G>A	p.Arg457Gln	p.R457Q	ENST00000369303	NM_004440.3	457	cGg/cAg	6/17	1	2	FACETS	0.348	0.303	0.398	0.348	0.303	0.398	SUBCLONAL	1	TRUE	1	0.44266378259564	2		490	908	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005515	150005515	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	187	552	0	ENST00000253339.5:c.710del	p.Pro237HisfsTer6	p.P237Hfs*6	ENST00000253339		237	cCa/ca	3/7	1	2	FACETS	0.829	0.765	0.895	0.829	0.765	0.895	CLONAL	1	TRUE	1	0.44266378259564	2		552	1019	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411729	116411729	+	intron_variant	Intron	SNP	A	A	G	rs1359046151	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	68	549	0	ENST00000397752.3:c.2887+21A>G		p.*963*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.364	0.316	0.416	0.364	0.316	0.416	SUBCLONAL	1	TRUE	1	0.44266378259564	2		549	844	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850820	128850820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780718707	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	103	417	0	ENST00000249373.3:c.1667G>A	p.Ser556Asn	p.S556N	ENST00000249373	NM_005631.4	556	aGt/aAt	10/12	1	2	FACETS	0.532	0.476	0.593	0.532	0.476	0.593	SUBCLONAL	1	TRUE	1	0.44266378259564	2		417	874	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965666	90965666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	29	386	2	ENST00000265433.3:c.1651del	p.Arg551GlyfsTer8	p.R551Gfs*8	ENST00000265433	NM_002485.4	551	Agg/gg	11/16	1	2	FACETS	0.341	0.274	0.418	0.341	0.274	0.418	SUBCLONAL	1	TRUE	1	0.44266378259564	2		388	384	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737323	145737323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369843844	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	136	664	0	ENST00000428558.2:c.3364G>A	p.Ala1122Thr	p.A1122T	ENST00000428558	NM_004260.3	1122	Gca/Aca	20/22	1	2	FACETS	0.508	0.46	0.558	0.508	0.46	0.558	SUBCLONAL	1	TRUE	1	0.44266378259564	2		664	1210	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2182174	2182174	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	87	387	0	ENST00000349721.2:c.4393G>T	p.Gly1465Cys	p.G1465C	ENST00000349721	NM_003070.3	1465	Ggc/Tgc	31/34	1	2	FACETS	0.544	0.481	0.611	0.544	0.481	0.611	SUBCLONAL	1	TRUE	1	0.44266378259564	2		387	723	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499706	8499706	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	89	531	0	ENST00000356435.5:c.2263G>T	p.Glu755Ter	p.E755*	ENST00000356435		755	Gaa/Taa	14/35	1	2	FACETS	0.391	0.346	0.44	0.391	0.346	0.44	SUBCLONAL	1	TRUE	1	0.44266378259564	2		531	1028	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020769	37020769	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	62	519	2	ENST00000358127.4:c.76G>T	p.Val26Phe	p.V26F	ENST00000358127	NM_001280556.1	26	Gtt/Ttt	2/10	1	2	FACETS	0.299	0.257	0.344	0.299	0.257	0.344	SUBCLONAL	1	TRUE	1	0.44266378259564	2		521	938	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	74	597	0	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.341	0.298	0.388	0.341	0.298	0.388	SUBCLONAL	1	TRUE	1	0.44266378259564	2		597	980	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797313	135797313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1279777367	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	119	550	0	ENST00000298552.3:c.556G>A	p.Ala186Thr	p.A186T	ENST00000298552	NM_001162426.1	186	Gca/Aca	7/23	1	2	FACETS	0.528	0.476	0.584	0.528	0.476	0.584	SUBCLONAL	1	TRUE	1	0.44266378259564	2		550	1018	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137313598	137313598	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	119	629	0	ENST00000481739.1:c.857T>C	p.Ile286Thr	p.I286T	ENST00000481739	NM_002957.4	286	aTc/aCc	6/10	1	2	FACETS	0.423	0.381	0.469	0.423	0.381	0.469	SUBCLONAL	1	TRUE	1	0.44266378259564	2		629	1270	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923086	39923087	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	100	265	0	ENST00000378444.4:c.3621dup	p.Gln1208ThrfsTer8	p.Q1208Tfs*8	ENST00000378444	NM_001123385.1	1207	-/A	8/15	1	1	FACETS	0.731	0.656	0.81	0.731	0.656	0.81	SUBCLONAL	1	TRUE	0	0.44266378259564	1		265	481	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47004901	47004901	+	intron_variant	Intron	SNP	G	G	A	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	181	357	0	ENST00000377604.3:c.-126+17G>A		p.*42*	ENST00000377604	NM_001204468.1	-/163			1	1	FACETS	0.821	0.758	0.885	0.821	0.758	0.885	CLONAL	1	TRUE	0	0.44266378259564	1		357	776	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224121	53224121	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	82	276	0	ENST00000375401.3:c.3430G>T	p.Gly1144Cys	p.G1144C	ENST00000375401	NM_004187.3	1144	Ggc/Tgc	22/26	1	1	FACETS	0.557	0.492	0.626	0.557	0.492	0.626	SUBCLONAL	1	TRUE	0	0.44266378259564	1		276	518	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412261	63412262	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	109	336	0	ENST00000330258.3:c.905dup	p.Asn302LysfsTer22	p.N302Kfs*22	ENST00000330258	NM_152424.3	302	aat/aaAt	2/2	1	1	FACETS	0.642	0.578	0.71	0.642	0.578	0.71	SUBCLONAL	1	TRUE	0	0.44266378259564	1		336	597	SUCCESS
AR	367	MSKCC	GRCh37	X	66766433	66766433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	55	160	0	ENST00000374690.3:c.1445G>A	p.Gly482Asp	p.G482D	ENST00000374690	NM_000044.3	482	gGc/gAc	1/8	1	1	FACETS	0.614	0.529	0.707	0.614	0.529	0.707	SUBCLONAL	1	TRUE	0	0.44266378259564	1		160	315	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152864529	152864529	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	94	177	0	ENST00000406277.2:c.1A>G	p.Met1?	p.M1?	ENST00000406277	NM_152274.4	1	Atg/Gtg	1/7	1		FACETS		0.752	0.931				CLONAL	1	TRUE	0	0.44266378259564	1		177	394	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438319	110438319	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs769951329	NA	P-0065610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	84	393	4	ENST00000375856.3:c.82A>C	p.Asn28His	p.N28H	ENST00000375856	NM_003749.2	28	Aac/Cac	1/2	1	2	FACETS	0.492	0.434	0.555	0.492	0.434	0.555	SUBCLONAL	1	TRUE	1	0.44266378259564	2		397	771	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065614-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	223	428	0	ENST00000397752.3:c.3028G>C	p.Asp1010His	p.D1010H	ENST00000397752	NM_000245.2	1010	Gat/Cat	14/21	0.293576616156343	3	FACETS	0.976	0.916	1	0.976	0.916	1	CLONAL	3	TRUE	0	0.297450279876823	3		428	588	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409038	4409038	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065614-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	49	374	0	ENST00000261254.3:c.733G>T	p.Ala245Ser	p.A245S	ENST00000261254	NM_001759.3	245	Gct/Tct	5/5	0.297450279876823	2	FACETS	0.802	0.68	0.934	0.401	0.34	0.467	CLONAL	1	TRUE	0	0.297450279876823	2		374	411	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827156	170827157	+	inframe_insertion,splice_region_variant	In_Frame_Ins	INS	-	-	TGA	rs746541921	NA	P-0065614-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	27	245	0	ENST00000296930.5:c.538_540dup	p.Asp180dup	p.D180dup	ENST00000296930	NM_002520.6	180	gat/gaTGAt		0.297450279876823	3	FACETS	0.612	0.487	0.754	0.306	0.243	0.377	SUBCLONAL	1	TRUE	1	0.297450279876823	3		245	341	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0065619-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	67	476	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.33057777391053	1	FACETS	0.685	0.597	0.78	0.685	0.597	0.78	SUBCLONAL	1	TRUE	0	0.357539388137162	1		476	449	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696430	47696430	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065619-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	82	495	0	ENST00000347630.2:c.393G>C	p.Trp131Cys	p.W131C	ENST00000347630	NM_001007230.1	131	tgG/tgC	6/11	1	2	FACETS	0.84	0.742	0.945	0.84	0.742	0.945	CLONAL	1	TRUE	1	0.357539388137162	2		495	546	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867267	68867267	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065619-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	84	564	0	ENST00000261769.5:c.2514C>G	p.Ser838Arg	p.S838R	ENST00000261769	NM_004360.3	838	agC/agG	16/16	1	2	FACETS	0.914	0.81	1	0.914	0.81	1	CLONAL	1	TRUE	1	0.357539388137162	2		564	514	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649029	37649030	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0065619-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	62	325	0	ENST00000447079.4:c.2135_2136del	p.Arg712LysfsTer16	p.R712Kfs*16	ENST00000447079	NM_015083.1	712	AGa/a	4/14	1	2	FACETS	0.865	0.75	0.989	0.865	0.75	0.989	CLONAL	1	TRUE	1	0.357539388137162	2		325	401	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0065620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	10	355	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.26	0.176	0.366	0.26	0.176	0.366	SUBCLONAL	1	TRUE	1	0.39	2		355	197	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0065620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	51	610	4	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.566	0.482	0.659	0.566	0.482	0.659	SUBCLONAL	1	TRUE	1	0.39	2		614	462	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	51	460	1	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	0.763	0.651	0.884	0.763	0.651	0.884	SUBCLONAL	1	TRUE	1	0.39	2		461	343	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0065620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	69	384	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.921	0.818	1	1	0.982	1	CLONAL	2	TRUE	1	0.39	2		384	192	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092815	27092815	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	116	461	0	ENST00000324856.7:c.2840del	p.Pro947HisfsTer21	p.P947Hfs*21	ENST00000324856	NM_006015.4	946	Ccc/cc	9/20	1	2	FACETS	0.862	0.786	0.94	1	0.988	1	CLONAL	2	TRUE	1	0.39	2		461	345	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233109	55233109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150899403	NA	P-0065620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	29	546	0	ENST00000275493.2:c.1859G>A	p.Cys620Tyr	p.C620Y	ENST00000275493	NM_005228.3	620	tGc/tAc	15/28	1	2	FACETS	0.378	0.303	0.464	0.378	0.303	0.464	SUBCLONAL	1	TRUE	1	0.39	2		546	393	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165786	108165786	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs753870656	NA	P-0065620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	33	430	0	ENST00000278616.4:c.4909G>T	p.Asp1637Tyr	p.D1637Y	ENST00000278616	NM_000051.3	1637	Gat/Tat	32/63	1	2	FACETS	0.711	0.583	0.854	0.711	0.583	0.854	SUBCLONAL	1	TRUE	1	0.39	2		430	238	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750639	128750639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775522201	NA	P-0065620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	124	566	0	ENST00000377970.2:c.176C>T	p.Ala59Val	p.A59V	ENST00000377970	NM_002467.4	59	gCg/gTg	2/3	1	2	FACETS	0.893	0.817	0.971	1	0.989	1	CLONAL	2	TRUE	1	0.39	2		566	356	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0065620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	42	294	2	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.778	0.653	0.914	0.778	0.653	0.914	CLONAL	1	TRUE	1	0.39	2		296	277	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296167	15296167	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	74	712	0	ENST00000263388.2:c.2197C>A	p.Leu733Met	p.L733M	ENST00000263388	NM_000435.2	733	Ctg/Atg	14/33	1	2	FACETS	0.986	0.868	1	0.986	0.868	1	CLONAL	1	TRUE	1	0.39	2		712	385	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405954	157405954	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	50	610	3	ENST00000346085.5:c.2201del	p.Gly734AlafsTer11	p.G734Afs*11	ENST00000346085	NM_020732.3	732	ccG/cc	6/20	1	2	FACETS	0.625	0.532	0.728	0.625	0.532	0.728	SUBCLONAL	1	TRUE	1	0.39	2		613	410	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527278	137527278	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146914620	NA	P-0065620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	28	378	0	ENST00000367739.4:c.368G>A	p.Arg123Gln	p.R123Q	ENST00000367739	NM_000416.2	123	cGa/cAa	3/7	1	2	FACETS	0.572	0.459	0.7	0.572	0.459	0.7	SUBCLONAL	1	TRUE	1	0.39	2		378	251	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434074	49434074	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	30	581	1	ENST00000301067.7:c.7479del	p.Phe2494SerfsTer49	p.F2494Sfs*49	ENST00000301067	NM_003482.3	2493	ggG/gg	31/54	1	2	FACETS	0.41	0.33	0.501	0.41	0.33	0.501	SUBCLONAL	1	TRUE	1	0.39	2		582	375	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0065620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	63	387	1	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.88	0.765	1	0.88	0.765	1	CLONAL	1	TRUE	1	0.39	2		388	367	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692871	89692871	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139767111	NA	P-0065620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	27	190	0	ENST00000371953.3:c.355G>T	p.Val119Phe	p.V119F	ENST00000371953	NM_000314.4	119	Gtt/Ttt	5/9	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.39	2		190	103	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274189	10274189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367543129	NA	P-0065620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	74	490	0	ENST00000330684.3:c.80C>T	p.Ala27Val	p.A27V	ENST00000330684	NM_001134407.1	27	gCg/gTg	2/13	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.39	2		490	281	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023957	27023957	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	83	494	0	ENST00000324856.7:c.1063C>T	p.Gln355Ter	p.Q355*	ENST00000324856	NM_006015.4	355	Caa/Taa	1/20	1	2	FACETS	0.8	0.716	0.888	1	0.982	1	SUBCLONAL	2	TRUE	1	0.39	2		494	266	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120469123	120469123	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs746314617	NA	P-0065620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	40	404	0	ENST00000256646.2:c.4004C>T	p.Pro1335Leu	p.P1335L	ENST00000256646	NM_024408.3	1335	cCg/cTg	24/34	1	2	FACETS	0.595	0.495	0.704	0.595	0.495	0.704	SUBCLONAL	1	TRUE	1	0.39	2		404	345	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435949	110435949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780816462	NA	P-0065620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	115	641	0	ENST00000375856.3:c.2452G>A	p.Gly818Arg	p.G818R	ENST00000375856	NM_003749.2	818	Ggg/Agg	1/2	1	2	FACETS	0.828	0.754	0.905	1	0.987	1	CLONAL	2	TRUE	1	0.39	2		641	356	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458705	120458705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	64	689	0	ENST00000256646.2:c.6640G>A	p.Ala2214Thr	p.A2214T	ENST00000256646	NM_024408.3	2214	Gcc/Acc	34/34	1	2	FACETS	0.789	0.686	0.9	0.789	0.686	0.9	SUBCLONAL	1	TRUE	1	0.39	2		689	416	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984352	201984353	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGATCCT	novel	NA	P-0065620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	19	512	0	ENST00000359651.3:c.1019_1026dup	p.Glu343ArgfsTer107	p.E343Rfs*107	ENST00000359651		339	-/GAGATCCT	8/8	1	2	FACETS	0.27	0.204	0.347	0.27	0.204	0.347	SUBCLONAL	1	TRUE	1	0.39	2		512	361	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433399	49433399	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	28	632	1	ENST00000301067.7:c.8048G>A	p.Arg2683His	p.R2683H	ENST00000301067	NM_003482.3	2683	cGc/cAc	32/54	1	2	FACETS	0.403	0.322	0.496	0.403	0.322	0.496	SUBCLONAL	1	TRUE	1	0.39	2		633	356	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639896	3639896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201294529	NA	P-0065620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	19	595	0	ENST00000294008.3:c.3743C>T	p.Ala1248Val	p.A1248V	ENST00000294008	NM_032444.2	1248	gCc/gTc	12/15	1	2	FACETS	0.28	0.212	0.36	0.28	0.212	0.36	SUBCLONAL	1	TRUE	1	0.39	2		595	348	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650667	67650667	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	136	520	0	ENST00000264010.4:c.972C>G	p.Cys324Trp	p.C324W	ENST00000264010	NM_006565.3	324	tgC/tgG	5/12	1	2	FACETS	0.945	0.87	1	1	0.991	1	CLONAL	2	TRUE	1	0.39	2		520	369	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270107	66270107	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	25	449	0	ENST00000273854.3:c.1775T>C	p.Val592Ala	p.V592A	ENST00000273854	NM_004439.5	592	gTc/gCc	8/18	1	2	FACETS	0.45	0.355	0.558	0.45	0.355	0.558	SUBCLONAL	1	TRUE	1	0.39	2		449	285	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591045	67591046	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAAGACTTGAAGAAGCAG	novel	NA	P-0065620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	50	418	0	ENST00000274335.5:c.1640_1657dup	p.Glu547_Gln552dup	p.E547_Q552dup	ENST00000274335		547	-/GAAGACTTGAAGAAGCAG	12/15	1	2	FACETS	0.994	0.851	1	0.994	0.851	1	CLONAL	1	TRUE	1	0.39	2		418	258	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508997	106508997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	31	602	0	ENST00000359195.3:c.991G>A	p.Gly331Arg	p.G331R	ENST00000359195	NM_002649.2	331	Gga/Aga	2/11	1	2	FACETS	0.443	0.358	0.538	0.443	0.358	0.538	SUBCLONAL	1	TRUE	1	0.39	2		602	359	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860245	151860245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	30	624	0	ENST00000262189.6:c.10417C>T	p.Pro3473Ser	p.P3473S	ENST00000262189	NM_170606.2	3473	Cca/Tca	43/59	1	2	FACETS	0.333	0.268	0.407	0.333	0.268	0.407	SUBCLONAL	1	TRUE	1	0.39	2		624	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519999	NA	P-0065621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	212	383	0	ENST00000269305.4:c.716A>G	p.Asn239Ser	p.N239S	ENST00000269305	NM_001126112.2	239	aAc/aGc	7/11	0.690001230804664	1	FACETS	0.982	0.928	1	0.982	0.928	1	CLONAL	1	TRUE	0	0.71007665658959	1		383	392	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433597	49433597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	60	568	0	ENST00000301067.7:c.7956G>A	p.Met2652Ile	p.M2652I	ENST00000301067	NM_003482.3	2652	atG/atA	31/54	1	2	FACETS	0.235	0.202	0.271	0.235	0.202	0.271	SUBCLONAL	1	TRUE	1	0.71007665658959	2		568	719	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0065622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	125	286	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.981	0.895	1	0.981	0.895	1	CLONAL	1	TRUE	1	0.615854735907222	2		286	414	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0065622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	210	430	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.615854735907222	1	FACETS	0.977	0.917	1	0.977	0.917	1	CLONAL	1	TRUE	0	0.615854735907222	1		430	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0065622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	182	449	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.615854735907222	1	FACETS	0.993	0.928	1	0.993	0.928	1	CLONAL	1	TRUE	0	0.615854735907222	1		451	412	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204642	108204642	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs747448699	NA	P-0065622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	150	330	0	ENST00000278616.4:c.7957A>G	p.Ile2653Val	p.I2653V	ENST00000278616	NM_000051.3	2653	Att/Gtt	54/63	1	2	FACETS	0.94	0.865	1	0.94	0.865	1	CLONAL	1	TRUE	1	0.615854735907222	2		330	518	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420885	49420885	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	230	557	0	ENST00000301067.7:c.14864C>G	p.Ser4955Cys	p.S4955C	ENST00000301067	NM_003482.3	4955	tCc/tGc	48/54	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.615854735907222	2		557	661	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130243	2130243	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45517295	NA	P-0065622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	259	656	0	ENST00000219476.3:c.3475C>T	p.Arg1159Trp	p.R1159W	ENST00000219476	NM_000548.3	1159	Cgg/Tgg	30/42	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.615854735907222	2		656	745	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274171	10274171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs960622904	NA	P-0065622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	173	486	0	ENST00000330684.3:c.98C>T	p.Ala33Val	p.A33V	ENST00000330684	NM_001134407.1	33	gCg/gTg	2/13	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.615854735907222	2		486	557	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291040	10291040	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	265	878	0	ENST00000340748.4:c.431A>T	p.Asp144Val	p.D144V	ENST00000340748		144	gAt/gTt	4/40	0.539405316210337	3	FACETS	0.9	0.843	0.96	0.45	0.421	0.48	CLONAL	1	TRUE	1	0.615854735907222	3		878	1250	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390094	89390094	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	149	451	0	ENST00000336596.2:c.843G>T	p.Leu281Phe	p.L281F	ENST00000336596	NM_005233.5	281	ttG/ttT	4/17	1	2	FACETS	0.923	0.849	1	0.923	0.849	1	CLONAL	1	TRUE	1	0.615854735907222	2		451	524	SUCCESS
APC	324	MSKCC	GRCh37	5	112175419	112175419	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	389	497	0	ENST00000257430.4:c.4128del	p.Tyr1376Ter	p.Y1376*	ENST00000257430	NM_000038.5	1376	taT/ta	16/16	0.610672876654284	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.615854735907222	2		497	623	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405027	405027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568315642	NA	P-0065622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	151	424	0	ENST00000380956.4:c.1109C>T	p.Ala370Val	p.A370V	ENST00000380956	NM_001195286.1	370	gCg/gTg	8/9	1	2	FACETS	0.963	0.887	1	0.963	0.887	1	CLONAL	1	TRUE	1	0.615854735907222	2		424	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578520	7578520	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	540	594	1	ENST00000269305.4:c.410T>A	p.Leu137Gln	p.L137Q	ENST00000269305	NM_001126112.2	137	cTg/cAg	5/11	0.486493026538736	4	FACETS	0.939	0.91	0.968	0.939	0.91	0.968	CLONAL	4	TRUE	0	0.517461180394752	4		595	843	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0065624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	69	286	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.959	0.84	1	0.959	0.84	1	CLONAL	1	TRUE	1	0.384757782499183	2		286	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579419	7579420	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs587783062	NA	P-0065624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	67	552	0	ENST00000269305.4:c.267dup	p.Ser90LeufsTer59	p.S90Lfs*59	ENST00000269305	NM_001126112.2	89	-/C	4/11	0.355617171826357	1	FACETS	0.815	0.713	0.924	0.815	0.713	0.924	CLONAL	1	TRUE	0	0.384757782499183	1		552	345	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0065624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	67	498	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	0.384757782499183	1	FACETS	0.973	0.854	1	0.973	0.854	1	CLONAL	1	TRUE	0	0.384757782499183	1		498	289	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755665	39755665	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	474	456	0	ENST00000288319.7:c.1100G>A	p.Arg367His	p.R367H	ENST00000288319	NM_182918.3	367	cGc/cAc	10/10	0.384757782499183	7	FACETS	0.979	0.944	1			1	CLONAL	6	TRUE	NA	0.384757782499183	7		456	823	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119642311	119642311	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	60	258	0	ENST00000316626.5:c.386A>C	p.Asn129Thr	p.N129T	ENST00000316626		129	aAt/aCt	4/12	1	2	FACETS	0.884	0.765	1	0.884	0.765	1	CLONAL	1	TRUE	1	0.384757782499183	2		258	353	SUCCESS
APC	324	MSKCC	GRCh37	5	112179749	112179749	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	32	471	0	ENST00000257430.4:c.8458A>T	p.Thr2820Ser	p.T2820S	ENST00000257430	NM_000038.5	2820	Act/Tct	16/16	1	2	FACETS	0.37	0.3	0.45	0.37	0.3	0.45	SUBCLONAL	1	TRUE	1	0.384757782499183	2		471	449	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840009	27840009	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	40	606	0	ENST00000328488.2:c.85A>G	p.Ser29Gly	p.S29G	ENST00000328488	NM_003533.2	29	Agc/Ggc	1/1	1	2	FACETS	0.453	0.376	0.538	0.453	0.376	0.538	SUBCLONAL	1	TRUE	1	0.384757782499183	2		606	459	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36846851	36846851	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1166397855	NA	P-0065624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	49	426	0	ENST00000358127.4:c.1088C>T	p.Pro363Leu	p.P363L	ENST00000358127	NM_001280556.1	363	cCg/cTg	9/10	0.384757782499183	1	FACETS	0.737	0.629	0.855	0.737	0.629	0.855	SUBCLONAL	1	TRUE	0	0.384757782499183	1		426	279	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	175	482	8	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.83	0.768	0.894	0.83	0.768	0.894	CLONAL	1	TRUE	1	0.682673144580431	2		490	618	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	327	910	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.682673144580431	2		916	942	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176338	24176338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	161	350	0	ENST00000263121.7:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000263121	NM_003073.3	377	Cgt/Tgt	9/9	1	2	FACETS	0.851	0.785	0.919	0.851	0.785	0.919	CLONAL	1	TRUE	1	0.682673144580431	2		350	554	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913837	32913837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359507	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	115	279	1	ENST00000380152.3:c.5351del	p.Asn1784ThrfsTer7	p.N1784Tfs*7	ENST00000380152		1782	cAa/ca	11/27	1	2	FACETS	0.936	0.852	1	0.936	0.852	1	CLONAL	1	TRUE	1	0.682673144580431	2		280	360	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867298	45867298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760337216	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	290	528	0	ENST00000391945.4:c.895C>T	p.Arg299Trp	p.R299W	ENST00000391945	NM_000400.3	299	Cgg/Tgg	10/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.682673144580431	2		528	816	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	238	498	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.802	0.75	0.856	0.802	0.75	0.856	CLONAL	1	TRUE	1	0.682673144580431	2		499	869	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	110	187	0	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	0.977	0.888	1	0.977	0.888	1	CLONAL	1	TRUE	1	0.682673144580431	2		187	330	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37038192	37038192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750206	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	194	408	0	ENST00000231790.2:c.199G>A	p.Gly67Arg	p.G67R	ENST00000231790	NM_000249.3	67	Ggg/Agg	2/19	1	2	FACETS	0.938	0.873	1	0.938	0.873	1	CLONAL	1	TRUE	1	0.682673144580431	2		408	606	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937164	39937164	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	246	195	0	ENST00000378444.4:c.19del	p.Leu7CysfsTer9	p.L7Cfs*9	ENST00000378444	NM_001123385.1	7	Ctg/tg	2/15	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.682673144580431	1		195	374	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	252	455	0	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.899	0.844	0.956	0.899	0.844	0.956	CLONAL	1	TRUE	1	0.682673144580431	2		455	821	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150022976	150022976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373625760	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	178	378	0	ENST00000253339.5:c.287G>A	p.Arg96Gln	p.R96Q	ENST00000253339		96	cGg/cAg	1/7	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.682673144580431	2		378	515	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931452	131931452	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507178	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	200	390	12	ENST00000265335.6:c.2165del	p.Lys722ArgfsTer14	p.K722Rfs*14	ENST00000265335		719	ctA/ct	13/25	1	2	FACETS	0.983	0.917	1	0.983	0.917	1	CLONAL	1	TRUE	1	0.682673144580431	2		402	596	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	285	520	6	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.682673144580431	2		526	831	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	280	583	3	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.999	0.942	1	0.999	0.942	1	CLONAL	1	TRUE	1	0.682673144580431	2		586	821	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171680	36171682	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs771972670	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	43	508	0	ENST00000300305.3:c.883_885del	p.Ser295del	p.S295del	ENST00000300305		295	TCT/-	7/8	1	2	FACETS	0.153	0.127	0.182	0.153	0.127	0.182	SUBCLONAL	1	TRUE	1	0.682673144580431	2		508	822	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725043	89725043	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1057517809	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	95	206	0	ENST00000371953.3:c.1027-1G>A		p.X343_splice	ENST00000371953	NM_000314.4	343			0.682673144580431	1	FACETS	0.945	0.863	1	0.945	0.863	1	CLONAL	1	TRUE	0	0.682673144580431	1		206	194	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260672	1260672	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201272197	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	262	572	0	ENST00000310581.5:c.2887G>A	p.Gly963Ser	p.G963S	ENST00000310581	NM_198253.2	963	Ggc/Agc	12/16	1	2	FACETS	0.968	0.91	1	0.968	0.91	1	CLONAL	1	TRUE	1	0.682673144580431	2		572	793	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275842	38275842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367715495	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	273	454	0	ENST00000425967.3:c.1427G>A	p.Arg476Gln	p.R476Q	ENST00000425967	NM_001174067.1	476	cGg/cAg	11/19	1	2	FACETS	0.961	0.905	1	0.961	0.905	1	CLONAL	1	TRUE	1	0.682673144580431	2		454	832	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	118	209	0	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	1	2	FACETS	0.993	0.907	1	0.993	0.907	1	CLONAL	1	TRUE	1	0.682673144580431	2		209	348	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733513	85733513	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs387906350	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	234	494	2	ENST00000370580.1:c.499del	p.Ser167LeufsTer6	p.S167Lfs*6	ENST00000370580	NM_003921.4	167	Tct/ct	3/3	1	2	FACETS	0.904	0.847	0.963	0.904	0.847	0.963	CLONAL	1	TRUE	1	0.682673144580431	2		496	758	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401198	139401198	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	282	524	0	ENST00000277541.6:c.3871T>G	p.Phe1291Val	p.F1291V	ENST00000277541	NM_017617.3	1291	Ttc/Gtc	23/34	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.682673144580431	2		524	810	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660807	227660808	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs747646240	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	173	564	0	ENST00000305123.5:c.2645_2647dup	p.Gln882dup	p.Q882dup	ENST00000305123	NM_005544.2	882	ccc/cAGCcc	1/2	1	2	FACETS	0.617	0.569	0.668	0.617	0.569	0.668	SUBCLONAL	1	TRUE	1	0.682673144580431	2		564	821	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437275	220437275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370513243	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	255	428	0	ENST00000243786.2:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000243786	NM_002191.3	60	cGa/cAa	1/2	1	2	FACETS	0.971	0.913	1	0.971	0.913	1	CLONAL	1	TRUE	1	0.682673144580431	2		428	769	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416952	416953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs771545848	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	245	520	2	ENST00000399788.2:c.3597dup	p.Gly1200ArgfsTer7	p.G1200Rfs*7	ENST00000399788	NM_001042603.1	1199	-/A	23/28	1	2	FACETS	0.896	0.84	0.953	0.896	0.84	0.953	CLONAL	1	TRUE	1	0.682673144580431	2		522	801	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821613	72821618	+	inframe_deletion	In_Frame_Del	DEL	CCGCCA	CCGCCA	-	rs761344900	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	66	483	9	ENST00000268489.5:c.10557_10562del	p.Gly3526_Gly3527del	p.G3526_G3527del	ENST00000268489	NM_006885.3	3519	ggTGGCGGc/ggc	10/10	1	2	FACETS	0.289	0.251	0.331	0.289	0.251	0.331	SUBCLONAL	1	TRUE	1	0.682673144580431	2		492	668	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107136	27107137	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	308	535	1	ENST00000324856.7:c.6749_6750del	p.Glu2250ValfsTer27	p.E2250Vfs*27	ENST00000324856	NM_006015.4	2249	tcAGag/tcag	20/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.682673144580431	2		536	885	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444519	187444519	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	246	413	0	ENST00000232014.4:c.1708G>A	p.Gly570Ser	p.G570S	ENST00000232014	NM_001130845.1	570	Ggt/Agt	7/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.682673144580431	2		413	676	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	313	460	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.682673144580431	2		463	895	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	221	421	1	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.874	0.816	0.933	0.874	0.816	0.933	CLONAL	1	TRUE	1	0.682673144580431	2		422	741	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	277	554	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.896	0.843	0.95	0.896	0.843	0.95	CLONAL	1	TRUE	1	0.682673144580431	2		554	906	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780277	9780277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	526	478	0	ENST00000377346.4:c.1447G>A	p.Val483Met	p.V483M	ENST00000377346	NM_005026.3	483	Gtg/Atg	11/24	0.682673144580431	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.682673144580431	3		478	1015	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291084	10291084	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	378	806	0	ENST00000340748.4:c.387del	p.Lys130AsnfsTer129	p.K130Nfs*129	ENST00000340748		129	ccC/cc	4/40	1	2	FACETS	0.91	0.864	0.957	0.91	0.864	0.957	CLONAL	1	TRUE	1	0.682673144580431	2		806	1217	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39762931	39762931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774038422	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	147	354	0	ENST00000288319.7:c.905G>A	p.Arg302His	p.R302H	ENST00000288319	NM_182918.3	302	cGc/cAc	9/10	1	2	FACETS	0.972	0.896	1	0.972	0.896	1	CLONAL	1	TRUE	1	0.682673144580431	2		354	443	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647310	23647310	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	165	407	0	ENST00000261584.4:c.557del	p.Asn186IlefsTer7	p.N186Ifs*7	ENST00000261584	NM_024675.3	186	aAt/at	4/13	1	2	FACETS	0.965	0.893	1	0.965	0.893	1	CLONAL	1	TRUE	1	0.682673144580431	2		407	501	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220134	5220134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115469963	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	285	483	0	ENST00000357368.4:c.3581G>A	p.Arg1194His	p.R1194H	ENST00000357368	NM_002850.3	1194	cGc/cAc	22/38	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.682673144580431	2		483	812	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991724	72991724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377474264	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	242	512	2	ENST00000268489.5:c.2321C>T	p.Ala774Val	p.A774V	ENST00000268489	NM_006885.3	774	gCg/gTg	2/10	1	2	FACETS	0.891	0.835	0.948	0.891	0.835	0.948	CLONAL	1	TRUE	1	0.682673144580431	2		514	796	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172413	7172413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764221583	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	228	412	0	ENST00000302850.5:c.1156G>A	p.Gly386Ser	p.G386S	ENST00000302850	NM_000208.2	386	Ggc/Agc	5/22	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.682673144580431	2		412	640	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256683	19256683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	226	445	0	ENST00000162023.5:c.1030G>A	p.Ala344Thr	p.A344T	ENST00000162023		344	Gcc/Acc	13/13	1	2	FACETS	0.951	0.89	1	0.951	0.89	1	CLONAL	1	TRUE	1	0.682673144580431	2		445	696	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639525	3639525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369846826	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	306	586	0	ENST00000294008.3:c.4114C>T	p.Arg1372Trp	p.R1372W	ENST00000294008	NM_032444.2	1372	Cgg/Tgg	12/15	1	2	FACETS	0.979	0.925	1	0.979	0.925	1	CLONAL	1	TRUE	1	0.682673144580431	2		586	916	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821610	72821618	+	inframe_deletion	In_Frame_Del	DEL	CCGCCGCCA	CCGCCGCCA	-	rs760306096	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	39	482	0	ENST00000268489.5:c.10557_10565del	p.Gly3525_Gly3527del	p.G3525_G3527del	ENST00000268489	NM_006885.3	3519	ggTGGCGGCGGc/ggc	10/10	1	2	FACETS	0.174	0.144	0.208	0.174	0.144	0.208	SUBCLONAL	1	TRUE	1	0.682673144580431	2		482	656	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216433	7216433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774633910	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	265	508	0	ENST00000380728.2:c.815G>A	p.Arg272His	p.R272H	ENST00000380728		272	cGc/cAc	10/11	1	2	FACETS	0.898	0.844	0.953	0.898	0.844	0.953	CLONAL	1	TRUE	1	0.682673144580431	2		508	865	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589648	69589648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	335	704	0	ENST00000168712.1:c.205G>A	p.Val69Ile	p.V69I	ENST00000168712	NM_002007.2	69	Gtc/Atc	1/3	1	2	FACETS	0.983	0.932	1	0.983	0.932	1	CLONAL	1	TRUE	1	0.682673144580431	2		704	998	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307462	118307462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782414402	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	222	325	0	ENST00000534358.1:c.235G>A	p.Ala79Thr	p.A79T	ENST00000534358	NM_005933.3	79	Gcc/Acc	1/36	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.682673144580431	2		325	595	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815622	139815622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	302	477	0	ENST00000247668.2:c.1093C>T	p.Arg365Cys	p.R365C	ENST00000247668	NM_021138.3	365	Cgc/Tgc	9/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.682673144580431	2		477	799	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691872	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs79375991	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	408	536	13	ENST00000295754.5:c.383del	p.Lys128SerfsTer35	p.K128Sfs*35	ENST00000295754	NM_003242.5	125	gAa/ga	3/7	1	2	FACETS	0.853	0.82	0.885	1	0.997	1	CLONAL	2	TRUE	1	0.682673144580431	2		549	701	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423550	47423550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1029166106	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	246	441	2	ENST00000404338.3:c.1618C>T	p.Arg540Cys	p.R540C	ENST00000404338	NM_004491.4	540	Cgt/Tgt	1/6	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.682673144580431	2		443	670	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914277	32914277	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	27	393	0	ENST00000380152.3:c.5785A>C	p.Ile1929Leu	p.I1929L	ENST00000380152		1929	Att/Ctt	11/27	1	2	FACETS	0.176	0.14	0.218	0.176	0.14	0.218	SUBCLONAL	1	TRUE	1	0.682673144580431	2		393	449	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435345	110435345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	283	568	1	ENST00000375856.3:c.3056del	p.Pro1019ArgfsTer87	p.P1019Rfs*87	ENST00000375856	NM_003749.2	1019	cCg/cg	1/2	1	2	FACETS	0.901	0.849	0.955	0.901	0.849	0.955	CLONAL	1	TRUE	1	0.682673144580431	2		569	920	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865913	56865913	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	197	379	0	ENST00000308159.5:c.1245G>A	p.Trp415Ter	p.W415*	ENST00000308159	NM_014669.4	415	tgG/tgA	11/22	1	2	FACETS	0.993	0.926	1	0.993	0.926	1	CLONAL	1	TRUE	1	0.682673144580431	2		379	581	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544249	86544249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	281	515	1	ENST00000262426.4:c.74C>T	p.Ala25Val	p.A25V	ENST00000262426	NM_001451.2	25	gCc/gTc	1/2	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.682673144580431	2		516	766	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923284	78923285	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	142	419	0	ENST00000306801.3:c.3311dup	p.Asn1105GlufsTer51	p.N1105Efs*51	ENST00000306801	NM_020761.2	1103	gaa/gAaa	28/34	1	2	FACETS	0.582	0.531	0.635	0.582	0.531	0.635	SUBCLONAL	1	TRUE	1	0.682673144580431	2		419	715	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219344	1219345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	237	502	0	ENST00000326873.7:c.402_403dup	p.Gly135ValfsTer27	p.G135Vfs*27	ENST00000326873	NM_000455.4	132	-/GT	3/10	1	2	FACETS	0.84	0.786	0.895	0.84	0.786	0.895	CLONAL	1	TRUE	1	0.682673144580431	2		502	827	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52729229	52729229	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780001633	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	261	486	0	ENST00000322088.6:c.1765G>A	p.Ala589Thr	p.A589T	ENST00000322088	NM_014225.5	589	Gcc/Acc	15/15	1	2	FACETS	0.993	0.934	1	0.993	0.934	1	CLONAL	1	TRUE	1	0.682673144580431	2		486	770	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067138	37067145	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGACTT	CAGGACTT	-	novel	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	139	250	0	ENST00000231790.2:c.1049_1056del	p.Pro350ArgfsTer9	p.P350Rfs*9	ENST00000231790	NM_000249.3	350	cCAGGACTT/c	12/19	1	2	FACETS	0.945	0.868	1	0.945	0.868	1	CLONAL	1	TRUE	1	0.682673144580431	2		250	431	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274872	41274872	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	230	465	0	ENST00000349496.5:c.1122T>G	p.Ser374Arg	p.S374R	ENST00000349496	NM_001904.3	374	agT/agG	8/15	1	2	FACETS	0.985	0.923	1	0.985	0.923	1	CLONAL	1	TRUE	1	0.682673144580431	2		465	684	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71161688	71161688	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	139	295	0	ENST00000318789.4:c.281A>G	p.Gln94Arg	p.Q94R	ENST00000318789	NM_032682.5	94	cAg/cGg	7/21	1	2	FACETS	0.911	0.836	0.988	0.911	0.836	0.988	CLONAL	1	TRUE	1	0.682673144580431	2		295	447	SUCCESS
ATR	545	MSKCC	GRCh37	3	142216026	142216027	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	154	271	0	ENST00000350721.4:c.5566_5567del	p.Met1856ValfsTer3	p.M1856Vfs*3	ENST00000350721	NM_001184.3	1856	ATg/g	33/47	1	2	FACETS	0.979	0.903	1	0.979	0.903	1	CLONAL	1	TRUE	1	0.682673144580431	2		271	461	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526597	31526597	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	159	313	0	ENST00000344624.3:c.443del	p.Pro148LeufsTer78	p.P148Lfs*78	ENST00000344624		148	cCt/ct	2/33	1	2	FACETS	0.814	0.75	0.88	0.814	0.75	0.88	CLONAL	1	TRUE	1	0.682673144580431	2		313	572	SUCCESS
APC	324	MSKCC	GRCh37	5	112178855	112178855	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	260	473	0	ENST00000257430.4:c.7564C>G	p.Pro2522Ala	p.P2522A	ENST00000257430	NM_000038.5	2522	Cca/Gca	16/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.682673144580431	2		473	742	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045936	26045936	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs777916771	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	368	547	0	ENST00000540144.1:c.298T>C	p.Tyr100His	p.Y100H	ENST00000540144	NM_003531.2	100	Tac/Cac	1/1	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.682673144580431	2		547	991	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005149	150005149	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	317	514	0	ENST00000253339.5:c.1076A>G	p.His359Arg	p.H359R	ENST00000253339		359	cAc/cGc	3/7	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.682673144580431	2		514	822	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976672	2976672	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	197	407	0	ENST00000396946.4:c.1340A>G	p.Gln447Arg	p.Q447R	ENST00000396946	NM_032415.4	447	cAg/cGg	9/25	1	2	FACETS	0.935	0.871	1	0.935	0.871	1	CLONAL	1	TRUE	1	0.682673144580431	2		407	617	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845200	151845202	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	265	493	0	ENST00000262189.6:c.13810_13812del	p.Glu4604del	p.E4604del	ENST00000262189	NM_170606.2	4604	GAG/-	52/59	1	2	FACETS	0.96	0.903	1	0.96	0.903	1	CLONAL	1	TRUE	1	0.682673144580431	2		493	809	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345919	70345919	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	230	192	0	ENST00000374080.3:c.2456G>A	p.Arg819Gln	p.R819Q	ENST00000374080		819	cGg/cAg	18/45	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.682673144580431	1		192	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0065635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	114	427	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.283151750994652	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	0	0.283151750994652	2		427	388	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41228521	41228521	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	68	406	0	ENST00000357654.3:c.4468G>C	p.Glu1490Gln	p.E1490Q	ENST00000357654	NM_007294.3	1490	Gaa/Caa	13/23	0.283151750994652	3	FACETS	0.923	0.81	1	0.615	0.54	0.695	CLONAL	2	TRUE	0	0.283151750994652	3		406	297	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	111	658	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.283151750994652	3	FACETS	0.971	0.878	1	0.971	0.878	1	CLONAL	2	TRUE	1	0.283151750994652	3		658	461	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952086	178952086	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	117	502	0	ENST00000263967.3:c.3141T>A	p.His1047Gln	p.H1047Q	ENST00000263967	NM_006218.2	1047	caT/caA	21/21	0.283151750994652	5	FACETS	1	0.944	1	0.707	0.64	0.778	CLONAL	2	TRUE	2	0.283151750994652	5		502	555	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589260	67589260	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0065635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	51	433	0	ENST00000274335.5:c.1248T>G	p.Tyr416Ter	p.Y416*	ENST00000274335		416	taT/taG	9/15	0.262156372063737	4	FACETS	0.951	0.816	1	0.951	0.816	1	CLONAL	2	TRUE	2	0.283151750994652	4		433	243	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934874	NA	P-0065636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	255	660	0	ENST00000269305.4:c.451C>A	p.Pro151Thr	p.P151T	ENST00000269305	NM_001126112.2	151	Ccc/Acc	5/11	0.0662854507834187	3	FACETS	0.891	0.853	0.929			1	INDETERMINATE	3	TRUE	NA	0.667575047309771	3		660	381	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727423	66727423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1049040928	NA	P-0065636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	230	485	0	ENST00000307102.5:c.139C>T	p.Arg47Ter	p.R47*	ENST00000307102	NM_002755.3	47	Cga/Tga	2/11	0.665859401339361	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.667575047309771	3		485	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578507	7578507	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519977	NA	P-0065637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	69	652	0	ENST00000269305.4:c.423C>G	p.Cys141Trp	p.C141W	ENST00000269305	NM_001126112.2	141	tgC/tgG	5/11	1	2	FACETS	0.521	0.452	0.596	0.521	0.452	0.596	SUBCLONAL	1	TRUE	1	0.28	2		652	946	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888847	76888847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	35	301	0	ENST00000373344.5:c.4982G>A	p.Arg1661His	p.R1661H	ENST00000373344	NM_000489.3	1661	cGt/cAt	19/35	1	1	FACETS	0.719	0.591	0.861	0.719	0.591	0.861	SUBCLONAL	1	TRUE	0	0.28	1		301	299	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119763	70119763	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	47	429	0	ENST00000245479.2:c.768del	p.Arg257AlafsTer22	p.R257Afs*22	ENST00000245479	NM_000346.3	255	gaG/ga	3/3	1	2	FACETS	0.546	0.46	0.641	0.546	0.46	0.641	SUBCLONAL	1	TRUE	1	0.28	2		429	615	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84406195	84406195	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	49	411	0	ENST00000321945.7:c.31T>A	p.Ser11Thr	p.S11T	ENST00000321945	NM_139076.2	11	Tcg/Acg	1/9	1	2	FACETS	0.516	0.436	0.605	0.516	0.436	0.605	SUBCLONAL	1	TRUE	1	0.28	2		411	678	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0065638-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	41	624	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		624	820	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842472	68842472	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0065638-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	36	708	0	ENST00000261769.5:c.531+2T>C		p.X177_splice	ENST00000261769	NM_004360.3	177			1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		708	778	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427633	72427633	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065639-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	54	568	0	ENST00000477973.2:c.857A>G	p.Asn286Ser	p.N286S	ENST00000477973	NM_012234.5	286	aAc/aGc	4/4	1	2	FACETS	0.164	0.139	0.191	0.164	0.139	0.191	SUBCLONAL	1	TRUE	1	0.673074748730723	2		568	980	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390631	139390631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065639-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1231	83	613	0	ENST00000277541.6:c.7560G>A	p.Trp2520Ter	p.W2520*	ENST00000277541	NM_017617.3	2520	tgG/tgA	34/34	0.673074748730723	3	FACETS	0.251	0.22	0.284	0.125	0.11	0.142	SUBCLONAL	1	TRUE	1	0.673074748730723	3		613	1314	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243801031	243801031	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	24	324	0	ENST00000263826.5:c.443T>A	p.Phe148Tyr	p.F148Y	ENST00000263826	NM_005465.4	148	tTt/tAt	5/13	1	2	FACETS	0.635	0.498	0.793	0.635	0.498	0.793	SUBCLONAL	1	TRUE	1	0.215357589724417	2		324	351	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427932	49427932	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	58	662	0	ENST00000301067.7:c.10658G>T	p.Gly3553Val	p.G3553V	ENST00000301067	NM_003482.3	3553	gGc/gTc	38/54	1	2	FACETS	0.701	0.601	0.811	0.701	0.601	0.811	SUBCLONAL	1	TRUE	1	0.215357589724417	2		662	768	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805063	89805063	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1176499940	NA	P-0065640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	78	666	0	ENST00000389301.3:c.4314C>A	p.Ser1438Arg	p.S1438R	ENST00000389301	NM_000135.2	1438	agC/agA	43/43	0.215357589724417	1	FACETS	0.757	0.664	0.857	0.757	0.664	0.857	SUBCLONAL	1	TRUE	0	0.215357589724417	1		666	854	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577067	7578089	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGCGGAGATTCTCTTCCTCTGTGCGCCGGTCTCTCCCAGGACAGGCACAAACACGCACCTCAAAGCTGTTCCGTCCCAGTAGATTACCACTACTCAGGATAGGAAAAGAGAAGCAAGAGGCAGTAAGGAAATCAGGTCCTACCTGTCCCATTTAAAAAACCAGGCTCCATCTACTCCCAACCACCCTTGTCCTTTCTGGAGCCTAAGCTCCAGCTCCAGGTAGGTGGAGGAGAAGCCACAGGTTAAGAGGTCCCAAAGCCAGAGAAAAGAAAACTGAGTGGGAGCAGTAAGGAGATTCCCCGCCGGGGATGTGATGAGAGGTGGATGGGTAGTAGTATGGAAGAAATCGGTAAGAGGTGGGCCCAGGGGTCAGAGGCAAGCAGAGGCTGGGGCACAGCAGGCCAGTGTGCAGGGTGGCAAGTGGCTCCTGACCTGGAGTCTTCCAGTGTGATGATGGTGAGGATGGGCCTCCGGTTCATGCCGCCCATGCAGGAACTGTTACACATGTAGTTGTAGTGGATGGTGGTACAGTCAGAGCCAACCTAGGAGATAACACAGGCCCAAGATGAGGCCAGTGCGCCTTGGGGAGACCTGTGGCAAGCAGGGGAGGCCTTTTTTTTTTTTTTTTGAGATGGAATCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGTGATCTCAGCTCACTGCAAGCTCCACCGCCCAGGTTCACGCCATTCTCCTTCCTCAGCCTCCCGAGTAGCTGGGACTACAGGTGCCCAGCACCACGCCCGGCTAATTTTTTTTTGTATTTTTCAGTAGAGACGGGGTTTCACCGTTAGCCAGGATGGTCTCGATCTCCCAACCTCGTGATCCGCCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTGCGCCCAGCCAAGCAGGGGAGGCCCTTAGCCTCTGTAAGCTTCAGTTTTTTCAACTGTGCAATAGTTAAACCCATTTACTTTGCACATCTCATGGGGTTATAGGGAGGTCAAATAAGCAGCA	TGCGGAGATTCTCTTCCTCTGTGCGCCGGTCTCTCCCAGGACAGGCACAAACACGCACCTCAAAGCTGTTCCGTCCCAGTAGATTACCACTACTCAGGATAGGAAAAGAGAAGCAAGAGGCAGTAAGGAAATCAGGTCCTACCTGTCCCATTTAAAAAACCAGGCTCCATCTACTCCCAACCACCCTTGTCCTTTCTGGAGCCTAAGCTCCAGCTCCAGGTAGGTGGAGGAGAAGCCACAGGTTAAGAGGTCCCAAAGCCAGAGAAAAGAAAACTGAGTGGGAGCAGTAAGGAGATTCCCCGCCGGGGATGTGATGAGAGGTGGATGGGTAGTAGTATGGAAGAAATCGGTAAGAGGTGGGCCCAGGGGTCAGAGGCAAGCAGAGGCTGGGGCACAGCAGGCCAGTGTGCAGGGTGGCAAGTGGCTCCTGACCTGGAGTCTTCCAGTGTGATGATGGTGAGGATGGGCCTCCGGTTCATGCCGCCCATGCAGGAACTGTTACACATGTAGTTGTAGTGGATGGTGGTACAGTCAGAGCCAACCTAGGAGATAACACAGGCCCAAGATGAGGCCAGTGCGCCTTGGGGAGACCTGTGGCAAGCAGGGGAGGCCTTTTTTTTTTTTTTTTGAGATGGAATCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGTGATCTCAGCTCACTGCAAGCTCCACCGCCCAGGTTCACGCCATTCTCCTTCCTCAGCCTCCCGAGTAGCTGGGACTACAGGTGCCCAGCACCACGCCCGGCTAATTTTTTTTTGTATTTTTCAGTAGAGACGGGGTTTCACCGTTAGCCAGGATGGTCTCGATCTCCCAACCTCGTGATCCGCCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTGCGCCCAGCCAAGCAGGGGAGGCCCTTAGCCTCTGTAAGCTTCAGTTTTTTCAACTGTGCAATAGTTAAACCCATTTACTTTGCACATCTCATGGGGTTATAGGGAGGTCAAATAAGCAGCA	-	novel	NA	P-0065640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	76	608	0	ENST00000269305.4:c.672+88_871del		p.X224_splice	ENST00000269305	NM_001126112.2	224		7-8/11	1	2	FACETS	0.863	0.756	0.979	0.863	0.756	0.979	CLONAL	1	TRUE	1	0.215357589724417	2		608	818	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78831616	78831617	+	missense_variant	Missense_Mutation	DNP	CG	CG	TT	novel	NA	P-0065640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	88	603	0	ENST00000306801.3:c.1425_1426delinsTT	p.Val476Leu	p.V476L	ENST00000306801	NM_020761.2	475	taCGtg/taTTtg	13/34	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.215357589724417	2		603	789	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0065641-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	691	602	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.88865078467228	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	1	0.88865078467228	3		602	1009	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434581	99434581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1461059080	NA	P-0065641-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	365	602	3	ENST00000268035.6:c.668C>T	p.Ala223Val	p.A223V	ENST00000268035	NM_000875.3	223	gCg/gTg	3/21	0.881863707234638	1	FACETS	0.937	0.907	0.966	0.937	0.907	0.966	CLONAL	1	TRUE	0	0.88865078467228	1		605	487	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798442	45798442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553128757	NA	P-0065641-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	365	731	0	ENST00000450313.1:c.569C>T	p.Ala190Val	p.A190V	ENST00000450313	NM_012222.2	190	gCt/gTt	7/16	1	2	FACETS	0.956	0.911	1	0.956	0.911	1	CLONAL	1	TRUE	1	0.88865078467228	2		731	859	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111473	8111473	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065641-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	401	568	0	ENST00000346208.3:c.959G>A	p.Cys320Tyr	p.C320Y	ENST00000346208		320	tGt/tAt	5/6	1	2	FACETS	0.994	0.95	1	0.994	0.95	1	CLONAL	1	TRUE	1	0.88865078467228	2		568	908	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945135	32945136	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs397507990	NA	P-0065641-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	238	435	0	ENST00000380152.3:c.8533dup	p.Arg2845LysfsTer24	p.R2845Kfs*24	ENST00000380152		2844	gaa/gAaa	20/27	0.881863707234638	1	FACETS	0.986	0.949	1	0.986	0.949	1	CLONAL	1	TRUE	0	0.88865078467228	1		435	302	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245287	41245287	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065641-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	330	579	0	ENST00000357654.3:c.2261G>T	p.Gly754Val	p.G754V	ENST00000357654	NM_007294.3	754	gGa/gTa	10/23	0.887084449637177	1	FACETS	0.964	0.933	0.994	0.964	0.933	0.994	CLONAL	1	TRUE	0	0.88865078467228	1		579	428	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590786	189590786	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0065641-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	440	521	0	ENST00000264731.3:c.1349+2T>C		p.X450_splice	ENST00000264731	NM_003722.4	450			0.88865078467228	3	FACETS	1	0.994	1	0.615	0.587	0.643	CLONAL	1	TRUE	1	0.88865078467228	3		521	1163	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056490	26056490	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs138831824	NA	P-0065641-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	368	557	0	ENST00000343677.2:c.167G>C	p.Gly56Ala	p.G56A	ENST00000343677	NM_005319.3	56	gGa/gCa	1/1	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.88865078467228	2		557	786	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400230	139400230	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065641-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	736	635	0	ENST00000277541.6:c.4118T>A	p.Leu1373Gln	p.L1373Q	ENST00000277541	NM_017617.3	1373	cTg/cAg	25/34	0.872793320099392	3	FACETS	0.99	0.963	1	0.99	0.963	1	CLONAL	2	TRUE	1	0.88865078467228	3		635	1208	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0065642-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	99	295	1	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.788	0.705	0.875	1	0.983	1	SUBCLONAL	2	TRUE	1	0.224009785421967	2		296	561	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0065642-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	38	384	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.224009785421967	2		384	298	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0065642-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	52	344	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	1	2	FACETS	1	0.924	1	1	0.978	1	CLONAL	2	TRUE	1	0.224009785421967	2		344	209	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624263	89624263	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065642-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	51	191	0	ENST00000371953.3:c.40del	p.Arg14GlyfsTer10	p.R14Gfs*10	ENST00000371953	NM_000314.4	13	Aaa/aa	1/9	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.224009785421967	2		191	312	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247516	123247516	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519795	NA	P-0065642-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	85	375	0	ENST00000358487.5:c.1975A>G	p.Lys659Glu	p.K659E	ENST00000358487	NM_000141.4	659	Aag/Gag	14/18	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.224009785421967	2		375	554	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433416	138433416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1194347036	NA	P-0065642-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	42	378	0	ENST00000289153.2:c.1196G>A	p.Arg399Gln	p.R399Q	ENST00000289153	NM_006219.2	399	cGa/cAa	7/22	1	2	FACETS	0.772	0.649	0.905	1	0.96	1	CLONAL	2	TRUE	1	0.224009785421967	2		378	243	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294240	11294240	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065642-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	53	551	0	ENST00000361445.4:c.2291C>G	p.Ala764Gly	p.A764G	ENST00000361445	NM_004958.3	764	gCc/gGc	14/58	1	2	FACETS	0.511	0.434	0.596	0.511	0.434	0.596	SUBCLONAL	1	TRUE	1	0.224009785421967	2		551	926	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922225	39922225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065642-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	111	533	0	ENST00000378444.4:c.3947G>A	p.Arg1316Lys	p.R1316K	ENST00000378444	NM_001123385.1	1316	aGg/aAg	9/15	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.224009785421967	2		533	881	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362617	118362617	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	135	494	0	ENST00000534358.1:c.4978A>G	p.Thr1660Ala	p.T1660A	ENST00000534358	NM_005933.3	1660	Acc/Gcc	15/36	1	2	FACETS	0.832	0.762	0.904	1	0.989	1	CLONAL	2	TRUE	1	0.352852188259845	2		494	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0065645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	202	485	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.269314172187122	2	FACETS	0.826	0.77	0.884	0.826	0.77	0.884	CLONAL	2	TRUE	0	0.389949666446066	2		485	627	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281934	39281934	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	37	264	0	ENST00000402219.2:c.541G>C	p.Glu181Gln	p.E181Q	ENST00000402219	NM_005633.3	181	Gaa/Caa	5/23	0.254467595933796	3	FACETS	0.945	0.812	1	1	0.959	1	CLONAL	3	TRUE	1	0.389949666446066	3		264	80	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578210	226578210	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200399922	NA	P-0065645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	232	518	0	ENST00000366794.5:c.518G>A	p.Arg173Gln	p.R173Q	ENST00000366794	NM_001618.3	173	cGg/cAg	4/23	0.389949666446066	4	FACETS	1	0.945	1	0.675	0.631	0.72	CLONAL	2	TRUE	1	0.389949666446066	4		518	817	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12043919	12043919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398054657	NA	P-0065645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	82	427	0	ENST00000396373.4:c.1298G>A	p.Arg433His	p.R433H	ENST00000396373	NM_001987.4	433	cGt/cAt	8/8	0.356719564393052	3	FACETS	1	0.926	1	0.531	0.47	0.596	CLONAL	1	TRUE	1	0.389949666446066	3		427	473	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999023	100999023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756847705	NA	P-0065645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	109	603	1	ENST00000325455.5:c.779C>T	p.Ala260Val	p.A260V	ENST00000325455	NM_001202474.3	260	gCg/gTg	1/8	0.146484464424724	2	FACETS	0.773	0.695	0.856	0.387	0.347	0.428	INDETERMINATE	1	TRUE	0	0.389949666446066	2		604	723	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099010	27099010	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	108	622	0	ENST00000324856.7:c.3429del	p.Gln1145ArgfsTer16	p.Q1145Rfs*16	ENST00000324856	NM_006015.4	1142	caG/ca	13/20	1	2	FACETS	0.842	0.757	0.932	0.842	0.757	0.932	CLONAL	1	TRUE	1	0.389949666446066	2		622	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	33	575	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.136	0.11	0.165	0.136	0.11	0.165	SUBCLONAL	1	TRUE	1	0.586389201236485	2		575	829	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	202	476	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.871	0.809	0.935	0.871	0.809	0.935	CLONAL	1	TRUE	1	0.586389201236485	2		476	791	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	227	515	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.586389201236485	2		515	754	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498433	89498433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369423490	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	196	483	0	ENST00000336596.2:c.2405C>T	p.Thr802Met	p.T802M	ENST00000336596	NM_005233.5	802	aCg/aTg	14/17	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.586389201236485	2		483	657	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	76	170	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.586389201236485	2		170	247	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	244	244	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.586389201236485	3	FACETS	0.929	0.876	0.983	0.929	0.876	0.983	CLONAL	2	TRUE	1	0.586389201236485	3		244	579	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255141	16255142	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	173	602	2	ENST00000375759.3:c.2417_2418dup	p.Arg807AspfsTer3	p.R807Dfs*3	ENST00000375759	NM_015001.2	802	-/GA	11/15	1	2	FACETS	0.6	0.552	0.651	0.6	0.552	0.651	SUBCLONAL	1	TRUE	1	0.586389201236485	2		604	983	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258735	16258735	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	57	729	3	ENST00000375759.3:c.6005del	p.Asn2002MetfsTer20	p.N2002Mfs*20	ENST00000375759	NM_015001.2	2000	ggA/gg	11/15	1	2	FACETS	0.186	0.158	0.216	0.186	0.158	0.216	SUBCLONAL	1	TRUE	1	0.586389201236485	2		732	1047	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262664	16262664	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	285	536	0	ENST00000375759.3:c.9929A>G	p.Asp3310Gly	p.D3310G	ENST00000375759	NM_015001.2	3310	gAc/gGc	11/15	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.586389201236485	2		536	786	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023744	27023744	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	218	592	0	ENST00000324856.7:c.854del	p.Gly285GlufsTer78	p.G285Efs*78	ENST00000324856	NM_006015.4	284	Ggg/gg	1/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.586389201236485	2		592	684	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057937	27057937	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	264	545	2	ENST00000324856.7:c.1650del	p.Tyr551ThrfsTer68	p.Y551Tfs*68	ENST00000324856	NM_006015.4	549	Ccc/cc	3/20	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.586389201236485	2		547	898	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	138	537	3	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.532	0.484	0.583	0.532	0.484	0.583	SUBCLONAL	1	TRUE	1	0.586389201236485	2		540	884	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330610	65330611	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	117	438	0	ENST00000342505.4:c.1035dup	p.Leu346ThrfsTer4	p.L346Tfs*4	ENST00000342505	NM_002227.2	345	-/A	8/25	1	2	FACETS	0.596	0.539	0.657	0.596	0.539	0.657	SUBCLONAL	1	TRUE	1	0.586389201236485	2		438	669	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612801	228612801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369460992	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	409	849	0	ENST00000366696.1:c.226G>A	p.Ala76Thr	p.A76T	ENST00000366696	NM_003493.2	76	Gct/Act	1/1	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.586389201236485	2		849	1157	SUCCESS
RET	5979	MSKCC	GRCh37	10	43572749	43572750	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	rs768132465	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	125	423	0	ENST00000355710.3:c.56_58dup	p.Leu19dup	p.L19dup	ENST00000355710	NM_020975.4	19	ttg/tTGCtg	1/20	1	2	FACETS	0.797	0.725	0.872	0.797	0.725	0.872	SUBCLONAL	1	TRUE	1	0.586389201236485	2		423	535	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850705	63850705	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs201178069	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	230	546	1	ENST00000279873.7:c.1489del	p.Ile497Ter	p.I497*	ENST00000279873	NM_032199.2	495	Aaa/aa	10/10	1	2	FACETS	0.961	0.898	1	0.961	0.898	1	CLONAL	1	TRUE	1	0.586389201236485	2		547	816	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653808	89653808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	80	216	0	ENST00000371953.3:c.106G>A	p.Gly36Arg	p.G36R	ENST00000371953	NM_000314.4	36	Gga/Aga	2/9	1	2	FACETS	0.875	0.777	0.977	0.875	0.777	0.977	CLONAL	1	TRUE	1	0.586389201236485	2		216	312	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	24	118	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.593	0.471	0.73	0.593	0.471	0.73	SUBCLONAL	1	TRUE	1	0.586389201236485	2		118	138	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154356	2154356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1260271030	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	296	683	0	ENST00000434045.2:c.572G>A	p.Arg191His	p.R191H	ENST00000434045	NM_001127598.1	191	cGt/cAt	5/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.586389201236485	2		683	938	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948208	71948209	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs749079348	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	227	644	0	ENST00000298229.2:c.2927dup	p.Pro977ThrfsTer7	p.P977Tfs*7	ENST00000298229	NM_001567.3	974	gcc/gCcc	26/28	1	2	FACETS	0.952	0.89	1	0.952	0.89	1	CLONAL	1	TRUE	1	0.586389201236485	2		644	813	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77961330	77961330	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	264	527	0	ENST00000361507.4:c.493A>G	p.Ser165Gly	p.S165G	ENST00000361507	NM_080491.2	165	Agc/Ggc	3/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.586389201236485	2		527	846	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180406	94180406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555005282	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	162	451	0	ENST00000323929.3:c.1762G>A	p.Gly588Arg	p.G588R	ENST00000323929	NM_005591.3	588	Gga/Aga	15/20	1	2	FACETS	0.901	0.831	0.975	0.901	0.831	0.975	CLONAL	1	TRUE	1	0.586389201236485	2		451	613	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69229705	69229705	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs549965230	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	162	336	0	ENST00000462284.1:c.781G>A	p.Asp261Asn	p.D261N	ENST00000462284	NM_002392.5	261	Gac/Aac	9/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.586389201236485	2		336	491	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432117	121432118	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776825	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	243	629	21	ENST00000257555.6:c.872dup	p.Gly292ArgfsTer25	p.G292Rfs*25	ENST00000257555		288	-/C	4/10	1	2	FACETS	0.976	0.914	1	0.976	0.914	1	CLONAL	1	TRUE	1	0.586389201236485	2		650	849	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041262	29041262	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	202	469	0	ENST00000282397.4:c.166del	p.Glu56LysfsTer12	p.E56Kfs*12	ENST00000282397	NM_002019.4	56	Gaa/aa	3/30	1	2	FACETS	0.972	0.904	1	0.972	0.904	1	CLONAL	1	TRUE	1	0.586389201236485	2		469	709	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434964	110434964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	234	703	2	ENST00000375856.3:c.3437G>A	p.Arg1146His	p.R1146H	ENST00000375856	NM_003749.2	1146	cGc/cAc	1/2	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.586389201236485	2		705	784	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061285	38061285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200059313	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	85	699	1	ENST00000250448.2:c.704C>T	p.Pro235Leu	p.P235L	ENST00000250448	NM_004496.3	235	cCg/cTg	2/2	1	2	FACETS	0.377	0.333	0.424	0.377	0.333	0.424	SUBCLONAL	1	TRUE	1	0.586389201236485	2		700	769	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51514629	51514629	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237240555	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	237	560	0	ENST00000260433.2:c.545C>T	p.Ser182Leu	p.S182L	ENST00000260433		182	tCg/tTg	5/10	1	2	FACETS	0.97	0.908	1	0.97	0.908	1	CLONAL	1	TRUE	1	0.586389201236485	2		560	833	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343713	343713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377025983	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	223	530	0	ENST00000262320.3:c.1961C>T	p.Ser654Leu	p.S654L	ENST00000262320	NM_003502.3	654	tCg/tTg	8/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.586389201236485	2		530	743	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821295	72821295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	205	518	0	ENST00000268489.5:c.10880C>T	p.Ala3627Val	p.A3627V	ENST00000268489	NM_006885.3	3627	gCg/gTg	10/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.586389201236485	2		518	666	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822033	72822034	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs372741038	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	197	672	0	ENST00000268489.5:c.10139_10141dup	p.Gln3380dup	p.Q3380dup	ENST00000268489	NM_006885.3	3380	cgg/cAGCgg	10/10	1	2	FACETS	0.676	0.626	0.728	0.676	0.626	0.728	SUBCLONAL	1	TRUE	1	0.586389201236485	2		672	994	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370236	40370236	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs761761205	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	128	394	7	ENST00000293328.3:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000293328	NM_012448.3	368	Cag/ag	9/19	1	2	FACETS	0.578	0.524	0.635	0.578	0.524	0.635	SUBCLONAL	1	TRUE	1	0.586389201236485	2		401	755	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2194554	2194555	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	186	469	0	ENST00000398665.3:c.635dup	p.His213AlafsTer30	p.H213Afs*30	ENST00000398665	NM_032482.2	210	gga/ggAa	7/28	1	2	FACETS	0.91	0.843	0.979	0.91	0.843	0.979	CLONAL	1	TRUE	1	0.586389201236485	2		469	697	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966835	18966835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	253	655	0	ENST00000262803.5:c.1646G>A	p.Arg549His	p.R549H	ENST00000262803	NM_002911.3	549	cGt/cAt	12/24	1	2	FACETS	0.883	0.827	0.941	0.883	0.827	0.941	CLONAL	1	TRUE	1	0.586389201236485	2		655	977	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222938	36222938	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	250	785	0	ENST00000222270.7:c.5572del	p.Arg1858ValfsTer37	p.R1858Vfs*37	ENST00000222270	NM_014727.1	1856	gCc/gc	27/37	1	2	FACETS	0.887	0.831	0.945	0.887	0.831	0.945	CLONAL	1	TRUE	1	0.586389201236485	2		785	961	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223273	36223274	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	283	745	1	ENST00000222270.7:c.5828dup	p.Pro1944SerfsTer28	p.P1944Sfs*28	ENST00000222270	NM_014727.1	1941	-/C	28/37	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.586389201236485	2		746	940	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424741	47424741	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	264	584	0	ENST00000404338.3:c.2814del	p.Phe938LeufsTer10	p.F938Lfs*10	ENST00000404338	NM_004491.4	937	Ttt/tt	1/6	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.586389201236485	2		584	826	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693886	47693886	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	143	356	0	ENST00000233146.2:c.1600del	p.Arg534ValfsTer9	p.R534Vfs*9	ENST00000233146	NM_000251.2	534	Cgt/gt	10/16	1	2	FACETS	0.991	0.91	1	0.991	0.91	1	CLONAL	1	TRUE	1	0.586389201236485	2		356	492	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702349	47702350	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	155	399	0	ENST00000233146.2:c.1946dup	p.Phe650IlefsTer4	p.F650Ifs*4	ENST00000233146	NM_000251.2	649	gca/gCca	12/16	1	2	FACETS	0.915	0.841	0.99	0.915	0.841	0.99	CLONAL	1	TRUE	1	0.586389201236485	2		399	578	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520134	9520135	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	180	479	0	ENST00000353224.5:c.2134dup	p.Leu712ProfsTer15	p.L712Pfs*15	ENST00000353224	NM_177990.2	712	ctc/cCtc	10/10	1	2	FACETS	0.9	0.833	0.97	0.9	0.833	0.97	CLONAL	1	TRUE	1	0.586389201236485	2		479	682	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877451	40877451	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	235	590	0	ENST00000373198.4:c.2245C>A	p.Gln749Lys	p.Q749K	ENST00000373198	NM_133170.3	749	Cag/Aag	15/32	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.586389201236485	2		590	753	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21347168	21347168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs935736801	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	253	608	1	ENST00000215739.8:c.1235G>A	p.Arg412His	p.R412H	ENST00000215739	NM_006767.3	412	cGc/cAc	11/21	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.586389201236485	2		609	856	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175879	24175879	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	226	506	0	ENST00000263121.7:c.1107del	p.Asp369GlufsTer7	p.D369Efs*7	ENST00000263121	NM_003073.3	369	gaC/ga	8/9	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.586389201236485	2		506	737	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281324	142281324	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	195	441	0	ENST00000350721.4:c.920C>T	p.Ala307Val	p.A307V	ENST00000350721	NM_001184.3	307	gCa/gTa	4/47	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.586389201236485	2		441	631	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260158	149260159	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	118	472	0	ENST00000360632.3:c.733_734dup	p.Arg246LysfsTer11	p.R246Kfs*11	ENST00000360632	NM_015472.4	245	gaa/gaGAa	4/7	1	2	FACETS	0.588	0.531	0.648	0.588	0.531	0.648	SUBCLONAL	1	TRUE	1	0.586389201236485	2		472	684	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	223	434	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.586389201236485	2		434	648	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294204	1294204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	266	794	0	ENST00000310581.5:c.797G>A	p.Ser266Asn	p.S266N	ENST00000310581	NM_198253.2	266	aGt/aAt	2/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.586389201236485	2		794	891	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31521250	31521250	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	170	369	0	ENST00000344624.3:c.927del	p.Glu310SerfsTer42	p.E310Sfs*42	ENST00000344624		309	aaA/aa	3/33	1	2	FACETS	0.966	0.893	1	0.966	0.893	1	CLONAL	1	TRUE	1	0.586389201236485	2		369	600	SUCCESS
APC	324	MSKCC	GRCh37	5	112175675	112175676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	222	572	0	ENST00000257430.4:c.4393_4394dup	p.Ser1465ArgfsTer9	p.S1465Rfs*9	ENST00000257430	NM_000038.5	1462	aag/aAGag	16/16	1	2	FACETS	0.914	0.853	0.978	0.914	0.853	0.978	CLONAL	1	TRUE	1	0.586389201236485	2		572	828	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675268	176675269	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	212	557	0	ENST00000439151.2:c.4591dup	p.Met1531AsnfsTer4	p.M1531Nfs*4	ENST00000439151	NM_022455.4	1528	-/A	11/23	1	2	FACETS	0.88	0.819	0.942	0.88	0.819	0.942	CLONAL	1	TRUE	1	0.586389201236485	2		557	822	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720964	176720964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	269	556	0	ENST00000439151.2:c.6595C>T	p.Arg2199Cys	p.R2199C	ENST00000439151	NM_022455.4	2199	Cgt/Tgt	23/23	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.586389201236485	2		556	887	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800429	32800429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750440758	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	289	677	0	ENST00000374899.4:c.1118G>A	p.Arg373His	p.R373H	ENST00000374899	NM_018833.2	373	cGc/cAc	6/12	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.586389201236485	2		677	880	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874739	151874739	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs960435496	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	239	616	0	ENST00000262189.6:c.7799C>T	p.Pro2600Leu	p.P2600L	ENST00000262189	NM_170606.2	2600	cCg/cTg	38/59	1	2	FACETS	0.938	0.878	1	0.938	0.878	1	CLONAL	1	TRUE	1	0.586389201236485	2		616	869	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38184338	38184339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	159	402	0	ENST00000317025.8:c.1617dup	p.Gln540AlafsTer14	p.Q540Afs*14	ENST00000317025	NM_023034.1	539	-/G	7/24	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.586389201236485	2		402	526	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27183457	27183457	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	168	439	0	ENST00000380036.4:c.1031G>A	p.Gly344Asp	p.G344D	ENST00000380036	NM_000459.3	344	gGc/gAc	8/23	1	2	FACETS	0.953	0.881	1	0.953	0.881	1	CLONAL	1	TRUE	1	0.586389201236485	2		439	601	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045701	47045701	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	283	778	0	ENST00000377604.3:c.2582T>G	p.Ile861Ser	p.I861S	ENST00000377604	NM_001204468.1	861	aTt/aGt	23/24	1	2	FACETS	0.998	0.94	1	0.998	0.94	1	CLONAL	1	TRUE	1	0.586389201236485	2		778	967	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361086	70361091	+	inframe_deletion	In_Frame_Del	DEL	CAGCAA	CAGCAA	-	novel	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	152	604	0	ENST00000374080.3:c.6285_6290del	p.Gln2114_Gln2115del	p.Q2114_Q2115del	ENST00000374080		2092	CAGCAA/-	43/45	1	2	FACETS	0.572	0.522	0.623	0.572	0.522	0.623	SUBCLONAL	1	TRUE	1	0.586389201236485	2		604	907	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361160	70361161	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCAGCAA	rs1433422316	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	115	778	0	ENST00000374080.3:c.6361_6369dup	p.Gln2121_Gln2123dup	p.Q2121_Q2123dup	ENST00000374080		2121	-/CAGCAGCAA	43/45	1	2	FACETS	0.424	0.382	0.47	0.424	0.382	0.47	SUBCLONAL	1	TRUE	1	0.586389201236485	2		778	924	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76954109	76954109	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1557151486	NA	P-0065646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	54	230	0	ENST00000373344.5:c.142A>G	p.Ser48Gly	p.S48G	ENST00000373344	NM_000489.3	48	Agt/Ggt	3/35	1	2	FACETS	0.633	0.544	0.728	0.633	0.544	0.728	SUBCLONAL	1	TRUE	1	0.586389201236485	2		230	291	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577123	7577123	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876660333	NA	P-0065647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	684	591	0	ENST00000269305.4:c.815T>G	p.Val272Gly	p.V272G	ENST00000269305	NM_001126112.2	272	gTg/gGg	8/11	0.823780606854302	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.823780606854302	1		591	921	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0065648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	179	594	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		594	870	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021785	71021785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs112795301	NA	P-0065648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	60	576	0	ENST00000318789.4:c.1573C>T	p.Arg525Ter	p.R525*	ENST00000318789	NM_032682.5	525	Cga/Tga	18/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		576	756	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067836	30067836	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315499	NA	P-0065648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	167	586	0	ENST00000338641.4:c.1021C>T	p.Arg341Ter	p.R341*	ENST00000338641	NM_000268.3	341	Cga/Tga	11/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		586	727	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170273	119170273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368696716	NA	P-0065648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	52	635	0	ENST00000264033.4:c.2503C>T	p.Arg835Trp	p.R835W	ENST00000264033	NM_005188.3	835	Cgg/Tgg	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		635	934	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799625	3799626	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	novel	NA	P-0065648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	23	112	0	ENST00000262367.5:c.3836+2dup		p.X1279_splice	ENST00000262367	NM_004380.2	1279			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		112	275	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981167	201981168	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	100	663	0	ENST00000359651.3:c.248dup	p.Asn83LysfsTer9	p.N83Kfs*9	ENST00000359651		82	-/A	2/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		663	988	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099864	27099864	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	166	687	0	ENST00000324856.7:c.3743C>A	p.Ser1248Ter	p.S1248*	ENST00000324856	NM_006015.4	1248	tCa/tAa	15/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		687	848	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0065648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	209	497	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		497	740	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55225370	55225370	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	70	460	0	ENST00000275493.2:c.1222C>T	p.Gln408Ter	p.Q408*	ENST00000275493	NM_005228.3	408	Cag/Tag	11/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		460	630	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223191	36223191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373804780	NA	P-0065648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	75	861	1	ENST00000222270.7:c.5741G>A	p.Arg1914His	p.R1914H	ENST00000222270	NM_014727.1	1914	cGt/cAt	28/37	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		862	1064	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858702	9858702	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	89	706	0	ENST00000330684.3:c.2699C>T	p.Ser900Leu	p.S900L	ENST00000330684	NM_001134407.1	900	tCa/tTa	13/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		706	895	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124737	108124737	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1060501539	NA	P-0065648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	121	455	0	ENST00000278616.4:c.2095G>C	p.Glu699Gln	p.E699Q	ENST00000278616	NM_000051.3	699	Gaa/Caa	13/63	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		455	581	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245724	46245724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565624116	NA	P-0065648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	98	795	0	ENST00000334344.6:c.3818G>A	p.Arg1273Gln	p.R1273Q	ENST00000334344	NM_152641.2	1273	cGa/cAa	15/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		795	986	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729551	41729551	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1356119994	NA	P-0065648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	106	659	0	ENST00000242208.4:c.978C>G	p.Phe326Leu	p.F326L	ENST00000242208	NM_002192.2	326	ttC/ttG	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		659	1024	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175411	108175411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	76	235	0	ENST00000278616.4:c.5506G>A	p.Asp1836Asn	p.D1836N	ENST00000278616	NM_000051.3	1836	Gac/Aac	37/63	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		235	426	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432905	432905	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	156	514	0	ENST00000399788.2:c.2011G>C	p.Asp671His	p.D671H	ENST00000399788	NM_001042603.1	671	Gat/Cat	15/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		514	778	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881490	48881490	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	37	230	0	ENST00000267163.4:c.212G>C	p.Arg71Thr	p.R71T	ENST00000267163	NM_000321.2	71	aGa/aCa	2/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		230	471	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103407	2103407	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	92	514	0	ENST00000219476.3:c.290C>A	p.Ala97Asp	p.A97D	ENST00000219476	NM_000548.3	97	gCc/gAc	4/42	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		514	654	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2214488	2214488	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	84	629	0	ENST00000398665.3:c.1816G>C	p.Glu606Gln	p.E606Q	ENST00000398665	NM_032482.2	606	Gag/Cag	19/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		629	818	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259632	89259633	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	AA	novel	NA	P-0065648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	56	630	2	ENST00000336596.2:c.776_777delinsAA	p.Cys259Ter	p.C259*	ENST00000336596	NM_005233.5	259	tGC/tAA	3/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		632	705	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109309883	109309883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	16	219	0	ENST00000436639.2:c.1432G>A	p.Asp478Asn	p.D478N	ENST00000436639	NM_014454.2	478	Gat/Aat	9/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		219	300	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138201353	138201353	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	60	651	0	ENST00000237289.4:c.2052G>C	p.Gln684His	p.Q684H	ENST00000237289	NM_001270507.1	684	caG/caC	8/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		651	850	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485995	8485995	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs985218104	NA	P-0065648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	153	733	0	ENST00000356435.5:c.2822C>T	p.Pro941Leu	p.P941L	ENST00000356435		941	cCa/cTa	17/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		733	846	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504299	8504299	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	59	538	0	ENST00000356435.5:c.1784C>T	p.Ala595Val	p.A595V	ENST00000356435		595	gCt/gTt	12/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		538	751	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293673	137293673	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	134	706	0	ENST00000481739.1:c.224A>T	p.His75Leu	p.H75L	ENST00000481739	NM_002957.4	75	cAc/cTc	2/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		706	914	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70355020	70355020	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	67	661	0	ENST00000374080.3:c.4942G>C	p.Val1648Leu	p.V1648L	ENST00000374080		1648	Gtc/Ctc	36/45	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		661	968	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0065649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	113	358	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.214878150496854	3	FACETS	1	0.951	1	0.539	0.488	0.593	INDETERMINATE	1	TRUE	1	0.601498146955054	3		358	453	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0065649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	126	639	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.507	0.458	0.557	0.507	0.458	0.557	SUBCLONAL	1	TRUE	1	0.601498146955054	2		639	827	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	99	324	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	1	2	FACETS	0.546	0.488	0.607	0.546	0.488	0.607	SUBCLONAL	1	TRUE	1	0.601498146955054	2		324	603	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913255	NA	P-0065649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	105	468	0	ENST00000369535.4:c.183A>C	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caC	3/7	1	2	FACETS	0.639	0.575	0.708	0.639	0.575	0.708	SUBCLONAL	1	TRUE	1	0.601498146955054	2		468	546	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879904	44879904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs912069418	NA	P-0065649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	69	426	0	ENST00000377967.4:c.493C>T	p.Arg165Ter	p.R165*	ENST00000377967	NM_021140.2	165	Cga/Tga	6/29	1	2	FACETS	0.372	0.324	0.424	0.372	0.324	0.424	SUBCLONAL	1	TRUE	1	0.601498146955054	2		426	617	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453132	140453132	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913365	NA	P-0065649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	298	387	0	ENST00000288602.6:c.1803A>C	p.Lys601Asn	p.K601N	ENST00000288602	NM_004333.4	601	aaA/aaC	15/18	0.601498146955054	3	FACETS	0.896	0.849	0.944	0.896	0.849	0.944	CLONAL	2	TRUE	1	0.601498146955054	3		387	719	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101611	27101612	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0065649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	117	651	0	ENST00000324856.7:c.4899dup	p.Met1634HisfsTer14	p.M1634Hfs*14	ENST00000324856	NM_006015.4	1631	-/C	18/20	1	2	FACETS	0.572	0.516	0.631	0.572	0.516	0.631	SUBCLONAL	1	TRUE	1	0.601498146955054	2		651	680	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692783	89692783	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	177	256	0	ENST00000371953.3:c.270del	p.Phe90LeufsTer9	p.F90Lfs*9	ENST00000371953	NM_000314.4	89	ccT/cc	5/9	0.36432138918355	3	FACETS	1	0.939	1	0.67	0.626	0.714	CLONAL	2	TRUE	0	0.601498146955054	3		256	381	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591212	67591246	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	GAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCA	GAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCA	-	novel	NA	P-0065649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	108	477	0	ENST00000274335.5:c.1746-35_1746-1del		p.X582_splice	ENST00000274335		582			1	2	FACETS	0.554	0.498	0.614	0.554	0.498	0.614	SUBCLONAL	1	TRUE	1	0.601498146955054	2		477	648	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0065650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	55	80	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.272477646650137	4	FACETS	0.836	0.725	0.954	0.836	0.725	0.954	INDETERMINATE	2	TRUE	2	0.465749612500099	4		80	207	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0065650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	235	250	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	0.272477646650137	4	FACETS	0.909	0.85	0.969	0.909	0.85	0.969	INDETERMINATE	2	TRUE	2	0.465749612500099	4		250	814	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012389	29012389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161996687	NA	P-0065650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	31	431	0	ENST00000282397.4:c.482C>T	p.Thr161Met	p.T161M	ENST00000282397	NM_002019.4	161	aCg/aTg	4/30	0.151915647618812	2	FACETS	0.265	0.213	0.323	0.132	0.106	0.162	INDETERMINATE	1	TRUE	0	0.465749612500099	2		431	503	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487154	56487154	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	277	503	0	ENST00000267101.3:c.1300A>G	p.Lys434Glu	p.K434E	ENST00000267101	NM_001982.3	434	Aag/Gag	12/28	0.422195813571573	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.465749612500099	4		503	797	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1749278	1749279	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0065650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	105	343	0	ENST00000378609.4:c.93_94del	p.Gln32AspfsTer46	p.Q32Dfs*46	ENST00000378609	NM_002074.3	31	tcTCag/tcag	4/12	0.465749612500099	3	FACETS	0.819	0.734	0.908	0.273	0.244	0.303	CLONAL	1	TRUE	0	0.465749612500099	3		343	679	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256628	16256628	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	45	543	0	ENST00000375759.3:c.3893C>G	p.Ser1298Cys	p.S1298C	ENST00000375759	NM_015001.2	1298	tCt/tGt	11/15	0.465749612500099	3	FACETS	0.323	0.271	0.382	0.108	0.09	0.128	SUBCLONAL	1	TRUE	0	0.465749612500099	3		543	737	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087370	27087370	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	446	475	0	ENST00000324856.7:c.1945del	p.Leu649SerfsTer9	p.L649Sfs*9	ENST00000324856	NM_006015.4	648	gaC/ga	5/20	0.465749612500099	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	0	0.465749612500099	3		475	768	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446291	70446291	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	190	635	0	ENST00000373644.4:c.5231G>C	p.Arg1744Thr	p.R1744T	ENST00000373644	NM_030625.2	1744	aGa/aCa	11/12	0.422195813571573	4	FACETS	1	0.964	1	0.537	0.496	0.58	CLONAL	1	TRUE	2	0.465749612500099	4		635	1113	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101112	41101112	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1322	167	665	0	ENST00000373198.4:c.1244C>A	p.Thr415Asn	p.T415N	ENST00000373198	NM_133170.3	415	aCc/aAc	8/32	0.465749612500099	6	FACETS	0.93	0.852	1	0.31	0.284	0.338	CLONAL	1	TRUE	3	0.465749612500099	6		665	1489	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211811	123211813	+	inframe_deletion	In_Frame_Del	DEL	ATA	ATA	-	novel	NA	P-0065650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	60	330	0	ENST00000218089.9:c.2680_2682del	p.Asn894del	p.N894del	ENST00000218089	NM_001042749.1	893	tATAat/tat	27/35	0.32353757085456	3	FACETS	0.711	0.614	0.816	0.355	0.307	0.408	SUBCLONAL	1	TRUE	1	0.465749612500099	3		330	447	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0065651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	10	80	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.204107006195712	4	FACETS	0.702	0.477	0.985	0.351	0.238	0.493	CLONAL	1	TRUE	2	0.211644695297993	4		80	163	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0065651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	226	656	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.211644695297993	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.211644695297993	2		656	988	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478923	56478923	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1308361325	NA	P-0065651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	101	500	0	ENST00000267101.3:c.379T>C	p.Ser127Pro	p.S127P	ENST00000267101	NM_001982.3	127	Tcc/Ccc	3/28	0.211644695297993	3	FACETS	1	0.964	1	0.593	0.529	0.661	CLONAL	1	TRUE	1	0.211644695297993	3		500	890	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101095	27101096	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0065651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	93	553	0	ENST00000324856.7:c.4377_4378del	p.Phe1459LeufsTer31	p.F1459Lfs*31	ENST00000324856	NM_006015.4	1459	ttTGgc/ttgc	18/20	0.211644695297993	3	FACETS	0.974	0.864	1	0.487	0.432	0.546	CLONAL	1	TRUE	1	0.211644695297993	3		553	998	SUCCESS
APC	324	MSKCC	GRCh37	5	112174175	112174175	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	39	414	0	ENST00000257430.4:c.2884G>C	p.Asp962His	p.D962H	ENST00000257430	NM_000038.5	962	Gat/Cat	16/16	0.203851563870296	3	FACETS	0.767	0.635	0.915	0.384	0.317	0.458	CLONAL	1	TRUE	1	0.211644695297993	3		414	531	SUCCESS
APC	324	MSKCC	GRCh37	5	112174842	112174843	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CACAGATA	novel	NA	P-0065651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	45	440	0	ENST00000257430.4:c.3552_3559dup	p.Ile1187ThrfsTer81	p.I1187Tfs*81	ENST00000257430	NM_000038.5	1184	gcc/gcCACAGATAc	16/16	0.203851563870296	3	FACETS	0.801	0.672	0.944	0.401	0.336	0.472	CLONAL	1	TRUE	1	0.211644695297993	3		440	587	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0065653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	34	286	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.191217139739198	2		286	272	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0065653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	63	829	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.191217139739198	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.191217139739198	1		829	441	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575200	48575200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500743	NA	P-0065653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	16	362	1	ENST00000342988.3:c.394C>T	p.His132Tyr	p.H132Y	ENST00000342988	NM_005359.5	132	Cac/Tac	3/12	0.191217139739198	1	FACETS	0.86	0.638	1	0.86	0.638	1	CLONAL	1	TRUE	0	0.191217139739198	1		363	176	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004276	150004276	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	14	406	0	ENST00000253339.5:c.1949T>A	p.Val650Glu	p.V650E	ENST00000253339		650	gTa/gAa	3/7	1	2	FACETS	0.755	0.547	1	0.755	0.547	1	CLONAL	1	TRUE	1	0.191217139739198	2		406	194	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974809	21974810	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	G	novel	NA	P-0065653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	73	721	0	ENST00000304494.5:c.17_18delinsC	p.Gly6AlafsTer20	p.G6Afs*20	ENST00000304494	NM_000077.4	6	gGG/gC	1/3	0.191217139739198	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.191217139739198	1		721	491	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50763871	50763871	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	33	454	0	ENST00000307179.4:c.728C>A	p.Ser243Tyr	p.S243Y	ENST00000307179		243	tCt/tAt	8/20	0.314709392682996	1	FACETS	0.832	0.691	0.984	0.832	0.691	0.984	CLONAL	1	TRUE	0	0.478848345233287	1		454	126	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0065654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	50	467	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.268590160557861	1	FACETS	0.679	0.582	0.783	0.679	0.582	0.783	INDETERMINATE	1	TRUE	0	0.478848345233287	1		467	234	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191571	10191591	+	inframe_deletion	In_Frame_Del	DEL	GGAAGACCACCCAAATGTGCA	GGAAGACCACCCAAATGTGCA	-	novel	NA	P-0065654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	79	498	0	ENST00000256474.2:c.565_585del	p.Glu189_Gln195del	p.E189_Q195del	ENST00000256474	NM_000551.3	188	ctGGAAGACCACCCAAATGTGCAg/ctg	3/3	0.478848345233287	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.478848345233287	1		498	224	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163163	47163185	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCCTTCTCCTCTTTCATCTAA	CCTCCTTCTCCTCTTTCATCTAA	-	novel	NA	P-0065654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	22	439	0	ENST00000409792.3:c.2941_2963del	p.Leu981ThrfsTer6	p.L981Tfs*6	ENST00000409792	NM_014159.6	981	TTAGATGAAAGAGGAGAAGGAGGa/a	3/21	0.478848345233287	1	FACETS	0.768	0.608	0.944	0.768	0.608	0.944	CLONAL	1	TRUE	0	0.478848345233287	1		439	91	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061240	38061240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	72	784	0	ENST00000250448.2:c.749C>T	p.Ser250Phe	p.S250F	ENST00000250448	NM_004496.3	250	tCc/tTc	2/2	1	2	FACETS	0.849	0.746	0.959	0.849	0.746	0.959	CLONAL	1	TRUE	1	0.43820377579416	2		784	387	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696431	47696431	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519969	NA	P-0065655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	83	506	0	ENST00000347630.2:c.392G>C	p.Trp131Ser	p.W131S	ENST00000347630	NM_001007230.1	131	tGg/tCg	6/11	1	2	FACETS	0.992	0.881	1	0.992	0.881	1	CLONAL	1	TRUE	1	0.43820377579416	2		506	382	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239419	105239419	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	76	791	0	ENST00000349310.3:c.968A>G	p.Asp323Gly	p.D323G	ENST00000349310	NM_001014432.1	323	gAc/gGc	12/15	1	2	FACETS	0.889	0.784	1	0.889	0.784	1	CLONAL	1	TRUE	1	0.43820377579416	2		791	390	SUCCESS
ALB	213	MSKCC	GRCh37	4	74270816	74270841	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTCTTCCCTTGCCCAGACAAGAGTG	TTTCTTCCCTTGCCCAGACAAGAGTG	-	novel	NA	P-0065655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	15	229	0	ENST00000295897.4:c.80-17_88del		p.X27_splice	ENST00000295897	NM_000477.5	27		2/15	1	2	FACETS	0.442	0.325	0.581	0.442	0.325	0.581	SUBCLONAL	1	TRUE	1	0.43820377579416	2		229	155	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940401	31940401	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	67	732	1	ENST00000375333.2:c.434C>T	p.Ser145Leu	p.S145L	ENST00000375333	NM_032454.1	145	tCg/tTg	3/8	1	2	FACETS	0.744	0.649	0.846	0.744	0.649	0.846	SUBCLONAL	1	TRUE	1	0.43820377579416	2		733	411	SUCCESS
APC	324	MSKCC	GRCh37	5	112175962	112175963	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	A	novel	NA	P-0065655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	48	433	0	ENST00000257430.4:c.4671_4672delinsA	p.Asp1558IlefsTer7	p.D1558Ifs*7	ENST00000257430	NM_000038.5	1557	atTGat/atAat	16/16	0.381799919941867	1	FACETS	0.671	0.572	0.778	0.671	0.572	0.778	SUBCLONAL	1	TRUE	0	0.43820377579416	1		433	255	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256495	115256495	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065663-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	170	353	0	ENST00000369535.4:c.216G>T	p.Met72Ile	p.M72I	ENST00000369535	NM_002524.4	72	atG/atT	3/7	1	2	FACETS	0.946	0.876	1	0.946	0.876	1	CLONAL	1	TRUE	1	0.691477205622026	2		353	520	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423432	116423432	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065663-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	285	319	0	ENST00000397752.3:c.3707G>T	p.Ser1236Ile	p.S1236I	ENST00000397752	NM_000245.2	1236	aGt/aTt	19/21	0.691477205622026	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.691477205622026	3		319	532	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528779	8528780	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	TC	TC	CA	novel	NA	P-0065663-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	188	384	0	ENST00000356435.5:c.353-1_353delinsTG		p.X118_splice	ENST00000356435		118		4/35	1	2	FACETS	0.957	0.89	1	0.957	0.89	1	CLONAL	1	TRUE	1	0.691477205622026	2		384	568	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0065664-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	101	602	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.246027899417919	2		602	691	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065664-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	114	551	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.246027899417919	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.246027899417919	1		551	652	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6213991	6213991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs898531747	NA	P-0065664-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	33	561	0	ENST00000252674.7:c.1366G>A	p.Glu456Lys	p.E456K	ENST00000252674	NM_005934.3	456	Gag/Aag	9/12	1	2	FACETS	0.443	0.359	0.537	0.443	0.359	0.537	SUBCLONAL	1	TRUE	1	0.246027899417919	2		561	606	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6214030	6214030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749861795	NA	P-0065664-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	30	539	1	ENST00000252674.7:c.1327G>A	p.Glu443Lys	p.E443K	ENST00000252674	NM_005934.3	443	Gag/Aag	9/12	1	2	FACETS	0.409	0.328	0.5	0.409	0.328	0.5	SUBCLONAL	1	TRUE	1	0.246027899417919	2		540	597	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6214046	6214046	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065664-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	30	528	0	ENST00000252674.7:c.1311G>C	p.Leu437Phe	p.L437F	ENST00000252674	NM_005934.3	437	ttG/ttC	9/12	1	2	FACETS	0.429	0.344	0.525	0.429	0.344	0.525	SUBCLONAL	1	TRUE	1	0.246027899417919	2		528	569	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31372604	31372604	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065664-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	40	561	0	ENST00000328111.2:c.245C>G	p.Ser82Cys	p.S82C	ENST00000328111	NM_006892.3	82	tCt/tGt	4/23	0.202204622230355	1	FACETS	0.417	0.345	0.497	0.417	0.345	0.497	SUBCLONAL	1	TRUE	0	0.246027899417919	1		561	684	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188386	32188386	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065664-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	57	807	0	ENST00000375023.3:c.955G>C	p.Glu319Gln	p.E319Q	ENST00000375023	NM_004557.3	319	Gag/Cag	6/30	1	2	FACETS	0.511	0.437	0.592	0.511	0.437	0.592	SUBCLONAL	1	TRUE	1	0.246027899417919	2		807	907	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109312032	109312032	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065664-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	82	394	0	ENST00000436639.2:c.1240T>A	p.Cys414Ser	p.C414S	ENST00000436639	NM_014454.2	414	Tgc/Agc	8/10	0.130178291718507	3	FACETS	1	0.966	1	0.631	0.557	0.71	INDETERMINATE	1	TRUE	1	0.246027899417919	3		394	593	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0065665-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	321	286	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.599562222063045	4	FACETS	0.957	0.906	1	0.957	0.906	1	CLONAL	2	TRUE	2	0.609500694253896	4		286	886	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0065665-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	107	80	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.229420782049916	3	FACETS	0.758	0.69	0.829	0.758	0.69	0.829	INDETERMINATE	2	TRUE	1	0.609500694253896	3		80	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0065665-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	426	442	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.609500694253896	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.609500694253896	3		442	889	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419986	41419986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372989163	NA	P-0065665-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	222	543	0	ENST00000373198.4:c.335G>A	p.Arg112His	p.R112H	ENST00000373198	NM_133170.3	112	cGt/cAt	3/32	0.599562222063045	4	FACETS	1	0.958	1	0.521	0.484	0.559	CLONAL	1	TRUE	2	0.609500694253896	4		543	1125	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0065665-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	161	375	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	1	2	FACETS	0.966	0.891	1	0.966	0.891	1	CLONAL	1	TRUE	1	0.609500694253896	2		375	547	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672347	86672347	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065665-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	208	359	0	ENST00000274376.6:c.2149A>T	p.Ile717Phe	p.I717F	ENST00000274376	NM_002890.2	717	Atc/Ttc	16/25	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.609500694253896	2		359	628	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114799877	114799878	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065665-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	157	325	0	ENST00000543371.1:c.545dup	p.His182GlnfsTer5	p.H182Qfs*5	ENST00000543371	NM_001198531.1	182	cac/cAac	5/14	1	2	FACETS	0.92	0.847	0.995	0.92	0.847	0.995	CLONAL	1	TRUE	1	0.609500694253896	2		325	560	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114905841	114905841	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065665-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	217	384	0	ENST00000543371.1:c.860A>G	p.Asn287Ser	p.N287S	ENST00000543371	NM_001198531.1	287	aAt/aGt	8/14	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.609500694253896	2		384	707	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918790	32918790	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1243544218	NA	P-0065665-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	109	244	0	ENST00000380152.3:c.6937G>A	p.Gly2313Ser	p.G2313S	ENST00000380152		2313	Ggc/Agc	12/27	0.609500694253896	3	FACETS	0.95	0.858	1	0.475	0.429	0.524	CLONAL	1	TRUE	1	0.609500694253896	3		244	491	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672254	86672254	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065665-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	235	434	0	ENST00000274376.6:c.2056A>G	p.Thr686Ala	p.T686A	ENST00000274376	NM_002890.2	686	Aca/Gca	16/25	1	2	FACETS	0.96	0.899	1	0.96	0.899	1	CLONAL	1	TRUE	1	0.609500694253896	2		434	803	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0065666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	15	286	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.534	0.389	0.71	0.534	0.389	0.71	SUBCLONAL	1	TRUE	1	0.13	2		286	432	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591888	48591888	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	48	600	0	ENST00000342988.3:c.1051G>T	p.Asp351Tyr	p.D351Y	ENST00000342988	NM_005359.5	351	Gat/Tat	9/12	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.13	2		600	724	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016571	12016571	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	31	383	0	ENST00000353533.5:c.707T>G	p.Leu236Arg	p.L236R	ENST00000353533	NM_003010.3	236	cTt/cGt	7/11	1	2	FACETS	0.96	0.775	1	0.96	0.775	1	CLONAL	1	TRUE	1	0.13	2		383	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576851	7576852	+	splice_donor_variant	Splice_Site	INS	-	-	C	novel	NA	P-0065666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	51	718	0	ENST00000269305.4:c.993+1dup		p.X331_splice	ENST00000269305	NM_001126112.2	331			1	2	FACETS	0.987	0.837	1	0.987	0.837	1	CLONAL	1	TRUE	1	0.13	2		718	795	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0065667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	57	566	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	1	2	FACETS	0.477	0.408	0.552	0.477	0.408	0.552	SUBCLONAL	1	FALSE	1	0.3	2		566	797	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866666	37866666	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs757811990	NA	P-0065667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	183	807	0	ENST00000269571.5:c.833C>A	p.Thr278Lys	p.T278K	ENST00000269571		278	aCg/aAg	7/27	0.134466077678529	3	FACETS	1	0.981	1	0.4	0.369	0.434	INDETERMINATE	1	FALSE	0	0.3	3		807	1168	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0065668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	127	602	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.322101451638744	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.322101451638744	2		602	339	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0065668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	121	244	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.322101451638744	4	FACETS	1	0.924	1	1	0.924	1	CLONAL	3	TRUE	1	0.322101451638744	4		244	328	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0065668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	79	352	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.322101451638744	4	FACETS	0.86	0.761	0.965	0.86	0.761	0.965	CLONAL	2	TRUE	2	0.322101451638744	4		352	377	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682399	52682400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	71	275	0	ENST00000394830.3:c.773dup	p.Asn258LysfsTer6	p.N258Kfs*6	ENST00000394830	NM_018313.4	258	aat/aaAt	8/30	0.322101451638744	2	FACETS	0.829	0.732	0.931	0.829	0.732	0.931	CLONAL	2	TRUE	0	0.322101451638744	2		275	266	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579575	7579575	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	399	571	0	ENST00000269305.4:c.112C>T	p.Gln38Ter	p.Q38*	ENST00000269305	NM_001126112.2	38	Caa/Taa	4/11	0.322101451638744	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.322101451638744	3		571	909	SUCCESS
APC	324	MSKCC	GRCh37	5	112173975	112173975	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0065668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	183	406	0	ENST00000257430.4:c.2684C>G	p.Ser895Ter	p.S895*	ENST00000257430	NM_000038.5	895	tCa/tGa	16/16	0.322101451638744	3	FACETS	0.89	0.824	0.959	0.89	0.824	0.959	CLONAL	2	TRUE	1	0.322101451638744	3		406	741	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217299	11217299	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519779	NA	P-0065668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	117	391	1	ENST00000361445.4:c.4379T>C	p.Leu1460Pro	p.L1460P	ENST00000361445	NM_004958.3	1460	cTt/cCt	30/58	0.322101451638744	3	FACETS	1	0.935	1	0.524	0.472	0.579	CLONAL	1	TRUE	1	0.322101451638744	3		392	805	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541486	187541486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	221	418	0	ENST00000441802.2:c.6254C>T	p.Pro2085Leu	p.P2085L	ENST00000441802	NM_005245.3	2085	cCc/cTc	10/27	0.322101451638744	4	FACETS	0.949	0.884	1	0.949	0.884	1	CLONAL	2	TRUE	2	0.322101451638744	4		418	956	SUCCESS
APC	324	MSKCC	GRCh37	5	112175617	112175617	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	134	509	1	ENST00000257430.4:c.4326del	p.Pro1443LeufsTer30	p.P1443Lfs*30	ENST00000257430	NM_000038.5	1442	ccT/cc	16/16	0.322101451638744	3	FACETS	0.988	0.896	1	0.494	0.448	0.542	CLONAL	1	TRUE	1	0.322101451638744	3		510	978	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241934	133241934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	114	420	0	ENST00000320574.5:c.2422C>T	p.His808Tyr	p.H808Y	ENST00000320574	NM_006231.2	808	Cac/Tac	21/49	0.322101451638744	4	FACETS	0.967	0.869	1	0.322	0.289	0.357	CLONAL	1	TRUE	1	0.322101451638744	4		420	968	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914446	32914446	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	24	367	0	ENST00000380152.3:c.5954C>A	p.Ser1985Tyr	p.S1985Y	ENST00000380152		1985	tCt/tAt	11/27	0.322101451638744	5	FACETS	0.67	0.525	0.836	0.167	0.131	0.209	SUBCLONAL	1	TRUE	1	0.322101451638744	5		367	330	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936680	32936680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80359009	NA	P-0065668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	54	289	0	ENST00000380152.3:c.7826G>A	p.Gly2609Asp	p.G2609D	ENST00000380152		2609	gGt/gAt	17/27	0.322101451638744	5	FACETS	1	0.881	1	0.258	0.221	0.3	CLONAL	1	TRUE	1	0.322101451638744	5		289	481	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871257	35871258	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	78	313	0	ENST00000216797.5:c.915dup	p.Asp306Ter	p.D306*	ENST00000216797	NM_020529.2	305	-/T	6/6	0.322101451638744	3	FACETS	0.853	0.75	0.964	0.427	0.375	0.482	CLONAL	1	TRUE	1	0.322101451638744	3		313	659	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376364	15376365	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAGGAGGATTCGGCT	novel	NA	P-0065668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	181	571	0	ENST00000263377.2:c.635_649dup	p.Gln212_Pro216dup	p.Q212_P216dup	ENST00000263377	NM_058243.2	212	cct/cAGCCGAATCCTCCTCct	5/20	0.322101451638744	3	FACETS	1	0.988	1	0.696	0.641	0.752	CLONAL	1	TRUE	1	0.322101451638744	3		571	938	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144380619	144380619	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	59	327	0	ENST00000262995.4:c.1757G>A	p.Ser586Asn	p.S586N	ENST00000262995	NM_207123.2	586	aGt/aAt	8/11	0.322101451638744	4	FACETS	0.874	0.759	0.997	0.874	0.759	0.997	CLONAL	2	TRUE	2	0.322101451638744	4		327	277	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522504	67522504	+	start_lost	Translation_Start_Site	SNP	A	A	T	novel	NA	P-0065668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	166	314	0	ENST00000274335.5:c.1A>T	p.Met1?	p.M1?	ENST00000274335		1	Atg/Ttg	1/15	0.322101451638744	3	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	1	0.322101451638744	3		314	595	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579368	7579368	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	434	690	0	ENST00000269305.4:c.319T>G	p.Tyr107Asp	p.Y107D	ENST00000269305	NM_001126112.2	107	Tac/Gac	4/11	0.634860763664965	3	FACETS	0.958	0.928	0.986	0.958	0.928	0.986	CLONAL	3	TRUE	0	0.669817240923696	3		690	602	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372044	55372044	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	86	697	1	ENST00000297316.4:c.734G>T	p.Cys245Phe	p.C245F	ENST00000297316	NM_022454.3	245	tGc/tTc	2/2	0.669817240923696	6	FACETS	0.471	0.415	0.531	0.118	0.103	0.133	SUBCLONAL	1	TRUE	2	0.669817240923696	6		698	1276	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721121	39721121	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	584	415	0	ENST00000361337.2:c.624A>C	p.Glu208Asp	p.E208D	ENST00000361337	NM_003286.2	208	gaA/gaC	9/21	0.61521573623597	5	FACETS	1	0.993	1			1	CLONAL	3	TRUE	NA	0.669817240923696	5		415	1059	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890084	76890084	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0065669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	304	307	0	ENST00000373344.5:c.4809+1G>A		p.X1603_splice	ENST00000373344	NM_000489.3	1603			0.672083491332	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.669817240923696	2		307	429	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030221	180030221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143739828	NA	P-0065671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	152	646	0	ENST00000261937.6:c.4063G>A	p.Val1355Met	p.V1355M	ENST00000261937	NM_182925.4	1355	Gtg/Atg	30/30	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.274455297073311	2		646	943	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844182	68844182	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	166	504	0	ENST00000261769.5:c.770A>T	p.Asp257Val	p.D257V	ENST00000261769	NM_004360.3	257	gAc/gTc	6/16	0.195505739249372	2	FACETS	1	0.989	1	0.747	0.687	0.809	CLONAL	1	FALSE	0	0.274455297073311	2		504	810	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579707	7579710	+	frameshift_variant	Frame_Shift_Del	DEL	TTGT	TTGT	-	novel	NA	P-0065671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	141	446	0	ENST00000269305.4:c.86_89del	p.Asn29ThrfsTer14	p.N29Tfs*14	ENST00000269305	NM_001126112.2	29	aACAAc/ac	3/11	0.197090490277756	2	FACETS	1	0.985	1	0.691	0.631	0.755	CLONAL	1	FALSE	0	0.274455297073311	2		446	743	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805883	46805883	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	183	670	2	ENST00000290295.7:c.73C>G	p.Arg25Gly	p.R25G	ENST00000290295	NM_006361.5	25	Cgg/Ggg	1/2	0.17343331538604	4	FACETS	1	0.989	1	0.741	0.683	0.802	CLONAL	1	FALSE	2	0.274455297073311	4		672	1147	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211146	55211146	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	120	451	0	ENST00000275493.2:c.389C>G	p.Thr130Ser	p.T130S	ENST00000275493	NM_005228.3	130	aCc/aGc	3/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.274455297073311	2		451	798	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911496	101911496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	83	345	0	ENST00000374994.4:c.1421G>A	p.Cys474Tyr	p.C474Y	ENST00000374994	NM_004612.2	474	tGt/tAt	9/9	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.274455297073311	2		345	528	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779545	3779545	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	473	699	0	ENST00000262367.5:c.5503G>T	p.Glu1835Ter	p.E1835*	ENST00000262367	NM_004380.2	1835	Gaa/Taa	31/31	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.841251430000593	2		699	1089	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033236	69033236	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	245	496	0	ENST00000288368.4:c.3676C>A	p.Pro1226Thr	p.P1226T	ENST00000288368	NM_024870.2	1226	Ccc/Acc	30/40	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.841251430000593	2		496	558	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0065673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	175	1407	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1407	447	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0065673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	344	532	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		532	613	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0065673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	327	554	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		554	490	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720671	89720671	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587782607	NA	P-0065673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	54	109	0	ENST00000371953.3:c.822G>A	p.Trp274Ter	p.W274*	ENST00000371953	NM_000314.4	274	tgG/tgA	8/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		109	85	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200413	138200413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756591879	NA	P-0065673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	64	634	0	ENST00000237289.4:c.1831G>A	p.Gly611Ser	p.G611S	ENST00000237289	NM_001270507.1	611	Ggc/Agc	7/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		634	1143	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420997	49420997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	205	558	0	ENST00000301067.7:c.14752C>T	p.Pro4918Ser	p.P4918S	ENST00000301067	NM_003482.3	4918	Cct/Tct	48/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		558	583	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350537	89350537	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	114	256	0	ENST00000301030.4:c.2413G>A	p.Glu805Lys	p.E805K	ENST00000301030	NM_001256183.1	805	Gaa/Aaa	9/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		256	383	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380283	25380283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913528	NA	P-0065674-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	11	565	0	ENST00000311936.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000311936	NM_004985.3	59	Gca/Aca	3/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		565	523	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412647	63412648	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065674-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	61	417	0	ENST00000330258.3:c.519dup	p.Ser174Ter	p.S174*	ENST00000330258	NM_152424.3	173	-/T	2/2	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		417	272	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0065675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	113	170	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.744986019900133	5	FACETS	1	0.933	1	1	0.933	1	CLONAL	3	TRUE	2	0.840056208265204	5		170	201	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744483	41744483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755240418	NA	P-0065675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	204	517	0	ENST00000301178.4:c.1103G>A	p.Arg368Gln	p.R368Q	ENST00000301178	NM_021913.4	368	cGg/cAg	8/20	0.840056208265204	3	FACETS	0.978	0.911	1	0.489	0.455	0.524	CLONAL	1	TRUE	1	0.840056208265204	3		517	705	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2116002	2116002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs281875238	NA	P-0065675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	229	511	0	ENST00000349721.2:c.3637C>T	p.Arg1213Trp	p.R1213W	ENST00000349721	NM_003070.3	1213	Cgg/Tgg	25/34	0.840056208265204	3	FACETS	1	0.978	1	0.55	0.515	0.586	CLONAL	1	TRUE	1	0.840056208265204	3		511	704	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0065676-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	135	426	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.531107785329952	2		426	489	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78854237	78854237	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065676-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	147	548	0	ENST00000306801.3:c.1532A>G	p.Lys511Arg	p.K511R	ENST00000306801	NM_020761.2	511	aAg/aGg	14/34	0.531107785329952	3	FACETS	0.93	0.851	1	0.465	0.425	0.507	CLONAL	1	TRUE	1	0.531107785329952	3		548	753	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0065678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	1741	476	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.555045132002358	14	FACETS	1	0.993	1	0.932	0.917	0.946	CLONAL	11	TRUE	2	0.555045132002358	14		476	2429	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0065678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	82	170	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.505057537868192	4	FACETS	0.919	0.813	1	0.306	0.271	0.344	CLONAL	1	TRUE	1	0.555045132002358	4		170	500	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101118	41101118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751886972	NA	P-0065678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	79	551	0	ENST00000373198.4:c.1238C>T	p.Ala413Val	p.A413V	ENST00000373198	NM_133170.3	413	gCg/gTg	8/32	0.336636726340274	4	FACETS	0.511	0.449	0.579			1	SUBCLONAL	1	TRUE	NA	0.555045132002358	4		551	866	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709469	176709469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	69	376	0	ENST00000439151.2:c.5896G>A	p.Glu1966Lys	p.E1966K	ENST00000439151	NM_022455.4	1966	Gaa/Aaa	19/23	0.325188971554084	3	FACETS	0.607	0.53	0.691	0.304	0.265	0.346	INDETERMINATE	1	TRUE	1	0.555045132002358	3		376	523	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50784085	50784085	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	78	427	0	ENST00000398568.2:c.476C>G	p.Ser159Cys	p.S159C	ENST00000398568	NM_001042412.1	159	tCc/tGc	3/18	0.191049108833638	2	FACETS	0.419	0.368	0.474	0.21	0.184	0.237	INDETERMINATE	1	TRUE	0	0.555045132002358	2		427	670	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652006	36652007	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0065678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	349	567	0	ENST00000244741.5:c.130dup	p.Glu44GlyfsTer4	p.E44Gfs*4	ENST00000244741	NM_000389.4	43	cag/caGg	2/3	0.430931839982387	3	FACETS	0.932	0.886	0.978	0.932	0.886	0.978	CLONAL	2	TRUE	1	0.555045132002358	3		567	862	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039176	49039176	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	278	283	1	ENST00000267163.4:c.2254del	p.Ile752LeufsTer2	p.I752Lfs*2	ENST00000267163	NM_000321.2	752	Att/tt	22/27	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.555045132002358	2		284	435	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374867	45374867	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	82	397	0	ENST00000262160.6:c.976G>C	p.Glu326Gln	p.E326Q	ENST00000262160	NM_005901.5	326	Gaa/Caa	8/11	0.255978517442769	2	FACETS	0.455	0.401	0.513	0.228	0.2	0.257	INDETERMINATE	1	TRUE	0	0.555045132002358	2		397	649	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560930	9560930	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	85	529	0	ENST00000353224.5:c.852G>T	p.Gln284His	p.Q284H	ENST00000353224	NM_177990.2	284	caG/caT	4/10	0.484083445035887	4	FACETS	0.469	0.413	0.529	0.234	0.206	0.265	SUBCLONAL	1	TRUE	2	0.555045132002358	4		529	1016	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280161	142280161	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	85	317	0	ENST00000350721.4:c.1273G>C	p.Asp425His	p.D425H	ENST00000350721	NM_001184.3	425	Gat/Cat	5/47	0.505057537868192	4	FACETS	0.563	0.497	0.634	0.188	0.165	0.212	SUBCLONAL	1	TRUE	1	0.555045132002358	4		317	846	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	894987	894987	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	67	308	0	ENST00000166345.3:c.178G>C	p.Glu60Gln	p.E60Q	ENST00000166345	NM_004237.3	60	Gag/Cag	2/13	0.555045132002358	7	FACETS	0.497	0.43	0.57	0.099	0.086	0.114	SUBCLONAL	1	TRUE	2	0.555045132002358	7		308	1160	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651924	36651933	+	frameshift_variant	Frame_Shift_Del	DEL	AAGGCCTGCC	AAGGCCTGCC	GCT	novel	NA	P-0065678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	200	546	1	ENST00000244741.5:c.46_55delinsGCT	p.Lys16AlafsTer13	p.K16Afs*13	ENST00000244741	NM_000389.4	16	AAGGCCTGCCgc/GCTgc	2/3	0.430931839982387	3	FACETS	1	0.979	1	0.569	0.528	0.611	CLONAL	1	TRUE	1	0.555045132002358	3		547	809	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0065680-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	17	491	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.156861160444582	2	FACETS	0.772	0.591	0.975	0.772	0.591	0.975	INDETERMINATE	2	FALSE	0	0.314481599062992	2		491	70	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578528	7578528	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065680-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	147	646	0	ENST00000269305.4:c.402T>G	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	ttT/ttG	5/11	0.314481599062992	2	FACETS	0.972	0.894	1	0.972	0.894	1	CLONAL	2	FALSE	0	0.314481599062992	2		646	481	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371654	55371654	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065680-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	36	641	0	ENST00000297316.4:c.344G>A	p.Arg115Gln	p.R115Q	ENST00000297316	NM_022454.3	115	cGg/cAg	2/2	1	2	FACETS	0.436	0.358	0.524	0.436	0.358	0.524	SUBCLONAL	1	FALSE	1	0.314481599062992	2		641	525	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136175	64136175	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0065680-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	47	617	0	ENST00000334205.4:c.1335-1G>C		p.X445_splice	ENST00000334205	NM_003942.2	445			1	2	FACETS	0.58	0.49	0.681	0.58	0.49	0.681	SUBCLONAL	1	FALSE	1	0.314481599062992	2		617	515	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513282	44513287	+	inframe_deletion	In_Frame_Del	DEL	CCACCG	CCACCG	-	rs745888281	NA	P-0065681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	9	485	0	ENST00000291552.4:c.648_653del	p.Gly222_Gly223del	p.G222_G223del	ENST00000291552	NM_006758.2	216	ggCGGTGGt/ggt	8/8	1	2	FACETS	0.134	0.088	0.193	0.134	0.088	0.193	SUBCLONAL	1	TRUE	1	0.469420370542317	2		485	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0065682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	33	472	0	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	1	2	FACETS	0.666	0.544	0.803	0.666	0.544	0.803	SUBCLONAL	1	FALSE	1	0.329223576900086	2		472	301	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602764	10602764	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	8	630	0	ENST00000171111.5:c.814C>T	p.Arg272Cys	p.R272C	ENST00000171111	NM_203500.1	272	Cgc/Tgc	3/6	0.189657815462402	3	FACETS	0.157	0.1	0.231	0.078	0.05	0.116	INDETERMINATE	1	FALSE	1	0.329223576900086	3		630	361	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162475165	162475165	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	10	444	0	ENST00000366898.1:c.576G>A	p.Met192Ile	p.M192I	ENST00000366898	NM_004562.2	192	atG/atA	5/12	1	2	FACETS	0.413	0.281	0.579	0.413	0.281	0.579	SUBCLONAL	1	FALSE	1	0.329223576900086	2		444	147	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266486	41266486	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775104326	NA	P-0065683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	16	485	0	ENST00000349496.5:c.283C>T	p.Arg95Ter	p.R95*	ENST00000349496	NM_001904.3	95	Cga/Tga	4/15	0.537936220138733	1	FACETS	0.154	0.113	0.202	0.154	0.113	0.202	SUBCLONAL	1	TRUE	0	0.537936220138733	1		485	283	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105861	27105861	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	99	530	0	ENST00000324856.7:c.5473del	p.Val1825TrpfsTer58	p.V1825Wfs*58	ENST00000324856	NM_006015.4	1824	gtG/gt	20/20	0.537936220138733	1	FACETS	0.879	0.795	0.967	0.879	0.795	0.967	CLONAL	1	TRUE	0	0.537936220138733	1		530	306	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438567	52438582	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGCGGCCCACACCT	GCTGCGGCCCACACCT	-	novel	NA	P-0065683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	99	552	0	ENST00000460680.1:c.1137_1152del	p.Gly380GlufsTer45	p.G380Efs*45	ENST00000460680	NM_004656.3	379	gcAGGTGTGGGCCGCAGC/gc	12/17	0.537936220138733	1	FACETS	0.894	0.808	0.982	0.894	0.808	0.982	CLONAL	1	TRUE	0	0.537936220138733	1		552	301	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0065684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	44	170	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.531792200687963	2		170	119	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0065684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	55	497	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.949	0.822	1	0.949	0.822	1	CLONAL	1	FALSE	1	0.531792200687963	2		497	218	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292745	91292745	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	85	486	0	ENST00000355112.3:c.247C>T	p.Gln83Ter	p.Q83*	ENST00000355112	NM_000057.2	83	Cag/Tag	3/22	1	2	FACETS	0.787	0.7	0.88	0.787	0.7	0.88	SUBCLONAL	1	FALSE	1	0.531792200687963	2		486	406	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971000	21971000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	311	681	0	ENST00000304494.5:c.358G>T	p.Glu120Ter	p.E120*	ENST00000304494	NM_000077.4	120	Gag/Tag	2/3	0.531792200687963	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	FALSE	0	0.531792200687963	2		681	519	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149917	202149917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	111	586	0	ENST00000358485.4:c.1358C>T	p.Pro453Leu	p.P453L	ENST00000358485	NM_001080125.1	453	cCg/cTg	8/9	0.150401518063722	0	FACETS	0.487	0.442	0.535			1	INDETERMINATE	1	FALSE	0	0.531792200687963	0		586	401	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781288	NA	P-0065684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	117	597	0	ENST00000269305.4:c.422G>T	p.Cys141Phe	p.C141F	ENST00000269305	NM_001126112.2	141	tGc/tTc	5/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	FALSE	1	0.531792200687963	2		597	424	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486130	8486130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	101	534	0	ENST00000356435.5:c.2687C>T	p.Ser896Leu	p.S896L	ENST00000356435		896	tCa/tTa	17/35	0.531792200687963	2	FACETS	0.922	0.83	1	0.461	0.415	0.509	CLONAL	1	FALSE	0	0.531792200687963	2		534	412	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278818	1278818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs939537185	NA	P-0065684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	131	562	0	ENST00000310581.5:c.2224C>T	p.Arg742Cys	p.R742C	ENST00000310581	NM_198253.2	742	Cgt/Tgt	6/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.531792200687963	2		562	373	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0065684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	136	675	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.531792200687963	2		675	438	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435240	49435240	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773708383	NA	P-0065684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	98	543	0	ENST00000301067.7:c.6313C>T	p.Arg2105Cys	p.R2105C	ENST00000301067	NM_003482.3	2105	Cgc/Tgc	31/54	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.531792200687963	2		543	329	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650657	67650657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	118	441	0	ENST00000264010.4:c.962C>T	p.Pro321Leu	p.P321L	ENST00000264010	NM_006565.3	321	cCt/cTt	5/12	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.531792200687963	2		441	398	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266824	41266824	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0065684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	92	475	0	ENST00000349496.5:c.496-1G>A		p.X166_splice	ENST00000349496	NM_001904.3	166			1	2	FACETS	0.938	0.84	1	0.938	0.84	1	CLONAL	1	FALSE	1	0.531792200687963	2		475	369	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448493	89448493	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	84	397	0	ENST00000336596.2:c.1457T>G	p.Ile486Ser	p.I486S	ENST00000336596	NM_005233.5	486	aTt/aGt	7/17	1	2	FACETS	0.969	0.864	1	0.969	0.864	1	CLONAL	1	FALSE	1	0.531792200687963	2		397	326	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157938	106157938	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	28	539	0	ENST00000380013.4:c.2839C>G	p.Gln947Glu	p.Q947E	ENST00000380013	NM_001127208.2	947	Caa/Gaa	3/11	0.170536950429563	2	FACETS	0.26	0.207	0.32	0.13	0.103	0.16	INDETERMINATE	1	FALSE	0	0.531792200687963	2		539	405	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413165	139413165	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	94	634	0	ENST00000277541.6:c.977G>C	p.Gly326Ala	p.G326A	ENST00000277541	NM_017617.3	326	gGc/gCc	6/34	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	FALSE	1	0.531792200687963	2		634	342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579426	7579441	+	frameshift_variant	Frame_Shift_Del	DEL	TGGTGCAGGGGCCGCC	TGGTGCAGGGGCCGCC	ACGCT	novel	NA	P-0065684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	160	694	3	ENST00000269305.4:c.246_261delinsAGCGT	p.Ala84CysfsTer61	p.A84Cfs*61	ENST00000269305	NM_001126112.2	82	ccGGCGGCCCCTGCACCA/ccAGCGT	4/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.531792200687963	2		697	498	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0065685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	107	322	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	0.750695249393456	2	FACETS	0.969	0.91	1	0.969	0.91	1	CLONAL	2	TRUE	0	0.767092969569641	2		322	144	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0065685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	281	656	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.972	0.918	1	0.972	0.918	1	CLONAL	1	TRUE	1	0.767092969569641	2		656	754	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941830	44941831	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	52	152	0	ENST00000377967.4:c.3160dup	p.Arg1054LysfsTer5	p.R1054Kfs*5	ENST00000377967	NM_021140.2	1052	gaa/gAaa	21/29	0.712152766543173	2	FACETS	0.858	0.746	0.976			1	CLONAL	1	TRUE	NA	0.767092969569641	2		152	158	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592115	67592115	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	194	600	0	ENST00000274335.5:c.1931G>A	p.Gly644Asp	p.G644D	ENST00000274335		644	gGc/gAc	14/15	1	2	FACETS	0.923	0.86	0.987	0.923	0.86	0.987	CLONAL	1	TRUE	1	0.767092969569641	2		600	548	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331719	68331719	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs751355274	NA	P-0065685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	43	137	1	ENST00000487270.1:c.316-1G>C		p.X106_splice	ENST00000487270	NM_133509.3	106			0.767092969569641	3	FACETS	1	0.966	1	0.746	0.644	0.85	CLONAL	1	TRUE	1	0.767092969569641	3		138	104	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333138	70333138	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	421	782	0	ENST00000373644.4:c.1043C>A	p.Ala348Asp	p.A348D	ENST00000373644	NM_030625.2	348	gCc/gAc	2/12	0.767092969569641	2	FACETS	0.996	0.967	1	0.996	0.967	1	CLONAL	2	TRUE	0	0.767092969569641	2		782	551	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719784	190719784	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	63	381	0	ENST00000441310.2:c.1786A>T	p.Thr596Ser	p.T596S	ENST00000441310	NM_000534.4	596	Act/Tct	9/13	1	2	FACETS	0.944	0.834	1	0.944	0.834	1	CLONAL	1	TRUE	1	0.767092969569641	2		381	174	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065695-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	20	663	0				ENST00000310581	NM_198253.2	-/1132			0.180852291151494	0	FACETS	0.805	0.633	0.995			1	CLONAL	3	FALSE	0	0.180844260643014	0		663	75	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0065695-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	188	532	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.986	0.919	1	1	0.995	1	CLONAL	4	FALSE	1	0.180844260643014	2		532	527	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25458637	25458637	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs781139634	NA	P-0065695-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	27	339	0	ENST00000264709.3:c.2536C>T	p.Gln846Ter	p.Q846*	ENST00000264709	NM_175629.2	846	Cag/Tag	22/23	1	2	FACETS	0.677	0.538	0.836	0.677	0.538	0.836	SUBCLONAL	1	FALSE	1	0.180844260643014	2		339	441	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211826	123211826	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065695-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	81	234	0	ENST00000218089.9:c.2693A>G	p.Asp898Gly	p.D898G	ENST00000218089	NM_001042749.1	898	gAt/gGt	27/35	1	1	FACETS	0.947	0.851	1	1	0.989	1	CLONAL	4	FALSE	0	0.180844260643014	1		234	215	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577151	64577151	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065695-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	40	401	0	ENST00000312049.6:c.431T>G	p.Phe144Cys	p.F144C	ENST00000312049	NM_130799.2	144	tTc/tGc	2/10	1	2	FACETS	0.676	0.561	0.806	0.676	0.561	0.806	SUBCLONAL	1	FALSE	1	0.180844260643014	2		401	654	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456394	99456395	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGAAGCCCTGGACTCAGTACGCCGTTTACG	novel	NA	P-0065695-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	116	465	0	ENST00000268035.6:c.1713_1742dup	p.Pro573_Lys582dup	p.P573_K582dup	ENST00000268035	NM_000875.3	573	ctg/cTGAAGCCCTGGACTCAGTACGCCGTTTACGtg	8/21	1	2	FACETS	0.916	0.827	1	1	0.988	1	CLONAL	2	FALSE	1	0.180844260643014	2		465	700	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065699-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	45	663	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.69	0.582	0.809	0.69	0.582	0.809	SUBCLONAL	1	TRUE	1	0.366340339933873	2		663	356	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602314	10602314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065699-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	106	460	0	ENST00000171111.5:c.1264G>A	p.Asp422Asn	p.D422N	ENST00000171111	NM_203500.1	422	Gat/Aat	3/6	1	2	FACETS	0.949	0.852	1	0.949	0.852	1	CLONAL	1	TRUE	1	0.366340339933873	2		460	610	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015147	71015147	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1292897246	NA	P-0065699-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	108	338	0	ENST00000318789.4:c.1783C>G	p.Leu595Val	p.L595V	ENST00000318789	NM_032682.5	595	Ctg/Gtg	20/21	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.366340339933873	2		338	576	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747137	40747137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752831315	NA	P-0065699-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	65	320	0	ENST00000373198.4:c.2945C>T	p.Pro982Leu	p.P982L	ENST00000373198	NM_133170.3	982	cCg/cTg	22/32	0.366340339933873	1	FACETS	0.592	0.514	0.676	0.592	0.514	0.676	SUBCLONAL	1	TRUE	0	0.366340339933873	1		320	490	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519920	NA	P-0065699-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	122	395	0	ENST00000397062.3:c.85G>C	p.Asp29His	p.D29H	ENST00000397062	NM_006164.4	29	Gat/Cat	2/5	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.366340339933873	2		395	646	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904835	101904835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065699-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	96	270	0	ENST00000374994.4:c.823C>T	p.Gln275Ter	p.Q275*	ENST00000374994	NM_004612.2	275	Cag/Tag	5/9	0.366340339933873	1	FACETS	0.913	0.817	1	0.913	0.817	1	CLONAL	1	TRUE	0	0.366340339933873	1		270	469	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117755	70117755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065699-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	123	439	0	ENST00000245479.2:c.223G>A	p.Glu75Lys	p.E75K	ENST00000245479	NM_000346.3	75	Gag/Aag	1/3	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.366340339933873	2		439	582	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184086	123184086	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065699-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	94	310	0	ENST00000218089.9:c.944G>A	p.Trp315Ter	p.W315*	ENST00000218089	NM_001042749.1	315	tGg/tAg	11/35	0.366340339933873	1	FACETS	0.886	0.792	0.986	0.886	0.792	0.986	CLONAL	1	TRUE	0	0.366340339933873	1		310	473	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0065704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	64	410	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.204481577332948	3	FACETS	0.981	0.855	1	0.491	0.427	0.558	INDETERMINATE	1	TRUE	1	0.474625196533848	3		410	340	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788659	3788659	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	28	332	0	ENST00000262367.5:c.4295C>G	p.Ser1432Cys	p.S1432C	ENST00000262367	NM_004380.2	1432	tCt/tGt	26/31	0.46994235124959	3	FACETS	0.624	0.501	0.762	0.312	0.25	0.381	SUBCLONAL	1	TRUE	1	0.474625196533848	3		332	234	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6213361	6213361	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	172	440	2	ENST00000252674.7:c.1538A>C	p.Asn513Thr	p.N513T	ENST00000252674	NM_005934.3	513	aAc/aCc	11/12	1	2	FACETS	0.971	0.906	1	0.971	0.906	1	CLONAL	1	TRUE	1	0.913021245539381	2		442	388	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391234	89391234	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	47	318	0	ENST00000336596.2:c.1300C>G	p.Gln434Glu	p.Q434E	ENST00000336596	NM_005233.5	434	Cag/Gag	5/17	1	2	FACETS	0.18	0.152	0.212	0.18	0.152	0.212	SUBCLONAL	1	TRUE	1	0.913021245539381	2		318	571	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853380	151853380	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	262	370	0	ENST00000262189.6:c.11722C>G	p.Pro3908Ala	p.P3908A	ENST00000262189	NM_170606.2	3908	Cca/Gca	45/59	0.875954649680472	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.913021245539381	1		370	296	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	58	663	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.807	0.708	0.909	0.807	0.708	0.909	CLONAL	1	TRUE	1	0.893082281455697	2		663	161	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711889	89711892	+	frameshift_variant	Frame_Shift_Del	DEL	CAGT	CAGT	-	novel	NA	P-0065706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	29	309	0	ENST00000371953.3:c.510_513del	p.Ser170ArgfsTer12	p.S170Rfs*12	ENST00000371953	NM_000314.4	169	ccCAGT/cc	6/9	0.79777363003212	1	FACETS	0.196	0.159	0.238	0.196	0.159	0.238	SUBCLONAL	1	TRUE	0	0.893082281455697	1		309	183	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0065706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	11	112	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.79777363003212	1	FACETS	0.262	0.186	0.351	0.262	0.186	0.351	SUBCLONAL	1	TRUE	0	0.893082281455697	1		112	52	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433843	49433843	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	135	670	1	ENST00000301067.7:c.7710del	p.Thr2571ProfsTer12	p.T2571Pfs*12	ENST00000301067	NM_003482.3	2570	ccC/cc	31/54	1	2	FACETS	0.819	0.754	0.887	0.819	0.754	0.887	CLONAL	1	TRUE	1	0.893082281455697	2		671	369	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103827	47103827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1244929991	NA	P-0065706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	160	467	0	ENST00000409792.3:c.6119G>A	p.Arg2040Gln	p.R2040Q	ENST00000409792	NM_014159.6	2040	cGa/cAa	14/21	1	2	FACETS	0.961	0.893	1	0.961	0.893	1	CLONAL	1	TRUE	1	0.893082281455697	2		467	373	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233037	55233037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1477025000	NA	P-0065706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	23889	445	0	ENST00000275493.2:c.1787C>T	p.Pro596Leu	p.P596L	ENST00000275493	NM_005228.3	596	cCg/cTg	15/28	0.893082281455697	46	FACETS	1	0.999	1			1	CLONAL	45	TRUE	NA	0.893082281455697	46		445	24388	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007110	152007110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	147	404	0	ENST00000262189.6:c.790C>T	p.Gln264Ter	p.Q264*	ENST00000262189	NM_170606.2	264	Cag/Tag	6/59	0.478733463404657	5	FACETS	1	0.976	1	0.393	0.359	0.427	INDETERMINATE	1	TRUE	2	0.893082281455697	5		404	654	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0065707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	118	491	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.175040541247737	5	FACETS	0.958	0.871	1	0.958	0.871	1	CLONAL	4	TRUE	1	0.175040541247737	5		491	444	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519920	NA	P-0065707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	13	395	0	ENST00000397062.3:c.85G>C	p.Asp29His	p.D29H	ENST00000397062	NM_006164.4	29	Gat/Cat	2/5	1	2	FACETS	0.326	0.232	0.443	0.326	0.232	0.443	SUBCLONAL	1	TRUE	1	0.175040541247737	2		395	455	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555604	21555604	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1231018689	NA	P-0065707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	34	406	0	ENST00000382592.4:c.2665+1G>T		p.X889_splice	ENST00000382592	NM_014572.2	889			1	2	FACETS	0.766	0.625	0.925	0.766	0.625	0.925	CLONAL	1	TRUE	1	0.175040541247737	2		406	507	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413151	63413151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	13	209	0	ENST00000330258.3:c.16G>A	p.Asp6Asn	p.D6N	ENST00000330258	NM_152424.3	6	Gat/Aat	2/2	1	1	FACETS	0.589	0.42	0.795	0.589	0.42	0.795	SUBCLONAL	1	TRUE	0	0.175040541247737	1		209	230	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486255	8486255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	37	434	0	ENST00000356435.5:c.2562G>T	p.Gln854His	p.Q854H	ENST00000356435		854	caG/caT	17/35	1	2	FACETS	0.877	0.723	1	0.877	0.723	1	CLONAL	1	TRUE	1	0.175040541247737	2		434	482	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550309	39550309	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	33	376	0	ENST00000262039.4:c.420G>T	p.Met140Ile	p.M140I	ENST00000262039	NM_002647.2	140	atG/atT	4/25	1	2	FACETS	0.781	0.635	0.945	0.781	0.635	0.945	CLONAL	1	TRUE	1	0.175040541247737	2		376	483	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326798	62326798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	51	610	0	ENST00000360203.5:c.3617C>T	p.Ser1206Leu	p.S1206L	ENST00000360203	NM_001283009.1	1206	tCa/tTa	34/35	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.175040541247737	2		610	553	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438188	56438188	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	26	448	0	ENST00000407977.2:c.805G>T	p.Ala269Ser	p.A269S	ENST00000407977		269	Gcc/Tcc	7/10	1	2	FACETS	0.637	0.504	0.791	0.637	0.504	0.791	SUBCLONAL	1	TRUE	1	0.175040541247737	2		448	466	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170552	11170552	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	36	533	0	ENST00000358026.2:c.4855G>T	p.Glu1619Ter	p.E1619*	ENST00000358026	NM_001128849.1	1619	Gaa/Taa	34/36	1	2	FACETS	0.896	0.737	1	0.896	0.737	1	CLONAL	1	TRUE	1	0.175040541247737	2		533	459	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388688	31388688	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	39	411	0	ENST00000328111.2:c.1953C>A	p.Cys651Ter	p.C651*	ENST00000328111	NM_006892.3	651	tgC/tgA	18/23	1	2	FACETS	0.975	0.808	1	0.975	0.808	1	CLONAL	1	TRUE	1	0.175040541247737	2		411	457	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971161	21971161	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	23	570	0	ENST00000304494.5:c.197A>T	p.His66Leu	p.H66L	ENST00000304494	NM_000077.4	66	cAc/cTc	2/3	1	2	FACETS	0.573	0.445	0.72	0.573	0.445	0.72	SUBCLONAL	1	TRUE	1	0.175040541247737	2		570	459	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940018	76940018	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	40	236	0	ENST00000373344.5:c.730A>T	p.Ile244Phe	p.I244F	ENST00000373344	NM_000489.3	244	Att/Ttt	9/35	1	1	FACETS	0.802	0.671	0.946	1	0.96	1	CLONAL	2	TRUE	0	0.175040541247737	1		236	260	SUCCESS
APC	324	MSKCC	GRCh37	5	112174144	112174144	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0065708-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	85	373	0	ENST00000257430.4:c.2853T>A	p.Tyr951Ter	p.Y951*	ENST00000257430	NM_000038.5	951	taT/taA	16/16	0.204001699568809	3	FACETS	0.883	0.783	0.99	0.883	0.783	0.99	CLONAL	2	TRUE	1	0.204001699568809	3		373	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577530	7577530	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065708-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	64	347	0	ENST00000269305.4:c.751A>T	p.Ile251Phe	p.I251F	ENST00000269305	NM_001126112.2	251	Atc/Ttc	7/11	0.204001699568809	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.204001699568809	1		347	485	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0065708-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	62	313	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.204001699568809	2		313	537	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914275	32914275	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065708-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	97	331	0	ENST00000380152.3:c.5785del	p.Ile1929PhefsTer34	p.I1929Ffs*34	ENST00000380152		1928	gAa/ga	11/27	0.204001699568809	3	FACETS	0.979	0.876	1	0.979	0.876	1	CLONAL	2	TRUE	1	0.204001699568809	3		331	535	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039831	47039831	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065708-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	12	176	0	ENST00000377604.3:c.1174A>T	p.Asn392Tyr	p.N392Y	ENST00000377604	NM_001204468.1	392	Aat/Tat	12/24	1	1	FACETS	0.534	0.375	0.728	0.534	0.375	0.728	SUBCLONAL	1	TRUE	0	0.204001699568809	1		176	198	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263192	115263192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	64	438	0	ENST00000438362.2:c.2158C>T	p.Arg720Cys	p.R720C	ENST00000438362	NM_001242891.1	720	Cgc/Tgc	17/20	1	2	FACETS	0.742	0.643	0.848	0.742	0.643	0.848	SUBCLONAL	1	TRUE	1	0.33	2		438	523	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	65	436	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.673	0.584	0.77	0.673	0.584	0.77	SUBCLONAL	1	TRUE	1	0.33	2		436	585	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	28	418	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.321	0.256	0.396	0.321	0.256	0.396	SUBCLONAL	1	TRUE	1	0.33	2		418	529	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	175	434	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.875	0.81	0.942	1	0.992	1	CLONAL	2	TRUE	1	0.33	2		434	606	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317082	11317082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	32	583	0	ENST00000361445.4:c.412G>A	p.Asp138Asn	p.D138N	ENST00000361445	NM_004958.3	138	Gac/Aac	4/58	1	2	FACETS	0.34	0.275	0.414	0.34	0.275	0.414	SUBCLONAL	1	TRUE	1	0.33	2		583	570	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317186	11317186	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763230714	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	190	530	0	ENST00000361445.4:c.308G>A	p.Arg103Gln	p.R103Q	ENST00000361445	NM_004958.3	103	cGa/cAa	4/58	1	2	FACETS	1	0.973	1	1	0.994	1	CLONAL	2	TRUE	1	0.33	2		530	531	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16248794	16248794	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	169	374	0	ENST00000375759.3:c.1800G>T	p.Glu600Asp	p.E600D	ENST00000375759	NM_015001.2	600	gaG/gaT	10/15	1	2	FACETS	0.919	0.85	0.99	1	0.992	1	CLONAL	2	TRUE	1	0.33	2		374	557	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261766	16261766	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs777176191	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	67	566	0	ENST00000375759.3:c.9031C>T	p.Arg3011Ter	p.R3011*	ENST00000375759	NM_015001.2	3011	Cga/Tga	11/15	1	2	FACETS	0.762	0.663	0.869	0.762	0.663	0.869	SUBCLONAL	1	TRUE	1	0.33	2		566	533	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097650	27097650	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	37	506	0	ENST00000324856.7:c.3239T>C	p.Leu1080Pro	p.L1080P	ENST00000324856	NM_006015.4	1080	cTc/cCc	12/20	1	2	FACETS	0.358	0.294	0.43	0.358	0.294	0.43	SUBCLONAL	1	TRUE	1	0.33	2		506	626	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	190	475	1	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	1	2	FACETS	0.941	0.874	1	1	0.993	1	CLONAL	2	TRUE	1	0.33	2		476	612	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106316	27106316	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	35	574	0	ENST00000324856.7:c.5927C>A	p.Ser1976Tyr	p.S1976Y	ENST00000324856	NM_006015.4	1976	tCt/tAt	20/20	1	2	FACETS	0.312	0.255	0.377	0.312	0.255	0.377	SUBCLONAL	1	TRUE	1	0.33	2		574	680	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106817	27106817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	39	618	1	ENST00000324856.7:c.6428G>A	p.Arg2143His	p.R2143H	ENST00000324856	NM_006015.4	2143	cGc/cAc	20/20	1	2	FACETS	0.357	0.295	0.426	0.357	0.295	0.426	SUBCLONAL	1	TRUE	1	0.33	2		619	663	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46736360	46736360	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	136	449	0	ENST00000371975.4:c.1072G>T	p.Glu358Ter	p.E358*	ENST00000371975	NM_003579.3	358	Gaa/Taa	10/18	1	2	FACETS	0.819	0.749	0.892	1	0.989	1	CLONAL	2	TRUE	1	0.33	2		449	503	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834543	156834543	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs578095133	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	39	622	0	ENST00000524377.1:c.311G>A	p.Arg104His	p.R104H	ENST00000524377	NM_002529.3	104	cGt/cAt	3/17	1	2	FACETS	0.451	0.373	0.538	0.451	0.373	0.538	SUBCLONAL	1	TRUE	1	0.33	2		622	524	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746018	162746018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	175	539	0	ENST00000367921.3:c.2141G>A	p.Arg714Gln	p.R714Q	ENST00000367921	NM_006182.2	714	cGa/cAa	16/18	1	2	FACETS	0.966	0.895	1	1	0.993	1	CLONAL	2	TRUE	1	0.33	2		539	549	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944333	206944333	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	33	519	0	ENST00000423557.1:c.297G>T	p.Glu99Asp	p.E99D	ENST00000423557	NM_000572.2	99	gaG/gaT	3/5	1	2	FACETS	0.353	0.286	0.428	0.353	0.286	0.428	SUBCLONAL	1	TRUE	1	0.33	2		519	567	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800978	243800978	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	64	383	0	ENST00000263826.5:c.496C>T	p.Arg166Ter	p.R166*	ENST00000263826	NM_005465.4	166	Cga/Tga	5/13	1	2	FACETS	0.726	0.63	0.831	0.726	0.63	0.831	SUBCLONAL	1	TRUE	1	0.33	2		383	534	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100762	8100762	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766641914	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	35	535	0	ENST00000346208.3:c.736G>A	p.Gly246Ser	p.G246S	ENST00000346208		246	Ggc/Agc	3/6	1	2	FACETS	0.48	0.393	0.577	0.48	0.393	0.577	SUBCLONAL	1	TRUE	1	0.33	2		535	442	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850870	63850870	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	216	542	0	ENST00000279873.7:c.1648G>T	p.Glu550Ter	p.E550*	ENST00000279873	NM_032199.2	550	Gaa/Taa	10/10	1	2	FACETS	1	0.975	1	1	0.995	1	CLONAL	2	TRUE	1	0.33	2		542	606	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692811	89692811	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	84	216	0	ENST00000371953.3:c.295G>T	p.Glu99Ter	p.E99*	ENST00000371953	NM_000314.4	99	Gaa/Taa	5/9	1	2	FACETS	0.899	0.804	0.999	1	0.984	1	CLONAL	2	TRUE	1	0.33	2		216	283	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	174	337	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.962	1	1	0.993	1	CLONAL	2	TRUE	1	0.33	2		337	499	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	216	516	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	1	0.975	1	1	0.995	1	CLONAL	2	TRUE	1	0.33	2		516	606	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10793142	10793142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867784949	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	56	351	0	ENST00000361367.2:c.2423C>T	p.Ala808Val	p.A808V	ENST00000361367	NM_014633.3	808	gCc/gTc	19/25	1	2	FACETS	0.568	0.486	0.657	0.568	0.486	0.657	SUBCLONAL	1	TRUE	1	0.33	2		351	598	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47599198	47599198	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	187	502	0	ENST00000430070.2:c.402T>G	p.Ile134Met	p.I134M	ENST00000430070	NM_018095.4	134	atT/atG	2/4	1	2	FACETS	0.952	0.885	1	1	0.993	1	CLONAL	2	TRUE	1	0.33	2		502	595	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588171	69588171	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	137	496	0	ENST00000168712.1:c.527G>T	p.Gly176Val	p.G176V	ENST00000168712	NM_002007.2	176	gGc/gTc	3/3	1	2	FACETS	0.762	0.696	0.83	1	0.987	1	SUBCLONAL	2	TRUE	1	0.33	2		496	545	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911881	94911881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1489329660	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	28	332	0	ENST00000536441.1:c.1049G>A	p.Arg350Gln	p.R350Q	ENST00000536441	NM_144665.3	350	cGa/cAa	7/10	1	2	FACETS	0.354	0.282	0.436	0.354	0.282	0.436	SUBCLONAL	1	TRUE	1	0.33	2		332	479	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920786	100920786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752995251	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	34	373	1	ENST00000325455.5:c.2362C>T	p.Arg788Trp	p.R788W	ENST00000325455	NM_001202474.3	788	Cgg/Tgg	6/8	1	2	FACETS	0.335	0.272	0.405	0.335	0.272	0.405	SUBCLONAL	1	TRUE	1	0.33	2		374	616	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102080254	102080254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193100333	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	28	366	0	ENST00000282441.5:c.991C>T	p.Arg331Trp	p.R331W	ENST00000282441	NM_001130145.2	331	Cgg/Tgg	6/9	1	2	FACETS	0.355	0.283	0.437	0.355	0.283	0.437	SUBCLONAL	1	TRUE	1	0.33	2		366	478	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115600	108115600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772821016	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	35	421	0	ENST00000278616.4:c.748C>T	p.Arg250Ter	p.R250*	ENST00000278616	NM_000051.3	250	Cga/Tga	7/63	1	2	FACETS	0.363	0.297	0.438	0.363	0.297	0.438	SUBCLONAL	1	TRUE	1	0.33	2		421	584	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142117	108142117	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	28	448	0	ENST00000278616.4:c.3061G>A	p.Val1021Ile	p.V1021I	ENST00000278616	NM_000051.3	1021	Gta/Ata	20/63	1	2	FACETS	0.304	0.242	0.374	0.304	0.242	0.374	SUBCLONAL	1	TRUE	1	0.33	2		448	559	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151824	108151824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200765255	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	56	402	0	ENST00000278616.4:c.3505G>A	p.Glu1169Lys	p.E1169K	ENST00000278616	NM_000051.3	1169	Gaa/Aaa	24/63	1	2	FACETS	0.667	0.572	0.771	0.667	0.572	0.771	SUBCLONAL	1	TRUE	1	0.33	2		402	509	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178655	108178656	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587781730	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	32	.	.	ENST00000278616.4:c.5712dup	p.Ser1905IlefsTer25	p.S1905Ifs*25	ENST00000278616	NM_000051.3	1902	-/A	38/63	1	2	FACETS	0.323	0.261	0.393	0.323	0.261	0.393	SUBCLONAL	1	TRUE	1	0.33	2		0	600	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190762	108190762	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	27	291	0	ENST00000278616.4:c.6429T>G	p.Phe2143Leu	p.F2143L	ENST00000278616	NM_000051.3	2143	ttT/ttG	44/63	1	2	FACETS	0.369	0.293	0.456	0.369	0.293	0.456	SUBCLONAL	1	TRUE	1	0.33	2		291	444	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342641	118342641	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	228	485	0	ENST00000534358.1:c.767T>G	p.Ile256Ser	p.I256S	ENST00000534358	NM_005933.3	256	aTt/aGt	3/36	1	2	FACETS	1	0.977	1	1	0.995	1	CLONAL	2	TRUE	1	0.33	2		485	635	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362576	118362576	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	45	486	1	ENST00000534358.1:c.4937C>A	p.Ser1646Tyr	p.S1646Y	ENST00000534358	NM_005933.3	1646	tCt/tAt	15/36	1	2	FACETS	0.461	0.387	0.544	0.461	0.387	0.544	SUBCLONAL	1	TRUE	1	0.33	2		487	591	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170466	119170466	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	28	442	0	ENST00000264033.4:c.2696C>A	p.Ser899Tyr	p.S899Y	ENST00000264033	NM_005188.3	899	tCt/tAt	16/16	1	2	FACETS	0.321	0.256	0.396	0.321	0.256	0.396	SUBCLONAL	1	TRUE	1	0.33	2		442	528	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871797	12871797	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	218	491	0	ENST00000228872.4:c.514G>T	p.Glu172Ter	p.E172*	ENST00000228872	NM_004064.3	172	Gaa/Taa	2/3	1	2	FACETS	1	0.971	1	1	0.995	1	CLONAL	2	TRUE	1	0.33	2		491	621	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435110	18435110	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	41	496	0	ENST00000266497.5:c.95C>A	p.Ser32Tyr	p.S32Y	ENST00000266497		32	tCt/tAt	1/31	1	2	FACETS	0.381	0.316	0.453	0.381	0.316	0.453	SUBCLONAL	1	TRUE	1	0.33	2		496	653	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18439785	18439785	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1248573211	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	25	308	0	ENST00000266497.5:c.683T>C	p.Ile228Thr	p.I228T	ENST00000266497		228	aTa/aCa	2/31	1	2	FACETS	0.335	0.263	0.418	0.335	0.263	0.418	SUBCLONAL	1	TRUE	1	0.33	2		308	452	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644394	18644394	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	29	377	0	ENST00000266497.5:c.2572A>G	p.Lys858Glu	p.K858E	ENST00000266497		858	Aag/Gag	18/31	1	2	FACETS	0.308	0.247	0.379	0.308	0.247	0.379	SUBCLONAL	1	TRUE	1	0.33	2		377	570	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691191	18691191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774205366	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	39	588	0	ENST00000266497.5:c.3302G>A	p.Arg1101His	p.R1101H	ENST00000266497		1101	cGt/cAt	23/31	1	2	FACETS	0.453	0.375	0.54	0.453	0.375	0.54	SUBCLONAL	1	TRUE	1	0.33	2		588	522	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425124	49425124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372839823	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	65	566	0	ENST00000301067.7:c.13364G>A	p.Arg4455His	p.R4455H	ENST00000301067	NM_003482.3	4455	cGc/cAc	39/54	1	2	FACETS	0.695	0.603	0.795	0.695	0.603	0.795	SUBCLONAL	1	TRUE	1	0.33	2		566	567	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426543	49426543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760983900	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	246	584	0	ENST00000301067.7:c.11945G>A	p.Arg3982Gln	p.R3982Q	ENST00000301067	NM_003482.3	3982	cGa/cAa	39/54	1	2	FACETS	1	0.965	1	1	0.995	1	CLONAL	2	TRUE	1	0.33	2		584	718	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50488303	50488303	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs750857733	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	28	418	1	ENST00000394963.4:c.1217C>A	p.Ser406Tyr	p.S406Y	ENST00000394963	NM_003076.4	406	tCt/tAt	10/13	1	2	FACETS	0.328	0.261	0.405	0.328	0.261	0.405	SUBCLONAL	1	TRUE	1	0.33	2		419	517	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489565	56489565	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	38	515	0	ENST00000267101.3:c.2030T>C	p.Met677Thr	p.M677T	ENST00000267101	NM_001982.3	677	aTg/aCg	17/28	1	2	FACETS	0.354	0.292	0.424	0.354	0.292	0.424	SUBCLONAL	1	TRUE	1	0.33	2		515	650	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495835	56495835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140679673	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	130	348	0	ENST00000267101.3:c.4025C>T	p.Thr1342Met	p.T1342M	ENST00000267101	NM_001982.3	1342	aCg/aTg	28/28	1	2	FACETS	0.929	0.85	1	1	0.99	1	CLONAL	2	TRUE	1	0.33	2		348	424	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112919983	112919983	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	29	267	0	ENST00000351677.2:c.1198G>T	p.Glu400Ter	p.E400*	ENST00000351677	NM_002834.3	400	Gaa/Taa	10/16	1	2	FACETS	0.467	0.375	0.572	0.467	0.375	0.572	SUBCLONAL	1	TRUE	1	0.33	2		267	376	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252078	133252078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1278939294	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	36	556	0	ENST00000320574.5:c.1132G>A	p.Val378Ile	p.V378I	ENST00000320574	NM_006231.2	378	Gtc/Atc	12/49	1	2	FACETS	0.413	0.339	0.497	0.413	0.339	0.497	SUBCLONAL	1	TRUE	1	0.33	2		556	528	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	158	419	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	1	0.931	1	1	0.992	1	CLONAL	2	TRUE	1	0.33	2		419	475	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589384	28589384	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	35	377	0	ENST00000241453.7:c.2663C>A	p.Pro888His	p.P888H	ENST00000241453	NM_004119.2	888	cCt/cAt	22/24	1	2	FACETS	0.485	0.398	0.584	0.485	0.398	0.584	SUBCLONAL	1	TRUE	1	0.33	2		377	437	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608309	28608309	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767430269	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	135	517	1	ENST00000241453.7:c.1747G>A	p.Gly583Ser	p.G583S	ENST00000241453	NM_004119.2	583	Ggc/Agc	14/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.33	2		518	584	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609661	28609661	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	33	502	0	ENST00000241453.7:c.1568C>A	p.Ser523Tyr	p.S523Y	ENST00000241453	NM_004119.2	523	tCt/tAt	12/24	1	2	FACETS	0.407	0.331	0.493	0.407	0.331	0.493	SUBCLONAL	1	TRUE	1	0.33	2		502	491	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893306	32893308	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	rs11571587	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	51	477	0	ENST00000380152.3:c.165_167del	p.Asn56del	p.N56del	ENST00000380152		54	AAC/-	3/27	1	2	FACETS	0.511	0.434	0.596	0.511	0.434	0.596	SUBCLONAL	1	TRUE	1	0.33	2		477	605	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911343	32911343	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	49	515	0	ENST00000380152.3:c.2851C>A	p.Leu951Ile	p.L951I	ENST00000380152		951	Ctt/Att	11/27	1	2	FACETS	0.525	0.444	0.614	0.525	0.444	0.614	SUBCLONAL	1	TRUE	1	0.33	2		515	566	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913254	32913254	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	40	513	0	ENST00000380152.3:c.4762G>T	p.Ala1588Ser	p.A1588S	ENST00000380152		1588	Gcc/Tcc	11/27	1	2	FACETS	0.39	0.323	0.465	0.39	0.323	0.465	SUBCLONAL	1	TRUE	1	0.33	2		513	621	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914821	32914821	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs80358873	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	34	501	0	ENST00000380152.3:c.6329A>C	p.Asp2110Ala	p.D2110A	ENST00000380152		2110	gAt/gCt	11/27	1	2	FACETS	0.342	0.278	0.413	0.342	0.278	0.413	SUBCLONAL	1	TRUE	1	0.33	2		501	603	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937356	32937356	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	34	365	0	ENST00000380152.3:c.8017A>C	p.Lys2673Gln	p.K2673Q	ENST00000380152		2673	Aaa/Caa	18/27	1	2	FACETS	0.379	0.309	0.459	0.379	0.309	0.459	SUBCLONAL	1	TRUE	1	0.33	2		365	543	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945130	32945130	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80359105	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	23	333	0	ENST00000380152.3:c.8525G>A	p.Arg2842His	p.R2842H	ENST00000380152		2842	cGc/cAc	20/27	1	2	FACETS	0.306	0.238	0.386	0.306	0.238	0.386	SUBCLONAL	1	TRUE	1	0.33	2		333	455	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934254	48934254	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1131690904	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	37	376	0	ENST00000267163.4:c.709G>T	p.Glu237Ter	p.E237*	ENST00000267163	NM_000321.2	237	Gaa/Taa	7/27	1	2	FACETS	0.428	0.352	0.513	0.428	0.352	0.513	SUBCLONAL	1	TRUE	1	0.33	2		376	524	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951075	48951075	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	25	289	0	ENST00000267163.4:c.1237G>T	p.Glu413Ter	p.E413*	ENST00000267163	NM_000321.2	413	Gaa/Taa	13/27	1	2	FACETS	0.392	0.308	0.488	0.392	0.308	0.488	SUBCLONAL	1	TRUE	1	0.33	2		289	387	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347916	73347916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139907646	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	27	417	0	ENST00000377767.4:c.1145G>A	p.Arg382Gln	p.R382Q	ENST00000377767	NM_014953.3	382	cGa/cAa	8/21	1	2	FACETS	0.295	0.234	0.365	0.295	0.234	0.365	SUBCLONAL	1	TRUE	1	0.33	2		417	555	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527822	103527822	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs768440346	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	36	518	0	ENST00000355739.4:c.3130G>T	p.Glu1044Ter	p.E1044*	ENST00000355739	NM_000123.3	1044	Gaa/Taa	15/15	1	2	FACETS	0.34	0.278	0.409	0.34	0.278	0.409	SUBCLONAL	1	TRUE	1	0.33	2		518	642	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562862	95562862	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	76	449	0	ENST00000393063.1:c.4395G>T	p.Lys1465Asn	p.K1465N	ENST00000393063	NM_030621.3	1465	aaG/aaT	24/28	1	2	FACETS	0.777	0.682	0.879	0.777	0.682	0.879	SUBCLONAL	1	TRUE	1	0.33	2		449	593	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95592924	95592924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755944755	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	140	275	0	ENST00000393063.1:c.896C>T	p.Ser299Leu	p.S299L	ENST00000393063	NM_030621.3	299	tCg/tTg	8/28	1	2	FACETS	1	0.941	1	1	0.992	1	CLONAL	2	TRUE	1	0.33	2		275	413	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961356	41961356	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	193	530	0	ENST00000219905.7:c.264C>A	p.Phe88Leu	p.F88L	ENST00000219905	NM_001164273.1	88	ttC/ttA	2/24	1	2	FACETS	0.953	0.886	1	1	0.993	1	CLONAL	2	TRUE	1	0.33	2		530	614	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701248	43701248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773338141	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	92	515	0	ENST00000382044.4:c.5447G>A	p.Arg1816Gln	p.R1816Q	ENST00000382044	NM_001141980.1	1816	cGa/cAa	26/28	1	2	FACETS	0.994	0.885	1	0.994	0.885	1	CLONAL	1	TRUE	1	0.33	2		515	561	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50789335	50789335	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	29	388	0	ENST00000307179.4:c.2945G>T	p.Arg982Ile	p.R982I	ENST00000307179		982	aGa/aTa	18/20	1	2	FACETS	0.317	0.253	0.389	0.317	0.253	0.389	SUBCLONAL	1	TRUE	1	0.33	2		388	555	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50789349	50789349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	31	391	1	ENST00000307179.4:c.2959C>A	p.His987Asn	p.H987N	ENST00000307179		987	Cat/Aat	18/20	1	2	FACETS	0.337	0.272	0.412	0.337	0.272	0.412	SUBCLONAL	1	TRUE	1	0.33	2		392	557	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67459118	67459118	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	29	460	0	ENST00000327367.4:c.534G>T	p.Glu178Asp	p.E178D	ENST00000327367	NM_005902.3	178	gaG/gaT	4/9	1	2	FACETS	0.335	0.268	0.412	0.335	0.268	0.412	SUBCLONAL	1	TRUE	1	0.33	2		460	524	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778773	3778773	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	54	608	1	ENST00000262367.5:c.6275C>A	p.Ser2092Ter	p.S2092*	ENST00000262367	NM_004380.2	2092	tCa/tAa	31/31	1	2	FACETS	0.59	0.503	0.684	0.59	0.503	0.684	SUBCLONAL	1	TRUE	1	0.33	2		609	555	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934583	9934583	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	33	493	0	ENST00000330684.3:c.1572C>A	p.Phe524Leu	p.F524L	ENST00000330684	NM_001134407.1	524	ttC/ttA	7/13	1	2	FACETS	0.376	0.305	0.456	0.376	0.305	0.456	SUBCLONAL	1	TRUE	1	0.33	2		493	532	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348769	11348769	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	27	433	0	ENST00000332029.2:c.567G>T	p.Glu189Asp	p.E189D	ENST00000332029	NM_003745.1	189	gaG/gaT	2/2	1	2	FACETS	0.421	0.334	0.519	0.421	0.334	0.519	SUBCLONAL	1	TRUE	1	0.33	2		433	389	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128544	30128544	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	29	577	1	ENST00000263025.4:c.838T>G	p.Tyr280Asp	p.Y280D	ENST00000263025	NM_002746.2	280	Tac/Gac	6/9	1	2	FACETS	0.33	0.264	0.406	0.33	0.264	0.406	SUBCLONAL	1	TRUE	1	0.33	2		578	532	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116170	67116170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761036715	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	62	427	0	ENST00000412916.2:c.454G>A	p.Glu152Lys	p.E152K	ENST00000412916		152	Gaa/Aaa	5/6	1	2	FACETS	0.611	0.527	0.702	0.611	0.527	0.702	SUBCLONAL	1	TRUE	1	0.33	2		427	615	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72863756	72863756	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	23	383	0	ENST00000268489.5:c.3451G>T	p.Glu1151Ter	p.E1151*	ENST00000268489	NM_006885.3	1151	Gaa/Taa	5/10	1	2	FACETS	0.313	0.243	0.394	0.313	0.243	0.394	SUBCLONAL	1	TRUE	1	0.33	2		383	445	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993131	72993131	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	38	569	0	ENST00000268489.5:c.914A>C	p.His305Pro	p.H305P	ENST00000268489	NM_006885.3	305	cAt/cCt	2/10	1	2	FACETS	0.396	0.327	0.474	0.396	0.327	0.474	SUBCLONAL	1	TRUE	1	0.33	2		569	581	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993477	72993477	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1404656543	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	71	614	1	ENST00000268489.5:c.568G>A	p.Val190Met	p.V190M	ENST00000268489	NM_006885.3	190	Gtg/Atg	2/10	1	2	FACETS	0.724	0.633	0.823	0.724	0.633	0.823	SUBCLONAL	1	TRUE	1	0.33	2		615	594	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805638	89805638	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	25	558	0	ENST00000389301.3:c.4070C>A	p.Ala1357Asp	p.A1357D	ENST00000389301	NM_000135.2	1357	gCt/gAt	41/43	1	2	FACETS	0.322	0.253	0.402	0.322	0.253	0.402	SUBCLONAL	1	TRUE	1	0.33	2		558	470	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89811449	89811449	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	173	489	0	ENST00000389301.3:c.3544C>T	p.Leu1182Phe	p.L1182F	ENST00000389301	NM_000135.2	1182	Ctc/Ttc	36/43	1	2	FACETS	0.953	0.883	1	1	0.993	1	CLONAL	2	TRUE	1	0.33	2		489	550	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974839	15974839	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	69	485	0	ENST00000268712.3:c.4036G>T	p.Glu1346Ter	p.E1346*	ENST00000268712	NM_006311.3	1346	Gaa/Taa	30/46	1	2	FACETS	0.671	0.585	0.765	0.671	0.585	0.765	SUBCLONAL	1	TRUE	1	0.33	2		485	623	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533378	29533378	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs878853865	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	54	438	0	ENST00000356175.3:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000356175	NM_000267.3	461	Cga/Tga	12/57	1	2	FACETS	0.57	0.487	0.662	0.57	0.487	0.662	SUBCLONAL	1	TRUE	1	0.33	2		438	574	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552212	29552212	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	148	362	0	ENST00000356175.3:c.1945G>T	p.Glu649Ter	p.E649*	ENST00000356175	NM_000267.3	649	Gaa/Taa	17/57	1	2	FACETS	0.871	0.8	0.944	1	0.99	1	CLONAL	2	TRUE	1	0.33	2		362	515	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	192	394	0	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	1	2	FACETS	1	0.938	1	1	0.994	1	CLONAL	2	TRUE	1	0.33	2		394	577	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370172	40370172	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	47	568	0	ENST00000293328.3:c.1166G>A	p.Arg389His	p.R389H	ENST00000293328	NM_012448.3	389	cGc/cAc	9/19	1	2	FACETS	0.42	0.353	0.493	0.42	0.353	0.493	SUBCLONAL	1	TRUE	1	0.33	2		568	679	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243770	41243770	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555587079	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	35	466	0	ENST00000357654.3:c.3778T>G	p.Leu1260Val	p.L1260V	ENST00000357654	NM_007294.3	1260	Tta/Gta	10/23	1	2	FACETS	0.335	0.273	0.404	0.335	0.273	0.404	SUBCLONAL	1	TRUE	1	0.33	2		466	634	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805444	46805444	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	32	514	0	ENST00000290295.7:c.512C>A	p.Ser171Tyr	p.S171Y	ENST00000290295	NM_006361.5	171	tCt/tAt	1/2	1	2	FACETS	0.323	0.261	0.393	0.323	0.261	0.393	SUBCLONAL	1	TRUE	1	0.33	2		514	601	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699338	47699338	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	186	432	0	ENST00000347630.2:c.170T>G	p.Phe57Cys	p.F57C	ENST00000347630	NM_001007230.1	57	tTt/tGt	4/11	1	2	FACETS	1	0.936	1	1	0.993	1	CLONAL	2	TRUE	1	0.33	2		432	560	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740526	58740526	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	178	511	0	ENST00000305921.3:c.1431T>G	p.Asn477Lys	p.N477K	ENST00000305921	NM_003620.3	477	aaT/aaG	6/6	1	2	FACETS	0.977	0.907	1	1	0.993	1	CLONAL	2	TRUE	1	0.33	2		511	552	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006674	62006674	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	156	564	0	ENST00000392795.3:c.605T>C	p.Ile202Thr	p.I202T	ENST00000392795	NM_001039933.1	202	aTt/aCt	6/6	1	2	FACETS	0.879	0.81	0.95	1	0.991	1	CLONAL	2	TRUE	1	0.33	2		564	538	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39575856	39575856	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs140660681	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	27	312	0	ENST00000262039.4:c.789G>T	p.Glu263Asp	p.E263D	ENST00000262039	NM_002647.2	263	gaG/gaT	8/25	1	2	FACETS	0.381	0.303	0.471	0.381	0.303	0.471	SUBCLONAL	1	TRUE	1	0.33	2		312	429	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372075	45372075	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	85	406	0	ENST00000262160.6:c.1094G>A	p.Arg365Lys	p.R365K	ENST00000262160	NM_005901.5	365	aGa/aAa	9/11	1	2	FACETS	0.845	0.747	0.948	0.845	0.747	0.948	CLONAL	1	TRUE	1	0.33	2		406	610	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611810	1611810	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs747096662	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	42	523	1	ENST00000344749.5:c.1852C>T	p.Arg618Ter	p.R618*	ENST00000344749	NM_001136139.2	618	Cga/Tga	19/19	1	2	FACETS	0.461	0.384	0.546	0.461	0.384	0.546	SUBCLONAL	1	TRUE	1	0.33	2		524	552	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291503	10291503	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	168	382	0	ENST00000340748.4:c.176A>C	p.Asn59Thr	p.N59T	ENST00000340748		59	aAt/aCt	3/40	1	2	FACETS	1	0.953	1	1	0.993	1	CLONAL	2	TRUE	1	0.33	2		382	491	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227852	36227852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751187730	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	81	566	0	ENST00000222270.7:c.7337G>A	p.Arg2446Gln	p.R2446Q	ENST00000222270	NM_014727.1	2446	cGa/cAa	32/37	1	2	FACETS	0.901	0.795	1	0.901	0.795	1	CLONAL	1	TRUE	1	0.33	2		566	545	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424921	47424921	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	204	491	0	ENST00000404338.3:c.2989C>T	p.Arg997Ter	p.R997*	ENST00000404338	NM_004491.4	997	Cga/Tga	1/6	1	2	FACETS	1	0.933	1	1	0.994	1	CLONAL	2	TRUE	1	0.33	2		491	618	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015023	27015023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202063570	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	73	425	0	ENST00000335756.4:c.125G>A	p.Arg42Gln	p.R42Q	ENST00000335756	NM_001809.3	42	cGg/cAg	2/5	1	2	FACETS	0.89	0.78	1	0.89	0.78	1	CLONAL	1	TRUE	1	0.33	2		425	497	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519902	29519902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200364883	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	32	471	0	ENST00000389048.3:c.1669C>T	p.Arg557Cys	p.R557C	ENST00000389048	NM_004304.4	557	Cgt/Tgt	9/29	1	2	FACETS	0.425	0.345	0.516	0.425	0.345	0.516	SUBCLONAL	1	TRUE	1	0.33	2		471	456	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39294834	39294834	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	39	372	0	ENST00000402219.2:c.148G>T	p.Glu50Ter	p.E50*	ENST00000402219	NM_005633.3	50	Gaa/Taa	2/23	1	2	FACETS	0.478	0.395	0.569	0.478	0.395	0.569	SUBCLONAL	1	TRUE	1	0.33	2		372	495	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698180	47698180	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63751411	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	163	393	0	ENST00000233146.2:c.1738G>T	p.Glu580Ter	p.E580*	ENST00000233146	NM_000251.2	580	Gaa/Taa	11/16	0.176681196959446	3	FACETS	0.98	0.904	1	0.98	0.904	1	INDETERMINATE	2	TRUE	1	0.33	3		393	587	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026938	48026938	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	219	459	0	ENST00000234420.5:c.1816A>C	p.Lys606Gln	p.K606Q	ENST00000234420	NM_000179.2	606	Aaa/Caa	4/10	0.176681196959446	3	FACETS	0.865	0.81	0.92	1	0.99	1	INDETERMINATE	3	TRUE	1	0.33	3		459	596	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027958	48027958	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1558666905	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	43	438	0	ENST00000234420.5:c.2836G>T	p.Glu946Ter	p.E946*	ENST00000234420	NM_000179.2	946	Gaa/Taa	4/10	0.176681196959446	3	FACETS	0.519	0.434	0.614	0.259	0.217	0.307	INDETERMINATE	1	TRUE	1	0.33	3		438	585	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630379	67630379	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	36	267	0	ENST00000272342.5:c.565G>T	p.Glu189Ter	p.E189*	ENST00000272342	NM_019002.3	189	Gaa/Taa	5/6	1	2	FACETS	0.399	0.327	0.479	0.399	0.327	0.479	SUBCLONAL	1	TRUE	1	0.33	2		267	547	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67632300	67632300	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	38	385	0	ENST00000272342.5:c.2486C>A	p.Ser829Tyr	p.S829Y	ENST00000272342	NM_019002.3	829	tCt/tAt	5/6	1	2	FACETS	0.448	0.37	0.536	0.448	0.37	0.536	SUBCLONAL	1	TRUE	1	0.33	2		385	514	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617589	158617589	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121912679	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	38	457	0	ENST00000263640.3:c.1067G>A	p.Gly356Asp	p.G356D	ENST00000263640	NM_001105.4	356	gGc/gAc	9/11	1	2	FACETS	0.441	0.364	0.527	0.441	0.364	0.527	SUBCLONAL	1	TRUE	1	0.33	2		457	522	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630626	158630626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912678	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	29	444	0	ENST00000263640.3:c.617G>A	p.Arg206His	p.R206H	ENST00000263640	NM_001105.4	206	cGc/cAc	6/11	1	2	FACETS	0.286	0.229	0.352	0.286	0.229	0.352	SUBCLONAL	1	TRUE	1	0.33	2		444	614	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630638	158630638	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs387906591	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	34	444	1	ENST00000263640.3:c.605G>T	p.Arg202Ile	p.R202I	ENST00000263640	NM_001105.4	202	aGa/aTa	6/11	1	2	FACETS	0.339	0.276	0.411	0.339	0.276	0.411	SUBCLONAL	1	TRUE	1	0.33	2		445	607	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273257	198273257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	30	455	0	ENST00000335508.6:c.953G>A	p.Arg318Gln	p.R318Q	ENST00000335508	NM_012433.2	318	cGa/cAa	8/25	1	2	FACETS	0.364	0.293	0.446	0.364	0.293	0.446	SUBCLONAL	1	TRUE	1	0.33	2		455	499	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141586	202141586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760898260	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	23	452	0	ENST00000358485.4:c.874C>T	p.Arg292Trp	p.R292W	ENST00000358485	NM_001080125.1	292	Cgg/Tgg	7/9	1	2	FACETS	0.226	0.175	0.285	0.226	0.175	0.285	SUBCLONAL	1	TRUE	1	0.33	2		452	617	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149589	202149589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1045485	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	188	527	0	ENST00000358485.4:c.1030G>A	p.Asp344Asn	p.D344N	ENST00000358485	NM_001080125.1	344	Gat/Aat	8/9	1	2	FACETS	0.976	0.907	1	1	0.993	1	CLONAL	2	TRUE	1	0.33	2		527	584	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736158	204736158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs963824682	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	42	459	2	ENST00000302823.3:c.515C>T	p.Ser172Leu	p.S172L	ENST00000302823	NM_005214.4	172	tCg/tTg	3/4	1	2	FACETS	0.424	0.353	0.503	0.424	0.353	0.503	SUBCLONAL	1	TRUE	1	0.33	2		461	600	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285173	212285173	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754420079	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	51	376	0	ENST00000342788.4:c.3128C>T	p.Ser1043Leu	p.S1043L	ENST00000342788	NM_005235.2	1043	tCg/tTg	25/28	1	2	FACETS	0.684	0.582	0.795	0.684	0.582	0.795	SUBCLONAL	1	TRUE	1	0.33	2		376	452	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735484	40735484	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	41	481	0	ENST00000373198.4:c.3389A>G	p.Asp1130Gly	p.D1130G	ENST00000373198	NM_133170.3	1130	gAc/gGc	25/32	0.210271357484023	0	FACETS	0.362	0.301	0.429			1	SUBCLONAL	1	TRUE	0	0.33	0		481	460	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281219	46281219	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	94	448	1	ENST00000371998.3:c.4016G>T	p.Arg1339Ile	p.R1339I	ENST00000371998		1339	aGa/aTa	21/23	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.33	2		449	545	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755756	39755756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	30	462	0	ENST00000288319.7:c.1009G>A	p.Gly337Arg	p.G337R	ENST00000288319	NM_182918.3	337	Ggg/Agg	10/10	1	2	FACETS	0.384	0.309	0.47	0.384	0.309	0.47	SUBCLONAL	1	TRUE	1	0.33	2		462	473	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074260	30074260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749326764	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	35	429	0	ENST00000338641.4:c.1522G>A	p.Asp508Asn	p.D508N	ENST00000338641	NM_000268.3	508	Gac/Aac	14/16	1	2	FACETS	0.381	0.311	0.459	0.381	0.311	0.459	SUBCLONAL	1	TRUE	1	0.33	2		429	557	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641905	12641905	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs755926381	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	37	470	0	ENST00000251849.4:c.844C>T	p.Arg282Ter	p.R282*	ENST00000251849	NM_002880.3	282	Cga/Tga	8/17	1	2	FACETS	0.377	0.31	0.452	0.377	0.31	0.452	SUBCLONAL	1	TRUE	1	0.33	2		470	595	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645643	12645643	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	26	473	0	ENST00000251849.4:c.826A>C	p.Met276Leu	p.M276L	ENST00000251849	NM_002880.3	276	Atg/Ctg	7/17	1	2	FACETS	0.311	0.246	0.387	0.311	0.246	0.387	SUBCLONAL	1	TRUE	1	0.33	2		473	506	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41279535	41279535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1376703203	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	31	423	0	ENST00000349496.5:c.2105C>T	p.Ala702Val	p.A702V	ENST00000349496	NM_001904.3	702	gCc/gTc	14/15	1	2	FACETS	0.322	0.26	0.393	0.322	0.26	0.393	SUBCLONAL	1	TRUE	1	0.33	2		423	583	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155365	47155365	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	159	397	0	ENST00000409792.3:c.4715+1G>A		p.X1572_splice	ENST00000409792	NM_014159.6	1572			1	2	FACETS	0.995	0.92	1	1	0.992	1	CLONAL	2	TRUE	1	0.33	2		397	484	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162904	47162904	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs757432733	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	153	497	0	ENST00000409792.3:c.3222G>T	p.Lys1074Asn	p.K1074N	ENST00000409792	NM_014159.6	1074	aaG/aaT	3/21	1	2	FACETS	0.822	0.756	0.89	1	0.99	1	CLONAL	2	TRUE	1	0.33	2		497	564	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164415	47164415	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	67	408	0	ENST00000409792.3:c.1711A>C	p.Asn571His	p.N571H	ENST00000409792	NM_014159.6	571	Aat/Cat	3/21	1	2	FACETS	0.633	0.55	0.724	0.633	0.55	0.724	SUBCLONAL	1	TRUE	1	0.33	2		408	641	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164999	47164999	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	35	445	0	ENST00000409792.3:c.1127A>C	p.Lys376Thr	p.K376T	ENST00000409792	NM_014159.6	376	aAa/aCa	3/21	1	2	FACETS	0.351	0.286	0.423	0.351	0.286	0.423	SUBCLONAL	1	TRUE	1	0.33	2		445	605	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165086	47165086	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	30	439	0	ENST00000409792.3:c.1040A>G	p.Lys347Arg	p.K347R	ENST00000409792	NM_014159.6	347	aAg/aGg	3/21	1	2	FACETS	0.32	0.257	0.391	0.32	0.257	0.391	SUBCLONAL	1	TRUE	1	0.33	2		439	569	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981696	63981696	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	45	612	1	ENST00000398590.3:c.2198C>A	p.Ser733Tyr	p.S733Y	ENST00000398590	NM_001177387.1	733	tCt/tAt	12/14	1	2	FACETS	0.428	0.359	0.505	0.428	0.359	0.505	SUBCLONAL	1	TRUE	1	0.33	2		613	637	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014100	70014100	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs750479971	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	66	435	0	ENST00000394351.3:c.961C>A	p.Leu321Ile	p.L321I	ENST00000394351	NM_000248.3	321	Ctt/Att	9/9	1	2	FACETS	0.704	0.612	0.804	0.704	0.612	0.804	SUBCLONAL	1	TRUE	1	0.33	2		435	568	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73112850	73112850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375938868	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	158	338	0	ENST00000356692.5:c.446G>A	p.Arg149Gln	p.R149Q	ENST00000356692		149	cGa/cAa	6/9	1	2	FACETS	1	0.931	1	1	0.992	1	CLONAL	2	TRUE	1	0.33	2		338	475	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89176379	89176379	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1321323037	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	51	288	0	ENST00000336596.2:c.109A>G	p.Thr37Ala	p.T37A	ENST00000336596	NM_005233.5	37	Aca/Gca	2/17	1	2	FACETS	0.775	0.66	0.9	0.775	0.66	0.9	SUBCLONAL	1	TRUE	1	0.33	2		288	399	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445035	89445035	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	31	438	0	ENST00000336596.2:c.1355G>T	p.Ser452Ile	p.S452I	ENST00000336596	NM_005233.5	452	aGc/aTc	6/17	1	2	FACETS	0.332	0.268	0.405	0.332	0.268	0.405	SUBCLONAL	1	TRUE	1	0.33	2		438	566	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468407	89468407	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs201062946	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	150	437	0	ENST00000336596.2:c.1941G>T	p.Glu647Asp	p.E647D	ENST00000336596	NM_005233.5	647	gaG/gaT	11/17	1	2	FACETS	0.965	0.889	1	1	0.992	1	CLONAL	2	TRUE	1	0.33	2		437	471	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468516	89468516	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1453560937	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	58	460	0	ENST00000336596.2:c.2050C>T	p.Arg684Ter	p.R684*	ENST00000336596	NM_005233.5	684	Cga/Tga	11/17	1	2	FACETS	0.662	0.569	0.763	0.662	0.569	0.763	SUBCLONAL	1	TRUE	1	0.33	2		460	531	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670461	134670461	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	26	474	0	ENST00000398015.3:c.372G>T	p.Lys124Asn	p.K124N	ENST00000398015	NM_004441.4	124	aaG/aaT	3/16	1	2	FACETS	0.321	0.253	0.399	0.321	0.253	0.399	SUBCLONAL	1	TRUE	1	0.33	2		474	491	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670619	134670619	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	25	470	0	ENST00000398015.3:c.530T>G	p.Phe177Cys	p.F177C	ENST00000398015	NM_004441.4	177	tTt/tGt	3/16	1	2	FACETS	0.31	0.243	0.387	0.31	0.243	0.387	SUBCLONAL	1	TRUE	1	0.33	2		470	489	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426050	138426050	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	60	339	0	ENST00000289153.2:c.1481A>C	p.Lys494Thr	p.K494T	ENST00000289153	NM_006219.2	494	aAa/aCa	9/22	1	2	FACETS	0.787	0.68	0.904	0.787	0.68	0.904	CLONAL	1	TRUE	1	0.33	2		339	462	SUCCESS
ATR	545	MSKCC	GRCh37	3	142180886	142180886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142918229	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	53	301	0	ENST00000350721.4:c.7088G>A	p.Arg2363Gln	p.R2363Q	ENST00000350721	NM_001184.3	2363	cGa/cAa	42/47	1	2	FACETS	0.678	0.578	0.786	0.678	0.578	0.786	SUBCLONAL	1	TRUE	1	0.33	2		301	474	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274850	142274850	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	33	420	0	ENST00000350721.4:c.2210A>G	p.His737Arg	p.H737R	ENST00000350721	NM_001184.3	737	cAt/cGt	10/47	1	2	FACETS	0.36	0.293	0.437	0.36	0.293	0.437	SUBCLONAL	1	TRUE	1	0.33	2		420	555	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281802	142281802	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	35	436	0	ENST00000350721.4:c.442G>T	p.Glu148Ter	p.E148*	ENST00000350721	NM_001184.3	148	Gaa/Taa	4/47	1	2	FACETS	0.358	0.293	0.432	0.358	0.293	0.432	SUBCLONAL	1	TRUE	1	0.33	2		436	592	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198077	185198077	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	148	458	0	ENST00000265026.3:c.2559C>A	p.Phe853Leu	p.F853L	ENST00000265026	NM_004721.4	853	ttC/ttA	13/14	1	2	FACETS	0.781	0.717	0.848	1	0.989	1	SUBCLONAL	2	TRUE	1	0.33	2		458	574	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444663	187444663	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	36	519	0	ENST00000232014.4:c.1564G>T	p.Glu522Ter	p.E522*	ENST00000232014	NM_001130845.1	522	Gag/Tag	7/10	1	2	FACETS	0.364	0.299	0.438	0.364	0.299	0.438	SUBCLONAL	1	TRUE	1	0.33	2		519	599	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749496	41749496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	23	431	0	ENST00000226382.2:c.299G>A	p.Arg100His	p.R100H	ENST00000226382	NM_003924.3	100	cGc/cAc	2/3	1	2	FACETS	0.333	0.259	0.42	0.333	0.259	0.42	SUBCLONAL	1	TRUE	1	0.33	2		431	418	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133904	55133904	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	48	405	0	ENST00000257290.5:c.1117A>C	p.Ile373Leu	p.I373L	ENST00000257290	NM_006206.4	373	Ata/Cta	7/23	1	2	FACETS	0.622	0.526	0.727	0.622	0.526	0.727	SUBCLONAL	1	TRUE	1	0.33	2		405	468	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948790	55948790	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	193	316	0	ENST00000263923.4:c.3675G>T	p.Gln1225His	p.Q1225H	ENST00000263923	NM_002253.2	1225	caG/caT	28/30	1	2	FACETS	1	0.983	1	1	0.994	1	CLONAL	2	TRUE	1	0.33	2		316	506	SUCCESS
REST	5978	MSKCC	GRCh37	4	57797908	57797908	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	35	447	0	ENST00000309042.7:c.2884A>C	p.Ile962Leu	p.I962L	ENST00000309042	NM_005612.4	962	Ata/Cta	4/4	1	2	FACETS	0.388	0.317	0.467	0.388	0.317	0.467	SUBCLONAL	1	TRUE	1	0.33	2		447	547	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217202	66217202	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	31	450	0	ENST00000273854.3:c.2413A>C	p.Asn805His	p.N805H	ENST00000273854	NM_004439.5	805	Aac/Cac	14/18	1	2	FACETS	0.352	0.284	0.429	0.352	0.284	0.429	SUBCLONAL	1	TRUE	1	0.33	2		450	534	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218787	66218787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	104	315	0	ENST00000273854.3:c.2271G>T	p.Glu757Asp	p.E757D	ENST00000273854	NM_004439.5	757	gaG/gaT	13/18	1	2	FACETS	0.847	0.765	0.932	1	0.986	1	CLONAL	2	TRUE	1	0.33	2		315	372	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230870	66230870	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765807043	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	30	407	0	ENST00000273854.3:c.2101G>A	p.Glu701Lys	p.E701K	ENST00000273854	NM_004439.5	701	Gaa/Aaa	12/18	1	2	FACETS	0.354	0.284	0.433	0.354	0.284	0.433	SUBCLONAL	1	TRUE	1	0.33	2		407	514	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157146	106157146	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	206	577	0	ENST00000380013.4:c.2047T>G	p.Phe683Val	p.F683V	ENST00000380013	NM_001127208.2	683	Ttt/Gtt	3/11	1	2	FACETS	1	0.963	1	1	0.994	1	CLONAL	2	TRUE	1	0.33	2		577	597	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094904	143094904	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	49	391	0	ENST00000262992.4:c.1240C>A	p.Leu414Ile	p.L414I	ENST00000262992	NM_001101669.1	414	Ctc/Atc	14/24	1	2	FACETS	0.511	0.432	0.598	0.511	0.432	0.598	SUBCLONAL	1	TRUE	1	0.33	2		391	581	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31405795	31405795	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	29	307	0	ENST00000344624.3:c.3983C>T	p.Ala1328Val	p.A1328V	ENST00000344624		1328	gCg/gTg	32/33	1	2	FACETS	0.349	0.279	0.428	0.349	0.279	0.428	SUBCLONAL	1	TRUE	1	0.33	2		307	504	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31511148	31511148	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	27	326	0	ENST00000344624.3:c.1426G>T	p.Asp476Tyr	p.D476Y	ENST00000344624		476	Gat/Tat	6/33	1	2	FACETS	0.357	0.284	0.442	0.357	0.284	0.442	SUBCLONAL	1	TRUE	1	0.33	2		326	458	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515145	31515145	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1202201920	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	48	500	0	ENST00000344624.3:c.1240C>T	p.Arg414Ter	p.R414*	ENST00000344624		414	Cga/Tga	5/33	1	2	FACETS	0.513	0.433	0.601	0.513	0.433	0.601	SUBCLONAL	1	TRUE	1	0.33	2		500	567	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950648	38950648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776074870	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	25	415	0	ENST00000357387.3:c.3302C>T	p.Ser1101Leu	p.S1101L	ENST00000357387	NM_152756.3	1101	tCg/tTg	31/38	1	2	FACETS	0.251	0.197	0.314	0.251	0.197	0.314	SUBCLONAL	1	TRUE	1	0.33	2		415	603	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952300	38952300	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs557642842	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	29	402	0	ENST00000357387.3:c.3125C>T	p.Ser1042Leu	p.S1042L	ENST00000357387	NM_152756.3	1042	tCg/tTg	30/38	1	2	FACETS	0.346	0.277	0.425	0.346	0.277	0.425	SUBCLONAL	1	TRUE	1	0.33	2		402	508	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181843	56181843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	27	314	0	ENST00000399503.3:c.4067G>A	p.Gly1356Asp	p.G1356D	ENST00000399503	NM_005921.1	1356	gGc/gAc	17/20	1	2	FACETS	0.315	0.25	0.389	0.315	0.25	0.389	SUBCLONAL	1	TRUE	1	0.33	2		314	520	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751158	57751158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149934516	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	62	457	0	ENST00000274289.3:c.1709C>T	p.Thr570Met	p.T570M	ENST00000274289	NM_006622.3	570	aCg/aTg	12/14	1	2	FACETS	0.728	0.63	0.835	0.728	0.63	0.835	SUBCLONAL	1	TRUE	1	0.33	2		457	516	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752839	57752839	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	34	437	0	ENST00000274289.3:c.1089C>A	p.Phe363Leu	p.F363L	ENST00000274289	NM_006622.3	363	ttC/ttA	8/14	1	2	FACETS	0.371	0.302	0.448	0.371	0.302	0.448	SUBCLONAL	1	TRUE	1	0.33	2		437	556	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589147	67589147	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	42	146	0	ENST00000274335.5:c.1135A>G	p.Lys379Glu	p.K379E	ENST00000274335		379	Aaa/Gaa	9/15	1	2	FACETS	0.471	0.393	0.559	0.471	0.393	0.559	SUBCLONAL	1	TRUE	1	0.33	2		146	540	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564611	86564611	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	162	622	0	ENST00000274376.6:c.343G>A	p.Ala115Thr	p.A115T	ENST00000274376	NM_002890.2	115	Gct/Act	1/25	1	2	FACETS	0.982	0.908	1	1	0.992	1	CLONAL	2	TRUE	1	0.33	2		622	500	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649005	86649005	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	154	346	0	ENST00000274376.6:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000274376	NM_002890.2	429	Gaa/Taa	9/25	1	2	FACETS	0.886	0.815	0.958	1	0.991	1	CLONAL	2	TRUE	1	0.33	2		346	527	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685312	86685312	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	167	352	0	ENST00000274376.6:c.3028C>T	p.Arg1010Ter	p.R1010*	ENST00000274376	NM_002890.2	1010	Cga/Tga	24/25	1	2	FACETS	1	0.966	1	1	0.993	1	CLONAL	2	TRUE	1	0.33	2		352	472	SUCCESS
APC	324	MSKCC	GRCh37	5	112175066	112175066	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs762391822	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	131	415	0	ENST00000257430.4:c.3775A>G	p.Ile1259Val	p.I1259V	ENST00000257430	NM_000038.5	1259	Ata/Gta	16/16	1	2	FACETS	0.759	0.692	0.828	1	0.987	1	SUBCLONAL	2	TRUE	1	0.33	2		415	523	SUCCESS
APC	324	MSKCC	GRCh37	5	112177354	112177354	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	198	489	0	ENST00000257430.4:c.6063C>A	p.Phe2021Leu	p.F2021L	ENST00000257430	NM_000038.5	2021	ttC/ttA	16/16	1	2	FACETS	1	0.959	1	1	0.994	1	CLONAL	2	TRUE	1	0.33	2		489	577	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977935	131977935	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1561661834	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	25	383	0	ENST00000265335.6:c.3818T>G	p.Phe1273Cys	p.F1273C	ENST00000265335		1273	tTt/tGt	25/25	1	2	FACETS	0.319	0.251	0.398	0.319	0.251	0.398	SUBCLONAL	1	TRUE	1	0.33	2		383	475	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911137	29911137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	45	490	0	ENST00000376809.5:c.436G>A	p.Asp146Asn	p.D146N	ENST00000376809	NM_002116.7	146	Gat/Aat	3/8	1	2	FACETS	0.617	0.519	0.725	0.617	0.519	0.725	SUBCLONAL	1	TRUE	1	0.33	2		490	442	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671416	30671416	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	44	576	0	ENST00000376406.3:c.5544G>T	p.Glu1848Asp	p.E1848D	ENST00000376406	NM_014641.2	1848	gaG/gaT	10/15	1	2	FACETS	0.416	0.348	0.492	0.416	0.348	0.492	SUBCLONAL	1	TRUE	1	0.33	2		576	641	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188823	32188823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs8192585	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	30	589	0	ENST00000375023.3:c.731C>T	p.Ser244Leu	p.S244L	ENST00000375023	NM_004557.3	244	tCg/tTg	4/30	1	2	FACETS	0.361	0.29	0.441	0.361	0.29	0.441	SUBCLONAL	1	TRUE	1	0.33	2		589	504	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64286793	64286793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	30	333	0	ENST00000370651.3:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000370651	NM_003463.4	3	cGa/cAa	2/6	1	2	FACETS	0.369	0.296	0.451	0.369	0.296	0.451	SUBCLONAL	1	TRUE	1	0.33	2		333	493	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536238	106536238	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	52	477	0	ENST00000369096.4:c.205T>G	p.Ser69Ala	p.S69A	ENST00000369096	NM_001198.3	69	Tct/Gct	2/7	1	2	FACETS	0.629	0.536	0.731	0.629	0.536	0.731	SUBCLONAL	1	TRUE	1	0.33	2		477	501	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106543511	106543511	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	30	430	0	ENST00000369096.4:c.313G>T	p.Glu105Ter	p.E105*	ENST00000369096	NM_001198.3	105	Gaa/Taa	3/7	1	2	FACETS	0.314	0.252	0.385	0.314	0.252	0.385	SUBCLONAL	1	TRUE	1	0.33	2		430	579	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609881	117609881	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	31	429	0	ENST00000368508.3:c.6818A>T	p.Asn2273Ile	p.N2273I	ENST00000368508	NM_002944.2	2273	aAc/aTc	43/43	1	2	FACETS	0.379	0.306	0.462	0.379	0.306	0.462	SUBCLONAL	1	TRUE	1	0.33	2		429	496	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609891	117609891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1302341778	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	32	442	0	ENST00000368508.3:c.6808G>A	p.Glu2270Lys	p.E2270K	ENST00000368508	NM_002944.2	2270	Gaa/Aaa	43/43	1	2	FACETS	0.388	0.314	0.471	0.388	0.314	0.471	SUBCLONAL	1	TRUE	1	0.33	2		442	500	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630083	117630083	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	43	377	0	ENST00000368508.3:c.6443G>T	p.Gly2148Val	p.G2148V	ENST00000368508	NM_002944.2	2148	gGa/gTa	41/43	1	2	FACETS	0.543	0.454	0.641	0.543	0.454	0.641	SUBCLONAL	1	TRUE	1	0.33	2		377	480	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117684012	117684012	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	197	422	0	ENST00000368508.3:c.3135G>T	p.Glu1045Asp	p.E1045D	ENST00000368508	NM_002944.2	1045	gaG/gaT	21/43	1	2	FACETS	1	0.978	1	1	0.994	1	CLONAL	2	TRUE	1	0.33	2		422	539	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519353	137519353	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	34	408	0	ENST00000367739.4:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000367739	NM_000416.2	429	Gaa/Taa	7/7	1	2	FACETS	0.402	0.328	0.486	0.402	0.328	0.486	SUBCLONAL	1	TRUE	1	0.33	2		408	512	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524672	137524672	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	34	373	0	ENST00000367739.4:c.697G>T	p.Glu233Ter	p.E233*	ENST00000367739	NM_000416.2	233	Gaa/Taa	5/7	1	2	FACETS	0.342	0.278	0.413	0.342	0.278	0.413	SUBCLONAL	1	TRUE	1	0.33	2		373	603	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100054	157100054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	129	530	0	ENST00000346085.5:c.991G>A	p.Ala331Thr	p.A331T	ENST00000346085	NM_020732.3	331	Gca/Aca	1/20	1	2	FACETS	1	0.916	1	1	0.991	1	CLONAL	2	TRUE	1	0.33	2		530	391	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683645	162683645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	46	514	0	ENST00000366898.1:c.324C>A	p.Ser108Arg	p.S108R	ENST00000366898	NM_004562.2	108	agC/agA	3/12	1	2	FACETS	0.596	0.502	0.699	0.596	0.502	0.699	SUBCLONAL	1	TRUE	1	0.33	2		514	468	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444317	50444317	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	31	559	0	ENST00000331340.3:c.247C>T	p.Arg83Ter	p.R83*	ENST00000331340	NM_006060.4	83	Cga/Tga	4/8	1	2	FACETS	0.339	0.273	0.414	0.339	0.273	0.414	SUBCLONAL	1	TRUE	1	0.33	2		559	554	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210997	55210997	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	30	428	0	ENST00000275493.2:c.241-1G>T		p.X81_splice	ENST00000275493	NM_005228.3	81			1	2	FACETS	0.379	0.305	0.463	0.379	0.305	0.463	SUBCLONAL	1	TRUE	1	0.33	2		428	480	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266437	55266437	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	151	418	0	ENST00000275493.2:c.2729T>G	p.Phe910Cys	p.F910C	ENST00000275493	NM_005228.3	910	tTt/tGt	23/28	1	2	FACETS	0.94	0.865	1	1	0.991	1	CLONAL	2	TRUE	1	0.33	2		418	487	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336634	81336634	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	123	362	0	ENST00000222390.5:c.1588C>A	p.Leu530Ile	p.L530I	ENST00000222390	NM_000601.4	530	Ctt/Att	14/18	1	2	FACETS	0.816	0.743	0.891	1	0.988	1	CLONAL	2	TRUE	1	0.33	2		362	457	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509227	106509227	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	34	522	0	ENST00000359195.3:c.1221G>T	p.Glu407Asp	p.E407D	ENST00000359195	NM_002649.2	407	gaG/gaT	2/11	1	2	FACETS	0.373	0.304	0.45	0.373	0.304	0.45	SUBCLONAL	1	TRUE	1	0.33	2		522	553	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520000	106520000	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs759433704	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	68	413	0	ENST00000359195.3:c.2428C>A	p.Pro810Thr	p.P810T	ENST00000359195	NM_002649.2	810	Cca/Aca	6/11	1	2	FACETS	0.864	0.753	0.983	0.864	0.753	0.983	CLONAL	1	TRUE	1	0.33	2		413	477	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340196	116340196	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	60	437	0	ENST00000397752.3:c.1058C>A	p.Ser353Tyr	p.S353Y	ENST00000397752	NM_000245.2	353	tCt/tAt	2/21	1	2	FACETS	0.666	0.574	0.766	0.666	0.574	0.766	SUBCLONAL	1	TRUE	1	0.33	2		437	546	SUCCESS
MET	4233	MSKCC	GRCh37	7	116381021	116381021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767715328	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	172	494	0	ENST00000397752.3:c.1643C>T	p.Ser548Leu	p.S548L	ENST00000397752	NM_000245.2	548	tCg/tTg	5/21	1	2	FACETS	0.853	0.789	0.919	1	0.991	1	CLONAL	2	TRUE	1	0.33	2		494	611	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124469359	124469359	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	52	264	0	ENST00000357628.3:c.1543C>A	p.Leu515Ile	p.L515I	ENST00000357628	NM_015450.2	515	Cta/Ata	16/19	1	2	FACETS	0.663	0.565	0.771	0.663	0.565	0.771	SUBCLONAL	1	TRUE	1	0.33	2		264	475	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860491	151860491	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	78	613	0	ENST00000262189.6:c.10171T>C	p.Phe3391Leu	p.F3391L	ENST00000262189	NM_170606.2	3391	Ttt/Ctt	43/59	1	2	FACETS	0.671	0.589	0.758	0.671	0.589	0.758	SUBCLONAL	1	TRUE	1	0.33	2		613	705	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891320	151891320	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	62	266	0	ENST00000262189.6:c.4534A>G	p.Ile1512Val	p.I1512V	ENST00000262189	NM_170606.2	1512	Att/Gtt	30/59	1	2	FACETS	0.767	0.663	0.879	0.767	0.663	0.879	SUBCLONAL	1	TRUE	1	0.33	2		266	490	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995501	68995501	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1326956245	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	45	373	0	ENST00000288368.4:c.1905G>T	p.Lys635Asn	p.K635N	ENST00000288368	NM_024870.2	635	aaG/aaT	18/40	1	2	FACETS	0.53	0.445	0.623	0.53	0.445	0.623	SUBCLONAL	1	TRUE	1	0.33	2		373	515	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74858910	74858910	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	39	378	0	ENST00000284811.8:c.294A>C	p.Glu98Asp	p.E98D	ENST00000284811		98	gaA/gaC	4/4	1	2	FACETS	0.434	0.359	0.518	0.434	0.359	0.518	SUBCLONAL	1	TRUE	1	0.33	2		378	544	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141582987	141582987	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	37	444	0	ENST00000220592.5:c.260T>G	p.Phe87Cys	p.F87C	ENST00000220592	NM_012154.3	87	tTt/tGt	3/19	1	2	FACETS	0.375	0.308	0.45	0.375	0.308	0.45	SUBCLONAL	1	TRUE	1	0.33	2		444	598	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090455	5090455	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	35	298	0	ENST00000381652.3:c.2771A>C	p.Asn924Thr	p.N924T	ENST00000381652	NM_004972.3	924	aAt/aCt	21/25	1	2	FACETS	0.499	0.409	0.6	0.499	0.409	0.6	SUBCLONAL	1	TRUE	1	0.33	2		298	425	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465499	8465499	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	136	435	0	ENST00000356435.5:c.3681C>A	p.Phe1227Leu	p.F1227L	ENST00000356435		1227	ttC/ttA	21/35	1	2	FACETS	0.939	0.861	1	1	0.99	1	CLONAL	2	TRUE	1	0.33	2		435	439	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020640	37020640	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	148	388	0	ENST00000358127.4:c.205C>A	p.Leu69Ile	p.L69I	ENST00000358127	NM_001280556.1	69	Ctt/Att	2/10	1	2	FACETS	0.99	0.912	1	1	0.992	1	CLONAL	2	TRUE	1	0.33	2		388	453	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815652	139815652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767258846	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	38	450	0	ENST00000247668.2:c.1123G>A	p.Ala375Thr	p.A375T	ENST00000247668	NM_021138.3	375	Gcc/Acc	9/11	1	2	FACETS	0.426	0.352	0.51	0.426	0.352	0.51	SUBCLONAL	1	TRUE	1	0.33	2		450	540	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933297	39933297	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	31	557	0	ENST00000378444.4:c.1302A>C	p.Lys434Asn	p.K434N	ENST00000378444	NM_001123385.1	434	aaA/aaC	4/15	1	2	FACETS	0.322	0.259	0.393	0.322	0.259	0.393	SUBCLONAL	1	TRUE	1	0.33	2		557	584	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732866	44732866	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	35	203	0	ENST00000377967.4:c.69G>T	p.Lys23Asn	p.K23N	ENST00000377967	NM_021140.2	23	aaG/aaT	1/29	1	2	FACETS	0.563	0.462	0.676	0.563	0.462	0.676	SUBCLONAL	1	TRUE	1	0.33	2		203	377	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426749	47426749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774324085	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	30	520	0	ENST00000377045.4:c.994G>A	p.Asp332Asn	p.D332N	ENST00000377045	NM_001654.4	332	Gat/Aat	10/16	1	2	FACETS	0.372	0.299	0.455	0.372	0.299	0.455	SUBCLONAL	1	TRUE	1	0.33	2		520	489	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342400	70342400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	71	497	1	ENST00000374080.3:c.1291C>T	p.Arg431Trp	p.R431W	ENST00000374080		431	Cgg/Tgg	9/45	1	2	FACETS	0.842	0.736	0.956	0.842	0.736	0.956	CLONAL	1	TRUE	1	0.33	2		498	511	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814238	76814238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	40	391	0	ENST00000373344.5:c.6406G>A	p.Asp2136Asn	p.D2136N	ENST00000373344	NM_000489.3	2136	Gac/Aac	29/35	1	2	FACETS	0.487	0.404	0.579	0.487	0.404	0.579	SUBCLONAL	1	TRUE	1	0.33	2		391	498	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76931726	76931726	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	28	419	0	ENST00000373344.5:c.3804G>T	p.Glu1268Asp	p.E1268D	ENST00000373344	NM_000489.3	1268	gaG/gaT	10/35	1	2	FACETS	0.329	0.262	0.405	0.329	0.262	0.405	SUBCLONAL	1	TRUE	1	0.33	2		419	516	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105551	27105551	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	186	484	0	ENST00000324856.7:c.5162del	p.Arg1721HisfsTer4	p.R1721Hfs*4	ENST00000324856	NM_006015.4	1721	cGa/ca	20/20	1	2	FACETS	0.929	0.862	0.997	1	0.993	1	CLONAL	2	TRUE	1	0.33	2		484	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578384	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	279	494	0	ENST00000269305.4:c.546C>A	p.Cys182Ter	p.C182*	ENST00000269305	NM_001126112.2	182	tgC/tgA	5/11	0.494638423062067	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.494638423062067	2		494	544	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422242	422242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769792722	NA	P-0065711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	169	326	0	ENST00000399788.2:c.3016G>A	p.Ala1006Thr	p.A1006T	ENST00000399788	NM_001042603.1	1006	Gct/Act	20/28	0.230301795358488	5	FACETS	0.835	0.775	0.897			1	INDETERMINATE	3	TRUE	NA	0.494638423062067	5		326	475	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286229	66286229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	153	314	0	ENST00000273854.3:c.1457C>T	p.Ser486Phe	p.S486F	ENST00000273854	NM_004439.5	486	tCt/tTt	6/18	0.263093471154593	5	FACETS	1	0.955	1	0.779	0.723	0.835	INDETERMINATE	3	TRUE	1	0.494638423062067	5		314	346	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229608	5229608	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	75	320	0	ENST00000357368.4:c.2243G>A	p.Arg748Gln	p.R748Q	ENST00000357368	NM_002850.3	748	cGg/cAg	15/38	0.430755054585379	4	FACETS	0.977	0.859	1	0.488	0.429	0.552	CLONAL	1	TRUE	2	0.494638423062067	4		320	464	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711237	114711242	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTTAGC	GTTAGC	-	novel	NA	P-0065711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	178	239	0	ENST00000543371.1:c.257-4_258del		p.X86_splice	ENST00000543371	NM_001198531.1	86		3/14	0.464702238417874	3	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	1	0.494638423062067	3		239	442	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066843	30066843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	88	332	0	ENST00000331968.5:c.2288C>T	p.Ser763Phe	p.S763F	ENST00000331968	NM_002742.2	763	tCt/tTt	16/18	0.494638423062067	2	FACETS	0.951	0.849	1	0.476	0.424	0.53	CLONAL	1	TRUE	0	0.494638423062067	2		332	374	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99491818	99491831	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCTGGGAGATCG	CCTCTGGGAGATCG	-	novel	NA	P-0065711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	31	332	1	ENST00000268035.6:c.3605_3618del	p.Leu1202HisfsTer33	p.L1202Hfs*33	ENST00000268035	NM_000875.3	1201	gtCCTCTGGGAGATCGcc/gtcc	20/21	0.430755054585379	4	FACETS	0.319	0.257	0.389	0.159	0.128	0.195	SUBCLONAL	1	TRUE	2	0.494638423062067	4		333	588	SUCCESS
ATR	545	MSKCC	GRCh37	3	142253963	142253963	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	74	239	0	ENST00000350721.4:c.3904C>G	p.His1302Asp	p.H1302D	ENST00000350721	NM_001184.3	1302	Cat/Gat	21/47	0.464702238417874	3	FACETS	1	0.935	1	0.546	0.481	0.614	CLONAL	1	TRUE	1	0.494638423062067	3		239	342	SUCCESS
ATR	545	MSKCC	GRCh37	3	142253983	142253983	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	82	255	0	ENST00000350721.4:c.3884A>G	p.Glu1295Gly	p.E1295G	ENST00000350721	NM_001184.3	1295	gAa/gGa	21/47	0.464702238417874	3	FACETS	1	0.952	1	0.568	0.504	0.635	CLONAL	1	TRUE	1	0.494638423062067	3		255	364	SUCCESS
APC	324	MSKCC	GRCh37	5	112175243	112175250	+	frameshift_variant	Frame_Shift_Del	DEL	GATCCTGT	GATCCTGT	-	novel	NA	P-0065711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	286	363	0	ENST00000257430.4:c.3954_3961del	p.Asp1318GlufsTer11	p.D1318Efs*11	ENST00000257430	NM_000038.5	1318	GATCCTGTg/g	16/16	0.494638423062067	3	FACETS	0.967	0.923	1	0.967	0.923	1	CLONAL	3	TRUE	0	0.494638423062067	3		363	497	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591115	67591123	+	inframe_deletion	In_Frame_Del	DEL	CTTATCCAG	CTTATCCAG	-	novel	NA	P-0065712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	61	348	1	ENST00000274335.5:c.1710_1718del	p.Ile571_Leu573del	p.I571_L573del	ENST00000274335		570	CTTATCCAG/-	12/15	0.704977065843106	4	FACETS	1	0.958	1			1	CLONAL	1	TRUE	NA	0.713078569625526	4		349	236	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098800	178098800	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	57	367	0	ENST00000397062.3:c.245A>C	p.Glu82Ala	p.E82A	ENST00000397062	NM_006164.4	82	gAa/gCa	2/5	0.166508123910984	3	FACETS	1	0.877	1	0.504	0.438	0.574	INDETERMINATE	1	TRUE	1	0.713078569625526	3		367	215	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685302	89685303	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	48	203	0	ENST00000371953.3:c.197_198insT	p.Lys66AsnfsTer8	p.K66Nfs*8	ENST00000371953	NM_000314.4	66	aag/aaTg	3/9	0.361244374373351	4	FACETS	0.994	0.866	1	0.994	0.866	1	INDETERMINATE	2	TRUE	2	0.713078569625526	4		203	116	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343285	118343285	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	35	306	0	ENST00000534358.1:c.1411C>T	p.Gln471Ter	p.Q471*	ENST00000534358	NM_005933.3	471	Caa/Taa	3/36	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.713078569625526	2		306	94	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416627	49416627	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0065712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	47	439	0	ENST00000301067.7:c.16084A>T	p.Lys5362Ter	p.K5362*	ENST00000301067	NM_003482.3	5362	Aag/Tag	51/54	0.123014923879913	4	FACETS	1	0.93	1	0.576	0.492	0.666	INDETERMINATE	1	TRUE	2	0.713078569625526	4		439	196	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176630	56176630	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0065712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	74	306	0	ENST00000399503.3:c.2179+1G>C		p.X727_splice	ENST00000399503	NM_005921.1	727			NA	2	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.713078569625526	2		306	151	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0065713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	56	449	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.54269588991573	6	FACETS	0.987	0.878	1			1	CLONAL	4	TRUE	NA	0.54269588991573	6		451	109	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851677	63851677	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	36	459	0	ENST00000279873.7:c.2455C>T	p.Leu819Phe	p.L819F	ENST00000279873	NM_032199.2	819	Ctc/Ttc	10/10	0.35271074732665	3	FACETS	0.878	0.745	1	0.878	0.745	1	CLONAL	2	TRUE	1	0.54269588991573	3		459	96	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21343088	21343088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776327053	NA	P-0065713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	18	393	0	ENST00000215739.8:c.520G>A	p.Ala174Thr	p.A174T	ENST00000215739	NM_006767.3	174	Gct/Act	6/21	0.35271074732665	3	FACETS	1	0.83	1	0.548	0.422	0.688	CLONAL	1	TRUE	1	0.54269588991573	3		393	77	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456474	189456474	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	27	406	0	ENST00000264731.3:c.235G>T	p.Glu79Ter	p.E79*	ENST00000264731	NM_003722.4	79	Gaa/Taa	3/14	0.546889088901796	5	FACETS	1	0.875	1	0.435	0.356	0.519	CLONAL	2	TRUE	0	0.54269588991573	5		406	83	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639160	176639160	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1035426339	NA	P-0065713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	45	437	0	ENST00000439151.2:c.3760C>A	p.Pro1254Thr	p.P1254T	ENST00000439151	NM_022455.4	1254	Ccc/Acc	5/23	0.520453934367092	5	FACETS	1	0.903	1	0.427	0.366	0.49	CLONAL	2	TRUE	0	0.54269588991573	5		437	141	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0065716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	120	485	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.3	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.38	1		485	385	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120115	70120115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	153	526	0	ENST00000245479.2:c.1121del	p.Pro374ArgfsTer9	p.P374Rfs*9	ENST00000245479	NM_000346.3	373	Ccc/cc	3/3	0.3	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.38	2		526	385	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0065716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	81	244	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.38	2		244	339	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343684	118343684	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	89	508	0	ENST00000534358.1:c.1810A>C	p.Met604Leu	p.M604L	ENST00000534358	NM_005933.3	604	Atg/Ctg	3/36	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.38	2		508	459	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376680	118376680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	118	615	0	ENST00000534358.1:c.10073G>A	p.Ser3358Asn	p.S3358N	ENST00000534358	NM_005933.3	3358	aGt/aAt	27/36	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.38	2		615	560	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829368	72829368	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201280219	NA	P-0065716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	83	544	0	ENST00000268489.5:c.7213G>A	p.Ala2405Thr	p.A2405T	ENST00000268489	NM_006885.3	2405	Gct/Act	9/10	1	2	FACETS	0.922	0.816	1	0.922	0.816	1	CLONAL	1	TRUE	1	0.38	2		544	474	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562641	29562641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854562	NA	P-0065716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	113	336	0	ENST00000356175.3:c.3721C>T	p.Arg1241Ter	p.R1241*	ENST00000356175	NM_000267.3	1241	Cga/Tga	28/57	1	2	FACETS	0.785	0.713	0.859	1	0.986	1	SUBCLONAL	2	TRUE	1	0.38	2		336	379	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654736	29654736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs797045139	NA	P-0065716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	48	555	0	ENST00000356175.3:c.5425C>T	p.Arg1809Cys	p.R1809C	ENST00000356175	NM_000267.3	1809	Cgc/Tgc	37/57	1	2	FACETS	0.424	0.358	0.497	0.424	0.358	0.497	SUBCLONAL	1	TRUE	1	0.38	2		555	596	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428299	33428299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368914740	NA	P-0065716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	86	577	0	ENST00000345365.6:c.824G>A	p.Arg275Gln	p.R275Q	ENST00000345365	NM_002878.3	275	cGg/cAg	9/10	1	2	FACETS	0.875	0.777	0.981	0.875	0.777	0.981	CLONAL	1	TRUE	1	0.38	2		577	517	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388078	31388078	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1477651398	NA	P-0065716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	127	495	1	ENST00000328111.2:c.1879G>A	p.Asp627Asn	p.D627N	ENST00000328111	NM_006892.3	627	Gac/Aac	17/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.38	2		496	516	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096243	71096244	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	87	486	0	ENST00000318789.4:c.513dup	p.Gln172ThrfsTer123	p.Q172Tfs*123	ENST00000318789	NM_032682.5	171	-/A	10/21	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.38	2		486	452	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0065716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	106	533	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.3	1	FACETS	0.941	0.848	1	0.941	0.848	1	CLONAL	1	TRUE	0	0.38	1		533	480	SUCCESS
APC	324	MSKCC	GRCh37	5	112173496	112173496	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	82	499	0	ENST00000257430.4:c.2205del	p.Lys736SerfsTer25	p.K736Sfs*25	ENST00000257430	NM_000038.5	735	gcG/gc	16/16	1	2	FACETS	0.946	0.838	1	0.946	0.838	1	CLONAL	1	TRUE	1	0.38	2		499	456	SUCCESS
APC	324	MSKCC	GRCh37	5	112175757	112175758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	88	555	0	ENST00000257430.4:c.4467dup	p.His1490ThrfsTer24	p.H1490Tfs*24	ENST00000257430	NM_000038.5	1489	tta/ttAa	16/16	1	2	FACETS	0.85	0.755	0.951	0.85	0.755	0.951	CLONAL	1	TRUE	1	0.38	2		555	545	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553617	106553617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773441438	NA	P-0065716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	94	668	0	ENST00000369096.4:c.1582G>A	p.Val528Met	p.V528M	ENST00000369096	NM_001198.3	528	Gtg/Atg	5/7	1	2	FACETS	0.852	0.759	0.949	0.852	0.759	0.949	CLONAL	1	TRUE	1	0.38	2		668	581	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44920620	44920620	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	79	132	0	ENST00000377967.4:c.1381C>T	p.Gln461Ter	p.Q461*	ENST00000377967	NM_021140.2	461	Cag/Tag	14/29	0.228588118140916	2	FACETS	1	0.935	1			1	CLONAL	2	TRUE	NA	0.38	2		132	197	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0065718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	116	491	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.188552873022587	5	FACETS	0.85	0.775	0.927			1	INDETERMINATE	3	TRUE	NA	0.438555212897503	5		491	344	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431516	49431516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1376941332	NA	P-0065718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	223	745	0	ENST00000301067.7:c.9623C>T	p.Ser3208Phe	p.S3208F	ENST00000301067	NM_003482.3	3208	tCc/tTc	34/54	0.109949692447816	5	FACETS	0.867	0.812	0.924			1	INDETERMINATE	3	TRUE	NA	0.438555212897503	5		745	648	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27172705	27172705	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	76	607	0	ENST00000380036.4:c.720C>G	p.Cys240Trp	p.C240W	ENST00000380036	NM_000459.3	240	tgC/tgG	5/23	0.36168940460086	0	FACETS	0.608	0.538	0.682			1	SUBCLONAL	1	TRUE	0	0.438555212897503	0		607	320	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214871	36214871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	211	627	4	ENST00000222270.7:c.3302del	p.Pro1101LeufsTer81	p.P1101Lfs*81	ENST00000222270	NM_014727.1	1099	ggC/gg	8/37	0.701623776240117	2	FACETS	0.984	0.92	1	0.492	0.46	0.525	CLONAL	1	TRUE	0	0.701623776240117	2		631	611	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	190	532	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.962	0.895	1	0.962	0.895	1	CLONAL	1	TRUE	1	0.701623776240117	2		532	563	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	516	910	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.701623776240117	2	FACETS	0.947	0.917	0.975	0.947	0.917	0.975	CLONAL	2	TRUE	0	0.701623776240117	2		916	777	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	153	610	4	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.615	0.564	0.669	0.615	0.564	0.669	SUBCLONAL	1	TRUE	1	0.701623776240117	2		614	709	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	122	261	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.885	0.807	0.965	0.885	0.807	0.965	CLONAL	1	TRUE	1	0.701623776240117	2		264	393	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	76	460	1	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	0.362	0.318	0.41	0.362	0.318	0.41	SUBCLONAL	1	TRUE	1	0.701623776240117	2		461	598	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691872	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs79375991	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	340	536	13	ENST00000295754.5:c.383del	p.Lys128SerfsTer35	p.K128Sfs*35	ENST00000295754	NM_003242.5	125	gAa/ga	3/7	0.701623776240117	2	FACETS	0.794	0.76	0.829	0.794	0.76	0.829	SUBCLONAL	2	TRUE	0	0.701623776240117	2		549	610	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	57	806	6	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	0.701623776240117	2	FACETS	0.26	0.223	0.301	0.13	0.111	0.151	SUBCLONAL	1	TRUE	0	0.701623776240117	2		812	624	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	106	664	3	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.378	0.339	0.42	0.378	0.339	0.42	SUBCLONAL	1	TRUE	1	0.701623776240117	2		667	799	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	232	594	0	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	0.925	0.866	0.985	0.925	0.866	0.985	CLONAL	1	TRUE	1	0.701623776240117	2		594	715	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105737	27105737	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1064794151	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	219	667	0	ENST00000324856.7:c.5351del	p.Asn1784MetfsTer5	p.N1784Mfs*5	ENST00000324856	NM_006015.4	1783	gAa/ga	20/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.701623776240117	2		667	601	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598212	28598212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769648213	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	237	702	0	ENST00000253063.3:c.184G>A	p.Glu62Lys	p.E62K	ENST00000253063	NM_031459.4	62	Gag/Aag	3/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.701623776240117	2		702	661	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436090	51436090	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	258	544	0	ENST00000262662.1:c.50A>G	p.Asp17Gly	p.D17G	ENST00000262662		17	gAc/gGc	3/4	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.701623776240117	2		544	630	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230461096	230461096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs932562245	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	194	519	0	ENST00000391860.1:c.994C>T	p.His332Tyr	p.H332Y	ENST00000391860	NM_001258311.1	332	Cac/Tac	6/7	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.701623776240117	2		519	520	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230468644	230468644	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	57	630	0	ENST00000391860.1:c.874T>C	p.Tyr292His	p.Y292H	ENST00000391860	NM_001258311.1	292	Tac/Cac	5/7	1	2	FACETS	0.25	0.214	0.29	0.25	0.214	0.29	SUBCLONAL	1	TRUE	1	0.701623776240117	2		630	649	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274678	123274678	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769880096	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	39	567	0	ENST00000358487.5:c.1240G>A	p.Ala414Thr	p.A414T	ENST00000358487	NM_000141.4	414	Gct/Act	9/18	1	2	FACETS	0.15	0.124	0.18	0.15	0.124	0.18	SUBCLONAL	1	TRUE	1	0.701623776240117	2		567	739	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199921	108199921	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	54	442	0	ENST00000278616.4:c.7263A>C	p.Lys2421Asn	p.K2421N	ENST00000278616	NM_000051.3	2421	aaA/aaC	49/63	1	2	FACETS	0.326	0.279	0.378	0.326	0.279	0.378	SUBCLONAL	1	TRUE	1	0.701623776240117	2		442	472	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344053	118344055	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1555036383	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	181	600	0	ENST00000534358.1:c.2184_2186del	p.Ser729del	p.S729del	ENST00000534358	NM_005933.3	727	TCT/-	3/36	1	2	FACETS	0.828	0.768	0.891	0.828	0.768	0.891	CLONAL	1	TRUE	1	0.701623776240117	2		600	623	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006400	12006400	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	227	613	0	ENST00000396373.4:c.368A>C	p.Gln123Pro	p.Q123P	ENST00000396373	NM_001987.4	123	cAg/cCg	4/8	1	2	FACETS	0.989	0.927	1	0.989	0.927	1	CLONAL	1	TRUE	1	0.701623776240117	2		613	654	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945008	31945008	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	280	694	0	ENST00000340398.3:c.93del	p.Ser32LeufsTer5	p.S32Lfs*5	ENST00000340398	NM_001013699.2	31	ccC/cc	1/1	1	2	FACETS	0.93	0.877	0.985	0.93	0.877	0.985	CLONAL	1	TRUE	1	0.701623776240117	2		694	858	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112323	115112324	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	rs1381943852	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	271	686	2	ENST00000257566.3:c.1416_1417del	p.Leu473ProfsTer218	p.L473Pfs*218	ENST00000257566	NM_016569.3	472	gcGCtc/gctc	7/8	0.701623776240117	2	FACETS	0.913	0.873	0.952	0.913	0.873	0.952	CLONAL	2	TRUE	0	0.701623776240117	2		688	423	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108105	30108105	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	20	381	0	ENST00000331968.5:c.702del	p.Lys234AsnfsTer30	p.K234Nfs*30	ENST00000331968	NM_002742.2	234	aaA/aa	5/18	1	2	FACETS	0.168	0.128	0.215	0.168	0.128	0.215	SUBCLONAL	1	TRUE	1	0.701623776240117	2		381	339	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42002912	42002912	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	102	418	0	ENST00000219905.7:c.2453del	p.Asn818IlefsTer10	p.N818Ifs*10	ENST00000219905	NM_001164273.1	817	Aaa/aa	8/24	1	2	FACETS	0.718	0.647	0.792	0.718	0.647	0.792	SUBCLONAL	1	TRUE	1	0.701623776240117	2		418	405	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996257	73996257	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775475628	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	65	114	0	ENST00000318443.5:c.991C>T	p.Arg331Cys	p.R331C	ENST00000318443	NM_001024736.1	331	Cgt/Tgt	5/10	0.701623776240117	2	FACETS	0.936	0.853	1	0.936	0.853	1	CLONAL	2	TRUE	0	0.701623776240117	2		114	99	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292816	91292817	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs781221411	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	413	556	0	ENST00000355112.3:c.320dup	p.Leu107PhefsTer36	p.L107Ffs*36	ENST00000355112	NM_000057.2	106	-/T	3/22	0.701623776240117	2	FACETS	0.895	0.862	0.926	0.895	0.862	0.926	CLONAL	2	TRUE	0	0.701623776240117	2		556	658	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990304	81990304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	219	516	0	ENST00000359376.3:c.3575G>A	p.Ser1192Asn	p.S1192N	ENST00000359376	NM_002661.3	1192	aGc/aAc	32/33	1	2	FACETS	0.978	0.916	1	0.978	0.916	1	CLONAL	1	TRUE	1	0.701623776240117	2		516	638	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044505	12044505	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	45	478	0	ENST00000353533.5:c.1128G>T	p.Glu376Asp	p.E376D	ENST00000353533	NM_003010.3	376	gaG/gaT	11/11	0.701623776240117	2	FACETS	0.249	0.209	0.293	0.125	0.104	0.147	SUBCLONAL	1	TRUE	0	0.701623776240117	2		478	515	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687471	37687472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs760014508	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	187	724	1	ENST00000447079.4:c.4382dup	p.Thr1463AsnfsTer50	p.T1463Nfs*50	ENST00000447079	NM_015083.1	1459	tgg/tGgg	14/14	1	2	FACETS	0.767	0.711	0.825	0.767	0.711	0.825	SUBCLONAL	1	TRUE	1	0.701623776240117	2		725	695	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761412	59761415	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	rs786203717	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	423	477	0	ENST00000259008.2:c.2992_2995del	p.Lys998GlufsTer60	p.K998Efs*60	ENST00000259008	NM_032043.2	998	AAGAga/ga	20/20	0.701623776240117	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.701623776240117	2		477	577	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031339	11031339	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	237	788	0	ENST00000327064.4:c.1339A>C	p.Ser447Arg	p.S447R	ENST00000327064	NM_199141.1	447	Agc/Cgc	12/16	1	2	FACETS	0.913	0.856	0.972	0.913	0.856	0.972	CLONAL	1	TRUE	1	0.701623776240117	2		788	740	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354058	15354058	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	108	450	0	ENST00000263377.2:c.2822del	p.Pro941LeufsTer8	p.P941Lfs*8	ENST00000263377	NM_058243.2	941	cCt/ct	14/20	1	2	FACETS	0.853	0.773	0.936	0.853	0.773	0.936	CLONAL	1	TRUE	1	0.701623776240117	2		450	361	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367969	15367969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759001252	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	30	566	0	ENST00000263377.2:c.1357C>T	p.Arg453Cys	p.R453C	ENST00000263377	NM_058243.2	453	Cgc/Tgc	8/20	1	2	FACETS	0.157	0.126	0.193	0.157	0.126	0.193	SUBCLONAL	1	TRUE	1	0.701623776240117	2		566	544	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945988	17945988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747131454	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	261	722	0	ENST00000458235.1:c.1951C>T	p.Arg651Trp	p.R651W	ENST00000458235	NM_000215.3	651	Cgg/Tgg	15/24	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.701623776240117	2		722	714	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	202	726	3	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	0.701623776240117	2	FACETS	0.924	0.862	0.988	0.462	0.431	0.494	CLONAL	1	TRUE	0	0.701623776240117	2		729	623	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150039	202150039	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1368296717	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	208	626	0	ENST00000358485.4:c.1480C>T	p.Arg494Ter	p.R494*	ENST00000358485	NM_001080125.1	494	Cga/Tga	8/9	1	2	FACETS	0.864	0.806	0.924	0.864	0.806	0.924	CLONAL	1	TRUE	1	0.701623776240117	2		626	686	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326764	62326764	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	228	762	0	ENST00000360203.5:c.3583G>A	p.Ala1195Thr	p.A1195T	ENST00000360203	NM_001283009.1	1195	Gcg/Acg	34/35	NA	2	FACETS	0.956	0.895	1			1	INDETERMINATE	1	TRUE	NA	0.701623776240117	2		762	680	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748023	41748028	+	inframe_deletion	In_Frame_Del	DEL	GCCGCG	GCCGCG	-	novel	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	48	230	0	ENST00000226382.2:c.741_746del	p.Ala259_Ala260del	p.A259_A260del	ENST00000226382	NM_003924.3	247	gcCGCGGCa/gca	3/3	1	2	FACETS	0.991	0.858	1	0.991	0.858	1	CLONAL	1	TRUE	1	0.701623776240117	2		230	138	SUCCESS
APC	324	MSKCC	GRCh37	5	112175211	112175211	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	184	550	0	ENST00000257430.4:c.3920del	p.Ile1307LysfsTer14	p.I1307Kfs*14	ENST00000257430	NM_000038.5	1307	aTa/aa	16/16	0.701623776240117	1	FACETS	0.91	0.854	0.967	0.91	0.854	0.967	CLONAL	1	TRUE	0	0.701623776240117	1		550	374	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520159	176520159	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766591955	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	215	753	0	ENST00000292408.4:c.1078G>A	p.Ala360Thr	p.A360T	ENST00000292408	NM_213647.1	360	Gca/Aca	9/18	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.701623776240117	2		753	612	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176700691	176700691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	220	477	0	ENST00000439151.2:c.5528C>T	p.Ala1843Val	p.A1843V	ENST00000439151	NM_022455.4	1843	gCa/gTa	17/23	1	2	FACETS	0.957	0.896	1	0.957	0.896	1	CLONAL	1	TRUE	1	0.701623776240117	2		477	655	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721024	176721024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	271	732	0	ENST00000439151.2:c.6655C>T	p.Arg2219Cys	p.R2219C	ENST00000439151	NM_022455.4	2219	Cgt/Tgt	23/23	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.701623776240117	2		732	739	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323265	31323265	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs41564218	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	97	274	0	ENST00000412585.2:c.724C>T	p.Gln242Ter	p.Q242*	ENST00000412585	NM_005514.6	242	Cag/Tag	4/8	1	2	FACETS	0.944	0.853	1	0.944	0.853	1	CLONAL	1	TRUE	1	0.701623776240117	2		274	293	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004256	150004256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	123	480	0	ENST00000253339.5:c.1969C>T	p.Arg657Cys	p.R657C	ENST00000253339		657	Cgt/Tgt	3/7	1	2	FACETS	0.932	0.852	1	0.932	0.852	1	CLONAL	1	TRUE	1	0.701623776240117	2		480	376	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397828	116397828	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	128	404	1	ENST00000397752.3:c.2102G>T	p.Ser701Ile	p.S701I	ENST00000397752	NM_000245.2	701	aGt/aTt	8/21	1	2	FACETS	0.96	0.88	1	0.96	0.88	1	CLONAL	1	TRUE	1	0.701623776240117	2		405	380	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879490	151879490	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	285	647	0	ENST00000262189.6:c.5455A>G	p.Met1819Val	p.M1819V	ENST00000262189	NM_170606.2	1819	Atg/Gtg	36/59	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.701623776240117	2		647	689	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345760	152345760	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	172	433	2	ENST00000359321.1:c.810del	p.Phe270LeufsTer27	p.F270Lfs*27	ENST00000359321	NM_005431.1	270	ttT/tt	3/3	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.701623776240117	2		435	484	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38184337	38184337	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	42	424	0	ENST00000317025.8:c.1619A>G	p.Gln540Arg	p.Q540R	ENST00000317025	NM_023034.1	540	cAa/cGa	7/24	1	2	FACETS	0.205	0.17	0.243	0.205	0.17	0.243	SUBCLONAL	1	TRUE	1	0.701623776240117	2		424	585	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371734	55371734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	197	710	0	ENST00000297316.4:c.424C>T	p.Arg142Cys	p.R142C	ENST00000297316	NM_022454.3	142	Cgc/Tgc	2/2	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.701623776240117	2		710	522	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5029792	5029792	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	93	418	0	ENST00000381652.3:c.236C>A	p.Pro79His	p.P79H	ENST00000381652	NM_004972.3	79	cCt/cAt	4/25	0.692800968246536	2	FACETS	0.887	0.798	0.979	0.443	0.399	0.49	CLONAL	1	TRUE	0	0.701623776240117	2		418	299	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486090	8486090	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	232	624	0	ENST00000356435.5:c.2727G>T	p.Lys909Asn	p.K909N	ENST00000356435		909	aaG/aaT	17/35	0.692800968246536	2	FACETS	1	0.961	1	0.516	0.484	0.548	CLONAL	1	TRUE	0	0.701623776240117	2		624	641	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894950	101894950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777965779	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	148	522	0	ENST00000374994.4:c.503G>A	p.Arg168His	p.R168H	ENST00000374994	NM_004612.2	168	cGc/cAc	3/9	1	2	FACETS	0.734	0.673	0.796	0.734	0.673	0.796	SUBCLONAL	1	TRUE	1	0.701623776240117	2		522	575	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249714	110249714	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	153	641	0	ENST00000374672.4:c.961C>A	p.Leu321Ile	p.L321I	ENST00000374672	NM_004235.4	321	Ctt/Att	3/5	1	2	FACETS	0.944	0.871	1	0.944	0.871	1	CLONAL	1	TRUE	1	0.701623776240117	2		641	462	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191804	123191805	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1392503050	NA	P-0065720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	17	355	0	ENST00000218089.9:c.1400dup	p.Phe468LeufsTer5	p.F468Lfs*5	ENST00000218089	NM_001042749.1	465	gtt/gTtt	15/35	0.701623776240117	1	FACETS	0.107	0.079	0.14	0.107	0.079	0.14	SUBCLONAL	1	TRUE	0	0.701623776240117	1		355	294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs530941076	NA	P-0065721-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	96	559	0	ENST00000269305.4:c.658T>A	p.Tyr220Asn	p.Y220N	ENST00000269305	NM_001126112.2	220	Tat/Aat	6/11	0.298993213298735	1	FACETS	0.795	0.713	0.881	1	0.983	1	SUBCLONAL	2	TRUE	0	0.26	1		559	404	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853215	68853215	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065721-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	143	592	0	ENST00000261769.5:c.1598T>G	p.Leu533Arg	p.L533R	ENST00000261769	NM_004360.3	533	cTg/cGg	11/16	0.288435438705033	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.26	2		592	446	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0065722-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	55	557	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	0.891	0.765	1	0.891	0.765	1	CLONAL	1	TRUE	1	0.314121570382209	2		557	393	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0065722-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	37	430	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.314121570382209	1	FACETS	0.807	0.67	0.959	0.807	0.67	0.959	CLONAL	1	TRUE	0	0.314121570382209	1		430	246	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0065722-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	94	381	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.196486311242786	4	FACETS	0.95	0.851	1	0.633	0.567	0.703	CLONAL	2	TRUE	1	0.314121570382209	4		381	414	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729154	66729154	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519731	NA	P-0065722-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	66	399	0	ENST00000307102.5:c.362G>C	p.Cys121Ser	p.C121S	ENST00000307102	NM_002755.3	121	tGc/tCc	3/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.314121570382209	2		399	345	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052633	42052633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065722-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	88	408	0	ENST00000219905.7:c.7304G>A	p.Arg2435Gln	p.R2435Q	ENST00000219905	NM_001164273.1	2435	cGg/cAg	20/24	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.314121570382209	2		408	418	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347553	118347553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555037629	NA	P-0065722-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	34	356	0	ENST00000534358.1:c.3190C>T	p.Arg1064Ter	p.R1064*	ENST00000534358	NM_005933.3	1064	Cga/Tga	4/36	1	2	FACETS	0.582	0.476	0.701	0.582	0.476	0.701	SUBCLONAL	1	TRUE	1	0.314121570382209	2		356	372	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448293	56448293	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065722-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	42	466	0	ENST00000407977.2:c.354del	p.Cys119AlafsTer39	p.C119Afs*39	ENST00000407977		118	ccC/cc	3/10	1	2	FACETS	0.604	0.504	0.714	0.604	0.504	0.714	SUBCLONAL	1	TRUE	1	0.314121570382209	2		466	443	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913527	NA	P-0065722-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	25	220	0	ENST00000311936.3:c.436G>C	p.Ala146Pro	p.A146P	ENST00000311936	NM_004985.3	146	Gca/Cca	4/5	0.172066632882213	5	FACETS	0.952	0.762	1	0.635	0.508	0.775	INDETERMINATE	2	TRUE	2	0.314121570382209	5		220	123	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282320	115282320	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs927733364	NA	P-0065722-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	15	281	0	ENST00000438362.2:c.330A>C	p.Lys110Asn	p.K110N	ENST00000438362	NM_001242891.1	110	aaA/aaC	3/20	0.122304168394054	3	FACETS	0.978	0.723	1	0.489	0.361	0.639	INDETERMINATE	1	TRUE	1	0.314121570382209	3		281	113	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435223	56435224	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0065722-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	68	584	0	ENST00000407977.2:c.1913dup	p.Ser638ArgfsTer109	p.S638Rfs*109	ENST00000407977		638	agt/agGt	9/10	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.314121570382209	2		584	354	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877363	40877363	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065722-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	26	401	0	ENST00000373198.4:c.2333T>A	p.Ile778Asn	p.I778N	ENST00000373198	NM_133170.3	778	aTc/aAc	15/32	0.314121570382209	1	FACETS	0.413	0.327	0.511	0.413	0.327	0.511	SUBCLONAL	1	TRUE	0	0.314121570382209	1		401	338	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0065723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	225	388	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.2342804987188	3	FACETS	0.847	0.791	0.904	0.847	0.791	0.904	CLONAL	3	TRUE	0	0.251177292848564	3		388	794	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875096	151875096	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0065723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	34	136	0	ENST00000262189.6:c.7443-1G>C		p.X2481_splice	ENST00000262189	NM_170606.2	2481			0.251177292848564	1	FACETS	0.958	0.788	1	0.958	0.788	1	CLONAL	1	TRUE	0	0.251177292848564	1		136	247	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127986	64127986	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0065723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	259	561	0	ENST00000334205.4:c.384C>G	p.Tyr128Ter	p.Y128*	ENST00000334205	NM_003942.2	128	taC/taG	4/17	0.18013459914614	4	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	2	0.251177292848564	4		561	1281	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447415	12447415	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	101	511	0	ENST00000287820.6:c.654G>C	p.Lys218Asn	p.K218N	ENST00000287820	NM_015869.4	218	aaG/aaC	5/7	0.251177292848564	3	FACETS	0.896	0.799	1	0.448	0.399	0.5	CLONAL	1	TRUE	1	0.251177292848564	3		511	1010	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0065724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	75	430	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.233307125340684	0	FACETS	0.888	0.78	1			1	CLONAL	1	TRUE	0	0.265304745324879	0		430	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0065724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	135	463	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.265304745324879	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.265304745324879	1		463	635	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0065724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	89	244	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.172599583725642	4	FACETS	0.96	0.856	1	0.96	0.856	1	CLONAL	2	TRUE	2	0.265304745324879	4		244	442	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0065724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	139	498	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.265304745324879	2		499	851	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0065724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	57	434	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.99	0.852	1	0.99	0.852	1	CLONAL	1	TRUE	1	0.265304745324879	2		434	434	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100999	41100999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1371429276	NA	P-0065724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	181	611	0	ENST00000373198.4:c.1357C>T	p.Arg453Cys	p.R453C	ENST00000373198	NM_133170.3	453	Cgc/Tgc	8/32	1	2	FACETS	1	0.947	1	1	0.993	1	CLONAL	2	TRUE	1	0.265304745324879	2		611	664	SUCCESS
APC	324	MSKCC	GRCh37	5	112175463	112175464	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	65	576	0	ENST00000257430.4:c.4174dup	p.Ser1392PhefsTer3	p.S1392Ffs*3	ENST00000257430	NM_000038.5	1391	agt/agTt	16/16	1	2	FACETS	0.937	0.813	1	0.937	0.813	1	CLONAL	1	TRUE	1	0.265304745324879	2		576	523	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638467	176638467	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784095	NA	P-0065724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	109	660	0	ENST00000439151.2:c.3067C>T	p.Arg1023Ter	p.R1023*	ENST00000439151	NM_022455.4	1023	Cga/Tga	5/23	0.10608061139548	0	FACETS	0.795	0.714	0.881			1	INDETERMINATE	1	TRUE	0	0.265304745324879	0		660	759	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553602	106553602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1562174876	NA	P-0065724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	107	664	0	ENST00000369096.4:c.1567G>A	p.Ala523Thr	p.A523T	ENST00000369096	NM_001198.3	523	Gcc/Acc	5/7	1	2	FACETS	0.859	0.769	0.954	0.859	0.769	0.954	CLONAL	1	TRUE	1	0.265304745324879	2		664	939	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100204	27100204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	231	746	1	ENST00000324856.7:c.4000C>T	p.Gln1334Ter	p.Q1334*	ENST00000324856	NM_006015.4	1334	Caa/Taa	16/20	1	2	FACETS	0.798	0.744	0.854	1	0.993	1	SUBCLONAL	2	TRUE	1	0.265304745324879	2		747	1091	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508112	106508112	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs142342118	NA	P-0065724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	87	684	0	ENST00000359195.3:c.106G>T	p.Glu36Ter	p.E36*	ENST00000359195	NM_002649.2	36	Gag/Tag	2/11	0.258510428680526	4	FACETS	1	0.945	1	0.371	0.328	0.417	CLONAL	1	TRUE	1	0.265304745324879	4		684	745	SUCCESS
APC	324	MSKCC	GRCh37	5	112174474	112174475	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	G	novel	NA	P-0065724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	49	546	0	ENST00000257430.4:c.3183_3184delinsG	p.Gln1062LysfsTer64	p.Q1062Kfs*64	ENST00000257430	NM_000038.5	1061	aaACaa/aaGaa	16/16	1	2	FACETS	0.97	0.824	1	0.97	0.824	1	CLONAL	1	TRUE	1	0.265304745324879	2		546	381	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231488893	231488894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs567805129	NA	P-0065725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	253	446	2	ENST00000295050.7:c.1263dup	p.Ile422TyrfsTer11	p.I422Yfs*11	ENST00000295050	NM_032018.5	419	aat/aaTt	5/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		448	895	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609105	43609105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1228204486	NA	P-0065725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	464	816	0	ENST00000355710.3:c.1861G>A	p.Glu621Lys	p.E621K	ENST00000355710	NM_020975.4	621	Gag/Aag	10/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		816	1032	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	441055	441055	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778756065	NA	P-0065725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	381	534	0	ENST00000399788.2:c.1703G>A	p.Arg568His	p.R568H	ENST00000399788	NM_001042603.1	568	cGt/cAt	13/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		534	891	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423500	88423500	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0065725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	235	449	0	ENST00000360948.2:c.2334+1G>T		p.X778_splice	ENST00000360948	NM_001012338.2	778			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		449	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0065725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	363	641	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		641	476	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410131	139410131	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	375	628	0	ENST00000277541.6:c.1707G>C	p.Glu569Asp	p.E569D	ENST00000277541	NM_017617.3	569	gaG/gaC	11/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		628	1191	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615581	100615581	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	601	544	1	ENST00000308731.7:c.751T>A	p.Trp251Arg	p.W251R	ENST00000308731	NM_000061.2	251	Tgg/Agg	8/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		545	1011	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578219	7578220	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	215	681	0	ENST00000269305.4:c.629dup	p.Asn210LysfsTer6	p.N210Kfs*6	ENST00000269305	NM_001126112.2	210	aac/aaAc	6/11	0.517499608307631	2	FACETS	0.978	0.922	1	0.978	0.922	1	CLONAL	2	TRUE	0	0.517499608307631	2		681	425	SUCCESS
APC	324	MSKCC	GRCh37	5	112116559	112116559	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	48	407	0	ENST00000257430.4:c.604G>T	p.Glu202Ter	p.E202*	ENST00000257430	NM_000038.5	202	Gaa/Taa	6/16	0.517499608307631	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.517499608307631	1		407	117	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7128950	7128950	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	175	485	0	ENST00000302850.5:c.2858A>G	p.Asn953Ser	p.N953S	ENST00000302850	NM_000208.2	953	aAt/aGt	15/22	0.290717161584586	5	FACETS	0.884	0.822	0.947	0.884	0.822	0.947	INDETERMINATE	3	TRUE	2	0.517499608307631	5		485	453	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280010	18280010	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555815294	NA	P-0065726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	93	605	0	ENST00000222254.8:c.2093A>C	p.His698Pro	p.H698P	ENST00000222254	NM_005027.3	698	cAc/cCc	16/16	0.290717161584586	5	FACETS	1	0.974	1	0.439	0.391	0.489	INDETERMINATE	1	TRUE	2	0.517499608307631	5		605	485	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336654	81336654	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	50	456	0	ENST00000222390.5:c.1568T>G	p.Leu523Trp	p.L523W	ENST00000222390	NM_000601.4	523	tTg/tGg	14/18	0.470195259475578	4	FACETS	0.971	0.829	1	0.485	0.414	0.563	CLONAL	1	TRUE	2	0.517499608307631	4		456	302	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0065727-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	108	491	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	1	0.609986114954541	2		491	345	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0065727-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	52	477	3	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	0.2191522006705	2	FACETS	0.408	0.348	0.473	0.204	0.174	0.237	INDETERMINATE	1	FALSE	0	0.609986114954541	2		480	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0065727-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	17	603	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.609986114954541	1	FACETS	0.159	0.119	0.208	0.159	0.119	0.208	SUBCLONAL	1	FALSE	0	0.609986114954541	1		603	243	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866663	37866663	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065727-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	121	628	0	ENST00000269571.5:c.830A>T	p.Asp277Val	p.D277V	ENST00000269571		277	gAc/gTc	7/27	0.609986114954541	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	0	0.609986114954541	1		628	250	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477853	140477853	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs180177036	NA	P-0065727-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	125	370	0	ENST00000288602.6:c.1455G>T	p.Leu485Phe	p.L485F	ENST00000288602	NM_004333.4	485	ttG/ttT	12/18	0.377581728125007	3	FACETS	1	0.958	1	0.545	0.496	0.596	CLONAL	1	FALSE	1	0.609986114954541	3		370	491	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793263	242793263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754424677	NA	P-0065727-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	57	510	2	ENST00000334409.5:c.814C>T	p.Arg272Trp	p.R272W	ENST00000334409	NM_005018.2	272	Cgg/Tgg	5/5	0.53424413332246	1	FACETS	0.565	0.49	0.644	0.565	0.49	0.644	SUBCLONAL	1	FALSE	0	0.609986114954541	1		512	230	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905560	50905560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065727-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	71	749	0	ENST00000440232.2:c.688G>A	p.Gly230Ser	p.G230S	ENST00000440232	NM_002691.3	230	Ggc/Agc	6/27	0.241373253046942	0	FACETS	0.338	0.298	0.379			1	INDETERMINATE	1	FALSE	0	0.609986114954541	0		749	269	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874644	35874644	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065727-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	116	352	0	ENST00000303115.3:c.800G>T	p.Arg267Met	p.R267M	ENST00000303115	NM_002185.3	267	aGg/aTg	6/8	1	2	FACETS	0.944	0.858	1	0.944	0.858	1	CLONAL	1	FALSE	1	0.609986114954541	2		352	403	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437100	110437100	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs893531150	NA	P-0065727-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	25	441	0	ENST00000375856.3:c.1301C>T	p.Pro434Leu	p.P434L	ENST00000375856	NM_003749.2	434	cCc/cTc	1/2	0.609986114954541	4	FACETS	0.32	0.252	0.399	0.107	0.084	0.133	SUBCLONAL	1	FALSE	1	0.609986114954541	4		441	412	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8111127	8111127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370931710	NA	P-0065727-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	77	407	0	ENST00000585124.1:c.80G>A	p.Arg27Gln	p.R27Q	ENST00000585124	NM_004217.3	27	cGa/cAa	3/9	0.609986114954541	1	FACETS	0.895	0.802	0.99	0.895	0.802	0.99	CLONAL	1	FALSE	0	0.609986114954541	1		407	196	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980729	40980729	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs374504796	NA	P-0065727-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	200	433	0	ENST00000373198.4:c.1757T>C	p.Ile586Thr	p.I586T	ENST00000373198	NM_133170.3	586	aTt/aCt	10/32	0.2191522006705	2	FACETS	0.786	0.739	0.834	0.786	0.739	0.834	INDETERMINATE	2	FALSE	0	0.609986114954541	2		433	417	SUCCESS
APC	324	MSKCC	GRCh37	5	112174732	112174732	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065727-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	135	460	0	ENST00000257430.4:c.3441C>A	p.Tyr1147Ter	p.Y1147*	ENST00000257430	NM_000038.5	1147	taC/taA	16/16	1	2	FACETS	0.898	0.821	0.977	0.898	0.821	0.977	CLONAL	1	FALSE	1	0.609986114954541	2		460	493	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968118	68968118	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065727-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	122	359	0	ENST00000288368.4:c.1147G>T	p.Glu383Ter	p.E383*	ENST00000288368	NM_024870.2	383	Gag/Tag	10/40	1	2	FACETS	0.973	0.887	1	0.973	0.887	1	CLONAL	1	FALSE	1	0.609986114954541	2		359	411	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058485	69058485	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1041364032	NA	P-0065727-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	38	346	0	ENST00000288368.4:c.4129C>G	p.Leu1377Val	p.L1377V	ENST00000288368	NM_024870.2	1377	Ctg/Gtg	34/40	1	2	FACETS	0.302	0.25	0.361	0.302	0.25	0.361	SUBCLONAL	1	FALSE	1	0.609986114954541	2		346	412	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0065728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	814	434	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.499826962547659	4	FACETS	1	0.997	1	1	0.997	1	CLONAL	4	TRUE	0	0.585697231505175	4		434	1012	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0065728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	389	656	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.585697231505175	3	FACETS	0.857	0.823	0.89	0.857	0.823	0.89	CLONAL	3	TRUE	0	0.585697231505175	3		656	668	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427369	49427369	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1565779294	NA	P-0065728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	216	735	0	ENST00000301067.7:c.11119C>T	p.Arg3707Ter	p.R3707*	ENST00000301067	NM_003482.3	3707	Cga/Tga	39/54	0.3678386167715	5	FACETS	1	0.974	1	0.719	0.672	0.767	CLONAL	2	TRUE	2	0.585697231505175	5		735	642	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066809	77066809	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	210	589	0	ENST00000356341.3:c.676G>A	p.Glu226Lys	p.E226K	ENST00000356341	NM_002576.4	226	Gaa/Aaa	7/15	0.22576115236525	5	FACETS	0.925	0.862	0.99	0.617	0.575	0.66	INDETERMINATE	2	TRUE	2	0.585697231505175	5		589	728	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907309	32907309	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	248	673	0	ENST00000380152.3:c.1695del	p.Thr566ProfsTer7	p.T566Pfs*7	ENST00000380152		565	gCc/gc	10/27	0.22576115236525	5	FACETS	0.857	0.807	0.907	0.857	0.807	0.907	INDETERMINATE	3	TRUE	2	0.585697231505175	5		673	619	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003528	42003528	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	167	462	0	ENST00000219905.7:c.3065C>G	p.Thr1022Arg	p.T1022R	ENST00000219905	NM_001164273.1	1022	aCa/aGa	8/24	0.161725490381508	5	FACETS	1	0.958	1	0.7	0.648	0.754	INDETERMINATE	2	TRUE	2	0.585697231505175	5		462	510	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936847	78936847	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	285	611	0	ENST00000306801.3:c.3929A>T	p.His1310Leu	p.H1310L	ENST00000306801	NM_020761.2	1310	cAc/cTc	33/34	0.585697231505175	4	FACETS	0.882	0.838	0.927			1	CLONAL	3	TRUE	NA	0.585697231505175	4		611	583	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602293	10602313	+	inframe_deletion	In_Frame_Del	DEL	CGACGGCATAGATGTGGCCAT	CGACGGCATAGATGTGGCCAT	-	novel	NA	P-0065728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	270	740	1	ENST00000171111.5:c.1265_1285del	p.Asp422_Val428del	p.D422_V428del	ENST00000171111	NM_203500.1	422	gATGGCCACATCTATGCCGTCGgc/ggc	3/6	0.585697231505175	5	FACETS	0.908	0.853	0.964	0.605	0.568	0.643	CLONAL	2	TRUE	2	0.585697231505175	5		741	954	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1962783	1962783	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	207	590	0	ENST00000382891.5:c.3277G>T	p.Val1093Phe	p.V1093F	ENST00000382891	NM_133335.3	1093	Gtt/Ttt	18/22	0.585697231505175	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.585697231505175	1		590	400	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196343	106196343	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	266	682	0	ENST00000380013.4:c.4676C>G	p.Ser1559Cys	p.S1559C	ENST00000380013	NM_001127208.2	1559	tCt/tGt	11/11	0.511622993153561	2	FACETS	0.907	0.861	0.952	0.907	0.861	0.952	CLONAL	2	TRUE	0	0.585697231505175	2		682	501	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910617	29910617	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	283	1026	0	ENST00000376809.5:c.157G>C	p.Asp53His	p.D53H	ENST00000376809	NM_002116.7	53	Gac/Cac	2/8	0.440309262273754	4	FACETS	0.845	0.796	0.895	0.845	0.796	0.895	CLONAL	2	TRUE	2	0.585697231505175	4		1026	907	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687370	117687370	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs535778217	NA	P-0065728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	144	557	0	ENST00000368508.3:c.2681G>T	p.Arg894Leu	p.R894L	ENST00000368508	NM_002944.2	894	cGg/cTg	18/43	0.440309262273754	4	FACETS	0.769	0.706	0.834	0.769	0.706	0.834	SUBCLONAL	2	TRUE	2	0.585697231505175	4		557	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0065730-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	201	442	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.375333868194982	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.375333868194982	2		442	465	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531806	46531807	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065730-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	102	239	0	ENST00000262741.5:c.540dup	p.Leu181ThrfsTer13	p.L181Tfs*13	ENST00000262741	NM_003629.3	180	-/A	5/10	0.371043515401289	3	FACETS	0.854	0.77	0.941	0.854	0.77	0.941	CLONAL	2	TRUE	1	0.375333868194982	3		239	378	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247943	59247943	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065730-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	114	603	0	ENST00000371222.2:c.800C>T	p.Ser267Phe	p.S267F	ENST00000371222	NM_002228.3	267	tCc/tTc	1/1	0.371043515401289	3	FACETS	1	0.922	1	0.513	0.462	0.567	CLONAL	1	TRUE	1	0.375333868194982	3		603	703	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266827	198266827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065730-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	81	366	2	ENST00000335508.6:c.2105G>A	p.Arg702Gln	p.R702Q	ENST00000335508	NM_012433.2	702	cGg/cAg	15/25	0.371043515401289	3	FACETS	0.872	0.769	0.982	0.436	0.384	0.491	CLONAL	1	TRUE	1	0.375333868194982	3		368	588	SUCCESS
APC	324	MSKCC	GRCh37	5	112164584	112164584	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs863225318	NA	P-0065730-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	201	351	0	ENST00000257430.4:c.1658G>A	p.Trp553Ter	p.W553*	ENST00000257430	NM_000038.5	553	tGg/tAg	14/16	0.375333868194982	3	FACETS	0.951	0.892	1	0.951	0.892	1	CLONAL	3	TRUE	0	0.375333868194982	3		351	446	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117771	70117772	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCTCAAAGGCTACGACTG	novel	NA	P-0065730-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	164	536	0	ENST00000245479.2:c.241_258dup	p.Leu81_Trp86dup	p.L81_W86dup	ENST00000245479	NM_000346.3	81	gtg/gtGCTCAAAGGCTACGACTGg	1/3	0.117519578901128	5	FACETS	0.981	0.903	1	0.654	0.602	0.708	INDETERMINATE	2	TRUE	2	0.375333868194982	5		536	696	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120236	70120237	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0065730-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	139	509	0	ENST00000245479.2:c.1239dup	p.Ser414LeufsTer164	p.S414Lfs*164	ENST00000245479	NM_000346.3	413	cac/caCc	3/3	0.117519578901128	5	FACETS	0.957	0.874	1	0.638	0.583	0.695	INDETERMINATE	2	TRUE	2	0.375333868194982	5		509	605	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590388	67590400	+	frameshift_variant	Frame_Shift_Del	DEL	ATTGAAGCATTTA	ATTGAAGCATTTA	-	novel	NA	P-0065730-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	131	323	0	ENST00000274335.5:c.1452_1464del	p.Ile484MetfsTer4	p.I484Mfs*4	ENST00000274335		484	ATTGAAGCATTTAat/at	11/15	0.371043515401289	3	FACETS	0.94	0.86	1	0.94	0.86	1	CLONAL	2	TRUE	1	0.375333868194982	3		323	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0065731-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	219	463	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.362020182692792	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.362020182692792	2		463	567	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0065731-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	179	303	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.362020182692792	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.362020182692792	2		303	403	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248749	212248749	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065731-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	105	447	1	ENST00000342788.4:c.3518C>A	p.Ser1173Tyr	p.S1173Y	ENST00000342788	NM_005235.2	1173	tCt/tAt	28/28	0.362020182692792	3	FACETS	1	0.982	1	0.718	0.647	0.793	CLONAL	1	TRUE	1	0.362020182692792	3		448	477	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659859	88659859	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065731-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	35	239	0	ENST00000372037.3:c.506T>A	p.Ile169Asn	p.I169N	ENST00000372037	NM_004329.2	169	aTc/aAc	7/13	1	2	FACETS	0.948	0.784	1	0.948	0.784	1	CLONAL	1	TRUE	1	0.362020182692792	2		239	204	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906618	32906618	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065731-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	217	422	0	ENST00000380152.3:c.1003G>T	p.Glu335Ter	p.E335*	ENST00000380152		335	Gaa/Taa	10/27	0.35573916996078	4	FACETS	0.924	0.87	0.977	0.924	0.87	0.977	CLONAL	4	TRUE	0	0.362020182692792	4		422	442	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492737	56492743	+	frameshift_variant	Frame_Shift_Del	DEL	CACCTTC	CACCTTC	-	novel	NA	P-0065731-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	190	476	0	ENST00000407977.2:c.196_202del	p.Glu66CysfsTer8	p.E66Cfs*8	ENST00000407977		66	GAAGGTGtg/tg	2/10	NA	2	FACETS	0.967	0.9	1			1	INDETERMINATE	2	TRUE	NA	0.362020182692792	2		476	543	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947827	178947827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	257	433	0	ENST00000263967.3:c.2702G>T	p.Cys901Phe	p.C901F	ENST00000263967	NM_006218.2	901	tGt/tTt	19/21	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.509607765017595	2		433	870	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875645	35875645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201449880	NA	P-0065732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	240	0	0	ENST00000303115.3:c.832G>A	p.Asp278Asn	p.D278N	ENST00000303115	NM_002185.3	278	Gat/Aat	7/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.509607765017595	2		0	808	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937606	76937606	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	138	408	0	ENST00000373344.5:c.3142A>G	p.Lys1048Glu	p.K1048E	ENST00000373344	NM_000489.3	1048	Aaa/Gaa	9/35	0.161610479175999	2	FACETS	0.645	0.587	0.706	0.322	0.293	0.353	INDETERMINATE	1	TRUE	0	0.509607765017595	2		408	840	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0065733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	189	286	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.332297183542315	3	FACETS	0.846	0.789	0.904	1	0.988	1	CLONAL	3	TRUE	1	0.345103818597963	3		286	506	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0065733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	73	602	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.645	0.564	0.732	0.645	0.564	0.732	SUBCLONAL	1	TRUE	1	0.345103818597963	2		602	656	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457303	67457303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768713596	NA	P-0065733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	281	749	1	ENST00000327367.4:c.277C>T	p.Arg93Ter	p.R93*	ENST00000327367	NM_005902.3	93	Cga/Tga	2/9	0.345103818597963	2	FACETS	0.995	0.939	1	0.995	0.939	1	CLONAL	2	TRUE	0	0.345103818597963	2		750	818	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	211	409	0	ENST00000262160.6:c.1391C>A	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tAa	11/11	0.345103818597963	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	0	0.345103818597963	2		409	608	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1623951	1623951	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs374988827	NA	P-0065733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	103	404	0	ENST00000344749.5:c.548C>T	p.Ser183Leu	p.S183L	ENST00000344749	NM_001136139.2	183	tCg/tTg	8/19	0.112376634533916	3	FACETS	1	0.97	1	0.608	0.545	0.674	INDETERMINATE	1	TRUE	1	0.345103818597963	3		404	576	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523630	41523630	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	272	601	0	ENST00000263253.7:c.1046A>G	p.His349Arg	p.H349R	ENST00000263253	NM_001429.3	349	cAc/cGc	4/31	0.345103818597963	2	FACETS	0.996	0.939	1	0.996	0.939	1	CLONAL	2	TRUE	0	0.345103818597963	2		601	791	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	59	224	0	ENST00000263967.3:c.1034A>G	p.Asn345Ser	p.N345S	ENST00000263967	NM_006218.2	345	aAt/aGt	5/21	1	2	FACETS	0.912	0.788	1	0.912	0.788	1	CLONAL	1	TRUE	1	0.345103818597963	2		224	375	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738639	145738639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769977498	NA	P-0065733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	118	751	0	ENST00000428558.2:c.2425G>A	p.Gly809Arg	p.G809R	ENST00000428558	NM_004260.3	809	Ggg/Agg	15/22	0.315609559441586	3	FACETS	0.996	0.899	1	0.498	0.449	0.55	CLONAL	1	TRUE	1	0.345103818597963	3		751	805	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900330	101900330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	103	301	0	ENST00000374994.4:c.764G>A	p.Arg255His	p.R255H	ENST00000374994	NM_004612.2	255	cGt/cAt	4/9	0.332297183542315	3	FACETS	1	0.923	1	0.518	0.464	0.576	CLONAL	1	TRUE	1	0.345103818597963	3		301	675	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966698	44966698	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	209	195	0	ENST00000377967.4:c.3922G>T	p.Glu1308Ter	p.E1308*	ENST00000377967	NM_021140.2	1308	Gaa/Taa	27/29	0.332689443567522	2	FACETS	1	0.976	1			1	CLONAL	4	TRUE	NA	0.345103818597963	2		195	293	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039903	47039903	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	97	223	0	ENST00000377604.3:c.1246C>T	p.Gln416Ter	p.Q416*	ENST00000377604	NM_001204468.1	416	Cag/Tag	12/24	0.332689443567522	2	FACETS	0.87	0.784	0.959			1	CLONAL	2	TRUE	NA	0.345103818597963	2		223	323	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77936216	77936216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373502813	NA	P-0065733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	96	495	0	ENST00000361507.4:c.1240C>T	p.Arg414Cys	p.R414C	ENST00000361507	NM_080491.2	414	Cgt/Tgt	5/10	1	2	FACETS	0.842	0.751	0.939	0.842	0.751	0.939	CLONAL	1	TRUE	1	0.345103818597963	2		495	661	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870891	12870892	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	157	590	0	ENST00000228872.4:c.118_119insT	p.Glu40ValfsTer85	p.E40Vfs*85	ENST00000228872	NM_004064.3	40	gag/gTag	1/3	0.332297183542315	3	FACETS	1	0.981	1	0.617	0.565	0.671	CLONAL	1	TRUE	1	0.345103818597963	3		590	865	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40742214	40742214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	197	579	0	ENST00000392038.2:c.910G>A	p.Gly304Arg	p.G304R	ENST00000392038	NM_001626.4	304	Ggg/Agg	10/14	0.112376634533916	3	FACETS	0.807	0.749	0.868	0.807	0.749	0.868	INDETERMINATE	2	TRUE	1	0.345103818597963	3		579	829	SUCCESS
APC	324	MSKCC	GRCh37	5	112174668	112174668	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	263	411	0	ENST00000257430.4:c.3377del	p.Ser1126ThrfsTer39	p.S1126Tfs*39	ENST00000257430	NM_000038.5	1126	aGc/ac	16/16	0.332297183542315	3	FACETS	0.893	0.843	0.944	1	0.992	1	CLONAL	3	TRUE	1	0.345103818597963	3		411	667	SUCCESS
APC	324	MSKCC	GRCh37	5	112175710	112175711	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	232	536	0	ENST00000257430.4:c.4419_4420insA	p.Ala1474SerfsTer13	p.A1474Sfs*13	ENST00000257430	NM_000038.5	1473	-/A	16/16	0.332297183542315	3	FACETS	0.921	0.86	0.983	0.921	0.86	0.983	CLONAL	2	TRUE	1	0.345103818597963	3		536	856	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100175	27100176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0065734-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	108	586	0	ENST00000324856.7:c.3977dup	p.Gln1327AlafsTer11	p.Q1327Afs*11	ENST00000324856	NM_006015.4	1324	tac/taCc	16/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		586	697	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551522	150551522	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065734-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	82	541	0	ENST00000369026.2:c.485C>G	p.Ser162Trp	p.S162W	ENST00000369026	NM_021960.4	162	tCg/tGg	1/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		541	838	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66522054	66522054	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0065734-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	57	291	0	ENST00000358598.2:c.708+1G>A		p.X236_splice	ENST00000358598	NM_212471.2	236			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		291	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574027	7574027	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882028	NA	P-0065734-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	83	349	0	ENST00000269305.4:c.1000G>T	p.Gly334Trp	p.G334W	ENST00000269305	NM_001126112.2	334	Ggg/Tgg	10/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		349	517	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163744	72163744	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065734-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	37	371	0	ENST00000357731.5:c.614C>A	p.Ala205Glu	p.A205E	ENST00000357731	NM_173808.2	205	gCg/gAg	4/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		371	425	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63898320	63898320	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065734-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	51	217	0	ENST00000398590.3:c.46G>T	p.Ala16Ser	p.A16S	ENST00000398590	NM_001177387.1	16	Gcg/Tcg	3/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		217	399	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241907	72241907	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065734-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	80	396	0	ENST00000357731.5:c.483G>T	p.Leu161Phe	p.L161F	ENST00000357731	NM_173808.2	161	ttG/ttT	3/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		396	628	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163824	152163824	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065734-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	66	387	1	ENST00000206249.3:c.545C>A	p.Thr182Asn	p.T182N	ENST00000206249	NM_000125.3	182	aCt/aAt	2/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		388	525	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467931	50467931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065734-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	68	534	0	ENST00000331340.3:c.1166C>T	p.Ser389Phe	p.S389F	ENST00000331340	NM_006060.4	389	tCc/tTc	8/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		534	621	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246498742	246498742	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065734-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	113	290	0	ENST00000388985.4:c.263A>G	p.Lys88Arg	p.K88R	ENST00000388985		88	aAa/aGa	3/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		290	554	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415178	109415178	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065734-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	74	446	0	ENST00000436639.2:c.99G>C	p.Leu33Phe	p.L33F	ENST00000436639	NM_014454.2	33	ttG/ttC	1/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		446	685	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607550	43607550	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065734-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	117	775	0	ENST00000355710.3:c.1526T>A	p.Val509Glu	p.V509E	ENST00000355710	NM_020975.4	509	gTg/gAg	8/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		775	922	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0065735-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	123	485	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.466208228630493	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.466208228630493	1		485	388	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0065735-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	94	286	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.466208228630493	2		286	403	SUCCESS
BLM	641	MSKCC	GRCh37	15	91328309	91328309	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1057516700	NA	P-0065735-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	93	281	0	ENST00000355112.3:c.2821C>T	p.Gln941Ter	p.Q941*	ENST00000355112	NM_000057.2	941	Cag/Tag	14/22	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.466208228630493	2		281	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	285	622	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.76470300370221	3	FACETS	0.926	0.893	0.957	0.926	0.893	0.957	CLONAL	3	TRUE	0	0.76470300370221	3		622	371	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	171	690	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	0.611014295348923	4	FACETS	1	0.971	1	0.536	0.5	0.572	CLONAL	2	TRUE	0	0.76470300370221	4		691	368	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	76	434	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.76470300370221	3	FACETS	0.904	0.817	0.99	0.603	0.545	0.66	CLONAL	2	TRUE	0	0.76470300370221	3		434	152	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	66	639	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	0.76470300370221	4	FACETS	0.793	0.692	0.902	0.198	0.173	0.226	CLONAL	1	TRUE	0	0.76470300370221	4		639	384	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	168	563	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	0.76470300370221	4	FACETS	0.974	0.907	1	0.487	0.453	0.521	CLONAL	2	TRUE	0	0.76470300370221	4		563	398	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797846	45797846	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138089183	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	205	586	0	ENST00000450313.1:c.925C>T	p.Arg309Cys	p.R309C	ENST00000450313	NM_012222.2	309	Cgc/Tgc	10/16	0.76470300370221	4	FACETS	0.99	0.928	1	0.495	0.464	0.526	CLONAL	2	TRUE	0	0.76470300370221	4		586	478	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872461	35872461	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	89	495	0	ENST00000216797.5:c.442del	p.Leu148TyrfsTer16	p.L148Yfs*16	ENST00000216797	NM_020529.2	148	Cta/ta	3/6	0.42901246186875	5	FACETS	0.77	0.683	0.863	0.257	0.227	0.288	INDETERMINATE	1	TRUE	2	0.76470300370221	5		495	649	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976624	7976624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	41	352	0	ENST00000319144.4:c.1768G>A	p.Ala590Thr	p.A590T	ENST00000319144	NM_001139.2	590	Gcc/Acc	14/15	0.76470300370221	3	FACETS	0.615	0.516	0.723	0.205	0.172	0.241	SUBCLONAL	1	TRUE	0	0.76470300370221	3		352	241	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435290	56435290	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	82	619	0	ENST00000407977.2:c.1847C>T	p.Pro616Leu	p.P616L	ENST00000407977		616	cCc/cTc	9/10	0.76470300370221	3	FACETS	0.859	0.764	0.96	0.286	0.254	0.32	CLONAL	1	TRUE	0	0.76470300370221	3		619	345	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743930	41743930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141302305	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	125	601	0	ENST00000301178.4:c.865G>A	p.Val289Met	p.V289M	ENST00000301178	NM_021913.4	289	Gtg/Atg	7/20	0.611014295348923	4	FACETS	0.962	0.884	1	0.481	0.442	0.52	CLONAL	2	TRUE	0	0.76470300370221	4		601	300	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743943	40743943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763964405	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	113	453	2	ENST00000373198.4:c.3052C>T	p.Arg1018Ter	p.R1018*	ENST00000373198	NM_133170.3	1018	Cga/Tga	23/32	0.710432381934944	2	FACETS	1	0.983	1	0.648	0.597	0.7	CLONAL	1	TRUE	0	0.76470300370221	2		455	228	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057302	30057302	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315496	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	64	469	0	ENST00000338641.4:c.784C>T	p.Arg262Ter	p.R262*	ENST00000338641	NM_000268.3	262	Cga/Tga	8/16	0.596623751237656	4	FACETS	0.965	0.843	1	0.241	0.21	0.274	CLONAL	1	TRUE	0	0.76470300370221	4		469	306	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890221	72890221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752101890	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	59	361	0	ENST00000325599.8:c.461G>A	p.Arg154Gln	p.R154Q	ENST00000325599	NM_018130.2	154	cGa/cAa	4/11	0.680239302765213	5	FACETS	0.879	0.759	1	0.176	0.151	0.202	CLONAL	1	TRUE	0	0.76470300370221	5		361	377	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413710	138413710	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	62	378	1	ENST00000289153.2:c.1810del	p.Arg604GlyfsTer4	p.R604Gfs*4	ENST00000289153	NM_006219.2	604	Cgg/gg	12/22	0.62783933017041	3	FACETS	0.801	0.698	0.91	0.4	0.349	0.455	CLONAL	1	TRUE	1	0.76470300370221	3		379	280	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204082	142204082	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	43	400	0	ENST00000350721.4:c.6121del	p.Tyr2041ThrfsTer9	p.Y2041Tfs*9	ENST00000350721	NM_001184.3	2041	Tac/ac	36/47	0.62783933017041	3	FACETS	0.758	0.642	0.884	0.379	0.321	0.442	SUBCLONAL	1	TRUE	1	0.76470300370221	3		400	205	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	65	568	3	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	0.76470300370221	3	FACETS	0.739	0.645	0.839	0.246	0.215	0.28	SUBCLONAL	1	TRUE	0	0.76470300370221	3		571	318	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31472189	31472189	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs779362571	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	92	436	0	ENST00000344624.3:c.2222T>C	p.Ile741Thr	p.I741T	ENST00000344624		741	aTt/aCt	14/33	0.62783933017041	3	FACETS	1	0.983	1	0.749	0.679	0.821	CLONAL	1	TRUE	1	0.76470300370221	3		436	222	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163855	32163855	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	66	448	0	ENST00000375023.3:c.5371del	p.Ala1791GlnfsTer11	p.A1791Qfs*11	ENST00000375023	NM_004557.3	1791	Gca/ca	30/30	0.708273200395407	4	FACETS	0.886	0.786	0.988	0.59	0.524	0.659	CLONAL	2	TRUE	1	0.76470300370221	4		448	172	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	55	534	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	0.76470300370221	4	FACETS	0.947	0.817	1	0.237	0.204	0.272	CLONAL	1	TRUE	0	0.76470300370221	4		534	268	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981872	70981872	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	116	559	0	ENST00000276594.2:c.224C>A	p.Pro75His	p.P75H	ENST00000276594	NM_024504.3	75	cCt/cAt	2/8	0.76470300370221	10	FACETS	0.754	0.679	0.833	0.167	0.15	0.185	SUBCLONAL	2	TRUE	1	0.76470300370221	10		559	817	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2039776	2039777	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAG	rs113070757	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	179	473	1	ENST00000349721.2:c.705_707dup	p.Gln238dup	p.Q238dup	ENST00000349721	NM_003070.3	238	-/CAG	4/34	0.76470300370221	8	FACETS	0.974	0.899	1	0.325	0.299	0.351	CLONAL	2	TRUE	2	0.76470300370221	8		474	792	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391014	139391014	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	133	594	0	ENST00000277541.6:c.7177C>T	p.Gln2393Ter	p.Q2393*	ENST00000277541	NM_017617.3	2393	Cag/Tag	34/34	0.76470300370221	6	FACETS	0.928	0.849	1	0.619	0.566	0.674	CLONAL	2	TRUE	3	0.76470300370221	6		594	474	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399409	139399411	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	rs761020817	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	95	571	2	ENST00000277541.6:c.4732_4734del	p.Val1578del	p.V1578del	ENST00000277541	NM_017617.3	1578	GTG/-	26/34	0.76470300370221	6	FACETS	1	0.944	1	0.364	0.324	0.406	CLONAL	1	TRUE	3	0.76470300370221	6		573	576	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793244	139793244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	74	454	0	ENST00000247668.2:c.52G>A	p.Gly18Ser	p.G18S	ENST00000247668	NM_021138.3	18	Ggc/Agc	2/11	0.76470300370221	6	FACETS	0.969	0.851	1	0.323	0.283	0.366	CLONAL	1	TRUE	3	0.76470300370221	6		454	505	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426118	47426118	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	70	528	0	ENST00000377045.4:c.638C>T	p.Thr213Met	p.T213M	ENST00000377045	NM_001654.4	213	aCg/aTg	7/16	0.643265764964049	2	FACETS	0.852	0.755	0.952	0.426	0.377	0.476	CLONAL	1	TRUE	0	0.76470300370221	2		528	215	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783272	9783272	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	68	525	0	ENST00000377346.4:c.2516T>G	p.Leu839Arg	p.L839R	ENST00000377346	NM_005026.3	839	cTc/cGc	20/24	0.625549143917999	5	FACETS	0.894	0.781	1	0.179	0.156	0.204	CLONAL	1	TRUE	0	0.76470300370221	5		525	427	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726411	46726411	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	51	467	0	ENST00000371975.4:c.490C>A	p.Leu164Met	p.L164M	ENST00000371975	NM_003579.3	164	Ctg/Atg	7/18	0.76470300370221	4	FACETS	0.55	0.468	0.639	0.137	0.117	0.16	SUBCLONAL	1	TRUE	0	0.76470300370221	4		467	428	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150919413	150919413	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	55	477	0	ENST00000271640.5:c.1192A>G	p.Met398Val	p.M398V	ENST00000271640	NM_001145415.1	398	Atg/Gtg	10/22	0.59973745239154	6	FACETS	0.756	0.648	0.875	0.252	0.216	0.292	SUBCLONAL	1	TRUE	3	0.76470300370221	6		477	481	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743274	162743274	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	30	387	0	ENST00000367921.3:c.1744G>T	p.Val582Leu	p.V582L	ENST00000367921	NM_006182.2	582	Gtg/Ttg	14/18	0.59973745239154	6	FACETS	0.692	0.559	0.841	0.231	0.186	0.281	SUBCLONAL	1	TRUE	3	0.76470300370221	6		387	287	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533451	533451	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	90	625	0	ENST00000451590.1:c.450+2T>C		p.X150_splice	ENST00000451590	NM_001130442.1	150			0.654634143488487	3	FACETS	0.723	0.645	0.806	0.241	0.215	0.269	SUBCLONAL	1	TRUE	0	0.76470300370221	3		625	450	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14303210	14303210	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	31	360	0	ENST00000256196.4:c.465G>T	p.Glu155Asp	p.E155D	ENST00000256196		155	gaG/gaT	5/6	0.654634143488487	3	FACETS	0.942	0.777	1	0.314	0.259	0.374	CLONAL	1	TRUE	0	0.76470300370221	3		360	119	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103387	77103387	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779686585	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	49	334	0	ENST00000356341.3:c.179C>A	p.Pro60His	p.P60H	ENST00000356341	NM_002576.4	60	cCt/cAt	2/15	0.654634143488487	3	FACETS	0.899	0.772	1	0.3	0.257	0.345	CLONAL	1	TRUE	0	0.76470300370221	3		334	197	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50490720	50490720	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	57	381	0	ENST00000394963.4:c.1357A>G	p.Asn453Asp	p.N453D	ENST00000394963	NM_003076.4	453	Aat/Gat	11/13	0.680239302765213	5	FACETS	1	0.91	1	0.214	0.185	0.246	CLONAL	1	TRUE	0	0.76470300370221	5		381	299	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249791	133249791	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1195703002	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	30	467	0	ENST00000320574.5:c.1432A>G	p.Ile478Val	p.I478V	ENST00000320574	NM_006231.2	478	Atc/Gtc	14/49	0.76470300370221	3	FACETS	0.5	0.405	0.606	0.167	0.135	0.202	SUBCLONAL	1	TRUE	0	0.76470300370221	3		467	217	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562826	21562826	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	54	582	0	ENST00000382592.4:c.1093A>G	p.Thr365Ala	p.T365A	ENST00000382592	NM_014572.2	365	Acc/Gcc	4/8	0.76470300370221	3	FACETS	0.59	0.506	0.68	0.197	0.168	0.227	SUBCLONAL	1	TRUE	0	0.76470300370221	3		582	331	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936806	32936806	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	125	406	0	ENST00000380152.3:c.7952G>T	p.Arg2651Met	p.R2651M	ENST00000380152		2651	aGg/aTg	17/27	0.76470300370221	3	FACETS	1	0.96	1	0.697	0.649	0.745	CLONAL	2	TRUE	0	0.76470300370221	3		406	216	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355862	73355862	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	62	473	0	ENST00000377767.4:c.109G>T	p.Ala37Ser	p.A37S	ENST00000377767	NM_014953.3	37	Gca/Tca	1/21	0.76470300370221	3	FACETS	0.97	0.849	1	0.323	0.283	0.366	CLONAL	1	TRUE	0	0.76470300370221	3		473	231	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508601	38508601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	187	471	0	ENST00000254066.5:c.649C>T	p.Arg217Cys	p.R217C	ENST00000254066	NM_000964.3	217	Cgt/Tgt	6/9	0.76470300370221	3	FACETS	1	0.99	1	0.808	0.767	0.847	CLONAL	2	TRUE	0	0.76470300370221	3		471	279	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390319	56390319	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	41	394	0	ENST00000348428.3:c.1058A>G	p.Tyr353Cys	p.Y353C	ENST00000348428	NM_006785.3	353	tAc/tGc	10/17	0.654634143488487	3	FACETS	0.814	0.687	0.952	0.271	0.229	0.318	CLONAL	1	TRUE	0	0.76470300370221	3		394	182	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217889	2217889	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	21	513	0	ENST00000398665.3:c.2663T>C	p.Val888Ala	p.V888A	ENST00000398665	NM_032482.2	888	gTg/gCg	22/28	0.654634143488487	3	FACETS	0.21	0.161	0.267	0.07	0.053	0.089	SUBCLONAL	1	TRUE	0	0.76470300370221	3		513	361	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353714	15353714	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs575892539	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	82	354	0	ENST00000263377.2:c.3166A>G	p.Thr1056Ala	p.T1056A	ENST00000263377	NM_058243.2	1056	Acc/Gcc	14/20	0.611014295348923	4	FACETS	1	0.97	1	0.318	0.283	0.354	CLONAL	1	TRUE	0	0.76470300370221	4		354	298	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257083	19257083	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	44	392	0	ENST00000162023.5:c.880A>G	p.Ser294Gly	p.S294G	ENST00000162023		294	Agt/Ggt	12/13	0.611014295348923	4	FACETS	1	0.919	1	0.282	0.24	0.328	CLONAL	1	TRUE	0	0.76470300370221	4		392	180	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631118	67631118	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	30	349	0	ENST00000272342.5:c.1304A>G	p.Asp435Gly	p.D435G	ENST00000272342	NM_019002.3	435	gAt/gGt	5/6	0.749091930190694	5	FACETS	0.682	0.552	0.828	0.227	0.184	0.276	SUBCLONAL	1	TRUE	2	0.76470300370221	5		349	247	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193528	99193528	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	145	576	2	ENST00000074304.5:c.2723T>C	p.Leu908Pro	p.L908P	ENST00000074304	NM_001134224.1	908	cTg/cCg	25/26	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.76470300370221	2		578	311	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274519	198274519	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	148	399	0	ENST00000335508.6:c.879G>A	p.Trp293Ter	p.W293*	ENST00000335508	NM_012433.2	293	tgG/tgA	7/25	0.749091930190694	5	FACETS	0.917	0.845	0.992	0.612	0.563	0.661	CLONAL	2	TRUE	2	0.76470300370221	5		399	453	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458238	12458238	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	51	378	0	ENST00000287820.6:c.855G>T	p.Met285Ile	p.M285I	ENST00000287820	NM_015869.4	285	atG/atT	6/7	0.680239302765213	5	FACETS	1	0.898	1	0.212	0.181	0.245	CLONAL	1	TRUE	0	0.76470300370221	5		378	270	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147591	47147591	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	128	468	0	ENST00000409792.3:c.4735T>C	p.Tyr1579His	p.Y1579H	ENST00000409792	NM_014159.6	1579	Tat/Cat	6/21	0.680239302765213	5	FACETS	0.969	0.888	1	0.387	0.355	0.421	CLONAL	2	TRUE	0	0.76470300370221	5		468	371	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119666170	119666170	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	51	306	0	ENST00000316626.5:c.311T>C	p.Leu104Pro	p.L104P	ENST00000316626		104	cTa/cCa	3/12	0.62783933017041	3	FACETS	0.955	0.824	1	0.478	0.412	0.548	CLONAL	1	TRUE	1	0.76470300370221	3		306	193	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191467	185191467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	50	426	0	ENST00000265026.3:c.2348G>A	p.Gly783Asp	p.G783D	ENST00000265026	NM_004721.4	783	gGc/gAc	11/14	0.62783933017041	3	FACETS	0.643	0.55	0.745	0.322	0.275	0.373	SUBCLONAL	1	TRUE	1	0.76470300370221	3		426	281	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446327	187446327	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs764890174	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	72	455	1	ENST00000232014.4:c.1361T>C	p.Met454Thr	p.M454T	ENST00000232014	NM_001130845.1	454	aTg/aCg	6/10	0.62783933017041	3	FACETS	1	0.902	1	0.51	0.451	0.572	CLONAL	1	TRUE	1	0.76470300370221	3		456	255	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539615	187539615	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	60	453	0	ENST00000441802.2:c.8125A>G	p.Thr2709Ala	p.T2709A	ENST00000441802	NM_005245.3	2709	Acc/Gcc	10/27	0.76470300370221	3	FACETS	1	0.954	1	0.397	0.348	0.448	CLONAL	1	TRUE	0	0.76470300370221	3		453	182	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295599	1295599	+	upstream_gene_variant	5'Flank	SNP	T	T	C	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	148	594	0				ENST00000310581	NM_198253.2	-/1132			0.62783933017041	3	FACETS	0.898	0.836	0.96	0.898	0.836	0.96	CLONAL	2	TRUE	1	0.76470300370221	3		594	298	SUCCESS
APC	324	MSKCC	GRCh37	5	112173333	112173333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	82	394	0	ENST00000257430.4:c.2042G>A	p.Cys681Tyr	p.C681Y	ENST00000257430	NM_000038.5	681	tGt/tAt	16/16	0.62783933017041	3	FACETS	0.81	0.732	0.889	0.81	0.732	0.889	CLONAL	2	TRUE	1	0.76470300370221	3		394	183	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131926992	131926992	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	40	360	0	ENST00000265335.6:c.1533del	p.Ala512GlnfsTer3	p.A512Qfs*3	ENST00000265335		510	gAa/ga	10/25	0.62783933017041	3	FACETS	0.679	0.57	0.798	0.339	0.285	0.399	SUBCLONAL	1	TRUE	1	0.76470300370221	3		360	213	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639163	176639163	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	79	484	0	ENST00000439151.2:c.3763A>G	p.Ser1255Gly	p.S1255G	ENST00000439151	NM_022455.4	1255	Agt/Ggt	5/23	0.62783933017041	3	FACETS	0.985	0.876	1	0.492	0.438	0.55	CLONAL	1	TRUE	1	0.76470300370221	3		484	290	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707817	176707817	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	64	413	0	ENST00000439151.2:c.5878del	p.Thr1960GlnfsTer9	p.T1960Qfs*9	ENST00000439151	NM_022455.4	1958	acA/ac	18/23	0.62783933017041	3	FACETS	0.821	0.717	0.93	0.41	0.358	0.465	CLONAL	1	TRUE	1	0.76470300370221	3		413	282	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117639352	117639352	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs753178466	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	45	333	0	ENST00000368508.3:c.6004A>G	p.Ser2002Gly	p.S2002G	ENST00000368508	NM_002944.2	2002	Agc/Ggc	37/43	0.708273200395407	4	FACETS	0.971	0.825	1	0.324	0.275	0.376	CLONAL	1	TRUE	1	0.76470300370221	4		333	214	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771139	161771139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	65	423	1	ENST00000366898.1:c.1390G>A	p.Asp464Asn	p.D464N	ENST00000366898	NM_004562.2	464	Gac/Aac	12/12	0.62783933017041	3	FACETS	0.894	0.783	1	0.447	0.391	0.505	CLONAL	1	TRUE	1	0.76470300370221	3		424	263	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976841	2976841	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	55	495	1	ENST00000396946.4:c.1171A>G	p.Thr391Ala	p.T391A	ENST00000396946	NM_032415.4	391	Aca/Gca	9/25	0.646374003768719	2	FACETS	0.625	0.541	0.715	0.313	0.27	0.358	SUBCLONAL	1	TRUE	0	0.76470300370221	2		496	230	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850379	128850379	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	71	422	0	ENST00000249373.3:c.1642A>G	p.Thr548Ala	p.T548A	ENST00000249373	NM_005631.4	548	Acc/Gcc	9/12	0.76470300370221	4	FACETS	0.981	0.863	1	0.245	0.215	0.277	CLONAL	1	TRUE	0	0.76470300370221	4		422	334	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853295	151853295	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs565261136	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	102	437	0	ENST00000262189.6:c.11807A>G	p.His3936Arg	p.H3936R	ENST00000262189	NM_170606.2	3936	cAt/cGt	45/59	0.76470300370221	4	FACETS	0.957	0.872	1	0.478	0.436	0.522	CLONAL	2	TRUE	0	0.76470300370221	4		437	246	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880096	151880096	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	60	318	0	ENST00000262189.6:c.5228G>T	p.Arg1743Ile	p.R1743I	ENST00000262189	NM_170606.2	1743	aGa/aTa	35/59	0.76470300370221	4	FACETS	1	0.898	1	0.259	0.225	0.296	CLONAL	1	TRUE	0	0.76470300370221	4		318	267	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030841	69030841	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	61	339	0	ENST00000288368.4:c.3383A>G	p.Gln1128Arg	p.Q1128R	ENST00000288368	NM_024870.2	1128	cAg/cGg	27/40	0.76470300370221	10	FACETS	0.922	0.795	1	0.102	0.088	0.118	CLONAL	1	TRUE	1	0.76470300370221	10		339	702	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046470	69046470	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	59	452	0	ENST00000288368.4:c.3943G>T	p.Gly1315Cys	p.G1315C	ENST00000288368	NM_024870.2	1315	Ggt/Tgt	32/40	0.76470300370221	10	FACETS	0.774	0.665	0.894	0.086	0.073	0.1	SUBCLONAL	1	TRUE	1	0.76470300370221	10		452	809	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739897	145739897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398698946	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	63	505	0	ENST00000428558.2:c.1633C>T	p.Pro545Ser	p.P545S	ENST00000428558	NM_004260.3	545	Cca/Tca	10/22	0.76470300370221	7	FACETS	0.819	0.708	0.939	0.164	0.141	0.188	CLONAL	1	TRUE	2	0.76470300370221	7		505	586	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2084198	2084198	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	41	270	0	ENST00000349721.2:c.2526+2T>C		p.X842_splice	ENST00000349721	NM_003070.3	842			0.76470300370221	8	FACETS	0.91	0.76	1	0.152	0.126	0.18	CLONAL	1	TRUE	2	0.76470300370221	8		270	388	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27109642	27109642	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	20	284	0	ENST00000380036.4:c.52+2T>C		p.X18_splice	ENST00000380036	NM_000459.3	18			0.76470300370221	8	FACETS	0.459	0.351	0.587	0.077	0.058	0.098	SUBCLONAL	1	TRUE	2	0.76470300370221	8		284	375	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97873780	97873780	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	66	598	0	ENST00000289081.3:c.1294C>A	p.Pro432Thr	p.P432T	ENST00000289081	NM_000136.2	432	Ccc/Acc	13/15	0.76470300370221	6	FACETS	0.97	0.845	1	0.323	0.281	0.369	CLONAL	1	TRUE	3	0.76470300370221	6		598	450	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348447	70348447	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	64	515	1	ENST00000374080.3:c.3355-1G>T		p.X1119_splice	ENST00000374080		1119			0.643265764964049	2	FACETS	0.854	0.753	0.96	0.427	0.376	0.48	CLONAL	1	TRUE	0	0.76470300370221	2		516	196	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123159740	123159741	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	105	320	0	ENST00000218089.9:c.101dup	p.Asn34LysfsTer11	p.N34Kfs*11	ENST00000218089	NM_001042749.1	32	gga/ggAa	4/35	0.643265764964049	2	FACETS	0.808	0.749	0.865	0.808	0.749	0.865	CLONAL	2	TRUE	0	0.76470300370221	2		320	170	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0065738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	21	575	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.616	0.474	0.782	0.616	0.474	0.782	SUBCLONAL	1	TRUE	1	0.19	2		575	359	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0065739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	295	449	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.290415870730117	3	FACETS	1	0.992	1	0.829	0.786	0.873	CLONAL	2	FALSE	0	0.419599192185519	3		451	684	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0065739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	120	434	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.235005677994378	3	FACETS	1	0.984	1	0.718	0.652	0.787	INDETERMINATE	1	FALSE	1	0.419599192185519	3		434	482	SUCCESS
APC	324	MSKCC	GRCh37	5	112128218	112128218	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	76	306	0	ENST00000257430.4:c.721G>T	p.Glu241Ter	p.E241*	ENST00000257430	NM_000038.5	241	Gaa/Taa	7/16	1	2	FACETS	0.821	0.723	0.926	0.821	0.723	0.926	CLONAL	1	FALSE	1	0.419599192185519	2		306	441	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239814	105239816	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0065739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	119	757	0	ENST00000349310.3:c.804_806del	p.Lys268del	p.K268del	ENST00000349310	NM_001014432.1	268	aaGAAc/aac	10/15	1	2	FACETS	0.873	0.789	0.96	0.873	0.789	0.96	CLONAL	1	FALSE	1	0.419599192185519	2		757	650	SUCCESS
APC	324	MSKCC	GRCh37	5	112175160	112175169	+	frameshift_variant	Frame_Shift_Del	DEL	ATCAGACGAC	ATCAGACGAC	-	novel	NA	P-0065739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	75	469	0	ENST00000257430.4:c.3870_3879del	p.Gln1291ArgfsTer11	p.Q1291Rfs*11	ENST00000257430	NM_000038.5	1290	aATCAGACGACa/aa	16/16	1	2	FACETS	0.69	0.606	0.78	0.69	0.606	0.78	SUBCLONAL	1	FALSE	1	0.419599192185519	2		469	518	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133748285	133748285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065740-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	33	462	0	ENST00000318560.5:c.946G>A	p.Glu316Lys	p.E316K	ENST00000318560	NM_005157.4	316	Gag/Aag	6/11	1	2	FACETS	0.158	0.128	0.192	0.158	0.128	0.192	SUBCLONAL	1	TRUE	1	0.863652462094031	2		462	483	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347802	70347802	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065740-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	161	538	0	ENST00000374080.3:c.3041A>T	p.Asn1014Ile	p.N1014I	ENST00000374080		1014	aAt/aTt	22/45	1	2	FACETS	0.617	0.569	0.668	0.617	0.569	0.668	SUBCLONAL	1	TRUE	1	0.863652462094031	2		538	604	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184621	185184621	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	129	519	0	ENST00000265026.3:c.1513C>T	p.Gln505Ter	p.Q505*	ENST00000265026	NM_004721.4	505	Caa/Taa	10/14	1	2	FACETS	0.874	0.793	0.96	0.874	0.793	0.96	CLONAL	1	TRUE	1	0.372125147592392	2		519	793	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44911001	44911002	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0065741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	118	630	0	ENST00000377967.4:c.705_706del	p.Asn236SerfsTer26	p.N236Sfs*26	ENST00000377967	NM_021140.2	234	acAGag/acag	9/29	0.372125147592392	1	FACETS	0.923	0.836	1	0.923	0.836	1	CLONAL	1	TRUE	0	0.372125147592392	1		630	559	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033823	49033823	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0065741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	105	392	0	ENST00000267163.4:c.1961-1G>C		p.X654_splice	ENST00000267163	NM_000321.2	654			0.372125147592392	1	FACETS	0.89	0.801	0.984	0.89	0.801	0.984	CLONAL	1	TRUE	0	0.372125147592392	1		392	516	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241487	105241487	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	174	652	0	ENST00000349310.3:c.493A>T	p.Ile165Phe	p.I165F	ENST00000349310	NM_001014432.1	165	Atc/Ttc	7/15	0.372125147592392	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.372125147592392	1		652	667	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989717	15989717	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	173	547	0	ENST00000268712.3:c.3056C>G	p.Pro1019Arg	p.P1019R	ENST00000268712	NM_006311.3	1019	cCt/cGt	23/46	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.372125147592392	2		547	822	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161922	47161922	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	131	445	0	ENST00000409792.3:c.4204G>T	p.Gly1402Trp	p.G1402W	ENST00000409792	NM_014159.6	1402	Ggg/Tgg	3/21	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.372125147592392	2		445	679	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0065742-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	13	286	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.736	0.524	0.997	0.736	0.524	0.997	CLONAL	1	TRUE	1	0.11	2		286	321	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274899	41274899	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065742-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	11	309	0	ENST00000349496.5:c.1149G>C	p.Trp383Cys	p.W383C	ENST00000349496	NM_001904.3	383	tgG/tgC	8/15	1	2	FACETS	0.461	0.317	0.642	0.461	0.317	0.642	SUBCLONAL	1	TRUE	1	0.11	2		309	434	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40872371	40872371	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs150955298	NA	P-0065742-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	33	435	0	ENST00000428826.2:c.584A>G	p.Asn195Ser	p.N195S	ENST00000428826		195	aAt/aGt	7/21	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.11	2		435	535	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562697	176562704	+	frameshift_variant	Frame_Shift_Del	DEL	AATCAGAG	AATCAGAG	-	novel	NA	P-0065742-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	35	454	1	ENST00000439151.2:c.596_603del	p.Ser199TrpfsTer9	p.S199Wfs*9	ENST00000439151	NM_022455.4	198	aAATCAGAG/a	2/23	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.11	2		455	491	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013719	170013719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388201066	NA	P-0065744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	18	212	0	ENST00000295797.4:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000295797	NM_002740.5	480	Cgc/Tgc	15/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		212	418	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0065744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	50	379	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		379	697	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0065744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	47	383	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		383	731	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795061	242795061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1203794937	NA	P-0065744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	64	638	0	ENST00000334409.5:c.148G>A	p.Ala50Thr	p.A50T	ENST00000334409	NM_005018.2	50	Gcc/Acc	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		638	1057	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425055	49425055	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200156008	NA	P-0065744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	56	623	0	ENST00000301067.7:c.13433G>A	p.Arg4478Gln	p.R4478Q	ENST00000301067	NM_003482.3	4478	cGg/cAg	39/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		623	1019	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554236	63554237	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	61	674	0	ENST00000307078.5:c.502dup	p.Ser168PhefsTer5	p.S168Ffs*5	ENST00000307078	NM_004655.3	168	tcc/tTcc	2/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		674	1044	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273053	18273053	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	63	580	0	ENST00000222254.8:c.943G>T	p.Val315Phe	p.V315F	ENST00000222254	NM_005027.3	315	Gtc/Ttc	8/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		580	1035	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686334	30686334	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	106	601	0	ENST00000295754.5:c.190C>T	p.Gln64Ter	p.Q64*	ENST00000295754	NM_003242.5	64	Cag/Tag	2/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		601	990	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044496	47044497	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	47	585	0	ENST00000377604.3:c.1998dup	p.Glu667ArgfsTer6	p.E667Rfs*6	ENST00000377604	NM_001204468.1	665	caa/cAaa	18/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		585	914	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971170	21971184	+	frameshift_variant	Frame_Shift_Del	DEL	AGCAGCTCCGCCACT	AGCAGCTCCGCCACT	G	novel	NA	P-0065744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	108	611	0	ENST00000304494.5:c.174_188delinsC	p.Val59AlafsTer56	p.V59Afs*56	ENST00000304494	NM_000077.4	58	cgAGTGGCGGAGCTGCTg/cgCg	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		611	981	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268766	41268766	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065745-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	54	430	0	ENST00000349496.5:c.1004A>C	p.Lys335Thr	p.K335T	ENST00000349496	NM_001904.3	335	aAa/aCa	7/15	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	FALSE	1	0.909896889741252	2		430	116	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696432	47696432	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519968	NA	P-0065746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	95	486	0	ENST00000347630.2:c.391T>G	p.Trp131Gly	p.W131G	ENST00000347630	NM_001007230.1	131	Tgg/Ggg	6/11	1	2	FACETS	0.87	0.776	0.97	0.87	0.776	0.97	CLONAL	1	TRUE	1	0.359729107487546	2		486	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0065746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	78	644	1	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	1	2	FACETS	0.627	0.55	0.709	0.627	0.55	0.709	SUBCLONAL	1	TRUE	1	0.359729107487546	2		645	692	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0065746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	83	587	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.359729107487546	1	FACETS	0.735	0.65	0.825	0.735	0.65	0.825	SUBCLONAL	1	TRUE	0	0.359729107487546	1		587	515	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061018	38061033	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGCGCCCTCTAGCT	GGCGCGCCCTCTAGCT	-	novel	NA	P-0065746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	14	631	0	ENST00000250448.2:c.956_971del	p.Gln319ArgfsTer26	p.Q319Rfs*26	ENST00000250448	NM_004496.3	319	cAGCTAGAGGGCGCGCCg/cg	2/2	1	2	FACETS	0.114	0.082	0.154	0.114	0.082	0.154	SUBCLONAL	1	TRUE	1	0.359729107487546	2		631	681	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137522074	137522074	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	31	237	0	ENST00000367739.4:c.805del	p.Tyr269IlefsTer8	p.Y269Ifs*8	ENST00000367739	NM_000416.2	269	Tat/at	6/7	1	2	FACETS	0.958	0.782	1	0.958	0.782	1	CLONAL	1	TRUE	1	0.359729107487546	2		237	180	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871016	12871016	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	118	647	0	ENST00000228872.4:c.245del	p.Gly82AlafsTer37	p.G82Afs*37	ENST00000228872	NM_004064.3	81	aaG/aa	1/3	1	2	FACETS	0.799	0.721	0.882	0.799	0.721	0.882	SUBCLONAL	1	TRUE	1	0.359729107487546	2		647	821	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060812	38060812	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	141	645	0	ENST00000250448.2:c.1177del	p.His393ThrfsTer47	p.H393Tfs*47	ENST00000250448	NM_004496.3	393	Cac/ac	2/2	1	2	FACETS	0.866	0.789	0.948	0.866	0.789	0.948	CLONAL	1	TRUE	1	0.359729107487546	2		645	905	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0065749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	23	80	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.508049518708764	4	FACETS	1	0.915	1			1	CLONAL	1	TRUE	NA	0.570047223181465	4		80	95	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121912651	NA	P-0065749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	302	543	0	ENST00000269305.4:c.742C>G	p.Arg248Gly	p.R248G	ENST00000269305	NM_001126112.2	248	Cgg/Ggg	7/11	0.512488049034538	2	FACETS	0.918	0.875	0.962	0.918	0.875	0.962	CLONAL	2	TRUE	0	0.570047223181465	2		543	577	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610650	52610650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	155	444	1	ENST00000394830.3:c.3523G>A	p.Glu1175Lys	p.E1175K	ENST00000394830	NM_018313.4	1175	Gaa/Aaa	23/30	0.484911546579625	3	FACETS	0.879	0.825	0.933	0.879	0.825	0.933	CLONAL	3	TRUE	0	0.570047223181465	3		445	265	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971098	21971098	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs878853647	NA	P-0065749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	318	631	0	ENST00000304494.5:c.260G>C	p.Arg87Pro	p.R87P	ENST00000304494	NM_000077.4	87	cGg/cCg	2/3	0.526147766325972	2	FACETS	0.974	0.93	1	0.974	0.93	1	CLONAL	2	TRUE	0	0.570047223181465	2		631	573	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8733827	8733827	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	124	524	0	ENST00000356435.5:c.17G>T	p.Arg6Met	p.R6M	ENST00000356435		6	aGg/aTg	1/35	0.526147766325972	2	FACETS	0.843	0.767	0.923	0.422	0.383	0.462	CLONAL	1	TRUE	0	0.570047223181465	2		524	516	SUCCESS
APC	324	MSKCC	GRCh37	5	112175908	112175909	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1554086015	NA	P-0065749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	184	512	0	ENST00000257430.4:c.4619_4620del	p.Glu1540AlafsTer3	p.E1540Afs*3	ENST00000257430	NM_000038.5	1539	tcAGag/tcag	16/16	0.540450085092207	2	FACETS	0.863	0.809	0.917	0.863	0.809	0.917	CLONAL	2	TRUE	0	0.570047223181465	2		512	374	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610715	52610715	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0065749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	121	322	1	ENST00000394830.3:c.3459-1G>A		p.X1153_splice	ENST00000394830	NM_018313.4	1153			0.484911546579625	3	FACETS	0.9	0.838	0.961	0.9	0.838	0.961	CLONAL	3	TRUE	0	0.570047223181465	3		323	202	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183592	10183592	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3289	314	743	0	ENST00000256474.2:c.61G>A	p.Glu21Lys	p.E21K	ENST00000256474	NM_000551.3	21	Gaa/Aaa	1/3	0.570047223181465	10	FACETS	1	0.94	1	0.111	0.104	0.119	CLONAL	1	TRUE	1	0.570047223181465	10		743	3603	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463186	25463186	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	152	658	0	ENST00000264709.3:c.2307C>G	p.Ile769Met	p.I769M	ENST00000264709	NM_175629.2	769	atC/atG	19/23	0.558121570917713	3	FACETS	0.947	0.867	1	0.473	0.433	0.515	CLONAL	1	TRUE	1	0.570047223181465	3		658	724	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427684	49427684	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1368	173	744	1	ENST00000301067.7:c.10804C>T	p.Gln3602Ter	p.Q3602*	ENST00000301067	NM_003482.3	3602	Caa/Taa	39/54	0.570047223181465	7	FACETS	0.955	0.876	1			1	CLONAL	1	TRUE	NA	0.570047223181465	7		745	1541	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427906	49427906	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	281	587	0	ENST00000301067.7:c.10684G>C	p.Glu3562Gln	p.E3562Q	ENST00000301067	NM_003482.3	3562	Gag/Cag	38/54	0.570047223181465	7	FACETS	0.913	0.856	0.971			1	CLONAL	2	TRUE	NA	0.570047223181465	7		587	1310	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438729	49438742	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGCGAAAGTACT	GAAGCGAAAGTACT	-	novel	NA	P-0065749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	778	607	1	ENST00000301067.7:c.4748_4761del	p.Gln1583ArgfsTer15	p.Q1583Rfs*15	ENST00000301067	NM_003482.3	1583	cAGTACTTTCGCTTC/c	19/54	0.570047223181465	7	FACETS	0.953	0.929	0.976			1	CLONAL	6	TRUE	NA	0.570047223181465	7		608	1158	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483885	88483885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767613437	NA	P-0065749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	220	575	0	ENST00000360948.2:c.1685C>T	p.Pro562Leu	p.P562L	ENST00000360948	NM_001012338.2	562	cCg/cTg	14/19	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.570047223181465	2		575	580	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193544	99193544	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	183	798	0	ENST00000074304.5:c.2739C>G	p.Ile913Met	p.I913M	ENST00000074304	NM_001134224.1	913	atC/atG	25/26	0.466186715484742	4	FACETS	1	0.936	1	0.508	0.468	0.549	CLONAL	1	TRUE	2	0.570047223181465	4		798	992	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63975907	63975907	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs376455162	NA	P-0065749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	258	742	0	ENST00000398590.3:c.1417G>C	p.Val473Leu	p.V473L	ENST00000398590	NM_001177387.1	473	Gtc/Ctc	10/14	0.484911546579625	3	FACETS	0.76	0.715	0.807	0.507	0.476	0.538	SUBCLONAL	2	TRUE	0	0.570047223181465	3		742	765	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185023	32185023	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	313	606	0	ENST00000375023.3:c.1645G>C	p.Glu549Gln	p.E549Q	ENST00000375023	NM_004557.3	549	Gag/Cag	10/30	0.466186715484742	4	FACETS	0.99	0.937	1	0.99	0.937	1	CLONAL	2	TRUE	2	0.570047223181465	4		606	871	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005691	150005691	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	115	576	1	ENST00000253339.5:c.534G>C	p.Trp178Cys	p.W178C	ENST00000253339		178	tgG/tgC	3/7	0.540450085092207	2	FACETS	0.911	0.826	0.999	0.455	0.413	0.5	CLONAL	1	TRUE	0	0.570047223181465	2		577	443	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346559	81346559	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	68	429	0	ENST00000222390.5:c.1394C>G	p.Pro465Arg	p.P465R	ENST00000222390	NM_000601.4	465	cCt/cGt	11/18	0.570047223181465	3	FACETS	0.73	0.637	0.829	0.365	0.318	0.415	SUBCLONAL	1	TRUE	1	0.570047223181465	3		429	420	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796930	78796934	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAT	GAAAT	AAAA	novel	NA	P-0065749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	126	471	1	ENST00000306801.3:c.1043_1047delinsAAAA	p.Arg348GlnfsTer10	p.R348Qfs*10	ENST00000306801	NM_020761.2	348	cGAAAT/cAAAA	9/34	0.507806310673921	3	FACETS	0.879	0.798	0.965	0.44	0.399	0.483	CLONAL	1	TRUE	1	0.570047223181465	3		472	646	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	230	1407	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.716780777819078	2		1407	583	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971187	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	349	849	1	ENST00000304494.5:c.171_172delinsTT	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	57	gcCCga/gcTTga	2/3	0.716780777819078	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.716780777819078	1		850	606	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509435	106509435	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138344795	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	287	773	0	ENST00000359195.3:c.1429C>T	p.Arg477Cys	p.R477C	ENST00000359195	NM_002649.2	477	Cgt/Tgt	2/11	0.172339987807701	3	FACETS	1	0.988	1	0.584	0.55	0.618	INDETERMINATE	1	TRUE	1	0.716780777819078	3		773	932	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032794	30032794	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434259	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	299	744	0	ENST00000338641.4:c.169C>T	p.Arg57Ter	p.R57*	ENST00000338641	NM_000268.3	57	Cga/Tga	2/16	1	2	FACETS	0.942	0.889	0.995	0.942	0.889	0.995	CLONAL	1	TRUE	1	0.716780777819078	2		744	886	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204678	108204678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	39	129	0	ENST00000278616.4:c.7993C>T	p.Pro2665Ser	p.P2665S	ENST00000278616	NM_000051.3	2665	Cct/Tct	54/63	0.716780777819078	1	FACETS	0.646	0.551	0.746	0.646	0.551	0.746	SUBCLONAL	1	TRUE	0	0.716780777819078	1		129	108	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259262	89259262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770780950	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	292	495	0	ENST00000336596.2:c.406C>T	p.Arg136Ter	p.R136*	ENST00000336596	NM_005233.5	136	Cga/Tga	3/17	0.637690203070089	3	FACETS	0.825	0.782	0.868	0.825	0.782	0.868	CLONAL	2	TRUE	1	0.716780777819078	3		495	671	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601918	43601918	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	387	864	0	ENST00000355710.3:c.962G>A	p.Gly321Glu	p.G321E	ENST00000355710	NM_020975.4	321	gGg/gAg	5/20	1	2	FACETS	0.971	0.924	1	0.971	0.924	1	CLONAL	1	TRUE	1	0.716780777819078	2		864	1112	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407472	139407472	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	197	309	0	ENST00000277541.6:c.2467+1G>A		p.X823_splice	ENST00000277541	NM_017617.3	823			0.692361984351602	3	FACETS	0.874	0.82	0.929	0.874	0.82	0.929	CLONAL	2	TRUE	1	0.716780777819078	3		309	427	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521838	157521838	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	293	657	0	ENST00000346085.5:c.4111-1G>A		p.X1371_splice	ENST00000346085	NM_020732.3	1371			1	2	FACETS	0.981	0.927	1	0.981	0.927	1	CLONAL	1	TRUE	1	0.716780777819078	2		657	833	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	319	688	0	ENST00000269305.4:c.991del	p.Gln331ArgfsTer14	p.Q331Rfs*14	ENST00000269305	NM_001126112.2	331	Cag/ag	9/11	1	2	FACETS	0.989	0.937	1	0.989	0.937	1	CLONAL	1	TRUE	1	0.716780777819078	2		688	900	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788647	3788647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	236	480	0	ENST00000262367.5:c.4307G>A	p.Ser1436Asn	p.S1436N	ENST00000262367	NM_004380.2	1436	aGt/aAt	26/31	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.716780777819078	2		480	648	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458549	120458549	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	397	1010	0	ENST00000256646.2:c.6796G>T	p.Glu2266Ter	p.E2266*	ENST00000256646	NM_024408.3	2266	Gag/Tag	34/34	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.716780777819078	2		1010	1053	SUCCESS
MAD2L2	10459	MSKCC	GRCh37	1	11737658	11737658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767807551	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	304	690	0	ENST00000235310.3:c.173C>T	p.Pro58Leu	p.P58L	ENST00000235310		58	cCg/cTg	6/11	1	2	FACETS	0.994	0.94	1	0.994	0.94	1	CLONAL	1	TRUE	1	0.716780777819078	2		690	853	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506414	120506414	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs376783592	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	257	556	0	ENST00000256646.2:c.1698G>T	p.Leu566Phe	p.L566F	ENST00000256646	NM_024408.3	566	ttG/ttT	11/34	1	2	FACETS	0.949	0.892	1	0.949	0.892	1	CLONAL	1	TRUE	1	0.716780777819078	2		556	756	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533873	533874	+	missense_variant	Missense_Mutation	DNP	CT	CT	TA	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	362	943	0	ENST00000451590.1:c.182_183delinsTA	p.Gln61Leu	p.Q61L	ENST00000451590	NM_001130442.1	61	cAG/cTA	3/5	1	2	FACETS	0.926	0.879	0.974	0.926	0.879	0.974	CLONAL	1	TRUE	1	0.716780777819078	2		943	1091	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	430245	430246	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	157	523	1	ENST00000399788.2:c.2456_2457delinsTT	p.Thr819Ile	p.T819I	ENST00000399788	NM_001042603.1	819	aCC/aTT	18/28	NA	2	FACETS	0.655	0.602	0.71			1	INDETERMINATE	1	TRUE	NA	0.716780777819078	2		524	669	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699278	18699278	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	138	334	0	ENST00000266497.5:c.3379G>C	p.Glu1127Gln	p.E1127Q	ENST00000266497		1127	Gag/Cag	24/31	1	2	FACETS	0.98	0.901	1	0.98	0.901	1	CLONAL	1	TRUE	1	0.716780777819078	2		334	393	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246497	46246498	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	256	653	0	ENST00000334344.6:c.4591_4592delinsTT	p.Pro1531Leu	p.P1531L	ENST00000334344	NM_152641.2	1531	CCa/TTa	15/21	1	2	FACETS	0.87	0.817	0.924	0.87	0.817	0.924	CLONAL	1	TRUE	1	0.716780777819078	2		653	821	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123880943	123880944	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	256	584	1	ENST00000330479.4:c.561_562delinsTT	p.Arg188Ter	p.R188*	ENST00000330479	NM_020382.3	187	gtCCga/gtTTga	5/9	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.716780777819078	2		585	687	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639602	3639602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	391	955	0	ENST00000294008.3:c.4037C>T	p.Pro1346Leu	p.P1346L	ENST00000294008	NM_032444.2	1346	cCc/cTc	12/15	1	2	FACETS	0.972	0.925	1	0.972	0.925	1	CLONAL	1	TRUE	1	0.716780777819078	2		955	1122	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129042	30129043	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	288	744	0	ENST00000263025.4:c.723_724delinsTT	p.Arg242Trp	p.R242W	ENST00000263025	NM_002746.2	241	aaCCgg/aaTTgg	5/9	1	2	FACETS	0.93	0.877	0.984	0.93	0.877	0.984	CLONAL	1	TRUE	1	0.716780777819078	2		744	864	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40460300	40460300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	312	679	0	ENST00000345506.4:c.2011C>T	p.Pro671Ser	p.P671S	ENST00000345506	NM_003152.3	671	Cct/Tct	17/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.716780777819078	2		679	870	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245824	41245824	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	83	164	0	ENST00000357654.3:c.1724A>T	p.Glu575Val	p.E575V	ENST00000357654	NM_007294.3	575	gAa/gTa	10/23	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.716780777819078	2		164	230	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246025	41246025	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398122637	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	99	286	0	ENST00000357654.3:c.1523C>T	p.Pro508Leu	p.P508L	ENST00000357654	NM_007294.3	508	cCt/cTt	10/23	1	2	FACETS	0.847	0.765	0.933	0.847	0.765	0.933	CLONAL	1	TRUE	1	0.716780777819078	2		286	326	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821801	59821801	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	64	127	0	ENST00000259008.2:c.2249G>A	p.Gly750Glu	p.G750E	ENST00000259008	NM_032043.2	750	gGa/gAa	15/20	1	2	FACETS	0.801	0.703	0.903	0.801	0.703	0.903	CLONAL	1	TRUE	1	0.716780777819078	2		127	223	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526153	63526153	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	346	746	0	ENST00000307078.5:c.2473G>A	p.Glu825Lys	p.E825K	ENST00000307078	NM_004655.3	825	Gag/Aag	11/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.716780777819078	2		746	934	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226749	2226750	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	366	1000	0	ENST00000398665.3:c.4229_4230delinsTT	p.Ala1410Val	p.A1410V	ENST00000398665	NM_032482.2	1410	gCC/gTT	27/28	1	2	FACETS	0.991	0.942	1	0.991	0.942	1	CLONAL	1	TRUE	1	0.716780777819078	2		1000	1030	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302560	15302561	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	341	912	0	ENST00000263388.2:c.797_798delinsAA	p.Trp266Ter	p.W266*	ENST00000263388	NM_000435.2	266	tGG/tAA	5/33	1	2	FACETS	0.896	0.849	0.944	0.896	0.849	0.944	CLONAL	1	TRUE	1	0.716780777819078	2		912	1062	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966319	25966319	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	270	673	0	ENST00000435504.4:c.2887C>T	p.Pro963Ser	p.P963S	ENST00000435504		963	Ccc/Tcc	13/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.716780777819078	2		673	732	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25990593	25990593	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	117	307	0	ENST00000435504.4:c.634A>G	p.Thr212Ala	p.T212A	ENST00000435504		212	Aca/Gca	8/13	1	2	FACETS	0.98	0.895	1	0.98	0.895	1	CLONAL	1	TRUE	1	0.716780777819078	2		307	333	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251631	212251631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	336	773	0	ENST00000342788.4:c.3428G>A	p.Gly1143Glu	p.G1143E	ENST00000342788	NM_005235.2	1143	gGa/gAa	27/28	1	2	FACETS	0.945	0.896	0.995	0.945	0.896	0.995	CLONAL	1	TRUE	1	0.716780777819078	2		773	992	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620508	52620509	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	279	604	0	ENST00000394830.3:c.3244_3245delinsAA	p.Gly1082Asn	p.G1082N	ENST00000394830	NM_018313.4	1082	GGt/AAt	21/30	0.716780777819078	1	FACETS	0.995	0.948	1	0.995	0.948	1	CLONAL	1	TRUE	0	0.716780777819078	1		604	502	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114701	73114701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	78	184	0	ENST00000356692.5:c.1082C>T	p.Ser361Phe	p.S361F	ENST00000356692		361	tCt/tTt	9/9	0.716780777819078	1	FACETS	0.956	0.869	1	0.956	0.869	1	CLONAL	1	TRUE	0	0.716780777819078	1		184	146	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356366	66356366	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	255	635	0	ENST00000273854.3:c.1131G>A	p.Trp377Ter	p.W377*	ENST00000273854	NM_004439.5	377	tgG/tgA	5/18	1	2	FACETS	0.891	0.836	0.946	0.891	0.836	0.946	CLONAL	1	TRUE	1	0.716780777819078	2		635	799	SUCCESS
ALB	213	MSKCC	GRCh37	4	74275113	74275114	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	89	282	0	ENST00000295897.4:c.524_525delinsTT	p.Ala175Val	p.A175V	ENST00000295897	NM_000477.5	175	gCC/gTT	5/15	1	2	FACETS	0.842	0.755	0.932	0.842	0.755	0.932	CLONAL	1	TRUE	1	0.716780777819078	2		282	295	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953192	38953192	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	51	102	0	ENST00000357387.3:c.2792G>A	p.Gly931Glu	p.G931E	ENST00000357387	NM_152756.3	931	gGa/gAa	29/38	1	2	FACETS	0.827	0.716	0.945	0.827	0.716	0.945	CLONAL	1	TRUE	1	0.716780777819078	2		102	172	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638337	176638338	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	289	795	0	ENST00000439151.2:c.2937_2938delinsTT	p.Pro980Ser	p.P980S	ENST00000439151	NM_022455.4	979	agCCct/agTTct	5/23	1	2	FACETS	0.871	0.821	0.922	0.871	0.821	0.922	CLONAL	1	TRUE	1	0.716780777819078	2		795	926	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948258	31948259	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	GT	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	277	641	1	ENST00000375333.2:c.846_847delinsGT	p.Arg283Ter	p.R283*	ENST00000375333	NM_032454.1	282	gtCCga/gtGTga	6/8	1	2	FACETS	0.938	0.884	0.993	0.938	0.884	0.993	CLONAL	1	TRUE	1	0.716780777819078	2		642	824	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468302	50468302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	341	702	0	ENST00000331340.3:c.1537G>A	p.Glu513Lys	p.E513K	ENST00000331340	NM_006060.4	513	Gag/Aag	8/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.716780777819078	2		702	895	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508260	106508260	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	419	841	1	ENST00000359195.3:c.254C>G	p.Ala85Gly	p.A85G	ENST00000359195	NM_002649.2	85	gCg/gGg	2/11	0.172339987807701	3	FACETS	0.767	0.733	0.802	0.767	0.733	0.802	INDETERMINATE	2	TRUE	1	0.716780777819078	3		842	1035	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942767	68942767	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs773741156	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	267	704	0	ENST00000288368.4:c.579C>A	p.Asp193Glu	p.D193E	ENST00000288368	NM_024870.2	193	gaC/gaA	6/40	1	2	FACETS	0.914	0.86	0.969	0.914	0.86	0.969	CLONAL	1	TRUE	1	0.716780777819078	2		704	815	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022067	5022067	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	128	337	0	ENST00000381652.3:c.80G>A	p.Gly27Glu	p.G27E	ENST00000381652	NM_004972.3	27	gGa/gAa	3/25	0.716780777819078	1	FACETS	0.885	0.819	0.951	0.885	0.819	0.951	CLONAL	1	TRUE	0	0.716780777819078	1		337	259	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054807	5054807	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1563961042	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	132	239	0	ENST00000381652.3:c.859A>G	p.Thr287Ala	p.T287A	ENST00000381652	NM_004972.3	287	Acc/Gcc	7/25	0.716780777819078	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.716780777819078	1		239	226	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430593	80430593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	30	33	0	ENST00000286548.4:c.415C>T	p.Pro139Ser	p.P139S	ENST00000286548	NM_002072.3	139	Cct/Tct	3/7	0.692361984351602	3	FACETS	0.932	0.79	1	0.932	0.79	1	CLONAL	2	TRUE	1	0.716780777819078	3		33	61	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390618	139390618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	402	836	0	ENST00000277541.6:c.7573C>T	p.Pro2525Ser	p.P2525S	ENST00000277541	NM_017617.3	2525	Ccg/Tcg	34/34	0.692361984351602	3	FACETS	1	0.979	1	0.528	0.501	0.555	CLONAL	1	TRUE	1	0.716780777819078	3		836	1443	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399784	139399784	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	414	861	0	ENST00000277541.6:c.4564C>T	p.Gln1522Ter	p.Q1522*	ENST00000277541	NM_017617.3	1522	Cag/Tag	25/34	0.692361984351602	3	FACETS	1	0.987	1	0.551	0.524	0.579	CLONAL	1	TRUE	1	0.716780777819078	3		861	1424	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732958	44732958	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	262	336	0	ENST00000377967.4:c.161G>A	p.Ser54Asn	p.S54N	ENST00000377967	NM_021140.2	54	aGc/aAc	1/29	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.716780777819078	1		336	354	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30060975	30060984	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCAGTTTACT	CCAGTTTACT	TAG	novel	NA	P-0065751-T01-IM7	NA	A	A	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	126	271	0	ENST00000338641.4:c.811-4_816delinsTAG		p.X271_splice	ENST00000338641	NM_000268.3	271		9/16	1	2	FACETS	0.961	0.88	1	0.961	0.88	1	CLONAL	1	TRUE	1	0.716780777819078	2		271	366	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665803	29665804	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	A	novel	NA	P-0065751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	46	78	0	ENST00000356175.3:c.6838_6839delinsA	p.Leu2280AsnfsTer18	p.L2280Nfs*18	ENST00000356175	NM_000267.3	2280	TTa/Aa	45/57	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.716780777819078	2		78	125	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579393	+	frameshift_variant	Frame_Shift_Del	DEL	GGGAA	GGGAA	-	novel	NA	P-0065752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	528	596	0	ENST00000269305.4:c.294_298del	p.Ser99GlufsTer48	p.S99Efs*48	ENST00000269305	NM_001126112.2	98	ccTTCCCag/ccag	4/11	0.848671316084489	3	FACETS	0.986	0.968	1	0.986	0.968	1	CLONAL	3	TRUE	0	0.848671316084489	3		596	599	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256433	115256433	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	28	293	0	ENST00000369535.4:c.278T>G	p.Ile93Ser	p.I93S	ENST00000369535	NM_002524.4	93	aTt/aGt	3/7	1	2	FACETS	0.33	0.265	0.402	0.33	0.265	0.402	SUBCLONAL	1	TRUE	1	0.848671316084489	2		293	200	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005517	42005517	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0065752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	130	507	0	ENST00000219905.7:c.3253A>T	p.Arg1085Ter	p.R1085*	ENST00000219905	NM_001164273.1	1085	Aga/Tga	9/24	0.848671316084489	2	FACETS	0.688	0.629	0.75	0.344	0.314	0.375	SUBCLONAL	1	TRUE	0	0.848671316084489	2		507	445	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61722624	61722624	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	64	284	0	ENST00000401558.2:c.1013A>G	p.Glu338Gly	p.E338G	ENST00000401558	NM_003400.3	338	gAa/gGa	11/25	0.840660883732331	3	FACETS	0.636	0.554	0.723	0.318	0.277	0.362	SUBCLONAL	1	TRUE	1	0.848671316084489	3		284	338	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097281	178097281	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	144	414	0	ENST00000397062.3:c.433C>A	p.Pro145Thr	p.P145T	ENST00000397062	NM_006164.4	145	Cct/Act	4/5	0.112585767036667	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.848671316084489	0		414	676	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532752	187532752	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	73	505	0	ENST00000441802.2:c.9641G>C	p.Gly3214Ala	p.G3214A	ENST00000441802	NM_005245.3	3214	gGc/gCc	14/27	0.848671316084489	1	FACETS	0.444	0.394	0.496	0.444	0.394	0.496	SUBCLONAL	1	TRUE	0	0.848671316084489	1		505	223	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348183	70348183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1474605735	NA	P-0065752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	17	299	1	ENST00000374080.3:c.3247G>A	p.Gly1083Ser	p.G1083S	ENST00000374080		1083	Ggc/Agc	23/45	1	1	FACETS	0.117	0.087	0.152	0.117	0.087	0.152	SUBCLONAL	1	TRUE	0	0.848671316084489	1		300	197	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0065755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	334	601	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.491721808663926	3	FACETS	0.894	0.855	0.932	0.894	0.855	0.932	CLONAL	3	TRUE	0	0.534063012590158	3		601	591	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584514	48584514	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	112	469	0	ENST00000342988.3:c.692del	p.Gly231AlafsTer10	p.G231Afs*10	ENST00000342988	NM_005359.5	229	ctG/ct	6/12	0.529311237549126	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	0	0.534063012590158	2		469	209	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192672	94192672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	43	172	0	ENST00000323929.3:c.1402G>A	p.Asp468Asn	p.D468N	ENST00000323929	NM_005591.3	468	Gat/Aat	13/20	0.476824380955969	3	FACETS	0.972	0.839	1	0.972	0.839	1	CLONAL	2	TRUE	1	0.534063012590158	3		172	105	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724619	43724619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1247584491	NA	P-0065755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	194	415	0	ENST00000382044.4:c.3448G>A	p.Glu1150Lys	p.E1150K	ENST00000382044	NM_001141980.1	1150	Gaa/Aaa	17/28	0.519899975332215	4	FACETS	0.899	0.851	0.945	0.899	0.851	0.945	CLONAL	4	TRUE	0	0.534063012590158	4		415	310	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220637	2220637	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	191	633	0	ENST00000326181.6:c.254G>T	p.Arg85Leu	p.R85L	ENST00000326181	NM_032271.2	85	cGc/cTc	5/21	0.460523730478057	3	FACETS	0.801	0.74	0.865	0.401	0.37	0.433	CLONAL	1	TRUE	1	0.534063012590158	3		633	1131	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600422	10600429	+	frameshift_variant	Frame_Shift_Del	DEL	AAGCCCCC	AAGCCCCC	-	novel	NA	P-0065755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	346	692	0	ENST00000171111.5:c.1426_1433del	p.Gly476Ter	p.G476*	ENST00000171111	NM_203500.1	476	GGGGGCTTt/t	4/6	NA	2	FACETS	0.899	0.857	0.94			1	INDETERMINATE	2	TRUE	NA	0.534063012590158	2		692	721	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169342	99169342	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	128	549	0	ENST00000074304.5:c.1272A>T	p.Gln424His	p.Q424H	ENST00000074304	NM_001134224.1	424	caA/caT	15/26	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.534063012590158	2		549	417	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430999	181430999	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1482	326	681	0	ENST00000325404.1:c.851C>G	p.Pro284Arg	p.P284R	ENST00000325404	NM_003106.3	284	cCg/cGg	1/1	0.415463663947931	6	FACETS	1	0.993	1	0.465	0.438	0.494	CLONAL	1	TRUE	3	0.534063012590158	6		681	1808	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613397	100613397	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	164	201	0	ENST00000308731.7:c.1003G>T	p.Val335Phe	p.V335F	ENST00000308731	NM_000061.2	335	Gtt/Ttt	12/19	0.534063012590158	3	FACETS	1	0.987	1			1	CLONAL	3	TRUE	NA	0.534063012590158	3		201	228	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0065789-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	409	441	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.677300091976651	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.677300091976651	3		441	805	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201059	NA	P-0065789-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	268	554	0	ENST00000269305.4:c.856G>T	p.Glu286Ter	p.E286*	ENST00000269305	NM_001126112.2	286	Gaa/Taa	8/11	0.677300091976651	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.677300091976651	1		554	467	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065789-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	162	313	0	ENST00000288602.6:c.1742A>T	p.Asn581Ile	p.N581I	ENST00000288602	NM_004333.4	581	aAt/aTt	15/18	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.677300091976651	2		313	424	SUCCESS
MAD2L2	10459	MSKCC	GRCh37	1	11736911	11736911	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065789-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	148	469	0	ENST00000235310.3:c.326C>A	p.Ser109Tyr	p.S109Y	ENST00000235310		109	tCc/tAc	7/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.677300091976651	2		469	430	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131229	202131229	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065789-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	198	428	0	ENST00000358485.4:c.197T>C	p.Leu66Pro	p.L66P	ENST00000358485	NM_001080125.1	66	cTt/cCt	2/9	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.677300091976651	2		428	550	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149238763	149238764	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0065789-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	389	479	0	ENST00000360632.3:c.1031_1032delinsTT	p.Gly344Val	p.G344V	ENST00000360632	NM_015472.4	344	gGA/gTT	7/7	0.677300091976651	3	FACETS	0.989	0.947	1	0.989	0.947	1	CLONAL	2	TRUE	1	0.677300091976651	3		479	777	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0065791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	56	491	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.28	2		491	395	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0065791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	16	118	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.922	0.688	1	0.922	0.688	1	CLONAL	1	TRUE	1	0.28	2		118	124	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0065791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	51	443	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.824	0.702	0.958	0.824	0.702	0.958	CLONAL	1	TRUE	1	0.28	2		443	442	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692790	89692790	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554898067	NA	P-0065791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	28	273	0	ENST00000371953.3:c.274G>T	p.Asp92Tyr	p.D92Y	ENST00000371953	NM_000314.4	92	Gac/Tac	5/9	1	2	FACETS	0.702	0.562	0.86	0.702	0.562	0.86	SUBCLONAL	1	TRUE	1	0.28	2		273	285	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589585	67589586	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATG	novel	NA	P-0065791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	50	353	0	ENST00000274335.5:c.1350_1352dup	p.His450_Glu451insAsp	p.H450_E451insD	ENST00000274335		450	cat/cATGat	10/15	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.28	2		353	314	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249247	10249247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	55	562	0	ENST00000340748.4:c.3935G>A	p.Arg1312Gln	p.R1312Q	ENST00000340748		1312	cGg/cAg	34/40	1	2	FACETS	0.931	0.798	1	0.931	0.798	1	CLONAL	1	TRUE	1	0.28	2		562	422	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088764	27088765	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0065791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	71	507	0	ENST00000324856.7:c.2374_2375del	p.Ser792HisfsTer24	p.S792Hfs*24	ENST00000324856	NM_006015.4	791	aaCTcc/aacc	7/20	1	2	FACETS	0.968	0.846	1	0.968	0.846	1	CLONAL	1	TRUE	1	0.28	2		507	524	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107013	27107026	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGCAGAGCCAGG	CCAGCAGAGCCAGG	-	novel	NA	P-0065791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	78	724	0	ENST00000324856.7:c.6629_6642del	p.Gln2210ProfsTer10	p.Q2210Pfs*10	ENST00000324856	NM_006015.4	2208	ttCCAGCAGAGCCAGGcc/ttcc	20/20	1	2	FACETS	0.984	0.866	1	0.984	0.866	1	CLONAL	1	TRUE	1	0.28	2		724	566	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913499	NA	P-0065792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	43	379	0	ENST00000345146.2:c.394C>A	p.Arg132Ser	p.R132S	ENST00000345146	NM_005896.2	132	Cgt/Agt	4/10	0.159027937246795	2	FACETS	1	0.889	1	1	0.966	1	CLONAL	3	TRUE	0	0.2162674205561	2		379	127	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs886039483	NA	P-0065792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	170	362	0	ENST00000269305.4:c.376T>G	p.Tyr126Asp	p.Y126D	ENST00000269305	NM_001126112.2	126	Tac/Gac	5/11	0.2162674205561	11	FACETS	1	0.968	1			1	CLONAL	13	TRUE	NA	0.2162674205561	11		362	233	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038893	12038893	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065793-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	17	378	0	ENST00000396373.4:c.1186A>G	p.Arg396Gly	p.R396G	ENST00000396373	NM_001987.4	396	Aga/Gga	7/8	0.330421566265395	5	FACETS	0.767	0.575	0.992	0.256	0.191	0.331	CLONAL	1	TRUE	2	0.412364238767423	5		378	174	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680751	88680751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201252722	NA	P-0065793-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	13	397	0	ENST00000360948.2:c.506G>A	p.Arg169His	p.R169H	ENST00000360948	NM_001012338.2	169	cGc/cAc	6/19	0.165416304764801	0	FACETS	0.457	0.331	0.605			1	INDETERMINATE	1	TRUE	0	0.412364238767423	0		397	81	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578260	7578260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204041	NA	P-0065793-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	57	607	0	ENST00000269305.4:c.589G>A	p.Val197Met	p.V197M	ENST00000269305	NM_001126112.2	197	Gtg/Atg	6/11	0.412364238767423	3	FACETS	1	0.885	1	1	0.885	1	CLONAL	2	TRUE	1	0.412364238767423	3		607	165	SUCCESS
APC	324	MSKCC	GRCh37	5	112175364	112175364	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881249	NA	P-0065793-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	21	425	0	ENST00000257430.4:c.4073C>T	p.Ala1358Val	p.A1358V	ENST00000257430	NM_000038.5	1358	gCg/gTg	16/16	0.237470419102323	2	FACETS	0.835	0.652	1	0.417	0.326	0.521	INDETERMINATE	1	TRUE	0	0.412364238767423	2		425	122	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974751	21974751	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1317637377	NA	P-0065793-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	12	488	0	ENST00000304494.5:c.76G>C	p.Glu26Gln	p.E26Q	ENST00000304494	NM_000077.4	26	Gag/Cag	1/3	0.412364238767423	1	FACETS	0.367	0.259	0.497	0.367	0.259	0.497	SUBCLONAL	1	TRUE	0	0.412364238767423	1		488	126	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0065794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	186	622	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.235207571708584	2	FACETS	0.837	0.775	0.901	1	0.985	1	CLONAL	3	TRUE	0	0.2	2		622	741	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	38	663	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	0	0.2	1		663	325	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436393	52436393	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1244342890	NA	P-0065794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	65	618	0	ENST00000460680.1:c.2101C>T	p.Arg701Cys	p.R701C	ENST00000460680	NM_004656.3	701	Cgc/Tgc	17/17	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.2	2		618	624	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957882	1957882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	37	470	0	ENST00000382891.5:c.2848G>A	p.Gly950Arg	p.G950R	ENST00000382891	NM_133335.3	950	Ggg/Agg	15/22	1	2	FACETS	0.686	0.565	0.823	0.686	0.565	0.823	SUBCLONAL	1	TRUE	1	0.2	2		470	539	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783856	50783857	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0065794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	55	502	0	ENST00000398568.2:c.248_249del	p.Phe83CysfsTer2	p.F83Cfs*2	ENST00000398568	NM_001042412.1	83	TTt/t	3/18	1	2	FACETS	0.845	0.722	0.98	0.845	0.722	0.98	CLONAL	1	TRUE	1	0.2	2		502	651	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2077691	2077691	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	37	475	0	ENST00000349721.2:c.2099C>G	p.Ser700Cys	p.S700C	ENST00000349721	NM_003070.3	700	tCc/tGc	14/34	1	2	FACETS	0.543	0.446	0.651	0.543	0.446	0.651	SUBCLONAL	1	TRUE	1	0.2	2		475	682	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436182	56436183	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0065794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	76	458	0	ENST00000407977.2:c.953_954dup	p.Gly319ArgfsTer101	p.G319Rfs*101	ENST00000407977		318	-/AG	9/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.2	2		458	521	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383617	42383617	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065796-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	32	542	0	ENST00000221972.3:c.392G>T	p.Arg131Met	p.R131M	ENST00000221972	NM_021601.3	131	aGg/aTg	3/5	1	2	FACETS	0.479	0.388	0.581	0.479	0.388	0.581	SUBCLONAL	1	TRUE	1	0.276335673332088	2		542	484	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673862	30673862	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs541015349	NA	P-0065796-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	65	427	0	ENST00000376406.3:c.3098C>T	p.Ser1033Phe	p.S1033F	ENST00000376406	NM_014641.2	1033	tCt/tTt	10/15	1	2	FACETS	0.813	0.705	0.929	0.813	0.705	0.929	CLONAL	1	TRUE	1	0.276335673332088	2		427	579	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0065797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	38	170	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.208712079947904	3	FACETS	1	0.912	1	0.574	0.48	0.678	INDETERMINATE	1	TRUE	1	0.406076215169487	3		170	196	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0065797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	21	337	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.341	0.263	0.433	0.341	0.263	0.433	SUBCLONAL	1	TRUE	1	0.406076215169487	2		337	303	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0065797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	149	337	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.406076215169487	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.406076215169487	3		337	371	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044463	12044463	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0065797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	18	327	0	ENST00000353533.5:c.1087-1G>A		p.X363_splice	ENST00000353533	NM_003010.3	363			1	2	FACETS	0.293	0.22	0.378	0.293	0.22	0.378	SUBCLONAL	1	TRUE	1	0.406076215169487	2		327	303	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034444	47034444	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	62	356	0	ENST00000377604.3:c.529G>T	p.Glu177Ter	p.E177*	ENST00000377604	NM_001204468.1	177	Gag/Tag	6/24	1	2	FACETS	0.985	0.857	1	0.985	0.857	1	CLONAL	1	TRUE	1	0.406076215169487	2		356	310	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281200	15281200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	65	637	0	ENST00000263388.2:c.5056G>T	p.Val1686Leu	p.V1686L	ENST00000263388	NM_000435.2	1686	Gtg/Ttg	27/33	0.208712079947904	3	FACETS	0.794	0.69	0.907	0.397	0.345	0.454	INDETERMINATE	1	TRUE	1	0.406076215169487	3		637	485	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742099	145742099	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	28	499	0	ENST00000428558.2:c.404C>G	p.Ser135Cys	p.S135C	ENST00000428558	NM_004260.3	135	tCt/tGt	5/22	0.279244919634621	3	FACETS	0.375	0.299	0.462	0.188	0.149	0.231	SUBCLONAL	1	TRUE	1	0.406076215169487	3		499	442	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0065798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	199	533	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		533	511	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827886	40827886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201911869	NA	P-0065798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	69	414	0	ENST00000373198.4:c.2542G>A	p.Gly848Arg	p.G848R	ENST00000373198	NM_133170.3	848	Gga/Aga	17/32	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		414	862	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185061	123185061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	10	199	0	ENST00000218089.9:c.1108C>T	p.Arg370Trp	p.R370W	ENST00000218089	NM_001042749.1	370	Cgg/Tgg	12/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		199	32	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670145	29670145	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	59	291	2	ENST00000356175.3:c.7121del	p.Leu2374Ter	p.L2374*	ENST00000356175	NM_000267.3	2373	cTt/ct	47/57	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		293	150	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30956843	30956866	+	inframe_deletion	In_Frame_Del	DEL	AATGCTATGCTACATTCCAATTCA	AATGCTATGCTACATTCCAATTCA	-	novel	NA	P-0065798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	205	380	0	ENST00000375687.4:c.170_193del	p.Asn57_Ser64del	p.N57_S64del	ENST00000375687	NM_015338.5	57	AATGCTATGCTACATTCCAATTCA/-	4/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		380	477	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0065799-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	95	602	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.538574620900824	2		602	285	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0065799-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	173	516	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.538574620900824	2		516	617	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725042	89725042	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1085308041	NA	P-0065799-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	50	268	0	ENST00000371953.3:c.1027-2A>G		p.X343_splice	ENST00000371953	NM_000314.4	343			1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.538574620900824	2		268	171	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692900	89692900	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1114167645	NA	P-0065799-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	57	289	0	ENST00000371953.3:c.384G>C	p.Lys128Asn	p.K128N	ENST00000371953	NM_000314.4	128	aaG/aaC	5/9	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.538574620900824	2		289	197	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778425	3778436	+	inframe_deletion	In_Frame_Del	DEL	TGTTGCTGCTGC	TGTTGCTGCTGC	-	rs750150018	NA	P-0065799-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	82	654	1	ENST00000262367.5:c.6612_6623del	p.Gln2213_Gln2216del	p.Q2213_Q2216del	ENST00000262367	NM_004380.2	2204	caGCAGCAGCAACAa/caa	31/31	1	2	FACETS	0.582	0.514	0.654	0.582	0.514	0.654	SUBCLONAL	1	TRUE	1	0.538574620900824	2		655	523	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100186	27100186	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065799-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	329	604	1	ENST00000324856.7:c.3982C>T	p.Gln1328Ter	p.Q1328*	ENST00000324856	NM_006015.4	1328	Cag/Tag	16/20	0.535647317154456	2	FACETS	0.91	0.868	0.953	0.91	0.868	0.953	CLONAL	2	TRUE	0	0.538574620900824	2		605	671	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0065820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	14	170	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.958	0.697	1	0.958	0.697	1	CLONAL	1	TRUE	1	0.201525581330216	2		170	145	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0065820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	50	388	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.201525581330216	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.201525581330216	1		388	396	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591865	48591865	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0065820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	35	450	0	ENST00000342988.3:c.1028C>G	p.Ser343Ter	p.S343*	ENST00000342988	NM_005359.5	343	tCa/tGa	9/12	0.201525581330216	1	FACETS	0.863	0.708	1	0.863	0.708	1	CLONAL	1	TRUE	0	0.201525581330216	1		450	362	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884028	37884028	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	71	544	0	ENST00000269571.5:c.3499C>G	p.Leu1167Val	p.L1167V	ENST00000269571		1167	Ctg/Gtg	27/27	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.201525581330216	2		544	638	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732266	74732266	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	67	536	0	ENST00000359995.5:c.643G>C	p.Glu215Gln	p.E215Q	ENST00000359995	NM_001195427.1	215	Gag/Cag	2/3	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.201525581330216	2		536	511	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910631	29910631	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	93	998	0	ENST00000376809.5:c.171C>G	p.Phe57Leu	p.F57L	ENST00000376809	NM_002116.7	57	ttC/ttG	2/8	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.201525581330216	2		998	914	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108079	30108079	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	31	314	0	ENST00000331968.5:c.728G>C	p.Arg243Pro	p.R243P	ENST00000331968	NM_002742.2	243	cGa/cCa	5/18	1	2	FACETS	0.983	0.797	1	0.983	0.797	1	CLONAL	1	TRUE	1	0.201525581330216	2		314	313	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560257	95560257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	46	345	0	ENST00000393063.1:c.5332G>C	p.Glu1778Gln	p.E1778Q	ENST00000393063	NM_030621.3	1778	Gag/Cag	25/28	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.201525581330216	2		345	400	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828585	72828585	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	48	534	0	ENST00000268489.5:c.7996C>G	p.Pro2666Ala	p.P2666A	ENST00000268489	NM_006885.3	2666	Ccg/Gcg	9/10	0.201525581330216	1	FACETS	0.948	0.802	1	0.948	0.802	1	CLONAL	1	TRUE	0	0.201525581330216	1		534	452	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290308	15290308	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0065820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	55	500	0	ENST00000263388.2:c.3328-1G>C		p.X1110_splice	ENST00000263388	NM_000435.2	1110			0.201525581330216	1	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	0	0.201525581330216	1		500	485	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	48	434	0	ENST00000373198.4:c.3281C>A	p.Pro1094Gln	p.P1094Q	ENST00000373198	NM_133170.3	1094	cCg/cAg	24/32	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.201525581330216	2		434	451	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158010	106158010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	63	613	0	ENST00000380013.4:c.2911G>A	p.Glu971Lys	p.E971K	ENST00000380013	NM_001127208.2	971	Gag/Aag	3/11	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.201525581330216	2		613	582	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755564	57755564	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	86	607	0	ENST00000274289.3:c.223G>A	p.Asp75Asn	p.D75N	ENST00000274289	NM_006622.3	75	Gac/Aac	1/14	1	2	FACETS	0.768	0.68	0.86	1	0.979	1	SUBCLONAL	2	TRUE	1	0.201525581330216	2		607	556	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31239534	31239534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs281860362	NA	P-0065820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	72	642	1	ENST00000376228.5:c.185G>A	p.Ser62Asn	p.S62N	ENST00000376228	NM_002117.5	62	aGc/aAc	2/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.201525581330216	2		643	573	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868507	117868507	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	25	288	0	ENST00000297338.2:c.835G>C	p.Asp279His	p.D279H	ENST00000297338	NM_006265.2	279	Gat/Cat	8/14	1	2	FACETS	0.768	0.606	0.954	0.768	0.606	0.954	CLONAL	1	TRUE	1	0.201525581330216	2		288	323	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152853834	152853834	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	24	128	0	ENST00000406277.2:c.730G>A	p.Glu244Lys	p.E244K	ENST00000406277	NM_152274.4	244	Gag/Aag	7/7	0.145522142779888	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.201525581330216	1		128	143	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579349	7579349	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1567555667	NA	P-0065824-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	235	465	0	ENST00000269305.4:c.338T>G	p.Phe113Cys	p.F113C	ENST00000269305	NM_001126112.2	113	tTc/tGc	4/11	0.536766369297951	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.536766369297951	1		465	625	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416500	49416500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065824-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	205	469	0	ENST00000301067.7:c.16211C>T	p.Ser5404Phe	p.S5404F	ENST00000301067	NM_003482.3	5404	tCc/tTc	51/54	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.536766369297951	2		469	763	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623229	52623229	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0065824-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	176	394	0	ENST00000394830.3:c.2822C>G	p.Ser941Ter	p.S941*	ENST00000394830	NM_018313.4	941	tCa/tGa	19/30	0.536766369297951	1	FACETS	0.937	0.87	1	0.937	0.87	1	CLONAL	1	TRUE	0	0.536766369297951	1		394	512	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476342	88476342	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065824-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	69	431	0	ENST00000360948.2:c.1790A>G	p.His597Arg	p.H597R	ENST00000360948	NM_001012338.2	597	cAt/cGt	15/19	0.421396736443319	1	FACETS	0.342	0.298	0.39	0.342	0.298	0.39	SUBCLONAL	1	TRUE	0	0.536766369297951	1		431	550	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539265	187539266	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0065824-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	86	480	0	ENST00000441802.2:c.8474dup	p.Ser2826LysfsTer2	p.S2826Kfs*2	ENST00000441802	NM_005245.3	2825	gga/ggGa	10/27	0.536766369297951	1	FACETS	0.445	0.394	0.499	0.445	0.394	0.499	SUBCLONAL	1	TRUE	0	0.536766369297951	1		480	527	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742994	17742994	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113719982	NA	P-0065824-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	78	480	1	ENST00000250003.3:c.902C>T	p.Pro301Leu	p.P301L	ENST00000250003	NM_002478.4	301	cCg/cTg	3/3	0.421396736443319	1	FACETS	0.287	0.251	0.325	0.287	0.251	0.325	SUBCLONAL	1	TRUE	0	0.536766369297951	1		481	742	SUCCESS
APC	324	MSKCC	GRCh37	5	112157678	112157678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878853417	NA	P-0065824-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	35	245	1	ENST00000257430.4:c.1398G>A	p.Met466Ile	p.M466I	ENST00000257430	NM_000038.5	466	atG/atA	11/16	0.421396736443319	1	FACETS	0.409	0.338	0.489	0.409	0.338	0.489	SUBCLONAL	1	TRUE	0	0.536766369297951	1		246	233	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427971	49427971	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065824-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	220	525	0	ENST00000301067.7:c.10619del	p.Lys3540ArgfsTer118	p.K3540Rfs*118	ENST00000301067	NM_003482.3	3540	aAg/ag	38/54	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.536766369297951	2		525	809	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060631	38060631	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065824-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	291	716	0	ENST00000250448.2:c.1358C>T	p.Ser453Leu	p.S453L	ENST00000250448	NM_004496.3	453	tCa/tTa	2/2	0.536766369297951	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.536766369297951	1		716	723	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310139	91310139	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0065824-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	68	145	0	ENST00000355112.3:c.2194-1G>C		p.X732_splice	ENST00000355112	NM_000057.2	732			0.421396736443319	1	FACETS	0.776	0.684	0.872	0.776	0.684	0.872	SUBCLONAL	1	TRUE	0	0.536766369297951	1		145	239	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016573	12016573	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065824-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	50	286	0	ENST00000353533.5:c.709C>A	p.Leu237Met	p.L237M	ENST00000353533	NM_003010.3	237	Ctg/Atg	7/11	0.536766369297951	1	FACETS	0.374	0.319	0.435	0.374	0.319	0.435	SUBCLONAL	1	TRUE	0	0.536766369297951	1		286	364	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67624671	67624671	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1432766010	NA	P-0065824-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	81	400	0	ENST00000272342.5:c.91G>C	p.Glu31Gln	p.E31Q	ENST00000272342	NM_019002.3	31	Gag/Cag	1/6	1	2	FACETS	0.516	0.455	0.581	0.516	0.455	0.581	SUBCLONAL	1	TRUE	1	0.536766369297951	2		400	585	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67624756	67624756	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065824-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	103	433	0	ENST00000272342.5:c.176G>C	p.Arg59Pro	p.R59P	ENST00000272342	NM_019002.3	59	cGa/cCa	1/6	1	2	FACETS	0.596	0.534	0.662	0.596	0.534	0.662	SUBCLONAL	1	TRUE	1	0.536766369297951	2		433	644	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853102	151853103	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0065824-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	88	398	0	ENST00000262189.6:c.11852_11853insAA	p.Phe3951LeufsTer37	p.F3951Lfs*37	ENST00000262189	NM_170606.2	3951	ttc/ttAAc	46/59	0.38819833197629	1	FACETS	0.366	0.324	0.41	0.366	0.324	0.41	SUBCLONAL	1	TRUE	0	0.536766369297951	1		398	656	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995601	68995601	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065824-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	30	300	0	ENST00000288368.4:c.2005C>G	p.Leu669Val	p.L669V	ENST00000288368	NM_024870.2	669	Ctt/Gtt	18/40	1	2	FACETS	0.399	0.322	0.486	0.399	0.322	0.486	SUBCLONAL	1	TRUE	1	0.536766369297951	2		300	280	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411969	63411970	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0065824-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	169	582	0	ENST00000330258.3:c.1197_1198delinsTT	p.Glu399_Glu400delinsAspTer	p.E399_E400delinsD*	ENST00000330258	NM_152424.3	399	gaGGag/gaTTag	2/2	0.421396736443319	1	FACETS	0.792	0.732	0.853	0.792	0.732	0.853	SUBCLONAL	1	TRUE	0	0.536766369297951	1		582	582	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0065825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	19	355	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.489	0.371	0.626	0.489	0.371	0.626	SUBCLONAL	1	FALSE	1	0.321307365412256	2		355	242	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0065825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	91	764	0	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	1	2	FACETS	0.678	0.602	0.761	0.678	0.602	0.761	SUBCLONAL	1	FALSE	1	0.321307365412256	2		764	835	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	62	679	0	ENST00000304494.5:c.143C>T	p.Pro48Leu	p.P48L	ENST00000304494	NM_000077.4	48	cCg/cTg	1/3	1	2	FACETS	0.644	0.556	0.74	0.644	0.556	0.74	SUBCLONAL	1	FALSE	1	0.321307365412256	2		679	599	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344287	118344287	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	66	666	0	ENST00000534358.1:c.2413C>T	p.Gln805Ter	p.Q805*	ENST00000534358	NM_005933.3	805	Cag/Tag	3/36	1	2	FACETS	0.512	0.443	0.586	0.512	0.443	0.586	SUBCLONAL	1	FALSE	1	0.321307365412256	2		666	803	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	138	430	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.273795901982073	1	FACETS	0.95	0.871	1	1	0.991	1	CLONAL	2	TRUE	0	0.273795901982073	1		430	458	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	447	910	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.108419684078361	3	FACETS	1	0.991	1	1	0.998	1	INDETERMINATE	5	TRUE	1	0.273795901982073	3		916	693	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965666	90965666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	33	386	2	ENST00000265433.3:c.1651del	p.Arg551GlyfsTer8	p.R551Gfs*8	ENST00000265433	NM_002485.4	551	Agg/gg	11/16	1	2	FACETS	0.487	0.396	0.59	0.487	0.396	0.59	SUBCLONAL	1	TRUE	1	0.273795901982073	2		388	495	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931452	131931452	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507178	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	190	390	12	ENST00000265335.6:c.2165del	p.Lys722ArgfsTer14	p.K722Rfs*14	ENST00000265335		719	ctA/ct	13/25	1	2	FACETS	1	0.981	1	1	0.994	1	CLONAL	2	TRUE	1	0.273795901982073	2		402	599	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	205	520	6	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	1	0.979	1	1	0.994	1	CLONAL	2	TRUE	1	0.273795901982073	2		526	665	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775955	9775955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	141	585	0	ENST00000377346.4:c.419G>A	p.Arg140His	p.R140H	ENST00000377346	NM_005026.3	140	cGc/cAc	5/24	1	2	FACETS	1	0.972	1	1	0.992	1	CLONAL	2	TRUE	1	0.273795901982073	2		585	455	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023016	27023016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1295137307	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	152	514	0	ENST00000324856.7:c.122C>T	p.Ala41Val	p.A41V	ENST00000324856	NM_006015.4	41	gCg/gTg	1/20	1	2	FACETS	0.853	0.787	0.92	1	0.993	1	CLONAL	3	TRUE	1	0.273795901982073	2		514	434	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150902567	150902567	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	174	388	0	ENST00000271640.5:c.385G>A	p.Asp129Asn	p.D129N	ENST00000271640	NM_001145415.1	129	Gat/Aat	3/22	1	2	FACETS	1	0.984	1	1	0.994	1	CLONAL	2	TRUE	1	0.273795901982073	2		388	520	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150912438	150912438	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	143	301	0	ENST00000271640.5:c.438del	p.Asp147ThrfsTer11	p.D147Tfs*11	ENST00000271640	NM_001145415.1	145	ccA/cc	4/22	1	2	FACETS	1	0.973	1	1	0.992	1	CLONAL	2	TRUE	1	0.273795901982073	2		301	460	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426934	70426934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241056232	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	181	469	0	ENST00000373644.4:c.4594C>T	p.Arg1532Trp	p.R1532W	ENST00000373644	NM_030625.2	1532	Cgg/Tgg	7/12	1	2	FACETS	1	0.986	1	1	0.994	1	CLONAL	2	TRUE	1	0.273795901982073	2		469	534	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256128	123256128	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	133	413	0	ENST00000358487.5:c.1781C>A	p.Pro594His	p.P594H	ENST00000358487	NM_000141.4	594	cCt/cAt	13/18	1	2	FACETS	0.911	0.832	0.994	1	0.99	1	CLONAL	2	TRUE	1	0.273795901982073	2		413	533	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998840	100998840	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	98	578	0	ENST00000325455.5:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000325455	NM_001202474.3	321	cGg/cAg	1/8	1	2	FACETS	1	0.938	1	1	0.988	1	CLONAL	2	TRUE	1	0.273795901982073	2		578	339	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	198	530	10	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	1	0.977	1	1	0.994	1	CLONAL	2	TRUE	1	0.273795901982073	2		540	649	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498154	498154	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	181	566	0	ENST00000399788.2:c.104T>C	p.Phe35Ser	p.F35S	ENST00000399788	NM_001042603.1	35	tTt/tCt	1/28	1	2	FACETS	1	0.971	1	1	0.993	1	CLONAL	2	TRUE	1	0.273795901982073	2		566	606	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480106	50480106	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	60	412	0	ENST00000394963.4:c.340C>T	p.Gln114Ter	p.Q114*	ENST00000394963	NM_003076.4	114	Cag/Tag	2/13	0.0477718009117942	4	FACETS	1	0.905	1	0.532	0.458	0.611	INDETERMINATE	1	TRUE	2	0.273795901982073	4		412	525	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	200	806	6	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	1	0.986	1	1	0.994	1	CLONAL	2	TRUE	1	0.273795901982073	2		812	600	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210819	133210819	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	92	522	0	ENST00000320574.5:c.5957del	p.Leu1986CysfsTer13	p.L1986Cfs*13	ENST00000320574	NM_006231.2	1986	tTg/tg	43/49	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.273795901982073	2		522	482	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562886	21562886	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	170	680	0	ENST00000382592.4:c.1033C>T	p.Gln345Ter	p.Q345*	ENST00000382592	NM_014572.2	345	Cag/Tag	4/8	1	2	FACETS	1	0.982	1	1	0.993	1	CLONAL	2	TRUE	1	0.273795901982073	2		680	522	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436644	110436644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	194	662	0	ENST00000375856.3:c.1757C>T	p.Pro586Leu	p.P586L	ENST00000375856	NM_003749.2	586	cCg/cTg	1/2	1	2	FACETS	0.888	0.828	0.949	1	0.995	1	CLONAL	3	TRUE	1	0.273795901982073	2		662	532	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748803	43748803	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	154	461	0	ENST00000382044.4:c.2003A>G	p.Glu668Gly	p.E668G	ENST00000382044	NM_001141980.1	668	gAg/gGg	12/28	1	2	FACETS	0.863	0.792	0.936	1	0.99	1	CLONAL	2	TRUE	1	0.273795901982073	2		461	652	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799215	88799215	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs779387312	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	68	466	0	ENST00000360948.2:c.170T>C	p.Leu57Pro	p.L57P	ENST00000360948	NM_001012338.2	57	cTg/cCg	2/19	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.273795901982073	NA		466	380	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354360	354360	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	223	472	1	ENST00000262320.3:c.1198C>T	p.Gln400Ter	p.Q400*	ENST00000262320	NM_003502.3	400	Cag/Tag	5/11	0.043976532664709	4	FACETS	1	0.981	1	1	0.993	1	INDETERMINATE	3	TRUE	2	0.273795901982073	4		473	619	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	139	511	3	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	0.273795901982073	1	FACETS	0.953	0.874	1	1	0.991	1	CLONAL	2	TRUE	0	0.273795901982073	1		514	460	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042196	14042196	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	203	493	0	ENST00000311895.7:c.2747del	p.Lys916SerfsTer4	p.K916Sfs*4	ENST00000311895	NM_005236.2	915	Aaa/aa	11/11	0.273795901982073	1	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	0	0.273795901982073	1		493	519	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831026	72831026	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs61737017	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	203	591	0	ENST00000268489.5:c.5555A>C	p.Gln1852Pro	p.Q1852P	ENST00000268489	NM_006885.3	1852	cAg/cCg	9/10	1	2	FACETS	0.852	0.796	0.91	1	0.995	1	CLONAL	3	TRUE	1	0.273795901982073	2		591	580	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81968118	81968118	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	110	395	0	ENST00000359376.3:c.2827del	p.Thr943ProfsTer5	p.T943Pfs*5	ENST00000359376	NM_002661.3	942	Aaa/aa	26/33	0.273795901982073	1	FACETS	0.834	0.755	0.916	1	0.986	1	CLONAL	2	TRUE	0	0.273795901982073	1		395	416	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618327	37618327	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	170	445	0	ENST00000447079.4:c.3G>A	p.Met1?	p.M1?	ENST00000447079	NM_015083.1	1	atG/atA	1/14	0.108419684078361	3	FACETS	0.881	0.816	0.948	1	0.987	1	INDETERMINATE	3	TRUE	1	0.273795901982073	3		445	534	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687472	37687472	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	184	525	2	ENST00000447079.4:c.4382del	p.Gly1461AlafsTer38	p.G1461Afs*38	ENST00000447079	NM_015083.1	1459	tGg/tg	14/14	0.108419684078361	3	FACETS	1	0.985	1	1	0.985	1	INDETERMINATE	2	TRUE	1	0.273795901982073	3		527	622	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40379634	40379634	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	163	389	0	ENST00000293328.3:c.198G>T	p.Gln66His	p.Q66H	ENST00000293328	NM_012448.3	66	caG/caT	3/19	0.108419684078361	3	FACETS	0.88	0.813	0.948	1	0.986	1	INDETERMINATE	3	TRUE	1	0.273795901982073	3		389	513	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453399	40453399	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs759027671	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	230	532	7	ENST00000345506.4:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000345506	NM_003152.3	366	Ccc/cc	10/20	0.108419684078361	3	FACETS	0.919	0.861	0.978	1	0.991	1	INDETERMINATE	3	TRUE	1	0.273795901982073	3		539	693	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40876402	40876402	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	205	426	0	ENST00000428826.2:c.287A>C	p.His96Pro	p.H96P	ENST00000428826		96	cAt/cCt	5/21	0.108419684078361	3	FACETS	1	0.959	1	1	0.992	1	INDETERMINATE	3	TRUE	1	0.273795901982073	3		426	549	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	200	531	3	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	0.108419684078361	3	FACETS	0.934	0.871	0.998	1	0.99	1	INDETERMINATE	3	TRUE	1	0.273795901982073	3		534	593	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604668	48604668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	172	429	0	ENST00000342988.3:c.1490G>A	p.Arg497His	p.R497H	ENST00000342988	NM_005359.5	497	cGc/cAc	12/12	0.273795901982073	1	FACETS	1	0.943	1	1	0.993	1	CLONAL	2	TRUE	0	0.273795901982073	1		429	531	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604704	48604704	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1060500744	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	158	534	1	ENST00000342988.3:c.1529del	p.Gly510AspfsTer27	p.G510Dfs*27	ENST00000342988	NM_005359.5	509	tGg/tg	12/12	0.273795901982073	1	FACETS	0.952	0.878	1	1	0.992	1	CLONAL	2	TRUE	0	0.273795901982073	1		535	523	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	113	523	1	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	0.273795901982073	1	FACETS	0.918	0.834	1	1	0.988	1	CLONAL	2	TRUE	0	0.273795901982073	1		524	388	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024683	11024683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	236	480	0	ENST00000327064.4:c.800G>A	p.Arg267His	p.R267H	ENST00000327064	NM_199141.1	267	cGc/cAc	6/16	0.0477718009117942	4	FACETS	0.88	0.827	0.934	1	0.994	1	INDETERMINATE	4	TRUE	2	0.273795901982073	4		480	624	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121173	11121173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	171	517	0	ENST00000358026.2:c.2240C>T	p.Ala747Val	p.A747V	ENST00000358026	NM_001128849.1	747	gCg/gTg	15/36	0.0477718009117942	4	FACETS	1	0.981	1	1	0.981	1	INDETERMINATE	2	TRUE	2	0.273795901982073	4		517	669	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288710	15288710	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	99	493	0	ENST00000263388.2:c.4029del	p.Cys1344ValfsTer76	p.C1344Vfs*76	ENST00000263388	NM_000435.2	1343	ccC/cc	24/33	0.273795901982073	1	FACETS	1	0.965	1	1	0.989	1	CLONAL	2	TRUE	0	0.273795901982073	1		493	274	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257082	19257082	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	31	440	0	ENST00000162023.5:c.881G>T	p.Ser294Ile	p.S294I	ENST00000162023		294	aGt/aTt	12/13	0.273795901982073	1	FACETS	0.628	0.509	0.763	0.628	0.509	0.763	SUBCLONAL	1	TRUE	0	0.273795901982073	1		440	311	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220070	36220070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	190	629	1	ENST00000222270.7:c.4790G>A	p.Arg1597Gln	p.R1597Q	ENST00000222270	NM_014727.1	1597	cGg/cAg	22/37	0.273795901982073	1	FACETS	0.993	0.923	1	1	0.993	1	CLONAL	2	TRUE	0	0.273795901982073	1		630	603	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223858	36223858	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	190	693	2	ENST00000222270.7:c.6413del	p.Pro2138ArgfsTer15	p.P2138Rfs*15	ENST00000222270	NM_014727.1	2136	ctC/ct	28/37	0.273795901982073	1	FACETS	1	0.977	1	1	0.994	1	CLONAL	2	TRUE	0	0.273795901982073	1		695	540	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140171	50140171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1437320392	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	196	594	0	ENST00000246792.3:c.254C>T	p.Ala85Val	p.A85V	ENST00000246792	NM_006270.3	85	gCg/gTg	3/6	0.108419684078361	3	FACETS	1	0.984	1	1	0.984	1	INDETERMINATE	2	TRUE	1	0.273795901982073	3		594	682	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	125	369	5	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	1	2	FACETS	1	0.95	1	1	0.991	1	CLONAL	2	TRUE	1	0.273795901982073	2		374	431	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728608	190728608	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	163	426	0	ENST00000441310.2:c.1996C>T	p.His666Tyr	p.H666Y	ENST00000441310	NM_000534.4	666	Cac/Tac	10/13	1	2	FACETS	1	0.976	1	1	0.993	1	CLONAL	2	TRUE	1	0.273795901982073	2		426	524	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422551	225422551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	103	248	0	ENST00000264414.4:c.89T>C	p.Val30Ala	p.V30A	ENST00000264414	NM_003590.4	30	gTa/gCa	2/16	0.0171375060064887	3	FACETS	1	0.97	1			1	INDETERMINATE	2	TRUE	NA	0.273795901982073	3		248	360	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29445999	29445999	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	163	555	2	ENST00000544604.2:c.1835del	p.Gly612AlafsTer54	p.G612Afs*54	ENST00000544604	NM_001206998.1	610	gcG/gc	8/9	0.273795901982073	1	FACETS	1	0.98	1	1	0.993	1	CLONAL	2	TRUE	0	0.273795901982073	1		557	444	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035100	37035100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750706	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	138	438	0	ENST00000231790.2:c.62C>T	p.Ala21Val	p.A21V	ENST00000231790	NM_000249.3	21	gCg/gTg	1/19	1	2	FACETS	0.979	0.896	1	1	0.991	1	CLONAL	2	TRUE	1	0.273795901982073	2		438	515	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165213	47165213	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	185	391	0	ENST00000409792.3:c.913del	p.Thr305GlnfsTer35	p.T305Qfs*35	ENST00000409792	NM_014159.6	305	Aca/ca	3/21	0.090222446607696	4	FACETS	1	0.96	1			1	INDETERMINATE	3	TRUE	NA	0.273795901982073	4		391	548	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70001001	70001001	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	74	389	1	ENST00000394351.3:c.598G>A	p.Ala200Thr	p.A200T	ENST00000394351	NM_000248.3	200	Gcc/Acc	6/9	1	2	FACETS	0.779	0.687	0.877	1	0.978	1	SUBCLONAL	2	TRUE	1	0.273795901982073	2		390	347	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374795	149374795	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	154	444	0	ENST00000360632.3:c.299C>T	p.Ala100Val	p.A100V	ENST00000360632	NM_015472.4	100	gCg/gTg	2/7	1	2	FACETS	1	0.983	1	1	0.993	1	CLONAL	2	TRUE	1	0.273795901982073	2		444	456	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146665	185146665	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1208061276	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	228	461	0	ENST00000265026.3:c.296A>G	p.Gln99Arg	p.Q99R	ENST00000265026	NM_004721.4	99	cAg/cGg	2/14	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	1	0.273795901982073	2		461	683	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99802232	99802232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200243582	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	29	56	0	ENST00000280892.6:c.661G>A	p.Ala221Thr	p.A221T	ENST00000280892	NM_001130678.1	221	Gca/Aca	7/7	1	2	FACETS	0.981	0.818	1	1	0.969	1	CLONAL	3	TRUE	1	0.273795901982073	2		56	72	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158446	106158447	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs748419340	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	121	431	0	ENST00000380013.4:c.3353dup	p.Asn1118LysfsTer12	p.N1118Kfs*12	ENST00000380013	NM_001127208.2	1116	ata/atAa	3/11	1	2	FACETS	1	0.93	1	1	0.99	1	CLONAL	2	TRUE	1	0.273795901982073	2		431	431	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754342	57754342	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	235	433	0	ENST00000274289.3:c.509T>A	p.Ile170Asn	p.I170N	ENST00000274289	NM_006622.3	170	aTt/aAt	4/14	1	2	FACETS	0.938	0.882	0.995	1	0.996	1	CLONAL	3	TRUE	1	0.273795901982073	2		433	610	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80160739	80160739	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	106	372	0	ENST00000265081.6:c.3108G>T	p.Glu1036Asp	p.E1036D	ENST00000265081	NM_002439.4	1036	gaG/gaT	22/24	1	2	FACETS	0.845	0.762	0.932	1	0.986	1	CLONAL	2	TRUE	1	0.273795901982073	2		372	458	SUCCESS
APC	324	MSKCC	GRCh37	5	112174982	112174982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573020080	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	48	435	0	ENST00000257430.4:c.3691C>T	p.Leu1231Phe	p.L1231F	ENST00000257430	NM_000038.5	1231	Ctc/Ttc	16/16	1	2	FACETS	0.781	0.661	0.913	0.781	0.661	0.913	CLONAL	1	TRUE	1	0.273795901982073	2		435	449	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31239494	31239494	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	132	756	0	ENST00000376228.5:c.225G>T	p.Trp75Cys	p.W75C	ENST00000376228	NM_002117.5	75	tgG/tgT	2/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.273795901982073	2		756	667	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652165	36652165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	184	537	0	ENST00000244741.5:c.287G>A	p.Gly96Asp	p.G96D	ENST00000244741	NM_000389.4	96	gGc/gAc	2/3	1	2	FACETS	1	0.973	1	1	0.994	1	CLONAL	2	TRUE	1	0.273795901982073	2		537	611	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199885	138199885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	230	571	0	ENST00000237289.4:c.1303C>T	p.Leu435Phe	p.L435F	ENST00000237289	NM_001270507.1	435	Ctc/Ttc	7/9	1	2	FACETS	1	0.981	1	1	0.995	1	CLONAL	2	TRUE	1	0.273795901982073	2		571	747	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517354	157517354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	159	356	0	ENST00000346085.5:c.3918G>A	p.Met1306Ile	p.M1306I	ENST00000346085	NM_020732.3	1306	atG/atA	16/20	1	2	FACETS	0.836	0.773	0.901	1	0.993	1	CLONAL	3	TRUE	1	0.273795901982073	2		356	463	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339935	116339935	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	232	401	0	ENST00000397752.3:c.797G>T	p.Arg266Met	p.R266M	ENST00000397752	NM_000245.2	266	aGg/aTg	2/21	1	2	FACETS	0.883	0.828	0.938	1	0.995	1	CLONAL	3	TRUE	1	0.273795901982073	2		401	640	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151946988	151946988	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	131	295	1	ENST00000262189.6:c.1786C>A	p.Leu596Ile	p.L596I	ENST00000262189	NM_170606.2	596	Ctt/Att	13/59	1	2	FACETS	0.846	0.776	0.918	1	0.992	1	CLONAL	3	TRUE	1	0.273795901982073	2		296	377	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336403	80336403	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	234	478	0	ENST00000286548.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000286548	NM_002072.3	306	Cga/Tga	7/7	1	2	FACETS	0.849	0.796	0.903	1	0.995	1	CLONAL	3	TRUE	1	0.273795901982073	2		478	671	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430562	80430562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	24	200	0	ENST00000286548.4:c.446G>A	p.Arg149Gln	p.R149Q	ENST00000286548	NM_002072.3	149	cGa/cAa	3/7	1	2	FACETS	0.581	0.456	0.724	0.581	0.456	0.724	SUBCLONAL	1	TRUE	1	0.273795901982073	2		200	302	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268793	98268793	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1554708751	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	187	497	2	ENST00000331920.6:c.290del	p.Asn97ThrfsTer20	p.N97Tfs*20	ENST00000331920	NM_000264.3	97	aAc/ac	2/24	1	2	FACETS	0.846	0.788	0.906	1	0.994	1	CLONAL	3	TRUE	1	0.273795901982073	2		499	538	SUCCESS
AR	367	MSKCC	GRCh37	X	66765119	66765119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs962089572	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	111	459	0	ENST00000374690.3:c.131C>T	p.Ala44Val	p.A44V	ENST00000374690	NM_000044.3	44	gCc/gTc	1/8	0.273795901982073	0	FACETS	0.746	0.683	0.811			1	SUBCLONAL	3	TRUE	0	0.273795901982073	0		459	263	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70362060	70362060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777818556	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	140	397	0	ENST00000374080.3:c.6526C>T	p.Arg2176Cys	p.R2176C	ENST00000374080		2176	Cgc/Tgc	45/45	0.273795901982073	0	FACETS	0.757	0.7	0.815			1	SUBCLONAL	3	TRUE	0	0.273795901982073	0		397	327	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920173	76920173	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	38	337	4	ENST00000373344.5:c.3904del	p.Arg1302GlufsTer44	p.R1302Efs*44	ENST00000373344	NM_000489.3	1302	Aga/ga	11/35	0.273795901982073	0	FACETS	0.549	0.455	0.654			1	SUBCLONAL	1	TRUE	0	0.273795901982073	0		341	367	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598066	55598066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201165084	NA	P-0065827-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	222	394	0	ENST00000288135.5:c.2263G>A	p.Ala755Thr	p.A755T	ENST00000288135	NM_000222.2	755	Gcc/Acc	16/21	0.188651519468386	3	FACETS	1	0.972	1	0.706	0.663	0.749	INDETERMINATE	2	TRUE	0	0.488647395930861	3		394	534	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218341	69218341	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065827-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	79	356	0	ENST00000462284.1:c.433G>T	p.Val145Leu	p.V145L	ENST00000462284	NM_002392.5	145	Gta/Tta	7/11	0.233045930189893	5	FACETS	1	0.969	1	0.436	0.385	0.491	INDETERMINATE	1	TRUE	2	0.488647395930861	5		356	428	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051002	180051002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs566339142	NA	P-0065827-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	324	540	0	ENST00000261937.6:c.1481C>T	p.Thr494Met	p.T494M	ENST00000261937	NM_182925.4	494	aCg/aTg	11/30	0.488647395930861	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.488647395930861	3		540	782	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	137	567	3	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.681	0.62	0.745	0.681	0.62	0.745	SUBCLONAL	1	TRUE	1	0.53974391288228	2		570	745	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	26	533	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.168	0.133	0.21	0.168	0.133	0.21	SUBCLONAL	1	TRUE	1	0.53974391288228	2		533	572	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	44	170	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.896	0.762	1	0.896	0.762	1	CLONAL	1	TRUE	1	0.53974391288228	2		170	182	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	201	583	3	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.979	0.91	1	0.979	0.91	1	CLONAL	1	TRUE	1	0.53974391288228	2		586	761	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	179	537	3	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.824	0.761	0.89	0.824	0.761	0.89	CLONAL	1	TRUE	1	0.53974391288228	2		540	805	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1749278	1749279	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	64	343	0	ENST00000378609.4:c.93_94del	p.Gln32AspfsTer46	p.Q32Dfs*46	ENST00000378609	NM_002074.3	31	tcTCag/tcag	4/12	1	2	FACETS	0.463	0.401	0.53	0.463	0.401	0.53	SUBCLONAL	1	TRUE	1	0.53974391288228	2		343	512	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	213	516	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.53974391288228	2	FACETS	1	0.938	1	0.503	0.469	0.539	CLONAL	1	TRUE	0	0.53974391288228	2		516	784	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	263	563	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.53974391288228	2		563	654	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807537	1807537	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146672976	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	185	606	0	ENST00000260795.2:c.1706C>T	p.Ala569Val	p.A569V	ENST00000260795		569	gCg/gTg	12/17	1	2	FACETS	0.963	0.892	1	0.963	0.892	1	CLONAL	1	TRUE	1	0.53974391288228	2		606	712	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671655	67671655	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1400980130	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	158	444	0	ENST00000264010.4:c.2070del	p.Glu691SerfsTer30	p.E691Sfs*30	ENST00000264010	NM_006565.3	688	gtA/gt	12/12	1	2	FACETS	0.895	0.823	0.97	0.895	0.823	0.97	CLONAL	1	TRUE	1	0.53974391288228	2		444	654	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121909229	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	184	347	0	ENST00000371953.3:c.389G>C	p.Arg130Pro	p.R130P	ENST00000371953	NM_000314.4	130	cGa/cCa	5/9	0.53974391288228	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.53974391288228	2		347	320	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778785	76778787	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1557042392	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	32	136	1	ENST00000373344.5:c.6792_6794del	p.Glu2265del	p.E2265del	ENST00000373344	NM_000489.3	2264	gaAGAg/gag	31/35	1	2	FACETS	0.354	0.288	0.429	0.354	0.288	0.429	SUBCLONAL	1	TRUE	1	0.53974391288228	2		137	335	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	214	664	3	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	0.53974391288228	2	FACETS	0.965	0.898	1	0.482	0.449	0.517	CLONAL	1	TRUE	0	0.53974391288228	2		667	822	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261555	142261555	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	25	96	0	ENST00000350721.4:c.3402del	p.Phe1134LeufsTer6	p.F1134Lfs*6	ENST00000350721	NM_001184.3	1134	ttT/tt	17/47	1	2	FACETS	0.305	0.24	0.379	0.305	0.24	0.379	SUBCLONAL	1	TRUE	1	0.53974391288228	2		96	304	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951852	2951852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770667388	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	179	428	0	ENST00000396946.4:c.3098C>T	p.Ala1033Val	p.A1033V	ENST00000396946	NM_032415.4	1033	gCg/gTg	23/25	1	2	FACETS	0.98	0.907	1	0.98	0.907	1	CLONAL	1	TRUE	1	0.53974391288228	2		428	677	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430901	181430901	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	104	697	2	ENST00000325404.1:c.758del	p.Pro253LeufsTer21	p.P253Lfs*21	ENST00000325404	NM_003106.3	251	agC/ag	1/1	1	2	FACETS	0.429	0.384	0.478	0.429	0.384	0.478	SUBCLONAL	1	TRUE	1	0.53974391288228	2		699	898	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101612	27101612	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	152	608	0	ENST00000324856.7:c.4899del	p.Met1634Ter	p.M1634*	ENST00000324856	NM_006015.4	1632	Ccc/cc	18/20	1	2	FACETS	0.726	0.665	0.79	0.726	0.665	0.79	SUBCLONAL	1	TRUE	1	0.53974391288228	2		608	776	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226627	1226627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781537	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	155	486	0	ENST00000326873.7:c.1283C>T	p.Ser428Leu	p.S428L	ENST00000326873	NM_000455.4	428	tCg/tTg	9/10	1	2	FACETS	0.977	0.898	1	0.977	0.898	1	CLONAL	1	TRUE	1	0.53974391288228	2		486	588	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023903	27023904	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	95	515	0	ENST00000324856.7:c.1015dup	p.Ala339GlyfsTer61	p.A339Gfs*61	ENST00000324856	NM_006015.4	337	tgg/tGgg	1/20	1	2	FACETS	0.704	0.629	0.783	0.704	0.629	0.783	SUBCLONAL	1	TRUE	1	0.53974391288228	2		515	500	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027676	48027678	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs587782858	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	88	333	0	ENST00000234420.5:c.2561_2563del	p.Lys854del	p.K854del	ENST00000234420	NM_000179.2	852	AAG/-	4/10	1	2	FACETS	0.627	0.557	0.701	0.627	0.557	0.701	SUBCLONAL	1	TRUE	1	0.53974391288228	2		333	520	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	183	385	0	ENST00000397062.3:c.246A>C	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaC	2/5	1	2	FACETS	0.966	0.894	1	0.966	0.894	1	CLONAL	1	TRUE	1	0.53974391288228	2		385	702	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466018	69466018	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	221	569	0	ENST00000227507.2:c.856A>G	p.Thr286Ala	p.T286A	ENST00000227507	NM_053056.2	286	Aca/Gca	5/5	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.53974391288228	2		569	809	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905061	50905061	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	125	333	0	ENST00000440232.2:c.347del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	115	Ccc/cc	4/27	1	2	FACETS	0.861	0.783	0.943	0.861	0.783	0.943	CLONAL	1	TRUE	1	0.53974391288228	2		333	538	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991949	72991949	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs753977275	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	118	506	0	ENST00000268489.5:c.2096del	p.Gly699AlafsTer125	p.G699Afs*125	ENST00000268489	NM_006885.3	699	gGc/gc	2/10	1	2	FACETS	0.647	0.584	0.713	0.647	0.584	0.713	SUBCLONAL	1	TRUE	1	0.53974391288228	2		506	676	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755553	39755554	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	63	529	0	ENST00000288319.7:c.1211dup	p.Glu405GlyfsTer61	p.E405Gfs*61	ENST00000288319	NM_182918.3	404	ccg/ccCg	10/10	1	2	FACETS	0.286	0.247	0.329	0.286	0.247	0.329	SUBCLONAL	1	TRUE	1	0.53974391288228	2		529	816	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723068	52723068	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1486388431	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	202	539	0	ENST00000322088.6:c.1253G>A	p.Arg418Gln	p.R418Q	ENST00000322088	NM_014225.5	418	cGg/cAg	10/15	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.53974391288228	2		539	730	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37628864	37628864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151307781	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	147	433	0	ENST00000249071.6:c.202C>T	p.Arg68Trp	p.R68W	ENST00000249071	NM_002872.4	68	Cgg/Tgg	3/7	1	2	FACETS	0.946	0.867	1	0.946	0.867	1	CLONAL	1	TRUE	1	0.53974391288228	2		433	576	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	95	450	2	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.43	0.382	0.481	0.43	0.382	0.481	SUBCLONAL	1	TRUE	1	0.53974391288228	2		452	819	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564491	41564491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555911073	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	40	381	0	ENST00000263253.7:c.3913C>T	p.Arg1305Cys	p.R1305C	ENST00000263253	NM_001429.3	1305	Cgt/Tgt	24/31	1	2	FACETS	0.226	0.187	0.269	0.226	0.187	0.269	SUBCLONAL	1	TRUE	1	0.53974391288228	2		381	657	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994829	73994829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751833994	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	67	241	0	ENST00000318443.5:c.313G>A	p.Ala105Thr	p.A105T	ENST00000318443	NM_001024736.1	105	Gca/Aca	3/10	1	2	FACETS	0.825	0.723	0.933	0.825	0.723	0.933	CLONAL	1	TRUE	1	0.53974391288228	2		241	301	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131495	202131495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	80	481	0	ENST00000358485.4:c.463G>A	p.Ala155Thr	p.A155T	ENST00000358485	NM_001080125.1	155	Gct/Act	2/9	1	2	FACETS	0.43	0.378	0.485	0.43	0.378	0.485	SUBCLONAL	1	TRUE	1	0.53974391288228	2		481	690	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946288	81946288	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	137	523	0	ENST00000359376.3:c.2021G>A	p.Arg674Gln	p.R674Q	ENST00000359376	NM_002661.3	674	cGa/cAa	19/33	1	2	FACETS	0.712	0.649	0.778	0.712	0.649	0.778	SUBCLONAL	1	TRUE	1	0.53974391288228	2		523	713	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158637068	158637069	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CA	CA	-	rs141073095	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	188	476	2	ENST00000263640.3:c.111_112del	p.Cys37Ter	p.C37*	ENST00000263640	NM_001105.4	37	tgTGaa/tgaa	4/11	1	2	FACETS	0.936	0.867	1	0.936	0.867	1	CLONAL	1	TRUE	1	0.53974391288228	2		478	744	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22412996	22412996	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	29	105	0	ENST00000344548.3:c.247del	p.Ser83GlnfsTer11	p.S83Qfs*11	ENST00000344548	NM_001039802.1	81	tgT/tg	5/7	1	2	FACETS	0.497	0.402	0.605	0.497	0.402	0.605	SUBCLONAL	1	TRUE	1	0.53974391288228	2		105	216	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137357	64137357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	79	435	0	ENST00000334205.4:c.1789G>A	p.Val597Ile	p.V597I	ENST00000334205	NM_003942.2	597	Gtc/Atc	14/17	1	2	FACETS	0.505	0.444	0.569	0.505	0.444	0.569	SUBCLONAL	1	TRUE	1	0.53974391288228	2		435	580	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027152	71027153	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	91	466	0	ENST00000318789.4:c.1174_1175del	p.Ser392GlnfsTer68	p.S392Qfs*68	ENST00000318789	NM_032682.5	392	TCc/c	15/21	1	2	FACETS	0.461	0.409	0.516	0.461	0.409	0.516	SUBCLONAL	1	TRUE	1	0.53974391288228	2		466	732	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040062	180040062	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376188634	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	162	541	0	ENST00000261937.6:c.3380G>A	p.Arg1127Gln	p.R1127Q	ENST00000261937	NM_182925.4	1127	cGg/cAg	25/30	0.53974391288228	2	FACETS	0.935	0.861	1	0.468	0.43	0.506	CLONAL	1	TRUE	0	0.53974391288228	2		541	642	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881596	37881596	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	46	501	0	ENST00000269571.5:c.2666T>C	p.Met889Thr	p.M889T	ENST00000269571		889	aTg/aCg	22/27	1	2	FACETS	0.246	0.206	0.29	0.246	0.206	0.29	SUBCLONAL	1	TRUE	1	0.53974391288228	2		501	693	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248011	59248011	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	231	632	0	ENST00000371222.2:c.732del	p.Ile245SerfsTer16	p.I245Sfs*16	ENST00000371222	NM_002228.3	244	ccC/cc	1/1	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.53974391288228	2		632	838	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447236	187447236	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	95	535	1	ENST00000232014.4:c.957del	p.Asn320MetfsTer4	p.N320Mfs*4	ENST00000232014	NM_001130845.1	319	ccC/cc	5/10	1	2	FACETS	0.527	0.469	0.588	0.527	0.469	0.588	SUBCLONAL	1	TRUE	1	0.53974391288228	2		536	668	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845609	63845609	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	54	390	0	ENST00000279873.7:c.1351del	p.Ser451AlafsTer28	p.S451Afs*28	ENST00000279873	NM_032199.2	450	Aaa/aa	9/10	1	2	FACETS	0.323	0.275	0.375	0.323	0.275	0.375	SUBCLONAL	1	TRUE	1	0.53974391288228	2		390	620	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47594883	47594883	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs756343868	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	120	586	0	ENST00000430070.2:c.1204del	p.Glu402ArgfsTer27	p.E402Rfs*27	ENST00000430070	NM_018095.4	402	Gag/ag	4/4	1	2	FACETS	0.547	0.494	0.603	0.547	0.494	0.603	SUBCLONAL	1	TRUE	1	0.53974391288228	2		586	813	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47492845	47492845	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	148	450	0	ENST00000404338.3:c.3949G>A	p.Val1317Met	p.V1317M	ENST00000404338	NM_004491.4	1317	Gtg/Atg	4/6	1	2	FACETS	0.896	0.822	0.974	0.896	0.822	0.974	CLONAL	1	TRUE	1	0.53974391288228	2		450	612	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150936799	150936800	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	56	491	0	ENST00000271640.5:c.3836_3837del	p.Cys1279LeufsTer6	p.C1279Lfs*6	ENST00000271640	NM_001145415.1	1279	TGt/t	22/22	0.516902061324752	3	FACETS	0.276	0.235	0.321	0.138	0.117	0.161	SUBCLONAL	1	TRUE	1	0.53974391288228	3		491	955	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318823	163318823	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	45	83	0	ENST00000271452.3:c.1213A>C	p.Ile405Leu	p.I405L	ENST00000271452	NM_145697.2	405	Att/Ctt	13/14	0.516902061324752	3	FACETS	0.685	0.579	0.802	0.343	0.289	0.401	SUBCLONAL	1	TRUE	1	0.53974391288228	3		83	309	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981489	201981489	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	69	500	0	ENST00000359651.3:c.403G>A	p.Glu135Lys	p.E135K	ENST00000359651		135	Gag/Aag	3/8	0.53974391288228	4	FACETS	0.415	0.36	0.474	0.138	0.12	0.158	SUBCLONAL	1	TRUE	1	0.53974391288228	4		500	949	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575551	64575551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1085307471	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	224	593	0	ENST00000312049.6:c.466G>A	p.Gly156Ser	p.G156S	ENST00000312049	NM_130799.2	156	Ggt/Agt	3/10	1	2	FACETS	0.993	0.926	1	0.993	0.926	1	CLONAL	1	TRUE	1	0.53974391288228	2		593	836	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518514	69518514	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	69	409	0	ENST00000294312.3:c.131T>C	p.Leu44Pro	p.L44P	ENST00000294312	NM_005117.2	44	cTg/cCg	1/3	1	2	FACETS	0.486	0.424	0.553	0.486	0.424	0.553	SUBCLONAL	1	TRUE	1	0.53974391288228	2		409	526	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962517	100962517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	116	370	0	ENST00000325455.5:c.1880G>A	p.Cys627Tyr	p.C627Y	ENST00000325455	NM_001202474.3	627	tGc/tAc	3/8	1	2	FACETS	0.806	0.73	0.887	0.806	0.73	0.887	CLONAL	1	TRUE	1	0.53974391288228	2		370	533	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160408	108160408	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1591663032	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	60	87	0	ENST00000278616.4:c.4316T>C	p.Leu1439Pro	p.L1439P	ENST00000278616	NM_000051.3	1439	cTt/cCt	29/63	1	2	FACETS	0.803	0.698	0.915	0.803	0.698	0.915	CLONAL	1	TRUE	1	0.53974391288228	2		87	277	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658336	18658336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1336348464	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	102	293	0	ENST00000266497.5:c.3141G>A	p.Met1047Ile	p.M1047I	ENST00000266497		1047	atG/atA	22/31	1	2	FACETS	0.851	0.766	0.941	0.851	0.766	0.941	CLONAL	1	TRUE	1	0.53974391288228	2		293	444	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109902	115109902	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	49	526	0	ENST00000257566.3:c.1976C>T	p.Ala659Val	p.A659V	ENST00000257566	NM_016569.3	659	gCc/gTc	8/8	1	2	FACETS	0.274	0.232	0.321	0.274	0.232	0.321	SUBCLONAL	1	TRUE	1	0.53974391288228	2		526	662	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41023338	41023338	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367685211	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	138	377	1	ENST00000267868.3:c.982G>A	p.Ala328Thr	p.A328T	ENST00000267868	NM_002875.4	328	Gcc/Acc	10/10	1	2	FACETS	0.81	0.74	0.884	0.81	0.74	0.884	CLONAL	1	TRUE	1	0.53974391288228	2		378	631	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828047	3828047	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	80	427	0	ENST00000262367.5:c.2078del	p.Pro693LeufsTer2	p.P693Lfs*2	ENST00000262367	NM_004380.2	693	cCt/ct	10/31	1	2	FACETS	0.441	0.388	0.498	0.441	0.388	0.498	SUBCLONAL	1	TRUE	1	0.53974391288228	2		427	672	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660500	67660501	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAAATGC	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	131	332	0	ENST00000264010.4:c.1401_1407dup	p.Arg470GlufsTer6	p.R470Efs*6	ENST00000264010	NM_006565.3	467	aag/aaGAAATGCg	8/12	1	2	FACETS	0.902	0.823	0.985	0.902	0.823	0.985	CLONAL	1	TRUE	1	0.53974391288228	2		332	538	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553589	29553589	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	118	274	0	ENST00000356175.3:c.2138T>C	p.Leu713Pro	p.L713P	ENST00000356175	NM_000267.3	713	cTc/cCc	18/57	1	2	FACETS	0.903	0.82	0.991	0.903	0.82	0.991	CLONAL	1	TRUE	1	0.53974391288228	2		274	484	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562645	29562645	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	111	237	0	ENST00000356175.3:c.3725T>G	p.Val1242Gly	p.V1242G	ENST00000356175	NM_000267.3	1242	gTt/gGt	28/57	1	2	FACETS	0.864	0.781	0.951	0.864	0.781	0.951	CLONAL	1	TRUE	1	0.53974391288228	2		237	476	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435455	56435455	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	185	566	0	ENST00000407977.2:c.1682G>T	p.Arg561Leu	p.R561L	ENST00000407977		561	cGg/cTg	9/10	1	2	FACETS	0.823	0.761	0.887	0.823	0.761	0.887	CLONAL	1	TRUE	1	0.53974391288228	2		566	833	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096047	11096048	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	37	519	0	ENST00000358026.2:c.326dup	p.Pro110AlafsTer19	p.P110Afs*19	ENST00000358026	NM_001128849.1	107	-/C	3/36	1	2	FACETS	0.197	0.161	0.236	0.197	0.161	0.236	SUBCLONAL	1	TRUE	1	0.53974391288228	2		519	697	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098590	11098590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1436490540	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	62	513	0	ENST00000358026.2:c.1108C>T	p.Arg370Cys	p.R370C	ENST00000358026	NM_001128849.1	370	Cgc/Tgc	6/36	1	2	FACETS	0.312	0.269	0.359	0.312	0.269	0.359	SUBCLONAL	1	TRUE	1	0.53974391288228	2		513	737	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18972888	18972888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	43	400	0	ENST00000262803.5:c.2527C>T	p.Arg843Trp	p.R843W	ENST00000262803	NM_002911.3	843	Cgg/Tgg	18/24	1	2	FACETS	0.258	0.215	0.306	0.258	0.215	0.306	SUBCLONAL	1	TRUE	1	0.53974391288228	2		400	617	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209140	36209141	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCG	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	129	579	0	ENST00000222270.7:c.222_225dup	p.Gly76ProfsTer41	p.G76Pfs*41	ENST00000222270	NM_014727.1	74	cgc/cGCCGgc	1/37	1	2	FACETS	0.755	0.686	0.827	0.755	0.686	0.827	SUBCLONAL	1	TRUE	1	0.53974391288228	2		579	633	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47601130	47601130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	104	377	0	ENST00000263735.4:c.368G>T	p.Gly123Val	p.G123V	ENST00000263735	NM_002354.2	123	gGg/gTg	3/9	1	2	FACETS	0.545	0.488	0.605	0.545	0.488	0.605	SUBCLONAL	1	TRUE	1	0.53974391288228	2		377	707	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99204040	99204040	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	69	292	0	ENST00000074304.5:c.2903C>T	p.Pro968Leu	p.P968L	ENST00000074304	NM_001134224.1	968	cCc/cTc	26/26	1	2	FACETS	0.424	0.369	0.483	0.424	0.369	0.483	SUBCLONAL	1	TRUE	1	0.53974391288228	2		292	603	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31381381	31381381	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	76	239	0	ENST00000328111.2:c.1106A>T	p.Lys369Ile	p.K369I	ENST00000328111	NM_006892.3	369	aAa/aTa	10/23	1	2	FACETS	0.722	0.637	0.813	0.722	0.637	0.813	SUBCLONAL	1	TRUE	1	0.53974391288228	2		239	390	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21349284	21349284	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	98	609	0	ENST00000215739.8:c.1911del	p.Arg638AlafsTer14	p.R638Afs*14	ENST00000215739	NM_006767.3	637	ccT/cc	16/21	1	2	FACETS	0.452	0.402	0.504	0.452	0.402	0.504	SUBCLONAL	1	TRUE	1	0.53974391288228	2		609	804	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627371	37627372	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	225	495	0	ENST00000249071.6:c.347dup	p.Leu117AlafsTer34	p.L117Afs*34	ENST00000249071	NM_002872.4	116	aag/aaAg	5/7	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.53974391288228	2		495	774	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468379	89468379	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	88	279	0	ENST00000336596.2:c.1913G>A	p.Gly638Asp	p.G638D	ENST00000336596	NM_005233.5	638	gGt/gAt	11/17	1	2	FACETS	0.663	0.589	0.741	0.663	0.589	0.741	SUBCLONAL	1	TRUE	1	0.53974391288228	2		279	492	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751137	57751137	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	153	323	0	ENST00000274289.3:c.1730A>G	p.His577Arg	p.H577R	ENST00000274289	NM_006622.3	577	cAt/cGt	12/14	0.53974391288228	2	FACETS	1	0.976	1	0.574	0.529	0.62	CLONAL	1	TRUE	0	0.53974391288228	2		323	494	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590977	67590986	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	ATTATGCATA	ATTATGCATA	-	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	143	194	0	ENST00000274335.5:c.1576_1585del	p.His526IlefsTer3	p.H526Ifs*3	ENST00000274335		524	ATTATGCATAat/at	12/15	0.53974391288228	2	FACETS	0.889	0.826	0.953	0.889	0.826	0.953	CLONAL	2	TRUE	0	0.53974391288228	2		194	298	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449583	149449583	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	59	523	0	ENST00000286301.3:c.1363C>A	p.Pro455Thr	p.P455T	ENST00000286301	NM_005211.3	455	Cct/Act	10/22	0.53974391288228	2	FACETS	0.314	0.269	0.362	0.157	0.134	0.181	SUBCLONAL	1	TRUE	0	0.53974391288228	2		523	697	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528729	157528729	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554238093	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	81	460	0	ENST00000346085.5:c.6454C>T	p.Gln2152Ter	p.Q2152*	ENST00000346085	NM_020732.3	2152	Cag/Tag	20/20	1	2	FACETS	0.464	0.409	0.523	0.464	0.409	0.523	SUBCLONAL	1	TRUE	1	0.53974391288228	2		460	647	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055722	152055722	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	22	244	0	ENST00000262189.6:c.200A>T	p.Asp67Val	p.D67V	ENST00000262189	NM_170606.2	67	gAc/gTc	2/59	1	2	FACETS	0.191	0.148	0.242	0.191	0.148	0.242	SUBCLONAL	1	TRUE	1	0.53974391288228	2		244	426	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912085	56912085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	67	227	0	ENST00000519728.1:c.1313C>T	p.Thr438Ile	p.T438I	ENST00000519728	NM_002350.3	438	aCc/aTc	12/13	1	2	FACETS	0.64	0.559	0.727	0.64	0.559	0.727	SUBCLONAL	1	TRUE	1	0.53974391288228	2		227	388	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2161735	2161735	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	141	346	0	ENST00000349721.2:c.4031A>G	p.Lys1344Arg	p.K1344R	ENST00000349721	NM_003070.3	1344	aAg/aGg	28/34	1	2	FACETS	0.824	0.753	0.898	0.824	0.753	0.898	CLONAL	1	TRUE	1	0.53974391288228	2		346	634	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347873	128347873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	97	423	0	ENST00000265960.3:c.632G>A	p.Cys211Tyr	p.C211Y	ENST00000265960	NM_001006617.1	211	tGc/tAc	5/12	1	2	FACETS	0.629	0.562	0.7	0.629	0.562	0.7	SUBCLONAL	1	TRUE	1	0.53974391288228	2		423	571	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171446	123171446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	49	75	0	ENST00000218089.9:c.363del	p.Phe121LeufsTer24	p.F121Lfs*24	ENST00000218089	NM_001042749.1	120	Ttt/tt	6/35	1	2	FACETS	0.841	0.72	0.97	0.841	0.72	0.97	CLONAL	1	TRUE	1	0.53974391288228	2		75	216	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205152	123205154	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	novel	NA	P-0065828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	38	163	0	ENST00000218089.9:c.2518_2520del	p.Asp840del	p.D840del	ENST00000218089	NM_001042749.1	838	GAT/-	25/35	1	2	FACETS	0.661	0.551	0.781	0.661	0.551	0.781	SUBCLONAL	1	TRUE	1	0.53974391288228	2		163	213	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0065830-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	299	427	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.723998097932917	4	FACETS	0.996	0.969	1	0.996	0.969	1	CLONAL	4	TRUE	0	0.770814908430647	4		427	345	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748472	162748472	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs773259518	NA	P-0065830-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	34	390	0	ENST00000367921.3:c.2386C>A	p.Gln796Lys	p.Q796K	ENST00000367921	NM_006182.2	796	Cag/Aag	17/18	0.479047383583321	3	FACETS	0.399	0.327	0.48	0.2	0.163	0.24	SUBCLONAL	1	TRUE	1	0.770814908430647	3		390	306	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004269	29004269	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs755914108	NA	P-0065830-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	12	307	0	ENST00000282397.4:c.1024C>G	p.Gln342Glu	p.Q342E	ENST00000282397	NM_002019.4	342	Cag/Gag	8/30	1	2	FACETS	0.162	0.114	0.222	0.162	0.114	0.222	SUBCLONAL	1	TRUE	1	0.770814908430647	2		307	192	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222869	5222916	+	inframe_deletion	In_Frame_Del	DEL	GGCAGGGCCCAGGGCACCGGCCTCCCGCACGGCCACCGTGTATTTGAC	GGCAGGGCCCAGGGCACCGGCCTCCCGCACGGCCACCGTGTATTTGAC	-	novel	NA	P-0065830-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	36	419	0	ENST00000357368.4:c.2887_2934del	p.Val963_Ala978del	p.V963_A978del	ENST00000357368	NM_002850.3	963	GTCAAATACACGGTGGCCGTGCGGGAGGCCGGTGCCCTGGGCCCTGCC/-	18/38	0.780760535685089	2	FACETS	0.653	0.546	0.768	0.327	0.273	0.385	SUBCLONAL	1	TRUE	0	0.770814908430647	2		419	143	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703545	47703545	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065830-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	102	396	0	ENST00000233146.2:c.2045C>G	p.Thr682Ser	p.T682S	ENST00000233146	NM_000251.2	682	aCt/aGt	13/16	0.398540224899445	5	FACETS	1	0.936	1	0.692	0.628	0.757	INDETERMINATE	2	TRUE	2	0.770814908430647	5		396	275	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622600	158622600	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065830-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	54	392	0	ENST00000263640.3:c.899T>A	p.Leu300Gln	p.L300Q	ENST00000263640	NM_001105.4	300	cTg/cAg	8/11	0.583776795001296	4	FACETS	0.684	0.586	0.789	0.342	0.293	0.395	SUBCLONAL	1	TRUE	2	0.770814908430647	4		392	363	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066608	94066633	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCCACAGGGAACACATTCGCCCTG	CTCCCACAGGGAACACATTCGCCCTG	-	novel	NA	P-0065830-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	27	433	0	ENST00000369303.4:c.1126_1151del	p.Gln376Ter	p.Q376*	ENST00000369303	NM_004440.3	376	CAGGGCGAATGTGTTCCCTGTGGGAGt/t	5/17	0.398540224899445	5	FACETS	0.538	0.429	0.661	0.179	0.143	0.221	INDETERMINATE	1	TRUE	2	0.770814908430647	5		433	281	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117870653	117870653	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065830-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	39	287	0	ENST00000297338.2:c.419T>G	p.Val140Gly	p.V140G	ENST00000297338	NM_006265.2	140	gTg/gGg	5/14	0.617388865085425	5	FACETS	0.574	0.477	0.683	0.191	0.159	0.228	SUBCLONAL	1	TRUE	2	0.770814908430647	5		287	380	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737558	145737603	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCCAGGGCCTGGCGCTCCCGGGCCTGCACACGGCCATAGAGGAA	GGGCCAGGGCCTGGCGCTCCCGGGCCTGCACACGGCCATAGAGGAA	-	novel	NA	P-0065830-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	118	596	0	ENST00000428558.2:c.3160_3205del	p.Phe1054ValfsTer12	p.F1054Vfs*12	ENST00000428558	NM_004260.3	1054	TTCCTCTATGGCCGTGTGCAGGCCCGGGAGCGCCAGGCCCTGGCCCgt/gt	19/22	0.617388865085425	5	FACETS	1	0.963	1	0.376	0.34	0.414	CLONAL	1	TRUE	2	0.770814908430647	5		596	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0065831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	65	414	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.200146900461407	2		414	517	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652251	36652251	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	36	452	0	ENST00000244741.5:c.373G>T	p.Glu125Ter	p.E125*	ENST00000244741	NM_000389.4	125	Gag/Tag	2/3	0.122687384030256	3	FACETS	0.666	0.546	0.801	0.333	0.273	0.401	SUBCLONAL	1	TRUE	1	0.200146900461407	3		452	594	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371981	55371981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1472360404	NA	P-0065831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	39	609	0	ENST00000297316.4:c.671C>T	p.Thr224Met	p.T224M	ENST00000297316	NM_022454.3	224	aCg/aTg	2/2	1	2	FACETS	0.698	0.578	0.833	0.698	0.578	0.833	SUBCLONAL	1	TRUE	1	0.200146900461407	2		609	558	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970969	21970969	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	90	583	0	ENST00000304494.5:c.389T>G	p.Leu130Arg	p.L130R	ENST00000304494	NM_000077.4	130	cTg/cGg	2/3	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.200146900461407	2		583	627	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243778453	243778453	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	24	271	0	ENST00000263826.5:c.572C>A	p.Ala191Glu	p.A191E	ENST00000263826	NM_005465.4	191	gCa/gAa	6/13	0.163961498944899	3	FACETS	0.882	0.693	1			1	CLONAL	1	TRUE	NA	0.200146900461407	3		271	299	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135986	64135986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	29	553	0	ENST00000334205.4:c.1247C>T	p.Ala416Val	p.A416V	ENST00000334205	NM_003942.2	416	gCg/gTg	11/17	1	2	FACETS	0.55	0.44	0.675	0.55	0.44	0.675	SUBCLONAL	1	TRUE	1	0.200146900461407	2		553	527	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953781	48953781	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0065831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	24	145	0	ENST00000267163.4:c.1384A>T	p.Lys462Ter	p.K462*	ENST00000267163	NM_000321.2	462	Aaa/Taa	14/27	0.200146900461407	1	FACETS	0.934	0.736	1	0.934	0.736	1	CLONAL	1	TRUE	0	0.200146900461407	1		145	231	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643510	38643510	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	33	429	0	ENST00000299084.4:c.980A>G	p.Lys327Arg	p.K327R	ENST00000299084	NM_152594.2	327	aAa/aGa	7/7	1	2	FACETS	0.605	0.492	0.733	0.605	0.492	0.733	SUBCLONAL	1	TRUE	1	0.200146900461407	2		429	545	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467174	99467174	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	26	365	0	ENST00000268035.6:c.2555G>T	p.Trp852Leu	p.W852L	ENST00000268035	NM_000875.3	852	tGg/tTg	12/21	1	2	FACETS	0.506	0.4	0.629	0.506	0.4	0.629	SUBCLONAL	1	TRUE	1	0.200146900461407	2		365	513	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020487	14020487	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913050	NA	P-0065831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	44	361	1	ENST00000311895.7:c.458G>T	p.Arg153Leu	p.R153L	ENST00000311895	NM_005236.2	153	cGc/cTc	3/11	1	2	FACETS	0.817	0.685	0.964	0.817	0.685	0.964	CLONAL	1	TRUE	1	0.200146900461407	2		362	538	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029171	14029171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	53	468	0	ENST00000311895.7:c.1382G>A	p.Arg461Lys	p.R461K	ENST00000311895	NM_005236.2	461	aGa/aAa	8/11	1	2	FACETS	0.951	0.811	1	0.951	0.811	1	CLONAL	1	TRUE	1	0.200146900461407	2		468	557	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541520	29541520	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs770201871	NA	P-0065831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	18	215	0	ENST00000356175.3:c.1444A>G	p.Thr482Ala	p.T482A	ENST00000356175	NM_000267.3	482	Aca/Gca	13/57	1	2	FACETS	0.983	0.744	1	0.983	0.744	1	CLONAL	1	TRUE	1	0.200146900461407	2		215	183	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78519566	78519566	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	42	406	0	ENST00000306801.3:c.137C>G	p.Ala46Gly	p.A46G	ENST00000306801	NM_020761.2	46	gCt/gGt	1/34	1	2	FACETS	0.867	0.724	1	0.867	0.724	1	CLONAL	1	TRUE	1	0.200146900461407	2		406	484	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145701	11145701	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	53	587	0	ENST00000358026.2:c.4063G>T	p.Glu1355Ter	p.E1355*	ENST00000358026	NM_001128849.1	1355	Gag/Tag	29/36	0.200146900461407	1	FACETS	0.835	0.712	0.97	0.835	0.712	0.97	CLONAL	1	TRUE	0	0.200146900461407	1		587	571	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936023	49936023	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	36	534	0	ENST00000296474.3:c.1647del	p.Asn550ThrfsTer32	p.N550Tfs*32	ENST00000296474	NM_002447.2	549	ggG/gg	4/20	1	2	FACETS	0.615	0.504	0.739	0.615	0.504	0.739	SUBCLONAL	1	TRUE	1	0.200146900461407	2		534	585	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259589	89259589	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	32	444	0	ENST00000336596.2:c.733A>G	p.Ser245Gly	p.S245G	ENST00000336596	NM_005233.5	245	Agt/Ggt	3/17	1	2	FACETS	0.58	0.47	0.706	0.58	0.47	0.706	SUBCLONAL	1	TRUE	1	0.200146900461407	2		444	551	SUCCESS
ATR	545	MSKCC	GRCh37	3	142224005	142224005	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	38	385	0	ENST00000350721.4:c.5172G>T	p.Arg1724Ser	p.R1724S	ENST00000350721	NM_001184.3	1724	agG/agT	29/47	1	2	FACETS	0.664	0.548	0.794	0.664	0.548	0.794	SUBCLONAL	1	TRUE	1	0.200146900461407	2		385	572	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535445	66535445	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	40	370	0	ENST00000273854.3:c.16C>A	p.Pro6Thr	p.P6T	ENST00000273854	NM_004439.5	6	Ccc/Acc	1/18	1	2	FACETS	0.934	0.777	1	0.934	0.777	1	CLONAL	1	TRUE	1	0.200146900461407	2		370	428	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80083478	80083478	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	39	351	0	ENST00000265081.6:c.2530G>T	p.Gly844Ter	p.G844*	ENST00000265081	NM_002439.4	844	Gga/Tga	18/24	1	2	FACETS	0.82	0.68	0.977	0.82	0.68	0.977	CLONAL	1	TRUE	1	0.200146900461407	2		351	475	SUCCESS
APC	324	MSKCC	GRCh37	5	112170825	112170825	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	39	361	0	ENST00000257430.4:c.1921A>T	p.Asn641Tyr	p.N641Y	ENST00000257430	NM_000038.5	641	Aat/Tat	15/16	1	2	FACETS	0.836	0.693	0.996	0.836	0.693	0.996	CLONAL	1	TRUE	1	0.200146900461407	2		361	466	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555204	106555205	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0065831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	67	443	0	ENST00000369096.4:c.2321_2322insC	p.Ser775ValfsTer19	p.S775Vfs*19	ENST00000369096	NM_001198.3	774	gtg/gtCg	7/7	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.200146900461407	2		443	613	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81399236	81399236	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs752758599	NA	P-0065831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	66	401	0	ENST00000222390.5:c.52C>A	p.His18Asn	p.H18N	ENST00000222390	NM_000601.4	18	Cat/Aat	1/18	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.200146900461407	2		401	517	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371947	55371947	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	49	567	0	ENST00000297316.4:c.637C>G	p.Pro213Ala	p.P213A	ENST00000297316	NM_022454.3	213	Ccg/Gcg	2/2	1	2	FACETS	0.82	0.694	0.959	0.82	0.694	0.959	CLONAL	1	TRUE	1	0.200146900461407	2		567	597	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87338512	87338512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	34	400	0	ENST00000277120.3:c.608C>T	p.Ala203Val	p.A203V	ENST00000277120		203	gCa/gTa	7/19	1	2	FACETS	0.642	0.524	0.776	0.642	0.524	0.776	SUBCLONAL	1	TRUE	1	0.200146900461407	2		400	529	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0065832-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	179	286	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.222416667594132	2	FACETS	0.892	0.832	0.953	1	0.993	1	CLONAL	4	TRUE	0	0.234883700373202	2		286	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0065832-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	349	467	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.235620347645488	1	FACETS	1	0.981	1	1	0.997	1	CLONAL	4	TRUE	0	0.234883700373202	1		467	629	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979319	40979319	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1217327426	NA	P-0065832-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	215	373	0	ENST00000373198.4:c.1814C>T	p.Thr605Met	p.T605M	ENST00000373198	NM_133170.3	605	aCg/aTg	11/32	NA	2	FACETS	1	0.968	1			1	INDETERMINATE	3	TRUE	NA	0.234883700373202	2		373	580	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77054949	77054949	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065832-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	209	335	0	ENST00000356341.3:c.913C>A	p.Gln305Lys	p.Q305K	ENST00000356341	NM_002576.4	305	Cag/Aag	10/15	0.199318507241166	4	FACETS	0.928	0.867	0.99	1	0.994	1	CLONAL	4	TRUE	2	0.234883700373202	4		335	592	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420197	88420197	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065832-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	199	366	0	ENST00000360948.2:c.2489C>A	p.Ala830Asp	p.A830D	ENST00000360948	NM_001012338.2	830	gCc/gAc	19/19	0.226683531524445	0	FACETS	0.854	0.798	0.91			1	CLONAL	3	TRUE	0	0.234883700373202	0		366	506	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065841-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	130	663	0				ENST00000310581	NM_198253.2	-/1132			0.173048236414618	2	FACETS	1	0.987	1	0.722	0.662	0.782	INDETERMINATE	1	TRUE	0	0.504654948589959	2		663	357	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0065841-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	376	786	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.504654948589959	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.504654948589959	2		786	679	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179050	123179050	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065841-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	142	145	0	ENST00000218089.9:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000218089	NM_001042749.1	167	Cag/Tag	8/35	1	1	FACETS	0.855	0.799	0.91	1	0.992	1	CLONAL	2	TRUE	0	0.504654948589959	1		145	246	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289323	33289323	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065841-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	121	325	0	ENST00000374542.5:c.229C>T	p.Gln77Ter	p.Q77*	ENST00000374542	NM_001141970.1	77	Cag/Tag	3/8	1	2	FACETS	0.955	0.868	1	0.955	0.868	1	CLONAL	1	TRUE	1	0.504654948589959	2		325	502	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041409	47041409	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065841-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	230	287	0	ENST00000377604.3:c.1753C>T	p.Gln585Ter	p.Q585*	ENST00000377604	NM_001204468.1	585	Cag/Tag	16/24	1	1	FACETS	0.837	0.794	0.88	1	0.995	1	CLONAL	2	TRUE	0	0.504654948589959	1		287	407	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791355	42791355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065841-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	182	526	0	ENST00000575354.2:c.415C>T	p.Arg139Trp	p.R139W	ENST00000575354	NM_015125.3	139	Cgg/Tgg	3/20	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.504654948589959	2		526	717	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196561	106196561	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1283023309	NA	P-0065841-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	301	410	0	ENST00000380013.4:c.4894C>T	p.Gln1632Ter	p.Q1632*	ENST00000380013	NM_001127208.2	1632	Caa/Taa	11/11	0.504654948589959	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.504654948589959	2		410	580	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431984	49431984	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065841-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	181	518	0	ENST00000301067.7:c.9155A>G	p.Tyr3052Cys	p.Y3052C	ENST00000301067	NM_003482.3	3052	tAt/tGt	34/54	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.504654948589959	2		518	694	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295733	15295733	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065841-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	189	445	0	ENST00000263388.2:c.2394C>A	p.Cys798Ter	p.C798*	ENST00000263388	NM_000435.2	798	tgC/tgA	15/33	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.504654948589959	2		445	626	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662262	227662262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1421163570	NA	P-0065841-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	210	549	2	ENST00000305123.5:c.1193G>A	p.Ser398Asn	p.S398N	ENST00000305123	NM_005544.2	398	aGt/aAt	1/2	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.504654948589959	2		551	754	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807660	1807660	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1176295260	NA	P-0065841-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	357	483	0	ENST00000260795.2:c.1829C>A	p.Ser610Tyr	p.S610Y	ENST00000260795		610	tCc/tAc	12/17	0.504654948589959	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.504654948589959	2		483	642	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945140	44945140	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065841-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	161	123	0	ENST00000377967.4:c.3464T>G	p.Val1155Gly	p.V1155G	ENST00000377967	NM_021140.2	1155	gTt/gGt	24/29	1	1	FACETS	0.817	0.765	0.868	1	0.992	1	CLONAL	2	TRUE	0	0.504654948589959	1		123	292	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805533	1805536	+	missense_variant	Missense_Mutation	ONP	CATC	CATC	TATT	novel	NA	P-0065841-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	385	416	0	ENST00000260795.2:c.1045_1048delinsTATT	p.His349_His350delinsTyrTyr	p.H349_H350delinsYY	ENST00000260795		349	CATCac/TATTac	7/17	0.504654948589959	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.504654948589959	2		416	681	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727514	88727514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770278704	NA	P-0065842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	120	463	4	ENST00000360948.2:c.265C>T	p.Arg89Cys	p.R89C	ENST00000360948	NM_001012338.2	89	Cgc/Tgc	3/19	1	2	FACETS	0.797	0.727	0.87	0.797	0.727	0.87	SUBCLONAL	1	TRUE	1	0.77	2		467	391	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793293	242793293	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	136	545	0	ENST00000334409.5:c.784C>T	p.Pro262Ser	p.P262S	ENST00000334409	NM_005018.2	262	Ccc/Tcc	5/5	1	2	FACETS	0.883	0.811	0.957	0.883	0.811	0.957	CLONAL	1	TRUE	1	0.77	2		545	400	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	31	663	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.57	0.46	0.694	0.57	0.46	0.694	SUBCLONAL	1	TRUE	1	0.216831599289761	2		663	502	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685307	89685307	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123317	NA	P-0065843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	23	211	0	ENST00000371953.3:c.202T>C	p.Tyr68His	p.Y68H	ENST00000371953	NM_000314.4	68	Tac/Cac	3/9	0.216831599289761	1	FACETS	0.876	0.686	1	0.876	0.686	1	CLONAL	1	TRUE	0	0.216831599289761	1		211	216	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217790	2217790	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	74	395	0	ENST00000398665.3:c.2564A>G	p.Tyr855Cys	p.Y855C	ENST00000398665	NM_032482.2	855	tAc/tGc	22/28	1	2	FACETS	0.91	0.796	1	0.91	0.796	1	CLONAL	1	TRUE	1	0.216831599289761	2		395	750	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763849	76763849	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	58	290	0	ENST00000373344.5:c.7459T>G	p.Ser2487Ala	p.S2487A	ENST00000373344	NM_000489.3	2487	Tcc/Gcc	35/35	1	2	FACETS	0.831	0.713	0.959	0.831	0.713	0.959	CLONAL	1	TRUE	1	0.216831599289761	2		290	644	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0065844-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	41	170	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		170	221	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039374	49039374	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853293	NA	P-0065844-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	278	365	0	ENST00000267163.4:c.2359C>T	p.Arg787Ter	p.R787*	ENST00000267163	NM_000321.2	787	Cga/Tga	23/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		365	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573999	7574008	+	frameshift_variant	Frame_Shift_Del	DEL	TCTCGGAACA	TCTCGGAACA	-	novel	NA	P-0065844-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	230	332	0	ENST00000269305.4:c.1019_1028del	p.Met340SerfsTer2	p.M340Sfs*2	ENST00000269305	NM_001126112.2	340	aTGTTCCGAGAg/ag	10/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		332	482	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254461	10254461	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065844-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	285	352	0	ENST00000340748.4:c.3049C>G	p.Arg1017Gly	p.R1017G	ENST00000340748		1017	Cgg/Ggg	28/40	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		352	781	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626737	28626737	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065844-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	438	318	0	ENST00000241453.7:c.559G>C	p.Glu187Gln	p.E187Q	ENST00000241453	NM_004119.2	187	Gag/Cag	5/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		318	707	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545799	41545799	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs143383109	NA	P-0065844-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	139	397	0	ENST00000263253.7:c.2414C>G	p.Ser805Cys	p.S805C	ENST00000263253	NM_001429.3	805	tCt/tGt	14/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		397	697	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548327	41548327	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065844-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	134	368	0	ENST00000263253.7:c.3115C>T	p.Pro1039Ser	p.P1039S	ENST00000263253	NM_001429.3	1039	Ccg/Tcg	16/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		368	642	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056623	26056623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs570629911	NA	P-0065844-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	271	412	0	ENST00000343677.2:c.34G>A	p.Ala12Thr	p.A12T	ENST00000343677	NM_005319.3	12	Gcg/Acg	1/1	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		412	767	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999030	100999031	+	missense_variant	Missense_Mutation	DNP	GC	GC	CT	novel	NA	P-0065845-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	98	533	0	ENST00000325455.5:c.771_772delinsAG	p.Pro258Ala	p.P258A	ENST00000325455	NM_001202474.3	257	ccGCcg/ccAGcg	1/8	1	2	FACETS	0.476	0.425	0.531	0.476	0.425	0.531	SUBCLONAL	1	TRUE	1	0.57991516105223	2		533	710	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965813	18965813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065845-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	191	440	3	ENST00000262803.5:c.1391C>T	p.Thr464Met	p.T464M	ENST00000262803	NM_002911.3	464	aCg/aTg	10/24	1	2	FACETS	0.934	0.867	1	0.934	0.867	1	CLONAL	1	TRUE	1	0.57991516105223	2		443	705	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163516	47163516	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065845-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	171	337	0	ENST00000409792.3:c.2610A>T	p.Leu870Phe	p.L870F	ENST00000409792	NM_014159.6	870	ttA/ttT	3/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.57991516105223	2		337	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0065846-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	20	622	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.321819923015625	2	FACETS	0.195	0.148	0.25	0.097	0.074	0.125	SUBCLONAL	1	TRUE	0	0.321819923015625	2		622	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0065846-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	113	472	0	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	0.321819923015625	2	FACETS	1	0.984	1	0.736	0.666	0.809	CLONAL	1	TRUE	0	0.321819923015625	2		472	477	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533500	533500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs772211333	NA	P-0065846-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	56	489	0	ENST00000451590.1:c.403C>T	p.Arg135Ter	p.R135*	ENST00000451590	NM_001130442.1	135	Cga/Tga	4/5	1	2	FACETS	0.559	0.478	0.647	0.559	0.478	0.647	SUBCLONAL	1	TRUE	1	0.321819923015625	2		489	623	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593613	55593613	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913521	NA	P-0065847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	298	315	0	ENST00000288135.5:c.1679T>A	p.Val560Asp	p.V560D	ENST00000288135	NM_000222.2	560	gTt/gAt	11/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.883949340626453	2		315	661	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770630	40770630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	46	298	0	ENST00000373198.4:c.2752G>A	p.Gly918Arg	p.G918R	ENST00000373198	NM_133170.3	918	Ggg/Agg	19/32	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		298	368	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0065848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	99	355	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		355	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578440	7578440	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs879254249	NA	P-0065848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	83	493	0	ENST00000269305.4:c.490A>G	p.Lys164Glu	p.K164E	ENST00000269305	NM_001126112.2	164	Aag/Gag	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		493	462	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003303	42003303	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0065848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	91	420	0	ENST00000219905.7:c.2840C>G	p.Ser947Ter	p.S947*	ENST00000219905	NM_001164273.1	947	tCa/tGa	8/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		420	403	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346879	89346879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760859183	NA	P-0065848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	60	529	0	ENST00000301030.4:c.6071C>T	p.Pro2024Leu	p.P2024L	ENST00000301030	NM_001256183.1	2024	cCg/cTg	9/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		529	362	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625194	69625194	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	56	469	0	ENST00000334134.2:c.599G>C	p.Arg200Thr	p.R200T	ENST00000334134	NM_005247.2	200	aGa/aCa	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		469	290	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112198	115112198	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	50	523	0	ENST00000257566.3:c.1542C>A	p.Asn514Lys	p.N514K	ENST00000257566	NM_016569.3	514	aaC/aaA	7/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		523	389	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346341	73346341	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	22	291	0	ENST00000377767.4:c.1459G>T	p.Asp487Tyr	p.D487Y	ENST00000377767	NM_014953.3	487	Gac/Tac	10/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		291	225	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291801	15291801	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	34	463	0	ENST00000263388.2:c.2965C>T	p.Leu989Phe	p.L989F	ENST00000263388	NM_000435.2	989	Ctc/Ttc	18/33	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		463	324	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443886	52443886	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	65	483	0	ENST00000460680.1:c.9G>C	p.Lys3Asn	p.K3N	ENST00000460680	NM_004656.3	3	aaG/aaC	1/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		483	433	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974648	21974738	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTGCTCCCGCTGCAGACCCTCTACCCACCTGGATCGGCCTCCGACCGTAACTATTCGGTGCGTTGGGCAGCGCCCCCGCCTCCAGCAGCG	CCTGCTCCCGCTGCAGACCCTCTACCCACCTGGATCGGCCTCCGACCGTAACTATTCGGTGCGTTGGGCAGCGCCCCCGCCTCCAGCAGCG	-	novel	NA	P-0065848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	16	487	0	ENST00000304494.5:c.89_150+29del		p.X30_splice	ENST00000304494	NM_000077.4	30		1/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		487	442	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0065849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	193	602	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.37359819953082	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.37359819953082	2		602	486	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0065849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	90	431	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.989	0.881	1	0.989	0.881	1	CLONAL	1	TRUE	1	0.37359819953082	2		431	487	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0065849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	107	475	0	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	1	2	FACETS	0.916	0.824	1	0.916	0.824	1	CLONAL	1	TRUE	1	0.37359819953082	2		475	625	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057630	27057647	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCTTTCCTACAGATTCC	TCCTTTCCTACAGATTCC	-	novel	NA	P-0065849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	93	372	0	ENST00000324856.7:c.1351-8_1360del		p.X451_splice	ENST00000324856	NM_006015.4	451		3/20	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.37359819953082	2		372	470	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106970	27107004	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTCCTGGGCTTCCTAGAGGACAGCCTTGCCGCC	ACCTCCTGGGCTTCCTAGAGGACAGCCTTGCCGCC	-	novel	NA	P-0065849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	130	538	0	ENST00000324856.7:c.6583_6617del	p.Leu2195ThrfsTer18	p.L2195Tfs*18	ENST00000324856	NM_006015.4	2194	aACCTCCTGGGCTTCCTAGAGGACAGCCTTGCCGCC/a	20/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.37359819953082	2		538	657	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136381	2136381	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs45517375	NA	P-0065850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	99	421	0	ENST00000219476.3:c.4849+1G>A		p.X1617_splice	ENST00000219476	NM_000548.3	1617			1	2	FACETS	0.802	0.716	0.893	0.802	0.716	0.893	CLONAL	1	TRUE	1	0.365290578617573	2		421	676	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623538	28623538	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	81	279	0	ENST00000241453.7:c.1019C>G	p.Ala340Gly	p.A340G	ENST00000241453	NM_004119.2	340	gCt/gGt	8/24	1	2	FACETS	0.938	0.829	1	0.938	0.829	1	CLONAL	1	TRUE	1	0.365290578617573	2		279	473	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006872	47006872	+	5_prime_UTR_variant	5'UTR	SNP	T	T	G	novel	NA	P-0065850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	92	180	0	ENST00000377604.3:c.-9T>G		p.*3*	ENST00000377604	NM_001204468.1	-/852		2/24	1	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.365290578617573	1		180	310	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138315	2138318	+	frameshift_variant	Frame_Shift_Del	DEL	CTCC	CTCC	GA	novel	NA	P-0065850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	127	510	0	ENST00000219476.3:c.5248_5251delinsGA	p.Leu1750GlufsTer24	p.L1750Efs*24	ENST00000219476	NM_000548.3	1750	CTCCgc/GAgc	41/42	1	2	FACETS	0.935	0.847	1	0.935	0.847	1	CLONAL	1	TRUE	1	0.365290578617573	2		510	744	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008412	71008412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368167189	NA	P-0065851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	49	316	0	ENST00000318789.4:c.2020G>A	p.Glu674Lys	p.E674K	ENST00000318789	NM_032682.5	674	Gag/Aag	21/21	0.654751928011681	1	FACETS	0.201	0.17	0.235	0.201	0.17	0.235	SUBCLONAL	1	TRUE	0	0.654751928011681	1		316	501	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265579	198265579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	205	257	0	ENST00000335508.6:c.2578G>A	p.Glu860Lys	p.E860K	ENST00000335508	NM_012433.2	860	Gaa/Aaa	18/25	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.654751928011681	2		257	613	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061219	38061219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	246	455	0	ENST00000250448.2:c.770G>A	p.Gly257Asp	p.G257D	ENST00000250448	NM_004496.3	257	gGc/gAc	2/2	0.648415803545754	1	FACETS	0.997	0.943	1	0.997	0.943	1	CLONAL	1	TRUE	0	0.654751928011681	1		455	507	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151932982	151932982	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs772146328	NA	P-0065851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	27	54	0	ENST00000262189.6:c.2689C>T	p.Arg897Ter	p.R897*	ENST00000262189	NM_170606.2	897	Cga/Tga	16/59	1	2	FACETS	0.589	0.475	0.715	0.589	0.475	0.715	SUBCLONAL	1	TRUE	1	0.654751928011681	2		54	140	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350447	89350447	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	247	332	1	ENST00000301030.4:c.2503G>A	p.Asp835Asn	p.D835N	ENST00000301030	NM_001256183.1	835	Gac/Aac	9/13	0.654751928011681	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.654751928011681	1		333	490	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222222	53222222	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782534108	NA	P-0065851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	256	380	0	ENST00000375401.3:c.4610C>T	p.Ser1537Leu	p.S1537L	ENST00000375401	NM_004187.3	1537	tCg/tTg	26/26	1	2	FACETS	0.964	0.906	1	0.964	0.906	1	CLONAL	1	TRUE	1	0.654751928011681	2		380	811	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870532	40870532	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	56	322	0	ENST00000428826.2:c.871C>A	p.Leu291Met	p.L291M	ENST00000428826		291	Ctg/Atg	9/21	1	2	FACETS	0.207	0.177	0.241	0.207	0.177	0.241	SUBCLONAL	1	TRUE	1	0.654751928011681	2		322	825	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94926619	94926619	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0065851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	143	176	0	ENST00000536441.1:c.144+2T>G		p.X48_splice	ENST00000536441	NM_144665.3	48			1	2	FACETS	0.958	0.88	1	0.958	0.88	1	CLONAL	1	TRUE	1	0.654751928011681	2		176	456	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51534986	51534986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1308017127	NA	P-0065851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	111	238	0	ENST00000260433.2:c.124G>A	p.Glu42Lys	p.E42K	ENST00000260433		42	Gag/Aag	2/10	1	2	FACETS	0.499	0.449	0.552	0.499	0.449	0.552	SUBCLONAL	1	TRUE	1	0.654751928011681	2		238	679	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857519	68857520	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0065851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	204	208	0	ENST00000261769.5:c.2155dup	p.Ala719GlyfsTer29	p.A719Gfs*29	ENST00000261769	NM_004360.3	718	-/G	13/16	0.654751928011681	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.654751928011681	1		208	392	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004694	16004694	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	287	298	0	ENST00000268712.3:c.2560G>T	p.Glu854Ter	p.E854*	ENST00000268712	NM_006311.3	854	Gaa/Taa	20/46	0.654751928011681	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.654751928011681	1		298	538	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022805	31022811	+	frameshift_variant	Frame_Shift_Del	DEL	CTACTGT	CTACTGT	-	novel	NA	P-0065851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	232	354	0	ENST00000375687.4:c.2291_2297del	p.Leu764ProfsTer6	p.L764Pfs*6	ENST00000375687	NM_015338.5	764	CTACTGTcc/cc	13/13	1	2	FACETS	0.917	0.858	0.977	0.917	0.858	0.977	CLONAL	1	TRUE	1	0.654751928011681	2		354	773	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177812	56177812	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	296	327	0	ENST00000399503.3:c.2785G>A	p.Glu929Lys	p.E929K	ENST00000399503	NM_005921.1	929	Gag/Aag	14/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.654751928011681	2		327	847	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930385	39930385	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	279	358	0	ENST00000378444.4:c.3079G>A	p.Glu1027Lys	p.E1027K	ENST00000378444	NM_001123385.1	1027	Gag/Aag	6/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.654751928011681	2		358	807	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0065858-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	180	644	1	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	0.216404952896364	2	FACETS	0.89	0.822	0.96	0.89	0.822	0.96	CLONAL	2	TRUE	0	0.252313689189411	2		645	802	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956164	55956164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780209077	NA	P-0065858-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	34	302	0	ENST00000263923.4:c.3151C>T	p.Arg1051Trp	p.R1051W	ENST00000263923	NM_002253.2	1051	Cgg/Tgg	23/30	0.199745727159006	2	FACETS	0.606	0.495	0.731	0.303	0.247	0.366	SUBCLONAL	1	TRUE	0	0.252313689189411	2		302	445	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349170	11349170	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065858-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	65	529	0	ENST00000332029.2:c.166C>T	p.Arg56Cys	p.R56C	ENST00000332029	NM_003745.1	56	Cgc/Tgc	2/2	1	2	FACETS	0.723	0.626	0.828	0.723	0.626	0.828	SUBCLONAL	1	TRUE	1	0.252313689189411	2		529	713	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196891	108196892	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs878853535	NA	P-0065858-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	32	285	0	ENST00000278616.4:c.6916_6917del	p.Leu2307CysfsTer65	p.L2307Cfs*65	ENST00000278616	NM_000051.3	2305	cAG/c	47/63	1	2	FACETS	0.49	0.397	0.595	0.49	0.397	0.595	SUBCLONAL	1	TRUE	1	0.252313689189411	2		285	518	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717683	89717707	+	frameshift_variant	Frame_Shift_Del	DEL	CAAGTTCATGTACTTTGAGTTCCCT	CAAGTTCATGTACTTTGAGTTCCCT	-	novel	NA	P-0065858-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	33	251	0	ENST00000371953.3:c.710_734del	p.Lys237SerfsTer11	p.K237Sfs*11	ENST00000371953	NM_000314.4	236	gaCAAGTTCATGTACTTTGAGTTCCCT/ga	7/9	0.216404952896364	2	FACETS	0.588	0.478	0.711	0.294	0.239	0.356	SUBCLONAL	1	TRUE	0	0.252313689189411	2		251	445	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180895	106180895	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065858-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	79	244	0	ENST00000380013.4:c.3923A>C	p.Lys1308Thr	p.K1308T	ENST00000380013	NM_001127208.2	1308	aAg/aCg	7/11	0.199745727159006	2	FACETS	0.751	0.664	0.844	0.751	0.664	0.844	SUBCLONAL	2	TRUE	0	0.252313689189411	2		244	417	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741178	145741178	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065858-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	226	520	0	ENST00000428558.2:c.1228G>T	p.Asp410Tyr	p.D410Y	ENST00000428558	NM_004260.3	410	Gat/Tat	6/22	0.226770850993587	4	FACETS	0.858	0.8	0.917	0.858	0.8	0.917	CLONAL	3	TRUE	1	0.252313689189411	4		520	872	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394942	394942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs944381620	NA	P-0065869-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	55	502	0	ENST00000380956.4:c.338G>A	p.Arg113Gln	p.R113Q	ENST00000380956	NM_001195286.1	113	cGg/cAg	3/9	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	FALSE	1	0.270591051180247	2		502	331	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6222578	6222578	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065869-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	22	553	0	ENST00000252674.7:c.664C>T	p.Gln222Ter	p.Q222*	ENST00000252674	NM_005934.3	222	Cag/Tag	6/12	1	2	FACETS	0.516	0.4	0.651	0.516	0.4	0.651	SUBCLONAL	1	FALSE	1	0.270591051180247	2		553	315	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065871-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	101	324	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	1	2	FACETS	0.963	0.861	1	0.963	0.861	1	CLONAL	1	TRUE	1	0.288796739614936	2		324	726	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0065871-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	154	473	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.257817107672168	2	FACETS	0.808	0.742	0.877	0.808	0.742	0.877	CLONAL	2	TRUE	0	0.288796739614936	2		473	660	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970971	21970971	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065871-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	165	665	0	ENST00000304494.5:c.387C>A	p.Tyr129Ter	p.Y129*	ENST00000304494	NM_000077.4	129	taC/taA	2/3	0.288796739614936	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.288796739614936	1		665	891	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023150	31023150	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065871-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	105	617	0	ENST00000375687.4:c.2635G>A	p.Asp879Asn	p.D879N	ENST00000375687	NM_015338.5	879	Gat/Aat	13/13	1	2	FACETS	0.888	0.795	0.986	0.888	0.795	0.986	CLONAL	1	TRUE	1	0.288796739614936	2		617	819	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941663	48941663	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065871-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	35	191	0	ENST00000267163.4:c.973T>A	p.Tyr325Asn	p.Y325N	ENST00000267163	NM_000321.2	325	Tat/Aat	10/27	0.288796739614936	1	FACETS	0.628	0.516	0.754	0.628	0.516	0.754	SUBCLONAL	1	TRUE	0	0.288796739614936	1		191	330	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683694	162683694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs566229879	NA	P-0065871-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	48	461	0	ENST00000366898.1:c.275C>T	p.Ala92Val	p.A92V	ENST00000366898	NM_004562.2	92	gCg/gTg	3/12	0.288796739614936	1	FACETS	0.459	0.388	0.539	0.459	0.388	0.539	SUBCLONAL	1	TRUE	0	0.288796739614936	1		461	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0065872-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	219	557	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.372217130453471	3	FACETS	0.835	0.786	0.884	0.835	0.786	0.884	CLONAL	3	TRUE	0	0.456884876231289	3		557	470	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0065872-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	203	631	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.456884876231289	2	FACETS	0.935	0.877	0.995	0.935	0.877	0.995	CLONAL	2	TRUE	0	0.456884876231289	2		631	475	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625348	69625348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1156753470	NA	P-0065872-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	205	623	0	ENST00000334134.2:c.445G>A	p.Ala149Thr	p.A149T	ENST00000334134	NM_005247.2	149	Gcc/Acc	3/3	0.395105228505402	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.456884876231289	3		623	508	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109879	115109879	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1268167495	NA	P-0065872-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	34	579	0	ENST00000257566.3:c.1999G>A	p.Ala667Thr	p.A667T	ENST00000257566	NM_016569.3	667	Gcg/Acg	8/8	0.456884876231289	3	FACETS	0.466	0.381	0.562	0.233	0.19	0.281	SUBCLONAL	1	TRUE	1	0.456884876231289	3		579	392	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89791101	89791101	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065872-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	33	414	0	ENST00000336032.3:c.488A>G	p.Asp163Gly	p.D163G	ENST00000336032	NM_006813.2	163	gAc/gGc	1/2	0.207708931921262	4	FACETS	0.625	0.509	0.754	0.312	0.254	0.377	INDETERMINATE	1	TRUE	2	0.456884876231289	4		414	337	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21643223	21643223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1065751	NA	P-0065873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	179	372	0	ENST00000421138.2:c.304G>A	p.Val102Ile	p.V102I	ENST00000421138		102	Gta/Ata	5/16	0.3	2	FACETS	0.938	0.872	1	0.938	0.872	1	CLONAL	2	TRUE	0	0.38	2		372	502	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346442	89346442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	73	594	2	ENST00000301030.4:c.6508G>A	p.Ala2170Thr	p.A2170T	ENST00000301030	NM_001256183.1	2170	Gcc/Acc	9/13	1	2	FACETS	0.7	0.613	0.793	0.7	0.613	0.793	SUBCLONAL	1	TRUE	1	0.38	2		596	549	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47440632	47440632	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	26	320	0	ENST00000404338.3:c.3793A>T	p.Ile1265Phe	p.I1265F	ENST00000404338	NM_004491.4	1265	Att/Ttt	2/6	1	2	FACETS	0.336	0.266	0.417	0.336	0.266	0.417	SUBCLONAL	1	TRUE	1	0.38	2		320	407	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183826	10183827	+	protein_altering_variant	In_Frame_Ins	INS	-	-	GTA	novel	NA	P-0065873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	90	513	0	ENST00000256474.2:c.295_296insGTA	p.Pro99delinsArgThr	p.P99delinsRT	ENST00000256474	NM_000551.3	99	cca/cGTAca	1/3	0.3	1	FACETS	0.927	0.827	1	0.927	0.827	1	CLONAL	1	TRUE	0	0.38	1		513	414	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065875-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	213	461	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	0.361588095546633	1	FACETS	0.762	0.712	0.814	0.762	0.712	0.814	SUBCLONAL	1	TRUE	0	0.594832657249982	1		461	660	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0065875-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	209	656	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.975	0.908	1	0.975	0.908	1	CLONAL	1	TRUE	1	0.594832657249982	2		656	721	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226330	2226330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778416555	NA	P-0065875-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	256	634	0	ENST00000326181.6:c.1943C>T	p.Ala648Val	p.A648V	ENST00000326181	NM_032271.2	648	gCg/gTg	20/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.594832657249982	2		634	753	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578471	7578471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065875-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	229	624	0	ENST00000269305.4:c.459del	p.Gly154AlafsTer16	p.G154Afs*16	ENST00000269305	NM_001126112.2	153	ccC/cc	5/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.594832657249982	2		624	712	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419949	152419949	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065875-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	184	459	0	ENST00000206249.3:c.1636G>A	p.Ala546Thr	p.A546T	ENST00000206249	NM_000125.3	546	Gcc/Acc	8/8	1	2	FACETS	0.967	0.896	1	0.967	0.896	1	CLONAL	1	TRUE	1	0.594832657249982	2		459	640	SUCCESS
APC	324	MSKCC	GRCh37	5	112137081	112137081	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0065875-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	93	343	0	ENST00000257430.4:c.834+1G>T		p.X278_splice	ENST00000257430	NM_000038.5	278			0.361588095546633	1	FACETS	0.912	0.825	1	0.912	0.825	1	CLONAL	1	TRUE	0	0.594832657249982	1		343	241	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132824	64132824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065875-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	65	559	0	ENST00000334205.4:c.958C>T	p.Pro320Ser	p.P320S	ENST00000334205	NM_003942.2	320	Ccc/Tcc	9/17	0.594832657249982	2	FACETS	0.313	0.27	0.358	0.156	0.135	0.179	SUBCLONAL	1	TRUE	0	0.594832657249982	2		559	699	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455042	50455042	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0065875-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	148	361	0	ENST00000331340.3:c.590-1G>C		p.X197_splice	ENST00000331340	NM_006060.4	197			0.594832657249982	3	FACETS	1	0.97	1	0.56	0.514	0.609	CLONAL	1	TRUE	1	0.594832657249982	3		361	576	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63898889	63898889	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	30	394	0	ENST00000398590.3:c.382del	p.Leu128SerfsTer95	p.L128Sfs*95	ENST00000398590	NM_001177387.1	128	Ctc/tc	4/14	0.200603929789722	1	FACETS	0.535	0.43	0.654	0.535	0.43	0.654	SUBCLONAL	1	TRUE	0	0.200603929789722	1		394	503	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913233	NA	P-0065877-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	57	650	0	ENST00000451590.1:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000451590	NM_001130442.1	61	cAg/cTg	3/5	1	2	FACETS	0.966	0.829	1	0.966	0.829	1	CLONAL	1	TRUE	1	0.21	2		650	562	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0065877-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	31	310	0	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	1	2	FACETS	0.879	0.712	1	0.879	0.712	1	CLONAL	1	TRUE	1	0.21	2		310	336	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0065877-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	53	575	1	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.21	2		576	464	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213956	2213957	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0065877-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	37	492	0	ENST00000398665.3:c.1773_1774del	p.Leu592ProfsTer74	p.L592Pfs*74	ENST00000398665	NM_032482.2	590	CGc/c	18/28	1	2	FACETS	0.801	0.66	0.958	0.801	0.66	0.958	CLONAL	1	TRUE	1	0.21	2		492	440	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227783	53227783	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370840799	NA	P-0065877-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	25	438	0	ENST00000375401.3:c.2405G>A	p.Arg802His	p.R802H	ENST00000375401	NM_004187.3	802	cGt/cAt	17/26	1	2	FACETS	0.51	0.401	0.636	0.51	0.401	0.636	SUBCLONAL	1	TRUE	1	0.21	2		438	467	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341609	70341609	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065877-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	45	543	0	ENST00000374080.3:c.1044C>A	p.Asp348Glu	p.D348E	ENST00000374080		348	gaC/gaA	7/45	1	2	FACETS	0.774	0.65	0.911	0.774	0.65	0.911	CLONAL	1	TRUE	1	0.21	2		543	554	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356847	70356847	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065877-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	43	547	0	ENST00000374080.3:c.5519G>T	p.Gly1840Val	p.G1840V	ENST00000374080		1840	gGc/gTc	38/45	1	2	FACETS	0.768	0.642	0.908	0.768	0.642	0.908	CLONAL	1	TRUE	1	0.21	2		547	533	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610687	81610687	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767693393	NA	P-0065903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	195	399	0	ENST00000298171.2:c.2285C>T	p.Thr762Met	p.T762M	ENST00000298171	NM_000369.2	762	aCg/aTg	10/10	1	2	FACETS	0.9	0.836	0.967	0.9	0.836	0.967	CLONAL	1	TRUE	1	0.594103302855197	2		399	729	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0065904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	154	601	2	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.490056066046698	1	FACETS	0.815	0.749	0.882	0.815	0.749	0.882	CLONAL	1	TRUE	0	0.494877023399352	1		603	575	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161814	47161815	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	59	483	0	ENST00000409792.3:c.4311dup	p.Val1438SerfsTer16	p.V1438Sfs*16	ENST00000409792	NM_014159.6	1437	-/A	3/21	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.16	2		483	729	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38135924	38135924	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	38	317	0	ENST00000317025.8:c.3767A>C	p.Glu1256Ala	p.E1256A	ENST00000317025	NM_023034.1	1256	gAg/gCg	22/24	0.142251432808593	1	FACETS	0.787	0.65	0.941	0.787	0.65	0.941	CLONAL	1	TRUE	0	0.16	1		317	555	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129632	11129632	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0065905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	55	449	0	ENST00000358026.2:c.2439-1G>A		p.X813_splice	ENST00000358026	NM_001128849.1	813			1	2	FACETS	0.955	0.815	1	0.955	0.815	1	CLONAL	1	TRUE	1	0.16	2		449	720	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967305	134967305	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	68	447	0	ENST00000398015.3:c.2644A>T	p.Ile882Phe	p.I882F	ENST00000398015	NM_004441.4	882	Atc/Ttc	14/16	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.16	2		447	806	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191508	10191509	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	T	novel	NA	P-0065905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	40	404	0	ENST00000256474.2:c.501_502delinsT	p.Ser168AlafsTer2	p.S168Afs*2	ENST00000256474	NM_000551.3	167	cgGAgc/cgTgc	3/3	1	2	FACETS	0.784	0.65	0.933	0.784	0.65	0.933	CLONAL	1	TRUE	1	0.16	2		404	638	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443599	52443601	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0065906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	76	504	0	ENST00000460680.1:c.91_93del	p.Glu31del	p.E31del	ENST00000460680	NM_004656.3	31	GAG/-	3/17	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.19	2		504	660	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850241	128850241	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	57	395	0	ENST00000249373.3:c.1504C>T	p.Gln502Ter	p.Q502*	ENST00000249373	NM_005631.4	502	Cag/Tag	9/12	0.171466859011769	3	FACETS	1	0.876	1	0.512	0.438	0.592	CLONAL	1	TRUE	1	0.19	3		395	642	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027195	48027196	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs267608083	NA	P-0065906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	38	523	0	ENST00000234420.5:c.2079dup	p.Cys694MetfsTer4	p.C694Mfs*4	ENST00000234420	NM_000179.2	691	-/A	4/10	1	2	FACETS	0.837	0.692	0.999	0.837	0.692	0.999	CLONAL	1	TRUE	1	0.19	2		523	478	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972896	25972896	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	52	432	1	ENST00000435504.4:c.1529C>A	p.Ser510Tyr	p.S510Y	ENST00000435504		510	tCt/tAt	12/13	1	2	FACETS	0.92	0.783	1	0.92	0.783	1	CLONAL	1	TRUE	1	0.19	2		433	595	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130246	2130246	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	79	507	0	ENST00000219476.3:c.3478A>G	p.Thr1160Ala	p.T1160A	ENST00000219476	NM_000548.3	1160	Act/Gct	30/42	1	2	FACETS	0.977	0.858	1	0.977	0.858	1	CLONAL	1	TRUE	1	0.19	2		507	851	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191583	10191583	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	52	389	0	ENST00000256474.2:c.578del	p.Asn193MetfsTer9	p.N193Mfs*9	ENST00000256474	NM_000551.3	192	ccA/cc	3/3	1	2	FACETS	0.667	0.566	0.778	0.667	0.566	0.778	SUBCLONAL	1	TRUE	1	0.19	2		389	821	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0065908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	273	425	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	NA	2	FACETS	0.821	0.775	0.868			1	INDETERMINATE	2	TRUE	NA	0.460991415374799	2		425	721	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435135	56435135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746854614	NA	P-0065909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	253	683	0	ENST00000407977.2:c.2002C>T	p.Arg668Trp	p.R668W	ENST00000407977		668	Cgg/Tgg	9/10	0.157203429129484	3	FACETS	0.765	0.717	0.814	0.765	0.717	0.814	INDETERMINATE	2	TRUE	1	0.44654590330889	3		683	906	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0065909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	42	170	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.44654590330889	2		170	183	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0065909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	141	417	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.44654590330889	1	FACETS	0.925	0.848	1	0.925	0.848	1	CLONAL	1	TRUE	0	0.44654590330889	1		417	530	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121333	29121333	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs756949505	NA	P-0065909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	139	359	0	ENST00000328354.6:c.342G>T	p.Trp114Cys	p.W114C	ENST00000328354	NM_007194.3	114	tgG/tgT	3/15	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.44654590330889	2		359	598	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851754	134851754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56396912	NA	P-0065909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	150	507	0	ENST00000398015.3:c.1160C>T	p.Thr387Met	p.T387M	ENST00000398015	NM_004441.4	387	aCg/aTg	5/16	1	2	FACETS	0.94	0.861	1	0.94	0.861	1	CLONAL	1	TRUE	1	0.44654590330889	2		507	715	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31239516	31239516	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs72558130	NA	P-0065909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	239	699	0	ENST00000376228.5:c.203G>C	p.Arg68Thr	p.R68T	ENST00000376228	NM_002117.5	68	aGa/aCa	2/8	1	2	FACETS	0.984	0.918	1	0.984	0.918	1	CLONAL	1	TRUE	1	0.44654590330889	2		699	1088	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989600	15989600	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0065909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	123	393	0	ENST00000268712.3:c.3173C>G	p.Ser1058Ter	p.S1058*	ENST00000268712	NM_006311.3	1058	tCa/tGa	23/46	0.44654590330889	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.44654590330889	1		393	420	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46254173	46254173	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	85	252	0	ENST00000371998.3:c.305C>G	p.Ser102Cys	p.S102C	ENST00000371998		102	tCt/tGt	5/23	1	2	FACETS	0.929	0.825	1	0.929	0.825	1	CLONAL	1	TRUE	1	0.44654590330889	2		252	410	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045756	26045756	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	220	683	0	ENST00000540144.1:c.118C>A	p.His40Asn	p.H40N	ENST00000540144	NM_003531.2	40	Cat/Aat	1/1	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.44654590330889	2		683	930	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	108	663	0				ENST00000310581	NM_198253.2	-/1132			0.601736375708799	3	FACETS	0.959	0.865	1	0.479	0.432	0.529	CLONAL	1	TRUE	1	0.601733249146895	3		663	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0065915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	497	592	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	0.601736375708799	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	0	0.601733249146895	3		592	700	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913233	NA	P-0065915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	819	650	0	ENST00000451590.1:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000451590	NM_001130442.1	61	cAg/cTg	3/5	0.586758178920048	5	FACETS	1	0.984	1	1	0.984	1	CLONAL	4	TRUE	1	0.601733249146895	5		650	1278	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942627	71942628	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0065915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	127	483	0	ENST00000298229.2:c.1583_1584delinsTT	p.Ser528Phe	p.S528F	ENST00000298229	NM_001567.3	528	tCC/tTT	13/28	0.600304917213958	4	FACETS	0.837	0.758	0.92	0.279	0.252	0.307	CLONAL	1	TRUE	1	0.601733249146895	4		483	808	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971059	21971060	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0065915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	324	556	0	ENST00000304494.5:c.297_298dup	p.Ala100GlyfsTer47	p.A100Gfs*47	ENST00000304494	NM_000077.4	100	gcc/gGGcc	2/3	0.601736375708799	2	FACETS	0.962	0.92	1	0.962	0.92	1	CLONAL	2	TRUE	0	0.601733249146895	2		556	560	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121912580	NA	P-0065916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	107	357	0	ENST00000342988.3:c.1157G>T	p.Gly386Val	p.G386V	ENST00000342988	NM_005359.5	386	gGt/gTt	10/12	0.336679939435713	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	0	0.336679939435713	1		357	472	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058039	27058040	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0065916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	134	486	0	ENST00000324856.7:c.1747_1748del	p.Gln583ValfsTer39	p.Q583Vfs*39	ENST00000324856	NM_006015.4	583	CAg/g	3/20	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	FALSE	1	0.336679939435713	2		486	784	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620415	43620415	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	81	405	0	ENST00000355710.3:c.3024G>T	p.Met1008Ile	p.M1008I	ENST00000355710	NM_020975.4	1008	atG/atT	18/20	1	2	FACETS	0.856	0.756	0.964	0.856	0.756	0.964	CLONAL	1	FALSE	1	0.336679939435713	2		405	562	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86546606	86546606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	88	471	0	ENST00000262426.4:c.1055C>T	p.Ala352Val	p.A352V	ENST00000262426	NM_001451.2	352	gCg/gTg	2/2	1	2	FACETS	0.857	0.76	0.96	0.857	0.76	0.96	CLONAL	1	FALSE	1	0.336679939435713	2		471	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579571	7579580	+	frameshift_variant	Frame_Shift_Del	DEL	GCTTGGGACG	GCTTGGGACG	-	novel	NA	P-0065916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	114	521	0	ENST00000269305.4:c.107_116del	p.Pro36GlnfsTer5	p.P36Qfs*5	ENST00000269305	NM_001126112.2	36	cCGTCCCAAGCa/ca	4/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.336679939435713	2		521	597	SUCCESS
APC	324	MSKCC	GRCh37	5	112175082	112175082	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	92	376	0	ENST00000257430.4:c.3791del	p.Val1264GlufsTer24	p.V1264Efs*24	ENST00000257430	NM_000038.5	1264	gTa/ga	16/16	0.314885441249553	1	FACETS	0.941	0.84	1	0.941	0.84	1	CLONAL	1	FALSE	0	0.336679939435713	1		376	483	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001277	150001277	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	48	459	0	ENST00000253339.5:c.2327A>C	p.Asp776Ala	p.D776A	ENST00000253339		776	gAc/gCc	4/7	0.330339073860624	1	FACETS	0.501	0.424	0.586	0.501	0.424	0.586	SUBCLONAL	1	FALSE	0	0.336679939435713	1		459	473	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0065917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	44	355	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.952	0.807	1	0.952	0.807	1	CLONAL	1	TRUE	1	0.427751892727688	2		355	216	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101300	27101300	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	308	637	0	ENST00000324856.7:c.4582C>T	p.Arg1528Ter	p.R1528*	ENST00000324856	NM_006015.4	1528	Cga/Tga	18/20	0.427751892727688	1	FACETS	0.884	0.841	0.928	1	0.996	1	CLONAL	2	TRUE	0	0.427751892727688	1		637	640	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970834	55970834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747693621	NA	P-0065917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	134	390	0	ENST00000263923.4:c.1963G>A	p.Val655Met	p.V655M	ENST00000263923	NM_002253.2	655	Gtg/Atg	13/30	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.427751892727688	2		390	590	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591259	67591259	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	102	465	0	ENST00000274335.5:c.1761del	p.Gly588ValfsTer7	p.G588Vfs*7	ENST00000274335		586	cAa/ca	13/15	1	2	FACETS	0.996	0.895	1	0.996	0.895	1	CLONAL	1	TRUE	1	0.427751892727688	2		465	479	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041266	47041266	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0065917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	184	614	1	ENST00000377604.3:c.1693+1G>A		p.X565_splice	ENST00000377604	NM_001204468.1	565			1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.427751892727688	2		615	671	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655479	67655479	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs769948988	NA	P-0065917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	80	353	0	ENST00000264010.4:c.1342C>T	p.Arg448Ter	p.R448*	ENST00000264010	NM_006565.3	448	Cga/Tga	7/12	1	2	FACETS	0.901	0.797	1	0.901	0.797	1	CLONAL	1	TRUE	1	0.427751892727688	2		353	415	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711874	89711874	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0065917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	88	315	0	ENST00000371953.3:c.493-1G>C		p.X165_splice	ENST00000371953	NM_000314.4	165			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.427751892727688	2		315	303	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617532	158617532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	166	498	1	ENST00000263640.3:c.1124G>A	p.Arg375His	p.R375H	ENST00000263640	NM_001105.4	375	cGt/cAt	9/11	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.427751892727688	2		499	762	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640455	3640455	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569194362	NA	P-0065917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	164	612	0	ENST00000294008.3:c.3184C>T	p.Arg1062Cys	p.R1062C	ENST00000294008	NM_032444.2	1062	Cgt/Tgt	12/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.427751892727688	2		612	635	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720853	89720853	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	33	165	0	ENST00000371953.3:c.1004del	p.Arg335HisfsTer9	p.R335Hfs*9	ENST00000371953	NM_000314.4	335	cGa/ca	8/9	1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	1	0.427751892727688	2		165	150	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924702	94924702	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	162	431	0	ENST00000536441.1:c.208G>C	p.Gly70Arg	p.G70R	ENST00000536441	NM_144665.3	70	Ggt/Cgt	3/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.427751892727688	2		431	622	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591117	67591118	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	99	411	0	ENST00000274335.5:c.1711dup	p.Ile571AsnfsTer31	p.I571Nfs*31	ENST00000274335		570	-/A	12/15	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.427751892727688	2		411	419	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	31	663	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.711	0.579	0.859	0.711	0.579	0.859	SUBCLONAL	1	TRUE	1	0.378946378864631	2		663	230	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0065918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	160	532	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.337385830398673	4	FACETS	0.933	0.865	1	0.933	0.865	1	CLONAL	3	TRUE	1	0.378946378864631	4		532	416	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736907	736907	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs986350587	NA	P-0065918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	33	242	0	ENST00000314574.4:c.1192C>T	p.Arg398Trp	p.R398W	ENST00000314574	NM_005433.3	398	Cgg/Tgg	10/12	1	2	FACETS	0.549	0.448	0.663	0.549	0.448	0.663	SUBCLONAL	1	TRUE	1	0.378946378864631	2		242	317	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256561	115256562	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0065918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	56	323	0	ENST00000369535.4:c.149_150delinsTT	p.Thr50Ile	p.T50I	ENST00000369535	NM_002524.4	50	aCC/aTT	3/7	1	2	FACETS	0.772	0.664	0.889	0.772	0.664	0.889	SUBCLONAL	1	TRUE	1	0.378946378864631	2		323	383	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0065918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	85	496	0	ENST00000304494.5:c.151-1G>A		p.X51_splice	ENST00000304494	NM_000077.4	51			0.378946378864631	1	FACETS	0.97	0.863	1	0.97	0.863	1	CLONAL	1	TRUE	0	0.378946378864631	1		496	375	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509636	106509636	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867282260	NA	P-0065918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	91	537	0	ENST00000359195.3:c.1630C>T	p.Arg544Ter	p.R544*	ENST00000359195	NM_002649.2	544	Cga/Tga	2/11	0.337385830398673	4	FACETS	0.926	0.822	1	0.309	0.274	0.346	CLONAL	1	TRUE	1	0.378946378864631	4		537	715	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190842	185190842	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	112	580	0	ENST00000265026.3:c.1723A>C	p.Met575Leu	p.M575L	ENST00000265026	NM_004721.4	575	Atg/Ctg	11/14	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.378946378864631	2		580	576	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707863	43707863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	97	515	0	ENST00000382044.4:c.5018G>A	p.Arg1673Lys	p.R1673K	ENST00000382044	NM_001141980.1	1673	aGa/aAa	23/28	1	2	FACETS	0.906	0.81	1	0.906	0.81	1	CLONAL	1	TRUE	1	0.378946378864631	2		515	565	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955082	55955082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	86	379	0	ENST00000263923.4:c.3463G>A	p.Glu1155Lys	p.E1155K	ENST00000263923	NM_002253.2	1155	Gag/Aag	26/30	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.378946378864631	2		379	441	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11206810	11206811	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0065918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	77	411	0	ENST00000361445.4:c.4608_4609delinsTT	p.Pro1537Ser	p.P1537S	ENST00000361445	NM_004958.3	1536	atCCct/atTTct	32/58	1	2	FACETS	0.848	0.747	0.957	0.848	0.747	0.957	CLONAL	1	TRUE	1	0.378946378864631	2		411	479	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641703	23641703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	57	300	0	ENST00000261584.4:c.1772C>T	p.Pro591Leu	p.P591L	ENST00000261584	NM_024675.3	591	cCa/cTa	5/13	1	2	FACETS	0.783	0.675	0.901	0.783	0.675	0.901	CLONAL	1	TRUE	1	0.378946378864631	2		300	384	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346148	152346148	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	84	395	0	ENST00000359321.1:c.422C>T	p.Pro141Leu	p.P141L	ENST00000359321	NM_005431.1	141	cCa/cTa	3/3	0.337385830398673	4	FACETS	0.895	0.791	1	0.298	0.263	0.336	CLONAL	1	TRUE	1	0.378946378864631	4		395	683	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954192	48954192	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	259	183	0	ENST00000267163.4:c.1393G>T	p.Glu465Ter	p.E465*	ENST00000267163	NM_000321.2	465	Gaa/Taa	15/27	0.916246230618884	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.916246230618884	2		183	276	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112326	115112326	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	440	440	0	ENST00000257566.3:c.1414G>T	p.Ala472Ser	p.A472S	ENST00000257566	NM_016569.3	472	Gcg/Tcg	7/8	0.916246230618884	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.916246230618884	3		440	688	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577157	7577157	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0065919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	653	453	0	ENST00000269305.4:c.783-2A>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.916246230618884	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.916246230618884	3		453	679	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165603	118165603	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	547	466	1	ENST00000369448.3:c.113G>T	p.Arg38Leu	p.R38L	ENST00000369448	NM_017709.3	38	cGa/cTa	2/2	0.497375111053987	4	FACETS	0.871	0.843	0.898	0.871	0.843	0.898	INDETERMINATE	3	TRUE	1	0.916246230618884	4		467	876	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606731	43606731	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1588871155	NA	P-0065919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	232	560	1	ENST00000355710.3:c.1340C>A	p.Ala447Asp	p.A447D	ENST00000355710	NM_020975.4	447	gCc/gAc	7/20	1	2	FACETS	0.947	0.891	1	0.947	0.891	1	CLONAL	1	TRUE	1	0.916246230618884	2		561	535	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943716	71943716	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	266	496	0	ENST00000298229.2:c.1759G>T	p.Asp587Tyr	p.D587Y	ENST00000298229	NM_001567.3	587	Gac/Tac	15/28	0.916246230618884	3	FACETS	0.927	0.871	0.985	0.464	0.435	0.493	CLONAL	1	TRUE	1	0.916246230618884	3		496	913	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420282	88420282	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	513	446	1	ENST00000360948.2:c.2404G>T	p.Val802Phe	p.V802F	ENST00000360948	NM_001012338.2	802	Gtc/Ttc	19/19	0.497375111053987	4	FACETS	0.882	0.853	0.91	0.882	0.853	0.91	INDETERMINATE	3	TRUE	1	0.916246230618884	4		447	811	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46266508	46266511	+	frameshift_variant	Frame_Shift_Del	DEL	TCAA	TCAA	-	novel	NA	P-0065919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	458	373	0	ENST00000371998.3:c.2493_2496del	p.Phe831LeufsTer8	p.F831Lfs*8	ENST00000371998		831	ttTCAA/tt	13/23	0.916246230618884	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.916246230618884	3		373	709	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045756	143045756	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	181	327	0	ENST00000262992.4:c.1878C>G	p.Ile626Met	p.I626M	ENST00000262992	NM_001101669.1	626	atC/atG	17/24	0.916246230618884	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.916246230618884	1		327	201	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686805	117686806	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0065919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	192	395	0	ENST00000368508.3:c.2911_2912delinsAT	p.Gly971Ile	p.G971I	ENST00000368508	NM_002944.2	971	GGt/ATt	19/43	0.916246230618884	3	FACETS	0.964	0.896	1	0.482	0.448	0.517	CLONAL	1	TRUE	1	0.916246230618884	3		395	634	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952136	76952136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs782377443	NA	P-0065919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	350	280	0	ENST00000373344.5:c.299A>G	p.Asp100Gly	p.D100G	ENST00000373344	NM_000489.3	100	gAt/gGt	5/35	0.804224601964663	4	FACETS	0.966	0.921	1	0.966	0.921	1	CLONAL	2	TRUE	2	0.916246230618884	4		280	758	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034356	123034356	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	274	277	0	ENST00000355640.3:c.1114del	p.Gln372LysfsTer21	p.Q372Kfs*21	ENST00000355640		371	ttC/tt	6/7	0.804224601964663	4	FACETS	0.843	0.796	0.89	0.843	0.796	0.89	CLONAL	2	TRUE	2	0.916246230618884	4		277	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0065920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	192	509	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.351770057135214	2	FACETS	0.796	0.74	0.853	0.796	0.74	0.853	SUBCLONAL	2	TRUE	0	0.391715907291681	2		509	616	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41219635	41219637	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	rs80358344	NA	P-0065920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	159	272	0	ENST00000357654.3:c.5062_5064del	p.Val1688del	p.V1688del	ENST00000357654	NM_007294.3	1688	GTT/-	16/23	0.318854310815578	3	FACETS	1	0.981	1	0.787	0.73	0.846	CLONAL	2	TRUE	0	0.391715907291681	3		272	411	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104588	69104588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143014630	NA	P-0065920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	75	372	0	ENST00000288368.4:c.4432G>A	p.Ala1478Thr	p.A1478T	ENST00000288368	NM_024870.2	1478	Gct/Act	37/40	0.317218868929416	3	FACETS	0.884	0.776	1	0.442	0.388	0.5	CLONAL	1	TRUE	1	0.391715907291681	3		372	518	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089691	27089691	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	101	512	0	ENST00000324856.7:c.2647A>C	p.Met883Leu	p.M883L	ENST00000324856	NM_006015.4	883	Atg/Ctg	8/20	0.317218868929416	3	FACETS	0.819	0.732	0.911	0.409	0.366	0.456	CLONAL	1	TRUE	1	0.391715907291681	3		512	753	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852414	63852469	+	frameshift_variant	Frame_Shift_Del	DEL	CGGATCAGAAGGCCACAAGCTTCCCCTCTCCTCCCCTATCTTCCCAGGTCTGTATT	CGGATCAGAAGGCCACAAGCTTCCCCTCTCCTCCCCTATCTTCCCAGGTCTGTATT	-	novel	NA	P-0065920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	150	414	0	ENST00000279873.7:c.3193_3248del	p.Gly1065ArgfsTer5	p.G1065Rfs*5	ENST00000279873	NM_032199.2	1064	ggCGGATCAGAAGGCCACAAGCTTCCCCTCTCCTCCCCTATCTTCCCAGGTCTGTATTcc/ggcc	10/10	0.295865528310504	4	FACETS	1	0.986	1	0.711	0.65	0.773	CLONAL	1	TRUE	2	0.391715907291681	4		414	750	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559705	29559740	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTATTTCTCAGATACTTCACATTATTTATGAACC	TTTTATTTCTCAGATACTTCACATTATTTATGAACC	-	novel	NA	P-0065920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	61	294	0	ENST00000356175.3:c.3315-9_3341del		p.X1105_splice	ENST00000356175	NM_000267.3	1105		26/57	0.335367070627329	1	FACETS	0.803	0.697	0.915	0.803	0.697	0.915	CLONAL	1	TRUE	0	0.391715907291681	1		294	312	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006783	47006783	+	5_prime_UTR_variant	5'UTR	SNP	T	T	G	novel	NA	P-0065920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	95	378	0	ENST00000377604.3:c.-98T>G		p.*33*	ENST00000377604	NM_001204468.1	-/852		2/24	0.310941906508877	2	FACETS	1	0.913	1	0.512	0.457	0.569	CLONAL	1	TRUE	0	0.391715907291681	2		378	474	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426496	47426496	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	82	547	0	ENST00000377045.4:c.839A>T	p.Glu280Val	p.E280V	ENST00000377045	NM_001654.4	280	gAg/gTg	9/16	0.310941906508877	2	FACETS	0.671	0.592	0.756	0.335	0.296	0.378	SUBCLONAL	1	TRUE	0	0.391715907291681	2		547	624	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0065921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	79	491	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.311657842124859	2		491	465	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0065921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	120	430	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.311657842124859	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.311657842124859	1		430	637	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002940	69002940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	90	362	0	ENST00000288368.4:c.2240G>A	p.Arg747Gln	p.R747Q	ENST00000288368	NM_024870.2	747	cGg/cAg	20/40	0.311657842124859	3	FACETS	0.962	0.854	1	0.481	0.427	0.539	CLONAL	1	TRUE	1	0.311657842124859	3		362	694	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577145	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTAGAT	novel	NA	P-0065921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	106	491	0	ENST00000269305.4:c.788_793dup	p.Leu264_Leu265insHisLeu	p.L264_L265insHL	ENST00000269305	NM_001126112.2	265	ctg/cATCTACtg	8/11	0.311657842124859	1	FACETS	0.949	0.853	1	0.949	0.853	1	CLONAL	1	TRUE	0	0.311657842124859	1		491	605	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229686	5229686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1393421847	NA	P-0065921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	69	351	0	ENST00000357368.4:c.2165C>T	p.Ala722Val	p.A722V	ENST00000357368	NM_002850.3	722	gCg/gTg	15/38	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.311657842124859	2		351	438	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	203	663	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		663	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0065922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	406	575	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		575	595	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880257	37880257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	269	593	0	ENST00000269571.5:c.2301C>G	p.Ile767Met	p.I767M	ENST00000269571		767	atC/atG	19/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		593	663	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100442	8100442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	230	623	0	ENST00000346208.3:c.416C>T	p.Ser139Phe	p.S139F	ENST00000346208		139	tCc/tTc	3/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		623	731	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099397	27099397	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	264	472	0	ENST00000324856.7:c.3634C>T	p.Gln1212Ter	p.Q1212*	ENST00000324856	NM_006015.4	1212	Cag/Tag	14/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		472	528	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489535	56489535	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	265	491	0	ENST00000267101.3:c.2000G>T	p.Arg667Leu	p.R667L	ENST00000267101	NM_001982.3	667	cGt/cTt	17/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		491	534	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650814	93650814	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	19	387	0	ENST00000375746.1:c.1740A>C	p.Glu580Asp	p.E580D	ENST00000375746	NM_001174167.1	580	gaA/gaC	13/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		387	360	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050841	49050845	+	frameshift_variant	Frame_Shift_Del	DEL	CTGAG	CTGAG	-	novel	NA	P-0065922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	88	278	0	ENST00000267163.4:c.2525_2529del	p.Ser842Ter	p.S842*	ENST00000267163	NM_000321.2	842	tCTGAG/t	25/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		278	261	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660566	67660566	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	244	392	0	ENST00000264010.4:c.1466A>G	p.His489Arg	p.H489R	ENST00000264010	NM_006565.3	489	cAc/cGc	8/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		392	444	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561447	9561447	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	69	535	0	ENST00000353224.5:c.335C>A	p.Ala112Asp	p.A112D	ENST00000353224	NM_177990.2	112	gCc/gAc	4/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		535	726	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672339	30672339	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	54	699	0	ENST00000376406.3:c.4621A>C	p.Thr1541Pro	p.T1541P	ENST00000376406	NM_014641.2	1541	Acc/Ccc	10/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		699	932	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396852	139396852	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	113	428	0	ENST00000277541.6:c.5256C>A	p.Cys1752Ter	p.C1752*	ENST00000277541	NM_017617.3	1752	tgC/tgA	28/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		428	566	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400132	139400132	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs750536515	NA	P-0065922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	216	504	0	ENST00000277541.6:c.4216A>T	p.Thr1406Ser	p.T1406S	ENST00000277541	NM_017617.3	1406	Aca/Tca	25/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		504	656	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0065928-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	183	622	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.159115072153218	2	FACETS	0.762	0.703	0.823	0.762	0.703	0.823	SUBCLONAL	2	TRUE	0	0.245181711155053	2		622	980	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0065928-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	154	631	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.245181711155053	2	FACETS	0.848	0.777	0.921	0.848	0.777	0.921	CLONAL	2	TRUE	0	0.245181711155053	2		631	741	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850736	63850736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149466999	NA	P-0065928-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	167	544	0	ENST00000279873.7:c.1514C>T	p.Ala505Val	p.A505V	ENST00000279873	NM_032199.2	505	gCg/gTg	10/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.245181711155053	2		544	917	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029445	16029446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065928-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	91	283	0	ENST00000268712.3:c.1584dup	p.Glu529ArgfsTer7	p.E529Rfs*7	ENST00000268712	NM_006311.3	528	-/A	15/46	0.159115072153218	2	FACETS	0.775	0.691	0.864	0.775	0.691	0.864	SUBCLONAL	2	TRUE	0	0.245181711155053	2		283	479	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920422	114920422	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065928-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	131	373	0	ENST00000543371.1:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000543371	NM_001198531.1	455	Cga/Tga	13/14	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.245181711155053	2		373	759	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366308	15366308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065928-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	122	485	0	ENST00000263377.2:c.1847G>A	p.Arg616Gln	p.R616Q	ENST00000263377	NM_058243.2	616	cGg/cAg	10/20	0.108890274682769	4	FACETS	1	0.983	1	0.721	0.652	0.795	INDETERMINATE	1	TRUE	2	0.245181711155053	4		485	859	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575186	48575186	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065928-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	88	302	0	ENST00000342988.3:c.380G>C	p.Cys127Ser	p.C127S	ENST00000342988	NM_005359.5	127	tGt/tCt	3/12	0.165583749808426	2	FACETS	0.816	0.726	0.91	0.816	0.726	0.91	CLONAL	2	TRUE	0	0.245181711155053	2		302	440	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0065930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	45	132	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.586	0.5	0.678	0.586	0.5	0.678	SUBCLONAL	1	TRUE	1	0.872104098164122	2		132	176	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928067	178928093	+	inframe_deletion	In_Frame_Del	DEL	CCTCATGGATTAGAAGATTTGCTGAAC	CCTCATGGATTAGAAGATTTGCTGAAC	-	novel	NA	P-0065930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	88	209	0	ENST00000263967.3:c.1348_1374del	p.His450_Pro458del	p.H450_P458del	ENST00000263967	NM_006218.2	449	CCTCATGGATTAGAAGATTTGCTGAAC/-	8/21	1	2	FACETS	0.582	0.52	0.647	0.582	0.52	0.647	SUBCLONAL	1	TRUE	1	0.872104098164122	2		209	347	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524749	187524749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372461501	NA	P-0065930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	32	420	0	ENST00000441802.2:c.10931C>T	p.Ala3644Val	p.A3644V	ENST00000441802	NM_005245.3	3644	gCg/gTg	19/27	NA	2	FACETS	0.117	0.095	0.143			1	INDETERMINATE	1	TRUE	NA	0.872104098164122	2		420	625	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644849	67644849	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	179	509	0	ENST00000264010.4:c.115del	p.His39ThrfsTer23	p.H39Tfs*23	ENST00000264010	NM_006565.3	38	tgC/tg	3/12	0.472403549374927	1	FACETS	0.381	0.353	0.41	0.381	0.353	0.41	INDETERMINATE	1	TRUE	0	0.872104098164122	1		509	607	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827875	72827876	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0065930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	153	388	0	ENST00000268489.5:c.8705dup	p.Tyr2902Ter	p.Y2902*	ENST00000268489	NM_006885.3	2902	tat/taAt	9/10	0.472403549374927	1	FACETS	0.393	0.361	0.425	0.393	0.361	0.425	INDETERMINATE	1	TRUE	0	0.872104098164122	1		388	504	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521281	187521281	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	139	459	0	ENST00000441802.2:c.11874G>T	p.Gln3958His	p.Q3958H	ENST00000441802	NM_005245.3	3958	caG/caT	22/27	NA	2	FACETS	0.554	0.507	0.604			1	INDETERMINATE	1	TRUE	NA	0.872104098164122	2		459	575	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178000	56178034	+	frameshift_variant	Frame_Shift_Del	DEL	ATCTGTACCAGCTGGCACTGCAACAGATGTCTCTA	ATCTGTACCAGCTGGCACTGCAACAGATGTCTCTA	-	novel	NA	P-0065930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	119	443	0	ENST00000399503.3:c.2974_3008del	p.Ser992AlafsTer2	p.S992Afs*2	ENST00000399503	NM_005921.1	991	ccATCTGTACCAGCTGGCACTGCAACAGATGTCTCTAag/ccag	14/20	1	2	FACETS	0.536	0.486	0.588	0.536	0.486	0.588	SUBCLONAL	1	TRUE	1	0.872104098164122	2		443	509	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180633	56180633	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	60	214	0	ENST00000399503.3:c.3962T>C	p.Leu1321Pro	p.L1321P	ENST00000399503	NM_005921.1	1321	cTc/cCc	16/20	1	2	FACETS	0.573	0.5	0.651	0.573	0.5	0.651	SUBCLONAL	1	TRUE	1	0.872104098164122	2		214	240	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151919086	151919086	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	44	138	0	ENST00000262189.6:c.3499G>C	p.Asp1167His	p.D1167H	ENST00000262189	NM_170606.2	1167	Gac/Cac	22/59	1	2	FACETS	0.5	0.424	0.581	0.5	0.424	0.581	SUBCLONAL	1	TRUE	1	0.872104098164122	2		138	202	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183797	10183797	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs5030807	NA	P-0065931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	53	464	0	ENST00000256474.2:c.266T>A	p.Leu89His	p.L89H	ENST00000256474	NM_000551.3	89	cTc/cAc	1/3	0.202258881195701	1	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	0	0.19	1		464	481	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626932	14626932	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	79	601	0	ENST00000254322.2:c.843A>G	p.Ile281Met	p.I281M	ENST00000254322	NM_006145.1	281	atA/atG	3/3	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.19	2		601	756	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643720	52643722	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	novel	NA	P-0065931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	47	382	0	ENST00000394830.3:c.2174_2176del	p.Val725del	p.V725del	ENST00000394830	NM_018313.4	725	gTTGag/gag	17/30	0.202258881195701	1	FACETS	0.88	0.742	1	0.88	0.742	1	CLONAL	1	TRUE	0	0.19	1		382	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577543	7577544	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065932-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	257	381	0	ENST00000269305.4:c.737dup	p.Met246IlefsTer18	p.M246Ifs*18	ENST00000269305	NM_001126112.2	246	atg/atTg	7/11	0.7092331963407	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.7092331963407	1		381	450	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841342	15841342	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367855979	NA	P-0065932-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	249	379	0	ENST00000307771.7:c.1426G>A	p.Val476Ile	p.V476I	ENST00000307771	NM_005089.3	476	Gtt/Att	11/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.7092331963407	2		379	687	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065933-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	68	663	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.743	0.653	0.838	0.743	0.653	0.838	SUBCLONAL	1	TRUE	1	0.675308716692587	2		663	271	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0065933-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12452	5618	421	0	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.675308716692587	57	FACETS	1	0.988	1	0.322	0.317	0.327	CLONAL	18	TRUE	1	0.675308716692587	57		421	18070	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351718	89351718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1414996600	NA	P-0065933-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	152	522	0	ENST00000301030.4:c.1232C>T	p.Ser411Leu	p.S411L	ENST00000301030	NM_001256183.1	411	tCg/tTg	9/13	1	2	FACETS	0.983	0.907	1	0.983	0.907	1	CLONAL	1	TRUE	1	0.675308716692587	2		522	458	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133208957	133208957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757559474	NA	P-0065933-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	80	528	0	ENST00000320574.5:c.6274G>A	p.Gly2092Ser	p.G2092S	ENST00000320574	NM_006231.2	2092	Ggt/Agt	45/49	1	2	FACETS	0.53	0.468	0.596	0.53	0.468	0.596	SUBCLONAL	1	TRUE	1	0.675308716692587	2		528	447	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231548	5231548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754436545	NA	P-0065933-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	119	440	0	ENST00000357368.4:c.1928C>T	p.Pro643Leu	p.P643L	ENST00000357368	NM_002850.3	643	cCg/cTg	14/38	1	2	FACETS	0.906	0.825	0.989	0.906	0.825	0.989	CLONAL	1	TRUE	1	0.675308716692587	2		440	389	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220329	55220329	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065933-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12859	969	368	0	ENST00000275493.2:c.719G>A	p.Cys240Tyr	p.C240Y	ENST00000275493	NM_005228.3	240	tGc/tAc	6/28	0.675308716692587	57	FACETS	1	0.975	1	0.073	0.069	0.076	CLONAL	4	TRUE	1	0.675308716692587	57		368	13828	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032007	10032007	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs778849362	NA	P-0065933-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	115	474	0	ENST00000330684.3:c.816T>A	p.Phe272Leu	p.F272L	ENST00000330684	NM_001134407.1	272	ttT/ttA	3/13	1	2	FACETS	0.894	0.813	0.978	0.894	0.813	0.978	CLONAL	1	TRUE	1	0.675308716692587	2		474	381	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720654	89720654	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0065934-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	42	151	0	ENST00000371953.3:c.805A>T	p.Lys269Ter	p.K269*	ENST00000371953	NM_000314.4	269	Aaa/Taa	8/9	0.415058665651238	3	FACETS	1	0.877	1	1	0.877	1	CLONAL	2	FALSE	1	0.434144724088131	3		151	115	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822645	72822645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149133285	NA	P-0065934-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	98	605	0	ENST00000268489.5:c.9530C>T	p.Ser3177Leu	p.S3177L	ENST00000268489	NM_006885.3	3177	tCg/tTg	10/10	0.397489412754064	3	FACETS	1	0.935	1	0.53	0.475	0.589	CLONAL	1	FALSE	1	0.434144724088131	3		605	518	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858202	9858202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065934-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	98	583	1	ENST00000330684.3:c.3199C>T	p.Arg1067Trp	p.R1067W	ENST00000330684	NM_001134407.1	1067	Cgg/Tgg	13/13	0.397489412754064	3	FACETS	1	0.939	1	0.534	0.478	0.594	CLONAL	1	FALSE	1	0.434144724088131	3		584	514	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940199	49940199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373567723	NA	P-0065934-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	54	608	0	ENST00000296474.3:c.844C>T	p.Arg282Trp	p.R282W	ENST00000296474	NM_002447.2	282	Cgg/Tgg	1/20	0.374507900928114	3	FACETS	0.562	0.48	0.651	0.187	0.16	0.217	SUBCLONAL	1	FALSE	0	0.434144724088131	3		608	539	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210754	5210754	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs768674983	NA	P-0065934-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	303	603	0	ENST00000357368.4:c.5297G>T	p.Arg1766Leu	p.R1766L	ENST00000357368	NM_002850.3	1766	cGc/cTc	34/38	0.434148664757766	5	FACETS	0.948	0.902	0.994	0.948	0.902	0.994	CLONAL	4	FALSE	1	0.434144724088131	5		603	608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0065935-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	72	442	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.235180996539483	1	FACETS	0.783	0.685	0.89	0.783	0.685	0.89	SUBCLONAL	1	TRUE	0	0.266821774970014	1		442	597	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696432	47696432	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519968	NA	P-0065935-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	109	486	0	ENST00000347630.2:c.391T>G	p.Trp131Gly	p.W131G	ENST00000347630	NM_001007230.1	131	Tgg/Ggg	6/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.266821774970014	2		486	693	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0065936-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	110	286	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.588747951456116	1	FACETS	0.966	0.882	1	0.966	0.882	1	CLONAL	1	TRUE	0	0.588747951456116	1		286	273	SUCCESS
APC	324	MSKCC	GRCh37	5	112178211	112178211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs901983934	NA	P-0065936-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	163	379	0	ENST00000257430.4:c.6920C>T	p.Ser2307Leu	p.S2307L	ENST00000257430	NM_000038.5	2307	tCg/tTg	16/16	0.588747951456116	1	FACETS	0.861	0.797	0.925	0.861	0.797	0.925	CLONAL	1	TRUE	0	0.588747951456116	1		379	454	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624298	89624298	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1320222638	NA	P-0065936-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	9	277	0	ENST00000371953.3:c.72C>G	p.Asp24Glu	p.D24E	ENST00000371953	NM_000314.4	24	gaC/gaG	1/9	0.502287598510706	0	FACETS	0.048	0.031	0.069			1	SUBCLONAL	1	TRUE	0	0.588747951456116	0		277	264	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821638	72821638	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs200561133	NA	P-0065936-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	103	454	0	ENST00000268489.5:c.10537A>G	p.Ser3513Gly	p.S3513G	ENST00000268489	NM_006885.3	3513	Agt/Ggt	10/10	0.507446593919241	3	FACETS	0.785	0.704	0.87	0.392	0.352	0.435	SUBCLONAL	1	TRUE	1	0.588747951456116	3		454	577	SUCCESS
APC	324	MSKCC	GRCh37	5	112174266	112174267	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065936-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	145	399	0	ENST00000257430.4:c.2976dup	p.Lys993Ter	p.K993*	ENST00000257430	NM_000038.5	992	agt/agTt	16/16	0.588747951456116	1	FACETS	0.822	0.757	0.888	0.822	0.757	0.888	CLONAL	1	TRUE	0	0.588747951456116	1		399	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576865	7576866	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0065936-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	193	475	0	ENST00000269305.4:c.980dup	p.Tyr327Ter	p.Y327*	ENST00000269305	NM_001126112.2	327	tat/taAt	9/11	0.588747951456116	1	FACETS	0.88	0.82	0.94	0.88	0.82	0.94	CLONAL	1	TRUE	0	0.588747951456116	1		475	526	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1686068	1686068	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1158577988	NA	P-0065936-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	180	485	0	ENST00000378625.1:c.1193C>T	p.Thr398Met	p.T398M	ENST00000378625	NM_001198994.1	398	aCg/aTg	10/14	1	2	FACETS	0.964	0.893	1	0.964	0.893	1	CLONAL	1	TRUE	1	0.588747951456116	2		485	634	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821601	72821616	+	protein_altering_variant	In_Frame_Del	DEL	CCGCCGCCGCCGCCGC	CCGCCGCCGCCGCCGC	G	novel	NA	P-0065936-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	73	444	0	ENST00000268489.5:c.10559_10574delinsC	p.Gly3520_Gly3525delinsAla	p.G3520_G3525delinsA	ENST00000268489	NM_006885.3	3520	gGCGGCGGCGGCGGCGGc/gCc	10/10	0.507446593919241	3	FACETS	0.529	0.463	0.6	0.264	0.231	0.3	SUBCLONAL	1	TRUE	1	0.588747951456116	3		444	607	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0065937-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	176	292	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	0.882	0.821	0.944	0.882	0.821	0.944	CLONAL	1	TRUE	1	0.87908259522408	2		292	454	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878062	48878062	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065937-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	30	443	0	ENST00000267163.4:c.19del	p.Arg7GlufsTer58	p.R7Efs*58	ENST00000267163	NM_000321.2	5	aCc/ac	1/27	0.634754944306397	1	FACETS	0.15	0.121	0.183	0.15	0.121	0.183	SUBCLONAL	1	TRUE	0	0.87908259522408	1		443	255	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003137	42003137	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065937-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	64	398	0	ENST00000219905.7:c.2678del	p.Pro893LeufsTer40	p.P893Lfs*40	ENST00000219905	NM_001164273.1	892	Ccc/cc	8/24	0.87908259522408	1	FACETS	0.262	0.228	0.297	0.262	0.228	0.297	SUBCLONAL	1	TRUE	0	0.87908259522408	1		398	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0065938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	164	373	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.762686724907699	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.762686724907699	1		373	257	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0065938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	111	268	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.762686724907699	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.762686724907699	1		268	169	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679748	33679748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs541914273	NA	P-0065938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	152	512	0	ENST00000308377.4:c.2333G>A	p.Arg778Gln	p.R778Q	ENST00000308377	NM_152270.3	778	cGa/cAa	5/5	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.762686724907699	2		512	398	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976636	90976636	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0065938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	235	278	0	ENST00000265433.3:c.994+2T>C		p.X332_splice	ENST00000265433	NM_002485.4	332			0.75533059941231	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	0	0.762686724907699	3		278	281	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0065939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	51	1407	0				ENST00000310581	NM_198253.2	-/1132			0.563830145490546	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.563830145490546	3		1407	93	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0065939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	210	533	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.563830145490546	5	FACETS	1	0.976	1	1	0.976	1	CLONAL	5	TRUE	0	0.563830145490546	5		533	269	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306689	41306689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868376470	NA	P-0065939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	64	386	0	ENST00000373198.4:c.970G>A	p.Glu324Lys	p.E324K	ENST00000373198	NM_133170.3	324	Gaa/Aaa	7/32	0.0816246933261714	5	FACETS	1	0.928	1	0.716	0.631	0.805	INDETERMINATE	2	TRUE	2	0.563830145490546	5		386	195	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293551	1293551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	65	488	0	ENST00000310581.5:c.1450G>A	p.Glu484Lys	p.E484K	ENST00000310581	NM_198253.2	484	Gaa/Aaa	2/16	0.563830145490546	3	FACETS	0.985	0.878	1	0.985	0.878	1	CLONAL	2	TRUE	1	0.563830145490546	3		488	150	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58711312	58711312	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	116	332	0	ENST00000305921.3:c.800C>T	p.Pro267Leu	p.P267L	ENST00000305921	NM_003620.3	267	cCt/cTt	3/6	0.563830145490546	4	FACETS	1	0.936	1	1	0.936	1	CLONAL	3	TRUE	1	0.563830145490546	4		332	212	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098407	108098407	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	101	331	1	ENST00000278616.4:c.56G>T	p.Arg19Ile	p.R19I	ENST00000278616	NM_000051.3	19	aGa/aTa	2/63	0.563830145490546	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.563830145490546	2		332	144	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670388	134670388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	93	423	0	ENST00000398015.3:c.299C>T	p.Pro100Leu	p.P100L	ENST00000398015	NM_004441.4	100	cCt/cTt	3/16	0.511967758372842	3	FACETS	0.927	0.855	0.997	1	0.985	1	CLONAL	3	TRUE	1	0.563830145490546	3		423	152	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417325	139417325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	41	495	0	ENST00000277541.6:c.719C>T	p.Thr240Ile	p.T240I	ENST00000277541	NM_017617.3	240	aCc/aTc	4/34	0.511967758372842	3	FACETS	1	0.931	1	0.594	0.503	0.691	CLONAL	1	TRUE	1	0.563830145490546	3		495	157	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21336728	21336728	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	96	474	0	ENST00000215739.8:c.68A>G	p.Lys23Arg	p.K23R	ENST00000215739	NM_006767.3	23	aAg/aGg	1/21	0.489158437820385	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.563830145490546	4		474	229	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850372	128850372	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	67	440	0	ENST00000249373.3:c.1635G>A	p.Trp545Ter	p.W545*	ENST00000249373	NM_005631.4	545	tgG/tgA	9/12	0.370893537475291	4	FACETS	0.856	0.756	0.961	0.856	0.756	0.961	CLONAL	2	TRUE	2	0.563830145490546	4		440	217	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758769	41758769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	60	485	0	ENST00000301178.4:c.1823C>T	p.Ser608Phe	p.S608F	ENST00000301178	NM_021913.4	608	tCt/tTt	16/20	0.563830145490546	3	FACETS	1	0.964	1	0.656	0.574	0.742	CLONAL	1	TRUE	1	0.563830145490546	3		485	208	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0065940-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	9	431	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.171	0.113	0.247	0.171	0.113	0.247	SUBCLONAL	1	TRUE	1	0.274945940895834	2		431	382	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412470	80412470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28764015	NA	P-0065940-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	79	373	0	ENST00000286548.4:c.571G>A	p.Glu191Lys	p.E191K	ENST00000286548	NM_002072.3	191	Gaa/Aaa	4/7	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.274945940895834	2		373	413	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338641	70338641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065940-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	28	147	0	ENST00000374080.3:c.37C>T	p.Pro13Ser	p.P13S	ENST00000374080		13	Ccc/Tcc	1/45	1	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.274945940895834	1		147	138	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15967483	15967483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065940-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	85	332	0	ENST00000268712.3:c.5120C>T	p.Ala1707Val	p.A1707V	ENST00000268712	NM_006311.3	1707	gCa/gTa	35/46	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.274945940895834	2		332	416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0065970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	164	454	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	0.405188145641518	2	FACETS	0.9	0.835	0.967	0.9	0.835	0.967	CLONAL	2	TRUE	0	0.405705009156873	2		454	449	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858095	40858095	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	150	356	0	ENST00000428826.2:c.1769G>T	p.Gly590Val	p.G590V	ENST00000428826		590	gGg/gTg	16/21	0.405188145641518	2	FACETS	0.963	0.891	1	0.963	0.891	1	CLONAL	2	TRUE	0	0.405705009156873	2		356	384	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857568	9857569	+	missense_variant	Missense_Mutation	DNP	TG	TG	AT	novel	NA	P-0065970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	56	404	1	ENST00000330684.3:c.3832_3833delinsAT	p.Gln1278Ile	p.Q1278I	ENST00000330684	NM_001134407.1	1278	CAa/ATa	13/13	0.35719908696666	3	FACETS	0.858	0.738	0.988	0.429	0.369	0.494	CLONAL	1	TRUE	1	0.405705009156873	3		405	387	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528448	29528448	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	148	276	0	ENST00000356175.3:c.1205C>A	p.Ser402Ter	p.S402*	ENST00000356175	NM_000267.3	402	tCa/tAa	11/57	0.405188145641518	2	FACETS	0.945	0.873	1	0.945	0.873	1	CLONAL	2	TRUE	0	0.405705009156873	2		276	386	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394727	394727	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	147	323	0	ENST00000399788.2:c.4968A>G	p.Ile1656Met	p.I1656M	ENST00000399788	NM_001042603.1	1656	atA/atG	28/28	0.234159991845135	5	FACETS	1	0.979	1			1	INDETERMINATE	2	TRUE	NA	0.405705009156873	5		323	490	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865294	57865294	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	64	381	1	ENST00000228682.2:c.2771C>A	p.Ser924Tyr	p.S924Y	ENST00000228682	NM_005269.2	924	tCc/tAc	12/12	0.250870292762529	6	FACETS	1	0.966	1	0.456	0.396	0.52	CLONAL	1	TRUE	3	0.405705009156873	6		382	418	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505379	157505379	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	76	263	0	ENST00000346085.5:c.3360G>C	p.Lys1120Asn	p.K1120N	ENST00000346085	NM_020732.3	1120	aaG/aaC	13/20	0.35719908696666	3	FACETS	1	0.884	1	0.502	0.442	0.566	CLONAL	1	TRUE	1	0.405705009156873	3		263	449	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342661	118342661	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	89	372	0	ENST00000534358.1:c.787A>T	p.Thr263Ser	p.T263S	ENST00000534358	NM_005933.3	263	Acg/Tcg	3/36	0.405705009156873	4	FACETS	1	0.93	1	0.266	0.236	0.298	CLONAL	1	TRUE	0	0.405705009156873	4		372	580	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0065971-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	99	476	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.165886077254345	2	FACETS	0.913	0.816	1	0.913	0.816	1	CLONAL	2	FALSE	0	0.165886077254345	2		476	654	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419986	41419986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372989163	NA	P-0065971-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	86	543	0	ENST00000373198.4:c.335G>A	p.Arg112His	p.R112H	ENST00000373198	NM_133170.3	112	cGt/cAt	3/32	0.165886077254345	3	FACETS	1	0.974	1	0.697	0.615	0.784	CLONAL	1	FALSE	1	0.165886077254345	3		543	806	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856529	111856529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065971-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	88	475	0	ENST00000341259.2:c.580G>A	p.Glu194Lys	p.E194K	ENST00000341259	NM_005475.2	194	Gag/Aag	2/8	0.165886077254345	2	FACETS	0.763	0.676	0.856	0.763	0.676	0.856	SUBCLONAL	2	FALSE	0	0.165886077254345	2		475	695	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0065971-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	142	465	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.165886077254345	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	FALSE	0	0.165886077254345	2		465	802	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115578	108115579	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0065971-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	88	296	0	ENST00000278616.4:c.727_728del	p.Leu243GlyfsTer10	p.L243Gfs*10	ENST00000278616	NM_000051.3	242	acTTtg/actg	7/63	0.165886077254345	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	2	FALSE	0	0.165886077254345	2		296	504	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109792	115109792	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065971-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	126	453	0	ENST00000257566.3:c.2086T>C	p.Ser696Pro	p.S696P	ENST00000257566	NM_016569.3	696	Tcc/Ccc	8/8	0.165886077254345	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	FALSE	0	0.165886077254345	2		453	710	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926885	112926885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507544	NA	P-0065972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	120	380	0	ENST00000351677.2:c.1505C>T	p.Ser502Leu	p.S502L	ENST00000351677	NM_002834.3	502	tCa/tTa	13/16	0.202601969734486	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.212074732929	3		380	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203436	NA	P-0065972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	65	758	0	ENST00000269305.4:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269305	NM_001126112.2	163	Tac/Cac	5/11	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.212074732929	2		758	562	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057988	27057988	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	63	546	0	ENST00000324856.7:c.1696C>T	p.Gln566Ter	p.Q566*	ENST00000324856	NM_006015.4	566	Cag/Tag	3/20	0.212074732929	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	0	0.212074732929	1		546	499	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473722	67473722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs794727798	NA	P-0065972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	108	435	1	ENST00000327367.4:c.802C>T	p.Arg268Cys	p.R268C	ENST00000327367	NM_005902.3	268	Cgc/Tgc	6/9	0.212074732929	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	0	0.212074732929	2		436	493	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581243	48581243	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	92	437	2	ENST00000342988.3:c.547C>T	p.Gln183Ter	p.Q183*	ENST00000342988	NM_005359.5	183	Cag/Tag	5/12	0.212074732929	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.212074732929	1		439	597	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790065	40790065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780417311	NA	P-0065972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	75	480	0	ENST00000373198.4:c.2666G>A	p.Arg889Gln	p.R889Q	ENST00000373198	NM_133170.3	889	cGg/cAg	18/32	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.212074732929	2		480	574	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61197641	61197641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	45	369	0	ENST00000301761.2:c.23C>T	p.Ser8Leu	p.S8L	ENST00000301761	NM_017841.2	8	tCg/tTg	1/4	1	2	FACETS	0.956	0.804	1	0.956	0.804	1	CLONAL	1	TRUE	1	0.212074732929	2		369	444	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39239474	39239474	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs397517156	NA	P-0065972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	41	258	0	ENST00000402219.2:c.2183A>T	p.Lys728Ile	p.K728I	ENST00000402219	NM_005633.3	728	aAa/aTa	14/23	1	2	FACETS	0.895	0.746	1	0.895	0.746	1	CLONAL	1	TRUE	1	0.212074732929	2		258	432	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980352	201980353	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0065972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	63	521	0	ENST00000359651.3:c.91_92del	p.Pro31CysfsTer8	p.P31Cfs*8	ENST00000359651		30	CCc/c	1/8	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.212074732929	2		521	583	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099754	157099757	+	frameshift_variant	Frame_Shift_Del	DEL	AATA	AATA	-	novel	NA	P-0065972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	63	303	0	ENST00000346085.5:c.692_695del	p.Asn231IlefsTer34	p.N231Ifs*34	ENST00000346085	NM_020732.3	231	AATAat/at	1/20	0.212074732929	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.212074732929	2		303	241	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439839	49439849	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTACTCACCC	GGTACTCACCC	-	novel	NA	P-0065972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	56	525	0	ENST00000301067.7:c.4692_4693+9del		p.X1564_splice	ENST00000301067	NM_003482.3	1564		17/54	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.212074732929	2		525	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0065974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	169	463	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.361550940371337	2	FACETS	0.825	0.765	0.887	0.825	0.765	0.887	CLONAL	2	TRUE	0	0.418086618244246	2		463	490	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0065974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	108	441	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.153276871741752	4	FACETS	0.807	0.728	0.889	0.807	0.728	0.889	INDETERMINATE	2	TRUE	2	0.418086618244246	4		441	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0065976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	25	366	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	1	2	FACETS	0.758	0.598	0.941	0.758	0.598	0.941	CLONAL	1	TRUE	1	0.219174886124534	2		366	301	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716327	52716327	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	155	466	0	ENST00000322088.6:c.771G>C	p.Trp257Cys	p.W257C	ENST00000322088	NM_014225.5	257	tgG/tgC	6/15	0.219174886124534	3	FACETS	0.95	0.879	1	1	0.992	1	CLONAL	4	TRUE	1	0.219174886124534	3		466	413	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686920	37686920	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs34070318	NA	P-0065976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	96	363	0	ENST00000447079.4:c.3824C>T	p.Pro1275Leu	p.P1275L	ENST00000447079	NM_015083.1	1275	cCg/cTg	14/14	0.219174886124534	4	FACETS	0.965	0.867	1	0.965	0.867	1	CLONAL	3	TRUE	1	0.219174886124534	4		363	369	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163425	108163425	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760542469	NA	P-0065976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	43	374	0	ENST00000278616.4:c.4516G>A	p.Val1506Met	p.V1506M	ENST00000278616	NM_000051.3	1506	Gtg/Atg	30/63	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.219174886124534	2		374	349	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468393	89468393	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	21	342	0	ENST00000336596.2:c.1927C>A	p.Pro643Thr	p.P643T	ENST00000336596	NM_005233.5	643	Cct/Act	11/17	1	2	FACETS	0.628	0.484	0.797	0.628	0.484	0.797	SUBCLONAL	1	TRUE	1	0.219174886124534	2		342	305	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0065978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	446	355	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.261475587930547	9	FACETS	1	0.987	1	0.934	0.9	0.969	CLONAL	8	TRUE	0	0.261475587930547	9		355	777	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456753	32456753	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1212035248	NA	P-0065978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	60	374	0	ENST00000332351.3:c.139G>A	p.Glu47Lys	p.E47K	ENST00000332351	NM_024426.4	47	Gag/Aag	1/10	1	2	FACETS	0.952	0.822	1	0.952	0.822	1	CLONAL	1	TRUE	1	0.261475587930547	2		374	482	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207088	1207089	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	78	366	0	ENST00000326873.7:c.178dup	p.Tyr60LeufsTer103	p.Y60Lfs*103	ENST00000326873	NM_000455.4	59	tct/tcTt	1/10	0.261475587930547	1	FACETS	0.952	0.838	1	0.952	0.838	1	CLONAL	1	TRUE	0	0.261475587930547	1		366	545	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035145	30035145	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	73	315	0	ENST00000338641.4:c.307G>T	p.Glu103Ter	p.E103*	ENST00000338641	NM_000268.3	103	Gag/Tag	3/16	0.261475587930547	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.261475587930547	1		315	449	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124499166	124499166	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	60	210	0	ENST00000357628.3:c.547G>T	p.Val183Leu	p.V183L	ENST00000357628	NM_015450.2	183	Gta/Tta	9/19	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.261475587930547	2		210	381	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388019	81388019	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs750225776	NA	P-0065978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	41	188	0	ENST00000222390.5:c.356A>G	p.Tyr119Cys	p.Y119C	ENST00000222390	NM_000601.4	119	tAt/tGt	3/18	1	2	FACETS	0.945	0.79	1	0.945	0.79	1	CLONAL	1	TRUE	1	0.261475587930547	2		188	332	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31369157	31369164	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGGCCGAA	AGGCCGAA	G	novel	NA	P-0065978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	63	300	0	ENST00000328111.2:c.143-2_148delinsG		p.X48_splice	ENST00000328111	NM_006892.3	48		3/23	1	2	FACETS	0.894	0.774	1	0.894	0.774	1	CLONAL	1	TRUE	1	0.261475587930547	2		300	539	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579346	7579348	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs764486868	NA	P-0065979-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	249	471	0	ENST00000269305.4:c.339_341del	p.Phe113del	p.F113del	ENST00000269305	NM_001126112.2	113	ttCTTg/ttg	4/11	0.263734223136863	3	FACETS	0.978	0.921	1	0.978	0.921	1	CLONAL	3	FALSE	0	0.313805148685777	3		471	626	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020827	26020827	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065979-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	143	556	0	ENST00000357647.3:c.110A>T	p.Lys37Ile	p.K37I	ENST00000357647	NM_003529.2	37	aAa/aTa	1/1	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.313805148685777	2		556	725	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0066000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	96	418	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.831	0.743	0.924	0.831	0.743	0.924	CLONAL	1	TRUE	1	0.461128216671652	2		418	501	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11999013	11999013	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0066000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	88	325	0	ENST00000353533.5:c.513+2T>C		p.X171_splice	ENST00000353533	NM_003010.3	171			0.461128216671652	1	FACETS	0.904	0.809	1	0.904	0.809	1	CLONAL	1	TRUE	0	0.461128216671652	1		325	325	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068433	26068433	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0066000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	59	200	0	ENST00000435504.4:c.58-1G>C		p.X20_splice	ENST00000435504		20			NA	2	FACETS	0.823	0.713	0.941			1	INDETERMINATE	1	TRUE	NA	0.461128216671652	2		200	311	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842735	68842735	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201511530	NA	P-0066000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	95	395	0	ENST00000261769.5:c.671G>A	p.Arg224His	p.R224H	ENST00000261769	NM_004360.3	224	cGc/cAc	5/16	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.461128216671652	2		395	388	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176176029	176176029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs989823943	NA	P-0066000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	164	572	0	ENST00000367669.3:c.86C>T	p.Ser29Leu	p.S29L	ENST00000367669	NM_022457.5	29	tCg/tTg	1/20	0.452340340017436	4	FACETS	0.992	0.917	1	0.992	0.917	1	CLONAL	2	TRUE	2	0.461128216671652	4		572	524	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003853	57003853	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	C	C	A	rs1000614668	NA	P-0066000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	71	602	0	ENST00000257254.3:c.626G>T	p.Gly209Val	p.G209V	ENST00000257254		209	gGc/gTc	1/2	0.426471293842125	1	FACETS	0.714	0.627	0.805	0.714	0.627	0.805	SUBCLONAL	1	TRUE	0	0.461128216671652	1		602	332	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778736	3778737	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0066000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	61	684	0	ENST00000262367.5:c.6311_6312delinsTT	p.Arg2104Leu	p.R2104L	ENST00000262367	NM_004380.2	2104	cGC/cTT	31/31	1	2	FACETS	0.733	0.635	0.838	0.733	0.635	0.838	SUBCLONAL	1	TRUE	1	0.461128216671652	2		684	361	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649416	23649416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs515726129	NA	P-0066000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	82	329	0	ENST00000261584.4:c.83A>G	p.Tyr28Cys	p.Y28C	ENST00000261584	NM_024675.3	28	tAc/tGc	2/13	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.461128216671652	2		329	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578558	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCTTGTTGAGGGCAGGGGAGTACTGT	ATCTTGTTGAGGGCAGGGGAGTACTGT	-	novel	NA	P-0066000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	90	548	0	ENST00000269305.4:c.376-4_398del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	0.461128216671652	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.461128216671652	1		548	291	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075172	16075172	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	127	452	0	ENST00000268712.3:c.380del	p.Leu127CysfsTer3	p.L127Cfs*3	ENST00000268712	NM_006311.3	127	tTg/tg	4/46	0.461128216671652	1	FACETS	0.965	0.881	1	0.965	0.881	1	CLONAL	1	TRUE	0	0.461128216671652	1		452	439	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936313	49936313	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	89	692	0	ENST00000296474.3:c.1535C>G	p.Ala512Gly	p.A512G	ENST00000296474	NM_002447.2	512	gCc/gGc	3/20	1	2	FACETS	0.995	0.888	1	0.995	0.888	1	CLONAL	1	TRUE	1	0.461128216671652	2		692	388	SUCCESS
ALB	213	MSKCC	GRCh37	4	74283279	74283279	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	90	378	1	ENST00000295897.4:c.1321C>A	p.Gln441Lys	p.Q441K	ENST00000295897	NM_000477.5	441	Caa/Aaa	11/15	0.422902811042709	1	FACETS	0.749	0.669	0.833	0.749	0.669	0.833	SUBCLONAL	1	TRUE	0	0.461128216671652	1		379	401	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963123	38963123	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	102	340	0	ENST00000357387.3:c.1421A>G	p.Asn474Ser	p.N474S	ENST00000357387	NM_152756.3	474	aAc/aGc	17/38	1	2	FACETS	0.813	0.73	0.901	0.813	0.73	0.901	CLONAL	1	TRUE	1	0.461128216671652	2		340	544	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638579	176638579	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	26	609	0	ENST00000439151.2:c.3179C>G	p.Pro1060Arg	p.P1060R	ENST00000439151	NM_022455.4	1060	cCa/cGa	5/23	1	2	FACETS	0.227	0.179	0.282	0.227	0.179	0.282	SUBCLONAL	1	TRUE	1	0.461128216671652	2		609	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0066001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	72	171	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.23995604045048	1	FACETS	0.979	0.858	1	0.979	0.858	1	CLONAL	1	TRUE	0	0.274035041514498	1		171	463	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244974	41244974	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	139	355	0	ENST00000357654.3:c.2574G>T	p.Gln858His	p.Q858H	ENST00000357654	NM_007294.3	858	caG/caT	10/23	0.268162597300654	2	FACETS	0.998	0.915	1	0.998	0.915	1	CLONAL	2	TRUE	0	0.274035041514498	2		355	508	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853907	59853907	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs757305097	NA	P-0066001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	92	311	0	ENST00000259008.2:c.1952T>A	p.Ile651Asn	p.I651N	ENST00000259008	NM_032043.2	651	aTt/aAt	14/20	0.268162597300654	2	FACETS	0.907	0.813	1	0.907	0.813	1	CLONAL	2	TRUE	0	0.274035041514498	2		311	370	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631465	67631465	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	39	346	0	ENST00000272342.5:c.1651T>G	p.Phe551Val	p.F551V	ENST00000272342	NM_019002.3	551	Ttt/Gtt	5/6	1	2	FACETS	0.771	0.641	0.917	0.771	0.641	0.917	CLONAL	1	TRUE	1	0.274035041514498	2		346	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0066019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	181	442	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.578257773643618	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.578257773643618	1		442	364	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736277	243736277	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs764214500	NA	P-0066019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	203	319	0	ENST00000263826.5:c.770C>G	p.Ser257Cys	p.S257C	ENST00000263826	NM_005465.4	257	tCt/tGt	8/13	0.263119719357083	2	FACETS	1	0.992	1	0.744	0.697	0.791	INDETERMINATE	1	TRUE	0	0.578257773643618	2		319	472	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682187	37682187	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	25	412	0	ENST00000447079.4:c.3378A>C	p.Gln1126His	p.Q1126H	ENST00000447079	NM_015083.1	1126	caA/caC	13/14	0.578257773643618	1	FACETS	0.15	0.117	0.187	0.15	0.117	0.187	SUBCLONAL	1	TRUE	0	0.578257773643618	1		412	411	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437618	52437618	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs765929006	NA	P-0066019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	18	482	0	ENST00000460680.1:c.1543A>C	p.Asn515His	p.N515H	ENST00000460680	NM_004656.3	515	Aac/Cac	13/17	0.463916819590331	0	FACETS	0.092	0.069	0.119			1	SUBCLONAL	1	TRUE	0	0.578257773643618	0		482	285	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420346	49420346	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs561594226	NA	P-0066019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	21	428	0	ENST00000301067.7:c.15403A>G	p.Met5135Val	p.M5135V	ENST00000301067	NM_003482.3	5135	Atg/Gtg	48/54	0.578257773643618	1	FACETS	0.124	0.095	0.158	0.124	0.095	0.158	SUBCLONAL	1	TRUE	0	0.578257773643618	1		428	417	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509367	149509367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1232469262	NA	P-0066019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	64	482	1	ENST00000261799.4:c.1532G>A	p.Arg511His	p.R511H	ENST00000261799	NM_002609.3	511	cGc/cAc	10/23	0.505420341879756	1	FACETS	0.319	0.276	0.364	0.319	0.276	0.364	SUBCLONAL	1	TRUE	0	0.578257773643618	1		483	494	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242491	+	protein_altering_variant	In_Frame_Del	DEL	TAAGAGAAGCAACATCTCCGAA	TAAGAGAAGCAACATCTCCGAA	CAAG	novel	NA	P-0066019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	171	345	1	ENST00000275493.2:c.2240_2261delinsCAAG	p.Leu747_Lys754delinsSerArg	p.L747_K754delinsSR	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCCGAAa/tCAAGa	19/28	0.544344639266972	2	FACETS	0.885	0.829	0.941	0.885	0.829	0.941	CLONAL	2	TRUE	0	0.578257773643618	2		346	334	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0066020-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	71	170	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.387298510496695	1	FACETS	0.939	0.826	1	0.939	0.826	1	CLONAL	1	FALSE	0	0.380366295313946	1		170	322	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060763	38060765	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0066020-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	24	530	0	ENST00000250448.2:c.1224_1226del	p.Ser409del	p.S409del	ENST00000250448	NM_004496.3	408	tcCTCg/tcg	2/2	0.375161621319757	0	FACETS	0.183	0.143	0.229			1	SUBCLONAL	1	FALSE	0	0.380366295313946	0		530	428	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636871	176636872	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0066020-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	102	428	0	ENST00000439151.2:c.1475dup	p.Pro493AlafsTer4	p.P493Afs*4	ENST00000439151	NM_022455.4	491	gaa/gAaa	5/23	NA	2	FACETS	0.754	0.675	0.839			1	INDETERMINATE	1	FALSE	NA	0.380366295313946	2		428	711	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423670	47423671	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0066020-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	111	401	0	ENST00000404338.3:c.1740dup	p.Pro581AlafsTer3	p.P581Afs*3	ENST00000404338	NM_004491.4	580	cgg/cGgg	1/6	1	2	FACETS	0.855	0.769	0.945	0.855	0.769	0.945	CLONAL	1	FALSE	1	0.380366295313946	2		401	683	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27016118	27016118	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066020-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	31	314	0	ENST00000335756.4:c.394A>T	p.Ile132Phe	p.I132F	ENST00000335756	NM_001809.3	132	Atc/Ttc	4/5	1	2	FACETS	0.312	0.252	0.381	0.312	0.252	0.381	SUBCLONAL	1	FALSE	1	0.380366295313946	2		314	522	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0066021-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	83	491	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.22743422120338	3	FACETS	0.809	0.72	0.902	0.809	0.72	0.902	CLONAL	2	TRUE	1	0.353038115760896	3		491	342	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971026	21971026	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066021-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	89	350	0	ENST00000304494.5:c.332del	p.Gly111AlafsTer35	p.G111Afs*35	ENST00000304494	NM_000077.4	111	gGc/gc	2/3	0.353038115760896	1	FACETS	0.842	0.749	0.941	0.842	0.749	0.941	CLONAL	1	TRUE	0	0.353038115760896	1		350	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577567	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0066021-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	69	276	0	ENST00000269305.4:c.713_714dup	p.Asn239ValfsTer9	p.N239Vfs*9	ENST00000269305	NM_001126112.2	238	-/GT	7/11	0.107079664153688	3	FACETS	0.864	0.754	0.984	0.288	0.251	0.328	INDETERMINATE	1	TRUE	0	0.353038115760896	3		276	532	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134988	41134988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	159	213	0	ENST00000379561.5:c.640C>T	p.Arg214Cys	p.R214C	ENST00000379561	NM_002015.3	214	Cgt/Tgt	2/3	1	2	FACETS	0.991	0.917	1	1	0.995	1	CLONAL	7	TRUE	1	0.104472801900669	2		213	439	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0066023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	71	1407	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.914	0.806	1	0.914	0.806	1	CLONAL	1	TRUE	1	0.533856493127643	2		1407	291	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486842	56486842	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	69	330	0	ENST00000267101.3:c.1256G>C	p.Gly419Ala	p.G419A	ENST00000267101	NM_001982.3	419	gGa/gCa	11/28	NA	2	FACETS	0.571	0.498	0.648			1	INDETERMINATE	1	TRUE	NA	0.533856493127643	2		330	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577123	7577123	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876660333	NA	P-0066023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	198	591	0	ENST00000269305.4:c.815T>G	p.Val272Gly	p.V272G	ENST00000269305	NM_001126112.2	272	gTg/gGg	8/11	0.496364551088147	2	FACETS	0.847	0.794	0.9	0.847	0.794	0.9	CLONAL	2	TRUE	0	0.533856493127643	2		591	438	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238593	142238593	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	65	263	0	ENST00000350721.4:c.4300G>T	p.Glu1434Ter	p.E1434*	ENST00000350721	NM_001184.3	1434	Gag/Tag	24/47	0.279319045442339	2	FACETS	0.56	0.487	0.638	0.28	0.243	0.319	INDETERMINATE	1	TRUE	0	0.533856493127643	2		263	435	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487326	56487326	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	65	329	0	ENST00000267101.3:c.1472G>A	p.Arg491Lys	p.R491K	ENST00000267101	NM_001982.3	491	aGa/aAa	12/28	NA	2	FACETS	0.577	0.502	0.658			1	INDETERMINATE	1	TRUE	NA	0.533856493127643	2		329	422	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348135	89348135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	70	413	0	ENST00000301030.4:c.4815G>A	p.Met1605Ile	p.M1605I	ENST00000301030	NM_001256183.1	1605	atG/atA	9/13	0.280183622633886	1	FACETS	0.41	0.358	0.465	0.41	0.358	0.465	INDETERMINATE	1	TRUE	0	0.533856493127643	1		413	469	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161385	55161385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	65	327	0	ENST00000257290.5:c.3216G>A	p.Met1072Ile	p.M1072I	ENST00000257290	NM_006206.4	1072	atG/atA	23/23	0.30782902161594	1	FACETS	0.429	0.373	0.489	0.429	0.373	0.489	INDETERMINATE	1	TRUE	0	0.533856493127643	1		327	416	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223370	2223370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561499135	NA	P-0066023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	76	435	0	ENST00000398665.3:c.3481G>A	p.Asp1161Asn	p.D1161N	ENST00000398665	NM_032482.2	1161	Gac/Aac	25/28	0.533856493127643	1	FACETS	0.555	0.49	0.625	0.555	0.49	0.625	SUBCLONAL	1	TRUE	0	0.533856493127643	1		435	376	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157366	106157367	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs746685650	NA	P-0066023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	119	342	0	ENST00000380013.4:c.2268dup	p.Leu757ThrfsTer12	p.L757Tfs*12	ENST00000380013	NM_001127208.2	756	ata/atAa	3/11	0.30782902161594	1	FACETS	0.64	0.58	0.702	0.64	0.58	0.702	INDETERMINATE	1	TRUE	0	0.533856493127643	1		342	511	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158637076	158637076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	61	406	0	ENST00000263640.3:c.104G>A	p.Cys35Tyr	p.C35Y	ENST00000263640	NM_001105.4	35	tGt/tAt	4/11	0.280183622633886	1	FACETS	0.375	0.324	0.43	0.375	0.324	0.43	INDETERMINATE	1	TRUE	0	0.533856493127643	1		406	447	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348084	89348084	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	65	430	0	ENST00000301030.4:c.4866G>C	p.Glu1622Asp	p.E1622D	ENST00000301030	NM_001256183.1	1622	gaG/gaC	9/13	0.280183622633886	1	FACETS	0.426	0.37	0.486	0.426	0.37	0.486	INDETERMINATE	1	TRUE	0	0.533856493127643	1		430	419	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357176	89357176	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs780204136	NA	P-0066023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	103	421	0	ENST00000301030.4:c.458C>G	p.Ser153Cys	p.S153C	ENST00000301030	NM_001256183.1	153	tCt/tGt	6/13	0.280183622633886	1	FACETS	0.526	0.472	0.583	0.526	0.472	0.583	INDETERMINATE	1	TRUE	0	0.533856493127643	1		421	538	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639622	47639622	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs63750488	NA	P-0066023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	53	265	0	ENST00000233146.2:c.715C>G	p.Gln239Glu	p.Q239E	ENST00000233146	NM_000251.2	239	Cag/Gag	4/16	1	2	FACETS	0.453	0.387	0.526	0.453	0.387	0.526	SUBCLONAL	1	TRUE	1	0.533856493127643	2		265	438	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262184	10262184	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	170	401	0	ENST00000340748.4:c.2107G>C	p.Glu703Gln	p.E703Q	ENST00000340748		703	Gag/Cag	23/40	0.533856493127643	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.533856493127643	1		401	417	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254635	16254635	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	127	348	0	ENST00000375759.3:c.1900G>C	p.Glu634Gln	p.E634Q	ENST00000375759	NM_015001.2	634	Gag/Cag	11/15	1	2	FACETS	0.933	0.85	1	0.933	0.85	1	CLONAL	1	TRUE	1	0.533856493127643	2		348	510	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006897	47006897	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	144	143	0	ENST00000377604.3:c.17+1del		p.R6fs	ENST00000377604	NM_001204468.1	6	cGt/ct	2/24	1	1	FACETS	0.794	0.743	0.845	1	0.991	1	SUBCLONAL	2	TRUE	0	0.533856493127643	1		143	249	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793531	42793531	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1353349876	NA	P-0066023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	265	381	0	ENST00000575354.2:c.1333G>A	p.Glu445Lys	p.E445K	ENST00000575354	NM_015125.3	445	Gag/Aag	8/20	0.51584952910418	3	FACETS	1	0.977	1	0.706	0.667	0.744	CLONAL	2	TRUE	0	0.533856493127643	3		381	594	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813519	32813519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	69	293	0	ENST00000354258.4:c.2264C>T	p.Ser755Leu	p.S755L	ENST00000354258	NM_000593.5	755	tCa/tTa	11/11	0.280183622633886	1	FACETS	0.525	0.46	0.594	0.525	0.46	0.594	INDETERMINATE	1	TRUE	0	0.533856493127643	1		293	361	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467797	99467797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	101	391	0	ENST00000268035.6:c.2666G>A	p.Gly889Glu	p.G889E	ENST00000268035	NM_000875.3	889	gGa/gAa	13/21	1	2	FACETS	0.683	0.612	0.758	0.683	0.612	0.758	SUBCLONAL	1	TRUE	1	0.533856493127643	2		391	554	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622224	117622224	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	57	264	0	ENST00000368508.3:c.6646C>T	p.Gln2216Ter	p.Q2216*	ENST00000368508	NM_002944.2	2216	Cag/Tag	42/43	0.30782902161594	1	FACETS	0.467	0.403	0.537	0.467	0.403	0.537	INDETERMINATE	1	TRUE	0	0.533856493127643	1		264	335	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523561	148523561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	42	239	0	ENST00000320356.2:c.892C>T	p.Arg298Cys	p.R298C	ENST00000320356	NM_004456.4	298	Cgt/Tgt	8/20	0.280183622633886	1	FACETS	0.308	0.257	0.363	0.308	0.257	0.363	INDETERMINATE	1	TRUE	0	0.533856493127643	1		239	375	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786851	135786851	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	77	310	0	ENST00000298552.3:c.1018G>C	p.Glu340Gln	p.E340Q	ENST00000298552	NM_001162426.1	340	Gaa/Caa	10/23	0.136043869036738	3	FACETS	0.647	0.569	0.731			1	INDETERMINATE	1	TRUE	NA	0.533856493127643	3		310	565	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517610	176517610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210567917	NA	P-0066023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	76	427	0	ENST00000292408.4:c.311G>A	p.Arg104Gln	p.R104Q	ENST00000292408	NM_213647.1	104	cGa/cAa	3/18	0.533856493127643	1	FACETS	0.616	0.544	0.691	0.616	0.544	0.691	SUBCLONAL	1	TRUE	0	0.533856493127643	1		427	339	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027219	49027219	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	167	278	0	ENST00000267163.4:c.1786del	p.Leu596SerfsTer15	p.L596Sfs*15	ENST00000267163	NM_000321.2	596	Ctc/tc	18/27	0.533856493127643	2	FACETS	0.886	0.827	0.945	0.886	0.827	0.945	CLONAL	2	TRUE	0	0.533856493127643	2		278	353	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409381	80409381	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	46	282	0	ENST00000286548.4:c.733G>A	p.Glu245Lys	p.E245K	ENST00000286548	NM_002072.3	245	Gag/Aag	5/7	0.280183622633886	1	FACETS	0.333	0.281	0.391	0.333	0.281	0.391	INDETERMINATE	1	TRUE	0	0.533856493127643	1		282	379	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223043	41223043	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	96	352	0	ENST00000357654.3:c.4888G>C	p.Glu1630Gln	p.E1630Q	ENST00000357654	NM_007294.3	1630	Gaa/Caa	15/23	0.286669019784544	2	FACETS	0.588	0.524	0.655	0.294	0.262	0.328	INDETERMINATE	1	TRUE	0	0.533856493127643	2		352	612	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752873	42752873	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	183	548	0	ENST00000222329.4:c.1391C>T	p.Pro464Leu	p.P464L	ENST00000222329	NM_006494.2	464	cCt/cTt	4/4	0.51584952910418	3	FACETS	1	0.987	1	0.431	0.399	0.464	CLONAL	1	TRUE	0	0.533856493127643	3		548	672	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0066024-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	488	170	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.672627873983171	8	FACETS	0.97	0.943	0.995	0.97	0.943	0.995	CLONAL	7	TRUE	1	0.672627873983171	8		170	645	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612371	1612371	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066024-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	174	384	0	ENST00000344749.5:c.1648G>A	p.Ala550Thr	p.A550T	ENST00000344749	NM_001136139.2	550	Gcc/Acc	18/19	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.672627873983171	2		384	439	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341650	70341651	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAG	novel	NA	P-0066024-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	148	397	0	ENST00000374080.3:c.1087_1089dup	p.Ser363dup	p.S363dup	ENST00000374080		363	ctc/ctCAGc	7/45	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.672627873983171	2		397	411	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	97	286	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.393201076821373	3	FACETS	0.897	0.809	0.989	0.897	0.809	0.989	CLONAL	2	TRUE	1	0.393201076821373	3		286	329	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099403	157099429	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAGCAACAG	CAGCAGCAGCAGCAGCAGCAGCAACAG	-	rs910569810	NA	P-0066025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	75	435	0	ENST00000346085.5:c.360_386del	p.Gln123_Gln131del	p.Q123_Q131del	ENST00000346085	NM_020732.3	114	CAGCAGCAGCAGCAGCAGCAGCAACAG/-	1/20	1	2	FACETS	0.67	0.588	0.759	0.67	0.588	0.759	SUBCLONAL	1	TRUE	1	0.393201076821373	2		435	569	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120684	115120684	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	195	394	0	ENST00000257566.3:c.322G>T	p.Glu108Ter	p.E108*	ENST00000257566	NM_016569.3	108	Gag/Tag	1/8	0.393201076821373	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.393201076821373	3		394	522	SUCCESS
APC	324	MSKCC	GRCh37	5	112175358	112175358	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1554085480	NA	P-0066025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	84	297	0	ENST00000257430.4:c.4067C>G	p.Ser1356Ter	p.S1356*	ENST00000257430	NM_000038.5	1356	tCa/tGa	16/16	0.37082414490305	3	FACETS	1	0.903	1	0.51	0.452	0.572	CLONAL	1	TRUE	1	0.393201076821373	3		297	501	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670597	134670597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1330628001	NA	P-0066025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	69	381	0	ENST00000398015.3:c.508C>T	p.Arg170Trp	p.R170W	ENST00000398015	NM_004441.4	170	Cgg/Tgg	3/16	1	2	FACETS	0.852	0.745	0.966	0.852	0.745	0.966	CLONAL	1	TRUE	1	0.393201076821373	2		381	412	SUCCESS
APC	324	MSKCC	GRCh37	5	112174885	112174886	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs864622106	NA	P-0066025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	140	343	0	ENST00000257430.4:c.3595_3596del	p.Lys1199GlufsTer8	p.K1199Efs*8	ENST00000257430	NM_000038.5	1198	tcAAag/tcag	16/16	0.37082414490305	3	FACETS	0.941	0.863	1	0.941	0.863	1	CLONAL	2	TRUE	1	0.393201076821373	3		343	453	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849212	76849212	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	46	290	0	ENST00000373344.5:c.6064C>A	p.Leu2022Ile	p.L2022I	ENST00000373344	NM_000489.3	2022	Ctt/Att	26/35	0.37082414490305	3	FACETS	0.745	0.629	0.872	0.372	0.314	0.436	SUBCLONAL	1	TRUE	1	0.393201076821373	3		290	376	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874152	155874152	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	269	342	0	ENST00000368323.3:c.379A>T	p.Thr127Ser	p.T127S	ENST00000368323	NM_006912.5	127	Aca/Tca	5/6	0.366435606544152	4	FACETS	0.973	0.919	1	0.973	0.919	1	CLONAL	3	TRUE	1	0.393201076821373	4		342	653	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042376	16042376	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	69	227	0	ENST00000268712.3:c.1298A>G	p.Asp433Gly	p.D433G	ENST00000268712	NM_006311.3	433	gAt/gGt	12/46	0.393201076821373	3	FACETS	1	0.959	1	0.614	0.538	0.695	CLONAL	1	TRUE	1	0.393201076821373	3		227	342	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120261	70120285	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCTTCAACCTCCCACACTACAGC	CCCCTTCAACCTCCCACACTACAGC	-	novel	NA	P-0066025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	244	396	0	ENST00000245479.2:c.1266_1290del	p.Phe423ProfsTer39	p.F423Pfs*39	ENST00000245479	NM_000346.3	421	agCCCCTTCAACCTCCCACACTACAGC/ag	3/3	0.393201076821373	3	FACETS	0.929	0.877	0.981	0.929	0.877	0.981	CLONAL	3	TRUE	0	0.393201076821373	3		396	533	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022795	12022795	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	91	493	0	ENST00000396373.4:c.903del	p.Lys302SerfsTer14	p.K302Sfs*14	ENST00000396373	NM_001987.4	301	Ggg/gg	5/8	0.393201076821373	3	FACETS	0.991	0.882	1	0.495	0.441	0.554	CLONAL	1	TRUE	1	0.393201076821373	3		493	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0066034-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	29	573	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	1	2	FACETS	0.25	0.201	0.306	0.25	0.201	0.306	SUBCLONAL	1	TRUE	1	0.72	2		573	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0066034-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	26	485	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.23	0.182	0.285	0.23	0.182	0.285	SUBCLONAL	1	TRUE	1	0.72	2		485	314	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937070	48937070	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066034-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	41	284	0	ENST00000267163.4:c.838G>T	p.Glu280Ter	p.E280*	ENST00000267163	NM_000321.2	280	Gaa/Taa	8/27	1	2	FACETS	0.357	0.298	0.422	0.357	0.298	0.422	SUBCLONAL	1	TRUE	1	0.72	2		284	319	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089499	27089499	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066034-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	27	499	0	ENST00000324856.7:c.2457del	p.Asn820MetfsTer13	p.N820Mfs*13	ENST00000324856	NM_006015.4	819	Ccc/cc	8/20	1	2	FACETS	0.246	0.196	0.303	0.246	0.196	0.303	SUBCLONAL	1	TRUE	1	0.72	2		499	305	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0066034-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	30	1407	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.505	0.411	0.609	0.505	0.411	0.609	SUBCLONAL	1	TRUE	1	0.72	2		1407	165	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639559	47639559	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066034-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	30	278	0	ENST00000233146.2:c.652C>G	p.Gln218Glu	p.Q218E	ENST00000233146	NM_000251.2	218	Caa/Gaa	4/16	1	2	FACETS	0.249	0.2	0.303	0.249	0.2	0.303	SUBCLONAL	1	TRUE	1	0.72	2		278	335	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677899	117677899	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066034-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	24	410	0	ENST00000368508.3:c.4034C>G	p.Ser1345Cys	p.S1345C	ENST00000368508	NM_002944.2	1345	tCt/tGt	25/43	1	2	FACETS	0.218	0.171	0.272	0.218	0.171	0.272	SUBCLONAL	1	TRUE	1	0.72	2		410	306	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0066041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	410	601	2	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.629522642290559	2	FACETS	0.976	0.94	1	0.976	0.94	1	CLONAL	2	TRUE	0	0.629522642290559	2		603	667	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	245	286	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.629411278224696	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.629522642290559	2		286	381	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0066041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	116	591	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.965	0.878	1	0.965	0.878	1	CLONAL	1	TRUE	1	0.629522642290559	2		591	382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0066041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	238	449	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.608863447377117	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.629522642290559	1		451	436	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604790	48604790	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1568211615	NA	P-0066041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	226	460	0	ENST00000342988.3:c.1612G>T	p.Glu538Ter	p.E538*	ENST00000342988	NM_005359.5	538	Gaa/Taa	12/12	0.629522642290559	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.629522642290559	1		460	454	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412095	63412095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852217	NA	P-0066041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	452	774	2	ENST00000330258.3:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000330258	NM_152424.3	358	Cga/Tga	2/2	NA	2	FACETS	0.864	0.831	0.897			1	INDETERMINATE	2	TRUE	NA	0.629522642290559	2		776	831	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927066	131927066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762188153	NA	P-0066041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	275	554	5	ENST00000265335.6:c.1603C>T	p.Arg535Cys	p.R535C	ENST00000265335		535	Cgt/Tgt	10/25	0.629522642290559	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.629522642290559	2		559	421	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710661	114710661	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	264	622	4	ENST00000543371.1:c.146T>C	p.Val49Ala	p.V49A	ENST00000543371	NM_001198531.1	49	gTc/gCc	1/14	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.629522642290559	2		626	754	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0066042-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	207	602	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.306876442767213	2	FACETS	1	0.992	1	0.738	0.692	0.785	INDETERMINATE	1	TRUE	0	0.571290034494825	2		602	491	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572495	41572495	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066042-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	105	757	0	ENST00000263253.7:c.5024A>G	p.His1675Arg	p.H1675R	ENST00000263253	NM_001429.3	1675	cAc/cGc	30/31	0.571290034494825	1	FACETS	0.491	0.441	0.543	0.491	0.441	0.543	SUBCLONAL	1	TRUE	0	0.571290034494825	1		757	535	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	90	286	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.197659914235795	4	FACETS	0.929	0.827	1	0.929	0.827	1	CLONAL	2	TRUE	2	0.240240619991721	4		286	500	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219389	1219389	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0066043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	183	488	0	ENST00000326873.7:c.443del	p.Phe148SerfsTer13	p.F148Sfs*13	ENST00000326873	NM_000455.4	147	cgT/cg	3/10	0.214684802969748	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.240240619991721	2		488	701	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610181	10610181	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	198	559	0	ENST00000171111.5:c.529C>T	p.Gln177Ter	p.Q177*	ENST00000171111	NM_203500.1	177	Cag/Tag	2/6	0.228207503410127	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.240240619991721	2		559	780	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211843	2211843	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0066043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	157	491	0	ENST00000398665.3:c.1557+2T>G		p.X519_splice	ENST00000398665	NM_032482.2	519			0.214684802969748	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.240240619991721	2		491	610	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989058	41989058	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	131	578	0	ENST00000219905.7:c.1850C>T	p.Pro617Leu	p.P617L	ENST00000219905	NM_001164273.1	617	cCa/cTa	3/24	0.145154937719931	4	FACETS	1	0.985	1	0.738	0.669	0.811	CLONAL	1	TRUE	2	0.240240619991721	4		578	916	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0066044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	144	491	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.902	0.83	0.977	1	0.991	1	CLONAL	2	TRUE	1	0.355445545277594	2		491	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0066044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	136	592	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	0.27719722731036	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.355445545277594	1		592	587	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120013	70120013	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	72	623	0	ENST00000245479.2:c.1015C>T	p.Gln339Ter	p.Q339*	ENST00000245479	NM_000346.3	339	Cag/Tag	3/3	1	2	FACETS	0.673	0.588	0.764	0.673	0.588	0.764	SUBCLONAL	1	TRUE	1	0.355445545277594	2		623	602	SUCCESS
APC	324	MSKCC	GRCh37	5	112175351	112175355	+	frameshift_variant	Frame_Shift_Del	DEL	TTTTC	TTTTC	-	novel	NA	P-0066044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	169	577	0	ENST00000257430.4:c.4062_4066del	p.Ser1355ArgfsTer18	p.S1355Rfs*18	ENST00000257430	NM_000038.5	1354	TTTTCt/t	16/16	1	2	FACETS	0.821	0.759	0.885	1	0.991	1	CLONAL	2	TRUE	1	0.355445545277594	2		577	579	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982134	93982134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773950345	NA	P-0066044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	53	523	0	ENST00000369303.4:c.1331C>T	p.Ser444Leu	p.S444L	ENST00000369303	NM_004440.3	444	tCg/tTg	6/17	1	2	FACETS	0.564	0.481	0.655	0.564	0.481	0.655	SUBCLONAL	1	TRUE	1	0.355445545277594	2		523	529	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114905823	114905824	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0066044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	98	520	0	ENST00000543371.1:c.845_846dup	p.Ala283GlnfsTer3	p.A283Qfs*3	ENST00000543371	NM_001198531.1	281	ccc/ccCAc	8/14	1	2	FACETS	0.99	0.886	1	0.99	0.886	1	CLONAL	1	TRUE	1	0.355445545277594	2		520	557	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120450	70120451	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0066044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	110	671	0	ENST00000245479.2:c.1452_1453del	p.Val486ProfsTer91	p.V486Pfs*91	ENST00000245479	NM_000346.3	484	tcTGgg/tcgg	3/3	1	2	FACETS	0.788	0.708	0.873	0.788	0.708	0.873	SUBCLONAL	1	TRUE	1	0.355445545277594	2		671	785	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265316	46265316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	1421	582	0	ENST00000371998.3:c.2186C>T	p.Pro729Leu	p.P729L	ENST00000371998		729	cCt/cTt	12/23	0.355445545277594	13	FACETS	0.977	0.962	0.992			1	CLONAL	13	TRUE	NA	0.355445545277594	13		582	1860	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281621	142281621	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763494560	NA	P-0066044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	64	442	0	ENST00000350721.4:c.623C>T	p.Thr208Ile	p.T208I	ENST00000350721	NM_001184.3	208	aCt/aTt	4/47	1	2	FACETS	0.63	0.545	0.721	0.63	0.545	0.721	SUBCLONAL	1	TRUE	1	0.355445545277594	2		442	572	SUCCESS
APC	324	MSKCC	GRCh37	5	112175101	112175102	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTTTCAAG	novel	NA	P-0066044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	134	517	0	ENST00000257430.4:c.3811_3818dup	p.Arg1273SerfsTer18	p.R1273Sfs*18	ENST00000257430	NM_000038.5	1270	-/TTTTCAAG	16/16	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.355445545277594	2		517	535	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188533	11188533	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	180	429	0	ENST00000361445.4:c.5888A>G	p.Asp1963Gly	p.D1963G	ENST00000361445	NM_004958.3	1963	gAc/gGc	42/58	1	2	FACETS	0.94	0.871	1	0.94	0.871	1	CLONAL	1	TRUE	1	0.62	2		429	618	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16203164	16203164	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	226	485	0	ENST00000375759.3:c.872G>A	p.Ser291Asn	p.S291N	ENST00000375759	NM_015001.2	291	aGc/aAc	3/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.62	2		485	691	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254929	16254929	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs751475729	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	85	575	0	ENST00000375759.3:c.2194C>T	p.Arg732Ter	p.R732*	ENST00000375759	NM_015001.2	732	Cga/Tga	11/15	1	2	FACETS	0.365	0.322	0.411	0.365	0.322	0.411	SUBCLONAL	1	TRUE	1	0.62	2		575	752	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795060	45795060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374655042	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	179	559	0	ENST00000450313.1:c.1568G>A	p.Arg523His	p.R523H	ENST00000450313	NM_012222.2	523	cGc/cAc	16/16	1	2	FACETS	0.827	0.765	0.892	0.827	0.765	0.892	CLONAL	1	TRUE	1	0.62	2		559	698	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306959	65306959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358494508	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	187	571	2	ENST00000342505.4:c.2618G>A	p.Arg873His	p.R873H	ENST00000342505	NM_002227.2	873	cGc/cAc	19/25	1	2	FACETS	0.84	0.778	0.904	0.84	0.778	0.904	CLONAL	1	TRUE	1	0.62	2		573	718	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251236	115251236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	193	465	0	ENST00000369535.4:c.490C>T	p.Arg164Cys	p.R164C	ENST00000369535	NM_002524.4	164	Cgc/Tgc	5/7	1	2	FACETS	0.912	0.847	0.978	0.912	0.847	0.978	CLONAL	1	TRUE	1	0.62	2		465	683	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263192	115263192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	197	438	0	ENST00000438362.2:c.2158C>T	p.Arg720Cys	p.R720C	ENST00000438362	NM_001242891.1	720	Cgc/Tgc	17/20	1	2	FACETS	0.981	0.912	1	0.981	0.912	1	CLONAL	1	TRUE	1	0.62	2		438	648	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275305	115275305	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	193	456	0	ENST00000438362.2:c.1108C>T	p.Arg370Ter	p.R370*	ENST00000438362	NM_001242891.1	370	Cga/Tga	10/20	1	2	FACETS	0.928	0.862	0.996	0.928	0.862	0.996	CLONAL	1	TRUE	1	0.62	2		456	671	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280667	115280667	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	173	382	0	ENST00000438362.2:c.364G>T	p.Asp122Tyr	p.D122Y	ENST00000438362	NM_001242891.1	122	Gac/Tac	4/20	1	2	FACETS	0.952	0.881	1	0.952	0.881	1	CLONAL	1	TRUE	1	0.62	2		382	586	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843452	156843452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs567093941	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	188	668	0	ENST00000524377.1:c.878C>T	p.Ala293Val	p.A293V	ENST00000524377	NM_002529.3	293	gCg/gTg	8/17	1	2	FACETS	0.876	0.813	0.942	0.876	0.813	0.942	CLONAL	1	TRUE	1	0.62	2		668	692	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849054	156849054	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786205449	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	180	601	0	ENST00000524377.1:c.1946G>A	p.Arg649Gln	p.R649Q	ENST00000524377	NM_002529.3	649	cGg/cAg	15/17	1	2	FACETS	0.952	0.882	1	0.952	0.882	1	CLONAL	1	TRUE	1	0.62	2		601	610	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107231	193107231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	141	496	0	ENST00000367435.3:c.440G>A	p.Arg147His	p.R147H	ENST00000367435	NM_024529.4	147	cGc/cAc	6/17	1	2	FACETS	0.825	0.756	0.898	0.825	0.756	0.898	CLONAL	1	TRUE	1	0.62	2		496	551	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564969	226564969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776941221	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	236	567	0	ENST00000366794.5:c.1781C>T	p.Thr594Met	p.T594M	ENST00000366794	NM_001618.3	594	aCg/aTg	13/23	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.62	2		567	730	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612974	228612974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756810829	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	250	582	1	ENST00000366696.1:c.53G>A	p.Arg18His	p.R18H	ENST00000366696	NM_003493.2	18	cGc/cAc	1/1	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.62	2		583	756	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601893	43601893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057521089	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	190	534	1	ENST00000355710.3:c.937C>T	p.Arg313Trp	p.R313W	ENST00000355710	NM_020975.4	313	Cgg/Tgg	5/20	1	2	FACETS	0.881	0.817	0.946	0.881	0.817	0.946	CLONAL	1	TRUE	1	0.62	2		535	696	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851924	63851924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199637139	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	216	588	0	ENST00000279873.7:c.2702C>T	p.Thr901Met	p.T901M	ENST00000279873	NM_032199.2	901	aCg/aTg	10/10	1	2	FACETS	0.916	0.854	0.979	0.916	0.854	0.979	CLONAL	1	TRUE	1	0.62	2		588	761	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	146	405	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	0.951	0.874	1	0.951	0.874	1	CLONAL	1	TRUE	1	0.62	2		405	495	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309776	104309776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202247756	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	211	453	0	ENST00000369902.3:c.367C>T	p.Arg123Cys	p.R123C	ENST00000369902	NM_016169.3	123	Cgt/Tgt	3/12	1	2	FACETS	0.947	0.883	1	0.947	0.883	1	CLONAL	1	TRUE	1	0.62	2		453	719	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625284	69625284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782801923	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	191	543	0	ENST00000334134.2:c.509G>A	p.Arg170His	p.R170H	ENST00000334134	NM_005247.2	170	cGc/cAc	3/3	1	2	FACETS	0.98	0.91	1	0.98	0.91	1	CLONAL	1	TRUE	1	0.62	2		543	629	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94908685	94908685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764427282	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	163	390	0	ENST00000536441.1:c.1369C>T	p.Arg457Trp	p.R457W	ENST00000536441	NM_144665.3	457	Cgg/Tgg	9/10	1	2	FACETS	0.907	0.836	0.979	0.907	0.836	0.979	CLONAL	1	TRUE	1	0.62	2		390	580	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343976	118343976	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	195	588	0	ENST00000534358.1:c.2102G>T	p.Arg701Ile	p.R701I	ENST00000534358	NM_005933.3	701	aGa/aTa	3/36	1	2	FACETS	0.874	0.811	0.938	0.874	0.811	0.938	CLONAL	1	TRUE	1	0.62	2		588	720	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103249	119103249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781738309	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	198	539	0	ENST00000264033.4:c.287G>A	p.Arg96His	p.R96H	ENST00000264033	NM_005188.3	96	cGt/cAt	2/16	1	2	FACETS	0.901	0.837	0.966	0.901	0.837	0.966	CLONAL	1	TRUE	1	0.62	2		539	709	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422224	422224	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	182	444	0	ENST00000399788.2:c.3034C>T	p.Gln1012Ter	p.Q1012*	ENST00000399788	NM_001042603.1	1012	Cag/Tag	20/28	1	2	FACETS	0.907	0.841	0.976	0.907	0.841	0.976	CLONAL	1	TRUE	1	0.62	2		444	647	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524215	18524215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769408892	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	170	428	0	ENST00000266497.5:c.1727C>T	p.Ala576Val	p.A576V	ENST00000266497		576	gCg/gTg	11/31	1	2	FACETS	0.967	0.895	1	0.967	0.895	1	CLONAL	1	TRUE	1	0.62	2		428	567	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793451	18793451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	128	394	0	ENST00000266497.5:c.4148C>T	p.Ser1383Phe	p.S1383F	ENST00000266497		1383	tCt/tTt	30/31	1	2	FACETS	0.839	0.765	0.916	0.839	0.765	0.916	CLONAL	1	TRUE	1	0.62	2		394	492	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421039	49421039	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123721	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	213	592	0	ENST00000301067.7:c.14710C>T	p.Arg4904Ter	p.R4904*	ENST00000301067	NM_003482.3	4904	Cga/Tga	48/54	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.62	2		592	686	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447310	49447310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747495428	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	222	536	0	ENST00000301067.7:c.788G>A	p.Arg263His	p.R263H	ENST00000301067	NM_003482.3	263	cGc/cAc	6/54	1	2	FACETS	0.949	0.886	1	0.949	0.886	1	CLONAL	1	TRUE	1	0.62	2		536	755	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	167	471	0	ENST00000267101.3:c.273G>T	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atT	3/28	1	2	FACETS	0.913	0.843	0.985	0.913	0.843	0.985	CLONAL	1	TRUE	1	0.62	2		471	590	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482409	56482409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372826813	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	209	555	0	ENST00000267101.3:c.957G>A	p.Met319Ile	p.M319I	ENST00000267101	NM_001982.3	319	atG/atA	8/28	1	2	FACETS	0.966	0.9	1	0.966	0.9	1	CLONAL	1	TRUE	1	0.62	2		555	698	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222593	69222593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194693256	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	197	447	0	ENST00000462284.1:c.566G>A	p.Arg189His	p.R189H	ENST00000462284	NM_002392.5	189	cGc/cAc	8/11	1	2	FACETS	0.896	0.833	0.962	0.896	0.833	0.962	CLONAL	1	TRUE	1	0.62	2		447	709	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811753	102811753	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369105057	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	238	630	0	ENST00000307046.8:c.431C>T	p.Thr144Met	p.T144M	ENST00000307046	NM_001111285.1	144	aCg/aTg	4/4	1	2	FACETS	0.962	0.901	1	0.962	0.901	1	CLONAL	1	TRUE	1	0.62	2		630	798	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926960	112926960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770363146	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	160	421	0	ENST00000351677.2:c.1580G>A	p.Arg527His	p.R527H	ENST00000351677	NM_002834.3	527	cGc/cAc	13/16	1	2	FACETS	0.967	0.892	1	0.967	0.892	1	CLONAL	1	TRUE	1	0.62	2		421	534	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233976	133233976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775271152	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	159	480	0	ENST00000320574.5:c.3418G>A	p.Ala1140Thr	p.A1140T	ENST00000320574	NM_006231.2	1140	Gcc/Acc	28/49	1	2	FACETS	0.88	0.81	0.951	0.88	0.81	0.951	CLONAL	1	TRUE	1	0.62	2		480	583	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250213	133250213	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs864622766	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	204	599	0	ENST00000320574.5:c.1307C>G	p.Pro436Arg	p.P436R	ENST00000320574	NM_006231.2	436	cCc/cGc	13/49	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.62	2		599	624	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562564	21562564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1452154404	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	110	423	0	ENST00000382592.4:c.1355C>T	p.Pro452Leu	p.P452L	ENST00000382592	NM_014572.2	452	cCg/cTg	4/8	1	2	FACETS	0.865	0.784	0.951	0.865	0.784	0.951	CLONAL	1	TRUE	1	0.62	2		423	410	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636179	28636179	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	157	476	0	ENST00000241453.7:c.193T>C	p.Cys65Arg	p.C65R	ENST00000241453	NM_004119.2	65	Tgt/Cgt	3/24	1	2	FACETS	0.793	0.729	0.859	0.793	0.729	0.859	SUBCLONAL	1	TRUE	1	0.62	2		476	639	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910976	32910977	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	152	532	0	ENST00000380152.3:c.2489dup	p.Asn830LysfsTer3	p.N830Kfs*3	ENST00000380152		828	-/A	11/27	1	2	FACETS	0.813	0.747	0.882	0.813	0.747	0.882	CLONAL	1	TRUE	1	0.62	2		532	603	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953953	32953953	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	179	438	0	ENST00000380152.3:c.9020G>T	p.Arg3007Ile	p.R3007I	ENST00000380152		3007	aGa/aTa	23/27	1	2	FACETS	0.959	0.889	1	0.959	0.889	1	CLONAL	1	TRUE	1	0.62	2		438	602	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134924	41134924	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	237	496	0	ENST00000379561.5:c.704C>A	p.Ser235Tyr	p.S235Y	ENST00000379561	NM_002015.3	235	tCt/tAt	2/3	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.62	2		496	683	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524624	103524624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377353991	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	203	479	0	ENST00000355739.4:c.2755C>T	p.Arg919Trp	p.R919W	ENST00000355739	NM_000123.3	919	Cgg/Tgg	13/15	1	2	FACETS	0.926	0.862	0.992	0.926	0.862	0.992	CLONAL	1	TRUE	1	0.62	2		479	707	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434889	110434889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1021457672	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	213	672	0	ENST00000375856.3:c.3512G>A	p.Arg1171His	p.R1171H	ENST00000375856	NM_003749.2	1171	cGc/cAc	1/2	1	2	FACETS	0.962	0.898	1	0.962	0.898	1	CLONAL	1	TRUE	1	0.62	2		672	714	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436128	110436128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	202	596	0	ENST00000375856.3:c.2273G>A	p.Gly758Asp	p.G758D	ENST00000375856	NM_003749.2	758	gGc/gAc	1/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.62	2		596	602	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609889	81609889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769777295	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	196	679	0	ENST00000298171.2:c.1487C>T	p.Thr496Met	p.T496M	ENST00000298171	NM_000369.2	496	aCg/aTg	10/10	1	2	FACETS	0.809	0.75	0.869	0.809	0.75	0.869	CLONAL	1	TRUE	1	0.62	2		679	782	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738669	43738669	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758253263	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	189	524	0	ENST00000382044.4:c.2956G>A	p.Val986Met	p.V986M	ENST00000382044	NM_001141980.1	986	Gtg/Atg	14/28	1	2	FACETS	0.864	0.801	0.928	0.864	0.801	0.928	CLONAL	1	TRUE	1	0.62	2		524	706	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310207	91310208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs747341586	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	172	327	0	ENST00000355112.3:c.2268dup	p.Asp757ArgfsTer18	p.D757Rfs*18	ENST00000355112	NM_000057.2	754	tca/tcAa	10/22	1	2	FACETS	0.94	0.87	1	0.94	0.87	1	CLONAL	1	TRUE	1	0.62	2		327	590	SUCCESS
BLM	641	MSKCC	GRCh37	15	91352484	91352484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1031421025	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	180	365	0	ENST00000355112.3:c.3869C>T	p.Ser1290Leu	p.S1290L	ENST00000355112	NM_000057.2	1290	tCg/tTg	20/22	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.62	2		365	579	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862749	9862749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150316865	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	164	525	0	ENST00000330684.3:c.2554G>A	p.Val852Met	p.V852M	ENST00000330684	NM_001134407.1	852	Gtg/Atg	12/13	1	2	FACETS	0.964	0.89	1	0.964	0.89	1	CLONAL	1	TRUE	1	0.62	2		525	549	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041930	14041930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141790888	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	205	559	0	ENST00000311895.7:c.2477C>T	p.Ala826Val	p.A826V	ENST00000311895	NM_005236.2	826	gCg/gTg	11/11	1	2	FACETS	0.935	0.871	1	0.935	0.871	1	CLONAL	1	TRUE	1	0.62	2		559	707	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655373	67655373	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	223	452	0	ENST00000264010.4:c.1236T>A	p.Cys412Ter	p.C412*	ENST00000264010	NM_006565.3	412	tgT/tgA	7/12	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.62	2		452	687	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867268	68867268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780121	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	186	546	0	ENST00000261769.5:c.2515G>A	p.Gly839Ser	p.G839S	ENST00000261769	NM_004360.3	839	Ggt/Agt	16/16	1	2	FACETS	0.823	0.762	0.886	0.823	0.762	0.886	CLONAL	1	TRUE	1	0.62	2		546	729	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991508	72991508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755878058	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	409	539	0	ENST00000268489.5:c.2537G>A	p.Arg846His	p.R846H	ENST00000268489	NM_006885.3	846	cGc/cAc	2/10	1	2	FACETS	0.959	0.923	0.995	1	0.997	1	CLONAL	2	TRUE	1	0.62	2		539	688	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992641	72992641	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	58	658	0	ENST00000268489.5:c.1404G>T	p.Glu468Asp	p.E468D	ENST00000268489	NM_006885.3	468	gaG/gaT	2/10	1	2	FACETS	0.262	0.224	0.303	0.262	0.224	0.303	SUBCLONAL	1	TRUE	1	0.62	2		658	714	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993128	72993128	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142256050	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	219	578	0	ENST00000268489.5:c.917G>A	p.Arg306Gln	p.R306Q	ENST00000268489	NM_006885.3	306	cGa/cAa	2/10	1	2	FACETS	0.933	0.871	0.997	0.933	0.871	0.997	CLONAL	1	TRUE	1	0.62	2		578	757	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81960768	81960768	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	163	539	0	ENST00000359376.3:c.2499G>T	p.Glu833Asp	p.E833D	ENST00000359376	NM_002661.3	833	gaG/gaT	23/33	1	2	FACETS	0.844	0.778	0.912	0.844	0.778	0.912	CLONAL	1	TRUE	1	0.62	2		539	623	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347584	89347584	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1048947362	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	200	615	0	ENST00000301030.4:c.5366G>A	p.Arg1789His	p.R1789H	ENST00000301030	NM_001256183.1	1789	cGc/cAc	9/13	1	2	FACETS	0.872	0.81	0.935	0.872	0.81	0.935	CLONAL	1	TRUE	1	0.62	2		615	740	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348059	89348059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1402377065	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	46	625	0	ENST00000301030.4:c.4891C>T	p.Arg1631Trp	p.R1631W	ENST00000301030	NM_001256183.1	1631	Cgg/Tgg	9/13	1	2	FACETS	0.197	0.165	0.232	0.197	0.165	0.232	SUBCLONAL	1	TRUE	1	0.62	2		625	755	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348652	89348652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1487348306	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	227	525	1	ENST00000301030.4:c.4298C>T	p.Ser1433Phe	p.S1433F	ENST00000301030	NM_001256183.1	1433	tCc/tTc	9/13	1	2	FACETS	0.949	0.887	1	0.949	0.887	1	CLONAL	1	TRUE	1	0.62	2		526	772	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349904	89349904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141871215	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	237	698	0	ENST00000301030.4:c.3046G>A	p.Asp1016Asn	p.D1016N	ENST00000301030	NM_001256183.1	1016	Gat/Aat	9/13	1	2	FACETS	0.887	0.829	0.946	0.887	0.829	0.946	CLONAL	1	TRUE	1	0.62	2		698	862	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044509	12044509	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771926980	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	163	452	0	ENST00000353533.5:c.1132G>A	p.Ala378Thr	p.A378T	ENST00000353533	NM_003010.3	378	Gca/Aca	11/11	1	2	FACETS	0.936	0.864	1	0.936	0.864	1	CLONAL	1	TRUE	1	0.62	2		452	562	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627887	37627887	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	252	585	0	ENST00000447079.4:c.1802C>A	p.Ser601Tyr	p.S601Y	ENST00000447079	NM_015083.1	601	tCt/tAt	2/14	1	2	FACETS	0.977	0.917	1	0.977	0.917	1	CLONAL	1	TRUE	1	0.62	2		585	832	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40872306	40872306	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs781642151	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	168	461	3	ENST00000428826.2:c.649C>T	p.Arg217Ter	p.R217*	ENST00000428826		217	Cga/Tga	7/21	1	2	FACETS	0.81	0.747	0.875	0.81	0.747	0.875	CLONAL	1	TRUE	1	0.62	2		464	669	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47684731	47684731	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	184	433	0	ENST00000347630.2:c.718C>T	p.Arg240Ter	p.R240*	ENST00000347630	NM_001007230.1	240	Cga/Tga	9/11	1	2	FACETS	0.976	0.906	1	0.976	0.906	1	CLONAL	1	TRUE	1	0.62	2		433	608	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554043	63554043	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	244	567	0	ENST00000307078.5:c.696G>T	p.Glu232Asp	p.E232D	ENST00000307078	NM_004655.3	232	gaG/gaT	2/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.62	2		567	728	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604790	48604790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	228	482	0	ENST00000342988.3:c.1612G>A	p.Glu538Lys	p.E538K	ENST00000342988	NM_005359.5	538	Gaa/Aaa	12/12	1	2	FACETS	0.977	0.913	1	0.977	0.913	1	CLONAL	1	TRUE	1	0.62	2		482	753	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218483	1218483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775595174	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	189	464	0	ENST00000326873.7:c.358G>A	p.Glu120Lys	p.E120K	ENST00000326873	NM_000455.4	120	Gaa/Aaa	2/10	1	2	FACETS	0.991	0.921	1	0.991	0.921	1	CLONAL	1	TRUE	1	0.62	2		464	615	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226233	2226233	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	63	570	0	ENST00000398665.3:c.3713G>A	p.Ser1238Asn	p.S1238N	ENST00000398665	NM_032482.2	1238	aGc/aAc	27/28	1	2	FACETS	0.313	0.27	0.359	0.313	0.27	0.359	SUBCLONAL	1	TRUE	1	0.62	2		570	650	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252856	10252856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370786558	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	239	574	0	ENST00000340748.4:c.3109G>A	p.Ala1037Thr	p.A1037T	ENST00000340748		1037	Gca/Aca	29/40	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.62	2		574	764	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943411	17943411	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	190	507	0	ENST00000458235.1:c.2597G>T	p.Arg866Met	p.R866M	ENST00000458235	NM_000215.3	866	aGg/aTg	19/24	1	2	FACETS	0.934	0.868	1	0.934	0.868	1	CLONAL	1	TRUE	1	0.62	2		507	656	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955108	17955108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56384680	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	185	559	0	ENST00000458235.1:c.119G>A	p.Arg40His	p.R40H	ENST00000458235	NM_000215.3	40	cGc/cAc	2/24	1	2	FACETS	0.983	0.913	1	0.983	0.913	1	CLONAL	1	TRUE	1	0.62	2		559	607	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220908	36220908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	183	547	1	ENST00000222270.7:c.4958G>A	p.Cys1653Tyr	p.C1653Y	ENST00000222270	NM_014727.1	1653	tGc/tAc	23/37	1	2	FACETS	0.93	0.862	0.999	0.93	0.862	0.999	CLONAL	1	TRUE	1	0.62	2		548	635	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741861	40741861	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745550650	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	196	635	1	ENST00000392038.2:c.1111C>T	p.Arg371Cys	p.R371C	ENST00000392038	NM_001626.4	371	Cgc/Tgc	11/14	1	2	FACETS	0.914	0.849	0.98	0.914	0.849	0.98	CLONAL	1	TRUE	1	0.62	2		636	692	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763485	41763485	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	199	568	0	ENST00000301178.4:c.2284C>A	p.Leu762Met	p.L762M	ENST00000301178	NM_021913.4	762	Ctg/Atg	19/20	1	2	FACETS	0.988	0.919	1	0.988	0.919	1	CLONAL	1	TRUE	1	0.62	2		568	650	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765694	41765694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61737385	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	182	651	0	ENST00000301178.4:c.2570C>T	p.Ala857Val	p.A857V	ENST00000301178	NM_021913.4	857	gCg/gTg	20/20	1	2	FACETS	0.948	0.879	1	0.948	0.879	1	CLONAL	1	TRUE	1	0.62	2		651	619	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383677	42383677	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1221821073	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	177	515	0	ENST00000221972.3:c.452T>C	p.Ile151Thr	p.I151T	ENST00000221972	NM_021601.3	151	aTc/aCc	3/5	1	2	FACETS	0.909	0.842	0.979	0.909	0.842	0.979	CLONAL	1	TRUE	1	0.62	2		515	628	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752816	42752816	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	215	669	0	ENST00000222329.4:c.1448G>A	p.Arg483His	p.R483H	ENST00000222329	NM_006494.2	483	cGc/cAc	4/4	1	2	FACETS	0.994	0.928	1	0.994	0.928	1	CLONAL	1	TRUE	1	0.62	2		669	698	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909523	50909523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	210	552	0	ENST00000440232.2:c.1327C>T	p.Arg443Trp	p.R443W	ENST00000440232	NM_002691.3	443	Cgg/Tgg	11/27	1	2	FACETS	0.945	0.881	1	0.945	0.881	1	CLONAL	1	TRUE	1	0.62	2		552	717	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716335	52716335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	163	507	0	ENST00000322088.6:c.779G>A	p.Arg260His	p.R260H	ENST00000322088	NM_014225.5	260	cGc/cAc	6/15	1	2	FACETS	0.907	0.836	0.979	0.907	0.836	0.979	CLONAL	1	TRUE	1	0.62	2		507	580	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505552	25505552	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	189	489	0	ENST00000264709.3:c.206C>A	p.Pro69His	p.P69H	ENST00000264709	NM_175629.2	69	cCt/cAt	4/23	1	2	FACETS	0.968	0.899	1	0.968	0.899	1	CLONAL	1	TRUE	1	0.62	2		489	630	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022295	26022295	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs944105395	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	196	493	0	ENST00000435504.4:c.362G>A	p.Gly121Asp	p.G121D	ENST00000435504		121	gGc/gAc	5/13	1	2	FACETS	0.846	0.786	0.909	0.846	0.786	0.909	CLONAL	1	TRUE	1	0.62	2		493	747	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607469	46607469	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201311893	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	205	601	0	ENST00000263734.3:c.1658C>T	p.Ala553Val	p.A553V	ENST00000263734	NM_001430.4	553	gCg/gTg	12/16	1	2	FACETS	0.92	0.856	0.985	0.92	0.856	0.985	CLONAL	1	TRUE	1	0.62	2		601	719	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025792	48025792	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	210	444	0	ENST00000234420.5:c.670G>T	p.Glu224Ter	p.E224*	ENST00000234420	NM_000179.2	224	Gaa/Taa	4/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.62	2		444	667	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033753	48033753	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1553333707	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	178	447	0	ENST00000234420.5:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000234420	NM_000179.2	1322	Gaa/Taa	9/10	1	2	FACETS	0.995	0.923	1	0.995	0.923	1	CLONAL	1	TRUE	1	0.62	2		447	577	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131514	202131514	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	204	471	0	ENST00000358485.4:c.482G>T	p.Arg161Met	p.R161M	ENST00000358485	NM_001080125.1	161	aGg/aTg	2/9	1	2	FACETS	0.929	0.865	0.995	0.929	0.865	0.995	CLONAL	1	TRUE	1	0.62	2		471	708	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149710	202149710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	226	586	0	ENST00000358485.4:c.1151G>A	p.Gly384Asp	p.G384D	ENST00000358485	NM_001080125.1	384	gGc/gAc	8/9	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.62	2		586	718	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251754	212251754	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	234	560	0	ENST00000342788.4:c.3305T>G	p.Phe1102Cys	p.F1102C	ENST00000342788	NM_005235.2	1102	tTt/tGt	27/28	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.62	2		560	712	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537975	212537975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267599192	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	191	430	0	ENST00000342788.4:c.1630C>T	p.Arg544Trp	p.R544W	ENST00000342788	NM_005235.2	544	Cgg/Tgg	14/28	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.62	2		430	601	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378259	225378259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	147	379	0	ENST00000264414.4:c.636G>A	p.Met212Ile	p.M212I	ENST00000264414	NM_003590.4	212	atG/atA	5/16	1	2	FACETS	0.891	0.819	0.967	0.891	0.819	0.967	CLONAL	1	TRUE	1	0.62	2		379	532	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662224	227662224	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	193	598	0	ENST00000305123.5:c.1231C>T	p.Arg411Ter	p.R411*	ENST00000305123	NM_005544.2	411	Cga/Tga	1/2	1	2	FACETS	0.876	0.813	0.94	0.876	0.813	0.94	CLONAL	1	TRUE	1	0.62	2		598	711	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100948	41100948	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	162	455	0	ENST00000373198.4:c.1408C>T	p.Arg470Ter	p.R470*	ENST00000373198	NM_133170.3	470	Cga/Tga	8/32	1	2	FACETS	0.837	0.771	0.906	0.837	0.771	0.906	CLONAL	1	TRUE	1	0.62	2		455	624	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256696	46256696	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768977330	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	197	417	0	ENST00000371998.3:c.752G>A	p.Arg251His	p.R251H	ENST00000371998		251	cGc/cAc	8/23	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.62	2		417	612	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256699	46256699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749607074	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	161	419	0	ENST00000371998.3:c.755G>A	p.Arg252His	p.R252H	ENST00000371998		252	cGc/cAc	8/23	1	2	FACETS	0.843	0.777	0.912	0.843	0.777	0.912	CLONAL	1	TRUE	1	0.62	2		419	616	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566524	41566525	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	206	467	2	ENST00000263253.7:c.4408dup	p.Met1470AsnfsTer3	p.M1470Nfs*3	ENST00000263253	NM_001429.3	1467	-/A	27/31	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.62	2		469	657	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181423	38181423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	245	538	0	ENST00000396334.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000396334	NM_002468.4	146	Gct/Act	2/5	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.62	2		538	735	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181460	38181460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1216607510	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	237	505	0	ENST00000396334.3:c.473C>T	p.Ala158Val	p.A158V	ENST00000396334	NM_002468.4	158	gCg/gTg	2/5	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.62	2		505	739	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438553	52438553	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770778299	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	214	524	0	ENST00000460680.1:c.1166G>A	p.Arg389His	p.R389H	ENST00000460680	NM_004656.3	389	cGc/cAc	12/17	1	2	FACETS	0.996	0.93	1	0.996	0.93	1	CLONAL	1	TRUE	1	0.62	2		524	693	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890351	72890351	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	180	367	0	ENST00000325599.8:c.332-1G>T		p.X111_splice	ENST00000325599	NM_018130.2	111			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.62	2		367	547	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89444986	89444986	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	218	563	0	ENST00000336596.2:c.1307-1G>T		p.X436_splice	ENST00000336596	NM_005233.5	436			1	2	FACETS	0.92	0.859	0.984	0.92	0.859	0.984	CLONAL	1	TRUE	1	0.62	2		563	764	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582302	119582302	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	242	540	0	ENST00000316626.5:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000316626		367	Cga/Tga	10/12	1	2	FACETS	0.953	0.893	1	0.953	0.893	1	CLONAL	1	TRUE	1	0.62	2		540	819	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426123	138426123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217537873	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	141	363	0	ENST00000289153.2:c.1408G>A	p.Glu470Lys	p.E470K	ENST00000289153	NM_006219.2	470	Gaa/Aaa	9/22	1	2	FACETS	0.89	0.816	0.967	0.89	0.816	0.967	CLONAL	1	TRUE	1	0.62	2		363	511	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177813	142177813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	137	404	0	ENST00000350721.4:c.7490G>A	p.Cys2497Tyr	p.C2497Y	ENST00000350721	NM_001184.3	2497	tGt/tAt	44/47	1	2	FACETS	0.976	0.894	1	0.976	0.894	1	CLONAL	1	TRUE	1	0.62	2		404	453	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013719	170013719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388201066	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	163	212	0	ENST00000295797.4:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000295797	NM_002740.5	480	Cgc/Tgc	15/18	1	2	FACETS	0.893	0.823	0.964	0.893	0.823	0.964	CLONAL	1	TRUE	1	0.62	2		212	589	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191157	185191157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs903937665	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	170	611	0	ENST00000265026.3:c.2038C>T	p.Arg680Trp	p.R680W	ENST00000265026	NM_004721.4	680	Cgg/Tgg	11/14	1	2	FACETS	0.893	0.825	0.963	0.893	0.825	0.963	CLONAL	1	TRUE	1	0.62	2		611	614	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902589	1902589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753748334	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	229	565	0	ENST00000382891.5:c.208G>A	p.Ala70Thr	p.A70T	ENST00000382891	NM_133335.3	70	Gcc/Acc	2/22	1	2	FACETS	0.914	0.854	0.976	0.914	0.854	0.976	CLONAL	1	TRUE	1	0.62	2		565	808	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953773	55953773	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	180	497	0	ENST00000263923.4:c.3662+1G>A		p.X1221_splice	ENST00000263923	NM_002253.2	1221			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.62	2		497	513	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968535	55968535	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	152	384	0	ENST00000263923.4:c.2128G>T	p.Asp710Tyr	p.D710Y	ENST00000263923	NM_002253.2	710	Gac/Tac	14/30	1	2	FACETS	0.965	0.889	1	0.965	0.889	1	CLONAL	1	TRUE	1	0.62	2		384	508	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201816	66201816	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556854839	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	189	519	0	ENST00000273854.3:c.2686C>T	p.Arg896Cys	p.R896C	ENST00000273854	NM_004439.5	896	Cgt/Tgt	16/18	1	2	FACETS	0.996	0.926	1	0.996	0.926	1	CLONAL	1	TRUE	1	0.62	2		519	612	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230813	66230813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748201189	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	165	497	0	ENST00000273854.3:c.2158G>A	p.Asp720Asn	p.D720N	ENST00000273854	NM_004439.5	720	Gat/Aat	12/18	1	2	FACETS	0.937	0.865	1	0.937	0.865	1	CLONAL	1	TRUE	1	0.62	2		497	568	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270102	66270102	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	155	437	0	ENST00000273854.3:c.1780C>A	p.Leu594Ile	p.L594I	ENST00000273854	NM_004439.5	594	Ctc/Atc	8/18	1	2	FACETS	0.917	0.845	0.992	0.917	0.845	0.992	CLONAL	1	TRUE	1	0.62	2		437	545	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	282	461	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.62	2		461	862	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539690	187539690	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs748166431	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	188	531	0	ENST00000441802.2:c.8050G>T	p.Glu2684Ter	p.E2684*	ENST00000441802	NM_005245.3	2684	Gaa/Taa	10/27	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.62	2		531	605	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260648	1260648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	243	559	0	ENST00000310581.5:c.2911C>T	p.Arg971Cys	p.R971C	ENST00000310581	NM_198253.2	971	Cgt/Tgt	12/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.62	2		559	771	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181881	56181881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	140	333	0	ENST00000399503.3:c.4105G>A	p.Asp1369Asn	p.D1369N	ENST00000399503	NM_005921.1	1369	Gat/Aat	17/20	1	2	FACETS	0.98	0.899	1	0.98	0.899	1	CLONAL	1	TRUE	1	0.62	2		333	461	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754884	57754884	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	181	408	0	ENST00000274289.3:c.306G>T	p.Leu102Phe	p.L102F	ENST00000274289	NM_006622.3	102	ttG/ttT	2/14	1	2	FACETS	0.94	0.871	1	0.94	0.871	1	CLONAL	1	TRUE	1	0.62	2		408	621	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	409	497	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	0.991	0.954	1	1	0.997	1	CLONAL	2	TRUE	1	0.62	2		497	666	SUCCESS
APC	324	MSKCC	GRCh37	5	112111328	112111328	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	125	282	0	ENST00000257430.4:c.425C>A	p.Ser142Ter	p.S142*	ENST00000257430	NM_000038.5	142	tCa/tAa	5/16	1	2	FACETS	0.969	0.885	1	0.969	0.885	1	CLONAL	1	TRUE	1	0.62	2		282	416	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	272	601	2	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.62	2		603	841	SUCCESS
APC	324	MSKCC	GRCh37	5	112176329	112176329	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs754122018	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	205	566	0	ENST00000257430.4:c.5038C>T	p.Gln1680Ter	p.Q1680*	ENST00000257430	NM_000038.5	1680	Cag/Tag	16/16	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.62	2		566	631	SUCCESS
APC	324	MSKCC	GRCh37	5	112177901	112177901	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs752654519	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	230	556	0	ENST00000257430.4:c.6610C>T	p.Arg2204Ter	p.R2204*	ENST00000257430	NM_000038.5	2204	Cga/Tga	16/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.62	2		556	715	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915194	131915194	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	142	350	0	ENST00000265335.6:c.551G>A	p.Arg184Lys	p.R184K	ENST00000265335		184	aGa/aAa	4/25	1	2	FACETS	0.979	0.899	1	0.979	0.899	1	CLONAL	1	TRUE	1	0.62	2		350	468	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435618	149435618	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	162	457	0	ENST00000286301.3:c.2525G>T	p.Gly842Val	p.G842V	ENST00000286301	NM_005211.3	842	gGc/gTc	19/22	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.62	2		457	503	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043377	180043377	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771345898	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	201	619	1	ENST00000261937.6:c.3209G>A	p.Arg1070His	p.R1070H	ENST00000261937	NM_182925.4	1070	cGc/cAc	23/30	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.62	2		620	626	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117632201	117632201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779401784	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	154	480	0	ENST00000368508.3:c.6215G>A	p.Arg2072Gln	p.R2072Q	ENST00000368508	NM_002944.2	2072	cGg/cAg	39/43	1	2	FACETS	0.92	0.847	0.995	0.92	0.847	0.995	CLONAL	1	TRUE	1	0.62	2		480	540	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681555	117681555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	190	395	0	ENST00000368508.3:c.3395C>T	p.Thr1132Ile	p.T1132I	ENST00000368508	NM_002944.2	1132	aCa/aTa	22/43	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.62	2		395	583	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715410	117715410	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769599473	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	138	391	0	ENST00000368508.3:c.1079G>T	p.Arg360Ile	p.R360I	ENST00000368508	NM_002944.2	360	aGa/aTa	10/43	1	2	FACETS	0.878	0.804	0.955	0.878	0.804	0.955	CLONAL	1	TRUE	1	0.62	2		391	507	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	219	533	0	ENST00000206249.3:c.1607T>C	p.Leu536Pro	p.L536P	ENST00000206249	NM_000125.3	536	cTc/cCc	8/8	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.62	2		533	705	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510830	157510830	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs902679026	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	195	573	0	ENST00000346085.5:c.3605C>T	p.Ser1202Phe	p.S1202F	ENST00000346085	NM_020732.3	1202	tCc/tTc	14/20	1	2	FACETS	0.917	0.852	0.984	0.917	0.852	0.984	CLONAL	1	TRUE	1	0.62	2		573	686	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043374	6043374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	31	65	0	ENST00000265849.7:c.300G>T	p.Gln100His	p.Q100H	ENST00000265849	NM_000535.5	100	caG/caT	4/15	1	2	FACETS	1	0.83	1	1	0.83	1	CLONAL	1	TRUE	1	0.62	2		65	100	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509806	106509806	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	183	532	0	ENST00000359195.3:c.1800G>T	p.Gln600His	p.Q600H	ENST00000359195	NM_002649.2	600	caG/caT	2/11	1	2	FACETS	0.924	0.856	0.993	0.924	0.856	0.993	CLONAL	1	TRUE	1	0.62	2		532	639	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843278	128843278	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41303402	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	174	543	0	ENST00000249373.3:c.385G>A	p.Val129Ile	p.V129I	ENST00000249373	NM_005631.4	129	Gta/Ata	2/12	1	2	FACETS	0.988	0.915	1	0.988	0.915	1	CLONAL	1	TRUE	1	0.62	2		543	568	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494257	140494257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1181422421	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	243	568	0	ENST00000288602.6:c.991C>T	p.Leu331Phe	p.L331F	ENST00000288602	NM_004333.4	331	Ctc/Ttc	8/18	1	2	FACETS	0.985	0.923	1	0.985	0.923	1	CLONAL	1	TRUE	1	0.62	2		568	796	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945341	151945341	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs906216502	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	30	88	0	ENST00000262189.6:c.2178G>T	p.Gln726His	p.Q726H	ENST00000262189	NM_170606.2	726	caG/caT	14/59	1	2	FACETS	0.739	0.605	0.885	0.739	0.605	0.885	SUBCLONAL	1	TRUE	1	0.62	2		88	131	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29197723	29197723	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs774219516	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	220	499	0	ENST00000240100.2:c.471C>A	p.Phe157Leu	p.F157L	ENST00000240100	NM_001394.6	157	ttC/ttA	2/4	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.62	2		499	632	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485824	8485824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs547908736	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	183	435	0	ENST00000356435.5:c.2993C>T	p.Thr998Met	p.T998M	ENST00000356435		998	aCg/aTg	17/35	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.62	2		435	561	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779084	135779084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769566267	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	224	480	0	ENST00000298552.3:c.2162G>A	p.Arg721His	p.R721H	ENST00000298552	NM_001162426.1	721	cGc/cAc	17/23	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.62	2		480	708	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399781	139399781	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746025437	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	201	528	0	ENST00000277541.6:c.4567C>T	p.Arg1523Cys	p.R1523C	ENST00000277541	NM_017617.3	1523	Cgt/Tgt	25/34	1	2	FACETS	0.883	0.821	0.947	0.883	0.821	0.947	CLONAL	1	TRUE	1	0.62	2		528	734	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317461	1317461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781459586	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	215	474	0	ENST00000400841.2:c.604G>A	p.Asp202Asn	p.D202N	ENST00000400841		202	Gac/Aac	5/6	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.62	2		474	627	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923603	39923603	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1048287551	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	206	543	1	ENST00000378444.4:c.3488G>A	p.Arg1163Gln	p.R1163Q	ENST00000378444	NM_001123385.1	1163	cGa/cAa	7/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.62	2		544	626	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041170	47041170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	174	550	0	ENST00000377604.3:c.1598C>T	p.Ala533Val	p.A533V	ENST00000377604	NM_001204468.1	533	gCt/gTt	15/24	1	2	FACETS	0.857	0.792	0.924	0.857	0.792	0.924	CLONAL	1	TRUE	1	0.62	2		550	655	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428244	47428244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	166	630	0	ENST00000377045.4:c.1204G>A	p.Asp402Asn	p.D402N	ENST00000377045	NM_001654.4	402	Gac/Aac	11/16	1	2	FACETS	0.811	0.748	0.877	0.811	0.748	0.877	CLONAL	1	TRUE	1	0.62	2		630	660	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650563	48650563	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	209	761	0	ENST00000376670.3:c.533G>T	p.Ser178Ile	p.S178I	ENST00000376670	NM_002049.3	178	aGc/aTc	3/6	1	2	FACETS	0.846	0.787	0.906	0.846	0.787	0.906	CLONAL	1	TRUE	1	0.62	2		761	797	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222414	53222414	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	177	580	0	ENST00000375401.3:c.4418C>T	p.Ala1473Val	p.A1473V	ENST00000375401	NM_004187.3	1473	gCc/gTc	26/26	1	2	FACETS	0.966	0.895	1	0.966	0.895	1	CLONAL	1	TRUE	1	0.62	2		580	591	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245075	53245075	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs782081983	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	176	568	0	ENST00000375401.3:c.865A>G	p.Lys289Glu	p.K289E	ENST00000375401	NM_004187.3	289	Aag/Gag	7/26	1	2	FACETS	0.908	0.841	0.978	0.908	0.841	0.978	CLONAL	1	TRUE	1	0.62	2		568	625	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346924	70346924	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	148	479	0	ENST00000374080.3:c.2791C>T	p.Arg931Trp	p.R931W	ENST00000374080		931	Cgg/Tgg	20/45	1	2	FACETS	0.839	0.77	0.911	0.839	0.77	0.911	CLONAL	1	TRUE	1	0.62	2		479	569	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874339	76874339	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	111	399	0	ENST00000373344.5:c.5383G>A	p.Val1795Ile	p.V1795I	ENST00000373344	NM_000489.3	1795	Gta/Ata	21/35	1	2	FACETS	0.744	0.673	0.82	0.744	0.673	0.82	SUBCLONAL	1	TRUE	1	0.62	2		399	481	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937230	76937230	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	173	574	0	ENST00000373344.5:c.3518C>A	p.Ser1173Ter	p.S1173*	ENST00000373344	NM_000489.3	1173	tCa/tAa	9/35	1	2	FACETS	0.897	0.83	0.967	0.897	0.83	0.967	CLONAL	1	TRUE	1	0.62	2		574	622	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939999	76939999	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	186	479	0	ENST00000373344.5:c.749G>A	p.Arg250Gln	p.R250Q	ENST00000373344	NM_000489.3	250	cGa/cAa	9/35	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.62	2		479	563	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611138	100611138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868978699	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	158	523	0	ENST00000308731.7:c.1468C>T	p.Arg490Cys	p.R490C	ENST00000308731	NM_000061.2	490	Cgc/Tgc	15/19	1	2	FACETS	0.845	0.778	0.915	0.845	0.778	0.915	CLONAL	1	TRUE	1	0.62	2		523	603	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866297	42866297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61735793	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	203	547	0	ENST00000398585.3:c.335C>T	p.Thr112Ile	p.T112I	ENST00000398585	NM_001135099.1	112	aCa/aTa	3/14	1	2	FACETS	0.937	0.872	1	0.937	0.872	1	CLONAL	1	TRUE	1	0.62	2		547	699	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11301713	11301713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201601333	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	159	421	0	ENST00000361445.4:c.1438G>A	p.Ala480Thr	p.A480T	ENST00000361445	NM_004958.3	480	Gcc/Acc	10/58	1	2	FACETS	0.842	0.775	0.911	0.842	0.775	0.911	CLONAL	1	TRUE	1	0.62	2		421	609	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1686893	1686893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	181	455	0	ENST00000378625.1:c.1043C>T	p.Ala348Val	p.A348V	ENST00000378625	NM_001198994.1	348	gCc/gTc	9/14	1	2	FACETS	0.971	0.901	1	0.971	0.901	1	CLONAL	1	TRUE	1	0.62	2		455	601	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1688687	1688687	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	211	481	0	ENST00000378625.1:c.638T>C	p.Val213Ala	p.V213A	ENST00000378625	NM_001198994.1	213	gTc/gCc	6/14	1	2	FACETS	0.947	0.883	1	0.947	0.883	1	CLONAL	1	TRUE	1	0.62	2		481	719	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255905	16255905	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	234	548	0	ENST00000375759.3:c.3170T>G	p.Leu1057Arg	p.L1057R	ENST00000375759	NM_015001.2	1057	cTt/cGt	11/15	1	2	FACETS	0.881	0.823	0.94	0.881	0.823	0.94	CLONAL	1	TRUE	1	0.62	2		548	857	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261667	16261667	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	210	622	1	ENST00000375759.3:c.8932C>A	p.Leu2978Met	p.L2978M	ENST00000375759	NM_015001.2	2978	Ctg/Atg	11/15	1	2	FACETS	0.865	0.805	0.927	0.865	0.805	0.927	CLONAL	1	TRUE	1	0.62	2		623	783	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17350485	17350485	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	139	395	0	ENST00000375499.3:c.625C>T	p.Pro209Ser	p.P209S	ENST00000375499	NM_003000.2	209	Cct/Tct	6/8	1	2	FACETS	0.784	0.717	0.854	0.784	0.717	0.854	SUBCLONAL	1	TRUE	1	0.62	2		395	572	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932429	36932429	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	208	559	0	ENST00000361632.4:c.2041-1G>T		p.X681_splice	ENST00000361632		681			1	2	FACETS	0.922	0.858	0.987	0.922	0.858	0.987	CLONAL	1	TRUE	1	0.62	2		559	728	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939132	36939132	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	203	655	0	ENST00000361632.4:c.577C>A	p.Leu193Met	p.L193M	ENST00000361632		193	Ctg/Atg	5/16	1	2	FACETS	0.906	0.843	0.971	0.906	0.843	0.971	CLONAL	1	TRUE	1	0.62	2		655	723	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248033	59248033	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762826057	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	188	657	0	ENST00000371222.2:c.710G>A	p.Gly237Asp	p.G237D	ENST00000371222	NM_002228.3	237	gGc/gAc	1/1	1	2	FACETS	0.889	0.825	0.956	0.889	0.825	0.956	CLONAL	1	TRUE	1	0.62	2		657	682	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428558	78428558	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	166	488	0	ENST00000370768.2:c.1241G>T	p.Arg414Ile	p.R414I	ENST00000370768	NM_003902.3	414	aGa/aTa	14/20	1	2	FACETS	0.872	0.805	0.942	0.872	0.805	0.942	CLONAL	1	TRUE	1	0.62	2		488	614	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282442	115282442	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	155	462	0	ENST00000438362.2:c.208C>A	p.Leu70Met	p.L70M	ENST00000438362	NM_001242891.1	70	Ctg/Atg	3/20	1	2	FACETS	0.947	0.872	1	0.947	0.872	1	CLONAL	1	TRUE	1	0.62	2		462	528	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115284276	115284276	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	180	449	0	ENST00000438362.2:c.10G>A	p.Val4Ile	p.V4I	ENST00000438362	NM_001242891.1	4	Gtt/Att	2/20	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.62	2		449	573	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510749	120510749	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	223	523	0	ENST00000256646.2:c.1215A>C	p.Gln405His	p.Q405H	ENST00000256646	NM_024408.3	405	caA/caC	7/34	1	2	FACETS	0.896	0.836	0.957	0.896	0.836	0.957	CLONAL	1	TRUE	1	0.62	2		523	803	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162750033	162750033	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	206	489	0	ENST00000367921.3:c.2565G>T	p.Glu855Asp	p.E855D	ENST00000367921	NM_006182.2	855	gaG/gaT	18/18	1	2	FACETS	0.973	0.907	1	0.973	0.907	1	CLONAL	1	TRUE	1	0.62	2		489	683	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132114	176132114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1444099543	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	108	353	0	ENST00000367669.3:c.653G>A	p.Arg218Lys	p.R218K	ENST00000367669	NM_022457.5	218	aGg/aAg	5/20	1	2	FACETS	0.799	0.722	0.88	0.799	0.722	0.88	SUBCLONAL	1	TRUE	1	0.62	2		353	436	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206943240	206943240	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	183	472	0	ENST00000423557.1:c.379-1G>T		p.X127_splice	ENST00000423557	NM_000572.2	127			1	2	FACETS	0.89	0.825	0.958	0.89	0.825	0.958	CLONAL	1	TRUE	1	0.62	2		472	663	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612764	228612764	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1482262254	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	304	722	0	ENST00000366696.1:c.263C>T	p.Ser88Leu	p.S88L	ENST00000366696	NM_003493.2	88	tCg/tTg	1/1	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.62	2		722	967	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667429	241667429	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	202	467	0	ENST00000366560.3:c.1021G>T	p.Asp341Tyr	p.D341Y	ENST00000366560	NM_000143.3	341	Gat/Tat	7/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.62	2		467	597	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243668619	243668619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	179	550	0	ENST00000263826.5:c.1372G>A	p.Asp458Asn	p.D458N	ENST00000263826	NM_005465.4	458	Gac/Aac	13/13	1	2	FACETS	0.867	0.802	0.934	0.867	0.802	0.934	CLONAL	1	TRUE	1	0.62	2		550	666	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615543	43615543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	70	571	0	ENST00000355710.3:c.2622C>A	p.Asp874Glu	p.D874E	ENST00000355710	NM_020975.4	874	gaC/gaA	15/20	1	2	FACETS	0.353	0.308	0.403	0.353	0.308	0.403	SUBCLONAL	1	TRUE	1	0.62	2		571	639	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112764385	112764385	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	157	378	0	ENST00000369452.4:c.994A>G	p.Lys332Glu	p.K332E	ENST00000369452	NM_007373.3	332	Aaa/Gaa	5/9	1	2	FACETS	0.884	0.814	0.956	0.884	0.814	0.956	CLONAL	1	TRUE	1	0.62	2		378	573	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154791	2154791	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753904854	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	179	642	0	ENST00000434045.2:c.430G>A	p.Ala144Thr	p.A144T	ENST00000434045	NM_001127598.1	144	Gcc/Acc	4/5	1	2	FACETS	0.87	0.805	0.937	0.87	0.805	0.937	CLONAL	1	TRUE	1	0.62	2		642	664	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003763	57003763	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	C	C	T	rs1446138644	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	67	601	0	ENST00000257254.3:c.716G>A	p.Gly239Asp	p.G239D	ENST00000257254		239	gGc/gAc	1/2	1	2	FACETS	0.355	0.308	0.405	0.355	0.308	0.405	SUBCLONAL	1	TRUE	1	0.62	2		601	609	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943296	71943296	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	234	570	0	ENST00000298229.2:c.1628C>A	p.Ala543Asp	p.A543D	ENST00000298229	NM_001567.3	543	gCt/gAt	14/28	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.62	2		570	739	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924678	94924678	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	232	579	0	ENST00000536441.1:c.232G>T	p.Val78Phe	p.V78F	ENST00000536441	NM_144665.3	78	Gtc/Ttc	3/10	1	2	FACETS	0.931	0.87	0.993	0.931	0.87	0.993	CLONAL	1	TRUE	1	0.62	2		579	804	SUCCESS
ATM	472	MSKCC	GRCh37	11	108099963	108099963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1412024666	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	162	424	0	ENST00000278616.4:c.244G>A	p.Val82Ile	p.V82I	ENST00000278616	NM_000051.3	82	Gta/Ata	4/63	1	2	FACETS	0.84	0.774	0.909	0.84	0.774	0.909	CLONAL	1	TRUE	1	0.62	2		424	622	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153599	108153599	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	131	322	0	ENST00000278616.4:c.3739T>G	p.Phe1247Val	p.F1247V	ENST00000278616	NM_000051.3	1247	Ttc/Gtc	25/63	1	2	FACETS	0.997	0.912	1	0.997	0.912	1	CLONAL	1	TRUE	1	0.62	2		322	424	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170512	108170512	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	178	431	0	ENST00000278616.4:c.5077G>T	p.Asp1693Tyr	p.D1693Y	ENST00000278616	NM_000051.3	1693	Gat/Tat	34/63	1	2	FACETS	0.975	0.904	1	0.975	0.904	1	CLONAL	1	TRUE	1	0.62	2		431	589	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196945	108196945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660924	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	174	350	0	ENST00000278616.4:c.6968G>A	p.Cys2323Tyr	p.C2323Y	ENST00000278616	NM_000051.3	2323	tGt/tAt	47/63	1	2	FACETS	0.969	0.898	1	0.969	0.898	1	CLONAL	1	TRUE	1	0.62	2		350	579	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205811	108205811	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	163	431	0	ENST00000278616.4:c.8126G>A	p.Gly2709Asp	p.G2709D	ENST00000278616	NM_000051.3	2709	gGc/gAc	55/63	1	2	FACETS	0.932	0.86	1	0.932	0.86	1	CLONAL	1	TRUE	1	0.62	2		431	564	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235846	108235846	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	223	532	0	ENST00000278616.4:c.8888A>T	p.Asn2963Ile	p.N2963I	ENST00000278616	NM_000051.3	2963	aAt/aTt	62/63	1	2	FACETS	0.991	0.926	1	0.991	0.926	1	CLONAL	1	TRUE	1	0.62	2		532	726	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343011	118343011	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	214	567	0	ENST00000534358.1:c.1142del	p.Lys381ArgfsTer19	p.K381Rfs*19	ENST00000534358	NM_005933.3	379	gcA/gc	3/36	1	2	FACETS	0.988	0.922	1	0.988	0.922	1	CLONAL	1	TRUE	1	0.62	2		567	699	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118379858	118379858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	190	437	0	ENST00000534358.1:c.10843G>A	p.Ala3615Thr	p.A3615T	ENST00000534358	NM_005933.3	3615	Gct/Act	29/36	1	2	FACETS	0.941	0.874	1	0.941	0.874	1	CLONAL	1	TRUE	1	0.62	2		437	651	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431625	431625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	175	409	0	ENST00000399788.2:c.2384C>T	p.Ala795Val	p.A795V	ENST00000399788	NM_001042603.1	795	gCt/gTt	17/28	1	2	FACETS	0.844	0.78	0.91	0.844	0.78	0.91	CLONAL	1	TRUE	1	0.62	2		409	669	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1042191	1042191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766945254	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	250	559	0	ENST00000358495.3:c.34C>T	p.Arg12Cys	p.R12C	ENST00000358495	NM_134424.2	12	Cgt/Tgt	2/12	1	2	FACETS	0.958	0.898	1	0.958	0.898	1	CLONAL	1	TRUE	1	0.62	2		559	842	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466902	18466902	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	153	426	0	ENST00000266497.5:c.1041C>A	p.His347Gln	p.H347Q	ENST00000266497		347	caC/caA	5/31	1	2	FACETS	0.914	0.841	0.989	0.914	0.841	0.989	CLONAL	1	TRUE	1	0.62	2		426	540	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656233	18656233	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	37	498	0	ENST00000266497.5:c.2912C>A	p.Pro971His	p.P971H	ENST00000266497		971	cCt/cAt	21/31	1	2	FACETS	0.212	0.174	0.254	0.212	0.174	0.254	SUBCLONAL	1	TRUE	1	0.62	2		498	564	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636402	21636402	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	134	445	0	ENST00000421138.2:c.608G>T	p.Arg203Ile	p.R203I	ENST00000421138		203	aGa/aTa	7/16	1	2	FACETS	0.843	0.77	0.918	0.843	0.77	0.918	CLONAL	1	TRUE	1	0.62	2		445	513	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205252	46205252	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	130	371	0	ENST00000334344.6:c.336G>T	p.Glu112Asp	p.E112D	ENST00000334344	NM_152641.2	112	gaG/gaT	4/21	1	2	FACETS	0.837	0.764	0.913	0.837	0.764	0.913	CLONAL	1	TRUE	1	0.62	2		371	501	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245012	46245012	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	215	665	0	ENST00000334344.6:c.3106G>T	p.Val1036Leu	p.V1036L	ENST00000334344	NM_152641.2	1036	Gta/Tta	15/21	1	2	FACETS	0.897	0.836	0.96	0.897	0.836	0.96	CLONAL	1	TRUE	1	0.62	2		665	773	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420822	49420822	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	204	601	0	ENST00000301067.7:c.14927C>A	p.Pro4976His	p.P4976H	ENST00000301067	NM_003482.3	4976	cCt/cAt	48/54	1	2	FACETS	0.923	0.859	0.989	0.923	0.859	0.989	CLONAL	1	TRUE	1	0.62	2		601	713	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425547	49425547	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	240	740	0	ENST00000301067.7:c.12941C>A	p.Pro4314His	p.P4314H	ENST00000301067	NM_003482.3	4314	cCt/cAt	39/54	1	2	FACETS	0.949	0.888	1	0.949	0.888	1	CLONAL	1	TRUE	1	0.62	2		740	816	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480040	50480040	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	185	556	0	ENST00000394963.4:c.274G>T	p.Ala92Ser	p.A92S	ENST00000394963	NM_003076.4	92	Gcc/Tcc	2/13	1	2	FACETS	0.972	0.902	1	0.972	0.902	1	CLONAL	1	TRUE	1	0.62	2		556	614	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480074	50480074	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	189	552	0	ENST00000394963.4:c.308C>A	p.Pro103His	p.P103H	ENST00000394963	NM_003076.4	103	cCt/cAt	2/13	1	2	FACETS	0.945	0.878	1	0.945	0.878	1	CLONAL	1	TRUE	1	0.62	2		552	645	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56474121	56474121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	138	405	0	ENST00000267101.3:c.37C>T	p.Leu13Phe	p.L13F	ENST00000267101	NM_001982.3	13	Ctt/Ttt	1/28	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.62	2		405	429	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490926	56490926	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	217	567	0	ENST00000267101.3:c.2372C>A	p.Pro791His	p.P791H	ENST00000267101	NM_001982.3	791	cCt/cAt	20/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.62	2		567	644	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865532	57865532	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	228	642	0	ENST00000228682.2:c.3009A>C	p.Lys1003Asn	p.K1003N	ENST00000228682	NM_005269.2	1003	aaA/aaC	12/12	1	2	FACETS	0.954	0.892	1	0.954	0.892	1	CLONAL	1	TRUE	1	0.62	2		642	771	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891156	112891156	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	247	555	0	ENST00000351677.2:c.490A>G	p.Lys164Glu	p.K164E	ENST00000351677	NM_002834.3	164	Aag/Gag	4/16	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.62	2		555	779	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926297	112926297	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	173	424	0	ENST00000351677.2:c.1430A>G	p.Asp477Gly	p.D477G	ENST00000351677	NM_002834.3	477	gAc/gGc	12/16	1	2	FACETS	0.922	0.853	0.994	0.922	0.853	0.994	CLONAL	1	TRUE	1	0.62	2		424	605	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112335	115112335	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	137	536	0	ENST00000257566.3:c.1405G>A	p.Glu469Lys	p.E469K	ENST00000257566	NM_016569.3	469	Gag/Aag	7/8	1	2	FACETS	0.865	0.791	0.941	0.865	0.791	0.941	CLONAL	1	TRUE	1	0.62	2		536	511	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133208912	133208912	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs774838300	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	236	524	0	ENST00000320574.5:c.6319T>C	p.Tyr2107His	p.Y2107H	ENST00000320574	NM_006231.2	2107	Tac/Cac	45/49	1	2	FACETS	0.898	0.84	0.957	0.898	0.84	0.957	CLONAL	1	TRUE	1	0.62	2		524	848	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133236001	133236001	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	222	582	0	ENST00000320574.5:c.3155C>T	p.Thr1052Met	p.T1052M	ENST00000320574	NM_006231.2	1052	aCg/aTg	26/49	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.62	2		582	654	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608229	28608229	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	199	549	0	ENST00000241453.7:c.1827T>A	p.Asn609Lys	p.N609K	ENST00000241453	NM_004119.2	609	aaT/aaA	14/24	1	2	FACETS	0.958	0.891	1	0.958	0.891	1	CLONAL	1	TRUE	1	0.62	2		549	670	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959139	28959139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747292637	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	216	487	0	ENST00000282397.4:c.1999C>T	p.Leu667Phe	p.L667F	ENST00000282397	NM_002019.4	667	Ctc/Ttc	14/30	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.62	2		487	685	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914362	32914362	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	154	473	0	ENST00000380152.3:c.5870T>A	p.Ile1957Lys	p.I1957K	ENST00000380152		1957	aTa/aAa	11/27	1	2	FACETS	0.89	0.819	0.964	0.89	0.819	0.964	CLONAL	1	TRUE	1	0.62	2		473	558	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281240	49281240	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	189	574	0	ENST00000282018.3:c.287A>G	p.Asp96Gly	p.D96G	ENST00000282018	NM_020377.2	96	gAc/gGc	1/1	1	2	FACETS	0.968	0.899	1	0.968	0.899	1	CLONAL	1	TRUE	1	0.62	2		574	630	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73334762	73334762	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	144	374	0	ENST00000377767.4:c.2698G>T	p.Val900Leu	p.V900L	ENST00000377767	NM_014953.3	900	Gtg/Ttg	20/21	1	2	FACETS	0.909	0.834	0.986	0.909	0.834	0.986	CLONAL	1	TRUE	1	0.62	2		374	511	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73348129	73348129	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	179	437	0	ENST00000377767.4:c.1056T>G	p.Asn352Lys	p.N352K	ENST00000377767	NM_014953.3	352	aaT/aaG	7/21	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.62	2		437	562	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518152	103518152	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	236	559	0	ENST00000355739.4:c.2090C>A	p.Ser697Tyr	p.S697Y	ENST00000355739	NM_000123.3	697	tCc/tAc	9/15	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.62	2		559	757	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527745	103527745	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	214	526	0	ENST00000355739.4:c.3053C>T	p.Ala1018Val	p.A1018V	ENST00000355739	NM_000123.3	1018	gCt/gTt	15/15	1	2	FACETS	0.899	0.838	0.962	0.899	0.838	0.962	CLONAL	1	TRUE	1	0.62	2		526	768	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437232	110437233	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	65	246	1	ENST00000375856.3:c.1168_1169insA	p.Leu390HisfsTer149	p.L390Hfs*149	ENST00000375856	NM_003749.2	390	ctg/cAtg	1/2	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.62	2		247	199	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872389	35872389	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	214	594	0	ENST00000216797.5:c.514C>A	p.Leu172Ile	p.L172I	ENST00000216797	NM_020529.2	172	Ctc/Atc	3/6	1	2	FACETS	0.831	0.773	0.89	0.831	0.773	0.89	CLONAL	1	TRUE	1	0.62	2		594	831	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988330	36988330	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	111	447	1	ENST00000354822.5:c.323T>G	p.Leu108Arg	p.L108R	ENST00000354822	NM_001079668.2	108	cTc/cGc	2/3	1	2	FACETS	0.923	0.837	1	0.923	0.837	1	CLONAL	1	TRUE	1	0.62	2		448	388	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610269	81610269	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	235	567	0	ENST00000298171.2:c.1867G>A	p.Ala623Thr	p.A623T	ENST00000298171	NM_000369.2	623	Gcc/Acc	10/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.62	2		567	660	SUCCESS
SCG5	6447	MSKCC	GRCh37	15	32972063	32972063	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	175	454	0	ENST00000300175.4:c.323G>T	p.Ser108Ile	p.S108I	ENST00000300175	NM_001144757.1	108	aGt/aTt	3/6	1	2	FACETS	0.954	0.883	1	0.954	0.883	1	CLONAL	1	TRUE	1	0.62	2		454	592	SUCCESS
SCG5	6447	MSKCC	GRCh37	15	32983929	32983929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753164742	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	186	452	0	ENST00000300175.4:c.508G>A	p.Glu170Lys	p.E170K	ENST00000300175	NM_001144757.1	170	Gag/Aag	5/6	1	2	FACETS	0.91	0.844	0.979	0.91	0.844	0.979	CLONAL	1	TRUE	1	0.62	2		452	659	SUCCESS
SCG5	6447	MSKCC	GRCh37	15	32983953	32983953	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200799739	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	186	449	0	ENST00000300175.4:c.532C>T	p.Arg178Ter	p.R178*	ENST00000300175	NM_001144757.1	178	Cga/Tga	5/6	1	2	FACETS	0.852	0.79	0.917	0.852	0.79	0.917	CLONAL	1	TRUE	1	0.62	2		449	704	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028608	42028608	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	202	573	0	ENST00000219905.7:c.4146C>A	p.Ser1382Arg	p.S1382R	ENST00000219905	NM_001164273.1	1382	agC/agA	13/24	1	2	FACETS	0.898	0.835	0.962	0.898	0.835	0.962	CLONAL	1	TRUE	1	0.62	2		573	726	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50731278	50731278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	134	337	0	ENST00000307179.4:c.8C>T	p.Ala3Val	p.A3V	ENST00000307179		3	gCt/gTt	2/20	1	2	FACETS	0.889	0.813	0.968	0.889	0.813	0.968	CLONAL	1	TRUE	1	0.62	2		337	486	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51503253	51503253	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1486608852	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	168	433	0	ENST00000260433.2:c.1264G>A	p.Val422Ile	p.V422I	ENST00000260433		422	Gtt/Att	10/10	1	2	FACETS	0.877	0.81	0.946	0.877	0.81	0.946	CLONAL	1	TRUE	1	0.62	2		433	618	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996048	73996048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	190	557	0	ENST00000318443.5:c.782G>A	p.Gly261Asp	p.G261D	ENST00000318443	NM_001024736.1	261	gGc/gAc	5/10	1	2	FACETS	0.965	0.897	1	0.965	0.897	1	CLONAL	1	TRUE	1	0.62	2		557	635	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576267	88576267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	159	417	0	ENST00000360948.2:c.1406C>T	p.Ala469Val	p.A469V	ENST00000360948	NM_001012338.2	469	gCt/gTt	13/19	1	2	FACETS	0.906	0.835	0.98	0.906	0.835	0.98	CLONAL	1	TRUE	1	0.62	2		417	566	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630471	90630471	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	223	572	0	ENST00000330062.3:c.840G>T	p.Lys280Asn	p.K280N	ENST00000330062	NM_002168.2	280	aaG/aaT	7/11	1	2	FACETS	0.98	0.916	1	0.98	0.916	1	CLONAL	1	TRUE	1	0.62	2		572	734	SUCCESS
BLM	641	MSKCC	GRCh37	15	91334015	91334015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555423111	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	179	510	0	ENST00000355112.3:c.2960C>T	p.Ser987Phe	p.S987F	ENST00000355112	NM_000057.2	987	tCt/tTt	15/22	1	2	FACETS	0.943	0.874	1	0.943	0.874	1	CLONAL	1	TRUE	1	0.62	2		510	612	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396415	396415	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	181	591	0	ENST00000262320.3:c.611C>A	p.Ser204Tyr	p.S204Y	ENST00000262320	NM_003502.3	204	tCt/tAt	2/11	1	2	FACETS	0.93	0.862	1	0.93	0.862	1	CLONAL	1	TRUE	1	0.62	2		591	628	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135303	2135303	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	184	464	0	ENST00000219476.3:c.4642C>A	p.Leu1548Met	p.L1548M	ENST00000219476	NM_000548.3	1548	Ctg/Atg	36/42	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.62	2		464	556	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647815	3647815	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	217	586	0	ENST00000294008.3:c.1349G>T	p.Arg450Met	p.R450M	ENST00000294008	NM_032444.2	450	aGg/aTg	6/15	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.62	2		586	687	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656511	3656511	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1485533770	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	198	585	0	ENST00000294008.3:c.724C>A	p.Pro242Thr	p.P242T	ENST00000294008	NM_032444.2	242	Cca/Aca	3/15	1	2	FACETS	0.905	0.841	0.97	0.905	0.841	0.97	CLONAL	1	TRUE	1	0.62	2		585	706	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658827	3658827	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	221	512	0	ENST00000294008.3:c.139T>C	p.Ser47Pro	p.S47P	ENST00000294008	NM_032444.2	47	Tct/Cct	2/15	1	2	FACETS	0.992	0.926	1	0.992	0.926	1	CLONAL	1	TRUE	1	0.62	2		512	719	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900866	3900866	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	196	532	0	ENST00000262367.5:c.230G>A	p.Gly77Asp	p.G77D	ENST00000262367	NM_004380.2	77	gGc/gAc	2/31	1	2	FACETS	0.897	0.833	0.962	0.897	0.833	0.962	CLONAL	1	TRUE	1	0.62	2		532	705	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14021896	14021896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	177	422	0	ENST00000311895.7:c.596C>T	p.Ala199Val	p.A199V	ENST00000311895	NM_005236.2	199	gCa/gTa	4/11	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.62	2		422	562	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129432	30129432	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	206	553	0	ENST00000263025.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000263025	NM_002746.2	199	gGc/gTc	4/9	1	2	FACETS	0.998	0.93	1	0.998	0.93	1	CLONAL	1	TRUE	1	0.62	2		553	666	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50821732	50821732	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	121	300	0	ENST00000398568.2:c.2068A>G	p.Ile690Val	p.I690V	ENST00000398568	NM_001042412.1	690	Att/Gtt	13/18	1	2	FACETS	0.839	0.763	0.919	0.839	0.763	0.919	CLONAL	1	TRUE	1	0.62	2		300	465	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663316	67663316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	229	530	0	ENST00000264010.4:c.1717C>T	p.His573Tyr	p.H573Y	ENST00000264010	NM_006565.3	573	Cat/Tat	10/12	1	2	FACETS	0.865	0.808	0.924	0.865	0.808	0.924	CLONAL	1	TRUE	1	0.62	2		530	854	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853317	68853317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886041160	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	176	434	0	ENST00000261769.5:c.1700C>T	p.Ala567Val	p.A567V	ENST00000261769	NM_004360.3	567	gCt/gTt	11/16	1	2	FACETS	0.957	0.887	1	0.957	0.887	1	CLONAL	1	TRUE	1	0.62	2		434	593	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828163	72828163	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	183	563	0	ENST00000268489.5:c.8418G>T	p.Lys2806Asn	p.K2806N	ENST00000268489	NM_006885.3	2806	aaG/aaT	9/10	1	2	FACETS	0.911	0.844	0.98	0.911	0.844	0.98	CLONAL	1	TRUE	1	0.62	2		563	648	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829198	72829198	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	238	619	0	ENST00000268489.5:c.7383G>T	p.Glu2461Asp	p.E2461D	ENST00000268489	NM_006885.3	2461	gaG/gaT	9/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.62	2		619	739	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832554	72832554	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	194	490	0	ENST00000268489.5:c.4027G>T	p.Asp1343Tyr	p.D1343Y	ENST00000268489	NM_006885.3	1343	Gat/Tat	9/10	1	2	FACETS	0.895	0.831	0.961	0.895	0.831	0.961	CLONAL	1	TRUE	1	0.62	2		490	699	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944204	81944204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1003077830	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	160	491	0	ENST00000359376.3:c.1813C>T	p.Leu605Phe	p.L605F	ENST00000359376	NM_002661.3	605	Ctc/Ttc	18/33	1	2	FACETS	0.905	0.835	0.979	0.905	0.835	0.979	CLONAL	1	TRUE	1	0.62	2		491	570	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544618	86544618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs918429732	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	123	590	1	ENST00000262426.4:c.443G>A	p.Cys148Tyr	p.C148Y	ENST00000262426	NM_001451.2	148	tGc/tAc	1/2	1	2	FACETS	0.728	0.661	0.798	0.728	0.661	0.798	SUBCLONAL	1	TRUE	1	0.62	2		591	545	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348820	89348820	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	259	677	0	ENST00000301030.4:c.4130G>A	p.Gly1377Asp	p.G1377D	ENST00000301030	NM_001256183.1	1377	gGc/gAc	9/13	1	2	FACETS	0.943	0.885	1	0.943	0.885	1	CLONAL	1	TRUE	1	0.62	2		677	886	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16056661	16056661	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	152	336	0	ENST00000268712.3:c.781G>A	p.Val261Ile	p.V261I	ENST00000268712	NM_006311.3	261	Gtt/Att	7/46	1	2	FACETS	0.89	0.818	0.964	0.89	0.818	0.964	CLONAL	1	TRUE	1	0.62	2		336	551	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684353	29684353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	47	445	0	ENST00000356175.3:c.7873G>A	p.Ala2625Thr	p.A2625T	ENST00000356175	NM_000267.3	2625	Gcc/Acc	53/57	1	2	FACETS	0.285	0.24	0.335	0.285	0.24	0.335	SUBCLONAL	1	TRUE	1	0.62	2		445	532	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686908	37686908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	143	506	0	ENST00000447079.4:c.3812G>A	p.Gly1271Glu	p.G1271E	ENST00000447079	NM_015083.1	1271	gGa/gAa	14/14	1	2	FACETS	0.746	0.683	0.813	0.746	0.683	0.813	SUBCLONAL	1	TRUE	1	0.62	2		506	618	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38792236	38792236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762623799	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	135	464	0	ENST00000348513.6:c.488G>A	p.Arg163His	p.R163H	ENST00000348513	NM_003079.4	163	cGc/cAc	7/11	1	2	FACETS	0.686	0.625	0.749	0.686	0.625	0.749	SUBCLONAL	1	TRUE	1	0.62	2		464	635	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40476738	40476738	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	167	533	0	ENST00000264657.5:c.1591A>C	p.Lys531Gln	p.K531Q	ENST00000264657	NM_139276.2	531	Aaa/Caa	17/24	1	2	FACETS	0.892	0.823	0.963	0.892	0.823	0.963	CLONAL	1	TRUE	1	0.62	2		533	604	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40879682	40879682	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	153	387	0	ENST00000428826.2:c.217C>T	p.Pro73Ser	p.P73S	ENST00000428826		73	Cct/Tct	4/21	1	2	FACETS	0.809	0.743	0.877	0.809	0.743	0.877	CLONAL	1	TRUE	1	0.62	2		387	610	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438299	56438299	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	165	499	0	ENST00000407977.2:c.694C>A	p.Leu232Ile	p.L232I	ENST00000407977		232	Ctt/Att	7/10	1	2	FACETS	0.937	0.865	1	0.937	0.865	1	CLONAL	1	TRUE	1	0.62	2		499	568	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677997	58677997	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	144	488	0	ENST00000305921.3:c.222G>T	p.Glu74Asp	p.E74D	ENST00000305921	NM_003620.3	74	gaG/gaT	1/6	1	2	FACETS	0.974	0.895	1	0.974	0.895	1	CLONAL	1	TRUE	1	0.62	2		488	477	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885847	59885847	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	179	473	0	ENST00000259008.2:c.899A>C	p.Glu300Ala	p.E300A	ENST00000259008	NM_032043.2	300	gAa/gCa	7/20	1	2	FACETS	0.904	0.837	0.973	0.904	0.837	0.973	CLONAL	1	TRUE	1	0.62	2		473	639	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936816	78936816	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1007443740	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	180	575	0	ENST00000306801.3:c.3898C>T	p.Arg1300Trp	p.R1300W	ENST00000306801	NM_020761.2	1300	Cgg/Tgg	33/34	1	2	FACETS	0.848	0.784	0.913	0.848	0.784	0.913	CLONAL	1	TRUE	1	0.62	2		575	685	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101018	4101018	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	147	504	0	ENST00000262948.5:c.704C>T	p.Ala235Val	p.A235V	ENST00000262948	NM_030662.3	235	gCt/gTt	6/11	1	2	FACETS	0.968	0.89	1	0.968	0.89	1	CLONAL	1	TRUE	1	0.62	2		504	490	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218493	5218493	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	196	579	0	ENST00000357368.4:c.3986A>G	p.Asp1329Gly	p.D1329G	ENST00000357368	NM_002850.3	1329	gAc/gGc	25/38	1	2	FACETS	0.798	0.741	0.858	0.798	0.741	0.858	SUBCLONAL	1	TRUE	1	0.62	2		579	792	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219978	5219978	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	163	505	0	ENST00000357368.4:c.3737T>C	p.Val1246Ala	p.V1246A	ENST00000357368	NM_002850.3	1246	gTg/gCg	22/38	1	2	FACETS	0.832	0.767	0.9	0.832	0.767	0.9	CLONAL	1	TRUE	1	0.62	2		505	632	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5239016	5239016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761297706	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	197	574	1	ENST00000357368.4:c.1763C>T	p.Thr588Met	p.T588M	ENST00000357368	NM_002850.3	588	aCg/aTg	13/38	1	2	FACETS	0.976	0.908	1	0.976	0.908	1	CLONAL	1	TRUE	1	0.62	2		575	651	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6222629	6222629	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1351320172	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	159	575	0	ENST00000252674.7:c.613C>T	p.Pro205Ser	p.P205S	ENST00000252674	NM_005934.3	205	Ccc/Tcc	6/12	1	2	FACETS	0.841	0.774	0.91	0.841	0.774	0.91	CLONAL	1	TRUE	1	0.62	2		575	610	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250888	10250888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	175	509	0	ENST00000340748.4:c.3592G>A	p.Val1198Ile	p.V1198I	ENST00000340748		1198	Gtc/Atc	32/40	1	2	FACETS	0.918	0.849	0.989	0.918	0.849	0.989	CLONAL	1	TRUE	1	0.62	2		509	615	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265352	10265352	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	212	601	1	ENST00000340748.4:c.1694A>C	p.Asp565Ala	p.D565A	ENST00000340748		565	gAc/gCc	20/40	1	2	FACETS	0.925	0.863	0.99	0.925	0.863	0.99	CLONAL	1	TRUE	1	0.62	2		602	739	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600354	10600354	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	243	612	0	ENST00000171111.5:c.1501A>G	p.Thr501Ala	p.T501A	ENST00000171111	NM_203500.1	501	Aca/Gca	4/6	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.62	2		612	737	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051635	13051635	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	229	551	0	ENST00000316448.5:c.894G>T	p.Glu298Asp	p.E298D	ENST00000316448	NM_004343.3	298	gaG/gaT	7/9	1	2	FACETS	0.945	0.883	1	0.945	0.883	1	CLONAL	1	TRUE	1	0.62	2		551	782	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295111	15295111	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	159	508	0	ENST00000263388.2:c.2561A>C	p.Asp854Ala	p.D854A	ENST00000263388	NM_000435.2	854	gAc/gCc	16/33	1	2	FACETS	0.805	0.741	0.872	0.805	0.741	0.872	CLONAL	1	TRUE	1	0.62	2		508	637	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379682	17379682	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1389676406	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	193	510	0	ENST00000359435.4:c.67C>A	p.Pro23Thr	p.P23T	ENST00000359435	NM_001033549.1	23	Cct/Act	2/9	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.62	2		510	615	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211136	36211136	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	213	616	0	ENST00000222270.7:c.887G>T	p.Gly296Val	p.G296V	ENST00000222270	NM_014727.1	296	gGc/gTc	3/37	1	2	FACETS	0.952	0.888	1	0.952	0.888	1	CLONAL	1	TRUE	1	0.62	2		616	722	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741238	40741238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1319165364	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	172	454	0	ENST00000392038.2:c.1195G>A	p.Asp399Asn	p.D399N	ENST00000392038	NM_001626.4	399	Gat/Aat	12/14	1	2	FACETS	0.972	0.899	1	0.972	0.899	1	CLONAL	1	TRUE	1	0.62	2		454	571	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47421976	47421976	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	237	550	0	ENST00000404338.3:c.44A>T	p.Asn15Ile	p.N15I	ENST00000404338	NM_004491.4	15	aAc/aTc	1/6	1	2	FACETS	0.974	0.912	1	0.974	0.912	1	CLONAL	1	TRUE	1	0.62	2		550	785	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424519	47424519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	228	591	0	ENST00000404338.3:c.2587C>T	p.Arg863Cys	p.R863C	ENST00000404338	NM_004491.4	863	Cgt/Tgt	1/6	1	2	FACETS	0.959	0.897	1	0.959	0.897	1	CLONAL	1	TRUE	1	0.62	2		591	767	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47502584	47502584	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	188	448	0	ENST00000404338.3:c.4060T>G	p.Leu1354Val	p.L1354V	ENST00000404338	NM_004491.4	1354	Ttg/Gtg	5/6	1	2	FACETS	0.967	0.898	1	0.967	0.898	1	CLONAL	1	TRUE	1	0.62	2		448	627	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714603	52714603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	168	538	0	ENST00000322088.6:c.361C>T	p.Pro121Ser	p.P121S	ENST00000322088	NM_014225.5	121	Ccc/Tcc	4/15	1	2	FACETS	0.829	0.764	0.895	0.829	0.764	0.895	CLONAL	1	TRUE	1	0.62	2		538	654	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085662	16085662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	224	521	0	ENST00000281043.3:c.838G>A	p.Val280Ile	p.V280I	ENST00000281043	NM_005378.4	280	Gtc/Atc	3/3	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.62	2		521	682	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973193	25973193	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	220	539	0	ENST00000435504.4:c.1232C>A	p.Ser411Tyr	p.S411Y	ENST00000435504		411	tCc/tAc	12/13	1	2	FACETS	0.893	0.833	0.954	0.893	0.833	0.954	CLONAL	1	TRUE	1	0.62	2		539	795	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250056	39250056	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	142	472	0	ENST00000402219.2:c.1513G>T	p.Asp505Tyr	p.D505Y	ENST00000402219	NM_005633.3	505	Gat/Tat	10/23	1	2	FACETS	0.787	0.72	0.856	0.787	0.72	0.856	SUBCLONAL	1	TRUE	1	0.62	2		472	582	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606953	47606953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	209	450	0	ENST00000263735.4:c.703G>A	p.Val235Ile	p.V235I	ENST00000263735	NM_002354.2	235	Gta/Ata	7/9	1	2	FACETS	0.962	0.897	1	0.962	0.897	1	CLONAL	1	TRUE	1	0.62	2		450	701	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637378	47637378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750902	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	219	522	0	ENST00000233146.2:c.512G>A	p.Arg171Lys	p.R171K	ENST00000233146	NM_000251.2	171	aGg/aAg	3/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.62	2		522	681	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018188	48018188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750143	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	38	523	0	ENST00000234420.5:c.383G>A	p.Arg128His	p.R128H	ENST00000234420	NM_000179.2	128	cGt/cAt	2/10	1	2	FACETS	0.166	0.137	0.2	0.166	0.137	0.2	SUBCLONAL	1	TRUE	1	0.62	2		523	737	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715828	61715828	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	189	490	0	ENST00000401558.2:c.2101G>T	p.Ala701Ser	p.A701S	ENST00000401558	NM_003400.3	701	Gct/Tct	18/25	1	2	FACETS	0.918	0.852	0.986	0.918	0.852	0.986	CLONAL	1	TRUE	1	0.62	2		490	664	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630859	67630859	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	208	568	0	ENST00000272342.5:c.1045A>G	p.Thr349Ala	p.T349A	ENST00000272342	NM_019002.3	349	Aca/Gca	5/6	1	2	FACETS	0.956	0.891	1	0.956	0.891	1	CLONAL	1	TRUE	1	0.62	2		568	702	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630932	67630932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	168	562	0	ENST00000272342.5:c.1118C>T	p.Ala373Val	p.A373V	ENST00000272342	NM_019002.3	373	gCa/gTa	5/6	1	2	FACETS	0.886	0.818	0.956	0.886	0.818	0.956	CLONAL	1	TRUE	1	0.62	2		562	612	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630976	67630976	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	176	548	0	ENST00000272342.5:c.1162G>T	p.Gly388Cys	p.G388C	ENST00000272342	NM_019002.3	388	Ggt/Tgt	5/6	1	2	FACETS	0.943	0.873	1	0.943	0.873	1	CLONAL	1	TRUE	1	0.62	2		548	602	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631994	67631994	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	181	536	0	ENST00000272342.5:c.2180C>A	p.Ser727Tyr	p.S727Y	ENST00000272342	NM_019002.3	727	tCt/tAt	5/6	1	2	FACETS	0.94	0.871	1	0.94	0.871	1	CLONAL	1	TRUE	1	0.62	2		536	621	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634692	158634692	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1269251512	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	232	592	0	ENST00000263640.3:c.494G>A	p.Gly165Asp	p.G165D	ENST00000263640	NM_001105.4	165	gGc/gAc	5/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.62	2		592	724	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270129	198270129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	198	487	0	ENST00000335508.6:c.1307C>T	p.Thr436Ile	p.T436I	ENST00000335508	NM_012433.2	436	aCa/aTa	10/25	1	2	FACETS	0.896	0.833	0.961	0.896	0.833	0.961	CLONAL	1	TRUE	1	0.62	2		487	713	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131387	202131387	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	190	543	0	ENST00000358485.4:c.355T>C	p.Ser119Pro	p.S119P	ENST00000358485	NM_001080125.1	119	Tcc/Ccc	2/9	1	2	FACETS	0.982	0.913	1	0.982	0.913	1	CLONAL	1	TRUE	1	0.62	2		543	624	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735646	204735646	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	183	480	0	ENST00000302823.3:c.447T>G	p.Ile149Met	p.I149M	ENST00000302823	NM_005214.4	149	atT/atG	2/4	1	2	FACETS	0.901	0.835	0.969	0.901	0.835	0.969	CLONAL	1	TRUE	1	0.62	2		480	655	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437343	220437343	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	162	519	0	ENST00000243786.2:c.247G>T	p.Ala83Ser	p.A83S	ENST00000243786	NM_002191.3	83	Gcc/Tcc	1/2	1	2	FACETS	0.94	0.867	1	0.94	0.867	1	CLONAL	1	TRUE	1	0.62	2		519	556	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30954261	30954261	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	199	497	0	ENST00000375687.4:c.132G>T	p.Lys44Asn	p.K44N	ENST00000375687	NM_015338.5	44	aaG/aaT	2/13	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.62	2		497	623	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380511	31380511	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	187	563	0	ENST00000328111.2:c.1001A>G	p.Glu334Gly	p.E334G	ENST00000328111	NM_006892.3	334	gAg/gGg	9/23	1	2	FACETS	0.944	0.876	1	0.944	0.876	1	CLONAL	1	TRUE	1	0.62	2		563	639	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39745013	39745013	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	154	485	0	ENST00000361337.2:c.1803G>T	p.Gln601His	p.Q601H	ENST00000361337	NM_003286.2	601	caG/caT	17/21	1	2	FACETS	0.806	0.741	0.874	0.806	0.741	0.874	CLONAL	1	TRUE	1	0.62	2		485	616	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46252732	46252732	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	178	339	0	ENST00000371998.3:c.161C>A	p.Ala54Asp	p.A54D	ENST00000371998		54	gCc/gAc	4/23	1	2	FACETS	0.992	0.919	1	0.992	0.919	1	CLONAL	1	TRUE	1	0.62	2		339	579	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46276092	46276092	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	208	510	0	ENST00000371998.3:c.3528G>T	p.Gln1176His	p.Q1176H	ENST00000371998		1176	caG/caT	18/23	1	2	FACETS	0.94	0.876	1	0.94	0.876	1	CLONAL	1	TRUE	1	0.62	2		510	714	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62309650	62309650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753838163	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	193	532	0	ENST00000360203.5:c.988G>A	p.Asp330Asn	p.D330N	ENST00000360203	NM_001283009.1	330	Gat/Aat	12/35	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.62	2		532	591	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42843788	42843788	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	213	463	0	ENST00000398585.3:c.1131G>T	p.Lys377Asn	p.K377N	ENST00000398585	NM_001135099.1	377	aaG/aaT	10/14	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.62	2		463	660	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21348913	21348913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs970027059	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	150	594	0	ENST00000215739.8:c.1682G>A	p.Arg561His	p.R561H	ENST00000215739	NM_006767.3	561	cGc/cAc	15/21	1	2	FACETS	0.805	0.739	0.874	0.805	0.739	0.874	CLONAL	1	TRUE	1	0.62	2		594	601	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21350356	21350356	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752191147	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	159	525	0	ENST00000215739.8:c.2174G>A	p.Arg725His	p.R725H	ENST00000215739	NM_006767.3	725	cGc/cAc	18/21	1	2	FACETS	0.901	0.831	0.974	0.901	0.831	0.974	CLONAL	1	TRUE	1	0.62	2		525	569	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21351005	21351005	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1474790426	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	222	537	0	ENST00000215739.8:c.2240A>G	p.Tyr747Cys	p.Y747C	ENST00000215739	NM_006767.3	747	tAc/tGc	19/21	1	2	FACETS	0.976	0.912	1	0.976	0.912	1	CLONAL	1	TRUE	1	0.62	2		537	734	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143237	24143237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	264	649	0	ENST00000263121.7:c.469G>A	p.Gly157Ser	p.G157S	ENST00000263121	NM_003073.3	157	Ggc/Agc	4/9	1	2	FACETS	0.998	0.938	1	0.998	0.938	1	CLONAL	1	TRUE	1	0.62	2		649	853	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29445520	29445520	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	164	590	0	ENST00000544604.2:c.1351T>G	p.Leu451Val	p.L451V	ENST00000544604	NM_001206998.1	451	Ttg/Gtg	8/9	1	2	FACETS	0.946	0.874	1	0.946	0.874	1	CLONAL	1	TRUE	1	0.62	2		590	559	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523654	41523654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	198	504	0	ENST00000263253.7:c.1070C>T	p.Ala357Val	p.A357V	ENST00000263253	NM_001429.3	357	gCc/gTc	4/31	1	2	FACETS	0.955	0.888	1	0.955	0.888	1	CLONAL	1	TRUE	1	0.62	2		504	669	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533698	41533698	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	207	493	0	ENST00000263253.7:c.1664C>A	p.Pro555His	p.P555H	ENST00000263253	NM_001429.3	555	cCt/cAt	8/31	1	2	FACETS	0.916	0.853	0.981	0.916	0.853	0.981	CLONAL	1	TRUE	1	0.62	2		493	729	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574236	41574236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	195	591	0	ENST00000263253.7:c.6521C>T	p.Thr2174Ile	p.T2174I	ENST00000263253	NM_001429.3	2174	aCc/aTc	31/31	1	2	FACETS	0.859	0.798	0.923	0.859	0.798	0.923	CLONAL	1	TRUE	1	0.62	2		591	732	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626654	12626654	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	92	614	0	ENST00000251849.4:c.1635G>T	p.Glu545Asp	p.E545D	ENST00000251849	NM_002880.3	545	gaG/gaT	15/17	1	2	FACETS	0.412	0.366	0.461	0.412	0.366	0.461	SUBCLONAL	1	TRUE	1	0.62	2		614	720	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626685	12626685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	81	619	1	ENST00000251849.4:c.1604G>A	p.Gly535Asp	p.G535D	ENST00000251849	NM_002880.3	535	gGc/gAc	15/17	1	2	FACETS	0.351	0.309	0.397	0.351	0.309	0.397	SUBCLONAL	1	TRUE	1	0.62	2		620	744	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713561	30713561	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	192	563	0	ENST00000295754.5:c.886G>T	p.Asp296Tyr	p.D296Y	ENST00000295754	NM_003242.5	296	Gac/Tac	4/7	1	2	FACETS	0.931	0.865	1	0.931	0.865	1	CLONAL	1	TRUE	1	0.62	2		563	665	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30733091	30733091	+	stop_lost	Nonstop_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	181	430	0	ENST00000295754.5:c.1704G>T	p.Ter568TyrextTer27	p.*568Yext*27	ENST00000295754	NM_003242.5	568	taG/taT	7/7	1	2	FACETS	0.988	0.916	1	0.988	0.916	1	CLONAL	1	TRUE	1	0.62	2		430	591	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280661	41280661	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	217	555	0	ENST00000349496.5:c.2174G>A	p.Gly725Asp	p.G725D	ENST00000349496	NM_001904.3	725	gGc/gAc	15/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.62	2		555	679	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52661317	52661317	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	204	488	0	ENST00000394830.3:c.1513T>C	p.Ser505Pro	p.S505P	ENST00000394830	NM_018313.4	505	Tct/Cct	14/30	1	2	FACETS	0.895	0.833	0.959	0.895	0.833	0.959	CLONAL	1	TRUE	1	0.62	2		488	735	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63975998	63975998	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	225	579	0	ENST00000398590.3:c.1508C>A	p.Ser503Tyr	p.S503Y	ENST00000398590	NM_001177387.1	503	tCt/tAt	10/14	1	2	FACETS	0.974	0.911	1	0.974	0.911	1	CLONAL	1	TRUE	1	0.62	2		579	745	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947115	178947115	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	159	423	0	ENST00000263967.3:c.2551G>A	p.Val851Met	p.V851M	ENST00000263967	NM_006218.2	851	Gtg/Atg	18/21	1	2	FACETS	0.826	0.76	0.894	0.826	0.76	0.894	CLONAL	1	TRUE	1	0.62	2		423	621	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430857	181430857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	231	664	0	ENST00000325404.1:c.709C>T	p.Leu237Phe	p.L237F	ENST00000325404	NM_003106.3	237	Ctt/Ttt	1/1	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.62	2		664	690	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526118	189526118	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	242	606	0	ENST00000264731.3:c.382T>C	p.Ser128Pro	p.S128P	ENST00000264731	NM_003722.4	128	Tcc/Ccc	4/14	1	2	FACETS	0.992	0.93	1	0.992	0.93	1	CLONAL	1	TRUE	1	0.62	2		606	787	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920309	1920309	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	172	480	0	ENST00000382891.5:c.1369G>T	p.Ala457Ser	p.A457S	ENST00000382891	NM_133335.3	457	Gca/Tca	5/22	1	2	FACETS	0.895	0.827	0.965	0.895	0.827	0.965	CLONAL	1	TRUE	1	0.62	2		480	620	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153649	55153649	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	183	542	0	ENST00000257290.5:c.2615A>G	p.Tyr872Cys	p.Y872C	ENST00000257290	NM_006206.4	872	tAc/tGc	19/23	1	2	FACETS	0.928	0.861	0.998	0.928	0.861	0.998	CLONAL	1	TRUE	1	0.62	2		542	636	SUCCESS
REST	5978	MSKCC	GRCh37	4	57777693	57777693	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	178	348	0	ENST00000309042.7:c.889A>G	p.Thr297Ala	p.T297A	ENST00000309042	NM_005612.4	297	Act/Gct	2/4	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.62	2		348	563	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796431	57796431	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	198	532	0	ENST00000309042.7:c.1407G>T	p.Glu469Asp	p.E469D	ENST00000309042	NM_005612.4	469	gaG/gaT	4/4	1	2	FACETS	0.882	0.82	0.947	0.882	0.82	0.947	CLONAL	1	TRUE	1	0.62	2		532	724	SUCCESS
REST	5978	MSKCC	GRCh37	4	57798053	57798053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	164	498	0	ENST00000309042.7:c.3029G>A	p.Gly1010Asp	p.G1010D	ENST00000309042	NM_005612.4	1010	gGc/gAc	4/4	1	2	FACETS	0.935	0.863	1	0.935	0.863	1	CLONAL	1	TRUE	1	0.62	2		498	566	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201695	66201695	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	141	505	0	ENST00000273854.3:c.2807T>C	p.Ile936Thr	p.I936T	ENST00000273854	NM_004439.5	936	aTa/aCa	16/18	1	2	FACETS	0.88	0.806	0.956	0.88	0.806	0.956	CLONAL	1	TRUE	1	0.62	2		505	517	SUCCESS
ALB	213	MSKCC	GRCh37	4	74279147	74279147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	174	408	1	ENST00000295897.4:c.854C>T	p.Ala285Val	p.A285V	ENST00000295897	NM_000477.5	285	gCc/gTc	8/15	1	2	FACETS	0.997	0.924	1	0.997	0.924	1	CLONAL	1	TRUE	1	0.62	2		409	563	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156325	106156325	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	259	696	0	ENST00000380013.4:c.1226C>A	p.Pro409His	p.P409H	ENST00000380013	NM_001127208.2	409	cCt/cAt	3/11	1	2	FACETS	0.999	0.939	1	0.999	0.939	1	CLONAL	1	TRUE	1	0.62	2		696	836	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542128	187542128	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1298258217	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	220	625	0	ENST00000441802.2:c.5612A>G	p.Asp1871Gly	p.D1871G	ENST00000441802	NM_005245.3	1871	gAc/gGc	10/27	1	2	FACETS	0.942	0.88	1	0.942	0.88	1	CLONAL	1	TRUE	1	0.62	2		625	753	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264628	1264628	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746883330	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	180	589	0	ENST00000310581.5:c.2734G>A	p.Glu912Lys	p.E912K	ENST00000310581	NM_198253.2	912	Gag/Aag	11/16	1	2	FACETS	0.965	0.894	1	0.965	0.894	1	CLONAL	1	TRUE	1	0.62	2		589	602	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295340	1295340	+	upstream_gene_variant	5'Flank	SNP	C	C	T	rs35265333	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	155	663	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.958	0.883	1	0.958	0.883	1	CLONAL	1	TRUE	1	0.62	2		663	522	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31401549	31401549	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	175	406	0	ENST00000344624.3:c.4115T>C	p.Ile1372Thr	p.I1372T	ENST00000344624		1372	aTc/aCc	33/33	1	2	FACETS	0.925	0.856	0.996	0.925	0.856	0.996	CLONAL	1	TRUE	1	0.62	2		406	610	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871313	35871313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs778642997	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	149	399	0	ENST00000303115.3:c.535A>G	p.Thr179Ala	p.T179A	ENST00000303115	NM_002185.3	179	Acg/Gcg	4/8	1	2	FACETS	0.93	0.855	1	0.93	0.855	1	CLONAL	1	TRUE	1	0.62	2		399	517	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80169096	80169096	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	138	428	0	ENST00000265081.6:c.3292A>G	p.Asn1098Asp	p.N1098D	ENST00000265081	NM_002439.4	1098	Aat/Gat	23/24	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.62	2		428	443	SUCCESS
APC	324	MSKCC	GRCh37	5	112178142	112178142	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs200468360	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	191	623	0	ENST00000257430.4:c.6851C>A	p.Pro2284His	p.P2284H	ENST00000257430	NM_000038.5	2284	cCt/cAt	16/16	1	2	FACETS	0.89	0.826	0.956	0.89	0.826	0.956	CLONAL	1	TRUE	1	0.62	2		623	692	SUCCESS
APC	324	MSKCC	GRCh37	5	112178304	112178304	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	150	547	0	ENST00000257430.4:c.7013C>A	p.Pro2338His	p.P2338H	ENST00000257430	NM_000038.5	2338	cCt/cAt	16/16	1	2	FACETS	0.787	0.722	0.854	0.787	0.722	0.854	SUBCLONAL	1	TRUE	1	0.62	2		547	615	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515433	149515433	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	165	499	0	ENST00000261799.4:c.49C>A	p.Leu17Met	p.L17M	ENST00000261799	NM_002609.3	17	Ctg/Atg	3/23	1	2	FACETS	0.935	0.864	1	0.935	0.864	1	CLONAL	1	TRUE	1	0.62	2		499	569	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522617	176522617	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	200	615	0	ENST00000292408.4:c.1714C>A	p.Leu572Ile	p.L572I	ENST00000292408	NM_213647.1	572	Ctc/Atc	13/18	1	2	FACETS	0.935	0.87	1	0.935	0.87	1	CLONAL	1	TRUE	1	0.62	2		615	690	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721915	176721915	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	258	651	0	ENST00000439151.2:c.7546T>C	p.Ser2516Pro	p.S2516P	ENST00000439151	NM_022455.4	2516	Tct/Cct	23/23	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.62	2		651	789	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038457	180038457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	155	552	0	ENST00000261937.6:c.3560C>T	p.Ala1187Val	p.A1187V	ENST00000261937	NM_182925.4	1187	gCc/gTc	27/30	1	2	FACETS	0.988	0.911	1	0.988	0.911	1	CLONAL	1	TRUE	1	0.62	2		552	506	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839850	27839850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	245	640	0	ENST00000328488.2:c.244G>A	p.Asp82Asn	p.D82N	ENST00000328488	NM_003533.2	82	Gat/Aat	1/1	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.62	2		640	738	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671834	30671834	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	207	621	0	ENST00000376406.3:c.5126C>A	p.Pro1709His	p.P1709H	ENST00000376406	NM_014641.2	1709	cCt/cAt	10/15	1	2	FACETS	0.888	0.827	0.951	0.888	0.827	0.951	CLONAL	1	TRUE	1	0.62	2		621	752	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324699	31324699	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs41552612	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	86	183	0	ENST00000412585.2:c.109T>A	p.Ser37Thr	p.S37T	ENST00000412585	NM_005514.6	37	Tcc/Acc	2/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.62	2		183	199	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940475	31940475	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	186	500	1	ENST00000375333.2:c.508G>A	p.Val170Met	p.V170M	ENST00000375333	NM_032454.1	170	Gtg/Atg	3/8	1	2	FACETS	0.992	0.921	1	0.992	0.921	1	CLONAL	1	TRUE	1	0.62	2		501	605	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188376	32188376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1317413244	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	199	655	0	ENST00000375023.3:c.965G>A	p.Gly322Asp	p.G322D	ENST00000375023	NM_004557.3	322	gGt/gAt	6/30	1	2	FACETS	0.884	0.822	0.948	0.884	0.822	0.948	CLONAL	1	TRUE	1	0.62	2		655	726	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964442	93964442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	149	485	0	ENST00000369303.4:c.2455G>A	p.Val819Ile	p.V819I	ENST00000369303	NM_004440.3	819	Gta/Ata	14/17	1	2	FACETS	0.885	0.813	0.96	0.885	0.813	0.96	CLONAL	1	TRUE	1	0.62	2		485	543	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117707003	117707003	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	179	485	0	ENST00000368508.3:c.2147G>T	p.Ser716Ile	p.S716I	ENST00000368508	NM_002944.2	716	aGc/aTc	15/43	1	2	FACETS	0.918	0.85	0.988	0.918	0.85	0.988	CLONAL	1	TRUE	1	0.62	2		485	629	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519676	137519676	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	176	482	0	ENST00000367739.4:c.962T>C	p.Val321Ala	p.V321A	ENST00000367739	NM_000416.2	321	gTc/gCc	7/7	1	2	FACETS	0.859	0.794	0.926	0.859	0.794	0.926	CLONAL	1	TRUE	1	0.62	2		482	661	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137540446	137540446	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	142	440	0	ENST00000367739.4:c.19C>A	p.Leu7Ile	p.L7I	ENST00000367739	NM_000416.2	7	Cta/Ata	1/7	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.62	2		440	455	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157470054	157470054	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1337652239	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	203	514	0	ENST00000346085.5:c.2848A>G	p.Met950Val	p.M950V	ENST00000346085	NM_020732.3	950	Atg/Gtg	9/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.62	2		514	645	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984022	2984022	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs753614569	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	188	511	0	ENST00000396946.4:c.508C>A	p.Arg170Ser	p.R170S	ENST00000396946	NM_032415.4	170	Cgc/Agc	5/25	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.62	2		511	597	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6439779	6439779	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	203	483	0	ENST00000356142.4:c.305C>T	p.Ser102Phe	p.S102F	ENST00000356142	NM_018890.3	102	tCc/tTc	5/7	1	2	FACETS	0.977	0.91	1	0.977	0.91	1	CLONAL	1	TRUE	1	0.62	2		483	670	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334722	81334722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	153	501	0	ENST00000222390.5:c.1994G>A	p.Gly665Glu	p.G665E	ENST00000222390	NM_000601.4	665	gGa/gAa	17/18	1	2	FACETS	0.869	0.799	0.941	0.869	0.799	0.941	CLONAL	1	TRUE	1	0.62	2		501	568	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509703	106509703	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1217690412	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	171	588	0	ENST00000359195.3:c.1697C>A	p.Pro566His	p.P566H	ENST00000359195	NM_002649.2	566	cCt/cAt	2/11	1	2	FACETS	0.987	0.913	1	0.987	0.913	1	CLONAL	1	TRUE	1	0.62	2		588	559	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436049	116436049	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	184	577	0	ENST00000397752.3:c.4044C>A	p.His1348Gln	p.H1348Q	ENST00000397752	NM_000245.2	1348	caC/caA	21/21	1	2	FACETS	0.891	0.826	0.958	0.891	0.826	0.958	CLONAL	1	TRUE	1	0.62	2		577	666	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851555	128851555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	175	416	0	ENST00000249373.3:c.1880C>T	p.Ala627Val	p.A627V	ENST00000249373	NM_005631.4	627	gCt/gTt	11/12	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.62	2		416	554	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512042	148512042	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	220	407	0	ENST00000320356.2:c.1636A>T	p.Asn546Tyr	p.N546Y	ENST00000320356	NM_004456.4	546	Aat/Tat	14/20	1	2	FACETS	0.967	0.903	1	0.967	0.903	1	CLONAL	1	TRUE	1	0.62	2		407	734	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849883	151849883	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201100798	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	201	473	0	ENST00000262189.6:c.12433C>T	p.Arg4145Cys	p.R4145C	ENST00000262189	NM_170606.2	4145	Cgt/Tgt	49/59	1	2	FACETS	0.965	0.898	1	0.965	0.898	1	CLONAL	1	TRUE	1	0.62	2		473	672	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859305	151859305	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	178	483	0	ENST00000262189.6:c.11357C>A	p.Ser3786Ter	p.S3786*	ENST00000262189	NM_170606.2	3786	tCa/tAa	43/59	1	2	FACETS	0.932	0.863	1	0.932	0.863	1	CLONAL	1	TRUE	1	0.62	2		483	616	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878155	151878155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	213	577	0	ENST00000262189.6:c.6790C>T	p.Pro2264Ser	p.P2264S	ENST00000262189	NM_170606.2	2264	Ccg/Tcg	36/59	1	2	FACETS	0.937	0.874	1	0.937	0.874	1	CLONAL	1	TRUE	1	0.62	2		577	733	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538802	23538802	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769852677	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	146	439	0	ENST00000380871.4:c.637G>A	p.Val213Met	p.V213M	ENST00000380871	NM_006167.3	213	Gtg/Atg	2/2	1	2	FACETS	0.887	0.814	0.962	0.887	0.814	0.962	CLONAL	1	TRUE	1	0.62	2		439	531	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187117	38187117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1481024329	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	193	487	0	ENST00000317025.8:c.1360C>T	p.Arg454Trp	p.R454W	ENST00000317025	NM_023034.1	454	Cgg/Tgg	6/24	1	2	FACETS	0.928	0.862	0.996	0.928	0.862	0.996	CLONAL	1	TRUE	1	0.62	2		487	671	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187408	38187408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243215593	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	166	423	1	ENST00000317025.8:c.1069C>T	p.Arg357Trp	p.R357W	ENST00000317025	NM_023034.1	357	Cgg/Tgg	6/24	1	2	FACETS	0.824	0.76	0.89	0.824	0.76	0.89	CLONAL	1	TRUE	1	0.62	2		424	650	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965389	68965389	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	167	482	0	ENST00000288368.4:c.1001C>T	p.Ala334Val	p.A334V	ENST00000288368	NM_024870.2	334	gCa/gTa	9/40	1	2	FACETS	0.947	0.875	1	0.947	0.875	1	CLONAL	1	TRUE	1	0.62	2		482	569	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981401	70981401	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	164	491	0	ENST00000276594.2:c.695G>T	p.Ser232Ile	p.S232I	ENST00000276594	NM_024504.3	232	aGc/aTc	2/8	1	2	FACETS	0.901	0.832	0.973	0.901	0.832	0.973	CLONAL	1	TRUE	1	0.62	2		491	587	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141545600	141545600	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	211	558	0	ENST00000220592.5:c.2238C>A	p.Phe746Leu	p.F746L	ENST00000220592	NM_012154.3	746	ttC/ttA	17/19	1	2	FACETS	0.916	0.854	0.98	0.916	0.854	0.98	CLONAL	1	TRUE	1	0.62	2		558	743	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740540	145740540	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	224	702	0	ENST00000428558.2:c.1477C>A	p.Leu493Met	p.L493M	ENST00000428558	NM_004260.3	493	Ctg/Atg	8/22	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.62	2		702	706	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2039719	2039719	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	183	600	0	ENST00000349721.2:c.609G>T	p.Gln203His	p.Q203H	ENST00000349721	NM_003070.3	203	caG/caT	4/34	1	2	FACETS	0.859	0.796	0.925	0.859	0.796	0.925	CLONAL	1	TRUE	1	0.62	2		600	687	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2161728	2161728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	214	495	0	ENST00000349721.2:c.4024C>T	p.Arg1342Trp	p.R1342W	ENST00000349721	NM_003070.3	1342	Cgg/Tgg	28/34	1	2	FACETS	0.964	0.9	1	0.964	0.9	1	CLONAL	1	TRUE	1	0.62	2		495	716	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5065019	5065019	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	53	429	0	ENST00000381652.3:c.1193G>A	p.Ser398Asn	p.S398N	ENST00000381652	NM_004972.3	398	aGc/aAc	9/25	1	2	FACETS	0.298	0.254	0.347	0.298	0.254	0.347	SUBCLONAL	1	TRUE	1	0.62	2		429	573	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5463032	5463032	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	248	510	0	ENST00000381577.3:c.593G>T	p.Arg198Ile	p.R198I	ENST00000381577	NM_014143.3	198	aGa/aTa	4/7	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.62	2		510	782	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465473	8465473	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	160	415	2	ENST00000356435.5:c.3707C>T	p.Ala1236Val	p.A1236V	ENST00000356435		1236	gCa/gTa	21/35	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.62	2		417	490	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504282	8504282	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	196	522	0	ENST00000356435.5:c.1801T>G	p.Ser601Ala	p.S601A	ENST00000356435		601	Tca/Gca	12/35	1	2	FACETS	0.951	0.884	1	0.951	0.884	1	CLONAL	1	TRUE	1	0.62	2		522	665	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606478	93606478	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	168	669	0	ENST00000375746.1:c.298G>A	p.Val100Ile	p.V100I	ENST00000375746	NM_001174167.1	100	Gtc/Atc	2/14	1	2	FACETS	0.954	0.882	1	0.954	0.882	1	CLONAL	1	TRUE	1	0.62	2		669	568	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606579	93606579	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	157	473	0	ENST00000375746.1:c.399G>T	p.Lys133Asn	p.K133N	ENST00000375746	NM_001174167.1	133	aaG/aaT	2/14	1	2	FACETS	0.961	0.886	1	0.961	0.886	1	CLONAL	1	TRUE	1	0.62	2		473	527	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97873753	97873753	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	181	615	0	ENST00000289081.3:c.1321C>T	p.Gln441Ter	p.Q441*	ENST00000289081	NM_000136.2	441	Cag/Tag	13/15	1	2	FACETS	0.909	0.843	0.978	0.909	0.843	0.978	CLONAL	1	TRUE	1	0.62	2		615	642	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900255	101900255	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	238	493	0	ENST00000374994.4:c.689C>T	p.Ala230Val	p.A230V	ENST00000374994	NM_004612.2	230	gCt/gTt	4/9	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.62	2		493	740	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738186	133738186	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	170	444	0	ENST00000318560.5:c.586G>A	p.Ala196Thr	p.A196T	ENST00000318560	NM_005157.4	196	Gcc/Acc	4/11	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.62	2		444	531	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293728	137293728	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	98	486	0	ENST00000481739.1:c.279G>T	p.Gln93His	p.Q93H	ENST00000481739	NM_002957.4	93	caG/caT	2/10	1	2	FACETS	0.674	0.604	0.748	0.674	0.604	0.748	SUBCLONAL	1	TRUE	1	0.62	2		486	469	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393563	139393563	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	169	635	0	ENST00000277541.6:c.6082+1G>A		p.X2028_splice	ENST00000277541	NM_017617.3	2028			1	2	FACETS	0.86	0.794	0.928	0.86	0.794	0.928	CLONAL	1	TRUE	1	0.62	2		635	634	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397757	139397757	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	163	545	0	ENST00000277541.6:c.5044A>G	p.Asn1682Asp	p.N1682D	ENST00000277541	NM_017617.3	1682	Aac/Gac	27/34	1	2	FACETS	0.929	0.857	1	0.929	0.857	1	CLONAL	1	TRUE	1	0.62	2		545	566	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410058	139410058	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	182	593	0	ENST00000277541.6:c.1780G>T	p.Gly594Cys	p.G594C	ENST00000277541	NM_017617.3	594	Ggc/Tgc	11/34	1	2	FACETS	0.886	0.82	0.953	0.886	0.82	0.953	CLONAL	1	TRUE	1	0.62	2		593	663	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921528	39921528	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369432845	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	193	527	0	ENST00000378444.4:c.4292C>T	p.Ser1431Phe	p.S1431F	ENST00000378444	NM_001123385.1	1431	tCc/tTc	10/15	1	2	FACETS	0.92	0.854	0.987	0.92	0.854	0.987	CLONAL	1	TRUE	1	0.62	2		527	677	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930249	39930249	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	205	563	0	ENST00000378444.4:c.3215C>G	p.Ala1072Gly	p.A1072G	ENST00000378444	NM_001123385.1	1072	gCa/gGa	6/15	1	2	FACETS	0.957	0.891	1	0.957	0.891	1	CLONAL	1	TRUE	1	0.62	2		563	691	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44921981	44921981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	88	283	0	ENST00000377967.4:c.1515G>A	p.Met505Ile	p.M505I	ENST00000377967	NM_021140.2	505	atG/atA	15/29	1	2	FACETS	0.722	0.644	0.805	0.722	0.644	0.805	SUBCLONAL	1	TRUE	1	0.62	2		283	393	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929019	44929019	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	197	431	0	ENST00000377967.4:c.2119G>T	p.Gly707Cys	p.G707C	ENST00000377967	NM_021140.2	707	Ggt/Tgt	17/29	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.62	2		431	603	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006879	47006879	+	5_prime_UTR_variant	5'UTR	SNP	A	A	G	rs2147065726	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	161	505	0	ENST00000377604.3:c.-2A>G		p.*1*	ENST00000377604	NM_001204468.1	-/852		2/24	1	2	FACETS	0.847	0.78	0.916	0.847	0.78	0.916	CLONAL	1	TRUE	1	0.62	2		505	613	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030479	47030479	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	155	520	0	ENST00000377604.3:c.254G>T	p.Arg85Leu	p.R85L	ENST00000377604	NM_001204468.1	85	cGg/cTg	4/24	1	2	FACETS	0.894	0.823	0.968	0.894	0.823	0.968	CLONAL	1	TRUE	1	0.62	2		520	559	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429039	47429039	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	199	607	0	ENST00000377045.4:c.1402G>T	p.Gly468Ter	p.G468*	ENST00000377045	NM_001654.4	468	Gga/Tga	13/16	1	2	FACETS	0.988	0.919	1	0.988	0.919	1	CLONAL	1	TRUE	1	0.62	2		607	650	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224165	53224165	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	182	586	0	ENST00000375401.3:c.3386A>G	p.Asp1129Gly	p.D1129G	ENST00000375401	NM_004187.3	1129	gAc/gGc	22/26	1	2	FACETS	0.927	0.86	0.997	0.927	0.86	0.997	CLONAL	1	TRUE	1	0.62	2		586	633	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413111	63413111	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	175	527	0	ENST00000330258.3:c.56G>T	p.Ser19Ile	p.S19I	ENST00000330258	NM_152424.3	19	aGt/aTt	2/2	1	2	FACETS	0.965	0.894	1	0.965	0.894	1	CLONAL	1	TRUE	1	0.62	2		527	585	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341282	70341282	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	197	538	0	ENST00000374080.3:c.841C>A	p.Leu281Ile	p.L281I	ENST00000374080		281	Ctc/Atc	6/45	1	2	FACETS	0.932	0.866	0.999	0.932	0.866	0.999	CLONAL	1	TRUE	1	0.62	2		538	682	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348997	70348997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	191	530	0	ENST00000374080.3:c.3509G>A	p.Arg1170Gln	p.R1170Q	ENST00000374080		1170	cGg/cAg	25/45	1	2	FACETS	0.905	0.84	0.972	0.905	0.84	0.972	CLONAL	1	TRUE	1	0.62	2		530	681	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349655	70349655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	219	620	0	ENST00000374080.3:c.3817G>A	p.Ala1273Thr	p.A1273T	ENST00000374080		1273	Gcc/Acc	27/45	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.62	2		620	659	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76777841	76777841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	164	530	0	ENST00000373344.5:c.6875C>T	p.Pro2292Leu	p.P2292L	ENST00000373344	NM_000489.3	2292	cCa/cTa	32/35	1	2	FACETS	0.864	0.797	0.934	0.864	0.797	0.934	CLONAL	1	TRUE	1	0.62	2		530	612	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874351	76874351	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	107	378	0	ENST00000373344.5:c.5371G>T	p.Asp1791Tyr	p.D1791Y	ENST00000373344	NM_000489.3	1791	Gat/Tat	21/35	1	2	FACETS	0.75	0.677	0.827	0.75	0.677	0.827	SUBCLONAL	1	TRUE	1	0.62	2		378	460	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888737	76888737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	140	469	0	ENST00000373344.5:c.5092C>T	p.Arg1698Trp	p.R1698W	ENST00000373344	NM_000489.3	1698	Cgg/Tgg	19/35	1	2	FACETS	0.792	0.725	0.863	0.792	0.725	0.863	SUBCLONAL	1	TRUE	1	0.62	2		469	570	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938838	76938838	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	186	506	0	ENST00000373344.5:c.1910A>C	p.Glu637Ala	p.E637A	ENST00000373344	NM_000489.3	637	gAg/gCg	9/35	1	2	FACETS	0.997	0.926	1	0.997	0.926	1	CLONAL	1	TRUE	1	0.62	2		506	602	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608218	100608218	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	184	441	0	ENST00000308731.7:c.1872G>T	p.Glu624Asp	p.E624D	ENST00000308731	NM_000061.2	624	gaG/gaT	18/19	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.62	2		441	542	SUCCESS
BTK	695	MSKCC	GRCh37	X	100624984	100624984	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	156	426	0	ENST00000308731.7:c.391+2T>C		p.X131_splice	ENST00000308731	NM_000061.2	131			1	2	FACETS	0.948	0.873	1	0.948	0.873	1	CLONAL	1	TRUE	1	0.62	2		426	531	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020207	123020207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	38	513	0	ENST00000355640.3:c.695G>A	p.Gly232Asp	p.G232D	ENST00000355640		232	gGc/gAc	2/7	1	2	FACETS	0.19	0.156	0.227	0.19	0.156	0.227	SUBCLONAL	1	TRUE	1	0.62	2		513	646	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197701	123197701	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	126	416	0	ENST00000218089.9:c.1825T>A	p.Leu609Met	p.L609M	ENST00000218089	NM_001042749.1	609	Ttg/Atg	20/35	1	2	FACETS	0.917	0.837	1	0.917	0.837	1	CLONAL	1	TRUE	1	0.62	2		416	443	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480563	123480563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	152	529	0	ENST00000371139.4:c.71G>A	p.Gly24Glu	p.G24E	ENST00000371139	NM_001114937.2	24	gGg/gAg	1/4	1	2	FACETS	0.895	0.823	0.969	0.895	0.823	0.969	CLONAL	1	TRUE	1	0.62	2		529	548	SUCCESS
PHF6	84295	MSKCC	GRCh37	X	133547958	133547958	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	198	390	0	ENST00000332070.3:c.691T>G	p.Phe231Val	p.F231V	ENST00000332070	NM_032458.2	231	Ttt/Gtt	7/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.62	2		390	522	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858080	152858080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	170	534	0	ENST00000406277.2:c.535G>A	p.Ala179Thr	p.A179T	ENST00000406277	NM_152274.4	179	Gcg/Acg	6/7	1	2	FACETS	0.926	0.856	0.998	0.926	0.856	0.998	CLONAL	1	TRUE	1	0.62	2		534	592	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0066047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	270	545	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.743228715594876	2		545	661	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624271	89624272	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs786204883	NA	P-0066047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	219	284	0	ENST00000371953.3:c.46dup	p.Tyr16LeufsTer28	p.Y16Lfs*28	ENST00000371953	NM_000314.4	15	-/T	1/9	0.724748402219837	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.743228715594876	2		284	281	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629143	14629143	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	204	579	0	ENST00000254322.2:c.19C>G	p.Gln7Glu	p.Q7E	ENST00000254322	NM_006145.1	7	Cag/Gag	1/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.743228715594876	2		579	514	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0066051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	133	491	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.192417358417619	3	FACETS	0.946	0.863	1			1	CLONAL	2	TRUE	NA	0.29	3		491	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0066051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	103	622	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.903	0.807	1	0.903	0.807	1	CLONAL	1	TRUE	1	0.29	2		622	787	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971124	21971125	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0066051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	89	751	0	ENST00000304494.5:c.233_234del	p.Leu78HisfsTer41	p.L78Hfs*41	ENST00000304494	NM_000077.4	78	cTC/c	2/3	1	2	FACETS	0.842	0.746	0.944	0.842	0.746	0.944	CLONAL	1	TRUE	1	0.29	2		751	729	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748297	43748297	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	80	727	0	ENST00000382044.4:c.2509C>T	p.Gln837Ter	p.Q837*	ENST00000382044	NM_001141980.1	837	Cag/Tag	12/28	1	2	FACETS	0.701	0.616	0.792	0.701	0.616	0.792	SUBCLONAL	1	TRUE	1	0.29	2		727	787	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244313	41244313	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	86	564	0	ENST00000357654.3:c.3235A>C	p.Lys1079Gln	p.K1079Q	ENST00000357654	NM_007294.3	1079	Aaa/Caa	10/23	1	2	FACETS	0.938	0.831	1	0.938	0.831	1	CLONAL	1	TRUE	1	0.29	2		564	632	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0066052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	119	295	1	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.402551054398987	2		296	540	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39535272	39535272	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	64	558	0	ENST00000262039.4:c.17del	p.Lys6SerfsTer18	p.K6Sfs*18	ENST00000262039	NM_002647.2	6	Aag/ag	1/25	1	2	FACETS	0.564	0.488	0.646	0.564	0.488	0.646	SUBCLONAL	1	TRUE	1	0.402551054398987	2		558	564	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	75	286	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.167515108785516	2	FACETS	1	0.945	1	0.566	0.498	0.639	INDETERMINATE	1	TRUE	0	0.286718944121058	2		286	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577095	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519984	NA	P-0066053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	139	612	0	ENST00000269305.4:c.843C>G	p.Asp281Glu	p.D281E	ENST00000269305	NM_001126112.2	281	gaC/gaG	8/11	0.167515108785516	2	FACETS	1	0.981	1	0.642	0.585	0.702	INDETERMINATE	1	TRUE	0	0.286718944121058	2		612	755	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220579	1220579	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0066053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	131	671	0	ENST00000326873.7:c.598-1G>T		p.X200_splice	ENST00000326873	NM_000455.4	200			0.167515108785516	2	FACETS	1	0.982	1	0.671	0.61	0.735	INDETERMINATE	1	TRUE	0	0.286718944121058	2		671	681	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150923452	150923452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	88	546	0	ENST00000271640.5:c.2099C>T	p.Thr700Ile	p.T700I	ENST00000271640	NM_001145415.1	700	aCc/aTc	13/22	0.207894683667009	4	FACETS	0.999	0.884	1	0.333	0.294	0.374	CLONAL	1	TRUE	1	0.286718944121058	4		546	791	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	58	663	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.412782640596513	2		663	213	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555526268	NA	P-0066054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	415	563	0	ENST00000269305.4:c.406C>G	p.Gln136Glu	p.Q136E	ENST00000269305	NM_001126112.2	136	Caa/Gaa	5/11	0.412782640596513	4	FACETS	0.908	0.876	0.938	1	0.994	1	CLONAL	5	TRUE	0	0.412782640596513	4		563	626	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243484	46243484	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	41	455	0	ENST00000334344.6:c.1837C>T	p.Gln613Ter	p.Q613*	ENST00000334344	NM_152641.2	613	Cag/Tag	14/21	0.194212760965321	5	FACETS	0.969	0.82	1	0.646	0.546	0.753	INDETERMINATE	2	TRUE	2	0.412782640596513	5		455	166	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350233	89350233	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763544660	NA	P-0066054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	248	554	0	ENST00000301030.4:c.2717G>A	p.Arg906Gln	p.R906Q	ENST00000301030	NM_001256183.1	906	cGa/cAa	9/13	0.412782640596513	2	FACETS	0.896	0.851	0.941	1	0.993	1	CLONAL	3	TRUE	0	0.412782640596513	2		554	447	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914458	32914458	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	52	509	0	ENST00000380152.3:c.5966C>T	p.Ser1989Leu	p.S1989L	ENST00000380152		1989	tCa/tTa	11/27	0.364472649477793	3	FACETS	1	0.96	1	0.45	0.388	0.517	CLONAL	1	TRUE	0	0.412782640596513	3		509	225	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732959	44732959	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0066054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	96	196	0	ENST00000377967.4:c.161+1G>T		p.X54_splice	ENST00000377967	NM_021140.2	54			0.412782640596513	2	FACETS	0.988	0.912	1			1	CLONAL	3	TRUE	NA	0.412782640596513	2		196	157	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940583	71940583	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0066054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	209	617	0	ENST00000298229.2:c.736del	p.Arg246AlafsTer16	p.R246Afs*16	ENST00000298229	NM_001567.3	245	aCc/ac	6/28	0.305739787902898	4	FACETS	0.98	0.913	1	0.98	0.913	1	CLONAL	2	TRUE	2	0.412782640596513	4		617	730	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729520	41729520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	69	599	0	ENST00000242208.4:c.1009G>A	p.Asp337Asn	p.D337N	ENST00000242208	NM_002192.2	337	Gac/Aac	3/3	0.412782640596513	5	FACETS	0.97	0.846	1	0.243	0.211	0.276	CLONAL	1	TRUE	1	0.412782640596513	5		599	558	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595399	141595399	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	246	598	0	ENST00000220592.5:c.34C>G	p.Pro12Ala	p.P12A	ENST00000220592	NM_012154.3	12	Cct/Gct	2/19	0.412782640596513	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.412782640596513	3		598	622	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350999	89350999	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	99	522	0	ENST00000301030.4:c.1951G>C	p.Glu651Gln	p.E651Q	ENST00000301030	NM_001256183.1	651	Gag/Cag	9/13	0.412782640596513	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.412782640596513	2		522	221	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350909	89350909	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0066054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	64	521	0	ENST00000301030.4:c.2041G>T	p.Glu681Ter	p.E681*	ENST00000301030	NM_001256183.1	681	Gaa/Taa	9/13	0.412782640596513	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	2	TRUE	0	0.412782640596513	2		521	151	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999684	100999684	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	35	560	0	ENST00000325455.5:c.118C>T	p.Gln40Ter	p.Q40*	ENST00000325455	NM_001202474.3	40	Cag/Tag	1/8	0.305739787902898	4	FACETS	0.597	0.49	0.718	0.299	0.245	0.359	SUBCLONAL	1	TRUE	2	0.412782640596513	4		560	401	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940452	13940452	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	48	341	0	ENST00000405192.2:c.1054T>A	p.Trp352Arg	p.W352R	ENST00000405192	NM_001163147.1	352	Tgg/Agg	11/12	0.412782640596513	5	FACETS	1	0.944	1	0.312	0.265	0.363	CLONAL	1	TRUE	1	0.412782640596513	5		341	302	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008501	70008501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147148433	NA	P-0066054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	100	495	0	ENST00000394351.3:c.788G>A	p.Arg263His	p.R263H	ENST00000394351	NM_000248.3	263	cGc/cAc	8/9	0.275424742109278	5	FACETS	0.95	0.854	1	0.633	0.569	0.7	CLONAL	2	TRUE	2	0.412782640596513	5		495	413	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664442	138664442	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	112	325	0	ENST00000330315.3:c.1123G>C	p.Asp375His	p.D375H	ENST00000330315	NM_023067.3	375	Gat/Cat	1/1	0.275424742109278	5	FACETS	0.996	0.91	1	0.996	0.91	1	CLONAL	3	TRUE	2	0.412782640596513	5		325	294	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350791	89350791	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1026259150	NA	P-0066054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	84	543	0	ENST00000301030.4:c.2159G>C	p.Arg720Thr	p.R720T	ENST00000301030	NM_001256183.1	720	aGa/aCa	9/13	0.412782640596513	2	FACETS	0.837	0.762	0.912	1	0.977	1	CLONAL	3	TRUE	0	0.412782640596513	2		543	162	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92404035	92404040	+	inframe_deletion	In_Frame_Del	DEL	GGCTCT	GGCTCT	-	novel	NA	P-0066054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	17	401	0	ENST00000265734.4:c.339_344del	p.Glu114_Pro115del	p.E114_P115del	ENST00000265734	NM_001259.6	113	ccAGAGCCt/cct	3/8	0.146594665606374	2	FACETS	0.512	0.384	0.661	0.256	0.192	0.331	INDETERMINATE	1	TRUE	0	0.412782640596513	2		401	161	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350558	89350558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	47	351	0	ENST00000301030.4:c.2392G>A	p.Asp798Asn	p.D798N	ENST00000301030	NM_001256183.1	798	Gat/Aat	9/13	0.412782640596513	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	0	0.412782640596513	2		351	98	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	56	663	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.886	0.773	1	0.886	0.773	1	CLONAL	1	TRUE	1	0.710025385661646	2		663	178	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0066055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	231	786	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.710025385661646	2	FACETS	0.98	0.937	1	0.98	0.937	1	CLONAL	2	TRUE	0	0.710025385661646	2		786	332	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779649	3779649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	137	559	1	ENST00000262367.5:c.5399G>A	p.Arg1800Gln	p.R1800Q	ENST00000262367	NM_004380.2	1800	cGg/cAg	31/31	1	2	FACETS	0.923	0.848	1	0.923	0.848	1	CLONAL	1	TRUE	1	0.710025385661646	2		560	418	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0066056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	40	554	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.298904381020566	2	FACETS	0.478	0.397	0.568	0.239	0.198	0.284	SUBCLONAL	1	TRUE	0	0.358967095462847	2		554	466	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175996806	175996806	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1272399205	NA	P-0066056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	133	499	0	ENST00000367669.3:c.1631A>G	p.Asn544Ser	p.N544S	ENST00000367669	NM_022457.5	544	aAt/aGt	15/20	0.299414251113288	4	FACETS	0.9	0.827	0.975	0.9	0.827	0.975	CLONAL	3	TRUE	1	0.358967095462847	4		499	373	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440843	52440843	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0066056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	141	516	0	ENST00000460680.1:c.659+2T>C		p.X220_splice	ENST00000460680	NM_004656.3	220			0.313222560061086	2	FACETS	1	0.988	1	0.748	0.685	0.813	CLONAL	1	TRUE	0	0.358967095462847	2		516	525	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80168958	80168958	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	104	472	0	ENST00000265081.6:c.3154T>C	p.Phe1052Leu	p.F1052L	ENST00000265081	NM_002439.4	1052	Ttt/Ctt	23/24	0.358967095462847	4	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	2	0.358967095462847	4		472	362	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347903	347907	+	frameshift_variant	Frame_Shift_Del	DEL	CGTGT	CGTGT	-	novel	NA	P-0066056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	159	752	0	ENST00000262320.3:c.1599_1603del	p.His534ProfsTer55	p.H534Pfs*55	ENST00000262320	NM_003502.3	533	cgACACGtc/cgtc	6/11	0.356125587549362	3	FACETS	1	0.986	1	0.69	0.634	0.749	CLONAL	1	TRUE	1	0.358967095462847	3		752	757	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0066058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	242	425	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.676571092802034	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.718616470052594	1		425	416	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829617	72829617	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	173	447	0	ENST00000268489.5:c.6964C>T	p.Arg2322Ter	p.R2322*	ENST00000268489	NM_006885.3	2322	Cga/Tga	9/10	0.284049022897141	3	FACETS	1	0.972	1	0.553	0.511	0.595	INDETERMINATE	1	TRUE	1	0.718616470052594	3		447	592	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36028518	36028518	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	150	388	0	ENST00000358208.4:c.860G>A	p.Gly287Glu	p.G287E	ENST00000358208		287	gGg/gAg	8/12	NA	2	FACETS	0.879	0.81	0.95			1	INDETERMINATE	1	TRUE	NA	0.718616470052594	2		388	475	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112434	115112435	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0066069-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	62	444	0	ENST00000257566.3:c.1305_1306del	p.Arg436ProfsTer2	p.R436Pfs*2	ENST00000257566	NM_016569.3	435	tcACgc/tcgc	7/8	0.211623491636644	4	FACETS	1	0.905	1	0.529	0.457	0.606	CLONAL	1	TRUE	2	0.294052769174518	4		444	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578262	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs483352697	NA	P-0066070-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	567	608	0	ENST00000269305.4:c.587G>C	p.Arg196Pro	p.R196P	ENST00000269305	NM_001126112.2	196	cGa/cCa	6/11	0.80717131549844	4	FACETS	0.977	0.959	0.994	0.977	0.959	0.994	CLONAL	4	TRUE	0	0.812938925370054	4		608	647	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748081	41748081	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066070-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	69	362	0	ENST00000226382.2:c.688G>A	p.Gly230Arg	p.G230R	ENST00000226382	NM_003924.3	230	Ggg/Agg	3/3	1	2	FACETS	0.923	0.82	1	0.923	0.82	1	CLONAL	1	TRUE	1	0.812938925370054	2		362	184	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098909	47098909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066071-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	180	474	0	ENST00000409792.3:c.6365G>A	p.Arg2122Gln	p.R2122Q	ENST00000409792	NM_014159.6	2122	cGg/cAg	15/21	0.516725348178082	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.516725348178082	1		474	458	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593605	55593610	+	inframe_deletion	In_Frame_Del	DEL	GAAGGT	GAAGGT	-	novel	NA	P-0066071-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	162	385	0	ENST00000288135.5:c.1671_1676del	p.Trp557_Val559delinsCys	p.W557_V559delinsC	ENST00000288135	NM_000222.2	557	tgGAAGGTt/tgt	11/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.516725348178082	2		385	603	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066072-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	129	663	0				ENST00000310581	NM_198253.2	-/1132			0.814981354435599	4	FACETS	0.775	0.712	0.84	0.775	0.712	0.84	SUBCLONAL	2	TRUE	2	0.937711769651418	4		663	344	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0066072-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	103	430	0	ENST00000349496.5:c.101G>A	p.Gly34Glu	p.G34E	ENST00000349496	NM_001904.3	34	gGa/gAa	3/15	0.814981354435599	4	FACETS	0.752	0.675	0.834	0.376	0.337	0.417	SUBCLONAL	1	TRUE	2	0.937711769651418	4		430	566	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945649	151945649	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066072-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	33	334	0	ENST00000262189.6:c.1870G>C	p.Asp624His	p.D624H	ENST00000262189	NM_170606.2	624	Gat/Cat	14/59	0.937711769651418	6	FACETS	0.778	0.637	0.936	0.259	0.212	0.312	CLONAL	1	TRUE	3	0.937711769651418	6		334	260	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945337	151945337	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066072-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	10	86	0	ENST00000262189.6:c.2182G>C	p.Glu728Gln	p.E728Q	ENST00000262189	NM_170606.2	728	Gaa/Caa	14/59	0.937711769651418	6	FACETS	0.829	0.57	1	0.276	0.19	0.381	CLONAL	1	TRUE	3	0.937711769651418	6		86	74	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945589	151945589	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747766860	NA	P-0066072-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	12	123	0	ENST00000262189.6:c.1930G>A	p.Glu644Lys	p.E644K	ENST00000262189	NM_170606.2	644	Gaa/Aaa	14/59	0.937711769651418	6	FACETS	0.701	0.497	0.946	0.234	0.165	0.316	CLONAL	1	TRUE	3	0.937711769651418	6		123	105	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933598	39933598	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066072-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	145	492	0	ENST00000378444.4:c.1001C>T	p.Pro334Leu	p.P334L	ENST00000378444	NM_001123385.1	334	cCc/cTc	4/15	0.506203768393711	4	FACETS	0.984	0.901	1	0.328	0.3	0.357	INDETERMINATE	1	TRUE	1	0.937711769651418	4		492	609	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190006	123190006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066072-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	39	337	0	ENST00000218089.9:c.1225G>A	p.Asp409Asn	p.D409N	ENST00000218089	NM_001042749.1	409	Gat/Aat	14/35	0.506203768393711	4	FACETS	0.971	0.817	1	0.324	0.272	0.379	INDETERMINATE	1	TRUE	1	0.937711769651418	4		337	166	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100948	41100948	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066073-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	216	455	0	ENST00000373198.4:c.1408C>T	p.Arg470Ter	p.R470*	ENST00000373198	NM_133170.3	470	Cga/Tga	8/32	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.644820256964075	2		455	622	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0066073-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	75	491	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.644820256964075	3	FACETS	0.91	0.818	1	0.91	0.818	1	CLONAL	2	TRUE	1	0.644820256964075	3		491	169	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0066073-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	31	407	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.2	0.161	0.244	0.2	0.161	0.244	SUBCLONAL	1	TRUE	1	0.644820256964075	2		407	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs786201057	NA	P-0066073-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	25	728	0	ENST00000269305.4:c.374C>G	p.Thr125Arg	p.T125R	ENST00000269305	NM_001126112.2	125	aCg/aGg	4/11	1	2	FACETS	0.145	0.113	0.181	0.145	0.113	0.181	SUBCLONAL	1	TRUE	1	0.644820256964075	2		728	536	SUCCESS
APC	324	MSKCC	GRCh37	5	112175651	112175651	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066073-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	214	556	0	ENST00000257430.4:c.4364del	p.Asn1455IlefsTer18	p.N1455Ifs*18	ENST00000257430	NM_000038.5	1454	Aaa/aa	16/16	0.644820256964075	2	FACETS	0.994	0.945	1	0.994	0.945	1	CLONAL	2	TRUE	0	0.644820256964075	2		556	334	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0066073-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	24	322	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	0.644820256964075	1	FACETS	0.587	0.472	0.711	0.587	0.472	0.711	SUBCLONAL	1	TRUE	0	0.644820256964075	1		322	86	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925316	114925317	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs745872748	NA	P-0066073-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	223	375	12	ENST00000543371.1:c.1403dup	p.Cys469ValfsTer8	p.C469Vfs*8	ENST00000543371	NM_001198531.1	465	aga/agAa	14/14	0.54135468677694	2	FACETS	0.784	0.74	0.828	0.784	0.74	0.828	SUBCLONAL	2	TRUE	0	0.644820256964075	2		387	441	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492817	56492817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066073-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	194	494	0	ENST00000407977.2:c.122C>T	p.Ser41Leu	p.S41L	ENST00000407977		41	tCa/tTa	2/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.644820256964075	2		494	539	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231774	36231774	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1569061768	NA	P-0066073-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	39	549	0	ENST00000300305.3:c.610C>T	p.Arg204Ter	p.R204*	ENST00000300305		204	Cga/Tga	5/8	1	2	FACETS	0.166	0.137	0.199	0.166	0.137	0.199	SUBCLONAL	1	TRUE	1	0.644820256964075	2		549	728	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158414	106158415	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0066073-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	37	418	0	ENST00000380013.4:c.3317_3318del	p.Glu1106ValfsTer23	p.E1106Vfs*23	ENST00000380013	NM_001127208.2	1105	atAGag/atag	3/11	1	2	FACETS	0.671	0.561	0.791	0.671	0.561	0.791	SUBCLONAL	1	TRUE	1	0.644820256964075	2		418	171	SUCCESS
APC	324	MSKCC	GRCh37	5	112173283	112173284	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0066073-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	28	432	0	ENST00000257430.4:c.1993_1994del	p.Leu665IlefsTer8	p.L665Ifs*8	ENST00000257430	NM_000038.5	664	acTTta/acta	16/16	0.644820256964075	2	FACETS	0.827	0.676	0.991	0.414	0.338	0.496	CLONAL	1	TRUE	0	0.644820256964075	2		432	105	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43766925	43766925	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066073-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	46	407	0	ENST00000382044.4:c.1126C>T	p.Arg376Ter	p.R376*	ENST00000382044	NM_001141980.1	376	Cga/Tga	10/28	1	2	FACETS	0.854	0.732	0.985	0.854	0.732	0.985	CLONAL	1	TRUE	1	0.644820256964075	2		407	167	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934069	39934070	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0066073-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	178	498	0	ENST00000378444.4:c.529_530del	p.Ser177ProfsTer8	p.S177Pfs*8	ENST00000378444	NM_001123385.1	177	AGc/c	4/15	1	2	FACETS	0.865	0.801	0.932	0.865	0.801	0.932	CLONAL	1	TRUE	1	0.644820256964075	2		498	638	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983037	201983037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868080326	NA	P-0066073-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	145	523	0	ENST00000359651.3:c.886G>A	p.Glu296Lys	p.E296K	ENST00000359651		296	Gag/Aag	7/8	0.251024010091534	3	FACETS	0.812	0.742	0.886	0.271	0.247	0.296	INDETERMINATE	1	TRUE	0	0.644820256964075	3		523	732	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910786	29910788	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0066073-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	47	345	0	ENST00000376809.5:c.328_330del	p.Asn110del	p.N110del	ENST00000376809	NM_002116.7	109	tACAac/tac	2/8	1	2	FACETS	0.35	0.295	0.409	0.35	0.295	0.409	SUBCLONAL	1	TRUE	1	0.644820256964075	2		345	417	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324102	31324102	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs41559014	NA	P-0066073-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	21	333	0	ENST00000412585.2:c.461T>C	p.Leu154Pro	p.L154P	ENST00000412585	NM_005514.6	154	cTg/cCg	3/8	1	2	FACETS	0.168	0.129	0.214	0.168	0.129	0.214	SUBCLONAL	1	TRUE	1	0.644820256964075	2		333	388	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	166	663	0				ENST00000310581	NM_198253.2	-/1132			0.334004630156818	4	FACETS	1	0.98	1	0.857	0.797	0.917	CLONAL	3	TRUE	0	0.334004630156818	4		663	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0066074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	210	372	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.303557769230885	3	FACETS	0.937	0.878	0.997	0.937	0.878	0.997	CLONAL	3	TRUE	0	0.334004630156818	3		372	522	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0066074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	13	476	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.303557769230885	3	FACETS	0.162	0.115	0.221	0.054	0.038	0.074	SUBCLONAL	1	TRUE	0	0.334004630156818	3		476	560	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729604	41729604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	81	496	0	ENST00000242208.4:c.925C>T	p.Arg309Trp	p.R309W	ENST00000242208	NM_002192.2	309	Cgg/Tgg	3/3	0.334004630156818	5	FACETS	0.859	0.755	0.97	0.286	0.251	0.324	CLONAL	1	TRUE	2	0.334004630156818	5		496	848	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827732	72827732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241554729	NA	P-0066074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	120	387	0	ENST00000268489.5:c.8849G>A	p.Arg2950His	p.R2950H	ENST00000268489	NM_006885.3	2950	cGc/cAc	9/10	0.334004630156818	3	FACETS	0.902	0.819	0.987	0.902	0.819	0.987	CLONAL	2	TRUE	1	0.334004630156818	3		387	465	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975459	13975459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80157564	NA	P-0066074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	110	513	0	ENST00000405192.2:c.428C>T	p.Thr143Met	p.T143M	ENST00000405192	NM_001163147.1	143	aCg/aTg	7/12	0.334004630156818	5	FACETS	1	0.98	1	0.459	0.412	0.508	CLONAL	1	TRUE	2	0.334004630156818	5		513	718	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942707	44942707	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	56	258	0	ENST00000377967.4:c.3288del	p.Trp1096Ter	p.W1096*	ENST00000377967	NM_021140.2	1096	tGg/tg	23/29	1	2	FACETS	0.83	0.722	0.944	1	0.974	1	CLONAL	2	TRUE	1	0.334004630156818	2		258	202	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305307	39305307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	46	402	0	ENST00000373001.3:c.1118C>T	p.Ser373Phe	p.S373F	ENST00000373001	NM_022157.3	373	tCt/tTt	7/7	0.299247629109898	4	FACETS	0.736	0.62	0.865	0.184	0.155	0.217	SUBCLONAL	1	TRUE	0	0.334004630156818	4		402	499	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894229	NA	P-0066074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	140	441	0	ENST00000451590.1:c.34G>T	p.Gly12Cys	p.G12C	ENST00000451590	NM_001130442.1	12	Ggc/Tgc	2/5	0.172791995248412	4	FACETS	1	0.96	1	1	0.96	1	INDETERMINATE	2	TRUE	2	0.334004630156818	4		441	518	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858459	9858459	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1567278391	NA	P-0066074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	35	366	0	ENST00000330684.3:c.2942A>G	p.Gln981Arg	p.Q981R	ENST00000330684	NM_001134407.1	981	cAg/cGg	13/13	0.292974517116952	2	FACETS	0.498	0.408	0.599	0.249	0.204	0.3	SUBCLONAL	1	TRUE	0	0.334004630156818	2		366	421	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984281	7984281	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	32	383	0	ENST00000319144.4:c.448C>A	p.Leu150Ile	p.L150I	ENST00000319144	NM_001139.2	150	Ctt/Att	4/15	0.303557769230885	3	FACETS	0.478	0.387	0.58	0.159	0.129	0.194	SUBCLONAL	1	TRUE	0	0.334004630156818	3		383	468	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41242984	41242984	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	29	372	0	ENST00000357654.3:c.4162C>G	p.Gln1388Glu	p.Q1388E	ENST00000357654	NM_007294.3	1388	Cag/Gag	11/23	0.303557769230885	3	FACETS	0.551	0.442	0.674	0.184	0.147	0.225	SUBCLONAL	1	TRUE	0	0.334004630156818	3		372	368	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62298881	62298881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772748212	NA	P-0066074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	59	411	0	ENST00000360203.5:c.674C>T	p.Pro225Leu	p.P225L	ENST00000360203	NM_001283009.1	225	cCg/cTg	8/35	0.334004630156818	5	FACETS	0.755	0.649	0.872	0.252	0.216	0.291	SUBCLONAL	1	TRUE	2	0.334004630156818	5		411	702	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948162	178948162	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0066074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	39	289	0	ENST00000263967.3:c.2934G>C	p.Glu978Asp	p.E978D	ENST00000263967	NM_006218.2	978	gaG/gaC	20/21	0.334004630156818	3	FACETS	0.816	0.678	0.968	0.408	0.339	0.484	CLONAL	1	TRUE	1	0.334004630156818	3		289	334	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908177	41908177	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	55	356	0	ENST00000372991.4:c.345G>T	p.Glu115Asp	p.E115D	ENST00000372991	NM_001760.3	115	gaG/gaT	2/5	0.334004630156818	3	FACETS	0.854	0.732	0.987	0.427	0.366	0.494	CLONAL	1	TRUE	1	0.334004630156818	3		356	450	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	27	1407	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.14	2		1407	342	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46215212	46215212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	10	241	0	ENST00000334344.6:c.647C>T	p.Ser216Phe	p.S216F	ENST00000334344	NM_152641.2	216	tCc/tTc	6/21	1	2	FACETS	0.756	0.512	1	0.756	0.512	1	CLONAL	1	TRUE	1	0.14	2		241	189	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594221	55594221	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913512	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	11	285	0	ENST00000288135.5:c.1924A>G	p.Lys642Glu	p.K642E	ENST00000288135	NM_000222.2	642	Aaa/Gaa	13/21	1	2	FACETS	0.462	0.318	0.643	0.462	0.318	0.643	SUBCLONAL	1	TRUE	1	0.14	2		285	340	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243778408	243778408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	21	291	0	ENST00000263826.5:c.617C>T	p.Pro206Leu	p.P206L	ENST00000263826	NM_005465.4	206	cCc/cTc	6/13	1	2	FACETS	1	0.791	1	1	0.791	1	CLONAL	1	TRUE	1	0.14	2		291	292	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412494	80412494	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	23	393	0	ENST00000286548.4:c.547C>T	p.Arg183Ter	p.R183*	ENST00000286548	NM_002072.3	183	Cga/Tga	4/7	1	2	FACETS	0.705	0.548	0.887	0.705	0.548	0.887	SUBCLONAL	1	TRUE	1	0.14	2		393	466	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770630	40770630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	22	298	0	ENST00000373198.4:c.2752G>A	p.Gly918Arg	p.G918R	ENST00000373198	NM_133170.3	918	Ggg/Agg	19/32	1	2	FACETS	0.731	0.565	0.924	0.731	0.565	0.924	CLONAL	1	TRUE	1	0.14	2		298	430	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517948	176517948	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	24	543	1	ENST00000292408.4:c.446G>A	p.Trp149Ter	p.W149*	ENST00000292408	NM_213647.1	149	tGg/tAg	5/18	1	2	FACETS	0.733	0.573	0.917	0.733	0.573	0.917	CLONAL	1	TRUE	1	0.14	2		544	468	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295204	1295204	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs2735943	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	25	460	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.14	2		460	291	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963907	2963907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	24	471	0	ENST00000396946.4:c.1900G>A	p.Glu634Lys	p.E634K	ENST00000396946	NM_032415.4	634	Gag/Aag	15/25	1	2	FACETS	0.754	0.59	0.943	0.754	0.59	0.943	CLONAL	1	TRUE	1	0.14	2		471	455	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	441056	441056	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766684341	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	23	410	0	ENST00000399788.2:c.1702C>T	p.Arg568Cys	p.R568C	ENST00000399788	NM_001042603.1	568	Cgt/Tgt	13/28	1	2	FACETS	0.721	0.561	0.907	0.721	0.561	0.907	CLONAL	1	TRUE	1	0.14	2		410	456	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233750	233750	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs746165168	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	30	248	0	ENST00000264932.6:c.1054C>T	p.Arg352Ter	p.R352*	ENST00000264932	NM_004168.2	352	Cga/Tga	8/15	1	2	FACETS	0.84	0.68	1	1	0.95	1	CLONAL	2	TRUE	1	0.14	2		248	255	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526735	106526735	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	24	307	0	ENST00000359195.3:c.3028C>T	p.Gln1010Ter	p.Q1010*	ENST00000359195	NM_002649.2	1010	Cag/Tag	10/11	1	2	FACETS	0.985	0.773	1	0.985	0.773	1	CLONAL	1	TRUE	1	0.14	2		307	348	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827984	40827984	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1174893851	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	22	470	0	ENST00000373198.4:c.2444G>A	p.Arg815Lys	p.R815K	ENST00000373198	NM_133170.3	815	aGg/aAg	17/32	1	2	FACETS	0.728	0.563	0.92	0.728	0.563	0.92	CLONAL	1	TRUE	1	0.14	2		470	432	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041180	29041180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	26	362	0	ENST00000282397.4:c.248G>A	p.Arg83Lys	p.R83K	ENST00000282397	NM_002019.4	83	aGa/aAa	3/30	1	2	FACETS	0.82	0.648	1	0.82	0.648	1	CLONAL	1	TRUE	1	0.14	2		362	453	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876472	35876472	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	26	446	0	ENST00000303115.3:c.1264C>T	p.Gln422Ter	p.Q422*	ENST00000303115	NM_002185.3	422	Caa/Taa	8/8	1	2	FACETS	0.718	0.568	0.892	0.718	0.568	0.892	SUBCLONAL	1	TRUE	1	0.14	2		446	517	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218892	193218892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1225502334	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	20	315	0	ENST00000367435.3:c.1450C>T	p.Arg484Cys	p.R484C	ENST00000367435	NM_024529.4	484	Cgt/Tgt	16/17	1	2	FACETS	0.758	0.579	0.968	0.758	0.579	0.968	CLONAL	1	TRUE	1	0.14	2		315	377	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264594	1264594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387907251	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	32	488	0	ENST00000310581.5:c.2768C>T	p.Pro923Leu	p.P923L	ENST00000310581	NM_198253.2	923	cCg/cTg	11/16	1	2	FACETS	0.925	0.75	1	0.925	0.75	1	CLONAL	1	TRUE	1	0.14	2		488	494	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033228	69033228	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	22	405	0	ENST00000288368.4:c.3668G>A	p.Trp1223Ter	p.W1223*	ENST00000288368	NM_024870.2	1223	tGg/tAg	30/40	1	2	FACETS	0.731	0.565	0.924	0.731	0.565	0.924	CLONAL	1	TRUE	1	0.14	2		405	430	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182309	38182309	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	24	427	0	ENST00000396334.3:c.745C>T	p.Gln249Ter	p.Q249*	ENST00000396334	NM_002468.4	249	Cag/Tag	4/5	1	2	FACETS	0.726	0.568	0.91	0.726	0.568	0.91	CLONAL	1	TRUE	1	0.14	2		427	472	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004205	29004205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	26	346	0	ENST00000282397.4:c.1088C>T	p.Pro363Leu	p.P363L	ENST00000282397	NM_002019.4	363	cCc/cTc	8/30	1	2	FACETS	0.825	0.653	1	0.825	0.653	1	CLONAL	1	TRUE	1	0.14	2		346	450	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189853	11189853	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	25	356	0	ENST00000361445.4:c.5656C>T	p.Gln1886Ter	p.Q1886*	ENST00000361445	NM_004958.3	1886	Cag/Tag	40/58	1	2	FACETS	0.842	0.663	1	0.842	0.663	1	CLONAL	1	TRUE	1	0.14	2		356	424	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729931	41729931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1379000367	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	24	438	0	ENST00000242208.4:c.598G>A	p.Glu200Lys	p.E200K	ENST00000242208	NM_002192.2	200	Gag/Aag	3/3	1	2	FACETS	0.736	0.576	0.921	0.736	0.576	0.921	CLONAL	1	TRUE	1	0.14	2		438	466	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27228230	27228230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536255448	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	16	337	0	ENST00000380036.4:c.3227G>A	p.Arg1076Gln	p.R1076Q	ENST00000380036	NM_000459.3	1076	cGg/cAg	22/23	1	2	FACETS	0.73	0.539	0.959	0.73	0.539	0.959	CLONAL	1	TRUE	1	0.14	2		337	313	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162639	47162639	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	23	376	0	ENST00000409792.3:c.3487C>A	p.Pro1163Thr	p.P1163T	ENST00000409792	NM_014159.6	1163	Cct/Act	3/21	1	2	FACETS	0.83	0.646	1	0.83	0.646	1	CLONAL	1	TRUE	1	0.14	2		376	396	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690618	33690618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	21	265	0	ENST00000308377.4:c.209C>T	p.Pro70Leu	p.P70L	ENST00000308377	NM_152270.3	70	cCc/cTc	2/5	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.14	2		265	257	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230492738	230492739	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	28	440	0	ENST00000391860.1:c.315_316delinsTT	p.Arg106Cys	p.R106C	ENST00000391860	NM_001258311.1	105	ttCCgc/ttTTgc	2/7	1	2	FACETS	0.875	0.699	1	0.875	0.699	1	CLONAL	1	TRUE	1	0.14	2		440	457	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925406	114925407	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	26	454	0	ENST00000543371.1:c.1484_1485insT	p.Ser496LeufsTer17	p.S496Lfs*17	ENST00000543371	NM_001198531.1	495	ccc/ccTc	14/14	1	2	FACETS	0.846	0.669	1	0.846	0.669	1	CLONAL	1	TRUE	1	0.14	2		454	439	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919220	48919220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	11	252	0	ENST00000267163.4:c.385C>T	p.His129Tyr	p.H129Y	ENST00000267163	NM_000321.2	129	Cat/Tat	4/27	1	2	FACETS	0.734	0.507	1	0.734	0.507	1	CLONAL	1	TRUE	1	0.14	2		252	214	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51514645	51514645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772438452	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	24	404	0	ENST00000260433.2:c.529G>A	p.Glu177Lys	p.E177K	ENST00000260433		177	Gag/Aag	5/10	1	2	FACETS	0.747	0.584	0.935	0.747	0.584	0.935	CLONAL	1	TRUE	1	0.14	2		404	459	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821275	72821275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750437411	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	22	395	0	ENST00000268489.5:c.10900C>T	p.Pro3634Ser	p.P3634S	ENST00000268489	NM_006885.3	3634	Cct/Tct	10/10	1	2	FACETS	0.714	0.552	0.903	0.714	0.552	0.903	CLONAL	1	TRUE	1	0.14	2		395	440	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991474	72991475	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	23	420	0	ENST00000268489.5:c.2570_2571delinsTT	p.Ala857Val	p.A857V	ENST00000268489	NM_006885.3	857	gCC/gTT	2/10	1	2	FACETS	0.729	0.567	0.917	0.729	0.567	0.917	CLONAL	1	TRUE	1	0.14	2		420	451	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593441	48593441	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	22	370	0	ENST00000342988.3:c.1192T>C	p.Trp398Arg	p.W398R	ENST00000342988	NM_005359.5	398	Tgg/Cgg	10/12	1	2	FACETS	0.722	0.559	0.913	0.722	0.559	0.913	CLONAL	1	TRUE	1	0.14	2		370	435	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61324638	61324638	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	15	293	0	ENST00000283752.5:c.478A>C	p.Lys160Gln	p.K160Q	ENST00000283752	NM_006919.2	160	Aaa/Caa	6/8	1	2	FACETS	0.763	0.557	1	0.763	0.557	1	CLONAL	1	TRUE	1	0.14	2		293	281	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950412	17950412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573731097	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	20	383	0	ENST00000458235.1:c.1315C>T	p.Leu439Phe	p.L439F	ENST00000458235	NM_000215.3	439	Ctt/Ttt	10/24	1	2	FACETS	0.718	0.548	0.918	0.718	0.548	0.918	CLONAL	1	TRUE	1	0.14	2		383	398	SUCCESS
AXL	558	MSKCC	GRCh37	19	41725372	41725372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	22	392	0	ENST00000301178.4:c.75G>A	p.Met25Ile	p.M25I	ENST00000301178	NM_021913.4	25	atG/atA	1/20	1	2	FACETS	0.89	0.69	1	0.89	0.69	1	CLONAL	1	TRUE	1	0.14	2		392	353	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867781	45867781	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	23	462	0	ENST00000391945.4:c.619T>C	p.Tyr207His	p.Y207H	ENST00000391945	NM_000400.3	207	Tat/Cat	8/23	1	2	FACETS	0.775	0.603	0.974	0.775	0.603	0.974	CLONAL	1	TRUE	1	0.14	2		462	424	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248631	212248631	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	25	497	0	ENST00000342788.4:c.3636T>A	p.Phe1212Leu	p.F1212L	ENST00000342788	NM_005235.2	1212	ttT/ttA	28/28	1	2	FACETS	0.752	0.591	0.937	0.752	0.591	0.937	CLONAL	1	TRUE	1	0.14	2		497	475	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251814	212251814	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	24	383	1	ENST00000342788.4:c.3245G>A	p.Arg1082Lys	p.R1082K	ENST00000342788	NM_005235.2	1082	aGa/aAa	27/28	1	2	FACETS	0.716	0.56	0.896	0.716	0.56	0.896	SUBCLONAL	1	TRUE	1	0.14	2		384	479	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546548	9546548	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	25	425	0	ENST00000353224.5:c.1474T>A	p.Phe492Ile	p.F492I	ENST00000353224	NM_177990.2	492	Ttc/Atc	5/10	1	2	FACETS	0.831	0.654	1	0.831	0.654	1	CLONAL	1	TRUE	1	0.14	2		425	430	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733229	40733229	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	26	429	0	ENST00000373198.4:c.3577C>A	p.Gln1193Lys	p.Q1193K	ENST00000373198	NM_133170.3	1193	Caa/Aaa	26/32	1	2	FACETS	0.797	0.63	0.989	0.797	0.63	0.989	CLONAL	1	TRUE	1	0.14	2		429	466	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877334	40877334	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	18	369	0	ENST00000373198.4:c.2362A>T	p.Lys788Ter	p.K788*	ENST00000373198	NM_133170.3	788	Aaa/Taa	15/32	1	2	FACETS	0.745	0.56	0.964	0.745	0.56	0.964	CLONAL	1	TRUE	1	0.14	2		369	345	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514476	41514476	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	22	393	0	ENST00000373198.4:c.185A>T	p.Lys62Ile	p.K62I	ENST00000373198	NM_133170.3	62	aAa/aTa	2/32	1	2	FACETS	0.802	0.621	1	0.802	0.621	1	CLONAL	1	TRUE	1	0.14	2		393	392	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256669	46256669	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	24	301	0	ENST00000371998.3:c.725T>A	p.Leu242Ter	p.L242*	ENST00000371998		242	tTg/tAg	8/23	1	2	FACETS	0.947	0.742	1	0.947	0.742	1	CLONAL	1	TRUE	1	0.14	2		301	362	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21344699	21344699	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	29	438	0	ENST00000215739.8:c.676C>G	p.Pro226Ala	p.P226A	ENST00000215739	NM_006767.3	226	Cca/Gca	8/21	1	2	FACETS	0.905	0.725	1	0.905	0.725	1	CLONAL	1	TRUE	1	0.14	2		438	458	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29445395	29445396	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	28	498	1	ENST00000544604.2:c.1226_1227delinsTT	p.Ser409Phe	p.S409F	ENST00000544604	NM_001206998.1	409	tCC/tTT	8/9	1	2	FACETS	0.749	0.597	0.923	0.749	0.597	0.923	CLONAL	1	TRUE	1	0.14	2		499	534	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274730	142274730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	19	300	0	ENST00000350721.4:c.2330C>T	p.Pro777Leu	p.P777L	ENST00000350721	NM_001184.3	777	cCa/cTa	10/47	1	2	FACETS	0.936	0.711	1	0.936	0.711	1	CLONAL	1	TRUE	1	0.14	2		300	290	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612217	189612217	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	24	434	0	ENST00000264731.3:c.1969G>T	p.Glu657Ter	p.E657*	ENST00000264731	NM_003722.4	657	Gag/Tag	14/14	1	2	FACETS	0.769	0.602	0.962	0.769	0.602	0.962	CLONAL	1	TRUE	1	0.14	2		434	446	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958873	55958873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	18	296	0	ENST00000263923.4:c.2980G>A	p.Asp994Asn	p.D994N	ENST00000263923	NM_002253.2	994	Gat/Aat	22/30	1	2	FACETS	0.832	0.626	1	0.832	0.626	1	CLONAL	1	TRUE	1	0.14	2		296	309	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094807	143094807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	14	280	0	ENST00000262992.4:c.1337C>T	p.Ser446Phe	p.S446F	ENST00000262992	NM_001101669.1	446	tCt/tTt	14/24	1	2	FACETS	0.714	0.516	0.955	0.714	0.516	0.955	CLONAL	1	TRUE	1	0.14	2		280	280	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295200	1295200	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	22	460	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.833	1	1	0.833	1	CLONAL	1	TRUE	1	0.14	2		460	288	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468103	31468104	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	30	340	0	ENST00000344624.3:c.2308_2309delinsTT	p.Pro770Leu	p.P770L	ENST00000344624		770	CCg/TTg	15/33	1	2	FACETS	0.948	0.763	1	0.948	0.763	1	CLONAL	1	TRUE	1	0.14	2		340	452	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526697	31526697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs989590447	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	30	533	0	ENST00000344624.3:c.343C>T	p.Pro115Ser	p.P115S	ENST00000344624		115	Cct/Tct	2/33	1	2	FACETS	0.85	0.684	1	0.85	0.684	1	CLONAL	1	TRUE	1	0.14	2		533	504	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871297	35871297	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	21	294	0	ENST00000303115.3:c.519G>T	p.Lys173Asn	p.K173N	ENST00000303115	NM_002185.3	173	aaG/aaT	4/8	1	2	FACETS	0.777	0.598	0.987	0.777	0.598	0.987	CLONAL	1	TRUE	1	0.14	2		294	386	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876455	35876455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1419531227	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	30	447	0	ENST00000303115.3:c.1247C>T	p.Pro416Leu	p.P416L	ENST00000303115	NM_002185.3	416	cCc/cTc	8/8	1	2	FACETS	0.812	0.653	0.993	0.812	0.653	0.993	CLONAL	1	TRUE	1	0.14	2		447	528	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755645	57755645	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	30	489	0	ENST00000274289.3:c.142C>T	p.Gln48Ter	p.Q48*	ENST00000274289	NM_006622.3	48	Cag/Tag	1/14	1	2	FACETS	0.994	0.801	1	0.994	0.801	1	CLONAL	1	TRUE	1	0.14	2		489	431	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149450111	149450111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	24	426	0	ENST00000286301.3:c.1106C>A	p.Pro369His	p.P369H	ENST00000286301	NM_005211.3	369	cCc/cAc	8/22	1	2	FACETS	0.794	0.621	0.993	0.794	0.621	0.993	CLONAL	1	TRUE	1	0.14	2		426	432	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504376	149504376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	20	432	0	ENST00000261799.4:c.1826G>A	p.Gly609Glu	p.G609E	ENST00000261799	NM_002609.3	609	gGg/gAg	13/23	1	2	FACETS	0.85	0.65	1	0.85	0.65	1	CLONAL	1	TRUE	1	0.14	2		432	336	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721985	176721986	+	missense_variant	Missense_Mutation	DNP	TT	TT	CA	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	45	514	1	ENST00000439151.2:c.7616_7617delinsCA	p.Leu2539Pro	p.L2539P	ENST00000439151	NM_022455.4	2539	cTT/cCA	23/23	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.14	2		515	550	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519172	137519172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	18	327	0	ENST00000367739.4:c.1466C>T	p.Ser489Leu	p.S489L	ENST00000367739	NM_000416.2	489	tCa/tTa	7/7	1	2	FACETS	0.75	0.564	0.97	0.75	0.564	0.97	CLONAL	1	TRUE	1	0.14	2		327	343	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624594	93624594	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	18	414	0	ENST00000375746.1:c.685C>A	p.Pro229Thr	p.P229T	ENST00000375746	NM_001174167.1	229	Ccc/Acc	4/14	1	2	FACETS	0.714	0.537	0.925	0.714	0.537	0.925	CLONAL	1	TRUE	1	0.14	2		414	360	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020236	123020236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	22	419	0	ENST00000355640.3:c.724G>A	p.Asp242Asn	p.D242N	ENST00000355640		242	Gat/Aat	2/7	1	2	FACETS	0.721	0.557	0.911	0.721	0.557	0.911	CLONAL	1	TRUE	1	0.14	2		419	436	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100944	41100944	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066076-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	100	440	0	ENST00000373198.4:c.1412T>A	p.Met471Lys	p.M471K	ENST00000373198	NM_133170.3	471	aTg/aAg	8/32	0.249490531541555	1	FACETS	0.557	0.499	0.618	0.557	0.499	0.618	INDETERMINATE	1	TRUE	0	0.523173009641999	1		440	507	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0066076-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	118	286	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.523173009641999	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.523173009641999	1		286	243	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906919	32906919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398122725	NA	P-0066076-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	82	496	0	ENST00000380152.3:c.1304G>A	p.Arg435Lys	p.R435K	ENST00000380152		435	aGa/aAa	10/27	1	2	FACETS	0.911	0.81	1	0.911	0.81	1	CLONAL	1	TRUE	1	0.523173009641999	2		496	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579449	7579450	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0066076-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	140	557	0	ENST00000269305.4:c.237_238del	p.Pro80TyrfsTer68	p.P80Yfs*68	ENST00000269305	NM_001126112.2	79	gcTCct/gcct	4/11	0.523173009641999	1	FACETS	0.913	0.839	0.989	0.913	0.839	0.989	CLONAL	1	TRUE	0	0.523173009641999	1		557	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0066077-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	119	594	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.12950050893877	5	FACETS	1	0.954	1	0.868	0.787	0.952	CLONAL	4	FALSE	0	0.12950050893877	5		594	506	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11071804	11071895	+	splice_donor_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	GAGGGGCGGGGGAGGCGCCGGGAAGTCGACGGCGCCGGCGGCTCCTGGTAAGGAACGCGGGCCGCGGGGGCAGCGCGGCGCGGGGCCGGGGA	GAGGGGCGGGGGAGGCGCCGGGAAGTCGACGGCGCCGGCGGCTCCTGGTAAGGAACGCGGGCCGCGGGGGCAGCGCGGCGCGGGGCCGGGGA	-	novel	NA	P-0066077-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	36	547	0	ENST00000358026.2:c.-77_-32+46del		p.X26_splice	ENST00000358026	NM_001128849.1	26		1/36	0.12950050893877	2	FACETS	0.995	0.816	1	0.497	0.408	0.598	CLONAL	1	FALSE	0	0.12950050893877	2		547	559	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0066078-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	136	466	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.199607267494944	4	FACETS	0.981	0.896	1	0.981	0.896	1	INDETERMINATE	2	TRUE	2	0.334499738572297	4		466	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0066078-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	313	645	0	ENST00000269305.4:c.548C>A	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tAa	5/11	0.334499738572297	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.334499738572297	3		645	638	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865770	57865770	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066078-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	53	507	0	ENST00000228682.2:c.3247A>T	p.Met1083Leu	p.M1083L	ENST00000228682	NM_005269.2	1083	Atg/Ttg	12/12	0.179699960442834	3	FACETS	0.731	0.624	0.848	0.244	0.208	0.283	INDETERMINATE	1	TRUE	0	0.334499738572297	3		507	506	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877816	151877816	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066078-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	69	440	0	ENST00000262189.6:c.7129G>A	p.Asp2377Asn	p.D2377N	ENST00000262189	NM_170606.2	2377	Gat/Aat	36/59	0.301113247893833	3	FACETS	1	0.927	1	0.545	0.476	0.619	CLONAL	1	TRUE	1	0.334499738572297	3		440	442	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0066079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	117	663	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.860894279201607	2		663	261	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0066079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	479	575	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.860894279201607	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.860894279201607	2		575	539	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0066079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	186	209	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	0.860894279201607	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.860894279201607	1		209	238	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650664	18650664	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0066079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	151	445	0	ENST00000266497.5:c.2875T>G	p.Ser959Ala	p.S959A	ENST00000266497		959	Tcc/Gcc	20/31	1	2	FACETS	0.911	0.843	0.98	0.911	0.843	0.98	CLONAL	1	TRUE	1	0.860894279201607	2		445	385	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450086	32450086	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0066080-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	55	523	0	ENST00000332351.3:c.726del	p.Ser243HisfsTer43	p.S243Hfs*43	ENST00000332351	NM_024426.4	242	caC/ca	2/10	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.313124863353551	2		523	303	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051412	13051412	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066080-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	75	582	0	ENST00000316448.5:c.760G>A	p.Asp254Asn	p.D254N	ENST00000316448	NM_004343.3	254	Gat/Aat	6/9	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.313124863353551	2		582	370	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251772	212251772	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0066080-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	80	487	0	ENST00000342788.4:c.3287G>A	p.Gly1096Asp	p.G1096D	ENST00000342788	NM_005235.2	1096	gGt/gAt	27/28	0.160469982563575	3	FACETS	1	0.97	1	0.654	0.578	0.735	INDETERMINATE	1	TRUE	1	0.313124863353551	3		487	452	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247149	153247191	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGATCTTACCTGTAATGAATAGACTCTATTAGTATGCCCCTGC	AGATCTTACCTGTAATGAATAGACTCTATTAGTATGCCCCTGC	-	novel	NA	P-0066080-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	19	353	0	ENST00000281708.4:c.1611_1644+9del		p.X537_splice	ENST00000281708	NM_033632.3	537		10/12	0.114342073358115	3	FACETS	0.463	0.351	0.595	0.232	0.175	0.298	INDETERMINATE	1	TRUE	1	0.313124863353551	3		353	303	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443614	52443660	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCCTTGACACCTGCGATGAGGAAAGGAAAGCAGTAGGGAAGGACAG	CCCCTTGACACCTGCGATGAGGAAAGGAAAGCAGTAGGGAAGGACAG	-	novel	NA	P-0066080-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	36	536	0	ENST00000460680.1:c.68-36_78del		p.X23_splice	ENST00000460680	NM_004656.3	23		3/17	0.313124863353551	1	FACETS	0.902	0.748	1	0.902	0.748	1	CLONAL	1	TRUE	0	0.313124863353551	1		536	215	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560935	9560935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145132727	NA	P-0066082-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	101	548	1	ENST00000353224.5:c.847C>T	p.Arg283Trp	p.R283W	ENST00000353224	NM_177990.2	283	Cgg/Tgg	4/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.624361141755251	2		549	279	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383185	42383185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782563209	NA	P-0066082-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	109	564	1	ENST00000221972.3:c.205G>A	p.Val69Ile	p.V69I	ENST00000221972	NM_021601.3	69	Gtc/Atc	2/5	0.625107552681787	3	FACETS	1	0.944	1	0.532	0.48	0.585	CLONAL	1	TRUE	1	0.624361141755251	3		565	431	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436611	8436611	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1439272694	NA	P-0066082-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	153	379	0	ENST00000356435.5:c.4067A>G	p.Lys1356Arg	p.K1356R	ENST00000356435		1356	aAg/aGg	24/35	0.625107552681787	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.624361141755251	3		379	303	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119566	108119829	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GATCGTGCTGTTCCACTCCAACCTGGGCAACAACAGCGAAACTCTGGCTCAAAAAAAAAAAAAAGAAAAAAGTGGATTTATTTTTATTTTACAGGTTTTTAATGAAGATACCAGATCCTTGGAGATTTCTCAATCTTACACTACTACACAAAGAGAATCTAGTGATTACAGTGTCCCTTGCAAAAGGAAGAAAATAGAACTAGGCTGGGAAGTAATAAAAGATCACCTTCAGAAGTCACAGAATGATTTTGATCTTGTGCCTTG	GATCGTGCTGTTCCACTCCAACCTGGGCAACAACAGCGAAACTCTGGCTCAAAAAAAAAAAAAAGAAAAAAGTGGATTTATTTTTATTTTACAGGTTTTTAATGAAGATACCAGATCCTTGGAGATTTCTCAATCTTACACTACTACACAAAGAGAATCTAGTGATTACAGTGTCCCTTGCAAAAGGAAGAAAATAGAACTAGGCTGGGAAGTAATAAAAGATCACCTTCAGAAGTCACAGAATGATTTTGATCTTGTGCCTTG	-	novel	NA	P-0066082-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	40	109	0	ENST00000278616.4:c.1066-93_1235+1del		p.X356_splice	ENST00000278616	NM_000051.3	356		9/63	0.625107552681787	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	2	TRUE	0	0.624361141755251	2		109	62	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988364	36988364	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762924398	NA	P-0066082-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	85	452	0	ENST00000354822.5:c.289G>A	p.Ala97Thr	p.A97T	ENST00000354822	NM_001079668.2	97	Gcc/Acc	2/3	0.625107552681787	2	FACETS	1	0.975	1	0.636	0.573	0.7	CLONAL	1	TRUE	0	0.624361141755251	2		452	214	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577533	7577548	+	frameshift_variant	Frame_Shift_Del	DEL	GCCTCCGGTTCATGCC	GCCTCCGGTTCATGCC	-	novel	NA	P-0066082-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	178	450	0	ENST00000269305.4:c.733_748del	p.Gly245ProfsTer95	p.G245Pfs*95	ENST00000269305	NM_001126112.2	245	GGCATGAACCGGAGGCcc/cc	7/11	0.625107552681787	2	FACETS	0.926	0.872	0.979	0.926	0.872	0.979	CLONAL	2	TRUE	0	0.624361141755251	2		450	308	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971097	21971100	+	stop_gained	Nonsense_Mutation	DEL	CCGG	CCGG	A	novel	NA	P-0066082-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	83	549	0	ENST00000579755.1:c.301_304delinsT	p.Pro101_Gly102delinsTer	p.P101_G102delins*	ENST00000579755		101	CCGGga/Tga	2/3	0.350204184365849	1	FACETS	0.799	0.717	0.883	0.799	0.717	0.883	INDETERMINATE	1	TRUE	0	0.624361141755251	1		549	229	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0066083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	220	425	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.481639121996257	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.481639121996257	2		425	412	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0066083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	136	525	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.129493204020263	6	FACETS	1	0.981	1	0.829	0.76	0.9	INDETERMINATE	2	TRUE	3	0.481639121996257	6		525	446	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0066083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	169	436	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.481639121996257	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.481639121996257	3		436	421	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0066083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	139	394	0	ENST00000263967.3:c.3073A>T	p.Thr1025Ser	p.T1025S	ENST00000263967	NM_006218.2	1025	Acc/Tcc	21/21	0.481639121996257	3	FACETS	0.997	0.92	1	0.997	0.92	1	CLONAL	2	TRUE	1	0.481639121996257	3		394	359	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845601	63845601	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0066083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	221	451	0	ENST00000279873.7:c.1342del	p.Ile448TyrfsTer31	p.I448Yfs*31	ENST00000279873	NM_032199.2	447	gAa/ga	9/10	0.129493204020263	6	FACETS	1	0.963	1	1	0.963	1	INDETERMINATE	3	TRUE	3	0.481639121996257	6		451	579	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624291	89624293	+	inframe_deletion	In_Frame_Del	DEL	ACT	ACT	-	novel	NA	P-0066083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	134	277	0	ENST00000371953.3:c.65_67del	p.Asp22_Leu23delinsVal	p.D22_L23delinsV	ENST00000371953	NM_000314.4	22	gACTta/gta	1/9	0.129493204020263	6	FACETS	0.984	0.905	1	0.984	0.905	1	INDETERMINATE	3	TRUE	3	0.481639121996257	6		277	370	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657313	29657313	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0066083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	134	368	0	ENST00000356175.3:c.5547-1G>A		p.X1849_splice	ENST00000356175	NM_000267.3	1849			0.481639121996257	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	0	0.481639121996257	2		368	276	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201890	67201890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375350949	NA	P-0066083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	19	546	0	ENST00000312629.5:c.1090C>T	p.Arg364Trp	p.R364W	ENST00000312629	NM_003952.2	364	Cgg/Tgg	13/15	0.466979716712615	2	FACETS	0.209	0.158	0.269	0.104	0.079	0.135	SUBCLONAL	1	TRUE	0	0.481639121996257	2		546	378	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492869	56492870	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0066083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	227	470	0	ENST00000407977.2:c.69dup	p.Gly24ArgfsTer16	p.G24Rfs*16	ENST00000407977		23	-/A	2/10	0.481639121996257	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.481639121996257	2		470	427	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927018	131927018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753680691	NA	P-0066084-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	77	418	0	ENST00000265335.6:c.1555C>T	p.Arg519Cys	p.R519C	ENST00000265335		519	Cgt/Tgt	10/25	0.601492126570208	1	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	0	0.601492126570208	1		418	179	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593558	48593558	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587781618	NA	P-0066084-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	66	362	0	ENST00000342988.3:c.1308+1G>T		p.X436_splice	ENST00000342988	NM_005359.5	436			0.601492126570208	1	FACETS	0.897	0.797	1	0.897	0.797	1	CLONAL	1	TRUE	0	0.601492126570208	1		362	171	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0066084-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	109	472	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.601492126570208	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.601492126570208	1		472	248	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929169	32929169	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0066084-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	84	510	0	ENST00000380152.3:c.7179G>A	p.Met2393Ile	p.M2393I	ENST00000380152		2393	atG/atA	14/27	0.601492126570208	1	FACETS	0.913	0.822	1	0.913	0.822	1	CLONAL	1	TRUE	0	0.601492126570208	1		510	214	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971122	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	GCACGGGTCGGG	GCACGGGTCGGG	TGATTAGT	novel	NA	P-0066084-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	22	583	2	ENST00000304494.5:c.236_247delinsACTAATCA	p.Thr79AsnfsTer2	p.T79Nfs*2	ENST00000304494	NM_000077.4	79	aCCCGACCCGTGCac/aACTAATCAac	2/3	0.601492126570208	1	FACETS	0.346	0.27	0.431	0.346	0.27	0.431	SUBCLONAL	1	TRUE	0	0.601492126570208	1		585	148	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324597	62324597	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs772031890	NA	P-0066086-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	46	572	0	ENST00000360203.5:c.2953C>G	p.Pro985Ala	p.P985A	ENST00000360203	NM_001283009.1	985	Ccc/Gcc	30/35	1	2	FACETS	0.318	0.269	0.372	0.318	0.269	0.372	SUBCLONAL	1	TRUE	1	0.973778924721493	2		572	297	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760462	133760462	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0066147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	41	684	0	ENST00000318560.5:c.2785G>T	p.Gly929Cys	p.G929C	ENST00000318560	NM_005157.4	929	Ggc/Tgc	11/11	1	2	FACETS	0.978	0.814	1	0.978	0.814	1	CLONAL	1	TRUE	1	0.16	2		684	524	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0000268-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	549	458	0				ENST00000310581	NM_198253.2	-/1132			0.689555985708497	7	FACETS	1	0.989	1	1	0.989	1	CLONAL	4	TRUE	3	0.689555985708497	7		458	1022	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458990	120458990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000268-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	532	564	1	ENST00000256646.2:c.6355C>T	p.Leu2119Phe	p.L2119F	ENST00000256646	NM_024408.3	2119	Ctt/Ttt	34/34	0.689555985708497	6	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	3	0.689555985708497	6		565	1115	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61722689	61722689	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000268-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	298	340	0	ENST00000401558.2:c.948G>C	p.Gln316His	p.Q316H	ENST00000401558	NM_003400.3	316	caG/caC	11/25	0.689555985708497	6	FACETS	1	0.986	1	0.756	0.713	0.799	CLONAL	2	TRUE	3	0.689555985708497	6		340	907	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66781598	66781598	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs754765552	NA	P-0000268-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	435	396	0	ENST00000307102.5:c.1006G>C	p.Asp336His	p.D336H	ENST00000307102	NM_002755.3	336	Gat/Cat	9/11	0.690186402383128	4	FACETS	1	0.994	1			1	CLONAL	3	TRUE	NA	0.689555985708497	4		396	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397516436	NA	P-0000268-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	577	541	0	ENST00000269305.4:c.637C>G	p.Arg213Gly	p.R213G	ENST00000269305	NM_001126112.2	213	Cga/Gga	6/11	0.690186402383128	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.689555985708497	3		541	685	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786117	3786117	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000268-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	301	485	0	ENST00000262367.5:c.4648G>C	p.Glu1550Gln	p.E1550Q	ENST00000262367	NM_004380.2	1550	Gaa/Caa	28/31	0.335048848982346	3	FACETS	1	0.987	1	0.727	0.694	0.761	INDETERMINATE	2	TRUE	0	0.689555985708497	3		485	538	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485136	57485387	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTGTGTATGGCTTCCACTCTTGCTGGCTGTTCATTGCGGTGGTTCTTTTTCAAACGGTCAGGCTGAAAACCCCCATCCCCCTCCCACCACCAAACCATAAAGGATCTATAAGAGAAGCAAGAAAAACGCACTCCCACTAATTCTCATATGGAAAAATCAGGGTTTTGAAGACTTCAGGAGCTACAGAGATGCTAGCACCCCAGCTCTGCTTGAATTTTAAATTACATTAATATGTATTCCCTTTTTATATA	GGTGTGTATGGCTTCCACTCTTGCTGGCTGTTCATTGCGGTGGTTCTTTTTCAAACGGTCAGGCTGAAAACCCCCATCCCCCTCCCACCACCAAACCATAAAGGATCTATAAGAGAAGCAAGAAAAACGCACTCCCACTAATTCTCATATGGAAAAATCAGGGTTTTGAAGACTTCAGGAGCTACAGAGATGCTAGCACCCCAGCTCTGCTTGAATTTTAAATTACATTAATATGTATTCCCTTTTTATATA	-	novel	NA	P-0000268-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	44	459	0	ENST00000371085.3:c.970+1_971-1del		p.X324_splice	ENST00000371085	NM_000516.4	324		11/13	0.690186402383128	4	FACETS	0.277	0.231	0.328	0.092	0.077	0.11	SUBCLONAL	1	TRUE	1	0.689555985708497	4		459	778	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678170	58678170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000268-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	397	509	0	ENST00000305921.3:c.395C>T	p.Ser132Leu	p.S132L	ENST00000305921	NM_003620.3	132	tCg/tTg	1/6	0.689555985708497	5	FACETS	1	0.98	1			1	CLONAL	2	TRUE	NA	0.689555985708497	5		509	1111	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710981	114710981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000268-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	109	282	0	ENST00000543371.1:c.205C>T	p.Pro69Ser	p.P69S	ENST00000543371	NM_001198531.1	69	Ccg/Tcg	2/14	0.318570002278208	5	FACETS	0.844	0.765	0.926	0.338	0.306	0.371	INDETERMINATE	2	TRUE	0	0.689555985708497	5		282	381	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902722	1902722	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs200319561	NA	P-0000268-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	181	537	0	ENST00000382891.5:c.341C>G	p.Thr114Ser	p.T114S	ENST00000382891	NM_133335.3	114	aCt/aGt	2/22	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.689555985708497	2		537	458	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922694	44922694	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs397514628	NA	P-0000268-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	106	224	0	ENST00000377967.4:c.1555C>G	p.Arg519Gly	p.R519G	ENST00000377967	NM_021140.2	519	Cga/Gga	16/29	0.690186402383128	2	FACETS	0.668	0.602	0.737			1	SUBCLONAL	1	TRUE	NA	0.689555985708497	2		224	460	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73633589	73633589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000268-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	136	355	0	ENST00000377687.4:c.124G>A	p.Asp42Asn	p.D42N	ENST00000377687	NM_001730.3	42	Gac/Aac	1/4	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.689555985708497	2		355	317	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150933602	150933604	+	frameshift_variant	Frame_Shift_Del	DEL	GAG	GAG	AA	novel	NA	P-0000268-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1631	176	501	0	ENST00000271640.5:c.3064_3066delinsAA	p.Glu1022LysfsTer8	p.E1022Kfs*8	ENST00000271640	NM_001145415.1	1022	GAG/AA	16/22	0.689555985708497	12	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.689555985708497	12		501	1807	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246490580	246490580	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000268-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	222	402	0	ENST00000388985.4:c.454C>G	p.Gln152Glu	p.Q152E	ENST00000388985		152	Caa/Gaa	5/12	0.689555985708497	5	FACETS	1	0.967	1			1	CLONAL	2	TRUE	NA	0.689555985708497	5		402	624	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362012	118362012	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000268-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	184	381	0	ENST00000534358.1:c.4798G>T	p.Glu1600Ter	p.E1600*	ENST00000534358	NM_005933.3	1600	Gag/Tag	14/36	0.256729741341343	3	FACETS	0.808	0.754	0.863	0.808	0.754	0.863	INDETERMINATE	2	TRUE	1	0.689555985708497	3		381	444	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123873987	123873987	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000268-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	135	548	0	ENST00000330479.4:c.18G>C	p.Lys6Asn	p.K6N	ENST00000330479	NM_020382.3	6	aaG/aaC	2/9	0.609289249330923	5	FACETS	0.876	0.796	0.961	0.292	0.265	0.321	CLONAL	1	TRUE	2	0.689555985708497	5		548	909	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95579475	95579475	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000268-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	122	387	0	ENST00000393063.1:c.1994C>T	p.Ser665Leu	p.S665L	ENST00000393063	NM_030621.3	665	tCa/tTa	13/28	0.690186402383128	3	FACETS	1	0.949	1	0.354	0.322	0.387	CLONAL	1	TRUE	0	0.689555985708497	3		387	448	SUCCESS
SCG5	6447	MSKCC	GRCh37	15	32972056	32972056	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000268-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	92	421	0	ENST00000300175.4:c.316G>C	p.Asp106His	p.D106H	ENST00000300175	NM_001144757.1	106	Gac/Cac	3/6	0.690186402383128	3	FACETS	0.873	0.781	0.97	0.291	0.26	0.324	CLONAL	1	TRUE	0	0.689555985708497	3		421	411	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473685	67473685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000268-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	98	480	0	ENST00000327367.4:c.765G>A	p.Met255Ile	p.M255I	ENST00000327367	NM_005902.3	255	atG/atA	6/9	0.690186402383128	4	FACETS	0.679	0.606	0.757			1	SUBCLONAL	1	TRUE	NA	0.689555985708497	4		480	707	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90645601	90645601	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000268-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	123	352	0	ENST00000330062.3:c.22G>C	p.Val8Leu	p.V8L	ENST00000330062	NM_002168.2	8	Gtg/Ctg	1/11	0.689555985708497	6	FACETS	1	0.959	1	0.222	0.2	0.245	CLONAL	1	TRUE	1	0.689555985708497	6		352	765	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99460076	99460076	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000268-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	185	409	0	ENST00000268035.6:c.2174del	p.Phe725SerfsTer114	p.F725Sfs*114	ENST00000268035	NM_000875.3	724	aaT/aa	10/21	0.666419439899814	5	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.689555985708497	5		409	830	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658741	3658741	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000268-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	343	486	0	ENST00000294008.3:c.225G>C	p.Lys75Asn	p.K75N	ENST00000294008	NM_032444.2	75	aaG/aaC	2/15	0.335048848982346	3	FACETS	1	0.993	1	0.785	0.753	0.817	INDETERMINATE	2	TRUE	0	0.689555985708497	3		486	568	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822553	72822553	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000268-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1321	208	712	0	ENST00000268489.5:c.9622C>T	p.Gln3208Ter	p.Q3208*	ENST00000268489	NM_006885.3	3208	Cag/Tag	10/10	0.689555985708497	6	FACETS	0.939	0.869	1	0.156	0.144	0.169	CLONAL	1	TRUE	0	0.689555985708497	6		712	1529	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216532	7216532	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1221616487	NA	P-0000268-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	178	530	0	ENST00000380728.2:c.803C>T	p.Ser268Leu	p.S268L	ENST00000380728		268	tCa/tTa	9/11	0.690186402383128	3	FACETS	0.917	0.847	0.99	0.306	0.282	0.33	CLONAL	1	TRUE	0	0.689555985708497	3		530	757	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217812	7217812	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000268-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	573	468	0	ENST00000380728.2:c.199G>T	p.Glu67Ter	p.E67*	ENST00000380728		67	Gaa/Taa	3/11	0.690186402383128	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.689555985708497	3		468	669	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607789	46607789	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000268-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	301	571	0	ENST00000263734.3:c.1978G>A	p.Glu660Lys	p.E660K	ENST00000263734	NM_001430.4	660	Gag/Aag	12/16	0.690186402383128	5	FACETS	0.89	0.839	0.941	0.593	0.559	0.628	CLONAL	2	TRUE	2	0.689555985708497	5		571	998	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627175	86627175	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000268-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	147	417	0	ENST00000274376.6:c.550G>A	p.Gly184Arg	p.G184R	ENST00000274376	NM_002890.2	184	Gga/Aga	2/25	0.690186402383128	3	FACETS	1	0.951	1	0.525	0.482	0.57	CLONAL	1	TRUE	1	0.689555985708497	3		417	546	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820219	32820219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000268-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	44	446	0	ENST00000354258.4:c.839C>T	p.Ser280Leu	p.S280L	ENST00000354258	NM_000593.5	280	tCa/tTa	2/11	0.690186402383128	3	FACETS	0.27	0.226	0.319	0.09	0.075	0.107	SUBCLONAL	1	TRUE	0	0.689555985708497	3		446	636	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820232	32820232	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000268-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	46	456	0	ENST00000354258.4:c.826C>G	p.Leu276Val	p.L276V	ENST00000354258	NM_000593.5	276	Cta/Gta	2/11	0.690186402383128	3	FACETS	0.283	0.238	0.333	0.094	0.079	0.111	SUBCLONAL	1	TRUE	0	0.689555985708497	3		456	634	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415270	109415270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000268-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	160	418	0	ENST00000436639.2:c.7G>A	p.Glu3Lys	p.E3K	ENST00000436639	NM_014454.2	3	Gaa/Aaa	1/10	0.690186402383128	3	FACETS	1	0.978	1	0.387	0.357	0.419	CLONAL	1	TRUE	0	0.689555985708497	3		418	537	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911521	131911521	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002794-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	134	372	0	ENST00000265335.6:c.266T>G	p.Val89Gly	p.V89G	ENST00000265335		89	gTc/gGc	3/25	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.258855059996739	2		372	883	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0002794-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	104	389	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.969	0.867	1	0.969	0.867	1	CLONAL	1	TRUE	1	0.258855059996739	2		389	829	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002794-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	81	391	0	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	0.258855059996739	1	FACETS	0.875	0.771	0.985	0.875	0.771	0.985	CLONAL	1	TRUE	0	0.258855059996739	1		391	623	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486211	8486211	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs994861872	NA	P-0002794-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	61	354	1	ENST00000356435.5:c.2606C>A	p.Thr869Asn	p.T869N	ENST00000356435		869	aCt/aAt	17/35	0.2484612238743	2	FACETS	0.637	0.548	0.733	0.318	0.274	0.367	SUBCLONAL	1	TRUE	0	0.258855059996739	2		355	740	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219537	133219537	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002794-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	76	279	1	ENST00000320574.5:c.4597G>T	p.Glu1533Ter	p.E1533*	ENST00000320574	NM_006231.2	1533	Gag/Tag	36/49	1	2	FACETS	0.953	0.837	1	0.953	0.837	1	CLONAL	1	TRUE	1	0.258855059996739	2		280	616	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472640	88472640	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002794-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	43	255	0	ENST00000360948.2:c.1915C>A	p.Leu639Ile	p.L639I	ENST00000360948	NM_001012338.2	639	Ctt/Att	16/19	1	2	FACETS	0.767	0.643	0.905	0.767	0.643	0.905	CLONAL	1	TRUE	1	0.258855059996739	2		255	433	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496947	29496947	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002794-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	92	303	0	ENST00000356175.3:c.518A>T	p.Asp173Val	p.D173V	ENST00000356175	NM_000267.3	173	gAt/gTt	5/57	0.258855059996739	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.258855059996739	1		303	596	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387081	31387081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs952998177	NA	P-0002794-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	76	395	1	ENST00000328111.2:c.1706C>T	p.Ala569Val	p.A569V	ENST00000328111	NM_006892.3	569	gCa/gTa	16/23	1	2	FACETS	0.855	0.749	0.968	0.855	0.749	0.968	CLONAL	1	TRUE	1	0.258855059996739	2		396	687	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225973	53225973	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002794-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	92	546	0	ENST00000375401.3:c.2876G>T	p.Ser959Ile	p.S959I	ENST00000375401	NM_004187.3	959	aGt/aTt	19/26	0.177090335629728	1	FACETS	0.639	0.566	0.716	0.639	0.566	0.716	SUBCLONAL	1	TRUE	0	0.258855059996739	1		546	969	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs11575997	NA	P-0003698-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	109	225	0	ENST00000269305.4:c.993+1G>T		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.498512981263596	6	FACETS	0.999	0.903	1			1	CLONAL	2	TRUE	NA	0.498512981263596	6		225	437	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933259	49933259	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003698-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	86	718	0	ENST00000296474.3:c.2851G>T	p.Asp951Tyr	p.D951Y	ENST00000296474	NM_002447.2	951	Gat/Tat	12/20	0.386421033605928	5	FACETS	1	0.902	1	0.34	0.301	0.382	CLONAL	1	TRUE	2	0.498512981263596	5		718	591	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435631	149435631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs690016557	NA	P-0003698-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	36	317	0	ENST00000286301.3:c.2512G>A	p.Val838Ile	p.V838I	ENST00000286301	NM_005211.3	838	Gtc/Atc	19/22	0.386421033605928	5	FACETS	0.701	0.577	0.839	0.234	0.192	0.28	SUBCLONAL	1	TRUE	2	0.498512981263596	5		317	360	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913797	32913797	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003698-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	162	942	0	ENST00000380152.3:c.5305G>C	p.Asp1769His	p.D1769H	ENST00000380152		1769	Gat/Cat	11/27	0.498512981263596	3	FACETS	0.791	0.725	0.86	0.395	0.362	0.43	SUBCLONAL	1	TRUE	1	0.498512981263596	3		942	1027	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914259	32914259	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003698-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	182	916	0	ENST00000380152.3:c.5767G>C	p.Asp1923His	p.D1923H	ENST00000380152		1923	Gac/Cac	11/27	0.498512981263596	3	FACETS	0.893	0.824	0.966	0.447	0.412	0.483	CLONAL	1	TRUE	1	0.498512981263596	3		916	1021	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136104	11136104	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003698-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	98	451	0	ENST00000358026.2:c.3088G>T	p.Gly1030Cys	p.G1030C	ENST00000358026	NM_001128849.1	1030	Ggc/Tgc	22/36	0.368337344132858	6	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.498512981263596	6		451	573	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543840	41543840	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003698-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	45	338	0	ENST00000263253.7:c.2132-1G>A		p.X711_splice	ENST00000263253	NM_001429.3	711			0.330470944675646	5	FACETS	0.759	0.638	0.891	0.253	0.212	0.297	SUBCLONAL	1	TRUE	2	0.498512981263596	5		338	416	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44920650	44920650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003698-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	194	344	0	ENST00000377967.4:c.1411C>T	p.Pro471Ser	p.P471S	ENST00000377967	NM_021140.2	471	Cca/Tca	14/29	0.410128180012904	2	FACETS	1	0.966	1			1	CLONAL	1	TRUE	NA	0.498512981263596	2		344	730	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	138	789	0				ENST00000310581	NM_198253.2	-/1132			0.754600643218786	4	FACETS	0.981	0.92	1	0.981	0.92	1	CLONAL	3	TRUE	1	0.754600643218786	4		789	218	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0003823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	727	576	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.754600643218786	8	FACETS	1	0.99	1			1	CLONAL	7	TRUE	NA	0.754600643218786	8		576	884	SUCCESS
INSRR	3645	MSKCC	GRCh37	1	156811907	156811907	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1317721002	NA	P-0003823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	101	295	0	ENST00000368195.3:c.3394G>A	p.Gly1132Arg	p.G1132R	ENST00000368195	NM_014215.2	1132	Ggg/Agg	19/22	1	2	FACETS	0.839	0.759	0.922	0.839	0.759	0.922	CLONAL	1	TRUE	1	0.754600643218786	2		295	319	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212571	133212587	+	frameshift_variant	Frame_Shift_Del	DEL	AGAAATTGTCAGAGAAT	AGAAATTGTCAGAGAAT	-	novel	NA	P-0003823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	36	239	0	ENST00000320574.5:c.5702_5718del	p.His1901LeufsTer15	p.H1901Lfs*15	ENST00000320574	NM_006231.2	1901	cATTCTCTGACAATTTCT/c	42/49	1	2	FACETS	0.47	0.39	0.558	0.47	0.39	0.558	SUBCLONAL	1	TRUE	1	0.754600643218786	2		239	203	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842414	68842415	+	protein_altering_variant	In_Frame_Ins	INS	-	-	ATA	novel	NA	P-0003823-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	88	354	0	ENST00000261769.5:c.475_476insATA	p.Pro159delinsHisThr	p.P159delinsHT	ENST00000261769	NM_004360.3	159	cct/cATAct	4/16	0.142715565436383	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.754600643218786	0		354	233	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443759	52443759	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004520-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	65	298	0	ENST00000460680.1:c.38G>T	p.Gly13Val	p.G13V	ENST00000460680	NM_004656.3	13	gGc/gTc	2/17	0.157747279407662	3	FACETS	1	0.97	1	0.713	0.622	0.812	INDETERMINATE	1	TRUE	1	0.28	3		298	371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0007181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	99	360	1	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.617992536522011	1	FACETS	0.648	0.586	0.711	0.648	0.586	0.711	SUBCLONAL	1	TRUE	0	0.695053208978885	1		361	287	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0007181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	114	601	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.618	0.558	0.68	0.618	0.558	0.68	SUBCLONAL	1	TRUE	1	0.695053208978885	2		601	531	SUCCESS
APC	324	MSKCC	GRCh37	5	112175760	112175761	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs398123122	NA	P-0007181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	55	249	0	ENST00000257430.4:c.4473dup	p.Ala1492CysfsTer22	p.A1492Cfs*22	ENST00000257430	NM_000038.5	1490	cat/caTt	16/16	0.617992536522011	1	FACETS	0.618	0.539	0.701	0.618	0.539	0.701	SUBCLONAL	1	TRUE	0	0.695053208978885	1		249	167	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259335	89259335	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750779844	NA	P-0007181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	64	470	1	ENST00000336596.2:c.479G>A	p.Arg160His	p.R160H	ENST00000336596	NM_005233.5	160	cGt/cAt	3/17	1	2	FACETS	0.579	0.505	0.658	0.579	0.505	0.658	SUBCLONAL	1	TRUE	1	0.695053208978885	2		471	318	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843614	156843614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs797045060	NA	P-0007181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	173	504	1	ENST00000524377.1:c.1040G>A	p.Arg347His	p.R347H	ENST00000524377	NM_002529.3	347	cGc/cAc	8/17	1	2	FACETS	0.796	0.736	0.859	0.796	0.736	0.859	SUBCLONAL	1	TRUE	1	0.695053208978885	2		505	625	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068102	94068102	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007181-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	260	706	0	ENST00000369303.4:c.860C>G	p.Ser287Cys	p.S287C	ENST00000369303	NM_004440.3	287	tCc/tGc	4/17	1	2	FACETS	0.828	0.777	0.88	0.828	0.777	0.88	CLONAL	1	TRUE	1	0.695053208978885	2		706	904	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0007779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	118	457	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.19	2		457	1180	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753975	57753975	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	112	376	0	ENST00000274289.3:c.649A>T	p.Met217Leu	p.M217L	ENST00000274289	NM_006622.3	217	Atg/Ttg	5/14	1	2	FACETS	0.981	0.88	1	0.981	0.88	1	CLONAL	1	TRUE	1	0.19	2		376	1202	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528852	157528852	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	52	430	0	ENST00000346085.5:c.6577G>T	p.Asp2193Tyr	p.D2193Y	ENST00000346085	NM_020732.3	2193	Gac/Tac	20/20	1	2	FACETS	0.664	0.564	0.775	0.664	0.564	0.775	SUBCLONAL	1	TRUE	1	0.19	2		430	824	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683782	162683782	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	44	310	0	ENST00000366898.1:c.187C>A	p.Gln63Lys	p.Q63K	ENST00000366898	NM_004562.2	63	Cag/Aag	3/12	1	2	FACETS	0.594	0.496	0.702	0.594	0.496	0.702	SUBCLONAL	1	TRUE	1	0.19	2		310	780	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460527	8460527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1489849541	NA	P-0007779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	76	483	1	ENST00000356435.5:c.3759G>A	p.Met1253Ile	p.M1253I	ENST00000356435		1253	atG/atA	22/35	1	2	FACETS	0.753	0.659	0.856	0.753	0.659	0.856	SUBCLONAL	1	TRUE	1	0.19	2		484	1062	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570329	95570329	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	53	346	0	ENST00000393063.1:c.3404A>G	p.Gln1135Arg	p.Q1135R	ENST00000393063	NM_030621.3	1135	cAa/cGa	22/28	1	2	FACETS	0.693	0.589	0.807	0.693	0.589	0.807	SUBCLONAL	1	TRUE	1	0.19	2		346	805	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110129	8110129	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	96	471	0	ENST00000585124.1:c.476G>T	p.Arg159Leu	p.R159L	ENST00000585124	NM_004217.3	159	cGc/cTc	6/9	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.19	2		471	793	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243620	41243620	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1333	111	600	0	ENST00000357654.3:c.3928A>T	p.Thr1310Ser	p.T1310S	ENST00000357654	NM_007294.3	1310	Aca/Tca	10/23	1	2	FACETS	0.809	0.725	0.899	0.809	0.725	0.899	CLONAL	1	TRUE	1	0.19	2		600	1444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577412	7577543	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCGGTAAGAGGTGGGCCCAGGGGTCAGAGGCAAGCAGAGGCTGGGGCACAGCAGGCCAGTGTGCAGGGTGGCAAGTGGCTCCTGACCTGGAGTCTTCCAGTGTGATGATGGTGAGGATGGGCCTCCGGTTC	ATCGGTAAGAGGTGGGCCCAGGGGTCAGAGGCAAGCAGAGGCTGGGGCACAGCAGGCCAGTGTGCAGGGTGGCAAGTGGCTCCTGACCTGGAGTCTTCCAGTGTGATGATGGTGAGGATGGGCCTCCGGTTC	-	novel	NA	P-0007779-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	73	210	0	ENST00000269305.4:c.738_782+87del		p.X246_splice	ENST00000269305	NM_001126112.2	246		7/11	1	2	FACETS	1	0.955	1	1	0.985	1	CLONAL	2	TRUE	1	0.19	2		210	327	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0007779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	368	457	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.257358905292569	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.34312945734353	3		457	1075	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753975	57753975	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	192	376	0	ENST00000274289.3:c.649A>T	p.Met217Leu	p.M217L	ENST00000274289	NM_006622.3	217	Atg/Ttg	5/14	0.276291078070526	4	FACETS	0.844	0.782	0.91	0.844	0.782	0.91	CLONAL	2	TRUE	2	0.34312945734353	4		376	890	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528852	157528852	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	127	430	0	ENST00000346085.5:c.6577G>T	p.Asp2193Tyr	p.D2193Y	ENST00000346085	NM_020732.3	2193	Gac/Tac	20/20	0.34312945734353	3	FACETS	1	0.929	1	0.515	0.466	0.566	CLONAL	1	TRUE	1	0.34312945734353	3		430	842	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683782	162683782	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	91	310	0	ENST00000366898.1:c.187C>A	p.Gln63Lys	p.Q63K	ENST00000366898	NM_004562.2	63	Cag/Aag	3/12	0.34312945734353	3	FACETS	0.971	0.863	1	0.485	0.431	0.543	CLONAL	1	TRUE	1	0.34312945734353	3		310	640	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460527	8460527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1489849541	NA	P-0007779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	182	483	1	ENST00000356435.5:c.3759G>A	p.Met1253Ile	p.M1253I	ENST00000356435		1253	atG/atA	22/35	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.34312945734353	2		484	773	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570329	95570329	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	86	346	0	ENST00000393063.1:c.3404A>G	p.Gln1135Arg	p.Q1135R	ENST00000393063	NM_030621.3	1135	cAa/cGa	22/28	0.34312945734353	3	FACETS	1	0.91	1	0.515	0.456	0.578	CLONAL	1	TRUE	1	0.34312945734353	3		346	570	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110129	8110129	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	306	471	0	ENST00000585124.1:c.476G>T	p.Arg159Leu	p.R159L	ENST00000585124	NM_004217.3	159	cGc/cTc	6/9	0.221828057331561	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.34312945734353	2		471	821	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243620	41243620	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	254	600	0	ENST00000357654.3:c.3928A>T	p.Thr1310Ser	p.T1310S	ENST00000357654	NM_007294.3	1310	Aca/Tca	10/23	0.201374123137947	4	FACETS	0.971	0.909	1	0.971	0.909	1	INDETERMINATE	2	TRUE	2	0.34312945734353	4		600	1024	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577412	7577543	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCGGTAAGAGGTGGGCCCAGGGGTCAGAGGCAAGCAGAGGCTGGGGCACAGCAGGCCAGTGTGCAGGGTGGCAAGTGGCTCCTGACCTGGAGTCTTCCAGTGTGATGATGGTGAGGATGGGCCTCCGGTTC	ATCGGTAAGAGGTGGGCCCAGGGGTCAGAGGCAAGCAGAGGCTGGGGCACAGCAGGCCAGTGTGCAGGGTGGCAAGTGGCTCCTGACCTGGAGTCTTCCAGTGTGATGATGGTGAGGATGGGCCTCCGGTTC	-	novel	NA	P-0007779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	232	210	0	ENST00000269305.4:c.738_782+87del		p.X246_splice	ENST00000269305	NM_001126112.2	246		7/11	0.221828057331561	2	FACETS	1	0.981	1	1	0.994	1	CLONAL	3	TRUE	0	0.34312945734353	2		210	420	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782690	135782690	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	60	470	0	ENST00000298552.3:c.1331C>T	p.Ser444Leu	p.S444L	ENST00000298552	NM_001162426.1	444	tCa/tTa	13/23	1	2	FACETS	0.44	0.378	0.508	0.44	0.378	0.508	SUBCLONAL	1	TRUE	1	0.34312945734353	2		470	794	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195085	123195085	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	48	389	0	ENST00000218089.9:c.1428T>A	p.His476Gln	p.H476Q	ENST00000218089	NM_001042749.1	476	caT/caA	16/35	0.260131115963148	2	FACETS	0.43	0.362	0.504	0.215	0.181	0.252	SUBCLONAL	1	TRUE	0	0.34312945734353	2		389	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578393	7578393	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876660821	NA	P-0008019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	314	156	0	ENST00000269305.4:c.537T>G	p.His179Gln	p.H179Q	ENST00000269305	NM_001126112.2	179	caT/caG	5/11	0.505165639329181	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.505165639329181	3		156	481	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0008019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	163	128	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.486063097178446	2	FACETS	0.943	0.88	1	0.943	0.88	1	CLONAL	2	TRUE	0	0.505165639329181	2		128	342	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859016	57859016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765428970	NA	P-0008019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	82	453	0	ENST00000228682.2:c.512G>A	p.Arg171Gln	p.R171Q	ENST00000228682	NM_005269.2	171	cGg/cAg	5/12	0.494628370679466	3	FACETS	0.334	0.293	0.378	0.167	0.146	0.189	SUBCLONAL	1	TRUE	1	0.505165639329181	3		453	1217	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528589	89528589	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	58	209	0	ENST00000336596.2:c.2889G>T	p.Lys963Asn	p.K963N	ENST00000336596	NM_005233.5	963	aaG/aaT	17/17	1	2	FACETS	0.435	0.374	0.502	0.435	0.374	0.502	SUBCLONAL	1	TRUE	1	0.505165639329181	2		209	528	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245506	153245506	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	82	246	0	ENST00000281708.4:c.1685C>A	p.Ser562Ter	p.S562*	ENST00000281708	NM_033632.3	562	tCa/tAa	11/12	0.309330466835722	1	FACETS	0.55	0.487	0.617	0.55	0.487	0.617	SUBCLONAL	1	TRUE	0	0.505165639329181	1		246	441	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520761	176520761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141530067	NA	P-0008019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	129	155	0	ENST00000292408.4:c.1504G>A	p.Val502Ile	p.V502I	ENST00000292408	NM_213647.1	502	Gtc/Atc	11/18	0.486063097178446	2	FACETS	1	0.936	1	0.516	0.47	0.563	CLONAL	1	TRUE	0	0.505165639329181	2		155	495	SUCCESS
BLM	641	MSKCC	GRCh37	15	91337522	91337522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008019-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	59	302	0	ENST00000355112.3:c.3145G>A	p.Gly1049Arg	p.G1049R	ENST00000355112	NM_000057.2	1049	Gga/Aga	16/22	0.151962023072489	3	FACETS	0.521	0.448	0.6	0.174	0.149	0.2	INDETERMINATE	1	TRUE	0	0.505165639329181	3		302	562	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008574-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	217	486	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.743396115485107	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.743396115485107	1		486	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578384	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008574-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	273	703	0	ENST00000269305.4:c.546C>A	p.Cys182Ter	p.C182*	ENST00000269305	NM_001126112.2	182	tgC/tgA	5/11	0.711179421337946	1	FACETS	0.99	0.944	1	0.99	0.944	1	CLONAL	1	TRUE	0	0.743396115485107	1		703	466	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667443	241667443	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008574-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	203	433	0	ENST00000366560.3:c.1007T>A	p.Met336Lys	p.M336K	ENST00000366560	NM_000143.3	336	aTg/aAg	7/10	0.740695640979218	3	FACETS	1	0.97	1	0.537	0.5	0.576	CLONAL	1	TRUE	1	0.743396115485107	3		433	697	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435559	18435559	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008574-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	198	508	0	ENST00000266497.5:c.544T>C	p.Phe182Leu	p.F182L	ENST00000266497		182	Ttc/Ctc	1/31	1	2	FACETS	0.879	0.819	0.941	0.879	0.819	0.941	CLONAL	1	TRUE	1	0.743396115485107	2		508	606	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353770	40353770	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008574-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	215	557	0	ENST00000293328.3:c.2350C>A	p.His784Asn	p.H784N	ENST00000293328	NM_012448.3	784	Cac/Aac	19/19	1	2	FACETS	0.951	0.89	1	0.951	0.89	1	CLONAL	1	TRUE	1	0.743396115485107	2		557	608	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508244	106508244	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008574-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	229	617	0	ENST00000359195.3:c.238G>C	p.Glu80Gln	p.E80Q	ENST00000359195	NM_002649.2	80	Gag/Cag	2/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.743396115485107	2		617	600	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978659	70978660	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0008574-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	465	606	1	ENST00000276594.2:c.993_994delinsAA	p.Arg332Ser	p.R332S	ENST00000276594	NM_024504.3	331	gcCCgc/gcAAgc	5/8	0.740695640979218	3	FACETS	0.953	0.917	0.99	0.953	0.917	0.99	CLONAL	2	TRUE	1	0.743396115485107	3		607	900	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014269	70014269	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008574-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	215	592	0	ENST00000394351.3:c.1130T>C	p.Ile377Thr	p.I377T	ENST00000394351	NM_000248.3	377	aTc/aCc	9/9	1	2	FACETS	0.933	0.873	0.995	0.933	0.873	0.995	CLONAL	1	TRUE	1	0.743396115485107	2		592	620	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681027	117681027	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008574-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	241	456	0	ENST00000368508.3:c.3593A>T	p.Tyr1198Phe	p.Y1198F	ENST00000368508	NM_002944.2	1198	tAt/tTt	23/43	0.743396115485107	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.743396115485107	1		456	376	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6439787	6439787	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008574-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	205	489	0	ENST00000356142.4:c.313A>C	p.Ser105Arg	p.S105R	ENST00000356142	NM_018890.3	105	Agt/Cgt	5/7	1	2	FACETS	0.961	0.898	1	0.961	0.898	1	CLONAL	1	TRUE	1	0.743396115485107	2		489	574	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0009071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	171	471	1	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	0.185042765676425	3	FACETS	0.888	0.815	0.964	0.888	0.815	0.964	CLONAL	2	TRUE	1	0.18	3		472	1166	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453100	140453100	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	56	303	0	ENST00000288602.6:c.1835A>G	p.Gln612Arg	p.Q612R	ENST00000288602	NM_004333.4	612	cAg/cGg	15/18	1	2	FACETS	0.957	0.819	1	0.957	0.819	1	CLONAL	1	TRUE	1	0.18	2		303	650	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989106	41989106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1584	153	831	1	ENST00000219905.7:c.1898G>A	p.Gly633Glu	p.G633E	ENST00000219905	NM_001164273.1	633	gGa/gAa	3/24	1	2	FACETS	0.979	0.892	1	0.979	0.892	1	CLONAL	1	TRUE	1	0.18	2		832	1737	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662442	67662442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009071-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	103	424	0	ENST00000264010.4:c.1688C>T	p.Thr563Ile	p.T563I	ENST00000264010	NM_006565.3	563	aCa/aTa	9/12	1	2	FACETS	0.919	0.82	1	0.919	0.82	1	CLONAL	1	TRUE	1	0.18	2		424	1245	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0009446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	91	462	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.856	0.76	0.958	1	0.983	1	CLONAL	2	TRUE	1	0.15	2		462	709	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	82	342	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.15	2		342	847	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579559	7579559	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010563-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	232	552	0	ENST00000269305.4:c.128del	p.Leu43Ter	p.L43*	ENST00000269305	NM_001126112.2	43	tTg/tg	4/11	0.493457344226592	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.521841037812658	2		552	436	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0010563-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	74	393	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.5206162049659	3	FACETS	0.964	0.849	1	0.482	0.424	0.543	CLONAL	1	TRUE	1	0.521841037812658	3		393	371	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56367749	56367749	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010563-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	78	343	0	ENST00000348428.3:c.575T>G	p.Val192Gly	p.V192G	ENST00000348428	NM_006785.3	192	gTt/gGt	4/17	0.169073852291953	3	FACETS	1	0.967	1	0.628	0.558	0.702	INDETERMINATE	1	TRUE	1	0.521841037812658	3		343	300	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89176389	89176389	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010563-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	54	270	0	ENST00000336596.2:c.119G>T	p.Gly40Val	p.G40V	ENST00000336596	NM_005233.5	40	gGg/gTg	2/17	0.282160369357236	5	FACETS	1	0.9	1	0.695	0.604	0.79	INDETERMINATE	2	TRUE	2	0.521841037812658	5		270	177	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114806	108114806	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010563-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	27	286	0	ENST00000278616.4:c.623A>C	p.Lys208Thr	p.K208T	ENST00000278616	NM_000051.3	208	aAa/aCa	6/63	0.5206162049659	4	FACETS	0.375	0.298	0.463	0.094	0.074	0.116	SUBCLONAL	1	TRUE	0	0.521841037812658	4		286	420	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61307004	61307005	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs745578463	NA	P-0010563-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	100	302	0	ENST00000341074.5:c.475dup	p.Ile159AsnfsTer2	p.I159Nfs*2	ENST00000341074	NM_002974.2	159	att/aAtt	6/8	0.169073852291953	3	FACETS	0.872	0.791	0.956	0.872	0.791	0.956	INDETERMINATE	2	TRUE	1	0.521841037812658	3		302	277	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630811	67630811	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010563-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	174	321	0	ENST00000272342.5:c.997G>C	p.Glu333Gln	p.E333Q	ENST00000272342	NM_019002.3	333	Gaa/Caa	5/6	0.161792633846199	5	FACETS	0.962	0.897	1			1	INDETERMINATE	3	TRUE	NA	0.521841037812658	5		321	412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0013437-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	54	381	0	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		381	217	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226596	2226596	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013437-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1415	239	668	0	ENST00000398665.3:c.4076A>T	p.Lys1359Met	p.K1359M	ENST00000398665	NM_032482.2	1359	aAg/aTg	27/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		668	1654	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251535	10251535	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013437-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	57	464	0	ENST00000340748.4:c.3397G>T	p.Glu1133Ter	p.E1133*	ENST00000340748		1133	Gag/Tag	31/40	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		464	295	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147615	61147617	+	splice_donor_variant,intron_variant	Splice_Site	TNP	TGG	TGG	CGT	novel	NA	P-0013437-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	28	304	0	ENST00000295025.8:c.1018+2_1018+4delinsCGT		p.X340_splice	ENST00000295025	NM_002908.2	340			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		304	398	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0013437-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	724	411	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		411	859	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738300	145738300	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013437-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	88	571	0	ENST00000428558.2:c.2685G>T	p.Arg895Ser	p.R895S	ENST00000428558	NM_004260.3	895	agG/agT	16/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		571	634	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035946	47035946	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013437-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	51	191	1	ENST00000377604.3:c.627del	p.Lys210SerfsTer56	p.K210Sfs*56	ENST00000377604	NM_001204468.1	208	gaC/ga	7/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		192	164	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24135796	24135796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013637-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	300	902	2	ENST00000263121.7:c.283G>A	p.Glu95Lys	p.E95K	ENST00000263121	NM_003073.3	95	Gaa/Aaa	3/9	0.508031661974545	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.508031661974545	1		904	777	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779172	135779172	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203631	NA	P-0013637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	109	240	0	ENST00000298552.3:c.2074C>T	p.Arg692Ter	p.R692*	ENST00000298552	NM_001162426.1	692	Cga/Tga	17/23	0.143323020723432	3	FACETS	1	0.966	1	0.585	0.526	0.646	INDETERMINATE	1	TRUE	1	0.364329782317867	3		240	605	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498490	89498490	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	68	324	0	ENST00000336596.2:c.2462G>C	p.Gly821Ala	p.G821A	ENST00000336596	NM_005233.5	821	gGa/gCa	14/17	0.26430272282158	0	FACETS	0.655	0.573	0.743			1	SUBCLONAL	1	TRUE	0	0.364329782317867	0		324	362	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436621	52436621	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	120	246	0	ENST00000460680.1:c.2053del	p.Glu685LysfsTer7	p.E685Kfs*7	ENST00000460680	NM_004656.3	685	Gaa/aa	16/17	0.364329782317867	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.364329782317867	1		246	452	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662928	52662928	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	73	291	0	ENST00000394830.3:c.1425del	p.Lys475AsnfsTer25	p.K475Nfs*25	ENST00000394830	NM_018313.4	475	aaA/aa	13/30	0.364329782317867	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.364329782317867	1		291	308	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539646	187539674	+	frameshift_variant	Frame_Shift_Del	DEL	CATTTCCGGTGGAAGGATTTTAACATAGA	CATTTCCGGTGGAAGGATTTTAACATAGA	-	novel	NA	P-0013637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	103	384	0	ENST00000441802.2:c.8066_8094del	p.Val2689AlafsTer32	p.V2689Afs*32	ENST00000441802	NM_005245.3	2689	gTCTATGTTAAAATCCTTCCACCGGAAATG/g	10/27	0.160515976198625	0	FACETS	0.824	0.742	0.91			1	INDETERMINATE	1	TRUE	0	0.364329782317867	0		384	436	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508577	106508577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	92	250	0	ENST00000359195.3:c.571C>T	p.Arg191Cys	p.R191C	ENST00000359195	NM_002649.2	191	Cgc/Tgc	2/11	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.364329782317867	2		250	480	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797330	135797330	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	98	310	0	ENST00000298552.3:c.539T>G	p.Leu180Arg	p.L180R	ENST00000298552	NM_001162426.1	180	cTc/cGc	7/23	0.143323020723432	3	FACETS	1	0.968	1	0.608	0.544	0.675	INDETERMINATE	1	TRUE	1	0.364329782317867	3		310	523	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188050	151188050	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519949	NA	P-0014812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	113	360	0	ENST00000262187.5:c.103T>A	p.Tyr35Asn	p.Y35N	ENST00000262187	NM_005614.3	35	Tac/Aac	2/8	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.63	2		360	351	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0015535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	167	256	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.987	0.908	1	0.987	0.908	1	CLONAL	1	TRUE	1	0.389698115763502	2		256	868	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0015535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	205	829	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	0.898	0.831	0.967	0.898	0.831	0.967	CLONAL	1	TRUE	1	0.389698115763502	2		829	1172	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534539	140534539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	120	475	1	ENST00000288602.6:c.374C>T	p.Ser125Phe	p.S125F	ENST00000288602	NM_004333.4	125	tCt/tTt	3/18	1	2	FACETS	0.805	0.727	0.887	0.805	0.727	0.887	CLONAL	1	TRUE	1	0.389698115763502	2		476	765	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206722	36206722	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	162	629	0	ENST00000300305.3:c.790C>T	p.Gln264Ter	p.Q264*	ENST00000300305		264	Cag/Tag	6/8	1	2	FACETS	0.826	0.758	0.899	0.826	0.758	0.899	CLONAL	1	TRUE	1	0.389698115763502	2		629	1006	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845618	68845618	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	210	590	0	ENST00000261769.5:c.864del	p.Asp288GlufsTer6	p.D288Efs*6	ENST00000261769	NM_004360.3	288	gaC/ga	7/16	0.374232057389073	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.389698115763502	1		590	774	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995270	15995270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	155	443	0	ENST00000268712.3:c.2923G>A	p.Glu975Lys	p.E975K	ENST00000268712	NM_006311.3	975	Gag/Aag	22/46	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.389698115763502	2		443	764	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629147	14629147	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0015535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	70	343	0	ENST00000254322.2:c.15C>G	p.Tyr5Ter	p.Y5*	ENST00000254322	NM_006145.1	5	taC/taG	1/3	1	2	FACETS	0.66	0.576	0.751	0.66	0.576	0.751	SUBCLONAL	1	TRUE	1	0.389698115763502	2		343	544	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149949	99149949	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	106	417	0	ENST00000074304.5:c.261G>C	p.Glu87Asp	p.E87D	ENST00000074304	NM_001134224.1	87	gaG/gaC	5/26	1	2	FACETS	0.703	0.63	0.78	0.703	0.63	0.78	SUBCLONAL	1	TRUE	1	0.389698115763502	2		417	774	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728798	190728798	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs201205478	NA	P-0015646-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	86	433	0	ENST00000441310.2:c.2186A>G	p.Asn729Ser	p.N729S	ENST00000441310	NM_000534.4	729	aAt/aGt	10/13	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.27	2		433	620	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496959	29496959	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015646-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	45	170	0	ENST00000356175.3:c.530T>G	p.Ile177Arg	p.I177R	ENST00000356175	NM_000267.3	177	aTa/aGa	5/57	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.27	2		170	282	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667635	29667635	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs1555535195	NA	P-0015646-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	61	355	0	ENST00000356175.3:c.6971T>G	p.Leu2324Ter	p.L2324*	ENST00000356175	NM_000267.3	2324	tTa/tGa	46/57	1	2	FACETS	0.866	0.748	0.994	0.866	0.748	0.994	CLONAL	1	TRUE	1	0.27	2		355	522	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0019539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	200	338	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.844624242940161	2		338	456	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602664	55602664	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs1057519713	NA	P-0019539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	466	343	0	ENST00000288135.5:c.2485G>C	p.Ala829Pro	p.A829P	ENST00000288135	NM_000222.2	829	Gct/Cct	18/21	0.844624242940161	4	FACETS	1	0.99	1			1	CLONAL	3	TRUE	NA	0.844624242940161	4		343	647	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003779	45003779	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	218	465	0	ENST00000558401.1:c.35T>G	p.Leu12Arg	p.L12R	ENST00000558401	NM_004048.2	12	cTa/cGa	1/4	0.843991801875799	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.844624242940161	1		465	253	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066763	94066764	+	missense_variant	Missense_Mutation	DNP	TG	TG	AT	novel	NA	P-0019539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	154	409	0	ENST00000369303.4:c.995_996delinsAT	p.Pro332His	p.P332H	ENST00000369303	NM_004440.3	332	cCA/cAT	5/17	0.844624242940161	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.844624242940161	1		409	201	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593584	55593598	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	ACCCATGTATGAAGT	ACCCATGTATGAAGT	-	rs587776804	NA	P-0020389-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	247	426	0	ENST00000288135.5:c.1652_1666del	p.Pro551_Val555del	p.P551_V555del	ENST00000288135	NM_000222.2	550	aaACCCATGTATGAAGTa/aaa	11/21	0.815279702383269	2	FACETS	0.98	0.946	1	0.98	0.946	1	CLONAL	2	TRUE	0	0.815279702383269	2		426	309	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964747	15964747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs945824338	NA	P-0020389-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	46	422	0	ENST00000268712.3:c.5849G>A	p.Arg1950His	p.R1950H	ENST00000268712	NM_006311.3	1950	cGt/cAt	37/46	0.815279702383269	3	FACETS	0.326	0.274	0.382	0.163	0.137	0.191	SUBCLONAL	1	TRUE	1	0.815279702383269	3		422	488	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956176	175956176	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020417-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	83	389	0	ENST00000367669.3:c.2036A>T	p.Lys679Met	p.K679M	ENST00000367669	NM_022457.5	679	aAg/aTg	18/20	1	2	FACETS	0.995	0.893	1	0.995	0.893	1	CLONAL	1	TRUE	1	0.722372346124075	2		389	231	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624491	140624491	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020417-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	107	647	0	ENST00000288602.6:c.13A>T	p.Ser5Cys	p.S5C	ENST00000288602	NM_004333.4	5	Agc/Tgc	1/18	0.337815602960298	5	FACETS	0.74	0.663	0.822	0.185	0.165	0.206	INDETERMINATE	1	TRUE	1	0.722372346124075	5		647	834	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0020748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	85	988	5	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	0.261514144901731	2	FACETS	1	0.895	1	0.506	0.448	0.569	CLONAL	1	TRUE	0	0.261514144901731	2		993	642	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310208	91310208	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs747341586	NA	P-0020748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	53	550	3	ENST00000355112.3:c.2268del	p.Asp757ThrfsTer4	p.D757Tfs*4	ENST00000355112	NM_000057.2	754	tcA/tc	10/22	1	2	FACETS	0.771	0.657	0.895	0.771	0.657	0.895	SUBCLONAL	1	TRUE	1	0.261514144901731	2		553	526	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	61	941	0	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	0.237589711661313	3	FACETS	0.604	0.519	0.696	0.302	0.259	0.348	SUBCLONAL	1	TRUE	1	0.261514144901731	3		941	874	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0020748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	58	555	2	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.792	0.681	0.914	0.792	0.681	0.914	CLONAL	1	TRUE	1	0.261514144901731	2		557	560	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0020748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	96	458	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.261514144901731	2	FACETS	0.966	0.868	1	0.966	0.868	1	CLONAL	2	TRUE	0	0.261514144901731	2		458	380	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791719	42791719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	66	640	0	ENST00000575354.2:c.605G>A	p.Arg202Gln	p.R202Q	ENST00000575354	NM_015125.3	202	cGg/cAg	5/20	1	2	FACETS	0.81	0.703	0.926	0.81	0.703	0.926	CLONAL	1	TRUE	1	0.261514144901731	2		640	623	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118918	70118918	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	118	908	2	ENST00000245479.2:c.490C>T	p.Gln164Ter	p.Q164*	ENST00000245479	NM_000346.3	164	Cag/Tag	2/3	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.261514144901731	2		910	805	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882050	36882050	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs780753361	NA	P-0020748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	95	881	9	ENST00000358127.4:c.963del	p.Ala322LeufsTer11	p.A322Lfs*11	ENST00000358127	NM_001280556.1	321	ccC/cc	8/10	0.188950735844411	3	FACETS	0.871	0.774	0.975	0.436	0.387	0.488	CLONAL	1	TRUE	1	0.261514144901731	3		890	943	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724244	52724244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	49	532	0	ENST00000322088.6:c.1376G>A	p.Arg459His	p.R459H	ENST00000322088	NM_014225.5	459	cGc/cAc	12/15	1	2	FACETS	0.69	0.584	0.807	0.69	0.584	0.807	SUBCLONAL	1	TRUE	1	0.261514144901731	2		532	543	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0020748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	65	743	1	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	0.261514144901731	2	FACETS	0.73	0.632	0.836	0.365	0.316	0.418	SUBCLONAL	1	TRUE	0	0.261514144901731	2		744	681	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	47	547	2	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.842	0.711	0.985	0.842	0.711	0.985	CLONAL	1	TRUE	1	0.261514144901731	2		549	427	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs753143066	NA	P-0020748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	55	923	5	ENST00000295797.4:c.826dup	p.Thr276AsnfsTer16	p.T276Nfs*16	ENST00000295797	NM_002740.5	273	tta/ttAa	9/18	1	2	FACETS	0.463	0.395	0.538	0.463	0.395	0.538	SUBCLONAL	1	TRUE	1	0.261514144901731	2		928	908	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958127	2958127	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs769192567	NA	P-0020748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	88	866	0	ENST00000396946.4:c.2605C>T	p.Arg869Trp	p.R869W	ENST00000396946	NM_032415.4	869	Cgg/Tgg	19/25	0.237589711661313	3	FACETS	0.866	0.766	0.973	0.433	0.383	0.487	CLONAL	1	TRUE	1	0.261514144901731	3		866	879	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445041	49445041	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	72	759	0	ENST00000301067.7:c.2425del	p.Gln809ArgfsTer121	p.Q809Rfs*121	ENST00000301067	NM_003482.3	809	Cag/ag	10/54	1	2	FACETS	0.826	0.721	0.938	0.826	0.721	0.938	CLONAL	1	TRUE	1	0.261514144901731	2		759	667	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748399150	NA	P-0020748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	110	690	5	ENST00000220592.5:c.1806del	p.Ala603ProfsTer92	p.A603Pfs*92	ENST00000220592	NM_012154.3	602	ccC/cc	14/19	0.237589711661313	3	FACETS	0.814	0.729	0.904	0.407	0.364	0.452	CLONAL	1	TRUE	1	0.261514144901731	3		695	1169	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809211	243809211	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	50	690	0	ENST00000263826.5:c.413C>G	p.Thr138Ser	p.T138S	ENST00000263826	NM_005465.4	138	aCc/aGc	4/13	1	2	FACETS	0.694	0.589	0.81	0.694	0.589	0.81	SUBCLONAL	1	TRUE	1	0.261514144901731	2		690	551	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998724	100998725	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	47	936	0	ENST00000325455.5:c.1077dup	p.Asp360ArgfsTer19	p.D360Rfs*19	ENST00000325455	NM_001202474.3	359	-/C	1/8	0.261514144901731	2	FACETS	0.533	0.449	0.627	0.267	0.224	0.314	SUBCLONAL	1	TRUE	0	0.261514144901731	2		936	674	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778282	3778282	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	46	758	0	ENST00000262367.5:c.6766del	p.Leu2256SerfsTer46	p.L2256Sfs*46	ENST00000262367	NM_004380.2	2256	Ctc/tc	31/31	1	2	FACETS	0.6	0.505	0.706	0.6	0.505	0.706	SUBCLONAL	1	TRUE	1	0.261514144901731	2		758	586	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56862947	56862947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	62	622	0	ENST00000308159.5:c.853G>A	p.Gly285Arg	p.G285R	ENST00000308159	NM_014669.4	285	Ggg/Agg	9/22	1	2	FACETS	0.77	0.665	0.884	0.77	0.665	0.884	SUBCLONAL	1	TRUE	1	0.261514144901731	2		622	616	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2220106	2220106	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0020748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	81	709	0	ENST00000398665.3:c.2692-1G>T		p.X898_splice	ENST00000398665	NM_032482.2	898			1	2	FACETS	0.829	0.73	0.936	0.829	0.73	0.936	CLONAL	1	TRUE	1	0.261514144901731	2		709	747	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2225404	2225404	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	67	694	4	ENST00000398665.3:c.3614C>T	p.Ala1205Val	p.A1205V	ENST00000398665	NM_032482.2	1205	gCa/gTa	26/28	1	2	FACETS	0.659	0.572	0.754	0.659	0.572	0.754	SUBCLONAL	1	TRUE	1	0.261514144901731	2		698	777	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965749	18965749	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	130	1067	0	ENST00000262803.5:c.1327C>A	p.His443Asn	p.H443N	ENST00000262803	NM_002911.3	443	Cac/Aac	10/24	1	2	FACETS	0.92	0.833	1	0.92	0.833	1	CLONAL	1	TRUE	1	0.261514144901731	2		1067	1081	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918147	50918147	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778972543	NA	P-0020748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	74	884	2	ENST00000440232.2:c.2464G>A	p.Asp822Asn	p.D822N	ENST00000440232	NM_002691.3	822	Gac/Aac	20/27	1	2	FACETS	0.837	0.733	0.95	0.837	0.733	0.95	CLONAL	1	TRUE	1	0.261514144901731	2		886	676	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686887	117686887	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	23	429	0	ENST00000368508.3:c.2830C>A	p.Pro944Thr	p.P944T	ENST00000368508	NM_002944.2	944	Cct/Act	19/43	0.188950735844411	3	FACETS	0.513	0.399	0.644	0.256	0.199	0.322	SUBCLONAL	1	TRUE	1	0.261514144901731	3		429	388	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214367	55214367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778252	NA	P-0020748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	74	865	0	ENST00000275493.2:c.493C>T	p.Arg165Trp	p.R165W	ENST00000275493	NM_005228.3	165	Cgg/Tgg	4/28	0.237589711661313	3	FACETS	0.671	0.586	0.764	0.336	0.293	0.382	SUBCLONAL	1	TRUE	1	0.261514144901731	3		865	953	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81340797	81340797	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs761396857	NA	P-0020748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	40	442	0	ENST00000222390.5:c.1444C>T	p.His482Tyr	p.H482Y	ENST00000222390	NM_000601.4	482	Cat/Tat	12/18	0.237589711661313	3	FACETS	0.799	0.664	0.949	0.399	0.332	0.475	CLONAL	1	TRUE	1	0.261514144901731	3		442	433	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860464	151860464	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147350420	NA	P-0020748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	86	726	1	ENST00000262189.6:c.10198C>T	p.Arg3400Cys	p.R3400C	ENST00000262189	NM_170606.2	3400	Cgt/Tgt	43/59	0.237589711661313	3	FACETS	0.86	0.759	0.968	0.43	0.379	0.484	CLONAL	1	TRUE	1	0.261514144901731	3		727	865	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275776	38275776	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	43	720	0	ENST00000425967.3:c.1493A>G	p.Glu498Gly	p.E498G	ENST00000425967	NM_001174067.1	498	gAa/gGa	11/19	0.237589711661313	3	FACETS	0.449	0.374	0.532	0.224	0.187	0.266	SUBCLONAL	1	TRUE	1	0.261514144901731	3		720	829	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863053	56863054	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	42	734	2	ENST00000519728.1:c.327dup	p.Glu110ArgfsTer40	p.E110Rfs*40	ENST00000519728	NM_002350.3	107	aca/acAa	5/13	0.237589711661313	3	FACETS	0.536	0.447	0.637	0.268	0.223	0.319	SUBCLONAL	1	TRUE	1	0.261514144901731	3		736	677	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215857	98215858	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	205	818	0	ENST00000331920.6:c.3351dup	p.Ala1118CysfsTer27	p.A1118Cfs*27	ENST00000331920	NM_000264.3	1117	-/T	20/24	0.188950735844411	3	FACETS	0.97	0.9	1	0.97	0.9	1	CLONAL	2	TRUE	1	0.261514144901731	3		818	914	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0022563-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	72	271	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.18	2		271	723	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101195	27101195	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022563-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	58	608	0	ENST00000324856.7:c.4477C>T	p.Gln1493Ter	p.Q1493*	ENST00000324856	NM_006015.4	1493	Cag/Tag	18/20	1	2	FACETS	0.718	0.615	0.831	0.718	0.615	0.831	SUBCLONAL	1	TRUE	1	0.18	2		608	897	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980299	201980300	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAACTACTTCAGTGCGATGTACAGCT	novel	NA	P-0022563-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	115	536	0	ENST00000359651.3:c.37_62dup	p.Glu22ThrfsTer30	p.E22Tfs*30	ENST00000359651		12	agc/agCAACTACTTCAGTGCGATGTACAGCTc	1/8	0.219650749653079	3	FACETS	1	0.981	1	0.698	0.627	0.772	CLONAL	1	TRUE	1	0.18	3		536	998	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16052778	16052778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022563-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	26	231	0	ENST00000268712.3:c.896C>T	p.Ala299Val	p.A299V	ENST00000268712	NM_006311.3	299	gCa/gTa	9/46	1	2	FACETS	0.802	0.636	0.994	0.802	0.636	0.994	CLONAL	1	TRUE	1	0.18	2		231	360	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591822	48591822	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022563-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	63	512	0	ENST00000342988.3:c.987del	p.Phe329LeufsTer7	p.F329Lfs*7	ENST00000342988	NM_005359.5	329	Ttt/tt	9/12	0.150237713744516	1	FACETS	0.818	0.706	0.94	0.818	0.706	0.94	CLONAL	1	TRUE	0	0.18	1		512	779	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938526	44938527	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0022563-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	47	413	0	ENST00000377967.4:c.3075_3076dup	p.Asn1026IlefsTer23	p.N1026Ifs*23	ENST00000377967	NM_021140.2	1025	agt/agTAt	20/29	1	2	FACETS	0.759	0.639	0.892	0.759	0.639	0.892	SUBCLONAL	1	TRUE	1	0.18	2		413	688	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398287	+	missense_variant	Missense_Mutation	TNP	CAG	CAG	AAC	novel	NA	P-0022563-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	30	0	0	ENST00000311936.3:c.32_34delinsGTT	p.Ala11_Gly12delinsGlyCys	p.A11_G12delinsGC	ENST00000311936	NM_004985.3	11	gCTGgt/gGTTgt	2/5	1	2	FACETS	0.644	0.517	0.787	0.644	0.517	0.787	SUBCLONAL	1	TRUE	1	0.18	2		0	518	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0025241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	289	482	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.584472039517768	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.584472039517768	1		482	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578207	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0025241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	408	744	0	ENST00000269305.4:c.642_643del	p.His214GlnfsTer7	p.H214Qfs*7	ENST00000269305	NM_001126112.2	214	caTAgt/cagt	6/11	0.584472039517768	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.584472039517768	1		744	955	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982386	25982386	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	209	406	0	ENST00000435504.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000435504		302	Cga/Tga	9/13	0.584472039517768	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.584472039517768	1		406	488	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710554	40710554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746059787	NA	P-0025241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	168	727	0	ENST00000373198.4:c.4297C>T	p.Arg1433Cys	p.R1433C	ENST00000373198	NM_133170.3	1433	Cgt/Tgt	31/32	0.112068451314793	5	FACETS	0.764	0.7	0.831	0.255	0.233	0.277	INDETERMINATE	1	TRUE	2	0.584472039517768	5		727	1413	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933464	100933464	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	120	283	0	ENST00000325455.5:c.1926C>A	p.Phe642Leu	p.F642L	ENST00000325455	NM_001202474.3	642	ttC/ttA	4/8	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.584472039517768	2		283	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578237	7578237	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	139	733	0	ENST00000269305.4:c.612G>T	p.Glu204Asp	p.E204D	ENST00000269305	NM_001126112.2	204	gaG/gaT	6/11	0.584472039517768	1	FACETS	0.351	0.319	0.385	0.351	0.319	0.385	SUBCLONAL	1	TRUE	0	0.584472039517768	1		733	958	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051644	30051644	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	67	436	0	ENST00000338641.4:c.578C>G	p.Ala193Gly	p.A193G	ENST00000338641	NM_000268.3	193	gCa/gGa	6/16	0.314840039791235	3	FACETS	0.356	0.309	0.408	0.119	0.103	0.136	INDETERMINATE	1	TRUE	0	0.584472039517768	3		436	832	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0025241-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	170	482	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.364232677594733	3	FACETS	0.921	0.862	0.978	0.921	0.862	0.978	CLONAL	3	TRUE	0	0.465594500384775	3		482	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578207	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0025241-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	165	744	0	ENST00000269305.4:c.642_643del	p.His214GlnfsTer7	p.H214Qfs*7	ENST00000269305	NM_001126112.2	214	caTAgt/cagt	6/11	0.279921531591938	3	FACETS	1	0.979	1	0.757	0.704	0.81	CLONAL	2	TRUE	0	0.465594500384775	3		744	385	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982386	25982386	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025241-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	227	406	0	ENST00000435504.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000435504		302	Cga/Tga	9/13	0.364232677594733	3	FACETS	0.999	0.947	1	0.999	0.947	1	CLONAL	3	TRUE	0	0.465594500384775	3		406	401	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710554	40710554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746059787	NA	P-0025241-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	46	727	0	ENST00000373198.4:c.4297C>T	p.Arg1433Cys	p.R1433C	ENST00000373198	NM_133170.3	1433	Cgt/Tgt	31/32	0.221595098362708	6	FACETS	0.699	0.588	0.821	0.233	0.196	0.274	INDETERMINATE	1	TRUE	3	0.465594500384775	6		727	546	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933464	100933464	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025241-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	95	283	0	ENST00000325455.5:c.1926C>A	p.Phe642Leu	p.F642L	ENST00000325455	NM_001202474.3	642	ttC/ttA	4/8	0.126195290623292	6	FACETS	1	0.967	1	0.787	0.707	0.869	INDETERMINATE	2	TRUE	3	0.465594500384775	6		283	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578237	7578237	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025241-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	92	733	0	ENST00000269305.4:c.612G>T	p.Glu204Asp	p.E204D	ENST00000269305	NM_001126112.2	204	gaG/gaT	6/11	0.279921531591938	3	FACETS	1	0.963	1	0.391	0.35	0.435	CLONAL	1	TRUE	0	0.465594500384775	3		733	415	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051644	30051644	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025241-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	65	436	0	ENST00000338641.4:c.578C>G	p.Ala193Gly	p.A193G	ENST00000338641	NM_000268.3	193	gCa/gGa	6/16	0.375219081899424	5	FACETS	0.976	0.848	1	0.244	0.212	0.279	CLONAL	1	TRUE	1	0.465594500384775	5		436	486	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593606	55593607	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGG	novel	NA	P-0025754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	729	387	0	ENST00000288135.5:c.1673_1675dup	p.Lys558_Val559insGlu	p.K558_V559insE	ENST00000288135	NM_000222.2	558	aag/aAGGag	11/21	0.825837303210926	2	FACETS	0.846	0.825	0.866	0.846	0.825	0.866	CLONAL	2	TRUE	0	0.825837303210926	2		387	1044	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509533	106509533	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs140765012	NA	P-0025754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1274	69	520	0	ENST00000359195.3:c.1527C>A	p.Asp509Glu	p.D509E	ENST00000359195	NM_002649.2	509	gaC/gaA	2/11	0.520587680860445	3	FACETS	0.176	0.152	0.202	0.088	0.076	0.101	SUBCLONAL	1	TRUE	1	0.825837303210926	3		520	1343	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593606	55593607	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGG	novel	NA	P-0025754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	625	387	0	ENST00000288135.5:c.1673_1675dup	p.Lys558_Val559insGlu	p.K558_V559insE	ENST00000288135	NM_000222.2	558	aag/aAGGag	11/21	0.89532089670171	2	FACETS	0.946	0.927	0.963	0.946	0.927	0.963	CLONAL	2	TRUE	0	0.89532089670171	2		387	738	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593606	55593607	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGG	novel	NA	P-0025754-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	356	387	0	ENST00000288135.5:c.1673_1675dup	p.Lys558_Val559insGlu	p.K558_V559insE	ENST00000288135	NM_000222.2	558	aag/aAGGag	11/21	0.765133822691967	2	FACETS	0.9	0.868	0.931	0.9	0.868	0.931	CLONAL	2	TRUE	0	0.765133822691967	2		387	517	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94209561	94209561	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587782845	NA	P-0025754-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	25	325	0	ENST00000323929.3:c.553C>G	p.Pro185Ala	p.P185A	ENST00000323929	NM_005591.3	185	Cca/Gca	7/20	1	2	FACETS	0.162	0.127	0.202	0.162	0.127	0.202	SUBCLONAL	1	TRUE	1	0.765133822691967	2		325	404	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593606	55593607	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGG	novel	NA	P-0025754-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	307	387	0	ENST00000288135.5:c.1673_1675dup	p.Lys558_Val559insGlu	p.K558_V559insE	ENST00000288135	NM_000222.2	558	aag/aAGGag	11/21	0.778630915674347	4	FACETS	0.96	0.935	0.982	0.96	0.935	0.982	CLONAL	4	TRUE	0	0.828703550665237	4		387	353	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442694	442694	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025754-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	172	544	0	ENST00000399788.2:c.1612A>C	p.Thr538Pro	p.T538P	ENST00000399788	NM_001042603.1	538	Acc/Ccc	12/28	0.717547815508209	4	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.828703550665237	4		544	582	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820171	139820171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025754-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	170	655	0	ENST00000247668.2:c.1324C>T	p.His442Tyr	p.H442Y	ENST00000247668	NM_021138.3	442	Cac/Tac	11/11	0.828703550665237	4	FACETS	0.94	0.866	1	0.47	0.433	0.509	CLONAL	1	TRUE	2	0.828703550665237	4		655	798	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0026314-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	66	500	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.188579936546925	2	FACETS	1	0.968	1	0.691	0.602	0.788	CLONAL	1	TRUE	0	0.218933667225539	2		500	436	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0026314-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	31	458	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.811	0.657	0.986	0.811	0.657	0.986	CLONAL	1	TRUE	1	0.218933667225539	2		458	349	SUCCESS
AXL	558	MSKCC	GRCh37	19	41737181	41737181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026314-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	26	719	1	ENST00000301178.4:c.761C>T	p.Pro254Leu	p.P254L	ENST00000301178	NM_021913.4	254	cCc/cTc	6/20	1	2	FACETS	0.493	0.389	0.612	0.493	0.389	0.612	SUBCLONAL	1	TRUE	1	0.218933667225539	2		720	482	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964962	55964962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026314-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	22	321	0	ENST00000263923.4:c.2275G>A	p.Glu759Lys	p.E759K	ENST00000263923	NM_002253.2	759	Gaa/Aaa	16/30	1	2	FACETS	0.661	0.513	0.833	0.661	0.513	0.833	SUBCLONAL	1	TRUE	1	0.218933667225539	2		321	304	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805400	46805400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026314-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	50	634	0	ENST00000290295.7:c.556G>A	p.Gly186Arg	p.G186R	ENST00000290295	NM_006361.5	186	Gga/Aga	1/2	1	2	FACETS	0.91	0.772	1	0.91	0.772	1	CLONAL	1	TRUE	1	0.218933667225539	2		634	502	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227102	2227102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026314-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	31	573	0	ENST00000398665.3:c.4582G>A	p.Gly1528Arg	p.G1528R	ENST00000398665	NM_032482.2	1528	Ggg/Agg	27/28	1	2	FACETS	0.561	0.453	0.684	0.561	0.453	0.684	SUBCLONAL	1	TRUE	1	0.218933667225539	2		573	505	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295217	1295217	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs796849347	NA	P-0026314-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	32	454	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.984	0.801	1	0.984	0.801	1	CLONAL	1	TRUE	1	0.218933667225539	2		454	297	SUCCESS
ALB	213	MSKCC	GRCh37	4	74283928	74283928	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs75920790	NA	P-0026314-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	47	452	0	ENST00000295897.4:c.1552G>A	p.Asp518Asn	p.D518N	ENST00000295897	NM_000477.5	518	Gat/Aat	12/15	0.126549034713793	3	FACETS	0.997	0.841	1	0.498	0.42	0.584	INDETERMINATE	1	TRUE	1	0.218933667225539	3		452	478	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156042	106156042	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026314-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	35	546	0	ENST00000380013.4:c.943T>G	p.Ser315Ala	p.S315A	ENST00000380013	NM_001127208.2	315	Tcc/Gcc	3/11	0.126549034713793	3	FACETS	0.707	0.578	0.851	0.353	0.289	0.426	INDETERMINATE	1	TRUE	1	0.218933667225539	3		546	502	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295169	1295169	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0026314-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	37	561	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.814	0.672	0.974	0.814	0.672	0.974	CLONAL	1	TRUE	1	0.218933667225539	2		561	415	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593580	55593580	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0026679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	113	435	0	ENST00000288135.5:c.1648-2A>T		p.X550_splice	ENST00000288135	NM_000222.2	550			1	2	FACETS	0.907	0.822	0.996	0.907	0.822	0.996	CLONAL	1	TRUE	1	0.559792634605944	2		435	445	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593586	55593606	+	inframe_deletion	In_Frame_Del	DEL	CCATGTATGAAGTACAGTGGA	CCATGTATGAAGTACAGTGGA	-	rs1560417385	NA	P-0026679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	118	442	0	ENST00000288135.5:c.1652_1672del	p.Pro551_Lys558delinsGln	p.P551_K558delinsQ	ENST00000288135	NM_000222.2	551	cCCATGTATGAAGTACAGTGGAag/cag	11/21	1	2	FACETS	0.923	0.838	1	0.923	0.838	1	CLONAL	1	TRUE	1	0.559792634605944	2		442	457	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045842	26045842	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	204	264	0	ENST00000540144.1:c.204C>G	p.Phe68Leu	p.F68L	ENST00000540144	NM_003531.2	68	ttC/ttG	1/1	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.559792634605944	2		264	663	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593580	55593580	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0026679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	262	435	0	ENST00000288135.5:c.1648-2A>T		p.X550_splice	ENST00000288135	NM_000222.2	550			0.660702147216223	2	FACETS	0.984	0.942	1	0.984	0.942	1	CLONAL	2	TRUE	0	0.684412482072412	2		435	389	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593586	55593606	+	inframe_deletion	In_Frame_Del	DEL	CCATGTATGAAGTACAGTGGA	CCATGTATGAAGTACAGTGGA	-	rs1560417385	NA	P-0026679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	272	442	0	ENST00000288135.5:c.1652_1672del	p.Pro551_Lys558delinsGln	p.P551_K558delinsQ	ENST00000288135	NM_000222.2	551	cCCATGTATGAAGTACAGTGGAag/cag	11/21	0.660702147216223	2	FACETS	0.989	0.947	1	0.989	0.947	1	CLONAL	2	TRUE	0	0.684412482072412	2		442	402	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913514	NA	P-0026679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	158	495	0	ENST00000288135.5:c.2466T>A	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaA	17/21	0.660702147216223	2	FACETS	1	0.934	1	0.505	0.467	0.544	CLONAL	1	TRUE	0	0.684412482072412	2		495	457	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0027419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	293	376	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.244898671362089	5	FACETS	0.871	0.819	0.925	0.871	0.819	0.925	CLONAL	3	TRUE	2	0.244898671362089	5		376	1252	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	223682	223682	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs369321221	NA	P-0027419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	157	287	0	ENST00000264932.6:c.149C>T	p.Ser50Phe	p.S50F	ENST00000264932	NM_004168.2	50	tCc/tTc	2/15	0.244898671362089	7	FACETS	0.93	0.851	1			1	CLONAL	2	TRUE	NA	0.244898671362089	7		287	1111	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357045	70357045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747305574	NA	P-0027419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	69	350	1	ENST00000374080.3:c.5560C>T	p.Arg1854Cys	p.R1854C	ENST00000374080		1854	Cgt/Tgt	39/45	0.132791624947693	2	FACETS	1	0.895	1			1	INDETERMINATE	1	TRUE	NA	0.244898671362089	2		351	547	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068998	30068998	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	91	587	0	ENST00000331968.5:c.1931A>T	p.Asn644Ile	p.N644I	ENST00000331968	NM_002742.2	644	aAt/aTt	14/18	0.184975796452903	3	FACETS	0.77	0.682	0.865			1	SUBCLONAL	1	TRUE	NA	0.244898671362089	3		587	1083	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799700	72799700	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	76	524	0	ENST00000325599.8:c.1469C>G	p.Ser490Cys	p.S490C	ENST00000325599	NM_018130.2	490	tCt/tGt	11/11	NA	2	FACETS	0.728	0.637	0.826			1	INDETERMINATE	1	TRUE	NA	0.244898671362089	2		524	853	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	223664	223664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1265	217	365	0	ENST00000264932.6:c.131C>T	p.Ser44Phe	p.S44F	ENST00000264932	NM_004168.2	44	tCt/tTt	2/15	0.244898671362089	7	FACETS	0.964	0.894	1			1	CLONAL	2	TRUE	NA	0.244898671362089	7		365	1482	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224491	224491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	55	122	1	ENST00000264932.6:c.167C>T	p.Pro56Leu	p.P56L	ENST00000264932	NM_004168.2	56	cCa/cTa	3/15	0.244898671362089	7	FACETS	1	0.927	1			1	CLONAL	2	TRUE	NA	0.244898671362089	7		123	322	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224617	224617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	127	330	0	ENST00000264932.6:c.293C>T	p.Ser98Leu	p.S98L	ENST00000264932	NM_004168.2	98	tCa/tTa	3/15	0.244898671362089	7	FACETS	0.91	0.823	1			1	CLONAL	2	TRUE	NA	0.244898671362089	7		330	919	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0027419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	468	376	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.287520285698138	11	FACETS	0.983	0.947	1	0.885	0.852	0.917	CLONAL	9	TRUE	1	0.287520285698138	11		376	844	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	223682	223682	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs369321221	NA	P-0027419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	31	287	0	ENST00000264932.6:c.149C>T	p.Ser50Phe	p.S50F	ENST00000264932	NM_004168.2	50	tCc/tTc	2/15	0.287520285698138	4	FACETS	0.499	0.403	0.609			1	SUBCLONAL	1	TRUE	NA	0.287520285698138	4		287	556	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	223664	223664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	37	365	0	ENST00000264932.6:c.131C>T	p.Ser44Phe	p.S44F	ENST00000264932	NM_004168.2	44	tCt/tTt	2/15	0.287520285698138	4	FACETS	0.456	0.374	0.547			1	SUBCLONAL	1	TRUE	NA	0.287520285698138	4		365	727	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224491	224491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	14	122	1	ENST00000264932.6:c.167C>T	p.Pro56Leu	p.P56L	ENST00000264932	NM_004168.2	56	cCa/cTa	3/15	0.287520285698138	4	FACETS	0.534	0.386	0.712			1	SUBCLONAL	1	TRUE	NA	0.287520285698138	4		123	235	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224617	224617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	30	330	0	ENST00000264932.6:c.293C>T	p.Ser98Leu	p.S98L	ENST00000264932	NM_004168.2	98	tCa/tTa	3/15	0.287520285698138	4	FACETS	0.469	0.377	0.574			1	SUBCLONAL	1	TRUE	NA	0.287520285698138	4		330	573	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961567	41961567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	36	418	0	ENST00000219905.7:c.475C>T	p.His159Tyr	p.H159Y	ENST00000219905	NM_001164273.1	159	Cat/Tat	2/24	0.105878141283372	0	FACETS	0.324	0.265	0.389			1	INDETERMINATE	1	TRUE	0	0.287520285698138	0		418	551	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390914	89390914	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	293	266	0	ENST00000336596.2:c.980C>G	p.Ser327Cys	p.S327C	ENST00000336596	NM_005233.5	327	tCt/tGt	5/17	0.287520285698138	12	FACETS	1	0.963	1			1	CLONAL	5	TRUE	NA	0.287520285698138	12		266	967	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0028857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	8	389	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	1	2	FACETS	0.155	0.099	0.227	0.155	0.099	0.227	SUBCLONAL	1	FALSE	1	0.346187709509921	2		389	299	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0028857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	37	293	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.194371864102535	5	FACETS	0.599	0.493	0.718	0.2	0.164	0.24	INDETERMINATE	1	FALSE	2	0.346187709509921	5		293	542	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	338	346	0	ENST00000263967.3:c.278G>T	p.Arg93Leu	p.R93L	ENST00000263967	NM_006218.2	93	cGg/cTg	2/21	0.346187709509921	7	FACETS	0.922	0.874	0.97			1	CLONAL	4	FALSE	NA	0.346187709509921	7		346	988	SUCCESS
APC	324	MSKCC	GRCh37	5	112173669	112173670	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0028857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	26	174	0	ENST00000257430.4:c.2379_2380del	p.Tyr796TrpfsTer2	p.Y796Wfs*2	ENST00000257430	NM_000038.5	793	cAA/c	16/16	0.164531243708039	4	FACETS	0.733	0.582	0.905	0.366	0.291	0.453	INDETERMINATE	1	FALSE	2	0.346187709509921	4		174	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579536	7579536	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567556930	NA	P-0028857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	73	650	0	ENST00000269305.4:c.151G>T	p.Glu51Ter	p.E51*	ENST00000269305	NM_001126112.2	51	Gaa/Taa	4/11	0.175198899737798	3	FACETS	0.815	0.713	0.925	0.408	0.356	0.463	INDETERMINATE	1	FALSE	1	0.346187709509921	3		650	607	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976706	2976706	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1044557293	NA	P-0028857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	31	385	0	ENST00000396946.4:c.1306C>T	p.Arg436Trp	p.R436W	ENST00000396946	NM_032415.4	436	Cgg/Tgg	9/25	0.346187709509921	1	FACETS	0.378	0.305	0.46	0.378	0.305	0.46	SUBCLONAL	1	FALSE	0	0.346187709509921	1		385	392	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243776973	243776973	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	45	421	0	ENST00000263826.5:c.696G>T	p.Glu232Asp	p.E232D	ENST00000263826	NM_005465.4	232	gaG/gaT	7/13	1	2	FACETS	0.574	0.483	0.675	0.574	0.483	0.675	SUBCLONAL	1	FALSE	1	0.346187709509921	2		421	453	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31390227	31390227	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	42	309	0	ENST00000328111.2:c.2182G>A	p.Ala728Thr	p.A728T	ENST00000328111	NM_006892.3	728	Gct/Act	20/23	0.346187709509921	3	FACETS	0.507	0.423	0.601	0.254	0.211	0.301	SUBCLONAL	1	FALSE	1	0.346187709509921	3		309	561	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526730	106526730	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	23	198	0	ENST00000359195.3:c.3023A>G	p.Lys1008Arg	p.K1008R	ENST00000359195	NM_002649.2	1008	aAa/aGa	10/11	0.120872518350983	4	FACETS	0.588	0.459	0.738	0.294	0.229	0.369	INDETERMINATE	1	FALSE	2	0.346187709509921	4		198	304	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0028857-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	282	293	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.697375490719838	3	FACETS	0.906	0.859	0.953	0.906	0.859	0.953	CLONAL	2	TRUE	1	0.697375490719838	3		293	602	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028857-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	142	346	0	ENST00000263967.3:c.278G>T	p.Arg93Leu	p.R93L	ENST00000263967	NM_006218.2	93	cGg/cTg	2/21	0.445855708154368	1	FACETS	0.436	0.398	0.474	0.436	0.398	0.474	SUBCLONAL	1	TRUE	0	0.697375490719838	1		346	609	SUCCESS
APC	324	MSKCC	GRCh37	5	112173669	112173670	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0028857-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	69	174	0	ENST00000257430.4:c.2379_2380del	p.Tyr796TrpfsTer2	p.Y796Wfs*2	ENST00000257430	NM_000038.5	793	cAA/c	16/16	0.574872074699575	1	FACETS	0.337	0.295	0.383	0.337	0.295	0.383	SUBCLONAL	1	TRUE	0	0.697375490719838	1		174	382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579536	7579536	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567556930	NA	P-0028857-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	583	650	0	ENST00000269305.4:c.151G>T	p.Glu51Ter	p.E51*	ENST00000269305	NM_001126112.2	51	Gaa/Taa	4/11	0.691856568256557	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.697375490719838	1		650	1081	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976706	2976706	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1044557293	NA	P-0028857-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	104	385	0	ENST00000396946.4:c.1306C>T	p.Arg436Trp	p.R436W	ENST00000396946	NM_032415.4	436	Cgg/Tgg	9/25	0.521324498229794	1	FACETS	0.236	0.211	0.263	0.236	0.211	0.263	SUBCLONAL	1	TRUE	0	0.697375490719838	1		385	822	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243776973	243776973	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028857-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	293	421	0	ENST00000263826.5:c.696G>T	p.Glu232Asp	p.E232D	ENST00000263826	NM_005465.4	232	gaG/gaT	7/13	0.670558719355118	2	FACETS	0.854	0.816	0.892	0.854	0.816	0.892	CLONAL	2	TRUE	0	0.697375490719838	2		421	492	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31390227	31390227	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028857-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	211	309	0	ENST00000328111.2:c.2182G>A	p.Ala728Thr	p.A728T	ENST00000328111	NM_006892.3	728	Gct/Act	20/23	1	2	FACETS	0.621	0.577	0.667	0.621	0.577	0.667	SUBCLONAL	1	TRUE	1	0.697375490719838	2		309	974	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526730	106526730	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028857-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	52	198	0	ENST00000359195.3:c.3023A>G	p.Lys1008Arg	p.K1008R	ENST00000359195	NM_002649.2	1008	aAa/aGa	10/11	0.521324498229794	1	FACETS	0.234	0.199	0.272	0.234	0.199	0.272	SUBCLONAL	1	TRUE	0	0.697375490719838	1		198	415	SUCCESS
APC	324	MSKCC	GRCh37	5	112175513	112175513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028857-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	139	175	0	ENST00000257430.4:c.4222G>T	p.Glu1408Ter	p.E1408*	ENST00000257430	NM_000038.5	1408	Gaa/Taa	16/16	0.574872074699575	1	FACETS	0.711	0.656	0.768	0.711	0.656	0.768	SUBCLONAL	1	TRUE	0	0.697375490719838	1		175	365	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473687	67473687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028857-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	180	408	0	ENST00000327367.4:c.767C>T	p.Thr256Ile	p.T256I	ENST00000327367	NM_005902.3	256	aCt/aTt	6/9	0.67544442985505	1	FACETS	0.478	0.442	0.516	0.478	0.442	0.516	SUBCLONAL	1	TRUE	0	0.697375490719838	1		408	703	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71064763	71064763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028857-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	100	249	0	ENST00000318789.4:c.911G>A	p.Gly304Glu	p.G304E	ENST00000318789	NM_032682.5	304	gGa/gAa	12/21	0.697375490719838	1	FACETS	0.486	0.438	0.537	0.486	0.438	0.537	SUBCLONAL	1	TRUE	0	0.697375490719838	1		249	384	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181849	56181849	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028857-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	108	228	0	ENST00000399503.3:c.4073C>A	p.Ser1358Ter	p.S1358*	ENST00000399503	NM_005921.1	1358	tCg/tAg	17/20	0.341271781047437	1	FACETS	0.619	0.562	0.677	0.619	0.562	0.677	INDETERMINATE	1	TRUE	0	0.697375490719838	1		228	326	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144445	58144445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754423955	NA	P-0029072-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	120	256	0	ENST00000257904.6:c.626G>A	p.Arg209His	p.R209H	ENST00000257904	NM_000075.3	209	cGt/cAt	5/8	1	2	FACETS	0.898	0.821	0.977	0.898	0.821	0.977	CLONAL	1	TRUE	1	0.781773552821615	2		256	342	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0029072-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	229	662	0	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.781773552821615	2		662	583	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161907	47161907	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029072-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	165	324	0	ENST00000409792.3:c.4219del	p.Arg1407GlyfsTer5	p.R1407Gfs*5	ENST00000409792	NM_014159.6	1407	Agg/gg	3/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.781773552821615	2		324	415	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030479	49030479	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029072-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	125	279	0	ENST00000267163.4:c.1959del	p.Val654CysfsTer4	p.V654Cfs*4	ENST00000267163	NM_000321.2	652	Aaa/aa	19/27	1	2	FACETS	0.914	0.837	0.992	0.914	0.837	0.992	CLONAL	1	TRUE	1	0.781773552821615	2		279	350	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0029072-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	150	365	0	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	1	2	FACETS	0.931	0.86	1	0.931	0.86	1	CLONAL	1	TRUE	1	0.781773552821615	2		365	412	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593618	55593662	+	inframe_deletion	In_Frame_Del	DEL	GAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTT	GAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTT	-	novel	NA	P-0029072-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	164	480	0	ENST00000288135.5:c.1684_1728del	p.Glu562_Leu576del	p.E562_L576del	ENST00000288135	NM_000222.2	562	GAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTT/-	11/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.781773552821615	2		480	408	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029072-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	214	550	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	0.895	0.837	0.954	0.895	0.837	0.954	CLONAL	1	TRUE	1	0.781773552821615	2		550	612	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467748	50467748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029072-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	195	501	0	ENST00000331340.3:c.983G>A	p.Arg328His	p.R328H	ENST00000331340	NM_006060.4	328	cGc/cAc	8/8	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.781773552821615	2		501	480	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630446	47630446	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs63750984	NA	P-0029072-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	247	731	0	ENST00000233146.2:c.119del	p.Gly40AlafsTer24	p.G40Afs*24	ENST00000233146	NM_000251.2	39	cGg/cg	1/16	0.781773552821615	1	FACETS	0.972	0.926	1	0.972	0.926	1	CLONAL	1	TRUE	0	0.781773552821615	1		731	396	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867626	78867626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781190662	NA	P-0029072-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	275	607	1	ENST00000306801.3:c.2362C>T	p.Arg788Cys	p.R788C	ENST00000306801	NM_020761.2	788	Cgc/Tgc	20/34	1	2	FACETS	0.991	0.936	1	0.991	0.936	1	CLONAL	1	TRUE	1	0.781773552821615	2		608	710	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410704	32410704	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139893274	NA	P-0029072-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	156	399	0	ENST00000332351.3:c.1454G>A	p.Arg485Gln	p.R485Q	ENST00000332351	NM_024426.4	485	cGg/cAg	10/10	1	2	FACETS	0.897	0.829	0.966	0.897	0.829	0.966	CLONAL	1	TRUE	1	0.781773552821615	2		399	445	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923722	72923722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1169589589	NA	P-0029072-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	242	588	1	ENST00000268489.5:c.3356G>A	p.Arg1119Gln	p.R1119Q	ENST00000268489	NM_006885.3	1119	cGa/cAa	4/10	NA	2	FACETS	0.947	0.89	1			1	INDETERMINATE	1	TRUE	NA	0.781773552821615	2		589	654	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425430	49425430	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778418522	NA	P-0029072-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	241	720	2	ENST00000301067.7:c.13058C>T	p.Pro4353Leu	p.P4353L	ENST00000301067	NM_003482.3	4353	cCg/cTg	39/54	1	2	FACETS	0.9	0.845	0.956	0.9	0.845	0.956	CLONAL	1	TRUE	1	0.781773552821615	2		722	685	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808000	3808000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029072-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	183	400	0	ENST00000262367.5:c.3419G>A	p.Arg1140Gln	p.R1140Q	ENST00000262367	NM_004380.2	1140	cGg/cAg	18/31	1	2	FACETS	0.988	0.92	1	0.988	0.92	1	CLONAL	1	TRUE	1	0.781773552821615	2		400	474	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222891	5222891	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029072-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	244	560	0	ENST00000357368.4:c.2912A>G	p.Glu971Gly	p.E971G	ENST00000357368	NM_002850.3	971	gAg/gGg	18/38	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.781773552821615	2		560	598	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500992	8500992	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029072-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	150	321	1	ENST00000356435.5:c.1890G>A	p.Trp630Ter	p.W630*	ENST00000356435		630	tgG/tgA	13/35	1	2	FACETS	0.992	0.917	1	0.992	0.917	1	CLONAL	1	TRUE	1	0.781773552821615	2		322	387	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593618	55593662	+	inframe_deletion	In_Frame_Del	DEL	GAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTT	GAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTT	-	novel	NA	P-0029072-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	161	480	0	ENST00000288135.5:c.1684_1728del	p.Glu562_Leu576del	p.E562_L576del	ENST00000288135	NM_000222.2	562	GAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTT/-	11/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.771805734458739	2		480	400	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524714	187524714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs192691397	NA	P-0029072-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	391	897	0	ENST00000441802.2:c.10966G>A	p.Val3656Ile	p.V3656I	ENST00000441802	NM_005245.3	3656	Gtt/Att	19/27	1	2	FACETS	0.965	0.919	1	0.965	0.919	1	CLONAL	1	TRUE	1	0.771805734458739	2		897	1050	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599322	55599322	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029072-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	136	492	0	ENST00000288135.5:c.2448C>A	p.Asp816Glu	p.D816E	ENST00000288135	NM_000222.2	816	gaC/gaA	17/21	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.771805734458739	2		492	338	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0030133-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	180	577	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	0.378420650794998	3	FACETS	1	0.947	1	0.683	0.634	0.733	CLONAL	2	TRUE	0	0.378420650794998	3		578	552	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115874	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752977342	NA	P-0030133-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	208	724	0	ENST00000346208.3:c.1220C>T	p.Ser407Leu	p.S407L	ENST00000346208		407	tCg/tTg	6/6	0.378420650794998	5	FACETS	1	0.986	1	0.812	0.757	0.869	CLONAL	2	TRUE	2	0.378420650794998	5		724	707	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183095	32183095	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030133-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	27	504	0	ENST00000375023.3:c.1929G>C	p.Gln643His	p.Q643H	ENST00000375023	NM_004557.3	643	caG/caC	12/30	0.322344974337506	4	FACETS	0.382	0.303	0.473	0.191	0.151	0.237	SUBCLONAL	1	TRUE	2	0.378420650794998	4		504	515	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0030133-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	131	513	0				ENST00000310581	NM_198253.2	-/1132			0.378420650794998	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.378420650794998	3		513	393	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162742035	162742035	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030133-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	180	521	0	ENST00000367921.3:c.1726G>A	p.Glu576Lys	p.E576K	ENST00000367921	NM_006182.2	576	Gag/Aag	13/18	0.378420650794998	4	FACETS	1	0.947	1	1	0.947	1	CLONAL	3	TRUE	1	0.378420650794998	4		521	430	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482363	56482363	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030133-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	46	490	0	ENST00000267101.3:c.911C>T	p.Ala304Val	p.A304V	ENST00000267101	NM_001982.3	304	gCc/gTc	8/28	0.234805087216373	3	FACETS	0.723	0.61	0.847	0.361	0.305	0.424	SUBCLONAL	1	TRUE	1	0.378420650794998	3		490	400	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929354	44929354	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030133-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	116	278	0	ENST00000377967.4:c.2454del	p.Pro819HisfsTer48	p.P819Hfs*48	ENST00000377967	NM_021140.2	818	tcA/tc	17/29	0.378420650794998	2	FACETS	0.989	0.904	1			1	CLONAL	2	TRUE	NA	0.378420650794998	2		278	310	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943670	9943670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375260513	NA	P-0030133-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	48	456	0	ENST00000330684.3:c.1271C>T	p.Pro424Leu	p.P424L	ENST00000330684	NM_001134407.1	424	cCc/cTc	5/13	0.180206044420101	5	FACETS	0.999	0.847	1	0.333	0.282	0.389	INDETERMINATE	1	TRUE	2	0.378420650794998	5		456	398	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701141	43701141	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030133-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	38	407	0	ENST00000382044.4:c.5554C>G	p.Leu1852Val	p.L1852V	ENST00000382044	NM_001141980.1	1852	Ctg/Gtg	26/28	0.322344974337506	4	FACETS	0.533	0.44	0.638	0.267	0.22	0.319	SUBCLONAL	1	TRUE	2	0.378420650794998	4		407	519	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115874	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752977342	NA	P-0030133-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	113	724	0	ENST00000346208.3:c.1220C>T	p.Ser407Leu	p.S407L	ENST00000346208		407	tCg/tTg	6/6	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.241960966464639	2		724	901	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0030133-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	86	513	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.821	0.73	0.917	1	0.982	1	CLONAL	2	TRUE	1	0.241960966464639	2		513	433	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162742035	162742035	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030133-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	85	521	0	ENST00000367921.3:c.1726G>A	p.Glu576Lys	p.E576K	ENST00000367921	NM_006182.2	576	Gag/Aag	13/18	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.241960966464639	2		521	605	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482363	56482363	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030133-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	85	490	0	ENST00000267101.3:c.911C>T	p.Ala304Val	p.A304V	ENST00000267101	NM_001982.3	304	gCc/gTc	8/28	0.0683953683788208	4	FACETS	1	0.963	1	0.613	0.541	0.689	INDETERMINATE	1	TRUE	2	0.241960966464639	4		490	712	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929354	44929354	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030133-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	94	278	0	ENST00000377967.4:c.2454del	p.Pro819HisfsTer48	p.P819Hfs*48	ENST00000377967	NM_021140.2	818	tcA/tc	17/29	0.158243346276082	2	FACETS	0.914	0.818	1			1	CLONAL	2	TRUE	NA	0.241960966464639	2		278	425	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218952	133218952	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030133-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	65	569	0	ENST00000320574.5:c.4984G>C	p.Glu1662Gln	p.E1662Q	ENST00000320574	NM_006231.2	1662	Gag/Cag	38/49	1	2	FACETS	0.809	0.701	0.926	0.809	0.701	0.926	CLONAL	1	TRUE	1	0.241960966464639	2		569	664	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332930	152332930	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0030133-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	75	399	0	ENST00000206249.3:c.1235+1G>T		p.X412_splice	ENST00000206249	NM_000125.3	412			0.241960966464639	1	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	0	0.241960966464639	1		399	528	SUCCESS
MAD2L2	10459	MSKCC	GRCh37	1	11737658	11737658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767807551	NA	P-0030133-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	68	538	0	ENST00000235310.3:c.173C>T	p.Pro58Leu	p.P58L	ENST00000235310		58	cCg/cTg	6/11	1	2	FACETS	0.798	0.694	0.912	0.798	0.694	0.912	CLONAL	1	TRUE	1	0.241960966464639	2		538	704	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157543	106157543	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030133-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	37	502	0	ENST00000380013.4:c.2444G>C	p.Arg815Thr	p.R815T	ENST00000380013	NM_001127208.2	815	aGa/aCa	3/11	1	2	FACETS	0.506	0.416	0.607	0.506	0.416	0.607	SUBCLONAL	1	TRUE	1	0.241960966464639	2		502	604	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030136-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	42	789	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.741	0.619	0.876	0.741	0.619	0.876	SUBCLONAL	1	TRUE	1	0.249161361604256	2		789	455	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151316	202151316	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0030136-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	94	280	0	ENST00000358485.4:c.1616G>C	p.Ter539SerextTer88	p.*539Sext*88	ENST00000358485	NM_001080125.1	539	tGa/tCa	9/9	0.249161361604256	2	FACETS	0.903	0.808	1	0.903	0.808	1	CLONAL	2	TRUE	0	0.249161361604256	2		280	418	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566521	41566521	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030136-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	141	392	0	ENST00000263253.7:c.4398G>C	p.Trp1466Cys	p.W1466C	ENST00000263253	NM_001429.3	1466	tgG/tgC	27/31	0.249161361604256	2	FACETS	0.998	0.913	1	0.998	0.913	1	CLONAL	2	TRUE	0	0.249161361604256	2		392	567	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257565	19257565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030136-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	95	667	0	ENST00000162023.5:c.661G>A	p.Gly221Arg	p.G221R	ENST00000162023		221	Gga/Aga	10/13	1	2	FACETS	0.881	0.783	0.985	0.881	0.783	0.985	CLONAL	1	TRUE	1	0.249161361604256	2		667	866	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593508	48593508	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793725	NA	P-0030136-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	71	393	0	ENST00000342988.3:c.1259G>A	p.Arg420His	p.R420H	ENST00000342988	NM_005359.5	420	cGt/cAt	10/12	1	2	FACETS	0.953	0.832	1	0.953	0.832	1	CLONAL	1	TRUE	1	0.249161361604256	2		393	598	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39240676	39240676	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030136-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	64	323	0	ENST00000402219.2:c.2092G>C	p.Glu698Gln	p.E698Q	ENST00000402219	NM_005633.3	698	Gag/Cag	13/23	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.249161361604256	2		323	493	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857517	57857517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs890327478	NA	P-0030136-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	94	571	0	ENST00000228682.2:c.43G>A	p.Glu15Lys	p.E15K	ENST00000228682	NM_005269.2	15	Gag/Aag	2/12	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.249161361604256	2		571	675	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143318	30143345	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGGGCGTAGACACGGAAGAGCGAGGG	CCCGGGCGTAGACACGGAAGAGCGAGGG	-	novel	NA	P-0030136-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	68	456	0	ENST00000389048.3:c.181_208del	p.Pro61ThrfsTer11	p.P61Tfs*11	ENST00000389048	NM_004304.4	61	CCCTCGCTCTTCCGTGTCTACGCCCGGGac/ac	1/29	1	2	FACETS	0.904	0.786	1	0.904	0.786	1	CLONAL	1	TRUE	1	0.249161361604256	2		456	604	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0030136-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	236	547	0	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	0.221594550026813	4	FACETS	0.947	0.886	1	0.947	0.886	1	CLONAL	3	TRUE	1	0.249161361604256	4		547	833	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869523	102869523	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030136-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	91	419	1	ENST00000307046.8:c.118C>A	p.Leu40Ile	p.L40I	ENST00000307046	NM_001111285.1	40	Ctc/Atc	2/4	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.249161361604256	2		420	580	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954339	48954339	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0030163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	78	341	0	ENST00000267163.4:c.1460T>A	p.Leu487Ter	p.L487*	ENST00000267163	NM_000321.2	487	tTg/tAg	16/27	0.48954199657318	2	FACETS	0.812	0.729	0.896	0.812	0.729	0.896	CLONAL	2	TRUE	0	0.497981284859851	2		341	193	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023055	31023055	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	132	622	0	ENST00000375687.4:c.2540C>G	p.Ser847Cys	p.S847C	ENST00000375687	NM_015338.5	847	tCc/tGc	13/13	0.497981284859851	3	FACETS	1	0.985	1	0.706	0.645	0.769	CLONAL	1	TRUE	1	0.497981284859851	3		622	469	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912145	76912145	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0030163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	50	144	0	ENST00000373344.5:c.4121-2A>T		p.X1374_splice	ENST00000373344	NM_000489.3	1374			0.497981284859851	2	FACETS	1	0.966	1			1	CLONAL	2	TRUE	NA	0.497981284859851	2		144	81	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139458	47139458	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	13	465	0	ENST00000409792.3:c.5129G>A	p.Arg1710His	p.R1710H	ENST00000409792	NM_014159.6	1710	cGt/cAt	9/21	1	2	FACETS	0.208	0.148	0.281	0.208	0.148	0.281	SUBCLONAL	1	TRUE	1	0.497981284859851	2		465	251	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542141	187542141	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	11	535	0	ENST00000441802.2:c.5599G>A	p.Val1867Ile	p.V1867I	ENST00000441802	NM_005245.3	1867	Gta/Ata	10/27	0.358149795293	3	FACETS	0.386	0.267	0.532	0.129	0.089	0.178	SUBCLONAL	1	TRUE	0	0.497981284859851	3		535	143	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913237	NA	P-0032363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	268	543	2	ENST00000369535.4:c.35G>T	p.Gly12Val	p.G12V	ENST00000369535	NM_002524.4	12	gGt/gTt	2/7	0.495118877673532	4	FACETS	1	0.977	1			1	CLONAL	2	TRUE	NA	0.495118877673532	4		545	757	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0032363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	284	585	0	ENST00000269305.4:c.375+1G>T		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.495118877673532	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.495118877673532	2		585	572	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939999	76939999	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	129	242	0	ENST00000373344.5:c.749G>A	p.Arg250Gln	p.R250Q	ENST00000373344	NM_000489.3	250	cGa/cAa	9/35	0.445847862405955	2	FACETS	1	0.981	1			1	CLONAL	2	TRUE	NA	0.495118877673532	2		242	225	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120707	115120707	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	203	755	0	ENST00000257566.3:c.299A>C	p.Glu100Ala	p.E100A	ENST00000257566	NM_016569.3	100	gAg/gCg	1/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.495118877673532	2		755	698	SUCCESS
APC	324	MSKCC	GRCh37	5	112175222	112175223	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0032363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	205	590	0	ENST00000257430.4:c.3932_3933dup	p.Gly1312LeufsTer10	p.G1312Lfs*10	ENST00000257430	NM_000038.5	1311	att/aTTtt	16/16	0.236743913949185	4	FACETS	1	0.958	1	1	0.958	1	INDETERMINATE	2	TRUE	2	0.495118877673532	4		590	598	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945052	151945052	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	37	360	0	ENST00000262189.6:c.2467A>T	p.Ile823Phe	p.I823F	ENST00000262189	NM_170606.2	823	Att/Ttt	14/59	0.322970890156368	4	FACETS	0.752	0.623	0.896	0.376	0.311	0.448	SUBCLONAL	1	TRUE	2	0.495118877673532	4		360	297	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066746	5066746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	40	413	0	ENST00000381652.3:c.1283G>A	p.Ser428Asn	p.S428N	ENST00000381652	NM_004972.3	428	aGt/aAt	10/25	0.351521593531454	4	FACETS	0.944	0.802	1	0.944	0.802	1	CLONAL	2	TRUE	2	0.495118877673532	4		413	128	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911614	114911614	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	CCGGC	novel	NA	P-0032363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	98	528	0	ENST00000543371.1:c.1132delinsCCGGC	p.Ala378ProfsTer46	p.A378Pfs*46	ENST00000543371	NM_001198531.1	378	Gcg/CCGGCcg	10/14	0.214529817171042	3	FACETS	0.829	0.741	0.922	0.276	0.247	0.308	INDETERMINATE	1	TRUE	0	0.495118877673532	3		528	596	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628974	187628974	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	40	657	0	ENST00000441802.2:c.2008G>T	p.Val670Leu	p.V670L	ENST00000441802	NM_005245.3	670	Gta/Tta	2/27	0.495118877673532	2	FACETS	0.283	0.235	0.338	0.142	0.117	0.169	SUBCLONAL	1	TRUE	0	0.495118877673532	2		657	570	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	93	789	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.889	0.806	0.973			1	INDETERMINATE	2	TRUE	NA	0.467017636049959	2		789	224	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570353	87570353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	84	623	0	ENST00000277120.3:c.2093G>A	p.Cys698Tyr	p.C698Y	ENST00000277120		698	tGc/tAc	17/19	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.467017636049959	2		623	340	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0033492-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	176	624	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.395343203910186	3	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	1	0.40802834261617	3		625	519	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034816	42034818	+	missense_variant	Missense_Mutation	TNP	TAC	TAC	AAG	novel	NA	P-0033492-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	118	503	0	ENST00000219905.7:c.4658_4660delinsAAG	p.Ile1553_Pro1554delinsLysAla	p.I1553_P1554delinsKA	ENST00000219905	NM_001164273.1	1553	aTACct/aAAGct	15/24	1	2	FACETS	0.987	0.893	1	0.987	0.893	1	CLONAL	1	TRUE	1	0.40802834261617	2		503	586	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782082	NA	P-0033492-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	205	410	0	ENST00000269305.4:c.745A>T	p.Arg249Trp	p.R249W	ENST00000269305	NM_001126112.2	249	Agg/Tgg	7/11	0.407956274718142	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.40802834261617	2		410	478	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520735	176520735	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750637669	NA	P-0033492-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	162	378	0	ENST00000292408.4:c.1478G>A	p.Arg493Gln	p.R493Q	ENST00000292408	NM_213647.1	493	cGg/cAg	11/18	0.40802834261617	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.40802834261617	2		378	382	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923161	48923161	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0034362-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	337	315	0	ENST00000267163.4:c.607+2T>G		p.X203_splice	ENST00000267163	NM_000321.2	203			0.568358577378571	5	FACETS	0.975	0.943	1	0.975	0.943	1	CLONAL	5	TRUE	0	0.569800375550891	5		315	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577540	7577541	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	A	novel	NA	P-0034362-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	583	463	0	ENST00000269305.4:c.740_741delinsT	p.Asn247IlefsTer98	p.N247Ifs*98	ENST00000269305	NM_001126112.2	247	aAC/aT	7/11	0.568358577378571	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.569800375550891	3		463	857	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248566	212248566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1210422013	NA	P-0034362-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	206	605	0	ENST00000342788.4:c.3701A>G	p.Lys1234Arg	p.K1234R	ENST00000342788	NM_005235.2	1234	aAg/aGg	28/28	0.568358577378571	3	FACETS	1	0.976	1	0.557	0.517	0.598	CLONAL	1	TRUE	1	0.569800375550891	3		605	834	SUCCESS
FH	2271	MSKCC	GRCh37	1	241676957	241676957	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034362-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	298	374	0	ENST00000366560.3:c.324G>C	p.Gln108His	p.Q108H	ENST00000366560	NM_000143.3	108	caG/caC	3/10	0.568358577378571	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.569800375550891	3		374	649	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154344	2154344	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034362-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	438	614	0	ENST00000434045.2:c.584G>C	p.Gly195Ala	p.G195A	ENST00000434045	NM_001127598.1	195	gGt/gCt	5/5	0.568358577378571	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.569800375550891	3		614	941	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10800494	10800494	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756415574	NA	P-0034362-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	193	526	0	ENST00000361367.2:c.3364C>T	p.Arg1122Cys	p.R1122C	ENST00000361367	NM_014633.3	1122	Cgc/Tgc	25/25	0.568358577378571	3	FACETS	1	0.952	1	0.518	0.48	0.558	CLONAL	1	TRUE	1	0.569800375550891	3		526	840	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944820	31944820	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034362-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	158	526	0	ENST00000340398.3:c.281A>T	p.Glu94Val	p.E94V	ENST00000340398	NM_001013699.2	94	gAg/gTg	1/1	0.535998889825666	4	FACETS	0.811	0.742	0.884	0.406	0.371	0.442	CLONAL	1	TRUE	2	0.569800375550891	4		526	1073	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424081	49424081	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034362-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	342	435	0	ENST00000301067.7:c.13981del	p.Ser4661ValfsTer5	p.S4661Vfs*5	ENST00000301067	NM_003482.3	4661	Agt/gt	42/54	0.535998889825666	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	2	0.569800375550891	4		435	913	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857253	9857253	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034362-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	587	605	0	ENST00000330684.3:c.4148C>A	p.Pro1383His	p.P1383H	ENST00000330684	NM_001134407.1	1383	cCc/cAc	13/13	0.568358577378571	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	1	0.569800375550891	4		605	1065	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923852	72923852	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034362-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	160	433	0	ENST00000268489.5:c.3226C>T	p.Gln1076Ter	p.Q1076*	ENST00000268489	NM_006885.3	1076	Cag/Tag	4/10	0.568358577378571	3	FACETS	0.99	0.91	1	0.495	0.455	0.537	CLONAL	1	TRUE	1	0.569800375550891	3		433	729	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042344	16042344	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034362-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	104	357	0	ENST00000268712.3:c.1330G>T	p.Glu444Ter	p.E444*	ENST00000268712	NM_006311.3	444	Gaa/Taa	12/46	0.568358577378571	3	FACETS	0.961	0.865	1	0.32	0.288	0.354	CLONAL	1	TRUE	0	0.569800375550891	3		357	488	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383305	42383305	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034362-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	391	583	0	ENST00000221972.3:c.325C>A	p.Gln109Lys	p.Q109K	ENST00000221972	NM_021601.3	109	Cag/Aag	2/5	0.323623028353245	5	FACETS	1	0.992	1	0.786	0.749	0.824	INDETERMINATE	2	TRUE	2	0.569800375550891	5		583	1079	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281945	39281945	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034362-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	84	303	0	ENST00000402219.2:c.530A>T	p.His177Leu	p.H177L	ENST00000402219	NM_005633.3	177	cAt/cTt	5/23	0.568358577378571	3	FACETS	0.947	0.842	1	0.474	0.421	0.53	CLONAL	1	TRUE	1	0.569800375550891	3		303	400	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61749764	61749764	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034362-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	138	367	0	ENST00000401558.2:c.283C>G	p.Pro95Ala	p.P95A	ENST00000401558	NM_003400.3	95	Cca/Gca	4/25	0.568358577378571	3	FACETS	0.976	0.89	1	0.488	0.445	0.532	CLONAL	1	TRUE	1	0.569800375550891	3		367	638	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631459	67631459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034362-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	448	553	0	ENST00000272342.5:c.1645G>A	p.Asp549Asn	p.D549N	ENST00000272342	NM_019002.3	549	Gat/Aat	5/6	0.568358577378571	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	1	0.569800375550891	4		553	800	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71050212	71050212	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0034362-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	143	394	0	ENST00000318789.4:c.975-2A>G		p.X325_splice	ENST00000318789	NM_032682.5	325			0.568358577378571	3	FACETS	1	0.914	1	0.5	0.457	0.545	CLONAL	1	TRUE	1	0.569800375550891	3		394	645	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525541	187525541	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034362-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	351	514	0	ENST00000441802.2:c.10538T>C	p.Leu3513Pro	p.L3513P	ENST00000441802	NM_005245.3	3513	cTg/cCg	18/27	0.568358577378571	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.569800375550891	2		514	598	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056154	26056154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1462256953	NA	P-0034362-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	233	633	0	ENST00000343677.2:c.503A>G	p.Lys168Arg	p.K168R	ENST00000343677	NM_005319.3	168	aAg/aGg	1/1	0.338661122445747	4	FACETS	1	0.986	1	0.603	0.562	0.645	INDETERMINATE	1	TRUE	2	0.569800375550891	4		633	1065	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0036177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	225	256	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.979	0.916	1	0.979	0.916	1	CLONAL	1	TRUE	1	0.667336570906232	2		256	689	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0036177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	216	338	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.945	0.883	1	0.945	0.883	1	CLONAL	1	TRUE	1	0.667336570906232	2		338	685	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0036177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	154	343	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	0.647963185637827	3	FACETS	0.996	0.915	1	0.498	0.457	0.54	CLONAL	1	TRUE	1	0.667336570906232	3		343	618	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781554	9781554	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	244	631	3	ENST00000377346.4:c.1864G>T	p.Glu622Ter	p.E622*	ENST00000377346	NM_005026.3	622	Gag/Tag	15/24	1	2	FACETS	0.948	0.89	1	0.948	0.89	1	CLONAL	1	TRUE	1	0.667336570906232	2		634	771	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226573318	226573318	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	206	527	0	ENST00000366794.5:c.898G>T	p.Gly300Cys	p.G300C	ENST00000366794	NM_001618.3	300	Ggt/Tgt	7/23	0.633684785110957	4	FACETS	0.94	0.871	1	0.47	0.435	0.506	CLONAL	1	TRUE	2	0.667336570906232	4		527	1095	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56867207	56867208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	250	604	0	ENST00000308159.5:c.1428dup	p.Ala477CysfsTer22	p.A477Cfs*22	ENST00000308159	NM_014669.4	476	gtt/gTtt	13/22	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.667336570906232	2		604	724	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953188	17953188	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1370621788	NA	P-0036177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	263	550	0	ENST00000458235.1:c.798C>A	p.Asp266Glu	p.D266E	ENST00000458235	NM_000215.3	266	gaC/gaA	6/24	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.667336570906232	2		550	734	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42848529	42848529	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	171	417	0	ENST00000398585.3:c.813del	p.Ala272GlnfsTer8	p.A272Qfs*8	ENST00000398585	NM_001135099.1	271	aaA/aa	8/14	1	2	FACETS	0.901	0.833	0.97	0.901	0.833	0.97	CLONAL	1	TRUE	1	0.667336570906232	2		417	569	SUCCESS
APC	324	MSKCC	GRCh37	5	112179371	112179371	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	213	446	0	ENST00000257430.4:c.8080A>C	p.Ile2694Leu	p.I2694L	ENST00000257430	NM_000038.5	2694	Att/Ctt	16/16	1	2	FACETS	0.95	0.887	1	0.95	0.887	1	CLONAL	1	TRUE	1	0.667336570906232	2		446	672	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282200	38282200	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	216	616	2	ENST00000425967.3:c.856C>T	p.Pro286Ser	p.P286S	ENST00000425967	NM_001174067.1	286	Ccc/Tcc	8/19	0.647963185637827	3	FACETS	1	0.937	1	0.503	0.468	0.539	CLONAL	1	TRUE	1	0.667336570906232	3		618	858	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650795	93650795	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0036177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	144	324	0	ENST00000375746.1:c.1723-2A>G		p.X575_splice	ENST00000375746	NM_001174167.1	575			1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.667336570906232	2		324	422	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434668	128434668	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	334	752	2	ENST00000265960.3:c.186G>T	p.Gln62His	p.Q62H	ENST00000265960	NM_001006617.1	62	caG/caT	2/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.667336570906232	2		754	975	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038723	47038723	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	248	664	0	ENST00000377604.3:c.730G>T	p.Glu244Ter	p.E244*	ENST00000377604	NM_001204468.1	244	Gag/Tag	9/24	0.667336570906232	1	FACETS	0.992	0.939	1	0.992	0.939	1	CLONAL	1	TRUE	0	0.667336570906232	1		664	499	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0036677-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	117	299	0	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	0.621017845423819	0	FACETS	0.661	0.612	0.71			1	SUBCLONAL	1	TRUE	NA	0.621017845423819	0		299	216	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs786201838	NA	P-0036677-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	263	755	0	ENST00000269305.4:c.578A>C	p.His193Pro	p.H193P	ENST00000269305	NM_001126112.2	193	cAt/cCt	6/11	0.621017845423819	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.621017845423819	1		755	571	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434795	49434795	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036677-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	247	816	0	ENST00000301067.7:c.6758A>G	p.Asp2253Gly	p.D2253G	ENST00000301067	NM_003482.3	2253	gAt/gGt	31/54	0.187592890827139	1	FACETS	0.807	0.758	0.856	0.807	0.758	0.856	INDETERMINATE	1	TRUE	0	0.621017845423819	1		816	680	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414941	78414941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036677-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	86	528	0	ENST00000370768.2:c.1825C>T	p.Pro609Ser	p.P609S	ENST00000370768	NM_003902.3	609	Cca/Tca	19/20	1	2	FACETS	0.523	0.463	0.586	0.523	0.463	0.586	SUBCLONAL	1	TRUE	1	0.621017845423819	2		528	530	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190691	108190691	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036677-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	30	360	0	ENST00000278616.4:c.6358G>C	p.Glu2120Gln	p.E2120Q	ENST00000278616	NM_000051.3	2120	Gaa/Caa	44/63	1	2	FACETS	0.393	0.318	0.477	0.393	0.318	0.477	SUBCLONAL	1	TRUE	1	0.621017845423819	2		360	246	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418947	116418947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037421-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	79	430	0	ENST00000397752.3:c.3458C>T	p.Pro1153Leu	p.P1153L	ENST00000397752	NM_000245.2	1153	cCg/cTg	17/21	0.327170653640872	1	FACETS	0.735	0.649	0.826	0.735	0.649	0.826	SUBCLONAL	1	TRUE	0	0.398644824335837	1		430	432	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625186	69625186	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs547457011	NA	P-0037421-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	77	546	0	ENST00000334134.2:c.607G>A	p.Gly203Ser	p.G203S	ENST00000334134	NM_005247.2	203	Ggt/Agt	3/3	0.398644824335837	6	FACETS	0.743	0.651	0.843	0.149	0.13	0.169	SUBCLONAL	1	TRUE	1	0.398644824335837	6		546	934	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448690	49448690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037421-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	87	555	0	ENST00000301067.7:c.169G>A	p.Asp57Asn	p.D57N	ENST00000301067	NM_003482.3	57	Gac/Aac	2/54	0.398644824335837	4	FACETS	0.756	0.668	0.849	0.252	0.222	0.283	SUBCLONAL	1	TRUE	1	0.398644824335837	4		555	808	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618688	37618688	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037421-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	420	558	0	ENST00000447079.4:c.365del	p.Leu122TyrfsTer2	p.L122Yfs*2	ENST00000447079	NM_015083.1	122	Tta/ta	1/14	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.398644824335837	2		558	938	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923507	9923507	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037421-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	49	353	0	ENST00000330684.3:c.1780C>A	p.Pro594Thr	p.P594T	ENST00000330684	NM_001134407.1	594	Ccc/Acc	9/13	1	2	FACETS	0.645	0.548	0.752	0.645	0.548	0.752	SUBCLONAL	1	TRUE	1	0.398644824335837	2		353	381	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032042	26032042	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037421-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	201	694	0	ENST00000244661.2:c.247C>G	p.Leu83Val	p.L83V	ENST00000244661	NM_003537.3	83	Ctt/Gtt	1/1	0.283823133345602	3	FACETS	1	0.95	1	0.517	0.478	0.557	CLONAL	1	TRUE	1	0.398644824335837	3		694	1170	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191479	10191479	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1559429613	NA	P-0039504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	38	468	0	ENST00000256474.2:c.472C>G	p.Leu158Val	p.L158V	ENST00000256474	NM_000551.3	158	Ctg/Gtg	3/3	NA	2	FACETS	0.41	0.339	0.49			1	INDETERMINATE	1	FALSE	NA	0.361875491224092	2		468	512	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563416	21563431	+	frameshift_variant	Frame_Shift_Del	DEL	GTCACTGGGGTTGGCA	GTCACTGGGGTTGGCA	-	novel	NA	P-0039504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	53	1103	0	ENST00000382592.4:c.488_503del	p.Met163SerfsTer19	p.M163Sfs*19	ENST00000382592	NM_014572.2	163	aTGCCAACCCCAGTGACg/ag	4/8	1	2	FACETS	0.312	0.265	0.364	0.312	0.265	0.364	SUBCLONAL	1	FALSE	1	0.361875491224092	2		1103	938	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165363	47165363	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0039504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	29	398	0	ENST00000409792.3:c.763A>T	p.Lys255Ter	p.K255*	ENST00000409792	NM_014159.6	255	Aag/Tag	3/21	1	2	FACETS	0.356	0.285	0.437	0.356	0.285	0.437	SUBCLONAL	1	FALSE	1	0.361875491224092	2		398	450	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53241070	53241070	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	53	361	0	ENST00000375401.3:c.1141G>T	p.Glu381Ter	p.E381*	ENST00000375401	NM_004187.3	381	Gaa/Taa	9/26	1	1	FACETS	0.65	0.556	0.752	0.65	0.556	0.752	SUBCLONAL	1	FALSE	0	0.361875491224092	1		361	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0039550-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	182	452	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.27262973286453	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.279246735864722	2		452	568	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980583	70980583	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039550-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	74	734	0	ENST00000276594.2:c.794A>G	p.His265Arg	p.H265R	ENST00000276594	NM_024504.3	265	cAt/cGt	4/8	0.262669907765148	4	FACETS	1	0.917	1	0.531	0.464	0.602	CLONAL	1	TRUE	2	0.279246735864722	4		734	639	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	28	433	0	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	0.101120345089616	3	FACETS	0.386	0.308	0.475	0.193	0.154	0.238	INDETERMINATE	1	TRUE	1	0.39	3		433	445	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	117	584	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.843	0.768	0.919	1	0.988	1	CLONAL	2	TRUE	1	0.39	2		584	356	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	72	495	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.776	0.687	0.868	1	0.978	1	SUBCLONAL	2	TRUE	1	0.39	2		495	238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	29	607	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.101120345089616	0	FACETS	0.16	0.127	0.197			1	INDETERMINATE	1	TRUE	0	0.39	0		607	568	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073509	8073509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	65	431	0	ENST00000377482.5:c.1150G>T	p.Glu384Ter	p.E384*	ENST00000377482	NM_018948.3	384	Gaa/Taa	4/4	1	2	FACETS	0.846	0.747	0.95	1	0.979	1	CLONAL	2	TRUE	1	0.39	2		431	197	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237633	16237633	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	14	405	0	ENST00000375759.3:c.1080G>T	p.Lys360Asn	p.K360N	ENST00000375759	NM_015001.2	360	aaG/aaT	5/15	1	2	FACETS	0.357	0.258	0.476	0.357	0.258	0.476	SUBCLONAL	1	TRUE	1	0.39	2		405	201	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264345	16264345	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	136	636	0	ENST00000375759.3:c.10548G>T	p.Lys3516Asn	p.K3516N	ENST00000375759	NM_015001.2	3516	aaG/aaT	13/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.39	2		636	500	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057932	27057932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	87	559	0	ENST00000324856.7:c.1640G>A	p.Ser547Asn	p.S547N	ENST00000324856	NM_006015.4	547	aGc/aAc	3/20	1	2	FACETS	0.637	0.564	0.716	0.637	0.564	0.716	SUBCLONAL	1	TRUE	1	0.39	2		559	700	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097631	27097631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	29	495	0	ENST00000324856.7:c.3220C>T	p.Arg1074Trp	p.R1074W	ENST00000324856	NM_006015.4	1074	Cgg/Tgg	12/20	1	2	FACETS	0.417	0.334	0.51	0.417	0.334	0.51	SUBCLONAL	1	TRUE	1	0.39	2		495	357	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101130	27101130	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs779806180	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	97	721	1	ENST00000324856.7:c.4412A>C	p.Asn1471Thr	p.N1471T	ENST00000324856	NM_006015.4	1471	aAt/aCt	18/20	1	2	FACETS	0.707	0.63	0.788	0.707	0.63	0.788	SUBCLONAL	1	TRUE	1	0.39	2		722	704	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932148	36932148	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	75	634	0	ENST00000361632.4:c.2321A>G	p.Gln774Arg	p.Q774R	ENST00000361632		774	cAg/cGg	16/16	1	2	FACETS	0.836	0.735	0.944	0.836	0.735	0.944	CLONAL	1	TRUE	1	0.39	2		634	460	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937198	36937198	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	61	779	0	ENST00000361632.4:c.1121C>A	p.Ser374Tyr	p.S374Y	ENST00000361632		374	tCt/tAt	9/16	1	2	FACETS	0.434	0.374	0.5	0.434	0.374	0.5	SUBCLONAL	1	TRUE	1	0.39	2		779	720	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305238	39305238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs890472037	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	51	474	0	ENST00000373001.3:c.1187G>A	p.Arg396Gln	p.R396Q	ENST00000373001	NM_022157.3	396	cGa/cAa	7/7	1	2	FACETS	0.493	0.418	0.574	0.493	0.418	0.574	SUBCLONAL	1	TRUE	1	0.39	2		474	531	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39317430	39317430	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	35	332	0	ENST00000373001.3:c.757-1G>T		p.X253_splice	ENST00000373001	NM_022157.3	253			1	2	FACETS	0.893	0.739	1	0.893	0.739	1	CLONAL	1	TRUE	1	0.39	2		332	201	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46733154	46733154	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	126	445	0	ENST00000371975.4:c.915G>T	p.Glu305Asp	p.E305D	ENST00000371975	NM_003579.3	305	gaG/gaT	9/18	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.39	2		445	469	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466316	120466316	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	30	465	0	ENST00000256646.2:c.4803G>T	p.Lys1601Asn	p.K1601N	ENST00000256646	NM_024408.3	1601	aaG/aaT	26/34	1	2	FACETS	0.47	0.38	0.573	0.47	0.38	0.573	SUBCLONAL	1	TRUE	1	0.39	2		465	327	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834155	156834155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	126	749	1	ENST00000524377.1:c.222G>T	p.Glu74Asp	p.E74D	ENST00000524377	NM_002529.3	74	gaG/gaT	2/17	1	2	FACETS	0.919	0.833	1	0.919	0.833	1	CLONAL	1	TRUE	1	0.39	2		750	703	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737052	162737052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765973930	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	88	437	0	ENST00000367921.3:c.1196G>A	p.Arg399Gln	p.R399Q	ENST00000367921	NM_006182.2	399	cGg/cAg	11/18	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.39	2		437	323	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317623	163317623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747173543	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	47	330	1	ENST00000271452.3:c.1019C>T	p.Ser340Leu	p.S340L	ENST00000271452	NM_145697.2	340	tCg/tTg	12/14	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.39	2		331	184	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094336	193094336	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886041158	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	40	337	0	ENST00000367435.3:c.226C>T	p.Arg76Ter	p.R76*	ENST00000367435	NM_024529.4	76	Cga/Tga	2/17	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.39	2		337	197	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193116996	193116996	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	40	265	0	ENST00000367435.3:c.730-1G>T		p.X244_splice	ENST00000367435	NM_024529.4	244			1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.39	2		265	150	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204512067	204512067	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	10	228	0	ENST00000367182.3:c.667A>G	p.Asn223Asp	p.N223D	ENST00000367182	NM_001278516.1	223	Aat/Gat	8/11	1	2	FACETS	0.564	0.386	0.782	0.564	0.386	0.782	SUBCLONAL	1	TRUE	1	0.39	2		228	91	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612948	228612948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750781461	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	57	738	0	ENST00000366696.1:c.79C>T	p.Arg27Cys	p.R27C	ENST00000366696	NM_003493.2	27	Cgc/Tgc	1/1	1	2	FACETS	0.674	0.579	0.776	0.674	0.579	0.776	SUBCLONAL	1	TRUE	1	0.39	2		738	434	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243675629	243675629	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	10	214	0	ENST00000263826.5:c.1351A>C	p.Lys451Gln	p.K451Q	ENST00000263826	NM_005465.4	451	Aaa/Caa	12/13	1	2	FACETS	0.458	0.312	0.638	0.458	0.312	0.638	SUBCLONAL	1	TRUE	1	0.39	2		214	112	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243801007	243801007	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	52	423	0	ENST00000263826.5:c.467A>C	p.Lys156Thr	p.K156T	ENST00000263826	NM_005465.4	156	aAa/aCa	5/13	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.39	2		423	243	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246490592	246490592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	18	516	0	ENST00000388985.4:c.442G>T	p.Val148Leu	p.V148L	ENST00000388985		148	Gta/Tta	5/12	1	2	FACETS	0.429	0.324	0.553	0.429	0.324	0.553	SUBCLONAL	1	TRUE	1	0.39	2		516	215	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246490612	246490612	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	15	450	0	ENST00000388985.4:c.422A>C	p.Lys141Thr	p.K141T	ENST00000388985		141	aAa/aCa	5/12	1	2	FACETS	0.416	0.305	0.548	0.416	0.305	0.548	SUBCLONAL	1	TRUE	1	0.39	2		450	185	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609030	43609030	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	23	634	1	ENST00000355710.3:c.1786C>T	p.Pro596Ser	p.P596S	ENST00000355710	NM_020975.4	596	Cct/Tct	10/20	1	2	FACETS	0.261	0.203	0.329	0.261	0.203	0.329	SUBCLONAL	1	TRUE	1	0.39	2		635	452	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851560	63851560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	132	572	0	ENST00000279873.7:c.2338C>T	p.Arg780Ter	p.R780*	ENST00000279873	NM_032199.2	780	Cga/Tga	10/10	1	2	FACETS	0.757	0.693	0.824	1	0.987	1	SUBCLONAL	2	TRUE	1	0.39	2		572	447	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332415	70332415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1419371452	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	40	584	0	ENST00000373644.4:c.320G>A	p.Arg107Gln	p.R107Q	ENST00000373644	NM_030625.2	107	cGa/cAa	2/12	1	2	FACETS	0.435	0.361	0.517	0.435	0.361	0.517	SUBCLONAL	1	TRUE	1	0.39	2		584	472	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405915	70405915	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1430579993	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	89	524	0	ENST00000373644.4:c.3429G>T	p.Lys1143Asn	p.K1143N	ENST00000373644	NM_030625.2	1143	aaG/aaT	4/12	1	2	FACETS	0.864	0.778	0.954	1	0.985	1	CLONAL	2	TRUE	1	0.39	2		524	264	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624245	89624245	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554890335	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	38	182	0	ENST00000371953.3:c.19G>T	p.Glu7Ter	p.E7*	ENST00000371953	NM_000314.4	7	Gag/Tag	1/9	1	2	FACETS	0.862	0.731	1	1	0.966	1	CLONAL	2	TRUE	1	0.39	2		182	113	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	78	445	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.93	0.832	1	1	0.984	1	CLONAL	2	TRUE	1	0.39	2		445	215	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112764488	112764488	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219277268	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	51	408	0	ENST00000369452.4:c.1097G>A	p.Arg366Gln	p.R366Q	ENST00000369452	NM_007373.3	366	cGa/cAa	5/9	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.39	2		408	190	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771387	112771387	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	22	558	0	ENST00000369452.4:c.1560A>C	p.Glu520Asp	p.E520D	ENST00000369452	NM_007373.3	520	gaA/gaC	9/9	1	2	FACETS	0.358	0.277	0.452	0.358	0.277	0.452	SUBCLONAL	1	TRUE	1	0.39	2		558	315	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248553	8248553	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757437334	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	225	699	1	ENST00000335790.3:c.334G>A	p.Asp112Asn	p.D112N	ENST00000335790	NM_002315.2	112	Gac/Aac	3/4	1	2	FACETS	0.795	0.743	0.848	1	0.993	1	SUBCLONAL	2	TRUE	1	0.39	2		700	726	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940539	71940539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	50	623	0	ENST00000298229.2:c.690G>T	p.Glu230Asp	p.E230D	ENST00000298229	NM_001567.3	230	gaG/gaT	6/28	1	2	FACETS	0.412	0.349	0.482	0.412	0.349	0.482	SUBCLONAL	1	TRUE	1	0.39	2		623	622	SUCCESS
EED	8726	MSKCC	GRCh37	11	85975288	85975288	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	19	279	0	ENST00000263360.6:c.709G>T	p.Asp237Tyr	p.D237Y	ENST00000263360	NM_003797.3	237	Gat/Tat	7/12	1	2	FACETS	0.492	0.375	0.629	0.492	0.375	0.629	SUBCLONAL	1	TRUE	1	0.39	2		279	198	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911895	94911895	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	23	504	0	ENST00000536441.1:c.1035T>G	p.His345Gln	p.H345Q	ENST00000536441	NM_144665.3	345	caT/caG	7/10	1	2	FACETS	0.491	0.384	0.615	0.491	0.384	0.615	SUBCLONAL	1	TRUE	1	0.39	2		504	240	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206852	102206852	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	49	343	0	ENST00000263464.3:c.1480G>T	p.Glu494Ter	p.E494*	ENST00000263464	NM_001165.4	494	Gaa/Taa	7/9	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.39	2		343	172	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207816	102207816	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	42	285	0	ENST00000263464.3:c.1798C>T	p.Arg600Cys	p.R600C	ENST00000263464	NM_001165.4	600	Cgt/Tgt	9/9	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.39	2		285	149	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115627	108115627	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	13	379	0	ENST00000278616.4:c.775C>A	p.Leu259Ile	p.L259I	ENST00000278616	NM_000051.3	259	Ctt/Att	7/63	1	2	FACETS	0.345	0.247	0.466	0.345	0.247	0.466	SUBCLONAL	1	TRUE	1	0.39	2		379	193	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121669	108121669	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750280306	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	18	423	1	ENST00000278616.4:c.1477C>T	p.Arg493Cys	p.R493C	ENST00000278616	NM_000051.3	493	Cgt/Tgt	10/63	1	2	FACETS	0.464	0.35	0.597	0.464	0.35	0.597	SUBCLONAL	1	TRUE	1	0.39	2		424	199	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163351	108163351	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	30	406	0	ENST00000278616.4:c.4442C>A	p.Ser1481Tyr	p.S1481Y	ENST00000278616	NM_000051.3	1481	tCt/tAt	30/63	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.39	2		406	142	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172385	108172385	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764389018	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	32	329	0	ENST00000278616.4:c.5188C>T	p.Arg1730Ter	p.R1730*	ENST00000278616	NM_000051.3	1730	Cga/Tga	35/63	1	2	FACETS	0.793	0.649	0.953	0.793	0.649	0.953	CLONAL	1	TRUE	1	0.39	2		329	207	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188112	108188112	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	35	244	0	ENST00000278616.4:c.6211T>G	p.Leu2071Val	p.L2071V	ENST00000278616	NM_000051.3	2071	Ttg/Gtg	43/63	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.39	2		244	145	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214089	108214089	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	21	281	0	ENST00000278616.4:c.8409G>T	p.Lys2803Asn	p.K2803N	ENST00000278616	NM_000051.3	2803	aaG/aaT	57/63	1	2	FACETS	0.657	0.509	0.825	0.657	0.509	0.825	SUBCLONAL	1	TRUE	1	0.39	2		281	164	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118355622	118355622	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	25	537	0	ENST00000534358.1:c.4264A>C	p.Ile1422Leu	p.I1422L	ENST00000534358	NM_005933.3	1422	Atc/Ctc	10/36	1	2	FACETS	0.427	0.337	0.531	0.427	0.337	0.531	SUBCLONAL	1	TRUE	1	0.39	2		537	300	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376449	118376449	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	12	435	0	ENST00000534358.1:c.9842C>A	p.Ser3281Tyr	p.S3281Y	ENST00000534358	NM_005933.3	3281	tCt/tAt	27/36	1	2	FACETS	0.293	0.206	0.4	0.293	0.206	0.4	SUBCLONAL	1	TRUE	1	0.39	2		435	210	SUCCESS
CBL	867	MSKCC	GRCh37	11	119146754	119146754	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	91	472	0	ENST00000264033.4:c.917G>T	p.Gly306Val	p.G306V	ENST00000264033	NM_005188.3	306	gGg/gTg	6/16	1	2	FACETS	0.783	0.704	0.866	1	0.983	1	SUBCLONAL	2	TRUE	1	0.39	2		472	298	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169179	119169179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150811339	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	95	463	1	ENST00000264033.4:c.2363G>A	p.Arg788Gln	p.R788Q	ENST00000264033	NM_005188.3	788	cGa/cAa	15/16	1	2	FACETS	0.779	0.695	0.869	0.779	0.695	0.869	SUBCLONAL	1	TRUE	1	0.39	2		464	625	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417087	417087	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1565528788	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	38	311	0	ENST00000399788.2:c.3463G>A	p.Val1155Met	p.V1155M	ENST00000399788	NM_001042603.1	1155	Gtg/Atg	23/28	0.101120345089616	3	FACETS	1	0.906	1	0.565	0.472	0.667	INDETERMINATE	1	TRUE	1	0.39	3		311	206	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	441022	441022	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	104	377	0	ENST00000399788.2:c.1736A>C	p.Asn579Thr	p.N579T	ENST00000399788	NM_001042603.1	579	aAc/aCc	13/28	0.101120345089616	3	FACETS	1	0.97	1	1	0.97	1	INDETERMINATE	2	TRUE	1	0.39	3		377	275	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	461472	461472	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	13	383	0	ENST00000399788.2:c.1048G>T	p.Glu350Ter	p.E350*	ENST00000399788	NM_001042603.1	350	Gaa/Taa	9/28	0.101120345089616	3	FACETS	0.314	0.223	0.424	0.157	0.111	0.212	INDETERMINATE	1	TRUE	1	0.39	3		383	254	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475146	475146	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	17	506	0	ENST00000399788.2:c.491G>T	p.Arg164Ile	p.R164I	ENST00000399788	NM_001042603.1	164	aGa/aTa	4/28	0.101120345089616	3	FACETS	0.386	0.288	0.502	0.193	0.144	0.251	INDETERMINATE	1	TRUE	1	0.39	3		506	270	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	495100	495100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374793802	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	58	342	0	ENST00000399788.2:c.206G>A	p.Arg69His	p.R69H	ENST00000399788	NM_001042603.1	69	cGt/cAt	2/28	0.101120345089616	3	FACETS	0.797	0.694	0.906	0.797	0.694	0.906	INDETERMINATE	2	TRUE	1	0.39	3		342	223	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385236	4385236	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	50	493	0	ENST00000261254.3:c.261C>A	p.Phe87Leu	p.F87L	ENST00000261254	NM_001759.3	87	ttC/ttA	2/5	0.101120345089616	3	FACETS	0.624	0.53	0.728	0.312	0.265	0.364	INDETERMINATE	1	TRUE	1	0.39	3		493	491	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4387995	4387995	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	30	509	0	ENST00000261254.3:c.481G>T	p.Glu161Ter	p.E161*	ENST00000261254	NM_001759.3	161	Gag/Tag	3/5	0.101120345089616	3	FACETS	0.442	0.356	0.54	0.221	0.178	0.27	INDETERMINATE	1	TRUE	1	0.39	3		509	416	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21627847	21627847	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	42	546	0	ENST00000421138.2:c.1283C>A	p.Ser428Ter	p.S428*	ENST00000421138		428	tCa/tAa	12/16	0.101120345089616	3	FACETS	0.817	0.685	0.962	0.409	0.342	0.481	INDETERMINATE	1	TRUE	1	0.39	3		546	315	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945093	31945093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	118	632	0	ENST00000340398.3:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000340398	NM_001013699.2	3	cGa/cAa	1/1	0.101120345089616	3	FACETS	1	0.947	1	0.536	0.484	0.59	INDETERMINATE	1	TRUE	1	0.39	3		632	675	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211548	46211548	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	19	291	0	ENST00000334344.6:c.514G>T	p.Glu172Ter	p.E172*	ENST00000334344	NM_152641.2	172	Gaa/Taa	5/21	0.101120345089616	3	FACETS	0.71	0.543	0.904	0.355	0.271	0.452	INDETERMINATE	1	TRUE	1	0.39	3		291	164	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244742	46244742	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	23	548	0	ENST00000334344.6:c.2836A>G	p.Ile946Val	p.I946V	ENST00000334344	NM_152641.2	946	Att/Gtt	15/21	0.101120345089616	3	FACETS	0.417	0.325	0.524	0.209	0.162	0.262	INDETERMINATE	1	TRUE	1	0.39	3		548	338	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245343	46245343	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	50	503	0	ENST00000334344.6:c.3437C>T	p.Ser1146Leu	p.S1146L	ENST00000334344	NM_152641.2	1146	tCg/tTg	15/21	0.101120345089616	3	FACETS	1	0.868	1	0.509	0.434	0.59	INDETERMINATE	1	TRUE	1	0.39	3		503	301	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287256	46287256	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	20	462	0	ENST00000334344.6:c.5201T>C	p.Val1734Ala	p.V1734A	ENST00000334344	NM_152641.2	1734	gTg/gCg	19/21	0.101120345089616	3	FACETS	0.407	0.311	0.519	0.204	0.155	0.26	INDETERMINATE	1	TRUE	1	0.39	3		462	301	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416114	49416114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	42	463	1	ENST00000301067.7:c.16361G>A	p.Arg5454Gln	p.R5454Q	ENST00000301067	NM_003482.3	5454	cGa/cAa	52/54	0.101120345089616	3	FACETS	0.617	0.516	0.729	0.309	0.258	0.365	INDETERMINATE	1	TRUE	1	0.39	3		464	417	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438728	49438728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290729871	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	70	692	0	ENST00000301067.7:c.4762G>A	p.Glu1588Lys	p.E1588K	ENST00000301067	NM_003482.3	1588	Gaa/Aaa	19/54	0.101120345089616	3	FACETS	0.671	0.585	0.764	0.336	0.292	0.382	INDETERMINATE	1	TRUE	1	0.39	3		692	639	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860063	57860063	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	84	788	0	ENST00000228682.2:c.803T>C	p.Phe268Ser	p.F268S	ENST00000228682	NM_005269.2	268	tTc/tCc	8/12	0.101120345089616	3	FACETS	0.584	0.515	0.659	0.292	0.257	0.33	INDETERMINATE	1	TRUE	1	0.39	3		788	881	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864595	57864595	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	66	845	0	ENST00000228682.2:c.2072G>T	p.Ser691Ile	p.S691I	ENST00000228682	NM_005269.2	691	aGc/aTc	12/12	0.101120345089616	3	FACETS	0.697	0.605	0.797	0.349	0.302	0.399	INDETERMINATE	1	TRUE	1	0.39	3		845	580	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865314	57865314	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	80	776	0	ENST00000228682.2:c.2791C>A	p.Leu931Met	p.L931M	ENST00000228682	NM_005269.2	931	Ctg/Atg	12/12	0.101120345089616	3	FACETS	0.908	0.801	1	0.454	0.4	0.511	INDETERMINATE	1	TRUE	1	0.39	3		776	540	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111886044	111886044	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769682050	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	97	560	0	ENST00000341259.2:c.1666G>A	p.Glu556Lys	p.E556K	ENST00000341259	NM_005475.2	556	Gaa/Aaa	8/8	0.101120345089616	3	FACETS	0.954	0.852	1	0.477	0.426	0.532	INDETERMINATE	1	TRUE	1	0.39	3		560	623	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117457	115117457	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	24	333	0	ENST00000257566.3:c.718-1G>T		p.X240_splice	ENST00000257566	NM_016569.3	240			0.101120345089616	3	FACETS	1	0.814	1	0.514	0.408	0.634	INDETERMINATE	1	TRUE	1	0.39	3		333	143	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416737	121416737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	284	789	0	ENST00000257555.6:c.166G>A	p.Glu56Lys	p.E56K	ENST00000257555		56	Gag/Aag	1/10	0.101120345089616	3	FACETS	1	0.96	1	1	0.96	1	INDETERMINATE	2	TRUE	1	0.39	3		789	851	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212602	133212602	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	15	432	0	ENST00000320574.5:c.5687C>A	p.Ser1896Ter	p.S1896*	ENST00000320574	NM_006231.2	1896	tCa/tAa	42/49	0.101120345089616	3	FACETS	0.393	0.287	0.519	0.196	0.143	0.26	INDETERMINATE	1	TRUE	1	0.39	3		432	234	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	159	403	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	0.101120345089616	3	FACETS	0.846	0.785	0.907	1	0.986	1	INDETERMINATE	3	TRUE	1	0.39	3		403	384	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557476	21557476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	43	594	0	ENST00000382592.4:c.2369G>A	p.Arg790Gln	p.R790Q	ENST00000382592	NM_014572.2	790	cGa/cAa	5/8	0.101120345089616	3	FACETS	0.619	0.518	0.73	0.309	0.259	0.365	INDETERMINATE	1	TRUE	1	0.39	3		594	426	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26978210	26978210	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776727772	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	24	465	0	ENST00000381527.3:c.1387C>T	p.Arg463Trp	p.R463W	ENST00000381527	NM_001260.1	463	Cgg/Tgg	13/13	0.101120345089616	3	FACETS	0.341	0.267	0.427	0.171	0.133	0.214	INDETERMINATE	1	TRUE	1	0.39	3		465	431	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589808	28589808	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568745490	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	92	482	0	ENST00000241453.7:c.2572G>A	p.Glu858Lys	p.E858K	ENST00000241453	NM_004119.2	858	Gaa/Aaa	21/24	0.101120345089616	3	FACETS	0.996	0.897	1	0.996	0.897	1	INDETERMINATE	2	TRUE	1	0.39	3		482	283	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608072	28608072	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	45	534	0	ENST00000241453.7:c.1894A>C	p.Ile632Leu	p.I632L	ENST00000241453	NM_004119.2	632	Att/Ctt	15/24	0.101120345089616	3	FACETS	1	0.881	1	0.524	0.444	0.612	INDETERMINATE	1	TRUE	1	0.39	3		534	263	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608234	28608234	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	13	497	0	ENST00000241453.7:c.1822G>T	p.Glu608Ter	p.E608*	ENST00000241453	NM_004119.2	608	Gaa/Taa	14/24	0.101120345089616	3	FACETS	0.398	0.284	0.537	0.199	0.142	0.269	INDETERMINATE	1	TRUE	1	0.39	3		497	200	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611324	28611324	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	19	381	0	ENST00000241453.7:c.1307G>T	p.Arg436Ile	p.R436I	ENST00000241453	NM_004119.2	436	aGa/aTa	10/24	0.101120345089616	3	FACETS	0.732	0.56	0.932	0.366	0.28	0.466	INDETERMINATE	1	TRUE	1	0.39	3		381	159	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893334	32893334	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	22	343	0	ENST00000380152.3:c.188A>C	p.Lys63Thr	p.K63T	ENST00000380152		63	aAa/aCa	3/27	0.101120345089616	3	FACETS	0.671	0.522	0.841	0.335	0.261	0.421	INDETERMINATE	1	TRUE	1	0.39	3		343	201	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32899248	32899248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375125172	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	15	250	0	ENST00000380152.3:c.352C>T	p.Arg118Cys	p.R118C	ENST00000380152		118	Cgc/Tgc	4/27	0.101120345089616	3	FACETS	0.609	0.448	0.8	0.304	0.224	0.4	INDETERMINATE	1	TRUE	1	0.39	3		250	151	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906567	32906567	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	27	337	0	ENST00000380152.3:c.952A>C	p.Lys318Gln	p.K318Q	ENST00000380152		318	Aaa/Caa	10/27	0.101120345089616	3	FACETS	0.752	0.61	0.907	0.752	0.61	0.907	INDETERMINATE	2	TRUE	1	0.39	3		337	110	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906894	32906894	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	11	445	1	ENST00000380152.3:c.1279G>T	p.Asp427Tyr	p.D427Y	ENST00000380152		427	Gac/Tac	10/27	0.101120345089616	3	FACETS	0.394	0.273	0.545	0.197	0.136	0.273	INDETERMINATE	1	TRUE	1	0.39	3		446	171	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906944	32906944	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs73169186	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	15	374	0	ENST00000380152.3:c.1329G>T	p.Glu443Asp	p.E443D	ENST00000380152		443	gaG/gaT	10/27	0.101120345089616	3	FACETS	0.55	0.404	0.724	0.275	0.202	0.362	INDETERMINATE	1	TRUE	1	0.39	3		374	167	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910943	32910943	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs767686668	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	23	383	0	ENST00000380152.3:c.2451G>T	p.Lys817Asn	p.K817N	ENST00000380152		817	aaG/aaT	11/27	0.101120345089616	3	FACETS	0.81	0.636	1	0.405	0.318	0.504	INDETERMINATE	1	TRUE	1	0.39	3		383	174	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914137	32914137	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs80358785	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	19	471	0	ENST00000380152.3:c.5645C>A	p.Ser1882Ter	p.S1882*	ENST00000380152		1882	tCa/tAa	11/27	0.101120345089616	3	FACETS	0.809	0.619	1	0.404	0.309	0.514	INDETERMINATE	1	TRUE	1	0.39	3		471	144	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945129	32945129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80359104	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	40	318	0	ENST00000380152.3:c.8524C>T	p.Arg2842Cys	p.R2842C	ENST00000380152		2842	Cgc/Tgc	20/27	0.101120345089616	3	FACETS	0.776	0.655	0.905	0.776	0.655	0.905	INDETERMINATE	2	TRUE	1	0.39	3		318	158	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134045	41134045	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	49	468	0	ENST00000379561.5:c.1583C>A	p.Ala528Asp	p.A528D	ENST00000379561	NM_002015.3	528	gCt/gAt	2/3	0.101120345089616	3	FACETS	0.649	0.55	0.757	0.324	0.275	0.379	INDETERMINATE	1	TRUE	1	0.39	3		468	463	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134459	41134459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756553520	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	127	505	0	ENST00000379561.5:c.1169C>T	p.Ser390Leu	p.S390L	ENST00000379561	NM_002015.3	390	tCg/tTg	2/3	0.101120345089616	3	FACETS	1	0.983	1	0.683	0.621	0.747	INDETERMINATE	1	TRUE	1	0.39	3		505	570	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942686	48942686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767011440	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	38	272	0	ENST00000267163.4:c.1073G>A	p.Arg358Gln	p.R358Q	ENST00000267163	NM_000321.2	358	cGa/cAa	11/27	0.101120345089616	3	FACETS	0.787	0.662	0.921	0.787	0.662	0.921	INDETERMINATE	2	TRUE	1	0.39	3		272	148	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337650	73337650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	55	228	0	ENST00000377767.4:c.2066G>A	p.Arg689Gln	p.R689Q	ENST00000377767	NM_014953.3	689	cGa/cAa	16/21	0.101120345089616	3	FACETS	1	0.936	1	1	0.936	1	INDETERMINATE	2	TRUE	1	0.39	3		228	151	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347871	73347871	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	12	272	0	ENST00000377767.4:c.1190G>T	p.Arg397Ile	p.R397I	ENST00000377767	NM_014953.3	397	aGa/aTa	8/21	0.101120345089616	3	FACETS	0.44	0.31	0.6	0.22	0.155	0.3	INDETERMINATE	1	TRUE	1	0.39	3		272	167	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347916	73347916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139907646	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	54	285	0	ENST00000377767.4:c.1145G>A	p.Arg382Gln	p.R382Q	ENST00000377767	NM_014953.3	382	cGa/cAa	8/21	0.101120345089616	3	FACETS	1	0.906	1	1	0.906	1	INDETERMINATE	2	TRUE	1	0.39	3		285	158	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73351596	73351596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760670933	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	12	231	0	ENST00000377767.4:c.616G>A	p.Glu206Lys	p.E206K	ENST00000377767	NM_014953.3	206	Gaa/Aaa	4/21	0.101120345089616	3	FACETS	0.359	0.252	0.49	0.179	0.126	0.245	INDETERMINATE	1	TRUE	1	0.39	3		231	205	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504585	103504585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747957305	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	29	245	0	ENST00000355739.4:c.206G>A	p.Arg69Gln	p.R69Q	ENST00000355739	NM_000123.3	69	cGa/cAa	2/15	0.101120345089616	3	FACETS	1	0.855	1	0.532	0.432	0.644	INDETERMINATE	1	TRUE	1	0.39	3		245	167	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515141	103515141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770246574	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	16	297	0	ENST00000355739.4:c.1642G>A	p.Glu548Lys	p.E548K	ENST00000355739	NM_000123.3	548	Gaa/Aaa	8/15	0.101120345089616	3	FACETS	0.766	0.571	0.994	0.383	0.285	0.497	INDETERMINATE	1	TRUE	1	0.39	3		297	128	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609532	81609532	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	30	514	0	ENST00000298171.2:c.1130C>A	p.Thr377Asn	p.T377N	ENST00000298171	NM_000369.2	377	aCt/aAt	10/10	0.101120345089616	3	FACETS	0.721	0.583	0.875	0.36	0.291	0.438	INDETERMINATE	1	TRUE	1	0.39	3		514	255	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675139	40675139	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	28	787	0	ENST00000249776.8:c.103C>A	p.Leu35Ile	p.L35I	ENST00000249776	NM_033286.3	35	Cta/Ata	1/9	0.101120345089616	0	FACETS	0.163	0.13	0.202			1	INDETERMINATE	1	TRUE	0	0.39	0		787	536	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961867	41961867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	12	350	0	ENST00000219905.7:c.775C>T	p.Arg259Trp	p.R259W	ENST00000219905	NM_001164273.1	259	Cgg/Tgg	2/24	0.101120345089616	0	FACETS	0.27	0.19	0.367			1	INDETERMINATE	1	TRUE	0	0.39	0		350	139	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988382	41988382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774833703	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	73	526	1	ENST00000219905.7:c.1174G>A	p.Glu392Lys	p.E392K	ENST00000219905	NM_001164273.1	392	Gaa/Aaa	3/24	0.101120345089616	0	FACETS	0.959	0.851	1			1	INDETERMINATE	1	TRUE	0	0.39	0		527	238	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019410	42019410	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs528009988	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	35	481	0	ENST00000219905.7:c.3463C>T	p.Arg1155Ter	p.R1155*	ENST00000219905	NM_001164273.1	1155	Cga/Tga	10/24	0.101120345089616	0	FACETS	0.433	0.356	0.517			1	INDETERMINATE	1	TRUE	0	0.39	0		481	253	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041074	42041074	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	47	668	1	ENST00000219905.7:c.5452C>T	p.Arg1818Ter	p.R1818*	ENST00000219905	NM_001164273.1	1818	Cga/Tga	16/24	0.101120345089616	0	FACETS	0.397	0.336	0.465			1	INDETERMINATE	1	TRUE	0	0.39	0		669	370	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054485	42054485	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	18	355	0	ENST00000219905.7:c.7669G>T	p.Asp2557Tyr	p.D2557Y	ENST00000219905	NM_001164273.1	2557	Gat/Tat	22/24	0.101120345089616	0	FACETS	0.235	0.177	0.303			1	INDETERMINATE	1	TRUE	0	0.39	0		355	240	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708548	43708548	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	26	608	0	ENST00000382044.4:c.4748G>T	p.Arg1583Ile	p.R1583I	ENST00000382044	NM_001141980.1	1583	aGa/aTa	22/28	0.101120345089616	0	FACETS	0.208	0.164	0.258			1	INDETERMINATE	1	TRUE	0	0.39	0		608	391	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724829	43724829	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	89	584	0	ENST00000382044.4:c.3238G>T	p.Glu1080Ter	p.E1080*	ENST00000382044	NM_001141980.1	1080	Gaa/Taa	17/28	0.101120345089616	0	FACETS	0.937	0.841	1			1	INDETERMINATE	1	TRUE	0	0.39	0		584	297	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007719	45007719	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	15	325	2	ENST00000558401.1:c.166G>T	p.Glu56Ter	p.E56*	ENST00000558401	NM_004048.2	56	Gaa/Taa	2/4	0.101120345089616	0	FACETS	0.264	0.193	0.348			1	INDETERMINATE	1	TRUE	0	0.39	0		327	178	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420174	88420174	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	35	420	0	ENST00000360948.2:c.2512C>A	p.Leu838Ile	p.L838I	ENST00000360948	NM_001012338.2	838	Ctt/Att	19/19	0.101120345089616	0	FACETS	0.327	0.268	0.392			1	INDETERMINATE	1	TRUE	0	0.39	0		420	335	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726694	88726694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766899479	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	121	456	0	ENST00000360948.2:c.350G>A	p.Ser117Asn	p.S117N	ENST00000360948	NM_001012338.2	117	aGc/aAc	4/19	0.101120345089616	0	FACETS	1	0.943	1			1	INDETERMINATE	1	TRUE	0	0.39	0		456	363	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292703	91292703	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746195311	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	11	472	0	ENST00000355112.3:c.205G>A	p.Glu69Lys	p.E69K	ENST00000355112	NM_000057.2	69	Gaa/Aaa	3/22	0.101120345089616	0	FACETS	0.156	0.108	0.217			1	INDETERMINATE	1	TRUE	0	0.39	0		472	220	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293078	91293078	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	52	421	0	ENST00000355112.3:c.580T>G	p.Phe194Val	p.F194V	ENST00000355112	NM_000057.2	194	Ttt/Gtt	3/22	0.101120345089616	0	FACETS	0.861	0.744	0.984			1	INDETERMINATE	1	TRUE	0	0.39	0		421	189	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459919	99459919	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	66	422	0	ENST00000268035.6:c.2015A>T	p.Lys672Met	p.K672M	ENST00000268035	NM_000875.3	672	aAg/aTg	10/21	0.101120345089616	0	FACETS	0.474	0.412	0.54			1	INDETERMINATE	1	TRUE	0	0.39	0		422	436	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465506	99465506	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	141	514	0	ENST00000268035.6:c.2331C>A	p.Phe777Leu	p.F777L	ENST00000268035	NM_000875.3	777	ttC/ttA	11/21	0.101120345089616	0	FACETS	0.872	0.799	0.947			1	INDETERMINATE	1	TRUE	0	0.39	0		514	506	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098664	2098664	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	42	573	0	ENST00000219476.3:c.48G>T	p.Lys16Asn	p.K16N	ENST00000219476	NM_000548.3	16	aaG/aaT	2/42	1	2	FACETS	0.465	0.388	0.55	0.465	0.388	0.55	SUBCLONAL	1	TRUE	1	0.39	2		573	463	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788637	3788637	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	94	394	0	ENST00000262367.5:c.4317C>A	p.Phe1439Leu	p.F1439L	ENST00000262367	NM_004380.2	1439	ttC/ttA	26/31	1	2	FACETS	0.834	0.752	0.919	1	0.985	1	CLONAL	2	TRUE	1	0.39	2		394	289	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807901	3807901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	76	503	2	ENST00000262367.5:c.3518G>A	p.Arg1173Gln	p.R1173Q	ENST00000262367	NM_004380.2	1173	cGa/cAa	18/31	1	2	FACETS	0.939	0.828	1	0.939	0.828	1	CLONAL	1	TRUE	1	0.39	2		505	415	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862740	9862740	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs796052564	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	91	564	0	ENST00000330684.3:c.2563G>A	p.Asp855Asn	p.D855N	ENST00000330684	NM_001134407.1	855	Gac/Aac	12/13	1	2	FACETS	0.836	0.744	0.934	0.836	0.744	0.934	CLONAL	1	TRUE	1	0.39	2		564	558	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916214	9916214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	20	497	0	ENST00000330684.3:c.2075G>A	p.Arg692Lys	p.R692K	ENST00000330684	NM_001134407.1	692	aGa/aAa	10/13	1	2	FACETS	0.38	0.291	0.484	0.38	0.291	0.484	SUBCLONAL	1	TRUE	1	0.39	2		497	270	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923313	9923313	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	43	518	0	ENST00000330684.3:c.1974T>G	p.Phe658Leu	p.F658L	ENST00000330684	NM_001134407.1	658	ttT/ttG	9/13	1	2	FACETS	0.662	0.556	0.779	0.662	0.556	0.779	SUBCLONAL	1	TRUE	1	0.39	2		518	333	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029332	14029332	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866657450	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	26	375	1	ENST00000311895.7:c.1543C>T	p.Arg515Cys	p.R515C	ENST00000311895	NM_005236.2	515	Cgt/Tgt	8/11	1	2	FACETS	0.771	0.616	0.945	0.771	0.616	0.945	CLONAL	1	TRUE	1	0.39	2		376	173	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646423	23646423	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	50	566	0	ENST00000261584.4:c.1444C>A	p.Leu482Ile	p.L482I	ENST00000261584	NM_024675.3	482	Ctc/Atc	4/13	1	2	FACETS	0.809	0.69	0.938	0.809	0.69	0.938	CLONAL	1	TRUE	1	0.39	2		566	317	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646683	23646683	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	12	505	0	ENST00000261584.4:c.1184C>A	p.Ser395Tyr	p.S395Y	ENST00000261584	NM_024675.3	395	tCt/tAt	4/13	1	2	FACETS	0.309	0.217	0.422	0.309	0.217	0.422	SUBCLONAL	1	TRUE	1	0.39	2		505	199	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647199	23647199	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	79	709	0	ENST00000261584.4:c.668T>G	p.Ile223Ser	p.I223S	ENST00000261584	NM_024675.3	223	aTt/aGt	4/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.39	2		709	291	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826550	50826550	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1567458272	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	13	266	0	ENST00000398568.2:c.2275G>T	p.Asp759Tyr	p.D759Y	ENST00000398568	NM_001042412.1	759	Gac/Tac	15/18	1	2	FACETS	0.399	0.285	0.537	0.399	0.285	0.537	SUBCLONAL	1	TRUE	1	0.39	2		266	167	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844172	68844172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	55	654	0	ENST00000261769.5:c.760G>A	p.Asp254Asn	p.D254N	ENST00000261769	NM_004360.3	254	Gat/Aat	6/16	1	2	FACETS	0.624	0.535	0.721	0.624	0.535	0.721	SUBCLONAL	1	TRUE	1	0.39	2		654	452	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827367	72827367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368568803	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	88	788	0	ENST00000268489.5:c.9214G>A	p.Val3072Ile	p.V3072I	ENST00000268489	NM_006885.3	3072	Gta/Ata	9/10	1	2	FACETS	0.789	0.7	0.883	0.789	0.7	0.883	SUBCLONAL	1	TRUE	1	0.39	2		788	572	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828578	72828578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1199271359	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	26	718	0	ENST00000268489.5:c.8003G>A	p.Arg2668Gln	p.R2668Q	ENST00000268489	NM_006885.3	2668	cGa/cAa	9/10	1	2	FACETS	0.282	0.223	0.351	0.282	0.223	0.351	SUBCLONAL	1	TRUE	1	0.39	2		718	472	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829200	72829200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779491169	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	234	658	0	ENST00000268489.5:c.7381G>A	p.Glu2461Lys	p.E2461K	ENST00000268489	NM_006885.3	2461	Gag/Aag	9/10	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.39	2		658	809	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831935	72831935	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	19	755	0	ENST00000268489.5:c.4646T>C	p.Val1549Ala	p.V1549A	ENST00000268489	NM_006885.3	1549	gTc/gCc	9/10	1	2	FACETS	0.274	0.208	0.353	0.274	0.208	0.353	SUBCLONAL	1	TRUE	1	0.39	2		755	355	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81960766	81960766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753762025	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	34	436	0	ENST00000359376.3:c.2497G>A	p.Glu833Lys	p.E833K	ENST00000359376	NM_002661.3	833	Gag/Aag	23/33	1	2	FACETS	0.438	0.358	0.528	0.438	0.358	0.528	SUBCLONAL	1	TRUE	1	0.39	2		436	398	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347939	89347939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	53	808	3	ENST00000301030.4:c.5011G>A	p.Ala1671Thr	p.A1671T	ENST00000301030	NM_001256183.1	1671	Gca/Aca	9/13	1	2	FACETS	0.476	0.406	0.553	0.476	0.406	0.553	SUBCLONAL	1	TRUE	1	0.39	2		811	571	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371709	89371709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1010844836	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	89	651	0	ENST00000301030.4:c.131G>A	p.Arg44His	p.R44H	ENST00000301030	NM_001256183.1	44	cGt/cAt	4/13	1	2	FACETS	0.566	0.501	0.635	0.566	0.501	0.635	SUBCLONAL	1	TRUE	1	0.39	2		651	807	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013707	12013707	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	28	334	0	ENST00000353533.5:c.649A>C	p.Asn217His	p.N217H	ENST00000353533	NM_003010.3	217	Aac/Cac	6/11	0.101120345089616	0	FACETS	0.484	0.39	0.589			1	INDETERMINATE	1	TRUE	0	0.39	0		334	181	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964768	15964768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1189783787	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	36	569	0	ENST00000268712.3:c.5828C>T	p.Ser1943Leu	p.S1943L	ENST00000268712	NM_006311.3	1943	tCg/tTg	37/46	0.101120345089616	0	FACETS	0.284	0.233	0.34			1	INDETERMINATE	1	TRUE	0	0.39	0		569	397	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16052790	16052790	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	73	364	0	ENST00000268712.3:c.884G>T	p.Arg295Ile	p.R295I	ENST00000268712	NM_006311.3	295	aGa/aTa	9/46	0.101120345089616	0	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	0	0.39	0		364	203	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552212	29552212	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	63	389	1	ENST00000356175.3:c.1945G>T	p.Glu649Ter	p.E649*	ENST00000356175	NM_000267.3	649	Gaa/Taa	17/57	0.101120345089616	0	FACETS	0.93	0.816	1			1	INDETERMINATE	1	TRUE	0	0.39	0		390	212	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560143	29560143	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	15	296	0	ENST00000356175.3:c.3620G>T	p.Arg1207Ile	p.R1207I	ENST00000356175	NM_000267.3	1207	aGa/aTa	27/57	0.101120345089616	0	FACETS	0.203	0.148	0.269			1	INDETERMINATE	1	TRUE	0	0.39	0		296	231	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	62	321	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	0.101120345089616	0	FACETS	1	0.888	1			1	INDETERMINATE	1	TRUE	0	0.39	0		321	192	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684041	29684041	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	26	521	0	ENST00000356175.3:c.7739C>A	p.Ser2580Ter	p.S2580*	ENST00000356175	NM_000267.3	2580	tCa/tAa	52/57	0.101120345089616	0	FACETS	0.259	0.205	0.321			1	INDETERMINATE	1	TRUE	0	0.39	0		521	314	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627509	37627509	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs371684674	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	84	572	0	ENST00000447079.4:c.1424C>A	p.Ser475Tyr	p.S475Y	ENST00000447079	NM_015083.1	475	tCt/tAt	2/14	0.101120345089616	0	FACETS	1	0.95	1			1	INDETERMINATE	1	TRUE	0	0.39	0		572	239	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883623	37883623	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1038581447	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	78	795	0	ENST00000269571.5:c.3235G>A	p.Glu1079Lys	p.E1079K	ENST00000269571		1079	Gaa/Aaa	26/27	0.101120345089616	0	FACETS	0.404	0.355	0.456			1	INDETERMINATE	1	TRUE	0	0.39	0		795	604	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40854906	40854906	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	58	490	0	ENST00000428826.2:c.2172C>A	p.Phe724Leu	p.F724L	ENST00000428826		724	ttC/ttA	20/21	0.101120345089616	0	FACETS	0.465	0.401	0.535			1	INDETERMINATE	1	TRUE	0	0.39	0		490	390	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234450	41234450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs4986849	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	45	461	1	ENST00000357654.3:c.4328G>A	p.Arg1443Gln	p.R1443Q	ENST00000357654	NM_007294.3	1443	cGa/cAa	12/23	0.101120345089616	0	FACETS	0.477	0.403	0.558			1	INDETERMINATE	1	TRUE	0	0.39	0		462	295	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256263	41256263	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	11	296	0	ENST00000357654.3:c.317A>C	p.Asn106Thr	p.N106T	ENST00000357654	NM_007294.3	106	aAt/aCt	6/23	0.101120345089616	0	FACETS	0.251	0.174	0.346			1	INDETERMINATE	1	TRUE	0	0.39	0		296	137	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774119	56774119	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1555594699	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	62	427	0	ENST00000337432.4:c.470T>G	p.Phe157Cys	p.F157C	ENST00000337432	NM_058216.2	157	tTt/tGt	3/9	0.101120345089616	0	FACETS	0.735	0.641	0.834			1	INDETERMINATE	1	TRUE	0	0.39	0		427	264	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740632	58740632	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs202221678	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	21	582	0	ENST00000305921.3:c.1537T>G	p.Leu513Val	p.L513V	ENST00000305921	NM_003620.3	513	Ttg/Gtg	6/6	0.101120345089616	0	FACETS	0.23	0.177	0.292			1	INDETERMINATE	1	TRUE	0	0.39	0		582	285	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763253	59763253	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	15	562	0	ENST00000259008.2:c.2849A>C	p.Lys950Thr	p.K950T	ENST00000259008	NM_032043.2	950	aAa/aCa	19/20	0.101120345089616	0	FACETS	0.166	0.121	0.221			1	INDETERMINATE	1	TRUE	0	0.39	0		562	282	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858338	59858338	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	20	396	0	ENST00000259008.2:c.1657C>A	p.Gln553Lys	p.Q553K	ENST00000259008	NM_032043.2	553	Caa/Aaa	12/20	0.101120345089616	0	FACETS	0.344	0.264	0.436			1	INDETERMINATE	1	TRUE	0	0.39	0		396	182	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59878821	59878821	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	21	230	0	ENST00000259008.2:c.933T>G	p.Tyr311Ter	p.Y311*	ENST00000259008	NM_032043.2	311	taT/taG	8/20	0.101120345089616	0	FACETS	0.664	0.521	0.823			1	INDETERMINATE	1	TRUE	0	0.39	0		230	99	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59938814	59938814	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769585673	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	26	354	0	ENST00000259008.2:c.87G>T	p.Met29Ile	p.M29I	ENST00000259008	NM_032043.2	29	atG/atT	2/20	0.101120345089616	0	FACETS	0.47	0.376	0.576			1	INDETERMINATE	1	TRUE	0	0.39	0		354	173	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550298	39550298	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749558522	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	18	210	0	ENST00000262039.4:c.409C>T	p.Arg137Cys	p.R137C	ENST00000262039	NM_002647.2	137	Cgc/Tgc	4/25	1	2	FACETS	0.71	0.54	0.906	0.71	0.54	0.906	CLONAL	1	TRUE	1	0.39	2		210	130	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394784	45394784	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	32	307	0	ENST00000262160.6:c.565G>T	p.Glu189Ter	p.E189*	ENST00000262160	NM_005901.5	189	Gaa/Taa	5/11	1	2	FACETS	0.707	0.578	0.852	0.707	0.578	0.852	SUBCLONAL	1	TRUE	1	0.39	2		307	232	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56381317	56381317	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	26	145	0	ENST00000348428.3:c.961G>T	p.Glu321Ter	p.E321*	ENST00000348428	NM_006785.3	321	Gaa/Taa	8/17	1	2	FACETS	0.784	0.639	0.941	1	0.944	1	CLONAL	2	TRUE	1	0.39	2		145	85	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231599	5231599	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	52	257	0	ENST00000357368.4:c.1877A>C	p.Lys626Thr	p.K626T	ENST00000357368	NM_002850.3	626	aAa/aCa	14/38	0.101120345089616	3	FACETS	0.926	0.792	1	0.463	0.396	0.536	INDETERMINATE	1	TRUE	1	0.39	3		257	344	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291465	10291465	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	45	580	0	ENST00000340748.4:c.214G>T	p.Glu72Ter	p.E72*	ENST00000340748		72	Gaa/Taa	3/40	0.101120345089616	3	FACETS	0.846	0.714	0.99	0.423	0.357	0.495	INDETERMINATE	1	TRUE	1	0.39	3		580	326	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15365013	15365013	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1453756538	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	194	592	1	ENST00000263377.2:c.2108C>T	p.Ser703Leu	p.S703L	ENST00000263377	NM_058243.2	703	tCg/tTg	11/20	0.101120345089616	3	FACETS	0.967	0.899	1	0.967	0.899	1	INDETERMINATE	2	TRUE	1	0.39	3		593	615	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945804	17945804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750102955	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	36	716	0	ENST00000458235.1:c.2056G>A	p.Asp686Asn	p.D686N	ENST00000458235	NM_000215.3	686	Gac/Aac	16/24	0.101120345089616	3	FACETS	0.343	0.281	0.412	0.171	0.14	0.206	INDETERMINATE	1	TRUE	1	0.39	3		716	644	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976416	18976416	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	290	936	0	ENST00000262803.5:c.3066G>T	p.Lys1022Asn	p.K1022N	ENST00000262803	NM_002911.3	1022	aaG/aaT	22/24	0.101120345089616	3	FACETS	1	0.971	1	1	0.971	1	INDETERMINATE	2	TRUE	1	0.39	3		936	851	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221273	36221273	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	86	772	0	ENST00000222270.7:c.5107C>A	p.Leu1703Ile	p.L1703I	ENST00000222270	NM_014727.1	1703	Ctc/Atc	24/37	0.101120345089616	3	FACETS	0.716	0.633	0.805	0.358	0.316	0.403	INDETERMINATE	1	TRUE	1	0.39	3		772	736	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754568	42754568	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	73	808	0	ENST00000222329.4:c.172A>G	p.Lys58Glu	p.K58E	ENST00000222329	NM_006494.2	58	Aaa/Gaa	2/4	0.101120345089616	3	FACETS	0.65	0.568	0.739	0.325	0.284	0.37	INDETERMINATE	1	TRUE	1	0.39	3		808	688	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085677	16085677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779959007	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	47	663	0	ENST00000281043.3:c.853C>T	p.Arg285Trp	p.R285W	ENST00000281043	NM_005378.4	285	Cgg/Tgg	3/3	1	2	FACETS	0.384	0.323	0.451	0.384	0.323	0.451	SUBCLONAL	1	TRUE	1	0.39	2		663	628	SUCCESS
ALK	238	MSKCC	GRCh37	2	29430136	29430136	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs74716434	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	23	409	0	ENST00000389048.3:c.3839C>T	p.Ala1280Val	p.A1280V	ENST00000389048	NM_004304.4	1280	gCg/gTg	26/29	1	2	FACETS	0.403	0.314	0.505	0.403	0.314	0.505	SUBCLONAL	1	TRUE	1	0.39	2		409	293	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498090	29498090	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	88	530	0	ENST00000389048.3:c.1916G>A	p.Ser639Asn	p.S639N	ENST00000389048	NM_004304.4	639	aGc/aAc	11/29	1	2	FACETS	0.914	0.823	1	1	0.986	1	CLONAL	2	TRUE	1	0.39	2		530	247	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551311	29551311	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	58	657	0	ENST00000389048.3:c.1319C>A	p.Ser440Tyr	p.S440Y	ENST00000389048	NM_004304.4	440	tCc/tAc	6/29	1	2	FACETS	0.527	0.453	0.608	0.527	0.453	0.608	SUBCLONAL	1	TRUE	1	0.39	2		657	564	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606679	29606679	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs865931787	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	86	544	0	ENST00000389048.3:c.1201C>T	p.Arg401Ter	p.R401*	ENST00000389048	NM_004304.4	401	Cga/Tga	5/29	1	2	FACETS	0.942	0.837	1	0.942	0.837	1	CLONAL	1	TRUE	1	0.39	2		544	468	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224414	39224414	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	64	460	0	ENST00000402219.2:c.2944C>T	p.Arg982Ter	p.R982*	ENST00000402219	NM_005633.3	982	Cga/Tga	18/23	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.39	2		460	253	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026015	48026015	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765237563	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	16	354	0	ENST00000234420.5:c.893G>A	p.Arg298Gln	p.R298Q	ENST00000234420	NM_000179.2	298	cGa/cAa	4/10	1	2	FACETS	0.326	0.24	0.427	0.326	0.24	0.427	SUBCLONAL	1	TRUE	1	0.39	2		354	252	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026290	48026290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147737737	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	39	508	1	ENST00000234420.5:c.1168G>A	p.Asp390Asn	p.D390N	ENST00000234420	NM_000179.2	390	Gat/Aat	4/10	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.39	2		509	159	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	15	536	0	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	0.319	0.233	0.422	0.319	0.233	0.422	SUBCLONAL	1	TRUE	1	0.39	2		536	241	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724120	61724120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781425578	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	21	288	0	ENST00000401558.2:c.782G>A	p.Arg261Gln	p.R261Q	ENST00000401558	NM_003400.3	261	cGa/cAa	10/25	1	2	FACETS	0.513	0.396	0.647	0.513	0.396	0.647	SUBCLONAL	1	TRUE	1	0.39	2		288	210	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61761022	61761022	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	22	266	0	ENST00000401558.2:c.11T>G	p.Ile4Ser	p.I4S	ENST00000401558	NM_003400.3	4	aTt/aGt	2/25	1	2	FACETS	0.762	0.597	0.95	0.762	0.597	0.95	CLONAL	1	TRUE	1	0.39	2		266	148	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046440	128046440	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	14	297	0	ENST00000285398.2:c.823G>A	p.Glu275Lys	p.E275K	ENST00000285398	NM_000122.1	275	Gaa/Aaa	7/15	1	2	FACETS	0.488	0.355	0.648	0.488	0.355	0.648	SUBCLONAL	1	TRUE	1	0.39	2		297	147	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622630	158622630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	46	420	0	ENST00000263640.3:c.869C>T	p.Ser290Leu	p.S290L	ENST00000263640	NM_001105.4	290	tCg/tTg	8/11	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.39	2		420	212	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098957	178098957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	21	300	0	ENST00000397062.3:c.88C>T	p.Leu30Phe	p.L30F	ENST00000397062	NM_006164.4	30	Ctt/Ttt	2/5	1	2	FACETS	0.769	0.599	0.963	0.769	0.599	0.963	CLONAL	1	TRUE	1	0.39	2		300	140	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288690	198288690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	29	377	0	ENST00000335508.6:c.37G>A	p.Ala13Thr	p.A13T	ENST00000335508	NM_012433.2	13	Gca/Aca	2/25	1	2	FACETS	0.676	0.546	0.822	0.676	0.546	0.822	SUBCLONAL	1	TRUE	1	0.39	2		377	220	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131364	202131364	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	16	454	1	ENST00000358485.4:c.332G>T	p.Arg111Ile	p.R111I	ENST00000358485	NM_001080125.1	111	aGa/aTa	2/9	1	2	FACETS	0.332	0.245	0.436	0.332	0.245	0.436	SUBCLONAL	1	TRUE	1	0.39	2		455	247	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131417	202131417	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	35	491	0	ENST00000358485.4:c.385A>C	p.Asn129His	p.N129H	ENST00000358485	NM_001080125.1	129	Aat/Cat	2/9	1	2	FACETS	0.721	0.594	0.861	0.721	0.594	0.861	SUBCLONAL	1	TRUE	1	0.39	2		491	249	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137360	202137360	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	24	314	0	ENST00000358485.4:c.589-1G>T		p.X197_splice	ENST00000358485	NM_001080125.1	197			1	2	FACETS	0.932	0.741	1	0.932	0.741	1	CLONAL	1	TRUE	1	0.39	2		314	132	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149974	202149974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301592633	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	40	630	0	ENST00000358485.4:c.1415G>A	p.Arg472Gln	p.R472Q	ENST00000358485	NM_001080125.1	472	cGa/cAa	8/9	1	2	FACETS	0.419	0.347	0.498	0.419	0.347	0.498	SUBCLONAL	1	TRUE	1	0.39	2		630	490	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736158	204736158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs963824682	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	35	344	0	ENST00000302823.3:c.515C>T	p.Ser172Leu	p.S172L	ENST00000302823	NM_005214.4	172	tCg/tTg	3/4	1	2	FACETS	0.653	0.537	0.781	0.653	0.537	0.781	SUBCLONAL	1	TRUE	1	0.39	2		344	275	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530096	212530096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	34	278	2	ENST00000342788.4:c.1823C>T	p.Ala608Val	p.A608V	ENST00000342788	NM_005235.2	608	gCt/gTt	15/28	1	2	FACETS	0.748	0.615	0.896	0.748	0.615	0.896	SUBCLONAL	1	TRUE	1	0.39	2		280	233	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793223	242793223	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762704059	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	107	758	0	ENST00000334409.5:c.854C>T	p.Ser285Phe	p.S285F	ENST00000334409	NM_005018.2	285	tCt/tTt	5/5	1	2	FACETS	0.716	0.642	0.795	0.716	0.642	0.795	SUBCLONAL	1	TRUE	1	0.39	2		758	766	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31020765	31020765	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	23	282	0	ENST00000375687.4:c.1062C>A	p.Phe354Leu	p.F354L	ENST00000375687	NM_015338.5	354	ttC/ttA	11/13	0.101120345089616	0	FACETS	0.402	0.315	0.5			1	INDETERMINATE	1	TRUE	0	0.39	0		282	179	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389107	31389107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749860839	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	100	464	0	ENST00000328111.2:c.2020G>A	p.Glu674Lys	p.E674K	ENST00000328111	NM_006892.3	674	Gaa/Aaa	19/23	0.101120345089616	0	FACETS	0.819	0.737	0.904			1	INDETERMINATE	1	TRUE	0	0.39	0		464	382	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730904	40730904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770182876	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	162	603	0	ENST00000373198.4:c.3631G>A	p.Glu1211Lys	p.E1211K	ENST00000373198	NM_133170.3	1211	Gag/Aag	27/32	0.101120345089616	0	FACETS	0.862	0.795	0.931			1	INDETERMINATE	1	TRUE	0	0.39	0		603	588	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281770	46281770	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	45	606	0	ENST00000371998.3:c.4217A>G	p.Asn1406Ser	p.N1406S	ENST00000371998		1406	aAc/aGc	22/23	0.101120345089616	0	FACETS	0.359	0.302	0.422			1	INDETERMINATE	1	TRUE	0	0.39	0		606	392	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231773	36231773	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1569061762	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	19	553	2	ENST00000300305.3:c.611G>A	p.Arg204Gln	p.R204Q	ENST00000300305		204	cGa/cAa	5/8	0.101120345089616	3	FACETS	0.172	0.13	0.223	0.086	0.065	0.112	INDETERMINATE	1	TRUE	1	0.39	3		555	676	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121349	29121349	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	21	530	0	ENST00000328354.6:c.326T>C	p.Val109Ala	p.V109A	ENST00000328354	NM_007194.3	109	gTg/gCg	3/15	0.101120345089616	0	FACETS	0.239	0.184	0.303			1	INDETERMINATE	1	TRUE	0	0.39	0		530	275	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41521867	41521867	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	28	484	0	ENST00000263253.7:c.730-1G>A		p.X244_splice	ENST00000263253	NM_001429.3	244			0.101120345089616	0	FACETS	0.456	0.367	0.556			1	INDETERMINATE	1	TRUE	0	0.39	0		484	192	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41562619	41562619	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	13	395	0	ENST00000263253.7:c.3823T>G	p.Cys1275Gly	p.C1275G	ENST00000263253	NM_001429.3	1275	Tgt/Ggt	23/31	0.101120345089616	0	FACETS	0.177	0.126	0.239			1	INDETERMINATE	1	TRUE	0	0.39	0		395	230	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434252	12434252	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	11	322	0	ENST00000287820.6:c.619+1G>A		p.X207_splice	ENST00000287820	NM_015869.4	207			1	2	FACETS	0.386	0.268	0.533	0.386	0.268	0.533	SUBCLONAL	1	TRUE	1	0.39	2		322	146	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691867	30691867	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	30	314	0	ENST00000295754.5:c.369G>T	p.Met123Ile	p.M123I	ENST00000295754	NM_003242.5	123	atG/atT	3/7	1	2	FACETS	0.702	0.57	0.851	0.702	0.57	0.851	SUBCLONAL	1	TRUE	1	0.39	2		314	219	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090086	37090086	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63751310	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	72	459	0	ENST00000231790.2:c.1975C>T	p.Arg659Ter	p.R659*	ENST00000231790	NM_000249.3	659	Cga/Tga	17/19	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.39	2		459	282	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098930	47098930	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	120	585	0	ENST00000409792.3:c.6344A>C	p.Lys2115Thr	p.K2115T	ENST00000409792	NM_014159.6	2115	aAa/aCa	15/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.39	2		585	428	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103716	47103716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs981018402	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	88	404	0	ENST00000409792.3:c.6230G>A	p.Arg2077Gln	p.R2077Q	ENST00000409792	NM_014159.6	2077	cGa/cAa	14/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.39	2		404	323	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158238	47158238	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	55	307	0	ENST00000409792.3:c.4461G>T	p.Lys1487Asn	p.K1487N	ENST00000409792	NM_014159.6	1487	aaG/aaT	4/21	1	2	FACETS	0.993	0.871	1	1	0.979	1	CLONAL	2	TRUE	1	0.39	2		307	142	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162161	47162161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147170912	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	13	417	1	ENST00000409792.3:c.3965G>A	p.Arg1322Gln	p.R1322Q	ENST00000409792	NM_014159.6	1322	cGa/cAa	3/21	1	2	FACETS	0.366	0.262	0.493	0.366	0.262	0.493	SUBCLONAL	1	TRUE	1	0.39	2		418	182	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162311	47162311	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	17	370	0	ENST00000409792.3:c.3815A>C	p.Gln1272Pro	p.Q1272P	ENST00000409792	NM_014159.6	1272	cAg/cCg	3/21	1	2	FACETS	0.459	0.344	0.595	0.459	0.344	0.595	SUBCLONAL	1	TRUE	1	0.39	2		370	190	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924860	49924860	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	63	743	0	ENST00000296474.3:c.4083G>T	p.Met1361Ile	p.M1361I	ENST00000296474	NM_002447.2	1361	atG/atT	20/20	1	2	FACETS	0.46	0.397	0.528	0.46	0.397	0.528	SUBCLONAL	1	TRUE	1	0.39	2		743	703	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940235	49940235	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	92	739	0	ENST00000296474.3:c.808A>G	p.Thr270Ala	p.T270A	ENST00000296474	NM_002447.2	270	Aca/Gca	1/20	1	2	FACETS	0.653	0.58	0.731	0.653	0.58	0.731	SUBCLONAL	1	TRUE	1	0.39	2		739	722	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678780	52678780	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	27	253	1	ENST00000394830.3:c.839T>G	p.Phe280Cys	p.F280C	ENST00000394830	NM_018313.4	280	tTt/tGt	9/30	1	2	FACETS	0.814	0.654	0.994	0.814	0.654	0.994	CLONAL	1	TRUE	1	0.39	2		254	170	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702632	52702632	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779102269	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	13	331	0	ENST00000394830.3:c.266C>A	p.Ser89Tyr	p.S89Y	ENST00000394830	NM_018313.4	89	tCt/tAt	4/30	1	2	FACETS	0.351	0.25	0.473	0.351	0.25	0.473	SUBCLONAL	1	TRUE	1	0.39	2		331	190	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72866499	72866499	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs748068509	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	19	275	0	ENST00000325599.8:c.764A>C	p.Lys255Thr	p.K255T	ENST00000325599	NM_018130.2	255	aAa/aCa	7/11	1	2	FACETS	0.613	0.468	0.78	0.613	0.468	0.78	SUBCLONAL	1	TRUE	1	0.39	2		275	159	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89444986	89444986	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs764527197	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	46	329	0	ENST00000336596.2:c.1307-1G>A		p.X436_splice	ENST00000336596	NM_005233.5	436			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.39	2		329	170	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480508	89480508	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	14	257	0	ENST00000336596.2:c.2345G>T	p.Arg782Ile	p.R782I	ENST00000336596	NM_005233.5	782	aGa/aTa	13/17	1	2	FACETS	0.42	0.304	0.559	0.42	0.304	0.559	SUBCLONAL	1	TRUE	1	0.39	2		257	171	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498444	89498444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	22	289	0	ENST00000336596.2:c.2416G>A	p.Asp806Asn	p.D806N	ENST00000336596	NM_005233.5	806	Gat/Aat	14/17	1	2	FACETS	0.57	0.444	0.714	0.57	0.444	0.714	SUBCLONAL	1	TRUE	1	0.39	2		289	198	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670461	134670461	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	27	554	0	ENST00000398015.3:c.372G>T	p.Lys124Asn	p.K124N	ENST00000398015	NM_004441.4	124	aaG/aaT	3/16	1	2	FACETS	0.398	0.317	0.491	0.398	0.317	0.491	SUBCLONAL	1	TRUE	1	0.39	2		554	348	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670668	134670668	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	98	615	0	ENST00000398015.3:c.579C>A	p.Phe193Leu	p.F193L	ENST00000398015	NM_004441.4	193	ttC/ttA	3/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.39	2		615	348	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825430	134825430	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	49	484	0	ENST00000398015.3:c.946G>T	p.Glu316Ter	p.E316*	ENST00000398015	NM_004441.4	316	Gaa/Taa	4/16	1	2	FACETS	0.535	0.453	0.624	0.535	0.453	0.624	SUBCLONAL	1	TRUE	1	0.39	2		484	470	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664718	138664718	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	35	165	0	ENST00000330315.3:c.847G>A	p.Ala283Thr	p.A283T	ENST00000330315	NM_023067.3	283	Gca/Aca	1/1	1	2	FACETS	0.613	0.504	0.734	0.613	0.504	0.734	SUBCLONAL	1	TRUE	1	0.39	2		165	293	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242845	142242845	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	54	378	0	ENST00000350721.4:c.4142T>G	p.Phe1381Cys	p.F1381C	ENST00000350721	NM_001184.3	1381	tTt/tGt	22/47	1	2	FACETS	0.761	0.661	0.866	1	0.97	1	SUBCLONAL	2	TRUE	1	0.39	2		378	182	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242899	142242899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750252420	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	77	450	0	ENST00000350721.4:c.4088C>T	p.Ala1363Val	p.A1363V	ENST00000350721	NM_001184.3	1363	gCg/gTg	22/47	1	2	FACETS	0.768	0.683	0.857	1	0.979	1	SUBCLONAL	2	TRUE	1	0.39	2		450	257	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921533	178921533	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1428379257	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	29	358	0	ENST00000263967.3:c.1015C>A	p.Leu339Ile	p.L339I	ENST00000263967	NM_006218.2	339	Ctt/Att	5/21	1	2	FACETS	0.991	0.806	1	0.991	0.806	1	CLONAL	1	TRUE	1	0.39	2		358	150	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937019	178937019	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	14	416	0	ENST00000263967.3:c.1700A>C	p.Lys567Thr	p.K567T	ENST00000263967	NM_006218.2	567	aAa/aCa	11/21	1	2	FACETS	0.303	0.219	0.405	0.303	0.219	0.405	SUBCLONAL	1	TRUE	1	0.39	2		416	237	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947872	178947872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	14	320	0	ENST00000263967.3:c.2747G>A	p.Arg916His	p.R916H	ENST00000263967	NM_006218.2	916	cGt/cAt	19/21	1	2	FACETS	0.397	0.287	0.528	0.397	0.287	0.528	SUBCLONAL	1	TRUE	1	0.39	2		320	181	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	22	389	0	ENST00000263967.3:c.3012G>T	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atT	21/21	1	2	FACETS	0.597	0.465	0.748	0.597	0.465	0.748	SUBCLONAL	1	TRUE	1	0.39	2		389	189	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182681824	182681824	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	25	392	0	ENST00000292782.4:c.234G>T	p.Glu78Asp	p.E78D	ENST00000292782	NM_020640.2	78	gaG/gaT	3/7	1	2	FACETS	0.619	0.491	0.765	0.619	0.491	0.765	SUBCLONAL	1	TRUE	1	0.39	2		392	207	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506913	186506913	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	11	202	0	ENST00000323963.5:c.1080-1G>T		p.X360_splice	ENST00000323963		360			1	2	FACETS	0.392	0.271	0.54	0.392	0.271	0.54	SUBCLONAL	1	TRUE	1	0.39	2		202	144	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584500	189584500	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	70	368	0	ENST00000264731.3:c.796C>T	p.Arg266Ter	p.R266*	ENST00000264731	NM_003722.4	266	Cga/Tga	6/14	1	2	FACETS	0.847	0.751	0.946	1	0.98	1	CLONAL	2	TRUE	1	0.39	2		368	212	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801476	1801476	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs200300532	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	79	859	0	ENST00000260795.2:c.382G>A	p.Ala128Thr	p.A128T	ENST00000260795		128	Gct/Act	3/17	0.101120345089616	3	FACETS	0.795	0.7	0.897	0.397	0.35	0.449	INDETERMINATE	1	TRUE	1	0.39	3		859	609	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750610	41750610	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	51	496	1	ENST00000226382.2:c.18T>G	p.Tyr6Ter	p.Y6*	ENST00000226382	NM_003924.3	6	taT/taG	1/3	0.101120345089616	3	FACETS	1	0.943	1	0.603	0.517	0.696	INDETERMINATE	1	TRUE	1	0.39	3		497	259	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146592	55146592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555347387	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	24	429	0	ENST00000257290.5:c.2266G>A	p.Asp756Asn	p.D756N	ENST00000257290	NM_006206.4	756	Gac/Aac	16/23	0.101120345089616	3	FACETS	0.799	0.631	0.99	0.4	0.315	0.495	INDETERMINATE	1	TRUE	1	0.39	3		429	184	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151567	55151567	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	16	404	0	ENST00000257290.5:c.2353G>T	p.Asp785Tyr	p.D785Y	ENST00000257290	NM_006206.4	785	Gat/Tat	17/23	0.101120345089616	3	FACETS	0.428	0.317	0.561	0.214	0.158	0.281	INDETERMINATE	1	TRUE	1	0.39	3		404	229	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55987288	55987288	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	20	375	0	ENST00000263923.4:c.137A>C	p.Asn46Thr	p.N46T	ENST00000263923	NM_002253.2	46	aAt/aCt	2/30	0.101120345089616	3	FACETS	0.607	0.466	0.77	0.303	0.233	0.385	INDETERMINATE	1	TRUE	1	0.39	3		375	202	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467623	66467623	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	25	346	1	ENST00000273854.3:c.646G>T	p.Asp216Tyr	p.D216Y	ENST00000273854	NM_004439.5	216	Gat/Tat	3/18	0.101120345089616	3	FACETS	0.811	0.643	1	0.405	0.321	0.5	INDETERMINATE	1	TRUE	1	0.39	3		347	189	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84390227	84390227	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	12	519	0	ENST00000321945.7:c.554C>T	p.Ser185Phe	p.S185F	ENST00000321945	NM_139076.2	185	tCc/tTc	6/9	0.101120345089616	3	FACETS	0.306	0.215	0.419	0.153	0.107	0.21	INDETERMINATE	1	TRUE	1	0.39	3		519	240	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155526	106155526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749618735	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	43	401	0	ENST00000380013.4:c.427G>A	p.Asp143Asn	p.D143N	ENST00000380013	NM_001127208.2	143	Gat/Aat	3/11	0.101120345089616	3	FACETS	0.771	0.655	0.895	0.771	0.655	0.895	INDETERMINATE	2	TRUE	1	0.39	3		401	171	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156199	106156199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	16	290	0	ENST00000380013.4:c.1100C>T	p.Ser367Phe	p.S367F	ENST00000380013	NM_001127208.2	367	tCt/tTt	3/11	0.101120345089616	3	FACETS	0.633	0.47	0.824	0.316	0.235	0.412	INDETERMINATE	1	TRUE	1	0.39	3		290	155	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158454	106158454	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1182812722	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	32	264	0	ENST00000380013.4:c.3355T>G	p.Leu1119Val	p.L1119V	ENST00000380013	NM_001127208.2	1119	Tta/Gta	3/11	0.101120345089616	3	FACETS	1	0.88	1	1	0.88	1	INDETERMINATE	2	TRUE	1	0.39	3		264	92	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114261	143114261	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866217456	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	50	290	0	ENST00000262992.4:c.1160G>T	p.Arg387Ile	p.R387I	ENST00000262992	NM_001101669.1	387	aGa/aTa	13/24	0.101120345089616	3	FACETS	0.88	0.76	1	0.88	0.76	1	INDETERMINATE	2	TRUE	1	0.39	3		290	174	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332586	153332586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768666009	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	19	337	0	ENST00000281708.4:c.370G>A	p.Asp124Asn	p.D124N	ENST00000281708	NM_033632.3	124	Gat/Aat	2/12	0.101120345089616	3	FACETS	0.689	0.526	0.878	0.344	0.263	0.439	INDETERMINATE	1	TRUE	1	0.39	3		337	169	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509853	187509853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748762429	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	89	293	0	ENST00000441802.2:c.13660G>A	p.Glu4554Lys	p.E4554K	ENST00000441802	NM_005245.3	4554	Gaa/Aaa	27/27	0.101120345089616	3	FACETS	1	0.979	1	0.725	0.648	0.807	INDETERMINATE	1	TRUE	1	0.39	3		293	376	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522476	187522476	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	25	554	0	ENST00000441802.2:c.11587T>C	p.Ser3863Pro	p.S3863P	ENST00000441802	NM_005245.3	3863	Tcc/Ccc	21/27	0.101120345089616	3	FACETS	0.488	0.385	0.606	0.244	0.192	0.303	INDETERMINATE	1	TRUE	1	0.39	3		554	314	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539727	187539727	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	13	363	0	ENST00000441802.2:c.8013C>A	p.Phe2671Leu	p.F2671L	ENST00000441802	NM_005245.3	2671	ttC/ttA	10/27	0.101120345089616	3	FACETS	0.424	0.303	0.571	0.212	0.151	0.286	INDETERMINATE	1	TRUE	1	0.39	3		363	188	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539951	187539951	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs777631605	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	73	461	0	ENST00000441802.2:c.7789C>T	p.Arg2597Ter	p.R2597*	ENST00000441802	NM_005245.3	2597	Cga/Tga	10/27	0.101120345089616	3	FACETS	0.94	0.834	1	0.94	0.834	1	INDETERMINATE	2	TRUE	1	0.39	3		461	238	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541096	187541096	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	28	410	0	ENST00000441802.2:c.6644T>C	p.Phe2215Ser	p.F2215S	ENST00000441802	NM_005245.3	2215	tTc/tCc	10/27	0.101120345089616	3	FACETS	0.515	0.412	0.633	0.258	0.206	0.317	INDETERMINATE	1	TRUE	1	0.39	3		410	333	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628927	187628927	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	38	637	0	ENST00000441802.2:c.2055G>T	p.Glu685Asp	p.E685D	ENST00000441802	NM_005245.3	685	gaG/gaT	2/27	0.101120345089616	3	FACETS	0.771	0.64	0.916	0.386	0.32	0.458	INDETERMINATE	1	TRUE	1	0.39	3		637	302	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31406984	31406984	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	30	580	0	ENST00000344624.3:c.3923G>T	p.Arg1308Ile	p.R1308I	ENST00000344624		1308	aGa/aTa	31/33	1	2	FACETS	0.436	0.351	0.532	0.436	0.351	0.532	SUBCLONAL	1	TRUE	1	0.39	2		580	353	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508814	31508814	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	155	622	0	ENST00000344624.3:c.1501G>A	p.Val501Ile	p.V501I	ENST00000344624		501	Gtt/Att	7/33	1	2	FACETS	0.773	0.713	0.836	1	0.989	1	SUBCLONAL	2	TRUE	1	0.39	2		622	514	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515591	31515591	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	38	336	0	ENST00000344624.3:c.1028C>A	p.Ser343Tyr	p.S343Y	ENST00000344624		343	tCt/tAt	4/33	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.39	2		336	133	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35860991	35860991	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	18	359	0	ENST00000303115.3:c.120C>A	p.Phe40Leu	p.F40L	ENST00000303115	NM_002185.3	40	ttC/ttA	2/8	1	2	FACETS	0.476	0.359	0.612	0.476	0.359	0.612	SUBCLONAL	1	TRUE	1	0.39	2		359	194	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944612	38944612	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs777123686	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	13	360	0	ENST00000357387.3:c.4849C>A	p.Leu1617Ile	p.L1617I	ENST00000357387	NM_152756.3	1617	Cta/Ata	36/38	1	2	FACETS	0.364	0.26	0.491	0.364	0.26	0.491	SUBCLONAL	1	TRUE	1	0.39	2		360	183	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950075	38950075	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs750741188	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	34	467	0	ENST00000357387.3:c.3875C>A	p.Ser1292Tyr	p.S1292Y	ENST00000357387	NM_152756.3	1292	tCt/tAt	31/38	1	2	FACETS	0.778	0.641	0.931	0.778	0.641	0.931	CLONAL	1	TRUE	1	0.39	2		467	224	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950648	38950648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776074870	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	10	351	0	ENST00000357387.3:c.3302C>T	p.Ser1101Leu	p.S1101L	ENST00000357387	NM_152756.3	1101	tCg/tTg	31/38	1	2	FACETS	0.335	0.227	0.47	0.335	0.227	0.47	SUBCLONAL	1	TRUE	1	0.39	2		351	153	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168741	56168741	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775802110	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	35	412	0	ENST00000399503.3:c.1595G>A	p.Arg532Gln	p.R532Q	ENST00000399503	NM_005921.1	532	cGa/cAa	9/20	1	2	FACETS	0.503	0.413	0.604	0.503	0.413	0.604	SUBCLONAL	1	TRUE	1	0.39	2		412	357	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177501	56177501	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	14	328	0	ENST00000399503.3:c.2474G>T	p.Arg825Ile	p.R825I	ENST00000399503	NM_005921.1	825	aGa/aTa	14/20	1	2	FACETS	0.357	0.258	0.476	0.357	0.258	0.476	SUBCLONAL	1	TRUE	1	0.39	2		328	201	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589609	67589609	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	17	242	1	ENST00000274335.5:c.1372G>T	p.Glu458Ter	p.E458*	ENST00000274335		458	Gaa/Taa	10/15	1	2	FACETS	0.535	0.401	0.691	0.535	0.401	0.691	SUBCLONAL	1	TRUE	1	0.39	2		243	163	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589618	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519838	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	13	240	0	ENST00000274335.5:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000274335		461	Cga/Tga	10/15	1	2	FACETS	0.394	0.282	0.531	0.394	0.282	0.531	SUBCLONAL	1	TRUE	1	0.39	2		240	169	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592099	67592099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	38	258	0	ENST00000274335.5:c.1915C>T	p.Arg639Ter	p.R639*	ENST00000274335		639	Cga/Tga	14/15	1	2	FACETS	0.631	0.523	0.75	0.631	0.523	0.75	SUBCLONAL	1	TRUE	1	0.39	2		258	309	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064749	80064749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148896355	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	36	399	1	ENST00000265081.6:c.2180G>A	p.Arg727Gln	p.R727Q	ENST00000265081	NM_002439.4	727	cGa/cAa	15/24	1	2	FACETS	0.705	0.582	0.84	0.705	0.582	0.84	SUBCLONAL	1	TRUE	1	0.39	2		400	262	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649005	86649005	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	50	284	0	ENST00000274376.6:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000274376	NM_002890.2	429	Gaa/Taa	9/25	1	2	FACETS	0.916	0.796	1	1	0.975	1	CLONAL	2	TRUE	1	0.39	2		284	140	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674299	86674299	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	10	301	0	ENST00000274376.6:c.2431C>A	p.His811Asn	p.H811N	ENST00000274376	NM_002890.2	811	Cat/Aat	18/25	1	2	FACETS	0.295	0.2	0.414	0.295	0.2	0.414	SUBCLONAL	1	TRUE	1	0.39	2		301	174	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681163	86681163	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	47	274	0	ENST00000274376.6:c.2804A>G	p.Lys935Arg	p.K935R	ENST00000274376	NM_002890.2	935	aAa/aGa	22/25	1	2	FACETS	0.843	0.727	0.964	1	0.971	1	CLONAL	2	TRUE	1	0.39	2		274	143	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86686657	86686657	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	10	251	0	ENST00000274376.6:c.3101A>G	p.Gln1034Arg	p.Q1034R	ENST00000274376	NM_002890.2	1034	cAa/cGa	25/25	1	2	FACETS	0.29	0.196	0.407	0.29	0.196	0.407	SUBCLONAL	1	TRUE	1	0.39	2		251	177	SUCCESS
APC	324	MSKCC	GRCh37	5	112173918	112173918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373428732	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	23	367	0	ENST00000257430.4:c.2627G>A	p.Arg876Gln	p.R876Q	ENST00000257430	NM_000038.5	876	cGa/cAa	16/16	1	2	FACETS	0.485	0.379	0.607	0.485	0.379	0.607	SUBCLONAL	1	TRUE	1	0.39	2		367	243	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	27	201	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	1	2	FACETS	0.805	0.659	0.961	1	0.948	1	CLONAL	2	TRUE	1	0.39	2		201	86	SUCCESS
APC	324	MSKCC	GRCh37	5	112178031	112178031	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1320484906	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	21	407	0	ENST00000257430.4:c.6740C>A	p.Ser2247Tyr	p.S2247Y	ENST00000257430	NM_000038.5	2247	tCt/tAt	16/16	1	2	FACETS	0.458	0.354	0.579	0.458	0.354	0.579	SUBCLONAL	1	TRUE	1	0.39	2		407	235	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131893065	131893065	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	22	317	0	ENST00000265335.6:c.49A>T	p.Ile17Leu	p.I17L	ENST00000265335		17	Ata/Tta	1/25	1	2	FACETS	0.446	0.346	0.561	0.446	0.346	0.561	SUBCLONAL	1	TRUE	1	0.39	2		317	253	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931279	131931279	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	18	331	0	ENST00000265335.6:c.1984G>A	p.Ala662Thr	p.A662T	ENST00000265335		662	Gcc/Acc	13/25	1	2	FACETS	0.442	0.333	0.569	0.442	0.333	0.569	SUBCLONAL	1	TRUE	1	0.39	2		331	209	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953803	131953803	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs769003601	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	14	309	0	ENST00000265335.6:c.3206G>T	p.Arg1069Ile	p.R1069I	ENST00000265335		1069	aGa/aTa	21/25	1	2	FACETS	0.499	0.362	0.661	0.499	0.362	0.661	SUBCLONAL	1	TRUE	1	0.39	2		309	144	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953874	131953874	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121912628	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	23	374	0	ENST00000265335.6:c.3277C>T	p.Arg1093Ter	p.R1093*	ENST00000265335		1093	Cga/Tga	21/25	1	2	FACETS	0.549	0.43	0.685	0.549	0.43	0.685	SUBCLONAL	1	TRUE	1	0.39	2		374	215	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503887	149503887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758280032	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	49	668	0	ENST00000261799.4:c.1949C>T	p.Ser650Leu	p.S650L	ENST00000261799	NM_002609.3	650	tCg/tTg	14/23	1	2	FACETS	0.464	0.393	0.543	0.464	0.393	0.543	SUBCLONAL	1	TRUE	1	0.39	2		668	541	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504328	149504328	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	70	675	0	ENST00000261799.4:c.1874C>A	p.Ser625Tyr	p.S625Y	ENST00000261799	NM_002609.3	625	tCt/tAt	13/23	1	2	FACETS	0.568	0.495	0.647	0.568	0.495	0.647	SUBCLONAL	1	TRUE	1	0.39	2		675	632	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518103	176518103	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs866476239	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	143	567	0	ENST00000292408.4:c.601C>T	p.Arg201Trp	p.R201W	ENST00000292408	NM_213647.1	201	Cgg/Tgg	5/18	1	2	FACETS	0.818	0.752	0.886	1	0.99	1	CLONAL	2	TRUE	1	0.39	2		567	448	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562156	176562156	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	33	480	0	ENST00000439151.2:c.52A>G	p.Asn18Asp	p.N18D	ENST00000439151	NM_022455.4	18	Aat/Gat	2/23	1	2	FACETS	0.557	0.455	0.671	0.557	0.455	0.671	SUBCLONAL	1	TRUE	1	0.39	2		480	304	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562934	176562934	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	50	451	0	ENST00000439151.2:c.830C>A	p.Ser277Tyr	p.S277Y	ENST00000439151	NM_022455.4	277	tCt/tAt	2/23	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.39	2		451	206	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709523	176709523	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs797045057	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	26	277	1	ENST00000439151.2:c.5950C>T	p.Arg1984Ter	p.R1984*	ENST00000439151	NM_022455.4	1984	Cga/Tga	19/23	1	2	FACETS	0.849	0.68	1	0.849	0.68	1	CLONAL	1	TRUE	1	0.39	2		278	157	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709530	176709530	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749277550	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	29	277	0	ENST00000439151.2:c.5957G>A	p.Arg1986His	p.R1986H	ENST00000439151	NM_022455.4	1986	cGc/cAc	19/23	1	2	FACETS	0.978	0.795	1	0.978	0.795	1	CLONAL	1	TRUE	1	0.39	2		277	152	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180049816	180049816	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	55	762	0	ENST00000261937.6:c.1572G>T	p.Gln524His	p.Q524H	ENST00000261937	NM_182925.4	524	caG/caT	12/30	1	2	FACETS	0.51	0.436	0.591	0.51	0.436	0.591	SUBCLONAL	1	TRUE	1	0.39	2		762	553	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395936	395936	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	43	379	0	ENST00000380956.4:c.492+1G>T		p.X164_splice	ENST00000380956	NM_001195286.1	164			0.101120345089616	3	FACETS	0.755	0.634	0.889	0.378	0.317	0.445	INDETERMINATE	1	TRUE	1	0.39	3		379	349	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407498	407498	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	64	360	0	ENST00000380956.4:c.1256A>G	p.Gln419Arg	p.Q419R	ENST00000380956	NM_001195286.1	419	cAa/cGa	9/9	0.101120345089616	3	FACETS	0.961	0.846	1	0.961	0.846	1	INDETERMINATE	2	TRUE	1	0.39	3		360	204	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020956	26020956	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	74	374	0	ENST00000357647.3:c.239A>C	p.Lys80Thr	p.K80T	ENST00000357647	NM_003529.2	80	aAa/aCa	1/1	0.101120345089616	3	FACETS	0.774	0.684	0.868	0.774	0.684	0.868	INDETERMINATE	2	TRUE	1	0.39	3		374	293	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045954	26045954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	43	403	0	ENST00000540144.1:c.316G>A	p.Glu106Lys	p.E106K	ENST00000540144	NM_003531.2	106	Gaa/Aaa	1/1	0.101120345089616	3	FACETS	0.676	0.566	0.796	0.338	0.283	0.398	INDETERMINATE	1	TRUE	1	0.39	3		403	390	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225789	26225789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	44	396	0	ENST00000360408.1:c.407C>T	p.Ala136Val	p.A136V	ENST00000360408	NM_003532.2	136	gCg/gTg	1/1	0.101120345089616	3	FACETS	0.7	0.589	0.823	0.35	0.294	0.412	INDETERMINATE	1	TRUE	1	0.39	3		396	385	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271502	26271502	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	35	384	0	ENST00000305910.3:c.111G>T	p.Lys37Asn	p.K37N	ENST00000305910	NM_003534.2	37	aaG/aaT	1/1	0.101120345089616	3	FACETS	0.72	0.592	0.862	0.36	0.296	0.431	INDETERMINATE	1	TRUE	1	0.39	3		384	298	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681943	30681943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772145482	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	16	390	0	ENST00000376406.3:c.154G>A	p.Gly52Arg	p.G52R	ENST00000376406	NM_014641.2	52	Ggg/Agg	3/15	0.101120345089616	3	FACETS	0.376	0.277	0.493	0.188	0.138	0.247	INDETERMINATE	1	TRUE	1	0.39	3		390	261	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180621	32180621	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	60	569	0	ENST00000375023.3:c.2506T>G	p.Tyr836Asp	p.Y836D	ENST00000375023	NM_004557.3	836	Tac/Gac	16/30	0.101120345089616	3	FACETS	0.691	0.596	0.795	0.346	0.298	0.398	INDETERMINATE	1	TRUE	1	0.39	3		569	532	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805778	32805778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	213	791	0	ENST00000374899.4:c.233C>T	p.Ser78Phe	p.S78F	ENST00000374899	NM_018833.2	78	tCc/tTc	2/12	0.101120345089616	3	FACETS	0.983	0.918	1	0.983	0.918	1	INDETERMINATE	2	TRUE	1	0.39	3		791	664	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43739012	43739012	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	51	377	0	ENST00000523873.1:c.29G>T	p.Trp10Leu	p.W10L	ENST00000523873		10	tGg/tTg	1/8	0.101120345089616	3	FACETS	0.675	0.574	0.785	0.338	0.287	0.393	INDETERMINATE	1	TRUE	1	0.39	3		377	463	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64286793	64286793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	25	376	0	ENST00000370651.3:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000370651	NM_003463.4	3	cGa/cAa	2/6	0.101120345089616	3	FACETS	0.755	0.598	0.932	0.377	0.299	0.466	INDETERMINATE	1	TRUE	1	0.39	3		376	203	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64289975	64289975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	34	356	0	ENST00000370651.3:c.418G>A	p.Ala140Thr	p.A140T	ENST00000370651	NM_003463.4	140	Gct/Act	6/6	0.101120345089616	3	FACETS	0.943	0.776	1	0.471	0.388	0.564	INDETERMINATE	1	TRUE	1	0.39	3		356	221	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662301	117662301	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	10	549	0	ENST00000368508.3:c.5076G>T	p.Gln1692His	p.Q1692H	ENST00000368508	NM_002944.2	1692	caG/caT	30/43	0.101120345089616	3	FACETS	0.311	0.21	0.437	0.156	0.105	0.219	INDETERMINATE	1	TRUE	1	0.39	3		549	197	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662397	117662397	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	15	447	0	ENST00000368508.3:c.4980G>T	p.Glu1660Asp	p.E1660D	ENST00000368508	NM_002944.2	1660	gaG/gaT	30/43	0.101120345089616	3	FACETS	0.547	0.402	0.72	0.274	0.201	0.36	INDETERMINATE	1	TRUE	1	0.39	3		447	168	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665230	117665230	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1258207555	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	23	258	0	ENST00000368508.3:c.4517G>T	p.Arg1506Ile	p.R1506I	ENST00000368508	NM_002944.2	1506	aGa/aTa	27/43	0.101120345089616	3	FACETS	1	0.909	1	0.653	0.518	0.802	INDETERMINATE	1	TRUE	1	0.39	3		258	108	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708157	117708157	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	12	350	0	ENST00000368508.3:c.2020G>T	p.Glu674Ter	p.E674*	ENST00000368508	NM_002944.2	674	Gaa/Taa	14/43	0.101120345089616	3	FACETS	0.373	0.262	0.509	0.187	0.131	0.255	INDETERMINATE	1	TRUE	1	0.39	3		350	197	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983213	149983213	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	19	513	0	ENST00000253339.5:c.3045C>A	p.Phe1015Leu	p.F1015L	ENST00000253339		1015	ttC/ttA	7/7	0.101120345089616	3	FACETS	0.403	0.306	0.517	0.201	0.153	0.259	INDETERMINATE	1	TRUE	1	0.39	3		513	289	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004834	150004834	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	21	419	0	ENST00000253339.5:c.1391C>A	p.Ser464Tyr	p.S464Y	ENST00000253339		464	tCt/tAt	3/7	0.101120345089616	3	FACETS	0.707	0.548	0.89	0.354	0.274	0.445	INDETERMINATE	1	TRUE	1	0.39	3		419	182	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206802	162206802	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	108	435	0	ENST00000366898.1:c.871+2T>C		p.X291_splice	ENST00000366898	NM_004562.2	291			0.101120345089616	3	FACETS	1	0.977	1	1	0.977	1	INDETERMINATE	2	TRUE	1	0.39	3		435	271	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042169	6042169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35629870	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	38	472	1	ENST00000265849.7:c.452G>A	p.Arg151His	p.R151H	ENST00000265849	NM_000535.5	151	cGc/cAc	5/15	0.101120345089616	3	FACETS	0.53	0.438	0.633	0.265	0.219	0.317	INDETERMINATE	1	TRUE	1	0.39	3		473	439	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14026311	14026311	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	11	217	0	ENST00000405192.2:c.134-1G>T		p.X45_splice	ENST00000405192	NM_001163147.1	45			0.101120345089616	3	FACETS	0.443	0.307	0.612	0.222	0.153	0.306	INDETERMINATE	1	TRUE	1	0.39	3		217	152	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240779	55240779	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	234	775	0	ENST00000275493.2:c.2023C>T	p.Arg675Trp	p.R675W	ENST00000275493	NM_005228.3	675	Cgg/Tgg	17/28	0.101120345089616	3	FACETS	0.924	0.865	0.985	0.924	0.865	0.985	INDETERMINATE	2	TRUE	1	0.39	3		775	776	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339547	81339547	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	13	368	0	ENST00000222390.5:c.1457C>A	p.Ser486Tyr	p.S486Y	ENST00000222390	NM_000601.4	486	tCt/tAt	13/18	0.101120345089616	3	FACETS	0.383	0.273	0.517	0.192	0.136	0.259	INDETERMINATE	1	TRUE	1	0.39	3		368	208	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397584	116397584	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	17	530	0	ENST00000397752.3:c.1956C>A	p.Phe652Leu	p.F652L	ENST00000397752	NM_000245.2	652	ttC/ttA	7/21	0.101120345089616	3	FACETS	0.409	0.305	0.531	0.204	0.152	0.266	INDETERMINATE	1	TRUE	1	0.39	3		530	255	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398532	116398532	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	14	420	0	ENST00000397752.3:c.2122G>T	p.Glu708Ter	p.E708*	ENST00000397752	NM_000245.2	708	Gaa/Taa	9/21	0.101120345089616	3	FACETS	0.44	0.318	0.586	0.22	0.159	0.293	INDETERMINATE	1	TRUE	1	0.39	3		420	195	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418997	116418997	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200754673	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	51	386	0	ENST00000397752.3:c.3508C>T	p.Arg1170Ter	p.R1170*	ENST00000397752	NM_000245.2	1170	Cga/Tga	17/21	0.101120345089616	3	FACETS	1	0.895	1	1	0.895	1	INDETERMINATE	2	TRUE	1	0.39	3		386	151	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140487360	140487360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507472	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	28	540	0	ENST00000288602.6:c.1165C>T	p.Arg389Cys	p.R389C	ENST00000288602	NM_004333.4	389	Cgt/Tgt	9/18	0.101120345089616	3	FACETS	0.592	0.474	0.725	0.296	0.237	0.363	INDETERMINATE	1	TRUE	1	0.39	3		540	290	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494130	140494130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	63	761	0	ENST00000288602.6:c.1118C>T	p.Thr373Ile	p.T373I	ENST00000288602	NM_004333.4	373	aCa/aTa	8/18	0.101120345089616	3	FACETS	1	0.96	1	0.637	0.555	0.724	INDETERMINATE	1	TRUE	1	0.39	3		761	303	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534596	140534596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1322163182	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	15	431	0	ENST00000288602.6:c.317G>A	p.Gly106Glu	p.G106E	ENST00000288602	NM_004333.4	106	gGa/gAa	3/18	0.101120345089616	3	FACETS	0.414	0.303	0.547	0.207	0.151	0.274	INDETERMINATE	1	TRUE	1	0.39	3		431	222	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523708	148523708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520183	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	14	267	0	ENST00000320356.2:c.745G>A	p.Glu249Lys	p.E249K	ENST00000320356	NM_004456.4	249	Gaa/Aaa	8/20	0.101120345089616	3	FACETS	0.604	0.439	0.801	0.302	0.219	0.401	INDETERMINATE	1	TRUE	1	0.39	3		267	142	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525973	148525973	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	10	243	0	ENST00000320356.2:c.485-1G>T		p.X162_splice	ENST00000320356	NM_004456.4	162			0.101120345089616	3	FACETS	0.417	0.283	0.584	0.208	0.141	0.292	INDETERMINATE	1	TRUE	1	0.39	3		243	147	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836804	151836804	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	101	487	0	ENST00000262189.6:c.14416C>T	p.Arg4806Ter	p.R4806*	ENST00000262189	NM_170606.2	4806	Cga/Tga	56/59	0.101120345089616	3	FACETS	0.921	0.832	1	0.921	0.832	1	INDETERMINATE	2	TRUE	1	0.39	3		487	336	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842334	151842334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777526116	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	38	277	0	ENST00000262189.6:c.14078G>A	p.Arg4693Gln	p.R4693Q	ENST00000262189	NM_170606.2	4693	cGa/cAa	54/59	0.101120345089616	3	FACETS	0.872	0.725	1	0.436	0.362	0.517	INDETERMINATE	1	TRUE	1	0.39	3		277	267	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879190	151879190	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	96	519	0	ENST00000262189.6:c.5755T>G	p.Ser1919Ala	p.S1919A	ENST00000262189	NM_170606.2	1919	Tct/Gct	36/59	0.101120345089616	3	FACETS	0.931	0.839	1	0.931	0.839	1	INDETERMINATE	2	TRUE	1	0.39	3		519	316	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900104	151900104	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	19	285	0	ENST00000262189.6:c.4007C>A	p.Ser1336Tyr	p.S1336Y	ENST00000262189	NM_170606.2	1336	tCt/tAt	26/59	0.101120345089616	3	FACETS	0.517	0.394	0.662	0.259	0.197	0.331	INDETERMINATE	1	TRUE	1	0.39	3		285	225	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151932981	151932981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1402089231	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	15	52	0	ENST00000262189.6:c.2690G>A	p.Arg897Gln	p.R897Q	ENST00000262189	NM_170606.2	897	cGa/cAa	16/59	0.101120345089616	3	FACETS	1	0.865	1	0.638	0.477	0.822	INDETERMINATE	1	TRUE	1	0.39	3		52	72	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151947996	151947996	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	21	434	1	ENST00000262189.6:c.1677G>T	p.Glu559Asp	p.E559D	ENST00000262189	NM_170606.2	559	gaG/gaT	12/59	0.101120345089616	3	FACETS	0.523	0.404	0.662	0.262	0.202	0.331	INDETERMINATE	1	TRUE	1	0.39	3		435	246	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187329	38187329	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2234552	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	23	507	1	ENST00000317025.8:c.1148G>A	p.Arg383Gln	p.R383Q	ENST00000317025	NM_023034.1	383	cGa/cAa	6/24	0.101120345089616	0	FACETS	0.291	0.227	0.365			1	INDETERMINATE	1	TRUE	0	0.39	0		508	247	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942742	68942742	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	20	365	0	ENST00000288368.4:c.554A>G	p.Lys185Arg	p.K185R	ENST00000288368	NM_024870.2	185	aAg/aGg	6/40	0.101120345089616	0	FACETS	0.194	0.148	0.248			1	INDETERMINATE	1	TRUE	0	0.39	0		365	323	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992692	68992692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529924687	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	32	498	0	ENST00000288368.4:c.1657G>A	p.Glu553Lys	p.E553K	ENST00000288368	NM_024870.2	553	Gaa/Aaa	16/40	0.101120345089616	0	FACETS	0.426	0.348	0.513			1	INDETERMINATE	1	TRUE	0	0.39	0		498	235	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69011978	69011978	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	18	569	0	ENST00000288368.4:c.2615C>A	p.Ser872Tyr	p.S872Y	ENST00000288368	NM_024870.2	872	tCt/tAt	23/40	0.101120345089616	0	FACETS	0.167	0.125	0.216			1	INDETERMINATE	1	TRUE	0	0.39	0		569	338	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981438	70981438	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	96	966	1	ENST00000276594.2:c.658C>A	p.His220Asn	p.H220N	ENST00000276594	NM_024504.3	220	Cac/Aac	2/8	0.101120345089616	0	FACETS	0.339	0.301	0.379			1	INDETERMINATE	1	TRUE	0	0.39	0		967	886	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90947838	90947838	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1554553893	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	18	241	0	ENST00000265433.3:c.2237A>G	p.Tyr746Cys	p.Y746C	ENST00000265433	NM_002485.4	746	tAc/tGc	16/16	0.101120345089616	0	FACETS	0.43	0.327	0.549			1	INDETERMINATE	1	TRUE	0	0.39	0		241	131	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967761	90967761	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	19	180	1	ENST00000265433.3:c.1147G>T	p.Glu383Ter	p.E383*	ENST00000265433	NM_002485.4	383	Gaa/Taa	10/16	0.101120345089616	0	FACETS	0.619	0.478	0.778			1	INDETERMINATE	1	TRUE	0	0.39	0		181	96	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864904	117864904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	11	296	0	ENST00000297338.2:c.1205G>T	p.Arg402Ile	p.R402I	ENST00000297338	NM_006265.2	402	aGa/aTa	10/14	0.101120345089616	0	FACETS	0.162	0.112	0.225			1	INDETERMINATE	1	TRUE	0	0.39	0		296	212	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750787	128750787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	58	643	0	ENST00000377970.2:c.324C>A	p.Phe108Leu	p.F108L	ENST00000377970	NM_002467.4	108	ttC/ttA	2/3	0.101120345089616	0	FACETS	0.384	0.33	0.442			1	INDETERMINATE	1	TRUE	0	0.39	0		643	473	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740736	145740736	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	70	660	0	ENST00000428558.2:c.1364C>T	p.Ser455Phe	p.S455F	ENST00000428558	NM_004260.3	455	tCc/tTc	7/22	0.101120345089616	0	FACETS	0.308	0.268	0.351			1	INDETERMINATE	1	TRUE	0	0.39	0		660	711	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050746	5050746	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	23	376	0	ENST00000381652.3:c.529G>T	p.Glu177Ter	p.E177*	ENST00000381652	NM_004972.3	177	Gaa/Taa	6/25	0.101120345089616	0	FACETS	0.358	0.28	0.447			1	INDETERMINATE	1	TRUE	0	0.39	0		376	201	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054768	5054768	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	30	325	0	ENST00000381652.3:c.820G>T	p.Glu274Ter	p.E274*	ENST00000381652	NM_004972.3	274	Gaa/Taa	7/25	0.101120345089616	0	FACETS	0.626	0.511	0.752			1	INDETERMINATE	1	TRUE	0	0.39	0		325	150	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072546	5072546	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	52	355	0	ENST00000381652.3:c.1696G>T	p.Glu566Ter	p.E566*	ENST00000381652	NM_004972.3	566	Gaa/Taa	13/25	0.101120345089616	0	FACETS	0.733	0.631	0.841			1	INDETERMINATE	1	TRUE	0	0.39	0		355	222	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072585	5072585	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	23	341	0	ENST00000381652.3:c.1735C>A	p.Leu579Ile	p.L579I	ENST00000381652	NM_004972.3	579	Ctt/Att	13/25	0.101120345089616	0	FACETS	0.327	0.256	0.409			1	INDETERMINATE	1	TRUE	0	0.39	0		341	220	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072613	5072613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1473044275	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	25	282	0	ENST00000381652.3:c.1763G>A	p.Arg588Lys	p.R588K	ENST00000381652	NM_004972.3	588	aGa/aAa	13/25	0.101120345089616	0	FACETS	0.439	0.349	0.542			1	INDETERMINATE	1	TRUE	0	0.39	0		282	178	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5077508	5077508	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	28	283	0	ENST00000381652.3:c.1920G>T	p.Lys640Asn	p.K640N	ENST00000381652	NM_004972.3	640	aaG/aaT	15/25	0.101120345089616	0	FACETS	0.534	0.431	0.648			1	INDETERMINATE	1	TRUE	0	0.39	0		283	164	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090520	5090520	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	23	334	0	ENST00000381652.3:c.2836G>T	p.Glu946Ter	p.E946*	ENST00000381652	NM_004972.3	946	Gaa/Taa	21/25	0.101120345089616	0	FACETS	0.458	0.36	0.569			1	INDETERMINATE	1	TRUE	0	0.39	0		334	157	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090825	5090825	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	13	267	0	ENST00000381652.3:c.2973A>C	p.Lys991Asn	p.K991N	ENST00000381652	NM_004972.3	991	aaA/aaC	22/25	0.101120345089616	0	FACETS	0.256	0.183	0.344			1	INDETERMINATE	1	TRUE	0	0.39	0		267	159	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5557744	5557744	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	44	342	0	ENST00000397747.3:c.758C>A	p.Ser253Tyr	p.S253Y	ENST00000397747	NM_025239.3	253	tCt/tAt	5/7	0.101120345089616	0	FACETS	0.81	0.69	0.938			1	INDETERMINATE	1	TRUE	0	0.39	0		342	170	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341701	8341701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766088715	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	25	438	2	ENST00000356435.5:c.4939G>A	p.Glu1647Lys	p.E1647K	ENST00000356435		1647	Gaa/Aaa	29/35	0.101120345089616	0	FACETS	0.339	0.268	0.419			1	INDETERMINATE	1	TRUE	0	0.39	0		440	231	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389318	8389318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	32	544	0	ENST00000356435.5:c.4300G>A	p.Glu1434Lys	p.E1434K	ENST00000356435		1434	Gaa/Aaa	26/35	0.101120345089616	0	FACETS	0.381	0.31	0.459			1	INDETERMINATE	1	TRUE	0	0.39	0		544	263	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185487	27185487	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	67	423	0	ENST00000380036.4:c.1187A>C	p.Lys396Thr	p.K396T	ENST00000380036	NM_000459.3	396	aAa/aCa	9/23	0.101120345089616	0	FACETS	1	0.924	1			1	INDETERMINATE	1	TRUE	0	0.39	0		423	198	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197465	27197465	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	28	719	0	ENST00000380036.4:c.1777G>T	p.Val593Phe	p.V593F	ENST00000380036	NM_000459.3	593	Gtt/Ttt	12/23	0.101120345089616	0	FACETS	0.183	0.146	0.226			1	INDETERMINATE	1	TRUE	0	0.39	0		719	478	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430668	80430668	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	56	494	0	ENST00000286548.4:c.340C>T	p.Arg114Ter	p.R114*	ENST00000286548	NM_002072.3	114	Cga/Tga	3/7	0.101120345089616	0	FACETS	0.706	0.611	0.808			1	INDETERMINATE	1	TRUE	0	0.39	0		494	248	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285871	87285871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408094711	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	71	488	0	ENST00000277120.3:c.208G>A	p.Glu70Lys	p.E70K	ENST00000277120		70	Gaa/Aaa	2/19	0.101120345089616	0	FACETS	0.584	0.513	0.661			1	INDETERMINATE	1	TRUE	0	0.39	0		488	380	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317081	87317081	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201490630	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	27	380	0	ENST00000277120.3:c.220G>A	p.Ala74Thr	p.A74T	ENST00000277120		74	Gca/Aca	3/19	0.101120345089616	0	FACETS	0.418	0.335	0.512			1	INDETERMINATE	1	TRUE	0	0.39	0		380	202	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317277	87317277	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	15	405	0	ENST00000277120.3:c.302C>A	p.Ser101Tyr	p.S101Y	ENST00000277120		101	tCt/tAt	4/19	0.101120345089616	0	FACETS	0.235	0.172	0.31			1	INDETERMINATE	1	TRUE	0	0.39	0		405	200	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317285	87317285	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	46	407	0	ENST00000277120.3:c.310A>C	p.Lys104Gln	p.K104Q	ENST00000277120		104	Aaa/Caa	4/19	0.101120345089616	0	FACETS	0.689	0.586	0.798			1	INDETERMINATE	1	TRUE	0	0.39	0		407	209	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87322770	87322770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781137734	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	18	348	0	ENST00000277120.3:c.371G>A	p.Arg124Gln	p.R124Q	ENST00000277120		124	cGa/cAa	5/19	0.101120345089616	0	FACETS	0.239	0.18	0.308			1	INDETERMINATE	1	TRUE	0	0.39	0		348	236	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342596	87342961	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCCAACCTCAGACCACCACTGGTGCATTCCATTCACTGTGAAAGGCAACCCCAAACCAGCGCTTCAGTGGTTCTATAACGGGGCAATATTGAATGAGTCCAAATACATCTGTACTAAAATACATGTTACCAATCACACGGAGTACCACGGCTGCCTCCAGCTGGATAATCCCACTCACATGAACAATGGGGACTACACTCTAATAGCCAAGAATGAGTATGGGAAGGATGAGAAACAGATTTCTGCTCACTTCATGGGCTGGCCTGGAATTGACGATGGTGAGTAACTGACACTTTTGTATGTGGGGAGAAGATAAAGTCTATCATTCACCTGTTGACAAAATCATGTATACAATAAGCCATCCC	CTCCAACCTCAGACCACCACTGGTGCATTCCATTCACTGTGAAAGGCAACCCCAAACCAGCGCTTCAGTGGTTCTATAACGGGGCAATATTGAATGAGTCCAAATACATCTGTACTAAAATACATGTTACCAATCACACGGAGTACCACGGCTGCCTCCAGCTGGATAATCCCACTCACATGAACAATGGGGACTACACTCTAATAGCCAAGAATGAGTATGGGAAGGATGAGAAACAGATTTCTGCTCACTTCATGGGCTGGCCTGGAATTGACGATGGTGAGTAACTGACACTTTTGTATGTGGGGAGAAGATAAAGTCTATCATTCACCTGTTGACAAAATCATGTATACAATAAGCCATCCC	TT	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	18	528	2	ENST00000277120.3:c.881_1159+87delinsTT		p.X294_splice	ENST00000277120		294		9/19	0.101120345089616	0	FACETS	0.175	0.131	0.227			1	INDETERMINATE	1	TRUE	0	0.39	0		530	322	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342787	87342787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	18	438	0	ENST00000277120.3:c.1072G>A	p.Asp358Asn	p.D358N	ENST00000277120		358	Gac/Aac	9/19	0.101120345089616	0	FACETS	0.247	0.186	0.319			1	INDETERMINATE	1	TRUE	0	0.39	0		438	228	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908824	101908824	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	38	446	0	ENST00000374994.4:c.1188C>A	p.Phe396Leu	p.F396L	ENST00000374994	NM_004612.2	396	ttC/ttA	7/9	0.101120345089616	0	FACETS	0.499	0.416	0.591			1	INDETERMINATE	1	TRUE	0	0.39	0		446	238	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128432180	128432180	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	14	333	0	ENST00000265960.3:c.266G>T	p.Arg89Ile	p.R89I	ENST00000265960	NM_001006617.1	89	aGa/aTa	3/12	0.101120345089616	0	FACETS	0.201	0.145	0.268			1	INDETERMINATE	1	TRUE	0	0.39	0		333	218	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798742	135798742	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	38	198	0	ENST00000298552.3:c.501G>T	p.Lys167Asn	p.K167N	ENST00000298552	NM_001162426.1	167	aaG/aaT	6/23	0.101120345089616	0	FACETS	0.907	0.766	1			1	INDETERMINATE	1	TRUE	0	0.39	0		198	131	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321067	137321067	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	75	611	1	ENST00000481739.1:c.1024G>A	p.Val342Met	p.V342M	ENST00000481739	NM_002957.4	342	Gtg/Atg	7/10	0.101120345089616	0	FACETS	0.396	0.347	0.449			1	INDETERMINATE	1	TRUE	0	0.39	0		612	592	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139794123	139794123	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs200834553	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	30	425	0	ENST00000247668.2:c.266C>T	p.Ser89Leu	p.S89L	ENST00000247668	NM_021138.3	89	tCg/tTg	3/11	0.101120345089616	0	FACETS	0.423	0.343	0.512			1	INDETERMINATE	1	TRUE	0	0.39	0		425	222	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325493	1325493	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	31	433	0	ENST00000400841.2:c.183-1G>T		p.X61_splice	ENST00000400841		61			1	2	FACETS	0.533	0.433	0.647	0.533	0.433	0.647	SUBCLONAL	1	TRUE	1	0.39	2		433	298	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44921917	44921917	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	29	437	0	ENST00000377967.4:c.1451G>T	p.Arg484Ile	p.R484I	ENST00000377967	NM_021140.2	484	aGa/aTa	15/29	1	2	FACETS	0.755	0.611	0.916	0.755	0.611	0.916	CLONAL	1	TRUE	1	0.39	2		437	197	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030535	47030535	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	189	796	0	ENST00000377604.3:c.310G>A	p.Asp104Asn	p.D104N	ENST00000377604	NM_001204468.1	104	Gac/Aac	4/24	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.39	2		796	669	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53253955	53253955	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	68	566	0	ENST00000375401.3:c.117G>T	p.Glu39Asp	p.E39D	ENST00000375401	NM_004187.3	39	gaG/gaT	1/26	1	2	FACETS	0.64	0.557	0.729	0.64	0.557	0.729	SUBCLONAL	1	TRUE	1	0.39	2		566	545	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412287	63412287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	146	874	2	ENST00000330258.3:c.880G>A	p.Val294Ile	p.V294I	ENST00000330258	NM_152424.3	294	Gta/Ata	2/2	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.39	2		876	531	SUCCESS
AR	367	MSKCC	GRCh37	X	66863230	66863230	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	27	488	0	ENST00000374690.3:c.1749C>A	p.Phe583Leu	p.F583L	ENST00000374690	NM_000044.3	583	ttC/ttA	2/8	1	2	FACETS	0.434	0.346	0.535	0.434	0.346	0.535	SUBCLONAL	1	TRUE	1	0.39	2		488	319	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347966	70347966	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770988288	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	21	564	0	ENST00000374080.3:c.3205G>A	p.Asp1069Asn	p.D1069N	ENST00000374080		1069	Gat/Aat	22/45	1	2	FACETS	0.259	0.199	0.33	0.259	0.199	0.33	SUBCLONAL	1	TRUE	1	0.39	2		564	415	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855270	76855270	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	15	308	0	ENST00000373344.5:c.5717G>T	p.Ser1906Ile	p.S1906I	ENST00000373344	NM_000489.3	1906	aGt/aTt	24/35	1	2	FACETS	0.472	0.347	0.621	0.472	0.347	0.621	SUBCLONAL	1	TRUE	1	0.39	2		308	163	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909681	76909681	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	22	321	0	ENST00000373344.5:c.4224G>T	p.Lys1408Asn	p.K1408N	ENST00000373344	NM_000489.3	1408	aaG/aaT	14/35	1	2	FACETS	0.752	0.589	0.938	0.752	0.589	0.938	CLONAL	1	TRUE	1	0.39	2		321	150	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937356	76937356	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	15	453	0	ENST00000373344.5:c.3392G>T	p.Arg1131Ile	p.R1131I	ENST00000373344	NM_000489.3	1131	aGa/aTa	9/35	1	2	FACETS	0.49	0.36	0.644	0.49	0.36	0.644	SUBCLONAL	1	TRUE	1	0.39	2		453	157	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937769	76937769	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs371962239	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	12	437	1	ENST00000373344.5:c.2979G>T	p.Lys993Asn	p.K993N	ENST00000373344	NM_000489.3	993	aaG/aaT	9/35	1	2	FACETS	0.256	0.18	0.351	0.256	0.18	0.351	SUBCLONAL	1	TRUE	1	0.39	2		438	240	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937850	76937850	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs138256318	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	60	507	0	ENST00000373344.5:c.2898G>T	p.Glu966Asp	p.E966D	ENST00000373344	NM_000489.3	966	gaG/gaT	9/35	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.39	2		507	236	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939893	76939893	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	12	522	0	ENST00000373344.5:c.855G>T	p.Glu285Asp	p.E285D	ENST00000373344	NM_000489.3	285	gaG/gaT	9/35	1	2	FACETS	0.305	0.214	0.416	0.305	0.214	0.416	SUBCLONAL	1	TRUE	1	0.39	2		522	202	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611795	100611795	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	58	473	0	ENST00000308731.7:c.1326C>A	p.Phe442Leu	p.F442L	ENST00000308731	NM_000061.2	442	ttC/ttA	14/19	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.39	2		473	212	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020196	123020196	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	81	688	0	ENST00000355640.3:c.684C>A	p.Phe228Leu	p.F228L	ENST00000355640		228	ttC/ttA	2/7	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.39	2		688	312	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034413	123034413	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	48	394	0	ENST00000355640.3:c.1170G>T	p.Lys390Asn	p.K390N	ENST00000355640		390	aaG/aaT	6/7	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.39	2		394	200	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176469	123176469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	47	272	0	ENST00000218089.9:c.436C>T	p.Arg146Ter	p.R146*	ENST00000218089	NM_001042749.1	146	Cga/Tga	7/35	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.39	2		272	187	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195645	123195645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	23	311	0	ENST00000218089.9:c.1559C>T	p.Ala520Val	p.A520V	ENST00000218089	NM_001042749.1	520	gCt/gTt	17/35	1	2	FACETS	0.867	0.685	1	0.867	0.685	1	CLONAL	1	TRUE	1	0.39	2		311	136	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210238	123210238	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	74	442	0	ENST00000218089.9:c.2590T>G	p.Leu864Val	p.L864V	ENST00000218089	NM_001042749.1	864	Tta/Gta	26/35	1	2	FACETS	0.753	0.668	0.842	1	0.978	1	SUBCLONAL	2	TRUE	1	0.39	2		442	252	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123499661	123499661	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	57	560	0	ENST00000371139.4:c.188C>A	p.Ser63Tyr	p.S63Y	ENST00000371139	NM_001114937.2	63	tCt/tAt	2/4	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.39	2		560	247	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111504	8111505	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0042114-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	413	470	0	ENST00000346208.3:c.992dup	p.Asn331LysfsTer21	p.N331Kfs*21	ENST00000346208		330	-/A	5/6	0.257879162626932	5	FACETS	0.853	0.814	0.892	0.853	0.814	0.892	INDETERMINATE	3	FALSE	2	0.581629078793888	5		470	1039	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23625396	23625396	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs766394024	NA	P-0042114-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	115	347	0	ENST00000261584.4:c.3130C>T	p.Gln1044Ter	p.Q1044*	ENST00000261584	NM_024675.3	1044	Caa/Taa	11/13	0.48718578434699	4	FACETS	0.899	0.819	0.981	0.899	0.819	0.981	CLONAL	2	FALSE	2	0.581629078793888	4		347	348	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056246	26056246	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042114-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	151	652	0	ENST00000343677.2:c.411G>T	p.Lys137Asn	p.K137N	ENST00000343677	NM_005319.3	137	aaG/aaT	1/1	0.581629078793888	6	FACETS	0.968	0.883	1	0.323	0.294	0.353	CLONAL	1	FALSE	3	0.581629078793888	6		652	1160	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416679	29416679	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042114-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	43	511	0	ENST00000389048.3:c.4274T>G	p.Leu1425Arg	p.L1425R	ENST00000389048	NM_004304.4	1425	cTg/cGg	29/29	0.567491844905836	3	FACETS	0.571	0.48	0.672	0.286	0.24	0.336	SUBCLONAL	1	FALSE	1	0.581629078793888	3		511	334	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685240	86685240	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042114-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	79	416	0	ENST00000274376.6:c.2956C>T	p.His986Tyr	p.H986Y	ENST00000274376	NM_002890.2	986	Cat/Tat	24/25	0.338474787907762	6	FACETS	1	0.966	1	0.318	0.28	0.358	INDETERMINATE	1	FALSE	2	0.581629078793888	6		416	462	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0042652-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	88	342	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.764	0.687	0.844	1	0.982	1	SUBCLONAL	2	TRUE	1	0.443001852406374	2		342	260	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175481	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0042652-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	132	465	0	ENST00000257430.4:c.4192_4193del	p.Arg1399PhefsTer9	p.R1399Ffs*9	ENST00000257430	NM_000038.5	1397	GAg/g	16/16	1	2	FACETS	0.988	0.9	1	0.988	0.9	1	CLONAL	1	TRUE	1	0.443001852406374	2		465	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0042652-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	192	598	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.443001852406374	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.443001852406374	1		598	578	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436952	49436952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748653082	NA	P-0042652-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	176	480	0	ENST00000301067.7:c.5551G>A	p.Val1851Met	p.V1851M	ENST00000301067	NM_003482.3	1851	Gtg/Atg	25/54	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.443001852406374	2		480	547	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610562	215610562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146946984	NA	P-0042652-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	81	374	0	ENST00000260947.4:c.1694G>A	p.Arg565His	p.R565H	ENST00000260947	NM_000465.2	565	cGt/cAt	8/11	1	2	FACETS	0.814	0.721	0.914	0.814	0.721	0.914	CLONAL	1	TRUE	1	0.443001852406374	2		374	449	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775497	39775497	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042652-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	188	542	1	ENST00000288319.7:c.523G>A	p.Asp175Asn	p.D175N	ENST00000288319	NM_182918.3	175	Gac/Aac	4/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.443001852406374	2		543	789	SUCCESS
APC	324	MSKCC	GRCh37	5	112164576	112164576	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1554082100	NA	P-0042652-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	77	329	0	ENST00000257430.4:c.1652del	p.Leu551CysfsTer7	p.L551Cfs*7	ENST00000257430	NM_000038.5	550	aaT/aa	14/16	1	2	FACETS	0.878	0.775	0.987	0.878	0.775	0.987	CLONAL	1	TRUE	1	0.443001852406374	2		329	396	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920435	114920435	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042652-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	163	385	0	ENST00000543371.1:c.1377del	p.Trp459CysfsTer32	p.W459Cfs*32	ENST00000543371	NM_001198531.1	459	tGg/tg	13/14	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.443001852406374	2		385	585	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139732	55139732	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042652-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	79	337	0	ENST00000257290.5:c.1393T>G	p.Leu465Val	p.L465V	ENST00000257290	NM_006206.4	465	Ttg/Gtg	10/23	1	2	FACETS	0.756	0.667	0.85	0.756	0.667	0.85	SUBCLONAL	1	TRUE	1	0.443001852406374	2		337	472	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139748	55139748	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0042652-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	89	380	1	ENST00000257290.5:c.1409C>G	p.Ser470Ter	p.S470*	ENST00000257290	NM_006206.4	470	tCa/tGa	10/23	1	2	FACETS	0.779	0.692	0.87	0.779	0.692	0.87	SUBCLONAL	1	TRUE	1	0.443001852406374	2		381	516	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715863	117715863	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042652-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	75	325	0	ENST00000368508.3:c.895del	p.Thr299LeufsTer3	p.T299Lfs*3	ENST00000368508	NM_002944.2	299	Act/ct	9/43	1	2	FACETS	0.965	0.851	1	0.965	0.851	1	CLONAL	1	TRUE	1	0.443001852406374	2		325	351	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0043085-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	173	556	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.983	0.911	1	0.983	0.911	1	CLONAL	1	TRUE	1	0.625011509614667	2		556	563	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942685	48942685	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913301	NA	P-0043085-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	65	308	0	ENST00000267163.4:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000267163	NM_000321.2	358	Cga/Tga	11/27	0.625011509614667	1	FACETS	0.454	0.396	0.515	0.454	0.396	0.515	SUBCLONAL	1	TRUE	0	0.625011509614667	1		308	315	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916948	178916950	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0043085-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	10	373	0	ENST00000263967.3:c.337_339del	p.Leu113del	p.L113del	ENST00000263967	NM_006218.2	112	aTCCtc/atc	2/21	1	2	FACETS	0.069	0.046	0.098	0.069	0.046	0.098	SUBCLONAL	1	TRUE	1	0.625011509614667	2		373	464	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876230	35876230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753614229	NA	P-0043085-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	158	602	1	ENST00000303115.3:c.1022G>A	p.Gly341Glu	p.G341E	ENST00000303115	NM_002185.3	341	gGa/gAa	8/8	1	2	FACETS	0.956	0.881	1	0.956	0.881	1	CLONAL	1	TRUE	1	0.625011509614667	2		603	529	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089651	27089652	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCTA	novel	NA	P-0043085-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	208	795	0	ENST00000324856.7:c.2608_2611dup	p.Asn871ThrfsTer2	p.N871Tfs*2	ENST00000324856	NM_006015.4	869	-/CCTA	8/20	1	2	FACETS	0.969	0.903	1	0.969	0.903	1	CLONAL	1	TRUE	1	0.625011509614667	2		795	687	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143980	11143980	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043085-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	165	871	3	ENST00000358026.2:c.3561G>T	p.Gln1187His	p.Q1187H	ENST00000358026	NM_001128849.1	1187	caG/caT	26/36	1	2	FACETS	0.987	0.912	1	0.987	0.912	1	CLONAL	1	TRUE	1	0.625011509614667	2		874	535	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29445670	29445671	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGAG	novel	NA	P-0043085-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	145	864	0	ENST00000544604.2:c.1504_1507dup	p.Gly503GlufsTer65	p.G503Efs*65	ENST00000544604	NM_001206998.1	501	ccg/cCGAGcg	8/9	0.625011509614667	1	FACETS	0.909	0.841	0.978	0.909	0.841	0.978	CLONAL	1	TRUE	0	0.625011509614667	1		864	351	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845528	151845529	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	G	novel	NA	P-0043085-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	174	667	0	ENST00000262189.6:c.13483_13484delinsC	p.Phe4495LeufsTer22	p.F4495Lfs*22	ENST00000262189	NM_170606.2	4495	TTt/Ct	52/59	1	2	FACETS	0.911	0.843	0.982	0.911	0.843	0.982	CLONAL	1	TRUE	1	0.625011509614667	2		667	611	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577594	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0043098-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	79	83	0	ENST00000269305.4:c.687T>A	p.Cys229Ter	p.C229*	ENST00000269305	NM_001126112.2	229	tgT/tgA	7/11	0.204650756103272	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.225388428487445	1		83	570	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868140	45868140	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043098-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	87	180	0	ENST00000391945.4:c.550G>T	p.Gly184Trp	p.G184W	ENST00000391945	NM_000400.3	184	Ggg/Tgg	7/23	1	2	FACETS	0.637	0.562	0.718	0.637	0.562	0.718	SUBCLONAL	1	TRUE	1	0.225388428487445	2		180	1212	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007353	143007353	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043098-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	32	50	0	ENST00000262992.4:c.2431C>T	p.Gln811Ter	p.Q811*	ENST00000262992	NM_001101669.1	811	Caa/Taa	22/24	0.225388428487445	1	FACETS	0.771	0.627	0.932	0.771	0.627	0.932	CLONAL	1	TRUE	0	0.225388428487445	1		50	327	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699426	47699426	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0043098-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	55	83	0	ENST00000347630.2:c.82A>T	p.Lys28Ter	p.K28*	ENST00000347630	NM_001007230.1	28	Aag/Tag	4/11	0.204650756103272	1	FACETS	0.993	0.852	1	0.993	0.852	1	CLONAL	1	TRUE	0	0.225388428487445	1		83	436	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690632	88690632	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043098-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	48	78	0	ENST00000360948.2:c.398A>T	p.Asn133Ile	p.N133I	ENST00000360948	NM_001012338.2	133	aAc/aTc	5/19	0.159100813580082	4	FACETS	0.979	0.828	1	0.49	0.414	0.573	CLONAL	1	TRUE	2	0.225388428487445	4		78	533	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679950	30680001	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGCTGTTAGGGAGGTGCCCTCCTCTGCATCTGTTTCACAGTCCCCATGCA	GAGGCTGTTAGGGAGGTGCCCTCCTCTGCATCTGTTTCACAGTCCCCATGCA	-	novel	NA	P-0043098-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	89	127	0	ENST00000376406.3:c.1718_1769del	p.Leu573GlnfsTer2	p.L573Qfs*2	ENST00000376406	NM_014641.2	573	cTGCATGGGGACTGTGAAACAGATGCAGAGGAGGGCACCTCCCTAACAGCCTCa/ca	5/15	1	2	FACETS	0.827	0.732	0.929	0.827	0.732	0.929	CLONAL	1	TRUE	1	0.225388428487445	2		127	955	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144446	11144447	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0043098-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	63	74	0	ENST00000358026.2:c.3779_3780del	p.Arg1260ThrfsTer54	p.R1260Tfs*54	ENST00000358026	NM_001128849.1	1260	AGa/a	27/36	1	2	FACETS	0.922	0.798	1	0.922	0.798	1	CLONAL	1	TRUE	1	0.225388428487445	2		74	606	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043419-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	143	486	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.768993583417944	2	FACETS	0.638	0.584	0.694	0.319	0.292	0.347	SUBCLONAL	1	TRUE	0	0.784671718693455	2		486	571	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115853	8115854	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0043419-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	347	551	0	ENST00000346208.3:c.1200dup	p.Ser401ValfsTer106	p.S401Vfs*106	ENST00000346208		400	atg/atGg	6/6	1	2	FACETS	0.936	0.889	0.984	0.936	0.889	0.984	CLONAL	1	TRUE	1	0.784671718693455	2		551	945	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629199	187629199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043419-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	86	458	0	ENST00000441802.2:c.1783G>A	p.Asp595Asn	p.D595N	ENST00000441802	NM_005245.3	595	Gat/Aat	2/27	0.398962694855627	3	FACETS	0.628	0.557	0.703	0.209	0.185	0.235	INDETERMINATE	1	TRUE	0	0.784671718693455	3		458	486	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971128	21971128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043419-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	164	515	0	ENST00000304494.5:c.230C>T	p.Thr77Ile	p.T77I	ENST00000304494	NM_000077.4	77	aCt/aTt	2/3	0.489546569359264	1	FACETS	0.444	0.41	0.48	0.444	0.41	0.48	SUBCLONAL	1	TRUE	0	0.784671718693455	1		515	572	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497562	125497562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043419-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	77	286	0	ENST00000428830.2:c.126G>A	p.Met42Ile	p.M42I	ENST00000428830	NM_001114121.2	42	atG/atA	3/14	0.769778188842939	2	FACETS	1	0.969	1	0.598	0.54	0.657	CLONAL	1	TRUE	0	0.784671718693455	2		286	164	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736393	85736393	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043419-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	73	369	0	ENST00000370580.1:c.254C>G	p.Ser85Cys	p.S85C	ENST00000370580	NM_003921.4	85	tCt/tGt	2/3	0.351549099726723	1	FACETS	0.357	0.314	0.401	0.357	0.314	0.401	INDETERMINATE	1	TRUE	0	0.784671718693455	1		369	317	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243708846	243708846	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043419-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	28	229	0	ENST00000263826.5:c.1217C>G	p.Ser406Cys	p.S406C	ENST00000263826	NM_005465.4	406	tCt/tGt	11/13	0.398962694855627	3	FACETS	0.438	0.352	0.535	0.146	0.117	0.179	INDETERMINATE	1	TRUE	0	0.784671718693455	3		229	227	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198283251	198283251	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043419-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	92	248	0	ENST00000335508.6:c.477A>C	p.Gln159His	p.Q159H	ENST00000335508	NM_012433.2	159	caA/caC	5/25	0.424699429222759	2	FACETS	0.92	0.83	1	0.46	0.415	0.506	INDETERMINATE	1	TRUE	0	0.784671718693455	2		248	255	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131893034	131893034	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043419-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	257	364	0	ENST00000265335.6:c.18G>C	p.Lys6Asn	p.K6N	ENST00000265335		6	aaG/aaC	1/25	0.175100166021546	6	FACETS	0.944	0.886	1	0.63	0.591	0.67	INDETERMINATE	2	TRUE	3	0.784671718693455	6		364	891	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914680	32914680	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043419-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	30	365	0	ENST00000380152.3:c.6188G>C	p.Gly2063Ala	p.G2063A	ENST00000380152		2063	gGa/gCa	11/27	0.784671718693455	1	FACETS	0.419	0.344	0.499	0.419	0.344	0.499	SUBCLONAL	1	TRUE	0	0.784671718693455	1		365	111	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934802	9934802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043419-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	79	340	0	ENST00000330684.3:c.1488G>A	p.Met496Ile	p.M496I	ENST00000330684	NM_001134407.1	496	atG/atA	6/13	0.656745025709764	5	FACETS	0.672	0.591	0.759	0.224	0.197	0.253	SUBCLONAL	1	TRUE	2	0.784671718693455	5		340	652	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690629	33690629	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043419-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	195	435	0	ENST00000308377.4:c.198G>T	p.Lys66Asn	p.K66N	ENST00000308377	NM_152270.3	66	aaG/aaT	2/5	0.120070728342175	4	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.784671718693455	4		435	633	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727940	41727940	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043419-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	144	402	0	ENST00000301178.4:c.565C>T	p.Gln189Ter	p.Q189*	ENST00000301178	NM_021913.4	189	Cag/Tag	4/20	0.784671718693455	3	FACETS	0.554	0.504	0.605	0.277	0.252	0.303	SUBCLONAL	1	TRUE	1	0.784671718693455	3		402	923	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023113	48023113	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043419-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	112	339	0	ENST00000234420.5:c.538G>C	p.Asp180His	p.D180H	ENST00000234420	NM_000179.2	180	Gat/Cat	3/10	0.425338534526491	3	FACETS	0.645	0.582	0.712	0.215	0.194	0.238	INDETERMINATE	1	TRUE	0	0.784671718693455	3		339	616	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449734	8449734	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043419-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	87	334	0	ENST00000356435.5:c.3979C>T	p.Gln1327Ter	p.Q1327*	ENST00000356435		1327	Caa/Taa	23/35	0.489546569359264	1	FACETS	0.413	0.369	0.459	0.413	0.369	0.459	SUBCLONAL	1	TRUE	0	0.784671718693455	1		334	326	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640853	3640853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs117707719	NA	P-0044010-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	317	525	0	ENST00000294008.3:c.2786C>T	p.Pro929Leu	p.P929L	ENST00000294008	NM_032444.2	929	cCg/cTg	12/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.935493203259738	2		525	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574032	7574034	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	TNP	ATC	ATC	GAT	novel	NA	P-0044010-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	507	146	2	ENST00000269305.4:c.994-1_995inv		p.X332_splice	ENST00000269305	NM_001126112.2	332		10/11	0.935493203259738	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.935493203259738	3		148	516	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37081756	37081756	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044010-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	222	104	0	ENST00000231790.2:c.1638G>C	p.Lys546Asn	p.K546N	ENST00000231790	NM_000249.3	546	aaG/aaC	14/19	0.935493203259738	5	FACETS	1	0.94	1	0.202	0.188	0.217	CLONAL	1	TRUE	0	0.935493203259738	5		104	1128	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959965	38959965	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044010-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	227	63	0	ENST00000357387.3:c.1967G>A	p.Ser656Asn	p.S656N	ENST00000357387	NM_152756.3	656	aGt/aAt	21/38	0.935493203259738	3	FACETS	1	0.939	1	0.502	0.469	0.535	CLONAL	1	TRUE	1	0.935493203259738	3		63	710	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924427	131924427	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044010-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	197	76	0	ENST00000265335.6:c.1100G>C	p.Arg367Thr	p.R367T	ENST00000265335		367	aGa/aCa	8/25	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.935493203259738	2		76	412	SUCCESS
AR	367	MSKCC	GRCh37	X	66941797	66941797	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044010-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4	622	59	0	ENST00000374690.3:c.2441T>C	p.Phe814Ser	p.F814S	ENST00000374690	NM_000044.3	814	tTc/tCc	6/8	0.885337010593957	3	FACETS	1	0.998	1			1	CLONAL	3	TRUE	NA	0.935493203259738	3		59	626	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593602	55593610	+	protein_altering_variant	In_Frame_Del	DEL	GTGGAAGGT	GTGGAAGGT	CAC	novel	NA	P-0045145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	134	330	1	ENST00000288135.5:c.1668_1676delinsCAC	p.Gln556_Val559delinsHisThr	p.Q556_V559delinsHT	ENST00000288135	NM_000222.2	556	caGTGGAAGGTt/caCACt	11/21	0.498044521449691	1	FACETS	0.853	0.782	0.926	0.853	0.782	0.926	CLONAL	1	FALSE	0	0.550080094894201	1		331	414	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0045145-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	162	365	0	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	1	2	FACETS	0.973	0.905	1	0.973	0.905	1	CLONAL	1	TRUE	1	0.88074851930636	2		365	378	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593602	55593610	+	protein_altering_variant	In_Frame_Del	DEL	GTGGAAGGT	GTGGAAGGT	CAC	novel	NA	P-0045145-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	171	330	1	ENST00000288135.5:c.1668_1676delinsCAC	p.Gln556_Val559delinsHisThr	p.Q556_V559delinsHT	ENST00000288135	NM_000222.2	556	caGTGGAAGGTt/caCACt	11/21	1	2	FACETS	0.959	0.893	1	0.959	0.893	1	CLONAL	1	TRUE	1	0.88074851930636	2		331	405	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0045302-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	15	393	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.465	0.338	0.618	0.465	0.338	0.618	SUBCLONAL	1	TRUE	1	0.12	2		393	538	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606697	29606697	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779282861	NA	P-0045302-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	25	407	1	ENST00000389048.3:c.1183C>A	p.Arg395Ser	p.R395S	ENST00000389048	NM_004304.4	395	Cgt/Agt	5/29	1	2	FACETS	0.916	0.721	1	0.916	0.721	1	CLONAL	1	TRUE	1	0.12	2		408	455	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0045481-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	64	415	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.144271243559517	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.144271243559517	3		415	385	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581201	48581201	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045481-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	42	481	0	ENST00000342988.3:c.505C>T	p.Gln169Ter	p.Q169*	ENST00000342988	NM_005359.5	169	Cag/Tag	5/12	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.144271243559517	2		481	462	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387324	17387324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374131612	NA	P-0045481-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	49	560	0	ENST00000359435.4:c.590C>T	p.Pro197Leu	p.P197L	ENST00000359435	NM_001033549.1	197	cCg/cTg	7/9	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.144271243559517	2		560	559	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568663	41568663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045481-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	28	427	0	ENST00000263253.7:c.4613C>T	p.Thr1538Ile	p.T1538I	ENST00000263253	NM_001429.3	1538	aCa/aTa	28/31	1	2	FACETS	0.848	0.676	1	0.848	0.676	1	CLONAL	1	TRUE	1	0.144271243559517	2		427	458	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163182	47163182	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045481-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	44	445	0	ENST00000409792.3:c.2944G>C	p.Asp982His	p.D982H	ENST00000409792	NM_014159.6	982	Gat/Cat	3/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.144271243559517	2		445	435	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964491	93964491	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045481-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	18	0	0	ENST00000369303.4:c.2406G>C	p.Trp802Cys	p.W802C	ENST00000369303	NM_004440.3	802	tgG/tgC	14/17	1	2	FACETS	0.609	0.457	0.789	0.609	0.457	0.789	SUBCLONAL	1	TRUE	1	0.144271243559517	2		0	410	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949031	44949031	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045481-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	41	176	0	ENST00000377967.4:c.3592G>A	p.Glu1198Lys	p.E1198K	ENST00000377967	NM_021140.2	1198	Gaa/Aaa	25/29	1	1	FACETS	0.93	0.784	1	1	0.976	1	CLONAL	3	TRUE	0	0.144271243559517	1		176	189	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851211	151851211	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045481-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	33	422	0	ENST00000262189.6:c.12160G>A	p.Asp4054Asn	p.D4054N	ENST00000262189	NM_170606.2	4054	Gac/Aac	48/59	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.144271243559517	2		422	451	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0047031-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	138	393	0	ENST00000288602.6:c.1397G>T	p.Gly466Val	p.G466V	ENST00000288602	NM_004333.4	466	gGa/gTa	11/18	0.167164698229815	2	FACETS	1	0.986	1	0.722	0.661	0.786	INDETERMINATE	1	TRUE	0	0.366214103768377	2		393	522	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913237	NA	P-0047031-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	126	543	2	ENST00000369535.4:c.35G>T	p.Gly12Val	p.G12V	ENST00000369535	NM_002524.4	12	gGt/gTt	2/7	0.359717002943863	1	FACETS	0.895	0.813	0.981	0.895	0.813	0.981	CLONAL	1	TRUE	0	0.366214103768377	1		545	628	SUCCESS
RET	5979	MSKCC	GRCh37	10	43613888	43613888	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047031-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	71	457	0	ENST00000355710.3:c.2354del	p.Pro785HisfsTer84	p.P785Hfs*84	ENST00000355710	NM_020975.4	784	caC/ca	13/20	1	2	FACETS	0.893	0.783	1	0.893	0.783	1	CLONAL	1	TRUE	1	0.366214103768377	2		457	434	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769051	112769051	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047031-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	107	404	0	ENST00000369452.4:c.1330C>T	p.Leu444Phe	p.L444F	ENST00000369452	NM_007373.3	444	Ctt/Ttt	7/9	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.366214103768377	2		404	569	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204925	94204925	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047031-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	112	415	0	ENST00000323929.3:c.660G>T	p.Arg220Ser	p.R220S	ENST00000323929	NM_005591.3	220	agG/agT	8/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.366214103768377	2		415	541	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344036	118344036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047031-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	61	577	0	ENST00000534358.1:c.2162G>A	p.Arg721Gln	p.R721Q	ENST00000534358	NM_005933.3	721	cGa/cAa	3/36	1	2	FACETS	0.424	0.365	0.488	0.424	0.365	0.488	SUBCLONAL	1	TRUE	1	0.366214103768377	2		577	786	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251059	99251059	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047031-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	57	559	0	ENST00000268035.6:c.363G>C	p.Glu121Asp	p.E121D	ENST00000268035	NM_000875.3	121	gaG/gaC	2/21	0.243392607004319	0	FACETS	0.456	0.392	0.525			1	SUBCLONAL	1	TRUE	0	0.366214103768377	0		559	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0047031-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	114	597	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.366214103768377	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.366214103768377	1		597	499	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873715	37873715	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047031-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	153	505	0	ENST00000269571.5:c.1880C>T	p.Pro627Leu	p.P627L	ENST00000269571		627	cCc/cTc	15/27	0.171766590536104	3	FACETS	0.834	0.766	0.904	0.834	0.766	0.904	INDETERMINATE	2	TRUE	1	0.366214103768377	3		505	593	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319080	62319080	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047031-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	111	722	0	ENST00000360203.5:c.1438G>T	p.Gly480Cys	p.G480C	ENST00000360203	NM_001283009.1	480	Ggc/Tgc	17/35	1	2	FACETS	0.931	0.838	1	0.931	0.838	1	CLONAL	1	TRUE	1	0.366214103768377	2		722	651	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947909	178947909	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047031-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	61	475	0	ENST00000263967.3:c.2784A>C	p.Gln928His	p.Q928H	ENST00000263967	NM_006218.2	928	caA/caC	19/21	1	2	FACETS	0.512	0.441	0.589	0.512	0.441	0.589	SUBCLONAL	1	TRUE	1	0.366214103768377	2		475	651	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197805	66197805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047031-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	54	458	0	ENST00000273854.3:c.2894G>A	p.Gly965Glu	p.G965E	ENST00000273854	NM_004439.5	965	gGg/gAg	17/18	1	2	FACETS	0.529	0.451	0.613	0.529	0.451	0.613	SUBCLONAL	1	TRUE	1	0.366214103768377	2		458	558	SUCCESS
APC	324	MSKCC	GRCh37	5	112174991	112174991	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047031-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	32	489	0	ENST00000257430.4:c.3700A>C	p.Ser1234Arg	p.S1234R	ENST00000257430	NM_000038.5	1234	Agt/Cgt	16/16	1	2	FACETS	0.302	0.245	0.368	0.302	0.245	0.368	SUBCLONAL	1	TRUE	1	0.366214103768377	2		489	578	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508695	106508695	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047031-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	63	610	0	ENST00000359195.3:c.689G>T	p.Ser230Ile	p.S230I	ENST00000359195	NM_002649.2	230	aGc/aTc	2/11	0.167164698229815	2	FACETS	0.505	0.436	0.58	0.253	0.218	0.29	INDETERMINATE	1	TRUE	0	0.366214103768377	2		610	681	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041007	47041007	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047031-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	66	331	0	ENST00000377604.3:c.1537G>T	p.Glu513Ter	p.E513*	ENST00000377604	NM_001204468.1	513	Gag/Tag	14/24	1	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.366214103768377	1		331	235	SUCCESS
AR	367	MSKCC	GRCh37	X	66942786	66942786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs9332971	NA	P-0047031-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	47	240	0	ENST00000374690.3:c.2567G>A	p.Arg856His	p.R856H	ENST00000374690	NM_000044.3	856	cGc/cAc	7/8	1	1	FACETS	0.835	0.711	0.97	0.835	0.711	0.97	CLONAL	1	TRUE	0	0.366214103768377	1		240	251	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0047553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	107	338	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.288872422760603	4	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	2	0.31047830088201	4		338	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0047553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	244	524	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.309194304327432	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.31047830088201	2		524	750	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586109	29586109	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	90	379	0	ENST00000356175.3:c.4329C>G	p.Phe1443Leu	p.F1443L	ENST00000356175	NM_000267.3	1443	ttC/ttG	32/57	0.31047830088201	3	FACETS	0.775	0.691	0.864	0.775	0.691	0.864	SUBCLONAL	2	TRUE	1	0.31047830088201	3		379	432	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799063	42799065	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs751580245	NA	P-0047553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	161	1423	0	ENST00000575354.2:c.4550_4552del	p.Lys1517del	p.K1517del	ENST00000575354	NM_015125.3	1516	cAGAag/cag	20/20	0.288872422760603	4	FACETS	1	0.946	1	0.523	0.478	0.57	CLONAL	1	TRUE	2	0.31047830088201	4		1423	1299	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873648	35873648	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	71	284	0	ENST00000303115.3:c.604G>C	p.Glu202Gln	p.E202Q	ENST00000303115	NM_002185.3	202	Gag/Cag	5/8	0.31047830088201	5	FACETS	0.826	0.724	0.934			1	CLONAL	2	TRUE	NA	0.31047830088201	5		284	406	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551058	41551058	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	65	518	2	ENST00000263253.7:c.3202C>T	p.Gln1068Ter	p.Q1068*	ENST00000263253	NM_001429.3	1068	Cag/Tag	17/31	0.31047830088201	3	FACETS	0.823	0.713	0.941	0.411	0.356	0.471	CLONAL	1	TRUE	1	0.31047830088201	3		520	588	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30302655	30302655	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	22	305	2	ENST00000322652.5:c.746C>T	p.Ser249Leu	p.S249L	ENST00000322652	NM_015355.2	249	tCg/tTg	7/16	0.31047830088201	3	FACETS	0.464	0.359	0.586	0.232	0.179	0.293	SUBCLONAL	1	TRUE	1	0.31047830088201	3		307	353	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117150	7117150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146490822	NA	P-0047553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	88	891	0	ENST00000302850.5:c.4066G>A	p.Glu1356Lys	p.E1356K	ENST00000302850	NM_000208.2	1356	Gag/Aag	22/22	0.309194304327432	2	FACETS	0.773	0.685	0.868	0.387	0.342	0.434	SUBCLONAL	1	TRUE	0	0.31047830088201	2		891	733	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141484	11141484	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	126	1041	0	ENST00000358026.2:c.3461T>G	p.Leu1154Arg	p.L1154R	ENST00000358026	NM_001128849.1	1154	cTc/cGc	25/36	0.309194304327432	2	FACETS	1	0.928	1	0.514	0.466	0.566	CLONAL	1	TRUE	0	0.31047830088201	2		1041	789	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851498	63851498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	63	564	0	ENST00000279873.7:c.2276G>A	p.Arg759Lys	p.R759K	ENST00000279873	NM_032199.2	759	aGa/aAa	10/10	1	2	FACETS	0.854	0.74	0.977	0.854	0.74	0.977	CLONAL	1	TRUE	1	0.31047830088201	2		564	475	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892212	9892212	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	320	713	0	ENST00000330684.3:c.2278G>T	p.Gly760Cys	p.G760C	ENST00000330684	NM_001134407.1	760	Ggt/Tgt	11/13	0.286358317600288	4	FACETS	0.933	0.887	0.979	0.933	0.887	0.979	CLONAL	4	TRUE	0	0.31047830088201	4		713	724	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141569579	141569582	+	frameshift_variant	Frame_Shift_Del	DEL	ACAA	ACAA	-	novel	NA	P-0047553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	51	491	0	ENST00000220592.5:c.702_705del	p.Cys235LysfsTer15	p.C235Kfs*15	ENST00000220592	NM_012154.3	234	gtTTGT/gt	6/19	0.31047830088201	4	FACETS	0.662	0.562	0.773	0.221	0.187	0.258	SUBCLONAL	1	TRUE	1	0.31047830088201	4		491	650	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753188	42753188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780415692	NA	P-0047553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	154	1233	0	ENST00000222329.4:c.1076C>T	p.Pro359Leu	p.P359L	ENST00000222329	NM_006494.2	359	cCg/cTg	4/4	0.288872422760603	4	FACETS	1	0.962	1	0.547	0.499	0.597	CLONAL	1	TRUE	2	0.31047830088201	4		1233	1188	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552123	29552123	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	29	170	0	ENST00000356175.3:c.1856G>A	p.Arg619Lys	p.R619K	ENST00000356175	NM_000267.3	619	aGa/aAa	17/57	0.31047830088201	3	FACETS	1	0.836	1	0.519	0.419	0.63	CLONAL	1	TRUE	1	0.31047830088201	3		170	208	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021843	246021843	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1336136860	NA	P-0047553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	101	743	0	ENST00000388985.4:c.1031T>A	p.Leu344Ter	p.L344*	ENST00000388985		344	tTg/tAg	10/12	0.31047830088201	3	FACETS	0.981	0.877	1	0.491	0.438	0.546	CLONAL	1	TRUE	1	0.31047830088201	3		743	766	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090400	77090400	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	140	477	0	ENST00000356341.3:c.325A>T	p.Thr109Ser	p.T109S	ENST00000356341	NM_002576.4	109	Aca/Tca	4/15	0.31047830088201	3	FACETS	0.981	0.898	1	0.981	0.898	1	CLONAL	2	TRUE	1	0.31047830088201	3		477	531	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022371	12022371	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	53	1051	0	ENST00000396373.4:c.477G>C	p.Gln159His	p.Q159H	ENST00000396373	NM_001987.4	159	caG/caC	5/8	0.288872422760603	4	FACETS	0.425	0.361	0.496	0.212	0.18	0.248	SUBCLONAL	1	TRUE	2	0.31047830088201	4		1051	1053	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022825	12022825	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	54	742	0	ENST00000396373.4:c.931G>T	p.Asp311Tyr	p.D311Y	ENST00000396373	NM_001987.4	311	Gac/Tac	5/8	0.288872422760603	4	FACETS	0.577	0.492	0.671	0.289	0.246	0.336	SUBCLONAL	1	TRUE	2	0.31047830088201	4		742	790	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120722	115120722	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	173	1056	0	ENST00000257566.3:c.284C>A	p.Pro95His	p.P95H	ENST00000257566	NM_016569.3	95	cCc/cAc	1/8	0.288872422760603	4	FACETS	1	0.988	1	0.725	0.667	0.786	CLONAL	1	TRUE	2	0.31047830088201	4		1056	1007	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129359	2129359	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	475	1129	0	ENST00000219476.3:c.3214A>C	p.Ser1072Arg	p.S1072R	ENST00000219476	NM_000548.3	1072	Agc/Cgc	28/42	0.31047830088201	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.31047830088201	3		1129	1012	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671675	67671675	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	158	565	0	ENST00000264010.4:c.2084A>C	p.Glu695Ala	p.E695A	ENST00000264010	NM_006565.3	695	gAg/gCg	12/12	0.309194304327432	2	FACETS	0.951	0.877	1	0.951	0.877	1	CLONAL	2	TRUE	0	0.31047830088201	2		565	535	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117680	70117680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	162	1211	0	ENST00000245479.2:c.148G>A	p.Glu50Lys	p.E50K	ENST00000245479	NM_000346.3	50	Gag/Aag	1/3	0.31047830088201	3	FACETS	1	0.974	1	0.575	0.527	0.626	CLONAL	1	TRUE	1	0.31047830088201	3		1211	1048	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793308	33793308	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	24	361	0	ENST00000498907.2:c.13G>C	p.Asp5His	p.D5H	ENST00000498907	NM_004364.3	5	Gac/Cac	1/1	0.288872422760603	4	FACETS	0.599	0.47	0.749	0.3	0.235	0.375	SUBCLONAL	1	TRUE	2	0.31047830088201	4		361	338	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920629	96920629	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	93	536	0	ENST00000258439.3:c.351del	p.Pro118ArgfsTer6	p.P118Rfs*6	ENST00000258439	NM_001193304.2	117	ggG/gg	3/4	0.288872422760603	4	FACETS	0.79	0.705	0.88	0.79	0.705	0.88	SUBCLONAL	2	TRUE	2	0.31047830088201	4		536	497	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128018917	128018917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	55	437	0	ENST00000285398.2:c.1951G>A	p.Val651Ile	p.V651I	ENST00000285398	NM_000122.1	651	Gtt/Att	13/15	1	2	FACETS	0.906	0.778	1	0.906	0.778	1	CLONAL	1	TRUE	1	0.31047830088201	2		437	391	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281574	198281574	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	66	549	1	ENST00000335508.6:c.557G>T	p.Gly186Val	p.G186V	ENST00000335508	NM_012433.2	186	gGa/gTa	6/25	1	2	FACETS	0.818	0.711	0.933	0.818	0.711	0.933	CLONAL	1	TRUE	1	0.31047830088201	2		550	520	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573970	41573970	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	100	774	0	ENST00000263253.7:c.6255C>G	p.Ile2085Met	p.I2085M	ENST00000263253	NM_001429.3	2085	atC/atG	31/31	0.31047830088201	3	FACETS	0.902	0.805	1	0.451	0.402	0.503	CLONAL	1	TRUE	1	0.31047830088201	3		774	825	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574076	41574076	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	91	700	1	ENST00000263253.7:c.6361C>T	p.Gln2121Ter	p.Q2121*	ENST00000263253	NM_001429.3	2121	Cag/Tag	31/31	0.31047830088201	3	FACETS	0.994	0.883	1	0.497	0.441	0.557	CLONAL	1	TRUE	1	0.31047830088201	3		701	681	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729930	41729930	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	87	893	1	ENST00000242208.4:c.599A>T	p.Glu200Val	p.E200V	ENST00000242208	NM_002192.2	200	gAg/gTg	3/3	0.31047830088201	5	FACETS	0.86	0.76	0.968	0.287	0.253	0.323	CLONAL	1	TRUE	2	0.31047830088201	5		894	955	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846104	128846104	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	277	1067	0	ENST00000249373.3:c.1034C>A	p.Ala345Asp	p.A345D	ENST00000249373	NM_005631.4	345	gCc/gAc	5/12	0.31047830088201	3	FACETS	1	0.954	1			1	CLONAL	2	TRUE	NA	0.31047830088201	3		1067	1013	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534663	140534663	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	52	250	0	ENST00000288602.6:c.250G>C	p.Glu84Gln	p.E84Q	ENST00000288602	NM_004333.4	84	Gaa/Caa	3/18	0.31047830088201	7	FACETS	1	0.932	1	0.234	0.199	0.273	CLONAL	1	TRUE	2	0.31047830088201	7		250	508	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740348	145740348	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs774637277	NA	P-0047553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	140	1389	0	ENST00000428558.2:c.1592C>G	p.Ser531Cys	p.S531C	ENST00000428558	NM_004260.3	531	tCt/tGt	9/22	0.31047830088201	4	FACETS	0.947	0.86	1	0.316	0.286	0.347	CLONAL	1	TRUE	1	0.31047830088201	4		1389	1248	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909659	76909659	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	56	344	0	ENST00000373344.5:c.4246C>T	p.Gln1416Ter	p.Q1416*	ENST00000373344	NM_000489.3	1416	Cag/Tag	14/35	0.309194304327432	2	FACETS	0.939	0.808	1	0.47	0.404	0.541	CLONAL	1	TRUE	0	0.31047830088201	2		344	384	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913492	NA	P-0048472-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	69	150	0	ENST00000286548.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000286548	NM_002072.3	209	cAa/cTa	5/7	0.726955533897173	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.726955533897173	1		150	101	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	219	202	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.86	2		202	489	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	131	988	5	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.295	0.267	0.325	0.295	0.267	0.325	SUBCLONAL	1	TRUE	1	0.86	2		993	1032	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	10	342	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.049	0.032	0.07	0.049	0.032	0.07	SUBCLONAL	1	TRUE	1	0.86	2		342	476	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	156	527	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	1	2	FACETS	0.453	0.415	0.493	0.453	0.415	0.493	SUBCLONAL	1	TRUE	1	0.86	2		527	800	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	358	200	12	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.86	2		212	639	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105978	27105979	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	318	542	0	ENST00000324856.7:c.5591_5592del	p.Glu1864AlafsTer36	p.E1864Afs*36	ENST00000324856	NM_006015.4	1863	acAGag/acag	20/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.86	2		542	701	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521525	46521525	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	377	387	0	ENST00000262741.5:c.883del	p.Met295Ter	p.M295*	ENST00000262741	NM_003629.3	295	Atg/tg	7/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.86	2		387	875	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256511	115256511	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	371	421	0	ENST00000369535.4:c.200T>C	p.Met67Thr	p.M67T	ENST00000369535	NM_002524.4	67	aTg/aCg	3/7	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.86	2		421	739	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100728	8100728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs771019738	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	419	870	4	ENST00000346208.3:c.708del	p.Ser237AlafsTer28	p.S237Afs*28	ENST00000346208		234	ttC/tt	3/6	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.86	2		874	966	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712017	89712017	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	116	181	0	ENST00000371953.3:c.634+1G>A		p.X212_splice	ENST00000371953	NM_000314.4	212			1	2	FACETS	0.921	0.843	1	0.921	0.843	1	CLONAL	1	TRUE	1	0.86	2		181	293	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717646	89717647	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	227	322	0	ENST00000371953.3:c.672dup	p.Tyr225IlefsTer18	p.Y225Ifs*18	ENST00000371953	NM_000314.4	224	ata/atAa	7/9	1	2	FACETS	0.931	0.875	0.988	0.931	0.875	0.988	CLONAL	1	TRUE	1	0.86	2		322	567	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572092	64572093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767319284	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	166	738	2	ENST00000312049.6:c.1546dup	p.Arg516ProfsTer15	p.R516Pfs*15	ENST00000312049	NM_130799.2	516	cgg/cCgg	10/10	1	2	FACETS	0.403	0.369	0.437	0.403	0.369	0.437	SUBCLONAL	1	TRUE	1	0.86	2		740	959	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996767	100996768	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	279	356	0	ENST00000325455.5:c.1759dup	p.Cys587LeufsTer2	p.C587Lfs*2	ENST00000325455	NM_001202474.3	587	tgt/tTgt	2/8	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.86	2		356	593	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111958674	111958674	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	137	514	0	ENST00000375549.3:c.146T>A	p.Ile49Lys	p.I49K	ENST00000375549	NM_003002.3	49	aTa/aAa	2/4	1	2	FACETS	0.429	0.391	0.47	0.429	0.391	0.47	SUBCLONAL	1	TRUE	1	0.86	2		514	742	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475143	475143	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	284	324	0	ENST00000399788.2:c.494T>A	p.Ile165Asn	p.I165N	ENST00000399788	NM_001042603.1	165	aTt/aAt	4/28	0.204463354913566	1	FACETS	0.593	0.562	0.624	0.593	0.562	0.624	INDETERMINATE	1	TRUE	0	0.86	1		324	635	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022514	12022514	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1463554644	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	398	807	0	ENST00000396373.4:c.620A>G	p.Asn207Ser	p.N207S	ENST00000396373	NM_001987.4	207	aAc/aGc	5/8	1	2	FACETS	0.978	0.934	1	0.978	0.934	1	CLONAL	1	TRUE	1	0.86	2		807	946	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431834	49431834	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	433	753	2	ENST00000301067.7:c.9305del	p.Pro3102LeufsTer17	p.P3102Lfs*17	ENST00000301067	NM_003482.3	3102	cCt/ct	34/54	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.86	2		755	896	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209309	133209309	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	456	899	0	ENST00000320574.5:c.6077G>T	p.Arg2026Met	p.R2026M	ENST00000320574	NM_006231.2	2026	aGg/aTg	44/49	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.86	2		899	1005	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944687	32944687	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	248	283	0	ENST00000380152.3:c.8480C>A	p.Pro2827His	p.P2827H	ENST00000380152		2827	cCt/cAt	19/27	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.86	2		283	547	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954052	32954052	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs397508038	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	201	183	0	ENST00000380152.3:c.9117+2T>C		p.X3039_splice	ENST00000380152		3039			1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.86	2		183	467	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434973	110434973	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	193	718	0	ENST00000375856.3:c.3428del	p.Gly1143AlafsTer116	p.G1143Afs*116	ENST00000375856	NM_003749.2	1143	gGc/gc	1/2	0.860016156572359	2	FACETS	0.449	0.415	0.485			1	SUBCLONAL	1	TRUE	NA	0.86	2		718	999	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437601	110437601	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	477	808	0	ENST00000375856.3:c.800C>A	p.Pro267His	p.P267H	ENST00000375856	NM_003749.2	267	cCc/cAc	1/2	0.860016156572359	2	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.86	2		808	1048	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574084	95574084	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	123	84	0	ENST00000393063.1:c.2665A>G	p.Thr889Ala	p.T889A	ENST00000393063	NM_030621.3	889	Act/Gct	18/28	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.86	2		84	279	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023394	33023397	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	122	695	0	ENST00000300177.4:c.505_508del	p.Arg169SerfsTer4	p.R169Sfs*4	ENST00000300177	NM_001191322.1	168	aAGAGa/aa	2/2	1	2	FACETS	0.305	0.275	0.336	0.305	0.275	0.336	SUBCLONAL	1	TRUE	1	0.86	2		695	931	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347983	347983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760961378	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	517	1130	1	ENST00000262320.3:c.1523del	p.Gly508ValfsTer197	p.G508Vfs*197	ENST00000262320	NM_003502.3	508	gGt/gt	6/11	1	2	FACETS	0.971	0.932	1	0.971	0.932	1	CLONAL	1	TRUE	1	0.86	2		1131	1238	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104366	2104366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	503	765	0	ENST00000219476.3:c.406C>A	p.Leu136Ile	p.L136I	ENST00000219476	NM_000548.3	136	Ctt/Att	5/42	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.86	2		765	1117	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820594	3820594	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	163	806	0	ENST00000262367.5:c.2857C>A	p.His953Asn	p.H953N	ENST00000262367	NM_004380.2	953	Cac/Aac	14/31	1	2	FACETS	0.338	0.31	0.368	0.338	0.31	0.368	SUBCLONAL	1	TRUE	1	0.86	2		806	1120	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274133	10274133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs796052542	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	442	778	0	ENST00000330684.3:c.136G>A	p.Val46Met	p.V46M	ENST00000330684	NM_001134407.1	46	Gtg/Atg	2/13	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.86	2		778	960	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830807	72830807	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	386	675	1	ENST00000268489.5:c.5774del	p.Gly1925ValfsTer72	p.G1925Vfs*72	ENST00000268489	NM_006885.3	1925	gGt/gt	9/10	1	2	FACETS	0.982	0.937	1	0.982	0.937	1	CLONAL	1	TRUE	1	0.86	2		676	914	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	329	724	7	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.994	0.945	1	0.994	0.945	1	CLONAL	1	TRUE	1	0.86	2		731	770	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527527	29527527	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	89	408	0	ENST00000356175.3:c.978del	p.Lys326AsnfsTer50	p.K326Nfs*50	ENST00000356175	NM_000267.3	326	Aaa/aa	9/57	1	2	FACETS	0.306	0.271	0.343	0.306	0.271	0.343	SUBCLONAL	1	TRUE	1	0.86	2		408	677	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552116	29552116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1131691135	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	34	104	0	ENST00000356175.3:c.1849G>A	p.Ala617Thr	p.A617T	ENST00000356175	NM_000267.3	617	Gca/Aca	17/57	1	2	FACETS	0.504	0.417	0.598	0.504	0.417	0.598	SUBCLONAL	1	TRUE	1	0.86	2		104	157	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487545	38487547	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	361	815	0	ENST00000254066.5:c.82_84del	p.Phe28del	p.F28del	ENST00000254066	NM_000964.3	25	gcCTTc/gcc	2/9	1	2	FACETS	0.925	0.88	0.97	0.925	0.88	0.97	CLONAL	1	TRUE	1	0.86	2		815	908	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677765	47677765	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	297	518	0	ENST00000347630.2:c.1100del	p.Pro367HisfsTer5	p.P367Hfs*5	ENST00000347630	NM_001007230.1	367	cCa/ca	11/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.86	2		518	673	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602329	10602329	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	553	1022	0	ENST00000171111.5:c.1249G>T	p.Gly417Trp	p.G417W	ENST00000171111	NM_203500.1	417	Ggg/Tgg	3/6	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.86	2		1022	1227	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602863	10602863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	512	942	0	ENST00000171111.5:c.715G>A	p.Val239Met	p.V239M	ENST00000171111	NM_203500.1	239	Gtg/Atg	3/6	1	2	FACETS	0.97	0.931	1	0.97	0.931	1	CLONAL	1	TRUE	1	0.86	2		942	1228	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610577	10610577	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	451	880	0	ENST00000171111.5:c.133T>A	p.Ser45Thr	p.S45T	ENST00000171111	NM_203500.1	45	Tcc/Acc	2/6	1	2	FACETS	0.992	0.95	1	0.992	0.95	1	CLONAL	1	TRUE	1	0.86	2		880	1057	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285059	15285059	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs367543285	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	466	894	0	ENST00000263388.2:c.4556T>C	p.Leu1519Pro	p.L1519P	ENST00000263388	NM_000435.2	1519	cTg/cCg	25/33	1	2	FACETS	0.962	0.922	1	0.962	0.922	1	CLONAL	1	TRUE	1	0.86	2		894	1126	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302812	15302812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	473	995	0	ENST00000263388.2:c.638G>A	p.Arg213Lys	p.R213K	ENST00000263388	NM_000435.2	213	aGg/aAg	4/33	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.86	2		995	1076	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210371	36210371	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	431	706	2	ENST00000222270.7:c.364G>T	p.Glu122Ter	p.E122*	ENST00000222270	NM_014727.1	122	Gag/Tag	2/37	1	2	FACETS	0.962	0.92	1	0.962	0.92	1	CLONAL	1	TRUE	1	0.86	2		708	1042	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605120	46605120	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	475	850	0	ENST00000263734.3:c.1337G>T	p.Ser446Ile	p.S446I	ENST00000263734	NM_001430.4	446	aGc/aTc	10/16	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.86	2		850	1001	SUCCESS
REL	5966	MSKCC	GRCh37	2	61144033	61144033	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	178	175	0	ENST00000295025.8:c.416A>C	p.Asp139Ala	p.D139A	ENST00000295025	NM_002908.2	139	gAt/gCt	5/11	1	2	FACETS	0.993	0.926	1	0.993	0.926	1	CLONAL	1	TRUE	1	0.86	2		175	417	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274578	198274578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	430	637	0	ENST00000335508.6:c.820C>T	p.Pro274Ser	p.P274S	ENST00000335508	NM_012433.2	274	Cca/Tca	7/25	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.86	2		637	974	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116180	209116180	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	232	268	0	ENST00000345146.2:c.96del	p.Tyr34ThrfsTer11	p.Y34Tfs*11	ENST00000345146	NM_005896.2	32	ttT/tt	3/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.86	2		268	527	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	62	610	2	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.125	0.107	0.144	0.125	0.107	0.144	SUBCLONAL	1	TRUE	1	0.86	2		612	1157	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368254	31368254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751741367	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	448	785	1	ENST00000328111.2:c.125G>A	p.Arg42His	p.R42H	ENST00000328111	NM_006892.3	42	cGc/cAc	2/23	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.86	2		786	963	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321553	62321553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	431	882	1	ENST00000360203.5:c.2255C>T	p.Ala752Val	p.A752V	ENST00000360203	NM_001283009.1	752	gCc/gTc	25/35	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.86	2		883	968	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525925	41525925	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	191	246	0	ENST00000263253.7:c.1200T>G	p.Ile400Met	p.I400M	ENST00000263253	NM_001429.3	400	atT/atG	5/31	1	2	FACETS	0.881	0.822	0.941	0.881	0.822	0.941	CLONAL	1	TRUE	1	0.86	2		246	504	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266134	41266136	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs587776850	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	195	308	0	ENST00000349496.5:c.133_135del	p.Ser45del	p.S45del	ENST00000349496	NM_001904.3	44	cCTTct/cct	3/15	1	2	FACETS	0.945	0.883	1	0.945	0.883	1	CLONAL	1	TRUE	1	0.86	2		308	480	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643587	52643587	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs748868964	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	86	360	0	ENST00000394830.3:c.2309A>G	p.His770Arg	p.H770R	ENST00000394830	NM_018313.4	770	cAt/cGt	17/30	1	2	FACETS	0.292	0.258	0.328	0.292	0.258	0.328	SUBCLONAL	1	TRUE	1	0.86	2		360	685	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	71	277	0	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	1	2	FACETS	0.357	0.312	0.405	0.357	0.312	0.405	SUBCLONAL	1	TRUE	1	0.86	2		277	463	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664989	138664989	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	125	237	0	ENST00000330315.3:c.576del	p.Lys193SerfsTer78	p.K193Sfs*78	ENST00000330315	NM_023067.3	192	ccC/cc	1/1	1	2	FACETS	0.87	0.798	0.944	0.87	0.798	0.944	CLONAL	1	TRUE	1	0.86	2		237	334	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916726	178916726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772110575	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	83	241	1	ENST00000263967.3:c.113G>A	p.Arg38His	p.R38H	ENST00000263967	NM_006218.2	38	cGt/cAt	2/21	1	2	FACETS	0.472	0.419	0.528	0.472	0.419	0.528	SUBCLONAL	1	TRUE	1	0.86	2		242	409	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	10	400	1	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.05	0.033	0.071	0.05	0.033	0.071	SUBCLONAL	1	TRUE	1	0.86	2		401	468	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	77	250	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	1	2	FACETS	0.335	0.294	0.378	0.335	0.294	0.378	SUBCLONAL	1	TRUE	1	0.86	2		250	535	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920102	1920102	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	468	707	0	ENST00000382891.5:c.1162A>T	p.Lys388Ter	p.K388*	ENST00000382891	NM_133335.3	388	Aag/Tag	5/22	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.86	2		707	1057	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509085	66509085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	43	202	0	ENST00000273854.3:c.242del	p.Asn81MetfsTer24	p.N81Mfs*24	ENST00000273854	NM_004439.5	81	aAt/at	2/18	1	2	FACETS	0.33	0.277	0.388	0.33	0.277	0.388	SUBCLONAL	1	TRUE	1	0.86	2		202	303	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518020	187518020	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755404071	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	311	535	0	ENST00000441802.2:c.12674C>T	p.Thr4225Met	p.T4225M	ENST00000441802	NM_005245.3	4225	aCg/aTg	25/27	1	2	FACETS	0.985	0.935	1	0.985	0.935	1	CLONAL	1	TRUE	1	0.86	2		535	734	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1268653	1268653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775014633	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	483	903	1	ENST00000310581.5:c.2564C>T	p.Ala855Val	p.A855V	ENST00000310581	NM_198253.2	855	gCg/gTg	9/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.86	2		904	1092	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38949853	38949853	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	175	182	0	ENST00000357387.3:c.4097T>C	p.Met1366Thr	p.M1366T	ENST00000357387	NM_152756.3	1366	aTg/aCg	31/38	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.86	2		182	381	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036914	180036914	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	196	677	0	ENST00000261937.6:c.3798A>C	p.Lys1266Asn	p.K1266N	ENST00000261937	NM_182925.4	1266	aaA/aaC	28/30	1	2	FACETS	0.522	0.483	0.561	0.522	0.483	0.561	SUBCLONAL	1	TRUE	1	0.86	2		677	874	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793664	89793664	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	195	188	0	ENST00000336032.3:c.733A>C	p.Ile245Leu	p.I245L	ENST00000336032	NM_006813.2	245	Att/Ctt	2/2	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.86	2		188	451	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935613	13935613	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs761964463	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	311	483	0	ENST00000405192.2:c.1243A>G	p.Met415Val	p.M415V	ENST00000405192	NM_001163147.1	415	Atg/Gtg	12/12	0.0929188346725953	3	FACETS	0.782	0.744	0.821	0.782	0.744	0.821	INDETERMINATE	2	TRUE	1	0.86	3		483	661	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012386	152012386	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	33	149	0	ENST00000262189.6:c.427del	p.Ser143ValfsTer3	p.S143Vfs*3	ENST00000262189	NM_170606.2	143	Agt/gt	4/59	1	2	FACETS	0.194	0.158	0.235	0.194	0.158	0.235	SUBCLONAL	1	TRUE	1	0.86	2		149	396	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371789	55371789	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	145	218	0	ENST00000297316.4:c.479C>G	p.Ala160Gly	p.A160G	ENST00000297316	NM_022454.3	160	gCt/gGt	2/2	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.86	2		218	281	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117861270	117861270	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	39	209	0	ENST00000297338.2:c.1621-2A>G		p.X541_splice	ENST00000297338	NM_006265.2	541			1	2	FACETS	0.184	0.152	0.219	0.184	0.152	0.219	SUBCLONAL	1	TRUE	1	0.86	2		209	494	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572642	141572642	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	392	714	0	ENST00000220592.5:c.428T>C	p.Leu143Ser	p.L143S	ENST00000220592	NM_012154.3	143	tTa/tCa	4/19	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.86	2		714	847	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020768	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs926053251	NA	P-0048528-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	20	523	0	ENST00000358127.4:c.77T>G	p.Val26Gly	p.V26G	ENST00000358127	NM_001280556.1	26	gTt/gGt	2/10	1	2	FACETS	0.056	0.042	0.072	0.056	0.042	0.072	SUBCLONAL	1	TRUE	1	0.86	2		523	831	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0048544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	552	618	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.740731343110195	4	FACETS	0.925	0.907	0.943	0.925	0.907	0.943	CLONAL	4	TRUE	0	0.863020760912893	4		618	644	SUCCESS
YES1	7525	MSKCC	GRCh37	18	747978	747978	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	78	410	0	ENST00000314574.4:c.412A>G	p.Lys138Glu	p.K138E	ENST00000314574	NM_005433.3	138	Aag/Gag	4/12	NA	2	FACETS	0.479	0.424	0.539			1	INDETERMINATE	1	TRUE	NA	0.863020760912893	2		410	377	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876310	35876310	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	124	396	0	ENST00000303115.3:c.1102A>C	p.Thr368Pro	p.T368P	ENST00000303115	NM_002185.3	368	Aca/Cca	8/8	0.863020760912893	6	FACETS	0.96	0.869	1	0.24	0.217	0.264	CLONAL	1	TRUE	2	0.863020760912893	6		396	816	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890147	76890147	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0048544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	64	191	1	ENST00000373344.5:c.4747A>T	p.Lys1583Ter	p.K1583*	ENST00000373344	NM_000489.3	1583	Aag/Tag	17/35	1	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.863020760912893	1		192	74	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0048704-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	304	293	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.557333310805224	5	FACETS	0.98	0.931	1	0.98	0.931	1	CLONAL	3	TRUE	2	0.557333310805224	5		293	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0048704-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	445	660	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.542435991184619	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.557333310805224	2		660	773	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575109	48575109	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048704-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	130	474	0	ENST00000342988.3:c.303G>T	p.Trp101Cys	p.W101C	ENST00000342988	NM_005359.5	101	tgG/tgT	3/12	0.557333310805224	1	FACETS	0.9	0.825	0.976	0.9	0.825	0.976	CLONAL	1	TRUE	0	0.557333310805224	1		474	374	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100949	27100949	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048704-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	427	501	0	ENST00000324856.7:c.4231C>T	p.Gln1411Ter	p.Q1411*	ENST00000324856	NM_006015.4	1411	Cag/Tag	18/20	0.543319131640632	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.557333310805224	3		501	917	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376665	8376665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753080783	NA	P-0048704-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	127	437	0	ENST00000356435.5:c.4448C>T	p.Thr1483Met	p.T1483M	ENST00000356435		1483	aCg/aTg	27/35	0.518199898343733	3	FACETS	1	0.912	1	0.334	0.304	0.366	CLONAL	1	TRUE	0	0.557333310805224	3		437	581	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895664	28895664	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048704-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	73	424	0	ENST00000282397.4:c.3110A>C	p.Lys1037Thr	p.K1037T	ENST00000282397	NM_002019.4	1037	aAg/aCg	23/30	1	2	FACETS	0.439	0.384	0.498	0.439	0.384	0.498	SUBCLONAL	1	TRUE	1	0.557333310805224	2		424	597	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355035	73355035	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048704-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	150	449	0	ENST00000377767.4:c.335T>C	p.Val112Ala	p.V112A	ENST00000377767	NM_014953.3	112	gTg/gCg	2/21	1	2	FACETS	0.993	0.913	1	0.993	0.913	1	CLONAL	1	TRUE	1	0.557333310805224	2		449	542	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0050403-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	6205	487	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.541910621279902	29	FACETS	0.985	0.98	0.989			1	CLONAL	29	TRUE	NA	0.541910621279902	29		487	6669	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440904	56440904	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1458799446	NA	P-0050403-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	312	662	0	ENST00000407977.2:c.433C>T	p.Arg145Ter	p.R145*	ENST00000407977		145	Cga/Tga	4/10	0.541910621279902	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.541910621279902	2		662	529	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240375	98240375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1293146883	NA	P-0050403-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	115	394	0	ENST00000331920.6:c.1309G>A	p.Val437Ile	p.V437I	ENST00000331920	NM_000264.3	437	Gtc/Atc	9/24	0.525941189723993	4	FACETS	1	0.946	1	0.357	0.322	0.394	CLONAL	1	TRUE	1	0.541910621279902	4		394	611	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847399	68847399	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0050403-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	268	380	0	ENST00000261769.5:c.1320+1G>T		p.X440_splice	ENST00000261769	NM_004360.3	440			0.541910621279902	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.541910621279902	2		380	439	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918577	94918577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050403-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	111	390	0	ENST00000536441.1:c.605C>T	p.Ala202Val	p.A202V	ENST00000536441	NM_144665.3	202	gCt/gTt	5/10	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.541910621279902	2		390	383	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208043	5208043	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050403-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	27	511	0	ENST00000357368.4:c.5668T>C	p.Phe1890Leu	p.F1890L	ENST00000357368	NM_002850.3	1890	Ttc/Ctc	37/38	1	2	FACETS	0.199	0.158	0.247	0.199	0.158	0.247	SUBCLONAL	1	TRUE	1	0.541910621279902	2		511	500	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858298	27858298	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050403-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	130	598	0	ENST00000359303.2:c.273G>A	p.Met91Ile	p.M91I	ENST00000359303	NM_003535.2	91	atG/atA	1/1	0.522296385339268	3	FACETS	0.829	0.752	0.909	0.414	0.376	0.455	CLONAL	1	TRUE	1	0.541910621279902	3		598	736	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359017	81359017	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050403-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	26	398	0	ENST00000222390.5:c.944G>C	p.Gly315Ala	p.G315A	ENST00000222390	NM_000601.4	315	gGc/gCc	8/18	0.522296385339268	3	FACETS	0.265	0.209	0.329	0.132	0.104	0.165	SUBCLONAL	1	TRUE	1	0.541910621279902	3		398	461	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981363	68981363	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050403-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	60	242	0	ENST00000288368.4:c.1435A>T	p.Ile479Phe	p.I479F	ENST00000288368	NM_024870.2	479	Att/Ttt	12/40	0.473266854443794	4	FACETS	1	0.937	1	0.569	0.494	0.649	CLONAL	1	TRUE	2	0.541910621279902	4		242	300	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0050532-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	2641	457	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.37824199791091	37	FACETS	0.992	0.982	1	0.992	0.982	1	CLONAL	33	TRUE	4	0.37824199791091	37		457	3250	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268969	55268969	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050532-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	3257	527	0	ENST00000275493.2:c.3035A>T	p.Asp1012Val	p.D1012V	ENST00000275493	NM_005228.3	1012	gAt/gTt	25/28	0.37824199791091	37	FACETS	0.986	0.977	0.996	0.986	0.977	0.996	CLONAL	33	TRUE	4	0.37824199791091	37		527	4032	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63973786	63973786	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050532-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	90	444	0	ENST00000398590.3:c.1147G>A	p.Asp383Asn	p.D383N	ENST00000398590	NM_001177387.1	383	Gat/Aat	9/14	0.376811127213384	3	FACETS	0.879	0.78	0.984	0.439	0.39	0.492	CLONAL	1	TRUE	1	0.37824199791091	3		444	644	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204782	128204782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050532-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	94	499	0	ENST00000341105.2:c.659G>A	p.Ser220Asn	p.S220N	ENST00000341105	NM_032638.4	220	aGc/aAc	3/6	0.315047435584328	4	FACETS	0.895	0.796	1	0.448	0.398	0.501	CLONAL	1	TRUE	2	0.37824199791091	4		499	765	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490653	20490653	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050532-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	58	436	0	ENST00000346618.3:c.1390T>G	p.Cys464Gly	p.C464G	ENST00000346618	NM_001949.4	464	Tgt/Ggt	7/7	0.311970586217232	3	FACETS	0.795	0.684	0.915	0.397	0.342	0.458	CLONAL	1	TRUE	1	0.37824199791091	3		436	459	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050545-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	148	789	0				ENST00000310581	NM_198253.2	-/1132			0.374295569178699	4	FACETS	0.831	0.762	0.903	0.831	0.762	0.903	CLONAL	2	TRUE	2	0.410618725077334	4		789	612	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0050545-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	438	534	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.410618725077334	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.410618725077334	3		534	784	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8497247	8497247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050545-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	99	285	0	ENST00000356435.5:c.2344G>A	p.Glu782Lys	p.E782K	ENST00000356435		782	Gaa/Aaa	15/35	0.159210542436891	4	FACETS	0.85	0.765	0.94	0.85	0.765	0.94	INDETERMINATE	2	TRUE	2	0.410618725077334	4		285	400	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25990544	25990544	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0050545-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	91	374	0	ENST00000435504.4:c.683C>G	p.Ser228Ter	p.S228*	ENST00000435504		228	tCa/tGa	8/13	0.398181920746696	3	FACETS	0.813	0.722	0.91	0.407	0.361	0.455	CLONAL	1	TRUE	1	0.410618725077334	3		374	657	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050980	49050980	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0050545-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	204	334	0	ENST00000267163.4:c.2663+1G>A		p.X888_splice	ENST00000267163	NM_000321.2	888			0.410552888315604	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.410618725077334	2		334	477	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17359601	17359601	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050545-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	217	385	0	ENST00000375499.3:c.240G>C	p.Lys80Asn	p.K80N	ENST00000375499	NM_003000.2	80	aaG/aaC	3/8	0.36735128284536	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.410618725077334	3		385	568	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793095	33793095	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050545-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	113	372	0	ENST00000498907.2:c.226G>T	p.Glu76Ter	p.E76*	ENST00000498907	NM_004364.3	76	Gag/Tag	1/1	0.30731987650506	3	FACETS	1	0.946	1			1	CLONAL	1	TRUE	NA	0.410618725077334	3		372	619	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738308	190738308	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1238956903	NA	P-0050545-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	190	331	0	ENST00000441310.2:c.2560C>G	p.Leu854Val	p.L854V	ENST00000441310	NM_000534.4	854	Ctt/Gtt	12/13	0.410552888315604	2	FACETS	0.935	0.872	0.998	0.935	0.872	0.998	CLONAL	2	TRUE	0	0.410618725077334	2		331	495	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400125	41400125	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050545-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	153	382	0	ENST00000373198.4:c.634C>T	p.Gln212Ter	p.Q212*	ENST00000373198	NM_133170.3	212	Cag/Tag	5/32	0.242441228249751	3	FACETS	0.762	0.701	0.827	0.762	0.701	0.827	INDETERMINATE	2	TRUE	1	0.410618725077334	3		382	589	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260723	16260724	+	missense_variant	Missense_Mutation	DNP	TC	TC	GA	novel	NA	P-0050545-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	168	507	0	ENST00000375759.3:c.7988_7989inv	p.Val2663Gly	p.V2663G	ENST00000375759	NM_015001.2	2663	gTC/gGA	11/15	0.36735128284536	3	FACETS	1	0.962	1	0.538	0.495	0.584	CLONAL	1	TRUE	1	0.410618725077334	3		507	916	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433707	49433707	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050545-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	165	538	0	ENST00000301067.7:c.7846C>G	p.Leu2616Val	p.L2616V	ENST00000301067	NM_003482.3	2616	Ctg/Gtg	31/54	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.410618725077334	2		538	686	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960951	15960951	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050545-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	371	393	0	ENST00000268712.3:c.6269C>G	p.Ser2090Cys	p.S2090C	ENST00000268712	NM_006311.3	2090	tCt/tGt	40/46	0.410618725077334	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	0	0.410618725077334	3		393	697	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855828	45855828	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050545-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	172	532	0	ENST00000391945.4:c.1982C>A	p.Ala661Asp	p.A661D	ENST00000391945	NM_000400.3	661	gCc/gAc	21/23	0.36735128284536	3	FACETS	1	0.982	1	0.613	0.565	0.664	CLONAL	1	TRUE	1	0.410618725077334	3		532	823	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617491	158617491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050545-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	135	424	0	ENST00000263640.3:c.1165G>A	p.Glu389Lys	p.E389K	ENST00000263640	NM_001105.4	389	Gaa/Aaa	9/11	0.410552888315604	2	FACETS	1	0.962	1	0.55	0.501	0.6	CLONAL	1	TRUE	0	0.410618725077334	2		424	598	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716169	243716169	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050545-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	73	340	0	ENST00000263826.5:c.1025G>A	p.Gly342Glu	p.G342E	ENST00000263826	NM_005465.4	342	gGg/gAg	10/13	0.374295569178699	4	FACETS	0.761	0.665	0.864	0.381	0.332	0.432	SUBCLONAL	1	TRUE	2	0.410618725077334	4		340	659	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95599689	95599689	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050545-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	96	346	0	ENST00000393063.1:c.107C>G	p.Ala36Gly	p.A36G	ENST00000393063	NM_030621.3	36	gCa/gGa	3/28	0.36735128284536	3	FACETS	0.928	0.829	1	0.464	0.414	0.517	CLONAL	1	TRUE	1	0.410618725077334	3		346	607	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149985	202149985	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050545-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	117	508	0	ENST00000358485.4:c.1426G>C	p.Glu476Gln	p.E476Q	ENST00000358485	NM_001080125.1	476	Gag/Cag	8/9	0.410552888315604	2	FACETS	0.833	0.752	0.918	0.417	0.376	0.459	CLONAL	1	TRUE	0	0.410618725077334	2		508	684	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523603	106523603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050545-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	87	381	0	ENST00000359195.3:c.2755G>A	p.Glu919Lys	p.E919K	ENST00000359195	NM_002649.2	919	Gaa/Aaa	8/11	0.398181920746696	3	FACETS	0.873	0.774	0.978	0.437	0.387	0.489	CLONAL	1	TRUE	1	0.410618725077334	3		381	585	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325652	87325652	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050545-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	49	377	0	ENST00000277120.3:c.529C>A	p.Leu177Met	p.L177M	ENST00000277120		177	Ctg/Atg	6/19	1	2	FACETS	0.484	0.41	0.566	0.484	0.41	0.566	SUBCLONAL	1	TRUE	1	0.410618725077334	2		377	493	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057835	27057837	+	missense_variant	Missense_Mutation	TNP	CAG	CAG	TTT	novel	NA	P-0050545-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	264	566	0	ENST00000324856.7:c.1543_1545delinsTTT	p.Gln515Phe	p.Q515F	ENST00000324856	NM_006015.4	515	CAG/TTT	3/20	0.36735128284536	3	FACETS	0.891	0.837	0.946	0.891	0.837	0.946	CLONAL	2	TRUE	1	0.410618725077334	3		566	870	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690813	89690813	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1554897861	NA	P-0051116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	41	291	0	ENST00000371953.3:c.220A>T	p.Arg74Ter	p.R74*	ENST00000371953	NM_000314.4	74	Aga/Tga	4/9	0.469024404056222	1	FACETS	0.816	0.69	0.951	0.816	0.69	0.951	CLONAL	1	TRUE	0	0.469024404056222	1		291	164	SUCCESS
ATM	472	MSKCC	GRCh37	11	108181006	108181006	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs56399311	NA	P-0051116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	34	323	0	ENST00000278616.4:c.5882A>G	p.Tyr1961Cys	p.Y1961C	ENST00000278616	NM_000051.3	1961	tAt/tGt	39/63	1	2	FACETS	0.763	0.63	0.91	0.763	0.63	0.91	CLONAL	1	TRUE	1	0.469024404056222	2		323	190	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094969	11094969	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	154	796	0	ENST00000358026.2:c.142G>C	p.Gly48Arg	p.G48R	ENST00000358026	NM_001128849.1	48	Ggg/Cgg	2/36	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.469024404056222	2		796	589	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458586	12458586	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	245	576	0	ENST00000287820.6:c.1203G>T	p.Lys401Asn	p.K401N	ENST00000287820	NM_015869.4	401	aaG/aaT	6/7	0.265190269571722	3	FACETS	1	0.988	1	0.785	0.74	0.829	INDETERMINATE	2	TRUE	0	0.469024404056222	3		576	548	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179175	123179175	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	18	448	0	ENST00000218089.9:c.624del	p.Asp209ThrfsTer16	p.D209Tfs*16	ENST00000218089	NM_001042749.1	208	tcT/tc	8/35	1	2	FACETS	0.257	0.193	0.332	0.257	0.193	0.332	SUBCLONAL	1	TRUE	1	0.469024404056222	2		448	299	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0051742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	240	702	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.536898958459578	1	FACETS	0.93	0.873	0.989	0.93	0.873	0.989	CLONAL	1	FALSE	0	0.536898958459578	1		702	703	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0051742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	166	293	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.94	0.866	1	0.94	0.866	1	CLONAL	1	FALSE	1	0.536898958459578	2		293	658	SUCCESS
APC	324	MSKCC	GRCh37	5	112175411	112175411	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	243	280	0	ENST00000257430.4:c.4120G>T	p.Glu1374Ter	p.E1374*	ENST00000257430	NM_000038.5	1374	Gaa/Taa	16/16	0.536898958459578	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	FALSE	0	0.536898958459578	2		280	420	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380283	25380283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913528	NA	P-0051742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	180	537	0	ENST00000311936.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000311936	NM_004985.3	59	Gca/Aca	3/5	1	2	FACETS	0.896	0.829	0.967	0.896	0.829	0.967	CLONAL	1	FALSE	1	0.536898958459578	2		537	748	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939207	36939207	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs760685785	NA	P-0051742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	211	772	0	ENST00000361632.4:c.502C>T	p.Gln168Ter	p.Q168*	ENST00000361632		168	Cag/Tag	5/16	0.222876583966742	1	FACETS	0.83	0.774	0.887	0.83	0.774	0.887	INDETERMINATE	1	FALSE	0	0.536898958459578	1		772	693	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121015	29121015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121908701	NA	P-0051742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	228	702	0	ENST00000328354.6:c.542G>A	p.Arg181His	p.R181H	ENST00000328354	NM_007194.3	181	cGt/cAt	4/15	1	2	FACETS	0.956	0.893	1	0.956	0.893	1	CLONAL	1	FALSE	1	0.536898958459578	2		702	888	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974813	21974813	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	24	203	0	ENST00000304494.5:c.14C>G	p.Ala5Gly	p.A5G	ENST00000304494	NM_000077.4	5	gCg/gGg	1/3	1	2	FACETS	0.483	0.381	0.599	0.483	0.381	0.599	SUBCLONAL	1	FALSE	1	0.536898958459578	2		203	185	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1688616	1688616	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395863965	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	105	381	0	ENST00000378625.1:c.709C>T	p.Arg237Cys	p.R237C	ENST00000378625	NM_001198994.1	237	Cgc/Tgc	6/14	0.732596527885158	3	FACETS	0.89	0.802	0.982	0.445	0.401	0.491	CLONAL	1	TRUE	1	0.732596527885158	3		381	440	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935322	36935323	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs747437399	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	43	660	3	ENST00000361632.4:c.1404dup	p.Ser469GlnfsTer5	p.S469Qfs*5	ENST00000361632		468	-/C	10/16	0.732596527885158	3	FACETS	0.233	0.195	0.277	0.117	0.097	0.139	SUBCLONAL	1	TRUE	1	0.732596527885158	3		663	687	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818261	43818261	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	215	754	0	ENST00000372470.3:c.1726G>A	p.Glu576Lys	p.E576K	ENST00000372470	NM_005373.2	576	Gag/Aag	12/12	0.732596527885158	3	FACETS	1	0.983	1	0.579	0.541	0.619	CLONAL	1	TRUE	1	0.732596527885158	3		754	692	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46714200	46714200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	155	652	0	ENST00000371975.4:c.20C>T	p.Pro7Leu	p.P7L	ENST00000371975	NM_003579.3	7	cCc/cTc	2/18	0.732596527885158	3	FACETS	0.912	0.838	0.989	0.456	0.419	0.495	CLONAL	1	TRUE	1	0.732596527885158	3		652	634	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736510	85736511	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs387906351	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	113	590	1	ENST00000370580.1:c.136dup	p.Ile46AsnfsTer4	p.I46Nfs*4	ENST00000370580	NM_003921.4	46	ata/aAta	2/3	0.732596527885158	3	FACETS	0.776	0.701	0.855	0.388	0.35	0.428	SUBCLONAL	1	TRUE	1	0.732596527885158	3		591	543	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261277	115261277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	155	519	0	ENST00000438362.2:c.2444G>A	p.Arg815His	p.R815H	ENST00000438362	NM_001242891.1	815	cGc/cAc	19/20	0.732596527885158	1	FACETS	0.982	0.92	1	0.982	0.92	1	CLONAL	1	TRUE	0	0.732596527885158	1		519	273	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491115	120491115	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	177	674	0	ENST00000256646.2:c.2674C>G	p.Gln892Glu	p.Q892E	ENST00000256646	NM_024408.3	892	Cag/Gag	17/34	0.732596527885158	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.732596527885158	1		674	295	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844755	156844755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs17425856	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	454	855	0	ENST00000524377.1:c.1309C>T	p.Leu437Phe	p.L437F	ENST00000524377	NM_002529.3	437	Ctt/Ttt	11/17	0.729542174227755	3	FACETS	0.973	0.936	1	0.973	0.936	1	CLONAL	2	TRUE	1	0.732596527885158	3		855	870	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193172935	193172935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	114	443	0	ENST00000367435.3:c.983C>A	p.Ser328Tyr	p.S328Y	ENST00000367435	NM_024529.4	328	tCt/tAt	11/17	0.567128912697806	4	FACETS	1	0.935	1	0.348	0.314	0.383	CLONAL	1	TRUE	1	0.732596527885158	4		443	517	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518380	204518380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	400	705	0	ENST00000367182.3:c.1043C>T	p.Ala348Val	p.A348V	ENST00000367182	NM_001278516.1	348	gCc/gTc	11/11	0.567128912697806	4	FACETS	0.909	0.873	0.944	0.909	0.873	0.944	CLONAL	3	TRUE	1	0.732596527885158	4		705	694	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666693	206666693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782183853	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	153	637	0	ENST00000367120.3:c.2027G>A	p.Arg676Gln	p.R676Q	ENST00000367120	NM_014002.3	676	cGa/cAa	20/22	0.729542174227755	3	FACETS	0.936	0.859	1	0.468	0.429	0.508	CLONAL	1	TRUE	1	0.732596527885158	3		637	610	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610162	43610162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	386	778	0	ENST00000355710.3:c.2114C>T	p.Ser705Phe	p.S705F	ENST00000355710	NM_020975.4	705	tCc/tTc	11/20	0.729542174227755	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.732596527885158	3		778	704	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404939	70404939	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	155	601	0	ENST00000373644.4:c.2453G>A	p.Gly818Glu	p.G818E	ENST00000373644	NM_030625.2	818	gGg/gAg	4/12	0.729542174227755	3	FACETS	0.962	0.885	1	0.481	0.442	0.521	CLONAL	1	TRUE	1	0.732596527885158	3		601	601	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625291	69625291	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	47	756	0	ENST00000334134.2:c.502A>G	p.Lys168Glu	p.K168E	ENST00000334134	NM_005247.2	168	Aag/Gag	3/3	0.654447360132024	3	FACETS	0.243	0.205	0.287	0.122	0.102	0.144	SUBCLONAL	1	TRUE	1	0.732596527885158	3		756	720	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180459	94180459	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	133	643	0	ENST00000323929.3:c.1709G>C	p.Arg570Thr	p.R570T	ENST00000323929	NM_005591.3	570	aGa/aCa	15/20	0.732596527885158	1	FACETS	0.78	0.721	0.84	0.78	0.721	0.84	SUBCLONAL	1	TRUE	0	0.732596527885158	1		643	295	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427168	49427168	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	227	810	0	ENST00000301067.7:c.11320C>T	p.Gln3774Ter	p.Q3774*	ENST00000301067	NM_003482.3	3774	Cag/Tag	39/54	0.729542174227755	3	FACETS	1	0.98	1	0.559	0.523	0.597	CLONAL	1	TRUE	1	0.732596527885158	3		810	757	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865627	57865627	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	389	796	0	ENST00000228682.2:c.3104A>G	p.Asn1035Ser	p.N1035S	ENST00000228682	NM_005269.2	1035	aAc/aGc	12/12	0.729542174227755	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.732596527885158	3		796	723	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885301	111885301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762026350	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	104	592	0	ENST00000341259.2:c.1189C>T	p.Arg397Trp	p.R397W	ENST00000341259	NM_005475.2	397	Cgg/Tgg	6/8	0.371357341757168	3	FACETS	0.792	0.712	0.875	0.264	0.237	0.292	INDETERMINATE	1	TRUE	0	0.732596527885158	3		592	490	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954242	32954243	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	263	582	0	ENST00000380152.3:c.9216_9217delinsAA	p.Asp3073Asn	p.D3073N	ENST00000380152		3072	gtGGac/gtAAac	24/27	0.732596527885158	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.732596527885158	2		582	350	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240204	41240204	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	21	528	0	ENST00000379561.5:c.146C>A	p.Ala49Asp	p.A49D	ENST00000379561	NM_002015.3	49	gCt/gAt	1/3	0.732596527885158	2	FACETS	0.165	0.127	0.21	0.083	0.063	0.105	SUBCLONAL	1	TRUE	0	0.732596527885158	2		528	347	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942697	48942698	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	222	398	0	ENST00000267163.4:c.1086dup	p.Asp363Ter	p.D363*	ENST00000267163	NM_000321.2	362	ctt/cTtt	11/27	0.732596527885158	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.732596527885158	2		398	285	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434655	110434655	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	371	710	0	ENST00000375856.3:c.3746A>T	p.Asn1249Ile	p.N1249I	ENST00000375856	NM_003749.2	1249	aAt/aTt	1/2	0.732596527885158	2	FACETS	0.997	0.964	1	0.997	0.964	1	CLONAL	2	TRUE	0	0.732596527885158	2		710	508	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647957	3647957	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	482	712	0	ENST00000294008.3:c.1207A>G	p.Ser403Gly	p.S403G	ENST00000294008	NM_032444.2	403	Agc/Ggc	6/15	0.732596527885158	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.732596527885158	2		712	576	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789685	3789685	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	206	611	0	ENST00000262367.5:c.4174C>T	p.Arg1392Ter	p.R1392*	ENST00000262367	NM_004380.2	1392	Cga/Tga	25/31	0.732596527885158	2	FACETS	1	0.987	1	0.598	0.561	0.636	CLONAL	1	TRUE	0	0.732596527885158	2		611	470	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646609	23646609	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587782446	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	361	626	0	ENST00000261584.4:c.1258C>T	p.Gln420Ter	p.Q420*	ENST00000261584	NM_024675.3	420	Cag/Tag	4/13	0.732596527885158	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.732596527885158	2		626	463	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831357	72831358	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTG	rs34918837	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	91	707	3	ENST00000268489.5:c.5221_5223dup	p.Gln1741dup	p.Q1741dup	ENST00000268489	NM_006885.3	1741	-/CAA	9/10	0.732596527885158	2	FACETS	0.475	0.423	0.53	0.238	0.211	0.265	SUBCLONAL	1	TRUE	0	0.732596527885158	2		710	523	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441496	40441496	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	352	605	0	ENST00000345506.4:c.67G>T	p.Gly23Cys	p.G23C	ENST00000345506	NM_003152.3	23	Ggc/Tgc	3/20	0.732596527885158	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.732596527885158	2		605	444	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246062	41246062	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28897676	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	30	633	0	ENST00000357654.3:c.1486C>T	p.Arg496Cys	p.R496C	ENST00000357654	NM_007294.3	496	Cgt/Tgt	10/23	0.732596527885158	2	FACETS	0.191	0.154	0.234	0.096	0.077	0.117	SUBCLONAL	1	TRUE	0	0.732596527885158	2		633	428	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39576621	39576621	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	197	464	0	ENST00000262039.4:c.911C>T	p.Pro304Leu	p.P304L	ENST00000262039	NM_002647.2	304	cCa/cTa	9/25	0.671022560212885	4	FACETS	0.996	0.932	1	0.996	0.932	1	CLONAL	2	TRUE	2	0.732596527885158	4		464	468	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632363	1632363	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143787476	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	385	673	0	ENST00000344749.5:c.187G>A	p.Asp63Asn	p.D63N	ENST00000344749	NM_001136139.2	63	Gac/Aac	4/19	0.729542174227755	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.732596527885158	3		673	657	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240223	5240223	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	159	606	0	ENST00000357368.4:c.1691A>G	p.Asp564Gly	p.D564G	ENST00000357368	NM_002850.3	564	gAc/gGc	12/38	0.729542174227755	3	FACETS	0.985	0.907	1	0.493	0.453	0.533	CLONAL	1	TRUE	1	0.732596527885158	3		606	602	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276230	15276230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs114813086	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	157	637	0	ENST00000263388.2:c.5764G>A	p.Val1922Met	p.V1922M	ENST00000263388	NM_000435.2	1922	Gtg/Atg	31/33	0.729542174227755	3	FACETS	0.946	0.87	1	0.473	0.435	0.513	CLONAL	1	TRUE	1	0.732596527885158	3		637	619	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966801	18966801	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	199	677	0	ENST00000262803.5:c.1612G>A	p.Gly538Arg	p.G538R	ENST00000262803	NM_002911.3	538	Ggg/Agg	12/24	0.729542174227755	3	FACETS	0.986	0.916	1	0.493	0.458	0.529	CLONAL	1	TRUE	1	0.732596527885158	3		677	753	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383628	42383628	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555843712	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	198	662	1	ENST00000221972.3:c.403G>A	p.Asp135Asn	p.D135N	ENST00000221972	NM_021601.3	135	Gac/Aac	3/5	0.729542174227755	3	FACETS	1	0.982	1	0.58	0.539	0.621	CLONAL	1	TRUE	1	0.732596527885158	3		663	637	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	148	642	4	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	0.732596527885158	3	FACETS	0.811	0.742	0.882	0.405	0.371	0.441	CLONAL	1	TRUE	1	0.732596527885158	3		646	681	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251725	212251725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144311212	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	178	697	0	ENST00000342788.4:c.3334C>T	p.Arg1112Cys	p.R1112C	ENST00000342788	NM_005235.2	1112	Cgc/Tgc	27/28	0.732596527885158	2	FACETS	1	0.977	1	0.553	0.516	0.592	CLONAL	1	TRUE	0	0.732596527885158	2		697	439	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54956602	54956602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45483697	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	227	511	0	ENST00000312783.6:c.592G>A	p.Gly198Ser	p.G198S	ENST00000312783	NM_198436.1	198	Ggt/Agt	7/10	0.644459677438661	4	FACETS	0.88	0.826	0.936	0.88	0.826	0.936	CLONAL	2	TRUE	2	0.732596527885158	4		511	610	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764346	39764347	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	121	520	0	ENST00000288319.7:c.765dup	p.Arg256GlnfsTer29	p.R256Qfs*29	ENST00000288319	NM_182918.3	255	-/C	7/10	0.675590928384171	3	FACETS	0.903	0.82	0.989	0.451	0.41	0.495	CLONAL	1	TRUE	1	0.732596527885158	3		520	500	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30733050	30733052	+	missense_variant	Missense_Mutation	TNP	GAG	GAG	AAT	novel	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	556	627	0	ENST00000295754.5:c.1663_1665delinsAAT	p.Glu555Asn	p.E555N	ENST00000295754	NM_003242.5	555	GAG/AAT	7/7	0.732596527885158	4	FACETS	0.965	0.944	0.986	0.965	0.944	0.986	CLONAL	4	TRUE	0	0.732596527885158	4		627	681	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682399	52682400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	584	262	1	ENST00000394830.3:c.773dup	p.Asn258LysfsTer6	p.N258Kfs*6	ENST00000394830	NM_018313.4	258	aat/aaAt	8/30	0.732596527885158	4	FACETS	0.937	0.915	0.958	0.937	0.915	0.958	CLONAL	4	TRUE	0	0.732596527885158	4		263	737	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456617	138456617	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1452619662	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	219	490	1	ENST00000289153.2:c.733G>T	p.Asp245Tyr	p.D245Y	ENST00000289153	NM_006219.2	245	Gat/Tat	4/22	0.732596527885158	6	FACETS	0.936	0.873	1	0.468	0.436	0.501	CLONAL	2	TRUE	2	0.732596527885158	6		491	787	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803592	1803592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs949596399	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	611	788	3	ENST00000260795.2:c.770C>T	p.Ala257Val	p.A257V	ENST00000260795		257	gCg/gTg	6/17	0.732596527885158	5	FACETS	1	0.967	1			1	CLONAL	3	TRUE	NA	0.732596527885158	5		791	1167	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806067	1806067	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	164	570	0	ENST00000260795.2:c.1086G>T	p.Glu362Asp	p.E362D	ENST00000260795		362	gaG/gaT	8/17	0.732596527885158	5	FACETS	0.963	0.883	1			1	CLONAL	1	TRUE	NA	0.732596527885158	5		570	976	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1941423	1941423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1189008609	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	355	577	0	ENST00000382891.5:c.1799G>A	p.Arg600Gln	p.R600Q	ENST00000382891	NM_133335.3	600	cGa/cAa	9/22	0.732596527885158	5	FACETS	1	0.985	1			1	CLONAL	2	TRUE	NA	0.732596527885158	5		577	934	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541258	187541258	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	349	699	0	ENST00000441802.2:c.6482del	p.Asn2161ThrfsTer15	p.N2161Tfs*15	ENST00000441802	NM_005245.3	2161	aAc/ac	10/27	0.732596527885158	2	FACETS	0.945	0.911	0.978	0.945	0.911	0.978	CLONAL	2	TRUE	0	0.732596527885158	2		699	504	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515324	31515324	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs187981384	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	42	497	0	ENST00000344624.3:c.1061G>A	p.Arg354His	p.R354H	ENST00000344624		354	cGc/cAc	5/33	0.729542174227755	3	FACETS	0.284	0.236	0.337	0.142	0.118	0.169	SUBCLONAL	1	TRUE	1	0.732596527885158	3		497	552	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967241	93967241	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	151	430	0	ENST00000369303.4:c.2111G>A	p.Gly704Glu	p.G704E	ENST00000369303	NM_004440.3	704	gGg/gAg	12/17	0.732596527885158	2	FACETS	0.912	0.86	0.962	0.912	0.86	0.962	CLONAL	2	TRUE	0	0.732596527885158	2		430	226	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041072	112041073	+	missense_variant	Missense_Mutation	DNP	GA	GA	AC	novel	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	340	637	0	ENST00000368678.4:c.182_183delinsGT	p.Leu61Arg	p.L61R	ENST00000368678		61	cTC/cGT	3/13	0.732596527885158	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.732596527885158	2		637	449	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528132	157528132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1562353202	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	393	785	1	ENST00000346085.5:c.5857C>T	p.Arg1953Cys	p.R1953C	ENST00000346085	NM_020732.3	1953	Cgt/Tgt	20/20	0.732596527885158	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.732596527885158	2		786	535	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6029553	6029553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	280	407	0	ENST00000265849.7:c.1022G>A	p.Arg341Lys	p.R341K	ENST00000265849	NM_000535.5	341	aGg/aAg	10/15	0.732596527885158	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.732596527885158	2		407	375	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035167	6035167	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	rs757409701	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	371	573	0	ENST00000265849.7:c.901A>T	p.Lys301Ter	p.K301*	ENST00000265849	NM_000535.5	301	Aag/Tag	8/15	0.732596527885158	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.732596527885158	2		573	489	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864602	56864602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	253	558	0	ENST00000519728.1:c.565G>A	p.Asp189Asn	p.D189N	ENST00000519728	NM_002350.3	189	Gat/Aat	7/13	0.671022560212885	4	FACETS	0.905	0.852	0.959	0.905	0.852	0.959	CLONAL	2	TRUE	2	0.732596527885158	4		558	661	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117875375	117875375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057522888	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	463	500	0	ENST00000297338.2:c.268C>T	p.Arg90Trp	p.R90W	ENST00000297338	NM_006265.2	90	Cgg/Tgg	3/14	0.732596527885158	7	FACETS	1	0.988	1	0.85	0.818	0.882	CLONAL	4	TRUE	2	0.732596527885158	7		500	842	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376626	8376626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772303653	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	254	514	1	ENST00000356435.5:c.4487G>A	p.Arg1496Gln	p.R1496Q	ENST00000356435		1496	cGa/cAa	27/35	0.732596527885158	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.732596527885158	2		515	332	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911378	39911378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053323-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	298	301	0	ENST00000378444.4:c.5252C>T	p.Ser1751Leu	p.S1751L	ENST00000378444	NM_001123385.1	1751	tCa/tTa	15/15	0.699561145316258	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.732596527885158	2		301	345	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0053651-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	11	624	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.118410010158319	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		625	245	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0053822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	107	801	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.516856838457246	1	FACETS	0.346	0.31	0.385	0.346	0.31	0.385	SUBCLONAL	1	TRUE	0	0.516856838457246	1		801	887	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442539	52442540	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	188	509	0	ENST00000460680.1:c.205dup	p.Thr69AsnfsTer5	p.T69Nfs*5	ENST00000460680	NM_004656.3	69	acg/aAcg	4/17	0.516856838457246	1	FACETS	0.929	0.863	0.995	0.929	0.863	0.995	CLONAL	1	TRUE	0	0.516856838457246	1		509	581	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374776	118374778	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0053822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	141	328	0	ENST00000534358.1:c.8174_8176del	p.Asp2725del	p.D2725del	ENST00000534358	NM_005933.3	2723	gtTGAt/gtt	27/36	1	2	FACETS	0.976	0.893	1	0.976	0.893	1	CLONAL	1	TRUE	1	0.516856838457246	2		328	559	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114790	108114790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	149	344	0	ENST00000278616.4:c.607G>A	p.Asp203Asn	p.D203N	ENST00000278616	NM_000051.3	203	Gac/Aac	6/63	0.860913455915078	1	FACETS	0.946	0.901	0.988	0.946	0.901	0.988	CLONAL	1	TRUE	0	0.903928505046347	1		344	191	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595518	55595519	+	missense_variant	Missense_Mutation	DNP	AC	AC	GA	novel	NA	P-0053921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	109	338	0	ENST00000288135.5:c.2008_2009delinsGA	p.Thr670Glu	p.T670E	ENST00000288135	NM_000222.2	670	ACa/GAa	14/21	0.903928505046347	1	FACETS	0.972	0.92	1	0.972	0.92	1	CLONAL	1	TRUE	0	0.903928505046347	1		338	136	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720807	89720807	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	44	125	0	ENST00000371953.3:c.958T>A	p.Leu320Ile	p.L320I	ENST00000371953	NM_000314.4	320	Tta/Ata	8/9	1	2	FACETS	0.761	0.653	0.873	0.761	0.653	0.873	SUBCLONAL	1	TRUE	1	0.903928505046347	2		125	128	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593605	55593611	+	protein_altering_variant	In_Frame_Del	DEL	GAAGGTT	GAAGGTT	TAAG	novel	NA	P-0053921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	190	391	1	ENST00000288135.5:c.1671_1677delinsTAAG	p.Trp557_Val559delinsCysLys	p.W557_V559delinsCK	ENST00000288135	NM_000222.2	557	tgGAAGGTT/tgTAAG	11/21	0.903928505046347	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.903928505046347	1		392	227	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0053977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	72	400	1	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.278498457772994	2		401	414	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0053977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	57	487	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.989	0.851	1	0.989	0.851	1	CLONAL	1	TRUE	1	0.278498457772994	2		487	414	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249002	55249003	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGTGGA	rs397517109	NA	P-0053977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	93	593	0	ENST00000275493.2:c.2303_2311dup	p.Ser768_Asp770dup	p.S768_D770dup	ENST00000275493	NM_005228.3	768	gcc/gcCAGCGTGGAc	20/28	1	2	FACETS	0.667	0.592	0.748	0.667	0.592	0.748	SUBCLONAL	1	TRUE	1	0.278498457772994	2		593	1001	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578471	7578471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	257	1016	1	ENST00000269305.4:c.459del	p.Gly154AlafsTer16	p.G154Afs*16	ENST00000269305	NM_001126112.2	153	ccC/cc	5/11	0.160170744917522	2	FACETS	1	0.991	1	0.683	0.638	0.729	INDETERMINATE	1	TRUE	0	0.278498457772994	2		1017	1352	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286793	33286793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	49	665	0	ENST00000374542.5:c.2144C>T	p.Pro715Leu	p.P715L	ENST00000374542	NM_001141970.1	715	cCt/cTt	7/8	1	2	FACETS	0.365	0.308	0.428	0.365	0.308	0.428	SUBCLONAL	1	TRUE	1	0.278498457772994	2		665	964	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0054557-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	382	354	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.642970157763525	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.656376747157024	2		354	566	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223194	36223194	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746724776	NA	P-0054557-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	286	1343	0	ENST00000222270.7:c.5744G>A	p.Arg1915His	p.R1915H	ENST00000222270	NM_014727.1	1915	cGt/cAt	28/37	0.626782637563244	3	FACETS	0.953	0.896	1	0.477	0.448	0.507	CLONAL	1	TRUE	1	0.656376747157024	3		1343	1214	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214067	36214067	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054557-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	503	499	0	ENST00000222270.7:c.2893C>T	p.Arg965Ter	p.R965*	ENST00000222270	NM_014727.1	965	Cga/Tga	6/37	0.626782637563244	3	FACETS	0.985	0.948	1	0.985	0.948	1	CLONAL	2	TRUE	1	0.656376747157024	3		499	1033	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998939	100998939	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054557-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	215	533	0	ENST00000325455.5:c.863C>T	p.Pro288Leu	p.P288L	ENST00000325455	NM_001202474.3	288	cCg/cTg	1/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.656376747157024	2		533	585	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654802	29654802	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1436590774	NA	P-0054557-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	181	389	0	ENST00000356175.3:c.5491G>A	p.Gly1831Arg	p.G1831R	ENST00000356175	NM_000267.3	1831	Ggg/Agg	37/57	0.46923203836987	4	FACETS	0.829	0.77	0.89	0.829	0.77	0.89	CLONAL	2	TRUE	2	0.656376747157024	4		389	551	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120179	70120179	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054557-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	133	535	0	ENST00000245479.2:c.1181G>C	p.Arg394Pro	p.R394P	ENST00000245479	NM_000346.3	394	cGa/cCa	3/3	0.323504342295446	5	FACETS	1	0.983	1	0.448	0.408	0.489	INDETERMINATE	1	TRUE	2	0.656376747157024	5		535	599	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216284	2216284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054557-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	190	695	0	ENST00000398665.3:c.1928G>A	p.Ser643Asn	p.S643N	ENST00000398665	NM_032482.2	643	aGc/aAc	20/28	NA	2	FACETS	1	0.945	1			1	INDETERMINATE	1	TRUE	NA	0.656376747157024	2		695	569	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251697	212251697	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054557-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	129	489	0	ENST00000342788.4:c.3362A>G	p.Glu1121Gly	p.E1121G	ENST00000342788	NM_005235.2	1121	gAg/gGg	27/28	0.656376747157024	4	FACETS	0.925	0.84	1	0.308	0.28	0.338	CLONAL	1	TRUE	1	0.656376747157024	4		489	704	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191642	10191642	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054557-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	148	306	0	ENST00000256474.2:c.635G>T	p.Gly212Val	p.G212V	ENST00000256474	NM_000551.3	212	gGa/gTa	3/3	0.172342409259738	3	FACETS	1	0.966	1	0.548	0.503	0.595	INDETERMINATE	1	TRUE	1	0.656376747157024	3		306	546	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155613	106155613	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054557-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	104	448	0	ENST00000380013.4:c.514A>T	p.Ser172Cys	p.S172C	ENST00000380013	NM_001127208.2	172	Agt/Tgt	3/11	1	2	FACETS	0.834	0.753	0.918	0.834	0.753	0.918	CLONAL	1	TRUE	1	0.656376747157024	2		448	380	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903714	41903714	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054557-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	736	562	0	ENST00000372991.4:c.843del	p.Ser282AlafsTer22	p.S282Afs*22	ENST00000372991	NM_001760.3	281	acC/ac	5/5	0.656376747157024	3	FACETS	0.994	0.971	1	0.994	0.971	1	CLONAL	3	TRUE	0	0.656376747157024	3		562	999	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0054557-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	271	354	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.871865453311835	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.871865453311835	2		354	293	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214067	36214067	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054557-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	122	499	0	ENST00000222270.7:c.2893C>T	p.Arg965Ter	p.R965*	ENST00000222270	NM_014727.1	965	Cga/Tga	6/37	1	2	FACETS	0.945	0.868	1	0.945	0.868	1	CLONAL	1	TRUE	1	0.871865453311835	2		499	296	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998939	100998939	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054557-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	86	533	0	ENST00000325455.5:c.863C>T	p.Pro288Leu	p.P288L	ENST00000325455	NM_001202474.3	288	cCg/cTg	1/8	0.713237826704917	3	FACETS	0.938	0.839	1	0.469	0.419	0.521	CLONAL	1	TRUE	1	0.871865453311835	3		533	302	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654802	29654802	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1436590774	NA	P-0054557-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	140	389	0	ENST00000356175.3:c.5491G>A	p.Gly1831Arg	p.G1831R	ENST00000356175	NM_000267.3	1831	Ggg/Agg	37/57	1	2	FACETS	0.994	0.92	1	0.994	0.92	1	CLONAL	1	TRUE	1	0.871865453311835	2		389	323	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191642	10191642	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054557-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	163	306	0	ENST00000256474.2:c.635G>T	p.Gly212Val	p.G212V	ENST00000256474	NM_000551.3	212	gGa/gTa	3/3	0.871865453311835	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.871865453311835	2		306	176	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155613	106155613	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054557-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	165	448	0	ENST00000380013.4:c.514A>T	p.Ser172Cys	p.S172C	ENST00000380013	NM_001127208.2	172	Agt/Tgt	3/11	0.444523279643098	2	FACETS	0.782	0.74	0.822	0.782	0.74	0.822	INDETERMINATE	2	TRUE	0	0.871865453311835	2		448	242	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903714	41903714	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054557-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	266	562	0	ENST00000372991.4:c.843del	p.Ser282AlafsTer22	p.S282Afs*22	ENST00000372991	NM_001760.3	281	acC/ac	5/5	0.871865453311835	2	FACETS	0.972	0.943	0.998	0.972	0.943	0.998	CLONAL	2	TRUE	0	0.871865453311835	2		562	314	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647564	117647564	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054557-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	112	330	0	ENST00000368508.3:c.5380A>C	p.Asn1794His	p.N1794H	ENST00000368508	NM_002944.2	1794	Aat/Cat	33/43	0.435134633689921	3	FACETS	1	0.971	1	0.578	0.527	0.631	INDETERMINATE	1	TRUE	1	0.871865453311835	3		330	319	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37622747	37622747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141308774	NA	P-0054557-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	128	424	0	ENST00000249071.6:c.545C>T	p.Thr182Met	p.T182M	ENST00000249071	NM_002872.4	182	aCg/aTg	6/7	0.871865453311835	1	FACETS	0.796	0.744	0.847	0.796	0.744	0.847	SUBCLONAL	1	TRUE	0	0.871865453311835	1		424	208	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158414	108158414	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054557-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	144	291	0	ENST00000278616.4:c.4081C>G	p.Gln1361Glu	p.Q1361E	ENST00000278616	NM_000051.3	1361	Cag/Gag	27/63	0.713237826704917	3	FACETS	0.926	0.866	0.987	0.926	0.866	0.987	CLONAL	2	TRUE	1	0.871865453311835	3		291	256	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984220	7984220	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1373779217	NA	P-0054557-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	97	477	0	ENST00000319144.4:c.509G>C	p.Arg170Pro	p.R170P	ENST00000319144	NM_001139.2	170	cGc/cCc	4/15	0.871865453311835	2	FACETS	0.73	0.658	0.803	0.365	0.329	0.402	SUBCLONAL	1	TRUE	0	0.871865453311835	2		477	305	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93973591	93973591	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054557-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	37	256	0	ENST00000369303.4:c.1785G>C	p.Glu595Asp	p.E595D	ENST00000369303	NM_004440.3	595	gaG/gaC	9/17	0.435134633689921	3	FACETS	0.512	0.425	0.608	0.256	0.212	0.304	INDETERMINATE	1	TRUE	1	0.871865453311835	3		256	238	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93973607	93973607	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054557-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	39	275	0	ENST00000369303.4:c.1769A>G	p.Gln590Arg	p.Q590R	ENST00000369303	NM_004440.3	590	cAa/cGa	9/17	0.435134633689921	3	FACETS	0.5	0.417	0.591	0.25	0.208	0.296	INDETERMINATE	1	TRUE	1	0.871865453311835	3		275	257	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123880952	123880952	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054648-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	26	467	0	ENST00000330479.4:c.570C>G	p.Ser190Arg	p.S190R	ENST00000330479	NM_020382.3	190	agC/agG	5/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		467	51	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094677	2094677	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1288936702	NA	P-0054648-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	30	480	0	ENST00000219066.1:c.503A>G	p.Asp168Gly	p.D168G	ENST00000219066	NM_002528.5	168	gAt/gGt	3/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		480	113	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215973	36215979	+	frameshift_variant	Frame_Shift_Del	DEL	CCGTGTG	CCGTGTG	GGA	novel	NA	P-0054648-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	27	543	0	ENST00000222270.7:c.3513_3519delinsGGA	p.Arg1172GlufsTer9	p.R1172Efs*9	ENST00000222270	NM_014727.1	1171	gtCCGTGTG/gtGGA	10/37	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		543	106	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383160	42383165	+	inframe_deletion	In_Frame_Del	DEL	CAACGC	CAACGC	-	novel	NA	P-0054648-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	16	643	0	ENST00000221972.3:c.185_190del	p.Ala62_Asn63del	p.A62_N63del	ENST00000221972	NM_021601.3	60	aaCAACGCc/aac	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		643	56	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044472	47044472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556781457	NA	P-0054648-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	17	264	0	ENST00000377604.3:c.1969C>T	p.Arg657Cys	p.R657C	ENST00000377604	NM_001204468.1	657	Cgc/Tgc	18/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		264	25	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916903	178916903	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054648-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	6	0	0	ENST00000263967.3:c.290C>A	p.Pro97His	p.P97H	ENST00000263967	NM_006218.2	97	cCc/cAc	2/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		0	11	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257536	16257536	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054648-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	3	0	0	ENST00000375759.3:c.4801G>C	p.Asp1601His	p.D1601H	ENST00000375759	NM_015001.2	1601	Gac/Cac	11/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		0	35	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870953	12870953	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054719-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	462	776	0	ENST00000228872.4:c.180G>T	p.Trp60Cys	p.W60C	ENST00000228872	NM_004064.3	60	tgG/tgT	1/3	1	2	FACETS	0.997	0.956	1	0.997	0.956	1	CLONAL	1	TRUE	1	0.919361250240988	2		776	1008	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576847	7577286	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAGTACCTGAAGGGTGAAATATTCTCCATCCAGTGGTTTCTTCTTTGGCTGGGGAGAGGAGCTGGTGTTGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAAGTGAATCTGAGGCATAACTGCACCCTTGGTCTCCTCCACCGCTTCTTGTCCTGCTTGCTTACCTCGCTTAGTGCTCCCTGGGGGCAGCTCGTGGTGAGGCTCCCCTTTCTTGCGGAGATTCTCTTCCTCTGTGCGCCGGTCTCTCCCAGGACAGGCACAAACACGCACCTCAAAGCTGTTCCGTCCCAGTAGATTACCACTACTCAGGATAGGAAAAGAGAAGCAAGAGGCAGTAAGGAAATCAGGTCCTACCTGTCCCATTTAAAAAACCAGGCTCCATCTACTCCCAACCACCCTTGTCCTTTCTGGAGCCTAAGCTCCAGCTCCAGG	TAGTACCTGAAGGGTGAAATATTCTCCATCCAGTGGTTTCTTCTTTGGCTGGGGAGAGGAGCTGGTGTTGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAAGTGAATCTGAGGCATAACTGCACCCTTGGTCTCCTCCACCGCTTCTTGTCCTGCTTGCTTACCTCGCTTAGTGCTCCCTGGGGGCAGCTCGTGGTGAGGCTCCCCTTTCTTGCGGAGATTCTCTTCCTCTGTGCGCCGGTCTCTCCCAGGACAGGCACAAACACGCACCTCAAAGCTGTTCCGTCCCAGTAGATTACCACTACTCAGGATAGGAAAAGAGAAGCAAGAGGCAGTAAGGAAATCAGGTCCTACCTGTCCCATTTAAAAAACCAGGCTCCATCTACTCCCAACCACCCTTGTCCTTTCTGGAGCCTAAGCTCCAGCTCCAGG	-	novel	NA	P-0054819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	41	582	0	ENST00000269305.4:c.783-131_993+6del		p.X261_splice	ENST00000269305	NM_001126112.2	261		8-9/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		582	255	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097859	8097859	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs759839816	NA	P-0055220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	127	543	0	ENST00000346208.3:c.241G>A	p.Gly81Arg	p.G81R	ENST00000346208		81	Ggg/Agg	2/6	0.306847533434017	1	FACETS	0.594	0.545	0.644	0.594	0.545	0.644	INDETERMINATE	1	TRUE	0	0.76518026587796	1		543	345	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0055298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	322	418	0	ENST00000269305.4:c.376-1G>T		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.799548224910556	2	FACETS	0.982	0.951	1	0.982	0.951	1	CLONAL	2	TRUE	0	0.799548224910556	2		418	410	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593609	55593609	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	145	461	0	ENST00000288135.5:c.1675G>T	p.Val559Phe	p.V559F	ENST00000288135	NM_000222.2	559	Gtt/Ttt	11/21	0.799548224910556	2	FACETS	1	0.94	1	0.509	0.471	0.549	CLONAL	1	TRUE	0	0.799548224910556	2		461	356	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880219	37880220	+	missense_variant	Missense_Mutation	DNP	TT	TT	CC	rs121913469	NA	P-0055318-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	256	420	0	ENST00000269571.5:c.2263_2264delinsCC	p.Leu755Pro	p.L755P	ENST00000269571		755	TTg/CCg	19/27	0.303996940359124	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.438254425845025	4		420	735	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143129653	143129653	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055318-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	30	270	0	ENST00000262992.4:c.997G>T	p.Gly333Ter	p.G333*	ENST00000262992	NM_001101669.1	333	Gga/Tga	12/24	0.241311526656417	3	FACETS	0.66	0.534	0.801	0.22	0.178	0.267	INDETERMINATE	1	TRUE	0	0.438254425845025	3		270	253	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10286249	10286250	+	missense_variant	Missense_Mutation	DNP	CG	CG	AT	novel	NA	P-0055318-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	54	416	0	ENST00000340748.4:c.566_567delinsAT	p.Ser189Tyr	p.S189Y	ENST00000340748		189	tCG/tAT	6/40	1	2	FACETS	0.52	0.444	0.602	0.52	0.444	0.602	SUBCLONAL	1	TRUE	1	0.438254425845025	2		416	474	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934268	39934268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055318-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	70	474	0	ENST00000378444.4:c.331G>A	p.Gly111Ser	p.G111S	ENST00000378444	NM_001123385.1	111	Ggc/Agc	4/15	1	2	FACETS	0.543	0.474	0.618	0.543	0.474	0.618	SUBCLONAL	1	TRUE	1	0.438254425845025	2		474	588	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0055841-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	248	256	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.840210761973642	4	FACETS	0.96	0.906	1	0.96	0.906	1	CLONAL	2	TRUE	2	0.850642126117833	4		256	562	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137360	202137360	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0055841-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	224	473	0	ENST00000358485.4:c.589-1G>A		p.X197_splice	ENST00000358485	NM_001080125.1	197			0.850642126117833	1	FACETS	0.976	0.935	1	0.976	0.935	1	CLONAL	1	TRUE	0	0.850642126117833	1		473	310	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576198	88576198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768882070	NA	P-0055841-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	226	460	0	ENST00000360948.2:c.1475C>T	p.Ser492Leu	p.S492L	ENST00000360948	NM_001012338.2	492	tCg/tTg	13/19	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.850642126117833	2		460	524	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445170	49445170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055841-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	300	607	2	ENST00000301067.7:c.2296G>A	p.Glu766Lys	p.E766K	ENST00000301067	NM_003482.3	766	Gag/Aag	10/54	0.801784042961513	3	FACETS	1	0.957	1	0.508	0.479	0.538	CLONAL	1	TRUE	1	0.850642126117833	3		609	989	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443812	49443812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055841-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	320	546	0	ENST00000301067.7:c.3559G>A	p.Glu1187Lys	p.E1187K	ENST00000301067	NM_003482.3	1187	Gag/Aag	11/54	0.801784042961513	3	FACETS	1	0.989	1	0.584	0.553	0.616	CLONAL	1	TRUE	1	0.850642126117833	3		546	918	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444157	49444157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756805095	NA	P-0055841-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	302	590	0	ENST00000301067.7:c.3214G>A	p.Glu1072Lys	p.E1072K	ENST00000301067	NM_003482.3	1072	Gag/Aag	11/54	0.801784042961513	3	FACETS	1	0.981	1	0.542	0.512	0.573	CLONAL	1	TRUE	1	0.850642126117833	3		590	933	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157138	106157138	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055841-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	282	516	0	ENST00000380013.4:c.2039G>C	p.Arg680Thr	p.R680T	ENST00000380013	NM_001127208.2	680	aGa/aCa	3/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.850642126117833	2		516	623	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863224499	NA	P-0055905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	338	538	0	ENST00000269305.4:c.672+1G>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.782018256563376	2	FACETS	0.885	0.856	0.914	0.885	0.856	0.914	CLONAL	2	TRUE	0	0.84275360496036	2		538	453	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984848	11984848	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0055905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	144	250	0	ENST00000353533.5:c.393+1G>A		p.X131_splice	ENST00000353533	NM_003010.3	131			0.782018256563376	2	FACETS	0.949	0.905	0.99	0.949	0.905	0.99	CLONAL	2	TRUE	0	0.84275360496036	2		250	180	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398625	116398625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45587940	NA	P-0055905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	66	212	0	ENST00000397752.3:c.2215C>T	p.Arg739Cys	p.R739C	ENST00000397752	NM_000245.2	739	Cgt/Tgt	9/21	0.107826061147029	1	FACETS	0.458	0.404	0.513	0.458	0.404	0.513	INDETERMINATE	1	TRUE	0	0.84275360496036	1		212	198	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602807	10602807	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	220	1016	0	ENST00000171111.5:c.771C>G	p.Cys257Trp	p.C257W	ENST00000171111	NM_203500.1	257	tgC/tgG	3/6	0.34795475083896	1	FACETS	0.56	0.526	0.595	0.56	0.526	0.595	INDETERMINATE	1	TRUE	0	0.84275360496036	1		1016	539	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0056146-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	74	732	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.356754908169914	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.423624785792112	4		732	202	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0056146-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	91	550	0	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	0.423624785792112	6	FACETS	0.909	0.817	1	0.545	0.49	0.603	CLONAL	3	TRUE	1	0.423624785792112	6		550	291	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820938	36820938	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056146-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	46	749	0	ENST00000373129.3:c.439C>G	p.His147Asp	p.H147D	ENST00000373129	NM_032017.1	147	Cat/Gat	6/12	0.248620012385731	2	FACETS	1	0.945	1	0.617	0.528	0.712	INDETERMINATE	1	TRUE	0	0.423624785792112	2		749	176	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003773	57003773	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	G	G	A	rs758461358	NA	P-0056146-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	18	681	0	ENST00000257254.3:c.706C>T	p.Arg236Cys	p.R236C	ENST00000257254		236	Cgc/Tgc	1/2	0.288690403621502	0	FACETS	0.69	0.533	0.864			1	SUBCLONAL	1	TRUE	0	0.423624785792112	0		681	71	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198847	67198848	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0056146-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	64	517	0	ENST00000312629.5:c.320_321del	p.Val107AlafsTer12	p.V107Afs*12	ENST00000312629	NM_003952.2	106	atTGtg/attg	5/15	0.423624785792112	6	FACETS	1	0.962	1			1	CLONAL	1	TRUE	NA	0.423624785792112	6		517	427	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490323	56490324	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0056146-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	54	556	0	ENST00000267101.3:c.2093_2094del	p.Lys698SerfsTer15	p.K698Sfs*15	ENST00000267101	NM_001982.3	698	AAa/a	18/28	0.423624785792112	5	FACETS	1	0.952	1	0.318	0.273	0.367	CLONAL	1	TRUE	1	0.423624785792112	5		556	328	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937079	48937080	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0056146-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	15	319	0	ENST00000267163.4:c.848_849del	p.Cys283Ter	p.C283*	ENST00000267163	NM_000321.2	283	TGt/t	8/27	0.278913250792269	2	FACETS	0.694	0.514	0.904	0.347	0.257	0.452	SUBCLONAL	1	TRUE	0	0.423624785792112	2		319	102	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054308	42055330	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTATTCTGTTAACTTACAGGTAAGACAGAAGAAGTGGTCCTGAAGAAGCTAGAGTATATTTATGCAAAACAGCAAGCACTAGAGGCACAAAAAAGAAAAAAGAAGATGGGATCAGATGAGTTTGACATATCTCCCAGAATTAGCAAACAGCAGGAAGGATCTTCTGCATCATCTGTAGATCTTGGACAGATGTTTATAAATAACAGGAGGGGGAAACCTTTGATTCTTTCCAGAAAAAAAGACCAGGCCACAGGTAGGAGGGACATTCTTCGCTTTCCTTAATGTAGATATACATCAGTTGACTTTAGTGGACTGACCACCTTCTCTTGTCCACATTTTTAGTTTTGTGTGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGAGACAGCTCTGTCGCCCAGGCTGCAGTTGCAGTGATGTGATCTCAGCTCATTGCAACCTCCACCTCCCAGGTTCAAGCGATTATCTGCTTCAGCCTCCTGAGTAGCTGGGACTACAGCGAGCACCACCATGCCCAATTTGTTTTTTTAATTTTTTAGTAGAGATGGGATTTTGCCCTGTTGGCCAGGCTAGTCTCAAACTCTTGACCTCAAGTGATCCACCCGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCAACCACACCCAGCCCACAGTTTTAGTTTTAATTAAATGAATTAAAGATGGGTTGTATAAAAAGTAGAATATTAACTACATTCGATTTTGGTTTCTGGTTGTAATACACACTCATGCAAATCCTGAGAAGTTACCAGTCCTGGTAGCATATTAGTCTATAGTCATGTATTTTTAATGAGTAGTTTTTTAAACTTATCTTTTCAGACTTATACTTGACTTCGTGATTTCCCTGCAGTTCTACTGATGGGTTTAAGAAGTTGGGTCTAGCTGAGACCAATAAATGGGAAATTTTTTGTAAAATTTAATTTTGTCAAATCAGGCTCTATTTTTCTTTCTTCCTTTTTTTTTTTTTTTTTTTTTTTTTGAGACAGAGTCTTGC	GTATTCTGTTAACTTACAGGTAAGACAGAAGAAGTGGTCCTGAAGAAGCTAGAGTATATTTATGCAAAACAGCAAGCACTAGAGGCACAAAAAAGAAAAAAGAAGATGGGATCAGATGAGTTTGACATATCTCCCAGAATTAGCAAACAGCAGGAAGGATCTTCTGCATCATCTGTAGATCTTGGACAGATGTTTATAAATAACAGGAGGGGGAAACCTTTGATTCTTTCCAGAAAAAAAGACCAGGCCACAGGTAGGAGGGACATTCTTCGCTTTCCTTAATGTAGATATACATCAGTTGACTTTAGTGGACTGACCACCTTCTCTTGTCCACATTTTTAGTTTTGTGTGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGAGACAGCTCTGTCGCCCAGGCTGCAGTTGCAGTGATGTGATCTCAGCTCATTGCAACCTCCACCTCCCAGGTTCAAGCGATTATCTGCTTCAGCCTCCTGAGTAGCTGGGACTACAGCGAGCACCACCATGCCCAATTTGTTTTTTTAATTTTTTAGTAGAGATGGGATTTTGCCCTGTTGGCCAGGCTAGTCTCAAACTCTTGACCTCAAGTGATCCACCCGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCAACCACACCCAGCCCACAGTTTTAGTTTTAATTAAATGAATTAAAGATGGGTTGTATAAAAAGTAGAATATTAACTACATTCGATTTTGGTTTCTGGTTGTAATACACACTCATGCAAATCCTGAGAAGTTACCAGTCCTGGTAGCATATTAGTCTATAGTCATGTATTTTTAATGAGTAGTTTTTTAAACTTATCTTTTCAGACTTATACTTGACTTCGTGATTTCCCTGCAGTTCTACTGATGGGTTTAAGAAGTTGGGTCTAGCTGAGACCAATAAATGGGAAATTTTTTGTAAAATTTAATTTTGTCAAATCAGGCTCTATTTTTCTTTCTTCCTTTTTTTTTTTTTTTTTTTTTTTTTGAGACAGAGTCTTGC	-	novel	NA	P-0056146-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	18	372	0	ENST00000219905.7:c.7511-19_7744+770del		p.X2504_splice	ENST00000219905	NM_001164273.1	2504		22/24	0.278570122513213	5	FACETS	0.885	0.671	1	0.295	0.223	0.378	CLONAL	1	TRUE	2	0.423624785792112	5		372	157	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56409194	56409195	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0056146-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	41	428	0	ENST00000348428.3:c.1702_1703del	p.Glu568IlefsTer4	p.E568Ifs*4	ENST00000348428	NM_006785.3	567	acAGaa/acaa	14/17	0.432055187221659	3	FACETS	1	0.897	1			1	CLONAL	1	TRUE	NA	0.423624785792112	3		428	215	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705501	47705502	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0056146-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	43	464	0	ENST00000233146.2:c.2302_2303del	p.Glu768IlefsTer18	p.E768Ifs*18	ENST00000233146	NM_000251.2	767	tcAGaa/tcaa	14/16	0.19735891886875	5	FACETS	1	0.85	1	0.667	0.567	0.773	INDETERMINATE	2	TRUE	2	0.423624785792112	5		464	166	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056434-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	33	789	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.718	0.584	0.868	0.718	0.584	0.868	SUBCLONAL	1	TRUE	1	0.21	2		789	438	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608348	43608348	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056434-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	26	0	0	ENST00000355710.3:c.1696C>T	p.Pro566Ser	p.P566S	ENST00000355710	NM_020975.4	566	Ccc/Tcc	9/20	1	2	FACETS	0.291	0.229	0.363	0.291	0.229	0.363	SUBCLONAL	1	TRUE	1	0.21	2		0	850	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348204	348216	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCCCTGGGGGC	CGGCCCTGGGGGC	-	novel	NA	P-0056434-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	66	536	0	ENST00000262320.3:c.1290_1302del	p.Pro431ValfsTer45	p.P431Vfs*45	ENST00000262320	NM_003502.3	430	ggGCCCCCAGGGCCG/gg	6/11	1	2	FACETS	0.972	0.843	1	0.972	0.843	1	CLONAL	1	TRUE	1	0.21	2		536	647	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660256	227660257	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056434-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	28	0	0	ENST00000305123.5:c.3198dup	p.Gly1067TrpfsTer14	p.G1067Wfs*14	ENST00000305123	NM_005544.2	1066	-/T	1/2	1	2	FACETS	0.405	0.322	0.499	0.405	0.322	0.499	SUBCLONAL	1	TRUE	1	0.21	2		0	659	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139563125	139563125	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056434-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	27	414	0	ENST00000308874.7:c.197G>T	p.Arg66Leu	p.R66L	ENST00000308874		66	cGa/cTa	4/10	1	2	FACETS	0.501	0.398	0.62	0.501	0.398	0.62	SUBCLONAL	1	TRUE	1	0.21	2		414	513	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715778	18715778	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056434-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	22	0	0	ENST00000266497.5:c.3609G>T	p.Arg1203Ser	p.R1203S	ENST00000266497		1203	agG/agT	25/31	1	2	FACETS	0.469	0.362	0.593	0.469	0.362	0.593	SUBCLONAL	1	TRUE	1	0.21	2		0	447	SUCCESS
BLM	641	MSKCC	GRCh37	15	91337418	91337418	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056434-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	22	328	0	ENST00000355112.3:c.3041A>C	p.His1014Pro	p.H1014P	ENST00000355112	NM_000057.2	1014	cAt/cCt	16/22	1	2	FACETS	0.539	0.417	0.681	0.539	0.417	0.681	SUBCLONAL	1	TRUE	1	0.21	2		328	389	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0056787-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	3	177	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.174	0.081	0.317	0.174	0.081	0.317	SUBCLONAL	1	TRUE	1	0.43	2		177	80	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218089	108218089	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587779874	NA	P-0056787-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	18	186	0	ENST00000278616.4:c.8668C>G	p.Leu2890Val	p.L2890V	ENST00000278616	NM_000051.3	2890	Cta/Gta	59/63	1	2	FACETS	0.432	0.326	0.555	0.432	0.326	0.555	SUBCLONAL	1	TRUE	1	0.43	2		186	194	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109308811	109308811	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs201885358	NA	P-0056787-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	33	223	0	ENST00000436639.2:c.1592T>C	p.Ile531Thr	p.I531T	ENST00000436639	NM_014454.2	531	aTa/aCa	10/10	1	2	FACETS	0.475	0.388	0.573	0.475	0.388	0.573	SUBCLONAL	1	TRUE	1	0.43	2		223	323	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796754	135796754	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203434	NA	P-0056846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	28	174	0	ENST00000298552.3:c.733C>T	p.Arg245Ter	p.R245*	ENST00000298552	NM_001162426.1	245	Cga/Tga	8/23	0.428048259267142	1	FACETS	0.719	0.583	0.87	0.719	0.583	0.87	SUBCLONAL	1	TRUE	0	0.428048259267142	1		174	143	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651921	36651924	+	frameshift_variant	Frame_Shift_Del	DEL	AGCA	AGCA	-	novel	NA	P-0056846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	152	965	0	ENST00000244741.5:c.45_48del	p.Ser15ArgfsTer15	p.S15Rfs*15	ENST00000244741	NM_000389.4	15	AGCAag/ag	2/3	1	2	FACETS	0.995	0.912	1	0.995	0.912	1	CLONAL	1	TRUE	1	0.428048259267142	2		965	714	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917701	94917701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	65	330	0	ENST00000536441.1:c.820G>A	p.Glu274Lys	p.E274K	ENST00000536441	NM_144665.3	274	Gaa/Aaa	6/10	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.428048259267142	2		330	296	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172184	38172184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs769879162	NA	P-0056846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	57	289	0	ENST00000317025.8:c.2223C>G	p.Ile741Met	p.I741M	ENST00000317025	NM_023034.1	741	atC/atG	12/24	1	2	FACETS	0.812	0.701	0.932	0.812	0.701	0.932	CLONAL	1	TRUE	1	0.428048259267142	2		289	328	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172269	38172269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1456616250	NA	P-0056846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	74	292	0	ENST00000317025.8:c.2138C>T	p.Ser713Phe	p.S713F	ENST00000317025	NM_023034.1	713	tCt/tTt	12/24	1	2	FACETS	0.91	0.801	1	0.91	0.801	1	CLONAL	1	TRUE	1	0.428048259267142	2		292	380	SUCCESS
AR	367	MSKCC	GRCh37	X	66942786	66942786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs9332971	NA	P-0056934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	55	240	0	ENST00000374690.3:c.2567G>A	p.Arg856His	p.R856H	ENST00000374690	NM_000044.3	856	cGc/cAc	7/8	0.110231161453158	2	FACETS	0.82	0.703	0.947			1	INDETERMINATE	1	TRUE	NA	0.309793080183316	2		240	433	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106648	27106648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553153748	NA	P-0056934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	165	730	0	ENST00000324856.7:c.6259G>A	p.Gly2087Arg	p.G2087R	ENST00000324856	NM_006015.4	2087	Gga/Aga	20/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.309793080183316	2		730	894	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882025	NA	P-0056934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	174	791	0	ENST00000269305.4:c.646G>C	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ctg	6/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.309793080183316	2		791	859	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913250	NA	P-0056934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	98	492	0	ENST00000369535.4:c.34G>C	p.Gly12Arg	p.G12R	ENST00000369535	NM_002524.4	12	Ggt/Cgt	2/7	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.309793080183316	2		492	609	SUCCESS
APC	324	MSKCC	GRCh37	5	112174276	112174276	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	29	341	0	ENST00000257430.4:c.2985C>A	p.Cys995Ter	p.C995*	ENST00000257430	NM_000038.5	995	tgC/tgA	16/16	0.309793080183316	1	FACETS	0.833	0.674	1	0.833	0.674	1	CLONAL	1	TRUE	0	0.309793080183316	1		341	190	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782303	9782303	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	52	788	0	ENST00000377346.4:c.2236G>A	p.Val746Met	p.V746M	ENST00000377346	NM_005026.3	746	Gtg/Atg	18/24	1	2	FACETS	0.476	0.404	0.554	0.476	0.404	0.554	SUBCLONAL	1	TRUE	1	0.309793080183316	2		788	706	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24135791	24135791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	94	579	1	ENST00000263121.7:c.278C>T	p.Ala93Val	p.A93V	ENST00000263121	NM_003073.3	93	gCc/gTc	3/9	1	2	FACETS	0.697	0.619	0.78	0.697	0.619	0.78	SUBCLONAL	1	TRUE	1	0.309793080183316	2		580	871	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026792	71026792	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0056934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	16	228	0	ENST00000318789.4:c.1428+2T>G		p.X476_splice	ENST00000318789	NM_032682.5	476			1	2	FACETS	0.76	0.566	0.987	0.76	0.566	0.987	CLONAL	1	TRUE	1	0.309793080183316	2		228	136	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0057034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	181	773	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	1	2	FACETS	0.991	0.913	1	0.991	0.913	1	CLONAL	1	TRUE	1	0.363525487598061	2		773	1005	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557596	21557596	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	177	660	0	ENST00000382592.4:c.2249G>T	p.Gly750Val	p.G750V	ENST00000382592	NM_014572.2	750	gGt/gTt	5/8	NA	2	FACETS	1	0.956	1			1	INDETERMINATE	1	TRUE	NA	0.363525487598061	2		660	924	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0057101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	103	624	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.496911559226546	2		625	405	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0057101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	125	477	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	0.496911559226546	1	FACETS	0.817	0.744	0.892	0.817	0.744	0.892	CLONAL	1	TRUE	0	0.496911559226546	1		477	463	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100375	27100375	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	179	736	0	ENST00000324856.7:c.4087C>T	p.Gln1363Ter	p.Q1363*	ENST00000324856	NM_006015.4	1363	Caa/Taa	17/20	1	2	FACETS	0.817	0.753	0.883	0.817	0.753	0.883	CLONAL	1	TRUE	1	0.496911559226546	2		736	882	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163720	32163720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253487294	NA	P-0057101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	153	697	0	ENST00000375023.3:c.5506G>A	p.Glu1836Lys	p.E1836K	ENST00000375023	NM_004557.3	1836	Gag/Aag	30/30	0.112356004016393	4	FACETS	1	0.986	1	0.688	0.631	0.747	INDETERMINATE	1	TRUE	2	0.496911559226546	4		697	670	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057961	27057961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	185	775	0	ENST00000324856.7:c.1669C>T	p.Gln557Ter	p.Q557*	ENST00000324856	NM_006015.4	557	Cag/Tag	3/20	1	2	FACETS	0.839	0.775	0.905	0.839	0.775	0.905	CLONAL	1	TRUE	1	0.496911559226546	2		775	888	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710987	114710987	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	152	587	0	ENST00000543371.1:c.211C>T	p.Arg71Cys	p.R71C	ENST00000543371	NM_001198531.1	71	Cgc/Tgc	2/14	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.496911559226546	2		587	584	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742145	145742145	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs571635676	NA	P-0057101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	157	805	0	ENST00000428558.2:c.358G>A	p.Gly120Arg	p.G120R	ENST00000428558	NM_004260.3	120	Gga/Aga	5/22	1	2	FACETS	0.931	0.855	1	0.931	0.855	1	CLONAL	1	TRUE	1	0.496911559226546	2		805	679	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627238	86627238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	103	350	1	ENST00000274376.6:c.613C>T	p.Leu205Phe	p.L205F	ENST00000274376	NM_002890.2	205	Ctt/Ttt	2/25	0.112356004016393	4	FACETS	1	0.939	1	0.533	0.478	0.591	INDETERMINATE	1	TRUE	2	0.496911559226546	4		351	582	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289223	33289223	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	170	638	0	ENST00000374542.5:c.329C>G	p.Ser110Cys	p.S110C	ENST00000374542	NM_001141970.1	110	tCt/tGt	3/8	0.112356004016393	4	FACETS	1	0.983	1	0.624	0.574	0.675	INDETERMINATE	1	TRUE	2	0.496911559226546	4		638	821	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850290	128850292	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs758836898	NA	P-0057101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	135	795	0	ENST00000249373.3:c.1556_1558del	p.Lys519del	p.K519del	ENST00000249373	NM_005631.4	518	gAGAag/gag	9/12	1	2	FACETS	0.754	0.686	0.825	0.754	0.686	0.825	SUBCLONAL	1	TRUE	1	0.496911559226546	2		795	721	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699388	117699388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	153	593	0	ENST00000369458.3:c.253G>A	p.Glu85Lys	p.E85K	ENST00000369458	NM_024626.3	85	Gaa/Aaa	3/6	1	2	FACETS	0.902	0.827	0.979	0.902	0.827	0.979	CLONAL	1	TRUE	1	0.496911559226546	2		593	683	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237653	16237653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	115	473	0	ENST00000375759.3:c.1100C>T	p.Ser367Leu	p.S367L	ENST00000375759	NM_015001.2	367	tCa/tTa	5/15	1	2	FACETS	0.87	0.787	0.957	0.87	0.787	0.957	CLONAL	1	TRUE	1	0.496911559226546	2		473	532	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114905817	114905817	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	166	618	0	ENST00000543371.1:c.836C>G	p.Pro279Arg	p.P279R	ENST00000543371	NM_001198531.1	279	cCc/cGc	8/14	1	2	FACETS	0.87	0.8	0.942	0.87	0.8	0.942	CLONAL	1	TRUE	1	0.496911559226546	2		618	768	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434689	49434689	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	199	1129	0	ENST00000301067.7:c.6864G>C	p.Lys2288Asn	p.K2288N	ENST00000301067	NM_003482.3	2288	aaG/aaC	31/54	0.112356004016393	4	FACETS	1	0.987	1	0.651	0.603	0.7	INDETERMINATE	1	TRUE	2	0.496911559226546	4		1129	921	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492557	56492557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	188	700	0	ENST00000267101.3:c.2707G>A	p.Glu903Lys	p.E903K	ENST00000267101	NM_001982.3	903	Gag/Aag	23/28	0.112356004016393	4	FACETS	1	0.988	1	0.668	0.618	0.72	INDETERMINATE	1	TRUE	2	0.496911559226546	4		700	848	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060765	38060765	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	238	1108	1	ENST00000250448.2:c.1224del	p.Ser409ArgfsTer31	p.S409Rfs*31	ENST00000250448	NM_004496.3	408	tcC/tc	2/2	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.496911559226546	2		1109	919	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748954	43748954	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	196	855	0	ENST00000382044.4:c.1852G>A	p.Glu618Lys	p.E618K	ENST00000382044	NM_001141980.1	618	Gaa/Aaa	12/28	1	2	FACETS	0.967	0.897	1	0.967	0.897	1	CLONAL	1	TRUE	1	0.496911559226546	2		855	816	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849553	68849553	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	183	753	0	ENST00000261769.5:c.1458del	p.Phe486LeufsTer36	p.F486Lfs*36	ENST00000261769	NM_004360.3	486	Ttt/tt	10/16	0.496911559226546	1	FACETS	0.927	0.86	0.996	0.927	0.86	0.996	CLONAL	1	TRUE	0	0.496911559226546	1		753	597	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81954851	81954851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368910187	NA	P-0057101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	150	592	1	ENST00000359376.3:c.2284C>T	p.Pro762Ser	p.P762S	ENST00000359376	NM_002661.3	762	Ccc/Tcc	21/33	0.496911559226546	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.496911559226546	1		593	434	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865232	40865232	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	177	647	0	ENST00000428826.2:c.1199C>G	p.Ser400Cys	p.S400C	ENST00000428826		400	tCt/tGt	11/21	1	2	FACETS	0.868	0.801	0.938	0.868	0.801	0.938	CLONAL	1	TRUE	1	0.496911559226546	2		647	821	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688788	47688788	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	119	416	0	ENST00000347630.2:c.512C>A	p.Ser171Tyr	p.S171Y	ENST00000347630	NM_001007230.1	171	tCt/tAt	7/11	1	2	FACETS	0.979	0.889	1	0.979	0.889	1	CLONAL	1	TRUE	1	0.496911559226546	2		416	489	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52693375	52693375	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	201	886	1	ENST00000322088.6:c.26C>T	p.Ser9Leu	p.S9L	ENST00000322088	NM_014225.5	9	tCg/tTg	1/15	1	2	FACETS	0.965	0.896	1	0.965	0.896	1	CLONAL	1	TRUE	1	0.496911559226546	2		887	838	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010494	48010494	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	104	539	0	ENST00000234420.5:c.122C>G	p.Ser41Cys	p.S41C	ENST00000234420	NM_000179.2	41	tCt/tGt	1/10	1	2	FACETS	0.922	0.83	1	0.922	0.83	1	CLONAL	1	TRUE	1	0.496911559226546	2		539	454	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161716	56161720	+	frameshift_variant	Frame_Shift_Del	DEL	CGTAA	CGTAA	-	novel	NA	P-0057101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	112	497	0	ENST00000399503.3:c.1214_1218del	p.Arg405HisfsTer19	p.R405Hfs*19	ENST00000399503	NM_005921.1	405	CGTAAc/c	6/20	0.112356004016393	4	FACETS	1	0.967	1	0.584	0.526	0.644	INDETERMINATE	1	TRUE	2	0.496911559226546	4		497	578	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167795	56167795	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	115	484	0	ENST00000399503.3:c.1360G>T	p.Glu454Ter	p.E454*	ENST00000399503	NM_005921.1	454	Gaa/Taa	7/20	0.112356004016393	4	FACETS	1	0.955	1	0.549	0.495	0.605	INDETERMINATE	1	TRUE	2	0.496911559226546	4		484	631	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38153399	38153399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2312	160	615	0	ENST00000317025.8:c.2830G>A	p.Glu944Lys	p.E944K	ENST00000317025	NM_023034.1	944	Gaa/Aaa	16/24	0.496911559226546	12	FACETS	0.908	0.828	0.992			1	CLONAL	1	TRUE	NA	0.496911559226546	12		615	2472	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162194	38162194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1809	119	511	0	ENST00000317025.8:c.2522C>T	p.Ser841Phe	p.S841F	ENST00000317025	NM_023034.1	841	tCc/tTc	14/24	0.496911559226546	12	FACETS	0.866	0.778	0.96			1	CLONAL	1	TRUE	NA	0.496911559226546	12		511	1928	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0057790-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	108	467	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.219071723680484	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	0	0.219071723680484	2		467	472	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44896923	44896923	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1402339766	NA	P-0057790-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	28	297	0	ENST00000377967.4:c.643T>C	p.Tyr215His	p.Y215H	ENST00000377967	NM_021140.2	215	Tat/Cat	8/29	0.209743967255475	1	FACETS	0.985	0.792	1	0.985	0.792	1	CLONAL	1	TRUE	0	0.219071723680484	1		297	231	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76812977	76812978	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0057790-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	38	508	0	ENST00000373344.5:c.6642_6643dup	p.Leu2215TyrfsTer2	p.L2215Yfs*2	ENST00000373344	NM_000489.3	2215	tta/tATta	30/35	0.209743967255475	1	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	TRUE	0	0.219071723680484	1		508	303	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	73	379	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.29	2		379	501	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612948	228612948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750781461	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	112	738	0	ENST00000366696.1:c.79C>T	p.Arg27Cys	p.R27C	ENST00000366696	NM_003493.2	27	Cgc/Tgc	1/1	1	2	FACETS	0.894	0.803	0.99	0.894	0.803	0.99	CLONAL	1	TRUE	1	0.29	2		738	864	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	117	557	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.29	2		558	769	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263395	123263395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536181987	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	107	554	4	ENST00000358487.5:c.1348C>T	p.Arg450Cys	p.R450C	ENST00000358487	NM_000141.4	450	Cgc/Tgc	10/18	1	2	FACETS	0.911	0.817	1	0.911	0.817	1	CLONAL	1	TRUE	1	0.29	2		558	810	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278061	18278061	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519801	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	138	772	0	ENST00000222254.8:c.1681A>G	p.Asn561Asp	p.N561D	ENST00000222254	NM_005027.3	561	Aac/Gac	13/16	1	2	FACETS	0.937	0.851	1	0.937	0.851	1	CLONAL	1	TRUE	1	0.29	2		772	1016	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149728	202149728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	59	721	0	ENST00000358485.4:c.1173del	p.Ile392SerfsTer4	p.I392Sfs*4	ENST00000358485	NM_001080125.1	390	gCc/gc	8/9	1	2	FACETS	0.507	0.435	0.586	0.507	0.435	0.586	SUBCLONAL	1	TRUE	1	0.29	2		721	802	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528710	8528710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768826930	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	95	494	1	ENST00000356435.5:c.422G>A	p.Arg141His	p.R141H	ENST00000356435		141	cGc/cAc	4/35	1	2	FACETS	0.87	0.775	0.972	0.87	0.775	0.972	CLONAL	1	TRUE	1	0.29	2		495	753	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504057	123504057	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	62	221	0	ENST00000371139.4:c.233G>A	p.Arg78Gln	p.R78Q	ENST00000371139	NM_001114937.2	78	cGg/cAg	3/4	0.243797662575717	2	FACETS	1	0.969	1			1	CLONAL	1	TRUE	NA	0.29	2		221	298	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351871	89351871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752417963	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	66	898	0	ENST00000301030.4:c.1079C>T	p.Pro360Leu	p.P360L	ENST00000301030	NM_001256183.1	360	cCg/cTg	9/13	1	2	FACETS	0.438	0.378	0.502	0.438	0.378	0.502	SUBCLONAL	1	TRUE	1	0.29	2		898	1040	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225607	133225607	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs141619382	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	178	952	5	ENST00000320574.5:c.4057A>G	p.Ser1353Gly	p.S1353G	ENST00000320574	NM_006231.2	1353	Agt/Ggt	32/49	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.29	2		957	1027	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050708	30050708	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	90	457	0	ENST00000338641.4:c.514del	p.Arg172GlyfsTer2	p.R172Gfs*2	ENST00000338641	NM_000268.3	170	ccA/cc	5/16	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.29	2		457	543	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467083	25467083	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs568207978	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	152	866	1	ENST00000264709.3:c.1792C>T	p.Arg598Ter	p.R598*	ENST00000264709	NM_175629.2	598	Cga/Tga	15/23	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.29	2		867	1044	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110129	8110130	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs745673717	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	102	743	0	ENST00000585124.1:c.475dup	p.Arg159ProfsTer15	p.R159Pfs*15	ENST00000585124	NM_004217.3	159	cgc/cCgc	6/9	1	2	FACETS	0.757	0.676	0.844	0.757	0.676	0.844	SUBCLONAL	1	TRUE	1	0.29	2		743	929	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574081	41574081	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	125	682	0	ENST00000263253.7:c.6370del	p.Val2124SerfsTer10	p.V2124Sfs*10	ENST00000263253	NM_001429.3	2122	caG/ca	31/31	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.29	2		682	827	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094798	2094798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370228590	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	162	871	0	ENST00000219066.1:c.382C>T	p.Arg128Cys	p.R128C	ENST00000219066	NM_002528.5	128	Cgc/Tgc	3/6	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.29	2		871	1020	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441499	6441499	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	43	344	0	ENST00000356142.4:c.346T>C	p.Trp116Arg	p.W116R	ENST00000356142	NM_018890.3	116	Tgg/Cgg	6/7	1	2	FACETS	0.676	0.566	0.797	0.676	0.566	0.797	SUBCLONAL	1	TRUE	1	0.29	2		344	439	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662690	117662690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148310006	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	78	539	1	ENST00000368508.3:c.4775G>A	p.Arg1592His	p.R1592H	ENST00000368508	NM_002944.2	1592	cGt/cAt	29/43	0.224215762600561	1	FACETS	0.676	0.594	0.765	0.676	0.594	0.765	SUBCLONAL	1	TRUE	0	0.29	1		540	680	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434005	49434005	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	143	1075	0	ENST00000301067.7:c.7548del	p.Asn2517IlefsTer26	p.N2517Ifs*26	ENST00000301067	NM_003482.3	2516	ccC/cc	31/54	1	2	FACETS	0.863	0.785	0.945	0.863	0.785	0.945	CLONAL	1	TRUE	1	0.29	2		1075	1143	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250906	153250906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	63	352	1	ENST00000281708.4:c.1154C>T	p.Thr385Ile	p.T385I	ENST00000281708	NM_033632.3	385	aCa/aTa	8/12	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.29	2		353	386	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129042	30129042	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745793573	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	130	735	0	ENST00000263025.4:c.724C>T	p.Arg242Trp	p.R242W	ENST00000263025	NM_002746.2	242	Cgg/Tgg	5/9	1	2	FACETS	0.865	0.783	0.951	0.865	0.783	0.951	CLONAL	1	TRUE	1	0.29	2		735	1037	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413893	139413893	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1164392989	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	131	822	0	ENST00000277541.6:c.865+2C>T		p.X289_splice	ENST00000277541	NM_017617.3	289			1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.29	2		822	902	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572273	64572273	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765306552	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	89	664	0	ENST00000312049.6:c.1366C>T	p.Arg456Cys	p.R456C	ENST00000312049	NM_130799.2	456	Cgc/Tgc	10/10	1	2	FACETS	0.787	0.697	0.883	0.787	0.697	0.883	SUBCLONAL	1	TRUE	1	0.29	2		664	780	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420184	49420184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555185701	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	144	733	0	ENST00000301067.7:c.15565G>A	p.Gly5189Arg	p.G5189R	ENST00000301067	NM_003482.3	5189	Gga/Aga	48/54	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.29	2		733	920	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222822	5222822	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370623380	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	92	478	0	ENST00000357368.4:c.2981C>T	p.Ala994Val	p.A994V	ENST00000357368	NM_002850.3	994	gCg/gTg	18/38	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.29	2		478	605	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131926963	131926963	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	40	258	0	ENST00000265335.6:c.1504del	p.Met502TrpfsTer3	p.M502Wfs*3	ENST00000265335		500	ttA/tt	10/25	1	2	FACETS	0.923	0.77	1	0.923	0.77	1	CLONAL	1	TRUE	1	0.29	2		258	299	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572962	7572963	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	106	678	0	ENST00000269305.4:c.1146dup	p.Leu383ThrfsTer9	p.L383Tfs*9	ENST00000269305	NM_001126112.2	382	-/A	11/11	1	2	FACETS	0.861	0.771	0.956	0.861	0.771	0.956	CLONAL	1	TRUE	1	0.29	2		678	849	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107748	30107748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775384193	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	84	610	0	ENST00000331968.5:c.932G>A	p.Arg311His	p.R311H	ENST00000331968	NM_002742.2	311	cGt/cAt	6/18	1	2	FACETS	0.843	0.745	0.949	0.843	0.745	0.949	CLONAL	1	TRUE	1	0.29	2		610	687	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330567	65330567	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290427088	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	46	604	0	ENST00000342505.4:c.1079G>A	p.Arg360Gln	p.R360Q	ENST00000342505	NM_002227.2	360	cGg/cAg	8/25	1	2	FACETS	0.379	0.318	0.447	0.379	0.318	0.447	SUBCLONAL	1	TRUE	1	0.29	2		604	837	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411636	63411636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	267	430	0	ENST00000330258.3:c.1531C>T	p.Pro511Ser	p.P511S	ENST00000330258	NM_152424.3	511	Cca/Tca	2/2	0.243797662575717	2	FACETS	1	0.963	1			1	CLONAL	3	TRUE	NA	0.29	2		430	600	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256128	123256128	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	101	759	0	ENST00000358487.5:c.1781C>A	p.Pro594His	p.P594H	ENST00000358487	NM_000141.4	594	cCt/cAt	13/18	1	2	FACETS	0.818	0.73	0.911	0.818	0.73	0.911	CLONAL	1	TRUE	1	0.29	2		759	852	SUCCESS
ATM	472	MSKCC	GRCh37	11	108126979	108126979	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	104	583	0	ENST00000278616.4:c.2165del	p.Leu722TrpfsTer13	p.L722Wfs*13	ENST00000278616	NM_000051.3	721	cTt/ct	14/63	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.29	2		583	709	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244977	46244977	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	59	636	0	ENST00000334344.6:c.3071A>C	p.Gln1024Pro	p.Q1024P	ENST00000334344	NM_152641.2	1024	cAg/cCg	15/21	1	2	FACETS	0.502	0.431	0.58	0.502	0.431	0.58	SUBCLONAL	1	TRUE	1	0.29	2		636	811	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893286	32893286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	52	344	0	ENST00000380152.3:c.140C>T	p.Ala47Val	p.A47V	ENST00000380152		47	gCa/gTa	3/27	1	2	FACETS	0.747	0.637	0.868	0.747	0.637	0.868	SUBCLONAL	1	TRUE	1	0.29	2		344	480	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930636	32930636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782191	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	61	495	0	ENST00000380152.3:c.7507G>A	p.Val2503Ile	p.V2503I	ENST00000380152		2503	Gtc/Atc	15/27	1	2	FACETS	0.725	0.626	0.834	0.725	0.626	0.834	SUBCLONAL	1	TRUE	1	0.29	2		495	580	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994936	73994936	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	40	351	0	ENST00000318443.5:c.418+2T>C		p.X140_splice	ENST00000318443	NM_001024736.1	140			1	2	FACETS	0.718	0.598	0.852	0.718	0.598	0.852	SUBCLONAL	1	TRUE	1	0.29	2		351	384	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226164	2226164	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	123	1088	0	ENST00000326181.6:c.1861T>C	p.Tyr621His	p.Y621H	ENST00000326181	NM_032271.2	621	Tac/Cac	19/21	1	2	FACETS	0.773	0.697	0.853	0.773	0.697	0.853	SUBCLONAL	1	TRUE	1	0.29	2		1088	1098	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796947	78796947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	99	566	0	ENST00000306801.3:c.1060G>A	p.Glu354Lys	p.E354K	ENST00000306801	NM_020761.2	354	Gaa/Aaa	9/34	1	2	FACETS	0.866	0.773	0.966	0.866	0.773	0.966	CLONAL	1	TRUE	1	0.29	2		566	788	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132497	11132497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555778721	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	103	976	1	ENST00000358026.2:c.2713C>T	p.Arg905Cys	p.R905C	ENST00000358026	NM_001128849.1	905	Cgc/Tgc	19/36	1	2	FACETS	0.723	0.645	0.805	0.723	0.645	0.805	SUBCLONAL	1	TRUE	1	0.29	2		977	983	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145590	11145590	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	138	785	0	ENST00000358026.2:c.3952C>T	p.Arg1318Cys	p.R1318C	ENST00000358026	NM_001128849.1	1318	Cgc/Tgc	29/36	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.29	2		785	923	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964986	25964986	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	96	661	1	ENST00000435504.4:c.4220T>C	p.Met1407Thr	p.M1407T	ENST00000435504		1407	aTg/aCg	13/13	1	2	FACETS	0.804	0.716	0.899	0.804	0.716	0.899	CLONAL	1	TRUE	1	0.29	2		662	823	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046943	128046944	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCT	rs761456808	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	73	658	1	ENST00000285398.2:c.789_791dup	p.Glu264dup	p.E264dup	ENST00000285398	NM_000122.1	264	gag/gaAGAg	6/15	1	2	FACETS	0.638	0.557	0.726	0.638	0.557	0.726	SUBCLONAL	1	TRUE	1	0.29	2		659	789	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067263	37067263	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	88	492	0	ENST00000231790.2:c.1174A>T	p.Lys392Ter	p.K392*	ENST00000231790	NM_000249.3	392	Aag/Tag	12/19	1	2	FACETS	0.855	0.757	0.959	0.855	0.757	0.959	CLONAL	1	TRUE	1	0.29	2		492	710	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47061327	47061327	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	24	397	0	ENST00000409792.3:c.7354T>C	p.Ser2452Pro	p.S2452P	ENST00000409792	NM_014159.6	2452	Tcg/Ccg	19/21	1	2	FACETS	0.345	0.269	0.432	0.345	0.269	0.432	SUBCLONAL	1	TRUE	1	0.29	2		397	480	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037156	71037156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149759021	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	79	491	0	ENST00000318789.4:c.1135G>A	p.Ala379Thr	p.A379T	ENST00000318789	NM_032682.5	379	Gcc/Acc	14/21	1	2	FACETS	0.801	0.705	0.905	0.801	0.705	0.905	CLONAL	1	TRUE	1	0.29	2		491	680	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928047	178928047	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	73	531	0	ENST00000263967.3:c.1325C>A	p.Ala442Asp	p.A442D	ENST00000263967	NM_006218.2	442	gCt/gAt	8/21	1	2	FACETS	0.782	0.684	0.887	0.782	0.684	0.887	SUBCLONAL	1	TRUE	1	0.29	2		531	644	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0058424-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	208	458	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.734516327218138	2		458	523	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0058424-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	216	389	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.734516327218138	2		389	539	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646270	3646270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780697002	NA	P-0058424-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	245	671	0	ENST00000294008.3:c.1808C>T	p.Ser603Leu	p.S603L	ENST00000294008	NM_032444.2	603	tCg/tTg	8/15	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.734516327218138	2		671	662	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982405	201982405	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058424-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	282	635	0	ENST00000359651.3:c.784del	p.Glu262ArgfsTer32	p.E262Rfs*32	ENST00000359651		262	Gag/ag	6/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.734516327218138	2		635	737	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465602	8465602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058424-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	116	529	0	ENST00000356435.5:c.3578C>T	p.Ala1193Val	p.A1193V	ENST00000356435		1193	gCc/gTc	21/35	0.725738375994802	3	FACETS	0.547	0.493	0.605	0.274	0.246	0.303	SUBCLONAL	1	TRUE	1	0.734516327218138	3		529	789	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533455	533455	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs1064796999	NA	P-0058424-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	669	729	1	ENST00000451590.1:c.448C>T	p.Gln150Ter	p.Q150*	ENST00000451590	NM_001130442.1	150	Cag/Tag	4/5	0.734516327218138	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.734516327218138	2		730	904	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894230	NA	P-0058424-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	543	579	0	ENST00000451590.1:c.35G>C	p.Gly12Ala	p.G12A	ENST00000451590	NM_001130442.1	12	gGc/gCc	2/5	0.734516327218138	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.734516327218138	2		579	724	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38157033	38157033	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0058424-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	478	457	0	ENST00000317025.8:c.2687C>G	p.Ser896Ter	p.S896*	ENST00000317025	NM_023034.1	896	tCa/tGa	15/24	0.734516327218138	3	FACETS	0.996	0.959	1	0.996	0.959	1	CLONAL	2	TRUE	1	0.734516327218138	3		457	893	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443695	29443695	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs863225281	NA	P-0058991-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	139	431	0	ENST00000389048.3:c.3522C>A	p.Phe1174Leu	p.F1174L	ENST00000389048	NM_004304.4	1174	ttC/ttA	23/29	0.77886239065968	5	FACETS	1	0.974	1	0.39	0.355	0.426	CLONAL	1	TRUE	2	0.78137125156207	5		431	661	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50773990	50773990	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058991-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	111	470	0	ENST00000307179.4:c.1531G>T	p.Glu511Ter	p.E511*	ENST00000307179		511	Gaa/Taa	11/20	0.78137125156207	5	FACETS	0.945	0.851	1	0.315	0.283	0.348	CLONAL	1	TRUE	2	0.78137125156207	5		470	653	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372233	55372233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1416373847	NA	P-0058991-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	29	625	0	ENST00000297316.4:c.923G>A	p.Gly308Glu	p.G308E	ENST00000297316	NM_022454.3	308	gGg/gAg	2/2	0.343477643581388	5	FACETS	0.428	0.343	0.524	0.143	0.114	0.175	INDETERMINATE	1	TRUE	2	0.78137125156207	5		625	377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0059141-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	243	714	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.321746855448809	1	FACETS	0.834	0.782	0.887	1	0.994	1	CLONAL	2	TRUE	0	0.321746855448809	1		714	760	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423610	88423610	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059141-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	112	501	0	ENST00000360948.2:c.2225T>C	p.Ile742Thr	p.I742T	ENST00000360948	NM_001012338.2	742	aTc/aCc	18/19	0.321746855448809	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.321746855448809	1		501	476	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961413	54961413	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs971358516	NA	P-0059141-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	32	255	0	ENST00000312783.6:c.219T>G	p.Asn73Lys	p.N73K	ENST00000312783	NM_198436.1	73	aaT/aaG	4/10	1	2	FACETS	0.737	0.6	0.889	0.737	0.6	0.889	SUBCLONAL	1	TRUE	1	0.321746855448809	2		255	270	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891182	101891182	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059141-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	141	433	0	ENST00000374994.4:c.143G>C	p.Cys48Ser	p.C48S	ENST00000374994	NM_004612.2	48	tGt/tCt	2/9	0.321746855448809	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.321746855448809	1		433	603	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971266	15971278	+	frameshift_variant	Frame_Shift_Del	DEL	CCGATAAACCTCG	CCGATAAACCTCG	-	novel	NA	P-0059442-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	467	666	0	ENST00000268712.3:c.4671_4683del	p.Glu1558AlafsTer53	p.E1558Afs*53	ENST00000268712	NM_006311.3	1557	ggCGAGGTTTATCGG/gg	32/46	0.932172951400074	2	FACETS	0.99	0.973	1	0.99	0.973	1	CLONAL	2	TRUE	0	0.91943463371961	2		666	513	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164744	32164744	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059442-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	2372	687	0	ENST00000375023.3:c.5158C>A	p.Leu1720Met	p.L1720M	ENST00000375023	NM_004557.3	1720	Ctg/Atg	28/30	0.91943463371961	8	FACETS	0.951	0.94	0.961	1	0.999	1	CLONAL	7	TRUE	2	0.91943463371961	8		687	2913	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0059527-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	180	452	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.462724224245223	1	FACETS	0.909	0.843	0.976	0.909	0.843	0.976	CLONAL	1	TRUE	0	0.520556401727195	1		452	563	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0059527-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	92	500	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.519692838467925	1	FACETS	0.533	0.475	0.594	0.533	0.475	0.594	SUBCLONAL	1	TRUE	0	0.520556401727195	1		500	491	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371962	55371962	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059527-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	272	583	0	ENST00000297316.4:c.652C>A	p.Pro218Thr	p.P218T	ENST00000297316	NM_022454.3	218	Ccg/Acg	2/2	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.520556401727195	2		583	757	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519920	NA	P-0059527-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	155	456	0	ENST00000397062.3:c.85G>A	p.Asp29Asn	p.D29N	ENST00000397062	NM_006164.4	29	Gat/Aat	2/5	1	2	FACETS	0.951	0.874	1	0.951	0.874	1	CLONAL	1	TRUE	1	0.520556401727195	2		456	626	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803005	32803005	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059527-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	138	531	0	ENST00000374899.4:c.871C>T	p.Arg291Ter	p.R291*	ENST00000374899	NM_018833.2	291	Cga/Tga	5/12	0.521865750261144	1	FACETS	0.665	0.607	0.725	0.665	0.607	0.725	SUBCLONAL	1	TRUE	0	0.520556401727195	1		531	590	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778526	3778526	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059527-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	171	651	0	ENST00000262367.5:c.6522G>T	p.Met2174Ile	p.M2174I	ENST00000262367	NM_004380.2	2174	atG/atT	31/31	0.512324526742015	2	FACETS	0.837	0.771	0.905	0.418	0.385	0.453	CLONAL	1	TRUE	0	0.520556401727195	2		651	785	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976501	18976501	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059527-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	41	588	0	ENST00000262803.5:c.3151C>T	p.Gln1051Ter	p.Q1051*	ENST00000262803	NM_002911.3	1051	Cag/Tag	22/24	1	2	FACETS	0.198	0.164	0.236	0.198	0.164	0.236	SUBCLONAL	1	TRUE	1	0.520556401727195	2		588	797	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050770	5050770	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059527-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	30	354	0	ENST00000381652.3:c.553G>C	p.Asp185His	p.D185H	ENST00000381652	NM_004972.3	185	Gat/Cat	6/25	0.521865750261144	1	FACETS	0.251	0.202	0.306	0.251	0.202	0.306	SUBCLONAL	1	TRUE	0	0.520556401727195	1		354	340	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518238	8518238	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059527-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	98	391	0	ENST00000356435.5:c.1153C>T	p.Pro385Ser	p.P385S	ENST00000356435		385	Ccc/Tcc	10/35	0.521865750261144	1	FACETS	0.763	0.687	0.843	0.763	0.687	0.843	SUBCLONAL	1	TRUE	0	0.520556401727195	1		391	365	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120508082	120508082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059527-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	121	380	0	ENST00000256646.2:c.1675G>A	p.Ala559Thr	p.A559T	ENST00000256646	NM_024408.3	559	Gcc/Acc	10/34	0.521865750261144	3	FACETS	0.765	0.691	0.842	0.382	0.345	0.421	SUBCLONAL	1	TRUE	1	0.520556401727195	3		380	766	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220054	5220054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059527-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	177	583	0	ENST00000357368.4:c.3661C>T	p.His1221Tyr	p.H1221Y	ENST00000357368	NM_002850.3	1221	Cat/Tat	22/38	0.310566952521424	1	FACETS	0.702	0.648	0.757	0.702	0.648	0.757	INDETERMINATE	1	TRUE	0	0.520556401727195	1		583	717	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098846	178098846	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059527-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	203	489	0	ENST00000397062.3:c.199G>C	p.Glu67Gln	p.E67Q	ENST00000397062	NM_006164.4	67	Gag/Cag	2/5	1	2	FACETS	0.961	0.892	1	0.961	0.892	1	CLONAL	1	TRUE	1	0.520556401727195	2		489	812	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205838	128205838	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059527-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	185	520	1	ENST00000341105.2:c.37C>A	p.His13Asn	p.H13N	ENST00000341105	NM_032638.4	13	Cac/Aac	2/6	1	2	FACETS	0.97	0.898	1	0.97	0.898	1	CLONAL	1	TRUE	1	0.520556401727195	2		521	733	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807569	1807569	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059527-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	204	647	0	ENST00000260795.2:c.1738G>T	p.Asp580Tyr	p.D580Y	ENST00000260795		580	Gac/Tac	12/17	0.169488140505469	3	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.520556401727195	3		647	942	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55130085	55130085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059527-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	128	444	1	ENST00000257290.5:c.619G>A	p.Ala207Thr	p.A207T	ENST00000257290	NM_006206.4	207	Gct/Act	4/23	1	2	FACETS	0.948	0.863	1	0.948	0.863	1	CLONAL	1	TRUE	1	0.520556401727195	2		445	519	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384032	84384032	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060503252	NA	P-0059527-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	98	413	0	ENST00000321945.7:c.820C>T	p.Pro274Ser	p.P274S	ENST00000321945	NM_139076.2	274	Cct/Tct	9/9	1	2	FACETS	0.808	0.724	0.896	0.808	0.724	0.896	CLONAL	1	TRUE	1	0.520556401727195	2		413	466	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815305	32815305	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059527-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	43	518	0	ENST00000354258.4:c.2068C>T	p.Gln690Ter	p.Q690*	ENST00000354258	NM_000593.5	690	Cag/Tag	9/11	0.474678244908466	1	FACETS	0.188	0.157	0.223	0.188	0.157	0.223	SUBCLONAL	1	TRUE	0	0.520556401727195	1		518	650	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547361	106547361	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059527-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	205	483	0	ENST00000369096.4:c.598T>A	p.Tyr200Asn	p.Y200N	ENST00000369096	NM_001198.3	200	Tat/Aat	4/7	1	2	FACETS	0.909	0.845	0.976	0.909	0.845	0.976	CLONAL	1	TRUE	1	0.520556401727195	2		483	866	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509206	106509206	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059527-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	168	593	0	ENST00000359195.3:c.1203del	p.Lys402AsnfsTer28	p.K402Nfs*28	ENST00000359195	NM_002649.2	400	agC/ag	2/11	NA	2	FACETS	0.828	0.762	0.896			1	INDETERMINATE	1	TRUE	NA	0.520556401727195	2		593	780	SUCCESS
PHF6	84295	MSKCC	GRCh37	X	133527630	133527630	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059527-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	77	461	0	ENST00000332070.3:c.340C>T	p.Gln114Ter	p.Q114*	ENST00000332070	NM_032458.2	114	Caa/Taa	4/10	0.519985827974943	1	FACETS	0.598	0.528	0.672	0.598	0.528	0.672	SUBCLONAL	1	TRUE	0	0.520556401727195	1		461	366	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858138	152858138	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059527-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	60	595	0	ENST00000406277.2:c.477G>T	p.Trp159Cys	p.W159C	ENST00000406277	NM_152274.4	159	tgG/tgT	6/7	0.519985827974943	1	FACETS	0.287	0.247	0.331	0.287	0.247	0.331	SUBCLONAL	1	TRUE	0	0.520556401727195	1		595	594	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152864519	152864519	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059527-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	34	356	0	ENST00000406277.2:c.11C>A	p.Pro4Gln	p.P4Q	ENST00000406277	NM_152274.4	4	cCg/cAg	1/7	0.519985827974943		FACETS		0.229	0.337				SUBCLONAL	1	TRUE	0	0.520556401727195	1		356	345	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220587	1220588	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0059527-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	38	554	0	ENST00000326873.7:c.605_606insG	p.His202GlnfsTer64	p.H202Qfs*64	ENST00000326873	NM_000455.4	202	cac/caGc	5/10	0.521865750261144	1	FACETS	0.201	0.166	0.241	0.201	0.166	0.241	SUBCLONAL	1	TRUE	0	0.520556401727195	1		554	537	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220588	1220604	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGTTCGCGGCGGACG	CCCGTTCGCGGCGGACG	GCCC	novel	NA	P-0059527-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	38	563	0	ENST00000326873.7:c.606_622delinsGCCC	p.His202GlnfsTer81	p.H202Qfs*81	ENST00000326873	NM_000455.4	202	caCCCGTTCGCGGCGGACGac/caGCCCac	5/10	0.521865750261144	1	FACETS	0.201	0.166	0.241	0.201	0.166	0.241	SUBCLONAL	1	TRUE	0	0.520556401727195	1		563	537	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0059749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	88	250	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	0.174888126730302	3	FACETS	0.921	0.822	1	0.921	0.822	1	CLONAL	2	TRUE	1	0.285753379986515	3		250	382	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322645	30322645	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	162	193	0	ENST00000322652.5:c.1658del	p.Gln553ArgfsTer29	p.Q553Rfs*29	ENST00000322652	NM_015355.2	553	cAg/cg	14/16	0.285753379986515	5	FACETS	1	0.959	1			1	CLONAL	4	TRUE	NA	0.285753379986515	5		193	387	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546031	29546042	+	frameshift_variant	Frame_Shift_Del	DEL	AAAACAGGGGCC	AAAACAGGGGCC	CAAA	novel	NA	P-0059749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	184	222	2	ENST00000356175.3:c.1536_1547delinsCAAA	p.Arg512SerfsTer43	p.R512Sfs*43	ENST00000356175	NM_000267.3	512	agAAAACAGGGGCCc/agCAAAc	14/57	0.285753379986515	5	FACETS	1	0.957	1			1	CLONAL	4	TRUE	NA	0.285753379986515	5		224	445	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0060060-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	133	342	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.510984035657879	2		342	467	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1720604	1720605	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060060-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	222	675	0	ENST00000378609.4:c.803dup	p.Asn268LysfsTer45	p.N268Kfs*45	ENST00000378609	NM_002074.3	268	aac/aaAc	10/12	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.510984035657879	2		675	830	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127719	64127719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060060-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	242	684	0	ENST00000334205.4:c.212C>T	p.Ala71Val	p.A71V	ENST00000334205	NM_003942.2	71	gCg/gTg	3/17	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.510984035657879	2		684	848	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981650	63981664	+	inframe_deletion	In_Frame_Del	DEL	TCCTCCTCCTCTTCC	TCCTCCTCCTCTTCC	-	rs754388483	NA	P-0060060-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	146	855	0	ENST00000398590.3:c.2166_2180del	p.Ser724_Ser728del	p.S724_S728del	ENST00000398590	NM_001177387.1	718	TCCTCCTCCTCTTCC/-	12/14	1	2	FACETS	0.575	0.524	0.628	0.575	0.524	0.628	SUBCLONAL	1	TRUE	1	0.510984035657879	2		855	994	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0060306-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	24	256	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.1671178241404	4	FACETS	0.859	0.678	1	0.429	0.339	0.532	INDETERMINATE	1	TRUE	2	0.432927941930239	4		256	185	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0060306-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	377	642	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.348904195446321	2	FACETS	0.808	0.768	0.848	0.808	0.768	0.848	CLONAL	2	TRUE	0	0.432927941930239	2		642	1078	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150030	202150030	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs931648756	NA	P-0060306-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	136	581	0	ENST00000358485.4:c.1471C>T	p.Arg491Ter	p.R491*	ENST00000358485	NM_001080125.1	491	Cga/Tga	8/9	0.432927941930239	3	FACETS	0.697	0.632	0.765	0.348	0.316	0.383	SUBCLONAL	1	TRUE	1	0.432927941930239	3		581	1097	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996699	73996699	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060306-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	12	71	0	ENST00000318443.5:c.1255T>G	p.Leu419Val	p.L419V	ENST00000318443	NM_001024736.1	419	Ttg/Gtg	6/10	0.396765881559213	3	FACETS	0.489	0.345	0.663	0.244	0.172	0.332	SUBCLONAL	1	TRUE	1	0.432927941930239	3		71	138	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872186	37872186	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758497995	NA	P-0060306-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	115	596	0	ENST00000269571.5:c.1507G>A	p.Glu503Lys	p.E503K	ENST00000269571		503	Gag/Aag	12/27	0.432927941930239	3	FACETS	0.6	0.539	0.665	0.2	0.179	0.222	SUBCLONAL	1	TRUE	0	0.432927941930239	3		596	1077	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55143609	55143609	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1452541160	NA	P-0060306-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	135	548	0	ENST00000257290.5:c.1841G>C	p.Gly614Ala	p.G614A	ENST00000257290	NM_006206.4	614	gGa/gCa	13/23	0.354252189588926	2	FACETS	0.791	0.72	0.867	0.396	0.36	0.434	SUBCLONAL	1	TRUE	0	0.432927941930239	2		548	788	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216590	108216590	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060497-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	315	356	0	ENST00000278616.4:c.8539G>C	p.Glu2847Gln	p.E2847Q	ENST00000278616	NM_000051.3	2847	Gag/Cag	58/63	0.370566737277955	3	FACETS	0.943	0.896	0.99	0.943	0.896	0.99	CLONAL	3	TRUE	0	0.375263857406486	3		356	705	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106159	27106159	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060497-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	207	433	0	ENST00000324856.7:c.5770G>T	p.Glu1924Ter	p.E1924*	ENST00000324856	NM_006015.4	1924	Gag/Tag	20/20	0.364267516236938	3	FACETS	0.966	0.901	1	0.966	0.901	1	CLONAL	2	TRUE	1	0.375263857406486	3		433	678	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207093	1207093	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060497-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	278	440	0	ENST00000326873.7:c.181G>C	p.Gly61Arg	p.G61R	ENST00000326873	NM_000455.4	61	Ggc/Cgc	1/10	0.375263857406486	3	FACETS	0.973	0.922	1	0.973	0.922	1	CLONAL	3	TRUE	0	0.375263857406486	3		440	603	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054393	13054393	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530463916	NA	P-0060497-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	98	406	0	ENST00000316448.5:c.1003G>A	p.Asp335Asn	p.D335N	ENST00000316448	NM_004343.3	335	Gat/Aat	8/9	0.375263857406486	3	FACETS	1	0.902	1	0.337	0.301	0.375	CLONAL	1	TRUE	0	0.375263857406486	3		406	614	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178197	56178198	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0060497-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	113	395	0	ENST00000399503.3:c.3171dup	p.His1058ThrfsTer7	p.H1058Tfs*7	ENST00000399503	NM_005921.1	1057	ata/atAa	14/20	0.366130519295638	3	FACETS	0.925	0.833	1	0.463	0.416	0.512	CLONAL	1	TRUE	1	0.375263857406486	3		395	773	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211612	36211612	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060497-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	219	377	0	ENST00000222270.7:c.1363G>T	p.Glu455Ter	p.E455*	ENST00000222270	NM_014727.1	455	Gaa/Taa	3/37	0.354762586111382	5	FACETS	1	0.962	1	1	0.962	1	CLONAL	3	TRUE	2	0.375263857406486	5		377	586	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153562	108153564	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0060497-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	152	254	0	ENST00000278616.4:c.3703_3705del	p.Pro1235del	p.P1235del	ENST00000278616	NM_000051.3	1234	ttTCCt/ttt	25/63	0.370566737277955	3	FACETS	0.837	0.775	0.9	0.837	0.775	0.9	CLONAL	3	TRUE	0	0.375263857406486	3		254	383	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398280	25398281	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0060497-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	184	285	0	ENST00000311936.3:c.38_39delinsTT	p.Gly13Val	p.G13V	ENST00000311936	NM_004985.3	13	gGC/gTT	2/5	0.375263857406486	4	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	2	0.375263857406486	4		285	672	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519797	29519797	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060497-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	86	359	0	ENST00000389048.3:c.1774C>A	p.Leu592Met	p.L592M	ENST00000389048	NM_004304.4	592	Ctg/Atg	9/29	0.364267516236938	3	FACETS	0.913	0.809	1	0.457	0.404	0.513	CLONAL	1	TRUE	1	0.375263857406486	3		359	596	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281488	198281489	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060497-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	100	346	2	ENST00000335508.6:c.642dup	p.Leu215ThrfsTer20	p.L215Tfs*20	ENST00000335508	NM_012433.2	214	-/A	6/25	0.316580913453195	4	FACETS	0.945	0.843	1	0.472	0.421	0.526	CLONAL	1	TRUE	2	0.375263857406486	4		348	776	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747138	40747138	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060497-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	167	352	0	ENST00000373198.4:c.2944C>A	p.Pro982Thr	p.P982T	ENST00000373198	NM_133170.3	982	Ccg/Acg	22/32	0.229060344685135	5	FACETS	1	0.973	1	0.745	0.688	0.805	CLONAL	2	TRUE	2	0.375263857406486	5		352	622	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980820	40980820	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060497-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	174	427	0	ENST00000373198.4:c.1666C>A	p.Leu556Met	p.L556M	ENST00000373198	NM_133170.3	556	Ctg/Atg	10/32	0.229060344685135	5	FACETS	1	0.961	1	0.708	0.654	0.764	CLONAL	2	TRUE	2	0.375263857406486	5		427	682	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270188	66270188	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060497-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	75	363	0	ENST00000273854.3:c.1694C>A	p.Ala565Glu	p.A565E	ENST00000273854	NM_004439.5	565	gCa/gAa	8/18	0.364267516236938	3	FACETS	0.827	0.725	0.936	0.414	0.362	0.468	CLONAL	1	TRUE	1	0.375263857406486	3		363	574	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314937	1314937	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1233819869	NA	P-0060497-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	101	370	0	ENST00000400841.2:c.724C>A	p.Leu242Met	p.L242M	ENST00000400841		242	Ctg/Atg	6/6	0.364267516236938	3	FACETS	1	0.959	1	0.569	0.51	0.631	CLONAL	1	TRUE	1	0.375263857406486	3		370	562	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280099	115280099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1039006812	NA	P-0060497-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	88	282	0	ENST00000438362.2:c.533G>A	p.Arg178His	p.R178H	ENST00000438362	NM_001242891.1	178	cGt/cAt	5/20	0.364267516236938	3	FACETS	1	0.908	1	0.513	0.455	0.574	CLONAL	1	TRUE	1	0.375263857406486	3		282	543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0060509-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	384	513	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.656779896221676	2	FACETS	0.97	0.934	1	0.97	0.934	1	CLONAL	2	TRUE	0	0.656779896221676	2		513	603	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030473	49030473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060509-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	90	324	0	ENST00000267163.4:c.1951del	p.Tyr651IlefsTer7	p.Y651Ifs*7	ENST00000267163	NM_000321.2	650	Ttt/tt	19/27	0.603788529869747	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.656779896221676	2		324	134	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0060509-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	130	513	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.3	1	FACETS	0.952	0.865	1	0.952	0.865	1	CLONAL	1	TRUE	0	0.34	1		513	667	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030473	49030473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060509-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	137	324	0	ENST00000267163.4:c.1951del	p.Tyr651IlefsTer7	p.Y651Ifs*7	ENST00000267163	NM_000321.2	650	Ttt/tt	19/27	0.279729307193734	2	FACETS	0.798	0.73	0.868	0.798	0.73	0.868	SUBCLONAL	2	TRUE	0	0.34	2		324	505	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416546	49416546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	45	674	0	ENST00000301067.7:c.16165C>T	p.Arg5389Trp	p.R5389W	ENST00000301067	NM_003482.3	5389	Cgg/Tgg	51/54	0.274530998875896	2	FACETS	0.377	0.316	0.444	0.188	0.158	0.222	SUBCLONAL	1	TRUE	0	0.377422522918029	2		674	633	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209101853	209101853	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	69	409	0	ENST00000345146.2:c.1195G>T	p.Asp399Tyr	p.D399Y	ENST00000345146	NM_005896.2	399	Gat/Tat	10/10	0.292296036061562	3	FACETS	1	0.902	1	0.519	0.453	0.589	CLONAL	1	TRUE	1	0.377422522918029	3		409	419	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0060755-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	116	412	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	0.971	0.881	1	0.971	0.881	1	CLONAL	1	TRUE	1	0.529962785735359	2		412	451	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0060755-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	56	181	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.529962785735359	2		181	182	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0060820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	140	495	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.27974211069711	2	FACETS	0.88	0.805	0.957	0.88	0.805	0.957	CLONAL	2	TRUE	0	0.27974211069711	2		495	569	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0060820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	70	342	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.27974211069711	3	FACETS	0.838	0.741	0.938	1	0.966	1	CLONAL	3	TRUE	1	0.27974211069711	3		342	227	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0060820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	58	549	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.909	0.783	1	0.909	0.783	1	CLONAL	1	TRUE	1	0.27974211069711	2		549	456	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0060820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	32	419	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.776	0.631	0.937	0.776	0.631	0.937	CLONAL	1	TRUE	1	0.27974211069711	2		419	295	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102132	27102132	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	102	407	0	ENST00000324856.7:c.5058G>A	p.Trp1686Ter	p.W1686*	ENST00000324856	NM_006015.4	1686	tgG/tgA	19/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.27974211069711	2		407	540	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120419	70121441	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	GCCCCATGTACACCCCCATCGCCGACACCTCTGGGGTCCCTTCCATCCCGCAGACCCACAGCCCCCAGCACTGGGAACAACCCGTCTACACACAGCTCACTCGACCTTGAGGAGGCCTCCCACGAAGGGCGAAGATGGCCGAGATGATCCTAAAAATAACCGAAGAAAGAGAGGACCAACCAGAATTCCCTTTGGACATTTGTGTTTTTTTGTTTTTTTATTTTGTTTTGTTTTTTCTTCTTCTTCTTCTTCCTTAAAGACATTTAAGCTAAAGGCAACTCGTACCCAAATTTCCAAGACACAAACATGACCTATCCAAGCGCATTACCCACTTGTGGCCAATCAGTGGCCAGGCCAACCTTGGCTAAATGGAGCAGCGAAATCAACGAGAAACTGGACTTTTTAAACCCTCTTCAGAGCAAGCGTGGAGGATGATGGAGAATCGTGTGATCAGTGTGCTAAATCTCTCTGCCTGTTTGGACTTTGTAATTATTTTTTTAGCAGTAATTAAAGAAAAAAGTCCTCTGTGAGGAATATTCTCTATTTTAAATATTTTTAGTATGTACTGTGTATGATTCATTACCATTTTGAGGGGATTTATACATATTTTTAGATAAAATTAAATGCTCTTATTTTTCCAACAGCTAAACTACTCTTAGTTGAACAGTGTGCCCTAGCTTTTCTTGCAACCAGAGTATTTTTGTACAGATTTGCTTTCTCTTACAAAAAGAAAAAAAAAATCCTGTTGTATTAACATTTAAAAACAGAATTGTGTTATGTGATCAGTTTTGGGGGTTAACTTTGCTTAATTCCTCAGGCTTTGCGATTTAAGGAGGAGCTGCCTTAAAAAAAAATAAAGGCCTTATTTTGCAATTATGGGAGTAAACAATAGTCTAGAGAAGCATTTGGTAAGCTTTATCATATATATATTTTTTAAAGAAGAGAAAAACACCTTGAGCCTTAAAACGGTGCTGCTGGGAAACATTTGCACTCTTTTAGTGCATTTCCTCCTGCCTTTGCTTG	GCCCCATGTACACCCCCATCGCCGACACCTCTGGGGTCCCTTCCATCCCGCAGACCCACAGCCCCCAGCACTGGGAACAACCCGTCTACACACAGCTCACTCGACCTTGAGGAGGCCTCCCACGAAGGGCGAAGATGGCCGAGATGATCCTAAAAATAACCGAAGAAAGAGAGGACCAACCAGAATTCCCTTTGGACATTTGTGTTTTTTTGTTTTTTTATTTTGTTTTGTTTTTTCTTCTTCTTCTTCTTCCTTAAAGACATTTAAGCTAAAGGCAACTCGTACCCAAATTTCCAAGACACAAACATGACCTATCCAAGCGCATTACCCACTTGTGGCCAATCAGTGGCCAGGCCAACCTTGGCTAAATGGAGCAGCGAAATCAACGAGAAACTGGACTTTTTAAACCCTCTTCAGAGCAAGCGTGGAGGATGATGGAGAATCGTGTGATCAGTGTGCTAAATCTCTCTGCCTGTTTGGACTTTGTAATTATTTTTTTAGCAGTAATTAAAGAAAAAAGTCCTCTGTGAGGAATATTCTCTATTTTAAATATTTTTAGTATGTACTGTGTATGATTCATTACCATTTTGAGGGGATTTATACATATTTTTAGATAAAATTAAATGCTCTTATTTTTCCAACAGCTAAACTACTCTTAGTTGAACAGTGTGCCCTAGCTTTTCTTGCAACCAGAGTATTTTTGTACAGATTTGCTTTCTCTTACAAAAAGAAAAAAAAAATCCTGTTGTATTAACATTTAAAAACAGAATTGTGTTATGTGATCAGTTTTGGGGGTTAACTTTGCTTAATTCCTCAGGCTTTGCGATTTAAGGAGGAGCTGCCTTAAAAAAAAATAAAGGCCTTATTTTGCAATTATGGGAGTAAACAATAGTCTAGAGAAGCATTTGGTAAGCTTTATCATATATATATTTTTTAAAGAAGAGAAAAACACCTTGAGCCTTAAAACGGTGCTGCTGGGAAACATTTGCACTCTTTTAGTGCATTTCCTCCTGCCTTTGCTTG	-	novel	NA	P-0060820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	61	583	0	ENST00000245479.2:c.1421_*913del		p.*474*	ENST00000245479	NM_000346.3	474		3/3	1	2	FACETS	0.635	0.547	0.731	0.635	0.547	0.731	SUBCLONAL	1	TRUE	1	0.27974211069711	2		583	687	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131361	202131362	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0060820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	60	397	0	ENST00000358485.4:c.332_333del	p.Arg111AsnfsTer18	p.R111Nfs*18	ENST00000358485	NM_001080125.1	110	aAG/a	2/9	1	2	FACETS	0.86	0.742	0.988	0.86	0.742	0.988	CLONAL	1	TRUE	1	0.27974211069711	2		397	499	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0060885-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	208	256	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.582131304488418	4	FACETS	0.977	0.923	1			1	CLONAL	3	TRUE	NA	0.625505867755301	4		256	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0060885-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	270	473	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.625505867755301	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.625505867755301	1		473	560	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98002928	98002929	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	novel	NA	P-0060885-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	112	276	0	ENST00000289081.3:c.345+2dup		p.X115_splice	ENST00000289081	NM_000136.2	115			1	2	FACETS	0.869	0.788	0.954	0.869	0.788	0.954	CLONAL	1	TRUE	1	0.625505867755301	2		276	412	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0061333-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	24	338	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.207367664931647	3	FACETS	1	0.83	1	0.532	0.419	0.662	CLONAL	1	TRUE	1	0.207367664931647	3		338	240	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1688714	1688714	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061333-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	27	505	0	ENST00000378625.1:c.611G>T	p.Trp204Leu	p.W204L	ENST00000378625	NM_001198994.1	204	tGg/tTg	6/14	1	2	FACETS	0.607	0.482	0.75	0.607	0.482	0.75	SUBCLONAL	1	TRUE	1	0.207367664931647	2		505	429	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798120	45798120	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061333-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	36	669	0	ENST00000450313.1:c.731G>T	p.Cys244Phe	p.C244F	ENST00000450313	NM_012222.2	244	tGc/tTc	9/16	1	2	FACETS	0.739	0.607	0.887	0.739	0.607	0.887	SUBCLONAL	1	TRUE	1	0.207367664931647	2		669	470	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119470	193119470	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061333-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	48	455	0	ENST00000367435.3:c.865G>T	p.Ala289Ser	p.A289S	ENST00000367435	NM_024529.4	289	Gcc/Tcc	9/17	0.123598979975185	3	FACETS	1	0.864	1	0.341	0.288	0.4	INDETERMINATE	1	TRUE	0	0.207367664931647	3		455	499	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120806019	120806019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061333-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	84	659	0	ENST00000257552.2:c.158G>T	p.Arg53Leu	p.R53L	ENST00000257552	NM_002442.3	53	cGg/cTg	3/15	0.207367664931647	3	FACETS	0.858	0.76	0.963	0.858	0.76	0.963	CLONAL	2	TRUE	1	0.207367664931647	3		659	521	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588647	28588647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061333-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	33	450	0	ENST00000241453.7:c.2801C>T	p.Pro934Leu	p.P934L	ENST00000241453	NM_004119.2	934	cCa/cTa	23/24	1	2	FACETS	0.663	0.539	0.803	0.663	0.539	0.803	SUBCLONAL	1	TRUE	1	0.207367664931647	2		450	480	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001456	29001456	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0061333-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	35	446	0	ENST00000282397.4:c.1277-1G>C		p.X426_splice	ENST00000282397	NM_002019.4	426			1	2	FACETS	0.846	0.694	1	0.846	0.694	1	CLONAL	1	TRUE	1	0.207367664931647	2		446	399	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349395	73349395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061333-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	26	434	0	ENST00000377767.4:c.941G>A	p.Gly314Asp	p.G314D	ENST00000377767	NM_014953.3	314	gGt/gAt	6/21	1	2	FACETS	0.63	0.499	0.781	0.63	0.499	0.781	SUBCLONAL	1	TRUE	1	0.207367664931647	2		434	398	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420329	88420329	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061333-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	40	559	0	ENST00000360948.2:c.2357del	p.Gly786ValfsTer30	p.G786Vfs*30	ENST00000360948	NM_001012338.2	786	gGt/gt	19/19	1	2	FACETS	0.875	0.727	1	0.875	0.727	1	CLONAL	1	TRUE	1	0.207367664931647	2		559	441	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805753	46805753	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061333-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	40	765	0	ENST00000290295.7:c.203G>A	p.Gly68Glu	p.G68E	ENST00000290295	NM_006361.5	68	gGg/gAg	1/2	1	2	FACETS	0.805	0.669	0.957	0.805	0.669	0.957	CLONAL	1	TRUE	1	0.207367664931647	2		765	479	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440903	56440903	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs151209912	NA	P-0061333-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	49	614	0	ENST00000407977.2:c.434G>T	p.Arg145Leu	p.R145L	ENST00000407977		145	cGa/cTa	4/10	1	2	FACETS	0.964	0.817	1	0.964	0.817	1	CLONAL	1	TRUE	1	0.207367664931647	2		614	490	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207009	1207009	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061333-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	35	606	0	ENST00000326873.7:c.97G>T	p.Glu33Ter	p.E33*	ENST00000326873	NM_000455.4	33	Gag/Tag	1/10	0.207367664931647	1	FACETS	0.764	0.627	0.918	0.764	0.627	0.918	CLONAL	1	TRUE	0	0.207367664931647	1		606	396	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610431	10610432	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0061333-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	49	698	0	ENST00000171111.5:c.278_279del	p.Phe93TyrfsTer33	p.F93Yfs*33	ENST00000171111	NM_203500.1	93	tTC/t	2/6	0.207367664931647	1	FACETS	0.892	0.756	1	0.892	0.756	1	CLONAL	1	TRUE	0	0.207367664931647	1		698	475	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416388	29416388	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs771352312	NA	P-0061333-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	28	628	0	ENST00000389048.3:c.4565T>G	p.Ile1522Arg	p.I1522R	ENST00000389048	NM_004304.4	1522	aTa/aGa	29/29	1	2	FACETS	0.561	0.448	0.691	0.561	0.448	0.691	SUBCLONAL	1	TRUE	1	0.207367664931647	2		628	481	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67632049	67632049	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061333-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	28	373	0	ENST00000272342.5:c.2235T>G	p.Cys745Trp	p.C745W	ENST00000272342	NM_019002.3	745	tgT/tgG	5/6	1	2	FACETS	0.785	0.628	0.964	0.785	0.628	0.964	CLONAL	1	TRUE	1	0.207367664931647	2		373	344	SUCCESS
ATR	545	MSKCC	GRCh37	3	142222253	142222253	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061333-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	17	320	0	ENST00000350721.4:c.5239G>T	p.Gly1747Cys	p.G1747C	ENST00000350721	NM_001184.3	1747	Ggt/Tgt	30/47	1	2	FACETS	0.482	0.359	0.629	0.482	0.359	0.629	SUBCLONAL	1	TRUE	1	0.207367664931647	2		320	340	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851522	128851522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061333-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	26	523	0	ENST00000249373.3:c.1847C>T	p.Ser616Phe	p.S616F	ENST00000249373	NM_005631.4	616	tCt/tTt	11/12	1	2	FACETS	0.63	0.499	0.781	0.63	0.499	0.781	SUBCLONAL	1	TRUE	1	0.207367664931647	2		523	398	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066928	30066928	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061333-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	33	429	0	ENST00000331968.5:c.2203G>T	p.Gly735Ter	p.G735*	ENST00000331968	NM_002742.2	735	Gga/Tga	16/18	1	2	FACETS	0.8	0.652	0.966	0.8	0.652	0.966	CLONAL	1	TRUE	1	0.207367664931647	2		429	398	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0061333-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	222	338	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.385891789711044	3	FACETS	1	0.989	1	0.764	0.726	0.801	INDETERMINATE	2	TRUE	0	0.747445401833119	3		338	356	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1688714	1688714	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061333-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	49	505	0	ENST00000378625.1:c.611G>T	p.Trp204Leu	p.W204L	ENST00000378625	NM_001198994.1	204	tGg/tTg	6/14	0.450422690285901	1	FACETS	0.344	0.294	0.397	0.344	0.294	0.397	SUBCLONAL	1	TRUE	0	0.747445401833119	1		505	239	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798120	45798120	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061333-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	234	669	0	ENST00000450313.1:c.731G>T	p.Cys244Phe	p.C244F	ENST00000450313	NM_012222.2	244	tGc/tTc	9/16	0.450422690285901	1	FACETS	0.847	0.801	0.893	0.847	0.801	0.893	CLONAL	1	TRUE	0	0.747445401833119	1		669	463	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119470	193119470	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061333-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	195	455	0	ENST00000367435.3:c.865G>T	p.Ala289Ser	p.A289S	ENST00000367435	NM_024529.4	289	Gcc/Tcc	9/17	0.612832986542559	3	FACETS	0.753	0.704	0.802	0.502	0.469	0.535	SUBCLONAL	2	TRUE	0	0.747445401833119	3		455	476	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120806019	120806019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061333-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	292	659	0	ENST00000257552.2:c.158G>T	p.Arg53Leu	p.R53L	ENST00000257552	NM_002442.3	53	cGg/cTg	3/15	0.385891789711044	3	FACETS	1	0.992	1	0.769	0.736	0.802	INDETERMINATE	2	TRUE	0	0.747445401833119	3		659	465	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588647	28588647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061333-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	198	450	0	ENST00000241453.7:c.2801C>T	p.Pro934Leu	p.P934L	ENST00000241453	NM_004119.2	934	cCa/cTa	23/24	1	2	FACETS	0.994	0.928	1	0.994	0.928	1	CLONAL	1	TRUE	1	0.747445401833119	2		450	533	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001456	29001456	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0061333-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	138	446	0	ENST00000282397.4:c.1277-1G>C		p.X426_splice	ENST00000282397	NM_002019.4	426			1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.747445401833119	2		446	360	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349395	73349395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061333-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	153	434	0	ENST00000377767.4:c.941G>A	p.Gly314Asp	p.G314D	ENST00000377767	NM_014953.3	314	gGt/gAt	6/21	1	2	FACETS	0.975	0.901	1	0.975	0.901	1	CLONAL	1	TRUE	1	0.747445401833119	2		434	420	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420329	88420329	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061333-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	195	559	0	ENST00000360948.2:c.2357del	p.Gly786ValfsTer30	p.G786Vfs*30	ENST00000360948	NM_001012338.2	786	gGt/gt	19/19	0.3848816438725	1	FACETS	0.807	0.757	0.856	0.807	0.757	0.856	INDETERMINATE	1	TRUE	0	0.747445401833119	1		559	405	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805753	46805753	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061333-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	185	765	0	ENST00000290295.7:c.203G>A	p.Gly68Glu	p.G68E	ENST00000290295	NM_006361.5	68	gGg/gAg	1/2	0.395422358307734	3	FACETS	1	0.987	1	0.632	0.588	0.677	INDETERMINATE	1	TRUE	1	0.747445401833119	3		765	538	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440903	56440903	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs151209912	NA	P-0061333-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	152	614	0	ENST00000407977.2:c.434G>T	p.Arg145Leu	p.R145L	ENST00000407977		145	cGa/cTa	4/10	0.395422358307734	3	FACETS	1	0.956	1	0.529	0.487	0.573	INDETERMINATE	1	TRUE	1	0.747445401833119	3		614	528	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207009	1207009	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061333-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	173	606	0	ENST00000326873.7:c.97G>T	p.Glu33Ter	p.E33*	ENST00000326873	NM_000455.4	33	Gag/Tag	1/10	0.747445401833119	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.747445401833119	1		606	263	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610431	10610432	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0061333-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	200	698	0	ENST00000171111.5:c.278_279del	p.Phe93TyrfsTer33	p.F93Yfs*33	ENST00000171111	NM_203500.1	93	tTC/t	2/6	0.747445401833119	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.747445401833119	1		698	289	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416388	29416388	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs771352312	NA	P-0061333-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	159	628	0	ENST00000389048.3:c.4565T>G	p.Ile1522Arg	p.I1522R	ENST00000389048	NM_004304.4	1522	aTa/aGa	29/29	1	2	FACETS	0.96	0.889	1	0.96	0.889	1	CLONAL	1	TRUE	1	0.747445401833119	2		628	443	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67632049	67632049	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061333-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	160	373	0	ENST00000272342.5:c.2235T>G	p.Cys745Trp	p.C745W	ENST00000272342	NM_019002.3	745	tgT/tgG	5/6	1	2	FACETS	0.975	0.903	1	0.975	0.903	1	CLONAL	1	TRUE	1	0.747445401833119	2		373	439	SUCCESS
ATR	545	MSKCC	GRCh37	3	142222253	142222253	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061333-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	102	320	0	ENST00000350721.4:c.5239G>T	p.Gly1747Cys	p.G1747C	ENST00000350721	NM_001184.3	1747	Ggt/Tgt	30/47	0.3848816438725	1	FACETS	0.718	0.655	0.782	0.718	0.655	0.782	INDETERMINATE	1	TRUE	0	0.747445401833119	1		320	238	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851522	128851522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061333-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	190	523	0	ENST00000249373.3:c.1847C>T	p.Ser616Phe	p.S616F	ENST00000249373	NM_005631.4	616	tCt/tTt	11/12	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.747445401833119	2		523	486	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066928	30066928	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061333-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	108	429	0	ENST00000331968.5:c.2203G>T	p.Gly735Ter	p.G735*	ENST00000331968	NM_002742.2	735	Gga/Tga	16/18	1	2	FACETS	0.944	0.859	1	0.944	0.859	1	CLONAL	1	TRUE	1	0.747445401833119	2		429	306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0061482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	177	529	0	ENST00000269305.4:c.97-1G>A		p.X33_splice	ENST00000269305	NM_001126112.2	33			NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.324958937001714	2		529	842	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178941899	178941899	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	59	424	0	ENST00000263967.3:c.2218A>T	p.Arg740Trp	p.R740W	ENST00000263967	NM_006218.2	740	Agg/Tgg	15/21	0.324958937001714	5	FACETS	0.768	0.66	0.887	0.256	0.22	0.296	SUBCLONAL	1	TRUE	2	0.324958937001714	5		424	703	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762440	41762440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773403341	NA	P-0061482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	115	558	0	ENST00000301178.4:c.2120G>A	p.Arg707His	p.R707H	ENST00000301178	NM_021913.4	707	cGt/cAt	18/20	1	2	FACETS	0.743	0.669	0.823	0.743	0.669	0.823	SUBCLONAL	1	TRUE	1	0.324958937001714	2		558	952	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483946	212483946	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	49	449	0	ENST00000342788.4:c.2257C>G	p.Leu753Val	p.L753V	ENST00000342788	NM_005235.2	753	Ctt/Gtt	19/28	1	2	FACETS	0.973	0.829	1	0.973	0.829	1	CLONAL	1	TRUE	1	0.324958937001714	2		449	310	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144146	11144146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	125	496	0	ENST00000358026.2:c.3727C>T	p.Arg1243Trp	p.R1243W	ENST00000358026	NM_001128849.1	1243	Cgg/Tgg	26/36	1	2	FACETS	0.837	0.757	0.922	0.837	0.757	0.922	CLONAL	1	TRUE	1	0.324958937001714	2		496	919	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149006	119149174	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTACGGATCTAAACAGCGACTTTTTTCAGCTATGTAATAACCTTGGAAAATTCGGTATTATATAGCCTTTACTGATACAAGGGGTGGCCTGGCTTTTGGGGTTAGGTTTAAACTTTTACTTTTTTTTGATCTCTAGGAAATGTATTTTCTAGTAGATTAATATTTTA	AGGTACGGATCTAAACAGCGACTTTTTTCAGCTATGTAATAACCTTGGAAAATTCGGTATTATATAGCCTTTACTGATACAAGGGGTGGCCTGGCTTTTGGGGTTAGGTTTAAACTTTTACTTTTTTTTGATCTCTAGGAAATGTATTTTCTAGTAGATTAATATTTTA	-	novel	NA	P-0061482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	168	460	0	ENST00000264033.4:c.1227+1_1228-44del		p.X409_splice	ENST00000264033	NM_005188.3	409		8/16	0.303541108797883	2	FACETS	1	0.989	1	0.74	0.682	0.8	CLONAL	1	TRUE	0	0.324958937001714	2		460	699	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435739	110435739	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	310	595	0	ENST00000375856.3:c.2662G>A	p.Val888Met	p.V888M	ENST00000375856	NM_003749.2	888	Gtg/Atg	1/2	0.324958937001714	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.324958937001714	3		595	998	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864613	37864613	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	141	595	0	ENST00000269571.5:c.265A>G	p.Asn89Asp	p.N89D	ENST00000269571		89	Aac/Gac	3/27	0.303541108797883	2	FACETS	0.915	0.833	1	0.458	0.416	0.501	CLONAL	1	TRUE	0	0.324958937001714	2		595	948	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285295	212285295	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	103	469	0	ENST00000342788.4:c.3006G>T	p.Lys1002Asn	p.K1002N	ENST00000342788	NM_005235.2	1002	aaG/aaT	25/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.324958937001714	2		469	503	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63898067	63898529	+	splice_acceptor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	AGCCCGCGCCGCGGACTTTGAGCCCGGGGCGGGGGGTGGCCTTGAGGAGGCGGGCTCGGGGGGCTGGGCGGCCATGGGGGCGCTGTCAGCGTGCCCCACCCGGTCCGCGGGCCGCGCACGCCGCCGGAACTCCCTGGCGCCTCCTTAAAAAACGGCCCCCGCGCGACTCTTTCCCCCTTTTTTTTGTTACATTGTAGGAGCGGAAAGAATGTCGGAGCGGGCCGCGGATGACGTCAGGGGGGAGCCGCGCCGCGCGGCGGCGGCGGCGGGCGGAGCAGCGGCCGCGGCCGCCCGGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCCGCCGCCTCCGCAGCCCCAGCGGCAGCAGCACCCGCCACCGCCGCCACGGCGCACACGGCCGGAGGACGGCGGGCCCGGCGCCGCCTCCACCTCGGCCGCCGCAATGGCGACGGTCGGGGAGCGCAGGCCTCTGCCC	AGCCCGCGCCGCGGACTTTGAGCCCGGGGCGGGGGGTGGCCTTGAGGAGGCGGGCTCGGGGGGCTGGGCGGCCATGGGGGCGCTGTCAGCGTGCCCCACCCGGTCCGCGGGCCGCGCACGCCGCCGGAACTCCCTGGCGCCTCCTTAAAAAACGGCCCCCGCGCGACTCTTTCCCCCTTTTTTTTGTTACATTGTAGGAGCGGAAAGAATGTCGGAGCGGGCCGCGGATGACGTCAGGGGGGAGCCGCGCCGCGCGGCGGCGGCGGCGGGCGGAGCAGCGGCCGCGGCCGCCCGGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCCGCCGCCTCCGCAGCCCCAGCGGCAGCAGCACCCGCCACCGCCGCCACGGCGCACACGGCCGGAGGACGGCGGGCCCGGCGCCGCCTCCACCTCGGCCGCCGCAATGGCGACGGTCGGGGAGCGCAGGCCTCTGCCC	-	novel	NA	P-0061482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	30	205	0	ENST00000398590.3:c.-11-195_257del		p.X4_splice	ENST00000398590	NM_001177387.1	4		3/14	0.303541108797883	2	FACETS	0.601	0.486	0.732	0.301	0.243	0.366	SUBCLONAL	1	TRUE	0	0.324958937001714	2		205	307	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818544	170819309	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGGAGTTCGATGGTCAACTCTTGAACATGGGGGCTTCTGCTGCTACTTTTATCAGAGGTGGAAAAACAGGTTCACTGGTTTGTTGATTTGGCTTATGTGTTTGCCTGTAATGTTTATTGTTCATTTTCTTCACATGTTTAGTGATGAAAAATTTCTCCCTTCTAGGTTTCCCTTGGGGGCTTTGAAATAACACCACCAGTGGTCTTAAGGTTGAAGTGTGGTTCAGGGCCAGTGCATATTAGTGGACAGCACTTAGTAGGTATGTTATTTTTATATATTATACTACTTAGTTTGTCCTCTTTAGTGCAGTTGCTTGGTTCCCAGTTTGGACTTAAAGCATGGGTATAGTACTACTGTCTTTTTAATAGGTTCCAATGTGAGTCTAGAAATTGGAGAGGACAAATAAATTTTTGGGGCGGGGGGGAGAGGAAATCTTGCTGTCACCCAGGCTAGAGTACAGTGGCACGATCTTGGCTCACTGGAACCTCTCCGGGATTCAAGCGATCCTCCTGTCTCAGCCTCCCCAGTAGCTGGGGCCACAGACGTGCACCACCAAGTCCAGTTGCGTTTCATAGTTATAGTAGAGAAGGGGTTTCGTGATGTTGGCCAGGCCGATCTTGAACTCCTGGCCTTAACGTGATCTGCACGCCCTGGCCTCTCAAAGTGCTAGTATTACACGTGTCAGCCACTGTGCCTGGCCTAAAAATTATTTTTTAATAAAGACAGTCTCATTATAACGGCTGGAGTGCAGTGATGTGATCATAG	CTGGAGTTCGATGGTCAACTCTTGAACATGGGGGCTTCTGCTGCTACTTTTATCAGAGGTGGAAAAACAGGTTCACTGGTTTGTTGATTTGGCTTATGTGTTTGCCTGTAATGTTTATTGTTCATTTTCTTCACATGTTTAGTGATGAAAAATTTCTCCCTTCTAGGTTTCCCTTGGGGGCTTTGAAATAACACCACCAGTGGTCTTAAGGTTGAAGTGTGGTTCAGGGCCAGTGCATATTAGTGGACAGCACTTAGTAGGTATGTTATTTTTATATATTATACTACTTAGTTTGTCCTCTTTAGTGCAGTTGCTTGGTTCCCAGTTTGGACTTAAAGCATGGGTATAGTACTACTGTCTTTTTAATAGGTTCCAATGTGAGTCTAGAAATTGGAGAGGACAAATAAATTTTTGGGGCGGGGGGGAGAGGAAATCTTGCTGTCACCCAGGCTAGAGTACAGTGGCACGATCTTGGCTCACTGGAACCTCTCCGGGATTCAAGCGATCCTCCTGTCTCAGCCTCCCCAGTAGCTGGGGCCACAGACGTGCACCACCAAGTCCAGTTGCGTTTCATAGTTATAGTAGAGAAGGGGTTTCGTGATGTTGGCCAGGCCGATCTTGAACTCCTGGCCTTAACGTGATCTGCACGCCCTGGCCTCTCAAAGTGCTAGTATTACACGTGTCAGCCACTGTGCCTGGCCTAAAAATTATTTTTTAATAAAGACAGTCTCATTATAACGGCTGGAGTGCAGTGATGTGATCATAG	-	novel	NA	P-0061482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	26	119	0	ENST00000296930.5:c.258+118_353-403del		p.X86_splice	ENST00000296930	NM_002520.6	86		4/11	1	2	FACETS	0.788	0.628	0.969	0.788	0.628	0.969	CLONAL	1	TRUE	1	0.324958937001714	2		119	203	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517415	157517415	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554234412	NA	P-0061482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	143	386	0	ENST00000346085.5:c.3979C>T	p.Gln1327Ter	p.Q1327*	ENST00000346085	NM_020732.3	1327	Cag/Tag	16/20	0.199218400179864	3	FACETS	1	0.986	1	0.715	0.653	0.78	CLONAL	1	TRUE	1	0.324958937001714	3		386	715	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061504-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	420	772	0	ENST00000269305.4:c.472C>G	p.Arg158Gly	p.R158G	ENST00000269305	NM_001126112.2	158	Cgc/Ggc	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		772	797	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46602865	46602865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061504-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	35	575	0	ENST00000263734.3:c.923G>A	p.Arg308Gln	p.R308Q	ENST00000263734	NM_001430.4	308	cGg/cAg	8/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		575	537	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31238074	31238075	+	missense_variant	Missense_Mutation	DNP	CT	CT	AC	novel	NA	P-0061504-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	10	33	0	ENST00000376228.5:c.807_808delinsGT	p.Ala270Ser	p.A270S	ENST00000376228	NM_002117.5	269	gcAGct/gcGTct	4/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		33	74	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913527	NA	P-0061504-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	3817	354	0	ENST00000311936.3:c.436G>C	p.Ala146Pro	p.A146P	ENST00000311936	NM_004985.3	146	Gca/Cca	4/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		354	4079	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933040	39933044	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTC	TTCTC	-	novel	NA	P-0061504-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	128	352	0	ENST00000378444.4:c.1555_1559del	p.Glu519GlnfsTer36	p.E519Qfs*36	ENST00000378444	NM_001123385.1	519	GAGAAc/c	4/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		352	249	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133697	2133701	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CTCCG	CTCCG	-	novel	NA	P-0061701-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	97	480	0	ENST00000219476.3:c.3886_3890del	p.Ser1296ArgfsTer24	p.S1296Rfs*24	ENST00000219476	NM_000548.3	1295	gaCTCCGcc/gacc	33/42	0.328794049719219	2	FACETS	0.981	0.887	1	0.981	0.887	1	CLONAL	2	TRUE	0	0.350616503640459	2		480	282	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1688633	1688633	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749009504	NA	P-0061701-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	15	356	0	ENST00000378625.1:c.692C>T	p.Thr231Met	p.T231M	ENST00000378625	NM_001198994.1	231	aCg/aTg	6/14	0.226042554633339	3	FACETS	0.524	0.384	0.691	0.175	0.128	0.231	SUBCLONAL	1	TRUE	0	0.350616503640459	3		356	192	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652024	36652025	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	T	novel	NA	P-0061701-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	112	565	0	ENST00000244741.5:c.146_147delinsT	p.Trp49LeufsTer99	p.W49Lfs*99	ENST00000244741	NM_000389.4	49	tGG/tT	2/3	0.3592170322906	4	FACETS	1	0.962	1			1	CLONAL	2	TRUE	NA	0.350616503640459	4		565	386	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051652	30051669	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGAGGCCGAGCCAGGTGA	CGAGGCCGAGCCAGGTGA	GCTC	novel	NA	P-0062186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	65	350	1	ENST00000338641.4:c.586_599+4delinsGCTC		p.X196_splice	ENST00000338641	NM_000268.3	196		6/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		351	362	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793211	139793212	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748531430	NA	P-0062198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	44	325	2	ENST00000247668.2:c.26dup	p.Gly10TrpfsTer70	p.G10Wfs*70	ENST00000247668	NM_021138.3	7	acc/aCcc	2/11	0.677360356282702	4	FACETS	0.665	0.56	0.78	0.222	0.186	0.26	SUBCLONAL	1	TRUE	1	0.673140693310782	4		327	329	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216476	108216477	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587782558	NA	P-0062198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	63	285	0	ENST00000278616.4:c.8432dup	p.Ser2812ValfsTer3	p.S2812Vfs*3	ENST00000278616	NM_000051.3	2809	caa/cAaa	58/63	0.677360356282702	2	FACETS	0.913	0.803	1	0.457	0.401	0.515	CLONAL	1	TRUE	0	0.673140693310782	2		285	205	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258566	16258566	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	87	607	0	ENST00000375759.3:c.5831T>C	p.Val1944Ala	p.V1944A	ENST00000375759	NM_015001.2	1944	gTt/gCt	11/15	0.677360356282702	5	FACETS	0.767	0.679	0.861	0.256	0.226	0.287	SUBCLONAL	1	TRUE	2	0.673140693310782	5		607	677	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607840	46607840	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	51	474	0	ENST00000263734.3:c.2029T>C	p.Ser677Pro	p.S677P	ENST00000263734	NM_001430.4	677	Tcc/Ccc	12/16	0.49462287052194	3	FACETS	0.519	0.442	0.603	0.26	0.221	0.302	SUBCLONAL	1	TRUE	1	0.673140693310782	3		474	390	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178942558	178942558	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	105	350	0	ENST00000263967.3:c.2365A>G	p.Met789Val	p.M789V	ENST00000263967	NM_006218.2	789	Atg/Gtg	16/21	0.673140693310782	7	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.673140693310782	7		350	665	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449548	187449548	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	121	443	0	ENST00000232014.4:c.332A>G	p.Tyr111Cys	p.Y111C	ENST00000232014	NM_001130845.1	111	tAc/tGc	4/10	0.677360356282702	4	FACETS	0.846	0.765	0.931	0.423	0.382	0.466	CLONAL	1	TRUE	2	0.673140693310782	4		443	711	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816828	32816828	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	103	432	0	ENST00000354258.4:c.1496T>C	p.Val499Ala	p.V499A	ENST00000354258	NM_000593.5	499	gTa/gCa	6/11	0.673140693310782	6	FACETS	1	0.939	1	0.178	0.159	0.198	CLONAL	1	TRUE	0	0.673140693310782	6		432	672	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914697	39914697	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062298-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	67	415	0	ENST00000378444.4:c.4665C>A	p.Asp1555Glu	p.D1555E	ENST00000378444	NM_001123385.1	1555	gaC/gaA	12/15	0.127327164982124	0	FACETS	0.31	0.271	0.351			1	INDETERMINATE	1	TRUE	0	0.56	0		415	340	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252155	226252155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553260624	NA	P-0062298-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	82	181	0	ENST00000366813.1:c.103G>A	p.Gly35Arg	p.G35R	ENST00000366813		35	Ggg/Agg	1/3	1	2	FACETS	0.933	0.831	1	0.933	0.831	1	CLONAL	1	TRUE	1	0.56	2		181	314	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398262	25398262	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913538	NA	P-0062298-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	125	293	0	ENST00000311936.3:c.57G>C	p.Leu19Phe	p.L19F	ENST00000311936	NM_004985.3	19	ttG/ttC	2/5	0.162388022960444	3	FACETS	0.762	0.697	0.829	0.762	0.697	0.829	INDETERMINATE	2	TRUE	1	0.56	3		293	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0062314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	44	745	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	1	2	FACETS	0.647	0.542	0.765	0.647	0.542	0.765	SUBCLONAL	1	TRUE	1	0.202034723940364	2		745	673	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	60	690	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.202034723940364	2		691	592	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0062314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	45	566	2	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.654	0.548	0.771	0.654	0.548	0.771	SUBCLONAL	1	TRUE	1	0.202034723940364	2		568	681	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0062314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	33	177	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.197728003494626	2	FACETS	0.978	0.807	1	0.978	0.807	1	CLONAL	2	TRUE	0	0.202034723940364	2		177	167	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	73	553	0	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.202034723940364	2		553	611	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106648	27106648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553153748	NA	P-0062314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	83	730	0	ENST00000324856.7:c.6259G>A	p.Gly2087Arg	p.G2087R	ENST00000324856	NM_006015.4	2087	Gga/Aga	20/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.202034723940364	2		730	683	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	15	482	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	0.197728003494626	2	FACETS	0.349	0.254	0.463	0.174	0.127	0.232	SUBCLONAL	1	TRUE	0	0.202034723940364	2		482	426	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653805	89653805	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659443	NA	P-0062314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	40	294	0	ENST00000371953.3:c.103A>G	p.Met35Val	p.M35V	ENST00000371953	NM_000314.4	35	Atg/Gtg	2/9	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.202034723940364	2		294	274	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0062314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	63	589	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.942	0.814	1	0.942	0.814	1	CLONAL	1	TRUE	1	0.202034723940364	2		589	662	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354428	40354428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs929910807	NA	P-0062314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	80	660	0	ENST00000293328.3:c.2167G>A	p.Ala723Thr	p.A723T	ENST00000293328	NM_012448.3	723	Gcc/Acc	18/19	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.202034723940364	2		660	659	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551952	150551952	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	52	605	1	ENST00000369026.2:c.55del	p.Ala19ProfsTer30	p.A19Pfs*30	ENST00000369026	NM_021960.4	19	Gcc/cc	1/3	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.202034723940364	2		606	493	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466040	69466040	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	124	687	0	ENST00000227507.2:c.878T>G	p.Val293Gly	p.V293G	ENST00000227507	NM_053056.2	293	gTg/gGg	5/5	0.202034723940364	3	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	1	0.202034723940364	3		687	638	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261246	16261246	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1466090335	NA	P-0062314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	68	634	6	ENST00000375759.3:c.8516del	p.Pro2839ArgfsTer50	p.P2839Rfs*50	ENST00000375759	NM_015001.2	2837	atC/at	11/15	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.202034723940364	2		640	667	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023715	27023716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0062314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	37	650	0	ENST00000324856.7:c.827dup	p.Gly277ArgfsTer123	p.G277Rfs*123	ENST00000324856	NM_006015.4	274	atg/atGg	1/20	1	2	FACETS	0.982	0.811	1	0.982	0.811	1	CLONAL	1	TRUE	1	0.202034723940364	2		650	373	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085824	16085824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763830786	NA	P-0062314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	28	499	0	ENST00000281043.3:c.1000G>A	p.Ala334Thr	p.A334T	ENST00000281043	NM_005378.4	334	Gcc/Acc	3/3	1	2	FACETS	0.5	0.399	0.617	0.5	0.399	0.617	SUBCLONAL	1	TRUE	1	0.202034723940364	2		499	554	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434408	49434408	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	62	653	0	ENST00000301067.7:c.7145del	p.Pro2382HisfsTer2	p.P2382Hfs*2	ENST00000301067	NM_003482.3	2382	cCa/ca	31/54	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.202034723940364	2		653	606	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221320	2221320	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	24	521	0	ENST00000326181.6:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000326181	NM_032271.2	135	tGc/tAc	6/21	1	2	FACETS	0.587	0.459	0.734	0.587	0.459	0.734	SUBCLONAL	1	TRUE	1	0.202034723940364	2		521	405	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352265	70352265	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	62	573	0	ENST00000374080.3:c.4292T>C	p.Leu1431Pro	p.L1431P	ENST00000374080		1431	cTc/cCc	31/45	1	2	FACETS	0.973	0.84	1	0.973	0.84	1	CLONAL	1	TRUE	1	0.202034723940364	2		573	631	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938039	76938039	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	32	482	0	ENST00000373344.5:c.2709A>T	p.Glu903Asp	p.E903D	ENST00000373344	NM_000489.3	903	gaA/gaT	9/35	1	2	FACETS	0.591	0.479	0.718	0.591	0.479	0.718	SUBCLONAL	1	TRUE	1	0.202034723940364	2		482	536	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1696784	1696784	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	30	456	0	ENST00000378625.1:c.62A>G	p.Tyr21Cys	p.Y21C	ENST00000378625	NM_001198994.1	21	tAc/tGc	2/14	1	2	FACETS	0.526	0.422	0.643	0.526	0.422	0.643	SUBCLONAL	1	TRUE	1	0.202034723940364	2		456	565	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650162	206650162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	56	631	0	ENST00000367120.3:c.682C>T	p.Arg228Trp	p.R228W	ENST00000367120	NM_014002.3	228	Cgg/Tgg	7/22	1	2	FACETS	0.906	0.776	1	0.906	0.776	1	CLONAL	1	TRUE	1	0.202034723940364	2		631	612	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850871	63850872	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0062314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	46	604	0	ENST00000279873.7:c.1652_1653del	p.Lys551ArgfsTer17	p.K551Rfs*17	ENST00000279873	NM_032199.2	550	gAA/g	10/10	1	2	FACETS	0.654	0.55	0.77	0.654	0.55	0.77	SUBCLONAL	1	TRUE	1	0.202034723940364	2		604	696	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692989	89692989	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	52	398	0	ENST00000371953.3:c.473T>A	p.Val158Glu	p.V158E	ENST00000371953	NM_000314.4	158	gTa/gAa	5/9	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.202034723940364	2		398	378	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003745	57003745	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	C	C	T	rs373852614	NA	P-0062314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	30	621	0	ENST00000257254.3:c.734G>A	p.Arg245Gln	p.R245Q	ENST00000257254		245	cGg/cAg	1/2	0.202034723940364	3	FACETS	0.55	0.441	0.673	0.275	0.22	0.337	SUBCLONAL	1	TRUE	1	0.202034723940364	3		621	595	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917760	29917760	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0062314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	32	525	0	ENST00000389048.3:c.908T>A	p.Leu303Ter	p.L303*	ENST00000389048	NM_004304.4	303	tTg/tAg	3/29	1	2	FACETS	0.608	0.493	0.739	0.608	0.493	0.739	SUBCLONAL	1	TRUE	1	0.202034723940364	2		525	521	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553120	106553120	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	38	612	0	ENST00000369096.4:c.1085C>A	p.Pro362His	p.P362H	ENST00000369096	NM_001198.3	362	cCt/cAt	5/7	1	2	FACETS	0.639	0.527	0.764	0.639	0.527	0.764	SUBCLONAL	1	TRUE	1	0.202034723940364	2		612	589	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0062419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	417	511	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.588276235112628	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	3	TRUE	1	0.588276235112628	4		511	748	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001425	29001425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	215	530	0	ENST00000282397.4:c.1307C>T	p.Ser436Leu	p.S436L	ENST00000282397	NM_002019.4	436	tCa/tTa	10/30	1	2	FACETS	0.932	0.869	0.997	0.932	0.869	0.997	CLONAL	1	TRUE	1	0.588276235112628	2		530	784	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579890	7579890	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659415	NA	P-0062419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	217	691	0	ENST00000269305.4:c.23C>T	p.Pro8Leu	p.P8L	ENST00000269305	NM_001126112.2	8	cCt/cTt	2/11	1	2	FACETS	0.967	0.902	1	0.967	0.902	1	CLONAL	1	TRUE	1	0.588276235112628	2		691	763	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873233	71873233	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	154	549	0	ENST00000357731.5:c.961G>A	p.Gly321Arg	p.G321R	ENST00000357731	NM_173808.2	321	Gga/Aga	7/7	1	2	FACETS	0.761	0.698	0.826	0.761	0.698	0.826	SUBCLONAL	1	TRUE	1	0.588276235112628	2		549	688	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514358	149514358	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	256	697	0	ENST00000261799.4:c.586G>A	p.Asp196Asn	p.D196N	ENST00000261799	NM_002609.3	196	Gac/Aac	4/23	1	2	FACETS	0.934	0.876	0.994	0.934	0.876	0.994	CLONAL	1	TRUE	1	0.588276235112628	2		697	932	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036029	180036029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	213	620	0	ENST00000261937.6:c.3832G>A	p.Val1278Met	p.V1278M	ENST00000261937	NM_182925.4	1278	Gtg/Atg	29/30	1	2	FACETS	0.879	0.818	0.941	0.879	0.818	0.941	CLONAL	1	TRUE	1	0.588276235112628	2		620	824	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706895	117706895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	163	519	0	ENST00000368508.3:c.2255C>T	p.Ala752Val	p.A752V	ENST00000368508	NM_002944.2	752	gCt/gTt	15/43	1	2	FACETS	0.946	0.872	1	0.946	0.872	1	CLONAL	1	TRUE	1	0.588276235112628	2		519	586	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149241	119149241	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867564832	NA	P-0062420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	245	578	0	ENST00000264033.4:c.1249C>T	p.Pro417Ser	p.P417S	ENST00000264033	NM_005188.3	417	Cct/Tct	9/16	0.559493371967447	2	FACETS	0.948	0.898	0.997	0.948	0.898	0.997	CLONAL	2	TRUE	0	0.559519594119028	2		578	462	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630235	100630235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868924845	NA	P-0062420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	252	367	0	ENST00000308731.7:c.38G>A	p.Arg13Gln	p.R13Q	ENST00000308731	NM_000061.2	13	cGa/cAa	2/19	0.502164595341669	2	FACETS	0.858	0.823	0.891			1	CLONAL	3	TRUE	NA	0.559519594119028	2		367	350	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109893	115109893	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239302522	NA	P-0062420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	313	764	0	ENST00000257566.3:c.1985C>T	p.Ser662Phe	p.S662F	ENST00000257566	NM_016569.3	662	tCc/tTc	8/8	0.557791176113098	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.559519594119028	2		764	545	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548866	29548866	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0062420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	95	298	0	ENST00000356175.3:c.1642-2A>G		p.X548_splice	ENST00000356175	NM_000267.3	548			0.558850000502321	2	FACETS	0.97	0.89	1	0.97	0.89	1	CLONAL	2	TRUE	0	0.559519594119028	2		298	175	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748066	41748066	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	134	396	0	ENST00000226382.2:c.703G>A	p.Glu235Lys	p.E235K	ENST00000226382	NM_003924.3	235	Gaa/Aaa	3/3	0.535126621154951	4	FACETS	0.95	0.872	1	0.95	0.872	1	CLONAL	2	TRUE	2	0.559519594119028	4		396	393	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450403	50450403	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	111	649	0	ENST00000331340.3:c.587C>T	p.Ser196Phe	p.S196F	ENST00000331340	NM_006060.4	196	tCc/tTc	5/8	0.559519594119028	4	FACETS	0.832	0.748	0.92	0.416	0.374	0.46	CLONAL	1	TRUE	2	0.559519594119028	4		649	744	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500976	8500976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866184934	NA	P-0062420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	247	674	0	ENST00000356435.5:c.1906G>A	p.Glu636Lys	p.E636K	ENST00000356435		636	Gaa/Aaa	13/35	0.559519594119028	5	FACETS	0.888	0.832	0.946	0.592	0.554	0.631	CLONAL	2	TRUE	2	0.559519594119028	5		674	914	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938701	76938702	+	stop_gained	Nonsense_Mutation	DNP	CA	CA	AG	novel	NA	P-0062420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	176	232	1	ENST00000373344.5:c.2046_2047delinsCT	p.Glu683Ter	p.E683*	ENST00000373344	NM_000489.3	682	aaTGaa/aaCTaa	9/35	0.502164595341669	2	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.559519594119028	2		233	267	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0062671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	53	476	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	1	2	FACETS	0.265	0.225	0.308	0.265	0.225	0.308	SUBCLONAL	1	TRUE	1	0.511504570607894	2		476	783	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0062671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	27	524	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	1	2	FACETS	0.124	0.098	0.154	0.124	0.098	0.154	SUBCLONAL	1	TRUE	1	0.511504570607894	2		524	853	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041308	42041309	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0062671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	53	496	0	ENST00000219905.7:c.5504-1_5504delinsTT		p.X1835_splice	ENST00000219905	NM_001164273.1	1835		17/24	1	2	FACETS	0.258	0.219	0.3	0.258	0.219	0.3	SUBCLONAL	1	TRUE	1	0.511504570607894	2		496	804	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21345982	21345982	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	54	593	0	ENST00000215739.8:c.857G>T	p.Gly286Val	p.G286V	ENST00000215739	NM_006767.3	286	gGg/gTg	9/21	1	2	FACETS	0.288	0.245	0.335	0.288	0.245	0.335	SUBCLONAL	1	TRUE	1	0.511504570607894	2		593	733	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352358	143352358	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	42	363	0	ENST00000262992.4:c.55G>T	p.Ala19Ser	p.A19S	ENST00000262992	NM_001101669.1	19	Gcc/Tcc	2/24	1	2	FACETS	0.278	0.232	0.33	0.278	0.232	0.33	SUBCLONAL	1	TRUE	1	0.511504570607894	2		363	590	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352364	143352364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	37	352	0	ENST00000262992.4:c.49C>T	p.Pro17Ser	p.P17S	ENST00000262992	NM_001101669.1	17	Cct/Tct	2/24	1	2	FACETS	0.244	0.2	0.293	0.244	0.2	0.293	SUBCLONAL	1	TRUE	1	0.511504570607894	2		352	593	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053239	180053239	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs934716331	NA	P-0062671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	42	550	0	ENST00000261937.6:c.1130G>T	p.Gly377Val	p.G377V	ENST00000261937	NM_182925.4	377	gGg/gTg	9/30	1	2	FACETS	0.237	0.197	0.282	0.237	0.197	0.282	SUBCLONAL	1	TRUE	1	0.511504570607894	2		550	692	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001263	150001263	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	71	432	0	ENST00000253339.5:c.2341G>T	p.Val781Leu	p.V781L	ENST00000253339		781	Gta/Tta	4/7	1	2	FACETS	0.479	0.418	0.544	0.479	0.418	0.544	SUBCLONAL	1	TRUE	1	0.511504570607894	2		432	580	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0062671-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	70	338	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.851	0.743	0.967	0.851	0.743	0.967	CLONAL	1	FALSE	1	0.309371746669846	2		338	532	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871286	35871286	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062671-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	108	360	0	ENST00000303115.3:c.508C>A	p.Arg170Ser	p.R170S	ENST00000303115	NM_002185.3	170	Cgc/Agc	4/8	0.309371746669846	6	FACETS	1	0.904	1	0.202	0.18	0.225	CLONAL	1	FALSE	1	0.309371746669846	6		360	1119	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589754	28589754	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062671-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	73	459	0	ENST00000241453.7:c.2626A>T	p.Ile876Leu	p.I876L	ENST00000241453	NM_004119.2	876	Ata/Tta	21/24	1	2	FACETS	0.837	0.733	0.949	0.837	0.733	0.949	CLONAL	1	FALSE	1	0.309371746669846	2		459	564	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575150	48575150	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062671-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	97	401	0	ENST00000342988.3:c.344G>T	p.Cys115Phe	p.C115F	ENST00000342988	NM_005359.5	115	tGt/tTt	3/12	0.309371746669846	1	FACETS	0.912	0.815	1	0.912	0.815	1	CLONAL	1	FALSE	0	0.309371746669846	1		401	581	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156492	106156492	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062671-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	64	566	0	ENST00000380013.4:c.1394del	p.Pro465HisfsTer21	p.P465Hfs*21	ENST00000380013	NM_001127208.2	465	Cca/ca	3/11	1	2	FACETS	0.483	0.417	0.555	0.483	0.417	0.555	SUBCLONAL	1	FALSE	1	0.309371746669846	2		566	856	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456461	32456461	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062671-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	71	562	1	ENST00000332351.3:c.431C>A	p.Pro144Gln	p.P144Q	ENST00000332351	NM_024426.4	144	cCg/cAg	1/10	1	2	FACETS	0.886	0.775	1	0.886	0.775	1	CLONAL	1	FALSE	1	0.309371746669846	2		563	518	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435128	18435128	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062671-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	127	541	0	ENST00000266497.5:c.113T>C	p.Leu38Pro	p.L38P	ENST00000266497		38	cTg/cCg	1/31	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	FALSE	1	0.309371746669846	2		541	771	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107915	30107915	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062671-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	78	440	0	ENST00000331968.5:c.892G>T	p.Gly298Cys	p.G298C	ENST00000331968	NM_002742.2	298	Ggc/Tgc	5/18	1	2	FACETS	0.62	0.544	0.702	0.62	0.544	0.702	SUBCLONAL	1	FALSE	1	0.309371746669846	2		440	813	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988571	41988571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062671-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	115	556	0	ENST00000219905.7:c.1365del	p.Ala456LeufsTer6	p.A456Lfs*6	ENST00000219905	NM_001164273.1	455	Aaa/aa	3/24	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	FALSE	1	0.309371746669846	2		556	734	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665752	29665755	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1555535032	NA	P-0062671-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	104	282	0	ENST00000356175.3:c.6789_6792del	p.Tyr2264ThrfsTer5	p.Y2264Tfs*5	ENST00000356175	NM_000267.3	2263	ACTTac/ac	45/57	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	FALSE	1	0.309371746669846	2		282	654	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508319	106508319	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062671-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	103	526	2	ENST00000359195.3:c.313C>A	p.Gln105Lys	p.Q105K	ENST00000359195	NM_002649.2	105	Cag/Aag	2/11	1	2	FACETS	0.946	0.847	1	0.946	0.847	1	CLONAL	1	FALSE	1	0.309371746669846	2		528	704	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028894	47028895	+	stop_gained,splice_region_variant	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0062671-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	150	477	0	ENST00000377604.3:c.198_199delinsTT	p.Glu67Ter	p.E67*	ENST00000377604	NM_001204468.1	66	gcGGag/gcTTag	3/24	0.309371746669846	3	FACETS	0.918	0.842	0.996	0.918	0.842	0.996	CLONAL	2	FALSE	1	0.309371746669846	3		477	610	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340830	70340830	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062671-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	81	497	0	ENST00000374080.3:c.563A>C	p.Gln188Pro	p.Q188P	ENST00000374080		188	cAg/cCg	5/45	1	2	FACETS	0.858	0.757	0.967	0.858	0.757	0.967	CLONAL	1	FALSE	1	0.309371746669846	2		497	610	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639639	3639650	+	inframe_deletion	In_Frame_Del	DEL	CAGAAGTTCCTG	CAGAAGTTCCTG	-	novel	NA	P-0062685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	565	626	0	ENST00000294008.3:c.3989_4000del	p.Pro1330_Asp1334delinsHis	p.P1330_D1334delinsH	ENST00000294008	NM_032444.2	1330	cCAGGAACTTCTGac/cac	12/15	1	2	FACETS	0.95	0.914	0.985	0.95	0.914	0.985	CLONAL	1	TRUE	1	0.947461660452781	2		626	1256	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99162489	99162489	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	544	447	0	ENST00000074304.5:c.1007C>T	p.Thr336Ile	p.T336I	ENST00000074304	NM_001134224.1	336	aCa/aTa	12/26	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.947461660452781	2		447	1120	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971199	21971199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894095	NA	P-0062849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	184	648	0	ENST00000304494.5:c.159G>A	p.Met53Ile	p.M53I	ENST00000304494	NM_000077.4	53	atG/atA	2/3	0.436949668393741	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.449355492579002	2		648	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0062849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	389	809	0	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	0.44937195569832	4	FACETS	1	0.989	1			1	CLONAL	3	TRUE	NA	0.449355492579002	4		809	764	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	204	678	0	ENST00000304494.5:c.143C>T	p.Pro48Leu	p.P48L	ENST00000304494	NM_000077.4	48	cCg/cTg	1/3	0.436949668393741	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.449355492579002	2		678	417	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271162	38271162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437821654	NA	P-0062849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	31	447	0	ENST00000425967.3:c.2546G>A	p.Gly849Glu	p.G849E	ENST00000425967	NM_001174067.1	849	gGa/gAa	19/19	0.449355492579002	5	FACETS	0.555	0.449	0.676			1	SUBCLONAL	1	TRUE	NA	0.449355492579002	5		447	416	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255074	16255075	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0062849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	112	660	0	ENST00000375759.3:c.2340dup	p.Arg781SerfsTer9	p.R781Sfs*9	ENST00000375759	NM_015001.2	780	tct/tcTt	11/15	0.379006379946749	3	FACETS	0.964	0.869	1	0.482	0.434	0.533	CLONAL	1	TRUE	1	0.449355492579002	3		660	633	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916799	48916803	+	frameshift_variant	Frame_Shift_Del	DEL	TAGAT	TAGAT	-	novel	NA	P-0062849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	108	313	1	ENST00000267163.4:c.329_333del	p.Leu110ArgfsTer8	p.L110Rfs*8	ENST00000267163	NM_000321.2	110	cTAGAT/c	3/27	0.449355492579002	2	FACETS	0.932	0.851	1	0.932	0.851	1	CLONAL	2	TRUE	0	0.449355492579002	2		314	258	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991578	72991578	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	190	646	0	ENST00000268489.5:c.2467A>G	p.Met823Val	p.M823V	ENST00000268489	NM_006885.3	823	Atg/Gtg	2/10	0.379006379946749	3	FACETS	0.918	0.855	0.983	0.918	0.855	0.983	CLONAL	2	TRUE	1	0.449355492579002	3		646	564	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051156	13051156	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	93	674	0	ENST00000316448.5:c.592G>C	p.Asp198His	p.D198H	ENST00000316448	NM_004343.3	198	Gac/Cac	5/9	0.0798762963192194	6	FACETS	1	0.976	1	0.454	0.404	0.507	INDETERMINATE	1	TRUE	3	0.449355492579002	6		674	577	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225637	26225637	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	94	989	0	ENST00000360408.1:c.255C>A	p.Phe85Leu	p.F85L	ENST00000360408	NM_003532.2	85	ttC/ttA	1/1	0.0798762963192194	6	FACETS	0.928	0.825	1	0.309	0.275	0.346	INDETERMINATE	1	TRUE	3	0.449355492579002	6		989	856	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271438	26271438	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	216	959	0	ENST00000305910.3:c.175A>C	p.Thr59Pro	p.T59P	ENST00000305910	NM_003534.2	59	Act/Cct	1/1	0.0798762963192194	6	FACETS	1	0.978	1	0.746	0.695	0.798	INDETERMINATE	2	TRUE	3	0.449355492579002	6		959	816	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5535001	5535001	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	153	524	0	ENST00000397747.3:c.312C>G	p.Ile104Met	p.I104M	ENST00000397747	NM_025239.3	104	atC/atG	3/7	0.436949668393741	2	FACETS	0.946	0.878	1	0.946	0.878	1	CLONAL	2	TRUE	0	0.449355492579002	2		524	360	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932555	39932555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	23	416	0	ENST00000378444.4:c.2044C>T	p.His682Tyr	p.H682Y	ENST00000378444	NM_001123385.1	682	Cac/Tac	4/15	0.13074331172804	2	FACETS	0.409	0.32	0.512			1	INDETERMINATE	1	TRUE	NA	0.449355492579002	2		416	250	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468186	25468186	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779323387	NA	P-0062944-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	361	677	0	ENST00000264709.3:c.1490G>A	p.Cys497Tyr	p.C497Y	ENST00000264709	NM_175629.2	497	tGt/tAt	13/23	0.185049500204998	1	FACETS	1	0.995	1	1	0.995	1	INDETERMINATE	1	TRUE	0	0.826718768217998	1		677	443	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29115452	29115452	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759734429	NA	P-0063073-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	55	352	0	ENST00000328354.6:c.614C>T	p.Thr205Ile	p.T205I	ENST00000328354	NM_007194.3	205	aCt/aTt	5/15	0.350762150154797	1	FACETS	0.479	0.411	0.552	0.479	0.411	0.552	SUBCLONAL	1	TRUE	0	0.462442537995674	1		352	382	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0063205-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	151	597	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.306014194853397	1	FACETS	0.919	0.843	0.998	0.919	0.843	0.998	CLONAL	1	TRUE	0	0.403478565861531	1		597	650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0063205-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	178	749	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.403478565861531	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.403478565861531	1		749	522	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106182959	106182959	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063205-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	123	449	0	ENST00000380013.4:c.3998T>G	p.Met1333Arg	p.M1333R	ENST00000380013	NM_001127208.2	1333	aTg/aGg	8/11	0.403478565861531	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.403478565861531	1		449	464	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0063239-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	27	342	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.183970833679706	2		342	208	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0063239-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	62	518	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	NA	2	FACETS	1	0.958	1			1	INDETERMINATE	1	TRUE	NA	0.183970833679706	2		518	522	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18960976	18960976	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1350475686	NA	P-0063239-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	46	549	0	ENST00000262803.5:c.554A>G	p.Asn185Ser	p.N185S	ENST00000262803	NM_002911.3	185	aAc/aGc	4/24	1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	1	0.183970833679706	2		549	496	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040911	47040911	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs782684857	NA	P-0063438-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	66	350	0	ENST00000377604.3:c.1441G>T	p.Glu481Ter	p.E481*	ENST00000377604	NM_001204468.1	481	Gag/Tag	14/24	1	1	FACETS	0.864	0.755	0.979	1	0.978	1	CLONAL	2	TRUE	0	0.212106149606923	1		350	322	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7167980	7167980	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063438-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	48	373	0	ENST00000302850.5:c.1609G>A	p.Ala537Thr	p.A537T	ENST00000302850	NM_000208.2	537	Gcc/Acc	7/22	1	2	FACETS	0.82	0.693	0.96	0.82	0.693	0.96	CLONAL	1	TRUE	1	0.212106149606923	2		373	552	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63898320	63898320	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063438-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	35	474	0	ENST00000398590.3:c.46G>T	p.Ala16Ser	p.A16S	ENST00000398590	NM_001177387.1	16	Gcg/Tcg	3/14	1	2	FACETS	0.871	0.715	1	0.871	0.715	1	CLONAL	1	TRUE	1	0.212106149606923	2		474	379	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0063438-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	31	265	0	ENST00000311936.3:c.34_35delinsTT	p.Gly12Phe	p.G12F	ENST00000311936	NM_004985.3	12	GGt/TTt	2/5	1	2	FACETS	0.58	0.468	0.707	0.58	0.468	0.707	SUBCLONAL	1	TRUE	1	0.212106149606923	2		265	504	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557732	21557732	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063438-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	50	510	0	ENST00000382592.4:c.2113C>G	p.Leu705Val	p.L705V	ENST00000382592	NM_014572.2	705	Ctg/Gtg	5/8	1	2	FACETS	0.784	0.665	0.916	0.784	0.665	0.916	CLONAL	1	TRUE	1	0.212106149606923	2		510	601	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43773212	43773212	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063438-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	52	454	0	ENST00000382044.4:c.380G>T	p.Gly127Val	p.G127V	ENST00000382044	NM_001141980.1	127	gGa/gTa	5/28	1	2	FACETS	0.812	0.691	0.945	0.812	0.691	0.945	CLONAL	1	TRUE	1	0.212106149606923	2		454	604	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337277	89337288	+	inframe_deletion	In_Frame_Del	DEL	CGGGCGTTGAAA	CGGGCGTTGAAA	-	novel	NA	P-0063438-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	49	336	0	ENST00000301030.4:c.7743_7754del	p.Phe2582_Arg2585del	p.F2582_R2585del	ENST00000301030	NM_001256183.1	2581	cgTTTCAACGCCCGc/cgc	12/13	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.212106149606923	2		336	379	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246491	41246491	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063438-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	68	588	0	ENST00000357654.3:c.1057T>C	p.Trp353Arg	p.W353R	ENST00000357654	NM_007294.3	353	Tgg/Cgg	10/23	0.167357662784912	3	FACETS	0.939	0.816	1	0.47	0.408	0.537	CLONAL	1	TRUE	1	0.212106149606923	3		588	755	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252859	10252859	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063438-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	46	510	1	ENST00000340748.4:c.3106C>A	p.His1036Asn	p.H1036N	ENST00000340748		1036	Cac/Aac	29/40	1	2	FACETS	0.82	0.69	0.963	0.82	0.69	0.963	CLONAL	1	TRUE	1	0.212106149606923	2		511	529	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935054	49935054	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063438-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	48	713	0	ENST00000296474.3:c.1945G>T	p.Ala649Ser	p.A649S	ENST00000296474	NM_002447.2	649	Gca/Tca	6/20	1	2	FACETS	0.717	0.605	0.841	0.717	0.605	0.841	SUBCLONAL	1	TRUE	1	0.212106149606923	2		713	631	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876487	35876487	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063438-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	74	576	0	ENST00000303115.3:c.1279A>T	p.Thr427Ser	p.T427S	ENST00000303115	NM_002185.3	427	Aca/Tca	8/8	0.167357662784912	3	FACETS	1	0.946	1	0.575	0.503	0.653	CLONAL	1	TRUE	1	0.212106149606923	3		576	671	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402594	20402595	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGC	rs559169760	NA	P-0063438-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	31	588	0	ENST00000346618.3:c.147_149dup	p.Ala53dup	p.A53dup	ENST00000346618	NM_001949.4	53	ttc/ttCGCc	1/7	0.167357662784912	3	FACETS	0.552	0.445	0.673	0.276	0.222	0.337	SUBCLONAL	1	TRUE	1	0.212106149606923	3		588	586	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31238849	31238849	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0063438-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	51	631	0	ENST00000376228.5:c.619+1G>C		p.X207_splice	ENST00000376228	NM_002117.5	207			0.167357662784912	3	FACETS	0.751	0.637	0.877	0.376	0.318	0.439	SUBCLONAL	1	TRUE	1	0.212106149606923	3		631	708	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729529	41729529	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs138538132	NA	P-0063438-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	59	592	0	ENST00000242208.4:c.1000G>T	p.Gly334Cys	p.G334C	ENST00000242208	NM_002192.2	334	Ggc/Tgc	3/3	1	2	FACETS	0.849	0.73	0.979	0.849	0.73	0.979	CLONAL	1	TRUE	1	0.212106149606923	2		592	655	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508384	106508384	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063438-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	63	515	0	ENST00000359195.3:c.378G>T	p.Lys126Asn	p.K126N	ENST00000359195	NM_002649.2	126	aaG/aaT	2/11	1	2	FACETS	0.963	0.833	1	0.963	0.833	1	CLONAL	1	TRUE	1	0.212106149606923	2		515	617	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230753	53230760	+	frameshift_variant	Frame_Shift_Del	DEL	TAGACGCC	TAGACGCC	-	novel	NA	P-0063438-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	25	229	0	ENST00000375401.3:c.2033_2040del	p.Arg678ProfsTer13	p.R678Pfs*13	ENST00000375401	NM_004187.3	678	cGGCGTCTA/c	14/26	1	1	FACETS	0.897	0.71	1	0.897	0.71	1	CLONAL	1	TRUE	0	0.212106149606923	1		229	235	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352765	70352765	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063438-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	55	213	0	ENST00000374080.3:c.4486C>A	p.Arg1496Ser	p.R1496S	ENST00000374080		1496	Cgc/Agc	32/45	1	1	FACETS	0.902	0.779	1	1	0.975	1	CLONAL	2	TRUE	0	0.212106149606923	1		213	257	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0063448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	612	524	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.722974832595501	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.722974832595501	2		524	820	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267784	46267784	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	200	381	0	ENST00000371998.3:c.2545C>G	p.Arg849Gly	p.R849G	ENST00000371998		849	Cgt/Ggt	14/23	0.689587439309427	4	FACETS	0.91	0.843	0.98	0.455	0.421	0.49	CLONAL	1	TRUE	2	0.722974832595501	4		381	1047	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106670	27106671	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0063584-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	170	502	0	ENST00000324856.7:c.6284dup	p.Ser2096PhefsTer3	p.S2096Ffs*3	ENST00000324856	NM_006015.4	2094	tgc/tgCc	20/20	0.67208667365583	2	FACETS	0.977	0.905	1	0.488	0.452	0.525	CLONAL	1	TRUE	0	0.67208667365583	2		502	518	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851554	63851554	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063584-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	130	420	0	ENST00000279873.7:c.2332C>G	p.Leu778Val	p.L778V	ENST00000279873	NM_032199.2	778	Ctg/Gtg	10/10	0.67208667365583	3	FACETS	0.923	0.841	1	0.461	0.42	0.505	CLONAL	1	TRUE	1	0.67208667365583	3		420	560	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186565	108186566	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0063584-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	196	295	0	ENST00000278616.4:c.6022_6023del	p.Ile2008LeufsTer9	p.I2008Lfs*9	ENST00000278616	NM_000051.3	2008	ATc/c	41/63	0.67208667365583	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.67208667365583	3		295	360	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382179	152382179	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063584-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	112	322	0	ENST00000206249.3:c.1289C>T	p.Ala430Val	p.A430V	ENST00000206249	NM_000125.3	430	gCt/gTt	6/8	0.620144904738586	3	FACETS	1	0.944	1	0.353	0.319	0.387	CLONAL	1	TRUE	0	0.67208667365583	3		322	421	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391150	89391150	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063676-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	150	373	0	ENST00000336596.2:c.1216A>T	p.Thr406Ser	p.T406S	ENST00000336596	NM_005233.5	406	Acc/Tcc	5/17	1	2	FACETS	0.963	0.886	1	0.963	0.886	1	CLONAL	1	TRUE	1	0.639949084671344	2		373	487	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0063676-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	388	388	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.639949084671344	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.639949084671344	3		388	512	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254733	46254733	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0063676-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	370	216	0	ENST00000334344.6:c.4922+1G>C		p.X1641_splice	ENST00000334344	NM_152641.2	1641			0.639949084671344	3	FACETS	0.988	0.955	1	0.988	0.955	1	CLONAL	3	TRUE	0	0.639949084671344	3		216	515	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111495	8111496	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGGA	novel	NA	P-0063740-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	211	532	0	ENST00000346208.3:c.982_985dup	p.Arg329MetfsTer24	p.R329Mfs*24	ENST00000346208		327	-/TGGA	5/6	1	2	FACETS	1	0.937	1	1	0.994	1	CLONAL	2	FALSE	1	0.345080705827252	2		532	610	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241726	55241726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767505234	NA	P-0063740-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	122	479	0	ENST00000275493.2:c.2174C>T	p.Thr725Met	p.T725M	ENST00000275493	NM_005228.3	725	aCg/aTg	18/28	1	2	FACETS	0.897	0.819	0.979	1	0.989	1	CLONAL	2	FALSE	1	0.345080705827252	2		479	394	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972509	81972509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755617580	NA	P-0063757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	28	446	0	ENST00000359376.3:c.3302C>T	p.Thr1101Met	p.T1101M	ENST00000359376	NM_002661.3	1101	aCg/aTg	29/33	0.891175506686617	1	FACETS	0.141	0.113	0.173	0.141	0.113	0.173	SUBCLONAL	1	TRUE	0	0.923385322922807	1		446	231	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198870	67198870	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	168	410	0	ENST00000312629.5:c.341C>G	p.Ala114Gly	p.A114G	ENST00000312629	NM_003952.2	114	gCa/gGa	5/15	1	2	FACETS	0.823	0.764	0.883	0.823	0.764	0.883	CLONAL	1	TRUE	1	0.923385322922807	2		410	442	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115941	8115942	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063875-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	211	570	0	ENST00000346208.3:c.1290dup	p.Gly431TrpfsTer76	p.G431Wfs*76	ENST00000346208		429	-/T	6/6	1	2	FACETS	0.877	0.819	0.937	0.877	0.819	0.937	CLONAL	1	TRUE	1	0.734568535067223	2		570	655	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100291	27100291	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0063875-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	72	613	0	ENST00000324856.7:c.4005-2A>T		p.X1335_splice	ENST00000324856	NM_006015.4	1335			0.733936762830581	1	FACETS	0.738	0.661	0.817	0.738	0.661	0.817	SUBCLONAL	1	TRUE	0	0.734568535067223	1		613	168	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597402	10597402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770453522	NA	P-0063879-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	135	491	0	ENST00000171111.5:c.1801C>T	p.Arg601Trp	p.R601W	ENST00000171111	NM_203500.1	601	Cgg/Tgg	6/6	0.328706656361572	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	0	0.328706656361572	2		491	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578262	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs483352697	NA	P-0063879-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	270	696	0	ENST00000269305.4:c.587G>C	p.Arg196Pro	p.R196P	ENST00000269305	NM_001126112.2	196	cGa/cCa	6/11	0.328706656361572	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	0	0.328706656361572	3		696	614	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219381	1219381	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063879-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	53	547	0	ENST00000326873.7:c.433G>T	p.Glu145Ter	p.E145*	ENST00000326873	NM_000455.4	145	Gag/Tag	3/10	0.259687071448831	1	FACETS	0.829	0.711	0.957	0.829	0.711	0.957	CLONAL	1	TRUE	0	0.328706656361572	1		547	325	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660083	12660084	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0063879-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	67	486	0	ENST00000251849.4:c.137_138delinsTT	p.Gly46Val	p.G46V	ENST00000251849	NM_002880.3	46	gGC/gTT	2/17	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.328706656361572	2		486	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0063922-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	263	571	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.355118011851886	3	FACETS	0.995	0.945	1	0.995	0.945	1	CLONAL	3	TRUE	0	0.431980619547154	3		572	496	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051053	180051053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755736057	NA	P-0063922-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	39	357	0	ENST00000261937.6:c.1430G>A	p.Arg477Gln	p.R477Q	ENST00000261937	NM_182925.4	477	cGg/cAg	11/30	1	2	FACETS	0.465	0.386	0.553	0.465	0.386	0.553	SUBCLONAL	1	TRUE	1	0.431980619547154	2		357	388	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063922-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	116	553	0	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.431980619547154	2		553	446	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249457	153249457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063922-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	41	317	0	ENST00000281708.4:c.1321C>T	p.Arg441Trp	p.R441W	ENST00000281708	NM_033632.3	441	Cgg/Tgg	9/12	1	2	FACETS	0.811	0.681	0.953	0.811	0.681	0.953	CLONAL	1	TRUE	1	0.431980619547154	2		317	234	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856181	111856181	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754838420	NA	P-0063922-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	88	393	0	ENST00000341259.2:c.232G>A	p.Glu78Lys	p.E78K	ENST00000341259	NM_005475.2	78	Gag/Aag	2/8	1	2	FACETS	0.963	0.858	1	0.963	0.858	1	CLONAL	1	TRUE	1	0.431980619547154	2		393	423	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265479	152265479	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766779326	NA	P-0063922-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	80	336	0	ENST00000206249.3:c.932C>T	p.Thr311Met	p.T311M	ENST00000206249	NM_000125.3	311	aCg/aTg	4/8	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.431980619547154	2		336	349	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584746	187584746	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs549688382	NA	P-0063922-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	25	342	0	ENST00000441802.2:c.3287G>A	p.Arg1096Gln	p.R1096Q	ENST00000441802	NM_005245.3	1096	cGa/cAa	3/27	0.351326799687937	2	FACETS	0.365	0.288	0.454	0.183	0.144	0.227	SUBCLONAL	1	TRUE	0	0.431980619547154	2		342	317	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910391	29910391	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063922-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	75	499	0	ENST00000376809.5:c.61C>T	p.Gln21Ter	p.Q21*	ENST00000376809	NM_002116.7	21	Cag/Tag	1/8	0.431980619547154	2	FACETS	0.734	0.645	0.829	0.367	0.322	0.415	SUBCLONAL	1	TRUE	0	0.431980619547154	2		499	473	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571819	64571819	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063922-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	25	316	0	ENST00000312049.6:c.1820G>A	p.Arg607His	p.R607H	ENST00000312049	NM_130799.2	607	cGc/cAc	10/10	0.279893983633386	3	FACETS	0.333	0.262	0.415	0.111	0.087	0.139	SUBCLONAL	1	TRUE	0	0.431980619547154	3		316	423	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427253	49427254	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCTGCTGCTGT	novel	NA	P-0063922-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	35	428	0	ENST00000301067.7:c.11223_11234dup	p.Gln3742_Gln3745dup	p.Q3742_Q3745dup	ENST00000301067	NM_003482.3	3742	cag/caACAGCAGCAGCAg	39/54	1	2	FACETS	0.331	0.271	0.399	0.331	0.271	0.399	SUBCLONAL	1	TRUE	1	0.431980619547154	2		428	489	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836386	89836386	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063922-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	51	448	0	ENST00000389301.3:c.2363C>A	p.Ala788Asp	p.A788D	ENST00000389301	NM_000135.2	788	gCc/gAc	26/43	1	2	FACETS	0.438	0.372	0.511	0.438	0.372	0.511	SUBCLONAL	1	TRUE	1	0.431980619547154	2		448	539	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375466	15375466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777186961	NA	P-0063922-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	46	413	0	ENST00000263377.2:c.961C>T	p.Arg321Trp	p.R321W	ENST00000263377	NM_058243.2	321	Cgg/Tgg	6/20	1	2	FACETS	0.37	0.311	0.436	0.37	0.311	0.436	SUBCLONAL	1	TRUE	1	0.431980619547154	2		413	575	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197714	66197714	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063922-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	72	286	0	ENST00000273854.3:c.2985C>A	p.Asp995Glu	p.D995E	ENST00000273854	NM_004439.5	995	gaC/gaA	17/18	0.431980619547154	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.431980619547154	1		286	227	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247157	153247157	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0063922-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	41	252	0	ENST00000281708.4:c.1644+1G>C		p.X548_splice	ENST00000281708	NM_033632.3	548			1	2	FACETS	0.944	0.795	1	0.944	0.795	1	CLONAL	1	TRUE	1	0.431980619547154	2		252	201	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253803	153253812	+	frameshift_variant	Frame_Shift_Del	DEL	GTAGCGACAT	GTAGCGACAT	-	novel	NA	P-0063922-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	16	251	0	ENST00000281708.4:c.921_930del	p.Cys308GlyfsTer31	p.C308Gfs*31	ENST00000281708	NM_033632.3	307	acATGTCGCTAC/ac	6/12	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.431980619547154	NA		251	230	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332556	153332556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063922-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	42	373	0	ENST00000281708.4:c.400G>A	p.Glu134Lys	p.E134K	ENST00000281708	NM_033632.3	134	Gaa/Aaa	2/12	0.351326799687937	2	FACETS	0.595	0.498	0.701	0.297	0.249	0.351	SUBCLONAL	1	TRUE	0	0.431980619547154	2		373	327	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332568	153332568	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063922-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	49	369	0	ENST00000281708.4:c.388G>C	p.Asp130His	p.D130H	ENST00000281708	NM_033632.3	130	Gat/Cat	2/12	0.351326799687937	2	FACETS	0.616	0.524	0.718	0.308	0.262	0.359	SUBCLONAL	1	TRUE	0	0.431980619547154	2		369	368	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911304	29911305	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACGCTGC	novel	NA	P-0063922-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	50	459	0	ENST00000376809.5:c.605_611dup	p.Gln204HisfsTer19	p.Q204Hfs*19	ENST00000376809	NM_002116.7	201	-/ACGCTGC	3/8	0.431980619547154	2	FACETS	0.519	0.441	0.605	0.26	0.22	0.303	SUBCLONAL	1	TRUE	0	0.431980619547154	2		459	446	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168679	32168679	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063922-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	52	350	0	ENST00000375023.3:c.4244T>A	p.Met1415Lys	p.M1415K	ENST00000375023	NM_004557.3	1415	aTg/aAg	23/30	0.431980619547154	2	FACETS	0.529	0.451	0.615	0.265	0.225	0.308	SUBCLONAL	1	TRUE	0	0.431980619547154	2		350	455	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759439	133759439	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063922-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	34	337	0	ENST00000318560.5:c.1762G>C	p.Glu588Gln	p.E588Q	ENST00000318560	NM_005157.4	588	Gag/Cag	11/11	0.24603919330739	2	FACETS	0.438	0.359	0.528	0.219	0.179	0.264	INDETERMINATE	1	TRUE	0	0.431980619547154	2		337	359	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0063941-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	114	342	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.172518761346278	4	FACETS	1	0.973	1	1	0.973	1	INDETERMINATE	3	TRUE	1	0.309834515959136	4		342	277	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520017	NA	P-0063941-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	23	920	0	ENST00000326873.7:c.647C>T	p.Ser216Phe	p.S216F	ENST00000326873	NM_000455.4	216	tCc/tTc	5/10	0.309834515959136	1	FACETS	0.884	0.697	1	0.884	0.697	1	CLONAL	1	TRUE	0	0.309834515959136	1		920	142	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220640	1220640	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690940	NA	P-0063941-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	28	902	0	ENST00000326873.7:c.658C>T	p.Gln220Ter	p.Q220*	ENST00000326873	NM_000455.4	220	Cag/Tag	5/10	0.309834515959136	1	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	0	0.309834515959136	1		902	143	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930404	39930404	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063941-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	48	828	0	ENST00000378444.4:c.3060G>A	p.Met1020Ile	p.M1020I	ENST00000378444	NM_001123385.1	1020	atG/atA	6/15	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.309834515959136	2		828	273	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953547	32953547	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063941-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	51	857	0	ENST00000380152.3:c.8848A>G	p.Lys2950Glu	p.K2950E	ENST00000380152		2950	Aag/Gag	22/27	1	2	FACETS	0.963	0.822	1	0.963	0.822	1	CLONAL	1	TRUE	1	0.309834515959136	2		857	342	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123615	108123615	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs766757573	NA	P-0063941-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	48	594	0	ENST00000278616.4:c.1874A>T	p.Asn625Ile	p.N625I	ENST00000278616	NM_000051.3	625	aAt/aTt	12/63	0.24400968295707	3	FACETS	1	0.886	1	0.526	0.447	0.613	CLONAL	1	TRUE	1	0.309834515959136	3		594	340	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351704	89351704	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063941-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	22	985	0	ENST00000301030.4:c.1246G>T	p.Ala416Ser	p.A416S	ENST00000301030	NM_001256183.1	416	Gcg/Tcg	9/13	1	2	FACETS	0.526	0.408	0.662	0.526	0.408	0.662	SUBCLONAL	1	TRUE	1	0.309834515959136	2		985	270	SUCCESS
YES1	7525	MSKCC	GRCh37	18	732851	732851	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063941-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	61	793	0	ENST00000314574.4:c.1406G>T	p.Gly469Val	p.G469V	ENST00000314574	NM_005433.3	469	gGc/gTc	11/12	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.309834515959136	2		793	298	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215553	36215553	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063941-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	34	740	0	ENST00000222270.7:c.3350A>T	p.Glu1117Val	p.E1117V	ENST00000222270	NM_014727.1	1117	gAa/gTa	9/37	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.309834515959136	2		740	182	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346876	70346877	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063941-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	25	793	0	ENST00000374080.3:c.2744dup	p.Ser917GlnfsTer5	p.S917Qfs*5	ENST00000374080		915	gtg/gTtg	20/45	1	2	FACETS	0.897	0.712	1	0.897	0.712	1	CLONAL	1	TRUE	1	0.309834515959136	2		793	180	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889119	76889119	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063941-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	50	745	0	ENST00000373344.5:c.4891G>T	p.Ala1631Ser	p.A1631S	ENST00000373344	NM_000489.3	1631	Gct/Tct	18/35	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.309834515959136	2		745	316	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520008	NA	P-0063950-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	456	644	2	ENST00000269305.4:c.613T>G	p.Tyr205Asp	p.Y205D	ENST00000269305	NM_001126112.2	205	Tat/Gat	6/11	0.590882808298811	2	FACETS	0.993	0.958	1	0.993	0.958	1	CLONAL	2	TRUE	0	0.597875186291548	2		646	768	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731479	47731479	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063950-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	406	533	0	ENST00000449228.1:c.313C>T	p.Arg105Cys	p.R105C	ENST00000449228	NM_001127240.2	105	Cgc/Tgc	2/4	0.597875186291548	3	FACETS	0.938	0.897	0.98	0.938	0.897	0.98	CLONAL	2	TRUE	1	0.597875186291548	3		533	940	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205138	38205138	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063950-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1301	129	472	0	ENST00000317025.8:c.552G>C	p.Glu184Asp	p.E184D	ENST00000317025	NM_023034.1	184	gaG/gaC	2/24	0.597875186291548	9	FACETS	0.933	0.843	1	0.117	0.105	0.129	CLONAL	1	TRUE	1	0.597875186291548	9		472	1430	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720815	89720817	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	AAA	AAA	GTAAATT	novel	NA	P-0063950-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	38	153	0	ENST00000371953.3:c.966_968delinsGTAAATT	p.Asn323Ter	p.N323*	ENST00000371953	NM_000314.4	322	aaAAAt/aaGTAAATTt	8/9	0.590882808298811	2	FACETS	0.757	0.651	0.865	0.757	0.651	0.865	SUBCLONAL	2	TRUE	0	0.597875186291548	2		153	84	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520008	NA	P-0063950-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	440	644	2	ENST00000269305.4:c.613T>G	p.Tyr205Asp	p.Y205D	ENST00000269305	NM_001126112.2	205	Tat/Gat	6/11	0.59785767475156	2	FACETS	0.976	0.94	1	0.976	0.94	1	CLONAL	2	TRUE	0	0.611824952690057	2		646	737	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731479	47731479	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063950-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	266	533	0	ENST00000449228.1:c.313C>T	p.Arg105Cys	p.R105C	ENST00000449228	NM_001127240.2	105	Cgc/Tgc	2/4	0.448265177393882	3	FACETS	0.871	0.822	0.92	0.871	0.822	0.92	CLONAL	2	TRUE	1	0.611824952690057	3		533	652	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720815	89720817	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	AAA	AAA	GTAAATT	novel	NA	P-0063950-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	75	153	0	ENST00000371953.3:c.966_968delinsGTAAATT	p.Asn323Ter	p.N323*	ENST00000371953	NM_000314.4	322	aaAAAt/aaGTAAATTt	8/9	0.611824952690057	2	FACETS	1	0.981	1	0.747	0.673	0.823	CLONAL	1	TRUE	0	0.611824952690057	2		153	164	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919006	50919024	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCCCAGCCTGGGCGACC	GCGCCCAGCCTGGGCGACC	-	novel	NA	P-0063950-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	67	504	0	ENST00000440232.2:c.2746_2764del	p.Pro916SerfsTer4	p.P916Sfs*4	ENST00000440232	NM_002691.3	915	GCGCCCAGCCTGGGCGACCgc/gc	22/27	0.448265177393882	3	FACETS	0.416	0.361	0.475	0.208	0.18	0.238	SUBCLONAL	1	TRUE	1	0.611824952690057	3		504	688	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs483352695	NA	P-0064005-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	177	427	0	ENST00000269305.4:c.736A>T	p.Met246Leu	p.M246L	ENST00000269305	NM_001126112.2	246	Atg/Ttg	7/11	0.497126999469416	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.497126999469416	1		427	474	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27168540	27168540	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1213348161	NA	P-0064005-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	70	367	0	ENST00000380036.4:c.412A>G	p.Asn138Asp	p.N138D	ENST00000380036	NM_000459.3	138	Aac/Gac	3/23	1	2	FACETS	0.853	0.75	0.964	0.853	0.75	0.964	CLONAL	1	TRUE	1	0.497126999469416	2		367	330	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436865	52436866	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	126	654	0	ENST00000460680.1:c.1912dup	p.Cys638LeufsTer5	p.C638Lfs*5	ENST00000460680	NM_004656.3	638	tgt/tTgt	15/17	0.3	0	FACETS	0.527	0.484	0.57			1	INDETERMINATE	1	TRUE	0	0.6	0		654	319	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100213	157100253	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCGGGGCCGCGAGCCTCAGCAAGGCGGCCGCCGGCTC	GGCGGCGGGGCCGCGAGCCTCAGCAAGGCGGCCGCCGGCTC	-	novel	NA	P-0064082-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	37	622	0	ENST00000346085.5:c.1160_1200del	p.Ala387GlyfsTer134	p.A387Gfs*134	ENST00000346085	NM_020732.3	384	GGCGGCGGGGCCGCGAGCCTCAGCAAGGCGGCCGCCGGCTCg/g	1/20	1	2	FACETS	0.759	0.629	0.904	0.759	0.629	0.904	CLONAL	1	TRUE	1	0.333712982855886	2		622	292	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106667	27106667	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064082-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	131	781	0	ENST00000324856.7:c.6280del	p.Cys2094AlafsTer41	p.C2094Afs*41	ENST00000324856	NM_006015.4	2093	gTt/gt	20/20	0.333712982855886	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.333712982855886	1		781	488	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332695	65332695	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064082-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	81	614	0	ENST00000342505.4:c.844G>T	p.Gly282Cys	p.G282C	ENST00000342505	NM_002227.2	282	Ggt/Tgt	7/25	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.333712982855886	2		614	446	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230655	46230655	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0064082-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	71	609	0	ENST00000334344.6:c.905del	p.Asn302MetfsTer26	p.N302Mfs*26	ENST00000334344	NM_152641.2	302	Aat/at	8/21	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.333712982855886	2		609	375	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	65	789	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.66	0.575	0.752	0.66	0.575	0.752	SUBCLONAL	1	TRUE	1	0.502446341490569	2		789	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0064163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	173	661	0	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.502446341490569	2		661	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780071	NA	P-0064163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	168	627	0	ENST00000269305.4:c.580C>T	p.Leu194Phe	p.L194F	ENST00000269305	NM_001126112.2	194	Ctt/Ttt	6/11	1	2	FACETS	0.991	0.914	1	0.991	0.914	1	CLONAL	1	TRUE	1	0.502446341490569	2		627	675	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024001	27024002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0064163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	72	395	0	ENST00000324856.7:c.1113dup	p.Gln372AlafsTer28	p.Q372Afs*28	ENST00000324856	NM_006015.4	369	-/G	1/20	1	2	FACETS	0.843	0.742	0.95	0.843	0.742	0.95	CLONAL	1	TRUE	1	0.502446341490569	2		395	340	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985680	60985680	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	52	570	0	ENST00000333681.4:c.220A>G	p.Thr74Ala	p.T74A	ENST00000333681		74	Acc/Gcc	2/3	1	2	FACETS	0.461	0.393	0.535	0.461	0.393	0.535	SUBCLONAL	1	TRUE	1	0.502446341490569	2		570	449	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047510	49047531	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGGTGAATCATTCGGGGTGAG	TTGGTGAATCATTCGGGGTGAG	-	novel	NA	P-0064163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	18	202	0	ENST00000267163.4:c.2505_2520+6del		p.X835_splice	ENST00000267163	NM_000321.2	835		24/27	0.502446341490569	1	FACETS	0.583	0.447	0.737	0.583	0.447	0.737	SUBCLONAL	1	TRUE	0	0.502446341490569	1		202	92	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43773132	43773132	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	140	450	0	ENST00000382044.4:c.460G>C	p.Asp154His	p.D154H	ENST00000382044	NM_001141980.1	154	Gat/Cat	5/28	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.502446341490569	2		450	502	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983214	7983214	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	65	501	0	ENST00000319144.4:c.800A>T	p.Gln267Leu	p.Q267L	ENST00000319144	NM_001139.2	267	cAg/cTg	7/15	1	2	FACETS	0.634	0.552	0.723	0.634	0.552	0.723	SUBCLONAL	1	TRUE	1	0.502446341490569	2		501	408	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61323049	61323049	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	71	678	0	ENST00000283752.5:c.1015del	p.Glu339ArgfsTer11	p.E339Rfs*11	ENST00000283752	NM_006919.2	339	Gag/ag	8/8	1	2	FACETS	0.44	0.384	0.501	0.44	0.384	0.501	SUBCLONAL	1	TRUE	1	0.502446341490569	2		678	642	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5239067	5239067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	79	591	0	ENST00000357368.4:c.1712G>A	p.Arg571Lys	p.R571K	ENST00000357368	NM_002850.3	571	aGg/aAg	13/38	0.502446341490569	3	FACETS	0.608	0.535	0.687	0.304	0.267	0.344	SUBCLONAL	1	TRUE	1	0.502446341490569	3		591	647	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47600976	47600976	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	112	447	0	ENST00000263735.4:c.214G>C	p.Glu72Gln	p.E72Q	ENST00000263735	NM_002354.2	72	Gaa/Caa	3/9	1	2	FACETS	0.953	0.862	1	0.953	0.862	1	CLONAL	1	TRUE	1	0.502446341490569	2		447	468	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139815	55139815	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	85	512	0	ENST00000257290.5:c.1476A>T	p.Lys492Asn	p.K492N	ENST00000257290	NM_006206.4	492	aaA/aaT	10/23	1	2	FACETS	0.647	0.573	0.725	0.647	0.573	0.725	SUBCLONAL	1	TRUE	1	0.502446341490569	2		512	523	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976615	55976615	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	50	477	0	ENST00000263923.4:c.1210A>T	p.Ile404Phe	p.I404F	ENST00000263923	NM_002253.2	404	Att/Ttt	9/30	0.384753401248647	1	FACETS	0.348	0.296	0.406	0.348	0.296	0.406	SUBCLONAL	1	TRUE	0	0.502446341490569	1		477	428	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876187	35876187	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	134	565	0	ENST00000303115.3:c.979A>G	p.Thr327Ala	p.T327A	ENST00000303115	NM_002185.3	327	Acg/Gcg	8/8	1	2	FACETS	0.942	0.86	1	0.942	0.86	1	CLONAL	1	TRUE	1	0.502446341490569	2		565	566	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187387	38187387	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	1771	492	0	ENST00000317025.8:c.1090G>C	p.Glu364Gln	p.E364Q	ENST00000317025	NM_023034.1	364	Gaa/Caa	6/24	0.502446341490569	14	FACETS	1	0.992	1			1	CLONAL	13	TRUE	NA	0.502446341490569	14		492	2165	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202434	123202434	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	59	147	0	ENST00000218089.9:c.2286del	p.Lys763AsnfsTer3	p.K763Nfs*3	ENST00000218089	NM_001042749.1	762	aaG/aa	24/35	1	1	FACETS	0.822	0.736	0.906	1	0.98	1	CLONAL	2	TRUE	0	0.502446341490569	1		147	107	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0064204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	172	393	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.821671029648432	2		393	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0064204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	334	660	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.821671029648432	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.821671029648432	1		660	426	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971031	21971040	+	frameshift_variant	Frame_Shift_Del	DEL	GGCATCGCGC	GGCATCGCGC	-	novel	NA	P-0064204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	283	657	0	ENST00000304494.5:c.318_327del	p.Arg107GlyfsTer36	p.R107Gfs*36	ENST00000304494	NM_000077.4	106	gtGCGCGATGCC/gt	2/3	0.821671029648432	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.821671029648432	1		657	358	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0064206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	65	598	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	1	2	FACETS	0.852	0.737	0.977	0.852	0.737	0.977	CLONAL	1	TRUE	1	0.18	2		598	848	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011150	12011150	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	24	340	0	ENST00000353533.5:c.557A>G	p.Asp186Gly	p.D186G	ENST00000353533	NM_003010.3	186	gAt/gGt	5/11	1	2	FACETS	0.169	0.132	0.211	0.169	0.132	0.211	SUBCLONAL	1	TRUE	1	0.78	2		340	365	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561352	9561352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773981325	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	11	505	0	ENST00000353224.5:c.430G>A	p.Glu144Lys	p.E144K	ENST00000353224	NM_177990.2	144	Gaa/Aaa	4/10	1	2	FACETS	0.079	0.054	0.11	0.079	0.054	0.11	SUBCLONAL	1	TRUE	1	0.78	2		505	359	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	199	475	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.78	2		475	445	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39317430	39317430	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	40	332	0	ENST00000373001.3:c.757-1G>T		p.X253_splice	ENST00000373001	NM_022157.3	253			1	2	FACETS	0.291	0.242	0.345	0.291	0.242	0.345	SUBCLONAL	1	TRUE	1	0.78	2		332	353	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	92	403	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	0.3	1	FACETS	0.615	0.556	0.675	0.615	0.556	0.675	INDETERMINATE	1	TRUE	0	0.78	1		403	234	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026290	48026290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147737737	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	155	508	1	ENST00000234420.5:c.1168G>A	p.Asp390Asn	p.D390N	ENST00000234420	NM_000179.2	390	Gat/Aat	4/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.78	2		509	336	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539951	187539951	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs777631605	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	144	461	0	ENST00000441802.2:c.7789C>T	p.Arg2597Ter	p.R2597*	ENST00000441802	NM_005245.3	2597	Cga/Tga	10/27	1	2	FACETS	0.93	0.858	1	0.93	0.858	1	CLONAL	1	TRUE	1	0.78	2		461	397	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418997	116418997	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200754673	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	177	386	0	ENST00000397752.3:c.3508C>T	p.Arg1170Ter	p.R1170*	ENST00000397752	NM_000245.2	1170	Cga/Tga	17/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.78	2		386	382	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630235	100630235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868924845	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	151	367	0	ENST00000308731.7:c.38G>A	p.Arg13Gln	p.R13Q	ENST00000308731	NM_000061.2	13	cGa/cAa	2/19	0.3	1	FACETS	0.75	0.698	0.802	0.75	0.698	0.802	INDETERMINATE	1	TRUE	0	0.78	1		367	315	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911514	131911514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143802516	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	155	311	1	ENST00000265335.6:c.259C>T	p.Arg87Cys	p.R87C	ENST00000265335		87	Cgt/Tgt	3/25	1	2	FACETS	0.999	0.925	1	0.999	0.925	1	CLONAL	1	TRUE	1	0.78	2		312	398	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913283	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	155	419	0	ENST00000263967.3:c.3129G>T	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atT	21/21	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.78	2		419	389	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641063	117641063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	149	539	0	ENST00000368508.3:c.5908G>A	p.Val1970Ile	p.V1970I	ENST00000368508	NM_002944.2	1970	Gtt/Att	36/43	1	2	FACETS	0.975	0.901	1	0.975	0.901	1	CLONAL	1	TRUE	1	0.78	2		539	392	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726669	88726669	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	200	375	0	ENST00000360948.2:c.375G>T	p.Lys125Asn	p.K125N	ENST00000360948	NM_001012338.2	125	aaG/aaT	4/19	1	2	FACETS	1	0.973	1	1	0.995	1	CLONAL	2	TRUE	1	0.78	2		375	252	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118950	115118950	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	134	394	0	ENST00000257566.3:c.391C>T	p.Arg131Ter	p.R131*	ENST00000257566	NM_016569.3	131	Cga/Tga	2/8	NA	3	FACETS	1	0.981	1	0.619	0.568	0.671	INDETERMINATE	1	TRUE	1	0.78	3		394	386	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244184	153244184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759610249	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	253	498	0	ENST00000281708.4:c.1973G>A	p.Arg658Gln	p.R658Q	ENST00000281708	NM_033632.3	658	cGa/cAa	12/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.78	2		498	554	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2972186	2972186	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748468563	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	89	320	0	ENST00000396946.4:c.1553G>A	p.Arg518Gln	p.R518Q	ENST00000396946	NM_032415.4	518	cGa/cAa	11/25	0.3	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.78	0		320	228	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164577	47164577	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	182	453	0	ENST00000409792.3:c.1549G>T	p.Glu517Ter	p.E517*	ENST00000409792	NM_014159.6	517	Gaa/Taa	3/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.78	2		453	419	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224793	123224793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	154	361	0	ENST00000218089.9:c.3557G>A	p.Arg1186Gln	p.R1186Q	ENST00000218089	NM_001042749.1	1186	cGa/cAa	32/35	0.3	1	FACETS	0.748	0.696	0.8	0.748	0.696	0.8	INDETERMINATE	1	TRUE	0	0.78	1		361	322	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50481162	50481162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	9	410	0	ENST00000394963.4:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000394963	NM_003076.4	183	cGa/cAa	5/13	NA	3	FACETS	0.089	0.058	0.129	0.045	0.029	0.065	INDETERMINATE	1	TRUE	1	0.78	3		410	359	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919244	48919244	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913296	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	127	275	0	ENST00000267163.4:c.409G>T	p.Glu137Ter	p.E137*	ENST00000267163	NM_000321.2	137	Gaa/Taa	4/27	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.78	2		275	317	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484414	57484414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	32	457	0	ENST00000371085.3:c.595C>T	p.Arg199Cys	p.R199C	ENST00000371085	NM_000516.4	199	Cgc/Tgc	8/13	1	2	FACETS	0.168	0.136	0.204	0.168	0.136	0.204	SUBCLONAL	1	TRUE	1	0.78	2		457	489	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29099515	29099515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	136	310	0	ENST00000328354.6:c.886G>A	p.Asp296Asn	p.D296N	ENST00000328354	NM_007194.3	296	Gat/Aat	8/15	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.78	2		310	337	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144880	47144880	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	136	368	0	ENST00000409792.3:c.4873C>T	p.Arg1625Cys	p.R1625C	ENST00000409792	NM_014159.6	1625	Cgt/Tgt	7/21	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.78	2		368	347	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188288	142188288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1470834016	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	179	396	0	ENST00000350721.4:c.6443G>A	p.Arg2148Gln	p.R2148Q	ENST00000350721	NM_001184.3	2148	cGa/cAa	38/47	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.78	2		396	402	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46527650	46527650	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1287980956	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	173	400	0	ENST00000262741.5:c.715G>T	p.Glu239Ter	p.E239*	ENST00000262741	NM_003629.3	239	Gaa/Taa	6/10	1	2	FACETS	0.973	0.904	1	0.973	0.904	1	CLONAL	1	TRUE	1	0.78	2		400	456	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632792	23632792	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	48	349	0	ENST00000261584.4:c.3004G>T	p.Glu1002Ter	p.E1002*	ENST00000261584	NM_024675.3	1002	Gaa/Taa	10/13	1	2	FACETS	0.452	0.385	0.526	0.452	0.385	0.526	SUBCLONAL	1	TRUE	1	0.78	2		349	272	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615593	43615593	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	124	484	0	ENST00000355710.3:c.2672C>T	p.Ser891Leu	p.S891L	ENST00000355710	NM_020975.4	891	tCg/tTg	15/20	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.78	2		484	318	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119509	193119509	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	165	379	0	ENST00000367435.3:c.904G>T	p.Glu302Ter	p.E302*	ENST00000367435	NM_024529.4	302	Gaa/Taa	9/17	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.78	2		379	387	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	603	369	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	NA	3	FACETS	1	0.995	1	1	0.998	1	INDETERMINATE	3	TRUE	1	0.78	3		369	685	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549095	87549095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	168	425	0	ENST00000277120.3:c.1652G>A	p.Arg551Gln	p.R551Q	ENST00000277120		551	cGa/cAa	15/19	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.78	2		425	343	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447384	187447384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780987785	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	159	557	0	ENST00000232014.4:c.809G>A	p.Arg270Gln	p.R270Q	ENST00000232014	NM_001130845.1	270	cGa/cAa	5/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.78	2		557	379	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260146	10260146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751754286	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	139	490	0	ENST00000340748.4:c.2521G>A	p.Glu841Lys	p.E841K	ENST00000340748		841	Gaa/Aaa	25/40	1	2	FACETS	0.921	0.848	0.996	0.921	0.848	0.996	CLONAL	1	TRUE	1	0.78	2		490	387	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033753	48033753	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1553333707	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	66	386	0	ENST00000234420.5:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000234420	NM_000179.2	1322	Gaa/Taa	9/10	1	2	FACETS	0.416	0.362	0.473	0.416	0.362	0.473	SUBCLONAL	1	TRUE	1	0.78	2		386	407	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610695	52610695	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	11	425	0	ENST00000394830.3:c.3478C>T	p.Arg1160Ter	p.R1160*	ENST00000394830	NM_018313.4	1160	Cga/Tga	23/30	1	2	FACETS	0.069	0.047	0.097	0.069	0.047	0.097	SUBCLONAL	1	TRUE	1	0.78	2		425	407	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164913	106164913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs898441677	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	9	337	0	ENST00000380013.4:c.3781C>T	p.Arg1261Cys	p.R1261C	ENST00000380013	NM_001127208.2	1261	Cgc/Tgc	6/11	1	2	FACETS	0.068	0.044	0.098	0.068	0.044	0.098	SUBCLONAL	1	TRUE	1	0.78	2		337	341	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351286	89351286	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	26	611	1	ENST00000301030.4:c.1664C>A	p.Ser555Tyr	p.S555Y	ENST00000301030	NM_001256183.1	555	tCt/tAt	9/13	0.3	1	FACETS	0.15	0.119	0.186	0.15	0.119	0.186	INDETERMINATE	1	TRUE	0	0.78	1		612	271	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074217	8074217	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372669618	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	246	546	0	ENST00000377482.5:c.442C>T	p.Arg148Trp	p.R148W	ENST00000377482	NM_018948.3	148	Cgg/Tgg	4/4	0.3	1	FACETS	0.603	0.567	0.639	0.603	0.567	0.639	INDETERMINATE	1	TRUE	0	0.78	1		546	638	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188035	151188035	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	137	290	0	ENST00000262187.5:c.118G>T	p.Glu40Ter	p.E40*	ENST00000262187	NM_005614.3	40	Gaa/Taa	2/8	1	2	FACETS	0.976	0.899	1	0.976	0.899	1	CLONAL	1	TRUE	1	0.78	2		290	360	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024649	14024649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202243691	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	27	360	0	ENST00000311895.7:c.875G>A	p.Arg292Gln	p.R292Q	ENST00000311895	NM_005236.2	292	cGa/cAa	5/11	1	2	FACETS	0.191	0.151	0.236	0.191	0.151	0.236	SUBCLONAL	1	TRUE	1	0.78	2		360	363	SUCCESS
APC	324	MSKCC	GRCh37	5	112177368	112177368	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	21	430	0	ENST00000257430.4:c.6077C>A	p.Ser2026Tyr	p.S2026Y	ENST00000257430	NM_000038.5	2026	tCt/tAt	16/16	1	2	FACETS	0.141	0.108	0.179	0.141	0.108	0.179	SUBCLONAL	1	TRUE	1	0.78	2		430	383	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976426	25976426	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	194	360	0	ENST00000435504.4:c.1119C>A	p.Phe373Leu	p.F373L	ENST00000435504		373	ttC/ttA	11/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.78	2		360	428	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094904	143094904	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	172	401	0	ENST00000262992.4:c.1240C>A	p.Leu414Ile	p.L414I	ENST00000262992	NM_001101669.1	414	Ctc/Atc	14/24	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.78	2		401	417	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115595	108115595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769166447	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	168	374	0	ENST00000278616.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000278616	NM_000051.3	248	cGa/cAa	7/63	1	2	FACETS	0.981	0.911	1	0.981	0.911	1	CLONAL	1	TRUE	1	0.78	2		374	439	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599320	55599320	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913506	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	179	419	0	ENST00000288135.5:c.2446G>A	p.Asp816Asn	p.D816N	ENST00000288135	NM_000222.2	816	Gac/Aac	17/21	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.78	2		419	399	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829368	72829368	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201280219	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	130	524	1	ENST00000268489.5:c.7213G>A	p.Ala2405Thr	p.A2405T	ENST00000268489	NM_006885.3	2405	Gct/Act	9/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.78	2		525	274	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257141	198257141	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	157	352	0	ENST00000335508.6:c.3801A>C	p.Lys1267Asn	p.K1267N	ENST00000335508	NM_012433.2	1267	aaA/aaC	25/25	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.78	2		352	390	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288751	11288751	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs770601118	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	174	454	0	ENST00000361445.4:c.3004C>T	p.Arg1002Ter	p.R1002*	ENST00000361445	NM_004958.3	1002	Cga/Tga	19/58	0.3	1	FACETS	0.793	0.743	0.844	0.793	0.743	0.844	INDETERMINATE	1	TRUE	0	0.78	1		454	343	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383233	31383233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771192296	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	21	494	0	ENST00000328111.2:c.1145G>A	p.Arg382His	p.R382H	ENST00000328111	NM_006892.3	382	cGc/cAc	11/23	1	2	FACETS	0.135	0.103	0.171	0.135	0.103	0.171	SUBCLONAL	1	TRUE	1	0.78	2		494	400	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725528	117725528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867759865	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	120	363	0	ENST00000368508.3:c.353G>A	p.Arg118Gln	p.R118Q	ENST00000368508	NM_002944.2	118	cGa/cAa	5/43	1	2	FACETS	0.98	0.898	1	0.98	0.898	1	CLONAL	1	TRUE	1	0.78	2		363	314	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724138	112724138	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	176	339	0	ENST00000369452.4:c.22G>T	p.Glu8Ter	p.E8*	ENST00000369452	NM_007373.3	8	Gaa/Taa	2/9	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.78	2		339	374	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77048440	77048440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1326439583	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	161	349	0	ENST00000356341.3:c.1145C>T	p.Ser382Leu	p.S382L	ENST00000356341	NM_002576.4	382	tCg/tTg	12/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.78	2		349	375	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762249	43762249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763084380	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	145	403	0	ENST00000382044.4:c.1196C>T	p.Thr399Met	p.T399M	ENST00000382044	NM_001141980.1	399	aCg/aTg	11/28	1	2	FACETS	0.944	0.871	1	0.944	0.871	1	CLONAL	1	TRUE	1	0.78	2		403	394	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678001	117678001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs62430836	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	168	458	0	ENST00000368508.3:c.3932G>A	p.Arg1311Gln	p.R1311Q	ENST00000368508	NM_002944.2	1311	cGa/cAa	25/43	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.78	2		458	419	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934254	48934254	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1131690904	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	125	378	2	ENST00000267163.4:c.709G>T	p.Glu237Ter	p.E237*	ENST00000267163	NM_000321.2	237	Gaa/Taa	7/27	1	2	FACETS	0.926	0.849	1	0.926	0.849	1	CLONAL	1	TRUE	1	0.78	2		380	346	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347793	70347793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	69	481	0	ENST00000374080.3:c.3032C>T	p.Ser1011Leu	p.S1011L	ENST00000374080		1011	tCg/tTg	22/45	0.3	1	FACETS	0.318	0.279	0.36	0.318	0.279	0.36	INDETERMINATE	1	TRUE	0	0.78	1		481	339	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343913	118343913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264831726	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	63	471	0	ENST00000534358.1:c.2039C>T	p.Ser680Leu	p.S680L	ENST00000534358	NM_005933.3	680	tCg/tTg	3/36	1	2	FACETS	0.372	0.323	0.426	0.372	0.323	0.426	SUBCLONAL	1	TRUE	1	0.78	2		471	434	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911247	32911247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs431825298	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	176	473	0	ENST00000380152.3:c.2755G>A	p.Glu919Lys	p.E919K	ENST00000380152		919	Gaa/Aaa	11/27	1	2	FACETS	0.897	0.833	0.963	0.897	0.833	0.963	CLONAL	1	TRUE	1	0.78	2		473	503	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990354	81990354	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	89	510	0	ENST00000359376.3:c.3625G>T	p.Glu1209Ter	p.E1209*	ENST00000359376	NM_002661.3	1209	Gaa/Taa	32/33	0.3	1	FACETS	0.37	0.33	0.412	0.37	0.33	0.412	INDETERMINATE	1	TRUE	0	0.78	1		510	376	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499478	89499479	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	195	464	1	ENST00000336596.2:c.2648_2649delinsAA	p.Arg883Gln	p.R883Q	ENST00000336596	NM_005233.5	883	cGG/cAA	15/17	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.78	2		465	463	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038524	47038524	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556777452	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	17	448	0	ENST00000377604.3:c.686G>A	p.Arg229His	p.R229H	ENST00000377604	NM_001204468.1	229	cGc/cAc	8/24	0.3	1	FACETS	0.096	0.071	0.126	0.096	0.071	0.126	INDETERMINATE	1	TRUE	0	0.78	1		448	276	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859878	117859878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780692465	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	182	423	0	ENST00000297338.2:c.1757G>A	p.Arg586Gln	p.R586Q	ENST00000297338	NM_006265.2	586	cGa/cAa	14/14	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.78	2		423	407	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217654	7217654	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	146	476	0	ENST00000380728.2:c.273G>T	p.Lys91Asn	p.K91N	ENST00000380728		91	aaG/aaT	4/11	1	2	FACETS	0.915	0.844	0.988	0.915	0.844	0.988	CLONAL	1	TRUE	1	0.78	2		476	409	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242692	16242692	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	38	444	0	ENST00000375759.3:c.1313G>T	p.Arg438Ile	p.R438I	ENST00000375759	NM_015001.2	438	aGa/aTa	6/15	1	2	FACETS	0.191	0.157	0.228	0.191	0.157	0.228	SUBCLONAL	1	TRUE	1	0.78	2		444	511	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019217	31019217	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs576447224	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	132	497	0	ENST00000375687.4:c.812G>A	p.Arg271Gln	p.R271Q	ENST00000375687	NM_015338.5	271	cGg/cAg	9/13	1	2	FACETS	0.94	0.864	1	0.94	0.864	1	CLONAL	1	TRUE	1	0.78	2		497	360	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939028	48939028	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	80	199	0	ENST00000267163.4:c.862-2A>T		p.X288_splice	ENST00000267163	NM_000321.2	288			1	2	FACETS	0.896	0.802	0.993	0.896	0.802	0.993	CLONAL	1	TRUE	1	0.78	2		199	229	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273905	10273905	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	100	496	0	ENST00000330684.3:c.364G>A	p.Val122Ile	p.V122I	ENST00000330684	NM_001134407.1	122	Gtc/Atc	2/13	0.3	1	FACETS	0.636	0.578	0.694	0.636	0.578	0.694	INDETERMINATE	1	TRUE	0	0.78	1		496	246	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647553	117647553	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	77	508	0	ENST00000368508.3:c.5391G>T	p.Gln1797His	p.Q1797H	ENST00000368508	NM_002944.2	1797	caG/caT	33/43	1	2	FACETS	0.475	0.418	0.534	0.475	0.418	0.534	SUBCLONAL	1	TRUE	1	0.78	2		508	416	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988119	85988119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	155	414	0	ENST00000263360.6:c.1064G>A	p.Arg355Gln	p.R355Q	ENST00000263360	NM_003797.3	355	cGa/cAa	10/12	1	2	FACETS	0.953	0.882	1	0.953	0.882	1	CLONAL	1	TRUE	1	0.78	2		414	417	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981172	55981172	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	169	379	0	ENST00000263923.4:c.527G>T	p.Arg176Ile	p.R176I	ENST00000263923	NM_002253.2	176	aGa/aTa	5/30	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.78	2		379	396	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761387	59761387	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs886053214	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	315	424	0	ENST00000259008.2:c.3020C>A	p.Ser1007Tyr	p.S1007Y	ENST00000259008	NM_032043.2	1007	tCt/tAt	20/20	0.3	2	FACETS	1	0.988	1	1	0.988	1	INDETERMINATE	2	TRUE	0	0.78	2		424	388	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937668	44937668	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	75	272	0	ENST00000377967.4:c.2856C>A	p.Phe952Leu	p.F952L	ENST00000377967	NM_021140.2	952	ttC/ttA	19/29	1	2	FACETS	0.687	0.608	0.769	0.687	0.608	0.769	SUBCLONAL	1	TRUE	1	0.78	2		272	280	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336400	80336400	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	83	573	0	ENST00000286548.4:c.919G>T	p.Glu307Ter	p.E307*	ENST00000286548	NM_002072.3	307	Gaa/Taa	7/7	1	2	FACETS	0.464	0.411	0.52	0.464	0.411	0.52	SUBCLONAL	1	TRUE	1	0.78	2		573	459	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641447	47641447	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	21	332	0	ENST00000233146.2:c.832G>T	p.Glu278Ter	p.E278*	ENST00000233146	NM_000251.2	278	Gaa/Taa	5/16	1	2	FACETS	0.138	0.105	0.175	0.138	0.105	0.175	SUBCLONAL	1	TRUE	1	0.78	2		332	391	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028656	12028656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	156	392	0	ENST00000353533.5:c.859C>T	p.Arg287Cys	p.R287C	ENST00000353533	NM_003010.3	287	Cgc/Tgc	8/11	1	2	FACETS	0.993	0.92	1	0.993	0.92	1	CLONAL	1	TRUE	1	0.78	2		392	403	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197726	123197726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755599197	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	93	369	0	ENST00000218089.9:c.1850G>A	p.Arg617Gln	p.R617Q	ENST00000218089	NM_001042749.1	617	cGg/cAg	20/35	0.3	1	FACETS	0.5	0.45	0.552	0.5	0.45	0.552	INDETERMINATE	1	TRUE	0	0.78	1		369	291	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646291	23646291	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	166	471	0	ENST00000261584.4:c.1576C>A	p.His526Asn	p.H526N	ENST00000261584	NM_024675.3	526	Cat/Aat	4/13	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.78	2		471	417	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592125	55592125	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	137	396	0	ENST00000288135.5:c.1449C>A	p.Phe483Leu	p.F483L	ENST00000288135	NM_000222.2	483	ttC/ttA	9/21	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.78	2		396	334	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098678	47098678	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	122	614	0	ENST00000409792.3:c.6596C>A	p.Ser2199Tyr	p.S2199Y	ENST00000409792	NM_014159.6	2199	tCt/tAt	15/21	1	2	FACETS	0.738	0.672	0.806	0.738	0.672	0.806	SUBCLONAL	1	TRUE	1	0.78	2		614	424	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519179	137519179	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1562281992	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	99	369	0	ENST00000367739.4:c.1459G>T	p.Glu487Ter	p.E487*	ENST00000367739	NM_000416.2	487	Gaa/Taa	7/7	1	2	FACETS	0.713	0.642	0.787	0.713	0.642	0.787	SUBCLONAL	1	TRUE	1	0.78	2		369	356	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212568	133212568	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	91	486	0	ENST00000320574.5:c.5721C>A	p.Phe1907Leu	p.F1907L	ENST00000320574	NM_006231.2	1907	ttC/ttA	42/49	0.3	1	FACETS	0.518	0.466	0.571	0.518	0.466	0.571	INDETERMINATE	1	TRUE	0	0.78	1		486	275	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041854	14041854	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	144	544	0	ENST00000311895.7:c.2401C>A	p.Leu801Ile	p.L801I	ENST00000311895	NM_005236.2	801	Ctc/Atc	11/11	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.78	2		544	369	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941876	44941876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	134	374	0	ENST00000377967.4:c.3200C>T	p.Ser1067Leu	p.S1067L	ENST00000377967	NM_021140.2	1067	tCg/tTg	21/29	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.78	2		374	336	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332599	65332599	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758451418	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	26	476	0	ENST00000342505.4:c.940G>A	p.Glu314Lys	p.E314K	ENST00000342505	NM_002227.2	314	Gaa/Aaa	7/25	1	2	FACETS	0.154	0.121	0.191	0.154	0.121	0.191	SUBCLONAL	1	TRUE	1	0.78	2		476	433	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38996935	38996935	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	78	399	0	ENST00000357387.3:c.442C>T	p.Arg148Ter	p.R148*	ENST00000357387	NM_152756.3	148	Cga/Tga	6/38	1	2	FACETS	0.444	0.392	0.501	0.444	0.392	0.501	SUBCLONAL	1	TRUE	1	0.78	2		399	450	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609843	117609843	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	168	438	0	ENST00000368508.3:c.6856G>T	p.Glu2286Ter	p.E2286*	ENST00000368508	NM_002944.2	2286	Gaa/Taa	43/43	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.78	2		438	393	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50482348	50482348	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	127	384	0	ENST00000394963.4:c.699C>A	p.Phe233Leu	p.F233L	ENST00000394963	NM_003076.4	233	ttC/ttA	6/13	NA	3	FACETS	1	0.956	1	0.538	0.491	0.586	INDETERMINATE	1	TRUE	1	0.78	3		384	421	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106519993	106519993	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	138	357	0	ENST00000359195.3:c.2421G>T	p.Lys807Asn	p.K807N	ENST00000359195	NM_002649.2	807	aaG/aaT	6/11	1	2	FACETS	0.946	0.871	1	0.946	0.871	1	CLONAL	1	TRUE	1	0.78	2		357	374	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285571	38285571	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	143	511	0	ENST00000425967.3:c.582G>T	p.Lys194Asn	p.K194N	ENST00000425967	NM_001174067.1	194	aaG/aaT	6/19	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.78	2		511	353	SUCCESS
APC	324	MSKCC	GRCh37	5	112174727	112174727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202168805	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	161	495	0	ENST00000257430.4:c.3436C>T	p.Arg1146Cys	p.R1146C	ENST00000257430	NM_000038.5	1146	Cgt/Tgt	16/16	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.78	2		495	410	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743317	743317	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	114	407	0	ENST00000314574.4:c.823G>T	p.Glu275Ter	p.E275*	ENST00000314574	NM_005433.3	275	Gaa/Taa	7/12	1	2	FACETS	0.771	0.701	0.844	0.771	0.701	0.844	SUBCLONAL	1	TRUE	1	0.78	2		407	379	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115524	108115524	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs769731317	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	39	320	0	ENST00000278616.4:c.672G>T	p.Lys224Asn	p.K224N	ENST00000278616	NM_000051.3	224	aaG/aaT	7/63	1	2	FACETS	0.269	0.223	0.32	0.269	0.223	0.32	SUBCLONAL	1	TRUE	1	0.78	2		320	372	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1978211	1978211	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	68	496	0	ENST00000382891.5:c.3631A>G	p.Thr1211Ala	p.T1211A	ENST00000382891	NM_133335.3	1211	Acc/Gcc	21/22	1	2	FACETS	0.414	0.361	0.471	0.414	0.361	0.471	SUBCLONAL	1	TRUE	1	0.78	2		496	421	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	339	402	0	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	0.3	2	FACETS	0.995	0.963	1	0.995	0.963	1	INDETERMINATE	2	TRUE	0	0.78	2		402	437	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424921	47424921	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	180	471	0	ENST00000404338.3:c.2989C>T	p.Arg997Ter	p.R997*	ENST00000404338	NM_004491.4	997	Cga/Tga	1/6	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.78	2		471	413	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1724732	1724732	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	101	379	0	ENST00000378609.4:c.449G>A	p.Arg150Gln	p.R150Q	ENST00000378609	NM_002074.3	150	cGa/cAa	8/12	0.3	1	FACETS	0.655	0.597	0.715	0.655	0.597	0.715	INDETERMINATE	1	TRUE	0	0.78	1		379	241	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186754	11186754	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs762212987	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	59	461	0	ENST00000361445.4:c.6451A>G	p.Ile2151Val	p.I2151V	ENST00000361445	NM_004958.3	2151	Att/Gtt	46/58	0.3	1	FACETS	0.294	0.254	0.336	0.294	0.254	0.336	INDETERMINATE	1	TRUE	0	0.78	1		461	314	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313324	65313324	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	124	414	0	ENST00000342505.4:c.1790T>C	p.Ile597Thr	p.I597T	ENST00000342505	NM_002227.2	597	aTc/aCc	13/25	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.78	2		414	313	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058614	72058614	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	148	378	0	ENST00000357731.5:c.826T>G	p.Phe276Val	p.F276V	ENST00000357731	NM_173808.2	276	Ttt/Gtt	6/7	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.78	2		378	338	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166274	118166274	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	182	580	0	ENST00000369448.3:c.784G>T	p.Glu262Ter	p.E262*	ENST00000369448	NM_017709.3	262	Gaa/Taa	2/2	1	2	FACETS	0.93	0.865	0.995	0.93	0.865	0.995	CLONAL	1	TRUE	1	0.78	2		580	502	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230492945	230492945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561944260	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	102	519	0	ENST00000391860.1:c.109C>T	p.Arg37Trp	p.R37W	ENST00000391860	NM_001258311.1	37	Cgg/Tgg	2/7	1	2	FACETS	0.893	0.809	0.978	0.893	0.809	0.978	CLONAL	1	TRUE	1	0.78	2		519	293	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63810695	63810695	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	214	402	0	ENST00000279873.7:c.782G>T	p.Arg261Ile	p.R261I	ENST00000279873	NM_032199.2	261	aGa/aTa	5/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.78	2		402	495	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405066	70405066	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1362476717	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	79	501	0	ENST00000373644.4:c.2580G>T	p.Glu860Asp	p.E860D	ENST00000373644	NM_030625.2	860	gaG/gaT	4/12	1	2	FACETS	0.58	0.514	0.65	0.58	0.514	0.65	SUBCLONAL	1	TRUE	1	0.78	2		501	349	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451438	70451438	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	184	475	0	ENST00000373644.4:c.6278A>C	p.Glu2093Ala	p.E2093A	ENST00000373644	NM_030625.2	2093	gAa/gCa	12/12	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.78	2		475	390	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717695	89717695	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	225	357	0	ENST00000371953.3:c.720C>A	p.Tyr240Ter	p.Y240*	ENST00000371953	NM_000314.4	240	taC/taA	7/9	1	2	FACETS	0.853	0.814	0.892	1	0.995	1	CLONAL	2	TRUE	1	0.78	2		357	338	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239471	123239471	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	88	573	0	ENST00000358487.5:c.2366C>A	p.Ser789Tyr	p.S789Y	ENST00000358487	NM_000141.4	789	tCt/tAt	18/18	1	2	FACETS	0.442	0.393	0.495	0.442	0.393	0.495	SUBCLONAL	1	TRUE	1	0.78	2		573	510	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123260457	123260457	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	179	471	0	ENST00000358487.5:c.1444A>G	p.Thr482Ala	p.T482A	ENST00000358487	NM_000141.4	482	Aca/Gca	11/18	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.78	2		471	426	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066720	77066720	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	146	431	0	ENST00000356341.3:c.765G>T	p.Glu255Asp	p.E255D	ENST00000356341	NM_002576.4	255	gaG/gaT	7/15	1	2	FACETS	0.945	0.873	1	0.945	0.873	1	CLONAL	1	TRUE	1	0.78	2		431	396	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180441	94180441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139461096	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	110	433	0	ENST00000323929.3:c.1727G>A	p.Arg576Gln	p.R576Q	ENST00000323929	NM_005591.3	576	cGa/cAa	15/20	1	2	FACETS	0.879	0.799	0.96	0.879	0.799	0.96	CLONAL	1	TRUE	1	0.78	2		433	321	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170543	108170543	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs772376652	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	126	381	0	ENST00000278616.4:c.5108T>C	p.Phe1703Ser	p.F1703S	ENST00000278616	NM_000051.3	1703	tTt/tCt	34/63	1	2	FACETS	0.892	0.817	0.969	0.892	0.817	0.969	CLONAL	1	TRUE	1	0.78	2		381	362	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235941	108235941	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs142322668	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	162	475	0	ENST00000278616.4:c.8983C>A	p.Leu2995Ile	p.L2995I	ENST00000278616	NM_000051.3	2995	Ctc/Atc	62/63	1	2	FACETS	0.984	0.913	1	0.984	0.913	1	CLONAL	1	TRUE	1	0.78	2		475	422	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406324	406324	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	143	444	0	ENST00000399788.2:c.4117C>A	p.Leu1373Ile	p.L1373I	ENST00000399788	NM_001042603.1	1373	Ctt/Att	25/28	0.3	1	FACETS	0.59	0.544	0.637	0.59	0.544	0.637	INDETERMINATE	1	TRUE	0	0.78	1		444	379	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	443431	443431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	147	366	0	ENST00000399788.2:c.1466G>A	p.Ser489Asn	p.S489N	ENST00000399788	NM_001042603.1	489	aGt/aAt	11/28	0.3	1	FACETS	0.581	0.536	0.626	0.581	0.536	0.626	INDETERMINATE	1	TRUE	0	0.78	1		366	396	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719992	18719992	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	91	233	0	ENST00000266497.5:c.3888+1G>T		p.X1296_splice	ENST00000266497		1296			NA	3	FACETS	1	0.979	1	0.679	0.613	0.746	INDETERMINATE	1	TRUE	1	0.78	3		233	239	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432650	49432650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1271513534	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	135	575	0	ENST00000301067.7:c.8489G>A	p.Arg2830Gln	p.R2830Q	ENST00000301067	NM_003482.3	2830	cGa/cAa	34/54	NA	3	FACETS	1	0.986	1	0.691	0.637	0.747	INDETERMINATE	1	TRUE	1	0.78	3		575	348	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589394	28589394	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	126	378	0	ENST00000241453.7:c.2654-1G>A		p.X885_splice	ENST00000241453	NM_004119.2	885			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.78	2		378	283	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910548	32910548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1135401896	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	138	364	0	ENST00000380152.3:c.2056C>T	p.Leu686Phe	p.L686F	ENST00000380152		686	Ctt/Ttt	11/27	1	2	FACETS	0.962	0.886	1	0.962	0.886	1	CLONAL	1	TRUE	1	0.78	2		364	368	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910564	32910564	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	164	408	0	ENST00000380152.3:c.2072C>G	p.Ala691Gly	p.A691G	ENST00000380152		691	gCa/gGa	11/27	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.78	2		408	401	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562899	95562899	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	151	440	0	ENST00000393063.1:c.4358T>C	p.Ile1453Thr	p.I1453T	ENST00000393063	NM_030621.3	1453	aTa/aCa	24/28	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.78	2		440	360	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991268	41991268	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	157	353	0	ENST00000219905.7:c.2099G>C	p.Arg700Thr	p.R700T	ENST00000219905	NM_001164273.1	700	aGa/aCa	5/24	1	2	FACETS	0.984	0.912	1	0.984	0.912	1	CLONAL	1	TRUE	1	0.78	2		353	409	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354557	91354557	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	155	483	0	ENST00000355112.3:c.3997G>T	p.Glu1333Ter	p.E1333*	ENST00000355112	NM_000057.2	1333	Gaa/Taa	21/22	1	2	FACETS	0.937	0.867	1	0.937	0.867	1	CLONAL	1	TRUE	1	0.78	2		483	424	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670646	67670646	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	123	398	0	ENST00000264010.4:c.1891G>T	p.Glu631Ter	p.E631*	ENST00000264010	NM_006565.3	631	Gaa/Taa	11/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.78	2		398	277	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821749	72821749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776585287	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	126	589	0	ENST00000268489.5:c.10426G>A	p.Asp3476Asn	p.D3476N	ENST00000268489	NM_006885.3	3476	Gac/Aac	10/10	1	2	FACETS	0.945	0.866	1	0.945	0.866	1	CLONAL	1	TRUE	1	0.78	2		589	342	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968904	15968904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	187	446	0	ENST00000268712.3:c.4846G>T	p.Asp1616Tyr	p.D1616Y	ENST00000268712	NM_006311.3	1616	Gat/Tat	33/46	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.78	2		446	435	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56401538	56401538	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	177	370	0	ENST00000348428.3:c.1401-1G>T		p.X467_splice	ENST00000348428	NM_006785.3	467			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.78	2		370	395	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299971	15299971	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1484483311	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	73	614	0	ENST00000263388.2:c.1207G>A	p.Glu403Lys	p.E403K	ENST00000263388	NM_000435.2	403	Gag/Aag	8/33	1	2	FACETS	0.731	0.648	0.819	0.731	0.648	0.819	SUBCLONAL	1	TRUE	1	0.78	2		614	256	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423344	47423344	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	44	462	0	ENST00000404338.3:c.1412C>T	p.Ser471Phe	p.S471F	ENST00000404338	NM_004491.4	471	tCt/tTt	1/6	1	2	FACETS	0.282	0.237	0.332	0.282	0.237	0.332	SUBCLONAL	1	TRUE	1	0.78	2		462	400	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474131	29474131	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1313368016	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	102	465	0	ENST00000389048.3:c.2044C>A	p.His682Asn	p.H682N	ENST00000389048	NM_004304.4	682	Cat/Aat	12/29	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.78	2		465	247	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39233605	39233605	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	179	332	0	ENST00000402219.2:c.2739G>T	p.Lys913Asn	p.K913N	ENST00000402219	NM_005633.3	913	aaG/aaT	17/23	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.78	2		332	413	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141636	202141636	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	25	493	0	ENST00000358485.4:c.924G>T	p.Glu308Asp	p.E308D	ENST00000358485	NM_001080125.1	308	gaG/gaT	7/9	1	2	FACETS	0.128	0.101	0.161	0.128	0.101	0.161	SUBCLONAL	1	TRUE	1	0.78	2		493	499	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39713126	39713126	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	127	353	0	ENST00000361337.2:c.532A>C	p.Asn178His	p.N178H	ENST00000361337	NM_003286.2	178	Aat/Cat	8/21	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.78	2		353	317	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729986	39729986	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	137	441	0	ENST00000361337.2:c.1301G>A	p.Arg434Gln	p.R434Q	ENST00000361337	NM_003286.2	434	cGa/cAa	13/21	1	2	FACETS	0.949	0.874	1	0.949	0.874	1	CLONAL	1	TRUE	1	0.78	2		441	370	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46266522	46266522	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs940267018	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	25	369	0	ENST00000371998.3:c.2507C>A	p.Ser836Tyr	p.S836Y	ENST00000371998		836	tCt/tAt	13/23	1	2	FACETS	0.156	0.122	0.194	0.156	0.122	0.194	SUBCLONAL	1	TRUE	1	0.78	2		369	412	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72861835	72861835	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	146	375	0	ENST00000325599.8:c.1047G>T	p.Lys349Asn	p.K349N	ENST00000325599	NM_018130.2	349	aaG/aaT	9/11	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.78	2		375	373	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114568	73114568	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	147	319	0	ENST00000356692.5:c.949G>T	p.Glu317Ter	p.E317*	ENST00000356692		317	Gaa/Taa	9/9	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.78	2		319	357	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275403	142275403	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	65	354	0	ENST00000350721.4:c.1900T>G	p.Ser634Ala	p.S634A	ENST00000350721	NM_001184.3	634	Tca/Gca	9/47	1	2	FACETS	0.448	0.39	0.51	0.448	0.39	0.51	SUBCLONAL	1	TRUE	1	0.78	2		354	372	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430728	181430728	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	160	685	0	ENST00000325404.1:c.580A>T	p.Met194Leu	p.M194L	ENST00000325404	NM_003106.3	194	Atg/Ttg	1/1	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.78	2		685	409	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902944	1902944	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	153	436	0	ENST00000382891.5:c.563T>G	p.Leu188Arg	p.L188R	ENST00000382891	NM_133335.3	188	cTt/cGt	2/22	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.78	2		436	332	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750620	41750620	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	113	409	1	ENST00000226382.2:c.8A>C	p.Lys3Thr	p.K3T	ENST00000226382	NM_003924.3	3	aAa/aCa	1/3	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.78	2		410	256	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573396	55573396	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	63	387	0	ENST00000288135.5:c.1058G>T	p.Arg353Ile	p.R353I	ENST00000288135	NM_000222.2	353	aGa/aTa	6/21	1	2	FACETS	0.492	0.429	0.561	0.492	0.429	0.561	SUBCLONAL	1	TRUE	1	0.78	2		387	328	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976902	55976902	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	156	419	0	ENST00000263923.4:c.1010A>C	p.Glu337Ala	p.E337A	ENST00000263923	NM_002253.2	337	gAa/gCa	8/30	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.78	2		419	399	SUCCESS
REST	5978	MSKCC	GRCh37	4	57776955	57776955	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	164	489	0	ENST00000309042.7:c.151A>C	p.Asn51His	p.N51H	ENST00000309042	NM_005612.4	51	Aat/Cat	2/4	1	2	FACETS	0.973	0.903	1	0.973	0.903	1	CLONAL	1	TRUE	1	0.78	2		489	432	SUCCESS
ALB	213	MSKCC	GRCh37	4	74279239	74279239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150388973	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	183	483	0	ENST00000295897.4:c.946G>A	p.Glu316Lys	p.E316K	ENST00000295897	NM_000477.5	316	Gaa/Aaa	8/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.78	2		483	422	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675638	86675638	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	163	330	0	ENST00000274376.6:c.2574A>C	p.Lys858Asn	p.K858N	ENST00000274376	NM_002890.2	858	aaA/aaC	19/25	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.78	2		330	414	SUCCESS
APC	324	MSKCC	GRCh37	5	112178682	112178682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	112	494	0	ENST00000257430.4:c.7391C>T	p.Ser2464Phe	p.S2464F	ENST00000257430	NM_000038.5	2464	tCt/tTt	16/16	1	2	FACETS	0.731	0.663	0.801	0.731	0.663	0.801	SUBCLONAL	1	TRUE	1	0.78	2		494	393	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398870	398870	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	106	454	0	ENST00000380956.4:c.680A>G	p.Glu227Gly	p.E227G	ENST00000380956	NM_001195286.1	227	gAg/gGg	6/9	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.78	2		454	266	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401581	401581	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	123	563	0	ENST00000380956.4:c.903G>T	p.Arg301Ser	p.R301S	ENST00000380956	NM_001195286.1	301	agG/agT	7/9	1	2	FACETS	0.986	0.904	1	0.986	0.904	1	CLONAL	1	TRUE	1	0.78	2		563	320	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662783	117662783	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	71	405	0	ENST00000368508.3:c.4682T>C	p.Val1561Ala	p.V1561A	ENST00000368508	NM_002944.2	1561	gTg/gCg	29/43	1	2	FACETS	0.519	0.455	0.586	0.519	0.455	0.586	SUBCLONAL	1	TRUE	1	0.78	2		405	351	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137522060	137522060	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	137	341	0	ENST00000367739.4:c.819T>G	p.Ile273Met	p.I273M	ENST00000367739	NM_000416.2	273	atT/atG	6/7	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.78	2		341	325	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397550	116397550	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	163	385	0	ENST00000397752.3:c.1922C>A	p.Ser641Ter	p.S641*	ENST00000397752	NM_000245.2	641	tCa/tAa	7/21	1	2	FACETS	0.967	0.897	1	0.967	0.897	1	CLONAL	1	TRUE	1	0.78	2		385	432	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397767	116397767	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	216	448	0	ENST00000397752.3:c.2041T>G	p.Tyr681Asp	p.Y681D	ENST00000397752	NM_000245.2	681	Tac/Gac	8/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.78	2		448	488	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124499094	124499094	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	142	341	0	ENST00000357628.3:c.619T>G	p.Leu207Val	p.L207V	ENST00000357628	NM_015450.2	207	Tta/Gta	9/19	1	2	FACETS	0.992	0.916	1	0.992	0.916	1	CLONAL	1	TRUE	1	0.78	2		341	367	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148507491	148507491	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	122	335	0	ENST00000320356.2:c.1963G>T	p.Glu655Ter	p.E655*	ENST00000320356	NM_004456.4	655	Gaa/Taa	17/20	1	2	FACETS	0.984	0.902	1	0.984	0.902	1	CLONAL	1	TRUE	1	0.78	2		335	318	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853346	151853346	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	93	489	0	ENST00000262189.6:c.11756G>T	p.Gly3919Val	p.G3919V	ENST00000262189	NM_170606.2	3919	gGt/gTt	45/59	1	2	FACETS	0.489	0.436	0.544	0.489	0.436	0.544	SUBCLONAL	1	TRUE	1	0.78	2		489	488	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319900	8319900	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	166	432	0	ENST00000356435.5:c.5601A>C	p.Glu1867Asp	p.E1867D	ENST00000356435		1867	gaA/gaC	34/35	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.78	2		432	406	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15833810	15833810	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	121	337	0	ENST00000307771.7:c.568A>G	p.Lys190Glu	p.K190E	ENST00000307771	NM_005089.3	190	Aaa/Gaa	8/11	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.78	2		337	299	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776265	76776265	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0064221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	99	328	0	ENST00000373344.5:c.7200+1G>A		p.X2400_splice	ENST00000373344	NM_000489.3	2400			0.3	1	FACETS	0.53	0.48	0.583	0.53	0.48	0.583	INDETERMINATE	1	TRUE	0	0.78	1		328	292	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188261	10188261	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0064225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	117	462	0	ENST00000256474.2:c.404T>G	p.Leu135Ter	p.L135*	ENST00000256474	NM_000551.3	135	tTa/tGa	2/3	0.295081255282807	2	FACETS	0.837	0.769	0.905	1	0.982	1	CLONAL	3	FALSE	0	0.358456802367285	2		462	260	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295708	212295708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775232357	NA	P-0064225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	28	527	0	ENST00000342788.4:c.2605G>A	p.Glu869Lys	p.E869K	ENST00000342788	NM_005235.2	869	Gaa/Aaa	21/28	0.347976117988893	3	FACETS	0.95	0.765	1	0.475	0.382	0.579	CLONAL	1	FALSE	1	0.358456802367285	3		527	194	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702625	52702625	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	27	392	0	ENST00000394830.3:c.273del	p.Ile92LeufsTer3	p.I92Lfs*3	ENST00000394830	NM_018313.4	91	ccC/cc	4/30	0.295081255282807	2	FACETS	1	0.93	1	0.685	0.556	0.826	CLONAL	1	FALSE	0	0.358456802367285	2		392	110	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1296255	1296255	+	upstream_gene_variant	5'Flank	SNP	A	A	G	novel	NA	P-0064225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	20	631	4				ENST00000310581	NM_198253.2	-/1132			0.30739720641585	5	FACETS	0.434	0.331	0.555	0.145	0.11	0.185	SUBCLONAL	1	FALSE	2	0.358456802367285	5		635	395	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817482	39817482	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064231-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	156	472	0	ENST00000288319.7:c.81C>A	p.His27Gln	p.H27Q	ENST00000288319	NM_182918.3	27	caC/caA	2/10	0.558700179072809	3	FACETS	1	0.945	1	0.519	0.476	0.563	CLONAL	1	TRUE	1	0.557790055715234	3		472	689	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690205	33690205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064231-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	84	416	0	ENST00000308377.4:c.622C>T	p.Pro208Ser	p.P208S	ENST00000308377	NM_152270.3	208	Cct/Tct	2/5	0.484356033044035	4	FACETS	0.994	0.881	1			1	CLONAL	1	TRUE	NA	0.557790055715234	4		416	472	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0064250-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	25	468	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	0.223405424309529	3	FACETS	1	0.874	1			1	INDETERMINATE	1	TRUE	NA	0.420799293976901	3		468	127	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845850	151846872	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGCCCAATTTCTTTAGAAATTCATCTATTTCATCCTCACAAGGTGGTTTAAATGTCCCCTTAGGGATTACAATATGAATGCTCCACTTCTTCCATTTCATTCCTCTCCATTTTTTATTGAGCGGCCTGCAATCTTCAAACCCACCATGGACAGCTCTTAGCCGAGGCTTCAGCTTGACTGTCACCTTCAGCTCATCTGGCTTGGCCTCGACTTGGGCTGCTTCAAAAGCAGGAGGGAAGGCGATGGGTGGTGAGGCAGGGGGAGAAGCTTTCTCTGGGAGCTGGGGGAGACAGTGCACATCCAAAGTGGAGATGTTGTTGCTGTACTGATGAAATGCTTTGGAAGGCGTTTCTCTCATAGGTGATTGTGGCAATGAAGGAATGGATTCCTGGGCAACATAAAGAAACCATGACAAAGAAAAATAATTCACAAGCCCGGAAAGCAATTCTTGTTAAGACAAGAAGCTGAGCAGTATGACTGAAGAGGATGGGTGACCTGAGGGGCAGAGGGAGAGTCAGCAGTAAGTGCTGGGGGCTCATGCACCGCAGAAGCTGACCATGCTCTAAGGTGCACAGGGATAGAGAGCGGGTGATGGCAGCTGTGCCGCGTCCTTTCGAGGCCTTTTCCACAAAGCCATAATTCTGGAGAATATTCTGCTCTTACACTTTCTGGGACAATCCCCTTTCTAACTATATTAAAACCAGAAAAAGAAAAAACACACACACACTCACAATGCTGTCAGAAGAGCTAATATAATTTGTACAATGGAACAGTGTTTTTTGTTTAACCAAATAAGAACGCTGCAGCATCGTTTCTTGAGAGCTTATCTCCACTCTAAAATTCACATCTGTTAATCTCAGCCTTAATCAATTGGTGTAAATGTTACAGAAAGGGAAGGAGCCCCTGTCAACAAATGAATCATACTAACTTTTCTCTGAGGCTTCTCAGCTCTGATCCGGCTGCTGAAACAGTTGAGCTGAGGGGAAATCTCCAATAGCTTATTTACTTTATGGTACAGAGTAT	TGCCCAATTTCTTTAGAAATTCATCTATTTCATCCTCACAAGGTGGTTTAAATGTCCCCTTAGGGATTACAATATGAATGCTCCACTTCTTCCATTTCATTCCTCTCCATTTTTTATTGAGCGGCCTGCAATCTTCAAACCCACCATGGACAGCTCTTAGCCGAGGCTTCAGCTTGACTGTCACCTTCAGCTCATCTGGCTTGGCCTCGACTTGGGCTGCTTCAAAAGCAGGAGGGAAGGCGATGGGTGGTGAGGCAGGGGGAGAAGCTTTCTCTGGGAGCTGGGGGAGACAGTGCACATCCAAAGTGGAGATGTTGTTGCTGTACTGATGAAATGCTTTGGAAGGCGTTTCTCTCATAGGTGATTGTGGCAATGAAGGAATGGATTCCTGGGCAACATAAAGAAACCATGACAAAGAAAAATAATTCACAAGCCCGGAAAGCAATTCTTGTTAAGACAAGAAGCTGAGCAGTATGACTGAAGAGGATGGGTGACCTGAGGGGCAGAGGGAGAGTCAGCAGTAAGTGCTGGGGGCTCATGCACCGCAGAAGCTGACCATGCTCTAAGGTGCACAGGGATAGAGAGCGGGTGATGGCAGCTGTGCCGCGTCCTTTCGAGGCCTTTTCCACAAAGCCATAATTCTGGAGAATATTCTGCTCTTACACTTTCTGGGACAATCCCCTTTCTAACTATATTAAAACCAGAAAAAGAAAAAACACACACACACTCACAATGCTGTCAGAAGAGCTAATATAATTTGTACAATGGAACAGTGTTTTTTGTTTAACCAAATAAGAACGCTGCAGCATCGTTTCTTGAGAGCTTATCTCCACTCTAAAATTCACATCTGTTAATCTCAGCCTTAATCAATTGGTGTAAATGTTACAGAAAGGGAAGGAGCCCCTGTCAACAAATGAATCATACTAACTTTTCTCTGAGGCTTCTCAGCTCTGATCCGGCTGCTGAAACAGTTGAGCTGAGGGGAAATCTCCAATAGCTTATTTACTTTATGGTACAGAGTAT	-	novel	NA	P-0064250-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	18	471	0	ENST00000262189.6:c.12775-635_13162del		p.X4259_splice	ENST00000262189	NM_170606.2	4259		52/59	0.228331375552292	2	FACETS	0.972	0.746	1	0.486	0.373	0.614	INDETERMINATE	1	TRUE	0	0.420799293976901	2		471	88	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38283681	38283681	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064250-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	31	527	0	ENST00000425967.3:c.797A>C	p.Glu266Ala	p.E266A	ENST00000425967	NM_001174067.1	266	gAg/gCg	7/19	1	2	FACETS	0.767	0.638	0.905	1	0.952	1	CLONAL	2	TRUE	1	0.420799293976901	2		527	96	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0064284-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	77	457	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.106754960840335	0	FACETS	1	0.95	1			1	INDETERMINATE	1	FALSE	0	0.288154650363392	0		457	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0064284-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	57	360	1	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.288154650363392	5	FACETS	1	0.945	1			1	CLONAL	2	FALSE	NA	0.288154650363392	5		361	240	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266713	198266713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776846119	NA	P-0064284-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	80	506	0	ENST00000335508.6:c.2219G>A	p.Gly740Glu	p.G740E	ENST00000335508	NM_012433.2	740	gGa/gAa	15/25	0.264625389795783	4	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	FALSE	2	0.288154650363392	4		506	332	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0064284-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	27	477	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	0.288154650363392	3	FACETS	0.567	0.451	0.7	0.284	0.225	0.35	SUBCLONAL	1	FALSE	1	0.288154650363392	3		477	378	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196855	108196855	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064284-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	97	546	0	ENST00000278616.4:c.6878T>C	p.Leu2293Pro	p.L2293P	ENST00000278616	NM_000051.3	2293	cTg/cCg	47/63	0.288154650363392	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	FALSE	0	0.288154650363392	2		546	318	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588594	28588594	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064284-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	16	482	0	ENST00000241453.7:c.2854G>C	p.Glu952Gln	p.E952Q	ENST00000241453	NM_004119.2	952	Gaa/Caa	23/24	0.288154650363392	0	FACETS	0.399	0.296	0.522			1	SUBCLONAL	1	FALSE	0	0.288154650363392	0		482	198	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0064306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	56	547	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	1	2	FACETS	0.947	0.81	1	0.947	0.81	1	CLONAL	1	TRUE	1	0.17	2		547	696	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262688	16262688	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	41	582	0	ENST00000375759.3:c.9953C>A	p.Ala3318Asp	p.A3318D	ENST00000375759	NM_015001.2	3318	gCc/gAc	11/15	1	2	FACETS	0.648	0.538	0.771	0.648	0.538	0.771	SUBCLONAL	1	TRUE	1	0.17	2		582	744	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94923045	94923045	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	39	426	0	ENST00000536441.1:c.423G>T	p.Trp141Cys	p.W141C	ENST00000536441	NM_144665.3	141	tgG/tgT	4/10	1	2	FACETS	0.925	0.766	1	0.925	0.766	1	CLONAL	1	TRUE	1	0.17	2		426	496	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664879	29664879	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060500342	NA	P-0064306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	41	505	0	ENST00000356175.3:c.6622T>C	p.Trp2208Arg	p.W2208R	ENST00000356175	NM_000267.3	2208	Tgg/Cgg	43/57	1	2	FACETS	0.937	0.78	1	0.937	0.78	1	CLONAL	1	TRUE	1	0.17	2		505	515	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204730	128204752	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCATAGTAGCTAGGCCTGGGC	GCCCATAGTAGCTAGGCCTGGGC	-	novel	NA	P-0064306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	47	735	0	ENST00000341105.2:c.689_711del	p.Arg230HisfsTer44	p.R230Hfs*44	ENST00000341105	NM_032638.4	230	cGCCCAGGCCTAGCTACTATGGGC/c	3/6	1	2	FACETS	0.61	0.513	0.717	0.61	0.513	0.717	SUBCLONAL	1	TRUE	1	0.17	2		735	907	SUCCESS
ATR	545	MSKCC	GRCh37	3	142232438	142232438	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	70	394	0	ENST00000350721.4:c.4546A>G	p.Ile1516Val	p.I1516V	ENST00000350721	NM_001184.3	1516	Att/Gtt	26/47	0.17289595642833	3	FACETS	1	0.972	1	0.729	0.636	0.83	CLONAL	1	TRUE	1	0.17	3		394	613	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604234	189604234	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	46	539	0	ENST00000264731.3:c.1401C>G	p.Asn467Lys	p.N467K	ENST00000264731	NM_003722.4	467	aaC/aaG	11/14	1	2	FACETS	0.797	0.67	0.938	0.797	0.67	0.938	CLONAL	1	TRUE	1	0.17	2		539	679	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056435	26056435	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs769566015	NA	P-0064306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	47	591	0	ENST00000343677.2:c.222G>C	p.Glu74Asp	p.E74D	ENST00000343677	NM_005319.3	74	gaG/gaC	1/1	1	2	FACETS	0.682	0.574	0.802	0.682	0.574	0.802	SUBCLONAL	1	TRUE	1	0.17	2		591	811	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064309-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	157	789	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.968	0.894	1	0.968	0.894	1	CLONAL	1	TRUE	1	0.656404908508195	2		789	494	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47594643	47594643	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	79	1027	2	ENST00000430070.2:c.1444C>A	p.Leu482Ile	p.L482I	ENST00000430070	NM_018095.4	482	Ctc/Atc	4/4	1	2	FACETS	0.816	0.72	0.919	0.816	0.72	0.919	CLONAL	1	TRUE	1	0.391136234240826	2		1029	495	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544689	65544689	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	29	979	0	ENST00000358664.4:c.237del	p.His79GlnfsTer91	p.H79Qfs*91	ENST00000358664	NM_002382.4	79	caC/ca	4/5	0.391136234240826	1	FACETS	0.28	0.224	0.343	0.28	0.224	0.343	SUBCLONAL	1	TRUE	0	0.391136234240826	1		979	426	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866399	42866399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138651919	NA	P-0064328-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	318	880	0	ENST00000398585.3:c.233C>T	p.Pro78Leu	p.P78L	ENST00000398585	NM_001135099.1	78	cCg/cTg	3/14	1	2	FACETS	0.942	0.896	0.989	0.942	0.896	0.989	CLONAL	1	TRUE	1	0.959012251301942	2		880	704	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622619	158622619	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064328-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	216	586	0	ENST00000263640.3:c.880T>C	p.Tyr294His	p.Y294H	ENST00000263640	NM_001105.4	294	Tat/Cat	8/11	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.959012251301942	2		586	448	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0064331-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	66	256	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.650184317710184	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.650184317710184	2		256	85	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332919	153332919	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs781123562	NA	P-0064331-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	14	492	2	ENST00000281708.4:c.37C>T	p.Arg13Ter	p.R13*	ENST00000281708	NM_033632.3	13	Cga/Tga	2/12	1	2	FACETS	0.161	0.116	0.215	0.161	0.116	0.215	SUBCLONAL	1	TRUE	1	0.650184317710184	2		494	268	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0064331-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	74	385	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.650184317710184	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.650184317710184	2		385	110	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266110	41266110	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064331-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	84	506	0	ENST00000349496.5:c.107A>C	p.His36Pro	p.H36P	ENST00000349496	NM_001904.3	36	cAt/cCt	3/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.650184317710184	2		506	225	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0064331-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	112	562	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.962	0.875	1	0.962	0.875	1	CLONAL	1	TRUE	1	0.650184317710184	2		562	358	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644856	67644856	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064331-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	34	553	0	ENST00000264010.4:c.124del	p.Gln42ArgfsTer20	p.Q42Rfs*20	ENST00000264010	NM_006565.3	41	Ccc/cc	3/12	0.642621988760882	1	FACETS	0.348	0.286	0.415	0.348	0.286	0.415	SUBCLONAL	1	TRUE	0	0.650184317710184	1		553	203	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644799	67644802	+	frameshift_variant	Frame_Shift_Del	DEL	AGAA	AGAA	-	novel	NA	P-0064331-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	43	547	0	ENST00000264010.4:c.67_70del	p.Lys23LeufsTer38	p.K23Lfs*38	ENST00000264010	NM_006565.3	22	AGAAag/ag	3/12	0.642621988760882	1	FACETS	0.463	0.392	0.539	0.463	0.392	0.539	SUBCLONAL	1	TRUE	0	0.650184317710184	1		547	193	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944491	40944491	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064331-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	35	514	0	ENST00000373198.4:c.2011G>T	p.Ala671Ser	p.A671S	ENST00000373198	NM_133170.3	671	Gcc/Tcc	12/32	1	2	FACETS	0.421	0.346	0.503	0.421	0.346	0.503	SUBCLONAL	1	TRUE	1	0.650184317710184	2		514	256	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249013	55249014	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATGGCC	novel	NA	P-0064356-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	24	939	0	ENST00000275493.2:c.2312_2313insTGGCCA	p.Asn771_Pro772insGlyHis	p.N771_P772insGH	ENST00000275493	NM_005228.3	771	aac/aATGGCCac	20/28	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		939	630	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0064404-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	29	624	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.192	0.153	0.237	0.192	0.153	0.237	SUBCLONAL	1	TRUE	1	0.45845342528366	2		625	658	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064404-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	115	342	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	0.95	0.86	1			1	INDETERMINATE	1	TRUE	NA	0.45845342528366	2		342	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0064404-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	252	607	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.459883109944507	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.45845342528366	1		607	759	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064404-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	147	414	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.459883109944507	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.45845342528366	1		414	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	135	766	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.401156691691942	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.401156691691942	1		767	490	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	58	369	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.763	0.658	0.876	0.763	0.658	0.876	SUBCLONAL	1	TRUE	1	0.401156691691942	2		373	379	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	48	293	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.906	0.772	1	0.906	0.772	1	CLONAL	1	TRUE	1	0.401156691691942	2		293	264	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	115	667	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.889	0.802	0.98	0.889	0.802	0.98	CLONAL	1	TRUE	1	0.401156691691942	2		668	645	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693003	89693003	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs786204900	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	65	323	0	ENST00000371953.3:c.491del	p.Lys164ArgfsTer3	p.K164Rfs*3	ENST00000371953	NM_000314.4	163	Aaa/aa	5/9	1	2	FACETS	0.991	0.865	1	0.991	0.865	1	CLONAL	1	TRUE	1	0.401156691691942	2		323	327	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	111	610	2	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.969	0.874	1	0.969	0.874	1	CLONAL	1	TRUE	1	0.401156691691942	2		612	571	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	53	277	0	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	0.401156691691942	1	FACETS	0.931	0.803	1	0.931	0.803	1	CLONAL	1	TRUE	0	0.401156691691942	1		277	227	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540040	187540040	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs116784674	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	112	512	0	ENST00000441802.2:c.7700G>A	p.Arg2567His	p.R2567H	ENST00000441802	NM_005245.3	2567	cGt/cAt	10/27	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.401156691691942	2		512	532	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	160	548	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.401156691691942	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.401156691691942	1		548	498	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523009	25523009	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	97	547	3	ENST00000264709.3:c.176del	p.Pro59ArgfsTer13	p.P59Rfs*13	ENST00000264709	NM_175629.2	59	cCg/cg	3/23	1	2	FACETS	0.928	0.83	1	0.928	0.83	1	CLONAL	1	TRUE	1	0.401156691691942	2		550	521	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022443	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	rs750318549	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	140	534	0	ENST00000375687.4:c.1933_1934del	p.Gly645TrpfsTer12	p.G645Wfs*12	ENST00000375687	NM_015338.5	643	GGg/g	13/13	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.401156691691942	2		534	608	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099165	157099166	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCC	rs770512547	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	68	538	0	ENST00000346085.5:c.121_123dup	p.Ser41dup	p.S41dup	ENST00000346085	NM_020732.3	41	-/TCC	1/20	0.401156691691942	1	FACETS	0.717	0.627	0.813	0.717	0.627	0.813	SUBCLONAL	1	TRUE	0	0.401156691691942	1		538	378	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243083	105243083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1396308032	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	124	532	0	ENST00000349310.3:c.200G>A	p.Arg67Gln	p.R67Q	ENST00000349310	NM_001014432.1	67	cGg/cAg	5/15	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.401156691691942	2		532	616	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579580	7579580	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781866	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	151	589	1	ENST00000269305.4:c.107C>T	p.Pro36Leu	p.P36L	ENST00000269305	NM_001126112.2	36	cCg/cTg	4/11	0.401156691691942	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.401156691691942	1		590	488	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044892	47044892	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	127	378	0	ENST00000377604.3:c.2218G>T	p.Glu740Ter	p.E740*	ENST00000377604	NM_001204468.1	740	Gag/Tag	20/24	1	1	FACETS	0.776	0.713	0.841	1	0.988	1	SUBCLONAL	2	TRUE	0	0.401156691691942	1		378	326	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184065	56184065	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	70	372	0	ENST00000399503.3:c.4270C>T	p.Gln1424Ter	p.Q1424*	ENST00000399503	NM_005921.1	1424	Caa/Taa	19/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.401156691691942	2		372	312	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781901	3781903	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs751071525	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	110	514	0	ENST00000262367.5:c.4764_4766del	p.Lys1588del	p.K1588del	ENST00000262367	NM_004380.2	1588	aaGAAc/aac	29/31	1	2	FACETS	0.916	0.825	1	0.916	0.825	1	CLONAL	1	TRUE	1	0.401156691691942	2		514	599	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741542	145741542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748212145	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	123	698	0	ENST00000428558.2:c.961G>A	p.Gly321Arg	p.G321R	ENST00000428558	NM_004260.3	321	Gga/Aga	5/22	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.401156691691942	2		698	587	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606273	93606273	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	91	555	0	ENST00000375746.1:c.98del	p.Gly33AlafsTer2	p.G33Afs*2	ENST00000375746	NM_001174167.1	31	caG/ca	2/14	0.324359351015606	3	FACETS	0.886	0.787	0.99	0.443	0.393	0.495	CLONAL	1	TRUE	1	0.401156691691942	3		555	615	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519505	137519506	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs780346130	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	98	502	14	ENST00000367739.4:c.1132_1133del	p.Ser378PhefsTer6	p.S378Ffs*6	ENST00000367739	NM_000416.2	378	AGt/t	7/7	0.401156691691942	1	FACETS	0.824	0.739	0.914	0.824	0.739	0.914	CLONAL	1	TRUE	0	0.401156691691942	1		516	474	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106917	27106917	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	125	681	0	ENST00000324856.7:c.6532del	p.Asp2178ThrfsTer22	p.D2178Tfs*22	ENST00000324856	NM_006015.4	2176	caG/ca	20/20	1	2	FACETS	0.908	0.824	0.998	0.908	0.824	0.998	CLONAL	1	TRUE	1	0.401156691691942	2		681	686	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285703	46285703	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	26	465	0	ENST00000334344.6:c.5061+2T>C		p.X1687_splice	ENST00000334344	NM_152641.2	1687			1	2	FACETS	0.279	0.22	0.346	0.279	0.22	0.346	SUBCLONAL	1	TRUE	1	0.401156691691942	2		465	465	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717719	89717720	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs780264945	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	74	322	0	ENST00000371953.3:c.750_751del	p.Cys250TrpfsTer2	p.C250Wfs*2	ENST00000371953	NM_000314.4	248	ccTGtg/cctg	7/9	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.401156691691942	2		322	357	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332000	81332000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543827901	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	76	446	0	ENST00000222390.5:c.2084G>A	p.Arg695His	p.R695H	ENST00000222390	NM_000601.4	695	cGt/cAt	18/18	1	2	FACETS	0.931	0.821	1	0.931	0.821	1	CLONAL	1	TRUE	1	0.401156691691942	2		446	407	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383271	31383271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753291521	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	144	471	0	ENST00000328111.2:c.1183G>A	p.Ala395Thr	p.A395T	ENST00000328111	NM_006892.3	395	Gca/Aca	11/23	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.401156691691942	2		471	632	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874914	151874914	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	133	491	1	ENST00000262189.6:c.7624del	p.Ser2542HisfsTer20	p.S2542Hfs*20	ENST00000262189	NM_170606.2	2542	Tca/ca	38/59	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.401156691691942	2		492	589	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082734	16082734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	54	295	0	ENST00000281043.3:c.548C>T	p.Ala183Val	p.A183V	ENST00000281043	NM_005378.4	183	gCc/gTc	2/3	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.401156691691942	2		295	260	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793272	242793272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765748069	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	114	546	0	ENST00000334409.5:c.805G>A	p.Asp269Asn	p.D269N	ENST00000334409	NM_005018.2	269	Gac/Aac	5/5	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.401156691691942	2		546	513	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593347	67593347	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	120	587	0	ENST00000274335.5:c.2093A>G	p.Tyr698Cys	p.Y698C	ENST00000274335		698	tAc/tGc	15/15	1	2	FACETS	0.989	0.896	1	0.989	0.896	1	CLONAL	1	TRUE	1	0.401156691691942	2		587	605	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123640	46123640	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	111	472	0	ENST00000334344.6:c.22del	p.Ala8ArgfsTer50	p.A8Rfs*50	ENST00000334344	NM_152641.2	7	aaG/aa	1/21	1	2	FACETS	0.992	0.895	1	0.992	0.895	1	CLONAL	1	TRUE	1	0.401156691691942	2		472	558	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436045	110436045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778993490	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	127	728	1	ENST00000375856.3:c.2356G>A	p.Ala786Thr	p.A786T	ENST00000375856	NM_003749.2	786	Gca/Aca	1/2	1	2	FACETS	0.976	0.886	1	0.976	0.886	1	CLONAL	1	TRUE	1	0.401156691691942	2		729	649	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557291	29557291	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	38	301	0	ENST00000356175.3:c.3004C>T	p.Leu1002Phe	p.L1002F	ENST00000356175	NM_000267.3	1002	Ctt/Ttt	23/57	1	2	FACETS	0.838	0.699	0.991	0.838	0.699	0.991	CLONAL	1	TRUE	1	0.401156691691942	2		301	226	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754825	29754825	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	121	572	0	ENST00000389048.3:c.1110G>T	p.Glu370Asp	p.E370D	ENST00000389048	NM_004304.4	370	gaG/gaT	4/29	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.401156691691942	2		572	573	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431010	181431011	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	45	636	0	ENST00000325404.1:c.867dup	p.Ser290GlnfsTer20	p.S290Qfs*20	ENST00000325404	NM_003106.3	288	gcc/gCcc	1/1	1	2	FACETS	0.361	0.302	0.425	0.361	0.302	0.425	SUBCLONAL	1	TRUE	1	0.401156691691942	2		636	622	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538967	187538967	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	161	543	0	ENST00000441802.2:c.8773G>T	p.Gly2925Trp	p.G2925W	ENST00000441802	NM_005245.3	2925	Ggg/Tgg	10/27	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.401156691691942	2		543	647	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048138	180048138	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064406-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	126	681	0	ENST00000261937.6:c.2135A>G	p.Tyr712Cys	p.Y712C	ENST00000261937	NM_182925.4	712	tAc/tGc	14/30	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.401156691691942	2		681	553	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064408-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	159	789	0				ENST00000310581	NM_198253.2	-/1132			0.479055486259339	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.471728524621835	3		789	361	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923060	44923060	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064408-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	364	229	0	ENST00000377967.4:c.1921C>T	p.Gln641Ter	p.Q641*	ENST00000377967	NM_021140.2	641	Cag/Tag	16/29	0.475184919775925	2	FACETS	1	0.993	1			1	CLONAL	3	TRUE	NA	0.471728524621835	2		229	472	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967255	134967255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751581569	NA	P-0064408-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	239	539	0	ENST00000398015.3:c.2594G>A	p.Arg865Gln	p.R865Q	ENST00000398015	NM_004441.4	865	cGg/cAg	14/16	0.471728524621835	5	FACETS	0.792	0.739	0.846	0.528	0.492	0.564	SUBCLONAL	2	TRUE	2	0.471728524621835	5		539	1093	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267361	198267361	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs754688962	NA	P-0064408-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	262	503	0	ENST00000335508.6:c.1996A>C	p.Lys666Gln	p.K666Q	ENST00000335508	NM_012433.2	666	Aag/Cag	14/25	0.479055486259339	3	FACETS	1	0.99	1	0.646	0.606	0.688	CLONAL	1	TRUE	1	0.471728524621835	3		503	1062	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265573	198265573	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064408-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	152	410	0	ENST00000335508.6:c.2584G>A	p.Glu862Lys	p.E862K	ENST00000335508	NM_012433.2	862	Gaa/Aaa	18/25	0.479055486259339	3	FACETS	0.963	0.881	1	0.482	0.44	0.524	CLONAL	1	TRUE	1	0.471728524621835	3		410	827	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77085411	77085411	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0064408-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	181	332	1	ENST00000356341.3:c.440-1G>A		p.X147_splice	ENST00000356341	NM_002576.4	147			0.152984629770242	2	FACETS	0.986	0.923	1	0.986	0.923	1	INDETERMINATE	2	TRUE	0	0.471728524621835	2		333	389	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532590	187532590	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064408-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	344	441	0	ENST00000441802.2:c.9803C>A	p.Ser3268Ter	p.S3268*	ENST00000441802	NM_005245.3	3268	tCa/tAa	14/27	0.479055486259339	2	FACETS	0.931	0.896	0.966	1	0.996	1	CLONAL	3	TRUE	0	0.471728524621835	2		441	522	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797300	135797300	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs118203402	NA	P-0064408-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	203	441	1	ENST00000298552.3:c.569G>A	p.Arg190His	p.R190H	ENST00000298552	NM_001162426.1	190	cGc/cAc	7/23	0.327983767025741	3	FACETS	0.755	0.703	0.809	0.755	0.703	0.809	SUBCLONAL	2	TRUE	1	0.471728524621835	3		442	704	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77937621	77937621	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064408-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	170	410	0	ENST00000361507.4:c.1097G>A	p.Trp366Ter	p.W366*	ENST00000361507	NM_080491.2	366	tGg/tAg	4/10	0.152984629770242	2	FACETS	0.885	0.824	0.947	0.885	0.824	0.947	INDETERMINATE	2	TRUE	0	0.471728524621835	2		410	407	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50763834	50763834	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064408-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	112	325	0	ENST00000307179.4:c.691A>T	p.Thr231Ser	p.T231S	ENST00000307179		231	Act/Tct	8/20	0.479055486259339	3	FACETS	0.892	0.803	0.985	0.446	0.401	0.493	CLONAL	1	TRUE	1	0.471728524621835	3		325	658	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966540	25966540	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064408-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	143	481	0	ENST00000435504.4:c.2666C>T	p.Ser889Phe	p.S889F	ENST00000435504		889	tCt/tTt	13/13	0.412149118092073	4	FACETS	0.906	0.825	0.991	0.302	0.275	0.331	CLONAL	1	TRUE	1	0.471728524621835	4		481	985	SUCCESS
ALB	213	MSKCC	GRCh37	4	74270839	74270839	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064408-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	27	349	1	ENST00000295897.4:c.86G>C	p.Ser29Thr	p.S29T	ENST00000295897	NM_000477.5	29	aGt/aCt	2/15	0.479055486259339	2	FACETS	0.231	0.183	0.286	0.115	0.091	0.143	SUBCLONAL	1	TRUE	0	0.471728524621835	2		350	496	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020772	26020772	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0064408-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	131	620	0	ENST00000357647.3:c.55A>T	p.Lys19Ter	p.K19*	ENST00000357647	NM_003529.2	19	Aaa/Taa	1/1	0.479055486259339	3	FACETS	0.855	0.776	0.938	0.427	0.388	0.469	CLONAL	1	TRUE	1	0.471728524621835	3		620	803	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0064429-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	197	511	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.211424397529053	5	FACETS	1	0.98	1	0.762	0.708	0.818	INDETERMINATE	2	TRUE	2	0.365215233555926	5		511	730	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0064429-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	261	753	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.365215233555926	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.365215233555926	2		753	695	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0064429-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	200	435	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	0.365215233555926	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	0	0.365215233555926	2		435	547	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861162	57861162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564027387	NA	P-0064429-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	333	587	0	ENST00000228682.2:c.959C>T	p.Thr320Met	p.T320M	ENST00000228682	NM_005269.2	320	aCg/aTg	9/12	0.365215233555926	4	FACETS	0.932	0.885	0.981	1	0.994	1	CLONAL	3	TRUE	2	0.365215233555926	4		587	890	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217906	2217906	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769883924	NA	P-0064429-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	65	609	3	ENST00000398665.3:c.2680G>A	p.Ala894Thr	p.A894T	ENST00000398665	NM_032482.2	894	Gcc/Acc	22/28	0.365215233555926	3	FACETS	0.618	0.535	0.708	0.309	0.267	0.354	SUBCLONAL	1	TRUE	1	0.365215233555926	3		612	681	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282202	38282202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064429-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	56	678	1	ENST00000425967.3:c.854G>A	p.Arg285Gln	p.R285Q	ENST00000425967	NM_001174067.1	285	cGg/cAg	8/19	0.214912043608229	4	FACETS	0.505	0.431	0.586	0.253	0.215	0.293	INDETERMINATE	1	TRUE	2	0.365215233555926	4		679	829	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416741	121416741	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064429-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	339	766	0	ENST00000257555.6:c.170T>C	p.Leu57Pro	p.L57P	ENST00000257555		57	cTg/cCg	1/10	0.338078225714322	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	0	0.365215233555926	3		766	699	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726868	61726868	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064429-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	82	314	0	ENST00000401558.2:c.570A>T	p.Lys190Asn	p.K190N	ENST00000401558	NM_003400.3	190	aaA/aaT	7/25	0.365215233555926	3	FACETS	0.978	0.864	1			1	CLONAL	1	TRUE	NA	0.365215233555926	3		314	543	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945360	54945360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064429-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	319	553	0	ENST00000312783.6:c.1066G>A	p.Ala356Thr	p.A356T	ENST00000312783	NM_198436.1	356	Gcc/Acc	10/10	0.365215233555926	7	FACETS	1	0.973	1	0.786	0.743	0.83	CLONAL	3	TRUE	3	0.365215233555926	7		553	1063	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0064502-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	160	457	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.207845522003121	3	FACETS	0.919	0.844	0.998	0.919	0.844	0.998	CLONAL	2	TRUE	1	0.234525282604919	3		457	829	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578538	7578538	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1131691037	NA	P-0064502-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	242	516	0	ENST00000269305.4:c.392A>T	p.Asn131Ile	p.N131I	ENST00000269305	NM_001126112.2	131	aAc/aTc	5/11	0.234525282604919	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	3	TRUE	1	0.234525282604919	4		516	821	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242287	98242287	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758585782	NA	P-0064502-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	48	535	0	ENST00000331920.6:c.1031G>A	p.Gly344Asp	p.G344D	ENST00000331920	NM_000264.3	344	gGt/gAt	7/24	1	2	FACETS	0.656	0.554	0.769	0.656	0.554	0.769	SUBCLONAL	1	TRUE	1	0.234525282604919	2		535	624	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141989	108141989	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1449057707	NA	P-0064502-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	48	388	0	ENST00000278616.4:c.2933C>T	p.Ser978Phe	p.S978F	ENST00000278616	NM_000051.3	978	tCt/tTt	20/63	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.234525282604919	2		388	328	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229653	5229653	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064502-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	85	462	3	ENST00000357368.4:c.2198A>G	p.Asn733Ser	p.N733S	ENST00000357368	NM_002850.3	733	aAc/aGc	15/38	0.234525282604919	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.234525282604919	1		465	491	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064504-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	80	789	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		789	454	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231335	5231335	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769069932	NA	P-0064517-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	34	422	1	ENST00000357368.4:c.2141G>A	p.Arg714His	p.R714H	ENST00000357368	NM_002850.3	714	cGc/cAc	14/38	0.3	1	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	0	0.27	1		423	204	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0064517-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	51	454	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.0458987845478775	3	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.27	3		454	310	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797357	135797357	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064517-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	45	422	0	ENST00000298552.3:c.512A>G	p.His171Arg	p.H171R	ENST00000298552	NM_001162426.1	171	cAc/cGc	7/23	0.3	1	FACETS	0.799	0.673	0.936	0.799	0.673	0.936	CLONAL	1	TRUE	0	0.27	1		422	361	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793432	18793432	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064517-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	25	367	0	ENST00000266497.5:c.4129C>A	p.Arg1377Ser	p.R1377S	ENST00000266497		1377	Cgt/Agt	30/31	0.169455679690385	5	FACETS	0.604	0.475	0.752	0.201	0.158	0.251	SUBCLONAL	1	TRUE	2	0.27	5		367	431	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864319	57864319	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064517-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	37	567	0	ENST00000228682.2:c.1796G>C	p.Gly599Ala	p.G599A	ENST00000228682	NM_005269.2	599	gGt/gCt	12/12	0.169455679690385	5	FACETS	1	0.877	1	0.36	0.297	0.429	CLONAL	1	TRUE	2	0.27	5		567	357	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588670	28588670	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064517-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	22	369	0	ENST00000241453.7:c.2778G>T	p.Trp926Cys	p.W926C	ENST00000241453	NM_004119.2	926	tgG/tgT	23/24	1	2	FACETS	0.458	0.354	0.578	0.458	0.354	0.578	SUBCLONAL	1	TRUE	1	0.27	2		369	356	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885970	59885970	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064517-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	94	428	0	ENST00000259008.2:c.776T>C	p.Ile259Thr	p.I259T	ENST00000259008	NM_032043.2	259	aTt/aCt	7/20	0.3	3	FACETS	1	0.978	1	0.711	0.634	0.792	CLONAL	1	TRUE	1	0.27	3		428	556	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143978	11143978	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064517-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	33	411	0	ENST00000358026.2:c.3559C>T	p.Gln1187Ter	p.Q1187*	ENST00000358026	NM_001128849.1	1187	Cag/Tag	26/36	0.3	1	FACETS	0.965	0.792	1	0.965	0.792	1	CLONAL	1	TRUE	0	0.27	1		411	219	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169993077	169993077	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0064517-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	35	211	0	ENST00000295797.4:c.705+2T>A		p.X235_splice	ENST00000295797	NM_002740.5	235			0.213922884919144	4	FACETS	0.927	0.762	1	0.464	0.381	0.557	CLONAL	1	TRUE	2	0.27	4		211	355	SUCCESS
ALB	213	MSKCC	GRCh37	4	74282072	74282072	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0064517-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	63	333	0	ENST00000295897.4:c.1289+2T>G		p.X430_splice	ENST00000295897	NM_000477.5	430			0.3	3	FACETS	1	0.968	1	0.706	0.614	0.806	CLONAL	1	TRUE	1	0.27	3		333	375	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197354	26197354	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064517-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	60	585	0	ENST00000356476.2:c.125A>T	p.Tyr42Phe	p.Y42F	ENST00000356476		42	tAc/tTc	1/1	0.3	3	FACETS	1	0.926	1	0.556	0.48	0.638	CLONAL	1	TRUE	1	0.27	3		585	454	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729817	41729818	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0064517-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	47	433	0	ENST00000242208.4:c.711_712delinsAA	p.Leu238Met	p.L238M	ENST00000242208	NM_002192.2	237	tcCCtg/tcAAtg	3/3	0.169455679690385	5	FACETS	1	0.939	1	0.412	0.348	0.482	CLONAL	1	TRUE	2	0.27	5		433	396	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730120	41730120	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064517-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	51	433	0	ENST00000242208.4:c.409C>A	p.His137Asn	p.H137N	ENST00000242208	NM_002192.2	137	Cac/Aac	3/3	0.169455679690385	5	FACETS	1	0.935	1	0.395	0.336	0.459	CLONAL	1	TRUE	2	0.27	5		433	448	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028038	69028038	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064517-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	68	409	0	ENST00000288368.4:c.3197A>T	p.Glu1066Val	p.E1066V	ENST00000288368	NM_024870.2	1066	gAg/gTg	26/40	0.224069458354669	5	FACETS	1	0.97	1	0.476	0.414	0.542	CLONAL	1	TRUE	2	0.27	5		409	496	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891451	76891451	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064517-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	36	195	0	ENST00000373344.5:c.4654G>T	p.Val1552Phe	p.V1552F	ENST00000373344	NM_000489.3	1552	Gtt/Ttt	16/35	0.182318061542577	2	FACETS	1	0.938	1			1	CLONAL	1	TRUE	NA	0.27	2		195	203	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262307	46262309	+	missense_variant	Missense_Mutation	TNP	CCG	CCG	TCC	novel	NA	P-0064517-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	59	443	0	ENST00000371998.3:c.891_893delinsTCC	p.Arg298Pro	p.R298P	ENST00000371998		297	atCCGa/atTCCa	9/23	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.27	2		443	417	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	190	789	0				ENST00000310581	NM_198253.2	-/1132			0.597179054904757	4	FACETS	1	0.983	1	0.402	0.372	0.433	CLONAL	1	TRUE	1	0.595706187579078	4		789	844	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88651892	88651892	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1589764265	NA	P-0064599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	116	291	0	ENST00000372037.3:c.239G>T	p.Gly80Val	p.G80V	ENST00000372037	NM_004329.2	80	gGa/gTa	5/13	0.597179054904757	3	FACETS	1	0.982	1	0.672	0.612	0.735	CLONAL	1	TRUE	1	0.595706187579078	3		291	376	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518527	69518527	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	67	528	0	ENST00000294312.3:c.118G>A	p.Asp40Asn	p.D40N	ENST00000294312	NM_005117.2	40	Gac/Aac	1/3	0.137561841760473	4	FACETS	0.692	0.602	0.788	0.346	0.301	0.394	INDETERMINATE	1	TRUE	2	0.595706187579078	4		528	519	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373989	118373989	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	30	521	0	ENST00000534358.1:c.7382G>A	p.Gly2461Glu	p.G2461E	ENST00000534358	NM_005933.3	2461	gGa/gAa	27/36	1	2	FACETS	0.179	0.144	0.22	0.179	0.144	0.22	SUBCLONAL	1	TRUE	1	0.595706187579078	2		521	562	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417160	417160	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	128	477	0	ENST00000399788.2:c.3390C>G	p.Phe1130Leu	p.F1130L	ENST00000399788	NM_001042603.1	1130	ttC/ttG	23/28	0.540919229413454	3	FACETS	0.947	0.861	1			1	CLONAL	1	TRUE	NA	0.595706187579078	3		477	589	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209274	133209274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs181570274	NA	P-0064599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	263	692	0	ENST00000320574.5:c.6112G>A	p.Glu2038Lys	p.E2038K	ENST00000320574	NM_006231.2	2038	Gag/Aag	44/49	0.56781544028864	4	FACETS	0.807	0.758	0.857	0.538	0.505	0.571	CLONAL	2	TRUE	1	0.595706187579078	4		692	873	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047527	49047527	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587778850	NA	P-0064599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	191	275	0	ENST00000267163.4:c.2520+1G>A		p.X840_splice	ENST00000267163	NM_000321.2	840			0.597179054904757	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.595706187579078	3		275	260	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66777418	66777418	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1238	103	580	0	ENST00000307102.5:c.784C>G	p.Pro262Ala	p.P262A	ENST00000307102	NM_002755.3	262	Ccc/Gcc	7/11	0.595706187579078	8	FACETS	0.719	0.641	0.802			1	SUBCLONAL	1	TRUE	NA	0.595706187579078	8		580	1341	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573991	7573991	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567542019	NA	P-0064599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	339	525	0	ENST00000269305.4:c.1036G>T	p.Glu346Ter	p.E346*	ENST00000269305	NM_001126112.2	346	Gag/Tag	10/11	0.597179054904757	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.595706187579078	2		525	497	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182123	99182123	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	40	445	0	ENST00000074304.5:c.2188G>C	p.Glu730Gln	p.E730Q	ENST00000074304	NM_001134224.1	730	Gag/Cag	21/26	0.597179054904757	4	FACETS	0.279	0.231	0.333	0.139	0.115	0.167	SUBCLONAL	1	TRUE	2	0.595706187579078	4		445	769	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180498	38180498	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	120	598	0	ENST00000396334.3:c.346C>A	p.Leu116Met	p.L116M	ENST00000396334	NM_002468.4	116	Ctg/Atg	1/5	0.597179054904757	3	FACETS	0.695	0.628	0.766	0.348	0.314	0.383	SUBCLONAL	1	TRUE	1	0.595706187579078	3		598	752	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808880	1808880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755526507	NA	P-0064599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	163	790	0	ENST00000260795.2:c.2312C>T	p.Ser771Phe	p.S771F	ENST00000260795		771	tCc/tTc	17/17	0.35413068165924	2	FACETS	0.756	0.695	0.819	0.378	0.347	0.41	INDETERMINATE	1	TRUE	0	0.595706187579078	2		790	724	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637208	176637208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	165	615	0	ENST00000439151.2:c.1808C>T	p.Ser603Phe	p.S603F	ENST00000439151	NM_022455.4	603	tCt/tTt	5/23	0.597179054904757	2	FACETS	0.866	0.798	0.936	0.433	0.399	0.468	CLONAL	1	TRUE	0	0.595706187579078	2		615	640	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673000	30673000	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	119	769	0	ENST00000376406.3:c.3960G>C	p.Lys1320Asn	p.K1320N	ENST00000376406	NM_014641.2	1320	aaG/aaC	10/15	0.432060443592719	3	FACETS	0.603	0.544	0.666	0.201	0.181	0.222	SUBCLONAL	1	TRUE	0	0.595706187579078	3		769	860	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675671	30675671	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	103	517	0	ENST00000376406.3:c.2685G>C	p.Glu895Asp	p.E895D	ENST00000376406	NM_014641.2	895	gaG/gaC	8/15	0.432060443592719	3	FACETS	0.709	0.635	0.787	0.236	0.211	0.263	SUBCLONAL	1	TRUE	0	0.595706187579078	3		517	633	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0064602-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	216	338	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		338	550	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064631-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	17	789	0				ENST00000310581	NM_198253.2	-/1132			0.283229644440628	1	FACETS	0.597	0.45	0.767	0.597	0.45	0.767	SUBCLONAL	1	TRUE	0	0.371311830142436	1		789	125	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149794	202149794	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064631-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	69	541	0	ENST00000358485.4:c.1235A>G	p.Lys412Arg	p.K412R	ENST00000358485	NM_001080125.1	412	aAa/aGa	8/9	0.161315375054156	4	FACETS	1	0.963	1	0.64	0.56	0.726	INDETERMINATE	1	TRUE	2	0.371311830142436	4		541	398	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413133	139413134	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064631-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	121	506	0	ENST00000277541.6:c.1008dup	p.Asp337Ter	p.D337*	ENST00000277541	NM_017617.3	336	-/T	6/34	0.371311830142436	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.371311830142436	2		506	287	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10776650	10776650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064631-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	68	434	0	ENST00000361367.2:c.290C>T	p.Ala97Val	p.A97V	ENST00000361367	NM_014633.3	97	gCt/gTt	3/25	0.169140415245729	5	FACETS	1	0.973	1	0.495	0.433	0.562	INDETERMINATE	1	TRUE	2	0.371311830142436	5		434	384	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576835	67576835	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0064631-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	47	298	0	ENST00000274335.5:c.916+1G>T		p.X306_splice	ENST00000274335		306			0.169140415245729	5	FACETS	1	0.962	1	0.496	0.421	0.577	INDETERMINATE	1	TRUE	2	0.371311830142436	5		298	265	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696688	47696688	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519971	NA	P-0064653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	269	243	0	ENST00000347630.2:c.260A>G	p.Tyr87Cys	p.Y87C	ENST00000347630	NM_001007230.1	87	tAc/tGc	5/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.751138599277424	2		243	679	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0064672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	32	612	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.209493622252034	5	FACETS	0.951	0.778	1	0.476	0.389	0.572	CLONAL	2	FALSE	1	0.209493622252034	5		612	211	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0064682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	17	457	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.365	0.272	0.476	0.365	0.272	0.476	SUBCLONAL	1	TRUE	1	0.282289720951933	2		457	330	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923138	48923138	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	13	191	0	ENST00000267163.4:c.586A>G	p.Ile196Val	p.I196V	ENST00000267163	NM_000321.2	196	Atc/Gtc	6/27	1	2	FACETS	0.774	0.557	1	0.774	0.557	1	CLONAL	1	TRUE	1	0.282289720951933	2		191	119	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0064684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	20	256	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.376175066898919	3	FACETS	1	0.924	1	0.747	0.59	0.918	CLONAL	1	TRUE	1	0.49934727262233	3		256	67	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224384	36224384	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs868232650	NA	P-0064684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	120	582	0	ENST00000222270.7:c.6934C>G	p.Gln2312Glu	p.Q2312E	ENST00000222270	NM_014727.1	2312	Cag/Gag	28/37	NA	2	FACETS	0.756	0.684	0.831			1	INDETERMINATE	1	TRUE	NA	0.49934727262233	2		582	636	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216566	108216566	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs876658958	NA	P-0064684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	35	336	0	ENST00000278616.4:c.8515T>A	p.Phe2839Ile	p.F2839I	ENST00000278616	NM_000051.3	2839	Ttc/Atc	58/63	0.49934727262233	2	FACETS	0.916	0.762	1	0.458	0.381	0.542	CLONAL	1	TRUE	0	0.49934727262233	2		336	153	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256583	16256583	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0064684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	85	493	0	ENST00000375759.3:c.3848C>G	p.Ser1283Ter	p.S1283*	ENST00000375759	NM_015001.2	1283	tCa/tGa	11/15	1	2	FACETS	0.765	0.679	0.856	0.765	0.679	0.856	SUBCLONAL	1	TRUE	1	0.49934727262233	2		493	445	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658304	18658304	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	29	365	0	ENST00000266497.5:c.3109G>C	p.Asp1037His	p.D1037H	ENST00000266497		1037	Gat/Cat	22/31	0.463438262207539	1	FACETS	0.333	0.268	0.406	0.333	0.268	0.406	SUBCLONAL	1	TRUE	0	0.49934727262233	1		365	262	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131627	2131627	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	109	456	0	ENST00000219476.3:c.3642C>G	p.Asn1214Lys	p.N1214K	ENST00000219476	NM_000548.3	1214	aaC/aaG	31/42	0.324949629320436	3	FACETS	0.823	0.74	0.911	0.411	0.37	0.456	CLONAL	1	TRUE	1	0.49934727262233	3		456	663	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868120	56868120	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	117	456	0	ENST00000308159.5:c.1618G>C	p.Glu540Gln	p.E540Q	ENST00000308159	NM_014669.4	540	Gag/Cag	14/22	0.426164953588233	2	FACETS	0.855	0.774	0.94	0.428	0.387	0.47	CLONAL	1	TRUE	0	0.49934727262233	2		456	548	SUCCESS
ALK	238	MSKCC	GRCh37	2	29420447	29420447	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	107	410	0	ENST00000389048.3:c.4034G>A	p.Gly1345Glu	p.G1345E	ENST00000389048	NM_004304.4	1345	gGa/gAa	27/29	0.491733443499107	3	FACETS	0.884	0.794	0.978	0.442	0.397	0.489	CLONAL	1	TRUE	1	0.49934727262233	3		410	606	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022919	31022919	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	92	497	0	ENST00000375687.4:c.2404G>A	p.Glu802Lys	p.E802K	ENST00000375687	NM_015338.5	802	Gag/Aag	13/13	0.285476606775611	4	FACETS	0.747	0.663	0.836	0.373	0.331	0.418	INDETERMINATE	1	TRUE	2	0.49934727262233	4		497	740	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023612	31023612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	114	467	0	ENST00000375687.4:c.3097G>A	p.Glu1033Lys	p.E1033K	ENST00000375687	NM_015338.5	1033	Gag/Aag	13/13	0.285476606775611	4	FACETS	0.944	0.851	1	0.472	0.425	0.522	INDETERMINATE	1	TRUE	2	0.49934727262233	4		467	725	SUCCESS
APC	324	MSKCC	GRCh37	5	112175986	112175986	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	37	407	0	ENST00000257430.4:c.4695T>A	p.Asp1565Glu	p.D1565E	ENST00000257430	NM_000038.5	1565	gaT/gaA	16/16	0.161863673351363	3	FACETS	0.531	0.438	0.633	0.177	0.146	0.211	INDETERMINATE	1	TRUE	0	0.49934727262233	3		407	349	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778071	27778071	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	154	646	0	ENST00000369163.2:c.220G>A	p.Glu74Lys	p.E74K	ENST00000369163	NM_003536.2	74	Gag/Aag	1/1	0.343364164980566	4	FACETS	0.9	0.822	0.981	0.45	0.411	0.491	CLONAL	1	TRUE	2	0.49934727262233	4		646	1028	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231868	36231870	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	novel	NA	P-0064684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	108	447	0	ENST00000300305.3:c.514_516del	p.Ser172del	p.S172del	ENST00000300305		172	AGC/-	5/8	0.323127472803995	3	FACETS	0.927	0.834	1	0.464	0.417	0.513	CLONAL	1	TRUE	1	0.49934727262233	3		447	583	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	27	789	0				ENST00000310581	NM_198253.2	-/1132			0.151393024130913	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.151393024130913	1		789	229	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0064685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	72	592	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	0.151393024130913	1	FACETS	0.781	0.683	0.886	1	0.976	1	SUBCLONAL	2	TRUE	0	0.151393024130913	1		592	563	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170695	7170695	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	63	575	0	ENST00000302850.5:c.1336C>T	p.Leu446Phe	p.L446F	ENST00000302850	NM_000208.2	446	Ctc/Ttc	6/22	0.151393024130913	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.151393024130913	1		575	520	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891519	76891519	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	112	204	0	ENST00000373344.5:c.4586C>A	p.Thr1529Asn	p.T1529N	ENST00000373344	NM_000489.3	1529	aCc/aAc	16/35	0.651864422539651	2	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.707600327446551	2		204	261	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221603	2221603	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	94	629	0	ENST00000326181.6:c.472T>G	p.Ser158Ala	p.S158A	ENST00000326181	NM_032271.2	158	Tca/Gca	7/21	0.414107412624835	4	FACETS	1	0.923	1	0.519	0.464	0.577	INDETERMINATE	1	TRUE	2	0.707600327446551	4		629	437	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593596	55593646	+	inframe_deletion	In_Frame_Del	DEL	AGTACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACAT	AGTACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACAT	-	novel	NA	P-0064686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	219	578	0	ENST00000288135.5:c.1664_1714del	p.Val555_Ile571del	p.V555_I571del	ENST00000288135	NM_000222.2	554	gaAGTACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATa/gaa	11/21	0.707600327446551	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.707600327446551	2		578	301	SUCCESS
PHF6	84295	MSKCC	GRCh37	X	133551265	133551266	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0064687-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	50	344	0	ENST00000332070.3:c.902dup	p.Tyr301Ter	p.Y301*	ENST00000332070	NM_032458.2	301	tac/tAac	9/10	0.27272499465939	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.27272499465939	1		344	261	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0064688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	291	513	0	ENST00000269305.4:c.375+1del		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.72843110738553	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.72843110738553	2		513	357	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907693	76907700	+	frameshift_variant	Frame_Shift_Del	DEL	TCAGTTTA	TCAGTTTA	-	novel	NA	P-0064688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	41	467	0	ENST00000373344.5:c.4461_4468del	p.Asp1487GlufsTer9	p.D1487Efs*9	ENST00000373344	NM_000489.3	1487	gaTAAACTGAga/gaga	15/35	0.72843110738553	1	FACETS	0.445	0.376	0.518	0.445	0.376	0.518	SUBCLONAL	1	TRUE	0	0.72843110738553	1		467	161	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0064697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	16	393	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.701	0.517	0.921	0.701	0.517	0.921	CLONAL	1	TRUE	1	0.14	2		393	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0064697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	25	692	0	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			1	2	FACETS	0.882	0.694	1	0.882	0.694	1	CLONAL	1	TRUE	1	0.14	2		692	405	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230472998	230472998	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	21	683	0	ENST00000391860.1:c.586G>A	p.Gly196Ser	p.G196S	ENST00000391860	NM_001258311.1	196	Ggc/Agc	4/7	1	2	FACETS	0.769	0.591	0.977	0.769	0.591	0.977	CLONAL	1	TRUE	1	0.14	2		683	390	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180318	27180318	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	46	632	0	ENST00000380036.4:c.982G>T	p.Gly328Ter	p.G328*	ENST00000380036	NM_000459.3	328	Gga/Tga	7/23	1	2	FACETS	0.383	0.322	0.452	0.383	0.322	0.452	SUBCLONAL	1	FALSE	1	0.284283257628032	2		632	844	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440346	52440351	+	inframe_deletion	In_Frame_Del	DEL	CGGGCA	CGGGCA	-	novel	NA	P-0064699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	83	817	0	ENST00000460680.1:c.701_706del	p.Val234_Pro235del	p.V234_P235del	ENST00000460680	NM_004656.3	234	gTGCCCGac/gac	9/17	1	2	FACETS	0.611	0.538	0.69	0.611	0.538	0.69	SUBCLONAL	1	FALSE	1	0.284283257628032	2		817	955	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641167	117641167	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	50	741	0	ENST00000368508.3:c.5804A>G	p.Glu1935Gly	p.E1935G	ENST00000368508	NM_002944.2	1935	gAa/gGa	36/43	1	2	FACETS	0.687	0.583	0.801	0.687	0.583	0.801	SUBCLONAL	1	FALSE	1	0.284283257628032	2		741	512	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	234	342	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.77798586443691	3	FACETS	0.926	0.878	0.974	0.926	0.878	0.974	CLONAL	2	TRUE	1	0.86299466345922	3		342	419	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78865562	78865562	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	268	536	0	ENST00000306801.3:c.2026A>G	p.Ser676Gly	p.S676G	ENST00000306801	NM_020761.2	676	Agc/Ggc	18/34	1	2	FACETS	0.899	0.848	0.95	0.899	0.848	0.95	CLONAL	1	TRUE	1	0.86299466345922	2		536	691	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385066	31385066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1037395724	NA	P-0064704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	291	630	0	ENST00000328111.2:c.1451G>A	p.Gly484Asp	p.G484D	ENST00000328111	NM_006892.3	484	gGc/gAc	14/23	1	2	FACETS	0.95	0.899	1	0.95	0.899	1	CLONAL	1	TRUE	1	0.86299466345922	2		630	710	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730335	133730335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	302	760	0	ENST00000318560.5:c.401G>A	p.Arg134His	p.R134H	ENST00000318560	NM_005157.4	134	cGc/cAc	3/11	0.49257718815646	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.512072033937411	3		760	711	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0064726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	111	350	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.447884525616001	3	FACETS	1	0.974	1	0.769	0.706	0.832	CLONAL	2	TRUE	0	0.509863083838102	3		350	237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0064726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	170	770	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	0.416469174041156	2	FACETS	1	0.989	1	0.708	0.657	0.76	CLONAL	1	TRUE	0	0.509863083838102	2		770	471	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459758	149459758	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1029057991	NA	P-0064726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	240	810	0	ENST00000286301.3:c.449G>A	p.Arg150His	p.R150H	ENST00000286301	NM_005211.3	150	cGc/cAc	4/22	0.437087110246244	3	FACETS	0.926	0.87	0.982	0.926	0.87	0.982	CLONAL	2	TRUE	1	0.509863083838102	3		810	638	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933904	39933904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	129	396	0	ENST00000378444.4:c.695C>T	p.Pro232Leu	p.P232L	ENST00000378444	NM_001123385.1	232	cCg/cTg	4/15	0.220812350932115	2	FACETS	0.894	0.826	0.963			1	INDETERMINATE	2	TRUE	NA	0.509863083838102	2		396	283	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971140	21971140	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	87	771	0	ENST00000304494.5:c.218C>G	p.Ala73Gly	p.A73G	ENST00000304494	NM_000077.4	73	gCc/gGc	2/3	0.509863083838102	1	FACETS	0.764	0.682	0.849	0.764	0.682	0.849	SUBCLONAL	1	TRUE	0	0.509863083838102	1		771	333	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971147	21971183	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCAC	TGGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCAC	-	novel	NA	P-0064726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	78	781	0	ENST00000304494.5:c.175_211del	p.Val59ThrfsTer75	p.V59Tfs*75	ENST00000304494	NM_000077.4	59	GTGGCGGAGCTGCTGCTGCTCCACGGCGCGGAGCCCAac/ac	2/3	0.509863083838102	1	FACETS	0.678	0.601	0.76	0.678	0.601	0.76	SUBCLONAL	1	TRUE	0	0.509863083838102	1		781	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0064742-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	135	342	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.258132923733791	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.258132923733791	2		342	501	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0064742-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	164	345	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.258132923733791	3	FACETS	0.927	0.857	0.999	0.927	0.857	0.999	CLONAL	3	TRUE	0	0.258132923733791	3		345	516	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626964	158626964	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064742-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	76	358	0	ENST00000263640.3:c.706A>T	p.Ile236Phe	p.I236F	ENST00000263640	NM_001105.4	236	Atc/Ttc	7/11	0.258132923733791	3	FACETS	1	0.906	1	0.519	0.455	0.588	CLONAL	1	TRUE	1	0.258132923733791	3		358	640	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983514	90983514	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0064742-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	63	226	0	ENST00000265433.3:c.589del	p.Tyr197ThrfsTer34	p.Y197Tfs*34	ENST00000265433	NM_002485.4	197	Tac/ac	6/16	0.258132923733791	5	FACETS	1	0.97	1	0.49	0.424	0.56	CLONAL	1	TRUE	2	0.258132923733791	5		226	461	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624296	89624296	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs786201995	NA	P-0064764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	20	375	0	ENST00000371953.3:c.70G>C	p.Asp24His	p.D24H	ENST00000371953	NM_000314.4	24	Gac/Cac	1/9	0.710540733033012	1	FACETS	0.214	0.164	0.271	0.214	0.164	0.271	SUBCLONAL	1	TRUE	0	0.710540733033012	1		375	170	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155200	108155200	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs863224566	NA	P-0064764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	67	377	0	ENST00000278616.4:c.3993G>C	p.Gln1331His	p.Q1331H	ENST00000278616	NM_000051.3	1331	caG/caC	26/63	0.710540733033012	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.710540733033012	1		377	112	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138054	2138054	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	44	641	0	ENST00000219476.3:c.5074G>T	p.Glu1692Ter	p.E1692*	ENST00000219476	NM_000548.3	1692	Gag/Tag	40/42	0.710540733033012	1	FACETS	0.262	0.22	0.307	0.262	0.22	0.307	SUBCLONAL	1	TRUE	0	0.710540733033012	1		641	305	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788575	3788576	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	22	361	0	ENST00000262367.5:c.4378dup	p.Tyr1460LeufsTer19	p.Y1460Lfs*19	ENST00000262367	NM_004380.2	1460	tat/tTat	26/31	0.710540733033012	1	FACETS	0.226	0.176	0.283	0.226	0.176	0.283	SUBCLONAL	1	TRUE	0	0.710540733033012	1		361	177	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203436	NA	P-0064764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	10	615	0	ENST00000269305.4:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269305	NM_001126112.2	163	Tac/Cac	5/11	0.710540733033012	1	FACETS	0.057	0.038	0.082	0.057	0.038	0.082	SUBCLONAL	1	TRUE	0	0.710540733033012	1		615	316	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039441	49039441	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	121	423	0	ENST00000267163.4:c.2426del	p.Leu809ArgfsTer17	p.L809Rfs*17	ENST00000267163	NM_000321.2	809	cTg/cg	23/27	0.710540733033012	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.710540733033012	1		423	187	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0064766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	137	70	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.753943208584548	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.753943208584548	1		70	222	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180984	108180984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	113	100	0	ENST00000278616.4:c.5860G>A	p.Ala1954Thr	p.A1954T	ENST00000278616	NM_000051.3	1954	Gct/Act	39/63	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.753943208584548	2		100	266	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459506	40459506	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	311	53	0	ENST00000345506.4:c.1767G>T	p.Trp589Cys	p.W589C	ENST00000345506	NM_003152.3	589	tgG/tgT	15/20	0.753943208584548	2	FACETS	0.987	0.952	1	0.987	0.952	1	CLONAL	2	TRUE	0	0.753943208584548	2		53	418	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180308	27180308	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	125	70	0	ENST00000380036.4:c.972T>A	p.Asp324Glu	p.D324E	ENST00000380036	NM_000459.3	324	gaT/gaA	7/23	1	2	FACETS	0.749	0.682	0.817	0.749	0.682	0.817	SUBCLONAL	1	TRUE	1	0.753943208584548	2		70	443	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128246863	128246863	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0064766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	140	94	0	ENST00000265960.3:c.1067-1G>A		p.X356_splice	ENST00000265960	NM_001006617.1	356			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.753943208584548	2		94	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7590694	7590694	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0064775-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	212	472	0	ENST00000269305.4:c.-29+1G>T		p.X10_splice	ENST00000269305	NM_001126112.2	10			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		472	383	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0064776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	400	393	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.653788641127581	4	FACETS	0.936	0.898	0.973	0.936	0.898	0.973	CLONAL	3	TRUE	1	0.653788641127581	4		393	721	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0064776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	247	571	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.653788641127581	1	FACETS	0.989	0.936	1	0.989	0.936	1	CLONAL	1	TRUE	0	0.653788641127581	1		572	514	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267371	198267371	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs778467242	NA	P-0064776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	229	561	0	ENST00000335508.6:c.1986C>A	p.His662Gln	p.H662Q	ENST00000335508	NM_012433.2	662	caC/caA	14/25	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.653788641127581	2		561	687	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922782	44922783	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0064776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	238	285	0	ENST00000377967.4:c.1644_1645dup	p.Arg549ThrfsTer45	p.R549Tfs*45	ENST00000377967	NM_021140.2	548	acc/acCAc	16/29	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.653788641127581	1		285	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578491	7578491	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1567553924	NA	P-0064777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	382	761	0	ENST00000269305.4:c.439del	p.Val147LeufsTer23	p.V147Lfs*23	ENST00000269305	NM_001126112.2	147	Gtt/tt	5/11	0.373629084415554	4	FACETS	0.967	0.926	1	0.967	0.926	1	CLONAL	4	TRUE	0	0.375396231851193	4		761	724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578440	7578440	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs879254249	NA	P-0064777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	14	785	0	ENST00000269305.4:c.490A>G	p.Lys164Glu	p.K164E	ENST00000269305	NM_001126112.2	164	Aag/Gag	5/11	0.373629084415554	4	FACETS	0.15	0.107	0.202	0.037	0.026	0.051	SUBCLONAL	1	TRUE	0	0.375396231851193	4		785	684	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95556899	95556899	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	128	349	0	ENST00000393063.1:c.5705C>G	p.Ser1902Cys	p.S1902C	ENST00000393063	NM_030621.3	1902	tCt/tGt	28/28	0.343900903924281	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.375396231851193	2		349	292	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7119581	7119581	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	63	531	0	ENST00000302850.5:c.3673G>T	p.Val1225Phe	p.V1225F	ENST00000302850	NM_000208.2	1225	Gtc/Ttc	21/22	1	2	FACETS	0.603	0.521	0.691	0.603	0.521	0.691	SUBCLONAL	1	TRUE	1	0.375396231851193	2		531	557	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220449	123220449	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	54	479	0	ENST00000218089.9:c.3106G>C	p.Asp1036His	p.D1036H	ENST00000218089	NM_001042749.1	1036	Gat/Cat	30/35	0.317562299744994	4	FACETS	0.741	0.633	0.859	0.371	0.316	0.43	SUBCLONAL	1	TRUE	2	0.375396231851193	4		479	534	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849260	76849260	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	95	606	0	ENST00000373344.5:c.6016G>T	p.Val2006Phe	p.V2006F	ENST00000373344	NM_000489.3	2006	Gtt/Ttt	26/35	NA	2	FACETS	1	0.927	1			1	INDETERMINATE	1	TRUE	NA	0.449814727150246	2		606	405	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064780-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	91	342	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.301079444786744	4	FACETS	0.898	0.803	0.999	0.898	0.803	0.999	CLONAL	2	TRUE	2	0.335776236981458	4		342	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0064780-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	136	431	0	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.330758070219151	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	0	0.335776236981458	2		431	397	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974760	21974762	+	frameshift_variant	Frame_Shift_Del	DEL	CCC	CCC	TA	novel	NA	P-0064780-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	125	597	0	ENST00000304494.5:c.65_67delinsTA	p.Arg22LeufsTer4	p.R22Lfs*4	ENST00000304494	NM_000077.4	22	cGGGgt/cTAgt	1/3	0.310027710814305	2	FACETS	0.856	0.781	0.934	0.856	0.781	0.934	CLONAL	2	TRUE	0	0.335776236981458	2		597	435	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	102	690	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.3	2		691	666	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	83	671	3	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.3	2		674	543	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	57	482	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.898	0.773	1	0.898	0.773	1	CLONAL	1	TRUE	1	0.3	2		482	423	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007620	45007620	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs111947448	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	35	466	0	ENST00000558401.1:c.68-1G>T		p.X23_splice	ENST00000558401	NM_004048.2	23			1	2	FACETS	0.508	0.416	0.612	0.508	0.416	0.612	SUBCLONAL	1	TRUE	1	0.3	2		466	459	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760106	133760106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2229071	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	74	549	0	ENST00000318560.5:c.2429C>T	p.Pro810Leu	p.P810L	ENST00000318560	NM_005157.4	810	cCg/cTg	11/11	1	2	FACETS	0.862	0.756	0.977	0.862	0.756	0.977	CLONAL	1	TRUE	1	0.3	2		549	572	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	104	692	3	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.952	0.853	1	0.952	0.853	1	CLONAL	1	TRUE	1	0.3	2		695	728	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128016978	128016978	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs4150521	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	79	557	1	ENST00000285398.2:c.2111C>T	p.Ser704Leu	p.S704L	ENST00000285398	NM_000122.1	704	tCg/tTg	14/15	1	2	FACETS	0.942	0.83	1	0.942	0.83	1	CLONAL	1	TRUE	1	0.3	2		558	559	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088788	27088788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	62	581	0	ENST00000324856.7:c.2402del	p.Gly801ValfsTer32	p.G801Vfs*32	ENST00000324856	NM_006015.4	799	caG/ca	7/20	1	2	FACETS	0.698	0.603	0.802	0.698	0.603	0.802	SUBCLONAL	1	TRUE	1	0.3	2		581	592	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131354	202131354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	55	544	0	ENST00000358485.4:c.322C>T	p.Gln108Ter	p.Q108*	ENST00000358485	NM_001080125.1	108	Cag/Tag	2/9	1	2	FACETS	0.733	0.628	0.848	0.733	0.628	0.848	SUBCLONAL	1	TRUE	1	0.3	2		544	500	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521114	187521114	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760053140	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	81	562	0	ENST00000441802.2:c.12041C>T	p.Thr4014Met	p.T4014M	ENST00000441802	NM_005245.3	4014	aCg/aTg	22/27	1	2	FACETS	0.831	0.732	0.936	0.831	0.732	0.936	CLONAL	1	TRUE	1	0.3	2		562	650	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907683	111907683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146318804	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	84	497	0	ENST00000393256.3:c.457C>T	p.Arg153Trp	p.R153W	ENST00000393256	NM_006538.4	153	Cgg/Tgg	3/4	1	2	FACETS	0.941	0.832	1	0.941	0.832	1	CLONAL	1	TRUE	1	0.3	2		497	595	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850704	63850705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	68	567	0	ENST00000279873.7:c.1489dup	p.Ile497AsnfsTer31	p.I497Nfs*31	ENST00000279873	NM_032199.2	494	-/A	10/10	1	2	FACETS	0.786	0.684	0.896	0.786	0.684	0.896	SUBCLONAL	1	TRUE	1	0.3	2		567	577	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200338	138200338	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753284576	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	120	673	1	ENST00000237289.4:c.1756G>A	p.Ala586Thr	p.A586T	ENST00000237289	NM_001270507.1	586	Gcc/Acc	7/9	1	2	FACETS	0.904	0.816	0.997	0.904	0.816	0.997	CLONAL	1	TRUE	1	0.3	2		674	885	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168682	32168682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs935064991	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	101	542	0	ENST00000375023.3:c.4241C>T	p.Ala1414Val	p.A1414V	ENST00000375023	NM_004557.3	1414	gCg/gTg	23/30	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.3	2		542	629	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112892380	112892380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	56	392	0	ENST00000351677.2:c.538G>A	p.Asp180Asn	p.D180N	ENST00000351677	NM_002834.3	180	Gac/Aac	5/16	1	2	FACETS	0.975	0.838	1	0.975	0.838	1	CLONAL	1	TRUE	1	0.3	2		392	383	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434182	12434182	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776687	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	46	501	1	ENST00000287820.6:c.556del	p.Ser186ValfsTer47	p.S186Vfs*47	ENST00000287820	NM_015869.4	184	Aaa/aa	4/7	0.301050038406521	2	FACETS	0.674	0.568	0.791	0.337	0.284	0.396	SUBCLONAL	1	TRUE	0	0.3	2		502	455	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223858	36223858	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	99	795	1	ENST00000222270.7:c.6413del	p.Pro2138ArgfsTer15	p.P2138Rfs*15	ENST00000222270	NM_014727.1	2136	ctC/ct	28/37	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.3	2		796	658	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380350	14380350	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	51	552	0	ENST00000256196.4:c.67G>T	p.Gly23Cys	p.G23C	ENST00000256196		23	Ggc/Tgc	1/6	1	2	FACETS	0.746	0.635	0.867	0.746	0.635	0.867	SUBCLONAL	1	TRUE	1	0.3	2		552	456	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609379	39609379	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749775725	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	63	407	1	ENST00000262039.4:c.1681C>T	p.Arg561Cys	p.R561C	ENST00000262039	NM_002647.2	561	Cgc/Tgc	15/25	1	2	FACETS	0.785	0.68	0.899	0.785	0.68	0.899	SUBCLONAL	1	TRUE	1	0.3	2		408	535	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235410	235410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258201485	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	100	536	0	ENST00000264932.6:c.1216G>A	p.Val406Met	p.V406M	ENST00000264932	NM_004168.2	406	Gtg/Atg	9/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.3	2		536	530	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399366	139399366	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	15	614	0	ENST00000277541.6:c.4777C>A	p.Leu1593Met	p.L1593M	ENST00000277541	NM_017617.3	1593	Ctg/Atg	26/34	1	2	FACETS	0.146	0.106	0.195	0.146	0.106	0.195	SUBCLONAL	1	TRUE	1	0.3	2		614	685	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031170	11031170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	116	654	0	ENST00000327064.4:c.1255C>T	p.Arg419Trp	p.R419W	ENST00000327064	NM_199141.1	419	Cgg/Tgg	11/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.3	2		654	670	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875613	35875613	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	71	421	0	ENST00000303115.3:c.801-1G>T		p.X267_splice	ENST00000303115	NM_002185.3	267			1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.3	2		421	412	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1959713	1959713	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs548600548	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	71	480	0	ENST00000382891.5:c.2935C>T	p.Arg979Ter	p.R979*	ENST00000382891	NM_133335.3	979	Cga/Tga	16/22	1	2	FACETS	0.822	0.718	0.934	0.822	0.718	0.934	CLONAL	1	TRUE	1	0.3	2		480	576	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796763	42796763	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	83	687	0	ENST00000575354.2:c.3221C>A	p.Pro1074His	p.P1074H	ENST00000575354	NM_015125.3	1074	cCt/cAt	14/20	1	2	FACETS	0.897	0.792	1	0.897	0.792	1	CLONAL	1	TRUE	1	0.3	2		687	617	SUCCESS
MET	4233	MSKCC	GRCh37	7	116414971	116414971	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45612435	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	84	627	0	ENST00000397752.3:c.3065G>A	p.Arg1022Gln	p.R1022Q	ENST00000397752	NM_000245.2	1022	cGa/cAa	15/21	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.3	2		627	477	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944312	76944312	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1180790039	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	36	376	0	ENST00000373344.5:c.593A>G	p.Lys198Arg	p.K198R	ENST00000373344	NM_000489.3	198	aAg/aGg	7/35	1	2	FACETS	0.906	0.749	1	0.906	0.749	1	CLONAL	1	TRUE	1	0.3	2		376	265	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912834	50912834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747628342	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	67	612	0	ENST00000440232.2:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000440232	NM_002691.3	689	Cgg/Tgg	17/27	1	2	FACETS	0.748	0.65	0.854	0.748	0.65	0.854	SUBCLONAL	1	TRUE	1	0.3	2		612	597	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160312	22160312	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	85	507	0	ENST00000215832.6:c.319C>A	p.Leu107Ile	p.L107I	ENST00000215832	NM_002745.4	107	Ctc/Atc	3/9	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.3	2		507	520	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489585	40489585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764674735	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	119	609	0	ENST00000264657.5:c.665C>T	p.Ala222Val	p.A222V	ENST00000264657	NM_139276.2	222	gCg/gTg	8/24	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.3	2		609	730	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450301	50450301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770551610	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	91	598	0	ENST00000331340.3:c.485G>A	p.Arg162Gln	p.R162Q	ENST00000331340	NM_006060.4	162	cGg/cAg	5/8	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.3	2		598	605	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462300	89462300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	55	464	0	ENST00000336596.2:c.1772C>T	p.Pro591Leu	p.P591L	ENST00000336596	NM_005233.5	591	cCa/cTa	10/17	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.3	2		464	330	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660618	67660618	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	72	459	0	ENST00000264010.4:c.1518G>T	p.Gln506His	p.Q506H	ENST00000264010	NM_006565.3	506	caG/caT	8/12	1	2	FACETS	0.901	0.788	1	0.901	0.788	1	CLONAL	1	TRUE	1	0.3	2		459	533	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973904	55973904	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	91	484	0	ENST00000263923.4:c.1412G>T	p.Ser471Ile	p.S471I	ENST00000263923	NM_002253.2	471	aGc/aTc	10/30	1	2	FACETS	0.925	0.822	1	0.925	0.822	1	CLONAL	1	TRUE	1	0.3	2		484	656	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574301	41574301	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	100	686	0	ENST00000263253.7:c.6586G>T	p.Gly2196Ter	p.G2196*	ENST00000263253	NM_001429.3	2196	Gga/Tga	31/31	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.3	2		686	614	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155568	106155568	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	33	546	0	ENST00000380013.4:c.469G>T	p.Glu157Ter	p.E157*	ENST00000380013	NM_001127208.2	157	Gaa/Taa	3/11	1	2	FACETS	0.433	0.352	0.525	0.433	0.352	0.525	SUBCLONAL	1	TRUE	1	0.3	2		546	508	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541661	187541661	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	51	642	0	ENST00000441802.2:c.6079C>A	p.Arg2027Ser	p.R2027S	ENST00000441802	NM_005245.3	2027	Cgc/Agc	10/27	1	2	FACETS	0.458	0.388	0.534	0.458	0.388	0.534	SUBCLONAL	1	TRUE	1	0.3	2		642	743	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858991	243858991	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	31	456	0	ENST00000263826.5:c.74G>T	p.Arg25Ile	p.R25I	ENST00000263826	NM_005465.4	25	aGa/aTa	2/13	1	2	FACETS	0.84	0.683	1	0.84	0.683	1	CLONAL	1	TRUE	1	0.3	2		456	246	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552144	29552144	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	47	493	1	ENST00000356175.3:c.1882del	p.Tyr628ThrfsTer3	p.Y628Tfs*3	ENST00000356175	NM_000267.3	626	cTt/ct	17/57	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.3	2		494	284	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47503744	47503746	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1387779417	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	93	633	0	ENST00000404338.3:c.4307_4309del	p.Phe1436del	p.F1436del	ENST00000404338	NM_004491.4	1433	ccCTTc/ccc	6/6	1	2	FACETS	0.854	0.759	0.955	0.854	0.759	0.955	CLONAL	1	TRUE	1	0.3	2		633	726	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88679173	88679174	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	14	180	0	ENST00000372037.3:c.1118dup	p.Asn373LysfsTer8	p.N373Kfs*8	ENST00000372037	NM_004329.2	371	-/A	10/13	1	2	FACETS	0.559	0.405	0.743	0.559	0.405	0.743	SUBCLONAL	1	TRUE	1	0.3	2		180	167	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588751	29588751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760703505	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	81	456	0	ENST00000356175.3:c.4537C>T	p.Arg1513Ter	p.R1513*	ENST00000356175	NM_000267.3	1513	Cga/Tga	34/57	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.3	2		456	493	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424841	47424841	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	105	583	1	ENST00000404338.3:c.2914del	p.Arg972GlyfsTer55	p.R972Gfs*55	ENST00000404338	NM_004491.4	970	tCc/tc	1/6	1	2	FACETS	0.951	0.852	1	0.951	0.852	1	CLONAL	1	TRUE	1	0.3	2		584	736	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124503667	124503667	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs797045168	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	57	425	0	ENST00000357628.3:c.283G>T	p.Gly95Cys	p.G95C	ENST00000357628	NM_015450.2	95	Ggt/Tgt	8/19	1	2	FACETS	0.876	0.753	1	0.876	0.753	1	CLONAL	1	TRUE	1	0.3	2		425	434	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073449	8073449	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	92	558	0	ENST00000377482.5:c.1210C>A	p.Leu404Met	p.L404M	ENST00000377482	NM_018948.3	404	Ctg/Atg	4/4	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.3	2		558	559	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259030	16259030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866283388	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	113	692	0	ENST00000375759.3:c.6295G>A	p.Ala2099Thr	p.A2099T	ENST00000375759	NM_015001.2	2099	Gct/Act	11/15	1	2	FACETS	0.982	0.884	1	0.982	0.884	1	CLONAL	1	TRUE	1	0.3	2		692	767	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749971	162749971	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	70	615	0	ENST00000367921.3:c.2503G>T	p.Asp835Tyr	p.D835Y	ENST00000367921	NM_006182.2	835	Gat/Tat	18/18	1	2	FACETS	0.813	0.709	0.925	0.813	0.709	0.925	CLONAL	1	TRUE	1	0.3	2		615	574	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981556	201981556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	35	495	0	ENST00000359651.3:c.470G>A	p.Gly157Glu	p.G157E	ENST00000359651		157	gGg/gAg	3/8	1	2	FACETS	0.45	0.368	0.542	0.45	0.368	0.542	SUBCLONAL	1	TRUE	1	0.3	2		495	519	SUCCESS
FH	2271	MSKCC	GRCh37	1	241676911	241676911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	61	347	0	ENST00000366560.3:c.370G>A	p.Ala124Thr	p.A124T	ENST00000366560	NM_000143.3	124	Gca/Aca	3/10	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.3	2		347	347	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727033	243727033	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	19	420	0	ENST00000263826.5:c.937C>A	p.Leu313Met	p.L313M	ENST00000263826	NM_005465.4	313	Ctg/Atg	9/13	1	2	FACETS	0.351	0.266	0.451	0.351	0.266	0.451	SUBCLONAL	1	TRUE	1	0.3	2		420	361	SUCCESS
RET	5979	MSKCC	GRCh37	10	43613924	43613924	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	75	485	0	ENST00000355710.3:c.2388G>T	p.Gln796His	p.Q796H	ENST00000355710	NM_020975.4	796	caG/caT	13/20	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.3	2		485	452	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620370	43620371	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	72	610	0	ENST00000355710.3:c.2983dup	p.Arg995LysfsTer17	p.R995Kfs*17	ENST00000355710	NM_020975.4	993	-/A	18/20	1	2	FACETS	0.749	0.654	0.851	0.749	0.654	0.851	SUBCLONAL	1	TRUE	1	0.3	2		610	641	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769084	112769084	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	16	421	0	ENST00000369452.4:c.1363C>A	p.Leu455Ile	p.L455I	ENST00000369452	NM_007373.3	455	Cta/Ata	7/9	1	2	FACETS	0.372	0.274	0.488	0.372	0.274	0.488	SUBCLONAL	1	TRUE	1	0.3	2		421	287	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57004136	57004136	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	C	C	T	rs780449482	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	80	639	1	ENST00000257254.3:c.343G>A	p.Ala115Thr	p.A115T	ENST00000257254		115	Gcc/Acc	1/2	1	2	FACETS	0.893	0.787	1	0.893	0.787	1	CLONAL	1	TRUE	1	0.3	2		640	597	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103171	119103171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	75	554	0	ENST00000264033.4:c.209G>A	p.Cys70Tyr	p.C70Y	ENST00000264033	NM_005188.3	70	tGt/tAt	2/16	1	2	FACETS	0.956	0.839	1	0.956	0.839	1	CLONAL	1	TRUE	1	0.3	2		554	523	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419096	419096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	82	542	1	ENST00000399788.2:c.3251G>A	p.Gly1084Glu	p.G1084E	ENST00000399788	NM_001042603.1	1084	gGg/gAg	22/28	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.3	2		543	478	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428610	49428610	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	92	683	0	ENST00000301067.7:c.10340C>T	p.Ala3447Val	p.A3447V	ENST00000301067	NM_003482.3	3447	gCa/gTa	35/54	1	2	FACETS	0.942	0.838	1	0.942	0.838	1	CLONAL	1	TRUE	1	0.3	2		683	651	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56474161	56474161	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	26	475	0	ENST00000267101.3:c.77A>G	p.Gln26Arg	p.Q26R	ENST00000267101	NM_001982.3	26	cAg/cGg	1/28	1	2	FACETS	0.39	0.308	0.483	0.39	0.308	0.483	SUBCLONAL	1	TRUE	1	0.3	2		475	445	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233130	69233130	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763077439	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	51	614	0	ENST00000462284.1:c.995G>A	p.Arg332His	p.R332H	ENST00000462284	NM_002392.5	332	cGt/cAt	11/11	1	2	FACETS	0.762	0.649	0.886	0.762	0.649	0.886	SUBCLONAL	1	TRUE	1	0.3	2		614	446	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112384	115112384	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	63	671	0	ENST00000257566.3:c.1356G>T	p.Glu452Asp	p.E452D	ENST00000257566	NM_016569.3	452	gaG/gaT	7/8	1	2	FACETS	0.722	0.624	0.827	0.722	0.624	0.827	SUBCLONAL	1	TRUE	1	0.3	2		671	582	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254021	133254021	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	73	526	0	ENST00000320574.5:c.729G>T	p.Trp243Cys	p.W243C	ENST00000320574	NM_006231.2	243	tgG/tgT	8/49	1	2	FACETS	0.851	0.745	0.965	0.851	0.745	0.965	CLONAL	1	TRUE	1	0.3	2		526	572	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557692	95557692	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	43	461	0	ENST00000393063.1:c.5375C>A	p.Ser1792Tyr	p.S1792Y	ENST00000393063	NM_030621.3	1792	tCt/tAt	26/28	1	2	FACETS	0.667	0.558	0.786	0.667	0.558	0.786	SUBCLONAL	1	TRUE	1	0.3	2		461	430	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724449	43724449	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	109	609	0	ENST00000382044.4:c.3618del	p.Ser1207ValfsTer39	p.S1207Vfs*39	ENST00000382044	NM_001141980.1	1206	ggG/gg	17/28	1	2	FACETS	0.973	0.874	1	0.973	0.874	1	CLONAL	1	TRUE	1	0.3	2		609	747	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832690	3832690	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	86	511	0	ENST00000262367.5:c.1568C>A	p.Pro523His	p.P523H	ENST00000262367	NM_004380.2	523	cCc/cAc	6/31	1	2	FACETS	0.879	0.778	0.987	0.879	0.778	0.987	CLONAL	1	TRUE	1	0.3	2		511	652	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14016015	14016015	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	52	391	0	ENST00000311895.7:c.335G>T	p.Arg112Met	p.R112M	ENST00000311895	NM_005236.2	112	aGg/aTg	2/11	1	2	FACETS	0.873	0.746	1	0.873	0.746	1	CLONAL	1	TRUE	1	0.3	2		391	397	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993206	72993206	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	72	596	0	ENST00000268489.5:c.839C>A	p.Pro280His	p.P280H	ENST00000268489	NM_006885.3	280	cCc/cAc	2/10	1	2	FACETS	0.697	0.608	0.792	0.697	0.608	0.792	SUBCLONAL	1	TRUE	1	0.3	2		596	689	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350284	89350284	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	103	652	0	ENST00000301030.4:c.2666G>T	p.Arg889Met	p.R889M	ENST00000301030	NM_001256183.1	889	aGg/aTg	9/13	1	2	FACETS	0.855	0.765	0.951	0.855	0.765	0.951	CLONAL	1	TRUE	1	0.3	2		652	803	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350353	89350353	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752743410	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	97	603	0	ENST00000301030.4:c.2597G>A	p.Arg866Lys	p.R866K	ENST00000301030	NM_001256183.1	866	aGg/aAg	9/13	1	2	FACETS	0.944	0.842	1	0.944	0.842	1	CLONAL	1	TRUE	1	0.3	2		603	685	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89818601	89818601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45501101	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	70	569	0	ENST00000389301.3:c.3011C>T	p.Ser1004Phe	p.S1004F	ENST00000389301	NM_000135.2	1004	tCt/tTt	31/43	1	2	FACETS	0.759	0.662	0.864	0.759	0.662	0.864	SUBCLONAL	1	TRUE	1	0.3	2		569	615	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216133	7216133	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	96	603	0	ENST00000380728.2:c.926C>A	p.Pro309His	p.P309H	ENST00000380728		309	cCt/cAt	11/11	1	2	FACETS	0.961	0.857	1	0.961	0.857	1	CLONAL	1	TRUE	1	0.3	2		603	666	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976209	7976210	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	86	576	0	ENST00000319144.4:c.1985_1986del	p.Ile662ArgfsTer34	p.I662Rfs*34	ENST00000319144	NM_001139.2	662	aTA/a	15/15	1	2	FACETS	0.94	0.832	1	0.94	0.832	1	CLONAL	1	TRUE	1	0.3	2		576	610	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665071	29665071	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	42	399	0	ENST00000356175.3:c.6670C>T	p.Gln2224Ter	p.Q2224*	ENST00000356175	NM_000267.3	2224	Caa/Taa	44/57	1	2	FACETS	0.784	0.657	0.925	0.784	0.657	0.925	CLONAL	1	TRUE	1	0.3	2		399	357	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627674	37627674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs555751910	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	74	559	0	ENST00000447079.4:c.1589C>T	p.Pro530Leu	p.P530L	ENST00000447079	NM_015083.1	530	cCc/cTc	2/14	1	2	FACETS	0.791	0.692	0.896	0.791	0.692	0.896	SUBCLONAL	1	TRUE	1	0.3	2		559	624	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883603	37883603	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	83	648	0	ENST00000269571.5:c.3215G>T	p.Arg1072Met	p.R1072M	ENST00000269571		1072	aGg/aTg	26/27	1	2	FACETS	0.916	0.809	1	0.916	0.809	1	CLONAL	1	TRUE	1	0.3	2		648	604	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533543	63533543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	40	611	0	ENST00000307078.5:c.1611G>T	p.Gln537His	p.Q537H	ENST00000307078	NM_004655.3	537	caG/caT	6/11	1	2	FACETS	0.405	0.336	0.483	0.405	0.336	0.483	SUBCLONAL	1	TRUE	1	0.3	2		611	658	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117616	70117616	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	99	700	0	ENST00000245479.2:c.84G>T	p.Glu28Asp	p.E28D	ENST00000245479	NM_000346.3	28	gaG/gaT	1/3	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.3	2		700	638	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857678	78857678	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	71	595	0	ENST00000306801.3:c.1748G>T	p.Arg583Met	p.R583M	ENST00000306801	NM_020761.2	583	aGg/aTg	16/34	1	2	FACETS	0.749	0.654	0.852	0.749	0.654	0.852	SUBCLONAL	1	TRUE	1	0.3	2		595	632	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39593457	39593457	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	34	402	0	ENST00000262039.4:c.1222T>G	p.Phe408Val	p.F408V	ENST00000262039	NM_002647.2	408	Ttt/Gtt	11/25	1	2	FACETS	0.651	0.533	0.784	0.651	0.533	0.784	SUBCLONAL	1	TRUE	1	0.3	2		402	348	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207680	2207680	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	63	533	0	ENST00000398665.3:c.963+1G>T		p.X321_splice	ENST00000398665	NM_032482.2	321			1	2	FACETS	0.797	0.69	0.913	0.797	0.69	0.913	CLONAL	1	TRUE	1	0.3	2		533	527	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6222225	6222225	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	117	707	0	ENST00000252674.7:c.1017G>T	p.Glu339Asp	p.E339D	ENST00000252674	NM_005934.3	339	gaG/gaT	6/12	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.3	2		707	761	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6262314	6262314	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	81	535	0	ENST00000252674.7:c.201G>T	p.Lys67Asn	p.K67N	ENST00000252674	NM_005934.3	67	aaG/aaT	3/12	1	2	FACETS	0.845	0.745	0.952	0.845	0.745	0.952	CLONAL	1	TRUE	1	0.3	2		535	639	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246906	10246906	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	112	641	0	ENST00000340748.4:c.4499T>C	p.Leu1500Pro	p.L1500P	ENST00000340748		1500	cTg/cCg	37/40	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.3	2		641	745	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273926	18273926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1041206635	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	98	552	0	ENST00000222254.8:c.1259G>A	p.Arg420Gln	p.R420Q	ENST00000222254	NM_005027.3	420	cGg/cAg	10/16	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.3	2		552	603	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422980	47422980	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	78	564	0	ENST00000404338.3:c.1048G>T	p.Ala350Ser	p.A350S	ENST00000404338	NM_004491.4	350	Gct/Tct	1/6	1	2	FACETS	0.875	0.77	0.988	0.875	0.77	0.988	CLONAL	1	TRUE	1	0.3	2		564	594	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99181224	99181224	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	77	601	0	ENST00000074304.5:c.2165A>G	p.Tyr722Cys	p.Y722C	ENST00000074304	NM_001134224.1	722	tAc/tGc	20/26	1	2	FACETS	0.715	0.627	0.809	0.715	0.627	0.809	SUBCLONAL	1	TRUE	1	0.3	2		601	718	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99181226	99181226	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	74	599	0	ENST00000074304.5:c.2167G>A	p.Gly723Arg	p.G723R	ENST00000074304	NM_001134224.1	723	Ggg/Agg	20/26	1	2	FACETS	0.678	0.593	0.769	0.678	0.593	0.769	SUBCLONAL	1	TRUE	1	0.3	2		599	728	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131451	202131451	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	69	523	0	ENST00000358485.4:c.419C>A	p.Thr140Asn	p.T140N	ENST00000358485	NM_001080125.1	140	aCt/aAt	2/9	1	2	FACETS	0.817	0.712	0.93	0.817	0.712	0.93	CLONAL	1	TRUE	1	0.3	2		523	563	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46255915	46255915	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	25	299	0	ENST00000371998.3:c.527C>A	p.Ser176Tyr	p.S176Y	ENST00000371998		176	tCt/tAt	6/23	1	2	FACETS	0.829	0.658	1	0.829	0.658	1	CLONAL	1	TRUE	1	0.3	2		299	201	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319496	62319496	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	66	638	0	ENST00000360203.5:c.1600T>G	p.Ser534Ala	p.S534A	ENST00000360203	NM_001283009.1	534	Tcc/Gcc	19/35	1	2	FACETS	0.753	0.654	0.861	0.753	0.654	0.861	SUBCLONAL	1	TRUE	1	0.3	2		638	584	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164520	36164520	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	76	603	0	ENST00000300305.3:c.1355T>C	p.Val452Ala	p.V452A	ENST00000300305		452	gTg/gCg	8/8	1	2	FACETS	0.911	0.8	1	0.911	0.8	1	CLONAL	1	TRUE	1	0.3	2		603	556	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627360	37627360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	112	634	0	ENST00000249071.6:c.359G>A	p.Arg120Gln	p.R120Q	ENST00000249071	NM_002872.4	120	cGg/cAg	5/7	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.3	2		634	719	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573809	41573809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	98	634	0	ENST00000263253.7:c.6094G>A	p.Gly2032Arg	p.G2032R	ENST00000263253	NM_001429.3	2032	Gga/Aga	31/31	1	2	FACETS	0.975	0.871	1	0.975	0.871	1	CLONAL	1	TRUE	1	0.3	2		634	670	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47079192	47079192	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	74	530	2	ENST00000409792.3:c.7314C>A	p.Asp2438Glu	p.D2438E	ENST00000409792	NM_014159.6	2438	gaC/gaA	18/21	0.301050038406521	2	FACETS	0.836	0.733	0.948	0.418	0.366	0.474	CLONAL	1	TRUE	0	0.3	2		532	590	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940240	49940240	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	59	652	0	ENST00000296474.3:c.803G>T	p.Ser268Ile	p.S268I	ENST00000296474	NM_002447.2	268	aGc/aTc	1/20	1	2	FACETS	0.595	0.511	0.686	0.595	0.511	0.686	SUBCLONAL	1	TRUE	1	0.3	2		652	661	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461502	138461502	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	51	403	0	ENST00000289153.2:c.519del	p.Lys173AsnfsTer16	p.K173Nfs*16	ENST00000289153	NM_006219.2	173	aaA/aa	3/22	1	2	FACETS	0.98	0.836	1	0.98	0.836	1	CLONAL	1	TRUE	1	0.3	2		403	347	SUCCESS
ATR	545	MSKCC	GRCh37	3	142285092	142285092	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	63	453	0	ENST00000350721.4:c.163C>A	p.Leu55Ile	p.L55I	ENST00000350721	NM_001184.3	55	Ctt/Att	3/47	1	2	FACETS	0.87	0.754	0.995	0.87	0.754	0.995	CLONAL	1	TRUE	1	0.3	2		453	483	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170016846	170016846	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	28	353	0	ENST00000295797.4:c.1651A>G	p.Asn551Asp	p.N551D	ENST00000295797	NM_002740.5	551	Aac/Gac	17/18	1	2	FACETS	0.587	0.47	0.72	0.587	0.47	0.72	SUBCLONAL	1	TRUE	1	0.3	2		353	318	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503811	186503814	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	78	470	0	ENST00000323963.5:c.490_493del	p.Phe164IlefsTer3	p.F164Ifs*3	ENST00000323963		163	gTGTTt/gt	5/11	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.3	2		470	505	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442822	187442822	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	91	605	0	ENST00000232014.4:c.1884G>T	p.Lys628Asn	p.K628N	ENST00000232014	NM_001130845.1	628	aaG/aaT	9/10	1	2	FACETS	0.831	0.738	0.931	0.831	0.738	0.931	CLONAL	1	TRUE	1	0.3	2		605	730	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164014	106164014	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	45	359	0	ENST00000380013.4:c.3524T>A	p.Ile1175Asn	p.I1175N	ENST00000380013	NM_001127208.2	1175	aTt/aAt	5/11	1	2	FACETS	0.952	0.804	1	0.952	0.804	1	CLONAL	1	TRUE	1	0.3	2		359	315	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144387356	144387356	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749694713	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	28	450	0	ENST00000262995.4:c.1994G>A	p.Gly665Glu	p.G665E	ENST00000262995	NM_207123.2	665	gGg/gAg	10/11	1	2	FACETS	0.47	0.375	0.578	0.47	0.375	0.578	SUBCLONAL	1	TRUE	1	0.3	2		450	397	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295376	1295376	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	83	734	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.3	2		734	495	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1296125	1296125	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	96	678	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.867	0.773	0.968	0.867	0.773	0.968	CLONAL	1	TRUE	1	0.3	2		678	738	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755549	57755549	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	74	574	0	ENST00000274289.3:c.238A>G	p.Lys80Glu	p.K80E	ENST00000274289	NM_006622.3	80	Aag/Gag	1/14	1	2	FACETS	0.873	0.765	0.989	0.873	0.765	0.989	CLONAL	1	TRUE	1	0.3	2		574	565	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682705	86682705	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	48	414	0	ENST00000274376.6:c.2910T>A	p.Phe970Leu	p.F970L	ENST00000274376	NM_002890.2	970	ttT/ttA	23/25	1	2	FACETS	0.967	0.821	1	0.967	0.821	1	CLONAL	1	TRUE	1	0.3	2		414	331	SUCCESS
APC	324	MSKCC	GRCh37	5	112176743	112176743	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	57	544	0	ENST00000257430.4:c.5452A>G	p.Asn1818Asp	p.N1818D	ENST00000257430	NM_000038.5	1818	Aat/Gat	16/16	1	2	FACETS	0.934	0.804	1	0.934	0.804	1	CLONAL	1	TRUE	1	0.3	2		544	407	SUCCESS
APC	324	MSKCC	GRCh37	5	112178076	112178076	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs878853465	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	82	595	0	ENST00000257430.4:c.6785G>T	p.Ser2262Ile	p.S2262I	ENST00000257430	NM_000038.5	2262	aGt/aTt	16/16	1	2	FACETS	0.781	0.688	0.88	0.781	0.688	0.88	SUBCLONAL	1	TRUE	1	0.3	2		595	700	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176563029	176563029	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	57	395	0	ENST00000439151.2:c.927del	p.Cys310ValfsTer10	p.C310Vfs*10	ENST00000439151	NM_022455.4	309	Ttt/tt	2/23	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.3	2		395	371	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030372	180030372	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	131	668	0	ENST00000261937.6:c.3912G>T	p.Gln1304His	p.Q1304H	ENST00000261937	NM_182925.4	1304	caG/caT	30/30	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.3	2		668	725	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858362	27858362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	106	760	0	ENST00000359303.2:c.209G>A	p.Arg70His	p.R70H	ENST00000359303	NM_003535.2	70	cGc/cAc	1/1	1	2	FACETS	0.863	0.773	0.958	0.863	0.773	0.958	CLONAL	1	TRUE	1	0.3	2		760	819	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800177	32800177	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750999800	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	89	650	0	ENST00000374899.4:c.1205G>A	p.Gly402Glu	p.G402E	ENST00000374899	NM_018833.2	402	gGg/gAg	7/12	1	2	FACETS	0.929	0.824	1	0.929	0.824	1	CLONAL	1	TRUE	1	0.3	2		650	639	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718087	117718087	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	58	420	0	ENST00000368508.3:c.770C>A	p.Thr257Asn	p.T257N	ENST00000368508	NM_002944.2	257	aCt/aAt	7/43	1	2	FACETS	0.969	0.836	1	0.969	0.836	1	CLONAL	1	TRUE	1	0.3	2		420	399	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157519944	157519944	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	64	439	0	ENST00000346085.5:c.4014-1G>T		p.X1338_splice	ENST00000346085	NM_020732.3	1338			1	2	FACETS	0.878	0.762	1	0.878	0.762	1	CLONAL	1	TRUE	1	0.3	2		439	486	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81340830	81340830	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	20	239	0	ENST00000222390.5:c.1411G>T	p.Gly471Cys	p.G471C	ENST00000222390	NM_000601.4	471	Ggt/Tgt	12/18	1	2	FACETS	0.794	0.611	1	0.794	0.611	1	CLONAL	1	TRUE	1	0.3	2		239	168	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124482876	124482876	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	23	366	0	ENST00000357628.3:c.1148C>A	p.Pro383His	p.P383H	ENST00000357628	NM_015450.2	383	cCt/cAt	13/19	1	2	FACETS	0.576	0.45	0.722	0.576	0.45	0.722	SUBCLONAL	1	TRUE	1	0.3	2		366	266	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148513831	148513831	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	62	481	0	ENST00000320356.2:c.1450C>A	p.Pro484Thr	p.P484T	ENST00000320356	NM_004456.4	484	Cca/Aca	12/20	1	2	FACETS	0.849	0.734	0.972	0.849	0.734	0.972	CLONAL	1	TRUE	1	0.3	2		481	487	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874296	151874296	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	63	524	1	ENST00000262189.6:c.8242C>A	p.Leu2748Ile	p.L2748I	ENST00000262189	NM_170606.2	2748	Ctc/Atc	38/59	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.3	2		525	393	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737451	145737451	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	64	712	0	ENST00000428558.2:c.3237-1G>T		p.X1079_splice	ENST00000428558	NM_004260.3	1079			1	2	FACETS	0.689	0.597	0.79	0.689	0.597	0.79	SUBCLONAL	1	TRUE	1	0.3	2		712	619	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2054603	2054603	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1279471313	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	79	472	0	ENST00000349721.2:c.1053G>T	p.Gln351His	p.Q351H	ENST00000349721	NM_003070.3	351	caG/caT	6/34	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.3	2		472	476	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404545	8404545	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	33	414	0	ENST00000356435.5:c.4202C>A	p.Ala1401Asp	p.A1401D	ENST00000356435		1401	gCt/gAt	25/35	1	2	FACETS	0.707	0.578	0.853	0.707	0.578	0.853	SUBCLONAL	1	TRUE	1	0.3	2		414	311	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270570	98270570	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	36	443	0	ENST00000331920.6:c.74del	p.Gly25AspfsTer55	p.G25Dfs*55	ENST00000331920	NM_000264.3	25	gGa/ga	1/24	1	2	FACETS	0.67	0.552	0.802	0.67	0.552	0.802	SUBCLONAL	1	TRUE	1	0.3	2		443	358	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20153899	20153899	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	41	299	0	ENST00000379607.5:c.161G>T	p.Gly54Val	p.G54V	ENST00000379607	NM_001412.3	54	gGt/gTt	3/7	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.3	2		299	259	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916486	39916486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	75	479	0	ENST00000378444.4:c.4517C>T	p.Ala1506Val	p.A1506V	ENST00000378444	NM_001123385.1	1506	gCt/gTt	11/15	1	2	FACETS	0.794	0.696	0.899	0.794	0.696	0.899	SUBCLONAL	1	TRUE	1	0.3	2		479	630	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933605	39933605	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	101	651	2	ENST00000378444.4:c.994C>A	p.Leu332Met	p.L332M	ENST00000378444	NM_001123385.1	332	Ctg/Atg	4/15	1	2	FACETS	0.926	0.828	1	0.926	0.828	1	CLONAL	1	TRUE	1	0.3	2		653	727	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942853	44942853	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	31	417	1	ENST00000377967.4:c.3433G>T	p.Gly1145Cys	p.G1145C	ENST00000377967	NM_021140.2	1145	Ggt/Tgt	23/29	1	2	FACETS	0.576	0.466	0.7	0.576	0.466	0.7	SUBCLONAL	1	TRUE	1	0.3	2		418	359	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247505	53247505	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	79	577	0	ENST00000375401.3:c.304A>G	p.Ile102Val	p.I102V	ENST00000375401	NM_004187.3	102	Att/Gtt	3/26	1	2	FACETS	0.929	0.818	1	0.929	0.818	1	CLONAL	1	TRUE	1	0.3	2		577	567	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250025	53250025	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520198	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	91	497	0	ENST00000375401.3:c.224T>C	p.Leu75Pro	p.L75P	ENST00000375401	NM_004187.3	75	cTa/cCa	2/26	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.3	2		497	605	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347970	70347970	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	69	535	0	ENST00000374080.3:c.3209G>T	p.Arg1070Met	p.R1070M	ENST00000374080		1070	aGg/aTg	22/45	1	2	FACETS	0.767	0.668	0.873	0.767	0.668	0.873	SUBCLONAL	1	TRUE	1	0.3	2		535	600	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019760	123019760	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs111626628	NA	P-0064782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	60	504	0	ENST00000355640.3:c.248A>G	p.His83Arg	p.H83R	ENST00000355640		83	cAc/cGc	2/7	1	2	FACETS	0.735	0.634	0.846	0.735	0.634	0.846	SUBCLONAL	1	TRUE	1	0.3	2		504	544	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064783-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	112	789	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.55	2		789	395	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0064783-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	128	511	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.974	0.888	1	0.974	0.888	1	CLONAL	1	TRUE	1	0.55	2		511	478	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0064783-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	90	387	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.841	0.752	0.936	0.841	0.752	0.936	CLONAL	1	TRUE	1	0.55	2		387	389	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200665	67200666	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTACGACATGCTCACTGGATCGGCAAGTCCAGCC	novel	NA	P-0064783-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	97	688	0	ENST00000312629.5:c.777_798+12dup		p.M259fs	ENST00000312629	NM_003952.2	259	atg/atGTACGACATGCTCACTGGATCGGCAAGTCCAGCCg	9/15	1	2	FACETS	0.521	0.465	0.581	0.521	0.465	0.581	SUBCLONAL	1	TRUE	1	0.55	2		688	677	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86686642	86686642	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064783-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	30	436	0	ENST00000274376.6:c.3086T>C	p.Ile1029Thr	p.I1029T	ENST00000274376	NM_002890.2	1029	aTa/aCa	25/25	1	2	FACETS	0.204	0.164	0.25	0.204	0.164	0.25	SUBCLONAL	1	TRUE	1	0.55	2		436	535	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184159	123184159	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064783-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	169	407	0	ENST00000218089.9:c.1017G>C	p.Lys339Asn	p.K339N	ENST00000218089	NM_001042749.1	339	aaG/aaC	11/35	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.55	2		407	500	SUCCESS
PHF6	84295	MSKCC	GRCh37	X	133559277	133559277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064783-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	47	385	0	ENST00000332070.3:c.1015G>A	p.Asp339Asn	p.D339N	ENST00000332070	NM_032458.2	339	Gat/Aat	10/10	1	2	FACETS	0.319	0.269	0.375	0.319	0.269	0.375	SUBCLONAL	1	TRUE	1	0.55	2		385	535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0064785-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	111	462	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.448720293998449	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.471286110263734	1		462	345	SUCCESS
APC	324	MSKCC	GRCh37	5	112175536	112175536	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064785-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	72	469	0	ENST00000257430.4:c.4245del	p.Ser1415ArgfsTer4	p.S1415Rfs*4	ENST00000257430	NM_000038.5	1415	agT/ag	16/16	1	2	FACETS	0.699	0.613	0.791	0.699	0.613	0.791	SUBCLONAL	1	TRUE	1	0.471286110263734	2		469	437	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625251	69625251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782147248	NA	P-0064785-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	122	552	2	ENST00000334134.2:c.542G>A	p.Arg181His	p.R181H	ENST00000334134	NM_005247.2	181	cGc/cAc	3/3	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.471286110263734	2		554	473	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993300	72993300	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745631900	NA	P-0064785-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	46	556	1	ENST00000268489.5:c.745G>A	p.Gly249Ser	p.G249S	ENST00000268489	NM_006885.3	249	Ggt/Agt	2/10	1	2	FACETS	0.338	0.284	0.398	0.338	0.284	0.398	SUBCLONAL	1	TRUE	1	0.471286110263734	2		557	577	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499651	8499651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064785-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	92	472	1	ENST00000356435.5:c.2318C>T	p.Ala773Val	p.A773V	ENST00000356435		773	gCa/gTa	14/35	1	2	FACETS	0.948	0.847	1	0.948	0.847	1	CLONAL	1	TRUE	1	0.471286110263734	2		473	412	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519132	103519132	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064785-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	142	398	1	ENST00000355739.4:c.2470A>G	p.Asn824Asp	p.N824D	ENST00000355739	NM_000123.3	824	Aac/Gac	11/15	0.471286110263734	3	FACETS	0.85	0.781	0.92	0.85	0.781	0.92	CLONAL	2	TRUE	1	0.471286110263734	3		399	438	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358539	67358539	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064785-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	150	549	1	ENST00000327367.4:c.47del	p.Leu16ArgfsTer100	p.L16Rfs*100	ENST00000327367	NM_005902.3	16	cTg/cg	1/9	0.426807376372309	2	FACETS	0.806	0.745	0.868	0.806	0.745	0.868	CLONAL	2	TRUE	0	0.471286110263734	2		550	395	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117543	70117543	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064785-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	91	570	2	ENST00000245479.2:c.11T>A	p.Leu4Gln	p.L4Q	ENST00000245479	NM_000346.3	4	cTg/cAg	1/3	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.471286110263734	2		572	376	SUCCESS
APC	324	MSKCC	GRCh37	5	112174035	112174035	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064785-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	68	548	0	ENST00000257430.4:c.2744del	p.Val915GlyfsTer40	p.V915Gfs*40	ENST00000257430	NM_000038.5	915	gTg/gg	16/16	1	2	FACETS	0.822	0.72	0.931	0.822	0.72	0.931	CLONAL	1	TRUE	1	0.471286110263734	2		548	351	SUCCESS
APC	324	MSKCC	GRCh37	5	112175852	112175852	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064786-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	88	610	0	ENST00000257430.4:c.4561G>T	p.Glu1521Ter	p.E1521*	ENST00000257430	NM_000038.5	1521	Gaa/Taa	16/16	1	2	FACETS	0.988	0.876	1	0.988	0.876	1	CLONAL	1	TRUE	1	0.273681449637448	2		610	651	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0064786-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	119	643	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.273681449637448	2		643	708	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860556	45860556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064786-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	110	690	1	ENST00000391945.4:c.1451C>T	p.Thr484Met	p.T484M	ENST00000391945	NM_000400.3	484	aCg/aTg	15/23	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.273681449637448	2		691	743	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28595739	28595739	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1038449460	NA	P-0064786-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	105	592	0	ENST00000253063.3:c.136G>A	p.Ala46Thr	p.A46T	ENST00000253063	NM_031459.4	46	Gcc/Acc	2/10	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.273681449637448	2		592	746	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748899	41748899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750167315	NA	P-0064786-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	104	666	0	ENST00000301178.4:c.1424G>A	p.Arg475Gln	p.R475Q	ENST00000301178	NM_021913.4	475	cGa/cAa	11/20	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.273681449637448	2		666	713	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0064786-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	60	462	0	ENST00000311936.3:c.180_181delinsAA	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggAAaa	3/5	1	2	FACETS	0.755	0.65	0.868	0.755	0.65	0.868	SUBCLONAL	1	TRUE	1	0.273681449637448	2		462	581	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497726	120497726	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064786-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	128	715	0	ENST00000256646.2:c.2156C>T	p.Ser719Leu	p.S719L	ENST00000256646	NM_024408.3	719	tCa/tTa	13/34	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.273681449637448	2		715	868	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622077	43622077	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757373375	NA	P-0064786-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	103	595	2	ENST00000355710.3:c.3094G>A	p.Gly1032Ser	p.G1032S	ENST00000355710	NM_020975.4	1032	Ggc/Agc	19/20	1	2	FACETS	0.997	0.892	1	0.997	0.892	1	CLONAL	1	TRUE	1	0.273681449637448	2		597	755	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794595	42794595	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064786-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	50	658	0	ENST00000575354.2:c.1675G>C	p.Ala559Pro	p.A559P	ENST00000575354	NM_015125.3	559	Gcc/Ccc	10/20	1	2	FACETS	0.485	0.411	0.568	0.485	0.411	0.568	SUBCLONAL	1	TRUE	1	0.273681449637448	2		658	753	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732951	30732951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223854	NA	P-0064786-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	102	609	0	ENST00000295754.5:c.1564G>A	p.Asp522Asn	p.D522N	ENST00000295754	NM_003242.5	522	Gac/Aac	7/7	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.273681449637448	2		609	600	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045872	180045872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064786-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	104	716	0	ENST00000261937.6:c.2899G>A	p.Ala967Thr	p.A967T	ENST00000261937	NM_182925.4	967	Gcc/Acc	21/30	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.273681449637448	2		716	692	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372533	55372533	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064786-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	101	581	0	ENST00000297316.4:c.1223A>T	p.Tyr408Phe	p.Y408F	ENST00000297316	NM_022454.3	408	tAc/tTc	2/2	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.273681449637448	2		581	633	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0064787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	36	500	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	0.301	0.247	0.362	0.301	0.247	0.362	SUBCLONAL	1	TRUE	1	0.50978776288804	2		500	469	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343507	343507	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567261095	NA	P-0064787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	29	520	0	ENST00000262320.3:c.2167C>T	p.Arg723Ter	p.R723*	ENST00000262320	NM_003502.3	723	Cga/Tga	8/11	1	2	FACETS	0.289	0.232	0.355	0.289	0.232	0.355	SUBCLONAL	1	TRUE	1	0.50978776288804	2		520	393	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221131	5221131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201447856	NA	P-0064787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	39	605	0	ENST00000357368.4:c.3335C>T	p.Thr1112Met	p.T1112M	ENST00000357368	NM_002850.3	1112	aCg/aTg	20/38	1	2	FACETS	0.273	0.226	0.326	0.273	0.226	0.326	SUBCLONAL	1	TRUE	1	0.50978776288804	2		605	560	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883770	37883770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747888253	NA	P-0064787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	49	657	0	ENST00000269571.5:c.3382G>A	p.Val1128Ile	p.V1128I	ENST00000269571		1128	Gtt/Att	26/27	1	2	FACETS	0.364	0.308	0.426	0.364	0.308	0.426	SUBCLONAL	1	TRUE	1	0.50978776288804	2		657	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0064818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	89	749	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.215895670745858	2	FACETS	1	0.967	1	0.617	0.548	0.69	CLONAL	1	TRUE	0	0.266584897770486	2		749	541	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375065	104375065	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	54	500	0	ENST00000369902.3:c.1063A>T	p.Ile355Phe	p.I355F	ENST00000369902	NM_016169.3	355	Atc/Ttc	9/12	0.161283919406997	1	FACETS	0.856	0.733	0.99	0.856	0.733	0.99	CLONAL	1	TRUE	0	0.266584897770486	1		500	410	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124532340	124532340	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	47	437	0	ENST00000357628.3:c.104C>T	p.Pro35Leu	p.P35L	ENST00000357628	NM_015450.2	35	cCa/cTa	6/19	0.266584897770486	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.266584897770486	1		437	228	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0064818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	53	749	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.191356875660172	2		749	454	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375065	104375065	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	43	500	0	ENST00000369902.3:c.1063A>T	p.Ile355Phe	p.I355F	ENST00000369902	NM_016169.3	355	Atc/Ttc	9/12	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	FALSE	1	0.191356875660172	2		500	387	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124532340	124532340	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	31	437	0	ENST00000357628.3:c.104C>T	p.Pro35Leu	p.P35L	ENST00000357628	NM_015450.2	35	cCa/cTa	6/19	1	2	FACETS	0.786	0.641	0.948	1	0.948	1	CLONAL	2	FALSE	1	0.191356875660172	2		437	206	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0064819-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	80	500	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		500	330	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064819-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	31	789	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		789	152	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0064819-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	52	618	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		618	301	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435228	49435228	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064819-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	43	562	0	ENST00000301067.7:c.6325C>T	p.Gln2109Ter	p.Q2109*	ENST00000301067	NM_003482.3	2109	Cag/Tag	31/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		562	299	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823847	3823847	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064819-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	131	591	0	ENST00000262367.5:c.2368C>T	p.Gln790Ter	p.Q790*	ENST00000262367	NM_004380.2	790	Cag/Tag	13/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		591	414	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578205	226578205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765820369	NA	P-0064819-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	108	552	0	ENST00000366794.5:c.523G>A	p.Glu175Lys	p.E175K	ENST00000366794	NM_001618.3	175	Gag/Aag	4/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		552	355	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256504	16256505	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0064819-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	126	689	0	ENST00000375759.3:c.3771dup	p.Thr1258AspfsTer14	p.T1258Dfs*14	ENST00000375759	NM_015001.2	1257	agg/aGgg	11/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		689	484	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377043	118377043	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555048374	NA	P-0064819-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	102	681	0	ENST00000534358.1:c.10436C>T	p.Ser3479Leu	p.S3479L	ENST00000534358	NM_005933.3	3479	tCa/tTa	27/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		681	331	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73638015	73638015	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064819-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	61	335	0	ENST00000377687.4:c.1189C>T	p.His397Tyr	p.H397Y	ENST00000377687	NM_001730.3	397	Cac/Tac	3/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		335	235	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424345	47424345	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064819-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	74	542	0	ENST00000404338.3:c.2413C>T	p.Gln805Ter	p.Q805*	ENST00000404338	NM_004491.4	805	Cag/Tag	1/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		542	367	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	113	789	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.927	0.849	1	0.927	0.849	1	CLONAL	1	TRUE	1	0.916866136369734	2		789	266	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0064820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	165	454	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	1	2	FACETS	0.923	0.859	0.988	0.923	0.859	0.988	CLONAL	1	TRUE	1	0.916866136369734	2		454	390	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982331	201982332	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0064821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	166	643	0	ENST00000359651.3:c.715dup	p.Asp239GlyfsTer62	p.D239Gfs*62	ENST00000359651		237	aag/aaGg	6/8	0.527128082541947	3	FACETS	1	0.965	1	0.543	0.5	0.587	CLONAL	1	TRUE	1	0.562105383432058	3		643	697	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243776975	243776975	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	55	400	0	ENST00000263826.5:c.694G>A	p.Glu232Lys	p.E232K	ENST00000263826	NM_005465.4	232	Gag/Aag	7/13	0.527128082541947	3	FACETS	0.853	0.735	0.98	0.426	0.367	0.49	CLONAL	1	TRUE	1	0.562105383432058	3		400	294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578393	7578393	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876660821	NA	P-0064821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	281	651	0	ENST00000269305.4:c.537T>A	p.His179Gln	p.H179Q	ENST00000269305	NM_001126112.2	179	caT/caA	5/11	0.536705860353069	2	FACETS	0.967	0.92	1	0.967	0.92	1	CLONAL	2	TRUE	0	0.562105383432058	2		651	517	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223419	2223419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1271868009	NA	P-0064821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	71	631	0	ENST00000398665.3:c.3530G>A	p.Gly1177Glu	p.G1177E	ENST00000398665	NM_032482.2	1177	gGg/gAg	25/28	0.554955214831429	2	FACETS	0.505	0.442	0.573	0.253	0.221	0.287	SUBCLONAL	1	TRUE	0	0.562105383432058	2		631	500	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754860	29754860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	130	582	0	ENST00000389048.3:c.1075G>A	p.Gly359Arg	p.G359R	ENST00000389048	NM_004304.4	359	Gga/Aga	4/29	0.527128082541947	3	FACETS	0.986	0.897	1	0.493	0.448	0.54	CLONAL	1	TRUE	1	0.562105383432058	3		582	601	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976857	55976857	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151317075	NA	P-0064821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	142	467	0	ENST00000263923.4:c.1055C>T	p.Ala352Val	p.A352V	ENST00000263923	NM_002253.2	352	gCg/gTg	8/30	0.502027622676507	3	FACETS	1	0.982	1	0.631	0.578	0.685	CLONAL	1	TRUE	1	0.562105383432058	3		467	513	SUCCESS
APC	324	MSKCC	GRCh37	5	112175050	112175050	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	92	434	0	ENST00000257430.4:c.3759del	p.Ile1254LeufsTer11	p.I1254Lfs*11	ENST00000257430	NM_000038.5	1253	tcT/tc	16/16	1	2	FACETS	0.986	0.885	1	0.986	0.885	1	CLONAL	1	TRUE	1	0.562105383432058	2		434	332	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371633	55371633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs931390946	NA	P-0064821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	91	494	0	ENST00000297316.4:c.323C>T	p.Ala108Val	p.A108V	ENST00000297316	NM_022454.3	108	gCg/gTg	2/2	1	2	FACETS	0.859	0.768	0.954	0.859	0.768	0.954	CLONAL	1	TRUE	1	0.562105383432058	2		494	377	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763997	76763997	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	222	285	0	ENST00000373344.5:c.7311G>T	p.Met2437Ile	p.M2437I	ENST00000373344	NM_000489.3	2437	atG/atT	35/35	0.470729785825446	2	FACETS	0.878	0.828	0.928			1	CLONAL	2	TRUE	NA	0.562105383432058	2		285	450	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	35	789	0				ENST00000310581	NM_198253.2	-/1132			0.322925915753168	1	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	FALSE	0	0.322925915753168	1		789	166	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0064822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	33	256	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	1	0.322925915753168	2		256	144	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0064822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	76	388	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.231639716342161	3	FACETS	1	0.93	1	0.709	0.63	0.792	CLONAL	2	FALSE	0	0.322925915753168	3		388	257	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150933642	150933642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	54	469	0	ENST00000271640.5:c.3104G>A	p.Gly1035Glu	p.G1035E	ENST00000271640	NM_001145415.1	1035	gGa/gAa	16/22	1	2	FACETS	0.947	0.813	1	0.947	0.813	1	CLONAL	1	FALSE	1	0.322925915753168	2		469	353	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100653	8100673	+	protein_altering_variant	In_Frame_Del	DEL	TGGAGCCTCCTCGTCGACCCA	TGGAGCCTCCTCGTCGACCCA	GTGGTGGGT	novel	NA	P-0064822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	28	632	1	ENST00000346208.3:c.627_647delinsGTGGTGGGT	p.Gly210_His216delinsTrpTrpVal	p.G210_H216delinsWWV	ENST00000346208		209	ggTGGAGCCTCCTCGTCGACCCAc/ggGTGGTGGGTc	3/6	1	2	FACETS	0.37	0.295	0.455	0.37	0.295	0.455	SUBCLONAL	1	FALSE	1	0.322925915753168	2		633	469	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446203	70446203	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	59	493	0	ENST00000373644.4:c.5143G>C	p.Asp1715His	p.D1715H	ENST00000373644	NM_030625.2	1715	Gac/Cac	11/12	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	FALSE	1	0.322925915753168	2		493	340	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106457	108106457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	16	419	0	ENST00000278616.4:c.392C>T	p.Ser131Leu	p.S131L	ENST00000278616	NM_000051.3	131	tCa/tTa	5/63	1	2	FACETS	0.42	0.31	0.55	0.42	0.31	0.55	SUBCLONAL	1	FALSE	1	0.322925915753168	2		419	236	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106544	108106544	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	13	389	0	ENST00000278616.4:c.479C>G	p.Ser160Cys	p.S160C	ENST00000278616	NM_000051.3	160	tCt/tGt	5/63	1	2	FACETS	0.338	0.241	0.457	0.338	0.241	0.457	SUBCLONAL	1	FALSE	1	0.322925915753168	2		389	238	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636175	28636175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764656426	NA	P-0064822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	64	487	0	ENST00000241453.7:c.197C>T	p.Ala66Val	p.A66V	ENST00000241453	NM_004119.2	66	gCg/gTg	3/24	0.322925915753168	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	FALSE	0	0.322925915753168	1		487	300	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007752	45007752	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	20	528	0	ENST00000558401.1:c.199G>C	p.Glu67Gln	p.E67Q	ENST00000558401	NM_004048.2	67	Gaa/Caa	2/4	0.322925915753168	1	FACETS	0.285	0.218	0.365	0.285	0.218	0.365	SUBCLONAL	1	FALSE	0	0.322925915753168	1		528	364	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16005069	16005069	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	35	442	0	ENST00000268712.3:c.2185G>T	p.Glu729Ter	p.E729*	ENST00000268712	NM_006311.3	729	Gaa/Taa	20/46	0.322925915753168	1	FACETS	0.761	0.627	0.908	0.761	0.627	0.908	CLONAL	1	FALSE	0	0.322925915753168	1		442	239	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820821	32820821	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	67	553	0	ENST00000354258.4:c.773C>G	p.Ser258Cys	p.S258C	ENST00000354258	NM_000593.5	258	tCt/tGt	1/11	0.191493612223878	2	FACETS	1	0.936	1	0.558	0.487	0.633	INDETERMINATE	1	FALSE	0	0.322925915753168	2		553	372	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150430	157150430	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057518951	NA	P-0064822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	48	551	0	ENST00000346085.5:c.1612C>T	p.Gln538Ter	p.Q538*	ENST00000346085	NM_020732.3	538	Cag/Tag	2/20	0.123898519842348	3	FACETS	0.836	0.708	0.976	0.418	0.354	0.488	INDETERMINATE	1	FALSE	1	0.322925915753168	3		551	413	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942724	44942724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1453322733	NA	P-0064822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	65	196	0	ENST00000377967.4:c.3304G>A	p.Glu1102Lys	p.E1102K	ENST00000377967	NM_021140.2	1102	Gag/Aag	23/29	0.151926486977713	2	FACETS	0.895	0.797	0.994			1	INDETERMINATE	3	FALSE	NA	0.322925915753168	2		196	150	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441813	49441813	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064823-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	10	544	0	ENST00000301067.7:c.4171G>C	p.Glu1391Gln	p.E1391Q	ENST00000301067	NM_003482.3	1391	Gag/Cag	14/54	0.358471681912532	5	FACETS	0.279	0.188	0.392	0.093	0.062	0.131	INDETERMINATE	1	TRUE	2	0.794096622647171	5		544	198	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115260795	115260795	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064823-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	12	375	0	ENST00000438362.2:c.2530G>A	p.Asp844Asn	p.D844N	ENST00000438362	NM_001242891.1	844	Gac/Aac	20/20	0.707794570464525	4	FACETS	0.231	0.162	0.316	0.115	0.081	0.158	SUBCLONAL	1	TRUE	2	0.794096622647171	4		375	235	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945076	31945076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064823-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	16	596	0	ENST00000340398.3:c.25C>T	p.Arg9Cys	p.R9C	ENST00000340398	NM_001013699.2	9	Cgt/Tgt	1/1	0.358471681912532	5	FACETS	0.365	0.27	0.478	0.122	0.09	0.16	INDETERMINATE	1	TRUE	2	0.794096622647171	5		596	242	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570408	95570408	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064823-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	10	509	0	ENST00000393063.1:c.3325T>A	p.Ser1109Thr	p.S1109T	ENST00000393063	NM_030621.3	1109	Tca/Aca	22/28	0.288415169096974	5	FACETS	0.381	0.258	0.533	0.127	0.086	0.178	INDETERMINATE	1	TRUE	2	0.794096622647171	5		509	145	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054561	42054561	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0064823-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	11	387	0	ENST00000219905.7:c.7744+1G>A		p.X2582_splice	ENST00000219905	NM_001164273.1	2582			0.121415580273233	4	FACETS	0.382	0.265	0.526	0.191	0.132	0.263	INDETERMINATE	1	TRUE	2	0.794096622647171	4		387	130	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244826	41244826	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80356978	NA	P-0064823-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	12	529	0	ENST00000357654.3:c.2722G>A	p.Glu908Lys	p.E908K	ENST00000357654	NM_007294.3	908	Gaa/Aaa	10/23	0.248904663293329	4	FACETS	0.414	0.292	0.561	0.207	0.146	0.281	INDETERMINATE	1	TRUE	2	0.794096622647171	4		529	131	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245662	41245662	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064823-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	11	533	0	ENST00000357654.3:c.1886G>C	p.Arg629Thr	p.R629T	ENST00000357654	NM_007294.3	629	aGa/aCa	10/23	0.248904663293329	4	FACETS	0.336	0.233	0.463	0.168	0.116	0.232	INDETERMINATE	1	TRUE	2	0.794096622647171	4		533	148	SUCCESS
APC	324	MSKCC	GRCh37	5	112128218	112128218	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064823-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	16	360	0	ENST00000257430.4:c.721G>T	p.Glu241Ter	p.E241*	ENST00000257430	NM_000038.5	241	Gaa/Taa	7/16	0.358471681912532	5	FACETS	0.496	0.368	0.648	0.165	0.122	0.216	INDETERMINATE	1	TRUE	2	0.794096622647171	5		360	178	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064824-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	23	342	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.972	0.758	1	0.972	0.758	1	CLONAL	1	TRUE	1	0.14	2		342	338	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440904	56440904	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1458799446	NA	P-0064824-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	13	662	0	ENST00000407977.2:c.433C>T	p.Arg145Ter	p.R145*	ENST00000407977		145	Cga/Tga	4/10	1	2	FACETS	0.374	0.265	0.507	0.374	0.265	0.507	SUBCLONAL	1	TRUE	1	0.14	2		662	497	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981088	201981089	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0064824-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	48	547	0	ENST00000359651.3:c.169dup	p.Ala57GlyfsTer35	p.A57Gfs*35	ENST00000359651		56	aag/aaGg	2/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.14	2		547	493	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591857	48591858	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTTA	novel	NA	P-0064824-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	12	584	0	ENST00000342988.3:c.1023_1024insAGTT	p.Pro342SerfsTer11	p.P342Sfs*11	ENST00000342988	NM_005359.5	340	-/GTTA	9/12	0.0853279505214107	0	FACETS	0.339	0.237	0.466			1	SUBCLONAL	1	TRUE	0	0.14	0		584	435	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0064825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	12	460	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.106	0.073	0.146	0.106	0.073	0.146	SUBCLONAL	1	TRUE	1	0.434496265963009	2		460	523	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604764	48604766	+	inframe_deletion	In_Frame_Del	DEL	TAC	TAC	-	novel	NA	P-0064825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	125	547	0	ENST00000342988.3:c.1586_1588del	p.Leu529_His530delinsTyr	p.L529_H530delinsY	ENST00000342988	NM_005359.5	529	tTACac/tac	12/12	0.434496265963009	1	FACETS	0.767	0.697	0.841	0.767	0.697	0.841	SUBCLONAL	1	TRUE	0	0.434496265963009	1		547	587	SUCCESS
APC	324	MSKCC	GRCh37	5	112175039	112175040	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs1114167583	NA	P-0064825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	108	438	0	ENST00000257430.4:c.3749_3750del	p.Lys1250SerfsTer5	p.K1250Sfs*5	ENST00000257430	NM_000038.5	1250	AAa/a	16/16	0.434496265963009	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.434496265963009	1		438	377	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21350094	21350094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	56	592	0	ENST00000215739.8:c.2002G>A	p.Asp668Asn	p.D668N	ENST00000215739	NM_006767.3	668	Gac/Aac	17/21	1	2	FACETS	0.537	0.461	0.62	0.537	0.461	0.62	SUBCLONAL	1	TRUE	1	0.434496265963009	2		592	480	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022913	27022938	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGCCGCCGCCAGCAGCCTGGGCAA	CCCGCCGCCGCCAGCAGCCTGGGCAA	-	rs797045262	NA	P-0064845-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	34	561	0	ENST00000324856.7:c.31_56del	p.Ser11AlafsTer91	p.S11Afs*91	ENST00000324856	NM_006015.4	7	CCCGCCGCCGCCAGCAGCCTGGGCAAc/c	1/20	0.357298395004081	1	FACETS	0.551	0.453	0.661	0.551	0.453	0.661	SUBCLONAL	1	TRUE	0	0.387048424178319	1		561	257	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067877	30067893	+	frameshift_variant	Frame_Shift_Del	DEL	TGAGTTGGAGAGGAGGC	TGAGTTGGAGAGGAGGC	-	novel	NA	P-0064845-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	73	602	0	ENST00000338641.4:c.1064_1080del	p.Glu355AlafsTer18	p.E355Afs*18	ENST00000338641	NM_000268.3	354	gaTGAGTTGGAGAGGAGGCtg/gatg	11/16	0.374027996043385	1	FACETS	0.882	0.777	0.993	0.882	0.777	0.993	CLONAL	1	TRUE	0	0.387048424178319	1		602	345	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713694	52713694	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0064845-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	137	544	0	ENST00000394830.3:c.34del	p.Ser12ProfsTer33	p.S12Pfs*33	ENST00000394830	NM_018313.4	12	Tcc/cc	2/30	0.364156722949932	2	FACETS	0.827	0.759	0.897	0.827	0.759	0.897	CLONAL	2	TRUE	0	0.387048424178319	2		544	428	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098969	178098969	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064846-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	149	509	0	ENST00000397062.3:c.76C>A	p.Gln26Lys	p.Q26K	ENST00000397062	NM_006164.4	26	Caa/Aaa	2/5	0.435947872265275	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.46742242140758	4		509	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579514	7579514	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064846-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	374	758	0	ENST00000269305.4:c.173del	p.Pro58GlnfsTer65	p.P58Qfs*65	ENST00000269305	NM_001126112.2	58	cCa/ca	4/11	0.46742242140758	5	FACETS	1	0.987	1			1	CLONAL	5	TRUE	NA	0.46742242140758	5		758	522	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102098300	102098300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064846-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	70	450	0	ENST00000282441.5:c.1264G>A	p.Glu422Lys	p.E422K	ENST00000282441	NM_001130145.2	422	Gag/Aag	8/9	0.467781196928652	1	FACETS	0.76	0.682	0.839	1	0.98	1	SUBCLONAL	2	TRUE	0	0.46742242140758	1		450	151	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424759	47424760	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064846-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	127	711	1	ENST00000404338.3:c.2834dup	p.Asn946GlufsTer11	p.N946Efs*11	ENST00000404338	NM_004491.4	943	gaa/gAaa	1/6	0.356897319360885	4	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	2	0.46742242140758	4		712	383	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	94	789	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		789	315	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0064847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	696	813	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		813	1090	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50789365	50789365	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752820652	NA	P-0064847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	242	644	1	ENST00000307179.4:c.2975G>A	p.Arg992Gln	p.R992Q	ENST00000307179		992	cGg/cAg	18/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		645	396	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0064848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	35	379	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.615	0.504	0.74	0.615	0.504	0.74	SUBCLONAL	1	FALSE	1	0.260382511614386	2		379	437	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220430	1220430	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0064848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	90	593	0	ENST00000326873.7:c.523A>T	p.Lys175Ter	p.K175*	ENST00000326873	NM_000455.4	175	Aag/Tag	4/10	0.201564597669922	1	FACETS	0.883	0.784	0.989	0.883	0.784	0.989	CLONAL	1	FALSE	0	0.260382511614386	1		593	681	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652501	48652501	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557020638	NA	P-0064848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	43	530	0	ENST00000376670.3:c.1172C>T	p.Thr391Met	p.T391M	ENST00000376670	NM_002049.3	391	aCg/aTg	6/6	0.234886833186238	1	FACETS	0.449	0.375	0.531	0.449	0.375	0.531	SUBCLONAL	1	FALSE	0	0.260382511614386	1		530	640	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809257	243809257	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	37	415	0	ENST00000263826.5:c.367T>A	p.Ser123Thr	p.S123T	ENST00000263826	NM_005465.4	123	Tca/Aca	4/13	0.260382511614386	4	FACETS	0.495	0.407	0.595	0.165	0.135	0.199	SUBCLONAL	1	FALSE	1	0.260382511614386	4		415	723	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524644	106524644	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	53	337	0	ENST00000359195.3:c.2805C>A	p.Tyr935Ter	p.Y935*	ENST00000359195	NM_002649.2	935	taC/taA	9/11	1	2	FACETS	0.872	0.744	1	0.872	0.744	1	CLONAL	1	FALSE	1	0.260382511614386	2		337	467	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412033	116412048	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTCCAGAAGGTATA	TTTTCCAGAAGGTATA	-	novel	NA	P-0064849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	204	502	0	ENST00000397752.3:c.3021_3028+8del		p.X1007_splice	ENST00000397752	NM_000245.2	1007		14/21	0.269107075155374	3	FACETS	0.945	0.882	1	0.945	0.882	1	CLONAL	3	TRUE	0	0.286794846499293	3		502	574	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929014	32929014	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	34	399	0	ENST00000380152.3:c.7024C>G	p.Gln2342Glu	p.Q2342E	ENST00000380152		2342	Caa/Gaa	14/27	0.286794846499293	1	FACETS	0.635	0.52	0.763	0.635	0.52	0.763	SUBCLONAL	1	TRUE	0	0.286794846499293	1		399	320	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129425	152129425	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	44	523	0	ENST00000206249.3:c.378G>C	p.Gln126His	p.Q126H	ENST00000206249	NM_000125.3	126	caG/caC	1/8	0.246231562094871	3	FACETS	0.9	0.756	1	0.45	0.378	0.529	CLONAL	1	TRUE	1	0.286794846499293	3		523	390	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0064850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	34	177	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.988	0.818	1	0.988	0.818	1	CLONAL	1	TRUE	1	0.417295541276969	2		177	165	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026140	36026140	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	145	568	0	ENST00000358208.4:c.742T>C	p.Cys248Arg	p.C248R	ENST00000358208		248	Tgc/Cgc	7/12	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.417295541276969	2		568	633	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942713	44942714	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	77	390	0	ENST00000377967.4:c.3293_3294insA	p.Gln1099AlafsTer4	p.Q1099Afs*4	ENST00000377967	NM_021140.2	1098	ttg/ttAg	23/29	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.417295541276969	2		390	345	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0064851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	259	256	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.507727020775297	6	FACETS	1	0.966	1	1	0.966	1	CLONAL	4	TRUE	2	0.575172439174368	6		256	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0064851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	307	443	0	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	0.575172439174368	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.575172439174368	2		443	501	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	171	468	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.344605681600745	3	FACETS	1	0.987	1	0.662	0.613	0.714	INDETERMINATE	1	TRUE	1	0.575172439174368	3		468	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573984	7573984	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0064851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	239	389	0	ENST00000269305.4:c.1043T>A	p.Leu348Ter	p.L348*	ENST00000269305	NM_001126112.2	348	tTg/tAg	10/11	0.575172439174368	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.575172439174368	2		389	394	SUCCESS
MAD2L2	10459	MSKCC	GRCh37	1	11736942	11736942	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766730327	NA	P-0064851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	165	427	1	ENST00000235310.3:c.295G>A	p.Val99Ile	p.V99I	ENST00000235310		99	Gtc/Atc	7/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.575172439174368	2		428	487	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112745473	112745473	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	141	314	0	ENST00000369452.4:c.791C>A	p.Thr264Asn	p.T264N	ENST00000369452	NM_007373.3	264	aCc/aAc	3/9	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.575172439174368	2		314	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0064852-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	292	462	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.539036705278828	2	FACETS	0.89	0.856	0.923	1	0.995	1	CLONAL	3	TRUE	0	0.534594084113613	2		462	409	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913215	32913215	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782013	NA	P-0064852-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	24	442	0	ENST00000380152.3:c.4723G>A	p.Asp1575Asn	p.D1575N	ENST00000380152		1575	Gac/Aac	11/27	0.474951193075468	2	FACETS	0.203	0.159	0.255	0.102	0.079	0.128	SUBCLONAL	1	TRUE	0	0.534594084113613	2		442	442	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50782607	50782607	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064852-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	46	453	0	ENST00000307179.4:c.2119G>C	p.Asp707His	p.D707H	ENST00000307179		707	Gat/Cat	14/20	0.44092333861628	2	FACETS	0.302	0.254	0.355	0.151	0.127	0.178	SUBCLONAL	1	TRUE	0	0.534594084113613	2		453	570	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52621383	52621383	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064852-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	199	346	0	ENST00000394830.3:c.3034G>A	p.Val1012Ile	p.V1012I	ENST00000394830	NM_018313.4	1012	Gtc/Atc	20/30	0.539036705278828	2	FACETS	0.859	0.817	0.898	1	0.992	1	CLONAL	3	TRUE	0	0.534594084113613	2		346	289	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0064853-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	157	766	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		767	539	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372289	55372289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs748072355	NA	P-0064853-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	132	1505	1	ENST00000297316.4:c.979C>A	p.Pro327Thr	p.P327T	ENST00000297316	NM_022454.3	327	Ccc/Acc	2/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1506	635	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239419	105239419	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064853-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	18	1263	2	ENST00000349310.3:c.968A>G	p.Asp323Gly	p.D323G	ENST00000349310	NM_001014432.1	323	gAc/gGc	12/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1265	710	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31947330	31947330	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1179338180	NA	P-0064853-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	72	676	2	ENST00000375333.2:c.815C>T	p.Thr272Met	p.T272M	ENST00000375333	NM_032454.1	272	aCg/aTg	5/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		678	559	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255347	16255347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747275202	NA	P-0064853-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	151	795	0	ENST00000375759.3:c.2612G>A	p.Arg871His	p.R871H	ENST00000375759	NM_015001.2	871	cGc/cAc	11/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		795	773	SUCCESS
ATM	472	MSKCC	GRCh37	11	108168047	108168047	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs997081415	NA	P-0064853-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	55	451	0	ENST00000278616.4:c.4943T>C	p.Val1648Ala	p.V1648A	ENST00000278616	NM_000051.3	1648	gTt/gCt	33/63	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		451	202	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29449565	29449565	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs776472367	NA	P-0064853-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	118	638	0	ENST00000544604.2:c.2768-2A>G		p.X923_splice	ENST00000544604	NM_001206998.1	923			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		638	493	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748035	41748035	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064853-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	89	952	2	ENST00000226382.2:c.734C>T	p.Ala245Val	p.A245V	ENST00000226382	NM_003924.3	245	gCg/gTg	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		954	216	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508431	106508431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064853-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	138	903	0	ENST00000359195.3:c.425C>T	p.Pro142Leu	p.P142L	ENST00000359195	NM_002649.2	142	cCg/cTg	2/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		903	574	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921481	39921481	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064853-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	141	968	0	ENST00000378444.4:c.4339C>T	p.Arg1447Cys	p.R1447C	ENST00000378444	NM_001123385.1	1447	Cgc/Tgc	10/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		968	612	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0064854-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	51	393	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.903	0.769	1	0.903	0.769	1	CLONAL	1	TRUE	1	0.244933926145351	2		393	461	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0064854-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	12	271	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	1	FACETS	0.293	0.205	0.402	0.293	0.205	0.402	SUBCLONAL	1	TRUE	0	0.244933926145351	1		271	293	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0064854-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	60	554	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.68	0.584	0.783	0.68	0.584	0.783	SUBCLONAL	1	TRUE	1	0.244933926145351	2		554	721	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181311	123181311	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs774761933	NA	P-0064854-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	39	152	0	ENST00000218089.9:c.775C>T	p.Arg259Ter	p.R259*	ENST00000218089	NM_001042749.1	259	Cga/Tga	9/35	1	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.244933926145351	1		152	200	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106178	27106178	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0064854-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	59	665	0	ENST00000324856.7:c.5789C>G	p.Ser1930Ter	p.S1930*	ENST00000324856	NM_006015.4	1930	tCa/tGa	20/20	1	2	FACETS	0.687	0.59	0.793	0.687	0.59	0.793	SUBCLONAL	1	TRUE	1	0.244933926145351	2		665	701	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779657	3779657	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064854-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	81	758	0	ENST00000262367.5:c.5391G>C	p.Lys1797Asn	p.K1797N	ENST00000262367	NM_004380.2	1797	aaG/aaC	31/31	1	2	FACETS	0.782	0.688	0.883	0.782	0.688	0.883	SUBCLONAL	1	TRUE	1	0.244933926145351	2		758	846	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544180	86544180	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064854-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	58	784	0	ENST00000262426.4:c.5C>G	p.Ser2Cys	p.S2C	ENST00000262426	NM_001451.2	2	tCt/tGt	1/2	1	2	FACETS	0.612	0.525	0.708	0.612	0.525	0.708	SUBCLONAL	1	TRUE	1	0.244933926145351	2		784	774	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47601169	47601169	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064854-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	54	491	0	ENST00000263735.4:c.407C>T	p.Ser136Phe	p.S136F	ENST00000263735	NM_002354.2	136	tCt/tTt	3/9	1	2	FACETS	0.806	0.689	0.935	0.806	0.689	0.935	CLONAL	1	TRUE	1	0.244933926145351	2		491	547	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513316	106513316	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064854-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	45	504	0	ENST00000359195.3:c.2220G>C	p.Glu740Asp	p.E740D	ENST00000359195	NM_002649.2	740	gaG/gaC	4/11	1	2	FACETS	0.668	0.561	0.787	0.668	0.561	0.787	SUBCLONAL	1	TRUE	1	0.244933926145351	2		504	550	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907793	76907797	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCT	CTCCT	-	novel	NA	P-0064854-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	55	259	0	ENST00000373344.5:c.4364_4368del	p.Glu1455GlyfsTer10	p.E1455Gfs*10	ENST00000373344	NM_000489.3	1455	gAGGAG/g	15/35	1	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.244933926145351	1		259	318	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66522040	66522043	+	missense_variant	Missense_Mutation	ONP	GAAG	GAAG	AAAA	novel	NA	P-0064854-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	43	481	0	ENST00000358598.2:c.695_698delinsAAAA	p.Arg232_Arg233delinsLysLys	p.R232_R233delinsKK	ENST00000358598	NM_212471.2	232	aGAAGa/aAAAAa	7/11	0.181934707618497	3	FACETS	0.687	0.574	0.812	0.343	0.287	0.406	SUBCLONAL	1	TRUE	1	0.244933926145351	3		481	574	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955064	93955064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151105732	NA	P-0064855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	134	335	0	ENST00000369303.4:c.2834C>T	p.Thr945Met	p.T945M	ENST00000369303	NM_004440.3	945	aCg/aTg	16/17	0.351575165611933	2	FACETS	0.895	0.823	0.97	0.895	0.823	0.97	CLONAL	2	TRUE	0	0.401202578093233	2		335	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574035	7574035	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs867389695	NA	P-0064855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	156	363	0	ENST00000269305.4:c.994-2A>G		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.401202578093233	2	FACETS	0.992	0.92	1	0.992	0.92	1	CLONAL	2	TRUE	0	0.401202578093233	2		363	392	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986745	36986746	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0064855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	229	514	0	ENST00000354822.5:c.943dup	p.His315ProfsTer124	p.H315Pfs*124	ENST00000354822	NM_001079668.2	315	cac/cCac	3/3	0.351575165611933	2	FACETS	0.906	0.85	0.963	0.906	0.85	0.963	CLONAL	2	TRUE	0	0.401202578093233	2		514	630	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211598	36211598	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	148	374	0	ENST00000222270.7:c.1349A>T	p.Gln450Leu	p.Q450L	ENST00000222270	NM_014727.1	450	cAa/cTa	3/37	0.40246757795944	4	FACETS	0.935	0.858	1	0.935	0.858	1	CLONAL	2	TRUE	2	0.401202578093233	4		374	553	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920478	134920478	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	152	400	0	ENST00000398015.3:c.2293C>G	p.Leu765Val	p.L765V	ENST00000398015	NM_004441.4	765	Ctc/Gtc	12/16	0.296240453937066	5	FACETS	0.818	0.749	0.889	0.545	0.499	0.593	CLONAL	2	TRUE	2	0.401202578093233	5		400	742	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970607	21971179	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCGCAGTCTAGGCCTTGAACTAGCAGAGGGTAGGTGTTTGGGTGGTGGTATGCTTTGGGAAGTATAATGTACAAAATGGGCTTTCACGTGCGCAAGTCCATTTCGGGATTATTTCCCATTTGCCGCCCTGGCGGGGCAGGGCGATAGGGAGACTCAGGCCGTCCCACCGATTGGCGCGTGAGCTGAGGCAAGACCGGAGACTGGTCTCCCGGGCTGAACTTTCTGTGCTGGAAAATGAATGCTCTGAGCTTTGGAAGCTCTCAGGGTACAAATTCTCAGATCATCAGTCCTCACCTGAGGGACCTTCCGCGGCATCTATGCGGGCATGGTTACTGCCTCTGGTGCCCCCCGCAGCCGCGCGCAGGTACCGTGCGACATCGCGATGGCCCAGCTCCTCAGCCAGGTCCACGGGCAGACGGCCCCAGGCATCGCGCACGTCCAGCCGCGCCCCGGCCCGGTGCAGCACCACCAGCGTGTCCAGGAAGCCCTCCCGGGCAGCGTCGTGCACGGGTCGGGTGAGAGTGGCGGGGTCGGCGCAGTTGGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCG	CCGCAGTCTAGGCCTTGAACTAGCAGAGGGTAGGTGTTTGGGTGGTGGTATGCTTTGGGAAGTATAATGTACAAAATGGGCTTTCACGTGCGCAAGTCCATTTCGGGATTATTTCCCATTTGCCGCCCTGGCGGGGCAGGGCGATAGGGAGACTCAGGCCGTCCCACCGATTGGCGCGTGAGCTGAGGCAAGACCGGAGACTGGTCTCCCGGGCTGAACTTTCTGTGCTGGAAAATGAATGCTCTGAGCTTTGGAAGCTCTCAGGGTACAAATTCTCAGATCATCAGTCCTCACCTGAGGGACCTTCCGCGGCATCTATGCGGGCATGGTTACTGCCTCTGGTGCCCCCCGCAGCCGCGCGCAGGTACCGTGCGACATCGCGATGGCCCAGCTCCTCAGCCAGGTCCACGGGCAGACGGCCCCAGGCATCGCGCACGTCCAGCCGCGCCCCGGCCCGGTGCAGCACCACCAGCGTGTCCAGGAAGCCCTCCCGGGCAGCGTCGTGCACGGGTCGGGTGAGAGTGGCGGGGTCGGCGCAGTTGGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCG	-	novel	NA	P-0064855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	71	35	0	ENST00000304494.5:c.179_457+294del		p.X60_splice	ENST00000304494	NM_000077.4	60		2/3	0.401202578093233	2	FACETS	0.994	0.928	1	1	0.988	1	CLONAL	4	TRUE	0	0.401202578093233	2		35	89	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0064856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	170	385	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.570252107777525	4	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	2	0.618071613273158	4		385	444	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023539	27023539	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0064856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	400	604	0	ENST00000324856.7:c.645C>G	p.Tyr215Ter	p.Y215*	ENST00000324856	NM_006015.4	215	taC/taG	1/20	0.618071613273158	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.618071613273158	3		604	513	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653775	89653788	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TACTCAGATATTTA	TACTCAGATATTTA	-	novel	NA	P-0064856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	87	325	0	ENST00000371953.3:c.80-6_87del		p.X27_splice	ENST00000371953	NM_000314.4	27		2/9	0.570252107777525	4	FACETS	0.769	0.689	0.853	0.769	0.689	0.853	SUBCLONAL	2	TRUE	2	0.618071613273158	4		325	296	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	315	497	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.618071613273158	3	FACETS	0.971	0.934	1	0.971	0.934	1	CLONAL	3	TRUE	0	0.618071613273158	3		497	458	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911541	134911541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	309	617	0	ENST00000398015.3:c.2006C>T	p.Ala669Val	p.A669V	ENST00000398015	NM_004441.4	669	gCg/gTg	11/16	0.570252107777525	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.618071613273158	4		617	798	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449659	187449659	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	288	527	0	ENST00000232014.4:c.221T>G	p.Leu74Arg	p.L74R	ENST00000232014	NM_001130845.1	74	cTa/cGa	4/10	0.570252107777525	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.618071613273158	4		527	724	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538936	187538936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs951647745	NA	P-0064856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	41	599	0	ENST00000441802.2:c.8804G>A	p.Gly2935Glu	p.G2935E	ENST00000441802	NM_005245.3	2935	gGg/gAg	10/27	0.618071613273158	3	FACETS	0.255	0.212	0.304	0.128	0.106	0.152	SUBCLONAL	1	TRUE	1	0.618071613273158	3		599	680	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971152	21971153	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0064856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	334	673	0	ENST00000304494.5:c.205dup	p.Glu69GlyfsTer51	p.E69Gfs*51	ENST00000304494	NM_000077.4	69	gag/gGag	2/3	0.618071613273158	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.618071613273158	2		673	532	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	121	789	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.804	0.733	0.877	0.804	0.733	0.877	CLONAL	1	TRUE	1	0.763826642871722	2		789	394	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	227	342	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.763826642871722	2	FACETS	0.901	0.86	0.94	0.901	0.86	0.94	CLONAL	2	TRUE	0	0.763826642871722	2		342	330	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023258	27023270	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCGGCGGTG	GGCGGCGGCGGTG	-	novel	NA	P-0064857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	179	547	0	ENST00000324856.7:c.365_377del	p.Gly122AlafsTer106	p.G122Afs*106	ENST00000324856	NM_006015.4	122	GGCGGCGGCGGTGgc/gc	1/20	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.763826642871722	2		547	459	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553609	29553609	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759679443	NA	P-0064857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	145	489	0	ENST00000356175.3:c.2158C>T	p.Arg720Trp	p.R720W	ENST00000356175	NM_000267.3	720	Cgg/Tgg	18/57	1	2	FACETS	0.761	0.699	0.825	0.761	0.699	0.825	SUBCLONAL	1	TRUE	1	0.763826642871722	2		489	499	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021641	31021642	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AG	novel	NA	P-0064857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	243	588	0	ENST00000375687.4:c.1640_1641delinsAG	p.Ser547Ter	p.S547*	ENST00000375687	NM_015338.5	547	tCC/tAG	12/13	1	2	FACETS	0.937	0.88	0.995	0.937	0.88	0.995	CLONAL	1	TRUE	1	0.763826642871722	2		588	679	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138402555	138402555	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	105	331	0	ENST00000289153.2:c.2390A>G	p.Glu797Gly	p.E797G	ENST00000289153	NM_006219.2	797	gAg/gGg	16/22	1	2	FACETS	0.989	0.9	1	0.989	0.9	1	CLONAL	1	TRUE	1	0.763826642871722	2		331	278	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848603	151848603	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	170	509	0	ENST00000262189.6:c.12590G>A	p.Trp4197Ter	p.W4197*	ENST00000262189	NM_170606.2	4197	tGg/tAg	50/59	1	2	FACETS	0.835	0.773	0.899	0.835	0.773	0.899	CLONAL	1	TRUE	1	0.763826642871722	2		509	533	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064872-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	87	789	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.556498909465663	2		789	269	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711915	89711915	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786204866	NA	P-0064872-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	144	340	0	ENST00000371953.3:c.533A>G	p.Tyr178Cys	p.Y178C	ENST00000371953	NM_000314.4	178	tAt/tGt	6/9	0.556498909465663	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.556498909465663	1		340	351	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215303	5215303	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064872-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	134	480	0	ENST00000357368.4:c.4315G>C	p.Glu1439Gln	p.E1439Q	ENST00000357368	NM_002850.3	1439	Gaa/Caa	28/38	1	2	FACETS	0.912	0.833	0.994	0.912	0.833	0.994	CLONAL	1	TRUE	1	0.556498909465663	2		480	528	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589598	67589599	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0064872-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	128	302	0	ENST00000274335.5:c.1362dup	p.Gln455SerfsTer10	p.Q455Sfs*10	ENST00000274335		454	act/acTt	10/15	1	2	FACETS	0.916	0.835	1	0.916	0.835	1	CLONAL	1	TRUE	1	0.556498909465663	2		302	502	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0064873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	42	393	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.686	0.576	0.807	0.686	0.576	0.807	SUBCLONAL	1	TRUE	1	0.434087747246032	2		393	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0064873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	322	607	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	NA	2	FACETS	0.941	0.894	0.99			1	INDETERMINATE	2	TRUE	NA	0.434087747246032	2		607	788	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152104	55152104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121908588	NA	P-0064873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	83	465	0	ENST00000257290.5:c.2536G>T	p.Asp846Tyr	p.D846Y	ENST00000257290	NM_006206.4	846	Gat/Tat	18/23	1	2	FACETS	0.592	0.523	0.666	0.592	0.523	0.666	SUBCLONAL	1	TRUE	1	0.434087747246032	2		465	646	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321399	1321399	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	50	482	0	ENST00000400841.2:c.356C>A	p.Pro119His	p.P119H	ENST00000400841		119	cCc/cAc	4/6	1	2	FACETS	0.312	0.264	0.365	0.312	0.264	0.365	SUBCLONAL	1	TRUE	1	0.434087747246032	2		482	739	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231047	53231047	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	187	521	0	ENST00000375401.3:c.1855del	p.Thr619LeufsTer40	p.T619Lfs*40	ENST00000375401	NM_004187.3	619	Act/ct	13/26	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.434087747246032	2		521	769	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0064874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	14	256	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.17	0.123	0.228	0.17	0.123	0.228	SUBCLONAL	1	TRUE	1	0.6605059663027	2		256	249	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0064874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	14	390	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.272001306965992	1	FACETS	0.056	0.04	0.075	0.056	0.04	0.075	INDETERMINATE	1	TRUE	0	0.6605059663027	1		390	511	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254826	16254826	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0064874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	43	456	0	ENST00000375759.3:c.2091C>G	p.Tyr697Ter	p.Y697*	ENST00000375759	NM_015001.2	697	taC/taG	11/15	1	2	FACETS	0.211	0.176	0.25	0.211	0.176	0.25	SUBCLONAL	1	TRUE	1	0.6605059663027	2		456	618	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099956	27099957	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0064874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	168	541	0	ENST00000324856.7:c.3836_3837del	p.Tyr1279SerfsTer7	p.Y1279Sfs*7	ENST00000324856	NM_006015.4	1279	TAt/t	15/20	1	2	FACETS	0.678	0.625	0.734	0.678	0.625	0.734	SUBCLONAL	1	TRUE	1	0.6605059663027	2		541	750	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024684	31024684	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	40	559	0	ENST00000375687.4:c.4169A>G	p.His1390Arg	p.H1390R	ENST00000375687	NM_015338.5	1390	cAt/cGt	13/13	1	2	FACETS	0.153	0.127	0.183	0.153	0.127	0.183	SUBCLONAL	1	TRUE	1	0.6605059663027	2		559	790	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059132	47059132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	171	379	0	ENST00000409792.3:c.7529G>A	p.Arg2510His	p.R2510H	ENST00000409792	NM_014159.6	2510	cGc/cAc	20/21	0.6605059663027	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.6605059663027	1		379	342	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0064874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	36	379	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	1	2	FACETS	0.198	0.162	0.239	0.198	0.162	0.239	SUBCLONAL	1	TRUE	1	0.6605059663027	2		379	550	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599234	55599234	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0064874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	25	302	0	ENST00000288135.5:c.2362-2A>G		p.X788_splice	ENST00000288135	NM_000222.2	788			1	2	FACETS	0.2	0.157	0.249	0.2	0.157	0.249	SUBCLONAL	1	TRUE	1	0.6605059663027	2		302	379	SUCCESS
APC	324	MSKCC	GRCh37	5	112154997	112154997	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	41	357	0	ENST00000257430.4:c.1268G>A	p.Trp423Ter	p.W423*	ENST00000257430	NM_000038.5	423	tGg/tAg	10/16	0.6605059663027	1	FACETS	0.208	0.173	0.246	0.208	0.173	0.246	SUBCLONAL	1	TRUE	0	0.6605059663027	1		357	400	SUCCESS
APC	324	MSKCC	GRCh37	5	112174842	112174842	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	24	382	0	ENST00000257430.4:c.3552del	p.Thr1185GlnfsTer80	p.T1185Qfs*80	ENST00000257430	NM_000038.5	1184	gCc/gc	16/16	0.6605059663027	1	FACETS	0.145	0.114	0.182	0.145	0.114	0.182	SUBCLONAL	1	TRUE	0	0.6605059663027	1		382	335	SUCCESS
APC	324	MSKCC	GRCh37	5	112174975	112174975	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	82	400	0	ENST00000257430.4:c.3684del	p.Asn1229IlefsTer36	p.N1229Ifs*36	ENST00000257430	NM_000038.5	1228	caG/ca	16/16	0.6605059663027	1	FACETS	0.521	0.464	0.582	0.521	0.464	0.582	SUBCLONAL	1	TRUE	0	0.6605059663027	1		400	319	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242470	+	missense_variant	Missense_Mutation	DNP	TT	TT	CC	rs397517096	NA	P-0064874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	196	335	0	ENST00000275493.2:c.2239_2240delinsCC	p.Leu747Pro	p.L747P	ENST00000275493	NM_005228.3	747	TTa/CCa	19/28	0.589925289679873	3	FACETS	1	0.985	1	0.612	0.569	0.656	CLONAL	1	TRUE	1	0.6605059663027	3		335	645	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624263	89624263	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0064875-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	87	185	0	ENST00000371953.3:c.40del	p.Arg14GlyfsTer10	p.R14Gfs*10	ENST00000371953	NM_000314.4	13	Aaa/aa	1/9	0.496239900188764	2	FACETS	0.943	0.856	1	0.943	0.856	1	CLONAL	2	TRUE	0	0.496239900188764	2		185	186	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0064875-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	210	524	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.496239900188764	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.496239900188764	2		524	415	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242486	+	inframe_deletion	In_Frame_Del	DEL	TTAAGAGAAGCAACATCT	TTAAGAGAAGCAACATCT	-	rs121913440	NA	P-0064875-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	243	371	0	ENST00000275493.2:c.2239_2256del	p.Leu747_Ser752del	p.L747_S752del	ENST00000275493	NM_005228.3	747	TTAAGAGAAGCAACATCT/-	19/28	0.496239900188764	6	FACETS	1	0.985	1	0.848	0.8	0.898	CLONAL	3	TRUE	2	0.496239900188764	6		371	575	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166815	32166815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064875-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	72	483	1	ENST00000375023.3:c.4423C>T	p.Arg1475Cys	p.R1475C	ENST00000375023	NM_004557.3	1475	Cgc/Tgc	24/30	0.450965154574703	4	FACETS	0.791	0.692	0.897	0.395	0.346	0.449	SUBCLONAL	1	TRUE	2	0.496239900188764	4		484	549	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	99	789	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.813	0.735	0.893	0.813	0.735	0.893	CLONAL	1	TRUE	1	0.825579958895782	2		789	295	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0064876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	218	576	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.993	0.932	1	0.993	0.932	1	CLONAL	1	TRUE	1	0.825579958895782	2		576	532	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056343	27056344	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0064876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	218	450	0	ENST00000324856.7:c.1341_1342del	p.Gln449AlafsTer173	p.Q449Afs*173	ENST00000324856	NM_006015.4	447	TAt/t	2/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.825579958895782	2		450	482	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038756	47038756	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	197	556	0	ENST00000377604.3:c.763C>T	p.Gln255Ter	p.Q255*	ENST00000377604	NM_001204468.1	255	Cag/Tag	9/24	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.825579958895782	2		556	477	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11181374	11181374	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	165	356	0	ENST00000361445.4:c.6862G>C	p.Glu2288Gln	p.E2288Q	ENST00000361445	NM_004958.3	2288	Gag/Cag	49/58	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.825579958895782	2		356	391	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131972841	131972841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	107	199	0	ENST00000265335.6:c.3424G>A	p.Glu1142Lys	p.E1142K	ENST00000265335		1142	Gaa/Aaa	22/25	1	2	FACETS	0.87	0.791	0.951	0.87	0.791	0.951	CLONAL	1	TRUE	1	0.825579958895782	2		199	298	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891600	151891600	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	182	391	0	ENST00000262189.6:c.4432C>T	p.Gln1478Ter	p.Q1478*	ENST00000262189	NM_170606.2	1478	Cag/Tag	29/59	1	2	FACETS	0.973	0.908	1	0.973	0.908	1	CLONAL	1	TRUE	1	0.825579958895782	2		391	453	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807271	3807290	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATGCTGCTTGACGCTTACCT	ATGCTGCTTGACGCTTACCT	-	novel	NA	P-0064876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	178	270	0	ENST00000262367.5:c.3697_3698+18del		p.X1233_splice	ENST00000262367	NM_004380.2	1233		19/31	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.825579958895782	2		270	401	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858180	9858180	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	227	538	0	ENST00000330684.3:c.3221C>A	p.Pro1074His	p.P1074H	ENST00000330684	NM_001134407.1	1074	cCt/cAt	13/13	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.825579958895782	2		538	545	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165371	47165371	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	52	431	0	ENST00000409792.3:c.755C>T	p.Ala252Val	p.A252V	ENST00000409792	NM_014159.6	252	gCa/gTa	3/21	1	2	FACETS	0.227	0.192	0.264	0.227	0.192	0.264	SUBCLONAL	1	TRUE	1	0.825579958895782	2		431	556	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864287	151864287	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	208	359	0	ENST00000262189.6:c.9694G>T	p.Glu3232Ter	p.E3232*	ENST00000262189	NM_170606.2	3232	Gaa/Taa	42/59	1	2	FACETS	0.931	0.872	0.992	0.931	0.872	0.992	CLONAL	1	TRUE	1	0.825579958895782	2		359	541	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572510	41572510	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748485911	NA	P-0064877-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	192	626	0	ENST00000263253.7:c.5039G>A	p.Arg1680His	p.R1680H	ENST00000263253	NM_001429.3	1680	cGc/cAc	30/31	0.65539174959507	2	FACETS	0.942	0.876	1	0.471	0.438	0.505	CLONAL	1	TRUE	0	0.664960784109519	2		626	613	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960039	134960039	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533462328	NA	P-0064877-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	158	586	0	ENST00000398015.3:c.2396G>A	p.Arg799His	p.R799H	ENST00000398015	NM_004441.4	799	cGc/cAc	13/16	0.634518650506411	3	FACETS	0.973	0.894	1	0.486	0.447	0.527	CLONAL	1	TRUE	1	0.664960784109519	3		586	651	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61717812	61717812	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064877-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	131	474	0	ENST00000401558.2:c.1987C>G	p.Gln663Glu	p.Q663E	ENST00000401558	NM_003400.3	663	Caa/Gaa	17/25	1	2	FACETS	0.923	0.845	1	0.923	0.845	1	CLONAL	1	TRUE	1	0.664960784109519	2		474	427	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591116	67591116	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064878-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	187	386	0	ENST00000274335.5:c.1709T>C	p.Leu570Pro	p.L570P	ENST00000274335		570	cTt/cCt	12/15	0.355350804994125	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	1	0.355350804994125	4		386	408	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595550	55595550	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064878-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	30	376	0	ENST00000288135.5:c.2045del	p.Leu682Ter	p.L682*	ENST00000288135	NM_000222.2	680	aaT/aa	14/21	1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	1	0.355350804994125	2		376	162	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110720	2110721	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0064878-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	127	580	0	ENST00000219476.3:c.1025_1026delinsAT	p.Ile342Asn	p.I342N	ENST00000219476	NM_000548.3	342	aTC/aAT	11/42	0.332372148984486	4	FACETS	0.82	0.745	0.898	0.82	0.745	0.898	CLONAL	2	TRUE	2	0.355350804994125	4		580	591	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183741	10183750	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCTCCCAG	GCCCTCCCAG	-	novel	NA	P-0064878-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	141	540	0	ENST00000256474.2:c.211_220del	p.Pro71SerfsTer85	p.P71Sfs*85	ENST00000256474	NM_000551.3	70	gaGCCCTCCCAG/ga	1/3	0.355350804994125	2	FACETS	0.864	0.794	0.937	0.864	0.794	0.937	CLONAL	2	TRUE	0	0.355350804994125	2		540	459	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584782	52584783	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0064878-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	123	504	0	ENST00000394830.3:c.4339_4340del	p.Gly1447LysfsTer61	p.G1447Kfs*61	ENST00000394830	NM_018313.4	1447	GGa/a	28/30	0.355350804994125	2	FACETS	0.916	0.837	0.997	0.916	0.837	0.997	CLONAL	2	TRUE	0	0.355350804994125	2		504	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	404	519	0	ENST00000269305.4:c.527G>C	p.Cys176Ser	p.C176S	ENST00000269305	NM_001126112.2	176	tGc/tCc	5/11	0.732728201047005	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.732728201047005	2		519	519	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120129	70120151	+	frameshift_variant	Frame_Shift_Del	DEL	ACAGGCGCACACGCTGACCACGC	ACAGGCGCACACGCTGACCACGC	CGT	novel	NA	P-0064879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	171	484	1	ENST00000245479.2:c.1131_1153delinsCGT	p.Gln378ValfsTer193	p.Q378Vfs*193	ENST00000245479	NM_000346.3	377	ccACAGGCGCACACGCTGACCACGCtg/ccCGTtg	3/3	0.732728201047005	2	FACETS	1	0.944	1	0.51	0.473	0.547	CLONAL	1	TRUE	0	0.732728201047005	2		485	458	SUCCESS
APC	324	MSKCC	GRCh37	5	112175454	112175455	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTCTGTCAGTTCACTTGATAGT	novel	NA	P-0064879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	204	439	0	ENST00000257430.4:c.4166_4187dup	p.Glu1397CysfsTer5	p.E1397Cfs*5	ENST00000257430	NM_000038.5	1388	act/acTTCTGTCAGTTCACTTGATAGTt	16/16	0.732728201047005	3	FACETS	1	0.991	1	0.461	0.431	0.492	CLONAL	1	TRUE	0	0.732728201047005	3		439	550	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140507851	140507851	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	74	288	0	ENST00000288602.6:c.620C>T	p.Pro207Leu	p.P207L	ENST00000288602	NM_004333.4	207	cCa/cTa	5/18	0.720205093238504	4	FACETS	0.774	0.68	0.875	0.258	0.226	0.292	SUBCLONAL	1	TRUE	1	0.732728201047005	4		288	452	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755477	133755480	+	frameshift_variant	Frame_Shift_Del	DEL	CCGG	CCGG	-	novel	NA	P-0064879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	255	419	0	ENST00000318560.5:c.1448_1451del	p.Arg483ProfsTer36	p.R483Pfs*36	ENST00000318560	NM_005157.4	482	gaCCGG/ga	9/11	0.732728201047005	3	FACETS	0.943	0.894	0.993	0.943	0.894	0.993	CLONAL	2	TRUE	1	0.732728201047005	3		419	504	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611835	100611836	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0064879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	137	160	0	ENST00000308731.7:c.1285_1286del	p.Ile429GlnfsTer10	p.I429Qfs*10	ENST00000308731	NM_000061.2	429	ATc/c	14/19	0.732728201047005	2	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.732728201047005	2		160	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0064880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	116	70	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		70	568	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509310	106509310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	95	416	0	ENST00000359195.3:c.1304G>A	p.Cys435Tyr	p.C435Y	ENST00000359195	NM_002649.2	435	tGc/tAc	2/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		416	935	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075582	8075582	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	121	391	0	ENST00000377482.5:c.98A>G	p.Tyr33Cys	p.Y33C	ENST00000377482	NM_018948.3	33	tAc/tGc	2/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		391	593	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851646	63851646	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	138	436	0	ENST00000279873.7:c.2424G>T	p.Glu808Asp	p.E808D	ENST00000279873	NM_032199.2	808	gaG/gaT	10/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		436	593	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118339504	118339512	+	inframe_deletion	In_Frame_Del	DEL	AGGTTTTGG	AGGTTTTGG	-	novel	NA	P-0064880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	40	376	0	ENST00000534358.1:c.447_455del	p.Leu149_Gly152delinsPhe	p.L149_G152delinsF	ENST00000534358	NM_005933.3	149	ttAGGTTTTGGc/ttc	2/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		376	567	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221331	2221331	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	119	441	0	ENST00000326181.6:c.415A>G	p.Lys139Glu	p.K139E	ENST00000326181	NM_032271.2	139	Aaa/Gaa	6/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		441	689	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100111	11100111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	134	440	0	ENST00000358026.2:c.1237C>T	p.Gln413Ter	p.Q413*	ENST00000358026	NM_001128849.1	413	Cag/Tag	7/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		440	590	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051205	13051205	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0064880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	74	476	0	ENST00000316448.5:c.641C>G	p.Ser214Ter	p.S214*	ENST00000316448	NM_004343.3	214	tCa/tGa	5/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		476	631	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303875	30303875	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0064880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	129	444	1	ENST00000262643.3:c.112-1G>T		p.X38_splice	ENST00000262643	NM_001238.2	38			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		445	588	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39708733	39708733	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	44	299	0	ENST00000361337.2:c.344A>T	p.Gln115Leu	p.Q115L	ENST00000361337	NM_003286.2	115	cAa/cTa	6/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		299	490	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475620	12475620	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	104	362	0	ENST00000287820.6:c.1494G>T	p.Gln498His	p.Q498H	ENST00000287820	NM_015869.4	498	caG/caT	7/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		362	618	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467589	66467589	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	41	397	0	ENST00000273854.3:c.680G>T	p.Arg227Leu	p.R227L	ENST00000273854	NM_004439.5	227	cGt/cTt	3/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		397	497	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509321	106509321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	90	441	0	ENST00000359195.3:c.1315C>T	p.Pro439Ser	p.P439S	ENST00000359195	NM_002649.2	439	Cca/Tca	2/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		441	969	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050726	69050726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	103	273	0	ENST00000288368.4:c.4061C>T	p.Pro1354Leu	p.P1354L	ENST00000288368	NM_024870.2	1354	cCa/cTa	33/40	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		273	527	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964321	70964321	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	57	201	0	ENST00000276594.2:c.1707A>C	p.Glu569Asp	p.E569D	ENST00000276594	NM_024504.3	569	gaA/gaC	8/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		201	415	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742123	145742123	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	62	444	1	ENST00000428558.2:c.380C>A	p.Pro127Gln	p.P127Q	ENST00000428558	NM_004260.3	127	cCg/cAg	5/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		445	893	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	53	342	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.146963572099784	3	FACETS	1	0.927	1	0.569	0.487	0.658	INDETERMINATE	1	TRUE	1	0.29	3		342	368	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903763	114903763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	68	367	0	ENST00000543371.1:c.767C>T	p.Pro256Leu	p.P256L	ENST00000543371	NM_001198531.1	256	cCg/cTg	7/14	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.29	2		367	440	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030464	47030464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	39	484	0	ENST00000377604.3:c.239G>A	p.Arg80His	p.R80H	ENST00000377604	NM_001204468.1	80	cGt/cAt	4/24	1	2	FACETS	0.476	0.394	0.568	0.476	0.394	0.568	SUBCLONAL	1	TRUE	1	0.29	2		484	565	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707824	43707824	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	35	512	0	ENST00000382044.4:c.5057A>G	p.Lys1686Arg	p.K1686R	ENST00000382044	NM_001141980.1	1686	aAg/aGg	23/28	1	2	FACETS	0.426	0.348	0.513	0.426	0.348	0.513	SUBCLONAL	1	TRUE	1	0.29	2		512	567	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961413	54961413	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	37	237	0	ENST00000312783.6:c.219T>A	p.Asn73Lys	p.N73K	ENST00000312783	NM_198436.1	73	aaT/aaA	4/10	0.298887856617291	3	FACETS	0.964	0.798	1	0.482	0.399	0.575	CLONAL	1	TRUE	1	0.29	3		237	303	SUCCESS
APC	324	MSKCC	GRCh37	5	112175383	112175384	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	76	430	0	ENST00000257430.4:c.4092_4093insA	p.Gly1365ArgfsTer10	p.G1365Rfs*10	ENST00000257430	NM_000038.5	1364	-/A	16/16	1	2	FACETS	0.998	0.878	1	0.998	0.878	1	CLONAL	1	TRUE	1	0.29	2		430	525	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0064882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	48	386	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.643	0.544	0.753	0.643	0.544	0.753	SUBCLONAL	1	TRUE	1	0.284237360675988	2		386	525	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0064882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	22	293	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.469	0.363	0.592	0.469	0.363	0.592	SUBCLONAL	1	TRUE	1	0.284237360675988	2		293	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578412	7578414	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0064882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	130	491	0	ENST00000269305.4:c.516_518del	p.Val173del	p.V173del	ENST00000269305	NM_001126112.2	172	gtTGTg/gtg	5/11	0.161224970516994	2	FACETS	1	0.959	1	0.55	0.499	0.604	INDETERMINATE	1	TRUE	0	0.284237360675988	2		491	831	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094396	27094396	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	47	422	0	ENST00000324856.7:c.3105del	p.Met1036TrpfsTer3	p.M1036Wfs*3	ENST00000324856	NM_006015.4	1035	gCc/gc	11/20	1	2	FACETS	0.49	0.412	0.576	0.49	0.412	0.576	SUBCLONAL	1	TRUE	1	0.284237360675988	2		422	675	SUCCESS
APC	324	MSKCC	GRCh37	5	112175233	112175234	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0064882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	59	430	0	ENST00000257430.4:c.3942_3943del	p.Arg1314SerfsTer3	p.R1314Sfs*3	ENST00000257430	NM_000038.5	1314	agGTca/agca	16/16	0.284237360675988	1	FACETS	0.579	0.498	0.668	0.579	0.498	0.668	SUBCLONAL	1	TRUE	0	0.284237360675988	1		430	615	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064883-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	37	472	3	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	1	0.831	1	1	0.831	1	CLONAL	1	TRUE	1	0.14	2		475	524	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855029	76855029	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1557085898	NA	P-0064883-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	15	222	0	ENST00000373344.5:c.5807A>G	p.Lys1936Arg	p.K1936R	ENST00000373344	NM_000489.3	1936	aAg/aGg	25/35	1	1	FACETS	0.791	0.583	1	1	0.898	1	CLONAL	2	TRUE	0	0.14	1		222	126	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274213	10274213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1302734897	NA	P-0064883-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	35	435	0	ENST00000330684.3:c.56G>A	p.Arg19His	p.R19H	ENST00000330684	NM_001134407.1	19	cGc/cAc	2/13	1	2	FACETS	0.833	0.682	1	0.833	0.682	1	CLONAL	1	TRUE	1	0.14	2		435	600	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145744	11145744	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1388796557	NA	P-0064883-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	43	506	0	ENST00000358026.2:c.4106G>A	p.Arg1369His	p.R1369H	ENST00000358026	NM_001128849.1	1369	cGt/cAt	29/36	1	2	FACETS	0.773	0.645	0.916	0.773	0.645	0.916	CLONAL	1	TRUE	1	0.14	2		506	795	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732911	30732911	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0064883-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	32	408	0	ENST00000295754.5:c.1525-1G>T		p.X509_splice	ENST00000295754	NM_003242.5	509			1	2	FACETS	0.715	0.579	0.87	0.715	0.579	0.87	SUBCLONAL	1	TRUE	1	0.14	2		408	639	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050348	37050348	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs267607755	NA	P-0064883-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	20	330	0	ENST00000231790.2:c.497T>A	p.Leu166Ter	p.L166*	ENST00000231790	NM_000249.3	166	tTa/tAa	6/19	1	2	FACETS	0.866	0.662	1	0.866	0.662	1	CLONAL	1	TRUE	1	0.14	2		330	330	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090630	71090630	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064883-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	34	398	0	ENST00000318789.4:c.718A>G	p.Thr240Ala	p.T240A	ENST00000318789	NM_032682.5	240	Act/Gct	11/21	1	2	FACETS	0.773	0.63	0.935	0.773	0.63	0.935	CLONAL	1	TRUE	1	0.14	2		398	628	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0064885-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	100	177	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.694057978058383	2		177	272	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49423200	49423200	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064885-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	212	497	0	ENST00000301067.7:c.14059C>G	p.Gln4687Glu	p.Q4687E	ENST00000301067	NM_003482.3	4687	Cag/Gag	43/54	1	2	FACETS	0.737	0.686	0.79	0.737	0.686	0.79	SUBCLONAL	1	TRUE	1	0.694057978058383	2		497	829	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105676	27105676	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064886-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	138	533	0	ENST00000324856.7:c.5287G>T	p.Glu1763Ter	p.E1763*	ENST00000324856	NM_006015.4	1763	Gaa/Taa	20/20	1	2	FACETS	0.873	0.794	0.956	0.873	0.794	0.956	CLONAL	1	TRUE	1	0.355227634014194	2		533	890	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111503	8111507	+	frameshift_variant	Frame_Shift_Del	DEL	GGAAT	GGAAT	-	novel	NA	P-0064886-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	105	491	0	ENST00000346208.3:c.990_994del	p.Arg330SerfsTer20	p.R330Sfs*20	ENST00000346208		330	aGGAAT/a	5/6	1	2	FACETS	0.815	0.731	0.905	0.815	0.731	0.905	CLONAL	1	TRUE	1	0.355227634014194	2		491	725	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577572	7577573	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTA	novel	NA	P-0064886-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	105	441	0	ENST00000269305.4:c.706_708dup	p.Tyr236dup	p.Y236dup	ENST00000269305	NM_001126112.2	236	-/TAC	7/11	0.236117821202328	2	FACETS	1	0.962	1	0.573	0.515	0.634	CLONAL	1	TRUE	0	0.355227634014194	2		441	516	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22153395	22153395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064886-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	112	467	0	ENST00000215832.6:c.515G>A	p.Arg172His	p.R172H	ENST00000215832	NM_002745.4	172	cGt/cAt	4/9	1	2	FACETS	0.909	0.818	1	0.909	0.818	1	CLONAL	1	TRUE	1	0.355227634014194	2		467	694	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0064898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	127	497	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	1	2	FACETS	0.912	0.835	0.992	0.912	0.835	0.992	CLONAL	1	TRUE	1	0.717835323947506	2		497	388	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	101	342	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.96	0.87	1	0.96	0.87	1	CLONAL	1	TRUE	1	0.717835323947506	2		342	293	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682399	52682400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0064898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	96	262	1	ENST00000394830.3:c.773dup	p.Asn258LysfsTer6	p.N258Kfs*6	ENST00000394830	NM_018313.4	258	aat/aaAt	8/30	1	2	FACETS	0.852	0.768	0.939	0.852	0.768	0.939	CLONAL	1	TRUE	1	0.717835323947506	2		263	314	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925316	114925317	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs745872748	NA	P-0064898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	193	367	13	ENST00000543371.1:c.1403dup	p.Cys469ValfsTer8	p.C469Vfs*8	ENST00000543371	NM_001198531.1	465	aga/agAa	14/14	0.708646413087787	2	FACETS	0.835	0.789	0.88	0.835	0.789	0.88	CLONAL	2	TRUE	0	0.717835323947506	2		380	322	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0064898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	15	469	0	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	0.717835323947506	1	FACETS	0.115	0.084	0.153	0.115	0.084	0.153	SUBCLONAL	1	TRUE	0	0.717835323947506	1		469	232	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604700	48604700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	162	451	1	ENST00000342988.3:c.1522G>A	p.Gly508Ser	p.G508S	ENST00000342988	NM_005359.5	508	Ggc/Agc	12/12	0.717835323947506	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.717835323947506	1		452	274	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344852	118344852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200209840	NA	P-0064898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	59	482	0	ENST00000534358.1:c.2978C>T	p.Thr993Ile	p.T993I	ENST00000534358	NM_005933.3	993	aCt/aTt	3/36	1	2	FACETS	0.353	0.304	0.406	0.353	0.304	0.406	SUBCLONAL	1	TRUE	1	0.717835323947506	2		482	466	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865720	57865720	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	186	608	0	ENST00000228682.2:c.3197A>G	p.Asp1066Gly	p.D1066G	ENST00000228682	NM_005269.2	1066	gAt/gGt	12/12	0.138469576383826	4	FACETS	0.894	0.833	0.956	0.894	0.833	0.956	INDETERMINATE	2	TRUE	2	0.717835323947506	4		608	498	SUCCESS
APC	324	MSKCC	GRCh37	5	112174356	112174357	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0064898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	75	356	0	ENST00000257430.4:c.3066_3067del	p.Pro1024AsnfsTer4	p.P1024Nfs*4	ENST00000257430	NM_000038.5	1022	gAT/g	16/16	1	2	FACETS	0.749	0.664	0.839	0.749	0.664	0.839	SUBCLONAL	1	TRUE	1	0.717835323947506	2		356	279	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843701	151843701	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	150	395	0	ENST00000262189.6:c.14014G>C	p.Ala4672Pro	p.A4672P	ENST00000262189	NM_170606.2	4672	Gca/Cca	53/59	0.717835323947506	3	FACETS	1	0.964	1	0.542	0.498	0.587	CLONAL	1	TRUE	1	0.717835323947506	3		395	524	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737816	145737819	+	missense_variant	Missense_Mutation	ONP	CGCC	CGCC	TGCT	novel	NA	P-0064898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	90	650	0	ENST00000428558.2:c.3011_3014delinsAGCA	p.Arg1004_Arg1005delinsGlnGln	p.R1004_R1005delinsQQ	ENST00000428558	NM_004260.3	1004	cGGCGg/cAGCAg	18/22	0.717835323947506	3	FACETS	0.499	0.443	0.559	0.249	0.221	0.28	SUBCLONAL	1	TRUE	1	0.717835323947506	3		650	683	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0064899-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	370	497	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	0.44064461569697	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.44064461569697	2		497	775	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064899-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	95	342	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.969	0.867	1	0.969	0.867	1	CLONAL	1	TRUE	1	0.44064461569697	2		342	445	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231551	5231551	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064899-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	61	480	0	ENST00000357368.4:c.1925C>T	p.Pro642Leu	p.P642L	ENST00000357368	NM_002850.3	642	cCg/cTg	14/38	1	2	FACETS	0.473	0.408	0.544	0.473	0.408	0.544	SUBCLONAL	1	TRUE	1	0.44064461569697	2		480	585	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647133	23647133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571063157	NA	P-0064899-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	60	455	0	ENST00000261584.4:c.734C>T	p.Ala245Val	p.A245V	ENST00000261584	NM_024675.3	245	gCg/gTg	4/13	0.163551200123858	2	FACETS	0.44	0.379	0.507	0.22	0.189	0.254	INDETERMINATE	1	TRUE	0	0.44064461569697	2		455	619	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593533	48593533	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064899-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	156	293	0	ENST00000342988.3:c.1284G>T	p.Lys428Asn	p.K428N	ENST00000342988	NM_005359.5	428	aaG/aaT	10/12	0.44064461569697	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.44064461569697	1		293	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577520	7577520	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064899-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	184	422	0	ENST00000269305.4:c.761T>C	p.Ile254Thr	p.I254T	ENST00000269305	NM_001126112.2	254	aTc/aCc	7/11	0.44064461569697	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.44064461569697	1		422	514	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900640	32900640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358747	NA	P-0064899-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	101	288	0	ENST00000380152.3:c.521G>A	p.Arg174His	p.R174H	ENST00000380152		174	cGt/cAt	7/27	1	2	FACETS	0.963	0.865	1	0.963	0.865	1	CLONAL	1	TRUE	1	0.44064461569697	2		288	476	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280398	1280398	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064899-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	158	548	0	ENST00000310581.5:c.1825C>A	p.His609Asn	p.H609N	ENST00000310581	NM_198253.2	609	Cat/Aat	4/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.44064461569697	2		548	634	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215848	98215848	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064899-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	177	357	0	ENST00000331920.6:c.3361C>T	p.His1121Tyr	p.H1121Y	ENST00000331920	NM_000264.3	1121	Cac/Tac	20/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.44064461569697	2		357	700	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593576	55593606	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	In_Frame_Del	DEL	CCACAGAAACCCATGTATGAAGTACAGTGGA	CCACAGAAACCCATGTATGAAGTACAGTGGA	-	novel	NA	P-0064900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	317	408	0	ENST00000288135.5:c.1648-6_1672del		p.K550_K558del	ENST00000288135	NM_000222.2	550		11/21	0.430837996101737	1	FACETS	0.7	0.669	0.73	0.7	0.669	0.73	INDETERMINATE	1	TRUE	0	0.897955357511957	1		408	556	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097818	27097818	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0064900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	149	489	0	ENST00000324856.7:c.3406+1G>C		p.X1136_splice	ENST00000324856	NM_006015.4	1136			0.23574067831072	1	FACETS	0.368	0.338	0.399	0.368	0.338	0.399	INDETERMINATE	1	TRUE	0	0.897955357511957	1		489	497	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101477	27101477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0064900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	151	526	0	ENST00000324856.7:c.4759del	p.Ser1587AlafsTer25	p.S1587Afs*25	ENST00000324856	NM_006015.4	1587	Agc/gc	18/20	0.23574067831072	1	FACETS	0.401	0.37	0.434	0.401	0.37	0.434	INDETERMINATE	1	TRUE	0	0.897955357511957	1		526	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0064901-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	198	441	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.638470668247723	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.638470668247723	1		441	390	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609651	46609651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064901-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	310	544	0	ENST00000263734.3:c.2375G>A	p.Gly792Glu	p.G792E	ENST00000263734	NM_001430.4	792	gGg/gAg	15/16	0.212531815333523	4	FACETS	0.906	0.857	0.956	0.906	0.857	0.956	INDETERMINATE	2	TRUE	2	0.638470668247723	4		544	878	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673029	30673029	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064901-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1698	159	736	0	ENST00000376406.3:c.3931A>T	p.Arg1311Trp	p.R1311W	ENST00000376406	NM_014641.2	1311	Agg/Tgg	10/15	0.638470668247723	5	FACETS	0.525	0.479	0.574	0.175	0.159	0.192	SUBCLONAL	1	TRUE	2	0.638470668247723	5		736	1857	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967677	90967677	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064901-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	77	317	0	ENST00000265433.3:c.1231T>A	p.Ser411Thr	p.S411T	ENST00000265433	NM_002485.4	411	Tct/Act	10/16	0.638470668247723	3	FACETS	0.533	0.468	0.603	0.267	0.234	0.302	SUBCLONAL	1	TRUE	1	0.638470668247723	3		317	597	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937719	76937720	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0064901-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	65	447	0	ENST00000373344.5:c.3028_3029delinsTT	p.Glu1010Leu	p.E1010L	ENST00000373344	NM_000489.3	1010	GAa/TTa	9/35	0.638470668247723	1	FACETS	0.419	0.365	0.476	0.419	0.365	0.476	SUBCLONAL	1	TRUE	0	0.638470668247723	1		447	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0064902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	764	560	0	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	0.822929079204232	2	FACETS	0.995	0.976	1	0.995	0.976	1	CLONAL	2	TRUE	0	0.822929079204232	2		560	933	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514940	103514940	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1008091379	NA	P-0064902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	844	477	0	ENST00000355739.4:c.1441G>T	p.Val481Leu	p.V481L	ENST00000355739	NM_000123.3	481	Gtg/Ttg	8/15	0.776574402801781	4	FACETS	0.986	0.962	1	0.986	0.962	1	CLONAL	3	TRUE	1	0.822929079204232	4		477	1264	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70411656	70411656	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	55	361	0	ENST00000373644.4:c.4330C>A	p.Pro1444Thr	p.P1444T	ENST00000373644	NM_030625.2	1444	Cca/Aca	5/12	0.822929079204232	3	FACETS	0.234	0.199	0.271	0.117	0.099	0.136	SUBCLONAL	1	TRUE	1	0.822929079204232	3		361	808	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421865	49421973	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGAGTTGGGGATCTTCATGCTCAGCAGCTCCGCCACTGCCACCATCACGCCATTCAGGTTCTGCCAGGGCCAGGGAAGGGATGGAAGAAACATATCAGCCAAGTGTCTG	GGAGTTGGGGATCTTCATGCTCAGCAGCTCCGCCACTGCCACCATCACGCCATTCAGGTTCTGCCAGGGCCAGGGAAGGGATGGAAGAAACATATCAGCCAAGTGTCTG	-	novel	NA	P-0064902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	534	552	0	ENST00000301067.7:c.14383-49_14442del		p.X4795_splice	ENST00000301067	NM_003482.3	4795		46/54	0.822172125259309	3	FACETS	0.839	0.808	0.87	0.839	0.808	0.87	CLONAL	2	TRUE	1	0.822929079204232	3		552	1092	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426196	49426196	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	680	575	0	ENST00000301067.7:c.12292C>G	p.Pro4098Ala	p.P4098A	ENST00000301067	NM_003482.3	4098	Cca/Gca	39/54	0.822172125259309	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.822929079204232	3		575	1158	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478170	99478170	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	585	467	0	ENST00000268035.6:c.3074A>G	p.Glu1025Gly	p.E1025G	ENST00000268035	NM_000875.3	1025	gAa/gGa	16/21	0.822929079204232	2	FACETS	0.99	0.968	1	0.99	0.968	1	CLONAL	2	TRUE	0	0.822929079204232	2		467	718	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	59	462	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.878	0.757	1	0.878	0.757	1	CLONAL	1	TRUE	1	0.284694979581326	2		462	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	80	660	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.914	0.805	1	0.914	0.805	1	CLONAL	1	TRUE	1	0.284694979581326	2		660	615	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	64	408	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.855	0.741	0.978	0.855	0.741	0.978	CLONAL	1	TRUE	1	0.284694979581326	2		408	526	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	80	684	1	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	1	2	FACETS	0.906	0.799	1	0.906	0.799	1	CLONAL	1	TRUE	1	0.284694979581326	2		685	620	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	124	667	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.792	0.719	0.868	1	0.987	1	SUBCLONAL	2	TRUE	1	0.284694979581326	2		668	550	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	105	685	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.227361201838381	3	FACETS	1	0.971	1	0.618	0.554	0.685	CLONAL	1	TRUE	1	0.284694979581326	3		685	682	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	179	601	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	1	0.96	1	1	0.993	1	CLONAL	2	TRUE	1	0.284694979581326	2		601	597	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434973	110434973	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	150	718	0	ENST00000375856.3:c.3428del	p.Gly1143AlafsTer116	p.G1143Afs*116	ENST00000375856	NM_003749.2	1143	gGc/gc	1/2	0.284694979581326	3	FACETS	0.933	0.856	1	0.933	0.856	1	CLONAL	2	TRUE	1	0.284694979581326	3		718	645	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296358	15296358	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	34	724	2	ENST00000263388.2:c.2084del	p.Pro695ArgfsTer165	p.P695Rfs*165	ENST00000263388	NM_000435.2	695	cCg/cg	13/33	1	2	FACETS	0.406	0.33	0.49	0.406	0.33	0.49	SUBCLONAL	1	TRUE	1	0.284694979581326	2		726	589	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644679	134644679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773064927	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	62	453	0	ENST00000398015.3:c.80C>T	p.Thr27Met	p.T27M	ENST00000398015	NM_004441.4	27	aCg/aTg	2/16	0.227361201838381	3	FACETS	0.874	0.756	1	0.437	0.378	0.502	CLONAL	1	TRUE	1	0.284694979581326	3		453	569	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679547	86679547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	35	246	0	ENST00000274376.6:c.2708G>A	p.Arg903Gln	p.R903Q	ENST00000274376	NM_002890.2	903	cGa/cAa	21/25	1	2	FACETS	0.957	0.789	1	0.957	0.789	1	CLONAL	1	TRUE	1	0.284694979581326	2		246	257	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698146	47698147	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs63750393	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	55	270	0	ENST00000233146.2:c.1705_1706del	p.Glu569IlefsTer2	p.E569Ifs*2	ENST00000233146	NM_000251.2	568	acAGaa/acaa	11/16	0.227361201838381	3	FACETS	1	0.885	1	0.518	0.444	0.599	CLONAL	1	TRUE	1	0.284694979581326	3		270	426	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100577	157100577	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1289149988	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	23	378	0	ENST00000346085.5:c.1518del	p.Gly507AspfsTer16	p.G507Dfs*16	ENST00000346085	NM_020732.3	505	aCc/ac	1/20	0.227361201838381	3	FACETS	0.455	0.354	0.572	0.227	0.177	0.286	SUBCLONAL	1	TRUE	1	0.284694979581326	3		378	406	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803222	1803222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	75	722	0	ENST00000260795.2:c.574G>A	p.Gly192Ser	p.G192S	ENST00000260795		192	Ggc/Agc	4/17	1	2	FACETS	0.958	0.841	1	0.958	0.841	1	CLONAL	1	TRUE	1	0.284694979581326	2		722	550	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591125	67591125	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	69	412	0	ENST00000274335.5:c.1718T>C	p.Leu573Pro	p.L573P	ENST00000274335		573	cTg/cCg	12/15	1	2	FACETS	0.941	0.821	1	0.941	0.821	1	CLONAL	1	TRUE	1	0.284694979581326	2		412	515	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259967	16259967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	74	663	0	ENST00000375759.3:c.7232C>T	p.Ser2411Leu	p.S2411L	ENST00000375759	NM_015001.2	2411	tCg/tTg	11/15	1	2	FACETS	0.843	0.738	0.955	0.843	0.738	0.955	CLONAL	1	TRUE	1	0.284694979581326	2		663	617	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549395	21549395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143631255	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	68	590	0	ENST00000382592.4:c.2881C>T	p.Arg961Trp	p.R961W	ENST00000382592	NM_014572.2	961	Cgg/Tgg	8/8	0.284694979581326	3	FACETS	1	0.883	1	0.507	0.442	0.578	CLONAL	1	TRUE	1	0.284694979581326	3		590	538	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097632	27097632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	67	534	0	ENST00000324856.7:c.3221G>A	p.Arg1074Gln	p.R1074Q	ENST00000324856	NM_006015.4	1074	cGg/cAg	12/20	1	2	FACETS	0.8	0.696	0.914	0.8	0.696	0.914	CLONAL	1	TRUE	1	0.284694979581326	2		534	588	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814869	139814869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1474752416	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	52	620	0	ENST00000247668.2:c.862G>A	p.Val288Ile	p.V288I	ENST00000247668	NM_021138.3	288	Gtc/Atc	8/11	1	2	FACETS	0.607	0.516	0.706	0.607	0.516	0.706	SUBCLONAL	1	TRUE	1	0.284694979581326	2		620	602	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347891	347891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370439934	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	87	870	1	ENST00000262320.3:c.1615G>A	p.Val539Ile	p.V539I	ENST00000262320	NM_003502.3	539	Gtc/Atc	6/11	1	2	FACETS	0.888	0.787	0.997	0.888	0.787	0.997	CLONAL	1	TRUE	1	0.284694979581326	2		871	688	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251724	212251724	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770460785	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	42	623	0	ENST00000342788.4:c.3335G>A	p.Arg1112His	p.R1112H	ENST00000342788	NM_005235.2	1112	cGc/cAc	27/28	0.227361201838381	3	FACETS	0.498	0.415	0.591	0.249	0.207	0.296	SUBCLONAL	1	TRUE	1	0.284694979581326	3		623	677	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18958623	18958623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	64	356	0	ENST00000262803.5:c.442C>T	p.Arg148Cys	p.R148C	ENST00000262803	NM_002911.3	148	Cgt/Tgt	3/24	1	2	FACETS	0.921	0.799	1	0.921	0.799	1	CLONAL	1	TRUE	1	0.284694979581326	2		356	488	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863054	56863054	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1266824391	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	121	443	0	ENST00000519728.1:c.327del	p.Glu110LysfsTer15	p.E110Kfs*15	ENST00000519728	NM_002350.3	107	acA/ac	5/13	0.284694979581326	3	FACETS	0.913	0.828	1	0.913	0.828	1	CLONAL	2	TRUE	1	0.284694979581326	3		443	532	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37622730	37622730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758461304	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	52	519	0	ENST00000249071.6:c.562G>A	p.Ala188Thr	p.A188T	ENST00000249071	NM_002872.4	188	Gcc/Acc	6/7	1	2	FACETS	0.777	0.662	0.903	0.777	0.662	0.903	CLONAL	1	TRUE	1	0.284694979581326	2		519	470	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828111	3828111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	78	436	0	ENST00000262367.5:c.2014C>T	p.Arg672Cys	p.R672C	ENST00000262367	NM_004380.2	672	Cgt/Tgt	10/31	1	2	FACETS	0.996	0.877	1	0.996	0.877	1	CLONAL	1	TRUE	1	0.284694979581326	2		436	550	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933162	49933162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375697146	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	80	634	0	ENST00000296474.3:c.2948G>A	p.Arg983Gln	p.R983Q	ENST00000296474	NM_002447.2	983	cGg/cAg	12/20	0.227361201838381	3	FACETS	1	0.919	1	0.528	0.465	0.595	CLONAL	1	TRUE	1	0.284694979581326	3		634	608	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343021	70343021	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs875989806	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	65	557	0	ENST00000374080.3:c.1562G>A	p.Arg521His	p.R521H	ENST00000374080		521	cGt/cAt	11/45	0.284694979581326	1	FACETS	0.798	0.693	0.911	0.798	0.693	0.911	CLONAL	1	TRUE	0	0.284694979581326	1		557	491	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439569	220439569	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	67	669	0	ENST00000243786.2:c.422G>A	p.Gly141Asp	p.G141D	ENST00000243786	NM_002191.3	141	gGc/gAc	2/2	0.227361201838381	3	FACETS	0.907	0.788	1	0.453	0.394	0.518	CLONAL	1	TRUE	1	0.284694979581326	3		669	593	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936750	78936750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	84	679	0	ENST00000306801.3:c.3832G>A	p.Ala1278Thr	p.A1278T	ENST00000306801	NM_020761.2	1278	Gcc/Acc	33/34	1	2	FACETS	0.992	0.877	1	0.992	0.877	1	CLONAL	1	TRUE	1	0.284694979581326	2		679	595	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110004	115110004	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1201751425	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	52	593	0	ENST00000257566.3:c.1874G>A	p.Arg625His	p.R625H	ENST00000257566	NM_016569.3	625	cGc/cAc	8/8	0.227361201838381	3	FACETS	0.955	0.815	1	0.477	0.407	0.554	CLONAL	1	TRUE	1	0.284694979581326	3		593	437	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89837023	89837023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777032467	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	42	453	1	ENST00000389301.3:c.2171C>T	p.Thr724Met	p.T724M	ENST00000389301	NM_000135.2	724	aCg/aTg	24/43	1	2	FACETS	0.625	0.522	0.74	0.625	0.522	0.74	SUBCLONAL	1	TRUE	1	0.284694979581326	2		454	472	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816535	32816535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373556147	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	81	587	0	ENST00000354258.4:c.1640G>A	p.Arg547His	p.R547H	ENST00000354258	NM_000593.5	547	cGc/cAc	7/11	0.227361201838381	3	FACETS	0.922	0.812	1	0.461	0.406	0.52	CLONAL	1	TRUE	1	0.284694979581326	3		587	705	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328378	137328380	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs763369916	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	54	577	0	ENST00000481739.1:c.1315_1317del	p.Phe439del	p.F439del	ENST00000481739	NM_002957.4	436	cTCTtc/ctc	10/10	1	2	FACETS	0.802	0.686	0.929	0.802	0.686	0.929	CLONAL	1	TRUE	1	0.284694979581326	2		577	473	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838362	156838362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372041586	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	234	781	1	ENST00000524377.1:c.640C>T	p.Arg214Trp	p.R214W	ENST00000524377	NM_002529.3	214	Cgg/Tgg	6/17	0.24005620891715	4	FACETS	0.907	0.849	0.967	0.907	0.849	0.967	CLONAL	3	TRUE	1	0.284694979581326	4		782	776	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394017	31394020	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	rs1406133758	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	45	319	0	ENST00000328111.2:c.2308_2311del	p.Lys770TyrfsTer4	p.K770Yfs*4	ENST00000328111	NM_006892.3	768	ttAAAG/tt	22/23	0.284694979581326	3	FACETS	0.79	0.665	0.929	0.395	0.332	0.465	CLONAL	1	TRUE	1	0.284694979581326	3		319	457	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31495464	31495464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	63	452	0	ENST00000344624.3:c.1684C>T	p.Arg562Cys	p.R562C	ENST00000344624		562	Cgt/Tgt	9/33	1	2	FACETS	0.827	0.716	0.948	0.827	0.716	0.948	CLONAL	1	TRUE	1	0.284694979581326	2		452	535	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276311	15276311	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754537422	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	71	595	0	ENST00000263388.2:c.5683C>T	p.Arg1895Cys	p.R1895C	ENST00000263388	NM_000435.2	1895	Cgc/Tgc	31/33	1	2	FACETS	0.978	0.855	1	0.978	0.855	1	CLONAL	1	TRUE	1	0.284694979581326	2		595	510	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052588	42052588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	68	493	0	ENST00000219905.7:c.7259C>T	p.Ala2420Val	p.A2420V	ENST00000219905	NM_001164273.1	2420	gCg/gTg	20/24	1	2	FACETS	0.769	0.669	0.877	0.769	0.669	0.877	SUBCLONAL	1	TRUE	1	0.284694979581326	2		493	621	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225652	133225652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751555395	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	140	646	0	ENST00000320574.5:c.4012G>A	p.Glu1338Lys	p.E1338K	ENST00000320574	NM_006231.2	1338	Gag/Aag	32/49	0.227361201838381	3	FACETS	0.927	0.847	1	0.927	0.847	1	CLONAL	2	TRUE	1	0.284694979581326	3		646	606	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133747514	133747516	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGG	AGG	-	novel	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	42	407	0	ENST00000318560.5:c.825_827del		p.X275_splice	ENST00000318560	NM_005157.4	275		5/11	1	2	FACETS	0.815	0.682	0.962	0.815	0.682	0.962	CLONAL	1	TRUE	1	0.284694979581326	2		407	362	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533153	63533153	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759825875	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	61	522	0	ENST00000307078.5:c.1741C>T	p.Arg581Cys	p.R581C	ENST00000307078	NM_004655.3	581	Cgc/Tgc	7/11	1	2	FACETS	0.862	0.745	0.989	0.862	0.745	0.989	CLONAL	1	TRUE	1	0.284694979581326	2		522	497	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730388	133730388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	57	478	0	ENST00000318560.5:c.454C>T	p.Arg152Cys	p.R152C	ENST00000318560	NM_005157.4	152	Cgt/Tgt	3/11	1	2	FACETS	0.782	0.672	0.902	0.782	0.672	0.902	CLONAL	1	TRUE	1	0.284694979581326	2		478	512	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7293878	7293878	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	67	833	7	ENST00000302850.5:c.25del	p.Ala9ArgfsTer56	p.A9Rfs*56	ENST00000302850	NM_000208.2	9	Gcg/cg	1/22	1	2	FACETS	0.938	0.816	1	0.938	0.816	1	CLONAL	1	TRUE	1	0.284694979581326	2		840	502	SUCCESS
MAD2L2	10459	MSKCC	GRCh37	1	11736959	11736959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151024263	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	44	506	0	ENST00000235310.3:c.278G>A	p.Arg93His	p.R93H	ENST00000235310		93	cGc/cAc	7/11	1	2	FACETS	0.631	0.529	0.744	0.631	0.529	0.744	SUBCLONAL	1	TRUE	1	0.284694979581326	2		506	490	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47492845	47492845	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	89	524	0	ENST00000404338.3:c.3949G>A	p.Val1317Met	p.V1317M	ENST00000404338	NM_004491.4	1317	Gtg/Atg	4/6	0.24005620891715	4	FACETS	1	0.969	1	0.422	0.374	0.473	CLONAL	1	TRUE	1	0.284694979581326	4		524	635	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717723	89717723	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	36	337	0	ENST00000371953.3:c.748T>C	p.Cys250Arg	p.C250R	ENST00000371953	NM_000314.4	250	Tgt/Cgt	7/9	1	2	FACETS	0.659	0.542	0.789	0.659	0.542	0.789	SUBCLONAL	1	TRUE	1	0.284694979581326	2		337	384	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023631	1023632	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	118	429	0	ENST00000358495.3:c.932_933del	p.Lys311ArgfsTer15	p.K311Rfs*15	ENST00000358495	NM_134424.2	311	aAA/a	10/12	0.227361201838381	3	FACETS	0.949	0.86	1	0.949	0.86	1	CLONAL	2	TRUE	1	0.284694979581326	3		429	499	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905510	11905510	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	32	429	1	ENST00000396373.4:c.160C>A	p.Leu54Met	p.L54M	ENST00000396373	NM_001987.4	54	Ctg/Atg	2/8	0.227361201838381	3	FACETS	0.515	0.417	0.625	0.257	0.208	0.313	SUBCLONAL	1	TRUE	1	0.284694979581326	3		430	499	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348854	11348854	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs758583756	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	45	518	0	ENST00000332029.2:c.482T>C	p.Met161Thr	p.M161T	ENST00000332029	NM_003745.1	161	aTg/aCg	2/2	1	2	FACETS	0.769	0.647	0.903	0.769	0.647	0.903	CLONAL	1	TRUE	1	0.284694979581326	2		518	411	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602464	10602464	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775901614	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	63	746	0	ENST00000171111.5:c.1114G>A	p.Gly372Arg	p.G372R	ENST00000171111	NM_203500.1	372	Ggg/Agg	3/6	1	2	FACETS	0.766	0.662	0.878	0.766	0.662	0.878	SUBCLONAL	1	TRUE	1	0.284694979581326	2		746	578	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030286	11030286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	51	537	0	ENST00000327064.4:c.1036C>T	p.Arg346Trp	p.R346W	ENST00000327064	NM_199141.1	346	Cgg/Tgg	9/16	1	2	FACETS	0.7	0.595	0.815	0.7	0.595	0.815	SUBCLONAL	1	TRUE	1	0.284694979581326	2		537	512	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156011	99156011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760166680	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	111	553	0	ENST00000074304.5:c.691C>T	p.Arg231Cys	p.R231C	ENST00000074304	NM_001134224.1	231	Cgc/Tgc	10/26	0.227361201838381	3	FACETS	0.842	0.76	0.928	0.842	0.76	0.928	CLONAL	2	TRUE	1	0.284694979581326	3		553	529	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728860	39728860	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	77	423	0	ENST00000361337.2:c.1140G>T	p.Glu380Asp	p.E380D	ENST00000361337	NM_003286.2	380	gaG/gaT	12/21	0.284694979581326	3	FACETS	1	0.963	1	0.625	0.55	0.706	CLONAL	1	TRUE	1	0.284694979581326	3		423	494	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940448	49940448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748625701	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	77	673	0	ENST00000296474.3:c.595G>A	p.Val199Met	p.V199M	ENST00000296474	NM_002447.2	199	Gtg/Atg	1/20	0.227361201838381	3	FACETS	0.972	0.853	1	0.486	0.426	0.55	CLONAL	1	TRUE	1	0.284694979581326	3		673	636	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281559	142281560	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	56	458	0	ENST00000350721.4:c.684dup	p.Leu229ThrfsTer13	p.L229Tfs*13	ENST00000350721	NM_001184.3	228	-/A	4/47	0.227361201838381	3	FACETS	0.829	0.711	0.959	0.415	0.355	0.48	CLONAL	1	TRUE	1	0.284694979581326	3		458	542	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278775	1278775	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374206276	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	66	553	0	ENST00000310581.5:c.2267G>A	p.Arg756His	p.R756H	ENST00000310581	NM_198253.2	756	cGc/cAc	6/16	1	2	FACETS	0.86	0.747	0.982	0.86	0.747	0.982	CLONAL	1	TRUE	1	0.284694979581326	2		553	539	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86667994	86667995	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	40	402	0	ENST00000274376.6:c.1760dup	p.Asn587LysfsTer2	p.N587Kfs*2	ENST00000274376	NM_002890.2	586	-/A	13/25	1	2	FACETS	0.531	0.441	0.632	0.531	0.441	0.632	SUBCLONAL	1	TRUE	1	0.284694979581326	2		402	529	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940429	31940429	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	38	691	0	ENST00000375333.2:c.462G>A	p.Met154Ile	p.M154I	ENST00000375333	NM_032454.1	154	atG/atA	3/8	0.227361201838381	3	FACETS	0.446	0.368	0.535	0.223	0.184	0.268	SUBCLONAL	1	TRUE	1	0.284694979581326	3		691	683	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555227	106555227	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	110	504	1	ENST00000369096.4:c.2344A>G	p.Asn782Asp	p.N782D	ENST00000369096	NM_001198.3	782	Aat/Gat	7/7	0.227361201838381	3	FACETS	1	0.983	1	0.746	0.672	0.824	CLONAL	1	TRUE	1	0.284694979581326	3		505	592	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665251	117665251	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	78	351	0	ENST00000368508.3:c.4496del	p.Asn1499ThrfsTer5	p.N1499Tfs*5	ENST00000368508	NM_002944.2	1499	aAc/ac	27/43	0.227361201838381	3	FACETS	1	0.971	1	0.677	0.597	0.763	CLONAL	1	TRUE	1	0.284694979581326	3		351	462	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146934	38146934	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	57	396	0	ENST00000317025.8:c.3208C>A	p.Pro1070Thr	p.P1070T	ENST00000317025	NM_023034.1	1070	Ccc/Acc	18/24	0.284694979581326	3	FACETS	0.878	0.754	1	0.439	0.377	0.507	CLONAL	1	TRUE	1	0.284694979581326	3		396	521	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050707	5050707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1168347611	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	41	319	0	ENST00000381652.3:c.490G>A	p.Gly164Arg	p.G164R	ENST00000381652	NM_004972.3	164	Gga/Aga	6/25	1	2	FACETS	0.726	0.605	0.859	0.726	0.605	0.859	SUBCLONAL	1	TRUE	1	0.284694979581326	2		319	397	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418200	139418200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	48	634	0	ENST00000277541.6:c.372G>T	p.Glu124Asp	p.E124D	ENST00000277541	NM_017617.3	124	gaG/gaT	3/34	1	2	FACETS	0.73	0.618	0.853	0.73	0.618	0.853	SUBCLONAL	1	TRUE	1	0.284694979581326	2		634	462	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741542	145741542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748212145	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	97	698	0	ENST00000428558.2:c.961G>A	p.Gly321Arg	p.G321R	ENST00000428558	NM_004260.3	321	Gga/Aga	5/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		698	950	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	103	629	0	ENST00000269305.4:c.880del	p.Glu294SerfsTer51	p.E294Sfs*51	ENST00000269305	NM_001126112.2	294	Gag/ag	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		629	877	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885901	111885901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs79819500	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	151	637	0	ENST00000341259.2:c.1523G>A	p.Arg508Gln	p.R508Q	ENST00000341259	NM_005475.2	508	cGg/cAg	8/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		637	931	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209513	98209513	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	43	629	0	ENST00000331920.6:c.4025G>T	p.Arg1342Leu	p.R1342L	ENST00000331920	NM_000264.3	1342	cGc/cTc	23/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		629	685	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469128	25469128	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1481248882	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	90	559	0	ENST00000264709.3:c.1330G>T	p.Glu444Ter	p.E444*	ENST00000264709	NM_175629.2	444	Gag/Tag	11/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		559	752	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790470	3790470	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	69	478	0	ENST00000262367.5:c.4063G>T	p.Gly1355Trp	p.G1355W	ENST00000262367	NM_004380.2	1355	Ggg/Tgg	24/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		478	740	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720871	176720871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1260544167	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	141	568	0	ENST00000439151.2:c.6502G>A	p.Gly2168Arg	p.G2168R	ENST00000439151	NM_022455.4	2168	Ggg/Agg	23/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		568	799	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484327	8484327	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	56	414	0	ENST00000356435.5:c.3205C>A	p.Gln1069Lys	p.Q1069K	ENST00000356435		1069	Cag/Aag	19/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		414	524	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042379	42042379	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	43	581	0	ENST00000219905.7:c.6574G>T	p.Glu2192Ter	p.E2192*	ENST00000219905	NM_001164273.1	2192	Gaa/Taa	17/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		581	691	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610538	215610538	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587780022	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	74	379	0	ENST00000260947.4:c.1718T>C	p.Ile573Thr	p.I573T	ENST00000260947	NM_000465.2	573	aTa/aCa	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		379	503	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729922	41729922	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	72	537	0	ENST00000242208.4:c.607G>T	p.Glu203Ter	p.E203*	ENST00000242208	NM_002192.2	203	Gaa/Taa	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		537	825	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101399	27101399	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	31	361	0	ENST00000324856.7:c.4681G>T	p.Val1561Leu	p.V1561L	ENST00000324856	NM_006015.4	1561	Gtg/Ttg	18/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		361	560	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910856	114910856	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	43	484	0	ENST00000543371.1:c.975G>C	p.Gln325His	p.Q325H	ENST00000543371	NM_001198531.1	325	caG/caC	9/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		484	691	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945086	31945086	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	119	586	0	ENST00000340398.3:c.15G>T	p.Lys5Asn	p.K5N	ENST00000340398	NM_001013699.2	5	aaG/aaT	1/1	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		586	1039	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123858	46123858	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	103	591	0	ENST00000334344.6:c.126del	p.Lys43ArgfsTer15	p.K43Rfs*15	ENST00000334344	NM_152641.2	42	Ggg/gg	2/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		591	889	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858636	57858636	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	145	631	0	ENST00000228682.2:c.374C>G	p.Ser125Cys	p.S125C	ENST00000228682	NM_005269.2	125	tCc/tGc	4/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		631	869	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061027	38061027	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1227249633	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	60	709	0	ENST00000250448.2:c.962A>T	p.Glu321Val	p.E321V	ENST00000250448	NM_004496.3	321	gAg/gTg	2/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		709	910	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984850	9984850	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	47	430	0	ENST00000330684.3:c.1115G>T	p.Trp372Leu	p.W372L	ENST00000330684	NM_001134407.1	372	tGg/tTg	4/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		430	604	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657502	37657502	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	30	283	0	ENST00000447079.4:c.2420-1G>T		p.X807_splice	ENST00000447079	NM_015083.1	807			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		283	354	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41197793	41197793	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	75	602	0	ENST00000357654.3:c.5494G>C	p.Val1832Leu	p.V1832L	ENST00000357654	NM_007294.3	1832	Gtg/Ctg	23/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		602	816	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858358	59858358	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	22	268	0	ENST00000259008.2:c.1637A>C	p.Asp546Ala	p.D546A	ENST00000259008	NM_032043.2	546	gAt/gCt	12/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		268	266	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610386	10610386	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	91	645	0	ENST00000171111.5:c.324G>T	p.Lys108Asn	p.K108N	ENST00000171111	NM_203500.1	108	aaG/aaT	2/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		645	922	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272501	15272501	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	95	623	0	ENST00000263388.2:c.5938G>T	p.Ala1980Ser	p.A1980S	ENST00000263388	NM_000435.2	1980	Gcc/Tcc	33/33	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		623	854	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046254	128046254	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	43	491	0	ENST00000285398.2:c.1009del	p.Val337SerfsTer15	p.V337Sfs*15	ENST00000285398	NM_000122.1	337	Gtc/tc	7/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		491	786	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149608	202149608	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	90	530	0	ENST00000358485.4:c.1049A>T	p.Gln350Leu	p.Q350L	ENST00000358485	NM_001080125.1	350	cAa/cTa	8/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		530	766	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21350154	21350154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587777178	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	93	700	0	ENST00000215739.8:c.2062C>T	p.Arg688Cys	p.R688C	ENST00000215739	NM_006767.3	688	Cgc/Tgc	17/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		700	785	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37628906	37628906	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	77	456	0	ENST00000249071.6:c.160G>T	p.Gly54Trp	p.G54W	ENST00000249071	NM_002872.4	54	Ggg/Tgg	3/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		456	646	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181416	185181416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	28	343	0	ENST00000265026.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000265026	NM_004721.4	453	Gaa/Aaa	8/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		343	467	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526183	189526183	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	57	716	0	ENST00000264731.3:c.447C>A	p.Tyr149Ter	p.Y149*	ENST00000264731	NM_003722.4	149	taC/taA	4/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		716	983	SUCCESS
REST	5978	MSKCC	GRCh37	4	57777127	57777127	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	163	502	0	ENST00000309042.7:c.323A>T	p.Asn108Ile	p.N108I	ENST00000309042	NM_005612.4	108	aAc/aTc	2/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		502	869	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180655	32180655	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs772156724	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	54	449	0	ENST00000375023.3:c.2472C>A	p.Ser824Arg	p.S824R	ENST00000375023	NM_004557.3	824	agC/agA	16/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		449	653	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748480	43748480	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1395807781	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	71	488	0	ENST00000523873.1:c.434G>C	p.Arg145Pro	p.R145P	ENST00000523873		145	cGa/cCa	6/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		488	766	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157454312	157454312	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	67	453	0	ENST00000346085.5:c.2522G>T	p.Gly841Val	p.G841V	ENST00000346085	NM_020732.3	841	gGt/gTt	8/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		453	616	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953040	2953040	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	89	622	0	ENST00000396946.4:c.2900G>T	p.Arg967Leu	p.R967L	ENST00000396946	NM_032415.4	967	cGc/cTc	22/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		622	894	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976855	2976855	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	70	560	0	ENST00000396946.4:c.1157G>T	p.Arg386Leu	p.R386L	ENST00000396946	NM_032415.4	386	cGa/cTa	9/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		560	747	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729839	41729839	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	93	526	0	ENST00000242208.4:c.690G>C	p.Leu230Phe	p.L230F	ENST00000242208	NM_002192.2	230	ttG/ttC	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		526	840	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845465	128845466	+	missense_variant	Missense_Mutation	DNP	TG	TG	CT	novel	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	69	474	0	ENST00000249373.3:c.762_763delinsCT	p.Asp255Tyr	p.D255Y	ENST00000249373	NM_005631.4	254	gcTGac/gcCTac	4/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		474	761	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877109	151877109	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	80	603	0	ENST00000262189.6:c.7252G>T	p.Gly2418Trp	p.G2418W	ENST00000262189	NM_170606.2	2418	Ggg/Tgg	37/59	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		603	904	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157832	27157833	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	58	425	0	ENST00000380036.4:c.56_57del	p.Thr19SerfsTer18	p.T19Sfs*18	ENST00000380036	NM_000459.3	19	aCT/a	2/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		425	468	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325626	87325626	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1369331924	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	32	414	0	ENST00000277120.3:c.503G>T	p.Ser168Ile	p.S168I	ENST00000277120		168	aGt/aTt	6/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		414	511	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405627	139405627	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	51	518	0	ENST00000277541.6:c.2564G>C	p.Cys855Ser	p.C855S	ENST00000277541	NM_017617.3	855	tGt/tCt	16/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		518	713	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325389	1325389	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	43	465	0	ENST00000400841.2:c.286T>A	p.Tyr96Asn	p.Y96N	ENST00000400841		96	Tat/Aat	3/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		465	699	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0064906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	39	293	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.605	0.503	0.718	0.605	0.503	0.718	SUBCLONAL	1	TRUE	1	0.394382530102581	2		293	327	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039407	47039407	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	92	579	0	ENST00000377604.3:c.1030G>T	p.Gly344Cys	p.G344C	ENST00000377604	NM_001204468.1	344	Ggc/Tgc	10/24	1	2	FACETS	0.695	0.618	0.778	0.695	0.618	0.778	SUBCLONAL	1	TRUE	1	0.394382530102581	2		579	671	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600407	10600407	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs867398451	NA	P-0064906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	111	671	0	ENST00000171111.5:c.1448G>T	p.Arg483Leu	p.R483L	ENST00000171111	NM_203500.1	483	cGc/cTc	4/6	0.316792687627531	1	FACETS	0.593	0.533	0.657	0.593	0.533	0.657	SUBCLONAL	1	TRUE	0	0.394382530102581	1		671	762	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207203	1207204	+	splice_donor_variant	Splice_Site	DEL	GT	GT	-	novel	NA	P-0064906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	93	496	0	ENST00000326873.7:c.290+1_290+2del		p.X97_splice	ENST00000326873	NM_000455.4	97			0.270557078259116	1	FACETS	0.643	0.573	0.718	0.643	0.573	0.718	SUBCLONAL	1	TRUE	0	0.394382530102581	1		496	589	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103513941	103513941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	65	370	0	ENST00000355739.4:c.757G>A	p.Glu253Lys	p.E253K	ENST00000355739	NM_000123.3	253	Gaa/Aaa	7/15	1	2	FACETS	0.64	0.556	0.731	0.64	0.556	0.731	SUBCLONAL	1	TRUE	1	0.394382530102581	2		370	515	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098380	11098380	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	98	625	0	ENST00000358026.2:c.898C>T	p.Gln300Ter	p.Q300*	ENST00000358026	NM_001128849.1	300	Cag/Tag	6/36	0.316792687627531	1	FACETS	0.611	0.546	0.68	0.611	0.546	0.68	SUBCLONAL	1	TRUE	0	0.394382530102581	1		625	653	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1686053	1686053	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	91	696	0	ENST00000378625.1:c.1208G>A	p.Gly403Glu	p.G403E	ENST00000378625	NM_001198994.1	403	gGg/gAg	10/14	1	2	FACETS	0.523	0.464	0.587	0.523	0.464	0.587	SUBCLONAL	1	TRUE	1	0.394382530102581	2		696	882	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133813	41133813	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	59	575	0	ENST00000379561.5:c.1815G>T	p.Met605Ile	p.M605I	ENST00000379561	NM_002015.3	605	atG/atT	2/3	1	2	FACETS	0.48	0.413	0.554	0.48	0.413	0.554	SUBCLONAL	1	TRUE	1	0.394382530102581	2		575	623	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877208	89877208	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	66	302	0	ENST00000389301.3:c.429G>C	p.Lys143Asn	p.K143N	ENST00000389301	NM_000135.2	143	aaG/aaC	5/43	1	2	FACETS	0.669	0.582	0.764	0.669	0.582	0.764	SUBCLONAL	1	TRUE	1	0.394382530102581	2		302	500	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47700121	47700122	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0064906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	86	433	0	ENST00000347630.2:c.51dup	p.Val18ArgfsTer3	p.V18Rfs*3	ENST00000347630	NM_001007230.1	17	-/C	3/11	1	2	FACETS	0.656	0.58	0.737	0.656	0.58	0.737	SUBCLONAL	1	TRUE	1	0.394382530102581	2		433	665	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719215	190719215	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	26	249	0	ENST00000441310.2:c.1217G>T	p.Cys406Phe	p.C406F	ENST00000441310	NM_000534.4	406	tGt/tTt	9/13	1	2	FACETS	0.459	0.364	0.568	0.459	0.364	0.568	SUBCLONAL	1	TRUE	1	0.394382530102581	2		249	287	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143129679	143129679	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	28	153	0	ENST00000262992.4:c.971C>A	p.Ser324Tyr	p.S324Y	ENST00000262992	NM_001101669.1	324	tCc/tAc	12/24	1	2	FACETS	0.706	0.569	0.861	0.706	0.569	0.861	SUBCLONAL	1	TRUE	1	0.394382530102581	2		153	201	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977895	131977895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1381323366	NA	P-0064906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	49	308	0	ENST00000265335.6:c.3778C>T	p.Arg1260Cys	p.R1260C	ENST00000265335		1260	Cgt/Tgt	25/25	1	2	FACETS	0.583	0.495	0.68	0.583	0.495	0.68	SUBCLONAL	1	TRUE	1	0.394382530102581	2		308	426	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190467	32190467	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	113	698	0	ENST00000375023.3:c.272C>A	p.Pro91His	p.P91H	ENST00000375023	NM_004557.3	91	cCc/cAc	3/30	1	2	FACETS	0.637	0.573	0.706	0.637	0.573	0.706	SUBCLONAL	1	TRUE	1	0.394382530102581	2		698	899	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545579	106545579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1436898471	NA	P-0064906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	75	346	0	ENST00000359195.3:c.3056C>T	p.Ala1019Val	p.A1019V	ENST00000359195	NM_002649.2	1019	gCc/gTc	11/11	1	2	FACETS	0.684	0.6	0.774	0.684	0.6	0.774	SUBCLONAL	1	TRUE	1	0.394382530102581	2		346	556	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845130	128845130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	104	572	0	ENST00000249373.3:c.624G>T	p.Glu208Asp	p.E208D	ENST00000249373	NM_005631.4	208	gaG/gaT	3/12	1	2	FACETS	0.7	0.627	0.778	0.7	0.627	0.778	SUBCLONAL	1	TRUE	1	0.394382530102581	2		572	753	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	29	789	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.504	0.404	0.62	0.504	0.404	0.62	SUBCLONAL	1	TRUE	1	0.2	2		789	575	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183765	10183765	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	82	537	0	ENST00000256474.2:c.234T>A	p.Asn78Lys	p.N78K	ENST00000256474	NM_000551.3	78	aaT/aaA	1/3	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.2	2		537	785	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928640	49928640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375490243	NA	P-0064907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	67	578	0	ENST00000296474.3:c.3634C>T	p.Arg1212Trp	p.R1212W	ENST00000296474	NM_002447.2	1212	Cgg/Tgg	17/20	1	2	FACETS	0.915	0.794	1	0.915	0.794	1	CLONAL	1	TRUE	1	0.2	2		578	732	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52663032	52663033	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0064907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	32	286	0	ENST00000394830.3:c.1320dup	p.Glu441ArgfsTer3	p.E441Rfs*3	ENST00000394830	NM_018313.4	440	-/A	13/30	1	2	FACETS	0.979	0.796	1	0.979	0.796	1	CLONAL	1	TRUE	1	0.2	2		286	327	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913409	NA	P-0064908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	326	391	0	ENST00000349496.5:c.134C>G	p.Ser45Cys	p.S45C	ENST00000349496	NM_001904.3	45	tCt/tGt	3/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		391	732	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421578	32421578	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	427	481	0	ENST00000332351.3:c.1014del	p.Tyr339ThrfsTer36	p.Y339Tfs*36	ENST00000332351	NM_024426.4	338	ggG/gg	6/10	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		481	905	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0064909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	422	571	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		572	549	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918967	76918970	+	frameshift_variant	Frame_Shift_Del	DEL	GCAA	GCAA	-	novel	NA	P-0064909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	131	212	0	ENST00000373344.5:c.4021_4024del	p.Leu1341GlyfsTer4	p.L1341Gfs*4	ENST00000373344	NM_000489.3	1341	TTGCgg/gg	12/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		212	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578429	7578429	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1567553148	NA	P-0064911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	1399	763	0	ENST00000269305.4:c.501del	p.Gln167HisfsTer3	p.Q167Hfs*3	ENST00000269305	NM_001126112.2	167	caG/ca	5/11	0.866756091268316	4	FACETS	1	0.998	1	1	0.998	1	CLONAL	4	TRUE	0	0.866756091268316	4		763	1462	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104613	209104613	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	349	483	0	ENST00000345146.2:c.965G>C	p.Gly322Ala	p.G322A	ENST00000345146	NM_005896.2	322	gGa/gCa	8/10	0.852076195936204	2	FACETS	0.97	0.944	0.994	0.97	0.944	0.994	CLONAL	2	TRUE	0	0.866756091268316	2		483	415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587781702	NA	P-0064912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	132	485	0	ENST00000269305.4:c.920-1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.366134661644513	1	FACETS	0.856	0.779	0.937	0.856	0.779	0.937	CLONAL	1	TRUE	0	0.366134661644513	1		485	688	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933434	36933434	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	97	711	1	ENST00000361632.4:c.1853C>A	p.Thr618Asn	p.T618N	ENST00000361632		618	aCc/aAc	13/16	1	2	FACETS	0.635	0.566	0.71	0.635	0.566	0.71	SUBCLONAL	1	TRUE	1	0.366134661644513	2		712	834	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0064914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	16	441	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	1	2	FACETS	0.758	0.56	0.994	0.758	0.56	0.994	CLONAL	1	TRUE	1	0.16	2		441	264	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0064914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	27	656	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.819	0.651	1	0.819	0.651	1	CLONAL	1	TRUE	1	0.16	2		660	412	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210728	2210728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745700742	NA	P-0064914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	25	582	0	ENST00000398665.3:c.1225C>T	p.Arg409Cys	p.R409C	ENST00000398665	NM_032482.2	409	Cgc/Tgc	14/28	1	2	FACETS	0.81	0.638	1	0.81	0.638	1	CLONAL	1	TRUE	1	0.16	2		582	386	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0064914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	19	511	1	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	0.63	0.477	0.81	0.63	0.477	0.81	SUBCLONAL	1	TRUE	1	0.16	2		512	377	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278032	18278032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756172410	NA	P-0064914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	24	445	0	ENST00000222254.8:c.1652C>T	p.Ser551Leu	p.S551L	ENST00000222254	NM_005027.3	551	tCg/tTg	13/16	1	2	FACETS	0.867	0.68	1	0.867	0.68	1	CLONAL	1	TRUE	1	0.16	2		445	346	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257874	19257874	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780635430	NA	P-0064914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	23	689	0	ENST00000162023.5:c.512G>A	p.Arg171Gln	p.R171Q	ENST00000162023		171	cGa/cAa	9/13	1	2	FACETS	0.7	0.545	0.879	0.7	0.545	0.879	SUBCLONAL	1	TRUE	1	0.16	2		689	411	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164751	106164751	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	14	376	0	ENST00000380013.4:c.3619G>T	p.Glu1207Ter	p.E1207*	ENST00000380013	NM_001127208.2	1207	Gag/Tag	6/11	1	2	FACETS	0.636	0.459	0.851	0.636	0.459	0.851	SUBCLONAL	1	TRUE	1	0.16	2		376	275	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080656	5080656	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs769318116	NA	P-0064914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	11	257	0	ENST00000381652.3:c.2407C>T	p.Arg803Ter	p.R803*	ENST00000381652	NM_004972.3	803	Cga/Tga	18/25	0.135625965378541	1	FACETS	0.897	0.622	1	0.897	0.622	1	CLONAL	1	TRUE	0	0.16	1		257	141	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436084	110436084	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	22	632	0	ENST00000375856.3:c.2317G>A	p.Asp773Asn	p.D773N	ENST00000375856	NM_003749.2	773	Gac/Aac	1/2	1	2	FACETS	0.755	0.585	0.954	0.755	0.585	0.954	CLONAL	1	TRUE	1	0.16	2		632	364	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432236	49432236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750788651	NA	P-0064914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	25	655	0	ENST00000301067.7:c.8903C>T	p.Pro2968Leu	p.P2968L	ENST00000301067	NM_003482.3	2968	cCg/cTg	34/54	0.135625965378541	3	FACETS	0.694	0.546	0.866	0.347	0.273	0.433	SUBCLONAL	1	TRUE	1	0.16	3		655	486	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150936207	150936207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	18	506	0	ENST00000271640.5:c.3659G>A	p.Arg1220His	p.R1220H	ENST00000271640	NM_001145415.1	1220	cGc/cAc	20/22	1	2	FACETS	0.676	0.508	0.874	0.676	0.508	0.874	SUBCLONAL	1	TRUE	1	0.16	2		506	333	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406426	70406426	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	26	454	0	ENST00000373644.4:c.3940G>T	p.Ala1314Ser	p.A1314S	ENST00000373644	NM_030625.2	1314	Gca/Tca	4/12	1	2	FACETS	0.913	0.723	1	0.913	0.723	1	CLONAL	1	TRUE	1	0.16	2		454	356	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100502	102100502	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	20	420	0	ENST00000282441.5:c.1346C>A	p.Pro449His	p.P449H	ENST00000282441	NM_001130145.2	449	cCt/cAt	9/9	1	2	FACETS	0.833	0.637	1	0.833	0.637	1	CLONAL	1	TRUE	1	0.16	2		420	300	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533131	63533131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1305562386	NA	P-0064914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	18	498	0	ENST00000307078.5:c.1763C>T	p.Pro588Leu	p.P588L	ENST00000307078	NM_004655.3	588	cCg/cTg	7/11	1	2	FACETS	0.804	0.605	1	0.804	0.605	1	CLONAL	1	TRUE	1	0.16	2		498	280	SUCCESS
APC	324	MSKCC	GRCh37	5	112177441	112177442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	15	362	0	ENST00000257430.4:c.6155dup	p.Pro2053AlafsTer7	p.P2053Afs*7	ENST00000257430	NM_000038.5	2050	-/A	16/16	1	2	FACETS	0.762	0.558	1	0.762	0.558	1	CLONAL	1	TRUE	1	0.16	2		362	246	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146929	38146930	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0064914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	13	305	1	ENST00000317025.8:c.3212dup	p.Pro1072SerfsTer8	p.P1072Sfs*8	ENST00000317025	NM_023034.1	1071	cct/ccCt	18/24	1	2	FACETS	0.763	0.545	1	0.763	0.545	1	CLONAL	1	TRUE	1	0.16	2		306	213	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628389	187628392	+	frameshift_variant	Frame_Shift_Del	DEL	TGTC	TGTC	-	novel	NA	P-0064914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	16	500	0	ENST00000441802.2:c.2590_2593del	p.Asp864GlnfsTer9	p.D864Qfs*9	ENST00000441802	NM_005245.3	864	GACAca/ca	2/27	1	2	FACETS	0.656	0.484	0.861	0.656	0.484	0.861	SUBCLONAL	1	TRUE	1	0.16	2		500	305	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0064915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	129	702	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.273308362987853	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	0	0.273308362987853	1		702	812	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0064915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	15	177	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.494	0.362	0.653	0.494	0.362	0.653	SUBCLONAL	1	TRUE	1	0.273308362987853	2		177	222	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0064915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	89	478	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	1	2	FACETS	0.816	0.723	0.916	0.816	0.723	0.916	CLONAL	1	TRUE	1	0.273308362987853	2		478	798	SUCCESS
APC	324	MSKCC	GRCh37	5	112170747	112170747	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1561568632	NA	P-0064915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	97	402	0	ENST00000257430.4:c.1847del	p.Leu616TrpfsTer14	p.L616Wfs*14	ENST00000257430	NM_000038.5	615	Ttt/tt	15/16	1	2	FACETS	0.924	0.824	1	0.924	0.824	1	CLONAL	1	TRUE	1	0.273308362987853	2		402	768	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172261	38172261	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	1066	469	0	ENST00000317025.8:c.2146C>T	p.Pro716Ser	p.P716S	ENST00000317025	NM_023034.1	716	Cct/Tct	12/24	0.273308362987853	20	FACETS	0.973	0.95	0.995			1	CLONAL	16	TRUE	NA	0.273308362987853	20		469	1734	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38176443	38176443	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs368291633	NA	P-0064915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	1208	272	1	ENST00000317025.8:c.1825C>G	p.Gln609Glu	p.Q609E	ENST00000317025	NM_023034.1	609	Cag/Gag	9/24	0.273308362987853	20	FACETS	0.993	0.975	1			1	CLONAL	19	TRUE	NA	0.273308362987853	20		273	1621	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0064916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	195	406	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.304266728619109	3	FACETS	1	0.963	1	0.699	0.652	0.747	CLONAL	2	TRUE	0	0.410462695771138	3		406	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578202	7578202	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520004	NA	P-0064916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	204	656	0	ENST00000269305.4:c.647T>G	p.Val216Gly	p.V216G	ENST00000269305	NM_001126112.2	216	gTg/gGg	6/11	0.268809346548597	2	FACETS	0.761	0.709	0.814	0.761	0.709	0.814	SUBCLONAL	2	TRUE	0	0.410462695771138	2		656	653	SUCCESS
APC	324	MSKCC	GRCh37	5	112175766	112175766	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	229	621	0	ENST00000257430.4:c.4476del	p.Thr1493ArgfsTer14	p.T1493Rfs*14	ENST00000257430	NM_000038.5	1492	gCc/gc	16/16	0.319664536987585	3	FACETS	1	0.989	1	0.82	0.771	0.869	CLONAL	2	TRUE	0	0.410462695771138	3		621	547	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224259	55224262	+	frameshift_variant	Frame_Shift_Del	DEL	ACTC	ACTC	-	novel	NA	P-0064916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	108	425	0	ENST00000275493.2:c.1044_1047del	p.Leu349ProfsTer2	p.L349Pfs*2	ENST00000275493	NM_005228.3	347	gACTCa/ga	9/28	0.223856196645963	5	FACETS	1	0.982	1	0.487	0.438	0.539	INDETERMINATE	1	TRUE	2	0.410462695771138	5		425	582	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577035	7577036	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0064917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	151	639	0	ENST00000269305.4:c.902dup	p.Gly302ArgfsTer4	p.G302Rfs*4	ENST00000269305	NM_001126112.2	301	cca/ccCa	8/11	0.367188060282843	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.367188060282843	1		639	547	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150933643	150933646	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	novel	NA	P-0064917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	92	473	0	ENST00000271640.5:c.3106_3109del	p.Asp1036SerfsTer17	p.D1036Sfs*17	ENST00000271640	NM_001145415.1	1035	ggAGAC/gg	16/22	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.367188060282843	2		473	493	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423659	88423659	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	84	474	0	ENST00000360948.2:c.2176G>T	p.Val726Leu	p.V726L	ENST00000360948	NM_001012338.2	726	Gtg/Ttg	18/19	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.367188060282843	2		474	395	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50816277	50816277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	83	355	0	ENST00000398568.2:c.1717C>T	p.Pro573Ser	p.P573S	ENST00000398568	NM_001042412.1	573	Cca/Tca	10/18	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.367188060282843	2		355	442	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135082	11135083	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCT	novel	NA	P-0064917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	97	529	0	ENST00000358026.2:c.3050_3053dup	p.Thr1019AlafsTer3	p.T1019Afs*3	ENST00000358026	NM_001128849.1	1017	ctg/cTGCTtg	21/36	0.367188060282843	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.367188060282843	1		529	401	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971159	21971162	+	frameshift_variant	Frame_Shift_Del	DEL	CGTG	CGTG	-	novel	NA	P-0064917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	144	679	0	ENST00000304494.5:c.196_199del	p.His66AlafsTer79	p.H66Afs*79	ENST00000304494	NM_000077.4	66	CACGgc/gc	2/3	0.367188060282843	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.367188060282843	1		679	461	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0064918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	116	511	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.500018731073183	2		511	447	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0064918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	8	177	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.500018731073183	1	FACETS	0.148	0.095	0.217	0.148	0.095	0.217	SUBCLONAL	1	TRUE	0	0.500018731073183	1		177	162	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031898	26031898	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	75	569	0	ENST00000244661.2:c.391A>G	p.Ile131Val	p.I131V	ENST00000244661	NM_003537.3	131	Att/Gtt	1/1	0.500018731073183	1	FACETS	0.288	0.252	0.327	0.288	0.252	0.327	SUBCLONAL	1	TRUE	0	0.500018731073183	1		569	781	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144146	11144146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	83	496	0	ENST00000358026.2:c.3727C>T	p.Arg1243Trp	p.R1243W	ENST00000358026	NM_001128849.1	1243	Cgg/Tgg	26/36	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.21	2		496	765	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562552	21562552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	48	471	0	ENST00000382592.4:c.1367C>T	p.Thr456Met	p.T456M	ENST00000382592	NM_014572.2	456	aCg/aTg	4/8	0.170696460252169	3	FACETS	0.855	0.722	1	0.427	0.361	0.501	CLONAL	1	TRUE	1	0.21	3		471	591	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846133	68846135	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	novel	NA	P-0064921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	56	449	0	ENST00000261769.5:c.1105_1107del	p.Asn369del	p.N369del	ENST00000261769	NM_004360.3	368	acCAAc/acc	8/16	1	2	FACETS	0.869	0.744	1	0.869	0.744	1	CLONAL	1	TRUE	1	0.21	2		449	614	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120258	70120259	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	75	562	0	ENST00000245479.2:c.1261dup	p.Ser421LysfsTer157	p.S421Kfs*157	ENST00000245479	NM_000346.3	420	-/A	3/3	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.21	2		562	667	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120325	70120326	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0064921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	72	591	0	ENST00000245479.2:c.1329dup	p.Asp444ArgfsTer134	p.D444Rfs*134	ENST00000245479	NM_000346.3	443	acc/aCcc	3/3	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.21	2		591	675	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615706	1615706	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	90	661	0	ENST00000344749.5:c.1565del	p.Lys522ArgfsTer21	p.K522Rfs*21	ENST00000344749	NM_001136139.2	522	aAg/ag	17/19	1	2	FACETS	0.997	0.883	1	0.997	0.883	1	CLONAL	1	TRUE	1	0.21	2		661	860	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374404	31374404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774911505	NA	P-0064921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	55	574	0	ENST00000328111.2:c.403G>A	p.Glu135Lys	p.E135K	ENST00000328111	NM_006892.3	135	Gag/Aag	5/23	1	2	FACETS	0.652	0.557	0.758	0.652	0.557	0.758	SUBCLONAL	1	TRUE	1	0.21	2		574	803	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412905	49412905	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519951	NA	P-0064921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	61	427	0	ENST00000418115.1:c.118G>A	p.Glu40Lys	p.E40K	ENST00000418115	NM_001664.2	40	Gag/Aag	2/5	1	2	FACETS	0.946	0.816	1	0.946	0.816	1	CLONAL	1	TRUE	1	0.21	2		427	614	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127487	55127487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759729258	NA	P-0064921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	61	451	0	ENST00000257290.5:c.275C>T	p.Ala92Val	p.A92V	ENST00000257290	NM_006206.4	92	gCg/gTg	3/23	1	2	FACETS	0.868	0.748	0.999	0.868	0.748	0.999	CLONAL	1	TRUE	1	0.21	2		451	669	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467999	66467999	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1397670613	NA	P-0064921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	29	337	0	ENST00000273854.3:c.270T>A	p.Asp90Glu	p.D90E	ENST00000273854	NM_004439.5	90	gaT/gaA	3/18	1	2	FACETS	0.719	0.577	0.881	0.719	0.577	0.881	SUBCLONAL	1	TRUE	1	0.21	2		337	384	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039843	47039843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	55	217	0	ENST00000377604.3:c.1186C>T	p.Arg396Cys	p.R396C	ENST00000377604	NM_001204468.1	396	Cgc/Tgc	12/24	1	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.21	1		217	316	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0064933-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	482	338	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.378021962469531	8	FACETS	1	0.975	1	1	0.975	1	CLONAL	7	TRUE	1	0.378021962469531	8		338	769	SUCCESS
ATM	472	MSKCC	GRCh37	11	108159816	108159816	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064933-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	13	89	0	ENST00000278616.4:c.4222C>G	p.Leu1408Val	p.L1408V	ENST00000278616	NM_000051.3	1408	Ctt/Gtt	28/63	0.378021962469531	5	FACETS	0.787	0.564	1	0.262	0.188	0.352	CLONAL	1	TRUE	2	0.378021962469531	5		89	137	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398021	4398022	+	missense_variant	Missense_Mutation	DNP	CA	CA	AT	novel	NA	P-0064933-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	45	450	0	ENST00000261254.3:c.585_586delinsAT	p.Met196Leu	p.M196L	ENST00000261254	NM_001759.3	195	gcCAtg/gcATtg	4/5	0.378021962469531	1	FACETS	0.623	0.526	0.729	0.623	0.526	0.729	SUBCLONAL	1	TRUE	0	0.378021962469531	1		450	310	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865755	57865755	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064933-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	222	599	0	ENST00000228682.2:c.3232T>A	p.Ser1078Thr	p.S1078T	ENST00000228682	NM_005269.2	1078	Tct/Act	12/12	0.347432448982578	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	1	0.378021962469531	3		599	688	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145018	58145018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064933-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	226	587	0	ENST00000257904.6:c.326C>T	p.Pro109Leu	p.P109L	ENST00000257904	NM_000075.3	109	cCa/cTa	3/8	0.347432448982578	3	FACETS	0.945	0.884	1	0.945	0.884	1	CLONAL	2	TRUE	1	0.378021962469531	3		587	752	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202722	133202722	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064933-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	192	566	0	ENST00000320574.5:c.6512A>T	p.Lys2171Ile	p.K2171I	ENST00000320574	NM_006231.2	2171	aAa/aTa	46/49	0.378021962469531	5	FACETS	1	0.945	1	0.512	0.474	0.55	CLONAL	2	TRUE	1	0.378021962469531	5		566	778	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068993	30068993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064933-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	142	366	0	ENST00000331968.5:c.1936G>A	p.Glu646Lys	p.E646K	ENST00000331968	NM_002742.2	646	Gag/Aag	14/18	0.347432448982578	3	FACETS	0.83	0.761	0.902	0.83	0.761	0.902	CLONAL	2	TRUE	1	0.378021962469531	3		366	538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0064933-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	174	500	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.378021962469531	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	0	0.378021962469531	2		500	451	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222191	2222191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064933-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	240	641	0	ENST00000398665.3:c.3023C>T	p.Ser1008Phe	p.S1008F	ENST00000398665	NM_032482.2	1008	tCc/tTc	24/28	0.378021962469531	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.378021962469531	2		641	581	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023328	31023328	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064933-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	195	506	0	ENST00000375687.4:c.2813C>G	p.Pro938Arg	p.P938R	ENST00000375687	NM_015338.5	938	cCt/cGt	13/13	0.347432448982578	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.378021962469531	3		506	593	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205731	128205731	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064933-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	105	584	0	ENST00000341105.2:c.144C>G	p.Phe48Leu	p.F48L	ENST00000341105	NM_032638.4	48	ttC/ttG	2/6	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.378021962469531	2		584	457	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278153	142278153	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064933-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	136	418	0	ENST00000350721.4:c.1672G>C	p.Asp558His	p.D558H	ENST00000350721	NM_001184.3	558	Gac/Cac	7/47	0.260884954375536	5	FACETS	1	0.942	1	0.693	0.634	0.756	CLONAL	2	TRUE	2	0.378021962469531	5		418	542	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189503	56189503	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064933-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	80	440	0	ENST00000399503.3:c.4535G>T	p.Trp1512Leu	p.W1512L	ENST00000399503	NM_005921.1	1512	tGg/tTg	20/20	1	2	FACETS	0.947	0.837	1	0.947	0.837	1	CLONAL	1	TRUE	1	0.378021962469531	2		440	447	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131894975	131894975	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs876658784	NA	P-0064933-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	50	217	0	ENST00000265335.6:c.130-1G>T		p.X44_splice	ENST00000265335		44			1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.378021962469531	2		217	219	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035208	6035208	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064933-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	129	555	0	ENST00000265849.7:c.860G>T	p.Arg287Ile	p.R287I	ENST00000265849	NM_000535.5	287	aGa/aTa	8/15	0.378021962469531	3	FACETS	1	0.958	1	0.548	0.497	0.602	CLONAL	1	TRUE	1	0.378021962469531	3		555	740	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132751	152132751	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064933-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	28	302	0	ENST00000262189.6:c.121C>G	p.Arg41Gly	p.R41G	ENST00000262189	NM_170606.2	41	Cgc/Ggc	1/59	0.378021962469531	3	FACETS	0.554	0.443	0.68			1	SUBCLONAL	1	TRUE	NA	0.378021962469531	3		302	318	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335040	81335040	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751819844	NA	P-0064940-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	173	393	0	ENST00000222390.5:c.1787C>T	p.Thr596Met	p.T596M	ENST00000222390	NM_000601.4	596	aCg/aTg	16/18	0.371794909912676	4	FACETS	0.942	0.87	1	0.942	0.87	1	CLONAL	2	TRUE	2	0.379249004864795	4		393	668	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42053955	42053955	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064940-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	182	400	0	ENST00000219905.7:c.7417G>T	p.Gly2473Ter	p.G2473*	ENST00000219905	NM_001164273.1	2473	Gga/Tga	21/24	0.379249004864795	2	FACETS	0.952	0.886	1	0.952	0.886	1	CLONAL	2	TRUE	0	0.379249004864795	2		400	504	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280125	66280125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064940-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	121	448	0	ENST00000273854.3:c.1564G>A	p.Glu522Lys	p.E522K	ENST00000273854	NM_004439.5	522	Gag/Aag	7/18	0.379249004864795	3	FACETS	1	0.914	1	0.506	0.457	0.557	CLONAL	1	TRUE	1	0.379249004864795	3		448	750	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217255	66217255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064940-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	141	445	0	ENST00000273854.3:c.2360G>T	p.Gly787Val	p.G787V	ENST00000273854	NM_004439.5	787	gGa/gTa	14/18	0.379249004864795	3	FACETS	1	0.979	1	0.619	0.564	0.675	CLONAL	1	TRUE	1	0.379249004864795	3		445	715	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372434	118372434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064940-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	418	492	0	ENST00000534358.1:c.6367C>T	p.Pro2123Ser	p.P2123S	ENST00000534358	NM_005933.3	2123	Cca/Tca	26/36	0.366845846613506	3	FACETS	1	0.983	1			1	CLONAL	3	TRUE	NA	0.379249004864795	3		492	834	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937683	76937683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781811015	NA	P-0064940-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	121	466	0	ENST00000373344.5:c.3065G>A	p.Arg1022Gln	p.R1022Q	ENST00000373344	NM_000489.3	1022	cGa/cAa	9/35	0.325096407003146	4	FACETS	1	0.942	1	0.53	0.478	0.584	CLONAL	1	TRUE	2	0.379249004864795	4		466	831	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0064940-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	526	306	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.379249004864795	7	FACETS	0.996	0.966	1	1	0.996	1	CLONAL	7	TRUE	1	0.379249004864795	7		306	775	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018140	48018140	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587779934	NA	P-0064940-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	143	452	0	ENST00000234420.5:c.335A>G	p.Asn112Ser	p.N112S	ENST00000234420	NM_000179.2	112	aAc/aGc	2/10	0.379249004864795	3	FACETS	1	0.918	1	0.504	0.459	0.551	CLONAL	1	TRUE	1	0.379249004864795	3		452	890	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593681	55593681	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064940-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	126	420	0	ENST00000288135.5:c.1747G>T	p.Glu583Ter	p.E583*	ENST00000288135	NM_000222.2	583	Gag/Tag	11/21	0.379249004864795	3	FACETS	1	0.975	1	0.609	0.553	0.668	CLONAL	1	TRUE	1	0.379249004864795	3		420	649	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885854	23885854	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064940-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	128	416	0	ENST00000374561.5:c.64C>A	p.Leu22Met	p.L22M	ENST00000374561	NM_002167.4	22	Ctg/Atg	1/3	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.379249004864795	2		416	624	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864175	57864175	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064940-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	160	538	0	ENST00000228682.2:c.1652C>A	p.Ser551Tyr	p.S551Y	ENST00000228682	NM_005269.2	551	tCt/tAt	12/12	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.379249004864795	2		538	775	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919684	28919685	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0064940-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	104	397	0	ENST00000282397.4:c.2252_2253delinsAA	p.Thr751Lys	p.T751K	ENST00000282397	NM_002019.4	751	aCC/aAA	16/30	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.379249004864795	2		397	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577499	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0064940-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	264	418	0	ENST00000269305.4:c.782_782+1delinsTT		p.X261_splice	ENST00000269305	NM_001126112.2	261		7/11	0.379249004864795	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.379249004864795	2		418	666	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724571	724571	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064940-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	130	258	0	ENST00000314574.4:c.1485G>T	p.Gln495His	p.Q495H	ENST00000314574	NM_005433.3	495	caG/caT	12/12	0.367870738084339	4	FACETS	0.965	0.881	1			1	CLONAL	2	TRUE	NA	0.379249004864795	4		258	490	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523511	41523511	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064940-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	120	438	0	ENST00000263253.7:c.927G>T	p.Gln309His	p.Q309H	ENST00000263253	NM_001429.3	309	caG/caT	4/31	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.379249004864795	2		438	610	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125320	47125320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064940-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	115	470	0	ENST00000409792.3:c.5950G>A	p.Glu1984Lys	p.E1984K	ENST00000409792	NM_014159.6	1984	Gag/Aag	12/21	1	2	FACETS	0.929	0.838	1	0.929	0.838	1	CLONAL	1	TRUE	1	0.379249004864795	2		470	653	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960059	134960059	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064940-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	268	542	0	ENST00000398015.3:c.2416G>T	p.Asp806Tyr	p.D806Y	ENST00000398015	NM_004441.4	806	Gac/Tac	13/16	0.379249004864795	3	FACETS	0.988	0.929	1	0.988	0.929	1	CLONAL	2	TRUE	1	0.379249004864795	3		542	851	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430204	181430204	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1227940600	NA	P-0064940-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	118	405	0	ENST00000325404.1:c.56G>T	p.Gly19Val	p.G19V	ENST00000325404	NM_003106.3	19	gGg/gTg	1/1	0.379249004864795	3	FACETS	1	0.922	1	0.512	0.462	0.565	CLONAL	1	TRUE	1	0.379249004864795	3		405	723	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748126	41748126	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1243150447	NA	P-0064940-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	106	424	0	ENST00000226382.2:c.643G>T	p.Gly215Cys	p.G215C	ENST00000226382	NM_003924.3	215	Ggc/Tgc	3/3	0.379249004864795	3	FACETS	1	0.934	1	0.526	0.472	0.583	CLONAL	1	TRUE	1	0.379249004864795	3		424	632	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524324	176524324	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064940-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	211	523	0	ENST00000292408.4:c.2185G>T	p.Ala729Ser	p.A729S	ENST00000292408	NM_213647.1	729	Gcg/Tcg	17/18	0.379249004864795	3	FACETS	0.814	0.758	0.872	0.814	0.758	0.872	CLONAL	2	TRUE	1	0.379249004864795	3		523	813	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922625	56922625	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064940-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	128	505	0	ENST00000519728.1:c.1495G>T	p.Asp499Tyr	p.D499Y	ENST00000519728	NM_002350.3	499	Gat/Tat	13/13	0.225775305122051	3	FACETS	0.97	0.879	1			1	INDETERMINATE	1	TRUE	NA	0.379249004864795	3		505	828	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0064941-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	12	149	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.335565708704688	1	FACETS	0.379	0.267	0.516	0.379	0.267	0.516	SUBCLONAL	1	TRUE	0	0.335565708704688	1		149	157	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535409	66535409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768337164	NA	P-0064941-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	37	542	0	ENST00000273854.3:c.52G>A	p.Gly18Ser	p.G18S	ENST00000273854	NM_004439.5	18	Ggc/Agc	1/18	1	2	FACETS	0.315	0.259	0.379	0.315	0.259	0.379	SUBCLONAL	1	TRUE	1	0.335565708704688	2		542	699	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101300	27101300	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064941-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	64	744	0	ENST00000324856.7:c.4582C>T	p.Arg1528Ter	p.R1528*	ENST00000324856	NM_006015.4	1528	Cga/Tga	18/20	0.327630994361425	3	FACETS	0.41	0.354	0.472	0.205	0.177	0.236	SUBCLONAL	1	TRUE	1	0.335565708704688	3		744	1086	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28929495	NA	P-0064941-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	322	524	0	ENST00000275493.2:c.2155G>T	p.Gly719Cys	p.G719C	ENST00000275493	NM_005228.3	719	Ggc/Tgc	18/28	0.335565708704688	4	FACETS	0.979	0.928	1	0.979	0.928	1	CLONAL	3	TRUE	1	0.335565708704688	4		524	873	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0064941-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	413	644	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.335565708704688	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	3	TRUE	1	0.335565708704688	4		644	1096	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0064948-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	4873	457	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.426339947539817	53	FACETS	0.999	0.995	1	0.999	0.995	1	CLONAL	53	FALSE	0	0.426339947539817	53		457	5126	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0064948-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5808	148	813	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.426339947539817	53	FACETS	1	0.983	1	0.026	0.023	0.029	CLONAL	1	FALSE	0	0.426339947539817	53		813	5956	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627889	37627889	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064948-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	71	557	1	ENST00000447079.4:c.1804C>T	p.Gln602Ter	p.Q602*	ENST00000447079	NM_015083.1	602	Cag/Tag	2/14	0.368006532549601	3	FACETS	0.978	0.858	1	0.326	0.286	0.369	CLONAL	1	FALSE	0	0.426339947539817	3		558	413	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7590694	7590694	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0064948-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	314	490	0	ENST00000269305.4:c.-29+1G>A		p.X10_splice	ENST00000269305	NM_001126112.2	10			0.368006532549601	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	FALSE	0	0.426339947539817	3		490	556	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954342	48954342	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064948-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	60	284	0	ENST00000267163.4:c.1463C>A	p.Ala488Glu	p.A488E	ENST00000267163	NM_000321.2	488	gCg/gAg	16/27	0.368006532549601	3	FACETS	1	0.957	1	0.79	0.699	0.883	CLONAL	2	FALSE	0	0.426339947539817	3		284	144	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533861	63533861	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	321	759	0	ENST00000307078.5:c.1293del	p.Tyr431Ter	p.Y431*	ENST00000307078	NM_004655.3	431	taC/ta	6/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.762483539423706	2		759	801	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593654	55593655	+	inframe_insertion	In_Frame_Ins	INS	-	-	CACAACTTCCTTATGATCACAAATGGGAGTTTCCCAGAAACAGGCTGAGTTTTGGTC	novel	NA	P-0064949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	118	511	0	ENST00000288135.5:c.1721_1774+3dup		p.T575_P594dup	ENST00000288135	NM_000222.2	575	aca/aCACAACTTCCTTATGATCACAAATGGGAGTTTCCCAGAAACAGGCTGAGTTTTGGTCca	11/21	1	2	FACETS	0.361	0.325	0.399	0.361	0.325	0.399	SUBCLONAL	1	TRUE	1	0.762483539423706	2		511	857	SUCCESS
APC	324	MSKCC	GRCh37	5	112175273	112175273	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123121	NA	P-0064950-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	294	606	0	ENST00000257430.4:c.3982C>T	p.Gln1328Ter	p.Q1328*	ENST00000257430	NM_000038.5	1328	Cag/Tag	16/16	0.51629700695893	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.51629700695893	2		606	561	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064950-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	94	527	0	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	1	2	FACETS	0.897	0.803	0.995	0.897	0.803	0.995	CLONAL	1	TRUE	1	0.51629700695893	2		527	406	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117642	70117642	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064950-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	515	921	0	ENST00000245479.2:c.110C>A	p.Ser37Ter	p.S37*	ENST00000245479	NM_000346.3	37	tCg/tAg	1/3	0.51629700695893	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.51629700695893	3		921	729	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417853	138417853	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064950-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	112	441	0	ENST00000289153.2:c.1666G>C	p.Asp556His	p.D556H	ENST00000289153	NM_006219.2	556	Gat/Cat	11/22	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.51629700695893	2		441	389	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253774	153253776	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0064950-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	86	418	0	ENST00000281708.4:c.957_959del	p.Leu320del	p.L320del	ENST00000281708	NM_033632.3	319	ctTCTc/ctc	6/12	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.51629700695893	2		418	323	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	91	624	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.31	2		625	563	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	142	680	2	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.31	2		682	913	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	72	386	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.946	0.829	1	0.946	0.829	1	CLONAL	1	TRUE	1	0.31	2		386	491	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	110	379	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.3	2	FACETS	0.941	0.854	1	0.941	0.854	1	CLONAL	2	TRUE	0	0.31	2		379	377	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073641	8073641	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	88	726	0	ENST00000377482.5:c.1018T>C	p.Ser340Pro	p.S340P	ENST00000377482	NM_018948.3	340	Tct/Cct	4/4	1	2	FACETS	0.607	0.537	0.683	0.607	0.537	0.683	SUBCLONAL	1	TRUE	1	0.31	2		726	935	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780177	9780177	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	171	819	0	ENST00000377346.4:c.1347G>T	p.Lys449Asn	p.K449N	ENST00000377346	NM_005026.3	449	aaG/aaT	11/24	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.31	2		819	925	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313336	65313336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1163622258	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	61	583	0	ENST00000342505.4:c.1778C>T	p.Thr593Met	p.T593M	ENST00000342505	NM_002227.2	593	aCg/aTg	13/25	1	2	FACETS	0.535	0.46	0.616	0.535	0.46	0.616	SUBCLONAL	1	TRUE	1	0.31	2		583	736	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980402	201980402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	104	787	0	ENST00000359651.3:c.142del	p.Gln48ArgfsTer107	p.Q48Rfs*107	ENST00000359651		46	aaC/aa	1/8	1	2	FACETS	0.696	0.622	0.775	0.696	0.622	0.775	SUBCLONAL	1	TRUE	1	0.31	2		787	964	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231488893	231488894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs567805129	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	39	542	0	ENST00000295050.7:c.1263dup	p.Ile422TyrfsTer11	p.I422Yfs*11	ENST00000295050	NM_032018.5	419	aat/aaTt	5/5	1	2	FACETS	0.447	0.37	0.533	0.447	0.37	0.533	SUBCLONAL	1	TRUE	1	0.31	2		542	563	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115794	8115794	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	112	691	0	ENST00000346208.3:c.1140C>G	p.Asp380Glu	p.D380E	ENST00000346208		380	gaC/gaG	6/6	1	2	FACETS	0.882	0.793	0.977	0.882	0.793	0.977	CLONAL	1	TRUE	1	0.31	2		691	819	SUCCESS
ATM	472	MSKCC	GRCh37	11	108183191	108183191	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	41	385	0	ENST00000278616.4:c.5977del	p.Ser1993ValfsTer7	p.S1993Vfs*7	ENST00000278616	NM_000051.3	1991	gAa/ga	40/63	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.31	2		385	248	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443789	49443789	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	178	792	0	ENST00000301067.7:c.3582del	p.Thr1195HisfsTer17	p.T1195Hfs*17	ENST00000301067	NM_003482.3	1194	ccC/cc	11/54	0.0650855355125226	4	FACETS	0.764	0.703	0.826	0.764	0.703	0.826	INDETERMINATE	2	TRUE	2	0.31	4		792	985	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481857	56481857	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519817	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	135	693	0	ENST00000267101.3:c.785C>A	p.Pro262His	p.P262H	ENST00000267101	NM_001982.3	262	cCt/cAt	7/28	0.0650855355125226	4	FACETS	1	0.984	1	0.706	0.642	0.773	INDETERMINATE	1	TRUE	2	0.31	4		693	808	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864184	57864184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	179	849	0	ENST00000228682.2:c.1661C>T	p.Thr554Ile	p.T554I	ENST00000228682	NM_005269.2	554	aCt/aTt	12/12	0.0650855355125226	4	FACETS	0.8	0.738	0.866	0.8	0.738	0.866	INDETERMINATE	2	TRUE	2	0.31	4		849	945	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874034	123874034	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs186822980	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	150	695	0	ENST00000330479.4:c.65T>C	p.Val22Ala	p.V22A	ENST00000330479	NM_020382.3	22	gTg/gCg	2/9	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.31	2		695	839	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249802	133249802	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	119	630	0	ENST00000320574.5:c.1421T>A	p.Val474Asp	p.V474D	ENST00000320574	NM_006231.2	474	gTc/gAc	14/49	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.31	2		630	699	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	27	581	4	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	0.501	0.398	0.617	0.501	0.398	0.617	SUBCLONAL	1	TRUE	1	0.31	2		585	348	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435949	110435949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780816462	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	107	807	0	ENST00000375856.3:c.2452G>A	p.Gly818Arg	p.G818R	ENST00000375856	NM_003749.2	818	Ggg/Agg	1/2	1	2	FACETS	0.92	0.826	1	0.92	0.826	1	CLONAL	1	TRUE	1	0.31	2		807	750	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986490	36986490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	63	730	0	ENST00000354822.5:c.1199C>T	p.Thr400Ile	p.T400I	ENST00000354822	NM_001079668.2	400	aCc/aTc	3/3	0.145462190053041	0	FACETS	0.419	0.362	0.481			1	INDETERMINATE	1	TRUE	0	0.31	0		730	669	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680766	88680766	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	98	562	0	ENST00000360948.2:c.491G>T	p.Cys164Phe	p.C164F	ENST00000360948	NM_001012338.2	164	tGc/tTc	6/19	0.3	1	FACETS	0.913	0.817	1	0.913	0.817	1	CLONAL	1	TRUE	0	0.31	1		562	585	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347484	91347484	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	102	589	0	ENST00000355112.3:c.3651del	p.Lys1217AsnfsTer62	p.K1217Nfs*62	ENST00000355112	NM_000057.2	1216	Aaa/aa	19/22	0.114485127873689	3	FACETS	1	0.972	1			1	INDETERMINATE	1	TRUE	NA	0.31	3		589	607	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348019	348019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	170	919	0	ENST00000262320.3:c.1487G>A	p.Ser496Asn	p.S496N	ENST00000262320	NM_003502.3	496	aGt/aAt	6/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.31	2		919	876	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121541	2121541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334081822	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	137	701	0	ENST00000219476.3:c.1870G>A	p.Asp624Asn	p.D624N	ENST00000219476	NM_000548.3	624	Gac/Aac	18/42	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.31	2		701	760	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825519	50825519	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	41	509	1	ENST00000398568.2:c.2156del	p.Asn719MetfsTer13	p.N719Mfs*13	ENST00000398568	NM_001042412.1	717	gAa/ga	14/18	1	2	FACETS	0.925	0.775	1	0.925	0.775	1	CLONAL	1	TRUE	1	0.31	2		510	286	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822055	72822055	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	166	800	0	ENST00000268489.5:c.10120G>C	p.Ala3374Pro	p.A3374P	ENST00000268489	NM_006885.3	3374	Gca/Cca	10/10	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.31	2		800	1043	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510749	38510749	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	99	433	0	ENST00000254066.5:c.1003A>G	p.Ile335Val	p.I335V	ENST00000254066	NM_000964.3	335	Atc/Gtc	7/9	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.31	2		433	608	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453399	40453399	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs759027671	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	153	645	8	ENST00000345506.4:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000345506	NM_003152.3	366	Ccc/cc	10/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.31	2		653	912	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118905	70118906	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	183	891	0	ENST00000245479.2:c.478dup	p.Arg160ProfsTer92	p.R160Pfs*92	ENST00000245479	NM_000346.3	159	-/C	2/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.31	2		891	988	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120114	70120115	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	145	699	0	ENST00000245479.2:c.1121dup	p.Gln375AlafsTer203	p.Q375Afs*203	ENST00000245479	NM_000346.3	372	-/C	3/3	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.31	2		699	789	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39567797	39567797	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	26	485	0	ENST00000262039.4:c.553G>T	p.Gly185Ter	p.G185*	ENST00000262039	NM_002647.2	185	Gga/Tga	5/25	1	2	FACETS	0.55	0.436	0.68	0.55	0.436	0.68	SUBCLONAL	1	TRUE	1	0.31	2		485	305	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221467	36221470	+	frameshift_variant	Frame_Shift_Del	DEL	TCTG	TCTG	-	novel	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	133	867	0	ENST00000222270.7:c.5230_5233del	p.Ser1744IlefsTer150	p.S1744Ifs*150	ENST00000222270	NM_014727.1	1742	acTCTG/ac	25/37	1	2	FACETS	0.934	0.847	1	0.934	0.847	1	CLONAL	1	TRUE	1	0.31	2		867	919	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082313	16082314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs780080562	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	33	793	1	ENST00000281043.3:c.134dup	p.Glu47GlyfsTer8	p.E47Gfs*8	ENST00000281043	NM_005378.4	43	acc/aCcc	2/3	1	2	FACETS	0.323	0.262	0.392	0.323	0.262	0.392	SUBCLONAL	1	TRUE	1	0.31	2		794	659	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197532	106197532	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	64	603	0	ENST00000380013.4:c.5865G>T	p.Glu1955Asp	p.E1955D	ENST00000380013	NM_001127208.2	1955	gaG/gaT	11/11	1	2	FACETS	0.55	0.475	0.631	0.55	0.475	0.631	SUBCLONAL	1	TRUE	1	0.31	2		603	751	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970922	79970922	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs71539687	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	69	490	1	ENST00000265081.6:c.1148A>G	p.Lys383Arg	p.K383R	ENST00000265081	NM_002439.4	383	aAg/aGg	7/24	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.31	2		491	443	SUCCESS
APC	324	MSKCC	GRCh37	5	112174956	112174956	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1114167614	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	120	574	0	ENST00000257430.4:c.3665C>A	p.Ser1222Ter	p.S1222*	ENST00000257430	NM_000038.5	1222	tCa/tAa	16/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.31	2		574	651	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	112	698	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	1	2	FACETS	0.912	0.821	1	0.912	0.821	1	CLONAL	1	TRUE	1	0.31	2		698	792	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324094	31324094	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	185	448	0	ENST00000412585.2:c.469T>G	p.Trp157Gly	p.W157G	ENST00000412585	NM_005514.6	157	Tgg/Ggg	3/8	0.0650855355125226	4	FACETS	0.899	0.835	0.964	1	0.989	1	INDETERMINATE	3	TRUE	2	0.31	4		448	580	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800564	32800564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148663600	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	180	716	0	ENST00000374899.4:c.983C>T	p.Ala328Val	p.A328V	ENST00000374899	NM_018833.2	328	gCg/gTg	6/12	0.0650855355125226	4	FACETS	1	0.989	1	0.726	0.669	0.786	INDETERMINATE	1	TRUE	2	0.31	4		716	1047	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816875	32816875	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	96	537	0	ENST00000354258.4:c.1449del	p.Val484TrpfsTer11	p.V484Wfs*11	ENST00000354258	NM_000593.5	483	aaA/aa	6/11	0.0650855355125226	4	FACETS	1	0.96	1	0.581	0.518	0.649	INDETERMINATE	1	TRUE	2	0.31	4		537	698	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652083	36652083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748758330	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	155	803	1	ENST00000244741.5:c.205C>T	p.Arg69Trp	p.R69W	ENST00000244741	NM_000389.4	69	Cgg/Tgg	2/3	0.0650855355125226	4	FACETS	1	0.984	1	0.662	0.605	0.721	INDETERMINATE	1	TRUE	2	0.31	4		804	990	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381466	81381466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	63	466	0	ENST00000222390.5:c.595G>A	p.Glu199Lys	p.E199K	ENST00000222390	NM_000601.4	199	Gaa/Aaa	5/18	1	2	FACETS	0.792	0.686	0.907	0.792	0.686	0.907	CLONAL	1	TRUE	1	0.31	2		466	513	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392136	81392136	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	30	396	0	ENST00000222390.5:c.141G>T	p.Lys47Asn	p.K47N	ENST00000222390	NM_000601.4	47	aaG/aaT	2/18	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.31	2		396	167	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836311	151836311	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	116	606	0	ENST00000262189.6:c.14494G>A	p.Asp4832Asn	p.D4832N	ENST00000262189	NM_170606.2	4832	Gac/Aac	57/59	1	2	FACETS	0.974	0.879	1	0.974	0.879	1	CLONAL	1	TRUE	1	0.31	2		606	768	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742041	145742041	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	75	737	0	ENST00000428558.2:c.462del	p.Val155SerfsTer25	p.V155Sfs*25	ENST00000428558	NM_004260.3	154	aaA/aa	5/22	0.190751131269917	4	FACETS	0.592	0.517	0.673	0.197	0.172	0.225	SUBCLONAL	1	TRUE	1	0.31	4		737	1071	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549526	5549526	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	51	673	2	ENST00000397747.3:c.557del	p.Pro186LeufsTer14	p.P186Lfs*14	ENST00000397747	NM_025239.3	185	Ccc/cc	4/7	1	2	FACETS	0.384	0.325	0.449	0.384	0.325	0.449	SUBCLONAL	1	TRUE	1	0.31	2		675	856	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934069	39934070	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	183	714	0	ENST00000378444.4:c.529_530del	p.Ser177ProfsTer8	p.S177Pfs*8	ENST00000378444	NM_001123385.1	177	AGc/c	4/15	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.31	2		714	863	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426763	47426763	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	69	778	0	ENST00000377045.4:c.1008G>T	p.Lys336Asn	p.K336N	ENST00000377045	NM_001654.4	336	aaG/aaT	10/16	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.31	NA		778	894	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2039765	2039791	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAACAGCAGCAGCAGCAG	CAGCAGCAGCAACAGCAGCAGCAGCAG	-	rs779149422	NA	P-0064952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	70	768	0	ENST00000349721.2:c.666_692del	p.Gln230_Gln238del	p.Q230_Q238del	ENST00000349721	NM_003070.3	219	CAGCAGCAGCAACAGCAGCAGCAGCAG/-	4/34	1	2	FACETS	0.529	0.46	0.604	0.529	0.46	0.604	SUBCLONAL	1	TRUE	1	0.31	2		768	854	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0064954-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	106	433	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.349833411244521	1	FACETS	0.66	0.599	0.723	0.66	0.599	0.723	INDETERMINATE	1	TRUE	0	0.669727945033647	1		433	319	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0064954-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	303	379	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.581443878681029	3	FACETS	0.979	0.931	1	0.979	0.931	1	CLONAL	2	TRUE	1	0.669727945033647	3		379	617	SUCCESS
APC	324	MSKCC	GRCh37	5	112154963	112154963	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660802	NA	P-0064954-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	127	634	1	ENST00000257430.4:c.1234C>T	p.Gln412Ter	p.Q412*	ENST00000257430	NM_000038.5	412	Cag/Tag	10/16	0.349833411244521	1	FACETS	0.426	0.387	0.467	0.426	0.387	0.467	INDETERMINATE	1	TRUE	0	0.669727945033647	1		635	592	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332919	153332919	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs781123562	NA	P-0064954-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	229	492	2	ENST00000281708.4:c.37C>T	p.Arg13Ter	p.R13*	ENST00000281708	NM_033632.3	13	Cga/Tga	2/12	1	2	FACETS	0.995	0.932	1	0.995	0.932	1	CLONAL	1	TRUE	1	0.669727945033647	2		494	687	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785724	50785724	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064954-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	204	481	2	ENST00000398568.2:c.714G>T	p.Leu238Phe	p.L238F	ENST00000398568	NM_001042412.1	238	ttG/ttT	4/18	1	2	FACETS	0.945	0.88	1	0.945	0.88	1	CLONAL	1	TRUE	1	0.669727945033647	2		483	645	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41560067	41560075	+	inframe_deletion	In_Frame_Del	DEL	TGTACAGAG	TGTACAGAG	-	novel	NA	P-0064954-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	85	470	0	ENST00000263253.7:c.3741_3749del	p.Thr1248_Cys1250del	p.T1248_C1250del	ENST00000263253	NM_001429.3	1247	TGTACAGAG/-	22/31	1	2	FACETS	0.459	0.406	0.515	0.459	0.406	0.515	SUBCLONAL	1	TRUE	1	0.669727945033647	2		470	553	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439885	52439885	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064954-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	286	730	2	ENST00000460680.1:c.827C>G	p.Ser276Cys	p.S276C	ENST00000460680	NM_004656.3	276	tCt/tGt	10/17	0.669727945033647	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.669727945033647	1		732	537	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729573	41729573	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064954-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	304	862	2	ENST00000242208.4:c.956A>G	p.Asn319Ser	p.N319S	ENST00000242208	NM_002192.2	319	aAc/aGc	3/3	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.669727945033647	2		864	906	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806092	1806092	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913484	NA	P-0064956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	55	619	0	ENST00000260795.2:c.1111A>T	p.Ser371Cys	p.S371C	ENST00000260795		371	Agt/Tgt	8/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		619	444	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813334	102813334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1430553116	NA	P-0064956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	30	658	0	ENST00000307046.8:c.355C>T	p.Arg119Cys	p.R119C	ENST00000307046	NM_001111285.1	119	Cgc/Tgc	3/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		658	568	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100541	8100541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1277364315	NA	P-0064956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	37	765	0	ENST00000346208.3:c.515C>T	p.Ser172Leu	p.S172L	ENST00000346208		172	tCg/tTg	3/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		765	564	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420273	49420273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1205083140	NA	P-0064956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	37	715	0	ENST00000301067.7:c.15476G>A	p.Arg5159Gln	p.R5159Q	ENST00000301067	NM_003482.3	5159	cGg/cAg	48/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		715	603	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	36	695	0	ENST00000227507.2:c.859C>A	p.Pro287Thr	p.P287T	ENST00000227507	NM_053056.2	287	Ccc/Acc	5/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		695	521	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100523	8100523	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	36	717	0	ENST00000346208.3:c.497C>G	p.Ser166Trp	p.S166W	ENST00000346208		166	tCg/tGg	3/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		717	489	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780035	9780035	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	30	717	0	ENST00000377346.4:c.1299G>T	p.Lys433Asn	p.K433N	ENST00000377346	NM_005026.3	433	aaG/aaT	10/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		717	560	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100550	8100550	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	35	789	0	ENST00000346208.3:c.524C>G	p.Ser175Trp	p.S175W	ENST00000346208		175	tCg/tGg	3/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		789	549	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447852	49447852	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	39	669	0	ENST00000301067.7:c.582C>G	p.His194Gln	p.H194Q	ENST00000301067	NM_003482.3	194	caC/caG	5/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		669	557	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46252735	46252735	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs200400305	NA	P-0064956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	67	424	0	ENST00000371998.3:c.164A>G	p.Asn55Ser	p.N55S	ENST00000371998		55	aAt/aGt	4/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		424	511	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564506	41564524	+	frameshift_variant	Frame_Shift_Del	DEL	CTGAGGCGACAGAATCACC	CTGAGGCGACAGAATCACC	-	novel	NA	P-0064956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	37	569	0	ENST00000263253.7:c.3933_3951del	p.Arg1311SerfsTer9	p.R1311Sfs*9	ENST00000263253	NM_001429.3	1310	CTGAGGCGACAGAATCACCct/ct	24/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		569	567	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638032	176638032	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	32	596	0	ENST00000439151.2:c.2632G>A	p.Asp878Asn	p.D878N	ENST00000439151	NM_022455.4	878	Gac/Aac	5/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		596	487	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860584	151860584	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1288334215	NA	P-0064956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	44	751	0	ENST00000262189.6:c.10078A>G	p.Ile3360Val	p.I3360V	ENST00000262189	NM_170606.2	3360	Ata/Gta	43/59	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		751	622	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772925	135772925	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397514871	NA	P-0064956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	30	549	0	ENST00000298552.3:c.2698C>T	p.Gln900Ter	p.Q900*	ENST00000298552	NM_001162426.1	900	Cag/Tag	21/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		549	444	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191480	10191480	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064957-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	98	524	0	ENST00000256474.2:c.473T>G	p.Leu158Arg	p.L158R	ENST00000256474	NM_000551.3	158	cTg/cGg	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		524	397	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931846	68931846	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064957-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	63	485	0	ENST00000288368.4:c.276A>T	p.Glu92Asp	p.E92D	ENST00000288368	NM_024870.2	92	gaA/gaT	3/40	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		485	288	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	178	342	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.457761078685266	3	FACETS	0.943	0.878	1			1	CLONAL	2	TRUE	NA	0.517521808798702	3		342	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0064958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	219	661	0	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	0.517521808798702	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.517521808798702	1		661	558	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0064958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	142	475	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.517521808798702	2		475	518	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148891	119148891	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs267606706	NA	P-0064958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	16	367	3	ENST00000264033.4:c.1111T>C	p.Tyr371His	p.Y371H	ENST00000264033	NM_005188.3	371	Tac/Cac	8/16	1	2	FACETS	0.153	0.112	0.201	0.153	0.112	0.201	SUBCLONAL	1	TRUE	1	0.517521808798702	2		370	405	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950066	38950066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1297105779	NA	P-0064958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	197	600	0	ENST00000357387.3:c.3884C>T	p.Thr1295Met	p.T1295M	ENST00000357387	NM_152756.3	1295	aCg/aTg	31/38	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.517521808798702	2		600	702	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90633818	90633818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371777275	NA	P-0064959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	70	735	0	ENST00000330062.3:c.266G>A	p.Arg89His	p.R89H	ENST00000330062	NM_002168.2	89	cGt/cAt	3/11	0.239221566835985	1	FACETS	0.44	0.383	0.501	0.44	0.383	0.501	SUBCLONAL	1	TRUE	0	0.394022540455991	1		735	649	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060635	38060635	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	3405	984	0	ENST00000250448.2:c.1354C>A	p.Pro452Thr	p.P452T	ENST00000250448	NM_004496.3	452	Ccc/Acc	2/2	0.394022540455991	20	FACETS	1	0.994	1			1	CLONAL	19	TRUE	NA	0.394022540455991	20		984	4117	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539227	187539227	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0064959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	43	715	0	ENST00000441802.2:c.8513C>G	p.Ser2838Ter	p.S2838*	ENST00000441802	NM_005245.3	2838	tCa/tGa	10/27	0.394022540455991	1	FACETS	0.369	0.309	0.436	0.369	0.309	0.436	SUBCLONAL	1	TRUE	0	0.394022540455991	1		715	475	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345240	70345240	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	51	602	0	ENST00000374080.3:c.2266G>C	p.Val756Leu	p.V756L	ENST00000374080		756	Gta/Cta	16/45	0.239221566835985	1	FACETS	0.405	0.344	0.472	0.405	0.344	0.472	SUBCLONAL	1	TRUE	0	0.394022540455991	1		602	513	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845382	76845382	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	61	461	0	ENST00000373344.5:c.6139C>G	p.Leu2047Val	p.L2047V	ENST00000373344	NM_000489.3	2047	Ctg/Gtg	27/35	0.239221566835985	1	FACETS	0.653	0.565	0.747	0.653	0.565	0.747	SUBCLONAL	1	TRUE	0	0.394022540455991	1		461	381	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0064962-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	171	475	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.514852123118396	2		475	570	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249002	55249003	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGTGGA	rs397517109	NA	P-0064962-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	124	593	0	ENST00000275493.2:c.2303_2311dup	p.Ser768_Asp770dup	p.S768_D770dup	ENST00000275493	NM_005228.3	768	gcc/gcCAGCGTGGAc	20/28	1	2	FACETS	0.967	0.88	1	0.967	0.88	1	CLONAL	1	TRUE	1	0.514852123118396	2		593	498	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261308	16261308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064962-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	177	772	0	ENST00000375759.3:c.8573C>T	p.Pro2858Leu	p.P2858L	ENST00000375759	NM_015001.2	2858	cCt/cTt	11/15	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.514852123118396	2		772	661	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845627	63845628	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0064962-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	84	610	0	ENST00000279873.7:c.1367_1368insCA	p.Glu456AspfsTer24	p.E456Dfs*24	ENST00000279873	NM_032199.2	456	gaa/gACaa	9/10	1	2	FACETS	0.463	0.408	0.521	0.463	0.408	0.521	SUBCLONAL	1	TRUE	1	0.514852123118396	2		610	705	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0064963-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	247	393	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.659788509129125	2	FACETS	0.87	0.831	0.908	0.87	0.831	0.908	CLONAL	2	TRUE	0	0.758754809920747	2		393	374	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0064963-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	129	527	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.754547083534765	1	FACETS	0.632	0.581	0.684	0.632	0.581	0.684	SUBCLONAL	1	TRUE	0	0.758754809920747	1		527	334	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0064963-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	85	552	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.456	0.404	0.511	0.456	0.404	0.511	SUBCLONAL	1	TRUE	1	0.758754809920747	2		552	491	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604790	48604790	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1568211615	NA	P-0064963-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	204	673	0	ENST00000342988.3:c.1612G>T	p.Glu538Ter	p.E538*	ENST00000342988	NM_005359.5	538	Gaa/Taa	12/12	0.758754809920747	1	FACETS	0.8	0.753	0.848	0.8	0.753	0.848	SUBCLONAL	1	TRUE	0	0.758754809920747	1		673	417	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001303	29001303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201407326	NA	P-0064963-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	157	555	1	ENST00000282397.4:c.1429G>A	p.Glu477Lys	p.E477K	ENST00000282397	NM_002019.4	477	Gaa/Aaa	10/30	1	2	FACETS	0.759	0.7	0.821	0.759	0.7	0.821	SUBCLONAL	1	TRUE	1	0.758754809920747	2		556	545	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450397	50450397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064963-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	72	726	0	ENST00000331340.3:c.581C>T	p.Thr194Met	p.T194M	ENST00000331340	NM_006060.4	194	aCg/aTg	5/8	0.760003885214185	3	FACETS	0.341	0.297	0.388	0.17	0.148	0.194	SUBCLONAL	1	TRUE	1	0.758754809920747	3		726	768	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578260	7578260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204041	NA	P-0064963-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	231	817	3	ENST00000269305.4:c.589G>A	p.Val197Met	p.V197M	ENST00000269305	NM_001126112.2	197	Gtg/Atg	6/11	0.721051852456815	1	FACETS	0.836	0.79	0.882	0.836	0.79	0.882	CLONAL	1	TRUE	0	0.758754809920747	1		820	452	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042116	6042116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881916	NA	P-0064963-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	34	293	0	ENST00000265849.7:c.505C>T	p.Arg169Cys	p.R169C	ENST00000265849	NM_000535.5	169	Cgc/Tgc	5/15	0.760003885214185	3	FACETS	0.253	0.206	0.306	0.126	0.103	0.153	SUBCLONAL	1	TRUE	1	0.758754809920747	3		293	489	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534665	140534665	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064963-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	65	493	0	ENST00000288602.6:c.248A>T	p.Glu83Val	p.E83V	ENST00000288602	NM_004333.4	83	gAa/gTa	3/18	0.760003885214185	3	FACETS	0.392	0.34	0.449	0.196	0.17	0.225	SUBCLONAL	1	TRUE	1	0.758754809920747	3		493	603	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	62	789	0				ENST00000310581	NM_198253.2	-/1132			0.188725188152611	0	FACETS	0.384	0.335	0.437			1	INDETERMINATE	1	TRUE	0	0.555568402254039	0		789	258	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476265	88476265	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	114	474	0	ENST00000360948.2:c.1867G>A	p.Gly623Arg	p.G623R	ENST00000360948	NM_001012338.2	623	Gga/Aga	15/19	0.555568402254039	3	FACETS	1	0.98	1	0.659	0.598	0.722	CLONAL	1	TRUE	1	0.555568402254039	3		474	398	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115733	108115733	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1370428326	NA	P-0064964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	36	438	0	ENST00000278616.4:c.881G>T	p.Gly294Val	p.G294V	ENST00000278616	NM_000051.3	294	gGa/gTa	7/63	0.542162517751946	2	FACETS	0.842	0.702	0.992	0.421	0.351	0.496	CLONAL	1	TRUE	0	0.555568402254039	2		438	154	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528987	157528987	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	88	548	0	ENST00000346085.5:c.6712G>A	p.Val2238Ile	p.V2238I	ENST00000346085	NM_020732.3	2238	Gtc/Atc	20/20	1	2	FACETS	0.769	0.685	0.857	0.769	0.685	0.857	SUBCLONAL	1	TRUE	1	0.555568402254039	2		548	412	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0064965-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	188	535	1	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.577111519639177	2		536	637	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0064965-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	326	552	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.577111519639177	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.577111519639177	2		552	535	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059162	27059172	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTAGGAGCTA	TGTAGGAGCTA	-	novel	NA	P-0064965-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	103	307	0	ENST00000324856.7:c.1804-4_1810del		p.X602_splice	ENST00000324856	NM_006015.4	602		4/20	1	2	FACETS	0.994	0.898	1	0.994	0.898	1	CLONAL	1	TRUE	1	0.577111519639177	2		307	359	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380276	+	missense_variant	Missense_Mutation	DNP	TT	TT	AA	novel	NA	P-0064965-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	100	435	0	ENST00000311936.3:c.182_183inv	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAA/cTT	3/5	1	2	FACETS	0.854	0.768	0.943	0.854	0.768	0.943	CLONAL	1	TRUE	1	0.577111519639177	2		435	406	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814231	76814231	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064965-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	58	228	0	ENST00000373344.5:c.6413C>A	p.Ser2138Tyr	p.S2138Y	ENST00000373344	NM_000489.3	2138	tCt/tAt	29/35	1	2	FACETS	0.885	0.77	1	0.885	0.77	1	CLONAL	1	TRUE	1	0.577111519639177	2		228	227	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871836	12871836	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	130	523	0	ENST00000228872.4:c.553G>C	p.Glu185Gln	p.E185Q	ENST00000228872	NM_004064.3	185	Gag/Cag	2/3	0.29378995990575	5	FACETS	1	0.969	1	0.385	0.349	0.423	INDETERMINATE	1	FALSE	2	0.576296306146815	5		523	728	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577520	+	inframe_deletion	In_Frame_Del	DEL	TGATGA	TGATGA	-	novel	NA	P-0064966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	554	576	0	ENST00000269305.4:c.761_766del	p.Ile254_Ile255del	p.I254_I255del	ENST00000269305	NM_001126112.2	254	aTCATCAca/aca	7/11	0.44870922756347	5	FACETS	1	0.993	1	0.862	0.836	0.887	CLONAL	4	FALSE	0	0.576296306146815	5		576	832	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69207359	69207359	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	67	396	0	ENST00000462284.1:c.125A>T	p.Lys42Met	p.K42M	ENST00000462284	NM_002392.5	42	aAg/aTg	3/11	0.321548855354829	6	FACETS	1	0.924	1	0.362	0.315	0.412	INDETERMINATE	1	FALSE	3	0.576296306146815	6		396	461	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832401	72832401	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	280	590	0	ENST00000268489.5:c.4180T>A	p.Ser1394Thr	p.S1394T	ENST00000268489	NM_006885.3	1394	Tca/Aca	9/10	0.535006645706448	4	FACETS	0.844	0.795	0.895	0.844	0.795	0.895	CLONAL	2	FALSE	2	0.576296306146815	4		590	907	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299894	15299894	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0064966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	377	691	0	ENST00000263388.2:c.1284del	p.Cys428TrpfsTer23	p.C428Wfs*23	ENST00000263388	NM_000435.2	428	tgT/tg	8/33	0.267768899378587	6	FACETS	1	0.986	1	0.809	0.772	0.847	INDETERMINATE	3	FALSE	2	0.576296306146815	6		691	870	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931302	131931302	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	129	397	0	ENST00000265335.6:c.2007C>G	p.Phe669Leu	p.F669L	ENST00000265335		669	ttC/ttG	13/25	0.351979777814875	5	FACETS	1	0.984	1			1	CLONAL	1	FALSE	NA	0.576296306146815	5		397	589	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124475468	124475468	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	211	372	0	ENST00000357628.3:c.1370G>A	p.Gly457Glu	p.G457E	ENST00000357628	NM_015450.2	457	gGa/gAa	15/19	0.419445473892458	6	FACETS	1	0.974	1	0.803	0.753	0.852	CLONAL	3	FALSE	2	0.576296306146815	6		372	491	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572718	141572718	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1242	85	613	0	ENST00000220592.5:c.352A>C	p.Thr118Pro	p.T118P	ENST00000220592	NM_012154.3	118	Acg/Ccg	4/19	0.576296306146815	8	FACETS	0.607	0.534	0.685	0.101	0.089	0.115	SUBCLONAL	1	FALSE	2	0.576296306146815	8		613	1327	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437795	52437795	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	170	767	0	ENST00000460680.1:c.1366C>T	p.Gln456Ter	p.Q456*	ENST00000460680	NM_004656.3	456	Cag/Tag	13/17	0.512079546510459	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.512079546510459	1		767	475	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218432	36218432	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	105	738	0	ENST00000222270.7:c.4211C>T	p.Ala1404Val	p.A1404V	ENST00000222270	NM_014727.1	1404	gCc/gTc	16/37	1	2	FACETS	0.655	0.588	0.726	0.655	0.588	0.726	SUBCLONAL	1	TRUE	1	0.512079546510459	2		738	626	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035102	30035102	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	76	593	0	ENST00000338641.4:c.265del	p.Glu89LysfsTer34	p.E89Kfs*34	ENST00000338641	NM_000268.3	88	aaG/aa	3/16	0.512079546510459	1	FACETS	0.769	0.682	0.861	0.769	0.682	0.861	SUBCLONAL	1	TRUE	0	0.512079546510459	1		593	287	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777967	27777967	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	102	883	0	ENST00000369163.2:c.116C>A	p.Pro39His	p.P39H	ENST00000369163	NM_003536.2	39	cCc/cAc	1/1	1	2	FACETS	0.507	0.453	0.564	0.507	0.453	0.564	SUBCLONAL	1	TRUE	1	0.512079546510459	2		883	786	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0064968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	53	458	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.529	0.45	0.617	0.529	0.45	0.617	SUBCLONAL	1	TRUE	1	0.236407887553892	2		458	847	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0064968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	94	627	1	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	NA	2	FACETS	0.677	0.6	0.759			1	INDETERMINATE	1	TRUE	NA	0.236407887553892	2		628	1175	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007842	45007842	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	66	531	0	ENST00000558401.1:c.289G>T	p.Glu97Ter	p.E97*	ENST00000558401	NM_004048.2	97	Gag/Tag	2/4	1	2	FACETS	0.558	0.483	0.64	0.558	0.483	0.64	SUBCLONAL	1	TRUE	1	0.236407887553892	2		531	1001	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406654	70406655	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0064968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	50	462	0	ENST00000373644.4:c.4170_4171dup	p.Ala1391ValfsTer11	p.A1391Vfs*11	ENST00000373644	NM_030625.2	1390	agt/aGTgt	4/12	1	2	FACETS	0.52	0.44	0.608	0.52	0.44	0.608	SUBCLONAL	1	TRUE	1	0.236407887553892	2		462	814	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924623	94924623	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	75	549	0	ENST00000536441.1:c.287T>G	p.Met96Arg	p.M96R	ENST00000536441	NM_144665.3	96	aTg/aGg	3/10	0.236407887553892	1	FACETS	0.576	0.503	0.655	0.576	0.503	0.655	SUBCLONAL	1	TRUE	0	0.236407887553892	1		549	971	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0064971-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	272	878	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.248095434335732	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.27	2		878	850	SUCCESS
APC	324	MSKCC	GRCh37	5	112175419	112175419	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0064971-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	123	709	0	ENST00000257430.4:c.4128T>G	p.Tyr1376Ter	p.Y1376*	ENST00000257430	NM_000038.5	1376	taT/taG	16/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.27	2		709	723	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0064971-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	107	719	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	0.248095434335732	2	FACETS	1	0.907	1	0.506	0.454	0.562	CLONAL	1	TRUE	0	0.27	2		719	783	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0064971-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	73	462	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	1	2	FACETS	0.964	0.844	1	0.964	0.844	1	CLONAL	1	TRUE	1	0.27	2		462	561	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476388	88476388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374759890	NA	P-0064971-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	157	564	0	ENST00000360948.2:c.1744C>T	p.Arg582Trp	p.R582W	ENST00000360948	NM_001012338.2	582	Cgg/Tgg	15/19	0.3	1	FACETS	0.837	0.77	0.906	1	0.99	1	CLONAL	2	TRUE	0	0.27	1		564	601	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920652	96920652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767739392	NA	P-0064971-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	85	686	0	ENST00000258439.3:c.328G>A	p.Ala110Thr	p.A110T	ENST00000258439	NM_001193304.2	110	Gct/Act	3/4	1	2	FACETS	0.899	0.795	1	0.899	0.795	1	CLONAL	1	TRUE	1	0.27	2		686	700	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0064972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	28	338	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	0.249798844856567	1	FACETS	0.405	0.324	0.496	0.405	0.324	0.496	SUBCLONAL	1	TRUE	0	0.380891082156953	1		338	294	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442567	52442567	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1253151209	NA	P-0064972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	107	419	0	ENST00000460680.1:c.178C>T	p.Arg60Ter	p.R60*	ENST00000460680	NM_004656.3	60	Cga/Tga	4/17	0.380891082156953	1	FACETS	0.782	0.703	0.864	0.782	0.703	0.864	SUBCLONAL	1	TRUE	0	0.380891082156953	1		419	582	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915853	127915853	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	149	267	0	ENST00000373547.4:c.628C>T	p.Arg210Ter	p.R210*	ENST00000373547	NM_002721.4	210	Cga/Tga	6/7	0.380891082156953	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	1	0.380891082156953	3		267	447	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178550	56178550	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	78	311	0	ENST00000399503.3:c.3523C>A	p.Gln1175Lys	p.Q1175K	ENST00000399503	NM_005921.1	1175	Caa/Aaa	14/20	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.380891082156953	2		311	384	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057712	27057713	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	70	713	0	ENST00000324856.7:c.1423dup	p.Ser475LysfsTer148	p.S475Kfs*148	ENST00000324856	NM_006015.4	474	caa/cAaa	3/20	1	2	FACETS	0.924	0.806	1	0.924	0.806	1	CLONAL	1	TRUE	1	0.26862024445327	2		713	564	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46587800	46587800	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	65	423	1	ENST00000263734.3:c.478A>G	p.Lys160Glu	p.K160E	ENST00000263734	NM_001430.4	160	Aaa/Gaa	5/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.26862024445327	2		424	390	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818129	32818129	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	51	442	0	ENST00000354258.4:c.1396G>C	p.Val466Leu	p.V466L	ENST00000354258	NM_000593.5	466	Gtg/Ctg	5/11	1	2	FACETS	0.94	0.801	1	0.94	0.801	1	CLONAL	1	TRUE	1	0.26862024445327	2		442	404	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0064974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	355	809	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.812683953480898	2		809	833	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582193	189582193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1198643405	NA	P-0064974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	101	636	0	ENST00000264731.3:c.752G>A	p.Arg251His	p.R251H	ENST00000264731	NM_003722.4	251	cGt/cAt	5/14	0.46753019581756	1	FACETS	0.332	0.298	0.368	0.332	0.298	0.368	INDETERMINATE	1	TRUE	0	0.812683953480898	1		636	444	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023364	33023364	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	150	815	0	ENST00000300177.4:c.473G>T	p.Cys158Phe	p.C158F	ENST00000300177	NM_001191322.1	158	tGc/tTc	2/2	0.785387073090258	2	FACETS	0.589	0.54	0.64	0.294	0.27	0.32	SUBCLONAL	1	TRUE	0	0.812683953480898	2		815	627	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614864	23614864	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	138	590	0	ENST00000261584.4:c.3477G>T	p.Trp1159Cys	p.W1159C	ENST00000261584	NM_024675.3	1159	tgG/tgT	13/13	1	2	FACETS	0.559	0.511	0.61	0.559	0.511	0.61	SUBCLONAL	1	TRUE	1	0.812683953480898	2		590	607	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791276	42791276	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	173	834	0	ENST00000575354.2:c.336C>G	p.His112Gln	p.H112Q	ENST00000575354	NM_015125.3	112	caC/caG	3/20	1	2	FACETS	0.559	0.515	0.604	0.559	0.515	0.604	SUBCLONAL	1	TRUE	1	0.812683953480898	2		834	762	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0064975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	42	624	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.513450376200938	3	FACETS	0.75	0.63	0.882	0.375	0.315	0.441	SUBCLONAL	1	TRUE	1	0.513450376200938	3		625	274	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	116	658	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.513450376200938	3	FACETS	1	0.966	1	0.571	0.517	0.628	CLONAL	1	TRUE	1	0.513450376200938	3		658	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0064975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	239	700	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	0.513450376200938	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.513450376200938	2		700	390	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128018820	128018820	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	61	500	0	ENST00000285398.2:c.2048A>T	p.Gln683Leu	p.Q683L	ENST00000285398	NM_000122.1	683	cAa/cTa	13/15	1	2	FACETS	0.928	0.809	1	0.928	0.809	1	CLONAL	1	TRUE	1	0.513450376200938	2		500	256	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434809	49434810	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	A	novel	NA	P-0064975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	128	896	0	ENST00000301067.7:c.6743_6744delinsT	p.Arg2248LeufsTer16	p.R2248Lfs*16	ENST00000301067	NM_003482.3	2248	cGC/cT	31/54	0.513450376200938	3	FACETS	1	0.969	1	0.572	0.52	0.625	CLONAL	1	TRUE	1	0.513450376200938	3		896	548	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0064976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	217	556	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.675894628425048	2		556	523	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193967	106193967	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	168	493	0	ENST00000380013.4:c.4429G>T	p.Glu1477Ter	p.E1477*	ENST00000380013	NM_001127208.2	1477	Gaa/Taa	10/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.675894628425048	2		493	476	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248151	110248151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	291	505	0	ENST00000374672.4:c.1321G>A	p.Asp441Asn	p.D441N	ENST00000374672	NM_004235.4	441	Gat/Aat	5/5	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.675894628425048	2		505	750	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89874715	89874715	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	221	545	0	ENST00000389301.3:c.583G>C	p.Glu195Gln	p.E195Q	ENST00000389301	NM_000135.2	195	Gag/Cag	6/43	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.675894628425048	2		545	608	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683807	117683807	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	157	460	0	ENST00000368508.3:c.3340C>T	p.Gln1114Ter	p.Q1114*	ENST00000368508	NM_002944.2	1114	Caa/Taa	21/43	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.675894628425048	2		460	422	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77051795	77051795	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	214	523	0	ENST00000356341.3:c.1012G>C	p.Asp338His	p.D338H	ENST00000356341	NM_002576.4	338	Gat/Cat	11/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.675894628425048	2		523	606	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11027383	11027383	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	325	768	0	ENST00000327064.4:c.950C>G	p.Ser317Cys	p.S317C	ENST00000327064	NM_199141.1	317	tCt/tGt	8/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.675894628425048	2		768	913	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424582	47424582	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1370417324	NA	P-0064976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	208	647	0	ENST00000404338.3:c.2650C>T	p.Gln884Ter	p.Q884*	ENST00000404338	NM_004491.4	884	Cag/Tag	1/6	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.675894628425048	2		647	602	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164583	47164583	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1019451348	NA	P-0064976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	142	412	0	ENST00000409792.3:c.1543G>C	p.Glu515Gln	p.E515Q	ENST00000409792	NM_014159.6	515	Gaa/Caa	3/21	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.675894628425048	2		412	400	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165778	47165778	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	232	572	0	ENST00000409792.3:c.348G>C	p.Met116Ile	p.M116I	ENST00000409792	NM_014159.6	116	atG/atC	3/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.675894628425048	2		572	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579463	7579463	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	586	952	0	ENST00000269305.4:c.224del	p.Pro75LeufsTer48	p.P75Lfs*48	ENST00000269305	NM_001126112.2	75	cCt/ct	4/11	1	2	FACETS	0.974	0.939	1	0.974	0.939	1	CLONAL	1	TRUE	1	0.921087633975808	2		952	1306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs587781702	NA	P-0064977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	592	512	0	ENST00000269305.4:c.920-1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.921087633975808	2		512	1222	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292534	15292534	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760472019	NA	P-0064977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	515	858	0	ENST00000263388.2:c.2645C>T	p.Pro882Leu	p.P882L	ENST00000263388	NM_000435.2	882	cCa/cTa	17/33	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.921087633975808	2		858	1071	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672779	47672779	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1445965781	NA	P-0064977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	180	112	0	ENST00000233146.2:c.1369A>G	p.Thr457Ala	p.T457A	ENST00000233146	NM_000251.2	457	Act/Gct	8/16	0.20114255449234	4	FACETS	0.955	0.893	1	0.955	0.893	1	INDETERMINATE	2	TRUE	2	0.921087633975808	4		112	393	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907666	111907666	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1321821639	NA	P-0064977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	93	360	0	ENST00000393256.3:c.440G>A	p.Trp147Ter	p.W147*	ENST00000393256	NM_006538.4	147	tGg/tAg	3/4	0.270569040399867	1	FACETS	0.112	0.099	0.126	0.112	0.099	0.126	INDETERMINATE	1	TRUE	0	0.921087633975808	1		360	972	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546983	9546983	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	367	630	0	ENST00000353224.5:c.1039T>A	p.Ser347Thr	p.S347T	ENST00000353224	NM_177990.2	347	Tct/Act	5/10	0.921087633975808	3	FACETS	0.936	0.887	0.985	0.468	0.443	0.493	CLONAL	1	TRUE	1	0.921087633975808	3		630	1244	SUCCESS
APC	324	MSKCC	GRCh37	5	112178912	112178912	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587778033	NA	P-0064978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	23	596	0	ENST00000257430.4:c.7621A>G	p.Ile2541Val	p.I2541V	ENST00000257430	NM_000038.5	2541	Atc/Gtc	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		596	422	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	67	464	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		464	853	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249017	55249018	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCA	rs1554350381	NA	P-0064978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	13	653	0	ENST00000275493.2:c.2317_2319dup	p.His773dup	p.H773dup	ENST00000275493	NM_005228.3	773	ccc/ccCCAc	20/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		653	415	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207065	1207065	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	60	748	0	ENST00000326873.7:c.157del	p.Asp53ThrfsTer11	p.D53Tfs*11	ENST00000326873	NM_000455.4	51	atG/at	1/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		748	779	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0064978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	63	827	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		827	612	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394654	394654	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	79	622	0	ENST00000399788.2:c.5041C>A	p.Leu1681Ile	p.L1681I	ENST00000399788	NM_001042603.1	1681	Cta/Ata	28/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		622	548	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422611	47422611	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	119	688	0	ENST00000404338.3:c.679G>T	p.Glu227Ter	p.E227*	ENST00000404338	NM_004491.4	227	Gag/Tag	1/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		688	749	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207070	1207070	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	68	735	0	ENST00000326873.7:c.158A>T	p.Asp53Val	p.D53V	ENST00000326873	NM_000455.4	53	gAc/gTc	1/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		735	772	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0064980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	130	643	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.183450278948923	2	FACETS	1	0.984	1	0.705	0.64	0.774	CLONAL	1	TRUE	0	0.231587883062812	2		643	796	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0064980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	135	888	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.231587883062812	2		888	1054	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17117130	17117130	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs879255683	NA	P-0064980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	122	729	0	ENST00000285071.4:c.1579C>T	p.Arg527Ter	p.R527*	ENST00000285071	NM_144997.5	527	Cga/Tga	14/14	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.231587883062812	2		729	825	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0064981-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	134	393	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.605372771720224	2		393	412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0064981-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	332	702	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.605372771720224	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.605372771720224	1		702	739	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0064981-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	191	462	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.605372771720224	2		462	592	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412095	63412095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852217	NA	P-0064981-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	289	392	0	ENST00000330258.3:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000330258	NM_152424.3	358	Cga/Tga	2/2	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.605372771720224	1		392	473	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449468	31449468	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064981-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	225	581	0	ENST00000344624.3:c.2741G>C	p.Arg914Thr	p.R914T	ENST00000344624		914	aGg/aCg	19/33	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.605372771720224	2		581	733	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740402	58740402	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064982-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	105	602	0	ENST00000305921.3:c.1307T>A	p.Ile436Lys	p.I436K	ENST00000305921	NM_003620.3	436	aTa/aAa	6/6	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.549810080363262	2		602	342	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0064983-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	247	558	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.794	0.745	0.843	1	0.994	1	SUBCLONAL	2	TRUE	1	0.42	2		558	741	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	19	477	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	1	2	FACETS	0.534	0.405	0.686	0.534	0.405	0.686	SUBCLONAL	1	TRUE	1	0.2332984478044	2		477	305	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	8	473	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	1	2	FACETS	0.278	0.178	0.407	0.278	0.178	0.407	SUBCLONAL	1	TRUE	1	0.2332984478044	2		473	247	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866444	37866444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	18	726	0	ENST00000269571.5:c.749C>T	p.Ser250Phe	p.S250F	ENST00000269571		250	tCt/tTt	6/27	1	2	FACETS	0.543	0.409	0.702	0.543	0.409	0.702	SUBCLONAL	1	TRUE	1	0.2332984478044	2		726	284	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497754	120497754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782066959	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	18	670	0	ENST00000256646.2:c.2128G>A	p.Glu710Lys	p.E710K	ENST00000256646	NM_024408.3	710	Gag/Aag	13/34	0.19145422214973	1	FACETS	0.417	0.313	0.539	0.417	0.313	0.539	SUBCLONAL	1	TRUE	0	0.2332984478044	1		670	327	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519925	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	15	470	0	ENST00000263967.3:c.1357G>C	p.Glu453Gln	p.E453Q	ENST00000263967	NM_006218.2	453	Gaa/Caa	8/21	1	2	FACETS	0.695	0.51	0.916	0.695	0.51	0.916	SUBCLONAL	1	TRUE	1	0.2332984478044	2		470	185	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416493	29416493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1182539285	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	22	740	0	ENST00000389048.3:c.4460C>T	p.Ser1487Leu	p.S1487L	ENST00000389048	NM_004304.4	1487	tCg/tTg	29/29	0.137361872561379	0	FACETS	0.643	0.5	0.807			1	INDETERMINATE	1	TRUE	0	0.2332984478044	0		740	225	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	9	738	0	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.2332984478044	6	FACETS	0.473	0.313	0.679			1	SUBCLONAL	1	TRUE	NA	0.2332984478044	6		738	239	SUCCESS
ALK	238	MSKCC	GRCh37	2	29450509	29450509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774004991	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	13	649	1	ENST00000389048.3:c.2845G>A	p.Glu949Lys	p.E949K	ENST00000389048	NM_004304.4	949	Gaa/Aaa	17/29	0.137361872561379	0	FACETS	0.464	0.332	0.625			1	INDETERMINATE	1	TRUE	0	0.2332984478044	0		650	184	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495239	212495239	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	11	567	0	ENST00000342788.4:c.2027G>T	p.Arg676Ile	p.R676I	ENST00000342788	NM_005235.2	676	aGa/aTa	17/28	0.2332984478044	0	FACETS	0.646	0.449	0.885			1	SUBCLONAL	1	TRUE	0	0.2332984478044	0		567	112	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129169	64129169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746466314	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	14	760	1	ENST00000334205.4:c.707C>T	p.Ser236Leu	p.S236L	ENST00000334205	NM_003942.2	236	tCg/tTg	7/17	0.2332984478044	6	FACETS	0.876	0.634	1			1	CLONAL	1	TRUE	NA	0.2332984478044	6		761	201	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200961	108200961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782310	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	15	492	0	ENST00000278616.4:c.7328G>A	p.Arg2443Gln	p.R2443Q	ENST00000278616	NM_000051.3	2443	cGa/cAa	50/63	1	2	FACETS	0.627	0.46	0.828	0.627	0.46	0.828	SUBCLONAL	1	TRUE	1	0.2332984478044	2		492	205	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57474036	57474036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750429818	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	27	519	0	ENST00000371085.3:c.253G>A	p.Asp85Asn	p.D85N	ENST00000371085	NM_000516.4	85	Gat/Aat	3/13	1	2	FACETS	0.772	0.615	0.95	0.772	0.615	0.95	CLONAL	1	TRUE	1	0.2332984478044	2		519	300	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716366	18716366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs935135637	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	22	558	0	ENST00000266497.5:c.3713C>T	p.Ser1238Leu	p.S1238L	ENST00000266497		1238	tCa/tTa	26/31	0.137361872561379	0	FACETS	0.626	0.487	0.787			1	INDETERMINATE	1	TRUE	0	0.2332984478044	0		558	231	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513224	106513224	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	14	559	0	ENST00000359195.3:c.2128C>T	p.Gln710Ter	p.Q710*	ENST00000359195	NM_002649.2	710	Cag/Tag	4/11	1	2	FACETS	0.5	0.361	0.668	0.5	0.361	0.668	SUBCLONAL	1	TRUE	1	0.2332984478044	2		559	240	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965767	18965767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	12	698	0	ENST00000262803.5:c.1345G>A	p.Glu449Lys	p.E449K	ENST00000262803	NM_002911.3	449	Gag/Aag	10/24	1	2	FACETS	0.631	0.445	0.859	0.631	0.445	0.859	SUBCLONAL	1	TRUE	1	0.2332984478044	2		698	163	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501213	140501213	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	12	381	0	ENST00000288602.6:c.859G>C	p.Asp287His	p.D287H	ENST00000288602	NM_004333.4	287	Gat/Cat	6/18	1	2	FACETS	0.69	0.487	0.938	0.69	0.487	0.938	SUBCLONAL	1	TRUE	1	0.2332984478044	2		381	149	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520766	176520766	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	14	362	0	ENST00000292408.4:c.1509G>C	p.Lys503Asn	p.K503N	ENST00000292408	NM_213647.1	503	aaG/aaC	11/18	1	2	FACETS	0.833	0.606	1	0.833	0.606	1	CLONAL	1	TRUE	1	0.2332984478044	2		362	144	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115284191	115284191	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs781456472	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	11	518	0	ENST00000438362.2:c.95C>G	p.Ser32Cys	p.S32C	ENST00000438362	NM_001242891.1	32	tCt/tGt	2/20	0.2332984478044	3	FACETS	0.524	0.362	0.725	0.175	0.12	0.242	SUBCLONAL	1	TRUE	0	0.2332984478044	3		518	201	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193181600	193181600	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	10	346	0	ENST00000367435.3:c.1147G>C	p.Asp383His	p.D383H	ENST00000367435	NM_024529.4	383	Gac/Cac	13/17	1	2	FACETS	0.487	0.33	0.684	0.487	0.33	0.684	SUBCLONAL	1	TRUE	1	0.2332984478044	2		346	176	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682952	241682952	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587778361	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	11	628	0	ENST00000366560.3:c.71C>G	p.Ser24Trp	p.S24W	ENST00000366560	NM_000143.3	24	tCg/tGg	1/10	1	2	FACETS	0.515	0.356	0.712	0.515	0.356	0.712	SUBCLONAL	1	TRUE	1	0.2332984478044	2		628	183	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404579	70404579	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs201182189	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	10	563	0	ENST00000373644.4:c.2093A>G	p.Asn698Ser	p.N698S	ENST00000373644	NM_030625.2	698	aAt/aGt	4/12	0.120647805739511	4	FACETS	0.556	0.377	0.782	0.278	0.188	0.391	INDETERMINATE	1	TRUE	2	0.2332984478044	4		563	190	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406721	70406721	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	13	447	0	ENST00000373644.4:c.4235C>T	p.Ser1412Phe	p.S1412F	ENST00000373644	NM_030625.2	1412	tCt/tTt	4/12	0.120647805739511	4	FACETS	0.764	0.546	1	0.382	0.273	0.514	INDETERMINATE	1	TRUE	2	0.2332984478044	4		447	180	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233137	46233137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	14	425	0	ENST00000334344.6:c.1356G>A	p.Met452Ile	p.M452I	ENST00000334344	NM_152641.2	452	atG/atA	11/21	0.120647805739511	4	FACETS	0.726	0.525	0.967	0.363	0.262	0.484	INDETERMINATE	1	TRUE	2	0.2332984478044	4		425	204	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40998443	40998443	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1048716857	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	23	419	0	ENST00000267868.3:c.294G>C	p.Glu98Asp	p.E98D	ENST00000267868	NM_002875.4	98	gaG/gaC	4/10	1	2	FACETS	0.846	0.662	1	0.846	0.662	1	CLONAL	1	TRUE	1	0.2332984478044	2		419	233	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43773107	43773107	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	16	514	0	ENST00000382044.4:c.485C>T	p.Ser162Phe	p.S162F	ENST00000382044	NM_001141980.1	162	tCc/tTc	5/28	1	2	FACETS	0.666	0.493	0.871	0.666	0.493	0.871	SUBCLONAL	1	TRUE	1	0.2332984478044	2		514	206	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351253	89351253	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	11	712	0	ENST00000301030.4:c.1697C>G	p.Ser566Ter	p.S566*	ENST00000301030	NM_001256183.1	566	tCa/tGa	9/13	1	2	FACETS	0.536	0.371	0.74	0.536	0.371	0.74	SUBCLONAL	1	TRUE	1	0.2332984478044	2		712	176	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231426	5231426	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1036934835	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	10	668	0	ENST00000357368.4:c.2050G>C	p.Glu684Gln	p.E684Q	ENST00000357368	NM_002850.3	684	Gag/Cag	14/38	0.137361872561379	0	FACETS	0.476	0.324	0.666			1	INDETERMINATE	1	TRUE	0	0.2332984478044	0		668	138	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17389822	17389822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	10	639	0	ENST00000359435.4:c.955G>A	p.Glu319Lys	p.E319K	ENST00000359435	NM_001033549.1	319	Gag/Aag	9/9	1	2	FACETS	0.617	0.419	0.863	0.617	0.419	0.863	SUBCLONAL	1	TRUE	1	0.2332984478044	2		639	139	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303897	30303897	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	11	686	0	ENST00000262643.3:c.133G>C	p.Glu45Gln	p.E45Q	ENST00000262643	NM_001238.2	45	Gaa/Caa	4/12	1	2	FACETS	0.462	0.319	0.64	0.462	0.319	0.64	SUBCLONAL	1	TRUE	1	0.2332984478044	2		686	204	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719346	190719346	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs779894503	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	13	478	0	ENST00000441310.2:c.1348C>T	p.Gln450Ter	p.Q450*	ENST00000441310	NM_000534.4	450	Cag/Tag	9/13	1	2	FACETS	0.652	0.466	0.876	0.652	0.466	0.876	SUBCLONAL	1	TRUE	1	0.2332984478044	2		478	171	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944387	40944387	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	16	626	0	ENST00000373198.4:c.2115C>G	p.Phe705Leu	p.F705L	ENST00000373198	NM_133170.3	705	ttC/ttG	12/32	1	2	FACETS	0.766	0.569	1	0.766	0.569	1	CLONAL	1	TRUE	1	0.2332984478044	2		626	179	SUCCESS
APC	324	MSKCC	GRCh37	5	112178985	112178985	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	14	550	0	ENST00000257430.4:c.7694G>C	p.Arg2565Thr	p.R2565T	ENST00000257430	NM_000038.5	2565	aGa/aCa	16/16	1	2	FACETS	0.536	0.387	0.715	0.536	0.387	0.715	SUBCLONAL	1	TRUE	1	0.2332984478044	2		550	224	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965677	93965677	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	11	535	0	ENST00000369303.4:c.2251G>A	p.Asp751Asn	p.D751N	ENST00000369303	NM_004440.3	751	Gat/Aat	13/17	0.2332984478044	0	FACETS	0.485	0.336	0.669			1	SUBCLONAL	1	TRUE	0	0.2332984478044	0		535	149	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120384	94120384	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	11	609	0	ENST00000369303.4:c.667G>A	p.Glu223Lys	p.E223K	ENST00000369303	NM_004440.3	223	Gaa/Aaa	3/17	0.2332984478044	0	FACETS	0.369	0.255	0.51			1	SUBCLONAL	1	TRUE	0	0.2332984478044	0		609	196	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878671	151878671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	14	642	0	ENST00000262189.6:c.6274G>A	p.Asp2092Asn	p.D2092N	ENST00000262189	NM_170606.2	2092	Gat/Aat	36/59	1	2	FACETS	0.594	0.43	0.792	0.594	0.43	0.792	SUBCLONAL	1	TRUE	1	0.2332984478044	2		642	202	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579369	7579369	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555526581	NA	P-0064985-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	774	608	0	ENST00000269305.4:c.318C>G	p.Ser106Arg	p.S106R	ENST00000269305	NM_001126112.2	106	agC/agG	4/11	0.568382576248369	3	FACETS	0.934	0.91	0.957	0.934	0.91	0.957	CLONAL	3	TRUE	0	0.624657621867188	3		608	1161	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654681	67654681	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750256116	NA	P-0064986-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	164	620	0	ENST00000264010.4:c.1168G>A	p.Asp390Asn	p.D390N	ENST00000264010	NM_006565.3	390	Gac/Aac	6/12	1	2	FACETS	0.716	0.658	0.777	0.716	0.658	0.777	SUBCLONAL	1	TRUE	1	0.531342636736647	2		620	862	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983145	7983145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064986-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	182	708	0	ENST00000319144.4:c.869C>T	p.Thr290Ile	p.T290I	ENST00000319144	NM_001139.2	290	aCa/aTa	7/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.531342636736647	2		708	648	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207061	1207076	+	frameshift_variant	Frame_Shift_Del	DEL	TGATGGGGGACCTGCT	TGATGGGGGACCTGCT	-	novel	NA	P-0064986-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	348	779	0	ENST00000326873.7:c.149_164del	p.Leu50ArgfsTer9	p.L50Rfs*9	ENST00000326873	NM_000455.4	50	cTGATGGGGGACCTGCTg/cg	1/10	0.4896696440036	2	FACETS	0.872	0.831	0.913	0.872	0.831	0.913	CLONAL	2	TRUE	0	0.531342636736647	2		779	751	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244279	5244279	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064986-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	582	831	0	ENST00000357368.4:c.1203G>C	p.Trp401Cys	p.W401C	ENST00000357368	NM_002850.3	401	tgG/tgC	11/38	0.4896696440036	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.531342636736647	2		831	1064	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600324	10600324	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064986-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	324	779	0	ENST00000171111.5:c.1531G>T	p.Gly511Cys	p.G511C	ENST00000171111	NM_203500.1	511	Ggc/Tgc	4/6	0.4896696440036	2	FACETS	0.772	0.733	0.811	0.772	0.733	0.811	SUBCLONAL	2	TRUE	0	0.531342636736647	2		779	790	SUCCESS
REL	5966	MSKCC	GRCh37	2	61121608	61121608	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064986-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	98	521	2	ENST00000295025.8:c.230A>G	p.His77Arg	p.H77R	ENST00000295025	NM_002908.2	77	cAt/cGt	3/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.531342636736647	2		523	327	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21348304	21348304	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064986-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	270	979	0	ENST00000215739.8:c.1447del	p.Gln483ArgfsTer73	p.Q483Rfs*73	ENST00000215739	NM_006767.3	482	gCc/gc	13/21	0.531342636736647	1	FACETS	0.973	0.917	1	0.973	0.917	1	CLONAL	1	TRUE	0	0.531342636736647	1		979	767	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289019	33289019	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064986-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	121	795	0	ENST00000374542.5:c.533C>G	p.Ser178Cys	p.S178C	ENST00000374542	NM_001141970.1	178	tCt/tGt	3/8	1	2	FACETS	0.452	0.407	0.499	0.452	0.407	0.499	SUBCLONAL	1	TRUE	1	0.531342636736647	2		795	1008	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965410	68965410	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064986-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	104	540	1	ENST00000288368.4:c.1022G>T	p.Cys341Phe	p.C341F	ENST00000288368	NM_024870.2	341	tGt/tTt	9/40	1	2	FACETS	0.844	0.759	0.932	0.844	0.759	0.932	CLONAL	1	TRUE	1	0.531342636736647	2		541	464	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300061	137300061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754761323	NA	P-0064986-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	237	670	0	ENST00000481739.1:c.346G>A	p.Val116Ile	p.V116I	ENST00000481739	NM_002957.4	116	Gtc/Atc	3/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.531342636736647	2		670	834	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038828	47038828	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064986-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	187	357	0	ENST00000377604.3:c.835C>T	p.Gln279Ter	p.Q279*	ENST00000377604	NM_001204468.1	279	Cag/Tag	9/24	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.531342636736647	1		357	387	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0064987-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	268	511	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.978	0.921	1	0.978	0.921	1	CLONAL	1	TRUE	1	0.717593746764062	2		511	764	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381466	81381466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064987-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	326	466	0	ENST00000222390.5:c.595G>A	p.Glu199Lys	p.E199K	ENST00000222390	NM_000601.4	199	Gaa/Aaa	5/18	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.717593746764062	2		466	877	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519277	137519277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064987-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	331	627	0	ENST00000367739.4:c.1361C>T	p.Ser454Phe	p.S454F	ENST00000367739	NM_000416.2	454	tCc/tTc	7/7	1	2	FACETS	0.989	0.937	1	0.989	0.937	1	CLONAL	1	TRUE	1	0.717593746764062	2		627	933	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211883	36211883	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202218975	NA	P-0064987-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	391	791	1	ENST00000222270.7:c.1634G>A	p.Arg545Gln	p.R545Q	ENST00000222270	NM_014727.1	545	cGa/cAa	3/37	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.717593746764062	2		792	1081	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857845	9857845	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064987-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	54	750	1	ENST00000330684.3:c.3556C>T	p.Leu1186Phe	p.L1186F	ENST00000330684	NM_001134407.1	1186	Ctc/Ttc	13/13	0.444557998271041	1	FACETS	0.116	0.098	0.135	0.116	0.098	0.135	SUBCLONAL	1	TRUE	0	0.717593746764062	1		751	832	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817451	39817451	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064987-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	239	655	0	ENST00000288319.7:c.112T>C	p.Ser38Pro	p.S38P	ENST00000288319	NM_182918.3	38	Tcc/Ccc	2/10	0.323710024594401	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.717593746764062	0		655	653	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817456	39817456	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064987-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	235	652	0	ENST00000288319.7:c.107C>T	p.Ser36Phe	p.S36F	ENST00000288319	NM_182918.3	36	tCc/tTc	2/10	0.323710024594401	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.717593746764062	0		652	655	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193767	106193767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064987-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	304	543	0	ENST00000380013.4:c.4229C>T	p.Pro1410Leu	p.P1410L	ENST00000380013	NM_001127208.2	1410	cCt/cTt	10/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.717593746764062	2		543	796	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111012	193111012	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064988-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	77	526	0	ENST00000367435.3:c.545T>A	p.Ile182Asn	p.I182N	ENST00000367435	NM_024529.4	182	aTt/aAt	7/17	1	2	FACETS	0.484	0.428	0.544	0.484	0.428	0.544	SUBCLONAL	1	TRUE	1	0.943357470379826	2		526	337	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	103	342	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		342	305	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0064989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	146	770	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		770	802	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032128	10032128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747198986	NA	P-0064989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	108	601	0	ENST00000330684.3:c.695C>T	p.Ser232Phe	p.S232F	ENST00000330684	NM_001134407.1	232	tCc/tTc	3/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		601	672	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051653	30051653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749176138	NA	P-0064989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	105	401	0	ENST00000338641.4:c.587G>A	p.Arg196Gln	p.R196Q	ENST00000338641	NM_000268.3	196	cGa/cAa	6/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		401	630	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11194430	11194430	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	115	553	0	ENST00000361445.4:c.5224del	p.Glu1742AsnfsTer11	p.E1742Nfs*11	ENST00000361445	NM_004958.3	1742	Gaa/aa	37/58	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		553	775	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590757	95590757	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	39	494	0	ENST00000393063.1:c.1152A>C	p.Leu384Phe	p.L384F	ENST00000393063	NM_030621.3	384	ttA/ttC	9/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		494	434	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857875	9857875	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1555482388	NA	P-0064989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	114	666	0	ENST00000330684.3:c.3526G>T	p.Glu1176Ter	p.E1176*	ENST00000330684	NM_001134407.1	1176	Gag/Tag	13/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		666	783	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158147	47158147	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	29	386	0	ENST00000409792.3:c.4552del	p.Glu1518LysfsTer9	p.E1518Kfs*9	ENST00000409792	NM_014159.6	1518	Gaa/aa	4/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		386	293	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324093	31324093	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	65	240	0	ENST00000412585.2:c.470G>C	p.Trp157Ser	p.W157S	ENST00000412585	NM_005514.6	157	tGg/tCg	3/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		240	324	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729933	41729933	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	123	630	0	ENST00000242208.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000242208	NM_002192.2	199	gGg/gTg	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		630	827	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392129	81392129	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	22	376	0	ENST00000222390.5:c.148C>G	p.Leu50Val	p.L50V	ENST00000222390	NM_000601.4	50	Cta/Gta	2/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		376	142	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485889	8485889	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	207	600	0	ENST00000356435.5:c.2928C>A	p.Asp976Glu	p.D976E	ENST00000356435		976	gaC/gaA	17/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		600	832	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	32	690	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.553	0.453	0.665	0.553	0.453	0.665	SUBCLONAL	1	TRUE	1	0.59	2		691	196	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	98	784	0	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.874	0.786	0.966	0.874	0.786	0.966	CLONAL	1	TRUE	1	0.59	2		784	380	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	44	400	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.59	2		400	122	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	123	829	0	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.979	0.892	1	0.979	0.892	1	CLONAL	1	TRUE	1	0.59	2		829	426	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223614	36223614	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	181	1007	0	ENST00000222270.7:c.6169del	p.Arg2057AlafsTer34	p.R2057Afs*34	ENST00000222270	NM_014727.1	2055	gCc/gc	28/37	0.245875138460896	4	FACETS	0.82	0.76	0.881	0.82	0.76	0.881	INDETERMINATE	2	TRUE	2	0.59	4		1007	595	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748399150	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	145	690	5	ENST00000220592.5:c.1806del	p.Ala603ProfsTer92	p.A603Pfs*92	ENST00000220592	NM_012154.3	602	ccC/cc	14/19	1	2	FACETS	0.968	0.888	1	0.968	0.888	1	CLONAL	1	TRUE	1	0.59	2		695	508	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665752	29665755	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1555535032	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	42	282	0	ENST00000356175.3:c.6789_6792del	p.Tyr2264ThrfsTer5	p.Y2264Tfs*5	ENST00000356175	NM_000267.3	2263	ACTTac/ac	45/57	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.59	2		282	140	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945092	38945092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769767383	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	11	541	0	ENST00000357387.3:c.4712C>T	p.Ser1571Leu	p.S1571L	ENST00000357387	NM_152756.3	1571	tCg/tTg	35/38	1	2	FACETS	0.187	0.129	0.26	0.187	0.129	0.26	SUBCLONAL	1	TRUE	1	0.59	2		541	199	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492721	56492721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764759712	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	35	640	0	ENST00000407977.2:c.218C>T	p.Ala73Val	p.A73V	ENST00000407977		73	gCt/gTt	2/10	1	2	FACETS	0.751	0.624	0.889	0.751	0.624	0.889	SUBCLONAL	1	TRUE	1	0.59	2		640	158	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	12	638	0	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	1	2	FACETS	0.096	0.067	0.133	0.096	0.067	0.133	SUBCLONAL	1	TRUE	1	0.59	2		638	422	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220275	55220275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751295137	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	8	572	1	ENST00000275493.2:c.665G>A	p.Arg222His	p.R222H	ENST00000275493	NM_005228.3	222	cGc/cAc	6/28	1	2	FACETS	0.074	0.047	0.109	0.074	0.047	0.109	SUBCLONAL	1	TRUE	1	0.59	2		573	366	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654643	67654643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs968244943	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	56	574	0	ENST00000264010.4:c.1130G>A	p.Arg377His	p.R377H	ENST00000264010	NM_006565.3	377	cGt/cAt	6/12	1	2	FACETS	0.744	0.644	0.852	0.744	0.644	0.852	SUBCLONAL	1	TRUE	1	0.59	2		574	255	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952088	178952088	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553826184	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	30	594	0	ENST00000263967.3:c.3143A>G	p.His1048Arg	p.H1048R	ENST00000263967	NM_006218.2	1048	cAt/cGt	21/21	1	2	FACETS	0.711	0.581	0.854	0.711	0.581	0.854	SUBCLONAL	1	TRUE	1	0.59	2		594	143	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099948	27099948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369087151	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	10	953	0	ENST00000324856.7:c.3827G>A	p.Arg1276Gln	p.R1276Q	ENST00000324856	NM_006015.4	1276	cGa/cAa	15/20	1	2	FACETS	0.071	0.048	0.101	0.071	0.048	0.101	SUBCLONAL	1	TRUE	1	0.59	2		953	476	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216631	2216631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769937964	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	203	902	0	ENST00000398665.3:c.2275C>T	p.Arg759Cys	p.R759C	ENST00000398665	NM_032482.2	759	Cgc/Tgc	20/28	0.245875138460896	4	FACETS	0.755	0.702	0.809	0.755	0.702	0.809	INDETERMINATE	2	TRUE	2	0.59	4		902	725	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534755	18534755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776582655	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	67	533	0	ENST00000266497.5:c.1813G>A	p.Val605Ile	p.V605I	ENST00000266497		605	Gta/Ata	12/31	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.59	2		533	184	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299983	15299983	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1390414547	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	164	874	1	ENST00000263388.2:c.1195G>A	p.Ala399Thr	p.A399T	ENST00000263388	NM_000435.2	399	Gcc/Acc	8/33	0.245875138460896	4	FACETS	1	0.988	1	0.715	0.659	0.773	INDETERMINATE	1	TRUE	2	0.59	4		875	618	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752695	42752695	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1366176199	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	97	746	2	ENST00000222329.4:c.1569del	p.Leu525SerfsTer6	p.L525Sfs*6	ENST00000222329	NM_006494.2	523	ggG/gg	4/4	0.245875138460896	4	FACETS	1	0.976	1	0.658	0.591	0.729	INDETERMINATE	1	TRUE	2	0.59	4		748	397	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	81	882	7	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.825	0.733	0.921	0.825	0.733	0.921	CLONAL	1	TRUE	1	0.59	2		889	333	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220614	1220614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881982	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	152	835	0	ENST00000326873.7:c.632G>A	p.Arg211Gln	p.R211Q	ENST00000326873	NM_000455.4	211	cGg/cAg	5/10	0.245875138460896	4	FACETS	0.752	0.691	0.814	0.752	0.691	0.814	INDETERMINATE	2	TRUE	2	0.59	4		835	545	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273026	18273026	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	152	703	0	ENST00000222254.8:c.921del	p.Lys308ArgfsTer33	p.K308Rfs*33	ENST00000222254	NM_005027.3	306	Ccc/cc	8/16	0.245875138460896	4	FACETS	0.816	0.751	0.882	0.816	0.751	0.882	INDETERMINATE	2	TRUE	2	0.59	4		703	502	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376248	15376248	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	73	484	3	ENST00000263377.2:c.766del	p.Gln256SerfsTer27	p.Q256Sfs*27	ENST00000263377	NM_058243.2	256	Cag/ag	5/20	0.245875138460896	4	FACETS	1	0.972	1	0.681	0.601	0.764	INDETERMINATE	1	TRUE	2	0.59	4		487	289	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933445	39933445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1177018779	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	91	824	0	ENST00000378444.4:c.1154C>T	p.Ala385Val	p.A385V	ENST00000378444	NM_001123385.1	385	gCg/gTg	4/15	0.112768084833348	1	FACETS	0.643	0.577	0.713	0.643	0.577	0.713	INDETERMINATE	1	TRUE	0	0.59	1		824	338	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307173	65307173	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs181919006	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	80	755	1	ENST00000342505.4:c.2515C>T	p.Arg839Ter	p.R839*	ENST00000342505	NM_002227.2	839	Cga/Tga	18/25	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.59	2		756	252	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332178	70332178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773402594	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	12	636	0	ENST00000373644.4:c.83G>A	p.Arg28Gln	p.R28Q	ENST00000373644	NM_030625.2	28	cGa/cAa	2/12	1	2	FACETS	0.192	0.134	0.262	0.192	0.134	0.262	SUBCLONAL	1	TRUE	1	0.59	2		636	212	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214094	36214094	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253599925	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	152	812	0	ENST00000222270.7:c.2920C>T	p.Arg974Cys	p.R974C	ENST00000222270	NM_014727.1	974	Cgt/Tgt	6/37	0.245875138460896	4	FACETS	0.802	0.738	0.867	0.802	0.738	0.867	INDETERMINATE	2	TRUE	2	0.59	4		812	511	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214714	36214714	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	94	706	1	ENST00000222270.7:c.3145del	p.Ala1049ArgfsTer133	p.A1049Rfs*133	ENST00000222270	NM_014727.1	1047	cGg/cg	8/37	0.245875138460896	4	FACETS	1	0.976	1	0.66	0.591	0.731	INDETERMINATE	1	TRUE	2	0.59	4		707	384	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096314	2096314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767591879	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	61	685	3	ENST00000219066.1:c.193C>T	p.Arg65Cys	p.R65C	ENST00000219066	NM_002528.5	65	Cgt/Tgt	2/6	1	2	FACETS	0.331	0.285	0.381	0.331	0.285	0.381	SUBCLONAL	1	TRUE	1	0.59	2		688	624	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001523	150001523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264217871	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	39	429	0	ENST00000253339.5:c.2081G>A	p.Arg694His	p.R694H	ENST00000253339		694	cGt/cAt	4/7	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.59	2		429	120	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284978	15284978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	172	783	2	ENST00000263388.2:c.4637G>A	p.Arg1546His	p.R1546H	ENST00000263388	NM_000435.2	1546	cGc/cAc	25/33	0.245875138460896	4	FACETS	0.922	0.855	0.99	0.922	0.855	0.99	INDETERMINATE	2	TRUE	2	0.59	4		785	503	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542848	187542848	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751475602	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	45	511	0	ENST00000441802.2:c.4892C>T	p.Ala1631Val	p.A1631V	ENST00000441802	NM_005245.3	1631	gCg/gTg	10/27	1	2	FACETS	0.838	0.715	0.97	0.838	0.715	0.97	CLONAL	1	TRUE	1	0.59	2		511	182	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223761	36223761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747697534	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	141	939	0	ENST00000222270.7:c.6311G>A	p.Arg2104Gln	p.R2104Q	ENST00000222270	NM_014727.1	2104	cGg/cAg	28/37	0.245875138460896	4	FACETS	0.826	0.758	0.896	0.826	0.758	0.896	INDETERMINATE	2	TRUE	2	0.59	4		939	460	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606379	93606379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757250931	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	109	856	0	ENST00000375746.1:c.199G>A	p.Glu67Lys	p.E67K	ENST00000375746	NM_001174167.1	67	Gag/Aag	2/14	0.112768084833348	1	FACETS	0.724	0.656	0.793	0.724	0.656	0.793	INDETERMINATE	1	TRUE	0	0.59	1		856	360	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93636954	93636955	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	84	673	0	ENST00000375746.1:c.1009dup	p.Gln337ProfsTer45	p.Q337Pfs*45	ENST00000375746	NM_001174167.1	335	ggc/ggCc	9/14	0.112768084833348	1	FACETS	0.601	0.535	0.67	0.601	0.535	0.67	INDETERMINATE	1	TRUE	0	0.59	1		673	334	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426732	47426732	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1313544010	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	124	835	0	ENST00000377045.4:c.977G>A	p.Arg326Gln	p.R326Q	ENST00000377045	NM_001654.4	326	cGa/cAa	10/16	0.112768084833348	1	FACETS	0.555	0.504	0.608	0.555	0.504	0.608	INDETERMINATE	1	TRUE	0	0.59	1		835	534	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259785	142259785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	62	567	1	ENST00000350721.4:c.3542G>A	p.Gly1181Asp	p.G1181D	ENST00000350721	NM_001184.3	1181	gGc/gAc	18/47	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.59	2		568	204	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068316	30068316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757547062	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	33	374	1	ENST00000331968.5:c.2083C>T	p.Arg695Trp	p.R695W	ENST00000331968	NM_002742.2	695	Cgg/Tgg	15/18	1	2	FACETS	0.973	0.81	1	0.973	0.81	1	CLONAL	1	TRUE	1	0.59	2		375	115	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2181665	2181665	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	14	308	1	ENST00000349721.2:c.4354del	p.Ile1452Ter	p.I1452*	ENST00000349721	NM_003070.3	1450	Aaa/aa	30/34	0.112768084833348	1	FACETS	0.558	0.414	0.721	0.558	0.414	0.721	INDETERMINATE	1	TRUE	0	0.59	1		309	60	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276462	115276462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	46	589	0	ENST00000438362.2:c.866C>T	p.Thr289Ile	p.T289I	ENST00000438362	NM_001242891.1	289	aCa/aTa	9/20	1	2	FACETS	0.939	0.805	1	0.939	0.805	1	CLONAL	1	TRUE	1	0.59	2		589	166	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648337	206648337	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	105	718	0	ENST00000367120.3:c.358G>A	p.Val120Met	p.V120M	ENST00000367120	NM_014002.3	120	Gtg/Atg	5/22	1	2	FACETS	0.784	0.706	0.865	0.784	0.706	0.865	SUBCLONAL	1	TRUE	1	0.59	2		718	454	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10785024	10785024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	50	508	0	ENST00000361367.2:c.896C>T	p.Thr299Ile	p.T299I	ENST00000361367	NM_014633.3	299	aCa/aTa	8/25	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.59	2		508	169	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102098232	102098232	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	19	498	0	ENST00000282441.5:c.1196A>G	p.Asp399Gly	p.D399G	ENST00000282441	NM_001130145.2	399	gAc/gGc	8/9	1	2	FACETS	0.297	0.226	0.38	0.297	0.226	0.38	SUBCLONAL	1	TRUE	1	0.59	2		498	217	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432367	432367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1237979376	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	41	200	0	ENST00000399788.2:c.2156G>A	p.Arg719His	p.R719H	ENST00000399788	NM_001042603.1	719	cGc/cAc	16/28	1	2	FACETS	0.933	0.791	1	0.933	0.791	1	CLONAL	1	TRUE	1	0.59	2		200	149	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437173	110437173	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	60	390	0	ENST00000375856.3:c.1228G>T	p.Gly410Cys	p.G410C	ENST00000375856	NM_003749.2	410	Ggc/Tgc	1/2	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.59	2		390	196	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220694	2220694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762612747	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	145	740	0	ENST00000326181.6:c.311G>A	p.Arg104His	p.R104H	ENST00000326181	NM_032271.2	104	cGc/cAc	5/21	1	2	FACETS	0.902	0.827	0.979	0.902	0.827	0.979	CLONAL	1	TRUE	1	0.59	2		740	545	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639230	3639230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs72778139	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	143	691	0	ENST00000294008.3:c.4409C>T	p.Pro1470Leu	p.P1470L	ENST00000294008	NM_032444.2	1470	cCg/cTg	12/15	1	2	FACETS	0.939	0.862	1	0.939	0.862	1	CLONAL	1	TRUE	1	0.59	2		691	516	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665110	29665110	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658541	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	50	481	0	ENST00000356175.3:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000356175	NM_000267.3	2237	Cga/Tga	44/57	1	2	FACETS	0.902	0.777	1	0.902	0.777	1	CLONAL	1	TRUE	1	0.59	2		481	188	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39620644	39620644	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	46	464	0	ENST00000262039.4:c.2042T>C	p.Phe681Ser	p.F681S	ENST00000262039	NM_002647.2	681	tTc/tCc	19/25	0.137467905924895	0	FACETS	0.447	0.384	0.513			1	INDETERMINATE	1	TRUE	0	0.59	0		464	143	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096044	11096044	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	184	809	0	ENST00000358026.2:c.321del	p.Pro109ArgfsTer194	p.P109Rfs*194	ENST00000358026	NM_001128849.1	106	atG/at	3/36	0.245875138460896	4	FACETS	0.932	0.867	0.999	0.932	0.867	0.999	INDETERMINATE	2	TRUE	2	0.59	4		809	532	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098443	11098443	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1344296942	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	111	627	0	ENST00000358026.2:c.961G>A	p.Ala321Thr	p.A321T	ENST00000358026	NM_001128849.1	321	Gcc/Acc	6/36	0.245875138460896	4	FACETS	0.763	0.692	0.837	0.763	0.692	0.837	INDETERMINATE	2	TRUE	2	0.59	4		627	392	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141427	11141427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	158	723	0	ENST00000358026.2:c.3404G>A	p.Arg1135Gln	p.R1135Q	ENST00000358026	NM_001128849.1	1135	cGg/cAg	25/36	0.245875138460896	4	FACETS	1	0.988	1	0.73	0.672	0.79	INDETERMINATE	1	TRUE	2	0.59	4		723	583	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753729	42753729	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372369574	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	147	968	0	ENST00000222329.4:c.535C>T	p.Arg179Cys	p.R179C	ENST00000222329	NM_006494.2	179	Cgc/Tgc	4/4	0.245875138460896	4	FACETS	1	0.985	1	0.666	0.61	0.723	INDETERMINATE	1	TRUE	2	0.59	4		968	595	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657041	47657041	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	17	428	0	ENST00000233146.2:c.1237del	p.Gln413AsnfsTer25	p.Q413Nfs*25	ENST00000233146	NM_000251.2	413	Caa/aa	7/16	1	2	FACETS	0.613	0.465	0.782	0.613	0.465	0.782	SUBCLONAL	1	TRUE	1	0.59	2		428	94	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660166	227660166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775121566	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	114	861	0	ENST00000305123.5:c.3289C>T	p.Arg1097Trp	p.R1097W	ENST00000305123	NM_005544.2	1097	Cgg/Tgg	1/2	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.59	2		861	366	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45648922	45648922	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780312517	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	121	600	0	ENST00000407780.3:c.904G>A	p.Val302Ile	p.V302I	ENST00000407780	NM_001283052.1	302	Gtt/Att	7/7	1	2	FACETS	0.961	0.875	1	0.961	0.875	1	CLONAL	1	TRUE	1	0.59	2		600	427	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29445349	29445349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765519314	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	136	847	0	ENST00000544604.2:c.1180G>A	p.Val394Ile	p.V394I	ENST00000544604	NM_001206998.1	394	Gtc/Atc	8/9	1	2	FACETS	0.929	0.85	1	0.929	0.85	1	CLONAL	1	TRUE	1	0.59	2		847	496	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595887	52595887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	112	697	0	ENST00000394830.3:c.4028C>T	p.Ala1343Val	p.A1343V	ENST00000394830	NM_018313.4	1343	gCt/gTt	26/30	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.59	2		697	373	SUCCESS
REST	5978	MSKCC	GRCh37	4	57797177	57797177	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	91	1105	0	ENST00000309042.7:c.2153C>A	p.Ser718Tyr	p.S718Y	ENST00000309042	NM_005612.4	718	tCt/tAt	4/4	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.59	2		1105	304	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521255	187521255	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	78	755	0	ENST00000441802.2:c.11900C>A	p.Pro3967His	p.P3967H	ENST00000441802	NM_005245.3	3967	cCt/cAt	22/27	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.59	2		755	219	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525678	187525678	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	55	623	0	ENST00000441802.2:c.10401G>T	p.Glu3467Asp	p.E3467D	ENST00000441802	NM_005245.3	3467	gaG/gaT	18/27	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.59	2		623	177	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111737	56111737	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	76	587	0	ENST00000399503.3:c.337C>A	p.Pro113Thr	p.P113T	ENST00000399503	NM_005921.1	113	Ccc/Acc	1/20	1	2	FACETS	0.965	0.857	1	0.965	0.857	1	CLONAL	1	TRUE	1	0.59	2		587	267	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564648	86564649	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	93	896	0	ENST00000274376.6:c.383_384del	p.Leu128ArgfsTer29	p.L128Rfs*29	ENST00000274376	NM_002890.2	127	aCT/a	1/25	1	2	FACETS	0.85	0.762	0.942	0.85	0.762	0.942	CLONAL	1	TRUE	1	0.59	2		896	371	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674310	86674313	+	frameshift_variant	Frame_Shift_Del	DEL	GAAA	GAAA	-	novel	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	29	431	0	ENST00000274376.6:c.2444_2447del	p.Lys815ThrfsTer4	p.K815Tfs*4	ENST00000274376	NM_002890.2	814	ttGAAA/tt	18/25	1	2	FACETS	0.902	0.74	1	0.902	0.74	1	CLONAL	1	TRUE	1	0.59	2		431	109	SUCCESS
APC	324	MSKCC	GRCh37	5	112176891	112176892	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGA	rs779014936	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	25	588	0	ENST00000257430.4:c.5612_5614dup	p.Asp1871dup	p.D1871dup	ENST00000257430	NM_000038.5	1871	ttt/ttTGAt	16/16	1	2	FACETS	0.678	0.542	0.828	0.678	0.542	0.828	SUBCLONAL	1	TRUE	1	0.59	2		588	125	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718177	117718177	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1459152647	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	39	513	0	ENST00000368508.3:c.680G>A	p.Gly227Asp	p.G227D	ENST00000368508	NM_002944.2	227	gGt/gAt	7/43	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.59	2		513	96	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969983	161969983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	108	556	0	ENST00000366898.1:c.986del	p.Gly329AlafsTer106	p.G329Afs*106	ENST00000366898	NM_004562.2	329	gGc/gc	9/12	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.59	2		556	344	SUCCESS
AR	367	MSKCC	GRCh37	X	66765908	66765908	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	59	875	0	ENST00000374690.3:c.920C>T	p.Ala307Val	p.A307V	ENST00000374690	NM_000044.3	307	gCt/gTt	1/8	0.112768084833348	1	FACETS	0.61	0.532	0.694	0.61	0.532	0.694	INDETERMINATE	1	TRUE	0	0.59	1		875	231	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340223	116340223	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs77523018	NA	P-0064991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	76	518	0	ENST00000397752.3:c.1085T>C	p.Met362Thr	p.M362T	ENST00000397752	NM_000245.2	362	aTg/aCg	2/21	0.326893572685876	3	FACETS	1	0.894	1	0.509	0.447	0.576	CLONAL	1	TRUE	1	0.326893572685876	3		518	531	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420032	41420032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	160	561	0	ENST00000373198.4:c.289G>A	p.Glu97Lys	p.E97K	ENST00000373198	NM_133170.3	97	Gag/Aag	3/32	0.326893572685876	1	FACETS	0.778	0.718	0.84	1	0.99	1	SUBCLONAL	2	TRUE	0	0.326893572685876	1		561	526	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539660	187539660	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	76	558	0	ENST00000441802.2:c.8080C>T	p.Leu2694Phe	p.L2694F	ENST00000441802	NM_005245.3	2694	Ctt/Ttt	10/27	1	2	FACETS	0.899	0.791	1	0.899	0.791	1	CLONAL	1	TRUE	1	0.326893572685876	2		558	517	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0064991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	93	641	0	ENST00000304494.5:c.151-1G>A		p.X51_splice	ENST00000304494	NM_000077.4	51			0.326893572685876	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.326893572685876	1		641	458	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0064991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	118	760	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	1	2	FACETS	0.977	0.882	1	0.977	0.882	1	CLONAL	1	TRUE	1	0.326893572685876	2		760	739	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561085	9561085	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	115	523	0	ENST00000353224.5:c.697C>T	p.Gln233Ter	p.Q233*	ENST00000353224	NM_177990.2	233	Caa/Taa	4/10	0.180279332096515	3	FACETS	0.803	0.726	0.882	0.803	0.726	0.882	INDETERMINATE	2	TRUE	1	0.326893572685876	3		523	510	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164865	36164865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	152	662	1	ENST00000300305.3:c.1010C>T	p.Pro337Leu	p.P337L	ENST00000300305		337	cCc/cTc	8/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.326893572685876	2		663	637	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279666	18279666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	43	610	0	ENST00000222254.8:c.1939C>T	p.Arg647Cys	p.R647C	ENST00000222254	NM_005027.3	647	Cgc/Tgc	15/16	1	2	FACETS	0.501	0.419	0.592	0.501	0.419	0.592	SUBCLONAL	1	TRUE	1	0.326893572685876	2		610	525	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945102	151945102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	18	234	0	ENST00000262189.6:c.2417C>T	p.Ser806Phe	p.S806F	ENST00000262189	NM_170606.2	806	tCc/tTc	14/59	0.326893572685876	3	FACETS	0.674	0.51	0.867	0.337	0.255	0.434	SUBCLONAL	1	TRUE	1	0.326893572685876	3		234	190	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453135	140453136	+	missense_variant	Missense_Mutation	DNP	CA	CA	AT	rs121913377	NA	P-0064991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	120	399	0	ENST00000288602.6:c.1799_1800delinsAT	p.Val600Asp	p.V600D	ENST00000288602	NM_004333.4	600	gTG/gAT	15/18	0.326893572685876	3	FACETS	0.924	0.84	1	0.924	0.84	1	CLONAL	2	TRUE	1	0.326893572685876	3		399	462	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674236	117674236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	79	507	0	ENST00000368508.3:c.4238G>A	p.Gly1413Glu	p.G1413E	ENST00000368508	NM_002944.2	1413	gGa/gAa	26/43	1	2	FACETS	0.869	0.766	0.98	0.869	0.766	0.98	CLONAL	1	TRUE	1	0.326893572685876	2		507	556	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728857	190728857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	66	394	0	ENST00000441310.2:c.2245C>T	p.Pro749Ser	p.P749S	ENST00000441310	NM_000534.4	749	Cca/Tca	10/13	0.326893572685876	1	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	0	0.326893572685876	1		394	325	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003523	57003523	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	110	740	0	ENST00000257254.3:c.956C>T	p.Ala319Val	p.A319V	ENST00000257254		319	gCc/gTc	1/2	0.326893572685876	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.326893572685876	1		740	542	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433234	49433234	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1231575034	NA	P-0064991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	103	689	0	ENST00000301067.7:c.8213C>T	p.Pro2738Leu	p.P2738L	ENST00000301067	NM_003482.3	2738	cCc/cTc	32/54	1	2	FACETS	0.974	0.873	1	0.974	0.873	1	CLONAL	1	TRUE	1	0.326893572685876	2		689	647	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608466	28608466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1051730013	NA	P-0064991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	82	451	0	ENST00000241453.7:c.1676C>T	p.Thr559Ile	p.T559I	ENST00000241453	NM_004119.2	559	aCc/aTc	13/24	0.180279332096515	3	FACETS	1	0.939	1	0.549	0.485	0.617	INDETERMINATE	1	TRUE	1	0.326893572685876	3		451	532	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835581	68835581	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501234	NA	P-0064991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	94	511	0	ENST00000261769.5:c.172G>A	p.Glu58Lys	p.E58K	ENST00000261769	NM_004360.3	58	Gaa/Aaa	3/16	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.326893572685876	2		511	572	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3113438	3113438	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	86	595	0	ENST00000078429.4:c.432C>A	p.Cys144Ter	p.C144*	ENST00000078429	NM_002067.2	144	tgC/tgA	3/7	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.326893572685876	2		595	503	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131300	202131300	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1559350009	NA	P-0064991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	106	512	0	ENST00000358485.4:c.268C>T	p.Pro90Ser	p.P90S	ENST00000358485	NM_001080125.1	90	Ccg/Tcg	2/9	0.326893572685876	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.326893572685876	1		512	522	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523325	9523325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	79	506	0	ENST00000353224.5:c.1912G>A	p.Asp638Asn	p.D638N	ENST00000353224	NM_177990.2	638	Gat/Aat	9/10	0.180279332096515	3	FACETS	0.987	0.869	1	0.493	0.434	0.556	INDETERMINATE	1	TRUE	1	0.326893572685876	3		506	570	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747057	40747057	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1485129344	NA	P-0064991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	137	495	0	ENST00000373198.4:c.3025G>A	p.Val1009Met	p.V1009M	ENST00000373198	NM_133170.3	1009	Gtg/Atg	22/32	0.326893572685876	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.326893572685876	1		495	475	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526591	31526591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	57	413	0	ENST00000344624.3:c.449C>T	p.Ser150Phe	p.S150F	ENST00000344624		150	tCc/tTc	2/33	0.326893572685876	1	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	0	0.326893572685876	1		413	285	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178631	56178631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	83	563	0	ENST00000399503.3:c.3604C>T	p.Leu1202Phe	p.L1202F	ENST00000399503	NM_005921.1	1202	Ctc/Ttc	14/20	0.326893572685876	1	FACETS	0.972	0.862	1	0.972	0.862	1	CLONAL	1	TRUE	0	0.326893572685876	1		563	437	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117645513	117645513	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	57	365	0	ENST00000368508.3:c.5623A>G	p.Thr1875Ala	p.T1875A	ENST00000368508	NM_002944.2	1875	Aca/Gca	34/43	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.326893572685876	2		365	304	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0064992-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	191	271	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.56	2		271	677	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0064992-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	13	556	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.072	0.051	0.099	0.072	0.051	0.099	SUBCLONAL	1	TRUE	1	0.56	2		556	642	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913476	NA	P-0064992-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	109	422	0	ENST00000358487.5:c.1647T>G	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaG	12/18	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.56	2		422	350	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220895	36220895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064992-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	183	688	0	ENST00000222270.7:c.4945G>A	p.Ala1649Thr	p.A1649T	ENST00000222270	NM_014727.1	1649	Gcc/Acc	23/37	1	2	FACETS	0.931	0.862	1	0.931	0.862	1	CLONAL	1	TRUE	1	0.56	2		688	702	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692920	89692920	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs370795352	NA	P-0064992-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	49	433	0	ENST00000371953.3:c.404T>A	p.Ile135Lys	p.I135K	ENST00000371953	NM_000314.4	135	aTa/aAa	5/9	1	2	FACETS	0.951	0.818	1	0.951	0.818	1	CLONAL	1	TRUE	1	0.56	2		433	184	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193458	99193458	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777173666	NA	P-0064992-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	156	697	0	ENST00000074304.5:c.2653C>T	p.Arg885Cys	p.R885C	ENST00000074304	NM_001134224.1	885	Cgc/Tgc	25/26	1	2	FACETS	0.86	0.79	0.932	0.86	0.79	0.932	CLONAL	1	TRUE	1	0.56	2		697	648	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106825	27106825	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0064992-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	225	848	0	ENST00000324856.7:c.6436A>T	p.Lys2146Ter	p.K2146*	ENST00000324856	NM_006015.4	2146	Aag/Tag	20/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.56	2		848	788	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966038	18966038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755352967	NA	P-0064992-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	43	646	0	ENST00000262803.5:c.1531C>T	p.Arg511Trp	p.R511W	ENST00000262803	NM_002911.3	511	Cgg/Tgg	11/24	1	2	FACETS	0.232	0.193	0.275	0.232	0.193	0.275	SUBCLONAL	1	TRUE	1	0.56	2		646	663	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589538	67589558	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	ATCAAGTTGTCAAAGAAGATA	ATCAAGTTGTCAAAGAAGATA	-	novel	NA	P-0064992-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	26	139	0	ENST00000274335.5:c.1303_1323del	p.Gln435_Asn441del	p.Q435_N441del	ENST00000274335		434	gATCAAGTTGTCAAAGAAGATAat/gat	10/15	1	2	FACETS	0.829	0.669	1	0.829	0.669	1	CLONAL	1	TRUE	1	0.56	2		139	112	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371714	55371715	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0064992-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	56	862	0	ENST00000297316.4:c.405dup	p.Lys136GlnfsTer26	p.K136Qfs*26	ENST00000297316	NM_022454.3	135	tac/taCc	2/2	1	2	FACETS	0.268	0.229	0.311	0.268	0.229	0.311	SUBCLONAL	1	TRUE	1	0.56	2		862	745	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577586	7577586	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587781589	NA	P-0064993-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	228	862	0	ENST00000269305.4:c.695T>G	p.Ile232Ser	p.I232S	ENST00000269305	NM_001126112.2	232	aTc/aGc	7/11	0.443590781200254	2	FACETS	0.882	0.829	0.935	0.882	0.829	0.935	CLONAL	2	TRUE	0	0.465067980347811	2		862	556	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601237	28601237	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064993-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	92	648	0	ENST00000241453.7:c.2195A>C	p.His732Pro	p.H732P	ENST00000241453	NM_004119.2	732	cAt/cCt	17/24	0.440381794077233	3	FACETS	0.949	0.846	1	0.316	0.282	0.353	CLONAL	1	TRUE	0	0.465067980347811	3		648	514	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48922000	48922000	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0064993-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	19	395	0	ENST00000267163.4:c.539+1G>C		p.X180_splice	ENST00000267163	NM_000321.2	180			0.440381794077233	3	FACETS	0.637	0.487	0.811	0.212	0.162	0.271	SUBCLONAL	1	TRUE	0	0.465067980347811	3		395	158	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197451	26197451	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0064993-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	138	1108	0	ENST00000356476.2:c.28A>T	p.Lys10Ter	p.K10*	ENST00000356476		10	Aag/Tag	1/1	0.348637956414877	4	FACETS	0.915	0.832	1	0.458	0.416	0.502	CLONAL	1	TRUE	2	0.465067980347811	4		1108	950	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	206	789	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.861782336242669	2		789	466	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	245	342	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.861782336242669	2		342	533	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692922	89692922	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201044	NA	P-0064994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	228	473	0	ENST00000371953.3:c.406T>C	p.Cys136Arg	p.C136R	ENST00000371953	NM_000314.4	136	Tgt/Cgt	5/9	1	2	FACETS	0.876	0.822	0.931	0.876	0.822	0.931	CLONAL	1	TRUE	1	0.861782336242669	2		473	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0064994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	341	476	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.861782336242669	2		476	706	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0064994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	20	536	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	0.06	0.045	0.077	0.06	0.045	0.077	SUBCLONAL	1	TRUE	1	0.861782336242669	2		536	775	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475550	12475550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479145908	NA	P-0064994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	348	642	0	ENST00000287820.6:c.1424C>T	p.Thr475Met	p.T475M	ENST00000287820	NM_015869.4	475	aCg/aTg	7/7	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.861782336242669	2		642	788	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117524	4117524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371852537	NA	P-0064994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	99	210	0	ENST00000262948.5:c.196G>A	p.Glu66Lys	p.E66K	ENST00000262948	NM_030662.3	66	Gaa/Aaa	2/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.861782336242669	2		210	220	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71161782	71161782	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	248	466	0	ENST00000318789.4:c.187C>T	p.Gln63Ter	p.Q63*	ENST00000318789	NM_032682.5	63	Cag/Tag	7/21	1	2	FACETS	0.976	0.92	1	0.976	0.92	1	CLONAL	1	TRUE	1	0.861782336242669	2		466	590	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27172734	27172734	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774928388	NA	P-0064994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	544	515	0	ENST00000380036.4:c.749C>T	p.Thr250Met	p.T250M	ENST00000380036	NM_000459.3	250	aCg/aTg	5/23	0.861782336242669	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.861782336242669	2		515	589	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711983	89711983	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554900638	NA	P-0064994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	252	301	0	ENST00000371953.3:c.601G>T	p.Glu201Ter	p.E201*	ENST00000371953	NM_000314.4	201	Gaa/Taa	6/9	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.861782336242669	2		301	498	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259947	16259947	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	399	843	0	ENST00000375759.3:c.7212G>C	p.Lys2404Asn	p.K2404N	ENST00000375759	NM_015001.2	2404	aaG/aaC	11/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.861782336242669	2		843	885	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494956	56494956	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	361	688	0	ENST00000267101.3:c.3313G>A	p.Glu1105Lys	p.E1105K	ENST00000267101	NM_001982.3	1105	Gag/Aag	27/28	1	2	FACETS	0.993	0.946	1	0.993	0.946	1	CLONAL	1	TRUE	1	0.861782336242669	2		688	844	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244262	5244262	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	329	790	0	ENST00000357368.4:c.1220C>G	p.Ser407Cys	p.S407C	ENST00000357368	NM_002850.3	407	tCc/tGc	11/38	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.861782336242669	2		790	754	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123693	11123693	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	326	593	0	ENST00000358026.2:c.2343G>T	p.Met781Ile	p.M781I	ENST00000358026	NM_001128849.1	781	atG/atT	16/36	1	2	FACETS	0.988	0.939	1	0.988	0.939	1	CLONAL	1	TRUE	1	0.861782336242669	2		593	766	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211342	36211342	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	394	785	0	ENST00000222270.7:c.1093G>T	p.Glu365Ter	p.E365*	ENST00000222270	NM_014727.1	365	Gaa/Taa	3/37	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.861782336242669	2		785	903	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159055	24159055	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	343	666	0	ENST00000263121.7:c.727C>G	p.Gln243Glu	p.Q243E	ENST00000263121	NM_003073.3	243	Cag/Gag	6/9	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.861782336242669	2		666	790	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629902	187629902	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	445	721	0	ENST00000441802.2:c.1080C>A	p.Phe360Leu	p.F360L	ENST00000441802	NM_005245.3	360	ttC/ttA	2/27	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.861782336242669	2		721	920	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938390	44938390	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0064994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	191	129	0	ENST00000377967.4:c.2939-1G>T		p.X980_splice	ENST00000377967	NM_021140.2	980			1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.861782336242669	1		129	202	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184063	123184067	+	frameshift_variant	Frame_Shift_Del	DEL	TTGCA	TTGCA	-	novel	NA	P-0064994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	284	245	0	ENST00000218089.9:c.924_928del	p.Cys308Ter	p.C308*	ENST00000218089	NM_001042749.1	307	atTTGCAtt/attt	11/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.861782336242669	1		245	332	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11177096	11177096	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878855328	NA	P-0064995-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	85	494	0	ENST00000361445.4:c.6981G>A	p.Met2327Ile	p.M2327I	ENST00000361445	NM_004958.3	2327	atG/atA	50/58	1	2	FACETS	0.301	0.266	0.338	0.301	0.266	0.338	SUBCLONAL	1	TRUE	1	0.832563372242246	2		494	679	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346894	73346894	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	213	505	0	ENST00000377767.4:c.1323T>G	p.His441Gln	p.H441Q	ENST00000377767	NM_014953.3	441	caT/caG	9/21	0.635588488016889	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.660175405294948	3		505	412	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983308	15983308	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	239	545	0	ENST00000268712.3:c.3471del	p.Ser1157ArgfsTer27	p.S1157Rfs*27	ENST00000268712	NM_006311.3	1157	agC/ag	26/46	0.50326966238627	4	FACETS	0.93	0.874	0.988	0.93	0.874	0.988	CLONAL	2	TRUE	2	0.660175405294948	4		545	646	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267373	198267373	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	61	562	0	ENST00000335508.6:c.1984C>G	p.His662Asp	p.H662D	ENST00000335508	NM_012433.2	662	Cac/Gac	14/25	1	2	FACETS	0.899	0.776	1	0.899	0.776	1	CLONAL	1	TRUE	1	0.252739147614808	2		562	537	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748083	41748083	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	34	432	0	ENST00000226382.2:c.686C>A	p.Pro229His	p.P229H	ENST00000226382	NM_003924.3	229	cCc/cAc	3/3	0.206141606515759	1	FACETS	0.825	0.677	0.99	0.825	0.677	0.99	CLONAL	1	TRUE	0	0.252739147614808	1		432	285	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266748	18266748	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	58	774	0	ENST00000222254.8:c.59C>G	p.Pro20Arg	p.P20R	ENST00000222254	NM_005027.3	20	cCg/cGg	2/16	1	2	FACETS	0.691	0.593	0.798	0.691	0.593	0.798	SUBCLONAL	1	TRUE	1	0.252739147614808	2		774	664	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045711	26045711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1217247868	NA	P-0064997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	89	806	0	ENST00000540144.1:c.73G>A	p.Ala25Thr	p.A25T	ENST00000540144	NM_003531.2	25	Gca/Aca	1/1	0.187011814947336	4	FACETS	1	0.94	1	0.547	0.485	0.614	CLONAL	1	TRUE	2	0.252739147614808	4		806	806	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900288	101900288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111854391	NA	P-0064998-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	15	188	0	ENST00000374994.4:c.722C>T	p.Ser241Leu	p.S241L	ENST00000374994	NM_004612.2	241	tCg/tTg	4/9	0.222936845813269	5	FACETS	0.605	0.442	0.801	0.202	0.147	0.267	SUBCLONAL	1	FALSE	2	0.222936845813269	5		188	297	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186756	108186756	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs774993357	NA	P-0064998-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	18	203	0	ENST00000278616.4:c.6114C>A	p.His2038Gln	p.H2038Q	ENST00000278616	NM_000051.3	2038	caC/caA	42/63	0.177312725656731	4	FACETS	0.796	0.6	1	0.398	0.3	0.514	CLONAL	1	FALSE	2	0.222936845813269	4		203	248	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061185	38061205	+	inframe_deletion	In_Frame_Del	DEL	GCACTTGAAGCGCTTCTGGCG	GCACTTGAAGCGCTTCTGGCG	-	novel	NA	P-0064998-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	81	726	0	ENST00000250448.2:c.784_804del	p.Arg262_Cys268del	p.R262_C268del	ENST00000250448	NM_004496.3	262	CGCCAGAAGCGCTTCAAGTGC/-	2/2	0.222936845813269	4	FACETS	0.753	0.664	0.848	0.753	0.664	0.848	SUBCLONAL	2	FALSE	2	0.222936845813269	4		726	590	SUCCESS
APC	324	MSKCC	GRCh37	5	112178803	112178803	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554088413	NA	P-0064998-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	25	275	0	ENST00000257430.4:c.7512G>A	p.Trp2504Ter	p.W2504*	ENST00000257430	NM_000038.5	2504	tgG/tgA	16/16	1	2	FACETS	1	0.823	1	1	0.823	1	CLONAL	1	FALSE	1	0.222936845813269	2		275	215	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685315	89685315	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1554897280	NA	P-0065000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	60	238	0	ENST00000371953.3:c.209+1G>T		p.X70_splice	ENST00000371953	NM_000314.4	70			0.593575327057331	2	FACETS	0.919	0.824	1	0.919	0.824	1	CLONAL	2	TRUE	0	0.593575327057331	2		238	110	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0065000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	293	824	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.593575327057331	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.593575327057331	2		824	433	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219336	1219336	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	170	748	0	ENST00000326873.7:c.388G>T	p.Glu130Ter	p.E130*	ENST00000326873	NM_000455.4	130	Gag/Tag	3/10	0.447300738486296	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.593575327057331	1		748	324	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033825	49033826	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	148	509	0	ENST00000267163.4:c.1963dup	p.Tyr655LeufsTer13	p.Y655Lfs*13	ENST00000267163	NM_000321.2	654	-/T	20/27	0.593575327057331	2	FACETS	0.948	0.887	1	0.948	0.887	1	CLONAL	2	TRUE	0	0.593575327057331	2		509	263	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647636	3647636	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	20	721	0	ENST00000294008.3:c.1427C>G	p.Ser476Cys	p.S476C	ENST00000294008	NM_032444.2	476	tCt/tGt	7/15	1	2	FACETS	0.187	0.143	0.239	0.187	0.143	0.239	SUBCLONAL	1	TRUE	1	0.593575327057331	2		721	360	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602913	10602913	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	236	665	0	ENST00000171111.5:c.665A>T	p.Asn222Ile	p.N222I	ENST00000171111	NM_203500.1	222	aAc/aTc	3/6	0.593575327057331	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.593575327057331	2		665	382	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040958	42040959	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0065000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	146	732	0	ENST00000219905.7:c.5341_5342del	p.Gln1781ThrfsTer12	p.Q1781Tfs*12	ENST00000219905	NM_001164273.1	1779	aAC/a	16/24	0.593575327057331	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.593575327057331	1		732	337	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602859	10602859	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	269	816	0	ENST00000171111.5:c.719G>C	p.Arg240Pro	p.R240P	ENST00000171111	NM_203500.1	240	cGc/cCc	3/6	0.593575327057331	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.593575327057331	2		816	446	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432453	49432453	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	112	803	0	ENST00000301067.7:c.8686C>T	p.Pro2896Ser	p.P2896S	ENST00000301067	NM_003482.3	2896	Cct/Tct	34/54	0.107039242887126	6	FACETS	1	0.983	1	0.486	0.438	0.536	INDETERMINATE	1	TRUE	3	0.593575327057331	6		803	566	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1959723	1959723	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	83	594	0	ENST00000382891.5:c.2945A>T	p.Gln982Leu	p.Q982L	ENST00000382891	NM_133335.3	982	cAg/cTg	16/22	0.180191221996787	3	FACETS	0.895	0.795	1	0.298	0.265	0.334	INDETERMINATE	1	TRUE	0	0.593575327057331	3		594	405	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970930	79970930	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	71	508	0	ENST00000265081.6:c.1156A>T	p.Ile386Phe	p.I386F	ENST00000265081	NM_002439.4	386	Att/Ttt	7/24	1	2	FACETS	0.893	0.788	1	0.893	0.788	1	CLONAL	1	TRUE	1	0.593575327057331	2		508	268	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562332	176562332	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	93	708	0	ENST00000439151.2:c.228G>T	p.Gln76His	p.Q76H	ENST00000439151	NM_022455.4	76	caG/caT	2/23	1	2	FACETS	0.836	0.749	0.927	0.836	0.749	0.927	CLONAL	1	TRUE	1	0.593575327057331	2		708	375	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091828	29091828	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	70	295	0	ENST00000328354.6:c.1129del	p.Glu377ArgfsTer5	p.E377Rfs*5	ENST00000328354	NM_007194.3	377	Gag/ag	11/15	0.593575327057331	2	FACETS	0.9	0.813	0.987	0.9	0.813	0.987	CLONAL	2	TRUE	0	0.593575327057331	2		295	131	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003747	45003749	+	start_lost	Translation_Start_Site	TNP	GTC	GTC	ATT	novel	NA	P-0065000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	91	643	0	ENST00000558401.1:c.3_5delinsATT	p.MetSer1_?2	p.MS1_?2	ENST00000558401	NM_004048.2	1	atGTCt/atATTt	1/4	0.593575327057331	1	FACETS	0.784	0.706	0.865	0.784	0.706	0.865	SUBCLONAL	1	TRUE	0	0.593575327057331	1		643	275	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0065001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	100	500	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.544830871037134	2	FACETS	0.991	0.913	1	0.991	0.913	1	CLONAL	2	TRUE	0	0.57352361797626	2		500	176	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	36	789	0				ENST00000310581	NM_198253.2	-/1132			0.560957439890634	1	FACETS	0.785	0.662	0.917	0.785	0.662	0.917	CLONAL	1	TRUE	0	0.57352361797626	1		789	114	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16235844	16235844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	165	522	0	ENST00000375759.3:c.910G>A	p.Asp304Asn	p.D304N	ENST00000375759	NM_015001.2	304	Gat/Aat	4/15	0.544830871037134	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	0	0.57352361797626	2		522	287	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14317322	14317322	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782597266	NA	P-0065001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	27	398	1	ENST00000256196.4:c.188G>A	p.Arg63Gln	p.R63Q	ENST00000256196		63	cGg/cAg	2/6	1	2	FACETS	0.951	0.775	1	0.951	0.775	1	CLONAL	1	TRUE	1	0.57352361797626	2		399	99	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123889569	123889569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs891671179	NA	P-0065001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	18	176	0	ENST00000330479.4:c.796C>T	p.Pro266Ser	p.P266S	ENST00000330479	NM_020382.3	266	Cct/Tct	7/9	1	2	FACETS	1	0.811	1	1	0.811	1	CLONAL	1	TRUE	1	0.57352361797626	2		176	60	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686905	37686905	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	130	580	0	ENST00000447079.4:c.3809C>T	p.Pro1270Leu	p.P1270L	ENST00000447079	NM_015083.1	1270	cCc/cTc	14/14	1	2	FACETS	0.967	0.883	1	0.967	0.883	1	CLONAL	1	TRUE	1	0.57352361797626	2		580	469	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369299	40369299	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	72	603	0	ENST00000293328.3:c.1259C>T	p.Ser420Phe	p.S420F	ENST00000293328	NM_012448.3	420	tCc/tTc	11/19	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.57352361797626	2		603	240	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61306888	61306888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	22	377	0	ENST00000341074.5:c.592G>A	p.Glu198Lys	p.E198K	ENST00000341074	NM_002974.2	198	Gaa/Aaa	6/8	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.57352361797626	2		377	74	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226646	2226646	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	55	803	0	ENST00000398665.3:c.4126C>A	p.Leu1376Met	p.L1376M	ENST00000398665	NM_032482.2	1376	Ctg/Atg	27/28	1	2	FACETS	0.501	0.43	0.578	0.501	0.43	0.578	SUBCLONAL	1	TRUE	1	0.57352361797626	2		803	383	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231574	5231575	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0065001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	70	444	0	ENST00000357368.4:c.1901_1902delinsTT	p.Ala634Val	p.A634V	ENST00000357368	NM_002850.3	634	gCC/gTT	14/38	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.57352361797626	2		444	236	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050363	13050363	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0065001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	94	671	1	ENST00000316448.5:c.315T>A	p.Cys105Ter	p.C105*	ENST00000316448	NM_004343.3	105	tgT/tgA	3/9	1	2	FACETS	0.872	0.782	0.966	0.872	0.782	0.966	CLONAL	1	TRUE	1	0.57352361797626	2		672	376	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292415	15292415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1379963173	NA	P-0065001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	42	630	0	ENST00000263388.2:c.2764G>A	p.Glu922Lys	p.E922K	ENST00000263388	NM_000435.2	922	Gaa/Aaa	17/33	1	2	FACETS	0.449	0.376	0.53	0.449	0.376	0.53	SUBCLONAL	1	TRUE	1	0.57352361797626	2		630	326	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36217247	36217247	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0065001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	82	530	0	ENST00000222270.7:c.3996T>G	p.Tyr1332Ter	p.Y1332*	ENST00000222270	NM_014727.1	1332	taT/taG	14/37	0.194825944610197	4	FACETS	0.752	0.671	0.838	0.752	0.671	0.838	INDETERMINATE	2	TRUE	2	0.57352361797626	4		530	299	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215595176	215595176	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658741	NA	P-0065001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	38	490	0	ENST00000260947.4:c.1960C>T	p.Pro654Ser	p.P654S	ENST00000260947	NM_000465.2	654	Cct/Tct	10/11	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.57352361797626	2		490	116	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215609821	215609821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	21	456	0	ENST00000260947.4:c.1873C>T	p.Leu625Phe	p.L625F	ENST00000260947	NM_000465.2	625	Ctc/Ttc	9/11	1	2	FACETS	0.882	0.696	1	0.882	0.696	1	CLONAL	1	TRUE	1	0.57352361797626	2		456	83	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437219	220437219	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	67	744	0	ENST00000243786.2:c.123G>T	p.Leu41Phe	p.L41F	ENST00000243786	NM_002191.3	41	ttG/ttT	1/2	1	2	FACETS	0.859	0.754	0.97	0.859	0.754	0.97	CLONAL	1	TRUE	1	0.57352361797626	2		744	272	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183871	10183872	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0065001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	57	569	0	ENST00000256474.2:c.340_340+1delinsAA		p.X114_splice	ENST00000256474	NM_000551.3	114		1/3	1	2	FACETS	0.773	0.67	0.884	0.773	0.67	0.884	SUBCLONAL	1	TRUE	1	0.57352361797626	2		569	257	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799688	72799688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	31	610	0	ENST00000325599.8:c.1481C>T	p.Pro494Leu	p.P494L	ENST00000325599	NM_018130.2	494	cCc/cTc	11/11	1	2	FACETS	0.819	0.674	0.977	0.819	0.674	0.977	CLONAL	1	TRUE	1	0.57352361797626	2		610	132	SUCCESS
ATR	545	MSKCC	GRCh37	3	142253934	142253934	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	24	322	0	ENST00000350721.4:c.3933G>C	p.Leu1311Phe	p.L1311F	ENST00000350721	NM_001184.3	1311	ttG/ttC	21/47	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.57352361797626	2		322	64	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259800	142259800	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	32	583	0	ENST00000350721.4:c.3527C>T	p.Thr1176Ile	p.T1176I	ENST00000350721	NM_001184.3	1176	aCc/aTc	18/47	1	2	FACETS	0.827	0.682	0.983	0.827	0.682	0.983	CLONAL	1	TRUE	1	0.57352361797626	2		583	135	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149375027	149375028	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0065001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	107	730	1	ENST00000360632.3:c.66_67delinsAA	p.Asp23Asn	p.D23N	ENST00000360632	NM_015472.4	22	caGGac/caAAac	2/7	1	2	FACETS	0.809	0.73	0.892	0.809	0.73	0.892	CLONAL	1	TRUE	1	0.57352361797626	2		731	461	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043464	180043464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	39	659	0	ENST00000261937.6:c.3122G>A	p.Arg1041Gln	p.R1041Q	ENST00000261937	NM_182925.4	1041	cGg/cAg	23/30	1	2	FACETS	0.477	0.397	0.565	0.477	0.397	0.565	SUBCLONAL	1	TRUE	1	0.57352361797626	2		659	285	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190368	32190368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	182	728	0	ENST00000375023.3:c.371C>T	p.Pro124Leu	p.P124L	ENST00000375023	NM_004557.3	124	cCc/cTc	3/30	0.57352361797626	4	FACETS	0.946	0.879	1	0.63	0.586	0.676	CLONAL	2	TRUE	1	0.57352361797626	4		728	528	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652171	36652171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760466052	NA	P-0065001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	75	702	0	ENST00000244741.5:c.293C>T	p.Ser98Leu	p.S98L	ENST00000244741	NM_000389.4	98	tCa/tTa	2/3	0.57352361797626	4	FACETS	0.881	0.775	0.995	0.294	0.258	0.332	CLONAL	1	TRUE	1	0.57352361797626	4		702	467	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964384	93964384	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	16	378	0	ENST00000369303.4:c.2513G>A	p.Trp838Ter	p.W838*	ENST00000369303	NM_004440.3	838	tGg/tAg	14/17	0.502952624065822	1	FACETS	0.865	0.668	1	0.865	0.668	1	CLONAL	1	TRUE	0	0.57352361797626	1		378	46	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552823	106552823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1042709746	NA	P-0065001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	41	689	0	ENST00000369096.4:c.788G>A	p.Gly263Glu	p.G263E	ENST00000369096	NM_001198.3	263	gGa/gAa	5/7	0.502952624065822	1	FACETS	0.675	0.573	0.785	0.675	0.573	0.785	SUBCLONAL	1	TRUE	0	0.57352361797626	1		689	151	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2949715	2949715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	46	535	0	ENST00000396946.4:c.3229C>T	p.Arg1077Trp	p.R1077W	ENST00000396946	NM_032415.4	1077	Cgg/Tgg	24/25	1	2	FACETS	0.779	0.664	0.902	0.779	0.664	0.902	CLONAL	1	TRUE	1	0.57352361797626	2		535	206	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332064	81332064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	56	442	0	ENST00000222390.5:c.2020G>A	p.Gly674Ser	p.G674S	ENST00000222390	NM_000601.4	674	Ggt/Agt	18/18	0.514200379342989	3	FACETS	0.849	0.745	0.956	0.849	0.745	0.956	CLONAL	2	TRUE	1	0.57352361797626	3		442	148	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934353	68934353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	30	315	0	ENST00000288368.4:c.419G>A	p.Arg140Lys	p.R140K	ENST00000288368	NM_024870.2	140	aGa/aAa	4/40	1	2	FACETS	0.918	0.781	1	1	0.964	1	CLONAL	2	TRUE	1	0.57352361797626	2		315	57	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956798	68956798	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	58	458	0	ENST00000288368.4:c.916G>A	p.Glu306Lys	p.E306K	ENST00000288368	NM_024870.2	306	Gaa/Aaa	8/40	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.57352361797626	2		458	191	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090890	5090890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777259241	NA	P-0065001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	16	337	0	ENST00000381652.3:c.3038C>T	p.Pro1013Leu	p.P1013L	ENST00000381652	NM_004972.3	1013	cCt/cTt	22/25	0.57352361797626	1	FACETS	0.884	0.684	1	0.884	0.684	1	CLONAL	1	TRUE	0	0.57352361797626	1		337	45	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492910	8492910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767627241	NA	P-0065001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	70	470	0	ENST00000356435.5:c.2419G>A	p.Gly807Arg	p.G807R	ENST00000356435		807	Gga/Aga	16/35	0.57352361797626	1	FACETS	0.936	0.833	1	0.936	0.833	1	CLONAL	1	TRUE	0	0.57352361797626	1		470	186	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0065002-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	19	338	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.356470828465392	10	FACETS	1	0.804	1	0.634	0.502	0.773	CLONAL	5	FALSE	2	0.356470828465392	10		338	51	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038831	47038831	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065002-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	41	646	0	ENST00000377604.3:c.838G>T	p.Gly280Ter	p.G280*	ENST00000377604	NM_001204468.1	280	Gga/Tga	9/24	0.312078043619308	1	FACETS	0.848	0.713	0.995	0.848	0.713	0.995	CLONAL	1	FALSE	0	0.356470828465392	1		646	223	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8252003	8252003	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065002-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	104	965	0	ENST00000335790.3:c.74C>A	p.Ala25Glu	p.A25E	ENST00000335790	NM_002315.2	25	gCg/gAg	2/4	0.356470828465392	3	FACETS	0.947	0.856	1	0.947	0.856	1	CLONAL	2	FALSE	1	0.356470828465392	3		965	363	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576910	7576946	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTGTTGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAA	GGTGTTGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAA	-	novel	NA	P-0065002-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	23	780	0	ENST00000269305.4:c.920-20_936del		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	0.327720332785698	2	FACETS	0.956	0.755	1	0.478	0.377	0.591	CLONAL	1	FALSE	0	0.356470828465392	2		780	135	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251466	10251466	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065002-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	45	803	0	ENST00000340748.4:c.3466C>A	p.His1156Asn	p.H1156N	ENST00000340748		1156	Cac/Aac	31/40	0.341592654040917	3	FACETS	0.806	0.679	0.945	0.269	0.226	0.315	CLONAL	1	FALSE	0	0.356470828465392	3		803	369	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662553	227662553	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065002-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	150	903	0	ENST00000305123.5:c.902G>C	p.Arg301Pro	p.R301P	ENST00000305123	NM_005544.2	301	cGc/cCc	1/2	0.212758312569611	5	FACETS	0.984	0.903	1	0.656	0.602	0.713	INDETERMINATE	2	FALSE	2	0.356470828465392	5		903	656	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324291	62324291	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065002-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	108	877	0	ENST00000360203.5:c.2786C>T	p.Ala929Val	p.A929V	ENST00000360203	NM_001283009.1	929	gCc/gTc	29/35	0.315849371160358	3	FACETS	0.781	0.705	0.861	0.781	0.705	0.861	SUBCLONAL	2	FALSE	1	0.356470828465392	3		877	457	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427694	72427694	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs765645254	NA	P-0065002-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	15	659	0	ENST00000477973.2:c.796A>T	p.Thr266Ser	p.T266S	ENST00000477973	NM_012234.5	266	Act/Tct	4/4	0.315849371160358	3	FACETS	0.58	0.426	0.763	0.29	0.213	0.382	SUBCLONAL	1	FALSE	1	0.356470828465392	3		659	171	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295270	1295270	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0065002-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	76	895	0				ENST00000310581	NM_198253.2	-/1132			0.356470828465392	3	FACETS	0.598	0.524	0.679	0.299	0.262	0.34	SUBCLONAL	1	FALSE	1	0.356470828465392	3		895	840	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161803	56161803	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065002-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	18	247	0	ENST00000399503.3:c.1300A>G	p.Ser434Gly	p.S434G	ENST00000399503	NM_005921.1	434	Agc/Ggc	6/20	0.356470828465392	3	FACETS	1	0.844	1	1	0.949	1	CLONAL	4	FALSE	1	0.356470828465392	3		247	29	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518382	8518382	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065002-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	47	566	0	ENST00000356435.5:c.1009A>G	p.Thr337Ala	p.T337A	ENST00000356435		337	Aca/Gca	10/35	0.291628475063351	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	FALSE	0	0.356470828465392	2		566	115	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760756	133760756	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065002-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	81	753	0	ENST00000318560.5:c.3079A>G	p.Ile1027Val	p.I1027V	ENST00000318560	NM_005157.4	1027	Atc/Gtc	11/11	0.356470828465392	3	FACETS	1	0.932	1	0.54	0.477	0.607	CLONAL	1	FALSE	1	0.356470828465392	3		753	496	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814733	139814733	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065002-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	121	783	0	ENST00000247668.2:c.726G>T	p.Glu242Asp	p.E242D	ENST00000247668	NM_021138.3	242	gaG/gaT	8/11	0.177396468194984	3	FACETS	0.997	0.909	1			1	INDETERMINATE	2	FALSE	NA	0.356470828465392	3		783	401	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606686	43606686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs552057730	NA	P-0065002-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	38	894	0	ENST00000355710.3:c.1295C>T	p.Ala432Val	p.A432V	ENST00000355710	NM_020975.4	432	gCa/gTa	7/20	0.356470828465392	3	FACETS	1	0.849	1	0.511	0.425	0.605	CLONAL	1	FALSE	1	0.356470828465392	3		894	246	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639230	3639230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs72778139	NA	P-0065003-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	67	691	0	ENST00000294008.3:c.4409C>T	p.Pro1470Leu	p.P1470L	ENST00000294008	NM_032444.2	1470	cCg/cTg	12/15	1	2	FACETS	0.468	0.406	0.534	0.468	0.406	0.534	SUBCLONAL	1	TRUE	1	0.45114524422626	2		691	635	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188177	11188177	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065003-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	249	608	0	ENST00000361445.4:c.5917A>T	p.Ile1973Phe	p.I1973F	ENST00000361445	NM_004958.3	1973	Atc/Ttc	43/58	0.45114524422626	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.45114524422626	2		608	547	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555230	226555230	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065003-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	209	572	0	ENST00000366794.5:c.2357G>C	p.Ser786Thr	p.S786T	ENST00000366794	NM_001618.3	786	aGc/aCc	17/23	0.45114524422626	2	FACETS	0.959	0.9	1	0.959	0.9	1	CLONAL	2	TRUE	0	0.45114524422626	2		572	483	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751484	57751484	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065003-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	61	559	0	ENST00000274289.3:c.1507T>C	p.Trp503Arg	p.W503R	ENST00000274289	NM_006622.3	503	Tgg/Cgg	11/14	1	2	FACETS	0.542	0.468	0.622	0.542	0.468	0.622	SUBCLONAL	1	TRUE	1	0.45114524422626	2		559	499	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821061	32821061	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065003-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	139	780	0	ENST00000354258.4:c.533C>A	p.Ser178Ter	p.S178*	ENST00000354258	NM_000593.5	178	tCa/tAa	1/11	0.45114524422626	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.45114524422626	1		780	453	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586419	189586419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1560280393	NA	P-0065004-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	361	598	0	ENST00000264731.3:c.1043C>T	p.Pro348Leu	p.P348L	ENST00000264731	NM_003722.4	348	cCa/cTa	8/14	1	2	FACETS	0.991	0.945	1	0.991	0.945	1	CLONAL	1	TRUE	1	0.89600117311212	2		598	813	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929070	44929071	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0065004-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	267	463	0	ENST00000377967.4:c.2172_2173del	p.Leu725AspfsTer4	p.L725Dfs*4	ENST00000377967	NM_021140.2	724	ATa/a	17/29	0.89600117311212	1	FACETS	0.991	0.958	1	0.991	0.958	1	CLONAL	1	TRUE	0	0.89600117311212	1		463	332	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124491979	124491980	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0065004-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	47	339	0	ENST00000357628.3:c.895_896del	p.Ala299GlnfsTer13	p.A299Qfs*13	ENST00000357628	NM_015450.2	299	GCc/c	11/19	1	2	FACETS	0.201	0.169	0.236	0.201	0.169	0.236	SUBCLONAL	1	TRUE	1	0.89600117311212	2		339	521	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399328	139399329	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACC	novel	NA	P-0065004-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	364	758	0	ENST00000277541.6:c.4812_4814dup	p.Val1605dup	p.V1605dup	ENST00000277541	NM_017617.3	1605	gtc/gtGGTc	26/34	0.89600117311212	1	FACETS	0.901	0.871	0.929	0.901	0.871	0.929	CLONAL	1	TRUE	0	0.89600117311212	1		758	498	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0065005-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	307	458	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		458	734	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646530	23646530	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs146434474	NA	P-0065005-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	290	536	1	ENST00000261584.4:c.1337A>T	p.Asp446Val	p.D446V	ENST00000261584	NM_024675.3	446	gAt/gTt	4/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		537	578	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295273	1295273	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0065005-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	332	807	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		807	900	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0065006-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	462	588	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.657211614022107	3	FACETS	0.995	0.966	1	0.995	0.966	1	CLONAL	3	TRUE	0	0.659599508152969	3		589	624	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415901	49415902	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0065006-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	204	607	0	ENST00000301067.7:c.16445_16446del	p.Val5482GlyfsTer7	p.V5482Gfs*7	ENST00000301067	NM_003482.3	5482	gTG/g	53/54	0.165183545705139	3	FACETS	1	0.988	1	0.64	0.596	0.684	INDETERMINATE	1	TRUE	1	0.659599508152969	3		607	643	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426022	49426022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1131691768	NA	P-0065006-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	291	839	0	ENST00000301067.7:c.12466C>T	p.Gln4156Ter	p.Q4156*	ENST00000301067	NM_003482.3	4156	Caa/Taa	39/54	0.165183545705139	3	FACETS	1	0.994	1	0.741	0.7	0.782	INDETERMINATE	1	TRUE	1	0.659599508152969	3		839	792	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155353	99155353	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0065006-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	168	362	0	ENST00000074304.5:c.580-1G>C		p.X194_splice	ENST00000074304	NM_001134224.1	194			NA	2	FACETS	0.997	0.923	1			1	INDETERMINATE	1	TRUE	NA	0.659599508152969	2		362	511	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32191698	32191698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065006-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	482	781	0	ENST00000375023.3:c.8C>T	p.Pro3Leu	p.P3L	ENST00000375023	NM_004557.3	3	cCc/cTc	1/30	0.660279807855942	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.659599508152969	2		781	664	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100328	157100328	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065006-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	164	465	0	ENST00000346085.5:c.1265T>A	p.Leu422Gln	p.L422Q	ENST00000346085	NM_020732.3	422	cTg/cAg	1/20	0.660279807855942	2	FACETS	1	0.976	1	0.563	0.521	0.604	CLONAL	1	TRUE	0	0.659599508152969	2		465	442	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223565	55223565	+	protein_altering_variant	In_Frame_Ins	INS	G	G	CCTA	novel	NA	P-0065006-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	91	687	0	ENST00000275493.2:c.932delinsCCTA	p.Cys311delinsSerTyr	p.C311delinsSY	ENST00000275493	NM_005228.3	311	tGt/tCCTAt	8/28	0.548645258636679	4	FACETS	0.502	0.445	0.563	0.167	0.148	0.188	SUBCLONAL	1	TRUE	1	0.659599508152969	4		687	912	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0065007-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	26	536	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	0.721	0.569	0.897	0.721	0.569	0.897	SUBCLONAL	1	TRUE	1	0.1	2		536	721	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880257	37880257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065007-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	20	476	0	ENST00000269571.5:c.2301C>G	p.Ile767Met	p.I767M	ENST00000269571		767	atC/atG	19/27	1	2	FACETS	0.567	0.432	0.728	0.567	0.432	0.728	SUBCLONAL	1	TRUE	1	0.1	2		476	705	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628590	187628590	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065007-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	41	586	0	ENST00000441802.2:c.2392G>C	p.Gly798Arg	p.G798R	ENST00000441802	NM_005245.3	798	Ggg/Cgg	2/27	1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	1	0.1	2		586	803	SUCCESS
APC	324	MSKCC	GRCh37	5	112173258	112173258	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065007-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	25	364	0	ENST00000257430.4:c.1967T>G	p.Leu656Arg	p.L656R	ENST00000257430	NM_000038.5	656	cTa/cGa	16/16	1	2	FACETS	1	0.816	1	1	0.816	1	CLONAL	1	TRUE	1	0.1	2		364	480	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0065008-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	183	256	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.66404840957906	5	FACETS	1	0.984	1			1	CLONAL	4	TRUE	NA	0.685456415178695	5		256	251	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0065008-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	159	395	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.823	0.758	0.889	0.823	0.758	0.889	CLONAL	1	TRUE	1	0.685456415178695	2		395	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572932	7572933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065008-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	236	357	0	ENST00000269305.4:c.1176dup	p.Asp393ArgfsTer78	p.D393Rfs*78	ENST00000269305	NM_001126112.2	392	-/A	11/11	0.685456415178695	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.685456415178695	1		357	409	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431079	49431079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065008-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	204	531	0	ENST00000301067.7:c.10060G>A	p.Gly3354Arg	p.G3354R	ENST00000301067	NM_003482.3	3354	Ggg/Agg	34/54	1	2	FACETS	0.913	0.851	0.977	0.913	0.851	0.977	CLONAL	1	TRUE	1	0.685456415178695	2		531	652	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50782459	50782459	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0065008-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	21	208	0	ENST00000307179.4:c.1972-1G>C		p.X658_splice	ENST00000307179		658			0.426261165441862	1	FACETS	0.172	0.133	0.218	0.172	0.133	0.218	SUBCLONAL	1	TRUE	0	0.685456415178695	1		208	234	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225722	26225722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1426924061	NA	P-0065008-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	253	520	0	ENST00000360408.1:c.340C>T	p.His114Tyr	p.H114Y	ENST00000360408	NM_003532.2	114	Cat/Tat	1/1	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.685456415178695	2		520	707	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937546	76937546	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065008-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	61	365	0	ENST00000373344.5:c.3202A>G	p.Thr1068Ala	p.T1068A	ENST00000373344	NM_000489.3	1068	Aca/Gca	9/35	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.685456415178695	2		365	170	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762464	41762464	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065010-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	167	539	0	ENST00000301178.4:c.2144G>A	p.Trp715Ter	p.W715*	ENST00000301178	NM_021913.4	715	tGg/tAg	18/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.437197868225564	2		539	732	SUCCESS
APC	324	MSKCC	GRCh37	5	112173835	112173838	+	frameshift_variant	Frame_Shift_Del	DEL	AGAT	AGAT	-	rs398123118	NA	P-0065010-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	111	463	0	ENST00000257430.4:c.2547_2550del	p.Asp849GlufsTer11	p.D849Efs*11	ENST00000257430	NM_000038.5	848	aaAGAT/aa	16/16	0.437197868225564	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.437197868225564	1		463	378	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77937766	77937775	+	frameshift_variant	Frame_Shift_Del	DEL	CCGGAACATC	CCGGAACATC	-	novel	NA	P-0065010-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	142	550	0	ENST00000361507.4:c.943_952del	p.Asp315ProfsTer22	p.D315Pfs*22	ENST00000361507	NM_080491.2	315	GATGTTCCGGcc/cc	4/10	1	2	FACETS	0.924	0.844	1	0.924	0.844	1	CLONAL	1	TRUE	1	0.437197868225564	2		550	703	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120843	115120843	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065010-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	154	621	0	ENST00000257566.3:c.163T>G	p.Ser55Ala	p.S55A	ENST00000257566	NM_016569.3	55	Tcg/Gcg	1/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.437197868225564	2		621	669	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014063	14014063	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754622238	NA	P-0065010-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	160	464	0	ENST00000311895.7:c.41C>T	p.Pro14Leu	p.P14L	ENST00000311895	NM_005236.2	14	cCg/cTg	1/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.437197868225564	2		464	622	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578521	7578522	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTGGCAAAAAAAA	novel	NA	P-0065010-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	295	619	0	ENST00000269305.4:c.408_409insTTTTTTTTGCCAA	p.Leu137PhefsTer16	p.L137Ffs*16	ENST00000269305	NM_001126112.2	136	-/TTTTTTTTGCCAA	5/11	0.349230860100229	3	FACETS	0.972	0.918	1	0.648	0.612	0.685	CLONAL	2	TRUE	0	0.437197868225564	3		619	846	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573604	48573604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065010-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	91	473	0	ENST00000342988.3:c.188C>T	p.Thr63Ile	p.T63I	ENST00000342988	NM_005359.5	63	aCa/aTa	2/12	0.437197868225564	1	FACETS	0.989	0.887	1	0.989	0.887	1	CLONAL	1	TRUE	0	0.437197868225564	1		473	329	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162275	38162275	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065010-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	100	360	0	ENST00000317025.8:c.2441G>A	p.Gly814Asp	p.G814D	ENST00000317025	NM_023034.1	814	gGc/gAc	14/24	0.437197868225564	1	FACETS	0.894	0.804	0.987	0.894	0.804	0.987	CLONAL	1	TRUE	0	0.437197868225564	1		360	400	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0065011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	217	662	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	0.165711955101945	3	FACETS	0.934	0.871	1	0.623	0.58	0.667	INDETERMINATE	2	TRUE	0	0.33	3		662	820	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099475	27099592	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAGGTGACTGATCTGATTGCTATTTGAACTTGTGCTCGTAAAGACAGGGCCAGTGAAATGGGGGGAAATCTTGAGAATGGCTCAGGGTTCTTGTGGAGCCATCCTCTGAGATAATGC	AAAGGTGACTGATCTGATTGCTATTTGAACTTGTGCTCGTAAAGACAGGGCCAGTGAAATGGGGGGAAATCTTGAGAATGGCTCAGGGTTCTTGTGGAGCCATCCTCTGAGATAATGC	-	novel	NA	P-0065011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	32	574	0	ENST00000324856.7:c.3713_3715+115del		p.X1238_splice	ENST00000324856	NM_006015.4	1238		14/20	1	2	FACETS	0.411	0.333	0.499	0.411	0.333	0.499	SUBCLONAL	1	TRUE	1	0.33	2		574	472	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444674	49444674	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	119	813	0	ENST00000301067.7:c.2792del	p.Pro931HisfsTer27	p.P931Hfs*27	ENST00000301067	NM_003482.3	931	cCa/ca	10/54	0.105930002381663	3	FACETS	1	0.935	1	0.523	0.472	0.577	INDETERMINATE	1	TRUE	1	0.33	3		813	803	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	203	789	0				ENST00000310581	NM_198253.2	-/1132			0.817425883550913	3	FACETS	0.956	0.902	1	0.956	0.902	1	CLONAL	2	TRUE	1	0.817425883550913	3		789	366	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432459	49432459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	399	619	0	ENST00000301067.7:c.8680C>T	p.Pro2894Ser	p.P2894S	ENST00000301067	NM_003482.3	2894	Ccg/Tcg	34/54	0.817425883550913	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.817425883550913	4		619	845	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777095	9777095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	196	662	0	ENST00000377346.4:c.859G>A	p.Asp287Asn	p.D287N	ENST00000377346	NM_005026.3	287	Gat/Aat	7/24	0.817425883550913	3	FACETS	1	0.959	1	0.521	0.485	0.559	CLONAL	1	TRUE	1	0.817425883550913	3		662	648	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217302	11217302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	306	480	0	ENST00000361445.4:c.4376C>T	p.Ala1459Val	p.A1459V	ENST00000361445	NM_004958.3	1459	gCc/gTc	30/58	0.817425883550913	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.817425883550913	3		480	490	SUCCESS
MAD2L2	10459	MSKCC	GRCh37	1	11735170	11735170	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	178	531	0	ENST00000235310.3:c.563C>G	p.Pro188Arg	p.P188R	ENST00000235310		188	cCa/cGa	10/11	0.817425883550913	3	FACETS	1	0.958	1	0.523	0.485	0.563	CLONAL	1	TRUE	1	0.817425883550913	3		531	586	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256378	16256378	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	390	650	0	ENST00000375759.3:c.3643C>T	p.Pro1215Ser	p.P1215S	ENST00000375759	NM_015001.2	1215	Cct/Tct	11/15	0.466389616832851	4	FACETS	0.86	0.826	0.894	1	0.995	1	INDETERMINATE	3	TRUE	2	0.817425883550913	4		650	672	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059176	27059176	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	218	331	0	ENST00000324856.7:c.1813C>T	p.Gln605Ter	p.Q605*	ENST00000324856	NM_006015.4	605	Caa/Taa	4/20	0.817425883550913	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.817425883550913	3		331	357	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363439	40363439	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	181	626	0	ENST00000397332.2:c.790C>T	p.Gln264Ter	p.Q264*	ENST00000397332	NM_001033082.2	264	Caa/Taa	3/3	0.817425883550913	3	FACETS	1	0.962	1	0.528	0.489	0.567	CLONAL	1	TRUE	1	0.817425883550913	3		626	591	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436151	51436151	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	168	400	0	ENST00000262662.1:c.111T>A	p.Phe37Leu	p.F37L	ENST00000262662		37	ttT/ttA	3/4	0.817425883550913	3	FACETS	1	0.98	1	0.581	0.538	0.625	CLONAL	1	TRUE	1	0.817425883550913	3		400	498	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258744	115258744	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121434596	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	147	425	0	ENST00000369535.4:c.38G>T	p.Gly13Val	p.G13V	ENST00000369535	NM_002524.4	13	gGt/gTt	2/7	0.817425883550913	3	FACETS	1	0.947	1	0.519	0.477	0.562	CLONAL	1	TRUE	1	0.817425883550913	3		425	488	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206664982	206664982	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1553390393	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	301	452	0	ENST00000367120.3:c.1735G>A	p.Val579Met	p.V579M	ENST00000367120	NM_014002.3	579	Gtg/Atg	18/22	0.755110909411672	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.817425883550913	4		452	650	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246091330	246091330	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1437168377	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	230	393	0	ENST00000388985.4:c.605C>T	p.Ser202Phe	p.S202F	ENST00000388985		202	tCt/tTt	7/12	0.755110909411672	4	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	2	0.817425883550913	4		393	511	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161519	2161519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	154	550	0	ENST00000434045.2:c.8C>T	p.Ser3Phe	p.S3F	ENST00000434045	NM_001127598.1	3	tCc/tTc	2/5	0.817425883550913	3	FACETS	1	0.951	1	0.521	0.48	0.564	CLONAL	1	TRUE	1	0.817425883550913	3		550	509	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404950	404950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765539853	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	255	407	0	ENST00000399788.2:c.4244C>T	p.Thr1415Ile	p.T1415I	ENST00000399788	NM_001042603.1	1415	aCc/aTc	26/28	0.795508991852383	4	FACETS	0.966	0.912	1			1	CLONAL	2	TRUE	NA	0.817425883550913	4		407	587	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434955	49434955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	377	627	0	ENST00000301067.7:c.6598C>T	p.Pro2200Ser	p.P2200S	ENST00000301067	NM_003482.3	2200	Cct/Tct	31/54	0.817425883550913	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.817425883550913	4		627	809	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481943	56481943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	315	448	0	ENST00000267101.3:c.871C>T	p.Pro291Ser	p.P291S	ENST00000267101	NM_001982.3	291	Ccc/Tcc	7/28	0.817425883550913	4	FACETS	0.999	0.95	1	0.999	0.95	1	CLONAL	2	TRUE	2	0.817425883550913	4		448	701	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21553868	21553868	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	270	423	0	ENST00000382592.4:c.2734C>T	p.Pro912Ser	p.P912S	ENST00000382592	NM_014572.2	912	Ccc/Tcc	7/8	0.755110909411672	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.817425883550913	4		423	534	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609763	28609763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	260	515	0	ENST00000241453.7:c.1466G>A	p.Arg489Lys	p.R489K	ENST00000241453	NM_004119.2	489	aGa/aAa	12/24	0.755110909411672	4	FACETS	0.988	0.934	1	0.988	0.934	1	CLONAL	2	TRUE	2	0.817425883550913	4		515	585	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900639	32900639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41293469	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	119	337	0	ENST00000380152.3:c.520C>T	p.Arg174Cys	p.R174C	ENST00000380152		174	Cgt/Tgt	7/27	0.755110909411672	4	FACETS	1	0.936	1	0.52	0.471	0.57	CLONAL	1	TRUE	2	0.817425883550913	4		337	509	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923112	48923112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770277291	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	106	141	0	ENST00000267163.4:c.560C>T	p.Ser187Phe	p.S187F	ENST00000267163	NM_000321.2	187	tCt/tTt	6/27	0.755110909411672	4	FACETS	0.958	0.876	1	0.958	0.876	1	CLONAL	2	TRUE	2	0.817425883550913	4		141	246	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43766937	43766937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749691200	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	253	385	0	ENST00000382044.4:c.1114C>T	p.Pro372Ser	p.P372S	ENST00000382044	NM_001141980.1	372	Cct/Tct	10/28	0.817425883550913	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.817425883550913	4		385	544	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096361	2096361	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	343	491	0	ENST00000219066.1:c.146G>A	p.Arg49Lys	p.R49K	ENST00000219066	NM_002528.5	49	aGg/aAg	2/6	0.817425883550913	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.817425883550913	4		491	724	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138326	2138327	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	GG	GG	A	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	363	669	0	ENST00000219476.3:c.5259_5259+1delinsA		p.X1753_splice	ENST00000219476	NM_000548.3	1753		41/42	0.817425883550913	4	FACETS	0.991	0.946	1	0.991	0.946	1	CLONAL	2	TRUE	2	0.817425883550913	4		669	814	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640413	3640413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	367	783	0	ENST00000294008.3:c.3226C>T	p.Pro1076Ser	p.P1076S	ENST00000294008	NM_032444.2	1076	Cca/Tca	12/15	0.817425883550913	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	2	0.817425883550913	4		783	813	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647394	3647394	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	161	572	0	ENST00000294008.3:c.1669C>T	p.Gln557Ter	p.Q557*	ENST00000294008	NM_032444.2	557	Cag/Tag	7/15	0.817425883550913	4	FACETS	0.961	0.883	1	0.48	0.441	0.521	CLONAL	1	TRUE	2	0.817425883550913	4		572	745	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857692	9857692	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1389208302	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	365	651	0	ENST00000330684.3:c.3709G>A	p.Asp1237Asn	p.D1237N	ENST00000330684	NM_001134407.1	1237	Gat/Aat	13/13	0.755110909411672	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.817425883550913	4		651	766	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858460	9858460	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	281	536	0	ENST00000330684.3:c.2941C>A	p.Gln981Lys	p.Q981K	ENST00000330684	NM_001134407.1	981	Cag/Aag	13/13	0.755110909411672	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.817425883550913	4		536	591	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032069	10032069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868215122	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	253	484	0	ENST00000330684.3:c.754G>A	p.Asp252Asn	p.D252N	ENST00000330684	NM_001134407.1	252	Gat/Aat	3/13	0.755110909411672	4	FACETS	0.983	0.929	1	0.983	0.929	1	CLONAL	2	TRUE	2	0.817425883550913	4		484	572	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826577	50826577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	185	240	0	ENST00000398568.2:c.2302C>T	p.Pro768Ser	p.P768S	ENST00000398568	NM_001042412.1	768	Cct/Tct	15/18	0.755110909411672	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.817425883550913	4		240	372	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993436	72993437	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	320	668	0	ENST00000268489.5:c.608_609delinsTT	p.Ser203Phe	p.S203F	ENST00000268489	NM_006885.3	203	tCC/tTT	2/10	0.755110909411672	4	FACETS	0.958	0.91	1	0.958	0.91	1	CLONAL	2	TRUE	2	0.817425883550913	4		668	743	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016613	12016613	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	162	427	0	ENST00000353533.5:c.749T>G	p.Ile250Ser	p.I250S	ENST00000353533	NM_003010.3	250	aTc/aGc	7/11	0.817425883550913	4	FACETS	1	0.963	1	0.54	0.497	0.585	CLONAL	1	TRUE	2	0.817425883550913	4		427	667	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509581	29509581	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	312	447	0	ENST00000356175.3:c.786del	p.Ala264GlnfsTer17	p.A264Qfs*17	ENST00000356175	NM_000267.3	262	cgT/cg	8/57	0.817425883550913	4	FACETS	0.969	0.92	1	0.969	0.92	1	CLONAL	2	TRUE	2	0.817425883550913	4		447	716	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654730	29654730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555533609	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	329	555	0	ENST00000356175.3:c.5419C>T	p.Arg1807Trp	p.R1807W	ENST00000356175	NM_000267.3	1807	Cgg/Tgg	37/57	0.817425883550913	4	FACETS	0.943	0.896	0.99	0.943	0.896	0.99	CLONAL	2	TRUE	2	0.817425883550913	4		555	776	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670070	29670070	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	248	369	0	ENST00000356175.3:c.7043G>A	p.Trp2348Ter	p.W2348*	ENST00000356175	NM_000267.3	2348	tGg/tAg	47/57	0.817425883550913	4	FACETS	0.99	0.935	1	0.99	0.935	1	CLONAL	2	TRUE	2	0.817425883550913	4		369	557	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872138	37872138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375382055	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	381	617	2	ENST00000269571.5:c.1459C>T	p.Arg487Trp	p.R487W	ENST00000269571		487	Cgg/Tgg	12/27	0.817425883550913	4	FACETS	0.988	0.944	1	0.988	0.944	1	CLONAL	2	TRUE	2	0.817425883550913	4		619	857	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40364021	40364021	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	193	347	0	ENST00000293328.3:c.1661C>T	p.Ser554Phe	p.S554F	ENST00000293328	NM_012448.3	554	tCc/tTc	13/19	0.817425883550913	4	FACETS	0.921	0.861	0.981	0.921	0.861	0.981	CLONAL	2	TRUE	2	0.817425883550913	4		347	466	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462547	40462547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	379	541	0	ENST00000345506.4:c.2245G>A	p.Asp749Asn	p.D749N	ENST00000345506	NM_003152.3	749	Gat/Aat	20/20	0.817425883550913	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.817425883550913	4		541	814	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435599	56435599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	150	631	0	ENST00000407977.2:c.1538C>T	p.Pro513Leu	p.P513L	ENST00000407977		513	cCt/cTt	9/10	0.817425883550913	4	FACETS	0.883	0.809	0.962	0.442	0.404	0.481	CLONAL	1	TRUE	2	0.817425883550913	4		631	755	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760842	59760842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	267	338	0	ENST00000259008.2:c.3565G>A	p.Asp1189Asn	p.D1189N	ENST00000259008	NM_032043.2	1189	Gat/Aat	20/20	0.817425883550913	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.817425883550913	4		338	555	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302983	15302983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142492710	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	188	608	0	ENST00000263388.2:c.467G>A	p.Arg156Gln	p.R156Q	ENST00000263388	NM_000435.2	156	cGa/cAa	4/33	0.817425883550913	3	FACETS	0.988	0.917	1	0.494	0.458	0.531	CLONAL	1	TRUE	1	0.817425883550913	3		608	656	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313222	30313222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	177	499	0	ENST00000262643.3:c.916C>T	p.His306Tyr	p.H306Y	ENST00000262643	NM_001238.2	306	Cat/Tat	10/12	0.817425883550913	3	FACETS	1	0.976	1	0.561	0.52	0.602	CLONAL	1	TRUE	1	0.817425883550913	3		499	544	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425573	47425573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	322	483	0	ENST00000404338.3:c.3641G>A	p.Arg1214Gln	p.R1214Q	ENST00000404338	NM_004491.4	1214	cGg/cAg	1/6	0.817425883550913	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.817425883550913	3		483	538	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469539	25469539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1401774585	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	162	558	0	ENST00000264709.3:c.1229C>T	p.Ala410Val	p.A410V	ENST00000264709	NM_175629.2	410	gCc/gTc	10/23	0.817425883550913	3	FACETS	1	0.925	1	0.501	0.462	0.541	CLONAL	1	TRUE	1	0.817425883550913	3		558	557	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609717	46609717	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765717751	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	153	568	0	ENST00000263734.3:c.2441C>T	p.Ser814Leu	p.S814L	ENST00000263734	NM_001430.4	814	tCg/tTg	15/16	0.817425883550913	3	FACETS	0.957	0.88	1	0.479	0.44	0.518	CLONAL	1	TRUE	1	0.817425883550913	3		568	551	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422375	225422376	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	82	272	0	ENST00000264414.4:c.264_264+1delinsAA		p.X88_splice	ENST00000264414	NM_003590.4	88		2/16	0.817425883550913	3	FACETS	1	0.906	1	0.508	0.454	0.565	CLONAL	1	TRUE	1	0.817425883550913	3		272	278	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076955	41076955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs724159838	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	210	403	0	ENST00000373198.4:c.1465C>T	p.Pro489Ser	p.P489S	ENST00000373198	NM_133170.3	489	Cct/Tct	9/32	0.755110909411672	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.817425883550913	4		403	418	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514518	41514518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	267	459	0	ENST00000373198.4:c.143G>A	p.Gly48Glu	p.G48E	ENST00000373198	NM_133170.3	48	gGg/gAg	2/32	0.755110909411672	4	FACETS	0.976	0.923	1	0.976	0.923	1	CLONAL	2	TRUE	2	0.817425883550913	4		459	608	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24158984	24158984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	163	442	0	ENST00000263121.7:c.656C>T	p.Ser219Leu	p.S219L	ENST00000263121	NM_003073.3	219	tCa/tTa	6/9	0.817425883550913	4	FACETS	0.989	0.91	1	0.494	0.454	0.536	CLONAL	1	TRUE	2	0.817425883550913	4		442	733	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447480	12447480	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150296212	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	339	562	1	ENST00000287820.6:c.719G>A	p.Arg240Gln	p.R240Q	ENST00000287820	NM_015869.4	240	cGg/cAg	5/7	0.817425883550913	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	2	0.817425883550913	4		563	747	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277850	41277850	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759171472	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	301	414	0	ENST00000349496.5:c.1814C>T	p.Ser605Phe	p.S605F	ENST00000349496	NM_001904.3	605	tCt/tTt	12/15	0.817425883550913	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	2	0.817425883550913	4		414	660	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668822	52668822	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	279	434	0	ENST00000394830.3:c.1097A>T	p.Tyr366Phe	p.Y366F	ENST00000394830	NM_018313.4	366	tAt/tTt	12/30	0.817425883550913	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.817425883550913	4		434	601	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63968053	63968053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370779210	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	317	472	0	ENST00000398590.3:c.944C>T	p.Pro315Leu	p.P315L	ENST00000398590	NM_001177387.1	315	cCg/cTg	7/14	0.817425883550913	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	2	0.817425883550913	4		472	701	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268448	142268448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564283952	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	361	396	0	ENST00000350721.4:c.3044G>A	p.Arg1015Gln	p.R1015Q	ENST00000350721	NM_001184.3	1015	cGa/cAa	15/47	0.817425883550913	5	FACETS	0.972	0.931	1	0.972	0.931	1	CLONAL	3	TRUE	2	0.817425883550913	5		396	674	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803142	1803142	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	407	625	2	ENST00000260795.2:c.494C>T	p.Ala165Val	p.A165V	ENST00000260795		165	gCc/gTc	4/17	0.795508991852383	4	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.817425883550913	4		627	809	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808562	1808562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377402598	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	361	731	0	ENST00000260795.2:c.2175G>A	p.Met725Ile	p.M725I	ENST00000260795		725	atG/atA	16/17	0.795508991852383	4	FACETS	0.998	0.952	1			1	CLONAL	2	TRUE	NA	0.817425883550913	4		731	804	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131118	55131118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139913632	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	151	423	0	ENST00000257290.5:c.661C>T	p.Leu221Phe	p.L221F	ENST00000257290	NM_006206.4	221	Ctt/Ttt	5/23	0.817425883550913	3	FACETS	1	0.981	1	0.6	0.553	0.647	CLONAL	1	TRUE	1	0.817425883550913	3		423	434	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155180	55155180	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600187	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	314	579	0	ENST00000257290.5:c.2779G>A	p.Glu927Lys	p.E927K	ENST00000257290	NM_006206.4	927	Gag/Aag	21/23	0.817425883550913	3	FACETS	0.959	0.916	1	0.959	0.916	1	CLONAL	2	TRUE	1	0.817425883550913	3		579	564	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953823	55953823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	133	472	0	ENST00000263923.4:c.3613G>A	p.Glu1205Lys	p.E1205K	ENST00000263923	NM_002253.2	1205	Gag/Aag	27/30	0.817425883550913	3	FACETS	0.953	0.871	1	0.477	0.435	0.519	CLONAL	1	TRUE	1	0.817425883550913	3		472	481	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953837	55953837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	130	472	0	ENST00000263923.4:c.3599C>T	p.Ser1200Phe	p.S1200F	ENST00000263923	NM_002253.2	1200	tCc/tTc	27/30	0.817425883550913	3	FACETS	0.911	0.831	0.993	0.455	0.415	0.497	CLONAL	1	TRUE	1	0.817425883550913	3		472	492	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955863	55955863	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868047715	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	225	349	0	ENST00000263923.4:c.3299C>T	p.Ser1100Phe	p.S1100F	ENST00000263923	NM_002253.2	1100	tCc/tTc	24/30	0.817425883550913	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.817425883550913	3		349	363	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956220	55956220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190050670	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	108	397	0	ENST00000263923.4:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000263923	NM_002253.2	1032	cGa/cAa	23/30	0.817425883550913	3	FACETS	1	0.916	1	0.506	0.458	0.555	CLONAL	1	TRUE	1	0.817425883550913	3		397	368	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961812	55961812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	211	369	0	ENST00000263923.4:c.2749G>A	p.Glu917Lys	p.E917K	ENST00000263923	NM_002253.2	917	Gaa/Aaa	20/30	0.817425883550913	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	1	0.817425883550913	3		369	362	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356298	66356298	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	154	632	0	ENST00000273854.3:c.1199C>T	p.Ser400Phe	p.S400F	ENST00000273854	NM_004439.5	400	tCc/tTc	5/18	0.817425883550913	3	FACETS	0.99	0.912	1	0.495	0.456	0.536	CLONAL	1	TRUE	1	0.817425883550913	3		632	536	SUCCESS
ALB	213	MSKCC	GRCh37	4	74272395	74272395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	123	396	0	ENST00000295897.4:c.187C>T	p.His63Tyr	p.H63Y	ENST00000295897	NM_000477.5	63	Cat/Tat	3/15	0.817425883550913	3	FACETS	1	0.976	1	0.595	0.545	0.648	CLONAL	1	TRUE	1	0.817425883550913	3		396	356	SUCCESS
ALB	213	MSKCC	GRCh37	4	74277813	74277813	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	271	409	0	ENST00000295897.4:c.814G>A	p.Gly272Arg	p.G272R	ENST00000295897	NM_000477.5	272	Gga/Aga	7/15	0.817425883550913	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.817425883550913	3		409	439	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196556	106196556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1351807056	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	150	515	0	ENST00000380013.4:c.4889C>T	p.Ser1630Leu	p.S1630L	ENST00000380013	NM_001127208.2	1630	tCa/tTa	11/11	0.817425883550913	3	FACETS	0.961	0.883	1	0.48	0.441	0.521	CLONAL	1	TRUE	1	0.817425883550913	3		515	538	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144359232	144359232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	119	421	0	ENST00000262995.4:c.674C>T	p.Ser225Phe	p.S225F	ENST00000262995	NM_207123.2	225	tCc/tTc	4/11	0.817425883550913	3	FACETS	0.856	0.777	0.939	0.428	0.388	0.47	CLONAL	1	TRUE	1	0.817425883550913	3		421	479	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	142	408	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.817425883550913	3	FACETS	1	0.918	1	0.5	0.459	0.543	CLONAL	1	TRUE	1	0.817425883550913	3		408	489	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541241	187541241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	311	572	0	ENST00000441802.2:c.6499G>A	p.Glu2167Lys	p.E2167K	ENST00000441802	NM_005245.3	2167	Gaa/Aaa	10/27	0.817425883550913	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	1	0.817425883550913	3		572	534	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1272320	1272320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	277	514	0	ENST00000310581.5:c.2362G>A	p.Asp788Asn	p.D788N	ENST00000310581	NM_198253.2	788	Gat/Aat	7/16	0.817425883550913	3	FACETS	0.992	0.946	1	0.992	0.946	1	CLONAL	2	TRUE	1	0.817425883550913	3		514	481	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280439	1280439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388629976	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	134	484	0	ENST00000310581.5:c.1784G>A	p.Arg595Lys	p.R595K	ENST00000310581	NM_198253.2	595	aGg/aAg	4/16	0.817425883550913	3	FACETS	0.915	0.836	0.996	0.457	0.418	0.498	CLONAL	1	TRUE	1	0.817425883550913	3		484	505	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35857138	35857138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	279	380	0	ENST00000303115.3:c.59G>A	p.Gly20Glu	p.G20E	ENST00000303115	NM_002185.3	20	gGa/gAa	1/8	0.817425883550913	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.817425883550913	3		380	466	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250484	26250484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1351044583	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	463	744	0	ENST00000446824.2:c.350G>A	p.Arg117Gln	p.R117Q	ENST00000446824	NM_021018.2	117	cGa/cAa	1/1	0.817425883550913	5	FACETS	1	0.977	1	0.515	0.493	0.538	CLONAL	2	TRUE	1	0.817425883550913	5		744	1223	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323331	31323331	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	75	224	0	ENST00000412585.2:c.658G>A	p.Asp220Asn	p.D220N	ENST00000412585	NM_005514.6	220	Gac/Aac	4/8	0.817425883550913	5	FACETS	1	0.939	1	0.276	0.243	0.311	CLONAL	1	TRUE	1	0.817425883550913	5		224	370	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183144	32183144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1394251155	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	147	539	0	ENST00000375023.3:c.1880C>T	p.Pro627Leu	p.P627L	ENST00000375023	NM_004557.3	627	cCc/cTc	12/30	0.817425883550913	5	FACETS	0.961	0.878	1	0.24	0.219	0.262	CLONAL	1	TRUE	1	0.817425883550913	5		539	833	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965706	93965706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	123	490	0	ENST00000369303.4:c.2222G>A	p.Gly741Glu	p.G741E	ENST00000369303	NM_004440.3	741	gGa/gAa	13/17	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.817425883550913	2		490	295	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120714	94120714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	113	453	0	ENST00000369303.4:c.337C>T	p.Pro113Ser	p.P113S	ENST00000369303	NM_004440.3	113	Cct/Tct	3/17	1	2	FACETS	0.95	0.868	1	0.95	0.868	1	CLONAL	1	TRUE	1	0.817425883550913	2		453	291	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536179	106536179	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	169	500	0	ENST00000369096.4:c.146G>A	p.Trp49Ter	p.W49*	ENST00000369096	NM_001198.3	49	tGg/tAg	2/7	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.817425883550913	2		500	345	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729727	41729727	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	330	570	0	ENST00000242208.4:c.802G>A	p.Glu268Lys	p.E268K	ENST00000242208	NM_002192.2	268	Gaa/Aaa	3/3	0.817425883550913	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	2	0.817425883550913	4		570	726	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372773	81372773	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	280	423	0	ENST00000222390.5:c.761G>A	p.Gly254Asp	p.G254D	ENST00000222390	NM_000601.4	254	gGc/gAc	7/18	0.817425883550913	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	2	0.817425883550913	4		423	616	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481403	140481403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913357	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	125	303	1	ENST00000288602.6:c.1405G>A	p.Gly469Arg	p.G469R	ENST00000288602	NM_004333.4	469	Gga/Aga	11/18	0.817425883550913	4	FACETS	1	0.956	1	0.542	0.493	0.593	CLONAL	1	TRUE	2	0.817425883550913	4		304	513	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277245	38277245	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	164	495	0	ENST00000425967.3:c.1183G>A	p.Glu395Lys	p.E395K	ENST00000425967	NM_001174067.1	395	Gag/Aag	10/19	0.817425883550913	3	FACETS	0.986	0.911	1	0.493	0.455	0.533	CLONAL	1	TRUE	1	0.817425883550913	3		495	573	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028113	69028113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	164	488	0	ENST00000288368.4:c.3272G>A	p.Gly1091Glu	p.G1091E	ENST00000288368	NM_024870.2	1091	gGa/gAa	26/40	0.817425883550913	3	FACETS	1	0.976	1	0.566	0.524	0.61	CLONAL	1	TRUE	1	0.817425883550913	3		488	499	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341851	8341851	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866497340	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	151	515	0	ENST00000356435.5:c.4789C>T	p.Gln1597Ter	p.Q1597*	ENST00000356435		1597	Caa/Taa	29/35	0.817425883550913	2	FACETS	1	0.958	1	0.523	0.485	0.562	CLONAL	1	TRUE	0	0.817425883550913	2		515	353	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389398	8389398	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	210	351	0	ENST00000356435.5:c.4220G>A	p.Gly1407Glu	p.G1407E	ENST00000356435		1407	gGa/gAa	26/35	0.817425883550913	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.817425883550913	2		351	245	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499700	8499700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	333	523	0	ENST00000356435.5:c.2269G>A	p.Gly757Ser	p.G757S	ENST00000356435		757	Ggt/Agt	14/35	0.817425883550913	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.817425883550913	2		523	394	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517993	8517993	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	236	446	0	ENST00000356435.5:c.1398G>A	p.Trp466Ter	p.W466*	ENST00000356435		466	tgG/tgA	10/35	0.817425883550913	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.817425883550913	2		446	271	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636826	8636826	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1353675904	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	289	479	0	ENST00000356435.5:c.83G>A	p.Arg28Gln	p.R28Q	ENST00000356435		28	cGa/cAa	2/35	0.817425883550913	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.817425883550913	2		479	322	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635199	87635199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	143	476	2	ENST00000277120.3:c.2251G>A	p.Asp751Asn	p.D751N	ENST00000277120		751	Gac/Aac	18/19	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.817425883550913	2		478	334	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606394	93606394	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	195	608	0	ENST00000375746.1:c.214G>C	p.Gly72Arg	p.G72R	ENST00000375746	NM_001174167.1	72	Ggc/Cgc	2/14	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.817425883550913	2		608	407	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038511	47038511	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	314	528	0	ENST00000377604.3:c.673C>T	p.Gln225Ter	p.Q225*	ENST00000377604	NM_001204468.1	225	Cag/Tag	8/24	0.684017964815903	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.817425883550913	4		528	671	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861646	152861646	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0065012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	273	485	0	ENST00000406277.2:c.107-1G>A		p.X36_splice	ENST00000406277	NM_152274.4	36			0.684017964815903		FACETS		0.939	1				CLONAL	2	TRUE	2	0.817425883550913	4		485	612	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0065015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	212	458	0				ENST00000310581	NM_198253.2	-/1132			0.516876345545642	5	FACETS	0.961	0.917	1	0.961	0.917	1	CLONAL	5	TRUE	0	0.516876345545642	5		458	303	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0065015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	100	487	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.877	0.788	0.971	0.877	0.788	0.971	CLONAL	1	TRUE	1	0.516876345545642	2		487	441	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41558779	41558779	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	44	291	0	ENST00000263253.7:c.3724G>C	p.Glu1242Gln	p.E1242Q	ENST00000263253	NM_001429.3	1242	Gaa/Caa	21/31	0.448433023078881	1	FACETS	0.391	0.329	0.459	0.391	0.329	0.459	SUBCLONAL	1	TRUE	0	0.516876345545642	1		291	323	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942739	44942739	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	121	194	0	ENST00000377967.4:c.3320del	p.Pro1107LeufsTer13	p.P1107Lfs*13	ENST00000377967	NM_021140.2	1107	Cct/ct	23/29	1	1	FACETS	0.786	0.728	0.842	1	0.989	1	SUBCLONAL	2	TRUE	0	0.516876345545642	1		194	221	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486842	56486842	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	103	507	0	ENST00000267101.3:c.1256G>C	p.Gly419Ala	p.G419A	ENST00000267101	NM_001982.3	419	gGa/gCa	11/28	1	2	FACETS	0.984	0.887	1	0.984	0.887	1	CLONAL	1	TRUE	1	0.516876345545642	2		507	405	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879854	37879854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	165	727	0	ENST00000269571.5:c.2149G>A	p.Glu717Lys	p.E717K	ENST00000269571		717	Gag/Aag	18/27	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.516876345545642	2		727	450	SUCCESS
ATR	545	MSKCC	GRCh37	3	142241638	142241638	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	118	432	0	ENST00000350721.4:c.4198C>G	p.Leu1400Val	p.L1400V	ENST00000350721	NM_001184.3	1400	Cta/Gta	23/47	1	2	FACETS	0.826	0.748	0.907	0.826	0.748	0.907	CLONAL	1	TRUE	1	0.516876345545642	2		432	553	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37672059	37672059	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs1489040904	NA	P-0065015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	112	376	0	ENST00000447079.4:c.2844C>G	p.Ile948Met	p.I948M	ENST00000447079	NM_015083.1	948	atC/atG	9/14	1	2	FACETS	0.965	0.874	1	0.965	0.874	1	CLONAL	1	TRUE	1	0.516876345545642	2		376	449	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618525	37618525	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	122	643	0	ENST00000447079.4:c.201C>G	p.Ile67Met	p.I67M	ENST00000447079	NM_015083.1	67	atC/atG	1/14	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.516876345545642	2		643	440	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957901	1957901	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	35	421	0	ENST00000382891.5:c.2867G>C	p.Arg956Thr	p.R956T	ENST00000382891	NM_133335.3	956	aGa/aCa	15/22	0.467508251020785	1	FACETS	0.373	0.307	0.447	0.373	0.307	0.447	SUBCLONAL	1	TRUE	0	0.516876345545642	1		421	269	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359956	87359956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137873897	NA	P-0065015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	247	466	0	ENST00000277120.3:c.1264G>A	p.Val422Ile	p.V422I	ENST00000277120		422	Gtc/Atc	11/19	0.516876345545642	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.516876345545642	2		466	451	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531892	41531892	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0065015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	58	393	0	ENST00000263253.7:c.1604C>G	p.Ser535Ter	p.S535*	ENST00000263253	NM_001429.3	535	tCa/tGa	7/31	0.448433023078881	1	FACETS	0.447	0.386	0.514	0.447	0.386	0.514	SUBCLONAL	1	TRUE	0	0.516876345545642	1		393	372	SUCCESS
FH	2271	MSKCC	GRCh37	1	241671932	241671932	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1553341321	NA	P-0065015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	138	382	0	ENST00000366560.3:c.709C>T	p.Gln237Ter	p.Q237*	ENST00000366560	NM_000143.3	237	Cag/Tag	5/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.516876345545642	2		382	411	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981202	201981202	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	116	609	0	ENST00000359651.3:c.281G>C	p.Arg94Pro	p.R94P	ENST00000359651		94	cGa/cCa	2/8	1	2	FACETS	0.957	0.868	1	0.957	0.868	1	CLONAL	1	TRUE	1	0.516876345545642	2		609	469	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074202	8074202	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	146	512	0	ENST00000377482.5:c.457C>G	p.Leu153Val	p.L153V	ENST00000377482	NM_018948.3	153	Ctt/Gtt	4/4	0.423970718908251	3	FACETS	1	0.971	1	0.567	0.519	0.617	CLONAL	1	TRUE	1	0.516876345545642	3		512	627	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056156	27056156	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	190	502	0	ENST00000324856.7:c.1153del	p.Asp385IlefsTer6	p.D385Ifs*6	ENST00000324856	NM_006015.4	384	atG/at	2/20	0.423970718908251	3	FACETS	0.874	0.815	0.935	0.874	0.815	0.935	CLONAL	2	TRUE	1	0.516876345545642	3		502	529	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346912	91346912	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776156059	NA	P-0065015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	47	416	1	ENST00000355112.3:c.3520G>A	p.Gly1174Arg	p.G1174R	ENST00000355112	NM_000057.2	1174	Gga/Aga	18/22	0.516876345545642	1	FACETS	0.335	0.283	0.392	0.335	0.283	0.392	SUBCLONAL	1	TRUE	0	0.516876345545642	1		417	403	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788642	3788642	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	231	406	0	ENST00000262367.5:c.4312C>G	p.His1438Asp	p.H1438D	ENST00000262367	NM_004380.2	1438	Cat/Gat	26/31	0.516876345545642	3	FACETS	0.999	0.939	1	0.999	0.939	1	CLONAL	2	TRUE	1	0.516876345545642	3		406	563	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004682	16004682	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	162	519	0	ENST00000268712.3:c.2572G>T	p.Glu858Ter	p.E858*	ENST00000268712	NM_006311.3	858	Gaa/Taa	20/46	0.516876345545642	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.516876345545642	1		519	351	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646853	37646853	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	96	401	0	ENST00000447079.4:c.1975G>A	p.Glu659Lys	p.E659K	ENST00000447079	NM_015083.1	659	Gaa/Aaa	3/14	1	2	FACETS	0.822	0.736	0.912	0.822	0.736	0.912	CLONAL	1	TRUE	1	0.516876345545642	2		401	452	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780589	56780589	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1411093088	NA	P-0065015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	173	398	0	ENST00000337432.4:c.604G>C	p.Asp202His	p.D202H	ENST00000337432	NM_058216.2	202	Gat/Cat	4/9	0.325800939392761	5	FACETS	0.862	0.796	0.931	0.575	0.531	0.621	CLONAL	2	TRUE	2	0.516876345545642	5		398	689	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424254	47424254	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	195	517	0	ENST00000404338.3:c.2322C>G	p.Ile774Met	p.I774M	ENST00000404338	NM_004491.4	774	atC/atG	1/6	0.149720396226341	3	FACETS	1	0.99	1	0.717	0.667	0.769	INDETERMINATE	1	TRUE	1	0.516876345545642	3		517	662	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262357	46262358	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0065015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	167	469	1	ENST00000371998.3:c.941_942delinsTT	p.Ser314Phe	p.S314F	ENST00000371998		314	tCC/tTT	9/23	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.516876345545642	2		470	604	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272425	21272425	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1397083945	NA	P-0065015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	180	664	0	ENST00000354336.3:c.203A>G	p.Asn68Ser	p.N68S	ENST00000354336	NM_005207.3	68	aAc/aGc	1/3	0.34254847359335	2	FACETS	0.831	0.776	0.887	0.831	0.776	0.887	CLONAL	2	TRUE	0	0.516876345545642	2		664	419	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37622804	37622804	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	27	548	0	ENST00000249071.6:c.488G>A	p.Arg163Lys	p.R163K	ENST00000249071	NM_002872.4	163	aGa/aAa	6/7	0.448433023078881	1	FACETS	0.277	0.22	0.341	0.277	0.22	0.341	SUBCLONAL	1	TRUE	0	0.516876345545642	1		548	280	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295273	1295273	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0065015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	293	638	0				ENST00000310581	NM_198253.2	-/1132			0.516876345545642	5	FACETS	0.984	0.947	1	0.984	0.947	1	CLONAL	5	TRUE	0	0.516876345545642	5		638	409	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821194	32821194	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	166	615	1	ENST00000354258.4:c.400G>A	p.Gly134Arg	p.G134R	ENST00000354258	NM_000593.5	134	Ggg/Agg	1/11	0.487311517051387	2	FACETS	0.83	0.772	0.888	0.83	0.772	0.888	CLONAL	2	TRUE	0	0.516876345545642	2		616	387	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874011	151874011	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	277	477	0	ENST00000262189.6:c.8527G>A	p.Asp2843Asn	p.D2843N	ENST00000262189	NM_170606.2	2843	Gat/Aat	38/59	0.447305301252941	4	FACETS	0.975	0.918	1	0.975	0.918	1	CLONAL	2	TRUE	2	0.516876345545642	4		477	834	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874026	151874026	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	292	482	0	ENST00000262189.6:c.8512G>T	p.Glu2838Ter	p.E2838*	ENST00000262189	NM_170606.2	2838	Gaa/Taa	38/59	0.447305301252941	4	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	2	0.516876345545642	4		482	849	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879574	151879574	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	281	531	0	ENST00000262189.6:c.5371C>T	p.Gln1791Ter	p.Q1791*	ENST00000262189	NM_170606.2	1791	Cag/Tag	36/59	0.447305301252941	4	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	2	0.516876345545642	4		531	818	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90947841	90947841	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0065015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	112	219	0	ENST00000265433.3:c.2235-1G>C		p.X745_splice	ENST00000265433	NM_002485.4	745			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.516876345545642	2		219	324	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781084	135781086	+	frameshift_variant	Frame_Shift_Del	DEL	CAG	CAG	A	novel	NA	P-0065015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	226	492	0	ENST00000298552.3:c.1879_1881delinsT	p.Leu627PhefsTer60	p.L627Ffs*60	ENST00000298552	NM_001162426.1	627	CTG/T	15/23	0.516876345545642	2	FACETS	0.951	0.897	1	0.951	0.897	1	CLONAL	2	TRUE	0	0.516876345545642	2		492	460	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0065016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	75	256	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.149742623352433	3	FACETS	1	0.951	1	0.577	0.508	0.651	INDETERMINATE	1	TRUE	1	0.39	3		256	398	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749987	162749987	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	155	406	0	ENST00000367921.3:c.2519C>T	p.Pro840Leu	p.P840L	ENST00000367921	NM_006182.2	840	cCc/cTc	18/18	0.21679844342632	3	FACETS	1	0.937	1	0.515	0.471	0.56	INDETERMINATE	1	TRUE	1	0.39	3		406	923	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206596	108206596	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	157	341	0	ENST00000278616.4:c.8176G>C	p.Ala2726Pro	p.A2726P	ENST00000278616	NM_000051.3	2726	Gct/Cct	56/63	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.39	2		341	720	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216529	108216530	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0065016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	49	336	0	ENST00000278616.4:c.8480_8481del	p.Phe2827SerfsTer20	p.F2827Sfs*20	ENST00000278616	NM_000051.3	2826	aaTTtt/aatt	58/63	1	2	FACETS	0.42	0.355	0.492	0.42	0.355	0.492	SUBCLONAL	1	TRUE	1	0.39	2		336	598	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913343	NA	P-0065017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	349	463	0	ENST00000269305.4:c.817C>A	p.Arg273Ser	p.R273S	ENST00000269305	NM_001126112.2	273	Cgt/Agt	8/11	0.857158168091925	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.857158168091925	1		463	445	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423532	47423532	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	287	479	0	ENST00000404338.3:c.1600C>T	p.Gln534Ter	p.Q534*	ENST00000404338	NM_004491.4	534	Caa/Taa	1/6	1	2	FACETS	0.979	0.927	1	0.979	0.927	1	CLONAL	1	TRUE	1	0.857158168091925	2		479	684	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077462	30077462	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	271	408	0	ENST00000338641.4:c.1609G>T	p.Glu537Ter	p.E537*	ENST00000338641	NM_000268.3	537	Gag/Tag	15/16	0.857158168091925	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.857158168091925	1		408	344	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41279522	41279522	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	267	413	0	ENST00000349496.5:c.2092C>G	p.Leu698Val	p.L698V	ENST00000349496	NM_001904.3	698	Ctt/Gtt	14/15	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.857158168091925	2		413	593	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221924	98221924	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	279	453	0	ENST00000331920.6:c.2845G>T	p.Val949Phe	p.V949F	ENST00000331920	NM_000264.3	949	Gtc/Ttc	17/24	1	2	FACETS	0.962	0.909	1	0.962	0.909	1	CLONAL	1	TRUE	1	0.857158168091925	2		453	677	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252691	133252691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	38	428	0	ENST00000320574.5:c.1009G>A	p.Glu337Lys	p.E337K	ENST00000320574	NM_006231.2	337	Gaa/Aaa	10/49	1	2	FACETS	0.625	0.516	0.746	0.625	0.516	0.746	SUBCLONAL	1	TRUE	1	0.275204893420658	2		428	442	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857275	9857275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426934537	NA	P-0065018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	80	509	0	ENST00000330684.3:c.4126C>T	p.Arg1376Cys	p.R1376C	ENST00000330684	NM_001134407.1	1376	Cgc/Tgc	13/13	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.275204893420658	2		509	440	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641146	23641146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148026749	NA	P-0065018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	40	478	0	ENST00000261584.4:c.2329G>A	p.Asp777Asn	p.D777N	ENST00000261584	NM_024675.3	777	Gac/Aac	5/13	1	2	FACETS	0.519	0.431	0.618	0.519	0.431	0.618	SUBCLONAL	1	TRUE	1	0.275204893420658	2		478	560	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740804	58740804	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	68	485	0	ENST00000305921.3:c.1709C>A	p.Ser570Ter	p.S570*	ENST00000305921	NM_003620.3	570	tCa/tAa	6/6	1	2	FACETS	0.694	0.603	0.793	0.694	0.603	0.793	SUBCLONAL	1	TRUE	1	0.275204893420658	2		485	712	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775168	73775168	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	72	641	0	ENST00000254810.4:c.88G>T	p.Ala30Ser	p.A30S	ENST00000254810	NM_005324.3	30	Gct/Tct	2/4	1	2	FACETS	0.643	0.561	0.732	0.643	0.561	0.732	SUBCLONAL	1	TRUE	1	0.275204893420658	2		641	814	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210838	36210838	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	36	624	0	ENST00000222270.7:c.589C>T	p.Leu197Phe	p.L197F	ENST00000222270	NM_014727.1	197	Ctc/Ttc	3/37	1	2	FACETS	0.543	0.446	0.652	0.543	0.446	0.652	SUBCLONAL	1	TRUE	1	0.275204893420658	2		624	482	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47503758	47503758	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	153	481	0	ENST00000404338.3:c.4313A>T	p.Asn1438Ile	p.N1438I	ENST00000404338	NM_004491.4	1438	aAt/aTt	6/6	1	2	FACETS	0.89	0.817	0.965	1	0.991	1	CLONAL	2	TRUE	1	0.275204893420658	2		481	625	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497920	25497920	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	163	391	0	ENST00000264709.3:c.529G>A	p.Glu177Lys	p.E177K	ENST00000264709	NM_175629.2	177	Gag/Aag	6/23	0.275204893420658	3	FACETS	0.867	0.801	0.935	1	0.986	1	CLONAL	3	TRUE	1	0.275204893420658	3		391	518	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475496	12475496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457864825	NA	P-0065018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	117	495	0	ENST00000287820.6:c.1370C>T	p.Ser457Leu	p.S457L	ENST00000287820	NM_015869.4	457	tCa/tTa	7/7	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.275204893420658	2		495	570	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946370	2946370	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201877328	NA	P-0065018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	95	487	0	ENST00000396946.4:c.3367G>A	p.Asp1123Asn	p.D1123N	ENST00000396946	NM_032415.4	1123	Gac/Aac	25/25	0.263221823489888	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.275204893420658	1		487	442	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371770	55371770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763824540	NA	P-0065018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	46	588	0	ENST00000297316.4:c.460G>A	p.Gly154Ser	p.G154S	ENST00000297316	NM_022454.3	154	Ggc/Agc	2/2	0.23941631249913	3	FACETS	0.761	0.641	0.893	0.38	0.32	0.447	SUBCLONAL	1	TRUE	1	0.275204893420658	3		588	500	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566340	141566340	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	64	468	1	ENST00000220592.5:c.1072G>A	p.Asp358Asn	p.D358N	ENST00000220592	NM_012154.3	358	Gac/Aac	9/19	0.23941631249913	3	FACETS	0.933	0.809	1	0.467	0.404	0.534	CLONAL	1	TRUE	1	0.275204893420658	3		469	567	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437220	52437234	+	frameshift_variant	Frame_Shift_Del	DEL	GTCCGTGGCTTCCAC	GTCCGTGGCTTCCAC	A	novel	NA	P-0065018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	124	522	0	ENST00000460680.1:c.1810_1824delinsT	p.Val604Ter	p.V604*	ENST00000460680	NM_004656.3	604	GTGGAAGCCACGGAC/T	14/17	0.275204893420658	1	FACETS	0.765	0.696	0.837	1	0.986	1	SUBCLONAL	2	TRUE	0	0.275204893420658	1		522	508	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77070044	77070044	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	223	373	0	ENST00000356341.3:c.496G>T	p.Glu166Ter	p.E166*	ENST00000356341	NM_002576.4	166	Gag/Tag	6/15	0.447751690295713	3	FACETS	0.908	0.85	0.968	0.908	0.85	0.968	CLONAL	2	TRUE	1	0.447751690295713	3		373	671	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427124	49427124	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	245	610	0	ENST00000301067.7:c.11364G>T	p.Gln3788His	p.Q3788H	ENST00000301067	NM_003482.3	3788	caG/caT	39/54	0.447751690295713	3	FACETS	0.857	0.804	0.912	0.857	0.804	0.912	CLONAL	2	TRUE	1	0.447751690295713	3		610	781	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0065019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	352	417	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.447751690295713	3	FACETS	0.962	0.92	1	0.962	0.92	1	CLONAL	3	TRUE	0	0.447751690295713	3		417	667	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872443	136872443	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	130	362	0	ENST00000241393.3:c.1055G>T	p.Ser352Ile	p.S352I	ENST00000241393	NM_003467.2	352	aGc/aTc	2/2	0.322306012899771	2	FACETS	1	0.977	1	0.606	0.553	0.661	CLONAL	1	TRUE	0	0.447751690295713	2		362	479	SUCCESS
ATR	545	MSKCC	GRCh37	3	142218547	142218547	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	100	297	0	ENST00000350721.4:c.5302G>A	p.Asp1768Asn	p.D1768N	ENST00000350721	NM_001184.3	1768	Gat/Aat	31/47	0.447751690295713	6	FACETS	1	0.966	1	0.241	0.215	0.268	CLONAL	1	TRUE	1	0.447751690295713	6		297	704	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163785	32163785	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	118	459	0	ENST00000375023.3:c.5441A>G	p.Asp1814Gly	p.D1814G	ENST00000375023	NM_004557.3	1814	gAt/gGt	30/30	0.373115714139001	3	FACETS	0.703	0.633	0.776	0.351	0.316	0.388	SUBCLONAL	1	TRUE	1	0.447751690295713	3		459	918	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681099	117681099	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	64	408	0	ENST00000368508.3:c.3521T>C	p.Val1174Ala	p.V1174A	ENST00000368508	NM_002944.2	1174	gTt/gCt	23/43	1	2	FACETS	0.557	0.483	0.637	0.557	0.483	0.637	SUBCLONAL	1	TRUE	1	0.447751690295713	2		408	513	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527349	157527349	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	128	382	0	ENST00000346085.5:c.5074A>T	p.Ile1692Phe	p.I1692F	ENST00000346085	NM_020732.3	1692	Att/Ttt	20/20	0.373115714139001	3	FACETS	1	0.983	1	0.674	0.614	0.737	CLONAL	1	TRUE	1	0.447751690295713	3		382	519	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423472	116423472	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	145	358	0	ENST00000397752.3:c.3747G>A	p.Trp1249Ter	p.W1249*	ENST00000397752	NM_000245.2	1249	tgG/tgA	19/21	0.446880237760221	3	FACETS	0.877	0.807	0.949	0.877	0.807	0.949	CLONAL	2	TRUE	1	0.447751690295713	3		358	452	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129954	69129954	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs367978709	NA	P-0065019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	83	447	0	ENST00000288368.4:c.4707+1G>T		p.X1569_splice	ENST00000288368	NM_024870.2	1569			0.447751690295713	4	FACETS	0.626	0.551	0.706	0.156	0.137	0.177	SUBCLONAL	1	TRUE	0	0.447751690295713	4		447	858	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562024	21562024	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065020-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	62	439	0	ENST00000382592.4:c.1895C>G	p.Ala632Gly	p.A632G	ENST00000382592	NM_014572.2	632	gCc/gGc	4/8	1	2	FACETS	0.219	0.189	0.252	0.219	0.189	0.252	SUBCLONAL	1	TRUE	1	0.794763706164614	2		439	712	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27173346	27173346	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065021-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	52	486	0	ENST00000380036.4:c.887T>C	p.Leu296Pro	p.L296P	ENST00000380036	NM_000459.3	296	cTg/cCg	6/23	1	2	FACETS	0.605	0.514	0.704	0.605	0.514	0.704	SUBCLONAL	1	TRUE	1	0.301182754121462	2		486	571	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0065054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	41	624	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	FALSE	1	0.40238513636246	2		625	174	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982331	201982332	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0065054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	107	643	0	ENST00000359651.3:c.715dup	p.Asp239GlyfsTer62	p.D239Gfs*62	ENST00000359651		237	aag/aaGg	6/8	1	2	FACETS	0.935	0.841	1	0.935	0.841	1	CLONAL	1	FALSE	1	0.40238513636246	2		643	569	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681717	30681717	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	105	897	0	ENST00000376406.3:c.380T>G	p.Leu127Arg	p.L127R	ENST00000376406	NM_014641.2	127	cTc/cGc	3/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.40238513636246	2		897	443	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020562	69020562	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	13	472	0	ENST00000288368.4:c.2934G>T	p.Glu978Asp	p.E978D	ENST00000288368	NM_024870.2	978	gaG/gaT	24/40	0.40238513636246	6	FACETS	0.523	0.373	0.706	0.105	0.074	0.142	SUBCLONAL	1	FALSE	1	0.40238513636246	6		472	223	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0065055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	184	766	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.163326087005645	14	FACETS	1	0.958	1			1	CLONAL	11	FALSE	NA	0.163326087005645	14		767	394	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0065055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	8	517	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	0.12112609361405	4	FACETS	0.376	0.241	0.552	0.188	0.12	0.276	SUBCLONAL	1	FALSE	2	0.163326087005645	4		517	303	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0065055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	72	819	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	1	0.931	1	1	0.987	1	CLONAL	3	FALSE	1	0.163326087005645	2		819	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781371	NA	P-0065055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	65	652	0	ENST00000269305.4:c.328C>T	p.Arg110Cys	p.R110C	ENST00000269305	NM_001126112.2	110	Cgt/Tgt	4/11	0.163326087005645	14	FACETS	0.949	0.829	1			1	CLONAL	5	FALSE	NA	0.163326087005645	14		652	332	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544748	65544748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	9	519	0	ENST00000358664.4:c.178C>T	p.Arg60Trp	p.R60W	ENST00000358664	NM_002382.4	60	Cgg/Tgg	4/5	1	2	FACETS	0.565	0.374	0.809	0.565	0.374	0.809	SUBCLONAL	1	FALSE	1	0.163326087005645	2		519	195	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920173	76920173	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	19	409	4	ENST00000373344.5:c.3904del	p.Arg1302GlufsTer44	p.R1302Efs*44	ENST00000373344	NM_000489.3	1302	Aga/ga	11/35	0.163326087005645	1	FACETS	0.848	0.651	1	1	0.925	1	CLONAL	2	FALSE	0	0.163326087005645	1		413	126	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0065057-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	71	773	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	1	2	FACETS	0.891	0.789	0.997	0.891	0.789	0.997	CLONAL	1	TRUE	1	0.696026753758025	2		773	229	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47108609	47108609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0065057-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	69	359	0	ENST00000409792.3:c.6061-1G>A		p.X2021_splice	ENST00000409792	NM_014159.6	2021			0.696026753758025	1	FACETS	0.904	0.812	0.997	0.904	0.812	0.997	CLONAL	1	TRUE	0	0.696026753758025	1		359	143	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571891	64571891	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065057-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	111	566	0	ENST00000312049.6:c.1748C>G	p.Ser583Trp	p.S583W	ENST00000312049	NM_130799.2	583	tCg/tGg	10/10	1	2	FACETS	0.886	0.805	0.97	0.886	0.805	0.97	CLONAL	1	TRUE	1	0.696026753758025	2		566	360	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424703	47424703	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065057-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	169	622	0	ENST00000404338.3:c.2771G>T	p.Cys924Phe	p.C924F	ENST00000404338	NM_004491.4	924	tGt/tTt	1/6	0.218761326001524	4	FACETS	0.865	0.802	0.929	0.865	0.802	0.929	INDETERMINATE	2	TRUE	2	0.696026753758025	4		622	476	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183825	10183825	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1559426115	NA	P-0065057-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	81	544	0	ENST00000256474.2:c.294C>G	p.Tyr98Ter	p.Y98*	ENST00000256474	NM_000551.3	98	taC/taG	1/3	0.696026753758025	1	FACETS	0.803	0.724	0.883	0.803	0.724	0.883	CLONAL	1	TRUE	0	0.696026753758025	1		544	189	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598176	52598176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065057-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	143	456	0	ENST00000394830.3:c.3690del	p.Leu1231PhefsTer13	p.L1231Ffs*13	ENST00000394830	NM_018313.4	1230	ctG/ct	24/30	0.696026753758025	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.696026753758025	1		456	257	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370715	55370715	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479682835	NA	P-0065057-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	90	542	0	ENST00000297316.4:c.17C>T	p.Ala6Val	p.A6V	ENST00000297316	NM_022454.3	6	gCg/gTg	1/2	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.696026753758025	2		542	210	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808641	1808651	+	frameshift_variant	Frame_Shift_Del	DEL	CTTACCGTGAC	CTTACCGTGAC	ACG	novel	NA	P-0065057-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	58	740	2	ENST00000260795.2:c.2254_2264delinsACG	p.Leu752ThrfsTer62	p.L752Tfs*62	ENST00000260795		752	CTTACCGTGACg/ACGg	16/17	0.518752758209511	1	FACETS	0.614	0.537	0.694	0.614	0.537	0.694	SUBCLONAL	1	TRUE	0	0.696026753758025	1		742	177	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0065058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	177	462	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.328600693800444	2	FACETS	0.846	0.785	0.908	0.846	0.785	0.908	CLONAL	2	TRUE	0	0.391112167190155	2		462	535	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115430	115115430	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	223	403	0	ENST00000257566.3:c.896T>C	p.Phe299Ser	p.F299S	ENST00000257566	NM_016569.3	299	tTt/tCt	5/8	0.391112167190155	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	1	0.391112167190155	4		403	478	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630870	67630870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	30	386	0	ENST00000272342.5:c.1056G>A	p.Met352Ile	p.M352I	ENST00000272342	NM_019002.3	352	atG/atA	5/6	0.372602976455001	3	FACETS	0.592	0.478	0.72	0.296	0.239	0.36	SUBCLONAL	1	TRUE	1	0.391112167190155	3		386	310	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952092	76952092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	23	121	0	ENST00000373344.5:c.343G>A	p.Asp115Asn	p.D115N	ENST00000373344	NM_000489.3	115	Gat/Aat	5/35	0.21059604388869	3	FACETS	0.873	0.687	1	0.437	0.343	0.543	INDETERMINATE	1	TRUE	1	0.391112167190155	3		121	161	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913476	NA	P-0065059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	184	422	0	ENST00000358487.5:c.1647T>G	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaG	12/18	1	2	FACETS	0.938	0.877	1	0.938	0.877	1	CLONAL	1	TRUE	1	0.931517458853444	2		422	421	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225886	2225886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	253	692	0	ENST00000326181.6:c.1678G>A	p.Gly560Ser	p.G560S	ENST00000326181	NM_032271.2	560	Ggc/Agc	18/21	1	2	FACETS	0.706	0.663	0.75	0.706	0.663	0.75	SUBCLONAL	1	TRUE	1	0.931517458853444	2		692	769	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348371	89348371	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777979146	NA	P-0065059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	396	720	0	ENST00000301030.4:c.4579G>A	p.Asp1527Asn	p.D1527N	ENST00000301030	NM_001256183.1	1527	Gat/Aat	9/13	0.931517458853444	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.931517458853444	1		720	447	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007645	45007645	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0065059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	539	503	0	ENST00000558401.1:c.92C>G	p.Ser31Ter	p.S31*	ENST00000558401	NM_004048.2	31	tCa/tGa	2/4	0.931517458853444	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.931517458853444	2		503	564	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426040	49426040	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	362	731	0	ENST00000301067.7:c.12448C>T	p.Gln4150Ter	p.Q4150*	ENST00000301067	NM_003482.3	4150	Cag/Tag	39/54	1	2	FACETS	0.981	0.936	1	0.981	0.936	1	CLONAL	1	TRUE	1	0.931517458853444	2		731	792	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222280	2222280	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	338	691	0	ENST00000398665.3:c.3112G>C	p.Glu1038Gln	p.E1038Q	ENST00000398665	NM_032482.2	1038	Gag/Cag	24/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.931517458853444	2		691	725	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117197	7117197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200400127	NA	P-0065059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	317	657	0	ENST00000302850.5:c.4019C>T	p.Ala1340Val	p.A1340V	ENST00000302850	NM_000208.2	1340	gCg/gTg	22/22	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.931517458853444	2		657	670	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439650	220439650	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	31	814	0	ENST00000243786.2:c.503C>G	p.Ser168Cys	p.S168C	ENST00000243786	NM_002191.3	168	tCt/tGt	2/2	0.931517458853444	1	FACETS	0.094	0.075	0.115	0.094	0.075	0.115	SUBCLONAL	1	TRUE	0	0.931517458853444	1		814	379	SUCCESS
REST	5978	MSKCC	GRCh37	4	57797021	57797021	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	384	846	0	ENST00000309042.7:c.1997T>C	p.Leu666Pro	p.L666P	ENST00000309042	NM_005612.4	666	cTg/cCg	4/4	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.931517458853444	2		846	763	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524902	187524902	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	43	652	0	ENST00000441802.2:c.10778C>G	p.Ser3593Cys	p.S3593C	ENST00000441802	NM_005245.3	3593	tCc/tGc	19/27	1	2	FACETS	0.137	0.114	0.163	0.137	0.114	0.163	SUBCLONAL	1	TRUE	1	0.931517458853444	2		652	672	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675558	86675558	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141119571	NA	P-0065059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	88	327	0	ENST00000274376.6:c.2494C>T	p.Pro832Ser	p.P832S	ENST00000274376	NM_002890.2	832	Cca/Tca	19/25	0.931517458853444	3	FACETS	0.893	0.8	0.991	0.447	0.4	0.496	CLONAL	1	TRUE	1	0.931517458853444	3		327	310	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518364	8518364	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	237	527	0	ENST00000356435.5:c.1027T>C	p.Trp343Arg	p.W343R	ENST00000356435		343	Tgg/Cgg	10/35	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.931517458853444	2		527	479	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412337	139412353	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGGAGCCCAGCGTGT	GAAGGAGCCCAGCGTGT	-	novel	NA	P-0065059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	330	662	0	ENST00000277541.6:c.1292_1308del	p.Asn431ArgfsTer75	p.N431Rfs*75	ENST00000277541	NM_017617.3	431	aACACGCTGGGCTCCTTC/a	8/34	1	2	FACETS	0.998	0.95	1	0.998	0.95	1	CLONAL	1	TRUE	1	0.931517458853444	2		662	710	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065060-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	63	789	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.897	0.776	1	0.897	0.776	1	CLONAL	1	TRUE	1	0.251716087769515	2		789	558	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380347	14380347	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065060-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	229	789	0	ENST00000256196.4:c.70G>T	p.Gly24Cys	p.G24C	ENST00000256196		24	Ggc/Tgc	1/6	0.251716087769515	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.251716087769515	3		789	930	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434181	49434181	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065060-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	133	959	0	ENST00000301067.7:c.7372C>T	p.Gln2458Ter	p.Q2458*	ENST00000301067	NM_003482.3	2458	Cag/Tag	31/54	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.251716087769515	2		959	939	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035145	30035145	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065060-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	166	652	0	ENST00000338641.4:c.307G>T	p.Glu103Ter	p.E103*	ENST00000338641	NM_000268.3	103	Gag/Tag	3/16	0.243354447851076	2	FACETS	0.986	0.909	1	0.986	0.909	1	CLONAL	2	TRUE	0	0.251716087769515	2		652	669	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989516	85989517	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065060-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	62	518	0	ENST00000263360.6:c.1276dup	p.Ile426AsnfsTer5	p.I426Nfs*5	ENST00000263360	NM_003797.3	425	-/A	12/12	0.251716087769515	1	FACETS	0.974	0.844	1	0.974	0.844	1	CLONAL	1	TRUE	0	0.251716087769515	1		518	442	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244230	46244230	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0065060-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	87	729	0	ENST00000334344.6:c.2324T>G	p.Leu775Ter	p.L775*	ENST00000334344	NM_152641.2	775	tTa/tGa	15/21	1	2	FACETS	0.808	0.715	0.909	0.808	0.715	0.909	CLONAL	1	TRUE	1	0.251716087769515	2		729	855	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434954	49434954	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065060-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	106	844	0	ENST00000301067.7:c.6599C>G	p.Pro2200Arg	p.P2200R	ENST00000301067	NM_003482.3	2200	cCt/cGt	31/54	1	2	FACETS	0.967	0.866	1	0.967	0.866	1	CLONAL	1	TRUE	1	0.251716087769515	2		844	871	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984488	7984488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065060-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	97	645	0	ENST00000319144.4:c.370G>A	p.Asp124Asn	p.D124N	ENST00000319144	NM_001139.2	124	Gac/Aac	3/15	0.251716087769515	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	0	0.251716087769515	1		645	660	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983957	15983957	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs916142118	NA	P-0065060-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	101	713	0	ENST00000268712.3:c.3262C>G	p.Leu1088Val	p.L1088V	ENST00000268712	NM_006311.3	1088	Ctt/Gtt	24/46	0.251716087769515	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.251716087769515	1		713	667	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690708	33690709	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs746280504	NA	P-0065060-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	90	663	0	ENST00000308377.4:c.118_119del	p.Asp40ProfsTer28	p.D40Pfs*28	ENST00000308377	NM_152270.3	40	GAc/c	2/5	1	2	FACETS	0.848	0.752	0.952	0.848	0.752	0.952	CLONAL	1	TRUE	1	0.251716087769515	2		663	843	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298703	15298703	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065060-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	95	658	1	ENST00000263388.2:c.1595G>T	p.Arg532Leu	p.R532L	ENST00000263388	NM_000435.2	532	cGc/cTc	10/33	1	2	FACETS	0.946	0.842	1	0.946	0.842	1	CLONAL	1	TRUE	1	0.251716087769515	2		659	798	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57470707	57470707	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065060-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	92	543	0	ENST00000371085.3:c.180G>C	p.Met60Ile	p.M60I	ENST00000371085	NM_000516.4	60	atG/atC	2/13	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.251716087769515	2		543	731	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572418	41572441	+	inframe_deletion	In_Frame_Del	DEL	GTCCACCATGTGCATGCTGGTGGA	GTCCACCATGTGCATGCTGGTGGA	-	novel	NA	P-0065060-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	281	955	0	ENST00000263253.7:c.4948_4971del	p.Ser1650_Glu1657del	p.S1650_E1657del	ENST00000263253	NM_001429.3	1649	tgGTCCACCATGTGCATGCTGGTGGAg/tgg	30/31	0.243354447851076	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.251716087769515	2		955	1007	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626634	12626634	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs775817988	NA	P-0065060-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	53	820	0	ENST00000251849.4:c.1655A>G	p.Asn552Ser	p.N552S	ENST00000251849	NM_002880.3	552	aAc/aGc	15/17	1	2	FACETS	0.455	0.386	0.53	0.455	0.386	0.53	SUBCLONAL	1	TRUE	1	0.251716087769515	2		820	926	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131951817	131951818	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065060-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	34	349	0	ENST00000265335.6:c.3163dup	p.Ser1055LysfsTer2	p.S1055Kfs*2	ENST00000265335		1053	-/A	20/25	1	2	FACETS	0.728	0.596	0.877	0.728	0.596	0.877	SUBCLONAL	1	TRUE	1	0.251716087769515	2		349	371	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371668	55371668	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1243637033	NA	P-0065060-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	109	843	0	ENST00000297316.4:c.358G>C	p.Glu120Gln	p.E120Q	ENST00000297316	NM_022454.3	120	Gag/Cag	2/2	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.251716087769515	2		843	820	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065061-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	117	789	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.969	0.886	1	0.969	0.886	1	CLONAL	1	TRUE	1	0.784113477883205	2		789	308	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172373	7172373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065061-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	188	529	0	ENST00000302850.5:c.1196G>A	p.Arg399Gln	p.R399Q	ENST00000302850	NM_000208.2	399	cGa/cAa	5/22	0.784113477883205	3	FACETS	0.868	0.804	0.934	0.434	0.402	0.467	CLONAL	1	TRUE	1	0.784113477883205	3		529	769	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0065061-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	126	237	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.784113477883205	2		237	290	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934413	39934413	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065061-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	197	705	0	ENST00000378444.4:c.186T>G	p.His62Gln	p.H62Q	ENST00000378444	NM_001123385.1	62	caT/caG	4/15	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.784113477883205	2		705	495	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347057	347057	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs773888441	NA	P-0065062-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	75	408	0	ENST00000262320.3:c.1954G>A	p.Gly652Arg	p.G652R	ENST00000262320	NM_003502.3	652	Ggg/Agg	7/11	0.315505076380317	4	FACETS	0.921	0.82	1			1	INDETERMINATE	2	FALSE	NA	0.544351157421925	4		408	231	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218404	1218424	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTCTGTCCCAGGGAAATTCA	TCTCTGTCCCAGGGAAATTCA	-	novel	NA	P-0065062-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	157	452	0	ENST00000326873.7:c.291-12_299del		p.X97_splice	ENST00000326873	NM_000455.4	97		2/10	0.444636249051133	2	FACETS	0.808	0.751	0.865	0.808	0.751	0.865	CLONAL	2	FALSE	0	0.544351157421925	2		452	357	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0065062-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	72	338	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.337722581414587	2		338	330	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219413	1219413	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0065062-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	99	297	0	ENST00000326873.7:c.464+1G>A		p.X155_splice	ENST00000326873	NM_000455.4	155			0.337722581414587	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.337722581414587	1		297	470	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462485	92462485	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065062-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	103	346	0	ENST00000265734.4:c.153G>T	p.Glu51Asp	p.E51D	ENST00000265734	NM_001259.6	51	gaG/gaT	2/8	0.299241703798545	1	FACETS	0.96	0.862	1	0.96	0.862	1	CLONAL	1	TRUE	0	0.337722581414587	1		346	528	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0065099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	173	259	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.833284444552327	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.833284444552327	3		259	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0065099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	190	354	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.833284444552327	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.833284444552327	2		354	227	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0065099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	39	406	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.833284444552327	3	FACETS	0.388	0.322	0.461	0.129	0.107	0.154	SUBCLONAL	1	TRUE	0	0.833284444552327	3		406	342	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175481	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0065099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	109	465	0	ENST00000257430.4:c.4192_4193del	p.Arg1399PhefsTer9	p.R1399Ffs*9	ENST00000257430	NM_000038.5	1397	GAg/g	16/16	0.833284444552327	3	FACETS	0.958	0.867	1	0.479	0.433	0.526	CLONAL	1	TRUE	1	0.833284444552327	3		465	387	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119041	70119041	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0065099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	292	549	0	ENST00000245479.2:c.613A>T	p.Lys205Ter	p.K205*	ENST00000245479	NM_000346.3	205	Aag/Tag	2/3	0.833284444552327	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.833284444552327	3		549	469	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003416	57003416	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	C	C	T	rs987154596	NA	P-0065099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	141	541	0	ENST00000257254.3:c.1063G>A	p.Gly355Ser	p.G355S	ENST00000257254		355	Ggc/Agc	1/2	0.833284444552327	3	FACETS	1	0.971	1	0.561	0.516	0.608	CLONAL	1	TRUE	1	0.833284444552327	3		541	427	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133282	30133282	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	122	551	0	ENST00000263025.4:c.216G>C	p.Lys72Asn	p.K72N	ENST00000263025	NM_002746.2	72	aaG/aaC	2/9	0.833284444552327	3	FACETS	1	0.95	1	0.53	0.484	0.579	CLONAL	1	TRUE	1	0.833284444552327	3		551	391	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248608	212248608	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	143	449	0	ENST00000342788.4:c.3659A>C	p.Glu1220Ala	p.E1220A	ENST00000342788	NM_005235.2	1220	gAg/gCg	28/28	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.833284444552327	2		449	314	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815376	32815376	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	221	433	0	ENST00000354258.4:c.1997A>C	p.Lys666Thr	p.K666T	ENST00000354258	NM_000593.5	666	aAg/aCg	9/11	0.797180433136321	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.833284444552327	4		433	446	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	76	789	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.883	0.783	0.989	0.883	0.783	0.989	CLONAL	1	TRUE	1	0.587220062535361	2		789	293	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	99	342	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.587220062535361	2		342	287	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	124	408	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.204766233897926	3	FACETS	1	0.97	1	0.576	0.524	0.63	INDETERMINATE	1	TRUE	1	0.587220062535361	3		408	474	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204864	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	18	175	0	ENST00000371953.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000371953	NM_000314.4	171	Cag/Tag	6/9	0.587220062535361	1	FACETS	0.177	0.133	0.228	0.177	0.133	0.228	SUBCLONAL	1	TRUE	0	0.587220062535361	1		175	245	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	49	197	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	1	2	FACETS	0.458	0.389	0.534	0.458	0.389	0.534	SUBCLONAL	1	TRUE	1	0.587220062535361	2		197	364	SUCCESS
AR	367	MSKCC	GRCh37	X	66766450	66766450	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	12	150	0	ENST00000374690.3:c.1462C>T	p.Gln488Ter	p.Q488*	ENST00000374690	NM_000044.3	488	Cag/Tag	1/8	1	1	FACETS	0.132	0.093	0.181	0.132	0.093	0.181	SUBCLONAL	1	TRUE	0	0.587220062535361	1		150	218	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022913	27022938	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGCCGCCGCCAGCAGCCTGGGCAA	CCCGCCGCCGCCAGCAGCCTGGGCAA	-	rs797045262	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	62	561	0	ENST00000324856.7:c.31_56del	p.Ser11AlafsTer91	p.S11Afs*91	ENST00000324856	NM_006015.4	7	CCCGCCGCCGCCAGCAGCCTGGGCAAc/c	1/20	1	2	FACETS	0.609	0.529	0.694	0.609	0.529	0.694	SUBCLONAL	1	TRUE	1	0.587220062535361	2		561	347	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478786	56478786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324972550	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	113	209	0	ENST00000267101.3:c.242G>A	p.Arg81Gln	p.R81Q	ENST00000267101	NM_001982.3	81	cGa/cAa	3/28	1	2	FACETS	0.987	0.896	1	0.987	0.896	1	CLONAL	1	TRUE	1	0.587220062535361	2		209	390	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549725	187549725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199516712	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	113	233	0	ENST00000441802.2:c.4516C>T	p.Arg1506Cys	p.R1506C	ENST00000441802	NM_005245.3	1506	Cgt/Tgt	8/27	0.204766233897926	3	FACETS	1	0.944	1	0.531	0.48	0.584	INDETERMINATE	1	TRUE	1	0.587220062535361	3		233	469	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185061	123185061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	44	43	0	ENST00000218089.9:c.1108C>T	p.Arg370Trp	p.R370W	ENST00000218089	NM_001042749.1	370	Cgg/Tgg	12/35	1	1	FACETS	0.666	0.568	0.77	0.666	0.568	0.77	SUBCLONAL	1	TRUE	0	0.587220062535361	1		43	159	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952349	17952349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201387977	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	116	311	0	ENST00000458235.1:c.991G>A	p.Glu331Lys	p.E331K	ENST00000458235	NM_000215.3	331	Gag/Aag	8/24	1	2	FACETS	0.954	0.867	1	0.954	0.867	1	CLONAL	1	TRUE	1	0.587220062535361	2		311	414	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244882	41244882	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	52	241	0	ENST00000357654.3:c.2666C>G	p.Ser889Cys	p.S889C	ENST00000357654	NM_007294.3	889	tCt/tGt	10/23	1	2	FACETS	0.431	0.368	0.5	0.431	0.368	0.5	SUBCLONAL	1	TRUE	1	0.587220062535361	2		241	411	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	12	363	0	ENST00000269571.5:c.829G>T	p.Asp277Tyr	p.D277Y	ENST00000269571		277	Gac/Tac	7/27	1	2	FACETS	0.069	0.048	0.096	0.069	0.048	0.096	SUBCLONAL	1	TRUE	1	0.587220062535361	2		363	591	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114241	115114241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	133	237	0	ENST00000257566.3:c.976G>A	p.Asp326Asn	p.D326N	ENST00000257566	NM_016569.3	326	Gat/Aat	6/8	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.587220062535361	2		237	435	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114679	108114679	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	71	77	2	ENST00000278616.4:c.497-1G>T		p.X166_splice	ENST00000278616	NM_000051.3	166			1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.587220062535361	2		79	228	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306588	41306588	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	107	220	0	ENST00000373198.4:c.1071G>T	p.Glu357Asp	p.E357D	ENST00000373198	NM_133170.3	357	gaG/gaT	7/32	NA	2	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.587220062535361	2		220	331	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134359	2134359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137854065	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	47	396	0	ENST00000219476.3:c.4136C>T	p.Ser1379Leu	p.S1379L	ENST00000219476	NM_000548.3	1379	tCg/tTg	34/42	1	2	FACETS	0.303	0.255	0.356	0.303	0.255	0.356	SUBCLONAL	1	TRUE	1	0.587220062535361	2		396	528	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258779	115258779	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	64	149	0	ENST00000369535.4:c.3G>A	p.Met1?	p.M1?	ENST00000369535	NM_002524.4	1	atG/atA	2/7	1	2	FACETS	0.632	0.55	0.719	0.632	0.55	0.719	SUBCLONAL	1	TRUE	1	0.587220062535361	2		149	345	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171749	36171749	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	61	240	0	ENST00000300305.3:c.816G>T	p.Gln272His	p.Q272H	ENST00000300305		272	caG/caT	7/8	1	2	FACETS	0.557	0.483	0.637	0.557	0.483	0.637	SUBCLONAL	1	TRUE	1	0.587220062535361	2		240	373	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	50	240	0	ENST00000308159.5:c.40G>C	p.Glu14Gln	p.E14Q	ENST00000308159	NM_014669.4	14	Gaa/Caa	2/22	1	2	FACETS	0.542	0.463	0.629	0.542	0.463	0.629	SUBCLONAL	1	TRUE	1	0.587220062535361	2		240	314	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918243	50918243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373650022	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	24	262	0	ENST00000440232.2:c.2560G>A	p.Asp854Asn	p.D854N	ENST00000440232	NM_002691.3	854	Gac/Aac	20/27	1	2	FACETS	0.203	0.158	0.254	0.203	0.158	0.254	SUBCLONAL	1	TRUE	1	0.587220062535361	2		262	403	SUCCESS
APC	324	MSKCC	GRCh37	5	112163655	112163655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	17	203	0	ENST00000257430.4:c.1578G>A	p.Met526Ile	p.M526I	ENST00000257430	NM_000038.5	526	atG/atA	13/16	1	2	FACETS	0.194	0.145	0.253	0.194	0.145	0.253	SUBCLONAL	1	TRUE	1	0.587220062535361	2		203	298	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190666	11190666	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762176419	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	118	351	2	ENST00000361445.4:c.5533G>A	p.Glu1845Lys	p.E1845K	ENST00000361445	NM_004958.3	1845	Gag/Aag	39/58	1	2	FACETS	0.827	0.75	0.907	0.827	0.75	0.907	CLONAL	1	TRUE	1	0.587220062535361	2		353	486	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855787	45855787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	129	342	0	ENST00000391945.4:c.2023G>T	p.Gly675Cys	p.G675C	ENST00000391945	NM_000400.3	675	Ggc/Tgc	21/23	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.587220062535361	2		342	394	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952048	178952048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	120	212	0	ENST00000263967.3:c.3103G>A	p.Ala1035Thr	p.A1035T	ENST00000263967	NM_006218.2	1035	Gct/Act	21/21	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.587220062535361	2		212	397	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42870072	42870072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	101	282	0	ENST00000398585.3:c.100G>A	p.Asp34Asn	p.D34N	ENST00000398585	NM_001135099.1	34	Gat/Aat	2/14	1	2	FACETS	0.615	0.551	0.683	0.615	0.551	0.683	SUBCLONAL	1	TRUE	1	0.587220062535361	2		282	559	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102098217	102098217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	108	174	0	ENST00000282441.5:c.1181G>A	p.Arg394Gln	p.R394Q	ENST00000282441	NM_001130145.2	394	cGa/cAa	8/9	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.587220062535361	2		174	343	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143423	30143423	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	100	262	0	ENST00000389048.3:c.103G>A	p.Gly35Arg	p.G35R	ENST00000389048	NM_004304.4	35	Ggg/Agg	1/29	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.587220062535361	2		262	323	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354253	70354253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1436223575	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	13	127	0	ENST00000374080.3:c.4664C>T	p.Thr1555Met	p.T1555M	ENST00000374080		1555	aCg/aTg	34/45	1	1	FACETS	0.142	0.101	0.192	0.142	0.101	0.192	SUBCLONAL	1	TRUE	0	0.587220062535361	1		127	220	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175942	176175942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs964768927	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	110	295	0	ENST00000367669.3:c.173C>T	p.Ser58Leu	p.S58L	ENST00000367669	NM_022457.5	58	tCg/tTg	1/20	1	2	FACETS	0.958	0.868	1	0.958	0.868	1	CLONAL	1	TRUE	1	0.587220062535361	2		295	391	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1690583	1690583	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	34	271	0	ENST00000378625.1:c.532C>T	p.Gln178Ter	p.Q178*	ENST00000378625	NM_001198994.1	178	Cag/Tag	5/14	1	2	FACETS	0.265	0.216	0.32	0.265	0.216	0.32	SUBCLONAL	1	TRUE	1	0.587220062535361	2		271	437	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1720648	1720648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	105	263	0	ENST00000378609.4:c.760G>A	p.Asp254Asn	p.D254N	ENST00000378609	NM_002074.3	254	Gac/Aac	10/12	1	2	FACETS	0.815	0.734	0.899	0.815	0.734	0.899	CLONAL	1	TRUE	1	0.587220062535361	2		263	439	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1735992	1735992	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	178	231	0	ENST00000378609.4:c.296G>A	p.Trp99Ter	p.W99*	ENST00000378609	NM_002074.3	99	tGg/tAg	7/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.587220062535361	2		231	470	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193193	11193193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	43	248	0	ENST00000361445.4:c.5308C>T	p.Pro1770Ser	p.P1770S	ENST00000361445	NM_004958.3	1770	Ccc/Tcc	38/58	1	2	FACETS	0.376	0.315	0.443	0.376	0.315	0.443	SUBCLONAL	1	TRUE	1	0.587220062535361	2		248	390	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259339	16259339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	26	334	0	ENST00000375759.3:c.6604G>A	p.Asp2202Asn	p.D2202N	ENST00000375759	NM_015001.2	2202	Gac/Aac	11/15	1	2	FACETS	0.172	0.136	0.214	0.172	0.136	0.214	SUBCLONAL	1	TRUE	1	0.587220062535361	2		334	514	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056221	27056227	+	frameshift_variant	Frame_Shift_Del	DEL	GACCTCC	GACCTCC	-	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	158	315	0	ENST00000324856.7:c.1218_1224del	p.Pro407GlnfsTer24	p.P407Qfs*24	ENST00000324856	NM_006015.4	406	gGACCTCCg/gg	2/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.587220062535361	2		315	506	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087548	27087548	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	48	328	0	ENST00000324856.7:c.2122C>G	p.Gln708Glu	p.Q708E	ENST00000324856	NM_006015.4	708	Cag/Gag	5/20	1	2	FACETS	0.365	0.309	0.427	0.365	0.309	0.427	SUBCLONAL	1	TRUE	1	0.587220062535361	2		328	448	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247943	59247943	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	146	374	0	ENST00000371222.2:c.800C>T	p.Ser267Phe	p.S267F	ENST00000371222	NM_002228.3	267	tCc/tTc	1/1	1	2	FACETS	0.936	0.86	1	0.936	0.86	1	CLONAL	1	TRUE	1	0.587220062535361	2		374	531	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737083	162737083	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	68	240	0	ENST00000367921.3:c.1227C>G	p.Ile409Met	p.I409M	ENST00000367921	NM_006182.2	409	atC/atG	11/18	1	2	FACETS	0.491	0.428	0.558	0.491	0.428	0.558	SUBCLONAL	1	TRUE	1	0.587220062535361	2		240	472	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651582	206651582	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	122	328	0	ENST00000367120.3:c.892T>C	p.Phe298Leu	p.F298L	ENST00000367120	NM_014002.3	298	Ttc/Ctc	9/22	1	2	FACETS	0.962	0.876	1	0.962	0.876	1	CLONAL	1	TRUE	1	0.587220062535361	2		328	432	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653813	89653839	+	inframe_deletion	In_Frame_Del	DEL	TCCTGCAGAAAGACTTGAAGGCGTATA	TCCTGCAGAAAGACTTGAAGGCGTATA	-	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	67	106	0	ENST00000371953.3:c.111_137del	p.Pro38_Tyr46del	p.P38_Y46del	ENST00000371953	NM_000314.4	37	ttTCCTGCAGAAAGACTTGAAGGCGTATAc/ttc	2/9	0.587220062535361	1	FACETS	0.698	0.615	0.785	0.698	0.615	0.785	SUBCLONAL	1	TRUE	0	0.587220062535361	1		106	231	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112745496	112745496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	15	162	1	ENST00000369452.4:c.814G>A	p.Glu272Lys	p.E272K	ENST00000369452	NM_007373.3	272	Gaa/Aaa	3/9	0.587220062535361	1	FACETS	0.158	0.115	0.209	0.158	0.115	0.209	SUBCLONAL	1	TRUE	0	0.587220062535361	1		163	229	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377148	118377148	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	32	344	0	ENST00000534358.1:c.10541C>G	p.Ser3514Cys	p.S3514C	ENST00000534358	NM_005933.3	3514	tCt/tGt	27/36	1	2	FACETS	0.218	0.177	0.266	0.218	0.177	0.266	SUBCLONAL	1	TRUE	1	0.587220062535361	2		344	499	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392649	118392649	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	22	276	0	ENST00000534358.1:c.11681A>T	p.Glu3894Val	p.E3894V	ENST00000534358	NM_005933.3	3894	gAg/gTg	36/36	1	2	FACETS	0.181	0.139	0.229	0.181	0.139	0.229	SUBCLONAL	1	TRUE	1	0.587220062535361	2		276	415	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416880	416880	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	129	312	0	ENST00000399788.2:c.3670G>C	p.Glu1224Gln	p.E1224Q	ENST00000399788	NM_001042603.1	1224	Gag/Cag	23/28	1	2	FACETS	0.953	0.87	1	0.953	0.87	1	CLONAL	1	TRUE	1	0.587220062535361	2		312	461	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416945	416945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	143	284	0	ENST00000399788.2:c.3605G>A	p.Ser1202Asn	p.S1202N	ENST00000399788	NM_001042603.1	1202	aGc/aAc	23/28	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.587220062535361	2		284	444	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416951	416951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	150	288	0	ENST00000399788.2:c.3599G>A	p.Gly1200Glu	p.G1200E	ENST00000399788	NM_001042603.1	1200	gGa/gAa	23/28	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.587220062535361	2		288	460	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	440990	440990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	54	239	0	ENST00000399788.2:c.1768G>A	p.Asp590Asn	p.D590N	ENST00000399788	NM_001042603.1	590	Gac/Aac	13/28	1	2	FACETS	0.456	0.391	0.528	0.456	0.391	0.528	SUBCLONAL	1	TRUE	1	0.587220062535361	2		239	403	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552592	18552592	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	76	189	0	ENST00000266497.5:c.2004-1G>A		p.X668_splice	ENST00000266497		668			1	2	FACETS	0.685	0.604	0.77	0.685	0.604	0.77	SUBCLONAL	1	TRUE	1	0.587220062535361	2		189	378	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432435	49432435	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	26	317	0	ENST00000301067.7:c.8704C>G	p.Gln2902Glu	p.Q2902E	ENST00000301067	NM_003482.3	2902	Cag/Gag	34/54	1	2	FACETS	0.172	0.135	0.214	0.172	0.135	0.214	SUBCLONAL	1	TRUE	1	0.587220062535361	2		317	515	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623662	28623662	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	79	209	0	ENST00000241453.7:c.895G>C	p.Glu299Gln	p.E299Q	ENST00000241453	NM_004119.2	299	Gag/Cag	8/24	1	2	FACETS	0.775	0.687	0.869	0.775	0.687	0.869	SUBCLONAL	1	TRUE	1	0.587220062535361	2		209	347	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988478	41988478	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	76	233	0	ENST00000219905.7:c.1270G>A	p.Glu424Lys	p.E424K	ENST00000219905	NM_001164273.1	424	Gag/Aag	3/24	1	2	FACETS	0.56	0.493	0.632	0.56	0.493	0.632	SUBCLONAL	1	TRUE	1	0.587220062535361	2		233	462	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988923	41988923	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	28	214	0	ENST00000219905.7:c.1715C>G	p.Ser572Ter	p.S572*	ENST00000219905	NM_001164273.1	572	tCa/tGa	3/24	1	2	FACETS	0.196	0.156	0.242	0.196	0.156	0.242	SUBCLONAL	1	TRUE	1	0.587220062535361	2		214	486	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51529083	51529083	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	112	222	0	ENST00000260433.2:c.269C>T	p.Ser90Phe	p.S90F	ENST00000260433		90	tCt/tTt	3/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.587220062535361	2		222	325	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459957	99459957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	20	245	0	ENST00000268035.6:c.2053G>A	p.Glu685Lys	p.E685K	ENST00000268035	NM_000875.3	685	Gag/Aag	10/21	1	2	FACETS	0.173	0.132	0.221	0.173	0.132	0.221	SUBCLONAL	1	TRUE	1	0.587220062535361	2		245	394	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56872905	56872905	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	102	182	0	ENST00000308159.5:c.2060C>T	p.Ser687Phe	p.S687F	ENST00000308159	NM_014669.4	687	tCc/tTc	19/22	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.587220062535361	2		182	334	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845824	72845824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	142	304	0	ENST00000268489.5:c.3643G>A	p.Glu1215Lys	p.E1215K	ENST00000268489	NM_006885.3	1215	Gag/Aag	6/10	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.587220062535361	2		304	469	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990302	81990302	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs201682723	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	39	252	0	ENST00000359376.3:c.3573G>C	p.Glu1191Asp	p.E1191D	ENST00000359376	NM_002661.3	1191	gaG/gaC	32/33	1	2	FACETS	0.333	0.276	0.396	0.333	0.276	0.396	SUBCLONAL	1	TRUE	1	0.587220062535361	2		252	399	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214658	5214658	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	27	327	0	ENST00000357368.4:c.4408G>A	p.Glu1470Lys	p.E1470K	ENST00000357368	NM_002850.3	1470	Gag/Aag	29/38	1	2	FACETS	0.195	0.155	0.242	0.195	0.155	0.242	SUBCLONAL	1	TRUE	1	0.587220062535361	2		327	471	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139651	202139651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	49	234	0	ENST00000358485.4:c.812C>T	p.Pro271Leu	p.P271L	ENST00000358485	NM_001080125.1	271	cCa/cTa	6/9	0.251392164188777	1	FACETS	0.316	0.268	0.368	0.316	0.268	0.368	INDETERMINATE	1	TRUE	0	0.587220062535361	1		234	373	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387119	31387119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	131	268	0	ENST00000328111.2:c.1744G>A	p.Asp582Asn	p.D582N	ENST00000328111	NM_006892.3	582	Gat/Aat	16/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.587220062535361	2		268	378	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548014	41548014	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	28	236	0	ENST00000263253.7:c.2995G>A	p.Glu999Lys	p.E999K	ENST00000263253	NM_001429.3	999	Gag/Aag	15/31	1	2	FACETS	0.24	0.191	0.295	0.24	0.191	0.295	SUBCLONAL	1	TRUE	1	0.587220062535361	2		236	398	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574921	41574921	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs780017165	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	137	290	0	ENST00000263253.7:c.7206G>C	p.Leu2402Phe	p.L2402F	ENST00000263253	NM_001429.3	2402	ttG/ttC	31/31	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.587220062535361	2		290	461	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49941018	49941018	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	133	394	0	ENST00000296474.3:c.25C>T	p.Gln9Ter	p.Q9*	ENST00000296474	NM_002447.2	9	Cag/Tag	1/20	1	2	FACETS	0.97	0.887	1	0.97	0.887	1	CLONAL	1	TRUE	1	0.587220062535361	2		394	467	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205834	128205855	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTGCGCCATCCAGCGCGGCT	GGGTGCGCCATCCAGCGCGGCT	-	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	100	280	0	ENST00000341105.2:c.20_41del	p.Gln7ArgfsTer4	p.Q7Rfs*4	ENST00000341105	NM_032638.4	7	cAGCCGCGCTGGATGGCGCACCCg/cg	2/6	1	2	FACETS	0.86	0.774	0.95	0.86	0.774	0.95	CLONAL	1	TRUE	1	0.587220062535361	2		280	396	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157156	106157156	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	30	274	0	ENST00000380013.4:c.2057G>C	p.Arg686Thr	p.R686T	ENST00000380013	NM_001127208.2	686	aGa/aCa	3/11	0.222375537754971	2	FACETS	0.22	0.176	0.269	0.11	0.088	0.135	INDETERMINATE	1	TRUE	0	0.587220062535361	2		274	465	SUCCESS
APC	324	MSKCC	GRCh37	5	112179206	112179206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	133	208	0	ENST00000257430.4:c.7915G>A	p.Glu2639Lys	p.E2639K	ENST00000257430	NM_000038.5	2639	Gaa/Aaa	16/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.587220062535361	2		208	417	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915031	131915035	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTC	AGCTC	-	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	88	143	0	ENST00000265335.6:c.388_392del	p.Ser130Ter	p.S130*	ENST00000265335		130	AGCTCt/t	4/25	1	2	FACETS	0.964	0.863	1	0.964	0.863	1	CLONAL	1	TRUE	1	0.587220062535361	2		143	311	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518076	176518076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	148	309	0	ENST00000292408.4:c.574C>T	p.His192Tyr	p.H192Y	ENST00000292408	NM_213647.1	192	Cat/Tat	5/18	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.587220062535361	2		309	464	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956640	93956640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	121	274	0	ENST00000369303.4:c.2596C>T	p.His866Tyr	p.H866Y	ENST00000369303	NM_004440.3	866	Cac/Tac	15/17	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.587220062535361	2		274	405	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332003	81332003	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	115	210	0	ENST00000222390.5:c.2081G>T	p.Gly694Val	p.G694V	ENST00000222390	NM_000601.4	694	gGt/gTt	18/18	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.587220062535361	2		210	355	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56860268	56860268	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs149135061	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	20	203	0	ENST00000519728.1:c.270G>T	p.Met90Ile	p.M90I	ENST00000519728	NM_002350.3	90	atG/atT	4/13	1	2	FACETS	0.228	0.174	0.291	0.228	0.174	0.291	SUBCLONAL	1	TRUE	1	0.587220062535361	2		203	299	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74868196	74868196	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	41	71	0	ENST00000284811.8:c.98G>C	p.Arg33Thr	p.R33T	ENST00000284811		33	aGa/aCa	3/4	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.587220062535361	2		71	135	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864111	97864130	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TTATCTCAGCAGTGTGAGCC	TTATCTCAGCAGTGTGAGCC	-	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	94	236	0	ENST00000289081.3:c.1536_1555del	p.Met512IlefsTer9	p.M512Ifs*9	ENST00000289081	NM_000136.2	512	atGGCTCACACTGCTGAGATAAct/atct	15/15	1	2	FACETS	0.811	0.726	0.899	0.811	0.726	0.899	CLONAL	1	TRUE	1	0.587220062535361	2		236	395	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413916	139413916	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	87	294	0	ENST00000277541.6:c.844C>G	p.Arg282Gly	p.R282G	ENST00000277541	NM_017617.3	282	Cgc/Ggc	5/34	1	2	FACETS	0.658	0.585	0.736	0.658	0.585	0.736	SUBCLONAL	1	TRUE	1	0.587220062535361	2		294	450	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922915	44922915	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	157	431	0	ENST00000377967.4:c.1776G>C	p.Leu592Phe	p.L592F	ENST00000377967	NM_021140.2	592	ttG/ttC	16/29	1	1	FACETS	0.758	0.714	0.802	1	0.992	1	SUBCLONAL	2	TRUE	0	0.587220062535361	1		431	249	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195692	123195692	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	14	65	0	ENST00000218089.9:c.1606C>T	p.His536Tyr	p.H536Y	ENST00000218089	NM_001042749.1	536	Cat/Tat	17/35	1	1	FACETS	0.226	0.164	0.3	0.226	0.164	0.3	SUBCLONAL	1	TRUE	0	0.587220062535361	1		65	149	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0065101-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	18	342	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.668	0.506	0.857	0.668	0.506	0.857	SUBCLONAL	1	TRUE	1	0.318912165970226	2		342	169	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0065101-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	20	390	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.302582720019015	1	FACETS	0.297	0.227	0.38	0.297	0.227	0.38	SUBCLONAL	1	TRUE	0	0.318912165970226	1		390	355	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579400	7579400	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065101-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	167	339	0	ENST00000269305.4:c.287del	p.Ser96LeufsTer27	p.S96Lfs*27	ENST00000269305	NM_001126112.2	96	tCt/tt	4/11	0.17076975422152	2	FACETS	1	0.977	1	0.584	0.537	0.634	INDETERMINATE	1	TRUE	0	0.318912165970226	2		339	896	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540654	NA	P-0065101-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	146	320	0	ENST00000269305.4:c.329G>A	p.Arg110His	p.R110H	ENST00000269305	NM_001126112.2	110	cGt/cAt	4/11	0.17076975422152	2	FACETS	1	0.977	1	0.597	0.545	0.651	INDETERMINATE	1	TRUE	0	0.318912165970226	2		320	767	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944160	71944160	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201836862	NA	P-0065101-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	77	367	0	ENST00000298229.2:c.1993C>T	p.Arg665Trp	p.R665W	ENST00000298229	NM_001567.3	665	Cgg/Tgg	17/28	1	2	FACETS	0.609	0.534	0.69	0.609	0.534	0.69	SUBCLONAL	1	TRUE	1	0.318912165970226	2		367	793	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105745	27105745	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065101-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	58	318	0	ENST00000324856.7:c.5356G>T	p.Glu1786Ter	p.E1786*	ENST00000324856	NM_006015.4	1786	Gag/Tag	20/20	1	2	FACETS	0.852	0.734	0.98	0.852	0.734	0.98	CLONAL	1	TRUE	1	0.318912165970226	2		318	427	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047135	77047135	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065101-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	56	258	0	ENST00000356341.3:c.1409T>C	p.Leu470Pro	p.L470P	ENST00000356341	NM_002576.4	470	cTg/cCg	13/15	1	2	FACETS	0.759	0.651	0.876	0.759	0.651	0.876	SUBCLONAL	1	TRUE	1	0.318912165970226	2		258	463	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912225	32912225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065102-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	45	220	0	ENST00000380152.3:c.3733G>A	p.Glu1245Lys	p.E1245K	ENST00000380152		1245	Gag/Aag	11/27	1	2	FACETS	0.706	0.595	0.828	0.706	0.595	0.828	SUBCLONAL	1	TRUE	1	0.342711583259423	2		220	372	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	78128725	78128725	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065102-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	92	383	0	ENST00000361507.4:c.42del	p.Lys15AsnfsTer8	p.K15Nfs*8	ENST00000361507	NM_080491.2	14	agG/ag	1/10	1	2	FACETS	0.862	0.767	0.963	0.862	0.767	0.963	CLONAL	1	TRUE	1	0.342711583259423	2		383	623	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093443	30093443	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065102-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	31	142	0	ENST00000331968.5:c.1820G>C	p.Arg607Thr	p.R607T	ENST00000331968	NM_002742.2	607	aGa/aCa	13/18	1	2	FACETS	0.887	0.723	1	0.887	0.723	1	CLONAL	1	TRUE	1	0.342711583259423	2		142	204	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0065104-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	10	349	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			1	2	FACETS	0.234	0.158	0.331	0.234	0.158	0.331	SUBCLONAL	1	TRUE	1	0.2	2		349	427	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809519	36809519	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065104-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	23	337	0	ENST00000373129.3:c.946C>G	p.Gln316Glu	p.Q316E	ENST00000373129	NM_032017.1	316	Cag/Gag	10/12	1	2	FACETS	0.68	0.53	0.854	0.68	0.53	0.854	SUBCLONAL	1	TRUE	1	0.2	2		337	338	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143993	11143993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568509370	NA	P-0065106-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	148	357	0	ENST00000358026.2:c.3574C>T	p.Arg1192Cys	p.R1192C	ENST00000358026	NM_001128849.1	1192	Cgc/Tgc	26/36	1	2	FACETS	0.943	0.865	1	0.943	0.865	1	CLONAL	1	TRUE	1	0.55	2		357	571	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497805	120497805	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0065106-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	175	363	0	ENST00000256646.2:c.2077A>T	p.Lys693Ter	p.K693*	ENST00000256646	NM_024408.3	693	Aag/Tag	13/34	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.55	2		363	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0065110-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	363	661	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.73091089808931	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.73091089808931	1		661	611	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030478	49030479	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1566234123	NA	P-0065110-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	207	392	0	ENST00000267163.4:c.1959dup	p.Val654SerfsTer14	p.V654Sfs*14	ENST00000267163	NM_000321.2	651	-/A	19/27	0.73091089808931	1	FACETS	0.915	0.862	0.966	0.915	0.862	0.966	CLONAL	1	TRUE	0	0.73091089808931	1		392	393	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786802	3786802	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs797044860	NA	P-0065110-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	226	492	0	ENST00000262367.5:c.4409A>G	p.His1470Arg	p.H1470R	ENST00000262367	NM_004380.2	1470	cAc/cGc	27/31	1	2	FACETS	0.887	0.83	0.945	0.887	0.83	0.945	CLONAL	1	TRUE	1	0.73091089808931	2		492	697	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607467	46607467	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065110-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	391	597	2	ENST00000263734.3:c.1656G>T	p.Leu552Phe	p.L552F	ENST00000263734	NM_001430.4	552	ttG/ttT	12/16	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.73091089808931	2		599	970	SUCCESS
ALB	213	MSKCC	GRCh37	4	74276072	74276073	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0065110-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	222	379	0	ENST00000295897.4:c.662_663del	p.Arg221ThrfsTer30	p.R221Tfs*30	ENST00000295897	NM_000477.5	220	cAG/c	6/15	1	2	FACETS	0.972	0.91	1	0.972	0.91	1	CLONAL	1	TRUE	1	0.73091089808931	2		379	625	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588168	67588168	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065110-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	253	442	0	ENST00000274335.5:c.998G>T	p.Trp333Leu	p.W333L	ENST00000274335		333	tGg/tTg	7/15	0.73091089808931	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.73091089808931	1		442	431	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348198	70348199	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0065110-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	381	282	1	ENST00000374080.3:c.3262_3263del	p.Leu1088GlufsTer9	p.L1088Efs*9	ENST00000374080		1088	CTg/g	23/45	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.73091089808931	1		283	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0065111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	49	534	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.466	0.393	0.546	0.466	0.393	0.546	SUBCLONAL	1	TRUE	1	0.27	2		534	779	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510730	120510730	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	66	538	0	ENST00000256646.2:c.1234T>G	p.Cys412Gly	p.C412G	ENST00000256646	NM_024408.3	412	Tgc/Ggc	7/34	1	2	FACETS	0.645	0.559	0.739	0.645	0.559	0.739	SUBCLONAL	1	TRUE	1	0.27	2		538	758	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156646	2156646	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	74	615	0	ENST00000434045.2:c.276G>T	p.Glu92Asp	p.E92D	ENST00000434045	NM_001127598.1	92	gaG/gaT	3/5	1	2	FACETS	0.613	0.535	0.697	0.613	0.535	0.697	SUBCLONAL	1	TRUE	1	0.27	2		615	894	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4388046	4388046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1488421614	NA	P-0065111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	74	544	0	ENST00000261254.3:c.532C>T	p.Arg178Cys	p.R178C	ENST00000261254	NM_001759.3	178	Cgc/Tgc	3/5	1	2	FACETS	0.732	0.64	0.831	0.732	0.64	0.831	SUBCLONAL	1	TRUE	1	0.27	2		544	749	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144445	58144445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754423955	NA	P-0065111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	38	256	0	ENST00000257904.6:c.626G>A	p.Arg209His	p.R209H	ENST00000257904	NM_000075.3	209	cGt/cAt	5/8	1	2	FACETS	0.394	0.324	0.472	0.394	0.324	0.472	SUBCLONAL	1	TRUE	1	0.27	2		256	715	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953760	48953760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913302	NA	P-0065111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	30	250	0	ENST00000267163.4:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000267163	NM_000321.2	455	Cga/Tga	14/27	1	2	FACETS	0.648	0.523	0.79	0.648	0.523	0.79	SUBCLONAL	1	TRUE	1	0.27	2		250	343	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039374	49039374	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853293	NA	P-0065111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	35	469	0	ENST00000267163.4:c.2359C>T	p.Arg787Ter	p.R787*	ENST00000267163	NM_000321.2	787	Cga/Tga	23/27	1	2	FACETS	0.367	0.3	0.443	0.367	0.3	0.443	SUBCLONAL	1	TRUE	1	0.27	2		469	706	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779750	3779751	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCCTGGGG	novel	NA	P-0065111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	49	560	0	ENST00000262367.5:c.5290_5297dup	p.Glu1766AspfsTer8	p.E1766Dfs*8	ENST00000262367	NM_004380.2	1766	gag/gaCCCCAGGAg	31/31	1	2	FACETS	0.472	0.399	0.553	0.472	0.399	0.553	SUBCLONAL	1	TRUE	1	0.27	2		560	769	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905736	50905736	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571623032	NA	P-0065111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	51	700	0	ENST00000440232.2:c.784G>A	p.Gly262Ser	p.G262S	ENST00000440232	NM_002691.3	262	Ggc/Agc	7/27	1	2	FACETS	0.429	0.364	0.502	0.429	0.364	0.502	SUBCLONAL	1	TRUE	1	0.27	2		700	880	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681600	30681600	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	42	557	0	ENST00000376406.3:c.497A>T	p.Glu166Val	p.E166V	ENST00000376406	NM_014641.2	166	gAg/gTg	3/15	1	2	FACETS	0.376	0.312	0.446	0.376	0.312	0.446	SUBCLONAL	1	TRUE	1	0.27	2		557	828	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953019	2953019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750407488	NA	P-0065111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	62	494	1	ENST00000396946.4:c.2921G>A	p.Arg974His	p.R974H	ENST00000396946	NM_032415.4	974	cGc/cAc	22/25	1	2	FACETS	0.64	0.552	0.735	0.64	0.552	0.735	SUBCLONAL	1	TRUE	1	0.27	2		495	718	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414397	6414397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	22	351	0	ENST00000356142.4:c.31G>A	p.Asp11Asn	p.D11N	ENST00000356142	NM_018890.3	11	Gac/Aac	1/7	1	2	FACETS	0.375	0.289	0.474	0.375	0.289	0.474	SUBCLONAL	1	TRUE	1	0.27	2		351	435	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56859043	56859043	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	38	316	0	ENST00000519728.1:c.169C>G	p.Gln57Glu	p.Q57E	ENST00000519728	NM_002350.3	57	Caa/Gaa	3/13	0.113330215756576	3	FACETS	0.556	0.458	0.665	0.278	0.229	0.333	INDETERMINATE	1	TRUE	1	0.27	3		316	575	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390716	139390717	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0065111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	59	732	0	ENST00000277541.6:c.7474_7475del	p.Ser2492AlafsTer14	p.S2492Afs*14	ENST00000277541	NM_017617.3	2492	TCg/g	34/34	1	2	FACETS	0.416	0.356	0.481	0.416	0.356	0.481	SUBCLONAL	1	TRUE	1	0.27	2		732	1051	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403423	139403423	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	61	564	0	ENST00000277541.6:c.3070G>A	p.Glu1024Lys	p.E1024K	ENST00000277541	NM_017617.3	1024	Gag/Aag	19/34	1	2	FACETS	0.534	0.459	0.616	0.534	0.459	0.616	SUBCLONAL	1	TRUE	1	0.27	2		564	846	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0065113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	22	256	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.711434929159918	3	FACETS	0.838	0.662	1	0.419	0.331	0.517	CLONAL	1	TRUE	1	0.711434929159918	3		256	100	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0065113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	333	576	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.954	0.904	1	0.954	0.904	1	CLONAL	1	TRUE	1	0.711434929159918	2		576	981	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546725	9546725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210292896	NA	P-0065113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	297	649	0	ENST00000353224.5:c.1297C>T	p.Arg433Trp	p.R433W	ENST00000353224	NM_177990.2	433	Cgg/Tgg	5/10	0.711434929159918	3	FACETS	0.933	0.878	0.99	0.467	0.439	0.495	CLONAL	1	TRUE	1	0.711434929159918	3		649	1213	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965581	15965581	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746171790	NA	P-0065113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	249	491	0	ENST00000268712.3:c.5225C>T	p.Ser1742Leu	p.S1742L	ENST00000268712	NM_006311.3	1742	tCa/tTa	36/46	1	2	FACETS	0.96	0.902	1	0.96	0.902	1	CLONAL	1	TRUE	1	0.711434929159918	2		491	729	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780172	9780172	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	123	580	0	ENST00000377346.4:c.1342G>A	p.Glu448Lys	p.E448K	ENST00000377346	NM_005026.3	448	Gag/Aag	11/24	1	2	FACETS	0.384	0.347	0.424	0.384	0.347	0.424	SUBCLONAL	1	TRUE	1	0.711434929159918	2		580	900	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845798	151845798	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	241	550	0	ENST00000262189.6:c.13214G>C	p.Cys4405Ser	p.C4405S	ENST00000262189	NM_170606.2	4405	tGt/tCt	52/59	0.711434929159918	1	FACETS	0.968	0.917	1	0.968	0.917	1	CLONAL	1	TRUE	0	0.711434929159918	1		550	451	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829029	72829029	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	336	696	0	ENST00000268489.5:c.7552C>T	p.Gln2518Ter	p.Q2518*	ENST00000268489	NM_006885.3	2518	Caa/Taa	9/10	1	2	FACETS	0.982	0.931	1	0.982	0.931	1	CLONAL	1	TRUE	1	0.711434929159918	2		696	962	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929245	44929245	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	149	535	0	ENST00000377967.4:c.2345C>T	p.Ala782Val	p.A782V	ENST00000377967	NM_021140.2	782	gCc/gTc	17/29	0.4237965888928	1	FACETS	0.426	0.391	0.463	0.426	0.391	0.463	INDETERMINATE	1	TRUE	0	0.711434929159918	1		535	633	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10785223	10785223	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	75	515	0	ENST00000361367.2:c.991C>G	p.Gln331Glu	p.Q331E	ENST00000361367	NM_014633.3	331	Caa/Gaa	9/25	1	2	FACETS	0.79	0.7	0.883	0.79	0.7	0.883	SUBCLONAL	1	TRUE	1	0.711434929159918	2		515	267	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022958	33022958	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	210	496	0	ENST00000300177.4:c.67G>A	p.Glu23Lys	p.E23K	ENST00000300177	NM_001191322.1	23	Gaa/Aaa	2/2	1	2	FACETS	0.876	0.817	0.936	0.876	0.817	0.936	CLONAL	1	TRUE	1	0.711434929159918	2		496	674	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740881	58740881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs541664685	NA	P-0065113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	191	458	0	ENST00000305921.3:c.1786C>T	p.His596Tyr	p.H596Y	ENST00000305921	NM_003620.3	596	Cat/Tat	6/6	0.711434929159918	2	FACETS	0.934	0.869	1	0.467	0.434	0.5	CLONAL	1	TRUE	0	0.711434929159918	2		458	575	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222467	39222467	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	98	477	0	ENST00000402219.2:c.3143G>T	p.Gly1048Val	p.G1048V	ENST00000402219	NM_005633.3	1048	gGt/gTt	20/23	1	2	FACETS	0.39	0.347	0.435	0.39	0.347	0.435	SUBCLONAL	1	TRUE	1	0.711434929159918	2		477	707	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326798	62326798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	355	679	0	ENST00000360203.5:c.3617C>T	p.Ser1206Leu	p.S1206L	ENST00000360203	NM_001283009.1	1206	tCa/tTa	34/35	0.711434929159918	3	FACETS	0.966	0.914	1	0.483	0.457	0.51	CLONAL	1	TRUE	1	0.711434929159918	3		679	1401	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934969	49934969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377444651	NA	P-0065113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	333	725	0	ENST00000296474.3:c.2030G>A	p.Arg677Lys	p.R677K	ENST00000296474	NM_002447.2	677	aGa/aAa	6/20	1	2	FACETS	0.98	0.929	1	0.98	0.929	1	CLONAL	1	TRUE	1	0.711434929159918	2		725	955	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643408	52643408	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	66	470	0	ENST00000394830.3:c.2488G>C	p.Glu830Gln	p.E830Q	ENST00000394830	NM_018313.4	830	Gaa/Caa	17/30	1	2	FACETS	0.406	0.353	0.463	0.406	0.353	0.463	SUBCLONAL	1	TRUE	1	0.711434929159918	2		470	457	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456713	138456713	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	88	402	0	ENST00000289153.2:c.637C>G	p.Gln213Glu	p.Q213E	ENST00000289153	NM_006219.2	213	Caa/Gaa	4/22	0.711434929159918	3	FACETS	0.919	0.82	1	0.459	0.41	0.511	CLONAL	1	TRUE	1	0.711434929159918	3		402	365	SUCCESS
REST	5978	MSKCC	GRCh37	4	57777187	57777187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1288824485	NA	P-0065113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	310	582	0	ENST00000309042.7:c.383C>T	p.Ser128Leu	p.S128L	ENST00000309042	NM_005612.4	128	tCa/tTa	2/4	1	2	FACETS	0.969	0.917	1	0.969	0.917	1	CLONAL	1	TRUE	1	0.711434929159918	2		582	899	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524105	187524105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	82	509	0	ENST00000441802.2:c.11434G>A	p.Glu3812Lys	p.E3812K	ENST00000441802	NM_005245.3	3812	Gag/Aag	20/27	1	2	FACETS	0.318	0.28	0.358	0.318	0.28	0.358	SUBCLONAL	1	TRUE	1	0.711434929159918	2		509	726	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839802	27839802	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	442	681	0	ENST00000328488.2:c.292G>T	p.Glu98Ter	p.E98*	ENST00000328488	NM_003533.2	98	Gag/Tag	1/1	0.711434929159918	2	FACETS	1	0.968	1	0.508	0.485	0.532	CLONAL	1	TRUE	0	0.711434929159918	2		681	1222	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287929	33287929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	757	600	0	ENST00000374542.5:c.1324G>A	p.Glu442Lys	p.E442K	ENST00000374542	NM_001141970.1	442	Gag/Aag	5/8	0.607400987944642	3	FACETS	0.895	0.874	0.917	0.895	0.874	0.917	CLONAL	3	TRUE	0	0.711434929159918	3		600	1074	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151850003	151850003	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	287	517	0	ENST00000262189.6:c.12313C>T	p.Leu4105Phe	p.L4105F	ENST00000262189	NM_170606.2	4105	Ctt/Ttt	49/59	0.711434929159918	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.711434929159918	1		517	508	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753924	133753924	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	219	431	0	ENST00000318560.5:c.1393C>T	p.Pro465Ser	p.P465S	ENST00000318560	NM_005157.4	465	Cca/Tca	8/11	1	2	FACETS	0.888	0.83	0.948	0.888	0.83	0.948	CLONAL	1	TRUE	1	0.711434929159918	2		431	693	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407539	139407539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	285	425	0	ENST00000277541.6:c.2401C>A	p.Leu801Met	p.L801M	ENST00000277541	NM_017617.3	801	Ctg/Atg	15/34	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.711434929159918	2		425	728	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923675	39923675	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0065113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	304	532	0	ENST00000378444.4:c.3416C>G	p.Ser1139Ter	p.S1139*	ENST00000378444	NM_001123385.1	1139	tCa/tGa	7/15	0.4237965888928	1	FACETS	0.862	0.819	0.904	0.862	0.819	0.904	INDETERMINATE	1	TRUE	0	0.711434929159918	1		532	639	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065115-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	231	789	0				ENST00000310581	NM_198253.2	-/1132			0.359370557370769	4	FACETS	0.992	0.932	1	0.992	0.932	1	CLONAL	3	FALSE	1	0.359370557370769	4		789	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0065115-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	182	462	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.340995726525426	3	FACETS	1	0.98	1	0.764	0.711	0.819	CLONAL	2	FALSE	0	0.359370557370769	3		462	521	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941720	48941720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065115-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	30	304	0	ENST00000267163.4:c.1030C>T	p.Gln344Ter	p.Q344*	ENST00000267163	NM_000321.2	344	Cag/Tag	10/27	1	2	FACETS	0.971	0.807	1	1	0.962	1	CLONAL	2	FALSE	1	0.359370557370769	2		304	86	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216590	108216590	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065115-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	18	356	0	ENST00000278616.4:c.8539G>C	p.Glu2847Gln	p.E2847Q	ENST00000278616	NM_000051.3	2847	Gag/Cag	58/63	1	2	FACETS	0.801	0.61	1	0.801	0.61	1	CLONAL	1	FALSE	1	0.359370557370769	2		356	125	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383227	31383227	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148132847	NA	P-0065115-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	211	680	0	ENST00000328111.2:c.1139G>A	p.Arg380Gln	p.R380Q	ENST00000328111	NM_006892.3	380	cGa/cAa	11/23	0.359370557370769	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	FALSE	1	0.359370557370769	3		680	661	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213594	36213594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201585209	NA	P-0065115-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	100	653	0	ENST00000222270.7:c.2696G>A	p.Arg899Gln	p.R899Q	ENST00000222270	NM_014727.1	899	cGg/cAg	5/37	0.359370557370769	4	FACETS	1	0.938	1	0.535	0.478	0.596	CLONAL	1	FALSE	2	0.359370557370769	4		653	707	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860081	57860081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065115-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	119	599	0	ENST00000228682.2:c.821G>A	p.Gly274Asp	p.G274D	ENST00000228682	NM_005269.2	274	gGc/gAc	8/12	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	FALSE	1	0.359370557370769	2		599	638	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984018	7984018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065115-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	156	561	0	ENST00000319144.4:c.608C>T	p.Ser203Phe	p.S203F	ENST00000319144	NM_001139.2	203	tCc/tTc	5/15	0.340995726525426	3	FACETS	1	0.965	1	0.719	0.663	0.775	CLONAL	2	FALSE	0	0.359370557370769	3		561	475	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512323	38512323	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065115-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	60	457	0	ENST00000254066.5:c.1234G>A	p.Glu412Lys	p.E412K	ENST00000254066	NM_000964.3	412	Gaa/Aaa	9/9	0.175256090287248	1	FACETS	0.875	0.759	0.999	0.875	0.759	0.999	INDETERMINATE	1	FALSE	0	0.359370557370769	1		457	313	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271758	18271758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065115-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	113	590	0	ENST00000222254.8:c.445G>A	p.Glu149Lys	p.E149K	ENST00000222254	NM_005027.3	149	Gag/Aag	4/16	0.227439845829438	3	FACETS	1	0.973	1	0.612	0.552	0.675	CLONAL	1	FALSE	1	0.359370557370769	3		590	606	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531892	41531892	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065115-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	21	468	0	ENST00000263253.7:c.1604C>A	p.Ser535Ter	p.S535*	ENST00000263253	NM_001429.3	535	tCa/tAa	7/31	0.359370557370769	1	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	FALSE	0	0.359370557370769	1		468	84	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176662925	176662925	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065115-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	38	480	0	ENST00000439151.2:c.3900G>C	p.Lys1300Asn	p.K1300N	ENST00000439151	NM_022455.4	1300	aaG/aaC	6/23	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	FALSE	1	0.359370557370769	2		480	166	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065116-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	103	789	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.804	0.724	0.888	0.804	0.724	0.888	CLONAL	1	TRUE	1	0.586000081376386	2		789	437	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0065116-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	139	511	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.552641195314243	3	FACETS	1	0.951	1	0.53	0.484	0.577	CLONAL	1	TRUE	1	0.586000081376386	3		511	579	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933732	39933732	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065116-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	108	327	0	ENST00000378444.4:c.867G>A	p.Trp289Ter	p.W289*	ENST00000378444	NM_001123385.1	289	tgG/tgA	4/15	1	1	FACETS	0.661	0.598	0.727	0.661	0.598	0.727	SUBCLONAL	1	TRUE	0	0.586000081376386	1		327	394	SUCCESS
YES1	7525	MSKCC	GRCh37	18	747976	747976	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1187206077	NA	P-0065116-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	96	320	0	ENST00000314574.4:c.414G>C	p.Lys138Asn	p.K138N	ENST00000314574	NM_005433.3	138	aaG/aaC	4/12	1	2	FACETS	0.499	0.445	0.556	0.499	0.445	0.556	SUBCLONAL	1	TRUE	1	0.586000081376386	2		320	657	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332463	153332463	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	186	342	0	ENST00000281708.4:c.493del	p.Thr165GlnfsTer4	p.T165Qfs*4	ENST00000281708	NM_033632.3	165	Aca/ca	2/12	0.637060327378944	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.637060327378944	1		342	371	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0065119-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	12	624	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.331	0.232	0.454	0.331	0.232	0.454	SUBCLONAL	1	TRUE	1	0.275438559436706	2		625	263	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793683	89793683	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs555301723	NA	P-0065119-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	34	481	1	ENST00000336032.3:c.752A>G	p.Lys251Arg	p.K251R	ENST00000336032	NM_006813.2	251	aAg/aGg	2/2	1	2	FACETS	0.882	0.723	1	0.882	0.723	1	CLONAL	1	TRUE	1	0.275438559436706	2		482	280	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910789	114910789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065119-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	35	473	0	ENST00000543371.1:c.908C>T	p.Thr303Met	p.T303M	ENST00000543371	NM_001198531.1	303	aCg/aTg	9/14	1	2	FACETS	0.444	0.363	0.535	0.444	0.363	0.535	SUBCLONAL	1	TRUE	1	0.275438559436706	2		473	573	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138771	64138771	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065119-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	77	387	0	ENST00000334205.4:c.2138A>G	p.Lys713Arg	p.K713R	ENST00000334205	NM_003942.2	713	aAg/aGg	17/17	0.184293037029228	3	FACETS	1	0.958	1	0.604	0.531	0.681	CLONAL	1	TRUE	1	0.275438559436706	3		387	527	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877124	151877124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771406657	NA	P-0065119-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	47	548	1	ENST00000262189.6:c.7237G>A	p.Ala2413Thr	p.A2413T	ENST00000262189	NM_170606.2	2413	Gca/Aca	37/59	1	2	FACETS	0.586	0.494	0.688	0.586	0.494	0.688	SUBCLONAL	1	TRUE	1	0.275438559436706	2		549	582	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0065124-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	101	379	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.899	0.815	0.987	0.899	0.815	0.987	CLONAL	1	TRUE	1	0.751168410182111	2		379	299	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0065124-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	506	495	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.721661869743821	3	FACETS	0.972	0.937	1	0.972	0.937	1	CLONAL	2	TRUE	1	0.751168410182111	3		495	953	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631878	90631878	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1319035463	NA	P-0065124-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	121	505	0	ENST00000330062.3:c.475C>T	p.Arg159Cys	p.R159C	ENST00000330062	NM_002168.2	159	Cgc/Tgc	4/11	1	2	FACETS	0.416	0.375	0.458	0.416	0.375	0.458	SUBCLONAL	1	TRUE	1	0.751168410182111	2		505	775	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411678	63411678	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065124-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	472	255	0	ENST00000330258.3:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000330258	NM_152424.3	497	Cga/Tga	2/2	0.707609695042301	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.751168410182111	2		255	546	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052636	42052636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1054243525	NA	P-0065124-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	245	428	0	ENST00000219905.7:c.7307G>A	p.Arg2436His	p.R2436H	ENST00000219905	NM_001164273.1	2436	cGt/cAt	20/24	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.751168410182111	2		428	648	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395158	139395158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554826860	NA	P-0065124-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	260	492	0	ENST00000277541.6:c.5780C>T	p.Thr1927Met	p.T1927M	ENST00000277541	NM_017617.3	1927	aCg/aTg	31/34	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.751168410182111	2		492	691	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0065124-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	215	342	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.751168410182111	3	FACETS	0.982	0.928	1	0.982	0.928	1	CLONAL	2	TRUE	1	0.751168410182111	3		342	401	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720841	89720841	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065124-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	44	116	0	ENST00000371953.3:c.992del	p.Asp331AlafsTer13	p.D331Afs*13	ENST00000371953	NM_000314.4	331	gAc/gc	8/9	1	2	FACETS	0.761	0.65	0.879	0.761	0.65	0.879	SUBCLONAL	1	TRUE	1	0.751168410182111	2		116	154	SUCCESS
APC	324	MSKCC	GRCh37	5	112173543	112173543	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065124-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	246	484	0	ENST00000257430.4:c.2252del	p.Ser751PhefsTer10	p.S751Ffs*10	ENST00000257430	NM_000038.5	751	tCt/tt	16/16	0.721661869743821	3	FACETS	1	0.959	1	0.516	0.483	0.55	CLONAL	1	TRUE	1	0.751168410182111	3		484	873	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0065125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	398	702	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.635208945799868	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.635208945799868	2		702	525	SUCCESS
APC	324	MSKCC	GRCh37	5	112170777	112170780	+	frameshift_variant	Frame_Shift_Del	DEL	CAGA	CAGA	-	rs878853420	NA	P-0065125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	66	418	0	ENST00000257430.4:c.1875_1878del	p.Asn627LeufsTer2	p.N627Lfs*2	ENST00000257430	NM_000038.5	625	CAGAca/ca	15/16	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.635208945799868	2		418	207	SUCCESS
APC	324	MSKCC	GRCh37	5	112175757	112175758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	96	435	0	ENST00000257430.4:c.4467dup	p.His1490ThrfsTer24	p.H1490Tfs*24	ENST00000257430	NM_000038.5	1489	tta/ttAa	16/16	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.635208945799868	2		435	284	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807539	1807539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	120	552	0	ENST00000260795.2:c.1708C>T	p.Arg570Trp	p.R570W	ENST00000260795		570	Cgg/Tgg	12/17	1	2	FACETS	0.947	0.863	1	0.947	0.863	1	CLONAL	1	TRUE	1	0.635208945799868	2		552	399	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380309	25380309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1407509439	NA	P-0065125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	55	312	0	ENST00000311936.3:c.149C>T	p.Thr50Ile	p.T50I	ENST00000311936	NM_004985.3	50	aCc/aTc	3/5	1	2	FACETS	0.951	0.828	1	0.951	0.828	1	CLONAL	1	TRUE	1	0.635208945799868	2		312	182	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	134	690	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.944	0.858	1	0.944	0.858	1	CLONAL	1	TRUE	1	0.335589516475565	2		691	846	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	92	466	5	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.805	0.716	0.9	0.805	0.716	0.9	CLONAL	1	TRUE	1	0.335589516475565	2		471	681	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	14	584	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.141	0.101	0.19	0.141	0.101	0.19	SUBCLONAL	1	TRUE	1	0.335589516475565	2		584	590	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	154	460	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.335589516475565	2		460	799	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	74	249	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.919	0.807	1	0.919	0.807	1	CLONAL	1	TRUE	1	0.335589516475565	2		250	480	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	75	527	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	1	2	FACETS	0.617	0.54	0.699	0.617	0.54	0.699	SUBCLONAL	1	TRUE	1	0.335589516475565	2		527	725	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1232964733	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	82	520	0	ENST00000324856.7:c.1015del	p.Ala339LeufsTer24	p.A339Lfs*24	ENST00000324856	NM_006015.4	337	tGg/tg	1/20	1	2	FACETS	0.879	0.776	0.988	0.879	0.776	0.988	CLONAL	1	TRUE	1	0.335589516475565	2		520	556	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653808	89653808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	27	263	0	ENST00000371953.3:c.106G>A	p.Gly36Arg	p.G36R	ENST00000371953	NM_000314.4	36	Gga/Aga	2/9	1	2	FACETS	0.377	0.299	0.466	0.377	0.299	0.466	SUBCLONAL	1	TRUE	1	0.335589516475565	2		263	427	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	94	413	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.335589516475565	2		413	545	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	113	368	1	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	1	2	FACETS	0.91	0.819	1	0.91	0.819	1	CLONAL	1	TRUE	1	0.335589516475565	2		369	740	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	49	662	0	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.505	0.427	0.591	0.505	0.427	0.591	SUBCLONAL	1	TRUE	1	0.335589516475565	2		662	578	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911589	39911589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768919602	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	89	433	0	ENST00000378444.4:c.5041C>T	p.Arg1681Cys	p.R1681C	ENST00000378444	NM_001123385.1	1681	Cgc/Tgc	15/15	1	2	FACETS	0.742	0.658	0.832	0.742	0.658	0.832	SUBCLONAL	1	TRUE	1	0.335589516475565	2		433	715	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254192	133254192	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500835	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	118	438	0	ENST00000320574.5:c.692G>A	p.Arg231His	p.R231H	ENST00000320574	NM_006231.2	231	cGc/cAc	7/49	1	2	FACETS	0.979	0.884	1	0.979	0.884	1	CLONAL	1	TRUE	1	0.335589516475565	2		438	718	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897445	78897445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334868419	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	130	549	1	ENST00000306801.3:c.2780G>A	p.Arg927Gln	p.R927Q	ENST00000306801	NM_020761.2	927	cGg/cAg	23/34	1	2	FACETS	0.966	0.877	1	0.966	0.877	1	CLONAL	1	TRUE	1	0.335589516475565	2		550	802	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052632	42052632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779811318	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	142	445	0	ENST00000219905.7:c.7303C>T	p.Arg2435Trp	p.R2435W	ENST00000219905	NM_001164273.1	2435	Cgg/Tgg	20/24	1	2	FACETS	0.896	0.816	0.98	0.896	0.816	0.98	CLONAL	1	TRUE	1	0.335589516475565	2		445	945	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	60	685	3	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.415	0.356	0.479	0.415	0.356	0.479	SUBCLONAL	1	TRUE	1	0.335589516475565	2		688	862	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	96	784	0	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.817	0.728	0.912	0.817	0.728	0.912	CLONAL	1	TRUE	1	0.335589516475565	2		784	700	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356452	70356454	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	136	533	0	ENST00000374080.3:c.5353_5355del	p.Lys1785del	p.K1785del	ENST00000374080		1783	AAG/-	37/45	1	2	FACETS	0.972	0.884	1	0.972	0.884	1	CLONAL	1	TRUE	1	0.335589516475565	2		533	834	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542687	141542687	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1435049396	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	73	417	0	ENST00000220592.5:c.2299G>A	p.Val767Ile	p.V767I	ENST00000220592	NM_012154.3	767	Gtc/Atc	18/19	1	2	FACETS	0.594	0.519	0.676	0.594	0.519	0.676	SUBCLONAL	1	TRUE	1	0.335589516475565	2		417	732	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468397	89468398	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1467832547	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	57	342	2	ENST00000336596.2:c.1938dup	p.Glu647ArgfsTer7	p.E647Rfs*7	ENST00000336596	NM_005233.5	644	tca/tcAa	11/17	1	2	FACETS	0.506	0.434	0.586	0.506	0.434	0.586	SUBCLONAL	1	TRUE	1	0.335589516475565	2		344	671	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384996	31384996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1169940446	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	91	388	0	ENST00000328111.2:c.1381C>T	p.Arg461Cys	p.R461C	ENST00000328111	NM_006892.3	461	Cgc/Tgc	14/23	1	2	FACETS	0.925	0.823	1	0.925	0.823	1	CLONAL	1	TRUE	1	0.335589516475565	2		388	586	SUCCESS
AR	367	MSKCC	GRCh37	X	66941694	66941694	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	98	386	0	ENST00000374690.3:c.2338C>T	p.Arg780Trp	p.R780W	ENST00000374690	NM_000044.3	780	Cgg/Tgg	6/8	1	2	FACETS	0.903	0.806	1	0.903	0.806	1	CLONAL	1	TRUE	1	0.335589516475565	2		386	647	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256134	123256134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768761510	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	127	444	1	ENST00000358487.5:c.1775G>A	p.Arg592His	p.R592H	ENST00000358487	NM_000141.4	592	cGt/cAt	13/18	1	2	FACETS	0.991	0.898	1	0.991	0.898	1	CLONAL	1	TRUE	1	0.335589516475565	2		445	764	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67646012	67646013	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	62	353	2	ENST00000264010.4:c.950_951dup	p.Gly318GlnfsTer16	p.G318Qfs*16	ENST00000264010	NM_006565.3	314	aac/aACac	4/12	1	2	FACETS	0.492	0.424	0.566	0.492	0.424	0.566	SUBCLONAL	1	TRUE	1	0.335589516475565	2		355	751	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142950056	142950056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568595082	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	33	304	0	ENST00000262992.4:c.2654G>A	p.Arg885His	p.R885H	ENST00000262992	NM_001101669.1	885	cGc/cAc	24/24	1	2	FACETS	0.367	0.298	0.445	0.367	0.298	0.445	SUBCLONAL	1	TRUE	1	0.335589516475565	2		304	536	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202352	133202352	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	37	465	0	ENST00000320574.5:c.6536G>T	p.Gly2179Val	p.G2179V	ENST00000320574	NM_006231.2	2179	gGg/gTg	47/49	1	2	FACETS	0.334	0.274	0.401	0.334	0.274	0.401	SUBCLONAL	1	TRUE	1	0.335589516475565	2		465	661	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14031682	14031682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs180919656	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	108	314	0	ENST00000311895.7:c.1871G>A	p.Arg624Gln	p.R624Q	ENST00000311895	NM_005236.2	624	cGg/cAg	9/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.335589516475565	2		314	576	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970919	70970919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1563439440	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	58	427	0	ENST00000276594.2:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000276594	NM_024504.3	448	Cgg/Tgg	6/8	1	2	FACETS	0.479	0.41	0.553	0.479	0.41	0.553	SUBCLONAL	1	TRUE	1	0.335589516475565	2		427	722	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100424	8100425	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs772396478	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	100	608	0	ENST00000346208.3:c.404dup	p.Ala136GlyfsTer167	p.A136Gfs*167	ENST00000346208		133	tac/taCc	3/6	1	2	FACETS	0.654	0.583	0.73	0.654	0.583	0.73	SUBCLONAL	1	TRUE	1	0.335589516475565	2		608	911	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485715	40485715	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	113	401	0	ENST00000264657.5:c.1025G>A	p.Gly342Asp	p.G342D	ENST00000264657	NM_139276.2	342	gGc/gAc	10/24	1	2	FACETS	0.921	0.83	1	0.921	0.83	1	CLONAL	1	TRUE	1	0.335589516475565	2		401	731	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339930	70339930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866469400	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	118	425	0	ENST00000374080.3:c.463C>T	p.Arg155Trp	p.R155W	ENST00000374080		155	Cgg/Tgg	4/45	1	2	FACETS	0.958	0.865	1	0.958	0.865	1	CLONAL	1	TRUE	1	0.335589516475565	2		425	734	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445949	49445949	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	115	603	0	ENST00000301067.7:c.1517del	p.Pro506HisfsTer424	p.P506Hfs*424	ENST00000301067	NM_003482.3	506	cCa/ca	10/54	1	2	FACETS	0.848	0.764	0.937	0.848	0.764	0.937	CLONAL	1	TRUE	1	0.335589516475565	2		603	808	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955099	1955099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	70	390	0	ENST00000382891.5:c.2186G>A	p.Arg729His	p.R729H	ENST00000382891	NM_133335.3	729	cGc/cAc	12/22	1	2	FACETS	0.528	0.459	0.602	0.528	0.459	0.602	SUBCLONAL	1	TRUE	1	0.335589516475565	2		390	790	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275305	115275305	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	52	398	0	ENST00000438362.2:c.1108C>T	p.Arg370Ter	p.R370*	ENST00000438362	NM_001242891.1	370	Cga/Tga	10/20	1	2	FACETS	0.508	0.432	0.592	0.508	0.432	0.592	SUBCLONAL	1	TRUE	1	0.335589516475565	2		398	610	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411417	63411417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370276785	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	141	585	0	ENST00000330258.3:c.1750C>T	p.Arg584Cys	p.R584C	ENST00000330258	NM_152424.3	584	Cgt/Tgt	2/2	1	2	FACETS	0.982	0.894	1	0.982	0.894	1	CLONAL	1	TRUE	1	0.335589516475565	2		585	856	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561505	141561505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	44	510	2	ENST00000220592.5:c.1300G>A	p.Val434Ile	p.V434I	ENST00000220592	NM_012154.3	434	Gtc/Atc	11/19	1	2	FACETS	0.327	0.273	0.386	0.327	0.273	0.386	SUBCLONAL	1	TRUE	1	0.335589516475565	2		512	803	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559777	29559777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs902739109	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	136	450	0	ENST00000356175.3:c.3374C>T	p.Ala1125Val	p.A1125V	ENST00000356175	NM_000267.3	1125	gCg/gTg	26/57	1	2	FACETS	0.915	0.831	1	0.915	0.831	1	CLONAL	1	TRUE	1	0.335589516475565	2		450	886	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563377	21563377	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1294740969	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	116	584	0	ENST00000382592.4:c.542C>T	p.Ala181Val	p.A181V	ENST00000382592	NM_014572.2	181	gCg/gTg	4/8	1	2	FACETS	0.913	0.823	1	0.913	0.823	1	CLONAL	1	TRUE	1	0.335589516475565	2		584	757	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056155	26056155	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	62	481	0	ENST00000343677.2:c.502A>G	p.Lys168Glu	p.K168E	ENST00000343677	NM_005319.3	168	Aag/Gag	1/1	1	2	FACETS	0.448	0.386	0.516	0.448	0.386	0.516	SUBCLONAL	1	TRUE	1	0.335589516475565	2		481	825	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821138	32821138	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	83	539	0	ENST00000354258.4:c.456G>A	p.Trp152Ter	p.W152*	ENST00000354258	NM_000593.5	152	tgG/tgA	1/11	1	2	FACETS	0.786	0.694	0.885	0.786	0.694	0.885	SUBCLONAL	1	TRUE	1	0.335589516475565	2		539	629	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166499	118166499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	45	503	0	ENST00000369448.3:c.1009G>A	p.Ala337Thr	p.A337T	ENST00000369448	NM_017709.3	337	Gcc/Acc	2/2	1	2	FACETS	0.346	0.289	0.408	0.346	0.289	0.408	SUBCLONAL	1	TRUE	1	0.335589516475565	2		503	776	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120508078	120508078	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	70	328	0	ENST00000256646.2:c.1679C>T	p.Thr560Ile	p.T560I	ENST00000256646	NM_024408.3	560	aCa/aTa	10/34	1	2	FACETS	0.757	0.661	0.861	0.757	0.661	0.861	SUBCLONAL	1	TRUE	1	0.335589516475565	2		328	551	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63662093	63662093	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	109	439	0	ENST00000279873.7:c.197G>A	p.Ser66Asn	p.S66N	ENST00000279873	NM_032199.2	66	aGc/aAc	2/10	1	2	FACETS	0.834	0.749	0.924	0.834	0.749	0.924	CLONAL	1	TRUE	1	0.335589516475565	2		439	779	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47594774	47594774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558994168	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	142	531	0	ENST00000430070.2:c.1313G>A	p.Arg438His	p.R438H	ENST00000430070	NM_018095.4	438	cGc/cAc	4/4	1	2	FACETS	0.938	0.855	1	0.938	0.855	1	CLONAL	1	TRUE	1	0.335589516475565	2		531	902	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416952	416952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	163	528	0	ENST00000399788.2:c.3598G>A	p.Gly1200Arg	p.G1200R	ENST00000399788	NM_001042603.1	1200	Gga/Aga	23/28	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.335589516475565	2		528	908	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951063	48951063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	33	229	0	ENST00000267163.4:c.1225G>A	p.Val409Met	p.V409M	ENST00000267163	NM_000321.2	409	Gtg/Atg	13/27	1	2	FACETS	0.559	0.456	0.675	0.559	0.456	0.675	SUBCLONAL	1	TRUE	1	0.335589516475565	2		229	352	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642787	3642787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	54	426	0	ENST00000294008.3:c.2240C>T	p.Ala747Val	p.A747V	ENST00000294008	NM_032444.2	747	gCc/gTc	11/15	1	2	FACETS	0.431	0.367	0.502	0.431	0.367	0.502	SUBCLONAL	1	TRUE	1	0.335589516475565	2		426	746	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670680	67670680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	47	416	0	ENST00000264010.4:c.1925C>T	p.Thr642Ile	p.T642I	ENST00000264010	NM_006565.3	642	aCc/aTc	11/12	1	2	FACETS	0.383	0.322	0.451	0.383	0.322	0.451	SUBCLONAL	1	TRUE	1	0.335589516475565	2		416	731	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855919	68855919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	76	410	1	ENST00000261769.5:c.1727C>T	p.Thr576Ile	p.T576I	ENST00000261769	NM_004360.3	576	aCt/aTt	12/16	1	2	FACETS	0.708	0.621	0.801	0.708	0.621	0.801	SUBCLONAL	1	TRUE	1	0.335589516475565	2		411	640	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264296	30264296	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	18	225	0	ENST00000322652.5:c.35del	p.Gly12AlafsTer60	p.G12Afs*60	ENST00000322652	NM_015355.2	11	Ggg/gg	1/16	1	2	FACETS	0.422	0.318	0.545	0.422	0.318	0.545	SUBCLONAL	1	TRUE	1	0.335589516475565	2		225	254	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39575909	39575909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	57	317	0	ENST00000262039.4:c.842C>A	p.Pro281His	p.P281H	ENST00000262039	NM_002647.2	281	cCt/cAt	8/25	1	2	FACETS	0.557	0.477	0.644	0.557	0.477	0.644	SUBCLONAL	1	TRUE	1	0.335589516475565	2		317	610	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110544	4110544	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs775213593	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	66	583	0	ENST00000262948.5:c.413A>G	p.Tyr138Cys	p.Y138C	ENST00000262948	NM_030662.3	138	tAc/tGc	3/11	1	2	FACETS	0.43	0.372	0.494	0.43	0.372	0.494	SUBCLONAL	1	TRUE	1	0.335589516475565	2		583	914	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422351	47422351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	115	475	0	ENST00000404338.3:c.419G>A	p.Gly140Glu	p.G140E	ENST00000404338	NM_004491.4	140	gGg/gAg	1/6	1	2	FACETS	0.889	0.801	0.982	0.889	0.801	0.982	CLONAL	1	TRUE	1	0.335589516475565	2		475	771	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423096	47423096	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	148	518	0	ENST00000404338.3:c.1164G>A	p.Trp388Ter	p.W388*	ENST00000404338	NM_004491.4	388	tgG/tgA	1/6	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.335589516475565	2		518	820	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128036849	128036849	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	118	375	0	ENST00000285398.2:c.1630T>C	p.Cys544Arg	p.C544R	ENST00000285398	NM_000122.1	544	Tgc/Cgc	10/15	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.335589516475565	2		375	681	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37059092	37059092	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs267607806	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	244	405	0	ENST00000231790.2:c.884+2T>C		p.X295_splice	ENST00000231790	NM_000249.3	295			0.335589516475565	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.335589516475565	2		405	675	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524336	187524337	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	112	426	0	ENST00000441802.2:c.11343_11344del	p.Cys3782GlnfsTer13	p.C3782Qfs*13	ENST00000441802	NM_005245.3	3781	ctCTgc/ctgc	19/27	1	2	FACETS	0.787	0.707	0.872	0.787	0.707	0.872	SUBCLONAL	1	TRUE	1	0.335589516475565	2		426	848	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295587	1295587	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	54	597	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.451	0.384	0.524	0.451	0.384	0.524	SUBCLONAL	1	TRUE	1	0.335589516475565	2		597	714	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710838	117710838	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	49	450	0	ENST00000368508.3:c.1434G>A	p.Met478Ile	p.M478I	ENST00000368508	NM_002944.2	478	atG/atA	12/43	1	2	FACETS	0.382	0.323	0.448	0.382	0.323	0.448	SUBCLONAL	1	TRUE	1	0.335589516475565	2		450	764	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124475438	124475438	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1410842025	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	45	292	0	ENST00000357628.3:c.1400C>T	p.Ser467Leu	p.S467L	ENST00000357628	NM_015450.2	467	tCg/tTg	15/19	1	2	FACETS	0.482	0.405	0.568	0.482	0.405	0.568	SUBCLONAL	1	TRUE	1	0.335589516475565	2		292	556	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835969	151835969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	49	399	0	ENST00000262189.6:c.14555C>T	p.Ala4852Val	p.A4852V	ENST00000262189	NM_170606.2	4852	gCa/gTa	58/59	1	2	FACETS	0.433	0.366	0.507	0.433	0.366	0.507	SUBCLONAL	1	TRUE	1	0.335589516475565	2		399	674	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38153318	38153318	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	46	329	0	ENST00000317025.8:c.2911T>C	p.Tyr971His	p.Y971H	ENST00000317025	NM_023034.1	971	Tac/Cac	16/24	1	2	FACETS	0.439	0.369	0.517	0.439	0.369	0.517	SUBCLONAL	1	TRUE	1	0.335589516475565	2		329	624	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127933387	127933388	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	39	294	0	ENST00000373547.4:c.147_148del	p.Cys51TrpfsTer9	p.C51Wfs*9	ENST00000373547	NM_002721.4	49	acAGtg/actg	2/7	1	2	FACETS	0.414	0.343	0.494	0.414	0.343	0.494	SUBCLONAL	1	TRUE	1	0.335589516475565	2		294	561	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128206785	128206785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	93	312	0	ENST00000265960.3:c.1438C>T	p.Leu480Phe	p.L480F	ENST00000265960	NM_001006617.1	480	Ctc/Ttc	11/12	1	2	FACETS	0.954	0.85	1	0.954	0.85	1	CLONAL	1	TRUE	1	0.335589516475565	2		312	581	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344049	70344049	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	105	431	0	ENST00000374080.3:c.1785C>A	p.Asn595Lys	p.N595K	ENST00000374080		595	aaC/aaA	13/45	1	2	FACETS	0.979	0.879	1	0.979	0.879	1	CLONAL	1	TRUE	1	0.335589516475565	2		431	639	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179101	123179101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765673108	NA	P-0065126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	84	319	0	ENST00000218089.9:c.550C>T	p.Arg184Trp	p.R184W	ENST00000218089	NM_001042749.1	184	Cgg/Tgg	8/35	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.335589516475565	2		319	357	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0065127-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	231	527	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	NA	2	FACETS	1	0.978	1			1	INDETERMINATE	2	TRUE	NA	0.31257297699927	2		527	677	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0065127-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	96	343	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	1	2	FACETS	0.899	0.802	1	0.899	0.802	1	CLONAL	1	TRUE	1	0.31257297699927	2		343	683	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127182	22127182	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065127-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	64	366	0	ENST00000215832.6:c.946T>C	p.Tyr316His	p.Y316H	ENST00000215832	NM_002745.4	316	Tat/Cat	7/9	1	2	FACETS	0.65	0.563	0.745	0.65	0.563	0.745	SUBCLONAL	1	TRUE	1	0.31257297699927	2		366	630	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0065128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	179	618	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.259066177932171	2	FACETS	0.868	0.802	0.936	0.868	0.802	0.936	CLONAL	2	TRUE	0	0.279327782588335	2		618	738	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781205	3781205	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	95	485	0	ENST00000262367.5:c.5160C>G	p.Cys1720Trp	p.C1720W	ENST00000262367	NM_004380.2	1720	tgC/tgG	30/31	0.222700301814516	3	FACETS	1	0.912	1	0.514	0.457	0.574	CLONAL	1	TRUE	1	0.279327782588335	3		485	754	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932976	49932976	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	91	552	0	ENST00000296474.3:c.2968C>T	p.Pro990Ser	p.P990S	ENST00000296474	NM_002447.2	990	Cct/Tct	13/20	0.259066177932171	2	FACETS	1	0.923	1	0.524	0.465	0.586	CLONAL	1	TRUE	0	0.279327782588335	2		552	622	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0065130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	31	259	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.159612262482553	1	FACETS	0.876	0.709	1	0.876	0.709	1	CLONAL	1	TRUE	0	0.159612262482553	1		259	408	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553578	106553578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1020395697	NA	P-0065130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	58	502	0	ENST00000369096.4:c.1543G>A	p.Gly515Arg	p.G515R	ENST00000369096	NM_001198.3	515	Ggg/Agg	5/7	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.159612262482553	2		502	705	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885263	111885263	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1179360058	NA	P-0065130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	50	559	0	ENST00000341259.2:c.1151A>G	p.Asp384Gly	p.D384G	ENST00000341259	NM_005475.2	384	gAt/gGt	6/8	1	2	FACETS	0.865	0.733	1	0.865	0.733	1	CLONAL	1	TRUE	1	0.159612262482553	2		559	724	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974294	18974294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	31	489	0	ENST00000262803.5:c.2648C>T	p.Pro883Leu	p.P883L	ENST00000262803	NM_002911.3	883	cCg/cTg	19/24	1	2	FACETS	0.658	0.531	0.803	0.658	0.531	0.803	SUBCLONAL	1	TRUE	1	0.159612262482553	2		489	590	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656898	45656898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	46	548	0	ENST00000407780.3:c.258G>A	p.Met86Ile	p.M86I	ENST00000407780	NM_001283052.1	86	atG/atA	3/7	0.159612262482553	1	FACETS	0.777	0.653	0.914	0.777	0.653	0.914	CLONAL	1	TRUE	0	0.159612262482553	1		548	683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0065131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	189	454	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.352003039685654	1	FACETS	0.825	0.767	0.885	0.825	0.767	0.885	CLONAL	1	TRUE	0	0.55642461447102	1		454	594	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593504	48593504	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	138	398	0	ENST00000342988.3:c.1255G>T	p.Gly419Trp	p.G419W	ENST00000342988	NM_005359.5	419	Ggg/Tgg	10/12	0.55642461447102	1	FACETS	0.897	0.825	0.971	0.897	0.825	0.971	CLONAL	1	TRUE	0	0.55642461447102	1		398	399	SUCCESS
APC	324	MSKCC	GRCh37	5	112174430	112174430	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs568149455	NA	P-0065131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	142	493	0	ENST00000257430.4:c.3139G>T	p.Glu1047Ter	p.E1047*	ENST00000257430	NM_000038.5	1047	Gaa/Taa	16/16	0.55642461447102	1	FACETS	0.982	0.906	1	0.982	0.906	1	CLONAL	1	TRUE	0	0.55642461447102	1		493	375	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543674	148543674	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1260470042	NA	P-0065131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	156	374	0	ENST00000320356.2:c.134A>G	p.Asn45Ser	p.N45S	ENST00000320356	NM_004456.4	45	aAt/aGt	3/20	0.295902904210475	3	FACETS	1	0.974	1	0.572	0.526	0.621	INDETERMINATE	1	TRUE	1	0.55642461447102	3		374	626	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578403	+	frameshift_variant	Frame_Shift_Ins	INS	GGGGGC	GGGGGC	AGGGGGA	novel	NA	P-0065131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	129	631	0	ENST00000269305.4:c.527_532delinsTCCCCCT	p.Cys176PhefsTer5	p.C176Ffs*5	ENST00000269305	NM_001126112.2	176	tGCCCCCac/tTCCCCCTac	5/11	0.352003039685654	1	FACETS	0.463	0.42	0.508	0.463	0.42	0.508	SUBCLONAL	1	TRUE	0	0.55642461447102	1		631	723	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0065132-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	558	376	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.383988371611553	8	FACETS	1	0.986	1	1	0.986	1	CLONAL	6	TRUE	2	0.383988371611553	8		376	1006	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006890	47006890	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065132-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	234	224	0	ENST00000377604.3:c.10G>T	p.Glu4Ter	p.E4*	ENST00000377604	NM_001204468.1	4	Gaa/Taa	2/24	0.357558610692027	2	FACETS	1	0.986	1			1	CLONAL	3	TRUE	NA	0.383988371611553	2		224	371	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857902	9857902	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065132-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	96	429	0	ENST00000330684.3:c.3499A>G	p.Met1167Val	p.M1167V	ENST00000330684	NM_001134407.1	1167	Atg/Gtg	13/13	0.373580171032222	4	FACETS	0.83	0.739	0.927	0.277	0.246	0.309	CLONAL	1	TRUE	1	0.383988371611553	4		429	834	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0065134-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	16	350	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.469	0.345	0.618	0.469	0.345	0.618	SUBCLONAL	1	TRUE	1	0.15	2		350	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0065134-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	36	694	1	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	1	2	FACETS	0.596	0.488	0.718	0.596	0.488	0.718	SUBCLONAL	1	TRUE	1	0.15	2		695	805	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0065135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	104	342	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.3	3	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	1	0.26	3		342	429	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023621	27023622	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	TA	novel	NA	P-0065135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	60	469	0	ENST00000324856.7:c.727_728delinsTA	p.Ala243Ter	p.A243*	ENST00000324856	NM_006015.4	243	GCg/TAg	1/20	1	2	FACETS	0.964	0.832	1	0.964	0.832	1	CLONAL	1	TRUE	1	0.26	2		469	479	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008307	29008307	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	81	429	0	ENST00000282397.4:c.564T>A	p.Ser188Arg	p.S188R	ENST00000282397	NM_002019.4	188	agT/agA	5/30	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.26	2		429	558	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986948	36986951	+	frameshift_variant	Frame_Shift_Del	DEL	CTTC	CTTC	TTT	novel	NA	P-0065135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	59	463	2	ENST00000354822.5:c.738_741delinsAAA	p.Met246IlefsTer49	p.M246Ifs*49	ENST00000354822	NM_001079668.2	246	atGAAG/atAAA	3/3	1	2	FACETS	0.942	0.811	1	0.942	0.811	1	CLONAL	1	TRUE	1	0.26	2		465	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0065136-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	68	534	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.283317251914354	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.283317251914354	1		534	378	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0065136-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	48	393	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.122037671941712	3	FACETS	1	0.936	1	0.601	0.51	0.699	INDETERMINATE	1	TRUE	1	0.283317251914354	3		393	322	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508177	38508177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749735817	NA	P-0065136-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	21	471	0	ENST00000254066.5:c.485G>A	p.Arg162Gln	p.R162Q	ENST00000254066	NM_000964.3	162	cGa/cAa	5/9	1	2	FACETS	0.36	0.276	0.458	0.36	0.276	0.458	SUBCLONAL	1	TRUE	1	0.283317251914354	2		471	412	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670702	134670703	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0065136-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	76	541	0	ENST00000398015.3:c.615_616del	p.Phe206SerfsTer54	p.F206Sfs*54	ENST00000398015	NM_004441.4	205	GTg/g	3/16	0.117236020451184	3	FACETS	1	0.966	1	0.428	0.376	0.483	INDETERMINATE	1	TRUE	0	0.283317251914354	3		541	477	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974755	21974777	+	frameshift_variant	Frame_Shift_Del	DEL	CCGACCCCGGGCCGCGGCCGTGG	CCGACCCCGGGCCGCGGCCGTGG	-	novel	NA	P-0065136-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	99	525	0	ENST00000304494.5:c.50_72del	p.Ala17GlyfsTer19	p.A17Gfs*19	ENST00000304494	NM_000077.4	17	gCCACGGCCGCGGCCCGGGGTCGG/g	1/3	0.283317251914354	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.283317251914354	1		525	482	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	58	789	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.417460417897839	2		789	261	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0065137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	125	766	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.417460417897839	2		767	553	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0065137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	313	547	0	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	0.417460417897839	3	FACETS	0.954	0.909	1	0.954	0.909	1	CLONAL	3	TRUE	0	0.417460417897839	3		547	633	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257698	16257698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	133	655	0	ENST00000375759.3:c.4963G>A	p.Glu1655Lys	p.E1655K	ENST00000375759	NM_015001.2	1655	Gag/Aag	11/15	1	2	FACETS	0.872	0.793	0.955	0.872	0.793	0.955	CLONAL	1	TRUE	1	0.417460417897839	2		655	731	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262208	115262208	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	117	371	0	ENST00000438362.2:c.2346G>A	p.Trp782Ter	p.W782*	ENST00000438362	NM_001242891.1	782	tgG/tgA	18/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.417460417897839	2		371	512	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914184	32914184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	65	463	0	ENST00000380152.3:c.5692G>A	p.Asp1898Asn	p.D1898N	ENST00000380152		1898	Gat/Aat	11/27	1	2	FACETS	0.913	0.797	1	0.913	0.797	1	CLONAL	1	TRUE	1	0.417460417897839	2		463	341	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129668	2129668	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs137854074	NA	P-0065137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	48	498	0	ENST00000219476.3:c.3395C>T	p.Ser1132Leu	p.S1132L	ENST00000219476	NM_000548.3	1132	tCg/tTg	29/42	1	2	FACETS	0.503	0.426	0.588	0.503	0.426	0.588	SUBCLONAL	1	TRUE	1	0.417460417897839	2		498	457	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589887	212589887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757597004	NA	P-0065137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	112	461	0	ENST00000342788.4:c.655G>A	p.Gly219Ser	p.G219S	ENST00000342788	NM_005235.2	219	Ggc/Agc	6/28	1	2	FACETS	0.96	0.866	1	0.96	0.866	1	CLONAL	1	TRUE	1	0.417460417897839	2		461	559	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916957	178916957	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200018596	NA	P-0065137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	71	350	0	ENST00000263967.3:c.344G>T	p.Arg115Leu	p.R115L	ENST00000263967	NM_006218.2	115	cGa/cTa	2/21	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.417460417897839	2		350	337	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549880	187549880	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	81	435	0	ENST00000441802.2:c.4361C>T	p.Pro1454Leu	p.P1454L	ENST00000441802	NM_005245.3	1454	cCt/cTt	8/27	0.416988660978742	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.417460417897839	1		435	292	SUCCESS
APC	324	MSKCC	GRCh37	5	112175640	112175640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782678	NA	P-0065137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	132	544	0	ENST00000257430.4:c.4349G>A	p.Arg1450Gln	p.R1450Q	ENST00000257430	NM_000038.5	1450	cGa/cAa	16/16	1	2	FACETS	0.965	0.879	1	0.965	0.879	1	CLONAL	1	TRUE	1	0.417460417897839	2		544	655	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55231495	55231495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	90	465	0	ENST00000275493.2:c.1701G>A	p.Met567Ile	p.M567I	ENST00000275493	NM_005228.3	567	atG/atA	14/28	1	2	FACETS	0.9	0.802	1	0.9	0.802	1	CLONAL	1	TRUE	1	0.417460417897839	2		465	479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0065138-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	177	571	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.768922009822129	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.768922009822129	2		572	226	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0065138-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	44	177	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.450217478544506	2	FACETS	0.773	0.684	0.859	0.773	0.684	0.859	INDETERMINATE	2	TRUE	0	0.768922009822129	2		177	74	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387087	31387087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778795266	NA	P-0065138-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	64	539	0	ENST00000328111.2:c.1712G>A	p.Arg571Gln	p.R571Q	ENST00000328111	NM_006892.3	571	cGa/cAa	16/23	0.501166938899474	3	FACETS	0.705	0.614	0.801	0.352	0.307	0.401	SUBCLONAL	1	TRUE	1	0.768922009822129	3		539	327	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004238	150004239	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065138-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	123	409	0	ENST00000253339.5:c.1986dup	p.Gln663ThrfsTer5	p.Q663Tfs*5	ENST00000253339		662	-/A	3/7	0.768922009822129	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.768922009822129	1		409	170	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739416	46739416	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065138-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	110	508	0	ENST00000371975.4:c.1607G>T	p.Arg536Leu	p.R536L	ENST00000371975	NM_003579.3	536	cGa/cTa	14/18	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.768922009822129	2		508	248	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599022	28599022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065138-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	83	448	0	ENST00000241453.7:c.2266C>T	p.His756Tyr	p.H756Y	ENST00000241453	NM_004119.2	756	Cat/Tat	18/24	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.768922009822129	2		448	191	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459694	40459694	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065138-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	20	584	0	ENST00000345506.4:c.1859G>A	p.Ser620Asn	p.S620N	ENST00000345506	NM_003152.3	620	aGt/aAt	16/20	0.49913543907985	3	FACETS	0.202	0.154	0.258	0.101	0.077	0.129	SUBCLONAL	1	TRUE	1	0.768922009822129	3		584	357	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78931480	78931480	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065138-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	73	534	0	ENST00000306801.3:c.3427G>C	p.Asp1143His	p.D1143H	ENST00000306801	NM_020761.2	1143	Gac/Cac	29/34	0.49913543907985	3	FACETS	0.885	0.782	0.994	0.443	0.391	0.497	CLONAL	1	TRUE	1	0.768922009822129	3		534	297	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47061257	47061257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065138-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	44	517	0	ENST00000409792.3:c.7424G>C	p.Arg2475Thr	p.R2475T	ENST00000409792	NM_014159.6	2475	aGa/aCa	19/21	0.400572035836596	3	FACETS	0.503	0.424	0.59	0.168	0.141	0.197	INDETERMINATE	1	TRUE	0	0.768922009822129	3		517	315	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109315689	109315689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760878307	NA	P-0065138-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	35	397	0	ENST00000436639.2:c.1096G>A	p.Glu366Lys	p.E366K	ENST00000436639	NM_014454.2	366	Gag/Aag	6/10	0.768922009822129	1	FACETS	0.379	0.315	0.447	0.379	0.315	0.447	SUBCLONAL	1	TRUE	0	0.768922009822129	1		397	148	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422727	47422727	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065138-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	65	475	0	ENST00000377045.4:c.199G>A	p.Gly67Arg	p.G67R	ENST00000377045	NM_001654.4	67	Gga/Aga	3/16	0.478644160630081	1	FACETS	0.542	0.478	0.608	0.542	0.478	0.608	SUBCLONAL	1	TRUE	0	0.768922009822129	1		475	192	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419922	41419922	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065139-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	76	512	0	ENST00000373198.4:c.399C>A	p.Asn133Lys	p.N133K	ENST00000373198	NM_133170.3	133	aaC/aaA	3/32	1	2	FACETS	0.266	0.232	0.302	0.266	0.232	0.302	SUBCLONAL	1	FALSE	1	0.706810346162144	2		512	809	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105907	27105907	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	213	507	0	ENST00000324856.7:c.5518G>A	p.Gly1840Ser	p.G1840S	ENST00000324856	NM_006015.4	1840	Ggc/Agc	20/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.631025582628095	2		507	670	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720670	89720670	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	32	162	0	ENST00000371953.3:c.821G>C	p.Trp274Ser	p.W274S	ENST00000371953	NM_000314.4	274	tGg/tCg	8/9	1	2	FACETS	0.86	0.712	1	0.86	0.712	1	CLONAL	1	TRUE	1	0.631025582628095	2		162	118	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639917	3639917	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773723496	NA	P-0065141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	188	503	0	ENST00000294008.3:c.3722G>A	p.Arg1241His	p.R1241H	ENST00000294008	NM_032444.2	1241	cGt/cAt	12/15	1	2	FACETS	0.928	0.862	0.997	0.928	0.862	0.997	CLONAL	1	TRUE	1	0.631025582628095	2		503	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576936	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTAGGAAAGA	CTAGGAAAGA	-	novel	NA	P-0065141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	243	593	0	ENST00000269305.4:c.920-10_920-1del		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.631025582628095				0.976	1				CLONAL	1	TRUE	0	0.631025582628095	1		593	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0065142-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	282	598	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.58462886816254	2	FACETS	0.944	0.899	0.989	0.944	0.899	0.989	CLONAL	2	TRUE	0	0.58462886816254	2		598	511	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29007999	29007999	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065142-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	70	445	1	ENST00000282397.4:c.770C>T	p.Pro257Leu	p.P257L	ENST00000282397	NM_002019.4	257	cCc/cTc	6/30	0.301274773938259	5	FACETS	0.895	0.782	1	0.298	0.26	0.339	INDETERMINATE	1	TRUE	2	0.58462886816254	5		446	502	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0065143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	123	393	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.111648008102413	14	FACETS	1	0.926	1	0.682	0.619	0.749	CLONAL	6	TRUE	5	0.111648008102413	14		393	599	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0065143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	91	646	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	1	2	FACETS	0.963	0.86	1	1	0.99	1	CLONAL	4	TRUE	1	0.111648008102413	2		646	423	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937694	76937694	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1184990999	NA	P-0065143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	44	591	0	ENST00000373344.5:c.3054G>T	p.Lys1018Asn	p.K1018N	ENST00000373344	NM_000489.3	1018	aaG/aaT	9/35	0.0911931624710247	3	FACETS	1	0.916	1	0.577	0.483	0.682	CLONAL	1	TRUE	1	0.111648008102413	3		591	721	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265313	152265313	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	27	491	0	ENST00000206249.3:c.766C>T	p.Arg256Ter	p.R256*	ENST00000206249	NM_000125.3	256	Cga/Tga	4/8	0.111648008102413	3	FACETS	1	0.868	1	0.564	0.448	0.697	CLONAL	1	TRUE	1	0.111648008102413	3		491	453	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453361	40453361	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372745237	NA	P-0065143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	31	575	0	ENST00000345506.4:c.1058G>A	p.Arg353His	p.R353H	ENST00000345506	NM_003152.3	353	cGc/cAc	10/20	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.111648008102413	2		575	383	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974681	21974682	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCGG	novel	NA	P-0065143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	58	663	0	ENST00000304494.5:c.142_145dup	p.Ile49ThrfsTer72	p.I49Tfs*72	ENST00000304494	NM_000077.4	49	atc/aCCGAtc	1/3	0.111648008102413	5	FACETS	1	0.908	1	0.538	0.462	0.62	CLONAL	2	TRUE	1	0.111648008102413	5		663	564	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194826	30194826	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	58	476	0	ENST00000331968.5:c.319G>T	p.Asp107Tyr	p.D107Y	ENST00000331968	NM_002742.2	107	Gac/Tac	2/18	1	2	FACETS	0.946	0.815	1	0.946	0.815	1	CLONAL	1	TRUE	1	0.308193644414917	2		476	398	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245832	46245832	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0065147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	66	511	0	ENST00000334344.6:c.3926C>G	p.Ser1309Ter	p.S1309*	ENST00000334344	NM_152641.2	1309	tCa/tGa	15/21	1	2	FACETS	0.965	0.84	1	0.965	0.84	1	CLONAL	1	TRUE	1	0.308193644414917	2		511	444	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231349	46231349	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	79	410	0	ENST00000334344.6:c.1189C>T	p.Gln397Ter	p.Q397*	ENST00000334344	NM_152641.2	397	Cag/Tag	10/21	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.308193644414917	2		410	428	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390779	139390779	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771318379	NA	P-0065147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	187	611	0	ENST00000277541.6:c.7412C>T	p.Ser2471Leu	p.S2471L	ENST00000277541	NM_017617.3	2471	tCg/tTg	34/34	1	2	FACETS	0.829	0.768	0.892	1	0.992	1	CLONAL	2	TRUE	1	0.308193644414917	2		611	732	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039278	47039278	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0065147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	65	529	0	ENST00000377604.3:c.902-1G>A		p.X301_splice	ENST00000377604	NM_001204468.1	301			0.308193644414917	1	FACETS	0.771	0.67	0.879	0.771	0.67	0.879	SUBCLONAL	1	TRUE	0	0.308193644414917	1		529	463	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415843	49415843	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	64	523	0	ENST00000301067.7:c.16504A>G	p.Ile5502Val	p.I5502V	ENST00000301067	NM_003482.3	5502	Atc/Gtc	53/54	1	2	FACETS	0.818	0.709	0.935	0.818	0.709	0.935	CLONAL	1	TRUE	1	0.308193644414917	2		523	508	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352596	68352596	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	44	430	0	ENST00000487270.1:c.463A>T	p.Ile155Leu	p.I155L	ENST00000487270	NM_133509.3	155	Ata/Tta	6/11	1	2	FACETS	0.879	0.74	1	0.879	0.74	1	CLONAL	1	TRUE	1	0.308193644414917	2		430	325	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51503086	51503086	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	75	454	0	ENST00000260433.2:c.1431G>T	p.Leu477Phe	p.L477F	ENST00000260433		477	ttG/ttT	10/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.308193644414917	2		454	406	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396605	396606	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0065147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	69	536	1	ENST00000262320.3:c.420_421delinsTT	p.Ala141Ser	p.A141S	ENST00000262320	NM_003502.3	140	ctGGcg/ctTTcg	2/11	1	2	FACETS	0.883	0.771	1	0.883	0.771	1	CLONAL	1	TRUE	1	0.308193644414917	2		537	507	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61306924	61306924	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	74	484	0	ENST00000341074.5:c.556T>A	p.Trp186Arg	p.W186R	ENST00000341074	NM_002974.2	186	Tgg/Agg	6/8	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.308193644414917	2		484	395	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220378	1220378	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	230	531	0	ENST00000326873.7:c.471del	p.Cys158ValfsTer3	p.C158Vfs*3	ENST00000326873	NM_000455.4	157	ttC/tt	4/10	0.299539848541884	3	FACETS	0.914	0.858	0.972	0.914	0.858	0.972	CLONAL	3	TRUE	0	0.308193644414917	3		531	628	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974277	18974277	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	77	490	0	ENST00000262803.5:c.2631G>C	p.Lys877Asn	p.K877N	ENST00000262803	NM_002911.3	877	aaG/aaC	19/24	0.299539848541884	3	FACETS	1	0.905	1	0.344	0.303	0.389	CLONAL	1	TRUE	0	0.308193644414917	3		490	558	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743908	40743908	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	75	470	0	ENST00000373198.4:c.3087C>A	p.Asp1029Glu	p.D1029E	ENST00000373198	NM_133170.3	1029	gaC/gaA	23/32	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.308193644414917	2		470	432	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522680	176522680	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	72	602	0	ENST00000292408.4:c.1777G>T	p.Ala593Ser	p.A593S	ENST00000292408	NM_213647.1	593	Gcc/Tcc	13/18	1	2	FACETS	0.827	0.723	0.939	0.827	0.723	0.939	CLONAL	1	TRUE	1	0.308193644414917	2		602	565	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120785	94120785	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	74	482	0	ENST00000369303.4:c.266G>A	p.Trp89Ter	p.W89*	ENST00000369303	NM_004440.3	89	tGg/tAg	3/17	0.308193644414917	1	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	0	0.308193644414917	1		482	395	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845415	151845415	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	41	642	0	ENST00000262189.6:c.13597C>T	p.Arg4533Ter	p.R4533*	ENST00000262189	NM_170606.2	4533	Cga/Tga	52/59	1	2	FACETS	0.833	0.7	0.978	0.833	0.7	0.978	CLONAL	1	TRUE	1	0.43	2		642	229	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0065150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	16	338	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		338	330	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432166	121432166	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	29	520	0	ENST00000257555.6:c.913C>G	p.Pro305Ala	p.P305A	ENST00000257555		305	Cct/Gct	4/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		520	538	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0065151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	80	457	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.237688283657434	2		457	613	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627451	37627454	+	frameshift_variant	Frame_Shift_Del	DEL	TCTG	TCTG	CC	novel	NA	P-0065151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	78	559	0	ENST00000447079.4:c.1366_1369delinsCC	p.Ser456ProfsTer5	p.S456Pfs*5	ENST00000447079	NM_015083.1	456	TCTGcc/CCcc	2/14	1	2	FACETS	0.902	0.792	1	0.902	0.792	1	CLONAL	1	TRUE	1	0.237688283657434	2		559	728	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0065151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	92	584	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.237688283657434	2		584	691	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978930	25978930	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	135	406	0	ENST00000435504.4:c.993C>A	p.Phe331Leu	p.F331L	ENST00000435504		331	ttC/ttA	10/13	0.437311100042004	1	FACETS	0.829	0.775	0.881	0.829	0.775	0.881	INDETERMINATE	1	TRUE	0	0.844273243771007	1		406	223	SUCCESS
APC	324	MSKCC	GRCh37	5	112170648	112170648	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	53	416	0	ENST00000257430.4:c.1744G>T	p.Glu582Ter	p.E582*	ENST00000257430	NM_000038.5	582	Gaa/Taa	15/16	0.844273243771007	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.844273243771007	1		416	61	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61322907	61322907	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	12	321	0	ENST00000283752.5:c.1157G>C	p.Arg386Thr	p.R386T	ENST00000283752	NM_006919.2	386	aGa/aCa	8/8	0.731386531849549	2	FACETS	0.711	0.52	0.923	0.355	0.26	0.462	CLONAL	1	TRUE	0	0.844273243771007	2		321	40	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798860	42798860	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	133	681	0	ENST00000575354.2:c.4434del	p.Gln1479ArgfsTer31	p.Q1479Rfs*31	ENST00000575354	NM_015125.3	1478	Ttt/tt	19/20	0.259421486988743	2	FACETS	1	0.986	1	0.64	0.595	0.685	INDETERMINATE	1	TRUE	0	0.844273243771007	2		681	246	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383804	84383805	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0065152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	57	500	0	ENST00000321945.7:c.1046_1047dup	p.Asp350Ter	p.D350*	ENST00000321945	NM_139076.2	349	-/TA	9/9	0.143408531392392	4	FACETS	0.996	0.882	1	0.996	0.882	1	INDETERMINATE	2	TRUE	2	0.844273243771007	4		500	125	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650825	48650825	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	33	516	0	ENST00000376670.3:c.694C>G	p.His232Asp	p.H232D	ENST00000376670	NM_002049.3	232	Cac/Gac	4/6	0.525843434755895	1	FACETS	0.601	0.497	0.714	0.601	0.497	0.714	SUBCLONAL	1	TRUE	0	0.557621424220604	1		516	142	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	66	789	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.969	0.842	1	0.969	0.842	1	CLONAL	1	FALSE	1	0.264532907855936	2		789	515	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806089	1806089	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913479	NA	P-0065167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	92	575	0	ENST00000260795.2:c.1108G>T	p.Gly370Cys	p.G370C	ENST00000260795		370	Ggc/Tgc	8/17	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.264532907855936	2		575	579	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842042	3842042	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783464	NA	P-0065167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	84	444	0	ENST00000262367.5:c.1270C>T	p.Arg424Ter	p.R424*	ENST00000262367	NM_004380.2	424	Cga/Tga	5/31	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.264532907855936	2		444	520	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197751	123197752	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	31	240	0	ENST00000218089.9:c.1876dup	p.Thr626AsnfsTer9	p.T626Nfs*9	ENST00000218089	NM_001042749.1	625	-/A	20/35	1	1	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	FALSE	0	0.264532907855936	1		240	194	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58725313	58725313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	97	487	0	ENST00000305921.3:c.887C>T	p.Thr296Ile	p.T296I	ENST00000305921	NM_003620.3	296	aCa/aTa	4/6	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.264532907855936	2		487	536	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3113410	3113410	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587777019	NA	P-0065167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	32	617	0	ENST00000078429.4:c.404T>A	p.Leu135Gln	p.L135Q	ENST00000078429	NM_002067.2	135	cTg/cAg	3/7	1	2	FACETS	0.411	0.332	0.5	0.411	0.332	0.5	SUBCLONAL	1	FALSE	1	0.264532907855936	2		617	589	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428444	72428445	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	36	455	0	ENST00000477973.2:c.557dup	p.Ile187AsnfsTer2	p.I187Nfs*2	ENST00000477973	NM_012234.5	187	att/aAtt	2/4	1	2	FACETS	0.531	0.435	0.637	0.531	0.435	0.637	SUBCLONAL	1	FALSE	1	0.264532907855936	2		455	513	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929420	44929423	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	novel	NA	P-0065167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	93	297	0	ENST00000377967.4:c.2520_2523del	p.Ser840ArgfsTer26	p.S840Rfs*26	ENST00000377967	NM_021140.2	840	agTGTT/ag	17/29	1	1	FACETS	0.872	0.782	0.965	1	0.985	1	CLONAL	2	FALSE	0	0.264532907855936	1		297	350	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928081	178928099	+	protein_altering_variant	In_Frame_Del	DEL	AGATTTGCTGAACCCTATT	AGATTTGCTGAACCCTATT	G	novel	NA	P-0065167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	32	421	0	ENST00000263967.3:c.1359_1377delinsG	p.Asp454_Ile459del	p.D454_I459del	ENST00000263967	NM_006218.2	453	gaAGATTTGCTGAACCCTATT/gaG	8/21	1	2	FACETS	0.516	0.418	0.626	0.516	0.418	0.626	SUBCLONAL	1	FALSE	1	0.264532907855936	2		421	469	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	31	789	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.841	0.682	1	0.841	0.682	1	CLONAL	1	TRUE	1	0.261440721520213	2		789	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	58	702	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.261440721520213	1	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	0	0.261440721520213	1		702	379	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186780	11186780	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	37	428	0	ENST00000361445.4:c.6425G>C	p.Gly2142Ala	p.G2142A	ENST00000361445	NM_004958.3	2142	gGa/gCa	46/58	1	2	FACETS	0.685	0.565	0.819	0.685	0.565	0.819	SUBCLONAL	1	TRUE	1	0.261440721520213	2		428	413	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	41	549	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.778	0.649	0.921	0.778	0.649	0.921	CLONAL	1	TRUE	1	0.261440721520213	2		549	403	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	132	562	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.234088347141461	2	FACETS	0.99	0.904	1	0.99	0.904	1	CLONAL	2	TRUE	0	0.261440721520213	2		562	510	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443892	52443892	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	57	547	0	ENST00000460680.1:c.3G>A	p.Met1?	p.M1?	ENST00000460680	NM_004656.3	1	atG/atA	1/17	0.261440721520213	1	FACETS	0.795	0.683	0.916	0.795	0.683	0.916	CLONAL	1	TRUE	0	0.261440721520213	1		547	477	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439727	140439727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507485	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	33	230	0	ENST00000288602.6:c.2012G>A	p.Arg671Gln	p.R671Q	ENST00000288602	NM_004333.4	671	cGa/cAa	17/18	0.222792279896656	3	FACETS	0.759	0.624	0.908	0.759	0.624	0.908	CLONAL	2	TRUE	1	0.261440721520213	3		230	188	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763509	59763509	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs578022079	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	26	351	0	ENST00000259008.2:c.2593C>T	p.Arg865Trp	p.R865W	ENST00000259008	NM_032043.2	865	Cgg/Tgg	19/20	0.222792279896656	3	FACETS	0.798	0.633	0.985	0.399	0.316	0.493	CLONAL	1	TRUE	1	0.261440721520213	3		351	282	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59937163	59937163	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	31	331	0	ENST00000259008.2:c.199C>G	p.Leu67Val	p.L67V	ENST00000259008	NM_032043.2	67	Ctt/Gtt	3/20	0.222792279896656	3	FACETS	0.918	0.745	1	0.459	0.372	0.557	CLONAL	1	TRUE	1	0.261440721520213	3		331	292	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784941	9784941	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778194087	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	60	492	1	ENST00000377346.4:c.2944C>T	p.Arg982Trp	p.R982W	ENST00000377346	NM_005026.3	982	Cgg/Tgg	23/24	1	2	FACETS	0.92	0.794	1	0.92	0.794	1	CLONAL	1	TRUE	1	0.261440721520213	2		493	499	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582062	189582062	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	64	454	0	ENST00000264731.3:c.621G>C	p.Lys207Asn	p.K207N	ENST00000264731	NM_003722.4	207	aaG/aaC	5/14	0.222792279896656	3	FACETS	1	0.891	1	0.515	0.447	0.59	CLONAL	1	TRUE	1	0.261440721520213	3		454	537	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541504	187541504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1272319296	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	66	496	0	ENST00000441802.2:c.6236C>T	p.Pro2079Leu	p.P2079L	ENST00000441802	NM_005245.3	2079	cCg/cTg	10/27	1	2	FACETS	0.996	0.866	1	0.996	0.866	1	CLONAL	1	TRUE	1	0.261440721520213	2		496	507	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	67	684	1	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	1	2	FACETS	0.951	0.827	1	0.951	0.827	1	CLONAL	1	TRUE	1	0.261440721520213	2		685	539	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28600622	28600622	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	50	430	0	ENST00000253063.3:c.973G>C	p.Asp325His	p.D325H	ENST00000253063	NM_031459.4	325	Gac/Cac	7/10	1	2	FACETS	0.949	0.807	1	0.949	0.807	1	CLONAL	1	TRUE	1	0.261440721520213	2		430	403	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150936104	150936104	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	136	502	0	ENST00000271640.5:c.3556G>A	p.Asp1186Asn	p.D1186N	ENST00000271640	NM_001145415.1	1186	Gac/Aac	20/22	0.222792279896656	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.261440721520213	3		502	545	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981486	201981486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	59	462	0	ENST00000359651.3:c.400G>A	p.Asp134Asn	p.D134N	ENST00000359651		134	Gat/Aat	3/8	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.261440721520213	2		462	340	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944752	71944752	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	53	524	0	ENST00000298229.2:c.2176G>C	p.Glu726Gln	p.E726Q	ENST00000298229	NM_001567.3	726	Gag/Cag	19/28	1	2	FACETS	0.956	0.817	1	0.956	0.817	1	CLONAL	1	TRUE	1	0.261440721520213	2		524	424	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343324	118343324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560915401	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	44	453	0	ENST00000534358.1:c.1450G>A	p.Val484Ile	p.V484I	ENST00000534358	NM_005933.3	484	Gtt/Att	3/36	1	2	FACETS	0.811	0.681	0.954	0.811	0.681	0.954	CLONAL	1	TRUE	1	0.261440721520213	2		453	415	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244447	46244447	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	59	559	0	ENST00000334344.6:c.2541C>G	p.Ile847Met	p.I847M	ENST00000334344	NM_152641.2	847	atC/atG	15/21	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.261440721520213	2		559	439	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117457	115117457	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	51	417	0	ENST00000257566.3:c.718-1G>A		p.X240_splice	ENST00000257566	NM_016569.3	240			1	2	FACETS	0.99	0.844	1	0.99	0.844	1	CLONAL	1	TRUE	1	0.261440721520213	2		417	394	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357452	89357452	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	68	501	0	ENST00000301030.4:c.366G>C	p.Gln122His	p.Q122H	ENST00000301030	NM_001256183.1	122	caG/caC	5/13	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.261440721520213	2		501	472	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244327	41244327	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786202155	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	46	423	0	ENST00000357654.3:c.3221G>C	p.Arg1074Thr	p.R1074T	ENST00000357654	NM_007294.3	1074	aGa/aCa	10/23	0.222792279896656	3	FACETS	1	0.941	1	0.624	0.528	0.729	CLONAL	1	TRUE	1	0.261440721520213	3		423	319	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245518	41245518	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	45	498	0	ENST00000357654.3:c.2030G>C	p.Gly677Ala	p.G677A	ENST00000357654	NM_007294.3	677	gGa/gCa	10/23	0.222792279896656	3	FACETS	0.968	0.815	1	0.484	0.407	0.569	CLONAL	1	TRUE	1	0.261440721520213	3		498	402	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6214012	6214012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559595286	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	34	486	0	ENST00000252674.7:c.1345G>A	p.Asp449Asn	p.D449N	ENST00000252674	NM_005934.3	449	Gac/Aac	9/12	1	2	FACETS	0.594	0.485	0.716	0.594	0.485	0.716	SUBCLONAL	1	TRUE	1	0.261440721520213	2		486	438	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961547	18961547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367878096	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	37	363	0	ENST00000262803.5:c.680C>T	p.Ser227Leu	p.S227L	ENST00000262803	NM_002911.3	227	tCg/tTg	5/24	1	2	FACETS	0.775	0.64	0.926	0.775	0.64	0.926	CLONAL	1	TRUE	1	0.261440721520213	2		363	365	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551316	29551316	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	53	492	0	ENST00000389048.3:c.1314G>T	p.Gln438His	p.Q438H	ENST00000389048	NM_004304.4	438	caG/caT	6/29	0.222792279896656	3	FACETS	0.953	0.814	1	0.477	0.407	0.553	CLONAL	1	TRUE	1	0.261440721520213	3		492	481	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564653	55564653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	50	411	1	ENST00000288135.5:c.541C>T	p.Arg181Trp	p.R181W	ENST00000288135	NM_000222.2	181	Cgg/Tgg	3/21	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.261440721520213	2		412	372	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280023	66280023	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	40	358	0	ENST00000273854.3:c.1666G>C	p.Glu556Gln	p.E556Q	ENST00000273854	NM_004439.5	556	Gag/Cag	7/18	1	2	FACETS	0.857	0.714	1	0.857	0.714	1	CLONAL	1	TRUE	1	0.261440721520213	2		358	357	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549788	187549788	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	55	426	0	ENST00000441802.2:c.4453G>T	p.Glu1485Ter	p.E1485*	ENST00000441802	NM_005245.3	1485	Gag/Tag	8/27	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.261440721520213	2		426	357	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590457	67590457	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	35	334	0	ENST00000274335.5:c.1519G>C	p.Glu507Gln	p.E507Q	ENST00000274335		507	Gaa/Caa	11/15	1	2	FACETS	0.914	0.752	1	0.914	0.752	1	CLONAL	1	TRUE	1	0.261440721520213	2		334	293	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821272	32821272	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	60	560	0	ENST00000354258.4:c.322G>T	p.Val108Leu	p.V108L	ENST00000354258	NM_000593.5	108	Gtg/Ttg	1/11	1	2	FACETS	0.744	0.641	0.856	0.744	0.641	0.856	SUBCLONAL	1	TRUE	1	0.261440721520213	2		560	617	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137313610	137313610	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	129	545	0	ENST00000481739.1:c.869C>T	p.Ser290Leu	p.S290L	ENST00000481739	NM_002957.4	290	tCa/tTa	6/10	0.166213754362707	3	FACETS	0.936	0.852	1	0.936	0.852	1	CLONAL	2	TRUE	1	0.261440721520213	3		545	596	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360708	70360708	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	53	460	0	ENST00000374080.3:c.6267+1G>A		p.X2089_splice	ENST00000374080		2089			0.261440721520213	3	FACETS	0.846	0.721	0.982	0.423	0.36	0.491	CLONAL	1	TRUE	1	0.261440721520213	3		460	542	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444684	49444684	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	G	G	TA	novel	NA	P-0065168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	67	609	0	ENST00000301067.7:c.2782delinsTA	p.Gln928Ter	p.Q928*	ENST00000301067	NM_003482.3	928	Cag/TAag	10/54	1	2	FACETS	0.912	0.793	1	0.912	0.793	1	CLONAL	1	TRUE	1	0.261440721520213	2		609	562	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0065170-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	55	393	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.863	0.742	0.995	0.863	0.742	0.995	CLONAL	1	TRUE	1	0.365043134087233	2		393	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0065170-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	87	766	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.365043134087233	1	FACETS	0.913	0.812	1	0.913	0.812	1	CLONAL	1	TRUE	0	0.365043134087233	1		767	427	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427735	72427735	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065170-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	93	438	0	ENST00000477973.2:c.755T>G	p.Val252Gly	p.V252G	ENST00000477973	NM_012234.5	252	gTg/gGg	4/4	1	2	FACETS	0.875	0.78	0.977	0.875	0.78	0.977	CLONAL	1	TRUE	1	0.365043134087233	2		438	582	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455578	189455578	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065170-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	108	450	0	ENST00000264731.3:c.112T>A	p.Ser38Thr	p.S38T	ENST00000264731	NM_003722.4	38	Tcc/Acc	2/14	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.365043134087233	2		450	497	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0065171-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	72	667	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.625	0.545	0.712	0.625	0.545	0.712	SUBCLONAL	1	TRUE	1	0.29	2		668	794	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405956	49405956	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065171-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	92	458	1	ENST00000418115.1:c.182C>A	p.Ala61Asp	p.A61D	ENST00000418115	NM_001664.2	61	gCt/gAt	3/5	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.29	2		459	621	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155929	119155929	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs774743605	NA	P-0065171-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	52	629	0	ENST00000264033.4:c.1594C>A	p.Pro532Thr	p.P532T	ENST00000264033	NM_005188.3	532	Cca/Aca	11/16	1	2	FACETS	0.414	0.351	0.483	0.414	0.351	0.483	SUBCLONAL	1	TRUE	1	0.29	2		629	866	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235284	235284	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs372738835	NA	P-0065171-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	19	324	0	ENST00000264932.6:c.1090G>C	p.Val364Leu	p.V364L	ENST00000264932	NM_004168.2	364	Gtc/Ctc	9/15	1	2	FACETS	0.356	0.27	0.458	0.356	0.27	0.458	SUBCLONAL	1	TRUE	1	0.29	2		324	368	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512326	149512326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371975483	NA	P-0065171-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	93	662	0	ENST00000261799.4:c.1114G>A	p.Val372Met	p.V372M	ENST00000261799	NM_002609.3	372	Gtg/Atg	7/23	1	2	FACETS	0.803	0.713	0.898	0.803	0.713	0.898	CLONAL	1	TRUE	1	0.29	2		662	799	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997427	149997430	+	frameshift_variant	Frame_Shift_Del	DEL	AAGA	AAGA	-	novel	NA	P-0065171-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	25	430	0	ENST00000253339.5:c.2849_2852del	p.Phe950TrpfsTer6	p.F950Wfs*6	ENST00000253339		950	tTCTTg/tg	6/7	1	2	FACETS	0.354	0.278	0.442	0.354	0.278	0.442	SUBCLONAL	1	TRUE	1	0.29	2		430	487	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913381	NA	P-0065172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	22	511	1	ENST00000304494.5:c.322G>A	p.Asp108Asn	p.D108N	ENST00000304494	NM_000077.4	108	Gat/Aat	2/3	0.646335765983803	0	FACETS		NA	1			1	NA	1	TRUE	0	0.690264239039613	0		512	153	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597401	10597401	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	150	424	0	ENST00000171111.5:c.1802G>T	p.Arg601Leu	p.R601L	ENST00000171111	NM_203500.1	601	cGg/cTg	6/6	0.682915073950999	1	FACETS	0.906	0.843	0.97	0.906	0.843	0.97	CLONAL	1	TRUE	0	0.690264239039613	1		424	314	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003303	42003303	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0065172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	86	470	0	ENST00000219905.7:c.2840C>G	p.Ser947Ter	p.S947*	ENST00000219905	NM_001164273.1	947	tCa/tGa	8/24	0.690264239039613	1	FACETS	0.796	0.719	0.874	0.796	0.719	0.874	SUBCLONAL	1	TRUE	0	0.690264239039613	1		470	205	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218415	1218415	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs112675807	NA	P-0065172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	111	397	0	ENST00000326873.7:c.291-1G>T		p.X97_splice	ENST00000326873	NM_000455.4	97			0.682915073950999	1	FACETS	0.916	0.842	0.99	0.916	0.842	0.99	CLONAL	1	TRUE	0	0.690264239039613	1		397	230	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645138	67645138	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	115	478	0	ENST00000264010.4:c.403C>T	p.Gln135Ter	p.Q135*	ENST00000264010	NM_006565.3	135	Cag/Tag	3/12	1	2	FACETS	0.986	0.899	1	0.986	0.899	1	CLONAL	1	TRUE	1	0.690264239039613	2		478	338	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984434	201984434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	158	416	0	ENST00000359651.3:c.1099C>T	p.Leu367Phe	p.L367F	ENST00000359651		367	Ctc/Ttc	8/8	0.690264239039613	3	FACETS	0.974	0.896	1	0.487	0.448	0.528	CLONAL	1	TRUE	1	0.690264239039613	3		416	632	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50751312	50751312	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	131	351	0	ENST00000307179.4:c.451A>G	p.Lys151Glu	p.K151E	ENST00000307179		151	Aaa/Gaa	5/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.690264239039613	2		351	350	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61306934	61306934	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	92	486	0	ENST00000341074.5:c.546C>G	p.Phe182Leu	p.F182L	ENST00000341074	NM_002974.2	182	ttC/ttG	6/8	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.690264239039613	2		486	247	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2202739	2202739	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	29	490	0	ENST00000398665.3:c.748G>T	p.Asp250Tyr	p.D250Y	ENST00000398665	NM_032482.2	250	Gat/Tat	9/28	0.682915073950999	1	FACETS	0.179	0.144	0.219	0.179	0.144	0.219	SUBCLONAL	1	TRUE	0	0.690264239039613	1		490	307	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212435	36212435	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	96	554	0	ENST00000222270.7:c.2186A>T	p.Asn729Ile	p.N729I	ENST00000222270	NM_014727.1	729	aAc/aTc	3/37	0.363640001512622	1	FACETS	0.46	0.413	0.51	0.46	0.413	0.51	INDETERMINATE	1	TRUE	0	0.690264239039613	1		554	396	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860473	151860473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	34	539	0	ENST00000262189.6:c.10189G>A	p.Glu3397Lys	p.E3397K	ENST00000262189	NM_170606.2	3397	Gaa/Aaa	43/59	1	2	FACETS	0.225	0.183	0.272	0.225	0.183	0.272	SUBCLONAL	1	TRUE	1	0.690264239039613	2		539	438	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860512	151860512	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	28	571	0	ENST00000262189.6:c.10150G>C	p.Glu3384Gln	p.E3384Q	ENST00000262189	NM_170606.2	3384	Gaa/Caa	43/59	1	2	FACETS	0.169	0.135	0.209	0.169	0.135	0.209	SUBCLONAL	1	TRUE	1	0.690264239039613	2		571	479	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597401	10597401	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065172-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	195	424	0	ENST00000171111.5:c.1802G>T	p.Arg601Leu	p.R601L	ENST00000171111	NM_203500.1	601	cGg/cTg	6/6	0.646601610216712	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.646601610216712	1		424	399	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003303	42003303	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0065172-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	212	470	0	ENST00000219905.7:c.2840C>G	p.Ser947Ter	p.S947*	ENST00000219905	NM_001164273.1	947	tCa/tGa	8/24	0.646601610216712	1	FACETS	0.99	0.932	1	0.99	0.932	1	CLONAL	1	TRUE	0	0.646601610216712	1		470	448	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218415	1218415	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs112675807	NA	P-0065172-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	185	397	0	ENST00000326873.7:c.291-1G>T		p.X97_splice	ENST00000326873	NM_000455.4	97			0.646601610216712	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.646601610216712	1		397	377	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645138	67645138	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065172-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	221	478	0	ENST00000264010.4:c.403C>T	p.Gln135Ter	p.Q135*	ENST00000264010	NM_006565.3	135	Cag/Tag	3/12	1	2	FACETS	0.965	0.902	1	0.965	0.902	1	CLONAL	1	TRUE	1	0.646601610216712	2		478	708	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984434	201984434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065172-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	202	416	0	ENST00000359651.3:c.1099C>T	p.Leu367Phe	p.L367F	ENST00000359651		367	Ctc/Ttc	8/8	0.646601610216712	3	FACETS	1	0.949	1	0.514	0.477	0.551	CLONAL	1	TRUE	1	0.646601610216712	3		416	805	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50751312	50751312	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065172-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	191	351	0	ENST00000307179.4:c.451A>G	p.Lys151Glu	p.K151E	ENST00000307179		151	Aaa/Gaa	5/20	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.646601610216712	2		351	582	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61306934	61306934	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065172-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	215	486	0	ENST00000341074.5:c.546C>G	p.Phe182Leu	p.F182L	ENST00000341074	NM_002974.2	182	ttC/ttG	6/8	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.646601610216712	2		486	653	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731242	162731242	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0065172-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	213	402	0	ENST00000367921.3:c.1097C>G	p.Ser366Ter	p.S366*	ENST00000367921	NM_006182.2	366	tCa/tGa	9/18	0.646601610216712	3	FACETS	1	0.939	1	0.505	0.47	0.542	CLONAL	1	TRUE	1	0.646601610216712	3		402	863	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141019	55141020	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAAATTCGCTGGAGGGTCATTGAATCAATC	novel	NA	P-0065173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	202	468	0	ENST00000257290.5:c.1666_1695dup	p.Glu556_Ile565dup	p.E556_I565dup	ENST00000257290	NM_006206.4	556	-/GAAATTCGCTGGAGGGTCATTGAATCAATC	12/23	0.576775949474359	3	FACETS	1	0.986	1	0.617	0.574	0.662	CLONAL	1	TRUE	1	0.577652110764776	3		468	730	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0065174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	198	441	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.490649481155718	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.52186074131785	1		441	552	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821601	72821618	+	inframe_deletion	In_Frame_Del	DEL	CCGCCGCCGCCGCCGCCA	CCGCCGCCGCCGCCGCCA	-	rs778016374	NA	P-0065174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	37	591	0	ENST00000268489.5:c.10557_10574del	p.Gly3522_Gly3527del	p.G3522_G3527del	ENST00000268489	NM_006885.3	3519	ggTGGCGGCGGCGGCGGCGGc/ggc	10/10	1	2	FACETS	0.208	0.171	0.25	0.208	0.171	0.25	SUBCLONAL	1	TRUE	1	0.52186074131785	2		591	682	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339499	81339499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	126	422	0	ENST00000222390.5:c.1505G>A	p.Arg502Gln	p.R502Q	ENST00000222390	NM_000601.4	502	cGa/cAa	13/18	0.364963236010054	4	FACETS	0.876	0.793	0.963	0.438	0.396	0.482	CLONAL	1	TRUE	2	0.52186074131785	4		422	839	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819721	81819721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370352962	NA	P-0065174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	162	566	1	ENST00000359376.3:c.127G>A	p.Val43Ile	p.V43I	ENST00000359376	NM_002661.3	43	Gtc/Atc	2/33	1	2	FACETS	0.881	0.81	0.954	0.881	0.81	0.954	CLONAL	1	TRUE	1	0.52186074131785	2		567	705	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749278	43749278	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	83	519	0	ENST00000382044.4:c.1528G>T	p.Gly510Trp	p.G510W	ENST00000382044	NM_001141980.1	510	Ggg/Tgg	12/28	0.511112811619225	2	FACETS	0.426	0.375	0.48	0.213	0.187	0.24	SUBCLONAL	1	TRUE	0	0.52186074131785	2		519	747	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165755	47165755	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	50	567	0	ENST00000409792.3:c.371del	p.Leu124TyrfsTer28	p.L124Yfs*28	ENST00000409792	NM_014159.6	124	tTa/ta	3/21	1	2	FACETS	0.255	0.216	0.299	0.255	0.216	0.299	SUBCLONAL	1	TRUE	1	0.52186074131785	2		567	751	SUCCESS
APC	324	MSKCC	GRCh37	5	112175393	112175394	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CACC	novel	NA	P-0065174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	284	581	0	ENST00000257430.4:c.4105_4108dup	p.Lys1370ThrfsTer6	p.K1370Tfs*6	ENST00000257430	NM_000038.5	1368	aca/aCACCca	16/16	0.495365458199973	2	FACETS	0.828	0.784	0.873	0.828	0.784	0.873	CLONAL	2	TRUE	0	0.52186074131785	2		581	657	SUCCESS
APC	324	MSKCC	GRCh37	5	112175400	112175400	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1365778107	NA	P-0065174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	296	563	0	ENST00000257430.4:c.4109A>G	p.Lys1370Arg	p.K1370R	ENST00000257430	NM_000038.5	1370	aAa/aGa	16/16	0.495365458199973	2	FACETS	0.903	0.858	0.949	0.903	0.858	0.949	CLONAL	2	TRUE	0	0.52186074131785	2		563	628	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0065174-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	50	256	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.380156788307756	4	FACETS	0.941	0.814	1	0.941	0.814	1	CLONAL	2	TRUE	2	0.506785092813111	4		256	158	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0065174-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	38	262	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.267461869104699	4	FACETS	0.763	0.642	0.894	0.763	0.642	0.894	INDETERMINATE	2	TRUE	2	0.506785092813111	4		262	148	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413010	49413010	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519952	NA	P-0065174-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	9	443	0	ENST00000418115.1:c.13C>T	p.Arg5Trp	p.R5W	ENST00000418115	NM_001664.2	5	Cgg/Tgg	2/5	0.288114297966061	5	FACETS	0.172	0.113	0.248	0.057	0.037	0.083	INDETERMINATE	1	TRUE	2	0.506785092813111	5		443	363	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0065174-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	97	386	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.436478094706668	2	FACETS	0.757	0.686	0.829	0.757	0.686	0.829	SUBCLONAL	2	TRUE	0	0.506785092813111	2		386	253	SUCCESS
APC	324	MSKCC	GRCh37	5	112175438	112175439	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0065174-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	29	520	0	ENST00000257430.4:c.4147_4148del	p.Met1383ValfsTer2	p.M1383Vfs*2	ENST00000257430	NM_000038.5	1383	ATg/g	16/16	0.267461869104699	4	FACETS	0.98	0.794	1	0.49	0.397	0.593	INDETERMINATE	1	TRUE	2	0.506785092813111	4		520	176	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028805	47028805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065174-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	179	283	6	ENST00000377604.3:c.109C>T	p.Arg37Trp	p.R37W	ENST00000377604	NM_001204468.1	37	Cgg/Tgg	3/24	0.506785092813111	4	FACETS	1	0.987	1			1	CLONAL	4	TRUE	NA	0.506785092813111	4		289	241	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577544	7577544	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587780074	NA	P-0065174-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	109	516	0	ENST00000269305.4:c.737T>G	p.Met246Arg	p.M246R	ENST00000269305	NM_001126112.2	246	aTg/aGg	7/11	0.506785092813111	5	FACETS	1	0.929	1	0.686	0.622	0.752	CLONAL	2	TRUE	2	0.506785092813111	5		516	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578178	7578178	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065174-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	135	640	0	ENST00000269305.4:c.671A>T	p.Glu224Val	p.E224V	ENST00000269305	NM_001126112.2	224	gAg/gTg	6/11	0.506785092813111	5	FACETS	1	0.925	1	0.674	0.617	0.733	CLONAL	2	TRUE	2	0.506785092813111	5		640	464	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741999	162741999	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065175-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	44	642	0	ENST00000367921.3:c.1690A>T	p.Thr564Ser	p.T564S	ENST00000367921	NM_006182.2	564	Act/Tct	13/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		642	591	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	359980	359980	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065175-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	84	595	0	ENST00000262320.3:c.1109A>G	p.His370Arg	p.H370R	ENST00000262320	NM_003502.3	370	cAc/cGc	4/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		595	804	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0065175-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	90	718	0	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		718	1117	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774786	73774786	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065175-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	72	564	0	ENST00000254810.4:c.301C>G	p.Leu101Val	p.L101V	ENST00000254810	NM_005324.3	101	Ctg/Gtg	4/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		564	947	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030275	11030275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065175-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	70	617	0	ENST00000327064.4:c.1025C>T	p.Thr342Ile	p.T342I	ENST00000327064	NM_199141.1	342	aCa/aTa	9/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		617	816	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422637	47422637	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065175-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	73	617	0	ENST00000404338.3:c.705C>A	p.Asn235Lys	p.N235K	ENST00000404338	NM_004491.4	235	aaC/aaA	1/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		617	610	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932906	49932906	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759642387	NA	P-0065175-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	96	706	0	ENST00000296474.3:c.3038C>T	p.Ser1013Leu	p.S1013L	ENST00000296474	NM_002447.2	1013	tCg/tTg	13/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		706	1092	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799656	72799656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065175-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	36	637	0	ENST00000325599.8:c.1513G>A	p.Val505Ile	p.V505I	ENST00000325599	NM_018130.2	505	Gtt/Att	11/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		637	611	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796747	57796747	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065175-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	23	613	0	ENST00000309042.7:c.1723A>T	p.Met575Leu	p.M575L	ENST00000309042	NM_005612.4	575	Atg/Ttg	4/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		613	370	SUCCESS
ALB	213	MSKCC	GRCh37	4	74272392	74272392	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065175-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	10	479	0	ENST00000295897.4:c.184G>T	p.Asp62Tyr	p.D62Y	ENST00000295897	NM_000477.5	62	Gat/Tat	3/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		479	89	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538307	187538307	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065175-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	11	564	0	ENST00000441802.2:c.8927G>T	p.Trp2976Leu	p.W2976L	ENST00000441802	NM_005245.3	2976	tGg/tTg	11/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		564	154	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539378	187539378	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065175-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	30	708	0	ENST00000441802.2:c.8362G>A	p.Glu2788Lys	p.E2788K	ENST00000441802	NM_005245.3	2788	Gag/Aag	10/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		708	514	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250439	26250439	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065175-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	80	749	0	ENST00000446824.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000446824	NM_021018.2	132	cGc/cTc	1/1	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		749	1202	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346448	152346448	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065175-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	18	509	0	ENST00000359321.1:c.122G>C	p.Gly41Ala	p.G41A	ENST00000359321	NM_005431.1	41	gGt/gCt	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		509	201	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370847	55370847	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065175-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	43	587	0	ENST00000297316.4:c.149C>A	p.Ala50Glu	p.A50E	ENST00000297316	NM_022454.3	50	gCg/gAg	1/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		587	781	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054648	5054648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765286468	NA	P-0065175-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	14	588	0	ENST00000381652.3:c.700C>T	p.Arg234Cys	p.R234C	ENST00000381652	NM_004972.3	234	Cgc/Tgc	7/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		588	141	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486320	8486320	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065175-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	40	468	1	ENST00000356435.5:c.2497C>A	p.His833Asn	p.H833N	ENST00000356435		833	Cac/Aac	17/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		469	484	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53253924	53253924	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065175-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	54	546	1	ENST00000375401.3:c.148G>T	p.Ala50Ser	p.A50S	ENST00000375401	NM_004187.3	50	Gcg/Tcg	1/26	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		547	796	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115982	8115983	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065176-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	292	616	0	ENST00000346208.3:c.1330dup	p.Ter444LeufsTer63	p.*444Lfs*63	ENST00000346208		443	ggt/ggTt	6/6	1	2	FACETS	0.982	0.928	1	0.982	0.928	1	CLONAL	1	TRUE	1	0.763510755385898	2		616	779	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575096	48575096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555685159	NA	P-0065178-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	206	463	0	ENST00000342988.3:c.290G>A	p.Arg97His	p.R97H	ENST00000342988	NM_005359.5	97	cGt/cAt	3/12	0.738211653995021	1	FACETS	0.939	0.887	0.991	0.939	0.887	0.991	CLONAL	1	TRUE	0	0.738211653995021	1		463	375	SUCCESS
APC	324	MSKCC	GRCh37	5	112175588	112175588	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065178-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	235	667	0	ENST00000257430.4:c.4298del	p.Pro1433GlnfsTer40	p.P1433Qfs*40	ENST00000257430	NM_000038.5	1433	Cca/ca	16/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.738211653995021	2		667	630	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432498	49432498	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763549369	NA	P-0065178-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	214	625	1	ENST00000301067.7:c.8641C>T	p.Arg2881Trp	p.R2881W	ENST00000301067	NM_003482.3	2881	Cgg/Tgg	34/54	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.738211653995021	2		626	532	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0065178-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	129	293	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.887	0.812	0.964	0.887	0.812	0.964	CLONAL	1	TRUE	1	0.738211653995021	2		293	394	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218140	36218140	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065178-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	64	541	0	ENST00000222270.7:c.4087T>C	p.Trp1363Arg	p.W1363R	ENST00000222270	NM_014727.1	1363	Tgg/Cgg	15/37	1	2	FACETS	0.339	0.294	0.388	0.339	0.294	0.388	SUBCLONAL	1	TRUE	1	0.738211653995021	2		541	511	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589863	212589863	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065178-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	83	584	0	ENST00000342788.4:c.679A>T	p.Ser227Cys	p.S227C	ENST00000342788	NM_005235.2	227	Agt/Tgt	6/28	0.294607328938447	3	FACETS	0.482	0.425	0.542	0.241	0.212	0.271	INDETERMINATE	1	TRUE	1	0.738211653995021	3		584	639	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253754	153253754	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065178-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	164	413	1	ENST00000281708.4:c.979G>T	p.Glu327Ter	p.E327*	ENST00000281708	NM_033632.3	327	Gaa/Taa	6/12	1	2	FACETS	0.951	0.881	1	0.951	0.881	1	CLONAL	1	TRUE	1	0.738211653995021	2		414	467	SUCCESS
APC	324	MSKCC	GRCh37	5	112174562	112174562	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065178-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	220	553	0	ENST00000257430.4:c.3272del	p.Pro1091HisfsTer35	p.P1091Hfs*35	ENST00000257430	NM_000038.5	1091	Cca/ca	16/16	1	2	FACETS	0.916	0.857	0.976	0.916	0.857	0.976	CLONAL	1	TRUE	1	0.738211653995021	2		553	651	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271372	26271372	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs141552598	NA	P-0065178-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	216	750	0	ENST00000305910.3:c.241A>G	p.Thr81Ala	p.T81A	ENST00000305910	NM_003534.2	81	Aca/Gca	1/1	1	2	FACETS	0.919	0.859	0.98	0.919	0.859	0.98	CLONAL	1	TRUE	1	0.738211653995021	2		750	637	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741777	145741778	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065178-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	38	697	0	ENST00000428558.2:c.725dup	p.Gln243ProfsTer53	p.Q243Pfs*53	ENST00000428558	NM_004260.3	242	ttc/ttTc	5/22	1	2	FACETS	0.165	0.135	0.197	0.165	0.135	0.197	SUBCLONAL	1	TRUE	1	0.738211653995021	2		697	625	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0065179-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	190	433	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.972	0.906	1	0.972	0.906	1	CLONAL	1	TRUE	1	0.748762489887598	2		433	522	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450366	50450366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065179-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	274	629	0	ENST00000331340.3:c.550C>T	p.Arg184Trp	p.R184W	ENST00000331340	NM_006060.4	184	Cgg/Tgg	5/8	0.174847383632878	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.748762489887598	0		629	719	SUCCESS
APC	324	MSKCC	GRCh37	5	112175225	112175225	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065179-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	268	556	0	ENST00000257430.4:c.3935del	p.Gly1312GlufsTer9	p.G1312Efs*9	ENST00000257430	NM_000038.5	1312	Gga/ga	16/16	1	2	FACETS	0.895	0.842	0.948	0.895	0.842	0.948	CLONAL	1	TRUE	1	0.748762489887598	2		556	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572991	7572991	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065179-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	411	617	1	ENST00000269305.4:c.1118del	p.Lys373ArgfsTer49	p.K373Rfs*49	ENST00000269305	NM_001126112.2	373	aAg/ag	11/11	0.748762489887598	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.748762489887598	1		618	599	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0065179-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	217	379	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.981	0.918	1	0.981	0.918	1	CLONAL	1	TRUE	1	0.748762489887598	2		379	591	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94224109	94224109	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs778229721	NA	P-0065179-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	153	323	1	ENST00000323929.3:c.43A>G	p.Ile15Val	p.I15V	ENST00000323929	NM_005591.3	15	Ata/Gta	3/20	1	2	FACETS	0.987	0.913	1	0.987	0.913	1	CLONAL	1	TRUE	1	0.748762489887598	2		324	414	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233429	69233429	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065179-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	319	643	1	ENST00000462284.1:c.1294G>T	p.Val432Leu	p.V432L	ENST00000462284	NM_002392.5	432	Gtg/Ttg	11/11	1	2	FACETS	0.967	0.916	1	0.967	0.916	1	CLONAL	1	TRUE	1	0.748762489887598	2		644	881	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900991	3900991	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065179-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	244	457	0	ENST00000262367.5:c.105C>A	p.Asp35Glu	p.D35E	ENST00000262367	NM_004380.2	35	gaC/gaA	2/31	1	2	FACETS	0.958	0.901	1	0.958	0.901	1	CLONAL	1	TRUE	1	0.748762489887598	2		457	680	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275120	41275120	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065179-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	358	651	2	ENST00000349496.5:c.1286G>C	p.Cys429Ser	p.C429S	ENST00000349496	NM_001904.3	429	tGc/tCc	9/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.748762489887598	2		653	935	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0065185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	203	342	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.253313180308293	4	FACETS	0.875	0.817	0.934	0.875	0.817	0.934	CLONAL	3	TRUE	1	0.373256482081332	4		342	569	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0065185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	34	478	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	0.338457883031305	3	FACETS	0.343	0.279	0.415	0.172	0.139	0.208	SUBCLONAL	1	TRUE	1	0.373256482081332	3		478	630	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0065185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	180	536	0	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	0.338457883031305	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.373256482081332	3		536	525	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579559	7579559	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	178	552	0	ENST00000269305.4:c.128del	p.Leu43Ter	p.L43*	ENST00000269305	NM_001126112.2	43	tTg/tg	4/11	0.373256482081332	2	FACETS	0.963	0.896	1	0.963	0.896	1	CLONAL	2	TRUE	0	0.373256482081332	2		552	495	SUCCESS
APC	324	MSKCC	GRCh37	5	112116538	112116538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs749479682	NA	P-0065185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	80	421	2	ENST00000257430.4:c.583C>T	p.Gln195Ter	p.Q195*	ENST00000257430	NM_000038.5	195	Caa/Taa	6/16	0.338457883031305	3	FACETS	0.944	0.832	1	0.472	0.416	0.532	CLONAL	1	TRUE	1	0.373256482081332	3		423	539	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437918	110437919	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCGGCGGGCGCG	rs1555316971	NA	P-0065185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	19	247	0	ENST00000375856.3:c.471_482dup	p.Ala158_Ala161dup	p.A158_A161dup	ENST00000375856	NM_003749.2	158	gcg/gcCGCGCCCGCCGCg	1/2	0.373256482081332	7	FACETS	0.688	0.522	0.883	0.115	0.087	0.148	SUBCLONAL	1	TRUE	1	0.373256482081332	7		247	286	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019514	123019514	+	start_lost	Translation_Start_Site	SNP	T	T	G	novel	NA	P-0065185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	95	353	2	ENST00000355640.3:c.2T>G	p.Met1?	p.M1?	ENST00000355640		1	aTg/aGg	2/7	0.28056406717711	5	FACETS	1	0.962	1	0.295	0.263	0.33	CLONAL	1	TRUE	1	0.373256482081332	5		355	672	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041052	42041053	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	A	novel	NA	P-0065185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	97	682	0	ENST00000219905.7:c.5430_5431delinsA	p.Leu1811PhefsTer27	p.L1811Ffs*27	ENST00000219905	NM_001164273.1	1810	caGCtt/caAtt	16/24	0.340620505118855	3	FACETS	0.763	0.68	0.852	0.382	0.34	0.426	SUBCLONAL	1	TRUE	1	0.373256482081332	3		682	808	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0065186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	250	479	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.426741053667832	2	FACETS	0.949	0.895	1	0.949	0.895	1	CLONAL	2	TRUE	0	0.437560096542326	2		479	602	SUCCESS
APC	324	MSKCC	GRCh37	5	112175328	112175328	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0065186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	236	437	0	ENST00000257430.4:c.4037C>G	p.Ser1346Ter	p.S1346*	ENST00000257430	NM_000038.5	1346	tCa/tGa	16/16	0.437560096542326	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.437560096542326	2		437	538	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2493255	2493255	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0065186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	32	375	0	ENST00000355716.4:c.694+1G>T		p.X232_splice	ENST00000355716	NM_003820.2	232			1	2	FACETS	0.287	0.232	0.349	0.287	0.232	0.349	SUBCLONAL	1	TRUE	1	0.437560096542326	2		375	510	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912198	114912198	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	89	331	0	ENST00000543371.1:c.1268A>G	p.Tyr423Cys	p.Y423C	ENST00000543371	NM_001198531.1	423	tAt/tGt	11/14	0.407832169324941	3	FACETS	0.968	0.861	1	0.484	0.43	0.541	CLONAL	1	TRUE	1	0.437560096542326	3		331	512	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212257	5212257	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs571743236	NA	P-0065186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	263	580	0	ENST00000357368.4:c.4774G>A	p.Gly1592Ser	p.G1592S	ENST00000357368	NM_002850.3	1592	Ggt/Agt	32/38	0.415301053642495	3	FACETS	0.985	0.927	1	0.985	0.927	1	CLONAL	2	TRUE	1	0.437560096542326	3		580	744	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0065187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	264	566	2	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.845	0.797	0.895	0.845	0.797	0.895	CLONAL	1	TRUE	1	0.878655952761468	2		568	711	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0065187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	150	369	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.951	0.881	1	0.951	0.881	1	CLONAL	1	TRUE	1	0.878655952761468	2		373	359	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0065187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	245	595	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	0.953	0.898	1	0.953	0.898	1	CLONAL	1	TRUE	1	0.878655952761468	2		595	585	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	252	656	2	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.893	0.842	0.946	0.893	0.842	0.946	CLONAL	1	TRUE	1	0.878655952761468	2		658	642	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0065187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	43	172	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	0.72	0.615	0.83	0.72	0.615	0.83	SUBCLONAL	1	TRUE	1	0.878655952761468	2		172	136	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238958	5238958	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	45	626	1	ENST00000357368.4:c.1821del	p.Val608TrpfsTer30	p.V608Wfs*30	ENST00000357368	NM_002850.3	607	ccC/cc	13/38	1	2	FACETS	0.186	0.156	0.22	0.186	0.156	0.22	SUBCLONAL	1	TRUE	1	0.878655952761468	2		627	550	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0065187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	278	654	7	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.997	0.943	1	0.997	0.943	1	CLONAL	1	TRUE	1	0.878655952761468	2		661	635	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693003	89693003	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs786204900	NA	P-0065187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	92	323	0	ENST00000371953.3:c.491del	p.Lys164ArgfsTer3	p.K164Rfs*3	ENST00000371953	NM_000314.4	163	Aaa/aa	5/9	1	2	FACETS	0.737	0.664	0.814	0.737	0.664	0.814	SUBCLONAL	1	TRUE	1	0.878655952761468	2		323	284	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952139	178952139	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1560150596	NA	P-0065187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	158	476	0	ENST00000263967.3:c.3194A>T	p.His1065Leu	p.H1065L	ENST00000263967	NM_006218.2	1065	cAt/cTt	21/21	1	2	FACETS	0.949	0.881	1	0.949	0.881	1	CLONAL	1	TRUE	1	0.878655952761468	2		476	379	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204992	128204992	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	29	713	2	ENST00000341105.2:c.449del	p.Gly150GlufsTer68	p.G150Efs*68	ENST00000341105	NM_032638.4	150	gGa/ga	3/6	1	2	FACETS	0.118	0.094	0.145	0.118	0.094	0.145	SUBCLONAL	1	TRUE	1	0.878655952761468	2		715	560	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0065187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	218	671	3	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	0.881	0.826	0.937	0.881	0.826	0.937	CLONAL	1	TRUE	1	0.878655952761468	2		674	563	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349019	89349019	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	292	645	0	ENST00000301030.4:c.3931C>T	p.Arg1311Ter	p.R1311*	ENST00000301030	NM_001256183.1	1311	Cga/Tga	9/13	1	2	FACETS	0.966	0.915	1	0.966	0.915	1	CLONAL	1	TRUE	1	0.878655952761468	2		645	688	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444081	49444081	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	263	713	0	ENST00000301067.7:c.3290del	p.Pro1097GlnfsTer22	p.P1097Qfs*22	ENST00000301067	NM_003482.3	1097	cCa/ca	11/54	1	2	FACETS	0.932	0.88	0.985	0.932	0.88	0.985	CLONAL	1	TRUE	1	0.878655952761468	2		713	642	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532579	63532579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878854724	NA	P-0065187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	327	711	0	ENST00000307078.5:c.2000G>A	p.Ser667Asn	p.S667N	ENST00000307078	NM_004655.3	667	aGc/aAc	8/11	1	2	FACETS	0.986	0.937	1	0.986	0.937	1	CLONAL	1	TRUE	1	0.878655952761468	2		711	755	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213932	2213932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	91	646	0	ENST00000326181.6:c.11G>A	p.Gly4Asp	p.G4D	ENST00000326181	NM_032271.2	4	gGc/gAc	2/21	1	2	FACETS	0.328	0.291	0.367	0.328	0.291	0.367	SUBCLONAL	1	TRUE	1	0.878655952761468	2		646	631	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560476	95560476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	246	543	0	ENST00000393063.1:c.5113G>A	p.Glu1705Lys	p.E1705K	ENST00000393063	NM_030621.3	1705	Gaa/Aaa	25/28	1	2	FACETS	0.941	0.887	0.996	0.941	0.887	0.996	CLONAL	1	TRUE	1	0.878655952761468	2		543	595	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199909	108199910	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	165	499	0	ENST00000278616.4:c.7255dup	p.Arg2419LysfsTer10	p.R2419Kfs*10	ENST00000278616	NM_000051.3	2417	-/A	49/63	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.878655952761468	2		499	359	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28885789	28885789	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	170	489	0	ENST00000282397.4:c.3573G>C	p.Glu1191Asp	p.E1191D	ENST00000282397	NM_002019.4	1191	gaG/gaC	27/30	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.878655952761468	2		489	365	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574294	95574294	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	169	474	0	ENST00000393063.1:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000393063	NM_030621.3	858	cTt/cGt	17/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.878655952761468	2		474	360	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511208	148511208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	49	541	0	ENST00000320356.2:c.1694G>A	p.Cys565Tyr	p.C565Y	ENST00000320356	NM_004456.4	565	tGc/tAc	15/20	1	2	FACETS	0.178	0.15	0.209	0.178	0.15	0.209	SUBCLONAL	1	TRUE	1	0.878655952761468	2		541	627	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877904	151877905	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	255	626	0	ENST00000262189.6:c.7040dup	p.Gln2348AlafsTer19	p.Q2348Afs*19	ENST00000262189	NM_170606.2	2347	cag/caAg	36/59	1	2	FACETS	0.899	0.847	0.951	0.899	0.847	0.951	CLONAL	1	TRUE	1	0.878655952761468	2		626	646	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617174	100617174	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	236	592	0	ENST00000308731.7:c.575C>A	p.Pro192His	p.P192H	ENST00000308731	NM_000061.2	192	cCt/cAt	7/19	1	2	FACETS	0.958	0.902	1	0.958	0.902	1	CLONAL	1	TRUE	1	0.878655952761468	2		592	561	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0065188-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	172	431	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	1	2	FACETS	0.95	0.878	1	0.95	0.878	1	CLONAL	1	TRUE	1	0.604732244928781	2		431	599	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057519990	NA	P-0065188-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	213	507	0	ENST00000269305.4:c.796G>T	p.Gly266Ter	p.G266*	ENST00000269305	NM_001126112.2	266	Gga/Tga	8/11	0.604732244928781	1	FACETS	0.999	0.938	1	0.999	0.938	1	CLONAL	1	TRUE	0	0.604732244928781	1		507	492	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065188-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	233	497	0	ENST00000257430.4:c.4199C>A	p.Ser1400Ter	p.S1400*	ENST00000257430	NM_000038.5	1400	tCg/tAg	16/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.604732244928781	2		497	722	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256532	115256532	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065188-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	203	442	0	ENST00000369535.4:c.179G>T	p.Gly60Val	p.G60V	ENST00000369535	NM_002524.4	60	gGa/gTa	3/7	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.604732244928781	2		442	671	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692881	89692881	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065188-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	127	231	0	ENST00000371953.3:c.365T>C	p.Ile122Thr	p.I122T	ENST00000371953	NM_000314.4	122	aTt/aCt	5/9	0.604732244928781	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.604732244928781	1		231	262	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50810132	50810132	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065188-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	174	462	0	ENST00000398568.2:c.956T>A	p.Met319Lys	p.M319K	ENST00000398568	NM_001042412.1	319	aTg/aAg	6/18	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.604732244928781	2		462	558	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212407	5212407	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065188-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	250	662	0	ENST00000357368.4:c.4710C>A	p.Phe1570Leu	p.F1570L	ENST00000357368	NM_002850.3	1570	ttC/ttA	31/38	1	2	FACETS	0.963	0.902	1	0.963	0.902	1	CLONAL	1	TRUE	1	0.604732244928781	2		662	859	SUCCESS
APC	324	MSKCC	GRCh37	5	112137081	112137081	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0065188-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	115	291	0	ENST00000257430.4:c.834+1G>T		p.X278_splice	ENST00000257430	NM_000038.5	278			1	2	FACETS	0.91	0.826	0.997	0.91	0.826	0.997	CLONAL	1	TRUE	1	0.604732244928781	2		291	418	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226283	2226283	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065189-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	130	584	0	ENST00000326181.6:c.1896C>G	p.Asn632Lys	p.N632K	ENST00000326181	NM_032271.2	632	aaC/aaG	20/21	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.28	2		584	915	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0065190-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	89	393	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.627242570108031	2		393	256	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095836	178095836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1328262363	NA	P-0065190-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	22	596	0	ENST00000397062.3:c.1495C>T	p.Arg499Trp	p.R499W	ENST00000397062	NM_006164.4	499	Cgg/Tgg	5/5	0.117753201941553	4	FACETS	0.264	0.204	0.334	0.132	0.102	0.167	INDETERMINATE	1	TRUE	2	0.627242570108031	4		596	433	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235935	108235935	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770641163	NA	P-0065190-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	122	530	0	ENST00000278616.4:c.8977C>T	p.Arg2993Ter	p.R2993*	ENST00000278616	NM_000051.3	2993	Cga/Tga	62/63	0.627242570108031	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.627242570108031	1		530	267	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950756	38950756	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199854036	NA	P-0065190-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	85	465	0	ENST00000357387.3:c.3194A>G	p.Asn1065Ser	p.N1065S	ENST00000357387	NM_152756.3	1065	aAt/aGt	31/38	1	2	FACETS	0.935	0.836	1	0.935	0.836	1	CLONAL	1	TRUE	1	0.627242570108031	2		465	290	SUCCESS
AR	367	MSKCC	GRCh37	X	66766432	66766432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065190-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	69	214	0	ENST00000374690.3:c.1444G>A	p.Gly482Ser	p.G482S	ENST00000374690	NM_000044.3	482	Ggc/Agc	1/8	1	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.627242570108031	1		214	128	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750672	39750672	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065190-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	32	312	0	ENST00000361337.2:c.2072T>C	p.Val691Ala	p.V691A	ENST00000361337	NM_003286.2	691	gTt/gCt	20/21	0.627242570108031	3	FACETS	0.423	0.344	0.512	0.211	0.172	0.256	SUBCLONAL	1	TRUE	1	0.627242570108031	3		312	317	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223880	53223880	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065190-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	21	334	0	ENST00000375401.3:c.3479del	p.Gly1160ValfsTer104	p.G1160Vfs*104	ENST00000375401	NM_004187.3	1160	gGt/gt	23/26	1	1	FACETS	0.17	0.13	0.215	0.17	0.13	0.215	SUBCLONAL	1	TRUE	0	0.627242570108031	1		334	271	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0065191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	17	524	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.475615685950189	1	FACETS	0.076	0.056	0.1	0.076	0.056	0.1	SUBCLONAL	1	TRUE	0	0.525409967098444	1		524	624	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0065191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	145	777	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.427621926493453	0	FACETS	0.435	0.398	0.473			1	SUBCLONAL	1	TRUE	0	0.525409967098444	0		777	602	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287412	46287412	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0065191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	173	485	1	ENST00000334344.6:c.5272-1G>T		p.X1758_splice	ENST00000334344	NM_152641.2	1758			0.525409967098444	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.525409967098444	1		486	482	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948832	17948832	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	230	668	0	ENST00000458235.1:c.1610G>T	p.Arg537Leu	p.R537L	ENST00000458235	NM_000215.3	537	cGg/cTg	12/24	1	2	FACETS	0.964	0.9	1	0.964	0.9	1	CLONAL	1	TRUE	1	0.525409967098444	2		668	908	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111485	8111485	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	215	641	0	ENST00000346208.3:c.971C>A	p.Thr324Lys	p.T324K	ENST00000346208		324	aCa/aAa	5/6	0.331903399522812	3	FACETS	1	0.976	1	0.555	0.516	0.595	CLONAL	1	TRUE	1	0.525409967098444	3		641	931	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518540	69518540	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	143	539	0	ENST00000294312.3:c.105C>A	p.His35Gln	p.H35Q	ENST00000294312	NM_005117.2	35	caC/caA	1/3	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.525409967098444	2		539	505	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437302	220437302	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	189	685	0	ENST00000243786.2:c.206A>T	p.His69Leu	p.H69L	ENST00000243786	NM_002191.3	69	cAc/cTc	1/2	1	2	FACETS	0.972	0.901	1	0.972	0.901	1	CLONAL	1	TRUE	1	0.525409967098444	2		685	740	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136799	55136799	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0065191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	123	320	0	ENST00000257290.5:c.1122-1G>T		p.X374_splice	ENST00000257290	NM_006206.4	374			1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.525409967098444	2		320	454	SUCCESS
AR	367	MSKCC	GRCh37	X	66766463	66766463	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	28	372	0	ENST00000374690.3:c.1475G>T	p.Gly492Val	p.G492V	ENST00000374690	NM_000044.3	492	gGc/gTc	1/8	0.525409967098444	0	FACETS	0.214	0.172	0.262			1	SUBCLONAL	1	TRUE	NA	0.525409967098444	0		372	236	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0065192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	91	584	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.292944886315573	2	FACETS	1	0.894	1	0.503	0.447	0.563	CLONAL	1	TRUE	0	0.29	2		584	624	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0065192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	49	379	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.758	0.643	0.884	0.758	0.643	0.884	SUBCLONAL	1	TRUE	1	0.29	2		379	446	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0065192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	113	400	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	0.292944886315573	2	FACETS	0.781	0.706	0.859	0.781	0.706	0.859	SUBCLONAL	2	TRUE	0	0.29	2		400	499	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99181109	99181109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757028003	NA	P-0065192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	57	561	0	ENST00000074304.5:c.2050G>A	p.Ala684Thr	p.A684T	ENST00000074304	NM_001134224.1	684	Gcc/Acc	20/26	1	2	FACETS	0.749	0.643	0.864	0.749	0.643	0.864	SUBCLONAL	1	TRUE	1	0.29	2		561	525	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	116	709	0	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.29	2		709	628	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466019	69466019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	89	609	0	ENST00000227507.2:c.857C>T	p.Thr286Ile	p.T286I	ENST00000227507	NM_053056.2	286	aCa/aTa	5/5	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.29	2		609	582	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0065192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	71	465	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.895	0.782	1	0.895	0.782	1	CLONAL	1	TRUE	1	0.29	2		465	547	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0065192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	87	517	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.29	2		517	567	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161221	56161221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781300314	NA	P-0065192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	87	378	0	ENST00000399503.3:c.1090C>T	p.Arg364Trp	p.R364W	ENST00000399503	NM_005921.1	364	Cgg/Tgg	5/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.29	2		378	539	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	83	549	0	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	1	2	FACETS	0.941	0.832	1	0.941	0.832	1	CLONAL	1	TRUE	1	0.29	2		549	608	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738360	133738360	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	122	569	0	ENST00000318560.5:c.760G>A	p.Gly254Arg	p.G254R	ENST00000318560	NM_005157.4	254	Ggg/Agg	4/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.29	2		569	676	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029437	16029439	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs774778469	NA	P-0065192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	76	432	0	ENST00000268712.3:c.1591_1593del	p.Glu531del	p.E531del	ENST00000268712	NM_006311.3	531	GAA/-	15/46	1	2	FACETS	0.967	0.85	1	0.967	0.85	1	CLONAL	1	TRUE	1	0.29	2		432	542	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156747	106156747	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs572712965	NA	P-0065192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	78	575	0	ENST00000380013.4:c.1648C>T	p.Arg550Ter	p.R550*	ENST00000380013	NM_001127208.2	550	Cga/Tga	3/11	1	2	FACETS	0.823	0.723	0.93	0.823	0.723	0.93	CLONAL	1	TRUE	1	0.29	2		575	654	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339175	65339175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180823763	NA	P-0065192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	85	633	0	ENST00000342505.4:c.361G>A	p.Asp121Asn	p.D121N	ENST00000342505	NM_002227.2	121	Gac/Aac	5/25	1	2	FACETS	0.95	0.841	1	0.95	0.841	1	CLONAL	1	TRUE	1	0.29	2		633	617	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371799	55371820	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCCGCGCTGGGCCCCGAG	GGCGGCCGCGCTGGGCCCCGAG	-	novel	NA	P-0065192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	74	595	0	ENST00000297316.4:c.499_520del	p.Leu167TrpfsTer213	p.L167Wfs*213	ENST00000297316	NM_022454.3	163	caGGCGGCCGCGCTGGGCCCCGAG/ca	2/2	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.29	2		595	416	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880957	134880957	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770406411	NA	P-0065192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	69	510	0	ENST00000398015.3:c.1520G>A	p.Arg507His	p.R507H	ENST00000398015	NM_004441.4	507	cGt/cAt	7/16	0.292944886315573	2	FACETS	0.896	0.782	1	0.448	0.391	0.51	CLONAL	1	TRUE	0	0.29	2		510	531	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546560	9546560	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771840400	NA	P-0065192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	82	550	0	ENST00000353224.5:c.1462C>T	p.Arg488Ter	p.R488*	ENST00000353224	NM_177990.2	488	Cga/Tga	5/10	1	2	FACETS	0.944	0.833	1	0.944	0.833	1	CLONAL	1	TRUE	1	0.29	2		550	599	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220069	36220069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1239076295	NA	P-0065192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	98	704	0	ENST00000222270.7:c.4789C>T	p.Arg1597Trp	p.R1597W	ENST00000222270	NM_014727.1	1597	Cgg/Tgg	22/37	1	2	FACETS	0.988	0.882	1	0.988	0.882	1	CLONAL	1	TRUE	1	0.29	2		704	684	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401690	401690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1182121626	NA	P-0065192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	99	732	0	ENST00000380956.4:c.1012G>A	p.Gly338Arg	p.G338R	ENST00000380956	NM_001195286.1	338	Ggg/Agg	7/9	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.29	2		732	678	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653405	206653405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782442134	NA	P-0065192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	121	600	2	ENST00000367120.3:c.1289G>A	p.Arg430Gln	p.R430Q	ENST00000367120	NM_014002.3	430	cGg/cAg	12/22	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.29	2		602	572	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40469199	40469199	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0065192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	106	400	0	ENST00000264657.5:c.2144+1G>A		p.X715_splice	ENST00000264657	NM_139276.2	715			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.29	2		400	501	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021646	31021646	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1299423705	NA	P-0065192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	90	613	0	ENST00000375687.4:c.1645C>T	p.Arg549Cys	p.R549C	ENST00000375687	NM_015338.5	549	Cgt/Tgt	12/13	1	2	FACETS	0.92	0.816	1	0.92	0.816	1	CLONAL	1	TRUE	1	0.29	2		613	675	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61323102	61323102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140650845	NA	P-0065192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	90	694	0	ENST00000283752.5:c.962G>A	p.Arg321His	p.R321H	ENST00000283752	NM_006919.2	321	cGc/cAc	8/8	1	2	FACETS	0.86	0.763	0.963	0.86	0.763	0.963	CLONAL	1	TRUE	1	0.29	2		694	722	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130307	11130307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1213692147	NA	P-0065192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	69	476	0	ENST00000358026.2:c.2546G>A	p.Arg849Gln	p.R849Q	ENST00000358026	NM_001128849.1	849	cGg/cAg	18/36	1	2	FACETS	0.868	0.757	0.988	0.868	0.757	0.988	CLONAL	1	TRUE	1	0.29	2		476	548	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027078	71027078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763468654	NA	P-0065192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	127	656	0	ENST00000318789.4:c.1249G>A	p.Val417Ile	p.V417I	ENST00000318789	NM_032682.5	417	Gtc/Atc	15/21	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.29	2		656	737	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0065195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	289	197	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		197	752	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	125	183	0	ENST00000269305.4:c.772G>C	p.Glu258Gln	p.E258Q	ENST00000269305	NM_001126112.2	258	Gaa/Caa	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		183	425	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577331	64577331	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	94	257	0	ENST00000312049.6:c.251C>A	p.Ser84Tyr	p.S84Y	ENST00000312049	NM_130799.2	84	tCt/tAt	2/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		257	601	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100460	102100461	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0065195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	67	227	0	ENST00000282441.5:c.1304_1305delinsTT	p.Pro435Leu	p.P435L	ENST00000282441	NM_001130145.2	435	cCC/cTT	9/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		227	555	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233252	69233273	+	frameshift_variant	Frame_Shift_Del	DEL	GTGAATGATTCCAGAGAGTCAT	GTGAATGATTCCAGAGAGTCAT	-	novel	NA	P-0065195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	203	248	0	ENST00000462284.1:c.1120_1141del	p.Asn374LeufsTer37	p.N374Lfs*37	ENST00000462284	NM_002392.5	373	GTGAATGATTCCAGAGAGTCATgt/gt	11/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		248	698	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73649905	73649905	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	62	242	0	ENST00000377687.4:c.1255G>A	p.Glu419Lys	p.E419K	ENST00000377687	NM_001730.3	419	Gag/Aag	4/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		242	456	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133065	30133065	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	52	195	0	ENST00000331968.5:c.536G>T	p.Gly179Val	p.G179V	ENST00000331968	NM_002742.2	179	gGg/gTg	4/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		195	551	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016003	31016003	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	135	249	0	ENST00000375687.4:c.325G>A	p.Glu109Lys	p.E109K	ENST00000375687	NM_015338.5	109	Gag/Aag	5/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		249	742	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750350	39750350	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	50	196	0	ENST00000361337.2:c.1965G>T	p.Lys655Asn	p.K655N	ENST00000361337	NM_003286.2	655	aaG/aaT	19/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		196	548	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490617	20490617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1330116976	NA	P-0065195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	73	219	0	ENST00000346618.3:c.1354G>A	p.Asp452Asn	p.D452N	ENST00000346618	NM_001949.4	452	Gat/Aat	7/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		219	507	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0065196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	137	393	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.699942441535134	2		393	375	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0065196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	210	495	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.939	0.877	1	0.939	0.877	1	CLONAL	1	TRUE	1	0.699942441535134	2		495	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577569	7577569	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519981	NA	P-0065196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	196	456	0	ENST00000269305.4:c.712T>A	p.Cys238Ser	p.C238S	ENST00000269305	NM_001126112.2	238	Tgt/Agt	7/11	0.699942441535134	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.699942441535134	1		456	337	SUCCESS
APC	324	MSKCC	GRCh37	5	112174117	112174117	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	129	441	0	ENST00000257430.4:c.2827del	p.Ser943GlnfsTer12	p.S943Qfs*12	ENST00000257430	NM_000038.5	942	aaT/aa	16/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.699942441535134	2		441	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0065197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	203	766	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.836381328374702	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.836381328374702	1		767	236	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513339	44513339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	154	460	0	ENST00000291552.4:c.596C>T	p.Ser199Phe	p.S199F	ENST00000291552	NM_006758.2	199	tCc/tTc	8/8	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.836381328374702	2		460	363	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211486	36211488	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	novel	NA	P-0065197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	66	345	5	ENST00000222270.7:c.1242_1244del	p.Pro416del	p.P416del	ENST00000222270	NM_014727.1	413	CCT/-	3/37	0.178892583089534	3	FACETS	0.921	0.81	1	0.461	0.405	0.519	INDETERMINATE	1	TRUE	1	0.836381328374702	3		350	243	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151167729	151167729	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	85	342	0	ENST00000262187.5:c.390T>G	p.Ser130Arg	p.S130R	ENST00000262187	NM_005614.3	130	agT/agG	7/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.836381328374702	2		342	186	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	103	789	0				ENST00000310581	NM_198253.2	-/1132			0.51943172985982	3	FACETS	0.948	0.867	1	0.948	0.867	1	CLONAL	2	TRUE	1	0.636351428453301	3		789	225	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0065198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	261	511	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.636351428453301	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.636351428453301	3		511	476	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141586	202141586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760898260	NA	P-0065198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	148	416	0	ENST00000358485.4:c.874C>T	p.Arg292Trp	p.R292W	ENST00000358485	NM_001080125.1	292	Cgg/Tgg	7/9	1	2	FACETS	0.985	0.907	1	0.985	0.907	1	CLONAL	1	TRUE	1	0.636351428453301	2		416	472	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0065198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	129	507	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.636351428453301	1	FACETS	0.973	0.899	1	0.973	0.899	1	CLONAL	1	TRUE	0	0.636351428453301	1		507	284	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817493	39817493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755303168	NA	P-0065198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	121	458	0	ENST00000288319.7:c.70G>A	p.Gly24Arg	p.G24R	ENST00000288319	NM_182918.3	24	Gga/Aga	2/10	1	2	FACETS	0.874	0.796	0.956	0.874	0.796	0.956	CLONAL	1	TRUE	1	0.636351428453301	2		458	435	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622458	28622458	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	119	407	0	ENST00000241453.7:c.1159C>T	p.Arg387Ter	p.R387*	ENST00000241453	NM_004119.2	387	Cga/Tga	9/24	0.513994671209199	1	FACETS	0.773	0.706	0.841	0.773	0.706	0.841	SUBCLONAL	1	TRUE	0	0.636351428453301	1		407	330	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0065198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	110	383	0				ENST00000310581	NM_198253.2	-/1132			0.51943172985982	3	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	1	0.636351428453301	3		383	225	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341284	89341284	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1402333853	NA	P-0065198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	43	116	0	ENST00000301030.4:c.7651C>T	p.Pro2551Ser	p.P2551S	ENST00000301030	NM_001256183.1	2551	Cca/Tca	11/13	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.636351428453301	2		116	108	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430557	78430557	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	97	339	0	ENST00000370768.2:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000370768	NM_003902.3	245	Caa/Taa	9/20	1	2	FACETS	0.894	0.805	0.987	0.894	0.805	0.987	CLONAL	1	TRUE	1	0.636351428453301	2		339	341	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505326	186505326	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	143	392	0	ENST00000323963.5:c.952G>A	p.Glu318Lys	p.E318K	ENST00000323963		318	Gaa/Aaa	9/11	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.636351428453301	2		392	445	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432908	432908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	139	442	0	ENST00000399788.2:c.2008C>T	p.Pro670Ser	p.P670S	ENST00000399788	NM_001042603.1	670	Cct/Tct	15/28	1	2	FACETS	0.964	0.885	1	0.964	0.885	1	CLONAL	1	TRUE	1	0.636351428453301	2		442	453	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858910	57858910	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	124	427	0	ENST00000228682.2:c.406C>A	p.Pro136Thr	p.P136T	ENST00000228682	NM_005269.2	136	Cca/Aca	5/12	0.156898922312223	3	FACETS	1	0.963	1	0.555	0.505	0.606	INDETERMINATE	1	TRUE	1	0.636351428453301	3		427	463	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622430	28622430	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1231767049	NA	P-0065198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	94	397	0	ENST00000241453.7:c.1187G>T	p.Gly396Val	p.G396V	ENST00000241453	NM_004119.2	396	gGt/gTt	9/24	0.513994671209199	1	FACETS	0.603	0.542	0.667	0.603	0.542	0.667	SUBCLONAL	1	TRUE	0	0.636351428453301	1		397	334	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423937	47423937	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	140	481	0	ENST00000404338.3:c.2005G>T	p.Glu669Ter	p.E669*	ENST00000404338	NM_004491.4	669	Gaa/Taa	1/6	1	2	FACETS	0.878	0.805	0.954	0.878	0.805	0.954	CLONAL	1	TRUE	1	0.636351428453301	2		481	501	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416437	29416437	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1553386991	NA	P-0065198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	157	488	0	ENST00000389048.3:c.4516A>G	p.Thr1506Ala	p.T1506A	ENST00000389048	NM_004304.4	1506	Acg/Gcg	29/29	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.636351428453301	2		488	481	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456665	138456665	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	108	352	0	ENST00000289153.2:c.685C>T	p.Gln229Ter	p.Q229*	ENST00000289153	NM_006219.2	229	Caa/Taa	4/22	1	2	FACETS	0.903	0.818	0.991	0.903	0.818	0.991	CLONAL	1	TRUE	1	0.636351428453301	2		352	376	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404548	8404548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	94	376	0	ENST00000356435.5:c.4199C>T	p.Ser1400Leu	p.S1400L	ENST00000356435		1400	tCa/tTa	25/35	0.636351428453301	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.636351428453301	1		376	186	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0065199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	73	624	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.292215598875344	2		625	469	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0065199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	79	527	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.923	0.812	1	0.923	0.812	1	CLONAL	1	TRUE	1	0.292215598875344	2		527	586	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0065199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	47	511	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.2898692013408	3	FACETS	0.72	0.608	0.844	0.36	0.304	0.422	SUBCLONAL	1	TRUE	1	0.292215598875344	3		511	512	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473647	67473647	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886039137	NA	P-0065199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	167	482	0	ENST00000327367.4:c.727C>T	p.Arg243Cys	p.R243C	ENST00000327367	NM_005902.3	243	Cgc/Tgc	6/9	0.292215598875344	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.292215598875344	2		482	513	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374935	45374935	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	161	448	0	ENST00000262160.6:c.908C>G	p.Thr303Arg	p.T303R	ENST00000262160	NM_005901.5	303	aCa/aGa	8/11	0.292215598875344	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.292215598875344	2		448	500	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500882	8500882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs191877533	NA	P-0065199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	86	499	0	ENST00000356435.5:c.2000C>T	p.Ser667Leu	p.S667L	ENST00000356435		667	tCg/tTg	13/35	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.292215598875344	2		499	486	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717749	89717749	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	99	345	0	ENST00000371953.3:c.775del	p.His259ThrfsTer7	p.H259Tfs*7	ENST00000371953	NM_000314.4	258	ttC/tt	7/9	0.292215598875344	2	FACETS	0.954	0.86	1	0.954	0.86	1	CLONAL	2	TRUE	0	0.292215598875344	2		345	355	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248443	212248443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141902440	NA	P-0065199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	156	604	0	ENST00000342788.4:c.3824G>A	p.Arg1275Gln	p.R1275Q	ENST00000342788	NM_005235.2	1275	cGg/cAg	28/28	0.2898692013408	3	FACETS	0.967	0.888	1	0.967	0.888	1	CLONAL	2	TRUE	1	0.292215598875344	3		604	633	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81574747	81574747	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	72	490	0	ENST00000298171.2:c.643G>T	p.Val215Phe	p.V215F	ENST00000298171	NM_000369.2	215	Gtt/Ttt	8/10	1	2	FACETS	0.97	0.849	1	0.97	0.849	1	CLONAL	1	TRUE	1	0.292215598875344	2		490	508	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786669	3786669	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	86	501	0	ENST00000262367.5:c.4542del	p.Ile1515SerfsTer35	p.I1515Sfs*35	ENST00000262367	NM_004380.2	1514	cgG/cg	27/31	1	2	FACETS	0.94	0.833	1	0.94	0.833	1	CLONAL	1	TRUE	1	0.292215598875344	2		501	626	SUCCESS
APC	324	MSKCC	GRCh37	5	112173723	112173723	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	50	493	0	ENST00000257430.4:c.2432C>A	p.Ser811Ter	p.S811*	ENST00000257430	NM_000038.5	811	tCa/tAa	16/16	1	2	FACETS	0.772	0.656	0.9	0.772	0.656	0.9	SUBCLONAL	1	TRUE	1	0.292215598875344	2		493	443	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864487	162864487	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	55	454	0	ENST00000366898.1:c.26C>A	p.Ser9Tyr	p.S9Y	ENST00000366898	NM_004562.2	9	tCc/tAc	2/12	1	2	FACETS	0.831	0.712	0.96	0.831	0.712	0.96	CLONAL	1	TRUE	1	0.292215598875344	2		454	453	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	54	789	0				ENST00000310581	NM_198253.2	-/1132			0.800964777267385	1	FACETS	0.525	0.458	0.594	0.525	0.458	0.594	SUBCLONAL	1	FALSE	0	0.800964777267385	1		789	154	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426649	121426649	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774996577	NA	P-0065200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	192	609	0	ENST00000257555.6:c.340C>T	p.Arg114Cys	p.R114C	ENST00000257555		114	Cgt/Tgt	2/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.800964777267385	2		609	464	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711882	89711883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AATA	novel	NA	P-0065200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	64	308	0	ENST00000371953.3:c.500_501insAATA	p.Pro169TyrfsTer12	p.P169Yfs*12	ENST00000371953	NM_000314.4	167	act/acAATAt	6/9	0.752711630035603	1	FACETS	0.798	0.717	0.879	0.798	0.717	0.879	SUBCLONAL	1	FALSE	0	0.800964777267385	1		308	120	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0065201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	175	615	0	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	0.226656237597476	3	FACETS	1	0.954	1	0.697	0.644	0.752	CLONAL	2	TRUE	0	0.282201450356719	3		615	677	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467123	99467123	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	98	551	0	ENST00000268035.6:c.2504C>A	p.Pro835His	p.P835H	ENST00000268035	NM_000875.3	835	cCt/cAt	12/21	0.282201450356719	7	FACETS	1	0.979	1	0.29	0.258	0.324	CLONAL	1	TRUE	2	0.282201450356719	7		551	817	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632322	215632323	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	219	474	0	ENST00000260947.4:c.1451dup	p.Ala485GlyfsTer11	p.A485Gfs*11	ENST00000260947	NM_000465.2	484	aag/aaAg	6/11	0.284160330442375	3	FACETS	0.907	0.848	0.967	0.907	0.848	0.967	CLONAL	3	TRUE	0	0.282201450356719	3		474	651	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138376612	138376612	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	79	425	0	ENST00000289153.2:c.2862G>C	p.Glu954Asp	p.E954D	ENST00000289153	NM_006219.2	954	gaG/gaC	20/22	0.223324247843945	4	FACETS	1	0.962	1	0.618	0.544	0.697	CLONAL	1	TRUE	2	0.282201450356719	4		425	581	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944418	76944418	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	26	401	0	ENST00000373344.5:c.487G>T	p.Asp163Tyr	p.D163Y	ENST00000373344	NM_000489.3	163	Gat/Tat	7/35	0.190159460728447	3	FACETS	0.422	0.333	0.524	0.211	0.166	0.262	SUBCLONAL	1	TRUE	1	0.282201450356719	3		401	498	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0065202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	23	624	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.52111773992023	6	FACETS	0.805	0.63	1	0.268	0.21	0.335	CLONAL	1	FALSE	3	0.52111773992023	6		625	224	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922915	44922915	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	30	431	0	ENST00000377967.4:c.1776G>C	p.Leu592Phe	p.L592F	ENST00000377967	NM_021140.2	592	ttG/ttC	16/29	0.461137279722386	2	FACETS	0.914	0.75	1	0.457	0.375	0.547	CLONAL	1	FALSE	0	0.52111773992023	2		431	126	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120469180	120469180	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	23	446	0	ENST00000256646.2:c.3947G>C	p.Gly1316Ala	p.G1316A	ENST00000256646	NM_024408.3	1316	gGa/gCa	24/34	0.239080981622152	4	FACETS	0.685	0.537	0.854	0.228	0.179	0.285	INDETERMINATE	1	FALSE	1	0.52111773992023	4		446	196	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978892	25978892	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0065202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	44	322	0	ENST00000435504.4:c.1031C>G	p.Ser344Ter	p.S344*	ENST00000435504		344	tCa/tGa	10/13	0.52111773992023	6	FACETS	1	0.949	1	0.333	0.281	0.389	CLONAL	1	FALSE	2	0.52111773992023	6		322	259	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075200	16075200	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1240701348	NA	P-0065202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	39	368	0	ENST00000268712.3:c.352C>G	p.His118Asp	p.H118D	ENST00000268712	NM_006311.3	118	Cat/Gat	4/46	0.278509376990935	5	FACETS	1	0.953	1			1	INDETERMINATE	1	FALSE	NA	0.52111773992023	5		368	185	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455533	189455533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144315591	NA	P-0065202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	42	335	0	ENST00000264731.3:c.67G>A	p.Val23Ile	p.V23I	ENST00000264731	NM_003722.4	23	Gta/Ata	2/14	0.52111773992023	6	FACETS	0.927	0.776	1	0.309	0.258	0.365	CLONAL	1	FALSE	3	0.52111773992023	6		335	355	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246196	41246196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	44	412	0	ENST00000357654.3:c.1352C>T	p.Ser451Leu	p.S451L	ENST00000357654	NM_007294.3	451	tCa/tTa	10/23	0.52111773992023	8	FACETS	1	0.944	1	0.259	0.218	0.305	CLONAL	1	FALSE	3	0.52111773992023	8		412	334	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487316	56487316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1394170153	NA	P-0065202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	47	378	2	ENST00000267101.3:c.1462C>T	p.Arg488Trp	p.R488W	ENST00000267101	NM_001982.3	488	Cgg/Tgg	12/28	0.52111773992023	8	FACETS	1	0.944	1	0.253	0.214	0.296	CLONAL	1	FALSE	3	0.52111773992023	8		380	366	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796923	78796923	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	24	354	0	ENST00000306801.3:c.1036C>G	p.Leu346Val	p.L346V	ENST00000306801	NM_020761.2	346	Ctg/Gtg	9/34	0.526463319013351	5	FACETS	0.726	0.572	0.903	0.242	0.19	0.301	CLONAL	1	FALSE	2	0.52111773992023	5		354	226	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50785016	50785016	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs148783236	NA	P-0065202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	10	209	2	ENST00000307179.4:c.2353A>G	p.Thr785Ala	p.T785A	ENST00000307179		785	Act/Gct	15/20	0.526463319013351	5	FACETS	0.768	0.526	1	0.256	0.175	0.355	CLONAL	1	FALSE	2	0.52111773992023	5		211	89	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6216464	6216464	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1279997160	NA	P-0065202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	19	506	0	ENST00000252674.7:c.1259C>T	p.Ser420Leu	p.S420L	ENST00000252674	NM_005934.3	420	tCg/tTg	8/12	1	2	FACETS	0.574	0.441	0.727	0.574	0.441	0.727	SUBCLONAL	1	FALSE	1	0.52111773992023	2		506	127	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257751	16257751	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	31	491	0	ENST00000375759.3:c.5016G>C	p.Lys1672Asn	p.K1672N	ENST00000375759	NM_015001.2	1672	aaG/aaC	11/15	0.52111773992023	10	FACETS	0.939	0.759	1			1	CLONAL	1	FALSE	NA	0.52111773992023	10		491	391	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165794	118165794	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	23	490	0	ENST00000369448.3:c.304G>C	p.Glu102Gln	p.E102Q	ENST00000369448	NM_017709.3	102	Gag/Cag	2/2	0.504304063432199	4	FACETS	0.592	0.463	0.739	0.296	0.231	0.37	SUBCLONAL	1	FALSE	2	0.52111773992023	4		490	227	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653872	206653872	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	28	466	0	ENST00000367120.3:c.1423G>C	p.Glu475Gln	p.E475Q	ENST00000367120	NM_014002.3	475	Gag/Cag	13/22	0.52111773992023	5	FACETS	0.836	0.672	1	0.209	0.168	0.256	CLONAL	1	FALSE	1	0.52111773992023	5		466	229	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918533	94918533	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	10	366	0	ENST00000536441.1:c.649G>C	p.Asp217His	p.D217H	ENST00000536441	NM_144665.3	217	Gat/Cat	5/10	0.239080981622152	4	FACETS	0.387	0.262	0.542	0.129	0.087	0.181	INDETERMINATE	1	FALSE	1	0.52111773992023	4		366	151	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115566	108115566	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	12	344	0	ENST00000278616.4:c.714C>G	p.Ile238Met	p.I238M	ENST00000278616	NM_000051.3	238	atC/atG	7/63	1	2	FACETS	0.305	0.215	0.415	0.305	0.215	0.415	SUBCLONAL	1	FALSE	1	0.52111773992023	2		344	151	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1036417	1036417	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	16	372	0	ENST00000358495.3:c.361C>A	p.His121Asn	p.H121N	ENST00000358495	NM_134424.2	121	Cat/Aat	6/12	0.504304063432199	4	FACETS	0.508	0.376	0.663	0.254	0.188	0.332	SUBCLONAL	1	FALSE	2	0.52111773992023	4		372	184	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489060	56489060	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	44	284	0	ENST00000267101.3:c.1879C>G	p.Gln627Glu	p.Q627E	ENST00000267101	NM_001982.3	627	Caa/Gaa	16/28	0.52111773992023	8	FACETS	1	0.924	1	0.235	0.197	0.276	CLONAL	1	FALSE	3	0.52111773992023	8		284	369	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874096	123874096	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	23	507	0	ENST00000330479.4:c.127G>T	p.Asp43Tyr	p.D43Y	ENST00000330479	NM_020382.3	43	Gac/Tac	2/9	0.526463319013351	3	FACETS	0.535	0.419	0.668	0.267	0.209	0.334	SUBCLONAL	1	FALSE	1	0.52111773992023	3		507	208	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240208	41240208	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	42	395	0	ENST00000379561.5:c.142G>C	p.Ala48Pro	p.A48P	ENST00000379561	NM_002015.3	48	Gcg/Ccg	1/3	0.504304063432199	4	FACETS	1	0.958	1	0.721	0.611	0.839	CLONAL	1	FALSE	2	0.52111773992023	4		395	170	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669585	88669585	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	13	340	0	ENST00000360948.2:c.1313T>A	p.Leu438His	p.L438H	ENST00000360948	NM_001012338.2	438	cTt/cAt	12/19	0.526463319013351	1	FACETS	0.455	0.33	0.603	0.455	0.33	0.603	SUBCLONAL	1	FALSE	0	0.52111773992023	1		340	81	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500577	99500577	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759627092	NA	P-0065202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	19	563	1	ENST00000268035.6:c.4010G>A	p.Arg1337His	p.R1337H	ENST00000268035	NM_000875.3	1337	cGc/cAc	21/21	0.52111773992023	5	FACETS	0.555	0.422	0.711	0.185	0.14	0.237	SUBCLONAL	1	FALSE	2	0.52111773992023	5		564	234	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639060	3639060	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	107	540	0	ENST00000294008.3:c.4579C>G	p.Pro1527Ala	p.P1527A	ENST00000294008	NM_032444.2	1527	Ccg/Gcg	12/15	0.367422243695225	6	FACETS	0.904	0.828	0.98	0.904	0.828	0.98	CLONAL	4	FALSE	2	0.52111773992023	6		540	232	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132542	11132542	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	39	577	0	ENST00000358026.2:c.2758G>T	p.Glu920Ter	p.E920*	ENST00000358026	NM_001128849.1	920	Gag/Tag	19/36	0.526463319013351	5	FACETS	1	0.935	1	0.417	0.349	0.492	CLONAL	1	FALSE	2	0.52111773992023	5		577	213	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021392	31021392	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	36	537	0	ENST00000375687.4:c.1391C>A	p.Pro464His	p.P464H	ENST00000375687	NM_015338.5	464	cCc/cAc	12/13	0.526463319013351	4	FACETS	0.815	0.673	0.971	0.272	0.224	0.324	CLONAL	1	FALSE	1	0.52111773992023	4		537	258	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924533	131924533	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	62	334	0	ENST00000265335.6:c.1206G>C	p.Glu402Asp	p.E402D	ENST00000265335		402	gaG/gaC	8/25	0.340888059210834	5	FACETS	1	0.881	1	0.402	0.352	0.454	CLONAL	2	FALSE	0	0.52111773992023	5		334	211	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278291	39278292	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	C	novel	NA	P-0065202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	17	300	0	ENST00000402219.2:c.857_858delinsG	p.Leu286TrpfsTer42	p.L286Wfs*42	ENST00000402219	NM_005633.3	286	tTA/tG	6/23	0.52111773992023	6	FACETS	0.843	0.633	1	0.211	0.158	0.273	CLONAL	1	FALSE	2	0.52111773992023	6		300	158	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735466	40735466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182388300	NA	P-0065206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	106	557	0	ENST00000373198.4:c.3407G>A	p.Arg1136His	p.R1136H	ENST00000373198	NM_133170.3	1136	cGt/cAt	25/32	0.36250740127424	5	FACETS	1	0.942	1			1	CLONAL	1	TRUE	NA	0.36250740127424	5		557	839	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796744	42796744	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370377701	NA	P-0065206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	103	733	0	ENST00000575354.2:c.3202G>A	p.Gly1068Ser	p.G1068S	ENST00000575354	NM_015125.3	1068	Ggt/Agt	14/20	0.376326247224108	3	FACETS	0.857	0.767	0.953			1	CLONAL	1	TRUE	NA	0.36250740127424	3		733	783	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0065206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	257	564	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.376326247224108	3	FACETS	0.875	0.825	0.926	0.875	0.825	0.926	CLONAL	3	TRUE	0	0.36250740127424	3		564	638	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913250	NA	P-0065206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	131	443	0	ENST00000369535.4:c.34G>T	p.Gly12Cys	p.G12C	ENST00000369535	NM_002524.4	12	Ggt/Tgt	2/7	0.34382401127998	3	FACETS	0.824	0.752	0.899	0.824	0.752	0.899	CLONAL	2	TRUE	1	0.36250740127424	3		443	518	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455173	29455173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746442213	NA	P-0065206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	85	559	1	ENST00000389048.3:c.2629G>A	p.Ala877Thr	p.A877T	ENST00000389048	NM_004304.4	877	Gca/Aca	15/29	NA	2	FACETS	0.872	0.772	0.978			1	INDETERMINATE	1	TRUE	NA	0.36250740127424	2		560	538	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665096	138665096	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs758370933	NA	P-0065206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	73	477	0	ENST00000330315.3:c.469C>G	p.Pro157Ala	p.P157A	ENST00000330315	NM_023067.3	157	Ccc/Gcc	1/1	0.364851857341344	4	FACETS	1	0.899	1	0.343	0.3	0.389	CLONAL	1	TRUE	1	0.36250740127424	4		477	533	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750638	128750638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	112	613	0	ENST00000377970.2:c.175G>A	p.Ala59Thr	p.A59T	ENST00000377970	NM_002467.4	59	Gcg/Acg	2/3	0.34382401127998	3	FACETS	0.873	0.785	0.967	0.437	0.392	0.484	CLONAL	1	TRUE	1	0.36250740127424	3		613	836	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373156	118373157	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0065206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	51	463	0	ENST00000534358.1:c.6549_6550delinsAT	p.Asp2183_Pro2184delinsGluSer	p.D2183_P2184delinsES	ENST00000534358	NM_005933.3	2183	gaTCct/gaATct	27/36	0.292257965327785	4	FACETS	0.643	0.546	0.75	0.322	0.273	0.375	SUBCLONAL	1	TRUE	2	0.36250740127424	4		463	596	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326235	62326235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142457144	NA	P-0065206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	97	577	0	ENST00000360203.5:c.3251C>T	p.Thr1084Ile	p.T1084I	ENST00000360203	NM_001283009.1	1084	aCa/aTa	32/35	0.36250740127424	6	FACETS	1	0.902	1	0.169	0.15	0.189	CLONAL	1	TRUE	0	0.36250740127424	6		577	910	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149375041	149375041	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	298	641	0	ENST00000360632.3:c.53T>C	p.Ile18Thr	p.I18T	ENST00000360632	NM_015472.4	18	aTc/aCc	2/7	0.364851857341344	4	FACETS	0.933	0.883	0.985	0.933	0.883	0.985	CLONAL	3	TRUE	1	0.36250740127424	4		641	800	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2115855	2115855	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	171	491	0	ENST00000349721.2:c.3490G>A	p.Gly1164Arg	p.G1164R	ENST00000349721	NM_003070.3	1164	Ggg/Agg	25/34	0.292257965327785	4	FACETS	0.937	0.865	1	0.937	0.865	1	CLONAL	2	TRUE	2	0.36250740127424	4		491	686	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0065207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	73	393	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.772	0.677	0.874	0.772	0.677	0.874	SUBCLONAL	1	TRUE	1	0.389903793520362	2		393	485	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0065207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	119	475	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.208259098176987	3	FACETS	1	0.941	1	0.528	0.477	0.581	INDETERMINATE	1	TRUE	1	0.389903793520362	3		475	691	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576110	88576110	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	75	512	0	ENST00000360948.2:c.1563C>A	p.His521Gln	p.H521Q	ENST00000360948	NM_001012338.2	521	caC/caA	13/19	1	2	FACETS	0.842	0.74	0.95	0.842	0.74	0.95	CLONAL	1	TRUE	1	0.389903793520362	2		512	457	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346340	73346340	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	101	434	0	ENST00000377767.4:c.1460A>T	p.Asp487Val	p.D487V	ENST00000377767	NM_014953.3	487	gAc/gTc	10/21	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.389903793520362	2		434	496	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144361484	144361484	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	114	561	0	ENST00000262995.4:c.1534G>T	p.Ala512Ser	p.A512S	ENST00000262995	NM_207123.2	512	Gca/Tca	6/11	1	2	FACETS	0.918	0.828	1	0.918	0.828	1	CLONAL	1	TRUE	1	0.389903793520362	2		561	637	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	44	624	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.647	0.546	0.757	0.647	0.546	0.757	SUBCLONAL	1	TRUE	1	0.523159590418057	2		625	260	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	34	584	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.533	0.438	0.638	0.533	0.438	0.638	SUBCLONAL	1	TRUE	1	0.523159590418057	2		584	244	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380346	14380346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	90	546	2	ENST00000256196.4:c.71G>A	p.Gly24Asp	p.G24D	ENST00000256196		24	gGc/gAc	1/6	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.523159590418057	2		548	316	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106648	27106648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553153748	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	117	730	0	ENST00000324856.7:c.6259G>A	p.Gly2087Arg	p.G2087R	ENST00000324856	NM_006015.4	2087	Gga/Aga	20/20	1	2	FACETS	0.968	0.879	1	0.968	0.879	1	CLONAL	1	TRUE	1	0.523159590418057	2		730	462	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	81	829	0	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.523159590418057	2		829	282	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	47	308	1	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	0.523159590418057	4	FACETS	1	0.925	1	0.382	0.325	0.443	CLONAL	1	TRUE	1	0.523159590418057	4		309	239	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412252	139412252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057523819	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	39	597	0	ENST00000277541.6:c.1393G>A	p.Ala465Thr	p.A465T	ENST00000277541	NM_017617.3	465	Gcc/Acc	8/34	1	2	FACETS	0.455	0.378	0.54	0.455	0.378	0.54	SUBCLONAL	1	TRUE	1	0.523159590418057	2		597	328	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216477	108216477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587782558	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	30	250	0	ENST00000278616.4:c.8432del	p.Lys2811SerfsTer46	p.K2811Sfs*46	ENST00000278616	NM_000051.3	2809	cAa/ca	58/63	1	2	FACETS	0.882	0.723	1	0.882	0.723	1	CLONAL	1	TRUE	1	0.523159590418057	2		250	130	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6036958	6036958	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	25	363	1	ENST00000265849.7:c.802del	p.Tyr268ThrfsTer39	p.Y268Tfs*39	ENST00000265849	NM_000535.5	268	Tac/ac	7/15	1	2	FACETS	0.508	0.403	0.627	0.508	0.403	0.627	SUBCLONAL	1	TRUE	1	0.523159590418057	2		364	188	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481412	140481412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913353	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	33	365	0	ENST00000288602.6:c.1396G>A	p.Gly466Arg	p.G466R	ENST00000288602	NM_004333.4	466	Gga/Aga	11/18	1	2	FACETS	0.667	0.549	0.798	0.667	0.549	0.798	SUBCLONAL	1	TRUE	1	0.523159590418057	2		365	189	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475061	40475063	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	43	508	0	ENST00000264657.5:c.1847_1849del	p.Glu616del	p.E616del	ENST00000264657	NM_139276.2	616	gAAGga/gga	20/24	1	2	FACETS	0.442	0.37	0.521	0.442	0.37	0.521	SUBCLONAL	1	TRUE	1	0.523159590418057	2		508	372	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	65	503	8	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.845	0.739	0.958	0.845	0.739	0.958	CLONAL	1	TRUE	1	0.523159590418057	2		511	294	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921567	178921567	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553821144	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	32	229	0	ENST00000263967.3:c.1049A>G	p.Asp350Gly	p.D350G	ENST00000263967	NM_006218.2	350	gAc/gGc	5/21	1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	TRUE	1	0.523159590418057	2		229	120	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443611	29443612	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	137	557	1	ENST00000389048.3:c.3605dup	p.Asp1203ArgfsTer82	p.D1203Rfs*82	ENST00000389048	NM_004304.4	1202	gga/ggGa	23/29	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.523159590418057	2		558	479	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233090	69233090	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746910913	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	32	540	1	ENST00000462284.1:c.961del	p.Leu321PhefsTer52	p.L321Ffs*52	ENST00000462284	NM_002392.5	319	Ccc/cc	11/11	1	2	FACETS	0.463	0.378	0.559	0.463	0.378	0.559	SUBCLONAL	1	TRUE	1	0.523159590418057	2		541	264	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781375	3781375	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	53	595	0	ENST00000262367.5:c.4990C>T	p.Arg1664Cys	p.R1664C	ENST00000262367	NM_004380.2	1664	Cgc/Tgc	30/31	1	2	FACETS	0.471	0.402	0.546	0.471	0.402	0.546	SUBCLONAL	1	TRUE	1	0.523159590418057	2		595	430	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771987	135771988	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs2234980	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	87	572	0	ENST00000298552.3:c.3127_3129dup	p.Ser1043dup	p.S1043dup	ENST00000298552	NM_001162426.1	1043	-/AGC	23/23	1	2	FACETS	0.696	0.618	0.778	0.696	0.618	0.778	SUBCLONAL	1	TRUE	1	0.523159590418057	2		572	478	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592641	28592641	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121909646	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	9	517	0	ENST00000241453.7:c.2504A>T	p.Asp835Val	p.D835V	ENST00000241453	NM_004119.2	835	gAt/gTt	20/24	1	2	FACETS	0.114	0.075	0.165	0.114	0.075	0.165	SUBCLONAL	1	TRUE	1	0.523159590418057	2		517	301	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218623	98218623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778629	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	136	587	0	ENST00000331920.6:c.3241G>A	p.Val1081Met	p.V1081M	ENST00000331920	NM_000264.3	1081	Gtg/Atg	19/24	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.523159590418057	2		587	510	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722906	49722906	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	rs747477010	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	12	130	1	ENST00000449682.2:c.1421del	p.Pro474GlnfsTer52	p.P474Qfs*52	ENST00000449682	NM_020998.3	474	cCa/ca	12/18	1	2	FACETS	0.559	0.399	0.75	0.559	0.399	0.75	SUBCLONAL	1	TRUE	1	0.523159590418057	2		131	82	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210417	2210417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	88	595	0	ENST00000398665.3:c.1024C>T	p.Arg342Trp	p.R342W	ENST00000398665	NM_032482.2	342	Cgg/Tgg	13/28	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.523159590418057	2		595	327	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829075	128829075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1247591045	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	62	450	0	ENST00000249373.3:c.88del	p.Ala30ArgfsTer25	p.A30Rfs*25	ENST00000249373	NM_005631.4	28	cGg/cg	1/12	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.523159590418057	2		450	235	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629075	187629075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	64	561	0	ENST00000441802.2:c.1907C>T	p.Ala636Val	p.A636V	ENST00000441802	NM_005245.3	636	gCa/gTa	2/27	1	2	FACETS	0.906	0.793	1	0.906	0.793	1	CLONAL	1	TRUE	1	0.523159590418057	2		561	270	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980558	1980559	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs752037034	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	116	642	10	ENST00000382891.5:c.4028dup	p.Glu1344ArgfsTer91	p.E1344Rfs*91	ENST00000382891	NM_133335.3	1340	-/C	22/22	0.523159590418057	1	FACETS	0.998	0.911	1	0.998	0.911	1	CLONAL	1	TRUE	0	0.523159590418057	1		652	328	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	131	685	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.523159590418057	2		685	467	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	94	200	12	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	1	2	FACETS	0.921	0.841	1	1	0.988	1	CLONAL	2	TRUE	1	0.523159590418057	2		212	195	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737551	145737551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773856131	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	144	792	1	ENST00000428558.2:c.3212G>A	p.Arg1071His	p.R1071H	ENST00000428558	NM_004260.3	1071	cGc/cAc	19/22	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.523159590418057	2		793	523	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81927337	81927337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1164040767	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	124	438	0	ENST00000359376.3:c.1010G>A	p.Arg337Gln	p.R337Q	ENST00000359376	NM_002661.3	337	cGg/cAg	12/33	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.523159590418057	2		438	394	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426771	49426772	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs944680171	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	88	694	0	ENST00000301067.7:c.11714_11716dup	p.Gln3905dup	p.Q3905dup	ENST00000301067	NM_003482.3	3905	ctg/cAGCtg	39/54	1	2	FACETS	0.635	0.564	0.71	0.635	0.564	0.71	SUBCLONAL	1	TRUE	1	0.523159590418057	2		694	530	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103666	47103666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	46	518	2	ENST00000409792.3:c.6280del	p.Arg2094GlyfsTer53	p.R2094Gfs*53	ENST00000409792	NM_014159.6	2094	Agg/gg	14/21	1	2	FACETS	0.371	0.312	0.436	0.371	0.312	0.436	SUBCLONAL	1	TRUE	1	0.523159590418057	2		520	474	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643770	52643770	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	22	460	0	ENST00000394830.3:c.2126T>A	p.Ile709Asn	p.I709N	ENST00000394830	NM_018313.4	709	aTt/aAt	17/30	1	2	FACETS	0.4	0.312	0.503	0.4	0.312	0.503	SUBCLONAL	1	TRUE	1	0.523159590418057	2		460	210	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223614	36223614	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	119	1007	0	ENST00000222270.7:c.6169del	p.Arg2057AlafsTer34	p.R2057Afs*34	ENST00000222270	NM_014727.1	2055	gCc/gc	28/37	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.523159590418057	2		1007	448	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230818	66230818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs910705978	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	49	366	0	ENST00000273854.3:c.2153G>A	p.Arg718His	p.R718H	ENST00000273854	NM_004439.5	718	cGc/cAc	12/18	1	2	FACETS	0.814	0.697	0.941	0.814	0.697	0.941	CLONAL	1	TRUE	1	0.523159590418057	2		366	230	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745836	745836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs185293600	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	19	313	0	ENST00000314574.4:c.596G>A	p.Arg199His	p.R199H	ENST00000314574	NM_005433.3	199	cGt/cAt	6/12	1	2	FACETS	0.294	0.223	0.377	0.294	0.223	0.377	SUBCLONAL	1	TRUE	1	0.523159590418057	2		313	247	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582070	189582070	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	60	593	0	ENST00000264731.3:c.629C>A	p.Pro210His	p.P210H	ENST00000264731	NM_003722.4	210	cCc/cAc	5/14	1	2	FACETS	0.549	0.474	0.629	0.549	0.474	0.629	SUBCLONAL	1	TRUE	1	0.523159590418057	2		593	418	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139642	202139642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1351320412	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	40	433	0	ENST00000358485.4:c.803C>T	p.Ser268Leu	p.S268L	ENST00000358485	NM_001080125.1	268	tCg/tTg	6/9	1	2	FACETS	0.5	0.417	0.591	0.5	0.417	0.591	SUBCLONAL	1	TRUE	1	0.523159590418057	2		433	306	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864003	97864003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs370974124	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	103	426	1	ENST00000289081.3:c.1663C>T	p.Arg555Ter	p.R555*	ENST00000289081	NM_000136.2	555	Cga/Tga	15/15	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.523159590418057	2		427	359	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760481	133760481	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143811852	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	113	564	2	ENST00000318560.5:c.2804C>T	p.Thr935Met	p.T935M	ENST00000318560	NM_005157.4	935	aCg/aTg	11/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.523159590418057	2		566	401	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528284	157528284	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs749055122	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	141	597	1	ENST00000346085.5:c.6013del	p.Val2005TrpfsTer16	p.V2005Wfs*16	ENST00000346085	NM_020732.3	2003	aaG/aa	20/20	1	2	FACETS	0.987	0.904	1	0.987	0.904	1	CLONAL	1	TRUE	1	0.523159590418057	2		598	546	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793484	42793484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780297917	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	121	591	2	ENST00000575354.2:c.1286C>T	p.Ala429Val	p.A429V	ENST00000575354	NM_015125.3	429	gCg/gTg	8/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.523159590418057	2		593	421	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220899	36220899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555731828	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	122	657	0	ENST00000222270.7:c.4949C>T	p.Thr1650Met	p.T1650M	ENST00000222270	NM_014727.1	1650	aCg/aTg	23/37	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.523159590418057	2		657	430	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229342	36229342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	49	599	0	ENST00000222270.7:c.8032C>T	p.Arg2678Cys	p.R2678C	ENST00000222270	NM_014727.1	2678	Cgc/Tgc	37/37	1	2	FACETS	0.421	0.357	0.491	0.421	0.357	0.491	SUBCLONAL	1	TRUE	1	0.523159590418057	2		599	445	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609918	81609918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762048531	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	118	671	0	ENST00000298171.2:c.1516G>A	p.Glu506Lys	p.E506K	ENST00000298171	NM_000369.2	506	Gag/Aag	10/10	1	2	FACETS	0.868	0.786	0.952	0.868	0.786	0.952	CLONAL	1	TRUE	1	0.523159590418057	2		671	520	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152009023	152009023	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	20	316	0	ENST00000262189.6:c.599C>A	p.Ser200Tyr	p.S200Y	ENST00000262189	NM_170606.2	200	tCt/tAt	5/59	1	2	FACETS	0.42	0.323	0.532	0.42	0.323	0.532	SUBCLONAL	1	TRUE	1	0.523159590418057	2		316	182	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393422	139393422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	53	632	0	ENST00000277541.6:c.6109G>A	p.Ala2037Thr	p.A2037T	ENST00000277541	NM_017617.3	2037	Gcc/Acc	33/34	1	2	FACETS	0.425	0.362	0.493	0.425	0.362	0.493	SUBCLONAL	1	TRUE	1	0.523159590418057	2		632	477	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439972	56439972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	120	537	3	ENST00000407977.2:c.620G>A	p.Gly207Asp	p.G207D	ENST00000407977		207	gGc/gAc	6/10	1	2	FACETS	0.98	0.891	1	0.98	0.891	1	CLONAL	1	TRUE	1	0.523159590418057	2		540	468	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480012	120480012	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	135	523	1	ENST00000256646.2:c.3415del	p.Leu1139TrpfsTer68	p.L1139Wfs*68	ENST00000256646	NM_024408.3	1139	Ctg/tg	21/34	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.523159590418057	2		524	486	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259059	16259059	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1557760629	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	122	652	0	ENST00000375759.3:c.6324G>T	p.Gln2108His	p.Q2108H	ENST00000375759	NM_015001.2	2108	caG/caT	11/15	1	2	FACETS	0.897	0.815	0.983	0.897	0.815	0.983	CLONAL	1	TRUE	1	0.523159590418057	2		652	520	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268982	115268982	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	64	388	0	ENST00000438362.2:c.1628A>C	p.Gln543Pro	p.Q543P	ENST00000438362	NM_001242891.1	543	cAg/cCg	14/20	1	2	FACETS	0.927	0.811	1	0.927	0.811	1	CLONAL	1	TRUE	1	0.523159590418057	2		388	264	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406186	70406186	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	76	468	0	ENST00000373644.4:c.3700A>T	p.Thr1234Ser	p.T1234S	ENST00000373644	NM_030625.2	1234	Aca/Tca	4/12	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.523159590418057	2		468	276	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724711	112724711	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	37	353	0	ENST00000369452.4:c.595C>A	p.Leu199Ile	p.L199I	ENST00000369452	NM_007373.3	199	Ctt/Att	2/9	1	2	FACETS	0.693	0.577	0.821	0.693	0.577	0.821	SUBCLONAL	1	TRUE	1	0.523159590418057	2		353	204	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10783587	10783587	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	13	194	0	ENST00000361367.2:c.835T>C	p.Phe279Leu	p.F279L	ENST00000361367	NM_014633.3	279	Ttt/Ctt	7/25	1	2	FACETS	0.401	0.288	0.536	0.401	0.288	0.536	SUBCLONAL	1	TRUE	1	0.523159590418057	2		194	124	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941183	71941183	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	127	794	1	ENST00000298229.2:c.958C>A	p.Leu320Met	p.L320M	ENST00000298229	NM_001567.3	320	Ctg/Atg	9/28	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.523159590418057	2		795	461	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202631	108202631	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	42	314	0	ENST00000278616.4:c.7655A>G	p.His2552Arg	p.H2552R	ENST00000278616	NM_000051.3	2552	cAc/cGc	52/63	1	2	FACETS	0.918	0.777	1	0.918	0.777	1	CLONAL	1	TRUE	1	0.523159590418057	2		314	175	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110061	115110061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755884541	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	104	503	0	ENST00000257566.3:c.1817C>T	p.Thr606Met	p.T606M	ENST00000257566	NM_016569.3	606	aCg/aTg	8/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.523159590418057	2		503	323	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263840	133263840	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1365779443	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	89	501	0	ENST00000320574.5:c.62G>T	p.Arg21Met	p.R21M	ENST00000320574	NM_006231.2	21	aGg/aTg	1/49	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.523159590418057	2		501	294	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240060	41240060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs970471060	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	21	252	0	ENST00000379561.5:c.290C>T	p.Ala97Val	p.A97V	ENST00000379561	NM_002015.3	97	gCg/gTg	1/3	1	2	FACETS	0.565	0.44	0.708	0.565	0.44	0.708	SUBCLONAL	1	TRUE	1	0.523159590418057	2		252	142	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572116	95572116	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	47	344	0	ENST00000393063.1:c.2992A>T	p.Asn998Tyr	p.N998Y	ENST00000393063	NM_030621.3	998	Aat/Tat	20/28	1	2	FACETS	0.889	0.76	1	0.889	0.76	1	CLONAL	1	TRUE	1	0.523159590418057	2		344	202	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643637	38643637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	62	430	0	ENST00000299084.4:c.1107G>A	p.Met369Ile	p.M369I	ENST00000299084	NM_152594.2	369	atG/atA	7/7	1	2	FACETS	0.817	0.712	0.93	0.817	0.712	0.93	CLONAL	1	TRUE	1	0.523159590418057	2		430	290	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096170	2096170	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	77	469	0	ENST00000219066.1:c.337C>A	p.Leu113Met	p.L113M	ENST00000219066	NM_002528.5	113	Ctg/Atg	2/6	1	2	FACETS	0.897	0.795	1	0.897	0.795	1	CLONAL	1	TRUE	1	0.523159590418057	2		469	328	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351960	89351960	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	62	585	0	ENST00000301030.4:c.990G>T	p.Lys330Asn	p.K330N	ENST00000301030	NM_001256183.1	330	aaG/aaT	9/13	1	2	FACETS	0.519	0.449	0.594	0.519	0.449	0.594	SUBCLONAL	1	TRUE	1	0.523159590418057	2		585	457	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118541	17118541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471793185	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	112	607	0	ENST00000285071.4:c.1390G>A	p.Glu464Lys	p.E464K	ENST00000285071	NM_144997.5	464	Gag/Aag	12/14	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.523159590418057	2		607	405	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120073	70120073	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	81	523	4	ENST00000245479.2:c.1079del	p.Pro360ArgfsTer23	p.P360Rfs*23	ENST00000245479	NM_000346.3	359	Ccc/cc	3/3	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.523159590418057	2		527	264	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291515	15291515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868655333	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	80	576	1	ENST00000263388.2:c.3119G>A	p.Cys1040Tyr	p.C1040Y	ENST00000263388	NM_000435.2	1040	tGc/tAc	19/33	1	2	FACETS	0.811	0.719	0.909	0.811	0.719	0.909	CLONAL	1	TRUE	1	0.523159590418057	2		577	377	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209046	36209050	+	frameshift_variant	Frame_Shift_Del	DEL	AGTGC	AGTGC	-	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	66	431	0	ENST00000222270.7:c.126_130del	p.Val43GlyfsTer71	p.V43Gfs*71	ENST00000222270	NM_014727.1	42	agAGTGCgg/aggg	1/37	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.523159590418057	2		431	229	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229405	36229405	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	51	597	0	ENST00000222270.7:c.8095A>T	p.Asn2699Tyr	p.N2699Y	ENST00000222270	NM_014727.1	2699	Aac/Tac	37/37	1	2	FACETS	0.407	0.346	0.474	0.407	0.346	0.474	SUBCLONAL	1	TRUE	1	0.523159590418057	2		597	479	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753230	42753230	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	76	703	0	ENST00000222329.4:c.1034C>A	p.Pro345His	p.P345H	ENST00000222329	NM_006494.2	345	cCt/cAt	4/4	1	2	FACETS	0.479	0.421	0.543	0.479	0.421	0.543	SUBCLONAL	1	TRUE	1	0.523159590418057	2		703	606	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033379	48033379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	66	403	0	ENST00000234420.5:c.3683C>T	p.Ala1228Val	p.A1228V	ENST00000234420	NM_000179.2	1228	gCa/gTa	8/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.523159590418057	2		403	217	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920640	96920640	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	46	527	0	ENST00000258439.3:c.340G>A	p.Asp114Asn	p.D114N	ENST00000258439	NM_001193304.2	114	Gat/Aat	3/4	1	2	FACETS	0.436	0.368	0.512	0.436	0.368	0.512	SUBCLONAL	1	TRUE	1	0.523159590418057	2		527	403	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131472	202131472	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	87	503	0	ENST00000358485.4:c.440G>T	p.Arg147Met	p.R147M	ENST00000358485	NM_001080125.1	147	aGg/aTg	2/9	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.523159590418057	2		503	302	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656839	45656840	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	78	559	0	ENST00000407780.3:c.316dup	p.Gln106ProfsTer24	p.Q106Pfs*24	ENST00000407780	NM_001283052.1	106	cag/cCag	3/7	1	2	FACETS	0.64	0.564	0.721	0.64	0.564	0.721	SUBCLONAL	1	TRUE	1	0.523159590418057	2		559	466	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41542800	41542800	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	45	515	0	ENST00000263253.7:c.2111C>A	p.Pro704His	p.P704H	ENST00000263253	NM_001429.3	704	cCt/cAt	11/31	0.210603600243986	1	FACETS	0.416	0.352	0.487	0.416	0.352	0.487	INDETERMINATE	1	TRUE	0	0.523159590418057	1		515	305	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63973888	63973888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61736570	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	66	519	1	ENST00000398590.3:c.1249G>A	p.Ala417Thr	p.A417T	ENST00000398590	NM_001177387.1	417	Gcc/Acc	9/14	1	2	FACETS	0.481	0.418	0.549	0.481	0.418	0.549	SUBCLONAL	1	TRUE	1	0.523159590418057	2		520	525	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138409906	138409906	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1195436796	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	21	332	0	ENST00000289153.2:c.1972A>G	p.Arg658Gly	p.R658G	ENST00000289153	NM_006219.2	658	Aga/Gga	13/22	1	2	FACETS	0.412	0.318	0.519	0.412	0.318	0.519	SUBCLONAL	1	TRUE	1	0.523159590418057	2		332	195	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413703	138413703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	102	440	1	ENST00000289153.2:c.1817C>T	p.Ala606Val	p.A606V	ENST00000289153	NM_006219.2	606	gCc/gTc	12/22	1	2	FACETS	0.997	0.899	1	0.997	0.899	1	CLONAL	1	TRUE	1	0.523159590418057	2		441	391	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554273	106554273	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	78	475	0	ENST00000369096.4:c.1801C>T	p.Arg601Trp	p.R601W	ENST00000369096	NM_001198.3	601	Cgg/Tgg	6/7	1	2	FACETS	0.84	0.743	0.942	0.84	0.743	0.942	CLONAL	1	TRUE	1	0.523159590418057	2		475	355	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346632	81346632	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1211202460	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	76	474	0	ENST00000222390.5:c.1321C>T	p.Arg441Ter	p.R441*	ENST00000222390	NM_000601.4	441	Cga/Tga	11/18	1	2	FACETS	0.949	0.841	1	0.949	0.841	1	CLONAL	1	TRUE	1	0.523159590418057	2		474	306	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960120	151960120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	42	245	0	ENST00000262189.6:c.1280C>T	p.Thr427Ile	p.T427I	ENST00000262189	NM_170606.2	427	aCc/aTc	9/59	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.523159590418057	2		245	125	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2083401	2083401	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	24	195	0	ENST00000349721.2:c.2403G>T	p.Lys801Asn	p.K801N	ENST00000349721	NM_003070.3	801	aaG/aaT	16/34	1	2	FACETS	0.496	0.391	0.615	0.496	0.391	0.615	SUBCLONAL	1	TRUE	1	0.523159590418057	2		195	185	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0065210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	141	441	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.37943989462207	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.397561417182647	1		441	531	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	118	463	0	ENST00000263967.3:c.3129G>C	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atC	21/21	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.397561417182647	2		463	574	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805601	46805601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	165	568	0	ENST00000290295.7:c.355G>A	p.Glu119Lys	p.E119K	ENST00000290295	NM_006361.5	119	Gag/Aag	1/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.397561417182647	2		568	675	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098559	47098559	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	147	647	0	ENST00000409792.3:c.6715del	p.Gln2239SerfsTer9	p.Q2239Sfs*9	ENST00000409792	NM_014159.6	2239	Cag/ag	15/21	0.397561417182647	1	FACETS	0.986	0.904	1	0.986	0.904	1	CLONAL	1	TRUE	0	0.397561417182647	1		647	601	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502213	157502213	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	100	569	0	ENST00000346085.5:c.3246G>C	p.Glu1082Asp	p.E1082D	ENST00000346085	NM_020732.3	1082	gaG/gaC	12/20	0.397561417182647	1	FACETS	0.781	0.7	0.866	0.781	0.7	0.866	SUBCLONAL	1	TRUE	0	0.397561417182647	1		569	516	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271246	38271246	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1421199406	NA	P-0065210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	123	660	0	ENST00000425967.3:c.2462C>T	p.Ser821Leu	p.S821L	ENST00000425967	NM_001174067.1	821	tCa/tTa	19/19	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.397561417182647	2		660	571	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0065211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	96	534	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.282539875031329	2		534	667	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0065211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	69	476	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	1	2	FACETS	0.899	0.784	1	0.899	0.784	1	CLONAL	1	TRUE	1	0.282539875031329	2		476	543	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873835	35873835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs923187160	NA	P-0065211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	68	401	0	ENST00000216797.5:c.16G>A	p.Glu6Lys	p.E6K	ENST00000216797	NM_020529.2	6	Gag/Aag	1/6	1	2	FACETS	0.901	0.785	1	0.901	0.785	1	CLONAL	1	TRUE	1	0.282539875031329	2		401	534	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873724	35873724	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs999467784	NA	P-0065211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	75	484	0	ENST00000216797.5:c.127G>C	p.Glu43Gln	p.E43Q	ENST00000216797	NM_020529.2	43	Gag/Cag	1/6	1	2	FACETS	0.892	0.782	1	0.892	0.782	1	CLONAL	1	TRUE	1	0.282539875031329	2		484	595	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741919	17741919	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	72	428	0	ENST00000250003.3:c.590C>G	p.Ser197Cys	p.S197C	ENST00000250003	NM_002478.4	197	tCc/tGc	1/3	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.282539875031329	2		428	489	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610364	10610364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	80	640	1	ENST00000171111.5:c.346C>T	p.Arg116Trp	p.R116W	ENST00000171111	NM_203500.1	116	Cgg/Tgg	2/6	0.282539875031329	1	FACETS	0.745	0.656	0.84	0.745	0.656	0.84	SUBCLONAL	1	TRUE	0	0.282539875031329	1		641	653	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758808	41758808	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	74	476	0	ENST00000301178.4:c.1862C>T	p.Pro621Leu	p.P621L	ENST00000301178	NM_021913.4	621	cCt/cTt	16/20	1	2	FACETS	0.803	0.703	0.911	0.803	0.703	0.911	CLONAL	1	TRUE	1	0.282539875031329	2		476	652	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218414	1218414	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0065211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	82	523	0	ENST00000326873.7:c.291-2A>T		p.X97_splice	ENST00000326873	NM_000455.4	97			0.282539875031329	1	FACETS	0.953	0.842	1	0.953	0.842	1	CLONAL	1	TRUE	0	0.282539875031329	1		523	523	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636057	28636057	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	83	498	0	ENST00000241453.7:c.315G>T	p.Trp105Cys	p.W105C	ENST00000241453	NM_004119.2	105	tgG/tgT	3/24	1	2	FACETS	0.981	0.867	1	0.981	0.867	1	CLONAL	1	TRUE	1	0.282539875031329	2		498	599	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10789474	10789474	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	112	474	0	ENST00000361367.2:c.1808C>G	p.Ser603Cys	p.S603C	ENST00000361367	NM_014633.3	603	tCt/tGt	14/25	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.282539875031329	2		474	733	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097073	11097087	+	frameshift_variant	Frame_Shift_Del	DEL	GATGCTGGCCAGGGG	GATGCTGGCCAGGGG	CA	novel	NA	P-0065211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	90	603	2	ENST00000358026.2:c.564_578delinsCA	p.Lys188AsnfsTer111	p.K188Nfs*111	ENST00000358026	NM_001128849.1	188	aaGATGCTGGCCAGGGGg/aaCAg	4/36	0.282539875031329	1	FACETS	0.901	0.801	1	0.901	0.801	1	CLONAL	1	TRUE	0	0.282539875031329	1		605	607	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448575	89448576	+	missense_variant	Missense_Mutation	DNP	AG	AG	TT	novel	NA	P-0065211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	78	456	1	ENST00000336596.2:c.1539_1540delinsTT	p.Ala514Ser	p.A514S	ENST00000336596	NM_005233.5	513	acAGcc/acTTcc	7/17	1	2	FACETS	0.834	0.733	0.943	0.834	0.733	0.943	CLONAL	1	TRUE	1	0.282539875031329	2		457	662	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909250	41909250	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	108	521	0	ENST00000372991.4:c.138G>C	p.Gln46His	p.Q46H	ENST00000372991	NM_001760.3	46	caG/caC	1/5	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.282539875031329	2		521	712	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524958	8524958	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	64	366	2	ENST00000356435.5:c.646C>A	p.Arg216Ser	p.R216S	ENST00000356435		216	Cgc/Agc	7/35	0.282539875031329	1	FACETS	0.89	0.773	1	0.89	0.773	1	CLONAL	1	TRUE	0	0.282539875031329	1		368	437	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045535	47045535	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	92	663	0	ENST00000377604.3:c.2502G>T	p.Lys834Asn	p.K834N	ENST00000377604	NM_001204468.1	834	aaG/aaT	22/24	1	2	FACETS	0.844	0.749	0.944	0.844	0.749	0.944	CLONAL	1	TRUE	1	0.282539875031329	2		663	772	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339229	70339229	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	59	368	0	ENST00000374080.3:c.106C>G	p.Leu36Val	p.L36V	ENST00000374080		36	Ctg/Gtg	2/45	1	2	FACETS	0.943	0.813	1	0.943	0.813	1	CLONAL	1	TRUE	1	0.282539875031329	2		368	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934874	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	252	711	0	ENST00000269305.4:c.451C>A	p.Pro151Thr	p.P151T	ENST00000269305	NM_001126112.2	151	Ccc/Acc	5/11	0.213663981589293	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.213663981589293	2		711	1006	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612028	189612028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs900140738	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	40	577	0	ENST00000264731.3:c.1780C>T	p.Arg594Ter	p.R594*	ENST00000264731	NM_003722.4	594	Cga/Tga	14/14	1	2	FACETS	0.546	0.452	0.65	0.546	0.452	0.65	SUBCLONAL	1	TRUE	1	0.213663981589293	2		577	686	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602583	10602583	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	129	794	0	ENST00000171111.5:c.995del	p.Gly332AlafsTer68	p.G332Afs*68	ENST00000171111	NM_203500.1	332	gGc/gc	3/6	0.213663981589293	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.213663981589293	1		794	900	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959247	2959247	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	146	605	0	ENST00000396946.4:c.2270-1G>T		p.X757_splice	ENST00000396946	NM_032415.4	757			1	2	FACETS	0.948	0.867	1	1	0.991	1	CLONAL	2	TRUE	1	0.213663981589293	2		605	721	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904847	101904847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	66	403	0	ENST00000374994.4:c.835G>A	p.Val279Met	p.V279M	ENST00000374994	NM_004612.2	279	Gtg/Atg	5/9	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.213663981589293	2		403	578	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120271	70120271	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	117	746	0	ENST00000245479.2:c.1273C>A	p.Leu425Ile	p.L425I	ENST00000245479	NM_000346.3	425	Ctc/Atc	3/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.213663981589293	2		746	875	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137850	64137850	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	70	764	0	ENST00000334205.4:c.1951G>T	p.Val651Phe	p.V651F	ENST00000334205	NM_003942.2	651	Gtc/Ttc	15/17	1	2	FACETS	0.745	0.648	0.851	0.745	0.648	0.851	SUBCLONAL	1	TRUE	1	0.213663981589293	2		764	879	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27228220	27228220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	58	407	0	ENST00000380036.4:c.3217C>A	p.Gln1073Lys	p.Q1073K	ENST00000380036	NM_000459.3	1073	Caa/Aaa	22/23	0.213663981589293	1	FACETS	0.978	0.841	1	0.978	0.841	1	CLONAL	1	TRUE	0	0.213663981589293	1		407	496	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291778	15291778	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	90	666	0	ENST00000263388.2:c.2988G>T	p.Gln996His	p.Q996H	ENST00000263388	NM_000435.2	996	caG/caT	18/33	0.213663981589293	1	FACETS	0.99	0.878	1	0.99	0.878	1	CLONAL	1	TRUE	0	0.213663981589293	1		666	760	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099387	27099399	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTGGGTATCAG	CCCTGGGTATCAG	-	novel	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	44	539	0	ENST00000324856.7:c.3627_3639del	p.Gly1210ValfsTer2	p.G1210Vfs*2	ENST00000324856	NM_006015.4	1208	aaCCCTGGGTATCAG/aa	14/20	0.213663981589293	1	FACETS	0.533	0.446	0.63	0.533	0.446	0.63	SUBCLONAL	1	TRUE	0	0.213663981589293	1		539	690	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956147	175956147	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	25	305	0	ENST00000367669.3:c.2065A>G	p.Lys689Glu	p.K689E	ENST00000367669	NM_022457.5	689	Aaa/Gaa	18/20	1	2	FACETS	0.508	0.399	0.633	0.508	0.399	0.633	SUBCLONAL	1	TRUE	1	0.213663981589293	2		305	461	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100793	8100793	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs763545775	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	49	695	0	ENST00000346208.3:c.767G>T	p.Arg256Leu	p.R256L	ENST00000346208		256	cGg/cTg	3/6	1	2	FACETS	0.638	0.539	0.747	0.638	0.539	0.747	SUBCLONAL	1	TRUE	1	0.213663981589293	2		695	719	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813319	102813319	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	44	631	0	ENST00000307046.8:c.370C>A	p.Gln124Lys	p.Q124K	ENST00000307046	NM_001111285.1	124	Cag/Aag	3/4	1	2	FACETS	0.512	0.428	0.606	0.512	0.428	0.606	SUBCLONAL	1	TRUE	1	0.213663981589293	2		631	804	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335500	73335500	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	53	305	0	ENST00000377767.4:c.2670+1G>T		p.X890_splice	ENST00000377767	NM_014953.3	890			0.213663981589293	1	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	0	0.213663981589293	1		305	439	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819658	81819658	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1423487027	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	53	622	0	ENST00000359376.3:c.64C>G	p.Leu22Val	p.L22V	ENST00000359376	NM_002661.3	22	Ctg/Gtg	2/33	1	2	FACETS	0.607	0.516	0.707	0.607	0.516	0.707	SUBCLONAL	1	TRUE	1	0.213663981589293	2		622	817	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351349	89351349	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	115	686	0	ENST00000301030.4:c.1601A>T	p.Gln534Leu	p.Q534L	ENST00000301030	NM_001256183.1	534	cAg/cTg	9/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.213663981589293	2		686	920	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119781	70119781	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs751690259	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	42	597	0	ENST00000245479.2:c.783G>T	p.Glu261Asp	p.E261D	ENST00000245479	NM_000346.3	261	gaG/gaT	3/3	1	2	FACETS	0.61	0.508	0.723	0.61	0.508	0.723	SUBCLONAL	1	TRUE	1	0.213663981589293	2		597	645	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727903	78727903	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	47	567	0	ENST00000306801.3:c.748G>A	p.Glu250Lys	p.E250K	ENST00000306801	NM_020761.2	250	Gag/Aag	6/34	1	2	FACETS	0.587	0.494	0.691	0.587	0.494	0.691	SUBCLONAL	1	TRUE	1	0.213663981589293	2		567	749	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2220143	2220143	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	94	651	0	ENST00000398665.3:c.2728C>T	p.Pro910Ser	p.P910S	ENST00000398665	NM_032482.2	910	Ccc/Tcc	23/28	0.213663981589293	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.213663981589293	1		651	708	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4094473	4094473	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	104	506	0	ENST00000262948.5:c.1070G>T	p.Arg357Leu	p.R357L	ENST00000262948	NM_030662.3	357	cGg/cTg	10/11	0.213663981589293	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.213663981589293	1		506	638	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982491	25982491	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	54	422	0	ENST00000435504.4:c.799G>C	p.Ala267Pro	p.A267P	ENST00000435504		267	Gct/Cct	9/13	1	2	FACETS	0.734	0.626	0.852	0.734	0.626	0.852	SUBCLONAL	1	TRUE	1	0.213663981589293	2		422	689	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225367752	225367752	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	33	296	0	ENST00000264414.4:c.1415G>T	p.Gly472Val	p.G472V	ENST00000264414	NM_003590.4	472	gGa/gTa	10/16	1	2	FACETS	0.599	0.487	0.725	0.599	0.487	0.725	SUBCLONAL	1	TRUE	1	0.213663981589293	2		296	516	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546898	9546898	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	91	657	0	ENST00000353224.5:c.1124C>G	p.Ser375Cys	p.S375C	ENST00000353224	NM_177990.2	375	tCt/tGt	5/10	0.213663981589293	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.213663981589293	1		657	689	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40709550	40709550	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	76	433	0	ENST00000373198.4:c.4352A>G	p.Glu1451Gly	p.E1451G	ENST00000373198	NM_133170.3	1451	gAg/gGg	32/32	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.213663981589293	2		433	646	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430717	181430717	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	122	880	0	ENST00000325404.1:c.569G>T	p.Gly190Val	p.G190V	ENST00000325404	NM_003106.3	190	gGc/gTc	1/1	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.213663981589293	2		880	1084	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557911	187557911	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	54	606	0	ENST00000441802.2:c.3800G>T	p.Arg1267Ile	p.R1267I	ENST00000441802	NM_005245.3	1267	aGa/aTa	5/27	0.186473973710527	0	FACETS	0.582	0.496	0.676			1	SUBCLONAL	1	TRUE	0	0.213663981589293	0		606	683	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961025	79961025	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	69	419	0	ENST00000265081.6:c.422G>C	p.Cys141Ser	p.C141S	ENST00000265081	NM_002439.4	141	tGc/tCc	3/24	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.213663981589293	2		419	641	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961156	79961156	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	35	320	0	ENST00000265081.6:c.553G>T	p.Asp185Tyr	p.D185Y	ENST00000265081	NM_002439.4	185	Gat/Tat	3/24	1	2	FACETS	0.565	0.462	0.681	0.565	0.462	0.681	SUBCLONAL	1	TRUE	1	0.213663981589293	2		320	580	SUCCESS
APC	324	MSKCC	GRCh37	5	112173650	112173650	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	41	426	0	ENST00000257430.4:c.2359A>T	p.Ser787Cys	p.S787C	ENST00000257430	NM_000038.5	787	Agt/Tgt	16/16	1	2	FACETS	0.612	0.509	0.727	0.612	0.509	0.727	SUBCLONAL	1	TRUE	1	0.213663981589293	2		426	627	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514459	149514459	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	54	663	0	ENST00000261799.4:c.485A>T	p.Glu162Val	p.E162V	ENST00000261799	NM_002609.3	162	gAg/gTg	4/23	0.199770227816648	1	FACETS	0.558	0.475	0.649	0.558	0.475	0.649	SUBCLONAL	1	TRUE	0	0.213663981589293	1		663	809	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250490	26250490	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs758807626	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	274	870	0	ENST00000446824.2:c.344C>G	p.Ala115Gly	p.A115G	ENST00000446824	NM_021018.2	115	gCc/gGc	1/1	0.213663981589293	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.213663981589293	2		870	1085	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519380	137519380	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	63	408	0	ENST00000367739.4:c.1258G>T	p.Glu420Ter	p.E420*	ENST00000367739	NM_000416.2	420	Gaa/Taa	7/7	0.213663981589293	1	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	0	0.213663981589293	1		408	524	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265514	152265514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	36	559	0	ENST00000206249.3:c.967G>A	p.Glu323Lys	p.E323K	ENST00000206249	NM_000125.3	323	Gag/Aag	4/8	0.213663981589293	1	FACETS	0.441	0.361	0.53	0.441	0.361	0.53	SUBCLONAL	1	TRUE	0	0.213663981589293	1		559	683	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969951	161969952	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	66	510	0	ENST00000366898.1:c.1017_1018delinsTT	p.Gly340Trp	p.G340W	ENST00000366898	NM_004562.2	339	gcGGgg/gcTTgg	9/12	0.213663981589293	1	FACETS	0.984	0.854	1	0.984	0.854	1	CLONAL	1	TRUE	0	0.213663981589293	1		510	561	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851991	128851991	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	194	723	0	ENST00000249373.3:c.2063C>A	p.Pro688His	p.P688H	ENST00000249373	NM_005631.4	688	cCc/cAc	12/12	0.185597852076116	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.213663981589293	2		723	827	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974648	21974803	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTGCTCCCGCTGCAGACCCTCTACCCACCTGGATCGGCCTCCGACCGTAACTATTCGGTGCGTTGGGCAGCGCCCCCGCCTCCAGCAGCGCCCGCACCTCCTCTACCCGACCCCGGGCCGCGGCCGTGGCCAGCCAGTCAGCCGAAGGCTCCATG	CCTGCTCCCGCTGCAGACCCTCTACCCACCTGGATCGGCCTCCGACCGTAACTATTCGGTGCGTTGGGCAGCGCCCCCGCCTCCAGCAGCGCCCGCACCTCCTCTACCCGACCCCGGGCCGCGGCCGTGGCCAGCCAGTCAGCCGAAGGCTCCATG	-	novel	NA	P-0065212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	108	723	0	ENST00000304494.5:c.24_150+29del		p.X8_splice	ENST00000304494	NM_000077.4	8		1/3	0.213663981589293	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.213663981589293	1		723	811	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593504	48593504	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	21	398	0	ENST00000342988.3:c.1255G>T	p.Gly419Trp	p.G419W	ENST00000342988	NM_005359.5	419	Ggg/Tgg	10/12	0.615118957266981	1	FACETS	0.15	0.115	0.19	0.15	0.115	0.19	SUBCLONAL	1	TRUE	0	0.647443652040856	1		398	293	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586250	48586250	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	37	358	0	ENST00000342988.3:c.919G>T	p.Glu307Ter	p.E307*	ENST00000342988	NM_005359.5	307	Gag/Tag	8/12	0.615118957266981	1	FACETS	0.477	0.399	0.562	0.477	0.399	0.562	SUBCLONAL	1	TRUE	0	0.647443652040856	1		358	162	SUCCESS
APC	324	MSKCC	GRCh37	5	112173956	112173956	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	456	443	0	ENST00000257430.4:c.2667del	p.Val890SerfsTer26	p.V890Sfs*26	ENST00000257430	NM_000038.5	889	Aaa/aa	16/16	0.627535148426665	4	FACETS	0.931	0.904	0.958	0.931	0.904	0.958	CLONAL	4	TRUE	0	0.647443652040856	4		443	623	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691039	NA	P-0065213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	197	614	0	ENST00000269305.4:c.919+1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.266227528759343	3	FACETS	1	0.989	1	0.655	0.61	0.701	INDETERMINATE	1	TRUE	1	0.647443652040856	3		614	615	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576905	7576914	+	frameshift_variant	Frame_Shift_Del	DEL	GAGCTGGTGT	GAGCTGGTGT	-	novel	NA	P-0065213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	163	611	0	ENST00000269305.4:c.932_941del	p.Asn311ThrfsTer31	p.N311Tfs*31	ENST00000269305	NM_001126112.2	311	aACACCAGCTCc/ac	9/11	0.266227528759343	3	FACETS	1	0.978	1	0.581	0.536	0.627	INDETERMINATE	1	TRUE	1	0.647443652040856	3		611	574	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554066	63554067	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATAGCCACACACGAT	novel	NA	P-0065213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	186	579	0	ENST00000307078.5:c.672_673insATCGTGTGTGGCTAT	p.Tyr224_Leu225insIleValCysGlyTyr	p.Y224_L225insIVCGY	ENST00000307078	NM_004655.3	224	-/ATCGTGTGTGGCTAT	2/11	0.648492871260614	3	FACETS	0.831	0.768	0.897	0.416	0.384	0.449	CLONAL	1	TRUE	1	0.647443652040856	3		579	915	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581148	48581149	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	AGCTCCATCAAGTATGATGGTGAAGGATGAATATGTGCATG	novel	NA	P-0065213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	12	324	0	ENST00000342988.3:c.455-1_494dup		p.X152_splice	ENST00000342988	NM_005359.5	152			0.615118957266981	1	FACETS	0.109	0.076	0.149	0.109	0.076	0.149	SUBCLONAL	1	TRUE	0	0.647443652040856	1		324	230	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512369	38512369	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	51	300	0	ENST00000254066.5:c.1280C>G	p.Pro427Arg	p.P427R	ENST00000254066	NM_000964.3	427	cCg/cGg	9/9	0.559114494143387	3	FACETS	0.527	0.448	0.612	0.263	0.224	0.306	SUBCLONAL	1	TRUE	1	0.591878787354328	3		300	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863224499	NA	P-0065215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	516	538	0	ENST00000269305.4:c.672+1G>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.940197749732945	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.940884188920834	1		538	549	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	525	723	0	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	0.863	0.829	0.898	0.863	0.829	0.898	CLONAL	1	TRUE	1	0.940884188920834	2		723	1293	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740749	58740749	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs779070661	NA	P-0065215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	449	434	0	ENST00000305921.3:c.1654C>T	p.Arg552Ter	p.R552*	ENST00000305921	NM_003620.3	552	Cga/Tga	6/6	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.940884188920834	2		434	928	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786795	3786795	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	406	479	0	ENST00000262367.5:c.4416G>T	p.Trp1472Cys	p.W1472C	ENST00000262367	NM_004380.2	1472	tgG/tgT	27/31	0.940884188920834	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.940884188920834	1		479	428	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434879	49434879	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	571	723	0	ENST00000301067.7:c.6674A>T	p.Glu2225Val	p.E2225V	ENST00000301067	NM_003482.3	2225	gAa/gTa	31/54	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.940884188920834	2		723	1200	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008041	29008041	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	306	331	0	ENST00000282397.4:c.728T>A	p.Leu243His	p.L243H	ENST00000282397	NM_002019.4	243	cTt/cAt	6/30	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.940884188920834	2		331	619	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244091	5244091	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	535	665	0	ENST00000357368.4:c.1391A>T	p.Tyr464Phe	p.Y464F	ENST00000357368	NM_002850.3	464	tAc/tTc	11/38	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.940884188920834	2		665	1124	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630747	67630748	+	missense_variant	Missense_Mutation	DNP	TA	TA	AT	novel	NA	P-0065215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	102	299	0	ENST00000272342.5:c.933_934delinsAT	p.Thr312Ser	p.T312S	ENST00000272342	NM_019002.3	311	acTAcc/acATcc	5/6	1	2	FACETS	0.439	0.394	0.486	0.439	0.394	0.486	SUBCLONAL	1	TRUE	1	0.940884188920834	2		299	494	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326576	62326576	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0065215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	543	630	0	ENST00000360203.5:c.3499+2T>A		p.X1167_splice	ENST00000360203	NM_001283009.1	1167			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.940884188920834	2		630	1145	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323235	31323235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs61759953	NA	P-0065215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	396	577	0	ENST00000412585.2:c.754A>G	p.Thr252Ala	p.T252A	ENST00000412585	NM_005514.6	252	Act/Gct	4/8	1	2	FACETS	0.825	0.787	0.864	0.825	0.787	0.864	CLONAL	1	TRUE	1	0.940884188920834	2		577	1020	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987230	2987230	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	384	466	0	ENST00000396946.4:c.199C>A	p.Pro67Thr	p.P67T	ENST00000396946	NM_032415.4	67	Cca/Aca	3/25	1	2	FACETS	0.945	0.902	0.988	0.945	0.902	0.988	CLONAL	1	TRUE	1	0.940884188920834	2		466	864	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222424	53222424	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	421	620	0	ENST00000375401.3:c.4408G>T	p.Asp1470Tyr	p.D1470Y	ENST00000375401	NM_004187.3	1470	Gat/Tat	26/26	0.131466252516511	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.940884188920834	0		620	963	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0065217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	95	338	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.189072117955876	4	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	2	0.189072117955876	4		338	546	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527870	103527870	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs761148901	NA	P-0065217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	53	556	0	ENST00000355739.4:c.3178A>G	p.Ile1060Val	p.I1060V	ENST00000355739	NM_000123.3	1060	Ata/Gta	15/15	1	2	FACETS	0.984	0.839	1	0.984	0.839	1	CLONAL	1	TRUE	1	0.189072117955876	2		556	570	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95595947	95595947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	47	372	0	ENST00000393063.1:c.596G>A	p.Cys199Tyr	p.C199Y	ENST00000393063	NM_030621.3	199	tGt/tAt	7/28	0.177710566557127	3	FACETS	1	0.955	1	0.692	0.585	0.81	CLONAL	1	TRUE	1	0.189072117955876	3		372	393	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40864402	40864402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1237409185	NA	P-0065217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	143	513	0	ENST00000428826.2:c.1306G>A	p.Gly436Arg	p.G436R	ENST00000428826		436	Ggg/Agg	12/21	0.189072117955876	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.189072117955876	4		513	774	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220505	1220505	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0065217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	177	691	0	ENST00000326873.7:c.597+1G>A		p.X199_splice	ENST00000326873	NM_000455.4	199			0.184647905774351	3	FACETS	0.883	0.815	0.953	0.883	0.815	0.953	CLONAL	3	TRUE	0	0.189072117955876	3		691	774	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602872	10602872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	225	628	0	ENST00000171111.5:c.706G>A	p.Asp236Asn	p.D236N	ENST00000171111	NM_203500.1	236	Gac/Aac	3/6	0.184647905774351	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	3	TRUE	0	0.189072117955876	3		628	835	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134297	11134297	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	162	486	0	ENST00000358026.2:c.2963T>G	p.Leu988Trp	p.L988W	ENST00000358026	NM_001128849.1	988	tTg/tGg	20/36	0.184647905774351	3	FACETS	0.981	0.904	1	0.981	0.904	1	CLONAL	3	TRUE	0	0.189072117955876	3		486	637	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0065229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	343	615	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	0.848	0.809	0.888	1	0.996	1	CLONAL	2	TRUE	1	0.55	2		615	735	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0065230-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	206	694	1	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.370258521555019	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.370258184599836	1		695	673	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0065230-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	165	601	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.370258184599836	2		601	721	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10786191	10786191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745924899	NA	P-0065230-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	74	511	0	ENST00000361367.2:c.1510G>A	p.Ala504Thr	p.A504T	ENST00000361367	NM_014633.3	504	Gcc/Acc	12/25	0.246478480590087	1	FACETS	0.607	0.532	0.687	0.607	0.532	0.687	SUBCLONAL	1	TRUE	0	0.370258184599836	1		511	537	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250381	10250381	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065230-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	76	680	0	ENST00000340748.4:c.3871G>A	p.Gly1291Ser	p.G1291S	ENST00000340748		1291	Ggc/Agc	33/40	1	2	FACETS	0.496	0.434	0.563	0.496	0.434	0.563	SUBCLONAL	1	TRUE	1	0.370258184599836	2		680	827	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602982	55602982	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065230-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	63	489	0	ENST00000288135.5:c.2692G>T	p.Glu898Ter	p.E898*	ENST00000288135	NM_000222.2	898	Gaa/Taa	19/21	0.31259130479242	1	FACETS	0.569	0.493	0.652	0.569	0.493	0.652	SUBCLONAL	1	TRUE	0	0.370258184599836	1		489	487	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0065231-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	106	256	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.791	0.717	0.868	0.791	0.717	0.868	SUBCLONAL	1	TRUE	1	0.795193152236485	2		256	337	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013715	12013719	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs777997110	NA	P-0065231-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	95	297	0	ENST00000353533.5:c.661_665del	p.Glu221LeufsTer22	p.E221Lfs*22	ENST00000353533	NM_003010.3	219	ttAAAAGaa/ttaa	6/11	0.498618306968536	1	FACETS	0.339	0.303	0.376	0.339	0.303	0.376	SUBCLONAL	1	TRUE	0	0.795193152236485	1		297	425	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0065231-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	174	256	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.782032511849937	2		256	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0065231-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	355	824	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.771975717590892	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.782032511849937	1		824	530	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013715	12013719	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs777997110	NA	P-0065231-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	214	297	0	ENST00000353533.5:c.661_665del	p.Glu221LeufsTer22	p.E221Lfs*22	ENST00000353533	NM_003010.3	219	ttAAAAGaa/ttaa	6/11	0.771975717590892	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.782032511849937	1		297	321	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752729	128752731	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1203089442	NA	P-0065232-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	323	650	0	ENST00000377970.2:c.892_894del	p.Ser298del	p.S298del	ENST00000377970	NM_002467.4	297	cCTTct/cct	3/3	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.86622410513926	2		650	719	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574027	7574027	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882028	NA	P-0065232-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	240	538	0	ENST00000269305.4:c.1000G>T	p.Gly334Trp	p.G334W	ENST00000269305	NM_001126112.2	334	Ggg/Tgg	10/11	0.86622410513926	1	FACETS	0.988	0.949	1	0.988	0.949	1	CLONAL	1	TRUE	0	0.86622410513926	1		538	318	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417947	32417947	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1423753702	NA	P-0065232-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	320	618	0	ENST00000332351.3:c.1105C>T	p.Arg369Ter	p.R369*	ENST00000332351	NM_024426.4	369	Cga/Tga	7/10	0.86622410513926	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.86622410513926	1		618	409	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11168338	11168338	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065232-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	245	446	0	ENST00000361445.4:c.7534G>T	p.Asp2512Tyr	p.D2512Y	ENST00000361445	NM_004958.3	2512	Gac/Tac	57/58	0.702411499199011	1	FACETS	0.864	0.825	0.902	0.864	0.825	0.902	CLONAL	1	TRUE	0	0.86622410513926	1		446	371	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942696	48942697	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0065232-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	267	373	0	ENST00000267163.4:c.1083_1084del	p.Leu362Ter	p.L362*	ENST00000267163	NM_000321.2	361	aaCCtt/aatt	11/27	0.86622410513926	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.86622410513926	1		373	333	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061126	38061191	+	inframe_deletion	In_Frame_Del	DEL	TTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTG	TTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTG	-	novel	NA	P-0065232-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	622	734	0	ENST00000250448.2:c.798_863del	p.Phe266_Lys288delinsLeu	p.F266_K288delinsL	ENST00000250448	NM_004496.3	266	ttCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGGCGCCAAg/ttg	2/2	0.67932173128962	3	FACETS	1	0.984	1			1	CLONAL	2	TRUE	NA	0.86622410513926	3		734	1007	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912041	127912041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1349509785	NA	P-0065232-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	324	563	0	ENST00000373547.4:c.829G>A	p.Val277Ile	p.V277I	ENST00000373547	NM_002721.4	277	Gta/Ata	7/7	0.780720963781224	1	FACETS	0.853	0.819	0.886	0.853	0.819	0.886	CLONAL	1	TRUE	0	0.86622410513926	1		563	497	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0065233-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	520	256	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.662025865069052	6	FACETS	1	0.993	1	1	0.993	1	CLONAL	6	TRUE	0	0.662025865069052	6		256	592	SUCCESS
APC	324	MSKCC	GRCh37	5	112175897	112175897	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065233-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	315	537	0	ENST00000257430.4:c.4606G>T	p.Glu1536Ter	p.E1536*	ENST00000257430	NM_000038.5	1536	Gaa/Taa	16/16	0.662025865069052	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.662025865069052	1		537	510	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434114	49434114	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065233-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	252	657	0	ENST00000301067.7:c.7439A>C	p.Lys2480Thr	p.K2480T	ENST00000301067	NM_003482.3	2480	aAg/aCg	31/54	0.237402974546074	4	FACETS	1	0.977	1	1	0.977	1	INDETERMINATE	2	TRUE	2	0.662025865069052	4		657	594	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574014	7574015	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGCGCTCACGCCCACGGATCTGC	novel	NA	P-0065233-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	159	452	1	ENST00000269305.4:c.994-4_1012dup	p.Phe338CysfsTer15	p.F338Cfs*15	ENST00000269305	NM_001126112.2	338	ttc/tGCAGATCCGTGGGCGTGAGCGCTtc	10/11	0.629589475742885	2	FACETS	1	0.986	1	0.629	0.584	0.674	CLONAL	1	TRUE	0	0.662025865069052	2		453	382	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843734	151843734	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065233-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	288	479	0	ENST00000262189.6:c.13981G>T	p.Glu4661Ter	p.E4661*	ENST00000262189	NM_170606.2	4661	Gag/Tag	53/59	0.237402974546074	4	FACETS	0.959	0.907	1	0.959	0.907	1	INDETERMINATE	2	TRUE	2	0.662025865069052	4		479	754	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763864	76763864	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065233-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	229	522	0	ENST00000373344.5:c.7444A>G	p.Lys2482Glu	p.K2482E	ENST00000373344	NM_000489.3	2482	Aaa/Gaa	35/35	0.193594151649132	4	FACETS	0.984	0.925	1	0.984	0.925	1	INDETERMINATE	2	TRUE	2	0.662025865069052	4		522	584	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0065234-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	18	350	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.189023689555295	3	FACETS	0.809	0.617	1	0.809	0.617	1	CLONAL	2	TRUE	1	0.214228136602699	3		350	115	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368208	45368208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065234-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	26	479	0	ENST00000262160.6:c.1394G>A	p.Ser465Asn	p.S465N	ENST00000262160	NM_005901.5	465	aGc/aAc	11/11	0.214228136602699	1	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	0	0.214228136602699	1		479	192	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065234-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	40	583	0	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	0.214228136602699	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.214228136602699	1		583	234	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435000	110435000	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065234-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	108	775	0	ENST00000375856.3:c.3401A>G	p.Lys1134Arg	p.K1134R	ENST00000375856	NM_003749.2	1134	aAg/aGg	1/2	0.150915804613408	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.214228136602699	1		775	699	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732964	30733022	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCCCGTCTCACAGCCCAGTGTGTGGCAGAACGCTTCAGTGAGCTGGAGCATCTGGAC	AGGCCCGTCTCACAGCCCAGTGTGTGGCAGAACGCTTCAGTGAGCTGGAGCATCTGGAC	-	novel	NA	P-0065234-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	75	570	0	ENST00000295754.5:c.1581_1639del	p.Arg528LeufsTer12	p.R528Lfs*12	ENST00000295754	NM_003242.5	526	gAGGCCCGTCTCACAGCCCAGTGTGTGGCAGAACGCTTCAGTGAGCTGGAGCATCTGGAC/g	7/7	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.214228136602699	2		570	597	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099980	27099980	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	CAT	novel	NA	P-0065234-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	79	728	0	ENST00000324856.7:c.3859delinsCAT	p.Arg1287HisfsTer3	p.R1287Hfs*3	ENST00000324856	NM_006015.4	1287	Aga/CATga	15/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.214228136602699	2		728	604	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0065235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	652	393	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.560077018130014	7	FACETS	0.972	0.951	0.993	0.972	0.951	0.993	CLONAL	7	TRUE	0	0.560077018130014	7		393	821	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562958	95562958	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	409	524	0	ENST00000393063.1:c.4299G>T	p.Lys1433Asn	p.K1433N	ENST00000393063	NM_030621.3	1433	aaG/aaT	24/28	0.431747975383515	5	FACETS	0.934	0.893	0.976	0.934	0.893	0.976	CLONAL	3	TRUE	2	0.560077018130014	5		524	959	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41999993	41999993	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	233	447	0	ENST00000219905.7:c.2256A>T	p.Leu752Phe	p.L752F	ENST00000219905	NM_001164273.1	752	ttA/ttT	6/24	0.537936016624396	2	FACETS	0.981	0.93	1	0.981	0.93	1	CLONAL	2	TRUE	0	0.560077018130014	2		447	424	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58725306	58725306	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	143	503	0	ENST00000305921.3:c.880C>G	p.Pro294Ala	p.P294A	ENST00000305921	NM_003620.3	294	Cca/Gca	4/6	0.539026384887977	4	FACETS	0.963	0.879	1	0.321	0.293	0.351	CLONAL	1	TRUE	1	0.560077018130014	4		503	827	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602488	10602488	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1397945617	NA	P-0065235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	536	788	0	ENST00000171111.5:c.1090G>T	p.Gly364Cys	p.G364C	ENST00000171111	NM_203500.1	364	Ggc/Tgc	3/6	0.536542463705898	3	FACETS	0.912	0.882	0.942	0.912	0.882	0.942	CLONAL	3	TRUE	0	0.560077018130014	3		788	895	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027718	48027718	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0065235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	240	478	0	ENST00000234420.5:c.2596A>T	p.Lys866Ter	p.K866*	ENST00000234420	NM_000179.2	866	Aaa/Taa	4/10	0.549978868365355	3	FACETS	0.927	0.872	0.982	0.927	0.872	0.982	CLONAL	2	TRUE	1	0.560077018130014	3		478	592	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378265	225378266	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	71	353	0	ENST00000264414.4:c.629dup	p.Leu210PhefsTer20	p.L210Ffs*20	ENST00000264414	NM_003590.4	210	ttg/ttTg	5/16	0.549978868365355	3	FACETS	0.664	0.581	0.753	0.332	0.29	0.377	SUBCLONAL	1	TRUE	1	0.560077018130014	3		353	489	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29279824	29279824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	88	76	0	ENST00000544604.2:c.70C>T	p.Arg24Cys	p.R24C	ENST00000544604	NM_001206998.1	24	Cgc/Tgc	1/9	0.537936016624396	2	FACETS	0.845	0.785	0.9	1	0.984	1	CLONAL	3	TRUE	0	0.560077018130014	2		76	124	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064391	30064391	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	269	498	0	ENST00000338641.4:c.955C>T	p.Gln319Ter	p.Q319*	ENST00000338641	NM_000268.3	319	Cag/Tag	10/16	0.537936016624396	2	FACETS	0.984	0.936	1	0.984	0.936	1	CLONAL	2	TRUE	0	0.560077018130014	2		498	488	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629415	187629415	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	353	628	0	ENST00000441802.2:c.1567G>T	p.Glu523Ter	p.E523*	ENST00000441802	NM_005245.3	523	Gaa/Taa	2/27	0.537936016624396	2	FACETS	0.977	0.935	1	0.977	0.935	1	CLONAL	2	TRUE	0	0.560077018130014	2		628	645	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	231091	231091	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	100	287	0	ENST00000264932.6:c.871G>T	p.Glu291Ter	p.E291*	ENST00000264932	NM_004168.2	291	Gag/Tag	7/15	0.549978868365355	3	FACETS	1	0.95	1	0.547	0.491	0.605	CLONAL	1	TRUE	1	0.560077018130014	3		287	418	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687261	117687261	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	140	439	0	ENST00000368508.3:c.2790G>T	p.Gln930His	p.Q930H	ENST00000368508	NM_002944.2	930	caG/caT	18/43	1	2	FACETS	0.958	0.877	1	0.958	0.877	1	CLONAL	1	TRUE	1	0.560077018130014	2		439	522	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981798	70981798	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	562	649	1	ENST00000276594.2:c.298C>G	p.Pro100Ala	p.P100A	ENST00000276594	NM_024504.3	100	Ccg/Gcg	2/8	0.560077018130014	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	1	0.560077018130014	4		650	987	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065237-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	122	789	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.74	0.671	0.812	0.74	0.671	0.812	SUBCLONAL	1	TRUE	1	0.552552675395211	2		789	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579321	7579322	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs587780067	NA	P-0065237-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	53	559	0	ENST00000269305.4:c.365_366del	p.Val122AspfsTer26	p.V122Dfs*26	ENST00000269305	NM_001126112.2	122	gTG/g	4/11	1	2	FACETS	0.222	0.189	0.259	0.222	0.189	0.259	SUBCLONAL	1	TRUE	1	0.552552675395211	2		559	863	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578518	7578518	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065237-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	65	576	1	ENST00000269305.4:c.412del	p.Ala138ProfsTer32	p.A138Pfs*32	ENST00000269305	NM_001126112.2	138	Gcc/cc	5/11	1	2	FACETS	0.223	0.192	0.256	0.223	0.192	0.256	SUBCLONAL	1	TRUE	1	0.552552675395211	2		577	1056	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624263	89624264	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs587776671	NA	P-0065237-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	60	203	0	ENST00000371953.3:c.39_40del	p.Arg14GlufsTer29	p.R14Efs*29	ENST00000371953	NM_000314.4	13	AAa/a	1/9	0.552552675395211	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.552552675395211	1		203	127	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562738	29562739	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555615472	NA	P-0065237-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	57	410	0	ENST00000356175.3:c.3822_3823del	p.Phe1275ProfsTer8	p.F1275Pfs*8	ENST00000356175	NM_000267.3	1273	aCT/a	28/57	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.552552675395211	2		410	175	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562657	29562660	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs1064794276	NA	P-0065237-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	41	411	0	ENST00000356175.3:c.3739_3742del	p.Phe1247IlefsTer18	p.F1247Ifs*18	ENST00000356175	NM_000267.3	1246	cTGTTt/ct	28/57	1	2	FACETS	0.957	0.811	1	0.957	0.811	1	CLONAL	1	TRUE	1	0.552552675395211	2		411	155	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257282	16257284	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs767260229	NA	P-0065237-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	12	624	0	ENST00000375759.3:c.4554_4556del	p.Glu1519del	p.E1519del	ENST00000375759	NM_015001.2	1516	aAAGaa/aaa	11/15	1	2	FACETS	0.243	0.171	0.331	0.243	0.171	0.331	SUBCLONAL	1	TRUE	1	0.552552675395211	2		624	179	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450066	32450066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1213160959	NA	P-0065237-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	293	576	0	ENST00000332351.3:c.746C>T	p.Pro249Leu	p.P249L	ENST00000332351	NM_024426.4	249	cCc/cTc	2/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.552552675395211	2		576	959	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281222	49281222	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147650408	NA	P-0065237-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	57	546	0	ENST00000282018.3:c.269C>T	p.Thr90Met	p.T90M	ENST00000282018	NM_020377.2	90	aCg/aTg	1/1	1	2	FACETS	0.96	0.835	1	0.96	0.835	1	CLONAL	1	TRUE	1	0.552552675395211	2		546	215	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271759	15271759	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065237-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	397	756	0	ENST00000263388.2:c.6680A>T	p.His2227Leu	p.H2227L	ENST00000263388	NM_000435.2	2227	cAc/cTc	33/33	0.116050300691067	4	FACETS	0.845	0.803	0.888	0.845	0.803	0.888	INDETERMINATE	2	TRUE	2	0.552552675395211	4		756	1320	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434243	12434244	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065237-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	52	412	0	ENST00000287820.6:c.612dup	p.His205SerfsTer2	p.H205Sfs*2	ENST00000287820	NM_015869.4	204	tct/tcTt	4/7	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.552552675395211	2		412	170	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573196	64573196	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065243-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	332	709	0	ENST00000312049.6:c.1096G>T	p.Glu366Ter	p.E366*	ENST00000312049	NM_130799.2	366	Gaa/Taa	8/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		709	469	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446834	29446834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375016509	NA	P-0065243-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	237	614	0	ENST00000544604.2:c.2665C>T	p.Arg889Trp	p.R889W	ENST00000544604	NM_001206998.1	889	Cgg/Tgg	8/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		614	592	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011150	12011150	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065244-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	134	340	0	ENST00000353533.5:c.557A>G	p.Asp186Gly	p.D186G	ENST00000353533	NM_003010.3	186	gAt/gGt	5/11	0.28841425788449	3	FACETS	1	0.936	1	1	0.936	1	CLONAL	3	TRUE	0	0.28841425788449	3		340	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579445	7579446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065244-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	267	636	0	ENST00000269305.4:c.241dup	p.Thr81AsnfsTer68	p.T81Nfs*68	ENST00000269305	NM_001126112.2	81	aca/aAca	4/11	0.28841425788449	3	FACETS	0.965	0.909	1	0.965	0.909	1	CLONAL	3	TRUE	0	0.28841425788449	3		636	732	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057580	180057580	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065244-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	57	492	0	ENST00000261937.6:c.375del	p.Ala126ProfsTer7	p.A126Pfs*7	ENST00000261937	NM_182925.4	125	gcC/gc	3/30	0.261129496061454	3	FACETS	1	0.902	1	0.531	0.456	0.611	CLONAL	1	TRUE	1	0.28841425788449	3		492	426	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154769	2154769	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1457247306	NA	P-0065245-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	502	578	0	ENST00000434045.2:c.452C>T	p.Ser151Leu	p.S151L	ENST00000434045	NM_001127598.1	151	tCg/tTg	4/5	0.8524514627286	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.8524514627286	3		578	792	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729982	41729982	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065245-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	268	557	0	ENST00000242208.4:c.547C>A	p.Gln183Lys	p.Q183K	ENST00000242208	NM_002192.2	183	Cag/Aag	3/3	0.8524514627286	3	FACETS	0.96	0.902	1	0.48	0.451	0.51	CLONAL	1	TRUE	1	0.8524514627286	3		557	934	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202925	27202925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749958421	NA	P-0065246-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	62	553	0	ENST00000380036.4:c.2017C>T	p.Arg673Cys	p.R673C	ENST00000380036	NM_000459.3	673	Cgt/Tgt	13/23	0.475157334659595	4	FACETS	1	0.954	1	0.607	0.53	0.689	CLONAL	1	TRUE	2	0.6424597049898	4		553	261	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608309	28608309	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767430269	NA	P-0065246-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	109	630	0	ENST00000241453.7:c.1747G>A	p.Gly583Ser	p.G583S	ENST00000241453	NM_004119.2	583	Ggc/Agc	14/24	0.6424597049898	8	FACETS	0.846	0.762	0.935	0.212	0.19	0.234	CLONAL	2	TRUE	0	0.6424597049898	8		630	587	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235946	108235946	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0065246-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	130	613	0	ENST00000278616.4:c.8987+1G>A		p.X2996_splice	ENST00000278616	NM_000051.3	2996			0.646498929061178	2	FACETS	0.859	0.82	0.894	1	0.991	1	CLONAL	3	TRUE	0	0.6424597049898	2		613	157	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100026	30100026	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065246-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	97	658	0	ENST00000331968.5:c.1594T>A	p.Trp532Arg	p.W532R	ENST00000331968	NM_002742.2	532	Tgg/Agg	10/18	0.461737407925663	4	FACETS	0.861	0.778	0.947	0.574	0.519	0.631	CLONAL	2	TRUE	1	0.6424597049898	4		658	288	SUCCESS
ALK	238	MSKCC	GRCh37	2	29420415	29420415	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065246-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	44	578	0	ENST00000389048.3:c.4066G>A	p.Gly1356Arg	p.G1356R	ENST00000389048	NM_004304.4	1356	Ggg/Agg	27/29	0.0604892970527429	4	FACETS	0.987	0.835	1			1	INDETERMINATE	1	TRUE	NA	0.6424597049898	4		578	228	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286839	33286839	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065246-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	215	792	0	ENST00000374542.5:c.2098A>T	p.Ile700Phe	p.I700F	ENST00000374542	NM_001141970.1	700	Atc/Ttc	7/8	0.6424597049898	6	FACETS	1	0.965	1	1	0.965	1	CLONAL	3	TRUE	3	0.6424597049898	6		792	491	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0065247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	358	500	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.705998685621531	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.706122255023894	2		500	499	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004922	150004922	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	240	649	0	ENST00000253339.5:c.1303C>T	p.Gln435Ter	p.Q435*	ENST00000253339		435	Cag/Tag	3/7	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.706122255023894	2		649	662	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	427	433	0	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	0.706122255023894	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.706122255023894	3		433	817	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661663	227661664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761880048	NA	P-0065247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	176	659	7	ENST00000305123.5:c.1791dup	p.His598AlafsTer13	p.H598Afs*13	ENST00000305123	NM_005544.2	597	-/G	1/2	1	2	FACETS	0.817	0.756	0.88	0.817	0.756	0.88	CLONAL	1	TRUE	1	0.706122255023894	2		666	610	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865804	57865804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267603606	NA	P-0065247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	195	565	0	ENST00000228682.2:c.3281C>T	p.Ser1094Phe	p.S1094F	ENST00000228682	NM_005269.2	1094	tCc/tTc	12/12	1	2	FACETS	0.99	0.923	1	0.99	0.923	1	CLONAL	1	TRUE	1	0.706122255023894	2		565	558	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367239	50367239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1045233686	NA	P-0065247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	170	521	0	ENST00000331340.3:c.46G>A	p.Glu16Lys	p.E16K	ENST00000331340	NM_006060.4	16	Gaa/Aaa	3/8	0.68322349787358	4	FACETS	0.978	0.9	1	0.326	0.3	0.353	CLONAL	1	TRUE	1	0.706122255023894	4		521	840	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164559	36164559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	179	607	0	ENST00000300305.3:c.1316C>T	p.Ser439Phe	p.S439F	ENST00000300305		439	tCc/tTc	8/8	1	2	FACETS	0.975	0.906	1	0.975	0.906	1	CLONAL	1	TRUE	1	0.706122255023894	2		607	520	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0065247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	137	524	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.915	0.84	0.992	0.915	0.84	0.992	CLONAL	1	TRUE	1	0.706122255023894	2		525	424	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436055	56436055	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1348903060	NA	P-0065247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	557	777	0	ENST00000407977.2:c.1082C>T	p.Pro361Leu	p.P361L	ENST00000407977		361	cCt/cTt	9/10	0.706122255023894	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.706122255023894	3		777	1019	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238323	98238323	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	205	483	0	ENST00000331920.6:c.1721C>T	p.Ser574Phe	p.S574F	ENST00000331920	NM_000264.3	574	tCc/tTc	12/24	0.706122255023894	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.706122255023894	1		483	341	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727078	40727078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs896375033	NA	P-0065247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	224	582	0	ENST00000373198.4:c.3886G>A	p.Glu1296Lys	p.E1296K	ENST00000373198	NM_133170.3	1296	Gag/Aag	28/32	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.706122255023894	2		582	633	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042100	42042100	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	155	464	0	ENST00000219905.7:c.6295C>T	p.Gln2099Ter	p.Q2099*	ENST00000219905	NM_001164273.1	2099	Caa/Taa	17/24	1	2	FACETS	0.918	0.848	0.991	0.918	0.848	0.991	CLONAL	1	TRUE	1	0.706122255023894	2		464	478	SUCCESS
CBL	867	MSKCC	GRCh37	11	119167699	119167699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368798262	NA	P-0065247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	190	475	0	ENST00000264033.4:c.2108C>T	p.Pro703Leu	p.P703L	ENST00000264033	NM_005188.3	703	cCc/cTc	13/16	0.706122255023894	1	FACETS	0.983	0.926	1	0.983	0.926	1	CLONAL	1	TRUE	0	0.706122255023894	1		475	354	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312909	30312909	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	220	518	0	ENST00000262643.3:c.712A>G	p.Lys238Glu	p.K238E	ENST00000262643	NM_001238.2	238	Aag/Gag	9/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.706122255023894	2		518	590	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560472	95560472	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	104	504	0	ENST00000393063.1:c.5117T>C	p.Phe1706Ser	p.F1706S	ENST00000393063	NM_030621.3	1706	tTc/tCc	25/28	0.336945840811893	6	FACETS	0.889	0.796	0.988	0.148	0.132	0.165	INDETERMINATE	1	TRUE	0	0.706122255023894	6		504	799	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645124	67645124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	203	559	0	ENST00000264010.4:c.389C>T	p.Ser130Leu	p.S130L	ENST00000264010	NM_006565.3	130	tCa/tTa	3/12	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.706122255023894	2		559	573	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626865	14626865	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	238	616	0	ENST00000254322.2:c.910C>A	p.Leu304Ile	p.L304I	ENST00000254322	NM_006145.1	304	Ctc/Atc	3/3	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.706122255023894	2		616	655	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36217255	36217255	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0065247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	150	421	0	ENST00000222270.7:c.4003+1G>A		p.X1335_splice	ENST00000222270	NM_014727.1	1335			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.706122255023894	2		421	414	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944430	40944430	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	227	541	0	ENST00000373198.4:c.2072G>A	p.Trp691Ter	p.W691*	ENST00000373198	NM_133170.3	691	tGg/tAg	12/32	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.706122255023894	2		541	612	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20153855	20153855	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0065247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	61	250	0	ENST00000379607.5:c.204+1G>A		p.X68_splice	ENST00000379607	NM_001412.3	68			1	2	FACETS	0.785	0.687	0.889	0.785	0.687	0.889	SUBCLONAL	1	TRUE	1	0.706122255023894	2		250	220	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446158	49446160	+	missense_variant	Missense_Mutation	TNP	CTC	CTC	TTT	novel	NA	P-0065247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	215	684	0	ENST00000301067.7:c.1306_1308delinsAAA	p.Glu436Lys	p.E436K	ENST00000301067	NM_003482.3	436	GAG/AAA	10/54	1	2	FACETS	0.927	0.866	0.989	0.927	0.866	0.989	CLONAL	1	TRUE	1	0.706122255023894	2		684	657	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	172	789	0				ENST00000310581	NM_198253.2	-/1132			0.652951194646958	4	FACETS	0.882	0.827	0.937	0.882	0.827	0.937	CLONAL	3	TRUE	1	0.652951194646958	4		789	329	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0065248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	100	534	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.624989726625641	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.652951194646958	1		534	204	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0065248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	230	736	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.652951194646958	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.652951194646958	2		736	329	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652323	36652323	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	170	477	0	ENST00000244741.5:c.445G>A	p.Asp149Asn	p.D149N	ENST00000244741	NM_000389.4	149	Gat/Aat	2/3	0.652951194646958	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.652951194646958	3		477	327	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561352	9561352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773981325	NA	P-0065248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	194	505	0	ENST00000353224.5:c.430G>A	p.Glu144Lys	p.E144K	ENST00000353224	NM_177990.2	144	Gaa/Aaa	4/10	0.652951194646958	4	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	2	0.652951194646958	4		505	487	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926270	112926270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918457	NA	P-0065248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	440	479	0	ENST00000351677.2:c.1403C>T	p.Thr468Met	p.T468M	ENST00000351677	NM_002834.3	468	aCg/aTg	12/16	0.652951194646958	5	FACETS	1	0.994	1			1	CLONAL	5	TRUE	NA	0.652951194646958	5		479	506	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979282	93979282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	145	560	0	ENST00000369303.4:c.1546C>T	p.Arg516Trp	p.R516W	ENST00000369303	NM_004440.3	516	Cgg/Tgg	7/17	0.652951194646958	3	FACETS	0.926	0.859	0.994	0.926	0.859	0.994	CLONAL	2	TRUE	1	0.652951194646958	3		560	318	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729162	66729162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519732	NA	P-0065248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	155	682	0	ENST00000307102.5:c.370C>T	p.Pro124Ser	p.P124S	ENST00000307102	NM_002755.3	124	Ccg/Tcg	3/11	0.622857670997931	4	FACETS	0.824	0.761	0.89	0.824	0.761	0.89	CLONAL	2	TRUE	2	0.652951194646958	4		682	476	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595852	52595852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276256973	NA	P-0065248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	207	633	0	ENST00000394830.3:c.4063G>A	p.Gly1355Arg	p.G1355R	ENST00000394830	NM_018313.4	1355	Ggg/Agg	26/30	0.652951194646958	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.652951194646958	2		633	308	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950660	38950660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759204549	NA	P-0065248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	97	542	2	ENST00000357387.3:c.3290G>A	p.Arg1097His	p.R1097H	ENST00000357387	NM_152756.3	1097	cGt/cAt	31/38	0.652951194646958	4	FACETS	1	0.934	1	0.352	0.315	0.391	CLONAL	1	TRUE	1	0.652951194646958	4		544	465	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217226	11217227	+	missense_variant	Missense_Mutation	DNP	GA	GA	AG	novel	NA	P-0065248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	239	560	2	ENST00000361445.4:c.4451_4452delinsCT	p.Leu1484Pro	p.L1484P	ENST00000361445	NM_004958.3	1484	cTC/cCT	30/58	0.597146565914767	5	FACETS	0.958	0.905	1	0.958	0.905	1	CLONAL	3	TRUE	2	0.652951194646958	5		562	504	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652837	29652838	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0065248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	152	346	0	ENST00000356175.3:c.4773-1_4773delinsAA		p.X1591_splice	ENST00000356175	NM_000267.3	1591		36/57	0.652951194646958	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.652951194646958	2		346	222	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61308183	61308183	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1913108160	NA	P-0065248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	88	192	0	ENST00000341074.5:c.394G>A	p.Glu132Lys	p.E132K	ENST00000341074	NM_002974.2	132	Gaa/Aaa	5/8	0.652951194646958	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.652951194646958	2		192	129	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794862	42794863	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0065248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	179	688	0	ENST00000575354.2:c.1942_1943delinsTT	p.Pro648Phe	p.P648F	ENST00000575354	NM_015125.3	648	CCc/TTc	10/20	0.652951194646958	3	FACETS	0.928	0.867	0.988	0.928	0.867	0.988	CLONAL	2	TRUE	1	0.652951194646958	3		688	392	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096232	178096232	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	225	733	0	ENST00000397062.3:c.1099G>T	p.Gly367Ter	p.G367*	ENST00000397062	NM_006164.4	367	Gga/Tga	5/5	0.652951194646958	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.652951194646958	4		733	538	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162431	47162431	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	196	621	0	ENST00000409792.3:c.3695A>T	p.Lys1232Ile	p.K1232I	ENST00000409792	NM_014159.6	1232	aAa/aTa	3/21	0.652951194646958	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.652951194646958	2		621	293	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056418	180056418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	74	642	0	ENST00000261937.6:c.826G>A	p.Gly276Ser	p.G276S	ENST00000261937	NM_182925.4	276	Ggt/Agt	7/30	0.652951194646958	3	FACETS	0.838	0.738	0.943	0.419	0.369	0.472	CLONAL	1	TRUE	1	0.652951194646958	3		642	359	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2054685	2054685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	199	505	0	ENST00000349721.2:c.1135G>A	p.Glu379Lys	p.E379K	ENST00000349721	NM_003070.3	379	Gaa/Aaa	6/34	0.652951194646958	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.652951194646958	2		505	282	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940008	76940008	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	76	508	0	ENST00000373344.5:c.740A>C	p.Asn247Thr	p.N247T	ENST00000373344	NM_000489.3	247	aAc/aCc	9/35	NA	2	FACETS	0.899	0.799	1			1	INDETERMINATE	1	TRUE	NA	0.652951194646958	2		508	259	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593603	55593606	+	protein_altering_variant	In_Frame_Del	DEL	TGGA	TGGA	C	novel	NA	P-0065249-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	211	466	0	ENST00000288135.5:c.1669_1672delinsC	p.Trp557_Lys558delinsGln	p.W557_K558delinsQ	ENST00000288135	NM_000222.2	557	TGGAag/Cag	11/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		466	501	SUCCESS
YES1	7525	MSKCC	GRCh37	18	742925	742925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388595429	NA	P-0065249-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	60	347	0	ENST00000314574.4:c.1053G>A	p.Met351Ile	p.M351I	ENST00000314574	NM_005433.3	351	atG/atA	8/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		347	418	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120529675	120529675	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065249-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	277	451	0	ENST00000256646.2:c.782T>C	p.Ile261Thr	p.I261T	ENST00000256646	NM_024408.3	261	aTt/aCt	5/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		451	556	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631391	117631391	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1022614558	NA	P-0065250-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	21	368	1	ENST00000368508.3:c.6287G>A	p.Arg2096Gln	p.R2096Q	ENST00000368508	NM_002944.2	2096	cGg/cAg	40/43	1	2	FACETS	0.7	0.538	0.889	0.7	0.538	0.889	SUBCLONAL	1	TRUE	1	0.15	2		369	400	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0065250-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	13	393	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.516	0.367	0.699	0.516	0.367	0.699	SUBCLONAL	1	TRUE	1	0.15	2		393	336	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190702	11190702	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065250-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	42	714	0	ENST00000361445.4:c.5497A>T	p.Thr1833Ser	p.T1833S	ENST00000361445	NM_004958.3	1833	Acc/Tcc	39/58	1	2	FACETS	0.699	0.582	0.83	0.699	0.582	0.83	SUBCLONAL	1	TRUE	1	0.15	2		714	801	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861168	57861168	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065250-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	38	529	0	ENST00000228682.2:c.965T>A	p.Leu322Gln	p.L322Q	ENST00000228682	NM_005269.2	322	cTg/cAg	9/12	1	2	FACETS	0.792	0.653	0.947	0.792	0.653	0.947	CLONAL	1	TRUE	1	0.15	2		529	640	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337743	73337743	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs781718393	NA	P-0065250-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	16	334	0	ENST00000377767.4:c.1973A>G	p.Glu658Gly	p.E658G	ENST00000377767	NM_014953.3	658	gAa/gGa	16/21	1	2	FACETS	0.688	0.508	0.904	0.688	0.508	0.904	SUBCLONAL	1	TRUE	1	0.15	2		334	310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0065251-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	213	661	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.41669430315185	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	0	0.41669430315185	1		661	732	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065251-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	89	202	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	0.181077296608422	2	FACETS	0.578	0.512	0.648	0.289	0.256	0.324	INDETERMINATE	1	FALSE	0	0.41669430315185	2		202	739	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620664	52620664	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065251-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	133	438	0	ENST00000394830.3:c.3089A>T	p.Asp1030Val	p.D1030V	ENST00000394830	NM_018313.4	1030	gAt/gTt	21/30	0.139515919642958	0	FACETS	0.56	0.509	0.613			1	INDETERMINATE	1	FALSE	0	0.41669430315185	0		438	665	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046324	69046324	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065251-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	41	470	0	ENST00000288368.4:c.3797T>G	p.Val1266Gly	p.V1266G	ENST00000288368	NM_024870.2	1266	gTt/gGt	32/40	1	2	FACETS	0.284	0.236	0.338	0.284	0.236	0.338	SUBCLONAL	1	FALSE	1	0.41669430315185	2		470	692	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500501	99500501	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065251-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	51	663	0	ENST00000268035.6:c.3934T>G	p.Ser1312Ala	p.S1312A	ENST00000268035	NM_000875.3	1312	Tcc/Gcc	21/21	1	2	FACETS	0.291	0.246	0.34	0.291	0.246	0.34	SUBCLONAL	1	FALSE	1	0.41669430315185	2		663	842	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163738	72163738	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065251-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	33	435	0	ENST00000357731.5:c.620del	p.Asn207MetfsTer8	p.N207Mfs*8	ENST00000357731	NM_173808.2	207	aAt/at	4/7	1	2	FACETS	0.271	0.22	0.329	0.271	0.22	0.329	SUBCLONAL	1	FALSE	1	0.41669430315185	2		435	585	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991647	72991647	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065251-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	53	597	1	ENST00000268489.5:c.2398A>C	p.Thr800Pro	p.T800P	ENST00000268489	NM_006885.3	800	Acc/Ccc	2/10	1	2	FACETS	0.321	0.273	0.374	0.321	0.273	0.374	SUBCLONAL	1	FALSE	1	0.41669430315185	2		598	792	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544707	86544707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065251-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	33	562	0	ENST00000262426.4:c.532G>A	p.Gly178Ser	p.G178S	ENST00000262426	NM_001451.2	178	Ggc/Agc	1/2	1	2	FACETS	0.251	0.203	0.304	0.251	0.203	0.304	SUBCLONAL	1	FALSE	1	0.41669430315185	2		562	632	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80088602	80088602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065251-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	129	442	0	ENST00000265081.6:c.2594C>T	p.Pro865Leu	p.P865L	ENST00000265081	NM_002439.4	865	cCt/cTt	19/24	0.281934014041442	1	FACETS	0.861	0.784	0.942	0.861	0.784	0.942	CLONAL	1	FALSE	0	0.41669430315185	1		442	569	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798424	32798424	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1255721269	NA	P-0065251-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	56	622	0	ENST00000374899.4:c.1432C>T	p.Pro478Ser	p.P478S	ENST00000374899	NM_018833.2	478	Ccc/Tcc	8/12	1	2	FACETS	0.348	0.297	0.403	0.348	0.297	0.403	SUBCLONAL	1	FALSE	1	0.41669430315185	2		622	773	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971164	21971175	+	inframe_deletion	In_Frame_Del	DEL	AGCAGCAGCAGC	AGCAGCAGCAGC	-	novel	NA	P-0065251-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	260	544	0	ENST00000304494.5:c.183_194del	p.Glu61_Leu65delinsAsp	p.E61_L65delinsD	ENST00000304494	NM_000077.4	61	gaGCTGCTGCTGCTc/gac	2/3	0.41669430315185	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	0	0.41669430315185	1		544	752	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0065259-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	68	256	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.381995176081216	5	FACETS	0.897	0.787	1	0.598	0.525	0.677	CLONAL	2	FALSE	2	0.381995176081216	5		256	312	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129418	64129418	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065259-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	23	529	1	ENST00000334205.4:c.850C>T	p.Arg284Ter	p.R284*	ENST00000334205	NM_003942.2	284	Cga/Tga	8/17	0.17896660785937	6	FACETS	0.47	0.365	0.591			1	INDETERMINATE	1	FALSE	NA	0.381995176081216	6		530	452	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873585	35873585	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065259-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	45	401	0	ENST00000303115.3:c.541G>T	p.Val181Leu	p.V181L	ENST00000303115	NM_002185.3	181	Gtg/Ttg	5/8	0.143343676912188	6	FACETS	1	0.931	1	0.399	0.336	0.468	INDETERMINATE	1	FALSE	3	0.381995176081216	6		401	347	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115698	8115834	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTAGATTAACAGACCCCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGG	TTAGATTAACAGACCCCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGG	-	novel	NA	P-0065259-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	166	356	0	ENST00000346208.3:c.1048-4_1180del		p.X350_splice	ENST00000346208		350		6/6	0.202218343552812	5	FACETS	1	0.974	1	0.75	0.692	0.809	INDETERMINATE	2	FALSE	2	0.381995176081216	5		356	608	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0065260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	9	256	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.335	0.221	0.479	0.335	0.221	0.479	SUBCLONAL	1	TRUE	1	0.28	2		256	192	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0065260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	44	607	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.893	0.751	1	0.893	0.751	1	CLONAL	1	TRUE	1	0.28	2		607	352	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89335056	89335056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	16	370	0	ENST00000301030.4:c.7822C>T	p.Arg2608Trp	p.R2608W	ENST00000301030	NM_001256183.1	2608	Cgg/Tgg	13/13	0.220070314886322	1	FACETS	0.697	0.519	0.906	0.697	0.519	0.906	SUBCLONAL	1	TRUE	0	0.28	1		370	141	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021848	69021848	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	11	378	0	ENST00000288368.4:c.3136C>T	p.Gln1046Ter	p.Q1046*	ENST00000288368	NM_024870.2	1046	Caa/Taa	25/40	0.220070314886322	1	FACETS	0.313	0.216	0.433	0.313	0.216	0.433	SUBCLONAL	1	TRUE	0	0.28	1		378	216	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980338	201980338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	32	489	0	ENST00000359651.3:c.74C>T	p.Thr25Ile	p.T25I	ENST00000359651		25	aCc/aTc	1/8	1	2	FACETS	0.697	0.567	0.843	0.697	0.567	0.843	SUBCLONAL	1	TRUE	1	0.28	2		489	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs878854073	NA	P-0065261-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	22	372	0	ENST00000269305.4:c.673-1G>A		p.X225_splice	ENST00000269305	NM_001126112.2	225			1	2	FACETS	0.894	0.693	1	0.894	0.693	1	CLONAL	1	TRUE	1	0.15	2		372	328	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245539	16245539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1471081719	NA	P-0065261-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	20	309	0	ENST00000375759.3:c.1514G>A	p.Arg505His	p.R505H	ENST00000375759	NM_015001.2	505	cGc/cAc	7/15	0.3	3	FACETS	0.781	0.597	0.998			1	CLONAL	1	TRUE	NA	0.15	3		309	367	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0065262-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	93	462	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.552764020809842	1	FACETS	0.796	0.718	0.877	0.796	0.718	0.877	SUBCLONAL	1	TRUE	0	0.597926667403061	1		462	274	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711927	89711928	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554900593	NA	P-0065262-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	218	286	0	ENST00000371953.3:c.548dup	p.Asn184GlufsTer6	p.N184Efs*6	ENST00000371953	NM_000314.4	182	tta/ttAa	6/9	1	2	FACETS	0.98	0.929	1	1	0.995	1	CLONAL	2	TRUE	1	0.597926667403061	2		286	372	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948187	71948187	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065262-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	210	490	0	ENST00000298229.2:c.2900del	p.Pro967LeufsTer164	p.P967Lfs*164	ENST00000298229	NM_001567.3	967	Cct/ct	26/28	0.543929774297642	2	FACETS	0.915	0.864	0.965	0.915	0.864	0.965	CLONAL	2	TRUE	0	0.597926667403061	2		490	384	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772298	68772299	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CG	novel	NA	P-0065262-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	116	453	0	ENST00000261769.5:c.150_151dup	p.Val51AlafsTer6	p.V51Afs*6	ENST00000261769	NM_004360.3	49	-/CG	2/16	0.597926667403061	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.597926667403061	1		453	260	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954215	17954215	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065262-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	57	516	0	ENST00000458235.1:c.394C>T	p.Pro132Ser	p.P132S	ENST00000458235	NM_000215.3	132	Cca/Tca	4/24	0.25375839782085	1	FACETS	0.413	0.356	0.474	0.413	0.356	0.474	INDETERMINATE	1	TRUE	0	0.597926667403061	1		516	324	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266837	+	protein_altering_variant	In_Frame_Del	DEL	TCTG	TCTG	C	novel	NA	P-0065262-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	113	335	0	ENST00000335508.6:c.2095_2098delinsG	p.Gln699_Lys700delinsGlu	p.Q699_K700delinsE	ENST00000335508	NM_012433.2	699	CAGAaa/Gaa	15/25	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.597926667403061	2		335	376	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0065263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	22	256	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.991	0.78	1	1	0.945	1	CLONAL	2	FALSE	1	0.191292248009316	2		256	116	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0065263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	28	342	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.904	0.73	1	1	0.952	1	CLONAL	2	FALSE	1	0.191292248009316	2		342	162	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692896	89692896	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs398123322	NA	P-0065263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	58	276	0	ENST00000371953.3:c.380G>T	p.Gly127Val	p.G127V	ENST00000371953	NM_000314.4	127	gGa/gTa	5/9	0.191292248009316	4	FACETS	0.966	0.844	1	1	0.962	1	CLONAL	4	FALSE	1	0.191292248009316	4		276	187	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0065263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	11	153	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.191292248009316	4	FACETS	1	0.812	1	0.419	0.292	0.574	CLONAL	1	FALSE	1	0.191292248009316	4		153	109	SUCCESS
APC	324	MSKCC	GRCh37	5	112178912	112178912	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587778033	NA	P-0065263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	65	596	0	ENST00000257430.4:c.7621A>G	p.Ile2541Val	p.I2541V	ENST00000257430	NM_000038.5	2541	Atc/Gtc	16/16	1	2	FACETS	1	0.954	1	1	0.983	1	CLONAL	2	FALSE	1	0.191292248009316	2		596	283	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212187	98212187	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065264-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	62	494	0	ENST00000331920.6:c.3485T>G	p.Leu1162Arg	p.L1162R	ENST00000331920	NM_000264.3	1162	cTc/cGc	21/24	0.233156959100753	3	FACETS	0.582	0.503	0.668	0.291	0.251	0.334	INDETERMINATE	1	TRUE	1	0.462491653779191	3		494	567	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940747	71940747	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs776487134	NA	P-0065264-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	144	725	0	ENST00000298229.2:c.794T>G	p.Val265Gly	p.V265G	ENST00000298229	NM_001567.3	265	gTg/gGg	7/28	0.307842961870235	1	FACETS	0.898	0.824	0.975	0.898	0.824	0.975	CLONAL	1	TRUE	0	0.462491653779191	1		725	533	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139221	108139222	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065264-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	55	496	0	ENST00000278616.4:c.2725dup	p.Thr909AsnfsTer11	p.T909Nfs*11	ENST00000278616	NM_000051.3	908	gta/gtAa	18/63	0.307842961870235	1	FACETS	0.386	0.33	0.446	0.386	0.33	0.446	SUBCLONAL	1	TRUE	0	0.462491653779191	1		496	474	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216494	108216494	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065264-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	94	347	0	ENST00000278616.4:c.8443G>T	p.Glu2815Ter	p.E2815*	ENST00000278616	NM_000051.3	2815	Gag/Tag	58/63	0.307842961870235	1	FACETS	0.941	0.846	1	0.941	0.846	1	CLONAL	1	TRUE	0	0.462491653779191	1		347	332	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0065265-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	34	594	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	1	2	FACETS	0.826	0.674	0.998	0.826	0.674	0.998	CLONAL	1	TRUE	1	0.14	2		594	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863224499	NA	P-0065265-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	51	538	0	ENST00000269305.4:c.672+1G>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.14	2		538	685	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0065265-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	19	351	0	ENST00000311936.3:c.34_35delinsAT	p.Gly12Ile	p.G12I	ENST00000311936	NM_004985.3	12	GGt/ATt	2/5	1	2	FACETS	0.672	0.509	0.864	0.672	0.509	0.864	SUBCLONAL	1	TRUE	1	0.14	2		351	404	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041533	42041533	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065265-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	35	497	0	ENST00000219905.7:c.5728C>T	p.Gln1910Ter	p.Q1910*	ENST00000219905	NM_001164273.1	1910	Caa/Taa	17/24	1	2	FACETS	0.806	0.659	0.972	0.806	0.659	0.972	CLONAL	1	TRUE	1	0.14	2		497	620	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81941330	81941330	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065265-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	30	387	0	ENST00000359376.3:c.1508T>A	p.Leu503Gln	p.L503Q	ENST00000359376	NM_002661.3	503	cTg/cAg	16/33	1	2	FACETS	0.938	0.755	1	0.938	0.755	1	CLONAL	1	TRUE	1	0.14	2		387	457	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983150	201983150	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	115	616	0	ENST00000359651.3:c.999G>A	p.Met333Ile	p.M333I	ENST00000359651		333	atG/atA	7/8	1	2	FACETS	0.883	0.801	0.969	0.883	0.801	0.969	CLONAL	1	TRUE	1	0.57627684894489	2		616	452	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196791	108196791	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	93	414	0	ENST00000278616.4:c.6814G>T	p.Glu2272Ter	p.E2272*	ENST00000278616	NM_000051.3	2272	Gaa/Taa	47/63	0.57627684894489	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.57627684894489	1		414	217	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037912	49037912	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	73	354	0	ENST00000267163.4:c.2152G>C	p.Asp718His	p.D718H	ENST00000267163	NM_000321.2	718	Gac/Cac	21/27	0.57627684894489	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.57627684894489	1		354	142	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696716	47696716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	100	421	0	ENST00000347630.2:c.232G>A	p.Glu78Lys	p.E78K	ENST00000347630	NM_001007230.1	78	Gaa/Aaa	5/11	0.295000064590066	3	FACETS	1	0.922	1	0.515	0.463	0.57	INDETERMINATE	1	TRUE	1	0.57627684894489	3		421	434	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978947	25978947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	116	394	0	ENST00000435504.4:c.976G>A	p.Ala326Thr	p.A326T	ENST00000435504		326	Gcc/Acc	10/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.57627684894489	2		394	287	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462371	89462371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866025221	NA	P-0065266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	73	496	0	ENST00000336596.2:c.1843G>A	p.Glu615Lys	p.E615K	ENST00000336596	NM_005233.5	615	Gaa/Aaa	10/17	0.57627684894489	1	FACETS	0.888	0.792	0.988	0.888	0.792	0.988	CLONAL	1	TRUE	0	0.57627684894489	1		496	203	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1296105	1296105	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs952924090	NA	P-0065266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	109	780	1				ENST00000310581	NM_198253.2	-/1132			0.57627684894489	2	FACETS	0.918	0.831	1	0.459	0.415	0.505	CLONAL	1	TRUE	0	0.57627684894489	2		781	412	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141570589	141570589	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	73	694	0	ENST00000220592.5:c.539C>G	p.Ser180Cys	p.S180C	ENST00000220592	NM_012154.3	180	tCc/tGc	5/19	0.260468341355322	3	FACETS	0.581	0.508	0.659	0.194	0.169	0.22	INDETERMINATE	1	TRUE	0	0.57627684894489	3		694	562	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971191	21971207	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CTGCCCATCATCATGAC	CTGCCCATCATCATGAC	-	novel	NA	P-0065266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	180	641	0	ENST00000304494.5:c.151_167del	p.Val51ArgfsTer63	p.V51Rfs*63	ENST00000304494	NM_000077.4	51	GTCATGATGATGGGCAGc/c	2/3	0.569342109791881	2	FACETS	0.856	0.802	0.91	0.856	0.802	0.91	CLONAL	2	TRUE	0	0.57627684894489	2		641	365	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044556	47044556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	136	821	0	ENST00000377604.3:c.2053C>T	p.Arg685Trp	p.R685W	ENST00000377604	NM_001204468.1	685	Cgg/Tgg	18/24	0.57627684894489	1	FACETS	0.936	0.862	1	0.936	0.862	1	CLONAL	1	TRUE	0	0.57627684894489	1		821	359	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243886	53243887	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0065266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	132	579	0	ENST00000375401.3:c.1106dup	p.Cys371ValfsTer7	p.C371Vfs*7	ENST00000375401	NM_004187.3	369	cca/ccCa	8/26	0.57627684894489	1	FACETS	0.924	0.849	1	0.924	0.849	1	CLONAL	1	TRUE	0	0.57627684894489	1		579	353	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0065267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	58	500	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		500	341	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0065267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	60	624	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		625	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0065267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	86	766	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		767	368	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983066	201983066	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	99	587	0	ENST00000359651.3:c.916del	p.Leu306CysfsTer19	p.L306Cfs*19	ENST00000359651		305	ttC/tt	7/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		587	433	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920444	114920444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1219807932	NA	P-0065267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	60	423	0	ENST00000543371.1:c.1385C>T	p.Pro462Leu	p.P462L	ENST00000543371	NM_001198531.1	462	cCg/cTg	13/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		423	358	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114905790	114905790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	62	390	0	ENST00000543371.1:c.809C>T	p.Pro270Leu	p.P270L	ENST00000543371	NM_001198531.1	270	cCa/cTa	8/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		390	337	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375954	8375954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	68	413	0	ENST00000356435.5:c.4643C>T	p.Pro1548Leu	p.P1548L	ENST00000356435		1548	cCg/cTg	28/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		413	380	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591153	67591153	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0065267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	38	458	0	ENST00000274335.5:c.1745+1G>A		p.X582_splice	ENST00000274335		582			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		458	339	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639064	176639064	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	74	487	0	ENST00000439151.2:c.3664A>C	p.Asn1222His	p.N1222H	ENST00000439151	NM_022455.4	1222	Aat/Cat	5/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		487	458	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922136	39922136	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	70	559	0	ENST00000378444.4:c.4036C>G	p.Leu1346Val	p.L1346V	ENST00000378444	NM_001123385.1	1346	Ctg/Gtg	9/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		559	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0065268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	43	587	0	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	1	2	FACETS	0.578	0.483	0.684	0.578	0.483	0.684	SUBCLONAL	1	FALSE	1	0.258705244379248	2		587	575	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467675	50467675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759124417	NA	P-0065268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	9	624	0	ENST00000331340.3:c.910G>A	p.Glu304Lys	p.E304K	ENST00000331340	NM_006060.4	304	Gaa/Aaa	8/8	1	2	FACETS	0.159	0.104	0.229	0.159	0.104	0.229	SUBCLONAL	1	FALSE	1	0.258705244379248	2		624	438	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026984	71026984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763413735	NA	P-0065268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	22	593	0	ENST00000318789.4:c.1343C>T	p.Ser448Leu	p.S448L	ENST00000318789	NM_032682.5	448	tCg/tTg	15/21	1	2	FACETS	0.255	0.196	0.323	0.255	0.196	0.323	SUBCLONAL	1	FALSE	1	0.258705244379248	2		593	668	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461101	120461101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs312262796	NA	P-0065268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	42	540	0	ENST00000256646.2:c.5857C>T	p.Arg1953Cys	p.R1953C	ENST00000256646	NM_024408.3	1953	Cgc/Tgc	32/34	1	2	FACETS	0.522	0.435	0.619	0.522	0.435	0.619	SUBCLONAL	1	FALSE	1	0.258705244379248	2		540	622	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476382	88476382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	42	461	0	ENST00000360948.2:c.1750G>A	p.Asp584Asn	p.D584N	ENST00000360948	NM_001012338.2	584	Gat/Aat	15/19	1	2	FACETS	0.639	0.533	0.757	0.639	0.533	0.757	SUBCLONAL	1	FALSE	1	0.258705244379248	2		461	508	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0065268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	17	541	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	1	2	FACETS	0.236	0.175	0.308	0.236	0.175	0.308	SUBCLONAL	1	FALSE	1	0.258705244379248	2		541	558	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020558	69020558	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753700	NA	P-0065268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	25	340	0	ENST00000288368.4:c.2930C>T	p.Ser977Leu	p.S977L	ENST00000288368	NM_024870.2	977	tCg/tTg	24/40	1	2	FACETS	0.43	0.338	0.537	0.43	0.338	0.537	SUBCLONAL	1	FALSE	1	0.258705244379248	2		340	449	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037501	12037501	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	57	507	0	ENST00000396373.4:c.1132C>T	p.Arg378Ter	p.R378*	ENST00000396373	NM_001987.4	378	Cga/Tga	6/8	1	2	FACETS	0.8	0.686	0.923	0.8	0.686	0.923	CLONAL	1	FALSE	1	0.258705244379248	2		507	551	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553584	106553584	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	48	535	0	ENST00000369096.4:c.1549C>T	p.Pro517Ser	p.P517S	ENST00000369096	NM_001198.3	517	Ccc/Tcc	5/7	1	2	FACETS	0.619	0.523	0.726	0.619	0.523	0.726	SUBCLONAL	1	FALSE	1	0.258705244379248	2		535	599	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21350158	21350158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555928965	NA	P-0065268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	49	583	0	ENST00000215739.8:c.2066C>T	p.Ser689Phe	p.S689F	ENST00000215739	NM_006767.3	689	tCc/tTc	17/21	1	2	FACETS	0.672	0.568	0.785	0.672	0.568	0.785	SUBCLONAL	1	FALSE	1	0.258705244379248	2		583	564	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100391	27100391	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0065268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	51	501	0	ENST00000324856.7:c.4101+2T>G		p.X1367_splice	ENST00000324856	NM_006015.4	1367			1	2	FACETS	0.592	0.502	0.691	0.592	0.502	0.691	SUBCLONAL	1	FALSE	1	0.258705244379248	2		501	666	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123353232	123353232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	39	477	0	ENST00000358487.5:c.100G>A	p.Glu34Lys	p.E34K	ENST00000358487	NM_000141.4	34	Gag/Aag	2/18	1	2	FACETS	0.554	0.459	0.661	0.554	0.459	0.661	SUBCLONAL	1	FALSE	1	0.258705244379248	2		477	544	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170241	119170241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	32	504	0	ENST00000264033.4:c.2471C>T	p.Pro824Leu	p.P824L	ENST00000264033	NM_005188.3	824	cCa/cTa	16/16	1	2	FACETS	0.419	0.339	0.51	0.419	0.339	0.51	SUBCLONAL	1	FALSE	1	0.258705244379248	2		504	590	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862210	68862210	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	rs786203544	NA	P-0065268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	30	421	0	ENST00000261769.5:c.2295+3G>A		p.X765_splice	ENST00000261769	NM_004360.3	765			1	2	FACETS	0.413	0.331	0.505	0.413	0.331	0.505	SUBCLONAL	1	FALSE	1	0.258705244379248	2		421	562	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61306551	61306551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	44	521	0	ENST00000341074.5:c.636G>A	p.Met212Ile	p.M212I	ENST00000341074	NM_002974.2	212	atG/atA	7/8	1	2	FACETS	0.484	0.405	0.572	0.484	0.405	0.572	SUBCLONAL	1	FALSE	1	0.258705244379248	2		521	703	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094879	11094879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	43	475	0	ENST00000358026.2:c.52C>T	p.Pro18Ser	p.P18S	ENST00000358026	NM_001128849.1	18	Ccg/Tcg	2/36	1	2	FACETS	0.712	0.596	0.84	0.712	0.596	0.84	SUBCLONAL	1	FALSE	1	0.258705244379248	2		475	467	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727915	41727916	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0065268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	46	474	0	ENST00000301178.4:c.540_541delinsAA	p.Ala181Thr	p.A181T	ENST00000301178	NM_021913.4	180	ctGGcc/ctAAcc	4/20	1	2	FACETS	0.789	0.665	0.925	0.789	0.665	0.925	CLONAL	1	FALSE	1	0.258705244379248	2		474	451	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095951	178095952	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0065268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	63	517	0	ENST00000397062.3:c.1379_1380delinsAA	p.Arg460Lys	p.R460K	ENST00000397062	NM_006164.4	460	aGG/aAA	5/5	1	2	FACETS	0.717	0.62	0.823	0.717	0.62	0.823	SUBCLONAL	1	FALSE	1	0.258705244379248	2		517	679	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21344695	21344696	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0065268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	33	512	0	ENST00000215739.8:c.672_673delinsAT	p.Pro225Ser	p.P225S	ENST00000215739	NM_006767.3	224	atCCcc/atATcc	8/21	1	2	FACETS	0.47	0.382	0.569	0.47	0.382	0.569	SUBCLONAL	1	FALSE	1	0.258705244379248	2		512	543	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281511	142281511	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	64	432	0	ENST00000350721.4:c.733A>G	p.Lys245Glu	p.K245E	ENST00000350721	NM_001184.3	245	Aaa/Gaa	4/47	0.258705244379248	1	FACETS	0.728	0.63	0.833	0.728	0.63	0.833	SUBCLONAL	1	FALSE	0	0.258705244379248	1		432	592	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426907	6426908	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0065268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	30	302	0	ENST00000356142.4:c.100_101delinsTT	p.Pro34Phe	p.P34F	ENST00000356142	NM_018890.3	34	CCt/TTt	2/7	1	2	FACETS	0.463	0.372	0.566	0.463	0.372	0.566	SUBCLONAL	1	FALSE	1	0.258705244379248	2		302	501	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124510991	124510991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	46	309	0	ENST00000357628.3:c.229G>A	p.Asp77Asn	p.D77N	ENST00000357628	NM_015450.2	77	Gat/Aat	7/19	1	2	FACETS	0.845	0.712	0.99	0.845	0.712	0.99	CLONAL	1	FALSE	1	0.258705244379248	2		309	421	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172995	38172995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	29	472	0	ENST00000317025.8:c.2054C>T	p.Ser685Phe	p.S685F	ENST00000317025	NM_023034.1	685	tCc/tTc	11/24	0.186892540123426	0	FACETS	0.315	0.252	0.387			1	SUBCLONAL	1	FALSE	0	0.258705244379248	0		472	528	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409145	139409145	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	45	539	0	ENST00000277541.6:c.2024G>A	p.Cys675Tyr	p.C675Y	ENST00000277541	NM_017617.3	675	tGt/tAt	13/34	1	2	FACETS	0.656	0.551	0.773	0.656	0.551	0.773	SUBCLONAL	1	FALSE	1	0.258705244379248	2		539	530	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0065269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	47	527	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.27662282306295	1	FACETS	0.796	0.673	0.93	0.796	0.673	0.93	CLONAL	1	TRUE	0	0.27662282306295	1		527	368	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115451	115115451	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0065269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	20	461	0	ENST00000257566.3:c.875T>A	p.Leu292Ter	p.L292*	ENST00000257566	NM_016569.3	292	tTa/tAa	5/8	1	2	FACETS	0.428	0.327	0.546	0.428	0.327	0.546	SUBCLONAL	1	TRUE	1	0.27662282306295	2		461	338	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864455	151864455	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554484302	NA	P-0065269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	43	370	0	ENST00000262189.6:c.9526C>T	p.Gln3176Ter	p.Q3176*	ENST00000262189	NM_170606.2	3176	Cag/Tag	42/59	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.27662282306295	2		370	288	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0065271-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	53	393	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.350831305775298	2		393	273	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591892	48591892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767345	NA	P-0065271-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	59	574	0	ENST00000342988.3:c.1055G>A	p.Gly352Glu	p.G352E	ENST00000342988	NM_005359.5	352	gGa/gAa	9/12	0.342237265613258	1	FACETS	0.853	0.739	0.976	0.853	0.739	0.976	CLONAL	1	TRUE	0	0.350831305775298	1		574	325	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764146326	NA	P-0065271-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	80	640	0	ENST00000269305.4:c.841G>T	p.Asp281Tyr	p.D281Y	ENST00000269305	NM_001126112.2	281	Gac/Tac	8/11	0.342237265613258	1	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	0	0.350831305775298	1		640	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0065272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	134	441	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.279936765643075	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.29	1		441	657	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0065272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	109	497	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	1	2	FACETS	0.978	0.878	1	0.978	0.878	1	CLONAL	1	TRUE	1	0.29	2		497	769	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645693	12645693	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397516827	NA	P-0065272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	109	485	0	ENST00000251849.4:c.776C>G	p.Ser259Cys	p.S259C	ENST00000251849	NM_002880.3	259	tCc/tGc	7/17	0.279936765643075	1	FACETS	0.964	0.866	1	0.964	0.866	1	CLONAL	1	TRUE	0	0.29	1		485	667	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942214	71942214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253875635	NA	P-0065272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	128	605	0	ENST00000298229.2:c.1478C>T	p.Thr493Met	p.T493M	ENST00000298229	NM_001567.3	493	aCg/aTg	12/28	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.29	2		605	821	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247169	153247169	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	208	440	0	ENST00000281708.4:c.1633T>A	p.Tyr545Asn	p.Y545N	ENST00000281708	NM_033632.3	545	Tat/Aat	10/12	0.285907187935966	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.29	3		440	673	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152482	56152482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	85	527	0	ENST00000399503.3:c.538C>T	p.Pro180Ser	p.P180S	ENST00000399503	NM_005921.1	180	Cca/Tca	2/20	1	2	FACETS	0.769	0.679	0.866	0.769	0.679	0.866	SUBCLONAL	1	TRUE	1	0.29	2		527	762	SUCCESS
APC	324	MSKCC	GRCh37	5	112175349	112175352	+	frameshift_variant	Frame_Shift_Del	DEL	AATT	AATT	-	novel	NA	P-0065272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	78	541	0	ENST00000257430.4:c.4058_4061del	p.Glu1353ValfsTer61	p.E1353Vfs*61	ENST00000257430	NM_000038.5	1353	gAATTt/gt	16/16	1	2	FACETS	0.761	0.668	0.861	0.761	0.668	0.861	SUBCLONAL	1	TRUE	1	0.29	2		541	707	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	126	789	0				ENST00000310581	NM_198253.2	-/1132			0.84313317074195	1	FACETS	0.977	0.92	1	0.977	0.92	1	CLONAL	1	TRUE	0	0.84313317074195	1		789	177	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0065274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	213	597	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.944	0.885	1	0.944	0.885	1	CLONAL	1	TRUE	1	0.84313317074195	2		597	535	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0065274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	73	228	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	1	2	FACETS	0.422	0.371	0.477	0.422	0.371	0.477	SUBCLONAL	1	TRUE	1	0.84313317074195	2		228	410	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791758	42791758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1380826096	NA	P-0065274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	25	549	0	ENST00000575354.2:c.644G>A	p.Arg215Gln	p.R215Q	ENST00000575354	NM_015125.3	215	cGg/cAg	5/20	0.84313317074195	1	FACETS	0.088	0.068	0.109	0.088	0.068	0.109	SUBCLONAL	1	TRUE	0	0.84313317074195	1		549	392	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928074	178928074	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	103	312	1	ENST00000263967.3:c.1352G>T	p.Gly451Val	p.G451V	ENST00000263967	NM_006218.2	451	gGa/gTa	8/21	1	2	FACETS	0.571	0.514	0.63	0.571	0.514	0.63	SUBCLONAL	1	TRUE	1	0.84313317074195	2		313	428	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0065274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	24	350	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.148	0.116	0.186	0.148	0.116	0.186	SUBCLONAL	1	TRUE	1	0.84313317074195	2		350	384	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059206	27059206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	36	290	0	ENST00000324856.7:c.1843G>A	p.Ala615Thr	p.A615T	ENST00000324856	NM_006015.4	615	Gcc/Acc	4/20	0.84313317074195	1	FACETS	0.207	0.171	0.246	0.207	0.171	0.246	SUBCLONAL	1	TRUE	0	0.84313317074195	1		290	239	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559728	29559728	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	60	333	0	ENST00000356175.3:c.3326del	p.Leu1109TyrfsTer3	p.L1109Yfs*3	ENST00000356175	NM_000267.3	1109	Tta/ta	26/57	1	2	FACETS	0.293	0.252	0.337	0.293	0.252	0.337	SUBCLONAL	1	TRUE	1	0.84313317074195	2		333	486	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798786	42798787	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	28	402	0	ENST00000575354.2:c.4359dup	p.Glu1454ArgfsTer3	p.E1454Rfs*3	ENST00000575354	NM_015125.3	1453	cta/ctAa	19/20	0.84313317074195	1	FACETS	0.153	0.122	0.188	0.153	0.122	0.188	SUBCLONAL	1	TRUE	0	0.84313317074195	1		402	251	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791758	42791758	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	11	549	0	ENST00000575354.2:c.644G>C	p.Arg215Pro	p.R215P	ENST00000575354	NM_015125.3	215	cGg/cCg	5/20	0.84313317074195	1	FACETS	0.039	0.026	0.054	0.039	0.026	0.054	SUBCLONAL	1	TRUE	0	0.84313317074195	1		549	392	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0065275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	125	438	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.339178851269769	3	FACETS	0.882	0.803	0.964	0.882	0.803	0.964	CLONAL	2	TRUE	1	0.350771353583744	3		438	475	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023339	31023339	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	102	645	0	ENST00000375687.4:c.2827del	p.Asp943IlefsTer2	p.D943Ifs*2	ENST00000375687	NM_015338.5	942	Ggg/gg	13/13	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.350771353583744	2		645	570	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280804	41280804	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	122	630	0	ENST00000349496.5:c.2317C>T	p.Gln773Ter	p.Q773*	ENST00000349496	NM_001904.3	773	Cag/Tag	15/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.350771353583744	2		630	612	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0065275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	52	256	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.888	0.76	1	0.888	0.76	1	CLONAL	1	TRUE	1	0.350771353583744	2		256	334	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253855	153253861	+	frameshift_variant	Frame_Shift_Del	DEL	AGCACAT	AGCACAT	-	novel	NA	P-0065275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	124	358	0	ENST00000281708.4:c.872_878del	p.Tyr291PhefsTer49	p.Y291Ffs*49	ENST00000281708	NM_033632.3	291	tATGTGCTt/tt	6/12	0.337638185337236	2	FACETS	0.875	0.799	0.954	0.875	0.799	0.954	CLONAL	2	TRUE	0	0.350771353583744	2		358	404	SUCCESS
APC	324	MSKCC	GRCh37	5	112170862	112170862	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1060503318	NA	P-0065275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	129	421	0	ENST00000257430.4:c.1958G>A	p.Arg653Lys	p.R653K	ENST00000257430	NM_000038.5	653	aGg/aAg	15/16	0.339178851269769	3	FACETS	0.825	0.752	0.901	0.825	0.752	0.901	CLONAL	2	TRUE	1	0.350771353583744	3		421	524	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0065275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	87	552	0	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	0.339178851269769	3	FACETS	0.94	0.833	1	0.47	0.416	0.528	CLONAL	1	TRUE	1	0.350771353583744	3		552	620	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910609	29910609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199474372	NA	P-0065275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	97	659	0	ENST00000376809.5:c.149G>A	p.Gly50Asp	p.G50D	ENST00000376809	NM_002116.7	50	gGc/gAc	2/8	1	2	FACETS	0.993	0.888	1	0.993	0.888	1	CLONAL	1	TRUE	1	0.350771353583744	2		659	557	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0065278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	188	256	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.773419068518057	3	FACETS	0.971	0.914	1	0.971	0.914	1	CLONAL	2	TRUE	1	0.773419068518057	3		256	347	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651970	36651980	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGCGACTGT	GCCGCGACTGT	-	novel	NA	P-0065278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	315	511	0	ENST00000244741.5:c.93_103del	p.Ser31ArgfsTer13	p.S31Rfs*13	ENST00000244741	NM_000389.4	31	aGCCGCGACTGT/a	2/3	1	2	FACETS	0.995	0.943	1	0.995	0.943	1	CLONAL	1	TRUE	1	0.773419068518057	2		511	819	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806089	1806089	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913479	NA	P-0065278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	301	575	0	ENST00000260795.2:c.1108G>T	p.Gly370Cys	p.G370C	ENST00000260795		370	Ggc/Tgc	8/17	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.773419068518057	2		575	776	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012190	16012190	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	222	439	0	ENST00000268712.3:c.2092C>T	p.Gln698Ter	p.Q698*	ENST00000268712	NM_006311.3	698	Caa/Taa	19/46	1	2	FACETS	0.93	0.872	0.99	0.93	0.872	0.99	CLONAL	1	TRUE	1	0.773419068518057	2		439	617	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170815004	170815004	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	111	180	0	ENST00000296930.5:c.52C>G	p.Leu18Val	p.L18V	ENST00000296930	NM_002520.6	18	Ctt/Gtt	1/11	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.773419068518057	2		180	285	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170456	108170456	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	166	278	0	ENST00000278616.4:c.5021G>T	p.Cys1674Phe	p.C1674F	ENST00000278616	NM_000051.3	1674	tGc/tTc	34/63	1	2	FACETS	0.852	0.788	0.917	0.852	0.788	0.917	CLONAL	1	TRUE	1	0.773419068518057	2		278	504	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426082	49426082	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123711	NA	P-0065278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	331	688	0	ENST00000301067.7:c.12406C>T	p.Gln4136Ter	p.Q4136*	ENST00000301067	NM_003482.3	4136	Cag/Tag	39/54	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.773419068518057	2		688	822	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0065278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	229	458	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.773419068518057	2		458	533	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342599	118342599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	290	364	0	ENST00000534358.1:c.725C>T	p.Ser242Leu	p.S242L	ENST00000534358	NM_005933.3	242	tCa/tTa	3/36	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.773419068518057	2		364	692	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628284	90628284	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	356	652	1	ENST00000330062.3:c.1127C>A	p.Thr376Lys	p.T376K	ENST00000330062	NM_002168.2	376	aCa/aAa	9/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.773419068518057	2		653	908	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281904	39281904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886041241	NA	P-0065278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	115	151	0	ENST00000402219.2:c.571G>A	p.Glu191Lys	p.E191K	ENST00000402219	NM_005633.3	191	Gaa/Aaa	5/23	1	2	FACETS	0.912	0.832	0.994	0.912	0.832	0.994	CLONAL	1	TRUE	1	0.773419068518057	2		151	326	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922749	44922749	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0065278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	312	273	0	ENST00000377967.4:c.1610C>G	p.Ser537Ter	p.S537*	ENST00000377967	NM_021140.2	537	tCa/tGa	16/29	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.773419068518057	1		273	402	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913651	32913651	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs80358740	NA	P-0065278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	107	155	0	ENST00000380152.3:c.5159C>G	p.Ser1720Ter	p.S1720*	ENST00000380152		1720	tCa/tGa	11/27	NA	2	FACETS	1	0.931	1			1	INDETERMINATE	1	TRUE	NA	0.773419068518057	2		155	270	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966401	25966401	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	292	564	0	ENST00000435504.4:c.2805G>A	p.Met935Ile	p.M935I	ENST00000435504		935	atG/atA	13/13	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.773419068518057	2		564	753	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088706	27088706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	297	506	0	ENST00000324856.7:c.2315C>T	p.Ser772Phe	p.S772F	ENST00000324856	NM_006015.4	772	tCt/tTt	7/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.773419068518057	2		506	699	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14300936	14300936	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	88	135	0	ENST00000256196.4:c.562G>C	p.Glu188Gln	p.E188Q	ENST00000256196		188	Gaa/Caa	6/6	1	2	FACETS	0.968	0.873	1	0.968	0.873	1	CLONAL	1	TRUE	1	0.773419068518057	2		135	235	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344537	118344537	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0065278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	337	535	0	ENST00000534358.1:c.2663C>G	p.Ser888Ter	p.S888*	ENST00000534358	NM_005933.3	888	tCa/tGa	3/36	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.773419068518057	2		535	829	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511703	66511703	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	215	353	0	ENST00000358598.2:c.163G>C	p.Glu55Gln	p.E55Q	ENST00000358598	NM_212471.2	55	Gag/Cag	2/11	1	2	FACETS	0.969	0.907	1	0.969	0.907	1	CLONAL	1	TRUE	1	0.773419068518057	2		353	574	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976889	18976889	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	246	452	0	ENST00000262803.5:c.3274G>C	p.Asp1092His	p.D1092H	ENST00000262803	NM_002911.3	1092	Gac/Cac	23/24	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.773419068518057	2		452	633	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436384	52436384	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	312	544	0	ENST00000460680.1:c.2110del	p.Val704SerfsTer32	p.V704Sfs*32	ENST00000460680	NM_004656.3	704	Gtc/tc	17/17	0.691661745800675	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.773419068518057	1		544	486	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73096464	73096464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	67	120	0	ENST00000356692.5:c.244G>A	p.Glu82Lys	p.E82K	ENST00000356692		82	Gaa/Aaa	3/9	1	2	FACETS	0.862	0.762	0.966	0.862	0.762	0.966	CLONAL	1	TRUE	1	0.773419068518057	2		120	201	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322566	109322566	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	232	300	0	ENST00000436639.2:c.471C>G	p.Phe157Leu	p.F157L	ENST00000436639	NM_014454.2	157	ttC/ttG	3/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.773419068518057	2		300	586	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864693	68864693	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	442	369	0	ENST00000288368.4:c.64C>A	p.Arg22Ser	p.R22S	ENST00000288368	NM_024870.2	22	Cgc/Agc	1/40	0.773419068518057	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.773419068518057	3		369	754	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0065279-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	21	350	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.8	0.615	1	0.8	0.615	1	CLONAL	1	TRUE	1	0.13	2		350	404	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063630	67063631	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065279-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	16	454	0	ENST00000412916.2:c.81dup	p.Lys28Ter	p.K28*	ENST00000412916		27	att/aTtt	2/6	1	2	FACETS	0.815	0.602	1	0.815	0.602	1	CLONAL	1	TRUE	1	0.13	2		454	302	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0065280-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	91	262	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.440406123217459	4	FACETS	0.872	0.783	0.966	0.872	0.783	0.966	CLONAL	2	TRUE	2	0.483531729766141	4		262	320	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519986	NA	P-0065280-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	287	599	0	ENST00000269305.4:c.809T>G	p.Phe270Cys	p.F270C	ENST00000269305	NM_001126112.2	270	tTt/tGt	8/11	0.483531729766141	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.483531729766141	2		599	542	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252066	226252066	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	24	207	0	ENST00000366813.1:c.14A>T	p.Lys5Met	p.K5M	ENST00000366813		5	aAg/aTg	1/3	0.654498292472726	4	FACETS	0.393	0.308	0.491	0.197	0.154	0.246	SUBCLONAL	1	FALSE	2	0.649666182415262	4		207	310	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245912910	245912910	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	23	528	0	ENST00000388985.4:c.1242G>C	p.Leu414Phe	p.L414F	ENST00000388985		414	ttG/ttC	12/12	0.654498292472726	4	FACETS	0.649	0.509	0.808	0.324	0.254	0.404	SUBCLONAL	1	FALSE	2	0.649666182415262	4		528	180	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427273	49427273	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	19	708	0	ENST00000301067.7:c.11215C>T	p.Gln3739Ter	p.Q3739*	ENST00000301067	NM_003482.3	3739	Cag/Tag	39/54	0.649666182415262	7	FACETS	0.414	0.313	0.532	0.103	0.078	0.133	SUBCLONAL	1	FALSE	3	0.649666182415262	7		708	371	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431879	49431880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	28	755	0	ENST00000301067.7:c.9259_9260insA	p.Arg3087GlnfsTer11	p.R3087Qfs*11	ENST00000301067	NM_003482.3	3087	cgg/cAgg	34/54	0.649666182415262	7	FACETS	0.544	0.434	0.669	0.136	0.108	0.168	SUBCLONAL	1	FALSE	3	0.649666182415262	7		755	416	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431466	121431466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193922600	NA	P-0065281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	19	624	0	ENST00000257555.6:c.670C>T	p.Pro224Ser	p.P224S	ENST00000257555		224	Cct/Tct	3/10	0.654498292472726	4	FACETS	0.412	0.313	0.528	0.206	0.156	0.264	SUBCLONAL	1	FALSE	2	0.649666182415262	4		624	234	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288346	15288346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1439729296	NA	P-0065281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	30	517	0	ENST00000263388.2:c.4393C>T	p.Arg1465Cys	p.R1465C	ENST00000263388	NM_000435.2	1465	Cgc/Tgc	24/33	0.649666182415262	5	FACETS	0.921	0.748	1	0.307	0.249	0.372	CLONAL	1	FALSE	2	0.649666182415262	5		517	198	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574338	41574338	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1211014285	NA	P-0065281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	34	679	0	ENST00000263253.7:c.6623A>G	p.His2208Arg	p.H2208R	ENST00000263253	NM_001429.3	2208	cAt/cGt	31/31	0.649666182415262	7	FACETS	0.725	0.593	0.873	0.181	0.148	0.219	SUBCLONAL	1	FALSE	3	0.649666182415262	7		679	379	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339782	116339782	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	27	600	0	ENST00000397752.3:c.644C>A	p.Ser215Ter	p.S215*	ENST00000397752	NM_000245.2	215	tCa/tAa	2/21	0.649666182415262	8	FACETS	0.518	0.411	0.641	0.13	0.102	0.161	SUBCLONAL	1	FALSE	4	0.649666182415262	8		600	473	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444062	49444064	+	frameshift_variant	Frame_Shift_Del	DEL	GCA	GCA	CC	novel	NA	P-0065281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	20	685	0	ENST00000301067.7:c.3307_3309delinsGG	p.Cys1103GlyfsTer16	p.C1103Gfs*16	ENST00000301067	NM_003482.3	1103	TGC/GG	11/54	0.649666182415262	7	FACETS	0.417	0.319	0.534	0.104	0.079	0.134	SUBCLONAL	1	FALSE	3	0.649666182415262	7		685	387	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781266	9781266	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	29	398	0	ENST00000377346.4:c.1771C>A	p.His591Asn	p.H591N	ENST00000377346	NM_005026.3	591	Cac/Aac	14/24	1	2	FACETS	0.561	0.451	0.688	0.561	0.451	0.688	SUBCLONAL	1	TRUE	1	0.271835976380955	2		398	380	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497748	120497748	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782035658	NA	P-0065286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	54	471	0	ENST00000256646.2:c.2134C>T	p.Pro712Ser	p.P712S	ENST00000256646	NM_024408.3	712	Ccc/Tcc	13/34	1	2	FACETS	0.854	0.731	0.989	0.854	0.731	0.989	CLONAL	1	TRUE	1	0.271835976380955	2		471	465	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162735842	162735842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	157	357	0	ENST00000367921.3:c.1151C>T	p.Pro384Leu	p.P384L	ENST00000367921	NM_006182.2	384	cCc/cTc	10/18	0.271835976380955	3	FACETS	0.851	0.785	0.919	0.851	0.785	0.919	CLONAL	3	TRUE	0	0.271835976380955	3		357	514	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	465673	465674	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0065286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	44	291	0	ENST00000399788.2:c.702_703delinsTT	p.Glu235Ter	p.E235*	ENST00000399788	NM_001042603.1	234	acGGaa/acTTaa	6/28	0.192605344847555	2	FACETS	1	0.889	1	0.534	0.45	0.626	CLONAL	1	TRUE	0	0.271835976380955	2		291	303	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18439832	18439832	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs971992008	NA	P-0065286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	57	281	0	ENST00000266497.5:c.730A>T	p.Ser244Cys	p.S244C	ENST00000266497		244	Agt/Tgt	2/31	0.192605344847555	2	FACETS	1	0.968	1	0.731	0.632	0.837	CLONAL	1	TRUE	0	0.271835976380955	2		281	287	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123891	46123891	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0065286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	99	436	0	ENST00000334344.6:c.157A>T	p.Arg53Ter	p.R53*	ENST00000334344	NM_152641.2	53	Aga/Tga	2/21	0.192605344847555	2	FACETS	0.873	0.785	0.966	0.873	0.785	0.966	CLONAL	2	TRUE	0	0.271835976380955	2		436	417	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445248	49445248	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	118	543	0	ENST00000301067.7:c.2218G>T	p.Gly740Trp	p.G740W	ENST00000301067	NM_003482.3	740	Ggg/Tgg	10/54	0.192605344847555	2	FACETS	1	0.984	1	0.737	0.667	0.811	CLONAL	1	TRUE	0	0.271835976380955	2		543	589	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527946	103527946	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	182	440	0	ENST00000355739.4:c.3254G>C	p.Gly1085Ala	p.G1085A	ENST00000355739	NM_000123.3	1085	gGt/gCt	15/15	0.241987204749717	3	FACETS	0.871	0.808	0.935	0.871	0.808	0.935	CLONAL	3	TRUE	0	0.271835976380955	3		440	582	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434835	99434835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1476643383	NA	P-0065286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	60	423	0	ENST00000268035.6:c.922C>T	p.Pro308Ser	p.P308S	ENST00000268035	NM_000875.3	308	Ccc/Tcc	3/21	0.188250229145258	3	FACETS	1	0.915	1	0.542	0.467	0.622	CLONAL	1	TRUE	1	0.271835976380955	3		423	463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0065286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	91	745	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	0.192605344847555	2	FACETS	1	0.973	1	0.651	0.58	0.727	CLONAL	1	TRUE	0	0.271835976380955	2		745	514	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654550	29654550	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	86	392	0	ENST00000356175.3:c.5239G>T	p.Glu1747Ter	p.E1747*	ENST00000356175	NM_000267.3	1747	Gag/Tag	37/57	0.192605344847555	2	FACETS	0.762	0.678	0.851	0.762	0.678	0.851	SUBCLONAL	2	TRUE	0	0.271835976380955	2		392	415	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37628000	37628000	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1376424345	NA	P-0065286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	70	383	0	ENST00000447079.4:c.1915G>C	p.Asp639His	p.D639H	ENST00000447079	NM_015083.1	639	Gat/Cat	2/14	0.192605344847555	2	FACETS	1	0.894	1	0.513	0.448	0.583	CLONAL	1	TRUE	0	0.271835976380955	2		383	502	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40384135	40384135	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	67	315	0	ENST00000293328.3:c.11G>A	p.Trp4Ter	p.W4*	ENST00000293328	NM_012448.3	4	tGg/tAg	2/19	0.192605344847555	2	FACETS	1	0.965	1	0.663	0.579	0.752	CLONAL	1	TRUE	0	0.271835976380955	2		315	372	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597401	10597401	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	48	364	0	ENST00000171111.5:c.1802G>A	p.Arg601Gln	p.R601Q	ENST00000171111	NM_203500.1	601	cGg/cAg	6/6	0.192605344847555	2	FACETS	0.859	0.728	1	0.43	0.364	0.502	CLONAL	1	TRUE	0	0.271835976380955	2		364	411	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610198	10610198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	105	488	0	ENST00000171111.5:c.512G>A	p.Cys171Tyr	p.C171Y	ENST00000171111	NM_203500.1	171	tGc/tAc	2/6	0.192605344847555	2	FACETS	1	0.982	1	0.739	0.664	0.817	CLONAL	1	TRUE	0	0.271835976380955	2		488	523	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279534	18279534	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0065286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	68	285	0	ENST00000222254.8:c.1809-2A>T		p.X603_splice	ENST00000222254	NM_005027.3	603			0.192605344847555	2	FACETS	0.872	0.766	0.984	0.872	0.766	0.984	CLONAL	2	TRUE	0	0.271835976380955	2		285	287	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99163151	99163151	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs771298129	NA	P-0065286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	60	337	0	ENST00000074304.5:c.1157A>G	p.Lys386Arg	p.K386R	ENST00000074304	NM_001134224.1	386	aAg/aGg	13/26	0.188250229145258	3	FACETS	1	0.949	1	0.607	0.525	0.696	CLONAL	1	TRUE	1	0.271835976380955	3		337	413	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737471	204737472	+	missense_variant	Missense_Mutation	DNP	AA	AA	TT	novel	NA	P-0065286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	42	389	0	ENST00000302823.3:c.608_609inv	p.Lys203Ile	p.K203I	ENST00000302823	NM_005214.4	203	aAA/aTT	4/4	0.188250229145258	3	FACETS	0.753	0.629	0.891	0.377	0.314	0.446	SUBCLONAL	1	TRUE	1	0.271835976380955	3		389	466	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295826	212295826	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0065286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	35	305	0	ENST00000342788.4:c.2488-1G>T		p.X830_splice	ENST00000342788	NM_005235.2	830			0.188250229145258	3	FACETS	0.758	0.622	0.91	0.379	0.311	0.455	CLONAL	1	TRUE	1	0.271835976380955	3		305	386	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944623	40944623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	79	349	0	ENST00000373198.4:c.1879G>A	p.Val627Ile	p.V627I	ENST00000373198	NM_133170.3	627	Gtt/Att	12/32	0.172756091972153	4	FACETS	1	0.977	1	0.748	0.66	0.842	CLONAL	1	TRUE	2	0.271835976380955	4		349	494	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193787	106193787	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs749210253	NA	P-0065286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	65	379	0	ENST00000380013.4:c.4249G>T	p.Val1417Phe	p.V1417F	ENST00000380013	NM_001127208.2	1417	Gtt/Ttt	10/11	0.192605344847555	2	FACETS	1	0.956	1	0.618	0.538	0.704	CLONAL	1	TRUE	0	0.271835976380955	2		379	387	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64288432	64288432	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	80	208	0	ENST00000370651.3:c.196C>T	p.Leu66Phe	p.L66F	ENST00000370651	NM_003463.4	66	Ctt/Ttt	3/6	0.188250229145258	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.271835976380955	3		208	284	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978318	2978330	+	frameshift_variant	Frame_Shift_Del	DEL	CTCGCAGCTCCTC	CTCGCAGCTCCTC	-	novel	NA	P-0065286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	78	352	0	ENST00000396946.4:c.1000_1012del	p.Glu334ThrfsTer28	p.E334Tfs*28	ENST00000396946	NM_032415.4	334	GAGGAGCTGCGAGac/ac	7/25	0.172756091972153	4	FACETS	0.8	0.706	0.901	0.8	0.706	0.901	CLONAL	2	TRUE	2	0.271835976380955	4		352	456	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946199	13946199	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	72	308	0	ENST00000405192.2:c.897G>T	p.Met299Ile	p.M299I	ENST00000405192	NM_001163147.1	299	atG/atT	10/12	0.172756091972153	4	FACETS	0.776	0.681	0.878	0.776	0.681	0.878	SUBCLONAL	2	TRUE	2	0.271835976380955	4		308	434	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0065286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	57	393	0	ENST00000288602.6:c.1397G>T	p.Gly466Val	p.G466V	ENST00000288602	NM_004333.4	466	gGa/gTa	11/18	0.172756091972153	4	FACETS	1	0.958	1	0.658	0.567	0.758	CLONAL	1	TRUE	2	0.271835976380955	4		393	405	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500753	8500753	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0065286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	67	352	0	ENST00000356435.5:c.2128+1G>T		p.X710_splice	ENST00000356435		710			0.192605344847555	2	FACETS	1	0.965	1	0.657	0.574	0.746	CLONAL	1	TRUE	0	0.271835976380955	2		352	375	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359956	87359956	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	71	349	0	ENST00000277120.3:c.1264G>T	p.Val422Phe	p.V422F	ENST00000277120		422	Gtc/Ttc	11/19	0.192605344847555	2	FACETS	1	0.968	1	0.668	0.586	0.756	CLONAL	1	TRUE	0	0.271835976380955	2		349	391	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920274	1920274	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	43	431	0	ENST00000382891.5:c.1334C>G	p.Thr445Arg	p.T445R	ENST00000382891	NM_133335.3	445	aCa/aGa	5/22	0.192097267374517	0	FACETS	1	0.859	1			1	CLONAL	1	TRUE	0	0.22	0		431	298	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852608	63852608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065287-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	32	424	0	ENST00000279873.7:c.3386G>A	p.Gly1129Glu	p.G1129E	ENST00000279873	NM_032199.2	1129	gGa/gAa	10/10	1	2	FACETS	0.317	0.257	0.386	0.317	0.257	0.386	SUBCLONAL	1	TRUE	1	0.394212747729842	2		424	512	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412046	116412046	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	T	novel	NA	P-0065287-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	60	442	0	ENST00000397752.3:c.3028+3A>T		p.X1010_splice	ENST00000397752	NM_000245.2	1010			1	2	FACETS	0.765	0.661	0.877	0.765	0.661	0.877	SUBCLONAL	1	TRUE	1	0.394212747729842	2		442	398	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0065288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	105	458	0				ENST00000310581	NM_198253.2	-/1132			0.482718565457234	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.482718565457234	1		458	294	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344170	118344170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1344397789	NA	P-0065288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	153	481	0	ENST00000534358.1:c.2296G>A	p.Glu766Lys	p.E766K	ENST00000534358	NM_005933.3	766	Gag/Aag	3/36	0.177984414623551	3	FACETS	1	0.974	1	0.574	0.526	0.623	INDETERMINATE	1	TRUE	1	0.482718565457234	3		481	686	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110031	115110031	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	121	367	0	ENST00000257566.3:c.1847C>G	p.Ser616Cys	p.S616C	ENST00000257566	NM_016569.3	616	tCt/tGt	8/8	0.482718565457234	3	FACETS	1	0.922	1	0.51	0.462	0.561	CLONAL	1	TRUE	1	0.482718565457234	3		367	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0065288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	339	496	0	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	0.480740529623495	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.482718565457234	2		496	675	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098804	178098804	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	126	364	0	ENST00000397062.3:c.241G>C	p.Gly81Arg	p.G81R	ENST00000397062	NM_006164.4	81	Ggt/Cgt	2/5	1	2	FACETS	0.949	0.863	1	0.949	0.863	1	CLONAL	1	TRUE	1	0.482718565457234	2		364	550	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286552	33286552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	144	343	0	ENST00000374542.5:c.2191G>A	p.Glu731Lys	p.E731K	ENST00000374542	NM_001141970.1	731	Gaa/Aaa	8/8	0.198513762156701	3	FACETS	0.798	0.734	0.865	0.798	0.734	0.865	INDETERMINATE	2	TRUE	1	0.482718565457234	3		343	464	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652049	36652050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0065288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	182	512	0	ENST00000244741.5:c.173dup	p.Leu59ThrfsTer4	p.L59Tfs*4	ENST00000244741	NM_000389.4	57	-/C	2/3	0.198513762156701	3	FACETS	1	0.984	1	0.622	0.575	0.67	INDETERMINATE	1	TRUE	1	0.482718565457234	3		512	753	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952931	2952931	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1460089226	NA	P-0065288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	113	345	0	ENST00000396946.4:c.3009C>G	p.Ile1003Met	p.I1003M	ENST00000396946	NM_032415.4	1003	atC/atG	22/25	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.482718565457234	2		345	436	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729551	41729551	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1356119994	NA	P-0065288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	158	500	0	ENST00000242208.4:c.978C>G	p.Phe326Leu	p.F326L	ENST00000242208	NM_002192.2	326	ttC/ttG	3/3	1	2	FACETS	0.983	0.904	1	0.983	0.904	1	CLONAL	1	TRUE	1	0.482718565457234	2		500	666	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128268597	128268597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	41	310	1	ENST00000265960.3:c.1058G>A	p.Arg353His	p.R353H	ENST00000265960	NM_001006617.1	353	cGc/cAc	8/12	1	2	FACETS	0.397	0.331	0.47	0.397	0.331	0.47	SUBCLONAL	1	TRUE	1	0.482718565457234	2		311	428	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003013	42003014	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	66	343	0	ENST00000219905.7:c.2551dup	p.Ser851PhefsTer10	p.S851Ffs*10	ENST00000219905	NM_001164273.1	850	-/T	8/24	0.547115923134181	1	FACETS	0.622	0.545	0.703	0.622	0.545	0.703	SUBCLONAL	1	TRUE	0	0.547115923134181	1		343	282	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007855	45007855	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	87	338	0	ENST00000558401.1:c.302del	p.Arg101LeufsTer2	p.R101Lfs*2	ENST00000558401	NM_004048.2	101	cGt/ct	2/4	0.547115923134181	1	FACETS	0.724	0.648	0.804	0.724	0.648	0.804	SUBCLONAL	1	TRUE	0	0.547115923134181	1		338	319	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21348511	21348511	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs990151749	NA	P-0065289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	86	465	0	ENST00000215739.8:c.1568del	p.Val523GlyfsTer33	p.V523Gfs*33	ENST00000215739	NM_006767.3	523	gTg/gg	14/21	0.530237913815377	1	FACETS	0.672	0.599	0.748	0.672	0.599	0.748	SUBCLONAL	1	TRUE	0	0.547115923134181	1		465	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0065290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	248	571	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.695403017866061	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.695403017866061	1		572	357	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0065290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	94	409	0	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	0.568782910088929	0	FACETS		NA	1			1	NA	1	TRUE	0	0.695403017866061	0		409	227	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916728	178916728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	8	304	0	ENST00000263967.3:c.115G>A	p.Glu39Lys	p.E39K	ENST00000263967	NM_006218.2	39	Gag/Aag	2/21	0.357932613496049	2	FACETS	0.06	0.038	0.089	0.03	0.019	0.045	INDETERMINATE	1	TRUE	0	0.695403017866061	2		304	381	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335630	81335630	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	36	312	0	ENST00000222390.5:c.1730C>A	p.Ser577Ter	p.S577*	ENST00000222390	NM_000601.4	577	tCa/tAa	15/18	0.559719991609846	2	FACETS	0.251	0.206	0.302	0.126	0.103	0.151	SUBCLONAL	1	TRUE	0	0.695403017866061	2		312	412	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251789	212251789	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	40	406	0	ENST00000342788.4:c.3270A>C	p.Glu1090Asp	p.E1090D	ENST00000342788	NM_005235.2	1090	gaA/gaC	27/28	0.391233207817398	1	FACETS	0.172	0.143	0.205	0.172	0.143	0.205	INDETERMINATE	1	TRUE	0	0.695403017866061	1		406	436	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967263	134967263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	268	438	0	ENST00000398015.3:c.2602C>T	p.Arg868Trp	p.R868W	ENST00000398015	NM_004441.4	868	Cgg/Tgg	14/16	0.470595921948789	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.695403017866061	1		438	491	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149440455	149440455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771977143	NA	P-0065290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	72	291	0	ENST00000286301.3:c.1939G>A	p.Val647Ile	p.V647I	ENST00000286301	NM_005211.3	647	Gtc/Atc	14/22	0.695403017866061	2	FACETS	0.577	0.507	0.651	0.288	0.253	0.326	SUBCLONAL	1	TRUE	0	0.695403017866061	2		291	359	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094466	27094467	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	244	402	0	ENST00000324856.7:c.3176dup	p.Glu1060GlyfsTer45	p.E1060Gfs*45	ENST00000324856	NM_006015.4	1058	-/A	11/20	0.695403017866061	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.695403017866061	1		402	354	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406702	70406702	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	56	342	0	ENST00000373644.4:c.4216C>G	p.Pro1406Ala	p.P1406A	ENST00000373644	NM_030625.2	1406	Cct/Gct	4/12	1	2	FACETS	0.337	0.289	0.389	0.337	0.289	0.389	SUBCLONAL	1	TRUE	1	0.695403017866061	2		342	478	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099201	4099201	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1172317151	NA	P-0065290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	76	324	0	ENST00000262948.5:c.917G>T	p.Ser306Ile	p.S306I	ENST00000262948	NM_030662.3	306	aGc/aTc	7/11	0.695403017866061	1	FACETS	0.495	0.439	0.554	0.495	0.439	0.554	SUBCLONAL	1	TRUE	0	0.695403017866061	1		324	288	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89176397	89176397	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	18	294	0	ENST00000336596.2:c.127G>C	p.Gly43Arg	p.G43R	ENST00000336596	NM_005233.5	43	Ggc/Cgc	2/17	0.470595921948789	1	FACETS	0.13	0.097	0.168	0.13	0.097	0.168	SUBCLONAL	1	TRUE	0	0.695403017866061	1		294	260	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604653	55604653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	25	330	0	ENST00000288135.5:c.2861C>T	p.Ser954Phe	p.S954F	ENST00000288135	NM_000222.2	954	tCt/tTt	21/21	0.476094231727312	1	FACETS	0.132	0.104	0.165	0.132	0.104	0.165	SUBCLONAL	1	TRUE	0	0.695403017866061	1		330	354	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31421399	31421399	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	64	265	0	ENST00000344624.3:c.3505C>G	p.His1169Asp	p.H1169D	ENST00000344624		1169	Cat/Gat	27/33	0.695403017866061	1	FACETS	0.354	0.308	0.403	0.354	0.308	0.403	SUBCLONAL	1	TRUE	0	0.695403017866061	1		265	339	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209394	98209394	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	23	422	0	ENST00000331920.6:c.4144C>A	p.His1382Asn	p.H1382N	ENST00000331920	NM_000264.3	1382	Cac/Aac	23/24	0.445243093427487	1	FACETS	0.102	0.079	0.129	0.102	0.079	0.129	SUBCLONAL	1	TRUE	0	0.695403017866061	1		422	422	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0065291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	223	535	1	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	0.394654669285409	1	FACETS	1	0.978	1	1	0.995	1	CLONAL	2	TRUE	0	0.394654669285409	1		536	424	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298642	11298642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	175	342	0	ENST00000361445.4:c.1819G>A	p.Ala607Thr	p.A607T	ENST00000361445	NM_004958.3	607	Gcg/Acg	12/58	0.394654669285409	1	FACETS	0.994	0.931	1	1	0.994	1	CLONAL	2	TRUE	0	0.394654669285409	1		342	358	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778200	27778200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	216	415	0	ENST00000369163.2:c.349C>T	p.Arg117Trp	p.R117W	ENST00000369163	NM_003536.2	117	Cgg/Tgg	1/1	1	2	FACETS	1	0.976	1	1	0.995	1	CLONAL	2	TRUE	1	0.394654669285409	2		415	508	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647501	3647511	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGGACACTG	GGAGGACACTG	C	novel	NA	P-0065291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	114	388	0	ENST00000294008.3:c.1552_1562delinsG	p.Gln518ValfsTer16	p.Q518Vfs*16	ENST00000294008	NM_032444.2	518	CAGTGTCCTCCt/Gt	7/15	0.394654669285409	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.394654669285409	1		388	370	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12647782	12647782	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1400058122	NA	P-0065309-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	104	268	0	ENST00000251849.4:c.598A>G	p.Thr200Ala	p.T200A	ENST00000251849	NM_002880.3	200	Act/Gct	6/17	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.756555136600947	2		268	236	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809196	243809196	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065309-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	78	274	0	ENST00000263826.5:c.428A>G	p.Lys143Arg	p.K143R	ENST00000263826	NM_005465.4	143	aAg/aGg	4/13	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.756555136600947	2		274	169	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085708	16085708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065309-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	177	366	0	ENST00000281043.3:c.884C>T	p.Thr295Ile	p.T295I	ENST00000281043	NM_005378.4	295	aCc/aTc	3/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.756555136600947	2		366	427	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531864	41531864	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065309-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	98	296	0	ENST00000263253.7:c.1576A>C	p.Ser526Arg	p.S526R	ENST00000263253	NM_001429.3	526	Agt/Cgt	7/31	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.756555136600947	2		296	234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0065310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	319	454	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.659206885021938	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.660283234668853	2		454	482	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380346	14380346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	262	546	2	ENST00000256196.4:c.71G>A	p.Gly24Asp	p.G24D	ENST00000256196		24	gGc/gAc	1/6	0.659206885021938	5	FACETS	0.927	0.877	0.977	0.927	0.877	0.977	CLONAL	3	TRUE	2	0.660283234668853	5		548	568	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177876	142177876	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777776233	NA	P-0065310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	545	375	0	ENST00000350721.4:c.7427G>A	p.Arg2476His	p.R2476H	ENST00000350721	NM_001184.3	2476	cGt/cAt	44/47	0.660283234668853	7	FACETS	0.922	0.891	0.953			1	CLONAL	5	TRUE	NA	0.660283234668853	7		375	949	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793049	42793062	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTCCTGTCCGTT	AGCTCCTGTCCGTT	-	novel	NA	P-0065310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	242	344	0	ENST00000575354.2:c.941_954del	p.Glu314GlyfsTer88	p.E314Gfs*88	ENST00000575354	NM_015125.3	314	gAGCTCCTGTCCGTT/g	7/20	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.660283234668853	2		344	345	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509616	106509616	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	290	482	0	ENST00000359195.3:c.1610A>G	p.Asp537Gly	p.D537G	ENST00000359195	NM_002649.2	537	gAc/gGc	2/11	0.659206885021938	3	FACETS	0.982	0.933	1	0.982	0.933	1	CLONAL	2	TRUE	1	0.660283234668853	3		482	595	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918335	44918344	+	frameshift_variant	Frame_Shift_Del	DEL	ATGGTGTTCA	ATGGTGTTCA	-	novel	NA	P-0065310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	166	309	0	ENST00000377967.4:c.962_971del	p.Trp321Ter	p.W321*	ENST00000377967	NM_021140.2	320	acATGGTGTTCA/ac	11/29	0.659206885021938	3	FACETS	0.855	0.796	0.915	0.855	0.796	0.915	CLONAL	2	TRUE	1	0.660283234668853	3		309	391	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589144	67589152	+	frameshift_variant	Frame_Shift_Del	DEL	AACAAATTA	AACAAATTA	T	novel	NA	P-0065310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	87	309	0	ENST00000274335.5:c.1132_1140delinsT	p.Asn378TyrfsTer14	p.N378Yfs*14	ENST00000274335		378	AACAAATTA/T	9/15	1	2	FACETS	0.834	0.746	0.926	0.834	0.746	0.926	CLONAL	1	TRUE	1	0.660283234668853	2		309	316	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065311-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	77	789	0				ENST00000310581	NM_198253.2	-/1132			0.16859032802937	7	FACETS	1	0.932	1	1	0.932	1	CLONAL	4	FALSE	3	0.16859032802937	7		789	303	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0065311-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	173	462	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.16859032802937	2	FACETS	0.972	0.909	1	1	0.994	1	CLONAL	6	FALSE	0	0.16859032802937	2		462	352	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919935	50919935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1044937882	NA	P-0065311-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	97	523	0	ENST00000440232.2:c.3022C>T	p.Arg1008Cys	p.R1008C	ENST00000440232	NM_002691.3	1008	Cgc/Tgc	24/27	0.16859032802937	7	FACETS	1	0.956	1	1	0.956	1	CLONAL	4	FALSE	3	0.16859032802937	7		523	367	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432459	49432459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065311-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	173	619	0	ENST00000301067.7:c.8680C>T	p.Pro2894Ser	p.P2894S	ENST00000301067	NM_003482.3	2894	Ccg/Tcg	34/54	0.16859032802937	8	FACETS	0.935	0.866	1	1	0.989	1	CLONAL	6	FALSE	4	0.16859032802937	8		619	551	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881523	48881523	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065311-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	143	319	0	ENST00000267163.4:c.245C>A	p.Ser82Ter	p.S82*	ENST00000267163	NM_000321.2	82	tCa/tAa	2/27	0.16859032802937	2	FACETS	1	0.971	1	1	0.993	1	CLONAL	5	FALSE	0	0.16859032802937	2		319	310	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432447	49432447	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065311-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	179	583	0	ENST00000301067.7:c.8692C>T	p.Gln2898Ter	p.Q2898*	ENST00000301067	NM_003482.3	2898	Cag/Tag	34/54	0.16859032802937	8	FACETS	0.933	0.866	1	1	0.989	1	CLONAL	6	FALSE	4	0.16859032802937	8		583	571	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217855	7217858	+	frameshift_variant	Frame_Shift_Del	DEL	CTTC	CTTC	-	novel	NA	P-0065311-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	150	456	0	ENST00000380728.2:c.153_156del	p.Lys53ArgfsTer9	p.K53Rfs*9	ENST00000380728		51	agGAAG/ag	3/11	0.16859032802937	2	FACETS	0.983	0.911	1	1	0.993	1	CLONAL	5	FALSE	0	0.16859032802937	2		456	362	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798880	135798880	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0065311-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	161	343	0	ENST00000298552.3:c.364-1G>A		p.X122_splice	ENST00000298552	NM_001162426.1	122			0.16859032802937	2	FACETS	0.939	0.876	1	1	0.994	1	CLONAL	6	FALSE	0	0.16859032802937	2		343	339	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65311195	65311195	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0065311-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	126	444	0	ENST00000342505.4:c.2115+1G>A		p.X705_splice	ENST00000342505	NM_002227.2	705			0.16859032802937	5	FACETS	0.961	0.876	1	1	0.98	1	CLONAL	4	FALSE	2	0.16859032802937	5		444	487	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799357	88799357	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065311-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	36	338	0	ENST00000360948.2:c.28T>C	p.Cys10Arg	p.C10R	ENST00000360948	NM_001012338.2	10	Tgt/Cgt	2/19	0.16859032802937	3	FACETS	0.767	0.633	0.916	0.511	0.422	0.611	CLONAL	2	FALSE	0	0.16859032802937	3		338	302	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143129587	143129587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065311-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	71	239	0	ENST00000262992.4:c.1063C>T	p.His355Tyr	p.H355Y	ENST00000262992	NM_001101669.1	355	Cac/Tac	12/24	0.16859032802937	3	FACETS	1	0.933	1	1	0.975	1	CLONAL	4	FALSE	0	0.16859032802937	3		239	213	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346338	73346338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065312-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	9	291	0	ENST00000377767.4:c.1462G>A	p.Asp488Asn	p.D488N	ENST00000377767	NM_014953.3	488	Gat/Aat	10/21	1	2	FACETS	0.064	0.042	0.093	0.064	0.042	0.093	SUBCLONAL	1	TRUE	1	0.778098460826426	2		291	361	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500635	99500635	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065312-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	34	424	0	ENST00000268035.6:c.4068G>C	p.Glu1356Asp	p.E1356D	ENST00000268035	NM_000875.3	1356	gaG/gaC	21/21	1	2	FACETS	0.164	0.133	0.198	0.164	0.133	0.198	SUBCLONAL	1	TRUE	1	0.778098460826426	2		424	534	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149437070	149437070	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065312-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	28	402	0	ENST00000286301.3:c.2218C>A	p.Gln740Lys	p.Q740K	ENST00000286301	NM_005211.3	740	Caa/Aaa	16/22	1	2	FACETS	0.143	0.114	0.177	0.143	0.114	0.177	SUBCLONAL	1	TRUE	1	0.778098460826426	2		402	503	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398831	398831	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065312-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	26	335	0	ENST00000380956.4:c.641G>C	p.Cys214Ser	p.C214S	ENST00000380956	NM_001195286.1	214	tGc/tCc	6/9	1	2	FACETS	0.132	0.104	0.164	0.132	0.104	0.164	SUBCLONAL	1	TRUE	1	0.778098460826426	2		335	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs878854073	NA	P-0065313-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	231	372	0	ENST00000269305.4:c.673-1G>A		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.753946929442814	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.753946929442814	1		372	352	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205596	38205596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065313-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	166	398	0	ENST00000317025.8:c.94G>A	p.Asp32Asn	p.D32N	ENST00000317025	NM_023034.1	32	Gat/Aat	2/24	0.468465892928702	1	FACETS	0.419	0.386	0.454	0.419	0.386	0.454	SUBCLONAL	1	TRUE	0	0.753946929442814	1		398	654	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0065314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	84	342	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.176832185659672	3	FACETS	1	0.961	1	0.781	0.696	0.869	CLONAL	2	TRUE	0	0.251565975877163	3		342	321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0065314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	97	660	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.192121677086763	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	2	TRUE	0	0.251565975877163	2		660	378	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845574	128845574	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1405848770	NA	P-0065314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	24	477	1	ENST00000249373.3:c.871C>T	p.Arg291Ter	p.R291*	ENST00000249373	NM_005631.4	291	Cga/Tga	4/12	0.172619795011342	3	FACETS	0.587	0.46	0.734	0.293	0.23	0.367	SUBCLONAL	1	TRUE	1	0.251565975877163	3		478	366	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416706	121416706	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	107	497	0	ENST00000257555.6:c.135del	p.Asp45GlufsTer110	p.D45Efs*110	ENST00000257555		45	gaC/ga	1/10	0.176832185659672	3	FACETS	0.867	0.785	0.953	0.867	0.785	0.953	CLONAL	3	TRUE	0	0.251565975877163	3		497	368	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119690	70119690	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	56	441	0	ENST00000245479.2:c.694del	p.Gln232ArgfsTer21	p.Q232Rfs*21	ENST00000245479	NM_000346.3	231	tCc/tc	3/3	0.0711184060389709	4	FACETS	0.803	0.691	0.923	0.803	0.691	0.923	INDETERMINATE	2	TRUE	2	0.251565975877163	4		441	347	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532650	187532650	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	67	466	0	ENST00000441802.2:c.9743A>G	p.Glu3248Gly	p.E3248G	ENST00000441802	NM_005245.3	3248	gAa/gGa	14/27	0.179028580680149	3	FACETS	1	0.956	1	0.618	0.538	0.704	CLONAL	1	TRUE	1	0.251565975877163	3		466	485	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065315-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	18	393	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	0.174158543892406	3	FACETS	0.93	0.704	1	0.465	0.352	0.598	CLONAL	1	FALSE	1	0.236564905937053	3		393	183	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0065316-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	30	342	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.57	0.461	0.694	0.57	0.461	0.694	SUBCLONAL	1	TRUE	1	0.345976297695829	2		342	304	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971077	21971078	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCGT	novel	NA	P-0065316-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	50	400	0	ENST00000304494.5:c.277_280dup	p.Leu94HisfsTer27	p.L94Hfs*27	ENST00000304494	NM_000077.4	94	ctg/cACGCtg	2/3	0.345976297695829	1	FACETS	0.695	0.592	0.807	0.695	0.592	0.807	SUBCLONAL	1	TRUE	0	0.345976297695829	1		400	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578486	7578488	+	frameshift_variant	Frame_Shift_Del	DEL	ATC	ATC	T	novel	NA	P-0065316-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	88	489	0	ENST00000269305.4:c.442_444delinsA	p.Asp148IlefsTer32	p.D148Ifs*32	ENST00000269305	NM_001126112.2	148	GAT/A	5/11	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.345976297695829	2		489	498	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	8	202	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	1	2	FACETS	0.093	0.059	0.137	0.093	0.059	0.137	SUBCLONAL	1	TRUE	1	0.65	2		202	264	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519893	NA	P-0065317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	14	387	0	ENST00000267101.3:c.310G>T	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ttg	3/28	1	2	FACETS	0.08	0.057	0.108	0.08	0.057	0.108	SUBCLONAL	1	TRUE	1	0.65	2		387	536	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0065317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	18	557	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.092	0.069	0.12	0.092	0.069	0.12	SUBCLONAL	1	TRUE	1	0.65	2		557	601	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0065317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	14	435	3	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	1	2	FACETS	0.1	0.072	0.135	0.1	0.072	0.135	SUBCLONAL	1	TRUE	1	0.65	2		438	430	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466025	69466026	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGA	novel	NA	P-0065317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	177	474	0	ENST00000227507.2:c.866_868dup	p.Asp289dup	p.D289dup	ENST00000227507	NM_053056.2	289	acc/acCGAc	5/5	1	2	FACETS	0.981	0.91	1	0.981	0.91	1	CLONAL	1	TRUE	1	0.65	2		474	555	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134230	11134230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1227826852	NA	P-0065317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	87	437	0	ENST00000358026.2:c.2896C>T	p.Arg966Trp	p.R966W	ENST00000358026	NM_001128849.1	966	Cgg/Tgg	20/36	NA	3	FACETS	0.73	0.648	0.816	0.365	0.324	0.408	INDETERMINATE	1	TRUE	1	0.65	3		437	486	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120267	70120267	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	172	544	0	ENST00000245479.2:c.1269del	p.Phe423LeufsTer47	p.F423Lfs*47	ENST00000245479	NM_000346.3	423	ttC/tt	3/3	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.65	2		544	493	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061526	38061539	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCCGCGCGGCTG	CGCCCGCGCGGCTG	AGCC	novel	NA	P-0065317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	25	486	1	ENST00000250448.2:c.450_463delinsGGCT	p.Ser151AlafsTer40	p.S151Afs*40	ENST00000250448	NM_004496.3	150	cgCAGCCGCGCGGGCGgc/cgGGCTgc	2/2	1	2	FACETS	0.179	0.141	0.224	0.179	0.141	0.224	SUBCLONAL	1	TRUE	1	0.65	2		487	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	243	459	0	ENST00000269305.4:c.313G>T	p.Gly105Cys	p.G105C	ENST00000269305	NM_001126112.2	105	Ggc/Tgc	4/11	0.446148117184052	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.453799975226751	2		459	497	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394888	394888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	206	378	0	ENST00000380956.4:c.284C>T	p.Thr95Met	p.T95M	ENST00000380956	NM_001195286.1	95	aCg/aTg	3/9	NA	2	FACETS	0.842	0.788	0.897			1	INDETERMINATE	2	TRUE	NA	0.453799975226751	2		378	539	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11205059	11205059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	197	331	0	ENST00000361445.4:c.4730C>T	p.Ala1577Val	p.A1577V	ENST00000361445	NM_004958.3	1577	gCg/gTg	33/58	0.439783310258789	3	FACETS	0.988	0.922	1	0.988	0.922	1	CLONAL	2	TRUE	1	0.453799975226751	3		331	539	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174875	11174880	+	inframe_deletion	In_Frame_Del	DEL	TAGCAT	TAGCAT	-	novel	NA	P-0065318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	58	224	0	ENST00000361445.4:c.7154_7159del	p.Asn2385_Ala2386del	p.N2385_A2386del	ENST00000361445	NM_004958.3	2385	aATGCTAtg/atg	52/58	0.439783310258789	3	FACETS	0.888	0.767	1	0.444	0.383	0.51	CLONAL	1	TRUE	1	0.453799975226751	3		224	353	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230459301	230459301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1558189111	NA	P-0065318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	231	362	0	ENST00000391860.1:c.1100C>T	p.Ala367Val	p.A367V	ENST00000391860	NM_001258311.1	367	gCc/gTc	7/7	0.439783310258789	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.453799975226751	3		362	619	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085899	16085899	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	104	404	0	ENST00000281043.3:c.1075C>G	p.Leu359Val	p.L359V	ENST00000281043	NM_005378.4	359	Ctc/Gtc	3/3	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.453799975226751	2		404	455	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161702	47161702	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	81	290	0	ENST00000409792.3:c.4424T>G	p.Leu1475Arg	p.L1475R	ENST00000409792	NM_014159.6	1475	cTt/cGt	3/21	0.439783310258789	3	FACETS	0.92	0.813	1	0.46	0.406	0.517	CLONAL	1	TRUE	1	0.453799975226751	3		290	476	SUCCESS
APC	324	MSKCC	GRCh37	5	112175647	112175654	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTAAAA	ACCTAAAA	-	novel	NA	P-0065318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	201	408	0	ENST00000257430.4:c.4357_4364del	p.Pro1453Ter	p.P1453*	ENST00000257430	NM_000038.5	1452	gtACCTAAAAat/gtat	16/16	0.453799975226751	2	FACETS	0.857	0.801	0.913	0.857	0.801	0.913	CLONAL	2	TRUE	0	0.453799975226751	2		408	517	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128849203	128849203	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	91	336	0	ENST00000249373.3:c.1431G>C	p.Gln477His	p.Q477H	ENST00000249373	NM_005631.4	477	caG/caC	8/12	0.411660569863014	4	FACETS	0.978	0.87	1	0.489	0.435	0.547	CLONAL	1	TRUE	2	0.453799975226751	4		336	596	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460354	149460354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437040009	NA	P-0065324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	63	436	1	ENST00000286301.3:c.283G>A	p.Ala95Thr	p.A95T	ENST00000286301	NM_005211.3	95	Gcc/Acc	3/22	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.30594848537599	2		437	400	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376262	225376262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	29	320	0	ENST00000264414.4:c.692C>T	p.Ser231Leu	p.S231L	ENST00000264414	NM_003590.4	231	tCa/tTa	6/16	1	2	FACETS	0.682	0.549	0.832	0.682	0.549	0.832	SUBCLONAL	1	TRUE	1	0.30594848537599	2		320	278	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150915366	150915366	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	71	504	0	ENST00000271640.5:c.712G>A	p.Gly238Arg	p.G238R	ENST00000271640	NM_001145415.1	238	Gga/Aga	7/22	1	2	FACETS	0.967	0.846	1	0.967	0.846	1	CLONAL	1	TRUE	1	0.30594848537599	2		504	480	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539957	187539957	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	37	512	0	ENST00000441802.2:c.7783C>G	p.Gln2595Glu	p.Q2595E	ENST00000441802	NM_005245.3	2595	Caa/Gaa	10/27	1	2	FACETS	0.497	0.409	0.595	0.497	0.409	0.595	SUBCLONAL	1	TRUE	1	0.30594848537599	2		512	487	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412034	116412070	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTCCAGAAGGTATATTTCAGTTTATTGTTCTGAGAA	TTTCCAGAAGGTATATTTCAGTTTATTGTTCTGAGAA	GAT	novel	NA	P-0065324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	74	568	1	ENST00000397752.3:c.3019_3028+27delinsGAT		p.X1007_splice	ENST00000397752	NM_000245.2	1007		14/21	0.30594848537599	1	FACETS	0.987	0.868	1	0.987	0.868	1	CLONAL	1	TRUE	0	0.30594848537599	1		569	415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0065326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	199	467	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		467	381	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109311921	109311921	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs749534099	NA	P-0065326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	145	342	0	ENST00000436639.2:c.1351A>G	p.Met451Val	p.M451V	ENST00000436639	NM_014454.2	451	Atg/Gtg	8/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		342	628	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446842	49446842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	133	546	0	ENST00000301067.7:c.968G>T	p.Cys323Phe	p.C323F	ENST00000301067	NM_003482.3	323	tGc/tTc	8/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		546	1068	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	69	789	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.853	0.747	0.966	0.853	0.747	0.966	CLONAL	1	TRUE	1	0.437468500247463	2		789	370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0065327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	164	519	1	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	0.409112971523632	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.437468500247463	1		520	484	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692803	89692803	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554898074	NA	P-0065327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	64	262	0	ENST00000371953.3:c.287C>T	p.Pro96Leu	p.P96L	ENST00000371953	NM_000314.4	96	cCa/cTa	5/9	0.437468500247463	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.437468500247463	1		262	196	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271151	38271151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17182463	NA	P-0065327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	95	433	0	ENST00000425967.3:c.2557C>T	p.Arg853Cys	p.R853C	ENST00000425967	NM_001174067.1	853	Cgc/Tgc	19/19	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.437468500247463	2		433	381	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021847	246021864	+	inframe_deletion	In_Frame_Del	DEL	GGCCGAGGTTGATGCAGG	GGCCGAGGTTGATGCAGG	-	novel	NA	P-0065327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	132	465	0	ENST00000388985.4:c.1010_1027del	p.Ala337_Leu343delinsVal	p.A337_L343delinsV	ENST00000388985		337	gCCTGCATCAACCTCGGCCtg/gtg	10/12	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.437468500247463	2		465	588	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	170	789	0				ENST00000310581	NM_198253.2	-/1132			0.643661615522676	5	FACETS	0.981	0.911	1	0.654	0.607	0.702	CLONAL	2	TRUE	2	0.824934043463999	5		789	470	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0065328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	277	256	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.824934043463999	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.824934043463999	3		256	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0065328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	334	588	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.824934043463999	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.824934043463999	2		589	395	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0065328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	98	389	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	0.461977867064781	1	FACETS	0.481	0.435	0.529	0.481	0.435	0.529	INDETERMINATE	1	TRUE	0	0.824934043463999	1		389	290	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211873	123211873	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1216415127	NA	P-0065328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	365	322	0	ENST00000218089.9:c.2740C>T	p.Gln914Ter	p.Q914*	ENST00000218089	NM_001042749.1	914	Cag/Tag	27/35	0.824934043463999	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.824934043463999	2		322	403	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651956	36651957	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	198	482	1	ENST00000244741.5:c.79dup	p.Ser27LysfsTer9	p.S27Kfs*9	ENST00000244741	NM_000389.4	26	-/A	2/3	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.824934043463999	2		483	464	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976408	18976408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550009751	NA	P-0065328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	99	485	0	ENST00000262803.5:c.3058C>T	p.Arg1020Cys	p.R1020C	ENST00000262803	NM_002911.3	1020	Cgc/Tgc	22/24	0.125954549670144	3	FACETS	0.726	0.651	0.805	0.363	0.325	0.403	INDETERMINATE	1	TRUE	1	0.824934043463999	3		485	467	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404592	70404592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756857307	NA	P-0065328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	212	423	0	ENST00000373644.4:c.2106G>A	p.Met702Ile	p.M702I	ENST00000373644	NM_030625.2	702	atG/atA	4/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.824934043463999	2		423	481	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878166	48878176	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGACCTGCC	GAGGACCTGCC	-	novel	NA	P-0065328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	291	463	0	ENST00000267163.4:c.118_128del	p.Glu40SerfsTer5	p.E40Sfs*5	ENST00000267163	NM_000321.2	40	GAGGACCTGCCt/t	1/27	0.824934043463999	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.824934043463999	2		463	347	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649195	23649195	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs730881899	NA	P-0065328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	86	286	0	ENST00000261584.4:c.187C>G	p.Leu63Val	p.L63V	ENST00000261584	NM_024675.3	63	Ctc/Gtc	3/13	0.725970588857149	2	FACETS	0.393	0.348	0.44	0.196	0.174	0.22	SUBCLONAL	1	TRUE	0	0.824934043463999	2		286	531	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821265	72821265	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1198448605	NA	P-0065328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	183	449	0	ENST00000268489.5:c.10910C>A	p.Ser3637Ter	p.S3637*	ENST00000268489	NM_006885.3	3637	tCa/tAa	10/10	0.768724460850607	1	FACETS	0.841	0.793	0.888	0.841	0.793	0.888	CLONAL	1	TRUE	0	0.824934043463999	1		449	310	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61304975	61304975	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs752728556	NA	P-0065328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	87	246	0	ENST00000341074.5:c.1151A>G	p.Tyr384Cys	p.Y384C	ENST00000341074	NM_002974.2	384	tAt/tGt	8/8	0.129870297082455	3	FACETS	1	0.949	1	0.548	0.491	0.606	INDETERMINATE	1	TRUE	1	0.824934043463999	3		246	272	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645284	215645284	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1559423185	NA	P-0065328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	259	344	0	ENST00000260947.4:c.1314G>T	p.Lys438Asn	p.K438N	ENST00000260947	NM_000465.2	438	aaG/aaT	4/11	0.824934043463999	2	FACETS	0.969	0.936	1	0.969	0.936	1	CLONAL	2	TRUE	0	0.824934043463999	2		344	324	SUCCESS
APC	324	MSKCC	GRCh37	5	112177136	112177136	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793815	NA	P-0065328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	35	463	0	ENST00000257430.4:c.5845G>A	p.Glu1949Lys	p.E1949K	ENST00000257430	NM_000038.5	1949	Gaa/Aaa	16/16	0.824934043463999	2	FACETS	0.2	0.164	0.241	0.1	0.082	0.121	SUBCLONAL	1	TRUE	0	0.824934043463999	2		463	424	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874398	151874398	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	173	349	0	ENST00000262189.6:c.8140G>A	p.Asp2714Asn	p.D2714N	ENST00000262189	NM_170606.2	2714	Gat/Aat	38/59	0.129870297082455	3	FACETS	1	0.989	1	0.675	0.628	0.723	INDETERMINATE	1	TRUE	1	0.824934043463999	3		349	439	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0065330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	69	500	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		500	558	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0065330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	42	458	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		458	408	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005117	150005117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56348064	NA	P-0065330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	97	653	0	ENST00000253339.5:c.1108C>T	p.Arg370Trp	p.R370W	ENST00000253339		370	Cgg/Tgg	3/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		653	758	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	21	297	0	ENST00000335508.6:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000335508	NM_012433.2	902	Gaa/Aaa	18/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		297	504	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8497265	8497265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1270795879	NA	P-0065330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	51	269	0	ENST00000356435.5:c.2326G>A	p.Glu776Lys	p.E776K	ENST00000356435		776	Gaa/Aaa	15/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		269	380	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679247	88679247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867521873	NA	P-0065330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	56	376	0	ENST00000360948.2:c.790C>T	p.His264Tyr	p.H264Y	ENST00000360948	NM_001012338.2	264	Cat/Tat	8/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		376	517	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320350	30320350	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	27	254	0	ENST00000322652.5:c.1291C>T	p.Gln431Ter	p.Q431*	ENST00000322652	NM_015355.2	431	Cag/Tag	11/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		254	397	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894230	NA	P-0065330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	32	457	0	ENST00000451590.1:c.35G>A	p.Gly12Asp	p.G12D	ENST00000451590	NM_001130442.1	12	gGc/gAc	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		457	590	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572002	64572002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779413959	NA	P-0065330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	77	582	0	ENST00000312049.6:c.1637C>T	p.Pro546Leu	p.P546L	ENST00000312049	NM_130799.2	546	cCg/cTg	10/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		582	648	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416740	29416740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	36	545	0	ENST00000389048.3:c.4213G>A	p.Val1405Met	p.V1405M	ENST00000389048	NM_004304.4	1405	Gtg/Atg	29/29	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		545	604	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21342323	21342323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	67	449	0	ENST00000215739.8:c.425C>T	p.Ser142Phe	p.S142F	ENST00000215739	NM_006767.3	142	tCc/tTc	5/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		449	554	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29090041	29090042	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0065330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	16	104	0	ENST00000328354.6:c.1439_1440delinsAT	p.Ala480Asp	p.A480D	ENST00000328354	NM_007194.3	480	gCC/gAT	13/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		104	164	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074224	30074224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	104	519	0	ENST00000338641.4:c.1486C>T	p.Pro496Ser	p.P496S	ENST00000338641	NM_000268.3	496	Cca/Tca	14/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		519	626	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478127	138478127	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	56	480	0	ENST00000289153.2:c.59T>C	p.Val20Ala	p.V20A	ENST00000289153	NM_006219.2	20	gTg/gCg	1/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		480	557	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604221	189604221	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	76	506	0	ENST00000264731.3:c.1388C>T	p.Ser463Phe	p.S463F	ENST00000264731	NM_003722.4	463	tCc/tTc	11/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		506	611	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332877	153332877	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	81	514	1	ENST00000281708.4:c.79C>T	p.Gln27Ter	p.Q27*	ENST00000281708	NM_033632.3	27	Cag/Tag	2/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		515	641	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0065330-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	147	458	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		458	323	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220274	55220274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065330-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15267	1053	372	0	ENST00000275493.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000275493	NM_005228.3	222	Cgc/Tgc	6/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		372	16320	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435779	56435779	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065330-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	230	690	0	ENST00000407977.2:c.1358A>G	p.Glu453Gly	p.E453G	ENST00000407977		453	gAa/gGa	9/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		690	515	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717769	89717770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065391-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	83	281	0	ENST00000371953.3:c.800dup	p.Asp268GlyfsTer30	p.D268Gfs*30	ENST00000371953	NM_000314.4	265	cta/ctAa	7/9	0.232778641616533	2	FACETS	0.941	0.837	1	0.941	0.837	1	CLONAL	2	TRUE	0	0.25	2		281	353	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs1057519842	NA	P-0065391-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	55	456	0	ENST00000274335.5:c.1727_1729del	p.Thr576del	p.T576del	ENST00000274335		575	aaGACg/aag	12/15	1	2	FACETS	0.905	0.775	1	0.905	0.775	1	CLONAL	1	TRUE	1	0.25	2		456	486	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912014	127912014	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773765410	NA	P-0065391-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	63	463	0	ENST00000373547.4:c.856C>T	p.Arg286Trp	p.R286W	ENST00000373547	NM_002721.4	286	Cgg/Tgg	7/7	1	2	FACETS	0.913	0.79	1	0.913	0.79	1	CLONAL	1	TRUE	1	0.25	2		463	552	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0065391-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	52	338	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.25	2		338	357	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094439	27094449	+	frameshift_variant	Frame_Shift_Del	DEL	GGACCTCTATC	GGACCTCTATC	-	novel	NA	P-0065391-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	77	543	0	ENST00000324856.7:c.3148_3158del	p.Asp1050ProfsTer51	p.D1050Pfs*51	ENST00000324856	NM_006015.4	1049	ctGGACCTCTATCgc/ctgc	11/20	1	2	FACETS	0.939	0.824	1	0.939	0.824	1	CLONAL	1	TRUE	1	0.25	2		543	656	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447293	187447293	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065391-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	95	659	0	ENST00000232014.4:c.900C>A	p.Ser300Arg	p.S300R	ENST00000232014	NM_001130845.1	300	agC/agA	5/10	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.25	2		659	723	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144359339	144359339	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	38	511	0	ENST00000262995.4:c.781C>A	p.Leu261Met	p.L261M	ENST00000262995	NM_207123.2	261	Ctg/Atg	4/11	1	2	FACETS	0.327	0.27	0.39	0.327	0.27	0.39	SUBCLONAL	1	TRUE	1	0.547154979261382	2		511	425	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881469	48881470	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	97	330	0	ENST00000267163.4:c.194dup	p.Ile66AspfsTer44	p.I66Dfs*44	ENST00000267163	NM_000321.2	64	tta/ttAa	2/27	0.36190810817811	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.36190810817811	1		330	398	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902252	50902252	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	96	498	0	ENST00000440232.2:c.144C>G	p.His48Gln	p.H48Q	ENST00000440232	NM_002691.3	48	caC/caG	2/27	0.36190810817811	1	FACETS	0.857	0.766	0.953	0.857	0.766	0.953	CLONAL	1	TRUE	0	0.36190810817811	1		498	507	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894230	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	128	457	0	ENST00000451590.1:c.35G>A	p.Gly12Asp	p.G12D	ENST00000451590	NM_001130442.1	12	gGc/gAc	2/5	1	2	FACETS	0.823	0.746	0.904	0.823	0.746	0.904	CLONAL	1	TRUE	1	0.397754980452443	2		457	782	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	108	338	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.397754980452443	2		338	422	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778839	9778839	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	206	597	0	ENST00000377346.4:c.1108del	p.Val370CysfsTer28	p.V370Cfs*28	ENST00000377346	NM_005026.3	370	Gtg/tg	9/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.397754980452443	2		597	966	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023165	27023222	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCGGGCCCGGCGCGGAGCCGGACCTGAAGAACTCGAACGGGAACGCGGGCCCTA	GGCGGCGGGCCCGGCGCGGAGCCGGACCTGAAGAACTCGAACGGGAACGCGGGCCCTA	-	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	92	495	0	ENST00000324856.7:c.274_331del	p.Gly92ProfsTer3	p.G92Pfs*3	ENST00000324856	NM_006015.4	91	GGCGGCGGGCCCGGCGCGGAGCCGGACCTGAAGAACTCGAACGGGAACGCGGGCCCTAgg/gg	1/20	1	2	FACETS	0.92	0.82	1	0.92	0.82	1	CLONAL	1	TRUE	1	0.397754980452443	2		495	503	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023744	27023744	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	118	568	1	ENST00000324856.7:c.854del	p.Gly285GlufsTer78	p.G285Efs*78	ENST00000324856	NM_006015.4	284	Ggg/gg	1/20	1	2	FACETS	0.965	0.873	1	0.965	0.873	1	CLONAL	1	TRUE	1	0.397754980452443	2		569	615	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058048	27058048	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	189	596	0	ENST00000324856.7:c.1756C>T	p.Gln586Ter	p.Q586*	ENST00000324856	NM_006015.4	586	Cag/Tag	3/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.397754980452443	2		596	842	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509532	46509533	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	154	443	0	ENST00000262741.5:c.1198dup	p.Glu400GlyfsTer82	p.E400Gfs*82	ENST00000262741	NM_003629.3	400	gaa/gGaa	10/10	1	2	FACETS	0.961	0.88	1	0.961	0.88	1	CLONAL	1	TRUE	1	0.397754980452443	2		443	806	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	167	690	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.994	0.914	1	0.994	0.914	1	CLONAL	1	TRUE	1	0.397754980452443	2		691	845	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339110	65339111	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	130	478	3	ENST00000342505.4:c.425dup	p.Ile143AspfsTer9	p.I143Dfs*9	ENST00000342505	NM_002227.2	142	aag/aaAg	5/25	1	2	FACETS	0.757	0.686	0.831	0.757	0.686	0.831	SUBCLONAL	1	TRUE	1	0.397754980452443	2		481	864	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429978	78429978	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	145	363	4	ENST00000370768.2:c.901del	p.Ile301TyrfsTer22	p.I301Yfs*22	ENST00000370768	NM_003902.3	301	Ata/ta	11/20	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.397754980452443	2		367	722	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444659	78444659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs908264837	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	175	521	3	ENST00000370768.2:c.30del	p.Ser11LeufsTer43	p.S11Lfs*43	ENST00000370768	NM_003902.3	10	ccC/cc	1/20	1	2	FACETS	0.806	0.741	0.873	0.806	0.741	0.873	CLONAL	1	TRUE	1	0.397754980452443	2		524	1092	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612686	228612686	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	201	657	0	ENST00000366696.1:c.341del	p.His114LeufsTer?	p.H114Lfs*?	ENST00000366696	NM_003493.2	114	cAt/ct	1/1	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.397754980452443	2		657	1006	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs121913292	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	189	313	0	ENST00000371953.3:c.389del	p.Arg130GlnfsTer4	p.R130Qfs*4	ENST00000371953	NM_000314.4	130	cGa/ca	5/9	0.397683518524376	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.397754980452443	2		313	445	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112767332	112767332	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	122	350	0	ENST00000369452.4:c.1205C>T	p.Thr402Ile	p.T402I	ENST00000369452	NM_007373.3	402	aCc/aTc	6/9	0.397683518524376	2	FACETS	1	0.968	1	0.574	0.521	0.63	CLONAL	1	TRUE	0	0.397754980452443	2		350	534	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	277	988	5	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.854	0.805	0.905	1	0.995	1	CLONAL	2	TRUE	1	0.397754980452443	2		993	815	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186743	108186743	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3218670	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	166	460	0	ENST00000278616.4:c.6101G>A	p.Arg2034Gln	p.R2034Q	ENST00000278616	NM_000051.3	2034	cGa/cAa	42/63	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.397754980452443	2		460	761	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420166	420166	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	120	472	0	ENST00000399788.2:c.3101C>A	p.Pro1034His	p.P1034H	ENST00000399788	NM_001042603.1	1034	cCt/cAt	21/28	1	2	FACETS	0.635	0.573	0.701	0.635	0.573	0.701	SUBCLONAL	1	TRUE	1	0.397754980452443	2		472	950	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420603	49420603	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	167	557	0	ENST00000301067.7:c.15146T>C	p.Leu5049Pro	p.L5049P	ENST00000301067	NM_003482.3	5049	cTg/cCg	48/54	1	2	FACETS	0.969	0.89	1	0.969	0.89	1	CLONAL	1	TRUE	1	0.397754980452443	2		557	867	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	138	466	5	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.904	0.823	0.988	0.904	0.823	0.988	CLONAL	1	TRUE	1	0.397754980452443	2		471	768	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337684	73337684	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771690280	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	114	320	7	ENST00000377767.4:c.2032del	p.Ile678PhefsTer59	p.I678Ffs*59	ENST00000377767	NM_014953.3	678	Att/tt	16/21	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.397754980452443	2		327	559	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060722	38060722	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	176	689	0	ENST00000250448.2:c.1267G>T	p.Ala423Ser	p.A423S	ENST00000250448	NM_004496.3	423	Gca/Tca	2/2	1	2	FACETS	0.883	0.813	0.956	0.883	0.813	0.956	CLONAL	1	TRUE	1	0.397754980452443	2		689	1002	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562560	95562560	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	195	563	0	ENST00000393063.1:c.4697T>C	p.Leu1566Pro	p.L1566P	ENST00000393063	NM_030621.3	1566	cTg/cCg	24/28	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.397754980452443	2		563	936	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	147	451	3	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.397754980452443	2		454	720	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51503057	51503057	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	175	411	0	ENST00000260433.2:c.1460T>C	p.Met487Thr	p.M487T	ENST00000260433		487	aTg/aCg	10/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.397754980452443	2		411	702	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310208	91310208	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs747341586	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	75	550	3	ENST00000355112.3:c.2268del	p.Asp757ThrfsTer4	p.D757Tfs*4	ENST00000355112	NM_000057.2	754	tcA/tc	10/22	1	2	FACETS	0.94	0.828	1	0.94	0.828	1	CLONAL	1	TRUE	1	0.397754980452443	2		553	401	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467855	99467856	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	81	446	0	ENST00000268035.6:c.2732_2733dup	p.Gly912LeufsTer26	p.G912Lfs*26	ENST00000268035	NM_000875.3	908	-/TC	13/21	1	2	FACETS	0.504	0.443	0.569	0.504	0.443	0.569	SUBCLONAL	1	TRUE	1	0.397754980452443	2		446	808	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	190	566	2	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.986	0.911	1	0.986	0.911	1	CLONAL	1	TRUE	1	0.397754980452443	2		568	969	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995333	15995333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768431009	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	168	459	0	ENST00000268712.3:c.2860G>A	p.Val954Met	p.V954M	ENST00000268712	NM_006311.3	954	Gtg/Atg	22/46	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.397754980452443	2		459	810	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682119	37682119	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	128	396	0	ENST00000447079.4:c.3310C>T	p.Leu1104Phe	p.L1104F	ENST00000447079	NM_015083.1	1104	Ctt/Ttt	13/14	1	2	FACETS	0.953	0.866	1	0.953	0.866	1	CLONAL	1	TRUE	1	0.397754980452443	2		396	675	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210893	36210893	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	162	639	2	ENST00000222270.7:c.649del	p.Arg217GlyfsTer22	p.R217Gfs*22	ENST00000222270	NM_014727.1	215	aCc/ac	3/37	1	2	FACETS	0.893	0.819	0.97	0.893	0.819	0.97	CLONAL	1	TRUE	1	0.397754980452443	2		641	912	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744385	41744385	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	107	461	0	ENST00000301178.4:c.1010del	p.Pro337LeufsTer29	p.P337Lfs*29	ENST00000301178	NM_021913.4	335	ggC/gg	8/20	1	2	FACETS	0.964	0.868	1	0.964	0.868	1	CLONAL	1	TRUE	1	0.397754980452443	2		461	558	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918134	50918140	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCGAC	GCCCGAC	-	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	135	546	0	ENST00000440232.2:c.2455_2461del	p.Asp819ThrfsTer67	p.D819Tfs*67	ENST00000440232	NM_002691.3	817	cgGCCCGAC/cg	20/27	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.397754980452443	2		546	640	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262550	39262550	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	161	351	0	ENST00000402219.2:c.956G>T	p.Gly319Val	p.G319V	ENST00000402219	NM_005633.3	319	gGg/gTg	7/23	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.397754980452443	2		351	622	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513282	44513287	+	inframe_deletion	In_Frame_Del	DEL	CCACCG	CCACCG	-	rs745888281	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	30	429	1	ENST00000291552.4:c.648_653del	p.Gly222_Gly223del	p.G222_G223del	ENST00000291552	NM_006758.2	216	ggCGGTGGt/ggt	8/8	1	2	FACETS	0.166	0.133	0.204	0.166	0.133	0.204	SUBCLONAL	1	TRUE	1	0.397754980452443	2		430	909	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143009	47143010	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	107	290	0	ENST00000409792.3:c.4953dup	p.Thr1652TyrfsTer14	p.T1652Yfs*14	ENST00000409792	NM_014159.6	1651	-/T	8/21	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.397754980452443	2		290	538	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403593	138403593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768628634	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	168	344	0	ENST00000289153.2:c.2189C>T	p.Ala730Val	p.A730V	ENST00000289153	NM_006219.2	730	gCc/gTc	15/22	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.397754980452443	2		344	662	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456576	138456576	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	61	308	0	ENST00000289153.2:c.774del	p.Phe258LeufsTer6	p.F258Lfs*6	ENST00000289153	NM_006219.2	258	ttT/tt	4/22	1	2	FACETS	0.682	0.589	0.781	0.682	0.589	0.781	SUBCLONAL	1	TRUE	1	0.397754980452443	2		308	450	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	126	584	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.926	0.84	1	0.926	0.84	1	CLONAL	1	TRUE	1	0.397754980452443	2		584	684	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808377	1808377	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886024	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	47	645	0	ENST00000260795.2:c.2135G>A	p.Arg712His	p.R712H	ENST00000260795		712	cGc/cAc	15/17	1	2	FACETS	0.262	0.22	0.308	0.262	0.22	0.308	SUBCLONAL	1	TRUE	1	0.397754980452443	2		645	903	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106194073	106194073	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	38	327	0	ENST00000380013.4:c.4535C>T	p.Ala1512Val	p.A1512V	ENST00000380013	NM_001127208.2	1512	gCa/gTa	10/11	1	2	FACETS	0.277	0.228	0.331	0.277	0.228	0.331	SUBCLONAL	1	TRUE	1	0.397754980452443	2		327	691	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510019	187510019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	152	503	0	ENST00000441802.2:c.13494G>A	p.Met4498Ile	p.M4498I	ENST00000441802	NM_005245.3	4498	atG/atA	27/27	1	2	FACETS	0.889	0.813	0.968	0.889	0.813	0.968	CLONAL	1	TRUE	1	0.397754980452443	2		503	860	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180643	56180646	+	frameshift_variant	Frame_Shift_Del	DEL	ATGG	ATGG	-	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	95	279	0	ENST00000399503.3:c.3976_3979del	p.Met1326GlnfsTer9	p.M1326Qfs*9	ENST00000399503	NM_005921.1	1324	gaATGG/ga	16/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.397754980452443	2		279	423	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588155	67588155	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	109	359	0	ENST00000274335.5:c.985C>T	p.Gln329Ter	p.Q329*	ENST00000274335		329	Caa/Taa	7/15	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.397754980452443	2		359	532	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	134	369	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.397754980452443	2		373	645	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564425	86564425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	158	632	0	ENST00000274376.6:c.157G>A	p.Val53Met	p.V53M	ENST00000274376	NM_002890.2	53	Gtg/Atg	1/25	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.397754980452443	2		632	769	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638251	176638251	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	170	473	0	ENST00000439151.2:c.2851G>T	p.Gly951Ter	p.G951*	ENST00000439151	NM_022455.4	951	Gga/Tga	5/23	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.397754980452443	2		473	850	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	179	680	2	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.967	0.891	1	0.967	0.891	1	CLONAL	1	TRUE	1	0.397754980452443	2		682	931	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720848	176720848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1327420643	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	187	430	0	ENST00000439151.2:c.6479C>T	p.Pro2160Leu	p.P2160L	ENST00000439151	NM_022455.4	2160	cCg/cTg	23/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.397754980452443	2		430	801	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31238011	31238011	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	168	336	0	ENST00000376228.5:c.871C>T	p.Gln291Ter	p.Q291*	ENST00000376228	NM_002117.5	291	Caa/Taa	4/8	1	2	FACETS	0.949	0.881	1	1	0.993	1	CLONAL	2	TRUE	1	0.397754980452443	2		336	445	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265511	152265511	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	165	450	0	ENST00000206249.3:c.964G>A	p.Ala322Thr	p.A322T	ENST00000206249	NM_000125.3	322	Gct/Act	4/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.397754980452443	2		450	735	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100159	157100159	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	101	499	0	ENST00000346085.5:c.1099del	p.Val367CysfsTer2	p.V367Cfs*2	ENST00000346085	NM_020732.3	366	Ggg/gg	1/20	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.397754980452443	2		499	497	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505503	157505503	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	123	443	0	ENST00000346085.5:c.3488del	p.Pro1163ArgfsTer48	p.P1163Rfs*48	ENST00000346085	NM_020732.3	1162	Ccc/cc	13/20	1	2	FACETS	0.869	0.786	0.955	0.869	0.786	0.955	CLONAL	1	TRUE	1	0.397754980452443	2		443	712	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370827	55370828	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	95	542	0	ENST00000297316.4:c.131_132dup	p.Lys45Ter	p.K45*	ENST00000297316	NM_022454.3	43	-/GT	1/2	1	2	FACETS	0.853	0.761	0.95	0.853	0.761	0.95	CLONAL	1	TRUE	1	0.397754980452443	2		542	560	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739433	145739433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762767243	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	73	521	0	ENST00000428558.2:c.1937G>A	p.Arg646His	p.R646H	ENST00000428558	NM_004260.3	646	cGc/cAc	12/22	1	2	FACETS	0.477	0.416	0.542	0.477	0.416	0.542	SUBCLONAL	1	TRUE	1	0.397754980452443	2		521	770	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400005	139400005	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1479377696	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	160	597	0	ENST00000277541.6:c.4343C>T	p.Ala1448Val	p.A1448V	ENST00000277541	NM_017617.3	1448	gCg/gTg	25/34	1	2	FACETS	0.978	0.897	1	0.978	0.897	1	CLONAL	1	TRUE	1	0.397754980452443	2		597	823	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	140	271	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.397754980452443	2		271	663	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930291	39930291	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	53	546	0	ENST00000378444.4:c.3173A>G	p.Gln1058Arg	p.Q1058R	ENST00000378444	NM_001123385.1	1058	cAg/cGg	6/15	1	2	FACETS	0.261	0.221	0.305	0.261	0.221	0.305	SUBCLONAL	1	TRUE	1	0.397754980452443	2		546	1021	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030443	47030443	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	114	436	2	ENST00000377604.3:c.221del	p.Pro74ArgfsTer60	p.P74Rfs*60	ENST00000377604	NM_001204468.1	73	tCc/tc	4/24	1	2	FACETS	0.887	0.8	0.979	0.887	0.8	0.979	CLONAL	1	TRUE	1	0.397754980452443	2		438	646	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409805	63409805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	81	468	0	ENST00000330258.3:c.3362C>T	p.Ala1121Val	p.A1121V	ENST00000330258	NM_152424.3	1121	gCc/gTc	2/2	1	2	FACETS	0.643	0.567	0.725	0.643	0.567	0.725	SUBCLONAL	1	TRUE	1	0.397754980452443	2		468	633	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0065396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	88	618	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.24	2		618	732	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699360	47699360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	106	279	0	ENST00000347630.2:c.148G>A	p.Glu50Lys	p.E50K	ENST00000347630	NM_001007230.1	50	Gaa/Aaa	4/11	0.184018886328676	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.24	2		279	395	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591118	67591129	+	inframe_deletion	In_Frame_Del	DEL	ATCCAGCTGAGA	ATCCAGCTGAGA	-	novel	NA	P-0065396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	12	330	0	ENST00000274335.5:c.1712_1723del	p.Ile571_Arg574del	p.I571_R574del	ENST00000274335		571	ATCCAGCTGAGA/-	12/15	1	2	FACETS	0.221	0.154	0.303	0.221	0.154	0.303	SUBCLONAL	1	TRUE	1	0.24	2		330	453	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416439	29416439	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	84	401	0	ENST00000389048.3:c.4514C>A	p.Pro1505Gln	p.P1505Q	ENST00000389048	NM_004304.4	1505	cCa/cAa	29/29	1	2	FACETS	0.797	0.703	0.899	0.797	0.703	0.899	SUBCLONAL	1	TRUE	1	0.24	2		401	878	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149608	202149613	+	inframe_deletion	In_Frame_Del	DEL	AAATCT	AAATCT	-	novel	NA	P-0065396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	141	425	0	ENST00000358485.4:c.1050_1055del	p.Gln350_Tyr352delinsHis	p.Q350_Y352delinsH	ENST00000358485	NM_001080125.1	350	cAAATCTat/cat	8/9	0.184018886328676	2	FACETS	0.831	0.758	0.907	0.831	0.758	0.907	CLONAL	2	TRUE	0	0.24	2		425	707	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589564	67589575	+	inframe_deletion	In_Frame_Del	DEL	GAAGCTGTAGGG	GAAGCTGTAGGG	-	novel	NA	P-0065396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	11	139	0	ENST00000274335.5:c.1327_1338del	p.Glu443_Gly446del	p.E443_G446del	ENST00000274335		443	GAAGCTGTAGGG/-	10/15	1	2	FACETS	0.521	0.36	0.72	0.521	0.36	0.72	SUBCLONAL	1	TRUE	1	0.24	2		139	176	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065397-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	224	789	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.823	0.771	0.876	0.823	0.771	0.876	CLONAL	1	TRUE	1	0.867044675063147	2		789	628	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806089	1806089	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913479	NA	P-0065397-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	680	575	0	ENST00000260795.2:c.1108G>T	p.Gly370Cys	p.G370C	ENST00000260795		370	Ggc/Tgc	8/17	0.867044675063147	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.867044675063147	2		575	762	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875096	151875096	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0065397-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	117	156	0	ENST00000262189.6:c.7443-1G>C		p.X2481_splice	ENST00000262189	NM_170606.2	2481			1	2	FACETS	0.954	0.874	1	0.954	0.874	1	CLONAL	1	TRUE	1	0.867044675063147	2		156	283	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860550	151860550	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0065397-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	405	709	0	ENST00000262189.6:c.10112C>G	p.Ser3371Ter	p.S3371*	ENST00000262189	NM_170606.2	3371	tCa/tGa	43/59	1	2	FACETS	0.998	0.954	1	0.998	0.954	1	CLONAL	1	TRUE	1	0.867044675063147	2		709	936	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677997	58677997	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065397-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	425	646	0	ENST00000305921.3:c.222G>C	p.Glu74Asp	p.E74D	ENST00000305921	NM_003620.3	74	gaG/gaC	1/6	0.852614380766504	3	FACETS	1	0.98	1	0.525	0.5	0.55	CLONAL	1	TRUE	1	0.867044675063147	3		646	1339	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0065399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	622	789	0				ENST00000310581	NM_198253.2	-/1132			0.831646605491682	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	1	0.831646605491682	4		789	913	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0065399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	248	511	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.831646605491682	2		511	500	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156606	106156606	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	331	585	0	ENST00000380013.4:c.1507G>C	p.Glu503Gln	p.E503Q	ENST00000380013	NM_001127208.2	503	Gag/Cag	3/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.831646605491682	2		585	793	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29662020	29662020	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	271	379	0	ENST00000356175.3:c.5914C>G	p.Gln1972Glu	p.Q1972E	ENST00000356175	NM_000267.3	1972	Caa/Gaa	39/57	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.831646605491682	2		379	598	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623110	52623110	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	270	484	0	ENST00000394830.3:c.2941G>A	p.Glu981Lys	p.E981K	ENST00000394830	NM_018313.4	981	Gaa/Aaa	19/30	1	2	FACETS	0.936	0.883	0.989	0.936	0.883	0.989	CLONAL	1	TRUE	1	0.831646605491682	2		484	694	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0065400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	51	465	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.176	0.148	0.206	0.176	0.148	0.206	SUBCLONAL	1	TRUE	1	0.606397865722061	2		465	957	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0065400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	223	595	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	0.763	0.711	0.817	0.763	0.711	0.817	SUBCLONAL	1	TRUE	1	0.606397865722061	2		595	964	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591125	67591126	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAGAAAGAC	novel	NA	P-0065400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	157	378	0	ENST00000274335.5:c.1723_1731dup	p.Lys575_Arg577dup	p.K575_R577dup	ENST00000274335		575	ctg/ctGAGAAAGACg	12/15	1	2	FACETS	0.769	0.707	0.834	0.769	0.707	0.834	SUBCLONAL	1	TRUE	1	0.606397865722061	2		378	673	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720671	89720671	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587782607	NA	P-0065400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	51	143	0	ENST00000371953.3:c.822G>A	p.Trp274Ter	p.W274*	ENST00000371953	NM_000314.4	274	tgG/tgA	8/9	0.606397865722061	3	FACETS	0.809	0.693	0.934	0.404	0.346	0.467	CLONAL	1	TRUE	1	0.606397865722061	3		143	271	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953748	48953748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759079385	NA	P-0065400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	133	201	0	ENST00000267163.4:c.1351C>T	p.Arg451Cys	p.R451C	ENST00000267163	NM_000321.2	451	Cgc/Tgc	14/27	1	2	FACETS	0.947	0.867	1	0.947	0.867	1	CLONAL	1	TRUE	1	0.606397865722061	2		201	463	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685269	89685269	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0065400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	177	231	0	ENST00000371953.3:c.165-1G>T		p.X55_splice	ENST00000371953	NM_000314.4	55			0.606397865722061	3	FACETS	0.876	0.817	0.937	0.876	0.817	0.937	CLONAL	2	TRUE	1	0.606397865722061	3		231	434	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058068	27058068	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	283	502	0	ENST00000324856.7:c.1777del	p.Ser593ProfsTer26	p.S593Pfs*26	ENST00000324856	NM_006015.4	592	taT/ta	3/20	1	2	FACETS	0.968	0.911	1	0.968	0.911	1	CLONAL	1	TRUE	1	0.606397865722061	2		502	964	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29108003	29108003	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs778212685	NA	P-0065400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	170	335	0	ENST00000328354.6:c.686G>T	p.Gly229Val	p.G229V	ENST00000328354	NM_007194.3	229	gGt/gTt	6/15	1	2	FACETS	0.925	0.855	0.998	0.925	0.855	0.998	CLONAL	1	TRUE	1	0.606397865722061	2		335	606	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589156	67589157	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0065400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	56	325	0	ENST00000274335.5:c.1146_1147del	p.Lys382AsnfsTer12	p.K382Nfs*12	ENST00000274335		382	AAa/a	9/15	1	2	FACETS	0.506	0.435	0.583	0.506	0.435	0.583	SUBCLONAL	1	TRUE	1	0.606397865722061	2		325	365	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849993	151849993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749141132	NA	P-0065400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	186	480	0	ENST00000262189.6:c.12323G>A	p.Arg4108Gln	p.R4108Q	ENST00000262189	NM_170606.2	4108	cGa/cAa	49/59	1	2	FACETS	0.673	0.621	0.726	0.673	0.621	0.726	SUBCLONAL	1	TRUE	1	0.606397865722061	2		480	912	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520176	9520176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	225	551	0	ENST00000353224.5:c.2093C>T	p.Pro698Leu	p.P698L	ENST00000353224	NM_177990.2	698	cCa/cTa	10/10	1	2	FACETS	0.885	0.829	0.942	0.885	0.829	0.942	CLONAL	1	TRUE	1	0.782534249270922	2		551	650	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976741	2976741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564294642	NA	P-0065404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	237	705	0	ENST00000396946.4:c.1271G>A	p.Arg424Gln	p.R424Q	ENST00000396946	NM_032415.4	424	cGg/cAg	9/25	1	2	FACETS	0.93	0.874	0.988	0.93	0.874	0.988	CLONAL	1	TRUE	1	0.782534249270922	2		705	651	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39708783	39708783	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	156	53	0	ENST00000361337.2:c.394G>T	p.Asp132Tyr	p.D132Y	ENST00000361337	NM_003286.2	132	Gat/Tat	6/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.782534249270922	2		53	371	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779598	3779598	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	301	895	2	ENST00000262367.5:c.5450C>T	p.Pro1817Leu	p.P1817L	ENST00000262367	NM_004380.2	1817	cCg/cTg	31/31	1	2	FACETS	0.958	0.907	1	0.958	0.907	1	CLONAL	1	TRUE	1	0.782534249270922	2		897	803	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598065	52598065	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0065404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	201	151	0	ENST00000394830.3:c.3800+1G>A		p.X1267_splice	ENST00000394830	NM_018313.4	1267			0.781447309450106	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.782534249270922	1		151	297	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46724358	46724358	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	190	215	0	ENST00000371975.4:c.211G>A	p.Glu71Lys	p.E71K	ENST00000371975	NM_003579.3	71	Gaa/Aaa	4/18	1	2	FACETS	0.995	0.929	1	0.995	0.929	1	CLONAL	1	TRUE	1	0.782534249270922	2		215	488	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555300	226555300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	269	654	0	ENST00000366794.5:c.2287G>A	p.Glu763Lys	p.E763K	ENST00000366794	NM_001618.3	763	Gaa/Aaa	17/23	1	2	FACETS	0.929	0.876	0.983	0.929	0.876	0.983	CLONAL	1	TRUE	1	0.782534249270922	2		654	740	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945021	31945021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	333	846	0	ENST00000340398.3:c.80G>A	p.Arg27Lys	p.R27K	ENST00000340398	NM_001013699.2	27	aGg/aAg	1/1	1	2	FACETS	0.97	0.921	1	0.97	0.921	1	CLONAL	1	TRUE	1	0.782534249270922	2		846	877	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191207	2191207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	272	698	0	ENST00000398665.3:c.461C>T	p.Thr154Ile	p.T154I	ENST00000398665	NM_032482.2	154	aCc/aTc	5/28	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.782534249270922	2		698	686	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961033	18961092	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGTGGTGCTGCTGTGCAGGTGAGTGGTCCCCAGATGTCTCCTGGGGGTGACCTTTAAGC	TGGTGGTGCTGCTGTGCAGGTGAGTGGTCCCCAGATGTCTCCTGGGGGTGACCTTTAAGC	-	novel	NA	P-0065404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	187	599	0	ENST00000262803.5:c.612_629+42del		p.X204_splice	ENST00000262803	NM_002911.3	204		4/24	1	2	FACETS	0.814	0.757	0.873	0.814	0.757	0.873	CLONAL	1	TRUE	1	0.782534249270922	2		599	587	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924790	49924790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	348	868	0	ENST00000296474.3:c.4153G>A	p.Gly1385Arg	p.G1385R	ENST00000296474	NM_002447.2	1385	Ggg/Agg	20/20	0.781447309450106	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.782534249270922	1		868	505	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340199	116340199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	283	514	0	ENST00000397752.3:c.1061C>T	p.Ala354Val	p.A354V	ENST00000397752	NM_000245.2	354	gCc/gTc	2/21	0.1368496537499	4	FACETS	0.914	0.865	0.965	0.914	0.865	0.965	INDETERMINATE	2	TRUE	2	0.782534249270922	4		514	705	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129903	69129904	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0065404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	224	707	0	ENST00000288368.4:c.4657_4658delinsAA	p.Gly1553Lys	p.G1553K	ENST00000288368	NM_024870.2	1553	GGa/AAa	38/40	1	2	FACETS	0.823	0.769	0.877	0.823	0.769	0.877	CLONAL	1	TRUE	1	0.782534249270922	2		707	696	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730453	133730453	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	202	466	0	ENST00000318560.5:c.519T>A	p.His173Gln	p.H173Q	ENST00000318560	NM_005157.4	173	caT/caA	3/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.782534249270922	2		466	496	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874423	76874423	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	94	57	0	ENST00000373344.5:c.5299G>A	p.Glu1767Lys	p.E1767K	ENST00000373344	NM_000489.3	1767	Gaa/Aaa	21/35	0.782534249270922	3	FACETS	0.774	0.703	0.845			1	SUBCLONAL	2	TRUE	NA	0.782534249270922	3		57	216	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0065406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	97	393	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.206661932795427	2	FACETS	0.805	0.722	0.892	0.805	0.722	0.892	CLONAL	2	TRUE	0	0.279061033817498	2		393	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782177	NA	P-0065406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	215	780	0	ENST00000269305.4:c.644G>T	p.Ser215Ile	p.S215I	ENST00000269305	NM_001126112.2	215	aGt/aTt	6/11	0.206661932795427	2	FACETS	0.767	0.712	0.823	0.767	0.712	0.823	SUBCLONAL	2	TRUE	0	0.279061033817498	2		780	1005	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088718	27088719	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	181	688	0	ENST00000324856.7:c.2329dup	p.Ser777PhefsTer40	p.S777Ffs*40	ENST00000324856	NM_006015.4	776	cct/ccTt	7/20	0.206661932795427	2	FACETS	1	0.989	1	0.717	0.662	0.775	CLONAL	1	TRUE	0	0.279061033817498	2		688	904	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134978	2134978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746246149	NA	P-0065407-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	264	736	0	ENST00000219476.3:c.4520C>T	p.Ser1507Phe	p.S1507F	ENST00000219476	NM_000548.3	1507	tCc/tTc	35/42	1	2	FACETS	0.981	0.922	1	0.981	0.922	1	CLONAL	1	TRUE	1	0.610638103381987	2		736	881	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479160	50479160	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065407-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	39	591	0	ENST00000394963.4:c.8C>A	p.Ala3Asp	p.A3D	ENST00000394963	NM_003076.4	3	gCc/gAc	1/13	1	2	FACETS	0.203	0.168	0.243	0.203	0.168	0.243	SUBCLONAL	1	TRUE	1	0.610638103381987	2		591	628	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162702	47162702	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065407-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	106	427	0	ENST00000409792.3:c.3424del	p.Glu1142LysfsTer12	p.E1142Kfs*12	ENST00000409792	NM_014159.6	1142	Gaa/aa	3/21	1	2	FACETS	0.793	0.715	0.874	0.793	0.715	0.874	SUBCLONAL	1	TRUE	1	0.610638103381987	2		427	438	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593635	55593661	+	inframe_deletion	In_Frame_Del	DEL	TTATGTTTACATAGACCCAACACAACT	TTATGTTTACATAGACCCAACACAACT	-	novel	NA	P-0065408-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	381	496	0	ENST00000288135.5:c.1702_1728del	p.Tyr568_Leu576del	p.Y568_L576del	ENST00000288135	NM_000222.2	567	aaTTATGTTTACATAGACCCAACACAACTt/aat	11/21	0.885862138000641	1	FACETS	0.986	0.957	1	0.986	0.957	1	CLONAL	1	TRUE	0	0.885862138000641	1		496	486	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0065409-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	52	393	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.983	0.84	1	0.983	0.84	1	CLONAL	1	TRUE	1	0.28	2		393	378	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222173	5222173	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065409-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	85	564	0	ENST00000357368.4:c.3162G>A	p.Trp1054Ter	p.W1054*	ENST00000357368	NM_002850.3	1054	tgG/tgA	19/38	1	2	FACETS	0.992	0.878	1	0.992	0.878	1	CLONAL	1	TRUE	1	0.28	2		564	612	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713271	30713271	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0065409-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	68	717	0	ENST00000295754.5:c.596C>G	p.Ser199Ter	p.S199*	ENST00000295754	NM_003242.5	199	tCa/tGa	4/7	1	2	FACETS	0.723	0.628	0.825	0.723	0.628	0.825	SUBCLONAL	1	TRUE	1	0.28	2		717	672	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715707	30715707	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065409-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	60	561	0	ENST00000295754.5:c.1365G>A	p.Trp455Ter	p.W455*	ENST00000295754	NM_003242.5	455	tgG/tgA	5/7	1	2	FACETS	0.749	0.646	0.862	0.749	0.646	0.862	SUBCLONAL	1	TRUE	1	0.28	2		561	572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1131691023	NA	P-0065425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	130	980	0	ENST00000269305.4:c.470T>A	p.Val157Asp	p.V157D	ENST00000269305	NM_001126112.2	157	gTc/gAc	5/11	0.32297783301559	1	FACETS	0.939	0.853	1	0.939	0.853	1	CLONAL	1	TRUE	0	0.32297783301559	1		980	719	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18963068	18963069	+	missense_variant	Missense_Mutation	DNP	TG	TG	CT	novel	NA	P-0065425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	102	798	1	ENST00000262803.5:c.935_936delinsCT	p.Leu312Pro	p.L312P	ENST00000262803	NM_002911.3	312	cTG/cCT	6/24	0.319050652003321	2	FACETS	0.953	0.853	1	0.476	0.426	0.529	CLONAL	1	TRUE	0	0.32297783301559	2		799	663	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0065426-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	335	441	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		441	647	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738792	145738792	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748416710	NA	P-0065426-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1858	108	1085	0	ENST00000428558.2:c.2273G>A	p.Arg758Gln	p.R758Q	ENST00000428558	NM_004260.3	758	cGa/cAa	14/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1085	1966	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260142	19260142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779592456	NA	P-0065426-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	396	636	4	ENST00000162023.5:c.151G>A	p.Ala51Thr	p.A51T	ENST00000162023		51	Gcc/Acc	7/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		640	699	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0065428-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	74	552	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.904	0.792	1	0.904	0.792	1	CLONAL	1	FALSE	1	0.276413819204383	2		552	592	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853184	68853185	+	stop_gained,frameshift_variant,splice_region_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0065428-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	28	693	0	ENST00000261769.5:c.1568dup	p.Tyr523Ter	p.Y523*	ENST00000261769	NM_004360.3	523	tat/tAat	11/16	1	2	FACETS	0.492	0.393	0.605	0.492	0.393	0.605	SUBCLONAL	1	FALSE	1	0.276413819204383	2		693	412	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645920	67645920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567609067	NA	P-0065428-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	20	730	0	ENST00000264010.4:c.848G>A	p.Arg283His	p.R283H	ENST00000264010	NM_006565.3	283	cGt/cAt	4/12	1	2	FACETS	0.368	0.281	0.471	0.368	0.281	0.471	SUBCLONAL	1	FALSE	1	0.276413819204383	2		730	393	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070567	67070567	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065428-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	44	660	0	ENST00000412916.2:c.191T>C	p.Leu64Pro	p.L64P	ENST00000412916		64	cTg/cCg	3/6	1	2	FACETS	0.812	0.682	0.955	0.812	0.682	0.955	CLONAL	1	FALSE	1	0.276413819204383	2		660	392	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729942	41729942	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200425294	NA	P-0065456-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	104	685	0	ENST00000242208.4:c.587G>A	p.Gly196Asp	p.G196D	ENST00000242208	NM_002192.2	196	gGc/gAc	3/3	1	2	FACETS	0.982	0.878	1	0.982	0.878	1	CLONAL	1	TRUE	1	0.23	2		685	921	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151932982	151932982	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs772146328	NA	P-0065456-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	24	106	0	ENST00000262189.6:c.2689C>T	p.Arg897Ter	p.R897*	ENST00000262189	NM_170606.2	897	Cga/Tga	16/59	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.23	2		106	166	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150919387	150919387	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065456-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	79	570	0	ENST00000271640.5:c.1166A>G	p.Tyr389Cys	p.Y389C	ENST00000271640	NM_001145415.1	389	tAt/tGt	10/22	1	2	FACETS	0.897	0.788	1	0.897	0.788	1	CLONAL	1	TRUE	1	0.23	2		570	766	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636864	73636865	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065456-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	105	551	0	ENST00000377687.4:c.1129dup	p.Tyr377LeufsTer24	p.Y377Lfs*24	ENST00000377687	NM_001730.3	376	gat/gaTt	2/4	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.23	2		551	909	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696716	47696716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	201	421	0	ENST00000347630.2:c.232G>A	p.Glu78Lys	p.E78K	ENST00000347630	NM_001007230.1	78	Gaa/Aaa	5/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.695565561917127	2		421	529	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	120	624	1	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.656	0.595	0.72	0.656	0.595	0.72	SUBCLONAL	1	TRUE	1	0.695565561917127	2		625	526	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	38	690	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.181	0.149	0.216	0.181	0.149	0.216	SUBCLONAL	1	TRUE	1	0.695565561917127	2		691	605	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	62	988	5	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.226	0.194	0.26	0.226	0.194	0.26	SUBCLONAL	1	TRUE	1	0.695565561917127	2		993	790	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143009	47143010	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	29	290	0	ENST00000409792.3:c.4953dup	p.Thr1652TyrfsTer14	p.T1652Yfs*14	ENST00000409792	NM_014159.6	1651	-/T	8/21	1	2	FACETS	0.222	0.178	0.272	0.222	0.178	0.272	SUBCLONAL	1	TRUE	1	0.695565561917127	2		290	376	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	144	369	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.892	0.82	0.967	0.892	0.82	0.967	CLONAL	1	TRUE	1	0.695565561917127	2		373	464	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100175	27100176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	220	652	0	ENST00000324856.7:c.3977dup	p.Gln1327AlafsTer11	p.Q1327Afs*11	ENST00000324856	NM_006015.4	1324	tac/taCc	16/20	1	2	FACETS	0.774	0.722	0.828	0.774	0.722	0.828	SUBCLONAL	1	TRUE	1	0.695565561917127	2		652	817	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	42	562	1	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.157	0.13	0.187	0.157	0.13	0.187	SUBCLONAL	1	TRUE	1	0.695565561917127	2		563	770	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	27	369	0	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	1	2	FACETS	0.199	0.158	0.245	0.199	0.158	0.245	SUBCLONAL	1	TRUE	1	0.695565561917127	2		369	391	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913237	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	147	360	0	ENST00000369535.4:c.35G>C	p.Gly12Ala	p.G12A	ENST00000369535	NM_002524.4	12	gGt/gCt	2/7	1	2	FACETS	0.864	0.795	0.936	0.864	0.795	0.936	CLONAL	1	TRUE	1	0.695565561917127	2		360	489	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589147	67589147	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	15	370	0	ENST00000274335.5:c.1135A>G	p.Lys379Glu	p.K379E	ENST00000274335		379	Aaa/Gaa	9/15	1	2	FACETS	0.182	0.133	0.241	0.182	0.133	0.241	SUBCLONAL	1	TRUE	1	0.695565561917127	2		370	237	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210735	2210735	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1238067958	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	53	710	1	ENST00000398665.3:c.1232G>A	p.Arg411His	p.R411H	ENST00000398665	NM_032482.2	411	cGc/cAc	14/28	1	2	FACETS	0.195	0.166	0.228	0.195	0.166	0.228	SUBCLONAL	1	TRUE	1	0.695565561917127	2		711	781	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533939	63533940	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs771001164	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	30	523	3	ENST00000307078.5:c.1214_1215del	p.Glu405GlyfsTer56	p.E405Gfs*56	ENST00000307078	NM_004655.3	405	gAG/g	6/11	1	2	FACETS	0.152	0.122	0.186	0.152	0.122	0.186	SUBCLONAL	1	TRUE	1	0.695565561917127	2		526	568	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258802	16258802	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs115691599	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	39	669	0	ENST00000375759.3:c.6067G>A	p.Val2023Met	p.V2023M	ENST00000375759	NM_015001.2	2023	Gtg/Atg	11/15	1	2	FACETS	0.147	0.121	0.176	0.147	0.121	0.176	SUBCLONAL	1	TRUE	1	0.695565561917127	2		669	765	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	176	750	0	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.618	0.57	0.668	0.618	0.57	0.668	SUBCLONAL	1	TRUE	1	0.695565561917127	2		750	819	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041262	29041262	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	28	434	1	ENST00000282397.4:c.166del	p.Glu56LysfsTer12	p.E56Kfs*12	ENST00000282397	NM_002019.4	56	Gaa/aa	3/30	1	2	FACETS	0.153	0.122	0.189	0.153	0.122	0.189	SUBCLONAL	1	TRUE	1	0.695565561917127	2		435	526	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197847	66197847	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	120	272	0	ENST00000273854.3:c.2853-1G>A		p.X951_splice	ENST00000273854	NM_004439.5	951			1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.695565561917127	2		272	341	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907720	76907720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	167	420	0	ENST00000373344.5:c.4441C>T	p.Arg1481Trp	p.R1481W	ENST00000373344	NM_000489.3	1481	Cgg/Tgg	15/35	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.695565561917127	2		420	467	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942195	71942195	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	38	611	0	ENST00000298229.2:c.1463del	p.Gly488AlafsTer43	p.G488Afs*43	ENST00000298229	NM_001567.3	487	Ggg/gg	12/28	1	2	FACETS	0.169	0.139	0.202	0.169	0.139	0.202	SUBCLONAL	1	TRUE	1	0.695565561917127	2		611	648	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187560922	187560922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769544525	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	75	388	0	ENST00000441802.2:c.3596C>T	p.Thr1199Met	p.T1199M	ENST00000441802	NM_005245.3	1199	aCg/aTg	4/27	1	2	FACETS	0.419	0.367	0.474	0.419	0.367	0.474	SUBCLONAL	1	TRUE	1	0.695565561917127	2		388	515	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040641	16040641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	24	280	0	ENST00000268712.3:c.1493G>A	p.Arg498His	p.R498H	ENST00000268712	NM_006311.3	498	cGc/cAc	14/46	1	2	FACETS	0.219	0.172	0.274	0.219	0.172	0.274	SUBCLONAL	1	TRUE	1	0.695565561917127	2		280	315	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386378	31386378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200193299	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	39	549	0	ENST00000328111.2:c.1603G>A	p.Val535Ile	p.V535I	ENST00000328111	NM_006892.3	535	Gtc/Atc	15/23	1	2	FACETS	0.188	0.155	0.225	0.188	0.155	0.225	SUBCLONAL	1	TRUE	1	0.695565561917127	2		549	596	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351594	89351595	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	133	587	0	ENST00000301030.4:c.1355dup	p.Asn452LysfsTer2	p.N452Kfs*2	ENST00000301030	NM_001256183.1	452	aat/aaAt	9/13	1	2	FACETS	0.575	0.523	0.629	0.575	0.523	0.629	SUBCLONAL	1	TRUE	1	0.695565561917127	2		587	665	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155727	119155727	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	162	562	1	ENST00000264033.4:c.1484del	p.Pro495ArgfsTer120	p.P495Rfs*120	ENST00000264033	NM_005188.3	494	Ccc/cc	10/16	1	2	FACETS	0.588	0.54	0.638	0.588	0.54	0.638	SUBCLONAL	1	TRUE	1	0.695565561917127	2		563	792	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	107	418	0	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	0.485	0.436	0.538	0.485	0.436	0.538	SUBCLONAL	1	TRUE	1	0.695565561917127	2		418	634	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857427	68857428	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs587781276	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	33	430	0	ENST00000261769.5:c.2064_2065del	p.Cys688Ter	p.C688*	ENST00000261769	NM_004360.3	688	TGt/t	13/16	1	2	FACETS	0.165	0.133	0.2	0.165	0.133	0.2	SUBCLONAL	1	TRUE	1	0.695565561917127	2		430	576	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023923	27023936	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTGCGGCGGCGG	AGCTGCGGCGGCGG	-	novel	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	204	591	0	ENST00000324856.7:c.1029_1042del	p.Ala344ArgfsTer51	p.A344Rfs*51	ENST00000324856	NM_006015.4	343	gcAGCTGCGGCGGCGGcc/gccc	1/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.695565561917127	2		591	567	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624265	89624266	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGGAGATATCAAG	novel	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	56	207	0	ENST00000371953.3:c.44_56dup	p.Asp19GlufsTer29	p.D19Efs*29	ENST00000371953	NM_000314.4	13	-/AGGAGATATCAAG	1/9	1	2	FACETS	0.988	0.864	1	0.988	0.864	1	CLONAL	1	TRUE	1	0.695565561917127	2		207	163	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219199	94219199	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	136	359	0	ENST00000323929.3:c.205A>G	p.Arg69Gly	p.R69G	ENST00000323929	NM_005591.3	69	Agg/Ggg	4/20	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.695565561917127	2		359	389	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350209	89350209	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	237	605	0	ENST00000301030.4:c.2741A>C	p.Asp914Ala	p.D914A	ENST00000301030	NM_001256183.1	914	gAt/gCt	9/13	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.695565561917127	2		605	678	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223120	1223121	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	231	552	0	ENST00000326873.7:c.1059_1060del	p.Phe354ArgfsTer5	p.F354Rfs*5	ENST00000326873	NM_000455.4	353	CTc/c	8/10	1	2	FACETS	0.984	0.922	1	0.984	0.922	1	CLONAL	1	TRUE	1	0.695565561917127	2		552	675	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943411	17943411	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	52	570	0	ENST00000458235.1:c.2597G>T	p.Arg866Met	p.R866M	ENST00000458235	NM_000215.3	866	aGg/aTg	19/24	1	2	FACETS	0.234	0.199	0.273	0.234	0.199	0.273	SUBCLONAL	1	TRUE	1	0.695565561917127	2		570	639	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794020	42794020	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs768530128	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	34	513	0	ENST00000575354.2:c.1381A>G	p.Thr461Ala	p.T461A	ENST00000575354	NM_015125.3	461	Act/Gct	9/20	1	2	FACETS	0.167	0.136	0.202	0.167	0.136	0.202	SUBCLONAL	1	TRUE	1	0.695565561917127	2		513	585	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169314	99169314	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	122	544	0	ENST00000074304.5:c.1244T>C	p.Ile415Thr	p.I415T	ENST00000074304	NM_001134224.1	415	aTc/aCc	15/26	1	2	FACETS	0.519	0.47	0.571	0.519	0.47	0.571	SUBCLONAL	1	TRUE	1	0.695565561917127	2		544	676	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37628931	37628931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	127	440	0	ENST00000249071.6:c.135G>A	p.Met45Ile	p.M45I	ENST00000249071	NM_002872.4	45	atG/atA	3/7	1	2	FACETS	0.739	0.673	0.808	0.739	0.673	0.808	SUBCLONAL	1	TRUE	1	0.695565561917127	2		440	494	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156969	89156969	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	30	378	0	ENST00000336596.2:c.71C>A	p.Pro24Gln	p.P24Q	ENST00000336596	NM_005233.5	24	cCg/cAg	1/17	1	2	FACETS	0.179	0.143	0.219	0.179	0.143	0.219	SUBCLONAL	1	TRUE	1	0.695565561917127	2		378	483	SUCCESS
ATR	545	MSKCC	GRCh37	3	142189011	142189011	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	74	309	0	ENST00000350721.4:c.6236G>T	p.Gly2079Val	p.G2079V	ENST00000350721	NM_001184.3	2079	gGa/gTa	37/47	1	2	FACETS	0.967	0.861	1	0.967	0.861	1	CLONAL	1	TRUE	1	0.695565561917127	2		309	220	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168479	56168479	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	75	291	0	ENST00000399503.3:c.1435T>C	p.Cys479Arg	p.C479R	ENST00000399503	NM_005921.1	479	Tgt/Cgt	8/20	1	2	FACETS	0.693	0.613	0.778	0.693	0.613	0.778	SUBCLONAL	1	TRUE	1	0.695565561917127	2		291	311	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202313	138202313	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	170	628	0	ENST00000237289.4:c.2230G>T	p.Gly744Cys	p.G744C	ENST00000237289	NM_001270507.1	744	Ggc/Tgc	9/9	1	2	FACETS	0.702	0.648	0.759	0.702	0.648	0.759	SUBCLONAL	1	TRUE	1	0.695565561917127	2		628	696	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38135907	38135907	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	131	389	0	ENST00000317025.8:c.3784A>G	p.Asn1262Asp	p.N1262D	ENST00000317025	NM_023034.1	1262	Aac/Gac	22/24	1	2	FACETS	0.723	0.659	0.789	0.723	0.659	0.789	SUBCLONAL	1	TRUE	1	0.695565561917127	2		389	521	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0065459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	4672	565	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.383014870041852	30	FACETS	1	0.995	1			1	CLONAL	30	TRUE	NA	0.383014870041852	30		565	5170	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738993	145738993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558451720	NA	P-0065459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	98	764	0	ENST00000428558.2:c.2162G>A	p.Arg721Gln	p.R721Q	ENST00000428558	NM_004260.3	721	cGa/cAa	13/22	0.383014870041852	1	FACETS	0.568	0.506	0.633	0.568	0.506	0.633	SUBCLONAL	1	TRUE	0	0.383014870041852	1		764	729	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274911	41274911	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs868651538	NA	P-0065459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	38	508	0	ENST00000349496.5:c.1161T>A	p.Asn387Lys	p.N387K	ENST00000349496	NM_001904.3	387	aaT/aaA	8/15	1	2	FACETS	0.274	0.226	0.329	0.274	0.226	0.329	SUBCLONAL	1	TRUE	1	0.383014870041852	2		508	724	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138885	64138885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1382584499	NA	P-0065459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	68	509	0	ENST00000334205.4:c.2252C>T	p.Pro751Leu	p.P751L	ENST00000334205	NM_003942.2	751	cCg/cTg	17/17	0.226620896618529	1	FACETS	0.56	0.488	0.637	0.56	0.488	0.637	INDETERMINATE	1	TRUE	0	0.383014870041852	1		509	513	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349640	89349641	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs772267579	NA	P-0065459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	111	549	3	ENST00000301030.4:c.3309dup	p.Asp1104ArgfsTer2	p.D1104Rfs*2	ENST00000301030	NM_001256183.1	1103	-/A	9/13	0.275979054868715	1	FACETS	0.772	0.696	0.853	0.772	0.696	0.853	SUBCLONAL	1	TRUE	0	0.383014870041852	1		552	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578210	7578212	+	missense_variant	Missense_Mutation	TNP	TCG	TCG	CCA	novel	NA	P-0065459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	143	595	0	ENST00000269305.4:c.637_639delinsTGG	p.Arg213Trp	p.R213W	ENST00000269305	NM_001126112.2	213	CGA/TGG	6/11	0.383014870041852	1	FACETS	0.948	0.867	1	0.948	0.867	1	CLONAL	1	TRUE	0	0.383014870041852	1		595	637	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600427	43600427	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1197513567	NA	P-0065459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	47	664	0	ENST00000355710.3:c.653C>A	p.Pro218Gln	p.P218Q	ENST00000355710	NM_020975.4	218	cCg/cAg	4/20	1	2	FACETS	0.32	0.269	0.376	0.32	0.269	0.376	SUBCLONAL	1	TRUE	1	0.383014870041852	2		664	767	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057642	27057642	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0065459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	176	521	0	ENST00000324856.7:c.1351-1G>A		p.X451_splice	ENST00000324856	NM_006015.4	451			0.345494995286545	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.383014870041852	1		521	572	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681438	88681438	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659155	NA	P-0065459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	33	327	0	ENST00000372037.3:c.1328G>A	p.Arg443His	p.R443H	ENST00000372037	NM_004329.2	443	cGt/cAt	11/13	0.226620896618529	1	FACETS	0.355	0.289	0.43	0.355	0.289	0.43	INDETERMINATE	1	TRUE	0	0.383014870041852	1		327	392	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277955	41277955	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	41	534	0	ENST00000349496.5:c.1919T>C	p.Leu640Pro	p.L640P	ENST00000349496	NM_001904.3	640	cTg/cCg	12/15	1	2	FACETS	0.306	0.254	0.364	0.306	0.254	0.364	SUBCLONAL	1	TRUE	1	0.383014870041852	2		534	700	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607611	43607611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0065459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	58	1173	0	ENST00000355710.3:c.1588del	p.Glu530SerfsTer108	p.E530Sfs*108	ENST00000355710	NM_020975.4	529	gaG/ga	8/20	1	2	FACETS	0.287	0.245	0.332	0.287	0.245	0.332	SUBCLONAL	1	TRUE	1	0.383014870041852	2		1173	1056	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26956976	26956976	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	82	345	0	ENST00000381527.3:c.482G>A	p.Gly161Asp	p.G161D	ENST00000381527	NM_001260.1	161	gGt/gAt	5/13	0.275979054868715	1	FACETS	0.686	0.606	0.77	0.686	0.606	0.77	SUBCLONAL	1	TRUE	0	0.383014870041852	1		345	505	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829892	72829892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs967126857	NA	P-0065459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	49	548	0	ENST00000268489.5:c.6689C>T	p.Ser2230Leu	p.S2230L	ENST00000268489	NM_006885.3	2230	tCg/tTg	9/10	0.275979054868715	1	FACETS	0.307	0.26	0.36	0.307	0.26	0.36	SUBCLONAL	1	TRUE	0	0.383014870041852	1		548	673	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573426	48573426	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	32	458	0	ENST00000342988.3:c.10A>G	p.Met4Val	p.M4V	ENST00000342988	NM_005359.5	4	Atg/Gtg	2/12	0.311284640846301	0	FACETS	0.226	0.183	0.274			1	SUBCLONAL	1	TRUE	0	0.383014870041852	0		458	457	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46254145	46254145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	36	345	0	ENST00000371998.3:c.277G>A	p.Asp93Asn	p.D93N	ENST00000371998		93	Gat/Aat	5/23	0.207305872277504	1	FACETS	0.316	0.259	0.38	0.316	0.259	0.38	INDETERMINATE	1	TRUE	0	0.383014870041852	1		345	481	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578529	7578529	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065460-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	221	592	0	ENST00000269305.4:c.401T>C	p.Phe134Ser	p.F134S	ENST00000269305	NM_001126112.2	134	tTt/tCt	5/11	0.52891067697956	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.518823506690067	1		592	469	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484129	8484129	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065460-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	108	384	0	ENST00000356435.5:c.3403G>C	p.Glu1135Gln	p.E1135Q	ENST00000356435		1135	Gag/Cag	19/35	0.130569751400762	3	FACETS	1	0.966	1	0.385	0.347	0.424	INDETERMINATE	1	TRUE	0	0.518823506690067	3		384	454	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965489	90965489	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065460-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	105	385	0	ENST00000265433.3:c.1828G>A	p.Glu610Lys	p.E610K	ENST00000265433	NM_002485.4	610	Gaa/Aaa	11/16	0.52891067697956	3	FACETS	0.907	0.815	1	0.454	0.407	0.502	CLONAL	1	TRUE	1	0.518823506690067	3		385	562	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230468640	230468640	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065460-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	184	556	0	ENST00000391860.1:c.878A>T	p.Asn293Ile	p.N293I	ENST00000391860	NM_001258311.1	293	aAc/aTc	5/7	0.370186554639765	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.518823506690067	1		556	459	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655421	67655421	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0065460-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	141	409	0	ENST00000264010.4:c.1284G>C	p.Gln428His	p.Q428H	ENST00000264010	NM_006565.3	428	caG/caC	7/12	0.52891067697956	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.518823506690067	1		409	338	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732314	74732314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0065460-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	265	559	0	ENST00000359995.5:c.595del	p.Glu199AsnfsTer33	p.E199Nfs*33	ENST00000359995	NM_001195427.1	199	Gaa/aa	2/3	0.52891067697956	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.518823506690067	1		559	574	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568599	41568599	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065460-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	89	462	0	ENST00000263253.7:c.4549A>G	p.Ile1517Val	p.I1517V	ENST00000263253	NM_001429.3	1517	Att/Gtt	28/31	0.306132067195857	1	FACETS	0.551	0.491	0.615	0.551	0.491	0.615	INDETERMINATE	1	TRUE	0	0.518823506690067	1		462	461	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201665	66201665	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065460-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	68	441	0	ENST00000273854.3:c.2837T>C	p.Val946Ala	p.V946A	ENST00000273854	NM_004439.5	946	gTt/gCt	16/18	0.370186554639765	1	FACETS	0.502	0.438	0.569	0.502	0.438	0.569	SUBCLONAL	1	TRUE	0	0.518823506690067	1		441	387	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598082	52598082	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065465-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	171	454	0	ENST00000394830.3:c.3784G>C	p.Glu1262Gln	p.E1262Q	ENST00000394830	NM_018313.4	1262	Gaa/Caa	24/30	0.502431515523911	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.502431515523911	1		454	458	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515086	148515086	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065465-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	234	601	0	ENST00000320356.2:c.1123A>T	p.Ile375Phe	p.I375F	ENST00000320356	NM_004456.4	375	Att/Ttt	10/20	0.502431515523911	2	FACETS	1	0.961	1	0.52	0.485	0.555	CLONAL	1	TRUE	0	0.502431515523911	2		601	896	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577152	7577152	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	TG	novel	NA	P-0065465-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	221	550	2	ENST00000269305.4:c.786delinsCA	p.Asn263LysfsTer9	p.N263Kfs*9	ENST00000269305	NM_001126112.2	262	ggT/ggCA	8/11	0.502431515523911	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.502431515523911	1		552	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577068	7577068	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005450-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	289	383	0	ENST00000269305.4:c.870del	p.Lys291ArgfsTer54	p.K291Rfs*54	ENST00000269305	NM_001126112.2	290	cgC/cg	8/11	0.763777108072784	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.763777108072784	1		383	453	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133815	55133815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005450-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	8578	333	0	ENST00000257290.5:c.1028C>T	p.Pro343Leu	p.P343L	ENST00000257290	NM_006206.4	343	cCa/cTa	7/23	0.763777108072784	32	FACETS	1	0.999	1	0.983	0.979	0.986	CLONAL	30	TRUE	1	0.763777108072784	32		333	9185	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101374	27101374	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	195	524	0	ENST00000324856.7:c.4656G>T	p.Gln1552His	p.Q1552H	ENST00000324856	NM_006015.4	1552	caG/caT	18/20	0.366344760103181	1	FACETS	0.829	0.783	0.875	0.829	0.783	0.875	INDETERMINATE	1	TRUE	0	0.819189527666454	1		524	339	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933165	36933165	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	106	739	0	ENST00000361632.4:c.1952G>T	p.Ser651Ile	p.S651I	ENST00000361632		651	aGc/aTc	14/16	0.366344760103181	1	FACETS	0.387	0.349	0.426	0.387	0.349	0.426	INDETERMINATE	1	TRUE	0	0.819189527666454	1		739	395	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797106	45797106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778540	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	522	821	1	ENST00000450313.1:c.1309C>T	p.Arg437Trp	p.R437W	ENST00000450313	NM_012222.2	437	Cgg/Tgg	13/16	0.468934270196446	3	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.819189527666454	3		822	778	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509362	46509362	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	227	644	2	ENST00000262741.5:c.1369C>A	p.Pro457Thr	p.P457T	ENST00000262741	NM_003629.3	457	Ccc/Acc	10/10	0.468934270196446	3	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.819189527666454	3		646	650	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743563	46743563	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs770776928	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	102	697	0	ENST00000371975.4:c.1944G>C	p.Glu648Asp	p.E648D	ENST00000371975	NM_003579.3	648	gaG/gaC	17/18	0.468934270196446	3	FACETS	0.529	0.474	0.588			1	INDETERMINATE	1	TRUE	NA	0.819189527666454	3		697	663	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301128	65301128	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	150	499	0	ENST00000342505.4:c.3320C>A	p.Thr1107Lys	p.T1107K	ENST00000342505	NM_002227.2	1107	aCg/aAg	24/25	0.515333036593646	3	FACETS	1	0.969	1			1	CLONAL	1	TRUE	NA	0.819189527666454	3		499	468	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551699	150551699	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	159	529	0	ENST00000369026.2:c.308G>T	p.Arg103Leu	p.R103L	ENST00000369026	NM_021960.4	103	cGc/cTc	1/3	0.360111214967019	6	FACETS	1	0.988	1	0.493	0.453	0.534	INDETERMINATE	1	TRUE	3	0.819189527666454	6		529	693	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745476	162745476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471671366	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	325	603	0	ENST00000367921.3:c.1891C>T	p.Arg631Trp	p.R631W	ENST00000367921	NM_006182.2	631	Cgg/Tgg	15/18	0.819189527666454	5	FACETS	0.855	0.809	0.902			1	CLONAL	2	TRUE	NA	0.819189527666454	5		603	1034	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163309184	163309184	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	558	691	0	ENST00000271452.3:c.523G>C	p.Glu175Gln	p.E175Q	ENST00000271452	NM_145697.2	175	Gaa/Caa	8/14	0.819189527666454	5	FACETS	0.998	0.964	1			1	CLONAL	3	TRUE	NA	0.819189527666454	5		691	1014	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226595555	226595555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	167	640	0	ENST00000366794.5:c.76G>A	p.Glu26Lys	p.E26K	ENST00000366794	NM_001618.3	26	Gag/Aag	1/23	0.305398444512377	3	FACETS	1	0.943	1	0.341	0.315	0.368	INDETERMINATE	1	TRUE	0	0.819189527666454	3		640	561	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828148	243828148	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	79	762	0	ENST00000263826.5:c.210C>G	p.Asn70Lys	p.N70K	ENST00000263826	NM_005465.4	70	aaC/aaG	3/13	0.305398444512377	3	FACETS	0.412	0.362	0.465	0.137	0.12	0.155	INDETERMINATE	1	TRUE	0	0.819189527666454	3		762	660	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615072	43615072	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	221	734	2	ENST00000355710.3:c.2486G>T	p.Ser829Ile	p.S829I	ENST00000355710	NM_020975.4	829	aGt/aTt	14/20	0.737569607308329	6	FACETS	0.988	0.917	1			1	CLONAL	1	TRUE	NA	0.819189527666454	6		736	1441	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851414	63851414	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	111	692	1	ENST00000279873.7:c.2192G>T	p.Ser731Ile	p.S731I	ENST00000279873	NM_032199.2	731	aGt/aTt	10/10	0.819189527666454	3	FACETS	0.38	0.341	0.422			1	SUBCLONAL	1	TRUE	NA	0.819189527666454	3		693	1005	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741802	17741802	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	64	511	0	ENST00000250003.3:c.473A>T	p.Glu158Val	p.E158V	ENST00000250003	NM_002478.4	158	gAg/gTg	1/3	0.150846150929389	4	FACETS	0.582	0.505	0.666			1	INDETERMINATE	1	TRUE	NA	0.819189527666454	4		511	488	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456447	32456447	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	124	525	0	ENST00000332351.3:c.445G>A	p.Ala149Thr	p.A149T	ENST00000332351	NM_024426.4	149	Gcg/Acg	1/10	0.150846150929389	4	FACETS	0.983	0.893	1			1	INDETERMINATE	1	TRUE	NA	0.819189527666454	4		525	560	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205796	108205796	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	330	561	0	ENST00000278616.4:c.8111G>T	p.Cys2704Phe	p.C2704F	ENST00000278616	NM_000051.3	2704	tGt/tTt	55/63	0.819189527666454	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.819189527666454	2		561	400	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398244	25398244	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	122	682	0	ENST00000311936.3:c.75G>C	p.Gln25His	p.Q25H	ENST00000311936	NM_004985.3	25	caG/caC	2/5	0.419597365983131	3	FACETS	0.616	0.557	0.677	0.205	0.185	0.226	INDETERMINATE	1	TRUE	0	0.819189527666454	3		682	682	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869579	102869579	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	113	625	0	ENST00000307046.8:c.64-2A>T		p.X22_splice	ENST00000307046	NM_001111285.1	22			0.429297765277739	2	FACETS	0.525	0.475	0.579	0.263	0.237	0.29	INDETERMINATE	1	TRUE	0	0.819189527666454	2		625	525	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112175	115112175	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	94	681	0	ENST00000257566.3:c.1565C>A	p.Pro522His	p.P522H	ENST00000257566	NM_016569.3	522	cCc/cAc	7/8	0.429297765277739	2	FACETS	0.423	0.377	0.471	0.211	0.188	0.236	INDETERMINATE	1	TRUE	0	0.819189527666454	2		681	543	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134698	41134698	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	257	440	1	ENST00000379561.5:c.930G>T	p.Trp310Cys	p.W310C	ENST00000379561	NM_002015.3	310	tgG/tgT	2/3	0.796926298939656	2	FACETS	0.925	0.891	0.958	0.925	0.891	0.958	CLONAL	2	TRUE	0	0.819189527666454	2		441	339	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050869	49050869	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1346717703	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	199	503	0	ENST00000267163.4:c.2553G>T	p.Met851Ile	p.M851I	ENST00000267163	NM_000321.2	851	atG/atT	25/27	0.796926298939656	2	FACETS	1	0.992	1	0.696	0.657	0.734	CLONAL	1	TRUE	0	0.819189527666454	2		503	349	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093372	30093372	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	355	703	0	ENST00000331968.5:c.1891G>T	p.Val631Phe	p.V631F	ENST00000331968	NM_002742.2	631	Gtt/Ttt	13/18	0.819189527666454	3	FACETS	0.968	0.927	1	0.968	0.927	1	CLONAL	2	TRUE	1	0.819189527666454	3		703	631	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093447	30093447	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	270	524	0	ENST00000331968.5:c.1816G>T	p.Gly606Ter	p.G606*	ENST00000331968	NM_002742.2	606	Gga/Tga	13/18	0.819189527666454	3	FACETS	0.993	0.946	1	0.993	0.946	1	CLONAL	2	TRUE	1	0.819189527666454	3		524	468	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060780	38060780	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	291	1083	0	ENST00000250448.2:c.1209C>A	p.Asn403Lys	p.N403K	ENST00000250448	NM_004496.3	403	aaC/aaA	2/2	0.819189527666454	3	FACETS	0.833	0.783	0.884	0.417	0.391	0.442	CLONAL	1	TRUE	1	0.819189527666454	3		1083	1202	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560440	65560440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	474	442	0	ENST00000358664.4:c.157C>T	p.Leu53Phe	p.L53F	ENST00000358664	NM_002382.4	53	Ctc/Ttc	3/5	0.479483785401797	5	FACETS	0.945	0.916	0.974			1	INDETERMINATE	4	TRUE	NA	0.819189527666454	5		442	682	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610566	81610566	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1406691651	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	94	427	0	ENST00000298171.2:c.2164C>G	p.Gln722Glu	p.Q722E	ENST00000298171	NM_000369.2	722	Caa/Gaa	10/10	0.722008044584553	3	FACETS	0.687	0.614	0.764	0.343	0.307	0.382	SUBCLONAL	1	TRUE	1	0.819189527666454	3		427	471	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058501	42058501	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	119	601	2	ENST00000219905.7:c.8221G>T	p.Glu2741Ter	p.E2741*	ENST00000219905	NM_001164273.1	2741	Gag/Tag	24/24	0.819189527666454	1	FACETS	0.853	0.794	0.912	0.853	0.794	0.912	CLONAL	1	TRUE	0	0.819189527666454	1		603	201	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43699682	43699682	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	375	744	0	ENST00000382044.4:c.5833C>T	p.Pro1945Ser	p.P1945S	ENST00000382044	NM_001141980.1	1945	Cct/Tct	28/28	0.355881939653971	1	FACETS	1	0.995	1	1	0.995	1	INDETERMINATE	1	TRUE	0	0.819189527666454	1		744	467	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007787	45007787	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	379	623	2	ENST00000558401.1:c.234G>T	p.Lys78Asn	p.K78N	ENST00000558401	NM_004048.2	78	aaG/aaT	2/4	0.355881939653971	1	FACETS	1	0.996	1	1	0.996	1	INDETERMINATE	1	TRUE	0	0.819189527666454	1		625	468	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250908	99250908	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	116	546	0	ENST00000268035.6:c.212G>T	p.Arg71Leu	p.R71L	ENST00000268035	NM_000875.3	71	cGc/cTc	2/21	0.658039865496021	3	FACETS	0.59	0.532	0.65	0.197	0.177	0.217	SUBCLONAL	1	TRUE	0	0.819189527666454	3		546	677	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808967	3808967	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	217	549	0	ENST00000262367.5:c.3257A>T	p.Lys1086Ile	p.K1086I	ENST00000262367	NM_004380.2	1086	aAa/aTa	17/31	0.366344760103181	1	FACETS	0.951	0.905	0.995	0.951	0.905	0.995	INDETERMINATE	1	TRUE	0	0.819189527666454	1		549	329	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346109	89346109	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	29	192	0	ENST00000301030.4:c.6841C>G	p.Gln2281Glu	p.Q2281E	ENST00000301030	NM_001256183.1	2281	Caa/Gaa	9/13	0.5050281772386	3	FACETS	0.525	0.425	0.637	0.175	0.141	0.213	SUBCLONAL	1	TRUE	0	0.819189527666454	3		192	190	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346769	89346769	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	97	466	2	ENST00000301030.4:c.6181G>T	p.Gly2061Trp	p.G2061W	ENST00000301030	NM_001256183.1	2061	Ggg/Tgg	9/13	0.5050281772386	3	FACETS	0.784	0.703	0.868	0.261	0.234	0.29	SUBCLONAL	1	TRUE	0	0.819189527666454	3		468	426	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89881022	89881022	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	96	590	0	ENST00000389301.3:c.190-1G>A		p.X64_splice	ENST00000389301	NM_000135.2	64			0.5050281772386	3	FACETS	0.554	0.495	0.618	0.185	0.165	0.206	SUBCLONAL	1	TRUE	0	0.819189527666454	3		590	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579410	7579410	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567556123	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	503	826	0	ENST00000269305.4:c.277del	p.Leu93CysfsTer30	p.L93Cfs*30	ENST00000269305	NM_001126112.2	93	Ctg/tg	4/11	0.819189527666454	2	FACETS	0.959	0.935	0.983	0.959	0.935	0.983	CLONAL	2	TRUE	0	0.819189527666454	2		826	640	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8109832	8109832	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	100	683	0	ENST00000585124.1:c.663G>C	p.Trp221Cys	p.W221C	ENST00000585124	NM_004217.3	221	tgG/tgC	7/9	0.819189527666454	2	FACETS	0.488	0.438	0.542	0.244	0.219	0.271	SUBCLONAL	1	TRUE	0	0.819189527666454	2		683	500	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30326004	30326005	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs769517721	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	64	423	0	ENST00000322652.5:c.2208dup	p.Gln737ThrfsTer20	p.Q737Tfs*20	ENST00000322652	NM_015355.2	734	-/A	16/16	0.524602810567318	3	FACETS	0.539	0.468	0.614	0.18	0.156	0.205	SUBCLONAL	1	TRUE	0	0.819189527666454	3		423	409	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62009619	62009620	+	start_lost	Translation_Start_Site	DNP	CA	CA	AT	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	89	804	1	ENST00000392795.3:c.2_3delinsAT	p.Met1?	p.M1?	ENST00000392795	NM_001039933.1	1	aTG/aAT	1/6	0.34946065462897	2	FACETS	0.429	0.382	0.48	0.215	0.191	0.24	INDETERMINATE	1	TRUE	0	0.819189527666454	2		805	506	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533925	63533925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555578117	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	176	545	1	ENST00000307078.5:c.1229C>T	p.Thr410Ile	p.T410I	ENST00000307078	NM_004655.3	410	aCa/aTa	6/11	0.34946065462897	2	FACETS	1	0.99	1	0.649	0.609	0.689	INDETERMINATE	1	TRUE	0	0.819189527666454	2		546	331	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610439	10610439	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs202181679	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	684	776	1	ENST00000171111.5:c.271G>T	p.Ala91Ser	p.A91S	ENST00000171111	NM_203500.1	91	Gcc/Tcc	2/6	0.813306605943443	3	FACETS	0.997	0.98	1	0.997	0.98	1	CLONAL	3	TRUE	0	0.819189527666454	3		777	787	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098340	11098340	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	580	727	0	ENST00000358026.2:c.860-2A>G		p.X287_splice	ENST00000358026	NM_001128849.1	287			0.813306605943443	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.819189527666454	3		727	657	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379622	17379622	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	60	328	0	ENST00000359435.4:c.7G>T	p.Val3Leu	p.V3L	ENST00000359435	NM_001033549.1	3	Gtg/Ttg	2/9	0.813306605943443	3	FACETS	0.566	0.49	0.648	0.189	0.163	0.216	SUBCLONAL	1	TRUE	0	0.819189527666454	3		328	365	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18956828	18956828	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	205	711	1	ENST00000262803.5:c.271G>T	p.Asp91Tyr	p.D91Y	ENST00000262803	NM_002911.3	91	Gac/Tac	2/24	0.813306605943443	3	FACETS	1	0.986	1	0.401	0.374	0.429	CLONAL	1	TRUE	0	0.819189527666454	3		712	586	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976935	18976935	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	499	702	1	ENST00000262803.5:c.3320A>T	p.Tyr1107Phe	p.Y1107F	ENST00000262803	NM_002911.3	1107	tAc/tTc	23/24	0.813306605943443	3	FACETS	0.972	0.951	0.992	0.972	0.951	0.992	CLONAL	3	TRUE	0	0.819189527666454	3		703	589	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214738	36214738	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	198	530	1	ENST00000222270.7:c.3164G>T	p.Arg1055Leu	p.R1055L	ENST00000222270	NM_014727.1	1055	cGg/cTg	8/37	0.712317983193125	4	FACETS	1	0.986	1	0.416	0.387	0.447	CLONAL	1	TRUE	1	0.819189527666454	4		531	704	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143339	30143339	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	229	739	0	ENST00000389048.3:c.187C>A	p.Leu63Ile	p.L63I	ENST00000389048	NM_004304.4	63	Ctc/Atc	1/29	0.459946526859173	3	FACETS	1	0.98	1	0.554	0.519	0.591	INDETERMINATE	1	TRUE	1	0.819189527666454	3		739	711	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46603835	46603835	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	261	666	4	ENST00000263734.3:c.1192G>T	p.Glu398Ter	p.E398*	ENST00000263734	NM_001430.4	398	Gag/Tag	9/16	0.459946526859173	3	FACETS	1	0.992	1	0.652	0.614	0.69	INDETERMINATE	1	TRUE	1	0.819189527666454	3		670	689	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724111	61724111	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	177	526	0	ENST00000401558.2:c.791C>G	p.Ser264Cys	p.S264C	ENST00000401558	NM_003400.3	264	tCt/tGt	10/25	0.459946526859173	3	FACETS	1	0.941	1	0.509	0.472	0.548	INDETERMINATE	1	TRUE	1	0.819189527666454	3		526	598	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	405	666	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	0.479483785401797	5	FACETS	0.991	0.945	1			1	INDETERMINATE	2	TRUE	NA	0.819189527666454	5		666	1112	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735360	204735360	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	57	341	0	ENST00000302823.3:c.161C>A	p.Ala54Asp	p.A54D	ENST00000302823	NM_005214.4	54	gCc/gAc	2/4	0.305398444512377	3	FACETS	0.562	0.485	0.646	0.187	0.161	0.216	INDETERMINATE	1	TRUE	0	0.819189527666454	3		341	349	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285248	212285248	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	156	644	0	ENST00000342788.4:c.3053A>T	p.Asp1018Val	p.D1018V	ENST00000342788	NM_005235.2	1018	gAt/gTt	25/28	0.305398444512377	3	FACETS	1	0.971	1	0.369	0.34	0.398	INDETERMINATE	1	TRUE	0	0.819189527666454	3		644	485	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286731	212286731	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	113	436	0	ENST00000342788.4:c.2964+1G>T		p.X988_splice	ENST00000342788	NM_005235.2	988			0.305398444512377	3	FACETS	0.985	0.894	1	0.328	0.298	0.36	INDETERMINATE	1	TRUE	0	0.819189527666454	3		436	395	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523261	9523261	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	214	747	2	ENST00000353224.5:c.1976T>A	p.Leu659Ter	p.L659*	ENST00000353224	NM_177990.2	659	tTa/tAa	9/10	0.819189527666454	4	FACETS	0.865	0.803	0.929			1	CLONAL	1	TRUE	NA	0.819189527666454	4		749	1099	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525116	9525116	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	161	559	0	ENST00000353224.5:c.1769G>T	p.Cys590Phe	p.C590F	ENST00000353224	NM_177990.2	590	tGt/tTt	8/10	0.819189527666454	4	FACETS	0.8	0.734	0.869			1	SUBCLONAL	1	TRUE	NA	0.819189527666454	4		559	894	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546560	9546560	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	171	673	0	ENST00000353224.5:c.1462C>G	p.Arg488Gly	p.R488G	ENST00000353224	NM_177990.2	488	Cga/Gga	5/10	0.819189527666454	4	FACETS	0.706	0.648	0.766			1	SUBCLONAL	1	TRUE	NA	0.819189527666454	4		673	1076	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742680	39742680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	128	534	0	ENST00000361337.2:c.1523G>A	p.Arg508His	p.R508H	ENST00000361337	NM_003286.2	508	cGt/cAt	15/21	0.658039865496021	3	FACETS	0.69	0.627	0.757	0.23	0.209	0.253	SUBCLONAL	1	TRUE	0	0.819189527666454	3		534	638	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419893	41419893	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	113	672	1	ENST00000373198.4:c.428C>A	p.Thr143Asn	p.T143N	ENST00000373198	NM_133170.3	143	aCt/aAt	3/32	0.658039865496021	3	FACETS	0.545	0.491	0.603	0.182	0.163	0.201	SUBCLONAL	1	TRUE	0	0.819189527666454	3		673	713	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36421171	36421171	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	16	575	0	ENST00000300305.3:c.26C>A	p.Ser9Ter	p.S9*	ENST00000300305		9	tCa/tAa	1/8	0.807562914958643	1	FACETS	0.083	0.061	0.109	0.083	0.061	0.109	SUBCLONAL	1	TRUE	0	0.819189527666454	1		575	278	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656921	45656921	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	318	833	2	ENST00000407780.3:c.235C>A	p.Arg79Ser	p.R79S	ENST00000407780	NM_001283052.1	79	Cgc/Agc	3/7	0.819189527666454	2	FACETS	1	0.987	1	0.554	0.526	0.581	CLONAL	1	TRUE	0	0.819189527666454	2		835	701	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556692	41556692	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	187	634	0	ENST00000263253.7:c.3637G>T	p.Val1213Phe	p.V1213F	ENST00000263253	NM_001429.3	1213	Gtt/Ttt	20/31	0.814610368593824	2	FACETS	0.888	0.827	0.95	0.444	0.413	0.475	CLONAL	1	TRUE	0	0.819189527666454	2		634	514	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940763	49940763	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	136	689	0	ENST00000296474.3:c.280G>T	p.Gly94Cys	p.G94C	ENST00000296474	NM_002447.2	94	Ggc/Tgc	1/20	0.392000358962975	2	FACETS	0.577	0.527	0.63	0.289	0.263	0.315	INDETERMINATE	1	TRUE	0	0.819189527666454	2		689	575	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588853	52588853	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	111	670	0	ENST00000394830.3:c.4175G>T	p.Gly1392Val	p.G1392V	ENST00000394830	NM_018313.4	1392	gGc/gTc	27/30	0.392000358962975	2	FACETS	0.513	0.463	0.566	0.257	0.231	0.283	INDETERMINATE	1	TRUE	0	0.819189527666454	2		670	528	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259406	89259406	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	125	709	0	ENST00000336596.2:c.550C>G	p.Gln184Glu	p.Q184E	ENST00000336596	NM_005233.5	184	Caa/Gaa	3/17	0.468934270196446	3	FACETS	0.657	0.596	0.721			1	INDETERMINATE	1	TRUE	NA	0.819189527666454	3		709	655	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480395	89480395	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	86	439	0	ENST00000336596.2:c.2232C>A	p.His744Gln	p.H744Q	ENST00000336596	NM_005233.5	744	caC/caA	13/17	0.468934270196446	3	FACETS	0.596	0.528	0.667			1	INDETERMINATE	1	TRUE	NA	0.819189527666454	3		439	497	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631596	119631596	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	305	537	0	ENST00000316626.5:c.670del	p.Ala224HisfsTer4	p.A224Hfs*4	ENST00000316626		224	Gca/ca	6/12	0.522940181861971	5	FACETS	1	0.99	1	0.78	0.74	0.821	CLONAL	2	TRUE	2	0.819189527666454	5		537	709	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205089	128205089	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	147	969	0	ENST00000341105.2:c.352G>T	p.Val118Leu	p.V118L	ENST00000341105	NM_032638.4	118	Gtg/Ttg	3/6	0.522940181861971	5	FACETS	0.727	0.662	0.794	0.242	0.22	0.265	SUBCLONAL	1	TRUE	2	0.819189527666454	5		969	1101	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205708	128205708	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	137	698	0	ENST00000341105.2:c.167G>T	p.Gly56Val	p.G56V	ENST00000341105	NM_032638.4	56	gGc/gTc	2/6	0.522940181861971	5	FACETS	0.801	0.728	0.878	0.267	0.242	0.293	CLONAL	1	TRUE	2	0.819189527666454	5		698	931	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138409981	138409981	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	253	467	0	ENST00000289153.2:c.1897G>T	p.Glu633Ter	p.E633*	ENST00000289153	NM_006219.2	633	Gaa/Taa	13/22	0.522940181861971	5	FACETS	1	0.988	1	0.78	0.737	0.825	CLONAL	2	TRUE	2	0.819189527666454	5		467	588	SUCCESS
ATR	545	MSKCC	GRCh37	3	142211975	142211975	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	270	512	0	ENST00000350721.4:c.6077A>T	p.Lys2026Met	p.K2026M	ENST00000350721	NM_001184.3	2026	aAg/aTg	35/47	0.522940181861971	5	FACETS	1	0.973	1	0.7	0.66	0.74	CLONAL	2	TRUE	2	0.819189527666454	5		512	700	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503829	186503829	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	90	543	0	ENST00000323963.5:c.506G>T	p.Arg169Ile	p.R169I	ENST00000323963		169	aGa/aTa	5/11	0.796856355536637	5	FACETS	0.437	0.386	0.491			1	SUBCLONAL	1	TRUE	NA	0.819189527666454	5		543	1121	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586462	189586462	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	257	525	0	ENST00000264731.3:c.1086G>T	p.Gln362His	p.Q362H	ENST00000264731	NM_003722.4	362	caG/caT	8/14	0.796856355536637	5	FACETS	1	0.992	1			1	CLONAL	1	TRUE	NA	0.819189527666454	5		525	968	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980388	55980388	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	83	630	0	ENST00000263923.4:c.703G>T	p.Glu235Ter	p.E235*	ENST00000263923	NM_002253.2	235	Gaa/Taa	6/30	0.819189527666454	1	FACETS	0.365	0.325	0.407	0.365	0.325	0.407	SUBCLONAL	1	TRUE	0	0.819189527666454	1		630	328	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31483685	31483685	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	129	461	0	ENST00000344624.3:c.2047C>G	p.Pro683Ala	p.P683A	ENST00000344624		683	Cca/Gca	13/33	1	2	FACETS	0.868	0.796	0.941	0.868	0.796	0.941	CLONAL	1	TRUE	1	0.819189527666454	2		461	363	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515224	31515224	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	82	905	0	ENST00000344624.3:c.1161C>G	p.Ile387Met	p.I387M	ENST00000344624		387	atC/atG	5/33	1	2	FACETS	0.274	0.241	0.31	0.274	0.241	0.31	SUBCLONAL	1	TRUE	1	0.819189527666454	2		905	730	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871286	35871286	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	159	488	0	ENST00000303115.3:c.508C>A	p.Arg170Ser	p.R170S	ENST00000303115	NM_002185.3	170	Cgc/Agc	4/8	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.819189527666454	2		488	386	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38964932	38964932	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	49	407	0	ENST00000357387.3:c.1362T>A	p.Asn454Lys	p.N454K	ENST00000357387	NM_152756.3	454	aaT/aaA	16/38	1	2	FACETS	0.488	0.417	0.565	0.488	0.417	0.565	SUBCLONAL	1	TRUE	1	0.819189527666454	2		407	245	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111822	56111822	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	121	96	0	ENST00000399503.3:c.422C>T	p.Ala141Val	p.A141V	ENST00000399503	NM_005921.1	141	gCc/gTc	1/20	0.622456830708066	5	FACETS	0.98	0.922	1			1	CLONAL	4	TRUE	NA	0.819189527666454	5		96	168	SUCCESS
APC	324	MSKCC	GRCh37	5	112175932	112175932	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	240	323	0	ENST00000257430.4:c.4641A>T	p.Glu1547Asp	p.E1547D	ENST00000257430	NM_000038.5	1547	gaA/gaT	16/16	0.819189527666454	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.819189527666454	2		323	284	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131976481	131976481	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	510	687	0	ENST00000265335.6:c.3736G>T	p.Ala1246Ser	p.A1246S	ENST00000265335		1246	Gca/Tca	24/25	0.468934270196446	3	FACETS	0.99	0.97	1			1	INDETERMINATE	3	TRUE	NA	0.819189527666454	3		687	591	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180037013	180037013	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	307	621	0	ENST00000261937.6:c.3699G>T	p.Trp1233Cys	p.W1233C	ENST00000261937	NM_182925.4	1233	tgG/tgT	28/30	0.817652380829449	2	FACETS	0.946	0.915	0.976	0.946	0.915	0.976	CLONAL	2	TRUE	0	0.819189527666454	2		621	396	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250668	26250668	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	130	635	0	ENST00000446824.2:c.166C>T	p.Gln56Ter	p.Q56*	ENST00000446824	NM_021018.2	56	Cag/Tag	1/1	0.819189527666454	2	FACETS	0.517	0.47	0.566	0.258	0.235	0.283	SUBCLONAL	1	TRUE	0	0.819189527666454	2		635	614	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536247	106536247	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	549	645	0	ENST00000369096.4:c.214G>T	p.Asp72Tyr	p.D72Y	ENST00000369096	NM_001198.3	72	Gat/Tat	2/7	0.563281262509528	5	FACETS	1	0.995	1	0.853	0.826	0.879	CLONAL	3	TRUE	1	0.819189527666454	5		645	876	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015727	112015727	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	103	572	3	ENST00000368678.4:c.1115C>A	p.Ala372Asp	p.A372D	ENST00000368678		372	gCt/gAt	11/13	0.563281262509528	5	FACETS	0.671	0.6	0.747	0.168	0.15	0.187	SUBCLONAL	1	TRUE	1	0.819189527666454	5		575	835	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674208	117674208	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	249	802	2	ENST00000368508.3:c.4266G>T	p.Lys1422Asn	p.K1422N	ENST00000368508	NM_002944.2	1422	aaG/aaT	26/43	0.563281262509528	5	FACETS	1	0.988	1	0.313	0.292	0.334	CLONAL	1	TRUE	1	0.819189527666454	5		804	1083	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335634	81335634	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	171	655	0	ENST00000222390.5:c.1726G>C	p.Gly576Arg	p.G576R	ENST00000222390	NM_000601.4	576	Gga/Cga	15/18	0.819189527666454	3	FACETS	0.888	0.819	0.958	0.444	0.409	0.479	CLONAL	1	TRUE	1	0.819189527666454	3		655	663	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350124	81350124	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	106	550	0	ENST00000222390.5:c.1208T>A	p.Leu403Ter	p.L403*	ENST00000222390	NM_000601.4	403	tTa/tAa	10/18	0.819189527666454	3	FACETS	0.484	0.434	0.538	0.242	0.217	0.269	SUBCLONAL	1	TRUE	1	0.819189527666454	3		550	753	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386511	81386511	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	127	520	0	ENST00000222390.5:c.476A>T	p.Glu159Val	p.E159V	ENST00000222390	NM_000601.4	159	gAa/gTa	4/18	0.819189527666454	3	FACETS	0.793	0.722	0.868	0.397	0.361	0.434	SUBCLONAL	1	TRUE	1	0.819189527666454	3		520	551	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846374	128846374	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	116	703	1	ENST00000249373.3:c.1210G>T	p.Val404Leu	p.V404L	ENST00000249373	NM_005631.4	404	Gtg/Ttg	6/12	0.479483785401797	5	FACETS	0.694	0.625	0.768			1	INDETERMINATE	1	TRUE	NA	0.819189527666454	5		704	909	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151947021	151947021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	222	576	0	ENST00000262189.6:c.1753G>T	p.Glu585Ter	p.E585*	ENST00000262189	NM_170606.2	585	Gaa/Taa	13/59	0.819189527666454	5	FACETS	1	0.945	1	0.34	0.315	0.365	CLONAL	1	TRUE	2	0.819189527666454	5		576	1186	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972978	68972978	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	266	592	1	ENST00000288368.4:c.1303G>T	p.Gly435Ter	p.G435*	ENST00000288368	NM_024870.2	435	Gga/Tga	11/40	0.784713292307676	2	FACETS	0.91	0.875	0.942	0.91	0.875	0.942	CLONAL	2	TRUE	0	0.819189527666454	2		593	357	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046504	69046504	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	338	637	0	ENST00000288368.4:c.3977C>T	p.Pro1326Leu	p.P1326L	ENST00000288368	NM_024870.2	1326	cCa/cTa	32/40	0.784713292307676	2	FACETS	0.978	0.949	1	0.978	0.949	1	CLONAL	2	TRUE	0	0.819189527666454	2		637	422	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982731	90982731	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	62	541	0	ENST00000265433.3:c.757A>T	p.Thr253Ser	p.T253S	ENST00000265433	NM_002485.4	253	Aca/Tca	7/16	0.784713292307676	2	FACETS	0.406	0.352	0.464	0.203	0.176	0.232	SUBCLONAL	1	TRUE	0	0.819189527666454	2		541	373	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528674	8528674	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	94	552	0	ENST00000356435.5:c.458C>T	p.Pro153Leu	p.P153L	ENST00000356435		153	cCg/cTg	4/35	0.796926298939656	2	FACETS	0.617	0.553	0.684	0.308	0.276	0.342	SUBCLONAL	1	TRUE	0	0.819189527666454	2		552	372	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650109	93650109	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs765007451	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	204	690	1	ENST00000375746.1:c.1660G>T	p.Asp554Tyr	p.D554Y	ENST00000375746	NM_001174167.1	554	Gat/Tat	12/14	0.409624549680059	3	FACETS	1	0.981	1	0.567	0.529	0.606	INDETERMINATE	1	TRUE	1	0.819189527666454	3		691	619	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755950	133755950	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	126	735	0	ENST00000318560.5:c.1577C>G	p.Pro526Arg	p.P526R	ENST00000318560	NM_005157.4	526	cCa/cGa	10/11	0.409624549680059	3	FACETS	0.641	0.582	0.704	0.321	0.291	0.352	INDETERMINATE	1	TRUE	1	0.819189527666454	3		735	676	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317514	1317514	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	273	917	1	ENST00000400841.2:c.551G>T	p.Trp184Leu	p.W184L	ENST00000400841		184	tGg/tTg	5/6	0.819189527666454	3	FACETS	0.927	0.87	0.984			1	CLONAL	1	TRUE	NA	0.819189527666454	3		918	1014	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044901	47044901	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	261	871	2	ENST00000377604.3:c.2227G>T	p.Glu743Ter	p.E743*	ENST00000377604	NM_001204468.1	743	Gag/Tag	20/24	1	2	FACETS	0.943	0.889	0.997	0.943	0.889	0.997	CLONAL	1	TRUE	1	0.819189527666454	2		873	676	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410142	63410142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	149	808	0	ENST00000330258.3:c.3025G>T	p.Glu1009Ter	p.E1009*	ENST00000330258	NM_152424.3	1009	Gag/Tag	2/2	0.819189527666454	3	FACETS	0.661	0.604	0.72	0.33	0.302	0.36	SUBCLONAL	1	TRUE	1	0.819189527666454	3		808	776	SUCCESS
AR	367	MSKCC	GRCh37	X	66943608	66943608	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	67	743	0	ENST00000374690.3:c.2688G>T	p.Met896Ile	p.M896I	ENST00000374690	NM_000044.3	896	atG/atT	8/8	0.819189527666454	3	FACETS	0.267	0.231	0.306	0.134	0.115	0.153	SUBCLONAL	1	TRUE	1	0.819189527666454	3		743	863	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937761	76937761	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	181	774	0	ENST00000373344.5:c.2987C>A	p.Ser996Ter	p.S996*	ENST00000373344	NM_000489.3	996	tCa/tAa	9/35	0.819189527666454	3	FACETS	0.774	0.715	0.835	0.387	0.357	0.418	SUBCLONAL	1	TRUE	1	0.819189527666454	3		774	805	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611069	100611069	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs781869026	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	257	854	0	ENST00000308731.7:c.1537G>C	p.Glu513Gln	p.E513Q	ENST00000308731	NM_000061.2	513	Gag/Cag	15/19	0.819189527666454	3	FACETS	1	0.973	1	0.532	0.499	0.565	CLONAL	1	TRUE	1	0.819189527666454	3		854	832	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630140	100630140	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	123	658	0	ENST00000308731.7:c.133G>T	p.Glu45Ter	p.E45*	ENST00000308731	NM_000061.2	45	Gaa/Taa	2/19	0.819189527666454	3	FACETS	0.665	0.602	0.73	0.332	0.301	0.365	SUBCLONAL	1	TRUE	1	0.819189527666454	3		658	637	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191739	123191740	+	missense_variant	Missense_Mutation	DNP	AG	AG	GT	novel	NA	P-0005783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	47	516	1	ENST00000218089.9:c.1328_1329delinsGT	p.Glu443Gly	p.E443G	ENST00000218089	NM_001042749.1	443	gAG/gGT	15/35	0.819189527666454	3	FACETS	0.286	0.241	0.336	0.143	0.12	0.168	SUBCLONAL	1	TRUE	1	0.819189527666454	3		517	566	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0005816-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	32	558	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	1	2	FACETS	0.778	0.631	0.945	0.778	0.631	0.945	CLONAL	1	TRUE	1	0.17	2		558	484	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644739	67644739	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005816-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	55	671	0	ENST00000264010.4:c.4G>T	p.Glu2Ter	p.E2*	ENST00000264010	NM_006565.3	2	Gaa/Taa	3/12	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.17	2		671	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0009202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	319	640	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.477058709921016	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.477058709921016	2		640	616	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086008	16086008	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	180	224	0	ENST00000281043.3:c.1184A>T	p.Asn395Ile	p.N395I	ENST00000281043	NM_005378.4	395	aAc/aTc	3/3	0.259005884592684	5	FACETS	1	0.986	1	0.831	0.773	0.892	INDETERMINATE	2	TRUE	2	0.477058709921016	5		224	519	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576854	212576854	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	104	316	0	ENST00000342788.4:c.1045G>T	p.Asp349Tyr	p.D349Y	ENST00000342788	NM_005235.2	349	Gat/Tat	9/28	0.447115738853535	2	FACETS	0.956	0.861	1	0.478	0.43	0.528	CLONAL	1	TRUE	0	0.477058709921016	2		316	456	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170249	32170249	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	107	244	0	ENST00000375023.3:c.3359A>C	p.Tyr1120Ser	p.Y1120S	ENST00000375023	NM_004557.3	1120	tAt/tCt	21/30	0.260648723941947	5	FACETS	1	0.945	1	0.709	0.642	0.778	INDETERMINATE	2	TRUE	2	0.477058709921016	5		244	362	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333254	70333254	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	77	372	0	ENST00000373644.4:c.1159G>C	p.Glu387Gln	p.E387Q	ENST00000373644	NM_030625.2	387	Gag/Cag	2/12	0.477058709921016	3	FACETS	0.763	0.671	0.861	0.381	0.335	0.431	SUBCLONAL	1	TRUE	1	0.477058709921016	3		372	524	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212555	133212555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	274	326	0	ENST00000320574.5:c.5734G>A	p.Glu1912Lys	p.E1912K	ENST00000320574	NM_006231.2	1912	Gaa/Aaa	42/49	0.260648723941947	5	FACETS	1	0.989	1	0.797	0.751	0.844	INDETERMINATE	2	TRUE	2	0.477058709921016	5		326	824	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467868	99467868	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	239	327	0	ENST00000268035.6:c.2737A>T	p.Asn913Tyr	p.N913Y	ENST00000268035	NM_000875.3	913	Aat/Tat	13/21	0.259005884592684	5	FACETS	1	0.988	1	0.806	0.756	0.857	INDETERMINATE	2	TRUE	2	0.477058709921016	5		327	711	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867265	68867265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121964872	NA	P-0009202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	168	286	0	ENST00000261769.5:c.2512A>G	p.Ser838Gly	p.S838G	ENST00000261769	NM_004360.3	838	Agc/Ggc	16/16	0.477058709921016	3	FACETS	0.755	0.697	0.814	0.755	0.697	0.814	SUBCLONAL	2	TRUE	1	0.477058709921016	3		286	578	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819671	81819671	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	338	488	0	ENST00000359376.3:c.77C>A	p.Thr26Lys	p.T26K	ENST00000359376	NM_002661.3	26	aCg/aAg	2/33	0.477058709921016	3	FACETS	0.876	0.83	0.922	0.876	0.83	0.922	CLONAL	2	TRUE	1	0.477058709921016	3		488	1002	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346165	89346165	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	97	218	1	ENST00000301030.4:c.6785G>C	p.Gly2262Ala	p.G2262A	ENST00000301030	NM_001256183.1	2262	gGc/gCc	9/13	0.477058709921016	3	FACETS	0.884	0.799	0.971	0.884	0.799	0.971	CLONAL	2	TRUE	1	0.477058709921016	3		219	285	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902142	50902142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772197667	NA	P-0009202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	105	475	0	ENST00000440232.2:c.34G>A	p.Gly12Arg	p.G12R	ENST00000440232	NM_002691.3	12	Ggg/Agg	2/27	0.477058709921016	2	FACETS	0.786	0.706	0.87	0.393	0.353	0.435	SUBCLONAL	1	TRUE	0	0.477058709921016	2		475	560	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417493	139417493	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	252	372	0	ENST00000277541.6:c.551del	p.Gln184ArgfsTer93	p.Q184Rfs*93	ENST00000277541	NM_017617.3	184	cAg/cg	4/34	0.420280228880584	5	FACETS	1	0.975	1	0.792	0.748	0.837	CLONAL	3	TRUE	1	0.477058709921016	5		372	572	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0009535-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	7160	644	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.83746907160037	31	FACETS	0.984	0.979	0.988	0.951	0.946	0.955	CLONAL	29	TRUE	1	0.83746907160037	31		644	7878	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196143	108196143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564652222	NA	P-0009535-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	50	408	0	ENST00000278616.4:c.6679C>T	p.Arg2227Cys	p.R2227C	ENST00000278616	NM_000051.3	2227	Cgc/Tgc	46/63	0.363968744390625	3	FACETS	0.516	0.44	0.599	0.258	0.22	0.3	INDETERMINATE	1	TRUE	1	0.83746907160037	3		408	328	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020502	14020502	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1012646362	NA	P-0009535-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	78	417	0	ENST00000311895.7:c.473G>A	p.Arg158His	p.R158H	ENST00000311895	NM_005236.2	158	cGt/cAt	3/11	0.621420629498359	4	FACETS	0.539	0.474	0.609	0.18	0.158	0.203	SUBCLONAL	1	TRUE	1	0.83746907160037	4		417	635	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790176	40790176	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009535-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	67	543	0	ENST00000373198.4:c.2555G>C	p.Gly852Ala	p.G852A	ENST00000373198	NM_133170.3	852	gGc/gCc	18/32	0.83746907160037	4	FACETS	0.397	0.345	0.455	0.132	0.115	0.152	SUBCLONAL	1	TRUE	1	0.83746907160037	4		543	740	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242481	+	inframe_deletion	In_Frame_Del	DEL	AATTAAGAGAAGCAA	AATTAAGAGAAGCAA	-	rs121913425	NA	P-0009535-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	5028	438	0	ENST00000275493.2:c.2237_2251del	p.Glu746_Thr751delinsAla	p.E746_T751delinsA	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAAca/gca	19/28	0.83746907160037	31	FACETS	1	0.997	1	0.969	0.964	0.974	CLONAL	29	TRUE	1	0.83746907160037	31		438	5428	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249091	55249091	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519861	NA	P-0009535-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4251	3453	657	0	ENST00000275493.2:c.2389T>A	p.Cys797Ser	p.C797S	ENST00000275493	NM_005228.3	797	Tgc/Agc	20/28	0.83746907160037	31	FACETS	1	0.989	1	0.469	0.461	0.476	CLONAL	14	TRUE	1	0.83746907160037	31		657	7704	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352765	70352765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759105512	NA	P-0009535-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	100	427	0	ENST00000374080.3:c.4486C>T	p.Arg1496Cys	p.R1496C	ENST00000374080		1496	Cgc/Tgc	32/45	0.448058379765094	4	FACETS	0.717	0.642	0.797	0.179	0.16	0.2	INDETERMINATE	1	TRUE	0	0.83746907160037	4		427	612	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139032	50139036	+	frameshift_variant	Frame_Shift_Del	DEL	GAGAC	GAGAC	T	novel	NA	P-0009535-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	100	709	0	ENST00000246792.3:c.527_531delinsA	p.Arg176GlnfsTer57	p.R176Qfs*57	ENST00000246792	NM_006270.3	176	cGTCTC/cA	5/6	0.782720291308682	3	FACETS	0.501	0.448	0.558	0.251	0.224	0.279	SUBCLONAL	1	TRUE	1	0.83746907160037	3		709	676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659675	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	183	408	0	ENST00000269305.4:c.764T>C	p.Ile255Thr	p.I255T	ENST00000269305	NM_001126112.2	255	aTc/aCc	7/11	0.959435330117305	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.959435330117305	1		408	190	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1785	129	458	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.959435330117305	9	FACETS	0.612	0.552	0.676			1	SUBCLONAL	1	TRUE	NA	0.959435330117305	9		458	1914	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790728	89790728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2231267	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	234	497	0	ENST00000336032.3:c.115C>T	p.Pro39Ser	p.P39S	ENST00000336032	NM_006813.2	39	Ccg/Tcg	1/2	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.959435330117305	2		497	435	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584787	48584787	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4	267	529	0	ENST00000342988.3:c.865C>T	p.Gln289Ter	p.Q289*	ENST00000342988	NM_005359.5	289	Cag/Tag	7/12	0.959435330117305	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.959435330117305	1		529	271	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14628978	14628978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	238	568	0	ENST00000254322.2:c.184G>A	p.Glu62Lys	p.E62K	ENST00000254322	NM_006145.1	62	Gag/Aag	1/3	NA	2	FACETS	1	0.949	1			1	INDETERMINATE	1	TRUE	NA	0.959435330117305	2		568	494	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244882	41244882	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	243	447	0	ENST00000357654.3:c.2666C>G	p.Ser889Cys	p.S889C	ENST00000357654	NM_007294.3	889	tCt/tGt	10/23	0.959435330117305	1	FACETS	0.903	0.873	0.93	0.903	0.873	0.93	CLONAL	1	TRUE	0	0.959435330117305	1		447	292	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067386	37067386	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs63750443	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	250	531	0	ENST00000231790.2:c.1297G>C	p.Glu433Gln	p.E433Q	ENST00000231790	NM_000249.3	433	Gaa/Caa	12/19	0.959435330117305	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.959435330117305	1		531	255	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028618	12028618	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	175	345	0	ENST00000353533.5:c.821G>T	p.Arg274Ile	p.R274I	ENST00000353533	NM_003010.3	274	aGa/aTa	8/11	0.959435330117305	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.959435330117305	1		345	185	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771344	68771344	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	190	316	0	ENST00000261769.5:c.26C>A	p.Ser9Ter	p.S9*	ENST00000261769	NM_004360.3	9	tCg/tAg	1/16	0.959435330117305	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.959435330117305	1		316	197	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728671	190728671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	234	367	0	ENST00000441310.2:c.2059G>A	p.Glu687Lys	p.E687K	ENST00000441310	NM_000534.4	687	Gaa/Aaa	10/13	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.959435330117305	2		367	468	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143033725	143033725	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	218	303	0	ENST00000262992.4:c.2246G>C	p.Gly749Ala	p.G749A	ENST00000262992	NM_001101669.1	749	gGa/gCa	20/24	0.959435330117305	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.959435330117305	1		303	223	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962679	38962679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	170	151	0	ENST00000357387.3:c.1576G>A	p.Glu526Lys	p.E526K	ENST00000357387	NM_152756.3	526	Gaa/Aaa	18/38	1	2	FACETS	0.958	0.894	1	0.958	0.894	1	CLONAL	1	TRUE	1	0.959435330117305	2		151	370	SUCCESS
APC	324	MSKCC	GRCh37	5	112177511	112177511	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	170	413	0	ENST00000257430.4:c.6220G>T	p.Glu2074Ter	p.E2074*	ENST00000257430	NM_000038.5	2074	Gaa/Taa	16/16	0.834967739284371	1	FACETS	0.862	0.824	0.896	0.862	0.824	0.896	CLONAL	1	TRUE	0	0.959435330117305	1		413	214	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163305	32163305	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	211	516	0	ENST00000375023.3:c.5921C>G	p.Pro1974Arg	p.P1974R	ENST00000375023	NM_004557.3	1974	cCg/cGg	30/30	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.959435330117305	2		516	436	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160508	108160508	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	217	324	0	ENST00000278616.4:c.4416G>C	p.Leu1472Phe	p.L1472F	ENST00000278616	NM_000051.3	1472	ttG/ttC	29/63	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.959435330117305	2		324	449	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233390	69233390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	275	417	0	ENST00000462284.1:c.1255G>A	p.Glu419Lys	p.E419K	ENST00000462284	NM_002392.5	419	Gag/Aag	11/11	0.234648001970881	3	FACETS	1	0.994	1	0.749	0.711	0.788	INDETERMINATE	1	TRUE	1	0.959435330117305	3		417	566	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945141	32945141	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	193	288	0	ENST00000380152.3:c.8536G>C	p.Glu2846Gln	p.E2846Q	ENST00000380152		2846	Gag/Cag	20/27	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.959435330117305	2		288	390	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78865559	78865559	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	225	458	0	ENST00000306801.3:c.2023G>C	p.Glu675Gln	p.E675Q	ENST00000306801	NM_020761.2	675	Gaa/Caa	18/34	0.959435330117305	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.959435330117305	1		458	236	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724609	724609	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	211	419	0	ENST00000314574.4:c.1447G>C	p.Glu483Gln	p.E483Q	ENST00000314574	NM_005433.3	483	Gaa/Caa	12/12	0.959435330117305	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.959435330117305	1		419	225	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592047	67592047	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	167	477	0	ENST00000274335.5:c.1863G>C	p.Glu621Asp	p.E621D	ENST00000274335		621	gaG/gaC	14/15	1	2	FACETS	0.81	0.752	0.868	0.81	0.752	0.868	CLONAL	1	TRUE	1	0.959435330117305	2		477	430	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931474	131931474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	32	402	1	ENST00000265335.6:c.2179G>A	p.Asp727Asn	p.D727N	ENST00000265335		727	Gat/Aat	13/25	0.959435330117305	1	FACETS	0.158	0.129	0.191	0.158	0.129	0.191	SUBCLONAL	1	TRUE	0	0.959435330117305	1		403	219	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439315	149439315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545858226	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	39	486	0	ENST00000286301.3:c.2080G>A	p.Glu694Lys	p.E694K	ENST00000286301	NM_005211.3	694	Gag/Aag	15/22	1	2	FACETS	0.133	0.11	0.159	0.133	0.11	0.159	SUBCLONAL	1	TRUE	1	0.959435330117305	2		486	610	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374703	118374703	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs956313303	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	40	491	0	ENST00000534358.1:c.8096G>A	p.Arg2699Gln	p.R2699Q	ENST00000534358	NM_005933.3	2699	cGa/cAa	27/36	1	2	FACETS	0.132	0.109	0.158	0.132	0.109	0.158	SUBCLONAL	1	TRUE	1	0.959435330117305	2		491	631	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866415	56866415	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	231	394	0	ENST00000519728.1:c.662G>C	p.Arg221Thr	p.R221T	ENST00000519728	NM_002350.3	221	aGa/aCa	8/13	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.959435330117305	2		394	476	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930115	68930115	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	94	335	0	ENST00000288368.4:c.176C>G	p.Ser59Ter	p.S59*	ENST00000288368	NM_024870.2	59	tCa/tGa	2/40	1	2	FACETS	0.505	0.452	0.56	0.505	0.452	0.56	SUBCLONAL	1	TRUE	1	0.959435330117305	2		335	388	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943776	71943776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	25	565	0	ENST00000298229.2:c.1819G>A	p.Asp607Asn	p.D607N	ENST00000298229	NM_001567.3	607	Gac/Aac	15/28	1	2	FACETS	0.123	0.097	0.154	0.123	0.097	0.154	SUBCLONAL	1	TRUE	1	0.959435330117305	2		565	423	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169787	11169787	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	208	332	0	ENST00000361445.4:c.7367-1G>C		p.X2456_splice	ENST00000361445	NM_004958.3	2456			0.959435330117305	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.959435330117305	1		332	218	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445893	49445893	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	223	646	0	ENST00000301067.7:c.1573G>A	p.Glu525Lys	p.E525K	ENST00000301067	NM_003482.3	525	Gag/Aag	10/54	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.959435330117305	2		646	464	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549380	21549380	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	225	490	0	ENST00000382592.4:c.2896G>C	p.Asp966His	p.D966H	ENST00000382592	NM_014572.2	966	Gac/Cac	8/8	1	2	FACETS	0.946	0.89	1	0.946	0.89	1	CLONAL	1	TRUE	1	0.959435330117305	2		490	496	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953980	32953980	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	25	278	0	ENST00000380152.3:c.9047C>G	p.Ser3016Cys	p.S3016C	ENST00000380152		3016	tCt/tGt	23/27	1	2	FACETS	0.13	0.102	0.163	0.13	0.102	0.163	SUBCLONAL	1	TRUE	1	0.959435330117305	2		278	400	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923368	9923368	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	200	492	0	ENST00000330684.3:c.1919T>C	p.Ile640Thr	p.I640T	ENST00000330684	NM_001134407.1	640	aTa/aCa	9/13	1	2	FACETS	0.757	0.706	0.808	0.757	0.706	0.808	SUBCLONAL	1	TRUE	1	0.959435330117305	2		492	551	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923383	9923383	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	180	485	0	ENST00000330684.3:c.1904C>A	p.Ala635Asp	p.A635D	ENST00000330684	NM_001134407.1	635	gCc/gAc	9/13	1	2	FACETS	0.707	0.656	0.758	0.707	0.656	0.758	SUBCLONAL	1	TRUE	1	0.959435330117305	2		485	531	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022284	26022284	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	64	494	0	ENST00000435504.4:c.373G>C	p.Glu125Gln	p.E125Q	ENST00000435504		125	Gag/Cag	5/13	1	2	FACETS	0.26	0.225	0.297	0.26	0.225	0.297	SUBCLONAL	1	TRUE	1	0.959435330117305	2		494	514	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630418	47630418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	170	413	0	ENST00000233146.2:c.88C>T	p.Pro30Ser	p.P30S	ENST00000233146	NM_000251.2	30	Ccg/Tcg	1/16	1	2	FACETS	0.802	0.745	0.86	0.802	0.745	0.86	CLONAL	1	TRUE	1	0.959435330117305	2		413	442	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155429	106155429	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	51	437	0	ENST00000380013.4:c.330G>C	p.Lys110Asn	p.K110N	ENST00000380013	NM_001127208.2	110	aaG/aaC	3/11	0.959435330117305	1	FACETS	0.212	0.181	0.245	0.212	0.181	0.245	SUBCLONAL	1	TRUE	0	0.959435330117305	1		437	261	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100116	157100117	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCGGC	rs797045268	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	120	519	0	ENST00000346085.5:c.1066_1071dup	p.Gly356_Gly357dup	p.G356_G357dup	ENST00000346085	NM_020732.3	356	-/GGCGGC	1/20	1	2	FACETS	0.578	0.525	0.632	0.578	0.525	0.632	SUBCLONAL	1	TRUE	1	0.959435330117305	2		519	433	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124481228	124481228	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	26	246	0	ENST00000357628.3:c.1168G>C	p.Glu390Gln	p.E390Q	ENST00000357628	NM_015450.2	390	Gaa/Caa	14/19	1	2	FACETS	0.172	0.136	0.213	0.172	0.136	0.213	SUBCLONAL	1	TRUE	1	0.959435330117305	2		246	316	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917620	151917620	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	13	248	0	ENST00000262189.6:c.3700G>C	p.Asp1234His	p.D1234H	ENST00000262189	NM_170606.2	1234	Gat/Cat	23/59	1	2	FACETS	0.131	0.093	0.177	0.131	0.093	0.177	SUBCLONAL	1	TRUE	1	0.959435330117305	2		248	207	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868512	117868512	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	17	268	0	ENST00000297338.2:c.830G>C	p.Ser277Thr	p.S277T	ENST00000297338	NM_006265.2	277	aGt/aCt	8/14	1	2	FACETS	0.118	0.087	0.154	0.118	0.087	0.154	SUBCLONAL	1	TRUE	1	0.959435330117305	2		268	301	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578245	7578245	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780072	NA	P-0012114-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	181	655	0	ENST00000269305.4:c.604C>T	p.Arg202Cys	p.R202C	ENST00000269305	NM_001126112.2	202	Cgt/Tgt	6/11	0.429754028402121	2	FACETS	1	0.984	1	0.618	0.572	0.666	CLONAL	1	TRUE	0	0.429754028402121	2		655	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519992	NA	P-0012114-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	259	625	0	ENST00000269305.4:c.641A>T	p.His214Leu	p.H214L	ENST00000269305	NM_001126112.2	214	cAt/cTt	6/11	0.429754028402121	2	FACETS	0.939	0.886	0.993	0.939	0.886	0.993	CLONAL	2	TRUE	0	0.429754028402121	2		625	642	SUCCESS
MET	4233	MSKCC	GRCh37	7	116417452	116417452	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012114-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	78	261	0	ENST00000397752.3:c.3269G>C	p.Gly1090Ala	p.G1090A	ENST00000397752	NM_000245.2	1090	gGt/gCt	16/21	1	2	FACETS	0.926	0.818	1	0.926	0.818	1	CLONAL	1	TRUE	1	0.429754028402121	2		261	392	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117799	108117799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202160435	NA	P-0013143-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	53	292	1	ENST00000278616.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000278616	NM_000051.3	337	cGt/cAt	8/63	0.310991966453652	3	FACETS	1	0.867	1			1	CLONAL	1	TRUE	NA	0.27	3		293	439	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242448	55242449	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTCCCGTCGCTATCAAGG	novel	NA	P-0013143-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	180	371	0	ENST00000275493.2:c.2219_2236dup	p.Lys745_Glu746insValProValAlaIleLys	p.K745_E746insVPVAIK	ENST00000275493	NM_005228.3	740	att/aTTCCCGTCGCTATCAAGGtt	19/28	0.310991966453652	4	FACETS	1	0.973	1	0.744	0.687	0.802	CLONAL	2	TRUE	1	0.27	4		371	759	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023968	27023975	+	frameshift_variant	Frame_Shift_Del	DEL	CCACGCGC	CCACGCGC	-	novel	NA	P-0013143-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	41	490	0	ENST00000324856.7:c.1077_1084del	p.Ala360GlufsTer37	p.A360Efs*37	ENST00000324856	NM_006015.4	358	caCCACGCGCcc/cacc	1/20	0.27963662452255	4	FACETS	0.528	0.439	0.629	0.264	0.219	0.315	SUBCLONAL	1	TRUE	2	0.27	4		490	730	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0014262-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	190	382	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.379647416863905	3	FACETS	0.908	0.844	0.975	0.908	0.844	0.975	CLONAL	2	TRUE	1	0.384850304093209	3		382	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs17849781	NA	P-0014262-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	343	632	0	ENST00000269305.4:c.832C>A	p.Pro278Thr	p.P278T	ENST00000269305	NM_001126112.2	278	Cct/Act	8/11	0.384850304093209	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.384850304093209	2		632	873	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0014262-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	143	557	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.384850304093209	2	FACETS	1	0.948	1	0.526	0.481	0.574	CLONAL	1	TRUE	0	0.384850304093209	2		557	706	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146499	185146499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35266179	NA	P-0014262-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	54	565	0	ENST00000265026.3:c.130G>A	p.Glu44Lys	p.E44K	ENST00000265026	NM_004721.4	44	Gag/Aag	2/14	0.384850304093209	2	FACETS	0.373	0.317	0.433	0.186	0.158	0.217	SUBCLONAL	1	TRUE	0	0.384850304093209	2		565	753	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240207	41240207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014262-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	106	454	0	ENST00000379561.5:c.143C>T	p.Ala48Val	p.A48V	ENST00000379561	NM_002015.3	48	gCg/gTg	1/3	0.35341926559916	4	FACETS	0.852	0.763	0.947	0.284	0.254	0.316	CLONAL	1	TRUE	1	0.384850304093209	4		454	895	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033962	48033962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014262-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	67	301	0	ENST00000234420.5:c.4046C>T	p.Ala1349Val	p.A1349V	ENST00000234420	NM_000179.2	1349	gCt/gTt	10/10	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.384850304093209	2		301	342	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212252715	212252715	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs1285745508	NA	P-0014262-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	91	439	0	ENST00000342788.4:c.3138T>G	p.Ser1046Arg	p.S1046R	ENST00000342788	NM_005235.2	1046	agT/agG	26/28	0.379647416863905	3	FACETS	0.864	0.767	0.966	0.432	0.383	0.483	CLONAL	1	TRUE	1	0.384850304093209	3		439	653	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73649903	73649903	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014262-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	270	569	0	ENST00000377687.4:c.1253A>C	p.Asp418Ala	p.D418A	ENST00000377687	NM_001730.3	418	gAt/gCt	4/4	0.35341926559916	4	FACETS	0.917	0.86	0.975	0.611	0.573	0.65	CLONAL	2	TRUE	1	0.384850304093209	4		569	1060	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225865	2225865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014262-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	165	643	0	ENST00000326181.6:c.1657C>T	p.His553Tyr	p.H553Y	ENST00000326181	NM_032271.2	553	Cac/Tac	18/21	0.365643679356329	4	FACETS	1	0.94	1	0.515	0.472	0.561	CLONAL	1	TRUE	2	0.384850304093209	4		643	1152	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637369	47637369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1244537662	NA	P-0014262-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	103	602	0	ENST00000233146.2:c.503C>T	p.Ser168Phe	p.S168F	ENST00000233146	NM_000251.2	168	tCc/tTc	3/16	1	2	FACETS	0.731	0.654	0.813	0.731	0.654	0.813	SUBCLONAL	1	TRUE	1	0.384850304093209	2		602	732	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0014262-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	135	382	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.32984614516646	5	FACETS	1	0.941	1	0.691	0.632	0.753	CLONAL	2	FALSE	2	0.411048390743229	5		382	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs17849781	NA	P-0014262-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	157	632	0	ENST00000269305.4:c.832C>A	p.Pro278Thr	p.P278T	ENST00000269305	NM_001126112.2	278	Cct/Act	8/11	0.411048390743229	2	FACETS	0.886	0.82	0.954	0.886	0.82	0.954	CLONAL	2	FALSE	0	0.411048390743229	2		632	431	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0014262-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	18	557	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.38088440847991	2	FACETS	0.129	0.097	0.168	0.065	0.048	0.084	SUBCLONAL	1	FALSE	0	0.411048390743229	2		557	677	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240207	41240207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014262-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	22	454	0	ENST00000379561.5:c.143C>T	p.Ala48Val	p.A48V	ENST00000379561	NM_002015.3	48	gCg/gTg	1/3	0.25216229406601	4	FACETS	0.368	0.285	0.466	0.123	0.095	0.156	SUBCLONAL	1	FALSE	1	0.411048390743229	4		454	410	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033962	48033962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014262-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	51	301	0	ENST00000234420.5:c.4046C>T	p.Ala1349Val	p.A1349V	ENST00000234420	NM_000179.2	1349	gCt/gTt	10/10	1	2	FACETS	0.493	0.419	0.574	0.493	0.419	0.574	SUBCLONAL	1	FALSE	1	0.411048390743229	2		301	503	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212252715	212252715	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs1285745508	NA	P-0014262-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	93	439	0	ENST00000342788.4:c.3138T>G	p.Ser1046Arg	p.S1046R	ENST00000342788	NM_005235.2	1046	agT/agG	26/28	0.375660667523662	3	FACETS	0.866	0.771	0.967	0.433	0.385	0.484	CLONAL	1	FALSE	1	0.411048390743229	3		439	630	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73649903	73649903	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014262-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	129	569	0	ENST00000377687.4:c.1253A>C	p.Asp418Ala	p.D418A	ENST00000377687	NM_001730.3	418	gAt/gCt	4/4	0.25216229406601	4	FACETS	1	0.964	1	0.376	0.34	0.413	CLONAL	1	FALSE	1	0.411048390743229	4		569	786	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250639	26250639	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1255819679	NA	P-0014262-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	44	794	0	ENST00000446824.2:c.195G>C	p.Lys65Asn	p.K65N	ENST00000446824	NM_021018.2	65	aaG/aaC	1/1	0.159312677088739	6	FACETS	0.447	0.373	0.529	0.149	0.124	0.177	INDETERMINATE	1	FALSE	3	0.411048390743229	6		794	873	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0015067-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	28	785	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.0999092235846185	3	FACETS	0.981	0.786	1	0.981	0.786	1	CLONAL	2	FALSE	1	0.0999092235846185	3		785	300	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015067-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	27	612	0				ENST00000310581	NM_198253.2	-/1132			0.0999092235846185	3	FACETS	1	0.904	1	1	0.904	1	CLONAL	2	FALSE	1	0.0999092235846185	3		612	229	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0015067-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	16	550	1	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	FALSE	1	0.0999092235846185	2		551	232	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248409	59248409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184098204	NA	P-0015067-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	38	1100	0	ENST00000371222.2:c.334G>A	p.Glu112Lys	p.E112K	ENST00000371222	NM_002228.3	112	Gag/Aag	1/1	0.0999092235846185	3	FACETS	1	0.936	1	0.66	0.545	0.79	CLONAL	1	FALSE	1	0.0999092235846185	3		1100	605	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770854	59770854	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015067-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	4	0	0	ENST00000259008.2:c.2512G>A	p.Asp838Asn	p.D838N	ENST00000259008	NM_032043.2	838	Gat/Aat	18/20	0.0999092235846185	3	FACETS	0.801	0.42	1	0.4	0.21	0.676	CLONAL	1	FALSE	1	0.0999092235846185	3		0	105	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652035	36652035	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015067-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	76	1035	0	ENST00000244741.5:c.159del	p.Phe53LeufsTer95	p.F53Lfs*95	ENST00000244741	NM_000389.4	53	Ttt/tt	2/3	0.0999092235846185	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	FALSE	1	0.0999092235846185	3		1035	655	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983222	149983223	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015067-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	20	684	0	ENST00000253339.5:c.3035dup	p.Ile1013AsnfsTer2	p.I1013Nfs*2	ENST00000253339		1012	aca/acCa	7/7	0.0999092235846185	3	FACETS	0.951	0.73	1	0.951	0.73	1	CLONAL	2	FALSE	1	0.0999092235846185	3		684	221	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983350	149983350	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015067-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	16	584	0	ENST00000253339.5:c.2908C>A	p.His970Asn	p.H970N	ENST00000253339		970	Cac/Aac	7/7	0.0999092235846185	3	FACETS	0.871	0.646	1	0.871	0.646	1	CLONAL	2	FALSE	1	0.0999092235846185	3		584	193	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889108	76889108	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015067-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	6	0	0	ENST00000373344.5:c.4902G>T	p.Trp1634Cys	p.W1634C	ENST00000373344	NM_000489.3	1634	tgG/tgT	18/35	0.0999092235846185	2	FACETS	1	0.701	1			1	CLONAL	1	FALSE	NA	0.0999092235846185	2		0	98	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712614	52712614	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0015067-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	5	0	0	ENST00000394830.3:c.139-1G>A		p.X47_splice	ENST00000394830	NM_018313.4	47			1	2	FACETS	0.382	0.215	0.617	0.382	0.215	0.617	SUBCLONAL	1	FALSE	1	0.0999092235846185	2		0	262	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289275	33289275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015814-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	91	444	1	ENST00000374542.5:c.277C>T	p.Gln93Ter	p.Q93*	ENST00000374542	NM_001141970.1	93	Caa/Taa	3/8	0.566031466539164	4	FACETS	0.735	0.653	0.822	0.245	0.217	0.274	SUBCLONAL	1	TRUE	1	0.603339871491321	4		445	658	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424289	47424289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015814-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	119	258	0	ENST00000377045.4:c.294G>A	p.Met98Ile	p.M98I	ENST00000377045	NM_001654.4	98	atG/atA	4/16	0.545927210139926	2	FACETS	1	0.957	1			1	CLONAL	1	TRUE	NA	0.603339871491321	2		258	365	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456680	32456680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015814-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	110	388	0	ENST00000332351.3:c.212C>T	p.Ser71Phe	p.S71F	ENST00000332351	NM_024426.4	71	tCc/tTc	1/10	0.559322536090476	2	FACETS	1	0.963	1	0.558	0.507	0.61	CLONAL	1	TRUE	0	0.603339871491321	2		388	327	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632270	215632270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015814-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	72	360	0	ENST00000260947.4:c.1504G>A	p.Ala502Thr	p.A502T	ENST00000260947	NM_000465.2	502	Gcc/Acc	6/11	0.570632048536857	3	FACETS	0.74	0.649	0.837	0.247	0.216	0.279	SUBCLONAL	1	TRUE	0	0.603339871491321	3		360	420	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264452	16264452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015814-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	132	427	0	ENST00000375759.3:c.10655G>A	p.Arg3552Lys	p.R3552K	ENST00000375759	NM_015001.2	3552	aGg/aAg	13/15	0.574580754158288	3	FACETS	1	0.955	1	0.537	0.49	0.586	CLONAL	1	TRUE	1	0.603339871491321	3		427	530	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737524	204737524	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015814-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	134	350	0	ENST00000302823.3:c.661C>G	p.Pro221Ala	p.P221A	ENST00000302823	NM_005214.4	221	Ccc/Gcc	4/4	0.603339871491321	3	FACETS	1	0.969	1	0.377	0.344	0.411	CLONAL	1	TRUE	0	0.603339871491321	3		350	511	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8109860	8109860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015814-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	99	415	0	ENST00000585124.1:c.635G>A	p.Gly212Glu	p.G212E	ENST00000585124	NM_004217.3	212	gGa/gAa	7/9	0.600486685440702	5	FACETS	0.891	0.795	0.992	0.297	0.265	0.331	CLONAL	1	TRUE	2	0.603339871491321	5		415	702	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073787	8073787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1188985552	NA	P-0015814-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	155	457	0	ENST00000377482.5:c.872C>T	p.Pro291Leu	p.P291L	ENST00000377482	NM_018948.3	291	cCt/cTt	4/4	0.603339871491321	4	FACETS	1	0.959	1			1	CLONAL	1	TRUE	NA	0.603339871491321	4		457	767	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103513962	103513962	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015814-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	91	393	0	ENST00000355739.4:c.778G>A	p.Gly260Arg	p.G260R	ENST00000355739	NM_000123.3	260	Gga/Aga	7/15	0.318566682633097	5	FACETS	1	0.94	1	0.361	0.322	0.404	INDETERMINATE	1	TRUE	2	0.603339871491321	5		393	530	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562161	95562161	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0015814-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	103	414	0	ENST00000393063.1:c.5095+1G>A		p.X1699_splice	ENST00000393063	NM_030621.3	1699			0.574580754158288	3	FACETS	0.87	0.781	0.963	0.435	0.39	0.482	CLONAL	1	TRUE	1	0.603339871491321	3		414	511	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38545396	38545396	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015814-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	74	310	0	ENST00000299084.4:c.10G>A	p.Glu4Lys	p.E4K	ENST00000299084	NM_152594.2	4	Gag/Aag	1/7	0.574580754158288	3	FACETS	0.931	0.821	1	0.465	0.41	0.524	CLONAL	1	TRUE	1	0.603339871491321	3		310	343	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50773820	50773820	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015814-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	134	451	0	ENST00000307179.4:c.1361C>T	p.Thr454Ile	p.T454I	ENST00000307179		454	aCt/aTt	11/20	0.603339871491321	4	FACETS	1	0.958	1			1	CLONAL	1	TRUE	NA	0.603339871491321	4		451	655	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096957	11096957	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555753081	NA	P-0015814-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	105	473	0	ENST00000358026.2:c.448G>A	p.Gly150Arg	p.G150R	ENST00000358026	NM_001128849.1	150	Gga/Aga	4/36	0.545927210139926	4	FACETS	0.806	0.723	0.895			1	CLONAL	1	TRUE	NA	0.603339871491321	4		473	692	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276615	15276615	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015814-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	126	487	0	ENST00000263388.2:c.5650G>T	p.Ala1884Ser	p.A1884S	ENST00000263388	NM_000435.2	1884	Gcc/Tcc	30/33	0.471567583616441	3	FACETS	0.947	0.861	1			1	CLONAL	1	TRUE	NA	0.603339871491321	3		487	574	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256779	19256779	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015814-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	93	418	0	ENST00000162023.5:c.934C>T	p.Pro312Ser	p.P312S	ENST00000162023		312	Ccg/Tcg	13/13	0.574580754158288	3	FACETS	0.856	0.764	0.952	0.428	0.382	0.476	CLONAL	1	TRUE	1	0.603339871491321	3		418	469	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223945	36223945	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015814-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	180	594	0	ENST00000222270.7:c.6495G>A	p.Trp2165Ter	p.W2165*	ENST00000222270	NM_014727.1	2165	tgG/tgA	28/37	NA	2	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.603339871491321	2		594	540	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825365	134825365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015814-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	106	464	0	ENST00000398015.3:c.881C>T	p.Pro294Leu	p.P294L	ENST00000398015	NM_004441.4	294	cCt/cTt	4/16	0.574580754158288	3	FACETS	0.885	0.796	0.978	0.442	0.398	0.489	CLONAL	1	TRUE	1	0.603339871491321	3		464	517	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981185	55981185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370917098	NA	P-0015814-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	251	324	0	ENST00000263923.4:c.514C>T	p.Pro172Ser	p.P172S	ENST00000263923	NM_002253.2	172	Cct/Tct	5/30	0.593337375635405	5	FACETS	0.882	0.832	0.933	0.662	0.624	0.7	CLONAL	3	TRUE	1	0.603339871491321	5		324	599	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372428	55372428	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015814-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	125	490	0	ENST00000297316.4:c.1118C>T	p.Pro373Leu	p.P373L	ENST00000297316	NM_022454.3	373	cCt/cTt	2/2	1	2	FACETS	0.899	0.819	0.982	0.899	0.819	0.982	CLONAL	1	TRUE	1	0.603339871491321	2		490	461	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295233	15295240	+	protein_altering_variant	In_Frame_Del	DEL	CTCGTCCA	CTCGTCCA	GGCCC	novel	NA	P-0015814-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	101	442	1	ENST00000263388.2:c.2432_2439delinsGGGCC	p.Val811_Glu813delinsGlyAla	p.V811_E813delinsGA	ENST00000263388	NM_000435.2	811	gTGGACGAG/gGGGCC	16/33	0.471567583616441	3	FACETS	0.917	0.824	1			1	CLONAL	1	TRUE	NA	0.603339871491321	3		443	475	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554545	63554545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015835-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	170	662	0	ENST00000307078.5:c.194C>T	p.Pro65Leu	p.P65L	ENST00000307078	NM_004655.3	65	cCg/cTg	2/11	1	2	FACETS	0.964	0.895	1	0.964	0.895	1	CLONAL	1	TRUE	1	0.764944110381615	2		662	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0015835-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	232	495	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.764944110381615	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.764944110381615	1		495	360	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038204	128038204	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs115481013	NA	P-0015835-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	172	454	0	ENST00000285398.2:c.1346A>G	p.Lys449Arg	p.K449R	ENST00000285398	NM_000122.1	449	aAg/aGg	9/15	0.764944110381615	3	FACETS	0.995	0.919	1	0.497	0.459	0.536	CLONAL	1	TRUE	1	0.764944110381615	3		454	625	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0015835-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	169	651	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.764944110381615	1	FACETS	0.961	0.904	1	0.961	0.904	1	CLONAL	1	TRUE	0	0.764944110381615	1		651	284	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0015835-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	285	516	0	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	0.764944110381615	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.764944110381615	2		516	357	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41222997	41222997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015835-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	203	567	0	ENST00000357654.3:c.4934G>A	p.Arg1645Lys	p.R1645K	ENST00000357654	NM_007294.3	1645	aGg/aAg	15/23	0.764944110381615	3	FACETS	0.954	0.887	1	0.477	0.443	0.512	CLONAL	1	TRUE	1	0.764944110381615	3		567	769	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848013	151848013	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015835-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	105	346	0	ENST00000262189.6:c.12746C>A	p.Thr4249Asn	p.T4249N	ENST00000262189	NM_170606.2	4249	aCt/aAt	51/59	0.764944110381615	3	FACETS	0.919	0.829	1	0.459	0.414	0.507	CLONAL	1	TRUE	1	0.764944110381615	3		346	413	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902934	1902934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015835-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	23	493	0	ENST00000382891.5:c.553G>A	p.Glu185Lys	p.E185K	ENST00000382891	NM_133335.3	185	Gaa/Aaa	2/22	1	2	FACETS	0.138	0.107	0.173	0.138	0.107	0.173	SUBCLONAL	1	TRUE	1	0.764944110381615	2		493	437	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405065	70405065	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015835-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	157	530	0	ENST00000373644.4:c.2579A>C	p.Glu860Ala	p.E860A	ENST00000373644	NM_030625.2	860	gAg/gCg	4/12	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.764944110381615	2		530	409	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423575	88423575	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015835-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	154	558	0	ENST00000360948.2:c.2260T>C	p.Trp754Arg	p.W754R	ENST00000360948	NM_001012338.2	754	Tgg/Cgg	18/19	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.764944110381615	2		558	357	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023002	31023002	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015835-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	176	635	0	ENST00000375687.4:c.2487A>C	p.Gln829His	p.Q829H	ENST00000375687	NM_015338.5	829	caA/caC	13/13	0.764944110381615	7	FACETS	0.996	0.915	1			1	CLONAL	1	TRUE	NA	0.764944110381615	7		635	1346	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979516	2979516	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015835-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	147	459	0	ENST00000396946.4:c.731A>C	p.Lys244Thr	p.K244T	ENST00000396946	NM_032415.4	244	aAg/aCg	6/25	0.764944110381615	5	FACETS	0.997	0.911	1	0.249	0.227	0.272	CLONAL	1	TRUE	1	0.764944110381615	5		459	828	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508587	106508587	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015835-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	135	547	0	ENST00000359195.3:c.581A>C	p.Lys194Thr	p.K194T	ENST00000359195	NM_002649.2	194	aAg/aCg	2/11	0.764944110381615	3	FACETS	1	0.949	1	0.526	0.481	0.572	CLONAL	1	TRUE	1	0.764944110381615	3		547	464	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0015964-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	41	176	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.708178511478216	3	FACETS	0.633	0.531	0.743	0.316	0.265	0.372	SUBCLONAL	1	TRUE	1	0.774961009864842	3		176	232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0015964-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	159	580	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.779404813072846	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.774961009864842	1		581	213	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015964-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	180	531	0	ENST00000263967.3:c.3012G>A	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atA	21/21	0.708178511478216	3	FACETS	1	0.984	1	0.601	0.558	0.645	CLONAL	1	TRUE	1	0.774961009864842	3		531	536	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251861	10251861	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015964-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	46	567	0	ENST00000340748.4:c.3266A>G	p.Tyr1089Cys	p.Y1089C	ENST00000340748		1089	tAt/tGt	30/40	1	2	FACETS	0.316	0.266	0.37	0.316	0.266	0.37	SUBCLONAL	1	TRUE	1	0.774961009864842	2		567	376	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770065	56770065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752608224	NA	P-0015964-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	110	607	0	ENST00000337432.4:c.61C>T	p.Pro21Ser	p.P21S	ENST00000337432	NM_058216.2	21	Cca/Tca	1/9	0.779404813072846	1	FACETS	0.654	0.598	0.711	0.654	0.598	0.711	SUBCLONAL	1	TRUE	0	0.774961009864842	1		607	266	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114901023	114901023	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs979684293	NA	P-0015964-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	133	708	0	ENST00000543371.1:c.633C>A	p.Phe211Leu	p.F211L	ENST00000543371	NM_001198531.1	211	ttC/ttA	6/14	0.389475809535184	1	FACETS	0.73	0.675	0.785	0.73	0.675	0.785	INDETERMINATE	1	TRUE	0	0.774961009864842	1		708	288	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494962	56494962	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015964-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	161	713	0	ENST00000267101.3:c.3319G>C	p.Glu1107Gln	p.E1107Q	ENST00000267101	NM_001982.3	1107	Gag/Cag	27/28	0.36366148854282	4	FACETS	1	0.946	1	1	0.946	1	INDETERMINATE	2	TRUE	2	0.774961009864842	4		713	362	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987165	36987165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015964-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	31	743	0	ENST00000354822.5:c.524C>T	p.Ser175Leu	p.S175L	ENST00000354822	NM_001079668.2	175	tCg/tTg	3/3	0.389475809535184	1	FACETS	0.325	0.266	0.389	0.325	0.266	0.389	INDETERMINATE	1	TRUE	0	0.774961009864842	1		743	151	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39595513	39595513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746929631	NA	P-0015964-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	65	472	0	ENST00000262039.4:c.1399G>A	p.Asp467Asn	p.D467N	ENST00000262039	NM_002647.2	467	Gat/Aat	12/25	0.779404813072846	1	FACETS	0.591	0.523	0.66	0.591	0.523	0.66	SUBCLONAL	1	TRUE	0	0.774961009864842	1		472	174	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3094724	3094724	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015964-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	82	608	0	ENST00000078429.4:c.75C>G	p.Ile25Met	p.I25M	ENST00000078429	NM_002067.2	25	atC/atG	1/7	0.779404813072846	1	FACETS	0.975	0.895	1	0.975	0.895	1	CLONAL	1	TRUE	0	0.774961009864842	1		608	133	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660992	227660992	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015964-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	274	823	0	ENST00000305123.5:c.2463C>A	p.Cys821Ter	p.C821*	ENST00000305123	NM_005544.2	821	tgC/tgA	1/2	0.682524044129004	3	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.774961009864842	3		823	774	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662172	227662172	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015964-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	206	770	0	ENST00000305123.5:c.1283C>A	p.Ser428Ter	p.S428*	ENST00000305123	NM_005544.2	428	tCg/tAg	1/2	0.682524044129004	3	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.774961009864842	3		770	610	SUCCESS
ATR	545	MSKCC	GRCh37	3	142218544	142218544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015964-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	58	406	0	ENST00000350721.4:c.5305G>A	p.Glu1769Lys	p.E1769K	ENST00000350721	NM_001184.3	1769	Gaa/Aaa	31/47	0.37329863166826	3	FACETS	0.547	0.471	0.628	0.273	0.235	0.314	INDETERMINATE	1	TRUE	1	0.774961009864842	3		406	380	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952478	38952478	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015964-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	59	508	0	ENST00000357387.3:c.2947G>C	p.Asp983His	p.D983H	ENST00000357387	NM_152756.3	983	Gat/Cat	30/38	0.37329863166826	3	FACETS	0.629	0.544	0.72	0.314	0.272	0.36	INDETERMINATE	1	TRUE	1	0.774961009864842	3		508	336	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176561	56176561	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1561198459	NA	P-0015964-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	174	513	0	ENST00000399503.3:c.2111C>G	p.Ser704Ter	p.S704*	ENST00000399503	NM_005921.1	704	tCa/tGa	12/20	0.779404813072846	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.774961009864842	1		513	246	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679733	30679733	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015964-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	165	759	0	ENST00000376406.3:c.1986G>T	p.Gln662His	p.Q662H	ENST00000376406	NM_014641.2	662	caG/caT	5/15	0.412879289263833	3	FACETS	1	0.977	1	0.571	0.528	0.616	INDETERMINATE	1	TRUE	1	0.774961009864842	3		759	517	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965690	93965690	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015964-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	154	521	0	ENST00000369303.4:c.2238G>C	p.Met746Ile	p.M746I	ENST00000369303	NM_004440.3	746	atG/atC	13/17	0.391258279598817	1	FACETS	0.919	0.861	0.975	0.919	0.861	0.975	INDETERMINATE	1	TRUE	0	0.774961009864842	1		521	265	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976761	2976761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015964-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	59	611	0	ENST00000396946.4:c.1251G>A	p.Met417Ile	p.M417I	ENST00000396946	NM_032415.4	417	atG/atA	9/25	0.779404813072846	1	FACETS	0.373	0.324	0.425	0.373	0.324	0.425	SUBCLONAL	1	TRUE	0	0.774961009864842	1		611	250	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975403	13975403	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015964-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	81	665	0	ENST00000405192.2:c.484G>T	p.Asp162Tyr	p.D162Y	ENST00000405192	NM_001163147.1	162	Gac/Tac	7/12	0.779404813072846	1	FACETS	0.498	0.445	0.554	0.498	0.445	0.554	SUBCLONAL	1	TRUE	0	0.774961009864842	1		665	257	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862873	117862875	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0015964-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	74	317	0	ENST00000297338.2:c.1602_1604del	p.Glu534del	p.E534del	ENST00000297338	NM_006265.2	534	gaAGAt/gat	12/14	0.779404813072846	4	FACETS	0.735	0.646	0.831			1	SUBCLONAL	1	TRUE	NA	0.774961009864842	4		317	461	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786752	3786752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519207	NA	P-0015964-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	109	532	0	ENST00000262367.5:c.4459C>T	p.His1487Tyr	p.H1487Y	ENST00000262367	NM_004380.2	1487	Cac/Tac	27/31	0.37329863166826	3	FACETS	1	0.917	1	0.507	0.459	0.557	INDETERMINATE	1	TRUE	1	0.774961009864842	3		532	385	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77934562	77934562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015964-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	147	621	0	ENST00000361507.4:c.1463C>T	p.Ser488Leu	p.S488L	ENST00000361507	NM_080491.2	488	tCa/tTa	6/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.774961009864842	2		621	341	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551376	150551376	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015964-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	54	880	0	ENST00000369026.2:c.631G>C	p.Glu211Gln	p.E211Q	ENST00000369026	NM_021960.4	211	Gag/Cag	1/3	0.344338389560078	1	FACETS	0.231	0.198	0.267	0.231	0.198	0.267	INDETERMINATE	1	TRUE	0	0.774961009864842	1		880	369	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175891	176175891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1227884588	NA	P-0015964-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	59	611	0	ENST00000367669.3:c.224C>T	p.Ser75Leu	p.S75L	ENST00000367669	NM_022457.5	75	tCg/tTg	1/20	0.344338389560078	1	FACETS	0.338	0.293	0.386	0.338	0.293	0.386	INDETERMINATE	1	TRUE	0	0.774961009864842	1		611	276	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108864	2108864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1345813917	NA	P-0015964-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	32	624	0	ENST00000219476.3:c.965C>T	p.Ser322Leu	p.S322L	ENST00000219476	NM_000548.3	322	tCa/tTa	10/42	0.37329863166826	3	FACETS	0.306	0.249	0.372	0.153	0.124	0.186	INDETERMINATE	1	TRUE	1	0.774961009864842	3		624	374	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965185	15965185	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0015964-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	55	643	0	ENST00000268712.3:c.5411C>G	p.Ser1804Ter	p.S1804*	ENST00000268712	NM_006311.3	1804	tCa/tGa	37/46	0.37329863166826	3	FACETS	0.379	0.325	0.439	0.19	0.162	0.22	INDETERMINATE	1	TRUE	1	0.774961009864842	3		643	519	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61323233	61323233	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs769440445	NA	P-0015964-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	19	192	0	ENST00000283752.5:c.831G>C	p.Glu277Asp	p.E277D	ENST00000283752	NM_006919.2	277	gaG/gaC	8/8	0.779404813072846	1	FACETS	0.91	0.748	1	0.91	0.748	1	CLONAL	1	TRUE	0	0.774961009864842	1		192	33	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4097307	4097307	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015964-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	13	501	0	ENST00000262948.5:c.954C>G	p.Ile318Met	p.I318M	ENST00000262948	NM_030662.3	318	atC/atG	8/11	0.779404813072846	1	FACETS	0.107	0.076	0.145	0.107	0.076	0.145	SUBCLONAL	1	TRUE	0	0.774961009864842	1		501	192	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219005	36219005	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015964-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	151	767	0	ENST00000222270.7:c.4504G>A	p.Glu1502Lys	p.E1502K	ENST00000222270	NM_014727.1	1502	Gaa/Aaa	19/37	0.449004433845842	1	FACETS	0.7	0.65	0.751	0.7	0.65	0.751	INDETERMINATE	1	TRUE	0	0.774961009864842	1		767	341	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279423	1279423	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015964-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	36	592	0	ENST00000310581.5:c.2113G>C	p.Glu705Gln	p.E705Q	ENST00000310581	NM_198253.2	705	Gag/Cag	5/16	0.37329863166826	3	FACETS	0.337	0.277	0.404	0.169	0.138	0.202	INDETERMINATE	1	TRUE	1	0.774961009864842	3		592	382	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031939	26031939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015964-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	291	816	1	ENST00000244661.2:c.350G>A	p.Arg117Gln	p.R117Q	ENST00000244661	NM_003537.3	117	cGa/cAa	1/1	0.412879289263833	3	FACETS	0.968	0.923	1	0.968	0.923	1	INDETERMINATE	2	TRUE	1	0.774961009864842	3		817	538	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124491947	124491947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015964-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	196	292	0	ENST00000357628.3:c.928G>A	p.Glu310Lys	p.E310K	ENST00000357628	NM_015450.2	310	Gaa/Aaa	11/19	0.582842980286718	3	FACETS	0.836	0.784	0.887	0.836	0.784	0.887	CLONAL	2	TRUE	1	0.774961009864842	3		292	420	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404662	8404662	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0015964-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	61	322	0	ENST00000356435.5:c.4087-2A>C		p.X1363_splice	ENST00000356435		1363			NA	2	FACETS	0.46	0.399	0.526			1	INDETERMINATE	1	TRUE	NA	0.774961009864842	2		322	342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0016108-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	439	580	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.835302413008898	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.835302413008898	1		581	566	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851267	156851267	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016108-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	361	642	0	ENST00000524377.1:c.2224C>T	p.Gln742Ter	p.Q742*	ENST00000524377	NM_002529.3	742	Cag/Tag	17/17	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.835302413008898	2		642	831	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244440	46244440	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016108-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	62	349	0	ENST00000334344.6:c.2534C>A	p.Thr845Asn	p.T845N	ENST00000334344	NM_152641.2	845	aCt/aAt	15/21	1	2	FACETS	0.169	0.145	0.195	0.169	0.145	0.195	SUBCLONAL	1	TRUE	1	0.835302413008898	2		349	879	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65568995	65569782	+	splice_donor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	CGGGAAGGAAGAAGCCCCAGGACTCACGTCGCTCTCCACCTCGATGTCATCGTTATCGCTCATTTCCTACGGCCCAGGGAGCGGCCACTGCAGCGGCGGCGGGGAGGGGAAGGGGTGAAGGGGAGGGGGAAGTCACCGACAACAACAAGCCGAGTCCCCCCCACACACACACTCACTCACTCACTCACTCGCTCTCTCACTCACACACACACACAACACGGGCAAGAACCACCTCCTCACTGCAGCACCGGATCAACGGCGGCACGCACGCCCGGTCGGCCCCCGCCACGTGACCAGGCTCGCAGCGCTGGGGCAGCCGAGACTTGTAGTTCTTGTCCCTCTAACAGACGGCCCGGGTAGCTCCAGAAAAACTACAAATCCCGGAAGAAACCGCATCCAGGCGACGCCAGCCCGGCTTGTTGACGGAGCCCAAGGCGCCTGCGCGTCCCGGGGAGGGGGGGGGGGGCGGGGGGGGGCGGGGAGAGCCGCGGCGCGGCGCCTCCTGGGAGTCGTAGTCCGCAGACCGCGAGTTGTCAGGAGATTTTCCTCCCGAGGCGGCAGAGGAGGCTGCTGGGAAGACAGGACACGTGGAGGGAGCTGGAACTCCTGGAGCCGGGCACCGTCTGCGCGCTGGACGCCGGGCCCAGGGGACTGGGTGGAGTCTCTGGGGGAGTAGCCGGCTGTCTAAATAATGCTGCCTCTCTTTGGTGTGACTGGTTATACTTTGTCTTCTTCATACGGAGTGGTTCCGTTTTGCGCCTAGGGGCGTAACCCGCCCGGGAGGGAAT	CGGGAAGGAAGAAGCCCCAGGACTCACGTCGCTCTCCACCTCGATGTCATCGTTATCGCTCATTTCCTACGGCCCAGGGAGCGGCCACTGCAGCGGCGGCGGGGAGGGGAAGGGGTGAAGGGGAGGGGGAAGTCACCGACAACAACAAGCCGAGTCCCCCCCACACACACACTCACTCACTCACTCACTCGCTCTCTCACTCACACACACACACAACACGGGCAAGAACCACCTCCTCACTGCAGCACCGGATCAACGGCGGCACGCACGCCCGGTCGGCCCCCGCCACGTGACCAGGCTCGCAGCGCTGGGGCAGCCGAGACTTGTAGTTCTTGTCCCTCTAACAGACGGCCCGGGTAGCTCCAGAAAAACTACAAATCCCGGAAGAAACCGCATCCAGGCGACGCCAGCCCGGCTTGTTGACGGAGCCCAAGGCGCCTGCGCGTCCCGGGGAGGGGGGGGGGGGCGGGGGGGGGCGGGGAGAGCCGCGGCGCGGCGCCTCCTGGGAGTCGTAGTCCGCAGACCGCGAGTTGTCAGGAGATTTTCCTCCCGAGGCGGCAGAGGAGGCTGCTGGGAAGACAGGACACGTGGAGGGAGCTGGAACTCCTGGAGCCGGGCACCGTCTGCGCGCTGGACGCCGGGCCCAGGGGACTGGGTGGAGTCTCTGGGGGAGTAGCCGGCTGTCTAAATAATGCTGCCTCTCTTTGGTGTGACTGGTTATACTTTGTCTTCTTCATACGGAGTGGTTCCGTTTTGCGCCTAGGGGCGTAACCCGCCCGGGAGGGAAT	-	novel	NA	P-0016108-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	68	393	0				ENST00000358664	NM_002382.4	-/160		1/5	0.835302413008898	1	FACETS	0.668	0.599	0.737	0.668	0.599	0.737	SUBCLONAL	1	TRUE	0	0.835302413008898	1		393	142	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210832	36210832	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016108-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	439	884	0	ENST00000222270.7:c.583G>A	p.Glu195Lys	p.E195K	ENST00000222270	NM_014727.1	195	Gaa/Aaa	3/37	1	2	FACETS	0.942	0.9	0.984	0.942	0.9	0.984	CLONAL	1	TRUE	1	0.835302413008898	2		884	1116	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880963	134880963	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016108-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	656	567	0	ENST00000398015.3:c.1526G>T	p.Arg509Leu	p.R509L	ENST00000398015	NM_004441.4	509	cGc/cTc	7/16	0.807199952596445	3	FACETS	0.987	0.957	1	0.987	0.957	1	CLONAL	2	TRUE	1	0.835302413008898	3		567	1128	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940435	76940435	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016108-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	106	221	0	ENST00000373344.5:c.658T>C	p.Cys220Arg	p.C220R	ENST00000373344	NM_000489.3	220	Tgt/Cgt	8/35	1	2	FACETS	0.878	0.799	0.96	0.878	0.799	0.96	CLONAL	1	TRUE	1	0.835302413008898	2		221	289	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	55	736	1	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.782	0.669	0.906	0.782	0.669	0.906	CLONAL	1	FALSE	1	0.261826117205921	2		737	537	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	31	542	7	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	FALSE	1	0.261826117205921	2		549	216	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	87	591	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.854	0.761	0.952	1	0.983	1	CLONAL	2	FALSE	1	0.261826117205921	2		591	389	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638911	176638911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367790484	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	69	629	0	ENST00000439151.2:c.3511C>T	p.Arg1171Cys	p.R1171C	ENST00000439151	NM_022455.4	1171	Cgt/Tgt	5/23	1	2	FACETS	0.854	0.744	0.973	0.854	0.744	0.973	CLONAL	1	FALSE	1	0.261826117205921	2		629	617	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	58	868	10	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.755	0.648	0.871	0.755	0.648	0.871	SUBCLONAL	1	FALSE	1	0.261826117205921	2		878	587	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	39	522	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.851	0.707	1	0.851	0.707	1	CLONAL	1	FALSE	1	0.261826117205921	2		522	350	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	19	285	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	1	0.767	1	1	0.767	1	CLONAL	1	FALSE	1	0.261826117205921	2		285	145	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494690	2494690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770694552	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	68	715	2	ENST00000355716.4:c.830C>T	p.Thr277Met	p.T277M	ENST00000355716	NM_003820.2	277	aCg/aTg	8/8	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	FALSE	1	0.261826117205921	2		717	473	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	86	684	2	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	FALSE	1	0.261826117205921	2		686	626	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216545	108216545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779872	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	24	416	0	ENST00000278616.4:c.8494C>T	p.Arg2832Cys	p.R2832C	ENST00000278616	NM_000051.3	2832	Cgt/Tgt	58/63	1	2	FACETS	0.736	0.579	0.916	0.736	0.579	0.916	CLONAL	1	FALSE	1	0.261826117205921	2		416	249	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	69	0	0	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	FALSE	1	0.261826117205921	2		0	519	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422384	47422384	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	39	572	4	ENST00000377045.4:c.23del	p.Pro8LeufsTer26	p.P8Lfs*26	ENST00000377045	NM_001654.4	6	ggC/gg	2/16	1	2	FACETS	0.628	0.521	0.749	0.628	0.521	0.749	SUBCLONAL	1	FALSE	1	0.261826117205921	2		576	474	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473647	67473647	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886039137	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	53	632	0	ENST00000327367.4:c.727C>T	p.Arg243Cys	p.R243C	ENST00000327367	NM_005902.3	243	Cgc/Tgc	6/9	1	2	FACETS	0.739	0.63	0.858	0.739	0.63	0.858	SUBCLONAL	1	FALSE	1	0.261826117205921	2		632	548	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139625	202139626	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	39	504	0	ENST00000358485.4:c.790dup	p.Val264GlyfsTer13	p.V264Gfs*13	ENST00000358485	NM_001080125.1	262	-/G	6/9	1	2	FACETS	0.849	0.705	1	0.849	0.705	1	CLONAL	1	FALSE	1	0.261826117205921	2		504	351	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711874	89711874	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs786204862	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	26	414	0	ENST00000371953.3:c.493-1G>A		p.X165_splice	ENST00000371953	NM_000314.4	165			1	2	FACETS	0.867	0.69	1	0.867	0.69	1	CLONAL	1	FALSE	1	0.261826117205921	2		414	229	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92354984	92354984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	88	544	0	ENST00000265734.4:c.493G>A	p.Gly165Ser	p.G165S	ENST00000265734	NM_001259.6	165	Ggc/Agc	4/8	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	FALSE	1	0.261826117205921	2		544	658	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276860	15276861	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs753725730	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	89	724	1	ENST00000263388.2:c.5404dup	p.Ala1802GlyfsTer8	p.A1802Gfs*8	ENST00000263388	NM_000435.2	1802	gct/gGct	30/33	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.261826117205921	2		725	513	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	45	707	1	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.747	0.628	0.878	0.747	0.628	0.878	SUBCLONAL	1	FALSE	1	0.261826117205921	2		708	460	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074255	8074255	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	93	688	0	ENST00000377482.5:c.404del	p.Asn135ThrfsTer40	p.N135Tfs*40	ENST00000377482	NM_018948.3	135	aAc/ac	4/4	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.261826117205921	2		688	549	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341730	8341730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41281783	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	47	571	0	ENST00000356435.5:c.4910C>T	p.Thr1637Met	p.T1637M	ENST00000356435		1637	aCg/aTg	29/35	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	1	0.261826117205921	2		571	313	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029257	14029257	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1367489461	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	48	651	0	ENST00000311895.7:c.1468C>T	p.Arg490Trp	p.R490W	ENST00000311895	NM_005236.2	490	Cgg/Tgg	8/11	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	FALSE	1	0.261826117205921	2		651	346	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37091976	37091976	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	112	561	0	ENST00000231790.2:c.2104-1G>C		p.X702_splice	ENST00000231790	NM_000249.3	702			0.261826117205921	1	FACETS	0.861	0.779	0.945	1	0.987	1	CLONAL	2	FALSE	0	0.261826117205921	1		561	432	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100172	157100172	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1235492881	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	42	700	0	ENST00000346085.5:c.1114del	p.Arg372GlyfsTer7	p.R372Gfs*7	ENST00000346085	NM_020732.3	370	tCc/tc	1/20	1	2	FACETS	0.842	0.705	0.994	0.842	0.705	0.994	CLONAL	1	FALSE	1	0.261826117205921	2		700	381	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467410	66467410	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761454685	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	76	636	0	ENST00000273854.3:c.859G>A	p.Gly287Arg	p.G287R	ENST00000273854	NM_004439.5	287	Ggg/Agg	3/18	1	2	FACETS	0.976	0.857	1	0.976	0.857	1	CLONAL	1	FALSE	1	0.261826117205921	2		636	595	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	53	980	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.676	0.576	0.786	0.676	0.576	0.786	SUBCLONAL	1	FALSE	1	0.261826117205921	2		981	599	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591129	67591130	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	75	444	0	ENST00000274335.5:c.1723_1724del	p.Lys575AspfsTer26	p.K575Dfs*26	ENST00000274335		574	agAAag/agag	12/15	1	2	FACETS	0.789	0.696	0.888	1	0.978	1	SUBCLONAL	2	FALSE	1	0.261826117205921	2		444	363	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466022	69466024	+	inframe_deletion	In_Frame_Del	DEL	CCA	CCA	-	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	64	803	0	ENST00000227507.2:c.862_864del	p.Thr288del	p.T288del	ENST00000227507	NM_053056.2	287	cCCAcc/ccc	5/5	1	2	FACETS	0.955	0.828	1	0.955	0.828	1	CLONAL	1	FALSE	1	0.261826117205921	2		803	512	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992478	72992478	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	49	712	0	ENST00000268489.5:c.1567C>A	p.Leu523Ile	p.L523I	ENST00000268489	NM_006885.3	523	Ctt/Att	2/10	1	2	FACETS	0.862	0.732	1	0.862	0.732	1	CLONAL	1	FALSE	1	0.261826117205921	2		712	434	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042481	16042481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	20	362	0	ENST00000268712.3:c.1193G>A	p.Arg398Gln	p.R398Q	ENST00000268712	NM_006311.3	398	cGg/cAg	12/46	1	2	FACETS	0.821	0.632	1	0.821	0.632	1	CLONAL	1	FALSE	1	0.261826117205921	2		362	186	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727832	78727832	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	44	567	0	ENST00000306801.3:c.677A>G	p.His226Arg	p.H226R	ENST00000306801	NM_020761.2	226	cAc/cGc	6/34	1	2	FACETS	0.913	0.768	1	0.913	0.768	1	CLONAL	1	FALSE	1	0.261826117205921	2		567	368	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600408	10600408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1412883238	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	61	704	0	ENST00000171111.5:c.1447C>T	p.Arg483Cys	p.R483C	ENST00000171111	NM_203500.1	483	Cgc/Tgc	4/6	1	2	FACETS	0.703	0.606	0.809	0.703	0.606	0.809	SUBCLONAL	1	FALSE	1	0.261826117205921	2		704	663	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471037	25471039	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	53	781	0	ENST00000264709.3:c.722_724del	p.Glu241del	p.E241del	ENST00000264709	NM_175629.2	241	gAGGcc/gcc	7/23	1	2	FACETS	0.733	0.625	0.852	0.733	0.625	0.852	SUBCLONAL	1	FALSE	1	0.261826117205921	2		781	552	SUCCESS
ATR	545	MSKCC	GRCh37	3	142184046	142184048	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	22	269	0	ENST00000350721.4:c.6932_6934del	p.Lys2311del	p.K2311del	ENST00000350721	NM_001184.3	2311	aAGAtt/att	41/47	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	FALSE	1	0.261826117205921	2		269	142	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048196	180048196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	45	773	0	ENST00000261937.6:c.2077G>A	p.Asp693Asn	p.D693N	ENST00000261937	NM_182925.4	693	Gac/Aac	14/30	1	2	FACETS	0.631	0.53	0.743	0.631	0.53	0.743	SUBCLONAL	1	FALSE	1	0.261826117205921	2		773	545	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417373	139417373	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	59	948	0	ENST00000277541.6:c.671C>A	p.Pro224His	p.P224H	ENST00000277541	NM_017617.3	224	cCc/cAc	4/34	1	2	FACETS	0.892	0.769	1	0.892	0.769	1	CLONAL	1	FALSE	1	0.261826117205921	2		948	505	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324681	31324681	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137854653	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	10	146	0	ENST00000412585.2:c.127G>A	p.Glu43Lys	p.E43K	ENST00000412585	NM_005514.6	43	Gag/Aag	2/8	1	2	FACETS	0.664	0.453	0.926	0.664	0.453	0.926	SUBCLONAL	1	FALSE	1	0.261826117205921	2		146	115	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216188	36216188	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	47	801	1	ENST00000222270.7:c.3596G>C	p.Gly1199Ala	p.G1199A	ENST00000222270	NM_014727.1	1199	gGc/gCc	11/37	1	2	FACETS	0.769	0.649	0.9	0.769	0.649	0.9	SUBCLONAL	1	FALSE	1	0.261826117205921	2		802	467	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778953	9778955	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs1259321686	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	56	670	0	ENST00000377346.4:c.1228_1230del	p.Lys410del	p.K410del	ENST00000377346	NM_005026.3	408	AAG/-	9/24	1	2	FACETS	0.795	0.681	0.919	0.795	0.681	0.919	CLONAL	1	FALSE	1	0.261826117205921	2		670	538	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859859	151859859	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	45	686	0	ENST00000262189.6:c.10803del	p.Lys3604ArgfsTer26	p.K3604Rfs*26	ENST00000262189	NM_170606.2	3601	aaA/aa	43/59	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	FALSE	1	0.261826117205921	2		686	308	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754505	42754505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1174086151	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	69	656	0	ENST00000222329.4:c.235G>A	p.Asp79Asn	p.D79N	ENST00000222329	NM_006494.2	79	Gac/Aac	2/4	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	FALSE	1	0.261826117205921	2		656	497	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948208	71948209	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	50	700	0	ENST00000298229.2:c.2926_2927dup	p.Pro977HisfsTer155	p.P977Hfs*155	ENST00000298229	NM_001567.3	974	gcc/gCCcc	26/28	1	2	FACETS	0.747	0.634	0.872	0.747	0.634	0.872	SUBCLONAL	1	FALSE	1	0.261826117205921	2		700	511	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231488893	231488894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs567805129	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	33	496	0	ENST00000295050.7:c.1263dup	p.Ile422TyrfsTer11	p.I422Yfs*11	ENST00000295050	NM_032018.5	419	aat/aaTt	5/5	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	FALSE	1	0.261826117205921	2		496	199	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958589	175958589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	30	405	0	ENST00000367669.3:c.1756C>T	p.Arg586Cys	p.R586C	ENST00000367669	NM_022457.5	586	Cgt/Tgt	16/20	1	2	FACETS	0.943	0.764	1	0.943	0.764	1	CLONAL	1	FALSE	1	0.261826117205921	2		405	243	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073583	8073583	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	110	762	0	ENST00000377482.5:c.1076T>G	p.Val359Gly	p.V359G	ENST00000377482	NM_018948.3	359	gTc/gGc	4/4	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.261826117205921	2		762	589	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165516	118165516	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	86	598	0	ENST00000369448.3:c.28del	p.Asp10IlefsTer37	p.D10Ifs*37	ENST00000369448	NM_017709.3	9	aGg/ag	2/2	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	FALSE	1	0.261826117205921	2		598	626	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163313620	163313620	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	11	267	0	ENST00000271452.3:c.772del	p.Met258Ter	p.M258*	ENST00000271452	NM_145697.2	256	gAa/ga	10/14	1	2	FACETS	0.824	0.574	1	0.824	0.574	1	CLONAL	1	FALSE	1	0.261826117205921	2		267	102	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77937796	77937796	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	39	697	0	ENST00000361507.4:c.922del	p.Asp308ThrfsTer4	p.D308Tfs*4	ENST00000361507	NM_080491.2	308	Gac/ac	4/10	1	2	FACETS	0.668	0.554	0.795	0.668	0.554	0.795	SUBCLONAL	1	FALSE	1	0.261826117205921	2		697	446	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307241	118307241	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	29	440	0	ENST00000534358.1:c.14G>A	p.Cys5Tyr	p.C5Y	ENST00000534358	NM_005933.3	5	tGt/tAt	1/36	1	2	FACETS	0.862	0.695	1	0.862	0.695	1	CLONAL	1	FALSE	1	0.261826117205921	2		440	257	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563065	21563065	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	70	985	0	ENST00000382592.4:c.854del	p.Gly285ValfsTer148	p.G285Vfs*148	ENST00000382592	NM_014572.2	285	gGt/gt	4/8	1	2	FACETS	0.957	0.835	1	0.957	0.835	1	CLONAL	1	FALSE	1	0.261826117205921	2		985	559	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428327	33428327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781813	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	64	630	0	ENST00000345365.6:c.796C>T	p.Arg266Cys	p.R266C	ENST00000345365	NM_002878.3	266	Cgc/Tgc	9/10	1	2	FACETS	0.858	0.743	0.982	0.858	0.743	0.982	CLONAL	1	FALSE	1	0.261826117205921	2		630	570	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47492866	47492866	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	57	527	0	ENST00000404338.3:c.3974del	p.Phe1325SerfsTer37	p.F1325Sfs*37	ENST00000404338	NM_004491.4	1324	Ttt/tt	4/6	1	2	FACETS	0.947	0.814	1	0.947	0.814	1	CLONAL	1	FALSE	1	0.261826117205921	2		527	460	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416157	29416157	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	67	661	0	ENST00000389048.3:c.4796del	p.Pro1599LeufsTer11	p.P1599Lfs*11	ENST00000389048	NM_004304.4	1599	cCt/ct	29/29	1	2	FACETS	0.99	0.862	1	0.99	0.862	1	CLONAL	1	FALSE	1	0.261826117205921	2		661	517	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587253	212587253	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	65	524	0	ENST00000342788.4:c.748A>G	p.Met250Val	p.M250V	ENST00000342788	NM_005235.2	250	Atg/Gtg	7/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.261826117205921	2		524	406	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265102	46265102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	60	704	0	ENST00000371998.3:c.1972G>A	p.Gly658Arg	p.G658R	ENST00000371998		658	Gga/Aga	12/23	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.261826117205921	2		704	366	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478847	57478847	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1555889131	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	70	530	0	ENST00000371085.3:c.432+1G>A		p.X144_splice	ENST00000371085	NM_000516.4	144			1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.261826117205921	2		530	440	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42838081	42838081	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	36	382	0	ENST00000398585.3:c.1579-1G>A		p.X527_splice	ENST00000398585	NM_001135099.1	527			1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	FALSE	1	0.261826117205921	2		382	245	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911573	131911574	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	23	351	0	ENST00000265335.6:c.323dup	p.Thr109AspfsTer4	p.T109Dfs*4	ENST00000265335		106	-/A	3/25	1	2	FACETS	1	0.802	1	1	0.802	1	CLONAL	1	FALSE	1	0.261826117205921	2		351	172	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099828	157099828	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	56	489	0	ENST00000346085.5:c.765T>A	p.His255Gln	p.H255Q	ENST00000346085	NM_020732.3	255	caT/caA	1/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.261826117205921	2		489	305	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70353047	70353047	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	42	536	0	ENST00000374080.3:c.4602A>T	p.Lys1534Asn	p.K1534N	ENST00000374080		1534	aaA/aaT	33/45	1	2	FACETS	0.713	0.595	0.843	0.713	0.595	0.843	SUBCLONAL	1	FALSE	1	0.261826117205921	2		536	450	SUCCESS
AR	367	MSKCC	GRCh37	X	66766402	66766402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	21	459	0	ENST00000374690.3:c.1414G>A	p.Gly472Ser	p.G472S	ENST00000374690	NM_000044.3	472	Ggc/Agc	1/8	1	2	FACETS	0.54	0.416	0.685	0.54	0.416	0.685	SUBCLONAL	1	FALSE	1	0.261826117205921	2		459	297	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111145	193111146	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGAGAG	novel	NA	P-0017883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	26	524	0	ENST00000367435.3:c.683_688dup	p.Glu228_Arg229dup	p.E228_R229dup	ENST00000367435	NM_024529.4	228	-/AGAGAG	7/17	1	2	FACETS	0.579	0.459	0.717	0.579	0.459	0.717	SUBCLONAL	1	FALSE	1	0.261826117205921	2		524	343	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0018029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	101	509	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.259166737184118	3	FACETS	0.985	0.88	1	0.492	0.44	0.549	CLONAL	1	TRUE	1	0.28	3		509	835	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925711	114925711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752060378	NA	P-0018029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	29	440	0	ENST00000543371.1:c.1789G>A	p.Val597Ile	p.V597I	ENST00000543371	NM_001198531.1	597	Gtc/Atc	14/14	1	2	FACETS	0.41	0.328	0.504	0.41	0.328	0.504	SUBCLONAL	1	TRUE	1	0.28	2		440	505	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205316	61205321	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CTTAGG	CTTAGG	-	novel	NA	P-0018029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	38	392	0	ENST00000301761.2:c.256_260+1del		p.X86_splice	ENST00000301761	NM_017841.2	86		2/4	1	2	FACETS	0.532	0.439	0.636	0.532	0.439	0.636	SUBCLONAL	1	TRUE	1	0.28	2		392	510	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120977	115120977	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	30	520	0	ENST00000257566.3:c.29T>C	p.Ile10Thr	p.I10T	ENST00000257566	NM_016569.3	10	aTt/aCt	1/8	1	2	FACETS	0.357	0.287	0.437	0.357	0.287	0.437	SUBCLONAL	1	TRUE	1	0.28	2		520	600	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21347136	21347136	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	56	534	0	ENST00000215739.8:c.1203C>A	p.Tyr401Ter	p.Y401*	ENST00000215739	NM_006767.3	401	taC/taA	11/21	1	2	FACETS	0.685	0.587	0.792	0.685	0.587	0.792	SUBCLONAL	1	TRUE	1	0.28	2		534	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0018237-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	114	710	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.579220656239406	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.583749171934915	2		710	170	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018237-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	192	473	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	0.518884009927846	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	TRUE	0	0.583749171934915	3		473	275	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196048	138196048	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018237-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	37	547	0	ENST00000237289.4:c.362T>C	p.Val121Ala	p.V121A	ENST00000237289	NM_001270507.1	121	gTa/gCa	3/9	0.457057611736758	5	FACETS	0.494	0.407	0.592	0.165	0.135	0.198	SUBCLONAL	1	TRUE	2	0.583749171934915	5		547	481	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226551738	226551738	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139425386	NA	P-0018659-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	246	452	1	ENST00000366794.5:c.2692G>A	p.Ala898Thr	p.A898T	ENST00000366794	NM_001618.3	898	Gct/Act	20/23	0.47376231090275	4	FACETS	1	0.979	1	0.726	0.682	0.771	CLONAL	2	TRUE	1	0.472601210722032	4		453	704	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946490	71946490	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018659-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	138	532	0	ENST00000298229.2:c.2654T>A	p.Leu885His	p.L885H	ENST00000298229	NM_001567.3	885	cTc/cAc	23/28	0.47376231090275	3	FACETS	1	0.965	1	0.555	0.507	0.606	CLONAL	1	TRUE	1	0.472601210722032	3		532	650	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794742	120794742	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018659-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	83	522	0	ENST00000257552.2:c.615C>A	p.Tyr205Ter	p.Y205*	ENST00000257552	NM_002442.3	205	taC/taA	9/15	0.47376231090275	3	FACETS	0.653	0.576	0.735	0.327	0.288	0.368	SUBCLONAL	1	TRUE	1	0.472601210722032	3		522	665	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001452	29001452	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018659-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	44	371	0	ENST00000282397.4:c.1280A>C	p.Lys427Thr	p.K427T	ENST00000282397	NM_002019.4	427	aAa/aCa	10/30	0.231522158366245	1	FACETS	0.348	0.292	0.409	0.348	0.292	0.409	INDETERMINATE	1	TRUE	0	0.472601210722032	1		371	409	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349146	89349146	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018659-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	269	544	0	ENST00000301030.4:c.3804del	p.Lys1269SerfsTer49	p.K1269Sfs*49	ENST00000301030	NM_001256183.1	1268	agG/ag	9/13	0.47376231090275	2	FACETS	0.983	0.931	1	0.983	0.931	1	CLONAL	2	TRUE	0	0.472601210722032	2		544	579	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487510	38487510	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018659-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	103	426	0	ENST00000254066.5:c.40G>T	p.Gly14Trp	p.G14W	ENST00000254066	NM_000964.3	14	Ggg/Tgg	2/9	0.472601210722032	5	FACETS	0.866	0.774	0.964	0.289	0.258	0.322	CLONAL	1	TRUE	2	0.472601210722032	5		426	860	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226238	2226243	+	inframe_deletion	In_Frame_Del	DEL	AAGTGG	AAGTGG	-	novel	NA	P-0018659-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	271	579	0	ENST00000398665.3:c.3722_3727del	p.Trp1241_Lys1242del	p.W1241_K1242del	ENST00000398665	NM_032482.2	1240	AAGTGG/-	27/28	0.47376231090275	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.472601210722032	2		579	551	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597440	52597440	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018659-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	61	433	0	ENST00000394830.3:c.3870A>T	p.Lys1290Asn	p.K1290N	ENST00000394830	NM_018313.4	1290	aaA/aaT	25/30	0.258311893050894	5	FACETS	0.586	0.504	0.675	0.195	0.168	0.225	INDETERMINATE	1	TRUE	2	0.472601210722032	5		433	753	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31472208	31472208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018659-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	56	463	0	ENST00000344624.3:c.2203G>A	p.Glu735Lys	p.E735K	ENST00000344624		735	Gaa/Aaa	14/33	0.47376231090275	2	FACETS	0.485	0.415	0.56	0.242	0.207	0.28	SUBCLONAL	1	TRUE	0	0.472601210722032	2		463	489	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589526	67589712	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AATCTTTCTAGGATCAAGTTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACACTCAGTTTCAAGAAAAAAGTCGAGAATATGATAGATTATATGAAGAATATACCCGCACATCCCAGGTGAGTTTTCTATGAAAATCAGATTAAAAAATAAGAGTTCTAAACTTTTA	AATCTTTCTAGGATCAAGTTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACACTCAGTTTCAAGAAAAAAGTCGAGAATATGATAGATTATATGAAGAATATACCCGCACATCCCAGGTGAGTTTTCTATGAAAATCAGATTAAAAAATAAGAGTTCTAAACTTTTA	-	novel	NA	P-0018659-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	10	250	0	ENST00000274335.5:c.1300-9_1425+52del		p.X434_splice	ENST00000274335		434		10/15	0.47376231090275	3	FACETS	0.393	0.267	0.55	0.197	0.133	0.275	SUBCLONAL	1	TRUE	1	0.472601210722032	3		250	133	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677840	117677840	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018659-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	193	381	0	ENST00000368508.3:c.4093C>A	p.Leu1365Met	p.L1365M	ENST00000368508	NM_002944.2	1365	Ctg/Atg	25/43	0.329329607897534	6	FACETS	1	0.982	1	0.587	0.545	0.63	CLONAL	2	TRUE	2	0.472601210722032	6		381	677	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714421	117714421	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018659-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	277	333	0	ENST00000368508.3:c.1228G>T	p.Ala410Ser	p.A410S	ENST00000368508	NM_002944.2	410	Gca/Tca	11/43	0.329329607897534	6	FACETS	0.935	0.885	0.984	0.935	0.885	0.984	CLONAL	4	TRUE	2	0.472601210722032	6		333	610	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683680	162683680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373593750	NA	P-0018659-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	72	452	0	ENST00000366898.1:c.289C>T	p.Arg97Trp	p.R97W	ENST00000366898	NM_004562.2	97	Cgg/Tgg	3/12	0.33240879825907	4	FACETS	0.692	0.605	0.787	0.173	0.151	0.197	SUBCLONAL	1	TRUE	0	0.472601210722032	4		452	648	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624399	140624422	+	inframe_deletion	In_Frame_Del	DEL	GGCCGCGGCGCCGGCGCCGGCGCC	GGCCGCGGCGCCGGCGCCGGCGCC	-	novel	NA	P-0018659-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	299	401	0	ENST00000288602.6:c.82_105del	p.Gly28_Ala35del	p.G28_A35del	ENST00000288602	NM_004333.4	28	GGCGCCGGCGCCGGCGCCGCGGCC/-	1/18	0.329329607897534	6	FACETS	0.95	0.902	0.998	0.95	0.902	0.998	CLONAL	4	TRUE	2	0.472601210722032	6		401	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0019098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	171	778	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	1	2	FACETS	0.75	0.69	0.812	1	0.989	1	SUBCLONAL	2	TRUE	1	0.265076770262178	2		778	860	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	50	711	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	0.261670377472218	3	FACETS	0.59	0.499	0.69	0.295	0.249	0.345	SUBCLONAL	1	TRUE	1	0.265076770262178	3		711	724	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220432	1220432	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	170	1041	0	ENST00000326873.7:c.526del	p.Asp176ThrfsTer111	p.D176Tfs*111	ENST00000326873	NM_000455.4	175	aaG/aa	4/10	0.177616358494145	2	FACETS	1	0.983	1	0.626	0.575	0.679	CLONAL	1	TRUE	0	0.265076770262178	2		1041	1025	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804977	43804977	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	107	598	0	ENST00000372470.3:c.427G>T	p.Gly143Cys	p.G143C	ENST00000372470	NM_005373.2	143	Ggt/Tgt	4/12	0.261670377472218	3	FACETS	1	0.982	1	0.743	0.668	0.823	CLONAL	1	TRUE	1	0.265076770262178	3		598	615	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841473	156841473	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	190	879	0	ENST00000524377.1:c.776A>G	p.Asn259Ser	p.N259S	ENST00000524377	NM_002529.3	259	aAc/aGc	7/17	0.265076770262178	3	FACETS	0.802	0.741	0.866	0.802	0.741	0.866	CLONAL	2	TRUE	1	0.265076770262178	3		879	1012	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165673	108165673	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	30	595	0	ENST00000278616.4:c.4796C>A	p.Ser1599Ter	p.S1599*	ENST00000278616	NM_000051.3	1599	tCa/tAa	32/63	1	2	FACETS	0.545	0.439	0.666	0.545	0.439	0.666	SUBCLONAL	1	TRUE	1	0.265076770262178	2		595	415	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432191	121432191	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	105	789	0	ENST00000257555.6:c.938C>A	p.Ser313Tyr	p.S313Y	ENST00000257555		313	tCc/tAc	4/10	1	2	FACETS	0.995	0.891	1	0.995	0.891	1	CLONAL	1	TRUE	1	0.265076770262178	2		789	796	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912420	32912420	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	25	747	0	ENST00000380152.3:c.3928A>C	p.Thr1310Pro	p.T1310P	ENST00000380152		1310	Act/Cct	11/27	1	2	FACETS	0.457	0.359	0.569	0.457	0.359	0.569	SUBCLONAL	1	TRUE	1	0.265076770262178	2		747	413	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74000680	74000680	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	70	806	2	ENST00000318443.5:c.1370G>T	p.Gly457Val	p.G457V	ENST00000318443	NM_001024736.1	457	gGg/gTg	7/10	0.261670377472218	3	FACETS	0.671	0.584	0.766	0.336	0.292	0.383	SUBCLONAL	1	TRUE	1	0.265076770262178	3		808	891	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678573	88678573	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs746542638	NA	P-0019098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	74	426	0	ENST00000360948.2:c.963C>G	p.Ile321Met	p.I321M	ENST00000360948	NM_001012338.2	321	atC/atG	9/19	0.261670377472218	3	FACETS	1	0.941	1	0.563	0.493	0.637	CLONAL	1	TRUE	1	0.265076770262178	3		426	562	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631908	90631908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777305434	NA	P-0019098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	141	1008	4	ENST00000330062.3:c.445C>T	p.Arg149Trp	p.R149W	ENST00000330062	NM_002168.2	149	Cgg/Tgg	4/11	0.261670377472218	3	FACETS	1	0.935	1	0.518	0.47	0.567	CLONAL	1	TRUE	1	0.265076770262178	3		1012	1164	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225512	2225512	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	77	966	0	ENST00000326181.6:c.1515C>G	p.Ile505Met	p.I505M	ENST00000326181	NM_032271.2	505	atC/atG	17/21	0.203838159761941	3	FACETS	0.692	0.606	0.785	0.346	0.303	0.393	SUBCLONAL	1	TRUE	1	0.265076770262178	3		966	951	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636680	2636776	+	frameshift_variant	Frame_Shift_Del	DEL	GACAATCTCCTGAGCCAGTTTGGCTGCATGCAGGTGTCTTCGTCCTCCTCCTCACACTCCCTGTCAGCCTCCGACACGGGCCTGCCCCAGAGGTCAG	GACAATCTCCTGAGCCAGTTTGGCTGCATGCAGGTGTCTTCGTCCTCCTCCTCACACTCCCTGTCAGCCTCCGACACGGGCCTGCCCCAGAGGTCAG	-	novel	NA	P-0019098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	54	620	0	ENST00000342085.4:c.1130_1226del	p.Asp377AlafsTer4	p.D377Afs*4	ENST00000342085	NM_002613.4	377	GACAATCTCCTGAGCCAGTTTGGCTGCATGCAGGTGTCTTCGTCCTCCTCCTCACACTCCCTGTCAGCCTCCGACACGGGCCTGCCCCAGAGGTCAGgc/gc	11/14	0.203838159761941	3	FACETS	0.701	0.598	0.814	0.351	0.299	0.407	SUBCLONAL	1	TRUE	1	0.265076770262178	3		620	658	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647990	3647990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	117	1149	2	ENST00000294008.3:c.1174C>T	p.His392Tyr	p.H392Y	ENST00000294008	NM_032444.2	392	Cac/Tac	6/15	0.203838159761941	3	FACETS	0.893	0.804	0.989	0.447	0.402	0.495	CLONAL	1	TRUE	1	0.265076770262178	3		1151	1119	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128507	30128507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1458119852	NA	P-0019098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	158	871	0	ENST00000263025.4:c.875G>A	p.Trp292Ter	p.W292*	ENST00000263025	NM_002746.2	292	tGg/tAg	6/9	0.203838159761941	3	FACETS	1	0.987	1	0.725	0.664	0.789	CLONAL	1	TRUE	1	0.265076770262178	3		871	931	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136097	11136097	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0019098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	140	949	3	ENST00000358026.2:c.3082-1G>T		p.X1028_splice	ENST00000358026	NM_001128849.1	1028			0.177616358494145	2	FACETS	1	0.981	1	0.639	0.582	0.698	CLONAL	1	TRUE	0	0.265076770262178	2		952	827	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467043	25467043	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	183	928	0	ENST00000264709.3:c.1832A>G	p.Asn611Ser	p.N611S	ENST00000264709	NM_175629.2	611	aAt/aGt	15/23	0.261670377472218	3	FACETS	0.889	0.821	0.96	0.889	0.821	0.96	CLONAL	2	TRUE	1	0.265076770262178	3		928	879	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416535	29416535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1174344092	NA	P-0019098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	174	819	2	ENST00000389048.3:c.4418G>A	p.Gly1473Glu	p.G1473E	ENST00000389048	NM_004304.4	1473	gGg/gAg	29/29	0.261670377472218	3	FACETS	0.871	0.802	0.942	0.871	0.802	0.942	CLONAL	2	TRUE	1	0.265076770262178	3		821	854	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212615376	212615376	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	54	763	0	ENST00000342788.4:c.610C>G	p.His204Asp	p.H204D	ENST00000342788	NM_005235.2	204	Cat/Gat	5/28	1	2	FACETS	0.6	0.512	0.697	0.6	0.512	0.697	SUBCLONAL	1	TRUE	1	0.265076770262178	2		763	679	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125764	47125764	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	48	561	0	ENST00000409792.3:c.5506C>G	p.Pro1836Ala	p.P1836A	ENST00000409792	NM_014159.6	1836	Ccg/Gcg	12/21	0.109014072724219	3	FACETS	0.698	0.589	0.817	0.349	0.294	0.409	INDETERMINATE	1	TRUE	1	0.265076770262178	3		561	588	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138400881	138400881	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	50	976	0	ENST00000289153.2:c.2432G>T	p.Arg811Leu	p.R811L	ENST00000289153	NM_006219.2	811	cGa/cTa	17/22	0.203838159761941	3	FACETS	0.68	0.576	0.795	0.34	0.288	0.398	SUBCLONAL	1	TRUE	1	0.265076770262178	3		976	628	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374772	149374772	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	48	456	1	ENST00000360632.3:c.322C>T	p.Gln108Ter	p.Q108*	ENST00000360632	NM_015472.4	108	Cag/Tag	2/7	0.203838159761941	3	FACETS	0.839	0.709	0.981	0.419	0.354	0.491	CLONAL	1	TRUE	1	0.265076770262178	3		457	489	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138614	55138614	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	63	810	0	ENST00000257290.5:c.1291C>A	p.Gln431Lys	p.Q431K	ENST00000257290	NM_006206.4	431	Cag/Aag	9/23	1	2	FACETS	0.541	0.467	0.623	0.541	0.467	0.623	SUBCLONAL	1	TRUE	1	0.265076770262178	2		810	878	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629388	187629388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778980929	NA	P-0019098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	45	1022	0	ENST00000441802.2:c.1594C>T	p.Arg532Trp	p.R532W	ENST00000441802	NM_005245.3	532	Cgg/Tgg	2/27	1	2	FACETS	0.414	0.346	0.488	0.414	0.346	0.488	SUBCLONAL	1	TRUE	1	0.265076770262178	2		1022	821	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499065	149499065	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	135	891	4	ENST00000261799.4:c.2763C>A	p.Tyr921Ter	p.Y921*	ENST00000261799	NM_002609.3	921	taC/taA	20/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.265076770262178	2		895	825	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520283	176520283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760787865	NA	P-0019098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	135	733	0	ENST00000292408.4:c.1202G>A	p.Arg401His	p.R401H	ENST00000292408	NM_213647.1	401	cGc/cAc	9/18	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.265076770262178	2		733	711	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30676006	30676006	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs142090899	NA	P-0019098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	149	844	1	ENST00000376406.3:c.2350G>T	p.Ala784Ser	p.A784S	ENST00000376406	NM_014641.2	784	Gca/Tca	8/15	0.163945412399746	2	FACETS	1	0.983	1	0.652	0.596	0.711	CLONAL	1	TRUE	0	0.265076770262178	2		845	862	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392035	81392035	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	38	560	1	ENST00000222390.5:c.242C>A	p.Pro81Gln	p.P81Q	ENST00000222390	NM_000601.4	81	cCa/cAa	2/18	0.265076770262178	3	FACETS	0.808	0.675	0.953	0.538	0.45	0.636	CLONAL	2	TRUE	0	0.265076770262178	3		561	201	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513335	106513335	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	178	722	0	ENST00000359195.3:c.2239C>T	p.Leu747Phe	p.L747F	ENST00000359195	NM_002649.2	747	Ctt/Ttt	4/11	0.265076770262178	3	FACETS	1	0.951	1	0.692	0.639	0.746	CLONAL	2	TRUE	0	0.265076770262178	3		722	733	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222334	53222334	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	96	1144	0	ENST00000375401.3:c.4498G>T	p.Glu1500Ter	p.E1500*	ENST00000375401	NM_004187.3	1500	Gag/Tag	26/26	0.265076770262178	1	FACETS	0.6	0.533	0.672	0.6	0.533	0.672	SUBCLONAL	1	TRUE	0	0.265076770262178	1		1144	1047	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0019605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	386	666	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.798903434496441	2		666	893	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0019605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	774	657	1	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	0.798903434496441	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.798903434496441	2		658	908	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971207	21971207	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	495	503	0	ENST00000304494.5:c.151del	p.Val51SerfsTer2	p.V51Sfs*2	ENST00000304494	NM_000077.4	51	Gtc/tc	2/3	0.785039200985088	2	FACETS	0.979	0.954	1	0.979	0.954	1	CLONAL	2	TRUE	0	0.798903434496441	2		503	633	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740106	162740106	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	233	422	0	ENST00000367921.3:c.1308G>T	p.Met436Ile	p.M436I	ENST00000367921	NM_006182.2	436	atG/atT	12/18	1	2	FACETS	0.98	0.921	1	0.98	0.921	1	CLONAL	1	TRUE	1	0.798903434496441	2		422	595	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786142	3786142	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	413	809	1	ENST00000262367.5:c.4623A>T	p.Glu1541Asp	p.E1541D	ENST00000262367	NM_004380.2	1541	gaA/gaT	28/31	1	2	FACETS	0.958	0.914	1	0.958	0.914	1	CLONAL	1	TRUE	1	0.798903434496441	2		810	1079	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224279	36224279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1166713872	NA	P-0019605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	429	715	1	ENST00000222270.7:c.6829C>T	p.Arg2277Cys	p.R2277C	ENST00000222270	NM_014727.1	2277	Cgc/Tgc	28/37	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.798903434496441	2		716	1015	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902125	50902125	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	270	557	2	ENST00000440232.2:c.17G>T	p.Arg6Leu	p.R6L	ENST00000440232	NM_002691.3	6	cGg/cTg	2/27	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.798903434496441	2		559	653	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713466	40713466	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	366	671	0	ENST00000373198.4:c.4049T>C	p.Ile1350Thr	p.I1350T	ENST00000373198	NM_133170.3	1350	aTa/aCa	30/32	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.798903434496441	2		671	883	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134885782	134885782	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0019605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	334	587	0	ENST00000398015.3:c.1695-2A>T		p.X565_splice	ENST00000398015	NM_004441.4	565			0.798903434496441	2	FACETS	1	0.971	1	0.516	0.49	0.542	CLONAL	1	TRUE	0	0.798903434496441	2		587	811	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253750	153253751	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	160	450	0	ENST00000281708.4:c.982dup	p.Glu328GlyfsTer4	p.E328Gfs*4	ENST00000281708	NM_033632.3	328	gag/gGag	6/12	0.798903434496441	1	FACETS	0.901	0.847	0.954	0.901	0.847	0.954	CLONAL	1	TRUE	0	0.798903434496441	1		450	267	SUCCESS
APC	324	MSKCC	GRCh37	5	112174483	112174483	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	111	341	0	ENST00000257430.4:c.3192del	p.Glu1064AspfsTer62	p.E1064Dfs*62	ENST00000257430	NM_000038.5	1064	gaG/ga	16/16	0.798903434496441	1	FACETS	0.865	0.801	0.928	0.865	0.801	0.928	CLONAL	1	TRUE	0	0.798903434496441	1		341	193	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662588	117662588	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	202	429	1	ENST00000368508.3:c.4877C>A	p.Ser1626Tyr	p.S1626Y	ENST00000368508	NM_002944.2	1626	tCt/tAt	29/43	0.38070267585181	1	FACETS	0.703	0.66	0.746	0.703	0.66	0.746	INDETERMINATE	1	TRUE	0	0.798903434496441	1		430	432	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163802	152163802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	244	563	2	ENST00000206249.3:c.523G>A	p.Ala175Thr	p.A175T	ENST00000206249	NM_000125.3	175	Gct/Act	2/8	1	2	FACETS	0.98	0.923	1	0.98	0.923	1	CLONAL	1	TRUE	1	0.798903434496441	2		565	623	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172063	38173085	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATAAAAGTGATGGGAACAAGATGTCCTAGGAGAGGTTGTCAGTGCACATTCCTGGCACAATCCCATTCATCTTTTCATGACTATCGAAATAAGTCATCTTACCAGTTTTACATTCCATGCAGATGAACTTGCTATCAGGAAGTGATGCCAATCCCAGGCACTCCAGGTGAAAGTGTTTGCAGCACTCTCCCTCACAAGGAATCAGAGAGTCACCAGAGCTTTCACAAATCTGTAATATGGCAAAAAGCAGTGGTTCTCAAACTTTGGCAAACATCAAGACCACATGGGCGGCTTGTTAAACACAAATTACCGGGTCCCTCACCCACAGACTGTGATTCAGTAGGTCTGGCGGGGGCCCCAAGAATGTGCATTTCTAATATGTATCCAGAAGATGCTGATATTGTTTGTCCTTGGCCTTCACTTTGAGAACCAGAGAACTAGACAATTACAGTATTTCCAGATACAATATGGTATAAAGTTTAAAGTCATACTTGATCTTTTAGGATTCCTTCTTTGGGATCTGCATATTTAAGTTTTCTTCACAGGGCAAAGCAGTATTTTTTCAAGAACGGTAAAAATACACTGAGAAAGTTATTACTTTAAAATTTTGAATTTAAGAAAGTTTTTCCAATCAGTCATCTGCCATTTACTTCCAATTAATTATAGTATATCACACTAAAGATTGGCATGTGGGTAAGTATTCCAACTCAGAAAGGGAAAAAAAGAACCACAAAGAGGTTTTATATCTGTAGCTTTAAAGTAATATCATAATAATTTGGAAACATATTATCCTCTTCAACAGGAGTTAAGTCTATTACTGGCAGAATATAATAGCAATTATTTCAAGCCATAGCACCAGTTACCTGCCTACCTGACATACAGTGTCCTTCTTACTCATTCCAGTGCCTCTTCTCGACAAACTTGAATCCATGGACTGCACATCAGAAACGTCTGCATCTGCAGTAGCTGAAGGGCTATCTACTTGCTTTCCAAAGCCTACCTACATAGAAAACATAGCATTTT	ATAAAAGTGATGGGAACAAGATGTCCTAGGAGAGGTTGTCAGTGCACATTCCTGGCACAATCCCATTCATCTTTTCATGACTATCGAAATAAGTCATCTTACCAGTTTTACATTCCATGCAGATGAACTTGCTATCAGGAAGTGATGCCAATCCCAGGCACTCCAGGTGAAAGTGTTTGCAGCACTCTCCCTCACAAGGAATCAGAGAGTCACCAGAGCTTTCACAAATCTGTAATATGGCAAAAAGCAGTGGTTCTCAAACTTTGGCAAACATCAAGACCACATGGGCGGCTTGTTAAACACAAATTACCGGGTCCCTCACCCACAGACTGTGATTCAGTAGGTCTGGCGGGGGCCCCAAGAATGTGCATTTCTAATATGTATCCAGAAGATGCTGATATTGTTTGTCCTTGGCCTTCACTTTGAGAACCAGAGAACTAGACAATTACAGTATTTCCAGATACAATATGGTATAAAGTTTAAAGTCATACTTGATCTTTTAGGATTCCTTCTTTGGGATCTGCATATTTAAGTTTTCTTCACAGGGCAAAGCAGTATTTTTTCAAGAACGGTAAAAATACACTGAGAAAGTTATTACTTTAAAATTTTGAATTTAAGAAAGTTTTTCCAATCAGTCATCTGCCATTTACTTCCAATTAATTATAGTATATCACACTAAAGATTGGCATGTGGGTAAGTATTCCAACTCAGAAAGGGAAAAAAAGAACCACAAAGAGGTTTTATATCTGTAGCTTTAAAGTAATATCATAATAATTTGGAAACATATTATCCTCTTCAACAGGAGTTAAGTCTATTACTGGCAGAATATAATAGCAATTATTTCAAGCCATAGCACCAGTTACCTGCCTACCTGACATACAGTGTCCTTCTTACTCATTCCAGTGCCTCTTCTCGACAAACTTGAATCCATGGACTGCACATCAGAAACGTCTGCATCTGCAGTAGCTGAAGGGCTATCTACTTGCTTTCCAAAGCCTACCTACATAGAAAACATAGCATTTT	-	novel	NA	P-0019605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	24	95	0	ENST00000317025.8:c.1987-23_2242+102del		p.X663_splice	ENST00000317025	NM_023034.1	663		11-12/24	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.798903434496441	NA		95	354	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121082	11121082	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020140-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	130	892	0	ENST00000358026.2:c.2149G>T	p.Glu717Ter	p.E717*	ENST00000358026	NM_001128849.1	717	Gaa/Taa	15/36	0.185599068894061	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.185599068894061	2		892	567	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0020140-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	50	588	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.185599068894061	2		588	505	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95563013	95563013	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020140-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	44	496	0	ENST00000393063.1:c.4244A>C	p.Glu1415Ala	p.E1415A	ENST00000393063	NM_030621.3	1415	gAg/gCg	24/28	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.185599068894061	2		496	346	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023273	33023273	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020140-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	73	859	0	ENST00000300177.4:c.382C>A	p.Pro128Thr	p.P128T	ENST00000300177	NM_001191322.1	128	Ccc/Acc	2/2	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.185599068894061	2		859	633	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652836	29652836	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0020140-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	27	293	0	ENST00000356175.3:c.4773-2A>T		p.X1591_splice	ENST00000356175	NM_000267.3	1591			1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.185599068894061	2		293	246	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653082	29653082	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1567611496	NA	P-0020140-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	36	554	0	ENST00000356175.3:c.5017G>T	p.Glu1673Ter	p.E1673*	ENST00000356175	NM_000267.3	1673	Gag/Tag	36/57	1	2	FACETS	0.982	0.808	1	0.982	0.808	1	CLONAL	1	TRUE	1	0.185599068894061	2		554	395	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219357	1219370	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGAAATGCTGGA	CAGGAAATGCTGGA	-	novel	NA	P-0020140-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	79	786	0	ENST00000326873.7:c.412_425del	p.Glu138ArgfsTer20	p.E138Rfs*20	ENST00000326873	NM_000455.4	137	CAGGAAATGCTGGAc/c	3/10	NA	2	FACETS	0.99	0.875	1			1	INDETERMINATE	2	TRUE	NA	0.185599068894061	2		786	430	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2206769	2206775	+	frameshift_variant	Frame_Shift_Del	DEL	TTCAGAA	TTCAGAA	-	novel	NA	P-0020140-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	110	783	0	ENST00000398665.3:c.830_836del	p.Phe277Ter	p.F277*	ENST00000398665	NM_032482.2	277	TTCAGAAta/ta	10/28	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	2	TRUE	NA	0.185599068894061	2		783	486	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250496	10250496	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	rs772176328	NA	P-0020140-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	90	617	1	ENST00000340748.4:c.3759-3C>T		p.X1253_splice	ENST00000340748		1253			0.185599068894061	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.185599068894061	2		618	396	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599909	10599909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020140-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	123	765	3	ENST00000171111.5:c.1667C>T	p.Ala556Val	p.A556V	ENST00000171111	NM_203500.1	556	gCc/gTc	5/6	0.185599068894061	2	FACETS	0.848	0.771	0.929	1	0.979	1	CLONAL	3	TRUE	0	0.185599068894061	2		768	521	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790176	40790176	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020140-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	33	498	0	ENST00000373198.4:c.2555G>T	p.Gly852Val	p.G852V	ENST00000373198	NM_133170.3	852	gGc/gTc	18/32	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.185599068894061	2		498	313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0020422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	183	504	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.151318913339513	3	FACETS	1	0.989	1	0.725	0.667	0.784	CLONAL	1	FALSE	1	0.233285331657982	3		504	1209	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265629	152265629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	37	404	0	ENST00000206249.3:c.1082C>T	p.Ala361Val	p.A361V	ENST00000206249	NM_000125.3	361	gCg/gTg	4/8	0.233285331657982	4	FACETS	0.589	0.484	0.707	0.196	0.161	0.236	SUBCLONAL	1	FALSE	1	0.233285331657982	4		404	664	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577563	7577563	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	45	663	1	ENST00000269305.4:c.718A>T	p.Ser240Cys	p.S240C	ENST00000269305	NM_001126112.2	240	Agt/Tgt	7/11	0.151318913339513	3	FACETS	0.436	0.365	0.516	0.218	0.182	0.258	SUBCLONAL	1	FALSE	1	0.233285331657982	3		664	987	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955567	55955567	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	56	781	0	ENST00000263923.4:c.3378G>T	p.Arg1126Ser	p.R1126S	ENST00000263923	NM_002253.2	1126	agG/agT	25/30	0.233285331657982	1	FACETS	0.419	0.358	0.487	0.419	0.358	0.487	SUBCLONAL	1	FALSE	0	0.233285331657982	1		781	1012	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063372	67063372	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	89	607	0	ENST00000412916.2:c.62T>G	p.Leu21Arg	p.L21R	ENST00000412916		21	cTg/cGg	1/6	0.233285331657982	1	FACETS	0.944	0.837	1	0.944	0.837	1	CLONAL	1	FALSE	0	0.233285331657982	1		607	714	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28601427	28601427	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs367797146	NA	P-0020422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	99	673	0	ENST00000253063.3:c.1112A>G	p.Tyr371Cys	p.Y371C	ENST00000253063	NM_031459.4	371	tAt/tGt	8/10	1	2	FACETS	0.958	0.854	1	0.958	0.854	1	CLONAL	1	FALSE	1	0.233285331657982	2		673	886	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058562	72058562	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1265992180	NA	P-0020422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	121	506	1	ENST00000357731.5:c.878G>T	p.Gly293Val	p.G293V	ENST00000357731	NM_173808.2	293	gGc/gTc	6/7	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.233285331657982	2		507	799	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844792	156844792	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	161	566	0	ENST00000524377.1:c.1346G>T	p.Gly449Val	p.G449V	ENST00000524377	NM_002529.3	449	gGg/gTg	11/17	0.174068224465151	4	FACETS	0.88	0.807	0.957	0.88	0.807	0.957	CLONAL	2	FALSE	2	0.233285331657982	4		566	967	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450669	70450669	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs146039331	NA	P-0020422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	168	501	1	ENST00000373644.4:c.5509G>T	p.Ala1837Ser	p.A1837S	ENST00000373644	NM_030625.2	1837	Gct/Tct	12/12	0.233285331657982	3	FACETS	0.937	0.862	1			1	CLONAL	2	FALSE	NA	0.233285331657982	3		502	858	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023177	1023177	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	179	671	0	ENST00000358495.3:c.1078T>G	p.Leu360Val	p.L360V	ENST00000358495	NM_134424.2	360	Ttg/Gtg	11/12	0.233285331657982	5	FACETS	0.764	0.703	0.829			1	SUBCLONAL	2	FALSE	NA	0.233285331657982	5		671	1355	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466978	18466978	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	56	504	2	ENST00000266497.5:c.1117C>A	p.Pro373Thr	p.P373T	ENST00000266497		373	Cca/Aca	5/31	1	2	FACETS	0.618	0.528	0.716	0.618	0.528	0.716	SUBCLONAL	1	FALSE	1	0.233285331657982	2		506	777	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426787	49426787	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	125	346	0	ENST00000301067.7:c.11701C>T	p.Gln3901Ter	p.Q3901*	ENST00000301067	NM_003482.3	3901	Cag/Tag	39/54	0.233285331657982	5	FACETS	0.882	0.801	0.965			1	CLONAL	3	FALSE	NA	0.233285331657982	5		346	547	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41021013	41021013	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	57	815	0	ENST00000267868.3:c.635T>A	p.Val212Glu	p.V212E	ENST00000267868	NM_002875.4	212	gTa/gAa	7/10	1	2	FACETS	0.447	0.382	0.518	0.447	0.382	0.518	SUBCLONAL	1	FALSE	1	0.233285331657982	2		815	1094	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988713	41988714	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	92	471	1	ENST00000219905.7:c.1507dup	p.Ala503GlyfsTer11	p.A503Gfs*11	ENST00000219905	NM_001164273.1	502	ttg/ttGg	3/24	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.233285331657982	2		472	719	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679753	88679753	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	229	691	1	ENST00000360948.2:c.710C>G	p.Pro237Arg	p.P237R	ENST00000360948	NM_001012338.2	237	cCc/cGc	7/19	0.233285331657982	4	FACETS	1	0.984	1	0.781	0.727	0.835	CLONAL	2	FALSE	1	0.233285331657982	4		692	1034	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591879	48591879	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	106	528	0	ENST00000342988.3:c.1042G>T	p.Val348Phe	p.V348F	ENST00000342988	NM_005359.5	348	Gtt/Ttt	9/12	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.233285331657982	2		528	824	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219360	1219360	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	164	841	8	ENST00000326873.7:c.412G>T	p.Glu138Ter	p.E138*	ENST00000326873	NM_000455.4	138	Gaa/Taa	3/10	0.233285331657982	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	0	0.233285331657982	1		849	1103	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793019	33793019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	31	240	0	ENST00000498907.2:c.302G>T	p.Gly101Val	p.G101V	ENST00000498907	NM_004364.3	101	gGc/gTc	1/1	0.151318913339513	3	FACETS	0.999	0.811	1	0.5	0.405	0.606	CLONAL	1	FALSE	1	0.233285331657982	3		240	297	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546802	9546802	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	26	294	2	ENST00000353224.5:c.1220C>A	p.Ser407Ter	p.S407*	ENST00000353224	NM_177990.2	407	tCa/tAa	5/10	0.233285331657982	3	FACETS	0.601	0.476	0.745	0.301	0.238	0.373	SUBCLONAL	1	FALSE	1	0.233285331657982	3		296	414	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42840397	42840397	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	59	623	0	ENST00000398585.3:c.1351T>C	p.Tyr451His	p.Y451H	ENST00000398585	NM_001135099.1	451	Tat/Cat	12/14	1	2	FACETS	0.584	0.501	0.675	0.584	0.501	0.675	SUBCLONAL	1	FALSE	1	0.233285331657982	2		623	866	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287410	33287410	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	122	468	0	ENST00000374542.5:c.1687G>T	p.Val563Leu	p.V563L	ENST00000374542	NM_001141970.1	563	Gtg/Ttg	6/8	0.185019279019337	2	FACETS	1	0.985	1	0.747	0.676	0.822	CLONAL	1	FALSE	0	0.233285331657982	2		468	700	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511333	157511333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149389876	NA	P-0020422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	28	311	1	ENST00000346085.5:c.3851G>A	p.Gly1284Glu	p.G1284E	ENST00000346085	NM_020732.3	1284	gGa/gAa	15/20	0.233285331657982	4	FACETS	0.567	0.452	0.699	0.189	0.15	0.233	SUBCLONAL	1	FALSE	1	0.233285331657982	4		312	522	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729646	41729646	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	88	516	1	ENST00000242208.4:c.883C>A	p.Leu295Met	p.L295M	ENST00000242208	NM_002192.2	295	Ctg/Atg	3/3	1	2	FACETS	0.987	0.874	1	0.987	0.874	1	CLONAL	1	FALSE	1	0.233285331657982	2		517	764	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967707	90967707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	120	338	1	ENST00000265433.3:c.1201C>T	p.Pro401Ser	p.P401S	ENST00000265433	NM_002485.4	401	Ccc/Tcc	10/16	0.233285331657982	4	FACETS	0.958	0.867	1	0.639	0.578	0.703	CLONAL	2	FALSE	1	0.233285331657982	4		339	662	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484198	8484198	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	46	583	0	ENST00000356435.5:c.3334C>A	p.Pro1112Thr	p.P1112T	ENST00000356435		1112	Cct/Act	19/35	0.197900029193711	1	FACETS	0.427	0.358	0.503	0.427	0.358	0.503	SUBCLONAL	1	FALSE	0	0.233285331657982	1		583	816	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250157	110250157	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1345414038	NA	P-0020422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	146	675	2	ENST00000374672.4:c.518A>G	p.Tyr173Cys	p.Y173C	ENST00000374672	NM_004235.4	173	tAt/tGt	3/5	0.185857546102936	2	FACETS	1	0.987	1	0.742	0.677	0.809	CLONAL	1	FALSE	0	0.233285331657982	2		677	844	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969467	44969468	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0020422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	71	585	2	ENST00000377967.4:c.4149_4150delinsTT	p.Met1384Leu	p.M1384L	ENST00000377967	NM_021140.2	1383	ctGAtg/ctTTtg	28/29	0.197900029193711	1	FACETS	0.691	0.602	0.787	0.691	0.602	0.787	SUBCLONAL	1	FALSE	0	0.233285331657982	1		587	778	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038741	47038741	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	137	783	0	ENST00000377604.3:c.748G>T	p.Gly250Cys	p.G250C	ENST00000377604	NM_001204468.1	250	Ggc/Tgc	9/24	0.197900029193711	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	0	0.233285331657982	1		783	962	SUCCESS
AR	367	MSKCC	GRCh37	X	66765502	66765502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	126	873	1	ENST00000374690.3:c.514C>T	p.Pro172Ser	p.P172S	ENST00000374690	NM_000044.3	172	Ccc/Tcc	1/8	0.197900029193711	1	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	FALSE	0	0.233285331657982	1		874	951	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626659	100626659	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	51	619	0	ENST00000308731.7:c.271C>G	p.Gln91Glu	p.Q91E	ENST00000308731	NM_000061.2	91	Caa/Gaa	4/19	0.197900029193711	1	FACETS	0.539	0.457	0.63	0.539	0.457	0.63	SUBCLONAL	1	FALSE	0	0.233285331657982	1		619	716	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931706	28931708	+	missense_variant	Missense_Mutation	TNP	ATG	ATG	GTT	novel	NA	P-0020422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	36	456	0	ENST00000282397.4:c.2231_2233delinsAAC	p.Ala744_Tyr745delinsGluHis	p.A744_Y745delinsEH	ENST00000282397	NM_002019.4	744	gCATac/gAACac	15/30	1	2	FACETS	0.468	0.383	0.563	0.468	0.383	0.563	SUBCLONAL	1	FALSE	1	0.233285331657982	2		456	660	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436297	110436302	+	inframe_deletion	In_Frame_Del	DEL	CGGCGG	CGGCGG	-	rs34412495	NA	P-0020693-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	293	1091	1	ENST00000375856.3:c.2099_2104del	p.Ala700_Ala701del	p.A700_A701del	ENST00000375856	NM_003749.2	700	gCCGCCGtg/gtg	1/2	0.555805754794495	5	FACETS	0.837	0.792	0.882	0.628	0.594	0.662	CLONAL	3	TRUE	1	0.620691788431668	5		1092	726	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117820	70117821	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCTCCT	novel	NA	P-0020693-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	242	895	0	ENST00000245479.2:c.294_295insTGGCTCC	p.Ser99TrpfsTer155	p.S99Wfs*155	ENST00000245479	NM_000346.3	96	-/GGCTCCT	1/3	0.575340007677101	4	FACETS	0.873	0.819	0.928	0.873	0.819	0.928	CLONAL	2	TRUE	2	0.620691788431668	4		895	724	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748056	72748056	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020693-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	115	800	0	ENST00000357731.5:c.122C>A	p.Pro41His	p.P41H	ENST00000357731	NM_173808.2	41	cCc/cAc	1/7	0.596088681828763	2	FACETS	1	0.911	1	0.501	0.455	0.548	CLONAL	1	TRUE	0	0.620691788431668	2		800	370	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77937720	77937720	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020693-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	122	827	0	ENST00000361507.4:c.998A>C	p.Asp333Ala	p.D333A	ENST00000361507	NM_080491.2	333	gAc/gCc	4/10	0.611363853147162	3	FACETS	0.921	0.836	1	0.461	0.418	0.506	CLONAL	1	TRUE	1	0.620691788431668	3		827	559	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657588	37657588	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020693-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	36	596	0	ENST00000447079.4:c.2505T>A	p.His835Gln	p.H835Q	ENST00000447079	NM_015083.1	835	caT/caA	6/14	0.575340007677101	4	FACETS	0.61	0.503	0.729	0.305	0.251	0.365	SUBCLONAL	1	TRUE	2	0.620691788431668	4		596	308	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239713	98240366	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCTGCAAGACCCTTCCGGTGAGAAGGACACACAGCACACAGGAGGCTGGCTGGGCCAAGCCTGGGGGCCGGGTGGCATTTGTCAACGGACAGCAGATAAATGGCTCCTTTAGTACCTGAGTTGTTGCAGCGTTAAAGGAAATTCCGATCAATGAGCACAGGCCCAGTCCTGCAGCCACTGACAGTGCAACCAGCAGGACGCCAGCCAGCCCCACGGCACCCTGGGACTTGGAGCAGTCCCAGCGCAGCATGGTTAGACAGGCATAGGCGAGCTGCAAGCAGAACAATGGGGGCACAGAACAAAAGCCGAACATTAGAATGTGTTGTGATTCTAATGTTTCCCTCCACCCATCACCCCAAATCAAAAGGCAGAACTTATCCAACAACAACAAAACTTTACATCAAGGGCGTCACATAAAATGACAGGAGTCAAAGGTAGGCAAACGGCAAATGGGAAAAATGCTTTACACGACCACTTTTAAACCACTGTGAAGCCACGCTCTCTCTGTCCTGGATGCACATCGATGTTAAGAGCAGTTAAGAAGCAGGAGCAGTCATGGAAAAGTAAAGACTAAAACAACCAAACCAAACTCCAGCCCCCAGGAGCATGGCATCGAGCGTTACCATGAGTAAGTAGCCGCTGGCCACGCGGAT	GGCTGCAAGACCCTTCCGGTGAGAAGGACACACAGCACACAGGAGGCTGGCTGGGCCAAGCCTGGGGGCCGGGTGGCATTTGTCAACGGACAGCAGATAAATGGCTCCTTTAGTACCTGAGTTGTTGCAGCGTTAAAGGAAATTCCGATCAATGAGCACAGGCCCAGTCCTGCAGCCACTGACAGTGCAACCAGCAGGACGCCAGCCAGCCCCACGGCACCCTGGGACTTGGAGCAGTCCCAGCGCAGCATGGTTAGACAGGCATAGGCGAGCTGCAAGCAGAACAATGGGGGCACAGAACAAAAGCCGAACATTAGAATGTGTTGTGATTCTAATGTTTCCCTCCACCCATCACCCCAAATCAAAAGGCAGAACTTATCCAACAACAACAAAACTTTACATCAAGGGCGTCACATAAAATGACAGGAGTCAAAGGTAGGCAAACGGCAAATGGGAAAAATGCTTTACACGACCACTTTTAAACCACTGTGAAGCCACGCTCTCTCTGTCCTGGATGCACATCGATGTTAAGAGCAGTTAAGAAGCAGGAGCAGTCATGGAAAAGTAAAGACTAAAACAACCAAACCAAACTCCAGCCCCCAGGAGCATGGCATCGAGCGTTACCATGAGTAAGTAGCCGCTGGCCACGCGGAT	-	novel	NA	P-0020693-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	57	228	0	ENST00000331920.6:c.1318_1503+116del		p.X440_splice	ENST00000331920	NM_000264.3	440		9-10/24	0.572806137458954	2	FACETS	0.759	0.673	0.846	0.759	0.673	0.846	SUBCLONAL	2	TRUE	0	0.620691788431668	2		228	121	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	183	612	0				ENST00000310581	NM_198253.2	-/1132			0.691524639356693	6	FACETS	0.837	0.779	0.897	0.837	0.779	0.897	CLONAL	3	TRUE	3	0.691524639356693	6		612	502	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776671	9776671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	209	663	0	ENST00000377346.4:c.774G>T	p.Gln258His	p.Q258H	ENST00000377346	NM_005026.3	258	caG/caT	6/24	0.140919818767576	4	FACETS	0.991	0.928	1			1	INDETERMINATE	2	TRUE	NA	0.691524639356693	4		663	516	SUCCESS
FH	2271	MSKCC	GRCh37	1	241661258	241661258	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	88	594	0	ENST00000366560.3:c.1403C>T	p.Ala468Val	p.A468V	ENST00000366560	NM_000143.3	468	gCa/gTa	10/10	0.691524639356693	5	FACETS	0.793	0.703	0.889	0.198	0.175	0.223	SUBCLONAL	1	TRUE	1	0.691524639356693	5		594	654	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710987	114710987	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	155	467	1	ENST00000543371.1:c.211C>G	p.Arg71Gly	p.R71G	ENST00000543371	NM_001198531.1	71	Cgc/Ggc	2/14	0.59257302301552	3	FACETS	0.777	0.72	0.835	0.777	0.72	0.835	SUBCLONAL	2	TRUE	1	0.691524639356693	3		468	388	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918436	94918436	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	111	567	0	ENST00000536441.1:c.746C>T	p.Ser249Leu	p.S249L	ENST00000536441	NM_144665.3	249	tCa/tTa	5/10	0.691524639356693	3	FACETS	1	0.915	1	0.506	0.458	0.556	CLONAL	1	TRUE	1	0.691524639356693	3		567	427	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878187	48878187	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0021266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	121	198	0	ENST00000267163.4:c.137+2T>G		p.X46_splice	ENST00000267163	NM_000321.2	46			0.691524639356693	3	FACETS	0.929	0.874	0.981	0.929	0.874	0.981	CLONAL	3	TRUE	0	0.691524639356693	3		198	169	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831437	89831437	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	116	675	0	ENST00000389301.3:c.2639G>C	p.Arg880Pro	p.R880P	ENST00000389301	NM_000135.2	880	cGa/cCa	28/43	0.633697291802986	2	FACETS	0.856	0.778	0.936	0.428	0.389	0.468	CLONAL	1	TRUE	0	0.691524639356693	2		675	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0021266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	279	715	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.633697291802986	2	FACETS	0.835	0.796	0.874	0.835	0.796	0.874	CLONAL	2	TRUE	0	0.691524639356693	2		715	483	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16046984	16046984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	77	531	1	ENST00000268712.3:c.1109C>T	p.Ser370Leu	p.S370L	ENST00000268712	NM_006311.3	370	tCa/tTa	11/46	0.633697291802986	2	FACETS	0.801	0.711	0.895	0.401	0.355	0.448	CLONAL	1	TRUE	0	0.691524639356693	2		532	278	SUCCESS
YES1	7525	MSKCC	GRCh37	18	732954	732954	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	211	551	2	ENST00000314574.4:c.1303C>A	p.Pro435Thr	p.P435T	ENST00000314574	NM_005433.3	435	Cca/Aca	11/12	0.552475446052306	4	FACETS	0.954	0.894	1	0.954	0.894	1	CLONAL	2	TRUE	2	0.691524639356693	4		553	541	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207162	1207162	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs137853076	NA	P-0021266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	550	869	1	ENST00000326873.7:c.250A>T	p.Lys84Ter	p.K84*	ENST00000326873	NM_000455.4	84	Aag/Tag	1/10	0.626173122404466	3	FACETS	0.968	0.943	0.993	0.968	0.943	0.993	CLONAL	3	TRUE	0	0.691524639356693	3		870	737	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748800	41748800	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0021266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	142	796	0	ENST00000301178.4:c.1325C>G	p.Ser442Ter	p.S442*	ENST00000301178	NM_021913.4	442	tCa/tGa	11/20	0.552475446052306	4	FACETS	0.891	0.812	0.973	0.445	0.406	0.487	CLONAL	1	TRUE	2	0.691524639356693	4		796	780	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917077	50917077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	188	924	0	ENST00000440232.2:c.2329G>A	p.Glu777Lys	p.E777K	ENST00000440232	NM_002691.3	777	Gag/Aag	19/27	0.104123926390079	6	FACETS	0.763	0.706	0.822			1	INDETERMINATE	2	TRUE	NA	0.691524639356693	6		924	849	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61717860	61717860	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs754930781	NA	P-0021266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	167	724	0	ENST00000401558.2:c.1939C>G	p.Gln647Glu	p.Q647E	ENST00000401558	NM_003400.3	647	Caa/Gaa	17/25	0.475615563601282	4	FACETS	1	0.93	1	0.506	0.465	0.548	CLONAL	1	TRUE	2	0.691524639356693	4		724	808	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160468	99160468	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	73	432	0	ENST00000074304.5:c.947G>A	p.Arg316Lys	p.R316K	ENST00000074304	NM_001134224.1	316	aGa/aAa	11/26	0.156135187649584	6	FACETS	1	0.949	1			1	INDETERMINATE	1	TRUE	NA	0.691524639356693	6		432	435	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439984	220439984	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	404	952	0	ENST00000243786.2:c.837G>T	p.Trp279Cys	p.W279C	ENST00000243786	NM_002191.3	279	tgG/tgT	2/2	0.552475446052306	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.691524639356693	4		952	973	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729966	39729966	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	97	556	0	ENST00000361337.2:c.1281C>G	p.Ile427Met	p.I427M	ENST00000361337	NM_003286.2	427	atC/atG	13/21	0.475615563601282	4	FACETS	0.953	0.853	1	0.476	0.426	0.529	CLONAL	1	TRUE	2	0.691524639356693	4		556	498	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729983	39729983	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	89	466	0	ENST00000361337.2:c.1298C>A	p.Ser433Ter	p.S433*	ENST00000361337	NM_003286.2	433	tCa/tAa	13/21	0.475615563601282	4	FACETS	0.961	0.856	1	0.481	0.428	0.536	CLONAL	1	TRUE	2	0.691524639356693	4		466	453	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743858	40743858	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs374930365	NA	P-0021266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	218	611	0	ENST00000373198.4:c.3137G>C	p.Arg1046Pro	p.R1046P	ENST00000373198	NM_133170.3	1046	cGc/cCc	23/32	0.475615563601282	4	FACETS	0.951	0.891	1	0.951	0.891	1	CLONAL	2	TRUE	2	0.691524639356693	4		611	561	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961352	54961352	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	243	571	0	ENST00000312783.6:c.280A>G	p.Asn94Asp	p.N94D	ENST00000312783	NM_198436.1	94	Aac/Gac	4/10	0.475615563601282	4	FACETS	0.935	0.879	0.991	0.935	0.879	0.991	CLONAL	2	TRUE	2	0.691524639356693	4		571	636	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52677333	52677333	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	125	569	1	ENST00000394830.3:c.926G>T	p.Arg309Ile	p.R309I	ENST00000394830	NM_018313.4	309	aGa/aTa	10/30	0.661822886485619	3	FACETS	0.916	0.833	1	0.458	0.416	0.502	CLONAL	1	TRUE	1	0.691524639356693	3		570	531	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189912	66189912	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	57	379	0	ENST00000273854.3:c.3034C>A	p.Leu1012Ile	p.L1012I	ENST00000273854	NM_004439.5	1012	Ctt/Att	18/18	0.59257302301552	3	FACETS	0.596	0.514	0.686	0.298	0.257	0.343	SUBCLONAL	1	TRUE	1	0.691524639356693	3		379	372	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456977	149456977	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	196	496	0	ENST00000286301.3:c.751G>C	p.Asp251His	p.D251H	ENST00000286301	NM_005211.3	251	Gac/Cac	6/22	0.628599668153419	3	FACETS	0.966	0.908	1	0.644	0.605	0.683	CLONAL	2	TRUE	0	0.691524639356693	3		496	395	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165243	32165243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	147	736	0	ENST00000375023.3:c.4885C>T	p.His1629Tyr	p.H1629Y	ENST00000375023	NM_004557.3	1629	Cac/Tac	27/30	0.594030374411183	4	FACETS	0.986	0.902	1	0.493	0.451	0.537	CLONAL	1	TRUE	2	0.691524639356693	4		736	729	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983885	2983885	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	187	823	0	ENST00000396946.4:c.645G>C	p.Lys215Asn	p.K215N	ENST00000396946	NM_032415.4	215	aaG/aaC	5/25	0.594030374411183	4	FACETS	1	0.971	1	0.548	0.507	0.591	CLONAL	1	TRUE	2	0.691524639356693	4		823	834	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450366	50450366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	234	571	1	ENST00000331340.3:c.550C>T	p.Arg184Trp	p.R184W	ENST00000331340	NM_006060.4	184	Cgg/Tgg	5/8	0.594030374411183	4	FACETS	0.894	0.84	0.95	0.894	0.84	0.95	CLONAL	2	TRUE	2	0.691524639356693	4		572	640	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197767	123197767	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	133	628	2	ENST00000218089.9:c.1891G>T	p.Ala631Ser	p.A631S	ENST00000218089	NM_001042749.1	631	Gca/Tca	20/35	0.346726101473054	4	FACETS	1	0.982	1	0.649	0.593	0.708	INDETERMINATE	1	TRUE	2	0.691524639356693	4		630	501	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864456	56864456	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	145	619	0	ENST00000308159.5:c.944G>T	p.Gly315Val	p.G315V	ENST00000308159	NM_014669.4	315	gGc/gTc	10/22	1	2	FACETS	0.863	0.786	0.943	0.863	0.786	0.943	CLONAL	1	TRUE	1	0.352794458265423	2		619	953	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224714	36224714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768250201	NA	P-0022001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	222	932	1	ENST00000222270.7:c.7100C>T	p.Pro2367Leu	p.P2367L	ENST00000222270	NM_014727.1	2367	cCc/cTc	30/37	1	2	FACETS	0.986	0.916	1	0.986	0.916	1	CLONAL	1	TRUE	1	0.352794458265423	2		933	1276	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894842	101894842	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	79	464	0	ENST00000374994.4:c.395G>A	p.Gly132Glu	p.G132E	ENST00000374994	NM_004612.2	132	gGa/gAa	3/9	0.352794458265423	1	FACETS	0.703	0.619	0.792	0.703	0.619	0.792	SUBCLONAL	1	TRUE	0	0.352794458265423	1		464	525	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0023172-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	107	580	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.421782848848553	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.421782848848553	3		581	248	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918514	44918514	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023172-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	53	227	0	ENST00000377967.4:c.997C>T	p.Gln333Ter	p.Q333*	ENST00000377967	NM_021140.2	333	Cag/Tag	12/29	0.388210133121482	2	FACETS	1	0.935	1			1	CLONAL	3	TRUE	NA	0.421782848848553	2		227	80	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060728	38060728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023172-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	51	704	0	ENST00000250448.2:c.1261G>A	p.Glu421Lys	p.E421K	ENST00000250448	NM_004496.3	421	Gaa/Aaa	2/2	0.421782848848553	2	FACETS	0.971	0.833	1	0.486	0.416	0.56	CLONAL	1	TRUE	0	0.421782848848553	2		704	249	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420213	49420213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267607237	NA	P-0023172-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	111	694	1	ENST00000301067.7:c.15536G>A	p.Arg5179His	p.R5179H	ENST00000301067	NM_003482.3	5179	cGt/cAt	48/54	0.421782848848553	5	FACETS	0.974	0.889	1	0.974	0.889	1	CLONAL	3	TRUE	2	0.421782848848553	5		695	294	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858254	59858254	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs780020495	NA	P-0023172-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	23	402	0	ENST00000259008.2:c.1741C>T	p.Arg581Ter	p.R581*	ENST00000259008	NM_032043.2	581	Cga/Tga	12/20	0.39382697145959	3	FACETS	1	0.857	1	0.555	0.439	0.684	CLONAL	1	TRUE	1	0.421782848848553	3		402	119	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347526	118347526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023172-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	23	413	0	ENST00000534358.1:c.3163G>A	p.Glu1055Lys	p.E1055K	ENST00000534358	NM_005933.3	1055	Gaa/Aaa	4/36	0.338171501977538	3	FACETS	1	0.796	1	0.504	0.398	0.623	CLONAL	1	TRUE	1	0.421782848848553	3		413	131	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427694	49427694	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023172-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	50	669	0	ENST00000301067.7:c.10794G>T	p.Lys3598Asn	p.K3598N	ENST00000301067	NM_003482.3	3598	aaG/aaT	39/54	0.421782848848553	5	FACETS	1	0.936	1	0.396	0.337	0.459	CLONAL	1	TRUE	2	0.421782848848553	5		669	326	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164370	47164370	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023172-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	11	409	0	ENST00000409792.3:c.1756C>T	p.His586Tyr	p.H586Y	ENST00000409792	NM_014159.6	586	Cat/Tat	3/21	0.39382697145959	3	FACETS	0.789	0.553	1	0.395	0.276	0.537	CLONAL	1	TRUE	1	0.421782848848553	3		409	80	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628697	187628698	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0023172-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	49	598	0	ENST00000441802.2:c.2283_2284dup	p.Asp762GlyfsTer6	p.D762Gfs*6	ENST00000441802	NM_005245.3	762	gat/gGGat	2/27	0.281281284132278	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	2	TRUE	0	0.421782848848553	2		598	116	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0023357-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	364	377	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.906662440628292	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.906662440628292	3		377	545	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0023357-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	363	358	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	0.906662440628292	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.906662440628292	3		358	548	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226174	2226174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023357-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	666	710	1	ENST00000326181.6:c.1871C>T	p.Ser624Phe	p.S624F	ENST00000326181	NM_032271.2	624	tCc/tTc	19/21	0.906662440628292	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	2	0.906662440628292	4		711	1303	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252880	36252880	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023357-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	492	483	0	ENST00000300305.3:c.482T>A	p.Leu161His	p.L161H	ENST00000300305		161	cTc/cAc	4/8	0.906662440628292	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.906662440628292	3		483	787	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827262	72827262	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023357-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	649	613	0	ENST00000268489.5:c.9319C>T	p.Gln3107Ter	p.Q3107*	ENST00000268489	NM_006885.3	3107	Cag/Tag	9/10	0.906662440628292	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.906662440628292	2		613	704	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217458	7217458	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023357-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	544	644	1	ENST00000380728.2:c.338C>A	p.Ser113Ter	p.S113*	ENST00000380728		113	tCa/tAa	5/11	0.906662440628292	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.906662440628292	2		645	584	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100041	157100055	+	inframe_deletion	In_Frame_Del	DEL	AGGAGGAGCAGGAGC	AGGAGGAGCAGGAGC	-	rs773423003	NA	P-0023357-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	88	805	0	ENST00000346085.5:c.993_1007del	p.Gly333_Gly337del	p.G333_G337del	ENST00000346085	NM_020732.3	326	ggAGGAGGAGCAGGAGCa/gga	1/20	0.906662440628292	3	FACETS	0.777	0.694	0.865	0.389	0.347	0.433	SUBCLONAL	1	TRUE	1	0.906662440628292	3		805	363	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100049	157100049	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1256773336	NA	P-0023357-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	25	813	5	ENST00000346085.5:c.986C>G	p.Ala329Gly	p.A329G	ENST00000346085	NM_020732.3	329	gCa/gGa	1/20	0.906662440628292	3	FACETS	0.214	0.168	0.267	0.107	0.084	0.134	SUBCLONAL	1	TRUE	1	0.906662440628292	3		818	374	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100055	157100055	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1462890053	NA	P-0023357-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	56	838	0	ENST00000346085.5:c.992C>G	p.Ala331Gly	p.A331G	ENST00000346085	NM_020732.3	331	gCa/gGa	1/20	0.906662440628292	3	FACETS	0.449	0.386	0.517	0.224	0.193	0.259	SUBCLONAL	1	TRUE	1	0.906662440628292	3		838	400	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849652	68849652	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023357-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	551	569	0	ENST00000261769.5:c.1555C>T	p.Gln519Ter	p.Q519*	ENST00000261769	NM_004360.3	519	Cag/Tag	10/16	0.906662440628292	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.906662440628292	2		569	605	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016559	12016559	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023357-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	463	410	0	ENST00000353533.5:c.695C>T	p.Pro232Leu	p.P232L	ENST00000353533	NM_003010.3	232	cCt/cTt	7/11	0.906662440628292	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.906662440628292	2		410	495	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118339493	118339493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782605513	NA	P-0023357-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	190	468	0	ENST00000534358.1:c.436G>A	p.Glu146Lys	p.E146K	ENST00000534358	NM_005933.3	146	Gag/Aag	2/36	0.906662440628292	3	FACETS	0.898	0.834	0.965	0.449	0.417	0.483	CLONAL	1	TRUE	1	0.906662440628292	3		468	678	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911982	32911982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023357-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	355	547	0	ENST00000380152.3:c.3490C>T	p.Leu1164Phe	p.L1164F	ENST00000380152		1164	Ctt/Ttt	11/27	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.906662440628292	2		547	701	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978815	13978815	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023357-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	616	437	0	ENST00000405192.2:c.292G>C	p.Glu98Gln	p.E98Q	ENST00000405192	NM_001163147.1	98	Gaa/Caa	6/12	0.84420251393575	4	FACETS	0.981	0.946	1	0.981	0.946	1	CLONAL	2	TRUE	2	0.906662440628292	4		437	1321	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44733219	44733219	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023357-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	365	418	0	ENST00000377967.4:c.211G>C	p.Ala71Pro	p.A71P	ENST00000377967	NM_021140.2	71	Gcc/Ccc	2/29	0.906662440628292	5	FACETS	1	0.963	1	1	0.963	1	CLONAL	3	TRUE	2	0.906662440628292	5		418	631	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223070	41223070	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023357-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	472	631	0	ENST00000357654.3:c.4861G>A	p.Asp1621Asn	p.D1621N	ENST00000357654	NM_007294.3	1621	Gat/Aat	15/23	0.906662440628292	2	FACETS	0.986	0.946	1	0.493	0.473	0.513	CLONAL	1	TRUE	0	0.906662440628292	2		631	1056	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29440871	29440871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372884606	NA	P-0023357-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	14	0	0	ENST00000544604.2:c.737G>A	p.Arg246His	p.R246H	ENST00000544604	NM_001206998.1	246	cGc/cAc	5/9	0.906662440628292	3	FACETS	0.06	0.043	0.082	0.03	0.021	0.041	SUBCLONAL	1	TRUE	1	0.906662440628292	3		0	744	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247304	153247304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023357-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	247	546	0	ENST00000281708.4:c.1498C>T	p.His500Tyr	p.H500Y	ENST00000281708	NM_033632.3	500	Cat/Tat	10/12	0.906662440628292	3	FACETS	1	0.977	1	0.54	0.507	0.574	CLONAL	1	TRUE	1	0.906662440628292	3		546	733	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099981	157099982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCGGCGGCGGCGGC	novel	NA	P-0023357-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	61	834	1	ENST00000346085.5:c.930_944dup	p.Gly315_Gly319dup	p.G315_G319dup	ENST00000346085	NM_020732.3	315	-/GGCGGCGGCGGCGGC	1/20	0.906662440628292	3	FACETS	0.29	0.249	0.334	0.145	0.124	0.167	SUBCLONAL	1	TRUE	1	0.906662440628292	3		835	675	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196061	138196075	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGTTCAGCACGCT	GCTGTTCAGCACGCT	C	novel	NA	P-0023357-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	48	563	0	ENST00000237289.4:c.375_389delinsC	p.Leu126GlnfsTer9	p.L126Qfs*9	ENST00000237289	NM_001270507.1	125	gcGCTGTTCAGCACGCTc/gcCc	3/9	0.906662440628292	3	FACETS	0.189	0.159	0.222	0.094	0.079	0.111	SUBCLONAL	1	TRUE	1	0.906662440628292	3		563	816	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0023926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	328	891	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			NA	2	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.393697481371476	2		891	776	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959118	28959118	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	206	618	0	ENST00000282397.4:c.2020A>G	p.Ile674Val	p.I674V	ENST00000282397	NM_002019.4	674	Atc/Gtc	14/30	0.393697481371476	2	FACETS	0.967	0.905	1	0.967	0.905	1	CLONAL	2	TRUE	0	0.393697481371476	2		618	541	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32931887	32931888	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0023926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	102	598	0	ENST00000380152.3:c.7626_7627del	p.Tyr2543TrpfsTer4	p.Y2543Wfs*4	ENST00000380152		2542	acGTat/acat	16/27	0.393697481371476	2	FACETS	0.969	0.869	1	0.484	0.434	0.537	CLONAL	1	TRUE	0	0.393697481371476	2		598	535	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636706	2636706	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	147	688	2	ENST00000342085.4:c.1155C>G	p.Cys385Trp	p.C385W	ENST00000342085	NM_002613.4	385	tgC/tgG	11/14	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.393697481371476	2		690	660	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821817	59821817	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	151	822	0	ENST00000259008.2:c.2233G>C	p.Ala745Pro	p.A745P	ENST00000259008	NM_032043.2	745	Gca/Cca	15/20	0.369431820393367	3	FACETS	0.917	0.838	1	0.459	0.419	0.501	CLONAL	1	TRUE	1	0.393697481371476	3		822	1001	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971053	21971053	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs137854598	NA	P-0023926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	100	590	0	ENST00000304494.5:c.305C>A	p.Ala102Glu	p.A102E	ENST00000304494	NM_000077.4	102	gCg/gAg	2/3	0.366952498666112	2	FACETS	1	0.978	1	0.667	0.6	0.736	CLONAL	1	TRUE	0	0.393697481371476	2		590	381	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0024249-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	42	287	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.15	2		287	554	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241894	133241894	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs757051826	NA	P-0024249-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	64	658	0	ENST00000320574.5:c.2462G>T	p.Arg821Leu	p.R821L	ENST00000320574	NM_006231.2	821	cGc/cTc	21/49	1	2	FACETS	0.926	0.799	1	0.926	0.799	1	CLONAL	1	TRUE	1	0.15	2		658	922	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0025657-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	131	578	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.275198628630697	3	FACETS	0.899	0.826	0.974	0.899	0.826	0.974	CLONAL	3	TRUE	0	0.321080783034698	3		578	351	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861055	35861055	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025657-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	55	351	0	ENST00000303115.3:c.184C>A	p.Pro62Thr	p.P62T	ENST00000303115	NM_002185.3	62	Cca/Aca	2/8	1	2	FACETS	0.684	0.585	0.791	0.684	0.585	0.791	SUBCLONAL	1	TRUE	1	0.321080783034698	2		351	501	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578209	7578209	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025657-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	253	530	0	ENST00000269305.4:c.640C>G	p.His214Asp	p.H214D	ENST00000269305	NM_001126112.2	214	Cat/Gat	6/11	0.318378866569522	3	FACETS	0.972	0.917	1	0.972	0.917	1	CLONAL	3	TRUE	0	0.321080783034698	3		530	627	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411879	116411900	+	splice_region_variant,intron_variant	Splice_Region	DEL	CTCTTTCTTTCTCTCTGTTTTA	CTCTTTCTTTCTCTCTGTTTTA	-	novel	NA	P-0025657-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	1360	848	0	ENST00000397752.3:c.2888-24_2888-3del		p.X963_splice	ENST00000397752	NM_000245.2	963			0.321080783034698	12	FACETS	0.968	0.951	0.985			1	CLONAL	12	TRUE	NA	0.321080783034698	12		848	1900	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667344	241667344	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025657-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	27	321	0	ENST00000366560.3:c.1106C>G	p.Pro369Arg	p.P369R	ENST00000366560	NM_000143.3	369	cCa/cGa	7/10	1	2	FACETS	0.394	0.313	0.487	0.394	0.313	0.487	SUBCLONAL	1	TRUE	1	0.321080783034698	2		321	427	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211690	36211690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025657-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	35	465	0	ENST00000222270.7:c.1441G>A	p.Glu481Lys	p.E481K	ENST00000222270	NM_014727.1	481	Gag/Aag	3/37	0.321080783034698	3	FACETS	0.404	0.33	0.487	0.202	0.165	0.244	SUBCLONAL	1	TRUE	1	0.321080783034698	3		465	627	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778239	27778239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025657-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	64	397	0	ENST00000369163.2:c.388C>T	p.Arg130Cys	p.R130C	ENST00000369163	NM_003536.2	130	Cgt/Tgt	1/1	0.321080783034698	0	FACETS	0.555	0.481	0.634			1	SUBCLONAL	1	TRUE	0	0.321080783034698	0		397	488	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138197217	138197217	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025657-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	38	387	0	ENST00000237289.4:c.719C>G	p.Ala240Gly	p.A240G	ENST00000237289	NM_001270507.1	240	gCc/gGc	5/9	0.144530564103324	3	FACETS	0.467	0.385	0.559	0.156	0.128	0.187	INDETERMINATE	1	TRUE	0	0.321080783034698	3		387	588	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0026521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	307	536	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.752367106693159	3	FACETS	0.965	0.92	1	0.965	0.92	1	CLONAL	2	TRUE	1	0.752367106693159	3		536	582	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462123	120462123	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	376	555	1	ENST00000256646.2:c.5593C>T	p.Gln1865Ter	p.Q1865*	ENST00000256646	NM_024408.3	1865	Cag/Tag	31/34	0.752367106693159	3	FACETS	0.991	0.95	1	0.991	0.95	1	CLONAL	2	TRUE	1	0.752367106693159	3		556	694	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	730	553	2	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	0.71859569031077	5	FACETS	0.916	0.892	0.94	0.916	0.892	0.94	CLONAL	4	TRUE	1	0.752367106693159	5		555	1127	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038529	47038529	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	477	342	0	ENST00000377604.3:c.691G>T	p.Glu231Ter	p.E231*	ENST00000377604	NM_001204468.1	231	Gag/Tag	8/24	0.752367106693159	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.752367106693159	2		342	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	882	660	0	ENST00000269305.4:c.880del	p.Glu294SerfsTer51	p.E294Sfs*51	ENST00000269305	NM_001126112.2	294	Gag/ag	8/11	0.733731325324602	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.752367106693159	3		660	1066	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610085	28610085	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	153	462	0	ENST00000241453.7:c.1405G>T	p.Asp469Tyr	p.D469Y	ENST00000241453	NM_004119.2	469	Gac/Tac	11/24	0.752367106693159	3	FACETS	0.93	0.854	1	0.465	0.427	0.504	CLONAL	1	TRUE	1	0.752367106693159	3		462	602	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774216	66774216	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1473690179	NA	P-0026521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	380	662	1	ENST00000307102.5:c.692C>T	p.Ser231Leu	p.S231L	ENST00000307102	NM_002755.3	231	tCg/tTg	6/11	0.360962807706524	5	FACETS	0.962	0.914	1	0.641	0.609	0.673	INDETERMINATE	2	TRUE	2	0.752367106693159	5		663	1118	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81399260	81399260	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1390087672	NA	P-0026521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	610	545	0	ENST00000222390.5:c.28C>A	p.Leu10Met	p.L10M	ENST00000222390	NM_000601.4	10	Ctg/Atg	1/18	0.752367106693159	5	FACETS	0.905	0.874	0.937			1	CLONAL	3	TRUE	NA	0.752367106693159	5		545	1271	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940083	76940083	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	208	223	0	ENST00000373344.5:c.665G>T	p.Trp222Leu	p.W222L	ENST00000373344	NM_000489.3	222	tGg/tTg	9/35	0.752367106693159	2	FACETS	1	0.987	1			1	CLONAL	2	TRUE	NA	0.752367106693159	2		223	259	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980335	201980335	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	262	678	0	ENST00000359651.3:c.71C>A	p.Ser24Tyr	p.S24Y	ENST00000359651		24	tCc/tAc	1/8	0.752367106693159	3	FACETS	0.921	0.863	0.98	0.46	0.431	0.49	CLONAL	1	TRUE	1	0.752367106693159	3		678	1041	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631170	69631170	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	576	605	0	ENST00000334134.2:c.242T>A	p.Val81Glu	p.V81E	ENST00000334134	NM_005247.2	81	gTg/gAg	2/3	0.752367106693159	4	FACETS	0.955	0.925	0.984	0.955	0.925	0.984	CLONAL	3	TRUE	1	0.752367106693159	4		605	937	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999179	100999179	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	790	653	4	ENST00000325455.5:c.623C>A	p.Ala208Asp	p.A208D	ENST00000325455	NM_001202474.3	208	gCc/gAc	1/8	0.714237450727175	5	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	2	0.752367106693159	5		657	1448	SUCCESS
ATM	472	MSKCC	GRCh37	11	108137947	108137947	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	205	402	0	ENST00000278616.4:c.2516A>T	p.Glu839Val	p.E839V	ENST00000278616	NM_000051.3	839	gAa/gTa	17/63	0.714237450727175	5	FACETS	0.876	0.817	0.937	0.584	0.544	0.625	CLONAL	2	TRUE	2	0.752367106693159	5		402	662	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509684	29509684	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1135402799	NA	P-0026521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	202	442	0	ENST00000356175.3:c.888+1G>A		p.X296_splice	ENST00000356175	NM_000267.3	296			0.752367106693159	3	FACETS	0.819	0.769	0.87	0.819	0.769	0.87	CLONAL	2	TRUE	1	0.752367106693159	3		442	451	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257165	198257166	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0026521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	164	355	0	ENST00000335508.6:c.3776_3777delinsTT	p.Arg1259Leu	p.R1259L	ENST00000335508	NM_012433.2	1259	cGG/cTT	25/25	0.6752163875037	4	FACETS	0.836	0.775	0.898	0.836	0.775	0.898	CLONAL	2	TRUE	2	0.752367106693159	4		355	457	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757450	40757450	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	409	602	0	ENST00000373198.4:c.2848C>G	p.Leu950Val	p.L950V	ENST00000373198	NM_133170.3	950	Ctg/Gtg	20/32	0.6752163875037	4	FACETS	0.888	0.847	0.929	0.888	0.847	0.929	CLONAL	2	TRUE	2	0.752367106693159	4		602	1073	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866424	42866424	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	587	818	0	ENST00000398585.3:c.208G>T	p.Val70Phe	p.V70F	ENST00000398585	NM_001135099.1	70	Gtc/Ttc	3/14	0.752367106693159	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.752367106693159	2		818	749	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523507	41523507	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	153	335	0	ENST00000263253.7:c.923C>A	p.Pro308Gln	p.P308Q	ENST00000263253	NM_001429.3	308	cCg/cAg	4/31	NA	2	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.752367106693159	2		335	357	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750464	41750464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	418	499	0	ENST00000226382.2:c.164C>T	p.Ser55Phe	p.S55F	ENST00000226382	NM_003924.3	55	tCc/tTc	1/3	0.752367106693159	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.752367106693159	4		499	906	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271240	1271240	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	100	253	0	ENST00000310581.5:c.2462G>T	p.Arg821Met	p.R821M	ENST00000310581	NM_198253.2	821	aGg/aTg	8/16	0.699015483937877	5	FACETS	1	0.929	1			1	CLONAL	1	TRUE	NA	0.752367106693159	5		253	541	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588928	67588928	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0026521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	85	242	0	ENST00000274335.5:c.1020-1G>T		p.X340_splice	ENST00000274335		340			0.528114772156794	1	FACETS	0.796	0.723	0.87	0.796	0.723	0.87	SUBCLONAL	1	TRUE	0	0.752367106693159	1		242	177	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520524	176520524	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763461529	NA	P-0026521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	375	792	0	ENST00000292408.4:c.1369G>A	p.Asp457Asn	p.D457N	ENST00000292408	NM_213647.1	457	Gac/Aac	10/18	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.752367106693159	2		792	832	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188563	32188563	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	555	656	0	ENST00000375023.3:c.892T>A	p.Tyr298Asn	p.Y298N	ENST00000375023	NM_004557.3	298	Tac/Aac	5/30	0.752367106693159	4	FACETS	0.841	0.812	0.87	1	0.996	1	CLONAL	3	TRUE	2	0.752367106693159	4		656	1025	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748574	43748574	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	367	347	0	ENST00000523873.1:c.528G>T	p.Trp176Cys	p.W176C	ENST00000523873		176	tgG/tgT	6/8	0.752367106693159	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.752367106693159	4		347	831	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965349	68965350	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0026521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	385	525	1	ENST00000288368.4:c.961_962delinsTT	p.Gly321Leu	p.G321L	ENST00000288368	NM_024870.2	321	GGa/TTa	9/40	0.71859569031077	5	FACETS	1	0.992	1	0.838	0.805	0.87	CLONAL	3	TRUE	1	0.752367106693159	5		526	650	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528761	8528761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	184	310	0	ENST00000356435.5:c.371G>T	p.Gly124Val	p.G124V	ENST00000356435		124	gGc/gTc	4/35	0.711872311426966	2	FACETS	0.913	0.867	0.956	0.913	0.867	0.956	CLONAL	2	TRUE	0	0.752367106693159	2		310	268	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965349	68965349	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	385	525	1	ENST00000288368.4:c.961G>T	p.Gly321Ter	p.G321*	ENST00000288368	NM_024870.2	321	Gga/Tga	9/40	0.71859569031077	5	FACETS	1	0.992	1	0.838	0.805	0.87	CLONAL	3	TRUE	1	0.752367106693159	5		526	650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0026547-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	529	691	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.433856448145871	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	FALSE	0	0.433856448145871	3		691	957	SUCCESS
AR	367	MSKCC	GRCh37	X	66766412	66766412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200390780	NA	P-0026547-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	102	280	0	ENST00000374690.3:c.1424C>T	p.Ala475Val	p.A475V	ENST00000374690	NM_000044.3	475	gCg/gTg	1/8	0.433856448145871	5	FACETS	0.915	0.824	1	0.458	0.412	0.506	CLONAL	2	FALSE	1	0.433856448145871	5		280	424	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112760274	112760274	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026547-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	32	238	0	ENST00000369452.4:c.943G>C	p.Glu315Gln	p.E315Q	ENST00000369452	NM_007373.3	315	Gag/Cag	4/9	0.433856448145871	3	FACETS	0.701	0.572	0.846	0.351	0.286	0.423	SUBCLONAL	1	FALSE	1	0.433856448145871	3		238	256	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547359	106547359	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026547-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	99	525	0	ENST00000369096.4:c.596G>T	p.Trp199Leu	p.W199L	ENST00000369096	NM_001198.3	199	tGg/tTg	4/7	0.200383931341297	3	FACETS	0.994	0.889	1	0.497	0.444	0.552	INDETERMINATE	1	FALSE	1	0.433856448145871	3		525	559	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411866	116411909	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGTCTTTAACAAGCTCTTTCTTTCTCTCTGTTTTAAGATCTGGG	CGTCTTTAACAAGCTCTTTCTTTCTCTCTGTTTTAAGATCTGGG	TGT	novel	NA	P-0026547-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	1017	664	2	ENST00000397752.3:c.2888-37_2894delinsTGT		p.X963_splice	ENST00000397752	NM_000245.2	963		14/21	0.433856448145871	8	FACETS	1	0.996	1			1	CLONAL	7	FALSE	NA	0.433856448145871	8		666	1442	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026839-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	47	612	0				ENST00000310581	NM_198253.2	-/1132			0.336333926250242	4	FACETS	1	0.932	1	1	0.932	1	INDETERMINATE	2	TRUE	2	0.700231685245328	4		612	103	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0026839-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	138	737	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.336333926250242	4	FACETS	1	0.926	1	1	0.926	1	INDETERMINATE	2	TRUE	2	0.700231685245328	4		737	334	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652147	36652148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026839-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	253	633	0	ENST00000244741.5:c.270dup	p.Gly91ArgfsTer38	p.G91Rfs*38	ENST00000244741	NM_000389.4	90	gga/ggAa	2/3	0.700231685245328	8	FACETS	1	0.985	1			1	CLONAL	3	TRUE	NA	0.700231685245328	8		633	657	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651893	36651894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026839-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	247	585	0	ENST00000244741.5:c.19dup	p.Asp7GlyfsTer29	p.D7Gfs*29	ENST00000244741	NM_000389.4	5	-/G	2/3	0.700231685245328	8	FACETS	0.975	0.92	1			1	CLONAL	4	TRUE	NA	0.700231685245328	8		585	561	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281768	49281768	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148425155	NA	P-0026839-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	74	568	1	ENST00000282018.3:c.815C>T	p.Thr272Met	p.T272M	ENST00000282018	NM_020377.2	272	aCg/aTg	1/1	0.630643710490813	4	FACETS	0.931	0.832	1	0.931	0.832	1	CLONAL	2	TRUE	2	0.700231685245328	4		569	193	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577188	64577188	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026839-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	250	603	0	ENST00000312049.6:c.394T>G	p.Ser132Ala	p.S132A	ENST00000312049	NM_130799.2	132	Tcc/Gcc	2/10	0.700231685245328	8	FACETS	0.949	0.896	1			1	CLONAL	4	TRUE	NA	0.700231685245328	8		603	583	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1976713	1976713	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026839-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	46	499	0	ENST00000382891.5:c.3496G>T	p.Val1166Phe	p.V1166F	ENST00000382891	NM_133335.3	1166	Gtc/Ttc	19/22	0.336333926250242	4	FACETS	0.531	0.447	0.622	0.265	0.223	0.311	INDETERMINATE	1	TRUE	2	0.700231685245328	4		499	421	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0027398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	531	516	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.491591371830409	6	FACETS	0.945	0.917	0.971			1	CLONAL	6	TRUE	NA	0.491591371830409	6		516	756	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203613	108203613	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs377349459	NA	P-0027398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	102	357	1	ENST00000278616.4:c.7913G>A	p.Trp2638Ter	p.W2638*	ENST00000278616	NM_000051.3	2638	tGg/tAg	53/63	0.491591371830409	2	FACETS	0.935	0.854	1	0.935	0.854	1	CLONAL	2	TRUE	0	0.491591371830409	2		358	222	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670136	86670136	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	86	407	3	ENST00000274376.6:c.1933G>A	p.Asp645Asn	p.D645N	ENST00000274376	NM_002890.2	645	Gat/Aat	14/25	0.163664404112236	5	FACETS	0.754	0.671	0.842	0.503	0.447	0.561	INDETERMINATE	2	TRUE	2	0.491591371830409	5		410	403	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027648-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	186	344	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.578857177508966	5	FACETS	0.951	0.889	1	0.951	0.889	1	CLONAL	3	TRUE	2	0.578857177508966	5		344	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0027648-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	281	633	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	NA	2	FACETS	0.971	0.925	1			1	INDETERMINATE	2	TRUE	NA	0.578857177508966	2		633	500	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435399	110435399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1264962918	NA	P-0027648-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	131	741	0	ENST00000375856.3:c.3002C>T	p.Ser1001Phe	p.S1001F	ENST00000375856	NM_003749.2	1001	tCc/tTc	1/2	0.578857177508966	3	FACETS	1	0.937	1	0.517	0.471	0.565	CLONAL	1	TRUE	1	0.578857177508966	3		741	564	SUCCESS
APC	324	MSKCC	GRCh37	5	112173600	112173600	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060503310	NA	P-0027648-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	193	396	0	ENST00000257430.4:c.2309C>G	p.Ser770Ter	p.S770*	ENST00000257430	NM_000038.5	770	tCa/tGa	16/16	0.539145599796638	2	FACETS	0.896	0.843	0.949	0.896	0.843	0.949	CLONAL	2	TRUE	0	0.578857177508966	2		396	372	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231689	66231689	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027648-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	37	216	0	ENST00000273854.3:c.2011G>C	p.Glu671Gln	p.E671Q	ENST00000273854	NM_004439.5	671	Gaa/Caa	11/18	0.578857177508966	1	FACETS	0.287	0.237	0.343	0.287	0.237	0.343	SUBCLONAL	1	TRUE	0	0.578857177508966	1		216	316	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098800	178098800	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	442	517	0	ENST00000397062.3:c.245A>G	p.Glu82Gly	p.E82G	ENST00000397062	NM_006164.4	82	gAa/gGa	2/5	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.807528196056256	2		517	997	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0029975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	656	414	0	ENST00000269305.4:c.673-2A>C		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.807528196056256	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.807528196056256	2		414	763	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971209	21971209	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1554654224	NA	P-0029975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	419	291	0	ENST00000304494.5:c.151-2A>G		p.X51_splice	ENST00000304494	NM_000077.4	51			0.807528196056256	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.807528196056256	2		291	491	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446130	49446130	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	472	663	0	ENST00000301067.7:c.1336G>C	p.Glu446Gln	p.E446Q	ENST00000301067	NM_003482.3	446	Gag/Cag	10/54	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.807528196056256	2		663	1131	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111588	56111588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1466506537	NA	P-0029975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	100	102	0	ENST00000399503.3:c.188G>A	p.Arg63His	p.R63H	ENST00000399503	NM_005921.1	63	cGc/cAc	1/20	0.807528196056256	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.807528196056256	1		102	132	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	51	701	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.17664293986747	2	FACETS	0.809	0.689	0.942	0.405	0.344	0.471	CLONAL	1	TRUE	0	0.268132772468719	2		701	470	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552891	106552891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771056895	NA	P-0030616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	41	785	1	ENST00000369096.4:c.856C>T	p.Arg286Cys	p.R286C	ENST00000369096	NM_001198.3	286	Cgt/Tgt	5/7	0.17664293986747	2	FACETS	0.58	0.483	0.689	0.29	0.241	0.345	SUBCLONAL	1	TRUE	0	0.268132772468719	2		786	527	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0030616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	122	697	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.268132772468719	2	FACETS	0.946	0.86	1	0.946	0.86	1	CLONAL	2	TRUE	0	0.268132772468719	2		697	481	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350251	15350251	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	44	758	0	ENST00000263377.2:c.3528C>G	p.Asp1176Glu	p.D1176E	ENST00000263377	NM_058243.2	1176	gaC/gaG	17/20	0.17664293986747	2	FACETS	0.736	0.618	0.867	0.368	0.309	0.434	SUBCLONAL	1	TRUE	0	0.268132772468719	2		758	446	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295909	1295909	+	upstream_gene_variant	5'Flank	SNP	C	C	T	rs1371469309	NA	P-0030616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	53	1120	1				ENST00000310581	NM_198253.2	-/1132			0.203857574308546	3	FACETS	0.717	0.611	0.834	0.359	0.305	0.417	SUBCLONAL	1	TRUE	1	0.268132772468719	3		1121	625	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713793	30713793	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	56	898	0	ENST00000295754.5:c.1118T>G	p.Met373Arg	p.M373R	ENST00000295754	NM_003242.5	373	aTg/aGg	4/7	1	2	FACETS	0.758	0.65	0.877	0.758	0.65	0.877	SUBCLONAL	1	TRUE	1	0.268132772468719	2		898	551	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140449177	140449177	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	20	82	0	ENST00000288602.6:c.1902C>G	p.Ser634Arg	p.S634R	ENST00000288602	NM_004333.4	634	agC/agG	16/18	0.268132772468719	5	FACETS	0.808	0.619	1	0.269	0.206	0.343	CLONAL	1	TRUE	2	0.268132772468719	5		82	259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0030797-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	101	421	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.835750661786997	3	FACETS	0.975	0.929	1	0.975	0.929	1	CLONAL	3	TRUE	0	0.837163116499693	3		421	117	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292583	15292583	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1176896295	NA	P-0030797-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	41	534	0	ENST00000263388.2:c.2596G>C	p.Asp866His	p.D866H	ENST00000263388	NM_000435.2	866	Gac/Cac	17/33	0.837163116499693	3	FACETS	0.602	0.505	0.707	0.301	0.252	0.354	SUBCLONAL	1	TRUE	1	0.837163116499693	3		534	231	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694604	176694604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030797-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	36	427	0	ENST00000439151.2:c.5188C>T	p.His1730Tyr	p.H1730Y	ENST00000439151	NM_022455.4	1730	Cat/Tat	15/23	0.837163116499693	5	FACETS	0.965	0.801	1	0.322	0.267	0.382	CLONAL	1	TRUE	2	0.837163116499693	5		427	201	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158404	26158404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030797-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	124	488	1	ENST00000289316.2:c.7G>A	p.Glu3Lys	p.E3K	ENST00000289316	NM_138720.2	3	Gaa/Aaa	1/2	0.69404379023479	6	FACETS	0.896	0.817	0.978	0.448	0.408	0.489	CLONAL	2	TRUE	2	0.837163116499693	6		489	442	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0030797-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	100	294	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.837163116499693	5	FACETS	0.966	0.888	1	0.966	0.888	1	CLONAL	3	TRUE	2	0.837163116499693	5		294	186	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371801	55371801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746536924	NA	P-0030797-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	23	593	0	ENST00000297316.4:c.491C>T	p.Ala164Val	p.A164V	ENST00000297316	NM_022454.3	164	gCg/gTg	2/2	NA	2	FACETS	0.555	0.441	0.681			1	INDETERMINATE	1	TRUE	NA	0.837163116499693	2		593	99	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397732	139397732	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs552065719	NA	P-0030797-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	26	595	0	ENST00000277541.6:c.5069C>T	p.Ser1690Leu	p.S1690L	ENST00000277541	NM_017617.3	1690	tCg/tTg	27/34	1	2	FACETS	0.565	0.456	0.684	0.565	0.456	0.684	SUBCLONAL	1	TRUE	1	0.837163116499693	2		595	110	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035969	47035969	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030797-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	17	485	0	ENST00000377604.3:c.647A>T	p.Asp216Val	p.D216V	ENST00000377604	NM_001204468.1	216	gAc/gTc	7/24	0.837163116499693	3	FACETS	0.345	0.259	0.446			1	SUBCLONAL	1	TRUE	NA	0.837163116499693	3		485	167	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0030859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	175	444	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.557810084202314	4	FACETS	1	0.975	1	0.787	0.746	0.827	CLONAL	3	TRUE	0	0.751881719499631	4		444	259	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0030859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	195	422	0	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	0.751881719499631	3	FACETS	0.868	0.828	0.907	0.868	0.828	0.907	CLONAL	3	TRUE	0	0.751881719499631	3		422	274	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325882	65325882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1490560356	NA	P-0030859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	159	466	0	ENST00000342505.4:c.1240C>T	p.Arg414Trp	p.R414W	ENST00000342505	NM_002227.2	414	Cgg/Tgg	9/25	0.751881719499631	3	FACETS	0.975	0.932	1	0.975	0.932	1	CLONAL	3	TRUE	0	0.751881719499631	3		466	199	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0030859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	199	336	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	0.743547069069022	2	FACETS	0.995	0.952	1	0.995	0.952	1	CLONAL	2	TRUE	0	0.751881719499631	2		336	266	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104269023	104269023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	193	409	0	ENST00000369902.3:c.280G>A	p.Gly94Ser	p.G94S	ENST00000369902	NM_016169.3	94	Ggc/Agc	2/12	0.743547069069022	2	FACETS	0.961	0.917	1	0.961	0.917	1	CLONAL	2	TRUE	0	0.751881719499631	2		409	267	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0030859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	20	524	5	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	0.751881719499631	3	FACETS	0.275	0.21	0.351			1	SUBCLONAL	1	TRUE	NA	0.751881719499631	3		529	266	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398279	25398279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894365	NA	P-0030859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	186	277	0	ENST00000311936.3:c.40G>A	p.Val14Ile	p.V14I	ENST00000311936	NM_004985.3	14	Gta/Ata	2/5	0.751881719499631	3	FACETS	0.974	0.934	1	0.974	0.934	1	CLONAL	3	TRUE	0	0.751881719499631	3		277	233	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438641	49438641	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759226682	NA	P-0030859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	34	486	0	ENST00000301067.7:c.4849C>T	p.Arg1617Trp	p.R1617W	ENST00000301067	NM_003482.3	1617	Cgg/Tgg	19/54	0.725199841105265	4	FACETS	0.58	0.476	0.696			1	SUBCLONAL	1	TRUE	NA	0.751881719499631	4		486	273	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481947	56481947	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs755433568	NA	P-0030859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	157	456	0	ENST00000267101.3:c.874+1G>A		p.X292_splice	ENST00000267101	NM_001982.3	292			0.751881719499631	3	FACETS	0.948	0.904	0.989	0.948	0.904	0.989	CLONAL	3	TRUE	0	0.751881719499631	3		456	202	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493456	56493456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781502670	NA	P-0030859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	180	436	0	ENST00000267101.3:c.2864G>A	p.Arg955His	p.R955H	ENST00000267101	NM_001982.3	955	cGc/cAc	24/28	0.751881719499631	3	FACETS	0.878	0.836	0.919	0.878	0.836	0.919	CLONAL	3	TRUE	0	0.751881719499631	3		436	250	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936983	48936983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690863	NA	P-0030859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	255	311	1	ENST00000267163.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000267163	NM_000321.2	251	Cga/Tga	8/27	0.751881719499631	3	FACETS	0.972	0.938	1	0.972	0.938	1	CLONAL	3	TRUE	0	0.751881719499631	3		312	320	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435007	110435007	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	94	595	0	ENST00000375856.3:c.3394G>A	p.Gly1132Ser	p.G1132S	ENST00000375856	NM_003749.2	1132	Ggc/Agc	1/2	0.743547069069022	2	FACETS	1	0.946	1	0.532	0.482	0.583	CLONAL	1	TRUE	0	0.751881719499631	2		595	235	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543210	65543210	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876659544	NA	P-0030859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	107	352	0	ENST00000358664.4:c.467G>A	p.Arg156Gln	p.R156Q	ENST00000358664	NM_002382.4	156	cGg/cAg	5/5	0.751881719499631	4	FACETS	0.963	0.879	1	0.963	0.879	1	CLONAL	2	TRUE	2	0.751881719499631	4		352	259	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052725	42052725	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	120	368	0	ENST00000219905.7:c.7396C>T	p.Arg2466Ter	p.R2466*	ENST00000219905	NM_001164273.1	2466	Cga/Tga	20/24	0.743547069069022	2	FACETS	0.923	0.866	0.976	0.923	0.866	0.976	CLONAL	2	TRUE	0	0.751881719499631	2		368	173	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442775	99442775	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	222	444	0	ENST00000268035.6:c.1172G>A	p.Arg391His	p.R391H	ENST00000268035	NM_000875.3	391	cGc/cAc	5/21	0.743547069069022	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.751881719499631	2		444	279	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120487	2120487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1800729	NA	P-0030859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	105	461	0	ENST00000219476.3:c.1747G>A	p.Ala583Thr	p.A583T	ENST00000219476	NM_000548.3	583	Gcc/Acc	17/42	0.751881719499631	2	FACETS	0.997	0.938	1	0.997	0.938	1	CLONAL	2	TRUE	0	0.751881719499631	2		461	140	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070640	67070643	+	frameshift_variant	Frame_Shift_Del	DEL	AGAA	AGAA	-	novel	NA	P-0030859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	23	407	0	ENST00000412916.2:c.267_270del	p.Arg90LysfsTer7	p.R90Kfs*7	ENST00000412916		88	ttAGAA/tt	3/6	0.751881719499631	2	FACETS	0.177	0.138	0.223	0.089	0.069	0.112	SUBCLONAL	1	TRUE	0	0.751881719499631	2		407	345	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349090	89349092	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0030859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	87	522	0	ENST00000301030.4:c.3858_3860del	p.Glu1287del	p.E1287del	ENST00000301030	NM_001256183.1	1286	gaAGAg/gag	9/13	0.743547069069022	2	FACETS	1	0.937	1	0.526	0.474	0.579	CLONAL	1	TRUE	0	0.751881719499631	2		522	220	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528489	29528489	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764079291	NA	P-0030859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	161	329	0	ENST00000356175.3:c.1246C>T	p.Arg416Ter	p.R416*	ENST00000356175	NM_000267.3	416	Cga/Tga	11/57	0.751881719499631	2	FACETS	0.996	0.948	1	0.996	0.948	1	CLONAL	2	TRUE	0	0.751881719499631	2		329	215	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370266	40370266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745315653	NA	P-0030859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	28	440	2	ENST00000293328.3:c.1072G>A	p.Gly358Arg	p.G358R	ENST00000293328	NM_012448.3	358	Ggg/Agg	9/19	0.751881719499631	3	FACETS	0.488	0.392	0.595	0.163	0.13	0.199	SUBCLONAL	1	TRUE	0	0.751881719499631	3		442	210	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223058	41223058	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	281	493	0	ENST00000357654.3:c.4873T>C	p.Tyr1625His	p.Y1625H	ENST00000357654	NM_007294.3	1625	Tat/Cat	15/23	0.751881719499631	3	FACETS	0.997	0.965	1	0.997	0.965	1	CLONAL	3	TRUE	0	0.751881719499631	3		493	344	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110587	4110587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1037950431	NA	P-0030859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	30	579	0	ENST00000262948.5:c.370G>A	p.Glu124Lys	p.E124K	ENST00000262948	NM_030662.3	124	Gaa/Aaa	3/11	0.751881719499631	4	FACETS	0.382	0.308	0.466	0.191	0.154	0.233	SUBCLONAL	1	TRUE	2	0.751881719499631	4		579	366	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11018783	11018783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	131	415	0	ENST00000327064.4:c.415G>A	p.Glu139Lys	p.E139K	ENST00000327064	NM_199141.1	139	Gag/Aag	3/16	0.718553777015161	4	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	2	0.751881719499631	4		415	304	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051574	13051574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767701623	NA	P-0030859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	294	505	0	ENST00000316448.5:c.833G>A	p.Arg278Gln	p.R278Q	ENST00000316448	NM_004343.3	278	cGg/cAg	7/9	0.718553777015161	4	FACETS	0.887	0.839	0.936	0.887	0.839	0.936	CLONAL	2	TRUE	2	0.751881719499631	4		505	772	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463307	25463307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757211277	NA	P-0030859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	146	440	0	ENST00000264709.3:c.2186G>A	p.Arg729Gln	p.R729Q	ENST00000264709	NM_175629.2	729	cGg/cAg	19/23	0.751881719499631	2	FACETS	0.986	0.935	1	0.986	0.935	1	CLONAL	2	TRUE	0	0.751881719499631	2		440	197	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703505	47703505	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs267607988	NA	P-0030859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	125	331	0	ENST00000233146.2:c.2006-1G>T		p.X669_splice	ENST00000233146	NM_000251.2	669			0.751881719499631	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.751881719499631	2		331	150	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035190	30035192	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs1555987732	NA	P-0030859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	21	364	0	ENST00000338641.4:c.357_359del	p.Phe119del	p.F119del	ENST00000338641	NM_000268.3	118	TTC/-	3/16	0.743547069069022	2	FACETS	0.339	0.262	0.426	0.169	0.131	0.213	SUBCLONAL	1	TRUE	0	0.751881719499631	2		364	165	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440292	187440292	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750212558	NA	P-0030859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	216	392	0	ENST00000232014.4:c.2075G>A	p.Arg692His	p.R692H	ENST00000232014	NM_001130845.1	692	cGc/cAc	10/10	0.751881719499631	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	0	0.751881719499631	3		392	257	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048156	180048156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747033940	NA	P-0030859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	76	535	0	ENST00000261937.6:c.2117C>T	p.Ala706Val	p.A706V	ENST00000261937	NM_182925.4	706	gCg/gTg	14/30	0.651553842330753	4	FACETS	0.805	0.718	0.895	0.805	0.718	0.895	CLONAL	2	TRUE	2	0.751881719499631	4		535	220	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524957	8524957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776042694	NA	P-0030859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	49	316	0	ENST00000356435.5:c.647G>A	p.Arg216His	p.R216H	ENST00000356435		216	cGc/cAc	7/35	0.751881719499631	7	FACETS	0.549	0.464	0.643	0.11	0.092	0.129	SUBCLONAL	1	TRUE	2	0.751881719499631	7		316	684	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426106	47426106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	87	226	0	ENST00000377045.4:c.626G>A	p.Arg209His	p.R209H	ENST00000377045	NM_001654.4	209	cGc/cAc	7/16	0.718103499728733	2	FACETS	0.857	0.769	0.948			1	CLONAL	1	TRUE	NA	0.751881719499631	2		226	270	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226066	53226066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556837402	NA	P-0030859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	94	263	2	ENST00000375401.3:c.2783C>T	p.Ala928Val	p.A928V	ENST00000375401	NM_004187.3	928	gCg/gTg	19/26	0.751881719499631	2	FACETS	1	0.984	1			1	CLONAL	2	TRUE	NA	0.751881719499631	2		265	111	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136209	2136209	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777539610	NA	P-0031214-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	177	579	1	ENST00000219476.3:c.4678G>A	p.Ala1560Thr	p.A1560T	ENST00000219476	NM_000548.3	1560	Gcc/Acc	37/42	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.680215109064538	2		580	497	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444746	49444746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031214-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	216	686	0	ENST00000301067.7:c.2720C>T	p.Pro907Leu	p.P907L	ENST00000301067	NM_003482.3	907	cCt/cTt	10/54	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.680215109064538	2		686	572	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438151	110438151	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031214-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	147	414	0	ENST00000375856.3:c.250A>G	p.Ser84Gly	p.S84G	ENST00000375856	NM_003749.2	84	Agc/Ggc	1/2	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.680215109064538	2		414	373	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064436	30064436	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1569302393	NA	P-0031214-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	114	406	0	ENST00000338641.4:c.999+1G>A		p.X333_splice	ENST00000338641	NM_000268.3	333			0.646721418251043	1	FACETS	0.941	0.866	1	0.941	0.866	1	CLONAL	1	TRUE	0	0.680215109064538	1		406	235	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663657	29663657	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031214-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	120	353	0	ENST00000356175.3:c.6089T>C	p.Ile2030Thr	p.I2030T	ENST00000356175	NM_000267.3	2030	aTt/aCt	41/57	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.680215109064538	2		353	353	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0033057-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	26	371	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.868	0.686	1	0.868	0.686	1	CLONAL	1	TRUE	1	0.13	2		371	461	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033057-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	26	612	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.791	0.625	0.981	0.791	0.625	0.981	CLONAL	1	TRUE	1	0.13	2		612	506	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125010	46125011	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0033057-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	36	484	0	ENST00000334344.6:c.198dup	p.Asn67GlufsTer8	p.N67Efs*8	ENST00000334344	NM_152641.2	66	aag/aaGg	3/21	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.13	2		484	533	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796945	42796945	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033057-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	31	0	0	ENST00000575354.2:c.3403C>G	p.Pro1135Ala	p.P1135A	ENST00000575354	NM_015125.3	1135	Ccc/Gcc	14/20	1	2	FACETS	0.498	0.401	0.61	0.498	0.401	0.61	SUBCLONAL	1	TRUE	1	0.13	2		0	957	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0033313-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	385	374	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.912332964557253	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	0	0.933249257851964	3		374	403	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0033313-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	649	294	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.933249257851964	7	FACETS	1	0.996	1	1	0.996	1	CLONAL	5	TRUE	2	0.933249257851964	7		294	849	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976787	2976787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033313-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	102	560	0	ENST00000396946.4:c.1225G>A	p.Glu409Lys	p.E409K	ENST00000396946	NM_032415.4	409	Gag/Aag	9/25	0.933249257851964	9	FACETS	0.868	0.774	0.967	0.124	0.11	0.139	CLONAL	1	TRUE	2	0.933249257851964	9		560	1075	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0033851-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	191	335	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.386663525041759	4	FACETS	0.9	0.838	0.964	0.9	0.838	0.964	CLONAL	2	TRUE	2	0.62060753144482	4		335	554	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412891	63412891	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033851-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	43	444	0	ENST00000330258.3:c.276G>T	p.Lys92Asn	p.K92N	ENST00000330258	NM_152424.3	92	aaG/aaT	2/2	0.320375900029341	3	FACETS	0.27	0.225	0.32	0.135	0.112	0.16	INDETERMINATE	1	TRUE	1	0.62060753144482	3		444	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577143	+	inframe_deletion	In_Frame_Del	DEL	AAGCTGTTCCGTCCC	AAGCTGTTCCGTCCC	-	novel	NA	P-0033851-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	249	436	0	ENST00000269305.4:c.795_809del	p.Gly266_Phe270del	p.G266_F270del	ENST00000269305	NM_001126112.2	265	ctGGGACGGAACAGCTTt/ctt	8/11	0.586725792670264	2	FACETS	0.82	0.777	0.864	0.82	0.777	0.864	CLONAL	2	TRUE	0	0.62060753144482	2		436	489	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391146	89391146	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034346-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	69	671	0	ENST00000336596.2:c.1212C>A	p.Asn404Lys	p.N404K	ENST00000336596	NM_005233.5	404	aaC/aaA	5/17	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	1	0.328644880771939	2		671	372	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549890	187549890	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034346-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	54	436	0	ENST00000441802.2:c.4351G>T	p.Asp1451Tyr	p.D1451Y	ENST00000441802	NM_005245.3	1451	Gac/Tac	8/27	1	2	FACETS	0.928	0.796	1	0.928	0.796	1	CLONAL	1	FALSE	1	0.328644880771939	2		436	354	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045187	47045187	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034346-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	66	920	0	ENST00000377604.3:c.2428G>T	p.Glu810Ter	p.E810*	ENST00000377604	NM_001204468.1	810	Gag/Tag	21/24	0.102452963696274	0	FACETS	0.733	0.639	0.833			1	INDETERMINATE	1	FALSE	0	0.328644880771939	0		920	368	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588125	69588125	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034346-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	57	887	1	ENST00000168712.1:c.573C>A	p.Asn191Lys	p.N191K	ENST00000168712	NM_002007.2	191	aaC/aaA	3/3	1	2	FACETS	0.93	0.801	1	0.93	0.801	1	CLONAL	1	FALSE	1	0.328644880771939	2		888	373	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335815	73335815	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034346-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	67	615	0	ENST00000377767.4:c.2480C>G	p.Ala827Gly	p.A827G	ENST00000377767	NM_014953.3	827	gCc/gGc	18/21	1	2	FACETS	0.985	0.859	1	0.985	0.859	1	CLONAL	1	FALSE	1	0.328644880771939	2		615	414	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046553	30046553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034346-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	66	856	1	ENST00000331968.5:c.2630G>A	p.Gly877Glu	p.G877E	ENST00000331968	NM_002742.2	877	gGg/gAg	18/18	1	2	FACETS	0.987	0.86	1	0.987	0.86	1	CLONAL	1	FALSE	1	0.328644880771939	2		857	407	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51504618	51504618	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034346-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	64	778	0	ENST00000260433.2:c.1162G>T	p.Val388Leu	p.V388L	ENST00000260433		388	Gtg/Ttg	9/10	1	2	FACETS	0.976	0.849	1	0.976	0.849	1	CLONAL	1	FALSE	1	0.328644880771939	2		778	399	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18960883	18960883	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0034346-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	65	576	0	ENST00000262803.5:c.462-1G>A		p.X154_splice	ENST00000262803	NM_002911.3	154			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.328644880771939	2		576	319	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271345	26271345	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034346-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	76	954	0	ENST00000305910.3:c.268G>T	p.Val90Leu	p.V90L	ENST00000305910	NM_003534.2	90	Gtg/Ttg	1/1	0.13407575966656	4	FACETS	1	0.939	1	0.557	0.489	0.629	INDETERMINATE	1	FALSE	2	0.328644880771939	4		954	552	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94067985	94067985	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034346-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	49	545	0	ENST00000369303.4:c.977T>C	p.Val326Ala	p.V326A	ENST00000369303	NM_004440.3	326	gTt/gCt	4/17	1	2	FACETS	0.819	0.696	0.953	0.819	0.696	0.953	CLONAL	1	FALSE	1	0.328644880771939	2		545	364	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50358680	50358680	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034346-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	97	443	0	ENST00000331340.3:c.23A>G	p.Asp8Gly	p.D8G	ENST00000331340	NM_006060.4	8	gAc/gGc	2/8	0.251833564193068	3	FACETS	0.976	0.879	1	0.976	0.879	1	CLONAL	2	FALSE	1	0.328644880771939	3		443	352	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412030	116412046	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TACTTTTCCAGAAGGTA	TACTTTTCCAGAAGGTA	-	novel	NA	P-0034346-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	133	595	0	ENST00000397752.3:c.3017_3028+5del		p.X1006_splice	ENST00000397752	NM_000245.2	1006		14/21	0.320175357998196	2	FACETS	0.809	0.739	0.882	0.809	0.739	0.882	CLONAL	2	FALSE	0	0.328644880771939	2		595	500	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002643	37002643	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0034346-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	61	864	0	ENST00000358127.4:c.604+2T>C		p.X202_splice	ENST00000358127	NM_001280556.1	202			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.328644880771939	2		864	295	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342671	87342671	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034346-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	76	632	0	ENST00000277120.3:c.956A>T	p.Tyr319Phe	p.Y319F	ENST00000277120		319	tAt/tTt	9/19	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	FALSE	1	0.328644880771939	2		632	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882019	NA	P-0034978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	160	761	0	ENST00000269305.4:c.455dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	ccg/ccCg	5/11	0.464325212489034	1	FACETS	0.564	0.52	0.609	0.564	0.52	0.609	SUBCLONAL	1	TRUE	0	0.683832404544769	1		761	546	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902711	50902711	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	130	637	0	ENST00000440232.2:c.286T>G	p.Phe96Val	p.F96V	ENST00000440232	NM_002691.3	96	Ttc/Gtc	3/27	0.306318973531293	2	FACETS	1	0.961	1	0.539	0.494	0.584	INDETERMINATE	1	TRUE	0	0.683832404544769	2		637	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0035710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	110	691	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.551571205642313	3	FACETS	0.862	0.777	0.953	0.431	0.388	0.477	CLONAL	1	TRUE	1	0.551571205642313	3		691	590	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106861	27106861	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	548	597	0	ENST00000324856.7:c.6472C>T	p.Arg2158Ter	p.R2158*	ENST00000324856	NM_006015.4	2158	Cga/Tga	20/20	0.551571205642313	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	0	0.551571205642313	3		597	841	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138473	11138473	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	238	428	0	ENST00000358026.2:c.3229C>T	p.Arg1077Ter	p.R1077*	ENST00000358026	NM_001128849.1	1077	Cga/Tga	24/36	0.551571205642313	2	FACETS	0.99	0.938	1	0.99	0.938	1	CLONAL	2	TRUE	0	0.551571205642313	2		428	436	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991872	72991872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	334	571	0	ENST00000268489.5:c.2173C>T	p.Pro725Ser	p.P725S	ENST00000268489	NM_006885.3	725	Cct/Tct	2/10	0.551571205642313	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.551571205642313	3		571	728	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	512	372	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.996	1			1	INDETERMINATE	1	TRUE	NA	0.808452548409319	2		372	995	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956552	93956552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754119070	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	265	527	0	ENST00000369303.4:c.2684G>A	p.Arg895Gln	p.R895Q	ENST00000369303	NM_004440.3	895	cGa/cAa	15/17	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.808452548409319	2		527	594	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262592	16262592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	444	857	0	ENST00000375759.3:c.9857C>A	p.Pro3286His	p.P3286H	ENST00000375759	NM_015001.2	3286	cCt/cAt	11/15	0.169292964671591	3	FACETS	1	0.996	1	0.715	0.684	0.747	INDETERMINATE	1	TRUE	1	0.808452548409319	3		857	1078	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023748	27023748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	314	796	0	ENST00000324856.7:c.854G>A	p.Gly285Glu	p.G285E	ENST00000324856	NM_006015.4	285	gGa/gAa	1/20	0.169292964671591	3	FACETS	1	0.994	1	0.712	0.675	0.749	INDETERMINATE	1	TRUE	1	0.808452548409319	3		796	766	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101423	27101423	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	296	635	0	ENST00000324856.7:c.4705C>T	p.Pro1569Ser	p.P1569S	ENST00000324856	NM_006015.4	1569	Cca/Tca	18/20	0.169292964671591	3	FACETS	0.758	0.719	0.798	0.758	0.719	0.798	INDETERMINATE	2	TRUE	1	0.808452548409319	3		635	678	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935268	36935268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	405	753	0	ENST00000361632.4:c.1459G>A	p.Gly487Arg	p.G487R	ENST00000361632		487	Ggg/Agg	10/16	0.169292964671591	3	FACETS	0.768	0.734	0.802	0.768	0.734	0.802	INDETERMINATE	2	TRUE	1	0.808452548409319	3		753	916	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166271	118166271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	469	792	0	ENST00000369448.3:c.781G>A	p.Glu261Lys	p.E261K	ENST00000369448	NM_017709.3	261	Gaa/Aaa	2/2	1	2	FACETS	0.987	0.946	1	0.987	0.946	1	CLONAL	1	TRUE	1	0.808452548409319	2		792	1175	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849128	156849128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	388	779	0	ENST00000524377.1:c.2020G>A	p.Asp674Asn	p.D674N	ENST00000524377	NM_002529.3	674	Gat/Aat	15/17	0.804873975230956	3	FACETS	0.952	0.903	1	0.476	0.451	0.501	CLONAL	1	TRUE	1	0.808452548409319	3		779	1416	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104377181	104377182	+	missense_variant	Missense_Mutation	DNP	TA	TA	CT	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	400	801	0	ENST00000369902.3:c.1292_1293delinsCT	p.Leu431Ser	p.L431S	ENST00000369902	NM_016169.3	431	tTA/tCT	10/12	1	2	FACETS	0.979	0.934	1	0.979	0.934	1	CLONAL	1	TRUE	1	0.808452548409319	2		801	1011	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256135	123256135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141929882	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	305	679	0	ENST00000358487.5:c.1774C>T	p.Arg592Cys	p.R592C	ENST00000358487	NM_000141.4	592	Cgt/Tgt	13/18	0.809383471346918	3	FACETS	0.937	0.883	0.992	0.468	0.441	0.496	CLONAL	1	TRUE	1	0.808452548409319	3		679	1131	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324081	123324081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	238	475	0	ENST00000358487.5:c.389C>T	p.Ser130Phe	p.S130F	ENST00000358487	NM_000141.4	130	tCc/tTc	4/18	0.809383471346918	3	FACETS	0.993	0.929	1	0.496	0.464	0.529	CLONAL	1	TRUE	1	0.808452548409319	3		475	833	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57004307	57004307	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	G	G	A	rs370702287	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	445	823	0	ENST00000257254.3:c.172C>T	p.Arg58Trp	p.R58W	ENST00000257254		58	Cgg/Tgg	1/2	1	2	FACETS	0.952	0.91	0.995	0.952	0.91	0.995	CLONAL	1	TRUE	1	0.808452548409319	2		823	1156	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141997	108141997	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780619	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	228	406	0	ENST00000278616.4:c.2941C>T	p.Arg981Cys	p.R981C	ENST00000278616	NM_000051.3	981	Cgt/Tgt	20/63	0.809383471346918	1	FACETS	0.977	0.932	1	0.977	0.932	1	CLONAL	1	TRUE	0	0.808452548409319	1		406	344	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103398	119103398	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	245	482	0	ENST00000264033.4:c.436C>T	p.Gln146Ter	p.Q146*	ENST00000264033	NM_005188.3	146	Cag/Tag	2/16	0.636308120325082	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.808452548409319	1		482	358	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417041	417041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	401	736	2	ENST00000399788.2:c.3509C>T	p.Ala1170Val	p.A1170V	ENST00000399788	NM_001042603.1	1170	gCc/gTc	23/28	NA	2	FACETS	0.99	0.945	1			1	INDETERMINATE	1	TRUE	NA	0.808452548409319	2		738	1002	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431735	49431735	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	359	874	0	ENST00000301067.7:c.9404C>T	p.Thr3135Ile	p.T3135I	ENST00000301067	NM_003482.3	3135	aCc/aTc	34/54	1	2	FACETS	0.926	0.88	0.972	0.926	0.88	0.972	CLONAL	1	TRUE	1	0.808452548409319	2		874	959	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112892368	112892368	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	160	285	0	ENST00000351677.2:c.526G>A	p.Glu176Lys	p.E176K	ENST00000351677	NM_002834.3	176	Gaa/Aaa	5/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.808452548409319	2		285	380	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112910803	112910803	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	212	361	0	ENST00000351677.2:c.812A>T	p.Gln271Leu	p.Q271L	ENST00000351677	NM_002834.3	271	cAa/cTa	7/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.808452548409319	2		361	509	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601256	28601256	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	225	528	0	ENST00000241453.7:c.2176T>C	p.Tyr726His	p.Y726H	ENST00000241453	NM_004119.2	726	Tac/Cac	17/24	1	2	FACETS	0.961	0.902	1	0.961	0.902	1	CLONAL	1	TRUE	1	0.808452548409319	2		528	579	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964022	28964022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	317	627	1	ENST00000282397.4:c.1880C>T	p.Ser627Phe	p.S627F	ENST00000282397	NM_002019.4	627	tCc/tTc	13/30	1	2	FACETS	0.985	0.934	1	0.985	0.934	1	CLONAL	1	TRUE	1	0.808452548409319	2		628	796	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005419	29005419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55687105	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	284	425	0	ENST00000282397.4:c.842G>A	p.Arg281Gln	p.R281Q	ENST00000282397	NM_002019.4	281	cGa/cAa	7/30	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.808452548409319	2		425	675	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012452	29012452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	237	486	0	ENST00000282397.4:c.419G>A	p.Ser140Asn	p.S140N	ENST00000282397	NM_002019.4	140	aGt/aAt	4/30	1	2	FACETS	0.964	0.907	1	0.964	0.907	1	CLONAL	1	TRUE	1	0.808452548409319	2		486	608	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944632	32944632	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	206	455	0	ENST00000380152.3:c.8425T>C	p.Phe2809Leu	p.F2809L	ENST00000380152		2809	Ttc/Ctc	19/27	1	2	FACETS	0.917	0.857	0.977	0.917	0.857	0.977	CLONAL	1	TRUE	1	0.808452548409319	2		455	556	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336134	73336134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	305	600	0	ENST00000377767.4:c.2269G>A	p.Gly757Arg	p.G757R	ENST00000377767	NM_014953.3	757	Gga/Aga	17/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.808452548409319	2		600	740	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569948	95569948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	423	854	0	ENST00000393063.1:c.3785C>T	p.Pro1262Leu	p.P1262L	ENST00000393063	NM_030621.3	1262	cCt/cTt	22/28	1	2	FACETS	0.99	0.946	1	0.99	0.946	1	CLONAL	1	TRUE	1	0.808452548409319	2		854	1057	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041734	42041734	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	387	731	0	ENST00000219905.7:c.5929C>T	p.Gln1977Ter	p.Q1977*	ENST00000219905	NM_001164273.1	1977	Cag/Tag	17/24	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.808452548409319	2		731	956	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052602	42052602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	364	741	0	ENST00000219905.7:c.7273C>T	p.Arg2425Cys	p.R2425C	ENST00000219905	NM_001164273.1	2425	Cgc/Tgc	20/24	1	2	FACETS	0.927	0.882	0.973	0.927	0.882	0.973	CLONAL	1	TRUE	1	0.808452548409319	2		741	971	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713311	43713311	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	497	829	0	ENST00000382044.4:c.4162C>G	p.Leu1388Val	p.L1388V	ENST00000382044	NM_001141980.1	1388	Ctt/Gtt	20/28	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.808452548409319	2		829	1157	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472652	88472652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	394	683	0	ENST00000360948.2:c.1903G>A	p.Asp635Asn	p.D635N	ENST00000360948	NM_001012338.2	635	Gat/Aat	16/19	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.808452548409319	2		683	950	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476280	88476280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	253	540	0	ENST00000360948.2:c.1852G>A	p.Glu618Lys	p.E618K	ENST00000360948	NM_001012338.2	618	Gaa/Aaa	15/19	1	2	FACETS	0.989	0.932	1	0.989	0.932	1	CLONAL	1	TRUE	1	0.808452548409319	2		540	633	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396431	396431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	388	764	0	ENST00000262320.3:c.595C>T	p.Pro199Ser	p.P199S	ENST00000262320	NM_003502.3	199	Ccc/Tcc	2/11	0.169292964671591	3	FACETS	1	0.996	1	0.737	0.704	0.771	INDETERMINATE	1	TRUE	1	0.808452548409319	3		764	914	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632744	23632744	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	204	474	0	ENST00000261584.4:c.3052G>T	p.Glu1018Ter	p.E1018*	ENST00000261584	NM_024675.3	1018	Gag/Tag	10/13	0.169292964671591	3	FACETS	1	0.986	1	0.606	0.565	0.647	INDETERMINATE	1	TRUE	1	0.808452548409319	3		474	585	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671678	67671679	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	320	732	0	ENST00000264010.4:c.2087_2088delinsTT	p.Pro696Leu	p.P696L	ENST00000264010	NM_006565.3	696	cCC/cTT	12/12	1	2	FACETS	0.859	0.813	0.905	0.859	0.813	0.905	CLONAL	1	TRUE	1	0.808452548409319	2		732	922	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346081	89346081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	144	305	0	ENST00000301030.4:c.6869C>T	p.Pro2290Leu	p.P2290L	ENST00000301030	NM_001256183.1	2290	cCc/cTc	9/13	1	2	FACETS	0.968	0.894	1	0.968	0.894	1	CLONAL	1	TRUE	1	0.808452548409319	2		305	368	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350869	89350869	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	298	592	0	ENST00000301030.4:c.2081T>G	p.Phe694Cys	p.F694C	ENST00000301030	NM_001256183.1	694	tTt/tGt	9/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.808452548409319	2		592	707	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958242	11958242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1261150954	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	129	273	0	ENST00000353533.5:c.152C>T	p.Pro51Leu	p.P51L	ENST00000353533	NM_003010.3	51	cCa/cTa	2/11	1	2	FACETS	0.904	0.83	0.98	0.904	0.83	0.98	CLONAL	1	TRUE	1	0.808452548409319	2		273	353	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554601	29554602	+	missense_variant	Missense_Mutation	DNP	AA	AA	GT	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	221	446	0	ENST00000356175.3:c.2386_2387delinsGT	p.Lys796Val	p.K796V	ENST00000356175	NM_000267.3	796	AAa/GTa	20/57	1	2	FACETS	0.816	0.763	0.87	0.816	0.763	0.87	CLONAL	1	TRUE	1	0.808452548409319	2		446	670	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576001	29576001	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	170	409	0	ENST00000356175.3:c.3975-1G>A		p.X1325_splice	ENST00000356175	NM_000267.3	1325			1	2	FACETS	0.841	0.78	0.904	0.841	0.78	0.904	CLONAL	1	TRUE	1	0.808452548409319	2		409	500	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653151	29653151	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	460	702	0	ENST00000356175.3:c.5086G>T	p.Glu1696Ter	p.E1696*	ENST00000356175	NM_000267.3	1696	Gag/Tag	36/57	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.808452548409319	2		702	977	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33681060	33681060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780673919	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	201	524	0	ENST00000308377.4:c.1217G>A	p.Arg406Gln	p.R406Q	ENST00000308377	NM_152270.3	406	cGa/cAa	4/5	1	2	FACETS	0.991	0.927	1	0.991	0.927	1	CLONAL	1	TRUE	1	0.808452548409319	2		524	502	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690521	33690521	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	367	737	0	ENST00000308377.4:c.306T>G	p.Cys102Trp	p.C102W	ENST00000308377	NM_152270.3	102	tgT/tgG	2/5	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.808452548409319	2		737	798	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864574	37864574	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	419	689	0	ENST00000269571.5:c.226G>A	p.Asp76Asn	p.D76N	ENST00000269571		76	Gat/Aat	3/27	0.237454820477616	3	FACETS	0.852	0.817	0.888	0.852	0.817	0.888	INDETERMINATE	2	TRUE	1	0.808452548409319	3		689	854	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857681	59857681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	210	378	0	ENST00000259008.2:c.1876G>A	p.Glu626Lys	p.E626K	ENST00000259008	NM_032043.2	626	Gaa/Aaa	13/20	1	2	FACETS	0.837	0.781	0.893	0.837	0.781	0.893	CLONAL	1	TRUE	1	0.808452548409319	2		378	621	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61305297	61305297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1448193250	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	46	206	0	ENST00000341074.5:c.829G>A	p.Glu277Lys	p.E277K	ENST00000341074	NM_002974.2	277	Gag/Aag	8/8	0.654217259174354	3	FACETS	0.549	0.465	0.641	0.275	0.232	0.321	SUBCLONAL	1	TRUE	1	0.808452548409319	3		206	291	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222899	36222899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	339	943	0	ENST00000222270.7:c.5528C>T	p.Pro1843Leu	p.P1843L	ENST00000222270	NM_014727.1	1843	cCt/cTt	27/37	0.654217259174354	3	FACETS	1	0.982	1	0.54	0.511	0.57	CLONAL	1	TRUE	1	0.808452548409319	3		943	1090	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792107	42792107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1382074611	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	393	773	0	ENST00000575354.2:c.911G>A	p.Gly304Asp	p.G304D	ENST00000575354	NM_015125.3	304	gGc/gAc	6/20	0.654217259174354	3	FACETS	1	0.993	1	0.609	0.58	0.639	CLONAL	1	TRUE	1	0.808452548409319	3		773	1120	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965017	25965017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	343	686	0	ENST00000435504.4:c.4189C>T	p.Pro1397Ser	p.P1397S	ENST00000435504		1397	Cct/Tct	13/13	0.169292964671591	3	FACETS	1	0.994	1	0.669	0.635	0.703	INDETERMINATE	1	TRUE	1	0.808452548409319	3		686	891	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185035	99185035	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	260	492	0	ENST00000074304.5:c.2437T>C	p.Phe813Leu	p.F813L	ENST00000074304	NM_001134224.1	813	Ttt/Ctt	23/26	NA	2	FACETS	0.915	0.862	0.969			1	INDETERMINATE	1	TRUE	NA	0.808452548409319	2		492	703	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538275	9538275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	341	554	0	ENST00000353224.5:c.1723C>T	p.Leu575Phe	p.L575F	ENST00000353224	NM_177990.2	575	Ctc/Ttc	7/10	1	2	FACETS	0.981	0.932	1	0.981	0.932	1	CLONAL	1	TRUE	1	0.808452548409319	2		554	860	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31015959	31015959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	376	683	0	ENST00000375687.4:c.281C>T	p.Pro94Leu	p.P94L	ENST00000375687	NM_015338.5	94	cCa/cTa	5/13	0.237454820477616	3	FACETS	0.751	0.716	0.786	0.751	0.716	0.786	INDETERMINATE	2	TRUE	1	0.808452548409319	3		683	870	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739115	40739115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	265	641	0	ENST00000373198.4:c.3169G>A	p.Glu1057Lys	p.E1057K	ENST00000373198	NM_133170.3	1057	Gag/Aag	24/32	0.237454820477616	3	FACETS	1	0.989	1	0.606	0.571	0.643	INDETERMINATE	1	TRUE	1	0.808452548409319	3		641	759	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827900	40827900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767977370	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	400	712	0	ENST00000373198.4:c.2528C>T	p.Ser843Phe	p.S843F	ENST00000373198	NM_133170.3	843	tCt/tTt	17/32	0.237454820477616	3	FACETS	0.754	0.72	0.788	0.754	0.72	0.788	INDETERMINATE	2	TRUE	1	0.808452548409319	3		712	922	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817438	39817438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748243137	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	377	689	0	ENST00000288319.7:c.125G>A	p.Gly42Glu	p.G42E	ENST00000288319	NM_182918.3	42	gGa/gAa	2/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.808452548409319	2		689	923	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852517	42852517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	244	668	0	ENST00000398585.3:c.569G>A	p.Gly190Glu	p.G190E	ENST00000398585	NM_001135099.1	190	gGa/gAa	6/14	1	2	FACETS	0.946	0.89	1	0.946	0.89	1	CLONAL	1	TRUE	1	0.808452548409319	2		668	638	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655440	45655440	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	369	711	0	ENST00000407780.3:c.412T>G	p.Phe138Val	p.F138V	ENST00000407780	NM_001283052.1	138	Ttc/Gtc	4/7	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.808452548409319	2		711	900	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035181	30035181	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	379	564	0	ENST00000338641.4:c.343C>T	p.Gln115Ter	p.Q115*	ENST00000338641	NM_000268.3	115	Caa/Taa	3/16	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.808452548409319	2		564	839	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259116	89259117	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	284	643	1	ENST00000336596.2:c.260_261delinsAT	p.Val87Asp	p.V87D	ENST00000336596	NM_005233.5	87	gTC/gAT	3/17	0.804873975230956	3	FACETS	0.935	0.88	0.992	0.468	0.44	0.496	CLONAL	1	TRUE	1	0.808452548409319	3		644	1055	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456447	189456447	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	602	543	0	ENST00000264731.3:c.208C>T	p.Gln70Ter	p.Q70*	ENST00000264731	NM_003722.4	70	Cag/Tag	3/14	0.799552382541931	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.808452548409319	2		543	743	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133586	55133586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501507	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	314	618	0	ENST00000257290.5:c.890G>A	p.Arg297Lys	p.R297K	ENST00000257290	NM_006206.4	297	aGg/aAg	6/23	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.808452548409319	2		618	772	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156489	55156489	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1290364180	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	227	473	0	ENST00000257290.5:c.2890A>G	p.Lys964Glu	p.K964E	ENST00000257290	NM_006206.4	964	Aaa/Gaa	22/23	1	2	FACETS	0.909	0.852	0.966	0.909	0.852	0.966	CLONAL	1	TRUE	1	0.808452548409319	2		473	618	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157485	106157485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747398674	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	320	668	0	ENST00000380013.4:c.2386G>A	p.Glu796Lys	p.E796K	ENST00000380013	NM_001127208.2	796	Gag/Aag	3/11	1	2	FACETS	0.975	0.925	1	0.975	0.925	1	CLONAL	1	TRUE	1	0.808452548409319	2		668	812	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541439	187541439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1246955615	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	334	769	0	ENST00000441802.2:c.6301C>T	p.Arg2101Cys	p.R2101C	ENST00000441802	NM_005245.3	2101	Cgc/Tgc	10/27	1	2	FACETS	0.911	0.864	0.958	0.911	0.864	0.958	CLONAL	1	TRUE	1	0.808452548409319	2		769	907	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295230	1295230	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs796516131	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	415	750	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.808452548409319	2		750	1005	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435618	149435618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	444	582	0	ENST00000286301.3:c.2525G>A	p.Gly842Asp	p.G842D	ENST00000286301	NM_005211.3	842	gGc/gAc	19/22	0.151551143892449	4	FACETS	0.96	0.919	1	0.96	0.919	1	INDETERMINATE	2	TRUE	2	0.808452548409319	4		582	1035	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500491	149500491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770930584	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	451	714	0	ENST00000261799.4:c.2546G>A	p.Arg849Gln	p.R849Q	ENST00000261799	NM_002609.3	849	cGa/cAa	18/23	0.151551143892449	4	FACETS	0.922	0.883	0.962	0.922	0.883	0.962	INDETERMINATE	2	TRUE	2	0.808452548409319	4		714	1094	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250700	26250700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	703	952	0	ENST00000446824.2:c.134G>A	p.Gly45Asp	p.G45D	ENST00000446824	NM_021018.2	45	gGt/gAt	1/1	0.793529689572465	3	FACETS	0.965	0.935	0.993	0.965	0.935	0.993	CLONAL	2	TRUE	1	0.808452548409319	3		952	1266	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797788	32797788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370090254	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	317	694	0	ENST00000374899.4:c.1714G>A	p.Glu572Lys	p.E572K	ENST00000374899	NM_018833.2	572	Gaa/Aaa	10/12	0.809383471346918	3	FACETS	1	0.968	1	0.518	0.489	0.547	CLONAL	1	TRUE	1	0.808452548409319	3		694	1063	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068097	94068097	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	262	461	0	ENST00000369303.4:c.865C>T	p.Gln289Ter	p.Q289*	ENST00000369303	NM_004440.3	289	Caa/Taa	4/17	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.808452548409319	2		461	629	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725567	117725567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767519397	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	238	499	0	ENST00000368508.3:c.314C>T	p.Pro105Leu	p.P105L	ENST00000368508	NM_002944.2	105	cCc/cTc	5/43	1	2	FACETS	0.902	0.847	0.957	0.902	0.847	0.957	CLONAL	1	TRUE	1	0.808452548409319	2		499	653	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6037030	6037030	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1562671039	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	383	353	1	ENST00000265849.7:c.730C>T	p.Gln244Ter	p.Q244*	ENST00000265849	NM_000535.5	244	Cag/Tag	7/15	0.653088451786631	4	FACETS	0.954	0.91	0.998	0.954	0.91	0.998	CLONAL	2	TRUE	2	0.808452548409319	4		354	898	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220344	55220344	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	438	481	0	ENST00000275493.2:c.734A>G	p.Glu245Gly	p.E245G	ENST00000275493	NM_005228.3	245	gAg/gGg	6/28	0.653088451786631	4	FACETS	0.919	0.879	0.959	0.919	0.879	0.959	CLONAL	2	TRUE	2	0.808452548409319	4		481	1066	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55232974	55232974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1249099747	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	503	573	0	ENST00000275493.2:c.1724G>A	p.Gly575Glu	p.G575E	ENST00000275493	NM_005228.3	575	gGa/gAa	15/28	0.653088451786631	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.808452548409319	4		573	1078	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359032	81359032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	1095	565	0	ENST00000222390.5:c.929G>A	p.Gly310Glu	p.G310E	ENST00000222390	NM_000601.4	310	gGa/gAa	8/18	0.809383471346918	6	FACETS	1	0.994	1	1	0.994	1	CLONAL	4	TRUE	2	0.808452548409319	6		565	1704	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945093	151945093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746147314	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	50	350	0	ENST00000262189.6:c.2426G>A	p.Gly809Glu	p.G809E	ENST00000262189	NM_170606.2	809	gGa/gAa	14/59	0.809383471346918	6	FACETS	0.748	0.635	0.87	0.187	0.158	0.218	SUBCLONAL	1	TRUE	2	0.808452548409319	6		350	433	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879289	56879289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	302	552	0	ENST00000519728.1:c.806G>A	p.Ser269Asn	p.S269N	ENST00000519728	NM_002350.3	269	aGt/aAt	9/13	0.654217259174354	3	FACETS	1	0.982	1	0.547	0.516	0.578	CLONAL	1	TRUE	1	0.808452548409319	3		552	959	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069575	69069575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	364	322	0	ENST00000288368.4:c.4250G>A	p.Gly1417Glu	p.G1417E	ENST00000288368	NM_024870.2	1417	gGa/gAa	35/40	0.654217259174354	3	FACETS	0.938	0.898	0.978	0.938	0.898	0.978	CLONAL	2	TRUE	1	0.808452548409319	3		322	674	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2029083	2029083	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	871	880	0	ENST00000349721.2:c.61C>T	p.Pro21Ser	p.P21S	ENST00000349721	NM_003070.3	21	Cct/Tct	2/34	0.808452548409319	2	FACETS	0.988	0.969	1	0.988	0.969	1	CLONAL	2	TRUE	0	0.808452548409319	2		880	1091	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2039699	2039699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	709	799	1	ENST00000349721.2:c.589C>T	p.Pro197Ser	p.P197S	ENST00000349721	NM_003070.3	197	Ccc/Tcc	4/34	0.808452548409319	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.808452548409319	2		800	873	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5055750	5055750	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs771912975	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	326	383	0	ENST00000381652.3:c.1018C>T	p.Arg340Ter	p.R340*	ENST00000381652	NM_004972.3	340	Cga/Tga	8/25	0.808452548409319	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.808452548409319	2		383	394	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524946	8524946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567730036	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	494	465	0	ENST00000356435.5:c.658C>T	p.Pro220Ser	p.P220S	ENST00000356435		220	Cct/Tct	7/35	0.808452548409319	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.808452548409319	2		465	597	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27228284	27228284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	437	376	0	ENST00000380036.4:c.3281G>A	p.Arg1094Lys	p.R1094K	ENST00000380036	NM_000459.3	1094	aGa/aAa	22/23	0.808452548409319	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.808452548409319	2		376	522	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317533	1317533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199794164	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	185	492	0	ENST00000400841.2:c.532G>A	p.Glu178Lys	p.E178K	ENST00000400841		178	Gag/Aag	5/6	1	1	FACETS	0.605	0.564	0.646	0.605	0.564	0.646	SUBCLONAL	1	TRUE	0	0.808452548409319	1		492	451	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913538	39913538	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	258	270	0	ENST00000378444.4:c.4790C>T	p.Thr1597Ile	p.T1597I	ENST00000378444	NM_001123385.1	1597	aCt/aTt	13/15	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.808452548409319	1		270	335	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223368	53223368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	431	320	0	ENST00000375401.3:c.3991C>T	p.Pro1331Ser	p.P1331S	ENST00000375401	NM_004187.3	1331	Cct/Tct	23/26	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.808452548409319	1		320	530	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938304	76938304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	287	264	0	ENST00000373344.5:c.2444C>T	p.Ser815Phe	p.S815F	ENST00000373344	NM_000489.3	815	tCt/tTt	9/35	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.808452548409319	1		264	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520000	NA	P-0036913-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	157	663	0	ENST00000269305.4:c.452C>A	p.Pro151His	p.P151H	ENST00000269305	NM_001126112.2	151	cCc/cAc	5/11	0.634437774284299	3	FACETS	1	0.98	1	0.597	0.55	0.646	CLONAL	1	TRUE	1	0.634437774284299	3		663	546	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036913-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	113	612	0				ENST00000310581	NM_198253.2	-/1132			0.634437774284299	3	FACETS	0.902	0.827	0.978	0.902	0.827	0.978	CLONAL	2	TRUE	1	0.634437774284299	3		612	260	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0036913-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	28	372	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	0.634437774284299	3	FACETS	1	0.843	1	0.519	0.423	0.624	CLONAL	1	TRUE	1	0.634437774284299	3		372	112	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631965	90631965	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036913-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	93	545	0	ENST00000330062.3:c.388A>G	p.Lys130Glu	p.K130E	ENST00000330062	NM_002168.2	130	Aag/Gag	4/11	0.634437774284299	2	FACETS	1	0.954	1	0.549	0.495	0.604	CLONAL	1	TRUE	0	0.634437774284299	2		545	267	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73113168	73113168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036913-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	101	306	0	ENST00000356692.5:c.509G>A	p.Gly170Glu	p.G170E	ENST00000356692		170	gGg/gAg	7/9	0.609578860010645	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.634437774284299	4		306	217	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436149	116436149	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200315561	NA	P-0036913-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	111	454	0	ENST00000397752.3:c.4144C>T	p.Arg1382Ter	p.R1382*	ENST00000397752	NM_000245.2	1382	Cga/Tga	21/21	0.634437774284299	6	FACETS	0.869	0.786	0.955			1	CLONAL	2	TRUE	NA	0.634437774284299	6		454	457	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328444	137328444	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036913-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	171	510	0	ENST00000481739.1:c.1373C>G	p.Pro458Arg	p.P458R	ENST00000481739	NM_002957.4	458	cCg/cGg	10/10	0.603410163239054	5	FACETS	1	0.932	1	0.671	0.621	0.721	CLONAL	2	TRUE	2	0.634437774284299	5		510	523	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63968627	63968627	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs773456165	NA	P-0036913-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	52	391	0	ENST00000398590.3:c.1025A>G	p.Asp342Gly	p.D342G	ENST00000398590	NM_001177387.1	342	gAt/gGt	8/14	0.609578860010645	4	FACETS	1	0.868	1	0.506	0.434	0.583	CLONAL	1	TRUE	2	0.634437774284299	4		391	265	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576865	7576865	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	rs879254077	NA	P-0037025-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	393	801	0	ENST00000269305.4:c.981T>G	p.Tyr327Ter	p.Y327*	ENST00000269305	NM_001126112.2	327	taT/taG	9/11	0.776098163605178	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.777372844250671	1		801	584	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907019	101907019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037025-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	296	354	0	ENST00000374994.4:c.979C>T	p.Pro327Ser	p.P327S	ENST00000374994	NM_004612.2	327	Cca/Tca	6/9	0.777372844250671	2	FACETS	0.89	0.855	0.923	0.89	0.855	0.923	CLONAL	2	TRUE	0	0.777372844250671	2		354	428	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763905	76763905	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037025-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	274	646	0	ENST00000373344.5:c.7403A>T	p.Gln2468Leu	p.Q2468L	ENST00000373344	NM_000489.3	2468	cAg/cTg	35/35	1	2	FACETS	0.935	0.882	0.989	0.935	0.882	0.989	CLONAL	1	TRUE	1	0.777372844250671	2		646	754	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395512	116395527	+	frameshift_variant	Frame_Shift_Del	DEL	GAGTTCTCCTTGGAAA	GAGTTCTCCTTGGAAA	TT	novel	NA	P-0037025-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	265	483	1	ENST00000397752.3:c.1805_1820delinsTT	p.Arg602IlefsTer2	p.R602Ifs*2	ENST00000397752	NM_000245.2	602	aGAGTTCTCCTTGGAAAt/aTTt	6/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.777372844250671	2		484	639	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64290026	64290026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040189-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	17	371	0	ENST00000370651.3:c.469C>T	p.Arg157Trp	p.R157W	ENST00000370651	NM_003463.4	157	Cgg/Tgg	6/6	1	2	FACETS	0.954	0.712	1	0.954	0.712	1	CLONAL	1	TRUE	1	0.12	2		371	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs17849781	NA	P-0040519-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	250	515	0	ENST00000269305.4:c.832C>G	p.Pro278Ala	p.P278A	ENST00000269305	NM_001126112.2	278	Cct/Gct	8/11	0.914448822248741	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.914448822248741	1		515	283	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133574	55133574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373948582	NA	P-0040519-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	253	468	0	ENST00000257290.5:c.878G>A	p.Arg293His	p.R293H	ENST00000257290	NM_006206.4	293	cGc/cAc	6/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.914448822248741	2		468	525	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218819	36218819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758281505	NA	P-0040519-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	36	724	1	ENST00000222270.7:c.4430G>A	p.Arg1477Gln	p.R1477Q	ENST00000222270	NM_014727.1	1477	cGg/cAg	18/37	1	2	FACETS	0.126	0.103	0.152	0.126	0.103	0.152	SUBCLONAL	1	TRUE	1	0.914448822248741	2		725	626	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040716-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	82	612	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.2	2		612	663	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744483	41744483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755240418	NA	P-0040716-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	53	640	0	ENST00000301178.4:c.1103G>A	p.Arg368Gln	p.R368Q	ENST00000301178	NM_021913.4	368	cGg/cAg	8/20	1	2	FACETS	0.749	0.637	0.871	0.749	0.637	0.871	SUBCLONAL	1	TRUE	1	0.2	2		640	708	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805651	43805651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040716-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	58	606	1	ENST00000372470.3:c.707C>T	p.Ala236Val	p.A236V	ENST00000372470	NM_005373.2	236	gCa/gTa	5/12	1	2	FACETS	0.885	0.76	1	0.885	0.76	1	CLONAL	1	TRUE	1	0.2	2		607	655	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371703	118371703	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040716-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	39	474	0	ENST00000534358.1:c.6160T>C	p.Cys2054Arg	p.C2054R	ENST00000534358	NM_005933.3	2054	Tgt/Cgt	25/36	1	2	FACETS	0.724	0.599	0.863	0.724	0.599	0.863	SUBCLONAL	1	TRUE	1	0.2	2		474	539	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121074	11121074	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040716-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	41	581	0	ENST00000358026.2:c.2141T>C	p.Val714Ala	p.V714A	ENST00000358026	NM_001128849.1	714	gTc/gCc	15/36	1	2	FACETS	0.569	0.472	0.676	0.569	0.472	0.676	SUBCLONAL	1	TRUE	1	0.2	2		581	721	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29383125	29383125	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040716-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	56	628	0	ENST00000544604.2:c.362T>C	p.Val121Ala	p.V121A	ENST00000544604	NM_001206998.1	121	gTa/gCa	2/9	1	2	FACETS	0.863	0.738	0.999	0.863	0.738	0.999	CLONAL	1	TRUE	1	0.2	2		628	649	SUCCESS
ALB	213	MSKCC	GRCh37	4	74270073	74270073	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040716-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	32	449	0	ENST00000295897.4:c.29T>G	p.Leu10Arg	p.L10R	ENST00000295897	NM_000477.5	10	cTt/cGt	1/15	1	2	FACETS	0.61	0.494	0.741	0.61	0.494	0.741	SUBCLONAL	1	TRUE	1	0.2	2		449	525	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133761024	133761024	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040716-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	53	626	0	ENST00000318560.5:c.3347A>T	p.Lys1116Met	p.K1116M	ENST00000318560	NM_005157.4	1116	aAg/aTg	11/11	1	2	FACETS	0.735	0.626	0.855	0.735	0.626	0.855	SUBCLONAL	1	TRUE	1	0.2	2		626	721	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912660	NA	P-0041041-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	84	770	0	ENST00000269305.4:c.839G>T	p.Arg280Ile	p.R280I	ENST00000269305	NM_001126112.2	280	aGa/aTa	8/11	1	2	FACETS	0.935	0.832	1	1	0.984	1	CLONAL	2	TRUE	1	0.252402239528424	2		770	356	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231134	98231134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1311707136	NA	P-0041041-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	21	798	0	ENST00000331920.6:c.2149G>A	p.Asp717Asn	p.D717N	ENST00000331920	NM_000264.3	717	Gac/Aac	14/24	0.232476572772521	2	FACETS	0.429	0.33	0.545	0.214	0.165	0.273	SUBCLONAL	1	TRUE	0	0.252402239528424	2		798	388	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630154	100630154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555980875	NA	P-0041041-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	19	455	0	ENST00000308731.7:c.119A>G	p.Tyr40Cys	p.Y40C	ENST00000308731	NM_000061.2	40	tAt/tGt	2/19	1	2	FACETS	0.997	0.763	1	0.997	0.763	1	CLONAL	1	TRUE	1	0.252402239528424	2		455	151	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332868	152332868	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041041-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	43	543	0	ENST00000206249.3:c.1174G>T	p.Val392Phe	p.V392F	ENST00000206249	NM_000125.3	392	Gtc/Ttc	5/8	0.242023511415576	3	FACETS	1	0.936	1	0.413	0.347	0.485	CLONAL	1	TRUE	0	0.252402239528424	3		543	310	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165890	118165890	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041041-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	41	744	0	ENST00000369448.3:c.400C>G	p.Leu134Val	p.L134V	ENST00000369448	NM_017709.3	134	Ctg/Gtg	2/2	0.252402239528424	3	FACETS	0.89	0.742	1	0.445	0.371	0.527	CLONAL	1	TRUE	1	0.252402239528424	3		744	411	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046620	30046620	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041041-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	46	620	0	ENST00000331968.5:c.2563A>G	p.Ile855Val	p.I855V	ENST00000331968	NM_002742.2	855	Atc/Gtc	18/18	0.252402239528424	2	FACETS	1	0.961	1	0.744	0.632	0.865	CLONAL	1	TRUE	0	0.252402239528424	2		620	245	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604643	48604643	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041041-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	34	614	0	ENST00000342988.3:c.1465G>T	p.Gly489Ter	p.G489*	ENST00000342988	NM_005359.5	489	Gga/Tga	12/12	0.252402239528424	1	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	0	0.252402239528424	1		614	208	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134277	11134278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TC	novel	NA	P-0041041-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	77	728	0	ENST00000358026.2:c.2943_2944inv	p.Lys981_Lys982delinsAsnGln	p.K981_K982delinsNQ	ENST00000358026	NM_001128849.1	981	aaGAag/aaTCag	20/36	0.232476572772521	2	FACETS	0.968	0.858	1	0.968	0.858	1	CLONAL	2	TRUE	0	0.252402239528424	2		728	315	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285157	15285157	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041041-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	91	854	0	ENST00000263388.2:c.4458G>C	p.Gln1486His	p.Q1486H	ENST00000263388	NM_000435.2	1486	caG/caC	25/33	0.232476572772521	2	FACETS	0.934	0.835	1	0.934	0.835	1	CLONAL	2	TRUE	0	0.252402239528424	2		854	386	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446913	29446913	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041041-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	39	680	0	ENST00000544604.2:c.2744G>C	p.Ser915Thr	p.S915T	ENST00000544604	NM_001206998.1	915	aGc/aCc	8/9	0.232476572772521	2	FACETS	0.888	0.738	1	0.444	0.369	0.527	CLONAL	1	TRUE	0	0.252402239528424	2		680	348	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575594	55575594	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041041-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	21	325	0	ENST00000288135.5:c.1120G>C	p.Val374Leu	p.V374L	ENST00000288135	NM_000222.2	374	Gta/Cta	7/21	0.252402239528424	5	FACETS	0.831	0.647	1	0.416	0.323	0.521	CLONAL	2	TRUE	1	0.252402239528424	5		325	138	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509134	106509134	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041041-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	53	861	0	ENST00000359195.3:c.1128C>A	p.Asn376Lys	p.N376K	ENST00000359195	NM_002649.2	376	aaC/aaA	2/11	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.252402239528424	2		861	400	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938382	76938383	+	missense_variant	Missense_Mutation	DNP	TC	TC	CA	novel	NA	P-0041041-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	11	457	1	ENST00000373344.5:c.2365_2366delinsTG	p.Asp789Cys	p.D789C	ENST00000373344	NM_000489.3	789	GAt/TGt	9/35	1	2	FACETS	1	0.768	1	1	0.768	1	CLONAL	1	TRUE	1	0.252402239528424	2		458	78	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613683	100613683	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041041-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	31	579	0	ENST00000308731.7:c.896G>C	p.Gly299Ala	p.G299A	ENST00000308731	NM_000061.2	299	gGg/gCg	11/19	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.252402239528424	2		579	221	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481671	56481671	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041381-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	39	456	1	ENST00000267101.3:c.706T>C	p.Ser236Pro	p.S236P	ENST00000267101	NM_001982.3	236	Tca/Cca	6/28	0.525967248521305	4	FACETS	0.789	0.657	0.934	0.394	0.328	0.467	CLONAL	1	TRUE	2	0.525953192333164	4		457	287	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974792	21974792	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs141798398	NA	P-0041381-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	19	476	0	ENST00000304494.5:c.35C>A	p.Ser12Ter	p.S12*	ENST00000304494	NM_000077.4	12	tCg/tAg	1/3	1	2	FACETS	0.363	0.276	0.464	0.363	0.276	0.464	SUBCLONAL	1	TRUE	1	0.525953192333164	2		476	199	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0041381-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	12	566	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.525967248521305	4	FACETS	0.348	0.245	0.475	0.174	0.122	0.238	SUBCLONAL	1	TRUE	2	0.525953192333164	4		566	200	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217662	7217662	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041381-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	29	377	0	ENST00000380728.2:c.265C>T	p.Gln89Ter	p.Q89*	ENST00000380728		89	Cag/Tag	4/11	0.525967248521305	4	FACETS	0.346	0.277	0.425	0.173	0.138	0.213	SUBCLONAL	1	TRUE	2	0.525953192333164	4		377	486	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437700	49437700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041381-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	19	478	0	ENST00000301067.7:c.5270G>A	p.Arg1757Gln	p.R1757Q	ENST00000301067	NM_003482.3	1757	cGa/cAa	22/54	0.525967248521305	4	FACETS	0.378	0.286	0.485	0.189	0.143	0.243	SUBCLONAL	1	TRUE	2	0.525953192333164	4		478	292	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607693	46607693	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1402437703	NA	P-0041381-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	13	483	0	ENST00000263734.3:c.1882C>G	p.Leu628Val	p.L628V	ENST00000263734	NM_001430.4	628	Ctc/Gtc	12/16	0.206445101227586	4	FACETS	0.322	0.23	0.435	0.161	0.115	0.218	INDETERMINATE	1	TRUE	2	0.525953192333164	4		483	234	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132862	152132862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041381-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	18	217	0	ENST00000262189.6:c.10G>A	p.Glu4Lys	p.E4K	ENST00000262189	NM_170606.2	4	Gag/Aag	1/59	1	2	FACETS	0.313	0.236	0.403	0.313	0.236	0.403	SUBCLONAL	1	TRUE	1	0.525953192333164	2		217	219	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111504	8111505	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0042114-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	210	651	0	ENST00000346208.3:c.992dup	p.Asn331LysfsTer21	p.N331Kfs*21	ENST00000346208		330	-/A	5/6	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.51710088053445	2		651	760	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857209	9857209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042114-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	78	808	1	ENST00000330684.3:c.4192G>A	p.Asp1398Asn	p.D1398N	ENST00000330684	NM_001134407.1	1398	Gac/Aac	13/13	0.143837391654084	2	FACETS	0.311	0.272	0.352	0.155	0.136	0.176	INDETERMINATE	1	TRUE	0	0.51710088053445	2		809	971	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563525	87563525	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1227692441	NA	P-0042114-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	43	583	0	ENST00000277120.3:c.1913A>T	p.His638Leu	p.H638L	ENST00000277120		638	cAt/cTt	16/19	1	2	FACETS	0.303	0.253	0.359	0.303	0.253	0.359	SUBCLONAL	1	TRUE	1	0.51710088053445	2		583	548	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054012	42054012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1411818407	NA	P-0042114-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	48	456	0	ENST00000219905.7:c.7474C>T	p.Arg2492Trp	p.R2492W	ENST00000219905	NM_001164273.1	2492	Cgg/Tgg	21/24	0.167896189186363	0	FACETS	0.22	0.186	0.257			1	INDETERMINATE	1	TRUE	0	0.51710088053445	0		456	408	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23625396	23625396	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs766394024	NA	P-0042114-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	76	425	0	ENST00000261584.4:c.3130C>T	p.Gln1044Ter	p.Q1044*	ENST00000261584	NM_024675.3	1044	Caa/Taa	11/13	0.143837391654084	2	FACETS	0.615	0.541	0.694	0.307	0.27	0.347	INDETERMINATE	1	TRUE	0	0.51710088053445	2		425	478	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150900287	150900287	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042114-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	76	776	0	ENST00000271640.5:c.97C>A	p.Leu33Met	p.L33M	ENST00000271640	NM_001145415.1	33	Ctg/Atg	2/22	0.241930711919348	2	FACETS	0.365	0.32	0.414	0.183	0.16	0.207	INDETERMINATE	1	TRUE	0	0.51710088053445	2		776	805	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230561520	230561520	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0042114-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	65	946	0				ENST00000391860	NM_001258311.1	-/409			0.167754158472432	3	FACETS	0.326	0.281	0.374	0.109	0.093	0.125	INDETERMINATE	1	TRUE	0	0.51710088053445	3		946	972	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005388	42005388	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0042114-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	37	760	0	ENST00000219905.7:c.3124A>T	p.Lys1042Ter	p.K1042*	ENST00000219905	NM_001164273.1	1042	Aaa/Taa	9/24	0.167896189186363	0	FACETS	0.106	0.087	0.128			1	INDETERMINATE	1	TRUE	0	0.51710088053445	0		760	651	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127653	2127663	+	frameshift_variant	Frame_Shift_Del	DEL	AGAATTCAAGG	AGAATTCAAGG	-	novel	NA	P-0042114-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	230	896	0	ENST00000219476.3:c.2895_2905del	p.Phe966LeufsTer15	p.F966Lfs*15	ENST00000219476	NM_000548.3	964	aaAGAATTCAAGGag/aaag	26/42	0.143837391654084	2	FACETS	0.949	0.886	1	0.475	0.443	0.508	INDETERMINATE	1	TRUE	0	0.51710088053445	2		896	937	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690025	33690025	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042114-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	121	695	0	ENST00000308377.4:c.802G>C	p.Asp268His	p.D268H	ENST00000308377	NM_152270.3	268	Gac/Cac	2/5	0.167670395502078	3	FACETS	0.805	0.728	0.886	0.402	0.364	0.443	INDETERMINATE	1	TRUE	1	0.51710088053445	3		695	732	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881573	111881573	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042114-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	74	759	0	ENST00000393256.3:c.251G>C	p.Arg84Thr	p.R84T	ENST00000393256	NM_006538.4	84	aGa/aCa	2/4	1	2	FACETS	0.375	0.327	0.426	0.375	0.327	0.426	SUBCLONAL	1	TRUE	1	0.51710088053445	2		759	764	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729979	39729979	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042114-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	100	571	0	ENST00000361337.2:c.1294A>G	p.Ser432Gly	p.S432G	ENST00000361337	NM_003286.2	432	Agt/Ggt	13/21	0.262448155357194	3	FACETS	0.663	0.592	0.738	0.332	0.296	0.369	INDETERMINATE	1	TRUE	1	0.51710088053445	3		571	734	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056246	26056246	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042114-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	43	835	0	ENST00000343677.2:c.411G>T	p.Lys137Asn	p.K137N	ENST00000343677	NM_005319.3	137	aaG/aaT	1/1	0.248026353156453	2	FACETS	0.195	0.162	0.231	0.097	0.081	0.116	INDETERMINATE	1	TRUE	0	0.51710088053445	2		835	853	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528701	8528701	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042114-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	99	688	1	ENST00000356435.5:c.431C>T	p.Thr144Ile	p.T144I	ENST00000356435		144	aCc/aTc	4/35	0.444734893777412	1	FACETS	0.497	0.445	0.553	0.497	0.445	0.553	SUBCLONAL	1	TRUE	0	0.51710088053445	1		689	571	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248998	55248999	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCAGCG	rs727504263	NA	P-0042261-T15-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	134	525	0	ENST00000275493.2:c.2300_2308dup	p.Ala767_Val769dup	p.A767_V769dup	ENST00000275493	NM_005228.3	767	atg/aTGGCCAGCGtg	20/28	0.329762625527474	4	FACETS	0.759	0.691	0.831	0.759	0.691	0.831	SUBCLONAL	2	FALSE	2	0.329762625527474	4		525	712	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779102	135779102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs986350787	NA	P-0042261-T15-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	52	525	0	ENST00000298552.3:c.2144G>A	p.Arg715Gln	p.R715Q	ENST00000298552	NM_001162426.1	715	cGg/cAg	17/23	0.238150105304286	2	FACETS	0.604	0.514	0.703	0.302	0.257	0.352	SUBCLONAL	1	FALSE	0	0.329762625527474	2		525	522	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465899	69465899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042261-T15-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	48	644	0	ENST00000227507.2:c.737C>T	p.Ala246Val	p.A246V	ENST00000227507	NM_053056.2	246	gCc/gTc	5/5	0.237779252620359	2	FACETS	0.545	0.461	0.638	0.273	0.23	0.319	SUBCLONAL	1	FALSE	0	0.329762625527474	2		644	534	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0042695-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	161	210	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.150357444647414	6	FACETS	0.888	0.82	0.958	0.888	0.82	0.958	INDETERMINATE	3	TRUE	3	0.422106130719212	6		210	528	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909490	50909490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774130423	NA	P-0042695-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	207	984	0	ENST00000440232.2:c.1294C>T	p.Arg432Trp	p.R432W	ENST00000440232	NM_002691.3	432	Cgg/Tgg	11/27	0.178950834658615	4	FACETS	0.862	0.802	0.924	0.862	0.802	0.924	INDETERMINATE	2	TRUE	2	0.422106130719212	4		984	809	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562695	95562697	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0042695-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	83	404	1	ENST00000393063.1:c.4560_4562del	p.Glu1520del	p.E1520del	ENST00000393063	NM_030621.3	1520	gaAGAt/gat	24/28	0.150357444647414	6	FACETS	0.996	0.879	1	0.332	0.293	0.374	INDETERMINATE	1	TRUE	3	0.422106130719212	6		405	728	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609639	81609639	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042990-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	368	712	1	ENST00000298171.2:c.1237G>T	p.Gly413Cys	p.G413C	ENST00000298171	NM_000369.2	413	Ggc/Tgc	10/10	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.832699122781901	2		713	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578520	7578568	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGA	AGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGA	-	novel	NA	P-0042990-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	237	636	0	ENST00000269305.4:c.376-14_410del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	0.835850580128887	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.832699122781901	1		636	306	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271273	38271273	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042990-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	245	649	0	ENST00000425967.3:c.2435C>G	p.Pro812Arg	p.P812R	ENST00000425967	NM_001174067.1	812	cCc/cGc	19/19	1	2	FACETS	0.943	0.888	0.999	0.943	0.888	0.999	CLONAL	1	TRUE	1	0.832699122781901	2		649	624	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47599155	47599155	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042990-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	64	612	0	ENST00000430070.2:c.445G>A	p.Glu149Lys	p.E149K	ENST00000430070	NM_018095.4	149	Gaa/Aaa	2/4	1	2	FACETS	0.225	0.195	0.259	0.225	0.195	0.259	SUBCLONAL	1	TRUE	1	0.832699122781901	2		612	682	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63985132	63985145	+	frameshift_variant	Frame_Shift_Del	DEL	GCACGTCCCTGACA	GCACGTCCCTGACA	-	novel	NA	P-0042990-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	32	460	0	ENST00000398590.3:c.2737_2750del	p.Thr913Ter	p.T913*	ENST00000398590	NM_001177387.1	912	gGCACGTCCCTGACA/g	14/14	0.42859770160165	2	FACETS	0.124	0.1	0.152	0.062	0.05	0.076	INDETERMINATE	1	TRUE	0	0.832699122781901	2		460	618	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98002947	98002960	+	frameshift_variant	Frame_Shift_Del	DEL	AGTTTTGATTGTCC	AGTTTTGATTGTCC	-	novel	NA	P-0042990-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	26	418	0	ENST00000289081.3:c.316_329del	p.Gly106Ter	p.G106*	ENST00000289081	NM_000136.2	106	GGACAATCAAAACTt/t	4/15	0.835850580128887	2	FACETS	0.16	0.126	0.198	0.08	0.063	0.099	SUBCLONAL	1	TRUE	0	0.832699122781901	2		418	391	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514961	148514974	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTCTTACCAGAGG	TGTCTTACCAGAGG	AGTTATT	novel	NA	P-0042990-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	31	516	1	ENST00000320356.2:c.1235_1240+8delinsAATAACT		p.X412_splice	ENST00000320356	NM_004456.4	412		10/20	NA	2	FACETS	0.134	0.108	0.164			1	INDETERMINATE	1	TRUE	NA	0.832699122781901	2		517	555	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0043925-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	49	482	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.194369959054812	2		482	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0043925-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	38	481	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	1	2	FACETS	0.905	0.749	1	0.905	0.749	1	CLONAL	1	TRUE	1	0.194369959054812	2		481	432	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890135	76890135	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043925-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	29	398	0	ENST00000373344.5:c.4759G>T	p.Gly1587Cys	p.G1587C	ENST00000373344	NM_000489.3	1587	Ggt/Tgt	17/35	1	2	FACETS	0.853	0.685	1	0.853	0.685	1	CLONAL	1	TRUE	1	0.194369959054812	2		398	350	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913075	32913075	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043925-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	36	444	0	ENST00000380152.3:c.4583G>T	p.Ser1528Ile	p.S1528I	ENST00000380152		1528	aGc/aTc	11/27	1	2	FACETS	0.786	0.646	0.944	0.786	0.646	0.944	CLONAL	1	TRUE	1	0.194369959054812	2		444	471	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435010	110435010	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043925-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	23	592	0	ENST00000375856.3:c.3391C>G	p.Arg1131Gly	p.R1131G	ENST00000375856	NM_003749.2	1131	Cgc/Ggc	1/2	1	2	FACETS	0.657	0.512	0.826	0.657	0.512	0.826	SUBCLONAL	1	TRUE	1	0.194369959054812	2		592	360	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149735	202149735	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043925-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	31	605	0	ENST00000358485.4:c.1176C>G	p.Ile392Met	p.I392M	ENST00000358485	NM_001080125.1	392	atC/atG	8/9	1	2	FACETS	0.687	0.555	0.837	0.687	0.555	0.837	SUBCLONAL	1	TRUE	1	0.194369959054812	2		605	464	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037198	71037198	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043925-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	46	484	0	ENST00000318789.4:c.1093A>C	p.Met365Leu	p.M365L	ENST00000318789	NM_032682.5	365	Atg/Ctg	14/21	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.194369959054812	2		484	464	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875958	76875958	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043925-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	39	395	0	ENST00000373344.5:c.5177A>T	p.Asn1726Ile	p.N1726I	ENST00000373344	NM_000489.3	1726	aAt/aTt	20/35	1	2	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	TRUE	1	0.194369959054812	2		395	394	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121082	11121082	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043925-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	53	892	0	ENST00000358026.2:c.2149G>T	p.Glu717Ter	p.E717*	ENST00000358026	NM_001128849.1	717	Gaa/Taa	15/36	1	2	FACETS	0.807	0.691	0.932	1	0.97	1	CLONAL	2	TRUE	1	0.194369959054812	2		892	338	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39618763	39618763	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043925-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	22	293	0	ENST00000262039.4:c.1987C>G	p.Leu663Val	p.L663V	ENST00000262039	NM_002647.2	663	Ctg/Gtg	18/25	0.194369959054812	1	FACETS	0.544	0.421	0.687	0.544	0.421	0.687	SUBCLONAL	1	TRUE	0	0.194369959054812	1		293	376	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144359542	144359542	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043925-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	39	507	2	ENST00000262995.4:c.984G>T	p.Leu328Phe	p.L328F	ENST00000262995	NM_207123.2	328	ttG/ttT	4/11	1	2	FACETS	0.944	0.783	1	0.944	0.783	1	CLONAL	1	TRUE	1	0.194369959054812	2		509	425	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439658	51439658	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	76	549	0	ENST00000262662.1:c.223C>G	p.His75Asp	p.H75D	ENST00000262662		75	Cat/Gat	4/4	0.277334632876096	4	FACETS	0.563	0.493	0.637	0.188	0.164	0.213	INDETERMINATE	1	TRUE	1	0.646543126988957	4		549	688	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0044996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	164	563	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.451936242224721	3	FACETS	1	0.954	1	0.684	0.639	0.729	CLONAL	2	TRUE	0	0.646543126988957	3		563	327	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047160	77047160	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	225	524	0	ENST00000356341.3:c.1384C>A	p.Pro462Thr	p.P462T	ENST00000356341	NM_002576.4	462	Cct/Act	13/15	0.646543126988957	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.646543126988957	3		524	396	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394786	394786	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	40	446	0	ENST00000399788.2:c.4909C>T	p.His1637Tyr	p.H1637Y	ENST00000399788	NM_001042603.1	1637	Cat/Tat	28/28	NA	2	FACETS	0.358	0.298	0.424			1	INDETERMINATE	1	TRUE	NA	0.646543126988957	2		446	346	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243893	41243893	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	109	510	0	ENST00000357654.3:c.3655G>T	p.Glu1219Ter	p.E1219*	ENST00000357654	NM_007294.3	1219	Gag/Tag	10/23	0.548037028916206	2	FACETS	0.791	0.729	0.854	0.791	0.729	0.854	SUBCLONAL	2	TRUE	0	0.646543126988957	2		510	213	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740467	58740467	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs773389405	NA	P-0044996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	49	436	0	ENST00000305921.3:c.1372C>G	p.Arg458Gly	p.R458G	ENST00000305921	NM_003620.3	458	Cga/Gga	6/6	0.646543126988957	3	FACETS	0.729	0.622	0.845	0.243	0.207	0.282	SUBCLONAL	1	TRUE	0	0.646543126988957	3		436	275	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46271095	46271095	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	72	449	0	ENST00000371998.3:c.3219C>G	p.Asp1073Glu	p.D1073E	ENST00000371998		1073	gaC/gaG	17/23	0.390302917690041	5	FACETS	0.981	0.861	1	0.327	0.287	0.371	CLONAL	1	TRUE	2	0.646543126988957	5		449	447	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62322099	62322153	+	splice_region_variant,intron_variant	Splice_Region	DEL	GCAGGGACCCCAGCTGGGGCCCCCCGTGGGCTTCACTGCGCACTCGGGTGCCCCT	GCAGGGACCCCAGCTGGGGCCCCCCGTGGGCTTCACTGCGCACTCGGGTGCCCCT	-	novel	NA	P-0044996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	48	233	0	ENST00000360203.5:c.2414-53_2415del		p.X805_splice	ENST00000360203	NM_001283009.1	805			0.390302917690041	5	FACETS	0.77	0.66	0.887	0.513	0.44	0.591	SUBCLONAL	2	TRUE	2	0.646543126988957	5		233	190	SUCCESS
REST	5978	MSKCC	GRCh37	4	57777321	57777321	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	43	525	0	ENST00000309042.7:c.517C>T	p.Gln173Ter	p.Q173*	ENST00000309042	NM_005612.4	173	Cag/Tag	2/4	0.277334632876096	4	FACETS	0.424	0.355	0.502	0.141	0.118	0.168	INDETERMINATE	1	TRUE	1	0.646543126988957	4		525	516	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251164	251164	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	36	231	0	ENST00000264932.6:c.1609G>C	p.Gly537Arg	p.G537R	ENST00000264932	NM_004168.2	537	Ggg/Cgg	12/15	0.427351324491006	6	FACETS	0.779	0.642	0.931	0.195	0.16	0.233	CLONAL	1	TRUE	2	0.646543126988957	6		231	328	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858456	27858547	+	frameshift_variant	Frame_Shift_Del	DEL	GCTTCTTCACACCGCCAGTCGCTGGAGCGCTTTTGCGCGCTGCCTTGGTGGCCAGCTGCTTCCGCGGTGCCTTGCCGCCGGTAGACTTGCGA	GCTTCTTCACACCGCCAGTCGCTGGAGCGCTTTTGCGCGCTGCCTTGGTGGCCAGCTGCTTCCGCGGTGCCTTGCCGCCGGTAGACTTGCGA	-	novel	NA	P-0044996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	88	667	0	ENST00000359303.2:c.24_115del	p.Arg9ProfsTer12	p.R9Pfs*12	ENST00000359303	NM_003535.2	8	gcTCGCAAGTCTACCGGCGGCAAGGCACCGCGGAAGCAGCTGGCCACCAAGGCAGCGCGCAAAAGCGCTCCAGCGACTGGCGGTGTGAAGAAGCcc/gccc	1/1	0.646543126988957	5	FACETS	0.661	0.585	0.743	0.22	0.195	0.248	SUBCLONAL	1	TRUE	2	0.646543126988957	5		667	811	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27109638	27109638	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	19	317	0	ENST00000380036.4:c.50C>A	p.Ser17Tyr	p.S17Y	ENST00000380036	NM_000459.3	17	tCt/tAt	1/23	0.646543126988957	3	FACETS	0.304	0.231	0.39	0.152	0.115	0.195	SUBCLONAL	1	TRUE	1	0.646543126988957	3		317	256	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1327790	1327790	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	28	336	0	ENST00000400841.2:c.91C>G	p.Gln31Glu	p.Q31E	ENST00000400841		31	Cag/Gag	2/6	0.390302917690041	5	FACETS	0.981	0.791	1	0.327	0.263	0.398	CLONAL	1	TRUE	2	0.646543126988957	5		336	174	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619161	37619162	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	218	731	0	ENST00000447079.4:c.839dup	p.Glu281GlyfsTer17	p.E281Gfs*17	ENST00000447079	NM_015083.1	279	-/A	1/14	0.738067675687639	3	FACETS	0.988	0.921	1	0.494	0.46	0.529	CLONAL	1	TRUE	1	0.73466035936651	3		731	821	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627610	37627610	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0045881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	366	539	0	ENST00000447079.4:c.1525A>T	p.Lys509Ter	p.K509*	ENST00000447079	NM_015083.1	509	Aaa/Taa	2/14	0.738067675687639	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.73466035936651	3		539	662	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480084	20480084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761207862	NA	P-0045881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	148	406	0	ENST00000346618.3:c.401G>A	p.Arg134Gln	p.R134Q	ENST00000346618	NM_001949.4	134	cGa/cAa	2/7	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.73466035936651	2		406	359	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412708	63412708	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	384	292	0	ENST00000330258.3:c.459A>T	p.Lys153Asn	p.K153N	ENST00000330258	NM_152424.3	153	aaA/aaT	2/2	0.738067675687639	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.73466035936651	2		292	429	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202482	123202482	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	151	86	0	ENST00000218089.9:c.2334C>G	p.Asn778Lys	p.N778K	ENST00000218089	NM_001042749.1	778	aaC/aaG	24/35	0.738067675687639	2	FACETS	1	0.99	1			1	CLONAL	2	TRUE	NA	0.73466035936651	2		86	180	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39321543	39321543	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046319-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	345	429	0	ENST00000373001.3:c.478A>C	p.Thr160Pro	p.T160P	ENST00000373001	NM_022157.3	160	Act/Cct	3/7	1	2	FACETS	0.988	0.941	1	0.988	0.941	1	CLONAL	1	TRUE	1	0.875145437236085	2		429	798	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248394	59248394	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046319-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	368	673	0	ENST00000371222.2:c.349G>T	p.Ala117Ser	p.A117S	ENST00000371222	NM_002228.3	117	Gcc/Tcc	1/1	1	2	FACETS	0.676	0.641	0.711	0.676	0.641	0.711	SUBCLONAL	1	TRUE	1	0.875145437236085	2		673	1245	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027156	49027159	+	frameshift_variant	Frame_Shift_Del	DEL	CAAT	CAAT	-	novel	NA	P-0046319-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	797	279	0	ENST00000267163.4:c.1726_1729del	p.Ser576ArgfsTer34	p.S576Rfs*34	ENST00000267163	NM_000321.2	575	CAATca/ca	18/27	0.875145437236085	2	FACETS	0.99	0.974	1	0.99	0.974	1	CLONAL	2	TRUE	0	0.875145437236085	2		279	920	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628736	187628736	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs369161430	NA	P-0046319-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	592	599	0	ENST00000441802.2:c.2246A>G	p.Asn749Ser	p.N749S	ENST00000441802	NM_005245.3	749	aAt/aGt	2/27	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.875145437236085	2		599	1332	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168768	32168768	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046319-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	77	572	0	ENST00000375023.3:c.4155G>T	p.Met1385Ile	p.M1385I	ENST00000375023	NM_004557.3	1385	atG/atT	23/30	1	2	FACETS	0.146	0.128	0.167	0.146	0.128	0.167	SUBCLONAL	1	TRUE	1	0.875145437236085	2		572	1202	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931610	39931610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046319-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	360	241	0	ENST00000378444.4:c.2989del	p.Ala997HisfsTer24	p.A997Hfs*24	ENST00000378444	NM_001123385.1	997	Gca/ca	4/15	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.875145437236085	1		241	428	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0046866-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	51	230	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.53591793008119	2		230	164	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046866-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	118	701	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.527436402959977	2	FACETS	0.935	0.849	1	0.467	0.424	0.513	CLONAL	1	TRUE	0	0.53591793008119	2		701	471	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237595	16237595	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0046866-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	106	345	0	ENST00000375759.3:c.1043-1G>C		p.X348_splice	ENST00000375759	NM_015001.2	348			1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.53591793008119	2		345	375	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265823	16265851	+	frameshift_variant	Frame_Shift_Del	DEL	TGAGTTCTCTGAGAGTCACCTGTCCCGCC	TGAGTTCTCTGAGAGTCACCTGTCCCGCC	-	novel	NA	P-0046866-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	148	623	0	ENST00000375759.3:c.10898_10926del	p.Glu3633GlyfsTer3	p.E3633Gfs*3	ENST00000375759	NM_015001.2	3632	tgTGAGTTCTCTGAGAGTCACCTGTCCCGCCtg/tgtg	15/15	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.53591793008119	2		623	528	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712712	43712712	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046866-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	138	658	0	ENST00000382044.4:c.4472T>A	p.Phe1491Tyr	p.F1491Y	ENST00000382044	NM_001141980.1	1491	tTt/tAt	21/28	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.53591793008119	2		658	509	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584587	48584587	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046866-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	141	604	0	ENST00000342988.3:c.760del	p.Thr254LeufsTer82	p.T254Lfs*82	ENST00000342988	NM_005359.5	254	Act/ct	6/12	0.53591793008119	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.53591793008119	1		604	377	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201753	66201753	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046866-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	102	597	0	ENST00000273854.3:c.2749A>C	p.Lys917Gln	p.K917Q	ENST00000273854	NM_004439.5	917	Aaa/Caa	16/18	1	2	FACETS	0.829	0.746	0.917	0.829	0.746	0.917	CLONAL	1	TRUE	1	0.53591793008119	2		597	459	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165339	32165349	+	frameshift_variant	Frame_Shift_Del	DEL	AGCAAACTGCT	AGCAAACTGCT	-	novel	NA	P-0046866-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	137	577	0	ENST00000375023.3:c.4779_4789del	p.Ala1594TrpfsTer17	p.A1594Wfs*17	ENST00000375023	NM_004557.3	1593	tcAGCAGTTTGCTgt/tcgt	27/30	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.53591793008119	2		577	470	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945702	151945702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1189672992	NA	P-0046866-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	54	301	0	ENST00000262189.6:c.1817C>T	p.Ser606Leu	p.S606L	ENST00000262189	NM_170606.2	606	tCa/tTa	14/59	1	2	FACETS	0.974	0.843	1	0.974	0.843	1	CLONAL	1	TRUE	1	0.53591793008119	2		301	207	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423781	47423781	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046866-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	170	642	0	ENST00000404338.3:c.1849C>T	p.Arg617Ter	p.R617*	ENST00000404338	NM_004491.4	617	Cga/Tga	1/6	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.53591793008119	2		642	528	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2076304	2076304	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046866-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	124	416	0	ENST00000349721.2:c.2011G>C	p.Glu671Gln	p.E671Q	ENST00000349721	NM_003070.3	671	Gag/Cag	13/34	0.316039793150293	3	FACETS	0.858	0.786	0.932	0.858	0.786	0.932	INDETERMINATE	2	TRUE	1	0.53591793008119	3		416	342	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0047181-T10-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	162	516	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.525295642021566	3	FACETS	0.828	0.771	0.886			1	CLONAL	2	TRUE	NA	0.729540811287363	3		516	366	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207118	1207118	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047181-T10-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	492	549	0	ENST00000326873.7:c.206C>A	p.Ser69Ter	p.S69*	ENST00000326873	NM_000455.4	69	tCg/tAg	1/10	0.729540811287363	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.729540811287363	2		549	665	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274541	198274541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047181-T10-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	183	429	0	ENST00000335508.6:c.857C>T	p.Ser286Phe	p.S286F	ENST00000335508	NM_012433.2	286	tCc/tTc	7/25	1	2	FACETS	0.899	0.835	0.964	0.899	0.835	0.964	CLONAL	1	TRUE	1	0.729540811287363	2		429	558	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054395	42054396	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047181-T10-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	147	376	0	ENST00000219905.7:c.7585dup	p.Arg2529LysfsTer9	p.R2529Kfs*9	ENST00000219905	NM_001164273.1	2527	caa/cAaa	22/24	1	2	FACETS	0.878	0.808	0.95	0.878	0.808	0.95	CLONAL	1	TRUE	1	0.729540811287363	2		376	459	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259196	89259196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047181-T10-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	184	409	0	ENST00000336596.2:c.340G>A	p.Gly114Arg	p.G114R	ENST00000336596	NM_005233.5	114	Gga/Aga	3/17	1	2	FACETS	0.952	0.885	1	0.952	0.885	1	CLONAL	1	TRUE	1	0.729540811287363	2		409	530	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227925	123227925	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047181-T10-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	108	316	0	ENST00000218089.9:c.3636G>C	p.Met1212Ile	p.M1212I	ENST00000218089	NM_001042749.1	1212	atG/atC	33/35	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.729540811287363	2		316	285	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0047218-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	121	516	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.892	0.813	0.974	0.892	0.813	0.974	CLONAL	1	TRUE	1	0.661537564582315	2		516	410	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0047218-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	105	424	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.45	0.403	0.5	0.45	0.403	0.5	SUBCLONAL	1	TRUE	1	0.661537564582315	2		424	705	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0047218-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	251	759	0	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.661132615091376	1	FACETS	0.908	0.858	0.959	0.908	0.858	0.959	CLONAL	1	TRUE	0	0.661537564582315	1		759	559	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896403	28896403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047218-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	157	484	0	ENST00000282397.4:c.3047G>A	p.Arg1016Lys	p.R1016K	ENST00000282397	NM_002019.4	1016	aGa/aAa	22/30	NA	2	FACETS	0.902	0.832	0.975			1	INDETERMINATE	1	TRUE	NA	0.661537564582315	2		484	526	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3634857	3634857	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1284986751	NA	P-0047218-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	501	640	0	ENST00000294008.3:c.4652A>G	p.Lys1551Arg	p.K1551R	ENST00000294008	NM_032444.2	1551	aAg/aGg	13/15	0.64261838549741	3	FACETS	0.954	0.918	0.991	0.954	0.918	0.991	CLONAL	2	TRUE	1	0.661537564582315	3		640	1056	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570432	39570432	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778354842	NA	P-0047218-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	63	149	0	ENST00000262039.4:c.628C>T	p.Arg210Ter	p.R210*	ENST00000262039	NM_002647.2	210	Cga/Tga	6/25	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.661537564582315	2		149	176	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602341	10602342	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0047218-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	63	948	0	ENST00000171111.5:c.1236_1237del	p.Arg413Ter	p.R413*	ENST00000171111	NM_203500.1	412	ccCCgt/ccgt	3/6	0.661132615091376	1	FACETS	0.19	0.164	0.218	0.19	0.164	0.218	SUBCLONAL	1	TRUE	0	0.661537564582315	1		948	672	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576872	212576872	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047218-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	209	446	0	ENST00000342788.4:c.1027A>T	p.Met343Leu	p.M343L	ENST00000342788	NM_005235.2	343	Atg/Ttg	9/28	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.661537564582315	2		446	515	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231351	98231351	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047218-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	357	992	0	ENST00000331920.6:c.1932del	p.Tyr645ThrfsTer48	p.Y645Tfs*48	ENST00000331920	NM_000264.3	644	ccC/cc	14/24	1	2	FACETS	0.979	0.928	1	0.979	0.928	1	CLONAL	1	TRUE	1	0.661537564582315	2		992	1103	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0047336-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	506	640	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.310935270929904	6	FACETS	0.938	0.904	0.972			1	CLONAL	6	TRUE	NA	0.310935270929904	6		640	938	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730915	40730915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753788938	NA	P-0047336-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	70	645	0	ENST00000373198.4:c.3620G>A	p.Arg1207His	p.R1207H	ENST00000373198	NM_133170.3	1207	cGt/cAt	27/32	0.312778254010007	3	FACETS	0.814	0.71	0.927			1	CLONAL	1	TRUE	NA	0.310935270929904	3		645	639	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435333	110435333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196624356	NA	P-0047336-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	104	749	0	ENST00000375856.3:c.3068C>T	p.Ala1023Val	p.A1023V	ENST00000375856	NM_003749.2	1023	gCg/gTg	1/2	0.312778254010007	3	FACETS	0.991	0.887	1	0.495	0.443	0.551	CLONAL	1	TRUE	1	0.310935270929904	3		749	780	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024432	31024432	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs769761920	NA	P-0047336-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	83	564	0	ENST00000375687.4:c.3917G>T	p.Gly1306Val	p.G1306V	ENST00000375687	NM_015338.5	1306	gGc/gTc	13/13	0.310935270929904	5	FACETS	0.977	0.862	1	0.244	0.215	0.276	CLONAL	1	TRUE	1	0.310935270929904	5		564	801	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877365	40877365	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047336-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	58	503	0	ENST00000373198.4:c.2331C>G	p.Ile777Met	p.I777M	ENST00000373198	NM_133170.3	777	atC/atG	15/32	0.312778254010007	3	FACETS	0.66	0.567	0.762			1	SUBCLONAL	1	TRUE	NA	0.310935270929904	3		503	653	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037192	71037192	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047336-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	58	518	0	ENST00000318789.4:c.1099A>G	p.Thr367Ala	p.T367A	ENST00000318789	NM_032682.5	367	Acc/Gcc	14/21	0.254905953437806	4	FACETS	0.713	0.612	0.824	0.356	0.306	0.412	SUBCLONAL	1	TRUE	2	0.310935270929904	4		518	686	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946216	13946216	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047336-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	42	322	0	ENST00000405192.2:c.880A>C	p.Lys294Gln	p.K294Q	ENST00000405192	NM_001163147.1	294	Aaa/Caa	10/12	0.312778254010007	3	FACETS	0.738	0.617	0.872	0.246	0.205	0.291	SUBCLONAL	1	TRUE	0	0.310935270929904	3		322	423	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242264	98242264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047336-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	65	473	0	ENST00000331920.6:c.1054G>A	p.Gly352Arg	p.G352R	ENST00000331920	NM_000264.3	352	Gga/Aga	7/24	0.301358314496043	2	FACETS	0.882	0.766	1	0.441	0.383	0.504	CLONAL	1	TRUE	0	0.310935270929904	2		473	474	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612286	189612286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048929-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	212	512	0	ENST00000264731.3:c.2038G>A	p.Glu680Lys	p.E680K	ENST00000264731	NM_003722.4	680	Gag/Aag	14/14	0.520640646987532	1	FACETS	0.73	0.69	0.769	0.73	0.69	0.769	INDETERMINATE	1	TRUE	0	0.874367876200321	1		512	374	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426810	212426810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1169977608	NA	P-0048929-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	43	461	0	ENST00000342788.4:c.2305G>A	p.Ala769Thr	p.A769T	ENST00000342788	NM_005235.2	769	Gct/Act	20/28	0.311477951760783	1	FACETS	0.104	0.087	0.124	0.104	0.087	0.124	INDETERMINATE	1	TRUE	0	0.874367876200321	1		461	531	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	63	344	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.786	0.687	0.892	0.786	0.687	0.892	SUBCLONAL	1	TRUE	1	0.582630567867251	2		344	275	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863224499	NA	P-0049139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	173	759	0	ENST00000269305.4:c.672+1G>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.582630567867251	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.582630567867251	1		759	413	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198402	108198402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	186	445	1	ENST00000278616.4:c.7006G>A	p.Glu2336Lys	p.E2336K	ENST00000278616	NM_000051.3	2336	Gaa/Aaa	48/63	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.582630567867251	2		446	468	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913514	NA	P-0049899-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	229	360	0	ENST00000288135.5:c.2466T>A	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaA	17/21	0.835223768751918	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.835223768751918	1		360	305	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593597	55593611	+	inframe_deletion	In_Frame_Del	DEL	GTACAGTGGAAGGTT	GTACAGTGGAAGGTT	-	novel	NA	P-0049899-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	222	411	0	ENST00000288135.5:c.1665_1679del	p.Gln556_Val560del	p.Q556_V560del	ENST00000288135	NM_000222.2	555	GTACAGTGGAAGGTT/-	11/21	0.835223768751918	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.835223768751918	1		411	301	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0050532-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	761	377	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.325190245369183	11	FACETS	0.979	0.952	1	0.979	0.952	1	CLONAL	9	TRUE	2	0.325190245369183	11		377	1308	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268969	55268969	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050532-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	976	560	0	ENST00000275493.2:c.3035A>T	p.Asp1012Val	p.D1012V	ENST00000275493	NM_005228.3	1012	gAt/gTt	25/28	0.325190245369183	11	FACETS	0.969	0.944	0.993	0.969	0.944	0.993	CLONAL	9	TRUE	2	0.325190245369183	11		560	1696	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63973786	63973786	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050532-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	58	447	0	ENST00000398590.3:c.1147G>A	p.Asp383Asn	p.D383N	ENST00000398590	NM_001177387.1	383	Gat/Aat	9/14	1	2	FACETS	0.601	0.516	0.693	0.601	0.516	0.693	SUBCLONAL	1	TRUE	1	0.325190245369183	2		447	594	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204782	128204782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050532-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	47	547	0	ENST00000341105.2:c.659G>A	p.Ser220Asn	p.S220N	ENST00000341105	NM_032638.4	220	aGc/aAc	3/6	1	2	FACETS	0.42	0.353	0.493	0.42	0.353	0.493	SUBCLONAL	1	TRUE	1	0.325190245369183	2		547	689	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490653	20490653	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050532-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	37	355	0	ENST00000346618.3:c.1390T>G	p.Cys464Gly	p.C464G	ENST00000346618	NM_001949.4	464	Tgt/Ggt	7/7	1	2	FACETS	0.478	0.394	0.572	0.478	0.394	0.572	SUBCLONAL	1	TRUE	1	0.325190245369183	2		355	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0050657-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	353	616	0	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	0.562312934221661	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.565479643502426	3		616	506	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942528	17942529	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0050657-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	177	558	0	ENST00000458235.1:c.2759_2760del	p.Arg920ProfsTer47	p.R920Pfs*47	ENST00000458235	NM_000215.3	920	cGC/c	20/24	0.562747762509086	2	FACETS	0.934	0.877	0.991	0.934	0.877	0.991	CLONAL	2	TRUE	0	0.565479643502426	2		558	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs483352695	NA	P-0050657-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	325	611	0	ENST00000269305.4:c.736A>T	p.Met246Leu	p.M246L	ENST00000269305	NM_001126112.2	246	Atg/Ttg	7/11	0.562312934221661	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	0	0.565479643502426	3		611	475	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412046	116412046	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	G	novel	NA	P-0050657-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	2704	719	0	ENST00000397752.3:c.3028+3A>G		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.565479643502426	17	FACETS	1	0.995	1			1	CLONAL	17	TRUE	NA	0.565479643502426	17		719	2939	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851446	63851446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050657-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	109	754	0	ENST00000279873.7:c.2224G>A	p.Asp742Asn	p.D742N	ENST00000279873	NM_032199.2	742	Gac/Aac	10/10	0.565479643502426	3	FACETS	0.878	0.791	0.97	0.439	0.395	0.485	CLONAL	1	TRUE	1	0.565479643502426	3		754	563	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124503667	124503667	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs797045168	NA	P-0050657-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	264	508	0	ENST00000357628.3:c.283G>T	p.Gly95Cys	p.G95C	ENST00000357628	NM_015450.2	95	Ggt/Tgt	8/19	0.565479643502426	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.565479643502426	2		508	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0050975-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	35	583	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.679	0.555	0.82	0.679	0.555	0.82	SUBCLONAL	1	TRUE	1	0.15	2		583	687	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050975-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	28	612	0				ENST00000310581	NM_198253.2	-/1132			0.119898347108003	3	FACETS	0.861	0.687	1	0.431	0.343	0.53	CLONAL	1	TRUE	1	0.15	3		612	466	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0050975-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	11	363	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.254	0.174	0.354	0.254	0.174	0.354	SUBCLONAL	1	TRUE	1	0.15	2		363	578	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0050975-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	80	667	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	0.843	0.742	0.95	1	0.98	1	CLONAL	2	TRUE	1	0.15	2		667	633	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136286	202136286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050975-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	20	0	0	ENST00000358485.4:c.530G>A	p.Arg177Lys	p.R177K	ENST00000358485	NM_001080125.1	177	aGg/aAg	3/9	1	2	FACETS	0.58	0.442	0.742	0.58	0.442	0.742	SUBCLONAL	1	TRUE	1	0.15	2		0	460	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090646	71090646	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050975-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	12	0	0	ENST00000318789.4:c.702A>T	p.Glu234Asp	p.E234D	ENST00000318789	NM_032682.5	234	gaA/gaT	11/21	1	2	FACETS	0.303	0.212	0.417	0.303	0.212	0.417	SUBCLONAL	1	TRUE	1	0.15	2		0	528	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968335	134968335	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0050975-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	23	463	0	ENST00000398015.3:c.2846+2T>C		p.X949_splice	ENST00000398015	NM_004441.4	949			1	2	FACETS	0.692	0.539	0.871	0.692	0.539	0.871	SUBCLONAL	1	TRUE	1	0.15	2		463	443	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275777	38275777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs923019674	NA	P-0050975-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	15	0	0	ENST00000425967.3:c.1492G>A	p.Glu498Lys	p.E498K	ENST00000425967	NM_001174067.1	498	Gaa/Aaa	11/19	1	2	FACETS	0.342	0.249	0.455	0.342	0.249	0.455	SUBCLONAL	1	TRUE	1	0.15	2		0	585	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106129	27106129	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051300-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	123	797	0	ENST00000324856.7:c.5740A>G	p.Met1914Val	p.M1914V	ENST00000324856	NM_006015.4	1914	Atg/Gtg	20/20	0.476816758324088	3	FACETS	0.829	0.75	0.912	0.414	0.375	0.456	CLONAL	1	TRUE	1	0.476816758324088	3		797	771	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499744	18499744	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051300-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	119	760	0	ENST00000266497.5:c.1599C>A	p.His533Gln	p.H533Q	ENST00000266497		533	caC/caA	10/31	0.357194982601793	3	FACETS	0.957	0.865	1	0.478	0.432	0.527	CLONAL	1	TRUE	1	0.476816758324088	3		760	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574027	7574069	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CACGGATCTGCAGCAACAGAGGAGGGGGAGAAGTAAGTATATA	CACGGATCTGCAGCAACAGAGGAGGGGGAGAAGTAAGTATATA	-	novel	NA	P-0051300-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	230	582	0	ENST00000269305.4:c.994-36_1000del		p.X332_splice	ENST00000269305	NM_001126112.2	332		10/11	0.476816758324088	3	FACETS	1	0.971	1	0.702	0.66	0.745	CLONAL	2	TRUE	0	0.476816758324088	3		582	567	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025674	48025750	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCATAAGTTGAACTGTCTTACATTATGGTTTTCCAAATTTTGATTTGTTTTTAAATACTCTTTCCTTGCCTGGCAGG	TCATAAGTTGAACTGTCTTACATTATGGTTTTCCAAATTTTGATTTGTTTTTAAATACTCTTTCCTTGCCTGGCAGG	-	novel	NA	P-0051300-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	35	200	0	ENST00000234420.5:c.628-75_629del		p.X210_splice	ENST00000234420	NM_000179.2	210		4/10	0.446968919401103	4	FACETS	0.763	0.636	0.901	0.763	0.636	0.901	CLONAL	2	TRUE	2	0.476816758324088	4		200	142	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027084	48027084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148592158	NA	P-0051300-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	86	740	0	ENST00000234420.5:c.1962G>A	p.Met654Ile	p.M654I	ENST00000234420	NM_000179.2	654	atG/atA	4/10	0.446968919401103	4	FACETS	0.861	0.762	0.966	0.43	0.381	0.483	CLONAL	1	TRUE	2	0.476816758324088	4		740	619	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590483	67590496	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCAATGAGAAAG	AGGCAATGAGAAAG	TTT	novel	NA	P-0051300-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	41	517	0	ENST00000274335.5:c.1545_1558delinsTTT	p.Glu515AspfsTer9	p.E515Dfs*9	ENST00000274335		515	gaAGGCAATGAGAAAGaa/gaTTTaa	11/15	0.326312085923634	2	FACETS	0.811	0.682	0.951	0.406	0.341	0.476	CLONAL	1	TRUE	0	0.476816758324088	2		517	212	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289247	33289247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1455644209	NA	P-0051469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	367	516	0	ENST00000374542.5:c.305C>T	p.Ser102Leu	p.S102L	ENST00000374542	NM_001141970.1	102	tCg/tTg	3/8	0.747130250997903	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.747130250997903	1		516	605	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920768	100920770	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	novel	NA	P-0051469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	181	388	0	ENST00000325455.5:c.2378_2380del	p.Ser793del	p.S793del	ENST00000325455	NM_001202474.3	793	tCATtc/ttc	6/8	0.747130250997903	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.747130250997903	1		388	293	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2115841	2115841	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs281875187	NA	P-0051469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	721	521	0	ENST00000349721.2:c.3476G>A	p.Arg1159Gln	p.R1159Q	ENST00000349721	NM_003070.3	1159	cGa/cAa	25/34	0.747130250997903	2	FACETS	0.985	0.962	1	0.985	0.962	1	CLONAL	2	TRUE	0	0.747130250997903	2		521	980	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0051880-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	268	377	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.386219468091525	4	FACETS	0.785	0.736	0.835	0.523	0.49	0.557	SUBCLONAL	2	TRUE	1	0.427745124075086	4		377	1140	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0051880-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	373	644	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.386219468091525	4	FACETS	0.975	0.925	1	0.65	0.616	0.684	CLONAL	2	TRUE	1	0.427745124075086	4		644	1277	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0051880-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	229	589	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.426601870653357	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.427745124075086	1		589	757	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61324115	61324115	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs61733410	NA	P-0051880-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	36	512	0	ENST00000283752.5:c.718G>C	p.Asp240His	p.D240H	ENST00000283752	NM_006919.2	240	Gat/Cat	7/8	0.308862805819366	1	FACETS	0.251	0.206	0.302	0.251	0.206	0.302	SUBCLONAL	1	TRUE	0	0.427745124075086	1		512	527	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0052316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	30	210	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.679	0.545	0.833	0.679	0.545	0.833	SUBCLONAL	1	TRUE	1	0.12	2		210	736	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691039	NA	P-0052316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	28	980	0	ENST00000269305.4:c.919+1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			1	2	FACETS	0.428	0.34	0.529	0.428	0.34	0.529	SUBCLONAL	1	TRUE	1	0.12	2		980	1091	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880827	28880827	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368266056	NA	P-0052316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	46	762	0	ENST00000282397.4:c.3803C>T	p.Ser1268Leu	p.S1268L	ENST00000282397	NM_002019.4	1268	tCg/tTg	29/30	1	2	FACETS	0.897	0.753	1	0.897	0.753	1	CLONAL	1	TRUE	1	0.12	2		762	855	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0052439-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	55	496	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	1	0.925	1	1	0.983	1	CLONAL	3	FALSE	1	0.189682256470801	2		496	177	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0052439-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	13	230	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.189682256470801	3	FACETS	0.974	0.767	1	1	0.932	1	CLONAL	7	FALSE	0	0.189682256470801	3		230	22	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056309	27056313	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCC	GGGCC	-	novel	NA	P-0052439-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	133	606	0	ENST00000324856.7:c.1309_1313del	p.Arg437AlafsTer184	p.R437Afs*184	ENST00000324856	NM_006015.4	435	caGGGCCgg/cagg	2/20	1	2	FACETS	0.996	0.916	1	1	0.993	1	CLONAL	4	FALSE	1	0.189682256470801	2		606	352	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798201	32798202	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0052439-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	63	548	0	ENST00000374899.4:c.1477_1478del	p.Leu493ThrfsTer4	p.L493Tfs*4	ENST00000374899	NM_018833.2	493	CTa/a	9/12	0.189682256470801	3	FACETS	1	0.915	1	1	0.982	1	CLONAL	4	FALSE	1	0.189682256470801	3		548	174	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0052439-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	15	210	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.252360641323546	3	FACETS	0.845	0.628	1	0.422	0.314	0.548	INDETERMINATE	1	FALSE	1	0.520349006166523	3		210	86	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245949	5245949	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052439-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	10	716	0	ENST00000357368.4:c.826G>A	p.Val276Met	p.V276M	ENST00000357368	NM_002850.3	276	Gtg/Atg	10/38	0.139492727912454	0	FACETS	0.097	0.065	0.136			1	INDETERMINATE	1	FALSE	0	0.520349006166523	0		716	191	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916781	48916781	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052439-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	16	329	0	ENST00000267163.4:c.311T>A	p.Phe104Tyr	p.F104Y	ENST00000267163	NM_000321.2	104	tTt/tAt	3/27	1	2	FACETS	0.831	0.628	1	0.831	0.628	1	CLONAL	1	FALSE	1	0.520349006166523	2		329	74	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100678	67100678	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052439-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	52	437	0	ENST00000412916.2:c.376G>T	p.Glu126Ter	p.E126*	ENST00000412916		126	Gag/Tag	4/6	0.520349006166523	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	0	0.520349006166523	1		437	124	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879621	151879621	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052439-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	45	521	0	ENST00000262189.6:c.5324del	p.Gln1775ArgfsTer2	p.Q1775Rfs*2	ENST00000262189	NM_170606.2	1775	cAg/cg	36/59	0.170710576910691	3	FACETS	0.795	0.684	0.913	0.795	0.684	0.913	INDETERMINATE	2	FALSE	1	0.520349006166523	3		521	137	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779127	3779127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769818976	NA	P-0052439-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	10	584	0	ENST00000262367.5:c.5921G>A	p.Arg1974Gln	p.R1974Q	ENST00000262367	NM_004380.2	1974	cGg/cAg	31/31	1	2	FACETS	0.226	0.153	0.318	0.226	0.153	0.318	SUBCLONAL	1	FALSE	1	0.520349006166523	2		584	170	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0052717-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	373	516	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.789688299229042	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.789688299229042	3		516	415	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339680	116339680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052717-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	390	429	2	ENST00000397752.3:c.542G>A	p.Gly181Glu	p.G181E	ENST00000397752	NM_000245.2	181	gGa/gAa	2/21	0.789688299229042	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.789688299229042	4		431	818	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619946	21619946	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052717-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	199	445	1	ENST00000382592.4:c.220C>T	p.Gln74Ter	p.Q74*	ENST00000382592	NM_014572.2	74	Cag/Tag	2/8	0.789688299229042	3	FACETS	1	0.958	1	0.521	0.484	0.558	CLONAL	1	TRUE	1	0.789688299229042	3		446	675	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222973	5222973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052717-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	344	462	1	ENST00000357368.4:c.2830G>C	p.Gly944Arg	p.G944R	ENST00000357368	NM_002850.3	944	Ggg/Cgg	18/38	0.69645519599344	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.789688299229042	4		463	768	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162097	22162098	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052717-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	334	395	2	ENST00000215832.6:c.157dup	p.Ile53AsnfsTer8	p.I53Nfs*8	ENST00000215832	NM_002745.4	53	atc/aAtc	2/9	0.789688299229042	3	FACETS	0.993	0.95	1	0.993	0.95	1	CLONAL	2	TRUE	1	0.789688299229042	3		397	594	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244265	153244265	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052717-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	342	398	1	ENST00000281708.4:c.1892A>T	p.Gln631Leu	p.Q631L	ENST00000281708	NM_033632.3	631	cAg/cTg	12/12	0.789688299229042	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.789688299229042	3		399	554	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293694	1293694	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052717-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	424	514	0	ENST00000310581.5:c.1307C>G	p.Ala436Gly	p.A436G	ENST00000310581	NM_198253.2	436	gCg/gGg	2/16	0.742936956800593	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.789688299229042	4		514	948	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755741	57755741	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052717-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	162	428	1	ENST00000274289.3:c.46A>G	p.Lys16Glu	p.K16E	ENST00000274289	NM_006622.3	16	Aaa/Gaa	1/14	0.789688299229042	3	FACETS	0.965	0.89	1	0.483	0.445	0.522	CLONAL	1	TRUE	1	0.789688299229042	3		429	593	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334827	81334827	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052717-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	256	347	1	ENST00000222390.5:c.1889G>T	p.Arg630Leu	p.R630L	ENST00000222390	NM_000601.4	630	cGa/cTa	17/18	0.789688299229042	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.789688299229042	4		348	565	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482242	87482242	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052717-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	184	455	1	ENST00000277120.3:c.1529C>A	p.Ser510Ter	p.S510*	ENST00000277120		510	tCg/tAg	14/19	0.789688299229042	3	FACETS	0.948	0.878	1	0.474	0.439	0.51	CLONAL	1	TRUE	1	0.789688299229042	3		456	686	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400173	139400173	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052717-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	223	493	1	ENST00000277541.6:c.4175T>A	p.Leu1392Gln	p.L1392Q	ENST00000277541	NM_017617.3	1392	cTg/cAg	25/34	0.721499654951825	3	FACETS	1	0.973	1	0.539	0.503	0.575	CLONAL	1	TRUE	1	0.789688299229042	3		494	731	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913517	NA	P-0053496-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	274	443	0	ENST00000288135.5:c.1676T>G	p.Val559Gly	p.V559G	ENST00000288135	NM_000222.2	559	gTt/gGt	11/21	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.840273348278331	2		443	575	SUCCESS
CBL	867	MSKCC	GRCh37	11	119158618	119158618	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053496-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	100	327	0	ENST00000264033.4:c.1999del	p.Ser667ProfsTer35	p.S667Pfs*35	ENST00000264033	NM_005188.3	666	ccT/cc	12/16	1	2	FACETS	0.409	0.366	0.455	0.409	0.366	0.455	SUBCLONAL	1	TRUE	1	0.840273348278331	2		327	582	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0054779-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	18	372	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.15	0.112	0.195	0.15	0.112	0.195	SUBCLONAL	1	TRUE	1	0.43	2		372	559	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156149	119156149	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054779-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	23	0	0	ENST00000264033.4:c.1814C>G	p.Ser605Cys	p.S605C	ENST00000264033	NM_005188.3	605	tCc/tGc	11/16	1	2	FACETS	0.12	0.093	0.152	0.12	0.093	0.152	SUBCLONAL	1	TRUE	1	0.43	2		0	890	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245811	46245811	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0054779-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	17	0	0	ENST00000334344.6:c.3905C>G	p.Ser1302Ter	p.S1302*	ENST00000334344	NM_152641.2	1302	tCa/tGa	15/21	1	2	FACETS	0.109	0.08	0.143	0.109	0.08	0.143	SUBCLONAL	1	TRUE	1	0.43	2		0	728	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50816365	50816365	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0054779-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	11	0	0	ENST00000398568.2:c.1805C>G	p.Ser602Ter	p.S602*	ENST00000398568	NM_001042412.1	602	tCa/tGa	10/18	1	2	FACETS	0.086	0.059	0.12	0.086	0.059	0.12	SUBCLONAL	1	TRUE	1	0.43	2		0	594	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615780	1615780	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054779-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	16	0	0	ENST00000344749.5:c.1491C>G	p.Ile497Met	p.I497M	ENST00000344749	NM_001136139.2	497	atC/atG	17/19	1	2	FACETS	0.103	0.075	0.136	0.103	0.075	0.136	SUBCLONAL	1	TRUE	1	0.43	2		0	725	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652072	36652072	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054779-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	9	0	0	ENST00000244741.5:c.194G>T	p.Trp65Leu	p.W65L	ENST00000244741	NM_000389.4	65	tGg/tTg	2/3	1	2	FACETS	0.052	0.034	0.076	0.052	0.034	0.076	SUBCLONAL	1	TRUE	1	0.43	2		0	799	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396239	139396239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054779-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	14	0	0	ENST00000277541.6:c.5599G>A	p.Val1867Ile	p.V1867I	ENST00000277541	NM_017617.3	1867	Gtt/Att	30/34	1	2	FACETS	0.088	0.063	0.119	0.088	0.063	0.119	SUBCLONAL	1	TRUE	1	0.43	2		0	736	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682399	52682400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054926-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	126	295	0	ENST00000394830.3:c.773dup	p.Asn258LysfsTer6	p.N258Kfs*6	ENST00000394830	NM_018313.4	258	aat/aaAt	8/30	0.593811441907728	1	FACETS	0.947	0.871	1	0.947	0.871	1	CLONAL	1	TRUE	0	0.593811441907728	1		295	315	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721028	61721028	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0054926-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	166	369	0	ENST00000401558.2:c.1245+1G>C		p.X415_splice	ENST00000401558	NM_003400.3	415			1	2	FACETS	0.964	0.89	1	0.964	0.89	1	CLONAL	1	TRUE	1	0.593811441907728	2		369	580	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443623	52443667	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCTGCGATGAGGAAAGGAAAGCAGTAGGGAAGGACAGCCCCTGA	ACCTGCGATGAGGAAAGGAAAGCAGTAGGGAAGGACAGCCCCTGA	-	novel	NA	P-0054926-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	213	444	0	ENST00000460680.1:c.68-43_69del		p.X23_splice	ENST00000460680	NM_004656.3	23		3/17	0.593811441907728	1	FACETS	0.963	0.903	1	0.963	0.903	1	CLONAL	1	TRUE	0	0.593811441907728	1		444	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs786203436	NA	P-0055109-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	66	924	0	ENST00000269305.4:c.487T>G	p.Tyr163Asp	p.Y163D	ENST00000269305	NM_001126112.2	163	Tac/Gac	5/11	0.199483856613683	2	FACETS	1	0.926	1	0.547	0.476	0.624	CLONAL	1	TRUE	0	0.245125701666196	2		924	492	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324615	31324615	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1050529	NA	P-0055109-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	16	333	2	ENST00000412585.2:c.193G>A	p.Ala65Thr	p.A65T	ENST00000412585	NM_005514.6	65	Gcg/Acg	2/8	0.229068305552063	3	FACETS	0.691	0.512	0.904	0.346	0.256	0.452	SUBCLONAL	1	TRUE	1	0.245125701666196	3		335	212	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0055109-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	152	344	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.245125701666196	4	FACETS	0.898	0.829	0.968	1	0.981	1	CLONAL	4	TRUE	1	0.245125701666196	4		344	430	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0055255-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	83	371	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		371	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0055502-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	82	631	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.313141810760453	3	FACETS	0.925	0.816	1	0.462	0.408	0.521	CLONAL	1	TRUE	1	0.313141810760453	3		631	655	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0055502-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	207	377	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.289085242905909	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.313141810760453	3		377	646	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003238	42003238	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055502-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	103	551	0	ENST00000219905.7:c.2777del	p.Lys926SerfsTer7	p.K926Sfs*7	ENST00000219905	NM_001164273.1	925	ccA/cc	8/24	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.313141810760453	2		551	615	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958178	54958178	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055502-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	75	431	0	ENST00000312783.6:c.429G>C	p.Lys143Asn	p.K143N	ENST00000312783	NM_198436.1	143	aaG/aaC	6/10	0.278993920614653	4	FACETS	1	0.882	1	0.503	0.441	0.57	CLONAL	1	TRUE	2	0.313141810760453	4		431	625	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069293	30069293	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055502-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	107	545	0	ENST00000338641.4:c.1158A>C	p.Glu386Asp	p.E386D	ENST00000338641	NM_000268.3	386	gaA/gaC	12/16	0.312714616499447	2	FACETS	1	0.968	1	0.592	0.532	0.655	CLONAL	1	TRUE	0	0.313141810760453	2		545	577	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046749	180046749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121909657	NA	P-0055502-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	103	705	1	ENST00000261937.6:c.2563G>A	p.Ala855Thr	p.A855T	ENST00000261937	NM_182925.4	855	Gcc/Acc	18/30	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.313141810760453	2		706	644	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288367	33288387	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCCTACGTGGGAAGACATAAA	GCCTACGTGGGAAGACATAAA	-	novel	NA	P-0055502-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	70	581	0	ENST00000374542.5:c.1040-19_1041del		p.X347_splice	ENST00000374542	NM_001141970.1	347		4/8	0.312714616499447	2	FACETS	0.668	0.582	0.761	0.334	0.291	0.381	SUBCLONAL	1	TRUE	0	0.313141810760453	2		581	669	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249092	55249092	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055502-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	105	568	0	ENST00000275493.2:c.2390G>C	p.Cys797Ser	p.C797S	ENST00000275493	NM_005228.3	797	tGc/tCc	20/28	0.289085242905909	3	FACETS	1	0.961	1	0.575	0.515	0.637	CLONAL	1	TRUE	1	0.313141810760453	3		568	675	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259439	55259439	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs397517126	NA	P-0055502-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	178	429	0	ENST00000275493.2:c.2497T>G	p.Leu833Val	p.L833V	ENST00000275493	NM_005228.3	833	Ttg/Gtg	21/28	0.289085242905909	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.313141810760453	3		429	547	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0056314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	205	287	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.500269498764523	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.500269498764523	3		287	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0056314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	327	523	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.500269498764523	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.500269498764523	2		523	642	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150923376	150923376	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056399-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	81	386	0	ENST00000271640.5:c.2023C>A	p.Pro675Thr	p.P675T	ENST00000271640	NM_001145415.1	675	Cct/Act	13/22	0.333203304576947	3	FACETS	0.768	0.678	0.865	0.384	0.339	0.433	SUBCLONAL	1	TRUE	1	0.476327623186568	3		386	548	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846125	68846126	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTGACACCAACGATAATC	novel	NA	P-0056399-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	178	422	0	ENST00000261769.5:c.1099_1116dup	p.Asp367_Pro372dup	p.D367_P372dup	ENST00000261769	NM_004360.3	367	act/aCTGACACCAACGATAATCct	8/16	0.476327623186568	3	FACETS	1	0.989	1	0.715	0.662	0.77	CLONAL	1	TRUE	1	0.476327623186568	3		422	647	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0056399-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	226	384	0	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	0.380535870453579	3	FACETS	1	0.985	1	0.759	0.714	0.804	CLONAL	2	TRUE	0	0.476327623186568	3		384	516	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279414	38279414	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056399-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	176	390	0	ENST00000425967.3:c.1075T>G	p.Leu359Val	p.L359V	ENST00000425967	NM_001174067.1	359	Tta/Gta	9/19	0.376265570588729	3	FACETS	0.808	0.749	0.869	0.808	0.749	0.869	CLONAL	2	TRUE	1	0.476327623186568	3		390	566	SUCCESS
APC	324	MSKCC	GRCh37	5	112155042	112155042	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs863225310	NA	P-0056873-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	175	488	0	ENST00000257430.4:c.1312+1G>A		p.X438_splice	ENST00000257430	NM_000038.5	438			0.530473545035329	2	FACETS	0.924	0.866	0.981	0.924	0.866	0.981	CLONAL	2	TRUE	0	0.569014405077998	2		488	333	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214708	36214708	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056873-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	107	615	0	ENST00000222270.7:c.3134C>G	p.Pro1045Arg	p.P1045R	ENST00000222270	NM_014727.1	1045	cCa/cGa	8/37	0.114696595885658	0	FACETS	0.405	0.366	0.446			1	INDETERMINATE	1	TRUE	0	0.569014405077998	0		615	400	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332890	152332890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056873-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	95	466	0	ENST00000206249.3:c.1196C>T	p.Pro399Leu	p.P399L	ENST00000206249	NM_000125.3	399	cCa/cTa	5/8	1	2	FACETS	0.938	0.843	1	0.938	0.843	1	CLONAL	1	TRUE	1	0.569014405077998	2		466	356	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115892	8115893	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0057256-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	57	470	0	ENST00000346208.3:c.1240dup	p.His414ProfsTer93	p.H414Pfs*93	ENST00000346208		413	agc/agCc	6/6	1	2	FACETS	0.724	0.623	0.834	0.724	0.623	0.834	SUBCLONAL	1	TRUE	1	0.3802055116275	2		470	414	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539759	187539759	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057256-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	67	407	0	ENST00000441802.2:c.7981C>A	p.Leu2661Ile	p.L2661I	ENST00000441802	NM_005245.3	2661	Ctc/Atc	10/27	0.3802055116275	4	FACETS	0.918	0.799	1	0.306	0.266	0.349	CLONAL	1	TRUE	1	0.3802055116275	4		407	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0057272-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	119	640	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.204772225570874	3	FACETS	1	0.939	1			1	CLONAL	2	TRUE	NA	0.204772225570874	3		640	610	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057272-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	28	475	0	ENST00000267101.3:c.850G>C	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Cga	7/28	1	2	FACETS	0.566	0.452	0.697	0.566	0.452	0.697	SUBCLONAL	1	TRUE	1	0.204772225570874	2		475	483	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864663	68864663	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773560075	NA	P-0057272-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	30	377	0	ENST00000288368.4:c.34G>A	p.Glu12Lys	p.E12K	ENST00000288368	NM_024870.2	12	Gag/Aag	1/40	0.180396475850943	3	FACETS	0.828	0.667	1	0.276	0.222	0.337	CLONAL	1	TRUE	0	0.204772225570874	3		377	390	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953759	48953759	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057272-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	63	204	0	ENST00000267163.4:c.1363del	p.Arg455GlufsTer2	p.R455Efs*2	ENST00000267163	NM_000321.2	454	taC/ta	14/27	0.204772225570874	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.204772225570874	2		204	262	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628317	90628317	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057272-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	69	650	0	ENST00000330062.3:c.1094G>T	p.Ser365Ile	p.S365I	ENST00000330062	NM_002168.2	365	aGc/aTc	9/11	0.19024900351858	4	FACETS	1	0.927	1	0.274	0.238	0.313	CLONAL	1	TRUE	0	0.204772225570874	4		650	740	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591113	67591133	+	inframe_deletion	In_Frame_Del	DEL	ACCTTATCCAGCTGAGAAAGA	ACCTTATCCAGCTGAGAAAGA	-	novel	NA	P-0057272-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	14	453	0	ENST00000274335.5:c.1706_1726del	p.Asp569_Thr576delinsAla	p.D569_T576delinsA	ENST00000274335		569	gACCTTATCCAGCTGAGAAAGAcg/gcg	12/15	0.198729010363169	3	FACETS	0.303	0.218	0.407	0.151	0.109	0.204	SUBCLONAL	1	TRUE	1	0.204772225570874	3		453	498	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202447	123202447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057272-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	14	307	0	ENST00000218089.9:c.2299G>A	p.Val767Ile	p.V767I	ENST00000218089	NM_001042749.1	767	Gta/Ata	24/35	1	2	FACETS	0.538	0.389	0.719	0.538	0.389	0.719	SUBCLONAL	1	TRUE	1	0.204772225570874	2		307	254	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397142	397142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs999945656	NA	P-0057291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	41	676	1	ENST00000380956.4:c.527G>A	p.Arg176Gln	p.R176Q	ENST00000380956	NM_001195286.1	176	cGa/cAa	5/9	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		677	578	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057382-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	95	934	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.400638951261394	2	FACETS	1	0.964	1	0.585	0.525	0.649	CLONAL	1	TRUE	0	0.400638951261394	2		934	405	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111504	8111505	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057382-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	72	651	0	ENST00000346208.3:c.992dup	p.Asn331LysfsTer21	p.N331Kfs*21	ENST00000346208		330	-/A	5/6	0.400638951261394	3	FACETS	0.999	0.876	1	0.499	0.438	0.565	CLONAL	1	TRUE	1	0.400638951261394	3		651	432	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609021	43609021	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878855059	NA	P-0057382-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	47	816	0	ENST00000355710.3:c.1777G>A	p.Gly593Arg	p.G593R	ENST00000355710	NM_020975.4	593	Gga/Aga	10/20	0.400638951261394	3	FACETS	0.684	0.578	0.8	0.342	0.289	0.4	SUBCLONAL	1	TRUE	1	0.400638951261394	3		816	412	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732517	74732517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057382-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	544	575	0	ENST00000359995.5:c.392G>A	p.Arg131Gln	p.R131Q	ENST00000359995	NM_001195427.1	131	cGg/cAg	2/3	0.400638951261394	16	FACETS	1	0.969	1			1	CLONAL	10	TRUE	NA	0.400638951261394	16		575	1028	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	91	542	7	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.356116584410956	2		549	481	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	46	343	4	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.356116584410956	2		347	232	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	60	651	1	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	0.862	0.745	0.987	0.862	0.745	0.987	CLONAL	1	TRUE	1	0.356116584410956	2		652	391	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350469	15350469	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	75	901	2	ENST00000263377.2:c.3445+1G>A		p.X1149_splice	ENST00000263377	NM_058243.2	1149			1	2	FACETS	0.934	0.821	1	0.934	0.821	1	CLONAL	1	TRUE	1	0.356116584410956	2		903	451	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	163	868	10	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.976	0.904	1	1	0.992	1	CLONAL	2	TRUE	1	0.356116584410956	2		878	469	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	124	1026	4	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.356116584410956	2		1030	563	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992721	68992721	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs764112302	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	47	628	1	ENST00000288368.4:c.1693del	p.Ser565ArgfsTer10	p.S565Rfs*10	ENST00000288368	NM_024870.2	562	cgT/cg	16/40	0.356116584410956	3	FACETS	0.682	0.576	0.799	0.227	0.192	0.267	SUBCLONAL	1	TRUE	0	0.356116584410956	3		629	456	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	82	684	2	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.356116584410956	2		686	387	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562995	95562997	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	rs544960260	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	45	494	0	ENST00000393063.1:c.4260_4262del	p.Glu1420del	p.E1420del	ENST00000393063	NM_030621.3	1420	gaGGAt/gat	24/28	1	2	FACETS	0.878	0.742	1	0.878	0.742	1	CLONAL	1	TRUE	1	0.356116584410956	2		494	288	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	109	884	9	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.356116584410956	2		893	566	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	38	523	3	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	0.356116584410956	4	FACETS	0.793	0.657	0.944	0.264	0.219	0.315	CLONAL	1	TRUE	1	0.356116584410956	4		526	365	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523145	176523145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746619070	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	89	885	2	ENST00000292408.4:c.1909G>A	p.Val637Ile	p.V637I	ENST00000292408	NM_213647.1	637	Gtc/Atc	14/18	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.356116584410956	2		887	479	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646085	215646085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	41	654	5	ENST00000260947.4:c.513del	p.Asp172MetfsTer40	p.D172Mfs*40	ENST00000260947	NM_000465.2	171	aaA/aa	4/11	1	2	FACETS	0.643	0.537	0.761	0.643	0.537	0.761	SUBCLONAL	1	TRUE	1	0.356116584410956	2		659	358	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	54	407	5	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.356116584410956	2		412	257	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782144	9782144	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	79	849	1	ENST00000377346.4:c.2167G>A	p.Ala723Thr	p.A723T	ENST00000377346	NM_005026.3	723	Gcc/Acc	17/24	1	2	FACETS	0.997	0.881	1	0.997	0.881	1	CLONAL	1	TRUE	1	0.356116584410956	2		850	445	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	66	1054	3	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	0.594	0.515	0.679	0.594	0.515	0.679	SUBCLONAL	1	TRUE	1	0.356116584410956	2		1057	624	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851848	134851848	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	73	839	1	ENST00000398015.3:c.1259del	p.Pro420HisfsTer28	p.P420Hfs*28	ENST00000398015	NM_004441.4	418	ttC/tt	5/16	0.347314993299674	3	FACETS	0.962	0.843	1	0.481	0.421	0.545	CLONAL	1	TRUE	1	0.356116584410956	3		840	502	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129749	108129749	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs780619951	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	49	370	0	ENST00000278616.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000278616	NM_000051.3	805	Cga/Tga	16/63	1	2	FACETS	0.908	0.774	1	0.908	0.774	1	CLONAL	1	TRUE	1	0.356116584410956	2		370	303	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149683	202149683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762734568	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	89	656	0	ENST00000358485.4:c.1124C>T	p.Ser375Phe	p.S375F	ENST00000358485	NM_001080125.1	375	tCc/tTc	8/9	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.356116584410956	2		656	376	SUCCESS
ATM	472	MSKCC	GRCh37	11	108137926	108137926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199875915	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	34	373	0	ENST00000278616.4:c.2495G>A	p.Arg832His	p.R832H	ENST00000278616	NM_000051.3	832	cGt/cAt	17/63	1	2	FACETS	0.868	0.715	1	0.868	0.715	1	CLONAL	1	TRUE	1	0.356116584410956	2		373	220	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971051	21971051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767642535	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	59	151	0	ENST00000304494.5:c.307C>T	p.Arg103Trp	p.R103W	ENST00000304494	NM_000077.4	103	Cgg/Tgg	2/3	0.347314993299674	3	FACETS	0.943	0.834	1	1	0.973	1	CLONAL	3	TRUE	1	0.356116584410956	3		151	138	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433482	138433482	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	64	473	0	ENST00000289153.2:c.1130del	p.Asn377MetfsTer35	p.N377Mfs*35	ENST00000289153	NM_006219.2	377	aAt/at	7/22	0.356116584410956	3	FACETS	1	0.899	1			1	CLONAL	1	TRUE	NA	0.356116584410956	3		473	407	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600425	10600425	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	121	1011	1	ENST00000171111.5:c.1430del	p.Gly477AlafsTer23	p.G477Afs*23	ENST00000171111	NM_203500.1	477	gGc/gc	4/6	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.356116584410956	2		1012	575	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190818	106190818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	62	578	0	ENST00000380013.4:c.4096C>T	p.Arg1366Cys	p.R1366C	ENST00000380013	NM_001127208.2	1366	Cgt/Tgt	9/11	1	2	FACETS	0.998	0.867	1	0.998	0.867	1	CLONAL	1	TRUE	1	0.356116584410956	2		578	349	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226860	2226860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	10	101	1	ENST00000398665.3:c.4340C>T	p.Ala1447Val	p.A1447V	ENST00000398665	NM_032482.2	1447	gCg/gTg	27/28	1	2	FACETS	0.802	0.552	1	0.802	0.552	1	CLONAL	1	TRUE	1	0.356116584410956	2		102	70	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468398	89468398	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1467832547	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	14	276	2	ENST00000336596.2:c.1938del	p.Glu647ArgfsTer9	p.E647Rfs*9	ENST00000336596	NM_005233.5	644	tcA/tc	11/17	0.356116584410956	2	FACETS	0.43	0.311	0.572	0.215	0.155	0.286	SUBCLONAL	1	TRUE	0	0.356116584410956	2		278	183	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213358	36213359	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	96	1031	2	ENST00000222270.7:c.2561_2562del	p.Glu854AlafsTer34	p.E854Afs*34	ENST00000222270	NM_014727.1	852	aAG/a	4/37	1	2	FACETS	0.836	0.746	0.932	0.836	0.746	0.932	CLONAL	1	TRUE	1	0.356116584410956	2		1033	645	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	84	737	6	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.985	0.873	1	0.985	0.873	1	CLONAL	1	TRUE	1	0.356116584410956	2		743	479	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508563	106508563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757016725	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	26	431	1	ENST00000359195.3:c.557C>T	p.Ala186Val	p.A186V	ENST00000359195	NM_002649.2	186	gCg/gTg	2/11	0.356116584410956	3	FACETS	0.608	0.482	0.751	0.304	0.241	0.376	SUBCLONAL	1	TRUE	1	0.356116584410956	3		432	283	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793363	242793363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	73	1131	1	ENST00000334409.5:c.714del	p.Val239CysfsTer39	p.V239Cfs*39	ENST00000334409	NM_005018.2	238	ccC/cc	5/5	1	2	FACETS	0.682	0.597	0.774	0.682	0.597	0.774	SUBCLONAL	1	TRUE	1	0.356116584410956	2		1132	601	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753149	42753151	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs199960550	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	91	812	11	ENST00000222329.4:c.1113_1115del	p.Ser373del	p.S373del	ENST00000222329	NM_006494.2	371	tcTTCc/tcc	4/4	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.356116584410956	2		823	485	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817720	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	19	520	0	ENST00000262367.5:c.3250dup	p.Ile1084AsnfsTer3	p.I1084Nfs*3	ENST00000262367	NM_004380.2	1084	atc/aAtc		1	2	FACETS	0.331	0.251	0.426	0.331	0.251	0.426	SUBCLONAL	1	TRUE	1	0.356116584410956	2		520	322	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753002	42753002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	87	793	0	ENST00000222329.4:c.1262del	p.Pro421ArgfsTer18	p.P421Rfs*18	ENST00000222329	NM_006494.2	421	cCg/cg	4/4	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.356116584410956	2		793	407	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405778	70405778	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	63	486	0	ENST00000373644.4:c.3297del	p.Val1100LeufsTer40	p.V1100Lfs*40	ENST00000373644	NM_030625.2	1098	Aaa/aa	4/12	0.356116584410956	2	FACETS	1	0.955	1	0.612	0.534	0.695	CLONAL	1	TRUE	0	0.356116584410956	2		486	289	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647921	3647921	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146021821	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	45	1161	0	ENST00000294008.3:c.1243G>A	p.Glu415Lys	p.E415K	ENST00000294008	NM_032444.2	415	Gag/Aag	6/15	1	2	FACETS	0.421	0.353	0.496	0.421	0.353	0.496	SUBCLONAL	1	TRUE	1	0.356116584410956	2		1161	601	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241993	105241993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060503071	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	122	849	1	ENST00000349310.3:c.431G>A	p.Arg144His	p.R144H	ENST00000349310	NM_001014432.1	144	cGc/cAc	6/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.356116584410956	2		850	538	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518687	103518687	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs570252494	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	50	383	2	ENST00000355739.4:c.2275C>T	p.Arg759Trp	p.R759W	ENST00000355739	NM_000123.3	759	Cgg/Tgg	10/15	0.175510406801611	4	FACETS	0.787	0.674	0.908	0.787	0.674	0.908	INDETERMINATE	2	TRUE	2	0.356116584410956	4		385	242	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101923	11101923	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502063	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	105	945	1	ENST00000358026.2:c.1343G>A	p.Arg448His	p.R448H	ENST00000358026	NM_001128849.1	448	cGc/cAc	8/36	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.356116584410956	2		946	535	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656682	3656682	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201769293	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	66	1039	0	ENST00000294008.3:c.553G>A	p.Asp185Asn	p.D185N	ENST00000294008	NM_032444.2	185	Gac/Aac	3/15	1	2	FACETS	0.649	0.564	0.742	0.649	0.564	0.742	SUBCLONAL	1	TRUE	1	0.356116584410956	2		1039	571	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858047	152858047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1432027234	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	53	335	2	ENST00000406277.2:c.568G>A	p.Ala190Thr	p.A190T	ENST00000406277	NM_152274.4	190	Gcc/Acc	6/7	1	1	FACETS	0.899	0.787	1	1	0.977	1	CLONAL	2	TRUE	0	0.356116584410956	1		337	136	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003780	45003781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	26	639	0	ENST00000558401.1:c.43_44dup	p.Ser16PhefsTer29	p.S16Ffs*29	ENST00000558401	NM_004048.2	12	-/CT	1/4	1	2	FACETS	0.351	0.277	0.435	0.351	0.277	0.435	SUBCLONAL	1	TRUE	1	0.356116584410956	2		639	416	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991400	72991400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201144589	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	108	954	1	ENST00000268489.5:c.2645C>T	p.Ser882Leu	p.S882L	ENST00000268489	NM_006885.3	882	tCg/tTg	2/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.356116584410956	2		955	540	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259254	16259254	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	18	477	0	ENST00000375759.3:c.6519G>T	p.Gln2173His	p.Q2173H	ENST00000375759	NM_015001.2	2173	caG/caT	11/15	1	2	FACETS	0.428	0.323	0.552	0.428	0.323	0.552	SUBCLONAL	1	TRUE	1	0.356116584410956	2		477	236	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260260	16260260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761667751	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	61	618	0	ENST00000375759.3:c.7525C>T	p.Arg2509Trp	p.R2509W	ENST00000375759	NM_015001.2	2509	Cgg/Tgg	11/15	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.356116584410956	2		618	309	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101167	27101167	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	90	843	0	ENST00000324856.7:c.4452del	p.Ile1485TyrfsTer20	p.I1485Yfs*20	ENST00000324856	NM_006015.4	1483	ggC/gg	18/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.356116584410956	2		843	454	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805226	43805226	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	84	811	0	ENST00000372470.3:c.676T>C	p.Ser226Pro	p.S226P	ENST00000372470	NM_005373.2	226	Tcc/Ccc	4/12	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.356116584410956	2		811	435	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282489	115282491	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	61	438	0	ENST00000438362.2:c.159_161del	p.Leu54del	p.L54del	ENST00000438362	NM_001242891.1	53	ctTCTc/ctc	3/20	1	2	FACETS	0.941	0.816	1	0.941	0.816	1	CLONAL	1	TRUE	1	0.356116584410956	2		438	364	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135607	64135607	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	27	944	1	ENST00000334205.4:c.1075T>C	p.Tyr359His	p.Y359H	ENST00000334205	NM_003942.2	359	Tac/Cac	10/17	1	2	FACETS	0.296	0.235	0.367	0.296	0.235	0.367	SUBCLONAL	1	TRUE	1	0.356116584410956	2		945	512	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196664	67196664	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	78	692	0	ENST00000312629.5:c.193C>A	p.His65Asn	p.H65N	ENST00000312629	NM_003952.2	65	Cac/Aac	3/15	1	2	FACETS	0.959	0.845	1	0.959	0.845	1	CLONAL	1	TRUE	1	0.356116584410956	2		692	457	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421806	49421807	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	120	1055	0	ENST00000301067.7:c.14500dup	p.Glu4834GlyfsTer3	p.E4834Gfs*3	ENST00000301067	NM_003482.3	4834	gaa/gGaa	46/54	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.356116584410956	2		1055	650	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986773	36986773	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	10	69	0	ENST00000354822.5:c.916G>A	p.Ala306Thr	p.A306T	ENST00000354822	NM_001079668.2	306	Gcg/Acg	3/3	1	2	FACETS	0.864	0.596	1	0.864	0.596	1	CLONAL	1	TRUE	1	0.356116584410956	2		69	65	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68878206	68878206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746531915	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	54	396	0	ENST00000487270.1:c.919C>T	p.Arg307Trp	p.R307W	ENST00000487270	NM_133509.3	307	Cgg/Tgg	9/11	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.356116584410956	2		396	296	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007772	45007776	+	frameshift_variant	Frame_Shift_Del	DEL	CTTGT	CTTGT	-	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	18	446	0	ENST00000558401.1:c.222_226del	p.Leu74PhefsTer14	p.L74Ffs*14	ENST00000558401	NM_004048.2	73	gaCTTGTct/gact	2/4	1	2	FACETS	0.338	0.254	0.437	0.338	0.254	0.437	SUBCLONAL	1	TRUE	1	0.356116584410956	2		446	299	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679822	88679822	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	73	558	0	ENST00000360948.2:c.641T>C	p.Val214Ala	p.V214A	ENST00000360948	NM_001012338.2	214	gTg/gCg	7/19	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.356116584410956	2		558	336	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358440	91358440	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	91	661	0	ENST00000355112.3:c.4185A>T	p.Lys1395Asn	p.K1395N	ENST00000355112	NM_000057.2	1395	aaA/aaT	22/22	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.356116584410956	2		661	495	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993644	72993644	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	94	823	1	ENST00000268489.5:c.401T>C	p.Val134Ala	p.V134A	ENST00000268489	NM_006885.3	134	gTc/gCc	2/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.356116584410956	2		824	443	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89833614	89833615	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs763378933	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	38	336	0	ENST00000389301.3:c.2535_2536del	p.Cys846GlnfsTer20	p.C846Qfs*20	ENST00000389301	NM_000135.2	845	ctCTgc/ctgc	27/43	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.356116584410956	2		336	196	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41197784	41197784	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs41293465	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	80	751	0	ENST00000357654.3:c.5503C>T	p.Arg1835Ter	p.R1835*	ENST00000357654	NM_007294.3	1835	Cga/Tga	23/23	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.356116584410956	2		751	447	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530191	63530191	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	39	508	0	ENST00000307078.5:c.2244A>C	p.Lys748Asn	p.K748N	ENST00000307078	NM_004655.3	748	aaA/aaC	10/11	1	2	FACETS	0.733	0.61	0.868	0.733	0.61	0.868	SUBCLONAL	1	TRUE	1	0.356116584410956	2		508	299	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56411594	56411594	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	29	338	0	ENST00000348428.3:c.1778A>C	p.Lys593Thr	p.K593T	ENST00000348428	NM_006785.3	593	aAg/aCg	15/17	1	2	FACETS	0.721	0.582	0.877	0.721	0.582	0.877	SUBCLONAL	1	TRUE	1	0.356116584410956	2		338	226	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213599	2213601	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	85	1007	0	ENST00000398665.3:c.1624_1626del	p.Glu542del	p.E542del	ENST00000398665	NM_032482.2	540	aAGGag/aag	17/28	1	2	FACETS	0.866	0.767	0.972	0.866	0.767	0.972	CLONAL	1	TRUE	1	0.356116584410956	2		1007	551	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169011	11169011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555795063	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	25	887	2	ENST00000358026.2:c.4601G>A	p.Arg1534His	p.R1534H	ENST00000358026	NM_001128849.1	1534	cGc/cAc	32/36	1	2	FACETS	0.285	0.224	0.356	0.285	0.224	0.356	SUBCLONAL	1	TRUE	1	0.356116584410956	2		889	492	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220866	36220866	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	21	226	0	ENST00000222270.7:c.4918-2A>G		p.X1640_splice	ENST00000222270	NM_014727.1	1640			1	2	FACETS	0.746	0.58	0.937	0.746	0.58	0.937	CLONAL	1	TRUE	1	0.356116584410956	2		226	158	SUCCESS
ALK	238	MSKCC	GRCh37	2	29541178	29541178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	19	566	0	ENST00000389048.3:c.1639C>T	p.Pro547Ser	p.P547S	ENST00000389048	NM_004304.4	547	Cca/Tca	8/29	1	2	FACETS	0.306	0.231	0.393	0.306	0.231	0.393	SUBCLONAL	1	TRUE	1	0.356116584410956	2		566	349	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269008	142269008	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	16	469	0	ENST00000350721.4:c.2942T>C	p.Val981Ala	p.V981A	ENST00000350721	NM_001184.3	981	gTt/gCt	14/47	0.356116584410956	3	FACETS	0.338	0.249	0.445	0.169	0.124	0.223	SUBCLONAL	1	TRUE	1	0.356116584410956	3		469	313	SUCCESS
ATR	545	MSKCC	GRCh37	3	142297488	142297488	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	62	649	0	ENST00000350721.4:c.59G>C	p.Ser20Thr	p.S20T	ENST00000350721	NM_001184.3	20	aGt/aCt	1/47	0.356116584410956	3	FACETS	0.819	0.708	0.938	0.409	0.354	0.469	CLONAL	1	TRUE	1	0.356116584410956	3		649	501	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189855	66189855	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	42	520	0	ENST00000273854.3:c.3091G>C	p.Val1031Leu	p.V1031L	ENST00000273854	NM_004439.5	1031	Gta/Cta	18/18	1	2	FACETS	0.808	0.678	0.95	0.808	0.678	0.95	CLONAL	1	TRUE	1	0.356116584410956	2		520	292	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956619	93956619	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	42	456	0	ENST00000369303.4:c.2617T>G	p.Trp873Gly	p.W873G	ENST00000369303	NM_004440.3	873	Tgg/Ggg	15/17	1	2	FACETS	0.831	0.697	0.977	0.831	0.697	0.977	CLONAL	1	TRUE	1	0.356116584410956	2		456	284	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339207	116339208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	74	380	0	ENST00000397752.3:c.73dup	p.Glu25GlyfsTer3	p.E25Gfs*3	ENST00000397752	NM_000245.2	23	-/G	2/21	0.356116584410956	3	FACETS	1	0.916	1	1	0.916	1	CLONAL	2	TRUE	1	0.356116584410956	3		380	236	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309155	137309155	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	106	972	0	ENST00000481739.1:c.765del	p.Leu256Ter	p.L256*	ENST00000481739	NM_002957.4	254	atG/at	5/10	0.347314993299674	3	FACETS	1	0.964	1	0.58	0.521	0.642	CLONAL	1	TRUE	1	0.356116584410956	3		972	605	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356308	70356308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778386823	NA	P-0057774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	46	454	0	ENST00000374080.3:c.5203C>T	p.Arg1735Cys	p.R1735C	ENST00000374080		1735	Cgc/Tgc	37/45	1	1	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	0	0.356116584410956	1		454	203	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0058056-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	111	287	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.31834670779581	4	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	TRUE	2	0.341218506122307	4		287	427	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118391551	118391551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058056-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	55	364	2	ENST00000534358.1:c.11464C>T	p.Arg3822Cys	p.R3822C	ENST00000534358	NM_005933.3	3822	Cgc/Tgc	34/36	0.341218506122307	3	FACETS	0.775	0.664	0.896	0.387	0.332	0.448	SUBCLONAL	1	TRUE	1	0.341218506122307	3		366	487	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228794	36228794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058157-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	119	571	0	ENST00000222270.7:c.7693C>T	p.Arg2565Cys	p.R2565C	ENST00000222270	NM_014727.1	2565	Cgt/Tgt	35/37	0.461271529794541	5	FACETS	1	0.955	1	0.365	0.33	0.403	CLONAL	1	TRUE	2	0.534575101937881	5		571	732	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577527	7577527	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555525470	NA	P-0058157-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	160	415	0	ENST00000269305.4:c.754del	p.Leu252SerfsTer93	p.L252Sfs*93	ENST00000269305	NM_001126112.2	252	Ctc/tc	7/11	0.514284636037669	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	0	0.534575101937881	2		415	299	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0058157-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	698	287	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.534575101937881	13	FACETS	0.967	0.944	0.99			1	CLONAL	11	TRUE	NA	0.534575101937881	13		287	967	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058536	69058536	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753703	NA	P-0058282-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	11	420	0	ENST00000288368.4:c.4180C>T	p.Arg1394Trp	p.R1394W	ENST00000288368	NM_024870.2	1394	Cgg/Tgg	34/40	0.296606426675254	2	FACETS	0.297	0.206	0.408	0.148	0.103	0.204	INDETERMINATE	1	TRUE	0	0.570482615777439	2		420	130	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038274	30038281	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTAGGCT	GGTAGGCT	-	novel	NA	P-0058282-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	182	591	0	ENST00000338641.4:c.447_447+7del		p.X149_splice	ENST00000338641	NM_000268.3	149		4/16	0.559678062373083	1	FACETS	0.854	0.794	0.916	0.854	0.794	0.916	CLONAL	1	TRUE	0	0.570482615777439	1		591	534	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442062	52442062	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0058282-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	296	883	0	ENST00000460680.1:c.287T>A	p.Leu96Ter	p.L96*	ENST00000460680	NM_004656.3	96	tTg/tAg	5/17	0.559678062373083	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.570482615777439	1		883	724	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663840	29663840	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058282-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	167	570	1	ENST00000356175.3:c.6272C>T	p.Ala2091Val	p.A2091V	ENST00000356175	NM_000267.3	2091	gCc/gTc	41/57	1	2	FACETS	0.904	0.833	0.976	0.904	0.833	0.976	CLONAL	1	TRUE	1	0.570482615777439	2		571	648	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0058643-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	12	644	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	1	2	FACETS	0.142	0.099	0.196	0.142	0.099	0.196	SUBCLONAL	1	FALSE	1	0.376169371640551	2		644	448	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866444	37866444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058643-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	102	848	0	ENST00000269571.5:c.749C>T	p.Ser250Phe	p.S250F	ENST00000269571		250	tCt/tTt	6/27	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	FALSE	1	0.376169371640551	2		848	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0058643-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	16	616	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.338509250933599	1	FACETS	0.18	0.132	0.237	0.18	0.132	0.237	SUBCLONAL	1	FALSE	0	0.376169371640551	1		616	384	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119974	70120026	+	frameshift_variant	Frame_Shift_Del	DEL	GCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAGGCGCCGCC	GCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAGGCGCCGCC	-	novel	NA	P-0058643-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	39	762	0	ENST00000245479.2:c.984_1036del	p.Ser330AlafsTer230	p.S330Afs*230	ENST00000245479	NM_000346.3	326	GCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAGGCGCCGCCg/g	3/3	1	2	FACETS	0.487	0.403	0.579	0.487	0.403	0.579	SUBCLONAL	1	FALSE	1	0.376169371640551	2		762	426	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473627	67473627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058643-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	67	655	0	ENST00000327367.4:c.707C>T	p.Ser236Phe	p.S236F	ENST00000327367	NM_005902.3	236	tCc/tTc	6/9	1	2	FACETS	0.84	0.733	0.955	0.84	0.733	0.955	CLONAL	1	FALSE	1	0.376169371640551	2		655	424	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339062	65339070	+	inframe_deletion	In_Frame_Del	DEL	CAGATACTC	CAGATACTC	-	novel	NA	P-0058643-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	88	740	0	ENST00000342505.4:c.466_474del	p.Glu156_Leu158del	p.E156_L158del	ENST00000342505	NM_002227.2	156	GAGTATCTG/-	5/25	0.376169371640551	1	FACETS	0.933	0.832	1	0.933	0.832	1	CLONAL	1	FALSE	0	0.376169371640551	1		740	407	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112764367	112764367	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058643-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	49	339	0	ENST00000369452.4:c.976C>G	p.Leu326Val	p.L326V	ENST00000369452	NM_007373.3	326	Ctt/Gtt	5/9	0.342275974635963	2	FACETS	0.892	0.76	1	0.446	0.38	0.518	CLONAL	1	FALSE	0	0.376169371640551	2		339	292	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32890645	32890645	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058643-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	35	393	0	ENST00000380152.3:c.48G>C	p.Lys16Asn	p.K16N	ENST00000380152		16	aaG/aaC	2/27	NA	2	FACETS	0.782	0.645	0.933			1	INDETERMINATE	1	FALSE	NA	0.376169371640551	2		393	238	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034382	42034963	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCAAGACCAGCCTGACCAACATGGAGAAACCTTGTCTCTACTAAAAATACAAAAATTAGCTGGGTTTGGTGGTATGTGCCTGTAATCCCAGCTACTCGGGAAGGCTGAGGCAGGAGAATTGCTTGAACCTGGGAGACAGAGGTTGCAGTGAGCCGAGATCGCGCCATTGCACTCTAGCCTGGGCAACAAGAAAGAAACTCCATCTTAAAAAAGAAAAAAAAGAAATTGGCACAAATAATACAGGTAGGTAGTACCTGTAAGAAATTGACCCAGTAGTGCACAGTAAATGTCGGTAAGCACAGTCACTAAGAGGATAAAATATGAGAACTGAAGATTTTTGACCTGCAAATTTCTGTTTGCAGCGGCTCGACCCTCTCCTGGTGGTGTGTTCACACAGTTTGTGATGAGTAAAGTTGGAGCCTTGCAGCAGAAGATACCTGGAGTTAGCACACCCCAAACCCTGGCAGGGACACAGAAGTTCAGTATCAGACCTTCTCCAGTAATGGTCGTCACACCTGTGGTTTCTTCTGAGCCAGTTCAGGTGTGCAGCCCTGTGACTGCTGCTGTCACTACTACCACCCC	TCAAGACCAGCCTGACCAACATGGAGAAACCTTGTCTCTACTAAAAATACAAAAATTAGCTGGGTTTGGTGGTATGTGCCTGTAATCCCAGCTACTCGGGAAGGCTGAGGCAGGAGAATTGCTTGAACCTGGGAGACAGAGGTTGCAGTGAGCCGAGATCGCGCCATTGCACTCTAGCCTGGGCAACAAGAAAGAAACTCCATCTTAAAAAAGAAAAAAAAGAAATTGGCACAAATAATACAGGTAGGTAGTACCTGTAAGAAATTGACCCAGTAGTGCACAGTAAATGTCGGTAAGCACAGTCACTAAGAGGATAAAATATGAGAACTGAAGATTTTTGACCTGCAAATTTCTGTTTGCAGCGGCTCGACCCTCTCCTGGTGGTGTGTTCACACAGTTTGTGATGAGTAAAGTTGGAGCCTTGCAGCAGAAGATACCTGGAGTTAGCACACCCCAAACCCTGGCAGGGACACAGAAGTTCAGTATCAGACCTTCTCCAGTAATGGTCGTCACACCTGTGGTTTCTTCTGAGCCAGTTCAGGTGTGCAGCCCTGTGACTGCTGCTGTCACTACTACCACCCC	-	novel	NA	P-0058643-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	35	6	0	ENST00000219905.7:c.4586-357_4810del		p.X1529_splice	ENST00000219905	NM_001164273.1	1529		15/24	0.161384732974126	4	FACETS	0.54	0.442	0.65	0.27	0.221	0.325	INDETERMINATE	1	FALSE	2	0.376169371640551	4		6	474	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90645594	90645594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1234438811	NA	P-0058643-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	51	545	0	ENST00000330062.3:c.29C>T	p.Ser10Leu	p.S10L	ENST00000330062	NM_002168.2	10	tCg/tTg	1/11	1	2	FACETS	0.919	0.786	1	0.919	0.786	1	CLONAL	1	FALSE	1	0.376169371640551	2		545	295	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741498	39741498	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058643-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	69	597	0	ENST00000361337.2:c.1385G>T	p.Arg462Leu	p.R462L	ENST00000361337	NM_003286.2	462	cGa/cTa	14/21	1	2	FACETS	0.812	0.709	0.922	0.812	0.709	0.922	CLONAL	1	FALSE	1	0.376169371640551	2		597	452	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204917	128204917	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058643-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	157	792	0	ENST00000341105.2:c.524C>T	p.Pro175Leu	p.P175L	ENST00000341105	NM_032638.4	175	cCc/cTc	3/6	0.376169371640551	3	FACETS	0.963	0.888	1	0.963	0.888	1	CLONAL	2	FALSE	1	0.376169371640551	3		792	515	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151602	55151602	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058643-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	54	413	0	ENST00000257290.5:c.2388G>C	p.Leu796Phe	p.L796F	ENST00000257290	NM_006206.4	796	ttG/ttC	17/23	0.269516135212145	3	FACETS	0.917	0.786	1	0.458	0.393	0.53	CLONAL	1	FALSE	1	0.376169371640551	3		413	372	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592045	67592045	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058643-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	77	570	0	ENST00000274335.5:c.1861G>T	p.Glu621Ter	p.E621*	ENST00000274335		621	Gag/Tag	14/15	1	2	FACETS	0.882	0.777	0.994	0.882	0.777	0.994	CLONAL	1	FALSE	1	0.376169371640551	2		570	464	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860435	151860435	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058643-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	163	852	0	ENST00000262189.6:c.10227G>C	p.Glu3409Asp	p.E3409D	ENST00000262189	NM_170606.2	3409	gaG/gaC	43/59	NA	2	FACETS	0.768	0.709	0.829			1	INDETERMINATE	2	FALSE	NA	0.376169371640551	2		852	564	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134259	11134259	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058643-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	47	617	0	ENST00000358026.2:c.2925C>G	p.Phe975Leu	p.F975L	ENST00000358026	NM_001128849.1	975	ttC/ttG	20/36	0.376169371640551	1	FACETS	0.606	0.513	0.707	0.606	0.513	0.707	SUBCLONAL	1	FALSE	0	0.376169371640551	1		617	335	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5563195	5563195	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058643-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	48	484	0	ENST00000397747.3:c.802del	p.Glu268LysfsTer2	p.E268Kfs*2	ENST00000397747	NM_025239.3	267	aGg/ag	6/7	0.338509250933599	1	FACETS	0.717	0.61	0.833	0.717	0.61	0.833	SUBCLONAL	1	FALSE	0	0.376169371640551	1		484	289	SUCCESS
PHF6	84295	MSKCC	GRCh37	X	133547582	133547582	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058643-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	50	467	0	ENST00000332070.3:c.480G>C	p.Lys160Asn	p.K160N	ENST00000332070	NM_032458.2	160	aaG/aaC	6/10	1	2	FACETS	0.789	0.672	0.916	0.789	0.672	0.916	CLONAL	1	FALSE	1	0.376169371640551	2		467	337	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465510	99465510	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	72	463	0	ENST00000268035.6:c.2335G>C	p.Glu779Gln	p.E779Q	ENST00000268035	NM_000875.3	779	Gag/Cag	11/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.19	2		463	534	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1720648	1720648	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	36	448	0	ENST00000378609.4:c.760G>C	p.Asp254His	p.D254H	ENST00000378609	NM_002074.3	254	Gac/Cac	10/12	0.169470079225058	2	FACETS	0.592	0.485	0.712	0.296	0.242	0.356	SUBCLONAL	1	TRUE	0	0.19	2		448	640	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202735	16202735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	86	429	0	ENST00000375759.3:c.443C>T	p.Ala148Val	p.A148V	ENST00000375759	NM_015001.2	148	gCc/gTc	3/15	0.169470079225058	2	FACETS	1	0.976	1	0.72	0.637	0.808	CLONAL	1	TRUE	0	0.19	2		429	629	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105551	27105551	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	129	406	0	ENST00000324856.7:c.5162G>C	p.Arg1721Pro	p.R1721P	ENST00000324856	NM_006015.4	1721	cGa/cCa	20/20	0.169470079225058	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.19	2		406	608	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599944	28599944	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	40	489	0	ENST00000253063.3:c.826G>T	p.Glu276Ter	p.E276*	ENST00000253063	NM_031459.4	276	Gag/Tag	6/10	0.169470079225058	2	FACETS	0.859	0.714	1	0.43	0.357	0.511	CLONAL	1	TRUE	0	0.19	2		489	490	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938201	36938201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	99	427	0	ENST00000361632.4:c.760G>A	p.Glu254Lys	p.E254K	ENST00000361632		254	Gag/Aag	6/16	0.169470079225058	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.19	2		427	456	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551990	150551990	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	47	492	0	ENST00000369026.2:c.17G>C	p.Arg6Thr	p.R6T	ENST00000369026	NM_021960.4	6	aGa/aCa	1/3	1	2	FACETS	0.866	0.73	1	0.866	0.73	1	CLONAL	1	TRUE	1	0.19	2		492	571	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150933602	150933602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	83	439	0	ENST00000271640.5:c.3064G>A	p.Glu1022Lys	p.E1022K	ENST00000271640	NM_001145415.1	1022	Gag/Aag	16/22	1	2	FACETS	0.817	0.722	0.917	1	0.98	1	CLONAL	2	TRUE	1	0.19	2		439	535	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981202	201981202	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	32	504	0	ENST00000359651.3:c.281G>T	p.Arg94Leu	p.R94L	ENST00000359651		94	cGa/cTa	2/8	0.3	1	FACETS	0.554	0.449	0.674	0.554	0.449	0.674	SUBCLONAL	1	TRUE	0	0.19	1		504	550	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230493024	230493024	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	54	510	0	ENST00000391860.1:c.30C>G	p.Phe10Leu	p.F10L	ENST00000391860	NM_001258311.1	10	ttC/ttG	2/7	0.3	1	FACETS	0.904	0.772	1	0.904	0.772	1	CLONAL	1	TRUE	0	0.19	1		510	569	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920777	100920777	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	35	336	0	ENST00000325455.5:c.2371G>C	p.Glu791Gln	p.E791Q	ENST00000325455	NM_001202474.3	791	Gaa/Caa	6/8	1	2	FACETS	0.787	0.645	0.947	0.787	0.645	0.947	CLONAL	1	TRUE	1	0.19	2		336	468	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141845	108141845	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	53	315	0	ENST00000278616.4:c.2893G>A	p.Asp965Asn	p.D965N	ENST00000278616	NM_000051.3	965	Gat/Aat	19/63	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.19	2		315	469	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49430593	49431582	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTTTGCACCACTTCTCTTCAAGTCTTAAGCTTTCAACTTCACTACAGCTACAAAGGCTCTGCTAATTAGGCTTCATTCATACATTCATTCCATTTATTCAAACATCTGCTACATGCCTACTATATGCCAGGAACTGTTCTCTCTCTTCTTAAAAGCTACAGTGTTTCTGCCTCTACCACTAGTATGATATTTAGCCAAAGTTCTTTGTGTCCCATCTTAAGTAGGGATTATCTGAGGTCTCTAGCCTCAGTGCCCATTTAGGGATAACAATAATCACCCTGAGTAACTTGGCTATGTTACCAGCTGAGGTTACCTGTATCTGGGAAGAAGCTGTTTGCCAGCTGCTGCTGCATTGCCAATTGCTGCGGCTTCATGCACATGGAAGGTGGCATGGTGCCCATGGGCTTCTGTGATAGCACTGGCTGTGAGCTCTGCTGGGGTACCAAGCCTGCCTGCCCTCCATGCTGCCCACTTAGCATATGCCCTTGATTGGACACCATAGCCATGGATGGAGCCAGGCGTTGCTGGAGGGCATGAGCTGGTGGCTGGGTGGGCATCAGTGGCTGGGGCAAACCTGGCTGTCGGGCACCTGCAAGACCCAGGGAAAGCTGCTGTTGGGACCCAGCCAAACTGGGAGAAGAGCCCTCATGTGGCAAAGACATGGCCTGGGCAGGGCCTGGTGCAGACAGTAGGGAATGCTGCTGCTGCTGTTGCTGCTGCTGCTGGGCAGGCTGCAACTGTGCTGAAAGCTGCTGCTTCTTCTGCAGCTCCTTCTTCTCATGCTCCAACAGGTCCTCAATGAGCAGGGGTAACTCGCTGGCTACCAGTGAGCTCTCCATCTTGTCTAGCTCATCCCCAGATGCTGCAGGTCCACCAGGCAAGGTCAAAGCCCCACTCTCGAGCTCAAACTTTTCCAGCAGGGAGGATCCTCCTGGGCCACTCAGTGGGCTGGGGGTCAGCAGGTGAGCTGGTGGTCCTCCCGTGGCCC	TTTTTTGCACCACTTCTCTTCAAGTCTTAAGCTTTCAACTTCACTACAGCTACAAAGGCTCTGCTAATTAGGCTTCATTCATACATTCATTCCATTTATTCAAACATCTGCTACATGCCTACTATATGCCAGGAACTGTTCTCTCTCTTCTTAAAAGCTACAGTGTTTCTGCCTCTACCACTAGTATGATATTTAGCCAAAGTTCTTTGTGTCCCATCTTAAGTAGGGATTATCTGAGGTCTCTAGCCTCAGTGCCCATTTAGGGATAACAATAATCACCCTGAGTAACTTGGCTATGTTACCAGCTGAGGTTACCTGTATCTGGGAAGAAGCTGTTTGCCAGCTGCTGCTGCATTGCCAATTGCTGCGGCTTCATGCACATGGAAGGTGGCATGGTGCCCATGGGCTTCTGTGATAGCACTGGCTGTGAGCTCTGCTGGGGTACCAAGCCTGCCTGCCCTCCATGCTGCCCACTTAGCATATGCCCTTGATTGGACACCATAGCCATGGATGGAGCCAGGCGTTGCTGGAGGGCATGAGCTGGTGGCTGGGTGGGCATCAGTGGCTGGGGCAAACCTGGCTGTCGGGCACCTGCAAGACCCAGGGAAAGCTGCTGTTGGGACCCAGCCAAACTGGGAGAAGAGCCCTCATGTGGCAAAGACATGGCCTGGGCAGGGCCTGGTGCAGACAGTAGGGAATGCTGCTGCTGCTGTTGCTGCTGCTGCTGGGCAGGCTGCAACTGTGCTGAAAGCTGCTGCTTCTTCTGCAGCTCCTTCTTCTCATGCTCCAACAGGTCCTCAATGAGCAGGGGTAACTCGCTGGCTACCAGTGAGCTCTCCATCTTGTCTAGCTCATCCCCAGATGCTGCAGGTCCACCAGGCAAGGTCAAAGCCCCACTCTCGAGCTCAAACTTTTCCAGCAGGGAGGATCCTCCTGGGCCACTCAGTGGGCTGGGGGTCAGCAGGTGAGCTGGTGGTCCTCCCGTGGCCC	-	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	54	16	0	ENST00000301067.7:c.9557_10231+315del		p.X3186_splice	ENST00000301067	NM_003482.3	3186		34/54	1	2	FACETS	0.987	0.918	1	1	0.986	1	CLONAL	9	TRUE	1	0.19	2		16	64	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486842	56486842	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	97	429	0	ENST00000267101.3:c.1256G>C	p.Gly419Ala	p.G419A	ENST00000267101	NM_001982.3	419	gGa/gCa	11/28	1	2	FACETS	0.942	0.842	1	1	0.986	1	CLONAL	2	TRUE	1	0.19	2		429	542	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885334	111885334	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	71	358	0	ENST00000341259.2:c.1222C>T	p.Gln408Ter	p.Q408*	ENST00000341259	NM_005475.2	408	Cag/Tag	6/8	1	2	FACETS	0.903	0.791	1	1	0.98	1	CLONAL	2	TRUE	1	0.19	2		358	414	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245249	133245249	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	39	573	0	ENST00000320574.5:c.1998G>T	p.Lys666Asn	p.K666N	ENST00000320574	NM_006231.2	666	aaG/aaT	18/49	1	2	FACETS	0.65	0.537	0.775	0.65	0.537	0.775	SUBCLONAL	1	TRUE	1	0.19	2		573	632	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248909	133248909	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	72	450	0	ENST00000320574.5:c.1687-1G>C		p.X563_splice	ENST00000320574	NM_006231.2	563			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.19	2		450	559	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828827	26828827	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	32	441	0	ENST00000381527.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000381527	NM_001260.1	17	Gag/Aag	1/13	1	2	FACETS	0.69	0.559	0.838	0.69	0.559	0.838	SUBCLONAL	1	TRUE	1	0.19	2		441	488	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035314	42035314	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	36	467	0	ENST00000219905.7:c.5156C>A	p.Ser1719Tyr	p.S1719Y	ENST00000219905	NM_001164273.1	1719	tCt/tAt	15/24	1	2	FACETS	0.725	0.595	0.87	0.725	0.595	0.87	SUBCLONAL	1	TRUE	1	0.19	2		467	523	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647249	2647249	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	53	373	0	ENST00000342085.4:c.1527G>T	p.Lys509Asn	p.K509N	ENST00000342085	NM_002613.4	509	aaG/aaT	13/14	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.19	2		373	478	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50827573	50827573	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	25	281	0	ENST00000398568.2:c.2458C>G	p.Gln820Glu	p.Q820E	ENST00000398568	NM_001042412.1	820	Caa/Gaa	16/18	1	2	FACETS	0.643	0.506	0.801	0.643	0.506	0.801	SUBCLONAL	1	TRUE	1	0.19	2		281	409	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81960765	81960765	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	49	463	0	ENST00000359376.3:c.2496C>A	p.Phe832Leu	p.F832L	ENST00000359376	NM_002661.3	832	ttC/ttA	23/33	1	2	FACETS	0.982	0.832	1	0.982	0.832	1	CLONAL	1	TRUE	1	0.19	2		463	525	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882319	89882319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	38	469	0	ENST00000389301.3:c.155G>A	p.Arg52Gln	p.R52Q	ENST00000389301	NM_000135.2	52	cGa/cAa	2/43	1	2	FACETS	0.802	0.662	0.958	0.802	0.662	0.958	CLONAL	1	TRUE	1	0.19	2		469	499	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243563	41243563	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	41	474	0	ENST00000357654.3:c.3985G>T	p.Glu1329Ter	p.E1329*	ENST00000357654	NM_007294.3	1329	Gaa/Taa	10/23	1	2	FACETS	0.606	0.503	0.721	0.606	0.503	0.721	SUBCLONAL	1	TRUE	1	0.19	2		474	712	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923296	78923296	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	30	429	0	ENST00000306801.3:c.3319G>C	p.Glu1107Gln	p.E1107Q	ENST00000306801	NM_020761.2	1107	Gag/Cag	28/34	1	2	FACETS	0.618	0.497	0.756	0.618	0.497	0.756	SUBCLONAL	1	TRUE	1	0.19	2		429	511	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395628	45395628	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	61	325	0	ENST00000262160.6:c.506G>C	p.Arg169Thr	p.R169T	ENST00000262160	NM_005901.5	169	aGa/aCa	4/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.19	2		325	516	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985691	60985691	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	39	514	0	ENST00000333681.4:c.209C>A	p.Ser70Ter	p.S70*	ENST00000333681		70	tCg/tAg	2/3	1	2	FACETS	0.823	0.681	0.98	0.823	0.681	0.98	CLONAL	1	TRUE	1	0.19	2		514	499	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265192	5265192	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	68	453	0	ENST00000357368.4:c.395C>G	p.Ser132Cys	p.S132C	ENST00000357368	NM_002850.3	132	tCt/tGt	5/38	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.19	2		453	584	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220976	36220976	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	84	564	0	ENST00000222270.7:c.5026G>A	p.Asp1676Asn	p.D1676N	ENST00000222270	NM_014727.1	1676	Gat/Aat	23/37	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.19	2		564	637	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96931053	96931053	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	30	475	0	ENST00000258439.3:c.67C>G	p.Leu23Val	p.L23V	ENST00000258439	NM_001193304.2	23	Ctg/Gtg	2/4	1	2	FACETS	0.65	0.523	0.794	0.65	0.523	0.794	SUBCLONAL	1	TRUE	1	0.19	2		475	486	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248410	212248410	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1213182678	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	38	515	0	ENST00000342788.4:c.3857C>G	p.Ser1286Cys	p.S1286C	ENST00000342788	NM_005235.2	1286	tCt/tGt	28/28	1	2	FACETS	0.661	0.545	0.791	0.661	0.545	0.791	SUBCLONAL	1	TRUE	1	0.19	2		515	605	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662301	227662301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1289819083	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	61	548	0	ENST00000305123.5:c.1154C>T	p.Ser385Leu	p.S385L	ENST00000305123	NM_005544.2	385	tCg/tTg	1/2	1	2	FACETS	0.917	0.79	1	0.917	0.79	1	CLONAL	1	TRUE	1	0.19	2		548	700	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022422	31022422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370230857	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	83	553	0	ENST00000375687.4:c.1907C>T	p.Ala636Val	p.A636V	ENST00000375687	NM_015338.5	636	gCg/gTg	13/13	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.19	2		553	653	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827919	40827919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	42	551	0	ENST00000373198.4:c.2509G>A	p.Glu837Lys	p.E837K	ENST00000373198	NM_133170.3	837	Gaa/Aaa	17/32	1	2	FACETS	0.706	0.589	0.837	0.706	0.589	0.837	SUBCLONAL	1	TRUE	1	0.19	2		551	626	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408920	41408920	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	40	433	0	ENST00000373198.4:c.506C>G	p.Ser169Ter	p.S169*	ENST00000373198	NM_133170.3	169	tCa/tGa	4/32	1	2	FACETS	0.725	0.601	0.863	0.725	0.601	0.863	SUBCLONAL	1	TRUE	1	0.19	2		433	581	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262832	46262832	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	56	389	0	ENST00000371998.3:c.1005C>A	p.Phe335Leu	p.F335L	ENST00000371998		335	ttC/ttA	10/23	1	2	FACETS	0.955	0.818	1	0.955	0.818	1	CLONAL	1	TRUE	1	0.19	2		389	617	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281282	46281282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	36	385	0	ENST00000371998.3:c.4079C>T	p.Ser1360Leu	p.S1360L	ENST00000371998		1360	tCa/tTa	21/23	1	2	FACETS	0.573	0.47	0.69	0.573	0.47	0.69	SUBCLONAL	1	TRUE	1	0.19	2		385	661	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546185	41546185	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	35	431	0	ENST00000263253.7:c.2800C>T	p.Pro934Ser	p.P934S	ENST00000263253	NM_001429.3	934	Ccg/Tcg	14/31	1	2	FACETS	0.607	0.496	0.732	0.607	0.496	0.732	SUBCLONAL	1	TRUE	1	0.19	2		431	607	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732930	30732930	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	50	391	0	ENST00000295754.5:c.1543G>C	p.Glu515Gln	p.E515Q	ENST00000295754	NM_003242.5	515	Gag/Cag	7/7	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.19	2		391	525	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021828	71021828	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	50	358	0	ENST00000318789.4:c.1531-1G>C		p.X511_splice	ENST00000318789	NM_032682.5	511			1	2	FACETS	0.957	0.812	1	0.957	0.812	1	CLONAL	1	TRUE	1	0.19	2		358	550	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498490	89498490	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	35	377	0	ENST00000336596.2:c.2462G>C	p.Gly821Ala	p.G821A	ENST00000336596	NM_005233.5	821	gGa/gCa	14/17	1	2	FACETS	0.693	0.567	0.834	0.693	0.567	0.834	SUBCLONAL	1	TRUE	1	0.19	2		377	532	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332691	153332691	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	99	460	0	ENST00000281708.4:c.265G>T	p.Glu89Ter	p.E89*	ENST00000281708	NM_033632.3	89	Gag/Tag	2/12	1	2	FACETS	0.77	0.688	0.857	1	0.982	1	SUBCLONAL	2	TRUE	1	0.19	2		460	677	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519279	187519279	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	42	368	0	ENST00000441802.2:c.12104G>T	p.Gly4035Val	p.G4035V	ENST00000441802	NM_005245.3	4035	gGt/gTt	23/27	1	2	FACETS	0.917	0.766	1	0.917	0.766	1	CLONAL	1	TRUE	1	0.19	2		368	482	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538326	187538326	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	37	345	0	ENST00000441802.2:c.8908G>A	p.Glu2970Lys	p.E2970K	ENST00000441802	NM_005245.3	2970	Gaa/Aaa	11/27	1	2	FACETS	0.818	0.674	0.979	0.818	0.674	0.979	CLONAL	1	TRUE	1	0.19	2		345	476	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032111	26032111	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	46	693	0	ENST00000244661.2:c.178G>C	p.Glu60Gln	p.E60Q	ENST00000244661	NM_003537.3	60	Gag/Cag	1/1	1	2	FACETS	0.553	0.464	0.652	0.553	0.464	0.652	SUBCLONAL	1	TRUE	1	0.19	2		693	875	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158464	26158464	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs916752202	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	49	498	0	ENST00000289316.2:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000289316	NM_138720.2	23	Cag/Tag	1/2	1	2	FACETS	0.76	0.642	0.889	0.76	0.642	0.889	SUBCLONAL	1	TRUE	1	0.19	2		498	679	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652031	36652031	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	135	589	0	ENST00000244741.5:c.153C>G	p.Phe51Leu	p.F51L	ENST00000244741	NM_000389.4	51	ttC/ttG	2/3	1	2	FACETS	0.956	0.87	1	1	0.99	1	CLONAL	2	TRUE	1	0.19	2		589	743	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652140	36652140	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	40	577	0	ENST00000244741.5:c.262G>T	p.Glu88Ter	p.E88*	ENST00000244741	NM_000389.4	88	Gag/Tag	2/3	1	2	FACETS	0.637	0.528	0.759	0.637	0.528	0.759	SUBCLONAL	1	TRUE	1	0.19	2		577	661	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745314	43745314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	43	541	0	ENST00000523873.1:c.227C>T	p.Ser76Phe	p.S76F	ENST00000523873		76	tCc/tTc	3/8	1	2	FACETS	0.662	0.552	0.784	0.662	0.552	0.784	SUBCLONAL	1	TRUE	1	0.19	2		541	684	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681555	117681555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	53	363	0	ENST00000368508.3:c.3395C>T	p.Thr1132Ile	p.T1132I	ENST00000368508	NM_002944.2	1132	aCa/aTa	22/43	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.19	2		363	449	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997819	149997819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	36	449	0	ENST00000253339.5:c.2648C>T	p.Ser883Leu	p.S883L	ENST00000253339		883	tCa/tTa	5/7	1	2	FACETS	0.607	0.498	0.73	0.607	0.498	0.73	SUBCLONAL	1	TRUE	1	0.19	2		449	624	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505494	157505494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	29	424	0	ENST00000346085.5:c.3475G>A	p.Gly1159Arg	p.G1159R	ENST00000346085	NM_020732.3	1159	Ggg/Agg	13/20	1	2	FACETS	0.606	0.485	0.743	0.606	0.485	0.743	SUBCLONAL	1	TRUE	1	0.19	2		424	504	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505511	157505512	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	27	423	0	ENST00000346085.5:c.3492_3493delinsAA	p.Glu1165Lys	p.E1165K	ENST00000346085	NM_020732.3	1164	ccGGaa/ccAAaa	13/20	1	2	FACETS	0.543	0.431	0.672	0.543	0.431	0.672	SUBCLONAL	1	TRUE	1	0.19	2		423	523	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845334	151845334	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	37	555	0	ENST00000262189.6:c.13678C>T	p.Gln4560Ter	p.Q4560*	ENST00000262189	NM_170606.2	4560	Cag/Tag	52/59	1	2	FACETS	0.63	0.518	0.756	0.63	0.518	0.756	SUBCLONAL	1	TRUE	1	0.19	2		555	618	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874893	151874893	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1473097808	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	46	465	0	ENST00000262189.6:c.7645C>T	p.Gln2549Ter	p.Q2549*	ENST00000262189	NM_170606.2	2549	Cag/Tag	38/59	1	2	FACETS	0.715	0.601	0.842	0.715	0.601	0.842	SUBCLONAL	1	TRUE	1	0.19	2		465	677	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133819	38133819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	39	439	0	ENST00000317025.8:c.4067C>T	p.Pro1356Leu	p.P1356L	ENST00000317025	NM_023034.1	1356	cCa/cTa	23/24	1	2	FACETS	0.663	0.549	0.792	0.663	0.549	0.792	SUBCLONAL	1	TRUE	1	0.19	2		439	619	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146228	38146228	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	54	420	0	ENST00000317025.8:c.3278C>T	p.Ser1093Leu	p.S1093L	ENST00000317025	NM_023034.1	1093	tCa/tTa	19/24	1	2	FACETS	0.941	0.803	1	0.941	0.803	1	CLONAL	1	TRUE	1	0.19	2		420	604	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549178	87549178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	39	404	0	ENST00000277120.3:c.1735G>A	p.Glu579Lys	p.E579K	ENST00000277120		579	Gag/Aag	15/19	0.158253743235104	2	FACETS	0.793	0.656	0.945	0.396	0.328	0.473	CLONAL	1	TRUE	0	0.19	2		404	518	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195673	123195674	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	62	157	0	ENST00000218089.9:c.1589_1590dup	p.Gln531AspfsTer46	p.Q531Dfs*46	ENST00000218089	NM_001042749.1	529	-/AG	17/35	0.117077957936849	2	FACETS	0.84	0.733	0.953			1	CLONAL	3	TRUE	NA	0.19	2		157	259	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133182	38133182	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	28	0	0	ENST00000317025.8:c.4291C>A	p.His1431Asn	p.H1431N	ENST00000317025	NM_023034.1	1431	Cat/Aat	24/24	1	2	FACETS	0.465	0.37	0.574	0.465	0.37	0.574	SUBCLONAL	1	TRUE	1	0.19	2		0	634	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845920	72845920	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1167212887	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	22	0	0	ENST00000268489.5:c.3547G>C	p.Glu1183Gln	p.E1183Q	ENST00000268489	NM_006885.3	1183	Gag/Cag	6/10	1	2	FACETS	0.452	0.349	0.573	0.452	0.349	0.573	SUBCLONAL	1	TRUE	1	0.19	2		0	512	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197454	26197454	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	31	0	0	ENST00000356476.2:c.25C>G	p.Arg9Gly	p.R9G	ENST00000356476		9	Cgc/Ggc	1/1	1	2	FACETS	0.452	0.364	0.552	0.452	0.364	0.552	SUBCLONAL	1	TRUE	1	0.19	2		0	722	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786740	3786740	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	20	0	0	ENST00000262367.5:c.4471C>T	p.Gln1491Ter	p.Q1491*	ENST00000262367	NM_004380.2	1491	Caa/Taa	27/31	1	2	FACETS	0.452	0.344	0.578	0.452	0.344	0.578	SUBCLONAL	1	TRUE	1	0.19	2		0	466	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977167	85977167	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	11	0	0	ENST00000263360.6:c.769G>C	p.Asp257His	p.D257H	ENST00000263360	NM_003797.3	257	Gat/Cat	8/12	1	2	FACETS	0.429	0.295	0.595	0.429	0.295	0.595	SUBCLONAL	1	TRUE	1	0.19	2		0	270	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347245	89347245	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058654-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	18	0	0	ENST00000301030.4:c.5705C>A	p.Ser1902Tyr	p.S1902Y	ENST00000301030	NM_001256183.1	1902	tCc/tAc	9/13	1	2	FACETS	0.354	0.265	0.46	0.354	0.265	0.46	SUBCLONAL	1	TRUE	1	0.19	2		0	535	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0058930-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	103	578	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.304968142730531	1	FACETS	0.761	0.682	0.844	0.761	0.682	0.844	SUBCLONAL	1	TRUE	0	0.359838911446227	1		578	617	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584513	48584514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs377767334	NA	P-0058930-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	102	673	0	ENST00000342988.3:c.692dup	p.Ser232GlnfsTer3	p.S232Qfs*3	ENST00000342988	NM_005359.5	229	ctg/ctGg	6/12	0.304968142730531	1	FACETS	0.766	0.686	0.85	0.766	0.686	0.85	SUBCLONAL	1	TRUE	0	0.359838911446227	1		673	607	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539950	187539950	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058930-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	82	767	0	ENST00000441802.2:c.7790G>T	p.Arg2597Leu	p.R2597L	ENST00000441802	NM_005245.3	2597	cGa/cTa	10/27	0.2734252714237	3	FACETS	0.729	0.642	0.822	0.243	0.214	0.274	SUBCLONAL	1	TRUE	0	0.359838911446227	3		767	738	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0058930-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	137	545	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.271422110692767	3	FACETS	1	0.987	1	0.745	0.68	0.813	CLONAL	1	TRUE	1	0.359838911446227	3		545	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576900	7576956	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGAGGAGCTGGTGTTGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAA	GAGAGGAGCTGGTGTTGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAA	-	novel	NA	P-0058930-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	179	888	0	ENST00000269305.4:c.920-30_946del		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	0.268648339452431	2	FACETS	1	0.981	1	0.599	0.552	0.647	CLONAL	1	TRUE	0	0.359838911446227	2		888	831	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0059599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	61	372	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.392686019441366	2		372	294	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41905044	41905044	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	118	778	0	ENST00000372991.4:c.503T>A	p.Leu168His	p.L168H	ENST00000372991	NM_001760.3	168	cTc/cAc	3/5	0.392686019441366	1	FACETS	0.966	0.876	1	0.966	0.876	1	CLONAL	1	TRUE	0	0.392686019441366	1		778	500	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858738	9858738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149698593	NA	P-0059834-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	88	480	0	ENST00000330684.3:c.2663C>T	p.Thr888Met	p.T888M	ENST00000330684	NM_001134407.1	888	aCg/aTg	13/13	0.348931531585127	2	FACETS	0.841	0.754	0.931	0.841	0.754	0.931	CLONAL	2	TRUE	0	0.361010853401492	2		480	290	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068325	30068325	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758594741	NA	P-0059834-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	26	295	3	ENST00000331968.5:c.2074G>A	p.Val692Met	p.V692M	ENST00000331968	NM_002742.2	692	Gtg/Atg	15/18	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.361010853401492	2		298	134	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574815	41574815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748953233	NA	P-0059834-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	117	589	0	ENST00000263253.7:c.7100C>T	p.Pro2367Leu	p.P2367L	ENST00000263253	NM_001429.3	2367	cCg/cTg	31/31	0.275077446849779	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	2	TRUE	0	0.361010853401492	2		589	322	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30060979	30060979	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059834-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	59	274	0	ENST00000338641.4:c.813del	p.Phe271LeufsTer25	p.F271Lfs*25	ENST00000338641	NM_000268.3	271	Ttt/tt	9/16	0.275077446849779	2	FACETS	0.956	0.839	1	0.956	0.839	1	CLONAL	2	TRUE	0	0.361010853401492	2		274	171	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059865-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	172	612	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	1	0.985	1	1	0.994	1	CLONAL	2	TRUE	0	0.28	1		612	432	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971178	13971178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs904139873	NA	P-0059865-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	257	608	0	ENST00000405192.2:c.751C>T	p.Pro251Ser	p.P251S	ENST00000405192	NM_001163147.1	251	Ccc/Tcc	8/12	1	2	FACETS	1	0.986	1	1	0.996	1	CLONAL	3	TRUE	1	0.28	2		608	543	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881462	48881462	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060178-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	48	271	0	ENST00000267163.4:c.184C>T	p.Gln62Ter	p.Q62*	ENST00000267163	NM_000321.2	62	Cag/Tag	2/27	0.307891231107735	3	FACETS	0.834	0.714	0.963	0.556	0.476	0.642	CLONAL	2	TRUE	0	0.324704361246563	3		271	206	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579485	7579485	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs869312782	NA	P-0060178-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	469	537	0	ENST00000269305.4:c.202G>T	p.Glu68Ter	p.E68*	ENST00000269305	NM_001126112.2	68	Gag/Tag	4/11	0.324704361246563	8	FACETS	1	0.985	1	0.899	0.865	0.934	CLONAL	6	TRUE	1	0.324704361246563	8		537	906	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564741	41564741	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060178-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	85	468	0	ENST00000263253.7:c.4042G>A	p.Glu1348Lys	p.E1348K	ENST00000263253	NM_001429.3	1348	Gag/Aag	25/31	0.324704361246563	4	FACETS	1	0.971	1	0.436	0.386	0.489	CLONAL	1	TRUE	1	0.324704361246563	4		468	530	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239788	41239788	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060178-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	64	511	0	ENST00000379561.5:c.562G>C	p.Glu188Gln	p.E188Q	ENST00000379561	NM_002015.3	188	Gag/Cag	1/3	0.307891231107735	3	FACETS	0.722	0.625	0.827	0.241	0.208	0.276	SUBCLONAL	1	TRUE	0	0.324704361246563	3		511	635	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610421	10610421	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060178-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	321	435	0	ENST00000171111.5:c.289A>C	p.Lys97Gln	p.K97Q	ENST00000171111	NM_203500.1	97	Aag/Cag	2/6	0.324704361246563	6	FACETS	0.908	0.864	0.953	0.908	0.864	0.953	CLONAL	5	TRUE	1	0.324704361246563	6		435	718	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426780	121426780	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060178-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	64	560	0	ENST00000257555.6:c.471G>C	p.Gln157His	p.Q157H	ENST00000257555		157	caG/caC	2/10	0.324704361246563	3	FACETS	0.815	0.706	0.933	0.272	0.235	0.311	CLONAL	1	TRUE	0	0.324704361246563	3		560	562	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335833	73335833	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060178-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	90	473	0	ENST00000377767.4:c.2462A>C	p.His821Pro	p.H821P	ENST00000377767	NM_014953.3	821	cAc/cCc	18/21	0.322561232942607	2	FACETS	0.88	0.789	0.975	0.88	0.789	0.975	CLONAL	2	TRUE	0	0.324704361246563	2		473	315	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254450	10254450	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060178-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	208	312	0	ENST00000340748.4:c.3060G>C	p.Lys1020Asn	p.K1020N	ENST00000340748		1020	aaG/aaC	28/40	0.324704361246563	6	FACETS	1	0.955	1	0.819	0.767	0.872	CLONAL	4	TRUE	1	0.324704361246563	6		312	516	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748575	40748575	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060178-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	144	338	0	ENST00000392038.2:c.307A>G	p.Ile103Val	p.I103V	ENST00000392038	NM_001626.4	103	Atc/Gtc	5/14	0.324704361246563	5	FACETS	0.871	0.799	0.944	0.653	0.599	0.708	CLONAL	3	TRUE	1	0.324704361246563	5		338	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572928	7572929	+	frameshift_variant,stop_lost	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0060318-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	239	375	0	ENST00000269305.4:c.1180_1181del	p.Ter394ThrfsTer76	p.*394Tfs*76	ENST00000269305	NM_001126112.2	394	TGa/a	11/11	0.416496866835648	0	FACETS		NA	1			1	NA	3	TRUE	0	0.437637746606559	0		375	269	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193814	106193814	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1355157024	NA	P-0060318-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	112	426	0	ENST00000380013.4:c.4276G>A	p.Val1426Met	p.V1426M	ENST00000380013	NM_001127208.2	1426	Gtg/Atg	10/11	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.437637746606559	2		426	488	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222001	1222001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060320-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	31	499	0	ENST00000326873.7:c.916C>T	p.His306Tyr	p.H306Y	ENST00000326873	NM_000455.4	306	Cac/Tac	7/10	1	2	FACETS	0.48	0.388	0.583	0.48	0.388	0.583	SUBCLONAL	1	TRUE	1	0.351130576172954	2		499	368	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600336	10600336	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs751088754	NA	P-0060320-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	61	623	0	ENST00000171111.5:c.1519C>T	p.Arg507Ter	p.R507*	ENST00000171111	NM_203500.1	507	Cga/Tga	4/6	1	2	FACETS	0.702	0.606	0.805	0.702	0.606	0.805	SUBCLONAL	1	TRUE	1	0.351130576172954	2		623	495	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310181	91310181	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060320-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	39	378	0	ENST00000355112.3:c.2235A>C	p.Glu745Asp	p.E745D	ENST00000355112	NM_000057.2	745	gaA/gaC	10/22	1	2	FACETS	0.738	0.614	0.875	0.738	0.614	0.875	SUBCLONAL	1	TRUE	1	0.351130576172954	2		378	301	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023679	27023679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771542513	NA	P-0060320-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	25	643	0	ENST00000324856.7:c.785C>T	p.Ser262Leu	p.S262L	ENST00000324856	NM_006015.4	262	tCg/tTg	1/20	1	2	FACETS	0.301	0.236	0.376	0.301	0.236	0.376	SUBCLONAL	1	TRUE	1	0.351130576172954	2		643	473	SUCCESS
EED	8726	MSKCC	GRCh37	11	85956296	85956296	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs374657922	NA	P-0060320-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	44	455	0	ENST00000263360.6:c.25G>T	p.Ala9Ser	p.A9S	ENST00000263360	NM_003797.3	9	Gcg/Tcg	1/12	1	2	FACETS	0.731	0.615	0.858	0.731	0.615	0.858	SUBCLONAL	1	TRUE	1	0.351130576172954	2		455	343	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149102	119149275	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTGGGGTTAGGTTTAAACTTTTACTTTTTTTTGATCTCTAGGAAATGTATTTTCTAGTAGATTAATATTTTAAGTATTTTCAGATGCATCTGTTACTATCTTTTGCTTCTTCTGCAGGAATCAGAAGGTCAGGGCTGTCCTTTCTGCCGATGTGAAATTAAAGGTACTGAACC	TTTGGGGTTAGGTTTAAACTTTTACTTTTTTTTGATCTCTAGGAAATGTATTTTCTAGTAGATTAATATTTTAAGTATTTTCAGATGCATCTGTTACTATCTTTTGCTTCTTCTGCAGGAATCAGAAGGTCAGGGCTGTCCTTTCTGCCGATGTGAAATTAAAGGTACTGAACC	-	novel	NA	P-0060320-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	49	320	0	ENST00000264033.4:c.1227+95_1283del		p.X409_splice	ENST00000264033	NM_005188.3	409		9/16	1	2	FACETS	0.729	0.619	0.849	0.729	0.619	0.849	SUBCLONAL	1	TRUE	1	0.351130576172954	2		320	383	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455296	29455296	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060320-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	45	569	0	ENST00000389048.3:c.2506G>A	p.Val836Met	p.V836M	ENST00000389048	NM_004304.4	836	Gtg/Atg	15/29	1	2	FACETS	0.563	0.474	0.662	0.563	0.474	0.662	SUBCLONAL	1	TRUE	1	0.351130576172954	2		569	455	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527946	157527946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060320-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	51	628	0	ENST00000346085.5:c.5671G>T	p.Asp1891Tyr	p.D1891Y	ENST00000346085	NM_020732.3	1891	Gac/Tac	20/20	1	2	FACETS	0.551	0.468	0.642	0.551	0.468	0.642	SUBCLONAL	1	TRUE	1	0.351130576172954	2		628	527	SUCCESS
APC	324	MSKCC	GRCh37	5	112175235	112175235	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060679-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	36	571	0	ENST00000257430.4:c.3944C>A	p.Ser1315Ter	p.S1315*	ENST00000257430	NM_000038.5	1315	tCa/tAa	16/16	1	2	FACETS	0.636	0.521	0.767	0.636	0.521	0.767	SUBCLONAL	1	TRUE	1	0.14	2		571	808	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0060679-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	24	344	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.217	0.169	0.272	0.217	0.169	0.272	SUBCLONAL	1	TRUE	1	0.51	2		344	434	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0060679-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	85	287	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.768	0.682	0.859	0.768	0.682	0.859	SUBCLONAL	1	TRUE	1	0.51	2		287	434	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0060679-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	158	547	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.945	0.868	1	0.945	0.868	1	CLONAL	1	TRUE	1	0.51	2		547	656	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119762	70119763	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0060679-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	89	435	0	ENST00000245479.2:c.768dup	p.Arg257AlafsTer39	p.R257Afs*39	ENST00000245479	NM_000346.3	255	gag/gaGg	3/3	1	2	FACETS	0.776	0.691	0.865	0.776	0.691	0.865	SUBCLONAL	1	TRUE	1	0.51	2		435	450	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584582	52584583	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0060679-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	161	663	0	ENST00000394830.3:c.4430_4431del	p.Pro1477ArgfsTer31	p.P1477Rfs*31	ENST00000394830	NM_018313.4	1477	cCT/c	29/30	1	2	FACETS	0.83	0.762	0.9	0.83	0.762	0.9	CLONAL	1	TRUE	1	0.51	2		663	761	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612158	189612158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770997588	NA	P-0060679-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	174	607	0	ENST00000264731.3:c.1910G>A	p.Arg637His	p.R637H	ENST00000264731	NM_003722.4	637	cGt/cAt	14/14	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.51	2		607	668	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912159	114912159	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060679-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	86	409	0	ENST00000543371.1:c.1229A>G	p.His410Arg	p.H410R	ENST00000543371	NM_001198531.1	410	cAt/cGt	11/14	1	2	FACETS	0.594	0.526	0.666	0.594	0.526	0.666	SUBCLONAL	1	TRUE	1	0.51	2		409	568	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526083	66526083	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060679-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	238	579	0	ENST00000358598.2:c.914G>C	p.Arg305Pro	p.R305P	ENST00000358598	NM_212471.2	305	cGt/cCt	10/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.51	2		579	768	SUCCESS
APC	324	MSKCC	GRCh37	5	112151242	112151242	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060679-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	134	376	0	ENST00000257430.4:c.885del	p.Ser295ArgfsTer10	p.S295Rfs*10	ENST00000257430	NM_000038.5	295	agT/ag	9/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.51	2		376	485	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913294	NA	P-0060745-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	62	288	0	ENST00000371953.3:c.518G>C	p.Arg173Pro	p.R173P	ENST00000371953	NM_000314.4	173	cGc/cCc	6/9	0.49203498656333	1	FACETS	0.819	0.717	0.927	0.819	0.717	0.927	CLONAL	1	TRUE	0	0.49203498656333	1		288	232	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827934	40827934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61749502	NA	P-0060745-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	167	475	0	ENST00000373198.4:c.2494G>A	p.Ala832Thr	p.A832T	ENST00000373198	NM_133170.3	832	Gcc/Acc	17/32	0.248429498357556	5	FACETS	0.839	0.777	0.901	0.839	0.777	0.901	INDETERMINATE	3	TRUE	2	0.49203498656333	5		475	469	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481412	140481412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913353	NA	P-0060745-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	79	305	0	ENST00000288602.6:c.1396G>A	p.Gly466Arg	p.G466R	ENST00000288602	NM_004333.4	466	Gga/Aga	11/18	0.469124018838109	4	FACETS	1	0.971	1	0.662	0.586	0.742	CLONAL	1	TRUE	2	0.49203498656333	4		305	362	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347951	70347951	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060745-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	98	443	0	ENST00000374080.3:c.3190G>A	p.Gly1064Arg	p.G1064R	ENST00000374080		1064	Ggg/Agg	22/45	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.49203498656333	2		443	350	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575559	64575559	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060745-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	176	521	0	ENST00000312049.6:c.458A>C	p.Asp153Ala	p.D153A	ENST00000312049	NM_130799.2	153	gAc/gCc	3/10	NA	2	FACETS	1	0.941	1			1	INDETERMINATE	2	TRUE	NA	0.49203498656333	2		521	356	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560032	29560032	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060745-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	186	406	0	ENST00000356175.3:c.3509del	p.His1170ProfsTer14	p.H1170Pfs*14	ENST00000356175	NM_000267.3	1170	cAc/cc	27/57	0.49203498656333	4	FACETS	1	0.96	1			1	CLONAL	2	TRUE	NA	0.49203498656333	4		406	540	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872785	37872785	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060745-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	66	603	0	ENST00000269571.5:c.1664T>A	p.Val555Glu	p.V555E	ENST00000269571		555	gTg/gAg	14/27	0.49203498656333	2	FACETS	0.865	0.757	0.981	0.433	0.378	0.491	CLONAL	1	TRUE	0	0.49203498656333	2		603	310	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051601	13051601	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060745-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	91	549	0	ENST00000316448.5:c.860G>C	p.Gly287Ala	p.G287A	ENST00000316448	NM_004343.3	287	gGc/gCc	7/9	1	2	FACETS	0.927	0.829	1	0.927	0.829	1	CLONAL	1	TRUE	1	0.49203498656333	2		549	399	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68984803	68984803	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060745-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	45	317	0	ENST00000288368.4:c.1567C>T	p.Gln523Ter	p.Q523*	ENST00000288368	NM_024870.2	523	Cag/Tag	14/40	0.49203498656333	9	FACETS	0.785	0.659	0.926	0.112	0.094	0.133	CLONAL	1	TRUE	2	0.49203498656333	9		317	634	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868978	117868978	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060745-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	60	248	0	ENST00000297338.2:c.721A>G	p.Ile241Val	p.I241V	ENST00000297338	NM_006265.2	241	Atc/Gtc	7/14	0.49203498656333	9	FACETS	1	0.929	1	0.161	0.138	0.186	CLONAL	1	TRUE	2	0.49203498656333	9		248	589	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061129-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	76	612	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	FALSE	1	0.240544220272348	2		612	625	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061129-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	159	661	0	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	0.174182230919025	3	FACETS	0.849	0.779	0.923	0.849	0.779	0.923	CLONAL	2	FALSE	1	0.240544220272348	3		661	872	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778096	135778096	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203671	NA	P-0061129-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	63	464	0	ENST00000298552.3:c.2287C>T	p.Gln763Ter	p.Q763*	ENST00000298552	NM_001162426.1	763	Cag/Tag	18/23	0.232582929882813	1	FACETS	0.97	0.841	1	0.97	0.841	1	CLONAL	1	FALSE	0	0.240544220272348	1		464	475	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519927	NA	P-0061129-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	10	220	0	ENST00000263967.3:c.1625A>T	p.Glu542Val	p.E542V	ENST00000263967	NM_006218.2	542	gAa/gTa	10/21	1	2	FACETS	0.526	0.357	0.738	0.526	0.357	0.738	SUBCLONAL	1	FALSE	1	0.240544220272348	2		220	158	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184733	185184733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061129-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	37	515	0	ENST00000265026.3:c.1625C>T	p.Ser542Phe	p.S542F	ENST00000265026	NM_004721.4	542	tCt/tTt	10/14	1	2	FACETS	0.552	0.454	0.662	0.552	0.454	0.662	SUBCLONAL	1	FALSE	1	0.240544220272348	2		515	557	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211212	2211212	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0061129-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	33	560	0	ENST00000398665.3:c.1465+1G>T		p.X489_splice	ENST00000398665	NM_032482.2	489			1	2	FACETS	0.467	0.379	0.566	0.467	0.379	0.566	SUBCLONAL	1	FALSE	1	0.240544220272348	2		560	588	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426589	49426589	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061129-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	445	732	0	ENST00000301067.7:c.11899C>T	p.Gln3967Ter	p.Q3967*	ENST00000301067	NM_003482.3	3967	Caa/Taa	39/54	0.240544220272348	5	FACETS	1	0.978	1			1	CLONAL	4	FALSE	NA	0.240544220272348	5		732	1213	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437968	110437968	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061129-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	27	356	0	ENST00000375856.3:c.433G>C	p.Glu145Gln	p.E145Q	ENST00000375856	NM_003749.2	145	Gag/Cag	1/2	1	2	FACETS	0.831	0.664	1	0.831	0.664	1	CLONAL	1	FALSE	1	0.240544220272348	2		356	270	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43772132	43772132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1430354090	NA	P-0061129-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	30	433	0	ENST00000382044.4:c.583G>A	p.Val195Met	p.V195M	ENST00000382044	NM_001141980.1	195	Gtg/Atg	6/28	0.240544220272348	1	FACETS	0.498	0.4	0.608	0.498	0.4	0.608	SUBCLONAL	1	FALSE	0	0.240544220272348	1		433	441	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772254	68772254	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061129-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	27	539	1	ENST00000261769.5:c.103G>A	p.Glu35Lys	p.E35K	ENST00000261769	NM_004360.3	35	Gag/Aag	2/16	1	2	FACETS	0.434	0.345	0.537	0.434	0.345	0.537	SUBCLONAL	1	FALSE	1	0.240544220272348	2		540	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578548	7578563	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGAGTACTGTAGGAA	GGGAGTACTGTAGGAA	-	novel	NA	P-0061129-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	55	598	0	ENST00000269305.4:c.376-9_382del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	0.232582929882813	1	FACETS	0.668	0.571	0.774	0.668	0.571	0.774	SUBCLONAL	1	FALSE	0	0.240544220272348	1		598	602	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424011	47424011	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061129-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	126	501	0	ENST00000404338.3:c.2079A>T	p.Leu693Phe	p.L693F	ENST00000404338	NM_004491.4	693	ttA/ttT	1/6	0.174182230919025	3	FACETS	0.803	0.728	0.882	0.803	0.728	0.882	CLONAL	2	FALSE	1	0.240544220272348	3		501	731	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242266	98242266	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061129-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	51	509	0	ENST00000331920.6:c.1052C>T	p.Thr351Ile	p.T351I	ENST00000331920	NM_000264.3	351	aCt/aTt	7/24	1	2	FACETS	0.796	0.676	0.927	0.796	0.676	0.927	CLONAL	1	FALSE	1	0.240544220272348	2		509	533	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870202	44870209	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACAGAATG	ACAGAATG	-	novel	NA	P-0061129-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	10	82	0	ENST00000377967.4:c.385-4_388del		p.X129_splice	ENST00000377967	NM_021140.2	129		5/29	1	1	FACETS	0.778	0.532	1	0.778	0.532	1	CLONAL	1	FALSE	0	0.240544220272348	1		82	94	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0061438-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	78	297	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.670727575227785	2		297	213	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156719	20156719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061438-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	54	262	0	ENST00000379607.5:c.38G>A	p.Arg13His	p.R13H	ENST00000379607	NM_001412.3	13	cGc/cAc	2/7	1	2	FACETS	0.785	0.68	0.897	0.785	0.68	0.897	SUBCLONAL	1	TRUE	1	0.670727575227785	2		262	205	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50785016	50785016	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs148783236	NA	P-0061438-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	11	258	0	ENST00000307179.4:c.2353A>G	p.Thr785Ala	p.T785A	ENST00000307179		785	Act/Gct	15/20	1	2	FACETS	0.155	0.106	0.215	0.155	0.106	0.215	SUBCLONAL	1	TRUE	1	0.670727575227785	2		258	212	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856296	111856296	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061438-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	16	633	0	ENST00000341259.2:c.347C>T	p.Pro116Leu	p.P116L	ENST00000341259	NM_005475.2	116	cCc/cTc	2/8	1	2	FACETS	0.179	0.132	0.236	0.179	0.132	0.236	SUBCLONAL	1	TRUE	1	0.670727575227785	2		633	266	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790735	89790735	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs946884142	NA	P-0061438-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	254	811	0	ENST00000336032.3:c.122C>T	p.Pro41Leu	p.P41L	ENST00000336032	NM_006813.2	41	cCt/cTt	1/2	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.670727575227785	2		811	564	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790740	89790740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061438-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	245	808	0	ENST00000336032.3:c.127C>T	p.Pro43Ser	p.P43S	ENST00000336032	NM_006813.2	43	Ccc/Tcc	1/2	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.670727575227785	2		808	548	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790864	89790864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061438-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	193	729	2	ENST00000336032.3:c.251C>T	p.Ala84Val	p.A84V	ENST00000336032	NM_006813.2	84	gCc/gTc	1/2	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.670727575227785	2		731	488	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0061601-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	19	213	0	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	0.20072316111314	1	FACETS	0.767	0.584	0.981	0.767	0.584	0.981	CLONAL	1	TRUE	0	0.20072316111314	1		213	222	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578551	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061601-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	105	526	0	ENST00000269305.4:c.379T>A	p.Ser127Thr	p.S127T	ENST00000269305	NM_001126112.2	127	Tcc/Acc	5/11	0.171917754669119	3	FACETS	0.933	0.838	1			1	CLONAL	2	TRUE	NA	0.20072316111314	3		526	617	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291798	15291798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759991207	NA	P-0061601-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	39	577	0	ENST00000263388.2:c.2968G>A	p.Glu990Lys	p.E990K	ENST00000263388	NM_000435.2	990	Gag/Aag	18/33	0.20072316111314	1	FACETS	0.555	0.459	0.663	0.555	0.459	0.663	SUBCLONAL	1	TRUE	0	0.20072316111314	1		577	630	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971177	21971177	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913382	NA	P-0061634-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	232	618	0	ENST00000304494.5:c.181G>T	p.Glu61Ter	p.E61*	ENST00000304494	NM_000077.4	61	Gag/Tag	2/3	0.372310372720902	2	FACETS	0.984	0.923	1	0.984	0.923	1	CLONAL	2	TRUE	0	0.372003190032533	2		618	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs985033810	NA	P-0061634-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	294	474	0	ENST00000269305.4:c.731G>T	p.Gly244Val	p.G244V	ENST00000269305	NM_001126112.2	244	gGc/gTc	7/11	0.372310372720902	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	0	0.372003190032533	3		474	601	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381564	81381564	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061634-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	227	376	0	ENST00000222390.5:c.497G>T	p.Ser166Ile	p.S166I	ENST00000222390	NM_000601.4	166	aGc/aTc	5/18	0.372310372720902	4	FACETS	0.962	0.904	1	0.962	0.904	1	CLONAL	3	TRUE	1	0.372003190032533	4		376	580	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163878	47163878	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061634-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	128	534	0	ENST00000409792.3:c.2248G>T	p.Glu750Ter	p.E750*	ENST00000409792	NM_014159.6	750	Gaa/Taa	3/21	0.372310372720902	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.372003190032533	1		534	455	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220399	1220400	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0061634-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	250	614	0	ENST00000326873.7:c.492_493delinsTT	p.Glu165Ter	p.E165*	ENST00000326873	NM_000455.4	164	ctGGag/ctTTag	4/10	0.372310372720902	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.372003190032533	2		614	633	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716331	52716331	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061634-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	139	578	0	ENST00000322088.6:c.775G>T	p.Val259Phe	p.V259F	ENST00000322088	NM_014225.5	259	Gtc/Ttc	6/15	0.372310372720902	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.372003190032533	1		578	519	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607660	43607660	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061634-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	186	1040	0	ENST00000355710.3:c.1636G>T	p.Gly546Ter	p.G546*	ENST00000355710	NM_020975.4	546	Gga/Tga	8/20	0.32619879097357	3	FACETS	1	0.932	1	0.337	0.31	0.365	CLONAL	1	TRUE	0	0.372003190032533	3		1040	1173	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419080	419080	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061634-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	84	534	0	ENST00000399788.2:c.3267G>T	p.Arg1089Ser	p.R1089S	ENST00000399788	NM_001042603.1	1089	agG/agT	22/28	0.372310372720902	4	FACETS	0.797	0.704	0.898			1	SUBCLONAL	1	TRUE	NA	0.372003190032533	4		534	777	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610692	81610692	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061634-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	70	428	0	ENST00000298171.2:c.2290T>G	p.Leu764Val	p.L764V	ENST00000298171	NM_000369.2	764	Ttg/Gtg	10/10	0.372310372720902	2	FACETS	0.791	0.691	0.898	0.395	0.345	0.449	SUBCLONAL	1	TRUE	0	0.372003190032533	2		428	476	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503796	186503797	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0061634-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	138	484	0	ENST00000323963.5:c.474_475dup	p.Thr159IlefsTer10	p.T159Ifs*10	ENST00000323963		158	ggt/ggTAt	5/11	0.372310372720902	3	FACETS	0.835	0.764	0.909	0.835	0.764	0.909	CLONAL	2	TRUE	1	0.372003190032533	3		484	527	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120656	94120656	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061634-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	29	461	0	ENST00000369303.4:c.395A>G	p.Tyr132Cys	p.Y132C	ENST00000369303	NM_004440.3	132	tAt/tGt	3/17	NA	2	FACETS	0.342	0.274	0.42			1	INDETERMINATE	1	TRUE	NA	0.372003190032533	2		461	456	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279425	38279425	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061634-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	107	492	0	ENST00000425967.3:c.1064A>T	p.Glu355Val	p.E355V	ENST00000425967	NM_001174067.1	355	gAg/gTg	9/19	NA	2	FACETS	0.999	0.898	1			1	INDETERMINATE	1	TRUE	NA	0.372003190032533	2		492	576	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439366	149439368	+	missense_variant	Missense_Mutation	TNP	TTC	TTC	ATG	novel	NA	P-0061634-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	104	559	0	ENST00000286301.3:c.2027_2029delinsCAT	p.Arg676_Arg677delinsProTrp	p.R676_R677delinsPW	ENST00000286301	NM_005211.3	676	cGAAgg/cCATgg	15/22	1	2	FACETS	0.935	0.839	1	0.935	0.839	1	CLONAL	1	TRUE	1	0.372003190032533	2		559	598	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0061673-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	137	311	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.272828431455877	1	FACETS	0.943	0.864	1	1	0.991	1	CLONAL	2	FALSE	0	0.272828431455877	1		311	460	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0061673-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	282	557	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.153625171367684	3	FACETS	0.922	0.87	0.976	1	0.993	1	INDETERMINATE	3	FALSE	1	0.272828431455877	3		557	849	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0061673-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	143	329	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	0.272828431455877	2	FACETS	0.989	0.932	1	1	0.994	1	CLONAL	5	FALSE	0	0.272828431455877	2		329	212	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061673-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	442	500	0	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	0.272828431455877	2	FACETS	1	0.991	1	1	0.997	1	CLONAL	4	FALSE	0	0.272828431455877	2		500	747	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11194436	11194436	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	210	482	0	ENST00000361445.4:c.5218A>G	p.Lys1740Glu	p.K1740E	ENST00000361445	NM_004958.3	1740	Aag/Gag	37/58	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.61716292326714	2		482	659	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089778	27089778	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	234	566	0	ENST00000324856.7:c.2732+2T>C		p.X911_splice	ENST00000324856	NM_006015.4	911			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.61716292326714	2		566	692	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36824417	36824417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759918440	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	207	434	0	ENST00000373129.3:c.119G>A	p.Arg40His	p.R40H	ENST00000373129	NM_032017.1	40	cGt/cAt	4/12	1	2	FACETS	0.994	0.926	1	0.994	0.926	1	CLONAL	1	TRUE	1	0.61716292326714	2		434	675	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939417	36939417	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	277	649	0	ENST00000361632.4:c.433G>T	p.Glu145Ter	p.E145*	ENST00000361632		145	Gag/Tag	4/16	1	2	FACETS	0.993	0.935	1	0.993	0.935	1	CLONAL	1	TRUE	1	0.61716292326714	2		649	904	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797162	45797162	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	270	639	0	ENST00000450313.1:c.1253A>G	p.Lys418Arg	p.K418R	ENST00000450313	NM_012222.2	418	aAg/aGg	13/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.61716292326714	2		639	852	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46733130	46733130	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	154	405	0	ENST00000371975.4:c.892-1G>T		p.X298_splice	ENST00000371975	NM_003579.3	298			1	2	FACETS	0.883	0.813	0.956	0.883	0.813	0.956	CLONAL	1	TRUE	1	0.61716292326714	2		405	565	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400934	72400934	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	33	467	0	ENST00000357731.5:c.237del	p.Phe79LeufsTer18	p.F79Lfs*18	ENST00000357731	NM_173808.2	79	ttT/tt	2/7	1	2	FACETS	0.17	0.138	0.207	0.17	0.138	0.207	SUBCLONAL	1	TRUE	1	0.61716292326714	2		467	629	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843653	156843653	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371498291	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	322	715	1	ENST00000524377.1:c.1079C>T	p.Thr360Met	p.T360M	ENST00000524377	NM_002529.3	360	aCg/aTg	8/17	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.61716292326714	2		716	967	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306580	163306580	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	115	306	0	ENST00000271452.3:c.377A>G	p.Asn126Ser	p.N126S	ENST00000271452	NM_145697.2	126	aAc/aGc	6/14	1	2	FACETS	0.956	0.869	1	0.956	0.869	1	CLONAL	1	TRUE	1	0.61716292326714	2		306	390	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226561958	226561958	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	206	418	0	ENST00000366794.5:c.2039A>G	p.Glu680Gly	p.E680G	ENST00000366794	NM_001618.3	680	gAa/gGa	14/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.61716292326714	2		418	605	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230468700	230468700	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759059657	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	225	627	0	ENST00000391860.1:c.818C>T	p.Pro273Leu	p.P273L	ENST00000391860	NM_001258311.1	273	cCg/cTg	5/7	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.61716292326714	2		627	687	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717702	89717702	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	136	330	0	ENST00000371953.3:c.727T>C	p.Phe243Leu	p.F243L	ENST00000371953	NM_000314.4	243	Ttc/Ctc	7/9	1	2	FACETS	0.942	0.863	1	0.942	0.863	1	CLONAL	1	TRUE	1	0.61716292326714	2		330	468	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298192	123298192	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	183	455	0	ENST00000358487.5:c.662T>C	p.Val221Ala	p.V221A	ENST00000358487	NM_000141.4	221	gTg/gCg	6/18	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.61716292326714	2		455	585	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137202	64137202	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1448724977	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	269	582	1	ENST00000334205.4:c.1634C>T	p.Ala545Val	p.A545V	ENST00000334205	NM_003942.2	545	gCc/gTc	14/17	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.61716292326714	2		583	794	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066886	77066886	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	193	359	0	ENST00000356341.3:c.599T>C	p.Val200Ala	p.V200A	ENST00000356341	NM_002576.4	200	gTa/gCa	7/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.61716292326714	2		359	561	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196186	108196186	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786202583	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	153	393	0	ENST00000278616.4:c.6722A>G	p.Asn2241Ser	p.N2241S	ENST00000278616	NM_000051.3	2241	aAc/aGc	46/63	1	2	FACETS	0.953	0.878	1	0.953	0.878	1	CLONAL	1	TRUE	1	0.61716292326714	2		393	520	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691152	18691152	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	142	341	0	ENST00000266497.5:c.3263A>C	p.Asn1088Thr	p.N1088T	ENST00000266497		1088	aAc/aCc	23/31	1	2	FACETS	0.922	0.846	1	0.922	0.846	1	CLONAL	1	TRUE	1	0.61716292326714	2		341	499	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245708	46245708	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	110	625	0	ENST00000334344.6:c.3802A>G	p.Asn1268Asp	p.N1268D	ENST00000334344	NM_152641.2	1268	Aac/Gac	15/21	1	2	FACETS	0.454	0.407	0.503	0.454	0.407	0.503	SUBCLONAL	1	TRUE	1	0.61716292326714	2		625	786	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431874	49431874	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	262	700	2	ENST00000301067.7:c.9265del	p.Val3089TrpfsTer30	p.V3089Wfs*30	ENST00000301067	NM_003482.3	3089	Gtg/tg	34/54	1	2	FACETS	0.969	0.91	1	0.969	0.91	1	CLONAL	1	TRUE	1	0.61716292326714	2		702	876	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432396	49432396	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783729	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	271	695	0	ENST00000301067.7:c.8743C>T	p.Arg2915Ter	p.R2915*	ENST00000301067	NM_003482.3	2915	Cga/Tga	34/54	1	2	FACETS	0.998	0.939	1	0.998	0.939	1	CLONAL	1	TRUE	1	0.61716292326714	2		695	880	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69230484	69230484	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	139	350	0	ENST00000462284.1:c.873G>T	p.Glu291Asp	p.E291D	ENST00000462284	NM_002392.5	291	gaG/gaT	10/11	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.61716292326714	2		350	440	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813315	102813315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761462868	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	210	537	0	ENST00000307046.8:c.374G>A	p.Arg125His	p.R125H	ENST00000307046	NM_001111285.1	125	cGc/cAc	3/4	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.61716292326714	2		537	657	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120704	115120704	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	250	657	0	ENST00000257566.3:c.302A>G	p.Asp101Gly	p.D101G	ENST00000257566	NM_016569.3	101	gAc/gGc	1/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.61716292326714	2		657	739	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254265	133254265	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	175	373	0	ENST00000320574.5:c.619A>G	p.Thr207Ala	p.T207A	ENST00000320574	NM_006231.2	207	Acc/Gcc	7/49	1	2	FACETS	0.948	0.878	1	0.948	0.878	1	CLONAL	1	TRUE	1	0.61716292326714	2		373	598	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597587	28597588	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	117	367	0	ENST00000241453.7:c.2317dup	p.Arg773LysfsTer14	p.R773Kfs*14	ENST00000241453	NM_004119.2	773	agg/aAgg	19/24	0.61716292326714	1	FACETS	0.769	0.701	0.838	0.769	0.701	0.838	SUBCLONAL	1	TRUE	0	0.61716292326714	1		367	341	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937323	32937323	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1566245207	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	126	358	0	ENST00000380152.3:c.7984A>G	p.Thr2662Ala	p.T2662A	ENST00000380152		2662	Acg/Gcg	18/27	0.61716292326714	1	FACETS	0.998	0.92	1	0.998	0.92	1	CLONAL	1	TRUE	0	0.61716292326714	1		358	283	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027127	49027127	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	124	268	0	ENST00000267163.4:c.1696-2A>G		p.X566_splice	ENST00000267163	NM_000321.2	566			0.61716292326714	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.61716292326714	1		268	265	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81557457	81557457	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	133	340	0	ENST00000298171.2:c.437A>G	p.Lys146Arg	p.K146R	ENST00000298171	NM_000369.2	146	aAa/aGa	5/10	1	2	FACETS	0.998	0.914	1	0.998	0.914	1	CLONAL	1	TRUE	1	0.61716292326714	2		340	432	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571556	95571556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	156	411	0	ENST00000393063.1:c.3121C>T	p.His1041Tyr	p.H1041Y	ENST00000393063	NM_030621.3	1041	Cat/Tat	21/28	1	2	FACETS	0.999	0.921	1	0.999	0.921	1	CLONAL	1	TRUE	1	0.61716292326714	2		411	506	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95573957	95573957	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	146	354	0	ENST00000393063.1:c.2792T>C	p.Val931Ala	p.V931A	ENST00000393063	NM_030621.3	931	gTt/gCt	18/28	1	2	FACETS	0.96	0.882	1	0.96	0.882	1	CLONAL	1	TRUE	1	0.61716292326714	2		354	493	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241526	105241526	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	259	565	0	ENST00000349310.3:c.454T>C	p.Tyr152His	p.Y152H	ENST00000349310	NM_001014432.1	152	Tac/Cac	7/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.61716292326714	2		565	736	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40679379	40679379	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1434965351	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	165	321	0	ENST00000249776.8:c.457A>G	p.Thr153Ala	p.T153A	ENST00000249776	NM_033286.3	153	Act/Gct	4/9	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.61716292326714	2		321	518	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713250	43713250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1392592073	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	209	511	0	ENST00000382044.4:c.4223G>A	p.Arg1408His	p.R1408H	ENST00000382044	NM_001141980.1	1408	cGc/cAc	20/28	1	2	FACETS	0.984	0.918	1	0.984	0.918	1	CLONAL	1	TRUE	1	0.61716292326714	2		511	688	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43733727	43733727	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61758077	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	149	341	0	ENST00000382044.4:c.3095C>T	p.Ala1032Val	p.A1032V	ENST00000382044	NM_001141980.1	1032	gCc/gTc	15/28	1	2	FACETS	0.901	0.828	0.976	0.901	0.828	0.976	CLONAL	1	TRUE	1	0.61716292326714	2		341	536	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295019	91295019	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	137	320	0	ENST00000355112.3:c.802A>G	p.Asn268Asp	p.N268D	ENST00000355112	NM_000057.2	268	Aat/Gat	4/22	0.61716292326714	3	FACETS	1	0.945	1	0.522	0.477	0.569	CLONAL	1	TRUE	1	0.61716292326714	3		320	556	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250809	99250809	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	180	545	0	ENST00000268035.6:c.113A>G	p.Asp38Gly	p.D38G	ENST00000268035	NM_000875.3	38	gAc/gGc	2/21	0.61716292326714	3	FACETS	0.877	0.81	0.948	0.439	0.405	0.474	CLONAL	1	TRUE	1	0.61716292326714	3		545	870	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467770	99467770	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	185	522	0	ENST00000268035.6:c.2639T>A	p.Val880Glu	p.V880E	ENST00000268035	NM_000875.3	880	gTg/gAg	13/21	0.61716292326714	3	FACETS	0.866	0.8	0.935	0.433	0.4	0.468	CLONAL	1	TRUE	1	0.61716292326714	3		522	906	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647657	3647657	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs774532876	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	176	579	1	ENST00000294008.3:c.1406del	p.Pro469HisfsTer4	p.P469Hfs*4	ENST00000294008	NM_032444.2	469	cCa/ca	7/15	1	2	FACETS	0.794	0.734	0.857	0.794	0.734	0.857	SUBCLONAL	1	TRUE	1	0.61716292326714	2		580	718	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786797	3786797	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	159	435	0	ENST00000262367.5:c.4414T>C	p.Trp1472Arg	p.W1472R	ENST00000262367	NM_004380.2	1472	Tgg/Cgg	27/31	1	2	FACETS	0.961	0.887	1	0.961	0.887	1	CLONAL	1	TRUE	1	0.61716292326714	2		435	536	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129414	30129414	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	260	570	0	ENST00000263025.4:c.614T>C	p.Val205Ala	p.V205A	ENST00000263025	NM_002746.2	205	gTg/gCg	4/9	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.61716292326714	2		570	792	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845623	68845623	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	106	440	0	ENST00000261769.5:c.869A>G	p.Asp290Gly	p.D290G	ENST00000261769	NM_004360.3	290	gAc/gGc	7/16	1	2	FACETS	0.513	0.461	0.569	0.513	0.461	0.569	SUBCLONAL	1	TRUE	1	0.61716292326714	2		440	669	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828768	72828768	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	257	528	0	ENST00000268489.5:c.7813T>C	p.Ser2605Pro	p.S2605P	ENST00000268489	NM_006885.3	2605	Tca/Cca	9/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.61716292326714	2		528	729	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	217	736	1	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.81	0.754	0.868	0.81	0.754	0.868	CLONAL	1	TRUE	1	0.61716292326714	2		737	868	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346190	89346190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1003478010	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	241	670	0	ENST00000301030.4:c.6760G>A	p.Gly2254Arg	p.G2254R	ENST00000301030	NM_001256183.1	2254	Gga/Aga	9/13	1	2	FACETS	0.995	0.932	1	0.995	0.932	1	CLONAL	1	TRUE	1	0.61716292326714	2		670	785	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348230	89348230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	49	571	0	ENST00000301030.4:c.4720G>A	p.Gly1574Arg	p.G1574R	ENST00000301030	NM_001256183.1	1574	Ggg/Agg	9/13	1	2	FACETS	0.211	0.178	0.248	0.211	0.178	0.248	SUBCLONAL	1	TRUE	1	0.61716292326714	2		571	751	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216529	7216529	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	261	592	0	ENST00000380728.2:c.804+2T>C		p.X268_splice	ENST00000380728		268			0.61716292326714	1	FACETS	0.993	0.939	1	0.993	0.939	1	CLONAL	1	TRUE	0	0.61716292326714	1		592	589	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	193	447	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.61716292326714	1	FACETS	0.87	0.812	0.929	0.87	0.812	0.929	CLONAL	1	TRUE	0	0.61716292326714	1		447	497	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588751	29588751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760703505	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	140	373	0	ENST00000356175.3:c.4537C>T	p.Arg1513Ter	p.R1513*	ENST00000356175	NM_000267.3	1513	Cga/Tga	34/57	0.61716292326714	1	FACETS	0.862	0.795	0.93	0.862	0.795	0.93	CLONAL	1	TRUE	0	0.61716292326714	1		373	364	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667587	29667587	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	73	382	0	ENST00000356175.3:c.6923A>G	p.Asn2308Ser	p.N2308S	ENST00000356175	NM_000267.3	2308	aAc/aGc	46/57	0.61716292326714	1	FACETS	0.405	0.356	0.457	0.405	0.356	0.457	SUBCLONAL	1	TRUE	0	0.61716292326714	1		382	404	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40874831	40874831	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	208	383	0	ENST00000428826.2:c.469A>G	p.Lys157Glu	p.K157E	ENST00000428826		157	Aaa/Gaa	6/21	0.61716292326714	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.61716292326714	1		383	436	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246662	41246662	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs748675395	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	84	485	0	ENST00000357654.3:c.886A>T	p.Arg296Ter	p.R296*	ENST00000357654	NM_007294.3	296	Aga/Tga	10/23	0.61716292326714	1	FACETS	0.421	0.373	0.472	0.421	0.373	0.472	SUBCLONAL	1	TRUE	0	0.61716292326714	1		485	447	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858343	59858343	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs375246789	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	131	335	0	ENST00000259008.2:c.1652C>A	p.Ala551Glu	p.A551E	ENST00000259008	NM_032043.2	551	gCg/gAg	12/20	1	2	FACETS	0.994	0.91	1	0.994	0.91	1	CLONAL	1	TRUE	1	0.61716292326714	2		335	427	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526196	63526196	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	184	446	0	ENST00000307078.5:c.2430T>G	p.Asp810Glu	p.D810E	ENST00000307078	NM_004655.3	810	gaT/gaG	11/11	1	2	FACETS	0.953	0.884	1	0.953	0.884	1	CLONAL	1	TRUE	1	0.61716292326714	2		446	626	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526198	63526198	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140344858	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	201	495	0	ENST00000307078.5:c.2428G>A	p.Asp810Asn	p.D810N	ENST00000307078	NM_004655.3	810	Gat/Aat	11/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.61716292326714	2		495	629	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120022	70120022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	44	551	0	ENST00000245479.2:c.1024C>T	p.Pro342Ser	p.P342S	ENST00000245479	NM_000346.3	342	Ccg/Tcg	3/3	1	2	FACETS	0.21	0.176	0.249	0.21	0.176	0.249	SUBCLONAL	1	TRUE	1	0.61716292326714	2		551	678	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733010	74733010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	226	580	0	ENST00000359995.5:c.233C>T	p.Ala78Val	p.A78V	ENST00000359995	NM_001195427.1	78	gCc/gTc	1/3	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.61716292326714	2		580	717	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78617590	78617590	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	182	463	0	ENST00000306801.3:c.328T>C	p.Tyr110His	p.Y110H	ENST00000306801	NM_020761.2	110	Tac/Cac	3/34	1	2	FACETS	0.935	0.866	1	0.935	0.866	1	CLONAL	1	TRUE	1	0.61716292326714	2		463	631	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919472	78919472	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	195	401	0	ENST00000306801.3:c.3031A>G	p.Thr1011Ala	p.T1011A	ENST00000306801	NM_020761.2	1011	Acg/Gcg	26/34	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.61716292326714	2		401	630	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591880	48591880	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	218	538	0	ENST00000342988.3:c.1043T>C	p.Val348Ala	p.V348A	ENST00000342988	NM_005359.5	348	gTt/gCt	9/12	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.61716292326714	2		538	692	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210512	5210512	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	221	544	0	ENST00000357368.4:c.5455A>G	p.Ile1819Val	p.I1819V	ENST00000357368	NM_002850.3	1819	Atc/Gtc	35/38	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.61716292326714	2		544	695	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274314	5274314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761620469	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	180	538	0	ENST00000357368.4:c.133G>A	p.Val45Met	p.V45M	ENST00000357368	NM_002850.3	45	Gtg/Atg	3/38	1	2	FACETS	0.903	0.836	0.972	0.903	0.836	0.972	CLONAL	1	TRUE	1	0.61716292326714	2		538	646	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6270769	6270769	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	218	645	1	ENST00000252674.7:c.14G>A	p.Cys5Tyr	p.C5Y	ENST00000252674	NM_005934.3	5	tGc/tAc	2/12	1	2	FACETS	0.83	0.773	0.889	0.83	0.773	0.889	CLONAL	1	TRUE	1	0.61716292326714	2		646	851	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7120722	7120722	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1448499462	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	200	487	0	ENST00000302850.5:c.3568T>C	p.Tyr1190His	p.Y1190H	ENST00000302850	NM_000208.2	1190	Tac/Cac	20/22	1	2	FACETS	0.95	0.884	1	0.95	0.884	1	CLONAL	1	TRUE	1	0.61716292326714	2		487	682	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11019830	11019830	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	240	622	1	ENST00000327064.4:c.505A>G	p.Thr169Ala	p.T169A	ENST00000327064	NM_199141.1	169	Aca/Gca	4/16	1	2	FACETS	0.98	0.918	1	0.98	0.918	1	CLONAL	1	TRUE	1	0.61716292326714	2		623	794	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101976	11101976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555757709	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	224	505	0	ENST00000358026.2:c.1396C>T	p.Arg466Cys	p.R466C	ENST00000358026	NM_001128849.1	466	Cgc/Tgc	8/36	1	2	FACETS	0.973	0.909	1	0.973	0.909	1	CLONAL	1	TRUE	1	0.61716292326714	2		505	746	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132561	11132561	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555778797	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	220	598	0	ENST00000358026.2:c.2777A>G	p.Asn926Ser	p.N926S	ENST00000358026	NM_001128849.1	926	aAc/aGc	19/36	1	2	FACETS	0.887	0.827	0.948	0.887	0.827	0.948	CLONAL	1	TRUE	1	0.61716292326714	2		598	804	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629161	14629161	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	195	492	0	ENST00000254322.2:c.1A>G	p.Met1?	p.M1?	ENST00000254322	NM_006145.1	1	Atg/Gtg	1/3	1	2	FACETS	0.978	0.91	1	0.978	0.91	1	CLONAL	1	TRUE	1	0.61716292326714	2		492	646	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302448	15302448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750260409	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	233	658	0	ENST00000263388.2:c.823G>A	p.Val275Met	p.V275M	ENST00000263388	NM_000435.2	275	Gtg/Atg	6/33	1	2	FACETS	0.895	0.836	0.955	0.895	0.836	0.955	CLONAL	1	TRUE	1	0.61716292326714	2		658	844	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354182	15354182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	154	463	0	ENST00000263377.2:c.2698C>T	p.Leu900Phe	p.L900F	ENST00000263377	NM_058243.2	900	Ctc/Ttc	14/20	1	2	FACETS	0.914	0.841	0.989	0.914	0.841	0.989	CLONAL	1	TRUE	1	0.61716292326714	2		463	546	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15379832	15379832	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	135	359	0	ENST00000263377.2:c.307A>G	p.Thr103Ala	p.T103A	ENST00000263377	NM_058243.2	103	Acg/Gcg	3/20	1	2	FACETS	0.923	0.845	1	0.923	0.845	1	CLONAL	1	TRUE	1	0.61716292326714	2		359	474	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383717	15383717	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	220	602	0	ENST00000263377.2:c.194A>G	p.Tyr65Cys	p.Y65C	ENST00000263377	NM_058243.2	65	tAc/tGc	2/20	1	2	FACETS	0.892	0.832	0.954	0.892	0.832	0.954	CLONAL	1	TRUE	1	0.61716292326714	2		602	799	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792803	33792803	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1488417025	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	130	371	0	ENST00000498907.2:c.518T>C	p.Leu173Pro	p.L173P	ENST00000498907	NM_004364.3	173	cTg/cCg	1/1	1	2	FACETS	0.881	0.805	0.961	0.881	0.805	0.961	CLONAL	1	TRUE	1	0.61716292326714	2		371	478	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212177	36212177	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	122	332	0	ENST00000222270.7:c.1928G>A	p.Arg643Lys	p.R643K	ENST00000222270	NM_014727.1	643	aGg/aAg	3/37	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.61716292326714	2		332	373	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762854	40762855	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1444704050	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	34	512	0	ENST00000392038.2:c.153dup	p.Asn53LysfsTer77	p.N53Kfs*77	ENST00000392038	NM_001626.4	51	-/C	3/14	1	2	FACETS	0.17	0.138	0.206	0.17	0.138	0.206	SUBCLONAL	1	TRUE	1	0.61716292326714	2		512	648	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	315	658	0	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.61716292326714	2		658	977	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795600	42795600	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	276	835	0	ENST00000575354.2:c.2680T>C	p.Ser894Pro	p.S894P	ENST00000575354	NM_015125.3	894	Tcc/Ccc	10/20	1	2	FACETS	0.953	0.896	1	0.953	0.896	1	CLONAL	1	TRUE	1	0.61716292326714	2		835	939	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910250	50910250	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1313176102	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	42	411	0	ENST00000440232.2:c.1505A>G	p.Asp502Gly	p.D502G	ENST00000440232	NM_002691.3	502	gAc/gGc	13/27	1	2	FACETS	0.269	0.224	0.319	0.269	0.224	0.319	SUBCLONAL	1	TRUE	1	0.61716292326714	2		411	506	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714583	52714583	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	42	603	1	ENST00000322088.6:c.341C>T	p.Ala114Val	p.A114V	ENST00000322088	NM_014225.5	114	gCc/gTc	4/15	1	2	FACETS	0.193	0.16	0.229	0.193	0.16	0.229	SUBCLONAL	1	TRUE	1	0.61716292326714	2		604	706	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464460	25464460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779176507	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	147	484	0	ENST00000264709.3:c.2053G>A	p.Gly685Arg	p.G685R	ENST00000264709	NM_175629.2	685	Ggg/Agg	17/23	0.61716292326714	1	FACETS	0.915	0.847	0.984	0.915	0.847	0.984	CLONAL	1	TRUE	0	0.61716292326714	1		484	360	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451784	29451784	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs772809305	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	81	178	0	ENST00000389048.3:c.2781del	p.Cys928AlafsTer11	p.C928Afs*11	ENST00000389048	NM_004304.4	927	ggG/gg	16/29	0.61716292326714	1	FACETS	0.821	0.737	0.908	0.821	0.737	0.908	CLONAL	1	TRUE	0	0.61716292326714	1		178	221	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656984	47656984	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	125	363	0	ENST00000233146.2:c.1180T>C	p.Phe394Leu	p.F394L	ENST00000233146	NM_000251.2	394	Ttt/Ctt	7/16	0.61716292326714	1	FACETS	0.966	0.889	1	0.966	0.889	1	CLONAL	1	TRUE	0	0.61716292326714	1		363	290	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631819	67631819	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	179	401	0	ENST00000272342.5:c.2005A>G	p.Asn669Asp	p.N669D	ENST00000272342	NM_019002.3	669	Aat/Gat	5/6	0.61716292326714	1	FACETS	0.973	0.909	1	0.973	0.909	1	CLONAL	1	TRUE	0	0.61716292326714	1		401	412	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172172	99172172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372688727	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	240	689	0	ENST00000074304.5:c.1738G>A	p.Ala580Thr	p.A580T	ENST00000074304	NM_001134224.1	580	Gcc/Acc	17/26	1	2	FACETS	0.933	0.873	0.994	0.933	0.873	0.994	CLONAL	1	TRUE	1	0.61716292326714	2		689	834	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047382	128047382	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	221	470	0	ENST00000285398.2:c.540C>A	p.Cys180Ter	p.C180*	ENST00000285398	NM_000122.1	180	tgC/tgA	5/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.61716292326714	2		470	637	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198264857	198264857	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	158	414	0	ENST00000335508.6:c.2935T>C	p.Tyr979His	p.Y979H	ENST00000335508	NM_012433.2	979	Tat/Cat	20/25	1	2	FACETS	0.924	0.852	0.999	0.924	0.852	0.999	CLONAL	1	TRUE	1	0.61716292326714	2		414	554	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645459	215645459	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1172376225	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	212	487	0	ENST00000260947.4:c.1139A>G	p.Asn380Ser	p.N380S	ENST00000260947	NM_000465.2	380	aAc/aGc	4/11	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.61716292326714	2		487	675	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019228	31019228	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	202	482	0	ENST00000375687.4:c.823G>C	p.Ala275Pro	p.A275P	ENST00000375687	NM_015338.5	275	Gcc/Ccc	9/13	1	2	FACETS	0.96	0.894	1	0.96	0.894	1	CLONAL	1	TRUE	1	0.61716292326714	2		482	682	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	197	474	7	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.767	0.712	0.825	0.767	0.712	0.825	SUBCLONAL	1	TRUE	1	0.61716292326714	2		481	832	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022634	31022634	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	226	693	0	ENST00000375687.4:c.2119A>G	p.Thr707Ala	p.T707A	ENST00000375687	NM_015338.5	707	Acc/Gcc	13/13	1	2	FACETS	0.902	0.842	0.963	0.902	0.842	0.963	CLONAL	1	TRUE	1	0.61716292326714	2		693	812	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368214	31368214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775216151	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	231	613	0	ENST00000328111.2:c.85G>A	p.Asp29Asn	p.D29N	ENST00000328111	NM_006892.3	29	Gac/Aac	2/23	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.61716292326714	2		613	738	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739077	40739077	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	161	495	0	ENST00000373198.4:c.3207G>T	p.Trp1069Cys	p.W1069C	ENST00000373198	NM_133170.3	1069	tgG/tgT	24/32	1	2	FACETS	0.883	0.814	0.954	0.883	0.814	0.954	CLONAL	1	TRUE	1	0.61716292326714	2		495	591	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757459	40757459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303277916	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	169	499	1	ENST00000373198.4:c.2839C>T	p.Arg947Trp	p.R947W	ENST00000373198	NM_133170.3	947	Cgg/Tgg	20/32	1	2	FACETS	0.901	0.832	0.972	0.901	0.832	0.972	CLONAL	1	TRUE	1	0.61716292326714	2		500	608	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164578	36164578	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	183	476	0	ENST00000300305.3:c.1297A>G	p.Thr433Ala	p.T433A	ENST00000300305		433	Acc/Gcc	8/8	1	2	FACETS	0.977	0.906	1	0.977	0.906	1	CLONAL	1	TRUE	1	0.61716292326714	2		476	607	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574371	41574371	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	96	615	0	ENST00000263253.7:c.6656A>G	p.Tyr2219Cys	p.Y2219C	ENST00000263253	NM_001429.3	2219	tAc/tGc	31/31	0.349332140487971	1	FACETS	0.36	0.321	0.401	0.36	0.321	0.401	INDETERMINATE	1	TRUE	0	0.61716292326714	1		615	598	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266619	41266619	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	207	474	0	ENST00000349496.5:c.416T>C	p.Leu139Ser	p.L139S	ENST00000349496	NM_001904.3	139	tTg/tCg	4/15	0.61716292326714	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.61716292326714	1		474	462	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162561	47162561	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	161	461	0	ENST00000409792.3:c.3565A>G	p.Thr1189Ala	p.T1189A	ENST00000409792	NM_014159.6	1189	Acc/Gcc	3/21	0.61716292326714	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.61716292326714	1		461	354	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119562167	119562167	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	207	421	1	ENST00000316626.5:c.1169T>C	p.Leu390Pro	p.L390P	ENST00000316626		390	cTt/cCt	11/12	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.61716292326714	2		422	669	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200148	128200148	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	208	529	0	ENST00000341105.2:c.1157T>C	p.Leu386Pro	p.L386P	ENST00000341105	NM_032638.4	386	cTg/cCg	6/6	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.61716292326714	2		529	668	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670328	134670328	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	168	484	2	ENST00000398015.3:c.244del	p.Ala82ProfsTer12	p.A82Pfs*12	ENST00000398015	NM_004441.4	80	cGg/cg	3/16	1	2	FACETS	0.82	0.756	0.886	0.82	0.756	0.886	CLONAL	1	TRUE	1	0.61716292326714	2		486	664	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503738	186503738	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	167	366	0	ENST00000323963.5:c.415A>G	p.Thr139Ala	p.T139A	ENST00000323963		139	Aca/Gca	5/11	1	2	FACETS	0.936	0.865	1	0.936	0.865	1	CLONAL	1	TRUE	1	0.61716292326714	2		366	578	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1941386	1941386	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	147	392	1	ENST00000382891.5:c.1766del	p.Asn589IlefsTer9	p.N589Ifs*9	ENST00000382891	NM_133335.3	588	Aaa/aa	9/22	1	2	FACETS	0.911	0.837	0.988	0.911	0.837	0.988	CLONAL	1	TRUE	1	0.61716292326714	2		393	523	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	216	836	6	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	1	2	FACETS	0.923	0.861	0.987	0.923	0.861	0.987	CLONAL	1	TRUE	1	0.61716292326714	2		842	758	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133814	55133814	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	160	453	0	ENST00000257290.5:c.1027C>A	p.Pro343Thr	p.P343T	ENST00000257290	NM_006206.4	343	Cca/Aca	7/23	1	2	FACETS	0.885	0.815	0.957	0.885	0.815	0.957	CLONAL	1	TRUE	1	0.61716292326714	2		453	586	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161434	55161434	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	167	401	0	ENST00000257290.5:c.3265C>A	p.Leu1089Met	p.L1089M	ENST00000257290	NM_006206.4	1089	Ctg/Atg	23/23	1	2	FACETS	0.997	0.922	1	0.997	0.922	1	CLONAL	1	TRUE	1	0.61716292326714	2		401	543	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984933	55984933	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	156	368	0	ENST00000263923.4:c.196A>T	p.Asn66Tyr	p.N66Y	ENST00000263923	NM_002253.2	66	Aat/Tat	3/30	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.61716292326714	2		368	460	SUCCESS
REST	5978	MSKCC	GRCh37	4	57797005	57797005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	315	795	0	ENST00000309042.7:c.1981C>T	p.Pro661Ser	p.P661S	ENST00000309042	NM_005612.4	661	Cct/Tct	4/4	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.61716292326714	2		795	936	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509110	66509110	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	103	298	0	ENST00000273854.3:c.217C>A	p.Leu73Met	p.L73M	ENST00000273854	NM_004439.5	73	Ctg/Atg	2/18	1	2	FACETS	0.816	0.736	0.9	0.816	0.736	0.9	CLONAL	1	TRUE	1	0.61716292326714	2		298	409	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157039	106157039	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs763505294	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	259	592	0	ENST00000380013.4:c.1940T>C	p.Val647Ala	p.V647A	ENST00000380013	NM_001127208.2	647	gTg/gCg	3/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.61716292326714	2		592	776	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130114	143130114	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	131	332	0	ENST00000262992.4:c.902T>C	p.Leu301Pro	p.L301P	ENST00000262992	NM_001101669.1	301	cTt/cCt	11/24	1	2	FACETS	0.933	0.853	1	0.933	0.853	1	CLONAL	1	TRUE	1	0.61716292326714	2		332	455	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144258415	144258415	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	71	440	0	ENST00000262995.4:c.72+2T>C		p.X24_splice	ENST00000262995	NM_207123.2	24			1	2	FACETS	0.403	0.352	0.458	0.403	0.352	0.458	SUBCLONAL	1	TRUE	1	0.61716292326714	2		440	571	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295752	1295752	+	upstream_gene_variant	5'Flank	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	252	749	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.901	0.845	0.959	0.901	0.845	0.959	CLONAL	1	TRUE	1	0.61716292326714	2		749	906	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31451666	31451666	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	132	334	0	ENST00000344624.3:c.2656A>G	p.Thr886Ala	p.T886A	ENST00000344624		886	Act/Gct	18/33	1	2	FACETS	0.887	0.811	0.967	0.887	0.811	0.967	CLONAL	1	TRUE	1	0.61716292326714	2		334	482	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31495475	31495475	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	55	446	1	ENST00000344624.3:c.1673T>C	p.Ile558Thr	p.I558T	ENST00000344624		558	aTc/aCc	9/33	1	2	FACETS	0.293	0.25	0.34	0.293	0.25	0.34	SUBCLONAL	1	TRUE	1	0.61716292326714	2		447	608	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589648	67589648	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	134	328	0	ENST00000274335.5:c.1411A>G	p.Thr471Ala	p.T471A	ENST00000274335		471	Acc/Gcc	10/15	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.61716292326714	2		328	434	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	167	542	7	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.972	0.898	1	0.972	0.898	1	CLONAL	1	TRUE	1	0.61716292326714	2		549	557	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522432	176522432	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	238	594	0	ENST00000292408.4:c.1621A>G	p.Thr541Ala	p.T541A	ENST00000292408	NM_213647.1	541	Acc/Gcc	12/18	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.61716292326714	2		594	719	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562196	176562196	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	249	541	0	ENST00000439151.2:c.92C>A	p.Pro31His	p.P31H	ENST00000439151	NM_022455.4	31	cCt/cAt	2/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.61716292326714	2		541	745	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045934	26045934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	320	790	0	ENST00000540144.1:c.296C>T	p.Ala99Val	p.A99V	ENST00000540144	NM_003531.2	99	gCc/gTc	1/1	0.61716292326714	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.61716292326714	1		790	688	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26046012	26046012	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	223	624	0	ENST00000540144.1:c.374T>A	p.Ile125Asn	p.I125N	ENST00000540144	NM_003531.2	125	aTc/aAc	1/1	0.61716292326714	1	FACETS	0.972	0.914	1	0.972	0.914	1	CLONAL	1	TRUE	0	0.61716292326714	1		624	514	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911141	29911141	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	75	367	0	ENST00000376809.5:c.440A>G	p.Tyr147Cys	p.Y147C	ENST00000376809	NM_002116.7	147	tAc/tGc	3/8	0.61716292326714	1	FACETS	0.568	0.502	0.637	0.568	0.502	0.637	SUBCLONAL	1	TRUE	0	0.61716292326714	1		367	296	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675588	30675588	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	227	568	0	ENST00000376406.3:c.2768T>C	p.Val923Ala	p.V923A	ENST00000376406	NM_014641.2	923	gTa/gCa	8/15	0.61716292326714	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.61716292326714	1		568	494	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324717	31324717	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs41555918	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	336	519	0	ENST00000412585.2:c.91T>C	p.Tyr31His	p.Y31H	ENST00000412585	NM_005514.6	31	Tat/Cat	2/8	0.61716292326714	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.61716292326714	1		519	616	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745343	43745343	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	259	592	0	ENST00000523873.1:c.256T>C	p.Cys86Arg	p.C86R	ENST00000523873		86	Tgc/Cgc	3/8	0.303148642703665	1	FACETS	0.855	0.805	0.905	0.855	0.805	0.905	INDETERMINATE	1	TRUE	0	0.61716292326714	1		592	679	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979300	93979300	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	40	467	0	ENST00000369303.4:c.1528G>T	p.Val510Leu	p.V510L	ENST00000369303	NM_004440.3	510	Gtg/Ttg	7/17	0.61716292326714	2	FACETS	0.214	0.177	0.255	0.107	0.088	0.128	SUBCLONAL	1	TRUE	0	0.61716292326714	2		467	606	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553171	106553171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368185616	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	229	575	0	ENST00000369096.4:c.1136C>T	p.Ala379Val	p.A379V	ENST00000369096	NM_001198.3	379	gCg/gTg	5/7	0.61716292326714	2	FACETS	0.951	0.89	1	0.476	0.445	0.508	CLONAL	1	TRUE	0	0.61716292326714	2		575	780	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015592	112015592	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	172	515	0	ENST00000368678.4:c.1250A>G	p.Tyr417Cys	p.Y417C	ENST00000368678		417	tAc/tGc	11/13	0.61716292326714	2	FACETS	0.914	0.845	0.985	0.457	0.422	0.493	CLONAL	1	TRUE	0	0.61716292326714	2		515	610	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129213	152129213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	271	615	0	ENST00000206249.3:c.166G>A	p.Glu56Lys	p.E56K	ENST00000206249	NM_000125.3	56	Gag/Aag	1/8	0.61716292326714	2	FACETS	1	0.988	1	0.591	0.557	0.625	CLONAL	1	TRUE	0	0.61716292326714	2		615	743	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469764	157469764	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	215	542	0	ENST00000346085.5:c.2558A>G	p.Tyr853Cys	p.Y853C	ENST00000346085	NM_020732.3	853	tAc/tGc	9/20	0.61716292326714	2	FACETS	0.997	0.931	1	0.498	0.465	0.533	CLONAL	1	TRUE	0	0.61716292326714	2		542	699	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240750	55240750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	272	600	0	ENST00000275493.2:c.1994G>A	p.Gly665Asp	p.G665D	ENST00000275493	NM_005228.3	665	gGc/gAc	17/28	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.61716292326714	2		600	840	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273119	55273119	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	211	550	0	ENST00000275493.2:c.3442A>G	p.Asn1148Asp	p.N1148D	ENST00000275493	NM_005228.3	1148	Aac/Gac	28/28	1	2	FACETS	0.997	0.93	1	0.997	0.93	1	CLONAL	1	TRUE	1	0.61716292326714	2		550	686	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92354966	92354966	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	181	447	0	ENST00000265734.4:c.511A>G	p.Ser171Gly	p.S171G	ENST00000265734	NM_001259.6	171	Agt/Ggt	4/8	1	2	FACETS	0.965	0.895	1	0.965	0.895	1	CLONAL	1	TRUE	1	0.61716292326714	2		447	608	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853011	151853011	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	174	504	0	ENST00000262189.6:c.11944A>G	p.Asn3982Asp	p.N3982D	ENST00000262189	NM_170606.2	3982	Aat/Gat	46/59	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.61716292326714	2		504	552	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372093	55372093	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	227	632	2	ENST00000297316.4:c.788del	p.Pro263ArgfsTer124	p.P263Rfs*124	ENST00000297316	NM_022454.3	261	ggC/gg	2/2	1	2	FACETS	0.932	0.871	0.995	0.932	0.871	0.995	CLONAL	1	TRUE	1	0.61716292326714	2		634	789	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68984765	68984765	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	149	319	0	ENST00000288368.4:c.1529T>C	p.Val510Ala	p.V510A	ENST00000288368	NM_024870.2	510	gTg/gCg	14/40	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.61716292326714	2		319	457	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738802	145738802	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269867447	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	356	897	2	ENST00000428558.2:c.2263C>T	p.Arg755Trp	p.R755W	ENST00000428558	NM_004260.3	755	Cgg/Tgg	14/22	1	2	FACETS	0.952	0.902	1	0.952	0.902	1	CLONAL	1	TRUE	1	0.61716292326714	2		899	1212	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739020	145739020	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	232	644	0	ENST00000428558.2:c.2135A>G	p.Asp712Gly	p.D712G	ENST00000428558	NM_004260.3	712	gAc/gGc	13/22	1	2	FACETS	0.94	0.879	1	0.94	0.879	1	CLONAL	1	TRUE	1	0.61716292326714	2		644	800	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742525	145742525	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	207	557	0	ENST00000428558.2:c.263A>G	p.Lys88Arg	p.K88R	ENST00000428558	NM_004260.3	88	aAg/aGg	4/22	1	2	FACETS	0.961	0.895	1	0.961	0.895	1	CLONAL	1	TRUE	1	0.61716292326714	2		557	698	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742534	145742534	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756838362	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	209	558	0	ENST00000428558.2:c.254C>T	p.Ala85Val	p.A85V	ENST00000428558	NM_004260.3	85	gCt/gTt	4/22	1	2	FACETS	0.937	0.873	1	0.937	0.873	1	CLONAL	1	TRUE	1	0.61716292326714	2		558	723	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069923	5069923	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	109	274	0	ENST00000381652.3:c.1514-2A>G		p.X505_splice	ENST00000381652	NM_004972.3	505			0.61716292326714	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.61716292326714	1		274	239	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8526642	8526642	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	111	307	0	ENST00000356435.5:c.553G>A	p.Gly185Ser	p.G185S	ENST00000356435		185	Ggt/Agt	6/35	0.61716292326714	1	FACETS	0.953	0.872	1	0.953	0.872	1	CLONAL	1	TRUE	0	0.61716292326714	1		307	261	SUCCESS
MTAP	4507	MSKCC	GRCh37	9	21818108	21818108	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1292959582	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	140	437	0	ENST00000380172.4:c.254G>A	p.Gly85Asp	p.G85D	ENST00000380172	NM_002451.3	85	gGc/gAc	4/8	0.61716292326714	1	FACETS	0.931	0.86	1	0.931	0.86	1	CLONAL	1	TRUE	0	0.61716292326714	1		437	337	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs767894241	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	151	452	0	ENST00000358127.4:c.76dup	p.Val26GlyfsTer49	p.V26Gfs*49	ENST00000358127	NM_001280556.1	26	gtt/gGtt	2/10	1	2	FACETS	0.752	0.689	0.816	0.752	0.689	0.816	SUBCLONAL	1	TRUE	1	0.61716292326714	2		452	651	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97876968	97876968	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	143	368	0	ENST00000289081.3:c.1097A>G	p.Gln366Arg	p.Q366R	ENST00000289081	NM_000136.2	366	cAg/cGg	12/15	1	2	FACETS	0.95	0.872	1	0.95	0.872	1	CLONAL	1	TRUE	1	0.61716292326714	2		368	488	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250040	110250040	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	185	494	0	ENST00000374672.4:c.635A>G	p.Tyr212Cys	p.Y212C	ENST00000374672	NM_004235.4	212	tAc/tGc	3/5	1	2	FACETS	0.908	0.842	0.977	0.908	0.842	0.977	CLONAL	1	TRUE	1	0.61716292326714	2		494	660	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402780	139402780	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	239	632	0	ENST00000277541.6:c.3229A>G	p.Thr1077Ala	p.T1077A	ENST00000277541	NM_017617.3	1077	Acc/Gcc	20/34	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.61716292326714	2		632	772	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404254	139404254	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1433433969	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	248	610	0	ENST00000277541.6:c.2900A>G	p.Tyr967Cys	p.Y967C	ENST00000277541	NM_017617.3	967	tAc/tGc	18/34	1	2	FACETS	0.998	0.937	1	0.998	0.937	1	CLONAL	1	TRUE	1	0.61716292326714	2		610	805	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412354	139412354	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	220	592	0	ENST00000277541.6:c.1291A>G	p.Asn431Asp	p.N431D	ENST00000277541	NM_017617.3	431	Aac/Gac	8/34	1	2	FACETS	0.926	0.864	0.989	0.926	0.864	0.989	CLONAL	1	TRUE	1	0.61716292326714	2		592	770	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923070	39923070	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	234	560	0	ENST00000378444.4:c.3638A>G	p.His1213Arg	p.H1213R	ENST00000378444	NM_001123385.1	1213	cAc/cGc	8/15	0.61716292326714	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.61716292326714	1		560	492	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937723	44937723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	156	319	0	ENST00000377967.4:c.2911C>T	p.Arg971Cys	p.R971C	ENST00000377967	NM_021140.2	971	Cgt/Tgt	19/29	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.61716292326714	2		319	438	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429036	47429036	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	234	612	0	ENST00000377045.4:c.1399T>C	p.Ser467Pro	p.S467P	ENST00000377045	NM_001654.4	467	Tca/Cca	13/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.61716292326714	2		612	742	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351469	70351469	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs755920101	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	188	412	0	ENST00000374080.3:c.4117A>G	p.Asn1373Asp	p.N1373D	ENST00000374080		1373	Aat/Gat	29/45	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.61716292326714	2		412	607	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70355035	70355035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	261	528	0	ENST00000374080.3:c.4957C>T	p.Pro1653Ser	p.P1653S	ENST00000374080		1653	Cca/Tca	36/45	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.61716292326714	2		528	701	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872102	76872102	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	28	354	0	ENST00000373344.5:c.5545T>C	p.Tyr1849His	p.Y1849H	ENST00000373344	NM_000489.3	1849	Tac/Cac	22/35	1	2	FACETS	0.231	0.185	0.285	0.231	0.185	0.285	SUBCLONAL	1	TRUE	1	0.61716292326714	2		354	392	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1296485	1296485	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	32	93	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.96	0.798	1	0.96	0.798	1	CLONAL	1	TRUE	1	0.61716292326714	2		93	108	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831357	72831358	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTG	rs34918837	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	145	561	0	ENST00000268489.5:c.5221_5223dup	p.Gln1741dup	p.Q1741dup	ENST00000268489	NM_006885.3	1741	-/CAA	9/10	1	2	FACETS	0.661	0.604	0.72	0.661	0.604	0.72	SUBCLONAL	1	TRUE	1	0.61716292326714	2		561	711	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659840	227659841	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0061835-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	68	386	0	ENST00000305123.5:c.3614dup	p.Pro1206ThrfsTer10	p.P1206Tfs*10	ENST00000305123	NM_005544.2	1205	cca/ccCa	1/2	1	2	FACETS	0.704	0.617	0.796	0.704	0.617	0.796	SUBCLONAL	1	TRUE	1	0.61716292326714	2		386	313	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692977	89692977	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1313989099	NA	P-0061933-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	122	237	0	ENST00000371953.3:c.461T>C	p.Phe154Ser	p.F154S	ENST00000371953	NM_000314.4	154	tTc/tCc	5/9	0.881511351012024	1	FACETS	0.927	0.874	0.977	0.927	0.874	0.977	CLONAL	1	TRUE	0	0.881511351012024	1		237	167	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691022	NA	P-0061933-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	452	552	0	ENST00000269305.4:c.1024del	p.Arg342GlufsTer3	p.R342Efs*3	ENST00000269305	NM_001126112.2	342	Cga/ga	10/11	0.881511351012024	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.881511351012024	2		552	488	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734026	58734026	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1361336223	NA	P-0061933-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	56	473	0	ENST00000305921.3:c.1084A>G	p.Met362Val	p.M362V	ENST00000305921	NM_003620.3	362	Atg/Gtg	5/6	0.881511351012024	3	FACETS	0.239	0.204	0.277	0.119	0.102	0.139	SUBCLONAL	1	TRUE	1	0.881511351012024	3		473	767	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982488	25982488	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061962-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	35	356	0	ENST00000435504.4:c.802G>C	p.Asp268His	p.D268H	ENST00000435504		268	Gac/Cac	9/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		356	425	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274900	41274900	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061962-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	67	468	0	ENST00000349496.5:c.1150A>C	p.Thr384Pro	p.T384P	ENST00000349496	NM_001904.3	384	Act/Cct	8/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		468	340	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0062049-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	94	287	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.37819506512444	2		287	446	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986707	36986707	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062049-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	101	643	0	ENST00000354822.5:c.982C>T	p.Gln328Ter	p.Q328*	ENST00000354822	NM_001079668.2	328	Cag/Tag	3/3	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.37819506512444	2		643	414	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405950	49405950	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062049-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	108	454	0	ENST00000418115.1:c.188A>G	p.Gln63Arg	p.Q63R	ENST00000418115	NM_001664.2	63	cAg/cGg	3/5	1	2	FACETS	0.963	0.867	1	0.963	0.867	1	CLONAL	1	TRUE	1	0.37819506512444	2		454	593	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144146	11144146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062049-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	122	530	0	ENST00000358026.2:c.3727C>T	p.Arg1243Trp	p.R1243W	ENST00000358026	NM_001128849.1	1243	Cgg/Tgg	26/36	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.37819506512444	2		530	560	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987031	36987031	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062049-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	90	510	0	ENST00000354822.5:c.658G>T	p.Glu220Ter	p.E220*	ENST00000354822	NM_001079668.2	220	Gag/Tag	3/3	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.37819506512444	2		510	442	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190523	32190523	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062049-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	126	653	0	ENST00000375023.3:c.216G>T	p.Gln72His	p.Q72H	ENST00000375023	NM_004557.3	72	caG/caT	3/30	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.37819506512444	2		653	589	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426097	47426097	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062049-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	115	600	0	ENST00000377045.4:c.617C>A	p.Pro206His	p.P206H	ENST00000377045	NM_001654.4	206	cCc/cAc	7/16	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.37819506512444	2		600	575	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0062129-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	60	344	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.236599547904642	4	FACETS	0.845	0.739	0.956	1	0.961	1	CLONAL	3	FALSE	2	0.294617628928071	4		344	208	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578480	+	missense_variant	Missense_Mutation	DNP	GT	GT	AA	novel	NA	P-0062129-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	189	680	2	ENST00000269305.4:c.450_451delinsTT	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	150	acACcc/acTTcc	5/11	0.257686471263388	2	FACETS	0.788	0.73	0.849	0.788	0.73	0.849	SUBCLONAL	2	FALSE	0	0.294617628928071	2		682	814	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160158	22160158	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062129-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	37	521	0	ENST00000215832.6:c.473A>G	p.Asn158Ser	p.N158S	ENST00000215832	NM_002745.4	158	aAc/aGc	3/9	0.172340563584803	1	FACETS	0.332	0.272	0.398	0.332	0.272	0.398	INDETERMINATE	1	FALSE	0	0.294617628928071	1		521	646	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498465	89498465	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062129-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	63	437	0	ENST00000336596.2:c.2437G>A	p.Val813Ile	p.V813I	ENST00000336596	NM_005233.5	813	Gtt/Att	14/17	1	2	FACETS	0.839	0.726	0.96	0.839	0.726	0.96	CLONAL	1	FALSE	1	0.294617628928071	2		437	510	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178217	142178217	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062129-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	25	363	0	ENST00000350721.4:c.7201A>G	p.Met2401Val	p.M2401V	ENST00000350721	NM_001184.3	2401	Atg/Gtg	43/47	1	2	FACETS	0.908	0.721	1	0.908	0.721	1	CLONAL	1	FALSE	1	0.294617628928071	2		363	187	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168694	32168694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143040647	NA	P-0062149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	138	492	0	ENST00000375023.3:c.4229G>A	p.Arg1410His	p.R1410H	ENST00000375023	NM_004557.3	1410	cGc/cAc	23/30	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.706226373560259	2		492	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577557	7577558	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGAACTGTTACACATGTAGTTGTAGTGGATGGT	novel	NA	P-0062149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	94	406	0	ENST00000269305.4:c.691_723dup	p.Thr231_Ser241dup	p.T231_S241dup	ENST00000269305	NM_001126112.2	231	-/ACCATCCACTACAACTACATGTGTAACAGTTCC	7/11	0.68850549894644	1	FACETS	0.514	0.462	0.569	0.514	0.462	0.569	SUBCLONAL	1	TRUE	0	0.706226373560259	1		406	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	241	691	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.976	0.921	1	0.976	0.921	1	CLONAL	1	TRUE	1	0.906101229799573	2		691	545	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322583	39322585	+	missense_variant	Missense_Mutation	TNP	TTC	TTC	GTT	novel	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	199	389	0	ENST00000373001.3:c.407_409delinsAAC	p.Gly136_Thr137delinsGluPro	p.G136_T137delinsEP	ENST00000373001	NM_022157.3	136	gGAAca/gAACca	2/7	0.906101229799573	3	FACETS	1	0.972	1	0.539	0.502	0.577	CLONAL	1	TRUE	1	0.906101229799573	3		389	592	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736316	243736316	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	272	437	0	ENST00000263826.5:c.731C>T	p.Ser244Phe	p.S244F	ENST00000263826	NM_005465.4	244	tCt/tTt	8/13	1	2	FACETS	0.978	0.925	1	0.978	0.925	1	CLONAL	1	TRUE	1	0.906101229799573	2		437	614	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933464	100933464	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	147	298	0	ENST00000325455.5:c.1926C>A	p.Phe642Leu	p.F642L	ENST00000325455	NM_001202474.3	642	ttC/ttA	4/8	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.906101229799573	2		298	316	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374399	118374399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	295	551	0	ENST00000534358.1:c.7792G>A	p.Asp2598Asn	p.D2598N	ENST00000534358	NM_005933.3	2598	Gac/Aac	27/36	0.906101229799573	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.906101229799573	1		551	345	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025536	1025536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	262	508	0	ENST00000358495.3:c.839C>T	p.Ser280Phe	p.S280F	ENST00000358495	NM_134424.2	280	tCc/tTc	9/12	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.906101229799573	2		508	554	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905387	11905387	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	209	322	0	ENST00000396373.4:c.37G>A	p.Glu13Lys	p.E13K	ENST00000396373	NM_001987.4	13	Gaa/Aaa	2/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.906101229799573	2		322	453	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434612	49434612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1401415779	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	280	608	0	ENST00000301067.7:c.6941C>T	p.Thr2314Ile	p.T2314I	ENST00000301067	NM_003482.3	2314	aCc/aTc	31/54	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.906101229799573	2		608	613	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434964	49434964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	262	572	0	ENST00000301067.7:c.6589C>T	p.Pro2197Ser	p.P2197S	ENST00000301067	NM_003482.3	2197	Ccc/Tcc	31/54	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.906101229799573	2		572	565	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636188	28636188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	247	413	0	ENST00000241453.7:c.184G>A	p.Asp62Asn	p.D62N	ENST00000241453	NM_004119.2	62	Gac/Aac	3/24	1	2	FACETS	0.999	0.943	1	0.999	0.943	1	CLONAL	1	TRUE	1	0.906101229799573	2		413	546	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951052	48951052	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	152	217	0	ENST00000267163.4:c.1216-2A>T		p.X406_splice	ENST00000267163	NM_000321.2	406			0.906101229799573	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.906101229799573	2		217	166	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675047	40675048	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	167	414	0	ENST00000249776.8:c.11_12delinsTT	p.Pro4Leu	p.P4L	ENST00000249776	NM_033286.3	4	cCC/cTT	1/9	0.866361536852887	1	FACETS	0.921	0.878	0.961	0.921	0.878	0.961	CLONAL	1	TRUE	0	0.906101229799573	1		414	219	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43767835	43767835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	309	513	0	ENST00000382044.4:c.1013C>T	p.Ser338Phe	p.S338F	ENST00000382044	NM_001141980.1	338	tCc/tTc	9/28	0.866361536852887	1	FACETS	0.99	0.96	1	0.99	0.96	1	CLONAL	1	TRUE	0	0.906101229799573	1		513	377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057519990	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	260	465	0	ENST00000269305.4:c.796G>T	p.Gly266Ter	p.G266*	ENST00000269305	NM_001126112.2	266	Gga/Tga	8/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.906101229799573	2		465	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578490	7578490	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	373	545	0	ENST00000269305.4:c.440T>C	p.Val147Ala	p.V147A	ENST00000269305	NM_001126112.2	147	gTt/gCt	5/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.906101229799573	2		545	757	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653044	29653044	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	308	481	0	ENST00000356175.3:c.4979A>C	p.Asn1660Thr	p.N1660T	ENST00000356175	NM_000267.3	1660	aAc/aCc	36/57	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.906101229799573	2		481	671	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216983	2216983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329819181	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	235	518	0	ENST00000398665.3:c.2438C>T	p.Pro813Leu	p.P813L	ENST00000398665	NM_032482.2	813	cCc/cTc	21/28	1	2	FACETS	0.931	0.877	0.986	0.931	0.877	0.986	CLONAL	1	TRUE	1	0.906101229799573	2		518	557	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117532	4117532	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	101	159	0	ENST00000262948.5:c.188A>G	p.Lys63Arg	p.K63R	ENST00000262948	NM_030662.3	63	aAg/aGg	2/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.906101229799573	2		159	201	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280072	18280072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	201	435	0	ENST00000222254.8:c.2155C>T	p.Pro719Ser	p.P719S	ENST00000222254	NM_005027.3	719	Ccg/Tcg	16/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.906101229799573	2		435	428	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214687	36214688	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	178	515	0	ENST00000222270.7:c.3113_3114delinsTT	p.Ala1038Val	p.A1038V	ENST00000222270	NM_014727.1	1038	gCC/gTT	8/37	1	2	FACETS	0.929	0.866	0.992	0.929	0.866	0.992	CLONAL	1	TRUE	1	0.906101229799573	2		515	423	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860794	45860794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762837634	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	324	691	0	ENST00000391945.4:c.1315G>A	p.Asp439Asn	p.D439N	ENST00000391945	NM_000400.3	439	Gac/Aac	14/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.906101229799573	2		691	702	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917048	50917048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs556196668	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	264	563	0	ENST00000440232.2:c.2300C>T	p.Ser767Leu	p.S767L	ENST00000440232	NM_002691.3	767	tCg/tTg	19/27	1	2	FACETS	0.983	0.929	1	0.983	0.929	1	CLONAL	1	TRUE	1	0.906101229799573	2		563	593	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921183	50921184	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	177	429	2	ENST00000440232.2:c.3303_3304delinsTT	p.Pro1102Ser	p.P1102S	ENST00000440232	NM_002691.3	1101	ccCCct/ccTTct	27/27	1	2	FACETS	0.921	0.859	0.985	0.921	0.859	0.985	CLONAL	1	TRUE	1	0.906101229799573	2		431	424	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738354	190738354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	113	270	0	ENST00000441310.2:c.2606G>A	p.Arg869Lys	p.R869K	ENST00000441310	NM_000534.4	869	aGa/aAa	12/13	1	2	FACETS	0.931	0.852	1	0.931	0.852	1	CLONAL	1	TRUE	1	0.906101229799573	2		270	268	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561124	9561124	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	269	453	0	ENST00000353224.5:c.658C>T	p.Gln220Ter	p.Q220*	ENST00000353224	NM_177990.2	220	Cag/Tag	4/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.906101229799573	2		453	502	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162873	47162873	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	197	418	0	ENST00000409792.3:c.3253C>T	p.Pro1085Ser	p.P1085S	ENST00000409792	NM_014159.6	1085	Cct/Tct	3/21	0.906101229799573	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.906101229799573	1		418	233	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447676	187447676	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	319	643	0	ENST00000232014.4:c.517C>T	p.Pro173Ser	p.P173S	ENST00000232014	NM_001130845.1	173	Cct/Tct	5/10	0.906101229799573	3	FACETS	1	0.982	1	0.542	0.513	0.572	CLONAL	1	TRUE	1	0.906101229799573	3		643	943	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201686	66201687	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	166	447	0	ENST00000273854.3:c.2815_2816delinsTT	p.Pro939Leu	p.P939L	ENST00000273854	NM_004439.5	939	CCa/TTa	16/18	1	2	FACETS	0.872	0.81	0.935	0.872	0.81	0.935	CLONAL	1	TRUE	1	0.906101229799573	2		447	420	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190766	106190766	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1193684921	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	184	295	0	ENST00000380013.4:c.4045-1G>A		p.X1349_splice	ENST00000380013	NM_001127208.2	1349			1	2	FACETS	0.956	0.893	1	0.956	0.893	1	CLONAL	1	TRUE	1	0.906101229799573	2		295	425	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961034	79961034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs966254697	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	200	425	0	ENST00000265081.6:c.431C>T	p.Ser144Phe	p.S144F	ENST00000265081	NM_002439.4	144	tCt/tTt	3/24	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.906101229799573	2		425	415	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499039	149499039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	215	418	0	ENST00000261799.4:c.2789C>T	p.Ser930Phe	p.S930F	ENST00000261799	NM_002609.3	930	tCc/tTc	20/23	1	2	FACETS	0.972	0.914	1	0.972	0.914	1	CLONAL	1	TRUE	1	0.906101229799573	2		418	488	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26046035	26046035	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	244	468	0	ENST00000540144.1:c.397G>A	p.Gly133Arg	p.G133R	ENST00000540144	NM_003531.2	133	Ggg/Agg	1/1	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.906101229799573	2		468	527	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967964	93967964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	213	337	0	ENST00000369303.4:c.1963C>T	p.Pro655Ser	p.P655S	ENST00000369303	NM_004440.3	655	Cca/Tca	11/17	1	2	FACETS	0.994	0.934	1	0.994	0.934	1	CLONAL	1	TRUE	1	0.906101229799573	2		337	473	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552940	106552941	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	295	627	1	ENST00000369096.4:c.905_906delinsAA	p.Arg302Gln	p.R302Q	ENST00000369096	NM_001198.3	302	cGG/cAA	5/7	1	2	FACETS	0.938	0.889	0.988	0.938	0.889	0.988	CLONAL	1	TRUE	1	0.906101229799573	2		628	694	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196881	138196882	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	227	474	0	ENST00000237289.4:c.543_544delinsAA	p.Met181_Ala182delinsIleThr	p.M181_A182delinsIT	ENST00000237289	NM_001270507.1	181	atGGcc/atAAcc	4/9	1	2	FACETS	0.919	0.864	0.975	0.919	0.864	0.975	CLONAL	1	TRUE	1	0.906101229799573	2		474	545	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55238896	55238897	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	135	280	0	ENST00000275493.2:c.1909_1910delinsTT	p.Pro637Leu	p.P637L	ENST00000275493	NM_005228.3	637	CCa/TTa	16/28	1	2	FACETS	0.967	0.894	1	0.967	0.894	1	CLONAL	1	TRUE	1	0.906101229799573	2		280	308	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513314	106513314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559655430	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	248	427	0	ENST00000359195.3:c.2218G>A	p.Glu740Lys	p.E740K	ENST00000359195	NM_002649.2	740	Gag/Aag	4/11	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.906101229799573	2		427	546	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843800	151843800	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	189	367	0	ENST00000262189.6:c.13915G>A	p.Glu4639Lys	p.E4639K	ENST00000262189	NM_170606.2	4639	Gag/Aag	53/59	1	2	FACETS	0.97	0.908	1	0.97	0.908	1	CLONAL	1	TRUE	1	0.906101229799573	2		367	430	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875031	151875031	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	420	350	0	ENST00000262189.6:c.7507C>T	p.Gln2503Ter	p.Q2503*	ENST00000262189	NM_170606.2	2503	Cag/Tag	38/59	1	2	FACETS	1	0.987	1	1	0.998	1	CLONAL	2	TRUE	1	0.906101229799573	2		350	460	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518312	8518312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1428808899	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	225	362	0	ENST00000356435.5:c.1079C>T	p.Pro360Leu	p.P360L	ENST00000356435		360	cCt/cTt	10/35	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.906101229799573	2		362	459	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528674	8528674	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	281	429	0	ENST00000356435.5:c.458C>G	p.Pro153Arg	p.P153R	ENST00000356435		153	cCg/cGg	4/35	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.906101229799573	2		429	603	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738163	133738164	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	174	360	0	ENST00000318560.5:c.563_564delinsTT	p.Ser188Phe	p.S188F	ENST00000318560	NM_005157.4	188	tCC/tTT	4/11	1	2	FACETS	0.944	0.88	1	0.944	0.88	1	CLONAL	1	TRUE	1	0.906101229799573	2		360	407	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564762	139564762	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	181	421	0	ENST00000308874.7:c.551G>A	p.Arg184Lys	p.R184K	ENST00000308874		184	aGg/aAg	7/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.906101229799573	2		421	373	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058499	72058499	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0062239-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	89	438	0	ENST00000357731.5:c.940+1G>A		p.X314_splice	ENST00000357731	NM_173808.2	314			1	2	FACETS	0.594	0.527	0.665	0.594	0.527	0.665	SUBCLONAL	1	TRUE	1	0.501995871560159	2		438	597	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945382	151945382	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062239-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	59	211	0	ENST00000262189.6:c.2137del	p.Glu713AsnfsTer5	p.E713Nfs*5	ENST00000262189	NM_170606.2	713	Gaa/aa	14/59	1	2	FACETS	0.805	0.698	0.919	0.805	0.698	0.919	CLONAL	1	TRUE	1	0.501995871560159	2		211	292	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341275	341275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219986773	NA	P-0062239-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	35	440	0	ENST00000262320.3:c.2209C>T	p.Arg737Trp	p.R737W	ENST00000262320	NM_003502.3	737	Cgg/Tgg	9/11	1	2	FACETS	0.265	0.217	0.32	0.265	0.217	0.32	SUBCLONAL	1	TRUE	1	0.501995871560159	2		440	526	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431670	49431670	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180928884	NA	P-0062239-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	116	795	0	ENST00000301067.7:c.9469G>A	p.Gly3157Arg	p.G3157R	ENST00000301067	NM_003482.3	3157	Gga/Aga	34/54	1	2	FACETS	0.529	0.476	0.585	0.529	0.476	0.585	SUBCLONAL	1	TRUE	1	0.501995871560159	2		795	874	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852412	42852419	+	frameshift_variant	Frame_Shift_Del	DEL	ATGTCCCT	ATGTCCCT	-	novel	NA	P-0062239-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	114	628	0	ENST00000398585.3:c.667_674del	p.Arg223GlyfsTer3	p.R223Gfs*3	ENST00000398585	NM_001135099.1	223	AGGGACATg/g	6/14	0.439471724949738	3	FACETS	0.608	0.547	0.674	0.304	0.273	0.337	SUBCLONAL	1	TRUE	1	0.501995871560159	3		628	934	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0062310-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	431	287	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.711440607636801	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	3	TRUE	1	0.711440607636801	4		287	691	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0062310-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	40	534	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.169	0.14	0.202	0.169	0.14	0.202	SUBCLONAL	1	TRUE	1	0.711440607636801	2		534	665	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045823	180045823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1446557372	NA	P-0062310-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	270	759	0	ENST00000261937.6:c.2948C>T	p.Ala983Val	p.A983V	ENST00000261937	NM_182925.4	983	gCg/gTg	21/30	1	2	FACETS	0.949	0.893	1	0.949	0.893	1	CLONAL	1	TRUE	1	0.711440607636801	2		759	800	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932519	39932520	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0062310-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	268	356	0	ENST00000378444.4:c.2079dup	p.Gly694TrpfsTer46	p.G694Wfs*46	ENST00000378444	NM_001123385.1	693	-/T	4/15	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.711440607636801	1		356	390	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0062541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	109	442	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	0.530596011199488	3	FACETS	0.962	0.868	1	0.481	0.434	0.531	CLONAL	1	TRUE	1	0.558542194646932	3		442	519	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814933	43814933	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0062541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	103	535	0	ENST00000372470.3:c.1469-1G>C		p.X490_splice	ENST00000372470	NM_005373.2	490			0.520264170285288	3	FACETS	1	0.963	1	0.573	0.516	0.632	CLONAL	1	TRUE	1	0.558542194646932	3		535	412	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490397	20490397	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0062541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	104	345	0	ENST00000346618.3:c.1136-2A>G		p.X379_splice	ENST00000346618	NM_001949.4	379			0.530596011199488	3	FACETS	1	0.946	1	0.538	0.484	0.594	CLONAL	1	TRUE	1	0.558542194646932	3		345	443	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0062671-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	53	311	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.273152677212807	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.21	1		311	345	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044877	47044877	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062671-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	81	729	0	ENST00000377604.3:c.2203G>T	p.Glu735Ter	p.E735*	ENST00000377604	NM_001204468.1	735	Gag/Tag	20/24	1	2	FACETS	0.768	0.675	0.869	0.768	0.675	0.869	SUBCLONAL	1	TRUE	1	0.21	2		729	1004	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285338	212285338	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0062671-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	39	353	0	ENST00000342788.4:c.2965-2A>G		p.X989_splice	ENST00000342788	NM_005235.2	989			1	2	FACETS	0.727	0.602	0.866	0.727	0.602	0.866	SUBCLONAL	1	TRUE	1	0.21	2		353	511	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874182	151874182	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062671-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	41	411	0	ENST00000262189.6:c.8356G>T	p.Asp2786Tyr	p.D2786Y	ENST00000262189	NM_170606.2	2786	Gat/Tat	38/59	0.142890683995608	3	FACETS	0.682	0.567	0.81	0.341	0.283	0.405	SUBCLONAL	1	TRUE	1	0.21	3		411	633	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343493	70343493	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062671-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	64	426	0	ENST00000374080.3:c.1667G>T	p.Gly556Val	p.G556V	ENST00000374080		556	gGc/gTc	12/45	1	2	FACETS	0.767	0.663	0.88	0.767	0.663	0.88	SUBCLONAL	1	TRUE	1	0.21	2		426	795	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578464	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	87	795	0	ENST00000269305.4:c.466del	p.Arg156AlafsTer14	p.R156Afs*14	ENST00000269305	NM_001126112.2	156	Cgc/gc	5/11	0.193583719371631	4	FACETS	1	0.933	1	0.54	0.477	0.608	CLONAL	1	FALSE	2	0.206044881351757	4		795	943	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs730881677	NA	P-0062730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	98	703	1	ENST00000304494.5:c.151-1G>T		p.X51_splice	ENST00000304494	NM_000077.4	51			0.206044881351757	0	FACETS	0.786	0.7	0.878			1	SUBCLONAL	1	FALSE	0	0.206044881351757	0		704	961	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600470	10600470	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	76	680	0	ENST00000171111.5:c.1385G>T	p.Gly462Val	p.G462V	ENST00000171111	NM_203500.1	462	gGg/gTg	4/6	0.206044881351757	3	FACETS	1	0.966	1	0.649	0.569	0.735	CLONAL	1	FALSE	1	0.206044881351757	3		680	627	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716316	52716316	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	40	695	0	ENST00000322088.6:c.760G>C	p.Asp254His	p.D254H	ENST00000322088	NM_014225.5	254	Gac/Cac	6/15	1	2	FACETS	0.532	0.441	0.634	0.532	0.441	0.634	SUBCLONAL	1	FALSE	1	0.206044881351757	2		695	730	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750448	41750449	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0062730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	49	727	2	ENST00000226382.2:c.179_180delinsAA	p.Leu60Gln	p.L60Q	ENST00000226382	NM_003924.3	60	cTC/cAA	1/3	0.150163145424597	3	FACETS	0.869	0.735	1	0.434	0.367	0.508	CLONAL	1	FALSE	1	0.206044881351757	3		729	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0062737-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	59	795	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	0.169489540497968	1	FACETS	0.941	0.809	1	0.941	0.809	1	CLONAL	1	TRUE	0	0.18	1		795	634	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028431	42028431	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0062737-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	40	651	0	ENST00000219905.7:c.3969T>G	p.Tyr1323Ter	p.Y1323*	ENST00000219905	NM_001164273.1	1323	taT/taG	13/24	1	2	FACETS	0.705	0.585	0.84	0.705	0.585	0.84	SUBCLONAL	1	TRUE	1	0.18	2		651	630	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0062805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	190	424	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.62334854227752	2		424	605	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266569	115266569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	70	300	0	ENST00000438362.2:c.1946G>A	p.Arg649His	p.R649H	ENST00000438362	NM_001242891.1	649	cGc/cAc	16/20	0.62334854227752	1	FACETS	0.497	0.437	0.561	0.497	0.437	0.561	SUBCLONAL	1	TRUE	0	0.62334854227752	1		300	311	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426814	49426814	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	230	622	0	ENST00000301067.7:c.11674C>T	p.Gln3892Ter	p.Q3892*	ENST00000301067	NM_003482.3	3892	Cag/Tag	39/54	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.62334854227752	2		622	719	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425688	49425688	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	217	626	0	ENST00000301067.7:c.12800del	p.Pro4267LeufsTer11	p.P4267Lfs*11	ENST00000301067	NM_003482.3	4267	cCt/ct	39/54	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.62334854227752	2		626	683	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696405	47696405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	155	367	0	ENST00000347630.2:c.418G>A	p.Asp140Asn	p.D140N	ENST00000347630	NM_001007230.1	140	Gat/Aat	6/11	0.62334854227752	1	FACETS	0.986	0.917	1	0.986	0.917	1	CLONAL	1	TRUE	0	0.62334854227752	1		367	347	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21341816	21341816	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756852884	NA	P-0062805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	168	461	0	ENST00000215739.8:c.344C>T	p.Pro115Leu	p.P115L	ENST00000215739	NM_006767.3	115	cCg/cTg	4/21	0.62334854227752	1	FACETS	0.89	0.827	0.953	0.89	0.827	0.953	CLONAL	1	TRUE	0	0.62334854227752	1		461	417	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709798	176710820	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AACAATTCAATGAAAATTGGAGCTTATATCTTTGAGTATTTTTTCTACAGGATTACAAGTTTGAACTCAGAAAAGTACATAATTCTTTTTTATTTTATTTTACAGTTGAGAAAATTGTTAAATATTTAATTATTTTACTGATAAGATTATGTAAATTTTTTTTTAAAATTATTTTGAGACAGAGTCTCGTTCTGTCACCCAGGCTGGAGTACAGTGGCATGATCTCGGCTTGCTGCAACCTCTGCCTCCTGGGTTCAAGCGATTCTTCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGCATCCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACAAAGTTTCACCATGTTGGCCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCTGCCTGCCTCGGACTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCGCACCTGGCCTTAGTTTTTATAATAAAACCCTTTCTTGGTATTTACCTTTGTAAACATTTCTCAAATTGTGCACTAGGATTTGTGAGATCTTCACTTCCAGATATTCTGATCTTACTTTGGGATTGGGACTCCGCATTAGTATTTAAATCTCCTTAGGTGATTTCTAATGTGCATCTGGGTTGAAACTACCTAAATAGAAAGTGGGACAAGCTGCTATTTGTAGGGCAGTGGTCCTCAAACTTCAATGTAGTCAGAAACCCCTGGCAGCCTTGTTATATATAACGCAGAATGCTGCACCCCACAGTCTCTGCTTTAGTGTATTTGAAGCACAACCCAGGAATTTGCATGTCTAACAAATTGCCAAATGGTGATGGTGCTGGTCCAGGGATCACACTTTGAGAACCAAAGTTCTTTGGGATCTTTTCTCTGAGAGGTTCAGTCTTTACAAATAGAAACTCCAACTTATTAGAGAGAATAGTCAAATTTTAATCCACAGCAGAGGTCTCAGGAAGTCTGATGTGTAGCTTCTTTTGGAATTCTAGGACCGAATCATTGATGCTGGTCCCAAAGGAAAC	AACAATTCAATGAAAATTGGAGCTTATATCTTTGAGTATTTTTTCTACAGGATTACAAGTTTGAACTCAGAAAAGTACATAATTCTTTTTTATTTTATTTTACAGTTGAGAAAATTGTTAAATATTTAATTATTTTACTGATAAGATTATGTAAATTTTTTTTTAAAATTATTTTGAGACAGAGTCTCGTTCTGTCACCCAGGCTGGAGTACAGTGGCATGATCTCGGCTTGCTGCAACCTCTGCCTCCTGGGTTCAAGCGATTCTTCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGCATCCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACAAAGTTTCACCATGTTGGCCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCTGCCTGCCTCGGACTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCGCACCTGGCCTTAGTTTTTATAATAAAACCCTTTCTTGGTATTTACCTTTGTAAACATTTCTCAAATTGTGCACTAGGATTTGTGAGATCTTCACTTCCAGATATTCTGATCTTACTTTGGGATTGGGACTCCGCATTAGTATTTAAATCTCCTTAGGTGATTTCTAATGTGCATCTGGGTTGAAACTACCTAAATAGAAAGTGGGACAAGCTGCTATTTGTAGGGCAGTGGTCCTCAAACTTCAATGTAGTCAGAAACCCCTGGCAGCCTTGTTATATATAACGCAGAATGCTGCACCCCACAGTCTCTGCTTTAGTGTATTTGAAGCACAACCCAGGAATTTGCATGTCTAACAAATTGCCAAATGGTGATGGTGCTGGTCCAGGGATCACACTTTGAGAACCAAAGTTCTTTGGGATCTTTTCTCTGAGAGGTTCAGTCTTTACAAATAGAAACTCCAACTTATTAGAGAGAATAGTCAAATTTTAATCCACAGCAGAGGTCTCAGGAAGTCTGATGTGTAGCTTCTTTTGGAATTCTAGGACCGAATCATTGATGCTGGTCCCAAAGGAAAC	-	novel	NA	P-0062805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	55	43	0	ENST00000439151.2:c.6009+216_6042del		p.X2003_splice	ENST00000439151	NM_022455.4	2003		20/23	0.62334854227752	1	FACETS	0.855	0.787	0.916	1	0.983	1	CLONAL	2	TRUE	0	0.62334854227752	1		43	71	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0062821-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	98	339	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.23146829052686	2	FACETS	1	0.98	1	0.727	0.65	0.809	CLONAL	1	FALSE	0	0.23562658867258	2		339	572	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0062821-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	9	313	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	0.23146829052686	2	FACETS	0.386	0.255	0.552	0.193	0.127	0.276	SUBCLONAL	1	FALSE	0	0.23562658867258	2		313	198	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971110	21971110	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062821-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	84	406	0	ENST00000304494.5:c.248A>T	p.His83Leu	p.H83L	ENST00000304494	NM_000077.4	83	cAc/cTc	2/3	0.23562658867258	1	FACETS	0.93	0.822	1	0.93	0.822	1	CLONAL	1	FALSE	0	0.23562658867258	1		406	676	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241961	72241961	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs368631212	NA	P-0062821-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	17	327	0	ENST00000357731.5:c.429C>A	p.Asp143Glu	p.D143E	ENST00000357731	NM_173808.2	143	gaC/gaA	3/7	1	2	FACETS	0.744	0.557	0.964	0.744	0.557	0.964	CLONAL	1	FALSE	1	0.23562658867258	2		327	194	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684350	29684350	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062821-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	11	309	0	ENST00000356175.3:c.7870G>T	p.Glu2624Ter	p.E2624*	ENST00000356175	NM_000267.3	2624	Gag/Tag	53/57	1	2	FACETS	0.543	0.376	0.75	0.543	0.376	0.75	SUBCLONAL	1	FALSE	1	0.23562658867258	2		309	172	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682531	37682531	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062821-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	55	353	0	ENST00000447079.4:c.3722C>G	p.Pro1241Arg	p.P1241R	ENST00000447079	NM_015083.1	1241	cCc/cGc	13/14	1	2	FACETS	0.785	0.671	0.909	0.785	0.671	0.909	CLONAL	1	FALSE	1	0.23562658867258	2		353	595	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946189	13946189	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062821-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	40	326	0	ENST00000405192.2:c.907G>T	p.Gly303Ter	p.G303*	ENST00000405192	NM_001163147.1	303	Gga/Tga	10/12	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	FALSE	1	0.23562658867258	2		326	281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0062859-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	308	581	0	ENST00000269305.4:c.920-2A>C		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.620664539898282	3	FACETS	0.979	0.95	1			1	CLONAL	3	TRUE	NA	0.77939748538251	3		581	374	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627670	14627670	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062859-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	111	623	0	ENST00000254322.2:c.400T>G	p.Phe134Val	p.F134V	ENST00000254322	NM_006145.1	134	Ttc/Gtc	2/3	0.412259894179197	6	FACETS	0.904	0.819	0.992	0.452	0.409	0.496	INDETERMINATE	2	TRUE	2	0.77939748538251	6		623	403	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099323	193099323	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062859-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	80	271	0	ENST00000367435.3:c.257T>C	p.Val86Ala	p.V86A	ENST00000367435	NM_024529.4	86	gTt/gCt	3/17	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.77939748538251	2		271	187	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417840	32417840	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062859-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	104	423	0	ENST00000332351.3:c.1212G>C	p.Lys404Asn	p.K404N	ENST00000332351	NM_024426.4	404	aaG/aaC	7/10	0.297240555331868	5	FACETS	1	0.981	1	0.471	0.424	0.519	INDETERMINATE	1	TRUE	2	0.77939748538251	5		423	410	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148732	119149397	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGTTTAATAAAAAATAAACCACTGTTGTGACATTTTTATATAAGCAAAATTTGTATAGGAAACAAGTCTTCACTTTTTCTGTTAACATTTATAATTGCAGTTATTTATTCAACTAATAGTCTTTTAATTTTTTTTAATCAAAGGAACAATATGAATTATACTGTGAGATGGGCTCCACATTCCAACTATGTAAAATATGTGCTGAAAATGATAAGGATGTAAAGATTGAGCCCTGTGGACACCTCATGTGCACATCCTGTCTTACATCCTGGCAGGTACGGATCTAAACAGCGACTTTTTTCAGCTATGTAATAACCTTGGAAAATTCGGTATTATATAGCCTTTACTGATACAAGGGGTGGCCTGGCTTTTGGGGTTAGGTTTAAACTTTTACTTTTTTTTGATCTCTAGGAAATGTATTTTCTAGTAGATTAATATTTTAAGTATTTTCAGATGCATCTGTTACTATCTTTTGCTTCTTCTGCAGGAATCAGAAGGTCAGGGCTGTCCTTTCTGCCGATGTGAAATTAAAGGTACTGAACCCATCGTGGTAGATCCGTTTGATCCTAGAGGGAGTGGCAGCCTGTTGAGGCAAGGAGCAGAGGGAGCTCCCTCCCCAAATTATGATGATGATGATGATGAACGAGCTGATGATACTCTCTTCA	TGGTTTAATAAAAAATAAACCACTGTTGTGACATTTTTATATAAGCAAAATTTGTATAGGAAACAAGTCTTCACTTTTTCTGTTAACATTTATAATTGCAGTTATTTATTCAACTAATAGTCTTTTAATTTTTTTTAATCAAAGGAACAATATGAATTATACTGTGAGATGGGCTCCACATTCCAACTATGTAAAATATGTGCTGAAAATGATAAGGATGTAAAGATTGAGCCCTGTGGACACCTCATGTGCACATCCTGTCTTACATCCTGGCAGGTACGGATCTAAACAGCGACTTTTTTCAGCTATGTAATAACCTTGGAAAATTCGGTATTATATAGCCTTTACTGATACAAGGGGTGGCCTGGCTTTTGGGGTTAGGTTTAAACTTTTACTTTTTTTTGATCTCTAGGAAATGTATTTTCTAGTAGATTAATATTTTAAGTATTTTCAGATGCATCTGTTACTATCTTTTGCTTCTTCTGCAGGAATCAGAAGGTCAGGGCTGTCCTTTCTGCCGATGTGAAATTAAAGGTACTGAACCCATCGTGGTAGATCCGTTTGATCCTAGAGGGAGTGGCAGCCTGTTGAGGCAAGGAGCAGAGGGAGCTCCCTCCCCAAATTATGATGATGATGATGATGAACGAGCTGATGATACTCTCTTCA	-	novel	NA	P-0062859-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	21	155	0	ENST00000264033.4:c.1096-142_1407del		p.X366_splice	ENST00000264033	NM_005188.3	366		8-9/16	0.77939748538251	4	FACETS	1	0.858	1	0.71	0.579	0.844	CLONAL	2	TRUE	1	0.77939748538251	4		155	45	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448201	49448201	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0062859-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	98	516	0	ENST00000301067.7:c.401-2A>C		p.X134_splice	ENST00000301067	NM_003482.3	134			0.77939748538251	3	FACETS	0.932	0.838	1	0.311	0.279	0.344	CLONAL	1	TRUE	0	0.77939748538251	3		516	375	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030411	49030414	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	novel	NA	P-0062859-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	154	392	0	ENST00000267163.4:c.1887_1890del	p.Glu629AspfsTer13	p.E629Dfs*13	ENST00000267163	NM_000321.2	629	gAGACa/ga	19/27	0.723016583068536	2	FACETS	0.945	0.898	0.991	0.945	0.898	0.991	CLONAL	2	TRUE	0	0.77939748538251	2		392	209	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582127	95582127	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062859-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	83	463	0	ENST00000393063.1:c.1784A>T	p.Asp595Val	p.D595V	ENST00000393063	NM_030621.3	595	gAt/gTt	12/28	0.210575797481269	3	FACETS	1	0.975	1	0.655	0.588	0.724	INDETERMINATE	1	TRUE	1	0.77939748538251	3		463	226	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921101	50921101	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs541931950	NA	P-0062859-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	71	368	0	ENST00000440232.2:c.3221G>A	p.Arg1074Gln	p.R1074Q	ENST00000440232	NM_002691.3	1074	cGg/cAg	27/27	0.446759711117861	3	FACETS	1	0.969	1	0.639	0.569	0.712	INDETERMINATE	1	TRUE	1	0.77939748538251	3		368	198	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817399	39817399	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062859-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	98	512	0	ENST00000288319.7:c.164A>T	p.Asp55Val	p.D55V	ENST00000288319	NM_182918.3	55	gAt/gTt	2/10	0.77939748538251	3	FACETS	0.901	0.81	0.996	0.45	0.405	0.498	CLONAL	1	TRUE	1	0.77939748538251	3		512	388	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439862	52439862	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062859-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	98	501	0	ENST00000460680.1:c.850G>C	p.Glu284Gln	p.E284Q	ENST00000460680	NM_004656.3	284	Gag/Cag	10/17	0.742420368425318	3	FACETS	0.929	0.836	1	0.465	0.418	0.514	CLONAL	1	TRUE	1	0.77939748538251	3		501	376	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31407045	31407045	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062859-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	23	389	0	ENST00000344624.3:c.3862C>T	p.Gln1288Ter	p.Q1288*	ENST00000344624		1288	Cag/Tag	31/33	0.347202101282799	6	FACETS	0.404	0.314	0.507	0.135	0.104	0.169	INDETERMINATE	1	TRUE	3	0.77939748538251	6		389	374	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31238016	31238016	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062859-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	122	749	0	ENST00000376228.5:c.866G>C	p.Gly289Ala	p.G289A	ENST00000376228	NM_002117.5	289	gGg/gCg	4/8	0.77939748538251	4	FACETS	0.974	0.883	1	0.487	0.441	0.535	CLONAL	1	TRUE	2	0.77939748538251	4		749	572	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2123746	2123746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062859-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	97	456	0	ENST00000349721.2:c.3790G>A	p.Asp1264Asn	p.D1264N	ENST00000349721	NM_003070.3	1264	Gat/Aat	27/34	0.679304221521489	2	FACETS	0.847	0.765	0.931	0.423	0.382	0.466	CLONAL	1	TRUE	0	0.77939748538251	2		456	294	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944368	76944400	+	inframe_deletion	In_Frame_Del	DEL	ATTGACCTGTTGTCCACAAGCAGTGCAGCTCAC	ATTGACCTGTTGTCCACAAGCAGTGCAGCTCAC	-	novel	NA	P-0062859-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	43	342	0	ENST00000373344.5:c.505_537del	p.Val169_Asn179del	p.V169_N179del	ENST00000373344	NM_000489.3	169	GTGAGCTGCACTGCTTGTGGACAACAGGTCAAT/-	7/35	0.711943253788041	2	FACETS	0.741	0.631	0.856	0.37	0.315	0.428	SUBCLONAL	1	TRUE	0	0.77939748538251	2		342	149	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0062860-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	8	852	1	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	0.241017022076713	4	FACETS	0.101	0.064	0.149	0.05	0.032	0.075	INDETERMINATE	1	FALSE	2	0.712743390981253	4		853	381	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380282	25380282	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886029	NA	P-0062860-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	8	421	0	ENST00000311936.3:c.176C>T	p.Ala59Val	p.A59V	ENST00000311936	NM_004985.3	59	gCa/gTa	3/5	0.712743390981253	6	FACETS	0.155	0.099	0.228	0.052	0.033	0.076	SUBCLONAL	1	FALSE	3	0.712743390981253	6		421	351	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061477	38061477	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062860-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	121	803	0	ENST00000250448.2:c.512C>T	p.Pro171Leu	p.P171L	ENST00000250448	NM_004496.3	171	cCg/cTg	2/2	0.283341298355222	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.712743390981253	0		803	346	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0062959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	21	329	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	0.147246408879935	2	FACETS	1	0.824	1	1	0.824	1	INDETERMINATE	2	TRUE	0	0.36464189448516	2		329	56	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	34	599	0	ENST00000269305.4:c.398T>G	p.Met133Arg	p.M133R	ENST00000269305	NM_001126112.2	133	aTg/aGg	5/11	0.147246408879935	2	FACETS	0.78	0.642	0.934	0.39	0.321	0.467	INDETERMINATE	1	TRUE	0	0.36464189448516	2		599	239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0062959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	91	710	0	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	0.147246408879935	2	FACETS	1	0.98	1	0.725	0.65	0.804	INDETERMINATE	1	TRUE	0	0.36464189448516	2		710	344	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202365	138202365	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368859219	NA	P-0062959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	18	706	0	ENST00000237289.4:c.2282G>A	p.Arg761His	p.R761H	ENST00000237289	NM_001270507.1	761	cGt/cAt	9/9	0.186736134894448	2	FACETS	0.475	0.358	0.611	0.237	0.179	0.306	INDETERMINATE	1	TRUE	0	0.36464189448516	2		706	208	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061209	38061210	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAGTAGCAGCCGTTCTCG	novel	NA	P-0062959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	15	626	0	ENST00000250448.2:c.762_779dup	p.Phe254_Tyr259dup	p.F254_Y259dup	ENST00000250448	NM_004496.3	254	ttg/ttCGAGAACGGCTGCTACTTg	2/2	0.346270402881503	3	FACETS	0.685	0.504	0.899	0.343	0.252	0.45	SUBCLONAL	1	TRUE	1	0.36464189448516	3		626	142	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0062998-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	225	504	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.910307360997655	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.910307360997655	3		504	234	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249009	55249010	+	inframe_insertion	In_Frame_Ins	INS	-	-	GACAACCCC	novel	NA	P-0062998-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	287	521	0	ENST00000275493.2:c.2308_2316dup	p.Asp770_Pro772dup	p.D770_P772dup	ENST00000275493	NM_005228.3	770	-/GACAACCCC	20/28	0.910307360997655	5	FACETS	1	0.988	1	0.821	0.786	0.856	CLONAL	3	TRUE	1	0.910307360997655	5		521	454	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249019	55249019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062998-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	313	509	0	ENST00000275493.2:c.2317C>T	p.His773Tyr	p.H773Y	ENST00000275493	NM_005228.3	773	Cac/Tac	20/28	0.910307360997655	5	FACETS	0.989	0.956	1	0.989	0.956	1	CLONAL	4	TRUE	1	0.910307360997655	5		509	411	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105901	27105901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062998-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	189	585	1	ENST00000324856.7:c.5512G>A	p.Asp1838Asn	p.D1838N	ENST00000324856	NM_006015.4	1838	Gac/Aac	20/20	0.910307360997655	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.910307360997655	3		586	289	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0063001-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	64	344	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.471028360514286	5	FACETS	0.92	0.815	1	0.69	0.611	0.772	CLONAL	3	FALSE	1	0.471028360514286	5		344	168	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0063001-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	271	684	0	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	0.370686843747868	3	FACETS	1	0.991	1	0.817	0.774	0.86	CLONAL	2	FALSE	0	0.471028360514286	3		684	580	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132522	11132522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778175819	NA	P-0063001-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	11	0	0	ENST00000358026.2:c.2738C>T	p.Pro913Leu	p.P913L	ENST00000358026	NM_001128849.1	913	cCg/cTg	19/36	0.370686843747868	3	FACETS	0.109	0.075	0.153	0.036	0.025	0.051	SUBCLONAL	1	FALSE	0	0.471028360514286	3		0	528	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1255443	1255443	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763381198	NA	P-0063001-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	313	689	0	ENST00000310581.5:c.3116C>T	p.Thr1039Met	p.T1039M	ENST00000310581	NM_198253.2	1039	aCg/aTg	14/16	0.395105503643334	3	FACETS	0.909	0.867	0.952	0.909	0.867	0.952	CLONAL	3	FALSE	0	0.471028360514286	3		689	602	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087396	27087397	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0063001-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	96	561	0	ENST00000324856.7:c.1970_1971insC	p.Ser658GlufsTer18	p.S658Efs*18	ENST00000324856	NM_006015.4	657	ctg/ctCg	5/20	0.471028360514286	3	FACETS	1	0.909	1	0.509	0.455	0.566	CLONAL	1	FALSE	1	0.471028360514286	3		561	495	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31390242	31390242	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063001-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	270	575	0	ENST00000328111.2:c.2197C>T	p.Arg733Ter	p.R733*	ENST00000328111	NM_006892.3	733	Cga/Tga	20/23	0.471028360514286	6	FACETS	0.991	0.934	1	0.991	0.934	1	CLONAL	3	FALSE	3	0.471028360514286	6		575	749	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0063163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	51	848	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	1	2	FACETS	0.6	0.509	0.699	0.6	0.509	0.699	SUBCLONAL	1	FALSE	1	0.267476708880971	2		848	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0063163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	10	543	2	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	1	2	FACETS	0.174	0.117	0.246	0.174	0.117	0.246	SUBCLONAL	1	FALSE	1	0.267476708880971	2		545	430	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987002	36987002	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	44	586	0	ENST00000354822.5:c.687C>G	p.His229Gln	p.H229Q	ENST00000354822	NM_001079668.2	229	caC/caG	3/3	1	2	FACETS	0.882	0.742	1	0.882	0.742	1	CLONAL	1	FALSE	1	0.267476708880971	2		586	373	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729094	66729099	+	inframe_deletion	In_Frame_Del	DEL	TGGAGA	TGGAGA	-	novel	NA	P-0063163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	56	588	0	ENST00000307102.5:c.303_308del	p.Glu102_Ile103del	p.E102_I103del	ENST00000307102	NM_002755.3	101	cTGGAGAtc/ctc	3/11	1	2	FACETS	0.784	0.672	0.906	0.784	0.672	0.906	CLONAL	1	FALSE	1	0.267476708880971	2		588	534	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188122	108188207	+	frameshift_variant	Frame_Shift_Del	DEL	GCCATATTCTTTCCGTCTATTTAAAAGGATTGGATTATGAAAATAAAGACTGGTGTCCTGAACTAGAAGAACTTCATTACCAAGCA	GCCATATTCTTTCCGTCTATTTAAAAGGATTGGATTATGAAAATAAAGACTGGTGTCCTGAACTAGAAGAACTTCATTACCAAGCA	-	novel	NA	P-0063163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	50	380	1	ENST00000278616.4:c.6223_6308del	p.His2075MetfsTer23	p.H2075Mfs*23	ENST00000278616	NM_000051.3	2074	tGCCATATTCTTTCCGTCTATTTAAAAGGATTGGATTATGAAAATAAAGACTGGTGTCCTGAACTAGAAGAACTTCATTACCAAGCA/t	43/63	0.0621866531886994	3	FACETS	0.93	0.79	1	0.465	0.395	0.542	INDETERMINATE	1	FALSE	1	0.267476708880971	3		381	456	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85742005	85742005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	32	521	0	ENST00000370580.1:c.31G>A	p.Glu11Lys	p.E11K	ENST00000370580	NM_003921.4	11	Gag/Aag	1/3	1	2	FACETS	0.577	0.468	0.699	0.577	0.468	0.699	SUBCLONAL	1	FALSE	1	0.267476708880971	2		521	415	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374477	118374477	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	107	851	0	ENST00000534358.1:c.7870G>A	p.Ala2624Thr	p.A2624T	ENST00000534358	NM_005933.3	2624	Gcc/Acc	27/36	0.0621866531886994	3	FACETS	1	0.974	1	0.632	0.567	0.7	INDETERMINATE	1	FALSE	1	0.267476708880971	3		851	718	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796723	57796723	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	29	678	0	ENST00000309042.7:c.1699G>C	p.Glu567Gln	p.E567Q	ENST00000309042	NM_005612.4	567	Gag/Cag	4/4	1	2	FACETS	0.378	0.302	0.464	0.378	0.302	0.464	SUBCLONAL	1	FALSE	1	0.267476708880971	2		678	574	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222568	157222568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	43	789	0	ENST00000346085.5:c.1835C>T	p.Pro612Leu	p.P612L	ENST00000346085	NM_020732.3	612	cCa/cTa	4/20	1	2	FACETS	0.504	0.421	0.597	0.504	0.421	0.597	SUBCLONAL	1	FALSE	1	0.267476708880971	2		789	638	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873937	151873937	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1475341096	NA	P-0063163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	36	624	0	ENST00000262189.6:c.8601G>C	p.Lys2867Asn	p.K2867N	ENST00000262189	NM_170606.2	2867	aaG/aaC	38/59	1	2	FACETS	0.484	0.397	0.582	0.484	0.397	0.582	SUBCLONAL	1	FALSE	1	0.267476708880971	2		624	556	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636843	8637078	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGCTGAAATAAAAAATAAACATCACAGTTAAATTGAAAACTGAAATACAGACTATTATCCTACTACCGCTGCTCTCCCCACCATCCTCAACCACACCGCCATCAAGACATACATTTTTACAATGCACTATGGGATTACAAAATTAGAAAAGCATCTTTTACTTTTGAGGGTAGTTTAAAGGGGAAGGACATAACTTTCTGGTTAAGTTATCTATTAGTGCTTTTATTGCTGAAATC	TGCTGAAATAAAAAATAAACATCACAGTTAAATTGAAAACTGAAATACAGACTATTATCCTACTACCGCTGCTCTCCCCACCATCCTCAACCACACCGCCATCAAGACATACATTTTTACAATGCACTATGGGATTACAAAATTAGAAAAGCATCTTTTACTTTTGAGGGTAGTTTAAAGGGGAAGGACATAACTTTCTGGTTAAGTTATCTATTAGTGCTTTTATTGCTGAAATC	-	novel	NA	P-0063163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	25	485	0	ENST00000356435.5:c.65-234_66del		p.X22_splice	ENST00000356435		22		2/35	0.267476708880971	1	FACETS	0.366	0.288	0.457	0.366	0.288	0.457	SUBCLONAL	1	FALSE	0	0.267476708880971	1		485	442	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225338975	225338976	+	frameshift_variant	Frame_Shift_Ins	INS	GT	GT	ACTTTGC	novel	NA	P-0063163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	48	402	0	ENST00000264414.4:c.2293_2294delinsGCAAAGT	p.Thr765AlafsTer5	p.T765Afs*5	ENST00000264414	NM_003590.4	765	ACa/GCAAAGTa	16/16	1	2	FACETS	0.909	0.77	1	0.909	0.77	1	CLONAL	1	FALSE	1	0.267476708880971	2		402	395	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0063164-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	81	516	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.208713254573268	2	FACETS	0.915	0.81	1	0.915	0.81	1	CLONAL	2	TRUE	0	0.208713254573268	2		516	424	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221313	1221314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs121913321	NA	P-0063164-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	161	593	1	ENST00000326873.7:c.842dup	p.Leu282AlafsTer3	p.L282Afs*3	ENST00000326873	NM_000455.4	279	ggc/ggCc	6/10	0.208713254573268	2	FACETS	0.986	0.906	1	0.986	0.906	1	CLONAL	2	TRUE	0	0.208713254573268	2		594	782	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0063164-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	83	603	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.208713254573268	1	FACETS	0.946	0.834	1	0.946	0.834	1	CLONAL	1	TRUE	0	0.208713254573268	1		603	753	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602301	10602301	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063164-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	148	584	0	ENST00000171111.5:c.1277A>G	p.Tyr426Cys	p.Y426C	ENST00000171111	NM_203500.1	426	tAt/tGt	3/6	0.208713254573268	2	FACETS	0.904	0.827	0.986	0.904	0.827	0.986	CLONAL	2	TRUE	0	0.208713254573268	2		584	784	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115740	8115740	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063164-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	56	486	0	ENST00000346208.3:c.1086G>T	p.Gln362His	p.Q362H	ENST00000346208		362	caG/caT	6/6	1	2	FACETS	0.78	0.667	0.903	0.78	0.667	0.903	CLONAL	1	TRUE	1	0.208713254573268	2		486	688	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230492996	230492996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063164-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	123	470	0	ENST00000391860.1:c.58C>T	p.Leu20Phe	p.L20F	ENST00000391860	NM_001258311.1	20	Ctc/Ttc	2/7	0.208713254573268	5	FACETS	0.888	0.803	0.979	0.592	0.535	0.653	CLONAL	2	TRUE	2	0.208713254573268	5		470	871	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396576	30396576	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063164-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	62	429	0	ENST00000331968.5:c.143del	p.Gly48AlafsTer10	p.G48Afs*10	ENST00000331968	NM_002742.2	48	gGc/gc	1/18	0.204804919046441	3	FACETS	1	0.918	1	0.363	0.313	0.417	CLONAL	1	TRUE	0	0.208713254573268	3		429	603	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149511637	149511637	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063164-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	127	440	0	ENST00000261799.4:c.1148T>C	p.Leu383Pro	p.L383P	ENST00000261799	NM_002609.3	383	cTg/cCg	8/23	0.208713254573268	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.208713254573268	2		440	569	SUCCESS
PHF6	84295	MSKCC	GRCh37	X	133551227	133551227	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063164-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	23	297	0	ENST00000332070.3:c.863C>G	p.Ala288Gly	p.A288G	ENST00000332070	NM_032458.2	288	gCt/gGt	9/10	1	2	FACETS	0.54	0.42	0.679	0.54	0.42	0.679	SUBCLONAL	1	TRUE	1	0.208713254573268	2		297	408	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0063247-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	439	529	2	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.777674972786454	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.813613915542776	2		531	538	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77931482	77931483	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0063247-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	70	548	0	ENST00000361507.4:c.1769_1770del	p.Pro590ArgfsTer16	p.P590Rfs*16	ENST00000361507	NM_080491.2	590	cCA/c	9/10	1	2	FACETS	0.271	0.236	0.309	0.271	0.236	0.309	SUBCLONAL	1	TRUE	1	0.813613915542776	2		548	634	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293818	1293818	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063247-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	364	822	0	ENST00000310581.5:c.1183G>T	p.Glu395Ter	p.E395*	ENST00000310581	NM_198253.2	395	Gag/Tag	2/16	0.236453559232189	1	FACETS	0.674	0.643	0.705	0.674	0.643	0.705	INDETERMINATE	1	TRUE	0	0.813613915542776	1		822	788	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0063308-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	24	176	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.814	1	1	0.814	1	CLONAL	1	FALSE	1	0.275257871391464	2		176	169	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852415	63852415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778543737	NA	P-0063308-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	49	626	0	ENST00000279873.7:c.3193G>A	p.Gly1065Arg	p.G1065R	ENST00000279873	NM_032199.2	1065	Gga/Aga	10/10	0.275257871391464	3	FACETS	0.689	0.583	0.806	0.344	0.291	0.403	SUBCLONAL	1	FALSE	1	0.275257871391464	3		626	588	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0063349-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1354	100	458	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.78077195186873	3	FACETS	0.245	0.218	0.274	0.122	0.109	0.137	SUBCLONAL	1	TRUE	1	0.78077195186873	3		458	1454	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063349-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	214	612	0				ENST00000310581	NM_198253.2	-/1132			0.37016012959052	4	FACETS	0.831	0.778	0.886	0.831	0.778	0.886	INDETERMINATE	2	TRUE	2	0.78077195186873	4		612	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0063349-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	514	580	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.78077195186873	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.78077195186873	1		581	682	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129169	64129169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746466314	NA	P-0063349-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	255	885	0	ENST00000334205.4:c.707C>T	p.Ser236Leu	p.S236L	ENST00000334205	NM_003942.2	236	tCg/tTg	7/17	1	2	FACETS	0.873	0.821	0.927	0.873	0.821	0.927	CLONAL	1	TRUE	1	0.78077195186873	2		885	748	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348912	11348912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765480579	NA	P-0063349-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	2279	831	0	ENST00000332029.2:c.424G>A	p.Glu142Lys	p.E142K	ENST00000332029	NM_003745.1	142	Gag/Aag	2/2	0.78077195186873	9	FACETS	0.986	0.975	0.996			1	CLONAL	8	TRUE	NA	0.78077195186873	9		831	2763	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49929248	49929248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763498892	NA	P-0063349-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	285	716	0	ENST00000296474.3:c.3295G>A	p.Gly1099Arg	p.G1099R	ENST00000296474	NM_002447.2	1099	Gga/Aga	15/20	0.3002469799388	3	FACETS	1	0.99	1	0.615	0.58	0.651	INDETERMINATE	1	TRUE	1	0.78077195186873	3		716	825	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831980	72831980	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063349-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	278	833	0	ENST00000268489.5:c.4601C>G	p.Thr1534Ser	p.T1534S	ENST00000268489	NM_006885.3	1534	aCt/aGt	9/10	0.337299637434125	4	FACETS	1	0.99	1	0.315	0.296	0.335	INDETERMINATE	1	TRUE	0	0.78077195186873	4		833	1005	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089914	16089914	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063349-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	339	639	0	ENST00000268712.3:c.196C>T	p.Arg66Ter	p.R66*	ENST00000268712	NM_006311.3	66	Cga/Tga	3/46	0.78077195186873	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.78077195186873	1		639	485	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17349200	17349200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063349-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	92	710	0	ENST00000375499.3:c.668G>A	p.Arg223Lys	p.R223K	ENST00000375499	NM_003000.2	223	aGa/aAa	7/8	0.78077195186873	3	FACETS	0.278	0.246	0.312	0.139	0.123	0.156	SUBCLONAL	1	TRUE	1	0.78077195186873	3		710	1180	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353782	40353782	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063349-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	434	933	0	ENST00000293328.3:c.2338C>T	p.Gln780Ter	p.Q780*	ENST00000293328	NM_012448.3	780	Cag/Tag	19/19	0.78077195186873	3	FACETS	1	0.981	1	0.529	0.504	0.555	CLONAL	1	TRUE	1	0.78077195186873	3		933	1461	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058004	27058004	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs969170076	NA	P-0063349-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	917	990	0	ENST00000324856.7:c.1712C>T	p.Ser571Leu	p.S571L	ENST00000324856	NM_006015.4	571	tCg/tTg	3/20	0.78077195186873	3	FACETS	0.975	0.949	1	0.975	0.949	1	CLONAL	2	TRUE	1	0.78077195186873	3		990	1674	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058013	27058015	+	stop_gained	Nonsense_Mutation	TNP	CCC	CCC	TTT	novel	NA	P-0063349-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	723	961	0	ENST00000324856.7:c.1721_1723delinsTTT	p.Ser574_Gln575delinsPheTer	p.S574_Q575delinsF*	ENST00000324856	NM_006015.4	574	tCCCag/tTTTag	3/20	0.78077195186873	3	FACETS	0.883	0.855	0.911	0.883	0.855	0.911	CLONAL	2	TRUE	1	0.78077195186873	3		961	1458	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699322	117699322	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063349-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	406	855	0	ENST00000369458.3:c.319C>G	p.Gln107Glu	p.Q107E	ENST00000369458	NM_024626.3	107	Caa/Gaa	3/6	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.78077195186873	2		855	897	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444241	49444241	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063349-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	126	1151	0	ENST00000301067.7:c.3130C>G	p.Pro1044Ala	p.P1044A	ENST00000301067	NM_003482.3	1044	Cct/Gct	11/54	1	2	FACETS	0.366	0.331	0.403	0.366	0.331	0.403	SUBCLONAL	1	TRUE	1	0.78077195186873	2		1151	882	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233202	69233202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063349-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	150	762	0	ENST00000462284.1:c.1067C>T	p.Ser356Leu	p.S356L	ENST00000462284	NM_002392.5	356	tCa/tTa	11/11	1	2	FACETS	0.687	0.631	0.745	0.687	0.631	0.745	SUBCLONAL	1	TRUE	1	0.78077195186873	2		762	559	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912387	32912387	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063349-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	18	362	0	ENST00000380152.3:c.3895G>A	p.Glu1299Lys	p.E1299K	ENST00000380152		1299	Gaa/Aaa	11/27	0.427272175779644	3	FACETS	0.28	0.211	0.361	0.14	0.105	0.181	INDETERMINATE	1	TRUE	1	0.78077195186873	3		362	229	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73649905	73649905	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063349-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	244	708	0	ENST00000377687.4:c.1255G>C	p.Glu419Gln	p.E419Q	ENST00000377687	NM_001730.3	419	Gag/Cag	4/4	0.649822579605776	3	FACETS	0.866	0.81	0.925	0.433	0.405	0.463	CLONAL	1	TRUE	1	0.78077195186873	3		708	1003	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831280	72831280	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063349-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	314	941	0	ENST00000268489.5:c.5301C>G	p.Ile1767Met	p.I1767M	ENST00000268489	NM_006885.3	1767	atC/atG	9/10	0.337299637434125	4	FACETS	1	0.991	1	0.312	0.294	0.33	INDETERMINATE	1	TRUE	0	0.78077195186873	4		941	1148	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805480	46805480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063349-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1322	128	963	0	ENST00000290295.7:c.476G>A	p.Arg159Gln	p.R159Q	ENST00000290295	NM_006361.5	159	cGa/cAa	1/2	0.78077195186873	3	FACETS	0.314	0.284	0.347	0.157	0.142	0.174	SUBCLONAL	1	TRUE	1	0.78077195186873	3		963	1450	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628380	86628380	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0063349-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	39	529	0	ENST00000274376.6:c.749C>G	p.Ser250Ter	p.S250*	ENST00000274376	NM_002890.2	250	tCa/tGa	3/25	1	2	FACETS	0.653	0.55	0.763	0.653	0.55	0.763	SUBCLONAL	1	TRUE	1	0.78077195186873	2		529	153	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978734	70978734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063349-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	44	599	0	ENST00000276594.2:c.919G>A	p.Glu307Lys	p.E307K	ENST00000276594	NM_024504.3	307	Gaa/Aaa	5/8	0.24059855012681	2	FACETS	0.235	0.197	0.278	0.118	0.098	0.139	INDETERMINATE	1	TRUE	0	0.78077195186873	2		599	479	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922945	39922945	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063349-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	510	388	0	ENST00000378444.4:c.3763G>C	p.Glu1255Gln	p.E1255Q	ENST00000378444	NM_001123385.1	1255	Gag/Cag	8/15	0.747432671590162	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.78077195186873	2		388	585	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410730	63410730	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063349-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	483	482	0	ENST00000330258.3:c.2437G>A	p.Asp813Asn	p.D813N	ENST00000330258	NM_152424.3	813	Gat/Aat	2/2	0.747432671590162	2	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.78077195186873	2		482	581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0063367-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	10	691	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.121273262681283	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		691	453	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0063367-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	7	285	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		285	233	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	773	810	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.863316294075326	5	FACETS	1	0.996	1	1	0.996	1	CLONAL	5	FALSE	0	0.863046476879188	5		810	810	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761414	59761417	+	frameshift_variant	Frame_Shift_Del	DEL	TTTG	TTTG	-	rs771028677	NA	P-0063492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	189	424	0	ENST00000259008.2:c.2990_2993del	p.Thr997ArgfsTer61	p.T997Rfs*61	ENST00000259008	NM_032043.2	997	aCAAAg/ag	20/20	0.85977019587333	4	FACETS	0.783	0.73	0.838	0.783	0.73	0.838	SUBCLONAL	2	FALSE	2	0.863046476879188	4		424	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0063545-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	567	640	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.428021137955186	3	FACETS	0.944	0.91	0.978	0.944	0.91	0.978	CLONAL	3	FALSE	0	0.423295095924992	3		640	1146	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063545-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	189	612	0				ENST00000310581	NM_198253.2	-/1132			0.366547099387081	5	FACETS	1	0.99	1	0.5	0.461	0.539	CLONAL	1	FALSE	2	0.423295095924992	5		612	974	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440372	52440372	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063545-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	348	768	0	ENST00000460680.1:c.680G>C	p.Arg227Pro	p.R227P	ENST00000460680	NM_004656.3	227	cGc/cCc	9/17	0.317375994556299	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	FALSE	2	0.423295095924992	4		768	1114	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380346	14380346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063545-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	50	621	0	ENST00000256196.4:c.71G>A	p.Gly24Asp	p.G24D	ENST00000256196		24	gGc/gAc	1/6	0.236798086019092	5	FACETS	0.479	0.405	0.56			1	INDETERMINATE	1	FALSE	NA	0.423295095924992	5		621	807	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412638	63412638	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369902795	NA	P-0063545-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	222	353	1	ENST00000330258.3:c.529C>T	p.Arg177Cys	p.R177C	ENST00000330258	NM_152424.3	177	Cgc/Tgc	2/2	0.262960407561217	2	FACETS	1	0.986	1			1	CLONAL	2	FALSE	NA	0.423295095924992	2		354	457	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878051	48878051	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0063545-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	278	688	0	ENST00000267163.4:c.3G>A	p.Met1?	p.M1?	ENST00000267163	NM_000321.2	1	atG/atA	1/27	0.372179764327172	2	FACETS	0.82	0.773	0.868	0.82	0.773	0.868	CLONAL	2	FALSE	0	0.423295095924992	2		688	801	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031994	26031994	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063545-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	42	0	0	ENST00000244661.2:c.295G>A	p.Ala99Thr	p.A99T	ENST00000244661	NM_003537.3	99	Gcc/Acc	1/1	0.428021137955186	3	FACETS	0.191	0.159	0.228	0.096	0.079	0.114	SUBCLONAL	1	FALSE	1	0.423295095924992	3		0	1256	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971073	21971074	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0063545-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	583	715	0	ENST00000304494.5:c.284_285del	p.Val95GlyfsTer24	p.V95Gfs*24	ENST00000304494	NM_000077.4	95	gTG/g	2/3	0.428021137955186	3	FACETS	0.943	0.91	0.976			1	CLONAL	3	FALSE	NA	0.423295095924992	3		715	1180	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196743	123196755	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCCTTTAGGTGC	TTCCTTTAGGTGC	-	novel	NA	P-0063545-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	88	175	0	ENST00000218089.9:c.1639-7_1644del		p.X547_splice	ENST00000218089	NM_001042749.1	547		18/35	0.262960407561217	2	FACETS	0.936	0.846	1			1	CLONAL	2	FALSE	NA	0.423295095924992	2		175	222	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56870579	56870579	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063545-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	47	505	0	ENST00000308159.5:c.1849G>C	p.Glu617Gln	p.E617Q	ENST00000308159	NM_014669.4	617	Gaa/Caa	17/22	0.24581329999218	5	FACETS	0.472	0.397	0.555	0.157	0.132	0.185	INDETERMINATE	1	FALSE	2	0.423295095924992	5		505	769	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40747856	40747856	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063545-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	260	679	0	ENST00000392038.2:c.562A>T	p.Ile188Phe	p.I188F	ENST00000392038	NM_001626.4	188	Atc/Ttc	6/14	0.428021137955186	3	FACETS	0.758	0.711	0.806	0.758	0.711	0.806	SUBCLONAL	2	FALSE	1	0.423295095924992	3		679	982	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96931057	96931057	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1573977946	NA	P-0063545-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	78	775	0	ENST00000258439.3:c.63C>A	p.Ser21Arg	p.S21R	ENST00000258439	NM_001193304.2	21	agC/agA	2/4	0.300401357998038	5	FACETS	0.536	0.469	0.608			1	SUBCLONAL	1	FALSE	NA	0.423295095924992	5		775	1124	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0063555-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	286	447	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.363159283657334	2	FACETS	0.987	0.933	1	0.987	0.933	1	CLONAL	2	TRUE	0	0.384342511282932	2		447	754	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524486	44524486	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063555-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	184	505	0	ENST00000291552.4:c.71T>C	p.Ile24Thr	p.I24T	ENST00000291552	NM_006758.2	24	aTt/aCt	2/8	0.374686119311238	4	FACETS	0.985	0.913	1	0.985	0.913	1	CLONAL	2	TRUE	2	0.384342511282932	4		505	673	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057056	180057056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142274156	NA	P-0063555-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	123	749	0	ENST00000261937.6:c.563G>A	p.Arg188Gln	p.R188Q	ENST00000261937	NM_182925.4	188	cGg/cAg	5/30	0.186036776537211	4	FACETS	1	0.925	1	0.513	0.464	0.566	INDETERMINATE	1	TRUE	2	0.384342511282932	4		749	863	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0063555-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	379	453	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.388183681256411	4	FACETS	0.926	0.887	0.966	0.926	0.887	0.966	CLONAL	4	TRUE	0	0.384342511282932	4		453	737	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226052	226052	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776193478	NA	P-0063559-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	39	82	0	ENST00000264932.6:c.511C>T	p.Arg171Cys	p.R171C	ENST00000264932	NM_004168.2	171	Cgt/Tgt	5/15	0.276354344375897	6	FACETS	0.974	0.837	1			1	CLONAL	5	FALSE	NA	0.276354344375897	6		82	90	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0063651-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	238	691	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.478302473188406	2	FACETS	0.862	0.812	0.913	0.862	0.812	0.913	CLONAL	2	TRUE	0	0.488478119018415	2		691	565	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941729	48941730	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0063651-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	109	268	0	ENST00000267163.4:c.1040_1041del	p.Ser347TyrfsTer5	p.S347Yfs*5	ENST00000267163	NM_000321.2	347	TCt/t	10/27	0.452616491980231	2	FACETS	0.907	0.831	0.984	0.907	0.831	0.984	CLONAL	2	TRUE	0	0.488478119018415	2		268	246	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714408	117714408	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs770589705	NA	P-0063651-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	127	393	0	ENST00000368508.3:c.1241T>C	p.Ile414Thr	p.I414T	ENST00000368508	NM_002944.2	414	aTt/aCt	11/43	0.154963580629853	2	FACETS	1	0.977	1	0.607	0.555	0.662	INDETERMINATE	1	TRUE	0	0.488478119018415	2		393	428	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464574	25464577	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	ONP	GCCC	GCCC	CCCA	novel	NA	P-0063651-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	110	497	0	ENST00000264709.3:c.1937-1_1939delinsTGGG		p.X646_splice	ENST00000264709	NM_175629.2	646		17/23	1	2	FACETS	0.892	0.805	0.983	0.892	0.805	0.983	CLONAL	1	TRUE	1	0.488478119018415	2		497	505	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0063662-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	34	280	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.200051645095764	0	FACETS	0.254	0.209	0.305			1	INDETERMINATE	1	TRUE	0	0.527209213063369	0		280	240	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735466	40735466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182388300	NA	P-0063662-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	52	866	5	ENST00000373198.4:c.3407G>A	p.Arg1136His	p.R1136H	ENST00000373198	NM_133170.3	1136	cGt/cAt	25/32	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.527209213063369	2		871	183	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411678	63411678	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063662-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	63	776	0	ENST00000330258.3:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000330258	NM_152424.3	497	Cga/Tga	2/2	0.527209213063369	2	FACETS	1	0.971	1			1	CLONAL	2	TRUE	NA	0.527209213063369	2		776	99	SUCCESS
APC	324	MSKCC	GRCh37	5	112175799	112175799	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063662-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	111	483	0	ENST00000257430.4:c.4508C>A	p.Ser1503Ter	p.S1503*	ENST00000257430	NM_000038.5	1503	tCa/tAa	16/16	0.527209213063369	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	0	0.527209213063369	2		483	209	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788651	3788651	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063662-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	30	317	0	ENST00000262367.5:c.4303G>T	p.Asp1435Tyr	p.D1435Y	ENST00000262367	NM_004380.2	1435	Gat/Tat	26/31	1	2	FACETS	0.774	0.633	0.93	0.774	0.633	0.93	CLONAL	1	TRUE	1	0.527209213063369	2		317	147	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266831	18266831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1011337615	NA	P-0063662-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	56	496	0	ENST00000222254.8:c.142G>A	p.Glu48Lys	p.E48K	ENST00000222254	NM_005027.3	48	Gag/Aag	2/16	0.178209483186068	4	FACETS	1	0.966	1	0.705	0.611	0.805	INDETERMINATE	1	TRUE	2	0.527209213063369	4		496	230	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435649	110435649	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1441639943	NA	P-0063662-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	53	582	0	ENST00000375856.3:c.2752G>A	p.Glu918Lys	p.E918K	ENST00000375856	NM_003749.2	918	Gag/Aag	1/2	1	2	FACETS	0.971	0.84	1	0.971	0.84	1	CLONAL	1	TRUE	1	0.527209213063369	2		582	207	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981536	201981536	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063662-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	85	529	0	ENST00000359651.3:c.451del	p.Gln151ArgfsTer4	p.Q151Rfs*4	ENST00000359651		150	ttC/tt	3/8	1	2	FACETS	0.768	0.693	0.845	1	0.983	1	SUBCLONAL	2	TRUE	1	0.527209213063369	2		529	210	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681453	88681453	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs766986283	NA	P-0063662-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	32	290	0	ENST00000372037.3:c.1342+1G>A		p.X448_splice	ENST00000372037	NM_004329.2	448			1	2	FACETS	0.66	0.541	0.791	0.66	0.541	0.791	SUBCLONAL	1	TRUE	1	0.527209213063369	2		290	184	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251866	8251866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063662-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	69	642	0	ENST00000335790.3:c.211C>T	p.Leu71Phe	p.L71F	ENST00000335790	NM_002315.2	71	Ctc/Ttc	2/4	0.104317993606523	0	FACETS	0.598	0.53	0.669			1	INDETERMINATE	1	TRUE	0	0.527209213063369	0		642	207	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457361	67457361	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906854	NA	P-0063662-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	119	644	0	ENST00000327367.4:c.335C>T	p.Ala112Val	p.A112V	ENST00000327367	NM_005902.3	112	gCc/gTc	2/9	0.461590712548909	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	0	0.527209213063369	2		644	221	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371777	45371777	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063662-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	54	392	0	ENST00000262160.6:c.1214T>A	p.Val405Asp	p.V405D	ENST00000262160	NM_005901.5	405	gTc/gAc	10/11	0.200051645095764	0	FACETS	0.453	0.391	0.518			1	INDETERMINATE	1	TRUE	0	0.527209213063369	0		392	214	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375021	45375021	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063662-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	15	406	0	ENST00000262160.6:c.822G>A	p.Trp274Ter	p.W274*	ENST00000262160	NM_005901.5	274	tgG/tgA	8/11	0.200051645095764	0	FACETS	0.156	0.114	0.206			1	INDETERMINATE	1	TRUE	0	0.527209213063369	0		406	172	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110251267	110251267	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063662-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	39	542	0	ENST00000374672.4:c.70G>A	p.Ala24Thr	p.A24T	ENST00000374672	NM_004235.4	24	Gcg/Acg	2/5	1	2	FACETS	0.624	0.521	0.737	0.624	0.521	0.737	SUBCLONAL	1	TRUE	1	0.527209213063369	2		542	237	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	24	612	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.826	0.647	1	0.826	0.647	1	CLONAL	1	TRUE	1	0.14	2		612	415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0063705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	32	566	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	1	2	FACETS	0.987	0.801	1	0.987	0.801	1	CLONAL	1	TRUE	1	0.14	2		566	463	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797482	45797482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778538	NA	P-0063705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	43	709	0	ENST00000450313.1:c.1037C>T	p.Ser346Leu	p.S346L	ENST00000450313	NM_012222.2	346	tCg/tTg	12/16	1	2	FACETS	0.875	0.731	1	0.875	0.731	1	CLONAL	1	TRUE	1	0.14	2		709	702	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685313	89685313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	13	262	0	ENST00000371953.3:c.208C>G	p.Leu70Val	p.L70V	ENST00000371953	NM_000314.4	70	Ctt/Gtt	3/9	1	2	FACETS	0.952	0.68	1	0.952	0.68	1	CLONAL	1	TRUE	1	0.14	2		262	195	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918491	44918491	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0063705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	16	197	0	ENST00000377967.4:c.975-1G>C		p.X325_splice	ENST00000377967	NM_021140.2	325			1	1	FACETS	1	0.779	1	1	0.779	1	CLONAL	1	TRUE	0	0.14	1		197	201	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78865595	78865595	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	29	448	0	ENST00000306801.3:c.2059G>C	p.Glu687Gln	p.E687Q	ENST00000306801	NM_020761.2	687	Gaa/Caa	18/34	1	2	FACETS	0.955	0.766	1	0.955	0.766	1	CLONAL	1	TRUE	1	0.14	2		448	434	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31472189	31472189	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs779362571	NA	P-0063705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	51	427	1	ENST00000344624.3:c.2222T>C	p.Ile741Thr	p.I741T	ENST00000344624		741	aTt/aCt	14/33	1	2	FACETS	0.834	0.71	0.969	1	0.969	1	CLONAL	2	TRUE	1	0.14	2		428	437	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31947235	31947235	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	26	512	0	ENST00000375333.2:c.720G>C	p.Gln240His	p.Q240H	ENST00000375333	NM_032454.1	240	caG/caC	5/8	1	2	FACETS	0.833	0.659	1	0.833	0.659	1	CLONAL	1	TRUE	1	0.14	2		512	446	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293499	137293499	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	36	618	0	ENST00000481739.1:c.50C>A	p.Ser17Tyr	p.S17Y	ENST00000481739	NM_002957.4	17	tCc/tAc	2/10	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.14	2		618	512	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604724	48604724	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063739-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	23	461	0	ENST00000342988.3:c.1546C>T	p.Gln516Ter	p.Q516*	ENST00000342988	NM_005359.5	516	Cag/Tag	12/12	1	2	FACETS	0.44	0.344	0.55	0.44	0.344	0.55	SUBCLONAL	1	TRUE	1	0.42	2		461	249	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0063875-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	54	341	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.236526134087232	2		341	417	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913286	NA	P-0063875-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	23	214	0	ENST00000263967.3:c.1636C>G	p.Gln546Glu	p.Q546E	ENST00000263967	NM_006218.2	546	Cag/Gag	10/21	1	2	FACETS	0.997	0.782	1	0.997	0.782	1	CLONAL	1	TRUE	1	0.236526134087232	2		214	195	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099331	193099331	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063875-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	34	278	0	ENST00000367435.3:c.265C>T	p.Pro89Ser	p.P89S	ENST00000367435	NM_024529.4	89	Cct/Tct	3/17	0.236526134087232	1	FACETS	0.971	0.798	1	0.971	0.798	1	CLONAL	1	TRUE	0	0.236526134087232	1		278	261	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115941	8115942	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063875-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	70	501	0	ENST00000346208.3:c.1290dup	p.Gly431TrpfsTer76	p.G431Wfs*76	ENST00000346208		429	-/T	6/6	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.236526134087232	2		501	592	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0063876-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	122	344	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.309747798526506	5	FACETS	0.854	0.781	0.929	0.854	0.781	0.929	CLONAL	3	TRUE	2	0.444877376004101	5		344	357	SUCCESS
APC	324	MSKCC	GRCh37	5	112154942	112154942	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779780	NA	P-0063876-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	144	663	0	ENST00000257430.4:c.1213C>T	p.Arg405Ter	p.R405*	ENST00000257430	NM_000038.5	405	Cga/Tga	10/16	0.331606350174845	2	FACETS	0.773	0.711	0.835	0.773	0.711	0.835	SUBCLONAL	2	TRUE	0	0.444877376004101	2		663	419	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974744	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAGCAGCGCCCGCA	CCTCCAGCAGCGCCCGCA	-	novel	NA	P-0063876-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	185	847	0	ENST00000304494.5:c.83_100del	p.Val28_Glu33del	p.V28_E33del	ENST00000304494	NM_000077.4	28	gTGCGGGCGCTGCTGGAGGcg/gcg	1/3	0.382176508873355	2	FACETS	0.84	0.783	0.899	0.84	0.783	0.899	CLONAL	2	TRUE	0	0.444877376004101	2		847	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578552	7578552	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063876-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	116	709	1	ENST00000269305.4:c.378C>A	p.Tyr126Ter	p.Y126*	ENST00000269305	NM_001126112.2	126	taC/taA	5/11	0.382176508873355	2	FACETS	1	0.982	1	0.676	0.614	0.739	CLONAL	1	TRUE	0	0.444877376004101	2		710	386	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295509	1295509	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0063876-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	43	1069	0				ENST00000310581	NM_198253.2	-/1132			0.305365780088539	5	FACETS	0.434	0.362	0.514	0.145	0.12	0.172	SUBCLONAL	1	TRUE	2	0.444877376004101	5		1069	743	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0063877-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	126	495	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.319601811734795	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.319601811734795	1		495	649	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0063877-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	59	282	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.319601811734795	2		282	334	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619927	21619927	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063877-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	114	477	0	ENST00000382592.4:c.239T>A	p.Ile80Asn	p.I80N	ENST00000382592	NM_014572.2	80	aTc/aAc	2/8	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.319601811734795	2		477	701	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591882	48591882	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063877-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	108	494	0	ENST00000342988.3:c.1045A>C	p.Thr349Pro	p.T349P	ENST00000342988	NM_005359.5	349	Act/Cct	9/12	0.319601811734795	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.319601811734795	1		494	519	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971187	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0063877-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	86	427	0	ENST00000304494.5:c.171_172del	p.Arg58SerfsTer61	p.R58Sfs*61	ENST00000304494	NM_000077.4	57	gcCCga/gcga	2/3	0.319601811734795	0	FACETS	0.821	0.73	0.918			1	CLONAL	1	TRUE	0	0.319601811734795	0		427	446	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070640	67070643	+	frameshift_variant	Frame_Shift_Del	DEL	AGAA	AGAA	-	novel	NA	P-0063878-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	178	407	0	ENST00000412916.2:c.267_270del	p.Arg90LysfsTer7	p.R90Kfs*7	ENST00000412916		88	ttAGAA/tt	3/6	0.689674780343412	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.689674780343412	1		407	326	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115701	8115701	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0063878-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	162	415	0	ENST00000346208.3:c.1048-1G>A		p.X350_splice	ENST00000346208		350			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.689674780343412	2		415	436	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168509	56168509	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063882-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	54	199	0	ENST00000399503.3:c.1465C>T	p.Pro489Ser	p.P489S	ENST00000399503	NM_005921.1	489	Ccc/Tcc	8/20	0.906168583183338	3	FACETS	0.821	0.71	0.938	0.41	0.355	0.469	CLONAL	1	TRUE	1	0.906168583183338	3		199	211	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880175	151880175	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1277391709	NA	P-0063882-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	69	529	0	ENST00000262189.6:c.5149A>G	p.Lys1717Glu	p.K1717E	ENST00000262189	NM_170606.2	1717	Aaa/Gaa	35/59	0.906168583183338	3	FACETS	0.958	0.846	1	0.479	0.423	0.538	CLONAL	1	TRUE	1	0.906168583183338	3		529	231	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243859016	243859016	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs397514606	NA	P-0063884-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	142	153	0	ENST00000263826.5:c.49G>A	p.Glu17Lys	p.E17K	ENST00000263826	NM_005465.4	17	Gaa/Aaa	2/13	0.627860109388265	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.627860109388265	2		153	210	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379748	17379748	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202199976	NA	P-0063884-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	191	770	0	ENST00000359435.4:c.133G>A	p.Val45Met	p.V45M	ENST00000359435	NM_001033549.1	45	Gtg/Atg	2/9	0.627860109388265	3	FACETS	0.97	0.899	1	0.485	0.449	0.522	CLONAL	1	TRUE	1	0.627860109388265	3		770	824	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0063947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	42	516	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.220193704945569	2		516	346	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0063947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	66	557	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.220193704945569	1	FACETS	0.779	0.675	0.891	0.779	0.675	0.891	SUBCLONAL	1	TRUE	0	0.220193704945569	1		557	685	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0063947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	61	813	2	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	1	2	FACETS	0.725	0.624	0.835	0.725	0.624	0.835	SUBCLONAL	1	TRUE	1	0.220193704945569	2		815	764	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587781525	NA	P-0063947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	56	837	0	ENST00000269305.4:c.842A>T	p.Asp281Val	p.D281V	ENST00000269305	NM_001126112.2	281	gAc/gTc	8/11	1	2	FACETS	0.73	0.624	0.845	0.73	0.624	0.845	SUBCLONAL	1	TRUE	1	0.220193704945569	2		837	697	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21565435	21565435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1217575272	NA	P-0063947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	42	795	1	ENST00000382592.4:c.451C>T	p.Arg151Trp	p.R151W	ENST00000382592	NM_014572.2	151	Cgg/Tgg	3/8	1	2	FACETS	0.559	0.466	0.664	0.559	0.466	0.664	SUBCLONAL	1	TRUE	1	0.220193704945569	2		796	682	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974762	21974762	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	89	799	0	ENST00000304494.5:c.65G>C	p.Arg22Pro	p.R22P	ENST00000304494	NM_000077.4	22	cGg/cCg	1/3	0.220193704945569	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.220193704945569	1		799	645	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274147	10274147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	68	715	0	ENST00000330684.3:c.122G>A	p.Gly41Asp	p.G41D	ENST00000330684	NM_001134407.1	41	gGt/gAt	2/13	0.220193704945569	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.220193704945569	1		715	479	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602716	10602716	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	100	754	0	ENST00000171111.5:c.862T>G	p.Cys288Gly	p.C288G	ENST00000171111	NM_203500.1	288	Tgc/Ggc	3/6	0.220193704945569	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.220193704945569	1		754	708	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587133	189587133	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	71	499	0	ENST00000264731.3:c.1150G>T	p.Gly384Cys	p.G384C	ENST00000264731	NM_003722.4	384	Ggt/Tgt	9/14	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.220193704945569	2		499	572	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193202147	193202147	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	37	568	0	ENST00000367435.3:c.1179G>C	p.Lys393Asn	p.K393N	ENST00000367435	NM_024529.4	393	aaG/aaC	14/17	0.195204296594574	3	FACETS	0.67	0.551	0.803	0.335	0.275	0.402	SUBCLONAL	1	TRUE	1	0.220193704945569	3		568	557	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942541	71942541	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0063947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	32	574	0	ENST00000298229.2:c.1498-1G>A		p.X500_splice	ENST00000298229	NM_001567.3	500			1	2	FACETS	0.562	0.455	0.683	0.562	0.455	0.683	SUBCLONAL	1	TRUE	1	0.220193704945569	2		574	517	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863385	57863385	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	59	732	0	ENST00000228682.2:c.1480A>T	p.Thr494Ser	p.T494S	ENST00000228682	NM_005269.2	494	Act/Tct	11/12	1	2	FACETS	0.739	0.635	0.853	0.739	0.635	0.853	SUBCLONAL	1	TRUE	1	0.220193704945569	2		732	725	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557630	95557630	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	46	634	0	ENST00000393063.1:c.5437G>C	p.Glu1813Gln	p.E1813Q	ENST00000393063	NM_030621.3	1813	Gag/Cag	26/28	1	2	FACETS	0.627	0.527	0.738	0.627	0.527	0.738	SUBCLONAL	1	TRUE	1	0.220193704945569	2		634	666	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90633735	90633735	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	118	833	0	ENST00000330062.3:c.349A>C	p.Thr117Pro	p.T117P	ENST00000330062	NM_002168.2	117	Acc/Ccc	3/11	0.216577788683893	2	FACETS	1	0.984	1	0.74	0.668	0.816	CLONAL	1	TRUE	0	0.220193704945569	2		833	724	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612361	1612361	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201939465	NA	P-0063947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	38	820	1	ENST00000344749.5:c.1658C>T	p.Ala553Val	p.A553V	ENST00000344749	NM_001136139.2	553	gCg/gTg	18/19	0.220193704945569	1	FACETS	0.495	0.408	0.593	0.495	0.408	0.593	SUBCLONAL	1	TRUE	0	0.220193704945569	1		821	620	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110266	3110266	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	96	821	0	ENST00000078429.4:c.256G>T	p.Ala86Ser	p.A86S	ENST00000078429	NM_002067.2	86	Gcc/Tcc	2/7	0.220193704945569	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.220193704945569	1		821	695	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209154	36209154	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	144	1021	0	ENST00000222270.7:c.235del	p.Arg79GlyfsTer88	p.R79Gfs*88	ENST00000222270	NM_014727.1	78	cgC/cg	1/37	0.220193704945569	5	FACETS	0.788	0.717	0.862			1	SUBCLONAL	2	TRUE	NA	0.220193704945569	5		1021	1104	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380541	31380541	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	48	744	0	ENST00000328111.2:c.1031G>C	p.Gly344Ala	p.G344A	ENST00000328111	NM_006892.3	344	gGg/gCg	9/23	0.161975125542762	3	FACETS	0.635	0.535	0.745	0.212	0.178	0.249	SUBCLONAL	1	TRUE	0	0.220193704945569	3		744	762	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99809095	99809095	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	17	371	0	ENST00000280892.6:c.290A>T	p.Asn97Ile	p.N97I	ENST00000280892	NM_001130678.1	97	aAc/aTc	4/7	1	2	FACETS	0.54	0.403	0.703	0.54	0.403	0.703	SUBCLONAL	1	TRUE	1	0.220193704945569	2		371	286	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156606	106156606	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	44	680	0	ENST00000380013.4:c.1507G>C	p.Glu503Gln	p.E503Q	ENST00000380013	NM_001127208.2	503	Gag/Cag	3/11	1	2	FACETS	0.652	0.546	0.77	0.652	0.546	0.77	SUBCLONAL	1	TRUE	1	0.220193704945569	2		680	613	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294132	1294132	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	47	912	0	ENST00000310581.5:c.869C>G	p.Ser290Cys	p.S290C	ENST00000310581	NM_198253.2	290	tCt/tGt	2/16	0.220193704945569	5	FACETS	0.645	0.543	0.759	0.129	0.108	0.152	SUBCLONAL	1	TRUE	0	0.220193704945569	5		912	880	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933505	39933505	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063947-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	52	436	0	ENST00000378444.4:c.1094C>G	p.Ser365Cys	p.S365C	ENST00000378444	NM_001123385.1	365	tCc/tGc	4/15	1	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.220193704945569	1		436	352	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917782	29917782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56077855	NA	P-0063980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	11	447	0	ENST00000389048.3:c.886G>A	p.Glu296Lys	p.E296K	ENST00000389048	NM_004304.4	296	Gag/Aag	3/29	1	2	FACETS	0.324	0.223	0.448	0.324	0.223	0.448	SUBCLONAL	1	FALSE	1	0.325156384844086	2		447	209	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374828	149374828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	139	411	0	ENST00000360632.3:c.266C>T	p.Ser89Leu	p.S89L	ENST00000360632	NM_015472.4	89	tCg/tTg	2/7	1	2	FACETS	1	0.963	1	1	0.993	1	CLONAL	3	FALSE	1	0.325156384844086	2		411	270	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625087	69625180	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCCAGCTGGGAGCCCAGTCTCGAAGCCTGAACGTGAGAGGGCTCCAGGTTATCCGGGCTCTGCTTCTGCCGCCGCCGTCGGGGCTGGACCCC	CCTCCAGCTGGGAGCCCAGTCTCGAAGCCTGAACGTGAGAGGGCTCCAGGTTATCCGGGCTCTGCTTCTGCCGCCGCCGTCGGGGCTGGACCCC	-	novel	NA	P-0063980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	26	403	0	ENST00000334134.2:c.613_706del	p.Gly205ProfsTer?	p.G205Pfs*?	ENST00000334134	NM_005247.2	205	GGGGTCCAGCCCCGACGGCGGCGGCAGAAGCAGAGCCCGGATAACCTGGAGCCCTCTCACGTTCAGGCTTCGAGACTGGGCTCCCAGCTGGAGGcc/cc	3/3	1	2	FACETS	1	0.8	1	1	0.8	1	CLONAL	1	FALSE	1	0.325156384844086	2		403	160	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0064001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	482	669	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.393903229799984	3	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.763502472245348	3		669	716	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271835	15271835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748776589	NA	P-0064001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	128	606	0	ENST00000263388.2:c.6604G>A	p.Val2202Ile	p.V2202I	ENST00000263388	NM_000435.2	2202	Gtc/Atc	33/33	1	2	FACETS	0.363	0.329	0.4	0.363	0.329	0.4	SUBCLONAL	1	TRUE	1	0.763502472245348	2		606	923	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662795	227662795	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	278	490	6	ENST00000305123.5:c.660C>A	p.Phe220Leu	p.F220L	ENST00000305123	NM_005544.2	220	ttC/ttA	1/2	1	2	FACETS	0.957	0.903	1	0.957	0.903	1	CLONAL	1	TRUE	1	0.763502472245348	2		496	761	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579365	7579366	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTAGCTGCCCTGGTAG	novel	NA	P-0064001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	230	515	2	ENST00000269305.4:c.306_321dup	p.Gly108LeufsTer46	p.G108Lfs*46	ENST00000269305	NM_001126112.2	107	-/CTACCAGGGCAGCTAC	4/11	0.763502472245348	1	FACETS	0.666	0.626	0.707	0.666	0.626	0.707	SUBCLONAL	1	TRUE	0	0.763502472245348	1		517	559	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260168	19260168	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	311	461	8	ENST00000162023.5:c.125A>T	p.Glu42Val	p.E42V	ENST00000162023		42	gAg/gTg	7/13	0.762917816225285	1	FACETS	0.993	0.951	1	0.993	0.951	1	CLONAL	1	TRUE	0	0.763502472245348	1		469	507	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032002	26032002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	126	597	0	ENST00000244661.2:c.287C>T	p.Ala96Val	p.A96V	ENST00000244661	NM_003537.3	96	gCt/gTt	1/1	1	2	FACETS	0.321	0.29	0.354	0.321	0.29	0.354	SUBCLONAL	1	TRUE	1	0.763502472245348	2		597	1028	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064024-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	102	344	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.884	0.795	0.978	0.884	0.795	0.978	CLONAL	1	TRUE	1	0.492976934611628	2		344	468	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295773	212295773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1299031105	NA	P-0064024-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	97	459	2	ENST00000342788.4:c.2540G>A	p.Arg847His	p.R847H	ENST00000342788	NM_005235.2	847	cGt/cAt	21/28	1	2	FACETS	0.832	0.745	0.923	0.832	0.745	0.923	CLONAL	1	TRUE	1	0.492976934611628	2		461	473	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679910	33679910	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064024-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	156	640	0	ENST00000308377.4:c.2171G>C	p.Arg724Thr	p.R724T	ENST00000308377	NM_152270.3	724	aGa/aCa	5/5	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.492976934611628	2		640	578	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575197	48575197	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064024-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	136	317	0	ENST00000342988.3:c.391T>A	p.Tyr131Asn	p.Y131N	ENST00000342988	NM_005359.5	131	Tat/Aat	3/12	0.492976934611628	1	FACETS	0.936	0.858	1	0.936	0.858	1	CLONAL	1	TRUE	0	0.492976934611628	1		317	444	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735553	40735553	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064024-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	111	643	0	ENST00000373198.4:c.3320C>A	p.Ala1107Asp	p.A1107D	ENST00000373198	NM_133170.3	1107	gCt/gAt	25/32	0.492976934611628	1	FACETS	0.722	0.653	0.795	0.722	0.653	0.795	SUBCLONAL	1	TRUE	0	0.492976934611628	1		643	470	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242909	142242909	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064024-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	142	538	0	ENST00000350721.4:c.4078G>T	p.Glu1360Ter	p.E1360*	ENST00000350721	NM_001184.3	1360	Gaa/Taa	22/47	1	2	FACETS	0.963	0.881	1	0.963	0.881	1	CLONAL	1	TRUE	1	0.492976934611628	2		538	598	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0064036-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	453	294	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.739966996206778	4	FACETS	0.984	0.952	1	0.984	0.952	1	CLONAL	3	TRUE	1	0.813330075285261	4		294	684	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0064036-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	460	529	2	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.763212315237808	3	FACETS	0.916	0.892	0.939	0.916	0.892	0.939	CLONAL	3	TRUE	0	0.813330075285261	3		531	579	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735351	204735351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759766975	NA	P-0064036-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	261	603	0	ENST00000302823.3:c.152G>A	p.Arg51Gln	p.R51Q	ENST00000302823	NM_005214.4	51	cGa/cAa	2/4	0.813330075285261	3	FACETS	1	0.97	1	0.525	0.493	0.558	CLONAL	1	TRUE	1	0.813330075285261	3		603	859	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262364	39262364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064036-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	129	363	0	ENST00000402219.2:c.1063G>A	p.Glu355Lys	p.E355K	ENST00000402219	NM_005633.3	355	Gaa/Aaa	8/23	0.782603774777733	3	FACETS	1	0.956	1	0.535	0.489	0.582	CLONAL	1	TRUE	1	0.813330075285261	3		363	417	SUCCESS
MAD2L2	10459	MSKCC	GRCh37	1	11736130	11736130	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064036-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	221	512	0	ENST00000235310.3:c.400G>A	p.Asp134Asn	p.D134N	ENST00000235310		134	Gat/Aat	8/11	0.803439306405351	2	FACETS	1	0.955	1	0.51	0.479	0.541	CLONAL	1	TRUE	0	0.813330075285261	2		512	533	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115252327	115252327	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064036-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	158	456	0	ENST00000369535.4:c.313G>A	p.Asp105Asn	p.D105N	ENST00000369535	NM_002524.4	105	Gac/Aac	4/7	0.803439306405351	2	FACETS	0.932	0.863	1	0.466	0.431	0.501	CLONAL	1	TRUE	0	0.813330075285261	2		456	417	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123889486	123889486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61955123	NA	P-0064036-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	69	206	0	ENST00000330479.4:c.713G>A	p.Arg238Gln	p.R238Q	ENST00000330479	NM_020382.3	238	cGg/cAg	7/9	0.794026634991509	2	FACETS	0.992	0.885	1	0.496	0.442	0.551	CLONAL	1	TRUE	0	0.813330075285261	2		206	171	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993813	72993813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064036-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	234	766	0	ENST00000268489.5:c.232G>A	p.Glu78Lys	p.E78K	ENST00000268489	NM_006885.3	78	Gag/Aag	2/10	0.792176570131523	3	FACETS	0.874	0.816	0.934	0.291	0.272	0.312	CLONAL	1	TRUE	0	0.813330075285261	3		766	926	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727114	41727114	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064036-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	231	499	0	ENST00000301178.4:c.372G>C	p.Gln124His	p.Q124H	ENST00000301178	NM_021913.4	124	caG/caC	3/20	0.782603774777733	3	FACETS	1	0.978	1	0.548	0.513	0.584	CLONAL	1	TRUE	1	0.813330075285261	3		499	729	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719518	190719518	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0064036-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	127	497	0	ENST00000441310.2:c.1520C>G	p.Ser507Ter	p.S507*	ENST00000441310	NM_000534.4	507	tCa/tGa	9/13	1	2	FACETS	0.967	0.889	1	0.967	0.889	1	CLONAL	1	TRUE	1	0.813330075285261	2		497	323	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293997	1293997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064036-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1255	255	717	0	ENST00000310581.5:c.1004C>T	p.Ser335Leu	p.S335L	ENST00000310581	NM_198253.2	335	tCa/tTa	2/16	0.664414187427276	5	FACETS	0.922	0.861	0.985	0.23	0.215	0.247	CLONAL	1	TRUE	1	0.813330075285261	5		717	1510	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637460	176637460	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064036-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	200	514	0	ENST00000439151.2:c.2060C>G	p.Ser687Cys	p.S687C	ENST00000439151	NM_022455.4	687	tCt/tGt	5/23	0.813330075285261	6	FACETS	1	0.97	1	0.219	0.202	0.236	CLONAL	1	TRUE	1	0.813330075285261	6		514	1181	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415043	109415043	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064036-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	183	548	0	ENST00000436639.2:c.234C>G	p.Phe78Leu	p.F78L	ENST00000436639	NM_014454.2	78	ttC/ttG	1/10	0.215047416915559	3	FACETS	1	0.988	1	0.646	0.601	0.691	INDETERMINATE	1	TRUE	1	0.813330075285261	3		548	490	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064046-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	77	344	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.529471479685582	2		344	250	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064046-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	195	736	0	ENST00000269305.4:c.859G>T	p.Glu287Ter	p.E287*	ENST00000269305	NM_001126112.2	287	Gag/Tag	8/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.529471479685582	2		736	569	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0064046-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	109	606	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.529471479685582	2		606	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0064046-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	125	561	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	1	2	FACETS	0.984	0.896	1	0.984	0.896	1	CLONAL	1	TRUE	1	0.529471479685582	2		561	480	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406573	70406573	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064046-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	68	615	0	ENST00000373644.4:c.4087G>T	p.Gly1363Ter	p.G1363*	ENST00000373644	NM_030625.2	1363	Gga/Tga	4/12	1	2	FACETS	0.678	0.593	0.769	0.678	0.593	0.769	SUBCLONAL	1	TRUE	1	0.529471479685582	2		615	379	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040788	47040788	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064046-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	125	788	0	ENST00000377604.3:c.1423C>T	p.Pro475Ser	p.P475S	ENST00000377604	NM_001204468.1	475	Ccc/Tcc	13/24	1	2	FACETS	0.881	0.801	0.964	0.881	0.801	0.964	CLONAL	1	TRUE	1	0.529471479685582	2		788	536	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845715	151845715	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759582255	NA	P-0064046-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	151	725	1	ENST00000262189.6:c.13297G>A	p.Ala4433Thr	p.A4433T	ENST00000262189	NM_170606.2	4433	Gct/Act	52/59	0.529471479685582	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.529471479685582	1		726	391	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631129	176631129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	275	392	0	ENST00000439151.2:c.1072C>T	p.Arg358Trp	p.R358W	ENST00000439151	NM_022455.4	358	Cgg/Tgg	4/23	1	2	FACETS	0.969	0.918	1	0.969	0.918	1	CLONAL	1	TRUE	1	0.925562811330006	2		392	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782082	NA	P-0064048-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	49	531	0	ENST00000269305.4:c.745A>T	p.Arg249Trp	p.R249W	ENST00000269305	NM_001126112.2	249	Agg/Tgg	7/11	0.423402538175796	1	FACETS	0.992	0.853	1	0.992	0.853	1	CLONAL	1	FALSE	0	0.423402538175796	1		531	184	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696598	47696598	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064048-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	67	551	0	ENST00000347630.2:c.350T>C	p.Met117Thr	p.M117T	ENST00000347630	NM_001007230.1	117	aTg/aCg	5/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.423402538175796	2		551	212	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076651	102076651	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064048-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	53	541	0	ENST00000282441.5:c.830C>A	p.Ala277Asp	p.A277D	ENST00000282441	NM_001130145.2	277	gCt/gAt	5/9	1	2	FACETS	0.75	0.642	0.866	0.75	0.642	0.866	SUBCLONAL	1	FALSE	1	0.423402538175796	2		541	334	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455265	29455265	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064048-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	51	652	0	ENST00000389048.3:c.2537G>T	p.Gly846Val	p.G846V	ENST00000389048	NM_004304.4	846	gGc/gTc	15/29	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	FALSE	1	0.423402538175796	2		652	236	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63898536	63898536	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064048-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	45	735	0	ENST00000398590.3:c.262G>C	p.Glu88Gln	p.E88Q	ENST00000398590	NM_001177387.1	88	Gaa/Caa	3/14	1	2	FACETS	0.679	0.573	0.795	0.679	0.573	0.795	SUBCLONAL	1	FALSE	1	0.423402538175796	2		735	313	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0064050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	85	377	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.718	0.635	0.807	0.718	0.635	0.807	SUBCLONAL	1	TRUE	1	0.35218853045106	2		377	672	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557283	29557283	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	35	274	0	ENST00000356175.3:c.2996T>C	p.Val999Ala	p.V999A	ENST00000356175	NM_000267.3	999	gTt/gCt	23/57	1	2	FACETS	0.364	0.298	0.439	0.364	0.298	0.439	SUBCLONAL	1	TRUE	1	0.35218853045106	2		274	546	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63983298	63983298	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs554990824	NA	P-0064050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	32	265	0	ENST00000398590.3:c.2663A>G	p.Asp888Gly	p.D888G	ENST00000398590	NM_001177387.1	888	gAt/gGt	13/14	1	2	FACETS	0.334	0.27	0.406	0.334	0.27	0.406	SUBCLONAL	1	TRUE	1	0.35218853045106	2		265	544	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039656	47039656	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	108	416	0	ENST00000377604.3:c.1108del	p.Leu370SerfsTer115	p.L370Sfs*115	ENST00000377604	NM_001204468.1	370	Ctc/tc	11/24	1	2	FACETS	0.792	0.711	0.879	0.792	0.711	0.879	SUBCLONAL	1	TRUE	1	0.35218853045106	2		416	774	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0064051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	191	593	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.439563070693769	2		593	648	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225923	133225923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	100	643	0	ENST00000320574.5:c.3974G>A	p.Ser1325Asn	p.S1325N	ENST00000320574	NM_006231.2	1325	aGc/aAc	31/49	1	2	FACETS	0.829	0.742	0.92	0.829	0.742	0.92	CLONAL	1	TRUE	1	0.439563070693769	2		643	549	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918159	50918159	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	83	734	0	ENST00000440232.2:c.2476T>G	p.Cys826Gly	p.C826G	ENST00000440232	NM_002691.3	826	Tgc/Ggc	20/27	1	2	FACETS	0.725	0.641	0.814	0.725	0.641	0.814	SUBCLONAL	1	TRUE	1	0.439563070693769	2		734	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579349	7579352	+	frameshift_variant	Frame_Shift_Del	DEL	AAGC	AAGC	-	novel	NA	P-0064078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	492	688	0	ENST00000269305.4:c.335_338del	p.Gly112AlafsTer10	p.G112Afs*10	ENST00000269305	NM_001126112.2	112	gGCTTc/gc	4/11	0.693972447516783	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	FALSE	0	0.69429526444471	2		688	705	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149238599	149238599	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	117	510	0	ENST00000360632.3:c.1196G>C	p.Trp399Ser	p.W399S	ENST00000360632	NM_015472.4	399	tGg/tCg	7/7	0.693972447516783	4	FACETS	0.665	0.599	0.734	0.332	0.299	0.367	SUBCLONAL	1	FALSE	2	0.69429526444471	4		510	859	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247222	153247222	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	218	518	0	ENST00000281708.4:c.1580A>G	p.Asp527Gly	p.D527G	ENST00000281708	NM_033632.3	527	gAt/gGt	10/12	0.179036434075747	3	FACETS	1	0.991	1	0.686	0.642	0.73	INDETERMINATE	1	FALSE	1	0.69429526444471	3		518	617	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668799	52668799	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	29	416	0	ENST00000394830.3:c.1120G>T	p.Glu374Ter	p.E374*	ENST00000394830	NM_018313.4	374	Gaa/Taa	12/30	0.204128579069187	0	FACETS	0.351	0.281	0.43			1	SUBCLONAL	1	TRUE	0	0.29	0		416	405	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210526	5210526	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	54	664	0	ENST00000357368.4:c.5441A>G	p.Asn1814Ser	p.N1814S	ENST00000357368	NM_002850.3	1814	aAc/aGc	35/38	1	2	FACETS	0.527	0.45	0.613	0.527	0.45	0.613	SUBCLONAL	1	TRUE	1	0.29	2		664	706	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591826	48591826	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	36	451	0	ENST00000342988.3:c.989A>T	p.Glu330Val	p.E330V	ENST00000342988	NM_005359.5	330	gAa/gTa	9/12	0.296731896720635	1	FACETS	0.501	0.411	0.6	0.501	0.411	0.6	SUBCLONAL	1	TRUE	0	0.29	1		451	424	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813324	102813324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377124814	NA	P-0064079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	83	598	0	ENST00000307046.8:c.365G>A	p.Arg122His	p.R122H	ENST00000307046	NM_001111285.1	122	cGt/cAt	3/4	1	2	FACETS	0.931	0.822	1	0.931	0.822	1	CLONAL	1	TRUE	1	0.29	2		598	615	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893461	32893461	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0064079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	93	341	0	ENST00000380152.3:c.315del	p.Gly106GlufsTer15	p.G106Efs*15	ENST00000380152		105	ttA/tt	3/27	0.270834141194149	3	FACETS	0.944	0.845	1	0.944	0.845	1	CLONAL	2	TRUE	1	0.29	3		341	389	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38064144	38064153	+	frameshift_variant	Frame_Shift_Del	DEL	TTTCATGCCC	TTTCATGCCC	-	novel	NA	P-0064079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	144	809	0	ENST00000250448.2:c.25_34del	p.Gly9ProfsTer23	p.G9Pfs*23	ENST00000250448	NM_004496.3	9	GGGCATGAAAcc/cc	1/2	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.29	2		809	860	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127911957	127911957	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	113	477	0	ENST00000373547.4:c.913C>A	p.Leu305Ile	p.L305I	ENST00000373547	NM_002721.4	305	Ctt/Att	7/7	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.29	2		477	652	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0064080-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	21	287	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.598	0.472	0.738	0.598	0.472	0.738	SUBCLONAL	1	TRUE	1	0.835676524840408	2		287	84	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591933	48591933	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060500733	NA	P-0064080-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	13	556	0	ENST00000342988.3:c.1096C>T	p.Gln366Ter	p.Q366*	ENST00000342988	NM_005359.5	366	Caa/Taa	9/12	0.835676524840408	1	FACETS	0.1	0.071	0.134	0.1	0.071	0.134	SUBCLONAL	1	TRUE	0	0.835676524840408	1		556	182	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984356	201984357	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0064080-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	29	535	0	ENST00000359651.3:c.1021_1022del	p.Ile341ProfsTer129	p.I341Pfs*129	ENST00000359651		341	ATc/c	8/8	1	2	FACETS	0.12	0.095	0.147	0.12	0.095	0.147	SUBCLONAL	1	TRUE	1	0.835676524840408	2		535	580	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573664	48573697	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTTAGTCTTATAAGAGTTTTTCTATACCCTCT	AGGTTAGTCTTATAAGAGTTTTTCTATACCCTCT	-	novel	NA	P-0064080-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	33	468	0	ENST00000342988.3:c.249_249+33del		p.X83_splice	ENST00000342988	NM_005359.5	83		2/12	0.835676524840408	1	FACETS	0.851	0.74	0.957	0.851	0.74	0.957	CLONAL	1	TRUE	0	0.835676524840408	1		468	54	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581336	48581336	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064080-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	15	466	0	ENST00000342988.3:c.642del	p.Asn216ThrfsTer25	p.N216Tfs*25	ENST00000342988	NM_005359.5	214	Ttt/tt	5/12	0.835676524840408	1	FACETS	0.079	0.057	0.104	0.079	0.057	0.104	SUBCLONAL	1	TRUE	0	0.835676524840408	1		466	266	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422541	47422542	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0064080-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	36	560	0	ENST00000404338.3:c.610_611dup	p.Gly205LysfsTer15	p.G205Kfs*15	ENST00000404338	NM_004491.4	203	-/GA	1/6	1	2	FACETS	0.163	0.134	0.196	0.163	0.134	0.196	SUBCLONAL	1	TRUE	1	0.835676524840408	2		560	528	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041396	47041396	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064080-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	19	350	0	ENST00000377604.3:c.1740del	p.Tyr581ThrfsTer123	p.Y581Tfs*123	ENST00000377604	NM_001204468.1	580	taC/ta	16/24	1	1	FACETS	0.075	0.057	0.097	0.075	0.057	0.097	SUBCLONAL	1	TRUE	0	0.835676524840408	1		350	352	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112892422	112892422	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	90	278	0	ENST00000351677.2:c.580G>C	p.Val194Leu	p.V194L	ENST00000351677	NM_002834.3	194	Gtg/Ctg	5/16	1	2	FACETS	0.959	0.857	1	0.959	0.857	1	CLONAL	1	TRUE	1	0.455344367944546	2		278	412	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103508416	103508416	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	72	302	0	ENST00000355739.4:c.482A>G	p.Asp161Gly	p.D161G	ENST00000355739	NM_000123.3	161	gAt/gGt	5/15	1	2	FACETS	0.97	0.854	1	0.97	0.854	1	CLONAL	1	TRUE	1	0.455344367944546	2		302	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0064090-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	257	721	2	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.298887322477262	4	FACETS	1	0.986	1	0.858	0.809	0.907	CLONAL	3	TRUE	0	0.32	4		723	618	SUCCESS
FH	2271	MSKCC	GRCh37	1	241676941	241676941	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064090-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	47	347	0	ENST00000366560.3:c.340C>G	p.Pro114Ala	p.P114A	ENST00000366560	NM_000143.3	114	Cca/Gca	3/10	0.272589207949472	2	FACETS	0.761	0.644	0.89	0.381	0.322	0.445	SUBCLONAL	1	TRUE	0	0.32	2		347	386	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661966	29661966	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064090-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	52	374	0	ENST00000356175.3:c.5860C>G	p.Leu1954Val	p.L1954V	ENST00000356175	NM_000267.3	1954	Ctt/Gtt	39/57	0.298887322477262	4	FACETS	0.89	0.759	1			1	CLONAL	1	TRUE	NA	0.32	4		374	482	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664497	29664497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1212510392	NA	P-0064090-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	63	401	0	ENST00000356175.3:c.6476C>T	p.Ser2159Phe	p.S2159F	ENST00000356175	NM_000267.3	2159	tCc/tTc	42/57	0.298887322477262	4	FACETS	0.92	0.796	1			1	CLONAL	1	TRUE	NA	0.32	4		401	565	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983018	149983018	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064090-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	50	330	0	ENST00000253339.5:c.3240C>A	p.Phe1080Leu	p.F1080L	ENST00000253339		1080	ttC/ttA	7/7	1	2	FACETS	0.735	0.625	0.856	0.735	0.625	0.856	SUBCLONAL	1	TRUE	1	0.32	2		330	425	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437777	52437804	+	frameshift_variant	Frame_Shift_Del	DEL	GAATTGAGAGGTCCTTCTGGGACTCTTT	GAATTGAGAGGTCCTTCTGGGACTCTTT	-	novel	NA	P-0064100-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	129	670	0	ENST00000460680.1:c.1357_1384del	p.Lys453LeufsTer109	p.K453Lfs*109	ENST00000460680	NM_004656.3	453	AAAGAGTCCCAGAAGGACCTCTCAATTCct/ct	13/17	0.40204796345369	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.406502450409278	1		670	496	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958831	38958831	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064100-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	163	547	1	ENST00000357387.3:c.2281G>T	p.Asp761Tyr	p.D761Y	ENST00000357387	NM_152756.3	761	Gat/Tat	23/38	1	2	FACETS	0.988	0.907	1	0.988	0.907	1	CLONAL	1	TRUE	1	0.406502450409278	2		548	812	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064112-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	527	344	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.48986051320241	10	FACETS	1	0.989	1	0.92	0.89	0.95	CLONAL	7	TRUE	2	0.48986051320241	10		344	865	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567556006	NA	P-0064112-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	439	847	0	ENST00000269305.4:c.298del	p.Gln100ArgfsTer23	p.Q100Rfs*23	ENST00000269305	NM_001126112.2	100	Cag/ag	4/11	0.44943616975512	2	FACETS	0.904	0.866	0.943	0.904	0.866	0.943	CLONAL	2	TRUE	0	0.48986051320241	2		847	991	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673767	37673767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1212731319	NA	P-0064112-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	172	694	0	ENST00000447079.4:c.2921C>T	p.Pro974Leu	p.P974L	ENST00000447079	NM_015083.1	974	cCg/cTg	10/14	0.490723279313003	3	FACETS	0.919	0.846	0.996	0.46	0.423	0.498	CLONAL	1	TRUE	1	0.48986051320241	3		694	951	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030862	69030862	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064112-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	82	514	0	ENST00000288368.4:c.3404G>T	p.Ser1135Ile	p.S1135I	ENST00000288368	NM_024870.2	1135	aGt/aTt	27/40	0.33764431745648	3	FACETS	0.756	0.668	0.851	0.378	0.334	0.426	SUBCLONAL	1	TRUE	1	0.48986051320241	3		514	551	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051598	30051598	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064112-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	193	432	0	ENST00000338641.4:c.532C>T	p.Gln178Ter	p.Q178*	ENST00000338641	NM_000268.3	178	Cag/Tag	6/16	0.44943616975512	2	FACETS	0.856	0.801	0.913	0.856	0.801	0.913	CLONAL	2	TRUE	0	0.48986051320241	2		432	460	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488724	212488724	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064112-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	128	706	0	ENST00000342788.4:c.2125C>G	p.Gln709Glu	p.Q709E	ENST00000342788	NM_005235.2	709	Caa/Gaa	18/28	1	2	FACETS	0.714	0.648	0.784	0.714	0.648	0.784	SUBCLONAL	1	TRUE	1	0.48986051320241	2		706	732	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941824	44941824	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064112-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	145	305	0	ENST00000377967.4:c.3148G>T	p.Glu1050Ter	p.E1050*	ENST00000377967	NM_021140.2	1050	Gaa/Taa	21/29	0.460024143646106	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	0	0.48986051320241	2		305	290	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3795318	3795318	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064112-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	180	666	0	ENST00000262367.5:c.3874C>T	p.Gln1292Ter	p.Q1292*	ENST00000262367	NM_004380.2	1292	Cag/Tag	22/31	1	2	FACETS	0.953	0.881	1	0.953	0.881	1	CLONAL	1	TRUE	1	0.48986051320241	2		666	771	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941972	44941972	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064112-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	185	464	0	ENST00000377967.4:c.3222G>T	p.Arg1074Ser	p.R1074S	ENST00000377967	NM_021140.2	1074	agG/agT	22/29	0.460024143646106	2	FACETS	0.937	0.877	0.997	0.937	0.877	0.997	CLONAL	2	TRUE	0	0.48986051320241	2		464	403	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90634821	90634823	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0064112-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	178	705	0	ENST00000330062.3:c.169_171del	p.Glu57del	p.E57del	ENST00000330062	NM_002168.2	57	GAG/-	2/11	1	2	FACETS	0.879	0.811	0.949	0.879	0.811	0.949	CLONAL	1	TRUE	1	0.48986051320241	2		705	827	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41558784	41558784	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0064112-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	249	290	0	ENST00000263253.7:c.3728+1G>A		p.X1243_splice	ENST00000263253	NM_001429.3	1243			0.463392378930298	4	FACETS	0.935	0.891	0.978	0.935	0.891	0.978	CLONAL	4	TRUE	0	0.48986051320241	4		290	405	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0064116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	345	516	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.62747627233785	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.62747627233785	3		516	678	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	210	595	0	ENST00000326873.7:c.667G>T	p.Glu223Ter	p.E223*	ENST00000326873	NM_000455.4	223	Gag/Tag	5/10	0.62747627233785	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.62747627233785	1		595	450	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781324	3781326	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs587783502	NA	P-0064116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	224	546	0	ENST00000262367.5:c.5039_5041del	p.Ser1680del	p.S1680del	ENST00000262367	NM_004380.2	1680	tCCTtg/ttg	30/31	1	2	FACETS	0.964	0.901	1	0.964	0.901	1	CLONAL	1	TRUE	1	0.62747627233785	2		546	741	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073667	8073667	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	222	545	0	ENST00000377482.5:c.992G>T	p.Arg331Leu	p.R331L	ENST00000377482	NM_018948.3	331	cGc/cTc	4/4	1	2	FACETS	0.937	0.875	1	0.937	0.875	1	CLONAL	1	TRUE	1	0.62747627233785	2		545	755	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331813	68331813	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	153	353	0	ENST00000487270.1:c.409G>A	p.Ala137Thr	p.A137T	ENST00000487270	NM_133509.3	137	Gct/Act	5/11	1	2	FACETS	0.936	0.862	1	0.936	0.862	1	CLONAL	1	TRUE	1	0.62747627233785	2		353	521	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106813	27106813	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	272	579	0	ENST00000324856.7:c.6424A>T	p.Ser2142Cys	p.S2142C	ENST00000324856	NM_006015.4	2142	Agc/Tgc	20/20	1	2	FACETS	0.955	0.898	1	0.955	0.898	1	CLONAL	1	TRUE	1	0.62747627233785	2		579	908	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588650	28588650	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	194	356	0	ENST00000241453.7:c.2798G>T	p.Arg933Leu	p.R933L	ENST00000241453	NM_004119.2	933	cGg/cTg	23/24	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.62747627233785	2		356	589	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141526	11141526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	204	505	0	ENST00000358026.2:c.3503C>T	p.Ala1168Val	p.A1168V	ENST00000358026	NM_001128849.1	1168	gCa/gTa	25/36	0.62747627233785	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.62747627233785	1		505	434	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300087	15300087	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs147782884	NA	P-0064116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	250	531	0	ENST00000263388.2:c.1189A>G	p.Ile397Val	p.I397V	ENST00000263388	NM_000435.2	397	Atc/Gtc	7/33	0.62747627233785	1	FACETS	0.994	0.939	1	0.994	0.939	1	CLONAL	1	TRUE	0	0.62747627233785	1		531	550	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794469	242794469	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	179	399	0	ENST00000334409.5:c.473C>A	p.Pro158His	p.P158H	ENST00000334409	NM_005018.2	158	cCc/cAc	3/5	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.62747627233785	2		399	548	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867554	101867613	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCGGCGGCGGCGCTGCTCCCGGGGGCGACGGGTGAGCGGCGGCGCGGCGGGCGGGCGACT	GCGGCGGCGGCGCTGCTCCCGGGGGCGACGGGTGAGCGGCGGCGCGGCGGGCGGGCGACT	-	novel	NA	P-0064116-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	212	377	0	ENST00000374994.4:c.71_97+33del		p.X24_splice	ENST00000374994	NM_004612.2	24		1/9	0.62747627233785	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.62747627233785	1		377	411	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	174	612	0				ENST00000310581	NM_198253.2	-/1132			0.488160747677064	4	FACETS	1	0.979	1	0.393	0.362	0.426	CLONAL	1	TRUE	1	0.488160747677064	4		612	899	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578513	7578513	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	233	813	0	ENST00000269305.4:c.417G>C	p.Lys139Asn	p.K139N	ENST00000269305	NM_001126112.2	139	aaG/aaC	5/11	0.1874185961075	3	FACETS	1	0.988	1	0.634	0.592	0.678	INDETERMINATE	1	TRUE	1	0.488160747677064	3		813	936	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0064117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	320	882	0	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	0.1874185961075	3	FACETS	0.835	0.79	0.881	0.835	0.79	0.881	INDETERMINATE	2	TRUE	1	0.488160747677064	3		882	977	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792017	42792017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	527	865	0	ENST00000575354.2:c.821G>A	p.Arg274Gln	p.R274Q	ENST00000575354	NM_015125.3	274	cGa/cAa	6/20	0.357929349816368	5	FACETS	0.899	0.862	0.936			1	CLONAL	3	TRUE	NA	0.488160747677064	5		865	1387	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870853	12870853	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	186	798	0	ENST00000228872.4:c.80C>A	p.Ser27Ter	p.S27*	ENST00000228872	NM_004064.3	27	tCg/tAg	1/3	1	2	FACETS	0.938	0.868	1	0.938	0.868	1	CLONAL	1	TRUE	1	0.488160747677064	2		798	812	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671570	30671570	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	278	784	0	ENST00000376406.3:c.5390C>G	p.Ser1797Cys	p.S1797C	ENST00000376406	NM_014641.2	1797	tCt/tGt	10/15	0.488160747677064	3	FACETS	1	0.988	1	0.604	0.567	0.642	CLONAL	1	TRUE	1	0.488160747677064	3		784	1173	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18975039	18975039	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759670824	NA	P-0064117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	42	551	0	ENST00000262803.5:c.2836G>A	p.Val946Ile	p.V946I	ENST00000262803	NM_002911.3	946	Gtc/Atc	20/24	1	2	FACETS	0.33	0.275	0.391	0.33	0.275	0.391	SUBCLONAL	1	TRUE	1	0.488160747677064	2		551	521	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	893162	893162	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	424	638	0	ENST00000166345.3:c.49G>C	p.Glu17Gln	p.E17Q	ENST00000166345	NM_004237.3	17	Gag/Cag	1/13	0.488160747677064	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	1	0.488160747677064	4		638	836	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271321	26271321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	1232	980	0	ENST00000305910.3:c.292G>A	p.Glu98Lys	p.E98K	ENST00000305910	NM_003534.2	98	Gag/Aag	1/1	0.488160747677064	6	FACETS	0.961	0.94	0.982	0.961	0.94	0.982	CLONAL	5	TRUE	1	0.488160747677064	6		980	2075	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041424	47041424	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	261	495	0	ENST00000377604.3:c.1768T>C	p.Tyr590His	p.Y590H	ENST00000377604	NM_001204468.1	590	Tat/Cat	16/24	1	1	FACETS	0.792	0.752	0.833	1	0.995	1	SUBCLONAL	2	TRUE	0	0.488160747677064	1		495	510	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0064128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	183	444	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.721247873218531	1	FACETS	0.998	0.94	1	0.998	0.94	1	CLONAL	1	FALSE	0	0.721247873218531	1		444	325	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0064128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	205	533	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.721247873218531	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	0	0.721247873218531	1		533	355	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220706	1220706	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878853992	NA	P-0064128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	8	738	0	ENST00000326873.7:c.724G>A	p.Gly242Arg	p.G242R	ENST00000326873	NM_000455.4	242	Ggg/Agg	5/10	0.292516308237235	1	FACETS	0.04	0.025	0.059	0.04	0.025	0.059	INDETERMINATE	1	FALSE	0	0.721247873218531	1		738	358	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0064128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	111	282	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.46209066300591	1	FACETS	0.837	0.769	0.906	0.837	0.769	0.906	CLONAL	1	FALSE	0	0.721247873218531	1		282	235	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922165	100922165	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	16	319	0	ENST00000325455.5:c.2347A>G	p.Ile783Val	p.I783V	ENST00000325455	NM_001202474.3	783	Ata/Gta	5/8	1	2	FACETS	0.151	0.111	0.199	0.151	0.111	0.199	SUBCLONAL	1	FALSE	1	0.721247873218531	2		319	294	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575141	48575141	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	62	531	0	ENST00000342988.3:c.335T>G	p.Val112Gly	p.V112G	ENST00000342988	NM_005359.5	112	gTt/gGt	3/12	0.721247873218531	1	FACETS	0.519	0.454	0.586	0.519	0.454	0.586	SUBCLONAL	1	FALSE	0	0.721247873218531	1		531	212	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575161	48575161	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	12	440	0	ENST00000342988.3:c.355T>C	p.Phe119Leu	p.F119L	ENST00000342988	NM_005359.5	119	Ttt/Ctt	3/12	0.721247873218531	1	FACETS	0.111	0.078	0.152	0.111	0.078	0.152	SUBCLONAL	1	FALSE	0	0.721247873218531	1		440	192	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231488898	231488898	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	36	383	0	ENST00000295050.7:c.1261T>G	p.Phe421Val	p.F421V	ENST00000295050	NM_032018.5	421	Ttt/Gtt	5/5	1	2	FACETS	0.938	0.773	1	0.938	0.773	1	CLONAL	1	TRUE	1	0.22	2		383	349	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424921	47424921	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	126	517	0	ENST00000404338.3:c.2989C>T	p.Arg997Ter	p.R997*	ENST00000404338	NM_004491.4	997	Cga/Tga	1/6	1	2	FACETS	1	0.933	1	1	0.99	1	CLONAL	2	TRUE	1	0.22	2		517	555	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	45	283	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.889	0.755	1	1	0.969	1	CLONAL	2	TRUE	1	0.22	2		283	230	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	32	348	0	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.22	2		348	280	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381472	81381472	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777593933	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	35	423	0	ENST00000222390.5:c.589C>T	p.Arg197Cys	p.R197C	ENST00000222390	NM_000601.4	197	Cgc/Tgc	5/18	1	2	FACETS	0.614	0.503	0.74	0.614	0.503	0.74	SUBCLONAL	1	TRUE	1	0.22	2		423	518	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	50	464	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	0.986	0.838	1	0.986	0.838	1	CLONAL	1	TRUE	1	0.22	2		464	461	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410486	63410486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779325879	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	31	751	0	ENST00000330258.3:c.2681G>A	p.Arg894His	p.R894H	ENST00000330258	NM_152424.3	894	cGc/cAc	2/2	1	2	FACETS	0.55	0.444	0.671	0.55	0.444	0.671	SUBCLONAL	1	TRUE	1	0.22	2		751	512	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468516	89468516	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1453560937	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	30	367	0	ENST00000336596.2:c.2050C>T	p.Arg684Ter	p.R684*	ENST00000336596	NM_005233.5	684	Cga/Tga	11/17	1	2	FACETS	0.703	0.566	0.858	0.703	0.566	0.858	SUBCLONAL	1	TRUE	1	0.22	2		367	388	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	17	437	0	ENST00000394830.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000394830	NM_018313.4	710	Cga/Tga	17/30	1	2	FACETS	0.426	0.317	0.556	0.426	0.317	0.556	SUBCLONAL	1	TRUE	1	0.22	2		437	363	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715979	52715979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205227	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	18	678	0	ENST00000322088.6:c.544C>T	p.Arg182Trp	p.R182W	ENST00000322088	NM_014225.5	182	Cgg/Tgg	5/15	1	2	FACETS	0.298	0.223	0.386	0.298	0.223	0.386	SUBCLONAL	1	TRUE	1	0.22	2		678	550	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159104	143159104	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1405228238	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	24	227	0	ENST00000262992.4:c.749G>A	p.Arg250Gln	p.R250Q	ENST00000262992	NM_001101669.1	250	cGa/cAa	10/24	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.22	2		227	179	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268762	41268762	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1245266458	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	33	357	0	ENST00000349496.5:c.1000G>A	p.Glu334Lys	p.E334K	ENST00000349496	NM_001904.3	334	Gaa/Aaa	7/15	1	2	FACETS	0.855	0.697	1	0.855	0.697	1	CLONAL	1	TRUE	1	0.22	2		357	351	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615593	43615593	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	58	684	0	ENST00000355710.3:c.2672C>T	p.Ser891Leu	p.S891L	ENST00000355710	NM_020975.4	891	tCg/tTg	15/20	1	2	FACETS	0.962	0.827	1	0.962	0.827	1	CLONAL	1	TRUE	1	0.22	2		684	548	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972801	32972801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358397	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	27	426	0	ENST00000380152.3:c.10151G>A	p.Arg3384Gln	p.R3384Q	ENST00000380152		3384	cGa/cAa	27/27	1	2	FACETS	0.641	0.51	0.791	0.641	0.51	0.791	SUBCLONAL	1	TRUE	1	0.22	2		426	383	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	67	309	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	1	0.93	1	1	0.983	1	CLONAL	2	TRUE	1	0.22	2		309	280	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912525	32912525	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	20	284	0	ENST00000380152.3:c.4033G>T	p.Asp1345Tyr	p.D1345Y	ENST00000380152		1345	Gat/Tat	11/27	1	2	FACETS	0.64	0.49	0.816	0.64	0.49	0.816	SUBCLONAL	1	TRUE	1	0.22	2		284	284	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203492	108203492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs138941496	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	14	232	0	ENST00000278616.4:c.7792C>T	p.Arg2598Ter	p.R2598*	ENST00000278616	NM_000051.3	2598	Cga/Tga	53/63	1	2	FACETS	0.795	0.577	1	0.795	0.577	1	CLONAL	1	TRUE	1	0.22	2		232	160	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542861	187542861	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1340793072	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	11	340	0	ENST00000441802.2:c.4879C>T	p.Arg1627Ter	p.R1627*	ENST00000441802	NM_005245.3	1627	Cga/Tga	10/27	1	2	FACETS	0.298	0.205	0.414	0.298	0.205	0.414	SUBCLONAL	1	TRUE	1	0.22	2		340	336	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480542	50480542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559383300	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	22	458	0	ENST00000394963.4:c.412C>T	p.Arg138Cys	p.R138C	ENST00000394963	NM_003076.4	138	Cgt/Tgt	4/13	1	2	FACETS	0.472	0.365	0.596	0.472	0.365	0.596	SUBCLONAL	1	TRUE	1	0.22	2		458	424	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314969	1314969	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	38	494	0	ENST00000400841.2:c.692A>C	p.Lys231Thr	p.K231T	ENST00000400841		231	aAa/aCa	6/6	1	2	FACETS	0.636	0.525	0.761	0.636	0.525	0.761	SUBCLONAL	1	TRUE	1	0.22	2		494	543	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026290	48026290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147737737	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	43	588	1	ENST00000234420.5:c.1168G>A	p.Asp390Asn	p.D390N	ENST00000234420	NM_000179.2	390	Gat/Aat	4/10	1	2	FACETS	0.814	0.682	0.962	0.814	0.682	0.962	CLONAL	1	TRUE	1	0.22	2		589	480	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121756	108121756	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	20	388	0	ENST00000278616.4:c.1564G>T	p.Glu522Ter	p.E522*	ENST00000278616	NM_000051.3	522	Gaa/Taa	10/63	1	2	FACETS	0.535	0.408	0.683	0.535	0.408	0.683	SUBCLONAL	1	TRUE	1	0.22	2		388	340	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56787287	56787287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267606997	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	32	330	0	ENST00000337432.4:c.773G>A	p.Arg258His	p.R258H	ENST00000337432	NM_058216.2	258	cGt/cAt	5/9	1	2	FACETS	0.853	0.694	1	0.853	0.694	1	CLONAL	1	TRUE	1	0.22	2		330	341	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587160	189587160	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs941268998	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	30	388	0	ENST00000264731.3:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000264731	NM_003722.4	393	Cga/Tga	9/14	1	2	FACETS	0.819	0.661	0.998	0.819	0.661	0.998	CLONAL	1	TRUE	1	0.22	2		388	333	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109315691	109315692	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	16	229	0	ENST00000436639.2:c.1093dup	p.Arg365LysfsTer11	p.R365Kfs*11	ENST00000436639	NM_014454.2	365	aga/aAga	6/10	1	2	FACETS	0.505	0.373	0.663	0.505	0.373	0.663	SUBCLONAL	1	TRUE	1	0.22	2		229	288	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218876	133218876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	57	697	0	ENST00000320574.5:c.5060C>T	p.Ser1687Phe	p.S1687F	ENST00000320574	NM_006231.2	1687	tCc/tTc	38/49	1	2	FACETS	0.796	0.682	0.92	0.796	0.682	0.92	CLONAL	1	TRUE	1	0.22	2		697	651	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438728	49438728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290729871	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	46	571	0	ENST00000301067.7:c.4762G>A	p.Glu1588Lys	p.E1588K	ENST00000301067	NM_003482.3	1588	Gaa/Aaa	19/54	1	2	FACETS	0.706	0.594	0.831	0.706	0.594	0.831	SUBCLONAL	1	TRUE	1	0.22	2		571	592	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109312010	109312010	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	27	313	0	ENST00000436639.2:c.1262C>A	p.Ser421Tyr	p.S421Y	ENST00000436639	NM_014454.2	421	tCt/tAt	8/10	1	2	FACETS	0.963	0.769	1	0.963	0.769	1	CLONAL	1	TRUE	1	0.22	2		313	255	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40993283	40993283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1428987216	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	21	355	0	ENST00000267868.3:c.109G>A	p.Asp37Asn	p.D37N	ENST00000267868	NM_002875.4	37	Gat/Aat	3/10	1	2	FACETS	0.55	0.423	0.698	0.55	0.423	0.698	SUBCLONAL	1	TRUE	1	0.22	2		355	347	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226778	142226778	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	24	296	0	ENST00000350721.4:c.5026T>G	p.Leu1676Val	p.L1676V	ENST00000350721	NM_001184.3	1676	Tta/Gta	28/47	1	2	FACETS	0.72	0.565	0.898	0.72	0.565	0.898	SUBCLONAL	1	TRUE	1	0.22	2		296	303	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800592	32800592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771425114	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	57	600	0	ENST00000374899.4:c.955C>T	p.Arg319Trp	p.R319W	ENST00000374899	NM_018833.2	319	Cgg/Tgg	6/12	1	2	FACETS	0.861	0.738	0.995	0.861	0.738	0.995	CLONAL	1	TRUE	1	0.22	2		600	602	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910943	32910943	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs767686668	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	22	355	0	ENST00000380152.3:c.2451G>T	p.Lys817Asn	p.K817N	ENST00000380152		817	aaG/aaT	11/27	1	2	FACETS	0.752	0.584	0.946	0.752	0.584	0.946	CLONAL	1	TRUE	1	0.22	2		355	266	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538970	23538970	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	40	626	0	ENST00000380871.4:c.469C>A	p.Leu157Met	p.L157M	ENST00000380871	NM_006167.3	157	Ctg/Atg	2/2	1	2	FACETS	0.699	0.581	0.832	0.699	0.581	0.832	SUBCLONAL	1	TRUE	1	0.22	2		626	520	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633425	8633425	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	21	401	0	ENST00000356435.5:c.244C>A	p.Leu82Ile	p.L82I	ENST00000356435		82	Ctc/Atc	3/35	1	2	FACETS	0.598	0.461	0.759	0.598	0.461	0.759	SUBCLONAL	1	TRUE	1	0.22	2		401	319	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336607	81336607	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	17	260	0	ENST00000222390.5:c.1615C>T	p.Arg539Ter	p.R539*	ENST00000222390	NM_000601.4	539	Cga/Tga	14/18	1	2	FACETS	0.626	0.467	0.813	0.626	0.467	0.813	SUBCLONAL	1	TRUE	1	0.22	2		260	247	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428417	49428417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1439926284	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	49	730	0	ENST00000301067.7:c.10388C>T	p.Ser3463Leu	p.S3463L	ENST00000301067	NM_003482.3	3463	tCg/tTg	36/54	1	2	FACETS	0.706	0.597	0.826	0.706	0.597	0.826	SUBCLONAL	1	TRUE	1	0.22	2		730	631	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679887	33679887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200734680	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	50	585	0	ENST00000308377.4:c.2194C>T	p.Arg732Cys	p.R732C	ENST00000308377	NM_152270.3	732	Cgc/Tgc	5/5	1	2	FACETS	0.874	0.742	1	0.874	0.742	1	CLONAL	1	TRUE	1	0.22	2		585	520	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31238855	31238855	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs281860547	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	43	746	0	ENST00000376228.5:c.614G>A	p.Arg205His	p.R205H	ENST00000376228	NM_002117.5	205	cGc/cAc	3/8	1	2	FACETS	0.687	0.574	0.812	0.687	0.574	0.812	SUBCLONAL	1	TRUE	1	0.22	2		746	569	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724437	162724437	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	33	587	0	ENST00000367921.3:c.209G>T	p.Gly70Val	p.G70V	ENST00000367921	NM_006182.2	70	gGa/gTa	5/18	1	2	FACETS	0.508	0.412	0.616	0.508	0.412	0.616	SUBCLONAL	1	TRUE	1	0.22	2		587	591	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600628	43600628	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	70	699	0	ENST00000355710.3:c.854T>C	p.Phe285Ser	p.F285S	ENST00000355710	NM_020975.4	285	tTc/tCc	4/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.22	2		699	550	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463350	463350	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	43	343	0	ENST00000399788.2:c.921A>C	p.Lys307Asn	p.K307N	ENST00000399788	NM_001042603.1	307	aaA/aaC	8/28	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.22	2		343	350	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691163	18691163	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	19	287	0	ENST00000266497.5:c.3274T>G	p.Phe1092Val	p.F1092V	ENST00000266497		1092	Ttt/Gtt	23/31	1	2	FACETS	0.61	0.463	0.783	0.61	0.463	0.783	SUBCLONAL	1	TRUE	1	0.22	2		287	283	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21630888	21630888	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	41	443	0	ENST00000421138.2:c.716G>C	p.Gly239Ala	p.G239A	ENST00000421138		239	gGt/gCt	8/16	1	2	FACETS	0.841	0.701	0.997	0.841	0.701	0.997	CLONAL	1	TRUE	1	0.22	2		443	443	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910972	32910972	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	18	323	0	ENST00000380152.3:c.2480A>C	p.Asn827Thr	p.N827T	ENST00000380152		827	aAt/aCt	11/27	1	2	FACETS	0.568	0.428	0.734	0.568	0.428	0.734	SUBCLONAL	1	TRUE	1	0.22	2		323	288	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	69061270	69061270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	14	207	0	ENST00000487270.1:c.1105C>T	p.Pro369Ser	p.P369S	ENST00000487270	NM_133509.3	369	Cct/Tct	11/11	1	2	FACETS	0.677	0.49	0.901	0.677	0.49	0.901	SUBCLONAL	1	TRUE	1	0.22	2		207	188	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829967	72829967	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	45	598	0	ENST00000268489.5:c.6614A>C	p.Lys2205Thr	p.K2205T	ENST00000268489	NM_006885.3	2205	aAg/aCg	9/10	1	2	FACETS	0.718	0.603	0.845	0.718	0.603	0.845	SUBCLONAL	1	TRUE	1	0.22	2		598	570	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350101	89350101	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1457323549	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	39	829	0	ENST00000301030.4:c.2849A>G	p.Asp950Gly	p.D950G	ENST00000301030	NM_001256183.1	950	gAc/gGc	9/13	1	2	FACETS	0.506	0.418	0.604	0.506	0.418	0.604	SUBCLONAL	1	TRUE	1	0.22	2		829	701	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132465	11132465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	40	741	0	ENST00000358026.2:c.2681C>T	p.Thr894Met	p.T894M	ENST00000358026	NM_001128849.1	894	aCg/aTg	19/36	1	2	FACETS	0.589	0.489	0.702	0.589	0.489	0.702	SUBCLONAL	1	TRUE	1	0.22	2		741	617	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797800	42797800	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	40	648	0	ENST00000575354.2:c.3852G>T	p.Glu1284Asp	p.E1284D	ENST00000575354	NM_015125.3	1284	gaG/gaT	16/20	1	2	FACETS	0.717	0.596	0.853	0.717	0.596	0.853	SUBCLONAL	1	TRUE	1	0.22	2		648	507	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645974	215645974	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1559425523	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	22	408	0	ENST00000260947.4:c.624G>T	p.Lys208Asn	p.K208N	ENST00000260947	NM_000465.2	208	aaG/aaT	4/11	1	2	FACETS	0.504	0.39	0.637	0.504	0.39	0.637	SUBCLONAL	1	TRUE	1	0.22	2		408	397	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62322268	62322268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465400494	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	36	540	0	ENST00000360203.5:c.2524G>A	p.Glu842Lys	p.E842K	ENST00000360203	NM_001283009.1	842	Gaa/Aaa	27/35	1	2	FACETS	0.777	0.639	0.932	0.777	0.639	0.932	CLONAL	1	TRUE	1	0.22	2		540	421	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63973831	63973831	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	49	569	0	ENST00000398590.3:c.1192T>G	p.Leu398Val	p.L398V	ENST00000398590	NM_001177387.1	398	Ttg/Gtg	9/14	1	2	FACETS	0.714	0.604	0.835	0.714	0.604	0.835	SUBCLONAL	1	TRUE	1	0.22	2		569	624	SUCCESS
ATR	545	MSKCC	GRCh37	3	142185323	142185323	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	17	273	0	ENST00000350721.4:c.6740A>C	p.Lys2247Thr	p.K2247T	ENST00000350721	NM_001184.3	2247	aAa/aCa	40/47	1	2	FACETS	0.636	0.475	0.827	0.636	0.475	0.827	SUBCLONAL	1	TRUE	1	0.22	2		273	243	SUCCESS
ALB	213	MSKCC	GRCh37	4	74272351	74272351	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	21	282	0	ENST00000295897.4:c.143T>C	p.Leu48Ser	p.L48S	ENST00000295897	NM_000477.5	48	tTg/tCg	3/15	1	2	FACETS	0.856	0.662	1	0.856	0.662	1	CLONAL	1	TRUE	1	0.22	2		282	223	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84393430	84393430	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	17	169	0	ENST00000321945.7:c.227C>A	p.Ser76Tyr	p.S76Y	ENST00000321945	NM_139076.2	76	tCt/tAt	4/9	1	2	FACETS	0.641	0.479	0.833	0.641	0.479	0.833	SUBCLONAL	1	TRUE	1	0.22	2		169	241	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143044557	143044557	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	33	282	0	ENST00000262992.4:c.1905G>C	p.Leu635Phe	p.L635F	ENST00000262992	NM_001101669.1	635	ttG/ttC	18/24	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.22	2		282	258	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534351	187534351	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	56	582	0	ENST00000441802.2:c.9375C>A	p.Phe3125Leu	p.F3125L	ENST00000441802	NM_005245.3	3125	ttC/ttA	13/27	1	2	FACETS	0.914	0.783	1	0.914	0.783	1	CLONAL	1	TRUE	1	0.22	2		582	557	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912109	56912109	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	31	285	0	ENST00000519728.1:c.1336+1G>A		p.X446_splice	ENST00000519728	NM_002350.3	446			1	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	TRUE	1	0.22	2		285	271	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5463058	5463058	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	51	469	0	ENST00000381577.3:c.619T>G	p.Phe207Val	p.F207V	ENST00000381577	NM_014143.3	207	Ttc/Gtc	4/7	1	2	FACETS	0.978	0.832	1	0.978	0.832	1	CLONAL	1	TRUE	1	0.22	2		469	474	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5465601	5465601	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	55	554	0	ENST00000381577.3:c.785G>T	p.Arg262Ile	p.R262I	ENST00000381577	NM_014143.3	262	aGa/aTa	5/7	1	2	FACETS	0.971	0.831	1	0.971	0.831	1	CLONAL	1	TRUE	1	0.22	2		554	515	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889071	76889071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358105128	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	16	294	0	ENST00000373344.5:c.4939G>A	p.Asp1647Asn	p.D1647N	ENST00000373344	NM_000489.3	1647	Gat/Aat	18/35	1	2	FACETS	0.727	0.539	0.951	0.727	0.539	0.951	CLONAL	1	TRUE	1	0.22	2		294	200	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937351	76937351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	32	286	0	ENST00000373344.5:c.3397G>A	p.Glu1133Lys	p.E1133K	ENST00000373344	NM_000489.3	1133	Gaa/Aaa	9/35	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.22	2		286	233	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054254	30054254	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs1555994854	NA	P-0064138-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	85	471	6	ENST00000338641.4:c.675+1G>C		p.X225_splice	ENST00000338641	NM_000268.3	225			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		477	233	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0064139-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	96	534	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		534	458	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0064139-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	40	386	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		386	270	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685270	89685271	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0064139-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	32	303	0	ENST00000371953.3:c.170dup	p.Leu57PhefsTer6	p.L57Ffs*6	ENST00000371953	NM_000314.4	55	-/T	3/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		303	201	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064139-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	75	465	1	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		466	460	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663300	67663300	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0064139-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	85	401	0	ENST00000264010.4:c.1702-1G>C		p.X568_splice	ENST00000264010	NM_006565.3	568			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		401	393	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989691	15989691	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064139-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	91	547	0	ENST00000268712.3:c.3082C>T	p.Arg1028Ter	p.R1028*	ENST00000268712	NM_006311.3	1028	Cga/Tga	23/46	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		547	590	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056425	26056427	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	rs774779034	NA	P-0064139-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	60	568	0	ENST00000343677.2:c.230_232del	p.Asn77del	p.N77del	ENST00000343677	NM_005319.3	77	aACAgc/agc	1/1	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		568	456	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593315	67593318	+	protein_altering_variant	In_Frame_Del	DEL	GTAC	GTAC	A	novel	NA	P-0064139-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	67	530	0	ENST00000274335.5:c.2061_2064delinsA	p.Tyr688del	p.Y688del	ENST00000274335		687	ttGTAC/ttA	15/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		530	483	SUCCESS
APC	324	MSKCC	GRCh37	5	112175643	112175643	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554085817	NA	P-0064140-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	171	590	0	ENST00000257430.4:c.4353del	p.Val1452TyrfsTer21	p.V1452Yfs*21	ENST00000257430	NM_000038.5	1451	gAa/ga	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		590	709	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0064140-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	164	317	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		317	396	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873442	45873442	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0064140-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	157	460	0	ENST00000391945.4:c.54C>G	p.Tyr18Ter	p.Y18*	ENST00000391945	NM_000400.3	18	taC/taG	2/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		460	413	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754303	57754303	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064140-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	53	467	0	ENST00000274289.3:c.548G>C	p.Arg183Pro	p.R183P	ENST00000274289	NM_006622.3	183	cGa/cCa	4/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		467	506	SUCCESS
APC	324	MSKCC	GRCh37	5	112174159	112174159	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064140-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	117	513	0	ENST00000257430.4:c.2868C>A	p.Tyr956Ter	p.Y956*	ENST00000257430	NM_000038.5	956	taC/taA	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		513	483	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	113	557	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.246523659532024	2		557	665	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577529	7577529	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs730882027	NA	P-0064141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	81	486	0	ENST00000269305.4:c.752T>G	p.Ile251Ser	p.I251S	ENST00000269305	NM_001126112.2	251	aTc/aGc	7/11	0.167020574201528	2	FACETS	1	0.962	1	0.612	0.54	0.689	CLONAL	1	TRUE	0	0.246523659532024	2		486	537	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922698	44922737	+	stop_gained	Nonsense_Mutation	DEL	CTACTGGAATTCCTAATGGGCCAACAGCTGACTCATCACT	CTACTGGAATTCCTAATGGGCCAACAGCTGACTCATCACT	A	novel	NA	P-0064141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	35	468	0	ENST00000377967.4:c.1559_1598delinsA	p.Ser520_Leu533delinsTer	p.S520_L533delins*	ENST00000377967	NM_021140.2	520	tCTACTGGAATTCCTAATGGGCCAACAGCTGACTCATCACTg/tAg	16/29	1	2	FACETS	0.563	0.461	0.678	0.563	0.461	0.678	SUBCLONAL	1	TRUE	1	0.246523659532024	2		468	504	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0064146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	170	557	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.626988989694668	2		557	524	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0064146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	19	222	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.456	0.349	0.578	0.456	0.349	0.578	SUBCLONAL	1	TRUE	1	0.626988989694668	2		222	133	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499064	149499064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143067190	NA	P-0064146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	151	502	0	ENST00000261799.4:c.2764C>T	p.Arg922Cys	p.R922C	ENST00000261799	NM_002609.3	922	Cgc/Tgc	20/23	1	2	FACETS	0.912	0.839	0.988	0.912	0.839	0.988	CLONAL	1	TRUE	1	0.626988989694668	2		502	528	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624270	89624270	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs398123324	NA	P-0064146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	74	178	0	ENST00000371953.3:c.44G>T	p.Arg15Ile	p.R15I	ENST00000371953	NM_000314.4	15	aGa/aTa	1/9	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.626988989694668	2		178	185	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092945	27092957	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGGGATGGCAGC	CAGGGATGGCAGC	-	novel	NA	P-0064146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	122	456	0	ENST00000324856.7:c.2879_2891del		p.X960_splice	ENST00000324856	NM_006015.4	960		10/20	1	2	FACETS	0.824	0.75	0.902	0.824	0.75	0.902	CLONAL	1	TRUE	1	0.626988989694668	2		456	472	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624304	89624312	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGTATCCA	CTGTATCCA	-	novel	NA	P-0064146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	88	334	0	ENST00000371953.3:c.78_79+7del		p.X26_splice	ENST00000371953	NM_000314.4	26		1/9	1	2	FACETS	0.858	0.768	0.953	0.858	0.768	0.953	CLONAL	1	TRUE	1	0.626988989694668	2		334	327	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786084	3786084	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	154	470	0	ENST00000262367.5:c.4681G>T	p.Glu1561Ter	p.E1561*	ENST00000262367	NM_004380.2	1561	Gag/Tag	28/31	1	2	FACETS	0.986	0.909	1	0.986	0.909	1	CLONAL	1	TRUE	1	0.626988989694668	2		470	498	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38506048	38506048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1434179064	NA	P-0064146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	162	445	0	ENST00000254066.5:c.340C>T	p.Arg114Cys	p.R114C	ENST00000254066	NM_000964.3	114	Cgc/Tgc	4/9	1	2	FACETS	0.97	0.895	1	0.97	0.895	1	CLONAL	1	TRUE	1	0.626988989694668	2		445	533	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0064147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	13	282	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.375	0.266	0.508	0.375	0.266	0.508	SUBCLONAL	1	TRUE	1	0.19	2		282	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0064147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	50	617	0	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	1	2	FACETS	0.834	0.707	0.974	0.834	0.707	0.974	CLONAL	1	TRUE	1	0.19	2		617	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs886039483	NA	P-0064148-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	18	544	0	ENST00000269305.4:c.376T>G	p.Tyr126Asp	p.Y126D	ENST00000269305	NM_001126112.2	126	Tac/Gac	5/11	1	2	FACETS	0.152	0.114	0.197	0.152	0.114	0.197	SUBCLONAL	1	TRUE	1	0.616474401920252	2		544	385	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	33	344	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.370207580131334	2		344	130	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473723	67473723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223740	NA	P-0064149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	13	471	0	ENST00000327367.4:c.803G>A	p.Arg268His	p.R268H	ENST00000327367	NM_005902.3	268	cGc/cAc	6/9	1	2	FACETS	0.436	0.312	0.586	0.436	0.312	0.586	SUBCLONAL	1	TRUE	1	0.370207580131334	2		471	161	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845356	89845356	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs753980264	NA	P-0064149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	39	513	0	ENST00000389301.3:c.1771C>T	p.Arg591Ter	p.R591*	ENST00000389301	NM_000135.2	591	Cga/Tga	19/43	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.370207580131334	2		513	189	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045488	47045488	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	30	287	0	ENST00000377604.3:c.2455G>T	p.Ala819Ser	p.A819S	ENST00000377604	NM_001204468.1	819	Gct/Tct	22/24	1	1	FACETS	0.88	0.737	1	1	0.96	1	CLONAL	2	TRUE	0	0.370207580131334	1		287	75	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134535	2134535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778925833	NA	P-0064149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	40	677	0	ENST00000219476.3:c.4312C>T	p.Arg1438Trp	p.R1438W	ENST00000219476	NM_000548.3	1438	Cgg/Tgg	34/42	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.370207580131334	2		677	177	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73637991	73637991	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	29	343	0	ENST00000377687.4:c.1165C>A	p.His389Asn	p.H389N	ENST00000377687	NM_001730.3	389	Cat/Aat	3/4	1	2	FACETS	0.911	0.739	1	0.911	0.739	1	CLONAL	1	TRUE	1	0.370207580131334	2		343	172	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593523	48593535	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTTCATAAGAT	CTGTTCATAAGAT	-	novel	NA	P-0064149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	30	333	0	ENST00000342988.3:c.1276_1288del	p.Val426ThrfsTer6	p.V426Tfs*6	ENST00000342988	NM_005359.5	425	gCTGTTCATAAGATc/gc	10/12	0.370207580131334	1	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	0	0.370207580131334	1		333	123	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045705	26045705	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs745690555	NA	P-0064149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	40	622	0	ENST00000540144.1:c.67A>G	p.Thr23Ala	p.T23A	ENST00000540144	NM_003531.2	23	Act/Gct	1/1	1	2	FACETS	0.956	0.801	1	0.956	0.801	1	CLONAL	1	TRUE	1	0.370207580131334	2		622	226	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	226	658	0	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.859	0.803	0.917	0.859	0.803	0.917	CLONAL	1	TRUE	1	0.679597995531169	2		658	774	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	124	474	7	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.549	0.497	0.603	0.549	0.497	0.603	SUBCLONAL	1	TRUE	1	0.679597995531169	2		481	665	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	25	444	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.118	0.093	0.148	0.118	0.093	0.148	SUBCLONAL	1	TRUE	1	0.679597995531169	2		444	621	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	441	868	10	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.788	0.757	0.818	1	0.997	1	SUBCLONAL	2	TRUE	1	0.679597995531169	2		878	824	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	229	402	3	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	0.398770175488558	3	FACETS	1	0.99	1	0.656	0.614	0.699	INDETERMINATE	1	TRUE	1	0.679597995531169	3		405	688	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	51	90	2	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.926	0.803	1	0.926	0.803	1	CLONAL	1	TRUE	1	0.679597995531169	2		92	162	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	92	261	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.783	0.702	0.867	0.783	0.702	0.867	SUBCLONAL	1	TRUE	1	0.679597995531169	2		261	346	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560514	65560514	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	118	325	0	ENST00000358664.4:c.83A>G	p.His28Arg	p.H28R	ENST00000358664	NM_002382.4	28	cAt/cGt	3/5	1	2	FACETS	0.715	0.648	0.784	0.715	0.648	0.784	SUBCLONAL	1	TRUE	1	0.679597995531169	2		325	486	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700232	117700232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146533107	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	115	279	0	ENST00000368508.3:c.2587C>T	p.Arg863Trp	p.R863W	ENST00000368508	NM_002944.2	863	Cgg/Tgg	17/43	1	2	FACETS	0.827	0.751	0.906	0.827	0.751	0.906	CLONAL	1	TRUE	1	0.679597995531169	2		279	409	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	155	338	4	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	1	2	FACETS	0.846	0.779	0.915	0.846	0.779	0.915	CLONAL	1	TRUE	1	0.679597995531169	2		342	539	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216358	2216358	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370276763	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	179	519	1	ENST00000398665.3:c.2002G>A	p.Ala668Thr	p.A668T	ENST00000398665	NM_032482.2	668	Gcc/Acc	20/28	1	2	FACETS	0.821	0.76	0.883	0.821	0.76	0.883	CLONAL	1	TRUE	1	0.679597995531169	2		520	642	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953229	81953229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	69	373	0	ENST00000359376.3:c.2195G>A	p.Arg732His	p.R732H	ENST00000359376	NM_002661.3	732	cGc/cAc	20/33	1	2	FACETS	0.338	0.294	0.385	0.338	0.294	0.385	SUBCLONAL	1	TRUE	1	0.679597995531169	2		373	601	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92247520	92247520	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs902137115	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	109	375	0	ENST00000265734.4:c.700G>A	p.Val234Met	p.V234M	ENST00000265734	NM_001259.6	234	Gtg/Atg	7/8	0.679597995531169	3	FACETS	0.629	0.566	0.697	0.315	0.283	0.349	SUBCLONAL	1	TRUE	1	0.679597995531169	3		375	683	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681061	117681061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749977900	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	47	373	0	ENST00000368508.3:c.3559G>A	p.Val1187Ile	p.V1187I	ENST00000368508	NM_002944.2	1187	Gtt/Att	23/43	1	2	FACETS	0.286	0.241	0.336	0.286	0.241	0.336	SUBCLONAL	1	TRUE	1	0.679597995531169	2		373	483	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951085	17951085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	113	287	1	ENST00000458235.1:c.1208G>A	p.Arg403His	p.R403H	ENST00000458235	NM_000215.3	403	cGc/cAc	9/24	1	2	FACETS	0.726	0.657	0.798	0.726	0.657	0.798	SUBCLONAL	1	TRUE	1	0.679597995531169	2		288	458	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265353	152265353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188957694	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	136	404	0	ENST00000206249.3:c.806G>A	p.Arg269His	p.R269H	ENST00000206249	NM_000125.3	269	cGc/cAc	4/8	1	2	FACETS	0.8	0.732	0.871	0.8	0.732	0.871	SUBCLONAL	1	TRUE	1	0.679597995531169	2		404	500	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003059	42003059	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	141	397	0	ENST00000219905.7:c.2596C>T	p.Arg866Ter	p.R866*	ENST00000219905	NM_001164273.1	866	Cga/Tga	8/24	0.593363918675686	1	FACETS	0.678	0.624	0.733	0.678	0.624	0.733	SUBCLONAL	1	TRUE	0	0.679597995531169	1		397	404	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716329	52716329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863225094	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	26	448	0	ENST00000322088.6:c.773G>A	p.Arg258His	p.R258H	ENST00000322088	NM_014225.5	258	cGc/cAc	6/15	1	2	FACETS	0.135	0.106	0.168	0.135	0.106	0.168	SUBCLONAL	1	TRUE	1	0.679597995531169	2		448	568	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340177	116340177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200074800	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	172	377	0	ENST00000397752.3:c.1039G>A	p.Ala347Thr	p.A347T	ENST00000397752	NM_000245.2	347	Gca/Aca	2/21	0.679597995531169	3	FACETS	0.892	0.823	0.965	0.446	0.411	0.483	CLONAL	1	TRUE	1	0.679597995531169	3		377	760	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347432	89347432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144003224	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	199	505	0	ENST00000301030.4:c.5518G>A	p.Ala1840Thr	p.A1840T	ENST00000301030	NM_001256183.1	1840	Gcg/Acg	9/13	1	2	FACETS	0.818	0.76	0.877	0.818	0.76	0.877	CLONAL	1	TRUE	1	0.679597995531169	2		505	716	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2111996	2111996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374936223	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	195	477	1	ENST00000219476.3:c.1244C>T	p.Ala415Val	p.A415V	ENST00000219476	NM_000548.3	415	gCg/gTg	12/42	1	2	FACETS	0.911	0.847	0.976	0.911	0.847	0.976	CLONAL	1	TRUE	1	0.679597995531169	2		478	630	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948824	17948824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747854515	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	38	481	0	ENST00000458235.1:c.1618C>T	p.Arg540Cys	p.R540C	ENST00000458235	NM_000215.3	540	Cgc/Tgc	12/24	1	2	FACETS	0.174	0.143	0.208	0.174	0.143	0.208	SUBCLONAL	1	TRUE	1	0.679597995531169	2		481	644	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427951	49427951	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	159	400	0	ENST00000301067.7:c.10639C>T	p.Arg3547Cys	p.R3547C	ENST00000301067	NM_003482.3	3547	Cgc/Tgc	38/54	1	2	FACETS	0.78	0.718	0.844	0.78	0.718	0.844	SUBCLONAL	1	TRUE	1	0.679597995531169	2		400	600	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821381	72821382	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	72	394	0	ENST00000268489.5:c.10793dup	p.Pro3599SerfsTer67	p.P3599Sfs*67	ENST00000268489	NM_006885.3	3598	cct/ccCt	10/10	1	2	FACETS	0.444	0.389	0.503	0.444	0.389	0.503	SUBCLONAL	1	TRUE	1	0.679597995531169	2		394	477	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425056	49425056	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs562043836	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	36	531	0	ENST00000301067.7:c.13432C>T	p.Arg4478Trp	p.R4478W	ENST00000301067	NM_003482.3	4478	Cgg/Tgg	39/54	1	2	FACETS	0.152	0.124	0.183	0.152	0.124	0.183	SUBCLONAL	1	TRUE	1	0.679597995531169	2		531	698	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120795696	120795696	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	104	272	0	ENST00000257552.2:c.457G>A	p.Gly153Arg	p.G153R	ENST00000257552	NM_002442.3	153	Ggg/Agg	8/15	1	2	FACETS	0.765	0.69	0.843	0.765	0.69	0.843	SUBCLONAL	1	TRUE	1	0.679597995531169	2		272	400	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858194	40858194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs905112048	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	98	309	0	ENST00000428826.2:c.1670G>A	p.Arg557His	p.R557H	ENST00000428826		557	cGt/cAt	16/21	1	2	FACETS	0.642	0.576	0.712	0.642	0.576	0.712	SUBCLONAL	1	TRUE	1	0.679597995531169	2		309	449	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540214	23540219	+	inframe_deletion	In_Frame_Del	DEL	CTCTGG	CTCTGG	-	novel	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	99	543	0	ENST00000380871.4:c.184_189del	p.Pro62_Glu63del	p.P62_E63del	ENST00000380871	NM_006167.3	62	CCAGAG/-	1/2	1	2	FACETS	0.497	0.445	0.553	0.497	0.445	0.553	SUBCLONAL	1	TRUE	1	0.679597995531169	2		543	586	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983971	2983971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	170	443	0	ENST00000396946.4:c.559C>T	p.Arg187Trp	p.R187W	ENST00000396946	NM_032415.4	187	Cgg/Tgg	5/25	0.679597995531169	3	FACETS	0.891	0.821	0.964	0.446	0.41	0.482	CLONAL	1	TRUE	1	0.679597995531169	3		443	752	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434581	99434581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1461059080	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	157	431	1	ENST00000268035.6:c.668C>T	p.Ala223Val	p.A223V	ENST00000268035	NM_000875.3	223	gCg/gTg	3/21	1	2	FACETS	0.797	0.733	0.862	0.797	0.733	0.862	SUBCLONAL	1	TRUE	1	0.679597995531169	2		432	580	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022435	12022435	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149660037	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	255	572	0	ENST00000396373.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000396373	NM_001987.4	181	Cgc/Tgc	5/8	1	2	FACETS	0.931	0.874	0.989	0.931	0.874	0.989	CLONAL	1	TRUE	1	0.679597995531169	2		572	806	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085677	16085677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779959007	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	135	391	0	ENST00000281043.3:c.853C>T	p.Arg285Trp	p.R285W	ENST00000281043	NM_005378.4	285	Cgg/Tgg	3/3	1	2	FACETS	0.782	0.715	0.852	0.782	0.715	0.852	SUBCLONAL	1	TRUE	1	0.679597995531169	2		391	508	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964205	28964206	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	107	332	0	ENST00000282397.4:c.1696dup	p.Met566AsnfsTer15	p.M566Nfs*15	ENST00000282397	NM_002019.4	566	atg/aAtg	13/30	1	2	FACETS	0.67	0.604	0.739	0.67	0.604	0.739	SUBCLONAL	1	TRUE	1	0.679597995531169	2		332	470	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240974	53240974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs907851319	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	26	179	0	ENST00000375401.3:c.1237G>A	p.Val413Met	p.V413M	ENST00000375401	NM_004187.3	413	Gtg/Atg	9/26	1	1	FACETS	0.181	0.143	0.224	0.181	0.143	0.224	SUBCLONAL	1	TRUE	0	0.679597995531169	1		179	279	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627355	37627355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs910521882	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	186	464	0	ENST00000249071.6:c.364G>A	p.Asp122Asn	p.D122N	ENST00000249071	NM_002872.4	122	Gac/Aac	5/7	1	2	FACETS	0.899	0.835	0.965	0.899	0.835	0.965	CLONAL	1	TRUE	1	0.679597995531169	2		464	609	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434667	99434667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375391097	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	43	475	0	ENST00000268035.6:c.754C>T	p.Arg252Cys	p.R252C	ENST00000268035	NM_000875.3	252	Cgc/Tgc	3/21	1	2	FACETS	0.2	0.167	0.237	0.2	0.167	0.237	SUBCLONAL	1	TRUE	1	0.679597995531169	2		475	633	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206761	27206761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376225163	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	133	292	0	ENST00000380036.4:c.2546G>A	p.Arg849Gln	p.R849Q	ENST00000380036	NM_000459.3	849	cGg/cAg	15/23	1	2	FACETS	0.856	0.784	0.932	0.856	0.784	0.932	CLONAL	1	TRUE	1	0.679597995531169	2		292	457	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249223	133249223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766276875	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	146	415	0	ENST00000320574.5:c.1676G>A	p.Arg559Gln	p.R559Q	ENST00000320574	NM_006231.2	559	cGg/cAg	15/49	1	2	FACETS	0.831	0.763	0.901	0.831	0.763	0.901	CLONAL	1	TRUE	1	0.679597995531169	2		415	517	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324506	31324507	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	211	653	0	ENST00000412585.2:c.301_302del	p.Ser101ProfsTer37	p.S101Pfs*37	ENST00000412585	NM_005514.6	101	AGc/c	2/8	1	2	FACETS	0.712	0.662	0.764	0.712	0.662	0.764	SUBCLONAL	1	TRUE	1	0.679597995531169	2		653	872	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508205	106508205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	372	458	0	ENST00000359195.3:c.199G>A	p.Val67Met	p.V67M	ENST00000359195	NM_002649.2	67	Gtg/Atg	2/11	0.679597995531169	3	FACETS	0.954	0.911	0.996	0.954	0.911	0.996	CLONAL	2	TRUE	1	0.679597995531169	3		458	769	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602698	10602698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145222481	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	212	485	1	ENST00000171111.5:c.880G>A	p.Asp294Asn	p.D294N	ENST00000171111	NM_203500.1	294	Gac/Aac	3/6	1	2	FACETS	0.938	0.876	1	0.938	0.876	1	CLONAL	1	TRUE	1	0.679597995531169	2		486	665	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120479976	120479976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782503548	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	136	476	0	ENST00000256646.2:c.3451G>A	p.Asp1151Asn	p.D1151N	ENST00000256646	NM_024408.3	1151	Gat/Aat	21/34	1	2	FACETS	0.684	0.624	0.746	0.684	0.624	0.746	SUBCLONAL	1	TRUE	1	0.679597995531169	2		476	585	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199609	16199609	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751080105	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	162	393	0	ENST00000375759.3:c.382C>T	p.Arg128Cys	p.R128C	ENST00000375759	NM_015001.2	128	Cgt/Tgt	2/15	1	2	FACETS	0.861	0.794	0.929	0.861	0.794	0.929	CLONAL	1	TRUE	1	0.679597995531169	2		393	554	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121573	193121573	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	132	290	0	ENST00000367435.3:c.971C>T	p.Thr324Met	p.T324M	ENST00000367435	NM_024529.4	324	aCg/aTg	10/17	1	2	FACETS	0.981	0.9	1	0.981	0.9	1	CLONAL	1	TRUE	1	0.679597995531169	2		290	396	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104359288	104359288	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	103	364	0	ENST00000369902.3:c.1009C>T	p.His337Tyr	p.H337Y	ENST00000369902	NM_016169.3	337	Cac/Tac	8/12	1	2	FACETS	0.6	0.539	0.664	0.6	0.539	0.664	SUBCLONAL	1	TRUE	1	0.679597995531169	2		364	505	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450142	32450142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767419243	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	169	462	0	ENST00000332351.3:c.670G>A	p.Gly224Arg	p.G224R	ENST00000332351	NM_024426.4	224	Ggg/Agg	2/10	1	2	FACETS	0.896	0.829	0.965	0.896	0.829	0.965	CLONAL	1	TRUE	1	0.679597995531169	2		462	555	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998346	100998346	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	82	351	0	ENST00000325455.5:c.1456A>G	p.Ser486Gly	p.S486G	ENST00000325455	NM_001202474.3	486	Agc/Ggc	1/8	1	2	FACETS	0.672	0.597	0.751	0.672	0.597	0.751	SUBCLONAL	1	TRUE	1	0.679597995531169	2		351	359	SUCCESS
ATM	472	MSKCC	GRCh37	11	108128307	108128307	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	123	246	0	ENST00000278616.4:c.2350A>G	p.Thr784Ala	p.T784A	ENST00000278616	NM_000051.3	784	Aca/Gca	15/63	1	2	FACETS	0.992	0.907	1	0.992	0.907	1	CLONAL	1	TRUE	1	0.679597995531169	2		246	365	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133967	41133967	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139398811	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	188	552	0	ENST00000379561.5:c.1661G>A	p.Arg554His	p.R554H	ENST00000379561	NM_002015.3	554	cGc/cAc	2/3	1	2	FACETS	0.769	0.713	0.828	0.769	0.713	0.828	SUBCLONAL	1	TRUE	1	0.679597995531169	2		552	719	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585395	29585395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138227618	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	103	309	0	ENST00000356175.3:c.4144G>A	p.Gly1382Ser	p.G1382S	ENST00000356175	NM_000267.3	1382	Ggt/Agt	31/57	1	2	FACETS	0.658	0.591	0.727	0.658	0.591	0.727	SUBCLONAL	1	TRUE	1	0.679597995531169	2		309	461	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244459	41244459	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	158	412	0	ENST00000357654.3:c.3089A>G	p.Asn1030Ser	p.N1030S	ENST00000357654	NM_007294.3	1030	aAc/aGc	10/23	1	2	FACETS	0.932	0.86	1	0.932	0.86	1	CLONAL	1	TRUE	1	0.679597995531169	2		412	499	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107036	11107038	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs747503505	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	13	455	0	ENST00000358026.2:c.1746_1748del	p.Lys588del	p.K588del	ENST00000358026	NM_001128849.1	581	AAG/-	10/36	1	2	FACETS	0.06	0.042	0.081	0.06	0.042	0.081	SUBCLONAL	1	TRUE	1	0.679597995531169	2		455	643	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054705	13054705	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	61	472	0	ENST00000316448.5:c.1232G>A	p.Gly411Asp	p.G411D	ENST00000316448	NM_004343.3	411	gGc/gAc	9/9	1	2	FACETS	0.284	0.244	0.326	0.284	0.244	0.326	SUBCLONAL	1	TRUE	1	0.679597995531169	2		472	633	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298755	15298755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	124	403	0	ENST00000263388.2:c.1543C>T	p.Pro515Ser	p.P515S	ENST00000263388	NM_000435.2	515	Ccc/Tcc	10/33	1	2	FACETS	0.781	0.712	0.854	0.781	0.712	0.854	SUBCLONAL	1	TRUE	1	0.679597995531169	2		403	467	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546656	9546656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	42	460	0	ENST00000353224.5:c.1366G>A	p.Gly456Arg	p.G456R	ENST00000353224	NM_177990.2	456	Ggg/Agg	5/10	1	2	FACETS	0.214	0.178	0.254	0.214	0.178	0.254	SUBCLONAL	1	TRUE	1	0.679597995531169	2		460	578	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629144	187629144	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	154	420	0	ENST00000441802.2:c.1838A>T	p.Asp613Val	p.D613V	ENST00000441802	NM_005245.3	613	gAt/gTt	2/27	1	2	FACETS	0.78	0.717	0.845	0.78	0.717	0.845	SUBCLONAL	1	TRUE	1	0.679597995531169	2		420	581	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289209	33289209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	60	478	0	ENST00000374542.5:c.343C>T	p.Arg115Trp	p.R115W	ENST00000374542	NM_001141970.1	115	Cgg/Tgg	3/8	1	2	FACETS	0.254	0.218	0.293	0.254	0.218	0.293	SUBCLONAL	1	TRUE	1	0.679597995531169	2		478	695	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959066	2959066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772566311	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	112	443	0	ENST00000396946.4:c.2450C>T	p.Ala817Val	p.A817V	ENST00000396946	NM_032415.4	817	gCg/gTg	18/25	0.679597995531169	3	FACETS	0.537	0.483	0.595	0.269	0.241	0.298	SUBCLONAL	1	TRUE	1	0.679597995531169	3		443	822	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935601	13935601	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1348279586	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	188	394	0	ENST00000405192.2:c.1255A>G	p.Ile419Val	p.I419V	ENST00000405192	NM_001163147.1	419	Atc/Gtc	12/12	0.679597995531169	3	FACETS	1	0.956	1	0.521	0.483	0.561	CLONAL	1	TRUE	1	0.679597995531169	3		394	711	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404282	139404282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	44	523	0	ENST00000277541.6:c.2872G>A	p.Ala958Thr	p.A958T	ENST00000277541	NM_017617.3	958	Gcc/Acc	18/34	1	2	FACETS	0.199	0.166	0.236	0.199	0.166	0.236	SUBCLONAL	1	TRUE	1	0.679597995531169	2		523	650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0064151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	145	515	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.456793220271649	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.456793220271649	1		515	429	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99460079	99460079	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	36	388	0	ENST00000268035.6:c.2175C>A	p.Phe725Leu	p.F725L	ENST00000268035	NM_000875.3	725	ttC/ttA	10/21	0.180667644381772	3	FACETS	0.398	0.326	0.478	0.199	0.163	0.239	INDETERMINATE	1	TRUE	1	0.456793220271649	3		388	487	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556236	29556240	+	frameshift_variant	Frame_Shift_Del	DEL	GTCCA	GTCCA	-	novel	NA	P-0064151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	108	370	0	ENST00000356175.3:c.2606_2610del	p.Pro869GlnfsTer2	p.P869Qfs*2	ENST00000356175	NM_000267.3	868	gGTCCA/g	21/57	0.456793220271649	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.456793220271649	1		370	335	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87475589	87476040	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATGATCTCTCCACTAAGGGGGAAGAAAGAAAGTGAGAAAGAAAGAAAACAGCTCAGAGCCCTTAACCCTGGGTTGTGGCTATTTTTCTCATAGACAGGCTGCTCTCTCTTATCTGATTGGAGCCTCCGTGTTCTCTGAATAGGAAATAAATCTCTACACAAAAATCCAAGGGTTAGTTTCCAGGTGTTTGATAGGAAGCTTTCATCCCAAGTGGTTTGTTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTTTGTCGGGGGGAGTTTGTTGCATTATTTGACCAAGGACAGTGTTGACCACCTCCGGTTTCTACTTCTCTTTCGAAGTTTATTTTATGTTTTGTTGTGGTTTTCAGATTTCTCATGGTTTGGATTTGGGAAAGTAAAATCAAGACAAGGTGTTGGTAAGTAGTTAACTCACTCCTTCTTTGGATAAGTAATG	ATGATCTCTCCACTAAGGGGGAAGAAAGAAAGTGAGAAAGAAAGAAAACAGCTCAGAGCCCTTAACCCTGGGTTGTGGCTATTTTTCTCATAGACAGGCTGCTCTCTCTTATCTGATTGGAGCCTCCGTGTTCTCTGAATAGGAAATAAATCTCTACACAAAAATCCAAGGGTTAGTTTCCAGGTGTTTGATAGGAAGCTTTCATCCCAAGTGGTTTGTTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTTTGTCGGGGGGAGTTTGTTGCATTATTTGACCAAGGACAGTGTTGACCACCTCCGGTTTCTACTTCTCTTTCGAAGTTTATTTTATGTTTTGTTGTGGTTTTCAGATTTCTCATGGTTTGGATTTGGGAAAGTAAAATCAAGACAAGGTGTTGGTAAGTAGTTAACTCACTCCTTCTTTGGATAAGTAATG	-	novel	NA	P-0064151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2	59	12	0	ENST00000277120.3:c.1397-365_1444+39del		p.X466_splice	ENST00000277120		466		13/19	1	2	FACETS	1	0.982	1	1	0.988	1	CLONAL	4	TRUE	1	0.456793220271649	2		12	61	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579381	7579381	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	266	490	0	ENST00000269305.4:c.306del	p.Tyr103ThrfsTer20	p.Y103Tfs*20	ENST00000269305	NM_001126112.2	102	acC/ac	4/11	0.461599841152435	4	FACETS	0.974	0.93	1	0.974	0.93	1	CLONAL	4	TRUE	0	0.482005449594655	4		490	420	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780589	56780589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	47	251	0	ENST00000337432.4:c.604G>A	p.Asp202Asn	p.D202N	ENST00000337432	NM_058216.2	202	Gat/Aat	4/9	0.475070343652694	3	FACETS	0.883	0.751	1	0.294	0.25	0.343	CLONAL	1	TRUE	0	0.482005449594655	3		251	274	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876997	151877000	+	frameshift_variant	Frame_Shift_Del	DEL	TATC	TATC	-	novel	NA	P-0064151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	47	445	0	ENST00000262189.6:c.7361_7364del	p.Arg2454MetfsTer21	p.R2454Mfs*21	ENST00000262189	NM_170606.2	2454	aGATAt/at	37/59	0.462540038457521	1	FACETS	0.722	0.617	0.835	0.722	0.617	0.835	SUBCLONAL	1	TRUE	0	0.482005449594655	1		445	205	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97876986	97876986	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs730881721	NA	P-0064151-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	180	311	0	ENST00000289081.3:c.1079C>G	p.Pro360Arg	p.P360R	ENST00000289081	NM_000136.2	360	cCt/cGt	12/15	0.476529809190399	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	3	TRUE	0	0.482005449594655	3		311	300	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	156	460	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.43	2		460	706	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249857	133249857	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1565972665	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	134	356	0	ENST00000320574.5:c.1366G>C	p.Ala456Pro	p.A456P	ENST00000320574	NM_006231.2	456	Gcc/Ccc	14/49	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.43	2		356	582	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	50	354	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.919	0.787	1	0.919	0.787	1	CLONAL	1	TRUE	1	0.43	2		354	253	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038133	128038133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369244363	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	118	301	0	ENST00000285398.2:c.1417G>A	p.Glu473Lys	p.E473K	ENST00000285398	NM_000122.1	473	Gaa/Aaa	9/15	1	2	FACETS	0.977	0.884	1	0.977	0.884	1	CLONAL	1	TRUE	1	0.43	2		301	562	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	77	344	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.95	0.839	1	0.95	0.839	1	CLONAL	1	TRUE	1	0.43	2		344	377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	55	583	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.349	0.297	0.405	0.349	0.297	0.405	SUBCLONAL	1	TRUE	1	0.43	2		583	734	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	28	283	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.728	0.587	0.885	0.728	0.587	0.885	SUBCLONAL	1	TRUE	1	0.43	2		283	179	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	43	274	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.952	0.806	1	0.952	0.806	1	CLONAL	1	TRUE	1	0.43	2		274	210	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102080254	102080254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193100333	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	41	270	0	ENST00000282441.5:c.991C>T	p.Arg331Trp	p.R331W	ENST00000282441	NM_001130145.2	331	Cgg/Tgg	6/9	1	2	FACETS	0.722	0.605	0.85	0.722	0.605	0.85	SUBCLONAL	1	TRUE	1	0.43	2		270	264	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510160	149510160	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772355478	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	129	392	0	ENST00000261799.4:c.1309C>T	p.Arg437Cys	p.R437C	ENST00000261799	NM_002609.3	437	Cgt/Tgt	9/23	1	2	FACETS	0.855	0.776	0.937	0.855	0.776	0.937	CLONAL	1	TRUE	1	0.43	2		392	702	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224207	53224207	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202160290	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	144	458	0	ENST00000375401.3:c.3344G>A	p.Arg1115His	p.R1115H	ENST00000375401	NM_004187.3	1115	cGc/cAc	22/26	1	2	FACETS	0.961	0.878	1	0.961	0.878	1	CLONAL	1	TRUE	1	0.43	2		458	697	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208010	5208010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	159	494	0	ENST00000357368.4:c.5701C>T	p.Arg1901Trp	p.R1901W	ENST00000357368	NM_002850.3	1901	Cgg/Tgg	37/38	1	2	FACETS	0.958	0.879	1	0.958	0.879	1	CLONAL	1	TRUE	1	0.43	2		494	772	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332565	70332565	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs185830524	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	73	281	0	ENST00000373644.4:c.470C>T	p.Ser157Leu	p.S157L	ENST00000373644	NM_030625.2	157	tCg/tTg	2/12	1	2	FACETS	0.877	0.771	0.99	0.877	0.771	0.99	CLONAL	1	TRUE	1	0.43	2		281	387	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245866	41245866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	51	321	0	ENST00000357654.3:c.1682C>T	p.Ser561Phe	p.S561F	ENST00000357654	NM_007294.3	561	tCt/tTt	10/23	0.123278900452651	0	FACETS	0.58	0.498	0.668			1	INDETERMINATE	1	TRUE	0	0.43	0		321	233	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484414	57484414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	106	373	0	ENST00000371085.3:c.595C>T	p.Arg199Cys	p.R199C	ENST00000371085	NM_000516.4	199	Cgc/Tgc	8/13	1	2	FACETS	0.882	0.793	0.976	0.882	0.793	0.976	CLONAL	1	TRUE	1	0.43	2		373	559	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051645	13051645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375135016	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	105	429	0	ENST00000316448.5:c.904G>A	p.Asp302Asn	p.D302N	ENST00000316448	NM_004343.3	302	Gat/Aat	7/9	1	2	FACETS	0.76	0.681	0.842	0.76	0.681	0.842	SUBCLONAL	1	TRUE	1	0.43	2		429	643	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267600319	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	107	357	0	ENST00000257430.4:c.4199C>T	p.Ser1400Leu	p.S1400L	ENST00000257430	NM_000038.5	1400	tCg/tTg	16/16	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.43	2		357	474	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021728	71021728	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1559602356	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	84	330	0	ENST00000318789.4:c.1630C>T	p.Arg544Ter	p.R544*	ENST00000318789	NM_032682.5	544	Cga/Tga	18/21	1	2	FACETS	0.913	0.81	1	0.913	0.81	1	CLONAL	1	TRUE	1	0.43	2		330	428	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670875	134670875	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	96	366	0	ENST00000398015.3:c.786G>T	p.Glu262Asp	p.E262D	ENST00000398015	NM_004441.4	262	gaG/gaT	3/16	1	2	FACETS	0.758	0.677	0.844	0.758	0.677	0.844	SUBCLONAL	1	TRUE	1	0.43	2		366	589	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518309	187518309	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs191917852	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	109	412	0	ENST00000441802.2:c.12385G>A	p.Asp4129Asn	p.D4129N	ENST00000441802	NM_005245.3	4129	Gac/Aac	25/27	1	2	FACETS	0.889	0.801	0.982	0.889	0.801	0.982	CLONAL	1	TRUE	1	0.43	2		412	570	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956553	93956553	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1035177735	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	63	333	1	ENST00000369303.4:c.2683C>T	p.Arg895Ter	p.R895*	ENST00000369303	NM_004440.3	895	Cga/Tga	15/17	1	2	FACETS	0.819	0.712	0.933	0.819	0.712	0.933	CLONAL	1	TRUE	1	0.43	2		334	358	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674233	86674233	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1463885690	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	35	306	0	ENST00000274376.6:c.2365C>T	p.Arg789Ter	p.R789*	ENST00000274376	NM_002890.2	789	Cga/Tga	18/25	1	2	FACETS	0.656	0.541	0.784	0.656	0.541	0.784	SUBCLONAL	1	TRUE	1	0.43	2		306	248	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839785	42839785	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773001010	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	117	340	0	ENST00000398585.3:c.1454C>T	p.Ser485Leu	p.S485L	ENST00000398585	NM_001135099.1	485	tCg/tTg	13/14	1	2	FACETS	0.938	0.849	1	0.938	0.849	1	CLONAL	1	TRUE	1	0.43	2		340	580	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877391	40877391	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372713520	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	121	392	0	ENST00000373198.4:c.2305G>A	p.Val769Met	p.V769M	ENST00000373198	NM_133170.3	769	Gtg/Atg	15/32	1	2	FACETS	0.906	0.821	0.996	0.906	0.821	0.996	CLONAL	1	TRUE	1	0.43	2		392	621	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250046	53250046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1569282235	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	106	396	0	ENST00000375401.3:c.203G>A	p.Arg68Gln	p.R68Q	ENST00000375401	NM_004187.3	68	cGa/cAa	2/26	1	2	FACETS	0.927	0.834	1	0.927	0.834	1	CLONAL	1	TRUE	1	0.43	2		396	532	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156011	119156011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143034856	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	155	459	0	ENST00000264033.4:c.1676G>A	p.Arg559Gln	p.R559Q	ENST00000264033	NM_005188.3	559	cGa/cAa	11/16	1	2	FACETS	0.92	0.843	1	0.92	0.843	1	CLONAL	1	TRUE	1	0.43	2		459	784	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925397	114925397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773530340	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	68	432	0	ENST00000543371.1:c.1475C>T	p.Ser492Leu	p.S492L	ENST00000543371	NM_001198531.1	492	tCg/tTg	14/14	1	2	FACETS	0.494	0.43	0.564	0.494	0.43	0.564	SUBCLONAL	1	TRUE	1	0.43	2		432	640	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589618	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519838	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	30	259	0	ENST00000274335.5:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000274335		461	Cga/Tga	10/15	1	2	FACETS	1	0.821	1	1	0.821	1	CLONAL	1	TRUE	1	0.43	2		259	139	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685312	86685312	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	80	284	0	ENST00000274376.6:c.3028C>T	p.Arg1010Ter	p.R1010*	ENST00000274376	NM_002890.2	1010	Cga/Tga	24/25	1	2	FACETS	0.899	0.795	1	0.899	0.795	1	CLONAL	1	TRUE	1	0.43	2		284	414	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911140	29911140	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	128	404	0	ENST00000376809.5:c.439T>G	p.Tyr147Asp	p.Y147D	ENST00000376809	NM_002116.7	147	Tac/Gac	3/8	1	2	FACETS	0.971	0.883	1	0.971	0.883	1	CLONAL	1	TRUE	1	0.43	2		404	613	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958788	55958788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780764266	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	54	247	0	ENST00000263923.4:c.3065G>A	p.Arg1022Gln	p.R1022Q	ENST00000263923	NM_002253.2	1022	cGa/cAa	22/30	1	2	FACETS	0.973	0.839	1	0.973	0.839	1	CLONAL	1	TRUE	1	0.43	2		247	258	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030396	49030396	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	56	310	0	ENST00000267163.4:c.1871C>A	p.Ser624Tyr	p.S624Y	ENST00000267163	NM_000321.2	624	tCt/tAt	19/27	1	2	FACETS	0.883	0.762	1	0.883	0.762	1	CLONAL	1	TRUE	1	0.43	2		310	295	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504590	103504590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1400329743	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	57	264	0	ENST00000355739.4:c.211C>T	p.Arg71Cys	p.R71C	ENST00000355739	NM_000123.3	71	Cgt/Tgt	2/15	1	2	FACETS	0.989	0.857	1	0.989	0.857	1	CLONAL	1	TRUE	1	0.43	2		264	268	SUCCESS
APC	324	MSKCC	GRCh37	5	112177368	112177368	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	61	361	0	ENST00000257430.4:c.6077C>A	p.Ser2026Tyr	p.S2026Y	ENST00000257430	NM_000038.5	2026	tCt/tAt	16/16	1	2	FACETS	0.887	0.77	1	0.887	0.77	1	CLONAL	1	TRUE	1	0.43	2		361	320	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42002991	42002991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375278041	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	64	353	0	ENST00000219905.7:c.2528G>A	p.Gly843Asp	p.G843D	ENST00000219905	NM_001164273.1	843	gGt/gAt	8/24	1	2	FACETS	0.858	0.747	0.976	0.858	0.747	0.976	CLONAL	1	TRUE	1	0.43	2		353	347	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690230	47690230	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63749947	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	43	299	0	ENST00000233146.2:c.1447G>T	p.Glu483Ter	p.E483*	ENST00000233146	NM_000251.2	483	Gaa/Taa	9/16	1	2	FACETS	0.877	0.741	1	0.877	0.741	1	CLONAL	1	TRUE	1	0.43	2		299	228	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417818	138417818	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	58	270	0	ENST00000289153.2:c.1701G>T	p.Glu567Asp	p.E567D	ENST00000289153	NM_006219.2	567	gaG/gaT	11/22	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.43	2		270	241	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265314	152265314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781741770	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	86	342	0	ENST00000206249.3:c.767G>A	p.Arg256Gln	p.R256Q	ENST00000206249	NM_000125.3	256	cGa/cAa	4/8	1	2	FACETS	0.893	0.793	0.998	0.893	0.793	0.998	CLONAL	1	TRUE	1	0.43	2		342	448	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471048	8471048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	62	289	0	ENST00000356435.5:c.3451C>T	p.Arg1151Cys	p.R1151C	ENST00000356435		1151	Cgc/Tgc	20/35	1	2	FACETS	0.921	0.802	1	0.921	0.802	1	CLONAL	1	TRUE	1	0.43	2		289	313	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622451	28622451	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	50	317	0	ENST00000241453.7:c.1166C>A	p.Ser389Ter	p.S389*	ENST00000241453	NM_004119.2	389	tCa/tAa	9/24	1	2	FACETS	0.825	0.705	0.955	0.825	0.705	0.955	CLONAL	1	TRUE	1	0.43	2		317	282	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964530	70964530	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	118	436	0	ENST00000276594.2:c.1498G>T	p.Ala500Ser	p.A500S	ENST00000276594	NM_024504.3	500	Gcc/Tcc	8/8	1	2	FACETS	0.827	0.747	0.91	0.827	0.747	0.91	CLONAL	1	TRUE	1	0.43	2		436	664	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914736	32914736	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	34	352	0	ENST00000380152.3:c.6244G>A	p.Glu2082Lys	p.E2082K	ENST00000380152		2082	Gaa/Aaa	11/27	1	2	FACETS	0.841	0.694	1	0.841	0.694	1	CLONAL	1	TRUE	1	0.43	2		352	188	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013719	170013719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388201066	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	44	227	0	ENST00000295797.4:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000295797	NM_002740.5	480	Cgc/Tgc	15/18	1	2	FACETS	0.829	0.7	0.968	0.829	0.7	0.968	CLONAL	1	TRUE	1	0.43	2		227	247	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016182	31016182	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144437064	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	74	387	0	ENST00000375687.4:c.428G>A	p.Arg143Gln	p.R143Q	ENST00000375687	NM_015338.5	143	cGa/cAa	6/13	1	2	FACETS	0.72	0.632	0.814	0.72	0.632	0.814	SUBCLONAL	1	TRUE	1	0.43	2		387	478	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188981	142188981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1032148842	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	19	289	0	ENST00000350721.4:c.6266G>A	p.Arg2089Gln	p.R2089Q	ENST00000350721	NM_001184.3	2089	cGa/cAa	37/47	1	2	FACETS	0.581	0.445	0.739	0.581	0.445	0.739	SUBCLONAL	1	TRUE	1	0.43	2		289	152	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026606	48026606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1358771617	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	107	378	0	ENST00000234420.5:c.1484G>A	p.Arg495Gln	p.R495Q	ENST00000234420	NM_000179.2	495	cGa/cAa	4/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.43	2		378	442	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128201272	128201272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779657195	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	166	415	0	ENST00000265960.3:c.1463C>T	p.Ser488Leu	p.S488L	ENST00000265960	NM_001006617.1	488	tCg/tTg	12/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.43	2		415	632	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55729505	55729505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1409691153	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	127	383	0	ENST00000284073.2:c.773C>T	p.Ala258Val	p.A258V	ENST00000284073	NM_138962.2	258	gCg/gTg	11/14	1	2	FACETS	0.923	0.838	1	0.923	0.838	1	CLONAL	1	TRUE	1	0.43	2		383	640	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420778	49420778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1427665021	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	168	502	0	ENST00000301067.7:c.14971C>T	p.Arg4991Trp	p.R4991W	ENST00000301067	NM_003482.3	4991	Cgg/Tgg	48/54	1	2	FACETS	0.932	0.858	1	0.932	0.858	1	CLONAL	1	TRUE	1	0.43	2		502	838	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526547	66526547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	89	375	0	ENST00000358598.2:c.1103G>A	p.Arg368Gln	p.R368Q	ENST00000358598	NM_212471.2	368	cGa/cAa	11/11	1	2	FACETS	0.741	0.658	0.828	0.741	0.658	0.828	SUBCLONAL	1	TRUE	1	0.43	2		375	559	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163297332	163297332	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1292835761	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	29	280	0	ENST00000271452.3:c.178C>T	p.Arg60Ter	p.R60*	ENST00000271452	NM_145697.2	60	Cga/Tga	3/14	1	2	FACETS	0.937	0.762	1	0.937	0.762	1	CLONAL	1	TRUE	1	0.43	2		280	144	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733583	85733583	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	75	360	0	ENST00000370580.1:c.429C>A	p.Phe143Leu	p.F143L	ENST00000370580	NM_003921.4	143	ttC/ttA	3/3	1	2	FACETS	0.908	0.801	1	0.908	0.801	1	CLONAL	1	TRUE	1	0.43	2		360	384	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277291	41277291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	92	326	0	ENST00000349496.5:c.1760G>A	p.Arg587Gln	p.R587Q	ENST00000349496	NM_001904.3	587	cGa/cAa	11/15	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.43	2		326	420	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525837	148525837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765147666	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	41	353	0	ENST00000320356.2:c.620G>A	p.Arg207Gln	p.R207Q	ENST00000320356	NM_004456.4	207	cGa/cAa	6/20	1	2	FACETS	0.717	0.601	0.844	0.717	0.601	0.844	SUBCLONAL	1	TRUE	1	0.43	2		353	266	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056830	102056830	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	49	274	0	ENST00000282441.5:c.770C>A	p.Ser257Tyr	p.S257Y	ENST00000282441	NM_001130145.2	257	tCt/tAt	4/9	1	2	FACETS	0.873	0.746	1	0.873	0.746	1	CLONAL	1	TRUE	1	0.43	2		274	261	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350048	89350048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1164325679	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	171	527	0	ENST00000301030.4:c.2902C>T	p.Pro968Ser	p.P968S	ENST00000301030	NM_001256183.1	968	Ccc/Tcc	9/13	1	2	FACETS	0.899	0.827	0.973	0.899	0.827	0.973	CLONAL	1	TRUE	1	0.43	2		527	885	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881515	48881515	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	35	291	0	ENST00000267163.4:c.237G>T	p.Glu79Asp	p.E79D	ENST00000267163	NM_000321.2	79	gaG/gaT	2/27	1	2	FACETS	0.711	0.587	0.848	0.711	0.587	0.848	SUBCLONAL	1	TRUE	1	0.43	2		291	229	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258560	19258560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372543417	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	180	494	0	ENST00000162023.5:c.340C>T	p.Arg114Trp	p.R114W	ENST00000162023		114	Cgg/Tgg	8/13	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.43	2		494	785	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650701	67650701	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	117	332	0	ENST00000264010.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000264010	NM_006565.3	336	Gaa/Taa	5/12	1	2	FACETS	0.864	0.781	0.951	0.864	0.781	0.951	CLONAL	1	TRUE	1	0.43	2		332	630	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281633	142281633	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	53	300	0	ENST00000350721.4:c.611T>G	p.Phe204Cys	p.F204C	ENST00000350721	NM_001184.3	204	tTt/tGt	4/47	1	2	FACETS	0.91	0.782	1	0.91	0.782	1	CLONAL	1	TRUE	1	0.43	2		300	271	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662661	227662661	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776343218	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	152	475	0	ENST00000305123.5:c.794G>A	p.Arg265His	p.R265H	ENST00000305123	NM_005544.2	265	cGc/cAc	1/2	1	2	FACETS	0.971	0.89	1	0.971	0.89	1	CLONAL	1	TRUE	1	0.43	2		475	728	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527595	41527595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	135	376	0	ENST00000263253.7:c.1486C>T	p.Pro496Ser	p.P496S	ENST00000263253	NM_001429.3	496	Cct/Tct	6/31	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.43	2		376	615	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332918	153332918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471232420	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	96	368	0	ENST00000281708.4:c.38G>A	p.Arg13Gln	p.R13Q	ENST00000281708	NM_033632.3	13	cGa/cAa	2/12	1	2	FACETS	0.923	0.826	1	0.923	0.826	1	CLONAL	1	TRUE	1	0.43	2		368	484	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218892	193218892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1225502334	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	29	287	0	ENST00000367435.3:c.1450C>T	p.Arg484Cys	p.R484C	ENST00000367435	NM_024529.4	484	Cgt/Tgt	16/17	1	2	FACETS	0.729	0.59	0.884	0.729	0.59	0.884	SUBCLONAL	1	TRUE	1	0.43	2		287	185	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145001	58145001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772938517	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	178	460	0	ENST00000257904.6:c.343G>A	p.Glu115Lys	p.E115K	ENST00000257904	NM_000075.3	115	Gaa/Aaa	3/8	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.43	2		460	805	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641346	23641346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759024828	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	94	408	0	ENST00000261584.4:c.2129C>T	p.Thr710Met	p.T710M	ENST00000261584	NM_024675.3	710	aCg/aTg	5/13	1	2	FACETS	0.913	0.816	1	0.913	0.816	1	CLONAL	1	TRUE	1	0.43	2		408	479	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740765	58740765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201236946	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	101	420	0	ENST00000305921.3:c.1670G>A	p.Arg557Gln	p.R557Q	ENST00000305921	NM_003620.3	557	cGa/cAa	6/6	1	2	FACETS	0.827	0.741	0.918	0.827	0.741	0.918	CLONAL	1	TRUE	1	0.43	2		420	568	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430375	78430375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569612114	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	26	356	1	ENST00000370768.2:c.793C>T	p.Arg265Trp	p.R265W	ENST00000370768	NM_003902.3	265	Cgg/Tgg	10/20	1	2	FACETS	0.474	0.377	0.585	0.474	0.377	0.585	SUBCLONAL	1	TRUE	1	0.43	2		357	255	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804954	43804954	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	112	382	0	ENST00000372470.3:c.404C>T	p.Pro135Leu	p.P135L	ENST00000372470	NM_005373.2	135	cCc/cTc	4/12	1	2	FACETS	0.861	0.776	0.95	0.861	0.776	0.95	CLONAL	1	TRUE	1	0.43	2		382	605	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255206	16255206	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780359509	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	37	426	0	ENST00000375759.3:c.2471G>A	p.Arg824His	p.R824H	ENST00000375759	NM_015001.2	824	cGc/cAc	11/15	1	2	FACETS	0.359	0.295	0.429	0.359	0.295	0.429	SUBCLONAL	1	TRUE	1	0.43	2		426	480	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425854	49425854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760279999	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	174	535	0	ENST00000301067.7:c.12634C>T	p.Arg4212Trp	p.R4212W	ENST00000301067	NM_003482.3	4212	Cgg/Tgg	39/54	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.43	2		535	795	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151932991	151932991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759973306	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	32	94	0	ENST00000262189.6:c.2680C>T	p.Arg894Trp	p.R894W	ENST00000262189	NM_170606.2	894	Cgg/Tgg	16/59	1	2	FACETS	0.924	0.76	1	0.924	0.76	1	CLONAL	1	TRUE	1	0.43	2		94	161	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281068	49281068	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	63	365	0	ENST00000282018.3:c.115G>T	p.Glu39Ter	p.E39*	ENST00000282018	NM_020377.2	39	Gaa/Taa	1/1	1	2	FACETS	0.936	0.816	1	0.936	0.816	1	CLONAL	1	TRUE	1	0.43	2		365	313	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095927	29095927	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555915589	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	92	318	0	ENST00000328354.6:c.909-2A>G		p.X303_splice	ENST00000328354	NM_007194.3	303			1	2	FACETS	0.973	0.869	1	0.973	0.869	1	CLONAL	1	TRUE	1	0.43	2		318	440	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435826	116435826	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1436537175	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	90	380	0	ENST00000397752.3:c.3916G>A	p.Glu1306Lys	p.E1306K	ENST00000397752	NM_000245.2	1306	Gaa/Aaa	20/21	1	2	FACETS	0.87	0.775	0.971	0.87	0.775	0.971	CLONAL	1	TRUE	1	0.43	2		380	481	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190656564	190656564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370084230	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	66	290	0	ENST00000441310.2:c.29G>A	p.Arg10Gln	p.R10Q	ENST00000441310	NM_000534.4	10	cGa/cAa	2/13	1	2	FACETS	0.95	0.831	1	0.95	0.831	1	CLONAL	1	TRUE	1	0.43	2		290	323	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845478	151845478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs375361560	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	101	432	0	ENST00000262189.6:c.13534C>A	p.His4512Asn	p.H4512N	ENST00000262189	NM_170606.2	4512	Cat/Aat	52/59	1	2	FACETS	0.86	0.771	0.954	0.86	0.771	0.954	CLONAL	1	TRUE	1	0.43	2		432	546	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190075	123190075	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	41	224	0	ENST00000218089.9:c.1294C>A	p.Leu432Ile	p.L432I	ENST00000218089	NM_001042749.1	432	Ctc/Atc	14/35	1	2	FACETS	0.953	0.803	1	0.953	0.803	1	CLONAL	1	TRUE	1	0.43	2		224	200	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200823	67200823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750710697	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	132	487	0	ENST00000312629.5:c.811G>A	p.Ala271Thr	p.A271T	ENST00000312629	NM_003952.2	271	Gca/Aca	10/15	1	2	FACETS	0.849	0.772	0.93	0.849	0.772	0.93	CLONAL	1	TRUE	1	0.43	2		487	723	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496961	29496961	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	40	186	0	ENST00000356175.3:c.532G>T	p.Glu178Ter	p.E178*	ENST00000356175	NM_000267.3	178	Gaa/Taa	5/57	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.43	2		186	183	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6213975	6213976	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs772076449	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	68	380	1	ENST00000252674.7:c.1381dup	p.Gln461ProfsTer23	p.Q461Pfs*23	ENST00000252674	NM_005934.3	461	cag/cCag	9/12	1	2	FACETS	0.549	0.478	0.626	0.549	0.478	0.626	SUBCLONAL	1	TRUE	1	0.43	2		381	576	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95583017	95583017	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886037672	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	33	336	0	ENST00000393063.1:c.1525C>T	p.Arg509Ter	p.R509*	ENST00000393063	NM_030621.3	509	Cga/Tga	11/28	1	2	FACETS	0.624	0.511	0.75	0.624	0.511	0.75	SUBCLONAL	1	TRUE	1	0.43	2		336	246	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39318060	39318060	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	37	250	0	ENST00000373001.3:c.742A>C	p.Asn248His	p.N248H	ENST00000373001	NM_022157.3	248	Aat/Cat	4/7	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.43	2		250	155	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94926679	94926679	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1336039287	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	32	253	0	ENST00000536441.1:c.86G>T	p.Arg29Ile	p.R29I	ENST00000536441	NM_144665.3	29	aGa/aTa	2/10	1	2	FACETS	0.8	0.656	0.96	0.8	0.656	0.96	CLONAL	1	TRUE	1	0.43	2		253	186	SUCCESS
ATM	472	MSKCC	GRCh37	11	108099904	108099904	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1259911051	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	27	203	0	ENST00000278616.4:c.186-1G>A		p.X62_splice	ENST00000278616	NM_000051.3	62			1	2	FACETS	0.903	0.729	1	0.903	0.729	1	CLONAL	1	TRUE	1	0.43	2		203	139	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112919990	112919990	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	58	224	0	ENST00000351677.2:c.1205A>C	p.Lys402Thr	p.K402T	ENST00000351677	NM_002834.3	402	aAa/aCa	10/16	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.43	2		224	260	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032258	10032258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs766473924	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	85	380	0	ENST00000330684.3:c.565A>G	p.Thr189Ala	p.T189A	ENST00000330684	NM_001134407.1	189	Acc/Gcc	3/13	1	2	FACETS	0.756	0.67	0.848	0.756	0.67	0.848	SUBCLONAL	1	TRUE	1	0.43	2		380	523	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56376693	56376693	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	55	370	0	ENST00000348428.3:c.733G>A	p.Val245Ile	p.V245I	ENST00000348428	NM_006785.3	245	Gtt/Att	5/17	1	2	FACETS	0.68	0.584	0.785	0.68	0.584	0.785	SUBCLONAL	1	TRUE	1	0.43	2		370	376	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468157	25468157	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	131	376	0	ENST00000264709.3:c.1519C>A	p.Pro507Thr	p.P507T	ENST00000264709	NM_175629.2	507	Ccc/Acc	13/23	1	2	FACETS	0.869	0.79	0.952	0.869	0.79	0.952	CLONAL	1	TRUE	1	0.43	2		376	701	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528165	157528165	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1206220417	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	155	449	0	ENST00000346085.5:c.5890G>A	p.Glu1964Lys	p.E1964K	ENST00000346085	NM_020732.3	1964	Gaa/Aaa	20/20	0.139648455630131	3	FACETS	1	0.974	1	0.577	0.529	0.627	INDETERMINATE	1	TRUE	1	0.43	3		449	759	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732802	44732802	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	123	342	0	ENST00000377967.4:c.5A>C	p.Lys2Thr	p.K2T	ENST00000377967	NM_021140.2	2	aAa/aCa	1/29	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.43	2		342	548	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743776	46743776	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	148	499	0	ENST00000371975.4:c.2066A>G	p.Gln689Arg	p.Q689R	ENST00000371975	NM_003579.3	689	cAg/cGg	18/18	1	2	FACETS	0.931	0.852	1	0.931	0.852	1	CLONAL	1	TRUE	1	0.43	2		499	739	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166204	118166204	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	151	504	0	ENST00000369448.3:c.714A>C	p.Glu238Asp	p.E238D	ENST00000369448	NM_017709.3	238	gaA/gaC	2/2	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.43	2		504	700	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404661	70404661	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	69	433	0	ENST00000373644.4:c.2175T>G	p.Asp725Glu	p.D725E	ENST00000373644	NM_030625.2	725	gaT/gaG	4/12	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.43	2		433	284	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69458665	69458665	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	134	353	0	ENST00000227507.2:c.480C>A	p.Phe160Leu	p.F160L	ENST00000227507	NM_053056.2	160	ttC/ttA	3/5	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.43	2		353	593	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984923	101984923	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587777249	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	72	264	0	ENST00000282441.5:c.370C>T	p.Arg124Ter	p.R124*	ENST00000282441	NM_001130145.2	124	Cga/Tga	2/9	1	2	FACETS	0.833	0.731	0.942	0.833	0.731	0.942	CLONAL	1	TRUE	1	0.43	2		264	402	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207756	102207756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1304922616	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	38	337	0	ENST00000263464.3:c.1738G>A	p.Asp580Asn	p.D580N	ENST00000263464	NM_001165.4	580	Gat/Aat	9/9	1	2	FACETS	0.921	0.77	1	0.921	0.77	1	CLONAL	1	TRUE	1	0.43	2		337	192	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028672	42028672	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	83	439	0	ENST00000219905.7:c.4210G>T	p.Asp1404Tyr	p.D1404Y	ENST00000219905	NM_001164273.1	1404	Gac/Tac	13/24	1	2	FACETS	0.871	0.772	0.976	0.871	0.772	0.976	CLONAL	1	TRUE	1	0.43	2		439	443	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50789335	50789335	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	35	327	0	ENST00000307179.4:c.2945G>T	p.Arg982Ile	p.R982I	ENST00000307179		982	aGa/aTa	18/20	1	2	FACETS	0.631	0.52	0.754	0.631	0.52	0.754	SUBCLONAL	1	TRUE	1	0.43	2		327	258	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934807	9934807	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1555494769	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	67	365	0	ENST00000330684.3:c.1483G>T	p.Gly495Ter	p.G495*	ENST00000330684	NM_001134407.1	495	Gga/Tga	6/13	1	2	FACETS	0.878	0.767	0.996	0.878	0.767	0.996	CLONAL	1	TRUE	1	0.43	2		365	355	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014167	14014167	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	110	425	0	ENST00000311895.7:c.145C>A	p.Leu49Ile	p.L49I	ENST00000311895	NM_005236.2	49	Ctc/Atc	1/11	1	2	FACETS	0.893	0.805	0.986	0.893	0.805	0.986	CLONAL	1	TRUE	1	0.43	2		425	573	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063359	67063359	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	93	367	0	ENST00000412916.2:c.49T>C	p.Phe17Leu	p.F17L	ENST00000412916		17	Ttt/Ctt	1/6	1	2	FACETS	0.748	0.667	0.835	0.748	0.667	0.835	SUBCLONAL	1	TRUE	1	0.43	2		367	578	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665815	29665815	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	26	247	0	ENST00000356175.3:c.6850C>A	p.Leu2284Ile	p.L2284I	ENST00000356175	NM_000267.3	2284	Ctt/Att	45/57	1	2	FACETS	0.817	0.655	0.998	0.817	0.655	0.998	CLONAL	1	TRUE	1	0.43	2		247	148	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33434081	33434081	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	135	404	0	ENST00000345365.6:c.406G>T	p.Asp136Tyr	p.D136Y	ENST00000345365	NM_002878.3	136	Gat/Tat	5/10	1	2	FACETS	0.965	0.879	1	0.965	0.879	1	CLONAL	1	TRUE	1	0.43	2		404	651	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243926	41243926	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	81	440	0	ENST00000357654.3:c.3622A>C	p.Lys1208Gln	p.K1208Q	ENST00000357654	NM_007294.3	1208	Aaa/Caa	10/23	0.123278900452651	0	FACETS	0.505	0.447	0.567			1	INDETERMINATE	1	TRUE	0	0.43	0		440	425	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740867	58740867	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	76	345	0	ENST00000305921.3:c.1772G>T	p.Gly591Val	p.G591V	ENST00000305921	NM_003620.3	591	gGa/gTa	6/6	1	2	FACETS	0.752	0.662	0.849	0.752	0.662	0.849	SUBCLONAL	1	TRUE	1	0.43	2		345	470	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59820496	59820496	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	64	304	0	ENST00000259008.2:c.2258-1G>T		p.X753_splice	ENST00000259008	NM_032043.2	753			1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.43	2		304	296	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244481	5244481	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1218428122	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	121	376	0	ENST00000357368.4:c.1001C>T	p.Ala334Val	p.A334V	ENST00000357368	NM_002850.3	334	gCt/gTt	11/38	1	2	FACETS	0.866	0.784	0.952	0.866	0.784	0.952	CLONAL	1	TRUE	1	0.43	2		376	650	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152033	11152033	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1384070535	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	145	399	0	ENST00000358026.2:c.4317G>T	p.Lys1439Asn	p.K1439N	ENST00000358026	NM_001128849.1	1439	aaG/aaT	31/36	1	2	FACETS	0.945	0.863	1	0.945	0.863	1	CLONAL	1	TRUE	1	0.43	2		399	714	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145558	61145558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188947380	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	53	336	0	ENST00000295025.8:c.670G>A	p.Asp224Asn	p.D224N	ENST00000295025	NM_002908.2	224	Gat/Aat	7/11	1	2	FACETS	0.798	0.684	0.92	0.798	0.684	0.92	CLONAL	1	TRUE	1	0.43	2		336	309	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67632097	67632097	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	49	339	0	ENST00000272342.5:c.2283A>G	p.Ile761Met	p.I761M	ENST00000272342	NM_019002.3	761	atA/atG	5/6	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.43	2		339	197	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215609789	215609789	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1574737047	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	46	259	0	ENST00000260947.4:c.1903+2T>C		p.X635_splice	ENST00000260947	NM_000465.2	635			1	2	FACETS	0.817	0.693	0.951	0.817	0.693	0.951	CLONAL	1	TRUE	1	0.43	2		259	262	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225360581	225360581	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	42	235	0	ENST00000264414.4:c.1810C>A	p.Leu604Ile	p.L604I	ENST00000264414	NM_003590.4	604	Ctc/Atc	13/16	1	2	FACETS	0.763	0.642	0.896	0.763	0.642	0.896	SUBCLONAL	1	TRUE	1	0.43	2		235	256	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324191	62324191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769828971	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	126	426	0	ENST00000360203.5:c.2686G>A	p.Ala896Thr	p.A896T	ENST00000360203	NM_001283009.1	896	Gcc/Acc	29/35	1	2	FACETS	0.893	0.811	0.98	0.893	0.811	0.98	CLONAL	1	TRUE	1	0.43	2		426	656	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29442705	29442705	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	106	345	0	ENST00000544604.2:c.746A>C	p.Asn249Thr	p.N249T	ENST00000544604	NM_001206998.1	249	aAt/aCt	6/9	1	2	FACETS	0.976	0.879	1	0.976	0.879	1	CLONAL	1	TRUE	1	0.43	2		345	505	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162778	47162778	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	44	328	0	ENST00000409792.3:c.3348A>T	p.Lys1116Asn	p.K1116N	ENST00000409792	NM_014159.6	1116	aaA/aaT	3/21	1	2	FACETS	0.701	0.591	0.821	0.701	0.591	0.821	SUBCLONAL	1	TRUE	1	0.43	2		328	292	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940120	49940120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761090501	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	163	496	0	ENST00000296474.3:c.923G>A	p.Arg308His	p.R308H	ENST00000296474	NM_002447.2	308	cGc/cAc	1/20	1	2	FACETS	0.939	0.863	1	0.939	0.863	1	CLONAL	1	TRUE	1	0.43	2		496	807	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433368	138433368	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	40	286	0	ENST00000289153.2:c.1244A>C	p.Lys415Thr	p.K415T	ENST00000289153	NM_006219.2	415	aAa/aCa	7/22	1	2	FACETS	0.894	0.751	1	0.894	0.751	1	CLONAL	1	TRUE	1	0.43	2		286	208	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266637	142266637	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	41	342	0	ENST00000350721.4:c.3287T>G	p.Ile1096Arg	p.I1096R	ENST00000350721	NM_001184.3	1096	aTa/aGa	16/47	1	2	FACETS	0.939	0.791	1	0.939	0.791	1	CLONAL	1	TRUE	1	0.43	2		342	203	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1936895	1936895	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	70	339	0	ENST00000382891.5:c.1580A>C	p.Asn527Thr	p.N527T	ENST00000382891	NM_133335.3	527	aAc/aCc	7/22	1	2	FACETS	0.899	0.789	1	0.899	0.789	1	CLONAL	1	TRUE	1	0.43	2		339	362	SUCCESS
REST	5978	MSKCC	GRCh37	4	57797635	57797635	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	109	460	0	ENST00000309042.7:c.2611A>C	p.Asn871His	p.N871H	ENST00000309042	NM_005612.4	871	Aat/Cat	4/4	1	2	FACETS	0.939	0.846	1	0.939	0.846	1	CLONAL	1	TRUE	1	0.43	2		460	540	SUCCESS
ALB	213	MSKCC	GRCh37	4	74283341	74283341	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	54	315	0	ENST00000295897.4:c.1383T>G	p.Cys461Trp	p.C461W	ENST00000295897	NM_000477.5	461	tgT/tgG	11/15	1	2	FACETS	0.934	0.804	1	0.934	0.804	1	CLONAL	1	TRUE	1	0.43	2		315	269	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156006	106156006	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	141	451	0	ENST00000380013.4:c.907A>C	p.Asn303His	p.N303H	ENST00000380013	NM_001127208.2	303	Aat/Cat	3/11	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.43	2		451	655	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156867	106156867	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	111	459	0	ENST00000380013.4:c.1768C>A	p.Leu590Ile	p.L590I	ENST00000380013	NM_001127208.2	590	Ctt/Att	3/11	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.43	2		459	507	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876283	35876283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	98	382	0	ENST00000303115.3:c.1075G>A	p.Glu359Lys	p.E359K	ENST00000303115	NM_002185.3	359	Gaa/Aaa	8/8	1	2	FACETS	0.789	0.705	0.877	0.789	0.705	0.877	SUBCLONAL	1	TRUE	1	0.43	2		382	578	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456997	149456997	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	101	373	0	ENST00000286301.3:c.731T>G	p.Leu244Arg	p.L244R	ENST00000286301	NM_005211.3	244	cTc/cGc	6/22	1	2	FACETS	0.876	0.786	0.972	0.876	0.786	0.972	CLONAL	1	TRUE	1	0.43	2		373	536	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515188	149515188	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	159	485	0	ENST00000261799.4:c.294C>A	p.Tyr98Ter	p.Y98*	ENST00000261799	NM_002609.3	98	taC/taA	3/23	1	2	FACETS	0.976	0.896	1	0.976	0.896	1	CLONAL	1	TRUE	1	0.43	2		485	758	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030262	180030262	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772644486	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	152	456	1	ENST00000261937.6:c.4022C>T	p.Ser1341Leu	p.S1341L	ENST00000261937	NM_182925.4	1341	tCg/tTg	30/30	1	2	FACETS	0.975	0.894	1	0.975	0.894	1	CLONAL	1	TRUE	1	0.43	2		457	725	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910780	29910780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	171	388	0	ENST00000376809.5:c.320G>A	p.Gly107Asp	p.G107D	ENST00000376809	NM_002116.7	107	gGc/gAc	2/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.43	2		388	621	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441589	6441589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	23	100	0	ENST00000356142.4:c.436G>A	p.Glu146Lys	p.E146K	ENST00000356142	NM_018890.3	146	Gag/Aag	6/7	1	2	FACETS	1	0.823	1	1	0.823	1	CLONAL	1	TRUE	1	0.43	2		100	103	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729540	41729540	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	150	487	0	ENST00000242208.4:c.989T>G	p.Phe330Cys	p.F330C	ENST00000242208	NM_002192.2	330	tTc/tGc	3/3	1	2	FACETS	0.94	0.861	1	0.94	0.861	1	CLONAL	1	TRUE	1	0.43	2		487	742	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526676	106526676	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	75	296	0	ENST00000359195.3:c.2969A>C	p.Asp990Ala	p.D990A	ENST00000359195	NM_002649.2	990	gAc/gCc	10/11	1	2	FACETS	0.925	0.816	1	0.925	0.816	1	CLONAL	1	TRUE	1	0.43	2		296	377	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514978	148514978	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	101	355	0	ENST00000320356.2:c.1231A>G	p.Ser411Gly	p.S411G	ENST00000320356	NM_004456.4	411	Agc/Ggc	10/20	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.43	2		355	464	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055690	152055690	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	52	317	0	ENST00000262189.6:c.232G>T	p.Glu78Ter	p.E78*	ENST00000262189	NM_170606.2	78	Gaa/Taa	2/59	1	2	FACETS	0.773	0.662	0.893	0.773	0.662	0.893	SUBCLONAL	1	TRUE	1	0.43	2		317	313	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146216	38146216	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	97	395	0	ENST00000317025.8:c.3290G>A	p.Arg1097His	p.R1097H	ENST00000317025	NM_023034.1	1097	cGc/cAc	19/24	1	2	FACETS	0.806	0.72	0.896	0.806	0.72	0.896	CLONAL	1	TRUE	1	0.43	2		395	560	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146267	38146267	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	99	339	0	ENST00000317025.8:c.3239A>C	p.Lys1080Thr	p.K1080T	ENST00000317025	NM_023034.1	1080	aAa/aCa	19/24	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.43	2		339	445	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981971	70981971	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	137	481	0	ENST00000276594.2:c.125G>A	p.Ser42Asn	p.S42N	ENST00000276594	NM_024504.3	42	aGc/aAc	2/8	1	2	FACETS	0.913	0.832	0.998	0.913	0.832	0.998	CLONAL	1	TRUE	1	0.43	2		481	698	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859902	117859902	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	40	317	0	ENST00000297338.2:c.1733C>T	p.Ser578Phe	p.S578F	ENST00000297338	NM_006265.2	578	tCt/tTt	14/14	1	2	FACETS	0.538	0.448	0.637	0.538	0.448	0.637	SUBCLONAL	1	TRUE	1	0.43	2		317	346	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2029198	2029198	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755744610	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	117	471	0	ENST00000349721.2:c.176C>T	p.Thr59Met	p.T59M	ENST00000349721	NM_003070.3	59	aCg/aTg	2/34	1	2	FACETS	0.888	0.803	0.977	0.888	0.803	0.977	CLONAL	1	TRUE	1	0.43	2		471	613	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080282	5080282	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	43	277	0	ENST00000381652.3:c.2185A>C	p.Asn729His	p.N729H	ENST00000381652	NM_004972.3	729	Aat/Cat	17/25	1	2	FACETS	0.866	0.731	1	0.866	0.731	1	CLONAL	1	TRUE	1	0.43	2		277	231	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779169	135779169	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	101	395	0	ENST00000298552.3:c.2077G>T	p.Asp693Tyr	p.D693Y	ENST00000298552	NM_001162426.1	693	Gac/Tac	17/23	1	2	FACETS	0.824	0.739	0.915	0.824	0.739	0.915	CLONAL	1	TRUE	1	0.43	2		395	570	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340843	70340843	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	116	362	0	ENST00000374080.3:c.576G>T	p.Lys192Asn	p.K192N	ENST00000374080		192	aaG/aaT	5/45	1	2	FACETS	0.974	0.881	1	0.974	0.881	1	CLONAL	1	TRUE	1	0.43	2		362	554	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938195	76938195	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	45	323	0	ENST00000373344.5:c.2553A>C	p.Glu851Asp	p.E851D	ENST00000373344	NM_000489.3	851	gaA/gaC	9/35	1	2	FACETS	0.68	0.574	0.795	0.68	0.574	0.795	SUBCLONAL	1	TRUE	1	0.43	2		323	308	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217343	123217343	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	37	244	0	ENST00000218089.9:c.2997T>G	p.Phe999Leu	p.F999L	ENST00000218089	NM_001042749.1	999	ttT/ttG	29/35	1	2	FACETS	0.865	0.72	1	0.865	0.72	1	CLONAL	1	TRUE	1	0.43	2		244	199	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	290	460	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.956	0.906	1	0.956	0.906	1	CLONAL	1	TRUE	1	0.87	2		460	697	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249857	133249857	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1565972665	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	224	356	0	ENST00000320574.5:c.1366G>C	p.Ala456Pro	p.A456P	ENST00000320574	NM_006231.2	456	Gcc/Ccc	14/49	1	2	FACETS	0.966	0.908	1	0.966	0.908	1	CLONAL	1	TRUE	1	0.87	2		356	533	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021428	42021428	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	229	407	0	ENST00000219905.7:c.3724C>T	p.Arg1242Ter	p.R1242*	ENST00000219905	NM_001164273.1	1242	Cga/Tga	11/24	1	2	FACETS	0.809	0.758	0.86	0.809	0.758	0.86	CLONAL	1	TRUE	1	0.87	2		407	651	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	194	283	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.995	0.932	1	0.995	0.932	1	CLONAL	1	TRUE	1	0.87	2		283	448	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	165	274	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.914	0.849	0.98	0.914	0.849	0.98	CLONAL	1	TRUE	1	0.87	2		274	415	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910943	32910943	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs767686668	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	177	355	0	ENST00000380152.3:c.2451G>T	p.Lys817Asn	p.K817N	ENST00000380152		817	aaG/aaT	11/27	1	2	FACETS	0.985	0.919	1	0.985	0.919	1	CLONAL	1	TRUE	1	0.87	2		355	413	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051645	13051645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375135016	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	250	429	0	ENST00000316448.5:c.904G>A	p.Asp302Asn	p.D302N	ENST00000316448	NM_004343.3	302	Gat/Aat	7/9	1	2	FACETS	0.899	0.847	0.952	0.899	0.847	0.952	CLONAL	1	TRUE	1	0.87	2		429	639	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674233	86674233	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1463885690	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	171	306	0	ENST00000274376.6:c.2365C>T	p.Arg789Ter	p.R789*	ENST00000274376	NM_002890.2	789	Cga/Tga	18/25	1	2	FACETS	0.809	0.75	0.869	0.809	0.75	0.869	CLONAL	1	TRUE	1	0.87	2		306	486	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589618	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519838	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	209	259	0	ENST00000274335.5:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000274335		461	Cga/Tga	10/15	1	2	FACETS	0.969	0.935	0.999	1	0.996	1	CLONAL	2	TRUE	1	0.87	2		259	248	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685312	86685312	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	196	284	0	ENST00000274376.6:c.3028C>T	p.Arg1010Ter	p.R1010*	ENST00000274376	NM_002890.2	1010	Cga/Tga	24/25	1	2	FACETS	0.949	0.887	1	0.949	0.887	1	CLONAL	1	TRUE	1	0.87	2		284	475	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958788	55958788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780764266	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	166	247	0	ENST00000263923.4:c.3065G>A	p.Arg1022Gln	p.R1022Q	ENST00000263923	NM_002253.2	1022	cGa/cAa	22/30	1	2	FACETS	0.933	0.867	1	0.933	0.867	1	CLONAL	1	TRUE	1	0.87	2		247	409	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504590	103504590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1400329743	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	206	264	0	ENST00000355739.4:c.211C>T	p.Arg71Cys	p.R71C	ENST00000355739	NM_000123.3	71	Cgt/Tgt	2/15	1	2	FACETS	0.978	0.917	1	0.978	0.917	1	CLONAL	1	TRUE	1	0.87	2		264	484	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471048	8471048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	183	289	0	ENST00000356435.5:c.3451C>T	p.Arg1151Cys	p.R1151C	ENST00000356435		1151	Cgc/Tgc	20/35	1	2	FACETS	0.983	0.918	1	0.983	0.918	1	CLONAL	1	TRUE	1	0.87	2		289	428	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013719	170013719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388201066	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	140	227	0	ENST00000295797.4:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000295797	NM_002740.5	480	Cgc/Tgc	15/18	1	2	FACETS	0.894	0.825	0.965	0.894	0.825	0.965	CLONAL	1	TRUE	1	0.87	2		227	360	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026606	48026606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1358771617	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	281	378	0	ENST00000234420.5:c.1484G>A	p.Arg495Gln	p.R495Q	ENST00000234420	NM_000179.2	495	cGa/cAa	4/10	1	2	FACETS	0.927	0.876	0.978	0.927	0.876	0.978	CLONAL	1	TRUE	1	0.87	2		378	697	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526547	66526547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	292	375	0	ENST00000358598.2:c.1103G>A	p.Arg368Gln	p.R368Q	ENST00000358598	NM_212471.2	368	cGa/cAa	11/11	1	2	FACETS	0.959	0.908	1	0.959	0.908	1	CLONAL	1	TRUE	1	0.87	2		375	700	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277291	41277291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	225	326	0	ENST00000349496.5:c.1760G>A	p.Arg587Gln	p.R587Q	ENST00000349496	NM_001904.3	587	cGa/cAa	11/15	1	2	FACETS	0.949	0.892	1	0.949	0.892	1	CLONAL	1	TRUE	1	0.87	2		326	545	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056830	102056830	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	190	274	0	ENST00000282441.5:c.770C>A	p.Ser257Tyr	p.S257Y	ENST00000282441	NM_001130145.2	257	tCt/tAt	4/9	1	2	FACETS	0.958	0.895	1	0.958	0.895	1	CLONAL	1	TRUE	1	0.87	2		274	456	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641346	23641346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759024828	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	305	408	0	ENST00000261584.4:c.2129C>T	p.Thr710Met	p.T710M	ENST00000261584	NM_024675.3	710	aCg/aTg	5/13	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.87	2		408	692	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281068	49281068	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	226	365	0	ENST00000282018.3:c.115G>T	p.Glu39Ter	p.E39*	ENST00000282018	NM_020377.2	39	Gaa/Taa	1/1	1	2	FACETS	0.913	0.857	0.969	0.913	0.857	0.969	CLONAL	1	TRUE	1	0.87	2		365	569	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190656564	190656564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370084230	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	216	290	0	ENST00000441310.2:c.29G>A	p.Arg10Gln	p.R10Q	ENST00000441310	NM_000534.4	10	cGa/cAa	2/13	1	2	FACETS	0.948	0.889	1	0.948	0.889	1	CLONAL	1	TRUE	1	0.87	2		290	524	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845478	151845478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs375361560	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	338	432	0	ENST00000262189.6:c.13534C>A	p.His4512Asn	p.H4512N	ENST00000262189	NM_170606.2	4512	Cat/Aat	52/59	1	2	FACETS	0.995	0.947	1	0.995	0.947	1	CLONAL	1	TRUE	1	0.87	2		432	781	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190075	123190075	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	175	224	0	ENST00000218089.9:c.1294C>A	p.Leu432Ile	p.L432I	ENST00000218089	NM_001042749.1	432	Ctc/Atc	14/35	1	2	FACETS	0.993	0.927	1	0.993	0.927	1	CLONAL	1	TRUE	1	0.87	2		224	405	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496961	29496961	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	129	186	0	ENST00000356175.3:c.532G>T	p.Glu178Ter	p.E178*	ENST00000356175	NM_000267.3	178	Gaa/Taa	5/57	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.87	2		186	290	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39318060	39318060	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	125	250	0	ENST00000373001.3:c.742A>C	p.Asn248His	p.N248H	ENST00000373001	NM_022157.3	248	Aat/Cat	4/7	1	2	FACETS	0.939	0.863	1	0.939	0.863	1	CLONAL	1	TRUE	1	0.87	2		250	306	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94926679	94926679	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1336039287	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	162	253	0	ENST00000536441.1:c.86G>T	p.Arg29Ile	p.R29I	ENST00000536441	NM_144665.3	29	aGa/aTa	2/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.87	2		253	331	SUCCESS
ATM	472	MSKCC	GRCh37	11	108099904	108099904	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1259911051	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	126	203	0	ENST00000278616.4:c.186-1G>A		p.X62_splice	ENST00000278616	NM_000051.3	62			1	2	FACETS	0.989	0.91	1	0.989	0.91	1	CLONAL	1	TRUE	1	0.87	2		203	293	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112919990	112919990	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	145	224	0	ENST00000351677.2:c.1205A>C	p.Lys402Thr	p.K402T	ENST00000351677	NM_002834.3	402	aAa/aCa	10/16	1	2	FACETS	0.95	0.879	1	0.95	0.879	1	CLONAL	1	TRUE	1	0.87	2		224	351	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032258	10032258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs766473924	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	239	380	0	ENST00000330684.3:c.565A>G	p.Thr189Ala	p.T189A	ENST00000330684	NM_001134407.1	189	Acc/Gcc	3/13	1	2	FACETS	0.967	0.911	1	0.967	0.911	1	CLONAL	1	TRUE	1	0.87	2		380	568	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56376693	56376693	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	242	370	0	ENST00000348428.3:c.733G>A	p.Val245Ile	p.V245I	ENST00000348428	NM_006785.3	245	Gtt/Att	5/17	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.87	2		370	533	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468157	25468157	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	264	376	0	ENST00000264709.3:c.1519C>A	p.Pro507Thr	p.P507T	ENST00000264709	NM_175629.2	507	Ccc/Acc	13/23	1	2	FACETS	0.941	0.888	0.994	0.941	0.888	0.994	CLONAL	1	TRUE	1	0.87	2		376	645	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528165	157528165	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1206220417	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	299	449	0	ENST00000346085.5:c.5890G>A	p.Glu1964Lys	p.E1964K	ENST00000346085	NM_020732.3	1964	Gaa/Aaa	20/20	1	2	FACETS	0.921	0.873	0.971	0.921	0.873	0.971	CLONAL	1	TRUE	1	0.87	2		449	746	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732802	44732802	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	228	342	0	ENST00000377967.4:c.5A>C	p.Lys2Thr	p.K2T	ENST00000377967	NM_021140.2	2	aAa/aCa	1/29	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.87	2		342	515	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783342	9783342	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	222	363	0	ENST00000377346.4:c.2586G>T	p.Lys862Asn	p.K862N	ENST00000377346	NM_005026.3	862	aaG/aaT	20/24	1	2	FACETS	0.91	0.854	0.966	0.91	0.854	0.966	CLONAL	1	TRUE	1	0.87	2		363	561	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305346	39305346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs553068233	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	193	358	0	ENST00000373001.3:c.1079G>A	p.Arg360Gln	p.R360Q	ENST00000373001	NM_022157.3	360	cGa/cAa	7/7	1	2	FACETS	0.84	0.784	0.898	0.84	0.784	0.898	CLONAL	1	TRUE	1	0.87	2		358	528	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803818	43803818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147938568	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	271	427	0	ENST00000372470.3:c.128G>A	p.Arg43Gln	p.R43Q	ENST00000372470	NM_005373.2	43	cGa/cAa	2/12	1	2	FACETS	0.934	0.882	0.986	0.934	0.882	0.986	CLONAL	1	TRUE	1	0.87	2		427	667	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743827	46743827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	284	469	0	ENST00000371975.4:c.2117G>T	p.Trp706Leu	p.W706L	ENST00000371975	NM_003579.3	706	tGg/tTg	18/18	1	2	FACETS	0.949	0.898	1	0.949	0.898	1	CLONAL	1	TRUE	1	0.87	2		469	688	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321352	65321352	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	262	401	0	ENST00000342505.4:c.1488G>T	p.Lys496Asn	p.K496N	ENST00000342505	NM_002227.2	496	aaG/aaT	11/25	1	2	FACETS	0.968	0.915	1	0.968	0.915	1	CLONAL	1	TRUE	1	0.87	2		401	622	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344748	65344748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781744573	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	247	358	0	ENST00000342505.4:c.289G>A	p.Val97Ile	p.V97I	ENST00000342505	NM_002227.2	97	Gtt/Att	4/25	1	2	FACETS	0.988	0.931	1	0.988	0.931	1	CLONAL	1	TRUE	1	0.87	2		358	575	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263192	115263192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	37	291	0	ENST00000438362.2:c.2158C>T	p.Arg720Cys	p.R720C	ENST00000438362	NM_001242891.1	720	Cgc/Tgc	17/20	1	2	FACETS	0.152	0.125	0.183	0.152	0.125	0.183	SUBCLONAL	1	TRUE	1	0.87	2		291	558	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150549852	150549852	+	stop_lost	Nonstop_Mutation	SNP	T	T	G	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	238	358	0	ENST00000369026.2:c.1052A>C	p.Ter351SerextTer8	p.*351Sext*8	ENST00000369026	NM_021960.4	351	tAg/tCg	3/3	1	2	FACETS	0.96	0.904	1	0.96	0.904	1	CLONAL	1	TRUE	1	0.87	2		358	570	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843724	156843724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	311	579	0	ENST00000524377.1:c.1150G>A	p.Glu384Lys	p.E384K	ENST00000524377	NM_002529.3	384	Gag/Aag	8/17	1	2	FACETS	0.921	0.873	0.97	0.921	0.873	0.97	CLONAL	1	TRUE	1	0.87	2		579	776	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724987	162724987	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1291613281	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	299	388	0	ENST00000367921.3:c.459G>T	p.Lys153Asn	p.K153N	ENST00000367921	NM_006182.2	153	aaG/aaT	6/18	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.87	2		388	677	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740212	162740212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219740609	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	293	424	0	ENST00000367921.3:c.1414G>A	p.Asp472Asn	p.D472N	ENST00000367921	NM_006182.2	472	Gat/Aat	12/18	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.87	2		424	640	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749901	162749901	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	269	363	0	ENST00000367921.3:c.2434-1G>T		p.X812_splice	ENST00000367921	NM_006182.2	812			1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.87	2		363	608	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176105666	176105666	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	81	194	0	ENST00000367669.3:c.849G>T	p.Gln283His	p.Q283H	ENST00000367669	NM_022457.5	283	caG/caT	7/20	1	2	FACETS	0.76	0.68	0.843	0.76	0.68	0.843	SUBCLONAL	1	TRUE	1	0.87	2		194	245	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104712	193104712	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	150	291	0	ENST00000367435.3:c.416G>T	p.Arg139Leu	p.R139L	ENST00000367435	NM_024529.4	139	cGa/cTa	5/17	1	2	FACETS	0.971	0.9	1	0.971	0.9	1	CLONAL	1	TRUE	1	0.87	2		291	355	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111048	193111048	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	223	296	0	ENST00000367435.3:c.581G>T	p.Arg194Ile	p.R194I	ENST00000367435	NM_024529.4	194	aGa/aTa	7/17	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.87	2		296	489	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231488487	231488487	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	217	363	0	ENST00000295050.7:c.850C>A	p.Leu284Ile	p.L284I	ENST00000295050	NM_032018.5	284	Ctt/Att	5/5	1	2	FACETS	0.896	0.84	0.952	0.896	0.84	0.952	CLONAL	1	TRUE	1	0.87	2		363	557	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70442644	70442644	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	264	333	0	ENST00000373644.4:c.4966C>T	p.Arg1656Cys	p.R1656C	ENST00000373644	NM_030625.2	1656	Cgt/Tgt	10/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.87	2		333	570	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925523	114925523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780741000	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	271	415	0	ENST00000543371.1:c.1601C>T	p.Pro534Leu	p.P534L	ENST00000543371	NM_001198531.1	534	cCg/cTg	14/14	1	2	FACETS	0.976	0.923	1	0.976	0.923	1	CLONAL	1	TRUE	1	0.87	2		415	638	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10785389	10785389	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	231	342	0	ENST00000361367.2:c.1157C>A	p.Ala386Asp	p.A386D	ENST00000361367	NM_014633.3	386	gCt/gAt	9/25	1	2	FACETS	0.937	0.881	0.993	0.937	0.881	0.993	CLONAL	1	TRUE	1	0.87	2		342	567	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10789920	10789920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	197	302	0	ENST00000361367.2:c.1991G>A	p.Arg664His	p.R664H	ENST00000361367	NM_014633.3	664	cGt/cAt	16/25	1	2	FACETS	0.926	0.866	0.987	0.926	0.866	0.987	CLONAL	1	TRUE	1	0.87	2		302	489	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47598975	47598975	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	44	358	0	ENST00000430070.2:c.625G>T	p.Asp209Tyr	p.D209Y	ENST00000430070	NM_018095.4	209	Gat/Tat	2/4	1	2	FACETS	0.153	0.127	0.181	0.153	0.127	0.181	SUBCLONAL	1	TRUE	1	0.87	2		358	663	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200245	67200245	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	67	473	0	ENST00000312629.5:c.553C>T	p.Leu185Phe	p.L185F	ENST00000312629	NM_003952.2	185	Ctc/Ttc	7/15	1	2	FACETS	0.23	0.199	0.263	0.23	0.199	0.263	SUBCLONAL	1	TRUE	1	0.87	2		473	670	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518517	69518517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	208	391	0	ENST00000294312.3:c.128G>A	p.Arg43His	p.R43H	ENST00000294312	NM_005117.2	43	cGc/cAc	1/3	1	2	FACETS	0.968	0.908	1	0.968	0.908	1	CLONAL	1	TRUE	1	0.87	2		391	494	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939289	71939289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	347	520	0	ENST00000298229.2:c.238G>A	p.Ala80Thr	p.A80T	ENST00000298229	NM_001567.3	80	Gct/Act	2/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.87	2		520	772	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945598	71945598	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	221	326	0	ENST00000298229.2:c.2354C>T	p.Ala785Val	p.A785V	ENST00000298229	NM_001567.3	785	gCc/gTc	21/28	1	2	FACETS	0.981	0.922	1	0.981	0.922	1	CLONAL	1	TRUE	1	0.87	2		326	518	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77991746	77991746	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762481298	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	260	364	0	ENST00000361507.4:c.277C>T	p.Arg93Cys	p.R93C	ENST00000361507	NM_080491.2	93	Cgc/Tgc	2/10	1	2	FACETS	0.918	0.866	0.971	0.918	0.866	0.971	CLONAL	1	TRUE	1	0.87	2		364	651	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94910926	94910926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145434950	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	163	285	0	ENST00000536441.1:c.1204C>T	p.Arg402Cys	p.R402C	ENST00000536441	NM_144665.3	402	Cgc/Tgc	8/10	1	2	FACETS	0.878	0.814	0.942	0.878	0.814	0.942	CLONAL	1	TRUE	1	0.87	2		285	427	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962550	100962550	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	220	263	0	ENST00000325455.5:c.1847G>T	p.Arg616Ile	p.R616I	ENST00000325455	NM_001202474.3	616	aGa/aTa	3/8	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.87	2		263	494	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	169	251	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.952	0.886	1	0.952	0.886	1	CLONAL	1	TRUE	1	0.87	2		251	408	SUCCESS
ATM	472	MSKCC	GRCh37	11	108168106	108168106	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs747317946	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	174	257	0	ENST00000278616.4:c.5002C>A	p.Leu1668Ile	p.L1668I	ENST00000278616	NM_000051.3	1668	Cta/Ata	33/63	1	2	FACETS	0.966	0.9	1	0.966	0.9	1	CLONAL	1	TRUE	1	0.87	2		257	414	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111958593	111958593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555186772	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	139	226	0	ENST00000375549.3:c.65G>A	p.Arg22Gln	p.R22Q	ENST00000375549	NM_003002.3	22	cGa/cAa	2/4	1	2	FACETS	0.918	0.847	0.99	0.918	0.847	0.99	CLONAL	1	TRUE	1	0.87	2		226	348	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344780	118344780	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	266	364	0	ENST00000534358.1:c.2906T>C	p.Leu969Pro	p.L969P	ENST00000534358	NM_005933.3	969	cTg/cCg	3/36	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.87	2		364	605	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118368660	118368660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555044474	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	236	304	0	ENST00000534358.1:c.5674C>T	p.Arg1892Cys	p.R1892C	ENST00000534358	NM_005933.3	1892	Cgt/Tgt	21/36	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.87	2		304	508	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374499	118374499	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	346	540	0	ENST00000534358.1:c.7892T>G	p.Phe2631Cys	p.F2631C	ENST00000534358	NM_005933.3	2631	tTt/tGt	27/36	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.87	2		540	764	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402183	402183	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1398896426	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	255	366	0	ENST00000399788.2:c.4608G>T	p.Lys1536Asn	p.K1536N	ENST00000399788	NM_001042603.1	1536	aaG/aaT	27/28	1	2	FACETS	0.932	0.879	0.986	0.932	0.879	0.986	CLONAL	1	TRUE	1	0.87	2		366	629	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427534	427534	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	265	378	0	ENST00000399788.2:c.2635G>T	p.Asp879Tyr	p.D879Y	ENST00000399788	NM_001042603.1	879	Gat/Tat	19/28	1	2	FACETS	0.944	0.892	0.998	0.944	0.892	0.998	CLONAL	1	TRUE	1	0.87	2		378	645	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463387	463387	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	158	269	0	ENST00000399788.2:c.884T>C	p.Val295Ala	p.V295A	ENST00000399788	NM_001042603.1	295	gTt/gCt	8/28	1	2	FACETS	0.863	0.799	0.928	0.863	0.799	0.928	CLONAL	1	TRUE	1	0.87	2		269	421	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006411	12006411	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	272	419	0	ENST00000396373.4:c.379C>T	p.Arg127Trp	p.R127W	ENST00000396373	NM_001987.4	127	Cgg/Tgg	4/8	1	2	FACETS	0.949	0.897	1	0.949	0.897	1	CLONAL	1	TRUE	1	0.87	2		419	659	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544106	18544106	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	146	292	0	ENST00000266497.5:c.1923G>T	p.Glu641Asp	p.E641D	ENST00000266497		641	gaG/gaT	13/31	1	2	FACETS	0.935	0.865	1	0.935	0.865	1	CLONAL	1	TRUE	1	0.87	2		292	359	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715817	18715817	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	38	304	0	ENST00000266497.5:c.3648A>C	p.Lys1216Asn	p.K1216N	ENST00000266497		1216	aaA/aaC	25/31	1	2	FACETS	0.176	0.145	0.21	0.176	0.145	0.21	SUBCLONAL	1	TRUE	1	0.87	2		304	497	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644577	21644577	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	194	324	0	ENST00000421138.2:c.90A>C	p.Glu30Asp	p.E30D	ENST00000421138		30	gaA/gaC	4/16	1	2	FACETS	0.817	0.761	0.873	0.817	0.761	0.873	CLONAL	1	TRUE	1	0.87	2		324	546	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231364	46231364	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	182	326	0	ENST00000334344.6:c.1204G>T	p.Glu402Ter	p.E402*	ENST00000334344	NM_152641.2	402	Gag/Tag	10/21	1	2	FACETS	0.833	0.775	0.893	0.833	0.775	0.893	CLONAL	1	TRUE	1	0.87	2		326	502	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427720	49427720	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	311	526	0	ENST00000301067.7:c.10768A>G	p.Asn3590Asp	p.N3590D	ENST00000301067	NM_003482.3	3590	Aat/Gat	39/54	1	2	FACETS	0.966	0.917	1	0.966	0.917	1	CLONAL	1	TRUE	1	0.87	2		526	740	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427743	49427743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	292	475	0	ENST00000301067.7:c.10745G>A	p.Arg3582Gln	p.R3582Q	ENST00000301067	NM_003482.3	3582	cGg/cAg	39/54	1	2	FACETS	0.938	0.888	0.988	0.938	0.888	0.988	CLONAL	1	TRUE	1	0.87	2		475	716	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50482348	50482348	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	196	291	0	ENST00000394963.4:c.699C>A	p.Phe233Leu	p.F233L	ENST00000394963	NM_003076.4	233	ttC/ttA	6/13	1	2	FACETS	0.982	0.919	1	0.982	0.919	1	CLONAL	1	TRUE	1	0.87	2		291	459	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50482388	50482388	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	200	291	0	ENST00000394963.4:c.739G>T	p.Asp247Tyr	p.D247Y	ENST00000394963	NM_003076.4	247	Gac/Tac	6/13	1	2	FACETS	0.989	0.926	1	0.989	0.926	1	CLONAL	1	TRUE	1	0.87	2		291	465	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865545	57865545	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	299	543	0	ENST00000228682.2:c.3022A>T	p.Asn1008Tyr	p.N1008Y	ENST00000228682	NM_005269.2	1008	Aac/Tac	12/12	1	2	FACETS	0.938	0.888	0.988	0.938	0.888	0.988	CLONAL	1	TRUE	1	0.87	2		543	733	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112893775	112893775	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	179	258	0	ENST00000351677.2:c.664A>C	p.Asn222His	p.N222H	ENST00000351677	NM_002834.3	222	Aat/Cat	6/16	1	2	FACETS	0.968	0.903	1	0.968	0.903	1	CLONAL	1	TRUE	1	0.87	2		258	425	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210824	133210824	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	263	460	0	ENST00000320574.5:c.5952G>T	p.Gln1984His	p.Q1984H	ENST00000320574	NM_006231.2	1984	caG/caT	43/49	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.87	2		460	575	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215787	133215787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762000608	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	30	373	0	ENST00000320574.5:c.5476C>T	p.Arg1826Trp	p.R1826W	ENST00000320574	NM_006231.2	1826	Cgg/Tgg	40/49	1	2	FACETS	0.138	0.111	0.17	0.138	0.111	0.17	SUBCLONAL	1	TRUE	1	0.87	2		373	498	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549196	21549196	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376701545	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	305	505	0	ENST00000382592.4:c.3080C>T	p.Ser1027Leu	p.S1027L	ENST00000382592	NM_014572.2	1027	tCg/tTg	8/8	1	2	FACETS	0.904	0.856	0.952	0.904	0.856	0.952	CLONAL	1	TRUE	1	0.87	2		505	776	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609736	28609736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	241	414	0	ENST00000241453.7:c.1493G>A	p.Ser498Asn	p.S498N	ENST00000241453	NM_004119.2	498	aGc/aAc	12/24	1	2	FACETS	0.907	0.853	0.961	0.907	0.853	0.961	CLONAL	1	TRUE	1	0.87	2		414	611	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611388	28611388	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	185	329	0	ENST00000241453.7:c.1243G>T	p.Glu415Ter	p.E415*	ENST00000241453	NM_004119.2	415	Gaa/Taa	10/24	1	2	FACETS	0.939	0.876	1	0.939	0.876	1	CLONAL	1	TRUE	1	0.87	2		329	453	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896448	28896448	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	191	310	0	ENST00000282397.4:c.3002C>A	p.Ser1001Tyr	p.S1001Y	ENST00000282397	NM_002019.4	1001	tCt/tAt	22/30	1	2	FACETS	0.919	0.858	0.98	0.919	0.858	0.98	CLONAL	1	TRUE	1	0.87	2		310	478	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001942	29001942	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	210	258	0	ENST00000282397.4:c.1223G>A	p.Ser408Asn	p.S408N	ENST00000282397	NM_002019.4	408	aGc/aAc	9/30	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.87	2		258	462	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911836	32911836	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	215	299	0	ENST00000380152.3:c.3344C>A	p.Ser1115Tyr	p.S1115Y	ENST00000380152		1115	tCt/tAt	11/27	1	2	FACETS	0.929	0.871	0.987	0.929	0.871	0.987	CLONAL	1	TRUE	1	0.87	2		299	532	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930736	32930736	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	239	341	0	ENST00000380152.3:c.7607C>A	p.Ser2536Tyr	p.S2536Y	ENST00000380152		2536	tCt/tAt	15/27	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.87	2		341	534	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	163	178	0	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			1	2	FACETS	1	0.975	1	1	0.995	1	CLONAL	2	TRUE	1	0.87	2		178	185	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352499	73352499	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	155	288	0	ENST00000377767.4:c.406G>T	p.Glu136Ter	p.E136*	ENST00000377767	NM_014953.3	136	Gaa/Taa	3/21	1	2	FACETS	0.916	0.849	0.984	0.916	0.849	0.984	CLONAL	1	TRUE	1	0.87	2		288	389	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514997	103514997	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137877463	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	264	375	0	ENST00000355739.4:c.1498C>T	p.Arg500Trp	p.R500W	ENST00000355739	NM_000123.3	500	Cgg/Tgg	8/15	1	2	FACETS	0.929	0.877	0.982	0.929	0.877	0.982	CLONAL	1	TRUE	1	0.87	2		375	653	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061352	38061352	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	275	463	0	ENST00000250448.2:c.637C>T	p.Arg213Cys	p.R213C	ENST00000250448	NM_004496.3	213	Cgc/Tgc	2/2	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.87	2		463	630	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554305	81554305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777252114	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	187	297	0	ENST00000298171.2:c.325C>T	p.Arg109Trp	p.R109W	ENST00000298171	NM_000369.2	109	Cgg/Tgg	4/10	1	2	FACETS	0.921	0.859	0.983	0.921	0.859	0.983	CLONAL	1	TRUE	1	0.87	2		297	467	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609462	81609462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200523471	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	251	403	0	ENST00000298171.2:c.1060G>A	p.Val354Ile	p.V354I	ENST00000298171	NM_000369.2	354	Gtc/Atc	10/10	1	2	FACETS	0.951	0.896	1	0.951	0.896	1	CLONAL	1	TRUE	1	0.87	2		403	607	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95563005	95563005	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1421729263	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	254	413	0	ENST00000393063.1:c.4252G>A	p.Glu1418Lys	p.E1418K	ENST00000393063	NM_030621.3	1418	Gag/Aag	24/28	1	2	FACETS	0.918	0.865	0.971	0.918	0.865	0.971	CLONAL	1	TRUE	1	0.87	2		413	636	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40678613	40678613	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	220	309	0	ENST00000249776.8:c.355G>T	p.Glu119Ter	p.E119*	ENST00000249776	NM_033286.3	119	Gaa/Taa	3/9	1	2	FACETS	0.933	0.876	0.991	0.933	0.876	0.991	CLONAL	1	TRUE	1	0.87	2		309	542	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748983	43748983	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	295	426	0	ENST00000382044.4:c.1823G>A	p.Gly608Asp	p.G608D	ENST00000382044	NM_001141980.1	608	gGt/gAt	12/28	1	2	FACETS	0.923	0.874	0.972	0.923	0.874	0.972	CLONAL	1	TRUE	1	0.87	2		426	735	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50731339	50731339	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	108	210	0	ENST00000307179.4:c.69G>T	p.Lys23Asn	p.K23N	ENST00000307179		23	aaG/aaT	2/20	1	2	FACETS	0.937	0.856	1	0.937	0.856	1	CLONAL	1	TRUE	1	0.87	2		210	265	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472621	88472621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1429499898	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	226	380	1	ENST00000360948.2:c.1934G>A	p.Arg645His	p.R645H	ENST00000360948	NM_001012338.2	645	cGc/cAc	16/19	1	2	FACETS	0.891	0.836	0.947	0.891	0.836	0.947	CLONAL	1	TRUE	1	0.87	2		381	583	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303988	91303988	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	239	413	1	ENST00000355112.3:c.1385C>A	p.Ser462Tyr	p.S462Y	ENST00000355112	NM_000057.2	462	tCt/tAt	7/22	1	2	FACETS	0.882	0.829	0.936	0.882	0.829	0.936	CLONAL	1	TRUE	1	0.87	2		414	623	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832852	3832852	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	235	327	0	ENST00000262367.5:c.1406C>A	p.Ser469Tyr	p.S469Y	ENST00000262367	NM_004380.2	469	tCt/tAt	6/31	1	2	FACETS	0.936	0.881	0.992	0.936	0.881	0.992	CLONAL	1	TRUE	1	0.87	2		327	577	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857172	9857172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555481986	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	281	460	0	ENST00000330684.3:c.4229C>T	p.Ser1410Leu	p.S1410L	ENST00000330684	NM_001134407.1	1410	tCg/tTg	13/13	1	2	FACETS	0.938	0.887	0.989	0.938	0.887	0.989	CLONAL	1	TRUE	1	0.87	2		460	689	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892311	9892311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555488144	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	229	392	0	ENST00000330684.3:c.2179G>A	p.Ala727Thr	p.A727T	ENST00000330684	NM_001134407.1	727	Gct/Act	11/13	1	2	FACETS	0.991	0.933	1	0.991	0.933	1	CLONAL	1	TRUE	1	0.87	2		392	531	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128084	30128084	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	288	473	0	ENST00000263025.4:c.1045G>A	p.Ala349Thr	p.A349T	ENST00000263025	NM_002746.2	349	Gcc/Acc	8/9	1	2	FACETS	0.958	0.907	1	0.958	0.907	1	CLONAL	1	TRUE	1	0.87	2		473	691	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129055	30129055	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	235	441	0	ENST00000263025.4:c.711G>T	p.Glu237Asp	p.E237D	ENST00000263025	NM_002746.2	237	gaG/gaT	5/9	1	2	FACETS	0.9	0.846	0.955	0.9	0.846	0.955	CLONAL	1	TRUE	1	0.87	2		441	600	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785743	50785743	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	166	258	0	ENST00000398568.2:c.733G>T	p.Glu245Ter	p.E245*	ENST00000398568	NM_001042412.1	245	Gaa/Taa	4/18	1	2	FACETS	0.894	0.83	0.959	0.894	0.83	0.959	CLONAL	1	TRUE	1	0.87	2		258	427	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56862974	56862974	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	256	376	0	ENST00000308159.5:c.880C>T	p.Arg294Ter	p.R294*	ENST00000308159	NM_014669.4	294	Cga/Tga	9/22	1	2	FACETS	0.949	0.896	1	0.949	0.896	1	CLONAL	1	TRUE	1	0.87	2		376	620	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56871634	56871634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764196494	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	209	299	0	ENST00000308159.5:c.2014G>A	p.Glu672Lys	p.E672K	ENST00000308159	NM_014669.4	672	Gaa/Aaa	18/22	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.87	2		299	478	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853319	68853319	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060501242	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	231	319	0	ENST00000261769.5:c.1702A>G	p.Thr568Ala	p.T568A	ENST00000261769	NM_004360.3	568	Aca/Gca	11/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.87	2		319	515	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984472	72984472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781364785	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	310	454	0	ENST00000268489.5:c.3112G>A	p.Val1038Met	p.V1038M	ENST00000268489	NM_006885.3	1038	Gtg/Atg	3/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.87	2		454	682	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028639	12028639	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	224	333	0	ENST00000353533.5:c.842G>A	p.Arg281Gln	p.R281Q	ENST00000353533	NM_003010.3	281	cGa/cAa	8/11	1	2	FACETS	0.981	0.922	1	0.981	0.922	1	CLONAL	1	TRUE	1	0.87	2		333	525	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942851	15942851	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs751936193	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	227	384	0	ENST00000268712.3:c.6851T>C	p.Val2284Ala	p.V2284A	ENST00000268712	NM_006311.3	2284	gTt/gCt	44/46	1	2	FACETS	0.965	0.907	1	0.965	0.907	1	CLONAL	1	TRUE	1	0.87	2		384	541	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012109	16012109	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	158	276	0	ENST00000268712.3:c.2173G>A	p.Asp725Asn	p.D725N	ENST00000268712	NM_006311.3	725	Gac/Aac	19/46	1	2	FACETS	0.879	0.815	0.945	0.879	0.815	0.945	CLONAL	1	TRUE	1	0.87	2		276	413	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012219	16012219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	190	262	0	ENST00000268712.3:c.2063G>A	p.Arg688Gln	p.R688Q	ENST00000268712	NM_006311.3	688	cGa/cAa	19/46	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.87	2		262	427	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075269	16075269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	227	321	0	ENST00000268712.3:c.283G>A	p.Gly95Ser	p.G95S	ENST00000268712	NM_006311.3	95	Ggc/Agc	4/46	1	2	FACETS	0.889	0.835	0.944	0.889	0.835	0.944	CLONAL	1	TRUE	1	0.87	2		321	587	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17124884	17124884	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502367	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	234	419	0	ENST00000285071.4:c.838G>A	p.Glu280Lys	p.E280K	ENST00000285071	NM_144997.5	280	Gag/Aag	8/14	1	2	FACETS	0.897	0.843	0.951	0.897	0.843	0.951	CLONAL	1	TRUE	1	0.87	2		419	600	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322591	30322591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	148	267	0	ENST00000322652.5:c.1604G>A	p.Arg535Gln	p.R535Q	ENST00000322652	NM_015355.2	535	cGa/cAa	14/16	1	2	FACETS	0.851	0.785	0.917	0.851	0.785	0.917	CLONAL	1	TRUE	1	0.87	2		267	400	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690684	33690684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773776714	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	269	446	0	ENST00000308377.4:c.143G>A	p.Arg48Gln	p.R48Q	ENST00000308377	NM_152270.3	48	cGg/cAg	2/5	1	2	FACETS	0.909	0.858	0.961	0.909	0.858	0.961	CLONAL	1	TRUE	1	0.87	2		446	680	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872590	37872590	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759579850	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	86	443	0	ENST00000269571.5:c.1550G>A	p.Arg517Gln	p.R517Q	ENST00000269571		517	cGa/cAa	13/27	1	2	FACETS	0.303	0.268	0.341	0.303	0.268	0.341	SUBCLONAL	1	TRUE	1	0.87	2		443	652	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879672	37879672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	276	507	0	ENST00000269571.5:c.2047C>T	p.Arg683Trp	p.R683W	ENST00000269571		683	Cgg/Tgg	17/27	1	2	FACETS	0.836	0.789	0.884	0.836	0.789	0.884	CLONAL	1	TRUE	1	0.87	2		507	759	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223001	41223001	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs397509205	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	258	419	0	ENST00000357654.3:c.4930G>T	p.Glu1644Ter	p.E1644*	ENST00000357654	NM_007294.3	1644	Gaa/Taa	15/23	1	2	FACETS	0.907	0.855	0.959	0.907	0.855	0.959	CLONAL	1	TRUE	1	0.87	2		419	654	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243927	41243927	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	289	439	0	ENST00000357654.3:c.3621G>T	p.Lys1207Asn	p.K1207N	ENST00000357654	NM_007294.3	1207	aaG/aaT	10/23	1	2	FACETS	0.941	0.891	0.992	0.941	0.891	0.992	CLONAL	1	TRUE	1	0.87	2		439	706	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436128	56436128	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	277	495	0	ENST00000407977.2:c.1009C>T	p.Arg337Ter	p.R337*	ENST00000407977		337	Cga/Tga	9/10	1	2	FACETS	0.903	0.853	0.954	0.903	0.853	0.954	CLONAL	1	TRUE	1	0.87	2		495	705	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440644	56440644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	295	437	0	ENST00000407977.2:c.574C>T	p.Pro192Ser	p.P192S	ENST00000407977		192	Ccg/Tcg	5/10	1	2	FACETS	0.999	0.947	1	0.999	0.947	1	CLONAL	1	TRUE	1	0.87	2		437	679	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740668	58740668	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs759850701	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	318	411	0	ENST00000305921.3:c.1573G>T	p.Glu525Ter	p.E525*	ENST00000305921	NM_003620.3	525	Gaa/Taa	6/6	1	2	FACETS	0.984	0.934	1	0.984	0.934	1	CLONAL	1	TRUE	1	0.87	2		411	743	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763428	59763428	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	193	337	0	ENST00000259008.2:c.2674C>A	p.Leu892Ile	p.L892I	ENST00000259008	NM_032043.2	892	Ctt/Att	19/20	1	2	FACETS	0.907	0.847	0.968	0.907	0.847	0.968	CLONAL	1	TRUE	1	0.87	2		337	489	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926518	59926518	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1330277587	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	148	284	0	ENST00000259008.2:c.479G>T	p.Arg160Ile	p.R160I	ENST00000259008	NM_032043.2	160	aGa/aTa	5/20	1	2	FACETS	0.995	0.922	1	0.995	0.922	1	CLONAL	1	TRUE	1	0.87	2		284	342	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743319	743319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752661671	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	239	351	0	ENST00000314574.4:c.821G>A	p.Arg274Gln	p.R274Q	ENST00000314574	NM_005433.3	274	cGa/cAa	7/12	1	2	FACETS	0.951	0.895	1	0.951	0.895	1	CLONAL	1	TRUE	1	0.87	2		351	578	SUCCESS
YES1	7525	MSKCC	GRCh37	18	747987	747987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202083013	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	180	272	0	ENST00000314574.4:c.403G>A	p.Ala135Thr	p.A135T	ENST00000314574	NM_005433.3	135	Gct/Act	4/12	1	2	FACETS	0.867	0.808	0.929	0.867	0.808	0.929	CLONAL	1	TRUE	1	0.87	2		272	477	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39576681	39576681	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1321481448	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	116	186	0	ENST00000262039.4:c.971C>T	p.Thr324Met	p.T324M	ENST00000262039	NM_002647.2	324	aCg/aTg	9/25	1	2	FACETS	0.952	0.873	1	0.952	0.873	1	CLONAL	1	TRUE	1	0.87	2		186	280	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61305171	61305171	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1221398490	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	223	454	0	ENST00000341074.5:c.955T>G	p.Trp319Gly	p.W319G	ENST00000341074	NM_002974.2	319	Tgg/Ggg	8/8	1	2	FACETS	0.804	0.752	0.856	0.804	0.752	0.856	CLONAL	1	TRUE	1	0.87	2		454	638	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226588	1226588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775978755	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	228	430	0	ENST00000326873.7:c.1244G>A	p.Arg415His	p.R415H	ENST00000326873	NM_000455.4	415	cGc/cAc	9/10	1	2	FACETS	0.95	0.893	1	0.95	0.893	1	CLONAL	1	TRUE	1	0.87	2		430	552	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5216734	5216734	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	213	328	0	ENST00000357368.4:c.4093G>T	p.Glu1365Ter	p.E1365*	ENST00000357368	NM_002850.3	1365	Gaa/Taa	26/38	1	2	FACETS	0.975	0.916	1	0.975	0.916	1	CLONAL	1	TRUE	1	0.87	2		328	502	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375310	15375310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	271	446	0	ENST00000263377.2:c.1117G>A	p.Ala373Thr	p.A373T	ENST00000263377	NM_058243.2	373	Gcc/Acc	6/20	1	2	FACETS	0.994	0.94	1	0.994	0.94	1	CLONAL	1	TRUE	1	0.87	2		446	627	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17947965	17947965	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	225	338	0	ENST00000458235.1:c.1759C>A	p.Leu587Ile	p.L587I	ENST00000458235	NM_000215.3	587	Ctc/Atc	13/24	1	2	FACETS	0.934	0.877	0.991	0.934	0.877	0.991	CLONAL	1	TRUE	1	0.87	2		338	554	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948832	17948832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778413	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	240	468	0	ENST00000458235.1:c.1610G>A	p.Arg537Gln	p.R537Q	ENST00000458235	NM_000215.3	537	cGg/cAg	12/24	1	2	FACETS	0.9	0.847	0.954	0.9	0.847	0.954	CLONAL	1	TRUE	1	0.87	2		468	613	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214067	36214067	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	264	484	0	ENST00000222270.7:c.2893C>T	p.Arg965Ter	p.R965*	ENST00000222270	NM_014727.1	965	Cga/Tga	6/37	1	2	FACETS	0.913	0.861	0.965	0.913	0.861	0.965	CLONAL	1	TRUE	1	0.87	2		484	665	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741996	40741996	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs980537301	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	303	502	0	ENST00000392038.2:c.976G>T	p.Asp326Tyr	p.D326Y	ENST00000392038	NM_001626.4	326	Gac/Tac	11/14	1	2	FACETS	0.932	0.884	0.982	0.932	0.884	0.982	CLONAL	1	TRUE	1	0.87	2		502	747	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425290	47425290	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178800275	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	300	498	0	ENST00000404338.3:c.3358C>T	p.Arg1120Trp	p.R1120W	ENST00000404338	NM_004491.4	1120	Cgg/Tgg	1/6	1	2	FACETS	0.915	0.866	0.964	0.915	0.866	0.964	CLONAL	1	TRUE	1	0.87	2		498	754	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085942	16085942	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	237	399	0	ENST00000281043.3:c.1118G>A	p.Arg373Gln	p.R373Q	ENST00000281043	NM_005378.4	373	cGa/cAa	3/3	1	2	FACETS	0.946	0.89	1	0.946	0.89	1	CLONAL	1	TRUE	1	0.87	2		399	576	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973114	25973114	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	261	370	0	ENST00000435504.4:c.1311A>C	p.Gln437His	p.Q437H	ENST00000435504		437	caA/caC	12/13	1	2	FACETS	0.857	0.808	0.907	0.857	0.808	0.907	CLONAL	1	TRUE	1	0.87	2		370	700	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46608835	46608835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	256	451	0	ENST00000263734.3:c.2146G>A	p.Glu716Lys	p.E716K	ENST00000263734	NM_001430.4	716	Gag/Aag	13/16	1	2	FACETS	0.982	0.928	1	0.982	0.928	1	CLONAL	1	TRUE	1	0.87	2		451	599	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61706056	61706056	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	220	339	0	ENST00000401558.2:c.3115G>T	p.Glu1039Ter	p.E1039*	ENST00000401558	NM_003400.3	1039	Gaa/Taa	25/25	1	2	FACETS	0.974	0.916	1	0.974	0.916	1	CLONAL	1	TRUE	1	0.87	2		339	519	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631894	67631894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751087948	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	204	417	0	ENST00000272342.5:c.2080C>T	p.His694Tyr	p.H694Y	ENST00000272342	NM_019002.3	694	Cat/Tat	5/6	1	2	FACETS	0.916	0.857	0.975	0.916	0.857	0.975	CLONAL	1	TRUE	1	0.87	2		417	512	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149884	99149884	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	93	346	0	ENST00000074304.5:c.196A>C	p.Ser66Arg	p.S66R	ENST00000074304	NM_001134224.1	66	Agt/Cgt	5/26	1	2	FACETS	0.352	0.313	0.393	0.352	0.313	0.393	SUBCLONAL	1	TRUE	1	0.87	2		346	607	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273230	198273230	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	222	357	0	ENST00000335508.6:c.980C>T	p.Pro327Leu	p.P327L	ENST00000335508	NM_012433.2	327	cCg/cTg	8/25	1	2	FACETS	0.881	0.827	0.937	0.881	0.827	0.937	CLONAL	1	TRUE	1	0.87	2		357	579	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131412	202131412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339962485	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	267	398	0	ENST00000358485.4:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000358485	NM_001080125.1	127	cGa/cAa	2/9	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.87	2		398	589	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737524	204737524	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	191	322	0	ENST00000302823.3:c.661C>A	p.Pro221Thr	p.P221T	ENST00000302823	NM_005214.4	221	Ccc/Acc	4/4	1	2	FACETS	0.996	0.932	1	0.996	0.932	1	CLONAL	1	TRUE	1	0.87	2		322	441	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262885	46262885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761607812	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	216	306	0	ENST00000371998.3:c.1058G>A	p.Arg353Gln	p.R353Q	ENST00000371998		353	cGa/cAa	10/23	1	2	FACETS	0.946	0.888	1	0.946	0.888	1	CLONAL	1	TRUE	1	0.87	2		306	525	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39762950	39762950	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	144	227	0	ENST00000288319.7:c.886C>A	p.Leu296Ile	p.L296I	ENST00000288319	NM_182918.3	296	Ctt/Att	9/10	1	2	FACETS	0.853	0.787	0.921	0.853	0.787	0.921	CLONAL	1	TRUE	1	0.87	2		227	388	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514879	44514879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	280	359	0	ENST00000291552.4:c.368C>T	p.Ala123Val	p.A123V	ENST00000291552	NM_006758.2	123	gCg/gTg	6/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.87	2		359	622	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057302	30057302	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315496	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	239	386	1	ENST00000338641.4:c.784C>T	p.Arg262Ter	p.R262*	ENST00000338641	NM_000268.3	262	Cga/Tga	8/16	1	2	FACETS	0.902	0.849	0.957	0.902	0.849	0.957	CLONAL	1	TRUE	1	0.87	2		387	609	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548243	41548243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775368605	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	207	309	0	ENST00000263253.7:c.3031G>A	p.Glu1011Lys	p.E1011K	ENST00000263253	NM_001429.3	1011	Gaa/Aaa	16/31	1	2	FACETS	0.954	0.894	1	0.954	0.894	1	CLONAL	1	TRUE	1	0.87	2		309	499	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458576	12458576	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	284	420	0	ENST00000287820.6:c.1193T>C	p.Phe398Ser	p.F398S	ENST00000287820	NM_015869.4	398	tTt/tCt	6/7	1	2	FACETS	0.985	0.932	1	0.985	0.932	1	CLONAL	1	TRUE	1	0.87	2		420	663	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042449	37042449	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63749829	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	103	203	0	ENST00000231790.2:c.211G>T	p.Glu71Ter	p.E71*	ENST00000231790	NM_000249.3	71	Gaa/Taa	3/19	1	2	FACETS	0.904	0.823	0.987	0.904	0.823	0.987	CLONAL	1	TRUE	1	0.87	2		203	262	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913403	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	287	360	0	ENST00000349496.5:c.110C>A	p.Ser37Tyr	p.S37Y	ENST00000349496	NM_001904.3	37	tCt/tAt	3/15	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.87	2		360	657	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266472	41266472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	231	362	0	ENST00000349496.5:c.269G>A	p.Arg90Gln	p.R90Q	ENST00000349496	NM_001904.3	90	cGa/cAa	4/15	1	2	FACETS	0.884	0.83	0.938	0.884	0.83	0.938	CLONAL	1	TRUE	1	0.87	2		362	601	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277233	41277233	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	236	359	0	ENST00000349496.5:c.1702G>T	p.Glu568Ter	p.E568*	ENST00000349496	NM_001904.3	568	Gaa/Taa	11/15	1	2	FACETS	0.952	0.896	1	0.952	0.896	1	CLONAL	1	TRUE	1	0.87	2		359	570	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162161	47162161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147170912	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	316	426	0	ENST00000409792.3:c.3965G>A	p.Arg1322Gln	p.R1322Q	ENST00000409792	NM_014159.6	1322	cGa/cAa	3/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.87	2		426	699	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595936	52595936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	228	337	0	ENST00000394830.3:c.3979C>T	p.Arg1327Trp	p.R1327W	ENST00000394830	NM_018313.4	1327	Cgg/Tgg	26/30	1	2	FACETS	0.899	0.844	0.955	0.899	0.844	0.955	CLONAL	1	TRUE	1	0.87	2		337	583	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702632	52702632	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779102269	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	141	226	0	ENST00000394830.3:c.266C>A	p.Ser89Tyr	p.S89Y	ENST00000394830	NM_018313.4	89	tCt/tAt	4/30	1	2	FACETS	0.988	0.914	1	0.988	0.914	1	CLONAL	1	TRUE	1	0.87	2		226	328	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69986988	69986988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs994568417	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	218	355	0	ENST00000394351.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000394351	NM_000248.3	17	Gaa/Aaa	2/9	1	2	FACETS	0.91	0.853	0.967	0.91	0.853	0.967	CLONAL	1	TRUE	1	0.87	2		355	551	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259477	89259477	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200567888	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	282	401	0	ENST00000336596.2:c.621G>T	p.Lys207Asn	p.K207N	ENST00000336596	NM_005233.5	207	aaG/aaT	3/17	1	2	FACETS	0.987	0.934	1	0.987	0.934	1	CLONAL	1	TRUE	1	0.87	2		401	657	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445035	89445035	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	262	392	0	ENST00000336596.2:c.1355G>T	p.Ser452Ile	p.S452I	ENST00000336596	NM_005233.5	452	aGc/aTc	6/17	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.87	2		392	593	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521758	89521758	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	236	335	0	ENST00000336596.2:c.2835G>T	p.Lys945Asn	p.K945N	ENST00000336596	NM_005233.5	945	aaG/aaT	16/17	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.87	2		335	531	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528586	89528586	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	181	306	0	ENST00000336596.2:c.2886G>T	p.Gln962His	p.Q962H	ENST00000336596	NM_005233.5	962	caG/caT	17/17	1	2	FACETS	0.937	0.874	1	0.937	0.874	1	CLONAL	1	TRUE	1	0.87	2		306	444	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851603	134851603	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1410626849	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	214	376	0	ENST00000398015.3:c.1009T>C	p.Ser337Pro	p.S337P	ENST00000398015	NM_004441.4	337	Tcc/Ccc	5/16	1	2	FACETS	0.908	0.851	0.965	0.908	0.851	0.965	CLONAL	1	TRUE	1	0.87	2		376	542	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898718	134898718	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	28	331	0	ENST00000398015.3:c.1776G>T	p.Lys592Asn	p.K592N	ENST00000398015	NM_004441.4	592	aaG/aaT	10/16	1	2	FACETS	0.117	0.093	0.145	0.117	0.093	0.145	SUBCLONAL	1	TRUE	1	0.87	2		331	550	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911445	134911445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571583026	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	216	395	0	ENST00000398015.3:c.1910G>A	p.Arg637His	p.R637H	ENST00000398015	NM_004441.4	637	cGt/cAt	11/16	1	2	FACETS	0.911	0.854	0.969	0.911	0.854	0.969	CLONAL	1	TRUE	1	0.87	2		395	545	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231180	142231180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	250	321	0	ENST00000350721.4:c.4774G>A	p.Ala1592Thr	p.A1592T	ENST00000350721	NM_001184.3	1592	Gca/Aca	27/47	1	2	FACETS	0.982	0.927	1	0.982	0.927	1	CLONAL	1	TRUE	1	0.87	2		321	585	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272221	142272221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141606250	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	205	240	0	ENST00000350721.4:c.2653G>A	p.Val885Ile	p.V885I	ENST00000350721	NM_001184.3	885	Gta/Ata	13/47	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.87	2		240	446	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178942501	178942501	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	154	293	0	ENST00000263967.3:c.2308C>T	p.Arg770Ter	p.R770*	ENST00000263967	NM_006218.2	770	Cga/Tga	16/21	1	2	FACETS	0.892	0.826	0.959	0.892	0.826	0.959	CLONAL	1	TRUE	1	0.87	2		293	397	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182679076	182679076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777384692	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	75	267	0	ENST00000292782.4:c.458G>A	p.Arg153Gln	p.R153Q	ENST00000292782	NM_020640.2	153	cGa/cAa	4/7	1	2	FACETS	0.607	0.538	0.68	0.607	0.538	0.68	SUBCLONAL	1	TRUE	1	0.87	2		267	284	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612028	189612028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs900140738	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	243	371	0	ENST00000264731.3:c.1780C>T	p.Arg594Ter	p.R594*	ENST00000264731	NM_003722.4	594	Cga/Tga	14/14	1	2	FACETS	0.929	0.875	0.984	0.929	0.875	0.984	CLONAL	1	TRUE	1	0.87	2		371	601	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612078	189612078	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs957895088	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	252	409	0	ENST00000264731.3:c.1830C>A	p.Phe610Leu	p.F610L	ENST00000264731	NM_003722.4	610	ttC/ttA	14/14	1	2	FACETS	0.915	0.862	0.969	0.915	0.862	0.969	CLONAL	1	TRUE	1	0.87	2		409	633	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604629	55604629	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779103998	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	202	319	0	ENST00000288135.5:c.2837G>A	p.Arg946Gln	p.R946Q	ENST00000288135	NM_000222.2	946	cGa/cAa	21/21	1	2	FACETS	0.857	0.801	0.914	0.857	0.801	0.914	CLONAL	1	TRUE	1	0.87	2		319	542	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961109	55961109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374755237	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	209	326	1	ENST00000263923.4:c.2831G>A	p.Arg944Gln	p.R944Q	ENST00000263923	NM_002253.2	944	cGa/cAa	21/30	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.87	2		327	475	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332699	153332699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780061054	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	276	442	0	ENST00000281708.4:c.257C>T	p.Ser86Leu	p.S86L	ENST00000281708	NM_033632.3	86	tCg/tTg	2/12	1	2	FACETS	0.984	0.931	1	0.984	0.931	1	CLONAL	1	TRUE	1	0.87	2		442	645	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31401640	31401640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561462275	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	30	248	1	ENST00000344624.3:c.4024C>T	p.Arg1342Trp	p.R1342W	ENST00000344624		1342	Cgg/Tgg	33/33	1	2	FACETS	0.155	0.124	0.189	0.155	0.124	0.189	SUBCLONAL	1	TRUE	1	0.87	2		249	446	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38960517	38960517	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	231	321	0	ENST00000357387.3:c.1834C>A	p.Leu612Ile	p.L612I	ENST00000357387	NM_152756.3	612	Ctt/Att	20/38	1	2	FACETS	0.937	0.881	0.993	0.937	0.881	0.993	CLONAL	1	TRUE	1	0.87	2		321	567	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183244	56183244	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	208	327	0	ENST00000399503.3:c.4154G>T	p.Arg1385Ile	p.R1385I	ENST00000399503	NM_005921.1	1385	aGa/aTa	18/20	1	2	FACETS	0.863	0.807	0.92	0.863	0.807	0.92	CLONAL	1	TRUE	1	0.87	2		327	554	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750466	57750466	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	196	341	0	ENST00000274289.3:c.2002G>T	p.Glu668Ter	p.E668*	ENST00000274289	NM_006622.3	668	Gaa/Taa	14/14	1	2	FACETS	0.92	0.86	0.98	0.92	0.86	0.98	CLONAL	1	TRUE	1	0.87	2		341	490	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522751	67522751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747723877	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	224	423	0	ENST00000274335.5:c.248C>T	p.Ser83Leu	p.S83L	ENST00000274335		83	tCg/tTg	1/15	1	2	FACETS	0.848	0.795	0.902	0.848	0.795	0.902	CLONAL	1	TRUE	1	0.87	2		423	607	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649000	86649000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755634472	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	58	215	0	ENST00000274376.6:c.1280G>A	p.Arg427Gln	p.R427Q	ENST00000274376	NM_002890.2	427	cGa/cAa	9/25	1	2	FACETS	0.481	0.417	0.55	0.481	0.417	0.55	SUBCLONAL	1	TRUE	1	0.87	2		215	277	SUCCESS
APC	324	MSKCC	GRCh37	5	112154753	112154753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	231	323	0	ENST00000257430.4:c.1024G>A	p.Asp342Asn	p.D342N	ENST00000257430	NM_000038.5	342	Gac/Aac	10/16	1	2	FACETS	0.974	0.917	1	0.974	0.917	1	CLONAL	1	TRUE	1	0.87	2		323	545	SUCCESS
APC	324	MSKCC	GRCh37	5	112154829	112154829	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	233	384	0	ENST00000257430.4:c.1100C>A	p.Ser367Tyr	p.S367Y	ENST00000257430	NM_000038.5	367	tCt/tAt	10/16	1	2	FACETS	0.928	0.873	0.984	0.928	0.873	0.984	CLONAL	1	TRUE	1	0.87	2		384	577	SUCCESS
APC	324	MSKCC	GRCh37	5	112154969	112154969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137854567	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	223	370	0	ENST00000257430.4:c.1240C>T	p.Arg414Cys	p.R414C	ENST00000257430	NM_000038.5	414	Cgc/Tgc	10/16	1	2	FACETS	0.866	0.812	0.921	0.866	0.812	0.921	CLONAL	1	TRUE	1	0.87	2		370	592	SUCCESS
APC	324	MSKCC	GRCh37	5	112178000	112178000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768922431	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	270	335	0	ENST00000257430.4:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000257430	NM_000038.5	2237	Cga/Tga	16/16	1	2	FACETS	0.897	0.847	0.948	0.897	0.847	0.948	CLONAL	1	TRUE	1	0.87	2		335	692	SUCCESS
APC	324	MSKCC	GRCh37	5	112178781	112178781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141010008	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	317	425	0	ENST00000257430.4:c.7490C>T	p.Ser2497Leu	p.S2497L	ENST00000257430	NM_000038.5	2497	tCg/tTg	16/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.87	2		425	702	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131895051	131895051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370769989	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	101	161	0	ENST00000265335.6:c.205G>A	p.Asp69Asn	p.D69N	ENST00000265335		69	Gat/Aat	2/25	1	2	FACETS	0.971	0.885	1	0.971	0.885	1	CLONAL	1	TRUE	1	0.87	2		161	239	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930643	131930643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763432574	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	158	257	0	ENST00000265335.6:c.1876G>A	p.Glu626Lys	p.E626K	ENST00000265335		626	Gaa/Aaa	12/25	1	2	FACETS	0.859	0.795	0.923	0.859	0.795	0.923	CLONAL	1	TRUE	1	0.87	2		257	423	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170814959	170814959	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	80	116	0	ENST00000296930.5:c.7G>T	p.Asp3Tyr	p.D3Y	ENST00000296930	NM_002520.6	3	Gat/Tat	1/11	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.87	2		116	180	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170834708	170834708	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	141	282	0	ENST00000296930.5:c.776G>A	p.Gly259Asp	p.G259D	ENST00000296930	NM_002520.6	259	gGt/gAt	10/11	1	2	FACETS	0.86	0.793	0.928	0.86	0.793	0.928	CLONAL	1	TRUE	1	0.87	2		282	377	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176618949	176618949	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	221	300	0	ENST00000439151.2:c.992T>G	p.Phe331Cys	p.F331C	ENST00000439151	NM_022455.4	331	tTc/tGc	3/23	1	2	FACETS	0.924	0.867	0.981	0.924	0.867	0.981	CLONAL	1	TRUE	1	0.87	2		300	550	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176678828	176678828	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	301	367	0	ENST00000439151.2:c.4739A>C	p.Lys1580Thr	p.K1580T	ENST00000439151	NM_022455.4	1580	aAa/aCa	12/23	1	2	FACETS	0.998	0.947	1	0.998	0.947	1	CLONAL	1	TRUE	1	0.87	2		367	693	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056980	180056980	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	280	477	0	ENST00000261937.6:c.639G>T	p.Gln213His	p.Q213H	ENST00000261937	NM_182925.4	213	caG/caT	5/30	1	2	FACETS	0.974	0.922	1	0.974	0.922	1	CLONAL	1	TRUE	1	0.87	2		477	661	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480168	20480168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765868574	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	198	282	0	ENST00000346618.3:c.485G>A	p.Arg162Gln	p.R162Q	ENST00000346618	NM_001949.4	162	cGa/cAa	2/7	1	2	FACETS	0.942	0.882	1	0.942	0.882	1	CLONAL	1	TRUE	1	0.87	2		282	483	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20486948	20486948	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs773975473	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	156	231	0	ENST00000346618.3:c.913C>T	p.Arg305Ter	p.R305*	ENST00000346618	NM_001949.4	305	Cga/Tga	5/7	1	2	FACETS	0.931	0.864	1	0.931	0.864	1	CLONAL	1	TRUE	1	0.87	2		231	385	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681866	30681866	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	232	403	0	ENST00000376406.3:c.231G>T	p.Glu77Asp	p.E77D	ENST00000376406	NM_014641.2	77	gaG/gaT	3/15	1	2	FACETS	0.826	0.774	0.878	0.826	0.774	0.878	CLONAL	1	TRUE	1	0.87	2		403	646	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803500	32803500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550712305	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	47	391	2	ENST00000374899.4:c.659G>A	p.Arg220Gln	p.R220Q	ENST00000374899	NM_018833.2	220	cGa/cAa	4/12	1	2	FACETS	0.178	0.15	0.209	0.178	0.15	0.209	SUBCLONAL	1	TRUE	1	0.87	2		393	607	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32814856	32814856	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	269	387	0	ENST00000354258.4:c.2209A>C	p.Ser737Arg	p.S737R	ENST00000354258	NM_000593.5	737	Agc/Cgc	10/11	1	2	FACETS	0.954	0.902	1	0.954	0.902	1	CLONAL	1	TRUE	1	0.87	2		387	648	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024169	112024169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465963577	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	236	363	0	ENST00000368678.4:c.616C>T	p.Arg206Cys	p.R206C	ENST00000368678		206	Cgc/Tgc	7/13	1	2	FACETS	0.926	0.871	0.981	0.926	0.871	0.981	CLONAL	1	TRUE	1	0.87	2		363	586	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023160	150023160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	241	315	0	ENST00000253339.5:c.103C>T	p.Arg35Trp	p.R35W	ENST00000253339		35	Cgg/Tgg	1/7	1	2	FACETS	0.93	0.875	0.985	0.93	0.875	0.985	CLONAL	1	TRUE	1	0.87	2		315	596	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522598	157522598	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554236040	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	206	373	0	ENST00000346085.5:c.4870C>T	p.Arg1624Ter	p.R1624*	ENST00000346085	NM_020732.3	1624	Cga/Tga	18/20	1	2	FACETS	0.872	0.816	0.929	0.872	0.816	0.929	CLONAL	1	TRUE	1	0.87	2		373	543	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946090	13946090	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1419462186	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	189	316	0	ENST00000405192.2:c.1006C>T	p.Arg336Ter	p.R336*	ENST00000405192	NM_001163147.1	336	Cga/Tga	10/12	1	2	FACETS	0.959	0.896	1	0.959	0.896	1	CLONAL	1	TRUE	1	0.87	2		316	453	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730125	41730125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142519810	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	208	343	0	ENST00000242208.4:c.404C>T	p.Thr135Met	p.T135M	ENST00000242208	NM_002192.2	135	aCg/aTg	3/3	1	2	FACETS	0.92	0.861	0.979	0.92	0.861	0.979	CLONAL	1	TRUE	1	0.87	2		343	520	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367287	50367287	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866731167	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	214	413	0	ENST00000331340.3:c.94C>T	p.Pro32Ser	p.P32S	ENST00000331340	NM_006060.4	32	Ccg/Tcg	3/8	1	2	FACETS	0.937	0.879	0.996	0.937	0.879	0.996	CLONAL	1	TRUE	1	0.87	2		413	525	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467637	50467637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1262982300	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	218	350	0	ENST00000331340.3:c.872C>T	p.Thr291Met	p.T291M	ENST00000331340	NM_006060.4	291	aCg/aTg	8/8	1	2	FACETS	0.969	0.91	1	0.969	0.91	1	CLONAL	1	TRUE	1	0.87	2		350	517	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350155	81350155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758567520	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	136	226	0	ENST00000222390.5:c.1177C>T	p.Arg393Cys	p.R393C	ENST00000222390	NM_000601.4	393	Cgt/Tgt	10/18	1	2	FACETS	0.953	0.88	1	0.953	0.88	1	CLONAL	1	TRUE	1	0.87	2		226	328	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508169	106508169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381484125	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	246	415	0	ENST00000359195.3:c.163G>A	p.Glu55Lys	p.E55K	ENST00000359195	NM_002649.2	55	Gaa/Aaa	2/11	1	2	FACETS	0.944	0.89	0.999	0.944	0.89	0.999	CLONAL	1	TRUE	1	0.87	2		415	599	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509747	106509747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761655879	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	275	400	0	ENST00000359195.3:c.1741G>A	p.Glu581Lys	p.E581K	ENST00000359195	NM_002649.2	581	Gaa/Aaa	2/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.87	2		400	628	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398665	116398665	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1351264833	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	145	222	0	ENST00000397752.3:c.2255C>A	p.Ser752Tyr	p.S752Y	ENST00000397752	NM_000245.2	752	tCt/tAt	9/21	1	2	FACETS	0.983	0.911	1	0.983	0.911	1	CLONAL	1	TRUE	1	0.87	2		222	339	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411854	116411854	+	intron_variant	Intron	SNP	G	G	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	345	480	0	ENST00000397752.3:c.2888-49G>A		p.*963*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.925	0.88	0.972	0.925	0.88	0.972	CLONAL	1	TRUE	1	0.87	2		480	857	SUCCESS
MET	4233	MSKCC	GRCh37	7	116422041	116422041	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	154	265	0	ENST00000397752.3:c.3523-1G>T		p.X1175_splice	ENST00000397752	NM_000245.2	1175			1	2	FACETS	0.932	0.864	1	0.932	0.864	1	CLONAL	1	TRUE	1	0.87	2		265	380	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845580	151845580	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1287135873	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	296	441	1	ENST00000262189.6:c.13432C>T	p.Arg4478Ter	p.R4478*	ENST00000262189	NM_170606.2	4478	Cga/Tga	52/59	1	2	FACETS	0.937	0.888	0.987	0.937	0.888	0.987	CLONAL	1	TRUE	1	0.87	2		442	726	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012226	152012226	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	214	293	0	ENST00000262189.6:c.587G>T	p.Arg196Ile	p.R196I	ENST00000262189	NM_170606.2	196	aGa/aTa	4/59	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.87	2		293	446	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538897	23538897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1200957711	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	233	383	0	ENST00000380871.4:c.542G>A	p.Arg181Gln	p.R181Q	ENST00000380871	NM_006167.3	181	cGa/cAa	2/2	1	2	FACETS	0.85	0.798	0.903	0.85	0.798	0.903	CLONAL	1	TRUE	1	0.87	2		383	630	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993708	90993708	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	147	223	0	ENST00000265433.3:c.215C>A	p.Ser72Tyr	p.S72Y	ENST00000265433	NM_002485.4	72	tCt/tAt	3/16	1	2	FACETS	0.941	0.871	1	0.941	0.871	1	CLONAL	1	TRUE	1	0.87	2		223	359	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737702	145737702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137853232	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	382	602	0	ENST00000428558.2:c.3061C>T	p.Arg1021Trp	p.R1021W	ENST00000428558	NM_004260.3	1021	Cgg/Tgg	19/22	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.87	2		602	859	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090868	5090868	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	139	297	0	ENST00000381652.3:c.3016G>T	p.Glu1006Ter	p.E1006*	ENST00000381652	NM_004972.3	1006	Gaa/Taa	22/25	1	2	FACETS	0.937	0.865	1	0.937	0.865	1	CLONAL	1	TRUE	1	0.87	2		297	341	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376626	8376626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772303653	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	197	274	0	ENST00000356435.5:c.4487G>A	p.Arg1496Gln	p.R1496Q	ENST00000356435		1496	cGa/cAa	27/35	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.87	2		274	449	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449817	8449817	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs748111632	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	235	318	0	ENST00000356435.5:c.3896C>A	p.Ser1299Tyr	p.S1299Y	ENST00000356435		1299	tCt/tAt	23/35	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.87	2		318	523	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504402	8504402	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	173	268	0	ENST00000356435.5:c.1681C>T	p.Arg561Ter	p.R561*	ENST00000356435		561	Cga/Tga	12/35	1	2	FACETS	0.938	0.873	1	0.938	0.873	1	CLONAL	1	TRUE	1	0.87	2		268	424	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317111	87317111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	218	339	0	ENST00000277120.3:c.250G>A	p.Glu84Lys	p.E84K	ENST00000277120		84	Gaa/Aaa	3/19	1	2	FACETS	0.86	0.805	0.915	0.86	0.805	0.915	CLONAL	1	TRUE	1	0.87	2		339	583	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342853	87342853	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	238	354	0	ENST00000277120.3:c.1138G>A	p.Gly380Ser	p.G380S	ENST00000277120		380	Ggc/Agc	9/19	1	2	FACETS	0.937	0.882	0.993	0.937	0.882	0.993	CLONAL	1	TRUE	1	0.87	2		354	584	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570412	87570412	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	252	472	0	ENST00000277120.3:c.2152T>C	p.Tyr718His	p.Y718H	ENST00000277120		718	Tac/Cac	17/19	1	2	FACETS	0.931	0.878	0.985	0.931	0.878	0.985	CLONAL	1	TRUE	1	0.87	2		472	622	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641216	93641216	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	201	262	0	ENST00000375746.1:c.1562C>T	p.Ala521Val	p.A521V	ENST00000375746	NM_001174167.1	521	gCt/gTt	11/14	1	2	FACETS	0.939	0.879	1	0.939	0.879	1	CLONAL	1	TRUE	1	0.87	2		262	492	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209721	98209721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749244396	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	262	427	0	ENST00000331920.6:c.3817G>A	p.Glu1273Lys	p.E1273K	ENST00000331920	NM_000264.3	1273	Gaa/Aaa	23/24	1	2	FACETS	0.915	0.864	0.968	0.915	0.864	0.968	CLONAL	1	TRUE	1	0.87	2		427	658	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215809	98215809	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	241	342	0	ENST00000331920.6:c.3400C>A	p.Leu1134Met	p.L1134M	ENST00000331920	NM_000264.3	1134	Ctg/Atg	20/24	1	2	FACETS	0.936	0.881	0.991	0.936	0.881	0.991	CLONAL	1	TRUE	1	0.87	2		342	592	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347843	128347843	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758476607	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	209	259	1	ENST00000265960.3:c.662C>T	p.Pro221Leu	p.P221L	ENST00000265960	NM_001006617.1	221	cCg/cTg	5/12	1	2	FACETS	0.957	0.897	1	0.957	0.897	1	CLONAL	1	TRUE	1	0.87	2		260	502	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133710899	133710899	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	137	286	0	ENST00000318560.5:c.66C>A	p.Ser22Arg	p.S22R	ENST00000318560	NM_005157.4	22	agC/agA	1/11	1	2	FACETS	0.908	0.837	0.98	0.908	0.837	0.98	CLONAL	1	TRUE	1	0.87	2		286	347	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760802	133760802	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	276	396	0	ENST00000318560.5:c.3125C>A	p.Ala1042Asp	p.A1042D	ENST00000318560	NM_005157.4	1042	gCc/gAc	11/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.87	2		396	624	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418237	139418237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768625801	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	292	431	0	ENST00000277541.6:c.335G>A	p.Arg112His	p.R112H	ENST00000277541	NM_017617.3	112	cGc/cAc	3/34	1	2	FACETS	0.992	0.94	1	0.992	0.94	1	CLONAL	1	TRUE	1	0.87	2		431	677	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317570	1317570	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	100	186	0	ENST00000400841.2:c.495A>C	p.Glu165Asp	p.E165D	ENST00000400841		165	gaA/gaC	5/6	1	2	FACETS	0.938	0.854	1	0.938	0.854	1	CLONAL	1	TRUE	1	0.87	2		186	245	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916526	39916526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265777184	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	200	332	1	ENST00000378444.4:c.4477C>T	p.Arg1493Trp	p.R1493W	ENST00000378444	NM_001123385.1	1493	Cgg/Tgg	11/15	1	2	FACETS	0.859	0.803	0.917	0.859	0.803	0.917	CLONAL	1	TRUE	1	0.87	2		333	535	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879905	44879905	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	183	299	0	ENST00000377967.4:c.494G>A	p.Arg165Gln	p.R165Q	ENST00000377967	NM_021140.2	165	cGa/cAa	6/29	1	2	FACETS	0.891	0.831	0.953	0.891	0.831	0.953	CLONAL	1	TRUE	1	0.87	2		299	472	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918695	44918695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746746824	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	196	317	0	ENST00000377967.4:c.1178G>A	p.Arg393Gln	p.R393Q	ENST00000377967	NM_021140.2	393	cGa/cAa	12/29	1	2	FACETS	0.971	0.909	1	0.971	0.909	1	CLONAL	1	TRUE	1	0.87	2		317	464	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426513	47426513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376276271	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	322	564	0	ENST00000377045.4:c.856G>A	p.Asp286Asn	p.D286N	ENST00000377045	NM_001654.4	286	Gat/Aat	9/16	1	2	FACETS	0.98	0.931	1	0.98	0.931	1	CLONAL	1	TRUE	1	0.87	2		564	755	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223539	53223539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	263	458	0	ENST00000375401.3:c.3820G>A	p.Glu1274Lys	p.E1274K	ENST00000375401	NM_004187.3	1274	Gag/Aag	23/26	1	2	FACETS	0.993	0.938	1	0.993	0.938	1	CLONAL	1	TRUE	1	0.87	2		458	609	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223853	53223853	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	301	507	0	ENST00000375401.3:c.3506C>T	p.Ser1169Leu	p.S1169L	ENST00000375401	NM_004187.3	1169	tCg/tTg	23/26	1	2	FACETS	0.969	0.919	1	0.969	0.919	1	CLONAL	1	TRUE	1	0.87	2		507	714	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228066	53228066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	241	424	0	ENST00000375401.3:c.2248C>T	p.Arg750Trp	p.R750W	ENST00000375401	NM_004187.3	750	Cgg/Tgg	16/26	1	2	FACETS	0.881	0.828	0.934	0.881	0.828	0.934	CLONAL	1	TRUE	1	0.87	2		424	629	SUCCESS
AR	367	MSKCC	GRCh37	X	66765677	66765677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1315081227	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	309	528	0	ENST00000374690.3:c.689C>T	p.Ser230Leu	p.S230L	ENST00000374690	NM_000044.3	230	tCg/tTg	1/8	1	2	FACETS	0.931	0.883	0.98	0.931	0.883	0.98	CLONAL	1	TRUE	1	0.87	2		528	763	SUCCESS
AR	367	MSKCC	GRCh37	X	66941716	66941716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764684648	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	242	345	0	ENST00000374690.3:c.2360G>A	p.Arg787Gln	p.R787Q	ENST00000374690	NM_000044.3	787	cGa/cAa	6/8	1	2	FACETS	0.929	0.874	0.984	0.929	0.874	0.984	CLONAL	1	TRUE	1	0.87	2		345	599	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349688	70349688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	298	462	0	ENST00000374080.3:c.3850C>T	p.Arg1284Cys	p.R1284C	ENST00000374080		1284	Cgc/Tgc	27/45	1	2	FACETS	0.966	0.916	1	0.966	0.916	1	CLONAL	1	TRUE	1	0.87	2		462	709	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912144	76912144	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	100	195	0	ENST00000373344.5:c.4121-1G>T		p.X1374_splice	ENST00000373344	NM_000489.3	1374			1	2	FACETS	0.923	0.84	1	0.923	0.84	1	CLONAL	1	TRUE	1	0.87	2		195	249	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918987	76918987	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1569536694	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	194	293	0	ENST00000373344.5:c.4004G>T	p.Arg1335Ile	p.R1335I	ENST00000373344	NM_000489.3	1335	aGa/aTa	12/35	1	2	FACETS	0.947	0.885	1	0.947	0.885	1	CLONAL	1	TRUE	1	0.87	2		293	471	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937356	76937356	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	175	332	0	ENST00000373344.5:c.3392G>T	p.Arg1131Ile	p.R1131I	ENST00000373344	NM_000489.3	1131	aGa/aTa	9/35	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.87	2		332	387	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938029	76938029	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	261	360	1	ENST00000373344.5:c.2719C>T	p.Arg907Ter	p.R907*	ENST00000373344	NM_000489.3	907	Cga/Tga	9/35	1	2	FACETS	0.89	0.839	0.942	0.89	0.839	0.942	CLONAL	1	TRUE	1	0.87	2		361	674	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76954061	76954061	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	100	163	0	ENST00000373344.5:c.189+1G>T		p.X63_splice	ENST00000373344	NM_000489.3	63			1	2	FACETS	0.97	0.883	1	0.97	0.883	1	CLONAL	1	TRUE	1	0.87	2		163	237	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227989	123227989	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	106	201	0	ENST00000218089.9:c.3700G>T	p.Asp1234Tyr	p.D1234Y	ENST00000218089	NM_001042749.1	1234	Gat/Tat	33/35	1	2	FACETS	0.873	0.795	0.953	0.873	0.795	0.953	CLONAL	1	TRUE	1	0.87	2		201	279	SUCCESS
PHF6	84295	MSKCC	GRCh37	X	133549146	133549146	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064152-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	114	224	0	ENST00000332070.3:c.830G>T	p.Arg277Ile	p.R277I	ENST00000332070	NM_032458.2	277	aGa/aTa	8/10	1	2	FACETS	0.956	0.876	1	0.956	0.876	1	CLONAL	1	TRUE	1	0.87	2		224	274	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0064158-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	98	712	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.377845370781298	1	FACETS	0.425	0.38	0.473	0.425	0.38	0.473	SUBCLONAL	1	TRUE	0	0.555850892470745	1		712	599	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0064158-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	215	684	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.377845370781298	1	FACETS	0.911	0.852	0.971	0.911	0.852	0.971	CLONAL	1	TRUE	0	0.555850892470745	1		684	613	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337696	73337696	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064158-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	16	158	0	ENST00000377767.4:c.2020G>T	p.Val674Phe	p.V674F	ENST00000377767	NM_014953.3	674	Gtt/Ttt	16/21	0.377845370781298	1	FACETS	0.368	0.275	0.476	0.368	0.275	0.476	SUBCLONAL	1	TRUE	0	0.555850892470745	1		158	113	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731679	47731679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064158-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	66	604	0	ENST00000449228.1:c.113G>A	p.Arg38His	p.R38H	ENST00000449228	NM_001127240.2	38	cGc/cAc	2/4	0.297752974335521	1	FACETS	0.509	0.444	0.578	0.509	0.444	0.578	INDETERMINATE	1	TRUE	0	0.555850892470745	1		604	337	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374333	81374333	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064158-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	24	162	0	ENST00000222390.5:c.729C>A	p.His243Gln	p.H243Q	ENST00000222390	NM_000601.4	243	caC/caA	6/18	0.286383832663377	0	FACETS	0.362	0.289	0.442			1	INDETERMINATE	1	TRUE	0	0.555850892470745	0		162	106	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221992	1221992	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064158-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	137	500	0	ENST00000326873.7:c.907A>T	p.Ile303Phe	p.I303F	ENST00000326873	NM_000455.4	303	Atc/Ttc	7/10	0.555850892470745	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.555850892470745	1		500	295	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100889	27100889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201172639	NA	P-0064158-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	65	552	0	ENST00000324856.7:c.4171G>A	p.Val1391Met	p.V1391M	ENST00000324856	NM_006015.4	1391	Gtg/Atg	18/20	0.550615621557421	1	FACETS	0.506	0.441	0.575	0.506	0.441	0.575	SUBCLONAL	1	TRUE	0	0.555850892470745	1		552	334	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150935462	150935462	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064158-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	123	391	0	ENST00000271640.5:c.3304C>G	p.Leu1102Val	p.L1102V	ENST00000271640	NM_001145415.1	1102	Ctg/Gtg	19/22	0.297752974335521	1	FACETS	0.929	0.85	1	0.929	0.85	1	INDETERMINATE	1	TRUE	0	0.555850892470745	1		391	344	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909954	100909954	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064158-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	36	145	0	ENST00000325455.5:c.2695del	p.Arg899GlyfsTer3	p.R899Gfs*3	ENST00000325455	NM_001202474.3	899	Cgg/gg	8/8	0.555850892470745	1	FACETS	0.779	0.655	0.912	0.779	0.655	0.912	CLONAL	1	TRUE	0	0.555850892470745	1		145	120	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435317	121435317	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064158-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	163	674	0	ENST00000257555.6:c.1350C>A	p.Asn450Lys	p.N450K	ENST00000257555		450	aaC/aaA	7/10	0.550417265543903	2	FACETS	0.774	0.72	0.828	0.774	0.72	0.828	SUBCLONAL	2	TRUE	0	0.555850892470745	2		674	379	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281201	49281201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064158-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	21	226	0	ENST00000282018.3:c.248C>T	p.Ser83Leu	p.S83L	ENST00000282018	NM_020377.2	83	tCa/tTa	1/1	0.377845370781298	1	FACETS	0.361	0.281	0.454	0.361	0.281	0.454	SUBCLONAL	1	TRUE	0	0.555850892470745	1		226	151	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281248	49281248	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064158-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	18	263	0	ENST00000282018.3:c.295C>A	p.Leu99Ile	p.L99I	ENST00000282018	NM_020377.2	99	Ctt/Att	1/1	0.377845370781298	1	FACETS	0.368	0.28	0.47	0.368	0.28	0.47	SUBCLONAL	1	TRUE	0	0.555850892470745	1		263	127	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641056	23641056	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1567217339	NA	P-0064158-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	112	371	0	ENST00000261584.4:c.2419C>G	p.Pro807Ala	p.P807A	ENST00000261584	NM_024675.3	807	Cca/Gca	5/13	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.555850892470745	2		371	401	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216703	36216703	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064158-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	97	568	0	ENST00000222270.7:c.3869G>T	p.Arg1290Leu	p.R1290L	ENST00000222270	NM_014727.1	1290	cGc/cTc	13/37	0.297752974335521	1	FACETS	0.477	0.427	0.531	0.477	0.427	0.531	INDETERMINATE	1	TRUE	0	0.555850892470745	1		568	528	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560884	9560884	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776471547	NA	P-0064158-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	104	544	0	ENST00000353224.5:c.898G>A	p.Gly300Arg	p.G300R	ENST00000353224	NM_177990.2	300	Gga/Aga	4/10	0.297752974335521	1	FACETS	0.761	0.688	0.837	0.761	0.688	0.837	INDETERMINATE	1	TRUE	0	0.555850892470745	1		544	355	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31379506	31379506	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064158-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	48	215	0	ENST00000328111.2:c.913G>T	p.Ala305Ser	p.A305S	ENST00000328111	NM_006892.3	305	Gct/Tct	8/23	0.297752974335521	1	FACETS	0.697	0.598	0.801	0.697	0.598	0.801	INDETERMINATE	1	TRUE	0	0.555850892470745	1		215	179	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502367	186502367	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064158-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	15	252	0	ENST00000323963.5:c.90G>C	p.Glu30Asp	p.E30D	ENST00000323963		30	gaG/gaC	3/11	0.377845370781298	1	FACETS	0.28	0.206	0.368	0.28	0.206	0.368	SUBCLONAL	1	TRUE	0	0.555850892470745	1		252	139	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31421442	31421442	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064158-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	112	148	0	ENST00000344624.3:c.3462G>T	p.Met1154Ile	p.M1154I	ENST00000344624		1154	atG/atT	27/33	0.459946828355243	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	TRUE	1	0.555850892470745	4		148	193	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513460	149513460	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064158-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	38	642	0	ENST00000261799.4:c.743C>A	p.Thr248Lys	p.T248K	ENST00000261799	NM_002609.3	248	aCa/aAa	5/23	0.555850892470745	1	FACETS	0.362	0.3	0.429	0.362	0.3	0.429	SUBCLONAL	1	TRUE	0	0.555850892470745	1		642	273	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178647	32178647	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs775055374	NA	P-0064158-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	128	528	0	ENST00000375023.3:c.2747G>T	p.Cys916Phe	p.C916F	ENST00000375023	NM_004557.3	916	tGc/tTc	18/30	0.555850892470745	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.555850892470745	1		528	304	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517413	157517413	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064158-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	71	330	0	ENST00000346085.5:c.3977G>T	p.Arg1326Leu	p.R1326L	ENST00000346085	NM_020732.3	1326	cGc/cTc	16/20	0.555850892470745	1	FACETS	0.951	0.846	1	0.951	0.846	1	CLONAL	1	TRUE	0	0.555850892470745	1		330	194	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0064159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	221	504	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.595579257567324	3	FACETS	0.849	0.806	0.891	0.849	0.806	0.891	CLONAL	3	TRUE	0	0.619368048801069	3		504	367	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71050185	71050185	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	108	415	0	ENST00000318789.4:c.1000G>C	p.Asp334His	p.D334H	ENST00000318789	NM_032682.5	334	Gac/Cac	13/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.619368048801069	2		415	313	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1721992	1721992	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	84	550	0	ENST00000378609.4:c.541del	p.Thr181ProfsTer8	p.T181Pfs*8	ENST00000378609	NM_002074.3	181	Acc/cc	9/12	1	2	FACETS	0.84	0.749	0.935	0.84	0.749	0.935	CLONAL	1	TRUE	1	0.619368048801069	2		550	323	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133015	30133015	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0064159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	83	413	0	ENST00000331968.5:c.586del	p.Cys196AlafsTer4	p.C196Afs*4	ENST00000331968	NM_002742.2	196	Tgc/gc	4/18	1	2	FACETS	0.985	0.881	1	0.985	0.881	1	CLONAL	1	TRUE	1	0.619368048801069	2		413	272	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50820772	50820773	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0064159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	51	284	0	ENST00000398568.2:c.1949_1950del	p.Tyr650CysfsTer14	p.Y650Cfs*14	ENST00000398568	NM_001042412.1	649	ggATat/ggat	12/18	0.619368048801069	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.619368048801069	1		284	97	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063629	67063629	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1292377961	NA	P-0064159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	90	445	0	ENST00000412916.2:c.79-1G>A		p.X27_splice	ENST00000412916		27			0.619368048801069	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.619368048801069	1		445	162	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511599	66511599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	109	434	0	ENST00000358598.2:c.59T>C	p.Leu20Pro	p.L20P	ENST00000358598	NM_212471.2	20	cTc/cCc	2/11	0.619368048801069	2	FACETS	0.994	0.902	1	0.497	0.451	0.545	CLONAL	1	TRUE	0	0.619368048801069	2		434	354	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295459	1295459	+	upstream_gene_variant	5'Flank	SNP	G	G	C	novel	NA	P-0064159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	47	662	0				ENST00000310581	NM_198253.2	-/1132			0.274523915115005	0	FACETS	0.419	0.361	0.479			1	INDETERMINATE	1	TRUE	0	0.619368048801069	0		662	138	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13949284	13949284	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	165	371	0	ENST00000405192.2:c.844A>G	p.Thr282Ala	p.T282A	ENST00000405192	NM_001163147.1	282	Acc/Gcc	9/12	0.619368048801069	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.619368048801069	2		371	240	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922747	44922747	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	66	524	0	ENST00000377967.4:c.1608del	p.Ser537GlnfsTer11	p.S537Qfs*11	ENST00000377967	NM_021140.2	536	aaC/aa	16/29	0.619368048801069	3	FACETS	0.648	0.564	0.738	0.324	0.282	0.369	SUBCLONAL	1	TRUE	1	0.619368048801069	3		524	431	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469672	NA	P-0064161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	178	335	0	ENST00000374080.3:c.131G>A	p.Gly44Asp	p.G44D	ENST00000374080		44	gGt/gAt	2/45	0.886734367525013	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.886734367525013	1		335	214	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0064162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	682	712	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.843739261808929	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.849974111990885	2		712	783	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156187	106156187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs17253672	NA	P-0064162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	278	261	20	ENST00000380013.4:c.1088C>T	p.Pro363Leu	p.P363L	ENST00000380013	NM_001127208.2	363	cCt/cTt	3/11	0.849974111990885	4	FACETS	1	0.976	1			1	CLONAL	2	TRUE	NA	0.849974111990885	4		281	577	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515226	106515226	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139231934	NA	P-0064162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	129	436	0	ENST00000359195.3:c.2369G>T	p.Gly790Val	p.G790V	ENST00000359195	NM_002649.2	790	gGa/gTa	5/11	0.849974111990885	3	FACETS	0.808	0.737	0.883	0.404	0.368	0.442	CLONAL	1	TRUE	1	0.849974111990885	3		436	535	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006827	47006827	+	5_prime_UTR_variant	5'UTR	SNP	C	C	T	novel	NA	P-0064162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	247	269	0	ENST00000377604.3:c.-54C>T		p.*18*	ENST00000377604	NM_001204468.1	-/852		2/24	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.849974111990885	1		269	280	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281357	142281357	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0064162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	158	447	0	ENST00000350721.4:c.887C>G	p.Ser296Ter	p.S296*	ENST00000350721	NM_001184.3	296	tCa/tGa	4/47	0.612626040124737	5	FACETS	1	0.985	1	0.443	0.407	0.48	CLONAL	1	TRUE	2	0.849974111990885	5		447	637	SUCCESS
ATM	472	MSKCC	GRCh37	11	108225540	108225540	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1060501572	NA	P-0064162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	223	339	0	ENST00000278616.4:c.8789G>T	p.Cys2930Phe	p.C2930F	ENST00000278616	NM_000051.3	2930	tGc/tTc	61/63	0.849974111990885	3	FACETS	0.951	0.901	1	0.951	0.901	1	CLONAL	2	TRUE	1	0.849974111990885	3		339	393	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425020	49425020	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	127	591	0	ENST00000301067.7:c.13468C>T	p.His4490Tyr	p.H4490Y	ENST00000301067	NM_003482.3	4490	Cac/Tac	39/54	0.439067393168491	1	FACETS	0.344	0.313	0.377	0.344	0.313	0.377	INDETERMINATE	1	TRUE	0	0.849974111990885	1		591	499	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	98	363	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.836	0.752	0.923	0.836	0.752	0.923	CLONAL	1	TRUE	1	0.653311201786565	2		363	359	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	145	466	0	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	1	2	FACETS	0.917	0.843	0.994	0.917	0.843	0.994	CLONAL	1	TRUE	1	0.653311201786565	2		466	484	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	112	522	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.934	0.849	1	0.934	0.849	1	CLONAL	1	TRUE	1	0.653311201786565	2		522	367	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971153	21971153	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913383	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	123	500	0	ENST00000304494.5:c.205G>T	p.Glu69Ter	p.E69*	ENST00000304494	NM_000077.4	69	Gag/Tag	2/3	0.653311201786565	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.653311201786565	1		500	236	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486134	8486134	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	136	549	0	ENST00000356435.5:c.2683C>T	p.Leu895Phe	p.L895F	ENST00000356435		895	Ctc/Ttc	17/35	0.653311201786565	1	FACETS	0.987	0.915	1	0.987	0.915	1	CLONAL	1	TRUE	0	0.653311201786565	1		549	284	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950622	38950622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748585755	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	88	442	0	ENST00000357387.3:c.3328C>T	p.Arg1110Cys	p.R1110C	ENST00000357387	NM_152756.3	1110	Cgt/Tgt	31/38	1	2	FACETS	0.797	0.713	0.885	0.797	0.713	0.885	SUBCLONAL	1	TRUE	1	0.653311201786565	2		442	338	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341130	8341130	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	104	381	0	ENST00000356435.5:c.5086G>A	p.Gly1696Arg	p.G1696R	ENST00000356435		1696	Gga/Aga	30/35	0.653311201786565	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.653311201786565	1		381	196	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876193	35876193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	120	497	0	ENST00000303115.3:c.985C>T	p.Pro329Ser	p.P329S	ENST00000303115	NM_002185.3	329	Cct/Tct	8/8	1	2	FACETS	0.959	0.875	1	0.959	0.875	1	CLONAL	1	TRUE	1	0.653311201786565	2		497	383	SUCCESS
AR	367	MSKCC	GRCh37	X	66931523	66931523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769862197	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	114	419	0	ENST00000374690.3:c.2165C>T	p.Ala722Val	p.A722V	ENST00000374690	NM_000044.3	722	gCc/gTc	4/8	1	2	FACETS	0.98	0.892	1	0.98	0.892	1	CLONAL	1	TRUE	1	0.653311201786565	2		419	356	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587251	212587251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868149408	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	155	362	0	ENST00000342788.4:c.750G>A	p.Met250Ile	p.M250I	ENST00000342788	NM_005235.2	250	atG/atA	7/28	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.653311201786565	2		362	382	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436150	116436150	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752694306	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	157	407	0	ENST00000397752.3:c.4145G>A	p.Arg1382Gln	p.R1382Q	ENST00000397752	NM_000245.2	1382	cGa/cAa	21/21	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.653311201786565	2		407	448	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324982	123324982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	135	514	0	ENST00000358487.5:c.346G>A	p.Glu116Lys	p.E116K	ENST00000358487	NM_000141.4	116	Gaa/Aaa	3/18	1	2	FACETS	0.849	0.776	0.923	0.849	0.776	0.923	CLONAL	1	TRUE	1	0.653311201786565	2		514	487	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317623	163317623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747173543	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	107	345	0	ENST00000271452.3:c.1019C>T	p.Ser340Leu	p.S340L	ENST00000271452	NM_145697.2	340	tCg/tTg	12/14	0.653311201786565	3	FACETS	1	0.91	1	0.504	0.455	0.555	CLONAL	1	TRUE	1	0.653311201786565	3		345	431	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421280	12421280	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	146	508	0	ENST00000287820.6:c.160G>A	p.Glu54Lys	p.E54K	ENST00000287820	NM_015869.4	54	Gaa/Aaa	2/7	1	2	FACETS	0.903	0.83	0.978	0.903	0.83	0.978	CLONAL	1	TRUE	1	0.653311201786565	2		508	495	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157971	27157971	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746368893	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	163	534	0	ENST00000380036.4:c.195G>A	p.Met65Ile	p.M65I	ENST00000380036	NM_000459.3	65	atG/atA	2/23	0.653311201786565	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.653311201786565	1		534	322	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851369	151851369	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1261796800	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	136	433	0	ENST00000262189.6:c.12122C>T	p.Pro4041Leu	p.P4041L	ENST00000262189	NM_170606.2	4041	cCt/cTt	47/59	1	2	FACETS	0.944	0.866	1	0.944	0.866	1	CLONAL	1	TRUE	1	0.653311201786565	2		433	441	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962554	100962554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	81	273	0	ENST00000325455.5:c.1843C>T	p.Arg615Cys	p.R615C	ENST00000325455	NM_001202474.3	615	Cgc/Tgc	3/8	1	2	FACETS	0.749	0.666	0.837	0.749	0.666	0.837	SUBCLONAL	1	TRUE	1	0.653311201786565	2		273	331	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242416	55242416	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	77	271	0	ENST00000275493.2:c.2186G>A	p.Gly729Glu	p.G729E	ENST00000275493	NM_005228.3	729	gGa/gAa	19/28	1	2	FACETS	0.939	0.836	1	0.939	0.836	1	CLONAL	1	TRUE	1	0.653311201786565	2		271	251	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608258	28608258	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	119	438	0	ENST00000241453.7:c.1798G>A	p.Asp600Asn	p.D600N	ENST00000241453	NM_004119.2	600	Gat/Aat	14/24	1	2	FACETS	0.941	0.858	1	0.941	0.858	1	CLONAL	1	TRUE	1	0.653311201786565	2		438	387	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749110	43749110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763646261	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	106	538	0	ENST00000382044.4:c.1696C>T	p.Pro566Ser	p.P566S	ENST00000382044	NM_001141980.1	566	Cct/Tct	12/28	1	2	FACETS	0.841	0.76	0.925	0.841	0.76	0.925	CLONAL	1	TRUE	1	0.653311201786565	2		538	386	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190780	11190780	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	116	490	0	ENST00000361445.4:c.5419C>T	p.Gln1807Ter	p.Q1807*	ENST00000361445	NM_004958.3	1807	Cag/Tag	39/58	1	2	FACETS	0.879	0.799	0.962	0.879	0.799	0.962	CLONAL	1	TRUE	1	0.653311201786565	2		490	404	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319348	11319349	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	106	449	0	ENST00000361445.4:c.118_119delinsTT	p.Ala40Phe	p.A40F	ENST00000361445	NM_004958.3	40	GCc/TTc	2/58	1	2	FACETS	0.822	0.742	0.904	0.822	0.742	0.904	CLONAL	1	TRUE	1	0.653311201786565	2		449	395	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261941	16261941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	136	588	0	ENST00000375759.3:c.9206C>T	p.Ser3069Phe	p.S3069F	ENST00000375759	NM_015001.2	3069	tCc/tTc	11/15	1	2	FACETS	0.909	0.833	0.988	0.909	0.833	0.988	CLONAL	1	TRUE	1	0.653311201786565	2		588	458	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385218	4385218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	89	402	0	ENST00000261254.3:c.243G>A	p.Met81Ile	p.M81I	ENST00000261254	NM_001759.3	81	atG/atA	2/5	1	2	FACETS	0.801	0.717	0.89	0.801	0.717	0.89	CLONAL	1	TRUE	1	0.653311201786565	2		402	340	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557410	95557410	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	134	366	0	ENST00000393063.1:c.5564G>T	p.Arg1855Leu	p.R1855L	ENST00000393063	NM_030621.3	1855	cGa/cTa	27/28	1	2	FACETS	0.986	0.904	1	0.986	0.904	1	CLONAL	1	TRUE	1	0.653311201786565	2		366	416	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570398	95570398	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	104	390	0	ENST00000393063.1:c.3335A>G	p.Asn1112Ser	p.N1112S	ENST00000393063	NM_030621.3	1112	aAc/aGc	22/28	1	2	FACETS	0.812	0.733	0.895	0.812	0.733	0.895	CLONAL	1	TRUE	1	0.653311201786565	2		390	392	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669579	88669579	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	126	375	0	ENST00000360948.2:c.1319C>T	p.Ala440Val	p.A440V	ENST00000360948	NM_001012338.2	440	gCt/gTt	12/19	1	2	FACETS	0.992	0.907	1	0.992	0.907	1	CLONAL	1	TRUE	1	0.653311201786565	2		375	389	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817901	3817901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	126	402	0	ENST00000262367.5:c.3070G>A	p.Glu1024Lys	p.E1024K	ENST00000262367	NM_004380.2	1024	Gag/Aag	16/31	1	2	FACETS	0.979	0.895	1	0.979	0.895	1	CLONAL	1	TRUE	1	0.653311201786565	2		402	394	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315340	30315340	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	152	317	0	ENST00000322652.5:c.1025G>A	p.Arg342Lys	p.R342K	ENST00000322652	NM_015355.2	342	aGg/aAg	10/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.653311201786565	2		317	402	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744015	41744015	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	129	586	0	ENST00000301178.4:c.950C>T	p.Pro317Leu	p.P317L	ENST00000301178	NM_021913.4	317	cCc/cTc	7/20	1	2	FACETS	0.963	0.881	1	0.963	0.881	1	CLONAL	1	TRUE	1	0.653311201786565	2		586	410	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37628888	37628888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	103	408	0	ENST00000249071.6:c.178G>A	p.Gly60Arg	p.G60R	ENST00000249071	NM_002872.4	60	Ggg/Agg	3/7	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.653311201786565	2		408	311	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37056000	37056000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750198	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	99	305	0	ENST00000231790.2:c.755C>T	p.Ser252Leu	p.S252L	ENST00000231790	NM_000249.3	252	tCa/tTa	9/19	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.653311201786565	2		305	293	SUCCESS
REST	5978	MSKCC	GRCh37	4	57777225	57777225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	122	491	0	ENST00000309042.7:c.421C>T	p.Pro141Ser	p.P141S	ENST00000309042	NM_005612.4	141	Ccc/Tcc	2/4	1	2	FACETS	0.772	0.702	0.845	0.772	0.702	0.845	SUBCLONAL	1	TRUE	1	0.653311201786565	2		491	484	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517967	176517967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	142	609	0	ENST00000292408.4:c.465G>A	p.Met155Ile	p.M155I	ENST00000292408	NM_213647.1	155	atG/atA	5/18	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.653311201786565	2		609	413	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509147	106509147	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	155	540	0	ENST00000359195.3:c.1141G>A	p.Val381Ile	p.V381I	ENST00000359195	NM_002649.2	381	Gtt/Att	2/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.653311201786565	2		540	453	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412023	63412023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	147	685	0	ENST00000330258.3:c.1144G>A	p.Glu382Lys	p.E382K	ENST00000330258	NM_152424.3	382	Gaa/Aaa	2/2	1	2	FACETS	0.876	0.804	0.949	0.876	0.804	0.949	CLONAL	1	TRUE	1	0.653311201786565	2		685	514	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0064166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	234	354	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.972	0.914	1	0.972	0.914	1	CLONAL	1	TRUE	1	0.787690863599049	2		354	611	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0064166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	286	372	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.787690863599049	2		372	721	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711910	89711910	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs1057522285	NA	P-0064166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	247	420	0	ENST00000371953.3:c.528T>G	p.Tyr176Ter	p.Y176*	ENST00000371953	NM_000314.4	176	taT/taG	6/9	0.787690863599049	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.787690863599049	1		420	343	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708541	43708541	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	431	632	0	ENST00000382044.4:c.4755G>A	p.Trp1585Ter	p.W1585*	ENST00000382044	NM_001141980.1	1585	tgG/tgA	22/28	0.787690863599049	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.787690863599049	1		632	619	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396290	396290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	415	629	0	ENST00000262320.3:c.736G>A	p.Glu246Lys	p.E246K	ENST00000262320	NM_003502.3	246	Gaa/Aaa	2/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.787690863599049	2		629	1000	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196978	106196978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	178	540	0	ENST00000380013.4:c.5311G>A	p.Gly1771Ser	p.G1771S	ENST00000380013	NM_001127208.2	1771	Ggc/Agc	11/11	0.386846493412991	1	FACETS	0.368	0.339	0.397	0.368	0.339	0.397	INDETERMINATE	1	TRUE	0	0.787690863599049	1		540	745	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	28	612	0				ENST00000310581	NM_198253.2	-/1132			0.411995582593504	0	FACETS	0.628	0.524	0.734			1	SUBCLONAL	2	FALSE	0	0.406974055968681	0		612	65	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0064167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	108	522	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.264213542924091	1	FACETS	0.903	0.828	0.979	1	0.989	1	CLONAL	2	FALSE	0	0.406974055968681	1		522	234	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406133	70406133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780978887	NA	P-0064167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	66	482	0	ENST00000373644.4:c.3647C>T	p.Ser1216Leu	p.S1216L	ENST00000373644	NM_030625.2	1216	tCg/tTg	4/12	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	1	0.406974055968681	2		482	283	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845843	151845843	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	31	577	1	ENST00000262189.6:c.13169T>G	p.Leu4390Arg	p.L4390R	ENST00000262189	NM_170606.2	4390	cTt/cGt	52/59	0.230665396836373	2	FACETS	0.762	0.621	0.918	0.381	0.31	0.459	INDETERMINATE	1	FALSE	0	0.406974055968681	2		578	200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0064168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	285	640	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.274706436054215	3	FACETS	0.898	0.85	0.947	0.898	0.85	0.947	CLONAL	3	TRUE	0	0.362173861682156	3		640	690	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786730	3786730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	155	533	0	ENST00000262367.5:c.4481C>T	p.Pro1494Leu	p.P1494L	ENST00000262367	NM_004380.2	1494	cCc/cTc	27/31	0.104169230313195	5	FACETS	0.986	0.905	1	0.493	0.452	0.535	INDETERMINATE	2	TRUE	1	0.362173861682156	5		533	670	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0064169-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	65	516	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.808	0.704	0.92	1	0.975	1	CLONAL	2	TRUE	1	0.21	2		516	383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0064169-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	38	490	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	1	2	FACETS	0.513	0.423	0.615	0.513	0.423	0.615	SUBCLONAL	1	TRUE	1	0.21	2		490	705	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460566	8460566	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064169-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	36	467	0	ENST00000356435.5:c.3720G>T	p.Met1240Ile	p.M1240I	ENST00000356435		1240	atG/atT	22/35	1	2	FACETS	0.705	0.579	0.847	0.705	0.579	0.847	SUBCLONAL	1	TRUE	1	0.21	2		467	486	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933200	39933200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064169-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	25	329	0	ENST00000378444.4:c.1399G>T	p.Val467Phe	p.V467F	ENST00000378444	NM_001123385.1	467	Gtt/Ttt	4/15	1	1	FACETS	0.541	0.426	0.673	0.541	0.426	0.673	SUBCLONAL	1	TRUE	0	0.21	1		329	394	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064170-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	8	344	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.141768483012331	4	FACETS	0.843	0.547	1	0.421	0.273	0.609	INDETERMINATE	1	TRUE	2	0.275175652175984	4		344	88	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0064170-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	12	714	0	ENST00000269305.4:c.97-1G>T		p.X33_splice	ENST00000269305	NM_001126112.2	33			1	2	FACETS	1	0.746	1	1	0.746	1	CLONAL	1	TRUE	1	0.275175652175984	2		714	83	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956675	93956675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776802108	NA	P-0064170-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	15	554	0	ENST00000369303.4:c.2561G>A	p.Arg854His	p.R854H	ENST00000369303	NM_004440.3	854	cGt/cAt	15/17	0.102799753596411	4	FACETS	1	0.866	1	0.656	0.485	0.855	INDETERMINATE	1	TRUE	2	0.275175652175984	4		554	106	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123875327	123875327	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064170-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	16	455	0	ENST00000330479.4:c.283C>T	p.Arg95Ter	p.R95*	ENST00000330479	NM_020382.3	95	Cga/Tga	3/9	0.262416194607253	1	FACETS	1	0.807	1	1	0.807	1	CLONAL	1	TRUE	0	0.275175652175984	1		455	92	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436347	110436347	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064170-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	60	1058	0	ENST00000375856.3:c.2054C>G	p.Ala685Gly	p.A685G	ENST00000375856	NM_003749.2	685	gCc/gGc	1/2	0.239464177076646	4	FACETS	1	0.943	1	1	0.978	1	CLONAL	3	TRUE	2	0.275175652175984	4		1058	165	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0064171-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	58	505	1	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.823	0.709	0.947	0.823	0.709	0.947	CLONAL	1	TRUE	1	0.321749062513287	2		506	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0064171-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	215	661	2	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.321749062513287	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.321749062513287	2		663	661	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0064171-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	117	464	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.321749062513287	2	FACETS	0.954	0.869	1	0.954	0.869	1	CLONAL	2	TRUE	0	0.321749062513287	2		464	381	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919596	28919596	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1244106213	NA	P-0064171-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	51	453	0	ENST00000282397.4:c.2341C>T	p.Arg781Ter	p.R781*	ENST00000282397	NM_002019.4	781	Cga/Tga	16/30	0.321749062513287	4	FACETS	0.77	0.655	0.897	0.257	0.218	0.299	SUBCLONAL	1	TRUE	1	0.321749062513287	4		453	544	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775941	9775941	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064171-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	84	584	0	ENST00000377346.4:c.405A>C	p.Glu135Asp	p.E135D	ENST00000377346	NM_005026.3	135	gaA/gaC	5/24	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.321749062513287	2		584	500	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73637974	73637974	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064171-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	46	409	0	ENST00000377687.4:c.1148T>A	p.Val383Asp	p.V383D	ENST00000377687	NM_001730.3	383	gTt/gAt	3/4	0.321749062513287	4	FACETS	0.764	0.643	0.896	0.255	0.214	0.299	SUBCLONAL	1	TRUE	1	0.321749062513287	4		409	495	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185032	99185032	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0064171-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	59	436	0	ENST00000074304.5:c.2436-2A>C		p.X812_splice	ENST00000074304	NM_001134224.1	812			0.172257866892859	5	FACETS	1	0.873	1	0.338	0.291	0.39	INDETERMINATE	1	TRUE	2	0.321749062513287	5		436	536	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193503	99193503	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064171-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	63	633	0	ENST00000074304.5:c.2698G>T	p.Asp900Tyr	p.D900Y	ENST00000074304	NM_001134224.1	900	Gac/Tac	25/26	0.172257866892859	5	FACETS	0.792	0.684	0.91	0.264	0.228	0.304	INDETERMINATE	1	TRUE	2	0.321749062513287	5		633	733	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023028	31023028	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064171-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1331	79	680	0	ENST00000375687.4:c.2513A>T	p.Lys838Met	p.K838M	ENST00000375687	NM_015338.5	838	aAg/aTg	13/13	0.321749062513287	10	FACETS	0.797	0.698	0.904	0.1	0.087	0.113	CLONAL	1	TRUE	2	0.321749062513287	10		680	1410	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161965	47161965	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064171-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	65	543	0	ENST00000409792.3:c.4161A>C	p.Lys1387Asn	p.K1387N	ENST00000409792	NM_014159.6	1387	aaA/aaC	3/21	0.321749062513287	3	FACETS	0.885	0.768	1	0.442	0.384	0.506	CLONAL	1	TRUE	1	0.321749062513287	3		543	530	SUCCESS
REST	5978	MSKCC	GRCh37	4	57797800	57797800	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064171-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	72	590	0	ENST00000309042.7:c.2776T>G	p.Leu926Val	p.L926V	ENST00000309042	NM_005612.4	926	Ttg/Gtg	4/4	0.284221318448007	4	FACETS	0.79	0.689	0.899	0.395	0.344	0.45	SUBCLONAL	1	TRUE	2	0.321749062513287	4		590	749	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515187	149515187	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064171-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	80	673	1	ENST00000261799.4:c.295T>C	p.Phe99Leu	p.F99L	ENST00000261799	NM_002609.3	99	Ttt/Ctt	3/23	0.321749062513287	2	FACETS	0.775	0.682	0.874	0.387	0.341	0.437	SUBCLONAL	1	TRUE	0	0.321749062513287	2		674	642	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371819	55371819	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064171-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	77	603	0	ENST00000297316.4:c.509A>G	p.Glu170Gly	p.E170G	ENST00000297316	NM_022454.3	170	gAg/gGg	2/2	0.321749062513287	5	FACETS	0.93	0.816	1	0.233	0.204	0.264	CLONAL	1	TRUE	1	0.321749062513287	5		603	763	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0064172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	93	553	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.746093699814889	4	FACETS	0.751	0.676	0.828	0.5	0.45	0.552	SUBCLONAL	2	TRUE	1	0.746093699814889	4		553	290	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0064172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	72	557	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.746093699814889	2		557	180	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041662	47041663	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0064172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	141	326	0	ENST00000377604.3:c.1887_1888del	p.Ala631ThrfsTer41	p.A631Tfs*41	ENST00000377604	NM_001204468.1	629	acAGgg/acgg	17/24	0.746093699814889	2	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.746093699814889	2		326	173	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375002	45375002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	164	508	0	ENST00000262160.6:c.841G>A	p.Glu281Lys	p.E281K	ENST00000262160	NM_005901.5	281	Gaa/Aaa	8/11	0.746093699814889	4	FACETS	1	0.982	1	0.768	0.718	0.819	CLONAL	2	TRUE	1	0.746093699814889	4		508	333	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844098	68844098	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0064172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	93	489	0	ENST00000261769.5:c.688-2A>C		p.X230_splice	ENST00000261769	NM_004360.3	230			0.746093699814889	2	FACETS	1	0.984	1	0.704	0.644	0.764	CLONAL	1	TRUE	0	0.746093699814889	2		489	177	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100391	8100391	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1225263875	NA	P-0064172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	58	833	0	ENST00000346208.3:c.365T>C	p.Ile122Thr	p.I122T	ENST00000346208		122	aTc/aCc	3/6	0.305800539634579	3	FACETS	0.962	0.837	1	0.321	0.279	0.365	INDETERMINATE	1	TRUE	0	0.746093699814889	3		833	222	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047261	77047263	+	inframe_deletion	In_Frame_Del	DEL	GGG	GGG	-	novel	NA	P-0064172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	75	594	0	ENST00000356341.3:c.1281_1283del	p.Pro428del	p.P428del	ENST00000356341	NM_002576.4	427	acCCCa/aca	13/15	0.746093699814889	3	FACETS	1	0.922	1	0.525	0.465	0.587	CLONAL	1	TRUE	1	0.746093699814889	3		594	263	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690584	88690584	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs368222977	NA	P-0064172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	33	459	0	ENST00000360948.2:c.446C>A	p.Thr149Lys	p.T149K	ENST00000360948	NM_001012338.2	149	aCg/aAg	5/19	0.657538090366442	5	FACETS	0.528	0.431	0.638	0.176	0.143	0.213	SUBCLONAL	1	TRUE	2	0.746093699814889	5		459	355	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944382	40944382	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	51	500	0	ENST00000373198.4:c.2120C>A	p.Ala707Glu	p.A707E	ENST00000373198	NM_133170.3	707	gCa/gAa	12/32	0.379833154219746	3	FACETS	0.792	0.68	0.912	0.396	0.34	0.456	INDETERMINATE	1	TRUE	1	0.746093699814889	3		500	237	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422927	12422927	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	19	455	0	ENST00000287820.6:c.417del	p.Arg140ValfsTer30	p.R140Vfs*30	ENST00000287820	NM_015869.4	139	tgT/tg	3/7	0.639248687092778	3	FACETS	0.275	0.209	0.353			1	SUBCLONAL	1	TRUE	NA	0.746093699814889	3		455	254	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645657	12645657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	48	539	0	ENST00000251849.4:c.812C>T	p.Pro271Leu	p.P271L	ENST00000251849	NM_002880.3	271	cCt/cTt	7/17	0.639248687092778	3	FACETS	0.837	0.716	0.967			1	CLONAL	1	TRUE	NA	0.746093699814889	3		539	211	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748225	41748225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	11	536	0	ENST00000226382.2:c.544G>A	p.Asp182Asn	p.D182N	ENST00000226382	NM_003924.3	182	Gac/Aac	3/3	0.746093699814889	3	FACETS	0.186	0.128	0.258	0.093	0.064	0.129	SUBCLONAL	1	TRUE	1	0.746093699814889	3		536	218	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064178-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	30	344	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.889	0.718	1	0.889	0.718	1	CLONAL	1	TRUE	1	0.208986160655639	2		344	323	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038526	47038526	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064178-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	36	136	0	ENST00000377604.3:c.688C>T	p.Arg230Ter	p.R230*	ENST00000377604	NM_001204468.1	230	Cga/Tga	8/24	1	1	FACETS	0.767	0.637	0.911	1	0.954	1	CLONAL	2	TRUE	0	0.208986160655639	1		136	201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520008	NA	P-0064178-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	47	305	0	ENST00000269305.4:c.613T>G	p.Tyr205Asp	p.Y205D	ENST00000269305	NM_001126112.2	205	Tat/Gat	6/11	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.208986160655639	2		305	434	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591931	48591931	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064178-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	20	261	0	ENST00000342988.3:c.1094G>T	p.Gly365Val	p.G365V	ENST00000342988	NM_005359.5	365	gGt/gTt	9/12	0.208986160655639	1	FACETS	0.487	0.372	0.622	0.487	0.372	0.622	SUBCLONAL	1	TRUE	0	0.208986160655639	1		261	352	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119642328	119642328	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064178-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	39	150	0	ENST00000316626.5:c.369A>C	p.Lys123Asn	p.K123N	ENST00000316626		123	aaA/aaC	4/12	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.208986160655639	2		150	340	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	50	344	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.519788415827556	2		344	176	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0064180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	288	660	0	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	0.489899002557601	2	FACETS	0.849	0.804	0.893	0.849	0.804	0.893	CLONAL	2	TRUE	0	0.519788415827556	2		660	653	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803183	1803183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764712450	NA	P-0064180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	158	530	2	ENST00000260795.2:c.535G>A	p.Ala179Thr	p.A179T	ENST00000260795		179	Gct/Act	4/17	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.519788415827556	2		532	538	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535430	66535430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	74	424	0	ENST00000273854.3:c.31C>T	p.Arg11Cys	p.R11C	ENST00000273854	NM_004439.5	11	Cgc/Tgc	1/18	1	2	FACETS	0.85	0.75	0.956	0.85	0.75	0.956	CLONAL	1	TRUE	1	0.519788415827556	2		424	335	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0064180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	107	495	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	1	2	FACETS	0.849	0.765	0.937	0.849	0.765	0.937	CLONAL	1	TRUE	1	0.519788415827556	2		495	485	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133916	38133916	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	354	490	0	ENST00000317025.8:c.3970T>G	p.Cys1324Gly	p.C1324G	ENST00000317025	NM_023034.1	1324	Tgt/Ggt	23/24	0.519788415827556	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.519788415827556	3		490	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577035	7577036	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0064182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	359	681	0	ENST00000269305.4:c.902dup	p.Gly302ArgfsTer4	p.G302Rfs*4	ENST00000269305	NM_001126112.2	301	cca/ccCa	8/11	0.706699141173512	1	FACETS	0.919	0.878	0.96	0.919	0.878	0.96	CLONAL	1	TRUE	0	0.706699141173512	1		681	715	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798749	45798767	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CCTTCCTCCCCTGGAGTCA	CCTTCCTCCCCTGGAGTCA	-	novel	NA	P-0064182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	594	603	0	ENST00000450313.1:c.462+2_462+20del		p.X154_splice	ENST00000450313	NM_012222.2	154			0.706699141173512	2	FACETS	0.998	0.971	1	0.998	0.971	1	CLONAL	2	TRUE	0	0.706699141173512	2		603	842	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70432749	70432749	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	117	451	0	ENST00000373644.4:c.4771G>C	p.Gly1591Arg	p.G1591R	ENST00000373644	NM_030625.2	1591	Ggt/Cgt	8/12	1	2	FACETS	0.427	0.385	0.472	0.427	0.385	0.472	SUBCLONAL	1	TRUE	1	0.706699141173512	2		451	775	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434832	49434832	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	507	727	0	ENST00000301067.7:c.6721C>G	p.Pro2241Ala	p.P2241A	ENST00000301067	NM_003482.3	2241	Cct/Gct	31/54	0.436185384966953	3	FACETS	0.848	0.814	0.882	0.848	0.814	0.882	CLONAL	2	TRUE	1	0.706699141173512	3		727	1145	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56769924	56770014	+	coding_sequence_variant,5_prime_UTR_variant	Frame_Shift_Del	DEL	CTTTACGTCTGACGTCACGCCGCACGCCCCAGCGAGGGCGTGCGGAGTTTGGCTGCTCCGGGGTTAGCAGGTGAGCCTGCGATGCGCGGGA	CTTTACGTCTGACGTCACGCCGCACGCCCCAGCGAGGGCGTGCGGAGTTTGGCTGCTCCGGGGTTAGCAGGTGAGCCTGCGATGCGCGGGA	-	novel	NA	P-0064182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	265	241	0				ENST00000337432	NM_058216.2	?-4/376		1/9	0.706699141173512	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.706699141173512	1		241	359	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117421	4117421	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	41	497	0	ENST00000262948.5:c.299G>T	p.Arg100Met	p.R100M	ENST00000262948	NM_030662.3	100	aGg/aTg	2/11	0.641532347017467	1	FACETS	0.117	0.096	0.139	0.117	0.096	0.139	SUBCLONAL	1	TRUE	0	0.706699141173512	1		497	644	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266632	142266632	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	93	444	0	ENST00000350721.4:c.3292G>C	p.Ala1098Pro	p.A1098P	ENST00000350721	NM_001184.3	1098	Gcc/Ccc	16/47	0.706699141173512	3	FACETS	0.422	0.374	0.472	0.211	0.187	0.236	SUBCLONAL	1	TRUE	1	0.706699141173512	3		444	845	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177408	56177426	+	frameshift_variant	Frame_Shift_Del	DEL	TGCTGTCCCTCTTAACCTT	TGCTGTCCCTCTTAACCTT	-	novel	NA	P-0064182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	88	418	0	ENST00000399503.3:c.2385_2403del	p.Ser796CysfsTer20	p.S796Cfs*20	ENST00000399503	NM_005921.1	794	cTGCTGTCCCTCTTAACCTTt/ct	14/20	0.706699141173512	1	FACETS	0.402	0.358	0.448	0.402	0.358	0.448	SUBCLONAL	1	TRUE	0	0.706699141173512	1		418	401	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289208	33289208	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	310	614	0	ENST00000374542.5:c.344G>T	p.Arg115Leu	p.R115L	ENST00000374542	NM_001141970.1	115	cGg/cTg	3/8	1	2	FACETS	0.927	0.877	0.979	0.927	0.877	0.979	CLONAL	1	TRUE	1	0.706699141173512	2		614	946	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981860	70981860	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	159	619	0	ENST00000276594.2:c.236G>C	p.Ser79Thr	p.S79T	ENST00000276594	NM_024504.3	79	aGc/aCc	2/8	1	2	FACETS	0.506	0.463	0.55	0.506	0.463	0.55	SUBCLONAL	1	TRUE	1	0.706699141173512	2		619	890	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054702	5054728	+	inframe_deletion	In_Frame_Del	DEL	CTTAAGTATCTTATAAATCTGGAAACT	CTTAAGTATCTTATAAATCTGGAAACT	-	novel	NA	P-0064182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	125	495	0	ENST00000381652.3:c.756_782del	p.Lys253_Leu261del	p.K253_L261del	ENST00000381652	NM_004972.3	252	CTTAAGTATCTTATAAATCTGGAAACT/-	7/25	0.705732861867474	1	FACETS	0.361	0.327	0.396	0.361	0.327	0.396	SUBCLONAL	1	TRUE	0	0.706699141173512	1		495	634	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817757	3817757	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs947598568	NA	P-0064182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	125	496	0	ENST00000262367.5:c.3214T>G	p.Ser1072Ala	p.S1072A	ENST00000262367	NM_004380.2	1072	Tct/Gct	16/31	0.628338623825925	1	FACETS	0.326	0.295	0.358	0.326	0.295	0.358	SUBCLONAL	1	TRUE	0	0.706699141173512	1		496	702	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241677	55241677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504256	NA	P-0064183-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	10397	484	4	ENST00000275493.2:c.2125G>A	p.Glu709Lys	p.E709K	ENST00000275493	NM_005228.3	709	Gaa/Aaa	18/28	0.536589384599681	47	FACETS	1	0.999	1			1	CLONAL	46	TRUE	NA	0.536589384599681	47		488	10935	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0064183-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	8662	404	6	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.536589384599681	47	FACETS	1	0.999	1			1	CLONAL	46	TRUE	NA	0.536589384599681	47		410	9108	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0064183-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	249	496	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.430737525841181	2	FACETS	0.808	0.763	0.854	0.808	0.763	0.854	CLONAL	2	TRUE	0	0.536589384599681	2		496	574	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872674	37872674	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064183-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	105	656	1	ENST00000269571.5:c.1634G>T	p.Arg545Leu	p.R545L	ENST00000269571		545	cGa/cTa	13/27	0.485679714286546	3	FACETS	0.475	0.424	0.529	0.158	0.141	0.177	SUBCLONAL	1	TRUE	0	0.536589384599681	3		657	1045	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648428	30648428	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	28	525	0	ENST00000295754.5:c.53C>A	p.Thr18Lys	p.T18K	ENST00000295754	NM_003242.5	18	aCg/aAg	1/7	1	2	FACETS	0.884	0.706	1	0.884	0.706	1	CLONAL	1	TRUE	1	0.16	2		525	396	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981315	68981315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866864487	NA	P-0064185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	52	279	0	ENST00000288368.4:c.1387C>T	p.Arg463Cys	p.R463C	ENST00000288368	NM_024870.2	463	Cgc/Tgc	12/40	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.694980386516329	2		279	111	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891406	76891406	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1483369109	NA	P-0064185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	51	336	0	ENST00000373344.5:c.4699G>A	p.Gly1567Ser	p.G1567S	ENST00000373344	NM_000489.3	1567	Ggt/Agt	16/35	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.694980386516329	2		336	130	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578202	7578202	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520004	NA	P-0064186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	183	580	0	ENST00000269305.4:c.647T>G	p.Val216Gly	p.V216G	ENST00000269305	NM_001126112.2	216	gTg/gGg	6/11	0.300205315160436	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.33	2		580	519	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448199	49448199	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	38	544	0	ENST00000301067.7:c.401G>C	p.Gly134Ala	p.G134A	ENST00000301067	NM_003482.3	134	gGg/gCg	4/54	0.0909463375609101	4	FACETS	0.551	0.455	0.659	0.275	0.227	0.33	INDETERMINATE	1	TRUE	2	0.33	4		544	556	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050926	49050926	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	51	471	0	ENST00000267163.4:c.2610A>T	p.Lys870Asn	p.K870N	ENST00000267163	NM_000321.2	870	aaA/aaT	25/27	0.0909463375609101	4	FACETS	0.747	0.635	0.871	0.374	0.317	0.436	INDETERMINATE	1	TRUE	2	0.33	4		471	550	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181433	38181434	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0064186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	132	518	0	ENST00000396334.3:c.446_447delinsAT	p.Ser149Asn	p.S149N	ENST00000396334	NM_002468.4	149	aGC/aAT	2/5	0.147360423569749	3	FACETS	0.876	0.799	0.956	0.876	0.799	0.956	INDETERMINATE	2	TRUE	1	0.33	3		518	532	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271404	26271404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1436484851	NA	P-0064186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	68	655	0	ENST00000305910.3:c.209G>A	p.Arg70His	p.R70H	ENST00000305910	NM_003534.2	70	cGc/cAc	1/1	0.161917045626932	3	FACETS	0.609	0.529	0.696	0.203	0.176	0.232	INDETERMINATE	1	TRUE	0	0.33	3		655	788	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692901	89692901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786204929	NA	P-0064187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	291	499	0	ENST00000371953.3:c.385G>A	p.Gly129Arg	p.G129R	ENST00000371953	NM_000314.4	129	Gga/Aga	5/9	0.627714502508289	3	FACETS	0.971	0.933	1	0.971	0.933	1	CLONAL	3	TRUE	0	0.627714502508289	3		499	418	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0064187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	29	639	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	0.578324195145972	3	FACETS	0.169	0.135	0.208	0.085	0.067	0.104	SUBCLONAL	1	TRUE	1	0.627714502508289	3		639	718	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916836	178916836	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	147	652	0	ENST00000263967.3:c.223C>G	p.Gln75Glu	p.Q75E	ENST00000263967	NM_006218.2	75	Caa/Gaa	2/21	0.627714502508289	3	FACETS	1	0.94	1	0.515	0.472	0.56	CLONAL	1	TRUE	1	0.627714502508289	3		652	597	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748480	43748480	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395807781	NA	P-0064187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	161	603	0	ENST00000523873.1:c.434G>A	p.Arg145Gln	p.R145Q	ENST00000523873		145	cGa/cAa	6/8	0.627714502508289	3	FACETS	0.959	0.882	1	0.479	0.441	0.52	CLONAL	1	TRUE	1	0.627714502508289	3		603	703	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340820	70340820	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0064187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	310	643	0	ENST00000374080.3:c.554-1G>A		p.X185_splice	ENST00000374080		185			0.627714502508289	2	FACETS	0.998	0.956	1	0.998	0.956	1	CLONAL	2	TRUE	0	0.627714502508289	2		643	495	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839699	27839699	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	398	924	0	ENST00000328488.2:c.395G>C	p.Arg132Pro	p.R132P	ENST00000328488	NM_003533.2	132	cGa/cCa	1/1	0.627714502508289	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.627714502508289	3		924	829	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400783	72400783	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	113	551	0	ENST00000357731.5:c.388C>T	p.Gln130Ter	p.Q130*	ENST00000357731	NM_173808.2	130	Cag/Tag	2/7	1	2	FACETS	0.968	0.88	1	0.968	0.88	1	CLONAL	1	TRUE	1	0.627714502508289	2		551	372	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10792095	10792095	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	198	680	0	ENST00000361367.2:c.2288G>C	p.Arg763Thr	p.R763T	ENST00000361367	NM_014633.3	763	aGa/aCa	18/25	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.627714502508289	2		680	567	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418598	49418598	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	351	762	0	ENST00000301067.7:c.15916G>A	p.Glu5306Lys	p.E5306K	ENST00000301067	NM_003482.3	5306	Gaa/Aaa	49/54	0.578324195145972	3	FACETS	0.941	0.896	0.985	0.941	0.896	0.985	CLONAL	2	TRUE	1	0.627714502508289	3		762	781	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134607	41134607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	67	838	0	ENST00000379561.5:c.1021G>A	p.Gly341Arg	p.G341R	ENST00000379561	NM_002015.3	341	Ggg/Agg	2/3	0.627714502508289	3	FACETS	0.326	0.282	0.373	0.109	0.094	0.125	SUBCLONAL	1	TRUE	0	0.627714502508289	3		838	861	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578197	7578198	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CACCACCA	novel	NA	P-0064187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	570	879	0	ENST00000269305.4:c.651_652insTGGTGGTG	p.Val218TrpfsTer32	p.V218Wfs*32	ENST00000269305	NM_001126112.2	217	-/TGGTGGTG	6/11	0.627714502508289	3	FACETS	0.914	0.887	0.941	0.914	0.887	0.941	CLONAL	3	TRUE	0	0.627714502508289	3		879	870	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085644	16085644	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	162	714	0	ENST00000281043.3:c.820G>C	p.Glu274Gln	p.E274Q	ENST00000281043	NM_005378.4	274	Gag/Cag	3/3	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.627714502508289	2		714	508	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553172	41553172	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0064187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	106	523	0	ENST00000263253.7:c.3262-1G>T		p.X1088_splice	ENST00000263253	NM_001429.3	1088			0.627714502508289	2	FACETS	0.824	0.744	0.907	0.412	0.372	0.454	CLONAL	1	TRUE	0	0.627714502508289	2		523	410	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268816	41268816	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	138	624	0	ENST00000349496.5:c.1054A>T	p.Ser352Cys	p.S352C	ENST00000349496	NM_001904.3	352	Agt/Tgt	7/15	1	2	FACETS	0.885	0.81	0.962	0.885	0.81	0.962	CLONAL	1	TRUE	1	0.627714502508289	2		624	497	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911520	134911520	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	233	832	0	ENST00000398015.3:c.1985G>C	p.Arg662Pro	p.R662P	ENST00000398015	NM_004441.4	662	cGt/cCt	11/16	0.627714502508289	3	FACETS	1	0.986	1	0.597	0.558	0.637	CLONAL	1	TRUE	1	0.627714502508289	3		832	817	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958908	38958908	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	96	640	0	ENST00000357387.3:c.2204A>T	p.His735Leu	p.H735L	ENST00000357387	NM_152756.3	735	cAt/cTt	23/38	0.627714502508289	7	FACETS	0.863	0.767	0.964	0.216	0.191	0.241	CLONAL	1	TRUE	3	0.627714502508289	7		640	911	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161990395	161990395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	157	647	0	ENST00000366898.1:c.925G>A	p.Glu309Lys	p.E309K	ENST00000366898	NM_004562.2	309	Gaa/Aaa	8/12	0.627714502508289	3	FACETS	0.999	0.918	1	0.499	0.459	0.542	CLONAL	1	TRUE	1	0.627714502508289	3		647	658	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829145	128829145	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	155	568	0	ENST00000249373.3:c.153C>A	p.Ser51Arg	p.S51R	ENST00000249373	NM_005631.4	51	agC/agA	1/12	0.578324195145972	3	FACETS	1	0.945	1	0.518	0.476	0.562	CLONAL	1	TRUE	1	0.627714502508289	3		568	626	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0064190-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	18	176	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.817	1	1	0.817	1	CLONAL	1	FALSE	1	0.408803589220845	2		176	82	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0064190-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	22	287	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.727	0.569	0.907	0.727	0.569	0.907	CLONAL	1	FALSE	1	0.408803589220845	2		287	148	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0064190-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	64	523	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.389962175816481	1	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	FALSE	0	0.408803589220845	1		523	246	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0064190-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	47	639	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	1	2	FACETS	0.902	0.767	1	0.902	0.767	1	CLONAL	1	FALSE	1	0.408803589220845	2		639	255	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0064190-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	58	791	6	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	0.389962175816481	1	FACETS	0.745	0.645	0.853	0.745	0.645	0.853	SUBCLONAL	1	FALSE	0	0.408803589220845	1		797	303	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411366	63411366	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064190-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	68	519	0	ENST00000330258.3:c.1801C>T	p.Arg601Ter	p.R601*	ENST00000330258	NM_152424.3	601	Cga/Tga	2/2	1	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	0	0.408803589220845	1		519	181	SUCCESS
APC	324	MSKCC	GRCh37	5	112175902	112175903	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906236	NA	P-0064190-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	28	481	0	ENST00000257430.4:c.4612_4613del	p.Glu1538IlefsTer5	p.E1538Ifs*5	ENST00000257430	NM_000038.5	1537	acAGaa/acaa	16/16	1	2	FACETS	0.806	0.651	0.979	0.806	0.651	0.979	CLONAL	1	FALSE	1	0.408803589220845	2		481	170	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831326	89831326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747220449	NA	P-0064190-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	68	751	0	ENST00000389301.3:c.2750G>A	p.Arg917Gln	p.R917Q	ENST00000389301	NM_000135.2	917	cGa/cAa	28/43	0.389242936821226	3	FACETS	1	0.965	1	0.646	0.567	0.731	CLONAL	1	FALSE	1	0.408803589220845	3		751	310	SUCCESS
APC	324	MSKCC	GRCh37	5	112173795	112173795	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064190-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	29	449	0	ENST00000257430.4:c.2504del	p.Ser835PhefsTer7	p.S835Ffs*7	ENST00000257430	NM_000038.5	835	tCt/tt	16/16	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	FALSE	1	0.408803589220845	2		449	135	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	157	612	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.962	0.89	1	0.962	0.89	1	CLONAL	1	TRUE	1	0.779371546279231	2		612	419	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	181	465	1	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	0.779371546279231	1	FACETS	0.998	0.944	1	0.998	0.944	1	CLONAL	1	TRUE	0	0.779371546279231	1		466	284	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439706	51439706	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	159	385	0	ENST00000262662.1:c.271G>A	p.Glu91Lys	p.E91K	ENST00000262662		91	Gag/Aag	4/4	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.779371546279231	2		385	400	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0064192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	35	287	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.676	0.556	0.809	0.676	0.556	0.809	SUBCLONAL	1	TRUE	1	0.345405156501726	2		287	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0064192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	91	523	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.345405156501726	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.345405156501726	1		523	400	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0064192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	81	534	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.345405156501726	2		534	361	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509619	106509619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142822484	NA	P-0064192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	32	517	0	ENST00000359195.3:c.1613C>T	p.Pro538Leu	p.P538L	ENST00000359195	NM_002649.2	538	cCg/cTg	2/11	0.171351405956865	3	FACETS	0.411	0.333	0.499	0.205	0.166	0.25	INDETERMINATE	1	TRUE	1	0.345405156501726	3		517	529	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211580	98211580	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762040036	NA	P-0064192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	47	507	0	ENST00000331920.6:c.3575G>T	p.Arg1192Leu	p.R1192L	ENST00000331920	NM_000264.3	1192	cGc/cTc	22/24	1	2	FACETS	0.692	0.586	0.81	0.692	0.586	0.81	SUBCLONAL	1	TRUE	1	0.345405156501726	2		507	393	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	130	612	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.781	0.714	0.851	0.781	0.714	0.851	SUBCLONAL	1	TRUE	1	0.742851931980557	2		612	448	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164799	36164799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	740	845	0	ENST00000300305.3:c.1076C>T	p.Pro359Leu	p.P359L	ENST00000300305		359	cCg/cTg	8/8	0.724713406395174	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.742851931980557	2		845	975	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435832	110435832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	272	786	0	ENST00000375856.3:c.2569G>A	p.Gly857Ser	p.G857S	ENST00000375856	NM_003749.2	857	Ggc/Agc	1/2	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.742851931980557	2		786	730	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215617263	215617263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375515606	NA	P-0064193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	22	237	0	ENST00000260947.4:c.1585C>T	p.Arg529Trp	p.R529W	ENST00000260947	NM_000465.2	529	Cgg/Tgg	7/11	1	2	FACETS	0.623	0.493	0.768	0.623	0.493	0.768	SUBCLONAL	1	TRUE	1	0.742851931980557	2		237	95	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729179	66729179	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	99	530	0	ENST00000307102.5:c.387C>G	p.Phe129Leu	p.F129L	ENST00000307102	NM_002755.3	129	ttC/ttG	3/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.742851931980557	2		530	237	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534285	534285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894226	NA	P-0064193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	244	684	0	ENST00000451590.1:c.38G>A	p.Gly13Asp	p.G13D	ENST00000451590	NM_001130442.1	13	gGt/gAt	2/5	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.742851931980557	2		684	645	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141426	11141426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	157	645	0	ENST00000358026.2:c.3403C>T	p.Arg1135Trp	p.R1135W	ENST00000358026	NM_001128849.1	1135	Cgg/Tgg	25/36	1	2	FACETS	0.999	0.925	1	0.999	0.925	1	CLONAL	1	TRUE	1	0.742851931980557	2		645	423	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89345591	89345591	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	10	30	0	ENST00000301030.4:c.7359del	p.Ile2454SerfsTer37	p.I2454Sfs*37	ENST00000301030	NM_001256183.1	2453	aaG/aa	9/13	1	2	FACETS	1	0.833	1	1	0.833	1	CLONAL	1	TRUE	1	0.742851931980557	2		30	22	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184745	185184745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs956527659	NA	P-0064193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	47	433	0	ENST00000265026.3:c.1637C>T	p.Thr546Ile	p.T546I	ENST00000265026	NM_004721.4	546	aCc/aTc	10/14	1	2	FACETS	0.758	0.65	0.872	0.758	0.65	0.872	SUBCLONAL	1	TRUE	1	0.742851931980557	2		433	167	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554903	187554903	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	57	480	0	ENST00000441802.2:c.4258G>T	p.Glu1420Ter	p.E1420*	ENST00000441802	NM_005245.3	1420	Gaa/Taa	7/27	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.742851931980557	2		480	136	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628303	187628304	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	88	598	0	ENST00000441802.2:c.2678dup	p.Leu893PhefsTer4	p.L893Ffs*4	ENST00000441802	NM_005245.3	893	tta/ttTa	2/27	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.742851931980557	2		598	232	SUCCESS
APC	324	MSKCC	GRCh37	5	112174736	112174738	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs761327787	NA	P-0064193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	36	359	0	ENST00000257430.4:c.3451_3453del	p.Glu1151del	p.E1151del	ENST00000257430	NM_000038.5	1149	GAA/-	16/16	1	2	FACETS	0.95	0.804	1	0.95	0.804	1	CLONAL	1	TRUE	1	0.742851931980557	2		359	102	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412327	139412327	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	460	722	0	ENST00000277541.6:c.1318T>G	p.Cys440Gly	p.C440G	ENST00000277541	NM_017617.3	440	Tgt/Ggt	8/34	0.695217245846022	2	FACETS	0.999	0.97	1	0.999	0.97	1	CLONAL	2	TRUE	0	0.742851931980557	2		722	620	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0064196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	344	366	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.850408795236974	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.850408795236974	1		366	416	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986611	36986611	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	175	476	0	ENST00000354822.5:c.1078C>A	p.Leu360Met	p.L360M	ENST00000354822	NM_001079668.2	360	Ctg/Atg	3/3	0.148092891780879	5	FACETS	1	0.987	1	0.452	0.417	0.488	INDETERMINATE	1	TRUE	2	0.850408795236974	5		476	691	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138465	2138465	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	439	520	0	ENST00000219476.3:c.5278T>G	p.Tyr1760Asp	p.Y1760D	ENST00000219476	NM_000548.3	1760	Tac/Gac	42/42	0.850408795236974	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.850408795236974	1		520	536	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545666	63545666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	56	430	0	ENST00000307078.5:c.928G>A	p.Asp310Asn	p.D310N	ENST00000307078	NM_004655.3	310	Gat/Aat	3/11	0.850408795236974	1	FACETS	0.144	0.123	0.166	0.144	0.123	0.166	SUBCLONAL	1	TRUE	0	0.850408795236974	1		430	527	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430814	47430814	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	157	496	0	ENST00000377045.4:c.1779G>C	p.Glu593Asp	p.E593D	ENST00000377045	NM_001654.4	593	gaG/gaC	16/16	0.494963372161173	1	FACETS	0.319	0.292	0.346	0.319	0.292	0.346	INDETERMINATE	1	TRUE	0	0.850408795236974	1		496	666	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0064218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	75	372	0				ENST00000310581	NM_198253.2	-/1132			0.435410917932451	3	FACETS	1	0.945	1	0.564	0.497	0.635	CLONAL	1	TRUE	1	0.435410917932451	3		372	372	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735466	40735466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182388300	NA	P-0064218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	100	866	5	ENST00000373198.4:c.3407G>A	p.Arg1136His	p.R1136H	ENST00000373198	NM_133170.3	1136	cGt/cAt	25/32	1	2	FACETS	0.947	0.85	1	0.947	0.85	1	CLONAL	1	TRUE	1	0.435410917932451	2		871	485	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0064218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	383	533	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.435410917932451	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.435410917932451	3		533	645	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0064218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	244	691	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.36669995577706	3	FACETS	0.841	0.794	0.888	0.841	0.794	0.888	CLONAL	3	TRUE	0	0.435410917932451	3		691	541	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141586	202141586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760898260	NA	P-0064218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	114	371	0	ENST00000358485.4:c.874C>T	p.Arg292Trp	p.R292W	ENST00000358485	NM_001080125.1	292	Cgg/Tgg	7/9	0.385264362836415	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.435410917932451	1		371	405	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14027714	14027714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	91	303	0	ENST00000405192.2:c.130G>A	p.Glu44Lys	p.E44K	ENST00000405192	NM_001163147.1	44	Gaa/Aaa	3/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.435410917932451	2		303	370	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440430	49440431	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0064218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	138	548	0	ENST00000301067.7:c.4379dup	p.Leu1461ThrfsTer30	p.L1461Tfs*30	ENST00000301067	NM_003482.3	1460	cca/ccCa	15/54	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.435410917932451	2		548	605	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598323	28598323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	129	522	0	ENST00000253063.3:c.295C>A	p.Leu99Met	p.L99M	ENST00000253063	NM_031459.4	99	Ctg/Atg	3/10	1	2	FACETS	0.97	0.882	1	0.97	0.882	1	CLONAL	1	TRUE	1	0.435410917932451	2		522	611	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145118	58145118	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	107	497	0	ENST00000257904.6:c.226G>A	p.Asp76Asn	p.D76N	ENST00000257904	NM_000075.3	76	Gac/Aac	3/8	1	2	FACETS	0.842	0.757	0.931	0.842	0.757	0.931	CLONAL	1	TRUE	1	0.435410917932451	2		497	584	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743861	41743864	+	missense_variant	Missense_Mutation	ONP	AACG	AACG	GACA	novel	NA	P-0064218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	129	488	0	ENST00000301178.4:c.796_799delinsGACA	p.Asn266_Asp267delinsAspAsn	p.N266_D267delinsDN	ENST00000301178	NM_021913.4	266	AACGat/GACAat	7/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.435410917932451	2		488	510	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	99	354	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.409794886335575	2		354	372	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	77	283	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.409794886335575	2		283	283	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259477	89259477	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200567888	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	116	401	0	ENST00000336596.2:c.621G>T	p.Lys207Asn	p.K207N	ENST00000336596	NM_005233.5	207	aaG/aaT	3/17	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.409794886335575	2		401	460	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	150	507	0	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.409794886335575	2		507	558	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	45	325	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	1	2	FACETS	0.59	0.497	0.693	0.59	0.497	0.693	SUBCLONAL	1	TRUE	1	0.409794886335575	2		325	372	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	137	383	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.808	0.742	0.875	1	0.989	1	CLONAL	2	TRUE	1	0.409794886335575	2		383	414	SUCCESS
AR	367	MSKCC	GRCh37	X	66942700	66942700	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs200801099	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	93	270	0	ENST00000374690.3:c.2481C>A	p.Phe827Leu	p.F827L	ENST00000374690	NM_000044.3	827	ttC/ttA	7/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.409794886335575	2		270	332	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941657	48941657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1060503077	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	40	135	0	ENST00000267163.4:c.967G>T	p.Glu323Ter	p.E323*	ENST00000267163	NM_000321.2	323	Gaa/Taa	10/27	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.409794886335575	2		135	152	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673064	30673064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144657716	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	239	683	1	ENST00000376406.3:c.3896G>A	p.Arg1299Gln	p.R1299Q	ENST00000376406	NM_014641.2	1299	cGa/cAa	10/15	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.409794886335575	2		684	903	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106803	27106804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	175	529	0	ENST00000324856.7:c.6420dup	p.Phe2141LeufsTer9	p.F2141Lfs*9	ENST00000324856	NM_006015.4	2138	-/C	20/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.409794886335575	2		529	624	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778864	76778864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	71	297	0	ENST00000373344.5:c.6715G>A	p.Glu2239Lys	p.E2239K	ENST00000373344	NM_000489.3	2239	Gag/Aag	31/35	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.409794886335575	2		297	268	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047336	128047336	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	125	393	0	ENST00000285398.2:c.586G>A	p.Glu196Lys	p.E196K	ENST00000285398	NM_000122.1	196	Gaa/Aaa	5/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.409794886335575	2		393	497	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181926	38181926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1559484615	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	166	473	0	ENST00000396334.3:c.550G>A	p.Asp184Asn	p.D184N	ENST00000396334	NM_002468.4	184	Gac/Aac	3/5	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.409794886335575	2		473	595	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211837	123211837	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	32	406	0	ENST00000218089.9:c.2704G>T	p.Glu902Ter	p.E902*	ENST00000218089	NM_001042749.1	902	Gaa/Taa	27/35	1	2	FACETS	0.435	0.353	0.527	0.435	0.353	0.527	SUBCLONAL	1	TRUE	1	0.409794886335575	2		406	359	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692838	89692838	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	29	88	0	ENST00000371953.3:c.322C>T	p.Leu108Phe	p.L108F	ENST00000371953	NM_000314.4	108	Ctt/Ttt	5/9	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.409794886335575	2		88	100	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662700	117662700	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	147	390	0	ENST00000368508.3:c.4765G>T	p.Glu1589Ter	p.E1589*	ENST00000368508	NM_002944.2	1589	Gaa/Taa	29/43	0.111171523651337	0	FACETS	0.762	0.699	0.827			1	INDETERMINATE	1	TRUE	0	0.409794886335575	0		390	556	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350734	89350734	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146294483	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	88	398	0	ENST00000301030.4:c.2216C>T	p.Ser739Leu	p.S739L	ENST00000301030	NM_001256183.1	739	tCg/tTg	9/13	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.409794886335575	2		398	416	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938995	76938995	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs886044898	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	100	311	0	ENST00000373344.5:c.1753G>T	p.Glu585Ter	p.E585*	ENST00000373344	NM_000489.3	585	Gaa/Taa	9/35	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.409794886335575	2		311	410	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228801	36228801	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	191	530	0	ENST00000222270.7:c.7700G>A	p.Arg2567His	p.R2567H	ENST00000222270	NM_014727.1	2567	cGt/cAt	35/37	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.409794886335575	2		530	633	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516857	187516857	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769928509	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	32	360	0	ENST00000441802.2:c.13124C>T	p.Ser4375Leu	p.S4375L	ENST00000441802	NM_005245.3	4375	tCg/tTg	26/27	1	2	FACETS	0.332	0.269	0.403	0.332	0.269	0.403	SUBCLONAL	1	TRUE	1	0.409794886335575	2		360	471	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475146	475146	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	21	385	0	ENST00000399788.2:c.491G>T	p.Arg164Ile	p.R164I	ENST00000399788	NM_001042603.1	164	aGa/aTa	4/28	1	2	FACETS	0.249	0.191	0.316	0.249	0.191	0.316	SUBCLONAL	1	TRUE	1	0.409794886335575	2		385	412	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692944	89692944	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786202047	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	77	338	0	ENST00000371953.3:c.428G>A	p.Gly143Asp	p.G143D	ENST00000371953	NM_000314.4	143	gGc/gAc	5/9	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.409794886335575	2		338	354	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347871	73347871	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	87	320	0	ENST00000377767.4:c.1190G>T	p.Arg397Ile	p.R397I	ENST00000377767	NM_014953.3	397	aGa/aTa	8/21	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.409794886335575	2		320	374	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250214	133250214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	123	455	0	ENST00000320574.5:c.1306C>T	p.Pro436Ser	p.P436S	ENST00000320574	NM_006231.2	436	Ccc/Tcc	13/49	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.409794886335575	2		455	483	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180553	56180553	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	14	281	0	ENST00000399503.3:c.3882G>T	p.Glu1294Asp	p.E1294D	ENST00000399503	NM_005921.1	1294	gaG/gaT	16/20	1	2	FACETS	0.259	0.187	0.346	0.259	0.187	0.346	SUBCLONAL	1	TRUE	1	0.409794886335575	2		281	264	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897021	28897021	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	129	409	0	ENST00000282397.4:c.2859G>T	p.Lys953Asn	p.K953N	ENST00000282397	NM_002019.4	953	aaG/aaT	21/30	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.409794886335575	2		409	528	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630836	67630836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs547474628	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	54	382	0	ENST00000272342.5:c.1022G>A	p.Arg341Gln	p.R341Q	ENST00000272342	NM_019002.3	341	cGa/cAa	5/6	1	2	FACETS	0.701	0.601	0.81	0.701	0.601	0.81	SUBCLONAL	1	TRUE	1	0.409794886335575	2		382	376	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250273	39250273	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	93	390	0	ENST00000402219.2:c.1296G>T	p.Trp432Cys	p.W432C	ENST00000402219	NM_005633.3	432	tgG/tgT	10/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.409794886335575	2		390	340	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10789919	10789919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1391585643	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	102	340	0	ENST00000361367.2:c.1990C>T	p.Arg664Cys	p.R664C	ENST00000361367	NM_014633.3	664	Cgt/Tgt	16/25	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.409794886335575	2		340	389	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163313609	163313609	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	41	157	0	ENST00000271452.3:c.756G>T	p.Lys252Asn	p.K252N	ENST00000271452	NM_145697.2	252	aaG/aaT	10/14	0.409794886335575	3	FACETS	0.927	0.778	1	0.464	0.389	0.546	CLONAL	1	TRUE	1	0.409794886335575	3		157	260	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175723	176175723	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	100	441	0	ENST00000367669.3:c.392G>T	p.Ser131Ile	p.S131I	ENST00000367669	NM_022457.5	131	aGc/aTc	1/20	0.409794886335575	3	FACETS	1	0.9	1	0.503	0.45	0.558	CLONAL	1	TRUE	1	0.409794886335575	3		441	585	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231488467	231488467	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	91	369	0	ENST00000295050.7:c.830C>T	p.Ala277Val	p.A277V	ENST00000295050	NM_032018.5	277	gCc/gTc	5/5	0.409794886335575	3	FACETS	1	0.967	1	0.611	0.545	0.68	CLONAL	1	TRUE	1	0.409794886335575	3		369	438	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246093171	246093171	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	35	329	0	ENST00000388985.4:c.599+1G>A		p.X200_splice	ENST00000388985		200			0.409794886335575	3	FACETS	0.339	0.277	0.409	0.17	0.138	0.205	SUBCLONAL	1	TRUE	1	0.409794886335575	3		329	607	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14317320	14317320	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	93	251	1	ENST00000256196.4:c.190C>A	p.Leu64Ile	p.L64I	ENST00000256196		64	Cta/Ata	2/6	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.409794886335575	2		252	320	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77934635	77934635	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	145	456	0	ENST00000361507.4:c.1390G>T	p.Ala464Ser	p.A464S	ENST00000361507	NM_080491.2	464	Gcc/Tcc	6/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.409794886335575	2		456	490	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250243	133250243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374920539	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	132	448	0	ENST00000320574.5:c.1277C>T	p.Ala426Val	p.A426V	ENST00000320574	NM_006231.2	426	gCg/gTg	13/49	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.409794886335575	2		448	480	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68878245	68878245	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1229788470	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	131	373	0	ENST00000487270.1:c.957+1G>A		p.X319_splice	ENST00000487270	NM_133509.3	319			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.409794886335575	2		373	527	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003088	42003088	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	162	411	0	ENST00000219905.7:c.2625A>C	p.Gln875His	p.Q875H	ENST00000219905	NM_001164273.1	875	caA/caC	8/24	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.409794886335575	2		411	541	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650675	67650675	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	159	389	0	ENST00000264010.4:c.980G>C	p.Cys327Ser	p.C327S	ENST00000264010	NM_006565.3	327	tGc/tCc	5/12	1	2	FACETS	0.771	0.712	0.832	1	0.99	1	SUBCLONAL	2	TRUE	1	0.409794886335575	2		389	503	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981534	63981534	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	172	477	0	ENST00000398590.3:c.2036C>A	p.Ser679Tyr	p.S679Y	ENST00000398590	NM_001177387.1	679	tCt/tAt	12/14	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.409794886335575	2		477	649	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390213	89390213	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	86	377	0	ENST00000336596.2:c.962C>A	p.Ala321Asp	p.A321D	ENST00000336596	NM_005233.5	321	gCt/gAt	4/17	1	2	FACETS	0.746	0.661	0.836	0.746	0.661	0.836	SUBCLONAL	1	TRUE	1	0.409794886335575	2		377	563	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413627	138413627	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	151	349	0	ENST00000289153.2:c.1892+1G>A		p.X631_splice	ENST00000289153	NM_006219.2	631			1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.409794886335575	2		349	514	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081579	143081579	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	136	373	0	ENST00000262992.4:c.1495G>T	p.Asp499Tyr	p.D499Y	ENST00000262992	NM_001101669.1	499	Gac/Tac	15/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.409794886335575	2		373	498	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554870	187554870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	148	377	0	ENST00000441802.2:c.4291G>A	p.Ala1431Thr	p.A1431T	ENST00000441802	NM_005245.3	1431	Gct/Act	7/27	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.409794886335575	2		377	543	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117730801	117730801	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	125	322	0	ENST00000368508.3:c.233A>G	p.Glu78Gly	p.E78G	ENST00000368508	NM_002944.2	78	gAg/gGg	4/43	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.409794886335575	2		322	425	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412266	63412266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776745995	NA	P-0064220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	170	571	0	ENST00000330258.3:c.901C>T	p.Pro301Ser	p.P301S	ENST00000330258	NM_152424.3	301	Ccc/Tcc	2/2	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.409794886335575	2		571	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0064223-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	132	580	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.388088817345168	1	FACETS	0.85	0.774	0.93	0.85	0.774	0.93	CLONAL	1	TRUE	0	0.388088817345168	1		581	645	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351208	89351208	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1376769382	NA	P-0064223-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	80	516	0	ENST00000301030.4:c.1742C>T	p.Ser581Phe	p.S581F	ENST00000301030	NM_001256183.1	581	tCt/tTt	9/13	0.16336027090841	1	FACETS	0.594	0.524	0.67	0.594	0.524	0.67	INDETERMINATE	1	TRUE	0	0.388088817345168	1		516	559	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243708883	243708883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs942187513	NA	P-0064223-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	22	253	0	ENST00000263826.5:c.1180G>A	p.Asp394Asn	p.D394N	ENST00000263826	NM_005465.4	394	Gat/Aat	11/13	1	2	FACETS	0.834	0.654	1	0.834	0.654	1	CLONAL	1	TRUE	1	0.388088817345168	2		253	136	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124467306	124467306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064223-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	22	330	1	ENST00000357628.3:c.1648G>A	p.Asp550Asn	p.D550N	ENST00000357628	NM_015450.2	550	Gat/Aat	17/19	1	2	FACETS	0.84	0.659	1	0.84	0.659	1	CLONAL	1	TRUE	1	0.388088817345168	2		331	135	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636664	73636684	+	protein_altering_variant	In_Frame_Del	DEL	TGGAAGTCCAGATAGACAAGC	TGGAAGTCCAGATAGACAAGC	ACAAGT	novel	NA	P-0064223-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	121	638	2	ENST00000377687.4:c.927_947delinsACAAGT	p.Gly310_Ala316delinsGlnVal	p.G310_A316delinsQV	ENST00000377687	NM_001730.3	309	ccTGGAAGTCCAGATAGACAAGCa/ccACAAGTa	2/4	0.279028577788093	1	FACETS	0.64	0.578	0.705	0.64	0.578	0.705	SUBCLONAL	1	TRUE	0	0.388088817345168	1		640	785	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0064224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	171	458	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.771469699820617	2		458	430	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0064224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	134	363	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.771469699820617	2		363	347	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230459233	230459233	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	115	494	0	ENST00000391860.1:c.1168C>A	p.Gln390Lys	p.Q390K	ENST00000391860	NM_001258311.1	390	Cag/Aag	7/7	1	2	FACETS	0.994	0.909	1	0.994	0.909	1	CLONAL	1	TRUE	1	0.771469699820617	2		494	300	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456404	32456404	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	122	442	0	ENST00000332351.3:c.488A>T	p.His163Leu	p.H163L	ENST00000332351	NM_024426.4	163	cAc/cTc	1/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.771469699820617	2		442	289	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369241	118369241	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs781805661	NA	P-0064224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	154	342	0	ENST00000534358.1:c.5959G>A	p.Glu1987Lys	p.E1987K	ENST00000534358	NM_005933.3	1987	Gaa/Aaa	22/36	1	2	FACETS	0.953	0.881	1	0.953	0.881	1	CLONAL	1	TRUE	1	0.771469699820617	2		342	419	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245349	46245349	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0064224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	308	470	0	ENST00000334344.6:c.3443T>G	p.Leu1148Ter	p.L1148*	ENST00000334344	NM_152641.2	1148	tTa/tGa	15/21	0.771469699820617	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.771469699820617	2		470	396	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873760	35873760	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	116	425	0	ENST00000216797.5:c.91G>C	p.Asp31His	p.D31H	ENST00000216797	NM_020529.2	31	Gac/Cac	1/6	0.670545299237904	1	FACETS	0.919	0.853	0.984	0.919	0.853	0.984	CLONAL	1	TRUE	0	0.771469699820617	1		425	201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579198	7579893	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGACAGGAAGCCAAAGGGTGAAGAGGAATCCCAAAGTTCCAAACAAAAGAAATGCAGGGGGATACGGCCAGGCATTGAAGTCTCATGGAAGCCAGCCCCTCAGGGCAACTGACCGTGCAAGTCACAGACTTGGCTGTCCCAGAATGCAAGAAGCCCAGACGGAAACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGGACAGAAGATGACAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTGCAGGGGCCACGGGGGGAGCAGCCTCTGGCATTCTGGGAGCTTCATCTGGACCTGGGTCTTCAGTGAACCATTGTTCAATATCGTCCGGGGACAGCATCAAATCATCCATTGCTTGGGACGGCAAGGGGGACTGTAGATGGGTGAAAAGAGCAGTCAGAGGACCAGGTCCTCAGCCCCCCAGCCCCCCAGCCCTCCAGGTCCCCAGCCCTCCAGGTCCCCAGCCCAACCCTTGTCCTTACCAGAACGTTGTTTTCAGGAAGTCTGAAAGACAAGAGCAGAAAGTCAGTCCCATGGAATTTTCGCTTCCCACAGGTCTCTGCTAGGGGGCTGGGGTTGGGGTGGGGGTGGTGGGCCTGCCCTTCCAATGGATCCACTCACAGTTTCCATAGGTCTGAAAATGTTTCCTGACTCAGAGGGGGCTCGACGCTAGGAT	CTGACAGGAAGCCAAAGGGTGAAGAGGAATCCCAAAGTTCCAAACAAAAGAAATGCAGGGGGATACGGCCAGGCATTGAAGTCTCATGGAAGCCAGCCCCTCAGGGCAACTGACCGTGCAAGTCACAGACTTGGCTGTCCCAGAATGCAAGAAGCCCAGACGGAAACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGGACAGAAGATGACAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTGCAGGGGCCACGGGGGGAGCAGCCTCTGGCATTCTGGGAGCTTCATCTGGACCTGGGTCTTCAGTGAACCATTGTTCAATATCGTCCGGGGACAGCATCAAATCATCCATTGCTTGGGACGGCAAGGGGGACTGTAGATGGGTGAAAAGAGCAGTCAGAGGACCAGGTCCTCAGCCCCCCAGCCCCCCAGCCCTCCAGGTCCCCAGCCCTCCAGGTCCCCAGCCCAACCCTTGTCCTTACCAGAACGTTGTTTTCAGGAAGTCTGAAAGACAAGAGCAGAAAGTCAGTCCCATGGAATTTTCGCTTCCCACAGGTCTCTGCTAGGGGGCTGGGGTTGGGGTGGGGGTGGTGGGCCTGCCCTTCCAATGGATCCACTCACAGTTTCCATAGGTCTGAAAATGTTTCCTGACTCAGAGGGGGCTCGACGCTAGGAT	-	novel	NA	P-0064224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	66	143	0	ENST00000269305.4:c.20_375+114del		p.X7_splice	ENST00000269305	NM_001126112.2	7		2-4/11	0.753860871833039	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.771469699820617	1		143	87	SUCCESS
APC	324	MSKCC	GRCh37	5	112116515	112116515	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	83	257	0	ENST00000257430.4:c.561del	p.Arg187SerfsTer18	p.R187Sfs*18	ENST00000257430	NM_000038.5	187	aGg/ag	6/16	0.771469699820617	1	FACETS	0.842	0.767	0.917	0.842	0.767	0.917	CLONAL	1	TRUE	0	0.771469699820617	1		257	157	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508836	106508836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	109	520	1	ENST00000359195.3:c.830G>A	p.Arg277Gln	p.R277Q	ENST00000359195	NM_002649.2	277	cGg/cAg	2/11	0.639500998309897	3	FACETS	0.837	0.756	0.922	0.418	0.378	0.461	CLONAL	1	TRUE	1	0.771469699820617	3		521	468	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064226-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	65	934	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.422548660102878	1	FACETS	0.971	0.852	1	0.971	0.852	1	CLONAL	1	TRUE	0	0.422548660102878	1		934	250	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593464	55593464	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs3822214	NA	P-0064226-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	9	566	0	ENST00000288135.5:c.1621A>C	p.Met541Leu	p.M541L	ENST00000288135	NM_000222.2	541	Atg/Ctg	10/21	0.422548660102878	3	FACETS	0.227	0.15	0.326	0.114	0.075	0.163	SUBCLONAL	1	TRUE	1	0.422548660102878	3		566	227	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041400	42041400	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064226-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	105	783	3	ENST00000219905.7:c.5595T>A	p.Asn1865Lys	p.N1865K	ENST00000219905	NM_001164273.1	1865	aaT/aaA	17/24	0.218619024124516	5	FACETS	0.938	0.846	1	0.625	0.564	0.689	INDETERMINATE	2	TRUE	2	0.422548660102878	5		786	433	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9928076	9928076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064227-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	105	516	0	ENST00000330684.3:c.1663G>A	p.Ala555Thr	p.A555T	ENST00000330684	NM_001134407.1	555	Gcc/Acc	8/13	0.449408592367818	0	FACETS	0.412	0.373	0.454			1	SUBCLONAL	1	TRUE	0	0.583769146992748	0		516	363	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434697	49434697	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064227-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	124	823	0	ENST00000301067.7:c.6856G>T	p.Glu2286Ter	p.E2286*	ENST00000301067	NM_003482.3	2286	Gag/Tag	31/54	1	2	FACETS	0.936	0.853	1	0.936	0.853	1	CLONAL	1	TRUE	1	0.583769146992748	2		823	454	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439806	220439806	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142337821	NA	P-0064227-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	121	754	1	ENST00000243786.2:c.659G>A	p.Arg220Gln	p.R220Q	ENST00000243786	NM_002191.3	220	cGg/cAg	2/2	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.583769146992748	2		755	372	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0064229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	296	599	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.231429642370456	3	FACETS	0.902	0.851	0.955	0.902	0.851	0.955	CLONAL	3	TRUE	0	0.263545109361883	3		599	939	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0064229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	15	304	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	0.263545109361883	5	FACETS	0.291	0.212	0.388	0.097	0.07	0.13	SUBCLONAL	1	TRUE	2	0.263545109361883	5		304	545	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370879	55370879	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	95	606	0	ENST00000297316.4:c.181C>T	p.Arg61Ter	p.R61*	ENST00000297316	NM_022454.3	61	Cga/Tga	1/2	0.266192307184076	1	FACETS	0.856	0.762	0.956	0.856	0.762	0.956	CLONAL	1	TRUE	0	0.263545109361883	1		606	731	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476252	88476252	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	133	486	0	ENST00000360948.2:c.1880A>C	p.Lys627Thr	p.K627T	ENST00000360948	NM_001012338.2	627	aAg/aCg	15/19	0.266192307184076	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.263545109361883	1		486	667	SUCCESS
AR	367	MSKCC	GRCh37	X	66766393	66766393	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	60	230	0	ENST00000374690.3:c.1405G>T	p.Gly469Cys	p.G469C	ENST00000374690	NM_000044.3	469	Ggc/Tgc	1/8	0.266192307184076	0	FACETS	1	0.953	1			1	CLONAL	1	TRUE	NA	0.263545109361883	0		230	275	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579329	7579329	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912658	NA	P-0064230-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	314	595	1	ENST00000269305.4:c.358A>G	p.Lys120Glu	p.K120E	ENST00000269305	NM_001126112.2	120	Aag/Gag	4/11	0.514952920330535	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.53593358104361	2		596	520	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817482	39817482	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064231-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	81	616	0	ENST00000288319.7:c.81C>A	p.His27Gln	p.H27Q	ENST00000288319	NM_182918.3	27	caC/caA	2/10	0.585871813498095	3	FACETS	0.829	0.734	0.931	0.415	0.367	0.466	CLONAL	1	TRUE	1	0.585871813498095	3		616	431	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690205	33690205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064231-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	95	706	0	ENST00000308377.4:c.622C>T	p.Pro208Ser	p.P208S	ENST00000308377	NM_152270.3	208	Cct/Tct	2/5	0.57576095175491	4	FACETS	0.96	0.857	1			1	CLONAL	1	TRUE	NA	0.585871813498095	4		706	536	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160227	22160227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064232-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	67	576	0	ENST00000215832.6:c.404G>A	p.Arg135Lys	p.R135K	ENST00000215832	NM_002745.4	135	aGa/aAa	3/9	0.375590246890835	1	FACETS	0.349	0.305	0.397	0.349	0.305	0.397	INDETERMINATE	1	TRUE	0	0.690326145263517	1		576	364	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265993	41266240	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTA	GCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTA	-	novel	NA	P-0064232-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	41	447	0	ENST00000349496.5:c.14-21_240del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	1	2	FACETS	0.579	0.488	0.679	0.579	0.488	0.679	SUBCLONAL	1	TRUE	1	0.690326145263517	2		447	205	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064233-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	97	344	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.355437911779222	2		344	408	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0064233-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	99	810	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.355437911779222	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	0	0.355437911779222	1		810	454	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783301	9783301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763402967	NA	P-0064233-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	23	689	0	ENST00000377346.4:c.2545G>A	p.Ala849Thr	p.A849T	ENST00000377346	NM_005026.3	849	Gcc/Acc	20/24	0.198314204265084	1	FACETS	0.247	0.192	0.312	0.247	0.192	0.312	INDETERMINATE	1	TRUE	0	0.355437911779222	1		689	430	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575055	48575055	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0064233-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	49	461	0	ENST00000342988.3:c.250-1G>A		p.X84_splice	ENST00000342988	NM_005359.5	84			0.355437911779222	1	FACETS	0.875	0.748	1	0.875	0.748	1	CLONAL	1	TRUE	0	0.355437911779222	1		461	259	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033249	69033249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs114811202	NA	P-0064233-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	68	624	0	ENST00000288368.4:c.3689G>A	p.Arg1230Gln	p.R1230Q	ENST00000288368	NM_024870.2	1230	cGg/cAg	30/40	1	2	FACETS	0.868	0.757	0.986	0.868	0.757	0.986	CLONAL	1	TRUE	1	0.355437911779222	2		624	441	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0064234-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	161	578	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.275425369195369	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.275425369195369	1		578	919	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0064234-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	131	453	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.163525418660486	3	FACETS	1	0.976	1	0.616	0.558	0.676	INDETERMINATE	1	TRUE	1	0.275425369195369	3		453	879	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579347	7579348	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0064234-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	158	601	0	ENST00000269305.4:c.339_340del	p.Leu114AlafsTer34	p.L114Afs*34	ENST00000269305	NM_001126112.2	113	ttCTtg/tttg	4/11	0.275425369195369	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.275425369195369	1		601	877	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686391	30686392	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCT	novel	NA	P-0064234-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	143	620	0	ENST00000295754.5:c.248_250dup	p.Val83_Cys84insPhe	p.V83_C84insF	ENST00000295754	NM_003242.5	83	gtc/gTCTtc	2/7	0.275425369195369	1	FACETS	0.938	0.854	1	0.938	0.854	1	CLONAL	1	TRUE	0	0.275425369195369	1		620	955	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050331	128050331	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755616510	NA	P-0064235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	226	515	0	ENST00000285398.2:c.326G>A	p.Arg109Gln	p.R109Q	ENST00000285398	NM_000122.1	109	cGa/cAa	3/15	1	2	FACETS	0.914	0.855	0.975	0.914	0.855	0.975	CLONAL	1	TRUE	1	0.671640248188052	2		515	736	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984362	201984363	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	297	514	0	ENST00000359651.3:c.1029dup	p.Arg344ThrfsTer127	p.R344Tfs*127	ENST00000359651		343	gaa/gAaa	8/8	1	2	FACETS	0.783	0.745	0.82	1	0.995	1	SUBCLONAL	2	TRUE	1	0.671640248188052	2		514	565	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70360787	70360792	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TAAAGG	TAAAGG	-	novel	NA	P-0064235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	107	271	0	ENST00000373644.4:c.1967_1968+4del		p.X656_splice	ENST00000373644	NM_030625.2	656		3/12	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.671640248188052	2		271	298	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061862	38061862	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	48	686	0	ENST00000250448.2:c.127T>G	p.Ser43Ala	p.S43A	ENST00000250448	NM_004496.3	43	Tcc/Gcc	2/2	1	2	FACETS	0.17	0.143	0.2	0.17	0.143	0.2	SUBCLONAL	1	TRUE	1	0.671640248188052	2		686	839	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740398	58740399	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0064235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	99	518	0	ENST00000305921.3:c.1307_1308dup	p.Pro437TyrfsTer15	p.P437Yfs*15	ENST00000305921	NM_003620.3	435	cat/cATat	6/6	0.343106143707385	1	FACETS	0.357	0.32	0.397	0.357	0.32	0.397	INDETERMINATE	1	TRUE	0	0.671640248188052	1		518	548	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564740	86564750	+	frameshift_variant	Frame_Shift_Del	DEL	TCTCTGGATGG	TCTCTGGATGG	-	novel	NA	P-0064235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	219	665	0	ENST00000274376.6:c.472_482del	p.Ser158ThrfsTer18	p.S158Tfs*18	ENST00000274376	NM_002890.2	158	TCTCTGGATGGa/a	1/25	0.671640248188052	1	FACETS	0.996	0.939	1	0.996	0.939	1	CLONAL	1	TRUE	0	0.671640248188052	1		665	435	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162892	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	GATA	novel	NA	P-0064235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	16	346	0	ENST00000257430.4:c.1496_1499dup	p.Tyr500Ter	p.Y500*	ENST00000257430	NM_000038.5	499	cga/cGATAga	12/16	0.671640248188052	1	FACETS	0.149	0.11	0.195	0.149	0.11	0.195	SUBCLONAL	1	TRUE	0	0.671640248188052	1		346	213	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873718	35873719	+	frameshift_variant	Frame_Shift_Ins	INS	TC	TC	GAT	novel	NA	P-0064235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	144	496	1	ENST00000216797.5:c.132_133delinsATC	p.Met45SerfsTer41	p.M45Sfs*41	ENST00000216797	NM_020529.2	44	caGAtg/caATCtg	1/6	1	2	FACETS	0.846	0.776	0.918	0.846	0.776	0.918	CLONAL	1	TRUE	1	0.671640248188052	2		497	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0064236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	142	583	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.266947683827733	2	FACETS	0.987	0.904	1	0.987	0.904	1	CLONAL	2	TRUE	0	0.266947683827733	2		583	539	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909464	50909464	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199576140	NA	P-0064236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	54	754	2	ENST00000440232.2:c.1268G>A	p.Arg423His	p.R423H	ENST00000440232	NM_002691.3	423	cGt/cAt	11/27	0.266947683827733	1	FACETS	0.804	0.688	0.93	0.804	0.688	0.93	CLONAL	1	TRUE	0	0.266947683827733	1		756	436	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402172	402172	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0064236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	48	677	0	ENST00000399788.2:c.4619del	p.Leu1540Ter	p.L1540*	ENST00000399788	NM_001042603.1	1540	tTa/ta	27/28	0.26494737681531	5	FACETS	0.676	0.57	0.793	0.225	0.19	0.265	SUBCLONAL	1	TRUE	2	0.266947683827733	5		677	745	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418482	49418482	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	42	735	0	ENST00000301067.7:c.15931G>T	p.Val5311Leu	p.V5311L	ENST00000301067	NM_003482.3	5311	Gtg/Ttg	50/54	0.266947683827733	2	FACETS	0.621	0.518	0.735	0.31	0.259	0.368	SUBCLONAL	1	TRUE	0	0.266947683827733	2		735	507	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720802	89720809	+	frameshift_variant	Frame_Shift_Del	DEL	TTACTTTA	TTACTTTA	ATT	novel	NA	P-0064236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	57	183	0	ENST00000371953.3:c.953_960delinsATT	p.Leu318HisfsTer5	p.L318Hfs*5	ENST00000371953	NM_000314.4	318	cTTACTTTA/cATT	8/9	0.266947683827733	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	0	0.266947683827733	2		183	190	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520000	NA	P-0064237-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	368	663	0	ENST00000269305.4:c.452C>A	p.Pro151His	p.P151H	ENST00000269305	NM_001126112.2	151	cCc/cAc	5/11	0.501934223486604	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.501425955325513	2		663	689	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298036	15298042	+	frameshift_variant	Frame_Shift_Del	DEL	AGCCAGG	AGCCAGG	-	novel	NA	P-0064237-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	127	670	0	ENST00000263388.2:c.1714_1720del	p.Pro572ThrfsTer25	p.P572Tfs*25	ENST00000263388	NM_000435.2	572	CCTGGCTac/ac	11/33	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.501425955325513	NA		670	729	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497275	149497275	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064237-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	117	547	0	ENST00000261799.4:c.3043A>T	p.Asn1015Tyr	p.N1015Y	ENST00000261799	NM_002609.3	1015	Aat/Tat	22/23	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.501425955325513	2		547	465	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101750	71101751	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0064238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	26	500	2	ENST00000318789.4:c.447dup	p.Gln150ThrfsTer20	p.Q150Tfs*20	ENST00000318789	NM_032682.5	149	-/A	9/21	1	2	FACETS	0.722	0.574	0.891	0.722	0.574	0.891	SUBCLONAL	1	TRUE	1	0.271703940474859	2		502	265	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797263	135797271	+	inframe_deletion	In_Frame_Del	DEL	AAAGGAGAC	AAAGGAGAC	-	novel	NA	P-0064238-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	32	611	0	ENST00000298552.3:c.598_606del	p.Val200_Phe202del	p.V200_F202del	ENST00000298552	NM_001162426.1	200	GTCTCCTTT/-	7/23	1	2	FACETS	0.626	0.509	0.759	0.626	0.509	0.759	SUBCLONAL	1	TRUE	1	0.271703940474859	2		611	376	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911679	32911679	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876657678	NA	P-0064244-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	104	457	0	ENST00000380152.3:c.3187C>T	p.Gln1063Ter	p.Q1063*	ENST00000380152		1063	Cag/Tag	11/27	0.579061828078083	1	FACETS	0.889	0.808	0.973	0.889	0.808	0.973	CLONAL	1	TRUE	0	0.579061828078083	1		457	287	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150933618	150933618	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0064244-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	175	568	0	ENST00000271640.5:c.3080C>G	p.Ser1027Ter	p.S1027*	ENST00000271640	NM_001145415.1	1027	tCa/tGa	16/22	1	2	FACETS	0.928	0.858	1	0.928	0.858	1	CLONAL	1	TRUE	1	0.579061828078083	2		568	651	SUCCESS
BLM	641	MSKCC	GRCh37	15	91337549	91337549	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064244-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	27	347	0	ENST00000355112.3:c.3172C>A	p.His1058Asn	p.H1058N	ENST00000355112	NM_000057.2	1058	Cac/Aac	16/22	1	2	FACETS	0.235	0.187	0.291	0.235	0.187	0.291	SUBCLONAL	1	TRUE	1	0.579061828078083	2		347	396	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106514799	106515271	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATGTGCTGGAAAGAAAACTACAGTATTAATTCCTTAGCATCACCCTCAGAGCATACTTCTCTACTTGGATTGTGTTGGTGTCTATGTGTTATCCCACATATATTCACATATTTCTGTCCCCTGTTGTAGTATGTGTACATGGTTATGTTGCTCACCTTAAGCCCAATGTATCTTGCCACCTCATATGGTTAGCTCCTCAAAGGCAGGGCCCACCCACATTTCTCCTGCTCTACACCAGAACAAATATATAGAATGCTATGAATAAATGTGTTCTCAGGAAATGTAATAGATAATATTGATGATTTCTGGAACTCACATAACTCTTGTGTACTTTTGACAATTACAGTTATTTCACAACTTAAACAAAAGCTTGAAAACCTGCAGAATTCTCAACTCCCCGAAAGCTTTAGAGTTCCATATGATCCTGGACTGAAAGCAGGAGCGCTGGCAGTAGGTATCACTTGGATGTCTCC	ATGTGCTGGAAAGAAAACTACAGTATTAATTCCTTAGCATCACCCTCAGAGCATACTTCTCTACTTGGATTGTGTTGGTGTCTATGTGTTATCCCACATATATTCACATATTTCTGTCCCCTGTTGTAGTATGTGTACATGGTTATGTTGCTCACCTTAAGCCCAATGTATCTTGCCACCTCATATGGTTAGCTCCTCAAAGGCAGGGCCCACCCACATTTCTCCTGCTCTACACCAGAACAAATATATAGAATGCTATGAATAAATGTGTTCTCAGGAAATGTAATAGATAATATTGATGATTTCTGGAACTCACATAACTCTTGTGTACTTTTGACAATTACAGTTATTTCACAACTTAAACAAAAGCTTGAAAACCTGCAGAATTCTCAACTCCCCGAAAGCTTTAGAGTTCCATATGATCCTGGACTGAAAGCAGGAGCGCTGGCAGTAGGTATCACTTGGATGTCTCC	-	novel	NA	P-0064244-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4	32	8	0	ENST00000359195.3:c.2288-341_2391+28del		p.X763_splice	ENST00000359195	NM_002649.2	763		5/11	1	2	FACETS	1	0.936	1	1	0.977	1	CLONAL	3	TRUE	1	0.579061828078083	2		8	36	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576926	7576927	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GC	GC	AT	novel	NA	P-0064246-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	42	567	0	ENST00000269305.4:c.920-1_920delinsAT		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	1	2	FACETS	0.269	0.223	0.319	0.269	0.223	0.319	SUBCLONAL	1	TRUE	1	0.395292441258939	2		567	791	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061228	38061229	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	T	novel	NA	P-0064246-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	131	564	0	ENST00000250448.2:c.760_761delinsA	p.Phe254ThrfsTer67	p.F254Tfs*67	ENST00000250448	NM_004496.3	254	TTc/Ac	2/2	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.395292441258939	2		564	628	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0064247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	63	631	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.256343420392505	2		631	386	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0064247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	94	311	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.256343420392505	5	FACETS	0.917	0.823	1	0.688	0.617	0.762	CLONAL	3	TRUE	1	0.256343420392505	5		311	369	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	79	557	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.191815171941702	2	FACETS	0.769	0.68	0.863	0.769	0.68	0.863	SUBCLONAL	2	TRUE	0	0.256343420392505	2		557	401	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949090	71949090	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	35	666	0	ENST00000298229.2:c.3557C>G	p.Pro1186Arg	p.P1186R	ENST00000298229	NM_001567.3	1186	cCg/cGg	27/28	1	2	FACETS	0.525	0.43	0.633	0.525	0.43	0.633	SUBCLONAL	1	TRUE	1	0.256343420392505	2		666	520	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131972863	131972863	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	20	267	0	ENST00000265335.6:c.3446A>G	p.Asp1149Gly	p.D1149G	ENST00000265335		1149	gAc/gGc	22/25	0.254380263023424	1	FACETS	0.515	0.394	0.656	0.515	0.394	0.656	SUBCLONAL	1	TRUE	0	0.256343420392505	1		267	264	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790781	89790784	+	frameshift_variant	Frame_Shift_Del	DEL	CCTC	CCTC	-	novel	NA	P-0064247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	83	607	0	ENST00000336032.3:c.172_175del	p.Pro58IlefsTer3	p.P58Ifs*3	ENST00000336032	NM_006813.2	56	ttCCTC/tt	1/2	0.145770617923116	3	FACETS	1	0.973	1	0.678	0.599	0.761	INDETERMINATE	1	TRUE	1	0.256343420392505	3		607	539	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239069	98239069	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	67	417	0	ENST00000331920.6:c.1574C>T	p.Thr525Ile	p.T525I	ENST00000331920	NM_000264.3	525	aCa/aTa	11/24	0.256343420392505	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.256343420392505	1		417	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0064248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	245	583	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.310633421531336	3	FACETS	1	0.975	1	0.707	0.666	0.749	CLONAL	2	TRUE	0	0.482467015534299	3		583	594	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656934	47656936	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs1295803849	NA	P-0064248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	140	306	0	ENST00000233146.2:c.1134_1136del	p.Glu378del	p.E378del	ENST00000233146	NM_000251.2	377	cAAGaa/caa	7/16	0.298758006416836	4	FACETS	0.931	0.855	1	0.931	0.855	1	CLONAL	2	TRUE	2	0.482467015534299	4		306	462	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606131	81606131	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	91	502	0	ENST00000298171.2:c.801G>T	p.Leu267Phe	p.L267F	ENST00000298171	NM_000369.2	267	ttG/ttT	9/10	0.482467015534299	4	FACETS	1	0.911	1	0.513	0.457	0.573	CLONAL	1	TRUE	2	0.482467015534299	4		502	545	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192534	138192534	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	76	541	0	ENST00000237289.4:c.170G>T	p.Cys57Phe	p.C57F	ENST00000237289	NM_001270507.1	57	tGt/tTt	2/9	0.482467015534299	3	FACETS	0.486	0.426	0.552	0.243	0.213	0.276	SUBCLONAL	1	TRUE	1	0.482467015534299	3		541	804	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100366	157100366	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	163	389	0	ENST00000346085.5:c.1304del	p.Gly435AlafsTer67	p.G435Afs*67	ENST00000346085	NM_020732.3	435	Ggc/gc	1/20	0.482467015534299	3	FACETS	0.756	0.697	0.815	0.756	0.697	0.815	SUBCLONAL	2	TRUE	1	0.482467015534299	3		389	555	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334707	81334707	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	62	355	0	ENST00000222390.5:c.2009A>T	p.Glu670Val	p.E670V	ENST00000222390	NM_000601.4	670	gAg/gTg	17/18	0.482467015534299	5	FACETS	1	0.95	1	0.402	0.349	0.46	CLONAL	1	TRUE	2	0.482467015534299	5		355	367	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0064249-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	47	282	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.886	0.756	1	0.886	0.756	1	CLONAL	1	TRUE	1	0.517759290017396	2		282	205	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727513	88727513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374069724	NA	P-0064249-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	77	531	1	ENST00000360948.2:c.266G>A	p.Arg89His	p.R89H	ENST00000360948	NM_001012338.2	89	cGc/cAc	3/19	1	2	FACETS	0.365	0.319	0.413	0.365	0.319	0.413	SUBCLONAL	1	TRUE	1	0.517759290017396	2		532	816	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs878854073	NA	P-0064249-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	129	449	0	ENST00000269305.4:c.673-1G>A		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.517759290017396	1	FACETS	0.892	0.816	0.97	0.892	0.816	0.97	CLONAL	1	TRUE	0	0.517759290017396	1		449	414	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142863	7142863	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064249-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	190	562	0	ENST00000302850.5:c.2506G>T	p.Val836Leu	p.V836L	ENST00000302850	NM_000208.2	836	Gtg/Ttg	12/22	0.186622028716516	4	FACETS	1	0.987	1	0.651	0.603	0.702	INDETERMINATE	1	TRUE	2	0.517759290017396	4		562	855	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710567	40710567	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064249-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	117	457	0	ENST00000373198.4:c.4284C>G	p.Ile1428Met	p.I1428M	ENST00000373198	NM_133170.3	1428	atC/atG	31/32	1	2	FACETS	0.846	0.766	0.93	0.846	0.766	0.93	CLONAL	1	TRUE	1	0.517759290017396	2		457	534	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0064258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	53	430	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	1	2	FACETS	0.822	0.699	0.956	0.822	0.699	0.956	CLONAL	1	TRUE	1	0.17	2		430	759	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998711	100998711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	69	485	0	ENST00000325455.5:c.1091C>T	p.Pro364Leu	p.P364L	ENST00000325455	NM_001202474.3	364	cCg/cTg	1/8	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.17	2		485	740	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544587	86544587	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	37	537	0	ENST00000262426.4:c.412C>T	p.Arg138Trp	p.R138W	ENST00000262426	NM_001451.2	138	Cgg/Tgg	1/2	1	2	FACETS	0.677	0.557	0.812	0.677	0.557	0.812	SUBCLONAL	1	TRUE	1	0.17	2		537	643	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520291	176520291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779369671	NA	P-0064258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	30	245	0	ENST00000292408.4:c.1210G>A	p.Ala404Thr	p.A404T	ENST00000292408	NM_213647.1	404	Gcc/Acc	9/18	1	2	FACETS	0.9	0.726	1	0.9	0.726	1	CLONAL	1	TRUE	1	0.17	2		245	392	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0064259-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	34	176	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.211186607371505	3	FACETS	0.845	0.698	1	1	0.929	1	CLONAL	3	TRUE	1	0.16	3		176	181	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061240	38061241	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0064259-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	39	872	1	ENST00000250448.2:c.748_749delinsAA	p.Ser250Asn	p.S250N	ENST00000250448	NM_004496.3	250	TCc/AAc	2/2	1	2	FACETS	0.756	0.625	0.902	0.756	0.625	0.902	CLONAL	1	TRUE	1	0.16	2		873	645	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212289018	212289018	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064259-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	30	407	0	ENST00000342788.4:c.2728A>C	p.Ile910Leu	p.I910L	ENST00000342788	NM_005235.2	910	Ata/Cta	23/28	0.291749964178339	1	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	0	0.16	1		407	326	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031280	36031280	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064259-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	38	607	0	ENST00000358208.4:c.1399C>A	p.Pro467Thr	p.P467T	ENST00000358208		467	Cct/Act	11/12	1	2	FACETS	0.838	0.691	1	0.838	0.691	1	CLONAL	1	TRUE	1	0.16	2		607	567	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0064261-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	209	466	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	0.29296854443317	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	3	TRUE	1	0.291444156550065	4		466	598	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0064261-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	72	516	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.29296854443317	4	FACETS	0.925	0.82	1	0.925	0.82	1	CLONAL	3	TRUE	1	0.291444156550065	4		516	230	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0064261-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	63	443	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.29296854443317	4	FACETS	1	0.868	1	0.334	0.289	0.383	CLONAL	1	TRUE	1	0.291444156550065	4		443	557	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0064261-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	41	184	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.29296854443317	3	FACETS	1	0.868	1	1	0.868	1	CLONAL	2	TRUE	1	0.291444156550065	3		184	157	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999560	100999560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778465984	NA	P-0064261-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	84	556	0	ENST00000325455.5:c.242C>T	p.Ser81Leu	p.S81L	ENST00000325455	NM_001202474.3	81	tCg/tTg	1/8	0.29296854443317	3	FACETS	1	0.96	1	0.597	0.528	0.671	CLONAL	1	TRUE	1	0.291444156550065	3		556	553	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803483	32803483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536291251	NA	P-0064261-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	144	433	0	ENST00000374899.4:c.676C>T	p.Arg226Trp	p.R226W	ENST00000374899	NM_018833.2	226	Cgg/Tgg	4/12	0.291444156550065	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	2	0.291444156550065	4		433	598	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933739	36933739	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1460105307	NA	P-0064261-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	73	599	0	ENST00000361632.4:c.1660C>A	p.Leu554Met	p.L554M	ENST00000361632		554	Ctg/Atg	12/16	0.29296854443317	3	FACETS	0.998	0.874	1	0.499	0.437	0.566	CLONAL	1	TRUE	1	0.291444156550065	3		599	575	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114917829	114917829	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0064261-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	108	307	0	ENST00000543371.1:c.1318+1G>T		p.X440_splice	ENST00000543371	NM_001198531.1	440			0.29296854443317	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.291444156550065	3		307	377	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924945	49924945	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064261-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	70	446	0	ENST00000296474.3:c.3998C>A	p.Thr1333Asn	p.T1333N	ENST00000296474	NM_002447.2	1333	aCc/aAc	20/20	0.29296854443317	3	FACETS	1	0.95	1	0.588	0.514	0.667	CLONAL	1	TRUE	1	0.291444156550065	3		446	468	SUCCESS
ALB	213	MSKCC	GRCh37	4	74279138	74279138	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs889031471	NA	P-0064261-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	32	332	0	ENST00000295897.4:c.845C>T	p.Ala282Val	p.A282V	ENST00000295897	NM_000477.5	282	gCg/gTg	8/15	0.29296854443317	3	FACETS	0.801	0.652	0.969	0.401	0.326	0.485	CLONAL	1	TRUE	1	0.291444156550065	3		332	314	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0064272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	106	409	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.575310535835421	2		409	349	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220579	1220579	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0064272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	234	739	0	ENST00000326873.7:c.598-1G>T		p.X200_splice	ENST00000326873	NM_000455.4	200			0.575310535835421	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.575310535835421	1		739	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0064272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	172	714	0	ENST00000269305.4:c.97-1G>T		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.575310535835421	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.575310535835421	1		714	384	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589711	69589711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	61	1178	0	ENST00000168712.1:c.142G>A	p.Glu48Lys	p.E48K	ENST00000168712	NM_002007.2	48	Gag/Aag	1/3	1	2	FACETS	0.364	0.314	0.419	0.364	0.314	0.419	SUBCLONAL	1	TRUE	1	0.575310535835421	2		1178	582	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955487	48955548	+	frameshift_variant	Frame_Shift_Del	DEL	TTTATCAAAGCAGAAGGCAACTTGACAAGAGAAATGATAAAACATTTAGAACGATGTGAACA	TTTATCAAAGCAGAAGGCAACTTGACAAGAGAAATGATAAAACATTTAGAACGATGTGAACA	-	novel	NA	P-0064272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	53	359	0	ENST00000267163.4:c.1604_1665del	p.Phe535SerfsTer16	p.F535Sfs*16	ENST00000267163	NM_000321.2	535	TTTATCAAAGCAGAAGGCAACTTGACAAGAGAAATGATAAAACATTTAGAACGATGTGAACAt/t	17/27	0.575310535835421	1	FACETS	0.608	0.525	0.696	0.608	0.525	0.696	SUBCLONAL	1	TRUE	0	0.575310535835421	1		359	216	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349357	73349357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	137	447	0	ENST00000377767.4:c.979G>A	p.Glu327Lys	p.E327K	ENST00000377767	NM_014953.3	327	Gaa/Aaa	6/21	0.230547294491315	3	FACETS	0.884	0.815	0.954	0.884	0.815	0.954	INDETERMINATE	2	TRUE	1	0.575310535835421	3		447	347	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133006	30133006	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	246	521	0	ENST00000331968.5:c.595G>T	p.Val199Leu	p.V199L	ENST00000331968	NM_002742.2	199	Gtg/Ttg	4/18	0.351874038394835	3	FACETS	0.994	0.938	1	0.663	0.625	0.7	CLONAL	2	TRUE	0	0.575310535835421	3		521	554	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679770	33679770	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	41	617	0	ENST00000308377.4:c.2311C>T	p.Gln771Ter	p.Q771*	ENST00000308377	NM_152270.3	771	Cag/Tag	5/5	1	2	FACETS	0.239	0.198	0.284	0.239	0.198	0.284	SUBCLONAL	1	TRUE	1	0.575310535835421	2		617	597	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202807	128202807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	124	700	1	ENST00000341105.2:c.913C>A	p.Leu305Ile	p.L305I	ENST00000341105	NM_032638.4	305	Ctc/Atc	4/6	1	2	FACETS	0.84	0.764	0.92	0.84	0.764	0.92	CLONAL	1	TRUE	1	0.575310535835421	2		701	513	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191077	185191077	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs747496570	NA	P-0064272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	131	738	0	ENST00000265026.3:c.1958A>G	p.His653Arg	p.H653R	ENST00000265026	NM_004721.4	653	cAt/cGt	11/14	1	2	FACETS	0.768	0.699	0.84	0.768	0.699	0.84	SUBCLONAL	1	TRUE	1	0.575310535835421	2		738	593	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803469	32803470	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	76	569	0	ENST00000374899.4:c.689dup	p.Ser231LeufsTer15	p.S231Lfs*15	ENST00000374899	NM_018833.2	230	ttc/ttTc	4/12	0.208142083181353	3	FACETS	0.581	0.51	0.657	0.194	0.17	0.219	INDETERMINATE	1	TRUE	0	0.575310535835421	3		569	586	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371902	116371902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	34	494	0	ENST00000397752.3:c.1381C>T	p.Arg461Cys	p.R461C	ENST00000397752	NM_000245.2	461	Cgc/Tgc	3/21	1	2	FACETS	0.27	0.221	0.327	0.27	0.221	0.327	SUBCLONAL	1	TRUE	1	0.575310535835421	2		494	437	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465643	8465643	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	89	452	0	ENST00000356435.5:c.3537C>A	p.Ser1179Arg	p.S1179R	ENST00000356435		1179	agC/agA	21/35	0.144090669276145	0	FACETS	0.417	0.374	0.463			1	INDETERMINATE	1	TRUE	0	0.575310535835421	0		452	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0064275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	35	566	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	1	2	FACETS	0.861	0.704	1	0.861	0.704	1	CLONAL	1	TRUE	1	0.14	2		566	581	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597395	10597395	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	32	609	0	ENST00000171111.5:c.1808G>T	p.Gly603Val	p.G603V	ENST00000171111	NM_203500.1	603	gGg/gTg	6/6	1	2	FACETS	0.851	0.69	1	0.851	0.69	1	CLONAL	1	TRUE	1	0.14	2		609	537	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435229	110435229	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1443489792	NA	P-0064275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	52	786	0	ENST00000375856.3:c.3172G>A	p.Ala1058Thr	p.A1058T	ENST00000375856	NM_003749.2	1058	Gcc/Acc	1/2	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.14	2		786	632	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220695	1220696	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0064275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	37	629	0	ENST00000326873.7:c.714_715del	p.Ile238MetfsTer27	p.I238Mfs*27	ENST00000326873	NM_000455.4	238	aTC/a	5/10	1	2	FACETS	0.972	0.8	1	0.972	0.8	1	CLONAL	1	TRUE	1	0.14	2		629	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0064276-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	25	687	0	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.145569843466771	2	FACETS	0.857	0.677	1	0.429	0.338	0.532	CLONAL	1	TRUE	0	0.197093953232073	2		687	296	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913253	39913253	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064276-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	34	640	1	ENST00000378444.4:c.4862del	p.Pro1621GlnfsTer53	p.P1621Qfs*53	ENST00000378444	NM_001123385.1	1621	cCa/ca	14/15	0.197093953232073	1	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	0	0.197093953232073	1		641	288	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321300	65321300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757281554	NA	P-0064276-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	28	691	0	ENST00000342505.4:c.1540C>T	p.Arg514Cys	p.R514C	ENST00000342505	NM_002227.2	514	Cgc/Tgc	11/25	1	2	FACETS	0.807	0.646	0.991	0.807	0.646	0.991	CLONAL	1	TRUE	1	0.197093953232073	2		691	352	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111965530	111965530	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064276-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	24	347	0	ENST00000375549.3:c.316G>T	p.Gly106Cys	p.G106C	ENST00000375549	NM_003002.3	106	Ggc/Tgc	4/4	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.197093953232073	2		347	216	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715665	18715665	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064276-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	13	464	0	ENST00000266497.5:c.3496C>T	p.Pro1166Ser	p.P1166S	ENST00000266497		1166	Cct/Tct	25/31	0.197093953232073	1	FACETS	0.734	0.525	0.986	0.734	0.525	0.986	CLONAL	1	TRUE	0	0.197093953232073	1		464	162	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222872	36222872	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064276-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	29	693	0	ENST00000222270.7:c.5501G>T	p.Arg1834Leu	p.R1834L	ENST00000222270	NM_014727.1	1834	cGc/cTc	27/37	1	2	FACETS	0.881	0.708	1	0.881	0.708	1	CLONAL	1	TRUE	1	0.197093953232073	2		693	334	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100319	27100319	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064276-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	18	763	0	ENST00000324856.7:c.4032del	p.Thr1345ProfsTer136	p.T1345Pfs*136	ENST00000324856	NM_006015.4	1344	tCc/tc	17/20	1	2	FACETS	0.595	0.448	0.769	0.595	0.448	0.769	SUBCLONAL	1	TRUE	1	0.197093953232073	2		763	307	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610120	43610120	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064276-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	43	791	0	ENST00000355710.3:c.2072G>T	p.Gly691Val	p.G691V	ENST00000355710	NM_020975.4	691	gGt/gTt	11/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.197093953232073	2		791	333	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243817	46243817	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0064276-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	13	388	0	ENST00000334344.6:c.1913-2A>T		p.X638_splice	ENST00000334344	NM_152641.2	638			0.197093953232073	1	FACETS	0.837	0.601	1	0.837	0.601	1	CLONAL	1	TRUE	0	0.197093953232073	1		388	142	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869457	102869457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064276-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	30	463	0	ENST00000307046.8:c.184C>T	p.Leu62Phe	p.L62F	ENST00000307046	NM_001111285.1	62	Ctt/Ttt	2/4	0.195478102496751	2	FACETS	1	0.858	1	0.538	0.435	0.654	CLONAL	1	TRUE	0	0.197093953232073	2		463	283	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817799	3817799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064276-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	18	508	0	ENST00000262367.5:c.3172G>A	p.Glu1058Lys	p.E1058K	ENST00000262367	NM_004380.2	1058	Gaa/Aaa	16/31	1	2	FACETS	0.664	0.5	0.858	0.664	0.5	0.858	SUBCLONAL	1	TRUE	1	0.197093953232073	2		508	275	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89806508	89806508	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0064276-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	32	483	0	ENST00000389301.3:c.3829-1G>A		p.X1277_splice	ENST00000389301	NM_000135.2	1277			0.161647056433916	2	FACETS	1	0.894	1	0.574	0.467	0.693	CLONAL	1	TRUE	0	0.197093953232073	2		483	283	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2202727	2202727	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064276-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	30	532	0	ENST00000398665.3:c.736G>T	p.Gly246Cys	p.G246C	ENST00000398665	NM_032482.2	246	Ggt/Tgt	9/28	1	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	TRUE	1	0.197093953232073	2		532	291	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229612	5229612	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064276-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	25	568	0	ENST00000357368.4:c.2239G>T	p.Gly747Cys	p.G747C	ENST00000357368	NM_002850.3	747	Ggc/Tgc	15/38	1	2	FACETS	1	0.838	1	1	0.838	1	CLONAL	1	TRUE	1	0.197093953232073	2		568	237	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015109	27015109	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0064276-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	14	308	0	ENST00000335756.4:c.210+1G>T		p.X70_splice	ENST00000335756	NM_001809.3	70			1	2	FACETS	0.555	0.401	0.742	0.555	0.401	0.742	SUBCLONAL	1	TRUE	1	0.197093953232073	2		308	256	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570117	212570117	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0064276-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	11	338	0	ENST00000342788.4:c.1125-1G>T		p.X375_splice	ENST00000342788	NM_005235.2	375			1	2	FACETS	0.792	0.549	1	0.792	0.549	1	CLONAL	1	TRUE	1	0.197093953232073	2		338	141	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446322	29446322	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064276-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	38	552	0	ENST00000544604.2:c.2153C>G	p.Pro718Arg	p.P718R	ENST00000544604	NM_001206998.1	718	cCc/cGc	8/9	0.197093953232073	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.197093953232073	1		552	260	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231656	66231656	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064276-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	14	382	0	ENST00000273854.3:c.2044G>T	p.Gly682Ter	p.G682*	ENST00000273854	NM_004439.5	682	Gga/Tga	11/18	1	2	FACETS	0.872	0.633	1	0.872	0.633	1	CLONAL	1	TRUE	1	0.197093953232073	2		382	163	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0064277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	1031	382	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.503791188105611	15	FACETS	0.992	0.973	1	0.992	0.973	1	CLONAL	13	TRUE	2	0.503791188105611	15		382	1357	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0064277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	219	643	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.478697034045623	2	FACETS	0.975	0.919	1	0.975	0.919	1	CLONAL	2	TRUE	0	0.503791188105611	2		643	446	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220382	1220382	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	72	612	0	ENST00000326873.7:c.475C>T	p.Gln159Ter	p.Q159*	ENST00000326873	NM_000455.4	159	Cag/Tag	4/10	0.133798019886441	5	FACETS	0.798	0.697	0.906			1	INDETERMINATE	1	TRUE	NA	0.503791188105611	5		612	629	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939154	76939154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	43	546	0	ENST00000373344.5:c.1594C>T	p.Leu532Phe	p.L532F	ENST00000373344	NM_000489.3	532	Ctt/Ttt	9/35	NA	2	FACETS	0.423	0.354	0.498			1	INDETERMINATE	1	TRUE	NA	0.503791188105611	2		546	404	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162722953	162722953	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	191	498	0	ENST00000367921.3:c.151C>G	p.Gln51Glu	p.Q51E	ENST00000367921	NM_006182.2	51	Cag/Gag	4/18	0.449201097481784	4	FACETS	0.878	0.816	0.943	0.878	0.816	0.943	CLONAL	2	TRUE	2	0.503791188105611	4		498	649	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0064278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	111	294	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.352100486692935	2		294	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519986	NA	P-0064278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	104	538	0	ENST00000269305.4:c.809T>C	p.Phe270Ser	p.F270S	ENST00000269305	NM_001126112.2	270	tTt/tCt	8/11	0.352100486692935	1	FACETS	0.979	0.881	1	0.979	0.881	1	CLONAL	1	TRUE	0	0.352100486692935	1		538	497	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136840	55136840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1227372630	NA	P-0064278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	38	144	0	ENST00000257290.5:c.1162G>A	p.Asp388Asn	p.D388N	ENST00000257290	NM_006206.4	388	Gac/Aac	8/23	1	2	FACETS	0.685	0.568	0.815	0.685	0.568	0.815	SUBCLONAL	1	TRUE	1	0.352100486692935	2		144	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0064279-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	44	570	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	1	2	FACETS	0.79	0.663	0.929	0.79	0.663	0.929	CLONAL	1	TRUE	1	0.28	2		570	398	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350469	15350469	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0064279-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	35	901	2	ENST00000263377.2:c.3445+1G>A		p.X1149_splice	ENST00000263377	NM_058243.2	1149			1	2	FACETS	0.704	0.578	0.845	0.704	0.578	0.845	SUBCLONAL	1	TRUE	1	0.28	2		903	355	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057619	27057640	+	splice_region_variant,intron_variant	Splice_Region	DEL	AAAGTATATTTTCCTTTCCTAC	AAAGTATATTTTCCTTTCCTAC	-	novel	NA	P-0064279-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	27	391	0	ENST00000324856.7:c.1351-23_1351-2del		p.X451_splice	ENST00000324856	NM_006015.4	451			1	2	FACETS	0.492	0.391	0.607	0.492	0.391	0.607	SUBCLONAL	1	TRUE	1	0.28	2		391	392	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528107	29528108	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0064279-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	33	145	0	ENST00000356175.3:c.1116dup	p.Val373CysfsTer6	p.V373Cfs*6	ENST00000356175	NM_000267.3	372	gat/gaTt	10/57	0.209948258661837	3	FACETS	0.902	0.737	1	0.451	0.368	0.543	CLONAL	1	TRUE	1	0.28	3		145	298	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588859	29588872	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGAATTTATGAC	GAGGAATTTATGAC	-	novel	NA	P-0064279-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	30	288	0	ENST00000356175.3:c.4645_4658del	p.Glu1549Ter	p.E1549*	ENST00000356175	NM_000267.3	1549	GAGGAATTTATGACt/t	34/57	0.209948258661837	3	FACETS	0.597	0.481	0.729	0.299	0.24	0.365	SUBCLONAL	1	TRUE	1	0.28	3		288	409	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747937	41747938	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0064279-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	54	456	0	ENST00000226382.2:c.831dup	p.Gly278ArgfsTer82	p.G278Rfs*82	ENST00000226382	NM_003924.3	277	-/C	3/3	1	2	FACETS	0.945	0.81	1	0.945	0.81	1	CLONAL	1	TRUE	1	0.28	2		456	408	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665719	86665719	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0064279-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	27	75	0	ENST00000274376.6:c.1698+2T>A		p.X566_splice	ENST00000274376	NM_002890.2	566			1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.28	2		75	159	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748448	162748448	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064280-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	44	488	0	ENST00000367921.3:c.2364del	p.Tyr789IlefsTer39	p.Y789Ifs*39	ENST00000367921	NM_006182.2	788	Ccc/cc	17/18	1	2	FACETS	0.456	0.381	0.539	0.456	0.381	0.539	SUBCLONAL	1	TRUE	1	0.308369911148497	2		488	626	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249013	55249014	+	protein_altering_variant	In_Frame_Ins	INS	-	-	GGG	novel	NA	P-0064280-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	891	586	0	ENST00000275493.2:c.2311_2312insGGG	p.Asn771delinsArgAsp	p.N771delinsRD	ENST00000275493	NM_005228.3	771	aac/aGGGac	20/28	0.308369911148497	12	FACETS	1	0.985	1	0.922	0.899	0.945	CLONAL	10	TRUE	1	0.308369911148497	12		586	1448	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100006	157100035	+	inframe_deletion	In_Frame_Del	DEL	GGAGGAGGAGGAGGCAGCGGAGGAGGAGGA	GGAGGAGGAGGAGGCAGCGGAGGAGGAGGA	-	novel	NA	P-0064280-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	52	724	0	ENST00000346085.5:c.956_985del	p.Gly319_Gly328del	p.G319_G328del	ENST00000346085	NM_020732.3	315	GGAGGAGGAGGAGGCAGCGGAGGAGGAGGA/-	1/20	1	2	FACETS	0.444	0.377	0.518	0.444	0.377	0.518	SUBCLONAL	1	TRUE	1	0.308369911148497	2		724	759	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	46	612	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.93	0.791	1	0.93	0.791	1	CLONAL	1	TRUE	1	0.44353481338073	2		612	223	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246482	105246482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	95	530	0	ENST00000349310.3:c.118G>A	p.Glu40Lys	p.E40K	ENST00000349310	NM_001014432.1	40	Gag/Aag	4/15	0.44353481338073	1	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	0	0.44353481338073	1		530	332	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176493	123176493	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	66	83	0	ENST00000218089.9:c.460G>T	p.Glu154Ter	p.E154*	ENST00000218089	NM_001042749.1	154	Gag/Tag	7/35	1	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.44353481338073	1		83	164	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	61	542	7	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.835	0.726	0.952	0.835	0.726	0.952	CLONAL	1	TRUE	1	0.491808063149859	2		549	297	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	143	753	4	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.825	0.753	0.899	0.825	0.753	0.899	CLONAL	1	TRUE	1	0.491808063149859	2		757	705	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836816	151836816	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	126	609	0	ENST00000262189.6:c.14404G>A	p.Gly4802Arg	p.G4802R	ENST00000262189	NM_170606.2	4802	Ggg/Agg	56/59	1	2	FACETS	0.942	0.857	1	0.942	0.857	1	CLONAL	1	TRUE	1	0.491808063149859	2		609	544	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101267	27101268	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	207	834	0	ENST00000324856.7:c.4555dup	p.Gln1519ProfsTer13	p.Q1519Pfs*13	ENST00000324856	NM_006015.4	1517	gcc/gCcc	18/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.491808063149859	2		834	802	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	216	868	10	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.918	0.854	0.984	0.918	0.854	0.984	CLONAL	1	TRUE	1	0.491808063149859	2		878	957	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743932	41743933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs778012871	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	173	895	3	ENST00000301178.4:c.874dup	p.His292ProfsTer47	p.H292Pfs*47	ENST00000301178	NM_021913.4	289	-/C	7/20	1	2	FACETS	0.866	0.798	0.937	0.866	0.798	0.937	CLONAL	1	TRUE	1	0.491808063149859	2		898	812	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	167	915	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.823	0.757	0.892	0.823	0.757	0.892	CLONAL	1	TRUE	1	0.491808063149859	2		916	825	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244184	153244184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759610249	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	166	779	0	ENST00000281708.4:c.1973G>A	p.Arg658Gln	p.R658Q	ENST00000281708	NM_033632.3	658	cGa/cAa	12/12	1	2	FACETS	0.976	0.899	1	0.976	0.899	1	CLONAL	1	TRUE	1	0.491808063149859	2		779	692	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	164	892	1	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	1	2	FACETS	0.796	0.731	0.863	0.796	0.731	0.863	SUBCLONAL	1	TRUE	1	0.491808063149859	2		893	838	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088788	27088788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	168	731	2	ENST00000324856.7:c.2402del	p.Gly801ValfsTer32	p.G801Vfs*32	ENST00000324856	NM_006015.4	799	caG/ca	7/20	1	2	FACETS	0.994	0.917	1	0.994	0.917	1	CLONAL	1	TRUE	1	0.491808063149859	2		733	687	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	417	1026	4	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.996	0.955	1	1	0.997	1	CLONAL	2	TRUE	1	0.491808063149859	2		1030	851	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	136	733	2	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.936	0.854	1	0.936	0.854	1	CLONAL	1	TRUE	1	0.491808063149859	2		735	591	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882049	36882050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs780753361	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	129	825	1	ENST00000358127.4:c.963dup	p.Ala322ArgfsTer19	p.A322Rfs*19	ENST00000358127	NM_001280556.1	321	-/C	8/10	1	2	FACETS	0.789	0.717	0.864	0.789	0.717	0.864	SUBCLONAL	1	TRUE	1	0.491808063149859	2		826	665	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210728	2210728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745700742	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	55	954	0	ENST00000398665.3:c.1225C>T	p.Arg409Cys	p.R409C	ENST00000398665	NM_032482.2	409	Cgc/Tgc	14/28	1	2	FACETS	0.286	0.244	0.333	0.286	0.244	0.333	SUBCLONAL	1	TRUE	1	0.491808063149859	2		954	781	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419957	41419957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369230837	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	171	799	0	ENST00000373198.4:c.364G>A	p.Val122Ile	p.V122I	ENST00000373198	NM_133170.3	122	Gtc/Atc	3/32	1	2	FACETS	0.966	0.891	1	0.966	0.891	1	CLONAL	1	TRUE	1	0.491808063149859	2		799	720	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396792	396792	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	194	908	1	ENST00000262320.3:c.234del	p.Thr79ProfsTer5	p.T79Pfs*5	ENST00000262320	NM_003502.3	78	ccC/cc	2/11	1	2	FACETS	0.952	0.882	1	0.952	0.882	1	CLONAL	1	TRUE	1	0.491808063149859	2		909	829	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257102	19257102	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	113	648	0	ENST00000162023.5:c.861del	p.Ala288ProfsTer?	p.A288Pfs*?	ENST00000162023		287	ccC/cc	12/13	1	2	FACETS	0.857	0.775	0.944	0.857	0.775	0.944	CLONAL	1	TRUE	1	0.491808063149859	2		648	536	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275254	41275254	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1553631860	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	169	775	0	ENST00000349496.5:c.1420C>T	p.Arg474Ter	p.R474*	ENST00000349496	NM_001904.3	474	Cga/Tga	9/15	1	2	FACETS	0.996	0.919	1	0.996	0.919	1	CLONAL	1	TRUE	1	0.491808063149859	2		775	690	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922363	178922363	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	10	278	0	ENST00000263967.3:c.1132T>C	p.Cys378Arg	p.C378R	ENST00000263967	NM_006218.2	378	Tgt/Cgt	6/21	1	2	FACETS	0.2	0.135	0.282	0.2	0.135	0.282	SUBCLONAL	1	TRUE	1	0.491808063149859	2		278	203	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992721	68992721	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs764112302	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	60	628	1	ENST00000288368.4:c.1693del	p.Ser565ArgfsTer10	p.S565Rfs*10	ENST00000288368	NM_024870.2	562	cgT/cg	16/40	1	2	FACETS	0.924	0.804	1	0.924	0.804	1	CLONAL	1	TRUE	1	0.491808063149859	2		629	264	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261246	16261246	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1466090335	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	170	875	1	ENST00000375759.3:c.8516del	p.Pro2839ArgfsTer50	p.P2839Rfs*50	ENST00000375759	NM_015001.2	2837	atC/at	11/15	1	2	FACETS	0.917	0.845	0.992	0.917	0.845	0.992	CLONAL	1	TRUE	1	0.491808063149859	2		876	754	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910615	29910615	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	192	1166	0	ENST00000376809.5:c.155T>C	p.Val52Ala	p.V52A	ENST00000376809	NM_002116.7	52	gTg/gCg	2/8	1	2	FACETS	0.733	0.677	0.791	0.733	0.677	0.791	SUBCLONAL	1	TRUE	1	0.491808063149859	2		1166	1065	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012386	152012386	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	87	578	0	ENST00000262189.6:c.427del	p.Ser143ValfsTer3	p.S143Vfs*3	ENST00000262189	NM_170606.2	143	Agt/gt	4/59	1	2	FACETS	0.964	0.86	1	0.964	0.86	1	CLONAL	1	TRUE	1	0.491808063149859	2		578	367	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777751	3777751	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	198	765	0	ENST00000262367.5:c.7297del	p.Asp2433ThrfsTer3	p.D2433Tfs*3	ENST00000262367	NM_004380.2	2433	Gac/ac	31/31	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.491808063149859	2		765	744	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564667	86564667	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	176	1024	0	ENST00000274376.6:c.402del	p.Pro136LeufsTer38	p.P136Lfs*38	ENST00000274376	NM_002890.2	133	ggT/gg	1/25	1	2	FACETS	0.85	0.784	0.919	0.85	0.784	0.919	CLONAL	1	TRUE	1	0.491808063149859	2		1024	842	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777114	9777114	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs754116182	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	188	934	4	ENST00000377346.4:c.883del	p.Gln295ArgfsTer39	p.Q295Rfs*39	ENST00000377346	NM_005026.3	293	gCc/gc	7/24	1	2	FACETS	0.944	0.874	1	0.944	0.874	1	CLONAL	1	TRUE	1	0.491808063149859	2		938	810	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1978301	1978301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774737951	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	194	864	0	ENST00000382891.5:c.3721G>A	p.Glu1241Lys	p.E1241K	ENST00000382891	NM_133335.3	1241	Gag/Aag	21/22	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.491808063149859	2		864	746	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37672049	37672049	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	38	496	0	ENST00000447079.4:c.2834T>C	p.Leu945Pro	p.L945P	ENST00000447079	NM_015083.1	945	cTa/cCa	9/14	1	2	FACETS	0.339	0.28	0.405	0.339	0.28	0.405	SUBCLONAL	1	TRUE	1	0.491808063149859	2		496	456	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437222	220437223	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1286117855	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	62	880	0	ENST00000243786.2:c.132dup	p.Ala45ArgfsTer29	p.A45Rfs*29	ENST00000243786	NM_002191.3	42	-/C	1/2	1	2	FACETS	0.336	0.29	0.387	0.336	0.29	0.387	SUBCLONAL	1	TRUE	1	0.491808063149859	2		880	750	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842705	68842705	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	159	681	1	ENST00000261769.5:c.641T>C	p.Leu214Pro	p.L214P	ENST00000261769	NM_004360.3	214	cTg/cCg	5/16	0.491808063149859	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.491808063149859	1		682	480	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598805	28598805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763209004	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	176	772	1	ENST00000253063.3:c.365G>A	p.Arg122His	p.R122H	ENST00000253063	NM_031459.4	122	cGc/cAc	4/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.491808063149859	2		773	675	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678391	88678391	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	155	748	2	ENST00000360948.2:c.1145del	p.Asn382ThrfsTer32	p.N382Tfs*32	ENST00000360948	NM_001012338.2	382	aAc/ac	9/19	1	2	FACETS	0.961	0.882	1	0.961	0.882	1	CLONAL	1	TRUE	1	0.491808063149859	2		750	656	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214734	36214734	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	158	736	0	ENST00000222270.7:c.3163del	p.Arg1055GlyfsTer127	p.R1055Gfs*127	ENST00000222270	NM_014727.1	1054	Ccc/cc	8/37	1	2	FACETS	0.978	0.899	1	0.978	0.899	1	CLONAL	1	TRUE	1	0.491808063149859	2		736	657	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518577	69518577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	158	715	0	ENST00000294312.3:c.68G>A	p.Arg23His	p.R23H	ENST00000294312	NM_005117.2	23	cGc/cAc	1/3	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.491808063149859	2		715	639	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	246	402	3	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.828	0.78	0.877	1	0.994	1	CLONAL	2	TRUE	1	0.491808063149859	2		405	604	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965863	90965863	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200891292	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	20	440	0	ENST00000265433.3:c.1454C>T	p.Thr485Met	p.T485M	ENST00000265433	NM_002485.4	485	aCg/aTg	11/16	1	2	FACETS	0.253	0.193	0.323	0.253	0.193	0.323	SUBCLONAL	1	TRUE	1	0.491808063149859	2		440	322	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88679160	88679160	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	36	162	0	ENST00000372037.3:c.1100A>G	p.Asn367Ser	p.N367S	ENST00000372037	NM_004329.2	367	aAc/aGc	10/13	1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	1	0.491808063149859	2		162	144	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10789525	10789525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372968145	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	167	785	0	ENST00000361367.2:c.1859G>A	p.Arg620Gln	p.R620Q	ENST00000361367	NM_014633.3	620	cGa/cAa	14/25	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.491808063149859	2		785	668	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022382	12022382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	202	948	1	ENST00000396373.4:c.488G>A	p.Arg163Lys	p.R163K	ENST00000396373	NM_001987.4	163	aGg/aAg	5/8	1	2	FACETS	0.97	0.9	1	0.97	0.9	1	CLONAL	1	TRUE	1	0.491808063149859	2		949	847	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115386	115115386	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	85	475	0	ENST00000257566.3:c.940A>G	p.Arg314Gly	p.R314G	ENST00000257566	NM_016569.3	314	Aga/Gga	5/8	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.491808063149859	2		475	330	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21553915	21553915	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	93	476	0	ENST00000382592.4:c.2687G>T	p.Trp896Leu	p.W896L	ENST00000382592	NM_014572.2	896	tGg/tTg	7/8	1	2	FACETS	0.914	0.817	1	0.914	0.817	1	CLONAL	1	TRUE	1	0.491808063149859	2		476	414	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436422	110436422	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	213	1032	0	ENST00000375856.3:c.1979C>A	p.Ala660Glu	p.A660E	ENST00000375856	NM_003749.2	660	gCg/gAg	1/2	1	2	FACETS	0.961	0.894	1	0.961	0.894	1	CLONAL	1	TRUE	1	0.491808063149859	2		1032	901	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609323	81609323	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	128	618	0	ENST00000298171.2:c.921G>T	p.Gln307His	p.Q307H	ENST00000298171	NM_000369.2	307	caG/caT	10/10	0.491808063149859	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.491808063149859	1		618	383	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220011	5220011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759472181	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	173	796	0	ENST00000357368.4:c.3704G>A	p.Gly1235Asp	p.G1235D	ENST00000357368	NM_002850.3	1235	gGc/gAc	22/38	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.491808063149859	2		796	667	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319690	62319692	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs779176651	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	175	778	0	ENST00000360203.5:c.1678_1680del	p.Phe560del	p.F560del	ENST00000360203	NM_001283009.1	558	aTCTtc/atc	20/35	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.491808063149859	2		778	706	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21350077	21350077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200248773	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	184	859	2	ENST00000215739.8:c.1985C>T	p.Ala662Val	p.A662V	ENST00000215739	NM_006767.3	662	gCg/gTg	17/21	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.491808063149859	2		861	719	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630372	187630372	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1289428034	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	57	802	0	ENST00000441802.2:c.610A>G	p.Ile204Val	p.I204V	ENST00000441802	NM_005245.3	204	Ata/Gta	2/27	0.491808063149859	1	FACETS	0.321	0.275	0.371	0.321	0.275	0.371	SUBCLONAL	1	TRUE	0	0.491808063149859	1		802	545	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564426	86564426	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	173	903	0	ENST00000274376.6:c.158T>C	p.Val53Ala	p.V53A	ENST00000274376	NM_002890.2	53	gTg/gCg	1/25	1	2	FACETS	0.955	0.881	1	0.955	0.881	1	CLONAL	1	TRUE	1	0.491808063149859	2		903	737	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682703	86682703	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	64	386	0	ENST00000274376.6:c.2912del	p.Leu971Ter	p.L971*	ENST00000274376	NM_002890.2	970	Ttt/tt	23/25	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.491808063149859	2		386	206	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271324	26271324	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	222	1094	0	ENST00000305910.3:c.289T>G	p.Cys97Gly	p.C97G	ENST00000305910	NM_003534.2	97	Tgc/Ggc	1/1	1	2	FACETS	0.871	0.811	0.934	0.871	0.811	0.934	CLONAL	1	TRUE	1	0.491808063149859	2		1094	1036	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821138	32821138	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	238	895	3	ENST00000354258.4:c.456G>A	p.Trp152Ter	p.W152*	ENST00000354258	NM_000593.5	152	tgG/tgA	1/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.491808063149859	2		898	890	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852003	128852004	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1258200617	NA	P-0064283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	138	784	0	ENST00000249373.3:c.2081dup	p.Ala695CysfsTer122	p.A695Cfs*122	ENST00000249373	NM_005631.4	692	cac/caCc	12/12	1	2	FACETS	0.844	0.77	0.921	0.844	0.77	0.921	CLONAL	1	TRUE	1	0.491808063149859	2		784	665	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0064284-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	798	377	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.443023345514228	9	FACETS	1	0.98	1	1	0.98	1	CLONAL	7	TRUE	2	0.443023345514228	9		377	1302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0064284-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	220	687	0	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.370109049622174	2	FACETS	1	0.992	1	0.731	0.684	0.78	CLONAL	1	TRUE	0	0.443023345514228	2		687	679	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230561589	230561589	+	upstream_gene_variant	5'Flank	SNP	G	G	C	novel	NA	P-0064284-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	58	714	0				ENST00000391860	NM_001258311.1	-/409			0.258353637324932	3	FACETS	0.368	0.315	0.426	0.123	0.105	0.142	INDETERMINATE	1	TRUE	0	0.443023345514228	3		714	869	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101985106	101985106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064284-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	45	410	0	ENST00000282441.5:c.553G>A	p.Gly185Ser	p.G185S	ENST00000282441	NM_001130145.2	185	Ggt/Agt	2/9	0.370109049622174	2	FACETS	0.465	0.391	0.546	0.232	0.195	0.273	SUBCLONAL	1	TRUE	0	0.443023345514228	2		410	437	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196855	108196855	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064284-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	167	446	0	ENST00000278616.4:c.6878T>C	p.Leu2293Pro	p.L2293P	ENST00000278616	NM_000051.3	2293	cTg/cCg	47/63	0.370109049622174	2	FACETS	0.855	0.794	0.917	0.855	0.794	0.917	CLONAL	2	TRUE	0	0.443023345514228	2		446	441	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266713	198266713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776846119	NA	P-0064284-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	29	378	0	ENST00000335508.6:c.2219G>A	p.Gly740Glu	p.G740E	ENST00000335508	NM_012433.2	740	gGa/gAa	15/25	1	2	FACETS	0.377	0.303	0.462	0.377	0.303	0.462	SUBCLONAL	1	TRUE	1	0.443023345514228	2		378	347	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21351063	21351063	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064284-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	51	592	0	ENST00000215739.8:c.2298G>C	p.Met766Ile	p.M766I	ENST00000215739	NM_006767.3	766	atG/atC	19/21	0.189555974730047	2	FACETS	0.315	0.267	0.368	0.157	0.133	0.184	INDETERMINATE	1	TRUE	0	0.443023345514228	2		592	731	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31504699	31504699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1032572786	NA	P-0064284-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	36	419	0	ENST00000344624.3:c.1631G>A	p.Arg544His	p.R544H	ENST00000344624		544	cGc/cAc	8/33	0.38765449963281	4	FACETS	0.359	0.294	0.432	0.18	0.147	0.216	SUBCLONAL	1	TRUE	2	0.443023345514228	4		419	653	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411901	116411901	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0064284-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	39	578	0	ENST00000397752.3:c.2888-2A>G		p.X963_splice	ENST00000397752	NM_000245.2	963			0.235880258857565	5	FACETS	0.356	0.294	0.426	0.119	0.098	0.142	INDETERMINATE	1	TRUE	2	0.443023345514228	5		578	823	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441304	52441304	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	174	960	0	ENST00000460680.1:c.466C>T	p.Gln156Ter	p.Q156*	ENST00000460680	NM_004656.3	156	Cag/Tag	7/17	0.424235268287552	2	FACETS	0.814	0.755	0.874	0.814	0.755	0.874	CLONAL	2	TRUE	0	0.424235268287552	2		960	504	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499733	18499733	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	128	768	0	ENST00000266497.5:c.1588T>G	p.Tyr530Asp	p.Y530D	ENST00000266497		530	Tat/Gat	10/31	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.424235268287552	2		768	582	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578393	7578393	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876660821	NA	P-0064292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	11	988	0	ENST00000269305.4:c.537T>A	p.His179Gln	p.H179Q	ENST00000269305	NM_001126112.2	179	caT/caA	5/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		988	443	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938099	76938100	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0064293-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	81	338	0	ENST00000373344.5:c.2648_2649del	p.Gln883ArgfsTer13	p.Q883Rfs*13	ENST00000373344	NM_000489.3	883	cAA/c	9/35	0.723301132888117	2	FACETS	1	0.968	1			1	CLONAL	1	TRUE	NA	0.723301132888117	2		338	188	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866440	42866440	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064293-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	66	943	0	ENST00000398585.3:c.192del	p.Ala65HisfsTer30	p.A65Hfs*30	ENST00000398585	NM_001135099.1	64	ccC/cc	3/14	0.22964594532084	2	FACETS	0.702	0.616	0.793	0.351	0.308	0.397	INDETERMINATE	1	TRUE	0	0.723301132888117	2		943	260	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247271	153247271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064293-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	73	731	0	ENST00000281708.4:c.1531G>A	p.Gly511Ser	p.G511S	ENST00000281708	NM_033632.3	511	Ggc/Agc	10/12	0.588726003350178	3	FACETS	0.895	0.79	1	0.448	0.395	0.503	CLONAL	1	TRUE	1	0.723301132888117	3		731	307	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0064295-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	134	651	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.365025937449757	2		651	711	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064295-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	285	770	1	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	0.361957476134875	2	FACETS	0.936	0.883	0.99	0.936	0.883	0.99	CLONAL	2	TRUE	0	0.365025937449757	2		771	834	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702612	52702614	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0064295-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	81	434	0	ENST00000394830.3:c.284_286del	p.Met95del	p.M95del	ENST00000394830	NM_018313.4	95	aTGAaa/aaa	4/30	0.365025937449757	1	FACETS	0.916	0.812	1	0.916	0.812	1	CLONAL	1	TRUE	0	0.365025937449757	1		434	396	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100155	27100161	+	frameshift_variant	Frame_Shift_Del	DEL	GATGTAT	GATGTAT	-	novel	NA	P-0064295-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	183	1017	0	ENST00000324856.7:c.3951_3957del	p.Met1318LeufsTer161	p.M1318Lfs*161	ENST00000324856	NM_006015.4	1317	ggGATGTAT/gg	16/20	0.365025937449757	1	FACETS	0.997	0.922	1	0.997	0.922	1	CLONAL	1	TRUE	0	0.365025937449757	1		1017	822	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127253	22127253	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064295-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	109	670	0	ENST00000215832.6:c.875A>C	p.Lys292Thr	p.K292T	ENST00000215832	NM_002745.4	292	aAa/aCa	7/9	1	2	FACETS	0.959	0.863	1	0.959	0.863	1	CLONAL	1	TRUE	1	0.365025937449757	2		670	623	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061517	38061519	+	inframe_deletion	In_Frame_Del	DEL	CGC	CGC	-	novel	NA	P-0064296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	8	910	1	ENST00000250448.2:c.470_472del	p.Gly157del	p.G157del	ENST00000250448	NM_004496.3	157	gGCGac/gac	2/2	0.492937254975604	2	FACETS	0.085	0.054	0.125	0.042	0.027	0.063	SUBCLONAL	1	TRUE	0	0.493068039507767	2		911	383	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670810	134670816	+	protein_altering_variant	In_Frame_Del	DEL	AACGGGG	AACGGGG	T	novel	NA	P-0064296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	244	863	0	ENST00000398015.3:c.721_727delinsT	p.Asn241_Asp243delinsTyr	p.N241_D243delinsY	ENST00000398015	NM_004441.4	241	AACGGGGat/Tat	3/16	0.492937254975604	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.493068039507767	3		863	565	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446849	49446849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1204392134	NA	P-0064297-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	219	870	0	ENST00000301067.7:c.961C>T	p.Arg321Trp	p.R321W	ENST00000301067	NM_003482.3	321	Cgg/Tgg	8/54	0.281908296599954	6	FACETS	1	0.988	1	0.828	0.773	0.884	INDETERMINATE	2	TRUE	3	0.474848593087426	6		870	724	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923756	72923756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771775824	NA	P-0064297-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	211	746	0	ENST00000268489.5:c.3322C>T	p.Arg1108Cys	p.R1108C	ENST00000268489	NM_006885.3	1108	Cgc/Tgc	4/10	0.319230838984302	5	FACETS	0.893	0.836	0.951	0.893	0.836	0.951	CLONAL	3	TRUE	2	0.474848593087426	5		746	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579483	7579492	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTGGCATT	CTCTGGCATT	-	novel	NA	P-0064297-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	444	879	0	ENST00000269305.4:c.195_204del	p.Met66LeufsTer54	p.M66Lfs*54	ENST00000269305	NM_001126112.2	65	agAATGCCAGAG/ag	4/11	0.474848593087426	3	FACETS	1	0.993	1			1	CLONAL	3	TRUE	NA	0.474848593087426	3		879	700	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121262	29121262	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064297-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	64	608	0	ENST00000328354.6:c.413C>A	p.Thr138Lys	p.T138K	ENST00000328354	NM_007194.3	138	aCa/aAa	3/15	0.216483762188109	5	FACETS	1	0.946	1	0.758	0.667	0.853	INDETERMINATE	2	TRUE	2	0.474848593087426	5		608	203	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962545	100962545	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064297-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	106	466	0	ENST00000325455.5:c.1852A>T	p.Asn618Tyr	p.N618Y	ENST00000325455	NM_001202474.3	618	Aac/Tac	3/8	0.474848593087426	5	FACETS	0.82	0.739	0.905	0.547	0.493	0.604	CLONAL	2	TRUE	2	0.474848593087426	5		466	466	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55962477	55962477	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064297-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	23	442	0	ENST00000263923.4:c.2647A>T	p.Met883Leu	p.M883L	ENST00000263923	NM_002253.2	883	Atg/Ttg	19/30	0.319230838984302	5	FACETS	0.528	0.412	0.663	0.176	0.137	0.221	SUBCLONAL	1	TRUE	2	0.474848593087426	5		442	314	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656888	45656888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566695508	NA	P-0064297-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	45	879	0	ENST00000407780.3:c.268G>A	p.Gly90Ser	p.G90S	ENST00000407780	NM_001283052.1	90	Ggc/Agc	3/7	0.659574246280593	1	FACETS	0.182	0.153	0.215	0.182	0.153	0.215	SUBCLONAL	1	TRUE	0	0.659574246280593	1		879	502	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446849	49446849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1204392134	NA	P-0064297-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	301	870	0	ENST00000301067.7:c.961C>T	p.Arg321Trp	p.R321W	ENST00000301067	NM_003482.3	321	Cgg/Tgg	8/54	0.292651513775487	4	FACETS	0.845	0.798	0.893			1	INDETERMINATE	2	TRUE	NA	0.659574246280593	4		870	896	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923756	72923756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771775824	NA	P-0064297-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	177	746	0	ENST00000268489.5:c.3322C>T	p.Arg1108Cys	p.R1108C	ENST00000268489	NM_006885.3	1108	Cgc/Tgc	4/10	NA	2	FACETS	0.893	0.827	0.961			1	INDETERMINATE	1	TRUE	NA	0.659574246280593	2		746	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579483	7579492	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTGGCATT	CTCTGGCATT	-	novel	NA	P-0064297-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	427	879	0	ENST00000269305.4:c.195_204del	p.Met66LeufsTer54	p.M66Lfs*54	ENST00000269305	NM_001126112.2	65	agAATGCCAGAG/ag	4/11	0.586659573739041	2	FACETS	0.962	0.928	0.995	0.962	0.928	0.995	CLONAL	2	TRUE	0	0.659574246280593	2		879	673	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121262	29121262	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064297-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	187	608	0	ENST00000328354.6:c.413C>A	p.Thr138Lys	p.T138K	ENST00000328354	NM_007194.3	138	aCa/aAa	3/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.659574246280593	2		608	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579335	7579336	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0064298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	360	810	0	ENST00000269305.4:c.350_351dup	p.Thr118GlyfsTer6	p.T118Gfs*6	ENST00000269305	NM_001126112.2	117	-/GG	4/11	0.570916328703432	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.570916328703432	2		810	612	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567317	226567317	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	208	540	0	ENST00000366794.5:c.1569G>T	p.Met523Ile	p.M523I	ENST00000366794	NM_001618.3	523	atG/atT	11/23	0.570933420945639	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.570916328703432	3		540	438	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78933999	78933999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763624128	NA	P-0064298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	314	736	0	ENST00000306801.3:c.3599G>A	p.Ser1200Asn	p.S1200N	ENST00000306801	NM_020761.2	1200	aGc/aAc	30/34	0.570933420945639	3	FACETS	0.99	0.941	1	0.99	0.941	1	CLONAL	2	TRUE	1	0.570916328703432	3		736	714	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467818	66467818	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	81	579	0	ENST00000273854.3:c.451T>A	p.Phe151Ile	p.F151I	ENST00000273854	NM_004439.5	151	Ttt/Att	3/18	0.56370965478309	2	FACETS	1	0.933	1	0.531	0.474	0.591	CLONAL	1	TRUE	0	0.570916328703432	2		579	267	SUCCESS
APC	324	MSKCC	GRCh37	5	112128182	112128182	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	130	319	0	ENST00000257430.4:c.685C>A	p.Leu229Ile	p.L229I	ENST00000257430	NM_000038.5	229	Ctt/Att	7/16	0.56370965478309	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.570916328703432	2		319	211	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397162	397162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	334	936	0	ENST00000380956.4:c.547C>T	p.Pro183Ser	p.P183S	ENST00000380956	NM_001195286.1	183	Ccg/Tcg	5/9	0.353718795787413	4	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	2	0.570916328703432	4		936	902	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs121913292	NA	P-0064299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	28	158	0	ENST00000371953.3:c.389del	p.Arg130GlnfsTer4	p.R130Qfs*4	ENST00000371953	NM_000314.4	130	cGa/ca	5/9	1	2	FACETS	0.936	0.748	1	0.936	0.748	1	CLONAL	1	TRUE	1	0.15	2		158	399	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0064299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	39	374	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.668	0.551	0.798	0.668	0.551	0.798	SUBCLONAL	1	TRUE	1	0.15	2		374	779	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0064299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	46	855	0	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	1	2	FACETS	0.947	0.796	1	0.947	0.796	1	CLONAL	1	TRUE	1	0.15	2		855	648	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717609	89717609	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs876661024	NA	P-0064299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	32	165	0	ENST00000371953.3:c.635-1G>A		p.X212_splice	ENST00000371953	NM_000314.4	212			1	2	FACETS	0.853	0.692	1	0.853	0.692	1	CLONAL	1	TRUE	1	0.15	2		165	500	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384651	31384651	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	32	723	0	ENST00000328111.2:c.1359del	p.Leu454SerfsTer136	p.L454Sfs*136	ENST00000328111	NM_006892.3	451	gaG/ga	13/23	1	2	FACETS	0.796	0.645	0.967	0.796	0.645	0.967	CLONAL	1	TRUE	1	0.15	2		723	536	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991757	72991758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760959844	NA	P-0064299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	43	1123	2	ENST00000268489.5:c.2287dup	p.Glu763GlyfsTer26	p.E763Gfs*26	ENST00000268489	NM_006885.3	763	gag/gGag	2/10	1	2	FACETS	0.779	0.65	0.923	0.779	0.65	0.923	CLONAL	1	TRUE	1	0.15	2		1125	736	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589223	67589225	+	inframe_deletion	In_Frame_Del	DEL	TAA	TAA	-	novel	NA	P-0064299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	16	133	0	ENST00000274335.5:c.1214_1216del	p.Ile405del	p.I405del	ENST00000274335		404	tTAAta/tta	9/15	0.140569116990015	3	FACETS	0.43	0.317	0.567	0.215	0.158	0.284	SUBCLONAL	1	TRUE	1	0.15	3		133	533	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164586	36164586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253570532	NA	P-0064299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	32	898	0	ENST00000300305.3:c.1289C>T	p.Pro430Leu	p.P430L	ENST00000300305		430	cCg/cTg	8/8	1	2	FACETS	0.847	0.686	1	0.847	0.686	1	CLONAL	1	TRUE	1	0.15	2		898	504	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968279	15968279	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	32	321	0	ENST00000268712.3:c.5006del	p.Gly1669GlufsTer93	p.G1669Efs*93	ENST00000268712	NM_006311.3	1669	gGa/ga	34/46	1	2	FACETS	0.731	0.592	0.888	0.731	0.592	0.888	SUBCLONAL	1	TRUE	1	0.15	2		321	584	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468296	50468296	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	43	794	0	ENST00000331340.3:c.1531C>T	p.Arg511Ter	p.R511*	ENST00000331340	NM_006060.4	511	Cga/Tga	8/8	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.15	2		794	530	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905289	50905289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750144413	NA	P-0064299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	44	1171	0	ENST00000440232.2:c.497G>A	p.Arg166Gln	p.R166Q	ENST00000440232	NM_002691.3	166	cGg/cAg	5/27	1	2	FACETS	0.901	0.754	1	0.901	0.754	1	CLONAL	1	TRUE	1	0.15	2		1171	651	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371818	118371818	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	38	546	0	ENST00000534358.1:c.6275A>G	p.His2092Arg	p.H2092R	ENST00000534358	NM_005933.3	2092	cAt/cGt	25/36	0.140569116990015	3	FACETS	0.922	0.761	1	0.461	0.38	0.551	CLONAL	1	TRUE	1	0.15	3		546	591	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99482496	99482496	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753856067	NA	P-0064299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	35	553	0	ENST00000268035.6:c.3364G>A	p.Gly1122Ser	p.G1122S	ENST00000268035	NM_000875.3	1122	Ggc/Agc	18/21	1	2	FACETS	0.796	0.651	0.96	0.796	0.651	0.96	CLONAL	1	TRUE	1	0.15	2		553	586	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813097	89813097	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0064299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	31	844	0	ENST00000389301.3:c.3409-1G>T		p.X1137_splice	ENST00000389301	NM_000135.2	1137			1	2	FACETS	0.812	0.656	0.99	0.812	0.656	0.99	CLONAL	1	TRUE	1	0.15	2		844	509	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222838	5222838	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1359440247	NA	P-0064299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	23	967	0	ENST00000357368.4:c.2965C>T	p.Pro989Ser	p.P989S	ENST00000357368	NM_002850.3	989	Ccg/Tcg	18/38	1	2	FACETS	0.667	0.519	0.839	0.667	0.519	0.839	SUBCLONAL	1	TRUE	1	0.15	2		967	460	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213530	36213530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	37	1049	0	ENST00000222270.7:c.2632G>A	p.Ala878Thr	p.A878T	ENST00000222270	NM_014727.1	878	Gcc/Acc	5/37	1	2	FACETS	0.811	0.668	0.973	0.811	0.668	0.973	CLONAL	1	TRUE	1	0.15	2		1049	608	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446306	187446306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	38	870	1	ENST00000232014.4:c.1382G>A	p.Ser461Asn	p.S461N	ENST00000232014	NM_001130845.1	461	aGc/aAc	6/10	1	2	FACETS	0.905	0.747	1	0.905	0.747	1	CLONAL	1	TRUE	1	0.15	2		871	560	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540025	187540025	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1310271235	NA	P-0064299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	39	366	0	ENST00000441802.2:c.7715A>G	p.Asp2572Gly	p.D2572G	ENST00000441802	NM_005245.3	2572	gAt/gGt	10/27	1	2	FACETS	0.788	0.651	0.941	0.788	0.651	0.941	CLONAL	1	TRUE	1	0.15	2		366	660	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589486	67589540	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGTTATTTGATTAAATACCTTATCCATTGAATTTATTTTAATCTTTCTAGGATC	TTGTTATTTGATTAAATACCTTATCCATTGAATTTATTTTAATCTTTCTAGGATC	-	novel	NA	P-0064299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	19	44	0	ENST00000274335.5:c.1300-51_1303del		p.X434_splice	ENST00000274335		434		10/15	0.140569116990015	3	FACETS	0.939	0.713	1	0.47	0.356	0.603	CLONAL	1	TRUE	1	0.15	3		44	290	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100443	157100443	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	11	413	0	ENST00000346085.5:c.1384del	p.Ala462ArgfsTer40	p.A462Rfs*40	ENST00000346085	NM_020732.3	460	gcG/gc	1/20	1	2	FACETS	0.784	0.542	1	0.784	0.542	1	CLONAL	1	TRUE	1	0.15	2		413	187	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946272	2946272	+	stop_lost	Nonstop_Mutation	SNP	T	T	C	novel	NA	P-0064299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	24	903	0	ENST00000396946.4:c.3465A>G	p.Ter1155TrpextTer16	p.*1155Wext*16	ENST00000396946	NM_032415.4	1155	tgA/tgG	25/25	1	2	FACETS	0.668	0.523	0.837	0.668	0.523	0.837	SUBCLONAL	1	TRUE	1	0.15	2		903	479	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402577	139402577	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	44	1067	0	ENST00000277541.6:c.3340C>A	p.Arg1114Ser	p.R1114S	ENST00000277541	NM_017617.3	1114	Cgc/Agc	21/34	1	2	FACETS	0.999	0.837	1	0.999	0.837	1	CLONAL	1	TRUE	1	0.15	2		1067	587	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76764041	76764041	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	56	388	0	ENST00000373344.5:c.7267C>T	p.Gln2423Ter	p.Q2423*	ENST00000373344	NM_000489.3	2423	Cag/Tag	35/35	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.15	2		388	617	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735466	40735466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182388300	NA	P-0064300-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	165	866	5	ENST00000373198.4:c.3407G>A	p.Arg1136His	p.R1136H	ENST00000373198	NM_133170.3	1136	cGt/cAt	25/32	0.503434657599193	3	FACETS	0.916	0.841	0.994	0.458	0.42	0.497	CLONAL	1	TRUE	1	0.503434657599193	3		871	896	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0064300-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	191	691	0	ENST00000269305.4:c.673-2A>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.503434657599193	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.503434657599193	1		691	536	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748850	41748850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138698106	NA	P-0064300-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	219	938	1	ENST00000301178.4:c.1375G>A	p.Val459Met	p.V459M	ENST00000301178	NM_021913.4	459	Gtg/Atg	11/20	0.294019901097418	1	FACETS	0.843	0.787	0.901	0.843	0.787	0.901	INDETERMINATE	1	TRUE	0	0.503434657599193	1		939	772	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794439	42794439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370252719	NA	P-0064300-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	244	1074	2	ENST00000575354.2:c.1519C>T	p.Arg507Cys	p.R507C	ENST00000575354	NM_015125.3	507	Cgc/Tgc	10/20	0.294019901097418	1	FACETS	0.794	0.743	0.847	0.794	0.743	0.847	INDETERMINATE	1	TRUE	0	0.503434657599193	1		1076	913	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21347150	21347150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375451574	NA	P-0064300-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	261	941	5	ENST00000215739.8:c.1217C>T	p.Thr406Met	p.T406M	ENST00000215739	NM_006767.3	406	aCg/aTg	11/21	0.503434657599193	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.503434657599193	1		946	740	SUCCESS
APC	324	MSKCC	GRCh37	5	112175456	112175457	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0064300-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	121	321	1	ENST00000257430.4:c.4166_4167del	p.Ser1389CysfsTer5	p.S1389Cfs*5	ENST00000257430	NM_000038.5	1389	TCt/t	16/16	NA	2	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.503434657599193	2		322	406	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738165	133738165	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064300-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	142	599	2	ENST00000318560.5:c.565G>T	p.Glu189Ter	p.E189*	ENST00000318560	NM_005157.4	189	Gag/Tag	4/11	0.503434657599193	1	FACETS	0.989	0.909	1	0.989	0.909	1	CLONAL	1	TRUE	0	0.503434657599193	1		601	427	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760019	133760019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753588128	NA	P-0064300-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	218	760	3	ENST00000318560.5:c.2342C>T	p.Thr781Met	p.T781M	ENST00000318560	NM_005157.4	781	aCg/aTg	11/11	0.503434657599193	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.503434657599193	1		763	600	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0064301-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	393	1053	2	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.416497806611127	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.441799246242762	2		1055	858	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692920	89692920	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs370795352	NA	P-0064301-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	199	605	0	ENST00000371953.3:c.404T>A	p.Ile135Lys	p.I135K	ENST00000371953	NM_000314.4	135	aTa/aAa	5/9	0.416497806611127	2	FACETS	0.908	0.849	0.968	0.908	0.849	0.968	CLONAL	2	TRUE	0	0.441799246242762	2		605	496	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0064302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	312	836	6	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	1	2	FACETS	0.918	0.868	0.97	0.918	0.868	0.97	CLONAL	1	TRUE	1	0.709920597885787	2		842	957	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0064302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	178	542	7	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.869	0.806	0.934	0.869	0.806	0.934	CLONAL	1	TRUE	1	0.709920597885787	2		549	577	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0064302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	366	646	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.709920597885787	2		646	783	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0064302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	373	707	1	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.709920597885787	2		708	911	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175857	24175859	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs875989800	NA	P-0064302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	328	613	1	ENST00000263121.7:c.1091_1093del	p.Lys364del	p.K364del	ENST00000263121	NM_003073.3	362	gAGAag/gag	8/9	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.709920597885787	2		614	754	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0064302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	394	776	3	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.709920597885787	2		779	888	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181765	56181765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1287268127	NA	P-0064302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	32	305	0	ENST00000399503.3:c.3989C>T	p.Ser1330Leu	p.S1330L	ENST00000399503	NM_005921.1	1330	tCg/tTg	17/20	1	2	FACETS	0.214	0.173	0.259	0.214	0.173	0.259	SUBCLONAL	1	TRUE	1	0.709920597885787	2		305	422	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272336	15272337	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs771517374	NA	P-0064302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	326	822	2	ENST00000263388.2:c.6102dup	p.Gly2035ArgfsTer60	p.G2035Rfs*60	ENST00000263388	NM_000435.2	2034	-/C	33/33	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.709920597885787	2		824	910	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835781	68835781	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060501215	NA	P-0064302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	393	731	1	ENST00000261769.5:c.377del	p.Pro126ArgfsTer89	p.P126Rfs*89	ENST00000261769	NM_004360.3	124	cgC/cg	3/16	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.709920597885787	2		732	905	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920173	76920173	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	240	163	1	ENST00000373344.5:c.3904del	p.Arg1302GlufsTer44	p.R1302Efs*44	ENST00000373344	NM_000489.3	1302	Aga/ga	11/35	1	1	FACETS		NA	1	1	0.996	1	NA	2	TRUE	0	0.709920597885787	1		164	274	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552710	226552710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	56	699	0	ENST00000366794.5:c.2651C>T	p.Ala884Val	p.A884V	ENST00000366794	NM_001618.3	884	gCg/gTg	19/23	1	2	FACETS	0.184	0.157	0.214	0.184	0.157	0.214	SUBCLONAL	1	TRUE	1	0.709920597885787	2		699	856	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396886	139396886	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752754662	NA	P-0064302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	337	576	0	ENST00000277541.6:c.5222C>T	p.Ala1741Val	p.A1741V	ENST00000277541	NM_017617.3	1741	gCg/gTg	28/34	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.709920597885787	2		576	663	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281574	15281574	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	43	690	0	ENST00000263388.2:c.4799G>A	p.Cys1600Tyr	p.C1600Y	ENST00000263388	NM_000435.2	1600	tGc/tAc	26/33	1	2	FACETS	0.182	0.151	0.215	0.182	0.151	0.215	SUBCLONAL	1	TRUE	1	0.709920597885787	2		690	667	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223175	36223175	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	471	956	0	ENST00000222270.7:c.5730del	p.Arg1911AspfsTer23	p.R1911Dfs*23	ENST00000222270	NM_014727.1	1909	Ccc/cc	28/37	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.709920597885787	2		956	977	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428494	72428496	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0064302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	290	475	0	ENST00000477973.2:c.506_508del	p.Lys170del	p.K170del	ENST00000477973	NM_012234.5	170	AAG/-	2/4	0.709920597885787	2	FACETS	1	0.988	1	0.571	0.54	0.602	CLONAL	1	TRUE	0	0.709920597885787	2		475	716	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247295	153247295	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	372	595	1	ENST00000281708.4:c.1507G>A	p.Ala503Thr	p.A503T	ENST00000281708	NM_033632.3	503	Gca/Aca	10/12	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.709920597885787	2		596	794	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306559	163306559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781627921	NA	P-0064302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	116	192	0	ENST00000271452.3:c.356G>A	p.Arg119Gln	p.R119Q	ENST00000271452	NM_145697.2	119	cGg/cAg	6/14	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.709920597885787	2		192	272	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852248	63852248	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	320	760	0	ENST00000279873.7:c.3026C>G	p.Ala1009Gly	p.A1009G	ENST00000279873	NM_032199.2	1009	gCg/gGg	10/10	1	2	FACETS	0.984	0.932	1	0.984	0.932	1	CLONAL	1	TRUE	1	0.709920597885787	2		760	916	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196093	138196093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1405321250	NA	P-0064302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	44	694	1	ENST00000237289.4:c.407G>A	p.Arg136His	p.R136H	ENST00000237289	NM_001270507.1	136	cGc/cAc	3/9	1	2	FACETS	0.148	0.123	0.176	0.148	0.123	0.176	SUBCLONAL	1	TRUE	1	0.709920597885787	2		695	837	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458044	120458045	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	403	773	0	ENST00000256646.2:c.7300dup	p.Ser2434PhefsTer2	p.S2434Ffs*2	ENST00000256646	NM_024408.3	2434	tct/tTct	34/34	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.709920597885787	2		773	918	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425941	49425941	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	413	1004	0	ENST00000301067.7:c.12547C>T	p.Gln4183Ter	p.Q4183*	ENST00000301067	NM_003482.3	4183	Cag/Tag	39/54	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.709920597885787	2		1004	880	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420193	49420193	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	392	781	0	ENST00000301067.7:c.15556del	p.His5186ThrfsTer57	p.H5186Tfs*57	ENST00000301067	NM_003482.3	5186	Cac/ac	48/54	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.709920597885787	2		781	875	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026924	71026987	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTCTACAAGAATTGCAGATTACAACTCTACGTGAGGCAAAAGGTGGAGTATCTACCTGACGAAA	GTCTACAAGAATTGCAGATTACAACTCTACGTGAGGCAAAAGGTGGAGTATCTACCTGACGAAA	-	novel	NA	P-0064302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	683	545	0	ENST00000318789.4:c.1340_1349-51del		p.X447_splice	ENST00000318789	NM_032682.5	447		15/21	0.709920597885787	2	FACETS		NA	1	1	0.998	1	NA	3	TRUE	0	0.709920597885787	2		545	740	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124503540	124503540	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587777475	NA	P-0064302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	216	513	0	ENST00000357628.3:c.410G>A	p.Arg137His	p.R137H	ENST00000357628	NM_015450.2	137	cGt/cAt	8/19	1	2	FACETS	0.918	0.858	0.979	0.918	0.858	0.979	CLONAL	1	TRUE	1	0.709920597885787	2		513	663	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230472953	230472953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	131	640	0	ENST00000391860.1:c.631G>A	p.Ala211Thr	p.A211T	ENST00000391860	NM_001258311.1	211	Gcc/Acc	4/7	1	2	FACETS	0.581	0.529	0.636	0.581	0.529	0.636	SUBCLONAL	1	TRUE	1	0.709920597885787	2		640	635	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257121	19257121	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	250	505	0	ENST00000162023.5:c.842C>G	p.Ser281Trp	p.S281W	ENST00000162023		281	tCg/tGg	12/13	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.709920597885787	2		505	500	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583389	46583389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	73	525	0	ENST00000263734.3:c.317G>A	p.Gly106Asp	p.G106D	ENST00000263734	NM_001430.4	106	gGc/gAc	3/16	1	2	FACETS	0.263	0.23	0.3	0.263	0.23	0.3	SUBCLONAL	1	TRUE	1	0.709920597885787	2		525	781	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29445371	29445371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1169381583	NA	P-0064302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	90	841	1	ENST00000544604.2:c.1202G>A	p.Arg401Gln	p.R401Q	ENST00000544604	NM_001206998.1	401	cGg/cAg	8/9	1	2	FACETS	0.26	0.23	0.292	0.26	0.23	0.292	SUBCLONAL	1	TRUE	1	0.709920597885787	2		842	976	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970825	79970825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373961048	NA	P-0064302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	170	241	0	ENST00000265081.6:c.1051G>A	p.Asp351Asn	p.D351N	ENST00000265081	NM_002439.4	351	Gat/Aat	7/24	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.709920597885787	2		241	430	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752964	128752964	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	420	688	0	ENST00000377970.2:c.1125C>A	p.Asn375Lys	p.N375K	ENST00000377970	NM_002467.4	375	aaC/aaA	3/3	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.709920597885787	2		688	933	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0064304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	175	599	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.498598230530425	2	FACETS	0.997	0.934	1	0.997	0.934	1	CLONAL	2	TRUE	0	0.498598230530425	2		599	352	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642814	3642814	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	100	670	0	ENST00000294008.3:c.2213T>A	p.Val738Asp	p.V738D	ENST00000294008	NM_032444.2	738	gTc/gAc	11/15	0.426471122332501	4	FACETS	1	0.918	1	0.515	0.461	0.572	CLONAL	1	TRUE	2	0.498598230530425	4		670	584	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141418	11141418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555783136	NA	P-0064304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	118	650	1	ENST00000358026.2:c.3395C>T	p.Ala1132Val	p.A1132V	ENST00000358026	NM_001128849.1	1132	gCg/gTg	25/36	0.475932604111506	3	FACETS	1	0.967	1	0.573	0.519	0.629	CLONAL	1	TRUE	1	0.498598230530425	3		651	516	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250170	39250170	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	67	355	0	ENST00000402219.2:c.1399T>G	p.Leu467Val	p.L467V	ENST00000402219	NM_005633.3	467	Tta/Gta	10/23	0.498598230530425	4	FACETS	1	0.962	1	0.422	0.369	0.478	CLONAL	1	TRUE	1	0.498598230530425	4		355	318	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589001	67589002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0064304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	107	327	0	ENST00000274335.5:c.1093dup	p.His365ProfsTer3	p.H365Pfs*3	ENST00000274335		364	-/C	8/15	0.47507254849752	3	FACETS	0.921	0.85	0.992	0.921	0.85	0.992	CLONAL	3	TRUE	0	0.498598230530425	3		327	194	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121336	29121338	+	frameshift_variant	Frame_Shift_Del	DEL	GTA	GTA	AT	novel	NA	P-0064304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	10	331	0	ENST00000328354.6:c.337_339delinsAT	p.Tyr113IlefsTer18	p.Y113Ifs*18	ENST00000328354	NM_007194.3	113	TAC/AT	3/15	0.498598230530425	2	FACETS	0.209	0.141	0.294	0.104	0.07	0.147	SUBCLONAL	1	TRUE	0	0.498598230530425	2		331	192	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064305-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	341	652	0	ENST00000269305.4:c.406del	p.Gln136AsnfsTer34	p.Q136Nfs*34	ENST00000269305	NM_001126112.2	136	Caa/aa	5/11	0.596853458129122	2	FACETS	0.967	0.926	1	0.967	0.926	1	CLONAL	2	TRUE	0	0.596853458129122	2		652	591	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951156	48951156	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064305-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	102	315	0	ENST00000267163.4:c.1318G>T	p.Glu440Ter	p.E440*	ENST00000267163	NM_000321.2	440	Gaa/Taa	13/27	0.596853458129122	1	FACETS	0.908	0.826	0.993	0.908	0.826	0.993	CLONAL	1	TRUE	0	0.596853458129122	1		315	264	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063360	67063360	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064305-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	103	572	0	ENST00000412916.2:c.50T>C	p.Phe17Ser	p.F17S	ENST00000412916		17	tTt/tCt	1/6	0.596853458129122	1	FACETS	0.91	0.828	0.994	0.91	0.828	0.994	CLONAL	1	TRUE	0	0.596853458129122	1		572	266	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674348	86674348	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064305-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	77	330	0	ENST00000274376.6:c.2480C>A	p.Ser827Tyr	p.S827Y	ENST00000274376	NM_002890.2	827	tCt/tAt	18/25	0.596853458129122	1	FACETS	0.854	0.763	0.947	0.854	0.763	0.947	CLONAL	1	TRUE	0	0.596853458129122	1		330	212	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0064307-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	446	631	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.660591963752659	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.660591963752659	2		631	667	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880998	37880998	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs144434331	NA	P-0064307-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	842	862	0	ENST00000269571.5:c.2327G>T	p.Gly776Val	p.G776V	ENST00000269571		776	gGt/gTt	20/27	0.659507273373974	3	FACETS	0.98	0.959	1	0.98	0.959	1	CLONAL	3	TRUE	0	0.660591963752659	3		862	1153	SUCCESS
APC	324	MSKCC	GRCh37	5	112175568	112175569	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0064307-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	430	863	0	ENST00000257430.4:c.4277_4278insTA	p.Pro1427ThrfsTer47	p.P1427Tfs*47	ENST00000257430	NM_000038.5	1426	agc/agTAc	16/16	0.645452142216005	2	FACETS	0.95	0.917	0.983	0.95	0.917	0.983	CLONAL	2	TRUE	0	0.660591963752659	2		863	685	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0064308-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	455	504	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.747849031669791	3	FACETS	0.999	0.974	1	0.999	0.974	1	CLONAL	3	TRUE	0	0.747849031669791	3		504	558	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150936830	150936830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064308-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	178	517	0	ENST00000271640.5:c.3866G>A	p.Arg1289His	p.R1289H	ENST00000271640	NM_001145415.1	1289	cGt/cAt	22/22	0.696537676428194	4	FACETS	1	0.957	1	0.527	0.487	0.569	CLONAL	1	TRUE	2	0.747849031669791	4		517	789	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437749	110437749	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064308-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	103	576	0	ENST00000375856.3:c.652C>G	p.Arg218Gly	p.R218G	ENST00000375856	NM_003749.2	218	Cgt/Ggt	1/2	0.747849031669791	2	FACETS	0.613	0.552	0.678	0.307	0.276	0.339	SUBCLONAL	1	TRUE	0	0.747849031669791	2		576	449	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052593	42052593	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064308-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	162	660	0	ENST00000219905.7:c.7264G>C	p.Ala2422Pro	p.A2422P	ENST00000219905	NM_001164273.1	2422	Gct/Cct	20/24	0.705356549485723	3	FACETS	0.903	0.832	0.978	0.452	0.416	0.489	CLONAL	1	TRUE	1	0.747849031669791	3		660	659	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234513	41234549	+	frameshift_variant	Frame_Shift_Del	DEL	CCATGCTGTTCTAACACAGCTTCTAGTTCAGCCATTT	CCATGCTGTTCTAACACAGCTTCTAGTTCAGCCATTT	-	novel	NA	P-0064308-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	166	504	0	ENST00000357654.3:c.4229_4265del	p.Glu1410GlyfsTer12	p.E1410Gfs*12	ENST00000357654	NM_007294.3	1410	gAAATGGCTGAACTAGAAGCTGTGTTAGAACAGCATGGg/gg	12/23	0.747849031669791	2	FACETS	0.879	0.814	0.946	0.44	0.407	0.473	CLONAL	1	TRUE	0	0.747849031669791	2		504	505	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46603832	46603832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369754100	NA	P-0064308-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	120	623	1	ENST00000263734.3:c.1189C>T	p.Pro397Ser	p.P397S	ENST00000263734	NM_001430.4	397	Ccc/Tcc	9/16	0.696537676428194	4	FACETS	0.754	0.681	0.831	0.377	0.34	0.416	SUBCLONAL	1	TRUE	2	0.747849031669791	4		624	744	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845360	42845360	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064308-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	172	673	2	ENST00000398585.3:c.902C>G	p.Pro301Arg	p.P301R	ENST00000398585	NM_001135099.1	301	cCg/cGg	9/14	0.632548778093929	4	FACETS	0.917	0.844	0.993	0.458	0.422	0.497	CLONAL	1	TRUE	2	0.747849031669791	4		675	877	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750383	133750383	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064308-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	337	584	0	ENST00000318560.5:c.1214G>A	p.Trp405Ter	p.W405*	ENST00000318560	NM_005157.4	405	tGg/tAg	7/11	0.747849031669791	2	FACETS	0.988	0.955	1	0.988	0.955	1	CLONAL	2	TRUE	0	0.747849031669791	2		584	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0064313-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	106	679	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.341014544703224	3	FACETS	1	0.979	1	0.831	0.76	0.903	CLONAL	2	FALSE	0	0.428429927732351	3		679	241	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057642	27057642	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0064313-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	44	703	0	ENST00000324856.7:c.1351-1G>A		p.X451_splice	ENST00000324856	NM_006015.4	451			0.163299535288169	4	FACETS	1	0.924	1	0.58	0.49	0.678	INDETERMINATE	1	FALSE	2	0.428429927732351	4		703	253	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513287	106513287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753731201	NA	P-0064313-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	90	700	0	ENST00000359195.3:c.2191G>A	p.Asp731Asn	p.D731N	ENST00000359195	NM_002649.2	731	Gac/Aac	4/11	0.26946399363358	3	FACETS	0.886	0.796	0.979	0.59	0.53	0.653	CLONAL	2	FALSE	0	0.428429927732351	3		700	288	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105240299	105240299	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064313-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	43	737	0	ENST00000349310.3:c.652C>G	p.Gln218Glu	p.Q218E	ENST00000349310	NM_001014432.1	218	Cag/Gag	9/15	0.428429927732351	3	FACETS	0.941	0.793	1	0.471	0.396	0.551	CLONAL	1	FALSE	1	0.428429927732351	3		737	259	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247378	71247378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757649540	NA	P-0064313-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	92	890	0	ENST00000318789.4:c.155C>T	p.Ala52Val	p.A52V	ENST00000318789	NM_032682.5	52	gCc/gTc	6/21	0.428429927732351	3	FACETS	0.957	0.852	1	0.478	0.426	0.534	CLONAL	1	FALSE	1	0.428429927732351	3		890	545	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197582	106197582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064313-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	78	802	0	ENST00000380013.4:c.5915C>T	p.Ala1972Val	p.A1972V	ENST00000380013	NM_001127208.2	1972	gCc/gTc	11/11	0.191062619309405	3	FACETS	1	0.967	1	0.635	0.562	0.712	INDETERMINATE	1	FALSE	1	0.428429927732351	3		802	348	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628371	86628371	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064313-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	21	483	0	ENST00000274376.6:c.740C>T	p.Ser247Phe	p.S247F	ENST00000274376	NM_002890.2	247	tCt/tTt	3/25	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	FALSE	1	0.428429927732351	2		483	85	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212869	27212869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064313-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	30	796	0	ENST00000380036.4:c.2851G>A	p.Gly951Ser	p.G951S	ENST00000380036	NM_000459.3	951	Ggc/Agc	17/23	0.428429927732351	3	FACETS	0.41	0.33	0.5	0.205	0.165	0.25	SUBCLONAL	1	FALSE	1	0.428429927732351	3		796	415	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644703	134644703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536029159	NA	P-0064315-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	79	607	2	ENST00000398015.3:c.104C>T	p.Thr35Met	p.T35M	ENST00000398015	NM_004441.4	35	aCg/aTg	2/16	1	2	FACETS	0.904	0.797	1	0.904	0.797	1	CLONAL	1	TRUE	1	0.32	2		609	546	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817459	39817459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs993206522	NA	P-0064315-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	63	776	0	ENST00000288319.7:c.104C>T	p.Ala35Val	p.A35V	ENST00000288319	NM_182918.3	35	gCg/gTg	2/10	1	2	FACETS	0.617	0.533	0.708	0.617	0.533	0.708	SUBCLONAL	1	TRUE	1	0.32	2		776	638	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372447	118372447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782001089	NA	P-0064315-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	74	738	0	ENST00000534358.1:c.6380G>A	p.Arg2127Gln	p.R2127Q	ENST00000534358	NM_005933.3	2127	cGa/cAa	26/36	1	2	FACETS	0.741	0.649	0.84	0.741	0.649	0.84	SUBCLONAL	1	TRUE	1	0.32	2		738	624	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532696	187532701	+	inframe_deletion	In_Frame_Del	DEL	GGTACT	GGTACT	-	novel	NA	P-0064315-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	85	755	0	ENST00000441802.2:c.9692_9697del	p.Glu3231_Arg3233delinsGly	p.E3231_R3233delinsG	ENST00000441802	NM_005245.3	3231	gAGTACCgt/ggt	14/27	1	2	FACETS	0.824	0.728	0.925	0.824	0.728	0.925	CLONAL	1	TRUE	1	0.32	2		755	645	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685269	89685269	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0064316-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	37	120	0	ENST00000371953.3:c.165-1G>T		p.X55_splice	ENST00000371953	NM_000314.4	55			0.657174867893766	1	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	0	0.657174867893766	1		120	74	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573987	7573987	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397516434	NA	P-0064316-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	188	611	0	ENST00000269305.4:c.1040C>T	p.Ala347Val	p.A347V	ENST00000269305	NM_001126112.2	347	gCc/gTc	10/11	0.657174867893766	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.657174867893766	1		611	309	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366149	15366149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35824241	NA	P-0064316-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	90	680	0	ENST00000263377.2:c.2006G>A	p.Arg669His	p.R669H	ENST00000263377	NM_058243.2	669	cGc/cAc	10/20	1	2	FACETS	0.565	0.503	0.63	0.565	0.503	0.63	SUBCLONAL	1	TRUE	1	0.657174867893766	2		680	485	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189293	99189293	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766300586	NA	P-0064316-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	80	653	0	ENST00000074304.5:c.2549G>A	p.Arg850His	p.R850H	ENST00000074304	NM_001134224.1	850	cGc/cAc	24/26	0.38038917423745	1	FACETS	0.339	0.299	0.382	0.339	0.299	0.382	INDETERMINATE	1	TRUE	0	0.657174867893766	1		653	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0064318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	119	691	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.656186006847577	1	FACETS	0.966	0.894	1	0.966	0.894	1	CLONAL	1	TRUE	0	0.705374346194747	1		691	226	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496977	29496978	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAATGTAA	novel	NA	P-0064318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	19	100	0	ENST00000356175.3:c.554_555insAACAATGT	p.Asp186ThrfsTer8	p.D186Tfs*8	ENST00000356175	NM_000267.3	183	atc/atCAATGTAAc	5/57	0.656186006847577	1	FACETS	0.415	0.322	0.519	0.415	0.322	0.519	SUBCLONAL	1	TRUE	0	0.705374346194747	1		100	84	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223233	5223233	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	90	799	0	ENST00000357368.4:c.2570G>T	p.Gly857Val	p.G857V	ENST00000357368	NM_002850.3	857	gGc/gTc	18/38	0.257377965956856	4	FACETS	0.769	0.691	0.85	0.769	0.691	0.85	INDETERMINATE	2	TRUE	2	0.705374346194747	4		799	283	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541691	187541719	+	frameshift_variant	Frame_Shift_Del	DEL	GGATGTGATAAAACAAAGGCTCATTGATT	GGATGTGATAAAACAAAGGCTCATTGATT	-	novel	NA	P-0064318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	203	1143	0	ENST00000441802.2:c.6021_6049del	p.Ile2008GlnfsTer7	p.I2008Qfs*7	ENST00000441802	NM_005245.3	2007	ccAATCAATGAGCCTTTGTTTTATCACATCCtc/cctc	10/27	0.705374346194747	2	FACETS	0.959	0.913	1	0.959	0.913	1	CLONAL	2	TRUE	0	0.705374346194747	2		1143	300	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496987	29496991	+	missense_variant	Missense_Mutation	ONP	TTGTG	TTGTG	ATGTT	novel	NA	P-0064318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	17	133	0	ENST00000356175.3:c.558_562delinsATGTT	p.Asp186_Ala188delinsGluCysSer	p.D186_A188delinsECS	ENST00000356175	NM_000267.3	186	gaTTGTGca/gaATGTTca	5/57	0.656186006847577	1	FACETS	0.363	0.276	0.462	0.363	0.276	0.462	SUBCLONAL	1	TRUE	0	0.705374346194747	1		133	86	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0064321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	335	361	0	ENST00000374690.3:c.2105T>A	p.Leu702His	p.L702H	ENST00000374690	NM_000044.3	702	cTc/cAc	4/8	1	1	FACETS	1	0.996	1	1	0.997	1	CLONAL	3	FALSE	0	0.419796637761501	1		361	366	SUCCESS
AR	367	MSKCC	GRCh37	X	66943552	66943552	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137852578	NA	P-0064321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	18	301	0	ENST00000374690.3:c.2632A>G	p.Thr878Ala	p.T878A	ENST00000374690	NM_000044.3	878	Act/Gct	8/8	1	1	FACETS	0.252	0.189	0.326	0.252	0.189	0.326	SUBCLONAL	1	FALSE	0	0.419796637761501	1		301	269	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0064321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	220	522	4	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	1	2	FACETS	0.985	0.925	1	1	0.994	1	CLONAL	2	FALSE	1	0.419796637761501	2		526	532	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028026	69028026	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775893443	NA	P-0064321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	183	424	0	ENST00000288368.4:c.3185G>A	p.Arg1062His	p.R1062H	ENST00000288368	NM_024870.2	1062	cGt/cAt	26/40	0.419796637761501	4	FACETS	0.99	0.918	1	0.66	0.612	0.71	CLONAL	2	FALSE	1	0.419796637761501	4		424	625	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204494703	204494703	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs148900701	NA	P-0064321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	194	468	0	ENST00000367182.3:c.57C>G	p.Ile19Met	p.I19M	ENST00000367182	NM_001278516.1	19	atC/atG	2/11	1	2	FACETS	1	0.957	1	1	0.994	1	CLONAL	2	FALSE	1	0.419796637761501	2		468	449	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371830	55371830	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	46	782	0	ENST00000297316.4:c.520G>T	p.Val174Leu	p.V174L	ENST00000297316	NM_022454.3	174	Gtg/Ttg	2/2	0.419796637761501	4	FACETS	0.435	0.365	0.512	0.145	0.121	0.171	SUBCLONAL	1	FALSE	1	0.419796637761501	4		782	716	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064337-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	282	612	0				ENST00000310581	NM_198253.2	-/1132			0.399310135631282	5	FACETS	1	0.988	1	0.785	0.739	0.832	CLONAL	2	FALSE	2	0.396655238555827	5		612	963	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0064337-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	109	374	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.396655238555827	6	FACETS	0.992	0.895	1			1	CLONAL	2	FALSE	NA	0.396655238555827	6		374	497	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8246257	8246257	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064337-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	89	438	0	ENST00000335790.3:c.377del	p.Gly126GlufsTer6	p.G126Efs*6	ENST00000335790	NM_002315.2	126	gGa/ga	4/4	0.265573006309325	3	FACETS	0.766	0.679	0.859	0.383	0.339	0.43	SUBCLONAL	1	FALSE	1	0.396655238555827	3		438	702	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911049	94911049	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064337-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	16	363	0	ENST00000536441.1:c.1081T>C	p.Phe361Leu	p.F361L	ENST00000536441	NM_144665.3	361	Ttc/Ctc	8/10	0.285725036550559	0	FACETS	0.737	0.56	0.937			1	CLONAL	1	FALSE	0	0.396655238555827	0		363	66	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480335	56480335	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064337-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	65	418	0	ENST00000267101.3:c.442T>C	p.Tyr148His	p.Y148H	ENST00000267101	NM_001982.3	148	Tat/Cat	4/28	0.399310135631282	1	FACETS	0.831	0.726	0.944	0.831	0.726	0.944	CLONAL	1	FALSE	0	0.396655238555827	1		418	316	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577096	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0064337-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	44	604	0	ENST00000269305.4:c.842_843del	p.Asp281AlafsTer24	p.D281Afs*24	ENST00000269305	NM_001126112.2	281	gAC/g	8/11	0.396655238555827	6	FACETS	0.767	0.643	0.904			1	CLONAL	1	FALSE	NA	0.396655238555827	6		604	519	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941830	44941830	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064337-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	39	176	0	ENST00000377967.4:c.3154G>T	p.Glu1052Ter	p.E1052*	ENST00000377967	NM_021140.2	1052	Gaa/Taa	21/29	0.252074294481083	2	FACETS	1	0.943	1			1	CLONAL	2	FALSE	NA	0.396655238555827	2		176	82	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941837	44941837	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064337-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	46	186	0	ENST00000377967.4:c.3161G>T	p.Arg1054Ile	p.R1054I	ENST00000377967	NM_021140.2	1054	aGa/aTa	21/29	0.252074294481083	2	FACETS	0.85	0.746	0.953			1	CLONAL	3	FALSE	NA	0.396655238555827	2		186	91	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064337-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	195	612	0				ENST00000310581	NM_198253.2	-/1132			0.529372988804715	4	FACETS	0.899	0.845	0.953	0.899	0.845	0.953	CLONAL	3	TRUE	1	0.577578460759767	4		612	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0064337-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	334	374	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.520419751153163	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.577578460759767	4		374	848	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8246257	8246257	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064337-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	96	438	0	ENST00000335790.3:c.377del	p.Gly126GlufsTer6	p.G126Efs*6	ENST00000335790	NM_002315.2	126	gGa/ga	4/4	0.577578460759767	3	FACETS	0.906	0.811	1	0.453	0.405	0.503	CLONAL	1	TRUE	1	0.577578460759767	3		438	473	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911049	94911049	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064337-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	161	363	0	ENST00000536441.1:c.1081T>C	p.Phe361Leu	p.F361L	ENST00000536441	NM_144665.3	361	Ttc/Ctc	8/10	0.577578460759767	3	FACETS	0.855	0.793	0.919	0.855	0.793	0.919	CLONAL	2	TRUE	1	0.577578460759767	3		363	420	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480335	56480335	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064337-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	131	418	0	ENST00000267101.3:c.442T>C	p.Tyr148His	p.Y148H	ENST00000267101	NM_001982.3	148	Tat/Cat	4/28	0.54361340642707	4	FACETS	1	0.932	1			1	CLONAL	1	TRUE	NA	0.577578460759767	4		418	695	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577096	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0064337-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	304	604	0	ENST00000269305.4:c.842_843del	p.Asp281AlafsTer24	p.D281Afs*24	ENST00000269305	NM_001126112.2	281	gAC/g	8/11	0.520419751153163	4	FACETS	0.908	0.858	0.96	0.908	0.858	0.96	CLONAL	2	TRUE	2	0.577578460759767	4		604	914	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941830	44941830	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064337-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	136	176	0	ENST00000377967.4:c.3154G>T	p.Glu1052Ter	p.E1052*	ENST00000377967	NM_021140.2	1052	Gaa/Taa	21/29	0.54361340642707	2	FACETS	1	0.985	1			1	CLONAL	2	TRUE	NA	0.577578460759767	2		176	201	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941837	44941837	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064337-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	142	186	0	ENST00000377967.4:c.3161G>T	p.Arg1054Ile	p.R1054I	ENST00000377967	NM_021140.2	1054	aGa/aTa	21/29	0.54361340642707	2	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.577578460759767	2		186	200	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003977	57003977	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	G	G	A	rs373170562	NA	P-0064337-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	126	566	1	ENST00000257254.3:c.502C>T	p.Arg168Cys	p.R168C	ENST00000257254		168	Cgc/Tgc	1/2	0.577578460759767	3	FACETS	0.96	0.872	1	0.48	0.436	0.526	CLONAL	1	TRUE	1	0.577578460759767	3		567	586	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992838	72992838	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064337-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	121	483	0	ENST00000268489.5:c.1207C>G	p.Leu403Val	p.L403V	ENST00000268489	NM_006885.3	403	Ctt/Gtt	2/10	0.577578460759767	3	FACETS	0.936	0.848	1	0.468	0.424	0.514	CLONAL	1	TRUE	1	0.577578460759767	3		483	577	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945097	38945097	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064337-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	128	435	0	ENST00000357387.3:c.4707G>T	p.Lys1569Asn	p.K1569N	ENST00000357387	NM_152756.3	1569	aaG/aaT	35/38	0.529372988804715	4	FACETS	0.973	0.883	1	0.324	0.294	0.356	CLONAL	1	TRUE	1	0.577578460759767	4		435	719	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836275	151836275	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1469176725	NA	P-0064337-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	136	436	0	ENST00000262189.6:c.14530G>A	p.Ala4844Thr	p.A4844T	ENST00000262189	NM_170606.2	4844	Gca/Aca	57/59	0.520419751153163	4	FACETS	1	0.958	1	0.544	0.495	0.595	CLONAL	1	TRUE	2	0.577578460759767	4		436	683	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0064338-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	89	651	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.307675320705724	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	0	0.307675320705724	1		651	477	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0064338-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	77	287	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.307675320705724	2		287	380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0064338-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	116	523	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.307675320705724	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.307675320705724	1		523	528	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958219	2958219	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064338-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	79	577	0	ENST00000396946.4:c.2513C>T	p.Ala838Val	p.A838V	ENST00000396946	NM_032415.4	838	gCc/gTc	19/25	1	2	FACETS	0.887	0.781	1	0.887	0.781	1	CLONAL	1	TRUE	1	0.307675320705724	2		577	579	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650462	48650462	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064338-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	91	872	0	ENST00000376670.3:c.432C>A	p.Asp144Glu	p.D144E	ENST00000376670	NM_002049.3	144	gaC/gaA	3/6	1	2	FACETS	0.795	0.706	0.891	0.795	0.706	0.891	SUBCLONAL	1	TRUE	1	0.307675320705724	2		872	744	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222554	2222554	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064338-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	102	686	0	ENST00000326181.6:c.748C>A	p.His250Asn	p.H250N	ENST00000326181	NM_032271.2	250	Cac/Aac	9/21	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.307675320705724	2		686	629	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971144	21971209	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGTTGGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCTGCCCATCATCATGACCT	AGTTGGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCTGCCCATCATCATGACCT	-	novel	NA	P-0064338-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	91	721	0	ENST00000304494.5:c.151-2_214del		p.X51_splice	ENST00000304494	NM_000077.4	51		2/3	0.307675320705724	1	FACETS	0.913	0.813	1	0.913	0.813	1	CLONAL	1	TRUE	0	0.307675320705724	1		721	548	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0064339-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	120	466	0	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	0.351924914132456	4	FACETS	1	0.941	1	1	0.941	1	CLONAL	3	FALSE	1	0.446268220305675	4		466	253	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123695	11123695	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064339-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	287	440	0	ENST00000358026.2:c.2345G>A	p.Gly782Asp	p.G782D	ENST00000358026	NM_001128849.1	782	gGc/gAc	16/36	0.343826088177367	5	FACETS	1	0.982	1	1	0.982	1	CLONAL	4	FALSE	1	0.446268220305675	5		440	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0064340-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	98	631	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.322343776042336	3	FACETS	0.931	0.838	1	0.62	0.559	0.685	CLONAL	2	TRUE	0	0.348255493400896	3		631	355	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0064340-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	59	516	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.253424804647226	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	2	TRUE	0	0.348255493400896	2		516	166	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411276	63411276	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064340-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	72	434	0	ENST00000330258.3:c.1891C>T	p.Arg631Ter	p.R631*	ENST00000330258	NM_152424.3	631	Cga/Tga	2/2	1	1	FACETS	1	0.914	1	1	0.985	1	CLONAL	2	TRUE	0	0.348255493400896	1		434	167	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764328	39764328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747584221	NA	P-0064340-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	30	531	0	ENST00000288319.7:c.784G>A	p.Gly262Ser	p.G262S	ENST00000288319	NM_182918.3	262	Ggt/Agt	7/10	0.267136632374476	3	FACETS	0.578	0.466	0.705	0.289	0.233	0.353	SUBCLONAL	1	TRUE	1	0.348255493400896	3		531	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064340-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	10	718	0	ENST00000269305.4:c.469G>C	p.Val157Leu	p.V157L	ENST00000269305	NM_001126112.2	157	Gtc/Ctc	5/11	0.322343776042336	3	FACETS	0.153	0.103	0.217	0.051	0.034	0.073	SUBCLONAL	1	TRUE	0	0.348255493400896	3		718	441	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710654	114710655	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0064340-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	132	563	0	ENST00000543371.1:c.142_143del	p.Leu48SerfsTer3	p.L48Sfs*3	ENST00000543371	NM_001198531.1	47	TCt/t	1/14	0.267136632374476	3	FACETS	0.953	0.871	1	0.953	0.871	1	CLONAL	2	TRUE	1	0.348255493400896	3		563	467	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163363	108163363	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064340-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	20	441	0	ENST00000278616.4:c.4454A>T	p.Asp1485Val	p.D1485V	ENST00000278616	NM_000051.3	1485	gAt/gTt	30/63	0.298991282559845	3	FACETS	1	0.89	1	0.636	0.494	0.796	CLONAL	1	TRUE	1	0.348255493400896	3		441	106	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350305	89350305	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs759995499	NA	P-0064340-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	51	697	0	ENST00000301030.4:c.2645A>C	p.Lys882Thr	p.K882T	ENST00000301030	NM_001256183.1	882	aAg/aCg	9/13	0.298991282559845	3	FACETS	0.764	0.65	0.889	0.382	0.325	0.445	SUBCLONAL	1	TRUE	1	0.348255493400896	3		697	450	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229685	5229686	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCGCTGGGCACTGGCGGGCGGGAGGGG	novel	NA	P-0064340-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	14	361	0	ENST00000357368.4:c.2156-17_2165dup	p.Pro723_Pro724insSerArgProProValProSerAlaPro	p.P723_P724insSRPPVPSAP	ENST00000357368	NM_002850.3	722	gcg/gcCCCCTCCCGCCCGCCAGTGCCCAGCGCg	15/38	0.274369702466743	0	FACETS	0.294	0.213	0.392			1	SUBCLONAL	1	TRUE	0	0.348255493400896	0		361	178	SUCCESS
APC	324	MSKCC	GRCh37	5	112175856	112175857	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064340-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	29	560	0	ENST00000257430.4:c.4567dup	p.Arg1523LysfsTer10	p.R1523Kfs*10	ENST00000257430	NM_000038.5	1522	tta/ttAa	16/16	0.34623730858431	1	FACETS	0.923	0.751	1	0.923	0.751	1	CLONAL	1	TRUE	0	0.348255493400896	1		560	149	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0064341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	101	515	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.801	0.718	0.888	0.801	0.718	0.888	CLONAL	1	TRUE	1	0.479426503934439	2		515	526	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57004037	57004037	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	C	C	T	rs576092494	NA	P-0064341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	116	841	0	ENST00000257254.3:c.442G>A	p.Val148Met	p.V148M	ENST00000257254		148	Gtg/Atg	1/2	1	2	FACETS	0.699	0.631	0.771	0.699	0.631	0.771	SUBCLONAL	1	TRUE	1	0.479426503934439	2		841	692	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727183	40727183	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	46	657	0	ENST00000373198.4:c.3781C>T	p.Gln1261Ter	p.Q1261*	ENST00000373198	NM_133170.3	1261	Cag/Tag	28/32	1	2	FACETS	0.301	0.253	0.355	0.301	0.253	0.355	SUBCLONAL	1	TRUE	1	0.479426503934439	2		657	637	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191507	10191507	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs5030821	NA	P-0064341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	136	571	0	ENST00000256474.2:c.500G>C	p.Arg167Pro	p.R167P	ENST00000256474	NM_000551.3	167	cGg/cCg	3/3	0.462296533770506	1	FACETS	0.882	0.807	0.96	0.882	0.807	0.96	CLONAL	1	TRUE	0	0.479426503934439	1		571	489	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437818	52437818	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0064341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	28	687	0	ENST00000460680.1:c.1343del	p.Leu448TrpfsTer123	p.L448Wfs*123	ENST00000460680	NM_004656.3	448	tTg/tg	13/17	0.462296533770506	1	FACETS	0.164	0.131	0.203	0.164	0.131	0.203	SUBCLONAL	1	TRUE	0	0.479426503934439	1		687	540	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584654	52584654	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0064341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	157	738	0	ENST00000394830.3:c.4360-1G>A		p.X1454_splice	ENST00000394830	NM_018313.4	1454			0.462296533770506	1	FACETS	0.891	0.82	0.963	0.891	0.82	0.963	CLONAL	1	TRUE	0	0.479426503934439	1		738	559	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604722	48604722	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	44	593	0	ENST00000342988.3:c.1544G>T	p.Arg515Ile	p.R515I	ENST00000342988	NM_005359.5	515	aGa/aTa	12/12	0.307443057921682	1	FACETS	0.433	0.362	0.511	0.433	0.362	0.511	SUBCLONAL	1	TRUE	0	0.307443057921682	1		593	560	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953270	81953270	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0064343-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	133	416	0	ENST00000359376.3:c.2235+1G>T		p.X745_splice	ENST00000359376	NM_002661.3	745			0.649476169215074	2	FACETS	0.788	0.719	0.859	0.394	0.359	0.43	SUBCLONAL	1	TRUE	0	0.649476169215074	2		416	520	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943616	9943616	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064343-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	56	408	0	ENST00000330684.3:c.1325T>C	p.Ile442Thr	p.I442T	ENST00000330684	NM_001134407.1	442	aTc/aCc	5/13	0.649476169215074	3	FACETS	0.344	0.294	0.399	0.172	0.147	0.2	SUBCLONAL	1	TRUE	1	0.649476169215074	3		408	664	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127432	17127838	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATGGGGCCTTCACGGCCAGGGCAGACCTGGAGGGACACCGGCGACTCAGACAGCCCTTTCCTCGCTTAGTGACACCAAATCAAAGCCTCTTCTTCAGACTTTTCAGAGTCAGCTGGCACAAATCAGCCAGCGTTAATAACGGGGAGAGTGGCACAGTGGGGGCCATGAGAGCCGAAGACTGTACTCTTCTGCTCCTGTGATCAAGCTTCCAACAACACTTGTCATTGTGGACTGCAAGGGCCGGTAACAAGGCTTATTGCTTTTCTTCCACCTTGAGCCATAAATAACTCCCATGCATATGTCACACCTCTCCCAGACTCAAATGTACCAGCTTACTCACCTGGAGCATGCAGAAGAACCAGCAGGTCAGAGCAGCCACTGCACTCTCCCTGCACTGAAATCCGCAC	ATGGGGCCTTCACGGCCAGGGCAGACCTGGAGGGACACCGGCGACTCAGACAGCCCTTTCCTCGCTTAGTGACACCAAATCAAAGCCTCTTCTTCAGACTTTTCAGAGTCAGCTGGCACAAATCAGCCAGCGTTAATAACGGGGAGAGTGGCACAGTGGGGGCCATGAGAGCCGAAGACTGTACTCTTCTGCTCCTGTGATCAAGCTTCCAACAACACTTGTCATTGTGGACTGCAAGGGCCGGTAACAAGGCTTATTGCTTTTCTTCCACCTTGAGCCATAAATAACTCCCATGCATATGTCACACCTCTCCCAGACTCAAATGTACCAGCTTACTCACCTGGAGCATGCAGAAGAACCAGCAGGTCAGAGCAGCCACTGCACTCTCCCTGCACTGAAATCCGCAC	-	novel	NA	P-0064343-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	80	464	0	ENST00000285071.4:c.397-381_422del		p.X133_splice	ENST00000285071	NM_144997.5	133		6/14	0.398225860446334	4	FACETS	0.688	0.606	0.775	0.172	0.151	0.194	SUBCLONAL	1	TRUE	0	0.649476169215074	4		464	591	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624802	9624802	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064343-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	294	424	0	ENST00000353224.5:c.175A>T	p.Ile59Phe	p.I59F	ENST00000353224	NM_177990.2	59	Atc/Ttc	3/10	0.562789768837717	4	FACETS	0.997	0.943	1	0.997	0.943	1	CLONAL	2	TRUE	2	0.649476169215074	4		424	749	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0064344-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	116	583	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.213038896108867	2	FACETS	1	0.97	1	0.595	0.537	0.656	CLONAL	1	TRUE	0	0.302841088077565	2		583	644	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660629	227660629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064344-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	48	599	0	ENST00000305123.5:c.2826G>A	p.Met942Ile	p.M942I	ENST00000305123	NM_005544.2	942	atG/atA	1/2	0.19599443354487	3	FACETS	0.534	0.45	0.626	0.267	0.225	0.313	SUBCLONAL	1	TRUE	1	0.302841088077565	3		599	684	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611814	100611814	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064344-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	19	374	0	ENST00000308731.7:c.1307C>A	p.Ser436Tyr	p.S436Y	ENST00000308731	NM_000061.2	436	tCc/tAc	14/19	1	2	FACETS	0.364	0.275	0.468	0.364	0.275	0.468	SUBCLONAL	1	TRUE	1	0.302841088077565	2		374	345	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822609	72822609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771122441	NA	P-0064345-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	229	572	0	ENST00000268489.5:c.9566C>T	p.Ala3189Val	p.A3189V	ENST00000268489	NM_006885.3	3189	gCg/gTg	10/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.561976793706916	2		572	750	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805074	89805074	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs74977201	NA	P-0064345-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	38	522	3	ENST00000389301.3:c.4303G>A	p.Ala1435Thr	p.A1435T	ENST00000389301	NM_000135.2	1435	Gcc/Acc	43/43	1	2	FACETS	0.206	0.17	0.247	0.206	0.17	0.247	SUBCLONAL	1	TRUE	1	0.561976793706916	2		525	656	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548938	29548938	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660135	NA	P-0064345-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	16	163	0	ENST00000356175.3:c.1714del	p.Glu572ArgfsTer14	p.E572Rfs*14	ENST00000356175	NM_000267.3	571	tGg/tg	15/57	1	2	FACETS	0.581	0.436	0.749	0.581	0.436	0.749	SUBCLONAL	1	TRUE	1	0.561976793706916	2		163	98	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654553	29654553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876657714	NA	P-0064345-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	143	347	0	ENST00000356175.3:c.5242C>T	p.Arg1748Ter	p.R1748*	ENST00000356175	NM_000267.3	1748	Cga/Tga	37/57	1	2	FACETS	0.817	0.747	0.889	0.817	0.747	0.889	CLONAL	1	TRUE	1	0.561976793706916	2		347	623	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223073	41223073	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064345-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	179	554	0	ENST00000357654.3:c.4858A>T	p.Thr1620Ser	p.T1620S	ENST00000357654	NM_007294.3	1620	Act/Tct	15/23	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.561976793706916	2		554	609	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220698	1220699	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0064345-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	134	535	0	ENST00000326873.7:c.716_717delinsCT	p.Trp239Ser	p.W239S	ENST00000326873	NM_000455.4	239	tGG/tCT	5/10	0.561976793706916	1	FACETS	0.84	0.771	0.912	0.84	0.771	0.912	CLONAL	1	TRUE	0	0.561976793706916	1		535	408	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231345	5231345	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765642813	NA	P-0064345-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	171	510	0	ENST00000357368.4:c.2131G>A	p.Val711Met	p.V711M	ENST00000357368	NM_002850.3	711	Gtg/Atg	14/38	0.561976793706916	1	FACETS	0.927	0.861	0.995	0.927	0.861	0.995	CLONAL	1	TRUE	0	0.561976793706916	1		510	472	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607808	46607808	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149676792	NA	P-0064345-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	179	579	0	ENST00000263734.3:c.1997C>T	p.Pro666Leu	p.P666L	ENST00000263734	NM_001430.4	666	cCg/cTg	12/16	1	2	FACETS	0.904	0.836	0.974	0.904	0.836	0.974	CLONAL	1	TRUE	1	0.561976793706916	2		579	705	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561444	9561444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064345-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	205	553	0	ENST00000353224.5:c.338C>T	p.Ser113Phe	p.S113F	ENST00000353224	NM_177990.2	113	tCc/tTc	4/10	1	2	FACETS	0.919	0.854	0.985	0.919	0.854	0.985	CLONAL	1	TRUE	1	0.561976793706916	2		553	794	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980855	40980855	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs375343257	NA	P-0064345-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	164	480	0	ENST00000373198.4:c.1631A>G	p.Lys544Arg	p.K544R	ENST00000373198	NM_133170.3	544	aAg/aGg	10/32	1	2	FACETS	0.941	0.868	1	0.941	0.868	1	CLONAL	1	TRUE	1	0.561976793706916	2		480	620	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712520	52712520	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064345-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	102	367	0	ENST00000394830.3:c.232C>T	p.Arg78Ter	p.R78*	ENST00000394830	NM_018313.4	78	Cga/Tga	3/30	0.561976793706916	1	FACETS	0.623	0.561	0.688	0.623	0.561	0.688	SUBCLONAL	1	TRUE	0	0.561976793706916	1		367	419	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542813	187542813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064345-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	144	474	0	ENST00000441802.2:c.4927G>A	p.Gly1643Ser	p.G1643S	ENST00000441802	NM_005245.3	1643	Ggc/Agc	10/27	1	2	FACETS	0.925	0.848	1	0.925	0.848	1	CLONAL	1	TRUE	1	0.561976793706916	2		474	554	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225387	26225387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776406667	NA	P-0064345-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	187	511	1	ENST00000360408.1:c.5C>T	p.Ala2Val	p.A2V	ENST00000360408	NM_003532.2	2	gCg/gTg	1/1	1	2	FACETS	0.908	0.841	0.977	0.908	0.841	0.977	CLONAL	1	TRUE	1	0.561976793706916	2		512	733	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790900	89790900	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064345-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	160	510	0	ENST00000336032.3:c.287A>T	p.Lys96Met	p.K96M	ENST00000336032	NM_006813.2	96	aAg/aTg	1/2	1	2	FACETS	0.92	0.847	0.995	0.92	0.847	0.995	CLONAL	1	TRUE	1	0.561976793706916	2		510	619	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951903	2951903	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064345-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	165	426	0	ENST00000396946.4:c.3047G>T	p.Arg1016Ile	p.R1016I	ENST00000396946	NM_032415.4	1016	aGa/aTa	23/25	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.561976793706916	2		426	540	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636759	8636759	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1318804406	NA	P-0064345-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	29	444	0	ENST00000356435.5:c.150C>A	p.Asp50Glu	p.D50E	ENST00000356435		50	gaC/gaA	2/35	0.561976793706916	1	FACETS	0.148	0.118	0.183	0.148	0.118	0.183	SUBCLONAL	1	TRUE	0	0.561976793706916	1		444	500	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410981	63410981	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064345-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	64	592	0	ENST00000330258.3:c.2186A>C	p.Glu729Ala	p.E729A	ENST00000330258	NM_152424.3	729	gAg/gCg	2/2	0.47702598731128	1	FACETS	0.316	0.274	0.362	0.316	0.274	0.362	SUBCLONAL	1	TRUE	0	0.561976793706916	1		592	518	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412309	139412309	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064364-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	79	547	0	ENST00000277541.6:c.1336G>T	p.Gly446Cys	p.G446C	ENST00000277541	NM_017617.3	446	Ggc/Tgc	8/34	0.358477172786906	1	FACETS	0.911	0.806	1	0.911	0.806	1	CLONAL	1	TRUE	0	0.358477172786906	1		547	397	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701263	43701263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1157211964	NA	P-0064364-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	69	497	0	ENST00000382044.4:c.5432C>T	p.Ala1811Val	p.A1811V	ENST00000382044	NM_001141980.1	1811	gCg/gTg	26/28	1	2	FACETS	0.958	0.838	1	0.958	0.838	1	CLONAL	1	TRUE	1	0.358477172786906	2		497	402	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441235	52441235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910211860	NA	P-0064364-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	83	568	0	ENST00000460680.1:c.535C>T	p.Arg179Trp	p.R179W	ENST00000460680	NM_004656.3	179	Cgg/Tgg	7/17	0.358477172786906	1	FACETS	0.934	0.829	1	0.934	0.829	1	CLONAL	1	TRUE	0	0.358477172786906	1		568	407	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665824	29665824	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1060500355	NA	P-0064364-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	30	281	0	ENST00000356175.3:c.6858+1G>T		p.X2286_splice	ENST00000356175	NM_000267.3	2286			0.358477172786906	1	FACETS	0.848	0.691	1	0.848	0.691	1	CLONAL	1	TRUE	0	0.358477172786906	1		281	162	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092731	27092731	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs141432631	NA	P-0064364-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	46	421	0	ENST00000324856.7:c.2752A>G	p.Met918Val	p.M918V	ENST00000324856	NM_006015.4	918	Atg/Gtg	9/20	1	2	FACETS	0.643	0.543	0.754	0.643	0.543	0.754	SUBCLONAL	1	TRUE	1	0.358477172786906	2		421	399	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858557	57858557	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064364-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	92	561	0	ENST00000228682.2:c.295A>T	p.Ile99Phe	p.I99F	ENST00000228682	NM_005269.2	99	Atc/Ttc	4/12	1	2	FACETS	0.951	0.847	1	0.951	0.847	1	CLONAL	1	TRUE	1	0.358477172786906	2		561	540	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133225	30133225	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064364-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	86	533	1	ENST00000263025.4:c.273C>G	p.Ile91Met	p.I91M	ENST00000263025	NM_002746.2	91	atC/atG	2/9	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.358477172786906	2		534	480	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288744	15288744	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1037739385	NA	P-0064364-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	44	407	0	ENST00000263388.2:c.3995C>T	p.Pro1332Leu	p.P1332L	ENST00000263388	NM_000435.2	1332	cCg/cTg	24/33	0.358477172786906	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.358477172786906	1		407	173	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158201	47158201	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064364-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	33	317	0	ENST00000409792.3:c.4498G>C	p.Glu1500Gln	p.E1500Q	ENST00000409792	NM_014159.6	1500	Gag/Cag	4/21	0.358477172786906	1	FACETS	0.609	0.499	0.732	0.609	0.499	0.732	SUBCLONAL	1	TRUE	0	0.358477172786906	1		317	248	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519154	187519154	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064364-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	34	430	0	ENST00000441802.2:c.12229C>T	p.Gln4077Ter	p.Q4077*	ENST00000441802	NM_005245.3	4077	Cag/Tag	23/27	0.181329881152213	2	FACETS	0.527	0.431	0.634	0.263	0.215	0.317	INDETERMINATE	1	TRUE	0	0.358477172786906	2		430	360	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864702	68864702	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064364-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	41	393	0	ENST00000288368.4:c.73G>T	p.Val25Leu	p.V25L	ENST00000288368	NM_024870.2	25	Gtg/Ttg	1/40	0.309148102436609	1	FACETS	0.663	0.555	0.782	0.663	0.555	0.782	SUBCLONAL	1	TRUE	0	0.358477172786906	1		393	283	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913381	NA	P-0064367-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	39	567	0	ENST00000304494.5:c.322G>A	p.Asp108Asn	p.D108N	ENST00000304494	NM_000077.4	108	Gat/Aat	2/3	1	2	FACETS	0.935	0.773	1	0.935	0.773	1	CLONAL	1	TRUE	1	0.13	2		567	642	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519927	NA	P-0064369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	55	220	0	ENST00000263967.3:c.1625A>T	p.Glu542Val	p.E542V	ENST00000263967	NM_006218.2	542	gAa/gTa	10/21	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.508697239013264	2		220	176	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0064369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	8	396	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	0.085	0.054	0.126	0.085	0.054	0.126	SUBCLONAL	1	TRUE	1	0.508697239013264	2		396	368	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720674	89720674	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs886044679	NA	P-0064369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	96	175	0	ENST00000371953.3:c.827del	p.Asn276IlefsTer15	p.N276Ifs*15	ENST00000371953	NM_000314.4	275	gtA/gt	8/9	0.508697239013264	3	FACETS	0.907	0.833	0.98	0.907	0.833	0.98	CLONAL	3	TRUE	0	0.508697239013264	3		175	174	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0064369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	107	560	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.508697239013264	2		560	415	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266112	41266112	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913228	NA	P-0064369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	124	512	0	ENST00000349496.5:c.109T>G	p.Ser37Ala	p.S37A	ENST00000349496	NM_001904.3	37	Tct/Gct	3/15	1	2	FACETS	0.995	0.905	1	0.995	0.905	1	CLONAL	1	TRUE	1	0.508697239013264	2		512	490	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0064370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	105	516	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.489199740688377	5	FACETS	1	0.933	1	0.692	0.626	0.76	CLONAL	2	TRUE	2	0.515722714542155	5		516	348	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	180	612	0				ENST00000310581	NM_198253.2	-/1132			0.515722714542155	5	FACETS	0.998	0.941	1	0.998	0.941	1	CLONAL	4	TRUE	1	0.515722714542155	5		612	310	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059260	27059260	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	340	347	0	ENST00000324856.7:c.1897C>T	p.Gln633Ter	p.Q633*	ENST00000324856	NM_006015.4	633	Cag/Tag	4/20	0.515722714542155	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.515722714542155	3		347	490	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442932	49442932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886049484	NA	P-0064370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	125	398	0	ENST00000301067.7:c.3976C>T	p.Arg1326Trp	p.R1326W	ENST00000301067	NM_003482.3	1326	Cgg/Tgg	12/54	0.489199740688377	5	FACETS	1	0.96	1	0.37	0.335	0.407	CLONAL	1	TRUE	2	0.515722714542155	5		398	774	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864138	57864138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	237	558	0	ENST00000228682.2:c.1615C>T	p.Leu539Phe	p.L539F	ENST00000228682	NM_005269.2	539	Ctt/Ttt	12/12	0.489199740688377	5	FACETS	1	0.954	1	0.683	0.639	0.727	CLONAL	2	TRUE	2	0.515722714542155	5		558	796	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828006	72828006	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	125	428	0	ENST00000268489.5:c.8575A>G	p.Thr2859Ala	p.T2859A	ENST00000268489	NM_006885.3	2859	Acg/Gcg	9/10	0.515722714542155	3	FACETS	1	0.945	1	0.528	0.48	0.579	CLONAL	1	TRUE	1	0.515722714542155	3		428	577	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562716	29562716	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876660667	NA	P-0064370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	176	337	0	ENST00000356175.3:c.3796G>C	p.Glu1266Gln	p.E1266Q	ENST00000356175	NM_000267.3	1266	Gaa/Caa	28/57	0.496261432740176	4	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	2	0.515722714542155	4		337	501	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29120997	29120997	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	58	308	0	ENST00000328354.6:c.560C>G	p.Ser187Cys	p.S187C	ENST00000328354	NM_007194.3	187	tCt/tGt	4/15	0.191092473216437	5	FACETS	1	0.951	1	0.41	0.355	0.47	INDETERMINATE	1	TRUE	2	0.515722714542155	5		308	324	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508733	106508733	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	289	462	0	ENST00000359195.3:c.727G>T	p.Ala243Ser	p.A243S	ENST00000359195	NM_002649.2	243	Gcc/Tcc	2/11	0.515722714542155	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.515722714542155	2		462	501	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	227	239	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	0.307007516016104	2	FACETS	0.917	0.877	0.955			1	INDETERMINATE	3	TRUE	NA	0.515722714542155	2		239	320	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023637	27023638	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTCCAAGCCGC	novel	NA	P-0064371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	55	523	0	ENST00000324856.7:c.748_758dup	p.Ser255ArgfsTer112	p.S255Rfs*112	ENST00000324856	NM_006015.4	248	ggc/ggCTCCAAGCCGCc	1/20	0.410373968976635	1	FACETS	0.826	0.713	0.946	0.826	0.713	0.946	CLONAL	1	TRUE	0	0.410373968976635	1		523	258	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088706	27088706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	75	476	0	ENST00000324856.7:c.2315C>T	p.Ser772Phe	p.S772F	ENST00000324856	NM_006015.4	772	tCt/tTt	7/20	0.410373968976635	1	FACETS	0.981	0.869	1	0.981	0.869	1	CLONAL	1	TRUE	0	0.410373968976635	1		476	296	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828330	50828330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	35	435	0	ENST00000398568.2:c.2668G>A	p.Asp890Asn	p.D890N	ENST00000398568	NM_001042412.1	890	Gat/Aat	17/18	1	2	FACETS	0.437	0.359	0.526	0.437	0.359	0.526	SUBCLONAL	1	TRUE	1	0.410373968976635	2		435	390	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220631	1220632	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0064371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	108	544	0	ENST00000326873.7:c.649_650insT	p.Pro217LeufsTer49	p.P217Lfs*49	ENST00000326873	NM_000455.4	217	ccg/cTcg	5/10	0.410373968976635	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.410373968976635	1		544	328	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610488	10610498	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGCTGAGCC	CTGGCTGAGCC	-	novel	NA	P-0064371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	144	520	0	ENST00000171111.5:c.212_222del	p.Arg71ProfsTer4	p.R71Pfs*4	ENST00000171111	NM_203500.1	71	cGGCTCAGCCAG/c	2/6	0.410373968976635	1	FACETS	0.781	0.722	0.841	1	0.99	1	SUBCLONAL	2	TRUE	0	0.410373968976635	1		520	357	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560863	9560863	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	71	528	0	ENST00000353224.5:c.919C>T	p.His307Tyr	p.H307Y	ENST00000353224	NM_177990.2	307	Cat/Tat	4/10	1	2	FACETS	0.933	0.819	1	0.933	0.819	1	CLONAL	1	TRUE	1	0.410373968976635	2		528	371	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087417	27087417	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0064372-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	89	694	0	ENST00000324856.7:c.1991C>G	p.Ser664Ter	p.S664*	ENST00000324856	NM_006015.4	664	tCa/tGa	5/20	1	2	FACETS	0.948	0.843	1	0.948	0.843	1	CLONAL	1	TRUE	1	0.364516890023188	2		694	515	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245922	46245923	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0064372-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	37	590	0	ENST00000334344.6:c.4017_4018del	p.Asn1340LeufsTer12	p.N1340Lfs*12	ENST00000334344	NM_152641.2	1339	cAG/c	15/21	1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	1	0.364516890023188	2		590	197	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100143	30100143	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064372-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	52	563	0	ENST00000331968.5:c.1477G>T	p.Glu493Ter	p.E493*	ENST00000331968	NM_002742.2	493	Gaa/Taa	10/18	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.364516890023188	2		563	280	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2047314	2047321	+	frameshift_variant	Frame_Shift_Del	DEL	CGCAGCCG	CGCAGCCG	-	novel	NA	P-0064372-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	12	144	0	ENST00000349721.2:c.885_892del	p.Gln296ArgfsTer59	p.Q296Rfs*59	ENST00000349721	NM_003070.3	292	ccCGCAGCCGcg/cccg	5/34	1	2	FACETS	0.573	0.405	0.774	0.573	0.405	0.774	SUBCLONAL	1	TRUE	1	0.364516890023188	2		144	115	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064373-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	11	612	0				ENST00000310581	NM_198253.2	-/1132			0.3	0	FACETS	0.511	0.354	0.705			1	SUBCLONAL	1	TRUE	0	0.21	0		612	162	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023408	27023408	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064373-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	43	666	0	ENST00000324856.7:c.514C>T	p.Gln172Ter	p.Q172*	ENST00000324856	NM_006015.4	172	Caa/Taa	1/20	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.21	2		666	357	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230772	46230772	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064373-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	21	390	0	ENST00000334344.6:c.1021G>T	p.Glu341Ter	p.E341*	ENST00000334344	NM_152641.2	341	Gag/Tag	8/21	0.170640820834149	3	FACETS	0.58	0.446	0.737	0.29	0.223	0.369	SUBCLONAL	1	TRUE	1	0.21	3		390	381	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145094	58145094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064373-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	41	799	0	ENST00000257904.6:c.250G>A	p.Asp84Asn	p.D84N	ENST00000257904	NM_000075.3	84	Gac/Aac	3/8	0.170640820834149	3	FACETS	0.552	0.458	0.657	0.276	0.229	0.329	SUBCLONAL	1	TRUE	1	0.21	3		799	782	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41999925	41999925	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0064373-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	20	303	0	ENST00000219905.7:c.2189-1G>A		p.X730_splice	ENST00000219905	NM_001164273.1	730			0.0944733049633826	3	FACETS	0.806	0.618	1	0.403	0.309	0.514	INDETERMINATE	1	TRUE	1	0.21	3		303	261	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069316	30069316	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064373-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	36	700	0	ENST00000338641.4:c.1181A>T	p.Glu394Val	p.E394V	ENST00000338641	NM_000268.3	394	gAg/gTg	12/16	1	2	FACETS	0.82	0.675	0.983	0.82	0.675	0.983	CLONAL	1	TRUE	1	0.21	2		700	418	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041720	47041720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064373-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	10	329	0	ENST00000377604.3:c.1945C>T	p.Gln649Ter	p.Q649*	ENST00000377604	NM_001204468.1	649	Caa/Taa	17/24	0.3	2	FACETS	0.488	0.331	0.686	0.244	0.165	0.343	SUBCLONAL	1	TRUE	0	0.21	2		329	195	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150923236	150923236	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	67	682	0	ENST00000271640.5:c.1883A>C	p.Lys628Thr	p.K628T	ENST00000271640	NM_001145415.1	628	aAg/aCg	13/22	1	2	FACETS	0.538	0.467	0.615	0.538	0.467	0.615	SUBCLONAL	1	TRUE	1	0.37970022842172	2		682	656	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860062	57860062	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	59	633	0	ENST00000228682.2:c.802T>G	p.Phe268Val	p.F268V	ENST00000228682	NM_005269.2	268	Ttc/Gtc	8/12	1	2	FACETS	0.539	0.463	0.621	0.539	0.463	0.621	SUBCLONAL	1	TRUE	1	0.37970022842172	2		633	577	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519078	103519078	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	29	537	0	ENST00000355739.4:c.2416A>C	p.Thr806Pro	p.T806P	ENST00000355739	NM_000123.3	806	Acc/Ccc	11/15	1	2	FACETS	0.313	0.251	0.384	0.313	0.251	0.384	SUBCLONAL	1	TRUE	1	0.37970022842172	2		537	488	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560322	95560322	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1423918933	NA	P-0064374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	88	518	0	ENST00000393063.1:c.5267A>G	p.Lys1756Arg	p.K1756R	ENST00000393063	NM_030621.3	1756	aAg/aGg	25/28	1	2	FACETS	0.829	0.736	0.928	0.829	0.736	0.928	CLONAL	1	TRUE	1	0.37970022842172	2		518	559	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50788264	50788264	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	28	371	0	ENST00000307179.4:c.2878A>G	p.Ser960Gly	p.S960G	ENST00000307179		960	Agt/Ggt	17/20	1	2	FACETS	0.493	0.395	0.605	0.493	0.395	0.605	SUBCLONAL	1	TRUE	1	0.37970022842172	2		371	299	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490375	29490375	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	45	504	0	ENST00000356175.3:c.460T>G	p.Phe154Val	p.F154V	ENST00000356175	NM_000267.3	154	Ttt/Gtt	4/57	1	2	FACETS	0.529	0.445	0.622	0.529	0.445	0.622	SUBCLONAL	1	TRUE	1	0.37970022842172	2		504	448	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690030	33690030	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	47	658	0	ENST00000308377.4:c.797A>G	p.Asp266Gly	p.D266G	ENST00000308377	NM_152270.3	266	gAc/gGc	2/5	1	2	FACETS	0.5	0.422	0.586	0.5	0.422	0.586	SUBCLONAL	1	TRUE	1	0.37970022842172	2		658	495	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59878729	59878729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	34	521	0	ENST00000259008.2:c.1025G>A	p.Ser342Asn	p.S342N	ENST00000259008	NM_032043.2	342	aGc/aAc	8/20	1	2	FACETS	0.493	0.403	0.594	0.493	0.403	0.594	SUBCLONAL	1	TRUE	1	0.37970022842172	2		521	363	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219424	5219424	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	129	684	1	ENST00000357368.4:c.3820del	p.Gln1274SerfsTer13	p.Q1274Sfs*13	ENST00000357368	NM_002850.3	1274	Cag/ag	23/38	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.37970022842172	2		685	542	SUCCESS
AXL	558	MSKCC	GRCh37	19	41759574	41759574	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	52	590	0	ENST00000301178.4:c.1997A>T	p.Lys666Met	p.K666M	ENST00000301178	NM_021913.4	666	aAg/aTg	17/20	1	2	FACETS	0.453	0.386	0.528	0.453	0.386	0.528	SUBCLONAL	1	TRUE	1	0.37970022842172	2		590	604	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610460	215610460	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	29	422	0	ENST00000260947.4:c.1796A>C	p.Glu599Ala	p.E599A	ENST00000260947	NM_000465.2	599	gAg/gCg	8/11	1	2	FACETS	0.404	0.324	0.495	0.404	0.324	0.495	SUBCLONAL	1	TRUE	1	0.37970022842172	2		422	378	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419872	41419872	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	68	657	0	ENST00000373198.4:c.449A>G	p.Glu150Gly	p.E150G	ENST00000373198	NM_133170.3	150	gAg/gGg	3/32	1	2	FACETS	0.544	0.472	0.62	0.544	0.472	0.62	SUBCLONAL	1	TRUE	1	0.37970022842172	2		657	659	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164758	36164758	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	95	817	0	ENST00000300305.3:c.1117T>A	p.Ser373Thr	p.S373T	ENST00000300305		373	Tcg/Acg	8/8	1	2	FACETS	0.672	0.598	0.75	0.672	0.598	0.75	SUBCLONAL	1	TRUE	1	0.37970022842172	2		817	745	SUCCESS
APC	324	MSKCC	GRCh37	5	112155041	112155041	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	28	522	0	ENST00000257430.4:c.1312A>C	p.Met438Leu	p.M438L	ENST00000257430	NM_000038.5	438	Atg/Ctg	10/16	0.37970022842172	1	FACETS	0.326	0.261	0.401	0.326	0.261	0.401	SUBCLONAL	1	TRUE	0	0.37970022842172	1		522	366	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672002	30672002	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	39	780	0	ENST00000376406.3:c.4958T>G	p.Val1653Gly	p.V1653G	ENST00000376406	NM_014641.2	1653	gTt/gGt	10/15	1	2	FACETS	0.313	0.259	0.374	0.313	0.259	0.374	SUBCLONAL	1	TRUE	1	0.37970022842172	2		780	656	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520100	106520100	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	22	351	0	ENST00000359195.3:c.2528T>G	p.Leu843Arg	p.L843R	ENST00000359195	NM_002649.2	843	cTt/cGt	6/11	0.37970022842172	1	FACETS	0.417	0.324	0.524	0.417	0.324	0.524	SUBCLONAL	1	TRUE	0	0.37970022842172	1		351	225	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874232	151874232	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1485265672	NA	P-0064374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	29	550	0	ENST00000262189.6:c.8306A>G	p.Lys2769Arg	p.K2769R	ENST00000262189	NM_170606.2	2769	aAg/aGg	38/59	0.37970022842172	1	FACETS	0.43	0.346	0.525	0.43	0.346	0.525	SUBCLONAL	1	TRUE	0	0.37970022842172	1		550	288	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820349	139820349	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	56	555	0	ENST00000247668.2:c.1502T>C	p.Leu501Pro	p.L501P	ENST00000247668	NM_021138.3	501	cTc/cCc	11/11	0.185893534529856	4	FACETS	0.735	0.629	0.85	0.184	0.157	0.213	INDETERMINATE	1	TRUE	0	0.37970022842172	4		555	554	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0064376-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	102	580	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.224669128187865	2		581	638	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0064376-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	62	374	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.876	0.756	1	0.876	0.756	1	CLONAL	1	TRUE	1	0.224669128187865	2		374	630	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0064376-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	15	292	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.224669128187865	1	FACETS	0.593	0.434	0.782	0.593	0.434	0.782	SUBCLONAL	1	TRUE	0	0.224669128187865	1		292	200	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604668	48604668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064376-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	55	537	0	ENST00000342988.3:c.1490G>A	p.Arg497His	p.R497H	ENST00000342988	NM_005359.5	497	cGc/cAc	12/12	0.224669128187865	1	FACETS	0.919	0.787	1	0.919	0.787	1	CLONAL	1	TRUE	0	0.224669128187865	1		537	473	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514758	103514758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143667470	NA	P-0064376-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	86	668	0	ENST00000355739.4:c.1259G>A	p.Arg420His	p.R420H	ENST00000355739	NM_000123.3	420	cGt/cAt	8/15	0.224669128187865	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.224669128187865	1		668	547	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920753	100920753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064376-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	39	414	0	ENST00000325455.5:c.2395C>T	p.Leu799Phe	p.L799F	ENST00000325455	NM_001202474.3	799	Ctt/Ttt	6/8	0.173699584847078	2	FACETS	1	0.933	1	0.627	0.522	0.742	CLONAL	1	TRUE	0	0.224669128187865	2		414	277	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443695	29443695	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs863225281	NA	P-0064377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	106	524	0	ENST00000389048.3:c.3522C>A	p.Phe1174Leu	p.F1174L	ENST00000389048	NM_004304.4	1174	ttC/ttA	23/29	0.533941759856114	3	FACETS	0.97	0.873	1	0.485	0.436	0.536	CLONAL	1	TRUE	1	0.538688383997803	3		524	515	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064378-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	43	612	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.769	0.657	0.888	0.769	0.657	0.888	SUBCLONAL	1	TRUE	1	0.787779566816221	2		612	142	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264515	30264515	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs933237275	NA	P-0064378-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	52	327	0	ENST00000322652.5:c.250G>A	p.Glu84Lys	p.E84K	ENST00000322652	NM_015355.2	84	Gag/Aag	1/16	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.787779566816221	2		327	120	SUCCESS
ALK	238	MSKCC	GRCh37	2	29430040	29430040	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064378-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	85	440	0	ENST00000389048.3:c.3935C>A	p.Thr1312Lys	p.T1312K	ENST00000389048	NM_004304.4	1312	aCa/aAa	26/29	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.787779566816221	2		440	212	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0064378-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	203	737	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.787779566816221	2		737	399	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565919	55565919	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064378-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	73	359	0	ENST00000288135.5:c.743G>C	p.Arg248Thr	p.R248T	ENST00000288135	NM_000222.2	248	aGa/aCa	4/21	1	2	FACETS	0.95	0.848	1	0.95	0.848	1	CLONAL	1	TRUE	1	0.787779566816221	2		359	195	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247367	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747241612	NA	P-0064378-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	105	442	0	ENST00000281708.4:c.1435C>G	p.Arg479Gly	p.R479G	ENST00000281708	NM_033632.3	479	Cga/Gga	10/12	1	2	FACETS	0.995	0.906	1	0.995	0.906	1	CLONAL	1	TRUE	1	0.787779566816221	2		442	268	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0064385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	203	631	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.327200582331995	3	FACETS	1	0.988	1	0.815	0.765	0.865	CLONAL	2	TRUE	0	0.461543853479027	3		631	443	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913294	NA	P-0064385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	17	288	0	ENST00000371953.3:c.518G>C	p.Arg173Pro	p.R173P	ENST00000371953	NM_000314.4	173	cGc/cCc	6/9	0.313213153336653	3	FACETS	0.2	0.149	0.262	0.067	0.049	0.088	SUBCLONAL	1	TRUE	0	0.461543853479027	3		288	453	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262447	16262635	+	inframe_deletion	In_Frame_Del	DEL	GATGCCAAAGCTGCCCCCACCCCCACCCCTGCCCCCGTCCCTGTCCCTGTCCCCCTTCCTGCCCCTGCTCCTGCCCCTCATGGTGAGGCCCGTATCCTCACAGTTACCCCCAGTAACCAACTCCAGGGGCTGCCTCTGACCCCTCCTGTGGTGGTGACCCATGGGGTGCAGATTGTGCACTCCAGCGGG	GATGCCAAAGCTGCCCCCACCCCCACCCCTGCCCCCGTCCCTGTCCCTGTCCCCCTTCCTGCCCCTGCTCCTGCCCCTCATGGTGAGGCCCGTATCCTCACAGTTACCCCCAGTAACCAACTCCAGGGGCTGCCTCTGACCCCTCCTGTGGTGGTGACCCATGGGGTGCAGATTGTGCACTCCAGCGGG	-	novel	NA	P-0064385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	155	444	0	ENST00000375759.3:c.9714_9902del	p.Asp3238_Gly3300del	p.D3238_G3300del	ENST00000375759	NM_015001.2	3238	GATGCCAAAGCTGCCCCCACCCCCACCCCTGCCCCCGTCCCTGTCCCTGTCCCCCTTCCTGCCCCTGCTCCTGCCCCTCATGGTGAGGCCCGTATCCTCACAGTTACCCCCAGTAACCAACTCCAGGGGCTGCCTCTGACCCCTCCTGTGGTGGTGACCCATGGGGTGCAGATTGTGCACTCCAGCGGG/-	11/15	0.481285817582422	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.461543853479027	3		444	359	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420195	420195	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	259	372	0	ENST00000399788.2:c.3072G>T	p.Glu1024Asp	p.E1024D	ENST00000399788	NM_001042603.1	1024	gaG/gaT	21/28	0.439372447457291	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.461543853479027	4		372	743	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436186	56436186	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0064385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	166	372	0	ENST00000407977.2:c.953-2A>C		p.X318_splice	ENST00000407977		318			0.329356880916161	3	FACETS	1	0.982	1	0.775	0.721	0.828	CLONAL	2	TRUE	0	0.461543853479027	3		372	381	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414661	56414661	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	154	353	0	ENST00000348428.3:c.2062T>G	p.Leu688Val	p.L688V	ENST00000348428	NM_006785.3	688	Tta/Gta	17/17	0.221654602262886	5	FACETS	1	0.972	1	0.747	0.688	0.807	INDETERMINATE	2	TRUE	2	0.461543853479027	5		353	504	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295961	1295961	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0064385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	495	665	0				ENST00000310581	NM_198253.2	-/1132			0.461543853479027	7	FACETS	1	0.982	1			1	CLONAL	5	TRUE	NA	0.461543853479027	7		665	898	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040044	180040044	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	126	531	0	ENST00000261937.6:c.3398G>T	p.Arg1133Met	p.R1133M	ENST00000261937	NM_182925.4	1133	aGg/aTg	25/30	0.42587288447678	2	FACETS	0.941	0.867	1	0.941	0.867	1	CLONAL	2	TRUE	0	0.461543853479027	2		531	290	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939396	76939396	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	49	511	2	ENST00000373344.5:c.1352C>A	p.Ala451Asp	p.A451D	ENST00000373344	NM_000489.3	451	gCt/gAt	9/35	0.183362762444812	0	FACETS	0.626	0.532	0.728			1	INDETERMINATE	1	TRUE	0	0.309200544078542	0		513	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577514	7577515	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0064386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	171	466	0	ENST00000269305.4:c.766dup	p.Thr256AsnfsTer8	p.T256Nfs*8	ENST00000269305	NM_001126112.2	256	aca/aAca	7/11	0.309200544078542	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.309200544078542	2		466	480	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428619	49428619	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	40	651	0	ENST00000301067.7:c.10331T>A	p.Ile3444Asn	p.I3444N	ENST00000301067	NM_003482.3	3444	aTt/aAt	35/54	0.309200544078542	3	FACETS	0.435	0.361	0.519			1	SUBCLONAL	1	TRUE	NA	0.309200544078542	3		651	686	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438225	110438225	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	42	490	0	ENST00000375856.3:c.176A>T	p.Glu59Val	p.E59V	ENST00000375856	NM_003749.2	59	gAg/gTg	1/2	0.309200544078542	2	FACETS	0.65	0.543	0.768	0.325	0.271	0.384	SUBCLONAL	1	TRUE	0	0.309200544078542	2		490	418	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169514	11169514	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	177	493	0	ENST00000358026.2:c.4680C>A	p.Asp1560Glu	p.D1560E	ENST00000358026	NM_001128849.1	1560	gaC/gaA	33/36	0.244101910256687	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.309200544078542	4		493	625	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856389	45856389	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1416467153	NA	P-0064386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	27	607	0	ENST00000391945.4:c.1783A>G	p.Ile595Val	p.I595V	ENST00000391945	NM_000400.3	595	Atc/Gtc	19/23	0.309200544078542	2	FACETS	0.327	0.259	0.405	0.164	0.129	0.203	SUBCLONAL	1	TRUE	0	0.309200544078542	2		607	534	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888710	76888710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1356091230	NA	P-0064386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	37	377	0	ENST00000373344.5:c.5119G>A	p.Ala1707Thr	p.A1707T	ENST00000373344	NM_000489.3	1707	Gct/Act	19/35	0.183362762444812	0	FACETS	0.588	0.487	0.7			1	INDETERMINATE	1	TRUE	0	0.309200544078542	0		377	281	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40876390	40876394	+	frameshift_variant	Frame_Shift_Del	DEL	CTCAT	CTCAT	ACAG	novel	NA	P-0064386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	66	512	1	ENST00000428826.2:c.295_299delinsCTGT	p.Met99LeufsTer4	p.M99Lfs*4	ENST00000428826		99	ATGAGg/CTGTg	5/21	0.309200544078542	5	FACETS	0.919	0.797	1	0.184	0.159	0.211	CLONAL	1	TRUE	0	0.309200544078542	5		513	680	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	16	612	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.61	0.451	0.801	0.61	0.451	0.801	SUBCLONAL	1	TRUE	1	0.19	2		612	276	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692896	89692896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123322	NA	P-0064387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	39	274	0	ENST00000371953.3:c.380G>A	p.Gly127Glu	p.G127E	ENST00000371953	NM_000314.4	127	gGa/gAa	5/9	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.19	2		274	397	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692899	89692899	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	21	294	0	ENST00000371953.3:c.383A>C	p.Lys128Thr	p.K128T	ENST00000371953	NM_000314.4	128	aAg/aCg	5/9	1	2	FACETS	0.52	0.4	0.661	0.52	0.4	0.661	SUBCLONAL	1	TRUE	1	0.19	2		294	425	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47595191	47595191	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	30	437	0	ENST00000430070.2:c.896A>C	p.His299Pro	p.H299P	ENST00000430070	NM_018095.4	299	cAt/cCt	4/4	1	2	FACETS	0.529	0.425	0.648	0.529	0.425	0.648	SUBCLONAL	1	TRUE	1	0.19	2		437	597	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946384	71946384	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs748648191	NA	P-0064387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	67	535	0	ENST00000298229.2:c.2548C>T	p.Gln850Ter	p.Q850*	ENST00000298229	NM_001567.3	850	Caa/Taa	23/28	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.19	2		535	686	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339577	339577	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	39	370	0	ENST00000262320.3:c.2325del	p.Ser776ValfsTer25	p.S776Vfs*25	ENST00000262320	NM_003502.3	775	ggG/gg	10/11	1	2	FACETS	0.811	0.672	0.967	0.811	0.672	0.967	CLONAL	1	TRUE	1	0.19	2		370	506	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285935	39285935	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	36	282	0	ENST00000402219.2:c.224A>G	p.Gln75Arg	p.Q75R	ENST00000402219	NM_005633.3	75	cAa/cGa	3/23	1	2	FACETS	0.892	0.733	1	0.892	0.733	1	CLONAL	1	TRUE	1	0.19	2		282	425	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163413	47163414	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0064387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	43	398	0	ENST00000409792.3:c.2711_2712dup	p.Ser905HisfsTer9	p.S905Hfs*9	ENST00000409792	NM_014159.6	904	-/CA	3/21	1	2	FACETS	0.747	0.624	0.884	0.747	0.624	0.884	SUBCLONAL	1	TRUE	1	0.19	2		398	606	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976906	55976906	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	32	365	0	ENST00000263923.4:c.1006A>G	p.Met336Val	p.M336V	ENST00000263923	NM_002253.2	336	Atg/Gtg	8/30	1	2	FACETS	0.61	0.494	0.742	0.61	0.494	0.742	SUBCLONAL	1	TRUE	1	0.19	2		365	552	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22412935	22412935	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	64	328	0	ENST00000344548.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000344548	NM_001039802.1	61	cAa/cGa	5/7	1	2	FACETS	0.991	0.863	1	0.991	0.863	1	CLONAL	1	TRUE	1	0.35	2		328	369	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0064394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	94	553	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.280500163516984	4	FACETS	1	0.902	1	0.508	0.451	0.568	CLONAL	1	TRUE	2	0.280500163516984	4		553	845	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591117	67591118	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0064394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	100	490	0	ENST00000274335.5:c.1711_1712del	p.Ile571ProfsTer30	p.I571Pfs*30	ENST00000274335		570	ctTAtc/cttc	12/15	0.280500163516984	2	FACETS	1	0.964	1	0.587	0.525	0.653	CLONAL	1	TRUE	0	0.280500163516984	2		490	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578483	7578484	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0064394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	252	676	0	ENST00000269305.4:c.446_447insA	p.Thr150HisfsTer31	p.T150Hfs*31	ENST00000269305	NM_001126112.2	149	tcc/tcAc	5/11	0.280500163516984	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.280500163516984	3		676	915	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	311	344	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.694230150763529	3	FACETS	0.993	0.96	1	0.993	0.96	1	CLONAL	3	TRUE	0	0.694230150763529	3		344	405	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135385	30135385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	111	426	0	ENST00000331968.5:c.433C>T	p.Arg145Cys	p.R145C	ENST00000331968	NM_002742.2	145	Cgt/Tgt	3/18	0.694230150763529	3	FACETS	0.907	0.82	0.998	0.453	0.41	0.499	CLONAL	1	TRUE	1	0.694230150763529	3		426	475	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438475	52438475	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	66	557	0	ENST00000460680.1:c.1244C>T	p.Ala415Val	p.A415V	ENST00000460680	NM_004656.3	415	gCc/gTc	12/17	0.331946197725919	2	FACETS	0.427	0.372	0.487	0.214	0.186	0.244	INDETERMINATE	1	TRUE	0	0.694230150763529	2		557	445	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249471	153249471	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	125	465	0	ENST00000281708.4:c.1307G>A	p.Ser436Asn	p.S436N	ENST00000281708	NM_033632.3	436	aGt/aAt	9/12	1	2	FACETS	0.96	0.878	1	0.96	0.878	1	CLONAL	1	TRUE	1	0.694230150763529	2		465	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0064396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	174	599	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.340464861628311	2	FACETS	0.771	0.716	0.826	0.771	0.716	0.826	SUBCLONAL	2	TRUE	0	0.485504185038653	2		599	465	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448297	56448298	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1567880599	NA	P-0064396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	204	697	3	ENST00000407977.2:c.349dup	p.Arg117ProfsTer8	p.R117Pfs*8	ENST00000407977		117	cgc/cCgc	3/10	0.340464861628311	2	FACETS	0.76	0.71	0.811	0.76	0.71	0.811	SUBCLONAL	2	TRUE	0	0.485504185038653	2		700	553	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133731	2133731	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs62642481	NA	P-0064396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	106	687	0	ENST00000219476.3:c.3919G>A	p.Glu1307Lys	p.E1307K	ENST00000219476	NM_000548.3	1307	Gag/Aag	33/42	0.300706067129437	3	FACETS	0.898	0.807	0.995	0.449	0.403	0.498	CLONAL	1	TRUE	1	0.485504185038653	3		687	604	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423602	88423602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767450627	NA	P-0064396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	134	518	0	ENST00000360948.2:c.2233C>T	p.Arg745Trp	p.R745W	ENST00000360948	NM_001012338.2	745	Cgg/Tgg	18/19	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.485504185038653	2		518	400	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486217	99486217	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	78	604	0	ENST00000268035.6:c.3523C>G	p.Pro1175Ala	p.P1175A	ENST00000268035	NM_000875.3	1175	Ccc/Gcc	19/21	1	2	FACETS	0.611	0.538	0.689	0.611	0.538	0.689	SUBCLONAL	1	TRUE	1	0.485504185038653	2		604	526	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781812	3781812	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	66	619	0	ENST00000262367.5:c.4855C>T	p.Gln1619Ter	p.Q1619*	ENST00000262367	NM_004380.2	1619	Cag/Tag	29/31	0.300706067129437	3	FACETS	0.664	0.577	0.757	0.332	0.288	0.379	SUBCLONAL	1	TRUE	1	0.485504185038653	3		619	509	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924223	11924223	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	85	749	0	ENST00000353533.5:c.20G>C	p.Ser7Thr	p.S7T	ENST00000353533	NM_003010.3	7	aGc/aCc	1/11	0.340464861628311	2	FACETS	0.826	0.734	0.923	0.413	0.367	0.462	CLONAL	1	TRUE	0	0.485504185038653	2		749	424	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198189	185198189	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	112	585	0	ENST00000265026.3:c.2671C>T	p.Gln891Ter	p.Q891*	ENST00000265026	NM_004721.4	891	Cag/Tag	13/14	0.300706067129437	3	FACETS	1	0.921	1	0.512	0.462	0.565	CLONAL	1	TRUE	1	0.485504185038653	3		585	560	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415702	152415702	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	159	548	0	ENST00000206249.3:c.1552A>G	p.Ser518Gly	p.S518G	ENST00000206249	NM_000125.3	518	Agt/Ggt	7/8	0.345701343603167	2	FACETS	0.751	0.695	0.808	0.751	0.695	0.808	SUBCLONAL	2	TRUE	0	0.485504185038653	2		548	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0064397-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	62	712	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	NA	2	FACETS	0.708	0.61	0.815			1	INDETERMINATE	1	TRUE	NA	0.2	2		712	876	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341250	341250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371459615	NA	P-0064397-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	44	479	0	ENST00000262320.3:c.2234C>T	p.Ala745Val	p.A745V	ENST00000262320	NM_003502.3	745	gCg/gTg	9/11	1	2	FACETS	0.838	0.703	0.988	0.838	0.703	0.988	CLONAL	1	TRUE	1	0.2	2		479	525	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0064397-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	85	558	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.2	2		558	705	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2086862	2086862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064397-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	43	585	0	ENST00000349721.2:c.2560C>T	p.His854Tyr	p.H854Y	ENST00000349721	NM_003070.3	854	Cac/Tac	18/34	1	2	FACETS	0.6	0.5	0.71	0.6	0.5	0.71	SUBCLONAL	1	TRUE	1	0.2	2		585	717	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860082	152860082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs918989098	NA	P-0064397-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	37	222	0	ENST00000406277.2:c.346C>T	p.Arg116Trp	p.R116W	ENST00000406277	NM_152274.4	116	Cgg/Tgg	5/7	1		FACETS		0.832	1				CLONAL	1	TRUE	0	0.2	1		222	331	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0064398-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	286	482	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.579100558759639	3	FACETS	0.969	0.929	1	0.969	0.929	1	CLONAL	3	TRUE	0	0.579100558759639	3		482	438	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792314	33792314	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064398-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	109	494	0	ENST00000498907.2:c.1007A>G	p.Asp336Gly	p.D336G	ENST00000498907	NM_004364.3	336	gAc/gGc	1/1	0.579100558759639	5	FACETS	0.998	0.897	1	0.333	0.299	0.369	CLONAL	1	TRUE	2	0.579100558759639	5		494	705	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105258937	105258937	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs368797346	NA	P-0064398-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	95	397	0	ENST00000349310.3:c.44G>A	p.Arg15Gln	p.R15Q	ENST00000349310	NM_001014432.1	15	cGa/cAa	3/15	0.571721410550122	3	FACETS	1	0.945	1	0.541	0.485	0.6	CLONAL	1	TRUE	1	0.579100558759639	3		397	391	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111663	56111663	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs982925395	NA	P-0064398-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	231	484	0	ENST00000399503.3:c.263C>T	p.Ser88Leu	p.S88L	ENST00000399503	NM_005921.1	88	tCg/tTg	1/20	0.579100558759639	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.579100558759639	3		484	490	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0064399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	93	287	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.370876735810799	2		287	495	SUCCESS
APC	324	MSKCC	GRCh37	5	112175952	112175952	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587783031	NA	P-0064399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	119	521	0	ENST00000257430.4:c.4666del	p.Thr1556LeufsTer9	p.T1556Lfs*9	ENST00000257430	NM_000038.5	1554	gAa/ga	16/16	1	2	FACETS	0.822	0.742	0.906	0.822	0.742	0.906	CLONAL	1	TRUE	1	0.370876735810799	2		521	781	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0064399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	233	515	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.370876735810799	2	FACETS	0.982	0.921	1	0.982	0.921	1	CLONAL	2	TRUE	0	0.370876735810799	2		515	640	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575089	48575089	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	122	453	0	ENST00000342988.3:c.283T>C	p.Tyr95His	p.Y95H	ENST00000342988	NM_005359.5	95	Tat/Cat	3/12	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.370876735810799	2		453	651	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0064399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	104	416	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.370876735810799	2		416	529	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952086	178952086	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519932	NA	P-0064399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	116	501	0	ENST00000263967.3:c.3141T>G	p.His1047Gln	p.H1047Q	ENST00000263967	NM_006218.2	1047	caT/caG	21/21	1	2	FACETS	0.974	0.88	1	0.974	0.88	1	CLONAL	1	TRUE	1	0.370876735810799	2		501	642	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706974	117706974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776027945	NA	P-0064399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	139	504	0	ENST00000368508.3:c.2176G>A	p.Val726Ile	p.V726I	ENST00000368508	NM_002944.2	726	Gtt/Att	15/43	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.370876735810799	2		504	680	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803144	1803144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219348193	NA	P-0064399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	93	682	0	ENST00000260795.2:c.496G>A	p.Val166Met	p.V166M	ENST00000260795		166	Gtg/Atg	4/17	1	2	FACETS	0.878	0.783	0.98	0.878	0.783	0.98	CLONAL	1	TRUE	1	0.370876735810799	2		682	571	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262538	16262538	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375130938	NA	P-0064399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	113	482	1	ENST00000375759.3:c.9803G>A	p.Arg3268His	p.R3268H	ENST00000375759	NM_015001.2	3268	cGt/cAt	11/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.370876735810799	2		483	543	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068433	26068433	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0064399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	84	210	0	ENST00000435504.4:c.58-1G>A		p.X20_splice	ENST00000435504		20			0.370876735810799	2	FACETS	0.784	0.7	0.871	0.784	0.7	0.871	SUBCLONAL	2	TRUE	0	0.370876735810799	2		210	289	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575102	48575102	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	103	469	0	ENST00000342988.3:c.297del	p.Trp99Ter	p.W99*	ENST00000342988	NM_005359.5	99	tGg/tg	3/12	1	2	FACETS	0.889	0.797	0.986	0.889	0.797	0.986	CLONAL	1	TRUE	1	0.370876735810799	2		469	625	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604756	48604756	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	138	593	0	ENST00000342988.3:c.1578A>T	p.Glu526Asp	p.E526D	ENST00000342988	NM_005359.5	526	gaA/gaT	12/12	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.370876735810799	2		593	701	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358999	81358999	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064399-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	103	459	0	ENST00000222390.5:c.962G>T	p.Trp321Leu	p.W321L	ENST00000222390	NM_000601.4	321	tGg/tTg	8/18	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.370876735810799	2		459	550	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0064400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	241	403	0	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.542945687960032	2	FACETS	0.847	0.8	0.895	0.847	0.8	0.895	CLONAL	2	TRUE	0	0.542945687960032	2		403	524	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431178	49431178	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs793888512	NA	P-0064400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	385	716	1	ENST00000301067.7:c.9961C>T	p.Arg3321Ter	p.R3321*	ENST00000301067	NM_003482.3	3321	Cga/Tga	34/54	0.525667554415522	2	FACETS	0.966	0.926	1	0.966	0.926	1	CLONAL	2	TRUE	0	0.542945687960032	2		717	734	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075424	8075424	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374119208	NA	P-0064400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	83	466	0	ENST00000377482.5:c.146C>T	p.Pro49Leu	p.P49L	ENST00000377482	NM_018948.3	49	cCg/cTg	3/4	0.367188028849845	2	FACETS	0.505	0.446	0.568	0.252	0.223	0.284	SUBCLONAL	1	TRUE	0	0.542945687960032	2		466	606	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612974	228612974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756810829	NA	P-0064400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	228	812	0	ENST00000366696.1:c.53G>A	p.Arg18His	p.R18H	ENST00000366696	NM_003493.2	18	cGc/cAc	1/1	0.114623482145467	3	FACETS	1	0.976	1	0.367	0.342	0.393	INDETERMINATE	1	TRUE	0	0.542945687960032	3		812	970	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770035	56770035	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1567782755	NA	P-0064400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	132	429	0	ENST00000337432.4:c.31C>T	p.Gln11Ter	p.Q11*	ENST00000337432	NM_058216.2	11	Cag/Tag	1/9	1	2	FACETS	0.894	0.815	0.976	0.894	0.815	0.976	CLONAL	1	TRUE	1	0.542945687960032	2		429	544	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21343151	21343151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758338373	NA	P-0064400-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	306	448	0	ENST00000215739.8:c.583G>A	p.Gly195Ser	p.G195S	ENST00000215739	NM_006767.3	195	Ggc/Agc	6/21	0.525667554415522	2	FACETS	0.944	0.899	0.989	0.944	0.899	0.989	CLONAL	2	TRUE	0	0.542945687960032	2		448	597	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0064401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	14	457	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	0.526	0.378	0.705	0.526	0.378	0.705	SUBCLONAL	1	TRUE	1	0.12	2		457	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0064401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	15	616	0	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	1	2	FACETS	0.411	0.299	0.546	0.411	0.299	0.546	SUBCLONAL	1	TRUE	1	0.12	2		616	609	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560442	65560442	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	32	424	0	ENST00000358664.4:c.155C>A	p.Ser52Ter	p.S52*	ENST00000358664	NM_002382.4	52	tCa/tAa	3/5	1	2	FACETS	0.975	0.79	1	0.975	0.79	1	CLONAL	1	TRUE	1	0.12	2		424	547	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50815160	50815160	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	27	398	0	ENST00000398568.2:c.1513del	p.Asp505MetfsTer21	p.D505Mfs*21	ENST00000398568	NM_001042412.1	505	Gat/at	9/18	1	2	FACETS	1	0.802	1	1	0.802	1	CLONAL	1	TRUE	1	0.12	2		398	446	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222727	5222727	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746980740	NA	P-0064411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	47	428	0	ENST00000357368.4:c.3076C>T	p.Arg1026Cys	p.R1026C	ENST00000357368	NM_002850.3	1026	Cgc/Tgc	18/38	0.236974010659547	4	FACETS	0.887	0.75	1	0.443	0.375	0.518	CLONAL	1	TRUE	2	0.385528585518904	4		428	381	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0064411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	155	553	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.385528585518904	4	FACETS	0.932	0.857	1	0.932	0.857	1	CLONAL	2	TRUE	2	0.385528585518904	4		553	598	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	113	344	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.385528585518904	4	FACETS	1	0.908	1	1	0.908	1	CLONAL	2	TRUE	2	0.385528585518904	4		344	406	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519896	NA	P-0064411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	105	429	0	ENST00000281708.4:c.1514G>A	p.Arg505His	p.R505H	ENST00000281708	NM_033632.3	505	cGc/cAc	10/12	0.381538343029824	3	FACETS	1	0.973	1	0.62	0.557	0.686	CLONAL	1	TRUE	1	0.385528585518904	3		429	524	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139079	37139079	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	163	541	0	ENST00000373509.5:c.419A>C	p.Gln140Pro	p.Q140P	ENST00000373509	NM_002648.3	140	cAa/cCa	4/6	0.385528585518904	4	FACETS	0.971	0.896	1	0.971	0.896	1	CLONAL	2	TRUE	2	0.385528585518904	4		541	603	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139175	37139175	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	154	584	0	ENST00000373509.5:c.515A>G	p.Asn172Ser	p.N172S	ENST00000373509	NM_002648.3	172	aAc/aGc	4/6	0.385528585518904	4	FACETS	0.844	0.775	0.916	0.844	0.775	0.916	CLONAL	2	TRUE	2	0.385528585518904	4		584	656	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124487049	124487049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	17	246	0	ENST00000357628.3:c.953C>T	p.Ser318Phe	p.S318F	ENST00000357628	NM_015450.2	318	tCt/tTt	12/19	0.385528585518904	4	FACETS	0.359	0.268	0.469	0.18	0.134	0.235	SUBCLONAL	1	TRUE	2	0.385528585518904	4		246	340	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549107	87549107	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	41	436	0	ENST00000277120.3:c.1664T>C	p.Val555Ala	p.V555A	ENST00000277120		555	gTt/gCt	15/19	0.385528585518904	4	FACETS	0.589	0.491	0.699	0.295	0.245	0.35	SUBCLONAL	1	TRUE	2	0.385528585518904	4		436	500	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259397	11259397	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	37	581	0	ENST00000361445.4:c.4171C>G	p.Arg1391Gly	p.R1391G	ENST00000361445	NM_004958.3	1391	Cga/Gga	28/58	0.54697838498619	2	FACETS	0.203	0.166	0.243	0.101	0.083	0.122	SUBCLONAL	1	TRUE	0	0.555907410857299	2		581	657	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100095	27100095	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	396	737	0	ENST00000324856.7:c.3893del	p.Gly1298GlufsTer3	p.G1298Efs*3	ENST00000324856	NM_006015.4	1297	gaG/ga	16/20	0.54697838498619	2	FACETS	0.96	0.921	0.999	0.96	0.921	0.999	CLONAL	2	TRUE	0	0.555907410857299	2		737	742	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0064412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	44	147	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.53487468091763	3	FACETS	0.973	0.843	1	0.648	0.562	0.737	CLONAL	2	TRUE	0	0.555907410857299	3		147	104	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258036	123258036	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519045	NA	P-0064412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	194	367	0	ENST00000358487.5:c.1645A>C	p.Asn549His	p.N549H	ENST00000358487	NM_000141.4	549	Aat/Cat	12/18	0.53487468091763	3	FACETS	0.918	0.858	0.979	0.612	0.572	0.653	CLONAL	2	TRUE	0	0.555907410857299	3		367	486	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608322	28608322	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	93	505	0	ENST00000241453.7:c.1734G>T	p.Met578Ile	p.M578I	ENST00000241453	NM_004119.2	578	atG/atT	14/24	1	2	FACETS	0.892	0.8	0.989	0.892	0.8	0.989	CLONAL	1	TRUE	1	0.555907410857299	2		505	375	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172090	99172091	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0064412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	337	623	2	ENST00000074304.5:c.1657_1658del	p.Arg553AlafsTer7	p.R553Afs*7	ENST00000074304	NM_001134224.1	552	gaGCgg/gagg	17/26	0.533730535476769	3	FACETS	0.953	0.906	1	0.953	0.906	1	CLONAL	2	TRUE	1	0.555907410857299	3		625	813	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99179930	99179930	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	134	457	0	ENST00000074304.5:c.1873G>T	p.Glu625Ter	p.E625*	ENST00000074304	NM_001134224.1	625	Gaa/Taa	19/26	0.533730535476769	3	FACETS	0.994	0.906	1	0.497	0.453	0.543	CLONAL	1	TRUE	1	0.555907410857299	3		457	620	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630626	158630626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912678	NA	P-0064412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	104	421	0	ENST00000263640.3:c.617G>A	p.Arg206His	p.R206H	ENST00000263640	NM_001105.4	206	cGc/cAc	6/11	0.533730535476769	3	FACETS	0.842	0.756	0.933	0.421	0.378	0.467	CLONAL	1	TRUE	1	0.555907410857299	3		421	568	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790170	40790170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373191879	NA	P-0064412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	104	486	0	ENST00000373198.4:c.2561G>A	p.Arg854His	p.R854H	ENST00000373198	NM_133170.3	854	cGc/cAc	18/32	1	2	FACETS	0.803	0.723	0.887	0.803	0.723	0.887	CLONAL	1	TRUE	1	0.555907410857299	2		486	466	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550950	150550950	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064413-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	243	510	0	ENST00000369026.2:c.706G>C	p.Asp236His	p.D236H	ENST00000369026	NM_021960.4	236	Gac/Cac	2/3	0.45448815288426	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.45448815288426	1		510	734	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592251	29592251	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs797044942	NA	P-0064413-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	88	287	0	ENST00000356175.3:c.4666C>T	p.Gln1556Ter	p.Q1556*	ENST00000356175	NM_000267.3	1556	Cag/Tag	35/57	0.45448815288426	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.45448815288426	1		287	296	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051607	30051607	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064413-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	127	351	0	ENST00000338641.4:c.542del	p.Pro181ArgfsTer28	p.P181Rfs*28	ENST00000338641	NM_000268.3	181	Ccg/cg	6/16	0.45448815288426	1	FACETS	0.848	0.773	0.927	0.848	0.773	0.927	CLONAL	1	TRUE	0	0.45448815288426	1		351	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578420	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0064414-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	396	578	0	ENST00000269305.4:c.510_511delinsTT	p.Glu171Ter	p.E171*	ENST00000269305	NM_001126112.2	170	acGGag/acTTag	5/11	0.510944053774061	4	FACETS	1	0.993	1	0.859	0.826	0.892	CLONAL	3	TRUE	0	0.535246062025193	4		578	661	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317120	87317120	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064414-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	146	427	0	ENST00000277120.3:c.259G>T	p.Val87Phe	p.V87F	ENST00000277120		87	Gtt/Ttt	3/19	0.355527350568496	5	FACETS	0.86	0.795	0.927	0.86	0.795	0.927	CLONAL	3	TRUE	2	0.535246062025193	5		427	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0064415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	212	892	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.465611147483317	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	0	0.487589572559736	2		892	435	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724120	61724120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781425578	NA	P-0064415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	80	579	0	ENST00000401558.2:c.782G>A	p.Arg261Gln	p.R261Q	ENST00000401558	NM_003400.3	261	cGa/cAa	10/25	0.410344095292676	5	FACETS	1	0.941	1	0.369	0.326	0.416	CLONAL	1	TRUE	2	0.487589572559736	5		579	513	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670357	134670357	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369940994	NA	P-0064415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	109	625	1	ENST00000398015.3:c.268C>T	p.Arg90Cys	p.R90C	ENST00000398015	NM_004441.4	90	Cgc/Tgc	3/16	0.437852521369623	3	FACETS	1	0.967	1	0.584	0.527	0.644	CLONAL	1	TRUE	1	0.487589572559736	3		626	476	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914811	32914811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	66	602	0	ENST00000380152.3:c.6319C>T	p.Pro2107Ser	p.P2107S	ENST00000380152		2107	Cct/Tct	11/27	0.487589572559736	7	FACETS	0.936	0.812	1	0.187	0.162	0.214	CLONAL	1	TRUE	2	0.487589572559736	7		602	642	SUCCESS
APC	324	MSKCC	GRCh37	5	112173306	112173307	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0064415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	136	499	0	ENST00000257430.4:c.2016_2017del	p.His672GlnfsTer7	p.H672Qfs*7	ENST00000257430	NM_000038.5	672	cAT/c	16/16	0.465611147483317	2	FACETS	0.958	0.888	1	0.958	0.888	1	CLONAL	2	TRUE	0	0.487589572559736	2		499	291	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446208	29446208	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs374188635	NA	P-0064415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	61	601	0	ENST00000389048.3:c.3359G>A	p.Arg1120Gln	p.R1120Q	ENST00000389048	NM_004304.4	1120	cGg/cAg	20/29	0.410344095292676	5	FACETS	0.799	0.69	0.918	0.266	0.23	0.306	CLONAL	1	TRUE	2	0.487589572559736	5		601	542	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629276	187629277	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACAAAGGT	novel	NA	P-0064415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	73	688	0	ENST00000441802.2:c.1698_1705dup	p.Phe569TyrfsTer7	p.F569Yfs*7	ENST00000441802	NM_005245.3	569	ttt/tACCTTTGTtt	2/27	0.437852521369623	3	FACETS	0.699	0.612	0.792	0.349	0.306	0.396	SUBCLONAL	1	TRUE	1	0.487589572559736	3		688	533	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612157	189612157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	120	529	0	ENST00000264731.3:c.1909C>T	p.Arg637Cys	p.R637C	ENST00000264731	NM_003722.4	637	Cgt/Tgt	14/14	0.42018714139805	3	FACETS	1	0.983	1	0.684	0.622	0.749	CLONAL	1	TRUE	1	0.469812711469042	3		529	461	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998700	100998700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	87	571	0	ENST00000325455.5:c.1102G>A	p.Glu368Lys	p.E368K	ENST00000325455	NM_001202474.3	368	Gag/Aag	1/8	0.474073705984038	3	FACETS	1	0.929	1	0.529	0.471	0.591	CLONAL	1	TRUE	1	0.469812711469042	3		571	432	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214663	133214663	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	195	439	0	ENST00000320574.5:c.5615T>G	p.Ile1872Ser	p.I1872S	ENST00000320574	NM_006231.2	1872	aTc/aGc	41/49	0.324092132460752	5	FACETS	1	0.968	1	0.715	0.664	0.766	CLONAL	2	TRUE	2	0.469812711469042	5		439	660	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214676	133214676	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	215	455	0	ENST00000320574.5:c.5602T>C	p.Phe1868Leu	p.F1868L	ENST00000320574	NM_006231.2	1868	Ttc/Ctc	41/49	0.324092132460752	5	FACETS	1	0.984	1	0.78	0.728	0.832	CLONAL	2	TRUE	2	0.469812711469042	5		455	667	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577516	7577517	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATGATGGTGAGGATGGGCCTCCGGTTC	novel	NA	P-0064416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	187	393	0	ENST00000269305.4:c.738_764dup	p.Met246_Ile254dup	p.M246_I254dup	ENST00000269305	NM_001126112.2	246	atc/atGAACCGGAGGCCCATCCTCACCATCATc	7/11	0.474073705984038	3	FACETS	0.887	0.825	0.951	0.591	0.55	0.634	CLONAL	2	TRUE	0	0.469812711469042	3		393	554	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057333	180057334	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0064416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	40	498	0	ENST00000261937.6:c.404_405del	p.Phe135Ter	p.F135*	ENST00000261937	NM_182925.4	135	tTT/t	4/30	NA	2	FACETS	0.474	0.395	0.562			1	INDETERMINATE	1	TRUE	NA	0.469812711469042	2		498	359	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	67	344	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.15548051680043	4	FACETS	0.777	0.686	0.87	0.777	0.686	0.87	INDETERMINATE	2	TRUE	2	0.726771075002482	4		344	205	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0064417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	232	374	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.726771075002482	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.726771075002482	1		374	379	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602764	10602764	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	10	449	0	ENST00000171111.5:c.814C>T	p.Arg272Cys	p.R272C	ENST00000171111	NM_203500.1	272	Cgc/Tgc	3/6	0.726771075002482	1	FACETS	0.038	0.025	0.055	0.038	0.025	0.055	SUBCLONAL	1	TRUE	0	0.726771075002482	1		449	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0064418-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	256	447	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.377373665770464	1	FACETS	0.847	0.798	0.896	1	0.994	1	CLONAL	2	FALSE	0	0.377373665770464	1		447	650	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0064418-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	143	339	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.377373665770464	2		339	546	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0064418-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	247	317	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.309299009787452	4	FACETS	1	0.986	1			1	CLONAL	3	FALSE	NA	0.377373665770464	4		317	531	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245229	46245230	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0064418-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	114	468	0	ENST00000334344.6:c.3327dup	p.Gly1110TrpfsTer50	p.G1110Wfs*50	ENST00000334344	NM_152641.2	1108	ggt/ggTt	15/21	0.377373665770464	1	FACETS	0.831	0.75	0.916	0.831	0.75	0.916	CLONAL	1	FALSE	0	0.377373665770464	1		468	590	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549250	21549250	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064418-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	75	464	0	ENST00000382592.4:c.3026G>T	p.Ser1009Ile	p.S1009I	ENST00000382592	NM_014572.2	1009	aGc/aTc	8/8	1	2	FACETS	0.424	0.371	0.482	0.424	0.371	0.482	SUBCLONAL	1	FALSE	1	0.377373665770464	2		464	937	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715614	30715614	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0064418-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	90	429	0	ENST00000295754.5:c.1272C>G	p.Tyr424Ter	p.Y424*	ENST00000295754	NM_003242.5	424	taC/taG	5/7	1	2	FACETS	0.701	0.623	0.786	0.701	0.623	0.786	SUBCLONAL	1	FALSE	1	0.377373665770464	2		429	680	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0064419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	66	176	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.269858305336963	1	FACETS	0.986	0.874	1	0.986	0.874	1	INDETERMINATE	1	TRUE	0	0.542225426013409	1		176	180	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0064419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	44	85	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.269858305336963	1	FACETS	0.903	0.775	1	0.903	0.775	1	INDETERMINATE	1	TRUE	0	0.542225426013409	1		85	131	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178257	56178257	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0064419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	104	265	0	ENST00000399503.3:c.3230C>G	p.Ser1077Ter	p.S1077*	ENST00000399503	NM_005921.1	1077	tCa/tGa	14/20	0.542225426013409	1	FACETS	0.926	0.84	1	0.926	0.84	1	CLONAL	1	TRUE	0	0.542225426013409	1		265	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0064419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	100	276	0	ENST00000269305.4:c.375+1G>T		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.537669361059866	1	FACETS	0.978	0.887	1	0.978	0.887	1	CLONAL	1	TRUE	0	0.542225426013409	1		276	275	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860569	45860569	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs757100147	NA	P-0064419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	133	300	0	ENST00000391945.4:c.1438A>G	p.Thr480Ala	p.T480A	ENST00000391945	NM_000400.3	480	Acc/Gcc	15/23	0.269858305336963	1	FACETS	0.868	0.796	0.942	0.868	0.796	0.942	INDETERMINATE	1	TRUE	0	0.542225426013409	1		300	412	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150935552	150935552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	75	227	0	ENST00000271640.5:c.3394G>A	p.Asp1132Asn	p.D1132N	ENST00000271640	NM_001145415.1	1132	Gat/Aat	19/22	0.269858305336963	1	FACETS	0.507	0.446	0.571	0.507	0.446	0.571	INDETERMINATE	1	TRUE	0	0.542225426013409	1		227	398	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303679	30303679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	134	313	0	ENST00000262643.3:c.107C>T	p.Thr36Ile	p.T36I	ENST00000262643	NM_001238.2	36	aCc/aTc	3/12	0.269858305336963	1	FACETS	0.91	0.835	0.986	0.91	0.835	0.986	INDETERMINATE	1	TRUE	0	0.542225426013409	1		313	396	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808294	99808294	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	17	109	0	ENST00000280892.6:c.395G>T	p.Arg132Leu	p.R132L	ENST00000280892	NM_001130678.1	132	cGa/cTa	5/7	1	2	FACETS	0.271	0.203	0.353	0.271	0.203	0.353	SUBCLONAL	1	TRUE	1	0.542225426013409	2		109	231	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0064423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	8	440	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		440	294	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0064424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	129	282	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.518436662328241	3	FACETS	0.787	0.721	0.856	0.787	0.721	0.856	SUBCLONAL	2	TRUE	1	0.518436662328241	3		282	398	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0064424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	142	534	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.518436662328241	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.518436662328241	1		534	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28934577	NA	P-0064424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	105	420	0	ENST00000269305.4:c.770T>C	p.Leu257Pro	p.L257P	ENST00000269305	NM_001126112.2	257	cTg/cCg	7/11	0.518436662328241	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.518436662328241	1		420	298	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131505	202131505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	85	439	0	ENST00000358485.4:c.473C>T	p.Ser158Phe	p.S158F	ENST00000358485	NM_001080125.1	158	tCt/tTt	2/9	0.186300436550186	1	FACETS	0.491	0.435	0.55	0.491	0.435	0.55	INDETERMINATE	1	TRUE	0	0.518436662328241	1		439	495	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969327	44969327	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	66	331	0	ENST00000377967.4:c.4009G>T	p.Glu1337Ter	p.E1337*	ENST00000377967	NM_021140.2	1337	Gag/Tag	28/29	0.45236749836366	1	FACETS	0.776	0.682	0.875	0.776	0.682	0.875	SUBCLONAL	1	TRUE	0	0.518436662328241	1		331	243	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131480	202131480	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	82	443	0	ENST00000358485.4:c.448C>T	p.Gln150Ter	p.Q150*	ENST00000358485	NM_001080125.1	150	Cag/Tag	2/9	0.186300436550186	1	FACETS	0.462	0.408	0.519	0.462	0.408	0.519	INDETERMINATE	1	TRUE	0	0.518436662328241	1		443	507	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32903606	32903606	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	37	254	0	ENST00000380152.3:c.658G>T	p.Val220Leu	p.V220L	ENST00000380152		220	Gta/Tta	8/27	0.518436662328241	3	FACETS	0.708	0.587	0.841	0.354	0.293	0.421	SUBCLONAL	1	TRUE	1	0.518436662328241	3		254	254	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665765	241665765	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	86	368	0	ENST00000366560.3:c.1214T>C	p.Leu405Ser	p.L405S	ENST00000366560	NM_000143.3	405	tTg/tCg	8/10	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.518436662328241	2		368	324	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931771	39931771	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	27	503	0	ENST00000378444.4:c.2828G>T	p.Gly943Val	p.G943V	ENST00000378444	NM_001123385.1	943	gGa/gTa	4/15	0.45236749836366	1	FACETS	0.217	0.172	0.268	0.217	0.172	0.268	SUBCLONAL	1	TRUE	0	0.518436662328241	1		503	356	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057916	27057916	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	76	502	0	ENST00000324856.7:c.1624C>T	p.Gln542Ter	p.Q542*	ENST00000324856	NM_006015.4	542	Cag/Tag	3/20	1	2	FACETS	0.962	0.847	1	0.962	0.847	1	CLONAL	1	TRUE	1	0.33462337162618	2		502	472	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0064425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	77	522	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.33462337162618	2		522	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577599	7577600	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1567550002	NA	P-0064425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	68	315	0	ENST00000269305.4:c.681dup	p.Asp228Ter	p.D228*	ENST00000269305	NM_001126112.2	227	-/T	7/11	0.273955799350143	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.33462337162618	1		315	292	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984806	11984806	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0064425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	31	315	1	ENST00000353533.5:c.352A>T	p.Lys118Ter	p.K118*	ENST00000353533	NM_003010.3	118	Aaa/Taa	3/11	0.273955799350143	1	FACETS	0.465	0.376	0.564	0.465	0.376	0.564	SUBCLONAL	1	TRUE	0	0.33462337162618	1		316	332	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0064425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	37	278	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.73	0.604	0.87	0.73	0.604	0.87	SUBCLONAL	1	TRUE	1	0.33462337162618	2		278	303	SUCCESS
APC	324	MSKCC	GRCh37	5	112175600	112175600	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0064425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	61	487	0	ENST00000257430.4:c.4312del	p.Thr1438HisfsTer35	p.T1438Hfs*35	ENST00000257430	NM_000038.5	1437	Aaa/aa	16/16	1	2	FACETS	0.777	0.672	0.891	0.777	0.672	0.891	SUBCLONAL	1	TRUE	1	0.33462337162618	2		487	469	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0064426-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	33	338	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		338	242	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0064427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	72	166	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.628773693242228	2		166	219	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251625	212251625	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	196	522	0	ENST00000342788.4:c.3434T>G	p.Leu1145Arg	p.L1145R	ENST00000342788	NM_005235.2	1145	cTg/cGg	27/28	1	2	FACETS	0.872	0.81	0.936	0.872	0.81	0.936	CLONAL	1	TRUE	1	0.628773693242228	2		522	715	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217488	142217488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	88	340	1	ENST00000350721.4:c.5509G>A	p.Ala1837Thr	p.A1837T	ENST00000350721	NM_001184.3	1837	Gca/Aca	32/47	1	2	FACETS	0.651	0.58	0.726	0.651	0.58	0.726	SUBCLONAL	1	TRUE	1	0.628773693242228	2		341	430	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591211	67591251	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGG	TGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGG	-	novel	NA	P-0064427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	165	403	0	ENST00000274335.5:c.1746-36_1750del		p.X582_splice	ENST00000274335		582		13/15	1	2	FACETS	0.919	0.849	0.992	0.919	0.849	0.992	CLONAL	1	TRUE	1	0.628773693242228	2		403	571	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855943	76855943	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	136	211	0	ENST00000373344.5:c.5657C>G	p.Pro1886Arg	p.P1886R	ENST00000373344	NM_000489.3	1886	cCt/cGt	23/35	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.628773693242228	1		211	243	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0064429-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	143	371	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.469172273198114	5	FACETS	0.875	0.809	0.942	0.875	0.809	0.942	CLONAL	3	FALSE	2	0.593525288410359	5		371	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0064429-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	352	579	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.591331976897415	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	FALSE	0	0.593525288410359	2		579	574	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0064429-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	203	375	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	0.593525288410359	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	FALSE	0	0.593525288410359	2		375	335	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861162	57861162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564027387	NA	P-0064429-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	336	453	0	ENST00000228682.2:c.959C>T	p.Thr320Met	p.T320M	ENST00000228682	NM_005269.2	320	aCg/aTg	9/12	0.272539575736926	6	FACETS	1	0.988	1	1	0.988	1	INDETERMINATE	3	FALSE	3	0.593525288410359	6		453	741	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2972184	2972184	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064429-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	36	387	0	ENST00000396946.4:c.1555A>G	p.Thr519Ala	p.T519A	ENST00000396946	NM_032415.4	519	Aca/Gca	11/25	0.469172273198114	5	FACETS	0.398	0.326	0.479	0.133	0.108	0.16	SUBCLONAL	1	FALSE	2	0.593525288410359	5		387	576	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416741	121416741	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064429-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	440	548	1	ENST00000257555.6:c.170T>C	p.Leu57Pro	p.L57P	ENST00000257555		57	cTg/cCg	1/10	0.566152521511674	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	FALSE	0	0.593525288410359	3		549	619	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383676	15383676	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064429-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	49	507	0	ENST00000263377.2:c.235T>C	p.Phe79Leu	p.F79L	ENST00000263377	NM_058243.2	79	Ttt/Ctt	2/20	0.593525288410359	3	FACETS	0.323	0.273	0.379	0.162	0.136	0.19	SUBCLONAL	1	FALSE	1	0.593525288410359	3		507	662	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086121	16086121	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064429-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	51	546	0	ENST00000281043.3:c.1297C>A	p.Leu433Ile	p.L433I	ENST00000281043	NM_005378.4	433	Ctc/Atc	3/3	0.593525288410359	2	FACETS	0.412	0.351	0.479	0.206	0.175	0.24	SUBCLONAL	1	FALSE	0	0.593525288410359	2		546	417	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726868	61726868	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064429-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	61	359	0	ENST00000401558.2:c.570A>T	p.Lys190Asn	p.K190N	ENST00000401558	NM_003400.3	190	aaA/aaT	7/25	0.425618881396472	5	FACETS	0.957	0.839	1	0.638	0.559	0.721	CLONAL	2	FALSE	2	0.593525288410359	5		359	203	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945360	54945360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064429-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	213	478	0	ENST00000312783.6:c.1066G>A	p.Ala356Thr	p.A356T	ENST00000312783	NM_198436.1	356	Gcc/Acc	10/10	0.593525288410359	6	FACETS	0.913	0.855	0.973	0.913	0.855	0.973	CLONAL	3	FALSE	3	0.593525288410359	6		478	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520000	NA	P-0064431-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	227	663	0	ENST00000269305.4:c.452C>A	p.Pro151His	p.P151H	ENST00000269305	NM_001126112.2	151	cCc/cAc	5/11	0.319646963307504	2	FACETS	0.992	0.929	1	0.992	0.929	1	CLONAL	2	TRUE	0	0.333992512727307	2		663	685	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339226	70339226	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064431-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	66	268	0	ENST00000374080.3:c.103G>A	p.Glu35Lys	p.E35K	ENST00000374080		35	Gaa/Aaa	2/45	1	2	FACETS	0.948	0.826	1	0.948	0.826	1	CLONAL	1	TRUE	1	0.333992512727307	2		268	417	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37863251	37863251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564064363	NA	P-0064431-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	88	474	0	ENST00000269571.5:c.82G>A	p.Gly28Ser	p.G28S	ENST00000269571		28	Ggc/Agc	2/27	0.311019149143333	3	FACETS	1	0.954	1	0.572	0.507	0.64	CLONAL	1	TRUE	1	0.333992512727307	3		474	538	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566442	41566442	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064431-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	103	354	0	ENST00000263253.7:c.4319C>G	p.Pro1440Arg	p.P1440R	ENST00000263253	NM_001429.3	1440	cCa/cGa	27/31	0.333992512727307	3	FACETS	1	0.975	1	0.646	0.58	0.716	CLONAL	1	TRUE	1	0.333992512727307	3		354	557	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041180	29041180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064431-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	80	392	0	ENST00000282397.4:c.248G>A	p.Arg83Lys	p.R83K	ENST00000282397	NM_002019.4	83	aGa/aAa	3/30	0.311019149143333	3	FACETS	0.927	0.817	1	0.464	0.408	0.523	CLONAL	1	TRUE	1	0.333992512727307	3		392	603	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21344759	21344759	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064431-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	41	391	0	ENST00000215739.8:c.736C>A	p.Gln246Lys	p.Q246K	ENST00000215739	NM_006767.3	246	Caa/Aaa	8/21	0.311019149143333	3	FACETS	0.461	0.383	0.548	0.23	0.191	0.274	SUBCLONAL	1	TRUE	1	0.333992512727307	3		391	622	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445791	49445791	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064431-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	153	636	0	ENST00000301067.7:c.1675G>T	p.Glu559Ter	p.E559*	ENST00000301067	NM_003482.3	559	Gag/Tag	10/54	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.333992512727307	2		636	772	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562148	21562148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064431-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	104	575	0	ENST00000382592.4:c.1771G>A	p.Glu591Lys	p.E591K	ENST00000382592	NM_014572.2	591	Gag/Aag	4/8	0.311019149143333	3	FACETS	0.862	0.771	0.959	0.431	0.385	0.48	CLONAL	1	TRUE	1	0.333992512727307	3		575	843	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570392	95570392	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1278843875	NA	P-0064431-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	85	348	0	ENST00000393063.1:c.3341C>G	p.Ser1114Cys	p.S1114C	ENST00000393063	NM_030621.3	1114	tCt/tGt	22/28	1	2	FACETS	0.925	0.82	1	0.925	0.82	1	CLONAL	1	TRUE	1	0.333992512727307	2		348	550	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215674192	215674192	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064431-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	59	354	0	ENST00000260947.4:c.102G>T	p.Trp34Cys	p.W34C	ENST00000260947	NM_000465.2	34	tgG/tgT	1/11	1	2	FACETS	0.897	0.774	1	0.897	0.774	1	CLONAL	1	TRUE	1	0.333992512727307	2		354	394	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794945	242794945	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064431-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	95	573	0	ENST00000334409.5:c.264G>C	p.Gln88His	p.Q88H	ENST00000334409	NM_005018.2	88	caG/caC	2/5	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.333992512727307	2		573	533	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917547	178917547	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200619412	NA	P-0064431-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	64	369	0	ENST00000263967.3:c.422G>A	p.Arg141Lys	p.R141K	ENST00000263967	NM_006218.2	141	aGa/aAa	3/21	0.25151221704426	3	FACETS	0.964	0.837	1	0.482	0.418	0.551	CLONAL	1	TRUE	1	0.333992512727307	3		369	464	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721721	176721721	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs200115665	NA	P-0064431-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	104	445	0	ENST00000439151.2:c.7352G>C	p.Arg2451Thr	p.R2451T	ENST00000439151	NM_022455.4	2451	aGa/aCa	23/23	0.333992512727307	1	FACETS	0.945	0.849	1	0.945	0.849	1	CLONAL	1	TRUE	0	0.333992512727307	1		445	549	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432188	49432190	+	frameshift_variant	Frame_Shift_Del	DEL	CCA	CCA	T	novel	NA	P-0064431-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	81	574	0	ENST00000301067.7:c.8949_8951delinsA	p.Gly2984GlufsTer5	p.G2984Efs*5	ENST00000301067	NM_003482.3	2983	gcTGGg/gcAg	34/54	1	2	FACETS	0.776	0.684	0.875	0.776	0.684	0.875	SUBCLONAL	1	TRUE	1	0.333992512727307	2		574	625	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0064433-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	40	516	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.837	1	1	0.837	1	CLONAL	1	TRUE	1	0.31	2		516	258	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220442	1220442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064433-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	40	510	0	ENST00000326873.7:c.535C>T	p.Pro179Ser	p.P179S	ENST00000326873	NM_000455.4	179	Ccg/Tcg	4/10	0.253094622940532	1	FACETS	0.859	0.718	1	0.859	0.718	1	CLONAL	1	TRUE	0	0.31	1		510	254	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508054	106508054	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064433-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	30	368	0	ENST00000359195.3:c.48C>A	p.Asn16Lys	p.N16K	ENST00000359195	NM_002649.2	16	aaC/aaA	2/11	0.155697308052386	4	FACETS	0.968	0.783	1	0.484	0.391	0.588	INDETERMINATE	1	TRUE	2	0.31	4		368	262	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150936528	150936528	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064434-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	64	474	0	ENST00000271640.5:c.3727C>T	p.Arg1243Cys	p.R1243C	ENST00000271640	NM_001145415.1	1243	Cgc/Tgc	21/22	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.245133934718031	2		474	504	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064434-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	34	379	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.245133934718031	3	FACETS	0.822	0.672	0.99	0.411	0.336	0.495	CLONAL	1	TRUE	1	0.245133934718031	3		379	379	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847275	68847277	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0064434-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	134	445	0	ENST00000261769.5:c.1199_1201del	p.Asp400del	p.D400del	ENST00000261769	NM_004360.3	399	acTGAt/act	9/16	0.245133934718031	3	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	1	0.245133934718031	3		445	602	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023021	27023021	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1329001050	NA	P-0064434-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	35	447	0	ENST00000324856.7:c.127G>A	p.Ala43Thr	p.A43T	ENST00000324856	NM_006015.4	43	Gca/Aca	1/20	1	2	FACETS	0.93	0.765	1	0.93	0.765	1	CLONAL	1	TRUE	1	0.245133934718031	2		447	307	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206942067	206942067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064434-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	41	315	0	ENST00000423557.1:c.451G>A	p.Glu151Lys	p.E151K	ENST00000423557	NM_000572.2	151	Gag/Aag	5/5	1	2	FACETS	0.793	0.661	0.939	0.793	0.661	0.939	CLONAL	1	TRUE	1	0.245133934718031	2		315	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0064435-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	143	504	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.376698370345678	2	FACETS	0.956	0.882	1	0.956	0.882	1	CLONAL	2	TRUE	0	0.385511981367961	2		504	388	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625159	69625159	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554980306	NA	P-0064435-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	53	708	1	ENST00000334134.2:c.634C>T	p.Arg212Trp	p.R212W	ENST00000334134	NM_005247.2	212	Cgg/Tgg	3/3	0.22391274455349	3	FACETS	0.839	0.718	0.971	0.419	0.359	0.486	INDETERMINATE	1	TRUE	1	0.385511981367961	3		709	391	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566818	212566818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762866612	NA	P-0064435-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	23	519	0	ENST00000342788.4:c.1363G>A	p.Ala455Thr	p.A455T	ENST00000342788	NM_005235.2	455	Gca/Aca	12/28	1	2	FACETS	0.497	0.389	0.622	0.497	0.389	0.622	SUBCLONAL	1	TRUE	1	0.385511981367961	2		519	240	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041074	180041076	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs587776833	NA	P-0064435-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	69	654	0	ENST00000261937.6:c.3323_3325del	p.Phe1108del	p.F1108del	ENST00000261937	NM_182925.4	1108	tTCTct/tct	24/30	1	2	FACETS	0.888	0.777	1	0.888	0.777	1	CLONAL	1	TRUE	1	0.385511981367961	2		654	403	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814576	43814576	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064435-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	47	724	0	ENST00000372470.3:c.1371C>A	p.Tyr457Ter	p.Y457*	ENST00000372470	NM_005373.2	457	taC/taA	9/12	0.168632272238574	2	FACETS	0.445	0.375	0.522	0.222	0.187	0.261	INDETERMINATE	1	TRUE	0	0.385511981367961	2		724	548	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748166	72748166	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064435-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	32	463	0	ENST00000357731.5:c.12G>T	p.Met4Ile	p.M4I	ENST00000357731	NM_173808.2	4	atG/atT	1/7	0.168632272238574	2	FACETS	0.502	0.408	0.607	0.251	0.204	0.304	INDETERMINATE	1	TRUE	0	0.385511981367961	2		463	331	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940202	49940202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064435-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	211	721	0	ENST00000296474.3:c.841G>A	p.Ala281Thr	p.A281T	ENST00000296474	NM_002447.2	281	Gca/Aca	1/20	0.385511981367961	3	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	1	0.385511981367961	3		721	651	SUCCESS
APC	324	MSKCC	GRCh37	5	112174033	112174033	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0064435-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	59	594	2	ENST00000257430.4:c.2742T>A	p.Cys914Ter	p.C914*	ENST00000257430	NM_000038.5	914	tgT/tgA	16/16	NA	2	FACETS	0.773	0.676	0.875			1	INDETERMINATE	2	TRUE	NA	0.385511981367961	2		596	198	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940151	31940151	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064435-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	207	878	0	ENST00000375333.2:c.293A>G	p.His98Arg	p.H98R	ENST00000375333	NM_032454.1	98	cAt/cGt	2/8	0.250838651607494	5	FACETS	1	0.971	1	0.722	0.671	0.773	CLONAL	2	TRUE	2	0.385511981367961	5		878	783	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467800	50467800	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064435-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	149	651	0	ENST00000331340.3:c.1035C>A	p.Ser345Arg	p.S345R	ENST00000331340	NM_006060.4	345	agC/agA	8/8	0.385511981367961	3	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	1	0.385511981367961	3		651	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578491	7578491	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1567553924	NA	P-0064436-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	94	823	0	ENST00000269305.4:c.439del	p.Val147LeufsTer23	p.V147Lfs*23	ENST00000269305	NM_001126112.2	147	Gtt/tt	5/11	0.24244870324261	3	FACETS	1	0.967	1	0.779	0.702	0.857	CLONAL	2	TRUE	0	0.338567918410798	3		823	278	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50784049	50784049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747924691	NA	P-0064436-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	40	576	0	ENST00000398568.2:c.440G>A	p.Arg147His	p.R147H	ENST00000398568	NM_001042412.1	147	cGc/cAc	3/18	1	2	FACETS	0.78	0.651	0.922	0.78	0.651	0.922	CLONAL	1	TRUE	1	0.338567918410798	2		576	303	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295105	15295105	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0064436-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	22	587	0	ENST00000263388.2:c.2566+1G>A		p.X856_splice	ENST00000263388	NM_000435.2	856			0.338567918410798	7	FACETS	0.808	0.627	1	0.162	0.125	0.204	CLONAL	1	TRUE	2	0.338567918410798	7		587	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0064437-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	315	580	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.493446712234653	2	FACETS	0.975	0.929	1	0.975	0.929	1	CLONAL	2	TRUE	0	0.515419528060365	2		581	627	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0064437-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	46	292	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.515419528060365	1	FACETS	0.744	0.636	0.86	0.744	0.636	0.86	SUBCLONAL	1	TRUE	0	0.515419528060365	1		292	178	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879674	123879674	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064437-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	11	167	0	ENST00000330479.4:c.370C>A	p.Leu124Met	p.L124M	ENST00000330479	NM_020382.3	124	Ctg/Atg	4/9	1	2	FACETS	0.381	0.265	0.523	0.381	0.265	0.523	SUBCLONAL	1	TRUE	1	0.515419528060365	2		167	112	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30103717	30103717	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064437-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	74	493	0	ENST00000331968.5:c.1221G>T	p.Met407Ile	p.M407I	ENST00000331968	NM_002742.2	407	atG/atT	8/18	1	2	FACETS	0.772	0.68	0.87	0.772	0.68	0.87	SUBCLONAL	1	TRUE	1	0.515419528060365	2		493	372	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591246	67591246	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0064437-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	106	569	0	ENST00000274335.5:c.1746-2A>C		p.X582_splice	ENST00000274335		582			0.515419528060365	1	FACETS	0.975	0.886	1	0.975	0.886	1	CLONAL	1	TRUE	0	0.515419528060365	1		569	313	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356251	70356251	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064437-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	115	339	0	ENST00000374080.3:c.5146C>T	p.Arg1716Ter	p.R1716*	ENST00000374080		1716	Cga/Tga	37/45	0.447625281826425	2	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.515419528060365	2		339	358	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064438-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	18	634	0	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		634	747	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0064439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	245	631	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.433574041511504	1	FACETS	0.727	0.689	0.765	0.727	0.689	0.765	INDETERMINATE	1	TRUE	0	0.843743775581944	1		631	462	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0064439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	208	505	1	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.433574041511504	1	FACETS	0.702	0.662	0.743	0.702	0.662	0.743	INDETERMINATE	1	TRUE	0	0.843743775581944	1		506	406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576851	7576851	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0064439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	150	770	0	ENST00000269305.4:c.993+2T>G		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.433574041511504	1	FACETS	0.382	0.351	0.414	0.382	0.351	0.414	INDETERMINATE	1	TRUE	0	0.843743775581944	1		770	538	SUCCESS
APC	324	MSKCC	GRCh37	5	112137081	112137081	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0064439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	116	348	0	ENST00000257430.4:c.834+1G>C		p.X278_splice	ENST00000257430	NM_000038.5	278			0.843743775581944	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.843743775581944	1		348	150	SUCCESS
AR	367	MSKCC	GRCh37	X	66941695	66941695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768366293	NA	P-0064439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	47	306	0	ENST00000374690.3:c.2339G>A	p.Arg780Gln	p.R780Q	ENST00000374690	NM_000044.3	780	cGg/cAg	6/8	1	1	FACETS	0.301	0.257	0.349	0.301	0.257	0.349	SUBCLONAL	1	TRUE	0	0.843743775581944	1		306	214	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0064441-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	28	176	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.374131099592419	2		176	138	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115111972	115111972	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064441-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	103	558	0	ENST00000257566.3:c.1768C>T	p.Gln590Ter	p.Q590*	ENST00000257566	NM_016569.3	590	Cag/Tag	7/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.374131099592419	2		558	501	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117430	115117431	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0064441-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	89	484	0	ENST00000257566.3:c.743dup	p.Tyr248Ter	p.Y248*	ENST00000257566	NM_016569.3	248	tac/taAc	4/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.374131099592419	2		484	418	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064441-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	71	379	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.374131099592419	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	0	0.374131099592419	1		379	299	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721102	61721102	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1336923235	NA	P-0064441-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	62	430	0	ENST00000401558.2:c.1172C>T	p.Ser391Phe	p.S391F	ENST00000401558	NM_003400.3	391	tCt/tTt	12/25	1	2	FACETS	0.969	0.842	1	0.969	0.842	1	CLONAL	1	TRUE	1	0.374131099592419	2		430	342	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55524236	55524236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1490714621	NA	P-0064441-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	99	477	3	ENST00000288135.5:c.55C>T	p.Arg19Cys	p.R19C	ENST00000288135	NM_000222.2	19	Cgc/Tgc	1/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.374131099592419	2		480	462	SUCCESS
APC	324	MSKCC	GRCh37	5	112174466	112174466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253882360	NA	P-0064441-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	70	401	0	ENST00000257430.4:c.3175G>A	p.Glu1059Lys	p.E1059K	ENST00000257430	NM_000038.5	1059	Gaa/Aaa	16/16	1	2	FACETS	0.998	0.875	1	0.998	0.875	1	CLONAL	1	TRUE	1	0.374131099592419	2		401	375	SUCCESS
APC	324	MSKCC	GRCh37	5	112175154	112175154	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064441-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	75	402	0	ENST00000257430.4:c.3863G>C	p.Gly1288Ala	p.G1288A	ENST00000257430	NM_000038.5	1288	gGa/gCa	16/16	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.374131099592419	2		402	377	SUCCESS
APC	324	MSKCC	GRCh37	5	112175226	112175226	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587779791	NA	P-0064441-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	77	425	0	ENST00000257430.4:c.3935G>C	p.Gly1312Ala	p.G1312A	ENST00000257430	NM_000038.5	1312	gGa/gCa	16/16	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.374131099592419	2		425	385	SUCCESS
APC	324	MSKCC	GRCh37	5	112175846	112175846	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064441-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	86	467	0	ENST00000257430.4:c.4555G>C	p.Asp1519His	p.D1519H	ENST00000257430	NM_000038.5	1519	Gat/Cat	16/16	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.374131099592419	2		467	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0064442-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	172	633	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.578967861452639	2	FACETS	0.874	0.824	0.922	0.874	0.824	0.922	CLONAL	2	FALSE	0	0.713394768501199	2		633	276	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285902	39285902	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064442-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	46	345	0	ENST00000402219.2:c.257C>A	p.Ala86Glu	p.A86E	ENST00000402219	NM_005633.3	86	gCa/gAa	3/23	0.69533815587044	3	FACETS	1	0.919	1	0.554	0.475	0.637	CLONAL	1	FALSE	1	0.713394768501199	3		345	158	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132532	11132532	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064442-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	177	842	0	ENST00000358026.2:c.2748C>G	p.Asn916Lys	p.N916K	ENST00000358026	NM_001128849.1	916	aaC/aaG	19/36	0.709500845607628	4	FACETS	0.941	0.876	1	0.941	0.876	1	CLONAL	2	FALSE	2	0.713394768501199	4		842	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0064443-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	206	523	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		523	486	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781207	9781207	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064443-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	348	626	0	ENST00000377346.4:c.1712G>T	p.Trp571Leu	p.W571L	ENST00000377346	NM_005026.3	571	tGg/tTg	14/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		626	592	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842731	68842732	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064443-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	199	487	0	ENST00000261769.5:c.669dup	p.Arg224ThrfsTer20	p.R224Tfs*20	ENST00000261769	NM_004360.3	223	gaa/gAaa	5/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		487	462	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723609	49723609	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064443-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	83	203	0	ENST00000449682.2:c.1033T>G	p.Phe345Val	p.F345V	ENST00000449682	NM_020998.3	345	Ttc/Gtc	9/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		203	224	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974715	21974780	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCCCCCGCCTCCAGCAGCGCCCGCACCTCCTCTACCCGACCCCGGGCCGCGGCCGTGGCCA	GCAGCGCCCCCGCCTCCAGCAGCGCCCGCACCTCCTCTACCCGACCCCGGGCCGCGGCCGTGGCCA	-	novel	NA	P-0064443-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	205	742	0	ENST00000304494.5:c.47_112del	p.Leu16_Leu37del	p.L16_L37del	ENST00000304494	NM_000077.4	16	cTGGCCACGGCCGCGGCCCGGGGTCGGGTAGAGGAGGTGCGGGCGCTGCTGGAGGCGGGGGCGCTGCcc/ccc	1/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		742	513	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845939	72845982	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TAAAAGAGAAAGTAGAAGATGCAATACAGCAGCCAGACCAGGCC	TAAAAGAGAAAGTAGAAGATGCAATACAGCAGCCAGACCAGGCC	CA	novel	NA	P-0064443-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	144	529	2	ENST00000268489.5:c.3530-45_3530-2delinsTG		p.X1177_splice	ENST00000268489	NM_006885.3	1177			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		531	388	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0064444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	29	297	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	0.905	0.753	1	0.905	0.753	1	CLONAL	1	TRUE	1	0.843118803593357	2		297	76	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442552	52442561	+	frameshift_variant	Frame_Shift_Del	DEL	AGGTAGAGAC	AGGTAGAGAC	-	novel	NA	P-0064444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	159	606	2	ENST00000460680.1:c.184_193del	p.Val62TrpfsTer7	p.V62Wfs*7	ENST00000460680	NM_004656.3	62	GTCTCTACCTtg/tg	4/17	0.843118803593357	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.843118803593357	1		608	204	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038467	180038467	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1005859117	NA	P-0064444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	144	714	2	ENST00000261937.6:c.3550G>T	p.Val1184Phe	p.V1184F	ENST00000261937	NM_182925.4	1184	Gtc/Ttc	27/30	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.843118803593357	2		716	331	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0064459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	32	176	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.762	0.618	0.925	0.762	0.618	0.925	CLONAL	1	TRUE	1	0.19	2		176	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0064459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	36	599	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.503	0.412	0.606	0.503	0.412	0.606	SUBCLONAL	1	TRUE	1	0.19	2		599	753	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913237	NA	P-0064459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	90	475	0	ENST00000369535.4:c.35G>C	p.Gly12Ala	p.G12A	ENST00000369535	NM_002524.4	12	gGt/gCt	2/7	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.19	2		475	744	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560980	9560980	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	65	729	0	ENST00000353224.5:c.802C>T	p.Pro268Ser	p.P268S	ENST00000353224	NM_177990.2	268	Cca/Tca	4/10	0.226043503464999	3	FACETS	0.703	0.607	0.807	0.351	0.303	0.404	SUBCLONAL	1	TRUE	1	0.19	3		729	1066	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577586	7577586	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587781589	NA	P-0064459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	60	557	0	ENST00000269305.4:c.695T>C	p.Ile232Thr	p.I232T	ENST00000269305	NM_001126112.2	232	aTc/aCc	7/11	1	2	FACETS	0.816	0.702	0.941	0.816	0.702	0.941	CLONAL	1	TRUE	1	0.19	2		557	774	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867360	68867360	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	104	650	0	ENST00000261769.5:c.2607C>G	p.Phe869Leu	p.F869L	ENST00000261769	NM_004360.3	869	ttC/ttG	16/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.19	2		650	911	SUCCESS
APC	324	MSKCC	GRCh37	5	112175142	112175142	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0064459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	64	560	0	ENST00000257430.4:c.3852del	p.Asp1285MetfsTer3	p.D1285Mfs*3	ENST00000257430	NM_000038.5	1284	gAa/ga	16/16	1	2	FACETS	0.885	0.765	1	0.885	0.765	1	CLONAL	1	TRUE	1	0.19	2		560	761	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061231	38061231	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064460-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	197	790	0	ENST00000250448.2:c.758T>A	p.Met253Lys	p.M253K	ENST00000250448	NM_004496.3	253	aTg/aAg	2/2	1	2	FACETS	0.854	0.791	0.919	0.854	0.791	0.919	CLONAL	1	TRUE	1	0.520738081629042	2		790	886	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464450	25464450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369713081	NA	P-0064460-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	207	614	0	ENST00000264709.3:c.2063G>A	p.Arg688His	p.R688H	ENST00000264709	NM_175629.2	688	cGc/cAc	17/23	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.520738081629042	2		614	781	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28931588	NA	P-0064460-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	158	653	0	ENST00000349496.5:c.94G>C	p.Asp32His	p.D32H	ENST00000349496	NM_001904.3	32	Gac/Cac	3/15	1	2	FACETS	0.677	0.62	0.737	0.677	0.62	0.737	SUBCLONAL	1	TRUE	1	0.520738081629042	2		653	896	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89851351	89851351	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064460-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	104	571	0	ENST00000389301.3:c.1381G>T	p.Gly461Cys	p.G461C	ENST00000389301	NM_000135.2	461	Ggc/Tgc	15/43	1	2	FACETS	0.561	0.502	0.623	0.561	0.502	0.623	SUBCLONAL	1	TRUE	1	0.520738081629042	2		571	712	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964890	15964891	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0064460-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	218	657	0	ENST00000268712.3:c.5705_5706del	p.Glu1902GlyfsTer5	p.E1902Gfs*5	ENST00000268712	NM_006311.3	1902	gAG/g	37/46	1	2	FACETS	0.993	0.926	1	0.993	0.926	1	CLONAL	1	TRUE	1	0.520738081629042	2		657	843	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0064461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	73	721	2	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.14	2		723	835	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772199	68772199	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0064461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	27	504	0	ENST00000261769.5:c.49del		p.X17_splice	ENST00000261769	NM_004360.3	17			1	2	FACETS	0.746	0.592	0.923	0.746	0.592	0.923	CLONAL	1	TRUE	1	0.14	2		504	517	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0064462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	28	283	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.677	0.54	0.834	0.677	0.54	0.834	SUBCLONAL	1	TRUE	1	0.16	2		283	517	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	36	344	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	TRUE	1	0.16	2		344	439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573009	7573009	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0064462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	52	600	0	ENST00000269305.4:c.1101-1G>T		p.X367_splice	ENST00000269305	NM_001126112.2	367			1	2	FACETS	0.87	0.739	1	0.87	0.739	1	CLONAL	1	TRUE	1	0.16	2		600	747	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106861	27106861	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	92	597	0	ENST00000324856.7:c.6472C>T	p.Arg2158Ter	p.R2158*	ENST00000324856	NM_006015.4	2158	Cga/Tga	20/20	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.17	2		597	994	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256469	115256470	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0064463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	51	529	0	ENST00000369535.4:c.241_242del	p.Val81IlefsTer5	p.V81Ifs*5	ENST00000369535	NM_002524.4	81	GTa/a	3/7	1	2	FACETS	0.916	0.777	1	0.916	0.777	1	CLONAL	1	TRUE	1	0.17	2		529	655	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692839	89692839	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	21	188	0	ENST00000371953.3:c.323T>G	p.Leu108Arg	p.L108R	ENST00000371953	NM_000314.4	108	cTt/cGt	5/9	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.17	2		188	177	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827334	72827334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769133893	NA	P-0064463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	65	886	2	ENST00000268489.5:c.9247C>T	p.Arg3083Trp	p.R3083W	ENST00000268489	NM_006885.3	3083	Cgg/Tgg	9/10	1	2	FACETS	0.962	0.832	1	0.962	0.832	1	CLONAL	1	TRUE	1	0.17	2		888	795	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	22	650	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	1	2	FACETS	0.422	0.325	0.534	0.422	0.325	0.534	SUBCLONAL	1	TRUE	1	0.17	2		650	614	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158612	26158612	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	33	469	0	ENST00000289316.2:c.215A>G	p.Glu72Gly	p.E72G	ENST00000289316	NM_138720.2	72	gAg/gGg	1/2	1	2	FACETS	0.938	0.764	1	0.938	0.764	1	CLONAL	1	TRUE	1	0.17	2		469	414	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978658	70978658	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	70	811	0	ENST00000276594.2:c.995G>A	p.Arg332His	p.R332H	ENST00000276594	NM_024504.3	332	cGc/cAc	5/8	1	2	FACETS	0.998	0.869	1	0.998	0.869	1	CLONAL	1	TRUE	1	0.17	2		811	825	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400248	139400248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758787267	NA	P-0064463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	58	847	0	ENST00000277541.6:c.4100C>T	p.Pro1367Leu	p.P1367L	ENST00000277541	NM_017617.3	1367	cCg/cTg	25/34	1	2	FACETS	0.956	0.82	1	0.956	0.82	1	CLONAL	1	TRUE	1	0.17	2		847	714	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0064464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	22	516	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.236538662470513	2	FACETS	1	0.924	1	0.744	0.584	0.924	CLONAL	1	TRUE	0	0.236538662470513	2		516	125	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220698	1220698	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs730881975	NA	P-0064464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	67	650	0	ENST00000326873.7:c.716G>C	p.Trp239Ser	p.W239S	ENST00000326873	NM_000455.4	239	tGg/tCg	5/10	0.234067023444032	2	FACETS	0.902	0.79	1	0.902	0.79	1	CLONAL	2	TRUE	0	0.236538662470513	2		650	314	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325318	39325318	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0064464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	50	685	0	ENST00000373001.3:c.1A>G	p.Met1?	p.M1?	ENST00000373001	NM_022157.3	1	Atg/Gtg	1/7	0.191717176732467	4	FACETS	0.822	0.701	0.953	0.822	0.701	0.953	CLONAL	2	TRUE	2	0.236538662470513	4		685	318	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226476	133226476	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0064464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	65	420	0	ENST00000320574.5:c.3583-1G>T		p.X1195_splice	ENST00000320574	NM_006231.2	1195			0.104033312866404	3	FACETS	1	0.942	1	1	0.942	1	INDETERMINATE	2	TRUE	1	0.236538662470513	3		420	271	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870014	40870014	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	21	542	0	ENST00000428826.2:c.1003A>T	p.Thr335Ser	p.T335S	ENST00000428826		335	Aca/Tca	10/21	0.22160670517468	3	FACETS	0.749	0.578	0.948	0.375	0.289	0.474	CLONAL	1	TRUE	1	0.236538662470513	3		542	265	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770012	56770012	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555591761	NA	P-0064464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	27	530	0	ENST00000337432.4:c.8G>C	p.Gly3Ala	p.G3A	ENST00000337432	NM_058216.2	3	gGg/gCg	1/9	0.22160670517468	3	FACETS	0.902	0.72	1	0.451	0.36	0.555	CLONAL	1	TRUE	1	0.236538662470513	3		530	283	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713688	30713689	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0064464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	85	794	0	ENST00000295754.5:c.1015_1016del	p.Arg339AlafsTer25	p.R339Afs*25	ENST00000295754	NM_003242.5	338	aCG/a	4/7	0.236538662470513	2	FACETS	0.946	0.842	1	0.946	0.842	1	CLONAL	2	TRUE	0	0.236538662470513	2		794	380	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528388	157528388	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	70	785	0	ENST00000346085.5:c.6113del	p.Ser2038LeufsTer61	p.S2038Lfs*61	ENST00000346085	NM_020732.3	2038	tCt/tt	20/20	0.236538662470513	2	FACETS	0.902	0.793	1	0.902	0.793	1	CLONAL	2	TRUE	0	0.236538662470513	2		785	328	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879321	151879321	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	98	760	0	ENST00000262189.6:c.5624A>T	p.Gln1875Leu	p.Q1875L	ENST00000262189	NM_170606.2	1875	cAg/cTg	36/59	0.191717176732467	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	2	0.236538662470513	4		760	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579718	7579718	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0064465-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	30	493	0	ENST00000269305.4:c.78del	p.Pro27LeufsTer17	p.P27Lfs*17	ENST00000269305	NM_001126112.2	26	ctT/ct	3/11	1	2	FACETS	0.703	0.566	0.858	0.703	0.566	0.858	SUBCLONAL	1	TRUE	1	0.2	2		493	427	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0064465-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	52	457	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	0.875	0.745	1	0.875	0.745	1	CLONAL	1	TRUE	1	0.2	2		457	594	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971081	21971081	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064465-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	50	560	0	ENST00000304494.5:c.277del	p.Thr93ArgfsTer53	p.T93Rfs*53	ENST00000304494	NM_000077.4	93	Acg/cg	2/3	0.164307551229648	1	FACETS	0.951	0.808	1	0.951	0.808	1	CLONAL	1	TRUE	0	0.2	1		560	473	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064466-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	48	344	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.138902471122022	3	FACETS	1	0.954	1	0.684	0.578	0.799	CLONAL	1	TRUE	1	0.16	3		344	474	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0064466-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	70	515	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.16	2		515	739	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345240	73345240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	50	650	0	ENST00000377767.4:c.1649C>T	p.Ser550Phe	p.S550F	ENST00000377767	NM_014953.3	550	tCc/tTc	12/21	1	2	FACETS	0.73	0.62	0.852	0.73	0.62	0.852	SUBCLONAL	1	TRUE	1	0.260287819677754	2		650	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587781845	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	210	932	0	ENST00000269305.4:c.511G>T	p.Glu171Ter	p.E171*	ENST00000269305	NM_001126112.2	171	Gag/Tag	5/11	0.260287819677754	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.260287819677754	2		932	710	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133761036	133761036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1456042173	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	46	672	0	ENST00000318560.5:c.3359C>T	p.Ser1120Leu	p.S1120L	ENST00000318560	NM_005157.4	1120	tCg/tTg	11/11	0.260287819677754	1	FACETS	0.526	0.442	0.618	0.526	0.442	0.618	SUBCLONAL	1	TRUE	0	0.260287819677754	1		672	585	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856364	111856364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	83	762	3	ENST00000341259.2:c.415C>T	p.Arg139Cys	p.R139C	ENST00000341259	NM_005475.2	139	Cgc/Tgc	2/8	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.260287819677754	2		765	542	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412688	63412688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	74	392	0	ENST00000330258.3:c.479C>T	p.Pro160Leu	p.P160L	ENST00000330258	NM_152424.3	160	cCc/cTc	2/2	1	1	FACETS	0.899	0.796	1	1	0.982	1	CLONAL	2	TRUE	0	0.260287819677754	1		392	275	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584548	189584548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	109	752	0	ENST00000264731.3:c.844G>A	p.Gly282Arg	p.G282R	ENST00000264731	NM_003722.4	282	Gga/Aga	6/14	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.260287819677754	2		752	656	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937878	36937878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3918018	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	117	995	0	ENST00000361632.4:c.958G>A	p.Asp320Asn	p.D320N	ENST00000361632		320	Gac/Aac	7/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.260287819677754	2		995	832	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944527	40944527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371433526	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	93	797	0	ENST00000373198.4:c.1975G>A	p.Asp659Asn	p.D659N	ENST00000373198	NM_133170.3	659	Gat/Aat	12/32	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.260287819677754	2		797	669	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	53	803	3				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.845	0.721	0.98	0.845	0.721	0.98	CLONAL	1	TRUE	1	0.260287819677754	2		806	482	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156585	55156585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779173667	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	110	801	0	ENST00000257290.5:c.2986G>A	p.Glu996Lys	p.E996K	ENST00000257290	NM_006206.4	996	Gag/Aag	22/23	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.260287819677754	2		801	670	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100445	8100445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157299467	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	108	1114	0	ENST00000346208.3:c.419C>T	p.Ser140Phe	p.S140F	ENST00000346208		140	tCc/tTc	3/6	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.260287819677754	2		1114	773	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793406	242793406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	211	841	0	ENST00000334409.5:c.671G>A	p.Gly224Glu	p.G224E	ENST00000334409	NM_005018.2	224	gGg/gAg	5/5	0.260287819677754	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.260287819677754	3		841	785	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706859	117706859	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	84	577	0	ENST00000368508.3:c.2291G>A	p.Gly764Glu	p.G764E	ENST00000368508	NM_002944.2	764	gGa/gAa	15/43	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.260287819677754	2		577	564	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2111962	2111962	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45457701	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	106	801	0	ENST00000219476.3:c.1210C>T	p.Gln404Ter	p.Q404*	ENST00000219476	NM_000548.3	404	Cag/Tag	12/42	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.260287819677754	2		801	747	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856004	111856004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	87	682	0	ENST00000341259.2:c.55C>T	p.Pro19Ser	p.P19S	ENST00000341259	NM_005475.2	19	Ccg/Tcg	2/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.260287819677754	2		682	581	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858238	9858238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	103	873	0	ENST00000330684.3:c.3163G>A	p.Glu1055Lys	p.E1055K	ENST00000330684	NM_001134407.1	1055	Gag/Aag	13/13	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.260287819677754	2		873	699	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36814336	36814336	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	112	867	0	ENST00000373129.3:c.704G>A	p.Gly235Glu	p.G235E	ENST00000373129	NM_032017.1	235	gGg/gAg	8/12	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.260287819677754	2		867	712	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436687	52436687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	99	849	0	ENST00000460680.1:c.1987G>A	p.Asp663Asn	p.D663N	ENST00000460680	NM_004656.3	663	Gat/Aat	16/17	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.260287819677754	2		849	684	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673271	30673271	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	159	966	0	ENST00000376406.3:c.3689G>C	p.Gly1230Ala	p.G1230A	ENST00000376406	NM_014641.2	1230	gGa/gCa	10/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.260287819677754	2		966	1011	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998141	169998141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1428010723	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	67	522	0	ENST00000295797.4:c.832C>T	p.Arg278Cys	p.R278C	ENST00000295797	NM_002740.5	278	Cgt/Tgt	9/18	1	2	FACETS	0.931	0.81	1	0.931	0.81	1	CLONAL	1	TRUE	1	0.260287819677754	2		522	553	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426719	47426719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	143	402	0	ENST00000377045.4:c.964G>A	p.Gly322Ser	p.G322S	ENST00000377045	NM_001654.4	322	Ggc/Agc	10/16	1	1	FACETS	1	0.98	1	1	0.992	1	CLONAL	2	TRUE	0	0.260287819677754	1		402	397	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185195175	185195175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749182070	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	66	524	0	ENST00000265026.3:c.2492G>A	p.Arg831Gln	p.R831Q	ENST00000265026	NM_004721.4	831	cGa/cAa	12/14	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.260287819677754	2		524	460	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	177	274	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	0.23493722483865	3	FACETS	0.949	0.88	1	0.949	0.88	1	CLONAL	3	TRUE	0	0.260287819677754	3		274	540	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750545	41750545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	103	773	0	ENST00000226382.2:c.83C>T	p.Ser28Leu	p.S28L	ENST00000226382	NM_003924.3	28	tCa/tTa	1/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.260287819677754	2		773	560	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577217	64577217	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	113	909	0	ENST00000312049.6:c.365C>G	p.Ser122Cys	p.S122C	ENST00000312049	NM_130799.2	122	tCc/tGc	2/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.260287819677754	2		909	738	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804377	43804377	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	71	689	0	ENST00000372470.3:c.377T>A	p.Phe126Tyr	p.F126Y	ENST00000372470	NM_005373.2	126	tTt/tAt	3/12	1	2	FACETS	0.926	0.809	1	0.926	0.809	1	CLONAL	1	TRUE	1	0.260287819677754	2		689	589	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150916454	150916454	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1195596229	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	91	557	0	ENST00000271640.5:c.934C>T	p.Pro312Ser	p.P312S	ENST00000271640	NM_001145415.1	312	Ccc/Tcc	8/22	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.260287819677754	2		557	624	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163325209	163325209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	51	500	0	ENST00000271452.3:c.1345G>A	p.Asp449Asn	p.D449N	ENST00000271452	NM_145697.2	449	Gat/Aat	14/14	1	2	FACETS	0.889	0.757	1	0.889	0.757	1	CLONAL	1	TRUE	1	0.260287819677754	2		500	441	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425335	49425335	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	95	924	0	ENST00000301067.7:c.13153G>A	p.Glu4385Lys	p.E4385K	ENST00000301067	NM_003482.3	4385	Gaa/Aaa	39/54	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.260287819677754	2		924	726	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490935	56490935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1303381079	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	91	794	0	ENST00000267101.3:c.2381C>T	p.Ser794Phe	p.S794F	ENST00000267101	NM_001982.3	794	tCt/tTt	20/28	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.260287819677754	2		794	688	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86545145	86545145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1434187368	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	105	814	0	ENST00000262426.4:c.970G>A	p.Glu324Lys	p.E324K	ENST00000262426	NM_001451.2	324	Gag/Aag	1/2	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.260287819677754	2		814	655	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348016	89348016	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	109	822	0	ENST00000301030.4:c.4934T>C	p.Leu1645Pro	p.L1645P	ENST00000301030	NM_001256183.1	1645	cTg/cCg	9/13	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.260287819677754	2		822	744	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38788467	38788467	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1026195254	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	192	577	0	ENST00000348513.6:c.694C>T	p.Gln232Ter	p.Q232*	ENST00000348513	NM_003079.4	232	Cag/Tag	8/11	0.23493722483865	3	FACETS	0.972	0.905	1	0.972	0.905	1	CLONAL	3	TRUE	0	0.260287819677754	3		577	572	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7141698	7141698	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	87	658	0	ENST00000302850.5:c.2672A>G	p.Tyr891Cys	p.Y891C	ENST00000302850	NM_000208.2	891	tAt/tGt	13/22	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.260287819677754	2		658	627	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607471	46607471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	110	909	0	ENST00000263734.3:c.1660G>A	p.Glu554Lys	p.E554K	ENST00000263734	NM_001430.4	554	Gag/Aag	12/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.260287819677754	2		909	762	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67632453	67632453	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	62	481	0	ENST00000272342.5:c.2639A>T	p.Lys880Ile	p.K880I	ENST00000272342	NM_019002.3	880	aAa/aTa	5/6	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.260287819677754	2		481	453	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748575	40748575	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1166829821	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	52	455	0	ENST00000373198.4:c.2941G>A	p.Gly981Ser	p.G981S	ENST00000373198	NM_133170.3	981	Ggt/Agt	21/32	1	2	FACETS	0.929	0.793	1	0.929	0.793	1	CLONAL	1	TRUE	1	0.260287819677754	2		455	430	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933524	49933524	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746705991	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	147	980	0	ENST00000296474.3:c.2666C>T	p.Ala889Val	p.A889V	ENST00000296474	NM_002447.2	889	gCt/gTt	11/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.260287819677754	2		980	919	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443876	52443877	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	70	800	0	ENST00000460680.1:c.18_19delinsAA	p.Glu7Lys	p.E7K	ENST00000460680	NM_004656.3	6	ctGGag/ctAAag	1/17	1	2	FACETS	0.91	0.794	1	0.91	0.794	1	CLONAL	1	TRUE	1	0.260287819677754	2		800	591	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623257	52623257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	106	563	0	ENST00000394830.3:c.2794G>T	p.Glu932Ter	p.E932*	ENST00000394830	NM_018313.4	932	Gaa/Taa	19/30	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.260287819677754	2		563	668	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713622	52713623	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	95	684	0	ENST00000394830.3:c.105dup	p.Arg36GlufsTer17	p.R36Efs*17	ENST00000394830	NM_018313.4	35	-/G	2/30	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.260287819677754	2		684	702	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165632	185165632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	84	573	0	ENST00000265026.3:c.907G>A	p.Glu303Lys	p.E303K	ENST00000265026	NM_004721.4	303	Gaa/Aaa	5/14	1	2	FACETS	0.981	0.867	1	0.981	0.867	1	CLONAL	1	TRUE	1	0.260287819677754	2		573	658	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582039	189582039	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	87	736	0	ENST00000264731.3:c.598A>T	p.Lys200Ter	p.K200*	ENST00000264731	NM_003722.4	200	Aaa/Taa	5/14	1	2	FACETS	0.993	0.88	1	0.993	0.88	1	CLONAL	1	TRUE	1	0.260287819677754	2		736	673	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750557	41750557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	73	774	0	ENST00000226382.2:c.71C>T	p.Ser24Leu	p.S24L	ENST00000226382	NM_003924.3	24	tCg/tTg	1/3	1	2	FACETS	0.979	0.857	1	0.979	0.857	1	CLONAL	1	TRUE	1	0.260287819677754	2		774	573	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156479	55156479	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	52	520	0	ENST00000257290.5:c.2881-1G>A		p.X961_splice	ENST00000257290	NM_006206.4	961			1	2	FACETS	0.826	0.703	0.959	0.826	0.703	0.959	CLONAL	1	TRUE	1	0.260287819677754	2		520	484	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539627	187539627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	90	743	1	ENST00000441802.2:c.8113G>A	p.Glu2705Lys	p.E2705K	ENST00000441802	NM_005245.3	2705	Gaa/Aaa	10/27	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.260287819677754	2		744	660	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867548	35867548	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	56	507	1	ENST00000303115.3:c.362T>A	p.Ile121Lys	p.I121K	ENST00000303115	NM_002185.3	121	aTa/aAa	3/8	1	2	FACETS	0.8	0.685	0.925	0.8	0.685	0.925	CLONAL	1	TRUE	1	0.260287819677754	2		508	538	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722118	176722118	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	110	907	0	ENST00000439151.2:c.7749G>T	p.Met2583Ile	p.M2583I	ENST00000439151	NM_022455.4	2583	atG/atT	23/23	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.260287819677754	2		907	824	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700228	117700229	+	missense_variant	Missense_Mutation	DNP	CC	CC	GA	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	61	564	0	ENST00000368508.3:c.2590_2591delinsTC	p.Gly864Ser	p.G864S	ENST00000368508	NM_002944.2	864	GGa/TCa	17/43	1	2	FACETS	0.898	0.775	1	0.898	0.775	1	CLONAL	1	TRUE	1	0.260287819677754	2		564	522	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968268	2968268	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	82	767	0	ENST00000396946.4:c.1718T>G	p.Ile573Ser	p.I573S	ENST00000396946	NM_032415.4	573	aTc/aGc	13/25	1	2	FACETS	0.946	0.834	1	0.946	0.834	1	CLONAL	1	TRUE	1	0.260287819677754	2		767	666	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358999	81358999	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	90	617	0	ENST00000222390.5:c.962G>A	p.Trp321Ter	p.W321*	ENST00000222390	NM_000601.4	321	tGg/tAg	8/18	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.260287819677754	2		617	622	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359033	81359033	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	92	562	0	ENST00000222390.5:c.928G>A	p.Gly310Arg	p.G310R	ENST00000222390	NM_000601.4	310	Gga/Aga	8/18	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.260287819677754	2		562	624	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950499	68950499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	76	556	0	ENST00000288368.4:c.811C>T	p.Leu271Phe	p.L271F	ENST00000288368	NM_024870.2	271	Ctt/Ttt	7/40	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.260287819677754	2		556	482	SUCCESS
MTAP	4507	MSKCC	GRCh37	9	21818189	21818189	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	62	526	0	ENST00000380172.4:c.335A>G	p.Gln112Arg	p.Q112R	ENST00000380172	NM_002451.3	112	cAg/cGg	4/8	0.260287819677754	1	FACETS	0.999	0.866	1	0.999	0.866	1	CLONAL	1	TRUE	0	0.260287819677754	1		526	415	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624603	93624603	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0064467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	30	685	0	ENST00000375746.1:c.694A>T	p.Lys232Ter	p.K232*	ENST00000375746	NM_001174167.1	232	Aag/Tag	4/14	0.260287819677754	1	FACETS	0.408	0.328	0.498	0.408	0.328	0.498	SUBCLONAL	1	TRUE	0	0.260287819677754	1		685	492	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	12	344	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.187	0.131	0.257	0.187	0.131	0.257	SUBCLONAL	1	FALSE	1	0.392577151793803	2		344	327	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0064469-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	16	453	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		453	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577567	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1567549651	NA	P-0064470-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	165	603	0	ENST00000269305.4:c.714dup	p.Asn239Ter	p.N239*	ENST00000269305	NM_001126112.2	238	-/T	7/11	0.318092095790555	2	FACETS	0.841	0.775	0.908	0.841	0.775	0.908	CLONAL	2	TRUE	0	0.318092095790555	2		603	617	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399937	139399937	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1414066424	NA	P-0064470-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	214	809	0	ENST00000277541.6:c.4411G>A	p.Ala1471Thr	p.A1471T	ENST00000277541	NM_017617.3	1471	Gcg/Acg	25/34	0.308253113036077	3	FACETS	0.933	0.868	0.999	0.933	0.868	0.999	CLONAL	2	TRUE	1	0.318092095790555	3		809	836	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993195	72993195	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064470-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	240	714	0	ENST00000268489.5:c.850T>G	p.Cys284Gly	p.C284G	ENST00000268489	NM_006885.3	284	Tgt/Ggt	2/10	0.318092095790555	3	FACETS	0.977	0.914	1	0.977	0.914	1	CLONAL	2	TRUE	1	0.318092095790555	3		714	895	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	70	460	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.943	0.822	1	0.943	0.822	1	CLONAL	1	TRUE	1	0.2	2		460	742	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624245	89624245	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554890335	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	19	174	0	ENST00000371953.3:c.19G>T	p.Glu7Ter	p.E7*	ENST00000371953	NM_000314.4	7	Gag/Tag	1/9	1	2	FACETS	1	0.824	1	1	0.824	1	CLONAL	1	TRUE	1	0.2	2		174	173	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	47	447	1	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.2	2		448	385	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	48	554	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.978	0.827	1	0.978	0.827	1	CLONAL	1	TRUE	1	0.2	2		554	491	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642538	117642538	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	73	641	0	ENST00000368508.3:c.5661G>T	p.Lys1887Asn	p.K1887N	ENST00000368508	NM_002944.2	1887	aaG/aaT	35/43	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.2	2		641	588	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	14	283	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.423	0.305	0.567	0.423	0.305	0.567	SUBCLONAL	1	TRUE	1	0.2	2		283	331	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429757	78429757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755419864	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	65	568	0	ENST00000370768.2:c.1031G>A	p.Arg344Gln	p.R344Q	ENST00000370768	NM_003902.3	344	cGa/cAa	12/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.2	2		568	479	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919244	48919244	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913296	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	15	362	0	ENST00000267163.4:c.409G>T	p.Glu137Ter	p.E137*	ENST00000267163	NM_000321.2	137	Gaa/Taa	4/27	1	2	FACETS	0.538	0.393	0.712	0.538	0.393	0.712	SUBCLONAL	1	TRUE	1	0.2	2		362	279	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487277	56487277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035001455	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	59	576	0	ENST00000267101.3:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000267101	NM_001982.3	475	Cgg/Tgg	12/28	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.2	2		576	586	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10267124	10267124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751093624	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	27	540	0	ENST00000340748.4:c.1294G>A	p.Glu432Lys	p.E432K	ENST00000340748		432	Gaa/Aaa	17/40	1	2	FACETS	0.454	0.36	0.562	0.454	0.36	0.562	SUBCLONAL	1	TRUE	1	0.2	2		540	595	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698180	47698180	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63751411	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	21	425	0	ENST00000233146.2:c.1738G>T	p.Glu580Ter	p.E580*	ENST00000233146	NM_000251.2	580	Gaa/Taa	11/16	1	2	FACETS	0.522	0.401	0.664	0.522	0.401	0.664	SUBCLONAL	1	TRUE	1	0.2	2		425	402	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412494	80412494	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	29	624	0	ENST00000286548.4:c.547C>T	p.Arg183Ter	p.R183*	ENST00000286548	NM_002072.3	183	Cga/Tga	4/7	1	2	FACETS	0.47	0.376	0.578	0.47	0.376	0.578	SUBCLONAL	1	TRUE	1	0.2	2		624	617	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244664	41244664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80356955	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	51	694	0	ENST00000357654.3:c.2884G>A	p.Glu962Lys	p.E962K	ENST00000357654	NM_007294.3	962	Gaa/Aaa	10/23	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.2	2		694	505	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716094	243716094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	24	447	0	ENST00000263826.5:c.1100G>A	p.Arg367Gln	p.R367Q	ENST00000263826	NM_005465.4	367	cGa/cAa	10/13	1	2	FACETS	0.633	0.496	0.792	0.633	0.496	0.792	SUBCLONAL	1	TRUE	1	0.2	2		447	379	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649005	86649005	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	42	431	0	ENST00000274376.6:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000274376	NM_002890.2	429	Gaa/Taa	9/25	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.2	2		431	316	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793432	18793432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187869576	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	41	493	0	ENST00000266497.5:c.4129C>T	p.Arg1377Cys	p.R1377C	ENST00000266497		1377	Cgt/Tgt	30/31	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.2	2		493	386	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5077508	5077508	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	28	251	0	ENST00000381652.3:c.1920G>T	p.Lys640Asn	p.K640N	ENST00000381652	NM_004972.3	640	aaG/aaT	15/25	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.2	2		251	197	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285863	39285863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	31	401	0	ENST00000402219.2:c.296G>A	p.Arg99Gln	p.R99Q	ENST00000402219	NM_005633.3	99	cGa/cAa	3/23	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.2	2		401	287	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839671	42839671	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs572530227	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	58	651	0	ENST00000398585.3:c.1568G>A	p.Arg523Gln	p.R523Q	ENST00000398585	NM_001135099.1	523	cGa/cAa	13/14	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.2	2		651	548	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779424	3779424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1032604340	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	73	895	0	ENST00000262367.5:c.5624G>A	p.Arg1875His	p.R1875H	ENST00000262367	NM_004380.2	1875	cGc/cAc	31/31	1	2	FACETS	0.979	0.855	1	0.979	0.855	1	CLONAL	1	TRUE	1	0.2	2		895	746	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431404	121431404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780357	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	35	780	0	ENST00000257555.6:c.608G>A	p.Arg203His	p.R203H	ENST00000257555		203	cGt/cAt	3/10	1	2	FACETS	0.55	0.45	0.664	0.55	0.45	0.664	SUBCLONAL	1	TRUE	1	0.2	2		780	636	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745466	162745466	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	59	661	0	ENST00000367921.3:c.1881G>T	p.Lys627Asn	p.K627N	ENST00000367921	NM_006182.2	627	aaG/aaT	15/18	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.2	2		661	445	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012244	152012244	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748254163	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	48	533	0	ENST00000262189.6:c.569G>A	p.Arg190Gln	p.R190Q	ENST00000262189	NM_170606.2	190	cGa/cAa	4/59	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.2	2		533	430	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038130	128038130	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	35	586	0	ENST00000285398.2:c.1420G>T	p.Asp474Tyr	p.D474Y	ENST00000285398	NM_000122.1	474	Gat/Tat	9/15	1	2	FACETS	0.59	0.483	0.712	0.59	0.483	0.712	SUBCLONAL	1	TRUE	1	0.2	2		586	593	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231206	98231206	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	53	875	0	ENST00000331920.6:c.2077A>G	p.Thr693Ala	p.T693A	ENST00000331920	NM_000264.3	693	Aca/Gca	14/24	1	2	FACETS	0.72	0.613	0.838	0.72	0.613	0.838	SUBCLONAL	1	TRUE	1	0.2	2		875	736	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39237792	39237792	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	37	412	1	ENST00000402219.2:c.2443G>T	p.Glu815Ter	p.E815*	ENST00000402219	NM_005633.3	815	Gaa/Taa	15/23	1	2	FACETS	0.894	0.737	1	0.894	0.737	1	CLONAL	1	TRUE	1	0.2	2		413	414	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249471	153249471	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	41	578	0	ENST00000281708.4:c.1307G>T	p.Ser436Ile	p.S436I	ENST00000281708	NM_033632.3	436	aGt/aTt	9/12	1	2	FACETS	0.923	0.77	1	0.923	0.77	1	CLONAL	1	TRUE	1	0.2	2		578	444	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038531	47038531	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	51	609	0	ENST00000377604.3:c.693G>T	p.Glu231Asp	p.E231D	ENST00000377604	NM_001204468.1	231	gaG/gaT	8/24	1	2	FACETS	0.843	0.716	0.983	0.843	0.716	0.983	CLONAL	1	TRUE	1	0.2	2		609	605	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855977	76855977	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	25	619	0	ENST00000373344.5:c.5623G>T	p.Asp1875Tyr	p.D1875Y	ENST00000373344	NM_000489.3	1875	Gat/Tat	23/35	1	2	FACETS	0.604	0.475	0.752	0.604	0.475	0.752	SUBCLONAL	1	TRUE	1	0.2	2		619	414	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80171602	80171602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576204286	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	46	514	0	ENST00000265081.6:c.3335C>T	p.Thr1112Met	p.T1112M	ENST00000265081	NM_002439.4	1112	aCg/aTg	24/24	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.2	2		514	419	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738308	190738308	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	36	443	0	ENST00000441310.2:c.2560C>A	p.Leu854Ile	p.L854I	ENST00000441310	NM_000534.4	854	Ctt/Att	12/13	1	2	FACETS	1	0.828	1	1	0.828	1	CLONAL	1	TRUE	1	0.2	2		443	358	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136289	202136289	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	61	524	1	ENST00000358485.4:c.533C>A	p.Ser178Tyr	p.S178Y	ENST00000358485	NM_001080125.1	178	tCt/tAt	3/9	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.2	2		525	487	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557968	187557968	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	56	670	0	ENST00000441802.2:c.3743A>C	p.Lys1248Thr	p.K1248T	ENST00000441802	NM_005245.3	1248	aAg/aCg	5/27	1	2	FACETS	0.838	0.717	0.971	0.838	0.717	0.971	CLONAL	1	TRUE	1	0.2	2		670	668	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288839	33288839	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	35	764	0	ENST00000374542.5:c.713G>A	p.Arg238Gln	p.R238Q	ENST00000374542	NM_001141970.1	238	cGa/cAa	3/8	1	2	FACETS	0.591	0.483	0.713	0.591	0.483	0.713	SUBCLONAL	1	TRUE	1	0.2	2		764	592	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856060	151856060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751794784	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	39	590	0	ENST00000262189.6:c.11558G>A	p.Arg3853Gln	p.R3853Q	ENST00000262189	NM_170606.2	3853	cGg/cAg	44/59	1	2	FACETS	0.583	0.482	0.696	0.583	0.482	0.696	SUBCLONAL	1	TRUE	1	0.2	2		590	669	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230492780	230492780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	58	746	0	ENST00000391860.1:c.274C>T	p.Arg92Cys	p.R92C	ENST00000391860	NM_001258311.1	92	Cgc/Tgc	2/7	1	2	FACETS	0.943	0.81	1	0.943	0.81	1	CLONAL	1	TRUE	1	0.2	2		746	615	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944568	71944568	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	51	788	0	ENST00000298229.2:c.2122+2T>C		p.X708_splice	ENST00000298229	NM_001567.3	708			1	2	FACETS	0.87	0.739	1	0.87	0.739	1	CLONAL	1	TRUE	1	0.2	2		788	586	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192035	108192035	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	51	452	0	ENST00000278616.4:c.6460G>T	p.Glu2154Ter	p.E2154*	ENST00000278616	NM_000051.3	2154	Gaa/Taa	45/63	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.2	2		452	488	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624568	21624568	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	42	486	0	ENST00000421138.2:c.1461G>T	p.Lys487Asn	p.K487N	ENST00000421138		487	aaG/aaT	14/16	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.2	2		486	366	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111886023	111886023	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs548593303	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	63	794	1	ENST00000341259.2:c.1645C>T	p.Arg549Ter	p.R549*	ENST00000341259	NM_005475.2	549	Cga/Tga	8/8	1	2	FACETS	0.882	0.762	1	0.882	0.762	1	CLONAL	1	TRUE	1	0.2	2		795	714	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252327	133252327	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	35	592	0	ENST00000320574.5:c.1100T>G	p.Phe367Cys	p.F367C	ENST00000320574	NM_006231.2	367	tTt/tGt	11/49	1	2	FACETS	0.622	0.508	0.749	0.622	0.508	0.749	SUBCLONAL	1	TRUE	1	0.2	2		592	563	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608448	28608448	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs753639225	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	67	646	0	ENST00000241453.7:c.1694A>C	p.Lys565Thr	p.K565T	ENST00000241453	NM_004119.2	565	aAg/aCg	13/24	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.2	2		646	538	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907180	32907180	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	25	641	0	ENST00000380152.3:c.1565G>A	p.Gly522Asp	p.G522D	ENST00000380152		522	gGt/gAt	10/27	1	2	FACETS	0.605	0.476	0.754	0.605	0.476	0.754	SUBCLONAL	1	TRUE	1	0.2	2		641	413	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636030	73636030	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	31	641	1	ENST00000377687.4:c.293C>T	p.Pro98Leu	p.P98L	ENST00000377687	NM_001730.3	98	cCt/cTt	2/4	1	2	FACETS	0.598	0.483	0.73	0.598	0.483	0.73	SUBCLONAL	1	TRUE	1	0.2	2		642	518	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779686	3779686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064795794	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	58	880	3	ENST00000262367.5:c.5362G>A	p.Ala1788Thr	p.A1788T	ENST00000262367	NM_004380.2	1788	Gcc/Acc	31/31	1	2	FACETS	0.83	0.712	0.959	0.83	0.712	0.959	CLONAL	1	TRUE	1	0.2	2		883	699	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877401	89877401	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	67	658	0	ENST00000389301.3:c.362T>C	p.Val121Ala	p.V121A	ENST00000389301	NM_000135.2	121	gTg/gCg	4/43	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.2	2		658	670	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562747	29562747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137854556	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	40	519	0	ENST00000356175.3:c.3827G>A	p.Arg1276Gln	p.R1276Q	ENST00000356175	NM_000267.3	1276	cGa/cAa	28/57	1	2	FACETS	0.833	0.692	0.99	0.833	0.692	0.99	CLONAL	1	TRUE	1	0.2	2		519	480	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312955	30312955	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	33	705	0	ENST00000262643.3:c.758A>G	p.Tyr253Cys	p.Y253C	ENST00000262643	NM_001238.2	253	tAc/tGc	9/12	1	2	FACETS	0.556	0.451	0.674	0.556	0.451	0.674	SUBCLONAL	1	TRUE	1	0.2	2		705	594	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425543	47425543	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs985060376	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	73	715	0	ENST00000404338.3:c.3611T>C	p.Val1204Ala	p.V1204A	ENST00000404338	NM_004491.4	1204	gTc/gCc	1/6	1	2	FACETS	0.992	0.867	1	0.992	0.867	1	CLONAL	1	TRUE	1	0.2	2		715	736	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723073	52723073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	70	699	2	ENST00000322088.6:c.1258C>T	p.Arg420Trp	p.R420W	ENST00000322088	NM_014225.5	420	Cgg/Tgg	10/15	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.2	2		701	637	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498359	29498359	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	47	609	0	ENST00000389048.3:c.1821C>A	p.Phe607Leu	p.F607L	ENST00000389048	NM_004304.4	607	ttC/ttA	10/29	1	2	FACETS	0.835	0.704	0.979	0.835	0.704	0.979	CLONAL	1	TRUE	1	0.2	2		609	563	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630492	67630492	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	15	444	0	ENST00000272342.5:c.678G>T	p.Glu226Asp	p.E226D	ENST00000272342	NM_019002.3	226	gaG/gaT	5/6	1	2	FACETS	0.505	0.369	0.669	0.505	0.369	0.669	SUBCLONAL	1	TRUE	1	0.2	2		444	297	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391010	89391010	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	44	588	0	ENST00000336596.2:c.1076T>G	p.Phe359Cys	p.F359C	ENST00000336596	NM_005233.5	359	tTc/tGc	5/17	1	2	FACETS	0.866	0.726	1	0.866	0.726	1	CLONAL	1	TRUE	1	0.2	2		588	508	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204056	142204056	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	44	585	0	ENST00000350721.4:c.6147G>T	p.Leu2049Phe	p.L2049F	ENST00000350721	NM_001184.3	2049	ttG/ttT	36/47	1	2	FACETS	0.851	0.713	1	0.851	0.713	1	CLONAL	1	TRUE	1	0.2	2		585	517	SUCCESS
ATR	545	MSKCC	GRCh37	3	142286967	142286967	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1347107495	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	22	373	0	ENST00000350721.4:c.89T>C	p.Val30Ala	p.V30A	ENST00000350721	NM_001184.3	30	gTa/gCa	2/47	1	2	FACETS	0.615	0.476	0.776	0.615	0.476	0.776	SUBCLONAL	1	TRUE	1	0.2	2		373	358	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007315	143007315	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	34	390	0	ENST00000262992.4:c.2469T>G	p.Ile823Met	p.I823M	ENST00000262992	NM_001101669.1	823	atT/atG	22/24	1	2	FACETS	0.907	0.742	1	0.907	0.742	1	CLONAL	1	TRUE	1	0.2	2		390	375	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180621	56180621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	28	455	0	ENST00000399503.3:c.3950G>A	p.Ser1317Asn	p.S1317N	ENST00000399503	NM_005921.1	1317	aGc/aAc	16/20	1	2	FACETS	0.872	0.698	1	0.872	0.698	1	CLONAL	1	TRUE	1	0.2	2		455	321	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946364	2946364	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	39	654	0	ENST00000396946.4:c.3373T>C	p.Trp1125Arg	p.W1125R	ENST00000396946	NM_032415.4	1125	Tgg/Cgg	25/25	1	2	FACETS	0.74	0.613	0.882	0.74	0.613	0.882	SUBCLONAL	1	TRUE	1	0.2	2		654	527	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187329	38187329	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2234552	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	48	616	0	ENST00000317025.8:c.1148G>A	p.Arg383Gln	p.R383Q	ENST00000317025	NM_023034.1	383	cGa/cAa	6/24	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.2	2		616	477	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74868208	74868208	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	17	177	0	ENST00000284811.8:c.86T>G	p.Phe29Cys	p.F29C	ENST00000284811		29	tTt/tGt	3/4	1	2	FACETS	0.96	0.72	1	0.96	0.72	1	CLONAL	1	TRUE	1	0.2	2		177	177	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44921944	44921944	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1235361183	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	18	363	0	ENST00000377967.4:c.1478T>G	p.Leu493Arg	p.L493R	ENST00000377967	NM_021140.2	493	cTg/cGg	15/29	1	2	FACETS	0.606	0.456	0.783	0.606	0.456	0.783	SUBCLONAL	1	TRUE	1	0.2	2		363	297	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185224	123185224	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	25	340	0	ENST00000218089.9:c.1176A>T	p.Lys392Asn	p.K392N	ENST00000218089	NM_001042749.1	392	aaA/aaT	13/35	1	2	FACETS	0.698	0.55	0.869	0.698	0.55	0.869	SUBCLONAL	1	TRUE	1	0.2	2		340	358	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0064473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	185	467	0	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.238772468589748	3	FACETS	0.859	0.798	0.922	0.859	0.798	0.922	CLONAL	3	TRUE	0	0.279265173770107	3		467	586	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748530	43748530	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	103	686	0	ENST00000382044.4:c.2276C>A	p.Ser759Tyr	p.S759Y	ENST00000382044	NM_001141980.1	759	tCc/tAc	12/28	0.279265173770107	3	FACETS	1	0.899	1	0.503	0.449	0.56	CLONAL	1	TRUE	1	0.279265173770107	3		686	836	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830490	72830490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1597241053	NA	P-0064473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	45	703	0	ENST00000268489.5:c.6091C>T	p.Pro2031Ser	p.P2031S	ENST00000268489	NM_006885.3	2031	Cca/Tca	9/10	0.151394209862385	5	FACETS	0.571	0.478	0.674	0.19	0.159	0.225	INDETERMINATE	1	TRUE	2	0.279265173770107	5		703	801	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208270	5208270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	47	687	0	ENST00000357368.4:c.5620G>A	p.Gly1874Ser	p.G1874S	ENST00000357368	NM_002850.3	1874	Ggc/Agc	36/38	0.173170048976843	3	FACETS	0.511	0.43	0.601	0.17	0.143	0.201	SUBCLONAL	1	TRUE	0	0.279265173770107	3		687	750	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291942	15291942	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs777577687	NA	P-0064473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	45	678	0	ENST00000263388.2:c.2824G>C	p.Gly942Arg	p.G942R	ENST00000263388	NM_000435.2	942	Ggc/Cgc	18/33	0.173170048976843	3	FACETS	0.522	0.437	0.615	0.174	0.145	0.205	SUBCLONAL	1	TRUE	0	0.279265173770107	3		678	704	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138423337	138423337	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0064473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	179	267	0	ENST00000289153.2:c.1531-2A>G		p.X511_splice	ENST00000289153	NM_006219.2	511			0.279265173770107	5	FACETS	1	0.971	1	1	0.991	1	CLONAL	4	TRUE	2	0.279265173770107	5		267	423	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152853900	152853900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557025062	NA	P-0064473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	53	212	0	ENST00000406277.2:c.664G>A	p.Asp222Asn	p.D222N	ENST00000406277	NM_152274.4	222	Gac/Aac	7/7	0.279265173770107	2	FACETS	1	0.955	1			1	CLONAL	1	TRUE	NA	0.279265173770107	2		212	292	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0064481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	164	210	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.942	0.869	1	0.942	0.869	1	CLONAL	1	TRUE	1	0.598237652572675	2		210	582	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0064481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	131	372	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.598237652572675	2		372	366	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0064481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	199	551	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.978	0.91	1	0.978	0.91	1	CLONAL	1	TRUE	1	0.598237652572675	2		552	680	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206646622	206646622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	159	621	0	ENST00000367120.3:c.52G>A	p.Gly18Arg	p.G18R	ENST00000367120	NM_014002.3	18	Ggg/Agg	3/22	1	2	FACETS	0.913	0.841	0.988	0.913	0.841	0.988	CLONAL	1	TRUE	1	0.598237652572675	2		621	582	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632656	3632656	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	179	790	0	ENST00000294008.3:c.5192C>A	p.Ala1731Glu	p.A1731E	ENST00000294008	NM_032444.2	1731	gCa/gAa	15/15	1	2	FACETS	0.956	0.885	1	0.956	0.885	1	CLONAL	1	TRUE	1	0.598237652572675	2		790	626	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47700100	47700100	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	43	518	0	ENST00000347630.2:c.73A>G	p.Thr25Ala	p.T25A	ENST00000347630	NM_001007230.1	25	Aca/Gca	3/11	1	2	FACETS	0.22	0.184	0.261	0.22	0.184	0.261	SUBCLONAL	1	TRUE	1	0.598237652572675	2		518	652	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913492	NA	P-0064482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	203	318	0	ENST00000286548.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000286548	NM_002072.3	209	cAa/cTa	5/7	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.688023980178663	2		318	430	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0064483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	157	372	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.608530628910214	2		372	479	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221743	55221743	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519829	NA	P-0064483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1750	22526	878	0	ENST00000275493.2:c.787A>C	p.Thr263Pro	p.T263P	ENST00000275493	NM_005228.3	263	Acc/Ccc	7/28	0.608530628910214	48	FACETS	0.994	0.992	0.997			1	CLONAL	46	TRUE	NA	0.608530628910214	48		878	24276	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591135	67591137	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0064483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	160	473	0	ENST00000274335.5:c.1728_1730del	p.Arg577del	p.R577del	ENST00000274335		576	acGAGa/aca	12/15	1	2	FACETS	0.875	0.806	0.946	0.875	0.806	0.946	CLONAL	1	TRUE	1	0.608530628910214	2		473	601	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261244	115261244	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	225	551	0	ENST00000438362.2:c.2477A>G	p.Asp826Gly	p.D826G	ENST00000438362	NM_001242891.1	826	gAt/gGt	19/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.608530628910214	2		551	711	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0064484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	673	598	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	0.57325308989164	5	FACETS	0.949	0.921	0.976	0.949	0.921	0.976	CLONAL	4	TRUE	1	0.635653901590187	5		598	1090	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	223	655	2	ENST00000269305.4:c.379T>C	p.Ser127Pro	p.S127P	ENST00000269305	NM_001126112.2	127	Tcc/Ccc	5/11	0.57325308989164	5	FACETS	1	0.949	1	0.256	0.238	0.276	CLONAL	1	TRUE	1	0.635653901590187	5		657	1336	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040642	16040642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	75	324	0	ENST00000268712.3:c.1492C>T	p.Arg498Cys	p.R498C	ENST00000268712	NM_006311.3	498	Cgc/Tgc	14/46	0.57325308989164	5	FACETS	0.789	0.692	0.894	0.197	0.173	0.224	SUBCLONAL	1	TRUE	1	0.635653901590187	5		324	584	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046534	30046534	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	103	609	0	ENST00000331968.5:c.2649C>G	p.His883Gln	p.H883Q	ENST00000331968	NM_002742.2	883	caC/caG	18/18	0.361958106853692	3	FACETS	0.542	0.485	0.603	0.271	0.242	0.302	INDETERMINATE	1	TRUE	1	0.635653901590187	3		609	788	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184517	7184517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141484557	NA	P-0064484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	462	509	0	ENST00000302850.5:c.784G>A	p.Gly262Ser	p.G262S	ENST00000302850	NM_000208.2	262	Ggc/Agc	3/22	0.635653901590187	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.635653901590187	3		509	902	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515219	106515219	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	191	510	0	ENST00000359195.3:c.2362G>T	p.Asp788Tyr	p.D788Y	ENST00000359195	NM_002649.2	788	Gat/Tat	5/11	0.635653901590187	3	FACETS	1	0.947	1	0.514	0.476	0.553	CLONAL	1	TRUE	1	0.635653901590187	3		510	771	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814583	43814583	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	88	690	0	ENST00000372470.3:c.1378C>A	p.Gln460Lys	p.Q460K	ENST00000372470	NM_005373.2	460	Cag/Aag	9/12	0.422070573106327	3	FACETS	0.536	0.475	0.601	0.268	0.237	0.301	SUBCLONAL	1	TRUE	1	0.635653901590187	3		690	681	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624479	21624480	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0064484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	192	536	0	ENST00000421138.2:c.1549_1550delinsAT	p.Asp517Ile	p.D517I	ENST00000421138		517	GAt/ATt	14/16	0.635653901590187	2	FACETS	0.985	0.917	1	0.493	0.458	0.528	CLONAL	1	TRUE	0	0.635653901590187	2		536	613	SUCCESS
BLM	641	MSKCC	GRCh37	15	91341459	91341459	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1421330208	NA	P-0064484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	55	229	0	ENST00000355112.3:c.3250A>G	p.Ile1084Val	p.I1084V	ENST00000355112	NM_000057.2	1084	Att/Gtt	17/22	0.635653901590187	7	FACETS	0.79	0.676	0.915	0.132	0.112	0.153	CLONAL	1	TRUE	1	0.635653901590187	7		229	567	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226168	2226168	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	188	758	0	ENST00000326181.6:c.1865A>G	p.Asp622Gly	p.D622G	ENST00000326181	NM_032271.2	622	gAc/gGc	19/21	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.635653901590187	2		758	579	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16055294	16055294	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	109	242	0	ENST00000268712.3:c.808T>C	p.Ser270Pro	p.S270P	ENST00000268712	NM_006311.3	270	Tca/Cca	8/46	0.57325308989164	5	FACETS	1	0.958	1	0.28	0.251	0.309	CLONAL	1	TRUE	1	0.635653901590187	5		242	599	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290291	15290291	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1399228829	NA	P-0064484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	246	657	0	ENST00000263388.2:c.3344A>G	p.Asn1115Ser	p.N1115S	ENST00000263388	NM_000435.2	1115	aAt/aGt	21/33	0.635653901590187	3	FACETS	1	0.974	1	0.537	0.503	0.573	CLONAL	1	TRUE	1	0.635653901590187	3		657	949	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215633963	215633963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs957472472	NA	P-0064484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	365	386	0	ENST00000260947.4:c.1388C>T	p.Thr463Ile	p.T463I	ENST00000260947	NM_000465.2	463	aCa/aTa	5/11	0.635653901590187	3	FACETS	0.966	0.933	0.999	0.966	0.933	0.999	CLONAL	3	TRUE	0	0.635653901590187	3		386	522	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751448	57751448	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	438	616	0	ENST00000274289.3:c.1543G>A	p.Gly515Ser	p.G515S	ENST00000274289	NM_006622.3	515	Ggc/Agc	11/14	0.315382866307663	3	FACETS	1	0.971	1	0.676	0.649	0.704	INDETERMINATE	2	TRUE	0	0.635653901590187	3		616	895	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505130	149505130	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	428	628	0	ENST00000261799.4:c.1685A>C	p.Tyr562Ser	p.Y562S	ENST00000261799	NM_002609.3	562	tAc/tCc	12/23	0.315382866307663	3	FACETS	1	0.981	1	0.691	0.663	0.719	INDETERMINATE	2	TRUE	0	0.635653901590187	3		628	856	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005946	69005946	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	207	426	0	ENST00000288368.4:c.2357G>C	p.Cys786Ser	p.C786S	ENST00000288368	NM_024870.2	786	tGt/tCt	21/40	0.244532309934462	6	FACETS	1	0.984	1	0.78	0.728	0.834	INDETERMINATE	2	TRUE	3	0.635653901590187	6		426	632	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740774	145740774	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1392	226	738	0	ENST00000428558.2:c.1326G>T	p.Glu442Asp	p.E442D	ENST00000428558	NM_004260.3	442	gaG/gaT	7/22	0.635653901590187	6	FACETS	0.998	0.927	1			1	CLONAL	1	TRUE	NA	0.635653901590187	6		738	1618	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891415	76891415	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	75	290	0	ENST00000373344.5:c.4690C>G	p.Gln1564Glu	p.Q1564E	ENST00000373344	NM_000489.3	1564	Caa/Gaa	16/35	0.635653901590187	1	FACETS	0.865	0.775	0.958	0.865	0.775	0.958	CLONAL	1	TRUE	0	0.635653901590187	1		290	186	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0064485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	66	651	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	1	2	FACETS	0.992	0.861	1	0.992	0.861	1	CLONAL	1	TRUE	1	0.19	2		651	700	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0064487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	260	691	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.476371855560351	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.476371855560351	1		691	752	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753910	133753910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149852028	NA	P-0064487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	202	609	2	ENST00000318560.5:c.1379G>A	p.Arg460His	p.R460H	ENST00000318560	NM_005157.4	460	cGc/cAc	8/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.476371855560351	2		611	802	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140900	37140900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773910971	NA	P-0064487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	263	737	0	ENST00000373509.5:c.736G>A	p.Glu246Lys	p.E246K	ENST00000373509	NM_002648.3	246	Gaa/Aaa	5/6	0.476371855560351	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.476371855560351	1		737	810	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410656	32410656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	242	703	0	ENST00000332351.3:c.1502G>A	p.Arg501His	p.R501H	ENST00000332351	NM_024426.4	501	cGc/cAc	10/10	0.476371855560351	1	FACETS	0.977	0.916	1	0.977	0.916	1	CLONAL	1	TRUE	0	0.476371855560351	1		703	792	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654646	67654646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	239	622	0	ENST00000264010.4:c.1133C>T	p.Pro378Leu	p.P378L	ENST00000264010	NM_006565.3	378	cCg/cTg	6/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.476371855560351	2		622	948	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951170	48951170	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	115	323	0	ENST00000267163.4:c.1332G>T	p.Gln444His	p.Q444H	ENST00000267163	NM_000321.2	444	caG/caT	13/27	0.476371855560351	1	FACETS	0.929	0.844	1	0.929	0.844	1	CLONAL	1	TRUE	0	0.476371855560351	1		323	396	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289275	33289275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	236	444	1	ENST00000374542.5:c.277C>T	p.Gln93Ter	p.Q93*	ENST00000374542	NM_001141970.1	93	Caa/Taa	3/8	0.476371855560351	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.476371855560351	1		445	747	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348866	89348866	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748428674	NA	P-0064487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	317	873	0	ENST00000301030.4:c.4084G>A	p.Asp1362Asn	p.D1362N	ENST00000301030	NM_001256183.1	1362	Gac/Aac	9/13	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.476371855560351	2		873	1226	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851575	63851575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376632312	NA	P-0064487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	313	902	0	ENST00000279873.7:c.2353C>T	p.Arg785Cys	p.R785C	ENST00000279873	NM_032199.2	785	Cgc/Tgc	10/10	0.476371855560351	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.476371855560351	1		902	896	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0064487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	168	550	5	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.872	0.802	0.944	0.872	0.802	0.944	CLONAL	1	TRUE	1	0.476371855560351	2		555	809	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436300	110436300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	295	1055	0	ENST00000375856.3:c.2101G>A	p.Ala701Thr	p.A701T	ENST00000375856	NM_003749.2	701	Gcc/Acc	1/2	0.476371855560351	1	FACETS	0.967	0.911	1	0.967	0.911	1	CLONAL	1	TRUE	0	0.476371855560351	1		1055	976	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025857	48025860	+	frameshift_variant	Frame_Shift_Del	DEL	AAAA	AAAA	-	novel	NA	P-0064487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	214	701	0	ENST00000234420.5:c.738_741del	p.Lys246AsnfsTer32	p.K246Nfs*32	ENST00000234420	NM_000179.2	245	atAAAA/at	4/10	0.476371855560351	1	FACETS	0.941	0.878	1	0.941	0.878	1	CLONAL	1	TRUE	0	0.476371855560351	1		701	727	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0064488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	135	612	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.533987217776579	1	FACETS	0.92	0.844	0.997	0.92	0.844	0.997	CLONAL	1	TRUE	0	0.533987217776579	1		612	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0064488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	339	710	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.533987217776579	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.533987217776579	2		710	629	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970969	21970969	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	195	930	1	ENST00000304494.5:c.389T>A	p.Leu130Gln	p.L130Q	ENST00000304494	NM_000077.4	130	cTg/cAg	2/3	0.533987217776579	3	FACETS	0.937	0.867	1	0.468	0.433	0.505	CLONAL	1	TRUE	1	0.533987217776579	3		931	988	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100999	41100999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1371429276	NA	P-0064488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	350	731	1	ENST00000373198.4:c.1357C>T	p.Arg453Cys	p.R453C	ENST00000373198	NM_133170.3	453	Cgc/Tgc	8/32	0.216262360622899	6	FACETS	0.903	0.857	0.949	0.903	0.857	0.949	INDETERMINATE	3	TRUE	3	0.533987217776579	6		732	1001	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794868	242794868	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55679128	NA	P-0064488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	102	839	0	ENST00000334409.5:c.341G>A	p.Arg114Gln	p.R114Q	ENST00000334409	NM_005018.2	114	cGg/cAg	2/5	0.473096777902929	3	FACETS	0.583	0.521	0.649	0.292	0.26	0.325	SUBCLONAL	1	TRUE	1	0.533987217776579	3		839	830	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024584	11024584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757525257	NA	P-0064488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	353	737	1	ENST00000327064.4:c.701G>A	p.Arg234His	p.R234H	ENST00000327064	NM_199141.1	234	cGc/cAc	6/16	0.473096777902929	3	FACETS	0.976	0.929	1	0.976	0.929	1	CLONAL	2	TRUE	1	0.533987217776579	3		738	858	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405961	70405961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752034407	NA	P-0064488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	173	733	1	ENST00000373644.4:c.3475C>T	p.Arg1159Trp	p.R1159W	ENST00000373644	NM_030625.2	1159	Cgg/Tgg	4/12	0.533987217776579	3	FACETS	0.961	0.886	1	0.481	0.443	0.52	CLONAL	1	TRUE	1	0.533987217776579	3		734	854	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28885816	28885816	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	279	554	0	ENST00000282397.4:c.3546T>A	p.Phe1182Leu	p.F1182L	ENST00000282397	NM_002019.4	1182	ttT/ttA	27/30	0.216262360622899	6	FACETS	0.912	0.86	0.964	0.912	0.86	0.964	INDETERMINATE	3	TRUE	3	0.533987217776579	6		554	790	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0064489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	31	210	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.848	0.687	1	0.848	0.687	1	CLONAL	1	TRUE	1	0.21	2		210	348	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845590	63845590	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	47	670	0	ENST00000279873.7:c.1329del	p.Ile444SerfsTer35	p.I444Sfs*35	ENST00000279873	NM_032199.2	443	cgC/cg	9/10	1	2	FACETS	0.724	0.61	0.85	0.724	0.61	0.85	SUBCLONAL	1	TRUE	1	0.21	2		670	618	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692790	89692790	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	32	295	0	ENST00000371953.3:c.274G>C	p.Asp92His	p.D92H	ENST00000371953	NM_000314.4	92	Gac/Cac	5/9	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.21	2		295	204	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638911	176638911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367790484	NA	P-0064489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	48	629	0	ENST00000439151.2:c.3511C>T	p.Arg1171Cys	p.R1171C	ENST00000439151	NM_022455.4	1171	Cgt/Tgt	5/23	1	2	FACETS	0.61	0.515	0.716	0.61	0.515	0.716	SUBCLONAL	1	TRUE	1	0.21	2		629	749	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159751	20159751	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	16	388	0	ENST00000379607.5:c.8A>G	p.Lys3Arg	p.K3R	ENST00000379607	NM_001412.3	3	aAg/aGg	1/7	1	2	FACETS	0.586	0.433	0.769	0.586	0.433	0.769	SUBCLONAL	1	TRUE	1	0.21	2		388	260	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0064490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	157	371	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.445421826833708	2		371	588	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0064490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	130	372	0				ENST00000310581	NM_198253.2	-/1132			0.445421826833708	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.445421826833708	1		372	400	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797235	32797235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768383489	NA	P-0064490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	178	743	0	ENST00000374899.4:c.1874C>T	p.Pro625Leu	p.P625L	ENST00000374899	NM_018833.2	625	cCg/cTg	11/12	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.445421826833708	2		743	727	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740672	58740672	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	212	768	0	ENST00000305921.3:c.1577T>C	p.Ile526Thr	p.I526T	ENST00000305921	NM_003620.3	526	aTt/aCt	6/6	0.200450990715492	3	FACETS	1	0.98	1	0.574	0.533	0.616	INDETERMINATE	1	TRUE	1	0.445421826833708	3		768	1014	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212114	36212115	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0064490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	87	457	0	ENST00000222270.7:c.1865_1866delinsTT	p.Pro622Leu	p.P622L	ENST00000222270	NM_014727.1	622	cCC/cTT	3/37	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.445421826833708	2		457	372	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609647	46609647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	183	834	0	ENST00000263734.3:c.2371C>T	p.Pro791Ser	p.P791S	ENST00000263734	NM_001430.4	791	Ccc/Tcc	15/16	1	2	FACETS	0.96	0.887	1	0.96	0.887	1	CLONAL	1	TRUE	1	0.445421826833708	2		834	856	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0064498-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	874	347	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.262450008424989	22	FACETS	1	0.982	1	0.956	0.934	0.977	CLONAL	19	TRUE	2	0.262450008424989	22		347	1263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587782272	NA	P-0064498-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	80	369	0	ENST00000269305.4:c.994-1G>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.170177920188597	2	FACETS	1	0.977	1	0.747	0.661	0.838	CLONAL	1	TRUE	0	0.262450008424989	2		369	408	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150921904	150921904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064498-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	87	461	0	ENST00000271640.5:c.1483C>T	p.Arg495Ter	p.R495*	ENST00000271640	NM_001145415.1	495	Cga/Tga	12/22	0.143489349728386	4	FACETS	1	0.978	1	0.739	0.656	0.828	INDETERMINATE	1	TRUE	2	0.262450008424989	4		461	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0064513-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	197	445	0	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	0.203434016316452	4	FACETS	1	0.981	1			1	CLONAL	3	TRUE	NA	0.302871459517029	4		445	501	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216115	7216115	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs200535238	NA	P-0064513-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	129	566	0	ENST00000380728.2:c.944T>C	p.Phe315Ser	p.F315S	ENST00000380728		315	tTc/tCc	11/11	0.203434016316452	4	FACETS	0.913	0.83	0.999			1	CLONAL	2	TRUE	NA	0.302871459517029	4		566	608	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519234	187519234	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064513-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	120	434	0	ENST00000441802.2:c.12149A>G	p.Glu4050Gly	p.E4050G	ENST00000441802	NM_005245.3	4050	gAg/gGg	23/27	0.298231747498589	2	FACETS	0.955	0.869	1	0.955	0.869	1	CLONAL	2	TRUE	0	0.302871459517029	2		434	415	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31504675	31504675	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064513-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	55	451	0	ENST00000344624.3:c.1655A>G	p.Tyr552Cys	p.Y552C	ENST00000344624		552	tAt/tGt	8/33	0.197645363834779	4	FACETS	0.862	0.737	0.998	0.431	0.368	0.499	CLONAL	1	TRUE	2	0.302871459517029	4		451	549	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0064519-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	93	651	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.320721526960566	1	FACETS	0.938	0.837	1	0.938	0.837	1	CLONAL	1	TRUE	0	0.320721526960566	1		651	519	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458738	120458738	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs773806339	NA	P-0064519-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	120	897	0	ENST00000256646.2:c.6607A>G	p.Asn2203Asp	p.N2203D	ENST00000256646	NM_024408.3	2203	Aac/Gac	34/34	0.289089115919899	3	FACETS	0.948	0.855	1	0.474	0.427	0.523	CLONAL	1	TRUE	1	0.320721526960566	3		897	916	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551957	150551957	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1012747207	NA	P-0064519-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	101	842	1	ENST00000369026.2:c.50G>T	p.Gly17Val	p.G17V	ENST00000369026	NM_021960.4	17	gGg/gTg	1/3	0.289089115919899	3	FACETS	0.762	0.68	0.85	0.381	0.34	0.425	SUBCLONAL	1	TRUE	1	0.320721526960566	3		843	959	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544518	86544518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064519-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	93	837	0	ENST00000262426.4:c.343C>T	p.Arg115Trp	p.R115W	ENST00000262426	NM_001451.2	115	Cgg/Tgg	1/2	0.320721526960566	1	FACETS	0.851	0.759	0.95	0.851	0.759	0.95	CLONAL	1	TRUE	0	0.320721526960566	1		837	572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519985	NA	P-0064519-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	246	816	0	ENST00000269305.4:c.857A>T	p.Glu286Val	p.E286V	ENST00000269305	NM_001126112.2	286	gAa/gTa	8/11	0.306773606659496	2	FACETS	0.991	0.93	1	0.991	0.93	1	CLONAL	2	TRUE	0	0.320721526960566	2		816	774	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0064520-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	454	377	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.231794975216872	9	FACETS	0.976	0.933	1	0.976	0.933	1	CLONAL	6	TRUE	3	0.231794975216872	9		377	1212	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0064520-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	181	640	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.181965582615166	2	FACETS	0.904	0.834	0.976	0.904	0.834	0.976	CLONAL	2	TRUE	0	0.231794975216872	2		640	864	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51507906	51507906	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064520-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	19	325	0	ENST00000260433.2:c.852A>C	p.Leu284Phe	p.L284F	ENST00000260433		284	ttA/ttC	7/10	0.181965582615166	2	FACETS	0.467	0.354	0.6	0.234	0.177	0.3	SUBCLONAL	1	TRUE	0	0.231794975216872	2		325	351	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183605	10183731	+	frameshift_variant	Frame_Shift_Del	DEL	CTGAAGAAGACGGCGGGGAGGAGTCGGGCGCCGAGGAGTCCGGCCCGGAAGAGTCCGGCCCGGAGGAACTGGGCGCCGAGGAGGAGATGGAGGCCGGGCGGCCGCGGCCCGTGCTGCGCTCGGTGAA	CTGAAGAAGACGGCGGGGAGGAGTCGGGCGCCGAGGAGTCCGGCCCGGAAGAGTCCGGCCCGGAGGAACTGGGCGCCGAGGAGGAGATGGAGGCCGGGCGGCCGCGGCCCGTGCTGCGCTCGGTGAA	-	novel	NA	P-0064520-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	25	891	0	ENST00000256474.2:c.76_202del	p.Glu26ArgfsTer91	p.E26Rfs*91	ENST00000256474	NM_000551.3	25	cCTGAAGAAGACGGCGGGGAGGAGTCGGGCGCCGAGGAGTCCGGCCCGGAAGAGTCCGGCCCGGAGGAACTGGGCGCCGAGGAGGAGATGGAGGCCGGGCGGCCGCGGCCCGTGCTGCGCTCGGTGAAc/cc	1/3	0.18562300158536	3	FACETS	0.268	0.21	0.336	0.089	0.07	0.112	SUBCLONAL	1	TRUE	0	0.231794975216872	3		891	898	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544756	65544756	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0064526-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	37	426	0	ENST00000358664.4:c.172-2A>G		p.X58_splice	ENST00000358664	NM_002382.4	58			0.818472854867123	1	FACETS	0.206	0.171	0.245	0.206	0.171	0.245	SUBCLONAL	1	TRUE	0	0.818472854867123	1		426	259	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592358	29592359	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0064526-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	73	275	0	ENST00000356175.3:c.4772+2dup		p.X1591_splice	ENST00000356175	NM_000267.3	1591			1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.818472854867123	2		275	159	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267895	46267895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1224684974	NA	P-0064526-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	43	424	0	ENST00000371998.3:c.2656G>A	p.Gly886Ser	p.G886S	ENST00000371998		886	Ggt/Agt	14/23	1	2	FACETS	0.274	0.23	0.324	0.274	0.23	0.324	SUBCLONAL	1	TRUE	1	0.818472854867123	2		424	383	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045483	47045483	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064526-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	39	584	0	ENST00000377604.3:c.2450G>T	p.Arg817Leu	p.R817L	ENST00000377604	NM_001204468.1	817	cGt/cTt	22/24	1	2	FACETS	0.183	0.151	0.218	0.183	0.151	0.218	SUBCLONAL	1	TRUE	1	0.818472854867123	2		584	521	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0064527-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	206	533	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.332039181947797	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.332039181947797	2		533	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0064527-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	204	604	1	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.332039181947797	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.332039181947797	2		605	582	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0064527-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	84	396	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.332039181947797	2		396	418	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150030	202150030	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs931648756	NA	P-0064527-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	229	623	0	ENST00000358485.4:c.1471C>T	p.Arg491Ter	p.R491*	ENST00000358485	NM_001080125.1	491	Cga/Tga	8/9	0.332039181947797	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.332039181947797	2		623	649	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528673	157528673	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1226524520	NA	P-0064527-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	113	631	1	ENST00000346085.5:c.6398C>T	p.Ala2133Val	p.A2133V	ENST00000346085	NM_020732.3	2133	gCg/gTg	20/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.332039181947797	2		632	601	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910399	29910399	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064527-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	100	787	0	ENST00000376809.5:c.69G>A	p.Trp23Ter	p.W23*	ENST00000376809	NM_002116.7	23	tgG/tgA	1/8	1	2	FACETS	0.94	0.841	1	0.94	0.841	1	CLONAL	1	TRUE	1	0.332039181947797	2		787	641	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525003	187525003	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064527-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	103	536	0	ENST00000441802.2:c.10677C>A	p.Tyr3559Ter	p.Y3559*	ENST00000441802	NM_005245.3	3559	taC/taA	19/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.332039181947797	2		536	464	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480087	50480087	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064527-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	94	526	0	ENST00000394963.4:c.321del	p.Ile108SerfsTer55	p.I108Sfs*55	ENST00000394963	NM_003076.4	107	caG/ca	2/13	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.332039181947797	2		526	528	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604705	48604705	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs377767370	NA	P-0064527-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	103	599	0	ENST00000342988.3:c.1527G>A	p.Trp509Ter	p.W509*	ENST00000342988	NM_005359.5	509	tgG/tgA	12/12	0.332039181947797	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.332039181947797	1		599	508	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966984	25966984	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064527-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	86	632	0	ENST00000435504.4:c.2222G>T	p.Arg741Ile	p.R741I	ENST00000435504		741	aGa/aTa	13/13	1	2	FACETS	0.907	0.804	1	0.907	0.804	1	CLONAL	1	TRUE	1	0.332039181947797	2		632	571	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713586	30713586	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064527-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	113	664	0	ENST00000295754.5:c.911T>G	p.Ile304Arg	p.I304R	ENST00000295754	NM_003242.5	304	aTa/aGa	4/7	0.332039181947797	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.332039181947797	1		664	478	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723107	49723107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560388937	NA	P-0064527-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	56	332	0	ENST00000449682.2:c.1309G>A	p.Asp437Asn	p.D437N	ENST00000449682	NM_020998.3	437	Gat/Aat	11/18	0.332039181947797	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.332039181947797	1		332	222	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064528-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	9	569	0	ENST00000347630.2:c.399C>A	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttA	6/11	1	2	FACETS	0.292	0.192	0.42	0.292	0.192	0.42	SUBCLONAL	1	TRUE	1	0.17	2		569	363	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061249	38061249	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064528-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	33	903	0	ENST00000250448.2:c.740A>G	p.His247Arg	p.H247R	ENST00000250448	NM_004496.3	247	cAc/cGc	2/2	1	2	FACETS	0.936	0.762	1	0.936	0.762	1	CLONAL	1	TRUE	1	0.17	2		903	415	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915083	32915084	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs80359605	NA	P-0064528-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	28	588	0	ENST00000380152.3:c.6591_6592del	p.Glu2198AsnfsTer4	p.E2198Nfs*4	ENST00000380152		2197	acTGaa/acaa	11/27	1	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	TRUE	1	0.17	2		588	311	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2185894	2185894	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064528-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	22	509	0	ENST00000398665.3:c.166G>C	p.Glu56Gln	p.E56Q	ENST00000398665	NM_032482.2	56	Gag/Cag	3/28	1	2	FACETS	0.711	0.551	0.898	0.711	0.551	0.898	SUBCLONAL	1	TRUE	1	0.17	2		509	364	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0064529-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	71	447	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.222498752221703	1	FACETS	0.877	0.765	0.997	0.877	0.765	0.997	CLONAL	1	TRUE	0	0.222498752221703	1		447	647	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064529-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	100	612	0				ENST00000310581	NM_198253.2	-/1132			0.187581185950339	3	FACETS	0.803	0.718	0.893	0.803	0.718	0.893	CLONAL	2	TRUE	1	0.222498752221703	3		612	622	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0064529-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	86	282	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.222498752221703	2	FACETS	0.922	0.821	1	0.922	0.821	1	CLONAL	2	TRUE	0	0.222498752221703	2		282	419	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923060	44923060	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064529-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	59	176	0	ENST00000377967.4:c.1921C>T	p.Gln641Ter	p.Q641*	ENST00000377967	NM_021140.2	641	Cag/Tag	16/29	0.152773745955937	0	FACETS	0.701	0.608	0.801			1	SUBCLONAL	2	TRUE	NA	0.222498752221703	0		176	294	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123199756	123199756	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064529-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	43	116	0	ENST00000218089.9:c.2056C>T	p.Gln686Ter	p.Q686*	ENST00000218089	NM_001042749.1	686	Cag/Tag	21/35	1	1	FACETS	0.976	0.829	1	1	0.971	1	CLONAL	2	TRUE	0	0.222498752221703	1		116	176	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1685768	1685768	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064529-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	80	504	0	ENST00000378625.1:c.1333G>T	p.Asp445Tyr	p.D445Y	ENST00000378625	NM_001198994.1	445	Gat/Tat	11/14	1	2	FACETS	0.901	0.792	1	0.901	0.792	1	CLONAL	1	TRUE	1	0.222498752221703	2		504	798	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995230	15995230	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064529-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	76	343	0	ENST00000268712.3:c.2963G>C	p.Arg988Thr	p.R988T	ENST00000268712	NM_006311.3	988	aGa/aCa	22/46	0.222498752221703	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.222498752221703	1		343	572	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183763	10183763	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs869025621	NA	P-0064530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	163	309	0	ENST00000256474.2:c.232A>C	p.Asn78His	p.N78H	ENST00000256474	NM_000551.3	78	Aat/Cat	1/3	0.354069582559933	1	FACETS	0.994	0.914	1	0.994	0.914	1	CLONAL	1	TRUE	0	0.354069582559933	1		309	762	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435404	18435404	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1047384914	NA	P-0064530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	98	283	0	ENST00000266497.5:c.389T>C	p.Ile130Thr	p.I130T	ENST00000266497		130	aTa/aCa	1/31	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.354069582559933	2		283	537	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437820	52437826	+	frameshift_variant	Frame_Shift_Del	DEL	GACGTTG	GACGTTG	-	novel	NA	P-0064530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	128	319	0	ENST00000460680.1:c.1335_1341del	p.Asn446TrpfsTer123	p.N446Wfs*123	ENST00000460680	NM_004656.3	445	atCAACGTC/at	13/17	0.354069582559933	1	FACETS	0.992	0.902	1	0.992	0.902	1	CLONAL	1	TRUE	0	0.354069582559933	1		319	600	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729812	41729812	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	146	282	0	ENST00000242208.4:c.717C>A	p.Asp239Glu	p.D239E	ENST00000242208	NM_002192.2	239	gaC/gaA	3/3	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.354069582559933	2		282	787	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0064531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	55	651	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.284379237500213	1	FACETS	0.674	0.577	0.78	0.674	0.577	0.78	SUBCLONAL	1	TRUE	0	0.284379237500213	1		651	492	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097621	27097622	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	64	503	0	ENST00000324856.7:c.3216dup	p.Trp1073MetfsTer32	p.W1073Mfs*32	ENST00000324856	NM_006015.4	1070	-/A	12/20	0.284379237500213	1	FACETS	0.667	0.578	0.764	0.667	0.578	0.764	SUBCLONAL	1	TRUE	0	0.284379237500213	1		503	579	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439764	51439764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	79	540	0	ENST00000262662.1:c.329C>T	p.Ala110Val	p.A110V	ENST00000262662		110	gCt/gTt	4/4	1	2	FACETS	0.856	0.753	0.967	0.856	0.753	0.967	CLONAL	1	TRUE	1	0.284379237500213	2		540	649	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727456	66727470	+	inframe_deletion	In_Frame_Del	DEL	CAGAAGGTGGGAGAA	CAGAAGGTGGGAGAA	-	novel	NA	P-0064531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	54	372	0	ENST00000307102.5:c.173_187del	p.Gln58_Glu62del	p.Q58_E62del	ENST00000307102	NM_002755.3	58	CAGAAGGTGGGAGAA/-	2/11	1	2	FACETS	0.722	0.617	0.837	0.722	0.617	0.837	SUBCLONAL	1	TRUE	1	0.284379237500213	2		372	526	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934328	81934328	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	57	466	0	ENST00000359376.3:c.1305G>C	p.Glu435Asp	p.E435D	ENST00000359376	NM_002661.3	435	gaG/gaC	14/33	1	2	FACETS	0.837	0.719	0.965	0.837	0.719	0.965	CLONAL	1	TRUE	1	0.284379237500213	2		466	479	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504023	186504023	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	67	342	0	ENST00000323963.5:c.588A>T	p.Gln196His	p.Q196H	ENST00000323963		196	caA/caT	6/11	1	2	FACETS	0.817	0.71	0.932	0.817	0.71	0.932	CLONAL	1	TRUE	1	0.284379237500213	2		342	577	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41962140	41962140	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	139	401	0	ENST00000219905.7:c.1048C>T	p.Gln350Ter	p.Q350*	ENST00000219905	NM_001164273.1	350	Caa/Taa	2/24	0.61449028442331	1	FACETS	0.958	0.886	1	0.958	0.886	1	CLONAL	1	TRUE	0	0.61449028442331	1		401	327	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804218	46804218	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	147	585	0	ENST00000290295.7:c.789G>T	p.Trp263Cys	p.W263C	ENST00000290295	NM_006361.5	263	tgG/tgT	2/2	0.61449028442331	2	FACETS	0.933	0.857	1	0.466	0.428	0.506	CLONAL	1	TRUE	0	0.61449028442331	2		585	513	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0064533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	34	631	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.863	0.704	1	0.863	0.704	1	CLONAL	1	TRUE	1	0.14	2		631	563	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0064533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	22	287	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.847	0.656	1	0.847	0.656	1	CLONAL	1	TRUE	1	0.14	2		287	371	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0064533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	35	533	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	0.791	0.647	0.954	0.791	0.647	0.954	CLONAL	1	TRUE	1	0.14	2		533	632	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0064534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	24	580	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.595	0.465	0.747	0.595	0.465	0.747	SUBCLONAL	1	TRUE	1	0.12	2		581	672	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842752	68842752	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1567504977	NA	P-0064534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	28	414	0	ENST00000261769.5:c.687+1G>A		p.X229_splice	ENST00000261769	NM_004360.3	229			1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.12	2		414	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577138	7577138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780075	NA	P-0064535-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	103	499	0	ENST00000269305.4:c.800G>A	p.Arg267Gln	p.R267Q	ENST00000269305	NM_001126112.2	267	cGg/cAg	8/11	0.14542692427746	3	FACETS	1	0.968	1	0.394	0.354	0.435	INDETERMINATE	1	TRUE	0	0.518056582677784	3		499	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352697	NA	P-0064535-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	119	699	0	ENST00000269305.4:c.587G>A	p.Arg196Gln	p.R196Q	ENST00000269305	NM_001126112.2	196	cGa/cAa	6/11	0.14542692427746	3	FACETS	1	0.956	1	0.364	0.329	0.4	INDETERMINATE	1	TRUE	0	0.518056582677784	3		699	530	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710607	114710607	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064535-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	32	528	0	ENST00000543371.1:c.92G>T	p.Ser31Ile	p.S31I	ENST00000543371	NM_001198531.1	31	aGc/aTc	1/14	1	2	FACETS	0.225	0.182	0.273	0.225	0.182	0.273	SUBCLONAL	1	TRUE	1	0.518056582677784	2		528	550	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1688724	1688724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1335212018	NA	P-0064535-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	114	456	0	ENST00000378625.1:c.601C>T	p.Arg201Trp	p.R201W	ENST00000378625	NM_001198994.1	201	Cgg/Tgg	6/14	1	2	FACETS	0.919	0.832	1	0.919	0.832	1	CLONAL	1	TRUE	1	0.518056582677784	2		456	479	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133296	30133296	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776770058	NA	P-0064535-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	69	631	0	ENST00000263025.4:c.202G>A	p.Val68Met	p.V68M	ENST00000263025	NM_002746.2	68	Gtg/Atg	2/9	1	2	FACETS	0.454	0.395	0.517	0.454	0.395	0.517	SUBCLONAL	1	TRUE	1	0.518056582677784	2		631	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0064537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	221	681	0	ENST00000269305.4:c.97-1G>A		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.691309906468393	1	FACETS	0.915	0.863	0.968	0.915	0.863	0.968	CLONAL	1	TRUE	0	0.691309906468393	1		681	457	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098803	178098803	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	264	594	0	ENST00000397062.3:c.242G>T	p.Gly81Val	p.G81V	ENST00000397062	NM_006164.4	81	gGt/gTt	2/5	1	2	FACETS	0.996	0.937	1	0.996	0.937	1	CLONAL	1	TRUE	1	0.691309906468393	2		594	767	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204513697	204513711	+	inframe_deletion	In_Frame_Del	DEL	ATGACTTGTGGTTTT	ATGACTTGTGGTTTT	-	novel	NA	P-0064537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	179	493	0	ENST00000367182.3:c.707_721del	p.Asp236_Leu241delinsVal	p.D236_L241delinsV	ENST00000367182	NM_001278516.1	236	gATGACTTGTGGTTTTtg/gtg	9/11	1	2	FACETS	0.902	0.837	0.969	0.902	0.837	0.969	CLONAL	1	TRUE	1	0.691309906468393	2		493	574	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098380	11098380	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	261	757	0	ENST00000358026.2:c.898C>T	p.Gln300Ter	p.Q300*	ENST00000358026	NM_001128849.1	300	Cag/Tag	6/36	0.691309906468393	1	FACETS	0.929	0.88	0.978	0.929	0.88	0.978	CLONAL	1	TRUE	0	0.691309906468393	1		757	532	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378350	15378350	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	254	519	0	ENST00000263377.2:c.436A>G	p.Ile146Val	p.I146V	ENST00000263377	NM_058243.2	146	Ata/Gta	4/20	0.691309906468393	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.691309906468393	1		519	446	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708990	117708990	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	242	561	0	ENST00000368508.3:c.1967G>T	p.Arg656Met	p.R656M	ENST00000368508	NM_002944.2	656	aGg/aTg	13/43	0.691309906468393	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.691309906468393	1		561	432	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874839	151874839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1278081629	NA	P-0064537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	281	664	0	ENST00000262189.6:c.7699G>A	p.Asp2567Asn	p.D2567N	ENST00000262189	NM_170606.2	2567	Gac/Aac	38/59	0.691309906468393	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.691309906468393	1		664	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0064538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	265	616	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.869979515378068	2		616	598	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0064538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	223	551	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.949	0.892	1	0.949	0.892	1	CLONAL	1	TRUE	1	0.869979515378068	2		552	540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0064538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	214	570	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	1	2	FACETS	0.976	0.916	1	0.976	0.916	1	CLONAL	1	TRUE	1	0.869979515378068	2		570	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501195	NA	P-0064538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	273	722	0	ENST00000269305.4:c.313G>A	p.Gly105Ser	p.G105S	ENST00000269305	NM_001126112.2	105	Ggc/Agc	4/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.869979515378068	2		722	607	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060689	38060689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	393	881	0	ENST00000250448.2:c.1300C>T	p.Pro434Ser	p.P434S	ENST00000250448	NM_004496.3	434	Ccc/Tcc	2/2	1	2	FACETS	0.966	0.922	1	0.966	0.922	1	CLONAL	1	TRUE	1	0.869979515378068	2		881	935	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938357	76938357	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	233	486	0	ENST00000373344.5:c.2391del	p.Ala798LeufsTer5	p.A798Lfs*5	ENST00000373344	NM_000489.3	797	tcA/tc	9/35	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.869979515378068	2		486	477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0064539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	274	640	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.265186870911251	3	FACETS	1	0.971	1	0.701	0.659	0.743	CLONAL	2	TRUE	0	0.354894946508581	3		640	865	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976689	55976689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747477930	NA	P-0064539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	235	587	0	ENST00000263923.4:c.1136C>T	p.Ala379Val	p.A379V	ENST00000263923	NM_002253.2	379	gCg/gTg	9/30	0.354894946508581	4	FACETS	1	0.988	1	0.813	0.761	0.865	CLONAL	2	TRUE	1	0.354894946508581	4		587	736	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023717	27023717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1424580720	NA	P-0064539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	72	851	0	ENST00000324856.7:c.823G>A	p.Gly275Arg	p.G275R	ENST00000324856	NM_006015.4	275	Ggg/Agg	1/20	0.258158679801152	4	FACETS	0.588	0.512	0.67	0.294	0.256	0.335	SUBCLONAL	1	TRUE	2	0.354894946508581	4		851	935	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647978	3647978	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1596528058	NA	P-0064539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	73	642	0	ENST00000294008.3:c.1186C>G	p.Leu396Val	p.L396V	ENST00000294008	NM_032444.2	396	Ctg/Gtg	6/15	0.354894946508581	5	FACETS	0.602	0.525	0.686	0.201	0.175	0.229	SUBCLONAL	1	TRUE	2	0.354894946508581	5		642	1047	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858886	89858886	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs776751315	NA	P-0064539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	191	572	0	ENST00000389301.3:c.1076A>G	p.Tyr359Cys	p.Y359C	ENST00000389301	NM_000135.2	359	tAc/tGc	12/43	0.354894946508581	3	FACETS	0.829	0.769	0.892			1	CLONAL	2	TRUE	NA	0.354894946508581	3		572	764	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0064541-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	140	518	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.903	0.826	0.982	0.903	0.826	0.982	CLONAL	1	TRUE	1	0.565059354901621	2		518	549	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0064541-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	122	404	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	0.565059354901621	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.565059354901621	1		404	288	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061566	38061566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064541-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	152	657	0	ENST00000250448.2:c.423G>A	p.Met141Ile	p.M141I	ENST00000250448	NM_004496.3	141	atG/atA	2/2	1	2	FACETS	0.941	0.864	1	0.941	0.864	1	CLONAL	1	TRUE	1	0.565059354901621	2		657	572	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961404	41961404	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064541-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	159	528	0	ENST00000219905.7:c.312del	p.Met104IlefsTer9	p.M104Ifs*9	ENST00000219905	NM_001164273.1	104	atG/at	2/24	0.565059354901621	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.565059354901621	1		528	378	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162197	47162197	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064541-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	148	588	0	ENST00000409792.3:c.3929del	p.Ser1310Ter	p.S1310*	ENST00000409792	NM_014159.6	1310	tCa/ta	3/21	0.565059354901621	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.565059354901621	1		588	345	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222657	53222657	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064541-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	165	611	0	ENST00000375401.3:c.4279C>T	p.Gln1427Ter	p.Q1427*	ENST00000375401	NM_004187.3	1427	Cag/Tag	25/26	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.565059354901621	2		611	582	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0064542-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	53	282	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.843	0.722	0.975	0.843	0.722	0.975	CLONAL	1	TRUE	1	0.348232096637863	2		282	361	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207092	1207092	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs778376925	NA	P-0064542-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	319	724	0	ENST00000326873.7:c.180C>G	p.Tyr60Ter	p.Y60*	ENST00000326873	NM_000455.4	60	taC/taG	1/10	0.348232096637863	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.348232096637863	2		724	770	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603093	48603108	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCAGGAAACATCCC	TGGCAGGAAACATCCC	-	novel	NA	P-0064542-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	88	524	0	ENST00000342988.3:c.1398_1413del	p.Gly467GlnfsTer4	p.G467Qfs*4	ENST00000342988	NM_005359.5	465	gTGGCAGGAAACATCCCt/gt	11/12	0.348232096637863	1	FACETS	0.942	0.839	1	0.942	0.839	1	CLONAL	1	TRUE	0	0.348232096637863	1		524	443	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161259	56161259	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064542-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	34	409	0	ENST00000399503.3:c.1128G>T	p.Trp376Cys	p.W376C	ENST00000399503	NM_005921.1	376	tgG/tgT	5/20	1	2	FACETS	0.784	0.644	0.94	0.784	0.644	0.94	CLONAL	1	TRUE	1	0.348232096637863	2		409	249	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064544-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	24	344	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.142	0.111	0.178	0.142	0.111	0.178	SUBCLONAL	1	TRUE	1	0.91	2		344	372	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713724	30713724	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064544-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	49	624	0	ENST00000295754.5:c.1049T>C	p.Leu350Pro	p.L350P	ENST00000295754	NM_003242.5	350	cTg/cCg	4/7	1	2	FACETS	0.164	0.138	0.192	0.164	0.138	0.192	SUBCLONAL	1	TRUE	1	0.91	2		624	658	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005075	150005075	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs780721648	NA	P-0064544-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	48	569	0	ENST00000253339.5:c.1150C>T	p.Gln384Ter	p.Q384*	ENST00000253339		384	Caa/Taa	3/7	1	2	FACETS	0.144	0.121	0.17	0.144	0.121	0.17	SUBCLONAL	1	TRUE	1	0.91	2		569	731	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722761	49722761	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs62262682	NA	P-0064547-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	10	31	0	ENST00000449682.2:c.1478G>T	p.Arg493Leu	p.R493L	ENST00000449682	NM_020998.3	493	cGt/cTt	13/18	0.237040230768827	3	FACETS	0.761	0.526	1	0.761	0.526	1	CLONAL	2	TRUE	1	0.237040230768827	3		31	62	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235935	108235935	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770641163	NA	P-0064547-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	210	585	0	ENST00000278616.4:c.8977C>T	p.Arg2993Ter	p.R2993*	ENST00000278616	NM_000051.3	2993	Cga/Tga	62/63	0.237040230768827	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.237040230768827	3		585	903	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305355	65305355	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064547-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	64	584	0	ENST00000342505.4:c.2773G>C	p.Glu925Gln	p.E925Q	ENST00000342505	NM_002227.2	925	Gaa/Caa	20/25	0.237040230768827	2	FACETS	0.679	0.587	0.78	0.34	0.293	0.39	SUBCLONAL	1	TRUE	0	0.237040230768827	2		584	795	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203532	108203532	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064547-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	65	308	0	ENST00000278616.4:c.7832del	p.Ser2611IlefsTer20	p.S2611Ifs*20	ENST00000278616	NM_000051.3	2611	aGt/at	53/63	0.237040230768827	3	FACETS	1	0.965	1	0.676	0.587	0.771	CLONAL	1	TRUE	1	0.237040230768827	3		308	454	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143033711	143033711	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1364129144	NA	P-0064547-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	67	338	0	ENST00000262992.4:c.2260C>A	p.Gln754Lys	p.Q754K	ENST00000262992	NM_001101669.1	754	Caa/Aaa	20/24	0.237040230768827	3	FACETS	1	0.931	1	0.556	0.483	0.634	CLONAL	1	TRUE	1	0.237040230768827	3		338	569	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	126	612	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.877	0.802	0.954	0.877	0.802	0.954	CLONAL	1	TRUE	1	0.754293463069782	2		612	381	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	278	279	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.754293463069782	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.754293463069782	3		279	503	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561263	9561263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769939031	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	251	535	0	ENST00000353224.5:c.519G>A	p.Met173Ile	p.M173I	ENST00000353224	NM_177990.2	173	atG/atA	4/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.754293463069782	2		535	636	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274114	10274114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	197	657	0	ENST00000330684.3:c.155G>A	p.Arg52Gln	p.R52Q	ENST00000330684	NM_001134407.1	52	cGa/cAa	2/13	1	2	FACETS	0.975	0.91	1	0.975	0.91	1	CLONAL	1	TRUE	1	0.754293463069782	2		657	536	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804214	43804214	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	220	661	0	ENST00000372470.3:c.214G>A	p.Glu72Lys	p.E72K	ENST00000372470	NM_005373.2	72	Gag/Aag	3/12	1	2	FACETS	0.977	0.916	1	0.977	0.916	1	CLONAL	1	TRUE	1	0.754293463069782	2		661	597	SUCCESS
AR	367	MSKCC	GRCh37	X	66765598	66765598	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	267	887	2	ENST00000374690.3:c.610G>A	p.Glu204Lys	p.E204K	ENST00000374690	NM_000044.3	204	Gaa/Aaa	1/8	1	2	FACETS	0.954	0.899	1	0.954	0.899	1	CLONAL	1	TRUE	1	0.754293463069782	2		889	742	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	139	587	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.915	0.841	0.99	0.915	0.841	0.99	CLONAL	1	TRUE	1	0.754293463069782	2		587	403	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169586	27169586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	205	586	0	ENST00000380036.4:c.587G>A	p.Gly196Glu	p.G196E	ENST00000380036	NM_000459.3	196	gGa/gAa	4/23	0.754293463069782	1	FACETS	0.996	0.943	1	0.996	0.943	1	CLONAL	1	TRUE	0	0.754293463069782	1		586	340	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306547	41306547	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	168	447	0	ENST00000373198.4:c.1112G>A	p.Gly371Glu	p.G371E	ENST00000373198	NM_133170.3	371	gGa/gAa	7/32	0.181464207410203	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.754293463069782	0		447	422	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984893	55984893	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	198	453	0	ENST00000263923.4:c.236G>A	p.Cys79Tyr	p.C79Y	ENST00000263923	NM_002253.2	79	tGc/tAc	3/30	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.754293463069782	2		453	524	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495457	56495457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1281265231	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	281	708	0	ENST00000267101.3:c.3647C>T	p.Ser1216Phe	p.S1216F	ENST00000267101	NM_001982.3	1216	tCc/tTc	28/28	1	2	FACETS	0.918	0.865	0.971	0.918	0.865	0.971	CLONAL	1	TRUE	1	0.754293463069782	2		708	812	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166824	32166824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs544666247	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	488	616	0	ENST00000375023.3:c.4414C>T	p.Arg1472Trp	p.R1472W	ENST00000375023	NM_004557.3	1472	Cgg/Tgg	24/30	0.754293463069782	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.754293463069782	3		616	849	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604680	43604680	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	171	584	0	ENST00000355710.3:c.1263+2T>G		p.X421_splice	ENST00000355710	NM_020975.4	421			0.754293463069782	1	FACETS	0.991	0.933	1	0.991	0.933	1	CLONAL	1	TRUE	0	0.754293463069782	1		584	285	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560899	9560899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	245	598	0	ENST00000353224.5:c.883C>T	p.Pro295Ser	p.P295S	ENST00000353224	NM_177990.2	295	Ccg/Tcg	4/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.754293463069782	2		598	639	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911648	39911648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752359195	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	179	419	0	ENST00000378444.4:c.4982G>A	p.Arg1661Gln	p.R1661Q	ENST00000378444	NM_001123385.1	1661	cGa/cAa	15/15	1	2	FACETS	0.907	0.843	0.973	0.907	0.843	0.973	CLONAL	1	TRUE	1	0.754293463069782	2		419	523	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992931	72992931	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	252	657	0	ENST00000268489.5:c.1114C>T	p.Arg372Ter	p.R372*	ENST00000268489	NM_006885.3	372	Cga/Tga	2/10	1	2	FACETS	0.941	0.885	0.998	0.941	0.885	0.998	CLONAL	1	TRUE	1	0.754293463069782	2		657	710	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264866	46264866	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	261	564	0	ENST00000371998.3:c.1736C>T	p.Pro579Leu	p.P579L	ENST00000371998		579	cCa/cTa	12/23	1	2	FACETS	0.976	0.92	1	0.976	0.92	1	CLONAL	1	TRUE	1	0.754293463069782	2		564	709	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111124	193111124	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	266	568	0	ENST00000367435.3:c.657T>G	p.Asp219Glu	p.D219E	ENST00000367435	NM_024529.4	219	gaT/gaG	7/17	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.754293463069782	2		568	683	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564999	226564999	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	228	521	0	ENST00000366794.5:c.1751G>T	p.Trp584Leu	p.W584L	ENST00000366794	NM_001618.3	584	tGg/tTg	13/23	1	2	FACETS	0.948	0.888	1	0.948	0.888	1	CLONAL	1	TRUE	1	0.754293463069782	2		521	638	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231488758	231488758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	254	456	0	ENST00000295050.7:c.1121C>T	p.Ser374Phe	p.S374F	ENST00000295050	NM_032018.5	374	tCt/tTt	5/5	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.754293463069782	2		456	605	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900953	114900953	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	259	531	0	ENST00000543371.1:c.563T>G	p.Val188Gly	p.V188G	ENST00000543371	NM_001198531.1	188	gTg/gGg	6/14	0.754293463069782	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.754293463069782	1		531	415	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148955	119149036	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGATTGAGCCCTGTGGACACCTCATGTGCACATCCTGTCTTACATCCTGGCAGGTACGGATCTAAACAGCGACTTTTTTCAG	AGATTGAGCCCTGTGGACACCTCATGTGCACATCCTGTCTTACATCCTGGCAGGTACGGATCTAAACAGCGACTTTTTTCAG	-	novel	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	99	447	0	ENST00000264033.4:c.1175_1227+29del		p.X392_splice	ENST00000264033	NM_005188.3	392		8/16	0.747492221330781	1	FACETS	0.72	0.656	0.785	0.72	0.656	0.785	SUBCLONAL	1	TRUE	0	0.754293463069782	1		447	227	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864538	57864538	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	276	784	0	ENST00000228682.2:c.2015G>A	p.Gly672Glu	p.G672E	ENST00000228682	NM_005269.2	672	gGa/gAa	12/12	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.754293463069782	2		784	660	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911727	26911727	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	108	211	0	ENST00000381527.3:c.152T>C	p.Leu51Ser	p.L51S	ENST00000381527	NM_001260.1	51	tTa/tCa	2/13	1	2	FACETS	0.971	0.884	1	0.971	0.884	1	CLONAL	1	TRUE	1	0.754293463069782	2		211	295	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953629	32953629	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	173	366	0	ENST00000380152.3:c.8930A>T	p.Tyr2977Phe	p.Y2977F	ENST00000380152		2977	tAt/tTt	22/27	1	2	FACETS	0.972	0.903	1	0.972	0.903	1	CLONAL	1	TRUE	1	0.754293463069782	2		366	472	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42057255	42057255	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	232	401	0	ENST00000219905.7:c.7916T>G	p.Leu2639Arg	p.L2639R	ENST00000219905	NM_001164273.1	2639	cTa/cGa	23/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.754293463069782	2		401	545	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352021	89352021	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770269691	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	248	644	0	ENST00000301030.4:c.929C>T	p.Pro310Leu	p.P310L	ENST00000301030	NM_001256183.1	310	cCt/cTt	9/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.754293463069782	2		644	619	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813285	89813285	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	194	470	0	ENST00000389301.3:c.3362C>G	p.Ser1121Cys	p.S1121C	ENST00000389301	NM_000135.2	1121	tCc/tGc	34/43	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.754293463069782	2		470	485	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527555	29527556	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	112	408	0	ENST00000356175.3:c.1006dup	p.Trp336LeufsTer4	p.W336Lfs*4	ENST00000356175	NM_000267.3	335	aat/aaTt	9/57	1	2	FACETS	0.686	0.621	0.753	0.686	0.621	0.753	SUBCLONAL	1	TRUE	1	0.754293463069782	2		408	433	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652879	29652879	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	248	447	0	ENST00000356175.3:c.4814A>T	p.His1605Leu	p.H1605L	ENST00000356175	NM_000267.3	1605	cAt/cTt	36/57	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.754293463069782	2		447	601	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296479	15296479	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	201	637	0	ENST00000263388.2:c.1963A>G	p.Asn655Asp	p.N655D	ENST00000263388	NM_000435.2	655	Aac/Gac	13/33	1	2	FACETS	0.897	0.837	0.959	0.897	0.837	0.959	CLONAL	1	TRUE	1	0.754293463069782	2		637	594	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425587	47425587	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	256	568	0	ENST00000404338.3:c.3655C>G	p.Leu1219Val	p.L1219V	ENST00000404338	NM_004491.4	1219	Ctt/Gtt	1/6	1	2	FACETS	0.972	0.916	1	0.972	0.916	1	CLONAL	1	TRUE	1	0.754293463069782	2		568	698	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451758	29451758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	144	538	0	ENST00000389048.3:c.2807G>A	p.Gly936Glu	p.G936E	ENST00000389048	NM_004304.4	936	gGa/gAa	16/29	1	2	FACETS	0.862	0.793	0.933	0.862	0.793	0.933	CLONAL	1	TRUE	1	0.754293463069782	2		538	443	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661625	227661625	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	241	788	0	ENST00000305123.5:c.1830del	p.Asp610GlufsTer26	p.D610Efs*26	ENST00000305123	NM_005544.2	610	gaT/ga	1/2	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.754293463069782	2		788	636	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520130	9520130	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	206	479	0	ENST00000353224.5:c.2139G>A	p.Met713Ile	p.M713I	ENST00000353224	NM_177990.2	713	atG/atA	10/10	1	2	FACETS	0.975	0.912	1	0.975	0.912	1	CLONAL	1	TRUE	1	0.754293463069782	2		479	560	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375210	31375210	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1441646586	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	288	694	0	ENST00000328111.2:c.607C>T	p.Pro203Ser	p.P203S	ENST00000328111	NM_006892.3	203	Ccg/Tcg	6/23	1	2	FACETS	0.987	0.932	1	0.987	0.932	1	CLONAL	1	TRUE	1	0.754293463069782	2		694	774	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29445402	29445402	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs946096980	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	296	789	0	ENST00000544604.2:c.1233G>C	p.Gln411His	p.Q411H	ENST00000544604	NM_001206998.1	411	caG/caC	8/9	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.754293463069782	2		789	750	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180310	38180310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	457	788	0	ENST00000396334.3:c.158G>A	p.Arg53Gln	p.R53Q	ENST00000396334	NM_002468.4	53	cGg/cAg	1/5	0.754293463069782	3	FACETS	0.992	0.955	1	0.992	0.955	1	CLONAL	2	TRUE	1	0.754293463069782	3		788	841	SUCCESS
ALB	213	MSKCC	GRCh37	4	74276060	74276060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1485868409	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	169	401	0	ENST00000295897.4:c.647C>T	p.Ser216Leu	p.S216L	ENST00000295897	NM_000477.5	216	tCg/tTg	6/15	1	2	FACETS	0.951	0.883	1	0.951	0.883	1	CLONAL	1	TRUE	1	0.754293463069782	2		401	471	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518065	176518065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	258	674	0	ENST00000292408.4:c.563G>A	p.Gly188Glu	p.G188E	ENST00000292408	NM_213647.1	188	gGa/gAa	5/18	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.754293463069782	2		674	623	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036973	180036973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762732020	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	229	668	0	ENST00000261937.6:c.3739C>T	p.Arg1247Cys	p.R1247C	ENST00000261937	NM_182925.4	1247	Cgt/Tgt	28/30	0.130709421708009	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.754293463069782	0		668	653	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405048	405048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	228	490	0	ENST00000380956.4:c.1130C>T	p.Ser377Phe	p.S377F	ENST00000380956	NM_001195286.1	377	tCc/tTc	8/9	0.754293463069782	3	FACETS	1	0.962	1	0.52	0.486	0.556	CLONAL	1	TRUE	1	0.754293463069782	3		490	800	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120527	94120527	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	210	479	0	ENST00000369303.4:c.524G>A	p.Gly175Glu	p.G175E	ENST00000369303	NM_004440.3	175	gGa/gAa	3/17	1	2	FACETS	0.923	0.863	0.985	0.923	0.863	0.985	CLONAL	1	TRUE	1	0.754293463069782	2		479	603	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2029117	2029117	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	259	707	0	ENST00000349721.2:c.95G>C	p.Gly32Ala	p.G32A	ENST00000349721	NM_003070.3	32	gGa/gCa	2/34	1	2	FACETS	0.947	0.892	1	0.947	0.892	1	CLONAL	1	TRUE	1	0.754293463069782	2		707	725	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0064549-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	229	652	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.36050143680866	2	FACETS	0.913	0.855	0.972	0.913	0.855	0.972	CLONAL	2	TRUE	0	0.363123926842575	2		652	691	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151574	55151574	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0064549-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	67	331	0	ENST00000257290.5:c.2360C>G	p.Ser787Ter	p.S787*	ENST00000257290	NM_006206.4	787	tCa/tGa	17/23	1	2	FACETS	0.896	0.782	1	0.896	0.782	1	CLONAL	1	TRUE	1	0.363123926842575	2		331	412	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064550-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	142	344	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.514213364375333	3	FACETS	1	0.968	1	0.555	0.509	0.603	CLONAL	1	TRUE	1	0.657008417777104	3		344	517	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0064550-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	238	515	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.657008417777104	2		515	694	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664459	138664459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064550-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	61	375	0	ENST00000330315.3:c.1106C>T	p.Ala369Val	p.A369V	ENST00000330315	NM_023067.3	369	gCg/gTg	1/1	1	2	FACETS	0.535	0.464	0.611	0.535	0.464	0.611	SUBCLONAL	1	TRUE	1	0.657008417777104	2		375	347	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550309	39550309	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064550-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	194	536	0	ENST00000262039.4:c.420G>T	p.Met140Ile	p.M140I	ENST00000262039	NM_002647.2	140	atG/atT	4/25	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.657008417777104	2		536	582	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566853	212566853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1418847829	NA	P-0064550-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	254	668	0	ENST00000342788.4:c.1328C>T	p.Thr443Ile	p.T443I	ENST00000342788	NM_005235.2	443	aCc/aTc	12/28	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.657008417777104	2		668	723	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805586	32805586	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064550-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	286	769	0	ENST00000374899.4:c.425T>A	p.Leu142Gln	p.L142Q	ENST00000374899	NM_018833.2	142	cTg/cAg	2/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.657008417777104	2		769	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	268	599	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.686057156407021	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.680394250570622	2		599	341	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	82	753	4	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	0.686057156407021	4	FACETS	0.58	0.511	0.654	0.29	0.255	0.327	SUBCLONAL	1	TRUE	2	0.680394250570622	4		757	698	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485415	57485415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755974022	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	175	810	0	ENST00000371085.3:c.997C>T	p.Arg333Cys	p.R333C	ENST00000371085	NM_000516.4	333	Cgc/Tgc	12/13	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.680394250570622	2		810	410	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429373	47429373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	135	894	1	ENST00000377045.4:c.1501G>A	p.Glu501Lys	p.E501K	ENST00000377045	NM_001654.4	501	Gag/Aag	14/16	0.680394250570622	6	FACETS	0.773	0.705	0.844			1	SUBCLONAL	2	TRUE	NA	0.680394250570622	6		895	606	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417921	138417921	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs866345647	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	17	332	0	ENST00000289153.2:c.1598del	p.Lys533SerfsTer6	p.K533Sfs*6	ENST00000289153	NM_006219.2	533	aAg/ag	11/22	0.686057156407021	2	FACETS	0.219	0.164	0.285	0.11	0.081	0.143	SUBCLONAL	1	TRUE	0	0.680394250570622	2		332	228	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	89	1156	9	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	0.686057156407021	2	FACETS	0.944	0.849	1	0.472	0.424	0.522	CLONAL	1	TRUE	0	0.680394250570622	2		1165	277	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435136	110435136	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs780127725	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	99	1536	2	ENST00000375856.3:c.3265G>C	p.Ala1089Pro	p.A1089P	ENST00000375856	NM_003749.2	1089	Gcc/Ccc	1/2	0.686057156407021	2	FACETS	1	0.947	1	0.533	0.483	0.584	CLONAL	1	TRUE	0	0.680394250570622	2		1538	273	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29099524	29099525	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs772683219	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	401	366	0	ENST00000328354.6:c.876dup	p.Asp293Ter	p.D293*	ENST00000328354	NM_007194.3	292	-/T	8/15	0.680394250570622	8	FACETS	1	0.991	1			1	CLONAL	5	TRUE	NA	0.680394250570622	8		366	653	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87338624	87338624	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	112	476	0	ENST00000277120.3:c.720G>T	p.Met240Ile	p.M240I	ENST00000277120		240	atG/atT	7/19	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.680394250570622	2		476	299	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	197	540	30	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	0.366432279796077	2	FACETS	1	0.962	1	1	0.962	1	INDETERMINATE	2	TRUE	0	0.680394250570622	2		570	286	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128849225	128849225	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756828715	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	207	824	0	ENST00000249373.3:c.1453C>T	p.Arg485Trp	p.R485W	ENST00000249373	NM_005631.4	485	Cgg/Tgg	8/12	0.686057156407021	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.680394250570622	2		824	254	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241894	133241894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757051826	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	116	1149	1	ENST00000320574.5:c.2462G>A	p.Arg821His	p.R821H	ENST00000320574	NM_006231.2	821	cGc/cAc	21/49	0.665868937180828	6	FACETS	1	0.972	1	0.242	0.218	0.267	CLONAL	1	TRUE	1	0.680394250570622	6		1150	665	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023983	31023983	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	131	966	2	ENST00000375687.4:c.3473del	p.Asn1158ThrfsTer13	p.N1158Tfs*13	ENST00000375687	NM_015338.5	1156	ggA/gg	13/13	1	2	FACETS	0.939	0.86	1	0.939	0.86	1	CLONAL	1	TRUE	1	0.680394250570622	2		968	410	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059206	27059207	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	316	613	0	ENST00000324856.7:c.1848dup	p.Ser617LeufsTer6	p.S617Lfs*6	ENST00000324856	NM_006015.4	615	gcc/gCcc	4/20	0.686057156407021	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	0	0.680394250570622	3		613	414	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24133946	24133946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	96	845	0	ENST00000263121.7:c.97G>A	p.Gly33Arg	p.G33R	ENST00000263121	NM_003073.3	33	Gga/Aga	2/9	0.680394250570622	6	FACETS	0.861	0.767	0.961			1	CLONAL	1	TRUE	NA	0.680394250570622	6		845	774	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193202218	193202218	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	114	630	0	ENST00000367435.3:c.1250C>T	p.Thr417Ile	p.T417I	ENST00000367435	NM_024529.4	417	aCt/aTt	14/17	0.644503109912035	5	FACETS	1	0.972	1			1	CLONAL	1	TRUE	NA	0.680394250570622	5		630	562	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968244	2968244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161484391	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	79	1501	3	ENST00000396946.4:c.1742C>T	p.Ala581Val	p.A581V	ENST00000396946	NM_032415.4	581	gCg/gTg	13/25	0.680394250570622	8	FACETS	0.651	0.571	0.738			1	SUBCLONAL	1	TRUE	NA	0.680394250570622	8		1504	1084	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842735	68842735	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201511530	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	130	649	0	ENST00000261769.5:c.671G>A	p.Arg224His	p.R224H	ENST00000261769	NM_004360.3	224	cGc/cAc	5/16	0.269514370156386	6	FACETS	1	0.94	1	0.517	0.473	0.563	INDETERMINATE	2	TRUE	2	0.680394250570622	6		649	436	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256106	16256107	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	158	818	0	ENST00000375759.3:c.3379_3380dup	p.Asp1128LysfsTer27	p.D1128Kfs*27	ENST00000375759	NM_015001.2	1124	cca/ccAGa	11/15	0.28361015096512	5	FACETS	0.752	0.692	0.814			1	INDETERMINATE	2	TRUE	NA	0.680394250570622	5		818	624	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076786	72076786	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	300	840	3	ENST00000357731.5:c.711del	p.Gly238AspfsTer5	p.G238Dfs*5	ENST00000357731	NM_173808.2	237	ccC/cc	5/7	0.686057156407021	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.680394250570622	2		843	403	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572285	64572285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863224810	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	84	1735	1	ENST00000312049.6:c.1354C>T	p.Arg452Trp	p.R452W	ENST00000312049	NM_130799.2	452	Cgg/Tgg	10/10	0.594921948854023	3	FACETS	0.689	0.611	0.773	0.345	0.305	0.387	SUBCLONAL	1	TRUE	1	0.680394250570622	3		1736	480	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285676	46285676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780577038	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	134	601	2	ENST00000334344.6:c.5036G>A	p.Arg1679Gln	p.R1679Q	ENST00000334344	NM_152641.2	1679	cGg/cAg	17/21	0.602905249527082	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.680394250570622	1		603	235	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436031	49436031	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	108	1119	0	ENST00000301067.7:c.5950C>A	p.Pro1984Thr	p.P1984T	ENST00000301067	NM_003482.3	1984	Ccc/Acc	28/54	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.680394250570622	2		1119	290	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636110	73636110	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	22	397	0	ENST00000377687.4:c.373A>G	p.Thr125Ala	p.T125A	ENST00000377687	NM_001730.3	125	Act/Gct	2/4	0.686057156407021	2	FACETS	0.211	0.163	0.266	0.105	0.081	0.133	SUBCLONAL	1	TRUE	0	0.680394250570622	2		397	307	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354341	354341	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	77	1079	0	ENST00000262320.3:c.1217A>C	p.Glu406Ala	p.E406A	ENST00000262320	NM_003502.3	406	gAg/gCg	5/11	0.444756596203481	3	FACETS	1	0.95	1			1	CLONAL	1	TRUE	NA	0.680394250570622	3		1079	270	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877205	89877205	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	94	516	0	ENST00000389301.3:c.432G>T	p.Lys144Asn	p.K144N	ENST00000389301	NM_000135.2	144	aaG/aaT	5/43	0.269514370156386	6	FACETS	0.803	0.719	0.891	0.402	0.359	0.446	INDETERMINATE	2	TRUE	2	0.680394250570622	6		516	406	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557904	29557904	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	45	133	0	ENST00000356175.3:c.3158C>A	p.Ser1053Ter	p.S1053*	ENST00000356175	NM_000267.3	1053	tCa/tAa	24/57	0.677337458418231	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.680394250570622	1		133	63	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39573259	39573259	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	175	396	0	ENST00000262039.4:c.740T>C	p.Leu247Ser	p.L247S	ENST00000262039	NM_002647.2	247	tTa/tCa	7/25	0.686057156407021	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.680394250570622	2		396	211	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946804	17946804	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200075643	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	15	1072	0	ENST00000458235.1:c.1843C>T	p.Arg615Cys	p.R615C	ENST00000458235	NM_000215.3	615	Cgt/Tgt	14/24	0.189482749699267	1	FACETS	0.109	0.08	0.145	0.109	0.08	0.145	INDETERMINATE	1	TRUE	0	0.680394250570622	1		1072	266	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309569	30309569	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	166	840	1	ENST00000307677.4:c.453C>A	p.Cys151Ter	p.C151*	ENST00000307677	NM_138578.1	151	tgC/tgA	2/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.680394250570622	2		841	445	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29279801	29279801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1464069146	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	30	309	0	ENST00000544604.2:c.47G>A	p.Arg16His	p.R16H	ENST00000544604	NM_001206998.1	16	cGc/cAc	1/9	0.680394250570622	8	FACETS	1	0.854	1			1	CLONAL	2	TRUE	NA	0.680394250570622	8		309	128	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067328	37067329	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	375	925	0	ENST00000231790.2:c.1240dup	p.Glu414GlyfsTer3	p.E414Gfs*3	ENST00000231790	NM_000249.3	413	-/G	12/19	0.686057156407021	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	0	0.680394250570622	3		925	490	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683471	182683472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	13	410	0	ENST00000292782.4:c.73dup	p.Thr25AsnfsTer10	p.T25Nfs*10	ENST00000292782	NM_020640.2	25	aca/aAca	2/7	0.686057156407021	2	FACETS	0.227	0.162	0.306	0.114	0.081	0.153	SUBCLONAL	1	TRUE	0	0.680394250570622	2		410	168	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391358	84391358	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1560574509	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	85	405	1	ENST00000321945.7:c.474del	p.Gly159AspfsTer8	p.G159Dfs*8	ENST00000321945	NM_139076.2	158	aaA/aa	5/9	0.534128165094388	4	FACETS	1	0.949	1	0.558	0.497	0.623	CLONAL	1	TRUE	2	0.680394250570622	4		406	376	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295571	1295571	+	upstream_gene_variant	5'Flank	DEL	C	C	-	novel	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	95	1694	0				ENST00000310581	NM_198253.2	-/1132			0.594921948854023	3	FACETS	1	0.93	1	0.523	0.469	0.578	CLONAL	1	TRUE	1	0.680394250570622	3		1694	358	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295609	1295628	+	upstream_gene_variant	5'Flank	DEL	GGCCTGATCCGGAGACCCAG	GGCCTGATCCGGAGACCCAG	-	novel	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	99	1662	0				ENST00000310581	NM_198253.2	-/1132			0.594921948854023	3	FACETS	1	0.929	1	0.52	0.468	0.574	CLONAL	1	TRUE	1	0.680394250570622	3		1662	375	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005958	69005958	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	86	511	3	ENST00000288368.4:c.2368+1G>A		p.X790_splice	ENST00000288368	NM_024870.2	790			0.686057156407021	4	FACETS	1	0.946	1	0.552	0.491	0.616	CLONAL	1	TRUE	2	0.680394250570622	4		514	385	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224235	53224235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781871728	NA	P-0064551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	137	1081	3	ENST00000375401.3:c.3316G>A	p.Ala1106Thr	p.A1106T	ENST00000375401	NM_004187.3	1106	Gca/Aca	22/26	0.444756596203481	3	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.680394250570622	3		1084	458	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0064552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	63	516	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.28868027575182	3	FACETS	1	0.935	1	0.558	0.487	0.634	INDETERMINATE	1	TRUE	1	0.500538646380598	3		516	282	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150902479	150902479	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	100	521	0	ENST00000271640.5:c.297C>A	p.Phe99Leu	p.F99L	ENST00000271640	NM_001145415.1	99	ttC/ttA	3/22	1	2	FACETS	0.979	0.881	1	0.979	0.881	1	CLONAL	1	TRUE	1	0.500538646380598	2		521	408	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764146326	NA	P-0064552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	119	677	0	ENST00000269305.4:c.841G>T	p.Asp281Tyr	p.D281Y	ENST00000269305	NM_001126112.2	281	Gac/Tac	8/11	1	2	FACETS	0.995	0.903	1	0.995	0.903	1	CLONAL	1	TRUE	1	0.500538646380598	2		677	478	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579536	7579536	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567556930	NA	P-0064552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	103	788	0	ENST00000269305.4:c.151G>T	p.Glu51Ter	p.E51*	ENST00000269305	NM_001126112.2	51	Gaa/Taa	4/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.500538646380598	2		788	375	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390203	89390203	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	79	679	0	ENST00000336596.2:c.952C>A	p.Pro318Thr	p.P318T	ENST00000336596	NM_005233.5	318	Cca/Aca	4/17	0.500538646380598	3	FACETS	0.723	0.637	0.815	0.361	0.318	0.408	SUBCLONAL	1	TRUE	1	0.500538646380598	3		679	546	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245395	153245395	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	63	481	0	ENST00000281708.4:c.1796C>A	p.Ala599Glu	p.A599E	ENST00000281708	NM_033632.3	599	gCa/gAa	11/12	1	2	FACETS	0.902	0.788	1	0.902	0.788	1	CLONAL	1	TRUE	1	0.500538646380598	2		481	279	SUCCESS
APC	324	MSKCC	GRCh37	5	112162825	112162825	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	97	406	0	ENST00000257430.4:c.1429G>T	p.Glu477Ter	p.E477*	ENST00000257430	NM_000038.5	477	Gaa/Taa	12/16	0.500538646380598	2	FACETS	0.999	0.914	1	0.999	0.914	1	CLONAL	2	TRUE	0	0.500538646380598	2		406	194	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520171	176520171	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	171	790	0	ENST00000292408.4:c.1090G>T	p.Glu364Ter	p.E364*	ENST00000292408	NM_213647.1	364	Gag/Tag	9/18	0.500538646380598	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.500538646380598	2		790	299	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334743	81334743	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	80	528	0	ENST00000222390.5:c.1973G>T	p.Cys658Phe	p.C658F	ENST00000222390	NM_000601.4	658	tGt/tTt	17/18	0.500538646380598	3	FACETS	0.989	0.876	1	0.495	0.438	0.555	CLONAL	1	TRUE	1	0.500538646380598	3		528	404	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931898	68931898	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	147	406	0	ENST00000288368.4:c.328C>A	p.Leu110Ile	p.L110I	ENST00000288368	NM_024870.2	110	Ctt/Att	3/40	0.469537567565334	4	FACETS	0.933	0.866	0.999	0.933	0.866	0.999	CLONAL	3	TRUE	1	0.500538646380598	4		406	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0064553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	102	721	2	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.615517252581872	1	FACETS	0.856	0.78	0.934	0.856	0.78	0.934	CLONAL	1	TRUE	0	0.645531723582457	1		723	250	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417865	138417865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	65	347	0	ENST00000289153.2:c.1654G>A	p.Glu552Lys	p.E552K	ENST00000289153	NM_006219.2	552	Gaa/Aaa	11/22	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.645531723582457	2		347	179	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030892	36030892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867805553	NA	P-0064553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	139	593	0	ENST00000358208.4:c.1171C>T	p.Arg391Cys	p.R391C	ENST00000358208		391	Cgt/Tgt	10/12	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.645531723582457	2		593	411	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831915	72831915	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	116	540	0	ENST00000268489.5:c.4666C>T	p.Gln1556Ter	p.Q1556*	ENST00000268489	NM_006885.3	1556	Caa/Taa	9/10	0.645531723582457	1	FACETS	0.817	0.747	0.888	0.817	0.747	0.888	CLONAL	1	TRUE	0	0.645531723582457	1		540	298	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870953	12870953	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	184	641	0	ENST00000228872.4:c.180G>A	p.Trp60Ter	p.W60*	ENST00000228872	NM_004064.3	60	tgG/tgA	1/3	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.645531723582457	2		641	507	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513603	41513603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	152	649	0	ENST00000263253.7:c.507G>A	p.Met169Ile	p.M169I	ENST00000263253	NM_001429.3	169	atG/atA	2/31	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.645531723582457	2		649	452	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936168	71936168	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	109	501	0	ENST00000298229.2:c.140G>C	p.Arg47Pro	p.R47P	ENST00000298229	NM_001567.3	47	cGa/cCa	1/28	0.471584407294341	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.645531723582457	1		501	226	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097180	11097180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1368858108	NA	P-0064553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	148	615	0	ENST00000358026.2:c.671C>T	p.Ser224Leu	p.S224L	ENST00000358026	NM_001128849.1	224	tCg/tTg	4/36	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.645531723582457	2		615	445	SUCCESS
APC	324	MSKCC	GRCh37	5	112151216	112151216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	50	363	0	ENST00000257430.4:c.859G>T	p.Glu287Ter	p.E287*	ENST00000257430	NM_000038.5	287	Gaa/Taa	9/16	0.643149819762249	3	FACETS	0.751	0.642	0.868	0.375	0.321	0.434	SUBCLONAL	1	TRUE	1	0.645531723582457	3		363	273	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717642	89717642	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0064553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	148	394	1	ENST00000371953.3:c.668del	p.Lys223ArgfsTer33	p.K223Rfs*33	ENST00000371953	NM_000314.4	223	Aag/ag	7/9	0.641456743314485	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.645531723582457	2		395	217	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112247	115112248	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0064553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	124	675	0	ENST00000257566.3:c.1492dup	p.Leu498ProfsTer194	p.L498Pfs*194	ENST00000257566	NM_016569.3	498	ctg/cCtg	7/8	1	2	FACETS	0.863	0.787	0.943	0.863	0.787	0.943	CLONAL	1	TRUE	1	0.645531723582457	2		675	445	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835671	68835687	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCTACGGTTTCATAA	CCTCTACGGTTTCATAA	-	novel	NA	P-0064553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	157	566	0	ENST00000261769.5:c.264_280del	p.Leu89ThrfsTer73	p.L89Tfs*73	ENST00000261769	NM_004360.3	88	CCTCTACGGTTTCATAAc/c	3/16	0.645531723582457	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.645531723582457	1		566	309	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573934	7573934	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	15	389	0	ENST00000269305.4:c.1093C>A	p.His365Asn	p.H365N	ENST00000269305	NM_001126112.2	365	Cac/Aac	10/11	0.615517252581872	1	FACETS	0.134	0.098	0.177	0.134	0.098	0.177	SUBCLONAL	1	TRUE	0	0.645531723582457	1		389	235	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548886	29548886	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs953440640	NA	P-0064553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	16	314	0	ENST00000356175.3:c.1660C>T	p.Gln554Ter	p.Q554*	ENST00000356175	NM_000267.3	554	Cag/Tag	15/57	0.615517252581872	1	FACETS	0.839	0.654	1	0.839	0.654	1	CLONAL	1	TRUE	0	0.645531723582457	1		314	40	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39746834	39746834	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	70	254	0	ENST00000361337.2:c.1849del	p.Leu617PhefsTer28	p.L617Ffs*28	ENST00000361337	NM_003286.2	616	atC/at	18/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.645531723582457	2		254	197	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0064554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	249	598	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	0.64993975051446	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.64993975051446	1		598	462	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	283	625	0	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	0.361518010712364	1	FACETS	0.896	0.849	0.944	0.896	0.849	0.944	INDETERMINATE	1	TRUE	0	0.64993975051446	1		625	656	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976867	2976867	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	218	562	0	ENST00000396946.4:c.1145C>A	p.Ala382Asp	p.A382D	ENST00000396946	NM_032415.4	382	gCc/gAc	9/25	0.324465017541838	1	FACETS	0.873	0.819	0.926	0.873	0.819	0.926	INDETERMINATE	1	TRUE	0	0.64993975051446	1		562	519	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158610	26158610	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	56	332	0	ENST00000289316.2:c.213C>G	p.Phe71Leu	p.F71L	ENST00000289316	NM_138720.2	71	ttC/ttG	1/2	1	2	FACETS	0.449	0.386	0.517	0.449	0.386	0.517	SUBCLONAL	1	TRUE	1	0.64993975051446	2		332	384	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10257049	10257049	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064555-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	81	549	0	ENST00000340748.4:c.2824C>G	p.Pro942Ala	p.P942A	ENST00000340748		942	Ccc/Gcc	27/40	0.179313388723069	4	FACETS	0.853	0.755	0.958	0.853	0.755	0.958	CLONAL	2	FALSE	2	0.255778278719898	4		549	466	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742505	145742505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564810489	NA	P-0064555-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	55	677	0	ENST00000428558.2:c.283G>A	p.Gly95Arg	p.G95R	ENST00000428558	NM_004260.3	95	Ggg/Agg	4/22	0.246012101604257	3	FACETS	0.884	0.756	1	0.442	0.378	0.512	CLONAL	1	FALSE	1	0.255778278719898	3		677	549	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404311	139404311	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064555-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	70	764	0	ENST00000277541.6:c.2843A>T	p.Glu948Val	p.E948V	ENST00000277541	NM_017617.3	948	gAg/gTg	18/34	0.246012101604257	3	FACETS	0.994	0.867	1	0.497	0.433	0.566	CLONAL	1	FALSE	1	0.255778278719898	3		764	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0064556-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	138	784	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.529792434687455	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.529792434687455	2		784	247	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064556-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	39	344	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.856	0.719	1	0.856	0.719	1	CLONAL	1	TRUE	1	0.529792434687455	2		344	172	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992316	72992316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs62640001	NA	P-0064556-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	79	723	0	ENST00000268489.5:c.1729G>A	p.Val577Ile	p.V577I	ENST00000268489	NM_006885.3	577	Gtc/Atc	2/10	1	2	FACETS	0.941	0.835	1	0.941	0.835	1	CLONAL	1	TRUE	1	0.529792434687455	2		723	317	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494971	56494971	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs532910077	NA	P-0064556-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	57	644	0	ENST00000267101.3:c.3328G>A	p.Glu1110Lys	p.E1110K	ENST00000267101	NM_001982.3	1110	Gag/Aag	27/28	1	2	FACETS	0.92	0.798	1	0.92	0.798	1	CLONAL	1	TRUE	1	0.529792434687455	2		644	234	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913314	28913314	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064556-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	61	508	0	ENST00000282397.4:c.2479C>T	p.Leu827Phe	p.L827F	ENST00000282397	NM_002019.4	827	Ctt/Ttt	17/30	0.529462482167957	3	FACETS	0.952	0.827	1	0.476	0.413	0.543	CLONAL	1	TRUE	1	0.529792434687455	3		508	306	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133962	41133963	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0064556-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	143	750	0	ENST00000379561.5:c.1664_1665dup	p.Thr556Ter	p.T556*	ENST00000379561	NM_002015.3	555	-/TG	2/3	0.529462482167957	3	FACETS	0.987	0.912	1	0.987	0.912	1	CLONAL	2	TRUE	1	0.529792434687455	3		750	346	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983608	7983608	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064557-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	219	527	0	ENST00000319144.4:c.699G>C	p.Trp233Cys	p.W233C	ENST00000319144	NM_001139.2	233	tgG/tgC	6/15	0.602880122513072	4	FACETS	1	0.966	1			1	CLONAL	2	TRUE	NA	0.655727905788938	4		527	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0064569-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	142	447	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.24576622350418	2	FACETS	0.936	0.856	1	0.936	0.856	1	CLONAL	2	TRUE	0	0.24576622350418	2		447	617	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987341	2987341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145474800	NA	P-0064569-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	47	631	0	ENST00000396946.4:c.88C>T	p.Arg30Trp	p.R30W	ENST00000396946	NM_032415.4	30	Cgg/Tgg	3/25	1	2	FACETS	0.744	0.628	0.872	0.744	0.628	0.872	SUBCLONAL	1	TRUE	1	0.24576622350418	2		631	514	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248666	10248666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064569-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	76	631	0	ENST00000340748.4:c.4087C>T	p.Arg1363Trp	p.R1363W	ENST00000340748		1363	Cgg/Tgg	35/40	0.24576622350418	3	FACETS	1	0.969	1	0.666	0.586	0.753	CLONAL	1	TRUE	1	0.24576622350418	3		631	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0064570-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	157	495	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.393483429909074	1	FACETS	0.928	0.852	1	0.928	0.852	1	CLONAL	1	TRUE	0	0.393483429909074	1		495	691	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222488	39222488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1027223518	NA	P-0064570-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	98	485	0	ENST00000402219.2:c.3122G>A	p.Arg1041His	p.R1041H	ENST00000402219	NM_005633.3	1041	cGt/cAt	20/23	1	2	FACETS	0.836	0.747	0.93	0.836	0.747	0.93	CLONAL	1	TRUE	1	0.393483429909074	2		485	596	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114611	73114611	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1312972036	NA	P-0064570-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	42	237	0	ENST00000356692.5:c.992A>T	p.Asp331Val	p.D331V	ENST00000356692		331	gAt/gTt	9/9	1	2	FACETS	0.671	0.563	0.791	0.671	0.563	0.791	SUBCLONAL	1	TRUE	1	0.393483429909074	2		237	318	SUCCESS
MET	4233	MSKCC	GRCh37	7	116417493	116417493	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0064570-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	92	405	0	ENST00000397752.3:c.3310A>T	p.Lys1104Ter	p.K1104*	ENST00000397752	NM_000245.2	1104	Aaa/Taa	16/21	1	2	FACETS	0.974	0.869	1	0.974	0.869	1	CLONAL	1	TRUE	1	0.393483429909074	2		405	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0064571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	234	631	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.588325793240303	2	FACETS	0.918	0.871	0.964	0.918	0.871	0.964	CLONAL	2	TRUE	0	0.629603920260423	2		631	405	SUCCESS
APC	324	MSKCC	GRCh37	5	112175760	112175761	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs398123122	NA	P-0064571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	332	755	0	ENST00000257430.4:c.4473dup	p.Ala1492CysfsTer22	p.A1492Cfs*22	ENST00000257430	NM_000038.5	1490	cat/caTt	16/16	0.629603920260423	3	FACETS	0.986	0.95	1	0.986	0.95	1	CLONAL	3	TRUE	0	0.629603920260423	3		755	469	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0064571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	118	287	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.629603920260423	3	FACETS	0.824	0.755	0.895	0.824	0.755	0.895	CLONAL	2	TRUE	1	0.629603920260423	3		287	299	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121912580	NA	P-0064571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	87	524	0	ENST00000342988.3:c.1157G>T	p.Gly386Val	p.G386V	ENST00000342988	NM_005359.5	386	gGt/gTt	10/12	0.629603920260423	1	FACETS	0.915	0.827	1	0.915	0.827	1	CLONAL	1	TRUE	0	0.629603920260423	1		524	207	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943692	9943692	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749504561	NA	P-0064571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	243	871	0	ENST00000330684.3:c.1249G>A	p.Val417Ile	p.V417I	ENST00000330684	NM_001134407.1	417	Gtc/Atc	5/13	0.629603920260423	3	FACETS	0.967	0.913	1	0.967	0.913	1	CLONAL	2	TRUE	1	0.629603920260423	3		871	525	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278821	1278821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150819225	NA	P-0064571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	263	935	2	ENST00000310581.5:c.2221G>A	p.Val741Met	p.V741M	ENST00000310581	NM_198253.2	741	Gtg/Atg	6/16	0.629603920260423	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.629603920260423	3		937	498	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0064572-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	390	640	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.208827721243485	4	FACETS	0.919	0.874	0.965	0.919	0.874	0.965	CLONAL	4	TRUE	0	0.208827721243485	4		640	1228	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0064573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	93	580	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.322127686815189	1	FACETS	0.971	0.866	1	0.971	0.866	1	CLONAL	1	TRUE	0	0.322127686815189	1		581	499	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420351	88420351	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	63	608	0	ENST00000360948.2:c.2335G>A	p.Val779Ile	p.V779I	ENST00000360948	NM_001012338.2	779	Gtc/Atc	19/19	1	2	FACETS	0.825	0.715	0.944	0.825	0.715	0.944	CLONAL	1	TRUE	1	0.322127686815189	2		608	474	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619190	1619190	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	103	1120	0	ENST00000344749.5:c.1370G>T	p.Ser457Ile	p.S457I	ENST00000344749	NM_001136139.2	457	aGc/aTc	16/19	1	2	FACETS	0.906	0.811	1	0.906	0.811	1	CLONAL	1	TRUE	1	0.322127686815189	2		1120	706	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046387	69046387	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	163	689	0	ENST00000288368.4:c.3860A>G	p.Asn1287Ser	p.N1287S	ENST00000288368	NM_024870.2	1287	aAc/aGc	32/40	0.260994785494663	3	FACETS	0.918	0.846	0.993	0.918	0.846	0.993	CLONAL	2	TRUE	1	0.322127686815189	3		689	640	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0064575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	121	210	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.452390744595381	2		210	508	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520017	NA	P-0064575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	29	783	0	ENST00000326873.7:c.647C>T	p.Ser216Phe	p.S216F	ENST00000326873	NM_000455.4	216	tCc/tTc	5/10	1	2	FACETS	0.158	0.126	0.195	0.158	0.126	0.195	SUBCLONAL	1	TRUE	1	0.452390744595381	2		783	811	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477184	67477184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1320208623	NA	P-0064575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	167	673	0	ENST00000327367.4:c.991G>A	p.Val331Ile	p.V331I	ENST00000327367	NM_005902.3	331	Gtc/Atc	7/9	0.452390744595381	1	FACETS	0.957	0.884	1	0.957	0.884	1	CLONAL	1	TRUE	0	0.452390744595381	1		673	597	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732318	74732318	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	198	744	0	ENST00000359995.5:c.591G>C	p.Lys197Asn	p.K197N	ENST00000359995	NM_001195427.1	197	aaG/aaC	2/3	0.452390744595381	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.452390744595381	1		744	667	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732269	74732269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	174	700	0	ENST00000359995.5:c.640G>A	p.Glu214Lys	p.E214K	ENST00000359995	NM_001195427.1	214	Gaa/Aaa	2/3	0.452390744595381	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.452390744595381	1		700	585	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435945	116435945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395763398	NA	P-0064575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	38	617	0	ENST00000397752.3:c.3940G>A	p.Glu1314Lys	p.E1314K	ENST00000397752	NM_000245.2	1314	Gaa/Aaa	21/21	1	2	FACETS	0.238	0.196	0.286	0.238	0.196	0.286	SUBCLONAL	1	TRUE	1	0.452390744595381	2		617	705	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715410	117715410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	22	420	0	ENST00000368508.3:c.1079G>A	p.Arg360Lys	p.R360K	ENST00000368508	NM_002944.2	360	aGa/aAa	10/43	0.452390744595381	1	FACETS	0.237	0.184	0.3	0.237	0.184	0.3	SUBCLONAL	1	TRUE	0	0.452390744595381	1		420	317	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915891	127915891	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0064575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	111	557	0	ENST00000373547.4:c.590C>G	p.Ser197Ter	p.S197*	ENST00000373547	NM_002721.4	197	tCa/tGa	6/7	1	2	FACETS	0.887	0.8	0.979	0.887	0.8	0.979	CLONAL	1	TRUE	1	0.452390744595381	2		557	553	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16248841	16248845	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	GAAGG	GAAGG	-	novel	NA	P-0064575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	46	381	0	ENST00000375759.3:c.1847_1850+1del		p.X616_splice	ENST00000375759	NM_015001.2	616		10/15	1	2	FACETS	0.884	0.752	1	0.884	0.752	1	CLONAL	1	TRUE	1	0.452390744595381	2		381	230	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63760053	63760053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	33	554	0	ENST00000279873.7:c.706G>A	p.Glu236Lys	p.E236K	ENST00000279873	NM_032199.2	236	Gaa/Aaa	4/10	1	2	FACETS	0.247	0.2	0.3	0.247	0.2	0.3	SUBCLONAL	1	TRUE	1	0.452390744595381	2		554	591	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10785325	10785325	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	18	465	0	ENST00000361367.2:c.1093G>C	p.Glu365Gln	p.E365Q	ENST00000361367	NM_014633.3	365	Gag/Cag	9/25	1	2	FACETS	0.222	0.166	0.287	0.222	0.166	0.287	SUBCLONAL	1	TRUE	1	0.452390744595381	2		465	359	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69229709	69229709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	19	347	0	ENST00000462284.1:c.785C>T	p.Ser262Leu	p.S262L	ENST00000462284	NM_002392.5	262	tCa/tTa	9/11	0.450035256434112	3	FACETS	0.307	0.232	0.394	0.153	0.116	0.197	SUBCLONAL	1	TRUE	1	0.452390744595381	3		347	336	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042712	42042712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	124	589	0	ENST00000219905.7:c.6907G>A	p.Glu2303Lys	p.E2303K	ENST00000219905	NM_001164273.1	2303	Gaa/Aaa	17/24	0.452390744595381	1	FACETS	0.973	0.887	1	0.973	0.887	1	CLONAL	1	TRUE	0	0.452390744595381	1		589	436	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042790	42042790	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1469243680	NA	P-0064575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	100	524	0	ENST00000219905.7:c.6985G>A	p.Glu2329Lys	p.E2329K	ENST00000219905	NM_001164273.1	2329	Gag/Aag	17/24	0.452390744595381	1	FACETS	0.907	0.817	1	0.907	0.817	1	CLONAL	1	TRUE	0	0.452390744595381	1		524	377	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51503134	51503134	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	65	632	0	ENST00000260433.2:c.1383G>C	p.Lys461Asn	p.K461N	ENST00000260433		461	aaG/aaC	10/10	0.452390744595381	1	FACETS	0.478	0.415	0.546	0.478	0.415	0.546	SUBCLONAL	1	TRUE	0	0.452390744595381	1		632	465	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827856	72827856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	46	610	0	ENST00000268489.5:c.8725G>A	p.Glu2909Lys	p.E2909K	ENST00000268489	NM_006885.3	2909	Gaa/Aaa	9/10	1	2	FACETS	0.332	0.279	0.391	0.332	0.279	0.391	SUBCLONAL	1	TRUE	1	0.452390744595381	2		610	612	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664397	29664397	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	24	395	1	ENST00000356175.3:c.6376C>T	p.Gln2126Ter	p.Q2126*	ENST00000356175	NM_000267.3	2126	Caa/Taa	42/57	0.452390744595381	1	FACETS	0.25	0.196	0.313	0.25	0.196	0.313	SUBCLONAL	1	TRUE	0	0.452390744595381	1		396	328	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619091	37619091	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	56	671	1	ENST00000447079.4:c.767C>G	p.Ser256Trp	p.S256W	ENST00000447079	NM_015083.1	256	tCg/tGg	1/14	0.452390744595381	1	FACETS	0.311	0.266	0.36	0.311	0.266	0.36	SUBCLONAL	1	TRUE	0	0.452390744595381	1		672	616	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732259	74732259	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	165	682	0	ENST00000359995.5:c.650G>C	p.Gly217Ala	p.G217A	ENST00000359995	NM_001195427.1	217	gGa/gCa	2/3	0.452390744595381	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.452390744595381	1		682	538	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1646381	1646381	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	79	782	0	ENST00000344749.5:c.118C>A	p.Leu40Met	p.L40M	ENST00000344749	NM_001136139.2	40	Ctg/Atg	3/19	1	2	FACETS	0.422	0.37	0.477	0.422	0.37	0.477	SUBCLONAL	1	TRUE	1	0.452390744595381	2		782	828	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228572	36228572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1415120926	NA	P-0064575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	141	680	0	ENST00000222270.7:c.7586C>T	p.Ser2529Phe	p.S2529F	ENST00000222270	NM_014727.1	2529	tCc/tTc	34/37	1	2	FACETS	0.846	0.772	0.923	0.846	0.772	0.923	CLONAL	1	TRUE	1	0.452390744595381	2		680	737	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40761112	40761112	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	142	586	0	ENST00000392038.2:c.240G>C	p.Trp80Cys	p.W80C	ENST00000392038	NM_001626.4	80	tgG/tgC	4/14	1	2	FACETS	0.911	0.832	0.994	0.911	0.832	0.994	CLONAL	1	TRUE	1	0.452390744595381	2		586	689	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794857	42794857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	46	730	0	ENST00000575354.2:c.1937G>A	p.Arg646Lys	p.R646K	ENST00000575354	NM_015125.3	646	aGa/aAa	10/20	1	2	FACETS	0.272	0.228	0.32	0.272	0.228	0.32	SUBCLONAL	1	TRUE	1	0.452390744595381	2		730	749	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965662	25965662	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	48	598	0	ENST00000435504.4:c.3544G>C	p.Asp1182His	p.D1182H	ENST00000435504		1182	Gat/Cat	13/13	1	2	FACETS	0.301	0.253	0.353	0.301	0.253	0.353	SUBCLONAL	1	TRUE	1	0.452390744595381	2		598	706	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67632062	67632062	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	10	349	0	ENST00000272342.5:c.2248C>G	p.Leu750Val	p.L750V	ENST00000272342	NM_019002.3	750	Ctg/Gtg	5/6	1	2	FACETS	0.238	0.161	0.334	0.238	0.161	0.334	SUBCLONAL	1	TRUE	1	0.452390744595381	2		349	186	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272508	142272508	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	20	349	0	ENST00000350721.4:c.2607G>C	p.Leu869Phe	p.L869F	ENST00000350721	NM_001184.3	869	ttG/ttC	12/47	1	2	FACETS	0.423	0.325	0.537	0.423	0.325	0.537	SUBCLONAL	1	TRUE	1	0.452390744595381	2		349	209	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987359	2987359	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	36	610	0	ENST00000396946.4:c.70G>A	p.Glu24Lys	p.E24K	ENST00000396946	NM_032415.4	24	Gag/Aag	3/25	1	2	FACETS	0.225	0.184	0.272	0.225	0.184	0.272	SUBCLONAL	1	TRUE	1	0.452390744595381	2		610	706	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902283	151902283	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	10	90	0	ENST00000262189.6:c.3869G>C	p.Arg1290Thr	p.R1290T	ENST00000262189	NM_170606.2	1290	aGa/aCa	25/59	1	2	FACETS	0.388	0.264	0.541	0.388	0.264	0.541	SUBCLONAL	1	TRUE	1	0.452390744595381	2		90	114	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206782	27206782	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs755835455	NA	P-0064575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	66	560	0	ENST00000380036.4:c.2567G>C	p.Arg856Thr	p.R856T	ENST00000380036	NM_000459.3	856	aGa/aCa	15/23	1	2	FACETS	0.476	0.413	0.544	0.476	0.413	0.544	SUBCLONAL	1	TRUE	1	0.452390744595381	2		560	613	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321364	1321364	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	36	650	0	ENST00000400841.2:c.391C>A	p.Gln131Lys	p.Q131K	ENST00000400841		131	Cag/Aag	4/6	1	2	FACETS	0.227	0.186	0.274	0.227	0.186	0.274	SUBCLONAL	1	TRUE	1	0.452390744595381	2		650	700	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0064576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	76	372	0				ENST00000310581	NM_198253.2	-/1132			0.294430553276565	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	0	0.418195815308274	1		372	279	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0064576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	202	579	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.418195815308274	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.418195815308274	1		579	573	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151270	202151270	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	42	439	0	ENST00000358485.4:c.1570C>T	p.Gln524Ter	p.Q524*	ENST00000358485	NM_001080125.1	524	Cag/Tag	9/9	0.418195815308274	1	FACETS	0.339	0.283	0.402	0.339	0.283	0.402	SUBCLONAL	1	TRUE	0	0.418195815308274	1		439	468	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138867	64138867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	57	550	0	ENST00000334205.4:c.2234C>T	p.Ser745Phe	p.S745F	ENST00000334205	NM_003942.2	745	tCc/tTc	17/17	1	2	FACETS	0.62	0.533	0.714	0.62	0.533	0.714	SUBCLONAL	1	TRUE	1	0.418195815308274	2		550	440	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037492	12037492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	249	540	0	ENST00000396373.4:c.1123G>A	p.Gly375Arg	p.G375R	ENST00000396373	NM_001987.4	375	Gga/Aga	6/8	0.400798563313976	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.418195815308274	2		540	591	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73113194	73113194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	39	333	0	ENST00000356692.5:c.535C>T	p.Arg179Ter	p.R179*	ENST00000356692		179	Cga/Tga	7/9	0.418195815308274	1	FACETS	0.45	0.374	0.534	0.45	0.374	0.534	SUBCLONAL	1	TRUE	0	0.418195815308274	1		333	328	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149776	202149776	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	74	713	0	ENST00000358485.4:c.1217C>T	p.Ser406Phe	p.S406F	ENST00000358485	NM_001080125.1	406	tCc/tTc	8/9	0.418195815308274	1	FACETS	0.461	0.404	0.523	0.461	0.404	0.523	SUBCLONAL	1	TRUE	0	0.418195815308274	1		713	607	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300432	11300432	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs758857090	NA	P-0064576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	27	592	0	ENST00000361445.4:c.1714A>G	p.Thr572Ala	p.T572A	ENST00000361445	NM_004958.3	572	Acc/Gcc	11/58	1	2	FACETS	0.24	0.19	0.297	0.24	0.19	0.297	SUBCLONAL	1	TRUE	1	0.418195815308274	2		592	538	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427696	49427722	+	inframe_deletion	In_Frame_Del	DEL	TGTTCCGATATTCTGCCATGAGATTAG	TGTTCCGATATTCTGCCATGAGATTAG	-	novel	NA	P-0064576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	246	715	0	ENST00000301067.7:c.10766_10792del	p.Thr3589_Asn3597del	p.T3589_N3597del	ENST00000301067	NM_003482.3	3589	aCTAATCTCATGGCAGAATATCGGAACAag/aag	39/54	0.418195815308274	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.418195815308274	2		715	586	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3094686	3094686	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	49	484	1	ENST00000078429.4:c.37G>A	p.Asp13Asn	p.D13N	ENST00000078429	NM_002067.2	13	Gat/Aat	1/7	0.418195815308274	1	FACETS	0.639	0.545	0.742	0.639	0.545	0.742	SUBCLONAL	1	TRUE	0	0.418195815308274	1		485	290	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355045	15355045	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	49	625	0	ENST00000263377.2:c.2578C>G	p.Pro860Ala	p.P860A	ENST00000263377	NM_058243.2	860	Cca/Gca	13/20	0.300743010044194	1	FACETS	0.341	0.289	0.399	0.341	0.289	0.399	SUBCLONAL	1	TRUE	0	0.418195815308274	1		625	543	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147496	47147496	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	45	734	0	ENST00000409792.3:c.4830G>T	p.Lys1610Asn	p.K1610N	ENST00000409792	NM_014159.6	1610	aaG/aaT	6/21	0.418195815308274	1	FACETS	0.251	0.211	0.297	0.251	0.211	0.297	SUBCLONAL	1	TRUE	0	0.418195815308274	1		734	677	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939962	49939962	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	29	787	0	ENST00000296474.3:c.1081G>T	p.Gly361Cys	p.G361C	ENST00000296474	NM_002447.2	361	Ggc/Tgc	1/20	0.418195815308274	1	FACETS	0.196	0.156	0.241	0.196	0.156	0.241	SUBCLONAL	1	TRUE	0	0.418195815308274	1		787	560	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670320	134670320	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	53	552	0	ENST00000398015.3:c.231C>G	p.Ile77Met	p.I77M	ENST00000398015	NM_004441.4	77	atC/atG	3/16	0.188323797164872	3	FACETS	0.502	0.427	0.583	0.251	0.213	0.292	INDETERMINATE	1	TRUE	1	0.418195815308274	3		552	611	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577150	7577150	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	466	723	0	ENST00000269305.4:c.788del	p.Asn263IlefsTer82	p.N263Ifs*82	ENST00000269305	NM_001126112.2	263	aAt/at	8/11	0.920702764931588	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.920702764931588	1		723	493	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444311	50444311	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778251001	NA	P-0064577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	302	782	0	ENST00000331340.3:c.241G>A	p.Asp81Asn	p.D81N	ENST00000331340	NM_006060.4	81	Gat/Aat	4/8	0.722853234954737	1	FACETS	0.72	0.689	0.75	0.72	0.689	0.75	SUBCLONAL	1	TRUE	0	0.920702764931588	1		782	492	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856187	111856187	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	711	888	0	ENST00000341259.2:c.238C>A	p.Arg80Ser	p.R80S	ENST00000341259	NM_005475.2	80	Cgc/Agc	2/8	0.894004716058271	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.920702764931588	3		888	1118	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504614	103504614	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	91	203	0	ENST00000355739.4:c.235G>C	p.Asp79His	p.D79H	ENST00000355739	NM_000123.3	79	Gat/Cat	2/15	1	2	FACETS	0.871	0.788	0.955	0.871	0.788	0.955	CLONAL	1	TRUE	1	0.920702764931588	2		203	227	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132964	30132964	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	298	648	0	ENST00000331968.5:c.637A>T	p.Ser213Cys	p.S213C	ENST00000331968	NM_002742.2	213	Agc/Tgc	4/18	0.469237409997827	3	FACETS	1	0.987	1	0.572	0.541	0.604	INDETERMINATE	1	TRUE	1	0.920702764931588	3		648	826	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346933	89346933	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs933089649	NA	P-0064577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	344	1025	0	ENST00000301030.4:c.6017G>A	p.Gly2006Glu	p.G2006E	ENST00000301030	NM_001256183.1	2006	gGg/gAg	9/13	1	2	FACETS	0.977	0.93	1	0.977	0.93	1	CLONAL	1	TRUE	1	0.920702764931588	2		1025	765	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627354	37627354	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	383	868	0	ENST00000249071.6:c.365A>G	p.Asp122Gly	p.D122G	ENST00000249071	NM_002872.4	122	gAc/gGc	5/7	0.469237409997827	3	FACETS	1	0.994	1	0.634	0.604	0.664	INDETERMINATE	1	TRUE	1	0.920702764931588	3		868	958	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2969682	2969682	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	240	825	0	ENST00000396946.4:c.1597G>C	p.Asp533His	p.D533H	ENST00000396946	NM_032415.4	533	Gac/Cac	12/25	0.558887958277437	1	FACETS	0.404	0.379	0.43	0.404	0.379	0.43	SUBCLONAL	1	TRUE	0	0.920702764931588	1		825	696	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965594	90965594	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201745	NA	P-0064577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	44	111	0	ENST00000265433.3:c.1723G>T	p.Glu575Ter	p.E575*	ENST00000265433	NM_002485.4	575	Gaa/Taa	11/16	1	2	FACETS	0.838	0.724	0.957	0.838	0.724	0.957	CLONAL	1	TRUE	1	0.920702764931588	2		111	114	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27205050	27205050	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	103	555	0	ENST00000380036.4:c.2351C>A	p.Ala784Asp	p.A784D	ENST00000380036	NM_000459.3	784	gCc/gAc	14/23	0.469237409997827	3	FACETS	0.522	0.468	0.579	0.261	0.234	0.29	INDETERMINATE	1	TRUE	1	0.920702764931588	3		555	626	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400291	139400291	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	175	831	0	ENST00000277541.6:c.4057G>C	p.Gly1353Arg	p.G1353R	ENST00000277541	NM_017617.3	1353	Ggc/Cgc	25/34	0.469237409997827	3	FACETS	0.613	0.565	0.664	0.307	0.282	0.332	INDETERMINATE	1	TRUE	1	0.920702764931588	3		831	905	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578266	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs942158624	NA	P-0064578-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	864	1034	11	ENST00000269305.4:c.583A>T	p.Ile195Phe	p.I195F	ENST00000269305	NM_001126112.2	195	Atc/Ttc	6/11	0.899745891808871	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.899745891808871	2		1045	931	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154240	2154241	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0064578-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	352	863	0	ENST00000434045.2:c.687dup	p.Glu230ArgfsTer50	p.E230Rfs*50	ENST00000434045	NM_001127598.1	229	-/A	5/5	1	2	FACETS	0.929	0.884	0.974	0.929	0.884	0.974	CLONAL	1	TRUE	1	0.899745891808871	2		863	842	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433690	49433690	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064578-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	475	1028	3	ENST00000301067.7:c.7863del	p.Asp2622ThrfsTer69	p.D2622Tfs*69	ENST00000301067	NM_003482.3	2621	ccC/cc	31/54	1	2	FACETS	0.99	0.95	1	0.99	0.95	1	CLONAL	1	TRUE	1	0.899745891808871	2		1031	1066	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245941	5245941	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064578-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	321	1072	2	ENST00000357368.4:c.834G>A	p.Trp278Ter	p.W278*	ENST00000357368	NM_002850.3	278	tgG/tgA	10/38	0.899745891808871	2	FACETS	0.755	0.715	0.796	0.378	0.357	0.398	SUBCLONAL	1	TRUE	0	0.899745891808871	2		1074	945	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975472	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064578-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	260	793	1	ENST00000405192.2:c.415A>C	p.Thr139Pro	p.T139P	ENST00000405192	NM_001163147.1	139	Aca/Cca	7/12	1	2	FACETS	0.787	0.741	0.834	0.787	0.741	0.834	SUBCLONAL	1	TRUE	1	0.899745891808871	2		794	734	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	200	612	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.987	0.92	1	0.987	0.92	1	CLONAL	1	TRUE	1	0.678046965343612	2		612	598	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0064579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17012	15716	591	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.678046965343612	42	FACETS	0.982	0.975	0.989	0.491	0.487	0.495	CLONAL	21	TRUE	0	0.678046965343612	42		591	32728	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589333	28589333	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	152	361	0	ENST00000241453.7:c.2714G>A	p.Gly905Glu	p.G905E	ENST00000241453	NM_004119.2	905	gGa/gAa	22/24	0.678046965343612	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.678046965343612	1		361	281	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916767	48916767	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs794727481	NA	P-0064579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	65	237	0	ENST00000267163.4:c.297G>A	p.Trp99Ter	p.W99*	ENST00000267163	NM_000321.2	99	tgG/tgA	3/27	0.678046965343612	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.678046965343612	1		237	119	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075571	8075571	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370227993	NA	P-0064579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	240	607	0	ENST00000377482.5:c.109C>T	p.Arg37Cys	p.R37C	ENST00000377482	NM_018948.3	37	Cgc/Tgc	2/4	1	2	FACETS	0.933	0.874	0.992	0.933	0.874	0.992	CLONAL	1	TRUE	1	0.678046965343612	2		607	759	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064584-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	101	934	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.521335208920093	2	FACETS	0.505	0.451	0.562	0.252	0.225	0.281	SUBCLONAL	1	TRUE	0	0.521335208920093	2		934	768	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711904	89711904	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs786201867	NA	P-0064584-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	216	554	0	ENST00000371953.3:c.522T>A	p.Tyr174Ter	p.Y174*	ENST00000371953	NM_000314.4	174	taT/taA	6/9	0.510605984530159	2	FACETS	0.917	0.863	0.97	0.917	0.863	0.97	CLONAL	2	TRUE	0	0.521335208920093	2		554	452	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577466	64577468	+	frameshift_variant	Frame_Shift_Del	DEL	AAG	AAG	TT	novel	NA	P-0064584-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	153	820	1	ENST00000312049.6:c.114_116delinsAA	p.Leu39ArgfsTer80	p.L39Rfs*80	ENST00000312049	NM_130799.2	38	tcCTTg/tcAAg	2/10	0.521335208920093	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.521335208920093	1		821	418	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102874157	102874157	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0064584-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	61	466	0	ENST00000307046.8:c.3G>A	p.Met1?	p.M1?	ENST00000307046	NM_001111285.1	1	atG/atA	1/4	1	2	FACETS	0.688	0.597	0.786	0.688	0.597	0.786	SUBCLONAL	1	TRUE	1	0.521335208920093	2		466	340	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170909	56170910	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0064584-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	318	882	0	ENST00000399503.3:c.1743_1744del	p.Glu581AspfsTer9	p.E581Dfs*9	ENST00000399503	NM_005921.1	579	gtGAga/gtga	10/20	0.521335208920093	3	FACETS	0.9	0.853	0.948	0.9	0.853	0.948	CLONAL	2	TRUE	1	0.521335208920093	3		882	854	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945655	151945655	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064584-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	90	362	0	ENST00000262189.6:c.1864G>T	p.Glu622Ter	p.E622*	ENST00000262189	NM_170606.2	622	Gaa/Taa	14/59	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.521335208920093	2		362	309	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0064585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	128	372	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.97	0.892	1	0.97	0.892	1	CLONAL	1	TRUE	1	0.804229001537645	2		372	328	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0064585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	509	560	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.752976990335948	4	FACETS	1	0.971	1			1	CLONAL	3	TRUE	NA	0.804229001537645	4		560	760	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971176	21971177	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0064585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	352	887	0	ENST00000304494.5:c.181dup	p.Glu61GlyfsTer59	p.E61Gfs*59	ENST00000304494	NM_000077.4	61	gag/gGag	2/3	0.804229001537645	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.804229001537645	1		887	452	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657493	29657493	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	29	407	0	ENST00000356175.3:c.5726G>T	p.Cys1909Phe	p.C1909F	ENST00000356175	NM_000267.3	1909	tGt/tTt	38/57	0.412998037538371	1	FACETS	0.125	0.1	0.153	0.125	0.1	0.153	INDETERMINATE	1	TRUE	0	0.804229001537645	1		407	345	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095980	11095980	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751542188	NA	P-0064585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	31	772	2	ENST00000358026.2:c.254C>T	p.Ser85Leu	p.S85L	ENST00000358026	NM_001128849.1	85	tCg/tTg	3/36	0.118862867133223	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.804229001537645	0		774	484	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934967	49934967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	249	1033	0	ENST00000296474.3:c.2032G>A	p.Gly678Ser	p.G678S	ENST00000296474	NM_002447.2	678	Ggc/Agc	6/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.804229001537645	2		1033	607	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972993	68972993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	144	429	0	ENST00000288368.4:c.1318G>A	p.Glu440Lys	p.E440K	ENST00000288368	NM_024870.2	440	Gaa/Aaa	11/40	1	2	FACETS	0.918	0.847	0.991	0.918	0.847	0.991	CLONAL	1	TRUE	1	0.804229001537645	2		429	390	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778850	76778850	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	144	525	0	ENST00000373344.5:c.6729A>G	p.Ile2243Met	p.I2243M	ENST00000373344	NM_000489.3	2243	atA/atG	31/35	0.261086139528026	1	FACETS	0.541	0.498	0.584	0.541	0.498	0.584	INDETERMINATE	1	TRUE	0	0.804229001537645	1		525	396	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0064586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	44	377	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.405	0.339	0.479	0.405	0.339	0.479	SUBCLONAL	1	TRUE	1	0.34	2		377	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579364	7579364	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	82	777	0	ENST00000269305.4:c.323G>T	p.Gly108Val	p.G108V	ENST00000269305	NM_001126112.2	108	gGt/gTt	4/11	1	2	FACETS	0.687	0.606	0.775	0.687	0.606	0.775	SUBCLONAL	1	TRUE	1	0.34	2		777	702	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178190	142178190	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	31	470	0	ENST00000350721.4:c.7228A>C	p.Met2410Leu	p.M2410L	ENST00000350721	NM_001184.3	2410	Atg/Ctg	43/47	1	2	FACETS	0.402	0.324	0.489	0.402	0.324	0.489	SUBCLONAL	1	TRUE	1	0.34	2		470	454	SUCCESS
REST	5978	MSKCC	GRCh37	4	57777205	57777205	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	40	680	0	ENST00000309042.7:c.401A>G	p.Tyr134Cys	p.Y134C	ENST00000309042	NM_005612.4	134	tAc/tGc	2/4	1	2	FACETS	0.318	0.263	0.379	0.318	0.263	0.379	SUBCLONAL	1	TRUE	1	0.34	2		680	740	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242501	55242501	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	38	536	0	ENST00000275493.2:c.2271G>T	p.Lys757Asn	p.K757N	ENST00000275493	NM_005228.3	757	aaG/aaT	19/28	1	2	FACETS	0.418	0.345	0.5	0.418	0.345	0.5	SUBCLONAL	1	TRUE	1	0.34	2		536	535	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719967	18719967	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064587-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	187	40	0	ENST00000266497.5:c.3864A>T	p.Leu1288Phe	p.L1288F	ENST00000266497		1288	ttA/ttT	27/31	0.712474608393298	4	FACETS	0.993	0.929	1	0.993	0.929	1	CLONAL	2	TRUE	2	0.838433461295455	4		40	413	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578396	7578404	+	inframe_deletion	In_Frame_Del	DEL	GTGGGGGCA	GTGGGGGCA	-	novel	NA	P-0064587-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	602	937	0	ENST00000269305.4:c.526_534del	p.Cys176_His178del	p.C176_H178del	ENST00000269305	NM_001126112.2	176	TGCCCCCAC/-	5/11	0.833603119747763	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.838433461295455	2		937	710	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397205	397205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372869810	NA	P-0064588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	183	963	0	ENST00000380956.4:c.590C>T	p.Thr197Met	p.T197M	ENST00000380956	NM_001195286.1	197	aCg/aTg	5/9	0.68277766433577	4	FACETS	0.956	0.891	1	0.956	0.891	1	CLONAL	2	FALSE	2	0.68277766433577	4		963	472	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748048	41748048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	159	381	3	ENST00000226382.2:c.721G>A	p.Ala241Thr	p.A241T	ENST00000226382	NM_003924.3	241	Gca/Aca	3/3	0.68277766433577	3	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	FALSE	1	0.68277766433577	3		384	309	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425375	49425375	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	37	1015	0	ENST00000301067.7:c.13113C>A	p.Ser4371Arg	p.S4371R	ENST00000301067	NM_003482.3	4371	agC/agA	39/54	0.68277766433577	4	FACETS	0.455	0.375	0.544	0.227	0.187	0.272	SUBCLONAL	1	FALSE	2	0.68277766433577	4		1015	401	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391430	139391430	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	190	1047	0	ENST00000277541.6:c.6761A>T	p.Glu2254Val	p.E2254V	ENST00000277541	NM_017617.3	2254	gAg/gTg	34/34	0.601751936883678	5	FACETS	0.955	0.888	1	0.636	0.592	0.682	CLONAL	2	FALSE	2	0.68277766433577	5		1047	590	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0064596-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	216	210	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.418399751480482	3	FACETS	1	0.974	1	0.551	0.511	0.591	CLONAL	1	TRUE	1	0.445247497080885	3		210	1077	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061240	38061240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064596-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	236	820	0	ENST00000250448.2:c.749C>T	p.Ser250Phe	p.S250F	ENST00000250448	NM_004496.3	250	tCc/tTc	2/2	0.397754602765071	4	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.445247497080885	4		820	1356	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115979	8115980	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0064596-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	179	692	0	ENST00000346208.3:c.1328dup	p.Ter444LeufsTer63	p.*444Lfs*63	ENST00000346208		442	atg/atGg	6/6	0.380745167835683	3	FACETS	1	0.938	1	0.51	0.47	0.552	CLONAL	1	TRUE	1	0.445247497080885	3		692	963	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840008	27840008	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064596-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1698	259	1059	0	ENST00000328488.2:c.86G>C	p.Ser29Thr	p.S29T	ENST00000328488	NM_003533.2	29	aGc/aCc	1/1	0.445247497080885	4	FACETS	0.859	0.801	0.919	0.43	0.4	0.46	CLONAL	1	TRUE	2	0.445247497080885	4		1059	1957	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0064596-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	81	210	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.36872150293879	3	FACETS	1	0.972	1	0.666	0.591	0.746	CLONAL	1	TRUE	1	0.384640675135959	3		210	377	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061240	38061240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064596-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	184	820	0	ENST00000250448.2:c.749C>T	p.Ser250Phe	p.S250F	ENST00000250448	NM_004496.3	250	tCc/tTc	2/2	0.384640675135959	6	FACETS	1	0.936	1	0.507	0.468	0.547	CLONAL	2	TRUE	2	0.384640675135959	6		820	835	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115979	8115980	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0064596-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	83	692	0	ENST00000346208.3:c.1328dup	p.Ter444LeufsTer63	p.*444Lfs*63	ENST00000346208		442	atg/atGg	6/6	0.208849766498652	3	FACETS	0.909	0.804	1	0.303	0.268	0.341	INDETERMINATE	1	TRUE	0	0.384640675135959	3		692	566	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840008	27840008	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064596-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	153	1059	0	ENST00000328488.2:c.86G>C	p.Ser29Thr	p.S29T	ENST00000328488	NM_003533.2	29	aGc/aCc	1/1	0.383310032898154	4	FACETS	1	0.976	1	0.592	0.541	0.645	CLONAL	1	TRUE	2	0.384640675135959	4		1059	930	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064597-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	163	612	0				ENST00000310581	NM_198253.2	-/1132			0.205464460167672	5	FACETS	0.912	0.835	0.992	0.608	0.557	0.662	CLONAL	2	TRUE	2	0.205464460167672	5		612	1138	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0064597-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	219	547	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.191580415441697	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.205464460167672	2		547	965	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0064597-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	31	230	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.205464460167672	3	FACETS	0.967	0.791	1	0.967	0.791	1	CLONAL	2	TRUE	1	0.205464460167672	3		230	172	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971000	21971000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064597-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1188	674	1015	0	ENST00000304494.5:c.358G>T	p.Glu120Ter	p.E120*	ENST00000304494	NM_000077.4	120	Gag/Tag	2/3	0.205464460167672	5	FACETS	0.922	0.888	0.956	0.922	0.888	0.956	CLONAL	5	TRUE	0	0.205464460167672	5		1015	1862	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021492	42021492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064597-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	106	589	0	ENST00000219905.7:c.3788C>T	p.Ser1263Leu	p.S1263L	ENST00000219905	NM_001164273.1	1263	tCa/tTa	11/24	0.205464460167672	3	FACETS	1	0.965	1	0.591	0.529	0.657	CLONAL	1	TRUE	1	0.205464460167672	3		589	963	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287839	33287839	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064597-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1305	219	795	0	ENST00000374542.5:c.1414G>A	p.Glu472Lys	p.E472K	ENST00000374542	NM_001141970.1	472	Gag/Aag	5/8	0.205464460167672	4	FACETS	0.843	0.782	0.907	0.843	0.782	0.907	CLONAL	2	TRUE	2	0.205464460167672	4		795	1524	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870260	44870260	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064597-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	22	100	0	ENST00000377967.4:c.439C>T	p.Gln147Ter	p.Q147*	ENST00000377967	NM_021140.2	147	Cag/Tag	5/29	0.205464460167672	2	FACETS	0.817	0.641	1			1	CLONAL	2	TRUE	NA	0.205464460167672	2		100	131	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121856	2121856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745897413	NA	P-0064597-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	105	656	0	ENST00000219476.3:c.2018C>T	p.Ala673Val	p.A673V	ENST00000219476	NM_000548.3	673	gCg/gTg	19/42	0.205464460167672	3	FACETS	1	0.907	1	0.508	0.454	0.566	CLONAL	1	TRUE	1	0.205464460167672	3		656	1109	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786887	135786887	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554817388	NA	P-0064597-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	172	496	0	ENST00000298552.3:c.982C>T	p.Gln328Ter	p.Q328*	ENST00000298552	NM_001162426.1	328	Cag/Tag	10/23	0.205464460167672	2	FACETS	0.945	0.87	1	0.945	0.87	1	CLONAL	2	TRUE	0	0.205464460167672	2		496	886	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941240	71941240	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064597-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1303	204	979	0	ENST00000298229.2:c.1015G>C	p.Glu339Gln	p.E339Q	ENST00000298229	NM_001567.3	339	Gag/Cag	9/28	0.191580415441697	2	FACETS	1	0.987	1	0.659	0.609	0.711	CLONAL	1	TRUE	0	0.205464460167672	2		979	1507	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720342	43720342	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1220444634	NA	P-0064597-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	54	460	1	ENST00000382044.4:c.3700C>T	p.Gln1234Ter	p.Q1234*	ENST00000382044	NM_001141980.1	1234	Cag/Tag	18/28	0.205464460167672	3	FACETS	0.687	0.585	0.799	0.343	0.292	0.4	SUBCLONAL	1	TRUE	1	0.205464460167672	3		461	844	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410961	31410961	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064597-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	211	597	0	ENST00000344624.3:c.3559C>G	p.Gln1187Glu	p.Q1187E	ENST00000344624		1187	Cag/Gag	28/33	0.205464460167672	5	FACETS	0.992	0.919	1	0.661	0.613	0.712	CLONAL	2	TRUE	2	0.205464460167672	5		597	1354	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405991	70405991	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064597-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	124	591	0	ENST00000373644.4:c.3505C>G	p.Gln1169Glu	p.Q1169E	ENST00000373644	NM_030625.2	1169	Caa/Gaa	4/12	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.205464460167672	2		591	960	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940198	71940198	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064597-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	74	730	0	ENST00000298229.2:c.583G>T	p.Glu195Ter	p.E195*	ENST00000298229	NM_001567.3	195	Gaa/Taa	5/28	0.191580415441697	2	FACETS	0.599	0.523	0.683	0.3	0.261	0.342	SUBCLONAL	1	TRUE	0	0.205464460167672	2		730	1202	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33680016	33680016	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064597-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	89	516	0	ENST00000308377.4:c.2065C>G	p.Arg689Gly	p.R689G	ENST00000308377	NM_152270.3	689	Cgg/Ggg	5/5	0.205464460167672	3	FACETS	0.992	0.878	1			1	CLONAL	1	TRUE	NA	0.205464460167672	3		516	963	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220093	36220093	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064597-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1461	156	848	0	ENST00000222270.7:c.4813G>A	p.Glu1605Lys	p.E1605K	ENST00000222270	NM_014727.1	1605	Gag/Aag	22/37	0.205464460167672	4	FACETS	1	0.969	1	0.377	0.344	0.413	CLONAL	1	TRUE	1	0.205464460167672	4		848	1617	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424156	47424157	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0064597-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	398	619	0	ENST00000404338.3:c.2225dup	p.Tyr742Ter	p.Y742*	ENST00000404338	NM_004491.4	742	tac/tAac	1/6	0.205464460167672	4	FACETS	0.997	0.949	1	0.997	0.949	1	CLONAL	4	TRUE	0	0.205464460167672	4		619	1171	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439799	220439799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064597-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1288	92	847	0	ENST00000243786.2:c.652C>T	p.His218Tyr	p.H218Y	ENST00000243786	NM_002191.3	218	Cac/Tac	2/2	1	2	FACETS	0.649	0.574	0.729	0.649	0.574	0.729	SUBCLONAL	1	TRUE	1	0.205464460167672	2		847	1380	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446130	29446130	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773834473	NA	P-0064597-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	155	654	0	ENST00000544604.2:c.1961C>T	p.Ser654Leu	p.S654L	ENST00000544604	NM_001206998.1	654	tCg/tTg	8/9	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.205464460167672	2		654	1153	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202721	128202721	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064597-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	203	731	0	ENST00000341105.2:c.999C>G	p.Ile333Met	p.I333M	ENST00000341105	NM_032638.4	333	atC/atG	4/6	0.205464460167672	3	FACETS	0.892	0.825	0.961	0.892	0.825	0.961	CLONAL	2	TRUE	1	0.205464460167672	3		731	1222	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80169066	80169066	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs928453595	NA	P-0064597-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	41	430	0	ENST00000265081.6:c.3262C>G	p.His1088Asp	p.H1088D	ENST00000265081	NM_002439.4	1088	Cac/Gac	23/24	1	2	FACETS	0.808	0.673	0.958	0.808	0.673	0.958	CLONAL	1	TRUE	1	0.205464460167672	2		430	494	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402663	20402663	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064597-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1435	245	1005	0	ENST00000346618.3:c.200C>A	p.Thr67Asn	p.T67N	ENST00000346618	NM_001949.4	67	aCc/aAc	1/7	0.205464460167672	4	FACETS	0.856	0.797	0.917	0.856	0.797	0.917	CLONAL	2	TRUE	2	0.205464460167672	4		1005	1680	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287827	33287827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064597-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1300	219	780	0	ENST00000374542.5:c.1426G>A	p.Asp476Asn	p.D476N	ENST00000374542	NM_001141970.1	476	Gat/Aat	5/8	0.205464460167672	4	FACETS	0.846	0.784	0.91	0.846	0.784	0.91	CLONAL	2	TRUE	2	0.205464460167672	4		780	1519	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200207	123200208	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064597-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	44	139	0	ENST00000218089.9:c.2186_2187insA	p.Val730CysfsTer18	p.V730Cfs*18	ENST00000218089	NM_001042749.1	729	att/atAt	23/35	0.205464460167672	2	FACETS	0.909	0.776	1			1	CLONAL	3	TRUE	NA	0.205464460167672	2		139	157	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0064609-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	21	516	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.774	0.596	0.983	0.774	0.596	0.983	CLONAL	1	TRUE	1	0.16	2		516	339	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0064609-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	23	339	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.541	0.421	0.682	0.541	0.421	0.682	SUBCLONAL	1	TRUE	1	0.16	2		339	531	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032794	30032794	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434259	NA	P-0064609-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	78	1023	1	ENST00000338641.4:c.169C>T	p.Arg57Ter	p.R57*	ENST00000338641	NM_000268.3	57	Cga/Tga	2/16	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.16	2		1024	916	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207065	1207065	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064609-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	57	1180	0	ENST00000326873.7:c.157del	p.Asp53ThrfsTer11	p.D53Tfs*11	ENST00000326873	NM_000455.4	51	atG/at	1/10	0.3	3	FACETS	0.708	0.605	0.821			1	SUBCLONAL	1	TRUE	NA	0.16	3		1180	1087	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577524	7577524	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064609-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	33	943	0	ENST00000269305.4:c.757A>T	p.Thr253Ser	p.T253S	ENST00000269305	NM_001126112.2	253	Acc/Tcc	7/11	1	2	FACETS	0.505	0.409	0.613	0.505	0.409	0.613	SUBCLONAL	1	TRUE	1	0.16	2		943	817	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0064610-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	553	925	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.231431552481951	3	FACETS	0.947	0.913	0.98	0.631	0.609	0.654	INDETERMINATE	2	TRUE	0	0.749901421067974	3		925	1071	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0064610-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	739	579	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.723916222497414	2	FACETS	0.978	0.955	1	0.978	0.955	1	CLONAL	2	TRUE	0	0.749901421067974	2		579	1008	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952191	76952191	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0064610-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	26	44	0	ENST00000373344.5:c.244A>T	p.Lys82Ter	p.K82*	ENST00000373344	NM_000489.3	82	Aaa/Taa	5/35	0.272417526207756	4	FACETS	0.749	0.599	0.917	0.375	0.299	0.459	INDETERMINATE	1	TRUE	2	0.749901421067974	4		44	162	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222593	69222593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194693256	NA	P-0064611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	75	458	0	ENST00000462284.1:c.566G>A	p.Arg189His	p.R189H	ENST00000462284	NM_002392.5	189	cGc/cAc	8/11	1	2	FACETS	0.983	0.878	1	0.983	0.878	1	CLONAL	1	TRUE	1	0.755506391098478	2		458	202	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022899	27022899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	173	804	1	ENST00000324856.7:c.5C>T	p.Ala2Val	p.A2V	ENST00000324856	NM_006015.4	2	gCc/gTc	1/20	1	2	FACETS	0.974	0.905	1	0.974	0.905	1	CLONAL	1	TRUE	1	0.755506391098478	2		805	470	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266048	41266327	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAAT	ACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAAT	-	novel	NA	P-0064611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	42	691	0	ENST00000349496.5:c.46_241+84del		p.X16_splice	ENST00000349496	NM_001904.3	16		3/15	1	2	FACETS	0.461	0.388	0.541	0.461	0.388	0.541	SUBCLONAL	1	TRUE	1	0.755506391098478	2		691	241	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0064612-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	385	669	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.684775547581363	2	FACETS	0.925	0.891	0.958	0.925	0.891	0.958	CLONAL	2	TRUE	0	0.706780255859992	2		669	589	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0064612-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	243	557	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.975	0.916	1	0.975	0.916	1	CLONAL	1	TRUE	1	0.706780255859992	2		557	705	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778738	3778738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1489860615	NA	P-0064612-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	50	898	0	ENST00000262367.5:c.6310C>T	p.Arg2104Cys	p.R2104C	ENST00000262367	NM_004380.2	2104	Cgc/Tgc	31/31	1	2	FACETS	0.206	0.174	0.241	0.206	0.174	0.241	SUBCLONAL	1	TRUE	1	0.706780255859992	2		898	687	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193207	11193207	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064612-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	192	663	0	ENST00000361445.4:c.5294A>G	p.Asn1765Ser	p.N1765S	ENST00000361445	NM_004958.3	1765	aAt/aGt	38/58	1	2	FACETS	0.922	0.858	0.988	0.922	0.858	0.988	CLONAL	1	TRUE	1	0.706780255859992	2		663	589	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11276213	11276213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064612-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	169	511	0	ENST00000361445.4:c.3109C>T	p.Leu1037Phe	p.L1037F	ENST00000361445	NM_004958.3	1037	Ctc/Ttc	20/58	1	2	FACETS	0.956	0.886	1	0.956	0.886	1	CLONAL	1	TRUE	1	0.706780255859992	2		511	500	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40477018	40477018	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064612-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	57	745	0	ENST00000264657.5:c.1427C>A	p.Ser476Tyr	p.S476Y	ENST00000264657	NM_139276.2	476	tCc/tAc	16/24	1	2	FACETS	0.242	0.207	0.28	0.242	0.207	0.28	SUBCLONAL	1	TRUE	1	0.706780255859992	2		745	667	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	163	460	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.35	2		460	759	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624245	89624245	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554890335	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	43	174	0	ENST00000371953.3:c.19G>T	p.Glu7Ter	p.E7*	ENST00000371953	NM_000314.4	7	Gag/Tag	1/9	1	2	FACETS	0.758	0.645	0.879	1	0.962	1	SUBCLONAL	2	TRUE	1	0.35	2		174	162	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217225	11217225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	124	711	0	ENST00000361445.4:c.4453G>A	p.Glu1485Lys	p.E1485K	ENST00000361445	NM_004958.3	1485	Gag/Aag	30/58	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.35	2		711	708	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255802	16255802	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	116	848	0	ENST00000375759.3:c.3067T>C	p.Ser1023Pro	p.S1023P	ENST00000375759	NM_015001.2	1023	Tcc/Ccc	11/15	1	2	FACETS	0.952	0.859	1	0.952	0.859	1	CLONAL	1	TRUE	1	0.35	2		848	696	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46738152	46738152	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	75	601	0	ENST00000371975.4:c.1184G>T	p.Arg395Met	p.R395M	ENST00000371975	NM_003579.3	395	aGg/aTg	11/18	1	2	FACETS	0.959	0.843	1	0.959	0.843	1	CLONAL	1	TRUE	1	0.35	2		601	447	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439638	51439638	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750990884	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	103	718	0	ENST00000262662.1:c.203G>A	p.Arg68Gln	p.R68Q	ENST00000262662		68	cGa/cAa	4/4	1	2	FACETS	0.934	0.837	1	0.934	0.837	1	CLONAL	1	TRUE	1	0.35	2		718	630	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120508111	120508111	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	76	656	0	ENST00000256646.2:c.1646A>C	p.Asp549Ala	p.D549A	ENST00000256646	NM_024408.3	549	gAt/gCt	10/34	1	2	FACETS	0.79	0.694	0.893	0.79	0.694	0.893	SUBCLONAL	1	TRUE	1	0.35	2		656	550	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150936528	150936528	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	101	474	0	ENST00000271640.5:c.3727C>T	p.Arg1243Cys	p.R1243C	ENST00000271640	NM_001145415.1	1243	Cgc/Tgc	21/22	1	2	FACETS	0.91	0.815	1	0.91	0.815	1	CLONAL	1	TRUE	1	0.35	2		474	634	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163315482	163315482	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	43	350	0	ENST00000271452.3:c.822G>T	p.Glu274Asp	p.E274D	ENST00000271452	NM_145697.2	274	gaG/gaT	11/14	1	2	FACETS	0.894	0.752	1	0.894	0.752	1	CLONAL	1	TRUE	1	0.35	2		350	275	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193110987	193110987	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1186176634	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	42	310	0	ENST00000367435.3:c.520T>C	p.Ser174Pro	p.S174P	ENST00000367435	NM_024529.4	174	Tct/Cct	7/17	1	2	FACETS	0.811	0.68	0.954	0.811	0.68	0.954	CLONAL	1	TRUE	1	0.35	2		310	296	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204511917	204511917	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs991142439	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	31	307	0	ENST00000367182.3:c.517G>T	p.Asp173Tyr	p.D173Y	ENST00000367182	NM_001278516.1	173	Gac/Tac	8/11	1	2	FACETS	0.836	0.681	1	0.836	0.681	1	CLONAL	1	TRUE	1	0.35	2		307	212	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649639	206649639	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	118	930	0	ENST00000367120.3:c.474C>A	p.Phe158Leu	p.F158L	ENST00000367120	NM_014002.3	158	ttC/ttA	6/22	1	2	FACETS	0.873	0.788	0.963	0.873	0.788	0.963	CLONAL	1	TRUE	1	0.35	2		930	772	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231488898	231488898	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	52	383	0	ENST00000295050.7:c.1261T>G	p.Phe421Val	p.F421V	ENST00000295050	NM_032018.5	421	Ttt/Gtt	5/5	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.35	2		383	292	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100702	8100702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1330938980	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	44	821	0	ENST00000346208.3:c.676G>A	p.Val226Met	p.V226M	ENST00000346208		226	Gtg/Atg	3/6	1	2	FACETS	0.388	0.325	0.459	0.388	0.325	0.459	SUBCLONAL	1	TRUE	1	0.35	2		821	648	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406439	70406439	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	109	803	0	ENST00000373644.4:c.3953A>G	p.Gln1318Arg	p.Q1318R	ENST00000373644	NM_030625.2	1318	cAa/cGa	4/12	1	2	FACETS	0.899	0.808	0.995	0.899	0.808	0.995	CLONAL	1	TRUE	1	0.35	2		803	693	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683192	88683192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199907158	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	50	255	0	ENST00000372037.3:c.1402G>A	p.Glu468Lys	p.E468K	ENST00000372037	NM_004329.2	468	Gaa/Aaa	12/13	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.35	2		255	270	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692940	89692940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746152219	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	48	433	0	ENST00000371953.3:c.424C>T	p.Arg142Trp	p.R142W	ENST00000371953	NM_000314.4	142	Cgg/Tgg	5/9	1	2	FACETS	0.917	0.78	1	0.917	0.78	1	CLONAL	1	TRUE	1	0.35	2		433	299	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717696	89717696	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1554825207	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	83	425	0	ENST00000371953.3:c.721T>G	p.Phe241Val	p.F241V	ENST00000371953	NM_000314.4	241	Ttt/Gtt	7/9	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.35	2		425	396	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410647	32410647	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	115	739	0	ENST00000332351.3:c.1511A>C	p.Asn504Thr	p.N504T	ENST00000332351	NM_024426.4	504	aAc/aCc	10/10	1	2	FACETS	0.875	0.789	0.966	0.875	0.789	0.966	CLONAL	1	TRUE	1	0.35	2		739	751	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514265	69514265	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	38	873	0	ENST00000294312.3:c.416A>G	p.His139Arg	p.H139R	ENST00000294312	NM_005117.2	139	cAc/cGc	3/3	1	2	FACETS	0.292	0.241	0.35	0.292	0.241	0.35	SUBCLONAL	1	TRUE	1	0.35	2		873	743	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94922975	94922975	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1286895936	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	44	380	0	ENST00000536441.1:c.493C>T	p.Arg165Ter	p.R165*	ENST00000536441	NM_144665.3	165	Cga/Tga	4/10	1	2	FACETS	0.803	0.677	0.942	0.803	0.677	0.942	CLONAL	1	TRUE	1	0.35	2		380	313	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933279	100933279	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	90	668	0	ENST00000325455.5:c.2111A>G	p.Asp704Gly	p.D704G	ENST00000325455	NM_001202474.3	704	gAc/gGc	4/8	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.35	2		668	470	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962574	100962574	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	87	487	0	ENST00000325455.5:c.1823A>C	p.Asp608Ala	p.D608A	ENST00000325455	NM_001202474.3	608	gAc/gCc	3/8	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.35	2		487	475	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996757	100996757	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	45	497	0	ENST00000325455.5:c.1770C>A	p.Phe590Leu	p.F590L	ENST00000325455	NM_001202474.3	590	ttC/ttA	2/8	1	2	FACETS	0.627	0.528	0.737	0.627	0.528	0.737	SUBCLONAL	1	TRUE	1	0.35	2		497	410	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122583	108122583	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	61	424	0	ENST00000278616.4:c.1627A>G	p.Thr543Ala	p.T543A	ENST00000278616	NM_000051.3	543	Act/Gct	11/63	1	2	FACETS	0.898	0.778	1	0.898	0.778	1	CLONAL	1	TRUE	1	0.35	2		424	388	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143551	108143551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201780199	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	17	397	0	ENST00000278616.4:c.3256C>T	p.Arg1086Cys	p.R1086C	ENST00000278616	NM_000051.3	1086	Cgc/Tgc	22/63	1	2	FACETS	0.335	0.25	0.436	0.335	0.25	0.436	SUBCLONAL	1	TRUE	1	0.35	2		397	290	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216627	108216627	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	42	348	0	ENST00000278616.4:c.8576C>A	p.Ser2859Tyr	p.S2859Y	ENST00000278616	NM_000051.3	2859	tCt/tAt	58/63	1	2	FACETS	0.857	0.72	1	0.857	0.72	1	CLONAL	1	TRUE	1	0.35	2		348	280	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344108	118344108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	58	662	0	ENST00000534358.1:c.2234G>A	p.Arg745Gln	p.R745Q	ENST00000534358	NM_005933.3	745	cGa/cAa	3/36	1	2	FACETS	0.672	0.578	0.774	0.672	0.578	0.774	SUBCLONAL	1	TRUE	1	0.35	2		662	493	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360886	118360886	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	95	547	0	ENST00000534358.1:c.4618A>C	p.Thr1540Pro	p.T1540P	ENST00000534358	NM_005933.3	1540	Act/Cct	13/36	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.35	2		547	527	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475203	475203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754666448	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	52	529	0	ENST00000399788.2:c.434G>A	p.Arg145His	p.R145H	ENST00000399788	NM_001042603.1	145	cGc/cAc	4/28	1	2	FACETS	0.851	0.728	0.985	0.851	0.728	0.985	CLONAL	1	TRUE	1	0.35	2		529	349	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424958105	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	10	413	0	ENST00000334344.6:c.940C>T	p.Arg314Cys	p.R314C	ENST00000334344	NM_152641.2	314	Cgt/Tgt	8/21	1	2	FACETS	0.152	0.102	0.215	0.152	0.102	0.215	SUBCLONAL	1	TRUE	1	0.35	2		413	376	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	127	809	0	ENST00000320574.5:c.1231G>C	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ctg	13/49	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.35	2		809	623	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562160	21562160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	149	995	0	ENST00000382592.4:c.1759G>A	p.Glu587Lys	p.E587K	ENST00000382592	NM_014572.2	587	Gaa/Aaa	4/8	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.35	2		995	848	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004277	29004277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370686484	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	63	542	0	ENST00000282397.4:c.1016G>A	p.Arg339Gln	p.R339Q	ENST00000282397	NM_002019.4	339	cGa/cAa	8/30	1	2	FACETS	0.687	0.595	0.787	0.687	0.595	0.787	SUBCLONAL	1	TRUE	1	0.35	2		542	524	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041204	29041204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393191546	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	78	635	0	ENST00000282397.4:c.224G>A	p.Ser75Asn	p.S75N	ENST00000282397	NM_002019.4	75	aGc/aAc	3/30	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.35	2		635	433	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911185	32911185	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	40	221	0	ENST00000380152.3:c.2693G>T	p.Arg898Met	p.R898M	ENST00000380152		898	aGg/aTg	11/27	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.35	2		221	214	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281763	49281763	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	90	791	0	ENST00000282018.3:c.810C>A	p.His270Gln	p.H270Q	ENST00000282018	NM_020377.2	270	caC/caA	1/1	1	2	FACETS	0.79	0.701	0.884	0.79	0.701	0.884	SUBCLONAL	1	TRUE	1	0.35	2		791	651	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281931	49281931	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	36	628	0	ENST00000282018.3:c.978G>T	p.Gln326His	p.Q326H	ENST00000282018	NM_020377.2	326	caG/caT	1/1	1	2	FACETS	0.406	0.333	0.487	0.406	0.333	0.487	SUBCLONAL	1	TRUE	1	0.35	2		628	507	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73333989	73333989	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs775586661	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	21	267	0	ENST00000377767.4:c.2821A>G	p.Thr941Ala	p.T941A	ENST00000377767	NM_014953.3	941	Act/Gct	21/21	1	2	FACETS	0.561	0.433	0.708	0.561	0.433	0.708	SUBCLONAL	1	TRUE	1	0.35	2		267	214	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355012	73355012	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	46	433	0	ENST00000377767.4:c.358T>G	p.Phe120Val	p.F120V	ENST00000377767	NM_014953.3	120	Ttc/Gtc	2/21	1	2	FACETS	0.906	0.768	1	0.906	0.768	1	CLONAL	1	TRUE	1	0.35	2		433	290	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060887	38060887	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	88	975	0	ENST00000250448.2:c.1102G>A	p.Ala368Thr	p.A368T	ENST00000250448	NM_004496.3	368	Gcc/Acc	2/2	1	2	FACETS	0.705	0.625	0.791	0.705	0.625	0.791	SUBCLONAL	1	TRUE	1	0.35	2		975	713	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643539	38643539	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	98	603	0	ENST00000299084.4:c.1009T>C	p.Tyr337His	p.Y337H	ENST00000299084	NM_152594.2	337	Tac/Cac	7/7	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.35	2		603	444	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989128	41989128	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	74	482	0	ENST00000219905.7:c.1920G>T	p.Lys640Asn	p.K640N	ENST00000219905	NM_001164273.1	640	aaG/aaT	3/24	1	2	FACETS	0.944	0.829	1	0.944	0.829	1	CLONAL	1	TRUE	1	0.35	2		482	448	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021428	42021428	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	14	407	0	ENST00000219905.7:c.3724C>T	p.Arg1242Ter	p.R1242*	ENST00000219905	NM_001164273.1	1242	Cga/Tga	11/24	1	2	FACETS	0.166	0.119	0.223	0.166	0.119	0.223	SUBCLONAL	1	TRUE	1	0.35	2		407	482	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007811	45007811	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	71	563	0	ENST00000558401.1:c.258C>A	p.Tyr86Ter	p.Y86*	ENST00000558401	NM_004048.2	86	taC/taA	2/4	1	2	FACETS	0.847	0.741	0.961	0.847	0.741	0.961	CLONAL	1	TRUE	1	0.35	2		563	479	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007825	45007825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	81	589	0	ENST00000558401.1:c.276del	p.Thr93LeufsTer10	p.T93Lfs*10	ENST00000558401	NM_004048.2	91	aCc/ac	2/4	1	2	FACETS	0.933	0.825	1	0.933	0.825	1	CLONAL	1	TRUE	1	0.35	2		589	496	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842068	3842068	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	89	520	0	ENST00000262367.5:c.1244T>G	p.Ile415Ser	p.I415S	ENST00000262367	NM_004380.2	415	aTc/aGc	5/31	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.35	2		520	499	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900384	3900384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146887252	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	127	822	0	ENST00000262367.5:c.712G>A	p.Val238Met	p.V238M	ENST00000262367	NM_004380.2	238	Gtg/Atg	2/31	1	2	FACETS	0.947	0.859	1	0.947	0.859	1	CLONAL	1	TRUE	1	0.35	2		822	766	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998893	11998893	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	27	194	0	ENST00000353533.5:c.395G>T	p.Arg132Ile	p.R132I	ENST00000353533	NM_003010.3	132	aGa/aTa	4/11	1	2	FACETS	0.804	0.644	0.983	0.804	0.644	0.983	CLONAL	1	TRUE	1	0.35	2		194	192	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556451	29556451	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1443857560	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	54	469	0	ENST00000356175.3:c.2818A>G	p.Thr940Ala	p.T940A	ENST00000356175	NM_000267.3	940	Acc/Gcc	21/57	1	2	FACETS	0.938	0.805	1	0.938	0.805	1	CLONAL	1	TRUE	1	0.35	2		469	329	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325934	30325934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	49	344	0	ENST00000322652.5:c.2132G>A	p.Gly711Glu	p.G711E	ENST00000322652	NM_015355.2	711	gGa/gAa	16/16	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.35	2		344	267	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244451	41244451	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs273899698	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	37	325	0	ENST00000357654.3:c.3097G>T	p.Glu1033Ter	p.E1033*	ENST00000357654	NM_007294.3	1033	Gaa/Taa	10/23	1	2	FACETS	0.75	0.621	0.892	0.75	0.621	0.892	SUBCLONAL	1	TRUE	1	0.35	2		325	282	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805765	46805765	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1194735492	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	99	1030	0	ENST00000290295.7:c.191A>G	p.His64Arg	p.H64R	ENST00000290295	NM_006361.5	64	cAc/cGc	1/2	1	2	FACETS	0.851	0.76	0.947	0.851	0.76	0.947	CLONAL	1	TRUE	1	0.35	2		1030	665	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780560	56780560	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	30	265	0	ENST00000337432.4:c.575A>G	p.His192Arg	p.H192R	ENST00000337432	NM_058216.2	192	cAc/cGc	4/9	1	2	FACETS	0.769	0.623	0.931	0.769	0.623	0.931	CLONAL	1	TRUE	1	0.35	2		265	223	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861716	59861716	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	37	219	0	ENST00000259008.2:c.1543G>T	p.Glu515Ter	p.E515*	ENST00000259008	NM_032043.2	515	Gaa/Taa	11/20	1	2	FACETS	0.957	0.795	1	0.957	0.795	1	CLONAL	1	TRUE	1	0.35	2		219	221	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56402522	56402522	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	40	190	0	ENST00000348428.3:c.1564G>T	p.Asp522Tyr	p.D522Y	ENST00000348428	NM_006785.3	522	Gat/Tat	13/17	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.35	2		190	166	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211707	5211707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145108936	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	152	781	0	ENST00000357368.4:c.5128C>T	p.Arg1710Cys	p.R1710C	ENST00000357368	NM_002850.3	1710	Cgc/Tgc	33/38	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.35	2		781	761	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267596	7267596	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	108	780	0	ENST00000302850.5:c.412A>C	p.Asn138His	p.N138H	ENST00000302850	NM_000208.2	138	Aac/Cac	2/22	1	2	FACETS	0.834	0.749	0.924	0.834	0.749	0.924	CLONAL	1	TRUE	1	0.35	2		780	740	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229231	36229231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	156	963	0	ENST00000222270.7:c.7921G>A	p.Ala2641Thr	p.A2641T	ENST00000222270	NM_014727.1	2641	Gcc/Acc	37/37	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.35	2		963	847	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229337	36229337	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	128	920	0	ENST00000222270.7:c.8027C>T	p.Ala2676Val	p.A2676V	ENST00000222270	NM_014727.1	2676	gCc/gTc	37/37	1	2	FACETS	0.876	0.794	0.963	0.876	0.794	0.963	CLONAL	1	TRUE	1	0.35	2		920	835	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744051	41744051	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779526458	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	124	959	2	ENST00000301178.4:c.986C>T	p.Pro329Leu	p.P329L	ENST00000301178	NM_021913.4	329	cCg/cTg	7/20	1	2	FACETS	0.973	0.881	1	0.973	0.881	1	CLONAL	1	TRUE	1	0.35	2		961	728	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383276	42383276	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	37	903	1	ENST00000221972.3:c.296G>A	p.Ser99Asn	p.S99N	ENST00000221972	NM_021601.3	99	aGc/aAc	2/5	1	2	FACETS	0.306	0.251	0.367	0.306	0.251	0.367	SUBCLONAL	1	TRUE	1	0.35	2		904	692	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424672	47424672	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	93	698	0	ENST00000404338.3:c.2740G>T	p.Glu914Ter	p.E914*	ENST00000404338	NM_004491.4	914	Gaa/Taa	1/6	1	2	FACETS	0.901	0.802	1	0.901	0.802	1	CLONAL	1	TRUE	1	0.35	2		698	590	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424921	47424921	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	122	517	0	ENST00000404338.3:c.2989C>T	p.Arg997Ter	p.R997*	ENST00000404338	NM_004491.4	997	Cga/Tga	1/6	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.35	2		517	617	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027958	48027958	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1558666905	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	64	563	0	ENST00000234420.5:c.2836G>T	p.Glu946Ter	p.E946*	ENST00000234420	NM_000179.2	946	Gaa/Taa	4/10	1	2	FACETS	0.845	0.734	0.964	0.845	0.734	0.964	CLONAL	1	TRUE	1	0.35	2		563	433	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028161	48028161	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1060502920	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	68	499	0	ENST00000234420.5:c.3039G>T	p.Lys1013Asn	p.K1013N	ENST00000234420	NM_000179.2	1013	aaG/aaT	4/10	1	2	FACETS	0.991	0.867	1	0.991	0.867	1	CLONAL	1	TRUE	1	0.35	2		499	392	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038133	128038133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369244363	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	105	301	0	ENST00000285398.2:c.1417G>A	p.Glu473Lys	p.E473K	ENST00000285398	NM_000122.1	473	Gaa/Aaa	9/15	1	2	FACETS	0.884	0.793	0.98	0.884	0.793	0.98	CLONAL	1	TRUE	1	0.35	2		301	679	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095610	178095610	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	44	470	0	ENST00000397062.3:c.1721A>C	p.Lys574Thr	p.K574T	ENST00000397062	NM_006164.4	574	aAa/aCa	5/5	1	2	FACETS	0.656	0.552	0.772	0.656	0.552	0.772	SUBCLONAL	1	TRUE	1	0.35	2		470	383	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39690032	39690032	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	49	454	0	ENST00000361337.2:c.59-2A>C		p.X20_splice	ENST00000361337	NM_003286.2	20			1	2	FACETS	0.906	0.772	1	0.906	0.772	1	CLONAL	1	TRUE	1	0.35	2		454	309	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262242	46262242	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	28	348	0	ENST00000371998.3:c.826A>C	p.Lys276Gln	p.K276Q	ENST00000371998		276	Aag/Cag	9/23	1	2	FACETS	0.606	0.486	0.742	0.606	0.486	0.742	SUBCLONAL	1	TRUE	1	0.35	2		348	264	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268414	46268414	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	91	730	0	ENST00000371998.3:c.2801A>T	p.Asn934Ile	p.N934I	ENST00000371998		934	aAt/aTt	15/23	1	2	FACETS	0.88	0.783	0.983	0.88	0.783	0.983	CLONAL	1	TRUE	1	0.35	2		730	591	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042536	37042536	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63751221	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	30	300	0	ENST00000231790.2:c.298C>T	p.Arg100Ter	p.R100*	ENST00000231790	NM_000249.3	100	Cga/Tga	3/19	1	2	FACETS	0.772	0.626	0.936	0.772	0.626	0.936	CLONAL	1	TRUE	1	0.35	2		300	222	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125365	47125365	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	81	556	0	ENST00000409792.3:c.5905A>C	p.Lys1969Gln	p.K1969Q	ENST00000409792	NM_014159.6	1969	Aaa/Caa	12/21	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.35	2		556	425	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49929220	49929220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147999292	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	107	761	0	ENST00000296474.3:c.3323G>A	p.Arg1108Gln	p.R1108Q	ENST00000296474	NM_002447.2	1108	cGa/cAa	15/20	1	2	FACETS	0.928	0.833	1	0.928	0.833	1	CLONAL	1	TRUE	1	0.35	2		761	659	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720954	119720954	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	26	493	0	ENST00000316626.5:c.221A>C	p.Lys74Thr	p.K74T	ENST00000316626		74	aAa/aCa	2/12	1	2	FACETS	0.311	0.246	0.387	0.311	0.246	0.387	SUBCLONAL	1	TRUE	1	0.35	2		493	477	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911488	134911488	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	121	738	0	ENST00000398015.3:c.1953G>T	p.Lys651Asn	p.K651N	ENST00000398015	NM_004441.4	651	aaG/aaT	11/16	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.35	2		738	687	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	21	323	0	ENST00000263967.3:c.333G>T	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaT	2/21	1	2	FACETS	0.38	0.292	0.482	0.38	0.292	0.482	SUBCLONAL	1	TRUE	1	0.35	2		323	316	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155346	185155346	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	96	688	0	ENST00000265026.3:c.587A>C	p.Lys196Thr	p.K196T	ENST00000265026	NM_004721.4	196	aAa/aCa	3/14	1	2	FACETS	0.836	0.746	0.932	0.836	0.746	0.932	CLONAL	1	TRUE	1	0.35	2		688	656	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165687	185165687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	87	607	0	ENST00000265026.3:c.962C>T	p.Ala321Val	p.A321V	ENST00000265026	NM_004721.4	321	gCg/gTg	5/14	1	2	FACETS	0.765	0.677	0.858	0.765	0.677	0.858	SUBCLONAL	1	TRUE	1	0.35	2		607	650	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749479	41749479	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	123	600	0	ENST00000226382.2:c.316A>G	p.Thr106Ala	p.T106A	ENST00000226382	NM_003924.3	106	Acc/Gcc	2/3	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.35	2		600	568	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593480	55593480	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	54	468	0	ENST00000288135.5:c.1637A>C	p.Lys546Thr	p.K546T	ENST00000288135	NM_000222.2	546	aAa/aCa	10/21	1	2	FACETS	0.986	0.847	1	0.986	0.847	1	CLONAL	1	TRUE	1	0.35	2		468	313	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948129	55948129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	30	226	0	ENST00000263923.4:c.3842C>T	p.Ser1281Phe	p.S1281F	ENST00000263923	NM_002253.2	1281	tCt/tTt	29/30	1	2	FACETS	1	0.821	1	1	0.821	1	CLONAL	1	TRUE	1	0.35	2		226	170	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968660	55968660	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199774865	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	92	616	0	ENST00000263923.4:c.2003C>T	p.Thr668Met	p.T668M	ENST00000263923	NM_002253.2	668	aCg/aTg	14/30	1	2	FACETS	0.849	0.756	0.949	0.849	0.756	0.949	CLONAL	1	TRUE	1	0.35	2		616	619	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233120	66233120	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	31	378	0	ENST00000273854.3:c.1879A>C	p.Lys627Gln	p.K627Q	ENST00000273854	NM_004439.5	627	Aaa/Caa	10/18	1	2	FACETS	0.583	0.472	0.707	0.583	0.472	0.707	SUBCLONAL	1	TRUE	1	0.35	2		378	304	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	75	344	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.859	0.754	0.971	0.859	0.754	0.971	CLONAL	1	TRUE	1	0.35	2		344	499	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532867	187532867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762890230	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	51	464	0	ENST00000441802.2:c.9526G>A	p.Glu3176Lys	p.E3176K	ENST00000441802	NM_005245.3	3176	Gaa/Aaa	14/27	1	2	FACETS	0.823	0.703	0.955	0.823	0.703	0.955	CLONAL	1	TRUE	1	0.35	2		464	354	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293551	1293551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	34	825	0	ENST00000310581.5:c.1450G>A	p.Glu484Lys	p.E484K	ENST00000310581	NM_198253.2	484	Gaa/Aaa	2/16	1	2	FACETS	0.333	0.271	0.402	0.333	0.271	0.402	SUBCLONAL	1	TRUE	1	0.35	2		825	584	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295472	1295472	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	114	1013	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.35	2		1015	615	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295845	1295845	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	179	1069	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.35	2		1069	810	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180584	56180584	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	51	337	0	ENST00000399503.3:c.3913A>G	p.Asn1305Asp	p.N1305D	ENST00000399503	NM_005921.1	1305	Aac/Gac	16/20	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.35	2		337	267	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79960969	79960969	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1472947441	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	25	423	0	ENST00000265081.6:c.366G>T	p.Lys122Asn	p.K122N	ENST00000265081	NM_002439.4	122	aaG/aaT	3/24	1	2	FACETS	0.533	0.421	0.661	0.533	0.421	0.661	SUBCLONAL	1	TRUE	1	0.35	2		423	268	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659227	86659227	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	39	243	0	ENST00000274376.6:c.1516T>C	p.Tyr506His	p.Y506H	ENST00000274376	NM_002890.2	506	Tat/Cat	11/25	1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	1	0.35	2		243	220	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674234	86674234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	57	472	0	ENST00000274376.6:c.2366G>A	p.Arg789Gln	p.R789Q	ENST00000274376	NM_002890.2	789	cGa/cAa	18/25	1	2	FACETS	0.783	0.674	0.901	0.783	0.674	0.901	CLONAL	1	TRUE	1	0.35	2		472	416	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149511589	149511589	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	97	837	0	ENST00000261799.4:c.1196T>C	p.Phe399Ser	p.F399S	ENST00000261799	NM_002609.3	399	tTc/tCc	8/23	1	2	FACETS	0.853	0.761	0.95	0.853	0.761	0.95	CLONAL	1	TRUE	1	0.35	2		837	650	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819955	170819955	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	30	210	0	ENST00000296930.5:c.497A>G	p.Asp166Gly	p.D166G	ENST00000296930	NM_002520.6	166	gAt/gGt	6/11	1	2	FACETS	0.794	0.644	0.961	0.794	0.644	0.961	CLONAL	1	TRUE	1	0.35	2		210	216	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637210	176637210	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784076	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	32	684	0	ENST00000439151.2:c.1810C>T	p.Arg604Ter	p.R604*	ENST00000439151	NM_022455.4	604	Cga/Tga	5/23	1	2	FACETS	0.309	0.25	0.377	0.309	0.25	0.377	SUBCLONAL	1	TRUE	1	0.35	2		684	591	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176678730	176678730	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	96	486	0	ENST00000439151.2:c.4642-1G>T		p.X1548_splice	ENST00000439151	NM_022455.4	1548			1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.35	2		486	502	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053126	180053126	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	108	979	0	ENST00000261937.6:c.1243G>T	p.Glu415Ter	p.E415*	ENST00000261937	NM_182925.4	415	Gag/Tag	9/30	1	2	FACETS	0.877	0.787	0.971	0.877	0.787	0.971	CLONAL	1	TRUE	1	0.35	2		979	704	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490599	20490599	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749949370	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	81	698	0	ENST00000346618.3:c.1336G>A	p.Asp446Asn	p.D446N	ENST00000346618	NM_001949.4	446	Gat/Aat	7/7	1	2	FACETS	0.763	0.672	0.859	0.763	0.672	0.859	SUBCLONAL	1	TRUE	1	0.35	2		698	607	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552838	106552838	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367766895	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	111	832	0	ENST00000369096.4:c.803G>A	p.Arg268His	p.R268H	ENST00000369096	NM_001198.3	268	cGt/cAt	5/7	1	2	FACETS	0.964	0.868	1	0.964	0.868	1	CLONAL	1	TRUE	1	0.35	2		832	658	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112035560	112035560	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	18	347	1	ENST00000368678.4:c.334T>G	p.Leu112Val	p.L112V	ENST00000368678		112	Ttg/Gtg	4/13	1	2	FACETS	0.313	0.235	0.405	0.313	0.235	0.405	SUBCLONAL	1	TRUE	1	0.35	2		348	329	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642538	117642538	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	25	641	0	ENST00000368508.3:c.5661G>T	p.Lys1887Asn	p.K1887N	ENST00000368508	NM_002944.2	1887	aaG/aaT	35/43	1	2	FACETS	0.29	0.228	0.362	0.29	0.228	0.362	SUBCLONAL	1	TRUE	1	0.35	2		641	493	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683830	117683830	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs759947584	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	42	473	0	ENST00000368508.3:c.3317T>C	p.Val1106Ala	p.V1106A	ENST00000368508	NM_002944.2	1106	gTc/gCc	21/43	1	2	FACETS	0.845	0.709	0.994	0.845	0.709	0.994	CLONAL	1	TRUE	1	0.35	2		473	284	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683905	117683905	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	33	376	0	ENST00000368508.3:c.3242A>T	p.Lys1081Ile	p.K1081I	ENST00000368508	NM_002944.2	1081	aAa/aTa	21/43	1	2	FACETS	0.799	0.655	0.959	0.799	0.655	0.959	CLONAL	1	TRUE	1	0.35	2		376	236	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687431	117687431	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	67	587	0	ENST00000368508.3:c.2620G>T	p.Glu874Ter	p.E874*	ENST00000368508	NM_002944.2	874	Gaa/Taa	18/43	1	2	FACETS	0.895	0.78	1	0.895	0.78	1	CLONAL	1	TRUE	1	0.35	2		587	428	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6031648	6031648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs116314131	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	57	324	0	ENST00000265849.7:c.944G>A	p.Arg315Gln	p.R315Q	ENST00000265849	NM_000535.5	315	cGa/cAa	9/15	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.35	2		324	296	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509723	106509723	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	78	640	0	ENST00000359195.3:c.1717G>T	p.Glu573Ter	p.E573*	ENST00000359195	NM_002649.2	573	Gaa/Taa	2/11	1	2	FACETS	0.796	0.7	0.898	0.796	0.7	0.898	SUBCLONAL	1	TRUE	1	0.35	2		640	560	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509784	106509784	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	77	597	0	ENST00000359195.3:c.1778T>C	p.Phe593Ser	p.F593S	ENST00000359195	NM_002649.2	593	tTt/tCt	2/11	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.35	2		597	437	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520093	106520093	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	34	305	0	ENST00000359195.3:c.2521G>T	p.Asp841Tyr	p.D841Y	ENST00000359195	NM_002649.2	841	Gac/Tac	6/11	1	2	FACETS	0.841	0.692	1	0.841	0.692	1	CLONAL	1	TRUE	1	0.35	2		305	231	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511116	148511116	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139878257	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	137	726	0	ENST00000320356.2:c.1786G>A	p.Ala596Thr	p.A596T	ENST00000320356	NM_004456.4	596	Gct/Act	15/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.35	2		726	731	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148513849	148513849	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	83	568	0	ENST00000320356.2:c.1432G>T	p.Glu478Ter	p.E478*	ENST00000320356	NM_004456.4	478	Gaa/Taa	12/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.35	2		568	402	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879672	151879672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	43	444	0	ENST00000262189.6:c.5273G>A	p.Arg1758His	p.R1758H	ENST00000262189	NM_170606.2	1758	cGt/cAt	36/59	1	2	FACETS	0.692	0.581	0.815	0.692	0.581	0.815	SUBCLONAL	1	TRUE	1	0.35	2		444	355	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346431	152346431	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	53	365	0	ENST00000359321.1:c.139C>A	p.His47Asn	p.H47N	ENST00000359321	NM_005431.1	47	Cat/Aat	3/3	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.35	2		365	289	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031690	69031690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371787029	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	64	411	0	ENST00000288368.4:c.3445C>T	p.Arg1149Cys	p.R1149C	ENST00000288368	NM_024870.2	1149	Cgc/Tgc	28/40	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.35	2		411	342	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982065	70982065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1224728611	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	106	702	0	ENST00000276594.2:c.31C>T	p.Pro11Ser	p.P11S	ENST00000276594	NM_024504.3	11	Cct/Tct	2/8	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.35	2		702	571	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117870595	117870595	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	26	169	0	ENST00000297338.2:c.477T>G	p.Asp159Glu	p.D159E	ENST00000297338	NM_006265.2	159	gaT/gaG	5/14	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.35	2		169	136	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2115987	2115987	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	121	726	0	ENST00000349721.2:c.3622T>C	p.Ser1208Pro	p.S1208P	ENST00000349721	NM_003070.3	1208	Tct/Cct	25/34	1	2	FACETS	0.881	0.796	0.97	0.881	0.796	0.97	CLONAL	1	TRUE	1	0.35	2		726	785	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050791	5050791	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	52	386	0	ENST00000381652.3:c.574G>T	p.Glu192Ter	p.E192*	ENST00000381652	NM_004972.3	192	Gaa/Taa	6/25	1	2	FACETS	0.9	0.771	1	0.9	0.771	1	CLONAL	1	TRUE	1	0.35	2		386	330	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5070038	5070038	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	36	184	0	ENST00000381652.3:c.1627G>T	p.Glu543Ter	p.E543*	ENST00000381652	NM_004972.3	543	Gaa/Taa	12/25	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.35	2		184	175	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020774	37020774	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	106	686	0	ENST00000358127.4:c.71G>T	p.Gly24Val	p.G24V	ENST00000358127	NM_001280556.1	24	gGg/gTg	2/10	1	2	FACETS	0.98	0.88	1	0.98	0.88	1	CLONAL	1	TRUE	1	0.35	2		686	618	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636224	87636224	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	146	738	0	ENST00000277120.3:c.2389G>T	p.Glu797Ter	p.E797*	ENST00000277120		797	Gag/Tag	19/19	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.35	2		738	737	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244310	98244310	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1266754583	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	40	481	0	ENST00000331920.6:c.667C>A	p.Leu223Ile	p.L223I	ENST00000331920	NM_000264.3	223	Ctt/Att	5/24	1	2	FACETS	0.747	0.623	0.883	0.747	0.623	0.883	SUBCLONAL	1	TRUE	1	0.35	2		481	306	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891383	101891383	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	43	273	0	ENST00000374994.4:c.343+1G>T		p.X115_splice	ENST00000374994	NM_004612.2	115			1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.35	2		273	196	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309144	137309144	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	130	850	0	ENST00000481739.1:c.751G>A	p.Glu251Lys	p.E251K	ENST00000481739	NM_002957.4	251	Gag/Aag	5/10	1	2	FACETS	0.963	0.875	1	0.963	0.875	1	CLONAL	1	TRUE	1	0.35	2		850	771	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410037	139410037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749381544	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	178	992	0	ENST00000277541.6:c.1801G>A	p.Glu601Lys	p.E601K	ENST00000277541	NM_017617.3	601	Gag/Aag	11/34	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.35	2		992	765	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44920635	44920635	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	34	380	0	ENST00000377967.4:c.1396T>G	p.Ser466Ala	p.S466A	ENST00000377967	NM_021140.2	466	Tca/Gca	14/29	1	2	FACETS	0.501	0.409	0.603	0.501	0.409	0.603	SUBCLONAL	1	TRUE	1	0.35	2		380	388	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041215	47041215	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	137	893	0	ENST00000377604.3:c.1643C>T	p.Ala548Val	p.A548V	ENST00000377604	NM_001204468.1	548	gCt/gTt	15/24	1	2	FACETS	0.974	0.886	1	0.974	0.886	1	CLONAL	1	TRUE	1	0.35	2		893	804	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240738	53240738	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	86	644	0	ENST00000375401.3:c.1342G>T	p.Glu448Ter	p.E448*	ENST00000375401	NM_004187.3	448	Gaa/Taa	10/26	1	2	FACETS	0.907	0.804	1	0.907	0.804	1	CLONAL	1	TRUE	1	0.35	2		644	542	SUCCESS
AR	367	MSKCC	GRCh37	X	66942713	66942713	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	66	448	0	ENST00000374690.3:c.2494C>T	p.Arg832Ter	p.R832*	ENST00000374690	NM_000044.3	832	Cga/Tga	7/8	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.35	2		448	366	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345893	70345893	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	79	596	0	ENST00000374080.3:c.2430G>T	p.Glu810Asp	p.E810D	ENST00000374080		810	gaG/gaT	18/45	1	2	FACETS	0.739	0.65	0.834	0.739	0.65	0.834	SUBCLONAL	1	TRUE	1	0.35	2		596	611	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70355014	70355014	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	120	833	0	ENST00000374080.3:c.4936C>T	p.Arg1646Ter	p.R1646*	ENST00000374080		1646	Cga/Tga	36/45	1	2	FACETS	0.907	0.82	0.999	0.907	0.82	0.999	CLONAL	1	TRUE	1	0.35	2		833	756	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813031	76813031	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	75	466	0	ENST00000373344.5:c.6590G>A	p.Arg2197His	p.R2197H	ENST00000373344	NM_000489.3	2197	cGt/cAt	30/35	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.35	2		466	393	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814238	76814238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	23	269	0	ENST00000373344.5:c.6406G>A	p.Asp2136Asn	p.D2136N	ENST00000373344	NM_000489.3	2136	Gac/Aac	29/35	1	2	FACETS	0.635	0.497	0.792	0.635	0.497	0.792	SUBCLONAL	1	TRUE	1	0.35	2		269	207	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938161	76938161	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	34	430	0	ENST00000373344.5:c.2587C>A	p.Gln863Lys	p.Q863K	ENST00000373344	NM_000489.3	863	Caa/Aaa	9/35	1	2	FACETS	0.619	0.507	0.744	0.619	0.507	0.744	SUBCLONAL	1	TRUE	1	0.35	2		430	314	SUCCESS
BTK	695	MSKCC	GRCh37	X	100604914	100604914	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	32	314	0	ENST00000308731.7:c.1939C>A	p.Leu647Ile	p.L647I	ENST00000308731	NM_000061.2	647	Ctt/Att	19/19	1	2	FACETS	0.622	0.506	0.752	0.622	0.506	0.752	SUBCLONAL	1	TRUE	1	0.35	2		314	294	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615648	100615648	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	98	737	0	ENST00000308731.7:c.684G>T	p.Met228Ile	p.M228I	ENST00000308731	NM_000061.2	228	atG/atT	8/19	1	2	FACETS	0.909	0.812	1	0.909	0.812	1	CLONAL	1	TRUE	1	0.35	2		737	616	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179066	123179066	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	52	362	0	ENST00000218089.9:c.515A>C	p.Lys172Thr	p.K172T	ENST00000218089	NM_001042749.1	172	aAa/aCa	8/35	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.35	2		362	266	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185222	123185222	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	16	121	0	ENST00000218089.9:c.1174A>C	p.Lys392Gln	p.K392Q	ENST00000218089	NM_001042749.1	392	Aaa/Caa	13/35	1	2	FACETS	0.756	0.564	0.979	0.756	0.564	0.979	CLONAL	1	TRUE	1	0.35	2		121	121	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	95	753	4	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	0.152788842649372	4	FACETS	1	0.956	1	0.572	0.509	0.639	INDETERMINATE	1	TRUE	2	0.288520394267753	4		757	742	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519505	137519506	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs780346130	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	123	474	4	ENST00000367739.4:c.1132_1133del	p.Ser378PhefsTer6	p.S378Ffs*6	ENST00000367739	NM_000416.2	378	AGt/t	7/7	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.288520394267753	2		478	780	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411678	63411678	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	113	776	0	ENST00000330258.3:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000330258	NM_152424.3	497	Cga/Tga	2/2	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.288520394267753	2		776	709	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	104	591	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.288520394267753	2		591	693	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645423	67645423	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	144	407	0	ENST00000264010.4:c.688G>T	p.Glu230Ter	p.E230*	ENST00000264010	NM_006565.3	230	Gaa/Taa	3/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.288520394267753	2		407	776	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653796	89653798	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs1554893765	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	64	98	0	ENST00000371953.3:c.97_99del	p.Ile33del	p.I33del	ENST00000371953	NM_000314.4	32	ATT/-	2/9	0.288520394267753	2	FACETS	0.896	0.794	1	1	0.971	1	CLONAL	3	TRUE	0	0.288520394267753	2		98	165	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	136	815	5	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.288520394267753	2		820	862	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857475	57857475	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	115	734	0	ENST00000228682.2:c.1A>G	p.Met1?	p.M1?	ENST00000228682	NM_005269.2	1	Atg/Gtg	2/12	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.288520394267753	2		734	686	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	130	535	8	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.288520394267753	2		543	765	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023183	27023183	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	63	825	1	ENST00000324856.7:c.289G>T	p.Glu97Ter	p.E97*	ENST00000324856	NM_006015.4	97	Gag/Tag	1/20	1	2	FACETS	0.956	0.829	1	0.956	0.829	1	CLONAL	1	TRUE	1	0.288520394267753	2		826	457	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589663	67589663	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587777709	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	12	98	0	ENST00000274335.5:c.1425+1G>A		p.X475_splice	ENST00000274335		475			1	2	FACETS	0.467	0.329	0.637	0.467	0.329	0.637	SUBCLONAL	1	TRUE	1	0.288520394267753	2		98	178	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915588	131915588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769853458	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	51	147	0	ENST00000265335.6:c.586C>T	p.Arg196Cys	p.R196C	ENST00000265335		196	Cgt/Tgt	5/25	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.288520394267753	2		147	279	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466018	69466018	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	119	1016	0	ENST00000227507.2:c.856A>G	p.Thr286Ala	p.T286A	ENST00000227507	NM_053056.2	286	Aca/Gca	5/5	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.288520394267753	2		1016	801	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856217	111856217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879321203	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	32	885	0	ENST00000341259.2:c.268C>T	p.Arg90Trp	p.R90W	ENST00000341259	NM_005475.2	90	Cgg/Tgg	2/8	1	2	FACETS	0.424	0.343	0.516	0.424	0.343	0.516	SUBCLONAL	1	TRUE	1	0.288520394267753	2		885	523	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257510	16257510	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370305920	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	43	395	0	ENST00000375759.3:c.4775G>A	p.Arg1592Gln	p.R1592Q	ENST00000375759	NM_015001.2	1592	cGg/cAg	11/15	1	2	FACETS	0.44	0.367	0.521	0.44	0.367	0.521	SUBCLONAL	1	TRUE	1	0.288520394267753	2		395	678	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836816	151836816	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	136	609	0	ENST00000262189.6:c.14404G>A	p.Gly4802Arg	p.G4802R	ENST00000262189	NM_170606.2	4802	Ggg/Agg	56/59	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.288520394267753	2		609	751	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644567	3644567	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115866745	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	116	797	0	ENST00000294008.3:c.2047G>A	p.Ala683Thr	p.A683T	ENST00000294008	NM_032444.2	683	Gcc/Acc	10/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.288520394267753	2		797	713	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638731	176638731	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151165525	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	91	435	0	ENST00000439151.2:c.3331G>A	p.Asp1111Asn	p.D1111N	ENST00000439151	NM_022455.4	1111	Gat/Aat	5/23	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.288520394267753	2		435	627	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948755	71948755	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1565399032	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	114	1154	1	ENST00000298229.2:c.3470del	p.Gly1157AspfsTer45	p.G1157Dfs*45	ENST00000298229	NM_001567.3	1156	cGg/cg	26/28	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.288520394267753	2		1155	715	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370805	55370805	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	64	924	0	ENST00000297316.4:c.107T>C	p.Leu36Pro	p.L36P	ENST00000297316	NM_022454.3	36	cTg/cCg	1/2	1	2	FACETS	0.934	0.811	1	0.934	0.811	1	CLONAL	1	TRUE	1	0.288520394267753	2		924	475	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626895	14626895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143320658	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	164	919	0	ENST00000254322.2:c.880C>T	p.Arg294Trp	p.R294W	ENST00000254322	NM_006145.1	294	Cgg/Tgg	3/3	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.288520394267753	2		919	828	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852230	63852230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1367766830	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	125	837	0	ENST00000279873.7:c.3008C>T	p.Pro1003Leu	p.P1003L	ENST00000279873	NM_032199.2	1003	cCg/cTg	10/10	0.288520394267753	2	FACETS	1	0.97	1	0.585	0.53	0.644	CLONAL	1	TRUE	0	0.288520394267753	2		837	740	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557639	95557639	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	107	336	0	ENST00000393063.1:c.5428G>T	p.Asp1810Tyr	p.D1810Y	ENST00000393063	NM_030621.3	1810	Gat/Tat	26/28	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.288520394267753	2		336	619	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057943	27057943	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	140	843	0	ENST00000324856.7:c.1651del	p.Tyr551ThrfsTer68	p.Y551Tfs*68	ENST00000324856	NM_006015.4	551	Tac/ac	3/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.288520394267753	2		843	750	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094443	27094443	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	124	623	0	ENST00000324856.7:c.3151C>T	p.Leu1051Phe	p.L1051F	ENST00000324856	NM_006015.4	1051	Ctc/Ttc	11/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.288520394267753	2		623	744	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444257	49444258	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	110	1005	0	ENST00000301067.7:c.3113dup	p.Pro1039SerfsTer29	p.P1039Sfs*29	ENST00000301067	NM_003482.3	1038	cct/ccCt	11/54	0.117133751598588	3	FACETS	1	0.942	1	0.535	0.481	0.593	INDETERMINATE	1	TRUE	1	0.288520394267753	3		1005	815	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061822	38061822	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	121	1015	0	ENST00000250448.2:c.167G>A	p.Ser56Asn	p.S56N	ENST00000250448	NM_004496.3	56	aGc/aAc	2/2	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.288520394267753	2		1015	751	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422094	81422094	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	97	873	0	ENST00000298171.2:c.70T>C	p.Cys24Arg	p.C24R	ENST00000298171	NM_000369.2	24	Tgt/Cgt	1/10	1	2	FACETS	0.955	0.852	1	0.955	0.852	1	CLONAL	1	TRUE	1	0.288520394267753	2		873	704	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821577	72821577	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776065671	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	75	725	1	ENST00000268489.5:c.10598C>T	p.Ala3533Val	p.A3533V	ENST00000268489	NM_006885.3	3533	gCg/gTg	10/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.288520394267753	2		726	457	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830531	72830532	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	111	728	0	ENST00000268489.5:c.6049_6050del	p.Arg2017ValfsTer11	p.R2017Vfs*11	ENST00000268489	NM_006885.3	2017	AGg/g	9/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.288520394267753	2		728	669	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577037	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	154	929	0	ENST00000269305.4:c.901_902insA	p.Pro301HisfsTer5	p.P301Hfs*5	ENST00000269305	NM_001126112.2	301	cca/cAca	8/11	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.288520394267753	2		929	1022	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214667	5214667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	118	977	0	ENST00000357368.4:c.4399C>T	p.Pro1467Ser	p.P1467S	ENST00000357368	NM_002850.3	1467	Ccg/Tcg	29/38	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.288520394267753	2		977	780	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21342377	21342377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	112	538	0	ENST00000215739.8:c.479G>A	p.Gly160Asp	p.G160D	ENST00000215739	NM_006767.3	160	gGc/gAc	5/21	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.288520394267753	2		538	715	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593244	67593291	+	inframe_deletion	In_Frame_Del	DEL	GACGGCGAAGTAAAGCATTGTGTCATAAACAAAACAGCAACTGGCTAT	GACGGCGAAGTAAAGCATTGTGTCATAAACAAAACAGCAACTGGCTAT	-	novel	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	87	398	0	ENST00000274335.5:c.1991_2038del	p.Asp664_Tyr679del	p.D664_Y679del	ENST00000274335		664	GACGGCGAAGTAAAGCATTGTGTCATAAACAAAACAGCAACTGGCTAT/-	15/15	1	2	FACETS	0.977	0.866	1	0.977	0.866	1	CLONAL	1	TRUE	1	0.288520394267753	2		398	617	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2058432	2058432	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	103	460	0	ENST00000349721.2:c.1489C>T	p.Arg497Trp	p.R497W	ENST00000349721	NM_003070.3	497	Cgg/Tgg	8/34	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.288520394267753	2		460	668	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27205056	27205056	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	115	472	0	ENST00000380036.4:c.2357A>G	p.Gln786Arg	p.Q786R	ENST00000380036	NM_000459.3	786	cAa/cGa	14/23	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.288520394267753	2		472	675	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771992	135771992	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148931779	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	67	963	0	ENST00000298552.3:c.3125G>A	p.Ser1042Asn	p.S1042N	ENST00000298552	NM_001162426.1	1042	aGc/aAc	23/23	1	2	FACETS	0.552	0.478	0.631	0.552	0.478	0.631	SUBCLONAL	1	TRUE	1	0.288520394267753	2		963	842	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413189	139413189	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	110	939	0	ENST00000277541.6:c.953G>T	p.Gly318Val	p.G318V	ENST00000277541	NM_017617.3	318	gGc/gTc	6/34	1	2	FACETS	0.975	0.876	1	0.975	0.876	1	CLONAL	1	TRUE	1	0.288520394267753	2		939	782	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073899	8073899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	108	720	2	ENST00000377482.5:c.760G>A	p.Ala254Thr	p.A254T	ENST00000377482	NM_018948.3	254	Gct/Act	4/4	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.268498747098732	2		722	737	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139292	108139292	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	82	587	0	ENST00000278616.4:c.2794G>A	p.Asp932Asn	p.D932N	ENST00000278616	NM_000051.3	932	Gat/Aat	18/63	1	2	FACETS	0.885	0.78	0.998	0.885	0.78	0.998	CLONAL	1	TRUE	1	0.268498747098732	2		587	690	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038745	47038745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556777782	NA	P-0064616-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	82	474	2	ENST00000377604.3:c.752C>T	p.Thr251Met	p.T251M	ENST00000377604	NM_001204468.1	251	aCg/aTg	9/24	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	0	NA	2		476	355	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0064617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	199	631	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.399674650656377	1	FACETS	0.981	0.912	1	0.981	0.912	1	CLONAL	1	TRUE	0	0.434904514415247	1		631	730	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675071	40675071	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	223	518	0	ENST00000249776.8:c.35T>G	p.Val12Gly	p.V12G	ENST00000249776	NM_033286.3	12	gTt/gGt	1/9	1	2	FACETS	0.991	0.922	1	0.991	0.922	1	CLONAL	1	TRUE	1	0.434904514415247	2		518	1035	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602335	28602335	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	42	480	0	ENST00000241453.7:c.2033T>A	p.Leu678Gln	p.L678Q	ENST00000241453	NM_004119.2	678	cTg/cAg	16/24	0.361730134037436	2	FACETS	0.256	0.213	0.304	0.128	0.106	0.152	SUBCLONAL	1	TRUE	0	0.434904514415247	2		480	754	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955465	48955465	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	41	255	0	ENST00000267163.4:c.1581T>G	p.Asp527Glu	p.D527E	ENST00000267163	NM_000321.2	527	gaT/gaG	17/27	NA	2	FACETS	1	0.927	1			1	INDETERMINATE	1	TRUE	NA	0.434904514415247	2		255	161	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	233	612	0				ENST00000310581	NM_198253.2	-/1132			0.364439365940734	5	FACETS	1	0.967	1	1	0.967	1	CLONAL	3	TRUE	2	0.364439365940734	5		612	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0064622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	230	633	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.314655130820657	2	FACETS	0.856	0.801	0.913	0.856	0.801	0.913	CLONAL	2	TRUE	0	0.364439365940734	2		633	737	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551870	150551870	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	70	674	0	ENST00000369026.2:c.137G>C	p.Arg46Pro	p.R46P	ENST00000369026	NM_021960.4	46	cGa/cCa	1/3	0.364439365940734	5	FACETS	0.562	0.488	0.642	0.187	0.162	0.214	SUBCLONAL	1	TRUE	2	0.364439365940734	5		674	1058	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745184	41745184	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	91	545	0	ENST00000301178.4:c.1250G>A	p.Trp417Ter	p.W417*	ENST00000301178	NM_021913.4	417	tGg/tAg	9/20	0.316293650592504	5	FACETS	0.864	0.766	0.969	0.216	0.191	0.243	CLONAL	1	TRUE	1	0.364439365940734	5		545	894	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082380	16082380	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	134	633	0	ENST00000281043.3:c.194G>T	p.Arg65Leu	p.R65L	ENST00000281043	NM_005378.4	65	cGt/cTt	2/3	0.364439365940734	3	FACETS	1	0.953	1	0.539	0.489	0.59	CLONAL	1	TRUE	1	0.364439365940734	3		633	807	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164611	36164611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	158	571	0	ENST00000300305.3:c.1264G>A	p.Glu422Lys	p.E422K	ENST00000300305		422	Gag/Aag	8/8	0.239556132212879	4	FACETS	0.854	0.784	0.926	0.854	0.784	0.926	CLONAL	2	TRUE	2	0.364439365940734	4		571	693	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149243898	149243898	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767747431	NA	P-0064622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	164	366	0	ENST00000360632.3:c.920C>T	p.Ser307Leu	p.S307L	ENST00000360632	NM_015472.4	307	tCg/tTg	6/7	0.364439365940734	3	FACETS	0.896	0.826	0.967	0.896	0.826	0.967	CLONAL	2	TRUE	1	0.364439365940734	3		366	594	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515645	31515645	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	49	326	0	ENST00000344624.3:c.974A>G	p.Glu325Gly	p.E325G	ENST00000344624		325	gAa/gGa	4/33	0.364439365940734	5	FACETS	0.59	0.498	0.691	0.197	0.166	0.231	SUBCLONAL	1	TRUE	2	0.364439365940734	5		326	705	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997485	149997485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	134	299	0	ENST00000253339.5:c.2794G>A	p.Asp932Asn	p.D932N	ENST00000253339		932	Gat/Aat	6/7	0.267929911526452	2	FACETS	0.776	0.71	0.844	0.776	0.71	0.844	SUBCLONAL	2	TRUE	0	0.364439365940734	2		299	474	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	107	210	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.845	0.76	0.935	0.845	0.76	0.935	CLONAL	1	TRUE	1	0.43	2		210	589	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588751	29588751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760703505	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	115	373	0	ENST00000356175.3:c.4537C>T	p.Arg1513Ter	p.R1513*	ENST00000356175	NM_000267.3	1513	Cga/Tga	34/57	1	2	FACETS	0.853	0.77	0.94	0.853	0.77	0.94	CLONAL	1	TRUE	1	0.43	2		373	627	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	175	474	7	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.747	0.687	0.809	0.747	0.687	0.809	SUBCLONAL	1	TRUE	1	0.43	2		481	1090	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972785	25972785	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs200858310	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	178	606	0	ENST00000435504.4:c.1640A>G	p.Gln547Arg	p.Q547R	ENST00000435504		547	cAg/cGg	12/13	1	2	FACETS	0.946	0.873	1	0.946	0.873	1	CLONAL	1	TRUE	1	0.43	2		606	875	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609990	43609990	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs77711105	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	245	830	1	ENST00000355710.3:c.1942G>A	p.Val648Ile	p.V648I	ENST00000355710	NM_020975.4	648	Gtc/Atc	11/20	1	2	FACETS	0.898	0.838	0.96	0.898	0.838	0.96	CLONAL	1	TRUE	1	0.43	2		831	1269	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557909	187557909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564430066	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	234	708	0	ENST00000441802.2:c.3802C>T	p.Arg1268Trp	p.R1268W	ENST00000441802	NM_005245.3	1268	Cgg/Tgg	5/27	1	2	FACETS	0.942	0.878	1	0.942	0.878	1	CLONAL	1	TRUE	1	0.43	2		708	1155	SUCCESS
AR	367	MSKCC	GRCh37	X	66931504	66931504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1340026226	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	206	300	0	ENST00000374690.3:c.2146G>A	p.Val716Met	p.V716M	ENST00000374690	NM_000044.3	716	Gtg/Atg	4/8	1	1	FACETS	0.779	0.73	0.828	1	0.993	1	SUBCLONAL	2	TRUE	0	0.43	1		300	483	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518262	8518262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	167	485	0	ENST00000356435.5:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000356435		377	Cgc/Tgc	10/35	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.43	2		485	747	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216379	7216380	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1216832021	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	219	757	0	ENST00000380728.2:c.868dup	p.Gln290ProfsTer?	p.Q290Pfs*?	ENST00000380728		290	cag/cCag	10/11	1	2	FACETS	0.883	0.82	0.948	0.883	0.82	0.948	CLONAL	1	TRUE	1	0.43	2		757	1154	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652243	48652243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	217	330	0	ENST00000376670.3:c.914G>A	p.Arg305Gln	p.R305Q	ENST00000376670	NM_002049.3	305	cGa/cAa	6/6	1	1	FACETS	0.763	0.717	0.811	1	0.993	1	SUBCLONAL	2	TRUE	0	0.43	1		330	519	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215947	41215947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41293459	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	98	346	0	ENST00000357654.3:c.5096G>A	p.Arg1699Gln	p.R1699Q	ENST00000357654	NM_007294.3	1699	cGg/cAg	17/23	1	2	FACETS	0.908	0.813	1	0.908	0.813	1	CLONAL	1	TRUE	1	0.43	2		346	502	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36934823	36934823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145256322	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	139	556	0	ENST00000361632.4:c.1510G>A	p.Val504Met	p.V504M	ENST00000361632		504	Gtg/Atg	11/16	1	2	FACETS	0.779	0.709	0.852	0.779	0.709	0.852	SUBCLONAL	1	TRUE	1	0.43	2		556	830	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572906	41572906	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	229	751	0	ENST00000263253.7:c.5191C>T	p.Arg1731Cys	p.R1731C	ENST00000263253	NM_001429.3	1731	Cgc/Tgc	31/31	1	2	FACETS	0.996	0.928	1	0.996	0.928	1	CLONAL	1	TRUE	1	0.43	2		751	1069	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835975	151835975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	115	461	0	ENST00000262189.6:c.14549C>T	p.Ser4850Leu	p.S4850L	ENST00000262189	NM_170606.2	4850	tCg/tTg	58/59	0.219115676803763	3	FACETS	0.72	0.648	0.796	0.36	0.324	0.398	INDETERMINATE	1	TRUE	1	0.43	3		461	903	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830884	72830885	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	245	874	0	ENST00000268489.5:c.5696dup	p.Glu1900ArgfsTer29	p.E1900Rfs*29	ENST00000268489	NM_006885.3	1899	gga/ggGa	9/10	1	2	FACETS	0.885	0.825	0.946	0.885	0.825	0.946	CLONAL	1	TRUE	1	0.43	2		874	1288	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555724	21555724	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753361598	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	207	656	1	ENST00000382592.4:c.2546G>A	p.Arg849Gln	p.R849Q	ENST00000382592	NM_014572.2	849	cGg/cAg	6/8	1	2	FACETS	0.96	0.891	1	0.96	0.891	1	CLONAL	1	TRUE	1	0.43	2		657	1003	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462607	40462607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1387284839	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	218	714	0	ENST00000345506.4:c.2305C>T	p.Arg769Cys	p.R769C	ENST00000345506	NM_003152.3	769	Cgc/Tgc	20/20	1	2	FACETS	0.912	0.847	0.979	0.912	0.847	0.979	CLONAL	1	TRUE	1	0.43	2		714	1112	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905522	50905522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1408031137	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	248	904	0	ENST00000440232.2:c.650C>T	p.Pro217Leu	p.P217L	ENST00000440232	NM_002691.3	217	cCg/cTg	6/27	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.43	2		904	1097	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440489	49440489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910695111	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	261	677	0	ENST00000301067.7:c.4321C>T	p.Arg1441Cys	p.R1441C	ENST00000301067	NM_003482.3	1441	Cgc/Tgc	15/54	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.43	2		677	1080	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176491	123176491	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	64	109	0	ENST00000218089.9:c.458A>T	p.Asp153Val	p.D153V	ENST00000218089	NM_001042749.1	153	gAt/gTt	7/35	1	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.43	1		109	180	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47685237	47685237	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	67	270	0	ENST00000347630.2:c.713del	p.Lys238ArgfsTer17	p.K238Rfs*17	ENST00000347630	NM_001007230.1	238	aAg/ag	8/11	1	2	FACETS	0.803	0.701	0.912	0.803	0.701	0.912	CLONAL	1	TRUE	1	0.43	2		270	388	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	51	206	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.728	0.622	0.843	0.728	0.622	0.843	SUBCLONAL	1	TRUE	1	0.43	2		206	326	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363231	40363231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768216635	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	87	645	0	ENST00000397332.2:c.998C>T	p.Ala333Val	p.A333V	ENST00000397332	NM_001033082.2	333	gCg/gTg	3/3	1	2	FACETS	0.385	0.339	0.433	0.385	0.339	0.433	SUBCLONAL	1	TRUE	1	0.43	2		645	1052	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166620	118166620	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	206	585	0	ENST00000369448.3:c.1130C>A	p.Pro377Gln	p.P377Q	ENST00000369448	NM_017709.3	377	cCa/cAa	2/2	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.43	2		585	911	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891153	112891153	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730880992	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	174	566	0	ENST00000351677.2:c.487G>A	p.Gly163Ser	p.G163S	ENST00000351677	NM_002834.3	163	Ggc/Agc	4/16	1	2	FACETS	0.882	0.812	0.954	0.882	0.812	0.954	CLONAL	1	TRUE	1	0.43	2		566	918	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117740	115117740	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	175	423	0	ENST00000257566.3:c.695G>C	p.Gly232Ala	p.G232A	ENST00000257566	NM_016569.3	232	gGg/gCg	3/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.43	2		423	777	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563170	21563170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	253	888	1	ENST00000382592.4:c.749G>A	p.Gly250Asp	p.G250D	ENST00000382592	NM_014572.2	250	gGc/gAc	4/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.43	2		889	1110	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467821	99467821	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	65	628	0	ENST00000268035.6:c.2690A>G	p.Asn897Ser	p.N897S	ENST00000268035	NM_000875.3	897	aAc/aGc	13/21	1	2	FACETS	0.288	0.248	0.331	0.288	0.248	0.331	SUBCLONAL	1	TRUE	1	0.43	2		628	1051	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862158	68862158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530717933	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	220	654	0	ENST00000261769.5:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000261769	NM_004360.3	749	cGg/cAg	14/16	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.43	2		654	1009	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216418	7216419	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	221	771	0	ENST00000380728.2:c.829dup	p.Gln277ProfsTer?	p.Q277Pfs*?	ENST00000380728		277	cag/cCag	10/11	1	2	FACETS	0.814	0.756	0.874	0.814	0.756	0.874	CLONAL	1	TRUE	1	0.43	2		771	1263	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541502	29541502	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	18	97	0	ENST00000356175.3:c.1428del	p.Lys476AsnfsTer22	p.K476Nfs*22	ENST00000356175	NM_000267.3	476	Aaa/aa	13/57	1	2	FACETS	0.734	0.56	0.934	0.734	0.56	0.934	CLONAL	1	TRUE	1	0.43	2		97	114	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556373	29556373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765848298	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	129	510	0	ENST00000356175.3:c.2740C>T	p.Arg914Trp	p.R914W	ENST00000356175	NM_000267.3	914	Cgg/Tgg	21/57	1	2	FACETS	0.788	0.715	0.865	0.788	0.715	0.865	SUBCLONAL	1	TRUE	1	0.43	2		510	761	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619223	37619223	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	271	707	0	ENST00000447079.4:c.899G>T	p.Arg300Ile	p.R300I	ENST00000447079	NM_015083.1	300	aGa/aTa	1/14	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.43	2		707	1205	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687307	37687307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	218	746	1	ENST00000447079.4:c.4211G>A	p.Arg1404His	p.R1404H	ENST00000447079	NM_015083.1	1404	cGt/cAt	14/14	1	2	FACETS	0.951	0.884	1	0.951	0.884	1	CLONAL	1	TRUE	1	0.43	2		747	1066	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56367784	56367784	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	109	339	0	ENST00000348428.3:c.610T>A	p.Ser204Thr	p.S204T	ENST00000348428	NM_006785.3	204	Tca/Aca	4/17	1	2	FACETS	0.831	0.748	0.919	0.831	0.748	0.919	CLONAL	1	TRUE	1	0.43	2		339	610	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032414	11032414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	201	719	0	ENST00000327064.4:c.1808C>T	p.Thr603Ile	p.T603I	ENST00000327064	NM_199141.1	603	aCc/aTc	16/16	1	2	FACETS	0.904	0.838	0.973	0.904	0.838	0.973	CLONAL	1	TRUE	1	0.43	2		719	1034	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027214	48027214	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750832	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	154	504	1	ENST00000234420.5:c.2092C>T	p.Gln698Ter	p.Q698*	ENST00000234420	NM_000179.2	698	Cag/Tag	4/10	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.43	2		505	683	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757431	40757431	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	211	634	0	ENST00000373198.4:c.2867A>C	p.Asp956Ala	p.D956A	ENST00000373198	NM_133170.3	956	gAc/gCc	20/32	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.43	2		634	902	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29445929	29445929	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	198	622	0	ENST00000544604.2:c.1760G>A	p.Arg587His	p.R587H	ENST00000544604	NM_001206998.1	587	cGc/cAc	8/9	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.43	2		622	896	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626078	12626078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	174	681	0	ENST00000251849.4:c.1882G>A	p.Ala628Thr	p.A628T	ENST00000251849	NM_002880.3	628	Gca/Aca	17/17	1	2	FACETS	0.791	0.728	0.857	0.791	0.728	0.857	SUBCLONAL	1	TRUE	1	0.43	2		681	1023	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79965925	79965926	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	84	357	0	ENST00000265081.6:c.594dup	p.Asp199Ter	p.D199*	ENST00000265081	NM_002439.4	197	ctt/cTtt	4/24	1	2	FACETS	0.737	0.653	0.827	0.737	0.653	0.827	SUBCLONAL	1	TRUE	1	0.43	2		357	530	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524400	176524400	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	78	682	0	ENST00000292408.4:c.2259+2T>C		p.X753_splice	ENST00000292408	NM_213647.1	753			1	2	FACETS	0.391	0.343	0.444	0.391	0.343	0.444	SUBCLONAL	1	TRUE	1	0.43	2		682	927	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020740	26020740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	208	664	0	ENST00000357647.3:c.23C>T	p.Ala8Val	p.A8V	ENST00000357647	NM_003529.2	8	gCt/gTt	1/1	1	2	FACETS	0.9	0.835	0.968	0.9	0.835	0.968	CLONAL	1	TRUE	1	0.43	2		664	1075	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100063	157100063	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	67	887	0	ENST00000346085.5:c.1000G>T	p.Ala334Ser	p.A334S	ENST00000346085	NM_020732.3	334	Gca/Tca	1/20	1	2	FACETS	0.277	0.24	0.318	0.277	0.24	0.318	SUBCLONAL	1	TRUE	1	0.43	2		887	1123	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273524	38273524	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	89	672	0	ENST00000425967.3:c.1811T>C	p.Leu604Pro	p.L604P	ENST00000425967	NM_001174067.1	604	cTg/cCg	14/19	0.219115676803763	3	FACETS	0.464	0.41	0.522	0.232	0.205	0.261	INDETERMINATE	1	TRUE	1	0.43	3		672	1084	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74858923	74858923	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	149	335	0	ENST00000284811.8:c.281C>T	p.Pro94Leu	p.P94L	ENST00000284811		94	cCa/cTa	4/4	0.219115676803763	3	FACETS	1	0.988	1	0.736	0.676	0.799	INDETERMINATE	1	TRUE	1	0.43	3		335	572	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2039765	2039767	+	inframe_deletion	In_Frame_Del	DEL	CAG	CAG	-	novel	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	98	769	1	ENST00000349721.2:c.663_665del	p.Gln238del	p.Q238del	ENST00000349721	NM_003070.3	219	CAG/-	4/34	1	2	FACETS	0.429	0.382	0.48	0.429	0.382	0.48	SUBCLONAL	1	TRUE	1	0.43	2		770	1062	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2086920	2086920	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	165	613	0	ENST00000349721.2:c.2622del	p.Arg875GlufsTer5	p.R875Efs*5	ENST00000349721	NM_003070.3	873	gCc/gc	18/34	1	2	FACETS	0.755	0.693	0.821	0.755	0.693	0.821	SUBCLONAL	1	TRUE	1	0.43	2		613	1016	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069021	5069021	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	40	188	0	ENST00000381652.3:c.1327-1G>A		p.X443_splice	ENST00000381652	NM_004972.3	443			1	2	FACETS	0.651	0.543	0.769	0.651	0.543	0.769	SUBCLONAL	1	TRUE	1	0.43	2		188	286	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485794	8485794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	149	467	0	ENST00000356435.5:c.3023G>A	p.Ser1008Asn	p.S1008N	ENST00000356435		1008	aGt/aAt	17/35	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.43	2		467	687	SUCCESS
BTK	695	MSKCC	GRCh37	X	100609654	100609654	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	153	244	0	ENST00000308731.7:c.1595A>G	p.Gln532Arg	p.Q532R	ENST00000308731	NM_000061.2	532	cAa/cGa	16/19	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.43	1		244	383	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0064625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	114	287	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.304063792743936	3	FACETS	0.942	0.853	1	0.942	0.853	1	CLONAL	2	TRUE	1	0.316586947832041	3		287	443	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	77	612	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.316586947832041	2		612	448	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0064625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	62	298	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.316586947832041	2		298	375	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457264	67457264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750707381	NA	P-0064625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	142	892	0	ENST00000327367.4:c.238C>T	p.Arg80Trp	p.R80W	ENST00000327367	NM_005902.3	80	Cgg/Tgg	2/9	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.316586947832041	2		892	866	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568668	41568669	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0064625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	80	385	0	ENST00000263253.7:c.4617+2dup		p.X1539_splice	ENST00000263253	NM_001429.3	1539			1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.316586947832041	2		385	486	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0064626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	210	395	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.779118283924592	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.779118283924592	1		395	326	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064435	30064438	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTG	GGTG	-	novel	NA	P-0064626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	210	371	0	ENST00000338641.4:c.999_999+3del		p.X333_splice	ENST00000338641	NM_000268.3	333		10/16	0.779118283924592	1	FACETS	0.957	0.907	1	0.957	0.907	1	CLONAL	1	TRUE	0	0.779118283924592	1		371	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0064627-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	269	444	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.421767632999813	3	FACETS	1	0.985	1	0.739	0.699	0.779	CLONAL	2	TRUE	0	0.504238614231938	3		444	603	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0064627-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	21	230	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.504951444505313	4	FACETS	1	0.915	1			1	CLONAL	1	TRUE	NA	0.504238614231938	4		230	90	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47061259	47061259	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064627-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	243	538	0	ENST00000409792.3:c.7422C>G	p.Phe2474Leu	p.F2474L	ENST00000409792	NM_014159.6	2474	ttC/ttG	19/21	0.421767632999813	3	FACETS	0.902	0.855	0.948	0.902	0.855	0.948	CLONAL	3	TRUE	0	0.504238614231938	3		538	446	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845748	151845751	+	frameshift_variant	Frame_Shift_Del	DEL	GGTT	GGTT	-	novel	NA	P-0064627-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	272	652	0	ENST00000262189.6:c.13261_13264del	p.Asn4421LeufsTer9	p.N4421Lfs*9	ENST00000262189	NM_170606.2	4421	AACCtt/tt	52/59	0.504951444505313	4	FACETS	0.98	0.923	1			1	CLONAL	2	TRUE	NA	0.504238614231938	4		652	828	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0064628-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	264	444	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.733233276575779	1	FACETS	0.981	0.933	1	0.981	0.933	1	CLONAL	1	TRUE	0	0.733233276575779	1		444	465	SUCCESS
APC	324	MSKCC	GRCh37	5	112111408	112111411	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	-	rs387906231	NA	P-0064628-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	32	141	0	ENST00000257430.4:c.509_512del	p.Asp170ValfsTer4	p.D170Vfs*4	ENST00000257430	NM_000038.5	169	ATAGat/at	5/16	0.609810045963421	1	FACETS	0.635	0.533	0.743	0.635	0.533	0.743	SUBCLONAL	1	TRUE	0	0.733233276575779	1		141	87	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912140	114912140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064628-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	189	469	0	ENST00000543371.1:c.1210C>T	p.Arg404Trp	p.R404W	ENST00000543371	NM_001198531.1	404	Cgg/Tgg	11/14	1	2	FACETS	0.856	0.796	0.918	0.856	0.796	0.918	CLONAL	1	TRUE	1	0.733233276575779	2		469	602	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469938	157469938	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064628-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	57	719	0	ENST00000346085.5:c.2732G>T	p.Gly911Val	p.G911V	ENST00000346085	NM_020732.3	911	gGa/gTa	9/20	1	2	FACETS	0.214	0.183	0.249	0.214	0.183	0.249	SUBCLONAL	1	TRUE	1	0.733233276575779	2		719	725	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777792	3777792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200566758	NA	P-0064629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	306	831	0	ENST00000262367.5:c.7256C>T	p.Ala2419Val	p.A2419V	ENST00000262367	NM_004380.2	2419	gCg/gTg	31/31	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.728833586313168	2		831	766	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0064629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	256	534	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.728833586313168	3	FACETS	0.963	0.903	1	0.482	0.451	0.513	CLONAL	1	TRUE	1	0.728833586313168	3		534	995	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619279	37619280	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0064629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	299	759	0	ENST00000447079.4:c.956dup	p.Tyr319Ter	p.Y319*	ENST00000447079	NM_015083.1	319	tac/tAac	1/14	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.728833586313168	2		759	706	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37672008	37672008	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0064629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	167	343	0	ENST00000447079.4:c.2795del	p.Lys932ArgfsTer14	p.K932Rfs*14	ENST00000447079	NM_015083.1	931	acA/ac	9/14	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.728833586313168	2		343	442	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752713	128752724	+	inframe_deletion	In_Frame_Del	DEL	TCAGAGTCTGGA	TCAGAGTCTGGA	-	novel	NA	P-0064629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	703	668	0	ENST00000377970.2:c.877_888del	p.Glu293_Ser296del	p.E293_S296del	ENST00000377970	NM_002467.4	292	TCAGAGTCTGGA/-	3/3	0.728833586313168	6	FACETS	0.912	0.88	0.944	0.912	0.88	0.944	CLONAL	3	TRUE	3	0.728833586313168	6		668	1733	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0064630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	20	642	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.627295671484116	2	FACETS	0.082	0.062	0.106	0.041	0.031	0.053	SUBCLONAL	1	TRUE	0	0.627295671484116	2		642	774	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254929	16254929	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs751475729	NA	P-0064630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	530	609	0	ENST00000375759.3:c.2194C>T	p.Arg732Ter	p.R732*	ENST00000375759	NM_015001.2	732	Cga/Tga	11/15	0.624887782349985	2	FACETS	0.999	0.967	1	0.999	0.967	1	CLONAL	2	TRUE	0	0.627295671484116	2		609	846	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913384	NA	P-0064630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	518	656	0	ENST00000304494.5:c.262G>T	p.Glu88Ter	p.E88*	ENST00000304494	NM_000077.4	88	Gag/Tag	2/3	0.624887782349985	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.627295671484116	2		656	771	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782082	NA	P-0064630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	398	531	0	ENST00000269305.4:c.745A>T	p.Arg249Trp	p.R249W	ENST00000269305	NM_001126112.2	249	Agg/Tgg	7/11	0.627295671484116	2	FACETS	0.998	0.961	1	0.998	0.961	1	CLONAL	2	TRUE	0	0.627295671484116	2		531	636	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098806	178098806	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1553487947	NA	P-0064630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	463	528	0	ENST00000397062.3:c.239C>A	p.Thr80Lys	p.T80K	ENST00000397062	NM_006164.4	80	aCa/aAa	2/5	0.624887782349985	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.627295671484116	2		528	688	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831127	72831130	+	frameshift_variant	Frame_Shift_Del	DEL	GGTC	GGTC	-	novel	NA	P-0064630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	510	585	0	ENST00000268489.5:c.5451_5454del	p.Thr1818ValfsTer4	p.T1818Vfs*4	ENST00000268489	NM_006885.3	1817	gtGACC/gt	9/10	0.627295671484116	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.627295671484116	3		585	1033	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508503	29508503	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	178	236	0	ENST00000356175.3:c.650A>G	p.Glu217Gly	p.E217G	ENST00000356175	NM_000267.3	217	gAa/gGa	6/57	0.525567074606904	5	FACETS	1	0.931	1			1	CLONAL	2	TRUE	NA	0.627295671484116	5		236	549	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30302625	30302625	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	22	56	0	ENST00000322652.5:c.716C>G	p.Pro239Arg	p.P239R	ENST00000322652	NM_015355.2	239	cCt/cGt	7/16	0.525567074606904	5	FACETS	1	0.902	1			1	CLONAL	1	TRUE	NA	0.627295671484116	5		56	106	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298695	15298695	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	431	603	0	ENST00000263388.2:c.1603G>T	p.Glu535Ter	p.E535*	ENST00000263388	NM_000435.2	535	Gag/Tag	10/33	0.627295671484116	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.627295671484116	3		603	859	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424114	47424138	+	frameshift_variant	Frame_Shift_Del	DEL	CTTCAGTGTGTCTTTCTCGACCCTG	CTTCAGTGTGTCTTTCTCGACCCTG	-	novel	NA	P-0064630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	477	524	0	ENST00000404338.3:c.2186_2210del	p.Gln729LeufsTer19	p.Q729Lfs*19	ENST00000404338	NM_004491.4	728	CTTCAGTGTGTCTTTCTCGACCCTGct/ct	1/6	0.627295671484116	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.627295671484116	3		524	982	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451929	29451929	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	295	519	0	ENST00000389048.3:c.2636G>T	p.Gly879Val	p.G879V	ENST00000389048	NM_004304.4	879	gGt/gTt	16/29	0.610886844524702	3	FACETS	0.979	0.93	1	0.979	0.93	1	CLONAL	2	TRUE	1	0.627295671484116	3		519	631	SUCCESS
ATR	545	MSKCC	GRCh37	3	142285067	142285067	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	300	373	0	ENST00000350721.4:c.188C>G	p.Pro63Arg	p.P63R	ENST00000350721	NM_001184.3	63	cCa/cGa	3/47	0.627295671484116	5	FACETS	0.969	0.914	1	0.484	0.457	0.513	CLONAL	2	TRUE	1	0.627295671484116	5		373	958	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287616	33287616	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	199	572	2	ENST00000374542.5:c.1481A>G	p.Lys494Arg	p.K494R	ENST00000374542	NM_001141970.1	494	aAg/aGg	6/8	1	2	FACETS	0.849	0.789	0.911	0.849	0.789	0.911	CLONAL	1	TRUE	1	0.627295671484116	2		574	747	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873441	151873441	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	147	574	0	ENST00000262189.6:c.9097A>G	p.Ile3033Val	p.I3033V	ENST00000262189	NM_170606.2	3033	Att/Gtt	38/59	0.627295671484116	2	FACETS	0.606	0.554	0.661	0.303	0.277	0.331	SUBCLONAL	1	TRUE	0	0.627295671484116	2		574	773	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064631-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	38	612	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.713	0.588	0.854	0.713	0.588	0.854	SUBCLONAL	1	TRUE	1	0.167797550797582	2		612	635	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149794	202149794	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064631-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	57	758	0	ENST00000358485.4:c.1235A>G	p.Lys412Arg	p.K412R	ENST00000358485	NM_001080125.1	412	aAa/aGa	8/9	1	2	FACETS	0.826	0.707	0.956	0.826	0.707	0.956	CLONAL	1	TRUE	1	0.167797550797582	2		758	823	SUCCESS
APC	324	MSKCC	GRCh37	5	112179567	112179567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs538289470	NA	P-0064631-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	47	673	1	ENST00000257430.4:c.8276G>A	p.Arg2759His	p.R2759H	ENST00000257430	NM_000038.5	2759	cGt/cAt	16/16	1	2	FACETS	0.819	0.69	0.962	0.819	0.69	0.962	CLONAL	1	TRUE	1	0.167797550797582	2		674	684	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413133	139413134	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064631-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	145	750	0	ENST00000277541.6:c.1008dup	p.Asp337Ter	p.D337*	ENST00000277541	NM_017617.3	336	-/T	6/34	0.167797550797582	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	0	0.167797550797582	2		750	850	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10776650	10776650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064631-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	56	612	0	ENST00000361367.2:c.290C>T	p.Ala97Val	p.A97V	ENST00000361367	NM_014633.3	97	gCt/gTt	3/25	1	2	FACETS	0.982	0.84	1	0.982	0.84	1	CLONAL	1	TRUE	1	0.167797550797582	2		612	680	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576835	67576835	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0064631-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	32	369	0	ENST00000274335.5:c.916+1G>T		p.X306_splice	ENST00000274335		306			1	2	FACETS	0.873	0.708	1	0.873	0.708	1	CLONAL	1	TRUE	1	0.167797550797582	2		369	437	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81973519	81973519	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064631-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	52	604	0	ENST00000359376.3:c.3336C>G	p.Ile1112Met	p.I1112M	ENST00000359376	NM_002661.3	1112	atC/atG	30/33	1	2	FACETS	0.938	0.797	1	0.938	0.797	1	CLONAL	1	TRUE	1	0.167797550797582	2		604	661	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0064633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	21	772	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.485984830047001	3	FACETS	0.104	0.08	0.134	0.052	0.04	0.067	SUBCLONAL	1	TRUE	1	0.485984830047001	3		772	1028	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	208	701	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.485984830047001	2		701	777	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0064633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	49	588	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	1	2	FACETS	0.844	0.722	0.975	0.844	0.722	0.975	CLONAL	1	TRUE	1	0.485984830047001	2		588	239	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692901	89692901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786204929	NA	P-0064633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	90	499	0	ENST00000371953.3:c.385G>A	p.Gly129Arg	p.G129R	ENST00000371953	NM_000314.4	129	Gga/Aga	5/9	0.485984830047001	3	FACETS	0.899	0.81	0.991	0.899	0.81	0.991	CLONAL	2	TRUE	1	0.485984830047001	3		499	256	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916726	178916726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772110575	NA	P-0064633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	57	411	0	ENST00000263967.3:c.113G>A	p.Arg38His	p.R38H	ENST00000263967	NM_006218.2	38	cGt/cAt	2/21	1	2	FACETS	0.931	0.807	1	0.931	0.807	1	CLONAL	1	TRUE	1	0.485984830047001	2		411	252	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466003	69466038	+	inframe_deletion	In_Frame_Del	DEL	GTGGACCTGGCTTGCACACCCACCGACGTGCGGGAC	GTGGACCTGGCTTGCACACCCACCGACGTGCGGGAC	-	novel	NA	P-0064633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	137	898	0	ENST00000227507.2:c.847_882del	p.Leu283_Asp294del	p.L283_D294del	ENST00000227507	NM_053056.2	281	GTGGACCTGGCTTGCACACCCACCGACGTGCGGGAC/-	5/5	1	2	FACETS	0.861	0.785	0.94	0.861	0.785	0.94	CLONAL	1	TRUE	1	0.485984830047001	2		898	655	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720851	89720851	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	21	174	0	ENST00000371953.3:c.1003del	p.Arg335AspfsTer9	p.R335Dfs*9	ENST00000371953	NM_000314.4	334	aaC/aa	8/9	0.485984830047001	3	FACETS	1	0.864	1	0.571	0.449	0.708	CLONAL	1	TRUE	1	0.485984830047001	3		174	94	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268796	41268796	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	70	587	0	ENST00000349496.5:c.1034A>G	p.Lys345Arg	p.K345R	ENST00000349496	NM_001904.3	345	aAg/aGg	7/15	1	2	FACETS	0.86	0.755	0.971	0.86	0.755	0.971	CLONAL	1	TRUE	1	0.485984830047001	2		587	335	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274753	123274764	+	inframe_deletion	In_Frame_Del	DEL	CGATTAAGAAGA	CGATTAAGAAGA	-	novel	NA	P-0064633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	145	635	0	ENST00000358487.5:c.1154_1165del	p.Val385_Ile388del	p.V385_I388del	ENST00000358487	NM_000141.4	385	gTCTTCTTAATCGcc/gcc	9/18	0.485984830047001	3	FACETS	0.872	0.795	0.952	0.436	0.397	0.476	CLONAL	1	TRUE	1	0.485984830047001	3		635	851	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829819	72829820	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	33	785	0	ENST00000268489.5:c.6761dup	p.Arg2255GlufsTer16	p.R2255Efs*16	ENST00000268489	NM_006885.3	2254	ctg/ctTg	9/10	1	2	FACETS	0.214	0.174	0.26	0.214	0.174	0.26	SUBCLONAL	1	TRUE	1	0.485984830047001	2		785	634	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268753	41268753	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	55	532	0	ENST00000349496.5:c.991T>A	p.Tyr331Asn	p.Y331N	ENST00000349496	NM_001904.3	331	Tat/Aat	7/15	1	2	FACETS	0.686	0.59	0.79	0.686	0.59	0.79	SUBCLONAL	1	TRUE	1	0.485984830047001	2		532	330	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176666846	176666846	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757591029	NA	P-0064633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	28	428	0	ENST00000439151.2:c.4282G>A	p.Asp1428Asn	p.D1428N	ENST00000439151	NM_022455.4	1428	Gac/Aac	8/23	1	2	FACETS	0.486	0.39	0.594	0.486	0.39	0.594	SUBCLONAL	1	TRUE	1	0.485984830047001	2		428	237	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394129	31394129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1330224703	NA	P-0064634-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	38	466	0	ENST00000328111.2:c.2416G>A	p.Glu806Lys	p.E806K	ENST00000328111	NM_006892.3	806	Gaa/Aaa	22/23	1	2	FACETS	0.448	0.371	0.534	0.448	0.371	0.534	SUBCLONAL	1	TRUE	1	0.417794486545727	2		466	406	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838208	89838208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767396631	NA	P-0064634-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	41	755	0	ENST00000389301.3:c.2029G>A	p.Val677Met	p.V677M	ENST00000389301	NM_000135.2	677	Gtg/Atg	23/43	1	2	FACETS	0.294	0.244	0.35	0.294	0.244	0.35	SUBCLONAL	1	TRUE	1	0.417794486545727	2		755	667	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231111	142231111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	285	325	0	ENST00000350721.4:c.4843G>A	p.Asp1615Asn	p.D1615N	ENST00000350721	NM_001184.3	1615	Gac/Aac	27/47	0.716929694568265	2	FACETS	0.959	0.922	0.995	0.959	0.922	0.995	CLONAL	2	TRUE	0	0.738895534849377	2		325	402	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416666	121416666	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	403	814	0	ENST00000257555.6:c.95A>C	p.Glu32Ala	p.E32A	ENST00000257555		32	gAg/gCg	1/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.738895534849377	2		814	971	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098777	178098777	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	290	630	0	ENST00000397062.3:c.268C>G	p.Gln90Glu	p.Q90E	ENST00000397062	NM_006164.4	90	Cag/Gag	2/5	1	2	FACETS	0.962	0.909	1	0.962	0.909	1	CLONAL	1	TRUE	1	0.738895534849377	2		630	816	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16056691	16056691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	10	219	0	ENST00000268712.3:c.751C>T	p.His251Tyr	p.H251Y	ENST00000268712	NM_006311.3	251	Cat/Tat	7/46	1	2	FACETS	0.168	0.113	0.236	0.168	0.113	0.236	SUBCLONAL	1	TRUE	1	0.599881058646457	2		219	199	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858774	9858776	+	frameshift_variant	Frame_Shift_Del	DEL	ATG	ATG	TT	novel	NA	P-0064649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	171	599	0	ENST00000330684.3:c.2625_2627delinsAA	p.His875GlnfsTer13	p.H875Qfs*13	ENST00000330684	NM_001134407.1	875	caCATt/caAAt	13/13	1	2	FACETS	0.905	0.836	0.976	0.905	0.836	0.976	CLONAL	1	TRUE	1	0.599881058646457	2		599	630	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	110	612	0				ENST00000310581	NM_198253.2	-/1132			0.110645421199818	6	FACETS	1	0.96	1	0.747	0.675	0.822	INDETERMINATE	2	TRUE	3	0.362670470417013	6		612	467	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258744	115258744	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121434596	NA	P-0064650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	28	452	0	ENST00000369535.4:c.38G>T	p.Gly13Val	p.G13V	ENST00000369535	NM_002524.4	13	gGt/gTt	2/7	0.153349743246287	6	FACETS	0.372	0.296	0.459	0.124	0.098	0.153	INDETERMINATE	1	TRUE	3	0.362670470417013	6		452	716	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338639	70338639	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	300	576	0	ENST00000374080.3:c.35G>A	p.Arg12Gln	p.R12Q	ENST00000374080		12	cGg/cAg	1/45	0.362670470417013	5	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	2	0.362670470417013	5		576	750	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15822318	15822318	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	77	517	0	ENST00000307771.7:c.397G>C	p.Glu133Gln	p.E133Q	ENST00000307771	NM_005089.3	133	Gag/Cag	5/11	0.362670470417013	5	FACETS	1	0.923	1	0.357	0.313	0.403	CLONAL	1	TRUE	2	0.362670470417013	5		517	613	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344889	70344889	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	121	736	0	ENST00000374080.3:c.2119G>C	p.Glu707Gln	p.E707Q	ENST00000374080		707	Gag/Cag	15/45	0.362670470417013	5	FACETS	1	0.919	1	0.34	0.307	0.376	CLONAL	1	TRUE	2	0.362670470417013	5		736	1009	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184093	123184094	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	70	484	0	ENST00000218089.9:c.952dup	p.Met318AsnfsTer3	p.M318Nfs*3	ENST00000218089	NM_001042749.1	317	-/A	11/35	0.362670470417013	5	FACETS	0.842	0.739	0.952	0.561	0.492	0.635	CLONAL	2	TRUE	2	0.362670470417013	5		484	354	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0064651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	29	413	0	ENST00000397752.3:c.3028+1G>C		p.X1010_splice	ENST00000397752	NM_000245.2	1010			1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		413	544	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029285	143029285	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	13	179	0	ENST00000262992.4:c.2335G>T	p.Glu779Ter	p.E779*	ENST00000262992	NM_001101669.1	779	Gaa/Taa	21/24	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		179	248	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	503	612	0				ENST00000310581	NM_198253.2	-/1132			0.779515603123234	5	FACETS	0.953	0.918	0.989	0.953	0.918	0.989	CLONAL	3	TRUE	2	0.779515603123234	5		612	979	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956552	93956552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754119070	NA	P-0064654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	126	527	0	ENST00000369303.4:c.2684G>A	p.Arg895Gln	p.R895Q	ENST00000369303	NM_004440.3	895	cGa/cAa	15/17	1	2	FACETS	0.954	0.875	1	0.954	0.875	1	CLONAL	1	TRUE	1	0.779515603123234	2		527	339	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972913	55972913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	134	342	0	ENST00000263923.4:c.1477G>A	p.Gly493Arg	p.G493R	ENST00000263923	NM_002253.2	493	Gga/Aga	11/30	0.650252875031769	4	FACETS	0.9	0.829	0.972	0.9	0.829	0.972	CLONAL	2	TRUE	2	0.779515603123234	4		342	340	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455608	189455608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	225	602	0	ENST00000264731.3:c.142G>A	p.Glu48Lys	p.E48K	ENST00000264731	NM_003722.4	48	Gaa/Aaa	2/14	0.650252875031769	4	FACETS	0.878	0.824	0.933	0.878	0.824	0.933	CLONAL	2	TRUE	2	0.779515603123234	4		602	585	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892182	9892182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	217	792	0	ENST00000330684.3:c.2308C>T	p.Pro770Ser	p.P770S	ENST00000330684	NM_001134407.1	770	Cct/Tct	11/13	0.758851264322818	3	FACETS	0.919	0.856	0.984	0.459	0.428	0.492	CLONAL	1	TRUE	1	0.779515603123234	3		792	842	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750414	41750414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	405	776	0	ENST00000226382.2:c.214G>A	p.Asp72Asn	p.D72N	ENST00000226382	NM_003924.3	72	Gac/Aac	1/3	0.650252875031769	4	FACETS	0.926	0.884	0.969	0.926	0.884	0.969	CLONAL	2	TRUE	2	0.779515603123234	4		776	998	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968166	55968166	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	236	542	0	ENST00000263923.4:c.2164C>T	p.Leu722Phe	p.L722F	ENST00000263923	NM_002253.2	722	Ctc/Ttc	15/30	0.650252875031769	4	FACETS	0.857	0.805	0.909	0.857	0.805	0.909	CLONAL	2	TRUE	2	0.779515603123234	4		542	629	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0064654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	897	1073	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	0.779515603123234	5	FACETS	0.995	0.968	1	0.995	0.968	1	CLONAL	3	TRUE	2	0.779515603123234	5		1073	1672	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546788	9546788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772481025	NA	P-0064654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	480	881	0	ENST00000353224.5:c.1234C>T	p.Pro412Ser	p.P412S	ENST00000353224	NM_177990.2	412	Ccg/Tcg	5/10	0.650252875031769	4	FACETS	0.892	0.855	0.93	0.892	0.855	0.93	CLONAL	2	TRUE	2	0.779515603123234	4		881	1228	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343903	118343903	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	451	826	0	ENST00000534358.1:c.2029C>T	p.Arg677Ter	p.R677*	ENST00000534358	NM_005933.3	677	Cga/Tga	3/36	0.726197056451649	2	FACETS	0.921	0.893	0.948	0.921	0.893	0.948	CLONAL	2	TRUE	0	0.779515603123234	2		826	628	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872482	136872482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	326	709	0	ENST00000241393.3:c.1016C>T	p.Ser339Phe	p.S339F	ENST00000241393	NM_003467.2	339	tCt/tTt	2/2	0.758851264322818	3	FACETS	0.885	0.843	0.926	0.885	0.843	0.926	CLONAL	2	TRUE	1	0.779515603123234	3		709	657	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517376	157517376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437511816	NA	P-0064654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	173	525	0	ENST00000346085.5:c.3940C>T	p.Pro1314Ser	p.P1314S	ENST00000346085	NM_020732.3	1314	Ccc/Tcc	16/20	1	2	FACETS	0.891	0.827	0.957	0.891	0.827	0.957	CLONAL	1	TRUE	1	0.779515603123234	2		525	498	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298148	123298148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	543	693	0	ENST00000358487.5:c.706G>A	p.Glu236Lys	p.E236K	ENST00000358487	NM_000141.4	236	Gaa/Aaa	6/18	0.690694005519552	4	FACETS	0.891	0.861	0.92	0.891	0.861	0.92	CLONAL	3	TRUE	1	0.779515603123234	4		693	928	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47079248	47079248	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	206	644	0	ENST00000409792.3:c.7258C>T	p.Pro2420Ser	p.P2420S	ENST00000409792	NM_014159.6	2420	Cct/Tct	18/21	0.650252875031769	4	FACETS	0.977	0.906	1	0.488	0.453	0.525	CLONAL	1	TRUE	2	0.779515603123234	4		644	963	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914920	32914920	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149330893	NA	P-0064654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	57	366	0	ENST00000380152.3:c.6428C>T	p.Ser2143Leu	p.S2143L	ENST00000380152		2143	tCa/tTa	11/27	0.758851264322818	3	FACETS	0.869	0.772	0.966	0.869	0.772	0.966	CLONAL	2	TRUE	1	0.779515603123234	3		366	117	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347678	89347678	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	508	1067	0	ENST00000301030.4:c.5272C>T	p.Pro1758Ser	p.P1758S	ENST00000301030	NM_001256183.1	1758	Ccc/Tcc	9/13	0.758851264322818	3	FACETS	0.917	0.883	0.951	0.917	0.883	0.951	CLONAL	2	TRUE	1	0.779515603123234	3		1067	988	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562746	29562746	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs199474742	NA	P-0064654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	222	544	0	ENST00000356175.3:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000356175	NM_000267.3	1276	Cga/Tga	28/57	0.472926921845731	4	FACETS	0.838	0.785	0.891	0.838	0.785	0.891	CLONAL	2	TRUE	2	0.779515603123234	4		544	605	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725031	162725031	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	665	733	0	ENST00000367921.3:c.503C>T	p.Pro168Leu	p.P168L	ENST00000367921	NM_006182.2	168	cCa/cTa	6/18	0.779515603123234	6	FACETS	0.901	0.869	0.933	0.901	0.869	0.933	CLONAL	3	TRUE	3	0.779515603123234	6		733	1615	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949134	71949134	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2798	307	1043	0	ENST00000298229.2:c.3601A>T	p.Met1201Leu	p.M1201L	ENST00000298229	NM_001567.3	1201	Atg/Ttg	27/28	0.779515603123234	10	FACETS	1	0.965	1			1	CLONAL	1	TRUE	NA	0.779515603123234	10		1043	3105	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656266	18656266	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs979866570	NA	P-0064654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	125	576	0	ENST00000266497.5:c.2945A>C	p.His982Pro	p.H982P	ENST00000266497		982	cAt/cCt	21/31	0.758851264322818	3	FACETS	0.862	0.784	0.943	0.431	0.392	0.472	CLONAL	1	TRUE	1	0.779515603123234	3		576	517	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443710	49443710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	420	896	0	ENST00000301067.7:c.3661C>T	p.Pro1221Ser	p.P1221S	ENST00000301067	NM_003482.3	1221	Cct/Tct	11/54	0.758851264322818	3	FACETS	0.909	0.872	0.946	0.909	0.872	0.946	CLONAL	2	TRUE	1	0.779515603123234	3		896	824	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73995412	73995412	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	656	837	0	ENST00000318443.5:c.718C>T	p.Gln240Ter	p.Q240*	ENST00000318443	NM_001024736.1	240	Cag/Tag	4/10	0.690694005519552	4	FACETS	0.928	0.901	0.955	0.928	0.901	0.955	CLONAL	3	TRUE	1	0.779515603123234	4		837	1076	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222600	2222600	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	117	557	0	ENST00000326181.6:c.794G>A	p.Gly265Glu	p.G265E	ENST00000326181	NM_032271.2	265	gGg/gAg	9/21	0.758851264322818	3	FACETS	0.81	0.734	0.89	0.405	0.367	0.445	CLONAL	1	TRUE	1	0.779515603123234	3		557	515	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858663	9858663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	444	851	0	ENST00000330684.3:c.2738C>T	p.Ser913Leu	p.S913L	ENST00000330684	NM_001134407.1	913	tCa/tTa	13/13	0.758851264322818	3	FACETS	0.911	0.875	0.947	0.911	0.875	0.947	CLONAL	2	TRUE	1	0.779515603123234	3		851	869	SUCCESS
APC	324	MSKCC	GRCh37	5	112177985	112177985	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4197	319	688	0	ENST00000257430.4:c.6694C>T	p.His2232Tyr	p.H2232Y	ENST00000257430	NM_000038.5	2232	Cat/Tat	16/16	0.779515603123234	21	FACETS	0.762	0.714	0.812	0.08	0.075	0.086	SUBCLONAL	2	TRUE	2	0.779515603123234	21		688	4516	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394840	394840	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	203	694	0	ENST00000380956.4:c.236G>A	p.Gly79Glu	p.G79E	ENST00000380956	NM_001195286.1	79	gGa/gAa	3/9	0.779515603123234	5	FACETS	0.957	0.886	1	0.319	0.295	0.344	CLONAL	1	TRUE	2	0.779515603123234	5		694	1181	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686821	117686821	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	85	462	0	ENST00000368508.3:c.2896C>T	p.Gln966Ter	p.Q966*	ENST00000368508	NM_002944.2	966	Caa/Taa	19/43	1	2	FACETS	0.755	0.675	0.838	0.755	0.675	0.838	SUBCLONAL	1	TRUE	1	0.779515603123234	2		462	289	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687256	117687256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	120	493	0	ENST00000368508.3:c.2795C>T	p.Ser932Phe	p.S932F	ENST00000368508	NM_002944.2	932	tCc/tTc	18/43	1	2	FACETS	0.853	0.779	0.929	0.853	0.779	0.929	CLONAL	1	TRUE	1	0.779515603123234	2		493	361	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528486	29528489	+	frameshift_variant	Frame_Shift_Del	DEL	CATC	CATC	TT	novel	NA	P-0064654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	53	457	0	ENST00000356175.3:c.1243_1246delinsTT	p.His415LeufsTer13	p.H415Lfs*13	ENST00000356175	NM_000267.3	415	CATCga/TTga	11/57	0.472926921845731	4	FACETS	1	0.958	1	0.647	0.561	0.738	CLONAL	1	TRUE	2	0.779515603123234	4		457	187	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0064655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	36	518	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.428	0.35	0.516	0.428	0.35	0.516	SUBCLONAL	1	TRUE	1	0.2	2		518	841	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259442	55259442	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397517127	NA	P-0064655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	46	595	0	ENST00000275493.2:c.2500G>T	p.Val834Leu	p.V834L	ENST00000275493	NM_005228.3	834	Gtg/Ttg	21/28	1	2	FACETS	0.649	0.545	0.764	0.649	0.545	0.764	SUBCLONAL	1	TRUE	1	0.2	2		595	709	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058057	27058057	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	74	882	0	ENST00000324856.7:c.1765C>T	p.Gln589Ter	p.Q589*	ENST00000324856	NM_006015.4	589	Caa/Taa	3/20	1	2	FACETS	0.762	0.665	0.867	0.762	0.665	0.867	SUBCLONAL	1	TRUE	1	0.2	2		882	971	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0064656-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	70	631	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.193456238509172	1	FACETS	0.746	0.649	0.852	0.746	0.649	0.852	SUBCLONAL	1	FALSE	0	0.193456238509172	1		631	876	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604789	48604789	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064656-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	42	665	0	ENST00000342988.3:c.1611C>G	p.Asp537Glu	p.D537E	ENST00000342988	NM_005359.5	537	gaC/gaG	12/12	0.190397542188664	0	FACETS	0.456	0.379	0.542			1	SUBCLONAL	1	FALSE	0	0.193456238509172	0		665	768	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412124	63412124	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064656-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	49	412	0	ENST00000330258.3:c.1043del	p.Gly348AlafsTer16	p.G348Afs*16	ENST00000330258	NM_152424.3	348	gGc/gc	2/2	0.193456238509172	2	FACETS	1	0.932	1			1	CLONAL	1	FALSE	NA	0.193456238509172	2		412	429	SUCCESS
APC	324	MSKCC	GRCh37	5	112175643	112175643	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554085817	NA	P-0064656-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	110	590	0	ENST00000257430.4:c.4353del	p.Val1452TyrfsTer21	p.V1452Yfs*21	ENST00000257430	NM_000038.5	1451	gAa/ga	16/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.193456238509172	2		590	883	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0064656-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	39	461	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	0.193356476204356	3	FACETS	0.892	0.739	1	0.446	0.369	0.531	CLONAL	1	FALSE	1	0.193456238509172	3		461	496	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446230	29446230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773583710	NA	P-0064656-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	58	766	0	ENST00000389048.3:c.3337C>T	p.Arg1113Trp	p.R1113W	ENST00000389048	NM_004304.4	1113	Cgg/Tgg	20/29	1	2	FACETS	0.633	0.542	0.733	0.633	0.542	0.733	SUBCLONAL	1	FALSE	1	0.193456238509172	2		766	947	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710650	40710650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159836	NA	P-0064656-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	127	597	0	ENST00000373198.4:c.4201G>A	p.Gly1401Arg	p.G1401R	ENST00000373198	NM_133170.3	1401	Gga/Aga	31/32	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.193456238509172	2		597	914	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0064657-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	31	516	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.847	0.686	1	0.847	0.686	1	CLONAL	1	TRUE	1	0.215269831360978	2		516	340	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039408	47039408	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064657-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	105	572	0	ENST00000377604.3:c.1031G>T	p.Gly344Val	p.G344V	ENST00000377604	NM_001204468.1	344	gGc/gTc	10/24	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.215269831360978	2		572	687	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752639	42752639	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1178888044	NA	P-0064657-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	54	581	0	ENST00000222329.4:c.1625C>T	p.Ser542Phe	p.S542F	ENST00000222329	NM_006494.2	542	tCc/tTc	4/4	1	2	FACETS	0.833	0.711	0.967	0.833	0.711	0.967	CLONAL	1	TRUE	1	0.215269831360978	2		581	602	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422332	422332	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1428121714	NA	P-0064657-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	53	410	0	ENST00000399788.2:c.2926A>G	p.Ser976Gly	p.S976G	ENST00000399788	NM_001042603.1	976	Agc/Ggc	20/28	1	2	FACETS	0.839	0.715	0.975	0.839	0.715	0.975	CLONAL	1	TRUE	1	0.215269831360978	2		410	587	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107737	30107737	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0064657-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	81	448	0	ENST00000331968.5:c.943A>T	p.Lys315Ter	p.K315*	ENST00000331968	NM_002742.2	315	Aaa/Taa	6/18	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.215269831360978	2		448	748	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55597576	55597576	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064657-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	66	373	0	ENST00000288135.5:c.2224G>T	p.Val742Leu	p.V742L	ENST00000288135	NM_000222.2	742	Gtg/Ttg	15/21	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.215269831360978	2		373	480	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2058355	2058355	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064657-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	67	476	0	ENST00000349721.2:c.1412G>T	p.Gly471Val	p.G471V	ENST00000349721	NM_003070.3	471	gGa/gTa	8/34	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.215269831360978	2		476	592	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321334	1321335	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	T	novel	NA	P-0064657-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	96	556	0	ENST00000400841.2:c.420_421delinsA	p.Asp140GlufsTer33	p.D140Efs*33	ENST00000400841		140	gaCCtg/gaAtg	4/6	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.215269831360978	2		556	669	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653805	89653805	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659443	NA	P-0064658-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	51	64	0	ENST00000371953.3:c.103A>G	p.Met35Val	p.M35V	ENST00000371953	NM_000314.4	35	Atg/Gtg	2/9	0.738855389810732	2	FACETS	0.852	0.766	0.933	0.852	0.766	0.933	CLONAL	2	TRUE	0	0.758108725016853	2		64	79	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0064658-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	1050	796	1	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.738855389810732	2	FACETS	0.98	0.961	0.999	0.98	0.961	0.999	CLONAL	2	TRUE	0	0.758108725016853	2		797	1413	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61310406	61310406	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064658-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	74	107	0	ENST00000341074.5:c.211G>T	p.Ala71Ser	p.A71S	ENST00000341074	NM_002974.2	71	Gca/Tca	3/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.758108725016853	2		107	162	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508473	106508473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370328855	NA	P-0064658-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	288	538	0	ENST00000359195.3:c.467C>T	p.Ala156Val	p.A156V	ENST00000359195	NM_002649.2	156	gCg/gTg	2/11	1	2	FACETS	0.949	0.896	1	0.949	0.896	1	CLONAL	1	TRUE	1	0.758108725016853	2		538	801	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0064659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	73	371	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.804	0.708	0.906	1	0.978	1	CLONAL	2	TRUE	1	0.26	2		371	349	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	40	612	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.971	0.81	1	0.971	0.81	1	CLONAL	1	TRUE	1	0.26	2		612	317	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871573	37871573	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	52	698	1	ENST00000269571.5:c.1183G>T	p.Glu395Ter	p.E395*	ENST00000269571		395	Gag/Tag	10/27	1	2	FACETS	0.625	0.531	0.728	0.625	0.531	0.728	SUBCLONAL	1	TRUE	1	0.26	2		699	640	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612102	43612102	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	82	658	0	ENST00000355710.3:c.2207G>T	p.Gly736Val	p.G736V	ENST00000355710	NM_020975.4	736	gGa/gTa	12/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.26	2		658	527	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932093	39932093	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	109	387	0	ENST00000378444.4:c.2506G>T	p.Glu836Ter	p.E836*	ENST00000378444	NM_001123385.1	836	Gag/Tag	4/15	1	1	FACETS	1	0.92	1	1	0.989	1	CLONAL	2	TRUE	0	0.26	1		387	359	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035983	47035983	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0064659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	72	277	0	ENST00000377604.3:c.661A>T	p.Lys221Ter	p.K221*	ENST00000377604	NM_001204468.1	221	Aag/Tag	7/24	1	1	FACETS	0.899	0.795	1	1	0.981	1	CLONAL	2	TRUE	0	0.26	1		277	268	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	22	612	0				ENST00000310581	NM_198253.2	-/1132			0.184488076360919	1	FACETS	0.772	0.622	0.933	0.772	0.622	0.933	INDETERMINATE	1	TRUE	0	0.629549157504223	1		612	62	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	203	633	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.511440101700778	4	FACETS	0.848	0.798	0.899	0.848	0.798	0.899	CLONAL	3	TRUE	1	0.629549157504223	4		633	413	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	229	450	1	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	0.537200960136397	4	FACETS	0.905	0.878	0.929			1	CLONAL	5	TRUE	NA	0.629549157504223	4		451	262	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220489	98220489	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1060502278	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	80	482	0	ENST00000331920.6:c.2974G>T	p.Glu992Ter	p.E992*	ENST00000331920	NM_000264.3	992	Gaa/Taa	18/24	0.231409119855151	3	FACETS	1	0.943	1	0.365	0.324	0.408	INDETERMINATE	1	TRUE	0	0.629549157504223	3		482	305	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69230488	69230488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	42	187	0	ENST00000462284.1:c.877G>A	p.Asp293Asn	p.D293N	ENST00000462284	NM_002392.5	293	Gat/Aat	10/11	0.629549157504223	3	FACETS	1	0.933	1	0.395	0.336	0.458	CLONAL	1	TRUE	0	0.629549157504223	3		187	148	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185061	123185061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	23	58	0	ENST00000218089.9:c.1108C>T	p.Arg370Trp	p.R370W	ENST00000218089	NM_001042749.1	370	Cgg/Tgg	12/35	0.537200960136397	2	FACETS	0.84	0.671	1			1	CLONAL	1	TRUE	NA	0.629549157504223	2		58	87	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770065	56770065	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs752608224	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	109	441	0	ENST00000337432.4:c.61C>G	p.Pro21Ala	p.P21A	ENST00000337432	NM_058216.2	21	Cca/Gca	1/9	0.629549157504223	3	FACETS	1	0.95	1	0.539	0.488	0.593	CLONAL	1	TRUE	1	0.629549157504223	3		441	422	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038894	12038894	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	178	417	0	ENST00000396373.4:c.1187G>A	p.Arg396Lys	p.R396K	ENST00000396373	NM_001987.4	396	aGa/aAa	7/8	0.467297570123597	3	FACETS	1	0.987	1	0.797	0.75	0.843	CLONAL	2	TRUE	0	0.629549157504223	3		417	311	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005580	42005580	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	118	485	0	ENST00000219905.7:c.3316C>T	p.Arg1106Ter	p.R1106*	ENST00000219905	NM_001164273.1	1106	Cga/Tga	9/24	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.629549157504223	2		485	347	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404754	404754	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	179	423	0	ENST00000399788.2:c.4440C>G	p.Phe1480Leu	p.F1480L	ENST00000399788	NM_001042603.1	1480	ttC/ttG	26/28	0.629549157504223	4	FACETS	1	0.98	1	0.562	0.525	0.6	CLONAL	2	TRUE	0	0.629549157504223	4		423	412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576888	7576889	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	86	559	0	ENST00000269305.4:c.957_958insT	p.Lys320Ter	p.K320*	ENST00000269305	NM_001126112.2	319	-/T	9/11	0.511440101700778	4	FACETS	1	0.959	1	0.388	0.346	0.434	CLONAL	1	TRUE	1	0.629549157504223	4		559	382	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910626	29910626	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	100	843	0	ENST00000376809.5:c.166C>T	p.Gln56Ter	p.Q56*	ENST00000376809	NM_002116.7	56	Cag/Tag	2/8	0.629549157504223	7	FACETS	0.766	0.682	0.855	0.128	0.113	0.143	SUBCLONAL	1	TRUE	1	0.629549157504223	7		843	1068	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416652	121416652	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs750099601	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	64	463	0	ENST00000257555.6:c.81C>G	p.Ile27Met	p.I27M	ENST00000257555		27	atC/atG	1/10	0.629549157504223	2	FACETS	1	0.97	1	0.656	0.582	0.731	CLONAL	1	TRUE	0	0.629549157504223	2		463	155	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986535	36986535	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	28	572	0	ENST00000354822.5:c.1154C>G	p.Ser385Trp	p.S385W	ENST00000354822	NM_001079668.2	385	tCg/tGg	3/3	0.569919106853555	3	FACETS	0.726	0.587	0.881	0.363	0.293	0.441	SUBCLONAL	1	TRUE	1	0.629549157504223	3		572	161	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441441	40441441	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	58	436	0	ENST00000345506.4:c.12G>C	p.Trp4Cys	p.W4C	ENST00000345506	NM_003152.3	4	tgG/tgC	3/20	0.511440101700778	4	FACETS	1	0.933	1	0.375	0.325	0.428	CLONAL	1	TRUE	1	0.629549157504223	4		436	267	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430992	181430992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	74	629	0	ENST00000325404.1:c.844G>A	p.Glu282Lys	p.E282K	ENST00000325404	NM_003106.3	282	Gag/Aag	1/1	0.629549157504223	6	FACETS	1	0.925	1	0.269	0.236	0.304	CLONAL	1	TRUE	2	0.629549157504223	6		629	494	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170046	32170046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768387019	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	51	516	0	ENST00000375023.3:c.3562G>A	p.Asp1188Asn	p.D1188N	ENST00000375023	NM_004557.3	1188	Gat/Aat	21/30	0.603563561856758	3	FACETS	0.934	0.803	1	0.311	0.267	0.359	CLONAL	1	TRUE	0	0.629549157504223	3		516	228	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420859	49420859	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759822794	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	279	570	0	ENST00000301067.7:c.14890C>T	p.Arg4964Cys	p.R4964C	ENST00000301067	NM_003482.3	4964	Cgt/Tgt	48/54	0.629549157504223	5	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	2	0.629549157504223	5		570	496	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044916	47044916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	76	337	0	ENST00000377604.3:c.2242G>A	p.Glu748Lys	p.E748K	ENST00000377604	NM_001204468.1	748	Gag/Aag	20/24	0.629549157504223	2	FACETS	1	0.971	1			1	CLONAL	1	TRUE	NA	0.629549157504223	2		337	192	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223667	36223667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	91	756	0	ENST00000222270.7:c.6217G>A	p.Glu2073Lys	p.E2073K	ENST00000222270	NM_014727.1	2073	Gag/Aag	28/37	0.629549157504223	3	FACETS	1	0.92	1	0.516	0.462	0.574	CLONAL	1	TRUE	1	0.629549157504223	3		756	368	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141549428	141549428	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	58	392	0	ENST00000220592.5:c.2160G>C	p.Lys720Asn	p.K720N	ENST00000220592	NM_012154.3	720	aaG/aaC	16/19	NA	2	FACETS	0.596	0.516	0.683			1	INDETERMINATE	1	TRUE	NA	0.629549157504223	2		392	309	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169601	27169601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540914328	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	103	456	0	ENST00000380036.4:c.602C>T	p.Ser201Leu	p.S201L	ENST00000380036	NM_000459.3	201	tCg/tTg	4/23	0.402469972655219	5	FACETS	1	0.918	1	0.343	0.307	0.38	CLONAL	1	TRUE	2	0.629549157504223	5		456	619	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264423	30264423	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	128	614	0	ENST00000322652.5:c.158C>G	p.Ser53Trp	p.S53W	ENST00000322652	NM_015355.2	53	tCg/tGg	1/16	0.511440101700778	4	FACETS	1	0.984	1	0.465	0.424	0.508	CLONAL	1	TRUE	1	0.629549157504223	4		614	475	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922157	39922157	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	69	259	0	ENST00000378444.4:c.4015G>C	p.Glu1339Gln	p.E1339Q	ENST00000378444	NM_001123385.1	1339	Gag/Cag	9/15	0.629549157504223	2	FACETS	1	0.969	1			1	CLONAL	1	TRUE	NA	0.629549157504223	2		259	172	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118857	115118857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	85	410	0	ENST00000257566.3:c.484C>T	p.Arg162Cys	p.R162C	ENST00000257566	NM_016569.3	162	Cgt/Tgt	2/8	0.629549157504223	2	FACETS	1	0.939	1	0.534	0.479	0.591	CLONAL	1	TRUE	0	0.629549157504223	2		410	253	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416854	121416854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555210473	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	107	575	0	ENST00000257555.6:c.283G>A	p.Glu95Lys	p.E95K	ENST00000257555		95	Gag/Aag	1/10	0.629549157504223	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.629549157504223	2		575	162	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967237	25967237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	66	466	0	ENST00000435504.4:c.1969C>T	p.Leu657Phe	p.L657F	ENST00000435504		657	Ctt/Ttt	13/13	1	2	FACETS	0.649	0.567	0.736	0.649	0.567	0.736	SUBCLONAL	1	TRUE	1	0.629549157504223	2		466	323	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465510	99465510	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	75	463	0	ENST00000268035.6:c.2335G>C	p.Glu779Gln	p.E779Q	ENST00000268035	NM_000875.3	779	Gag/Cag	11/21	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.629549157504223	2		463	223	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176145127	176145127	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	18	186	0	ENST00000367669.3:c.484C>G	p.Gln162Glu	p.Q162E	ENST00000367669	NM_022457.5	162	Cag/Gag	3/20	0.629549157504223	7	FACETS	0.447	0.336	0.579	0.075	0.056	0.097	SUBCLONAL	1	TRUE	1	0.629549157504223	7		186	329	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22412961	22412961	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	46	169	0	ENST00000344548.3:c.208C>A	p.Leu70Met	p.L70M	ENST00000344548	NM_001039802.1	70	Ctg/Atg	5/7	0.591103432203112	4	FACETS	1	0.915	1	0.556	0.474	0.646	CLONAL	1	TRUE	2	0.629549157504223	4		169	214	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46725641	46725641	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	121	451	0	ENST00000371975.4:c.277C>A	p.Leu93Met	p.L93M	ENST00000371975	NM_003579.3	93	Ctg/Atg	5/18	0.629549157504223	2	FACETS	1	0.95	1	0.529	0.483	0.577	CLONAL	1	TRUE	0	0.629549157504223	2		451	363	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176153810	176153810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	40	166	0	ENST00000367669.3:c.426G>A	p.Met142Ile	p.M142I	ENST00000367669	NM_022457.5	142	atG/atA	2/20	0.629549157504223	7	FACETS	0.971	0.809	1	0.162	0.134	0.192	CLONAL	1	TRUE	1	0.629549157504223	7		166	337	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852225	63852225	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	154	495	0	ENST00000279873.7:c.3003G>T	p.Met1001Ile	p.M1001I	ENST00000279873	NM_032199.2	1001	atG/atT	10/10	0.184488076360919	1	FACETS	0.772	0.714	0.832	0.772	0.714	0.832	INDETERMINATE	1	TRUE	0	0.629549157504223	1		495	434	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377043	118377043	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	74	588	0	ENST00000534358.1:c.10436C>A	p.Ser3479Ter	p.S3479*	ENST00000534358	NM_005933.3	3479	tCa/tAa	27/36	0.629549157504223	3	FACETS	0.829	0.73	0.934	0.414	0.365	0.467	CLONAL	1	TRUE	1	0.629549157504223	3		588	373	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383262	4383262	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	21	542	0	ENST00000261254.3:c.56A>G	p.Asn19Ser	p.N19S	ENST00000261254	NM_001759.3	19	aAc/aGc	1/5	0.629549157504223	4	FACETS	0.392	0.302	0.497	0.098	0.075	0.125	SUBCLONAL	1	TRUE	0	0.629549157504223	4		542	277	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445982	49445982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	289	664	0	ENST00000301067.7:c.1484C>T	p.Ser495Phe	p.S495F	ENST00000301067	NM_003482.3	495	tCt/tTt	10/54	0.629549157504223	5	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	2	0.629549157504223	5		664	551	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15967466	15967466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	139	479	0	ENST00000268712.3:c.5137G>A	p.Glu1713Lys	p.E1713K	ENST00000268712	NM_006311.3	1713	Gag/Aag	35/46	0.511440101700778	4	FACETS	1	0.976	1	0.398	0.364	0.435	CLONAL	1	TRUE	1	0.629549157504223	4		479	602	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684074	29684074	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	81	371	0	ENST00000356175.3:c.7772A>C	p.Asp2591Ala	p.D2591A	ENST00000356175	NM_000267.3	2591	gAt/gCt	52/57	0.511440101700778	4	FACETS	1	0.961	1	0.397	0.352	0.444	CLONAL	1	TRUE	1	0.629549157504223	4		371	352	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881010	37881010	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	115	629	0	ENST00000269571.5:c.2339C>T	p.Pro780Leu	p.P780L	ENST00000269571		780	cCa/cTa	20/27	0.511440101700778	4	FACETS	0.787	0.716	0.861	0.525	0.477	0.574	SUBCLONAL	2	TRUE	1	0.629549157504223	4		629	378	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881019	37881019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	111	622	0	ENST00000269571.5:c.2348C>T	p.Ser783Phe	p.S783F	ENST00000269571		783	tCc/tTc	20/27	0.511440101700778	4	FACETS	0.789	0.717	0.865	0.526	0.478	0.577	SUBCLONAL	2	TRUE	1	0.629549157504223	4		622	364	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244120	41244120	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs80357434	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	81	337	0	ENST00000357654.3:c.3428C>G	p.Ser1143Cys	p.S1143C	ENST00000357654	NM_007294.3	1143	tCt/tGt	10/23	0.511440101700778	4	FACETS	1	0.975	1	0.455	0.405	0.508	CLONAL	1	TRUE	1	0.629549157504223	4		337	307	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926618	59926618	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	53	189	0	ENST00000259008.2:c.380-1G>C		p.X127_splice	ENST00000259008	NM_032043.2	127			0.629549157504223	3	FACETS	1	0.923	1	0.551	0.476	0.63	CLONAL	1	TRUE	1	0.629549157504223	3		189	201	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66521093	66521093	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	34	164	0	ENST00000358598.2:c.543G>C	p.Glu181Asp	p.E181D	ENST00000358598	NM_212471.2	181	gaG/gaC	6/11	0.629549157504223	3	FACETS	0.728	0.601	0.869	0.364	0.3	0.435	SUBCLONAL	1	TRUE	1	0.629549157504223	3		164	195	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254509	10254511	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	91	505	0	ENST00000340748.4:c.2999_3001del	p.Phe1000del	p.F1000del	ENST00000340748		1000	tTCTgt/tgt	28/40	0.629549157504223	3	FACETS	1	0.916	1	0.514	0.459	0.57	CLONAL	1	TRUE	1	0.629549157504223	3		505	370	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170510	11170510	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775433905	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	91	591	0	ENST00000358026.2:c.4813G>A	p.Glu1605Lys	p.E1605K	ENST00000358026	NM_001128849.1	1605	Gag/Aag	34/36	0.629549157504223	3	FACETS	0.987	0.883	1	0.494	0.441	0.549	CLONAL	1	TRUE	1	0.629549157504223	3		591	385	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627832	14627832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	267	736	0	ENST00000254322.2:c.238G>A	p.Gly80Ser	p.G80S	ENST00000254322	NM_006145.1	80	Ggt/Agt	2/3	0.629549157504223	3	FACETS	0.977	0.916	1	0.489	0.458	0.52	CLONAL	1	TRUE	1	0.629549157504223	3		736	1141	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223661	36223661	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	89	762	0	ENST00000222270.7:c.6211G>A	p.Glu2071Lys	p.E2071K	ENST00000222270	NM_014727.1	2071	Gag/Aag	28/37	0.629549157504223	3	FACETS	1	0.913	1	0.512	0.457	0.569	CLONAL	1	TRUE	1	0.629549157504223	3		762	363	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224577	36224577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	79	597	0	ENST00000222270.7:c.7039G>A	p.Glu2347Lys	p.E2347K	ENST00000222270	NM_014727.1	2347	Gaa/Aaa	29/37	0.629549157504223	3	FACETS	0.973	0.863	1	0.487	0.431	0.545	CLONAL	1	TRUE	1	0.629549157504223	3		597	339	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423832	47423832	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	115	502	0	ENST00000404338.3:c.1900G>C	p.Glu634Gln	p.E634Q	ENST00000404338	NM_004491.4	634	Gag/Cag	1/6	0.629549157504223	2	FACETS	1	0.973	1	0.584	0.533	0.636	CLONAL	1	TRUE	0	0.629549157504223	2		502	313	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424324	47424324	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	90	440	0	ENST00000404338.3:c.2392G>C	p.Asp798His	p.D798H	ENST00000404338	NM_004491.4	798	Gac/Cac	1/6	0.629549157504223	2	FACETS	1	0.95	1	0.546	0.491	0.602	CLONAL	1	TRUE	0	0.629549157504223	2		440	262	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505409	25505409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	68	420	0	ENST00000264709.3:c.349G>A	p.Glu117Lys	p.E117K	ENST00000264709	NM_175629.2	117	Gag/Aag	4/23	1	2	FACETS	0.777	0.683	0.877	0.777	0.683	0.877	SUBCLONAL	1	TRUE	1	0.629549157504223	2		420	278	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47643527	47643527	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs63750396	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	77	300	0	ENST00000233146.2:c.1035G>A	p.Trp345Ter	p.W345*	ENST00000233146	NM_000251.2	345	tgG/tgA	6/16	0.629549157504223	3	FACETS	1	0.924	1	0.527	0.467	0.59	CLONAL	1	TRUE	1	0.629549157504223	3		300	305	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027241	48027241	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	64	396	0	ENST00000234420.5:c.2119G>T	p.Glu707Ter	p.E707*	ENST00000234420	NM_000179.2	707	Gaa/Taa	4/10	0.629549157504223	3	FACETS	1	0.935	1	0.552	0.484	0.624	CLONAL	1	TRUE	1	0.629549157504223	3		396	242	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631899	67631899	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	94	401	0	ENST00000272342.5:c.2085G>C	p.Leu695Phe	p.L695F	ENST00000272342	NM_019002.3	695	ttG/ttC	5/6	0.629549157504223	3	FACETS	0.905	0.81	1	0.452	0.405	0.503	CLONAL	1	TRUE	1	0.629549157504223	3		401	434	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198262785	198262785	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	71	293	0	ENST00000335508.6:c.3190G>C	p.Glu1064Gln	p.E1064Q	ENST00000335508	NM_012433.2	1064	Gag/Cag	22/25	0.402469972655219	5	FACETS	0.815	0.72	0.916	0.543	0.48	0.611	CLONAL	2	TRUE	2	0.629549157504223	5		293	269	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342988	225342988	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	89	364	0	ENST00000264414.4:c.2104G>A	p.Glu702Lys	p.E702K	ENST00000264414	NM_003590.4	702	Gag/Aag	15/16	0.569919106853555	3	FACETS	0.879	0.784	0.979	0.439	0.392	0.49	CLONAL	1	TRUE	1	0.629549157504223	3		364	423	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326719	62326719	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs748758593	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	105	644	1	ENST00000360203.5:c.3538A>G	p.Lys1180Glu	p.K1180E	ENST00000360203	NM_001283009.1	1180	Aag/Gag	34/35	0.629549157504223	4	FACETS	1	0.958	1	0.559	0.503	0.618	CLONAL	1	TRUE	2	0.629549157504223	4		645	486	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981753	63981753	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	139	549	0	ENST00000398590.3:c.2255C>T	p.Ser752Phe	p.S752F	ENST00000398590	NM_001177387.1	752	tCt/tTt	12/14	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.629549157504223	2		549	365	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176465	142176465	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	84	296	0	ENST00000350721.4:c.7636C>T	p.Gln2546Ter	p.Q2546*	ENST00000350721	NM_001184.3	2546	Cag/Tag	45/47	0.229959638428889	2	FACETS	0.733	0.652	0.818	0.367	0.326	0.409	INDETERMINATE	1	TRUE	0	0.629549157504223	2		296	364	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807564	1807564	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	28	651	0	ENST00000260795.2:c.1733C>G	p.Ser578Cys	p.S578C	ENST00000260795		578	tCc/tGc	12/17	0.629549157504223	1	FACETS	0.635	0.52	0.758	0.635	0.52	0.758	SUBCLONAL	1	TRUE	0	0.629549157504223	1		651	96	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796702	57796708	+	frameshift_variant	Frame_Shift_Del	DEL	AAGGGTG	AAGGGTG	-	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	15	383	0	ENST00000309042.7:c.1679_1685del	p.Lys560ThrfsTer14	p.K560Tfs*14	ENST00000309042	NM_005612.4	560	AAGGGTGac/ac	4/4	NA	2	FACETS	0.181	0.132	0.24			1	INDETERMINATE	1	TRUE	NA	0.629549157504223	2		383	263	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527271	187527271	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	234	451	0	ENST00000441802.2:c.10303G>C	p.Asp3435His	p.D3435H	ENST00000441802	NM_005245.3	3435	Gac/Cac	17/27	0.629549157504223	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.629549157504223	3		451	451	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295853	1295853	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	25	768	2				ENST00000310581	NM_198253.2	-/1132			0.184488076360919	1	FACETS	0.273	0.217	0.338	0.273	0.217	0.338	INDETERMINATE	1	TRUE	0	0.629549157504223	1		770	199	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950199	38950199	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	97	403	0	ENST00000357387.3:c.3751G>C	p.Asp1251His	p.D1251H	ENST00000357387	NM_152756.3	1251	Gac/Cac	31/38	0.629549157504223	5	FACETS	0.935	0.834	1	0.312	0.278	0.347	CLONAL	1	TRUE	2	0.629549157504223	5		403	641	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056330	26056330	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	157	530	0	ENST00000343677.2:c.327G>C	p.Lys109Asn	p.K109N	ENST00000343677	NM_005319.3	109	aaG/aaC	1/1	0.629549157504223	7	FACETS	1	0.984	1	0.218	0.199	0.238	CLONAL	1	TRUE	1	0.629549157504223	7		530	980	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672225	30672225	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1247684520	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	117	580	0	ENST00000376406.3:c.4735C>A	p.Gln1579Lys	p.Q1579K	ENST00000376406	NM_014641.2	1579	Cag/Aag	10/15	0.629549157504223	7	FACETS	1	0.976	1	0.21	0.189	0.232	CLONAL	1	TRUE	1	0.629549157504223	7		580	760	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322273	31322273	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	54	303	0	ENST00000412585.2:c.1076C>G	p.Ser359Cys	p.S359C	ENST00000412585	NM_005514.6	359	tCt/tGt	7/8	0.603563561856758	3	FACETS	0.944	0.815	1	0.315	0.271	0.361	CLONAL	1	TRUE	0	0.629549157504223	3		303	239	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651988	36651989	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	523	526	0	ENST00000244741.5:c.112dup	p.Met38AsnfsTer10	p.M38Nfs*10	ENST00000244741	NM_000389.4	37	cta/ctAa	2/3	0.629549157504223	6	FACETS	1	0.995	1	0.909	0.885	0.932	CLONAL	5	TRUE	0	0.629549157504223	6		526	688	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547315	106547315	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	256	425	0	ENST00000369096.4:c.552C>G	p.Phe184Leu	p.F184L	ENST00000369096	NM_001198.3	184	ttC/ttG	4/7	0.629549157504223	2	FACETS	1	0.989	1	0.598	0.563	0.633	CLONAL	1	TRUE	0	0.629549157504223	2		425	680	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729904	41729904	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	65	501	0	ENST00000242208.4:c.625A>G	p.Lys209Glu	p.K209E	ENST00000242208	NM_002192.2	209	Aaa/Gaa	3/3	0.231409119855151	3	FACETS	0.714	0.622	0.813	0.238	0.207	0.271	INDETERMINATE	1	TRUE	0	0.629549157504223	3		501	380	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124503620	124503620	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	74	399	0	ENST00000357628.3:c.330G>C	p.Leu110Phe	p.L110F	ENST00000357628	NM_015450.2	110	ttG/ttC	8/19	0.629549157504223	3	FACETS	0.925	0.816	1	0.463	0.408	0.521	CLONAL	1	TRUE	1	0.629549157504223	3		399	334	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862913	117862913	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs199878247	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	20	189	0	ENST00000297338.2:c.1564C>G	p.Leu522Val	p.L522V	ENST00000297338	NM_006265.2	522	Ctg/Gtg	12/14	0.481279141564945	5	FACETS	0.792	0.61	1	0.264	0.203	0.334	CLONAL	1	TRUE	2	0.629549157504223	5		189	156	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922867	39922867	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	48	196	0	ENST00000378444.4:c.3841G>C	p.Glu1281Gln	p.E1281Q	ENST00000378444	NM_001123385.1	1281	Gaa/Caa	8/15	0.629549157504223	2	FACETS	1	0.957	1			1	CLONAL	1	TRUE	NA	0.629549157504223	2		196	120	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410858	63410858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	32	263	0	ENST00000330258.3:c.2309C>T	p.Ser770Leu	p.S770L	ENST00000330258	NM_152424.3	770	tCa/tTa	2/2	1	1	FACETS	0.774	0.648	0.907	0.774	0.648	0.907	CLONAL	1	TRUE	0	0.629549157504223	1		263	90	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	222	447	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.298397472235073	2	FACETS	0.85	0.794	0.907	0.85	0.794	0.907	CLONAL	2	TRUE	0	0.355296153508226	2		447	735	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	165	612	0				ENST00000310581	NM_198253.2	-/1132			0.24045926025271	5	FACETS	1	0.976	1	0.762	0.702	0.823	CLONAL	2	TRUE	2	0.355296153508226	5		612	623	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344736	65344736	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	237	543	0	ENST00000342505.4:c.301A>T	p.Met101Leu	p.M101L	ENST00000342505	NM_002227.2	101	Atg/Ttg	4/25	0.355296153508226	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.355296153508226	3		543	716	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162722922	162722922	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	147	585	0	ENST00000367921.3:c.120G>T	p.Gln40His	p.Q40H	ENST00000367921	NM_006182.2	40	caG/caT	4/18	0.355296153508226	5	FACETS	1	0.985	1	0.346	0.315	0.378	CLONAL	1	TRUE	1	0.355296153508226	5		585	917	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980415	201980416	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	183	621	0	ENST00000359651.3:c.152_153dup	p.Glu52TrpfsTer104	p.E52Wfs*104	ENST00000359651		51	ttg/tTGtg	1/8	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.355296153508226	2		621	737	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809238	243809238	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	172	380	0	ENST00000263826.5:c.386G>T	p.Gly129Val	p.G129V	ENST00000263826	NM_005465.4	129	gGa/gTa	4/13	0.355296153508226	4	FACETS	0.859	0.797	0.923	1	0.987	1	CLONAL	3	TRUE	2	0.355296153508226	4		380	509	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608311	43608311	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	70	970	0	ENST00000355710.3:c.1659G>C	p.Arg553Ser	p.R553S	ENST00000355710	NM_020975.4	553	agG/agC	9/20	0.25566588836167	3	FACETS	0.398	0.346	0.455	0.199	0.173	0.228	SUBCLONAL	1	TRUE	1	0.355296153508226	3		970	1165	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332790	70332790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545216411	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	126	468	0	ENST00000373644.4:c.695C>T	p.Thr232Ile	p.T232I	ENST00000373644	NM_030625.2	232	aCa/aTa	2/12	0.25566588836167	3	FACETS	1	0.978	1	0.632	0.573	0.693	CLONAL	1	TRUE	1	0.355296153508226	3		468	661	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514068	69514068	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	150	618	0	ENST00000294312.3:c.613G>T	p.Gly205Ter	p.G205*	ENST00000294312	NM_005117.2	205	Gga/Tga	3/3	0.192218203465583	4	FACETS	1	0.988	1	0.747	0.683	0.813	INDETERMINATE	1	TRUE	2	0.355296153508226	4		618	766	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936113	71936113	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	157	531	0	ENST00000298229.2:c.85G>C	p.Ala29Pro	p.A29P	ENST00000298229	NM_001567.3	29	Gcg/Ccg	1/28	0.192218203465583	4	FACETS	0.951	0.874	1	0.951	0.874	1	INDETERMINATE	2	TRUE	2	0.355296153508226	4		531	630	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119741	108119741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622650	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	89	272	0	ENST00000278616.4:c.1147C>T	p.Pro383Ser	p.P383S	ENST00000278616	NM_000051.3	383	Cct/Tct	9/63	0.192218203465583	4	FACETS	0.784	0.699	0.874	0.784	0.699	0.874	INDETERMINATE	2	TRUE	2	0.355296153508226	4		272	433	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440420	49440420	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	211	684	0	ENST00000301067.7:c.4390G>T	p.Val1464Phe	p.V1464F	ENST00000301067	NM_003482.3	1464	Gtc/Ttc	15/54	0.172603922116818	5	FACETS	0.96	0.892	1	0.64	0.595	0.687	INDETERMINATE	2	TRUE	2	0.355296153508226	5		684	948	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444172	49444172	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	226	769	0	ENST00000301067.7:c.3199G>A	p.Glu1067Lys	p.E1067K	ENST00000301067	NM_003482.3	1067	Gag/Aag	11/54	0.172603922116818	5	FACETS	1	0.953	1	0.685	0.638	0.733	INDETERMINATE	2	TRUE	2	0.355296153508226	5		769	949	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856313	111856313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747913408	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	30	590	1	ENST00000341259.2:c.364G>A	p.Glu122Lys	p.E122K	ENST00000341259	NM_005475.2	122	Gag/Aag	2/8	0.321810573078788	3	FACETS	0.395	0.318	0.484	0.198	0.159	0.242	SUBCLONAL	1	TRUE	1	0.355296153508226	3		591	503	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212510	133212510	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	99	487	0	ENST00000320574.5:c.5779G>T	p.Gly1927Ter	p.G1927*	ENST00000320574	NM_006231.2	1927	Gga/Tga	42/49	0.321810573078788	3	FACETS	1	0.901	1	0.504	0.45	0.561	CLONAL	1	TRUE	1	0.355296153508226	3		487	651	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636140	28636140	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	246	564	0	ENST00000241453.7:c.232G>T	p.Ala78Ser	p.A78S	ENST00000241453	NM_004119.2	78	Gct/Tct	3/24	0.346553663310344	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.355296153508226	2		564	666	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436045	110436045	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	374	741	0	ENST00000375856.3:c.2356G>C	p.Ala786Pro	p.A786P	ENST00000375856	NM_003749.2	786	Gca/Cca	1/2	0.335544790455983	3	FACETS	0.882	0.84	0.924	0.882	0.84	0.924	CLONAL	3	TRUE	0	0.355296153508226	3		741	937	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609750	81609750	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	262	730	0	ENST00000298171.2:c.1348C>A	p.Arg450Ser	p.R450S	ENST00000298171	NM_000369.2	450	Cgc/Agc	10/10	0.321810573078788	3	FACETS	0.946	0.888	1	0.946	0.888	1	CLONAL	2	TRUE	1	0.355296153508226	3		730	918	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423546	88423546	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	184	517	0	ENST00000360948.2:c.2289C>G	p.Ile763Met	p.I763M	ENST00000360948	NM_001012338.2	763	atC/atG	18/19	0.346553663310344	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	0	0.355296153508226	2		517	516	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472538	88472538	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	193	604	0	ENST00000360948.2:c.2017C>A	p.Gln673Lys	p.Q673K	ENST00000360948	NM_001012338.2	673	Cag/Aag	16/19	0.346553663310344	2	FACETS	0.846	0.786	0.907	0.846	0.786	0.907	CLONAL	2	TRUE	0	0.355296153508226	2		604	642	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341227	341227	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1362608628	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	95	472	0	ENST00000262320.3:c.2257G>T	p.Val753Leu	p.V753L	ENST00000262320	NM_003502.3	753	Gta/Tta	9/11	0.25566588836167	3	FACETS	1	0.931	1	0.529	0.472	0.59	CLONAL	1	TRUE	1	0.355296153508226	3		472	595	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639677	3639677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs778781581	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	134	864	0	ENST00000294008.3:c.3962C>G	p.Pro1321Arg	p.P1321R	ENST00000294008	NM_032444.2	1321	cCg/cGg	12/15	0.25566588836167	3	FACETS	0.893	0.81	0.98	0.446	0.405	0.49	CLONAL	1	TRUE	1	0.355296153508226	3		864	995	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943772	9943772	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	108	632	0	ENST00000330684.3:c.1169G>T	p.Trp390Leu	p.W390L	ENST00000330684	NM_001134407.1	390	tGg/tTg	5/13	0.25566588836167	3	FACETS	0.894	0.802	0.991	0.447	0.401	0.496	CLONAL	1	TRUE	1	0.355296153508226	3		632	801	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552174	29552174	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs780412565	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	88	427	0	ENST00000356175.3:c.1907C>G	p.Ser636Cys	p.S636C	ENST00000356175	NM_000267.3	636	tCt/tGt	17/57	0.172603922116818	5	FACETS	0.836	0.744	0.934	0.558	0.496	0.623	INDETERMINATE	2	TRUE	2	0.355296153508226	5		427	454	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690784	33690784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774335910	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	158	563	0	ENST00000308377.4:c.43C>T	p.Pro15Ser	p.P15S	ENST00000308377	NM_152270.3	15	Cca/Tca	2/5	0.172603922116818	5	FACETS	0.953	0.876	1	0.636	0.584	0.69	INDETERMINATE	2	TRUE	2	0.355296153508226	5		563	715	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602504	10602504	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	228	732	0	ENST00000171111.5:c.1074del	p.Gln359ArgfsTer41	p.Q359Rfs*41	ENST00000171111	NM_203500.1	358	ctG/ct	3/6	0.32610164560023	2	FACETS	0.894	0.836	0.952	0.894	0.836	0.952	CLONAL	2	TRUE	0	0.355296153508226	2		732	718	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292495	15292495	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144732188	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	250	734	0	ENST00000263388.2:c.2684C>T	p.Pro895Leu	p.P895L	ENST00000263388	NM_000435.2	895	cCc/cTc	17/33	0.32610164560023	2	FACETS	0.96	0.902	1	0.96	0.902	1	CLONAL	2	TRUE	0	0.355296153508226	2		734	733	SUCCESS
ALK	238	MSKCC	GRCh37	2	29448414	29448414	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	304	882	0	ENST00000389048.3:c.3085C>A	p.Pro1029Thr	p.P1029T	ENST00000389048	NM_004304.4	1029	Cca/Aca	19/29	0.172603922116818	5	FACETS	1	0.976	1	0.71	0.669	0.753	INDETERMINATE	2	TRUE	2	0.355296153508226	5		882	1231	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873267	136873267	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	218	670	0	ENST00000241393.3:c.231G>T	p.Arg77Ser	p.R77S	ENST00000241393	NM_003467.2	77	agG/agT	2/2	0.172603922116818	5	FACETS	1	0.945	1	0.678	0.631	0.726	INDETERMINATE	2	TRUE	2	0.355296153508226	5		670	925	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739075	40739075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	167	518	0	ENST00000373198.4:c.3209C>T	p.Pro1070Leu	p.P1070L	ENST00000373198	NM_133170.3	1070	cCt/cTt	24/32	0.192218203465583	4	FACETS	0.904	0.833	0.977	0.904	0.833	0.977	INDETERMINATE	2	TRUE	2	0.355296153508226	4		518	705	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573999	41573999	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	40	697	0	ENST00000263253.7:c.6284C>G	p.Ser2095Cys	p.S2095C	ENST00000263253	NM_001429.3	2095	tCt/tGt	31/31	0.331330717374102	3	FACETS	0.34	0.282	0.406	0.113	0.094	0.136	SUBCLONAL	1	TRUE	0	0.355296153508226	3		697	779	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169999684	169999684	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	78	199	0	ENST00000295797.4:c.995T>A	p.Ile332Lys	p.I332K	ENST00000295797	NM_002740.5	332	aTa/aAa	11/18	0.172603922116818	5	FACETS	1	0.95	1	0.753	0.668	0.842	INDETERMINATE	2	TRUE	2	0.355296153508226	5		199	298	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170020899	170020899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	30	63	0	ENST00000295797.4:c.1775C>T	p.Ala592Val	p.A592V	ENST00000295797	NM_002740.5	592	gCa/gTa	18/18	0.172603922116818	5	FACETS	1	0.835	1	0.679	0.557	0.813	INDETERMINATE	2	TRUE	2	0.355296153508226	5		63	127	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955231	1955231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	184	589	0	ENST00000382891.5:c.2318C>T	p.Ser773Leu	p.S773L	ENST00000382891	NM_133335.3	773	tCa/tTa	12/22	0.172603922116818	5	FACETS	0.983	0.908	1	0.655	0.605	0.706	INDETERMINATE	2	TRUE	2	0.355296153508226	5		589	808	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955054	55955054	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	165	443	0	ENST00000263923.4:c.3491T>A	p.Leu1164Ter	p.L1164*	ENST00000263923	NM_002253.2	1164	tTg/tAg	26/30	0.298397472235073	2	FACETS	0.914	0.846	0.984	0.914	0.846	0.984	CLONAL	2	TRUE	0	0.355296153508226	2		443	508	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875673	35875673	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	201	367	0	ENST00000303115.3:c.860G>T	p.Cys287Phe	p.C287F	ENST00000303115	NM_002185.3	287	tGt/tTt	7/8	0.355296153508226	5	FACETS	0.865	0.806	0.927	0.865	0.806	0.927	CLONAL	3	TRUE	2	0.355296153508226	5		367	668	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401502	401502	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	366	592	0	ENST00000380956.4:c.824G>T	p.Arg275Leu	p.R275L	ENST00000380956	NM_001195286.1	275	cGg/cTg	7/9	0.311256737202981	3	FACETS	1	0.987	1			1	CLONAL	3	TRUE	NA	0.355296153508226	3		592	749	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190423	32190423	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs140979766	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	405	815	0	ENST00000375023.3:c.316C>A	p.Leu106Ile	p.L106I	ENST00000375023	NM_004557.3	106	Ctc/Atc	3/30	0.355296153508226	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	0	0.355296153508226	3		815	873	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64286793	64286793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	91	360	0	ENST00000370651.3:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000370651	NM_003463.4	3	cGa/cAa	2/6	0.321810573078788	3	FACETS	1	0.98	1	0.741	0.662	0.824	CLONAL	1	TRUE	1	0.355296153508226	3		360	407	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462507	92462507	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	182	552	0	ENST00000265734.4:c.131G>T	p.Arg44Leu	p.R44L	ENST00000265734	NM_001259.6	44	cGc/cTc	2/8	0.346553663310344	2	FACETS	0.918	0.853	0.985	0.918	0.853	0.985	CLONAL	2	TRUE	0	0.355296153508226	2		552	558	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930139	68930139	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	65	458	0	ENST00000288368.4:c.200A>G	p.Glu67Gly	p.E67G	ENST00000288368	NM_024870.2	67	gAa/gGa	2/40	1	2	FACETS	0.869	0.756	0.991	0.869	0.756	0.991	CLONAL	1	TRUE	1	0.355296153508226	2		458	421	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741824	145741824	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	459	692	0	ENST00000428558.2:c.679G>C	p.Val227Leu	p.V227L	ENST00000428558	NM_004260.3	227	Gtc/Ctc	5/22	0.355296153508226	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	1	0.355296153508226	4		692	1004	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971056	21971056	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	233	686	0	ENST00000304494.5:c.302G>T	p.Gly101Val	p.G101V	ENST00000304494	NM_000077.4	101	gGg/gTg	2/3	0.318495404643802	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.355296153508226	2		686	651	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206623	27206623	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	174	446	1	ENST00000380036.4:c.2408T>A	p.Leu803Gln	p.L803Q	ENST00000380036	NM_000459.3	803	cTa/cAa	15/23	0.318495404643802	2	FACETS	0.993	0.922	1	0.993	0.922	1	CLONAL	2	TRUE	0	0.355296153508226	2		447	493	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922253	39922253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769942209	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	179	513	0	ENST00000378444.4:c.3919G>T	p.Ala1307Ser	p.A1307S	ENST00000378444	NM_001123385.1	1307	Gct/Tct	9/15	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.355296153508226	2		513	706	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931691	39931691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	104	522	0	ENST00000378444.4:c.2908G>A	p.Ala970Thr	p.A970T	ENST00000378444	NM_001123385.1	970	Gcg/Acg	4/15	1	2	FACETS	0.869	0.779	0.964	0.869	0.779	0.964	CLONAL	1	TRUE	1	0.355296153508226	2		522	674	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611108	100611108	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	203	589	0	ENST00000308731.7:c.1498G>T	p.Glu500Ter	p.E500*	ENST00000308731	NM_000061.2	500	Gag/Tag	15/19	0.318495404643802	2	FACETS	0.989	0.923	1	0.989	0.923	1	CLONAL	2	TRUE	0	0.355296153508226	2		589	578	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444307	49444307	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	AA	novel	NA	P-0064661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	262	788	0	ENST00000301067.7:c.3064delinsTT	p.Pro1022PhefsTer46	p.P1022Ffs*46	ENST00000301067	NM_003482.3	1022	Cct/TTct	11/54	0.172603922116818	5	FACETS	1	0.976	1	0.72	0.675	0.766	INDETERMINATE	2	TRUE	2	0.355296153508226	5		788	1047	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0064662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	15	287	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.476	0.346	0.633	0.476	0.346	0.633	SUBCLONAL	1	TRUE	1	0.13	2		287	485	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0064671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	123	372	0				ENST00000310581	NM_198253.2	-/1132			0.392883305813766	3	FACETS	0.925	0.844	1	0.925	0.844	1	CLONAL	2	TRUE	1	0.392883305813766	3		372	405	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534467	187534467	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375998390	NA	P-0064671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	105	571	0	ENST00000441802.2:c.9259C>T	p.Arg3087Cys	p.R3087C	ENST00000441802	NM_005245.3	3087	Cgt/Tgt	13/27	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.392883305813766	2		571	457	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920685	100920685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	70	310	2	ENST00000325455.5:c.2463G>A	p.Met821Ile	p.M821I	ENST00000325455	NM_001202474.3	821	atG/atA	6/8	0.392883305813766	3	FACETS	1	0.878	1	0.502	0.439	0.569	CLONAL	1	TRUE	1	0.392883305813766	3		312	425	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259646	89259646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	36	484	0	ENST00000336596.2:c.790G>A	p.Glu264Lys	p.E264K	ENST00000336596	NM_005233.5	264	Gaa/Aaa	3/17	0.327304389746398	4	FACETS	0.387	0.317	0.466	0.194	0.158	0.233	SUBCLONAL	1	TRUE	2	0.392883305813766	4		484	659	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148875	119148876	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0064671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	38	250	0	ENST00000264033.4:c.1096-1_1096delinsAA		p.X366_splice	ENST00000264033	NM_005188.3	366		8/16	0.392883305813766	1	FACETS	0.814	0.68	0.959	0.814	0.68	0.959	CLONAL	1	TRUE	0	0.392883305813766	1		250	191	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106519967	106519967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	89	297	0	ENST00000359195.3:c.2395G>A	p.Glu799Lys	p.E799K	ENST00000359195	NM_002649.2	799	Gaa/Aaa	6/11	0.392883305813766	5	FACETS	1	0.977	1	0.352	0.312	0.393	CLONAL	1	TRUE	1	0.392883305813766	5		297	512	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426678	212426678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	120	601	0	ENST00000342788.4:c.2437G>A	p.Asp813Asn	p.D813N	ENST00000342788	NM_005235.2	813	Gat/Aat	20/28	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.392883305813766	2		601	574	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009279	69009279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	141	374	0	ENST00000288368.4:c.2396C>T	p.Ala799Val	p.A799V	ENST00000288368	NM_024870.2	799	gCc/gTc	22/40	0.392883305813766	3	FACETS	0.862	0.791	0.936	0.862	0.791	0.936	CLONAL	2	TRUE	1	0.392883305813766	3		374	498	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864641	56864641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	111	395	0	ENST00000519728.1:c.604C>T	p.Pro202Ser	p.P202S	ENST00000519728	NM_002350.3	202	Ccc/Tcc	7/13	0.392883305813766	3	FACETS	1	0.978	1	0.655	0.591	0.722	CLONAL	1	TRUE	1	0.392883305813766	3		395	516	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249016	55249016	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	55	704	0	ENST00000275493.2:c.2314C>T	p.Pro772Ser	p.P772S	ENST00000275493	NM_005228.3	772	Ccc/Tcc	20/28	0.392883305813766	5	FACETS	0.601	0.513	0.698	0.15	0.128	0.175	SUBCLONAL	1	TRUE	1	0.392883305813766	5		704	740	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857920	9857920	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	216	718	1	ENST00000330684.3:c.3481G>A	p.Gly1161Arg	p.G1161R	ENST00000330684	NM_001134407.1	1161	Ggg/Agg	13/13	0.327304389746398	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.392883305813766	4		719	738	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995547	68995547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	133	378	0	ENST00000288368.4:c.1951G>A	p.Glu651Lys	p.E651K	ENST00000288368	NM_024870.2	651	Gaa/Aaa	18/40	0.392883305813766	3	FACETS	0.757	0.691	0.826	0.757	0.691	0.826	SUBCLONAL	2	TRUE	1	0.392883305813766	3		378	535	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429373	47429373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	169	894	1	ENST00000377045.4:c.1501G>A	p.Glu501Lys	p.E501K	ENST00000377045	NM_001654.4	501	Gag/Aag	14/16	0.20866756628013	4	FACETS	0.992	0.916	1	0.992	0.916	1	INDETERMINATE	2	TRUE	2	0.392883305813766	4		895	604	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	459825	459826	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0064671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	102	519	0	ENST00000399788.2:c.1269_1270delinsAA	p.Val424Met	p.V424M	ENST00000399788	NM_001042603.1	423	ccGGtg/ccAAtg	10/28	0.380509360880446	3	FACETS	1	0.947	1	0.544	0.488	0.604	CLONAL	1	TRUE	1	0.392883305813766	3		519	571	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134214	41134214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757179771	NA	P-0064671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	210	681	0	ENST00000379561.5:c.1414C>T	p.Pro472Ser	p.P472S	ENST00000379561	NM_002015.3	472	Ccc/Tcc	2/3	0.392883305813766	3	FACETS	0.953	0.889	1	0.953	0.889	1	CLONAL	2	TRUE	1	0.392883305813766	3		681	671	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81563018	81563018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	210	523	2	ENST00000298171.2:c.581G>A	p.Gly194Glu	p.G194E	ENST00000298171	NM_000369.2	194	gGa/gAa	7/10	0.392883305813766	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.392883305813766	3		525	607	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822430	72822430	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	253	935	0	ENST00000268489.5:c.9745G>A	p.Gly3249Arg	p.G3249R	ENST00000268489	NM_006885.3	3249	Ggg/Agg	10/10	0.327304389746398	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	2	0.392883305813766	4		935	870	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992897	72992897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757081224	NA	P-0064671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	178	660	0	ENST00000268489.5:c.1148C>T	p.Ser383Phe	p.S383F	ENST00000268489	NM_006885.3	383	tCc/tTc	2/10	0.327304389746398	4	FACETS	0.994	0.92	1	0.994	0.92	1	CLONAL	2	TRUE	2	0.392883305813766	4		660	635	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557336	29557336	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	279	357	1	ENST00000356175.3:c.3049C>T	p.Gln1017Ter	p.Q1017*	ENST00000356175	NM_000267.3	1017	Caa/Taa	23/57	0.392883305813766	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	4	TRUE	0	0.392883305813766	4		358	465	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4123801	4123802	+	missense_variant	Missense_Mutation	DNP	AG	AG	GA	novel	NA	P-0064671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	123	571	0	ENST00000262948.5:c.71_72delinsTC	p.Pro24Leu	p.P24L	ENST00000262948	NM_030662.3	24	cCT/cTC	1/11	0.20866756628013	4	FACETS	0.808	0.733	0.885	0.808	0.733	0.885	INDETERMINATE	2	TRUE	2	0.392883305813766	4		571	540	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793069	42793069	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	183	635	0	ENST00000575354.2:c.961C>T	p.Gln321Ter	p.Q321*	ENST00000575354	NM_015125.3	321	Cag/Tag	7/20	0.20866756628013	4	FACETS	1	0.953	1	1	0.953	1	INDETERMINATE	2	TRUE	2	0.392883305813766	4		635	626	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940154	49940155	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0064671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	208	785	0	ENST00000296474.3:c.888_889delinsAA	p.Val297Ile	p.V297I	ENST00000296474	NM_002447.2	296	ctGGtc/ctAAtc	1/20	0.380509360880446	3	FACETS	0.976	0.911	1	0.976	0.911	1	CLONAL	2	TRUE	1	0.392883305813766	3		785	649	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259649	89259649	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	35	472	0	ENST00000336596.2:c.793G>C	p.Glu265Gln	p.E265Q	ENST00000336596	NM_005233.5	265	Gaa/Caa	3/17	0.327304389746398	4	FACETS	0.382	0.312	0.461	0.191	0.156	0.231	SUBCLONAL	1	TRUE	2	0.392883305813766	4		472	649	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149290788	149290788	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0064671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	159	359	0	ENST00000360632.3:c.432-1G>A		p.X144_splice	ENST00000360632	NM_015472.4	144			0.327304389746398	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.392883305813766	4		359	511	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517815	187517816	+	missense_variant	Missense_Mutation	DNP	GT	GT	AA	novel	NA	P-0064671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	99	677	1	ENST00000441802.2:c.12878_12879delinsTT	p.His4293Leu	p.H4293L	ENST00000441802	NM_005245.3	4293	cAC/cTT	25/27	1	2	FACETS	0.953	0.853	1	0.953	0.853	1	CLONAL	1	TRUE	1	0.392883305813766	2		678	529	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79968671	79968671	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1580552356	NA	P-0064671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	161	377	0	ENST00000265081.6:c.1021G>A	p.Gly341Arg	p.G341R	ENST00000265081	NM_002439.4	341	Gga/Aga	6/24	0.327304389746398	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	2	0.392883305813766	4		377	537	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26046042	26046042	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1296022073	NA	P-0064671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	190	592	0	ENST00000540144.1:c.404G>A	p.Arg135Lys	p.R135K	ENST00000540144	NM_003531.2	135	aGg/aAg	1/1	0.392883305813766	5	FACETS	0.891	0.824	0.959	0.594	0.549	0.64	CLONAL	2	TRUE	2	0.392883305813766	5		592	863	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100137	157100137	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0064671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	90	710	0	ENST00000346085.5:c.1074T>A	p.Tyr358Ter	p.Y358*	ENST00000346085	NM_020732.3	358	taT/taA	1/20	0.392883305813766	3	FACETS	0.975	0.867	1	0.488	0.433	0.545	CLONAL	1	TRUE	1	0.392883305813766	3		710	562	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033161	69033161	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	145	361	2	ENST00000288368.4:c.3601C>T	p.Gln1201Ter	p.Q1201*	ENST00000288368	NM_024870.2	1201	Caa/Taa	30/40	0.392883305813766	3	FACETS	0.979	0.901	1	0.979	0.901	1	CLONAL	2	TRUE	1	0.392883305813766	3		363	451	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028799	47028813	+	inframe_deletion	In_Frame_Del	DEL	GACTACCGGGACATG	GACTACCGGGACATG	-	novel	NA	P-0064671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	159	675	0	ENST00000377604.3:c.111_125del	p.Asp38_Arg42del	p.D38_R42del	ENST00000377604	NM_001204468.1	35	GACTACCGGGACATG/-	3/24	0.20866756628013	4	FACETS	0.969	0.892	1	0.969	0.892	1	INDETERMINATE	2	TRUE	2	0.392883305813766	4		675	582	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123159758	123159758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	86	311	0	ENST00000218089.9:c.113G>A	p.Gly38Asp	p.G38D	ENST00000218089	NM_001042749.1	38	gGc/gAc	4/35	0.20866756628013	4	FACETS	0.78	0.694	0.87	0.78	0.694	0.87	INDETERMINATE	2	TRUE	2	0.392883305813766	4		311	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780071	NA	P-0064673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	79	849	0	ENST00000269305.4:c.580C>T	p.Leu194Phe	p.L194F	ENST00000269305	NM_001126112.2	194	Ctt/Ttt	6/11	1	2	FACETS	0.955	0.839	1	0.955	0.839	1	CLONAL	1	FALSE	1	0.220325872533922	2		849	751	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319959	8319959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745582718	NA	P-0064673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	62	520	0	ENST00000356435.5:c.5542G>A	p.Val1848Ile	p.V1848I	ENST00000356435		1848	Gtt/Att	34/35	0.144084117449868	0	FACETS	0.766	0.662	0.879			1	SUBCLONAL	1	FALSE	0	0.220325872533922	0		520	573	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396860	139396860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368396893	NA	P-0064673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	48	644	0	ENST00000277541.6:c.5248G>A	p.Val1750Met	p.V1750M	ENST00000277541	NM_017617.3	1750	Gtg/Atg	28/34	1	2	FACETS	0.723	0.61	0.847	0.723	0.61	0.847	SUBCLONAL	1	FALSE	1	0.220325872533922	2		644	603	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112370	115112370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371891930	NA	P-0064673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	51	808	0	ENST00000257566.3:c.1370C>T	p.Pro457Leu	p.P457L	ENST00000257566	NM_016569.3	457	cCg/cTg	7/8	1	2	FACETS	0.79	0.671	0.921	0.79	0.671	0.921	CLONAL	1	FALSE	1	0.220325872533922	2		808	586	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099346	27099347	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0064673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	60	619	0	ENST00000324856.7:c.3585_3586dup	p.Asp1196ValfsTer11	p.D1196Vfs*11	ENST00000324856	NM_006015.4	1195	agt/aGTgt	14/20	1	2	FACETS	0.894	0.77	1	0.894	0.77	1	CLONAL	1	FALSE	1	0.220325872533922	2		619	609	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21652500	21652500	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs566339459	NA	P-0064673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	13	211	0	ENST00000421138.2:c.5C>T	p.Ala2Val	p.A2V	ENST00000421138		2	gCg/gTg	3/16	1	2	FACETS	0.461	0.328	0.623	0.461	0.328	0.623	SUBCLONAL	1	FALSE	1	0.220325872533922	2		211	256	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436570	110436570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	57	859	0	ENST00000375856.3:c.1831C>T	p.Arg611Cys	p.R611C	ENST00000375856	NM_003749.2	611	Cgc/Tgc	1/2	1	2	FACETS	0.839	0.719	0.969	0.839	0.719	0.969	CLONAL	1	FALSE	1	0.220325872533922	2		859	617	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682397	52682397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	28	343	0	ENST00000394830.3:c.776C>T	p.Ala259Val	p.A259V	ENST00000394830	NM_018313.4	259	gCc/gTc	8/30	1	2	FACETS	0.507	0.405	0.625	0.507	0.405	0.625	SUBCLONAL	1	FALSE	1	0.220325872533922	2		343	501	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971039	+	frameshift_variant	Frame_Shift_Del	DEL	CGCG	CGCG	-	novel	NA	P-0064673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	55	789	0	ENST00000304494.5:c.319_322del	p.Arg107MetfsTer38	p.R107Mfs*38	ENST00000304494	NM_000077.4	107	CGCGat/at	2/3	0.144084117449868	0	FACETS	0.623	0.532	0.722			1	SUBCLONAL	1	FALSE	0	0.220325872533922	0		789	625	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135777047	135777047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397514814	NA	P-0064673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	41	484	0	ENST00000298552.3:c.2431C>T	p.Arg811Trp	p.R811W	ENST00000298552	NM_001162426.1	811	Cgg/Tgg	19/23	1	2	FACETS	0.689	0.573	0.818	0.689	0.573	0.818	SUBCLONAL	1	FALSE	1	0.220325872533922	2		484	540	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0064674-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	44	282	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.399312697191086	6	FACETS	1	0.897	1	0.271	0.228	0.319	CLONAL	1	TRUE	2	0.540614699331943	6		282	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0064674-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	460	1119	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.540614699331943	4	FACETS	0.918	0.895	0.94	1	0.996	1	CLONAL	5	TRUE	0	0.540614699331943	4		1119	571	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0064674-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	127	551	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.166101293881947	4	FACETS	1	0.979	1	1	0.979	1	INDETERMINATE	2	TRUE	2	0.540614699331943	4		552	302	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0064675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	45	305	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.465693778660866	2	FACETS	0.732	0.621	0.853	0.366	0.31	0.427	SUBCLONAL	1	TRUE	0	0.525194970062678	2		305	234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0064675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	289	374	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.436572246071012	2	FACETS	0.919	0.872	0.965	0.919	0.872	0.965	CLONAL	2	TRUE	0	0.525194970062678	2		374	599	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680489	241680489	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200007371	NA	P-0064675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	59	467	0	ENST00000366560.3:c.260G>A	p.Arg87His	p.R87H	ENST00000366560	NM_000143.3	87	cGc/cAc	2/10	0.426844423655329	3	FACETS	0.589	0.507	0.677	0.294	0.253	0.339	SUBCLONAL	1	TRUE	1	0.525194970062678	3		467	482	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846354	156846354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772229945	NA	P-0064675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	109	778	0	ENST00000524377.1:c.1795C>T	p.Arg599Cys	p.R599C	ENST00000524377	NM_002529.3	599	Cgc/Tgc	14/17	0.426844423655329	3	FACETS	0.836	0.752	0.924	0.418	0.376	0.462	CLONAL	1	TRUE	1	0.525194970062678	3		778	627	SUCCESS
APC	324	MSKCC	GRCh37	5	112174916	112174916	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	95	524	0	ENST00000257430.4:c.3625G>T	p.Glu1209Ter	p.E1209*	ENST00000257430	NM_000038.5	1209	Gaa/Taa	16/16	1	2	FACETS	0.841	0.753	0.934	0.841	0.753	0.934	CLONAL	1	TRUE	1	0.525194970062678	2		524	430	SUCCESS
AR	367	MSKCC	GRCh37	X	66863154	66863154	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	47	320	0	ENST00000374690.3:c.1673A>G	p.Lys558Arg	p.K558R	ENST00000374690	NM_000044.3	558	aAg/aGg	2/8	0.526852897086772	2	FACETS	0.421	0.356	0.493			1	SUBCLONAL	1	TRUE	NA	0.525194970062678	2		320	425	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245928	5245928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747508744	NA	P-0064675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	65	928	0	ENST00000357368.4:c.847G>A	p.Glu283Lys	p.E283K	ENST00000357368	NM_002850.3	283	Gag/Aag	10/38	0.526852897086772	3	FACETS	0.477	0.413	0.546	0.239	0.206	0.273	SUBCLONAL	1	TRUE	1	0.525194970062678	3		928	655	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911505	134911505	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	132	750	0	ENST00000398015.3:c.1970A>T	p.Tyr657Phe	p.Y657F	ENST00000398015	NM_004441.4	657	tAc/tTc	11/16	0.465693778660866	2	FACETS	0.882	0.804	0.963	0.441	0.402	0.482	CLONAL	1	TRUE	0	0.525194970062678	2		750	570	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52729013	52729013	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064676-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	132	1072	0	ENST00000322088.6:c.1705C>T	p.Gln569Ter	p.Q569*	ENST00000322088	NM_014225.5	569	Cag/Tag	14/15	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.306949643683975	2		1072	841	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163854	32163854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778992900	NA	P-0064676-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	47	863	0	ENST00000375023.3:c.5372C>T	p.Ala1791Val	p.A1791V	ENST00000375023	NM_004557.3	1791	gCa/gTa	30/30	1	2	FACETS	0.615	0.519	0.721	0.615	0.519	0.721	SUBCLONAL	1	TRUE	1	0.306949643683975	2		863	498	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0064677-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	181	623	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		623	489	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0064677-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	24	283	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.207	0.162	0.26	0.207	0.162	0.26	SUBCLONAL	1	TRUE	1	0.54	2		283	429	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0064677-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	34	440	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.20737741839288	3	FACETS	0.272	0.221	0.329	0.136	0.11	0.165	INDETERMINATE	1	TRUE	1	0.54	3		440	588	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211138	36211138	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064677-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	54	521	0	ENST00000222270.7:c.889C>T	p.Arg297Ter	p.R297*	ENST00000222270	NM_014727.1	297	Cga/Tga	3/37	1	2	FACETS	0.298	0.254	0.346	0.298	0.254	0.346	SUBCLONAL	1	TRUE	1	0.54	2		521	671	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031973	26031973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064677-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	44	597	0	ENST00000244661.2:c.316G>C	p.Glu106Gln	p.E106Q	ENST00000244661	NM_003537.3	106	Gag/Cag	1/1	1	2	FACETS	0.219	0.183	0.26	0.219	0.183	0.26	SUBCLONAL	1	TRUE	1	0.54	2		597	743	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429764	78429764	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064677-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	40	423	0	ENST00000370768.2:c.1024C>A	p.Leu342Ile	p.L342I	ENST00000370768	NM_003902.3	342	Ctt/Att	12/20	1	2	FACETS	0.238	0.197	0.284	0.238	0.197	0.284	SUBCLONAL	1	TRUE	1	0.54	2		423	623	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984818	72984819	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064677-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	31	458	0	ENST00000268489.5:c.2765dup	p.Val923GlyfsTer124	p.V923Gfs*124	ENST00000268489	NM_006885.3	922	ctg/ctTg	3/10	1	2	FACETS	0.191	0.154	0.233	0.191	0.154	0.233	SUBCLONAL	1	TRUE	1	0.54	2		458	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0064678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	38	631	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.849	0.699	1	0.849	0.699	1	CLONAL	1	TRUE	1	0.11	2		631	814	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0064678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	43	691	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.956	0.797	1	0.956	0.797	1	CLONAL	1	TRUE	1	0.11	2		691	818	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216472	2216486	+	inframe_deletion	In_Frame_Del	DEL	AGCATGAGCCCGGAG	AGCATGAGCCCGGAG	-	novel	NA	P-0064678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	52	746	0	ENST00000398665.3:c.2116_2130del	p.Ser706_Glu710del	p.S706_E710del	ENST00000398665	NM_032482.2	706	AGCATGAGCCCGGAG/-	20/28	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.11	2		746	926	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133954	38133954	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	46	561	0	ENST00000317025.8:c.3932A>T	p.Lys1311Met	p.K1311M	ENST00000317025	NM_023034.1	1311	aAg/aTg	23/24	1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	1	0.11	2		561	830	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	16	344	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.531	0.391	0.698	0.531	0.391	0.698	SUBCLONAL	1	TRUE	1	0.18	2		344	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0064679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	54	523	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.987	0.842	1	0.987	0.842	1	CLONAL	1	TRUE	1	0.18	2		523	608	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435239	18435239	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	43	622	0	ENST00000266497.5:c.224G>A	p.Gly75Glu	p.G75E	ENST00000266497		75	gGg/gAg	1/31	1	2	FACETS	0.896	0.75	1	0.896	0.75	1	CLONAL	1	TRUE	1	0.18	2		622	533	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0064695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	182	176	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.473450795492694	5	FACETS	0.916	0.867	0.964	1	0.987	1	CLONAL	5	TRUE	1	0.473450795492694	5		176	287	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338669	70338669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	81	504	0	ENST00000374080.3:c.65C>T	p.Pro22Leu	p.P22L	ENST00000374080		22	cCc/cTc	1/45	1	2	FACETS	0.932	0.827	1	0.932	0.827	1	CLONAL	1	TRUE	1	0.473450795492694	2		504	367	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0064696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	226	536	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.561521238437057	2		536	751	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727483	66727483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504317	NA	P-0064696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	287	629	1	ENST00000307102.5:c.199G>A	p.Asp67Asn	p.D67N	ENST00000307102	NM_002755.3	67	Gac/Aac	2/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.561521238437057	2		630	919	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560970	9560970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781706438	NA	P-0064696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	319	705	0	ENST00000353224.5:c.812C>T	p.Ser271Leu	p.S271L	ENST00000353224	NM_177990.2	271	tCg/tTg	4/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.561521238437057	2		705	1045	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578418	7578418	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	351	869	1	ENST00000269305.4:c.512A>G	p.Glu171Gly	p.E171G	ENST00000269305	NM_001126112.2	171	gAg/gGg	5/11	0.561521238437057	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.561521238437057	1		870	889	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155533	106155533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs114619974	NA	P-0064696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	200	581	0	ENST00000380013.4:c.434G>A	p.Ser145Asn	p.S145N	ENST00000380013	NM_001127208.2	145	aGt/aAt	3/11	0.47060997301747	1	FACETS	0.845	0.788	0.904	0.845	0.788	0.904	CLONAL	1	TRUE	0	0.561521238437057	1		581	606	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552876	106552876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1003783236	NA	P-0064696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	312	812	0	ENST00000369096.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000369096	NM_001198.3	281	Gat/Aat	5/7	0.561521238437057	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.561521238437057	1		812	782	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426279	49426279	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	340	850	0	ENST00000301067.7:c.12209C>T	p.Ser4070Phe	p.S4070F	ENST00000301067	NM_003482.3	4070	tCt/tTt	39/54	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.561521238437057	2		850	1149	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0064696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	265	372	0				ENST00000310581	NM_198253.2	-/1132			0.561521238437057	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.561521238437057	1		372	567	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213599	36213599	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754201347	NA	P-0064696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	292	691	0	ENST00000222270.7:c.2701C>T	p.Arg901Trp	p.R901W	ENST00000222270	NM_014727.1	901	Cgg/Tgg	5/37	NA	2	FACETS	0.977	0.92	1			1	INDETERMINATE	1	TRUE	NA	0.561521238437057	2		691	1064	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983445	90983445	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659811	NA	P-0064696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	45	197	0	ENST00000265433.3:c.658C>G	p.Gln220Glu	p.Q220E	ENST00000265433	NM_002485.4	220	Caa/Gaa	6/16	1	2	FACETS	0.716	0.607	0.833	0.716	0.607	0.833	SUBCLONAL	1	TRUE	1	0.561521238437057	2		197	224	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639012	3639012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190668825	NA	P-0064696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	300	714	0	ENST00000294008.3:c.4627G>A	p.Glu1543Lys	p.E1543K	ENST00000294008	NM_032444.2	1543	Gag/Aag	12/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.561521238437057	2		714	1038	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884960	111884960	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1341400435	NA	P-0064696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	311	823	0	ENST00000341259.2:c.958C>T	p.Pro320Ser	p.P320S	ENST00000341259	NM_005475.2	320	Ccc/Tcc	5/8	1	2	FACETS	0.936	0.882	0.99	0.936	0.882	0.99	CLONAL	1	TRUE	1	0.561521238437057	2		823	1184	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40874918	40874918	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	152	449	0	ENST00000428826.2:c.382G>A	p.Val128Ile	p.V128I	ENST00000428826		128	Gtt/Att	6/21	1	2	FACETS	0.838	0.769	0.91	0.838	0.769	0.91	CLONAL	1	TRUE	1	0.561521238437057	2		449	646	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794887	42794887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568514975	NA	P-0064696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	75	875	0	ENST00000575354.2:c.1967C>T	p.Ala656Val	p.A656V	ENST00000575354	NM_015125.3	656	gCc/gTc	10/20	0.445321705053008	1	FACETS	0.221	0.193	0.251	0.221	0.193	0.251	SUBCLONAL	1	TRUE	0	0.561521238437057	1		875	870	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213126	39213126	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	403	785	1	ENST00000402219.2:c.3841G>A	p.Glu1281Lys	p.E1281K	ENST00000402219	NM_005633.3	1281	Gaa/Aaa	23/23	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.561521238437057	2		786	1268	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630482	67630482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	63	224	0	ENST00000272342.5:c.668C>T	p.Ser223Leu	p.S223L	ENST00000272342	NM_019002.3	223	tCa/tTa	5/6	1	2	FACETS	0.98	0.859	1	0.98	0.859	1	CLONAL	1	TRUE	1	0.561521238437057	2		224	229	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384625	31384625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752929250	NA	P-0064696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	263	729	0	ENST00000328111.2:c.1327C>T	p.Pro443Ser	p.P443S	ENST00000328111	NM_006892.3	443	Ccc/Tcc	13/23	1	2	FACETS	0.941	0.882	1	0.941	0.882	1	CLONAL	1	TRUE	1	0.561521238437057	2		729	996	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573671	41573672	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0064696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	397	837	0	ENST00000263253.7:c.5956_5957delinsTT	p.Pro1986Leu	p.P1986L	ENST00000263253	NM_001429.3	1986	CCg/TTg	31/31	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.561521238437057	2		837	1353	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665021	138665021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	194	555	0	ENST00000330315.3:c.544G>A	p.Gly182Arg	p.G182R	ENST00000330315	NM_023067.3	182	Ggg/Agg	1/1	1	2	FACETS	0.966	0.897	1	0.966	0.897	1	CLONAL	1	TRUE	1	0.561521238437057	2		555	715	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447345	187447345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	685	801	0	ENST00000232014.4:c.848C>T	p.Pro283Leu	p.P283L	ENST00000232014	NM_001130845.1	283	cCt/cTt	5/10	0.515813272620299	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.561521238437057	3		801	1473	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31451711	31451711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372313396	NA	P-0064696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	114	414	2	ENST00000344624.3:c.2611C>T	p.Arg871Cys	p.R871C	ENST00000344624		871	Cgc/Tgc	18/33	0.561521238437057	1	FACETS	0.728	0.661	0.798	0.728	0.661	0.798	SUBCLONAL	1	TRUE	0	0.561521238437057	1		416	401	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979202	93979202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	63	382	0	ENST00000369303.4:c.1626G>A	p.Met542Ile	p.M542I	ENST00000369303	NM_004440.3	542	atG/atA	7/17	0.561521238437057	1	FACETS	0.751	0.659	0.847	0.751	0.659	0.847	SUBCLONAL	1	TRUE	0	0.561521238437057	1		382	215	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2029069	2029069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	291	805	0	ENST00000349721.2:c.47C>T	p.Ser16Leu	p.S16L	ENST00000349721	NM_003070.3	16	tCg/tTg	2/34	0.561521238437057	1	FACETS	0.946	0.894	0.999	0.946	0.894	0.999	CLONAL	1	TRUE	0	0.561521238437057	1		805	788	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520000	NA	P-0064698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	345	663	0	ENST00000269305.4:c.452C>A	p.Pro151His	p.P151H	ENST00000269305	NM_001126112.2	151	cCc/cAc	5/11	0.714825230071179	2	FACETS	0.942	0.908	0.976	0.942	0.908	0.976	CLONAL	2	TRUE	0	0.730707735334773	2		663	501	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183245	56183245	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	273	580	0	ENST00000399503.3:c.4155A>C	p.Arg1385Ser	p.R1385S	ENST00000399503	NM_005921.1	1385	agA/agC	18/20	0.725463496114434	2	FACETS	0.939	0.9	0.976	0.939	0.9	0.976	CLONAL	2	TRUE	0	0.730707735334773	2		580	398	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271246	26271246	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1561766854	NA	P-0064698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	314	871	0	ENST00000305910.3:c.367A>G	p.Lys123Glu	p.K123E	ENST00000305910	NM_003534.2	123	Aag/Gag	1/1	0.698304083419611	4	FACETS	0.903	0.855	0.951	0.451	0.427	0.476	CLONAL	2	TRUE	0	0.730707735334773	4		871	824	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821386	32821386	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	30	811	0	ENST00000354258.4:c.208del	p.Arg70AlafsTer53	p.R70Afs*53	ENST00000354258	NM_000593.5	70	Cgc/gc	1/11	0.698304083419611	4	FACETS	0.242	0.194	0.297	0.061	0.048	0.075	SUBCLONAL	1	TRUE	0	0.730707735334773	4		811	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0064700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	530	631	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.78254837406498	2	FACETS	0.961	0.935	0.985	0.961	0.935	0.985	CLONAL	2	TRUE	0	0.78254837406498	2		631	705	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023173	27023174	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCGGCGCGGAGCCGGA	novel	NA	P-0064700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	147	737	0	ENST00000324856.7:c.282_298dup	p.Leu100ProfsTer7	p.L100Pfs*7	ENST00000324856	NM_006015.4	93	-/CCCGGCGCGGAGCCGGA	1/20	1	2	FACETS	0.627	0.575	0.682	0.627	0.575	0.682	SUBCLONAL	1	TRUE	1	0.78254837406498	2		737	599	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057838	27057838	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1446574904	NA	P-0064700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	379	1048	0	ENST00000324856.7:c.1546C>G	p.Pro516Ala	p.P516A	ENST00000324856	NM_006015.4	516	Cct/Gct	3/20	1	2	FACETS	0.861	0.818	0.904	0.861	0.818	0.904	CLONAL	1	TRUE	1	0.78254837406498	2		1048	1125	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332704	70332704	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	35	523	0	ENST00000373644.4:c.609C>G	p.Ile203Met	p.I203M	ENST00000373644	NM_030625.2	203	atC/atG	2/12	1	2	FACETS	0.153	0.125	0.185	0.153	0.125	0.185	SUBCLONAL	1	TRUE	1	0.78254837406498	2		523	585	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427201	49427201	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	302	894	0	ENST00000301067.7:c.11287G>C	p.Val3763Leu	p.V3763L	ENST00000301067	NM_003482.3	3763	Gta/Cta	39/54	1	2	FACETS	0.945	0.894	0.996	0.945	0.894	0.996	CLONAL	1	TRUE	1	0.78254837406498	2		894	817	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929486	81929486	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	62	680	0	ENST00000359376.3:c.1147G>C	p.Asp383His	p.D383H	ENST00000359376	NM_002661.3	383	Gac/Cac	13/33	0.78254837406498	1	FACETS	0.193	0.167	0.222	0.193	0.167	0.222	SUBCLONAL	1	TRUE	0	0.78254837406498	1		680	499	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10259567	10259567	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	254	674	0	ENST00000340748.4:c.2665A>G	p.Lys889Glu	p.K889E	ENST00000340748		889	Aag/Gag	26/40	1	2	FACETS	0.889	0.836	0.943	0.889	0.836	0.943	CLONAL	1	TRUE	1	0.78254837406498	2		674	730	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149862	202149862	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	204	738	0	ENST00000358485.4:c.1303G>T	p.Glu435Ter	p.E435*	ENST00000358485	NM_001080125.1	435	Gag/Tag	8/9	1	2	FACETS	0.675	0.628	0.724	0.675	0.628	0.724	SUBCLONAL	1	TRUE	1	0.78254837406498	2		738	772	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8733830	8733830	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	269	583	0	ENST00000356435.5:c.14C>G	p.Ala5Gly	p.A5G	ENST00000356435		5	gCc/gGc	1/35	0.78254837406498	1	FACETS	0.951	0.908	0.994	0.951	0.908	0.994	CLONAL	1	TRUE	0	0.78254837406498	1		583	440	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0064703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	95	1026	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.81	0.72	0.906	0.81	0.72	0.906	CLONAL	1	TRUE	1	0.278215450570982	2		1026	843	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119781	70119781	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1274036689	NA	P-0064703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	104	856	0	ENST00000245479.2:c.788del	p.Gly263AlafsTer16	p.G263Afs*16	ENST00000245479	NM_000346.3	261	gaG/ga	3/3	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.278215450570982	2		856	626	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578196	7578196	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555525743	NA	P-0064703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	128	1076	0	ENST00000269305.4:c.653T>G	p.Val218Gly	p.V218G	ENST00000269305	NM_001126112.2	218	gTg/gGg	6/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.278215450570982	2		1076	847	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0064703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	42	516	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.719	0.601	0.85	0.719	0.601	0.85	SUBCLONAL	1	TRUE	1	0.278215450570982	2		516	420	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020820	112020820	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	93	692	0	ENST00000368678.4:c.751C>A	p.Pro251Thr	p.P251T	ENST00000368678		251	Cca/Aca	8/13	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.278215450570982	2		692	644	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411728	63411728	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	95	620	0	ENST00000330258.3:c.1439del	p.Glu480GlyfsTer61	p.E480Gfs*61	ENST00000330258	NM_152424.3	480	gAg/gg	2/2	0.278215450570982	0	FACETS	1	0.966	1			1	CLONAL	1	TRUE	NA	0.278215450570982	0		620	414	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0064723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	127	377	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.295148604207991	7	FACETS	0.956	0.882	1	1	0.976	1	CLONAL	6	TRUE	2	0.26	7		377	281	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243219	123243227	+	inframe_deletion	In_Frame_Del	DEL	GTTGTGAGA	GTTGTGAGA	-	novel	NA	P-0064723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	69	607	0	ENST00000358487.5:c.2286_2294del	p.Leu763_Thr765del	p.L763_T765del	ENST00000358487	NM_000141.4	762	acTCTCACAACc/acc	17/18	1	2	FACETS	0.981	0.856	1	0.981	0.856	1	CLONAL	1	TRUE	1	0.26	2		607	541	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77936178	77936178	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	72	482	0	ENST00000361507.4:c.1278G>C	p.Met426Ile	p.M426I	ENST00000361507	NM_080491.2	426	atG/atC	5/10	0.295148604207991	6	FACETS	0.929	0.81	1	0.232	0.202	0.265	CLONAL	1	TRUE	2	0.26	6		482	906	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578461	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CG	novel	NA	P-0064723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	265	602	0	ENST00000269305.4:c.468_469dup	p.Val157AlafsTer14	p.V157Afs*14	ENST00000269305	NM_001126112.2	157	gtc/gCGtc	5/11	0.249520529187737	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	3	TRUE	0	0.26	3		602	740	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350554	15350554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199839337	NA	P-0064723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	84	465	0	ENST00000263377.2:c.3361C>T	p.Arg1121Cys	p.R1121C	ENST00000263377	NM_058243.2	1121	Cgc/Tgc	16/20	0.295148604207991	6	FACETS	0.901	0.798	1	0.451	0.399	0.506	CLONAL	2	TRUE	2	0.26	6		465	545	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738710	145738722	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCGCACATCTG	GCCCGCACATCTG	-	novel	NA	P-0064723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	89	805	0	ENST00000428558.2:c.2342_2354del	p.Pro781LeufsTer58	p.P781Lfs*58	ENST00000428558	NM_004260.3	781	cCAGATGTGCGGGCt/ct	15/22	0.255637524680459	3	FACETS	1	0.959	1	0.589	0.522	0.66	CLONAL	1	TRUE	1	0.26	3		805	657	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	200	474	7	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.75	0.697	0.805	0.75	0.697	0.805	SUBCLONAL	1	TRUE	1	0.728429687667114	2		481	732	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	61	542	7	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.403	0.348	0.461	0.403	0.348	0.461	SUBCLONAL	1	TRUE	1	0.728429687667114	2		549	416	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	85	176	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.728429687667114	2		176	216	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190735	11190735	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1338775745	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	311	371	0	ENST00000361445.4:c.5464G>A	p.Gly1822Arg	p.G1822R	ENST00000361445	NM_004958.3	1822	Ggg/Agg	39/58	1	2	FACETS	0.928	0.878	0.979	0.928	0.878	0.979	CLONAL	1	TRUE	1	0.728429687667114	2		371	920	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248126	59248126	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs763958620	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	256	393	4	ENST00000371222.2:c.617A>C	p.Gln206Pro	p.Q206P	ENST00000371222	NM_002228.3	206	cAg/cCg	1/1	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.728429687667114	2		397	672	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163309204	163309204	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	45	201	0	ENST00000271452.3:c.543G>T	p.Lys181Asn	p.K181N	ENST00000271452	NM_145697.2	181	aaG/aaT	8/14	1	2	FACETS	0.324	0.273	0.381	0.324	0.273	0.381	SUBCLONAL	1	TRUE	1	0.728429687667114	2		201	381	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404833	70404833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376078561	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	100	193	0	ENST00000373644.4:c.2347G>A	p.Gly783Ser	p.G783S	ENST00000373644	NM_030625.2	783	Ggc/Agc	4/12	1	2	FACETS	0.728	0.656	0.804	0.728	0.656	0.804	SUBCLONAL	1	TRUE	1	0.728429687667114	2		193	377	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	414	505	1	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.975	0.944	1	1	0.997	1	CLONAL	2	TRUE	1	0.728429687667114	2		506	583	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123246892	123246892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	199	222	0	ENST00000358487.5:c.2033G>A	p.Arg678Lys	p.R678K	ENST00000358487	NM_000141.4	678	aGa/aAa	15/18	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.728429687667114	2		222	544	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939260	71939260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	95	409	1	ENST00000298229.2:c.209G>A	p.Arg70His	p.R70H	ENST00000298229	NM_001567.3	70	cGc/cAc	2/28	1	2	FACETS	0.357	0.318	0.399	0.357	0.318	0.399	SUBCLONAL	1	TRUE	1	0.728429687667114	2		410	730	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	56	451	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.226	0.193	0.263	0.226	0.193	0.263	SUBCLONAL	1	TRUE	1	0.728429687667114	2		452	679	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307301	118307301	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	51	134	0	ENST00000534358.1:c.77del	p.Gly26AlafsTer2	p.G26Afs*2	ENST00000534358	NM_005933.3	25	cGg/cg	1/36	1	2	FACETS	0.959	0.834	1	0.959	0.834	1	CLONAL	1	TRUE	1	0.728429687667114	2		134	146	SUCCESS
CBL	867	MSKCC	GRCh37	11	119168126	119168126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	117	201	0	ENST00000264033.4:c.2186G>A	p.Cys729Tyr	p.C729Y	ENST00000264033	NM_005188.3	729	tGt/tAt	14/16	1	2	FACETS	0.598	0.541	0.658	0.598	0.541	0.658	SUBCLONAL	1	TRUE	1	0.728429687667114	2		201	537	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	161	343	4	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.898	0.831	0.968	0.898	0.831	0.968	CLONAL	1	TRUE	1	0.728429687667114	2		347	492	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406317	406318	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	208	240	0	ENST00000399788.2:c.4123dup	p.Cys1375LeufsTer2	p.C1375Lfs*2	ENST00000399788	NM_001042603.1	1375	tgt/tTgt	25/28	1	2	FACETS	0.929	0.867	0.991	0.929	0.867	0.991	CLONAL	1	TRUE	1	0.728429687667114	2		240	615	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398148	4398148	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	73	223	0	ENST00000261254.3:c.712A>G	p.Thr238Ala	p.T238A	ENST00000261254	NM_001759.3	238	Aca/Gca	4/5	1	2	FACETS	0.361	0.316	0.41	0.361	0.316	0.41	SUBCLONAL	1	TRUE	1	0.728429687667114	2		223	555	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123836	46123837	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	141	282	0	ENST00000334344.6:c.109dup	p.Ile37AsnfsTer29	p.I37Nfs*29	ENST00000334344	NM_152641.2	34	-/A	2/21	1	2	FACETS	0.589	0.538	0.643	0.589	0.538	0.643	SUBCLONAL	1	TRUE	1	0.728429687667114	2		282	657	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426444	49426444	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	226	405	0	ENST00000301067.7:c.12044T>C	p.Leu4015Pro	p.L4015P	ENST00000301067	NM_003482.3	4015	cTg/cCg	39/54	1	2	FACETS	0.67	0.625	0.717	0.67	0.625	0.717	SUBCLONAL	1	TRUE	1	0.728429687667114	2		405	926	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	209	355	0	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.78	0.726	0.835	0.78	0.726	0.835	SUBCLONAL	1	TRUE	1	0.728429687667114	2		355	736	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481857	56481857	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519817	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	287	296	0	ENST00000267101.3:c.785C>A	p.Pro262His	p.P262H	ENST00000267101	NM_001982.3	262	cCt/cAt	7/28	1	2	FACETS	0.972	0.917	1	0.972	0.917	1	CLONAL	1	TRUE	1	0.728429687667114	2		296	811	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491680	56491682	+	inframe_deletion	In_Frame_Del	DEL	CTG	CTG	-	rs769041526	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	177	254	0	ENST00000267101.3:c.2576_2578del	p.Leu859del	p.L859del	ENST00000267101	NM_001982.3	858	CTG/-	21/28	1	2	FACETS	0.713	0.659	0.768	0.713	0.659	0.768	SUBCLONAL	1	TRUE	1	0.728429687667114	2		254	682	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562750	21562750	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1157842597	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	241	377	1	ENST00000382592.4:c.1169C>T	p.Pro390Leu	p.P390L	ENST00000382592	NM_014572.2	390	cCg/cTg	4/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.728429687667114	2		378	623	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133898	41133898	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	238	333	0	ENST00000379561.5:c.1730del	p.Gly577AlafsTer5	p.G577Afs*5	ENST00000379561	NM_002015.3	577	gGc/gc	2/3	1	2	FACETS	0.91	0.853	0.968	0.91	0.853	0.968	CLONAL	1	TRUE	1	0.728429687667114	2		333	718	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609331	81609331	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139286618	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	199	229	0	ENST00000298171.2:c.929G>A	p.Arg310His	p.R310H	ENST00000298171	NM_000369.2	310	cGc/cAc	10/10	1	2	FACETS	0.957	0.893	1	0.957	0.893	1	CLONAL	1	TRUE	1	0.728429687667114	2		229	571	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572555	95572555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	130	162	0	ENST00000393063.1:c.2810G>A	p.Arg937His	p.R937H	ENST00000393063	NM_030621.3	937	cGc/cAc	19/28	1	2	FACETS	0.899	0.824	0.977	0.899	0.824	0.977	CLONAL	1	TRUE	1	0.728429687667114	2		162	397	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961399	41961399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748756129	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	60	272	0	ENST00000219905.7:c.307C>T	p.Arg103Cys	p.R103C	ENST00000219905	NM_001164273.1	103	Cgc/Tgc	2/24	1	2	FACETS	0.287	0.247	0.33	0.287	0.247	0.33	SUBCLONAL	1	TRUE	1	0.728429687667114	2		272	575	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054516	42054516	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	106	219	0	ENST00000219905.7:c.7704del	p.Lys2569AsnfsTer3	p.K2569Nfs*3	ENST00000219905	NM_001164273.1	2567	aGg/ag	22/24	1	2	FACETS	0.691	0.624	0.762	0.691	0.624	0.762	SUBCLONAL	1	TRUE	1	0.728429687667114	2		219	421	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43739593	43739593	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1298106514	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	184	183	0	ENST00000382044.4:c.2807T>C	p.Leu936Ser	p.L936S	ENST00000382044	NM_001141980.1	936	tTg/tCg	13/28	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.728429687667114	2		183	480	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	229	289	0	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	1	2	FACETS	0.967	0.907	1	0.967	0.907	1	CLONAL	1	TRUE	1	0.728429687667114	2		289	650	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994652	73994652	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	283	405	0	ENST00000318443.5:c.136G>A	p.Ala46Thr	p.A46T	ENST00000318443	NM_001024736.1	46	Gcc/Acc	3/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.728429687667114	2		405	735	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354374	354374	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	168	221	0	ENST00000262320.3:c.1184G>A	p.Arg395His	p.R395H	ENST00000262320	NM_003502.3	395	cGc/cAc	5/11	1	2	FACETS	0.688	0.635	0.744	0.688	0.635	0.744	SUBCLONAL	1	TRUE	1	0.728429687667114	2		221	670	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656556	3656556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147872182	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	333	316	0	ENST00000294008.3:c.679G>A	p.Ala227Thr	p.A227T	ENST00000294008	NM_032444.2	227	Gct/Act	3/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.728429687667114	2		316	893	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781866	3781866	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	91	321	0	ENST00000262367.5:c.4801A>C	p.Ser1601Arg	p.S1601R	ENST00000262367	NM_004380.2	1601	Agc/Cgc	29/31	1	2	FACETS	0.297	0.263	0.334	0.297	0.263	0.334	SUBCLONAL	1	TRUE	1	0.728429687667114	2		321	840	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790470	3790470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774076896	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	174	238	0	ENST00000262367.5:c.4063G>A	p.Gly1355Arg	p.G1355R	ENST00000262367	NM_004380.2	1355	Ggg/Agg	24/31	1	2	FACETS	0.625	0.577	0.676	0.625	0.577	0.676	SUBCLONAL	1	TRUE	1	0.728429687667114	2		238	764	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614858	23614858	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	200	209	0	ENST00000261584.4:c.3483del	p.Phe1161LeufsTer2	p.F1161Lfs*2	ENST00000261584	NM_024675.3	1161	ttT/tt	13/13	1	2	FACETS	0.905	0.843	0.968	0.905	0.843	0.968	CLONAL	1	TRUE	1	0.728429687667114	2		209	607	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56878430	56878430	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771046738	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	95	269	1	ENST00000308159.5:c.2369G>A	p.Arg790His	p.R790H	ENST00000308159	NM_014669.4	790	cGc/cAc	22/22	1	2	FACETS	0.352	0.314	0.394	0.352	0.314	0.394	SUBCLONAL	1	TRUE	1	0.728429687667114	2		270	740	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991586	72991586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768340392	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	288	357	0	ENST00000268489.5:c.2459G>A	p.Arg820His	p.R820H	ENST00000268489	NM_006885.3	820	cGc/cAc	2/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.728429687667114	2		357	748	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346961	89346961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775491352	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	254	384	0	ENST00000301030.4:c.5989G>A	p.Ala1997Thr	p.A1997T	ENST00000301030	NM_001256183.1	1997	Gcg/Acg	9/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.728429687667114	2		384	655	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89880998	89880998	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	64	176	0	ENST00000389301.3:c.213del	p.Lys71AsnfsTer7	p.K71Nfs*7	ENST00000389301	NM_000135.2	71	aaA/aa	3/43	1	2	FACETS	0.319	0.276	0.365	0.319	0.276	0.365	SUBCLONAL	1	TRUE	1	0.728429687667114	2		176	551	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679886	33679886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746690453	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	262	288	0	ENST00000308377.4:c.2195G>A	p.Arg732His	p.R732H	ENST00000308377	NM_152270.3	732	cGc/cAc	5/5	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.728429687667114	2		288	676	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657676	37657677	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	116	200	0	ENST00000447079.4:c.2597dup	p.Leu866PhefsTer4	p.L866Ffs*4	ENST00000447079	NM_015083.1	865	att/aTtt	6/14	1	2	FACETS	0.895	0.815	0.977	0.895	0.815	0.977	CLONAL	1	TRUE	1	0.728429687667114	2		200	356	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370236	40370236	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs761761205	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	170	355	4	ENST00000293328.3:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000293328	NM_012448.3	368	Cag/ag	9/19	1	2	FACETS	0.653	0.602	0.706	0.653	0.602	0.706	SUBCLONAL	1	TRUE	1	0.728429687667114	2		359	715	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865379	40865379	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	100	242	0	ENST00000428826.2:c.1052A>G	p.His351Arg	p.H351R	ENST00000428826		351	cAc/cGc	11/21	1	2	FACETS	0.385	0.343	0.428	0.385	0.343	0.428	SUBCLONAL	1	TRUE	1	0.728429687667114	2		242	714	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	163	651	1	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	0.661	0.608	0.716	0.661	0.608	0.716	SUBCLONAL	1	TRUE	1	0.728429687667114	2		652	677	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63537617	63537617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502160	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	205	209	0	ENST00000307078.5:c.1015C>T	p.Arg339Cys	p.R339C	ENST00000307078	NM_004655.3	339	Cgc/Tgc	4/11	1	2	FACETS	0.921	0.86	0.984	0.921	0.86	0.984	CLONAL	1	TRUE	1	0.728429687667114	2		209	611	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526526	66526526	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	193	289	0	ENST00000358598.2:c.1082C>A	p.Pro361Gln	p.P361Q	ENST00000358598	NM_212471.2	361	cCa/cAa	11/11	1	2	FACETS	0.624	0.578	0.672	0.624	0.578	0.672	SUBCLONAL	1	TRUE	1	0.728429687667114	2		289	849	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732442	74732447	+	inframe_deletion	In_Frame_Del	DEL	CGAGAA	CGAGAA	-	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	175	359	0	ENST00000359995.5:c.462_467del	p.Arg158_Ser159del	p.R158_S159del	ENST00000359995	NM_001195427.1	154	cgTTCTCGa/cga	2/3	1	2	FACETS	0.611	0.563	0.66	0.611	0.563	0.66	SUBCLONAL	1	TRUE	1	0.728429687667114	2		359	787	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609313	39609313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760479037	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	130	179	0	ENST00000262039.4:c.1615C>T	p.Arg539Cys	p.R539C	ENST00000262039	NM_002647.2	539	Cgt/Tgt	15/25	1	2	FACETS	0.613	0.558	0.671	0.613	0.558	0.671	SUBCLONAL	1	TRUE	1	0.728429687667114	2		179	582	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142932	7142932	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs371294434	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	270	346	1	ENST00000302850.5:c.2437C>T	p.Arg813Ter	p.R813*	ENST00000302850	NM_000208.2	813	Cga/Tga	12/22	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.728429687667114	2		347	724	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311605	15311605	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1445073298	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	286	533	4	ENST00000263388.2:c.112del	p.Ala38LeufsTer198	p.A38Lfs*198	ENST00000263388	NM_000435.2	38	Gct/ct	1/33	1	2	FACETS	0.927	0.875	0.981	0.927	0.875	0.981	CLONAL	1	TRUE	1	0.728429687667114	2		537	847	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214398	36214398	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs868041281	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	237	287	0	ENST00000222270.7:c.3057del	p.Gly1020AlafsTer4	p.G1020Afs*4	ENST00000222270	NM_014727.1	1018	Aaa/aa	7/37	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.728429687667114	2		287	623	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224568	36224568	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755245377	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	180	385	0	ENST00000222270.7:c.7030G>A	p.Ala2344Thr	p.A2344T	ENST00000222270	NM_014727.1	2344	Gct/Act	29/37	1	2	FACETS	0.698	0.646	0.752	0.698	0.646	0.752	SUBCLONAL	1	TRUE	1	0.728429687667114	2		385	708	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227816	36227816	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190286476	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	310	404	0	ENST00000222270.7:c.7301C>T	p.Ala2434Val	p.A2434V	ENST00000222270	NM_014727.1	2434	gCg/gTg	32/37	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.728429687667114	2		404	794	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795269	42795269	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs34000070	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	69	365	0	ENST00000575354.2:c.2353del	p.Ala785ProfsTer139	p.A785Pfs*139	ENST00000575354	NM_015125.3	783	caG/ca	10/20	1	2	FACETS	0.307	0.267	0.35	0.307	0.267	0.35	SUBCLONAL	1	TRUE	1	0.728429687667114	2		365	617	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241025	39241025	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	40	156	0	ENST00000402219.2:c.2046A>G	p.Ile682Met	p.I682M	ENST00000402219	NM_005633.3	682	atA/atG	12/23	1	2	FACETS	0.37	0.308	0.437	0.37	0.308	0.437	SUBCLONAL	1	TRUE	1	0.728429687667114	2		156	297	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47612329	47612329	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	69	137	0	ENST00000263735.4:c.883G>T	p.Ala295Ser	p.A295S	ENST00000263735	NM_002354.2	295	Gca/Tca	8/9	1	2	FACETS	0.718	0.632	0.808	0.718	0.632	0.808	SUBCLONAL	1	TRUE	1	0.728429687667114	2		137	264	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	68	753	4	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.242	0.21	0.277	0.242	0.21	0.277	SUBCLONAL	1	TRUE	1	0.728429687667114	2		757	772	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719061	190719061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141084536	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	58	179	0	ENST00000441310.2:c.1063G>A	p.Ala355Thr	p.A355T	ENST00000441310	NM_000534.4	355	Gca/Aca	9/13	1	2	FACETS	0.531	0.459	0.608	0.531	0.459	0.608	SUBCLONAL	1	TRUE	1	0.728429687667114	2		179	300	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150022	202150022	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	80	331	0	ENST00000358485.4:c.1463T>C	p.Leu488Pro	p.L488P	ENST00000358485	NM_001080125.1	488	cTg/cCg	8/9	1	2	FACETS	0.279	0.245	0.316	0.279	0.245	0.316	SUBCLONAL	1	TRUE	1	0.728429687667114	2		331	786	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735313	204735313	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	86	284	0	ENST00000302823.3:c.114G>A	p.Met38Ile	p.M38I	ENST00000302823	NM_005214.4	38	atG/atA	2/4	1	2	FACETS	0.372	0.329	0.418	0.372	0.329	0.418	SUBCLONAL	1	TRUE	1	0.728429687667114	2		284	635	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645975	215645975	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs587780033	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	55	287	0	ENST00000260947.4:c.623del	p.Lys208ArgfsTer4	p.K208Rfs*4	ENST00000260947	NM_000465.2	208	aAg/ag	4/11	1	2	FACETS	0.264	0.225	0.306	0.264	0.225	0.306	SUBCLONAL	1	TRUE	1	0.728429687667114	2		287	573	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440169	220440169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777288649	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	231	315	0	ENST00000243786.2:c.1022G>A	p.Arg341His	p.R341H	ENST00000243786	NM_002191.3	341	cGc/cAc	2/2	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.728429687667114	2		315	631	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	78	357	0	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.286	0.251	0.324	0.286	0.251	0.324	SUBCLONAL	1	TRUE	1	0.728429687667114	2		357	749	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485415	57485415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755974022	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	255	810	0	ENST00000371085.3:c.997C>T	p.Arg333Cys	p.R333C	ENST00000371085	NM_000516.4	333	Cgc/Tgc	12/13	1	2	FACETS	0.921	0.866	0.978	0.921	0.866	0.978	CLONAL	1	TRUE	1	0.728429687667114	2		810	760	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62303918	62303918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1023502136	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	201	270	0	ENST00000360203.5:c.709G>A	p.Ala237Thr	p.A237T	ENST00000360203	NM_001283009.1	237	Gca/Aca	9/35	1	2	FACETS	0.778	0.724	0.834	0.778	0.724	0.834	SUBCLONAL	1	TRUE	1	0.728429687667114	2		270	709	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21347168	21347168	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	246	311	0	ENST00000215739.8:c.1235G>T	p.Arg412Leu	p.R412L	ENST00000215739	NM_006767.3	412	cGc/cTc	11/21	1	2	FACETS	0.957	0.899	1	0.957	0.899	1	CLONAL	1	TRUE	1	0.728429687667114	2		311	706	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29445208	29445209	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	298	333	0	ENST00000544604.2:c.1046_1047del	p.Val349GlyfsTer117	p.V349Gfs*117	ENST00000544604	NM_001206998.1	347	GTg/g	8/9	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.728429687667114	2		333	748	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37628864	37628864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151307781	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	205	271	0	ENST00000249071.6:c.202C>T	p.Arg68Trp	p.R68W	ENST00000249071	NM_002872.4	68	Cgg/Tgg	3/7	1	2	FACETS	0.903	0.843	0.965	0.903	0.843	0.965	CLONAL	1	TRUE	1	0.728429687667114	2		271	623	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691872	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs79375991	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	364	247	11	ENST00000295754.5:c.383del	p.Lys128SerfsTer35	p.K128Sfs*35	ENST00000295754	NM_003242.5	125	gAa/ga	3/7	0.728429687667114	2	FACETS	0.817	0.784	0.849	0.817	0.784	0.849	CLONAL	2	TRUE	0	0.728429687667114	2		258	612	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042546	37042546	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	245	144	0	ENST00000231790.2:c.306+2T>C		p.X102_splice	ENST00000231790	NM_000249.3	102			0.728429687667114	2	FACETS	0.904	0.863	0.944	0.904	0.863	0.944	CLONAL	2	TRUE	0	0.728429687667114	2		144	372	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582161	52582161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	356	338	0	ENST00000394830.3:c.4667C>T	p.Ala1556Val	p.A1556V	ENST00000394830	NM_018313.4	1556	gCa/gTa	30/30	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.728429687667114	2		338	944	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981832	63981832	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	271	389	1	ENST00000398590.3:c.2340del	p.Thr781ProfsTer11	p.T781Pfs*11	ENST00000398590	NM_001177387.1	778	ggC/gg	12/14	1	2	FACETS	0.849	0.799	0.901	0.849	0.799	0.901	CLONAL	1	TRUE	1	0.728429687667114	2		390	876	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204623	128204623	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	109	338	0	ENST00000341105.2:c.818del	p.Gly273AspfsTer53	p.G273Dfs*53	ENST00000341105	NM_032638.4	273	gGa/ga	3/6	1	2	FACETS	0.411	0.369	0.456	0.411	0.369	0.456	SUBCLONAL	1	TRUE	1	0.728429687667114	2		338	728	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916648	178916648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	79	211	0	ENST00000263967.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000263967	NM_006218.2	12	gGc/gAc	2/21	1	2	FACETS	0.548	0.484	0.615	0.548	0.484	0.615	SUBCLONAL	1	TRUE	1	0.728429687667114	2		211	396	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356200	66356200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770587480	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	189	309	0	ENST00000273854.3:c.1297G>A	p.Ala433Thr	p.A433T	ENST00000273854	NM_004439.5	433	Gct/Act	5/18	1	2	FACETS	0.688	0.638	0.741	0.688	0.638	0.741	SUBCLONAL	1	TRUE	1	0.728429687667114	2		309	754	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509922	187509922	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372186380	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	155	358	0	ENST00000441802.2:c.13591G>A	p.Ala4531Thr	p.A4531T	ENST00000441802	NM_005245.3	4531	Gct/Act	27/27	1	2	FACETS	0.51	0.467	0.555	0.51	0.467	0.555	SUBCLONAL	1	TRUE	1	0.728429687667114	2		358	835	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630783	187630783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	262	302	0	ENST00000441802.2:c.199G>A	p.Ala67Thr	p.A67T	ENST00000441802	NM_005245.3	67	Gcg/Acg	2/27	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.728429687667114	2		302	711	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260644	1260644	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	207	376	0	ENST00000310581.5:c.2915G>T	p.Arg972Leu	p.R972L	ENST00000310581	NM_198253.2	972	cGc/cTc	12/16	1	2	FACETS	0.691	0.643	0.742	0.691	0.643	0.742	SUBCLONAL	1	TRUE	1	0.728429687667114	2		376	822	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873630	35873631	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	39	241	0	ENST00000303115.3:c.588dup	p.Pro197ThrfsTer6	p.P197Tfs*6	ENST00000303115	NM_002185.3	196	caa/cAaa	5/8	1	2	FACETS	0.178	0.147	0.212	0.178	0.147	0.212	SUBCLONAL	1	TRUE	1	0.728429687667114	2		241	603	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111414	56111414	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1561156036	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	186	313	1	ENST00000399503.3:c.14C>G	p.Ala5Gly	p.A5G	ENST00000399503	NM_005921.1	5	gCg/gGg	1/20	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.728429687667114	2		314	503	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627198	86627200	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	231	223	0	ENST00000274376.6:c.577_579del	p.Glu193del	p.E193del	ENST00000274376	NM_002890.2	191	gcAGAa/gca	2/25	1	2	FACETS	0.911	0.854	0.97	0.911	0.854	0.97	CLONAL	1	TRUE	1	0.728429687667114	2		223	696	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	267	443	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.97	0.914	1	0.97	0.914	1	CLONAL	1	TRUE	1	0.728429687667114	2		443	756	SUCCESS
APC	324	MSKCC	GRCh37	5	112175952	112175952	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587783031	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	161	521	0	ENST00000257430.4:c.4666del	p.Thr1556LeufsTer9	p.T1556Lfs*9	ENST00000257430	NM_000038.5	1554	gAa/ga	16/16	1	2	FACETS	0.819	0.755	0.884	0.819	0.755	0.884	CLONAL	1	TRUE	1	0.728429687667114	2		521	540	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923763	131923763	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	37	177	0	ENST00000265335.6:c.1033G>A	p.Glu345Lys	p.E345K	ENST00000265335		345	Gaa/Aaa	7/25	1	2	FACETS	0.249	0.205	0.298	0.249	0.205	0.298	SUBCLONAL	1	TRUE	1	0.728429687667114	2		177	408	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977953	131977953	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375710541	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	145	185	0	ENST00000265335.6:c.3836G>A	p.Arg1279His	p.R1279H	ENST00000265335		1279	cGt/cAt	25/25	1	2	FACETS	0.998	0.92	1	0.998	0.92	1	CLONAL	1	TRUE	1	0.728429687667114	2		185	399	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459680	149459680	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	212	344	0	ENST00000286301.3:c.527A>G	p.Gln176Arg	p.Q176R	ENST00000286301	NM_005211.3	176	cAa/cGa	4/22	1	2	FACETS	0.768	0.715	0.822	0.768	0.715	0.822	SUBCLONAL	1	TRUE	1	0.728429687667114	2		344	758	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827157	170827159	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TGA	TGA	-	rs746541921	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	101	144	0	ENST00000296930.5:c.538_540del	p.Asp180del	p.D180del	ENST00000296930	NM_002520.6	175	gaTGAt/gat	7/11	1	2	FACETS	0.792	0.715	0.873	0.792	0.715	0.873	SUBCLONAL	1	TRUE	1	0.728429687667114	2		144	350	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045918	180045920	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CTC	CTC	-	rs746341092	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	203	342	0	ENST00000261937.6:c.2851_2853del	p.Glu951del	p.E951del	ENST00000261937	NM_182925.4	951	GAG/-	21/30	1	2	FACETS	0.971	0.907	1	0.971	0.907	1	CLONAL	1	TRUE	1	0.728429687667114	2		342	574	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322261	31322262	+	frameshift_variant,stop_lost	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	36	145	0	ENST00000412585.2:c.1087dup	p.Ter363LeufsTer37	p.*363Lfs*37	ENST00000412585	NM_005514.6	363	tga/tTga	7/8	0.728429687667114	2	FACETS	0.321	0.264	0.384	0.16	0.132	0.192	SUBCLONAL	1	TRUE	0	0.728429687667114	2		145	308	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323288	31323288	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	43	119	0	ENST00000412585.2:c.701C>A	p.Pro234His	p.P234H	ENST00000412585	NM_005514.6	234	cCt/cAt	4/8	0.728429687667114	2	FACETS	0.3	0.252	0.354	0.15	0.126	0.177	SUBCLONAL	1	TRUE	0	0.728429687667114	2		119	393	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622135	117622135	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	72	176	0	ENST00000368508.3:c.6733+2T>C		p.X2245_splice	ENST00000368508	NM_002944.2	2245			1	2	FACETS	0.679	0.599	0.764	0.679	0.599	0.764	SUBCLONAL	1	TRUE	1	0.728429687667114	2		176	291	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674204	117674204	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	69	252	0	ENST00000368508.3:c.4270C>A	p.Leu1424Ile	p.L1424I	ENST00000368508	NM_002944.2	1424	Cta/Ata	26/43	1	2	FACETS	0.298	0.259	0.34	0.298	0.259	0.34	SUBCLONAL	1	TRUE	1	0.728429687667114	2		252	635	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519505	137519506	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs780346130	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	165	474	4	ENST00000367739.4:c.1132_1133del	p.Ser378PhefsTer6	p.S378Ffs*6	ENST00000367739	NM_000416.2	378	AGt/t	7/7	1	2	FACETS	0.644	0.593	0.698	0.644	0.593	0.698	SUBCLONAL	1	TRUE	1	0.728429687667114	2		478	703	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137528164	137528164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs538147969	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	143	172	0	ENST00000367739.4:c.136G>A	p.Val46Ile	p.V46I	ENST00000367739	NM_000416.2	46	Gta/Ata	2/7	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.728429687667114	2		172	347	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129396	152129396	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	230	332	0	ENST00000206249.3:c.349C>A	p.Leu117Met	p.L117M	ENST00000206249	NM_000125.3	117	Ctg/Atg	1/8	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.728429687667114	2		332	608	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739873	41739873	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1261664857	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	260	264	0	ENST00000242208.4:c.100G>A	p.Asp34Asn	p.D34N	ENST00000242208	NM_002192.2	34	Gac/Aac	2/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.728429687667114	2		264	659	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444246	50444246	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	223	274	0	ENST00000331340.3:c.176T>C	p.Val59Ala	p.V59A	ENST00000331340	NM_006060.4	59	gTa/gCa	4/8	1	2	FACETS	0.926	0.867	0.987	0.926	0.867	0.987	CLONAL	1	TRUE	1	0.728429687667114	2		274	661	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240738	55240738	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	171	369	0	ENST00000275493.2:c.1982C>T	p.Ala661Val	p.A661V	ENST00000275493	NM_005228.3	661	gCc/gTc	17/28	1	2	FACETS	0.548	0.505	0.594	0.548	0.505	0.594	SUBCLONAL	1	TRUE	1	0.728429687667114	2		369	856	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	160	452	7	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	0.589	0.541	0.639	0.589	0.541	0.639	SUBCLONAL	1	TRUE	1	0.728429687667114	2		459	746	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862878	117862878	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	24	114	0	ENST00000297338.2:c.1599del	p.Glu534LysfsTer78	p.E534Kfs*78	ENST00000297338	NM_006265.2	533	aaA/aa	12/14	1	2	FACETS	0.29	0.228	0.361	0.29	0.228	0.361	SUBCLONAL	1	TRUE	1	0.728429687667114	2		114	227	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2039776	2039777	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAG	rs113070757	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	170	377	0	ENST00000349721.2:c.705_707dup	p.Gln238dup	p.Q238dup	ENST00000349721	NM_003070.3	238	-/CAG	4/34	1	2	FACETS	0.541	0.497	0.586	0.541	0.497	0.586	SUBCLONAL	1	TRUE	1	0.728429687667114	2		377	863	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331715	8331715	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	91	240	0	ENST00000356435.5:c.5401A>G	p.Arg1801Gly	p.R1801G	ENST00000356435		1801	Agg/Ggg	33/35	1	2	FACETS	0.37	0.329	0.415	0.37	0.329	0.415	SUBCLONAL	1	TRUE	1	0.728429687667114	2		240	675	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389269	8389269	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	55	204	0	ENST00000356435.5:c.4349C>T	p.Thr1450Ile	p.T1450I	ENST00000356435		1450	aCa/aTa	26/35	1	2	FACETS	0.381	0.327	0.44	0.381	0.327	0.44	SUBCLONAL	1	TRUE	1	0.728429687667114	2		204	396	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27172734	27172734	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774928388	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	217	214	0	ENST00000380036.4:c.749C>T	p.Thr250Met	p.T250M	ENST00000380036	NM_000459.3	250	aCg/aTg	5/23	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.728429687667114	2		214	585	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185545	27185545	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1564083506	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	82	275	0	ENST00000380036.4:c.1250del	p.Pro417LeufsTer10	p.P417Lfs*10	ENST00000380036	NM_000459.3	415	ctC/ct	9/23	1	2	FACETS	0.278	0.245	0.314	0.278	0.245	0.314	SUBCLONAL	1	TRUE	1	0.728429687667114	2		275	809	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321297	1321297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370445430	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	250	305	0	ENST00000400841.2:c.458G>A	p.Arg153Gln	p.R153Q	ENST00000400841		153	cGg/cAg	4/6	1	1	FACETS	0.583	0.548	0.62	0.583	0.548	0.62	SUBCLONAL	1	TRUE	0	0.728429687667114	1		305	748	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411246	63411246	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	262	210	0	ENST00000330258.3:c.1921C>T	p.Arg641Ter	p.R641*	ENST00000330258	NM_152424.3	641	Cga/Tga	2/2	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.728429687667114	1		210	358	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891544	76891544	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	111	81	0	ENST00000373344.5:c.4561A>T	p.Ile1521Leu	p.I1521L	ENST00000373344	NM_000489.3	1521	Ata/Tta	16/35	1	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.728429687667114	1		81	170	SUCCESS
BTK	695	MSKCC	GRCh37	X	100629548	100629549	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs886041148	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	85	113	0	ENST00000308731.7:c.215dup	p.Asn72LysfsTer13	p.N72Kfs*13	ENST00000308731	NM_000061.2	72	aat/aaAt	3/19	1	1	FACETS	0.687	0.619	0.756	0.687	0.619	0.756	SUBCLONAL	1	TRUE	0	0.728429687667114	1		113	216	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215311	123215311	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	101	62	0	ENST00000218089.9:c.2857C>T	p.Arg953Ter	p.R953*	ENST00000218089	NM_001042749.1	953	Cga/Tga	28/35	1	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.728429687667114	1		62	159	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49724809	49724809	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243595850	NA	P-0064724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	13	183	0	ENST00000449682.2:c.458C>T	p.Pro153Leu	p.P153L	ENST00000449682	NM_020998.3	153	cCa/cTa	4/18	0.728429687667114	2	FACETS	0.337	0.242	0.449	0.168	0.121	0.225	SUBCLONAL	1	TRUE	0	0.728429687667114	2		183	106	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593613	55593613	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913521	NA	P-0064725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	360	441	0	ENST00000288135.5:c.1679T>A	p.Val560Asp	p.V560D	ENST00000288135	NM_000222.2	560	gTt/gAt	11/21	0.920057000489878	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.920057000489878	1		441	399	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0064727-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	221	845	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	1	2	FACETS	0.799	0.743	0.857	0.799	0.743	0.857	SUBCLONAL	1	TRUE	1	0.502230844630351	2		845	1102	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492904	56492905	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0064727-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1408	167	637	0	ENST00000407977.2:c.34dup	p.Leu12ProfsTer28	p.L12Pfs*28	ENST00000407977		12	ctc/cCtc	2/10	0.502230844630351	9	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.502230844630351	9		637	1575	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0064728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	70	845	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	1	2	FACETS	0.992	0.868	1	0.992	0.868	1	CLONAL	1	TRUE	1	0.323849444844122	2		845	436	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0064728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	33	386	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.323849444844122	1	FACETS	0.933	0.768	1	0.933	0.768	1	CLONAL	1	TRUE	0	0.323849444844122	1		386	183	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440093	99440093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	43	478	0	ENST00000268035.6:c.1061C>T	p.Thr354Ile	p.T354I	ENST00000268035	NM_000875.3	354	aCc/aTc	4/21	1	2	FACETS	0.865	0.727	1	0.865	0.727	1	CLONAL	1	TRUE	1	0.323849444844122	2		478	307	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100149	27100150	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0064728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	67	957	0	ENST00000324856.7:c.3946dup	p.Ser1316PhefsTer7	p.S1316Ffs*7	ENST00000324856	NM_006015.4	1315	-/T	16/20	1	2	FACETS	0.926	0.807	1	0.926	0.807	1	CLONAL	1	TRUE	1	0.323849444844122	2		957	447	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0064734-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	78	176	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.472597419274917	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.472597419274917	1		176	236	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0064734-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	127	287	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.22444703968669	3	FACETS	0.816	0.746	0.889	0.816	0.746	0.889	INDETERMINATE	2	TRUE	1	0.472597419274917	3		287	407	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0064734-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	219	547	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.471799267708858	2	FACETS	0.865	0.812	0.918	0.865	0.812	0.918	CLONAL	2	TRUE	0	0.472597419274917	2		547	536	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022436	12022436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150089916	NA	P-0064734-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	91	701	3	ENST00000396373.4:c.542G>A	p.Arg181His	p.R181H	ENST00000396373	NM_001987.4	181	cGc/cAc	5/8	0.244843652010364	3	FACETS	0.557	0.494	0.625	0.278	0.247	0.313	INDETERMINATE	1	TRUE	1	0.472597419274917	3		704	855	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990615	7990615	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs143526675	NA	P-0064734-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	34	241	0	ENST00000319144.4:c.146C>T	p.Ala49Val	p.A49V	ENST00000319144	NM_001139.2	49	gCg/gTg	1/15	0.33780870334847	1	FACETS	0.445	0.365	0.533	0.445	0.365	0.533	SUBCLONAL	1	TRUE	0	0.472597419274917	1		241	247	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946245	55946245	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243160272	NA	P-0064734-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	75	489	0	ENST00000263923.4:c.3934G>A	p.Asp1312Asn	p.D1312N	ENST00000263923	NM_002253.2	1312	Gat/Aat	30/30	0.33780870334847	1	FACETS	0.399	0.349	0.452	0.399	0.349	0.452	SUBCLONAL	1	TRUE	0	0.472597419274917	1		489	608	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247847	59247847	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064734-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	162	565	0	ENST00000371222.2:c.896A>G	p.Asn299Ser	p.N299S	ENST00000371222	NM_002228.3	299	aAc/aGc	1/1	0.33780870334847	1	FACETS	0.767	0.705	0.83	0.767	0.705	0.83	SUBCLONAL	1	TRUE	0	0.472597419274917	1		565	683	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439883	52439883	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064735-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	113	471	0	ENST00000460680.1:c.829C>T	p.Gln277Ter	p.Q277*	ENST00000460680	NM_004656.3	277	Caa/Taa	10/17	1	2	FACETS	0.961	0.869	1	0.961	0.869	1	CLONAL	1	TRUE	1	0.48	2		471	490	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439246	52439246	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064735-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	105	583	0	ENST00000460680.1:c.996del	p.Lys333SerfsTer2	p.K333Sfs*2	ENST00000460680	NM_004656.3	332	ccC/cc	11/17	1	2	FACETS	0.884	0.795	0.977	0.884	0.795	0.977	CLONAL	1	TRUE	1	0.48	2		583	495	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271443	38271443	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	107	579	0	ENST00000425967.3:c.2378C>T	p.Ser793Phe	p.S793F	ENST00000425967	NM_001174067.1	793	tCc/tTc	18/19	0.359081952798678	3	FACETS	0.919	0.825	1	0.46	0.412	0.51	CLONAL	1	TRUE	1	0.381985309552296	3		579	726	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0064737-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	128	354	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.550281796667779	2		354	440	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0064737-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	201	290	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.508767294913557	2	FACETS	0.982	0.926	1	0.982	0.926	1	CLONAL	2	FALSE	0	0.550281796667779	2		290	372	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0064737-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	195	650	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.527608168279664	1	FACETS	0.919	0.857	0.983	0.919	0.857	0.983	CLONAL	1	FALSE	0	0.550281796667779	1		650	559	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589599	67589604	+	inframe_deletion	In_Frame_Del	DEL	TCAGTT	TCAGTT	-	novel	NA	P-0064737-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	90	286	0	ENST00000274335.5:c.1365_1370del	p.Phe456_Gln457del	p.F456_Q457del	ENST00000274335		454	acTCAGTTt/act	10/15	1	2	FACETS	0.87	0.778	0.967	0.87	0.778	0.967	CLONAL	1	FALSE	1	0.550281796667779	2		286	376	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55130043	55130043	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774431464	NA	P-0064737-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	124	446	0	ENST00000257290.5:c.577G>A	p.Val193Ile	p.V193I	ENST00000257290	NM_006206.4	193	Gtc/Atc	4/23	0.139247204262516	0	FACETS	0.419	0.381	0.458			1	INDETERMINATE	1	FALSE	0	0.550281796667779	0		446	484	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114905790	114905790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064737-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	123	298	0	ENST00000543371.1:c.809C>T	p.Pro270Leu	p.P270L	ENST00000543371	NM_001198531.1	270	cCa/cTa	8/14	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	1	0.550281796667779	2		298	441	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007713	45007713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148494241	NA	P-0064737-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	86	476	0	ENST00000558401.1:c.160G>A	p.Asp54Asn	p.D54N	ENST00000558401	NM_004048.2	54	Gac/Aac	2/4	0.294852180834196	1	FACETS	0.371	0.328	0.416	0.371	0.328	0.416	INDETERMINATE	1	FALSE	0	0.550281796667779	1		476	611	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780812	9780812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765797019	NA	P-0064737-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	146	519	0	ENST00000377346.4:c.1534C>T	p.Arg512Trp	p.R512W	ENST00000377346	NM_005026.3	512	Cgg/Tgg	13/24	1	2	FACETS	0.963	0.884	1	0.963	0.884	1	CLONAL	1	FALSE	1	0.550281796667779	2		519	551	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153569	108153569	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064737-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	52	318	0	ENST00000278616.4:c.3709A>G	p.Ile1237Val	p.I1237V	ENST00000278616	NM_000051.3	1237	Att/Gtt	25/63	0.294852180834196	1	FACETS	0.387	0.331	0.448	0.387	0.331	0.448	INDETERMINATE	1	FALSE	0	0.550281796667779	1		318	354	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827966	40827966	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064737-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	94	474	0	ENST00000373198.4:c.2462C>A	p.Ala821Asp	p.A821D	ENST00000373198	NM_133170.3	821	gCc/gAc	17/32	0.227049417562803	2	FACETS	0.604	0.538	0.673	0.302	0.269	0.337	INDETERMINATE	1	FALSE	0	0.550281796667779	2		474	566	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564172	139564173	+	inframe_insertion,splice_region_variant	In_Frame_Ins	INS	-	-	GGT	novel	NA	P-0064737-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	101	403	0	ENST00000308874.7:c.313+1_313+3dup		p.G103dup	ENST00000308874		103	-/GGT	5/10	1	2	FACETS	0.846	0.761	0.935	0.846	0.761	0.935	CLONAL	1	FALSE	1	0.550281796667779	2		403	434	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510648	38510648	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	41	616	0	ENST00000254066.5:c.902G>T	p.Gly301Val	p.G301V	ENST00000254066	NM_000964.3	301	gGc/gTc	7/9	1	2	FACETS	0.263	0.219	0.312	0.263	0.219	0.312	SUBCLONAL	1	TRUE	1	0.762863843771675	2		616	408	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510576	38510576	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	20	503	0	ENST00000254066.5:c.830A>G	p.Tyr277Cys	p.Y277C	ENST00000254066	NM_000964.3	277	tAc/tGc	7/9	1	2	FACETS	0.155	0.118	0.198	0.155	0.118	0.198	SUBCLONAL	1	TRUE	1	0.762863843771675	2		503	339	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	280	344	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.616482737402832	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	1	0.616482737402832	3		344	593	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368208	45368208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	170	349	0	ENST00000262160.6:c.1394G>A	p.Ser465Asn	p.S465N	ENST00000262160	NM_005901.5	465	aGc/aAc	11/11	0.616482737402832	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.616482737402832	1		349	362	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0064739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	574	430	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.613344505165537	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.616482737402832	3		430	778	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440379	52440379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	222	495	0	ENST00000460680.1:c.673G>A	p.Asp225Asn	p.D225N	ENST00000460680	NM_004656.3	225	Gac/Aac	9/17	0.606273386842165	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.616482737402832	1		495	477	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672759	86672759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	316	409	1	ENST00000274376.6:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000274376	NM_002890.2	749	cGa/cAa	17/25	0.616482737402832	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.616482737402832	2		410	504	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434793	99434793	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201529410	NA	P-0064739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	331	445	0	ENST00000268035.6:c.880G>A	p.Glu294Lys	p.E294K	ENST00000268035	NM_000875.3	294	Gag/Aag	3/21	0.616482737402832	2	FACETS	0.944	0.903	0.983	0.944	0.903	0.983	CLONAL	2	TRUE	0	0.616482737402832	2		445	569	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358581	67358581	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	406	505	0	ENST00000327367.4:c.89G>A	p.Trp30Ter	p.W30*	ENST00000327367	NM_005902.3	30	tGg/tAg	1/9	0.616482737402832	2	FACETS	0.954	0.918	0.991	0.954	0.918	0.991	CLONAL	2	TRUE	0	0.616482737402832	2		505	690	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217304	66217304	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs549914252	NA	P-0064739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	160	396	0	ENST00000273854.3:c.2311C>A	p.Gln771Lys	p.Q771K	ENST00000273854	NM_004439.5	771	Cag/Aag	14/18	0.160937652629316	0	FACETS	0.44	0.407	0.474			1	INDETERMINATE	1	TRUE	0	0.616482737402832	0		396	452	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299916	15299916	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	207	544	0	ENST00000263388.2:c.1262G>A	p.Arg421His	p.R421H	ENST00000263388	NM_000435.2	421	cGt/cAt	8/33	0.616482737402832	3	FACETS	0.9	0.835	0.967	0.45	0.417	0.484	CLONAL	1	TRUE	1	0.616482737402832	3		544	976	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348637	89348637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	388	493	0	ENST00000301030.4:c.4313C>T	p.Ser1438Phe	p.S1438F	ENST00000301030	NM_001256183.1	1438	tCc/tTc	9/13	0.616482737402832	3	FACETS	0.981	0.938	1	0.981	0.938	1	CLONAL	2	TRUE	1	0.616482737402832	3		493	839	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482338	56482338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	348	396	0	ENST00000267101.3:c.886G>A	p.Val296Met	p.V296M	ENST00000267101	NM_001982.3	296	Gtg/Atg	8/28	0.616482737402832	3	FACETS	0.943	0.898	0.988	0.943	0.898	0.988	CLONAL	2	TRUE	1	0.616482737402832	3		396	783	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794772	242794772	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0064739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	160	403	0	ENST00000334409.5:c.436+1G>A		p.X146_splice	ENST00000334409	NM_005018.2	146			0.616482737402832	3	FACETS	1	0.937	1	0.511	0.469	0.553	CLONAL	1	TRUE	1	0.616482737402832	3		403	665	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921533	178921534	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTTGTGCACTTG	novel	NA	P-0064739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	119	367	0	ENST00000263967.3:c.1023_1024insCTTGTTTGTGCA	p.Ala341_Thr342insLeuValCysAla	p.A341_T342insLVCA	ENST00000263967	NM_006218.2	339	ctt/cTTTGTGCACTTGtt	5/21	1	2	FACETS	0.796	0.722	0.873	0.796	0.722	0.873	SUBCLONAL	1	TRUE	1	0.616482737402832	2		367	485	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553423	106553423	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	187	471	0	ENST00000369096.4:c.1388C>A	p.Pro463His	p.P463H	ENST00000369096	NM_001198.3	463	cCc/cAc	5/7	1	2	FACETS	0.963	0.894	1	0.963	0.894	1	CLONAL	1	TRUE	1	0.616482737402832	2		471	630	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0064740-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	171	344	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.932	0.863	1	0.932	0.863	1	CLONAL	1	TRUE	1	0.681001781374488	2		344	539	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0064740-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	370	85	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.681001781374488	15	FACETS	1	0.963	1	0.391	0.371	0.411	CLONAL	5	TRUE	2	0.681001781374488	15		85	1160	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38632026	38632026	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0064740-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	169	342	0	ENST00000299084.4:c.512C>G	p.Ser171Ter	p.S171*	ENST00000299084	NM_152594.2	171	tCa/tGa	5/7	1	2	FACETS	0.944	0.874	1	0.944	0.874	1	CLONAL	1	TRUE	1	0.681001781374488	2		342	526	SUCCESS
EED	8726	MSKCC	GRCh37	11	85967435	85967435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064740-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	174	333	0	ENST00000263360.6:c.433G>A	p.Glu145Lys	p.E145K	ENST00000263360	NM_003797.3	145	Gaa/Aaa	5/12	0.680748845259666	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.681001781374488	1		333	303	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341230	89341230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064740-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	126	385	0	ENST00000301030.4:c.7705G>A	p.Glu2569Lys	p.E2569K	ENST00000301030	NM_001256183.1	2569	Gag/Aag	11/13	1	2	FACETS	0.964	0.882	1	0.964	0.882	1	CLONAL	1	TRUE	1	0.681001781374488	2		385	384	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119056	70119056	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201541265	NA	P-0064740-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	354	507	1	ENST00000245479.2:c.628G>A	p.Asp210Asn	p.D210N	ENST00000245479	NM_000346.3	210	Gac/Aac	2/3	0.658530463467916	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.681001781374488	3		508	688	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178577	56178577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064740-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	168	454	0	ENST00000399503.3:c.3550G>A	p.Glu1184Lys	p.E1184K	ENST00000399503	NM_005921.1	1184	Gaa/Aaa	14/20	0.290574143792321	3	FACETS	1	0.973	1	0.557	0.514	0.601	INDETERMINATE	1	TRUE	1	0.681001781374488	3		454	594	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0064741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	202	568	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.341563437062244	2	FACETS	0.985	0.922	1	0.985	0.922	1	CLONAL	2	TRUE	0	0.409968061864547	2		568	500	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692943	89692956	+	frameshift_variant	Frame_Shift_Del	DEL	GGCAAATTTTTAAA	GGCAAATTTTTAAA	-	novel	NA	P-0064741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	209	478	0	ENST00000371953.3:c.431_444del	p.Lys144ThrfsTer31	p.K144Tfs*31	ENST00000371953	NM_000314.4	143	GGCAAATTTTTAAAg/g	5/9	0.348425999326981	3	FACETS	1	0.988	1	0.822	0.771	0.874	CLONAL	2	TRUE	0	0.409968061864547	3		478	498	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264222	46264222	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	252	507	0	ENST00000371998.3:c.1269C>G	p.Ser423Arg	p.S423R	ENST00000371998		423	agC/agG	11/23	0.411331372338519	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.409968061864547	2		507	611	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212759	27212759	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	203	504	0	ENST00000380036.4:c.2741T>A	p.Leu914His	p.L914H	ENST00000380036	NM_000459.3	914	cTt/cAt	17/23	0.405535967673044	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.409968061864547	2		504	481	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0064756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	148	476	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.77	2		476	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782082	NA	P-0064759-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	13	531	0	ENST00000269305.4:c.745A>T	p.Arg249Trp	p.R249W	ENST00000269305	NM_001126112.2	249	Agg/Tgg	7/11	1	2	FACETS	0.276	0.196	0.375	0.276	0.196	0.375	SUBCLONAL	1	TRUE	1	0.23	2		531	409	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0064759-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	15	317	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.396	0.289	0.526	0.396	0.289	0.526	SUBCLONAL	1	TRUE	1	0.23	2		317	329	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0064760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	122	631	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.60951818866584	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.60951818866584	1		631	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0064761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	97	355	1	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.283601311705717	2	FACETS	0.753	0.678	0.831	0.753	0.678	0.831	SUBCLONAL	2	TRUE	0	0.37872105572906	2		356	340	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11552822	NA	P-0064761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	81	419	0	ENST00000304494.5:c.250G>T	p.Asp84Tyr	p.D84Y	ENST00000304494	NM_000077.4	84	Gac/Tac	2/3	0.273553959519518	2	FACETS	1	0.942	1	0.551	0.488	0.618	CLONAL	1	TRUE	0	0.37872105572906	2		419	388	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31401618	31401618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	36	303	0	ENST00000344624.3:c.4046G>A	p.Arg1349Lys	p.R1349K	ENST00000344624		1349	aGa/aAa	33/33	0.37872105572906	5	FACETS	0.651	0.535	0.781	0.217	0.178	0.261	SUBCLONAL	1	TRUE	2	0.37872105572906	5		303	458	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40364003	40364003	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	77	326	0	ENST00000293328.3:c.1679G>C	p.Arg560Thr	p.R560T	ENST00000293328	NM_012448.3	560	aGg/aCg	13/19	0.285267630297535	4	FACETS	0.774	0.684	0.87	0.774	0.684	0.87	SUBCLONAL	2	TRUE	2	0.37872105572906	4		326	362	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602803	10602803	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	236	475	0	ENST00000171111.5:c.775C>T	p.Gln259Ter	p.Q259*	ENST00000171111	NM_203500.1	259	Cag/Tag	3/6	0.37872105572906	3	FACETS	1	0.99	1	0.833	0.784	0.884	CLONAL	2	TRUE	0	0.37872105572906	3		475	593	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423001	47423001	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	229	397	0	ENST00000404338.3:c.1069G>T	p.Glu357Ter	p.E357*	ENST00000404338	NM_004491.4	357	Gaa/Taa	1/6	0.37872105572906	3	FACETS	0.901	0.848	0.955	0.901	0.848	0.955	CLONAL	3	TRUE	0	0.37872105572906	3		397	532	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426682	212426682	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	88	400	0	ENST00000342788.4:c.2433C>A	p.His811Gln	p.H811Q	ENST00000342788	NM_005235.2	811	caC/caA	20/28	0.291880465438939	3	FACETS	1	0.971	1	0.64	0.57	0.714	CLONAL	1	TRUE	1	0.37872105572906	3		400	432	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371690	225371691	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0064761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	45	366	0	ENST00000264414.4:c.913_914del	p.Arg305CysfsTer10	p.R305Cfs*10	ENST00000264414	NM_003590.4	305	CGt/t	7/16	0.291880465438939	3	FACETS	0.728	0.614	0.855	0.364	0.307	0.428	SUBCLONAL	1	TRUE	1	0.37872105572906	3		366	388	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386315	31386315	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1488463962	NA	P-0064761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	38	483	0	ENST00000328111.2:c.1540G>T	p.Ala514Ser	p.A514S	ENST00000328111	NM_006892.3	514	Gcc/Tcc	15/23	0.37872105572906	4	FACETS	0.451	0.372	0.539	0.15	0.124	0.18	SUBCLONAL	1	TRUE	1	0.37872105572906	4		483	614	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155417	47155417	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	76	324	0	ENST00000409792.3:c.4664T>G	p.Ile1555Arg	p.I1555R	ENST00000409792	NM_014159.6	1555	aTa/aGa	5/21	0.283601311705717	2	FACETS	1	0.934	1	0.544	0.48	0.612	CLONAL	1	TRUE	0	0.37872105572906	2		324	369	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045710	26045710	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	234	438	0	ENST00000540144.1:c.72A>T	p.Lys24Asn	p.K24N	ENST00000540144	NM_003531.2	24	aaA/aaT	1/1	0.37872105572906	4	FACETS	0.912	0.856	0.968	0.912	0.856	0.968	CLONAL	3	TRUE	1	0.37872105572906	4		438	623	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508220	106508220	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	226	429	0	ENST00000359195.3:c.214G>C	p.Ala72Pro	p.A72P	ENST00000359195	NM_002649.2	72	Gcc/Ccc	2/11	0.37872105572906	5	FACETS	1	0.942	1	1	0.942	1	CLONAL	3	TRUE	2	0.37872105572906	5		429	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0064763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	220	712	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.609941630650825	1	FACETS	0.957	0.899	1	0.957	0.899	1	CLONAL	1	TRUE	0	0.609941630650825	1		712	524	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	371	389	0	ENST00000397062.3:c.92G>C	p.Gly31Ala	p.G31A	ENST00000397062	NM_006164.4	31	gGa/gCa	2/5	0.598537435914664	2	FACETS	0.996	0.957	1	0.996	0.957	1	CLONAL	2	TRUE	0	0.609941630650825	2		389	611	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914004	32914004	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	53	473	0	ENST00000380152.3:c.5512G>C	p.Glu1838Gln	p.E1838Q	ENST00000380152		1838	Gag/Cag	11/27	1	2	FACETS	0.318	0.271	0.369	0.318	0.271	0.369	SUBCLONAL	1	TRUE	1	0.609941630650825	2		473	547	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0064765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	204	210	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.684731374624113	5	FACETS	0.972	0.9	1	0.243	0.225	0.262	CLONAL	1	TRUE	1	0.722493017905117	5		210	1211	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0064765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	126	496	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	0.419881819335999	1	FACETS	0.385	0.35	0.422	0.385	0.35	0.422	INDETERMINATE	1	TRUE	0	0.722493017905117	1		496	578	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs121913292	NA	P-0064765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	143	158	0	ENST00000371953.3:c.389del	p.Arg130GlnfsTer4	p.R130Qfs*4	ENST00000371953	NM_000314.4	130	cGa/ca	5/9	1	2	FACETS	0.985	0.907	1	0.985	0.907	1	CLONAL	1	TRUE	1	0.722493017905117	2		158	402	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615577	43615577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146838520	NA	P-0064765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	238	648	0	ENST00000355710.3:c.2656C>T	p.Arg886Trp	p.R886W	ENST00000355710	NM_020975.4	886	Cgg/Tgg	15/20	1	2	FACETS	0.943	0.884	1	0.943	0.884	1	CLONAL	1	TRUE	1	0.722493017905117	2		648	699	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370985	55370985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	107	520	0	ENST00000297316.4:c.287C>G	p.Ala96Gly	p.A96G	ENST00000297316	NM_022454.3	96	gCc/gGc	1/2	1	2	FACETS	0.465	0.418	0.515	0.465	0.418	0.515	SUBCLONAL	1	TRUE	1	0.722493017905117	2		520	637	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106617	27106617	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	132	762	0	ENST00000324856.7:c.6228C>A	p.Tyr2076Ter	p.Y2076*	ENST00000324856	NM_006015.4	2076	taC/taA	20/20	0.419881819335999	1	FACETS	0.356	0.324	0.39	0.356	0.324	0.39	INDETERMINATE	1	TRUE	0	0.722493017905117	1		762	655	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653751	89653781	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	AGATATTTCTTTCCTTAACTAAAGTACTCAG	AGATATTTCTTTCCTTAACTAAAGTACTCAG	-	novel	NA	P-0064765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	60	289	0	ENST00000371953.3:c.80-30_80del		p.X27_splice	ENST00000371953	NM_000314.4	27			1	2	FACETS	0.644	0.56	0.733	0.644	0.56	0.733	SUBCLONAL	1	TRUE	1	0.722493017905117	2		289	258	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765640	41765640	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	106	697	0	ENST00000301178.4:c.2516G>C	p.Gly839Ala	p.G839A	ENST00000301178	NM_021913.4	839	gGa/gCa	20/20	0.419881819335999	1	FACETS	0.329	0.296	0.365	0.329	0.296	0.365	INDETERMINATE	1	TRUE	0	0.722493017905117	1		697	569	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239881	53239881	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	144	577	0	ENST00000375401.3:c.1560T>A	p.Ser520Arg	p.S520R	ENST00000375401	NM_004187.3	520	agT/agA	11/26	1	2	FACETS	0.619	0.566	0.674	0.619	0.566	0.674	SUBCLONAL	1	TRUE	1	0.722493017905117	2		577	644	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0064767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	28	377	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.573	0.457	0.706	0.573	0.457	0.706	SUBCLONAL	1	TRUE	1	0.18	2		377	543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0064767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	57	473	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.18	2		473	554	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111467	56111467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	26	453	0	ENST00000399503.3:c.67G>A	p.Glu23Lys	p.E23K	ENST00000399503	NM_005921.1	23	Gag/Aag	1/20	1	2	FACETS	0.666	0.526	0.826	0.666	0.526	0.826	SUBCLONAL	1	TRUE	1	0.18	2		453	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0064770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	53	583	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.744104700558626	1	FACETS	0.877	0.778	0.975	0.877	0.778	0.975	CLONAL	1	TRUE	0	0.744104700558626	1		583	102	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074171	8074171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	62	460	0	ENST00000377482.5:c.488C>T	p.Ser163Phe	p.S163F	ENST00000377482	NM_018948.3	163	tCt/tTt	4/4	1	2	FACETS	0.921	0.811	1	0.921	0.811	1	CLONAL	1	TRUE	1	0.744104700558626	2		460	181	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0064770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	33	308	0	ENST00000311936.3:c.180_181delinsAA	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggAAaa	3/5	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.744104700558626	2		308	78	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	69061225	69061225	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	11	194	0	ENST00000487270.1:c.1060C>T	p.Gln354Ter	p.Q354*	ENST00000487270	NM_133509.3	354	Caa/Taa	11/11	0.744104700558626	1	FACETS	0.241	0.169	0.328	0.241	0.169	0.328	SUBCLONAL	1	TRUE	0	0.744104700558626	1		194	77	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479787	67479787	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	21	376	0	ENST00000327367.4:c.1094A>C	p.Gln365Pro	p.Q365P	ENST00000327367	NM_005902.3	365	cAg/cCg	8/9	0.221820534881091	1	FACETS	0.153	0.118	0.193	0.153	0.118	0.193	INDETERMINATE	1	TRUE	0	0.744104700558626	1		376	232	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812182	212812182	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064781-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	76	486	0	ENST00000342788.4:c.394C>T	p.Gln132Ter	p.Q132*	ENST00000342788	NM_005235.2	132	Caa/Taa	3/28	0.395302166838076	3	FACETS	0.934	0.821	1	0.467	0.41	0.527	CLONAL	1	TRUE	1	0.404416856027426	3		486	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579365	7579365	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782461	NA	P-0064781-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	218	600	0	ENST00000269305.4:c.322G>T	p.Gly108Cys	p.G108C	ENST00000269305	NM_001126112.2	108	Ggt/Tgt	4/11	0.404416856027426	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.404416856027426	2		600	531	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0064781-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	118	311	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.404416856027426	2	FACETS	0.938	0.859	1	0.938	0.859	1	CLONAL	2	TRUE	0	0.404416856027426	2		311	311	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748512	162748512	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064781-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	331	487	0	ENST00000367921.3:c.2426G>C	p.Gly809Ala	p.G809A	ENST00000367921	NM_006182.2	809	gGg/gCg	17/18	0.404416856027426	6	FACETS	0.97	0.923	1	0.97	0.923	1	CLONAL	4	TRUE	2	0.404416856027426	6		487	763	SUCCESS
SCG5	6447	MSKCC	GRCh37	15	32976867	32976867	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064781-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	165	450	0	ENST00000300175.4:c.486G>T	p.Lys162Asn	p.K162N	ENST00000300175	NM_001144757.1	162	aaG/aaT	4/6	0.395302166838076	3	FACETS	0.898	0.83	0.969	0.898	0.83	0.969	CLONAL	2	TRUE	1	0.404416856027426	3		450	546	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610237	10610237	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064781-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	218	612	0	ENST00000171111.5:c.473G>T	p.Gly158Val	p.G158V	ENST00000171111	NM_203500.1	158	gGt/gTt	2/6	0.404416856027426	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.404416856027426	2		612	512	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610276	10610276	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064781-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	234	647	0	ENST00000171111.5:c.434T>G	p.Ile145Ser	p.I145S	ENST00000171111	NM_203500.1	145	aTc/aGc	2/6	0.404416856027426	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.404416856027426	2		647	553	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0064795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	32	484	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	0.120368922335691	5	FACETS	0.956	0.782	1	0.478	0.391	0.575	INDETERMINATE	2	FALSE	1	0.209402977881628	5		484	210	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920786	100920786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752995251	NA	P-0064795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	16	447	0	ENST00000325455.5:c.2362C>T	p.Arg788Trp	p.R788W	ENST00000325455	NM_001202474.3	788	Cgg/Tgg	6/8	1	2	FACETS	1	0.767	1	1	0.767	1	CLONAL	1	FALSE	1	0.209402977881628	2		447	148	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589545	67589586	+	inframe_deletion	In_Frame_Del	DEL	TGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATTACA	TGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATTACA	-	novel	NA	P-0064795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	10	154	0	ENST00000274335.5:c.1310_1351del	p.Val437_His450del	p.V437_H450del	ENST00000274335		436	gtTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATTACAt/gtt	10/15	1	2	FACETS	1	0.802	1	1	0.802	1	CLONAL	1	FALSE	1	0.209402977881628	2		154	76	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221702	55221702	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0064795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	51	601	0	ENST00000275493.2:c.748-2A>G		p.X250_splice	ENST00000275493	NM_005228.3	250			1	2	FACETS	0.864	0.734	1	0.864	0.734	1	CLONAL	1	FALSE	1	0.209402977881628	2		601	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0064796-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	124	599	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.200411267271473	1	FACETS	1	0.973	1	1	0.991	1	CLONAL	2	FALSE	0	0.200411267271473	1		599	471	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427227	49427227	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064796-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	117	549	0	ENST00000301067.7:c.11261A>T	p.Gln3754Leu	p.Q3754L	ENST00000301067	NM_003482.3	3754	cAg/cTg	39/54	1	2	FACETS	0.835	0.754	0.921	1	0.986	1	CLONAL	2	FALSE	1	0.200411267271473	2		549	699	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0064797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	365	669	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.637937427761173	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.637937427761173	3		669	742	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0064797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	162	515	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.637937427761173	2		515	492	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0064797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	15	553	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.072	0.052	0.096	0.072	0.052	0.096	SUBCLONAL	1	TRUE	1	0.637937427761173	2		553	652	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131951771	131951771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	162	319	0	ENST00000265335.6:c.3113G>A	p.Arg1038Lys	p.R1038K	ENST00000265335		1038	aGa/aAa	20/25	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.637937427761173	2		319	507	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115435	115115437	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	rs1319662056	NA	P-0064797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	185	517	0	ENST00000257566.3:c.889_891del	p.Asn297del	p.N297del	ENST00000257566	NM_016569.3	297	AAC/-	5/8	1	2	FACETS	0.962	0.893	1	0.962	0.893	1	CLONAL	1	TRUE	1	0.637937427761173	2		517	603	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193530	99193530	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	222	616	0	ENST00000074304.5:c.2725G>C	p.Glu909Gln	p.E909Q	ENST00000074304	NM_001134224.1	909	Gag/Cag	25/26	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.637937427761173	2		616	595	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855936	68855938	+	inframe_deletion	In_Frame_Del	DEL	CTG	CTG	-	rs1555516823	NA	P-0064797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	189	580	0	ENST00000261769.5:c.1747_1749del	p.Leu583del	p.L583del	ENST00000261769	NM_004360.3	582	CTG/-	12/16	0.637937427761173	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.637937427761173	1		580	376	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221613	36221613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	226	672	0	ENST00000222270.7:c.5282C>T	p.Ser1761Phe	p.S1761F	ENST00000222270	NM_014727.1	1761	tCc/tTc	26/37	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.637937427761173	2		672	706	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748338	43748338	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0064797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	218	600	0	ENST00000382044.4:c.2468C>G	p.Ser823Ter	p.S823*	ENST00000382044	NM_001141980.1	823	tCa/tGa	12/28	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.637937427761173	2		600	640	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266822	18266822	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753372060	NA	P-0064797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	201	540	0	ENST00000222254.8:c.133G>A	p.Glu45Lys	p.E45K	ENST00000222254	NM_005027.3	45	Gag/Aag	2/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.637937427761173	2		540	554	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321345	65321345	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	37	598	0	ENST00000342505.4:c.1495C>T	p.Gln499Ter	p.Q499*	ENST00000342505	NM_002227.2	499	Cag/Tag	11/25	0.637937427761173	1	FACETS	0.188	0.154	0.225	0.188	0.154	0.225	SUBCLONAL	1	TRUE	0	0.637937427761173	1		598	421	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228965	36228965	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	244	644	0	ENST00000222270.7:c.7745C>T	p.Ser2582Leu	p.S2582L	ENST00000222270	NM_014727.1	2582	tCa/tTa	36/37	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.637937427761173	2		644	744	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830872	156830872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	241	572	0	ENST00000524377.1:c.146G>A	p.Arg49Gln	p.R49Q	ENST00000524377	NM_002529.3	49	cGa/cAa	1/17	0.320085351178764	6	FACETS	0.861	0.804	0.919	0.574	0.536	0.613	INDETERMINATE	2	TRUE	3	0.637937427761173	6		572	999	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690381	117690381	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	190	479	0	ENST00000369458.3:c.748C>T	p.His250Tyr	p.H250Y	ENST00000369458	NM_024626.3	250	Cac/Tac	5/6	0.637937427761173	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.637937427761173	1		479	383	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574808	64575830	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAAAATTCTGGGACCAGCCCTTTAATGGAGTCAAAGCAATTTCACATCTCAATTCTACTCTCCCAAGAGCCCTGGGAAAGGCCAGGCCAGGAATTACTAACCCATTTTTCCAGGAGGGGAAGCTGAAGCTCAGGAAGGGAAAGTGCCCCTGCCCAGGGTCCCACAGCAAGTCAAGTCTGGCCTAGCCCAGTCCTGCCCCATTGGCTCAGCCCTCACCTGCTGCAGCTGCAGAAGCTCCAGCGAGTCGGTGTGCAGGTCAATGGAAGGGTTGATGGCACACACCATGAACGCCACCTCCATCTTGCGGTCACAGCGCATGTATGATCCTTTCAGGTACAGCCAGCTCTTAGGGGGGGATGAGATCATTATGTCTCATGATGGCCCACCCTGTGCCTGCTTCAGGGAATGACAGCCAGGAAAAGGGGCTCTTCTGTCTTCCCTTCCTATGTGGGTGGTGATGGGAAGAAAGGGGTGTGGCCCAAGAAAATGGAGTCCCTTGGGTGGCTTGGGCTACTACAGTATGAAGGGGACAAGGCTGGGGGGAGGGAACAATACCCGCTCAGCCACACCGGCATTGACTGTCTGGCCCCTGCGGTCCTCGTTGCCCTTGCCGTGCCAGGTGACCTCAGCTGTCTGCTCCCCATTGGGCCCAAACACTACCCAGGCATGATCCTCAGACAGGGCGAGGTGGACATCCCGGAGACCCAGGGCCTGGCAGGCCCCAACCACAGCAAAGGCCACACCGGAGCTGTCCAATTTGGTGCCTGTGGAAGGGGGAGGTAATGAAAGAGGGTCCTCTGTGCTTTAACATGGGGAAAGGGGGCCAGGTAGTGATGGGCCACACTCCCTCCCACTCCCTTTCCAAGCCTGTGACCCAACCTCAGATTCTCCTGCCCACTATCCCTCCATCCCTTCCCTCCCACGTGTTCAAAGACTCTCTCCCTGTTTACACCCTCTATGTCCAACAAGATACCTTTCTGGATATCCTGTAGCTGACCCAGCCTTTGGCCCTACCTCGTCTTT	CAAAATTCTGGGACCAGCCCTTTAATGGAGTCAAAGCAATTTCACATCTCAATTCTACTCTCCCAAGAGCCCTGGGAAAGGCCAGGCCAGGAATTACTAACCCATTTTTCCAGGAGGGGAAGCTGAAGCTCAGGAAGGGAAAGTGCCCCTGCCCAGGGTCCCACAGCAAGTCAAGTCTGGCCTAGCCCAGTCCTGCCCCATTGGCTCAGCCCTCACCTGCTGCAGCTGCAGAAGCTCCAGCGAGTCGGTGTGCAGGTCAATGGAAGGGTTGATGGCACACACCATGAACGCCACCTCCATCTTGCGGTCACAGCGCATGTATGATCCTTTCAGGTACAGCCAGCTCTTAGGGGGGGATGAGATCATTATGTCTCATGATGGCCCACCCTGTGCCTGCTTCAGGGAATGACAGCCAGGAAAAGGGGCTCTTCTGTCTTCCCTTCCTATGTGGGTGGTGATGGGAAGAAAGGGGTGTGGCCCAAGAAAATGGAGTCCCTTGGGTGGCTTGGGCTACTACAGTATGAAGGGGACAAGGCTGGGGGGAGGGAACAATACCCGCTCAGCCACACCGGCATTGACTGTCTGGCCCCTGCGGTCCTCGTTGCCCTTGCCGTGCCAGGTGACCTCAGCTGTCTGCTCCCCATTGGGCCCAAACACTACCCAGGCATGATCCTCAGACAGGGCGAGGTGGACATCCCGGAGACCCAGGGCCTGGCAGGCCCCAACCACAGCAAAGGCCACACCGGAGCTGTCCAATTTGGTGCCTGTGGAAGGGGGAGGTAATGAAAGAGGGTCCTCTGTGCTTTAACATGGGGAAAGGGGGCCAGGTAGTGATGGGCCACACTCCCTCCCACTCCCTTTCCAAGCCTGTGACCCAACCTCAGATTCTCCTGCCCACTATCCCTCCATCCCTTCCCTCCCACGTGTTCAAAGACTCTCTCCCTGTTTACACCCTCTATGTCCAACAAGATACCTTTCTGGATATCCTGTAGCTGACCCAGCCTTTGGCCCTACCTCGTCTTT	-	novel	NA	P-0064797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	69	204	0	ENST00000312049.6:c.446-259_784-117del		p.X149_splice	ENST00000312049	NM_130799.2	149		3-4/10	1	2	FACETS	0.813	0.716	0.915	0.813	0.716	0.915	CLONAL	1	TRUE	1	0.637937427761173	2		204	266	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749392	43749392	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	154	378	0	ENST00000382044.4:c.1414C>G	p.Leu472Val	p.L472V	ENST00000382044	NM_001141980.1	472	Ctg/Gtg	12/28	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.637937427761173	2		378	474	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858517	9858517	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs765370528	NA	P-0064797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	176	622	0	ENST00000330684.3:c.2884G>C	p.Glu962Gln	p.E962Q	ENST00000330684	NM_001134407.1	962	Gaa/Caa	13/13	1	2	FACETS	0.89	0.824	0.958	0.89	0.824	0.958	CLONAL	1	TRUE	1	0.637937427761173	2		622	620	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223578	36223578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	273	670	0	ENST00000222270.7:c.6128C>T	p.Ser2043Phe	p.S2043F	ENST00000222270	NM_014727.1	2043	tCc/tTc	28/37	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.637937427761173	2		670	825	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228580	36228580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	222	629	0	ENST00000222270.7:c.7594C>T	p.Arg2532Trp	p.R2532W	ENST00000222270	NM_014727.1	2532	Cgg/Tgg	34/37	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.637937427761173	2		629	637	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67624602	67624602	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	166	485	0	ENST00000272342.5:c.22G>C	p.Asp8His	p.D8H	ENST00000272342	NM_019002.3	8	Gat/Cat	1/6	1	2	FACETS	0.945	0.873	1	0.945	0.873	1	CLONAL	1	TRUE	1	0.637937427761173	2		485	551	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149238666	149238666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	170	584	0	ENST00000360632.3:c.1129G>A	p.Glu377Lys	p.E377K	ENST00000360632	NM_015472.4	377	Gaa/Aaa	7/7	1	2	FACETS	0.888	0.821	0.958	0.888	0.821	0.958	CLONAL	1	TRUE	1	0.637937427761173	2		584	600	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149375015	149375015	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	221	612	0	ENST00000360632.3:c.79G>T	p.Asp27Tyr	p.D27Y	ENST00000360632	NM_015472.4	27	Gac/Tac	2/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.637937427761173	2		612	635	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540976	187540976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372329367	NA	P-0064797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	166	661	0	ENST00000441802.2:c.6764G>A	p.Arg2255His	p.R2255H	ENST00000441802	NM_005245.3	2255	cGc/cAc	10/27	1	2	FACETS	0.846	0.781	0.914	0.846	0.781	0.914	CLONAL	1	TRUE	1	0.637937427761173	2		661	615	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590490	67590490	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	185	468	0	ENST00000274335.5:c.1552G>C	p.Glu518Gln	p.E518Q	ENST00000274335		518	Gag/Cag	11/15	1	2	FACETS	0.997	0.926	1	0.997	0.926	1	CLONAL	1	TRUE	1	0.637937427761173	2		468	582	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510173	149510173	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	184	595	0	ENST00000261799.4:c.1296G>C	p.Gln432His	p.Q432H	ENST00000261799	NM_002609.3	432	caG/caC	9/23	1	2	FACETS	0.968	0.899	1	0.968	0.899	1	CLONAL	1	TRUE	1	0.637937427761173	2		595	596	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321319	1321319	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	181	561	0	ENST00000400841.2:c.436C>T	p.Leu146Phe	p.L146F	ENST00000400841		146	Ctc/Ttc	4/6	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.637937427761173	2		561	556	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0064830-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	32	311	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.954	0.778	1	0.954	0.778	1	CLONAL	1	TRUE	1	0.237800581079123	2		311	282	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0064830-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	53	1388	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.237800581079123	1	FACETS	0.94	0.803	1	0.94	0.803	1	CLONAL	1	TRUE	0	0.237800581079123	1		1388	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs11575997	NA	P-0064830-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	101	1514	0	ENST00000269305.4:c.993+1G>T		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.150620992228102	2	FACETS	0.797	0.715	0.884	0.797	0.715	0.884	SUBCLONAL	2	TRUE	0	0.237800581079123	2		1514	533	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636650	73636650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064830-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	113	1764	0	ENST00000377687.4:c.913C>T	p.Pro305Ser	p.P305S	ENST00000377687	NM_001730.3	305	Cca/Tca	2/4	0.0780170824338864	3	FACETS	1	0.982	1	0.714	0.642	0.789	INDETERMINATE	1	TRUE	1	0.237800581079123	3		1764	745	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479822	67479822	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064830-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	24	1331	0	ENST00000327367.4:c.1129G>C	p.Val377Leu	p.V377L	ENST00000327367	NM_005902.3	377	Gtc/Ctc	8/9	0.237800581079123	1	FACETS	0.446	0.349	0.558	0.446	0.349	0.558	SUBCLONAL	1	TRUE	0	0.237800581079123	1		1331	399	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976533	7976533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780420901	NA	P-0064830-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	53	1131	1	ENST00000319144.4:c.1859C>T	p.Pro620Leu	p.P620L	ENST00000319144	NM_001139.2	620	cCg/cTg	14/15	0.150620992228102	2	FACETS	1	0.959	1	0.677	0.581	0.782	CLONAL	1	TRUE	0	0.237800581079123	2		1132	329	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714390	40714391	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0064830-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	116	1332	0	ENST00000373198.4:c.4005_4006dup	p.Phe1336TyrfsTer16	p.F1336Yfs*16	ENST00000373198	NM_133170.3	1336	ttc/tATtc	29/32	0.235259415221612	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.237800581079123	3		1332	512	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522609	67522610	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0064830-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	70	1385	0	ENST00000274335.5:c.108dup	p.Val38SerfsTer7	p.V38Sfs*7	ENST00000274335		36	tcc/tCcc	1/15	0.237800581079123	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.237800581079123	1		1385	450	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0064831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	35	516	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.133	0.108	0.161	0.133	0.108	0.161	SUBCLONAL	1	TRUE	1	0.798775201266244	2		516	659	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0064833-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	141	560	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.256364804587815	3	FACETS	1	0.95	1	1	0.992	1	CLONAL	4	FALSE	1	0.256364804587815	3		560	301	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs121913292	NA	P-0064835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	45	158	0	ENST00000371953.3:c.389del	p.Arg130GlnfsTer4	p.R130Qfs*4	ENST00000371953	NM_000314.4	130	cGa/ca	5/9	0.70550187439182	3	FACETS	1	0.938	1	0.591	0.507	0.68	CLONAL	1	TRUE	1	0.70550187439182	3		158	146	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0064835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	74	646	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	0.70550187439182	3	FACETS	0.943	0.833	1	0.471	0.416	0.529	CLONAL	1	TRUE	1	0.70550187439182	3		646	301	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0064835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	45	377	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.700922089048578	3	FACETS	1	0.857	1	0.502	0.428	0.58	CLONAL	1	TRUE	1	0.70550187439182	3		377	172	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0064835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	185	772	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.70550187439182	3	FACETS	0.972	0.912	1	0.972	0.912	1	CLONAL	2	TRUE	1	0.70550187439182	3		772	365	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0064835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	82	283	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.70550187439182	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.70550187439182	3		283	146	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0064835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	74	341	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	0.700922089048578	3	FACETS	1	0.976	1	0.696	0.62	0.773	CLONAL	1	TRUE	1	0.70550187439182	3		341	204	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860342	42860342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779659161	NA	P-0064835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	110	1022	0	ENST00000398585.3:c.535G>A	p.Gly179Arg	p.G179R	ENST00000398585	NM_001135099.1	179	Ggg/Agg	5/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.70550187439182	2		1022	249	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456466	99456466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764375938	NA	P-0064835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	74	1146	0	ENST00000268035.6:c.1783C>T	p.Arg595Cys	p.R595C	ENST00000268035	NM_000875.3	595	Cgt/Tgt	8/21	1	2	FACETS	0.912	0.811	1	0.912	0.811	1	CLONAL	1	TRUE	1	0.70550187439182	2		1146	230	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468188	50468188	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	75	1146	0	ENST00000331340.3:c.1423G>A	p.Val475Ile	p.V475I	ENST00000331340	NM_006060.4	475	Gtc/Atc	8/8	0.700922089048578	3	FACETS	0.931	0.823	1	0.465	0.411	0.522	CLONAL	1	TRUE	1	0.70550187439182	3		1146	309	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100113	27100114	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCCCACA	novel	NA	P-0064835-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	93	1531	0	ENST00000324856.7:c.3913_3920dup	p.Asn1308HisfsTer176	p.N1308Hfs*176	ENST00000324856	NM_006015.4	1303	-/GCCCCACA	16/20	1	2	FACETS	0.969	0.874	1	0.969	0.874	1	CLONAL	1	TRUE	1	0.70550187439182	2		1531	272	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0064836-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	37	516	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.24	2		516	219	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0064836-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	37	578	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	1	2	FACETS	0.91	0.752	1	0.91	0.752	1	CLONAL	1	TRUE	1	0.24	2		578	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0064836-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	18	339	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	1	2	FACETS	0.487	0.366	0.63	0.487	0.366	0.63	SUBCLONAL	1	TRUE	1	0.24	2		339	308	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0064837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	119	712	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.615654827376484	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	0	0.615654827376484	1		712	234	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106621	27106621	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	152	944	0	ENST00000324856.7:c.6232G>T	p.Glu2078Ter	p.E2078*	ENST00000324856	NM_006015.4	2078	Gag/Tag	20/20	0.615654827376484	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	0	0.615654827376484	1		944	300	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154251	2154251	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	79	838	0	ENST00000434045.2:c.677del	p.Gly226AlafsTer30	p.G226Afs*30	ENST00000434045	NM_001127598.1	226	gGc/gc	5/5	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	FALSE	1	0.615654827376484	2		838	254	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112558	2112558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45484298	NA	P-0064837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	102	727	0	ENST00000219476.3:c.1318G>A	p.Gly440Ser	p.G440S	ENST00000219476	NM_000548.3	440	Ggc/Agc	13/42	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.615654827376484	2		727	262	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073643	8073643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746627277	NA	P-0064837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	30	876	0	ENST00000377482.5:c.1016C>T	p.Pro339Leu	p.P339L	ENST00000377482	NM_018948.3	339	cCg/cTg	4/4	0.615654827376484	1	FACETS	0.254	0.205	0.308	0.254	0.205	0.308	SUBCLONAL	1	FALSE	0	0.615654827376484	1		876	266	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098966	178098966	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	156	645	0	ENST00000397062.3:c.79G>C	p.Asp27His	p.D27H	ENST00000397062	NM_006164.4	27	Gat/Cat	2/5	1	2	FACETS	0.802	0.748	0.856	1	0.991	1	CLONAL	2	FALSE	1	0.615654827376484	2		645	316	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731195	162731195	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs769860361	NA	P-0064837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	51	849	0	ENST00000367921.3:c.1050C>A	p.Tyr350Ter	p.Y350*	ENST00000367921	NM_006182.2	350	taC/taA	9/18	1	2	FACETS	0.523	0.446	0.605	0.523	0.446	0.605	SUBCLONAL	1	FALSE	1	0.615654827376484	2		849	317	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200880	67200880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370899912	NA	P-0064837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	102	825	0	ENST00000312629.5:c.868C>T	p.Pro290Ser	p.P290S	ENST00000312629	NM_003952.2	290	Ccc/Tcc	10/15	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	1	0.615654827376484	2		825	315	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125089	46125089	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0064837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	51	601	0	ENST00000334344.6:c.276T>G	p.Tyr92Ter	p.Y92*	ENST00000334344	NM_152641.2	92	taT/taG	3/21	0.615654827376484	1	FACETS	0.549	0.472	0.63	0.549	0.472	0.63	SUBCLONAL	1	FALSE	0	0.615654827376484	1		601	209	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023129	33023129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1312888226	NA	P-0064837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	89	761	0	ENST00000300177.4:c.238G>A	p.Ala80Thr	p.A80T	ENST00000300177	NM_001191322.1	80	Gcc/Acc	2/2	0.615654827376484	2	FACETS	1	0.976	1	0.64	0.578	0.703	CLONAL	1	FALSE	0	0.615654827376484	2		761	226	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527477	29527477	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	70	569	0	ENST00000356175.3:c.926G>T	p.Gly309Val	p.G309V	ENST00000356175	NM_000267.3	309	gGc/gTc	9/57	0.615654827376484	2	FACETS	0.892	0.787	1	0.446	0.393	0.501	CLONAL	1	FALSE	0	0.615654827376484	2		569	255	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41222964	41222964	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	116	773	1	ENST00000357654.3:c.4967G>T	p.Gly1656Val	p.G1656V	ENST00000357654	NM_007294.3	1656	gGc/gTc	15/23	0.124893144359582	4	FACETS	0.841	0.766	0.918	0.841	0.766	0.918	INDETERMINATE	2	FALSE	2	0.615654827376484	4		774	362	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615799	1615799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145054379	NA	P-0064837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	13	747	0	ENST00000344749.5:c.1472C>T	p.Thr491Met	p.T491M	ENST00000344749	NM_001136139.2	491	aCg/aTg	17/19	0.615654827376484	1	FACETS	0.165	0.118	0.223	0.165	0.118	0.223	SUBCLONAL	1	FALSE	0	0.615654827376484	1		747	177	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607468	46607468	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	88	862	0	ENST00000263734.3:c.1657G>T	p.Ala553Ser	p.A553S	ENST00000263734	NM_001430.4	553	Gcg/Tcg	12/16	0.615654827376484	2	FACETS	0.888	0.795	0.985	0.444	0.397	0.493	CLONAL	1	FALSE	0	0.615654827376484	2		862	322	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259060	89259061	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CC	CC	-	novel	NA	P-0064837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	29	701	0	ENST00000336596.2:c.204_205del	p.Tyr68Ter	p.Y68*	ENST00000336596	NM_005233.5	68	taCCag/taag	3/17	0.615654827376484	2	FACETS	0.419	0.338	0.51	0.209	0.169	0.255	SUBCLONAL	1	FALSE	0	0.615654827376484	2		701	225	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204681	128204681	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	168	821	0	ENST00000341105.2:c.760C>A	p.Pro254Thr	p.P254T	ENST00000341105	NM_032638.4	254	Ccg/Acg	3/6	0.615654827376484	3	FACETS	0.959	0.895	1	0.64	0.596	0.683	CLONAL	2	FALSE	0	0.615654827376484	3		821	372	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144359249	144359249	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	114	721	0	ENST00000262995.4:c.691G>T	p.Gly231Ter	p.G231*	ENST00000262995	NM_207123.2	231	Gga/Tga	4/11	0.615654827376484	1	FACETS	0.967	0.887	1	0.967	0.887	1	CLONAL	1	FALSE	0	0.615654827376484	1		721	265	SUCCESS
APC	324	MSKCC	GRCh37	5	112175330	112175330	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	61	713	0	ENST00000257430.4:c.4039G>T	p.Ala1347Ser	p.A1347S	ENST00000257430	NM_000038.5	1347	Gcc/Tcc	16/16	0.615654827376484	1	FACETS	0.514	0.447	0.584	0.514	0.447	0.584	SUBCLONAL	1	FALSE	0	0.615654827376484	1		713	267	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271734	38271734	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	78	896	0	ENST00000425967.3:c.2215G>T	p.Glu739Ter	p.E739*	ENST00000425967	NM_001174067.1	739	Gaa/Taa	17/19	1	2	FACETS	0.895	0.796	1	0.895	0.796	1	CLONAL	1	FALSE	1	0.615654827376484	2		896	283	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0064913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	169	371	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.463580228886212	3	FACETS	0.922	0.856	0.988	0.922	0.856	0.988	CLONAL	2	TRUE	1	0.521917616742843	3		371	443	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223018	5223018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61729778	NA	P-0064913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	253	702	0	ENST00000357368.4:c.2785C>T	p.Arg929Cys	p.R929C	ENST00000357368	NM_002850.3	929	Cgt/Tgt	18/38	0.521917616742843	2	FACETS	0.945	0.895	0.995	0.945	0.895	0.995	CLONAL	2	TRUE	0	0.521917616742843	2		702	513	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793466	18793466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193113798	NA	P-0064913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	79	325	0	ENST00000266497.5:c.4163C>T	p.Thr1388Met	p.T1388M	ENST00000266497		1388	aCg/aTg	30/31	1	2	FACETS	0.929	0.824	1	0.929	0.824	1	CLONAL	1	TRUE	1	0.521917616742843	2		325	326	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007794	45007797	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0064913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	130	469	0	ENST00000558401.1:c.244_247del	p.Phe82IlefsTer20	p.F82Ifs*20	ENST00000558401	NM_004048.2	81	TCTTtc/tc	2/4	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.521917616742843	2		469	427	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591925	48591925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660556	NA	P-0064913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	231	470	0	ENST00000342988.3:c.1088G>A	p.Cys363Tyr	p.C363Y	ENST00000342988	NM_005359.5	363	tGt/tAt	9/12	0.521917616742843	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.521917616742843	2		470	431	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435790	110435790	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1446914389	NA	P-0064913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	35	603	0	ENST00000375856.3:c.2611C>T	p.Arg871Trp	p.R871W	ENST00000375856	NM_003749.2	871	Cgg/Tgg	1/2	1	2	FACETS	0.294	0.241	0.354	0.294	0.241	0.354	SUBCLONAL	1	TRUE	1	0.521917616742843	2		603	456	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251216	251216	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs376391115	NA	P-0064913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	35	196	0	ENST00000264932.6:c.1661G>A	p.Arg554Gln	p.R554Q	ENST00000264932	NM_004168.2	554	cGg/cAg	12/15	1	2	FACETS	0.794	0.659	0.941	0.794	0.659	0.941	CLONAL	1	TRUE	1	0.521917616742843	2		196	169	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437073	110437073	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	126	493	0	ENST00000375856.3:c.1328C>A	p.Thr443Asn	p.T443N	ENST00000375856	NM_003749.2	443	aCc/aAc	1/2	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.521917616742843	2		493	472	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492685	56492685	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs775059555	NA	P-0064913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	184	375	0	ENST00000407977.2:c.252+2C>G		p.X84_splice	ENST00000407977		84			0.521917616742843	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.521917616742843	2		375	337	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29279825	29279825	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	24	29	0	ENST00000544604.2:c.71del	p.Arg24ProfsTer98	p.R24Pfs*98	ENST00000544604	NM_001206998.1	24	cGc/cc	1/9	1	2	FACETS	0.754	0.616	0.898	1	0.941	1	SUBCLONAL	2	TRUE	1	0.521917616742843	2		29	61	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29279995	29280008	+	frameshift_variant	Frame_Shift_Del	DEL	CTCACGGGCCGCTT	CTCACGGGCCGCTT	-	novel	NA	P-0064913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	106	511	0	ENST00000544604.2:c.244_257del	p.Thr82AlafsTer22	p.T82Afs*22	ENST00000544604	NM_001206998.1	81	CTCACGGGCCGCTTc/c	1/9	1	2	FACETS	0.852	0.767	0.94	0.852	0.767	0.94	CLONAL	1	TRUE	1	0.521917616742843	2		511	477	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8733791	8733791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376714429	NA	P-0064913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	114	413	0	ENST00000356435.5:c.53C>T	p.Thr18Met	p.T18M	ENST00000356435		18	aCg/aTg	1/35	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.521917616742843	2		413	421	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0065022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	361	210	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.3	17	FACETS	1	0.948	1	0.313	0.296	0.331	CLONAL	5	TRUE	1	0.4	17		210	1441	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28971147	28971147	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	102	406	0	ENST00000282397.4:c.1610C>A	p.Ala537Asp	p.A537D	ENST00000282397	NM_002019.4	537	gCt/gAt	12/30	0.3	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.4	1		406	314	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779742	3779742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	155	605	0	ENST00000262367.5:c.5306G>A	p.Arg1769Gln	p.R1769Q	ENST00000262367	NM_004380.2	1769	cGg/cAg	31/31	0.0775230368837008	3	FACETS	1	0.953	1	1	0.953	1	INDETERMINATE	2	TRUE	1	0.4	3		605	446	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155356	106155356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	148	528	0	ENST00000380013.4:c.257C>T	p.Ser86Phe	p.S86F	ENST00000380013	NM_001127208.2	86	tCc/tTc	3/11	0.0775230368837008	3	FACETS	0.819	0.752	0.888	0.819	0.752	0.888	INDETERMINATE	2	TRUE	1	0.4	3		528	542	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11168338	11168338	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	134	421	0	ENST00000361445.4:c.7534G>C	p.Asp2512His	p.D2512H	ENST00000361445	NM_004958.3	2512	Gac/Cac	57/58	0.3	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.4	1		421	368	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10785293	10785293	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	116	479	0	ENST00000361367.2:c.1061G>T	p.Arg354Leu	p.R354L	ENST00000361367	NM_014633.3	354	cGa/cTa	9/25	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.4	2		479	407	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639061	176639061	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	197	505	0	ENST00000439151.2:c.3661C>T	p.Gln1221Ter	p.Q1221*	ENST00000439151	NM_022455.4	1221	Caa/Taa	5/23	0.3	0	FACETS	0.852	0.804	0.899			1	CLONAL	2	TRUE	0	0.4	0		505	347	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150917561	150917561	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	147	522	0	ENST00000271640.5:c.1117A>T	p.Ser373Cys	p.S373C	ENST00000271640	NM_001145415.1	373	Agc/Tgc	9/22	0.30246374956196	3	FACETS	0.896	0.82	0.975	0.448	0.41	0.488	INDETERMINATE	1	TRUE	1	0.607898504285039	3		522	704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0065039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	214	355	1	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.434432477111344	2	FACETS	0.809	0.762	0.856	0.809	0.762	0.856	CLONAL	2	TRUE	0	0.607898504285039	2		356	435	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920111	1920115	+	stop_gained	Nonsense_Mutation	ONP	AGAGA	AGAGA	TGAGG	novel	NA	P-0065039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	205	614	0	ENST00000382891.5:c.1171_1175delinsTGAGG	p.Arg391_Glu392delinsTer	p.R391_E392delins*	ENST00000382891	NM_133335.3	391	AGAGAa/TGAGGa	5/22	0.296707134038697	2	FACETS	1	0.99	1	0.672	0.629	0.715	INDETERMINATE	1	TRUE	0	0.607898504285039	2		614	502	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143044517	143044517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	81	394	0	ENST00000262992.4:c.1945G>A	p.Asp649Asn	p.D649N	ENST00000262992	NM_001101669.1	649	Gac/Aac	18/24	1	2	FACETS	0.833	0.741	0.93	0.833	0.741	0.93	CLONAL	1	TRUE	1	0.607898504285039	2		394	320	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0065040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	115	371	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.887	0.804	0.973	0.887	0.804	0.973	CLONAL	1	TRUE	1	0.560171900049124	2		371	463	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0065040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	237	612	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.560171900049124	2	FACETS	0.858	0.81	0.906	0.858	0.81	0.906	CLONAL	2	TRUE	0	0.560171900049124	2		612	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577507	7577507	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	235	400	0	ENST00000269305.4:c.774A>T	p.Glu258Asp	p.E258D	ENST00000269305	NM_001126112.2	258	gaA/gaT	7/11	0.560171900049124	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.560171900049124	1		400	484	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921555	178921555	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	131	342	0	ENST00000263967.3:c.1037T>A	p.Val346Glu	p.V346E	ENST00000263967	NM_006218.2	346	gTa/gAa	5/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.560171900049124	2		342	403	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249501	153249501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1316840275	NA	P-0065040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	156	475	0	ENST00000281708.4:c.1277C>T	p.Ser426Leu	p.S426L	ENST00000281708	NM_033632.3	426	tCa/tTa	9/12	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.560171900049124	2		475	515	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046766	42046766	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0065040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	217	442	0	ENST00000219905.7:c.7139+1G>A		p.X2380_splice	ENST00000219905	NM_001164273.1	2380			1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.560171900049124	2		442	603	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56852610	56852610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764790250	NA	P-0065040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	158	395	0	ENST00000308159.5:c.524G>A	p.Arg175Gln	p.R175Q	ENST00000308159	NM_014669.4	175	cGa/cAa	6/22	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.560171900049124	2		395	511	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110710	2110710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559727962	NA	P-0065040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	330	501	2	ENST00000219476.3:c.1015G>A	p.Val339Ile	p.V339I	ENST00000219476	NM_000548.3	339	Gtc/Atc	11/42	0.157418287231773	3	FACETS	1	0.979	1	0.699	0.665	0.733	INDETERMINATE	2	TRUE	0	0.560171900049124	3		503	719	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478915	56478915	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0065040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	214	482	0	ENST00000267101.3:c.371A>T	p.Asn124Ile	p.N124I	ENST00000267101	NM_001982.3	124	aAc/aTc	3/28	0.22423745430888	3	FACETS	1	0.991	1	0.72	0.672	0.769	INDETERMINATE	1	TRUE	1	0.560171900049124	3		482	679	SUCCESS
BLM	641	MSKCC	GRCh37	15	91306381	91306381	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	149	388	0	ENST00000355112.3:c.2068C>A	p.Pro690Thr	p.P690T	ENST00000355112	NM_000057.2	690	Ccg/Acg	8/22	1	2	FACETS	0.982	0.902	1	0.982	0.902	1	CLONAL	1	TRUE	1	0.560171900049124	2		388	542	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815823	32815823	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	31	458	0	ENST00000354258.4:c.1793G>T	p.Gly598Val	p.G598V	ENST00000354258	NM_000593.5	598	gGa/gTa	8/11	0.560171900049124	1	FACETS	0.163	0.131	0.199	0.163	0.131	0.199	SUBCLONAL	1	TRUE	0	0.560171900049124	1		458	489	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0065041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	153	631	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.536057893913965	1	FACETS	0.941	0.869	1	0.941	0.869	1	CLONAL	1	TRUE	0	0.536057893913965	1		631	444	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0065041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	198	465	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.285121207583019	1	FACETS	0.817	0.76	0.875	0.817	0.76	0.875	INDETERMINATE	1	TRUE	0	0.536057893913965	1		466	662	SUCCESS
APC	324	MSKCC	GRCh37	5	112174096	112174096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs137854575	NA	P-0065041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	169	540	0	ENST00000257430.4:c.2805C>A	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	taC/taA	16/16	1	2	FACETS	0.882	0.813	0.953	0.882	0.813	0.953	CLONAL	1	TRUE	1	0.536057893913965	2		540	715	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0065041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	174	466	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	0.895	0.827	0.967	0.895	0.827	0.967	CLONAL	1	TRUE	1	0.536057893913965	2		466	725	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0065041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	211	496	8	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.536057893913965	2		504	601	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575671	48575671	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0065041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	47	304	0	ENST00000342988.3:c.431C>G	p.Ser144Ter	p.S144*	ENST00000342988	NM_005359.5	144	tCa/tGa	4/12	0.536057893913965	1	FACETS	0.394	0.333	0.459	0.394	0.333	0.459	SUBCLONAL	1	TRUE	0	0.536057893913965	1		304	326	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908864	101908864	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	149	471	0	ENST00000374994.4:c.1228G>T	p.Glu410Ter	p.E410*	ENST00000374994	NM_004612.2	410	Gaa/Taa	7/9	0.536057893913965	1	FACETS	0.686	0.63	0.745	0.686	0.63	0.745	SUBCLONAL	1	TRUE	0	0.536057893913965	1		471	593	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28624343	28624343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065042-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	168	454	0	ENST00000241453.7:c.631C>T	p.Pro211Ser	p.P211S	ENST00000241453	NM_004119.2	211	Cca/Tca	6/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		454	575	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223936	2223936	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065042-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	124	514	0	ENST00000326181.6:c.1150C>G	p.Gln384Glu	p.Q384E	ENST00000326181	NM_032271.2	384	Cag/Gag	13/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		514	563	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305339	65305339	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0065043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	54	633	0	ENST00000342505.4:c.2789G>C	p.Arg930Thr	p.R930T	ENST00000342505	NM_002227.2	930	aGg/aCg	20/25	0.571814729708513	1	FACETS	0.285	0.244	0.33	0.285	0.244	0.33	SUBCLONAL	1	TRUE	0	0.636755227687318	1		633	405	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912146	114912146	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	124	513	0	ENST00000543371.1:c.1216G>T	p.Glu406Ter	p.E406*	ENST00000543371	NM_001198531.1	406	Gag/Tag	11/14	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.636755227687318	2		513	343	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0065043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	75	280	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.942	0.837	1	0.942	0.837	1	CLONAL	1	TRUE	1	0.636755227687318	2		280	250	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473722	67473722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs794727798	NA	P-0065043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	32	558	0	ENST00000327367.4:c.802C>T	p.Arg268Cys	p.R268C	ENST00000327367	NM_005902.3	268	Cgc/Tgc	6/9	1	2	FACETS	0.293	0.238	0.355	0.293	0.238	0.355	SUBCLONAL	1	TRUE	1	0.636755227687318	2		558	343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0065043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	172	785	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.636755227687318	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.636755227687318	1		785	360	SUCCESS
APC	324	MSKCC	GRCh37	5	112174352	112174353	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TAGA	novel	NA	P-0065043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	87	480	0	ENST00000257430.4:c.3064_3067dup	p.Thr1023ArgfsTer7	p.T1023Rfs*7	ENST00000257430	NM_000038.5	1021	cta/cTAGAta	16/16	1	2	FACETS	0.697	0.621	0.777	0.697	0.621	0.777	SUBCLONAL	1	TRUE	1	0.636755227687318	2		480	392	SUCCESS
APC	324	MSKCC	GRCh37	5	112175760	112175761	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs398123122	NA	P-0065043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	121	755	0	ENST00000257430.4:c.4473dup	p.Ala1492CysfsTer22	p.A1492Cfs*22	ENST00000257430	NM_000038.5	1490	cat/caTt	16/16	1	2	FACETS	0.797	0.724	0.872	0.797	0.724	0.872	SUBCLONAL	1	TRUE	1	0.636755227687318	2		755	477	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045963	26045963	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	137	745	0	ENST00000540144.1:c.325A>C	p.Asn109His	p.N109H	ENST00000540144	NM_003531.2	109	Aat/Cat	1/1	0.141188745169361	5	FACETS	0.779	0.712	0.848	0.389	0.356	0.424	INDETERMINATE	2	TRUE	1	0.636755227687318	5		745	540	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226998	53226998	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	371	275	0	ENST00000375401.3:c.2577G>T	p.Gln859His	p.Q859H	ENST00000375401	NM_004187.3	859	caG/caT	18/26	0.636755227687318	3	FACETS	0.881	0.859	0.901			1	CLONAL	4	TRUE	NA	0.636755227687318	3		275	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0065044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	859	784	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.702228814935725	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.702228814935725	3		784	1087	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554545	63554545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	831	662	0	ENST00000307078.5:c.194C>T	p.Pro65Leu	p.P65L	ENST00000307078	NM_004655.3	65	cCg/cTg	2/11	0.702228814935725	3	FACETS	0.976	0.956	0.996	0.976	0.956	0.996	CLONAL	3	TRUE	0	0.702228814935725	3		662	1092	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144027	11144027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770680174	NA	P-0065044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	530	819	0	ENST00000358026.2:c.3608G>A	p.Arg1203His	p.R1203H	ENST00000358026	NM_001128849.1	1203	cGc/cAc	26/36	0.702228814935725	4	FACETS	0.945	0.907	0.984	0.945	0.907	0.984	CLONAL	2	TRUE	2	0.702228814935725	4		819	1359	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168941	11168941	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1458830964	NA	P-0065044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	398	613	0	ENST00000358026.2:c.4531C>T	p.Arg1511Cys	p.R1511C	ENST00000358026	NM_001128849.1	1511	Cgt/Tgt	32/36	0.702228814935725	4	FACETS	0.954	0.91	0.999	0.954	0.91	0.999	CLONAL	2	TRUE	2	0.702228814935725	4		613	1011	SUCCESS
APC	324	MSKCC	GRCh37	5	112174026	112174027	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0065044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	285	579	0	ENST00000257430.4:c.2736dup	p.His913ThrfsTer6	p.H913Tfs*6	ENST00000257430	NM_000038.5	912	tta/ttAa	16/16	0.701981591231341	2	FACETS	0.978	0.939	1	0.978	0.939	1	CLONAL	2	TRUE	0	0.702228814935725	2		579	415	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983064	201983087	+	frameshift_variant	Frame_Shift_Del	DEL	TTCCTGCGCTCCGAGGCTGTGGCC	TTCCTGCGCTCCGAGGCTGTGGCC	GGCCACAGGAA	novel	NA	P-0065044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	503	776	1	ENST00000359651.3:c.913_936delinsGGCCACAGGAA	p.Phe305GlyfsTer16	p.F305Gfs*16	ENST00000359651		305	TTCCTGCGCTCCGAGGCTGTGGCC/GGCCACAGGAA	7/8	0.69385183448941	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.702228814935725	3		777	966	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354509	91354509	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730880251	NA	P-0065045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	134	744	0	ENST00000355112.3:c.3949G>A	p.Glu1317Lys	p.E1317K	ENST00000355112	NM_000057.2	1317	Gag/Aag	21/22	0.417989419569097	3	FACETS	0.802	0.729	0.879	0.401	0.364	0.44	CLONAL	1	TRUE	1	0.521168966863674	3		744	808	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222727	5222727	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746980740	NA	P-0065045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	174	428	0	ENST00000357368.4:c.3076C>T	p.Arg1026Cys	p.R1026C	ENST00000357368	NM_002850.3	1026	Cgc/Tgc	18/38	0.414903076050193	3	FACETS	1	0.989	1	0.704	0.651	0.758	CLONAL	1	TRUE	1	0.521168966863674	3		428	598	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59934572	59934572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769573395	NA	P-0065045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	275	577	0	ENST00000259008.2:c.226G>A	p.Val76Ile	p.V76I	ENST00000259008	NM_032043.2	76	Gta/Ata	4/20	0.443388729426093	3	FACETS	1	0.989	1	0.766	0.726	0.806	CLONAL	2	TRUE	0	0.521168966863674	3		577	579	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794718	42794718	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1296019502	NA	P-0065045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	139	810	0	ENST00000575354.2:c.1798C>T	p.Arg600Cys	p.R600C	ENST00000575354	NM_015125.3	600	Cgc/Tgc	10/20	0.429910317708832	5	FACETS	0.855	0.776	0.937	0.214	0.194	0.235	CLONAL	1	TRUE	1	0.521168966863674	5		810	1112	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579458	7579459	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCAGGCAGC	novel	NA	P-0065045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	417	997	0	ENST00000269305.4:c.228_229insGCTGCCTGCA	p.Pro77AlafsTer75	p.P77Afs*75	ENST00000269305	NM_001126112.2	76	-/GCTGCCTGCA	4/11	0.443388729426093	3	FACETS	1	0.969	1	0.678	0.648	0.708	CLONAL	2	TRUE	0	0.521168966863674	3		997	992	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139438482	139438482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	161	621	0	ENST00000277541.6:c.134C>T	p.Ala45Val	p.A45V	ENST00000277541	NM_017617.3	45	gCc/gTc	2/34	0.318188051277152	3	FACETS	1	0.986	1	0.671	0.619	0.726	CLONAL	1	TRUE	1	0.521168966863674	3		621	580	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	13	280	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.145	0.103	0.197	0.145	0.103	0.197	SUBCLONAL	1	TRUE	1	0.39	2		280	460	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	144	460	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.39	2		460	613	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106367	27106367	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	44	589	0	ENST00000324856.7:c.5978T>G	p.Phe1993Cys	p.F1993C	ENST00000324856	NM_006015.4	1993	tTt/tGt	20/20	1	2	FACETS	0.366	0.306	0.433	0.366	0.306	0.433	SUBCLONAL	1	TRUE	1	0.39	2		589	616	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805081	43805081	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	45	629	0	ENST00000372470.3:c.531G>T	p.Lys177Asn	p.K177N	ENST00000372470	NM_005373.2	177	aaG/aaT	4/12	1	2	FACETS	0.38	0.319	0.448	0.38	0.319	0.448	SUBCLONAL	1	TRUE	1	0.39	2		629	607	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428511	78428511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408536007	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	47	498	0	ENST00000370768.2:c.1288C>T	p.Arg430Cys	p.R430C	ENST00000370768	NM_003902.3	430	Cgt/Tgt	14/20	1	2	FACETS	0.411	0.346	0.483	0.411	0.346	0.483	SUBCLONAL	1	TRUE	1	0.39	2		498	586	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104712	193104712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	37	428	0	ENST00000367435.3:c.416G>A	p.Arg139Gln	p.R139Q	ENST00000367435	NM_024529.4	139	cGa/cAa	5/17	1	2	FACETS	0.379	0.312	0.454	0.379	0.312	0.454	SUBCLONAL	1	TRUE	1	0.39	2		428	501	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984434	201984434	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	127	551	0	ENST00000359651.3:c.1099C>A	p.Leu367Ile	p.L367I	ENST00000359651		367	Ctc/Atc	8/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.39	2		551	607	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852632	63852632	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	43	585	1	ENST00000279873.7:c.3410C>A	p.Ser1137Tyr	p.S1137Y	ENST00000279873	NM_032199.2	1137	tCt/tAt	10/10	1	2	FACETS	0.342	0.285	0.405	0.342	0.285	0.405	SUBCLONAL	1	TRUE	1	0.39	2		586	645	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624245	89624245	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554890335	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	30	174	0	ENST00000371953.3:c.19G>T	p.Glu7Ter	p.E7*	ENST00000371953	NM_000314.4	7	Gag/Tag	1/9	1	2	FACETS	0.836	0.68	1	0.836	0.68	1	CLONAL	1	TRUE	1	0.39	2		174	184	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685281	89685281	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	30	330	0	ENST00000371953.3:c.176C>A	p.Ser59Ter	p.S59*	ENST00000371953	NM_000314.4	59	tCa/tAa	3/9	1	2	FACETS	0.42	0.339	0.513	0.42	0.339	0.513	SUBCLONAL	1	TRUE	1	0.39	2		330	366	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	96	447	1	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	0.967	0.865	1	0.967	0.865	1	CLONAL	1	TRUE	1	0.39	2		448	509	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911587	114911587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	155	535	0	ENST00000543371.1:c.1105G>A	p.Val369Ile	p.V369I	ENST00000543371	NM_001198531.1	369	Gta/Ata	10/14	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.39	2		535	613	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14303203	14303203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316363049	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	119	455	0	ENST00000256196.4:c.472G>A	p.Ala158Thr	p.A158T	ENST00000256196		158	Gca/Aca	5/6	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.39	2		455	428	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69456170	69456170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	130	647	0	ENST00000227507.2:c.89C>T	p.Ala30Val	p.A30V	ENST00000227507	NM_053056.2	30	gCc/gTc	1/5	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.39	2		647	582	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625341	69625341	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs782008134	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	35	675	0	ENST00000334134.2:c.452G>T	p.Arg151Ile	p.R151I	ENST00000334134	NM_005247.2	151	aGa/aTa	3/3	1	2	FACETS	0.305	0.249	0.368	0.305	0.249	0.368	SUBCLONAL	1	TRUE	1	0.39	2		675	589	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195629	102195629	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	52	562	0	ENST00000263464.3:c.389A>G	p.Asn130Ser	p.N130S	ENST00000263464	NM_001165.4	130	aAc/aGc	2/9	1	2	FACETS	0.368	0.313	0.43	0.368	0.313	0.43	SUBCLONAL	1	TRUE	1	0.39	2		562	724	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205756	108205756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531980488	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	50	382	1	ENST00000278616.4:c.8071C>T	p.Arg2691Cys	p.R2691C	ENST00000278616	NM_000051.3	2691	Cgc/Tgc	55/63	1	2	FACETS	0.485	0.411	0.566	0.485	0.411	0.566	SUBCLONAL	1	TRUE	1	0.39	2		383	529	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481856	56481856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	111	640	1	ENST00000267101.3:c.784C>T	p.Pro262Ser	p.P262S	ENST00000267101	NM_001982.3	262	Cct/Tct	7/28	1	2	FACETS	0.912	0.822	1	0.912	0.822	1	CLONAL	1	TRUE	1	0.39	2		641	624	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811760	102811760	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	59	578	0	ENST00000307046.8:c.424A>G	p.Lys142Glu	p.K142E	ENST00000307046	NM_001111285.1	142	Aag/Gag	4/4	1	2	FACETS	0.42	0.361	0.485	0.42	0.361	0.485	SUBCLONAL	1	TRUE	1	0.39	2		578	720	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249857	133249857	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1565972665	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	129	356	0	ENST00000320574.5:c.1366G>C	p.Ala456Pro	p.A456P	ENST00000320574	NM_006231.2	456	Gcc/Ccc	14/49	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.39	2		356	582	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906927	32906927	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs765436962	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	57	519	0	ENST00000380152.3:c.1312G>T	p.Asp438Tyr	p.D438Y	ENST00000380152		438	Gat/Tat	10/27	1	2	FACETS	0.516	0.442	0.596	0.516	0.442	0.596	SUBCLONAL	1	TRUE	1	0.39	2		519	567	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913023	32913023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376338226	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	158	620	0	ENST00000380152.3:c.4531G>A	p.Glu1511Lys	p.E1511K	ENST00000380152		1511	Gaa/Aaa	11/27	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.39	2		620	667	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915065	32915065	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	43	506	0	ENST00000380152.3:c.6573A>C	p.Lys2191Asn	p.K2191N	ENST00000380152		2191	aaA/aaC	11/27	1	2	FACETS	0.38	0.317	0.449	0.38	0.317	0.449	SUBCLONAL	1	TRUE	1	0.39	2		506	581	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49054201	49054201	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs756634613	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	57	477	0	ENST00000267163.4:c.2781G>T	p.Glu927Asp	p.E927D	ENST00000267163	NM_000321.2	927	gaG/gaT	27/27	1	2	FACETS	0.623	0.536	0.719	0.623	0.536	0.719	SUBCLONAL	1	TRUE	1	0.39	2		477	469	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527667	103527667	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377390651	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	71	423	0	ENST00000355739.4:c.2975G>A	p.Arg992Gln	p.R992Q	ENST00000355739	NM_000123.3	992	cGa/cAa	15/15	1	2	FACETS	0.737	0.645	0.836	0.737	0.645	0.836	SUBCLONAL	1	TRUE	1	0.39	2		423	494	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041074	42041074	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	48	642	0	ENST00000219905.7:c.5452C>T	p.Arg1818Ter	p.R1818*	ENST00000219905	NM_001164273.1	1818	Cga/Tga	16/24	1	2	FACETS	0.348	0.293	0.409	0.348	0.293	0.409	SUBCLONAL	1	TRUE	1	0.39	2		642	707	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784215	43784215	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	78	491	0	ENST00000382044.4:c.271G>T	p.Glu91Ter	p.E91*	ENST00000382044	NM_001141980.1	91	Gaa/Taa	3/28	1	2	FACETS	0.606	0.532	0.685	0.606	0.532	0.685	SUBCLONAL	1	TRUE	1	0.39	2		491	660	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51507948	51507948	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	62	435	0	ENST00000260433.2:c.810G>T	p.Glu270Asp	p.E270D	ENST00000260433		270	gaG/gaT	7/10	1	2	FACETS	0.619	0.535	0.709	0.619	0.535	0.709	SUBCLONAL	1	TRUE	1	0.39	2		435	514	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857152	9857152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369508378	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	48	636	0	ENST00000330684.3:c.4249C>T	p.Arg1417Trp	p.R1417W	ENST00000330684	NM_001134407.1	1417	Cgg/Tgg	13/13	1	2	FACETS	0.394	0.333	0.463	0.394	0.333	0.463	SUBCLONAL	1	TRUE	1	0.39	2		636	624	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614911	23614911	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	33	530	0	ENST00000261584.4:c.3430C>A	p.Leu1144Ile	p.L1144I	ENST00000261584	NM_024675.3	1144	Ctc/Atc	13/13	1	2	FACETS	0.273	0.221	0.331	0.273	0.221	0.331	SUBCLONAL	1	TRUE	1	0.39	2		530	621	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813889	50813889	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	55	523	0	ENST00000398568.2:c.1443C>A	p.Phe481Leu	p.F481L	ENST00000398568	NM_001042412.1	481	ttC/ttA	8/18	1	2	FACETS	0.442	0.378	0.513	0.442	0.378	0.513	SUBCLONAL	1	TRUE	1	0.39	2		523	638	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50816375	50816375	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	118	429	0	ENST00000398568.2:c.1815C>A	p.Phe605Leu	p.F605L	ENST00000398568	NM_001042412.1	605	ttC/ttA	10/18	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.39	2		429	518	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654624	67654624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	47	492	0	ENST00000264010.4:c.1111C>T	p.Arg371Cys	p.R371C	ENST00000264010	NM_006565.3	371	Cgc/Tgc	6/12	1	2	FACETS	0.337	0.284	0.396	0.337	0.284	0.396	SUBCLONAL	1	TRUE	1	0.39	2		492	715	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862196	68862196	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	70	526	0	ENST00000261769.5:c.2284G>T	p.Glu762Ter	p.E762*	ENST00000261769	NM_004360.3	762	Gaa/Taa	14/16	1	2	FACETS	0.619	0.54	0.704	0.619	0.54	0.704	SUBCLONAL	1	TRUE	1	0.39	2		526	580	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829565	72829565	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1000233330	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	71	527	1	ENST00000268489.5:c.7016G>A	p.Arg2339His	p.R2339H	ENST00000268489	NM_006885.3	2339	cGc/cAc	9/10	1	2	FACETS	0.582	0.508	0.662	0.582	0.508	0.662	SUBCLONAL	1	TRUE	1	0.39	2		528	626	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925185	81925185	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	61	467	0	ENST00000359376.3:c.976T>G	p.Ser326Ala	p.S326A	ENST00000359376	NM_002661.3	326	Tca/Gca	11/33	1	2	FACETS	0.527	0.454	0.605	0.527	0.454	0.605	SUBCLONAL	1	TRUE	1	0.39	2		467	594	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528054	29528054	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	41	93	0	ENST00000356175.3:c.1063-1G>T		p.X355_splice	ENST00000356175	NM_000267.3	355			1	2	FACETS	0.983	0.843	1	1	0.972	1	CLONAL	2	TRUE	1	0.39	2		93	107	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	23	551	1	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	1	2	FACETS	0.185	0.143	0.234	0.185	0.143	0.234	SUBCLONAL	1	TRUE	1	0.39	2		552	637	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546065	29546065	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1135402815	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	101	534	1	ENST00000356175.3:c.1570G>T	p.Glu524Ter	p.E524*	ENST00000356175	NM_000267.3	524	Gaa/Taa	14/57	1	2	FACETS	0.691	0.617	0.769	0.691	0.617	0.769	SUBCLONAL	1	TRUE	1	0.39	2		535	750	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690567	33690567	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	63	572	0	ENST00000308377.4:c.260C>A	p.Ser87Tyr	p.S87Y	ENST00000308377	NM_152270.3	87	tCt/tAt	2/5	1	2	FACETS	0.538	0.465	0.617	0.538	0.465	0.617	SUBCLONAL	1	TRUE	1	0.39	2		572	601	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696405	47696405	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	127	522	0	ENST00000347630.2:c.418G>T	p.Asp140Tyr	p.D140Y	ENST00000347630	NM_001007230.1	140	Gat/Tat	6/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.39	2		522	559	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5256125	5256125	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	55	469	0	ENST00000357368.4:c.712C>T	p.Arg238Ter	p.R238*	ENST00000357368	NM_002850.3	238	Cga/Tga	9/38	0.100617535680206	3	FACETS	0.408	0.348	0.474	0.204	0.174	0.237	INDETERMINATE	1	TRUE	1	0.39	3		469	826	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107038	11107038	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	83	659	0	ENST00000358026.2:c.1743G>T	p.Lys581Asn	p.K581N	ENST00000358026	NM_001128849.1	581	aaG/aaT	10/36	0.100617535680206	3	FACETS	0.721	0.636	0.813	0.361	0.318	0.407	INDETERMINATE	1	TRUE	1	0.39	3		659	705	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794053	42794053	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	35	594	0	ENST00000575354.2:c.1414A>C	p.Thr472Pro	p.T472P	ENST00000575354	NM_015125.3	472	Acc/Ccc	9/20	0.100617535680206	3	FACETS	0.409	0.334	0.492	0.204	0.167	0.246	INDETERMINATE	1	TRUE	1	0.39	3		594	525	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425613	47425614	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	159	522	0	ENST00000404338.3:c.3681+1_3681+2dup		p.-1227fs	ENST00000404338	NM_004491.4	1227	-/GT		0.100617535680206	3	FACETS	0.776	0.714	0.84	0.776	0.714	0.84	INDETERMINATE	2	TRUE	1	0.39	3		522	628	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705261	52705261	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770424653	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	135	507	0	ENST00000322088.6:c.143G>A	p.Arg48Gln	p.R48Q	ENST00000322088	NM_014225.5	48	cGa/cAa	2/15	0.100617535680206	3	FACETS	1	0.984	1	0.689	0.629	0.753	INDETERMINATE	1	TRUE	1	0.39	3		507	600	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657077	47657077	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1064795063	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	35	384	0	ENST00000233146.2:c.1273G>T	p.Glu425Ter	p.E425*	ENST00000233146	NM_000251.2	425	Gaa/Taa	7/16	1	2	FACETS	0.323	0.264	0.389	0.323	0.264	0.389	SUBCLONAL	1	TRUE	1	0.39	2		384	556	SUCCESS
REL	5966	MSKCC	GRCh37	2	61128147	61128147	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1016724251	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	31	320	0	ENST00000295025.8:c.323G>A	p.Arg108Gln	p.R108Q	ENST00000295025	NM_002908.2	108	cGa/cAa	4/11	1	2	FACETS	0.34	0.275	0.415	0.34	0.275	0.415	SUBCLONAL	1	TRUE	1	0.39	2		320	467	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095740	178095740	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs762320240	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	38	529	0	ENST00000397062.3:c.1591C>A	p.His531Asn	p.H531N	ENST00000397062	NM_006164.4	531	Cat/Aat	5/5	1	2	FACETS	0.316	0.26	0.378	0.316	0.26	0.378	SUBCLONAL	1	TRUE	1	0.39	2		529	617	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533736	41533736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1046073854	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	43	506	0	ENST00000263253.7:c.1702C>T	p.Arg568Trp	p.R568W	ENST00000263253	NM_001429.3	568	Cgg/Tgg	8/31	1	2	FACETS	0.351	0.293	0.416	0.351	0.293	0.416	SUBCLONAL	1	TRUE	1	0.39	2		506	628	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	45	442	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	1	2	FACETS	0.405	0.34	0.477	0.405	0.34	0.477	SUBCLONAL	1	TRUE	1	0.39	2		442	570	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163575	47163575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	75	532	0	ENST00000409792.3:c.2551G>A	p.Glu851Lys	p.E851K	ENST00000409792	NM_014159.6	851	Gaa/Aaa	3/21	1	2	FACETS	0.701	0.615	0.793	0.701	0.615	0.793	SUBCLONAL	1	TRUE	1	0.39	2		532	549	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49399973	49399973	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	147	490	0	ENST00000418115.1:c.364C>T	p.Arg122Trp	p.R122W	ENST00000418115	NM_001664.2	122	Cgg/Tgg	4/5	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.39	2		490	669	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70005665	70005665	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	98	412	0	ENST00000394351.3:c.694C>T	p.Pro232Ser	p.P232S	ENST00000394351	NM_000248.3	232	Ccc/Tcc	7/9	1	2	FACETS	0.966	0.865	1	0.966	0.865	1	CLONAL	1	TRUE	1	0.39	2		412	520	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73112850	73112850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375938868	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	109	397	0	ENST00000356692.5:c.446G>A	p.Arg149Gln	p.R149Q	ENST00000356692		149	cGa/cAa	6/9	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.39	2		397	445	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	66	554	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.581	0.504	0.663	0.581	0.504	0.663	SUBCLONAL	1	TRUE	1	0.39	2		554	583	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	28	354	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.238	0.189	0.294	0.238	0.189	0.294	SUBCLONAL	1	TRUE	1	0.39	2		354	603	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921567	178921567	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553821144	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	9	413	0	ENST00000263967.3:c.1049A>G	p.Asp350Gly	p.D350G	ENST00000263967	NM_006218.2	350	gAc/gGc	5/21	1	2	FACETS	0.106	0.07	0.154	0.106	0.07	0.154	SUBCLONAL	1	TRUE	1	0.39	2		413	434	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136805	55136805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41279521	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	110	351	0	ENST00000257290.5:c.1127G>A	p.Arg376Gln	p.R376Q	ENST00000257290	NM_006206.4	376	cGa/cAa	8/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.39	2		351	505	SUCCESS
REST	5978	MSKCC	GRCh37	4	57777087	57777087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs909981105	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	128	562	0	ENST00000309042.7:c.283G>A	p.Glu95Lys	p.E95K	ENST00000309042	NM_005612.4	95	Gag/Aag	2/4	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.39	2		562	641	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196717	106196717	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	149	601	0	ENST00000380013.4:c.5050G>T	p.Gly1684Ter	p.G1684*	ENST00000380013	NM_001127208.2	1684	Gga/Tga	11/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.39	2		601	579	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159099	143159099	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1332432216	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	31	381	1	ENST00000262992.4:c.754C>T	p.Arg252Ter	p.R252*	ENST00000262992	NM_001101669.1	252	Cga/Tga	10/24	1	2	FACETS	0.371	0.3	0.452	0.371	0.3	0.452	SUBCLONAL	1	TRUE	1	0.39	2		382	428	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	154	660	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.39	2		660	722	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538206	187538206	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1327390871	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	56	506	0	ENST00000441802.2:c.9028G>T	p.Glu3010Ter	p.E3010*	ENST00000441802	NM_005245.3	3010	Gaa/Taa	11/27	1	2	FACETS	0.518	0.444	0.6	0.518	0.444	0.6	SUBCLONAL	1	TRUE	1	0.39	2		506	554	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522657	67522657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	152	566	0	ENST00000274335.5:c.154G>T	p.Glu52Ter	p.E52*	ENST00000274335		52	Gaa/Taa	1/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.39	2		566	647	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633825	86633825	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	57	393	0	ENST00000274376.6:c.934G>T	p.Glu312Ter	p.E312*	ENST00000274376	NM_002890.2	312	Gaa/Taa	5/25	1	2	FACETS	0.792	0.683	0.911	0.792	0.683	0.911	CLONAL	1	TRUE	1	0.39	2		393	369	SUCCESS
APC	324	MSKCC	GRCh37	5	112177167	112177167	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	57	492	0	ENST00000257430.4:c.5876C>A	p.Thr1959Asn	p.T1959N	ENST00000257430	NM_000038.5	1959	aCt/aAt	16/16	1	2	FACETS	0.444	0.381	0.514	0.444	0.381	0.514	SUBCLONAL	1	TRUE	1	0.39	2		492	658	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931342	131931342	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367925756	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	37	446	0	ENST00000265335.6:c.2047G>A	p.Val683Ile	p.V683I	ENST00000265335		683	Gtt/Att	13/25	1	2	FACETS	0.292	0.24	0.351	0.292	0.24	0.351	SUBCLONAL	1	TRUE	1	0.39	2		446	649	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176662822	176662822	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	38	420	0	ENST00000439151.2:c.3797C>T	p.Ala1266Val	p.A1266V	ENST00000439151	NM_022455.4	1266	gCt/gTt	6/23	1	2	FACETS	0.339	0.28	0.406	0.339	0.28	0.406	SUBCLONAL	1	TRUE	1	0.39	2		420	574	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709529	176709529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777258117	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	56	437	0	ENST00000439151.2:c.5956C>T	p.Arg1986Cys	p.R1986C	ENST00000439151	NM_022455.4	1986	Cgc/Tgc	19/23	1	2	FACETS	0.552	0.473	0.638	0.552	0.473	0.638	SUBCLONAL	1	TRUE	1	0.39	2		437	520	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672776	30672776	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	56	781	0	ENST00000376406.3:c.4184G>T	p.Arg1395Ile	p.R1395I	ENST00000376406	NM_014641.2	1395	aGa/aTa	10/15	1	2	FACETS	0.35	0.299	0.406	0.35	0.299	0.406	SUBCLONAL	1	TRUE	1	0.39	2		781	820	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672794	30672794	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1170303675	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	219	852	1	ENST00000376406.3:c.4166C>A	p.Ser1389Tyr	p.S1389Y	ENST00000376406	NM_014641.2	1389	tCt/tAt	10/15	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.39	2		853	886	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969087	93969087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1270476760	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	38	481	0	ENST00000369303.4:c.1909C>T	p.Arg637Cys	p.R637C	ENST00000369303	NM_004440.3	637	Cgt/Tgt	10/17	1	2	FACETS	0.37	0.305	0.442	0.37	0.305	0.442	SUBCLONAL	1	TRUE	1	0.39	2		481	527	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642530	117642530	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	58	611	0	ENST00000368508.3:c.5669A>T	p.Lys1890Ile	p.K1890I	ENST00000368508	NM_002944.2	1890	aAa/aTa	35/43	1	2	FACETS	0.424	0.363	0.49	0.424	0.363	0.49	SUBCLONAL	1	TRUE	1	0.39	2		611	702	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710875	117710875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140178288	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	122	618	0	ENST00000368508.3:c.1397G>A	p.Arg466Gln	p.R466Q	ENST00000368508	NM_002944.2	466	cGa/cAa	12/43	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.39	2		618	612	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459558	50459558	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	54	455	0	ENST00000331340.3:c.847C>A	p.Leu283Ile	p.L283I	ENST00000331340	NM_006060.4	283	Ctt/Att	7/8	1	2	FACETS	0.426	0.363	0.495	0.426	0.363	0.495	SUBCLONAL	1	TRUE	1	0.39	2		455	650	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92244540	92244540	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	39	563	0	ENST00000265734.4:c.895T>C	p.Tyr299His	p.Y299H	ENST00000265734	NM_001259.6	299	Tac/Cac	8/8	1	2	FACETS	0.323	0.267	0.385	0.323	0.267	0.385	SUBCLONAL	1	TRUE	1	0.39	2		563	620	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980478	70980478	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	35	554	0	ENST00000276594.2:c.899C>T	p.Ser300Phe	p.S300F	ENST00000276594	NM_024504.3	300	tCt/tTt	4/8	1	2	FACETS	0.307	0.251	0.371	0.307	0.251	0.371	SUBCLONAL	1	TRUE	1	0.39	2		554	584	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868912	117868912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746064262	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	42	397	0	ENST00000297338.2:c.787G>A	p.Asp263Asn	p.D263N	ENST00000297338	NM_006265.2	263	Gat/Aat	7/14	1	2	FACETS	0.446	0.372	0.528	0.446	0.372	0.528	SUBCLONAL	1	TRUE	1	0.39	2		397	483	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2054700	2054700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	61	454	1	ENST00000349721.2:c.1150C>T	p.Arg384Trp	p.R384W	ENST00000349721	NM_003070.3	384	Cgg/Tgg	6/34	1	2	FACETS	0.51	0.44	0.587	0.51	0.44	0.587	SUBCLONAL	1	TRUE	1	0.39	2		455	613	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912146	127912146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564144380	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	31	516	0	ENST00000373547.4:c.724G>A	p.Glu242Lys	p.E242K	ENST00000373547	NM_002721.4	242	Gaa/Aaa	7/7	1	2	FACETS	0.279	0.225	0.341	0.279	0.225	0.341	SUBCLONAL	1	TRUE	1	0.39	2		516	569	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841301	15841301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1195011512	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	53	706	0	ENST00000307771.7:c.1385G>A	p.Arg462Gln	p.R462Q	ENST00000307771	NM_005089.3	462	cGa/cAa	11/11	1	2	FACETS	0.436	0.371	0.507	0.436	0.371	0.507	SUBCLONAL	1	TRUE	1	0.39	2		706	624	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345265	70345265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	69	575	0	ENST00000374080.3:c.2291G>A	p.Arg764Gln	p.R764Q	ENST00000374080		764	cGa/cAa	16/45	1	2	FACETS	0.661	0.577	0.753	0.661	0.577	0.753	SUBCLONAL	1	TRUE	1	0.39	2		575	535	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938330	76938330	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	104	511	0	ENST00000373344.5:c.2418G>T	p.Lys806Asn	p.K806N	ENST00000373344	NM_000489.3	806	aaG/aaT	9/35	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.39	2		511	503	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197050	123197050	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	84	362	0	ENST00000218089.9:c.1816G>T	p.Glu606Ter	p.E606*	ENST00000218089	NM_001042749.1	606	Gaa/Taa	19/35	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.39	2		362	363	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220587	123220587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1443844104	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	118	446	0	ENST00000218089.9:c.3244C>T	p.Arg1082Trp	p.R1082W	ENST00000218089	NM_001042749.1	1082	Cgg/Tgg	30/35	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.39	2		446	519	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229252	123229252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0065047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	45	430	0	ENST00000218089.9:c.3736G>A	p.Glu1246Lys	p.E1246K	ENST00000218089	NM_001042749.1	1246	Gaa/Aaa	34/35	1	2	FACETS	0.394	0.331	0.465	0.394	0.331	0.465	SUBCLONAL	1	TRUE	1	0.39	2		430	585	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0001716-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	181	435	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		435	505	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519742	NA	P-0001716-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	239	616	0	ENST00000078429.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000078429	NM_002067.2	209	cAg/cCg	5/7	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		616	620	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0002842-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	69	600	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.891	0.774	1	0.891	0.774	1	CLONAL	1	TRUE	1	0.16	2		600	968	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270112	66270112	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002842-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	42	440	0	ENST00000273854.3:c.1770C>G	p.Ile590Met	p.I590M	ENST00000273854	NM_004439.5	590	atC/atG	8/18	0.3	1	FACETS	0.685	0.571	0.813	0.685	0.571	0.813	SUBCLONAL	1	TRUE	0	0.16	1		440	705	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846426	128846426	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002842-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	33	297	0	ENST00000249373.3:c.1262G>T	p.Arg421Leu	p.R421L	ENST00000249373	NM_005631.4	421	cGa/cTa	6/12	1	2	FACETS	0.909	0.74	1	0.909	0.74	1	CLONAL	1	TRUE	1	0.16	2		297	454	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874136	151874136	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002842-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	62	517	0	ENST00000262189.6:c.8402A>G	p.Asn2801Ser	p.N2801S	ENST00000262189	NM_170606.2	2801	aAc/aGc	38/59	1	2	FACETS	0.748	0.644	0.862	0.748	0.644	0.862	SUBCLONAL	1	TRUE	1	0.16	2		517	1036	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742486	145742486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs62530445	NA	P-0002842-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	37	329	1	ENST00000428558.2:c.302C>T	p.Ser101Leu	p.S101L	ENST00000428558	NM_004260.3	101	tCg/tTg	4/22	0.3	2	FACETS	0.709	0.583	0.851			1	SUBCLONAL	1	TRUE	NA	0.16	2		330	652	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438025	49438025	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002842-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	60	466	0	ENST00000301067.7:c.5146G>T	p.Ala1716Ser	p.A1716S	ENST00000301067	NM_003482.3	1716	Gca/Tca	21/54	1	2	FACETS	0.932	0.801	1	0.932	0.801	1	CLONAL	1	TRUE	1	0.16	2		466	805	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245759	41245759	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs55650082	NA	P-0002842-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	94	524	0	ENST00000357654.3:c.1789G>T	p.Glu597Ter	p.E597*	ENST00000357654	NM_007294.3	597	Gaa/Taa	10/23	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.16	2		524	932	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114772	108114772	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002842-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	120	455	0	ENST00000278616.4:c.590del	p.Gly197AspfsTer9	p.G197Dfs*9	ENST00000278616	NM_000051.3	197	Gga/ga	6/63	0.123245047293367	3	FACETS	0.936	0.845	1	0.624	0.563	0.689	CLONAL	2	TRUE	0	0.16	3		455	865	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0004313-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	75	515	0				ENST00000310581	NM_198253.2	-/1132			0.218427839359622	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.945069865143585	0		515	156	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0004313-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	227	449	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.945069865143585	2		449	459	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0004313-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	264	353	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.945069865143585	2		353	538	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797278	42797278	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs968289754	NA	P-0004313-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	257	595	0	ENST00000575354.2:c.3640C>T	p.Arg1214Ter	p.R1214*	ENST00000575354	NM_015125.3	1214	Cga/Tga	15/20	NA	2	FACETS	0.961	0.938	0.981			1	INDETERMINATE	2	TRUE	NA	0.945069865143585	2		595	283	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129605	47129605	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004313-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	144	370	0	ENST00000409792.3:c.5275C>T	p.Gln1759Ter	p.Q1759*	ENST00000409792	NM_014159.6	1759	Cag/Tag	10/21	0.945069865143585	1	FACETS	0.946	0.907	0.98	0.946	0.907	0.98	CLONAL	1	TRUE	0	0.945069865143585	1		370	170	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73633691	73633691	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004313-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	52	293	0	ENST00000377687.4:c.226A>G	p.Thr76Ala	p.T76A	ENST00000377687	NM_001730.3	76	Acc/Gcc	1/4	1	2	FACETS	0.636	0.551	0.726	0.636	0.551	0.726	SUBCLONAL	1	TRUE	1	0.945069865143585	2		293	173	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136105	11136105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004313-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	167	421	0	ENST00000358026.2:c.3089G>A	p.Gly1030Asp	p.G1030D	ENST00000358026	NM_001128849.1	1030	gGc/gAc	22/36	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.945069865143585	2		421	337	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0005604-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	178	515	0				ENST00000310581	NM_198253.2	-/1132			0.501882658395109	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.623707366889359	4		515	382	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397780	116397780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005604-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	256	394	0	ENST00000397752.3:c.2054G>A	p.Gly685Glu	p.G685E	ENST00000397752	NM_000245.2	685	gGg/gAg	8/21	0.626308707903863	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.623707366889359	2		394	347	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717679	89717679	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005604-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	166	399	0	ENST00000371953.3:c.704A>G	p.Glu235Gly	p.E235G	ENST00000371953	NM_000314.4	235	gAa/gGa	7/9	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.623707366889359	2		399	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577106	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0005604-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	259	512	0	ENST00000269305.4:c.832_833delinsTT	p.Pro278Phe	p.P278F	ENST00000269305	NM_001126112.2	278	CCt/TTt	8/11	0.626308707903863	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.623707366889359	2		512	380	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066482	94066482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542602078	NA	P-0005604-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	120	459	1	ENST00000369303.4:c.1277G>A	p.Arg426Gln	p.R426Q	ENST00000369303	NM_004440.3	426	cGa/cAa	5/17	0.626308707903863	3	FACETS	0.925	0.838	1	0.462	0.419	0.508	CLONAL	1	TRUE	1	0.623707366889359	3		460	546	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250808	99250808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005604-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	147	515	0	ENST00000268035.6:c.112G>A	p.Asp38Asn	p.D38N	ENST00000268035	NM_000875.3	38	Gac/Aac	2/21	0.626308707903863	3	FACETS	1	0.973	1	0.568	0.522	0.617	CLONAL	1	TRUE	1	0.623707366889359	3		515	544	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5246009	5246009	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1302033266	NA	P-0005604-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	129	580	0	ENST00000357368.4:c.766A>C	p.Ile256Leu	p.I256L	ENST00000357368	NM_002850.3	256	Atc/Ctc	10/38	0.496600688539213	4	FACETS	1	0.948	1	0.354	0.322	0.388	CLONAL	1	TRUE	1	0.623707366889359	4		580	632	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2097457	2097457	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005604-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	215	367	0	ENST00000349721.2:c.3064T>C	p.Phe1022Leu	p.F1022L	ENST00000349721	NM_003070.3	1022	Ttt/Ctt	21/34	0.626308707903863	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.623707366889359	2		367	332	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0006147-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	209	600	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA	2	FACETS	0.81	0.75	0.871			1	INDETERMINATE	2	TRUE	NA	0.220659803762403	2		600	1170	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593397	48593397	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs377767355	NA	P-0006147-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	107	414	0	ENST00000342988.3:c.1148T>A	p.Ile383Lys	p.I383K	ENST00000342988	NM_005359.5	383	aTa/aAa	10/12	0.220659803762403	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.220659803762403	1		414	794	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971138	21971138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760640852	NA	P-0006147-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	90	285	0	ENST00000304494.5:c.220G>A	p.Asp74Asn	p.D74N	ENST00000304494	NM_000077.4	74	Gac/Aac	2/3	0.220659803762403	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.220659803762403	1		285	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576891	7576891	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0006147-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	149	519	1	ENST00000269305.4:c.955A>T	p.Lys319Ter	p.K319*	ENST00000269305	NM_001126112.2	319	Aag/Tag	9/11	0.220659803762403	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.220659803762403	1		520	1031	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882992	89882992	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006147-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	59	355	0	ENST00000389301.3:c.32C>G	p.Ser11Trp	p.S11W	ENST00000389301	NM_000135.2	11	tCg/tGg	1/43	1	2	FACETS	0.86	0.739	0.991	0.86	0.739	0.991	CLONAL	1	TRUE	1	0.220659803762403	2		355	622	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0006280-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	18	454	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.174397099317195	3	FACETS	0.883	0.69	1	0.589	0.46	0.729	INDETERMINATE	2	TRUE	0	0.444710793335983	3		454	56	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082299	16082299	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs958489598	NA	P-0006280-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	9	0	0	ENST00000281043.3:c.113G>A	p.Gly38Asp	p.G38D	ENST00000281043	NM_005378.4	38	gGc/gAc	2/3	0.232175575707482	3	FACETS	1	0.761	1	0.575	0.392	0.792	INDETERMINATE	1	TRUE	1	0.444710793335983	3		0	43	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793305	242793305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006280-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	18	595	0	ENST00000334409.5:c.772G>A	p.Gly258Ser	p.G258S	ENST00000334409	NM_005018.2	258	Ggc/Agc	5/5	1	2	FACETS	0.778	0.61	0.959	1	0.923	1	CLONAL	2	TRUE	1	0.444710793335983	2		595	52	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577551	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0006280-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	13	488	2	ENST00000269305.4:c.730_731delinsTT	p.Gly244Phe	p.G244F	ENST00000269305	NM_001126112.2	244	GGc/TTc	7/11	0.449994192979568	1	FACETS	1	0.748	1	1	0.748	1	CLONAL	1	TRUE	0	0.444710793335983	1		490	45	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630703	90630704	+	missense_variant	Missense_Mutation	DNP	AC	AC	CT	novel	NA	P-0006280-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	13	549	0	ENST00000330062.3:c.782_783delinsAG	p.Arg261Gln	p.R261Q	ENST00000330062	NM_002168.2	261	cGT/cAG	6/11	0.232175575707482	3	FACETS	0.812	0.588	1	0.406	0.294	0.539	INDETERMINATE	1	TRUE	1	0.444710793335983	3		549	88	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	139	523	0				ENST00000310581	NM_198253.2	-/1132			0.360127904040045	3	FACETS	0.877	0.805	0.951	0.877	0.805	0.951	CLONAL	2	TRUE	1	0.435547042817948	3		523	443	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101358	27101358	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	116	647	0	ENST00000324856.7:c.4640C>T	p.Ser1547Phe	p.S1547F	ENST00000324856	NM_006015.4	1547	tCc/tTc	18/20	1	2	FACETS	0.826	0.746	0.91	0.826	0.746	0.91	CLONAL	1	TRUE	1	0.435547042817948	2		647	645	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812246	43812246	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	142	648	0	ENST00000372470.3:c.1111G>A	p.Ala371Thr	p.A371T	ENST00000372470	NM_005373.2	371	Gcc/Acc	7/12	1	2	FACETS	0.921	0.841	1	0.921	0.841	1	CLONAL	1	TRUE	1	0.435547042817948	2		648	708	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43817888	43817888	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1190279641	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	156	630	0	ENST00000372470.3:c.1567A>G	p.Arg523Gly	p.R523G	ENST00000372470	NM_005373.2	523	Aga/Gga	11/12	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.435547042817948	2		630	678	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615538	43615538	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	112	682	1	ENST00000355710.3:c.2617C>T	p.Arg873Trp	p.R873W	ENST00000355710	NM_020975.4	873	Cgg/Tgg	15/20	1	2	FACETS	0.875	0.789	0.965	0.875	0.789	0.965	CLONAL	1	TRUE	1	0.435547042817948	2		683	588	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851953	63851953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	167	662	0	ENST00000279873.7:c.2731C>T	p.Pro911Ser	p.P911S	ENST00000279873	NM_032199.2	911	Ccc/Tcc	10/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.435547042817948	2		662	667	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446314	70446314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868773920	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	132	670	0	ENST00000373644.4:c.5254C>T	p.Pro1752Ser	p.P1752S	ENST00000373644	NM_030625.2	1752	Ccc/Tcc	11/12	1	2	FACETS	0.859	0.781	0.94	0.859	0.781	0.94	CLONAL	1	TRUE	1	0.435547042817948	2		670	706	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201807	102201807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	102	540	0	ENST00000263464.3:c.1159G>A	p.Glu387Lys	p.E387K	ENST00000263464	NM_001165.4	387	Gaa/Aaa	6/9	0.419158233029454	1	FACETS	0.914	0.823	1	0.914	0.823	1	CLONAL	1	TRUE	0	0.435547042817948	1		540	401	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307319	118307319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	34	178	0	ENST00000534358.1:c.92C>T	p.Pro31Leu	p.P31L	ENST00000534358	NM_005933.3	31	cCg/cTg	1/36	0.419158233029454	1	FACETS	0.947	0.789	1	0.947	0.789	1	CLONAL	1	TRUE	0	0.435547042817948	1		178	129	SUCCESS
CBL	867	MSKCC	GRCh37	11	119167741	119167741	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	78	433	0	ENST00000264033.4:c.2150C>T	p.Ser717Leu	p.S717L	ENST00000264033	NM_005188.3	717	tCa/tTa	13/16	0.419158233029454	1	FACETS	0.763	0.675	0.857	0.763	0.675	0.857	SUBCLONAL	1	TRUE	0	0.435547042817948	1		433	367	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434469	49434469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1449737126	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	299	863	0	ENST00000301067.7:c.7084C>T	p.Pro2362Ser	p.P2362S	ENST00000301067	NM_003482.3	2362	Cct/Tct	31/54	0.408215295816558	2	FACETS	0.961	0.911	1	0.961	0.911	1	CLONAL	2	TRUE	0	0.435547042817948	2		863	714	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434936	49434936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1007923504	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	272	746	0	ENST00000301067.7:c.6617C>T	p.Pro2206Leu	p.P2206L	ENST00000301067	NM_003482.3	2206	cCt/cTt	31/54	0.408215295816558	2	FACETS	0.985	0.932	1	0.985	0.932	1	CLONAL	2	TRUE	0	0.435547042817948	2		746	634	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445394	49445394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	352	1017	0	ENST00000301067.7:c.2072C>T	p.Pro691Leu	p.P691L	ENST00000301067	NM_003482.3	691	cCa/cTa	10/54	0.408215295816558	2	FACETS	0.888	0.844	0.933	0.888	0.844	0.933	CLONAL	2	TRUE	0	0.435547042817948	2		1017	910	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445991	49445991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265398099	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	300	839	0	ENST00000301067.7:c.1475C>T	p.Ser492Leu	p.S492L	ENST00000301067	NM_003482.3	492	tCg/tTg	10/54	0.408215295816558	2	FACETS	0.872	0.825	0.919	0.872	0.825	0.919	CLONAL	2	TRUE	0	0.435547042817948	2		839	790	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863272	57863272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1305707895	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	236	713	0	ENST00000228682.2:c.1367G>A	p.Gly456Glu	p.G456E	ENST00000228682	NM_005269.2	456	gGg/gAg	11/12	0.408215295816558	2	FACETS	0.805	0.755	0.856	0.805	0.755	0.856	CLONAL	2	TRUE	0	0.435547042817948	2		713	673	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626755	28626755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750445891	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	98	527	0	ENST00000241453.7:c.541G>A	p.Ala181Thr	p.A181T	ENST00000241453	NM_004119.2	181	Gcc/Acc	5/24	0.419158233029454	1	FACETS	0.838	0.752	0.928	0.838	0.752	0.928	CLONAL	1	TRUE	0	0.435547042817948	1		527	420	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893575	28893575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	56	418	0	ENST00000282397.4:c.3271G>A	p.Glu1091Lys	p.E1091K	ENST00000282397	NM_002019.4	1091	Gaa/Aaa	24/30	0.419158233029454	1	FACETS	0.651	0.561	0.747	0.651	0.561	0.747	SUBCLONAL	1	TRUE	0	0.435547042817948	1		418	309	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640328	3640328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767093188	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	127	665	0	ENST00000294008.3:c.3311G>A	p.Arg1104Gln	p.R1104Q	ENST00000294008	NM_032444.2	1104	cGg/cAg	12/15	1	2	FACETS	0.951	0.864	1	0.951	0.864	1	CLONAL	1	TRUE	1	0.435547042817948	2		665	613	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857900	9857900	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	122	707	0	ENST00000330684.3:c.3501G>A	p.Met1167Ile	p.M1167I	ENST00000330684	NM_001134407.1	1167	atG/atA	13/13	1	2	FACETS	0.888	0.804	0.975	0.888	0.804	0.975	CLONAL	1	TRUE	1	0.435547042817948	2		707	631	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857935	9857935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	121	713	0	ENST00000330684.3:c.3466G>A	p.Glu1156Lys	p.E1156K	ENST00000330684	NM_001134407.1	1156	Gaa/Aaa	13/13	1	2	FACETS	0.878	0.795	0.965	0.878	0.795	0.965	CLONAL	1	TRUE	1	0.435547042817948	2		713	633	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	422	782	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.388911418427155	3	FACETS	0.925	0.887	0.964	0.925	0.887	0.964	CLONAL	3	TRUE	0	0.435547042817948	3		782	850	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496919	29496919	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	105	300	0	ENST00000356175.3:c.491del	p.Leu164Ter	p.L164*	ENST00000356175	NM_000267.3	164	Tta/ta	5/57	0.392157241260674	2	FACETS	0.79	0.718	0.865	0.79	0.718	0.865	SUBCLONAL	2	TRUE	0	0.435547042817948	2		300	305	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33680949	33680949	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	160	480	0	ENST00000308377.4:c.1328G>A	p.Arg443Lys	p.R443K	ENST00000308377	NM_152270.3	443	aGa/aAa	4/5	0.392157241260674	2	FACETS	0.829	0.768	0.892	0.829	0.768	0.892	CLONAL	2	TRUE	0	0.435547042817948	2		480	443	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690040	33690040	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	203	643	0	ENST00000308377.4:c.787G>A	p.Glu263Lys	p.E263K	ENST00000308377	NM_152270.3	263	Gaa/Aaa	2/5	0.392157241260674	2	FACETS	0.773	0.721	0.826	0.773	0.721	0.826	SUBCLONAL	2	TRUE	0	0.435547042817948	2		643	603	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55339533	55339533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	164	434	0	ENST00000284073.2:c.292C>T	p.Pro98Ser	p.P98S	ENST00000284073	NM_138962.2	98	Cct/Tct	5/14	0.378406480235241	3	FACETS	0.852	0.787	0.919	0.568	0.525	0.613	CLONAL	2	TRUE	0	0.435547042817948	3		434	538	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271682	15271682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	275	893	0	ENST00000263388.2:c.6757G>A	p.Glu2253Lys	p.E2253K	ENST00000263388	NM_000435.2	2253	Gag/Aag	33/33	0.378853343523845	3	FACETS	0.946	0.891	1	0.946	0.891	1	CLONAL	2	TRUE	1	0.435547042817948	3		893	813	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272089	15272089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	113	860	0	ENST00000263388.2:c.6350C>T	p.Ser2117Phe	p.S2117F	ENST00000263388	NM_000435.2	2117	tCc/tTc	33/33	0.378853343523845	3	FACETS	0.799	0.719	0.884	0.399	0.359	0.442	SUBCLONAL	1	TRUE	1	0.435547042817948	3		860	791	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214005	36214005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	163	791	0	ENST00000222270.7:c.2831C>T	p.Thr944Ile	p.T944I	ENST00000222270	NM_014727.1	944	aCc/aTc	6/37	0.378853343523845	3	FACETS	0.991	0.909	1	0.495	0.454	0.538	CLONAL	1	TRUE	1	0.435547042817948	3		791	920	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214864	36214864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	197	648	0	ENST00000222270.7:c.3290C>T	p.Pro1097Leu	p.P1097L	ENST00000222270	NM_014727.1	1097	cCc/cTc	8/37	0.378853343523845	3	FACETS	0.987	0.921	1	0.987	0.921	1	CLONAL	2	TRUE	1	0.435547042817948	3		648	558	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727079	41727079	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	88	584	0	ENST00000301178.4:c.337G>A	p.Gly113Arg	p.G113R	ENST00000301178	NM_021913.4	113	Gga/Aga	3/20	0.394795910448796	3	FACETS	0.734	0.651	0.824	0.367	0.325	0.412	SUBCLONAL	1	TRUE	1	0.435547042817948	3		584	670	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25459872	25459872	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs750597155	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	186	572	1	ENST00000264709.3:c.2411C>T	p.Pro804Leu	p.P804L	ENST00000264709	NM_175629.2	804	cCg/cTg	21/23	0.378406480235241	3	FACETS	0.835	0.775	0.896	0.556	0.516	0.598	CLONAL	2	TRUE	0	0.435547042817948	3		573	623	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537918	212537918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146197533	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	231	558	0	ENST00000342788.4:c.1687G>A	p.Glu563Lys	p.E563K	ENST00000342788	NM_005235.2	563	Gaa/Aaa	14/28	0.408215295816558	2	FACETS	0.97	0.912	1	0.97	0.912	1	CLONAL	2	TRUE	0	0.435547042817948	2		558	547	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546725	9546725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210292896	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	251	698	0	ENST00000353224.5:c.1297C>T	p.Arg433Trp	p.R433W	ENST00000353224	NM_177990.2	433	Cgg/Tgg	5/10	0.378853343523845	3	FACETS	0.871	0.817	0.925	0.871	0.817	0.925	CLONAL	2	TRUE	1	0.435547042817948	3		698	806	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713349	40713349	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	104	789	0	ENST00000373198.4:c.4166G>C	p.Arg1389Thr	p.R1389T	ENST00000373198	NM_133170.3	1389	aGg/aCg	30/32	0.435775340073312	3	FACETS	0.672	0.601	0.748	0.336	0.3	0.374	SUBCLONAL	1	TRUE	1	0.435547042817948	3		789	865	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827909	40827909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778174338	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	117	632	0	ENST00000373198.4:c.2519C>T	p.Ser840Phe	p.S840F	ENST00000373198	NM_133170.3	840	tCt/tTt	17/32	0.435775340073312	3	FACETS	0.888	0.801	0.979	0.444	0.4	0.49	CLONAL	1	TRUE	1	0.435547042817948	3		632	737	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944591	40944592	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	130	607	1	ENST00000373198.4:c.1910_1911delinsAA	p.Arg637Gln	p.R637Q	ENST00000373198	NM_133170.3	637	cGG/cAA	12/32	0.435775340073312	3	FACETS	1	0.938	1	0.521	0.473	0.571	CLONAL	1	TRUE	1	0.435547042817948	3		608	698	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306689	41306689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868376470	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	115	584	0	ENST00000373198.4:c.970G>A	p.Glu324Lys	p.E324K	ENST00000373198	NM_133170.3	324	Gaa/Aaa	7/32	0.435775340073312	3	FACETS	0.966	0.871	1	0.483	0.435	0.533	CLONAL	1	TRUE	1	0.435547042817948	3		584	666	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62323096	62323096	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	74	582	0	ENST00000360203.5:c.2558C>T	p.Ala853Val	p.A853V	ENST00000360203	NM_001283009.1	853	gCc/gTc	28/35	0.360127904040045	3	FACETS	0.711	0.623	0.806	0.356	0.311	0.403	SUBCLONAL	1	TRUE	1	0.435547042817948	3		582	582	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39763629	39763629	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542821839	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	71	428	0	ENST00000288319.7:c.823C>T	p.Pro275Ser	p.P275S	ENST00000288319	NM_182918.3	275	Cca/Tca	8/10	1	2	FACETS	0.807	0.708	0.913	0.807	0.708	0.913	CLONAL	1	TRUE	1	0.435547042817948	2		428	404	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421202	12421202	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	99	488	0	ENST00000287820.6:c.83-1G>A		p.X28_splice	ENST00000287820	NM_015869.4	28			1	2	FACETS	0.897	0.804	0.995	0.897	0.804	0.995	CLONAL	1	TRUE	1	0.435547042817948	2		488	507	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125764	47125764	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775677070	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	131	556	0	ENST00000409792.3:c.5506C>T	p.Pro1836Ser	p.P1836S	ENST00000409792	NM_014159.6	1836	Ccg/Tcg	12/21	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.435547042817948	2		556	593	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49929248	49929248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763498892	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	107	575	0	ENST00000296474.3:c.3295G>A	p.Gly1099Arg	p.G1099R	ENST00000296474	NM_002447.2	1099	Gga/Aga	15/20	1	2	FACETS	0.854	0.769	0.945	0.854	0.769	0.945	CLONAL	1	TRUE	1	0.435547042817948	2		575	575	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73096456	73096456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	42	208	0	ENST00000356692.5:c.236C>T	p.Pro79Leu	p.P79L	ENST00000356692		79	cCc/cTc	3/9	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.435547042817948	2		208	173	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430309	181430309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	69	425	0	ENST00000325404.1:c.161G>A	p.Gly54Glu	p.G54E	ENST00000325404	NM_003106.3	54	gGg/gAg	1/1	1	2	FACETS	0.903	0.791	1	0.903	0.791	1	CLONAL	1	TRUE	1	0.435547042817948	2		425	351	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584548	189584548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	142	518	0	ENST00000264731.3:c.844G>A	p.Gly282Arg	p.G282R	ENST00000264731	NM_003722.4	282	Gga/Aga	6/14	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.435547042817948	2		518	629	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1977063	1977063	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	90	624	0	ENST00000382891.5:c.3557A>C	p.Asn1186Thr	p.N1186T	ENST00000382891	NM_133335.3	1186	aAt/aCt	20/22	1	2	FACETS	0.753	0.669	0.841	0.753	0.669	0.841	SUBCLONAL	1	TRUE	1	0.435547042817948	2		624	549	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961101	55961101	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	82	517	0	ENST00000263923.4:c.2839C>T	p.Gln947Ter	p.Q947*	ENST00000263923	NM_002253.2	947	Caa/Taa	21/30	1	2	FACETS	0.813	0.72	0.913	0.813	0.72	0.913	CLONAL	1	TRUE	1	0.435547042817948	2		517	463	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55962398	55962398	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	82	389	0	ENST00000263923.4:c.2726G>A	p.Gly909Glu	p.G909E	ENST00000263923	NM_002253.2	909	gGa/gAa	19/30	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.435547042817948	2		389	369	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968583	55968583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	117	556	0	ENST00000263923.4:c.2080C>T	p.Pro694Ser	p.P694S	ENST00000263923	NM_002253.2	694	Ccc/Tcc	14/30	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.435547042817948	2		556	500	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155778	106155778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	135	688	0	ENST00000380013.4:c.679G>A	p.Glu227Lys	p.E227K	ENST00000380013	NM_001127208.2	227	Gaa/Aaa	3/11	0.419158233029454	1	FACETS	0.906	0.828	0.988	0.906	0.828	0.988	CLONAL	1	TRUE	0	0.435547042817948	1		688	535	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630059	187630059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866303516	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	154	780	0	ENST00000441802.2:c.923C>T	p.Ser308Phe	p.S308F	ENST00000441802	NM_005245.3	308	tCc/tTc	2/27	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.435547042817948	2		780	667	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630386	187630386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	139	698	0	ENST00000441802.2:c.596C>T	p.Pro199Leu	p.P199L	ENST00000441802	NM_005245.3	199	cCa/cTa	2/27	1	2	FACETS	0.977	0.892	1	0.977	0.892	1	CLONAL	1	TRUE	1	0.435547042817948	2		698	653	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264601	1264601	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	118	746	0	ENST00000310581.5:c.2761C>T	p.Gln921Ter	p.Q921*	ENST00000310581	NM_198253.2	921	Cag/Tag	11/16	0.360127904040045	3	FACETS	0.882	0.796	0.973	0.441	0.398	0.487	CLONAL	1	TRUE	1	0.435547042817948	3		746	748	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295201	1295201	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	68	559	0				ENST00000310581	NM_198253.2	-/1132			0.360127904040045	3	FACETS	0.886	0.774	1	0.443	0.387	0.504	CLONAL	1	TRUE	1	0.435547042817948	3		559	429	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409227	31409228	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AT	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	93	615	0	ENST00000344624.3:c.3789_3790delinsAT	p.Gln1264Ter	p.Q1264*	ENST00000344624		1263	tcCCag/tcATag	30/33	0.394795910448796	3	FACETS	0.805	0.716	0.899	0.403	0.358	0.45	CLONAL	1	TRUE	1	0.435547042817948	3		615	646	SUCCESS
APC	324	MSKCC	GRCh37	5	112116491	112116491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	52	385	0	ENST00000257430.4:c.536C>T	p.Ser179Phe	p.S179F	ENST00000257430	NM_000038.5	179	tCc/tTc	6/16	0.378853343523845	3	FACETS	0.729	0.622	0.845	0.364	0.311	0.423	SUBCLONAL	1	TRUE	1	0.435547042817948	3		385	399	SUCCESS
APC	324	MSKCC	GRCh37	5	112170771	112170771	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	175	615	0	ENST00000257430.4:c.1867C>G	p.Arg623Gly	p.R623G	ENST00000257430	NM_000038.5	623	Cgg/Ggg	15/16	0.378853343523845	3	FACETS	0.783	0.724	0.843	0.783	0.724	0.843	SUBCLONAL	2	TRUE	1	0.435547042817948	3		615	625	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066678	94066678	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	100	572	0	ENST00000369303.4:c.1081A>T	p.Asn361Tyr	p.N361Y	ENST00000369303	NM_004440.3	361	Aac/Tac	5/17	0.378853343523845	3	FACETS	0.841	0.752	0.935	0.42	0.376	0.468	CLONAL	1	TRUE	1	0.435547042817948	3		572	665	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609759	117609759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	93	563	0	ENST00000368508.3:c.6940G>A	p.Asp2314Asn	p.D2314N	ENST00000368508	NM_002944.2	2314	Gat/Aat	43/43	0.378853343523845	3	FACETS	0.894	0.796	0.997	0.447	0.398	0.499	CLONAL	1	TRUE	1	0.435547042817948	3		563	582	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662627	117662627	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	97	608	0	ENST00000368508.3:c.4838T>A	p.Phe1613Tyr	p.F1613Y	ENST00000368508	NM_002944.2	1613	tTt/tAt	29/43	0.378853343523845	3	FACETS	0.856	0.764	0.953	0.428	0.382	0.477	CLONAL	1	TRUE	1	0.435547042817948	3		608	634	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687430	117687430	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	194	572	0	ENST00000368508.3:c.2621A>T	p.Glu874Val	p.E874V	ENST00000368508	NM_002944.2	874	gAa/gTa	18/43	0.378853343523845	3	FACETS	0.906	0.843	0.97	0.906	0.843	0.97	CLONAL	2	TRUE	1	0.435547042817948	3		572	599	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202299	138202299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	97	692	0	ENST00000237289.4:c.2216C>T	p.Pro739Leu	p.P739L	ENST00000237289	NM_001270507.1	739	cCc/cTc	9/9	1	2	FACETS	0.693	0.618	0.772	0.693	0.618	0.772	SUBCLONAL	1	TRUE	1	0.435547042817948	2		692	643	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522556	157522556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1265377330	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	135	701	0	ENST00000346085.5:c.4828C>T	p.Pro1610Ser	p.P1610S	ENST00000346085	NM_020732.3	1610	Cct/Tct	18/20	1	2	FACETS	0.883	0.804	0.966	0.883	0.804	0.966	CLONAL	1	TRUE	1	0.435547042817948	2		701	702	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527357	157527357	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	110	557	0	ENST00000346085.5:c.5082T>G	p.Ile1694Met	p.I1694M	ENST00000346085	NM_020732.3	1694	atT/atG	20/20	1	2	FACETS	0.902	0.813	0.996	0.902	0.813	0.996	CLONAL	1	TRUE	1	0.435547042817948	2		557	560	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411852	116411852	+	intron_variant	Intron	SNP	G	G	A	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	171	735	0	ENST00000397752.3:c.2888-51G>A		p.*963*	ENST00000397752	NM_000245.2	-/1390			0.419158233029454	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.435547042817948	1		735	582	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194692	29194692	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	132	744	0	ENST00000240100.2:c.1036C>T	p.Pro346Ser	p.P346S	ENST00000240100	NM_001394.6	346	Ccc/Tcc	4/4	0.419158233029454	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.435547042817948	1		744	467	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939532	68939532	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	99	391	0	ENST00000288368.4:c.517A>G	p.Ile173Val	p.I173V	ENST00000288368	NM_024870.2	173	Ata/Gta	5/40	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.435547042817948	2		391	360	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942891	68942891	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	124	487	0	ENST00000288368.4:c.703G>A	p.Glu235Lys	p.E235K	ENST00000288368	NM_024870.2	235	Gag/Aag	6/40	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.435547042817948	2		487	526	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050711	69050711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	86	392	0	ENST00000288368.4:c.4046C>T	p.Ser1349Phe	p.S1349F	ENST00000288368	NM_024870.2	1349	tCc/tTc	33/40	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.435547042817948	2		392	368	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069556	69069556	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	76	315	0	ENST00000288368.4:c.4232-1G>A		p.X1411_splice	ENST00000288368	NM_024870.2	1411			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.435547042817948	2		315	306	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141570593	141570593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755867103	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	117	686	0	ENST00000220592.5:c.535C>T	p.Arg179Cys	p.R179C	ENST00000220592	NM_012154.3	179	Cgc/Tgc	5/19	1	2	FACETS	0.814	0.735	0.897	0.814	0.735	0.897	CLONAL	1	TRUE	1	0.435547042817948	2		686	660	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740797	145740797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769553486	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	164	769	0	ENST00000428558.2:c.1303C>T	p.Pro435Ser	p.P435S	ENST00000428558	NM_004260.3	435	Cct/Tct	7/22	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.435547042817948	2		769	695	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2086916	2086916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	214	674	0	ENST00000349721.2:c.2614G>A	p.Val872Met	p.V872M	ENST00000349721	NM_003070.3	872	Gtg/Atg	18/34	0.392157241260674	2	FACETS	0.777	0.727	0.829	0.777	0.727	0.829	SUBCLONAL	2	TRUE	0	0.435547042817948	2		674	632	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2104046	2104046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199759640	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	104	557	1	ENST00000349721.2:c.3169C>T	p.Arg1057Cys	p.R1057C	ENST00000349721	NM_003070.3	1057	Cgt/Tgt	23/34	0.392157241260674	2	FACETS	0.883	0.793	0.977	0.441	0.396	0.489	CLONAL	1	TRUE	0	0.435547042817948	2		558	541	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486281	8486281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	84	506	0	ENST00000356435.5:c.2536C>T	p.Pro846Ser	p.P846S	ENST00000356435		846	Ccg/Tcg	17/35	0.392157241260674	2	FACETS	0.787	0.698	0.883	0.394	0.349	0.442	SUBCLONAL	1	TRUE	0	0.435547042817948	2		506	490	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970900	21970900	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	220	622	2	ENST00000304494.5:c.457+1G>A		p.X153_splice	ENST00000304494	NM_000077.4	153			0.392157241260674	2	FACETS	0.937	0.88	0.995	0.937	0.88	0.995	CLONAL	2	TRUE	0	0.435547042817948	2		624	539	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966611	36966611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs984035588	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	209	624	0	ENST00000358127.4:c.715C>T	p.Arg239Cys	p.R239C	ENST00000358127	NM_001280556.1	239	Cgc/Tgc	6/10	0.392157241260674	2	FACETS	0.897	0.84	0.955	0.897	0.84	0.955	CLONAL	2	TRUE	0	0.435547042817948	2		624	535	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894928	101894928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	267	572	0	ENST00000374994.4:c.481G>A	p.Glu161Lys	p.E161K	ENST00000374994	NM_004612.2	161	Gaa/Aaa	3/9	0.392157241260674	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.435547042817948	2		572	563	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617194	100617194	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	185	642	0	ENST00000308731.7:c.555A>T	p.Lys185Asn	p.K185N	ENST00000308731	NM_000061.2	185	aaA/aaT	7/19	0.346927379774695	2	FACETS	0.82	0.763	0.878	0.82	0.763	0.878	CLONAL	2	TRUE	0	0.435547042817948	2		642	518	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504128	123504128	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008997-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	76	394	0	ENST00000371139.4:c.304G>T	p.Val102Phe	p.V102F	ENST00000371139	NM_001114937.2	102	Gtt/Ttt	3/4	0.346927379774695	2	FACETS	0.956	0.844	1	0.478	0.422	0.538	CLONAL	1	TRUE	0	0.435547042817948	2		394	365	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0009377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	195	301	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	1	2	FACETS	0.925	0.86	0.993	0.925	0.86	0.993	CLONAL	1	FALSE	1	0.604725704465406	2		301	697	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0009377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	201	404	2	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.843	0.783	0.904	0.843	0.783	0.904	CLONAL	1	FALSE	1	0.604725704465406	2		406	789	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	277	397	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	0.966	0.909	1	0.966	0.909	1	CLONAL	1	FALSE	1	0.604725704465406	2		397	948	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577524	7577525	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAG	novel	NA	P-0009377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	209	393	0	ENST00000269305.4:c.754_756dup	p.Leu252dup	p.L252dup	ENST00000269305	NM_001126112.2	252	-/CTC	7/11	0.604725704465406	1	FACETS	0.91	0.852	0.968	0.91	0.852	0.968	CLONAL	1	FALSE	0	0.604725704465406	1		393	530	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	204	712	3	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.846	0.785	0.908	0.846	0.785	0.908	CLONAL	1	TRUE	1	0.561555847562822	2		715	859	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519505	137519506	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs780346130	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	182	651	2	ENST00000367739.4:c.1132_1133del	p.Ser378PhefsTer6	p.S378Ffs*6	ENST00000367739	NM_000416.2	378	AGt/t	7/7	0.561555847562822	1	FACETS	0.936	0.871	1	0.936	0.871	1	CLONAL	1	TRUE	0	0.561555847562822	1		653	498	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	147	469	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.92	0.844	0.999	0.92	0.844	0.999	CLONAL	1	TRUE	1	0.561555847562822	2		472	569	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	184	597	0	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	0.561555847562822	1	FACETS	0.893	0.83	0.956	0.893	0.83	0.956	CLONAL	1	TRUE	0	0.561555847562822	1		597	528	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	98	399	0	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.561555847562822	1	FACETS	0.711	0.64	0.785	0.711	0.64	0.785	SUBCLONAL	1	TRUE	0	0.561555847562822	1		399	353	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567647	226567647	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	203	767	0	ENST00000366794.5:c.1519del	p.Ser507AlafsTer17	p.S507Afs*17	ENST00000366794	NM_001618.3	507	Agc/gc	10/23	1	2	FACETS	0.891	0.828	0.957	0.891	0.828	0.957	CLONAL	1	TRUE	1	0.561555847562822	2		767	811	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47595339	47595339	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	145	464	0	ENST00000430070.2:c.748A>G	p.Ile250Val	p.I250V	ENST00000430070	NM_018095.4	250	Att/Gtt	4/4	1	2	FACETS	0.98	0.899	1	0.98	0.899	1	CLONAL	1	TRUE	1	0.561555847562822	2		464	527	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206616	108206616	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	153	490	0	ENST00000278616.4:c.8196C>A	p.Phe2732Leu	p.F2732L	ENST00000278616	NM_000051.3	2732	ttC/ttA	56/63	1	2	FACETS	0.958	0.881	1	0.958	0.881	1	CLONAL	1	TRUE	1	0.561555847562822	2		490	569	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145018	58145018	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	127	758	0	ENST00000257904.6:c.326del	p.Pro109HisfsTer12	p.P109Hfs*12	ENST00000257904	NM_000075.3	109	cCa/ca	3/8	1	2	FACETS	0.561	0.508	0.617	0.561	0.508	0.617	SUBCLONAL	1	TRUE	1	0.561555847562822	2		758	806	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89345482	89345482	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	34	610	0	ENST00000301030.4:c.7468G>A	p.Val2490Met	p.V2490M	ENST00000301030	NM_001256183.1	2490	Gtg/Atg	9/13	1	2	FACETS	0.19	0.155	0.231	0.19	0.155	0.231	SUBCLONAL	1	TRUE	1	0.561555847562822	2		610	636	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845237	89845237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765036744	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	206	598	0	ENST00000389301.3:c.1798C>T	p.Arg600Cys	p.R600C	ENST00000389301	NM_000135.2	600	Cgt/Tgt	20/43	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.561555847562822	2		598	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579344	7579344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	207	695	0	ENST00000269305.4:c.343C>T	p.His115Tyr	p.H115Y	ENST00000269305	NM_001126112.2	115	Cat/Tat	4/11	1	2	FACETS	0.998	0.929	1	0.998	0.929	1	CLONAL	1	TRUE	1	0.561555847562822	2		695	739	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557880	29557880	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1567850142	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	51	179	0	ENST00000356175.3:c.3134T>C	p.Leu1045Pro	p.L1045P	ENST00000356175	NM_000267.3	1045	cTg/cCg	24/57	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.561555847562822	2		179	174	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512370	38512370	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567767560	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	117	371	0	ENST00000254066.5:c.1286del	p.Gly429ValfsTer214	p.G429Vfs*214	ENST00000254066	NM_000964.3	427	ccG/cc	9/9	1	2	FACETS	0.947	0.86	1	0.947	0.86	1	CLONAL	1	TRUE	1	0.561555847562822	2		371	440	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55339537	55339537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	161	405	0	ENST00000284073.2:c.296G>A	p.Arg99His	p.R99H	ENST00000284073	NM_138962.2	99	cGt/cAt	5/14	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.561555847562822	2		405	502	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118924	70118926	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	265	833	0	ENST00000245479.2:c.499_501del	p.Lys167del	p.K167del	ENST00000245479	NM_000346.3	166	AAG/-	2/3	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.561555847562822	2		833	938	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602586	10602586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773315433	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	204	761	0	ENST00000171111.5:c.992C>T	p.Ala331Val	p.A331V	ENST00000171111	NM_203500.1	331	gCg/gTg	3/6	1	2	FACETS	0.909	0.845	0.975	0.909	0.845	0.975	CLONAL	1	TRUE	1	0.561555847562822	2		761	799	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121082	11121082	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	207	655	0	ENST00000358026.2:c.2149G>T	p.Glu717Ter	p.E717*	ENST00000358026	NM_001128849.1	717	Gaa/Taa	15/36	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.561555847562822	2		655	705	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228593	36228594	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	234	730	0	ENST00000222270.7:c.7607_7608insT	p.Glu2536AspfsTer6	p.E2536Dfs*6	ENST00000222270	NM_014727.1	2536	gag/gaTg	34/37	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.561555847562822	2		730	798	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748448	40748448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	162	560	0	ENST00000392038.2:c.434C>T	p.Ala145Val	p.A145V	ENST00000392038	NM_001626.4	145	gCt/gTt	5/14	1	2	FACETS	0.895	0.824	0.968	0.895	0.824	0.968	CLONAL	1	TRUE	1	0.561555847562822	2		560	645	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607487	46607487	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	201	744	3	ENST00000263734.3:c.1681del	p.Gln561SerfsTer7	p.Q561Sfs*7	ENST00000263734	NM_001430.4	559	aCc/ac	12/16	1	2	FACETS	0.891	0.828	0.957	0.891	0.828	0.957	CLONAL	1	TRUE	1	0.561555847562822	2		747	803	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793331	242793331	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	185	752	1	ENST00000334409.5:c.746C>T	p.Ala249Val	p.A249V	ENST00000334409	NM_005018.2	249	gCc/gTc	5/5	1	2	FACETS	0.888	0.822	0.956	0.888	0.822	0.956	CLONAL	1	TRUE	1	0.561555847562822	2		753	742	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794422	242794422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758959367	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	195	687	0	ENST00000334409.5:c.520G>A	p.Val174Met	p.V174M	ENST00000334409	NM_005018.2	174	Gtg/Atg	3/5	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.561555847562822	2		687	691	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	208	810	0	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.894	0.831	0.958	0.894	0.831	0.958	CLONAL	1	TRUE	1	0.561555847562822	2		810	829	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098755	47098755	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	240	812	0	ENST00000409792.3:c.6519G>A	p.Met2173Ile	p.M2173I	ENST00000409792	NM_014159.6	2173	atG/atA	15/21	0.561555847562822	1	FACETS	0.937	0.88	0.995	0.937	0.88	0.995	CLONAL	1	TRUE	0	0.561555847562822	1		812	656	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588757	52588757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269557269	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	178	663	0	ENST00000394830.3:c.4271C>T	p.Pro1424Leu	p.P1424L	ENST00000394830	NM_018313.4	1424	cCg/cTg	27/30	0.561555847562822	1	FACETS	0.923	0.858	0.989	0.923	0.858	0.989	CLONAL	1	TRUE	0	0.561555847562822	1		663	494	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52621443	52621445	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	118	334	0	ENST00000394830.3:c.2972_2974del	p.Glu991del	p.E991del	ENST00000394830	NM_018313.4	991	gAAGtt/gtt	20/30	0.561555847562822	1	FACETS	0.924	0.845	1	0.924	0.845	1	CLONAL	1	TRUE	0	0.561555847562822	1		334	327	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204842	128204842	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs768767517	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	173	762	0	ENST00000341105.2:c.599del	p.Gly200ValfsTer18	p.G200Vfs*18	ENST00000341105	NM_032638.4	200	gGt/gt	3/6	1	2	FACETS	0.832	0.767	0.898	0.832	0.767	0.898	CLONAL	1	TRUE	1	0.561555847562822	2		762	741	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198253	185198253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370479462	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	205	686	1	ENST00000265026.3:c.2735C>T	p.Ala912Val	p.A912V	ENST00000265026	NM_004721.4	912	gCc/gTc	13/14	1	2	FACETS	0.964	0.897	1	0.964	0.897	1	CLONAL	1	TRUE	1	0.561555847562822	2		687	757	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs149680468	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	175	648	0	ENST00000281708.4:c.1513C>A	p.Arg505Ser	p.R505S	ENST00000281708	NM_033632.3	505	Cgc/Agc	10/12	1	2	FACETS	0.927	0.857	1	0.927	0.857	1	CLONAL	1	TRUE	1	0.561555847562822	2		648	672	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630275	187630275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	219	772	0	ENST00000441802.2:c.707G>A	p.Gly236Asp	p.G236D	ENST00000441802	NM_005245.3	236	gGc/gAc	2/27	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.561555847562822	2		772	767	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861061	35861061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398237911	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	127	533	0	ENST00000303115.3:c.190G>A	p.Val64Ile	p.V64I	ENST00000303115	NM_002185.3	64	Gtc/Atc	2/8	1	2	FACETS	0.802	0.729	0.878	0.802	0.729	0.878	CLONAL	1	TRUE	1	0.561555847562822	2		533	564	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950304	38950304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs895560221	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	152	581	0	ENST00000357387.3:c.3646C>T	p.Arg1216Cys	p.R1216C	ENST00000357387	NM_152756.3	1216	Cgt/Tgt	31/38	1	2	FACETS	0.873	0.802	0.947	0.873	0.802	0.947	CLONAL	1	TRUE	1	0.561555847562822	2		581	620	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665637	86665638	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	69	249	0	ENST00000274376.6:c.1619_1620del	p.Cys540PhefsTer9	p.C540Ffs*9	ENST00000274376	NM_002890.2	540	TGt/t	12/25	0.561555847562822	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.561555847562822	1		249	160	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845189	151845189	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201742813	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	219	674	0	ENST00000262189.6:c.13823G>A	p.Arg4608His	p.R4608H	ENST00000262189	NM_170606.2	4608	cGc/cAc	52/59	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.561555847562822	2		674	766	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGG	novel	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	230	640	1	ENST00000220592.5:c.1804_1806dup	p.Pro602dup	p.P602dup	ENST00000220592	NM_012154.3	602	-/CCC	14/19	0.561555847562822	3	FACETS	1	0.984	1	0.583	0.544	0.623	CLONAL	1	TRUE	1	0.561555847562822	3		641	900	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220434	98220434	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	195	668	0	ENST00000331920.6:c.3029C>A	p.Pro1010His	p.P1010H	ENST00000331920	NM_000264.3	1010	cCc/cAc	18/24	1	2	FACETS	0.982	0.912	1	0.982	0.912	1	CLONAL	1	TRUE	1	0.561555847562822	2		668	707	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760526	133760526	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	185	780	0	ENST00000318560.5:c.2849A>G	p.Gln950Arg	p.Q950R	ENST00000318560	NM_005157.4	950	cAg/cGg	11/11	1	2	FACETS	0.904	0.837	0.973	0.904	0.837	0.973	CLONAL	1	TRUE	1	0.561555847562822	2		780	729	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854916	76854916	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010331-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	123	521	0	ENST00000373344.5:c.5920G>T	p.Gly1974Ter	p.G1974*	ENST00000373344	NM_000489.3	1974	Gga/Tga	25/35	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.561555847562822	2		521	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573996	7573996	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121912662	NA	P-0011364-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	191	600	0	ENST00000269305.4:c.1031T>C	p.Leu344Pro	p.L344P	ENST00000269305	NM_001126112.2	344	cTg/cCg	10/11	0.637776701073915	2	FACETS	0.967	0.915	1	0.967	0.915	1	CLONAL	2	TRUE	0	0.639482955839872	2		600	309	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940238	71940238	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011364-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	126	789	0	ENST00000298229.2:c.625del	p.Arg209ValfsTer36	p.R209Vfs*36	ENST00000298229	NM_001567.3	208	aCc/ac	5/28	0.443999177364498	6	FACETS	1	0.965	1	0.285	0.257	0.313	CLONAL	1	TRUE	2	0.639482955839872	6		789	789	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125525123	125525126	+	frameshift_variant	Frame_Shift_Del	DEL	GATG	GATG	-	novel	NA	P-0011364-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	42	359	0	ENST00000428830.2:c.1342_1345del	p.Gly448TrpfsTer8	p.G448Wfs*8	ENST00000428830	NM_001114121.2	447	GATGga/ga	13/14	0.641330765633065	3	FACETS	0.81	0.683	0.948	0.405	0.341	0.474	CLONAL	1	TRUE	1	0.639482955839872	3		359	214	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490604	56490604	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373831196	NA	P-0011364-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	66	547	0	ENST00000267101.3:c.2248C>T	p.Arg750Trp	p.R750W	ENST00000267101	NM_001982.3	750	Cgg/Tgg	19/28	0.531461674679265	4	FACETS	1	0.885	1	0.507	0.443	0.575	CLONAL	1	TRUE	2	0.639482955839872	4		547	334	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705492	47705494	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	novel	NA	P-0011364-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	50	332	0	ENST00000233146.2:c.2292_2294del	p.Trp764_Ala765delinsCys	p.W764_A765delinsC	ENST00000233146	NM_000251.2	764	tgGGCt/tgt	14/16	0.641330765633065	3	FACETS	0.925	0.794	1	0.463	0.397	0.533	CLONAL	1	TRUE	1	0.639482955839872	3		332	223	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090519	71090519	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011364-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	101	778	0	ENST00000318789.4:c.829A>G	p.Thr277Ala	p.T277A	ENST00000318789	NM_032682.5	277	Acc/Gcc	11/21	0.641330765633065	4	FACETS	1	0.939	1	0.533	0.478	0.59	CLONAL	1	TRUE	2	0.639482955839872	4		778	486	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012146-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	258	564	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.65371842743131	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.65371842743131	1		564	460	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0012146-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	141	372	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.65371842743131	2		372	397	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138135	2138135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201206500	NA	P-0012146-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	249	745	0	ENST00000219476.3:c.5155G>A	p.Ala1719Thr	p.A1719T	ENST00000219476	NM_000548.3	1719	Gca/Aca	40/42	0.639957069758204	4	FACETS	0.964	0.9	1	0.321	0.3	0.344	CLONAL	1	TRUE	1	0.65371842743131	4		745	1307	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227959	123227959	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012146-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	62	286	0	ENST00000218089.9:c.3670G>A	p.Glu1224Lys	p.E1224K	ENST00000218089	NM_001042749.1	1224	Gag/Aag	33/35	1	2	FACETS	0.721	0.629	0.819	0.721	0.629	0.819	SUBCLONAL	1	TRUE	1	0.65371842743131	2		286	263	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849512	68849512	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012146-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	227	637	0	ENST00000261769.5:c.1416del	p.Val473SerfsTer8	p.V473Sfs*8	ENST00000261769	NM_004360.3	472	aCc/ac	10/16	0.65371842743131	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.65371842743131	1		637	457	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341536	89341536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012146-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	177	502	0	ENST00000301030.4:c.7534C>T	p.Arg2512Trp	p.R2512W	ENST00000301030	NM_001256183.1	2512	Cgg/Tgg	10/13	0.65371842743131	1	FACETS	0.967	0.904	1	0.967	0.904	1	CLONAL	1	TRUE	0	0.65371842743131	1		502	377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0014834-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	195	472	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	0.374216043697713	3	FACETS	0.876	0.821	0.932	0.876	0.821	0.932	CLONAL	3	TRUE	0	0.413382715674485	3		472	433	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658485	3658485	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014834-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	162	382	0	ENST00000294008.3:c.481C>G	p.Gln161Glu	p.Q161E	ENST00000294008	NM_032444.2	161	Cag/Gag	2/15	0.408044854886126	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.413382715674485	3		382	426	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857427	9857427	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014834-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	70	439	0	ENST00000330684.3:c.3974A>T	p.Tyr1325Phe	p.Y1325F	ENST00000330684	NM_001134407.1	1325	tAc/tTc	13/13	0.408044854886126	3	FACETS	1	0.901	1	0.516	0.452	0.585	CLONAL	1	TRUE	1	0.413382715674485	3		439	396	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984924	9984924	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014834-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	32	284	0	ENST00000330684.3:c.1041C>A	p.Asp347Glu	p.D347E	ENST00000330684	NM_001134407.1	347	gaC/gaA	4/13	0.408044854886126	3	FACETS	0.649	0.528	0.784	0.324	0.264	0.392	SUBCLONAL	1	TRUE	1	0.413382715674485	3		284	288	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763437	59763437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014834-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	130	305	0	ENST00000259008.2:c.2665C>T	p.Gln889Ter	p.Q889*	ENST00000259008	NM_032043.2	889	Caa/Taa	19/20	0.390350737475839	4	FACETS	0.896	0.832	0.96	0.896	0.832	0.96	CLONAL	4	TRUE	0	0.413382715674485	4		305	248	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935020	49935020	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014834-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	85	486	0	ENST00000296474.3:c.1979C>G	p.Thr660Ser	p.T660S	ENST00000296474	NM_002447.2	660	aCt/aGt	6/20	0.3889325344919	2	FACETS	1	0.97	1	0.631	0.563	0.702	CLONAL	1	TRUE	0	0.413382715674485	2		486	326	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402792	20402792	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014834-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	125	408	0	ENST00000346618.3:c.329C>A	p.Ala110Asp	p.A110D	ENST00000346618	NM_001949.4	110	gCc/gAc	1/7	0.413382715674485	6	FACETS	0.837	0.763	0.913	0.628	0.572	0.685	CLONAL	3	TRUE	2	0.413382715674485	6		408	440	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273548	38273548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768223019	NA	P-0014834-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	145	434	0	ENST00000425967.3:c.1787C>T	p.Ser596Phe	p.S596F	ENST00000425967	NM_001174067.1	596	tCc/tTc	14/19	0.3889325344919	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.413382715674485	2		434	285	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412136	63412136	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014834-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	161	441	0	ENST00000330258.3:c.1031T>C	p.Met344Thr	p.M344T	ENST00000330258	NM_152424.3	344	aTg/aCg	2/2	0.32263407068495	5	FACETS	0.838	0.774	0.903	0.838	0.774	0.903	CLONAL	3	TRUE	2	0.413382715674485	5		441	502	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0017626-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	38	454	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.073428032102822	3	FACETS	0.683	0.563	0.819	0.342	0.281	0.41	INDETERMINATE	1	TRUE	1	0.15	3		454	797	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017626-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	34	551	0	ENST00000269305.4:c.475del	p.Ala159ProfsTer11	p.A159Pfs*11	ENST00000269305	NM_001126112.2	159	Gcc/cc	5/11	1	2	FACETS	0.496	0.403	0.601	0.496	0.403	0.601	SUBCLONAL	1	TRUE	1	0.15	2		551	914	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851600	128851600	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017626-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	35	380	0	ENST00000249373.3:c.1925T>G	p.Val642Gly	p.V642G	ENST00000249373	NM_005631.4	642	gTg/gGg	11/12	0.073428032102822	3	FACETS	0.753	0.616	0.909	0.377	0.308	0.455	INDETERMINATE	1	TRUE	1	0.15	3		380	666	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444259	50444259	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017626-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	23	0	0	ENST00000331340.3:c.189T>G	p.Ser63Arg	p.S63R	ENST00000331340	NM_006060.4	63	agT/agG	4/8	0.073428032102822	3	FACETS	0.4	0.31	0.505	0.2	0.155	0.253	INDETERMINATE	1	TRUE	1	0.15	3		0	824	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	79	728	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.848	0.746	0.959	0.848	0.746	0.959	CLONAL	1	TRUE	1	0.26161628496602	2		728	712	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020047-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	104	523	0				ENST00000310581	NM_198253.2	-/1132			0.284448006025105	2	FACETS	0.809	0.728	0.893	0.809	0.728	0.893	CLONAL	2	TRUE	0	0.284448006025105	2		523	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0020047-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	148	485	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.26850901558576	3	FACETS	0.942	0.863	1			1	CLONAL	2	TRUE	NA	0.284448006025105	3		485	631	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217236	7217236	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs775804583	NA	P-0020047-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	135	226	0	ENST00000380728.2:c.469del	p.Gln157LysfsTer188	p.Q157Kfs*188	ENST00000380728		157	Caa/aa	6/11	0.26850901558576	3	FACETS	0.83	0.756	0.907			1	CLONAL	2	TRUE	NA	0.284448006025105	3		226	653	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371717	225371717	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020047-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	55	142	0	ENST00000264414.4:c.887T>G	p.Leu296Arg	p.L296R	ENST00000264414	NM_003590.4	296	cTt/cGt	7/16	0.268537537785901	3	FACETS	1	0.918	1	0.551	0.472	0.636	CLONAL	1	TRUE	1	0.284448006025105	3		142	401	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358920	81358920	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0020047-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	67	109	0	ENST00000222390.5:c.1040+1G>C		p.X347_splice	ENST00000222390	NM_000601.4	347			0.284448006025105	3	FACETS	1	0.908	1	0.527	0.458	0.6	CLONAL	1	TRUE	1	0.284448006025105	3		109	511	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928929	44928929	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020047-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	93	127	0	ENST00000377967.4:c.2029C>G	p.Gln677Glu	p.Q677E	ENST00000377967	NM_021140.2	677	Cag/Gag	17/29	0.284448006025105	3	FACETS	1	0.969	1	0.627	0.558	0.699	CLONAL	1	TRUE	1	0.284448006025105	3		127	596	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929161	44929182	+	frameshift_variant	Frame_Shift_Del	DEL	TGACGGCAGATGCTGTTTGCAG	TGACGGCAGATGCTGTTTGCAG	-	novel	NA	P-0020047-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	107	139	0	ENST00000377967.4:c.2262_2283del	p.Met754IlefsTer13	p.M754Ifs*13	ENST00000377967	NM_021140.2	754	aTGACGGCAGATGCTGTTTGCAGt/at	17/29	0.284448006025105	3	FACETS	1	0.976	1	0.646	0.58	0.716	CLONAL	1	TRUE	1	0.284448006025105	3		139	665	SUCCESS
AR	367	MSKCC	GRCh37	X	66766544	66766544	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020047-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	33	203	0	ENST00000374690.3:c.1556G>T	p.Cys519Phe	p.C519F	ENST00000374690	NM_000044.3	519	tGt/tTt	1/8	1	2	FACETS	0.449	0.365	0.544	0.449	0.365	0.544	SUBCLONAL	1	TRUE	1	0.284448006025105	2		203	517	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080307	5080307	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020047-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	43	149	0	ENST00000381652.3:c.2210G>A	p.Trp737Ter	p.W737*	ENST00000381652	NM_004972.3	737	tGg/tAg	17/25	0.284448006025105	4	FACETS	0.797	0.667	0.942	0.266	0.222	0.314	CLONAL	1	TRUE	1	0.284448006025105	4		149	487	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945142	44945157	+	frameshift_variant	Frame_Shift_Del	DEL	AACATAAATATTGGCC	AACATAAATATTGGCC	GTTATTCA	novel	NA	P-0020047-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	54	160	0	ENST00000377967.4:c.3466_3481delinsGTTATTCA	p.Asn1156ValfsTer5	p.N1156Vfs*5	ENST00000377967	NM_021140.2	1156	AACATAAATATTGGCCca/GTTATTCAca	24/29	0.284448006025105	3	FACETS	0.955	0.817	1	0.478	0.408	0.553	CLONAL	1	TRUE	1	0.284448006025105	3		160	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578181	7578181	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138983188	NA	P-0020150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	440	813	0	ENST00000269305.4:c.668C>T	p.Pro223Leu	p.P223L	ENST00000269305	NM_001126112.2	223	cCt/cTt	6/11	0.857588601582418	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.89194249069568	1		813	526	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023414	27023437	+	inframe_deletion	In_Frame_Del	DEL	GGCGGACAACAAAGCCCTGGCCTG	GGCGGACAACAAAGCCCTGGCCTG	-	novel	NA	P-0020150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	364	160	0	ENST00000324856.7:c.521_544del	p.Gly174_Leu181del	p.G174_L181del	ENST00000324856	NM_006015.4	174	GGCGGACAACAAAGCCCTGGCCTG/-	1/20	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.89194249069568	2		160	629	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505528	157505528	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	366	177	0	ENST00000346085.5:c.3509G>C	p.Gly1170Ala	p.G1170A	ENST00000346085	NM_020732.3	1170	gGg/gCg	13/20	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.89194249069568	2		177	593	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937611	76937615	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTT	CTTTT	-	novel	NA	P-0020541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	119	205	0	ENST00000373344.5:c.3133_3137del	p.Lys1045Ter	p.K1045*	ENST00000373344	NM_000489.3	1045	AAAAGt/t	9/35	0.677711378843027	2	FACETS	0.982	0.922	1			1	CLONAL	2	TRUE	NA	0.712773912885428	2		205	170	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577448	64577448	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	197	577	0	ENST00000312049.6:c.134A>C	p.Glu45Ala	p.E45A	ENST00000312049	NM_130799.2	45	gAg/gCg	2/10	0.712773912885428	2	FACETS	0.994	0.948	1	0.994	0.948	1	CLONAL	2	TRUE	0	0.712773912885428	2		577	278	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134971	2134971	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	144	546	0	ENST00000219476.3:c.4513T>C	p.Tyr1505His	p.Y1505H	ENST00000219476	NM_000548.3	1505	Tac/Cac	35/42	0.712773912885428	2	FACETS	1	0.989	1	0.706	0.657	0.756	CLONAL	1	TRUE	0	0.712773912885428	2		546	286	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258625	19258625	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021942-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	297	475	0	ENST00000162023.5:c.275G>T	p.Gly92Val	p.G92V	ENST00000162023		92	gGc/gTc	8/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		475	680	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818435	43818435	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021942-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	152	452	0	ENST00000372470.3:c.1900C>G	p.Gln634Glu	p.Q634E	ENST00000372470	NM_005373.2	634	Cag/Gag	12/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		452	425	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333886	70333886	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021942-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	128	405	0	ENST00000373644.4:c.1791C>A	p.Cys597Ter	p.C597*	ENST00000373644	NM_030625.2	597	tgC/tgA	2/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		405	654	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61197650	61197650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148425779	NA	P-0021942-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	234	321	0	ENST00000301761.2:c.32C>T	p.Ser11Leu	p.S11L	ENST00000301761	NM_017841.2	11	tCg/tTg	1/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		321	621	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129189	64129189	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021942-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	173	478	0	ENST00000334205.4:c.727G>C	p.Glu243Gln	p.E243Q	ENST00000334205	NM_003942.2	243	Gag/Cag	7/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		478	765	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082930	16082930	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021942-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	147	294	0	ENST00000281043.3:c.744C>A	p.Asp248Glu	p.D248E	ENST00000281043	NM_005378.4	248	gaC/gaA	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		294	658	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54963243	54963243	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021942-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	51	170	0	ENST00000312783.6:c.11C>A	p.Ser4Tyr	p.S4Y	ENST00000312783	NM_198436.1	4	tCt/tAt	3/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		170	403	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971098	55971098	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021942-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	77	301	0	ENST00000263923.4:c.1699del	p.Val567CysfsTer46	p.V567Cfs*46	ENST00000263923	NM_002253.2	567	Gtg/tg	13/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		301	356	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979403	2979403	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021942-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	99	300	0	ENST00000396946.4:c.844G>C	p.Glu282Gln	p.E282Q	ENST00000396946	NM_032415.4	282	Gag/Cag	6/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		300	806	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76856009	76856009	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021942-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	51	264	0	ENST00000373344.5:c.5591G>A	p.Gly1864Glu	p.G1864E	ENST00000373344	NM_000489.3	1864	gGa/gAa	23/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		264	230	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646300	23646319	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGGGTGCAGGCTGATTTT	CTGGGGTGCAGGCTGATTTT	-	novel	NA	P-0021942-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	196	359	0	ENST00000261584.4:c.1548_1567del	p.Arg516SerfsTer6	p.R516Sfs*6	ENST00000261584	NM_024675.3	516	agAAAATCAGCCTGCACCCCAGca/agca	4/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		359	841	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965568	25965568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs375180879	NA	P-0021942-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	133	394	0	ENST00000435504.4:c.3638G>T	p.Gly1213Val	p.G1213V	ENST00000435504		1213	gGa/gTa	13/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		394	778	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259866	142259876	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CTGTTCAAGGC	CTGTTCAAGGC	-	novel	NA	P-0021942-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	65	272	0	ENST00000350721.4:c.3451_3461del	p.Ala1151PhefsTer33	p.A1151Ffs*33	ENST00000350721	NM_001184.3	1151	GCCTTGAACAGt/t	18/47	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		272	383	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790975	89790975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021942-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	86	381	0	ENST00000336032.3:c.362G>A	p.Arg121Gln	p.R121Q	ENST00000336032	NM_006813.2	121	cGg/cAg	1/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		381	382	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517919	8517920	+	missense_variant	Missense_Mutation	DNP	TT	TT	AC	novel	NA	P-0021942-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	81	325	0	ENST00000356435.5:c.1471_1472delinsGT	p.Lys491Val	p.K491V	ENST00000356435		491	AAa/GTa	10/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		325	514	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023717-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	39	514	0	ENST00000304494.5:c.247C>A	p.His83Asn	p.H83N	ENST00000304494	NM_000077.4	83	Cac/Aac	2/3	0.494722370601513	2	FACETS	0.293	0.243	0.349	0.147	0.121	0.175	SUBCLONAL	1	TRUE	0	0.563912680314876	2		514	472	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136370	2136372	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	rs137854331	NA	P-0023717-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	227	526	0	ENST00000219476.3:c.4842_4844del	p.Ile1614del	p.I1614del	ENST00000219476	NM_000548.3	1613	gaCATc/gac	37/42	0.563912680314876	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.563912680314876	1		526	464	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288261	33288261	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023717-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	298	556	0	ENST00000374542.5:c.1147C>T	p.Gln383Ter	p.Q383*	ENST00000374542	NM_001141970.1	383	Caa/Taa	4/8	0.487951409664081	2	FACETS	0.855	0.813	0.898	0.855	0.813	0.898	CLONAL	2	TRUE	0	0.563912680314876	2		556	618	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923321	78923321	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023717-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	53	483	0	ENST00000306801.3:c.3344T>C	p.Leu1115Pro	p.L1115P	ENST00000306801	NM_020761.2	1115	cTc/cCc	28/34	1	2	FACETS	0.328	0.279	0.381	0.328	0.279	0.381	SUBCLONAL	1	TRUE	1	0.563912680314876	2		483	573	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577329	64577330	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs386134253	NA	P-0023717-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	265	440	0	ENST00000312049.6:c.252dup	p.Ile85TyrfsTer32	p.I85Yfs*32	ENST00000312049	NM_130799.2	84	-/T	2/10	0.377390543980032	3	FACETS	1	0.992	1	0.821	0.781	0.862	CLONAL	2	TRUE	0	0.563912680314876	3		440	489	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0025513-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	69	586	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.420486549353701	1	FACETS	0.301	0.263	0.341	0.301	0.263	0.341	INDETERMINATE	1	TRUE	0	0.751708696444423	1		586	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882019	NA	P-0025513-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	349	860	0	ENST00000269305.4:c.455dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	ccg/ccCg	5/11	0.751708696444423	1	FACETS	0.986	0.945	1	0.986	0.945	1	CLONAL	1	TRUE	0	0.751708696444423	1		860	588	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622544	28622544	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs34172843	NA	P-0025513-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	141	354	0	ENST00000241453.7:c.1073A>T	p.Asp358Val	p.D358V	ENST00000241453	NM_004119.2	358	gAt/gTt	9/24	0.372387623894669	3	FACETS	1	0.98	1	0.745	0.698	0.791	INDETERMINATE	2	TRUE	0	0.751708696444423	3		354	231	SUCCESS
APC	324	MSKCC	GRCh37	5	112136997	112136997	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025513-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	114	465	0	ENST00000257430.4:c.751del	p.Glu251LysfsTer42	p.E251Kfs*42	ENST00000257430	NM_000038.5	251	Gaa/aa	8/16	0.420486549353701	1	FACETS	0.699	0.64	0.758	0.699	0.64	0.758	INDETERMINATE	1	TRUE	0	0.751708696444423	1		465	271	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990400	81990400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370547009	NA	P-0025513-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	133	691	0	ENST00000359376.3:c.3671G>A	p.Arg1224His	p.R1224H	ENST00000359376	NM_002661.3	1224	cGc/cAc	32/33	0.440889261966928	1	FACETS	0.416	0.379	0.454	0.416	0.379	0.454	INDETERMINATE	1	TRUE	0	0.751708696444423	1		691	531	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118355631	118355631	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025513-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	294	550	0	ENST00000534358.1:c.4273T>G	p.Ser1425Ala	p.S1425A	ENST00000534358	NM_005933.3	1425	Tct/Gct	10/36	0.284078486499231	3	FACETS	0.947	0.902	0.993	0.947	0.902	0.993	INDETERMINATE	2	TRUE	1	0.751708696444423	3		550	568	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	461482	461482	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025513-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	52	378	0	ENST00000399788.2:c.1038C>G	p.Ser346Arg	p.S346R	ENST00000399788	NM_001042603.1	346	agC/agG	9/28	0.420486549353701	1	FACETS	0.366	0.315	0.421	0.366	0.315	0.421	INDETERMINATE	1	TRUE	0	0.751708696444423	1		378	236	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472222	472222	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025513-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	109	549	0	ENST00000399788.2:c.579G>T	p.Glu193Asp	p.E193D	ENST00000399788	NM_001042603.1	193	gaG/gaT	5/28	0.420486549353701	1	FACETS	0.417	0.377	0.459	0.417	0.377	0.459	INDETERMINATE	1	TRUE	0	0.751708696444423	1		549	434	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472238	472238	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025513-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	114	505	0	ENST00000399788.2:c.563T>G	p.Leu188Arg	p.L188R	ENST00000399788	NM_001042603.1	188	cTt/cGt	5/28	0.420486549353701	1	FACETS	0.461	0.418	0.505	0.461	0.418	0.505	INDETERMINATE	1	TRUE	0	0.751708696444423	1		505	411	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679635	33679635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147085136	NA	P-0025513-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	116	731	0	ENST00000308377.4:c.2446G>A	p.Ala816Thr	p.A816T	ENST00000308377	NM_152270.3	816	Gca/Aca	5/5	0.460448451519648	1	FACETS	0.39	0.353	0.429	0.39	0.353	0.429	SUBCLONAL	1	TRUE	0	0.751708696444423	1		731	494	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031883	26031884	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs758780418	NA	P-0026680-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	104	661	0	ENST00000244661.2:c.405_406del	p.Arg135SerfsTer12	p.R135Sfs*12	ENST00000244661	NM_003537.3	135	agAGcg/agcg	1/1	0.3	3	FACETS	0.825	0.737	0.918	0.412	0.368	0.459	CLONAL	1	TRUE	1	0.28	3		661	1027	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0026680-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	266	473	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.3	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.28	3		473	870	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717733	89717733	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1554825235	NA	P-0026680-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	264	441	0	ENST00000371953.3:c.758T>A	p.Ile253Asn	p.I253N	ENST00000371953	NM_000314.4	253	aTc/aAc	7/9	0.3	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	3	TRUE	0	0.28	3		441	695	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427614	49427614	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026680-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	281	823	0	ENST00000301067.7:c.10874C>T	p.Pro3625Leu	p.P3625L	ENST00000301067	NM_003482.3	3625	cCc/cTc	39/54	0.295691542496593	4	FACETS	0.965	0.905	1	0.965	0.905	1	CLONAL	2	TRUE	2	0.28	4		823	1331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574029	7574029	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026680-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	187	567	0	ENST00000269305.4:c.998G>C	p.Arg333Pro	p.R333P	ENST00000269305	NM_001126112.2	333	cGt/cCt	10/11	0.271106996557872	2	FACETS	0.949	0.879	1	0.949	0.879	1	CLONAL	2	TRUE	0	0.28	2		567	704	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78519487	78519487	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026680-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	129	724	0	ENST00000306801.3:c.58G>C	p.Asp20His	p.D20H	ENST00000306801	NM_020761.2	20	Gat/Cat	1/34	0.3	3	FACETS	0.945	0.855	1	0.473	0.427	0.521	CLONAL	1	TRUE	1	0.28	3		724	1111	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107150	27107156	+	frameshift_variant	Frame_Shift_Del	DEL	ACGAATC	ACGAATC	-	novel	NA	P-0026680-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	61	657	0	ENST00000324856.7:c.6764_6770del	p.Glu2255GlyfsTer10	p.E2255Gfs*10	ENST00000324856	NM_006015.4	2254	tACGAATCa/ta	20/20	1	2	FACETS	0.459	0.394	0.529	0.459	0.394	0.529	SUBCLONAL	1	TRUE	1	0.28	2		657	950	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092904	29092904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026680-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	29	481	0	ENST00000328354.6:c.1080G>T	p.Glu360Asp	p.E360D	ENST00000328354	NM_007194.3	360	gaG/gaT	10/15	0.271106996557872	2	FACETS	0.357	0.286	0.439	0.179	0.143	0.22	SUBCLONAL	1	TRUE	0	0.28	2		481	580	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260665	1260665	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026680-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1359	133	754	0	ENST00000310581.5:c.2894A>G	p.Lys965Arg	p.K965R	ENST00000310581	NM_198253.2	965	aAg/aGg	12/16	0.3	6	FACETS	0.993	0.899	1	0.248	0.224	0.274	CLONAL	1	TRUE	2	0.28	6		754	1492	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610496	10610496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027097-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1668	17	0	0	ENST00000171111.5:c.214C>T	p.Leu72Phe	p.L72F	ENST00000171111	NM_203500.1	72	Ctc/Ttc	2/6	1	2	FACETS	0.144	0.106	0.189	0.144	0.106	0.189	SUBCLONAL	1	TRUE	1	0.14	2		0	1685	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058015	27058015	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027097-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1712	23	0	0	ENST00000324856.7:c.1723C>T	p.Gln575Ter	p.Q575*	ENST00000324856	NM_006015.4	575	Cag/Tag	3/20	1	2	FACETS	0.189	0.146	0.24	0.189	0.146	0.24	SUBCLONAL	1	TRUE	1	0.14	2		0	1735	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396863	396863	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027097-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1728	18	0	0	ENST00000262320.3:c.163G>T	p.Glu55Ter	p.E55*	ENST00000262320	NM_003502.3	55	Gag/Tag	2/11	NA	2	FACETS	0.147	0.11	0.192			1	INDETERMINATE	1	TRUE	NA	0.14	2		0	1746	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0027351-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	147	454	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.411383574927372	2		454	663	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0027351-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	30	428	0	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	0.286370647808844	1	FACETS	0.17	0.136	0.208	0.17	0.136	0.208	SUBCLONAL	1	TRUE	0	0.411383574927372	1		428	682	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087528	27087528	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027351-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	218	595	0	ENST00000324856.7:c.2102G>T	p.Gly701Val	p.G701V	ENST00000324856	NM_006015.4	701	gGc/gTc	5/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.411383574927372	2		595	937	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039344	47039344	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027351-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	158	452	0	ENST00000377604.3:c.967T>G	p.Tyr323Asp	p.Y323D	ENST00000377604	NM_001204468.1	323	Tac/Gac	10/24	1	2	FACETS	0.985	0.904	1	0.985	0.904	1	CLONAL	1	TRUE	1	0.411383574927372	2		452	780	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931821	68931821	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027351-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	18	213	0	ENST00000288368.4:c.251A>T	p.His84Leu	p.H84L	ENST00000288368	NM_024870.2	84	cAt/cTt	3/40	0.395849438473574	1	FACETS	0.223	0.167	0.288	0.223	0.167	0.288	SUBCLONAL	1	TRUE	0	0.411383574927372	1		213	312	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0027419-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	131	473	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.503244936757754	4	FACETS	1	0.979	1	0.419	0.381	0.459	CLONAL	1	TRUE	1	0.503244936757754	4		473	622	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	223682	223682	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs369321221	NA	P-0027419-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	119	295	0	ENST00000264932.6:c.149C>T	p.Ser50Phe	p.S50F	ENST00000264932	NM_004168.2	50	tCc/tTc	2/15	0.503244936757754	8	FACETS	0.783	0.707	0.863	0.224	0.202	0.247	SUBCLONAL	2	TRUE	1	0.503244936757754	8		295	758	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	223664	223664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027419-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	152	368	0	ENST00000264932.6:c.131C>T	p.Ser44Phe	p.S44F	ENST00000264932	NM_004168.2	44	tCt/tTt	2/15	0.503244936757754	8	FACETS	0.765	0.699	0.834	0.219	0.199	0.239	SUBCLONAL	2	TRUE	1	0.503244936757754	8		368	991	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224491	224491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027419-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	54	133	0	ENST00000264932.6:c.167C>T	p.Pro56Leu	p.P56L	ENST00000264932	NM_004168.2	56	cCa/cTa	3/15	0.503244936757754	8	FACETS	0.91	0.783	1	0.26	0.223	0.299	CLONAL	2	TRUE	1	0.503244936757754	8		133	296	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224617	224617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027419-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	120	264	0	ENST00000264932.6:c.293C>T	p.Ser98Leu	p.S98L	ENST00000264932	NM_004168.2	98	tCa/tTa	3/15	0.503244936757754	8	FACETS	0.833	0.753	0.918	0.238	0.215	0.263	CLONAL	2	TRUE	1	0.503244936757754	8		264	718	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961567	41961567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027419-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	120	540	0	ENST00000219905.7:c.475C>T	p.His159Tyr	p.H159Y	ENST00000219905	NM_001164273.1	159	Cat/Tat	2/24	1	2	FACETS	0.907	0.822	0.995	0.907	0.822	0.995	CLONAL	1	TRUE	1	0.503244936757754	2		540	526	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390914	89390914	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027419-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	630	423	0	ENST00000336596.2:c.980C>G	p.Ser327Cys	p.S327C	ENST00000336596	NM_005233.5	327	tCt/tGt	5/17	0.503244936757754	11	FACETS	0.926	0.891	0.962			1	CLONAL	5	TRUE	NA	0.503244936757754	11		423	1765	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555165	106555165	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027419-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	144	646	0	ENST00000369096.4:c.2282C>G	p.Ala761Gly	p.A761G	ENST00000369096	NM_001198.3	761	gCc/gGc	7/7	0.503244936757754	3	FACETS	1	0.938	1	0.516	0.471	0.563	CLONAL	1	TRUE	1	0.503244936757754	3		646	694	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0029826-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	133	600	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.350290348655266	2	FACETS	0.882	0.808	0.957	0.882	0.808	0.957	CLONAL	2	TRUE	0	0.360085163091624	2		600	419	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527714	103527714	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0029826-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	55	415	0	ENST00000355739.4:c.3022A>T	p.Lys1008Ter	p.K1008*	ENST00000355739	NM_000123.3	1008	Aaa/Taa	15/15	1	2	FACETS	0.58	0.496	0.671	0.58	0.496	0.671	SUBCLONAL	1	TRUE	1	0.360085163091624	2		415	527	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527861	103527861	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029826-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	97	483	0	ENST00000355739.4:c.3169A>G	p.Lys1057Glu	p.K1057E	ENST00000355739	NM_000123.3	1057	Aag/Gag	15/15	1	2	FACETS	0.88	0.786	0.98	0.88	0.786	0.98	CLONAL	1	TRUE	1	0.360085163091624	2		483	612	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420326	88420326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370533197	NA	P-0029826-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	63	452	1	ENST00000360948.2:c.2360G>A	p.Arg787His	p.R787H	ENST00000360948	NM_001012338.2	787	cGt/cAt	19/19	0.144231113012222	3	FACETS	0.613	0.529	0.703	0.306	0.264	0.352	INDETERMINATE	1	TRUE	1	0.360085163091624	3		453	674	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574026	7574026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029826-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	91	359	0	ENST00000269305.4:c.1001G>T	p.Gly334Val	p.G334V	ENST00000269305	NM_001126112.2	334	gGg/gTg	10/11	0.339689953550191	1	FACETS	0.942	0.841	1	0.942	0.841	1	CLONAL	1	TRUE	0	0.360085163091624	1		359	440	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792953	33792953	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029826-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	95	354	0	ENST00000498907.2:c.368G>T	p.Gly123Val	p.G123V	ENST00000498907	NM_004364.3	123	gGa/gTa	1/1	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.360085163091624	2		354	497	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091139	29091139	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029826-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	50	191	0	ENST00000328354.6:c.1351G>T	p.Val451Phe	p.V451F	ENST00000328354	NM_007194.3	451	Gtc/Ttc	12/15	1	2	FACETS	0.868	0.74	1	0.868	0.74	1	CLONAL	1	TRUE	1	0.360085163091624	2		191	320	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916785	178916785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029826-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	63	320	0	ENST00000263967.3:c.172C>T	p.Leu58Phe	p.L58F	ENST00000263967	NM_006218.2	58	Ctc/Ttc	2/21	1	2	FACETS	0.837	0.727	0.956	0.837	0.727	0.956	CLONAL	1	TRUE	1	0.360085163091624	2		320	418	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875642	35875657	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGATCATAAGAAGA	CCCGATCATAAGAAGA	-	novel	NA	P-0029826-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	175	381	0	ENST00000303115.3:c.830_845del	p.Pro277LeufsTer13	p.P277Lfs*13	ENST00000303115	NM_002185.3	277	CCCGATCATAAGAAGAct/ct	7/8	0.345883469766191	3	FACETS	0.892	0.825	0.961	0.892	0.825	0.961	CLONAL	2	TRUE	1	0.360085163091624	3		381	643	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176671248	176671248	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029826-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	35	331	0	ENST00000439151.2:c.4355C>G	p.Ser1452Cys	p.S1452C	ENST00000439151	NM_022455.4	1452	tCt/tGt	9/23	0.345883469766191	3	FACETS	0.517	0.423	0.622	0.258	0.211	0.311	SUBCLONAL	1	TRUE	1	0.360085163091624	3		331	444	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469812	157469812	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029826-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	73	552	0	ENST00000346085.5:c.2606G>T	p.Gly869Val	p.G869V	ENST00000346085	NM_020732.3	869	gGc/gTc	9/20	0.209930707993515	1	FACETS	0.504	0.441	0.573	0.504	0.441	0.573	INDETERMINATE	1	TRUE	0	0.360085163091624	1		552	659	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340397	8340397	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029826-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	126	463	0	ENST00000356435.5:c.5199G>T	p.Trp1733Cys	p.W1733C	ENST00000356435		1733	tgG/tgT	31/35	0.360085163091624	1	FACETS	0.956	0.869	1	0.956	0.869	1	CLONAL	1	TRUE	0	0.360085163091624	1		463	600	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	89	372	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.891	0.792	0.995	1	0.984	1	CLONAL	2	TRUE	1	0.19	2		372	526	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	156	622	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.887	0.812	0.965	1	0.99	1	CLONAL	2	TRUE	1	0.19	2		626	926	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	64	380	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.858	0.742	0.985	0.858	0.742	0.985	CLONAL	1	TRUE	1	0.19	2		380	785	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	17	298	0	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	0.609	0.454	0.793	0.609	0.454	0.793	SUBCLONAL	1	TRUE	1	0.19	2		298	294	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	39	353	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.984	0.817	1	0.984	0.817	1	CLONAL	1	TRUE	1	0.19	2		353	417	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	44	539	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	1	2	FACETS	0.625	0.523	0.739	0.625	0.523	0.739	SUBCLONAL	1	TRUE	1	0.19	2		539	741	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700232	117700232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146533107	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	28	327	0	ENST00000368508.3:c.2587C>T	p.Arg863Trp	p.R863W	ENST00000368508	NM_002944.2	863	Cgg/Tgg	17/43	1	2	FACETS	0.864	0.691	1	0.864	0.691	1	CLONAL	1	TRUE	1	0.19	2		327	341	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626153	12626153	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1420280008	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	49	465	0	ENST00000251849.4:c.1807C>A	p.Leu603Met	p.L603M	ENST00000251849	NM_002880.3	603	Ctg/Atg	17/17	1	2	FACETS	0.773	0.654	0.905	0.773	0.654	0.905	CLONAL	1	TRUE	1	0.19	2		465	667	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874637	35874637	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	29	359	0	ENST00000303115.3:c.799del	p.Arg267GlyfsTer28	p.R267Gfs*28	ENST00000303115	NM_002185.3	265	Aaa/aa	6/8	1	2	FACETS	0.617	0.494	0.757	0.617	0.494	0.757	SUBCLONAL	1	TRUE	1	0.19	2		359	495	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890149	76890150	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	25	345	0	ENST00000373344.5:c.4744dup	p.Thr1582AsnfsTer19	p.T1582Nfs*19	ENST00000373344	NM_000489.3	1582	aca/aAca	17/35	1	2	FACETS	0.684	0.538	0.851	0.684	0.538	0.851	SUBCLONAL	1	TRUE	1	0.19	2		345	385	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133761036	133761036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1456042173	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	47	433	0	ENST00000318560.5:c.3359C>T	p.Ser1120Leu	p.S1120L	ENST00000318560	NM_005157.4	1120	tCg/tTg	11/11	1	2	FACETS	0.717	0.604	0.842	0.717	0.604	0.842	SUBCLONAL	1	TRUE	1	0.19	2		433	690	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861837	57861837	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs759838377	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	63	486	0	ENST00000228682.2:c.1138C>T	p.Arg380Ter	p.R380*	ENST00000228682	NM_005269.2	380	Cga/Tga	10/12	1	2	FACETS	0.945	0.816	1	0.945	0.816	1	CLONAL	1	TRUE	1	0.19	2		486	702	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952435	38952435	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138880117	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	49	436	0	ENST00000357387.3:c.2990G>A	p.Arg997His	p.R997H	ENST00000357387	NM_152756.3	997	cGc/cAc	30/38	1	2	FACETS	0.888	0.751	1	0.888	0.751	1	CLONAL	1	TRUE	1	0.19	2		436	581	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212185	98212185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113663584	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	61	452	0	ENST00000331920.6:c.3487G>A	p.Gly1163Ser	p.G1163S	ENST00000331920	NM_000264.3	1163	Ggc/Agc	21/24	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.19	2		452	634	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662140	227662140	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760127800	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	83	570	0	ENST00000305123.5:c.1315C>T	p.Arg439Trp	p.R439W	ENST00000305123	NM_005544.2	439	Cgg/Tgg	1/2	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.19	2		570	832	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511221	148511221	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1268069858	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	57	373	0	ENST00000320356.2:c.1681C>T	p.Arg561Cys	p.R561C	ENST00000320356	NM_004456.4	561	Cgc/Tgc	15/20	1	2	FACETS	0.998	0.856	1	0.998	0.856	1	CLONAL	1	TRUE	1	0.19	2		373	601	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294664	1294665	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1060502990	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	39	485	0	ENST00000310581.5:c.336dup	p.Glu113ArgfsTer79	p.E113Rfs*79	ENST00000310581	NM_198253.2	112	-/C	2/16	1	2	FACETS	0.689	0.57	0.822	0.689	0.57	0.822	SUBCLONAL	1	TRUE	1	0.19	2		485	596	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368217	45368217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773849578	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	32	420	0	ENST00000262160.6:c.1385G>A	p.Arg462His	p.R462H	ENST00000262160	NM_005901.5	462	cGt/cAt	11/11	1	2	FACETS	0.649	0.526	0.789	0.649	0.526	0.789	SUBCLONAL	1	TRUE	1	0.19	2		420	519	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202845	16202845	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148074613	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	62	487	0	ENST00000375759.3:c.553G>A	p.Ala185Thr	p.A185T	ENST00000375759	NM_015001.2	185	Gct/Act	3/15	1	2	FACETS	0.898	0.774	1	0.898	0.774	1	CLONAL	1	TRUE	1	0.19	2		487	727	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012175	16012175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184177098	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	52	361	0	ENST00000268712.3:c.2107G>A	p.Ala703Thr	p.A703T	ENST00000268712	NM_006311.3	703	Gct/Act	19/46	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.19	2		361	466	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753821	42753821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755151370	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	46	641	0	ENST00000222329.4:c.443C>T	p.Thr148Met	p.T148M	ENST00000222329	NM_006494.2	148	aCg/aTg	4/4	1	2	FACETS	0.551	0.463	0.65	0.551	0.463	0.65	SUBCLONAL	1	TRUE	1	0.19	2		641	878	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174426	11174426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1390645065	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	44	351	0	ENST00000361445.4:c.7249G>A	p.Val2417Met	p.V2417M	ENST00000361445	NM_004958.3	2417	Gtg/Atg	53/58	1	2	FACETS	0.751	0.628	0.886	0.751	0.628	0.886	SUBCLONAL	1	TRUE	1	0.19	2		351	617	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573556	48573556	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	40	352	0	ENST00000342988.3:c.140T>C	p.Leu47Pro	p.L47P	ENST00000342988	NM_005359.5	47	cTg/cCg	2/12	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.19	2		352	407	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794785	120794785	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375135447	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	51	437	0	ENST00000257552.2:c.572C>T	p.Ser191Leu	p.S191L	ENST00000257552	NM_002442.3	191	tCg/tTg	9/15	1	2	FACETS	0.792	0.672	0.924	0.792	0.672	0.924	CLONAL	1	TRUE	1	0.19	2		437	678	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112526	115112526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358091442	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	60	493	0	ENST00000257566.3:c.1214G>A	p.Arg405His	p.R405H	ENST00000257566	NM_016569.3	405	cGt/cAt	7/8	1	2	FACETS	0.945	0.814	1	0.945	0.814	1	CLONAL	1	TRUE	1	0.19	2		493	668	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609330	81609330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121908882	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	55	370	0	ENST00000298171.2:c.928C>T	p.Arg310Cys	p.R310C	ENST00000298171	NM_000369.2	310	Cgc/Tgc	10/10	1	2	FACETS	0.92	0.787	1	0.92	0.787	1	CLONAL	1	TRUE	1	0.19	2		370	629	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933223	100933223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1175582391	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	59	343	0	ENST00000325455.5:c.2167G>A	p.Glu723Lys	p.E723K	ENST00000325455	NM_001202474.3	723	Gag/Aag	4/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.19	2		343	497	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193462	99193462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746015383	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	43	445	0	ENST00000074304.5:c.2657G>A	p.Arg886His	p.R886H	ENST00000074304	NM_001134224.1	886	cGc/cAc	25/26	1	2	FACETS	0.717	0.599	0.849	0.717	0.599	0.849	SUBCLONAL	1	TRUE	1	0.19	2		445	631	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	19	213	1	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	0.673	0.511	0.864	0.673	0.511	0.864	SUBCLONAL	1	TRUE	1	0.19	2		214	297	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165941	118165941	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780173405	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	83	510	0	ENST00000369448.3:c.451C>T	p.Arg151Cys	p.R151C	ENST00000369448	NM_017709.3	151	Cgc/Tgc	2/2	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.19	2		510	756	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166505	118166505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs865949572	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	42	456	1	ENST00000369448.3:c.1015C>T	p.Arg339Cys	p.R339C	ENST00000369448	NM_017709.3	339	Cgt/Tgt	2/2	1	2	FACETS	0.57	0.474	0.677	0.57	0.474	0.677	SUBCLONAL	1	TRUE	1	0.19	2		457	776	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249857	133249857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	32	377	0	ENST00000320574.5:c.1366G>A	p.Ala456Thr	p.A456T	ENST00000320574	NM_006231.2	456	Gcc/Acc	14/49	1	2	FACETS	0.675	0.547	0.82	0.675	0.547	0.82	SUBCLONAL	1	TRUE	1	0.19	2		377	499	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636756	2636756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs75824263	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	60	513	0	ENST00000342085.4:c.1205C>T	p.Thr402Met	p.T402M	ENST00000342085	NM_002613.4	402	aCg/aTg	11/14	1	2	FACETS	0.844	0.726	0.973	0.844	0.726	0.973	CLONAL	1	TRUE	1	0.19	2		513	748	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658460	3658460	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776018346	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	36	390	0	ENST00000294008.3:c.506C>T	p.Ser169Leu	p.S169L	ENST00000294008	NM_032444.2	169	tCg/tTg	2/15	1	2	FACETS	0.559	0.458	0.673	0.559	0.458	0.673	SUBCLONAL	1	TRUE	1	0.19	2		390	678	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89828426	89828426	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	32	300	0	ENST00000389301.3:c.2783C>A	p.Thr928Asn	p.T928N	ENST00000389301	NM_000135.2	928	aCt/aAt	29/43	1	2	FACETS	0.836	0.679	1	0.836	0.679	1	CLONAL	1	TRUE	1	0.19	2		300	403	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456645	40456645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	68	486	0	ENST00000345506.4:c.1355G>A	p.Ser452Asn	p.S452N	ENST00000345506	NM_003152.3	452	aGc/aAc	12/20	1	2	FACETS	0.989	0.859	1	0.989	0.859	1	CLONAL	1	TRUE	1	0.19	2		486	724	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61324165	61324165	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151099886	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	41	422	0	ENST00000283752.5:c.668C>T	p.Ser223Leu	p.S223L	ENST00000283752	NM_006919.2	223	tCg/tTg	7/8	1	2	FACETS	0.841	0.7	0.998	0.841	0.7	0.998	CLONAL	1	TRUE	1	0.19	2		422	513	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2194544	2194544	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	47	379	0	ENST00000398665.3:c.619A>G	p.Lys207Glu	p.K207E	ENST00000398665	NM_032482.2	207	Aaa/Gaa	7/28	1	2	FACETS	0.847	0.714	0.994	0.847	0.714	0.994	CLONAL	1	TRUE	1	0.19	2		379	584	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130334	11130334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1480398200	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	49	420	0	ENST00000358026.2:c.2573C>T	p.Thr858Met	p.T858M	ENST00000358026	NM_001128849.1	858	aCg/aTg	18/36	1	2	FACETS	0.916	0.776	1	0.916	0.776	1	CLONAL	1	TRUE	1	0.19	2		420	563	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299868	15299868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757495623	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	81	516	0	ENST00000263388.2:c.1310C>T	p.Ser437Leu	p.S437L	ENST00000263388	NM_000435.2	437	tCg/tTg	8/33	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.19	2		516	752	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953879	17953879	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs138201425	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	78	542	0	ENST00000458235.1:c.523C>T	p.Arg175Ter	p.R175*	ENST00000458235	NM_000215.3	175	Cga/Tga	5/24	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.19	2		542	788	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219910	36219910	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	44	616	0	ENST00000222270.7:c.4712C>G	p.Ala1571Gly	p.A1571G	ENST00000222270	NM_014727.1	1571	gCc/gGc	21/37	1	2	FACETS	0.583	0.487	0.689	0.583	0.487	0.689	SUBCLONAL	1	TRUE	1	0.19	2		616	795	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422499	47422499	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	56	429	0	ENST00000404338.3:c.571del	p.Thr191GlnfsTer5	p.T191Qfs*5	ENST00000404338	NM_004491.4	189	gcA/gc	1/6	1	2	FACETS	0.877	0.751	1	0.877	0.751	1	CLONAL	1	TRUE	1	0.19	2		429	672	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714531	52714531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	66	511	0	ENST00000322088.6:c.289G>A	p.Ala97Thr	p.A97T	ENST00000322088	NM_014225.5	97	Gcc/Acc	4/15	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.19	2		511	687	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198260981	198260981	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	24	354	0	ENST00000335508.6:c.3338C>G	p.Thr1113Ser	p.T1113S	ENST00000335508	NM_012433.2	1113	aCt/aGt	23/25	1	2	FACETS	0.539	0.421	0.675	0.539	0.421	0.675	SUBCLONAL	1	TRUE	1	0.19	2		354	469	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730909	40730909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	45	469	0	ENST00000373198.4:c.3626G>T	p.Arg1209Leu	p.R1209L	ENST00000373198	NM_133170.3	1209	cGg/cTg	27/32	1	2	FACETS	0.766	0.643	0.903	0.766	0.643	0.903	CLONAL	1	TRUE	1	0.19	2		469	618	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803717	1803717	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	66	509	0	ENST00000260795.2:c.895G>T	p.Gly299Cys	p.G299C	ENST00000260795		299	Ggc/Tgc	6/17	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.19	2		509	686	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176972	56176972	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	38	320	0	ENST00000399503.3:c.2242T>A	p.Ser748Thr	p.S748T	ENST00000399503	NM_005921.1	748	Tca/Aca	13/20	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.19	2		320	364	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87322812	87322812	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	32	283	0	ENST00000277120.3:c.413T>C	p.Leu138Pro	p.L138P	ENST00000277120		138	cTt/cCt	5/19	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.19	2		283	292	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801009	135801009	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	48	355	0	ENST00000298552.3:c.328G>T	p.Ala110Ser	p.A110S	ENST00000298552	NM_001162426.1	110	Gca/Tca	5/23	1	2	FACETS	0.953	0.806	1	0.953	0.806	1	CLONAL	1	TRUE	1	0.19	2		355	530	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424266	47424267	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031078-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	40	458	0	ENST00000377045.4:c.273dup	p.Glu92Ter	p.E92*	ENST00000377045	NM_001654.4	91	ctt/cTtt	4/16	1	2	FACETS	0.644	0.534	0.767	0.644	0.534	0.767	SUBCLONAL	1	TRUE	1	0.19	2		458	654	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0031477-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	88	998	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.642110783958031	1	FACETS	0.896	0.817	0.974	0.896	0.817	0.974	CLONAL	1	TRUE	0	0.735299488919748	1		998	169	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117388	115117389	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTACA	novel	NA	P-0031477-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	52	653	0	ENST00000257566.3:c.785_786insTGTAA	p.Lys262AsnfsTer22	p.K262Nfs*22	ENST00000257566	NM_016569.3	262	aaa/aaTGTAAa	4/8	1	2	FACETS	0.837	0.726	0.954	0.837	0.726	0.954	CLONAL	1	TRUE	1	0.735299488919748	2		653	169	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0031803-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	240	662	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.694292367138987	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.694292367138987	1		662	420	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277230	41277230	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031803-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	131	526	0	ENST00000349496.5:c.1699G>A	p.Glu567Lys	p.E567K	ENST00000349496	NM_001904.3	567	Gaa/Aaa	11/15	0.350306387498652	1	FACETS	0.498	0.454	0.543	0.498	0.454	0.543	INDETERMINATE	1	TRUE	0	0.694292367138987	1		526	495	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0031803-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	150	406	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.694292367138987	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.694292367138987	1		406	281	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436108	51436108	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031803-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	175	508	1	ENST00000262662.1:c.68G>C	p.Ser23Thr	p.S23T	ENST00000262662		23	aGt/aCt	3/4	0.694292367138987	1	FACETS	0.994	0.933	1	0.994	0.933	1	CLONAL	1	TRUE	0	0.694292367138987	1		509	331	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865611	57865611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1027428919	NA	P-0031803-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	312	694	0	ENST00000228682.2:c.3088G>A	p.Glu1030Lys	p.E1030K	ENST00000228682	NM_005269.2	1030	Gaa/Aaa	12/12	0.694292367138987	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.694292367138987	1		694	548	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241496	105241496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031803-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	258	727	0	ENST00000349310.3:c.484G>A	p.Gly162Ser	p.G162S	ENST00000349310	NM_001014432.1	162	Ggc/Agc	7/15	0.694292367138987	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.694292367138987	1		727	446	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398255	25398255	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913236	NA	P-0031803-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	147	379	0	ENST00000311936.3:c.64C>A	p.Gln22Lys	p.Q22K	ENST00000311936	NM_004985.3	22	Cag/Aag	2/5	0.694292367138987	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.694292367138987	1		379	254	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57004264	57004264	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	G	G	A	rs376527330	NA	P-0031803-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	149	753	1	ENST00000257254.3:c.215C>T	p.Ala72Val	p.A72V	ENST00000257254		72	gCg/gTg	1/2	0.350306387498652	1	FACETS	0.495	0.454	0.537	0.495	0.454	0.537	INDETERMINATE	1	TRUE	0	0.694292367138987	1		754	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0032983-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	434	681	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.9054211891092	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.9054211891092	1		682	487	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059204	27059204	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0032983-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	355	285	0	ENST00000324856.7:c.1841C>G	p.Ser614Ter	p.S614*	ENST00000324856	NM_006015.4	614	tCa/tGa	4/20	0.9054211891092	2	FACETS	0.971	0.948	0.991	0.971	0.948	0.991	CLONAL	2	TRUE	0	0.9054211891092	2		285	404	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0032983-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	610	286	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	0.9054211891092	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.9054211891092	2		286	651	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622144	117622144	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032983-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	19	202	0	ENST00000368508.3:c.6726C>A	p.Ser2242Arg	p.S2242R	ENST00000368508	NM_002944.2	2242	agC/agA	42/43	1	2	FACETS	0.123	0.093	0.158	0.123	0.093	0.158	SUBCLONAL	1	TRUE	1	0.9054211891092	2		202	342	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	57	523	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.864	0.748	0.989	0.864	0.748	0.989	CLONAL	1	TRUE	1	0.474467900178533	2		523	278	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720703	89720703	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	34	97	0	ENST00000371953.3:c.856del	p.Thr286ProfsTer5	p.T286Pfs*5	ENST00000371953	NM_000314.4	285	gAa/ga	8/9	0.474467900178533	1	FACETS	0.804	0.668	0.95	0.804	0.668	0.95	CLONAL	1	TRUE	0	0.474467900178533	1		97	136	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588880	69588880	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1240828791	NA	P-0034065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	93	510	0	ENST00000168712.1:c.356C>G	p.Ser119Trp	p.S119W	ENST00000168712	NM_002007.2	119	tCg/tGg	2/3	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.474467900178533	2		510	364	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955383	48955383	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	123	289	0	ENST00000267163.4:c.1499G>T	p.Arg500Ile	p.R500I	ENST00000267163	NM_000321.2	500	aGa/aTa	17/27	0.474467900178533	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.474467900178533	1		289	350	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520090	106520090	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	94	352	0	ENST00000359195.3:c.2518C>T	p.Gln840Ter	p.Q840*	ENST00000359195	NM_002649.2	840	Caa/Taa	6/11	0.474467900178533	3	FACETS	0.956	0.853	1	0.478	0.426	0.532	CLONAL	1	TRUE	1	0.474467900178533	3		352	513	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325194	39325194	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	118	526	0	ENST00000373001.3:c.125G>A	p.Gly42Glu	p.G42E	ENST00000373001	NM_022157.3	42	gGa/gAa	1/7	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.474467900178533	2		526	395	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664851	29664852	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATTCCAACGTGCAAGTGGCTGGACCAGTGGACAGAACTAGCTCAAA	novel	NA	P-0034065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	65	425	0	ENST00000356175.3:c.6595_6640dup	p.Arg2214AsnfsTer22	p.R2214Nfs*22	ENST00000356175	NM_000267.3	2198	-/ATTCCAACGTGCAAGTGGCTGGACCAGTGGACAGAACTAGCTCAAA	43/57	1	2	FACETS	0.488	0.424	0.559	0.488	0.424	0.559	SUBCLONAL	1	TRUE	1	0.474467900178533	2		425	561	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	98	523	0				ENST00000310581	NM_198253.2	-/1132			0.216897134711919	4	FACETS	1	0.978	1	0.679	0.61	0.751	INDETERMINATE	1	TRUE	2	0.545713480860538	4		523	409	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	85	393	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.516926899926286	4	FACETS	0.995	0.894	1	0.995	0.894	1	CLONAL	2	TRUE	2	0.545713480860538	4		394	242	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	194	998	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.545713480860538	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.545713480860538	1		998	461	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	191	753	0	ENST00000269571.5:c.829G>C	p.Asp277His	p.D277H	ENST00000269571		277	Gac/Cac	7/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.545713480860538	2		753	610	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56477621	56477621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	90	594	0	ENST00000267101.3:c.169G>A	p.Glu57Lys	p.E57K	ENST00000267101	NM_001982.3	57	Gag/Aag	2/28	1	2	FACETS	0.679	0.604	0.757	0.679	0.604	0.757	SUBCLONAL	1	TRUE	1	0.545713480860538	2		594	486	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584674	187584674	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	124	638	0	ENST00000441802.2:c.3359C>T	p.Ser1120Leu	p.S1120L	ENST00000441802	NM_005245.3	1120	tCa/tTa	3/27	0.215320341100218	3	FACETS	1	0.976	1	0.604	0.549	0.66	INDETERMINATE	1	TRUE	1	0.545713480860538	3		638	479	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874166	155874166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777520196	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	134	609	0	ENST00000368323.3:c.365G>A	p.Arg122Gln	p.R122Q	ENST00000368323	NM_006912.5	122	cGa/cAa	5/6	0.545713480860538	3	FACETS	1	0.953	1	0.534	0.487	0.583	CLONAL	1	TRUE	1	0.545713480860538	3		609	585	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259830	16259830	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	99	757	0	ENST00000375759.3:c.7095G>C	p.Glu2365Asp	p.E2365D	ENST00000375759	NM_015001.2	2365	gaG/gaC	11/15	0.18264398090631	0	FACETS	0.38	0.341	0.421			1	INDETERMINATE	1	TRUE	0	0.545713480860538	0		757	434	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877972	151877972	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	76	634	0	ENST00000262189.6:c.6973C>T	p.Gln2325Ter	p.Q2325*	ENST00000262189	NM_170606.2	2325	Cag/Tag	36/59	0.280656875510408	1	FACETS	0.521	0.459	0.586	0.521	0.459	0.586	INDETERMINATE	1	TRUE	0	0.545713480860538	1		634	389	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573583	48573583	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	62	483	0	ENST00000342988.3:c.167C>T	p.Ser56Phe	p.S56F	ENST00000342988	NM_005359.5	56	tCt/tTt	2/12	0.545713480860538	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.545713480860538	1		483	153	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599209	28599209	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	93	757	1	ENST00000253063.3:c.655G>C	p.Glu219Gln	p.E219Q	ENST00000253063	NM_031459.4	219	Gag/Cag	5/10	0.232523190359183	2	FACETS	0.525	0.467	0.587	0.263	0.233	0.294	INDETERMINATE	1	TRUE	0	0.545713480860538	2		758	649	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112445	115112445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	162	868	0	ENST00000257566.3:c.1295C>T	p.Ser432Leu	p.S432L	ENST00000257566	NM_016569.3	432	tCg/tTg	7/8	1	2	FACETS	0.975	0.898	1	0.975	0.898	1	CLONAL	1	TRUE	1	0.545713480860538	2		868	609	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598902	28598902	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	115	748	0	ENST00000253063.3:c.462G>C	p.Glu154Asp	p.E154D	ENST00000253063	NM_031459.4	154	gaG/gaC	4/10	0.232523190359183	2	FACETS	0.589	0.531	0.651	0.295	0.265	0.326	INDETERMINATE	1	TRUE	0	0.545713480860538	2		748	715	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471809	120471809	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	85	653	0	ENST00000256646.2:c.3682G>A	p.Asp1228Asn	p.D1228N	ENST00000256646	NM_024408.3	1228	Gac/Aac	23/34	0.443602504184782	1	FACETS	0.445	0.394	0.499	0.445	0.394	0.499	SUBCLONAL	1	TRUE	0	0.545713480860538	1		653	509	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939533	71939533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	165	827	0	ENST00000298229.2:c.388G>A	p.Asp130Asn	p.D130N	ENST00000298229	NM_001567.3	130	Gat/Aat	3/28	1	2	FACETS	0.922	0.85	0.997	0.922	0.85	0.997	CLONAL	1	TRUE	1	0.545713480860538	2		827	656	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998871	100998871	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs373360839	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	114	778	0	ENST00000325455.5:c.931C>G	p.Leu311Val	p.L311V	ENST00000325455	NM_001202474.3	311	Ctc/Gtc	1/8	1	2	FACETS	0.985	0.894	1	0.985	0.894	1	CLONAL	1	TRUE	1	0.545713480860538	2		778	424	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100642	102100642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	119	440	0	ENST00000282441.5:c.1486G>A	p.Asp496Asn	p.D496N	ENST00000282441	NM_001130145.2	496	Gat/Aat	9/9	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.545713480860538	2		440	406	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129772	108129772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658688	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	55	322	0	ENST00000278616.4:c.2436G>A	p.Met812Ile	p.M812I	ENST00000278616	NM_000051.3	812	atG/atA	16/63	1	2	FACETS	0.951	0.824	1	0.951	0.824	1	CLONAL	1	TRUE	1	0.545713480860538	2		322	212	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372386	118372386	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	90	458	0	ENST00000534358.1:c.6320-1G>C		p.X2107_splice	ENST00000534358	NM_005933.3	2107			1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.545713480860538	2		458	313	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245258	46245258	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs757890582	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	83	733	0	ENST00000334344.6:c.3352C>T	p.Gln1118Ter	p.Q1118*	ENST00000334344	NM_152641.2	1118	Cag/Tag	15/21	1	2	FACETS	0.532	0.47	0.598	0.532	0.47	0.598	SUBCLONAL	1	TRUE	1	0.545713480860538	2		733	572	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780586	56780586	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs531838785	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	55	356	0	ENST00000337432.4:c.601C>G	p.Leu201Val	p.L201V	ENST00000337432	NM_058216.2	201	Ctt/Gtt	4/9	1	2	FACETS	0.869	0.752	0.994	0.869	0.752	0.994	CLONAL	1	TRUE	1	0.545713480860538	2		356	232	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41521980	41521980	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	102	409	0	ENST00000263253.7:c.842C>G	p.Ser281Ter	p.S281*	ENST00000263253	NM_001429.3	281	tCa/tGa	3/31	0.545713480860538	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.545713480860538	1		409	201	SUCCESS
ATR	545	MSKCC	GRCh37	3	142224090	142224090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1027616979	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	180	488	0	ENST00000350721.4:c.5087G>A	p.Arg1696Lys	p.R1696K	ENST00000350721	NM_001184.3	1696	aGa/aAa	29/47	0.349517237659819	3	FACETS	1	0.99	1	0.742	0.688	0.797	CLONAL	1	TRUE	1	0.545713480860538	3		488	566	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955040	55955040	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	72	408	0	ENST00000263923.4:c.3505C>G	p.Gln1169Glu	p.Q1169E	ENST00000263923	NM_002253.2	1169	Cag/Gag	26/30	0.545713480860538	1	FACETS	0.803	0.711	0.898	0.803	0.711	0.898	CLONAL	1	TRUE	0	0.545713480860538	1		408	239	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509799	106509799	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	50	596	0	ENST00000359195.3:c.1793G>T	p.Trp598Leu	p.W598L	ENST00000359195	NM_002649.2	598	tGg/tTg	2/11	0.280656875510408	1	FACETS	0.413	0.352	0.479	0.413	0.352	0.479	INDETERMINATE	1	TRUE	0	0.545713480860538	1		596	323	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879486	151879486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	58	658	0	ENST00000262189.6:c.5459C>T	p.Ser1820Phe	p.S1820F	ENST00000262189	NM_170606.2	1820	tCt/tTt	36/59	0.280656875510408	1	FACETS	0.448	0.387	0.514	0.448	0.387	0.514	INDETERMINATE	1	TRUE	0	0.545713480860538	1		658	345	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904851	101904851	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	37	401	1	ENST00000374994.4:c.839C>T	p.Ser280Leu	p.S280L	ENST00000374994	NM_004612.2	280	tCa/tTa	5/9	0.303840180407425	3	FACETS	0.473	0.39	0.565	0.158	0.13	0.189	INDETERMINATE	1	TRUE	0	0.545713480860538	3		402	365	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133756018	133756018	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	129	613	0	ENST00000318560.5:c.1645G>C	p.Glu549Gln	p.E549Q	ENST00000318560	NM_005157.4	549	Gag/Cag	10/11	0.482884339800031	3	FACETS	0.89	0.809	0.976	0.297	0.269	0.326	CLONAL	1	TRUE	0	0.545713480860538	3		613	676	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889158	76889158	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	80	186	0	ENST00000373344.5:c.4852G>T	p.Asp1618Tyr	p.D1618Y	ENST00000373344	NM_000489.3	1618	Gat/Tat	18/35	1	1	FACETS	0.756	0.69	0.821	1	0.984	1	SUBCLONAL	2	TRUE	0	0.545713480860538	1		186	141	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230561428	230561428	+	5_prime_UTR_variant	5'UTR	SNP	G	G	T	novel	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	102	1168	0	ENST00000391860.1:c.-99C>A		p.*33*	ENST00000391860	NM_001258311.1	-/409		1/7	0.540877083312201	1	FACETS	0.53	0.476	0.587	0.53	0.476	0.587	SUBCLONAL	1	TRUE	0	0.545713480860538	1		1168	513	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692811	89692811	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	21	193	0	ENST00000371953.3:c.295G>A	p.Glu99Lys	p.E99K	ENST00000371953	NM_000314.4	99	Gaa/Aaa	5/9	0.2430499539479	1	FACETS	0.441	0.343	0.551	0.441	0.343	0.551	INDETERMINATE	1	TRUE	0	0.545713480860538	1		193	127	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774215	56774215	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	69	445	0	ENST00000337432.4:c.566G>A	p.Gly189Glu	p.G189E	ENST00000337432	NM_058216.2	189	gGa/gAa	3/9	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.545713480860538	2		445	239	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981182	55981182	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	55	389	0	ENST00000263923.4:c.517G>T	p.Asp173Tyr	p.D173Y	ENST00000263923	NM_002253.2	173	Gat/Tat	5/30	0.545713480860538	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.545713480860538	1		389	141	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	893120	893120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	83	528	0	ENST00000166345.3:c.7G>A	p.Glu3Lys	p.E3K	ENST00000166345	NM_004237.3	3	Gag/Aag	1/13	0.216897134711919	4	FACETS	1	0.913	1	0.518	0.459	0.581	INDETERMINATE	1	TRUE	2	0.545713480860538	4		528	454	SUCCESS
APC	324	MSKCC	GRCh37	5	112102897	112102897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	56	341	0	ENST00000257430.4:c.232G>A	p.Asp78Asn	p.D78N	ENST00000257430	NM_000038.5	78	Gat/Aat	4/16	0.545713480860538	3	FACETS	0.892	0.77	1	0.446	0.385	0.512	CLONAL	1	TRUE	1	0.545713480860538	3		341	293	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032069	26032069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	199	966	0	ENST00000244661.2:c.220G>A	p.Glu74Lys	p.E74K	ENST00000244661	NM_003537.3	74	Gaa/Aaa	1/1	0.545713480860538	3	FACETS	1	0.986	1	0.625	0.58	0.67	CLONAL	1	TRUE	1	0.545713480860538	3		966	743	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636637	73636638	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034556-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	304	632	0	ENST00000377687.4:c.905dup	p.Ser303ValfsTer12	p.S303Vfs*12	ENST00000377687	NM_001730.3	300	-/C	2/4	1	2	FACETS	0.806	0.765	0.847	0.806	0.765	0.847	CLONAL	1	TRUE	1	1.1	2		632	686	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47088041	47088042	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034556-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	455	414	0	ENST00000409792.3:c.7033dup	p.Val2345GlyfsTer24	p.V2345Gfs*24	ENST00000409792	NM_014159.6	2345	gtg/gGtg	16/21	1	2	FACETS		NA	1	1	0.998	1	NA	2	TRUE	1	1.1	2		414	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764146326	NA	P-0036792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	461	743	0	ENST00000269305.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000269305	NM_001126112.2	281	Gac/Aac	8/11	0.755377515953454	2	FACETS	0.951	0.923	0.977	0.951	0.923	0.977	CLONAL	2	TRUE	0	0.777057898349687	2		743	624	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242442	55242443	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTAAAATTCCCGTCGCTA	novel	NA	P-0036792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1341	1479	527	0	ENST00000275493.2:c.2214_2231dup	p.Ile740_Lys745dup	p.I740_K745dup	ENST00000275493	NM_005228.3	740	gtt/gTTAAAATTCCCGTCGCTAtt	19/28	0.777057898349687	11	FACETS	1	0.987	1	0.607	0.594	0.62	CLONAL	6	TRUE	1	0.777057898349687	11		527	2820	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200617	67200617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	415	898	0	ENST00000312629.5:c.728G>A	p.Arg243His	p.R243H	ENST00000312629	NM_003952.2	243	cGc/cAc	9/15	0.391486613716573	2	FACETS	1	0.986	1	0.536	0.512	0.56	INDETERMINATE	1	TRUE	0	0.777057898349687	2		898	996	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14026312	14026312	+	splice_acceptor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0036792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	57	238	0	ENST00000405192.2:c.134-2del		p.X45_splice	ENST00000405192	NM_001163147.1	45			0.777057898349687	3	FACETS	0.429	0.368	0.495	0.214	0.184	0.248	SUBCLONAL	1	TRUE	1	0.777057898349687	3		238	475	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0036977-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	250	362	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.873944980007658	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	FALSE	1	0.873944980007658	3		362	383	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925316	114925317	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs745872748	NA	P-0036977-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	139	350	11	ENST00000543371.1:c.1403dup	p.Cys469ValfsTer8	p.C469Vfs*8	ENST00000543371	NM_001198531.1	465	aga/agAa	14/14	1	2	FACETS	0.869	0.801	0.939	0.869	0.801	0.939	CLONAL	1	FALSE	1	0.873944980007658	2		361	366	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480345	89480345	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs774448099	NA	P-0036977-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	202	299	0	ENST00000336596.2:c.2182C>T	p.Arg728Ter	p.R728*	ENST00000336596	NM_005233.5	728	Cga/Tga	13/17	0.323318484697376	4	FACETS	1	0.99	1			1	INDETERMINATE	1	FALSE	NA	0.873944980007658	4		299	622	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0036977-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	512	506	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.873944980007658	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	FALSE	0	0.873944980007658	2		506	569	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416417	49416417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565753611	NA	P-0036977-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	188	415	0	ENST00000301067.7:c.16294C>T	p.Arg5432Trp	p.R5432W	ENST00000301067	NM_003482.3	5432	Cgg/Tgg	51/54	0.873944980007658	3	FACETS	0.975	0.905	1	0.488	0.452	0.524	CLONAL	1	FALSE	1	0.873944980007658	3		415	634	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610030	81610030	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036977-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	275	494	0	ENST00000298171.2:c.1628T>G	p.Val543Gly	p.V543G	ENST00000298171	NM_000369.2	543	gTt/gGt	10/10	0.872089416843349	3	FACETS	1	0.975	1	0.531	0.5	0.563	CLONAL	1	FALSE	1	0.873944980007658	3		494	852	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545898	41545898	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774840930	NA	P-0036977-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	447	445	0	ENST00000263253.7:c.2513G>A	p.Arg838His	p.R838H	ENST00000263253	NM_001429.3	838	cGt/cAt	14/31	0.873944980007658	3	FACETS	0.993	0.958	1	0.993	0.958	1	CLONAL	2	FALSE	1	0.873944980007658	3		445	740	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288765	33288765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761608312	NA	P-0036977-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	269	407	0	ENST00000374542.5:c.787C>T	p.Arg263Cys	p.R263C	ENST00000374542	NM_001141970.1	263	Cgc/Tgc	3/8	0.873944980007658	5	FACETS	0.955	0.9	1	0.637	0.6	0.674	CLONAL	2	FALSE	2	0.873944980007658	5		407	745	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576886	212576886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036977-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	160	275	0	ENST00000342788.4:c.1013G>A	p.Gly338Asp	p.G338D	ENST00000342788	NM_005235.2	338	gGc/gAc	9/28	0.567723203604498	6	FACETS	1	0.98	1	0.303	0.277	0.329	CLONAL	1	FALSE	2	0.873944980007658	6		275	831	SUCCESS
APC	324	MSKCC	GRCh37	5	112175544	112175545	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036977-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	215	397	0	ENST00000257430.4:c.4255dup	p.Ser1419LysfsTer4	p.S1419Kfs*4	ENST00000257430	NM_000038.5	1418	ata/atAa	16/16	0.873944980007658	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	0	0.873944980007658	1		397	266	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38787071	38787071	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036977-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	220	402	0	ENST00000348513.6:c.922G>T	p.Ala308Ser	p.A308S	ENST00000348513	NM_003079.4	308	Gca/Tca	10/11	0.873944980007658	3	FACETS	0.902	0.841	0.964	0.451	0.42	0.482	CLONAL	1	FALSE	1	0.873944980007658	3		402	802	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99179973	99179973	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036977-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	220	432	0	ENST00000074304.5:c.1916A>C	p.Asp639Ala	p.D639A	ENST00000074304	NM_001134224.1	639	gAc/gCc	19/26	0.872089416843349	3	FACETS	0.953	0.89	1	0.477	0.445	0.509	CLONAL	1	FALSE	1	0.873944980007658	3		432	759	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465660	8465660	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs201604141	NA	P-0036977-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	171	293	0	ENST00000356435.5:c.3520T>C	p.Ser1174Pro	p.S1174P	ENST00000356435		1174	Tct/Cct	21/35	0.872089416843349	3	FACETS	1	0.97	1	0.544	0.504	0.585	CLONAL	1	FALSE	1	0.873944980007658	3		293	517	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202845	27202847	+	missense_variant	Missense_Mutation	TNP	AGA	AGA	CGG	novel	NA	P-0036977-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	75	323	0	ENST00000380036.4:c.1937_1939delinsCGG	p.Lys646_Ile647delinsThrVal	p.K646_I647delinsTV	ENST00000380036	NM_000459.3	646	aAGAtt/aCGGtt	13/23	1	2	FACETS	0.309	0.271	0.35	0.309	0.271	0.35	SUBCLONAL	1	FALSE	1	0.873944980007658	2		323	555	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638325	117638325	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3752566	NA	P-0039257-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	136	363	0	ENST00000368508.3:c.6116G>A	p.Arg2039His	p.R2039H	ENST00000368508	NM_002944.2	2039	cGt/cAt	38/43	0.675904821013217	3	FACETS	0.988	0.903	1	0.494	0.451	0.539	CLONAL	1	TRUE	1	0.682400003107225	3		363	541	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233459	69233459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039257-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4329	324	445	0	ENST00000462284.1:c.1324G>A	p.Glu442Lys	p.E442K	ENST00000462284	NM_002392.5	442	Gaa/Aaa	11/11	0.682400003107225	25	FACETS	0.903	0.846	0.961	0.082	0.076	0.088	CLONAL	2	TRUE	3	0.682400003107225	25		445	4653	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754505	42754505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1174086151	NA	P-0039257-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	210	492	0	ENST00000222329.4:c.235G>A	p.Asp79Asn	p.D79N	ENST00000222329	NM_006494.2	79	Gac/Aac	2/4	0.679210858490659	3	FACETS	1	0.933	1	0.502	0.466	0.538	CLONAL	1	TRUE	1	0.682400003107225	3		492	823	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155259	55155259	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039257-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	174	405	0	ENST00000257290.5:c.2858T>G	p.Leu953Arg	p.L953R	ENST00000257290	NM_006206.4	953	cTg/cGg	21/23	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.682400003107225	2		405	506	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808573	1808573	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039257-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	3220	646	0	ENST00000260795.2:c.2186A>C	p.Glu729Ala	p.E729A	ENST00000260795		729	gAg/gCg	16/17	0.682400003107225	15	FACETS	0.977	0.967	0.986			1	CLONAL	13	TRUE	NA	0.682400003107225	15		646	4040	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0039595-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	2832	473	1	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	0.295072475598004	29	FACETS	1	0.997	1			1	CLONAL	29	TRUE	NA	0.34	29		474	3177	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743534	46743534	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039595-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	127	677	0	ENST00000371975.4:c.1915A>C	p.Lys639Gln	p.K639Q	ENST00000371975	NM_003579.3	639	Aag/Cag	17/18	0.295072475598004	1	FACETS	0.937	0.85	1	0.937	0.85	1	CLONAL	1	TRUE	0	0.34	1		677	662	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434849	49434849	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039595-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	128	773	0	ENST00000301067.7:c.6704G>T	p.Arg2235Ile	p.R2235I	ENST00000301067	NM_003482.3	2235	aGa/aTa	31/54	1	2	FACETS	0.746	0.675	0.821	0.746	0.675	0.821	SUBCLONAL	1	TRUE	1	0.34	2		773	1009	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039732-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	258	564	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.638962475564715	2		564	806	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0039732-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	34	103	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.638962475564715	1	FACETS	0.747	0.628	0.871	0.747	0.628	0.871	SUBCLONAL	1	TRUE	0	0.638962475564715	1		103	97	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944178	71944178	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs748455961	NA	P-0039732-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	294	753	0	ENST00000298229.2:c.2011T>C	p.Tyr671His	p.Y671H	ENST00000298229	NM_001567.3	671	Tat/Cat	17/28	0.638962475564715	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.638962475564715	1		753	571	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900017	151900017	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0039732-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	79	239	0	ENST00000262189.6:c.4092+2T>G		p.X1364_splice	ENST00000262189	NM_170606.2	1364			1	2	FACETS	0.856	0.761	0.955	0.856	0.761	0.955	CLONAL	1	TRUE	1	0.638962475564715	2		239	289	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396760	139396760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039732-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	192	526	0	ENST00000277541.6:c.5348G>A	p.Arg1783Gln	p.R1783Q	ENST00000277541	NM_017617.3	1783	cGg/cAg	28/34	1	2	FACETS	0.976	0.907	1	0.976	0.907	1	CLONAL	1	TRUE	1	0.638962475564715	2		526	616	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0039776-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	303	728	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.389280098219728	6	FACETS	1	0.971	1	1	0.971	1	CLONAL	5	TRUE	1	0.389280098219728	6		728	541	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301888	65301888	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039776-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	16	371	0	ENST00000342505.4:c.3151G>C	p.Glu1051Gln	p.E1051Q	ENST00000342505	NM_002227.2	1051	Gaa/Caa	23/25	0.394060569687617	1	FACETS	0.366	0.271	0.478	0.366	0.271	0.478	SUBCLONAL	1	TRUE	0	0.389280098219728	1		371	181	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309866	65309866	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039776-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	27	509	0	ENST00000342505.4:c.2284G>C	p.Glu762Gln	p.E762Q	ENST00000342505	NM_002227.2	762	Gag/Cag	17/25	0.394060569687617	1	FACETS	0.417	0.332	0.513	0.417	0.332	0.513	SUBCLONAL	1	TRUE	0	0.389280098219728	1		509	268	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	78128764	78128764	+	start_lost	Translation_Start_Site	SNP	C	C	G	novel	NA	P-0039776-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	58	690	0	ENST00000361507.4:c.3G>C	p.Met1?	p.M1?	ENST00000361507	NM_080491.2	1	atG/atC	1/10	0.360622658279065	3	FACETS	0.731	0.629	0.842	0.365	0.314	0.421	SUBCLONAL	1	TRUE	1	0.389280098219728	3		690	487	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632636	3632636	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs556217576	NA	P-0039776-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	61	642	0	ENST00000294008.3:c.5212G>A	p.Gly1738Arg	p.G1738R	ENST00000294008	NM_032444.2	1738	Ggg/Agg	15/15	0.394060569687617	4	FACETS	0.831	0.718	0.954	0.277	0.239	0.318	CLONAL	1	TRUE	1	0.389280098219728	4		642	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519975	NA	P-0039776-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	84	697	0	ENST00000269305.4:c.403T>C	p.Cys135Arg	p.C135R	ENST00000269305	NM_001126112.2	135	Tgc/Cgc	5/11	0.33201217284119	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.389280098219728	1		697	313	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303277	15303277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039776-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	21	634	0	ENST00000263388.2:c.251C>T	p.Ser84Leu	p.S84L	ENST00000263388	NM_000435.2	84	tCa/tTa	3/33	1	2	FACETS	0.322	0.248	0.409	0.322	0.248	0.409	SUBCLONAL	1	TRUE	1	0.389280098219728	2		634	335	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220868	36220868	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039776-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	66	519	0	ENST00000222270.7:c.4918C>T	p.Arg1640Cys	p.R1640C	ENST00000222270	NM_014727.1	1640	Cgc/Tgc	23/37	0.389280098219728	7	FACETS	1	0.89	1			1	CLONAL	1	TRUE	NA	0.389280098219728	7		519	650	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917736	29917736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150966028	NA	P-0039776-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	26	528	1	ENST00000389048.3:c.932G>A	p.Arg311His	p.R311H	ENST00000389048	NM_004304.4	311	cGt/cAt	3/29	0.0317639732798485	3	FACETS	0.482	0.382	0.597			1	INDETERMINATE	1	TRUE	NA	0.389280098219728	3		529	331	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748066	41748066	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039776-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	39	290	0	ENST00000226382.2:c.703G>A	p.Glu235Lys	p.E235K	ENST00000226382	NM_003924.3	235	Gaa/Aaa	3/3	0.208731062830367	5	FACETS	0.786	0.658	0.925	0.524	0.438	0.617	INDETERMINATE	2	TRUE	2	0.389280098219728	5		290	202	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628235	187628235	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0039776-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	13	655	0	ENST00000441802.2:c.2747C>G	p.Ser916Ter	p.S916*	ENST00000441802	NM_005245.3	916	tCa/tGa	2/27	0.394060569687617	1	FACETS	0.238	0.169	0.321	0.238	0.169	0.321	SUBCLONAL	1	TRUE	0	0.389280098219728	1		655	226	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155725	56155726	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0039776-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	152	398	0	ENST00000399503.3:c.819_820del	p.Arg273SerfsTer27	p.R273Sfs*27	ENST00000399503	NM_005921.1	273	AGa/a	3/20	0.394060569687617	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	3	TRUE	0	0.389280098219728	3		398	295	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197136	26197136	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs535488676	NA	P-0039776-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	112	808	0	ENST00000356476.2:c.343G>T	p.Ala115Ser	p.A115S	ENST00000356476		115	Gcc/Tcc	1/1	0.208731062830367	5	FACETS	0.768	0.693	0.848	0.512	0.462	0.565	INDETERMINATE	2	TRUE	2	0.389280098219728	5		808	593	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974393	93974393	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039776-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	43	281	0	ENST00000369303.4:c.1661C>T	p.Pro554Leu	p.P554L	ENST00000369303	NM_004440.3	554	cCt/cTt	8/17	0.116907091050756	5	FACETS	0.825	0.698	0.963	0.413	0.349	0.482	INDETERMINATE	2	TRUE	1	0.389280098219728	5		281	212	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0040096-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	39	187	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.282083965908066	3	FACETS	1	0.856	1	0.516	0.429	0.611	CLONAL	1	TRUE	1	0.282083965908066	3		187	306	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79968073	79968073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760032154	NA	P-0040096-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	38	414	0	ENST00000265081.6:c.803G>A	p.Arg268Gln	p.R268Q	ENST00000265081	NM_002439.4	268	cGa/cAa	5/24	1	2	FACETS	0.527	0.435	0.63	0.527	0.435	0.63	SUBCLONAL	1	TRUE	1	0.282083965908066	2		414	511	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714125	43714125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040096-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	74	805	0	ENST00000382044.4:c.4028G>A	p.Arg1343Lys	p.R1343K	ENST00000382044	NM_001141980.1	1343	aGa/aAa	19/28	1	2	FACETS	0.561	0.489	0.638	0.561	0.489	0.638	SUBCLONAL	1	TRUE	1	0.282083965908066	2		805	936	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38506081	38506081	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040096-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	63	815	0	ENST00000254066.5:c.373C>G	p.His125Asp	p.H125D	ENST00000254066	NM_000964.3	125	Cac/Gac	4/9	0.10322304209465	3	FACETS	0.561	0.484	0.646			1	INDETERMINATE	1	TRUE	NA	0.282083965908066	3		815	908	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016276	150016276	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040096-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	44	433	0	ENST00000253339.5:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000253339		144	Caa/Taa	2/7	0.282083965908066	1	FACETS	0.53	0.444	0.624	0.53	0.444	0.624	SUBCLONAL	1	TRUE	0	0.282083965908066	1		433	506	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459176	120459176	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040096-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	80	998	0	ENST00000256646.2:c.6169G>C	p.Asp2057His	p.D2057H	ENST00000256646	NM_024408.3	2057	Gac/Cac	34/34	0.10322304209465	3	FACETS	0.564	0.495	0.639			1	INDETERMINATE	1	TRUE	NA	0.282083965908066	3		998	1147	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588796	69588796	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040096-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	62	599	0	ENST00000168712.1:c.440G>T	p.Gly147Val	p.G147V	ENST00000168712	NM_002007.2	147	gGc/gTc	2/3	0.282083965908066	7	FACETS	0.678	0.584	0.782			1	SUBCLONAL	1	TRUE	NA	0.282083965908066	7		599	1105	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540650	187540650	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040096-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	75	927	0	ENST00000441802.2:c.7090G>T	p.Asp2364Tyr	p.D2364Y	ENST00000441802	NM_005245.3	2364	Gat/Tat	10/27	1	2	FACETS	0.513	0.448	0.584	0.513	0.448	0.584	SUBCLONAL	1	TRUE	1	0.282083965908066	2		927	1036	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983350	149983350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040096-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	46	591	0	ENST00000253339.5:c.2908C>T	p.His970Tyr	p.H970Y	ENST00000253339		970	Cac/Tac	7/7	0.282083965908066	1	FACETS	0.424	0.357	0.5	0.424	0.357	0.5	SUBCLONAL	1	TRUE	0	0.282083965908066	1		591	660	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579378	7579378	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0040826-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	339	525	4	ENST00000269305.4:c.309C>G	p.Tyr103Ter	p.Y103*	ENST00000269305	NM_001126112.2	103	taC/taG	4/11	0.722510506867428	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.724291717787173	2		529	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0040853-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	400	850	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.581409694626741	2	FACETS	0.997	0.958	1	0.997	0.958	1	CLONAL	2	TRUE	0	0.581409694626741	2		852	690	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670777	134670777	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040853-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	173	699	0	ENST00000398015.3:c.688G>A	p.Glu230Lys	p.E230K	ENST00000398015	NM_004441.4	230	Gag/Aag	3/16	0.537587398267707	4	FACETS	0.995	0.916	1	0.497	0.458	0.539	CLONAL	1	TRUE	2	0.581409694626741	4		699	946	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431067	49431067	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040853-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	241	825	0	ENST00000301067.7:c.10072A>C	p.Ser3358Arg	p.S3358R	ENST00000301067	NM_003482.3	3358	Agt/Cgt	34/54	0.57161131706411	3	FACETS	1	0.984	1	0.579	0.541	0.618	CLONAL	1	TRUE	1	0.581409694626741	3		825	924	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0041463-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	327	547	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.591662658149409	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.591662658149409	2		548	503	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041463-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	336	564	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.591662658149409	3	FACETS	0.831	0.788	0.873	0.831	0.788	0.873	CLONAL	2	TRUE	1	0.591662658149409	3		564	886	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0041463-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	123	372	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.591662658149409	2		372	415	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446386	29446386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371521416	NA	P-0041463-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	102	608	0	ENST00000389048.3:c.3181C>T	p.Arg1061Trp	p.R1061W	ENST00000389048	NM_004304.4	1061	Cgg/Tgg	20/29	0.591662658149409	2	FACETS	0.555	0.497	0.617	0.278	0.248	0.309	SUBCLONAL	1	TRUE	0	0.591662658149409	2		608	621	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016634	12016634	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041463-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	280	412	1	ENST00000353533.5:c.770C>A	p.Ser257Tyr	p.S257Y	ENST00000353533	NM_003010.3	257	tCt/tAt	7/11	0.591662658149409	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.591662658149409	2		413	440	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591246	67591246	+	splice_acceptor_variant	Splice_Site	DEL	A	A	-	novel	NA	P-0041463-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	185	466	0	ENST00000274335.5:c.1746-2del		p.X582_splice	ENST00000274335		582			0.330107505412346	2	FACETS	0.776	0.726	0.826	0.776	0.726	0.826	INDETERMINATE	2	TRUE	0	0.591662658149409	2		466	403	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608966	100608966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041463-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	247	361	0	ENST00000308731.7:c.1642G>A	p.Asp548Asn	p.D548N	ENST00000308731	NM_000061.2	548	Gat/Aat	17/19	0.591662658149409	3	FACETS	0.998	0.943	1	0.998	0.943	1	CLONAL	2	TRUE	1	0.591662658149409	3		361	542	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182049	11182049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041463-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	79	357	1	ENST00000361445.4:c.6797G>A	p.Arg2266His	p.R2266H	ENST00000361445	NM_004958.3	2266	cGc/cAc	48/58	1	2	FACETS	0.612	0.541	0.689	0.612	0.541	0.689	SUBCLONAL	1	TRUE	1	0.591662658149409	2		358	436	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293080	91293080	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041463-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	81	497	0	ENST00000355112.3:c.582T>A	p.Phe194Leu	p.F194L	ENST00000355112	NM_000057.2	194	ttT/ttA	3/22	1	2	FACETS	0.606	0.536	0.68	0.606	0.536	0.68	SUBCLONAL	1	TRUE	1	0.591662658149409	2		497	452	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187221	38187222	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041463-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	327	425	0	ENST00000317025.8:c.1255dup	p.Thr419AsnfsTer28	p.T419Nfs*28	ENST00000317025	NM_023034.1	419	acc/aAcc	6/24	0.591662658149409	2	FACETS	0.961	0.919	1	0.961	0.919	1	CLONAL	2	TRUE	0	0.591662658149409	2		425	575	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0042047-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	221	648	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.310145024853655	3	FACETS	1	0.99	1	0.685	0.636	0.735	CLONAL	1	TRUE	1	0.311366917562548	3		648	1198	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943936	71943938	+	inframe_deletion	In_Frame_Del	DEL	CAG	CAG	-	novel	NA	P-0042047-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	144	694	0	ENST00000298229.2:c.1872_1874del	p.Ser624del	p.S624del	ENST00000298229	NM_001567.3	623	atCAGc/atc	16/28	1	2	FACETS	0.882	0.803	0.965	0.882	0.803	0.965	CLONAL	1	TRUE	1	0.311366917562548	2		694	1049	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764146326	NA	P-0042047-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	151	743	0	ENST00000269305.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000269305	NM_001126112.2	281	Gac/Aac	8/11	0.311366917562548	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.311366917562548	1		743	800	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37092115	37092115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374380262	NA	P-0042047-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	134	520	0	ENST00000231790.2:c.2242G>A	p.Asp748Asn	p.D748N	ENST00000231790	NM_000249.3	748	Gat/Aat	19/19	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.311366917562548	2		520	766	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545728	106545728	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042047-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	139	480	0	ENST00000359195.3:c.3205C>G	p.Leu1069Val	p.L1069V	ENST00000359195	NM_002649.2	1069	Ctt/Gtt	11/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.311366917562548	2		480	805	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274803	123274803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042758-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	85	543	0	ENST00000358487.5:c.1115C>T	p.Ser372Phe	p.S372F	ENST00000358487	NM_000141.4	372	tCc/tTc	9/18	0.263165709718624	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.263165709718624	1		543	530	SUCCESS
CBL	867	MSKCC	GRCh37	11	119168192	119168192	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0042758-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	33	335	0	ENST00000264033.4:c.2251+1G>C		p.X751_splice	ENST00000264033	NM_005188.3	751			1	2	FACETS	0.638	0.52	0.771	0.638	0.52	0.771	SUBCLONAL	1	TRUE	1	0.263165709718624	2		335	393	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434752	49434752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042758-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	43	664	0	ENST00000301067.7:c.6801del	p.Ala2268LeufsTer18	p.A2268Lfs*18	ENST00000301067	NM_003482.3	2267	aaA/aa	31/54	1	2	FACETS	0.438	0.365	0.519	0.438	0.365	0.519	SUBCLONAL	1	TRUE	1	0.263165709718624	2		664	746	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	338190	338190	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs370661416	NA	P-0042758-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	122	504	0	ENST00000262320.3:c.2521C>T	p.Arg841Ter	p.R841*	ENST00000262320	NM_003502.3	841	Cga/Tga	11/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.263165709718624	2		504	660	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274248	10274248	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555491563	NA	P-0042758-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	83	465	0	ENST00000330684.3:c.21G>A	p.Trp7Ter	p.W7*	ENST00000330684	NM_001134407.1	7	tgG/tgA	2/13	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.263165709718624	2		465	567	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679797	33679797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1049928797	NA	P-0042758-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	35	512	0	ENST00000308377.4:c.2284G>A	p.Glu762Lys	p.E762K	ENST00000308377	NM_152270.3	762	Gag/Aag	5/5	1	2	FACETS	0.437	0.358	0.528	0.437	0.358	0.528	SUBCLONAL	1	TRUE	1	0.263165709718624	2		512	608	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302837	15302837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042758-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	106	643	0	ENST00000263388.2:c.613C>T	p.Pro205Ser	p.P205S	ENST00000263388	NM_000435.2	205	Cca/Tca	4/33	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.263165709718624	2		643	723	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927992	49927992	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1235783876	NA	P-0042758-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	81	492	0	ENST00000296474.3:c.3736C>T	p.His1246Tyr	p.H1246Y	ENST00000296474	NM_002447.2	1246	Cac/Tac	18/20	1	2	FACETS	0.996	0.878	1	0.996	0.878	1	CLONAL	1	TRUE	1	0.263165709718624	2		492	618	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447763	187447763	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398495055	NA	P-0042758-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	73	563	0	ENST00000232014.4:c.430C>T	p.Leu144Phe	p.L144F	ENST00000232014	NM_001130845.1	144	Ctc/Ttc	5/10	1	2	FACETS	0.855	0.748	0.97	0.855	0.748	0.97	CLONAL	1	TRUE	1	0.263165709718624	2		563	649	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956128	55956128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042758-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	45	358	0	ENST00000263923.4:c.3187G>A	p.Gly1063Arg	p.G1063R	ENST00000263923	NM_002253.2	1063	Gga/Aga	23/30	0.251032718847039	1	FACETS	0.849	0.716	0.994	0.849	0.716	0.994	CLONAL	1	TRUE	0	0.263165709718624	1		358	350	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0042758-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	31	515	0				ENST00000310581	NM_198253.2	-/1132			0.263165709718624	1	FACETS	0.439	0.354	0.535	0.439	0.354	0.535	SUBCLONAL	1	TRUE	0	0.263165709718624	1		515	466	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490506	20490506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042758-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	31	492	0	ENST00000346618.3:c.1243C>T	p.Pro415Ser	p.P415S	ENST00000346618	NM_001949.4	415	Cct/Tct	7/7	0.251032718847039	1	FACETS	0.339	0.273	0.414	0.339	0.273	0.414	SUBCLONAL	1	TRUE	0	0.263165709718624	1		492	603	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0042758-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	62	372	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.116343839598005	3	FACETS	0.901	0.784	1	0.6	0.523	0.683	INDETERMINATE	2	TRUE	0	0.263165709718624	3		372	296	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275779	38275779	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042758-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	103	539	0	ENST00000425967.3:c.1490C>T	p.Pro497Leu	p.P497L	ENST00000425967	NM_001174067.1	497	cCc/cTc	11/19	0.259799319308576	3	FACETS	1	0.954	1	0.561	0.502	0.624	CLONAL	1	TRUE	1	0.263165709718624	3		539	789	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0042758-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	23	514	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	1	2	FACETS	0.413	0.321	0.52	0.413	0.321	0.52	SUBCLONAL	1	TRUE	1	0.263165709718624	2		514	423	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915925	127915925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042758-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	70	418	0	ENST00000373547.4:c.556C>T	p.Pro186Ser	p.P186S	ENST00000373547	NM_002721.4	186	Cct/Tct	6/7	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.263165709718624	2		418	451	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061212	38061232	+	inframe_deletion	In_Frame_Del	DEL	GTAGCAGCCGTTCTCGAACAT	GTAGCAGCCGTTCTCGAACAT	-	novel	NA	P-0043637-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	468	511	0	ENST00000250448.2:c.757_777del	p.Met253_Tyr259del	p.M253_Y259del	ENST00000250448	NM_004496.3	253	ATGTTCGAGAACGGCTGCTAC/-	2/2	0.741362358138721	5	FACETS	0.957	0.92	0.994			1	CLONAL	3	TRUE	NA	0.744031032516517	5		511	927	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543891	41543891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1354874707	NA	P-0043637-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	179	372	0	ENST00000263253.7:c.2182C>T	p.Arg728Trp	p.R728W	ENST00000263253	NM_001429.3	728	Cgg/Tgg	12/31	0.741362358138721	2	FACETS	1	0.946	1	0.51	0.474	0.546	CLONAL	1	TRUE	0	0.744031032516517	2		372	472	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43783907	43783907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043637-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	194	402	0	ENST00000382044.4:c.331C>T	p.Gln111Ter	p.Q111*	ENST00000382044	NM_001141980.1	111	Cag/Tag	4/28	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.744031032516517	2		402	509	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124610	108124611	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0043637-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	230	304	0	ENST00000278616.4:c.1970_1971del	p.Phe657Ter	p.F657*	ENST00000278616	NM_000051.3	656	acTTtt/actt	13/63	0.741362358138721	2	FACETS	0.912	0.871	0.952	0.912	0.871	0.952	CLONAL	2	TRUE	0	0.744031032516517	2		304	339	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426803	49426808	+	inframe_deletion	In_Frame_Del	DEL	GCCCAT	GCCCAT	-	novel	NA	P-0043637-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	230	587	0	ENST00000301067.7:c.11680_11685del	p.Met3894_Gly3895del	p.M3894_G3895del	ENST00000301067	NM_003482.3	3894	ATGGGC/-	39/54	0.741362358138721	3	FACETS	1	0.938	1	0.502	0.469	0.536	CLONAL	1	TRUE	1	0.744031032516517	3		587	845	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0044005-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	433	558	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.858620728012953	2	FACETS	0.985	0.963	1	0.985	0.963	1	CLONAL	2	TRUE	0	0.875591850370475	2		558	502	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170136	32170136	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771019003	NA	P-0044005-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	175	608	0	ENST00000375023.3:c.3472C>T	p.Arg1158Ter	p.R1158*	ENST00000375023	NM_004557.3	1158	Cga/Tga	21/30	1	2	FACETS	0.485	0.446	0.524	0.485	0.446	0.524	SUBCLONAL	1	TRUE	1	0.875591850370475	2		608	825	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0044005-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	112	292	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.875591850370475	1	FACETS	0.91	0.854	0.964	0.91	0.854	0.964	CLONAL	1	TRUE	0	0.875591850370475	1		292	158	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597396	10597396	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044005-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	479	514	0	ENST00000171111.5:c.1807G>T	p.Gly603Trp	p.G603W	ENST00000171111	NM_203500.1	603	Ggg/Tgg	6/6	0.867497145681922	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.875591850370475	2		514	546	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600572	43600572	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044005-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	501	610	0	ENST00000355710.3:c.798C>G	p.Asp266Glu	p.D266E	ENST00000355710	NM_020975.4	266	gaC/gaG	4/20	0.875591850370475	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.875591850370475	1		610	583	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279540	123279540	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044005-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	443	573	0	ENST00000358487.5:c.892G>C	p.Gly298Arg	p.G298R	ENST00000358487	NM_000141.4	298	Ggc/Cgc	7/18	0.523945411548581	1	FACETS	1	0.995	1	1	0.995	1	INDETERMINATE	1	TRUE	0	0.875591850370475	1		573	522	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136072	64136072	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044005-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	150	0	0	ENST00000334205.4:c.1333A>T	p.Arg445Trp	p.R445W	ENST00000334205	NM_003942.2	445	Agg/Tgg	11/17	0.453076291694665	2	FACETS	0.588	0.539	0.638	0.294	0.269	0.319	INDETERMINATE	1	TRUE	0	0.875591850370475	2		0	583	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732352	74732352	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs145534754	NA	P-0044005-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	651	690	0	ENST00000359995.5:c.557G>T	p.Arg186Leu	p.R186L	ENST00000359995	NM_001195427.1	186	cGg/cTg	2/3	0.875591850370475	3	FACETS	0.905	0.877	0.934	0.603	0.584	0.623	CLONAL	2	TRUE	0	0.875591850370475	3		690	1181	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213619	36213619	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044005-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	407	511	0	ENST00000222270.7:c.2721G>T	p.Glu907Asp	p.E907D	ENST00000222270	NM_014727.1	907	gaG/gaT	5/37	0.433197335127014	3	FACETS	0.855	0.82	0.89	0.855	0.82	0.89	INDETERMINATE	2	TRUE	1	0.875591850370475	3		511	782	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25459857	25459857	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044005-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	252	458	0	ENST00000264709.3:c.2426T>C	p.Val809Ala	p.V809A	ENST00000264709	NM_175629.2	809	gTg/gCg	21/23	0.875591850370475	3	FACETS	0.952	0.893	1	0.476	0.446	0.507	CLONAL	1	TRUE	1	0.875591850370475	3		458	869	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426799	212426799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044005-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	110	440	0	ENST00000342788.4:c.2316G>T	p.Met772Ile	p.M772I	ENST00000342788	NM_005235.2	772	atG/atT	20/28	0.406556877825512	5	FACETS	0.651	0.584	0.722	0.163	0.146	0.181	INDETERMINATE	1	TRUE	1	0.875591850370475	5		440	893	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196553	106196553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044005-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	350	526	0	ENST00000380013.4:c.4886C>T	p.Pro1629Leu	p.P1629L	ENST00000380013	NM_001127208.2	1629	cCa/cTa	11/11	0.867497145681922	2	FACETS	0.985	0.96	1	0.985	0.96	1	CLONAL	2	TRUE	0	0.875591850370475	2		526	406	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397530	116397530	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044005-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	507	401	0	ENST00000397752.3:c.1902C>G	p.Phe634Leu	p.F634L	ENST00000397752	NM_000245.2	634	ttC/ttG	7/21	0.875591850370475	5	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	2	0.875591850370475	5		401	807	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850288	128850290	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0044005-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1369	110	470	0	ENST00000249373.3:c.1552_1554del	p.Glu518del	p.E518del	ENST00000249373	NM_005631.4	517	gtGGAg/gtg	9/12	0.875591850370475	6	FACETS	0.467	0.418	0.52			1	SUBCLONAL	1	TRUE	NA	0.875591850370475	6		470	1479	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873836	151873836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044005-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	437	497	0	ENST00000262189.6:c.8702C>T	p.Pro2901Leu	p.P2901L	ENST00000262189	NM_170606.2	2901	cCt/cTt	38/59	0.863346321890408	3	FACETS	0.958	0.923	0.993	0.958	0.923	0.993	CLONAL	2	TRUE	1	0.875591850370475	3		497	749	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221354	36221354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766608261	NA	P-0044005-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	187	726	0	ENST00000222270.7:c.5188G>A	p.Val1730Met	p.V1730M	ENST00000222270	NM_014727.1	1730	Gtg/Atg	24/37	0.433197335127014	3	FACETS	0.568	0.524	0.613	0.284	0.262	0.307	INDETERMINATE	1	TRUE	1	0.875591850370475	3		726	1082	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2073231	2073231	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044005-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	571	426	0	ENST00000349721.2:c.1766A>T	p.Gln589Leu	p.Q589L	ENST00000349721	NM_003070.3	589	cAg/cTg	11/34	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.875591850370475	2		426	625	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	90	515	0				ENST00000310581	NM_198253.2	-/1132			0.20778522776024	2	FACETS	0.834	0.747	0.925	1	0.971	1	CLONAL	3	TRUE	0	0.214171550298818	2		515	336	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875642	35875642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	69	359	0	ENST00000303115.3:c.829C>T	p.Pro277Ser	p.P277S	ENST00000303115	NM_002185.3	277	Ccc/Tcc	7/8	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.214171550298818	2		359	520	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491360	18491360	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	26	231	0	ENST00000266497.5:c.1273G>A	p.Glu425Lys	p.E425K	ENST00000266497		425	Gaa/Aaa	8/31	1	2	FACETS	0.864	0.686	1	0.864	0.686	1	CLONAL	1	TRUE	1	0.214171550298818	2		231	281	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662582	117662582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	56	489	0	ENST00000368508.3:c.4883G>A	p.Gly1628Glu	p.G1628E	ENST00000368508	NM_002944.2	1628	gGa/gAa	29/43	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.214171550298818	2		489	445	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	109	429	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.214171550298818	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.214171550298818	3		429	451	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612028	189612028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs900140738	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	52	442	0	ENST00000264731.3:c.1780C>T	p.Arg594Ter	p.R594*	ENST00000264731	NM_003722.4	594	Cga/Tga	14/14	1	2	FACETS	0.861	0.733	1	0.861	0.733	1	CLONAL	1	TRUE	1	0.214171550298818	2		442	564	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3901001	3901001	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs865788612	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	66	329	0	ENST00000262367.5:c.95C>T	p.Ser32Leu	p.S32L	ENST00000262367	NM_004380.2	32	tCa/tTa	2/31	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.214171550298818	2		329	479	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933705	49933705	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751338048	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	97	634	0	ENST00000296474.3:c.2572C>T	p.Arg858Cys	p.R858C	ENST00000296474	NM_002447.2	858	Cgc/Tgc	10/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.214171550298818	2		634	696	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264412	46264412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746670862	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	81	510	0	ENST00000371998.3:c.1459C>T	p.Arg487Cys	p.R487C	ENST00000371998		487	Cgt/Tgt	11/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.214171550298818	2		510	551	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522095	157522095	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	77	632	0	ENST00000346085.5:c.4367C>T	p.Ser1456Phe	p.S1456F	ENST00000346085	NM_020732.3	1456	tCc/tTc	18/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.214171550298818	2		632	575	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253817	153253817	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	40	349	0	ENST00000281708.4:c.916C>T	p.Gln306Ter	p.Q306*	ENST00000281708	NM_033632.3	306	Cag/Tag	6/12	1	2	FACETS	0.869	0.722	1	0.869	0.722	1	CLONAL	1	TRUE	1	0.214171550298818	2		349	430	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271831	15271831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779902629	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	89	842	0	ENST00000263388.2:c.6608C>T	p.Ser2203Phe	p.S2203F	ENST00000263388	NM_000435.2	2203	tCc/tTc	33/33	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.214171550298818	2		842	679	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750750	128750750	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	71	518	0	ENST00000377970.2:c.287C>T	p.Ser96Phe	p.S96F	ENST00000377970	NM_002467.4	96	tCc/tTc	2/3	0.214171550298818	3	FACETS	1	0.892	1	0.513	0.447	0.584	CLONAL	1	TRUE	1	0.214171550298818	3		518	716	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295253	1295253	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1232074117	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	53	456	0				ENST00000310581	NM_198253.2	-/1132			0.20778522776024	2	FACETS	1	0.958	1	0.678	0.58	0.784	CLONAL	1	TRUE	0	0.214171550298818	2		456	365	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876352	35876352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	45	515	0	ENST00000303115.3:c.1144C>T	p.Leu382Phe	p.L382F	ENST00000303115	NM_002185.3	382	Ctc/Ttc	8/8	1	2	FACETS	0.787	0.661	0.926	0.787	0.661	0.926	CLONAL	1	TRUE	1	0.214171550298818	2		515	534	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732855	44732855	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1271145433	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	50	217	0	ENST00000377967.4:c.58G>A	p.Asp20Asn	p.D20N	ENST00000377967	NM_021140.2	20	Gat/Aat	1/29	1	1	FACETS	1	0.888	1	1	0.976	1	CLONAL	2	TRUE	0	0.214171550298818	1		217	201	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69011995	69011995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	105	379	0	ENST00000288368.4:c.2632C>T	p.Pro878Ser	p.P878S	ENST00000288368	NM_024870.2	878	Cct/Tct	23/40	0.214171550298818	3	FACETS	1	0.922	1	1	0.922	1	CLONAL	2	TRUE	1	0.214171550298818	3		379	527	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125533	7125533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867354196	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	62	508	0	ENST00000302850.5:c.3019C>T	p.Pro1007Ser	p.P1007S	ENST00000302850	NM_000208.2	1007	Cca/Tca	17/22	1	2	FACETS	0.91	0.786	1	0.91	0.786	1	CLONAL	1	TRUE	1	0.214171550298818	2		508	636	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612016	189612016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1560310917	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	53	490	0	ENST00000264731.3:c.1768C>T	p.Pro590Ser	p.P590S	ENST00000264731	NM_003722.4	590	Cct/Tct	14/14	1	2	FACETS	0.853	0.727	0.991	0.853	0.727	0.991	CLONAL	1	TRUE	1	0.214171550298818	2		490	580	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965690	93965690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	43	435	0	ENST00000369303.4:c.2238G>A	p.Met746Ile	p.M746I	ENST00000369303	NM_004440.3	746	atG/atA	13/17	1	2	FACETS	0.911	0.763	1	0.911	0.763	1	CLONAL	1	TRUE	1	0.214171550298818	2		435	441	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602269	10602269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751899258	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	53	546	0	ENST00000171111.5:c.1309C>T	p.His437Tyr	p.H437Y	ENST00000171111	NM_203500.1	437	Cac/Tac	3/6	1	2	FACETS	0.814	0.694	0.946	0.814	0.694	0.946	CLONAL	1	TRUE	1	0.214171550298818	2		546	608	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058530	69058530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	38	339	0	ENST00000288368.4:c.4174C>T	p.Pro1392Ser	p.P1392S	ENST00000288368	NM_024870.2	1392	Cct/Tct	34/40	0.214171550298818	3	FACETS	0.914	0.756	1	0.457	0.378	0.545	CLONAL	1	TRUE	1	0.214171550298818	3		339	430	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979602	55979602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	46	374	0	ENST00000263923.4:c.845G>A	p.Gly282Glu	p.G282E	ENST00000263923	NM_002253.2	282	gGg/gAg	7/30	1	2	FACETS	0.906	0.764	1	0.906	0.764	1	CLONAL	1	TRUE	1	0.214171550298818	2		374	474	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249511	153249512	+	stop_gained	Nonsense_Mutation	DNP	CA	CA	AC	novel	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	47	390	0	ENST00000281708.4:c.1266_1267delinsGT	p.Gly423Ter	p.G423*	ENST00000281708	NM_033632.3	422	ggTGga/ggGTga	9/12	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.214171550298818	2		390	413	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714445	117714445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1307627482	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	54	330	0	ENST00000368508.3:c.1204G>A	p.Glu402Lys	p.E402K	ENST00000368508	NM_002944.2	402	Gaa/Aaa	11/43	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.214171550298818	2		330	344	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914920	32914920	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149330893	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	41	317	0	ENST00000380152.3:c.6428C>T	p.Ser2143Leu	p.S2143L	ENST00000380152		2143	tCa/tTa	11/27	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.214171550298818	2		317	323	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546995	9546995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	77	489	0	ENST00000353224.5:c.1027C>T	p.Pro343Ser	p.P343S	ENST00000353224	NM_177990.2	343	Cca/Tca	5/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.214171550298818	2		489	529	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408909	41408909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	54	389	0	ENST00000373198.4:c.517C>T	p.His173Tyr	p.H173Y	ENST00000373198	NM_133170.3	173	Cat/Tat	4/32	1	2	FACETS	0.872	0.745	1	0.872	0.745	1	CLONAL	1	TRUE	1	0.214171550298818	2		389	578	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165542	47165542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	112	666	1	ENST00000409792.3:c.584C>T	p.Pro195Leu	p.P195L	ENST00000409792	NM_014159.6	195	cCa/cTa	3/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.214171550298818	2		667	868	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259036	153259036	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	43	378	0	ENST00000281708.4:c.779G>C	p.Cys260Ser	p.C260S	ENST00000281708	NM_033632.3	260	tGt/tCt	5/12	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.214171550298818	2		378	352	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715380	117715380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	27	350	0	ENST00000368508.3:c.1109C>T	p.Ser370Phe	p.S370F	ENST00000368508	NM_002944.2	370	tCt/tTt	10/43	1	2	FACETS	0.985	0.787	1	0.985	0.787	1	CLONAL	1	TRUE	1	0.214171550298818	2		350	256	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41209101	41209101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	79	415	0	ENST00000357654.3:c.5245C>T	p.Pro1749Ser	p.P1749S	ENST00000357654	NM_007294.3	1749	Cca/Tca	19/23	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.214171550298818	2		415	618	SUCCESS
ALB	213	MSKCC	GRCh37	4	74283931	74283931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	76	460	0	ENST00000295897.4:c.1555G>A	p.Glu519Lys	p.E519K	ENST00000295897	NM_000477.5	519	Gaa/Aaa	12/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.214171550298818	2		460	570	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466371	120466371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1392252497	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	76	474	0	ENST00000256646.2:c.4748C>T	p.Ser1583Phe	p.S1583F	ENST00000256646	NM_024408.3	1583	tCc/tTc	26/34	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.214171550298818	2		474	651	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612162	43612162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	72	555	0	ENST00000355710.3:c.2267C>T	p.Ala756Val	p.A756V	ENST00000355710	NM_020975.4	756	gCc/gTc	12/20	0.214171550298818	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.214171550298818	1		555	487	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133982	41133982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	86	606	0	ENST00000379561.5:c.1646C>T	p.Thr549Ile	p.T549I	ENST00000379561	NM_002015.3	549	aCc/aTc	2/3	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.214171550298818	2		606	733	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348383	89348383	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	78	618	0	ENST00000301030.4:c.4567C>T	p.Pro1523Ser	p.P1523S	ENST00000301030	NM_001256183.1	1523	Ccg/Tcg	9/13	1	2	FACETS	0.899	0.789	1	0.899	0.789	1	CLONAL	1	TRUE	1	0.214171550298818	2		618	810	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349579	89349580	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	64	551	0	ENST00000301030.4:c.3370_3371insGG	p.Glu1124GlyfsTer195	p.E1124Gfs*195	ENST00000301030	NM_001256183.1	1124	gag/gGGag	9/13	1	2	FACETS	0.949	0.821	1	0.949	0.821	1	CLONAL	1	TRUE	1	0.214171550298818	2		551	630	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744476	41744476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	77	458	0	ENST00000301178.4:c.1096G>A	p.Gly366Arg	p.G366R	ENST00000301178	NM_021913.4	366	Ggg/Agg	8/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.214171550298818	2		458	555	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795048	42795048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	63	622	0	ENST00000575354.2:c.2128G>A	p.Glu710Lys	p.E710K	ENST00000575354	NM_015125.3	710	Gaa/Aaa	10/20	1	2	FACETS	0.864	0.746	0.992	0.864	0.746	0.992	CLONAL	1	TRUE	1	0.214171550298818	2		622	681	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519901	29519901	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	55	426	0	ENST00000389048.3:c.1670G>C	p.Arg557Pro	p.R557P	ENST00000389048	NM_004304.4	557	cGt/cCt	9/29	1	2	FACETS	0.879	0.752	1	0.879	0.752	1	CLONAL	1	TRUE	1	0.214171550298818	2		426	584	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631157	67631157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	29	273	0	ENST00000272342.5:c.1343C>T	p.Ser448Phe	p.S448F	ENST00000272342	NM_019002.3	448	tCt/tTt	5/6	1	2	FACETS	0.906	0.729	1	0.906	0.729	1	CLONAL	1	TRUE	1	0.214171550298818	2		273	299	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446317	29446318	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	44	475	0	ENST00000544604.2:c.2148_2149delinsTT	p.Gln717Ter	p.Q717*	ENST00000544604	NM_001206998.1	716	ccCCag/ccTTag	8/9	1	2	FACETS	0.971	0.816	1	0.971	0.816	1	CLONAL	1	TRUE	1	0.214171550298818	2		475	423	SUCCESS
ALB	213	MSKCC	GRCh37	4	74272474	74272474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	37	329	0	ENST00000295897.4:c.266C>T	p.Ser89Leu	p.S89L	ENST00000295897	NM_000477.5	89	tCa/tTa	3/15	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.214171550298818	2		329	334	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681505	117681505	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs775665843	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	36	298	0	ENST00000368508.3:c.3445G>A	p.Glu1149Lys	p.E1149K	ENST00000368508	NM_002944.2	1149	Gaa/Aaa	22/43	1	2	FACETS	0.921	0.758	1	0.921	0.758	1	CLONAL	1	TRUE	1	0.214171550298818	2		298	365	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873411	151873411	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	64	474	0	ENST00000262189.6:c.9127G>C	p.Glu3043Gln	p.E3043Q	ENST00000262189	NM_170606.2	3043	Gag/Cag	38/59	0.214171550298818	3	FACETS	0.92	0.796	1	0.46	0.398	0.528	CLONAL	1	TRUE	1	0.214171550298818	3		474	719	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874629	151874629	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	63	526	0	ENST00000262189.6:c.7909C>T	p.His2637Tyr	p.H2637Y	ENST00000262189	NM_170606.2	2637	Cat/Tat	38/59	0.214171550298818	3	FACETS	0.913	0.789	1	0.457	0.394	0.525	CLONAL	1	TRUE	1	0.214171550298818	3		526	713	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884524	151884524	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770416252	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	66	410	0	ENST00000262189.6:c.4831C>T	p.Pro1611Ser	p.P1611S	ENST00000262189	NM_170606.2	1611	Cct/Tct	33/59	0.214171550298818	3	FACETS	1	0.954	1	0.616	0.535	0.703	CLONAL	1	TRUE	1	0.214171550298818	3		410	554	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128322037	128322038	+	missense_variant	Missense_Mutation	DNP	CA	CA	TT	novel	NA	P-0044788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	77	439	0	ENST00000265960.3:c.722_723delinsAA	p.Val241Glu	p.V241E	ENST00000265960	NM_001006617.1	241	gTG/gAA	6/12	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.214171550298818	2		439	572	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439824	220439824	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046260-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	70	577	0	ENST00000243786.2:c.677G>T	p.Gly226Val	p.G226V	ENST00000243786	NM_002191.3	226	gGa/gTa	2/2	0.656206544514889	3	FACETS	0.477	0.416	0.543			1	SUBCLONAL	1	TRUE	NA	0.656206544514889	3		577	594	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937657	32937657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046260-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	268	321	0	ENST00000380152.3:c.8318C>T	p.Ser2773Phe	p.S2773F	ENST00000380152		2773	tCt/tTt	18/27	0.62097691270865	4	FACETS	0.941	0.896	0.987	0.941	0.896	0.987	CLONAL	3	TRUE	1	0.656206544514889	4		321	479	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561282	9561282	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046260-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	55	464	0	ENST00000353224.5:c.500A>T	p.Lys167Met	p.K167M	ENST00000353224	NM_177990.2	167	aAg/aTg	4/10	0.591842714280029	1	FACETS	0.304	0.26	0.35	0.304	0.26	0.35	SUBCLONAL	1	TRUE	0	0.656206544514889	1		464	371	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375256	31375256	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046260-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	69	475	0	ENST00000328111.2:c.653A>G	p.Gln218Arg	p.Q218R	ENST00000328111	NM_006892.3	218	cAg/cGg	6/23	0.492611531056807	2	FACETS	0.375	0.327	0.427	0.187	0.163	0.214	SUBCLONAL	1	TRUE	0	0.656206544514889	2		475	561	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851793	134851793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046260-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	172	533	0	ENST00000398015.3:c.1199C>T	p.Thr400Ile	p.T400I	ENST00000398015	NM_004441.4	400	aCc/aTc	5/16	0.656206544514889	2	FACETS	1	0.987	1	0.639	0.595	0.684	CLONAL	1	TRUE	0	0.656206544514889	2		533	410	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006767	47006767	+	5_prime_UTR_variant	5'UTR	SNP	G	G	T	novel	NA	P-0046260-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	60	213	0	ENST00000377604.3:c.-114G>T		p.*38*	ENST00000377604	NM_001204468.1	-/852		2/24	0.656206544514889	2	FACETS	0.759	0.661	0.862			1	SUBCLONAL	1	TRUE	NA	0.656206544514889	2		213	241	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0046449-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	490	547	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.857952494175837	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.857952494175837	2		548	553	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046449-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	149	523	0				ENST00000310581	NM_198253.2	-/1132			0.857952494175837	1	FACETS	0.987	0.936	1	0.987	0.936	1	CLONAL	1	TRUE	0	0.857952494175837	1		523	201	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0046449-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	243	364	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	0.857952494175837	1	FACETS	0.989	0.95	1	0.989	0.95	1	CLONAL	1	TRUE	0	0.857952494175837	1		364	327	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657025	45657025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542311532	NA	P-0046449-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	267	517	0	ENST00000407780.3:c.131G>A	p.Arg44His	p.R44H	ENST00000407780	NM_001283052.1	44	cGt/cAt	3/7	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.857952494175837	2		517	598	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112884118	112884118	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587778635	NA	P-0046449-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	194	287	0	ENST00000351677.2:c.53A>G	p.Asn18Ser	p.N18S	ENST00000351677	NM_002834.3	18	aAc/aGc	2/16	0.238054785358182	1	FACETS	0.616	0.578	0.655	0.616	0.578	0.655	INDETERMINATE	1	TRUE	0	0.857952494175837	1		287	419	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194830	29194830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046449-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	336	601	0	ENST00000240100.2:c.898C>T	p.Arg300Trp	p.R300W	ENST00000240100	NM_001394.6	300	Cgg/Tgg	4/4	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.857952494175837	2		601	688	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050300	176050300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046449-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	172	310	0	ENST00000367669.3:c.1265G>A	p.Ser422Asn	p.S422N	ENST00000367669	NM_022457.5	422	aGt/aAt	11/20	1	2	FACETS	0.891	0.828	0.955	0.891	0.828	0.955	CLONAL	1	TRUE	1	0.857952494175837	2		310	450	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024637	14024639	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	TGA	TGA	-	novel	NA	P-0046449-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	197	364	0	ENST00000311895.7:c.863_865del	p.Leu288_Lys289delinsTer	p.L288_K289delins*	ENST00000311895	NM_005236.2	288	tTGAag/tag	5/11	0.18307286341644	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.857952494175837	0		364	482	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503879	149503879	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046449-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	283	507	0	ENST00000261799.4:c.1957A>G	p.Lys653Glu	p.K653E	ENST00000261799	NM_002609.3	653	Aag/Gag	14/23	0.857952494175837	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.857952494175837	1		507	349	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748488	43748488	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046449-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	311	476	0	ENST00000523873.1:c.442G>T	p.Gly148Ter	p.G148*	ENST00000523873		148	Gga/Tga	6/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.857952494175837	2		476	709	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0047326-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	270	614	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.231029538194864	4	FACETS	1	0.957	1	0.766	0.72	0.813	CLONAL	3	TRUE	0	0.254771416281806	4		614	868	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038893	12038894	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0047326-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	133	451	0	ENST00000396373.4:c.1188_1189del	p.Arg396SerfsTer29	p.R396Sfs*29	ENST00000396373	NM_001987.4	396	AGa/a	7/8	0.20556559161191	2	FACETS	0.827	0.753	0.904	0.827	0.753	0.904	CLONAL	2	TRUE	0	0.254771416281806	2		451	631	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525569	187525569	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0047326-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	97	524	0	ENST00000441802.2:c.10510A>T	p.Lys3504Ter	p.K3504*	ENST00000441802	NM_005245.3	3504	Aag/Tag	18/27	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.254771416281806	2		524	618	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144387353	144387353	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047326-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	82	452	0	ENST00000262995.4:c.1991C>A	p.Ser664Tyr	p.S664Y	ENST00000262995	NM_207123.2	664	tCt/tAt	10/11	0.254771416281806	5	FACETS	1	0.954	1	0.389	0.343	0.439	CLONAL	1	TRUE	2	0.254771416281806	5		452	762	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106237	27106237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1003835206	NA	P-0047505-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	134	557	0	ENST00000324856.7:c.5848C>T	p.Arg1950Trp	p.R1950W	ENST00000324856	NM_006015.4	1950	Cgg/Tgg	20/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		557	860	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579874	7579875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1555527002	NA	P-0047505-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	137	431	0	ENST00000269305.4:c.38dup	p.Leu14SerfsTer15	p.L14Sfs*15	ENST00000269305	NM_001126112.2	13	cct/ccCt	2/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		431	622	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913315	NA	P-0047505-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	84	553	0	ENST00000326873.7:c.580G>A	p.Asp194Asn	p.D194N	ENST00000326873	NM_000455.4	194	Gac/Aac	4/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		553	648	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047505-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	64	540	0	ENST00000326873.7:c.647C>A	p.Ser216Tyr	p.S216Y	ENST00000326873	NM_000455.4	216	tCc/tAc	5/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		540	667	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220677	1220677	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047505-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	53	493	0	ENST00000326873.7:c.695C>T	p.Ser232Phe	p.S232F	ENST00000326873	NM_000455.4	232	tCc/tTc	5/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		493	566	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221325	1221325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047505-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	49	513	0	ENST00000326873.7:c.848C>T	p.Ser283Phe	p.S283F	ENST00000326873	NM_000455.4	283	tCt/tTt	6/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		513	650	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098423	11098423	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs549254467	NA	P-0047505-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	110	446	1	ENST00000358026.2:c.941C>T	p.Ala314Val	p.A314V	ENST00000358026	NM_001128849.1	314	gCg/gTg	6/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		447	597	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568668	41568668	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0047505-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	205	389	0	ENST00000263253.7:c.4617+1G>C		p.X1539_splice	ENST00000263253	NM_001429.3	1539			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		389	580	SUCCESS
MET	4233	MSKCC	GRCh37	7	116422151	116422151	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047505-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	113	242	0	ENST00000397752.3:c.3632T>C	p.Met1211Thr	p.M1211T	ENST00000397752	NM_000245.2	1211	aTg/aCg	18/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		242	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0048335-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	89	623	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	NA	2	FACETS	0.632	0.562	0.706			1	INDETERMINATE	1	TRUE	NA	0.571350615073564	2		623	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0048335-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	26	850	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	0.154	0.121	0.191			1	INDETERMINATE	1	TRUE	NA	0.571350615073564	2		852	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0048335-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	18	692	0	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	NA	2	FACETS	0.107	0.08	0.139			1	INDETERMINATE	1	TRUE	NA	0.571350615073564	2		692	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782664	NA	P-0048335-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	11	506	0	ENST00000269305.4:c.711G>C	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atC	7/11	NA	2	FACETS	0.08	0.055	0.112			1	INDETERMINATE	1	TRUE	NA	0.571350615073564	2		506	480	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346338	73346338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048335-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	120	477	0	ENST00000377767.4:c.1462G>A	p.Asp488Asn	p.D488N	ENST00000377767	NM_014953.3	488	Gat/Aat	10/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.571350615073564	2		477	371	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560494	65560494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048335-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	167	484	0	ENST00000358664.4:c.103C>T	p.Arg35Cys	p.R35C	ENST00000358664	NM_002382.4	35	Cgt/Tgt	3/5	0.571350615073564	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.571350615073564	1		484	384	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288872	33288872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1450224002	NA	P-0048335-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	40	608	1	ENST00000374542.5:c.680G>A	p.Arg227Gln	p.R227Q	ENST00000374542	NM_001141970.1	227	cGg/cAg	3/8	1	2	FACETS	0.228	0.189	0.272	0.228	0.189	0.272	SUBCLONAL	1	TRUE	1	0.571350615073564	2		609	614	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199705	11199705	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048335-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	26	493	0	ENST00000361445.4:c.4883G>C	p.Arg1628Pro	p.R1628P	ENST00000361445	NM_004958.3	1628	cGt/cCt	35/58	1	2	FACETS	0.194	0.153	0.241	0.194	0.153	0.241	SUBCLONAL	1	TRUE	1	0.571350615073564	2		493	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577067	7577067	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0048579-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	406	591	0	ENST00000269305.4:c.871A>T	p.Lys291Ter	p.K291*	ENST00000269305	NM_001126112.2	291	Aag/Tag	8/11	0.907496336809607	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.907496336809607	1		591	466	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321727	62321729	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs771771098	NA	P-0048973-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	36	720	0	ENST00000360203.5:c.2351_2353del	p.Phe784del	p.F784del	ENST00000360203	NM_001283009.1	782	ccCTTc/ccc	26/35	0.179391635417384	3	FACETS	0.92	0.756	1	0.307	0.252	0.368	CLONAL	1	TRUE	0	0.199243248344746	3		720	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0049041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	166	547	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.958	1	1	0.992	1	CLONAL	2	TRUE	1	0.205824381585417	2		548	758	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0049041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	13	393	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.205824381585417	3	FACETS	0.294	0.208	0.399	0.147	0.104	0.2	SUBCLONAL	1	TRUE	1	0.205824381585417	3		394	474	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497901	25497901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1447483341	NA	P-0049041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	49	687	0	ENST00000264709.3:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000264709	NM_175629.2	183	cGg/cAg	6/23	0.205824381585417	1	FACETS	0.523	0.442	0.614	0.523	0.442	0.614	SUBCLONAL	1	TRUE	0	0.205824381585417	1		687	816	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170543	11170543	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	104	688	0	ENST00000358026.2:c.4846G>T	p.Glu1616Ter	p.E1616*	ENST00000358026	NM_001128849.1	1616	Gaa/Taa	34/36	0.205824381585417	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.205824381585417	1		688	690	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40864870	40864870	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	34	320	0	ENST00000373198.4:c.2398T>A	p.Leu800Met	p.L800M	ENST00000373198	NM_133170.3	800	Ttg/Atg	16/32	NA	2	FACETS	0.684	0.558	0.826			1	INDETERMINATE	1	TRUE	NA	0.205824381585417	2		320	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0049041-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	326	547	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.524047737845231	3	FACETS	0.859	0.824	0.893	0.859	0.824	0.893	CLONAL	3	TRUE	0	0.651507644074928	3		548	515	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497901	25497901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1447483341	NA	P-0049041-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	151	687	0	ENST00000264709.3:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000264709	NM_175629.2	183	cGg/cAg	6/23	0.351897587350358	3	FACETS	0.983	0.902	1	0.492	0.451	0.534	INDETERMINATE	1	TRUE	1	0.651507644074928	3		687	625	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170543	11170543	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049041-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	390	688	0	ENST00000358026.2:c.4846G>T	p.Glu1616Ter	p.E1616*	ENST00000358026	NM_001128849.1	1616	Gaa/Taa	34/36	0.61630197539399	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.651507644074928	2		688	570	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40864870	40864870	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049041-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	101	320	0	ENST00000373198.4:c.2398T>A	p.Leu800Met	p.L800M	ENST00000373198	NM_133170.3	800	Ttg/Atg	16/32	0.359797305636325	6	FACETS	0.813	0.731	0.899			1	INDETERMINATE	2	TRUE	NA	0.651507644074928	6		320	439	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955082	93955082	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764861058	NA	P-0049041-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	44	422	0	ENST00000369303.4:c.2816G>C	p.Arg939Thr	p.R939T	ENST00000369303	NM_004440.3	939	aGa/aCa	16/17	NA	2	FACETS	0.79	0.673	0.915			1	INDETERMINATE	1	TRUE	NA	0.651507644074928	2		422	171	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0049520-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	21	681	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.453	0.347	0.577	0.453	0.347	0.577	SUBCLONAL	1	TRUE	1	0.16	2		682	580	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061240	38061240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049652-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	557	570	0	ENST00000250448.2:c.749C>T	p.Ser250Phe	p.S250F	ENST00000250448	NM_004496.3	250	tCc/tTc	2/2	0.812480473698106	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.812480473698106	3		570	939	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231201	46231201	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0049652-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	21	314	0	ENST00000334344.6:c.1120+1G>A		p.X374_splice	ENST00000334344	NM_152641.2	374			1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.812480473698106	2		314	44	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103212	119103212	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1379287344	NA	P-0049652-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	197	487	0	ENST00000264033.4:c.250A>G	p.Ile84Val	p.I84V	ENST00000264033	NM_005188.3	84	Atc/Gtc	2/16	0.735471655771919	4	FACETS	1	0.977	1	0.562	0.521	0.604	CLONAL	1	TRUE	2	0.812480473698106	4		487	782	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720857	89720858	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0049652-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	10	111	0	ENST00000371953.3:c.1008_1009insG	p.Phe337ValfsTer6	p.F337Vfs*6	ENST00000371953	NM_000314.4	336	-/G	8/9	0.802938780851212	2	FACETS	0.947	0.683	1	0.473	0.341	0.615	CLONAL	1	TRUE	0	0.812480473698106	2		111	26	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22413210	22413210	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049652-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	35	199	0	ENST00000344548.3:c.337G>T	p.Val113Phe	p.V113F	ENST00000344548	NM_001039802.1	113	Gtt/Ttt	6/7	0.812480473698106	3	FACETS	0.748	0.621	0.886	0.374	0.31	0.443	SUBCLONAL	1	TRUE	1	0.812480473698106	3		199	162	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489429	56489485	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTTTCTATATATCCCATAGCAAAACCCATCTGACAATGGCTTTGACAGTGATAGCA	GGTTTCTATATATCCCATAGCAAAACCCATCTGACAATGGCTTTGACAGTGATAGCA	-	novel	NA	P-0049652-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	132	326	0	ENST00000267101.3:c.1914-18_1952del		p.X638_splice	ENST00000267101	NM_001982.3	638		17/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.812480473698106	2		326	280	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024212	31024212	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049652-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	156	570	0	ENST00000375687.4:c.3697G>C	p.Glu1233Gln	p.E1233Q	ENST00000375687	NM_015338.5	1233	Gag/Cag	13/13	0.735471655771919	4	FACETS	0.956	0.877	1	0.478	0.438	0.519	CLONAL	1	TRUE	2	0.812480473698106	4		570	728	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873107	134873107	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049652-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	188	431	0	ENST00000398015.3:c.1411T>A	p.Tyr471Asn	p.Y471N	ENST00000398015	NM_004441.4	471	Tac/Aac	6/16	0.774804313714022	6	FACETS	0.956	0.881	1	0.191	0.176	0.207	CLONAL	1	TRUE	1	0.812480473698106	6		431	1271	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880241	151880241	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049652-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	33	306	0	ENST00000262189.6:c.5083C>A	p.Gln1695Lys	p.Q1695K	ENST00000262189	NM_170606.2	1695	Caa/Aaa	35/59	0.812480473698106	6	FACETS	0.952	0.781	1	0.19	0.156	0.229	CLONAL	1	TRUE	1	0.812480473698106	6		306	224	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914194	32914221	+	protein_altering_variant	In_Frame_Del	DEL	AGGATATTCTTCATAACTCTCTAGATAA	AGGATATTCTTCATAACTCTCTAGATAA	GATATTC	novel	NA	P-0049652-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	28	468	1	ENST00000380152.3:c.5702_5729delinsGATATTC	p.Glu1901_Asn1910delinsGlyTyrSer	p.E1901_N1910delinsGYS	ENST00000380152		1901	gAGGATATTCTTCATAACTCTCTAGATAAt/gGATATTCt	11/27	0.812480473698106	1	FACETS	0.671	0.562	0.781	0.671	0.562	0.781	SUBCLONAL	1	TRUE	0	0.812480473698106	1		469	61	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164531	47164531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	12	568	0	ENST00000409792.3:c.1595C>T	p.Ser532Phe	p.S532F	ENST00000409792	NM_014159.6	532	tCt/tTt	3/21	0.285581210161046	0	FACETS	0.124	0.087	0.168			1	INDETERMINATE	1	TRUE	0	0.613386594292902	0		568	122	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129367	64129367	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	30	697	0	ENST00000334205.4:c.801del	p.Val268TrpfsTer107	p.V268Wfs*107	ENST00000334205	NM_003942.2	267	Ccc/cc	8/17	0.399422530260056	1	FACETS	0.278	0.225	0.338	0.278	0.225	0.338	SUBCLONAL	1	TRUE	0	0.613386594292902	1		697	244	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287304	33287304	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	53	728	0	ENST00000374542.5:c.1793C>G	p.Thr598Ser	p.T598S	ENST00000374542	NM_001141970.1	598	aCc/aGc	6/8	0.122087554305347	4	FACETS	0.738	0.631	0.853	0.369	0.315	0.427	INDETERMINATE	1	TRUE	2	0.613386594292902	4		728	378	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517936	8517936	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	21	492	0	ENST00000356435.5:c.1455G>T	p.Gln485His	p.Q485H	ENST00000356435		485	caG/caT	10/35	1	2	FACETS	0.405	0.314	0.51	0.405	0.314	0.51	SUBCLONAL	1	TRUE	1	0.613386594292902	2		492	169	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0050386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	241	213	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.554405444031105	4	FACETS	1	0.989	1	0.851	0.81	0.891	CLONAL	3	TRUE	0	0.57473678984096	4		213	388	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022899	33022899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868208266	NA	P-0050386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	81	302	2	ENST00000300177.4:c.8G>A	p.Arg3His	p.R3H	ENST00000300177	NM_001191322.1	3	cGc/cAc	2/2	0.528564581521917	3	FACETS	0.973	0.863	1	0.486	0.431	0.545	CLONAL	1	TRUE	1	0.57473678984096	3		304	373	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602667	10602667	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	551	868	0	ENST00000171111.5:c.911T>A	p.Ile304Asn	p.I304N	ENST00000171111	NM_203500.1	304	aTc/aAc	3/6	0.569059360027533	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.57473678984096	3		868	781	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691003	NA	P-0050386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	185	461	0	ENST00000269305.4:c.96+1G>T		p.X32_splice	ENST00000269305	NM_001126112.2	32			0.532347576094085	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.57473678984096	2		461	320	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249469	153249469	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	173	465	1	ENST00000281708.4:c.1309G>A	p.Gly437Arg	p.G437R	ENST00000281708	NM_033632.3	437	Gga/Aga	9/12	0.528564581521917	3	FACETS	0.811	0.753	0.87	0.811	0.753	0.87	CLONAL	2	TRUE	1	0.57473678984096	3		466	478	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877427	40877427	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	170	514	0	ENST00000373198.4:c.2269G>T	p.Glu757Ter	p.E757*	ENST00000373198	NM_133170.3	757	Gag/Tag	15/32	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.57473678984096	2		514	438	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945075	151945075	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs762187073	NA	P-0050386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	55	413	0	ENST00000262189.6:c.2444C>A	p.Thr815Asn	p.T815N	ENST00000262189	NM_170606.2	815	aCt/aAt	14/59	0.57473678984096	6	FACETS	0.977	0.838	1	0.244	0.209	0.282	CLONAL	1	TRUE	2	0.57473678984096	6		413	421	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714594	52714594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	292	750	0	ENST00000322088.6:c.352G>A	p.Glu118Lys	p.E118K	ENST00000322088	NM_014225.5	118	Gag/Aag	4/15	0.57473678984096	2	FACETS	0.934	0.89	0.978	0.934	0.89	0.978	CLONAL	2	TRUE	0	0.57473678984096	2		750	544	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115981	8115981	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	152	344	0	ENST00000346208.3:c.1327G>T	p.Gly443Cys	p.G443C	ENST00000346208		443	Ggt/Tgt	6/6	0.532347576094085	2	FACETS	0.931	0.87	0.992	0.931	0.87	0.992	CLONAL	2	TRUE	0	0.57473678984096	2		344	284	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608362	43608362	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs144015580	NA	P-0050386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	362	812	0	ENST00000355710.3:c.1710C>A	p.Cys570Ter	p.C570*	ENST00000355710	NM_020975.4	570	tgC/tgA	9/20	0.57473678984096	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.57473678984096	3		812	781	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244313	46244313	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	289	355	1	ENST00000334344.6:c.2408del	p.Gly803AlafsTer19	p.G803Afs*19	ENST00000334344	NM_152641.2	803	Ggc/gc	15/21	0.554405444031105	4	FACETS	0.927	0.89	0.964	0.927	0.89	0.964	CLONAL	4	TRUE	0	0.57473678984096	4		356	427	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646297	3646297	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	189	802	1	ENST00000294008.3:c.1781G>T	p.Gly594Val	p.G594V	ENST00000294008	NM_032444.2	594	gGc/gTc	8/15	0.57473678984096	3	FACETS	0.987	0.913	1	0.493	0.456	0.532	CLONAL	1	TRUE	1	0.57473678984096	3		803	858	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778918	3778918	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	324	671	0	ENST00000262367.5:c.6130G>T	p.Ala2044Ser	p.A2044S	ENST00000262367	NM_004380.2	2044	Gcc/Tcc	31/31	0.57473678984096	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.57473678984096	3		671	696	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992619	72992619	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	103	473	1	ENST00000268489.5:c.1426G>T	p.Glu476Ter	p.E476*	ENST00000268489	NM_006885.3	476	Gag/Tag	2/10	0.57473678984096	3	FACETS	1	0.946	1	0.538	0.484	0.594	CLONAL	1	TRUE	1	0.57473678984096	3		474	429	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657587	37657587	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	226	494	0	ENST00000447079.4:c.2504A>T	p.His835Leu	p.H835L	ENST00000447079	NM_015083.1	835	cAt/cTt	6/14	0.541388132700986	4	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	2	0.57473678984096	4		494	613	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865266	40865266	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	293	565	0	ENST00000428826.2:c.1165G>T	p.Asp389Tyr	p.D389Y	ENST00000428826		389	Gac/Tac	11/21	0.541388132700986	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.57473678984096	4		565	748	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606722	29606722	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	99	431	0	ENST00000389048.3:c.1158G>T	p.Trp386Cys	p.W386C	ENST00000389048	NM_004304.4	386	tgG/tgT	5/29	1	2	FACETS	0.996	0.898	1	0.996	0.898	1	CLONAL	1	TRUE	1	0.57473678984096	2		431	346	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655164	45655164	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	211	453	0	ENST00000407780.3:c.688A>T	p.Ser230Cys	p.S230C	ENST00000407780	NM_001283052.1	230	Agc/Tgc	4/7	0.555582864808863	4	FACETS	0.968	0.905	1	0.968	0.905	1	CLONAL	2	TRUE	2	0.57473678984096	4		453	597	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281546	142281546	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	219	437	0	ENST00000350721.4:c.698G>T	p.Gly233Val	p.G233V	ENST00000350721	NM_001184.3	233	gGt/gTt	4/47	0.541388132700986	4	FACETS	0.987	0.924	1	0.987	0.924	1	CLONAL	2	TRUE	2	0.57473678984096	4		437	608	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067053	143067053	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	89	282	1	ENST00000262992.4:c.1660G>T	p.Gly554Cys	p.G554C	ENST00000262992	NM_001101669.1	554	Ggc/Tgc	16/24	0.528564581521917	3	FACETS	1	0.944	1	0.545	0.487	0.606	CLONAL	1	TRUE	1	0.57473678984096	3		283	366	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754287	57754287	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	85	343	0	ENST00000274289.3:c.564G>T	p.Gln188His	p.Q188H	ENST00000274289	NM_006622.3	188	caG/caT	4/14	0.528564581521917	3	FACETS	0.886	0.787	0.99	0.443	0.393	0.495	CLONAL	1	TRUE	1	0.57473678984096	3		343	430	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508241	106508241	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763784435	NA	P-0050386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	204	487	0	ENST00000359195.3:c.235C>A	p.Leu79Met	p.L79M	ENST00000359195	NM_002649.2	79	Ctg/Atg	2/11	0.57473678984096	6	FACETS	0.962	0.894	1	0.481	0.447	0.516	CLONAL	2	TRUE	2	0.57473678984096	6		487	793	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031722	69031722	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	303	426	0	ENST00000288368.4:c.3477T>A	p.His1159Gln	p.H1159Q	ENST00000288368	NM_024870.2	1159	caT/caA	28/40	0.573045848155961	4	FACETS	0.971	0.925	1	0.971	0.925	1	CLONAL	3	TRUE	1	0.57473678984096	4		426	570	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737651	145737651	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	546	884	3	ENST00000428558.2:c.3112C>A	p.Arg1038Ser	p.R1038S	ENST00000428558	NM_004260.3	1038	Cgc/Agc	19/22	0.573045848155961	4	FACETS	0.978	0.944	1	0.978	0.944	1	CLONAL	3	TRUE	1	0.57473678984096	4		887	1020	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239885	53239885	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	294	304	0	ENST00000375401.3:c.1556G>C	p.Trp519Ser	p.W519S	ENST00000375401	NM_004187.3	519	tGg/tCg	11/26	0.541528825765925	2	FACETS	0.866	0.834	0.895			1	CLONAL	3	TRUE	NA	0.57473678984096	2		304	394	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0050416-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	137	411	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.477277082936297	2		411	557	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608224	28608224	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050416-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	106	528	0	ENST00000241453.7:c.1832A>T	p.Glu611Val	p.E611V	ENST00000241453	NM_004119.2	611	gAg/gTg	14/24	0.292240158021699	1	FACETS	0.713	0.643	0.788	0.713	0.643	0.788	SUBCLONAL	1	TRUE	0	0.477277082936297	1		528	474	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955571	55955571	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1380184007	NA	P-0050416-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	46	414	0	ENST00000263923.4:c.3374T>C	p.Met1125Thr	p.M1125T	ENST00000263923	NM_002253.2	1125	aTg/aCg	25/30	0.292240158021699	1	FACETS	0.439	0.371	0.514	0.439	0.371	0.514	SUBCLONAL	1	TRUE	0	0.477277082936297	1		414	334	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922030	39922030	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050416-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	126	259	0	ENST00000378444.4:c.4142G>A	p.Gly1381Glu	p.G1381E	ENST00000378444	NM_001123385.1	1381	gGg/gAg	9/15	1	1	FACETS	0.863	0.786	0.942	0.863	0.786	0.942	CLONAL	1	TRUE	0	0.477277082936297	1		259	466	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0051008-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	345	771	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.510227460181992	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	FALSE	0	0.591634150651738	3		771	466	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495462	56495462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051008-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	168	865	0	ENST00000267101.3:c.3652G>A	p.Glu1218Lys	p.E1218K	ENST00000267101	NM_001982.3	1218	Gag/Aag	28/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.591634150651738	2		865	502	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444310	49444310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051008-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	152	926	0	ENST00000301067.7:c.3061C>T	p.Pro1021Ser	p.P1021S	ENST00000301067	NM_003482.3	1021	Cct/Tct	11/54	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	FALSE	1	0.591634150651738	2		926	503	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223043	5223044	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0051008-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	113	896	0	ENST00000357368.4:c.2759dup	p.Leu921ProfsTer62	p.L921Pfs*62	ENST00000357368	NM_002850.3	920	gtc/gtTc	18/38	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.591634150651738	2		896	358	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805540	1805540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051008-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	414	660	0	ENST00000260795.2:c.1052C>T	p.Ser351Phe	p.S351F	ENST00000260795		351	tCt/tTt	7/17	0.510227460181992	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	FALSE	0	0.591634150651738	3		660	554	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806618	1806618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051008-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	480	795	0	ENST00000260795.2:c.1334C>T	p.Ser445Leu	p.S445L	ENST00000260795		445	tCa/tTa	9/17	0.510227460181992	3	FACETS	0.883	0.862	0.904	1	0.997	1	CLONAL	4	FALSE	0	0.591634150651738	3		795	595	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760412	133760412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1168825454	NA	P-0051008-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	121	838	0	ENST00000318560.5:c.2735G>A	p.Gly912Glu	p.G912E	ENST00000318560	NM_005157.4	912	gGa/gAa	11/11	0.591634150651738	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	0	0.591634150651738	1		838	252	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760976	133760976	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051008-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	97	666	0	ENST00000318560.5:c.3299G>A	p.Cys1100Tyr	p.C1100Y	ENST00000318560	NM_005157.4	1100	tGc/tAc	11/11	0.591634150651738	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	0	0.591634150651738	1		666	206	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786039	135786039	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051008-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	144	817	0	ENST00000298552.3:c.1182del	p.Pro395LeufsTer45	p.P395Lfs*45	ENST00000298552	NM_001162426.1	394	tcT/tc	12/23	0.591634150651738	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	0	0.591634150651738	1		817	304	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222203	53222204	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0051008-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	135	388	0	ENST00000375401.3:c.4628_4629insTT	p.Thr1544Ter	p.T1544*	ENST00000375401	NM_004187.3	1543	ctg/ctTTg	26/26	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	0	0.591634150651738	1		388	215	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144361352	144361352	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051008-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	190	725	0	ENST00000262995.4:c.1402C>T	p.Gln468Ter	p.Q468*	ENST00000262995	NM_207123.2	468	Cag/Tag	6/11	0.591446691449176	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	FALSE	0	0.591634150651738	2		725	317	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010443	48010443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201684	NA	P-0051715-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	106	1060	0	ENST00000234420.5:c.71C>T	p.Ser24Leu	p.S24L	ENST00000234420	NM_000179.2	24	tCg/tTg	1/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.29	2		1060	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578391	7578392	+	inframe_insertion	In_Frame_Ins	INS	-	-	CATGGTGGGGGCAGCGCC	novel	NA	P-0051715-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	238	1252	0	ENST00000269305.4:c.521_538dup	p.His179_Glu180insGlyArgCysProHisHis	p.H179_E180insGRCPHH	ENST00000269305	NM_001126112.2	180	gag/gGGCGCTGCCCCCACCATGag	5/11	0.295451578376142	3	FACETS	0.961	0.898	1	0.641	0.598	0.684	CLONAL	2	TRUE	0	0.29	3		1252	978	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132922	64132922	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs752239607	NA	P-0051715-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	110	1050	1	ENST00000334205.4:c.1056C>A	p.Asp352Glu	p.D352E	ENST00000334205	NM_003942.2	352	gaC/gaA	9/17	0.292332513995721	2	FACETS	0.925	0.831	1	0.463	0.415	0.513	CLONAL	1	TRUE	0	0.29	2		1051	820	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111681	56111681	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051715-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	80	979	0	ENST00000399503.3:c.281A>C	p.Glu94Ala	p.E94A	ENST00000399503	NM_005921.1	94	gAg/gCg	1/20	0.292332513995721	2	FACETS	1	0.97	1	0.657	0.581	0.737	CLONAL	1	TRUE	0	0.29	2		979	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	105	452	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.289480550967544	3	FACETS	1	0.965	1	0.589	0.528	0.654	CLONAL	1	FALSE	1	0.288929439448248	3		452	706	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587118	189587118	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	95	372	0	ENST00000264731.3:c.1135C>A	p.Arg379Ser	p.R379S	ENST00000264731	NM_003722.4	379	Cgt/Agt	9/14	0.289480550967544	3	FACETS	0.875	0.784	0.971	0.875	0.784	0.971	CLONAL	2	FALSE	1	0.288929439448248	3		372	430	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257865	133257865	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	91	631	0	ENST00000320574.5:c.63G>T	p.Arg21Ser	p.R21S	ENST00000320574	NM_006231.2	21	agG/agT	2/49	0.289480550967544	3	FACETS	0.883	0.784	0.99	0.442	0.392	0.495	CLONAL	1	FALSE	1	0.288929439448248	3		631	816	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112326	115112326	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	39	555	0	ENST00000257566.3:c.1414G>T	p.Ala472Ser	p.A472S	ENST00000257566	NM_016569.3	472	Gcg/Tcg	7/8	0.289480550967544	3	FACETS	0.563	0.466	0.671	0.281	0.233	0.336	SUBCLONAL	1	FALSE	1	0.288929439448248	3		555	549	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2089939	2089939	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1337853224	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	37	623	1	ENST00000219066.1:c.925G>A	p.Ala309Thr	p.A309T	ENST00000219066	NM_002528.5	309	Gcc/Acc	6/6	0.274781052370149	4	FACETS	0.456	0.375	0.548			1	SUBCLONAL	1	FALSE	NA	0.288929439448248	4		624	724	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259060	89259060	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	49	472	0	ENST00000336596.2:c.204C>A	p.Tyr68Ter	p.Y68*	ENST00000336596	NM_005233.5	68	taC/taA	3/17	0.263062216253128	2	FACETS	0.562	0.475	0.657	0.281	0.237	0.329	SUBCLONAL	1	FALSE	0	0.288929439448248	2		472	604	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031713	69031713	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	70	452	0	ENST00000288368.4:c.3468C>G	p.Asp1156Glu	p.D1156E	ENST00000288368	NM_024870.2	1156	gaC/gaG	28/40	1	2	FACETS	0.958	0.837	1	0.958	0.837	1	CLONAL	1	FALSE	1	0.288929439448248	2		452	506	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226579937	226579937	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1481258529	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	104	518	0	ENST00000366794.5:c.365G>A	p.Arg122Lys	p.R122K	ENST00000366794	NM_001618.3	122	aGa/aAa	3/23	0.289480550967544	4	FACETS	1	0.979	1	0.69	0.619	0.766	CLONAL	1	FALSE	2	0.288929439448248	4		518	672	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449557	187449557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	52	570	0	ENST00000232014.4:c.323C>T	p.Thr108Met	p.T108M	ENST00000232014	NM_001130845.1	108	aCg/aTg	4/10	0.289480550967544	3	FACETS	0.582	0.494	0.678	0.291	0.247	0.339	SUBCLONAL	1	FALSE	1	0.288929439448248	3		570	708	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372734	81372734	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs771889279	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	28	453	0	ENST00000222390.5:c.800C>A	p.Pro267Gln	p.P267Q	ENST00000222390	NM_000601.4	267	cCg/cAg	7/18	0.289480550967544	3	FACETS	0.398	0.317	0.49	0.199	0.158	0.245	SUBCLONAL	1	FALSE	1	0.288929439448248	3		453	558	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023810	27023810	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	104	588	0	ENST00000324856.7:c.916C>G	p.Arg306Gly	p.R306G	ENST00000324856	NM_006015.4	306	Cgg/Ggg	1/20	0.289480550967544	4	FACETS	1	0.978	1			1	CLONAL	1	FALSE	NA	0.288929439448248	4		588	685	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873248	71873248	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	85	462	0	ENST00000357731.5:c.946A>T	p.Ser316Cys	p.S316C	ENST00000357731	NM_173808.2	316	Agt/Tgt	7/7	0.289480550967544	3	FACETS	1	0.947	1	0.562	0.497	0.631	CLONAL	1	FALSE	1	0.288929439448248	3		462	599	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981855	201981855	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771105129	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	355	679	0	ENST00000359651.3:c.566C>T	p.Pro189Leu	p.P189L	ENST00000359651		189	cCc/cTc	4/8	0.288929439448248	6	FACETS	0.947	0.899	0.995	0.947	0.899	0.995	CLONAL	4	FALSE	2	0.288929439448248	6		679	1024	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404563	70404563	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	41	453	0	ENST00000373644.4:c.2077G>T	p.Glu693Ter	p.E693*	ENST00000373644	NM_030625.2	693	Gaa/Taa	4/12	1	2	FACETS	0.542	0.451	0.643	0.542	0.451	0.643	SUBCLONAL	1	FALSE	1	0.288929439448248	2		453	524	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449502	32449502	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	55	404	0	ENST00000332351.3:c.872G>A	p.Ser291Asn	p.S291N	ENST00000332351	NM_024426.4	291	aGt/aAt	3/10	0.261783159269254	4	FACETS	0.968	0.829	1	0.484	0.414	0.56	CLONAL	1	FALSE	2	0.288929439448248	4		404	507	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631086	69631086	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1554981074	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	57	672	0	ENST00000334134.2:c.324+2T>C		p.X108_splice	ENST00000334134	NM_005247.2	108			0.261783159269254	4	FACETS	0.755	0.647	0.873	0.377	0.323	0.437	SUBCLONAL	1	FALSE	2	0.288929439448248	4		672	674	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869552	102869552	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	125	508	0	ENST00000307046.8:c.89C>A	p.Ser30Ter	p.S30*	ENST00000307046	NM_001111285.1	30	tCg/tAg	2/4	0.289480550967544	3	FACETS	0.75	0.68	0.824	0.75	0.68	0.824	SUBCLONAL	2	FALSE	1	0.288929439448248	3		508	660	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112128	115112128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	141	702	0	ENST00000257566.3:c.1612G>A	p.Gly538Ser	p.G538S	ENST00000257566	NM_016569.3	538	Ggc/Agc	7/8	0.289480550967544	3	FACETS	1	0.986	1	0.739	0.674	0.807	CLONAL	1	FALSE	1	0.288929439448248	3		702	756	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614513	38614513	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	70	350	0	ENST00000299084.4:c.279G>T	p.Lys93Asn	p.K93N	ENST00000299084	NM_152594.2	93	aaG/aaT	3/7	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.288929439448248	2		350	411	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813807	50813812	+	frameshift_variant	Frame_Shift_Del	DEL	GTCCAC	GTCCAC	TTCTT	novel	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	133	602	0	ENST00000398568.2:c.1361_1366delinsTTCTT	p.Ser454IlefsTer14	p.S454Ifs*14	ENST00000398568	NM_001042412.1	454	aGTCCACcc/aTTCTTcc	8/18	0.274781052370149	4	FACETS	0.831	0.756	0.91			1	CLONAL	2	FALSE	NA	0.288929439448248	4		602	714	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267400	7267400	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	186	503	0	ENST00000302850.5:c.608G>T	p.Gly203Val	p.G203V	ENST00000302850	NM_000208.2	203	gGg/gTg	2/22	0.289480550967544	4	FACETS	1	0.985	1	0.833	0.773	0.895	CLONAL	2	FALSE	1	0.288929439448248	4		503	664	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366207	15366207	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	172	553	0	ENST00000263377.2:c.1948G>T	p.Asp650Tyr	p.D650Y	ENST00000263377	NM_058243.2	650	Gac/Tac	10/20	0.289480550967544	4	FACETS	1	0.981	1	0.797	0.736	0.859	CLONAL	2	FALSE	1	0.288929439448248	4		553	642	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010508	48010508	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	39	555	0	ENST00000234420.5:c.136G>T	p.Gly46Trp	p.G46W	ENST00000234420	NM_000179.2	46	Ggg/Tgg	1/10	0.261783159269254	4	FACETS	0.53	0.438	0.633	0.265	0.219	0.317	SUBCLONAL	1	FALSE	2	0.288929439448248	4		555	656	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584563	189584563	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	34	492	0	ENST00000264731.3:c.859C>A	p.Leu287Met	p.L287M	ENST00000264731	NM_003722.4	287	Ctg/Atg	6/14	0.289480550967544	3	FACETS	0.412	0.336	0.499	0.206	0.168	0.25	SUBCLONAL	1	FALSE	1	0.288929439448248	3		492	653	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249505	153249505	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	84	459	0	ENST00000281708.4:c.1273T>A	p.Trp425Arg	p.W425R	ENST00000281708	NM_033632.3	425	Tgg/Agg	9/12	0.289480550967544	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	FALSE	0	0.288929439448248	1		459	485	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220286	55220286	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	58	415	0	ENST00000275493.2:c.676A>T	p.Lys226Ter	p.K226*	ENST00000275493	NM_005228.3	226	Aag/Tag	6/28	0.288929439448248	6	FACETS	0.972	0.834	1	0.243	0.208	0.281	CLONAL	1	FALSE	2	0.288929439448248	6		415	652	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877938	151877938	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	95	621	1	ENST00000262189.6:c.7007C>A	p.Ala2336Glu	p.A2336E	ENST00000262189	NM_170606.2	2336	gCa/gAa	36/59	0.288929439448248	6	FACETS	1	0.961	1	0.295	0.262	0.33	CLONAL	1	FALSE	2	0.288929439448248	6		622	879	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989645	68989645	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	31	480	0	ENST00000288368.4:c.1583C>A	p.Thr528Asn	p.T528N	ENST00000288368	NM_024870.2	528	aCc/aAc	15/40	1	2	FACETS	0.437	0.353	0.533	0.437	0.353	0.533	SUBCLONAL	1	FALSE	1	0.288929439448248	2		480	491	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5456129	5456129	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	89	349	0	ENST00000381577.3:c.16G>C	p.Val6Leu	p.V6L	ENST00000381577	NM_014143.3	6	Gtc/Ctc	2/7	0.289480550967544	3	FACETS	0.809	0.721	0.902	0.809	0.721	0.902	CLONAL	2	FALSE	1	0.288929439448248	3		349	436	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577217	64577217	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	61	669	0	ENST00000312049.6:c.365C>G	p.Ser122Cys	p.S122C	ENST00000312049	NM_130799.2	122	tCc/tGc	2/10	0.261783159269254	4	FACETS	0.645	0.555	0.743	0.322	0.277	0.372	SUBCLONAL	1	FALSE	2	0.288929439448248	4		669	844	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986785	36986785	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	42	589	0	ENST00000354822.5:c.904G>T	p.Ala302Ser	p.A302S	ENST00000354822	NM_001079668.2	302	Gcg/Tcg	3/3	0.288929439448248	5	FACETS	0.596	0.496	0.707			1	SUBCLONAL	1	FALSE	NA	0.288929439448248	5		589	699	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90645544	90645544	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	30	346	0	ENST00000330062.3:c.79A>T	p.Thr27Ser	p.T27S	ENST00000330062	NM_002168.2	27	Aca/Tca	1/11	0.289480550967544	3	FACETS	0.577	0.465	0.704			1	SUBCLONAL	1	FALSE	NA	0.288929439448248	3		346	412	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61305237	61305237	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	53	352	0	ENST00000341074.5:c.889del	p.Asp297ThrfsTer3	p.D297Tfs*3	ENST00000341074	NM_002974.2	297	Gac/ac	8/8	1	2	FACETS	0.986	0.844	1	0.986	0.844	1	CLONAL	1	FALSE	1	0.288929439448248	2		352	372	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169040	11169040	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	134	492	0	ENST00000358026.2:c.4629+1G>C		p.X1543_splice	ENST00000358026	NM_001128849.1	1543			0.289480550967544	4	FACETS	1	0.966	1	0.745	0.68	0.812	CLONAL	2	FALSE	1	0.288929439448248	4		492	535	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281512	15281512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	38	504	0	ENST00000263388.2:c.4861G>A	p.Asp1621Asn	p.D1621N	ENST00000263388	NM_000435.2	1621	Gac/Aac	26/33	0.289480550967544	4	FACETS	0.648	0.535	0.775	0.216	0.178	0.259	SUBCLONAL	1	FALSE	1	0.288929439448248	4		504	523	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29445646	29445646	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377603629	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	47	684	0	ENST00000544604.2:c.1477C>T	p.Arg493Trp	p.R493W	ENST00000544604	NM_001206998.1	493	Cgg/Tgg	8/9	0.25371650482673	4	FACETS	0.591	0.498	0.695	0.296	0.249	0.348	SUBCLONAL	1	FALSE	2	0.288929439448248	4		684	709	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144359721	144359721	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	46	446	0	ENST00000262995.4:c.1163T>C	p.Ile388Thr	p.I388T	ENST00000262995	NM_207123.2	388	aTt/aCt	4/11	0.263062216253128	2	FACETS	0.602	0.507	0.707	0.301	0.253	0.354	SUBCLONAL	1	FALSE	0	0.288929439448248	2		446	529	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522470	187522470	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1427112919	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	24	408	0	ENST00000441802.2:c.11593C>A	p.His3865Asn	p.H3865N	ENST00000441802	NM_005245.3	3865	Cat/Aat	21/27	0.277625026775053	3	FACETS	0.408	0.319	0.511	0.136	0.106	0.171	SUBCLONAL	1	FALSE	0	0.288929439448248	3		408	466	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683610	162683610	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	36	514	0	ENST00000366898.1:c.359C>A	p.Ala120Asp	p.A120D	ENST00000366898	NM_004562.2	120	gCt/gAt	3/12	0.161972551983207	2	FACETS	0.516	0.424	0.619	0.258	0.212	0.31	INDETERMINATE	1	FALSE	0	0.288929439448248	2		514	483	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462405	92462405	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	30	433	0	ENST00000265734.4:c.233G>C	p.Arg78Thr	p.R78T	ENST00000265734	NM_001259.6	78	aGg/aCg	2/8	0.289480550967544	3	FACETS	0.447	0.359	0.547	0.223	0.179	0.274	SUBCLONAL	1	FALSE	1	0.288929439448248	3		433	532	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030879	69030879	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1371560750	NA	P-0053343-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	41	411	0	ENST00000288368.4:c.3421G>T	p.Gly1141Cys	p.G1141C	ENST00000288368	NM_024870.2	1141	Ggt/Tgt	27/40	1	2	FACETS	0.601	0.501	0.713	0.601	0.501	0.713	SUBCLONAL	1	FALSE	1	0.288929439448248	2		411	472	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0053403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	265	657	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.951	0.892	1	0.951	0.892	1	CLONAL	1	TRUE	1	0.544053532885031	2		657	1024	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0053403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	278	593	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	0.992	0.933	1	0.992	0.933	1	CLONAL	1	TRUE	1	0.544053532885031	2		593	1030	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211718	5211718	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	89	707	0	ENST00000357368.4:c.5117A>G	p.Lys1706Arg	p.K1706R	ENST00000357368	NM_002850.3	1706	aAg/aGg	33/38	1	2	FACETS	0.316	0.279	0.355	0.316	0.279	0.355	SUBCLONAL	1	TRUE	1	0.544053532885031	2		707	1037	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578493	7578493	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1206165503	NA	P-0053651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	278	838	0	ENST00000269305.4:c.437G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tGg/tAg	5/11	0.131186120045912	3	FACETS	1	0.993	1	0.499	0.468	0.531	INDETERMINATE	1	TRUE	0	0.322820413545015	3		838	1336	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441235	52441235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910211860	NA	P-0053651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	120	536	0	ENST00000460680.1:c.535C>T	p.Arg179Trp	p.R179W	ENST00000460680	NM_004656.3	179	Cgg/Tgg	7/17	0.181586099758509	2	FACETS	0.917	0.828	1	0.458	0.414	0.506	INDETERMINATE	1	TRUE	0	0.322820413545015	2		536	811	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0053657-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	93	338	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.605711417416411	3	FACETS	1	0.972	1	0.619	0.556	0.684	CLONAL	1	TRUE	1	0.603772769827586	3		338	324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0053657-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	163	595	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.605711417416411	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.603772769827586	3		595	308	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918644	44918644	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0053657-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	220	223	0	ENST00000377967.4:c.1127T>A	p.Leu376Ter	p.L376*	ENST00000377967	NM_021140.2	376	tTa/tAa	12/29	0.44975788377127	2	FACETS	0.98	0.951	1			1	CLONAL	3	TRUE	NA	0.603772769827586	2		223	248	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0053718-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	176	681	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.281024063845835	3	FACETS	0.864	0.801	0.929	1	0.987	1	CLONAL	3	TRUE	1	0.281024063845835	3		682	551	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035203	30035203	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0053718-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	91	209	0	ENST00000338641.4:c.363+2T>G		p.X121_splice	ENST00000338641	NM_000268.3	121			0.235792882937793	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.281024063845835	2		209	288	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046656	42046656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053718-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	35	172	0	ENST00000219905.7:c.7030G>A	p.Glu2344Lys	p.E2344K	ENST00000219905	NM_001164273.1	2344	Gag/Aag	18/24	1	2	FACETS	0.883	0.727	1	0.883	0.727	1	CLONAL	1	TRUE	1	0.281024063845835	2		172	282	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950384	38950384	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053718-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	45	125	0	ENST00000357387.3:c.3566T>G	p.Phe1189Cys	p.F1189C	ENST00000357387	NM_152756.3	1189	tTt/tGt	31/38	0.208002816514008	2	FACETS	1	0.882	1	0.527	0.445	0.616	CLONAL	1	TRUE	0	0.281024063845835	2		125	304	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69012077	69012077	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053718-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	26	76	0	ENST00000288368.4:c.2714A>C	p.Lys905Thr	p.K905T	ENST00000288368	NM_024870.2	905	aAg/aCg	23/40	0.204946648558544	4	FACETS	1	0.911	1	0.644	0.514	0.791	CLONAL	1	TRUE	2	0.281024063845835	4		76	184	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053752-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	243	523	0				ENST00000310581	NM_198253.2	-/1132			0.243067480969373	1	FACETS	0.642	0.603	0.681	0.642	0.603	0.681	INDETERMINATE	1	FALSE	0	0.723535104072309	1		523	668	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390656	139390656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1160184715	NA	P-0053752-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	395	521	0	ENST00000277541.6:c.7535C>T	p.Pro2512Leu	p.P2512L	ENST00000277541	NM_017617.3	2512	cCg/cTg	34/34	0.502946344424069	1	FACETS	0.827	0.791	0.863	0.827	0.791	0.863	CLONAL	1	FALSE	0	0.723535104072309	1		521	843	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517201	NA	P-0053752-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	65	192	0	ENST00000263967.3:c.1637A>C	p.Gln546Pro	p.Q546P	ENST00000263967	NM_006218.2	546	cAg/cCg	10/21	1	2	FACETS	0.993	0.878	1	0.993	0.878	1	CLONAL	1	FALSE	1	0.723535104072309	2		192	181	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030378	49030378	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0053752-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	757	303	0	ENST00000267163.4:c.1853C>G	p.Ser618Ter	p.S618*	ENST00000267163	NM_000321.2	618	tCa/tGa	19/27	0.723535104072309	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	4	FALSE	0	0.723535104072309	4		303	879	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579427	7579427	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053752-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	446	560	0	ENST00000269305.4:c.260del	p.Pro87GlnfsTer36	p.P87Qfs*36	ENST00000269305	NM_001126112.2	87	cCa/ca	4/11	0.722132198361734	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	0	0.723535104072309	1		560	754	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663871	241663871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1131691244	NA	P-0053752-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	76	140	0	ENST00000366560.3:c.1256C>T	p.Ser419Leu	p.S419L	ENST00000366560	NM_000143.3	419	tCa/tTa	9/10	0.645970110143603	3	FACETS	0.795	0.702	0.893	0.397	0.351	0.447	SUBCLONAL	1	FALSE	1	0.723535104072309	3		140	360	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211985	36211985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761171846	NA	P-0053752-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	354	513	0	ENST00000222270.7:c.1736C>T	p.Pro579Leu	p.P579L	ENST00000222270	NM_014727.1	579	cCa/cTa	3/37	1	2	FACETS	0.855	0.81	0.9	0.855	0.81	0.9	CLONAL	1	FALSE	1	0.723535104072309	2		513	1145	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980428	201980429	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0053752-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	361	404	0	ENST00000359651.3:c.163+2dup		p.X55_splice	ENST00000359651		55			0.374390839777299	5	FACETS	0.808	0.766	0.852			1	INDETERMINATE	2	FALSE	NA	0.723535104072309	5		404	1287	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045114	47045114	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0053752-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	350	265	0	ENST00000377604.3:c.2356-1G>A		p.X786_splice	ENST00000377604	NM_001204468.1	786			1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	FALSE	0	0.723535104072309	1		265	506	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106322	27106322	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053752-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	342	463	0	ENST00000324856.7:c.5934del	p.Lys1979SerfsTer36	p.K1979Sfs*36	ENST00000324856	NM_006015.4	1978	gCc/gc	20/20	1	2	FACETS	0.915	0.867	0.964	0.915	0.867	0.964	CLONAL	1	FALSE	1	0.723535104072309	2		463	1033	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982077	201982078	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0053752-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	395	452	0	ENST00000359651.3:c.602dup	p.Gly202TrpfsTer15	p.G202Wfs*15	ENST00000359651		201	act/aCct	5/8	0.374390839777299	5	FACETS	0.793	0.753	0.834			1	INDETERMINATE	2	FALSE	NA	0.723535104072309	5		452	1435	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202594	67202594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053752-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	457	560	0	ENST00000312629.5:c.1403C>T	p.Ser468Leu	p.S468L	ENST00000312629	NM_003952.2	468	tCa/tTa	15/15	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	FALSE	NA	0.723535104072309	2		560	1225	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070626	67070626	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053752-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	287	327	0	ENST00000412916.2:c.250G>C	p.Glu84Gln	p.E84Q	ENST00000412916		84	Gag/Cag	3/6	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	1	0.723535104072309	2		327	792	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961083	55961083	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053752-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	198	321	0	ENST00000263923.4:c.2857G>A	p.Gly953Arg	p.G953R	ENST00000263923	NM_002253.2	953	Gga/Aga	21/30	0.193960875929446	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.723535104072309	0		321	555	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467915	66467915	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053752-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	194	346	0	ENST00000273854.3:c.354C>G	p.Ile118Met	p.I118M	ENST00000273854	NM_004439.5	118	atC/atG	3/18	0.193960875929446	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.723535104072309	0		346	512	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467985	66467985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053752-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	138	320	0	ENST00000273854.3:c.284C>T	p.Pro95Leu	p.P95L	ENST00000273854	NM_004439.5	95	cCt/cTt	3/18	0.193960875929446	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.723535104072309	0		320	397	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521340	187521341	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053752-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	261	398	0	ENST00000441802.2:c.11814dup	p.Gly3939ArgfsTer10	p.G3939Rfs*10	ENST00000441802	NM_005245.3	3938	-/A	22/27	1	2	FACETS	0.935	0.879	0.991	0.935	0.879	0.991	CLONAL	1	FALSE	1	0.723535104072309	2		398	772	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629374	187629375	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0053752-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	285	469	0	ENST00000441802.2:c.1607_1608insTT	p.Arg537Ter	p.R537*	ENST00000441802	NM_005245.3	536	ctg/ctTTg	2/27	1	2	FACETS	0.875	0.825	0.927	0.875	0.825	0.927	CLONAL	1	FALSE	1	0.723535104072309	2		469	900	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860344	151860344	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053752-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	357	482	1	ENST00000262189.6:c.10318G>A	p.Glu3440Lys	p.E3440K	ENST00000262189	NM_170606.2	3440	Gag/Aag	43/59	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.723535104072309	2		483	945	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449761	8449761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053752-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	203	306	0	ENST00000356435.5:c.3952C>T	p.Pro1318Ser	p.P1318S	ENST00000356435		1318	Cct/Tct	23/35	0.723535104072309	1	FACETS	0.805	0.755	0.854	0.805	0.755	0.854	CLONAL	1	FALSE	0	0.723535104072309	1		306	445	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1685010	1685010	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053752-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	289	356	0	ENST00000378625.1:c.1615G>C	p.Asp539His	p.D539H	ENST00000378625	NM_001198994.1	539	Gac/Cac	13/14	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.723535104072309	2		356	770	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984426	201984427	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0053752-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	326	405	0	ENST00000359651.3:c.1094_1095dup	p.Val366ArgfsTer82	p.V366Rfs*82	ENST00000359651		364	gaa/gaAGa	8/8	0.374390839777299	5	FACETS	1	0.994	1			1	INDETERMINATE	1	FALSE	NA	0.723535104072309	5		405	1318	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865189	57865190	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGAAT	novel	NA	P-0053752-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	331	410	0	ENST00000228682.2:c.2666_2667insGGAAT	p.Thr890GlufsTer58	p.T890Efs*58	ENST00000228682	NM_005269.2	889	tcc/tcGGAATc	12/12	0.722132198361734	1	FACETS	0.957	0.915	1	0.957	0.915	1	CLONAL	1	FALSE	0	0.723535104072309	1		410	610	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636867	73636868	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0053752-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	289	377	0	ENST00000377687.4:c.1133dup	p.Gly379TrpfsTer22	p.G379Wfs*22	ENST00000377687	NM_001730.3	377	tac/taCc	2/4	0.723535104072309	4	FACETS	0.933	0.876	0.993	0.233	0.219	0.249	CLONAL	1	FALSE	0	0.723535104072309	4		377	1475	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21350313	21350313	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053752-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	295	481	0	ENST00000215739.8:c.2131G>T	p.Gly711Trp	p.G711W	ENST00000215739	NM_006767.3	711	Ggg/Tgg	18/21	1	2	FACETS	0.899	0.848	0.951	0.899	0.848	0.951	CLONAL	1	FALSE	1	0.723535104072309	2		481	907	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117874153	117874153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053752-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	133	263	0	ENST00000297338.2:c.301C>T	p.Arg101Trp	p.R101W	ENST00000297338	NM_006265.2	101	Cgg/Tgg	4/14	1	2	FACETS	0.948	0.87	1	0.948	0.87	1	CLONAL	1	FALSE	1	0.723535104072309	2		263	388	SUCCESS
PHF6	84295	MSKCC	GRCh37	X	133511718	133511718	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1556013227	NA	P-0053752-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	179	124	0	ENST00000332070.3:c.71G>C	p.Arg24Thr	p.R24T	ENST00000332070	NM_032458.2	24	aGa/aCa	2/10	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	FALSE	0	0.723535104072309	1		124	231	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176715909	176715910	+	frameshift_variant	Frame_Shift_Ins	INS	TT	TT	GAA	novel	NA	P-0053752-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	243	333	0	ENST00000439151.2:c.6241_6242delinsGAA	p.Leu2081GlufsTer32	p.L2081Efs*32	ENST00000439151	NM_022455.4	2081	TTg/GAAg	21/23	1	2	FACETS	0.9	0.845	0.957	0.9	0.845	0.957	CLONAL	1	FALSE	1	0.723535104072309	2		333	746	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0053781-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	137	949	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.3	2	FACETS	0.881	0.808	0.958	0.881	0.808	0.958	CLONAL	2	TRUE	0	0.33	2		950	471	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40855818	40855818	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053781-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	96	522	0	ENST00000428826.2:c.2038C>T	p.Arg680Trp	p.R680W	ENST00000428826		680	Cgg/Tgg	19/21	0.117645583406292	5	FACETS	0.925	0.828	1	0.617	0.552	0.685	INDETERMINATE	2	TRUE	2	0.33	5		522	470	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0054116-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	64	393	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.97	0.86	1	0.97	0.86	1	CLONAL	1	TRUE	1	0.799709873435418	2		394	165	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054116-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	104	362	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.985	0.897	1	0.985	0.897	1	CLONAL	1	TRUE	1	0.799709873435418	2		362	264	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473723	67473723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223740	NA	P-0054116-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	272	652	0	ENST00000327367.4:c.803G>A	p.Arg268His	p.R268H	ENST00000327367	NM_005902.3	268	cGc/cAc	6/9	0.797338676026471	2	FACETS	0.953	0.918	0.986	0.953	0.918	0.986	CLONAL	2	TRUE	0	0.799709873435418	2		652	357	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436026	56436026	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771831816	NA	P-0054116-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	337	917	0	ENST00000407977.2:c.1111C>T	p.Arg371Ter	p.R371*	ENST00000407977		371	Cga/Tga	9/10	0.797338676026471	2	FACETS	0.971	0.94	1	0.971	0.94	1	CLONAL	2	TRUE	0	0.799709873435418	2		917	434	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045136	47045136	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054116-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	174	804	0	ENST00000377604.3:c.2377C>T	p.Arg793Ter	p.R793*	ENST00000377604	NM_001204468.1	793	Cga/Tga	21/24	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.799709873435418	2		804	415	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981851	201981852	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0054116-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	143	837	0	ENST00000359651.3:c.566_567dup	p.Ser190ProfsTer65	p.S190Pfs*65	ENST00000359651		188	gcc/gCCcc	4/8	1	2	FACETS	0.783	0.719	0.848	0.783	0.719	0.848	SUBCLONAL	1	TRUE	1	0.799709873435418	2		837	457	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959180	2959180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184296576	NA	P-0054116-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	126	623	1	ENST00000396946.4:c.2336G>A	p.Arg779Gln	p.R779Q	ENST00000396946	NM_032415.4	779	cGg/cAg	18/25	1	2	FACETS	0.941	0.863	1	0.941	0.863	1	CLONAL	1	TRUE	1	0.799709873435418	2		624	335	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044463	12044463	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0054116-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	103	412	0	ENST00000353533.5:c.1087-1G>C		p.X363_splice	ENST00000353533	NM_003010.3	363			0.799709873435418	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.799709873435418	1		412	137	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849289	76849289	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054116-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	117	495	0	ENST00000373344.5:c.5987G>T	p.Ser1996Ile	p.S1996I	ENST00000373344	NM_000489.3	1996	aGc/aTc	26/35	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.799709873435418	2		495	289	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054434-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	328	362	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.584118697426997	4	FACETS	1	0.972	1			1	CLONAL	3	TRUE	NA	0.584118697426997	4		362	581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0054434-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	240	632	0	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	0.584118697426997	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.584118697426997	1		632	546	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246445	105246445	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054434-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	178	609	0	ENST00000349310.3:c.155T>G	p.Leu52Arg	p.L52R	ENST00000349310	NM_001014432.1	52	cTc/cGc	4/15	1	2	FACETS	0.96	0.889	1	0.96	0.889	1	CLONAL	1	TRUE	1	0.584118697426997	2		609	635	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631102	69631102	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121917704	NA	P-0054434-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	56	600	1	ENST00000334134.2:c.310C>T	p.Arg104Ter	p.R104*	ENST00000334134	NM_005247.2	104	Cga/Tga	2/3	1	2	FACETS	0.277	0.237	0.322	0.277	0.237	0.322	SUBCLONAL	1	TRUE	1	0.584118697426997	2		601	691	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797340	135797340	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054434-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	99	480	0	ENST00000298552.3:c.529C>G	p.Leu177Val	p.L177V	ENST00000298552	NM_001162426.1	177	Ctc/Gtc	7/23	0.584118697426997	1	FACETS	0.593	0.533	0.655	0.593	0.533	0.655	SUBCLONAL	1	TRUE	0	0.584118697426997	1		480	405	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124503600	124503600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1385542313	NA	P-0054434-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	66	497	0	ENST00000357628.3:c.350G>A	p.Arg117His	p.R117H	ENST00000357628	NM_015450.2	117	cGc/cAc	8/19	0.362154986333716	1	FACETS	0.346	0.3	0.394	0.346	0.3	0.394	SUBCLONAL	1	TRUE	0	0.584118697426997	1		497	463	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495072	56495073	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054434-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	218	638	0	ENST00000267101.3:c.3430dup	p.Thr1144AsnfsTer46	p.T1144Nfs*46	ENST00000267101	NM_001982.3	1143	-/A	27/28	1	2	FACETS	0.973	0.908	1	0.973	0.908	1	CLONAL	1	TRUE	1	0.584118697426997	2		638	767	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144045	11144045	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145476154	NA	P-0054434-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	185	574	1	ENST00000358026.2:c.3626G>A	p.Ser1209Asn	p.S1209N	ENST00000358026	NM_001128849.1	1209	aGc/aAc	26/36	1	2	FACETS	0.984	0.912	1	0.984	0.912	1	CLONAL	1	TRUE	1	0.584118697426997	2		575	644	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0055106-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	408	648	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.80655689778844	4	FACETS	1	0.991	1	0.742	0.712	0.773	CLONAL	2	TRUE	1	0.884006097906796	4		648	781	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055106-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	269	596	0	ENST00000269305.4:c.377del	p.Tyr126SerfsTer44	p.Y126Sfs*44	ENST00000269305	NM_001126112.2	126	tAc/tc	5/11	0.884006097906796	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.884006097906796	1		596	319	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999413	100999413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055106-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	35	793	0	ENST00000325455.5:c.389G>A	p.Ser130Asn	p.S130N	ENST00000325455	NM_001202474.3	130	aGc/aAc	1/8	1	2	FACETS	0.113	0.092	0.137	0.113	0.092	0.137	SUBCLONAL	1	TRUE	1	0.884006097906796	2		793	700	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218417	69218417	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055106-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	21	424	0	ENST00000462284.1:c.509C>G	p.Ala170Gly	p.A170G	ENST00000462284	NM_002392.5	170	gCa/gGa	7/11	0.379505303611605	1	FACETS	0.076	0.058	0.097	0.076	0.058	0.097	INDETERMINATE	1	TRUE	0	0.884006097906796	1		424	349	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045982	26045982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055106-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	131	717	0	ENST00000540144.1:c.344C>T	p.Ala115Val	p.A115V	ENST00000540144	NM_003531.2	115	gCt/gTt	1/1	0.170130602129051	4	FACETS	0.579	0.525	0.637	0.29	0.262	0.319	INDETERMINATE	1	TRUE	2	0.884006097906796	4		717	964	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518241	8518241	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055106-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	204	516	0	ENST00000356435.5:c.1150A>C	p.Ser384Arg	p.S384R	ENST00000356435		384	Agt/Cgt	10/35	1	2	FACETS	0.968	0.907	1	0.968	0.907	1	CLONAL	1	TRUE	1	0.884006097906796	2		516	477	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518307	8518307	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055106-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	228	446	0	ENST00000356435.5:c.1084A>C	p.Asn362His	p.N362H	ENST00000356435		362	Aac/Cac	10/35	1	2	FACETS	0.973	0.916	1	0.973	0.916	1	CLONAL	1	TRUE	1	0.884006097906796	2		446	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0055666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	168	464	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.709230893277155	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.709230893277155	1		464	292	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023324	31023324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	14	576	0	ENST00000375687.4:c.2809C>T	p.Pro937Ser	p.P937S	ENST00000375687	NM_015338.5	937	Cct/Tct	13/13	0.709230893277155	1	FACETS	0.103	0.074	0.138	0.103	0.074	0.138	SUBCLONAL	1	TRUE	0	0.709230893277155	1		576	248	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391586	139391586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	125	1006	1	ENST00000277541.6:c.6605C>T	p.Ser2202Phe	p.S2202F	ENST00000277541	NM_017617.3	2202	tCc/tTc	34/34	0.709230893277155	1	FACETS	0.679	0.623	0.737	0.679	0.623	0.737	SUBCLONAL	1	TRUE	0	0.709230893277155	1		1007	335	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030446	47030446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782698715	NA	P-0055666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	51	416	1	ENST00000377604.3:c.221C>T	p.Pro74Leu	p.P74L	ENST00000377604	NM_001204468.1	74	cCg/cTg	4/24	0.709230893277155	2	FACETS	0.564	0.483	0.651			1	SUBCLONAL	1	TRUE	NA	0.709230893277155	2		417	255	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579330	7579330	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055667-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	64	499	0	ENST00000269305.4:c.357del	p.Lys120SerfsTer3	p.K120Sfs*3	ENST00000269305	NM_001126112.2	119	gcC/gc	4/11	0.208411291310048	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.208411291310048	1		499	489	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602298	10602298	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055667-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	70	683	0	ENST00000171111.5:c.1280C>A	p.Ala427Asp	p.A427D	ENST00000171111	NM_203500.1	427	gCc/gAc	3/6	0.208411291310048	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.208411291310048	1		683	523	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628542	187628542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157383372	NA	P-0055667-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	79	522	0	ENST00000441802.2:c.2440G>A	p.Asp814Asn	p.D814N	ENST00000441802	NM_005245.3	814	Gat/Aat	2/27	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.208411291310048	2		522	616	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432546	49432546	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055667-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	89	548	1	ENST00000301067.7:c.8593G>A	p.Gly2865Ser	p.G2865S	ENST00000301067	NM_003482.3	2865	Ggt/Agt	34/54	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.208411291310048	2		549	611	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055936-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	45	523	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.94	0.8	1	0.94	0.8	1	CLONAL	1	TRUE	1	0.486269637441755	2		523	197	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577530	7577530	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055936-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	88	539	0	ENST00000269305.4:c.751A>T	p.Ile251Phe	p.I251F	ENST00000269305	NM_001126112.2	251	Atc/Ttc	7/11	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.486269637441755	2		539	344	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622458	28622458	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055936-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	65	501	0	ENST00000241453.7:c.1159C>T	p.Arg387Ter	p.R387*	ENST00000241453	NM_004119.2	387	Cga/Tga	9/24	1	2	FACETS	0.828	0.723	0.94	0.828	0.723	0.94	CLONAL	1	TRUE	1	0.486269637441755	2		501	323	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912140	114912140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055936-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	27	547	0	ENST00000543371.1:c.1210C>T	p.Arg404Trp	p.R404W	ENST00000543371	NM_001198531.1	404	Cgg/Tgg	11/14	0.221324365615452	1	FACETS	0.222	0.177	0.275	0.222	0.177	0.275	INDETERMINATE	1	TRUE	0	0.486269637441755	1		547	378	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371900	55371900	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055936-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	29	734	0	ENST00000297316.4:c.590C>T	p.Pro197Leu	p.P197L	ENST00000297316	NM_022454.3	197	cCg/cTg	2/2	0.221324365615452	1	FACETS	0.353	0.284	0.43	0.353	0.284	0.43	INDETERMINATE	1	TRUE	0	0.486269637441755	1		734	256	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060817	38060818	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0055936-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	64	861	0	ENST00000250448.2:c.1171dup	p.Asp391GlyfsTer24	p.D391Gfs*24	ENST00000250448	NM_004496.3	391	gac/gGac	2/2	1	2	FACETS	0.616	0.535	0.704	0.616	0.535	0.704	SUBCLONAL	1	TRUE	1	0.486269637441755	2		861	427	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983920	15983920	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0055936-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	140	559	0	ENST00000268712.3:c.3298+1G>T		p.X1100_splice	ENST00000268712	NM_006311.3	1100			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.486269637441755	2		559	519	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131103	55131103	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs766847405	NA	P-0055936-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	33	470	0	ENST00000257290.5:c.646C>A	p.Leu216Ile	p.L216I	ENST00000257290	NM_006206.4	216	Cta/Ata	5/23	0.221324365615452	1	FACETS	0.385	0.315	0.463	0.385	0.315	0.463	INDETERMINATE	1	TRUE	0	0.486269637441755	1		470	267	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294652	1294652	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055936-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	68	670	0	ENST00000310581.5:c.349A>T	p.Thr117Ser	p.T117S	ENST00000310581	NM_198253.2	117	Acc/Tcc	2/16	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.486269637441755	2		670	246	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449510	31449510	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055936-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	42	407	0	ENST00000344624.3:c.2699C>G	p.Pro900Arg	p.P900R	ENST00000344624		900	cCa/cGa	19/33	1	2	FACETS	0.555	0.466	0.654	0.555	0.466	0.654	SUBCLONAL	1	TRUE	1	0.486269637441755	2		407	311	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135780967	135780967	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs118203610	NA	P-0055936-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	123	553	0	ENST00000298552.3:c.1997+1G>A		p.X666_splice	ENST00000298552	NM_001162426.1	666			0.486269637441755	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.486269637441755	1		553	295	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949966	44949966	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0055936-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	99	210	0	ENST00000377967.4:c.3737-2A>T		p.X1246_splice	ENST00000377967	NM_021140.2	1246			0.486269637441755	2	FACETS	1	0.963	1			1	CLONAL	2	TRUE	NA	0.486269637441755	2		210	187	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150917546	150917546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055936-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	93	634	0	ENST00000271640.5:c.1102G>A	p.Glu368Lys	p.E368K	ENST00000271640	NM_001145415.1	368	Gag/Aag	9/22	1	2	FACETS	0.681	0.606	0.759	0.681	0.606	0.759	SUBCLONAL	1	TRUE	1	0.486269637441755	2		634	562	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991097	41991097	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055936-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	24	356	0	ENST00000219905.7:c.2050G>C	p.Glu684Gln	p.E684Q	ENST00000219905	NM_001164273.1	684	Gaa/Caa	4/24	0.221324365615452	1	FACETS	0.283	0.222	0.353	0.283	0.222	0.353	INDETERMINATE	1	TRUE	0	0.486269637441755	1		356	264	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459436	40459436	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055936-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	26	636	0	ENST00000345506.4:c.1697G>A	p.Trp566Ter	p.W566*	ENST00000345506	NM_003152.3	566	tGg/tAg	15/20	1	2	FACETS	0.3	0.237	0.371	0.3	0.237	0.371	SUBCLONAL	1	TRUE	1	0.486269637441755	2		636	357	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144381537	144381537	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867730397	NA	P-0055936-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	74	510	1	ENST00000262995.4:c.1790C>T	p.Ser597Phe	p.S597F	ENST00000262995	NM_207123.2	597	tCc/tTc	9/11	1	2	FACETS	0.809	0.713	0.912	0.809	0.713	0.912	CLONAL	1	TRUE	1	0.486269637441755	2		511	376	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638072	176638072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055936-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	41	534	0	ENST00000439151.2:c.2672C>T	p.Ser891Phe	p.S891F	ENST00000439151	NM_022455.4	891	tCt/tTt	5/23	0.486269637441755	1	FACETS	0.399	0.333	0.471	0.399	0.333	0.471	SUBCLONAL	1	TRUE	0	0.486269637441755	1		534	320	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446502	29446502	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055936-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	86	691	0	ENST00000544604.2:c.2333C>A	p.Pro778His	p.P778H	ENST00000544604	NM_001206998.1	778	cCc/cAc	8/9	0.318403477984809	1	FACETS	0.977	0.876	1	0.977	0.876	1	CLONAL	1	TRUE	0	0.486269637441755	1		691	274	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46588079	46588088	+	protein_altering_variant	In_Frame_Del	DEL	GTCTGTGTGG	GTCTGTGTGG	CAGA	novel	NA	P-0055936-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	93	717	1	ENST00000263734.3:c.629_638delinsCAGA	p.Ser210_Gly213delinsThrAsp	p.S210_G213delinsTD	ENST00000263734	NM_001430.4	210	aGTCTGTGTGGc/aCAGAc	6/16	1	2	FACETS	0.887	0.794	0.986	0.887	0.794	0.986	CLONAL	1	TRUE	1	0.486269637441755	2		718	431	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097741	27097753	+	frameshift_variant	Frame_Shift_Del	DEL	AGAAGACCCTCCC	AGAAGACCCTCCC	-	novel	NA	P-0056237-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	101	581	0	ENST00000324856.7:c.3330_3342del	p.Glu1111GlnfsTer46	p.E1111Qfs*46	ENST00000324856	NM_006015.4	1110	ggAGAAGACCCTCCC/gg	12/20	0.320706169747644	1	FACETS	0.859	0.771	0.952	0.859	0.771	0.952	CLONAL	1	TRUE	0	0.380795250527723	1		581	500	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032799	30032799	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056237-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	130	494	0	ENST00000338641.4:c.174A>T	p.Glu58Asp	p.E58D	ENST00000338641	NM_000268.3	58	gaA/gaT	2/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.380795250527723	2		494	608	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143330	108143342	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGAGGTGAGTTT	TTGAGGTGAGTTT	-	novel	NA	P-0056237-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	78	431	0	ENST00000278616.4:c.3152_3153+11del		p.X1051_splice	ENST00000278616	NM_000051.3	1051		21/63	0.380795250527723	1	FACETS	0.815	0.72	0.916	0.815	0.72	0.916	CLONAL	1	TRUE	0	0.380795250527723	1		431	407	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424099	47424099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056237-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	103	565	0	ENST00000404338.3:c.2167C>T	p.Gln723Ter	p.Q723*	ENST00000404338	NM_004491.4	723	Caa/Taa	1/6	1	2	FACETS	0.86	0.771	0.954	0.86	0.771	0.954	CLONAL	1	TRUE	1	0.380795250527723	2		565	629	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0056309-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	323	600	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.667090962420654	3	FACETS	0.994	0.96	1	0.994	0.96	1	CLONAL	3	FALSE	0	0.667090962420654	3		600	433	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0056309-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	54	393	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.667090962420654	3	FACETS	0.699	0.6	0.805	0.233	0.2	0.269	SUBCLONAL	1	FALSE	0	0.667090962420654	3		394	309	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0056309-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	403	662	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.653964739708704	2	FACETS	0.928	0.894	0.962	0.928	0.894	0.962	CLONAL	2	FALSE	0	0.667090962420654	2		662	651	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692790	89692790	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056309-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	161	294	0	ENST00000371953.3:c.274G>C	p.Asp92His	p.D92H	ENST00000371953	NM_000314.4	92	Gac/Cac	5/9	0.653964739708704	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	FALSE	0	0.667090962420654	2		294	231	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100147	27100147	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056309-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	238	902	0	ENST00000324856.7:c.3943G>C	p.Asp1315His	p.D1315H	ENST00000324856	NM_006015.4	1315	Gac/Cac	16/20	0.667090962420654	3	FACETS	0.905	0.845	0.968	0.453	0.422	0.484	CLONAL	1	FALSE	1	0.667090962420654	3		902	1051	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724664	43724664	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056309-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	417	742	0	ENST00000382044.4:c.3403G>C	p.Glu1135Gln	p.E1135Q	ENST00000382044	NM_001141980.1	1135	Gaa/Caa	17/28	0.653964739708704	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	FALSE	0	0.667090962420654	2		742	607	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968579	55968579	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056309-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	181	470	0	ENST00000263923.4:c.2084del	p.Pro695LeufsTer14	p.P695Lfs*14	ENST00000263923	NM_002253.2	695	cCt/ct	14/30	0.255140969579876	5	FACETS	0.816	0.756	0.879	0.544	0.504	0.586	INDETERMINATE	2	FALSE	2	0.667090962420654	5		470	665	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838393	156838393	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056309-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	396	781	0	ENST00000524377.1:c.671A>T	p.Gln224Leu	p.Q224L	ENST00000524377	NM_002529.3	224	cAg/cTg	6/17	0.667090962420654	5	FACETS	0.94	0.893	0.987	0.626	0.595	0.658	CLONAL	2	FALSE	2	0.667090962420654	5		781	1264	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050907	49050907	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056309-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	328	504	0	ENST00000267163.4:c.2592del	p.Gly865GlufsTer8	p.G865Efs*8	ENST00000267163	NM_000321.2	864	gAa/ga	25/27	0.653964739708704	2	FACETS	0.997	0.959	1	0.997	0.959	1	CLONAL	2	FALSE	0	0.667090962420654	2		504	493	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467616	66467616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056309-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	249	617	0	ENST00000273854.3:c.653G>A	p.Gly218Asp	p.G218D	ENST00000273854	NM_004439.5	218	gGt/gAt	3/18	0.255140969579876	5	FACETS	1	0.965	1	0.691	0.65	0.734	INDETERMINATE	2	FALSE	2	0.667090962420654	5		617	720	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7168003	7168003	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056309-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	322	569	0	ENST00000302850.5:c.1586G>T	p.Gly529Val	p.G529V	ENST00000302850	NM_000208.2	529	gGg/gTg	7/22	0.657171431242475	4	FACETS	0.998	0.947	1	0.998	0.947	1	CLONAL	2	FALSE	2	0.667090962420654	4		569	806	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045930	26045930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056309-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	218	903	0	ENST00000540144.1:c.292G>A	p.Glu98Lys	p.E98K	ENST00000540144	NM_003531.2	98	Gag/Aag	1/1	0.667090962420654	4	FACETS	0.817	0.758	0.879	0.204	0.189	0.22	CLONAL	1	FALSE	0	0.667090962420654	4		903	1333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0056388-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	267	619	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.56070924720915	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.576915785133652	1		619	609	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222704	69222704	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056388-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	189	476	1	ENST00000462284.1:c.677C>A	p.Ser226Ter	p.S226*	ENST00000462284	NM_002392.5	226	tCg/tAg	8/11	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.576915785133652	2		477	642	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819770	170819772	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0056388-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	83	160	1	ENST00000296930.5:c.410_412del	p.Ser137del	p.S137del	ENST00000296930	NM_002520.6	137	AGT/-	5/11	1	2	FACETS	0.953	0.85	1	0.953	0.85	1	CLONAL	1	TRUE	1	0.576915785133652	2		161	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0057124-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	150	850	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.176682137552721	4	FACETS	0.887	0.815	0.962			1	CLONAL	4	TRUE	NA	0.176682137552721	4		852	563	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732862	44732862	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057124-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	16	0	0	ENST00000377967.4:c.68del	p.Lys23ArgfsTer19	p.K23Rfs*19	ENST00000377967	NM_021140.2	22	gAa/ga	1/29	NA	2	FACETS	0.527	0.388	0.692			1	INDETERMINATE	1	TRUE	NA	0.176682137552721	2		0	344	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450166	32450166	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0057124-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	74	619	0	ENST00000332351.3:c.647-1G>T		p.X216_splice	ENST00000332351	NM_024426.4	216			0.160675508548013	2	FACETS	0.943	0.829	1	0.943	0.829	1	CLONAL	2	TRUE	0	0.176682137552721	2		619	444	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39573270	39573270	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057124-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	15	0	0	ENST00000262039.4:c.751G>C	p.Glu251Gln	p.E251Q	ENST00000262039	NM_002647.2	251	Gaa/Caa	7/25	0.176682137552721	2	FACETS	0.428	0.312	0.568	0.214	0.156	0.284	SUBCLONAL	1	TRUE	0	0.176682137552721	2		0	397	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794812	42794812	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057124-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	40	674	0	ENST00000575354.2:c.1892T>C	p.Leu631Pro	p.L631P	ENST00000575354	NM_015125.3	631	cTg/cCg	10/20	0.115019514279275	3	FACETS	1	0.839	1	0.505	0.419	0.6	CLONAL	1	TRUE	1	0.176682137552721	3		674	488	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239039	98239039	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0057124-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	61	451	0	ENST00000331920.6:c.1602+2T>C		p.X534_splice	ENST00000331920	NM_000264.3	534			0.160675508548013	2	FACETS	0.842	0.729	0.964	0.842	0.729	0.964	CLONAL	2	TRUE	0	0.176682137552721	2		451	410	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741578	145741578	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057124-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	60	717	0	ENST00000428558.2:c.925C>G	p.Gln309Glu	p.Q309E	ENST00000428558	NM_004260.3	309	Cag/Gag	5/22	0.176682137552721	5	FACETS	1	0.96	1	0.336	0.289	0.387	CLONAL	1	TRUE	1	0.176682137552721	5		717	640	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0057186-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	331	213	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.532169835725265	4	FACETS	0.999	0.963	1	0.999	0.963	1	CLONAL	4	TRUE	0	0.549882580185332	4		213	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0057186-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	382	471	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.420852052893985	3	FACETS	1	0.994	1	0.81	0.776	0.844	CLONAL	2	TRUE	0	0.549882580185332	3		471	729	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120085	70120085	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057186-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	975	475	0	ENST00000245479.2:c.1087C>T	p.Gln363Ter	p.Q363*	ENST00000245479	NM_000346.3	363	Cag/Tag	3/3	0.532169835725265	4	FACETS	1	0.997	1	1	0.997	1	CLONAL	4	TRUE	0	0.549882580185332	4		475	1263	SUCCESS
APC	324	MSKCC	GRCh37	5	112175302	112175303	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	CT	novel	NA	P-0057186-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	369	414	0	ENST00000257430.4:c.4011_4012delinsCT	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1337	ctGCag/ctCTag	16/16	0.549882580185332	3	FACETS	0.883	0.847	0.919	0.883	0.847	0.919	CLONAL	3	TRUE	0	0.549882580185332	3		414	646	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575188	48575188	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057186-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	180	264	0	ENST00000342988.3:c.382G>A	p.Val128Met	p.V128M	ENST00000342988	NM_005359.5	128	Gtg/Atg	3/12	0.549882580185332	2	FACETS	0.98	0.921	1	0.98	0.921	1	CLONAL	2	TRUE	0	0.549882580185332	2		264	334	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987141	36987141	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057186-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	147	484	0	ENST00000354822.5:c.548T>G	p.Met183Arg	p.M183R	ENST00000354822	NM_001079668.2	183	aTg/aGg	3/3	1	2	FACETS	0.888	0.814	0.965	0.888	0.814	0.965	CLONAL	1	TRUE	1	0.549882580185332	2		484	602	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800926	18800926	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057186-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	60	246	0	ENST00000266497.5:c.4302A>C	p.Lys1434Asn	p.K1434N	ENST00000266497		1434	aaA/aaC	31/31	0.532169835725265	4	FACETS	0.883	0.764	1	0.221	0.191	0.253	CLONAL	1	TRUE	0	0.549882580185332	4		246	383	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937484	32937484	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057186-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	95	378	0	ENST00000380152.3:c.8145A>C	p.Lys2715Asn	p.K2715N	ENST00000380152		2715	aaA/aaC	18/27	0.549882580185332	5	FACETS	0.647	0.575	0.724	0.216	0.191	0.242	SUBCLONAL	1	TRUE	2	0.549882580185332	5		378	975	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937561	32937561	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057186-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	96	362	0	ENST00000380152.3:c.8222A>C	p.Lys2741Thr	p.K2741T	ENST00000380152		2741	aAg/aCg	18/27	0.549882580185332	5	FACETS	0.546	0.484	0.611	0.182	0.161	0.204	SUBCLONAL	1	TRUE	2	0.549882580185332	5		362	1168	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253771	153253771	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057186-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	196	247	0	ENST00000281708.4:c.962G>A	p.Trp321Ter	p.W321*	ENST00000281708	NM_033632.3	321	tGg/tAg	6/12	0.45178030171414	3	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	1	0.549882580185332	3		247	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0057435-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	294	406	1	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.332133437788447	3	FACETS	1	0.988	1	0.752	0.714	0.791	CLONAL	2	TRUE	0	0.509218397021859	3		407	642	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470474	25470474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024296111	NA	P-0057435-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	156	514	0	ENST00000264709.3:c.1000G>A	p.Gly334Ser	p.G334S	ENST00000264709	NM_175629.2	334	Ggc/Agc	8/23	0.115484426267815	5	FACETS	0.851	0.782	0.922	0.425	0.391	0.461	INDETERMINATE	2	TRUE	1	0.509218397021859	5		514	635	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61197642	61197663	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACTTCGTCGCTGGTGAGGAGA	GACTTCGTCGCTGGTGAGGAGA	-	novel	NA	P-0057435-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	164	435	0	ENST00000301761.2:c.26_36+11del		p.X9_splice	ENST00000301761	NM_017841.2	9		1/4	0.160550906656077	2	FACETS	1	0.938	1	0.51	0.47	0.552	INDETERMINATE	1	TRUE	0	0.509218397021859	2		435	631	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590445	67590518	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGGTACAGCAAAGAATACATAGAAAAGTTTAAACGTGAAGGCAATGAGAAAGAAATACAAAGGTTGGTGTTTCC	CGGTACAGCAAAGAATACATAGAAAAGTTTAAACGTGAAGGCAATGAGAAAGAAATACAAAGGTTGGTGTTTCC	-	novel	NA	P-0057435-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	71	472	0	ENST00000274335.5:c.1508_1568+13del		p.X503_splice	ENST00000274335		503		11/15	0.362362012924251	3	FACETS	0.619	0.541	0.704	0.31	0.27	0.352	SUBCLONAL	1	TRUE	1	0.509218397021859	3		472	565	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190657	11190657	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057435-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	136	683	0	ENST00000361445.4:c.5542A>G	p.Asn1848Asp	p.N1848D	ENST00000361445	NM_004958.3	1848	Aac/Gac	39/58	0.441833962338334	3	FACETS	0.766	0.696	0.839	0.255	0.232	0.28	SUBCLONAL	1	TRUE	0	0.509218397021859	3		683	875	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176176062	176176062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057435-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	123	543	0	ENST00000367669.3:c.53C>T	p.Ser18Phe	p.S18F	ENST00000367669	NM_022457.5	18	tCc/tTc	1/20	0.205165520381795	3	FACETS	0.686	0.619	0.756	0.229	0.206	0.252	INDETERMINATE	1	TRUE	0	0.509218397021859	3		543	884	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966030	18966030	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057435-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	81	501	0	ENST00000262803.5:c.1523A>T	p.His508Leu	p.H508L	ENST00000262803	NM_002911.3	508	cAc/cTc	11/24	0.362362012924251	3	FACETS	0.648	0.571	0.73	0.324	0.285	0.365	SUBCLONAL	1	TRUE	1	0.509218397021859	3		501	616	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0057467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	83	372	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.844	0.748	0.946	0.844	0.748	0.946	CLONAL	1	TRUE	1	0.447003027468385	2		372	440	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TC	novel	NA	P-0057564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	24	492	0	ENST00000311936.3:c.180_181inv	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggGAaa	3/5	1	2	FACETS	0.494	0.385	0.621	0.494	0.385	0.621	SUBCLONAL	1	TRUE	1	0.11	2		492	883	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551522	150551522	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057571-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	139	464	0	ENST00000369026.2:c.485C>G	p.Ser162Trp	p.S162W	ENST00000369026	NM_021960.4	162	tCg/tGg	1/3	1	2	FACETS	0.331	0.3	0.364	0.331	0.3	0.364	SUBCLONAL	1	TRUE	1	0.637232921127002	2		464	1317	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873554	151873554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057571-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1417	80	456	0	ENST00000262189.6:c.8984C>T	p.Pro2995Leu	p.P2995L	ENST00000262189	NM_170606.2	2995	cCa/cTa	38/59	NA	2	FACETS	0.168	0.147	0.191			1	INDETERMINATE	1	TRUE	NA	0.637232921127002	2		456	1497	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748114	43748114	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057571-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	316	311	0	ENST00000382044.4:c.2692C>A	p.Gln898Lys	p.Q898K	ENST00000382044	NM_001141980.1	898	Caa/Aaa	12/28	0.206590342603097	1	FACETS	0.74	0.7	0.781	0.74	0.7	0.781	INDETERMINATE	1	TRUE	0	0.637232921127002	1		311	913	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59871083	59871083	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057571-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	55	239	0	ENST00000259008.2:c.1348G>C	p.Glu450Gln	p.E450Q	ENST00000259008	NM_032043.2	450	Gaa/Caa	10/20	1	2	FACETS	0.229	0.195	0.266	0.229	0.195	0.266	SUBCLONAL	1	TRUE	1	0.637232921127002	2		239	755	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	694	523	0				ENST00000310581	NM_198253.2	-/1132			0.405637308913275	9	FACETS	1	0.991	1	1	0.991	1	CLONAL	7	TRUE	2	0.405637308913275	9		523	1133	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941653	48941653	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	67	338	0	ENST00000267163.4:c.963C>G	p.Tyr321Ter	p.Y321*	ENST00000267163	NM_000321.2	321	taC/taG	10/27	0.231182114695664	3	FACETS	1	0.973	1	0.483	0.424	0.546	INDETERMINATE	1	TRUE	0	0.405637308913275	3		338	274	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924315	112924315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355732645	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	237	630	0	ENST00000351677.2:c.1261C>T	p.Arg421Trp	p.R421W	ENST00000351677	NM_002834.3	421	Cgg/Tgg	11/16	0.405637308913275	2	FACETS	0.938	0.881	0.995	0.938	0.881	0.995	CLONAL	2	TRUE	0	0.405637308913275	2		630	623	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051598	30051598	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	157	419	0	ENST00000338641.4:c.532C>T	p.Gln178Ter	p.Q178*	ENST00000338641	NM_000268.3	178	Cag/Tag	6/16	0.304002004697971	3	FACETS	1	0.925	1	0.667	0.617	0.72	CLONAL	2	TRUE	0	0.405637308913275	3		419	465	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652056	36652057	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGGGT	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	543	879	0	ENST00000244741.5:c.179_183dup	p.Asp62ArgfsTer88	p.D62Rfs*88	ENST00000244741	NM_000389.4	60	gag/gAGGGTag	2/3	0.408567857240278	4	FACETS	0.9	0.868	0.932	0.9	0.868	0.932	CLONAL	4	TRUE	0	0.405637308913275	4		879	1045	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577069	7577069	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	AA	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	370	765	0	ENST00000269305.4:c.869delinsTT	p.Arg290LeufsTer16	p.R290Lfs*16	ENST00000269305	NM_001126112.2	290	cGc/cTTc	8/11	0.408567857240278	3	FACETS	0.917	0.875	0.958	0.917	0.875	0.958	CLONAL	3	TRUE	0	0.405637308913275	3		765	798	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774092	66774092	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	174	669	0	ENST00000307102.5:c.569-1G>T		p.X190_splice	ENST00000307102	NM_002755.3	190			0.155830811991545	4	FACETS	0.925	0.855	0.997	0.925	0.855	0.997	INDETERMINATE	2	TRUE	2	0.405637308913275	4		669	652	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612198	189612198	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1023563516	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	57	637	0	ENST00000264731.3:c.1950C>G	p.Ile650Met	p.I650M	ENST00000264731	NM_003722.4	650	atC/atG	14/14	0.314854234849355	4	FACETS	0.486	0.416	0.563	0.243	0.208	0.282	SUBCLONAL	1	TRUE	2	0.405637308913275	4		637	813	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474420	40474420	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs747639500	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	55	637	0	ENST00000264657.5:c.1981G>T	p.Asp661Tyr	p.D661Y	ENST00000264657	NM_139276.2	661	Gat/Tat	21/24	1	2	FACETS	0.479	0.41	0.555	0.479	0.41	0.555	SUBCLONAL	1	TRUE	1	0.405637308913275	2		637	566	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843423	3843423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	115	614	0	ENST00000262367.5:c.1180C>T	p.His394Tyr	p.H394Y	ENST00000262367	NM_004380.2	394	Cac/Tac	4/31	0.405637308913275	2	FACETS	0.88	0.795	0.971	0.44	0.397	0.486	CLONAL	1	TRUE	0	0.405637308913275	2		614	644	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639587	47639587	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	109	292	0	ENST00000233146.2:c.680G>T	p.Arg227Ile	p.R227I	ENST00000233146	NM_000251.2	227	aGa/aTa	4/16	0.408567857240278	3	FACETS	1	0.984	1	0.494	0.447	0.544	CLONAL	1	TRUE	0	0.405637308913275	3		292	436	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750362	133750362	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	96	668	0	ENST00000318560.5:c.1193G>T	p.Gly398Val	p.G398V	ENST00000318560	NM_005157.4	398	gGa/gTa	7/11	0.186392106588844	2	FACETS	0.822	0.734	0.915	0.411	0.367	0.458	INDETERMINATE	1	TRUE	0	0.405637308913275	2		668	576	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021535	31021535	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs757832294	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	157	757	0	ENST00000375687.4:c.1534C>T	p.Gln512Ter	p.Q512*	ENST00000375687	NM_015338.5	512	Cag/Tag	12/13	0.304002004697971	3	FACETS	1	0.982	1	0.421	0.386	0.457	CLONAL	1	TRUE	0	0.405637308913275	3		757	738	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023154	1023154	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs766789173	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	68	650	0	ENST00000358495.3:c.1101G>C	p.Gln367His	p.Q367H	ENST00000358495	NM_134424.2	367	caG/caC	11/12	0.314854234849355	4	FACETS	0.657	0.571	0.751	0.329	0.285	0.376	SUBCLONAL	1	TRUE	2	0.405637308913275	4		650	717	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870933	12870933	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	139	729	0	ENST00000228872.4:c.160G>T	p.Glu54Ter	p.E54*	ENST00000228872	NM_004064.3	54	Gag/Tag	1/3	0.304002004697971	3	FACETS	1	0.963	1	0.369	0.336	0.403	CLONAL	1	TRUE	0	0.405637308913275	3		729	745	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550938	150550938	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	118	637	0	ENST00000369026.2:c.718G>A	p.Glu240Lys	p.E240K	ENST00000369026	NM_021960.4	240	Gaa/Aaa	2/3	0.338549817939202	2	FACETS	0.909	0.822	1	0.455	0.411	0.501	CLONAL	1	TRUE	0	0.405637308913275	2		637	640	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221270	1221270	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	67	806	0	ENST00000326873.7:c.793G>C	p.Glu265Gln	p.E265Q	ENST00000326873	NM_000455.4	265	Gag/Cag	6/10	1	2	FACETS	0.463	0.401	0.529	0.463	0.401	0.529	SUBCLONAL	1	TRUE	1	0.405637308913275	2		806	714	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28631597	28631597	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	19	304	0	ENST00000241453.7:c.371G>A	p.Gly124Glu	p.G124E	ENST00000241453	NM_004119.2	124	gGa/gAa	4/24	0.231182114695664	3	FACETS	0.303	0.229	0.39	0.101	0.076	0.13	INDETERMINATE	1	TRUE	0	0.405637308913275	3		304	372	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827170	170827170	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	76	315	0	ENST00000296930.5:c.538G>T	p.Asp180Tyr	p.D180Y	ENST00000296930	NM_002520.6	180	Gat/Tat	7/11	0.383462509064957	3	FACETS	1	0.948	1	0.569	0.502	0.641	CLONAL	1	TRUE	1	0.405637308913275	3		315	396	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45800152	45800152	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553131563	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	134	714	0	ENST00000450313.1:c.68G>A	p.Gly23Glu	p.G23E	ENST00000450313	NM_012222.2	23	gGa/gAa	2/16	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.405637308913275	2		714	635	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400926	72400926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	112	535	0	ENST00000357731.5:c.245G>A	p.Gly82Asp	p.G82D	ENST00000357731	NM_173808.2	82	gGt/gAt	2/7	0.408567857240278	3	FACETS	1	0.919	1	0.511	0.46	0.565	CLONAL	1	TRUE	1	0.405637308913275	3		535	650	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120496230	120496230	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	117	603	0	ENST00000256646.2:c.2301G>C	p.Gln767His	p.Q767H	ENST00000256646	NM_024408.3	767	caG/caC	14/34	0.408567857240278	3	FACETS	0.943	0.851	1	0.471	0.425	0.52	CLONAL	1	TRUE	1	0.405637308913275	3		603	736	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161293457	161293457	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	68	366	0	ENST00000367975.2:c.74G>C	p.Arg25Thr	p.R25T	ENST00000367975	NM_003001.3	25	aGa/aCa	2/6	0.338549817939202	2	FACETS	0.785	0.686	0.892	0.393	0.343	0.446	SUBCLONAL	1	TRUE	0	0.405637308913275	2		366	427	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161332165	161332165	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	54	235	0	ENST00000367975.2:c.452C>G	p.Ser151Cys	p.S151C	ENST00000367975	NM_003001.3	151	tCt/tGt	6/6	0.338549817939202	2	FACETS	1	0.92	1	0.548	0.473	0.628	CLONAL	1	TRUE	0	0.405637308913275	2		235	243	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226579983	226579983	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	117	612	0	ENST00000366794.5:c.319G>C	p.Glu107Gln	p.E107Q	ENST00000366794	NM_001618.3	107	Gag/Cag	3/23	0.338549817939202	2	FACETS	0.968	0.875	1	0.484	0.437	0.533	CLONAL	1	TRUE	0	0.405637308913275	2		612	596	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104357042	104357042	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	57	474	0	ENST00000369902.3:c.902C>A	p.Ser301Tyr	p.S301Y	ENST00000369902	NM_016169.3	301	tCt/tAt	7/12	0.338549817939202	2	FACETS	0.643	0.553	0.741	0.322	0.276	0.371	SUBCLONAL	1	TRUE	0	0.405637308913275	2		474	437	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426469	49426469	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs188017299	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	148	870	0	ENST00000301067.7:c.12019C>A	p.Gln4007Lys	p.Q4007K	ENST00000301067	NM_003482.3	4007	Caa/Aaa	39/54	0.405637308913275	2	FACETS	0.883	0.807	0.963	0.442	0.403	0.482	CLONAL	1	TRUE	0	0.405637308913275	2		870	826	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233279	69233279	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	101	553	0	ENST00000462284.1:c.1144G>C	p.Glu382Gln	p.E382Q	ENST00000462284	NM_002392.5	382	Gag/Cag	11/11	0.405637308913275	2	FACETS	0.793	0.71	0.881	0.396	0.355	0.441	SUBCLONAL	1	TRUE	0	0.405637308913275	2		553	628	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239678	105239678	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	76	799	0	ENST00000349310.3:c.867G>C	p.Lys289Asn	p.K289N	ENST00000349310	NM_001014432.1	289	aaG/aaC	11/15	0.337229550435551	2	FACETS	0.557	0.488	0.631	0.278	0.244	0.316	SUBCLONAL	1	TRUE	0	0.405637308913275	2		799	673	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644861	67644861	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	147	784	0	ENST00000264010.4:c.126G>C	p.Gln42His	p.Q42H	ENST00000264010	NM_006565.3	42	caG/caC	3/12	0.405637308913275	2	FACETS	0.94	0.859	1	0.47	0.429	0.512	CLONAL	1	TRUE	0	0.405637308913275	2		784	771	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644871	67644871	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	144	794	0	ENST00000264010.4:c.136G>T	p.Asp46Tyr	p.D46Y	ENST00000264010	NM_006565.3	46	Gat/Tat	3/12	0.405637308913275	2	FACETS	0.914	0.834	0.997	0.457	0.417	0.499	CLONAL	1	TRUE	0	0.405637308913275	2		794	777	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645297	67645297	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	129	732	0	ENST00000264010.4:c.562G>A	p.Asp188Asn	p.D188N	ENST00000264010	NM_006565.3	188	Gat/Aat	3/12	0.405637308913275	2	FACETS	0.909	0.825	0.996	0.454	0.412	0.498	CLONAL	1	TRUE	0	0.405637308913275	2		732	700	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110669	8110669	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	109	567	0	ENST00000585124.1:c.223G>C	p.Asp75His	p.D75H	ENST00000585124	NM_004217.3	75	Gat/Cat	5/9	0.408567857240278	3	FACETS	0.826	0.741	0.915	0.275	0.247	0.305	CLONAL	1	TRUE	0	0.405637308913275	3		567	783	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47684735	47684735	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	49	362	0	ENST00000347630.2:c.715-1G>A		p.X239_splice	ENST00000347630	NM_001007230.1	239			1	2	FACETS	0.599	0.509	0.699	0.599	0.509	0.699	SUBCLONAL	1	TRUE	1	0.405637308913275	2		362	403	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006805	62006805	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	106	793	0	ENST00000392795.3:c.583C>G	p.His195Asp	p.H195D	ENST00000392795	NM_001039933.1	195	Cac/Gac	5/6	1	2	FACETS	0.896	0.806	0.992	0.896	0.806	0.992	CLONAL	1	TRUE	1	0.405637308913275	2		793	583	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219394	1219394	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	120	683	0	ENST00000326873.7:c.446C>G	p.Pro149Arg	p.P149R	ENST00000326873	NM_000455.4	149	cCa/cGa	3/10	1	2	FACETS	0.994	0.901	1	0.994	0.901	1	CLONAL	1	TRUE	1	0.405637308913275	2		683	595	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094867	11094867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	60	721	0	ENST00000358026.2:c.40C>T	p.Pro14Ser	p.P14S	ENST00000358026	NM_001128849.1	14	Cca/Tca	2/36	1	2	FACETS	0.477	0.411	0.55	0.477	0.411	0.55	SUBCLONAL	1	TRUE	1	0.405637308913275	2		721	620	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100046	11100046	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	49	715	0	ENST00000358026.2:c.1172C>T	p.Ser391Phe	p.S391F	ENST00000358026	NM_001128849.1	391	tCc/tTc	7/36	1	2	FACETS	0.397	0.335	0.464	0.397	0.335	0.464	SUBCLONAL	1	TRUE	1	0.405637308913275	2		715	609	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374323	15374323	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	131	635	0	ENST00000263377.2:c.1249G>C	p.Glu417Gln	p.E417Q	ENST00000263377	NM_058243.2	417	Gag/Cag	7/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.405637308913275	2		635	599	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272525	142272525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	115	332	0	ENST00000350721.4:c.2590G>A	p.Glu864Lys	p.E864K	ENST00000350721	NM_001184.3	864	Gag/Aag	12/47	0.314854234849355	4	FACETS	1	0.964	1	0.573	0.517	0.633	CLONAL	1	TRUE	2	0.405637308913275	4		332	695	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155021	55155021	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	58	676	0	ENST00000257290.5:c.2730G>C	p.Lys910Asn	p.K910N	ENST00000257290	NM_006206.4	910	aaG/aaC	20/23	0.283071023829241	2	FACETS	0.481	0.413	0.555	0.24	0.206	0.278	SUBCLONAL	1	TRUE	0	0.405637308913275	2		676	595	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254585	1254585	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	81	580	0	ENST00000310581.5:c.3193C>G	p.Leu1065Val	p.L1065V	ENST00000310581	NM_198253.2	1065	Ctg/Gtg	15/16	0.405637308913275	9	FACETS	0.803	0.705	0.909	0.115	0.1	0.13	CLONAL	1	TRUE	2	0.405637308913275	9		580	1204	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685301	86685301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	68	488	0	ENST00000274376.6:c.3017C>T	p.Ser1006Leu	p.S1006L	ENST00000274376	NM_002890.2	1006	tCa/tTa	24/25	0.19770829270334	3	FACETS	0.845	0.737	0.962	0.423	0.368	0.481	INDETERMINATE	1	TRUE	1	0.405637308913275	3		488	477	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056024	26056024	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs750505144	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	122	613	0	ENST00000343677.2:c.633G>C	p.Lys211Asn	p.K211N	ENST00000343677	NM_005319.3	211	aaG/aaC	1/1	0.408567857240278	4	FACETS	1	0.938	1	0.262	0.237	0.289	CLONAL	1	TRUE	0	0.405637308913275	4		613	806	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778027	27778027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767895248	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	242	1039	0	ENST00000369163.2:c.176C>T	p.Thr59Ile	p.T59I	ENST00000369163	NM_003536.2	59	aCc/aTc	1/1	0.408567857240278	4	FACETS	1	0.991	1	0.354	0.33	0.378	CLONAL	1	TRUE	0	0.405637308913275	4		1039	1186	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172130	32172130	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	119	735	0	ENST00000375023.3:c.2902G>A	p.Glu968Lys	p.E968K	ENST00000375023	NM_004557.3	968	Gaa/Aaa	19/30	0.408567857240278	4	FACETS	0.96	0.866	1	0.24	0.216	0.265	CLONAL	1	TRUE	0	0.405637308913275	4		735	859	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33290687	33290687	+	5_prime_UTR_variant	5'UTR	SNP	C	C	T	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	100	491	0	ENST00000374542.5:c.-101G>A		p.*34*	ENST00000374542	NM_001141970.1	-/740		1/8	0.408567857240278	4	FACETS	1	0.946	1	0.273	0.244	0.304	CLONAL	1	TRUE	0	0.405637308913275	4		491	635	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2949706	2949706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	95	563	0	ENST00000396946.4:c.3238G>A	p.Glu1080Lys	p.E1080K	ENST00000396946	NM_032415.4	1080	Gag/Aag	24/25	0.408567857240278	4	FACETS	0.92	0.819	1	0.46	0.409	0.514	CLONAL	1	TRUE	2	0.405637308913275	4		563	716	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946090	13946090	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	41	399	0	ENST00000405192.2:c.1006C>G	p.Arg336Gly	p.R336G	ENST00000405192	NM_001163147.1	336	Cga/Gga	10/12	0.408567857240278	4	FACETS	0.423	0.352	0.504	0.212	0.176	0.252	SUBCLONAL	1	TRUE	2	0.405637308913275	4		399	671	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880148	151880148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	47	446	0	ENST00000262189.6:c.5176G>A	p.Asp1726Asn	p.D1726N	ENST00000262189	NM_170606.2	1726	Gat/Aat	35/59	0.313283714570331	3	FACETS	0.447	0.376	0.525	0.149	0.125	0.175	SUBCLONAL	1	TRUE	0	0.405637308913275	3		446	624	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2070427	2070427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	67	489	0	ENST00000349721.2:c.1702G>A	p.Glu568Lys	p.E568K	ENST00000349721	NM_003070.3	568	Gag/Aag	10/34	0.155830811991545	4	FACETS	0.946	0.824	1	0.473	0.412	0.539	INDETERMINATE	1	TRUE	2	0.405637308913275	4		489	491	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057722-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	57	523	0				ENST00000310581	NM_198253.2	-/1132			0.332901774674353	5	FACETS	1	0.895	1	0.767	0.673	0.865	CLONAL	3	TRUE	1	0.359774275260422	5		523	159	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941653	48941653	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0057722-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	67	338	0	ENST00000267163.4:c.963C>G	p.Tyr321Ter	p.Y321*	ENST00000267163	NM_000321.2	321	taC/taG	10/27	0.359774275260422	4	FACETS	0.954	0.847	1	1	0.975	1	CLONAL	3	TRUE	2	0.359774275260422	4		338	177	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924315	112924315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355732645	NA	P-0057722-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	46	630	0	ENST00000351677.2:c.1261C>T	p.Arg421Trp	p.R421W	ENST00000351677	NM_002834.3	421	Cgg/Tgg	11/16	0.359774275260422	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.359774275260422	1		630	193	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051598	30051598	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057722-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	44	419	0	ENST00000338641.4:c.532C>T	p.Gln178Ter	p.Q178*	ENST00000338641	NM_000268.3	178	Cag/Tag	6/16	0.359774275260422	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.359774275260422	1		419	142	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921807	111921807	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0057722-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	33	461	0	ENST00000393256.3:c.596G>C	p.Ter199SerextTer70	p.*199Sext*70	ENST00000393256	NM_006538.4	199	tGa/tCa	4/4	0.205471401790984	2	FACETS	0.734	0.601	0.882	0.367	0.3	0.441	INDETERMINATE	1	TRUE	0	0.359774275260422	2		461	250	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652056	36652057	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGGGT	novel	NA	P-0057722-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	118	879	0	ENST00000244741.5:c.179_183dup	p.Asp62ArgfsTer88	p.D62Rfs*88	ENST00000244741	NM_000389.4	60	gag/gAGGGTag	2/3	0.359774275260422	7	FACETS	1	0.932	1	0.514	0.468	0.562	CLONAL	3	TRUE	1	0.359774275260422	7		879	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577069	7577069	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	AA	novel	NA	P-0057722-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	70	765	0	ENST00000269305.4:c.869delinsTT	p.Arg290LeufsTer16	p.R290Lfs*16	ENST00000269305	NM_001126112.2	290	cGc/cTTc	8/11	0.334298592058409	2	FACETS	1	0.974	1	0.721	0.635	0.811	CLONAL	1	TRUE	0	0.359774275260422	2		765	270	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774092	66774092	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0057722-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	52	669	0	ENST00000307102.5:c.569-1G>T		p.X190_splice	ENST00000307102	NM_002755.3	190			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.359774275260422	2		669	220	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226589933	226589933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057722-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	40	608	0	ENST00000366794.5:c.268G>A	p.Glu90Lys	p.E90K	ENST00000366794	NM_001618.3	90	Gaa/Aaa	2/23	1	2	FACETS	0.818	0.683	0.965	0.818	0.683	0.965	CLONAL	1	TRUE	1	0.359774275260422	2		608	272	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0058090-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	44	764	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	0.467	0.39	0.552	0.467	0.39	0.552	SUBCLONAL	1	TRUE	1	0.257965531930602	2		764	731	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0058090-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	30	454	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.257965531930602	3	FACETS	0.479	0.385	0.586	0.24	0.192	0.293	SUBCLONAL	1	TRUE	1	0.257965531930602	3		454	548	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878151	48878151	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778869	NA	P-0058090-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	57	663	0	ENST00000267163.4:c.103C>T	p.Gln35Ter	p.Q35*	ENST00000267163	NM_000321.2	35	Cag/Tag	1/27	1	2	FACETS	0.726	0.622	0.839	0.726	0.622	0.839	SUBCLONAL	1	TRUE	1	0.257965531930602	2		663	609	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044898	47044898	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058090-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	38	459	0	ENST00000377604.3:c.2224C>T	p.Gln742Ter	p.Q742*	ENST00000377604	NM_001204468.1	742	Cag/Tag	20/24	1	1	FACETS	0.733	0.607	0.873	0.733	0.607	0.873	SUBCLONAL	1	TRUE	0	0.257965531930602	1		459	350	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057904	27057904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058090-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	24	0	0	ENST00000324856.7:c.1612C>T	p.Gln538Ter	p.Q538*	ENST00000324856	NM_006015.4	538	Cag/Tag	3/20	1	2	FACETS	0.261	0.204	0.328	0.261	0.204	0.328	SUBCLONAL	1	TRUE	1	0.257965531930602	2		0	712	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846107	151846107	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058090-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	124	679	0	ENST00000262189.6:c.12905C>T	p.Pro4302Leu	p.P4302L	ENST00000262189	NM_170606.2	4302	cCt/cTt	52/59	0.257965531930602	3	FACETS	1	0.985	1	0.746	0.676	0.821	CLONAL	1	TRUE	1	0.257965531930602	3		679	727	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	119	523	0				ENST00000310581	NM_198253.2	-/1132			0.162628480994145	2	FACETS	0.785	0.716	0.856	0.785	0.716	0.856	INDETERMINATE	2	TRUE	0	0.417452742309273	2		523	363	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273197	115273197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	114	481	0	ENST00000438362.2:c.1261C>T	p.His421Tyr	p.H421Y	ENST00000438362	NM_001242891.1	421	Cac/Tac	11/20	0.385228191212545	2	FACETS	0.942	0.85	1	0.471	0.425	0.519	CLONAL	1	TRUE	0	0.417452742309273	2		481	580	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885177	111885178	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	95	728	3	ENST00000341259.2:c.1065_1066delinsAA	p.Asp356Asn	p.D356N	ENST00000341259	NM_005475.2	355	acGGac/acAAac	6/8	0.417452742309273	3	FACETS	0.649	0.577	0.726	0.324	0.288	0.363	SUBCLONAL	1	TRUE	1	0.417452742309273	3		731	848	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32971034	32971034	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1566260055	NA	P-0058105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	50	261	0	ENST00000380152.3:c.9502-1G>A		p.X3168_splice	ENST00000380152		3168			0.230841032939554	4	FACETS	1	0.859	1	0.336	0.286	0.39	INDETERMINATE	1	TRUE	1	0.417452742309273	4		261	337	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955381	48955381	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0058105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	93	211	0	ENST00000267163.4:c.1499-2A>G		p.X500_splice	ENST00000267163	NM_000321.2	500			0.230841032939554	4	FACETS	1	0.964	1	0.766	0.69	0.843	INDETERMINATE	2	TRUE	1	0.417452742309273	4		211	275	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955382	48955383	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0058105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	52	206	0	ENST00000267163.4:c.1499-1_1499delinsAA		p.X500_splice	ENST00000267163	NM_000321.2	500		17/27	0.230841032939554	4	FACETS	1	0.947	1	0.412	0.353	0.475	INDETERMINATE	1	TRUE	1	0.417452742309273	4		206	286	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724811	43724811	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	509	673	0	ENST00000382044.4:c.3256C>T	p.His1086Tyr	p.H1086Y	ENST00000382044	NM_001141980.1	1086	Cat/Tat	17/28	0.417452742309273	6	FACETS	0.944	0.906	0.982	0.755	0.725	0.786	CLONAL	4	TRUE	1	0.417452742309273	6		673	1185	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983299	15983301	+	missense_variant	Missense_Mutation	TNP	GGA	GGA	AAT	novel	NA	P-0058105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	77	514	1	ENST00000268712.3:c.3478_3480delinsATT	p.Ser1160Ile	p.S1160I	ENST00000268712	NM_006311.3	1160	TCC/ATT	26/46	0.219594967619282	5	FACETS	0.958	0.842	1	0.319	0.28	0.362	INDETERMINATE	1	TRUE	2	0.417452742309273	5		515	626	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541575	29541575	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	139	291	0	ENST00000356175.3:c.1499T>A	p.Ile500Asn	p.I500N	ENST00000356175	NM_000267.3	500	aTt/aAt	13/57	0.269426054356157	3	FACETS	1	0.971	1	0.741	0.683	0.8	CLONAL	2	TRUE	0	0.417452742309273	3		291	362	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559841	29559842	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	64	342	0	ENST00000356175.3:c.3438_3439delinsTT	p.Leu1147Phe	p.L1147F	ENST00000356175	NM_000267.3	1146	gtCCtt/gtTTtt	26/57	0.269426054356157	3	FACETS	0.844	0.733	0.964	0.281	0.244	0.322	CLONAL	1	TRUE	0	0.417452742309273	3		342	439	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284907	15284907	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs551991530	NA	P-0058105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	303	1039	2	ENST00000263388.2:c.4708C>T	p.Arg1570Cys	p.R1570C	ENST00000263388	NM_000435.2	1570	Cgt/Tgt	25/33	0.417452742309273	5	FACETS	1	0.99	1	0.805	0.76	0.852	CLONAL	2	TRUE	2	0.417452742309273	5		1041	977	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15364971	15364971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	86	585	0	ENST00000263377.2:c.2150C>T	p.Ser717Phe	p.S717F	ENST00000263377	NM_058243.2	717	tCc/tTc	11/20	0.417452742309273	5	FACETS	0.974	0.862	1	0.325	0.287	0.365	CLONAL	1	TRUE	2	0.417452742309273	5		585	688	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762875	40762875	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763646270	NA	P-0058105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	127	809	0	ENST00000392038.2:c.133C>T	p.Pro45Ser	p.P45S	ENST00000392038	NM_001626.4	45	Cct/Tct	3/14	0.417452742309273	5	FACETS	1	0.952	1	0.361	0.327	0.398	CLONAL	1	TRUE	2	0.417452742309273	5		809	913	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742671	39742671	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1353973932	NA	P-0058105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	59	423	0	ENST00000361337.2:c.1514G>A	p.Cys505Tyr	p.C505Y	ENST00000361337	NM_003286.2	505	tGc/tAc	15/21	0.219594967619282	5	FACETS	0.628	0.539	0.725	0.209	0.179	0.242	INDETERMINATE	1	TRUE	2	0.417452742309273	5		423	732	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805444	1805444	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs775299111	NA	P-0058105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	134	864	0	ENST00000260795.2:c.956A>G	p.Lys319Arg	p.K319R	ENST00000260795		319	aAg/aGg	7/17	1	2	FACETS	0.881	0.801	0.964	0.881	0.801	0.964	CLONAL	1	TRUE	1	0.417452742309273	2		864	729	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593609	55593611	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	rs121913685	NA	P-0058105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3394	339	394	0	ENST00000288135.5:c.1679_1681del	p.Val560del	p.V560del	ENST00000288135	NM_000222.2	559	GTT/-	11/21	0.417452742309273	32	FACETS	1	0.971	1	0.105	0.099	0.112	CLONAL	3	TRUE	2	0.417452742309273	32		394	3733	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279483	1279483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	130	1093	1	ENST00000310581.5:c.2053G>A	p.Asp685Asn	p.D685N	ENST00000310581	NM_198253.2	685	Gat/Aat	5/16	0.162628480994145	2	FACETS	0.699	0.634	0.768	0.35	0.317	0.384	INDETERMINATE	1	TRUE	0	0.417452742309273	2		1094	891	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149436864	149436880	+	frameshift_variant	Frame_Shift_Del	DEL	GGAAGGCCATGCCCTGG	GGAAGGCCATGCCCTGG	-	novel	NA	P-0058105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	105	714	0	ENST00000286301.3:c.2289_2305del	p.Gln764ArgfsTer14	p.Q764Rfs*14	ENST00000286301	NM_005211.3	763	gcCCAGGGCATGGCCTTCCtc/gctc	17/22	0.230841032939554	4	FACETS	0.946	0.847	1	0.315	0.282	0.35	INDETERMINATE	1	TRUE	1	0.417452742309273	4		714	754	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672956	30672956	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	141	774	1	ENST00000376406.3:c.4004C>T	p.Ser1335Phe	p.S1335F	ENST00000376406	NM_014641.2	1335	tCc/tTc	10/15	0.417452742309273	6	FACETS	0.992	0.902	1	0.331	0.3	0.363	CLONAL	1	TRUE	3	0.417452742309273	6		775	1249	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066675	94066675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	190	588	1	ENST00000369303.4:c.1084G>A	p.Asp362Asn	p.D362N	ENST00000369303	NM_004440.3	362	Gat/Aat	5/17	0.286455507022562	4	FACETS	0.91	0.844	0.978	0.91	0.844	0.978	CLONAL	2	TRUE	2	0.417452742309273	4		589	709	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609887	117609887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749542060	NA	P-0058105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	181	558	1	ENST00000368508.3:c.6812G>A	p.Gly2271Glu	p.G2271E	ENST00000368508	NM_002944.2	2271	gGg/gAg	43/43	0.286455507022562	4	FACETS	0.916	0.848	0.986	0.916	0.848	0.986	CLONAL	2	TRUE	2	0.417452742309273	4		559	671	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725505	117725505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	160	443	0	ENST00000368508.3:c.376G>A	p.Gly126Arg	p.G126R	ENST00000368508	NM_002944.2	126	Gga/Aga	5/43	0.286455507022562	4	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	2	0.417452742309273	4		443	533	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741395	145741396	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	360	1102	0	ENST00000428558.2:c.1107_1108delinsTT	p.Arg370Cys	p.R370C	ENST00000428558	NM_004260.3	369	ctCCgt/ctTTgt	5/22	0.219594967619282	5	FACETS	1	0.951	1	0.67	0.634	0.706	INDETERMINATE	2	TRUE	2	0.417452742309273	5		1102	1396	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212875	27212875	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	129	725	0	ENST00000380036.4:c.2857G>A	p.Asp953Asn	p.D953N	ENST00000380036	NM_000459.3	953	Gac/Aac	17/23	0.165445766041202	2	FACETS	0.793	0.72	0.871	0.397	0.36	0.436	INDETERMINATE	1	TRUE	0	0.417452742309273	2		725	779	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933563	39933563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	97	853	1	ENST00000378444.4:c.1036C>T	p.Pro346Ser	p.P346S	ENST00000378444	NM_001123385.1	346	Ccc/Tcc	4/15	0.110143098684133	4	FACETS	0.816	0.727	0.911			1	INDETERMINATE	1	TRUE	NA	0.417452742309273	4		854	807	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776366	76776366	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1557041107	NA	P-0058105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	221	487	0	ENST00000373344.5:c.7100C>T	p.Ala2367Val	p.A2367V	ENST00000373344	NM_000489.3	2367	gCc/gTc	34/35	0.226788581746281	4	FACETS	0.885	0.831	0.941	0.664	0.623	0.706	INDETERMINATE	3	TRUE	0	0.417452742309273	4		487	565	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608325	100608325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	78	567	0	ENST00000308731.7:c.1765G>A	p.Glu589Lys	p.E589K	ENST00000308731	NM_000061.2	589	Gaa/Aaa	18/19	0.226788581746281	4	FACETS	0.863	0.759	0.974	0.216	0.189	0.244	INDETERMINATE	1	TRUE	0	0.417452742309273	4		567	614	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs967461896	NA	P-0058783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	1241	385	0	ENST00000269305.4:c.526T>A	p.Cys176Ser	p.C176S	ENST00000269305	NM_001126112.2	176	Tgc/Agc	5/11	0.734885307632444	7	FACETS	0.945	0.933	0.958			1	CLONAL	7	TRUE	NA	0.734885307632444	7		385	1448	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286237	66286238	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	167	521	0	ENST00000273854.3:c.1448dup	p.Asn483LysfsTer21	p.N483Kfs*21	ENST00000273854	NM_004439.5	483	aac/aaAc	6/18	0.737320392507044	2	FACETS	0.884	0.818	0.952	0.442	0.409	0.476	CLONAL	1	TRUE	0	0.734885307632444	2		521	514	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288296	33288296	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1462295871	NA	P-0058783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	332	511	0	ENST00000374542.5:c.1112G>A	p.Arg371Gln	p.R371Q	ENST00000374542	NM_001141970.1	371	cGg/cAg	4/8	0.700914554277554	4	FACETS	1	0.992	1	0.418	0.395	0.442	CLONAL	1	TRUE	1	0.734885307632444	4		511	1249	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974783	21974783	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658556	NA	P-0058783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	1534	769	0	ENST00000304494.5:c.44G>A	p.Trp15Ter	p.W15*	ENST00000304494	NM_000077.4	15	tGg/tAg	1/3	0.737320392507044	4	FACETS	1	0.996	1	1	0.996	1	CLONAL	4	TRUE	0	0.734885307632444	4		769	1773	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030469	47030469	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556772646	NA	P-0058783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	271	304	0	ENST00000377604.3:c.244C>T	p.Arg82Trp	p.R82W	ENST00000377604	NM_001204468.1	82	Cgg/Tgg	4/24	0.732996307441902	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.734885307632444	1		304	448	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775933	9775933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754053878	NA	P-0058783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	259	267	0	ENST00000377346.4:c.397G>A	p.Asp133Asn	p.D133N	ENST00000377346	NM_005026.3	133	Gac/Aac	5/24	0.6386844356413	4	FACETS	0.853	0.803	0.904			1	CLONAL	2	TRUE	NA	0.734885307632444	4		267	717	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495609	56495609	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs745487835	NA	P-0058783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	320	622	0	ENST00000267101.3:c.3799C>T	p.Arg1267Ter	p.R1267*	ENST00000267101	NM_001982.3	1267	Cga/Tga	28/28	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.734885307632444	2		622	820	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992125	11992125	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	221	515	0	ENST00000396373.4:c.215G>T	p.Trp72Leu	p.W72L	ENST00000396373	NM_001987.4	72	tGg/tTg	3/8	0.737320392507044	4	FACETS	0.938	0.873	1	0.469	0.436	0.504	CLONAL	1	TRUE	2	0.734885307632444	4		515	1112	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565575	41565575	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	159	253	0	ENST00000263253.7:c.4241A>C	p.Tyr1414Ser	p.Y1414S	ENST00000263253	NM_001429.3	1414	tAt/tCt	26/31	0.734885307632444	6	FACETS	0.909	0.837	0.983	0.303	0.279	0.328	CLONAL	2	TRUE	0	0.734885307632444	6		253	588	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219384	1219384	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	267	218	0	ENST00000326873.7:c.436A>G	p.Lys146Glu	p.K146E	ENST00000326873	NM_000455.4	146	Aag/Gag	3/10	0.734885307632444	6	FACETS	1	0.991	1	0.343	0.321	0.366	CLONAL	1	TRUE	2	0.734885307632444	6		218	1308	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100390	27100390	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0058783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	518	389	0	ENST00000324856.7:c.4101+1G>T		p.X1367_splice	ENST00000324856	NM_006015.4	1367			0.594580526813236	4	FACETS	1	0.996	1	0.862	0.838	0.886	CLONAL	3	TRUE	0	0.734885307632444	4		389	709	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163310209	163310209	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	168	358	0	ENST00000271452.3:c.662A>C	p.Lys221Thr	p.K221T	ENST00000271452	NM_145697.2	221	aAg/aCg	9/14	0.737320392507044	3	FACETS	0.975	0.9	1			1	CLONAL	1	TRUE	NA	0.734885307632444	3		358	641	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332392	70332392	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	234	487	0	ENST00000373644.4:c.297C>A	p.Cys99Ter	p.C99*	ENST00000373644	NM_030625.2	99	tgC/tgA	2/12	0.347937904351213	3	FACETS	1	0.991	1	0.676	0.634	0.718	INDETERMINATE	1	TRUE	1	0.734885307632444	3		487	644	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352362	73352363	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	rs1197150249	NA	P-0058783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	183	613	0	ENST00000377767.4:c.542_543del	p.Lys181ArgfsTer14	p.K181Rfs*14	ENST00000377767	NM_014953.3	181	aAA/a	3/21	0.735138661268995	3	FACETS	0.913	0.845	0.984	0.304	0.281	0.328	CLONAL	1	TRUE	0	0.734885307632444	3		613	746	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103520608	103520608	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0058783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	124	381	0	ENST00000355739.4:c.2678+1G>C		p.X893_splice	ENST00000355739	NM_000123.3	893			0.735138661268995	3	FACETS	0.864	0.785	0.946	0.288	0.261	0.316	CLONAL	1	TRUE	0	0.734885307632444	3		381	534	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646219	3646219	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	491	314	0	ENST00000294008.3:c.1859G>C	p.Arg620Thr	p.R620T	ENST00000294008	NM_032444.2	620	aGg/aCg	8/15	0.734885307632444	6	FACETS	0.972	0.933	1	0.972	0.933	1	CLONAL	3	TRUE	3	0.734885307632444	6		314	1132	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37680974	37680974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1357617308	NA	P-0058783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2869	327	379	0	ENST00000447079.4:c.3143G>A	p.Arg1048Gln	p.R1048Q	ENST00000447079	NM_015083.1	1048	cGa/cAa	12/14	0.734885307632444	19	FACETS	1	0.947	1			1	CLONAL	2	TRUE	NA	0.734885307632444	19		379	3196	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58725343	58725343	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	217	451	0	ENST00000305921.3:c.917A>G	p.His306Arg	p.H306R	ENST00000305921	NM_003620.3	306	cAc/cGc	4/6	0.737320392507044	3	FACETS	1	0.95	1	0.341	0.317	0.365	CLONAL	1	TRUE	0	0.734885307632444	3		451	790	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761289	59761290	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0058783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	250	542	0	ENST00000259008.2:c.3117_3118del	p.Lys1040AspfsTer4	p.K1040Dfs*4	ENST00000259008	NM_032043.2	1039	gaGAag/gaag	20/20	0.737320392507044	3	FACETS	0.996	0.933	1	0.332	0.311	0.354	CLONAL	1	TRUE	0	0.734885307632444	3		542	934	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222839	36222840	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0058783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	295	318	0	ENST00000222270.7:c.5471_5472del	p.Thr1824ArgfsTer9	p.T1824Rfs*9	ENST00000222270	NM_014727.1	1823	gAC/g	27/37	0.636590962515855	3	FACETS	1	0.994	1			1	CLONAL	1	TRUE	NA	0.734885307632444	3		318	765	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39212997	39212997	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	642	734	0	ENST00000402219.2:c.3970C>A	p.Pro1324Thr	p.P1324T	ENST00000402219	NM_005633.3	1324	Cca/Aca	23/23	0.561997033177829	4	FACETS	0.905	0.877	0.932	0.905	0.877	0.932	CLONAL	3	TRUE	1	0.734885307632444	4		734	1117	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152276	99152276	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	168	347	0	ENST00000074304.5:c.355G>C	p.Val119Leu	p.V119L	ENST00000074304	NM_001134224.1	119	Gtg/Ctg	6/26	0.443781672463234	6	FACETS	1	0.987	1	0.456	0.419	0.494	CLONAL	1	TRUE	3	0.734885307632444	6		347	826	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136239	202136239	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	164	421	0	ENST00000358485.4:c.483G>T	p.Arg161Ser	p.R161S	ENST00000358485	NM_001080125.1	161	agG/agT	3/9	0.737320392507044	3	FACETS	0.89	0.819	0.963	0.445	0.409	0.482	CLONAL	1	TRUE	1	0.734885307632444	3		421	686	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294481	1294481	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs145958962	NA	P-0058783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	306	385	0	ENST00000310581.5:c.520C>G	p.Pro174Ala	p.P174A	ENST00000310581	NM_198253.2	174	Ccg/Gcg	2/16	0.734885307632444	6	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.734885307632444	6		385	1489	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444452	50444452	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	241	512	1	ENST00000331340.3:c.384del	p.Asn130MetfsTer63	p.N130Mfs*63	ENST00000331340	NM_006060.4	128	Ggg/gg	4/8	0.737320392507044	3	FACETS	0.872	0.815	0.932	0.436	0.407	0.466	CLONAL	1	TRUE	1	0.734885307632444	3		513	1028	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133868	38133868	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	273	511	0	ENST00000317025.8:c.4018G>C	p.Asp1340His	p.D1340H	ENST00000317025	NM_023034.1	1340	Gac/Cac	23/24	0.737320392507044	4	FACETS	1	0.97	1			1	CLONAL	1	TRUE	NA	0.734885307632444	4		511	1222	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633389	8633390	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0058783-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	810	520	1	ENST00000356435.5:c.279_280delinsCT	p.Glu93_Ala94delinsAspSer	p.E93_A94delinsDS	ENST00000356435		93	gaGGcc/gaCTcc	3/35	0.737320392507044	4	FACETS	0.994	0.977	1	0.994	0.977	1	CLONAL	4	TRUE	0	0.734885307632444	4		521	962	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059038-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	81	523	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.697	0.621	0.777	0.697	0.621	0.777	SUBCLONAL	1	TRUE	1	0.785222114321664	2		523	296	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519920	NA	P-0059038-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	18	349	0	ENST00000397062.3:c.85G>A	p.Asp29Asn	p.D29N	ENST00000397062	NM_006164.4	29	Gat/Aat	2/5	1	2	FACETS	0.161	0.121	0.209	0.161	0.121	0.209	SUBCLONAL	1	TRUE	1	0.785222114321664	2		349	284	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685300	89685300	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs878853936	NA	P-0059038-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	111	220	0	ENST00000371953.3:c.195C>G	p.Tyr65Ter	p.Y65*	ENST00000371953	NM_000314.4	65	taC/taG	3/9	0.744020543924271	1	FACETS	0.981	0.913	1	0.981	0.913	1	CLONAL	1	TRUE	0	0.785222114321664	1		220	175	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390071	89390071	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760135022	NA	P-0059038-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	112	345	0	ENST00000336596.2:c.820C>T	p.Arg274Ter	p.R274*	ENST00000336596	NM_005233.5	274	Cga/Tga	4/17	1	2	FACETS	0.837	0.761	0.914	0.837	0.761	0.914	CLONAL	1	TRUE	1	0.785222114321664	2		345	341	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056165	27056165	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059038-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	143	397	0	ENST00000324856.7:c.1163del	p.Gly388AlafsTer3	p.G388Afs*3	ENST00000324856	NM_006015.4	387	atG/at	2/20	0.638928018990891	3	FACETS	0.959	0.879	1	0.479	0.439	0.521	CLONAL	1	TRUE	1	0.785222114321664	3		397	529	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087524	27087524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059038-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	316	574	0	ENST00000324856.7:c.2098G>A	p.Val700Ile	p.V700I	ENST00000324856	NM_006015.4	700	Gtt/Att	5/20	0.638928018990891	3	FACETS	0.952	0.908	0.995	0.952	0.908	0.995	CLONAL	2	TRUE	1	0.785222114321664	3		574	589	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089777	27089777	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0059038-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	278	495	0	ENST00000324856.7:c.2732+1G>C		p.X911_splice	ENST00000324856	NM_006015.4	911			0.638928018990891	3	FACETS	0.852	0.808	0.895	0.852	0.808	0.895	CLONAL	2	TRUE	1	0.785222114321664	3		495	579	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243904	41243904	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786203310	NA	P-0059038-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	215	480	0	ENST00000357654.3:c.3644A>G	p.Asn1215Ser	p.N1215S	ENST00000357654	NM_007294.3	1215	aAc/aGc	10/23	0.607323752720132	3	FACETS	1	0.974	1	0.543	0.507	0.58	CLONAL	1	TRUE	1	0.785222114321664	3		480	702	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007565	62007565	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059038-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	368	571	0	ENST00000392795.3:c.302A>G	p.Gln101Arg	p.Q101R	ENST00000392795	NM_001039933.1	101	cAg/cGg	3/6	0.607323752720132	3	FACETS	0.938	0.898	0.978	0.938	0.898	0.978	CLONAL	2	TRUE	1	0.785222114321664	3		571	696	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157519944	157519944	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs886044620	NA	P-0059038-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	128	355	0	ENST00000346085.5:c.4014-1G>A		p.X1338_splice	ENST00000346085	NM_020732.3	1338			1	2	FACETS	0.982	0.902	1	0.982	0.902	1	CLONAL	1	TRUE	1	0.785222114321664	2		355	332	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197047	123197047	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059038-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	63	293	0	ENST00000218089.9:c.1814del	p.Leu605Ter	p.L605*	ENST00000218089	NM_001042749.1	605	Tta/ta	19/35	1	2	FACETS	0.836	0.736	0.94	0.836	0.736	0.94	CLONAL	1	TRUE	1	0.785222114321664	2		293	192	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0059251-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	81	181	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	1	0.899	1	1	0.986	1	CLONAL	2	FALSE	1	0.340444779840371	2		181	237	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249330	133249332	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0059251-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	221	472	0	ENST00000320574.5:c.1567_1569del	p.Glu523del	p.E523del	ENST00000320574	NM_006231.2	523	GAG/-	15/49	1	2	FACETS	0.979	0.916	1	1	0.994	1	CLONAL	2	FALSE	1	0.340444779840371	2		472	663	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115698	8115704	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTAGATT	TTAGATT	A	novel	NA	P-0059251-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	161	320	0	ENST00000346208.3:c.1048-4_1050delinsA		p.X350_splice	ENST00000346208		350		6/6	1	2	FACETS	1	0.956	1	1	0.993	1	CLONAL	2	FALSE	1	0.340444779840371	2		320	452	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070562	67070571	+	protein_altering_variant	In_Frame_Del	DEL	CAATCTGTCT	CAATCTGTCT	A	novel	NA	P-0059251-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	231	349	0	ENST00000412916.2:c.186_195delinsA	p.Asn63_Ser65del	p.N63_S65del	ENST00000412916		62	acCAATCTGTCT/acA	3/6	0.340444779840371	0	FACETS	0.921	0.869	0.973			1	CLONAL	2	FALSE	0	0.340444779840371	0		349	486	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685289	89685289	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554897267	NA	P-0059254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	11	260	0	ENST00000371953.3:c.188del	p.Asn63ThrfsTer36	p.N63Tfs*36	ENST00000371953	NM_000314.4	62	Aaa/aa	3/9	0.3	1	FACETS	0.55	0.381	0.757	0.55	0.381	0.757	SUBCLONAL	1	TRUE	0	0.25	1		260	140	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795072	45795072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369410616	NA	P-0059254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	27	478	0	ENST00000450313.1:c.1556G>A	p.Arg519Gln	p.R519Q	ENST00000450313	NM_012222.2	519	cGg/cAg	16/16	1	2	FACETS	0.436	0.346	0.54	0.436	0.346	0.54	SUBCLONAL	1	TRUE	1	0.25	2		478	495	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325733	30325733	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	15	325	0	ENST00000322652.5:c.1931G>T	p.Gly644Val	p.G644V	ENST00000322652	NM_015355.2	644	gGa/gTa	16/16	0.0712325720301545	3	FACETS	0.574	0.42	0.759	0.287	0.21	0.38	INDETERMINATE	1	TRUE	1	0.25	3		325	235	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911032	32911032	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502457	NA	P-0059254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	13	426	0	ENST00000380152.3:c.2540G>A	p.Arg847Lys	p.R847K	ENST00000380152		847	aGa/aAa	11/27	0.0712325720301545	3	FACETS	0.676	0.484	0.91	0.338	0.242	0.455	INDETERMINATE	1	TRUE	1	0.25	3		426	173	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332654	153332654	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs767856434	NA	P-0059254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	36	522	0	ENST00000281708.4:c.302A>G	p.Asp101Gly	p.D101G	ENST00000281708	NM_033632.3	101	gAt/gGt	2/12	0.3	1	FACETS	0.565	0.464	0.678	0.565	0.464	0.678	SUBCLONAL	1	TRUE	0	0.25	1		522	446	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433387	49433387	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	31	539	0	ENST00000301067.7:c.8060G>A	p.Arg2687Gln	p.R2687Q	ENST00000301067	NM_003482.3	2687	cGa/cAa	32/54	0.0712325720301545	3	FACETS	0.578	0.466	0.704	0.289	0.233	0.352	INDETERMINATE	1	TRUE	1	0.25	3		539	483	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983015	111983015	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059254-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	34	494	0	ENST00000368678.4:c.1532A>T	p.Glu511Val	p.E511V	ENST00000368678		511	gAg/gTg	13/13	1	2	FACETS	0.545	0.445	0.658	0.545	0.445	0.658	SUBCLONAL	1	TRUE	1	0.25	2		494	499	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	65	523	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.973	0.85	1	0.973	0.85	1	CLONAL	1	TRUE	1	0.42127959662906	2		523	317	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539105	23539105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	140	669	0	ENST00000380871.4:c.334G>A	p.Ala112Thr	p.A112T	ENST00000380871	NM_006167.3	112	Gcc/Acc	2/2	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.42127959662906	2		669	589	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508856	106508856	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376958957	NA	P-0059494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	112	717	0	ENST00000359195.3:c.850G>A	p.Glu284Lys	p.E284K	ENST00000359195	NM_002649.2	284	Gaa/Aaa	2/11	0.42127959662906	3	FACETS	0.965	0.869	1	0.483	0.434	0.533	CLONAL	1	TRUE	1	0.42127959662906	3		717	667	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52677355	52677355	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	40	440	0	ENST00000394830.3:c.904C>T	p.Pro302Ser	p.P302S	ENST00000394830	NM_018313.4	302	Cca/Tca	10/30	1	2	FACETS	0.369	0.306	0.44	0.369	0.306	0.44	SUBCLONAL	1	TRUE	1	0.42127959662906	2		440	514	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533099	63533099	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	28	609	0	ENST00000307078.5:c.1795del	p.Ala599ProfsTer90	p.A599Pfs*90	ENST00000307078	NM_004655.3	599	Gcc/cc	7/11	1	2	FACETS	0.328	0.262	0.404	0.328	0.262	0.404	SUBCLONAL	1	TRUE	1	0.42127959662906	2		609	405	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117645494	117645494	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs780534001	NA	P-0059494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	104	302	0	ENST00000368508.3:c.5641+1G>T		p.X1881_splice	ENST00000368508	NM_002944.2	1881			1	2	FACETS	0.909	0.817	1	0.909	0.817	1	CLONAL	1	TRUE	1	0.42127959662906	2		302	543	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743374	162743374	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1571321327	NA	P-0060341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	97	543	0	ENST00000367921.3:c.1844A>T	p.Asn615Ile	p.N615I	ENST00000367921	NM_006182.2	615	aAc/aTc	14/18	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.551079567182552	2		543	277	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021967	246021967	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	166	421	0	ENST00000388985.4:c.907G>T	p.Glu303Ter	p.E303*	ENST00000388985		303	Gag/Tag	10/12	0.394642899558663	5	FACETS	1	0.944	1			1	CLONAL	3	TRUE	NA	0.551079567182552	5		421	362	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649959	88649959	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	147	477	0	ENST00000372037.3:c.208G>T	p.Asp70Tyr	p.D70Y	ENST00000372037	NM_004329.2	70	Gat/Tat	4/13	0.551079567182552	10	FACETS	0.854	0.782	0.93			1	CLONAL	3	TRUE	NA	0.551079567182552	10		477	667	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8284889	8284889	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	95	523	0	ENST00000335790.3:c.21G>C	p.Glu7Asp	p.E7D	ENST00000335790	NM_002315.2	7	gaG/gaC	1/4	0.182274846040887	2	FACETS	0.766	0.696	0.837	0.766	0.696	0.837	INDETERMINATE	2	TRUE	0	0.551079567182552	2		523	225	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10789413	10789413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	61	515	0	ENST00000361367.2:c.1747C>T	p.Pro583Ser	p.P583S	ENST00000361367	NM_014633.3	583	Cct/Tct	14/25	0.182274846040887	2	FACETS	0.796	0.693	0.906	0.398	0.346	0.453	INDETERMINATE	1	TRUE	0	0.551079567182552	2		515	278	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999369	100999369	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	127	749	1	ENST00000325455.5:c.433C>A	p.Pro145Thr	p.P145T	ENST00000325455	NM_001202474.3	145	Ccc/Acc	1/8	0.182274846040887	2	FACETS	0.817	0.754	0.881	0.817	0.754	0.881	INDETERMINATE	2	TRUE	0	0.551079567182552	2		750	282	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566220	95566220	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs767112987	NA	P-0060341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	160	544	0	ENST00000393063.1:c.4103G>T	p.Arg1368Leu	p.R1368L	ENST00000393063	NM_030621.3	1368	cGc/cTc	23/28	0.350888774552991	5	FACETS	0.916	0.851	0.982	0.916	0.851	0.982	CLONAL	3	TRUE	2	0.551079567182552	5		544	386	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052726	42052726	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	68	422	0	ENST00000219905.7:c.7397G>T	p.Arg2466Leu	p.R2466L	ENST00000219905	NM_001164273.1	2466	cGa/cTa	20/24	0.552728633918814	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.551079567182552	1		422	144	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708587	43708587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199716902	NA	P-0060341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	118	620	0	ENST00000382044.4:c.4709C>T	p.Ser1570Phe	p.S1570F	ENST00000382044	NM_001141980.1	1570	tCt/tTt	22/28	0.552728633918814	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.551079567182552	1		620	209	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029314	14029314	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	107	667	0	ENST00000311895.7:c.1525G>T	p.Asp509Tyr	p.D509Y	ENST00000311895	NM_005236.2	509	Gat/Tat	8/11	0.552728633918814	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.551079567182552	1		667	200	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349250	89349250	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	131	609	0	ENST00000301030.4:c.3700A>G	p.Asn1234Asp	p.N1234D	ENST00000301030	NM_001256183.1	1234	Aat/Gat	9/13	0.552728633918814	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.551079567182552	1		609	234	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836608	89836608	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	120	644	0	ENST00000389301.3:c.2282T>C	p.Val761Ala	p.V761A	ENST00000389301	NM_000135.2	761	gTg/gCg	25/43	NA	2	FACETS	0.857	0.79	0.925			1	INDETERMINATE	2	TRUE	NA	0.551079567182552	2		644	254	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0060341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	242	697	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.552728633918814	3	FACETS	0.978	0.932	1	0.978	0.932	1	CLONAL	3	TRUE	0	0.551079567182552	3		697	382	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546086	29546086	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057518134	NA	P-0060341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	149	606	0	ENST00000356175.3:c.1591C>T	p.Gln531Ter	p.Q531*	ENST00000356175	NM_000267.3	531	Caa/Taa	14/57	0.552728633918814	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.551079567182552	1		606	281	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61324563	61324563	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	40	565	0	ENST00000283752.5:c.553C>A	p.Gln185Lys	p.Q185K	ENST00000283752	NM_006919.2	185	Cag/Aag	6/8	0.552728633918814	0	FACETS	0.795	0.689	0.901			1	CLONAL	1	TRUE	0	0.551079567182552	0		565	82	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285159	15285159	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	68	713	0	ENST00000263388.2:c.4456C>T	p.Gln1486Ter	p.Q1486*	ENST00000263388	NM_000435.2	1486	Cag/Tag	25/33	0.552728633918814	1	FACETS	0.698	0.615	0.786	0.698	0.615	0.786	SUBCLONAL	1	TRUE	0	0.551079567182552	1		713	256	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791480	42791480	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	252	738	0	ENST00000575354.2:c.461C>A	p.Ser154Tyr	p.S154Y	ENST00000575354	NM_015125.3	154	tCc/tAc	4/20	0.552728633918814	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.551079567182552	2		738	419	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719697	190719697	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	47	471	0	ENST00000441310.2:c.1699A>T	p.Ser567Cys	p.S567C	ENST00000441310	NM_000534.4	567	Agc/Tgc	9/13	0.282528853232725	3	FACETS	0.863	0.748	0.983	0.863	0.748	0.983	INDETERMINATE	2	TRUE	1	0.551079567182552	3		471	126	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62303948	62303948	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	119	627	0	ENST00000360203.5:c.739G>T	p.Val247Leu	p.V247L	ENST00000360203	NM_001283009.1	247	Gtg/Ttg	9/35	0.192478497210159	4	FACETS	0.898	0.819	0.98	0.898	0.819	0.98	INDETERMINATE	2	TRUE	2	0.551079567182552	4		627	373	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326953	62326953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	106	679	0	ENST00000360203.5:c.3772C>T	p.Pro1258Ser	p.P1258S	ENST00000360203	NM_001283009.1	1258	Cct/Tct	34/35	0.192478497210159	4	FACETS	0.765	0.691	0.842	0.765	0.691	0.842	INDETERMINATE	2	TRUE	2	0.551079567182552	4		679	390	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441289	52441289	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	155	856	0	ENST00000460680.1:c.481G>T	p.Ala161Ser	p.A161S	ENST00000460680	NM_004656.3	161	Gca/Tca	7/17	0.192478497210159	4	FACETS	0.876	0.808	0.946	0.876	0.808	0.946	INDETERMINATE	2	TRUE	2	0.551079567182552	4		856	498	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541611	187541611	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	125	802	0	ENST00000441802.2:c.6129G>T	p.Gln2043His	p.Q2043H	ENST00000441802	NM_005245.3	2043	caG/caT	10/27	0.436875803592143	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.551079567182552	1		802	276	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295247	1295247	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0060341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	32	497	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.556	0.454	0.668	0.556	0.454	0.668	SUBCLONAL	1	TRUE	1	0.551079567182552	2		497	209	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79966001	79966001	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	121	590	0	ENST00000265081.6:c.665A>T	p.Asn222Ile	p.N222I	ENST00000265081	NM_002439.4	222	aAc/aTc	4/24	0.552728633918814	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.551079567182552	2		590	201	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31238896	31238896	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	59	413	0	ENST00000376228.5:c.573G>A	p.Trp191Ter	p.W191*	ENST00000376228	NM_002117.5	191	tgG/tgA	3/8	0.461265500732747	5	FACETS	1	0.958	1	0.427	0.37	0.489	CLONAL	1	TRUE	2	0.551079567182552	5		413	305	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444288	50444288	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	80	672	0	ENST00000331340.3:c.218T>C	p.Met73Thr	p.M73T	ENST00000331340	NM_006060.4	73	aTg/aCg	4/8	0.552728633918814	1	FACETS	0.779	0.694	0.867	0.779	0.694	0.867	SUBCLONAL	1	TRUE	0	0.551079567182552	1		672	270	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124465305	124465306	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0060341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	27	416	0	ENST00000357628.3:c.1792_1792+1delinsTT		p.X598_splice	ENST00000357628	NM_015450.2	598		18/19	0.342945534365834	1	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	0	0.551079567182552	1		416	66	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21993396	21994238	+	splice_donor_variant,splice_donor_5th_base_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACTAAAATACTATCAGTTGGGATTTCTCAGGAACAGTTCTACAGTTCTGTCGTTTGCTAAACATACGAGCATTGTCCCGAGCAGTTTCAATCACTCAGGCCGCCGGACCTCTACCTCTAACTCACAAAGAAAGCCCATTTCCCTGTTGGCTGCAAAACTCCCCCAAGAAGCAAGTGCTTGCTCCTCGCAGCAGTAACTGATCCTACGATCCTTGTTAGCATTTCAGGAAGTCGCTGCCTGCGTGCCCCGTATCTCACGGGTCCTCCACTCTCCTGGAAGGTGGGAGAGGGTGACCCCGCCGGGAGGCTGGGGAGAAAAAAGGCCGCCTCCAGAAAACTTAGATGGTTAGCAATAATTCTCCCCAAGGAGAAAGAAAGTGTGCTTGAAATACACCTTTCCTACTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTCTTAGTCATTCCCACCCAGGATATTCGGGACTCACTGACTTCTGAGGTGGGTTTAGAAGCTCTGTTCGCCTCAGTTTCCCACGATTGAGGGGCTGTGTGAAGGGAGGTCCAGGTTCAATGGTACTGCGAGAACCACATGTCTAAGTCGTTGTAACCCGAATGGGGAAGCCTCCACCGGCGGTTATCTCCTCCTCCTCCTAGCCTGGGCTAGAGACGAATTATCTGTTTACGAAATCACACCAAACAAAACAAGTGCCGAATGCGCCCCGGACTTTTCGAGGGCCTTTCCTACCTGGTCTTCTAGGAAGCGGCTGCTGCCCTAGACGCTGGCTCCTCAGTAGCATCAGCACGAGGGCCACAGCGGCGGGCGCCCCTGGCGCTGCCCACTCCCCC	GACTAAAATACTATCAGTTGGGATTTCTCAGGAACAGTTCTACAGTTCTGTCGTTTGCTAAACATACGAGCATTGTCCCGAGCAGTTTCAATCACTCAGGCCGCCGGACCTCTACCTCTAACTCACAAAGAAAGCCCATTTCCCTGTTGGCTGCAAAACTCCCCCAAGAAGCAAGTGCTTGCTCCTCGCAGCAGTAACTGATCCTACGATCCTTGTTAGCATTTCAGGAAGTCGCTGCCTGCGTGCCCCGTATCTCACGGGTCCTCCACTCTCCTGGAAGGTGGGAGAGGGTGACCCCGCCGGGAGGCTGGGGAGAAAAAAGGCCGCCTCCAGAAAACTTAGATGGTTAGCAATAATTCTCCCCAAGGAGAAAGAAAGTGTGCTTGAAATACACCTTTCCTACTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTCTTAGTCATTCCCACCCAGGATATTCGGGACTCACTGACTTCTGAGGTGGGTTTAGAAGCTCTGTTCGCCTCAGTTTCCCACGATTGAGGGGCTGTGTGAAGGGAGGTCCAGGTTCAATGGTACTGCGAGAACCACATGTCTAAGTCGTTGTAACCCGAATGGGGAAGCCTCCACCGGCGGTTATCTCCTCCTCCTCCTAGCCTGGGCTAGAGACGAATTATCTGTTTACGAAATCACACCAAACAAAACAAGTGCCGAATGCGCCCCGGACTTTTCGAGGGCCTTTCCTACCTGGTCTTCTAGGAAGCGGCTGCTGCCCTAGACGCTGGCTCCTCAGTAGCATCAGCACGAGGGCCACAGCGGCGGGCGCCCCTGGCGCTGCCCACTCCCCC	-	novel	NA	P-0060341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1	85	0	0	ENST00000579755.1:c.93_193+742del		p.X31_splice	ENST00000579755		31		1/3	0.435146555507977				NA	1				NA	5	TRUE	1	0.551079567182552	3		0	86	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937149	39937149	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	121	296	0	ENST00000378444.4:c.34C>G	p.His12Asp	p.H12D	ENST00000378444	NM_001123385.1	12	Cac/Gac	2/15	0.277927241151876	2	FACETS	0.856	0.805	0.905			1	INDETERMINATE	3	TRUE	NA	0.551079567182552	2		296	171	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861591	152861591	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	134	359	0	ENST00000406277.2:c.161A>T	p.His54Leu	p.H54L	ENST00000406277	NM_152274.4	54	cAt/cTt	4/7	1		FACETS		0.828	0.932				CLONAL	2	TRUE	0	0.551079567182552	1		359	200	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060822-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	131	523	0				ENST00000310581	NM_198253.2	-/1132			0.262337785739145	3	FACETS	1	0.985	1	0.741	0.673	0.813	CLONAL	1	FALSE	1	0.262337785739145	3		523	762	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0060822-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	141	764	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.262337785739145	3	FACETS	1	0.954	1	0.539	0.489	0.59	CLONAL	1	FALSE	1	0.262337785739145	3		764	1129	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593519	48593519	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060822-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	103	385	0	ENST00000342988.3:c.1270G>C	p.Asp424His	p.D424H	ENST00000342988	NM_005359.5	424	Gat/Cat	10/12	0.223269372869234	3	FACETS	1	0.982	1	0.741	0.665	0.822	CLONAL	1	FALSE	1	0.262337785739145	3		385	599	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461576	138461576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060822-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	25	377	0	ENST00000289153.2:c.445C>T	p.Arg149Ter	p.R149*	ENST00000289153	NM_006219.2	149	Cga/Tga	3/22	NA	2	FACETS	0.424	0.334	0.529			1	INDETERMINATE	1	FALSE	NA	0.262337785739145	2		377	449	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982095	201982096	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0060822-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	370	696	0	ENST00000359651.3:c.622dup	p.His208ProfsTer9	p.H208Pfs*9	ENST00000359651		207	tcc/tCcc	5/8	0.262337785739145	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	FALSE	0	0.262337785739145	3		696	978	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938435	44938435	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060822-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	59	155	0	ENST00000377967.4:c.2983G>T	p.Glu995Ter	p.E995*	ENST00000377967	NM_021140.2	995	Gaa/Taa	20/29	0.174222136756968	2	FACETS	0.961	0.837	1			1	CLONAL	2	FALSE	NA	0.262337785739145	2		155	234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578410	7578411	+	inframe_insertion	In_Frame_Ins	INS	-	-	TAC	novel	NA	P-0060822-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	218	675	0	ENST00000269305.4:c.519_520insGTA	p.Val173dup	p.V173dup	ENST00000269305	NM_001126112.2	173	-/GTA	5/11	0.262337785739145	3	FACETS	0.82	0.761	0.88	0.82	0.761	0.88	CLONAL	2	FALSE	1	0.262337785739145	3		675	1147	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222229	53222229	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060822-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	205	345	0	ENST00000375401.3:c.4603G>T	p.Gly1535Cys	p.G1535C	ENST00000375401	NM_004187.3	1535	Ggc/Tgc	26/26	0.174222136756968	2	FACETS	0.895	0.836	0.955			1	CLONAL	3	FALSE	NA	0.262337785739145	2		345	582	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0060881-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	16	210	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.26889840694504	3	FACETS	0.446	0.329	0.586	0.223	0.164	0.293	SUBCLONAL	1	TRUE	1	0.26	3		210	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0060881-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	34	552	0	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	1	2	FACETS	0.417	0.34	0.505	0.417	0.34	0.505	SUBCLONAL	1	TRUE	1	0.26	2		552	627	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969442	44969442	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060881-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	34	508	0	ENST00000377967.4:c.4124T>C	p.Leu1375Pro	p.L1375P	ENST00000377967	NM_021140.2	1375	cTa/cCa	28/29	1	2	FACETS	0.485	0.396	0.586	0.485	0.396	0.586	SUBCLONAL	1	TRUE	1	0.26	2		508	539	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220604	1220604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555738372	NA	P-0060881-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	48	764	0	ENST00000326873.7:c.622G>A	p.Asp208Asn	p.D208N	ENST00000326873	NM_000455.4	208	Gac/Aac	5/10	1	2	FACETS	0.534	0.45	0.626	0.534	0.45	0.626	SUBCLONAL	1	TRUE	1	0.26	2		764	692	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438619	49438619	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1186385716	NA	P-0060881-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	41	693	2	ENST00000301067.7:c.4871C>T	p.Ala1624Val	p.A1624V	ENST00000301067	NM_003482.3	1624	gCa/gTa	19/54	1	2	FACETS	0.444	0.368	0.528	0.444	0.368	0.528	SUBCLONAL	1	TRUE	1	0.26	2		695	711	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242014	105242014	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060881-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	36	691	0	ENST00000349310.3:c.410C>T	p.Ser137Phe	p.S137F	ENST00000349310	NM_001014432.1	137	tCc/tTc	6/15	1	2	FACETS	0.388	0.318	0.467	0.388	0.318	0.467	SUBCLONAL	1	TRUE	1	0.26	2		691	714	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372320	55372320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060891-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	126	612	0	ENST00000297316.4:c.1010C>T	p.Pro337Leu	p.P337L	ENST00000297316	NM_022454.3	337	cCg/cTg	2/2	0.419630789918974	4	FACETS	1	0.962	1	0.373	0.338	0.41	CLONAL	1	TRUE	1	0.419630789918974	4		612	762	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587782197	NA	P-0060891-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	232	460	1	ENST00000269305.4:c.434T>A	p.Leu145Gln	p.L145Q	ENST00000269305	NM_001126112.2	145	cTg/cAg	5/11	0.419630789918974	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.419630789918974	2		461	538	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411719	63411719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060891-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	30	234	0	ENST00000330258.3:c.1448C>T	p.Ser483Leu	p.S483L	ENST00000330258	NM_152424.3	483	tCa/tTa	2/2	0.216141769478925	3	FACETS	0.553	0.446	0.673			1	INDETERMINATE	1	TRUE	NA	0.419630789918974	3		234	313	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187719	11187719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767904339	NA	P-0060891-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	70	377	0	ENST00000361445.4:c.6178C>T	p.Arg2060Trp	p.R2060W	ENST00000361445	NM_004958.3	2060	Cgg/Tgg	44/58	0.320707163414585	3	FACETS	0.827	0.723	0.939	0.414	0.361	0.47	CLONAL	1	TRUE	1	0.419630789918974	3		377	488	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33680085	33680085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771227424	NA	P-0060891-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	51	200	0	ENST00000308377.4:c.1996G>A	p.Val666Ile	p.V666I	ENST00000308377	NM_152270.3	666	Gtc/Atc	5/5	0.221149991503006	5	FACETS	0.792	0.679	0.913	0.528	0.453	0.609	INDETERMINATE	2	TRUE	2	0.419630789918974	5		200	250	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461497	138461497	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060891-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	27	263	0	ENST00000289153.2:c.524C>G	p.Thr175Arg	p.T175R	ENST00000289153	NM_006219.2	175	aCa/aGa	3/22	0.359914353600713	3	FACETS	0.362	0.288	0.447	0.181	0.144	0.224	SUBCLONAL	1	TRUE	1	0.419630789918974	3		263	430	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549305	187549308	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TACC	TACC	-	novel	NA	P-0060891-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	77	303	0	ENST00000441802.2:c.4810_4810+3del		p.X1604_splice	ENST00000441802	NM_005245.3	1604		9/27	0.382423860279736	2	FACETS	0.836	0.737	0.942	0.418	0.368	0.471	CLONAL	1	TRUE	0	0.419630789918974	2		303	439	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061028-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	75	547	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.399773021060539	2	FACETS	1	0.959	1	0.599	0.529	0.672	CLONAL	1	TRUE	0	0.399052348938771	2		547	314	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0061028-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	61	482	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.399773021060539	3	FACETS	0.924	0.8	1	0.462	0.4	0.529	CLONAL	1	TRUE	1	0.399052348938771	3		482	397	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0061028-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	114	251	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	0.399773021060539	4	FACETS	0.892	0.823	0.961	1	0.979	1	CLONAL	4	TRUE	1	0.399052348938771	4		251	224	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448309	56448309	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781449421	NA	P-0061028-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	87	367	0	ENST00000407977.2:c.338G>A	p.Arg113Gln	p.R113Q	ENST00000407977		113	cGa/cAa	3/10	0.399773021060539	5	FACETS	0.842	0.75	0.939	0.561	0.5	0.626	CLONAL	2	TRUE	2	0.399052348938771	5		367	414	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052659	42052659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061028-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	64	372	0	ENST00000219905.7:c.7330G>A	p.Glu2444Lys	p.E2444K	ENST00000219905	NM_001164273.1	2444	Gag/Aag	20/24	0.399773021060539	4	FACETS	1	0.949	1	0.594	0.516	0.677	CLONAL	1	TRUE	2	0.399052348938771	4		372	378	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717695	89717696	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0061028-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	53	382	0	ENST00000371953.3:c.722_723dup	p.Glu242LeufsTer15	p.E242Lfs*15	ENST00000371953	NM_000314.4	240	-/TT	7/9	0.309442949274814	3	FACETS	0.895	0.777	1	0.597	0.518	0.68	CLONAL	2	TRUE	0	0.399052348938771	3		382	178	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129785	108129785	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587778067	NA	P-0061028-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	38	229	0	ENST00000278616.4:c.2449G>C	p.Asp817His	p.D817H	ENST00000278616	NM_000051.3	817	Gat/Cat	16/63	0.309442949274814	3	FACETS	1	0.947	1	0.453	0.38	0.533	CLONAL	1	TRUE	0	0.399052348938771	3		229	168	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169787	11169787	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0061028-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	55	139	0	ENST00000361445.4:c.7367-1G>C		p.X2456_splice	ENST00000361445	NM_004958.3	2456			0.399052348938771	9	FACETS	0.903	0.78	1			1	CLONAL	3	TRUE	NA	0.399052348938771	9		139	244	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406606	70406606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061028-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	79	435	0	ENST00000373644.4:c.4120G>A	p.Glu1374Lys	p.E1374K	ENST00000373644	NM_030625.2	1374	Gaa/Aaa	4/12	0.399052348938771	6	FACETS	0.804	0.71	0.903	0.536	0.473	0.602	CLONAL	2	TRUE	3	0.399052348938771	6		435	443	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68292285	68292285	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061028-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	56	297	0	ENST00000487270.1:c.189G>C	p.Lys63Asn	p.K63N	ENST00000487270	NM_133509.3	63	aaG/aaC	3/11	0.399773021060539	4	FACETS	1	0.928	1	0.563	0.484	0.647	CLONAL	1	TRUE	2	0.399052348938771	4		297	349	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481616	40481616	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061028-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	144	290	0	ENST00000264657.5:c.1189G>C	p.Glu397Gln	p.E397Q	ENST00000264657	NM_139276.2	397	Gaa/Caa	13/24	0.399052348938771	7	FACETS	0.91	0.839	0.983	0.91	0.839	0.983	CLONAL	4	TRUE	3	0.399052348938771	7		290	396	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38184274	38184274	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061028-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1791	737	381	0	ENST00000317025.8:c.1682C>T	p.Ser561Phe	p.S561F	ENST00000317025	NM_023034.1	561	tCt/tTt	7/24	0.399052348938771	50	FACETS	1	0.982	1			1	CLONAL	15	TRUE	NA	0.399052348938771	50		381	2528	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0061077-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	14	210	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.438	0.316	0.584	0.438	0.316	0.584	SUBCLONAL	1	TRUE	1	0.288284489782257	2		210	222	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0061077-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	112	493	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	0.288284489782257	3	FACETS	0.863	0.78	0.951	0.575	0.52	0.634	CLONAL	2	TRUE	0	0.288284489782257	3		493	515	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0061077-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	78	818	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.721	0.633	0.815	0.721	0.633	0.815	SUBCLONAL	1	TRUE	1	0.288284489782257	2		818	751	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0061077-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	12	699	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	1	2	FACETS	0.14	0.097	0.192	0.14	0.097	0.192	SUBCLONAL	1	TRUE	1	0.288284489782257	2		699	596	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457408	67457408	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061077-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	120	865	0	ENST00000327367.4:c.382C>T	p.Gln128Ter	p.Q128*	ENST00000327367	NM_005902.3	128	Cag/Tag	2/9	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.288284489782257	2		865	687	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708581	43708582	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0061077-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	114	708	1	ENST00000382044.4:c.4714dup	p.Glu1572GlyfsTer7	p.E1572Gfs*7	ENST00000382044	NM_001141980.1	1572	gaa/gGaa	22/28	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.288284489782257	2		709	544	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850290	128850292	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs758836898	NA	P-0061077-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	99	575	0	ENST00000249373.3:c.1556_1558del	p.Lys519del	p.K519del	ENST00000249373	NM_005631.4	518	gAGAag/gag	9/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.288284489782257	2		575	533	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254933	16254941	+	inframe_deletion	In_Frame_Del	DEL	GTCCACAGA	GTCCACAGA	-	novel	NA	P-0061077-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	58	732	0	ENST00000375759.3:c.2202_2210del	p.Gln735_Pro737del	p.Q735_P737del	ENST00000375759	NM_015001.2	733	cGTCCACAGAgt/cgt	11/15	0.159894701780804	1	FACETS	0.617	0.53	0.712	0.617	0.53	0.712	INDETERMINATE	1	TRUE	0	0.288284489782257	1		732	558	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772264	68772264	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061077-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	64	804	0	ENST00000261769.5:c.113del	p.Thr38SerfsTer18	p.T38Sfs*18	ENST00000261769	NM_004360.3	38	aCg/ag	2/16	1	2	FACETS	0.904	0.785	1	0.904	0.785	1	CLONAL	1	TRUE	1	0.288284489782257	2		804	491	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295508	1295508	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0061077-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	38	1008	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.432	0.356	0.517	0.432	0.356	0.517	SUBCLONAL	1	TRUE	1	0.288284489782257	2		1008	610	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0061090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	58	210	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.883	0.765	1	0.883	0.765	1	CLONAL	1	TRUE	1	0.46093271312263	2		210	285	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	98	523	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.773	0.692	0.859	0.773	0.692	0.859	SUBCLONAL	1	TRUE	1	0.46093271312263	2		523	550	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462205	120462211	+	frameshift_variant	Frame_Shift_Del	DEL	GAGAGAA	GAGAGAA	-	novel	NA	P-0061090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	50	449	0	ENST00000256646.2:c.5505_5511del	p.Ser1836GlufsTer7	p.S1836Efs*7	ENST00000256646	NM_024408.3	1835	gcTTCTCTC/gc	31/34	1	2	FACETS	0.377	0.319	0.44	0.377	0.319	0.44	SUBCLONAL	1	TRUE	1	0.46093271312263	2		449	576	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120469225	120469225	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	55	404	0	ENST00000256646.2:c.3902G>T	p.Cys1301Phe	p.C1301F	ENST00000256646	NM_024408.3	1301	tGt/tTt	24/34	1	2	FACETS	0.419	0.358	0.485	0.419	0.358	0.485	SUBCLONAL	1	TRUE	1	0.46093271312263	2		404	570	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0061090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	16	501	0	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	1	2	FACETS	0.127	0.093	0.167	0.127	0.093	0.167	SUBCLONAL	1	TRUE	1	0.46093271312263	2		501	548	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894230	NA	P-0061090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	60	502	0	ENST00000451590.1:c.35G>A	p.Gly12Asp	p.G12D	ENST00000451590	NM_001130442.1	12	gGc/gAc	2/5	1	2	FACETS	0.47	0.405	0.541	0.47	0.405	0.541	SUBCLONAL	1	TRUE	1	0.46093271312263	2		502	554	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336064	73336064	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	54	381	0	ENST00000377767.4:c.2339G>C	p.Arg780Thr	p.R780T	ENST00000377767	NM_014953.3	780	aGa/aCa	17/21	1	2	FACETS	0.449	0.383	0.52	0.449	0.383	0.52	SUBCLONAL	1	TRUE	1	0.46093271312263	2		381	522	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243630	41243630	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786202068	NA	P-0061090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	40	516	0	ENST00000357654.3:c.3918G>C	p.Leu1306Phe	p.L1306F	ENST00000357654	NM_007294.3	1306	ttG/ttC	10/23	1	2	FACETS	0.278	0.23	0.332	0.278	0.23	0.332	SUBCLONAL	1	TRUE	1	0.46093271312263	2		516	624	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599882	10599882	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	50	488	0	ENST00000171111.5:c.1694G>C	p.Arg565Thr	p.R565T	ENST00000171111	NM_203500.1	565	aGa/aCa	5/6	1	2	FACETS	0.349	0.295	0.408	0.349	0.295	0.408	SUBCLONAL	1	TRUE	1	0.46093271312263	2		488	622	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0061090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	33	428	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	1	2	FACETS	0.279	0.226	0.338	0.279	0.226	0.338	SUBCLONAL	1	TRUE	1	0.46093271312263	2		428	514	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149961	202149962	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs587776665	NA	P-0061090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	58	561	0	ENST00000358485.4:c.1405_1406del	p.Val469PhefsTer28	p.V469Ffs*28	ENST00000358485	NM_001080125.1	468	TGt/t	8/9	1	2	FACETS	0.378	0.325	0.437	0.378	0.325	0.437	SUBCLONAL	1	TRUE	1	0.46093271312263	2		561	665	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151181	202151181	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs1354563506	NA	P-0061090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	25	352	0	ENST00000358485.4:c.1482-1G>C		p.X494_splice	ENST00000358485	NM_001080125.1	494			1	2	FACETS	0.247	0.194	0.308	0.247	0.194	0.308	SUBCLONAL	1	TRUE	1	0.46093271312263	2		352	439	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413009	49413009	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519953	NA	P-0061090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	28	415	0	ENST00000418115.1:c.14G>T	p.Arg5Leu	p.R5L	ENST00000418115	NM_001664.2	5	cGg/cTg	2/5	1	2	FACETS	0.248	0.198	0.306	0.248	0.198	0.306	SUBCLONAL	1	TRUE	1	0.46093271312263	2		415	489	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0061090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	36	404	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	0.28	0.23	0.337	0.28	0.23	0.337	SUBCLONAL	1	TRUE	1	0.46093271312263	2		404	557	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525110	187525110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	38	385	1	ENST00000441802.2:c.10570C>T	p.Gln3524Ter	p.Q3524*	ENST00000441802	NM_005245.3	3524	Cag/Tag	19/27	1	2	FACETS	0.338	0.279	0.404	0.338	0.279	0.404	SUBCLONAL	1	TRUE	1	0.46093271312263	2		386	488	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323238	31323238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	112	448	0	ENST00000412585.2:c.751G>A	p.Asp251Asn	p.D251N	ENST00000412585	NM_005514.6	251	Gac/Aac	4/8	1	2	FACETS	0.968	0.875	1	0.968	0.875	1	CLONAL	1	TRUE	1	0.46093271312263	2		448	502	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323253	31323253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45445194	NA	P-0061090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	87	338	0	ENST00000412585.2:c.736G>A	p.Glu246Lys	p.E246K	ENST00000412585	NM_005514.6	246	Gag/Aag	4/8	1	2	FACETS	0.97	0.865	1	0.97	0.865	1	CLONAL	1	TRUE	1	0.46093271312263	2		338	389	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413070	63413070	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	44	513	0	ENST00000330258.3:c.97G>A	p.Ala33Thr	p.A33T	ENST00000330258	NM_152424.3	33	Gca/Aca	2/2	1	2	FACETS	0.32	0.268	0.378	0.32	0.268	0.378	SUBCLONAL	1	TRUE	1	0.46093271312263	2		513	597	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187368	32187368	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0061220-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	75	595	0	ENST00000375023.3:c.1510+1G>T		p.X504_splice	ENST00000375023	NM_004557.3	504			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		595	683	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987208	2987208	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0061220-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	52	413	0	ENST00000396946.4:c.220+1G>T		p.X74_splice	ENST00000396946	NM_032415.4	74			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		413	632	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0061333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	150	600	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.515821770747216	2		600	486	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207009	1207009	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	194	622	0	ENST00000326873.7:c.97G>T	p.Glu33Ter	p.E33*	ENST00000326873	NM_000455.4	33	Gag/Tag	1/10	0.506544213720347	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.515821770747216	1		622	545	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1688714	1688714	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	81	554	0	ENST00000378625.1:c.611G>T	p.Trp204Leu	p.W204L	ENST00000378625	NM_001198994.1	204	tGg/tTg	6/14	0.271106873814924	0	FACETS	0.33	0.291	0.371			1	INDETERMINATE	1	TRUE	0	0.515821770747216	0		554	461	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798120	45798120	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	152	747	0	ENST00000450313.1:c.731G>T	p.Cys244Phe	p.C244F	ENST00000450313	NM_012222.2	244	tGc/tTc	9/16	0.394251927788121	1	FACETS	0.758	0.696	0.822	0.758	0.696	0.822	SUBCLONAL	1	TRUE	0	0.515821770747216	1		747	577	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119470	193119470	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	132	487	0	ENST00000367435.3:c.865G>T	p.Ala289Ser	p.A289S	ENST00000367435	NM_024529.4	289	Gcc/Tcc	9/17	0.27739285260183	2	FACETS	0.929	0.847	1	0.464	0.423	0.507	INDETERMINATE	1	TRUE	0	0.515821770747216	2		487	551	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120806019	120806019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	180	706	0	ENST00000257552.2:c.158G>T	p.Arg53Leu	p.R53L	ENST00000257552	NM_002442.3	53	cGg/cTg	3/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.515821770747216	2		706	667	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588647	28588647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	132	547	0	ENST00000241453.7:c.2801C>T	p.Pro934Leu	p.P934L	ENST00000241453	NM_004119.2	934	cCa/cTa	23/24	1	2	FACETS	0.917	0.836	1	0.917	0.836	1	CLONAL	1	TRUE	1	0.515821770747216	2		547	558	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001456	29001456	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0061333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	135	425	0	ENST00000282397.4:c.1277-1G>C		p.X426_splice	ENST00000282397	NM_002019.4	426			1	2	FACETS	0.989	0.904	1	0.989	0.904	1	CLONAL	1	TRUE	1	0.515821770747216	2		425	529	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349395	73349395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	130	511	0	ENST00000377767.4:c.941G>A	p.Gly314Asp	p.G314D	ENST00000377767	NM_014953.3	314	gGt/gAt	6/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.515821770747216	2		511	462	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420329	88420329	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	127	558	0	ENST00000360948.2:c.2357del	p.Gly786ValfsTer30	p.G786Vfs*30	ENST00000360948	NM_001012338.2	786	gGt/gt	19/19	0.443898826458804	1	FACETS	0.738	0.673	0.806	0.738	0.673	0.806	SUBCLONAL	1	TRUE	0	0.515821770747216	1		558	495	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805753	46805753	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	166	690	0	ENST00000290295.7:c.203G>A	p.Gly68Glu	p.G68E	ENST00000290295	NM_006361.5	68	gGg/gAg	1/2	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.515821770747216	2		690	624	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440903	56440903	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs151209912	NA	P-0061333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	169	694	0	ENST00000407977.2:c.434G>T	p.Arg145Leu	p.R145L	ENST00000407977		145	cGa/cTa	4/10	1	2	FACETS	0.966	0.891	1	0.966	0.891	1	CLONAL	1	TRUE	1	0.515821770747216	2		694	678	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610431	10610432	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0061333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	176	747	0	ENST00000171111.5:c.278_279del	p.Phe93TyrfsTer33	p.F93Yfs*33	ENST00000171111	NM_203500.1	93	tTC/t	2/6	0.489923974193224	1	FACETS	0.961	0.892	1	0.961	0.892	1	CLONAL	1	TRUE	0	0.515821770747216	1		747	527	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416388	29416388	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs771352312	NA	P-0061333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	79	675	0	ENST00000389048.3:c.4565T>G	p.Ile1522Arg	p.I1522R	ENST00000389048	NM_004304.4	1522	aTa/aGa	29/29	0.305782454499304	2	FACETS	0.525	0.462	0.593	0.263	0.231	0.297	INDETERMINATE	1	TRUE	0	0.515821770747216	2		675	583	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67632049	67632049	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	52	441	0	ENST00000272342.5:c.2235T>G	p.Cys745Trp	p.C745W	ENST00000272342	NM_019002.3	745	tgT/tgG	5/6	NA	2	FACETS	0.457	0.39	0.531			1	INDETERMINATE	1	TRUE	NA	0.515821770747216	2		441	441	SUCCESS
ATR	545	MSKCC	GRCh37	3	142222253	142222253	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	60	327	0	ENST00000350721.4:c.5239G>T	p.Gly1747Cys	p.G1747C	ENST00000350721	NM_001184.3	1747	Ggt/Tgt	30/47	0.398747158476738	1	FACETS	0.541	0.469	0.618	0.541	0.469	0.618	SUBCLONAL	1	TRUE	0	0.515821770747216	1		327	319	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851522	128851522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	148	559	2	ENST00000249373.3:c.1847C>T	p.Ser616Phe	p.S616F	ENST00000249373	NM_005631.4	616	tCt/tTt	11/12	1	2	FACETS	0.974	0.894	1	0.974	0.894	1	CLONAL	1	TRUE	1	0.515821770747216	2		561	589	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066928	30066928	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	105	430	0	ENST00000331968.5:c.2203G>T	p.Gly735Ter	p.G735*	ENST00000331968	NM_002742.2	735	Gga/Tga	16/18	NA	2	FACETS	0.917	0.827	1			1	INDETERMINATE	1	TRUE	NA	0.515821770747216	2		430	444	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17355171	17355171	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	95	540	0	ENST00000375499.3:c.347G>T	p.Arg116Met	p.R116M	ENST00000375499	NM_003000.2	116	aGg/aTg	4/8	0.271106873814924	0	FACETS	0.338	0.302	0.377			1	INDETERMINATE	1	TRUE	0	0.515821770747216	0		540	527	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434595	49434595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	69	722	1	ENST00000301067.7:c.6958G>A	p.Glu2320Lys	p.E2320K	ENST00000301067	NM_003482.3	2320	Gag/Aag	31/54	0.249445456842253	3	FACETS	0.477	0.415	0.545	0.239	0.207	0.273	INDETERMINATE	1	TRUE	1	0.515821770747216	3		723	705	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900140	101900140	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0061333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	85	300	0	ENST00000374994.4:c.575-1G>T		p.X192_splice	ENST00000374994	NM_004612.2	192			0.515821770747216	1	FACETS	0.889	0.796	0.986	0.889	0.796	0.986	CLONAL	1	TRUE	0	0.515821770747216	1		300	275	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763833	76763833	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	23	457	0	ENST00000373344.5:c.7475T>A	p.Met2492Lys	p.M2492K	ENST00000373344	NM_000489.3	2492	aTg/aAg	35/35	0.379019300877796	0	FACETS	0.143	0.112	0.18			1	SUBCLONAL	1	TRUE	0	0.515821770747216	0		457	301	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63898340	63898377	+	frameshift_variant	Frame_Shift_Del	DEL	AGCAGCGGCCGCGGCCGCCCGGCAGCAGCAGCAGCAGC	AGCAGCGGCCGCGGCCGCCCGGCAGCAGCAGCAGCAGC	-	novel	NA	P-0061333-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	79	602	0	ENST00000398590.3:c.72_109del	p.Arg29AlafsTer47	p.R29Afs*47	ENST00000398590	NM_001177387.1	22	ggAGCAGCGGCCGCGGCCGCCCGGCAGCAGCAGCAGCAGCag/ggag	3/14	0.394251927788121	1	FACETS	0.475	0.418	0.534	0.475	0.418	0.534	SUBCLONAL	1	TRUE	0	0.515821770747216	1		602	479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0061422-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	249	662	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.57585766136318	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.590266267555575	2		662	420	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136153	11136153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061422-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	92	402	2	ENST00000358026.2:c.3137G>A	p.Cys1046Tyr	p.C1046Y	ENST00000358026	NM_001128849.1	1046	tGc/tAc	22/36	0.590266267555575	3	FACETS	0.926	0.827	1	0.463	0.413	0.515	CLONAL	1	TRUE	1	0.590266267555575	3		404	436	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981316	68981316	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061422-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	135	225	0	ENST00000288368.4:c.1388G>T	p.Arg463Leu	p.R463L	ENST00000288368	NM_024870.2	463	cGc/cTc	12/40	0.590266267555575	9	FACETS	0.954	0.868	1	0.382	0.347	0.418	CLONAL	2	TRUE	4	0.590266267555575	9		225	735	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50774049	50774049	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061422-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	126	513	0	ENST00000307179.4:c.1590T>A	p.Ser530Arg	p.S530R	ENST00000307179		530	agT/agA	11/20	0.590266267555575	3	FACETS	0.982	0.893	1	0.491	0.446	0.538	CLONAL	1	TRUE	1	0.590266267555575	3		513	563	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0061570-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	86	331	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.284785683948031	3	FACETS	0.918	0.817	1	0.918	0.817	1	CLONAL	2	TRUE	1	0.284785683948031	3		331	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0061570-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	198	619	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.284785683948031	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.284785683948031	2		619	630	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976857	55976857	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151317075	NA	P-0061570-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	147	611	0	ENST00000263923.4:c.1055C>T	p.Ala352Val	p.A352V	ENST00000263923	NM_002253.2	352	gCg/gTg	8/30	0.284785683948031	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.284785683948031	2		611	486	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974780	21974780	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs864622263	NA	P-0061570-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	140	678	0	ENST00000304494.5:c.47T>A	p.Leu16Gln	p.L16Q	ENST00000304494	NM_000077.4	16	cTg/cAg	1/3	0.284785683948031	1	FACETS	0.771	0.705	0.839	1	0.988	1	SUBCLONAL	2	TRUE	0	0.284785683948031	1		678	547	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0061677-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	37	591	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	1	2	FACETS	0.448	0.368	0.538	0.448	0.368	0.538	SUBCLONAL	1	TRUE	1	0.25	2		591	661	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453124	140453136	+	protein_altering_variant	In_Frame_Del	DEL	CATCGAGATTTCA	CATCGAGATTTCA	T	novel	NA	P-0061677-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	30	500	0	ENST00000288602.6:c.1799_1811delinsA	p.Val600_Trp604delinsGlu	p.V600_W604delinsE	ENST00000288602	NM_004333.4	600	gTGAAATCTCGATGg/gAg	15/18	1	2	FACETS	0.405	0.325	0.496	0.405	0.325	0.496	SUBCLONAL	1	TRUE	1	0.25	2		500	593	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295803	212295803	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061677-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	31	452	0	ENST00000342788.4:c.2510G>C	p.Arg837Thr	p.R837T	ENST00000342788	NM_005235.2	837	aGa/aCa	21/28	1	2	FACETS	0.493	0.398	0.601	0.493	0.398	0.601	SUBCLONAL	1	TRUE	1	0.25	2		452	503	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0061733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	136	448	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.18112222410899	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		448	386	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56377284	56377284	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	54	412	0	ENST00000348428.3:c.905A>G	p.Lys302Arg	p.K302R	ENST00000348428	NM_006785.3	302	aAg/aGg	6/17	0.233650876701869	4	FACETS	0.937	0.814	1	0.937	0.814	1	INDETERMINATE	2	TRUE	2	0.438398359604061	4		412	189	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244980	133244980	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115225325	NA	P-0061837-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	159	601	0	ENST00000320574.5:c.2135G>A	p.Arg712His	p.R712H	ENST00000320574	NM_006231.2	712	cGc/cAc	19/49	0.930861327084463	3	FACETS	0.88	0.812	0.952	0.44	0.406	0.476	CLONAL	1	TRUE	1	0.949439289797478	3		601	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0121494-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	41	525	0	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	0.159124712861991	3	FACETS	0.465	0.386	0.554	0.233	0.193	0.277	INDETERMINATE	1	NA	1	0.27	3		525	741	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922925	39922965	+	frameshift_variant	Frame_Shift_Del	DEL	CCTTTTCCTGCCAGGTTTCTCTTCAGTGATGTTAGTCCCCT	CCTTTTCCTGCCAGGTTTCTCTTCAGTGATGTTAGTCCCCT	AGGAAA	novel	NA	P-0121494-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	52	570	1	ENST00000378444.4:c.3743_3783delinsTTTCCT	p.Gln1248LeufsTer17	p.Q1248Lfs*17	ENST00000378444	NM_001123385.1	1248	cAGGGGACTAACATCACTGAAGAGAAACCTGGCAGGAAAAGG/cTTTCCT	8/15	1	2	FACETS	0.5	0.425	0.583	0.5	0.425	0.583	SUBCLONAL	1	NA	1	0.27	2		571	770	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289668	33289668	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	320	400	0	ENST00000374542.5:c.35A>G	p.Asp12Gly	p.D12G	ENST00000374542	NM_001141970.1	12	gAt/gGt	2/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.92	2		400	693	SUCCESS
APC	324	MSKCC	GRCh37	5	112175096	112175097	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs786203760	NA	P-0062047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	60	359	0	ENST00000257430.4:c.3807_3808del	p.Ile1269MetfsTer6	p.I1269Mfs*6	ENST00000257430	NM_000038.5	1269	ATa/a	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		359	495	SUCCESS
APC	324	MSKCC	GRCh37	5	112173387	112173387	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1060503336	NA	P-0062047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	32	415	0	ENST00000257430.4:c.2096G>A	p.Trp699Ter	p.W699*	ENST00000257430	NM_000038.5	699	tGg/tAg	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		415	620	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149245756	149245756	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	42	330	0	ENST00000360632.3:c.772G>A	p.Glu258Lys	p.E258K	ENST00000360632	NM_015472.4	258	Gaa/Aaa	5/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		330	585	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235269	235269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758817818	NA	P-0062047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	39	261	0	ENST00000264932.6:c.1075C>T	p.Pro359Ser	p.P359S	ENST00000264932	NM_004168.2	359	Cct/Tct	9/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		261	343	SUCCESS
APC	324	MSKCC	GRCh37	5	112175697	112175697	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	102	456	0	ENST00000257430.4:c.4407del	p.Ala1470LeufsTer3	p.A1470Lfs*3	ENST00000257430	NM_000038.5	1469	cAa/ca	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		456	736	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0062055-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	29	362	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.835	0.67	1	0.835	0.67	1	CLONAL	1	TRUE	1	0.16	2		362	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0062055-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	56	583	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	1	2	FACETS	0.997	0.853	1	0.997	0.853	1	CLONAL	1	TRUE	1	0.16	2		583	702	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062055-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	42	456	0	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	1	2	FACETS	0.735	0.612	0.873	0.735	0.612	0.873	SUBCLONAL	1	TRUE	1	0.16	2		456	714	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512288	38512289	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0062055-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	33	355	0	ENST00000254066.5:c.1201dup	p.Glu401GlyfsTer45	p.E401Gfs*45	ENST00000254066	NM_000964.3	400	atg/atGg	9/9	1	2	FACETS	0.658	0.534	0.798	0.658	0.534	0.798	SUBCLONAL	1	TRUE	1	0.16	2		355	627	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0062098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	13	411	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.707215208103527	3	FACETS	0.112	0.079	0.152	0.056	0.039	0.076	SUBCLONAL	1	FALSE	1	0.720337149649103	3		411	439	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777065	9777065	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	113	572	0	ENST00000377346.4:c.829G>T	p.Val277Phe	p.V277F	ENST00000377346	NM_005026.3	277	Gtc/Ttc	7/24	0.63555920872574	4	FACETS	0.952	0.859	1	0.476	0.429	0.525	CLONAL	1	FALSE	2	0.720337149649103	4		572	567	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797478	45797478	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1557465450	NA	P-0062098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	156	631	0	ENST00000450313.1:c.1041G>T	p.Glu347Asp	p.E347D	ENST00000450313	NM_012222.2	347	gaG/gaT	12/16	0.63555920872574	4	FACETS	1	0.948	1	0.522	0.479	0.567	CLONAL	1	FALSE	2	0.720337149649103	4		631	714	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246490516	246490516	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	72	403	0	ENST00000388985.4:c.518A>G	p.Glu173Gly	p.E173G	ENST00000388985		173	gAa/gGa	5/12	0.665764995043159	5	FACETS	0.675	0.59	0.767	0.225	0.196	0.256	SUBCLONAL	1	FALSE	2	0.720337149649103	5		403	616	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132834	64132834	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs752611628	NA	P-0062098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	86	573	0	ENST00000334205.4:c.968G>T	p.Arg323Leu	p.R323L	ENST00000334205	NM_003942.2	323	cGc/cTc	9/17	0.720337149649103	6	FACETS	0.621	0.548	0.699	0.155	0.137	0.175	SUBCLONAL	1	FALSE	2	0.720337149649103	6		573	939	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266571	41266571	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	151	466	0	ENST00000349496.5:c.368A>T	p.Gln123Leu	p.Q123L	ENST00000349496	NM_001904.3	123	cAg/cTg	4/15	0.707215208103527	3	FACETS	1	0.924	1	0.503	0.462	0.545	CLONAL	1	FALSE	1	0.720337149649103	3		466	567	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815847	32815847	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	98	414	0	ENST00000354258.4:c.1769C>A	p.Pro590His	p.P590H	ENST00000354258	NM_000593.5	590	cCt/cAt	8/11	0.63555920872574	4	FACETS	0.907	0.812	1	0.454	0.406	0.504	CLONAL	1	FALSE	2	0.720337149649103	4		414	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0062109-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	413	449	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.713921565361237	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.729656658633649	1		449	679	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137021	64137021	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062109-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	263	418	1	ENST00000334205.4:c.1532G>A	p.Arg511His	p.R511H	ENST00000334205	NM_003942.2	511	cGc/cAc	13/17	1	2	FACETS	0.992	0.934	1	0.992	0.934	1	CLONAL	1	TRUE	1	0.729656658633649	2		419	727	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602292	10602292	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062109-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	312	493	0	ENST00000171111.5:c.1286G>T	p.Gly429Val	p.G429V	ENST00000171111	NM_203500.1	429	gGc/gTc	3/6	0.729656658633649	1	FACETS	0.977	0.933	1	0.977	0.933	1	CLONAL	1	TRUE	0	0.729656658633649	1		493	556	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964433	55964433	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062109-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	278	362	0	ENST00000263923.4:c.2380G>T	p.Gly794Ter	p.G794*	ENST00000263923	NM_002253.2	794	Gga/Tga	17/30	0.713921565361237	1	FACETS	0.951	0.905	0.996	0.951	0.905	0.996	CLONAL	1	TRUE	0	0.729656658633649	1		362	509	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220409	1220409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062109-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	280	504	0	ENST00000326873.7:c.502C>T	p.His168Tyr	p.H168Y	ENST00000326873	NM_000455.4	168	Cat/Tat	4/10	0.729656658633649	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.729656658633649	1		504	483	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561794	55561794	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062109-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	39	380	0	ENST00000288135.5:c.184G>T	p.Gly62Cys	p.G62C	ENST00000288135	NM_000222.2	62	Ggc/Tgc	2/21	0.713921565361237	1	FACETS	0.13	0.107	0.155	0.13	0.107	0.155	SUBCLONAL	1	TRUE	0	0.729656658633649	1		380	523	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306544	41306544	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062109-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	243	311	0	ENST00000373198.4:c.1115C>A	p.Pro372Gln	p.P372Q	ENST00000373198	NM_133170.3	372	cCg/cAg	7/32	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.729656658633649	2		311	575	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946789	71946789	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062109-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	329	541	0	ENST00000298229.2:c.2730G>T	p.Gln910His	p.Q910H	ENST00000298229	NM_001567.3	910	caG/caT	24/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.729656658633649	2		541	830	SUCCESS
ATM	472	MSKCC	GRCh37	11	108154972	108154972	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062109-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	143	238	1	ENST00000278616.4:c.3765G>T	p.Leu1255Phe	p.L1255F	ENST00000278616	NM_000051.3	1255	ttG/ttT	26/63	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.729656658633649	2		239	371	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961231	41961231	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062109-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	258	388	0	ENST00000219905.7:c.139G>T	p.Ala47Ser	p.A47S	ENST00000219905	NM_001164273.1	47	Gcc/Tcc	2/24	0.438662456241478	1	FACETS	0.679	0.639	0.718	0.679	0.639	0.718	SUBCLONAL	1	TRUE	0	0.729656658633649	1		388	662	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858375	9858375	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062109-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	174	401	0	ENST00000330684.3:c.3026G>T	p.Arg1009Ile	p.R1009I	ENST00000330684	NM_001134407.1	1009	aGa/aTa	13/13	0.438662456241478	1	FACETS	0.466	0.431	0.503	0.466	0.431	0.503	SUBCLONAL	1	TRUE	0	0.729656658633649	1		401	650	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495236	212495236	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062109-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	237	334	0	ENST00000342788.4:c.2030G>T	p.Arg677Met	p.R677M	ENST00000342788	NM_005235.2	677	aGg/aTg	17/28	0.636785336946931	1	FACETS	0.832	0.786	0.878	0.832	0.786	0.878	CLONAL	1	TRUE	0	0.729656658633649	1		334	496	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749499	41749499	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062109-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	226	291	0	ENST00000226382.2:c.296G>T	p.Arg99Leu	p.R99L	ENST00000226382	NM_003924.3	99	cGg/cTg	2/3	0.713921565361237	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.729656658633649	1		291	385	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179197	123179197	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062142-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	219	187	0	ENST00000218089.9:c.646C>T	p.Arg216Ter	p.R216*	ENST00000218089	NM_001042749.1	216	Cga/Tga	8/35	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		187	243	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062262-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	84	523	0				ENST00000310581	NM_198253.2	-/1132			0.217032218621791	5	FACETS	1	0.906	1	0.672	0.604	0.743	INDETERMINATE	2	TRUE	2	0.778432308541287	5		523	232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0062262-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	286	850	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.758167420941721	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.778432308541287	2		852	358	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0062262-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	10	771	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.614324306598587	3	FACETS	0.087	0.058	0.124	0.044	0.029	0.062	SUBCLONAL	1	TRUE	1	0.778432308541287	3		771	409	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866444	37866444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062262-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	281	588	0	ENST00000269571.5:c.749C>T	p.Ser250Phe	p.S250F	ENST00000269571		250	tCt/tTt	6/27	0.777511990948769	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.778432308541287	4		588	595	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101327	27101327	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062262-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	481	537	0	ENST00000324856.7:c.4609C>T	p.Gln1537Ter	p.Q1537*	ENST00000324856	NM_006015.4	1537	Cag/Tag	18/20	0.778531208586222	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	1	0.778432308541287	4		537	653	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81954830	81954830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758623675	NA	P-0062262-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	184	361	0	ENST00000359376.3:c.2263G>A	p.Val755Ile	p.V755I	ENST00000359376	NM_002661.3	755	Gtc/Atc	21/33	0.227699849954013	6	FACETS	0.889	0.83	0.95	0.889	0.83	0.95	INDETERMINATE	3	TRUE	3	0.778432308541287	6		361	453	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651921	36651924	+	frameshift_variant	Frame_Shift_Del	DEL	AGCA	AGCA	-	novel	NA	P-0062262-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	413	555	0	ENST00000244741.5:c.45_48del	p.Ser15ArgfsTer15	p.S15Rfs*15	ENST00000244741	NM_000389.4	15	AGCAag/ag	2/3	0.778531208586222	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	1	0.778432308541287	4		555	540	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101181	27101181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062262-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	479	550	0	ENST00000324856.7:c.4463C>T	p.Ser1488Leu	p.S1488L	ENST00000324856	NM_006015.4	1488	tCa/tTa	18/20	0.778531208586222	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	1	0.778432308541287	4		550	677	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527839	157527839	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs771295398	NA	P-0062262-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	154	590	0	ENST00000346085.5:c.5564G>C	p.Arg1855Thr	p.R1855T	ENST00000346085	NM_020732.3	1855	aGa/aCa	20/20	0.176281362007856	3	FACETS	1	0.985	1	0.645	0.596	0.695	INDETERMINATE	1	TRUE	1	0.778432308541287	3		590	426	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435477	56435477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372129321	NA	P-0062262-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	271	536	0	ENST00000407977.2:c.1660C>T	p.Arg554Trp	p.R554W	ENST00000407977		554	Cgg/Tgg	9/10	0.777511990948769	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.778432308541287	4		536	582	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923438	9923438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062262-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	144	443	0	ENST00000330684.3:c.1849G>A	p.Val617Met	p.V617M	ENST00000330684	NM_001134407.1	617	Gtg/Atg	9/13	0.767739211877201	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.778432308541287	2		443	164	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945987	17945987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465717926	NA	P-0062262-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	104	509	0	ENST00000458235.1:c.1952G>A	p.Arg651Gln	p.R651Q	ENST00000458235	NM_000215.3	651	cGg/cAg	15/24	0.614324306598587	3	FACETS	0.88	0.793	0.97	0.44	0.396	0.485	CLONAL	1	TRUE	1	0.778432308541287	3		509	422	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971210	18971210	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062262-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	101	414	0	ENST00000262803.5:c.2263G>C	p.Glu755Gln	p.E755Q	ENST00000262803	NM_002911.3	755	Gag/Cag	16/24	0.614324306598587	3	FACETS	1	0.906	1	0.502	0.453	0.553	CLONAL	1	TRUE	1	0.778432308541287	3		414	359	SUCCESS
ATR	545	MSKCC	GRCh37	3	142286936	142286936	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062262-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	55	154	0	ENST00000350721.4:c.120C>G	p.Phe40Leu	p.F40L	ENST00000350721	NM_001184.3	40	ttC/ttG	2/47	0.778531208586222	6	FACETS	1	0.965	1	0.356	0.307	0.408	CLONAL	1	TRUE	2	0.778432308541287	6		154	254	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5064995	5064995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768074072	NA	P-0062262-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	235	295	0	ENST00000381652.3:c.1169C>T	p.Pro390Leu	p.P390L	ENST00000381652	NM_004972.3	390	cCa/cTa	9/25	0.755102938395425	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.778432308541287	2		295	291	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331652	8331652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062262-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	161	346	0	ENST00000356435.5:c.5464G>A	p.Asp1822Asn	p.D1822N	ENST00000356435		1822	Gac/Aac	33/35	0.778531208586222	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.778432308541287	1		346	210	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028595	42028597	+	stop_gained	Nonsense_Mutation	TNP	CTC	CTC	TTT	novel	NA	P-0062262-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	143	545	0	ENST00000219905.7:c.4133_4135delinsTTT	p.Ser1378_Gln1379delinsPheTer	p.S1378_Q1379delinsF*	ENST00000219905	NM_001164273.1	1378	tCTCag/tTTTag	13/24	0.778531208586222	3	FACETS	0.899	0.823	0.977	0.449	0.411	0.489	CLONAL	1	TRUE	1	0.778432308541287	3		545	568	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776661	9776661	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062262-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	15	405	0	ENST00000377346.4:c.764C>G	p.Pro255Arg	p.P255R	ENST00000377346	NM_005026.3	255	cCg/cGg	6/24	0.245551026782229	3	FACETS	0.229	0.167	0.303	0.076	0.055	0.101	INDETERMINATE	1	TRUE	0	0.778432308541287	3		405	234	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724033	61724033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776572018	NA	P-0062262-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	56	294	0	ENST00000401558.2:c.869C>T	p.Thr290Ile	p.T290I	ENST00000401558	NM_003400.3	290	aCa/aTa	10/25	0.688678624202544	4	FACETS	0.766	0.66	0.881	0.383	0.33	0.441	SUBCLONAL	1	TRUE	2	0.778432308541287	4		294	334	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007331	143007331	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062262-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	61	246	0	ENST00000262992.4:c.2453G>C	p.Arg818Thr	p.R818T	ENST00000262992	NM_001101669.1	818	aGa/aCa	22/24	0.665555419055471	4	FACETS	0.722	0.625	0.826	0.241	0.208	0.276	SUBCLONAL	1	TRUE	1	0.778432308541287	4		246	386	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876492	35876492	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062262-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	80	486	0	ENST00000303115.3:c.1284G>C	p.Leu428Phe	p.L428F	ENST00000303115	NM_002185.3	428	ttG/ttC	8/8	0.778531208586222	5	FACETS	0.631	0.555	0.713	0.21	0.185	0.238	SUBCLONAL	1	TRUE	2	0.778432308541287	5		486	706	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610198	10610198	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	114	501	0	ENST00000171111.5:c.512G>T	p.Cys171Phe	p.C171F	ENST00000171111	NM_203500.1	171	tGc/tTc	2/6	0.446241967815019	1	FACETS	0.888	0.805	0.975	0.888	0.805	0.975	CLONAL	1	TRUE	0	0.446241967815019	1		501	447	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718277	117718277	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1298952570	NA	P-0062301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	81	322	0	ENST00000368508.3:c.580C>T	p.Pro194Ser	p.P194S	ENST00000368508	NM_002944.2	194	Cct/Tct	7/43	0.446241967815019	1	FACETS	0.913	0.812	1	0.913	0.812	1	CLONAL	1	TRUE	0	0.446241967815019	1		322	309	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481417	140481417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913348	NA	P-0062301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	66	271	0	ENST00000288602.6:c.1391G>A	p.Gly464Glu	p.G464E	ENST00000288602	NM_004333.4	464	gGa/gAa	11/18	1	2	FACETS	0.875	0.765	0.993	0.875	0.765	0.993	CLONAL	1	TRUE	1	0.446241967815019	2		271	338	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42050038	42050038	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0062301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	55	258	0	ENST00000219905.7:c.7191+1G>T		p.X2397_splice	ENST00000219905	NM_001164273.1	2397			1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.446241967815019	2		258	243	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476310	88476310	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	90	392	0	ENST00000360948.2:c.1822G>T	p.Gly608Cys	p.G608C	ENST00000360948	NM_001012338.2	608	Ggc/Tgc	15/19	1	2	FACETS	0.954	0.851	1	0.954	0.851	1	CLONAL	1	TRUE	1	0.446241967815019	2		392	423	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220701	1220701	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730881976	NA	P-0062301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	112	430	0	ENST00000326873.7:c.719C>G	p.Ser240Trp	p.S240W	ENST00000326873	NM_000455.4	240	tCg/tGg	5/10	0.446241967815019	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.446241967815019	1		430	382	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50788274	50788274	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	71	284	0	ENST00000307179.4:c.2888C>G	p.Thr963Arg	p.T963R	ENST00000307179		963	aCa/aGa	17/20	1	2	FACETS	0.991	0.872	1	0.991	0.872	1	CLONAL	1	TRUE	1	0.446241967815019	2		284	321	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171694	36171694	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	128	442	0	ENST00000300305.3:c.871A>T	p.Ile291Phe	p.I291F	ENST00000300305		291	Att/Ttt	7/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.446241967815019	2		442	510	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161789	47161789	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	90	411	0	ENST00000409792.3:c.4337G>T	p.Gly1446Val	p.G1446V	ENST00000409792	NM_014159.6	1446	gGg/gTg	3/21	1	2	FACETS	0.855	0.761	0.953	0.855	0.761	0.953	CLONAL	1	TRUE	1	0.446241967815019	2		411	472	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117874128	117874128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	74	273	0	ENST00000297338.2:c.326C>T	p.Thr109Ile	p.T109I	ENST00000297338	NM_006265.2	109	aCt/aTt	4/14	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.446241967815019	2		273	308	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399919	139399919	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	118	542	0	ENST00000277541.6:c.4429G>T	p.Gly1477Cys	p.G1477C	ENST00000277541	NM_017617.3	1477	Ggt/Tgt	25/34	1	2	FACETS	0.902	0.817	0.992	0.902	0.817	0.992	CLONAL	1	TRUE	1	0.446241967815019	2		542	586	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038830	47038830	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	110	429	0	ENST00000377604.3:c.839del	p.Gly280GlufsTer28	p.G280Efs*28	ENST00000377604	NM_001204468.1	279	caG/ca	9/24	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.446241967815019	2		429	436	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0062309-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	70	470	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.897	0.782	1	0.897	0.782	1	CLONAL	1	TRUE	1	0.242739784665694	2		471	643	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0062309-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	40	309	0	ENST00000311936.3:c.34_35delinsCT	p.Gly12Leu	p.G12L	ENST00000311936	NM_004985.3	12	GGt/CTt	2/5	1	2	FACETS	0.854	0.711	1	0.854	0.711	1	CLONAL	1	TRUE	1	0.242739784665694	2		309	386	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231302	46231302	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062309-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	78	442	0	ENST00000334344.6:c.1142T>A	p.Leu381His	p.L381H	ENST00000334344	NM_152641.2	381	cTt/cAt	10/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.242739784665694	2		442	523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579585	7579586	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0062309-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	68	520	0	ENST00000269305.4:c.101_102insTT	p.Leu35SerfsTer10	p.L35Sfs*10	ENST00000269305	NM_001126112.2	34	ccc/ccTTc	4/11	0.242739784665694	1	FACETS	0.881	0.767	1	0.881	0.767	1	CLONAL	1	TRUE	0	0.242739784665694	1		520	559	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509097	66509097	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062309-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	41	330	0	ENST00000273854.3:c.230C>A	p.Ala77Asp	p.A77D	ENST00000273854	NM_004439.5	77	gCt/gAt	2/18	1	2	FACETS	0.906	0.756	1	0.906	0.756	1	CLONAL	1	TRUE	1	0.242739784665694	2		330	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579381	7579381	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	600	799	0	ENST00000269305.4:c.306del	p.Tyr103ThrfsTer20	p.Y103Tfs*20	ENST00000269305	NM_001126112.2	102	acC/ac	4/11	0.710227550404026	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.710227550404026	2		799	837	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881488	48881489	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0062384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	318	427	0	ENST00000267163.4:c.219_220dup	p.Ala74GlufsTer4	p.A74Efs*4	ENST00000267163	NM_000321.2	70	-/AG	2/27	0.663263206935931	3	FACETS	1	0.993	1	0.793	0.76	0.825	CLONAL	2	TRUE	0	0.710227550404026	3		427	510	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259652	89259653	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0062384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	35	554	0	ENST00000336596.2:c.798_799del	p.Gly267PhefsTer17	p.G267Ffs*17	ENST00000336596	NM_005233.5	266	AGa/a	3/17	1	2	FACETS	0.171	0.139	0.206	0.171	0.139	0.206	SUBCLONAL	1	TRUE	1	0.710227550404026	2		554	577	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188263	10188263	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs397516442	NA	P-0062427-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	166	440	0	ENST00000256474.2:c.408del	p.Phe136LeufsTer23	p.F136Lfs*23	ENST00000256474	NM_000551.3	136	Ttt/tt	2/3	0.529624761138706	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.529624761138706	1		440	420	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857466	68857466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426734014	NA	P-0062427-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	194	505	0	ENST00000261769.5:c.2101G>A	p.Val701Ile	p.V701I	ENST00000261769	NM_004360.3	701	Gtc/Atc	13/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.529624761138706	2		505	642	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018090	48018090	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062427-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	125	588	0	ENST00000234420.5:c.286del	p.Val96PhefsTer53	p.V96Ffs*53	ENST00000234420	NM_000179.2	95	ttG/tt	2/10	0.160445879586253	3	FACETS	0.862	0.781	0.946	0.431	0.39	0.473	INDETERMINATE	1	TRUE	1	0.529624761138706	3		588	693	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165285	47165285	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0062427-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	111	520	0	ENST00000409792.3:c.841A>T	p.Lys281Ter	p.K281*	ENST00000409792	NM_014159.6	281	Aaa/Taa	3/21	0.529624761138706	1	FACETS	0.917	0.834	1	0.917	0.834	1	CLONAL	1	TRUE	0	0.529624761138706	1		520	336	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651312	52651312	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062427-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	212	564	0	ENST00000394830.3:c.1784G>C	p.Arg595Pro	p.R595P	ENST00000394830	NM_018313.4	595	cGg/cCg	15/30	0.529624761138706	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.529624761138706	1		564	520	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062473-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	41	523	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.999	0.833	1	0.999	0.833	1	CLONAL	1	TRUE	1	0.21	2		523	391	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670013	29670025	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	ATTATCTTTAATA	ATTATCTTTAATA	-	novel	NA	P-0062473-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	39	375	0	ENST00000356175.3:c.7000-14_7000-2del		p.X2334_splice	ENST00000356175	NM_000267.3	2334			0.0899856229137364	0	FACETS	0.827	0.687	0.982			1	INDETERMINATE	1	TRUE	0	0.21	0		375	355	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775173	73775173	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062473-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	99	987	0	ENST00000254810.4:c.83A>T	p.Lys28Ile	p.K28I	ENST00000254810	NM_005324.3	28	aAa/aTa	2/4	1	2	FACETS	0.863	0.768	0.964	0.863	0.768	0.964	CLONAL	1	TRUE	1	0.21	2		987	1093	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937434	32937435	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0062503-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	113	549	0	ENST00000380152.3:c.8100_8101dup	p.Ser2701TyrfsTer33	p.S2701Yfs*33	ENST00000380152		2699	aat/aATat	18/27	0.373465188015593	3	FACETS	1	0.974	1	0.613	0.553	0.675	CLONAL	1	FALSE	1	0.412801165798611	3		549	539	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578428	7578457	+	inframe_deletion	In_Frame_Del	DEL	GCTGTGACTGCTTGTAGATGGCCATGGCGC	GCTGTGACTGCTTGTAGATGGCCATGGCGC	-	novel	NA	P-0062503-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	178	886	0	ENST00000269305.4:c.473_502del	p.Arg158_Gln167del	p.R158_Q167del	ENST00000269305	NM_001126112.2	158	cGCGCCATGGCCATCTACAAGCAGTCACAGCac/cac	5/11	0.252895783977165	2	FACETS	0.799	0.741	0.857	0.799	0.741	0.857	SUBCLONAL	2	FALSE	0	0.412801165798611	2		886	540	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0062646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	476	728	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.781404218877385	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.781404218877385	2		728	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	450	587	0	ENST00000269305.4:c.398T>A	p.Met133Lys	p.M133K	ENST00000269305	NM_001126112.2	133	aTg/aAg	5/11	0.781404218877385	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.781404218877385	1		587	569	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100603	67100603	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	323	467	0	ENST00000412916.2:c.301A>G	p.Met101Val	p.M101V	ENST00000412916		101	Atg/Gtg	4/6	0.781404218877385	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.781404218877385	1		467	453	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714441	117714441	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	51	447	0	ENST00000368508.3:c.1208T>C	p.Ile403Thr	p.I403T	ENST00000368508	NM_002944.2	403	aTt/aCt	11/43	0.55818663304731	3	FACETS	0.365	0.31	0.425	0.182	0.155	0.213	SUBCLONAL	1	TRUE	1	0.781404218877385	3		447	498	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912345	32912346	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359406	NA	P-0062646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	27	449	0	ENST00000380152.3:c.3860dup	p.Asn1287LysfsTer2	p.N1287Kfs*2	ENST00000380152		1285	gaa/gAaa	11/27	0.17817818158492	2	FACETS	0.157	0.124	0.194	0.078	0.062	0.097	INDETERMINATE	1	TRUE	0	0.781404218877385	2		449	441	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405019	70405019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	447	545	0	ENST00000373644.4:c.2533C>T	p.His845Tyr	p.H845Y	ENST00000373644	NM_030625.2	845	Cat/Tat	4/12	0.640203590231714	4	FACETS	0.999	0.957	1	0.666	0.638	0.694	CLONAL	2	TRUE	1	0.781404218877385	4		545	1020	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424072	49424072	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	305	365	0	ENST00000301067.7:c.13990del	p.Ala4664HisfsTer2	p.A4664Hfs*2	ENST00000301067	NM_003482.3	4664	Gca/ca	42/54	0.781404218877385	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.781404218877385	1		365	408	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005304	29005304	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	153	410	0	ENST00000282397.4:c.957C>A	p.Phe319Leu	p.F319L	ENST00000282397	NM_002019.4	319	ttC/ttA	7/30	0.17817818158492	2	FACETS	0.986	0.913	1	0.493	0.456	0.531	INDETERMINATE	1	TRUE	0	0.781404218877385	2		410	397	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929317	32929317	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	223	504	0	ENST00000380152.3:c.7327G>C	p.Asp2443His	p.D2443H	ENST00000380152		2443	Gat/Cat	14/27	0.17817818158492	2	FACETS	1	0.982	1	0.557	0.524	0.591	INDETERMINATE	1	TRUE	0	0.781404218877385	2		504	512	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016673	12016673	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	367	464	0	ENST00000353533.5:c.809T>A	p.Met270Lys	p.M270K	ENST00000353533	NM_003010.3	270	aTg/aAg	7/11	0.781404218877385	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.781404218877385	1		464	494	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2164202	2164202	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs780708540	NA	P-0062646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	46	394	0	ENST00000398665.3:c.19C>G	p.Leu7Val	p.L7V	ENST00000398665	NM_032482.2	7	Ctg/Gtg	1/28	0.711193661996692	1	FACETS	0.212	0.179	0.248	0.212	0.179	0.248	SUBCLONAL	1	TRUE	0	0.781404218877385	1		394	339	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637618	176637618	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752771282	NA	P-0062646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	250	624	0	ENST00000439151.2:c.2218C>T	p.His740Tyr	p.H740Y	ENST00000439151	NM_022455.4	740	Cac/Tac	5/23	0.479192495961757	1	FACETS	0.611	0.575	0.647	0.611	0.575	0.647	SUBCLONAL	1	TRUE	0	0.781404218877385	1		624	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0062672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	186	427	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	0.643974834505321	2	FACETS	0.984	0.938	1	0.984	0.938	1	CLONAL	2	TRUE	0	0.73546864058402	2		427	257	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937530	32937530	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397507966	NA	P-0062672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	100	466	0	ENST00000380152.3:c.8191C>T	p.Gln2731Ter	p.Q2731*	ENST00000380152		2731	Cag/Tag	18/27	0.606291591260948	2	FACETS	0.805	0.743	0.865	0.805	0.743	0.865	CLONAL	2	TRUE	0	0.73546864058402	2		466	169	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506922	186506940	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGGGGTCGATTTGGGAG	GAGGGGGTCGATTTGGGAG	-	novel	NA	P-0062672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	32	405	0	ENST00000323963.5:c.1090_1108del	p.Gly364LysfsTer5	p.G364Kfs*5	ENST00000323963		363	aGAGGGGGTCGATTTGGGAGg/ag	11/11	0.622042504316087	4	FACETS	0.651	0.532	0.784	0.325	0.266	0.392	SUBCLONAL	1	TRUE	2	0.73546864058402	4		405	232	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004292	150004292	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	42	421	0	ENST00000253339.5:c.1933C>T	p.Gln645Ter	p.Q645*	ENST00000253339		645	Caa/Taa	3/7	0.643974834505321	2	FACETS	0.993	0.852	1	0.497	0.426	0.57	CLONAL	1	TRUE	0	0.73546864058402	2		421	115	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5068984	5069554	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACTATCCCTCCCTTTCTTTATAATTAAACTTATACAGCGAGAAAATGTCATTGAATATAAACACTGTTTGATTACAAAAAATGAGAATGAAGAGTACAACCTCAGTGGGACAAAGAAGAACTTCAGCAGTCTTAAAGATCTTTTGAATTGTTACCAGATGGAAACTGTTCGCTCAGACAATATAATTTTCCAGTTTACTAAATGCTGTCCCCCAAAGCCAAAAGGTAAGATAATTTTCTAGTTATTTTTAAATTACTGGTCATGGATTGTTTATGTGGCGTGAAGTATCTTCAGTACATTGATTTCAAAGGATATATGAAAGAAGCAGCTCTAAAAGTTAATTTTATCTTATTCTATTGTACAAGCATCATCAAATAAGATTGTTTACTTTGGTTTTGGTGGTCTAGAAGTGACTTGAAGTTCAATTATTCTAAAATGAGATTTTAAACATAATGTGTGGTATGATGTCATTTATTGAACTGGAAGATCTCACTACTAAATTCTTATGTTGTTTTAAGTAAAAATTTTCATATACTTCGAGGATTTTAATTTCTGTATTTTAAAAATAAA	GACTATCCCTCCCTTTCTTTATAATTAAACTTATACAGCGAGAAAATGTCATTGAATATAAACACTGTTTGATTACAAAAAATGAGAATGAAGAGTACAACCTCAGTGGGACAAAGAAGAACTTCAGCAGTCTTAAAGATCTTTTGAATTGTTACCAGATGGAAACTGTTCGCTCAGACAATATAATTTTCCAGTTTACTAAATGCTGTCCCCCAAAGCCAAAAGGTAAGATAATTTTCTAGTTATTTTTAAATTACTGGTCATGGATTGTTTATGTGGCGTGAAGTATCTTCAGTACATTGATTTCAAAGGATATATGAAAGAAGCAGCTCTAAAAGTTAATTTTATCTTATTCTATTGTACAAGCATCATCAAATAAGATTGTTTACTTTGGTTTTGGTGGTCTAGAAGTGACTTGAAGTTCAATTATTCTAAAATGAGATTTTAAACATAATGTGTGGTATGATGTCATTTATTGAACTGGAAGATCTCACTACTAAATTCTTATGTTGTTTTAAGTAAAAATTTTCATATACTTCGAGGATTTTAATTTCTGTATTTTAAAAATAAA	-	novel	NA	P-0062672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	12	261	0	ENST00000381652.3:c.1327-35_1513+349del		p.X443_splice	ENST00000381652	NM_004972.3	443		11/25	0.643974834505321	2	FACETS	0.709	0.516	0.929	0.355	0.258	0.465	CLONAL	1	TRUE	0	0.73546864058402	2		261	46	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617222	100617222	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	162	503	0	ENST00000308731.7:c.527A>T	p.Lys176Ile	p.K176I	ENST00000308731	NM_000061.2	176	aAa/aTa	7/19	0.695754370169464	3	FACETS	0.871	0.812	0.93	0.871	0.812	0.93	CLONAL	2	TRUE	1	0.73546864058402	3		503	346	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506951	186506966	+	protein_altering_variant	In_Frame_Del	DEL	GCTATAAACTTTGTTA	GCTATAAACTTTGTTA	T	novel	NA	P-0062672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	32	423	0	ENST00000323963.5:c.1117_1132delinsT	p.Ala373_Thr378delinsSer	p.A373_T378delinsS	ENST00000323963		373	GCTATAAACTTTGTTAct/Tct	11/11	0.622042504316087	4	FACETS	0.624	0.509	0.752	0.312	0.254	0.376	SUBCLONAL	1	TRUE	2	0.73546864058402	4		423	242	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0062726-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	61	54	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.523347246001132	2		54	178	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530103	63530103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398258340	NA	P-0062726-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	165	245	0	ENST00000307078.5:c.2332C>T	p.Arg778Trp	p.R778W	ENST00000307078	NM_004655.3	778	Cgg/Tgg	10/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.523347246001132	2		245	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0062729-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	216	514	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.300377133091774	1	FACETS	0.948	0.88	1	0.948	0.88	1	CLONAL	1	TRUE	0	0.31	1		514	1242	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194865	30194865	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062729-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	33	401	0	ENST00000331968.5:c.280T>G	p.Phe94Val	p.F94V	ENST00000331968	NM_002742.2	94	Ttc/Gtc	2/18	1	2	FACETS	0.323	0.262	0.392	0.323	0.262	0.392	SUBCLONAL	1	TRUE	1	0.31	2		401	659	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919631	96919631	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062729-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	99	598	0	ENST00000258439.3:c.632T>G	p.Leu211Arg	p.L211R	ENST00000258439	NM_001193304.2	211	cTc/cGc	4/4	1	2	FACETS	0.572	0.509	0.64	0.572	0.509	0.64	SUBCLONAL	1	TRUE	1	0.31	2		598	1116	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0062810-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	111	850	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.313728336462933	1	FACETS	0.924	0.832	1	0.924	0.832	1	CLONAL	1	TRUE	0	0.313728336462933	1		852	646	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0062810-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	48	362	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.313728336462933	1	FACETS	0.816	0.694	0.95	0.816	0.694	0.95	CLONAL	1	TRUE	0	0.313728336462933	1		362	316	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591931	48591931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062810-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	87	584	0	ENST00000342988.3:c.1094G>A	p.Gly365Asp	p.G365D	ENST00000342988	NM_005359.5	365	gGt/gAt	9/12	0.313728336462933	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.313728336462933	1		584	426	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858047	152858047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1432027234	NA	P-0062810-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	81	709	0	ENST00000406277.2:c.568G>A	p.Ala190Thr	p.A190T	ENST00000406277	NM_152274.4	190	Gcc/Acc	6/7	1	2	FACETS	0.856	0.755	0.965	0.856	0.755	0.965	CLONAL	1	TRUE	1	0.313728336462933	2		709	603	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0062820-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	52	380	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	0.118142608247874	3	FACETS	0.872	0.749	1	0.581	0.499	0.67	INDETERMINATE	2	TRUE	0	0.26014615131883	3		380	259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0062820-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	77	681	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.118142608247874	3	FACETS	1	0.95	1	0.386	0.339	0.437	INDETERMINATE	1	TRUE	0	0.26014615131883	3		682	577	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913381	NA	P-0062820-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	65	657	0	ENST00000304494.5:c.322G>T	p.Asp108Tyr	p.D108Y	ENST00000304494	NM_000077.4	108	Gat/Tat	2/3	0.258697970866353	1	FACETS	0.753	0.653	0.862	0.753	0.653	0.862	SUBCLONAL	1	TRUE	0	0.26014615131883	1		657	577	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350272	89350272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1298734986	NA	P-0062820-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	112	654	0	ENST00000301030.4:c.2678G>A	p.Arg893Gln	p.R893Q	ENST00000301030	NM_001256183.1	893	cGg/cAg	9/13	0.177184099974288	3	FACETS	1	0.979	1	0.67	0.603	0.741	CLONAL	1	TRUE	1	0.26014615131883	3		654	726	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677260	29677260	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1199046022	NA	P-0062820-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	43	372	0	ENST00000356175.3:c.7318C>G	p.Leu2440Val	p.L2440V	ENST00000356175	NM_000267.3	2440	Ctt/Gtt	49/57	0.118142608247874	3	FACETS	1	0.951	1	0.458	0.385	0.537	INDETERMINATE	1	TRUE	0	0.26014615131883	3		372	272	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118692	11118692	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062820-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	39	443	0	ENST00000358026.2:c.2116A>T	p.Ile706Phe	p.I706F	ENST00000358026	NM_001128849.1	706	Atc/Ttc	14/36	NA	2	FACETS	0.582	0.482	0.694			1	INDETERMINATE	1	TRUE	NA	0.26014615131883	2		443	515	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664953	138664953	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062820-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	85	456	0	ENST00000330315.3:c.612G>C	p.Trp204Cys	p.W204C	ENST00000330315	NM_023067.3	204	tgG/tgC	1/1	0.26014615131883	5	FACETS	0.78	0.691	0.876	0.52	0.46	0.584	SUBCLONAL	2	TRUE	2	0.26014615131883	5		456	582	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117717381	117717381	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062820-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	88	404	0	ENST00000368508.3:c.826G>T	p.Glu276Ter	p.E276*	ENST00000368508	NM_002944.2	276	Gaa/Taa	8/43	1	2	FACETS	0.835	0.745	0.931	1	0.983	1	CLONAL	2	TRUE	1	0.26014615131883	2		404	405	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412020	116412082	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTACCGAGCTACTTTTCCAGAAGGTATATTTCAGTTTATTGTTCTGAGAAATACCTATACAT	ACTACCGAGCTACTTTTCCAGAAGGTATATTTCAGTTTATTGTTCTGAGAAATACCTATACAT	-	novel	NA	P-0062821-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	95	609	0	ENST00000397752.3:c.3006_3028+40del		p.X1002_splice	ENST00000397752	NM_000245.2	1002		14/21	0.156135340328914	3	FACETS	0.893	0.797	0.994	0.595	0.531	0.663	CLONAL	2	TRUE	0	0.20796146524258	3		609	565	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411256	63411256	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062821-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	27	665	0	ENST00000330258.3:c.1911G>T	p.Glu637Asp	p.E637D	ENST00000330258	NM_152424.3	637	gaG/gaT	2/2	0.20796146524258	0	FACETS	0.647	0.515	0.797			1	SUBCLONAL	1	TRUE	0	0.20796146524258	0		665	318	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220362	1220371	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTGCCCGCAG	CTGCCCGCAG	A	novel	NA	P-0062821-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	13	512	0	ENST00000326873.7:c.465-10_465-1delinsA		p.X155_splice	ENST00000326873	NM_000455.4	155			0.20796146524258	0	FACETS	0.303	0.215	0.41			1	SUBCLONAL	1	TRUE	0	0.20796146524258	0		512	327	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312689	91312689	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs765143263	NA	P-0062822-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	128	366	0	ENST00000355112.3:c.2428G>C	p.Asp810His	p.D810H	ENST00000355112	NM_000057.2	810	Gat/Cat	12/22	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.456674618400118	2		366	534	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206941996	206941996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062822-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	109	359	0	ENST00000423557.1:c.522G>A	p.Met174Ile	p.M174I	ENST00000423557	NM_000572.2	174	atG/atA	5/5	0.453778250334503	3	FACETS	0.931	0.837	1	0.465	0.418	0.515	CLONAL	1	TRUE	1	0.456674618400118	3		359	630	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219345	1219346	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	rs587782424	NA	P-0062822-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	173	528	0	ENST00000326873.7:c.402_403del	p.Cys134TrpfsTer28	p.C134Wfs*28	ENST00000326873	NM_000455.4	133	GTg/g	3/10	0.456674618400118	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.456674618400118	1		528	572	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287239	33287239	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062822-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	132	515	0	ENST00000374542.5:c.1858C>G	p.His620Asp	p.H620D	ENST00000374542	NM_001141970.1	620	Cac/Gac	6/8	1	2	FACETS	0.763	0.693	0.836	0.763	0.693	0.836	SUBCLONAL	1	TRUE	1	0.456674618400118	2		515	758	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984130	2984130	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062822-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	119	491	0	ENST00000396946.4:c.400G>A	p.Glu134Lys	p.E134K	ENST00000396946	NM_032415.4	134	Gag/Aag	5/25	1	2	FACETS	0.91	0.824	0.999	0.91	0.824	0.999	CLONAL	1	TRUE	1	0.456674618400118	2		491	573	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215674170	215674170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062822-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	48	481	0	ENST00000260947.4:c.124G>A	p.Asp42Asn	p.D42N	ENST00000260947	NM_000465.2	42	Gac/Aac	1/11	1	2	FACETS	0.422	0.357	0.494	0.422	0.357	0.494	SUBCLONAL	1	TRUE	1	0.456674618400118	2		481	498	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528086	29528086	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs864622107	NA	P-0062822-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	41	152	0	ENST00000356175.3:c.1094C>G	p.Ser365Ter	p.S365*	ENST00000356175	NM_000267.3	365	tCa/tGa	10/57	1	2	FACETS	0.767	0.644	0.901	0.767	0.644	0.901	CLONAL	1	TRUE	1	0.456674618400118	2		152	234	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602819	10602819	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062822-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	175	588	0	ENST00000171111.5:c.759del	p.Lys254SerfsTer23	p.K254Sfs*23	ENST00000171111	NM_203500.1	253	gtC/gt	3/6	0.456674618400118	1	FACETS	0.966	0.894	1	0.966	0.894	1	CLONAL	1	TRUE	0	0.456674618400118	1		588	612	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218059	108218059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062822-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	104	375	0	ENST00000278616.4:c.8638G>A	p.Glu2880Lys	p.E2880K	ENST00000278616	NM_000051.3	2880	Gag/Aag	59/63	1	2	FACETS	0.888	0.798	0.982	0.888	0.798	0.982	CLONAL	1	TRUE	1	0.456674618400118	2		375	513	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420191	88420191	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062822-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	155	447	0	ENST00000360948.2:c.2495C>G	p.Pro832Arg	p.P832R	ENST00000360948	NM_001012338.2	832	cCa/cGa	19/19	1	2	FACETS	0.963	0.884	1	0.963	0.884	1	CLONAL	1	TRUE	1	0.456674618400118	2		447	705	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350921	89350921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062822-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	133	388	0	ENST00000301030.4:c.2029G>A	p.Asp677Asn	p.D677N	ENST00000301030	NM_001256183.1	677	Gat/Aat	9/13	1	2	FACETS	0.935	0.852	1	0.935	0.852	1	CLONAL	1	TRUE	1	0.456674618400118	2		388	623	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664427	29664427	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062822-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	121	388	0	ENST00000356175.3:c.6406del	p.Ser2136HisfsTer43	p.S2136Hfs*43	ENST00000356175	NM_000267.3	2136	Tca/ca	42/57	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.456674618400118	2		388	517	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805846	46805846	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062822-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	154	622	0	ENST00000290295.7:c.110del	p.Pro37GlnfsTer6	p.P37Qfs*6	ENST00000290295	NM_006361.5	37	cCa/ca	1/2	1	2	FACETS	0.905	0.83	0.984	0.905	0.83	0.984	CLONAL	1	TRUE	1	0.456674618400118	2		622	745	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137638	202137638	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062822-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	139	495	0	ENST00000358485.4:c.745G>C	p.Glu249Gln	p.E249Q	ENST00000358485	NM_001080125.1	249	Gaa/Caa	5/9	1	2	FACETS	0.897	0.818	0.979	0.897	0.818	0.979	CLONAL	1	TRUE	1	0.456674618400118	2		495	679	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435365	18435365	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs768734704	NA	P-0062840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	161	556	0	ENST00000266497.5:c.350C>A	p.Pro117His	p.P117H	ENST00000266497		117	cCt/cAt	1/31	0.858701101052202	4	FACETS	0.9	0.837	0.965	0.9	0.837	0.965	CLONAL	2	FALSE	2	0.858701101052202	4		556	387	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55603385	55603385	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	73	395	0	ENST00000288135.5:c.2741del	p.Arg914AsnfsTer10	p.R914Nfs*10	ENST00000288135	NM_000222.2	914	aGa/aa	20/21	0.790547029034286	4	FACETS	0.903	0.795	1	0.301	0.265	0.339	CLONAL	1	FALSE	1	0.858701101052202	4		395	350	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455068	50455068	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0062840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	86	513	0	ENST00000331340.3:c.615T>A	p.Tyr205Ter	p.Y205*	ENST00000331340	NM_006060.4	205	taT/taA	6/8	0.802631133339613	2	FACETS	0.882	0.795	0.972	0.441	0.397	0.486	CLONAL	1	FALSE	0	0.858701101052202	2		513	227	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194623	29194623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	127	701	0	ENST00000240100.2:c.1105C>T	p.Pro369Ser	p.P369S	ENST00000240100	NM_001394.6	369	Ccg/Tcg	4/4	0.800165230301121	4	FACETS	1	0.962	1			1	CLONAL	1	FALSE	NA	0.858701101052202	4		701	498	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778763	76778763	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	307	425	0	ENST00000373344.5:c.6816del	p.Ala2273GlnfsTer13	p.A2273Qfs*13	ENST00000373344	NM_000489.3	2272	aaA/aa	31/35	0.858701101052202	5	FACETS	0.981	0.936	1	0.981	0.936	1	CLONAL	3	FALSE	2	0.858701101052202	5		425	556	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912016	127912106	+	protein_altering_variant	In_Frame_Del	DEL	AATAACTTTGGTTCTCTTGTATTTACATCTTTGAAGACCATGATCGAAGCAATATTTCCACAACGATAGCAGTAATTAGGAGCAGACCATA	AATAACTTTGGTTCTCTTGTATTTACATCTTTGAAGACCATGATCGAAGCAATATTTCCACAACGATAGCAGTAATTAGGAGCAGACCATA	GCTC	novel	NA	P-0062840-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	371	496	2	ENST00000373547.4:c.764_854delinsGAGC	p.Val255_Phe285delinsGlyAla	p.V255_F285delinsGA	ENST00000373547	NM_002721.4	255	gTATGGTCTGCTCCTAATTACTGCTATCGTTGTGGAAATATTGCTTCGATCATGGTCTTCAAAGATGTAAATACAAGAGAACCAAAGTTATTc/gGAGCc	7/7	0.858701101052202	5	FACETS	0.952	0.912	0.992	0.952	0.912	0.992	CLONAL	3	FALSE	2	0.858701101052202	5		498	692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0062911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	531	617	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.76019390535004	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.75053454130959	2		617	618	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626639	12626649	+	frameshift_variant	Frame_Shift_Del	DEL	GTGAGAATAAG	GTGAGAATAAG	-	novel	NA	P-0062911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	157	771	0	ENST00000251849.4:c.1640_1650del	p.Pro547HisfsTer21	p.P547Hfs*21	ENST00000251849	NM_002880.3	547	cCTTATTCTCAC/c	15/17	0.412563046604824	2	FACETS	0.499	0.457	0.543	0.25	0.228	0.272	INDETERMINATE	1	TRUE	0	0.75053454130959	2		771	838	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31239125	31239125	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	110	683	0	ENST00000376228.5:c.344G>C	p.Gly115Ala	p.G115A	ENST00000376228	NM_002117.5	115	gGg/gCg	3/8	1	2	FACETS	0.495	0.446	0.547	0.495	0.446	0.547	SUBCLONAL	1	TRUE	1	0.75053454130959	2		683	592	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0062932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	33	728	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.803	0.652	0.975	0.803	0.652	0.975	CLONAL	1	TRUE	1	0.11	2		728	747	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0062932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	53	850	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	0.962	0.817	1			1	INDETERMINATE	1	TRUE	NA	0.11	2		852	1002	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653782	89653782	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs886041877	NA	P-0062932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	25	263	0	ENST00000371953.3:c.80A>G	p.Tyr27Cys	p.Y27C	ENST00000371953	NM_000314.4	27	tAt/tGt	2/9	1	2	FACETS	1	0.836	1	1	0.836	1	CLONAL	1	TRUE	1	0.11	2		263	423	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679007	117679007	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	31	389	0	ENST00000368508.3:c.3814A>C	p.Asn1272His	p.N1272H	ENST00000368508	NM_002944.2	1272	Aat/Cat	24/43	1	2	FACETS	0.96	0.775	1	0.96	0.775	1	CLONAL	1	TRUE	1	0.11	2		389	587	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880113	151880114	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0062932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	33	467	0	ENST00000262189.6:c.5210_5211del	p.Lys1737ArgfsTer11	p.K1737Rfs*11	ENST00000262189	NM_170606.2	1737	aAA/a	35/59	1	2	FACETS	0.915	0.743	1	0.915	0.743	1	CLONAL	1	TRUE	1	0.11	2		467	656	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468186	25468186	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779323387	NA	P-0062944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	300	611	0	ENST00000264709.3:c.1490G>A	p.Cys497Tyr	p.C497Y	ENST00000264709	NM_175629.2	497	tGt/tAt	13/23	0.818984002140688	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.847152948272977	1		611	377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578217	7578217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062946-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	37	500	0	ENST00000269305.4:c.632C>T	p.Thr211Ile	p.T211I	ENST00000269305	NM_001126112.2	211	aCt/aTt	6/11	1	2	FACETS	0.324	0.267	0.388	0.324	0.267	0.388	SUBCLONAL	1	TRUE	1	0.453018723705373	2		500	504	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026649	6026649	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63751459	NA	P-0062946-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	20	0	0	ENST00000265849.7:c.1747G>A	p.Glu583Lys	p.E583K	ENST00000265849	NM_000535.5	583	Gaa/Aaa	11/15	1	2	FACETS	0.194	0.147	0.248	0.194	0.147	0.248	SUBCLONAL	1	TRUE	1	0.453018723705373	2		0	456	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28929495	NA	P-0062982-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	6250	364	0	ENST00000275493.2:c.2155G>A	p.Gly719Ser	p.G719S	ENST00000275493	NM_005228.3	719	Ggc/Agc	18/28	0.731272879648249	30	FACETS	1	0.999	1	1	0.999	1	CLONAL	29	TRUE	1	0.731272879648249	30		364	6533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0062982-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	780	464	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.379438158686846	4	FACETS	0.982	0.964	0.999			1	INDETERMINATE	4	TRUE	NA	0.731272879648249	4		464	940	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0062982-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	6450	303	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.731272879648249	30	FACETS	1	0.999	1	1	0.999	1	CLONAL	29	TRUE	1	0.731272879648249	30		303	6747	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039219	49039219	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062982-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	308	202	1	ENST00000267163.4:c.2297C>G	p.Thr766Arg	p.T766R	ENST00000267163	NM_000321.2	766	aCa/aGa	22/27	0.73130225701533	3	FACETS	0.913	0.88	0.944	0.913	0.88	0.944	CLONAL	3	TRUE	0	0.731272879648249	3		203	420	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039187	49039187	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062982-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	269	171	0	ENST00000267163.4:c.2265C>G	p.Phe755Leu	p.F755L	ENST00000267163	NM_000321.2	755	ttC/ttG	22/27	0.73130225701533	3	FACETS	0.908	0.872	0.941	0.908	0.872	0.941	CLONAL	3	TRUE	0	0.731272879648249	3		171	369	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039174	49039174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062982-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	250	154	0	ENST00000267163.4:c.2252C>T	p.Ser751Phe	p.S751F	ENST00000267163	NM_000321.2	751	tCt/tTt	22/27	0.73130225701533	3	FACETS	0.91	0.874	0.945	0.91	0.874	0.945	CLONAL	3	TRUE	0	0.731272879648249	3		154	342	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039240	49039241	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0062982-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	284	205	0	ENST00000267163.4:c.2318_2319delinsTT	p.Ser773Phe	p.S773F	ENST00000267163	NM_000321.2	773	tCC/tTT	22/27	0.73130225701533	3	FACETS	0.916	0.882	0.949	0.916	0.882	0.949	CLONAL	3	TRUE	0	0.731272879648249	3		205	386	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039139	49039139	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062982-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	192	116	0	ENST00000267163.4:c.2217C>G	p.Phe739Leu	p.F739L	ENST00000267163	NM_000321.2	739	ttC/ttG	22/27	0.73130225701533	3	FACETS	0.923	0.882	0.962	0.923	0.882	0.962	CLONAL	3	TRUE	0	0.731272879648249	3		116	259	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542851	187542851	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062982-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	419	304	0	ENST00000441802.2:c.4889A>T	p.Gln1630Leu	p.Q1630L	ENST00000441802	NM_005245.3	1630	cAa/cTa	10/27	0.73130225701533	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.731272879648249	2		304	534	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793799	89793799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062982-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	240	339	0	ENST00000336032.3:c.868C>T	p.Pro290Ser	p.P290S	ENST00000336032	NM_006813.2	290	Cct/Tct	2/2	0.73130225701533	3	FACETS	1	0.984	1	0.576	0.54	0.613	CLONAL	1	TRUE	1	0.731272879648249	3		339	778	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2047249	2047249	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062982-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	42	99	0	ENST00000349721.2:c.811G>A	p.Gly271Ser	p.G271S	ENST00000349721	NM_003070.3	271	Ggc/Agc	5/34	0.706867575463098	4	FACETS	0.839	0.706	0.984	0.42	0.353	0.492	CLONAL	1	TRUE	2	0.731272879648249	4		99	237	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28929495	NA	P-0062982-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	7632	364	0	ENST00000275493.2:c.2155G>A	p.Gly719Ser	p.G719S	ENST00000275493	NM_005228.3	719	Ggc/Agc	18/28	0.94903101682505	23	FACETS	1	0.999	1	0.978	0.975	0.981	CLONAL	22	TRUE	0	0.94903101682505	23		364	7839	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0062982-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	1140	464	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.94903101682505	4	FACETS	1	0.998	1	1	0.998	1	CLONAL	4	TRUE	0	0.94903101682505	4		464	1156	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0062982-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	8533	303	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.94903101682505	23	FACETS	0.98	0.977	0.982	0.98	0.977	0.982	CLONAL	23	TRUE	0	0.94903101682505	23		303	8750	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208064	5208064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753044393	NA	P-0062982-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	61	614	1	ENST00000357368.4:c.5647G>A	p.Gly1883Ser	p.G1883S	ENST00000357368	NM_002850.3	1883	Ggc/Agc	37/38	0.94903101682505	2	FACETS	0.162	0.139	0.187	0.081	0.069	0.094	SUBCLONAL	1	TRUE	0	0.94903101682505	2		615	795	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039219	49039219	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062982-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	139	202	1	ENST00000267163.4:c.2297C>G	p.Thr766Arg	p.T766R	ENST00000267163	NM_000321.2	766	aCa/aGa	22/27	0.94903101682505	3	FACETS	0.935	0.903	0.962	0.935	0.903	0.962	CLONAL	3	TRUE	0	0.94903101682505	3		203	154	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039187	49039187	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062982-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	113	171	0	ENST00000267163.4:c.2265C>G	p.Phe755Leu	p.F755L	ENST00000267163	NM_000321.2	755	ttC/ttG	22/27	0.94903101682505	3	FACETS	0.959	0.927	0.985	0.959	0.927	0.985	CLONAL	3	TRUE	0	0.94903101682505	3		171	122	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039174	49039174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062982-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	100	154	0	ENST00000267163.4:c.2252C>T	p.Ser751Phe	p.S751F	ENST00000267163	NM_000321.2	751	tCt/tTt	22/27	0.94903101682505	3	FACETS	0.95	0.914	0.979	0.95	0.914	0.979	CLONAL	3	TRUE	0	0.94903101682505	3		154	109	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039240	49039241	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0062982-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	114	205	0	ENST00000267163.4:c.2318_2319delinsTT	p.Ser773Phe	p.S773F	ENST00000267163	NM_000321.2	773	tCC/tTT	22/27	0.94903101682505	3	FACETS	0.923	0.885	0.954	0.923	0.885	0.954	CLONAL	3	TRUE	0	0.94903101682505	3		205	128	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039139	49039139	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062982-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4	76	116	0	ENST00000267163.4:c.2217C>G	p.Phe739Leu	p.F739L	ENST00000267163	NM_000321.2	739	ttC/ttG	22/27	0.94903101682505	3	FACETS	0.984	0.948	1	0.984	0.948	1	CLONAL	3	TRUE	0	0.94903101682505	3		116	80	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542851	187542851	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062982-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	484	304	0	ENST00000441802.2:c.4889A>T	p.Gln1630Leu	p.Q1630L	ENST00000441802	NM_005245.3	1630	cAa/cTa	10/27	0.94903101682505	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.94903101682505	2		304	507	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793799	89793799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062982-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	242	339	0	ENST00000336032.3:c.868C>T	p.Pro290Ser	p.P290S	ENST00000336032	NM_006813.2	290	Cct/Tct	2/2	0.215334512273734	6	FACETS	0.827	0.773	0.881	0.276	0.257	0.294	INDETERMINATE	2	TRUE	0	0.94903101682505	6		339	894	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2047249	2047249	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062982-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	79	99	0	ENST00000349721.2:c.811G>A	p.Gly271Ser	p.G271S	ENST00000349721	NM_003070.3	271	Ggc/Agc	5/34	0.94903101682505	5	FACETS	1	0.89	1	0.335	0.296	0.377	CLONAL	1	TRUE	2	0.94903101682505	5		99	401	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50827465	50827465	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062982-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	136	407	0	ENST00000398568.2:c.2350C>A	p.Gln784Lys	p.Q784K	ENST00000398568	NM_001042412.1	784	Cag/Aag	16/18	0.215334512273734	6	FACETS	0.935	0.85	1	0.156	0.141	0.171	INDETERMINATE	1	TRUE	0	0.94903101682505	6		407	888	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248678	212248678	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062982-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	89	550	0	ENST00000342788.4:c.3589A>G	p.Lys1197Glu	p.K1197E	ENST00000342788	NM_005235.2	1197	Aag/Gag	28/28	0.94903101682505	3	FACETS	0.277	0.245	0.312	0.092	0.081	0.104	SUBCLONAL	1	TRUE	0	0.94903101682505	3		550	998	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0062998-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	360	431	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.550541671055585	3	FACETS	0.835	0.801	0.868	0.835	0.801	0.868	CLONAL	3	TRUE	0	0.633087814110939	3		431	598	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0062998-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1393	34	473	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.633087814110939	7	FACETS	0.194	0.158	0.236	0.032	0.026	0.04	SUBCLONAL	1	TRUE	1	0.633087814110939	7		473	1427	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249009	55249010	+	inframe_insertion	In_Frame_Ins	INS	-	-	GACAACCCC	novel	NA	P-0062998-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	920	506	0	ENST00000275493.2:c.2308_2316dup	p.Asp770_Pro772dup	p.D770_P772dup	ENST00000275493	NM_005228.3	770	-/GACAACCCC	20/28	0.633087814110939	7	FACETS	0.944	0.919	0.968	0.786	0.766	0.807	CLONAL	5	TRUE	1	0.633087814110939	7		506	1591	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249092	55249092	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062998-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1280	138	465	0	ENST00000275493.2:c.2390G>C	p.Cys797Ser	p.C797S	ENST00000275493	NM_005228.3	797	tGc/tCc	20/28	0.633087814110939	7	FACETS	0.794	0.72	0.872	0.132	0.12	0.146	SUBCLONAL	1	TRUE	1	0.633087814110939	7		465	1418	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249019	55249019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062998-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	1046	500	0	ENST00000275493.2:c.2317C>T	p.His773Tyr	p.H773Y	ENST00000275493	NM_005228.3	773	Cac/Tac	20/28	0.633087814110939	7	FACETS	0.946	0.927	0.966	0.946	0.927	0.966	CLONAL	6	TRUE	1	0.633087814110939	7		500	1503	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105901	27105901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062998-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	336	545	0	ENST00000324856.7:c.5512G>A	p.Asp1838Asn	p.D1838N	ENST00000324856	NM_006015.4	1838	Gac/Aac	20/20	0.302779442125051	4	FACETS	0.963	0.914	1	0.963	0.914	1	INDETERMINATE	2	TRUE	2	0.633087814110939	4		545	900	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015093	37015093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062998-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	42	476	1	ENST00000358127.4:c.311G>A	p.Arg104His	p.R104H	ENST00000358127	NM_001280556.1	104	cGc/cAc	3/10	0.633087814110939	3	FACETS	0.217	0.18	0.258	0.072	0.06	0.086	SUBCLONAL	1	TRUE	0	0.633087814110939	3		477	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0063072-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	225	699	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.45214546853136	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.451062178829049	2		699	456	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533137	63533137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1598097941	NA	P-0063072-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	89	836	1	ENST00000307078.5:c.1757C>T	p.Thr586Met	p.T586M	ENST00000307078	NM_004655.3	586	aCg/aTg	7/11	0.451062178829049	8	FACETS	0.887	0.784	0.997	0.127	0.112	0.143	CLONAL	1	TRUE	1	0.451062178829049	8		837	1047	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225343	26225425	+	coding_sequence_variant,5_prime_UTR_variant	Frame_Shift_Del	DEL	CAAACCAATCTTCCTAACTCATTTACTTTGCAGATGAACTATGGCGCGTACTAAGCAGACGGCTCGTAAATCCACAGGCGGTA	CAAACCAATCTTCCTAACTCATTTACTTTGCAGATGAACTATGGCGCGTACTAAGCAGACGGCTCGTAAATCCACAGGCGGTA	-	novel	NA	P-0063072-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	62	536	0				ENST00000360408	NM_003532.2	?-15/136		1/1	0.25467633049401	5	FACETS	0.904	0.782	1	0.301	0.26	0.346	INDETERMINATE	1	TRUE	2	0.451062178829049	5		536	510	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426414	47426415	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0063072-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	82	1203	2	ENST00000377045.4:c.763dup	p.Arg255ProfsTer33	p.R255Pfs*33	ENST00000377045	NM_001654.4	253	acc/aCcc	9/16	0.273179910176615	4	FACETS	0.498	0.437	0.563	0.249	0.218	0.282	SUBCLONAL	1	TRUE	2	0.451062178829049	4		1205	1060	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156740	20156740	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063072-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	95	352	0	ENST00000379607.5:c.17G>A	p.Gly6Asp	p.G6D	ENST00000379607	NM_001412.3	6	gGt/gAt	2/7	0.672472091728072	4	FACETS	0.851	0.771	0.934	0.851	0.771	0.934	CLONAL	2	TRUE	2	0.812201666160956	4		352	249	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105841	27105842	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGAA	novel	NA	P-0063072-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	112	907	0	ENST00000324856.7:c.5453_5456dup	p.Asn1820GlufsTer3	p.N1820Efs*3	ENST00000324856	NM_006015.4	1818	cag/cAGAAag	20/20	0.77231696597326	3	FACETS	0.885	0.802	0.973	0.443	0.401	0.487	CLONAL	1	TRUE	1	0.812201666160956	3		907	438	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023725	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGGGAGGC	GGGGGGAGGC	-	novel	NA	P-0063072-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	185	910	0	ENST00000324856.7:c.824_833del	p.Gly275AlafsTer85	p.G275Afs*85	ENST00000324856	NM_006015.4	274	atGGGGGGAGGC/at	1/20	0.77231696597326	3	FACETS	0.793	0.742	0.844	0.793	0.742	0.844	SUBCLONAL	2	TRUE	1	0.812201666160956	3		910	404	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265145	198265145	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	170	477	0	ENST00000335508.6:c.2732T>G	p.Leu911Trp	p.L911W	ENST00000335508	NM_012433.2	911	tTg/tGg	19/25	0.411203500200291	1	FACETS	0.466	0.43	0.504	0.466	0.43	0.504	INDETERMINATE	1	TRUE	0	0.706187896836584	1		477	668	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0063082-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	26	372	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.663	0.524	0.823	0.663	0.524	0.823	SUBCLONAL	1	TRUE	1	0.15	2		372	523	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584513	48584514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs377767334	NA	P-0063082-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	37	471	0	ENST00000342988.3:c.692dup	p.Ser232GlnfsTer3	p.S232Qfs*3	ENST00000342988	NM_005359.5	229	ctg/ctGg	6/12	1	2	FACETS	0.862	0.71	1	0.862	0.71	1	CLONAL	1	TRUE	1	0.15	2		471	572	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187847	11187847	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063082-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	34	405	0	ENST00000361445.4:c.6050T>C	p.Ile2017Thr	p.I2017T	ENST00000361445	NM_004958.3	2017	aTc/aCc	44/58	0.112202005148134	3	FACETS	0.802	0.653	0.969	0.401	0.326	0.485	CLONAL	1	TRUE	1	0.15	3		405	608	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161742	47161742	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063082-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	42	511	0	ENST00000409792.3:c.4384G>T	p.Glu1462Ter	p.E1462*	ENST00000409792	NM_014159.6	1462	Gaa/Taa	3/21	1	2	FACETS	0.807	0.672	0.957	0.807	0.672	0.957	CLONAL	1	TRUE	1	0.15	2		511	694	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110674	2110674	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs754596133	NA	P-0063093-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	43	547	0	ENST00000219476.3:c.979A>G	p.Met327Val	p.M327V	ENST00000219476	NM_000548.3	327	Atg/Gtg	11/42	1	2	FACETS	0.42	0.35	0.498	0.42	0.35	0.498	SUBCLONAL	1	TRUE	1	0.28	2		547	731	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063096-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	73	523	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.547	0.482	0.617	0.547	0.482	0.617	SUBCLONAL	1	TRUE	1	0.755914289143442	2		523	353	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0063096-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	21	103	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.478107484521153	1	FACETS	0.288	0.225	0.36	0.288	0.225	0.36	SUBCLONAL	1	TRUE	0	0.755914289143442	1		103	120	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229279	36229279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063096-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	49	677	0	ENST00000222270.7:c.7969C>T	p.Pro2657Ser	p.P2657S	ENST00000222270	NM_014727.1	2657	Ccc/Tcc	37/37	1	2	FACETS	0.176	0.149	0.207	0.176	0.149	0.207	SUBCLONAL	1	TRUE	1	0.755914289143442	2		677	735	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211805	123211805	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0063096-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	182	592	0	ENST00000218089.9:c.2674-2A>C		p.X892_splice	ENST00000218089	NM_001042749.1	892			1	2	FACETS	0.663	0.614	0.715	0.663	0.614	0.715	SUBCLONAL	1	TRUE	1	0.755914289143442	2		592	726	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858044	152858044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557026036	NA	P-0063096-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	143	552	0	ENST00000406277.2:c.571G>A	p.Val191Met	p.V191M	ENST00000406277	NM_152274.4	191	Gtg/Atg	6/7	1	2	FACETS	0.632	0.578	0.687	0.632	0.578	0.687	SUBCLONAL	1	TRUE	1	0.755914289143442	2		552	599	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063160-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	123	523	0				ENST00000310581	NM_198253.2	-/1132			0.188802179801175	4	FACETS	0.926	0.846	1	1	0.984	1	CLONAL	3	TRUE	2	0.286918843227832	4		523	397	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0063160-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	84	623	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.286918843227832	2		623	468	SUCCESS
FH	2271	MSKCC	GRCh37	1	241661135	241661136	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	CA	novel	NA	P-0063160-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	21	380	0	ENST00000366560.3:c.1525_1526delinsTG	p.Pro509Ter	p.P509*	ENST00000366560	NM_000143.3	509	CCa/TGa	10/10	0.239878031516935	2	FACETS	0.4	0.307	0.508	0.2	0.153	0.254	SUBCLONAL	1	TRUE	0	0.286918843227832	2		380	366	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916747	48916747	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690915	NA	P-0063160-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	65	271	0	ENST00000267163.4:c.277C>T	p.Gln93Ter	p.Q93*	ENST00000267163	NM_000321.2	93	Caa/Taa	3/27	0.2542651977454	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	2	TRUE	0	0.286918843227832	2		271	213	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0063160-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	94	467	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.286918843227832	2		467	540	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007656	62007656	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs912718113	NA	P-0063160-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	83	558	0	ENST00000392795.3:c.211G>A	p.Ala71Thr	p.A71T	ENST00000392795	NM_001039933.1	71	Gcc/Acc	3/6	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.286918843227832	2		558	536	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911464	134911464	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063160-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	86	455	0	ENST00000398015.3:c.1929G>T	p.Lys643Asn	p.K643N	ENST00000398015	NM_004441.4	643	aaG/aaT	11/16	0.286918843227832	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.286918843227832	1		455	458	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27220064	27220064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780622660	NA	P-0063160-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	66	397	0	ENST00000380036.4:c.3121G>A	p.Gly1041Arg	p.G1041R	ENST00000380036	NM_000459.3	1041	Ggg/Agg	21/23	0.286918843227832	3	FACETS	0.95	0.825	1	0.475	0.412	0.542	CLONAL	1	TRUE	1	0.286918843227832	3		397	554	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039371	47039378	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGTCAT	CGCGTCAT	-	novel	NA	P-0063160-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	141	297	0	ENST00000377604.3:c.994_1001del	p.Arg332LysfsTer46	p.R332Kfs*46	ENST00000377604	NM_001204468.1	332	CGCGTCATa/a	10/24	0.241015234568397	2	FACETS	0.984	0.91	1			1	CLONAL	3	TRUE	NA	0.286918843227832	2		297	333	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063162-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	167	523	0				ENST00000310581	NM_198253.2	-/1132			0.884372750460064	1	FACETS	0.958	0.913	0.999	0.958	0.913	0.999	CLONAL	1	TRUE	0	0.884372750460064	1		523	220	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553249	106553249	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1415765117	NA	P-0063162-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	390	696	0	ENST00000369096.4:c.1214C>T	p.Ser405Leu	p.S405L	ENST00000369096	NM_001198.3	405	tCg/tTg	5/7	0.884372750460064	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.884372750460064	1		696	473	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0063162-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	573	222	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.884372750460064	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.884372750460064	2		222	641	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233100	69233100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867680779	NA	P-0063162-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	252	215	0	ENST00000462284.1:c.965C>T	p.Pro322Leu	p.P322L	ENST00000462284	NM_002392.5	322	cCa/cTa	11/11	1	2	FACETS	0.93	0.877	0.983	0.93	0.877	0.983	CLONAL	1	TRUE	1	0.884372750460064	2		215	613	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46276064	46276064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370656650	NA	P-0063162-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	371	562	0	ENST00000371998.3:c.3500C>T	p.Pro1167Leu	p.P1167L	ENST00000371998		1167	cCc/cTc	18/23	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.884372750460064	2		562	836	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879260	151879260	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063162-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	358	613	0	ENST00000262189.6:c.5685G>A	p.Met1895Ile	p.M1895I	ENST00000262189	NM_170606.2	1895	atG/atA	36/59	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.884372750460064	2		613	780	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1696691	1696691	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063162-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	120	454	0	ENST00000378625.1:c.155C>A	p.Ala52Asp	p.A52D	ENST00000378625	NM_001198994.1	52	gCc/gAc	2/14	0.884372750460064	2	FACETS	0.383	0.346	0.422	0.191	0.173	0.211	SUBCLONAL	1	TRUE	0	0.884372750460064	2		454	709	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667539	241667539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063162-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	524	225	0	ENST00000366560.3:c.911C>T	p.Pro304Leu	p.P304L	ENST00000366560	NM_000143.3	304	cCt/cTt	7/10	0.864874791581205	4	FACETS	0.976	0.947	1	0.732	0.71	0.753	CLONAL	3	TRUE	0	0.884372750460064	4		225	763	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595933	43595933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063162-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	287	498	0	ENST00000355710.3:c.100G>A	p.Asp34Asn	p.D34N	ENST00000355710	NM_020975.4	34	Gat/Aat	2/20	1	2	FACETS	0.979	0.927	1	0.979	0.927	1	CLONAL	1	TRUE	1	0.884372750460064	2		498	663	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724669	112724669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063162-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	220	147	0	ENST00000369452.4:c.553C>T	p.Pro185Ser	p.P185S	ENST00000369452	NM_007373.3	185	Cct/Tct	2/9	1	2	FACETS	0.932	0.875	0.989	0.932	0.875	0.989	CLONAL	1	TRUE	1	0.884372750460064	2		147	534	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245286	46245286	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063162-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	319	502	0	ENST00000334344.6:c.3380T>C	p.Val1127Ala	p.V1127A	ENST00000334344	NM_152641.2	1127	gTt/gCt	15/21	1	2	FACETS	0.974	0.925	1	0.974	0.925	1	CLONAL	1	TRUE	1	0.884372750460064	2		502	741	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354447	91354447	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063162-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	346	495	0	ENST00000355112.3:c.3887C>T	p.Ser1296Phe	p.S1296F	ENST00000355112	NM_000057.2	1296	tCc/tTc	21/22	0.884372750460064	3	FACETS	1	0.977	1	0.527	0.499	0.555	CLONAL	1	TRUE	1	0.884372750460064	3		495	1071	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857541	9857541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063162-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	282	512	0	ENST00000330684.3:c.3860G>A	p.Ser1287Asn	p.S1287N	ENST00000330684	NM_001134407.1	1287	aGc/aAc	13/13	1	2	FACETS	0.981	0.929	1	0.981	0.929	1	CLONAL	1	TRUE	1	0.884372750460064	2		512	650	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391170	139391171	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0063162-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	342	764	0	ENST00000277541.6:c.7020dup	p.Ser2341LeufsTer13	p.S2341Lfs*13	ENST00000277541	NM_017617.3	2340	-/C	34/34	0.884372750460064	1	FACETS	0.888	0.856	0.918	0.888	0.856	0.918	CLONAL	1	TRUE	0	0.884372750460064	1		764	486	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0063169-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	25	331	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.906	0.714	1	0.906	0.714	1	CLONAL	1	TRUE	1	0.16	2		331	345	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0063169-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	55	496	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.16	2		496	676	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324057	31324057	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs12697943	NA	P-0063169-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	57	458	0	ENST00000412585.2:c.506G>T	p.Arg169Leu	p.R169L	ENST00000412585	NM_005514.6	169	cGc/cTc	3/8	0.175528757529936	3	FACETS	1	0.919	1	0.554	0.474	0.641	CLONAL	1	TRUE	1	0.16	3		458	695	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916815	48916823	+	frameshift_variant	Frame_Shift_Del	DEL	CACTTTTAC	CACTTTTAC	T	novel	NA	P-0063169-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	15	324	0	ENST00000267163.4:c.345_353delinsT	p.Thr116Ter	p.T116*	ENST00000267163	NM_000321.2	115	ttCACTTTTACt/ttTt	3/27	1	2	FACETS	1	0.78	1	1	0.78	1	CLONAL	1	TRUE	1	0.16	2		324	175	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0063214-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	181	372	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.20668081176453	3	FACETS	0.759	0.706	0.812	0.759	0.706	0.812	INDETERMINATE	2	TRUE	1	0.647018364469217	3		372	488	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0063231-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	53	704	9	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.623	0.532	0.722	0.623	0.532	0.722	SUBCLONAL	1	FALSE	1	0.374685630385844	2		713	454	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124532352	124532352	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063231-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	18	342	0	ENST00000357628.3:c.92T>C	p.Phe31Ser	p.F31S	ENST00000357628	NM_015450.2	31	tTc/tCc	6/19	1	2	FACETS	0.717	0.545	0.916	0.717	0.545	0.916	CLONAL	1	FALSE	1	0.374685630385844	2		342	134	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652020	36652020	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1407742055	NA	P-0063238-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	53	519	0	ENST00000244741.5:c.142C>T	p.Arg48Ter	p.R48*	ENST00000244741	NM_000389.4	48	Cga/Tga	2/3	0.571484746522026	2	FACETS	0.203	0.172	0.236	0.101	0.086	0.118	SUBCLONAL	1	TRUE	0	0.683214554298409	2		519	766	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652120	36652139	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCCCGGCGAGGCCGGGAT	GGCCCCGGCGAGGCCGGGAT	-	novel	NA	P-0063238-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	464	567	0	ENST00000244741.5:c.243_262del	p.Pro82ValfsTer40	p.P82Vfs*40	ENST00000244741	NM_000389.4	81	gGGCCCCGGCGAGGCCGGGAT/g	2/3	0.571484746522026	2	FACETS	0.867	0.836	0.898	0.867	0.836	0.898	CLONAL	2	TRUE	0	0.683214554298409	2		567	783	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942732	44942732	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063238-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	155	119	0	ENST00000377967.4:c.3312del	p.Lys1105AsnfsTer15	p.K1105Nfs*15	ENST00000377967	NM_021140.2	1104	acT/ac	23/29	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.683214554298409	1		119	240	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591143	67591146	+	protein_altering_variant	In_Frame_Del	DEL	AATA	AATA	C	novel	NA	P-0063238-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	182	366	0	ENST00000274335.5:c.1736_1739delinsC	p.Gln579_Tyr580delinsPro	p.Q579_Y580delinsP	ENST00000274335		579	cAATAc/cCc	12/15	1	2	FACETS	0.914	0.848	0.981	0.914	0.848	0.981	CLONAL	1	TRUE	1	0.683214554298409	2		366	583	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713736	30713738	+	missense_variant	Missense_Mutation	TNP	TCG	TCG	CCC	novel	NA	P-0063238-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	227	536	0	ENST00000295754.5:c.1061_1063delinsCCC	p.Leu354_Ala355delinsProPro	p.L354_A355delinsPP	ENST00000295754	NM_003242.5	354	cTCGcc/cCCCcc	4/7	1	2	FACETS	0.888	0.831	0.948	0.888	0.831	0.948	CLONAL	1	TRUE	1	0.683214554298409	2		536	748	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	136	523	0				ENST00000310581	NM_198253.2	-/1132			0.100893599663695	3	FACETS	1	0.985	1	0.67	0.617	0.724	INDETERMINATE	1	TRUE	1	0.785322365829697	3		523	360	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683876	117683876	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs781304519	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	145	430	0	ENST00000368508.3:c.3271C>G	p.Gln1091Glu	p.Q1091E	ENST00000368508	NM_002944.2	1091	Caa/Gaa	21/43	1	2	FACETS	0.801	0.737	0.867	0.801	0.737	0.867	CLONAL	1	TRUE	1	0.785322365829697	2		430	461	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	119	420	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	0.375549969260171	1	FACETS	0.309	0.279	0.34	0.309	0.279	0.34	INDETERMINATE	1	TRUE	0	0.785322365829697	1		420	596	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047495	49047495	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs587778838	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	77	273	0	ENST00000267163.4:c.2490-1G>A		p.X830_splice	ENST00000267163	NM_000321.2	830			0.785322365829697	1	FACETS	0.559	0.5	0.62	0.559	0.5	0.62	SUBCLONAL	1	TRUE	0	0.785322365829697	1		273	213	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	328	702	0	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	0.785322365829697	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.785322365829697	1		702	467	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41962024	41962024	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	174	607	0	ENST00000219905.7:c.932C>G	p.Ser311Ter	p.S311*	ENST00000219905	NM_001164273.1	311	tCa/tGa	2/24	0.433229073970589	1	FACETS	0.482	0.447	0.519	0.482	0.447	0.519	INDETERMINATE	1	TRUE	0	0.785322365829697	1		607	558	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224296	55224296	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	92	561	0	ENST00000275493.2:c.1077C>G	p.Phe359Leu	p.F359L	ENST00000275493	NM_005228.3	359	ttC/ttG	9/28	0.543371291979137	1	FACETS	0.301	0.269	0.336	0.301	0.269	0.336	SUBCLONAL	1	TRUE	0	0.785322365829697	1		561	472	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830136	72830136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	132	647	1	ENST00000268489.5:c.6445C>T	p.Arg2149Cys	p.R2149C	ENST00000268489	NM_006885.3	2149	Cgc/Tgc	9/10	1	2	FACETS	0.535	0.487	0.586	0.535	0.487	0.586	SUBCLONAL	1	TRUE	1	0.785322365829697	2		648	628	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911771	26911771	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	82	350	0	ENST00000381527.3:c.196G>C	p.Glu66Gln	p.E66Q	ENST00000381527	NM_001260.1	66	Gaa/Caa	2/13	1	2	FACETS	0.507	0.449	0.568	0.507	0.449	0.568	SUBCLONAL	1	TRUE	1	0.785322365829697	2		350	412	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106822	27106822	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	106	714	0	ENST00000324856.7:c.6433G>T	p.Glu2145Ter	p.E2145*	ENST00000324856	NM_006015.4	2145	Gag/Tag	20/20	0.375549969260171	1	FACETS	0.286	0.257	0.317	0.286	0.257	0.317	INDETERMINATE	1	TRUE	0	0.785322365829697	1		714	573	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222530	2222530	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760394488	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	107	591	0	ENST00000398665.3:c.3362C>T	p.Ser1121Leu	p.S1121L	ENST00000398665	NM_032482.2	1121	tCg/tTg	24/28	0.537868752618116	1	FACETS	0.414	0.374	0.455	0.414	0.374	0.455	SUBCLONAL	1	TRUE	0	0.785322365829697	1		591	400	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46736381	46736381	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs559500678	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	108	546	0	ENST00000371975.4:c.1093C>T	p.Arg365Ter	p.R365*	ENST00000371975	NM_003579.3	365	Cga/Tga	10/18	0.375549969260171	1	FACETS	0.322	0.29	0.356	0.322	0.29	0.356	INDETERMINATE	1	TRUE	0	0.785322365829697	1		546	519	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830868	72830868	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	176	817	0	ENST00000268489.5:c.5713C>T	p.Pro1905Ser	p.P1905S	ENST00000268489	NM_006885.3	1905	Ccg/Tcg	9/10	1	2	FACETS	0.591	0.545	0.638	0.591	0.545	0.638	SUBCLONAL	1	TRUE	1	0.785322365829697	2		817	759	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965427	68965427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	245	506	0	ENST00000288368.4:c.1039G>A	p.Glu347Lys	p.E347K	ENST00000288368	NM_024870.2	347	Gaa/Aaa	9/40	1	2	FACETS	0.989	0.931	1	0.989	0.931	1	CLONAL	1	TRUE	1	0.785322365829697	2		506	631	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342518	118342518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	47	532	1	ENST00000534358.1:c.644C>T	p.Ser215Phe	p.S215F	ENST00000534358	NM_005933.3	215	tCt/tTt	3/36	0.785322365829697	1	FACETS	0.175	0.147	0.205	0.175	0.147	0.205	SUBCLONAL	1	TRUE	0	0.785322365829697	1		533	416	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805422	46805422	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	126	720	1	ENST00000290295.7:c.534G>A	p.Trp178Ter	p.W178*	ENST00000290295	NM_006361.5	178	tgG/tgA	1/2	1	2	FACETS	0.528	0.479	0.579	0.528	0.479	0.579	SUBCLONAL	1	TRUE	1	0.785322365829697	2		721	608	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802635	135802635	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203343	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	21	468	0	ENST00000298552.3:c.163C>T	p.Gln55Ter	p.Q55*	ENST00000298552	NM_001162426.1	55	Cag/Tag	4/23	0.785322365829697	1	FACETS	0.081	0.062	0.104	0.081	0.062	0.104	SUBCLONAL	1	TRUE	0	0.785322365829697	1		468	400	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78765262	78765262	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs765785590	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	60	366	0	ENST00000306801.3:c.843G>C	p.Gln281His	p.Q281H	ENST00000306801	NM_020761.2	281	caG/caC	7/34	1	2	FACETS	0.33	0.285	0.379	0.33	0.285	0.379	SUBCLONAL	1	TRUE	1	0.785322365829697	2		366	463	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675577	30675577	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	120	691	0	ENST00000376406.3:c.2779G>C	p.Glu927Gln	p.E927Q	ENST00000376406	NM_014641.2	927	Gag/Cag	8/15	1	2	FACETS	0.443	0.4	0.488	0.443	0.4	0.488	SUBCLONAL	1	TRUE	1	0.785322365829697	2		691	690	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981084	201981084	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	122	529	0	ENST00000359651.3:c.164-1G>C		p.X55_splice	ENST00000359651		55			0.375549969260171	1	FACETS	0.418	0.381	0.458	0.418	0.381	0.458	INDETERMINATE	1	TRUE	0	0.785322365829697	1		529	451	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426682	49426682	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	333	832	0	ENST00000301067.7:c.11806C>T	p.Gln3936Ter	p.Q3936*	ENST00000301067	NM_003482.3	3936	Cag/Tag	39/54	0.100893599663695	3	FACETS	1	0.992	1	0.617	0.585	0.65	INDETERMINATE	1	TRUE	1	0.785322365829697	3		832	957	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105846	27105846	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	108	641	0	ENST00000324856.7:c.5457G>C	p.Lys1819Asn	p.K1819N	ENST00000324856	NM_006015.4	1819	aaG/aaC	20/20	0.375549969260171	1	FACETS	0.298	0.268	0.329	0.298	0.268	0.329	INDETERMINATE	1	TRUE	0	0.785322365829697	1		641	561	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105979	27105979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1371851589	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	129	683	0	ENST00000324856.7:c.5590G>A	p.Glu1864Lys	p.E1864K	ENST00000324856	NM_006015.4	1864	Gag/Aag	20/20	0.375549969260171	1	FACETS	0.347	0.316	0.38	0.347	0.316	0.38	INDETERMINATE	1	TRUE	0	0.785322365829697	1		683	575	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439730	51439730	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs537858214	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	133	592	0	ENST00000262662.1:c.295G>C	p.Glu99Gln	p.E99Q	ENST00000262662		99	Gag/Cag	4/4	0.375549969260171	1	FACETS	0.367	0.334	0.401	0.367	0.334	0.401	INDETERMINATE	1	TRUE	0	0.785322365829697	1		592	561	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430755	78430755	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	299	558	0	ENST00000370768.2:c.634C>T	p.Gln212Ter	p.Q212*	ENST00000370768	NM_003902.3	212	Cag/Tag	8/20	0.375549969260171	1	FACETS	0.752	0.715	0.789	0.752	0.715	0.789	INDETERMINATE	1	TRUE	0	0.785322365829697	1		558	615	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150936790	150936790	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	156	650	0	ENST00000271640.5:c.3826G>T	p.Glu1276Ter	p.E1276*	ENST00000271640	NM_001145415.1	1276	Gag/Tag	22/22	0.375549969260171	1	FACETS	0.337	0.309	0.366	0.337	0.309	0.366	INDETERMINATE	1	TRUE	0	0.785322365829697	1		650	717	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415828	49415828	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	251	562	0	ENST00000301067.7:c.16519G>T	p.Glu5507Ter	p.E5507*	ENST00000301067	NM_003482.3	5507	Gag/Tag	53/54	0.100893599663695	3	FACETS	1	0.993	1	0.713	0.672	0.755	INDETERMINATE	1	TRUE	1	0.785322365829697	3		562	624	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436655	49436655	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	231	554	0	ENST00000301067.7:c.5651C>G	p.Pro1884Arg	p.P1884R	ENST00000301067	NM_003482.3	1884	cCc/cGc	26/54	0.100893599663695	3	FACETS	1	0.992	1	0.688	0.647	0.731	INDETERMINATE	1	TRUE	1	0.785322365829697	3		554	595	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123875220	123875220	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1423140279	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	80	200	0	ENST00000330479.4:c.176G>A	p.Ser59Asn	p.S59N	ENST00000330479	NM_020382.3	59	aGc/aAc	3/9	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.785322365829697	2		200	192	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680695	88680696	+	missense_variant	Missense_Mutation	DNP	AG	AG	TA	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	89	481	0	ENST00000360948.2:c.561_562delinsTA	p.Tyr188Asn	p.Y188N	ENST00000360948	NM_001012338.2	187	ctCTac/ctTAac	6/19	0.433229073970589	1	FACETS	0.339	0.302	0.378	0.339	0.302	0.378	INDETERMINATE	1	TRUE	0	0.785322365829697	1		481	406	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934338	81934338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	210	558	0	ENST00000359376.3:c.1315G>A	p.Asp439Asn	p.D439N	ENST00000359376	NM_002661.3	439	Gac/Aac	14/33	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.785322365829697	2		558	510	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944200	81944200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	172	605	0	ENST00000359376.3:c.1809C>A	p.Asp603Glu	p.D603E	ENST00000359376	NM_002661.3	603	gaC/gaA	18/33	1	2	FACETS	0.916	0.851	0.983	0.916	0.851	0.983	CLONAL	1	TRUE	1	0.785322365829697	2		605	478	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546113	29546113	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	108	534	0	ENST00000356175.3:c.1618G>C	p.Glu540Gln	p.E540Q	ENST00000356175	NM_000267.3	540	Gag/Cag	14/57	1	2	FACETS	0.4	0.359	0.444	0.4	0.359	0.444	SUBCLONAL	1	TRUE	1	0.785322365829697	2		534	687	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760956	59760956	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555572587	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	73	508	0	ENST00000259008.2:c.3451G>A	p.Glu1151Lys	p.E1151K	ENST00000259008	NM_032043.2	1151	Gaa/Aaa	20/20	1	2	FACETS	0.328	0.287	0.373	0.328	0.287	0.373	SUBCLONAL	1	TRUE	1	0.785322365829697	2		508	566	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222536	2222536	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	105	555	0	ENST00000398665.3:c.3368C>T	p.Ser1123Phe	p.S1123F	ENST00000398665	NM_032482.2	1123	tCt/tTt	24/28	0.537868752618116	1	FACETS	0.43	0.388	0.473	0.43	0.388	0.473	SUBCLONAL	1	TRUE	0	0.785322365829697	1		555	378	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2225428	2225428	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	118	498	0	ENST00000398665.3:c.3638C>G	p.Ser1213Cys	p.S1213C	ENST00000398665	NM_032482.2	1213	tCt/tGt	26/28	0.537868752618116	1	FACETS	0.446	0.406	0.488	0.446	0.406	0.488	SUBCLONAL	1	TRUE	0	0.785322365829697	1		498	409	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051177	128051177	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	108	633	0	ENST00000285398.2:c.146C>G	p.Ser49Ter	p.S49*	ENST00000285398	NM_000122.1	49	tCa/tGa	2/15	0.398387826470739	1	FACETS	0.319	0.287	0.352	0.319	0.287	0.352	INDETERMINATE	1	TRUE	0	0.785322365829697	1		633	524	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31390271	31390271	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	243	590	0	ENST00000328111.2:c.2226G>C	p.Met742Ile	p.M742I	ENST00000328111	NM_006892.3	742	atG/atC	20/23	1	2	FACETS	0.968	0.911	1	0.968	0.911	1	CLONAL	1	TRUE	1	0.785322365829697	2		590	639	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29279773	29279773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	54	249	0	ENST00000544604.2:c.19G>A	p.Gly7Arg	p.G7R	ENST00000544604	NM_001206998.1	7	Ggg/Agg	1/9	0.44218966906814	1	FACETS	0.407	0.353	0.466	0.407	0.353	0.466	INDETERMINATE	1	TRUE	0	0.785322365829697	1		249	205	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29442863	29442863	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	119	539	0	ENST00000544604.2:c.904G>T	p.Asp302Tyr	p.D302Y	ENST00000544604	NM_001206998.1	302	Gat/Tat	6/9	0.44218966906814	1	FACETS	0.345	0.313	0.379	0.345	0.313	0.379	INDETERMINATE	1	TRUE	0	0.785322365829697	1		539	533	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275257	41275257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	114	587	0	ENST00000349496.5:c.1423C>T	p.His475Tyr	p.H475Y	ENST00000349496	NM_001904.3	475	Cac/Tac	9/15	0.375549969260171	1	FACETS	0.294	0.265	0.325	0.294	0.265	0.325	INDETERMINATE	1	TRUE	0	0.785322365829697	1		587	599	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1941450	1941450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	123	544	0	ENST00000382891.5:c.1826C>T	p.Ser609Leu	p.S609L	ENST00000382891	NM_133335.3	609	tCa/tTa	9/22	0.207433344010594	6	FACETS	0.765	0.691	0.845			1	INDETERMINATE	1	TRUE	NA	0.785322365829697	6		544	1052	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020724	26020724	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1426138687	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	269	637	0	ENST00000357647.3:c.7C>T	p.Arg3Cys	p.R3C	ENST00000357647	NM_003529.2	3	Cgc/Tgc	1/1	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.785322365829697	2		637	657	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671586	30671586	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	131	733	0	ENST00000376406.3:c.5374G>C	p.Glu1792Gln	p.E1792Q	ENST00000376406	NM_014641.2	1792	Gaa/Caa	10/15	1	2	FACETS	0.542	0.494	0.594	0.542	0.494	0.594	SUBCLONAL	1	TRUE	1	0.785322365829697	2		733	615	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675692	30675692	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	125	603	0	ENST00000376406.3:c.2664G>C	p.Glu888Asp	p.E888D	ENST00000376406	NM_014641.2	888	gaG/gaC	8/15	1	2	FACETS	0.476	0.431	0.523	0.476	0.431	0.523	SUBCLONAL	1	TRUE	1	0.785322365829697	2		603	669	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163348	32163348	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	125	709	0	ENST00000375023.3:c.5878G>C	p.Gly1960Arg	p.G1960R	ENST00000375023	NM_004557.3	1960	Ggt/Cgt	30/30	1	2	FACETS	0.479	0.434	0.526	0.479	0.434	0.526	SUBCLONAL	1	TRUE	1	0.785322365829697	2		709	665	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109309883	109309883	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	41	359	0	ENST00000436639.2:c.1432G>C	p.Asp478His	p.D478H	ENST00000436639	NM_014454.2	478	Gat/Cat	9/10	1	2	FACETS	0.297	0.248	0.352	0.297	0.248	0.352	SUBCLONAL	1	TRUE	1	0.785322365829697	2		359	351	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322535	109322535	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	100	516	0	ENST00000436639.2:c.502G>C	p.Asp168His	p.D168H	ENST00000436639	NM_014454.2	168	Gat/Cat	3/10	1	2	FACETS	0.421	0.376	0.468	0.421	0.376	0.468	SUBCLONAL	1	TRUE	1	0.785322365829697	2		516	605	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851125	151851130	+	inframe_deletion	In_Frame_Del	DEL	TACAGA	TACAGA	-	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	197	512	0	ENST00000262189.6:c.12241_12246del	p.Ser4081_Val4082del	p.S4081_V4082del	ENST00000262189	NM_170606.2	4081	TCTGTA/-	48/59	0.491051170591188	1	FACETS	0.72	0.676	0.765	0.72	0.676	0.765	SUBCLONAL	1	TRUE	0	0.785322365829697	1		512	423	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864248	151864248	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063243-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	32	414	0	ENST00000262189.6:c.9733C>G	p.Gln3245Glu	p.Q3245E	ENST00000262189	NM_170606.2	3245	Cag/Gag	42/59	0.491051170591188	1	FACETS	0.147	0.119	0.178	0.147	0.119	0.178	SUBCLONAL	1	TRUE	0	0.785322365829697	1		414	337	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0063245-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	552	473	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.409163084725522	5	FACETS	1	0.994	1	1	0.994	1	CLONAL	5	TRUE	0	0.409163084725522	5		473	801	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0063245-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	221	575	0	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.409163084725522	2	FACETS	0.961	0.902	1	0.961	0.902	1	CLONAL	2	TRUE	0	0.409163084725522	2		575	562	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971155	21971155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501260	NA	P-0063245-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	126	812	0	ENST00000304494.5:c.203C>T	p.Ala68Val	p.A68V	ENST00000304494	NM_000077.4	68	gCg/gTg	2/3	0.409163084725522	1	FACETS	0.862	0.784	0.945	0.862	0.784	0.945	CLONAL	1	TRUE	0	0.409163084725522	1		812	568	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144258384	144258385	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755581817	NA	P-0063245-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	119	621	2	ENST00000262995.4:c.50dup	p.Glu18GlyfsTer34	p.E18Gfs*34	ENST00000262995	NM_207123.2	15	tcc/tCcc	1/11	0.305844474153055	4	FACETS	0.912	0.822	1			1	CLONAL	1	TRUE	NA	0.409163084725522	4		623	899	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163328	47163328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063245-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	123	638	0	ENST00000409792.3:c.2798G>A	p.Gly933Asp	p.G933D	ENST00000409792	NM_014159.6	933	gGt/gAt	3/21	0.409163084725522	1	FACETS	0.966	0.879	1	0.966	0.879	1	CLONAL	1	TRUE	0	0.409163084725522	1		638	495	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929350	44929354	+	frameshift_variant	Frame_Shift_Ins	INS	CTTCA	CTTCA	TCTTCACCAT	novel	NA	P-0063245-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	122	381	0	ENST00000377967.4:c.2450_2454delinsTCTTCACCAT	p.Ser817PhefsTer52	p.S817Ffs*52	ENST00000377967	NM_021140.2	817	tCTTCA/tTCTTCACCAT	17/29	0.305844474153055	2	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.409163084725522	2		381	444	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0063251-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	250	494	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.433558379126313	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.433558379126313	2		494	525	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063251-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	101	416	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.433558379126313	1	FACETS	0.992	0.894	1	0.992	0.894	1	CLONAL	1	TRUE	0	0.433558379126313	1		416	368	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063718	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0063251-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	89	441	1	ENST00000412916.2:c.165+2dup		p.X55_splice	ENST00000412916		55			0.433558379126313	1	FACETS	0.932	0.834	1	0.932	0.834	1	CLONAL	1	TRUE	0	0.433558379126313	1		442	345	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0063251-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	71	531	2	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			0.210553662313197	1	FACETS	0.559	0.489	0.634	0.559	0.489	0.634	INDETERMINATE	1	TRUE	0	0.433558379126313	1		533	459	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245500	153245500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1304288466	NA	P-0063251-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	58	489	0	ENST00000281708.4:c.1691G>A	p.Arg564His	p.R564H	ENST00000281708	NM_033632.3	564	cGt/cAt	11/12	0.221902647152303	1	FACETS	0.477	0.411	0.549	0.477	0.411	0.549	INDETERMINATE	1	TRUE	0	0.433558379126313	1		489	439	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696682	47696682	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0063251-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	123	552	0	ENST00000347630.2:c.266T>A	p.Leu89Ter	p.L89*	ENST00000347630	NM_001007230.1	89	tTa/tAa	5/11	0.433558379126313	1	FACETS	0.96	0.874	1	0.96	0.874	1	CLONAL	1	TRUE	0	0.433558379126313	1		552	463	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675407	241675407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200343823	NA	P-0063251-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	35	388	0	ENST00000366560.3:c.415G>A	p.Val139Met	p.V139M	ENST00000366560	NM_000143.3	139	Gtg/Atg	4/10	0.433558379126313	3	FACETS	0.376	0.307	0.453	0.188	0.153	0.227	SUBCLONAL	1	TRUE	1	0.433558379126313	3		388	523	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130514	29130514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881696	NA	P-0063251-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	76	570	1	ENST00000328354.6:c.196G>A	p.Val66Met	p.V66M	ENST00000328354	NM_007194.3	66	Gtg/Atg	2/15	0.210553662313197	1	FACETS	0.504	0.442	0.57	0.504	0.442	0.57	INDETERMINATE	1	TRUE	0	0.433558379126313	1		571	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579315	7579324	+	frameshift_variant	Frame_Shift_Del	DEL	GCAAGTCACA	GCAAGTCACA	TGCCT	novel	NA	P-0063251-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	123	565	0	ENST00000269305.4:c.363_372delinsAGGCA	p.Val122GlyfsTer25	p.V122Gfs*25	ENST00000269305	NM_001126112.2	121	tcTGTGACTTGC/tcAGGCA	4/11	0.433558379126313	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.433558379126313	1		565	435	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0063253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	376	518	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.245294632346474	5	FACETS	1	0.98	1	1	0.98	1	CLONAL	4	TRUE	1	0.245294632346474	5		518	996	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0063253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	173	523	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.224056791673175	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.245294632346474	3		523	656	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628074	187628074	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	90	571	0	ENST00000441802.2:c.2908G>T	p.Gly970Ter	p.G970*	ENST00000441802	NM_005245.3	970	Gga/Tga	2/27	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.245294632346474	2		571	682	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034471	47034471	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	82	434	0	ENST00000377604.3:c.556C>T	p.Arg186Ter	p.R186*	ENST00000377604	NM_001204468.1	186	Cga/Tga	6/24	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.245294632346474	2		434	561	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054048	42054048	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	30	346	0	ENST00000219905.7:c.7510G>C	p.Gly2504Arg	p.G2504R	ENST00000219905	NM_001164273.1	2504	Ggt/Cgt	21/24	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.245294632346474	2		346	226	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041647	42041647	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	128	596	1	ENST00000219905.7:c.5842C>T	p.Gln1948Ter	p.Q1948*	ENST00000219905	NM_001164273.1	1948	Cag/Tag	17/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.245294632346474	2		597	728	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873203	136873203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755899324	NA	P-0063253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	52	616	0	ENST00000241393.3:c.295G>A	p.Val99Met	p.V99M	ENST00000241393	NM_003467.2	99	Gtg/Atg	2/2	1	2	FACETS	0.498	0.423	0.581	0.498	0.423	0.581	SUBCLONAL	1	TRUE	1	0.245294632346474	2		616	851	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353811	68353811	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	70	479	0	ENST00000487270.1:c.646G>T	p.Val216Phe	p.V216F	ENST00000487270	NM_133509.3	216	Gtc/Ttc	7/11	0.245294632346474	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.245294632346474	1		479	358	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679389	29679389	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	99	540	0	ENST00000356175.3:c.7510del	p.Asp2504ThrfsTer23	p.D2504Tfs*23	ENST00000356175	NM_000267.3	2503	ctG/ct	50/57	0.245294632346474	5	FACETS	1	0.974	1	0.327	0.292	0.366	CLONAL	1	TRUE	1	0.245294632346474	5		540	843	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134289	11134289	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	73	507	0	ENST00000358026.2:c.2955G>T	p.Glu985Asp	p.E985D	ENST00000358026	NM_001128849.1	985	gaG/gaT	20/36	0.0769724158083447	3	FACETS	0.964	0.843	1	0.482	0.421	0.548	INDETERMINATE	1	TRUE	1	0.245294632346474	3		507	693	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519830	29519830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	107	524	0	ENST00000389048.3:c.1741G>A	p.Val581Ile	p.V581I	ENST00000389048	NM_004304.4	581	Gtc/Atc	9/29	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.245294632346474	2		524	673	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661463	227661463	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	148	798	0	ENST00000305123.5:c.1992G>C	p.Met664Ile	p.M664I	ENST00000305123	NM_005544.2	664	atG/atC	1/2	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.245294632346474	2		798	859	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492895	8492895	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	118	440	0	ENST00000356435.5:c.2434A>T	p.Ser812Cys	p.S812C	ENST00000356435		812	Agc/Tgc	16/35	0.245294632346474	2	FACETS	0.949	0.86	1	0.949	0.86	1	CLONAL	2	TRUE	0	0.245294632346474	2		440	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578446	7578446	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063256-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	445	590	0	ENST00000269305.4:c.484A>T	p.Ile162Phe	p.I162F	ENST00000269305	NM_001126112.2	162	Atc/Ttc	5/11	0.557142823483942	3	FACETS	0.972	0.94	1	0.972	0.94	1	CLONAL	3	TRUE	0	0.603080121162766	3		590	659	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023768	27023769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0063256-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	191	531	1	ENST00000324856.7:c.879dup	p.Thr294HisfsTer106	p.T294Hfs*106	ENST00000324856	NM_006015.4	292	acc/aCcc	1/20	0.327161245836465	2	FACETS	1	0.987	1	0.62	0.578	0.662	INDETERMINATE	1	TRUE	0	0.603080121162766	2		532	511	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256552	16256552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063256-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	250	587	0	ENST00000375759.3:c.3817G>A	p.Glu1273Lys	p.E1273K	ENST00000375759	NM_015001.2	1273	Gag/Aag	11/15	NA	2	FACETS	0.756	0.715	0.799			1	INDETERMINATE	2	TRUE	NA	0.603080121162766	2		587	548	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211449	98211449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779844193	NA	P-0063256-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	206	490	0	ENST00000331920.6:c.3706G>A	p.Glu1236Lys	p.E1236K	ENST00000331920	NM_000264.3	1236	Gag/Aag	22/24	0.55357575433099	2	FACETS	0.897	0.846	0.947	0.897	0.846	0.947	CLONAL	2	TRUE	0	0.603080121162766	2		490	381	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669523	88669523	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063256-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	114	350	0	ENST00000360948.2:c.1375C>G	p.Arg459Gly	p.R459G	ENST00000360948	NM_001012338.2	459	Cgg/Ggg	12/19	0.603080121162766	3	FACETS	1	0.938	1	0.523	0.474	0.575	CLONAL	1	TRUE	1	0.603080121162766	3		350	470	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21337317	21337317	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs886041418	NA	P-0063256-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	63	505	0	ENST00000215739.8:c.202C>T	p.Arg68Cys	p.R68C	ENST00000215739	NM_006767.3	68	Cgc/Tgc	2/21	0.55357575433099	2	FACETS	0.521	0.452	0.595	0.261	0.226	0.298	SUBCLONAL	1	TRUE	0	0.603080121162766	2		505	401	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144354644	144354644	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1196434138	NA	P-0063256-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	50	291	0	ENST00000262995.4:c.368A>G	p.Asp123Gly	p.D123G	ENST00000262995	NM_207123.2	123	gAt/gGt	3/11	0.603080121162766	2	FACETS	0.556	0.475	0.645	0.278	0.237	0.323	SUBCLONAL	1	TRUE	0	0.603080121162766	2		291	298	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0063274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	84	712	3	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.494	0.436	0.557	0.494	0.436	0.557	SUBCLONAL	1	TRUE	1	0.391482086577216	2		715	868	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097621	27097622	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0063274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	33	588	0	ENST00000324856.7:c.3216dup	p.Trp1073MetfsTer32	p.W1073Mfs*32	ENST00000324856	NM_006015.4	1070	-/A	12/20	1	2	FACETS	0.259	0.21	0.314	0.259	0.21	0.314	SUBCLONAL	1	TRUE	1	0.391482086577216	2		588	652	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs1057519842	NA	P-0063274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	51	449	0	ENST00000274335.5:c.1727_1729del	p.Thr576del	p.T576del	ENST00000274335		575	aaGACg/aag	12/15	1	2	FACETS	0.438	0.372	0.511	0.438	0.372	0.511	SUBCLONAL	1	TRUE	1	0.391482086577216	2		449	595	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0063274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	90	795	2	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.476	0.422	0.535	0.476	0.422	0.535	SUBCLONAL	1	TRUE	1	0.391482086577216	2		797	965	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121909229	NA	P-0063274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	94	419	0	ENST00000371953.3:c.389G>T	p.Arg130Leu	p.R130L	ENST00000371953	NM_000314.4	130	cGa/cTa	5/9	0.200510135716907	2	FACETS	0.974	0.87	1	0.487	0.435	0.542	INDETERMINATE	1	TRUE	0	0.391482086577216	2		419	493	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520273	176520273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759709290	NA	P-0063274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	71	691	0	ENST00000292408.4:c.1192C>T	p.Arg398Trp	p.R398W	ENST00000292408	NM_213647.1	398	Cgg/Tgg	9/18	1	2	FACETS	0.515	0.449	0.587	0.515	0.449	0.587	SUBCLONAL	1	TRUE	1	0.391482086577216	2		691	704	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0063274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	118	748	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.712	0.642	0.786	0.712	0.642	0.786	SUBCLONAL	1	TRUE	1	0.391482086577216	2		752	847	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739902	145739902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	79	626	0	ENST00000428558.2:c.1628G>A	p.Gly543Asp	p.G543D	ENST00000428558	NM_004260.3	543	gGc/gAc	10/22	1	2	FACETS	0.58	0.51	0.655	0.58	0.51	0.655	SUBCLONAL	1	TRUE	1	0.391482086577216	2		626	696	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440364	187440364	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1426858162	NA	P-0063274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	79	476	0	ENST00000232014.4:c.2003G>A	p.Arg668His	p.R668H	ENST00000232014	NM_001130845.1	668	cGt/cAt	10/10	1	2	FACETS	0.641	0.564	0.723	0.641	0.564	0.723	SUBCLONAL	1	TRUE	1	0.391482086577216	2		476	630	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254972	16254972	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	62	678	0	ENST00000375759.3:c.2237G>T	p.Arg746Met	p.R746M	ENST00000375759	NM_015001.2	746	aGg/aTg	11/15	1	2	FACETS	0.43	0.371	0.495	0.43	0.371	0.495	SUBCLONAL	1	TRUE	1	0.391482086577216	2		678	736	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88679200	88679201	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0063274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	19	304	0	ENST00000372037.3:c.1141_1142dup	p.Gly382TrpfsTer18	p.G382Wfs*18	ENST00000372037	NM_004329.2	380	-/CT	10/13	0.200510135716907	2	FACETS	0.273	0.206	0.351	0.136	0.103	0.176	INDETERMINATE	1	TRUE	0	0.391482086577216	2		304	356	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99473529	99473529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	26	451	0	ENST00000268035.6:c.2951C>T	p.Ala984Val	p.A984V	ENST00000268035	NM_000875.3	984	gCt/gTt	15/21	1	2	FACETS	0.264	0.208	0.328	0.264	0.208	0.328	SUBCLONAL	1	TRUE	1	0.391482086577216	2		451	504	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637556	23637556	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs753153576	NA	P-0063274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	54	402	0	ENST00000261584.4:c.2748+1G>T		p.X916_splice	ENST00000261584	NM_024675.3	916			1	2	FACETS	0.539	0.46	0.625	0.539	0.46	0.625	SUBCLONAL	1	TRUE	1	0.391482086577216	2		402	512	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99162518	99162518	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	62	534	0	ENST00000074304.5:c.1036C>T	p.Gln346Ter	p.Q346*	ENST00000074304	NM_001134224.1	346	Caa/Taa	12/26	1	2	FACETS	0.476	0.411	0.548	0.476	0.411	0.548	SUBCLONAL	1	TRUE	1	0.391482086577216	2		534	665	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631593	119631593	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	52	402	0	ENST00000316626.5:c.673C>A	p.Pro225Thr	p.P225T	ENST00000316626		225	Cca/Aca	6/12	1	2	FACETS	0.537	0.457	0.624	0.537	0.457	0.624	SUBCLONAL	1	TRUE	1	0.391482086577216	2		402	495	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158456	26158456	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs62623440	NA	P-0063274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	90	633	0	ENST00000289316.2:c.59C>G	p.Thr20Ser	p.T20S	ENST00000289316	NM_138720.2	20	aCt/aGt	1/2	1	2	FACETS	0.576	0.511	0.646	0.576	0.511	0.646	SUBCLONAL	1	TRUE	1	0.391482086577216	2		633	798	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371852	55371852	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	45	635	0	ENST00000297316.4:c.542T>C	p.Leu181Pro	p.L181P	ENST00000297316	NM_022454.3	181	cTc/cCc	2/2	1	2	FACETS	0.364	0.305	0.43	0.364	0.305	0.43	SUBCLONAL	1	TRUE	1	0.391482086577216	2		635	631	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2056730	2056730	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	80	648	0	ENST00000349721.2:c.1232A>C	p.Asn411Thr	p.N411T	ENST00000349721	NM_003070.3	411	aAc/aCc	7/34	1	2	FACETS	0.537	0.472	0.607	0.537	0.472	0.607	SUBCLONAL	1	TRUE	1	0.391482086577216	2		648	761	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0063275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	21	393	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.19	2		394	153	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106022	8106022	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	63	624	0	ENST00000346208.3:c.842A>G	p.His281Arg	p.H281R	ENST00000346208		281	cAc/cGc	4/6	1	2	FACETS	0.881	0.761	1	0.881	0.761	1	CLONAL	1	TRUE	1	0.19	2		624	753	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0063290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	59	362	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.975	0.84	1	0.975	0.84	1	CLONAL	1	FALSE	1	0.240998291328733	2		362	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0063290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	116	0	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			NA	2	FACETS	1	0.972	1			1	INDETERMINATE	1	FALSE	NA	0.240998291328733	2		0	790	SUCCESS
REST	5978	MSKCC	GRCh37	4	57777087	57777087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs909981105	NA	P-0063290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	52	435	0	ENST00000309042.7:c.283G>A	p.Glu95Lys	p.E95K	ENST00000309042	NM_005612.4	95	Gag/Aag	2/4	1	2	FACETS	0.556	0.472	0.649	0.556	0.472	0.649	SUBCLONAL	1	FALSE	1	0.240998291328733	2		435	776	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100175	27100176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0063324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	108	635	0	ENST00000324856.7:c.3977dup	p.Gln1327AlafsTer11	p.Q1327Afs*11	ENST00000324856	NM_006015.4	1324	tac/taCc	16/20	0.164085720651674	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	1	0.196269241808147	3		635	565	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971116	21971116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552823	NA	P-0063324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	103	593	0	ENST00000304494.5:c.242C>T	p.Pro81Leu	p.P81L	ENST00000304494	NM_000077.4	81	cCc/cTc	2/3	0.196269241808147	2	FACETS	0.841	0.758	0.928	1	0.975	1	CLONAL	3	TRUE	0	0.196269241808147	2		593	416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577123	7577123	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876660333	NA	P-0063324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	87	470	0	ENST00000269305.4:c.815T>A	p.Val272Glu	p.V272E	ENST00000269305	NM_001126112.2	272	gTg/gAg	8/11	0.19280962217849	2	FACETS	0.852	0.757	0.954	0.852	0.757	0.954	CLONAL	2	TRUE	0	0.196269241808147	2		470	520	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604748	48604748	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	74	410	0	ENST00000342988.3:c.1570T>G	p.Trp524Gly	p.W524G	ENST00000342988	NM_005359.5	524	Tgg/Ggg	12/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.196269241808147	2		410	518	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405963	49405963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	54	358	0	ENST00000418115.1:c.175G>A	p.Asp59Asn	p.D59N	ENST00000418115	NM_001664.2	59	Gac/Aac	3/5	0.154649405739141	3	FACETS	1	0.953	1	0.646	0.552	0.748	CLONAL	1	TRUE	1	0.196269241808147	3		358	468	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843477	156843477	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	58	584	0	ENST00000524377.1:c.906del	p.Phe303SerfsTer167	p.F303Sfs*167	ENST00000524377	NM_002529.3	301	atC/at	8/17	0.164085720651674	3	FACETS	1	0.933	1	0.574	0.493	0.663	CLONAL	1	TRUE	1	0.196269241808147	3		584	565	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244314	46244314	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	53	510	0	ENST00000334344.6:c.2408G>C	p.Gly803Ala	p.G803A	ENST00000334344	NM_152641.2	803	gGc/gCc	15/21	0.164085720651674	3	FACETS	1	0.874	1	0.514	0.438	0.597	CLONAL	1	TRUE	1	0.196269241808147	3		510	577	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326825	62326825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568726633	NA	P-0063324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	91	585	0	ENST00000360203.5:c.3644C>T	p.Ser1215Phe	p.S1215F	ENST00000360203	NM_001283009.1	1215	tCt/tTt	34/35	0.164085720651674	3	FACETS	0.936	0.833	1	0.936	0.833	1	CLONAL	2	TRUE	1	0.196269241808147	3		585	544	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474703	138474703	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	138	323	0	ENST00000289153.2:c.290G>T	p.Arg97Leu	p.R97L	ENST00000289153	NM_006219.2	97	cGa/cTa	2/22	0.196269241808147	5	FACETS	1	0.955	1	1	0.955	1	CLONAL	4	TRUE	1	0.196269241808147	5		323	429	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910356	29910356	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	46	835	0	ENST00000376809.5:c.26T>G	p.Leu9Arg	p.L9R	ENST00000376809	NM_002116.7	9	cTc/cGc	1/8	0.196269241808147	1	FACETS	0.709	0.597	0.834	0.709	0.597	0.834	SUBCLONAL	1	TRUE	0	0.196269241808147	1		835	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138729528	NA	P-0063348-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	103	1353	0	ENST00000269305.4:c.523C>G	p.Arg175Gly	p.R175G	ENST00000269305	NM_001126112.2	175	Cgc/Ggc	5/11	0.183464748523091	2	FACETS	0.912	0.817	1	0.456	0.408	0.506	INDETERMINATE	1	TRUE	0	0.346417223095619	2		1353	652	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624970	9624970	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063348-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	50	719	0	ENST00000353224.5:c.7G>T	p.Gly3Trp	p.G3W	ENST00000353224	NM_177990.2	3	Ggg/Tgg	3/10	1	2	FACETS	0.61	0.518	0.711	0.61	0.518	0.711	SUBCLONAL	1	TRUE	1	0.346417223095619	2		719	473	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134255	41134255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs994659376	NA	P-0063348-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	87	675	0	ENST00000379561.5:c.1373C>T	p.Ala458Val	p.A458V	ENST00000379561	NM_002015.3	458	gCg/gTg	2/3	0.346417223095619	4	FACETS	0.865	0.765	0.972	0.288	0.255	0.324	CLONAL	1	TRUE	1	0.346417223095619	4		675	782	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631323	117631323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063348-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	51	722	1	ENST00000368508.3:c.6355G>A	p.Gly2119Arg	p.G2119R	ENST00000368508	NM_002944.2	2119	Ggg/Agg	40/43	1	2	FACETS	0.671	0.571	0.78	0.671	0.571	0.78	SUBCLONAL	1	TRUE	1	0.346417223095619	2		723	439	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220544	133220544	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs200776293	NA	P-0063348-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	135	852	0	ENST00000320574.5:c.4169G>T	p.Arg1390Leu	p.R1390L	ENST00000320574	NM_006231.2	1390	cGc/cTc	33/49	0.346417223095619	3	FACETS	0.772	0.705	0.843	0.772	0.705	0.843	SUBCLONAL	2	TRUE	1	0.346417223095619	3		852	592	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248877	133248877	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1054837169	NA	P-0063348-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	159	1022	2	ENST00000320574.5:c.1718G>A	p.Arg573Gln	p.R573Q	ENST00000320574	NM_006231.2	573	cGg/cAg	16/49	0.346417223095619	3	FACETS	0.817	0.751	0.885	0.817	0.751	0.885	CLONAL	2	TRUE	1	0.346417223095619	3		1024	659	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435006	110435006	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063348-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	258	1712	0	ENST00000375856.3:c.3395G>T	p.Gly1132Val	p.G1132V	ENST00000375856	NM_003749.2	1132	gGc/gTc	1/2	0.346417223095619	6	FACETS	0.944	0.882	1	0.377	0.353	0.403	CLONAL	2	TRUE	1	0.346417223095619	6		1712	1336	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023218	33023218	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063348-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	91	1100	0	ENST00000300177.4:c.327C>A	p.Asn109Lys	p.N109K	ENST00000300177	NM_001191322.1	109	aaC/aaA	2/2	0.134672665711581	4	FACETS	1	0.945	1	0.552	0.49	0.617	INDETERMINATE	1	TRUE	2	0.346417223095619	4		1100	641	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953124	81953125	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0063348-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	112	996	1	ENST00000359376.3:c.2090_2091delinsTT	p.Arg697Leu	p.R697L	ENST00000359376	NM_002661.3	697	cGG/cTT	20/33	0.224099084101718	5	FACETS	0.795	0.717	0.878	0.53	0.478	0.585	SUBCLONAL	2	TRUE	2	0.346417223095619	5		997	618	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533034	63533034	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063348-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	161	1054	0	ENST00000307078.5:c.1860G>C	p.Trp620Cys	p.W620C	ENST00000307078	NM_004655.3	620	tgG/tgC	7/11	0.346417223095619	3	FACETS	0.778	0.715	0.843	0.778	0.715	0.843	SUBCLONAL	2	TRUE	1	0.346417223095619	3		1054	701	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143068	30143068	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063348-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	318	1379	0	ENST00000389048.3:c.458G>T	p.Gly153Val	p.G153V	ENST00000389048	NM_004304.4	153	gGt/gTt	1/29	0.346417223095619	3	FACETS	1	0.99	1	0.797	0.754	0.84	CLONAL	2	TRUE	0	0.346417223095619	3		1379	901	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027670	48027670	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063348-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	125	586	0	ENST00000234420.5:c.2548T>A	p.Tyr850Asn	p.Y850N	ENST00000234420	NM_000179.2	850	Tac/Aac	4/10	0.346417223095619	3	FACETS	0.8	0.728	0.876	0.534	0.485	0.584	SUBCLONAL	2	TRUE	0	0.346417223095619	3		586	529	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513208	41513208	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063348-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	102	639	0	ENST00000263253.7:c.112G>T	p.Asp38Tyr	p.D38Y	ENST00000263253	NM_001429.3	38	Gac/Tac	2/31	0.312606785403339	3	FACETS	0.775	0.697	0.856	0.516	0.464	0.571	SUBCLONAL	2	TRUE	0	0.346417223095619	3		639	446	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508841	31508841	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1182934007	NA	P-0063348-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	53	756	0	ENST00000344624.3:c.1474A>T	p.Thr492Ser	p.T492S	ENST00000344624		492	Acc/Tcc	7/33	0.346417223095619	5	FACETS	0.618	0.525	0.719	0.154	0.131	0.18	SUBCLONAL	1	TRUE	1	0.346417223095619	5		756	753	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106543518	106543518	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063348-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	69	629	0	ENST00000369096.4:c.320T>G	p.Ile107Arg	p.I107R	ENST00000369096	NM_001198.3	107	aTa/aGa	3/7	1	2	FACETS	0.777	0.677	0.883	0.777	0.677	0.883	SUBCLONAL	1	TRUE	1	0.346417223095619	2		629	513	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877076	151877076	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063348-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	172	1080	1	ENST00000262189.6:c.7285A>T	p.Asn2429Tyr	p.N2429Y	ENST00000262189	NM_170606.2	2429	Aac/Tac	37/59	0.346417223095619	3	FACETS	0.835	0.77	0.901	0.835	0.77	0.901	CLONAL	2	TRUE	1	0.346417223095619	3		1081	698	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341778	8341778	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063348-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	127	772	0	ENST00000356435.5:c.4862C>A	p.Pro1621Gln	p.P1621Q	ENST00000356435		1621	cCa/cAa	29/35	0.346417223095619	3	FACETS	1	0.985	1	0.723	0.657	0.792	CLONAL	1	TRUE	1	0.346417223095619	3		772	595	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0063350-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	173	998	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.66477699491819	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.66477699491819	1		998	313	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063350-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	23	716	0	ENST00000304494.5:c.143C>T	p.Pro48Leu	p.P48L	ENST00000304494	NM_000077.4	48	cCg/cTg	1/3	0.56403144704712	0	FACETS	0.161	0.127	0.2			1	SUBCLONAL	1	TRUE	0	0.66477699491819	0		716	144	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745976	745976	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063350-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	41	291	0	ENST00000314574.4:c.546C>G	p.Phe182Leu	p.F182L	ENST00000314574	NM_005433.3	182	ttC/ttG	5/12	0.444625771392468	4	FACETS	0.583	0.487	0.69			1	SUBCLONAL	1	TRUE	NA	0.66477699491819	4		291	352	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745990	745990	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063350-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	42	277	0	ENST00000314574.4:c.532C>G	p.Gln178Glu	p.Q178E	ENST00000314574	NM_005433.3	178	Caa/Gaa	5/12	0.444625771392468	4	FACETS	0.612	0.512	0.721			1	SUBCLONAL	1	TRUE	NA	0.66477699491819	4		277	344	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299869	15299869	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063350-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	69	697	0	ENST00000263388.2:c.1309T>C	p.Ser437Pro	p.S437P	ENST00000263388	NM_000435.2	437	Tcg/Ccg	8/33	0.533656867672844	1	FACETS	0.398	0.349	0.451	0.398	0.349	0.451	SUBCLONAL	1	TRUE	0	0.66477699491819	1		697	348	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226928	142226928	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063350-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	60	326	0	ENST00000350721.4:c.4876T>C	p.Tyr1626His	p.Y1626H	ENST00000350721	NM_001184.3	1626	Tat/Cat	28/47	0.251625535340905	4	FACETS	0.979	0.85	1	0.489	0.425	0.559	INDETERMINATE	1	TRUE	2	0.66477699491819	4		326	307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0063351-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	186	517	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.251156593079913	2	FACETS	0.988	0.916	1	1	0.99	1	CLONAL	3	TRUE	0	0.18	2		517	697	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914056	32914056	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0063351-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	37	480	0	ENST00000380152.3:c.5564C>G	p.Ser1855Ter	p.S1855*	ENST00000380152		1855	tCa/tGa	11/27	0.211861822999649	1	FACETS	0.889	0.733	1	0.889	0.733	1	CLONAL	1	TRUE	0	0.18	1		480	421	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837937	156837937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141021604	NA	P-0063351-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	122	622	0	ENST00000524377.1:c.470G>A	p.Arg157His	p.R157H	ENST00000524377	NM_002529.3	157	cGc/cAc	5/17	0.285241395785512	4	FACETS	0.935	0.845	1	0.624	0.563	0.687	CLONAL	2	TRUE	1	0.18	4		622	855	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914242	32914242	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs886040609	NA	P-0063351-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	31	485	0	ENST00000380152.3:c.5750C>G	p.Ser1917Ter	p.S1917*	ENST00000380152		1917	tCa/tGa	11/27	0.211861822999649	1	FACETS	0.708	0.572	0.861	0.708	0.572	0.861	SUBCLONAL	1	TRUE	0	0.18	1		485	443	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913477	32913477	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886040559	NA	P-0063351-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	41	504	0	ENST00000380152.3:c.4985C>T	p.Ser1662Leu	p.S1662L	ENST00000380152		1662	tCa/tTa	11/27	0.211861822999649	1	FACETS	0.921	0.768	1	0.921	0.768	1	CLONAL	1	TRUE	0	0.18	1		504	450	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914202	32914202	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55875643	NA	P-0063351-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	31	487	0	ENST00000380152.3:c.5710C>T	p.Leu1904Phe	p.L1904F	ENST00000380152		1904	Ctt/Ttt	11/27	0.211861822999649	1	FACETS	0.732	0.592	0.891	0.732	0.592	0.891	SUBCLONAL	1	TRUE	0	0.18	1		487	428	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780851	9780851	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777389	NA	P-0063351-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	64	562	0	ENST00000377346.4:c.1573G>A	p.Glu525Lys	p.E525K	ENST00000377346	NM_005026.3	525	Gag/Aag	13/24	0.3	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.18	1		562	599	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449809	29449809	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063351-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	84	713	0	ENST00000389048.3:c.3046G>A	p.Glu1016Lys	p.E1016K	ENST00000389048	NM_004304.4	1016	Gag/Aag	18/29	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.18	2		713	773	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923285	131923285	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063351-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	58	302	0	ENST00000265335.6:c.788C>G	p.Ser263Cys	p.S263C	ENST00000265335		263	tCt/tGt	6/25	0.239002404895432	3	FACETS	0.878	0.757	1	0.878	0.757	1	CLONAL	2	TRUE	1	0.18	3		302	400	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0063368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	279	728	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.199098018350698	6	FACETS	1	0.982	1			1	CLONAL	4	TRUE	NA	0.199098018350698	6		728	891	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521481	8521481	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760428875	NA	P-0063368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	72	592	0	ENST00000356435.5:c.757G>A	p.Val253Ile	p.V253I	ENST00000356435		253	Gtt/Att	9/35	0.199098018350698	1	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	0	0.199098018350698	1		592	632	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908874	101908874	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	103	576	0	ENST00000374994.4:c.1238G>T	p.Arg413Leu	p.R413L	ENST00000374994	NM_004612.2	413	cGa/cTa	7/9	1	2	FACETS	0.753	0.674	0.836	1	0.982	1	SUBCLONAL	2	TRUE	1	0.199098018350698	2		576	687	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578209	7578209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	129	689	0	ENST00000269305.4:c.640C>T	p.His214Tyr	p.H214Y	ENST00000269305	NM_001126112.2	214	Cat/Tat	6/11	0.185107371630323	2	FACETS	0.805	0.73	0.884	0.805	0.73	0.884	CLONAL	2	TRUE	0	0.199098018350698	2		689	805	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138600	2138600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376017665	NA	P-0063368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	71	599	0	ENST00000219476.3:c.5413G>A	p.Glu1805Lys	p.E1805K	ENST00000219476	NM_000548.3	1805	Gag/Aag	42/42	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.199098018350698	2		599	608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578202	7578203	+	missense_variant	Missense_Mutation	DNP	AC	AC	CT	novel	NA	P-0063368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	126	705	0	ENST00000269305.4:c.646_647delinsAG	p.Val216Arg	p.V216R	ENST00000269305	NM_001126112.2	216	GTg/AGg	6/11	0.185107371630323	2	FACETS	0.793	0.718	0.872	0.793	0.718	0.872	SUBCLONAL	2	TRUE	0	0.199098018350698	2		705	798	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0063379-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	128	484	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	0.872	0.793	0.954	0.872	0.793	0.954	CLONAL	1	TRUE	1	0.52168726471812	2		484	563	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347782	347782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063379-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	164	605	0	ENST00000262320.3:c.1724C>T	p.Ser575Phe	p.S575F	ENST00000262320	NM_003502.3	575	tCc/tTc	6/11	0.52168726471812	3	FACETS	0.81	0.743	0.88	0.405	0.371	0.44	CLONAL	1	TRUE	1	0.52168726471812	3		605	979	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106587	27106588	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATCTCGGGGCAGTTGGACCTATCTCCATACCCCGAGAGCAT	novel	NA	P-0063379-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	100	648	0	ENST00000324856.7:c.6199_6239dup	p.Cys2081SerfsTer68	p.C2081Sfs*68	ENST00000324856	NM_006015.4	2066	-/ATCTCGGGGCAGTTGGACCTATCTCCATACCCCGAGAGCAT	20/20	1	2	FACETS	0.447	0.398	0.498	0.447	0.398	0.498	SUBCLONAL	1	TRUE	1	0.52168726471812	2		648	858	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628275	90628275	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063379-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	194	725	0	ENST00000330062.3:c.1136T>A	p.Leu379Gln	p.L379Q	ENST00000330062	NM_002168.2	379	cTg/cAg	9/11	1	2	FACETS	0.985	0.914	1	0.985	0.914	1	CLONAL	1	TRUE	1	0.52168726471812	2		725	755	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138253	2138253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760395277	NA	P-0063379-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	160	659	0	ENST00000219476.3:c.5186G>A	p.Arg1729His	p.R1729H	ENST00000219476	NM_000548.3	1729	cGc/cAc	41/42	0.52168726471812	3	FACETS	0.922	0.846	1	0.461	0.423	0.501	CLONAL	1	TRUE	1	0.52168726471812	3		659	839	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562632	29562632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	172	389	1	ENST00000356175.3:c.3712G>A	p.Glu1238Lys	p.E1238K	ENST00000356175	NM_000267.3	1238	Gaa/Aaa	28/57	0.0933023598562452	4	FACETS	0.962	0.897	1	0.962	0.897	1	INDETERMINATE	2	TRUE	2	0.850694402350991	4		390	389	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38785213	38785213	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	191	573	0	ENST00000348513.6:c.1060C>T	p.Gln354Ter	p.Q354*	ENST00000348513	NM_003079.4	354	Caa/Taa	11/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.850694402350991	2		573	424	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288939	212288939	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	284	500	0	ENST00000342788.4:c.2807del	p.Gly936GlufsTer23	p.G936Efs*23	ENST00000342788	NM_005235.2	936	gGa/ga	23/28	0.850694402350991	2	FACETS	0.994	0.965	1	0.994	0.965	1	CLONAL	2	TRUE	0	0.850694402350991	2		500	336	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938733	76938733	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	155	304	0	ENST00000373344.5:c.2015del	p.Pro672LeufsTer2	p.P672Lfs*2	ENST00000373344	NM_000489.3	672	cCt/ct	9/35	1	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.850694402350991	1		304	204	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219341	1219341	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs760399253	NA	P-0063389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	67	555	0	ENST00000326873.7:c.393C>G	p.Tyr131Ter	p.Y131*	ENST00000326873	NM_000455.4	131	taC/taG	3/10	0.336573518801374	1	FACETS	0.818	0.713	0.929	0.818	0.713	0.929	CLONAL	1	TRUE	0	0.336573518801374	1		555	405	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206716	36206716	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	54	651	0	ENST00000300305.3:c.796C>T	p.Gln266Ter	p.Q266*	ENST00000300305		266	Cag/Tag	6/8	1	2	FACETS	0.583	0.498	0.677	0.583	0.498	0.677	SUBCLONAL	1	TRUE	1	0.336573518801374	2		651	550	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341136	8341136	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	64	395	0	ENST00000356435.5:c.5080G>T	p.Val1694Leu	p.V1694L	ENST00000356435		1694	Gta/Tta	30/35	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.336573518801374	2		395	363	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220449	98220449	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	68	494	1	ENST00000331920.6:c.3014G>T	p.Gly1005Val	p.G1005V	ENST00000331920	NM_000264.3	1005	gGg/gTg	18/24	1	2	FACETS	0.83	0.723	0.944	0.83	0.723	0.944	CLONAL	1	TRUE	1	0.336573518801374	2		495	487	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231421	98231421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751536947	NA	P-0063389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	69	505	0	ENST00000331920.6:c.1862G>A	p.Arg621Lys	p.R621K	ENST00000331920	NM_000264.3	621	aGa/aAa	14/24	1	2	FACETS	0.74	0.645	0.842	0.74	0.645	0.842	SUBCLONAL	1	TRUE	1	0.336573518801374	2		505	554	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600331	10600331	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	CC	novel	NA	P-0063389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	169	619	0	ENST00000171111.5:c.1524delinsGG	p.Ser508ArgfsTer19	p.S508Rfs*19	ENST00000171111	NM_203500.1	508	agC/agGG	4/6	0.273731437932738	3	FACETS	0.978	0.903	1	0.652	0.602	0.703	CLONAL	2	TRUE	0	0.336573518801374	3		619	600	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0063393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	132	210	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.947	1	1	0.994	1	CLONAL	5	TRUE	1	0.17	2		210	301	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	89	523	0				ENST00000310581	NM_198253.2	-/1132			0.252492103170876	1	FACETS	0.925	0.832	1	1	0.99	1	CLONAL	4	TRUE	0	0.17	1		523	259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0063393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	156	558	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.938	1	1	0.994	1	CLONAL	4	TRUE	1	0.17	2		558	451	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0063393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	173	771	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA	2	FACETS	0.903	0.839	0.967			1	INDETERMINATE	5	TRUE	NA	0.17	2		771	451	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100436	8100436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1220437638	NA	P-0063393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	281	586	0	ENST00000346208.3:c.410C>T	p.Ser137Leu	p.S137L	ENST00000346208		137	tCg/tTg	3/6	1	2	FACETS	1	0.957	1	1	0.997	1	CLONAL	5	TRUE	1	0.17	2		586	653	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100664	8100664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1477514775	NA	P-0063393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	239	491	0	ENST00000346208.3:c.638C>T	p.Ser213Leu	p.S213L	ENST00000346208		213	tCg/tTg	3/6	1	2	FACETS	1	0.979	1	1	0.996	1	CLONAL	5	TRUE	1	0.17	2		491	522	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029126	26029126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	163	332	0	ENST00000435504.4:c.224C>T	p.Pro75Leu	p.P75L	ENST00000435504		75	cCa/cTa	4/13	1	2	FACETS	0.966	0.898	1	1	0.995	1	CLONAL	5	TRUE	1	0.17	2		332	397	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794857	42794857	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	150	485	0	ENST00000575354.2:c.1937G>C	p.Arg646Thr	p.R646T	ENST00000575354	NM_015125.3	646	aGa/aCa	10/20	1	2	FACETS	1	0.972	1	1	0.994	1	CLONAL	4	TRUE	1	0.17	2		485	398	SUCCESS
APC	324	MSKCC	GRCh37	5	112178503	112178503	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	203	384	0	ENST00000257430.4:c.7212G>A	p.Met2404Ile	p.M2404I	ENST00000257430	NM_000038.5	2404	atG/atA	16/16	1	2	FACETS	1	0.961	1	1	0.996	1	CLONAL	5	TRUE	1	0.17	2		384	462	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060812	38060812	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	261	537	2	ENST00000250448.2:c.1177C>A	p.His393Asn	p.H393N	ENST00000250448	NM_004496.3	393	Cac/Aac	2/2	1	2	FACETS	0.963	0.908	1	1	0.996	1	CLONAL	5	TRUE	1	0.17	2		539	638	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432409	49432412	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	novel	NA	P-0063393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	247	534	0	ENST00000301067.7:c.8727_8730del	p.Ser2910ArgfsTer32	p.S2910Rfs*32	ENST00000301067	NM_003482.3	2909	gtAAGT/gt	34/54	1	2	FACETS	0.977	0.921	1	1	0.996	1	CLONAL	5	TRUE	1	0.17	2		534	595	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105237098	105237098	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	134	353	0	ENST00000349310.3:c.1347C>G	p.Ile449Met	p.I449M	ENST00000349310	NM_001014432.1	449	atC/atG	14/15	1	2	FACETS	1	0.941	1	1	0.993	1	CLONAL	4	TRUE	1	0.17	2		353	383	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794847	42794847	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778199	NA	P-0063393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	157	463	0	ENST00000575354.2:c.1927G>A	p.Gly643Ser	p.G643S	ENST00000575354	NM_015125.3	643	Ggc/Agc	10/20	1	2	FACETS	0.903	0.837	0.971	1	0.994	1	CLONAL	5	TRUE	1	0.17	2		463	409	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100427	8100427	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777735536	NA	P-0063393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	277	602	0	ENST00000346208.3:c.401C>T	p.Pro134Leu	p.P134L	ENST00000346208		134	cCc/cTc	3/6	1	2	FACETS	1	0.951	1	1	0.997	1	CLONAL	5	TRUE	1	0.17	2		602	648	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433302	49433302	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	195	488	0	ENST00000301067.7:c.8145del	p.Pro2716LeufsTer17	p.P2716Lfs*17	ENST00000301067	NM_003482.3	2715	ggG/gg	32/54	1	2	FACETS	0.964	0.901	1	1	0.995	1	CLONAL	5	TRUE	1	0.17	2		488	476	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244127	41244127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555587727	NA	P-0063393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	191	395	0	ENST00000357654.3:c.3421C>T	p.His1141Tyr	p.H1141Y	ENST00000357654	NM_007294.3	1141	Cat/Tat	10/23	1	2	FACETS	0.901	0.84	0.962	1	0.995	1	CLONAL	5	TRUE	1	0.17	2		395	499	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794788	42794788	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	161	479	0	ENST00000575354.2:c.1868G>C	p.Gly623Ala	p.G623A	ENST00000575354	NM_015125.3	623	gGa/gCa	10/20	1	2	FACETS	0.928	0.862	0.997	1	0.994	1	CLONAL	5	TRUE	1	0.17	2		479	408	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794841	42794841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	152	473	0	ENST00000575354.2:c.1921G>A	p.Glu641Lys	p.E641K	ENST00000575354	NM_015125.3	641	Gag/Aag	10/20	1	2	FACETS	1	0.966	1	1	0.994	1	CLONAL	4	TRUE	1	0.17	2		473	414	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795285	42795285	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	180	510	0	ENST00000575354.2:c.2365G>T	p.Gly789Trp	p.G789W	ENST00000575354	NM_015125.3	789	Ggg/Tgg	10/20	1	2	FACETS	0.965	0.9	1	1	0.995	1	CLONAL	5	TRUE	1	0.17	2		510	439	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21344765	21344765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869320686	NA	P-0063393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	188	453	0	ENST00000215739.8:c.742G>A	p.Gly248Arg	p.G248R	ENST00000215739	NM_006767.3	248	Gga/Aga	8/21	0.252492103170876	1	FACETS	1	0.975	1	1	0.995	1	CLONAL	4	TRUE	0	0.17	1		453	464	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144387287	144387287	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	199	372	0	ENST00000262995.4:c.1925G>A	p.Gly642Glu	p.G642E	ENST00000262995	NM_207123.2	642	gGa/gAa	10/11	1	2	FACETS	0.92	0.86	0.981	1	0.995	1	CLONAL	5	TRUE	1	0.17	2		372	509	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247311	153247311	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	257	396	0	ENST00000281708.4:c.1491G>C	p.Leu497Phe	p.L497F	ENST00000281708	NM_033632.3	497	ttG/ttC	10/12	1	2	FACETS	1	0.948	1	1	0.996	1	CLONAL	5	TRUE	1	0.17	2		396	602	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343052	70343052	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	160	387	0	ENST00000374080.3:c.1593G>C	p.Lys531Asn	p.K531N	ENST00000374080		531	aaG/aaC	11/45	0.252492103170876	1	FACETS	0.936	0.866	1	1	0.994	1	CLONAL	4	TRUE	0	0.17	1		387	460	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463268	25463268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	22	494	0	ENST00000264709.3:c.2225G>A	p.Arg742Gln	p.R742Q	ENST00000264709	NM_175629.2	742	cGg/cAg	19/23	1	2	FACETS	0.61	0.472	0.772	0.61	0.472	0.772	SUBCLONAL	1	TRUE	1	0.17	2		494	424	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0063393-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	37	210	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.782	0.656	0.916	0.782	0.656	0.916	CLONAL	1	TRUE	1	0.681136633595234	2		210	139	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063393-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	233	523	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.879	0.823	0.937	0.879	0.823	0.937	CLONAL	1	TRUE	1	0.681136633595234	2		523	778	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0063393-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	283	558	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.985	0.928	1	0.985	0.928	1	CLONAL	1	TRUE	1	0.681136633595234	2		558	844	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0063393-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	314	771	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA	2	FACETS	0.891	0.841	0.941			1	INDETERMINATE	1	TRUE	NA	0.681136633595234	2		771	1035	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100436	8100436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1220437638	NA	P-0063393-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	373	586	0	ENST00000346208.3:c.410C>T	p.Ser137Leu	p.S137L	ENST00000346208		137	tCg/tTg	3/6	1	2	FACETS	0.956	0.908	1	0.956	0.908	1	CLONAL	1	TRUE	1	0.681136633595234	2		586	1146	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100664	8100664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1477514775	NA	P-0063393-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	346	491	0	ENST00000346208.3:c.638C>T	p.Ser213Leu	p.S213L	ENST00000346208		213	tCg/tTg	3/6	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.681136633595234	2		491	1014	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029126	26029126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063393-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	121	332	0	ENST00000435504.4:c.224C>T	p.Pro75Leu	p.P75L	ENST00000435504		75	cCa/cTa	4/13	1	2	FACETS	0.871	0.794	0.951	0.871	0.794	0.951	CLONAL	1	TRUE	1	0.681136633595234	2		332	408	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794857	42794857	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063393-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	296	485	0	ENST00000575354.2:c.1937G>C	p.Arg646Thr	p.R646T	ENST00000575354	NM_015125.3	646	aGa/aCa	10/20	1	2	FACETS	0.891	0.84	0.942	0.891	0.84	0.942	CLONAL	1	TRUE	1	0.681136633595234	2		485	976	SUCCESS
APC	324	MSKCC	GRCh37	5	112178503	112178503	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063393-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	233	384	0	ENST00000257430.4:c.7212G>A	p.Met2404Ile	p.M2404I	ENST00000257430	NM_000038.5	2404	atG/atA	16/16	1	2	FACETS	0.999	0.936	1	0.999	0.936	1	CLONAL	1	TRUE	1	0.681136633595234	2		384	685	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060812	38060812	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063393-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	402	537	2	ENST00000250448.2:c.1177C>A	p.His393Asn	p.H393N	ENST00000250448	NM_004496.3	393	Cac/Aac	2/2	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.681136633595234	2		539	1163	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432409	49432412	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	novel	NA	P-0063393-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	317	534	0	ENST00000301067.7:c.8727_8730del	p.Ser2910ArgfsTer32	p.S2910Rfs*32	ENST00000301067	NM_003482.3	2909	gtAAGT/gt	34/54	1	2	FACETS	0.915	0.865	0.966	0.915	0.865	0.966	CLONAL	1	TRUE	1	0.681136633595234	2		534	1017	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105237098	105237098	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063393-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	252	353	0	ENST00000349310.3:c.1347C>G	p.Ile449Met	p.I449M	ENST00000349310	NM_001014432.1	449	atC/atG	14/15	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	1	TRUE	NA	0.681136633595234	2		353	711	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794847	42794847	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778199	NA	P-0063393-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	297	463	0	ENST00000575354.2:c.1927G>A	p.Gly643Ser	p.G643S	ENST00000575354	NM_015125.3	643	Ggc/Agc	10/20	1	2	FACETS	0.906	0.854	0.958	0.906	0.854	0.958	CLONAL	1	TRUE	1	0.681136633595234	2		463	963	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100427	8100427	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777735536	NA	P-0063393-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	389	602	0	ENST00000346208.3:c.401C>T	p.Pro134Leu	p.P134L	ENST00000346208		134	cCc/cTc	3/6	1	2	FACETS	0.995	0.947	1	0.995	0.947	1	CLONAL	1	TRUE	1	0.681136633595234	2		602	1148	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433302	49433302	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063393-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	352	488	0	ENST00000301067.7:c.8145del	p.Pro2716LeufsTer17	p.P2716Lfs*17	ENST00000301067	NM_003482.3	2715	ggG/gg	32/54	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.681136633595234	2		488	1008	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244127	41244127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555587727	NA	P-0063393-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	217	395	0	ENST00000357654.3:c.3421C>T	p.His1141Tyr	p.H1141Y	ENST00000357654	NM_007294.3	1141	Cat/Tat	10/23	1	2	FACETS	0.9	0.84	0.961	0.9	0.84	0.961	CLONAL	1	TRUE	1	0.681136633595234	2		395	708	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794788	42794788	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063393-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	296	479	0	ENST00000575354.2:c.1868G>C	p.Gly623Ala	p.G623A	ENST00000575354	NM_015125.3	623	gGa/gCa	10/20	1	2	FACETS	0.953	0.899	1	0.953	0.899	1	CLONAL	1	TRUE	1	0.681136633595234	2		479	912	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794841	42794841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063393-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	285	473	0	ENST00000575354.2:c.1921G>A	p.Glu641Lys	p.E641K	ENST00000575354	NM_015125.3	641	Gag/Aag	10/20	1	2	FACETS	0.877	0.826	0.929	0.877	0.826	0.929	CLONAL	1	TRUE	1	0.681136633595234	2		473	954	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795285	42795285	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063393-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	307	510	0	ENST00000575354.2:c.2365G>T	p.Gly789Trp	p.G789W	ENST00000575354	NM_015125.3	789	Ggg/Tgg	10/20	1	2	FACETS	0.927	0.876	0.98	0.927	0.876	0.98	CLONAL	1	TRUE	1	0.681136633595234	2		510	972	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21344765	21344765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869320686	NA	P-0063393-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	285	453	0	ENST00000215739.8:c.742G>A	p.Gly248Arg	p.G248R	ENST00000215739	NM_006767.3	248	Gga/Aga	8/21	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.681136633595234	2		453	812	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144387287	144387287	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063393-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	178	372	0	ENST00000262995.4:c.1925G>A	p.Gly642Glu	p.G642E	ENST00000262995	NM_207123.2	642	gGa/gAa	10/11	1	2	FACETS	0.87	0.806	0.935	0.87	0.806	0.935	CLONAL	1	TRUE	1	0.681136633595234	2		372	601	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247311	153247311	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063393-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	296	396	0	ENST00000281708.4:c.1491G>C	p.Leu497Phe	p.L497F	ENST00000281708	NM_033632.3	497	ttG/ttC	10/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.681136633595234	2		396	816	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343052	70343052	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063393-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	245	387	0	ENST00000374080.3:c.1593G>C	p.Lys531Asn	p.K531N	ENST00000374080		531	aaG/aaC	11/45	1	2	FACETS	0.942	0.883	1	0.942	0.883	1	CLONAL	1	TRUE	1	0.681136633595234	2		387	764	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878178	48878178	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1345893304	NA	P-0063393-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	64	477	0	ENST00000267163.4:c.130C>A	p.Leu44Ile	p.L44I	ENST00000267163	NM_000321.2	44	Ctc/Atc	1/27	1	2	FACETS	0.222	0.192	0.255	0.222	0.192	0.255	SUBCLONAL	1	TRUE	1	0.681136633595234	2		477	846	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0063396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	148	583	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	FALSE	NA	0.233600421550026	2		583	880	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107180	27107180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1308037041	NA	P-0063396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	59	404	3	ENST00000324856.7:c.6791C>T	p.Ser2264Leu	p.S2264L	ENST00000324856	NM_006015.4	2264	tCa/tTa	20/20	1	2	FACETS	0.638	0.547	0.737	0.638	0.547	0.737	SUBCLONAL	1	FALSE	1	0.233600421550026	2		407	792	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174420	11174420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587777900	NA	P-0063396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	39	325	0	ENST00000361445.4:c.7255G>A	p.Glu2419Lys	p.E2419K	ENST00000361445	NM_004958.3	2419	Gaa/Aaa	53/58	1	2	FACETS	0.664	0.55	0.791	0.664	0.55	0.791	SUBCLONAL	1	FALSE	1	0.233600421550026	2		325	503	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838389	156838389	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	82	544	0	ENST00000524377.1:c.667G>C	p.Glu223Gln	p.E223Q	ENST00000524377	NM_002529.3	223	Gag/Cag	6/17	1	2	FACETS	0.761	0.67	0.86	0.761	0.67	0.86	SUBCLONAL	1	FALSE	1	0.233600421550026	2		544	922	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63817051	63817051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	57	314	1	ENST00000279873.7:c.1022G>A	p.Arg341Gln	p.R341Q	ENST00000279873	NM_032199.2	341	cGa/cAa	6/10	0.233600421550026	3	FACETS	0.921	0.79	1			1	CLONAL	1	FALSE	NA	0.233600421550026	3		315	592	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018193	48018193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	45	392	0	ENST00000234420.5:c.388C>T	p.His130Tyr	p.H130Y	ENST00000234420	NM_000179.2	130	Cat/Tat	2/10	0.233600421550026	3	FACETS	0.574	0.481	0.678	0.287	0.24	0.339	SUBCLONAL	1	FALSE	1	0.233600421550026	3		392	749	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514650	103514650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	44	419	2	ENST00000355739.4:c.1151C>T	p.Ser384Leu	p.S384L	ENST00000355739	NM_000123.3	384	tCa/tTa	8/15	1	2	FACETS	0.489	0.408	0.578	0.489	0.408	0.578	SUBCLONAL	1	FALSE	1	0.233600421550026	2		421	771	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39283950	39283950	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	28	273	0	ENST00000402219.2:c.403G>C	p.Glu135Gln	p.E135Q	ENST00000402219	NM_005633.3	135	Gaa/Caa	4/23	0.233600421550026	3	FACETS	0.68	0.543	0.835	0.34	0.271	0.418	SUBCLONAL	1	FALSE	1	0.233600421550026	3		273	394	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942803	15942803	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749499082	NA	P-0063396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	43	356	1	ENST00000268712.3:c.6899C>T	p.Ser2300Leu	p.S2300L	ENST00000268712	NM_006311.3	2300	tCa/tTa	44/46	0.233600421550026	1	FACETS	0.499	0.417	0.591	0.499	0.417	0.591	SUBCLONAL	1	FALSE	0	0.233600421550026	1		357	651	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014224	14014224	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	95	332	2	ENST00000311895.7:c.202G>A	p.Glu68Lys	p.E68K	ENST00000311895	NM_005236.2	68	Gag/Aag	1/11	0.233600421550026	3	FACETS	1	0.906	1	0.51	0.454	0.571	CLONAL	1	FALSE	1	0.233600421550026	3		334	890	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348679	89348679	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	43	376	1	ENST00000301030.4:c.4271C>T	p.Ser1424Phe	p.S1424F	ENST00000301030	NM_001256183.1	1424	tCt/tTt	9/13	1	2	FACETS	0.589	0.492	0.697	0.589	0.492	0.697	SUBCLONAL	1	FALSE	1	0.233600421550026	2		377	625	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280281	1280281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	72	439	0	ENST00000310581.5:c.1942G>A	p.Glu648Lys	p.E648K	ENST00000310581	NM_198253.2	648	Gaa/Aaa	4/16	1	2	FACETS	0.757	0.66	0.862	0.757	0.66	0.862	SUBCLONAL	1	FALSE	1	0.233600421550026	2		439	814	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089618	27089618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	91	488	0	ENST00000324856.7:c.2574G>A	p.Met858Ile	p.M858I	ENST00000324856	NM_006015.4	858	atG/atA	8/20	1	2	FACETS	0.893	0.792	1	0.893	0.792	1	CLONAL	1	FALSE	1	0.233600421550026	2		488	872	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225674	26225674	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1341	146	879	0	ENST00000360408.1:c.292G>A	p.Glu98Lys	p.E98K	ENST00000360408	NM_003532.2	98	Gag/Aag	1/1	0.233600421550026	5	FACETS	1	0.967	1	0.284	0.258	0.311	CLONAL	1	FALSE	1	0.233600421550026	5		879	1487	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944785	31944785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	30	265	2	ENST00000340398.3:c.316G>A	p.Asp106Asn	p.D106N	ENST00000340398	NM_001013699.2	106	Gat/Aat	1/1	1	2	FACETS	0.535	0.43	0.654	0.535	0.43	0.654	SUBCLONAL	1	FALSE	1	0.233600421550026	2		267	480	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632215	215632215	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	28	258	0	ENST00000260947.4:c.1559G>C	p.Arg520Thr	p.R520T	ENST00000260947	NM_000465.2	520	aGa/aCa	6/11	0.233600421550026	1	FACETS	0.499	0.399	0.614	0.499	0.399	0.614	SUBCLONAL	1	FALSE	0	0.233600421550026	1		258	424	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911266	32911266	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs879255446	NA	P-0063396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	27	349	2	ENST00000380152.3:c.2774C>G	p.Ser925Cys	p.S925C	ENST00000380152		925	tCt/tGt	11/27	1	2	FACETS	0.541	0.43	0.669	0.541	0.43	0.669	SUBCLONAL	1	FALSE	1	0.233600421550026	2		351	427	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934234	48934234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1459523811	NA	P-0063396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	17	279	0	ENST00000267163.4:c.689C>T	p.Ser230Leu	p.S230L	ENST00000267163	NM_000321.2	230	tCa/tTa	7/27	1	2	FACETS	0.488	0.364	0.636	0.488	0.364	0.636	SUBCLONAL	1	FALSE	1	0.233600421550026	2		279	298	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641031	23641031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879254068	NA	P-0063396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	40	384	1	ENST00000261584.4:c.2444C>T	p.Ser815Leu	p.S815L	ENST00000261584	NM_024675.3	815	tCa/tTa	5/13	0.233600421550026	3	FACETS	0.562	0.466	0.67	0.281	0.233	0.335	SUBCLONAL	1	FALSE	1	0.233600421550026	3		385	680	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845901	72845901	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1264598448	NA	P-0063396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	37	372	0	ENST00000268489.5:c.3566C>G	p.Ser1189Cys	p.S1189C	ENST00000268489	NM_006885.3	1189	tCt/tGt	6/10	1	2	FACETS	0.549	0.452	0.658	0.549	0.452	0.658	SUBCLONAL	1	FALSE	1	0.233600421550026	2		372	577	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347467	89347467	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755632399	NA	P-0063396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	61	510	1	ENST00000301030.4:c.5483C>T	p.Ser1828Leu	p.S1828L	ENST00000301030	NM_001256183.1	1828	tCg/tTg	9/13	1	2	FACETS	0.633	0.545	0.729	0.633	0.545	0.729	SUBCLONAL	1	FALSE	1	0.233600421550026	2		511	825	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348106	89348106	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	63	412	4	ENST00000301030.4:c.4844C>A	p.Ser1615Tyr	p.S1615Y	ENST00000301030	NM_001256183.1	1615	tCc/tAc	9/13	1	2	FACETS	0.692	0.598	0.796	0.692	0.598	0.796	SUBCLONAL	1	FALSE	1	0.233600421550026	2		416	779	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302972	15302972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	75	505	0	ENST00000263388.2:c.478G>A	p.Asp160Asn	p.D160N	ENST00000263388	NM_000435.2	160	Gat/Aat	4/33	1	2	FACETS	0.647	0.566	0.736	0.647	0.566	0.736	SUBCLONAL	1	FALSE	1	0.233600421550026	2		505	992	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966240	25966240	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	46	452	3	ENST00000435504.4:c.2966G>A	p.Gly989Glu	p.G989E	ENST00000435504		989	gGg/gAg	13/13	0.233600421550026	3	FACETS	0.522	0.438	0.615	0.261	0.219	0.308	SUBCLONAL	1	FALSE	1	0.233600421550026	3		455	843	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631400	67631400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	54	299	3	ENST00000272342.5:c.1586C>T	p.Ser529Phe	p.S529F	ENST00000272342	NM_019002.3	529	tCt/tTt	5/6	0.233600421550026	3	FACETS	1	0.944	1	0.609	0.521	0.704	CLONAL	1	FALSE	1	0.233600421550026	3		302	424	SUCCESS
ATR	545	MSKCC	GRCh37	3	142224105	142224105	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	36	311	1	ENST00000350721.4:c.5072G>C	p.Gly1691Ala	p.G1691A	ENST00000350721	NM_001184.3	1691	gGa/gCa	29/47	0.233600421550026	3	FACETS	0.592	0.486	0.712	0.296	0.243	0.356	SUBCLONAL	1	FALSE	1	0.233600421550026	3		312	581	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056039	26056039	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs61742488	NA	P-0063396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	100	358	0	ENST00000343677.2:c.618G>C	p.Lys206Asn	p.K206N	ENST00000343677	NM_005319.3	206	aaG/aaC	1/1	0.233600421550026	5	FACETS	1	0.971	1	0.315	0.281	0.352	CLONAL	1	FALSE	1	0.233600421550026	5		358	917	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225698	26225698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1310	133	629	1	ENST00000360408.1:c.316G>A	p.Glu106Lys	p.E106K	ENST00000360408	NM_003532.2	106	Gag/Aag	1/1	0.233600421550026	5	FACETS	1	0.946	1	0.266	0.241	0.294	CLONAL	1	FALSE	1	0.233600421550026	5		630	1443	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250802	26250802	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	106	488	0	ENST00000446824.2:c.32C>G	p.Ser11Cys	p.S11C	ENST00000446824	NM_021018.2	11	tCc/tGc	1/1	0.233600421550026	5	FACETS	0.991	0.885	1	0.248	0.221	0.276	CLONAL	1	FALSE	1	0.233600421550026	5		488	1237	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675811	30675811	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	71	415	1	ENST00000376406.3:c.2545G>C	p.Glu849Gln	p.E849Q	ENST00000376406	NM_014641.2	849	Gag/Cag	8/15	0.215137703843467	4	FACETS	0.809	0.704	0.923	0.27	0.234	0.308	CLONAL	1	FALSE	1	0.233600421550026	4		416	927	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742099	145742099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	76	452	0	ENST00000428558.2:c.404C>T	p.Ser135Phe	p.S135F	ENST00000428558	NM_004260.3	135	tCt/tTt	5/22	0.196532833375292	1	FACETS	0.669	0.586	0.759	0.669	0.586	0.759	SUBCLONAL	1	FALSE	0	0.233600421550026	1		452	859	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44896904	44896905	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	24	197	1	ENST00000377967.4:c.627dup	p.His210SerfsTer7	p.H210Sfs*7	ENST00000377967	NM_021140.2	208	-/T	8/29	0.196532833375292	1	FACETS	0.617	0.485	0.77	0.617	0.485	0.77	SUBCLONAL	1	FALSE	0	0.233600421550026	1		198	294	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0063406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	86	549	0				ENST00000310581	NM_198253.2	-/1132			0.277495281972169	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	2	0.277495281972169	4		549	345	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225674	26225674	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	121	879	0	ENST00000360408.1:c.292G>A	p.Glu98Lys	p.E98K	ENST00000360408	NM_003532.2	98	Gag/Aag	1/1	0.278690926427536	3	FACETS	1	0.98	1	0.665	0.601	0.732	CLONAL	1	TRUE	1	0.277495281972169	3		879	747	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	198	587	0	ENST00000269305.4:c.398T>A	p.Met133Lys	p.M133K	ENST00000269305	NM_001126112.2	133	aTg/aAg	5/11	0.278690926427536	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.277495281972169	3		587	467	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662539	227662539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	24	701	0	ENST00000305123.5:c.916G>A	p.Glu306Lys	p.E306K	ENST00000305123	NM_005544.2	306	Gag/Aag	1/2	0.278690926427536	3	FACETS	0.411	0.321	0.515	0.206	0.16	0.258	SUBCLONAL	1	TRUE	1	0.277495281972169	3		701	479	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468065	50468065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749084924	NA	P-0063406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	77	633	1	ENST00000331340.3:c.1300G>A	p.Ala434Thr	p.A434T	ENST00000331340	NM_006060.4	434	Gcc/Acc	8/8	0.244088879202261	4	FACETS	1	0.973	1	0.467	0.411	0.527	CLONAL	1	TRUE	1	0.277495281972169	4		634	506	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244538	41244538	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786202534	NA	P-0063406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	45	421	0	ENST00000357654.3:c.3010G>C	p.Glu1004Gln	p.E1004Q	ENST00000357654	NM_007294.3	1004	Gag/Cag	10/23	0.176133228746105	4	FACETS	1	0.954	1	0.693	0.585	0.81	CLONAL	1	TRUE	2	0.277495281972169	4		421	299	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39294771	39294771	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	47	281	0	ENST00000402219.2:c.211G>C	p.Glu71Gln	p.E71Q	ENST00000402219	NM_005633.3	71	Gag/Cag	2/23	0.278690926427536	3	FACETS	1	0.942	1	0.622	0.528	0.725	CLONAL	1	TRUE	1	0.277495281972169	3		281	310	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733138	74733138	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	92	551	0	ENST00000359995.5:c.105G>C	p.Glu35Asp	p.E35D	ENST00000359995	NM_001195427.1	35	gaG/gaC	1/3	0.277495281972169	5	FACETS	0.862	0.768	0.961	0.574	0.512	0.641	CLONAL	2	TRUE	2	0.277495281972169	5		551	545	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780295	9780295	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	85	600	0	ENST00000377346.4:c.1465G>C	p.Glu489Gln	p.E489Q	ENST00000377346	NM_005026.3	489	Gag/Cag	11/24	0.277495281972169	6	FACETS	0.874	0.774	0.98	0.35	0.309	0.392	CLONAL	2	TRUE	1	0.277495281972169	6		600	545	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636680	2636680	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	83	501	0	ENST00000342085.4:c.1129G>C	p.Asp377His	p.D377H	ENST00000342085	NM_002613.4	377	Gac/Cac	11/14	0.278690926427536	3	FACETS	0.781	0.693	0.875	0.781	0.693	0.875	SUBCLONAL	2	TRUE	1	0.277495281972169	3		501	436	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89811480	89811480	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0063406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	54	454	0	ENST00000389301.3:c.3514-1G>A		p.X1172_splice	ENST00000389301	NM_000135.2	1172			0.278690926427536	3	FACETS	1	0.945	1	0.609	0.522	0.703	CLONAL	1	TRUE	1	0.277495281972169	3		454	364	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47684716	47684716	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	40	368	0	ENST00000347630.2:c.733G>C	p.Asp245His	p.D245H	ENST00000347630	NM_001007230.1	245	Gat/Cat	9/11	0.176133228746105	4	FACETS	1	0.861	1	0.519	0.432	0.615	CLONAL	1	TRUE	2	0.277495281972169	4		368	355	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612380	1612400	+	inframe_deletion	In_Frame_Del	DEL	TCTCCCGGTCCCTCAGGTCTT	TCTCCCGGTCCCTCAGGTCTT	-	novel	NA	P-0063406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	68	562	0	ENST00000344749.5:c.1619_1639del	p.Lys540_Glu546del	p.K540_E546del	ENST00000344749	NM_001136139.2	540	aAAGACCTGAGGGACCGGGAGAgg/agg	18/19	0.278690926427536	3	FACETS	1	0.963	1	0.646	0.564	0.734	CLONAL	1	TRUE	1	0.277495281972169	3		562	432	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142989	7142989	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376600434	NA	P-0063406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	82	560	0	ENST00000302850.5:c.2380G>A	p.Glu794Lys	p.E794K	ENST00000302850	NM_000208.2	794	Gag/Aag	12/22	0.278690926427536	3	FACETS	0.756	0.67	0.848	0.756	0.67	0.848	SUBCLONAL	2	TRUE	1	0.277495281972169	3		560	445	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	914666	914666	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	45	334	0	ENST00000166345.3:c.1107G>C	p.Leu369Phe	p.L369F	ENST00000166345	NM_004237.3	369	ttG/ttC	11/13	0.277495281972169	4	FACETS	0.955	0.803	1	0.477	0.401	0.561	CLONAL	1	TRUE	2	0.277495281972169	4		334	434	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38137162	38137162	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	48	418	0	ENST00000317025.8:c.3656C>G	p.Ser1219Cys	p.S1219C	ENST00000317025	NM_023034.1	1219	tCt/tGt	21/24	0.278690926427536	3	FACETS	1	0.922	1	0.571	0.484	0.665	CLONAL	1	TRUE	1	0.277495281972169	3		418	345	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141570495	141570495	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	81	543	0	ENST00000220592.5:c.633G>A	p.Trp211Ter	p.W211*	ENST00000220592	NM_012154.3	211	tgG/tgA	5/19	0.277495281972169	7	FACETS	1	0.977	1	0.299	0.263	0.338	CLONAL	1	TRUE	2	0.277495281972169	7		543	661	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971064	21971079	+	frameshift_variant	Frame_Shift_Del	DEL	GTGCAGCACCACCAGC	GTGCAGCACCACCAGC	-	novel	NA	P-0063406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	202	601	0	ENST00000304494.5:c.279_294del	p.Leu94GlyfsTer47	p.L94Gfs*47	ENST00000304494	NM_000077.4	93	acGCTGGTGGTGCTGCAC/ac	2/3	0.278690926427536	2	FACETS	1	0.969	1	1	0.993	1	CLONAL	3	TRUE	0	0.277495281972169	2		601	460	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679786	88679786	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	57	395	0	ENST00000360948.2:c.677A>G	p.Asn226Ser	p.N226S	ENST00000360948	NM_001012338.2	226	aAc/aGc	7/19	0.278690926427536	3	FACETS	1	0.946	1	0.604	0.52	0.695	CLONAL	1	TRUE	1	0.277495281972169	3		395	387	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745332	43745332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762664023	NA	P-0063413-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	1039	561	13	ENST00000523873.1:c.245G>A	p.Arg82Gln	p.R82Q	ENST00000523873		82	cGa/cAa	3/8	0.789356131194153	3	FACETS	1	0.996	1			1	CLONAL	3	TRUE	NA	0.789356131194153	3		574	1190	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341275	341275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219986773	NA	P-0063413-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	193	350	2	ENST00000262320.3:c.2209C>T	p.Arg737Trp	p.R737W	ENST00000262320	NM_003502.3	737	Cgg/Tgg	9/11	0.789356131194153	2	FACETS	1	0.949	1	0.509	0.476	0.543	CLONAL	1	TRUE	0	0.789356131194153	2		352	480	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096524	178096524	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063413-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	285	380	2	ENST00000397062.3:c.807C>A	p.Asn269Lys	p.N269K	ENST00000397062	NM_006164.4	269	aaC/aaA	5/5	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.789356131194153	2		382	706	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541306	187541306	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063413-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	220	374	5	ENST00000441802.2:c.6434C>A	p.Thr2145Asn	p.T2145N	ENST00000441802	NM_005245.3	2145	aCc/aAc	10/27	0.789356131194153	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.789356131194153	1		379	333	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609950	43609950	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs77709286	NA	P-0063414-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	515	472	0	ENST00000355710.3:c.1902C>G	p.Cys634Trp	p.C634W	ENST00000355710	NM_020975.4	634	tgC/tgG	11/20	0.370805222873186	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	FALSE	0	0.485008996631608	2		472	871	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541243	187541243	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063414-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	71	304	0	ENST00000441802.2:c.6497C>G	p.Ala2166Gly	p.A2166G	ENST00000441802	NM_005245.3	2166	gCg/gGg	10/27	1	2	FACETS	0.555	0.485	0.63	0.555	0.485	0.63	SUBCLONAL	1	FALSE	1	0.485008996631608	2		304	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0063415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	150	452	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.170104326792614	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	FALSE	0	0.180819713832956	2		452	718	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0063415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	33	292	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.180819713832956	1	FACETS	0.878	0.716	1	0.878	0.716	1	CLONAL	1	FALSE	0	0.180819713832956	1		292	378	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230668	46230668	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0063415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	108	352	0	ENST00000334344.6:c.917T>A	p.Leu306Ter	p.L306*	ENST00000334344	NM_152641.2	306	tTg/tAg	8/21	0.16972657626482	3	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	FALSE	1	0.180819713832956	3		352	616	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998924	11998928	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAC	AAAAC	-	novel	NA	P-0063415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	41	282	0	ENST00000353533.5:c.428_432del	p.Lys143ThrfsTer12	p.K143Tfs*12	ENST00000353533	NM_003010.3	142	caAAAACaa/caaa	4/11	0.170104326792614	2	FACETS	1	0.905	1	0.564	0.47	0.668	CLONAL	1	FALSE	0	0.180819713832956	2		282	402	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604790	48604790	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1568211615	NA	P-0063415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	118	345	0	ENST00000342988.3:c.1612G>T	p.Glu538Ter	p.E538*	ENST00000342988	NM_005359.5	538	Gaa/Taa	12/12	0.180819713832956	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	FALSE	0	0.180819713832956	2		345	623	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519378	176519378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148292303	NA	P-0063415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	37	445	0	ENST00000292408.4:c.784G>A	p.Val262Met	p.V262M	ENST00000292408	NM_213647.1	262	Gtg/Atg	7/18	1	2	FACETS	0.745	0.614	0.893	0.745	0.614	0.893	SUBCLONAL	1	FALSE	1	0.180819713832956	2		445	549	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0063424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	254	547	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.510553483656828	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.508408416883376	2		548	414	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	106	337	0	ENST00000308159.5:c.43C>G	p.Gln15Glu	p.Q15E	ENST00000308159	NM_014669.4	15	Cag/Gag	2/22	0.210853128888694	5	FACETS	1	0.98	1	0.462	0.416	0.511	INDETERMINATE	1	TRUE	2	0.508408416883376	5		337	530	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717642	89717642	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	101	331	0	ENST00000371953.3:c.668del	p.Lys223ArgfsTer33	p.K223Rfs*33	ENST00000371953	NM_000314.4	223	Aag/ag	7/9	0.510553483656828	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.508408416883376	1		331	291	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884942	111884942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548009613	NA	P-0063424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	284	504	0	ENST00000341259.2:c.940G>A	p.Glu314Lys	p.E314K	ENST00000341259	NM_005475.2	314	Gaa/Aaa	5/8	0.510553483656828	3	FACETS	0.84	0.792	0.889			1	CLONAL	2	TRUE	NA	0.508408416883376	3		504	834	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202258	133202258	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	250	538	0	ENST00000320574.5:c.6630G>C	p.Lys2210Asn	p.K2210N	ENST00000320574	NM_006231.2	2210	aaG/aaC	47/49	0.510553483656828	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	1	0.508408416883376	3		538	609	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993680	72993680	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	116	611	0	ENST00000268489.5:c.365A>G	p.Glu122Gly	p.E122G	ENST00000268489	NM_006885.3	122	gAg/gGg	2/10	NA	2	FACETS	0.608	0.548	0.672			1	INDETERMINATE	1	TRUE	NA	0.508408416883376	2		611	750	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654771	29654771	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	141	476	0	ENST00000356175.3:c.5460A>C	p.Gln1820His	p.Q1820H	ENST00000356175	NM_000267.3	1820	caA/caC	37/57	0.510553483656828	2	FACETS	1	0.921	1	0.503	0.461	0.548	CLONAL	1	TRUE	0	0.508408416883376	2		476	551	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664430	29664440	+	frameshift_variant	Frame_Shift_Del	DEL	TTACCCAAATT	TTACCCAAATT	-	novel	NA	P-0063424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	105	316	0	ENST00000356175.3:c.6413_6423del	p.Pro2138LeufsTer6	p.P2138Lfs*6	ENST00000356175	NM_000267.3	2137	TTACCCAAATTt/t	42/57	0.510553483656828	2	FACETS	0.954	0.86	1	0.477	0.43	0.526	CLONAL	1	TRUE	0	0.508408416883376	2		316	433	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33689827	33689827	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	127	430	1	ENST00000308377.4:c.1000G>T	p.Val334Leu	p.V334L	ENST00000308377	NM_152270.3	334	Gtg/Ttg	2/5	NA	2	FACETS	0.995	0.907	1			1	INDETERMINATE	1	TRUE	NA	0.508408416883376	2		431	502	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435930	56435930	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1436857798	NA	P-0063424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	359	583	1	ENST00000407977.2:c.1207C>T	p.Gln403Ter	p.Q403*	ENST00000407977		403	Cag/Tag	9/10	0.510553483656828	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.508408416883376	2		584	613	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22153378	22153378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	356	373	0	ENST00000215832.6:c.532C>T	p.His178Tyr	p.H178Y	ENST00000215832	NM_002745.4	178	Cat/Tat	4/9	0.510553483656828	4	FACETS	0.849	0.809	0.89	1	0.994	1	CLONAL	3	TRUE	2	0.508408416883376	4		373	829	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29442711	29442723	+	frameshift_variant	Frame_Shift_Del	DEL	TGAACAGGCTGGC	TGAACAGGCTGGC	-	novel	NA	P-0063424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	121	366	0	ENST00000544604.2:c.754_766del	p.Asn252CysfsTer4	p.N252Cfs*4	ENST00000544604	NM_001206998.1	251	aTGAACAGGCTGGCt/at	6/9	0.504281210746311	2	FACETS	1	0.982	1	0.652	0.595	0.71	CLONAL	1	TRUE	0	0.508408416883376	2		366	365	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100431	157100476	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCGGCGGCGGGGGCGGCGGCGGGCGGCCAGCAGGCGGCCGCG	GGCGGCGGCGGCGGGGGCGGCGGCGGGCGGCCAGCAGGCGGCCGCG	-	novel	NA	P-0063424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	119	158	0	ENST00000346085.5:c.1371_1416del	p.Ala458TrpfsTer29	p.A458Wfs*29	ENST00000346085	NM_020732.3	456	caGGCGGCGGCGGCGGGGGCGGCGGCGGGCGGCCAGCAGGCGGCCGCG/ca	1/20	0.510553483656828	1	FACETS	0.954	0.892	1	1	0.991	1	CLONAL	2	TRUE	0	0.508408416883376	1		158	183	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137326030	137326030	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	45	455	0	ENST00000481739.1:c.1218C>G	p.His406Gln	p.H406Q	ENST00000481739	NM_002957.4	406	caC/caG	9/10	0.28775445820452	2	FACETS	0.378	0.318	0.445	0.189	0.159	0.223	INDETERMINATE	1	TRUE	0	0.508408416883376	2		455	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0063425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	211	583	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.328548909956639	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.519024261019136	1		583	592	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430413	181430413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	123	474	0	ENST00000325404.1:c.265C>T	p.Pro89Ser	p.P89S	ENST00000325404	NM_003106.3	89	Ccg/Tcg	1/1	1	2	FACETS	0.836	0.759	0.917	0.836	0.759	0.917	CLONAL	1	TRUE	1	0.519024261019136	2		474	567	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0063426-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	956	454	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.252693815150147	16	FACETS	1	0.991	1	0.959	0.937	0.981	CLONAL	14	TRUE	1	0.252693815150147	16		454	1456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0063426-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	76	698	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.252693815150147	1	FACETS	0.932	0.818	1	0.932	0.818	1	CLONAL	1	TRUE	0	0.252693815150147	1		698	564	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792732	33792737	+	inframe_deletion	In_Frame_Del	DEL	GCGGGT	GCGGGT	-	rs762459325	NA	P-0063426-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	9	391	1	ENST00000498907.2:c.584_589del	p.His195_Pro196del	p.H195_P196del	ENST00000498907	NM_004364.3	195	cACCCGCcg/ccg	1/1	0.202711435700534	2	FACETS	0.188	0.124	0.271	0.094	0.062	0.136	SUBCLONAL	1	TRUE	0	0.252693815150147	2		392	379	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020669	37020669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063426-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	24	517	0	ENST00000358127.4:c.176G>A	p.Arg59Gln	p.R59Q	ENST00000358127	NM_001280556.1	59	cGg/cAg	2/10	0.252693815150147	1	FACETS	0.353	0.276	0.442	0.353	0.276	0.442	SUBCLONAL	1	TRUE	0	0.252693815150147	1		517	470	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0063427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	22	393	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.444	0.344	0.56	0.444	0.344	0.56	SUBCLONAL	1	TRUE	1	0.307994670106109	2		394	322	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0063427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	35	319	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.16540693735445	3	FACETS	0.492	0.403	0.593	0.246	0.201	0.297	INDETERMINATE	1	TRUE	1	0.307994670106109	3		319	533	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630626	158630626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912678	NA	P-0063427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	15	423	0	ENST00000263640.3:c.617G>A	p.Arg206His	p.R206H	ENST00000263640	NM_001105.4	206	cGc/cAc	6/11	1	2	FACETS	0.145	0.105	0.193	0.145	0.105	0.193	SUBCLONAL	1	TRUE	1	0.307994670106109	2		423	672	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023558	27023558	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	39	474	0	ENST00000324856.7:c.664del	p.Tyr222ThrfsTer10	p.Y222Tfs*10	ENST00000324856	NM_006015.4	222	Tac/ac	1/20	1	2	FACETS	0.539	0.446	0.642	0.539	0.446	0.642	SUBCLONAL	1	TRUE	1	0.307994670106109	2		474	470	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692878	89692884	+	frameshift_variant	Frame_Shift_Del	DEL	CAATTCA	CAATTCA	-	novel	NA	P-0063427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	71	198	0	ENST00000371953.3:c.363_369del	p.Ile122ValfsTer10	p.I122Vfs*10	ENST00000371953	NM_000314.4	121	gCAATTCAc/gc	5/9	0.16540693735445	3	FACETS	1	0.975	1	0.747	0.656	0.844	INDETERMINATE	1	TRUE	1	0.307994670106109	3		198	356	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828913	72828914	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0063427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	54	622	0	ENST00000268489.5:c.7667_7668insAC	p.Gln2557ArgfsTer56	p.Q2557Rfs*56	ENST00000268489	NM_006885.3	2556	gcg/gcACg	9/10	1	2	FACETS	0.451	0.384	0.524	0.451	0.384	0.524	SUBCLONAL	1	TRUE	1	0.307994670106109	2		622	778	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699368	47699368	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	50	354	0	ENST00000347630.2:c.140A>C	p.Glu47Ala	p.E47A	ENST00000347630	NM_001007230.1	47	gAa/gCa	4/11	1	2	FACETS	0.544	0.461	0.635	0.544	0.461	0.635	SUBCLONAL	1	TRUE	1	0.307994670106109	2		354	597	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324560	31324560	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	21	339	0	ENST00000412585.2:c.248A>G	p.Tyr83Cys	p.Y83C	ENST00000412585	NM_005514.6	83	tAt/tGt	2/8	1	2	FACETS	0.4	0.308	0.508	0.4	0.308	0.508	SUBCLONAL	1	TRUE	1	0.307994670106109	2		339	341	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682991	241682991	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1226883651	NA	P-0063431-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	173	493	0	ENST00000366560.3:c.32C>G	p.Ser11Trp	p.S11W	ENST00000366560	NM_000143.3	11	tCg/tGg	1/10	0.574114220879143	4	FACETS	1	0.923	1	0.334	0.307	0.362	CLONAL	1	TRUE	1	0.574114220879143	4		493	946	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692901	89692901	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063431-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	120	279	0	ENST00000371953.3:c.385G>C	p.Gly129Arg	p.G129R	ENST00000371953	NM_000314.4	129	Gga/Cga	5/9	0.574114220879143	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.574114220879143	1		279	288	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941200	71941200	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063431-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	259	732	0	ENST00000298229.2:c.975G>C	p.Lys325Asn	p.K325N	ENST00000298229	NM_001567.3	325	aaG/aaC	9/28	1	2	FACETS	0.956	0.897	1	0.956	0.897	1	CLONAL	1	TRUE	1	0.574114220879143	2		732	944	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646346	3646346	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1202254236	NA	P-0063431-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	111	567	0	ENST00000294008.3:c.1732G>C	p.Glu578Gln	p.E578Q	ENST00000294008	NM_032444.2	578	Gag/Cag	8/15	0.536644643101956	3	FACETS	0.56	0.503	0.621	0.28	0.251	0.311	SUBCLONAL	1	TRUE	1	0.574114220879143	3		567	889	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849631	68849631	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063431-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	230	487	0	ENST00000261769.5:c.1534G>T	p.Glu512Ter	p.E512*	ENST00000261769	NM_004360.3	512	Gag/Tag	10/16	0.574114220879143	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.574114220879143	1		487	548	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120527	70120527	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0063431-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	234	595	0	ENST00000245479.2:c.1529G>C	p.Ter510SerextTer49	p.*510Sext*49	ENST00000245479	NM_000346.3	510	tGa/tCa	3/3	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.574114220879143	2		595	752	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39713113	39713113	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063431-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	98	287	0	ENST00000361337.2:c.519G>T	p.Leu173Phe	p.L173F	ENST00000361337	NM_003286.2	173	ttG/ttT	8/21	0.574114220879143	2	FACETS	0.829	0.744	0.917	0.414	0.372	0.459	CLONAL	1	TRUE	0	0.574114220879143	2		287	412	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940438	49940438	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063431-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	99	645	0	ENST00000296474.3:c.605C>A	p.Ser202Ter	p.S202*	ENST00000296474	NM_002447.2	202	tCa/tAa	1/20	1	2	FACETS	0.444	0.396	0.496	0.444	0.396	0.496	SUBCLONAL	1	TRUE	1	0.574114220879143	2		645	776	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948174	55948174	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063431-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	114	309	0	ENST00000263923.4:c.3797C>T	p.Ser1266Leu	p.S1266L	ENST00000263923	NM_002253.2	1266	tCa/tTa	29/30	1	2	FACETS	0.881	0.798	0.967	0.881	0.798	0.967	CLONAL	1	TRUE	1	0.574114220879143	2		309	451	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045649	26045649	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063431-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	206	555	0	ENST00000540144.1:c.11C>G	p.Thr4Arg	p.T4R	ENST00000540144	NM_003531.2	4	aCg/aGg	1/1	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.574114220879143	2		555	688	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101895013	101895013	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063431-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	154	404	0	ENST00000374994.4:c.566C>A	p.Ser189Tyr	p.S189Y	ENST00000374994	NM_004612.2	189	tCt/tAt	3/9	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.574114220879143	2		404	506	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806089	1806089	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913479	NA	P-0063432-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	48	526	0	ENST00000260795.2:c.1108G>T	p.Gly370Cys	p.G370C	ENST00000260795		370	Ggc/Tgc	8/17	0.112198742708782	5	FACETS	1	0.911	1	0.536	0.464	0.613	INDETERMINATE	2	TRUE	1	0.597371268277257	5		526	142	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445832	49445832	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs886039399	NA	P-0063432-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	24	651	0	ENST00000301067.7:c.1634del	p.Leu545ArgfsTer385	p.L545Rfs*385	ENST00000301067	NM_003482.3	545	cTg/cg	10/54	1	2	FACETS	0.945	0.761	1	0.945	0.761	1	CLONAL	1	TRUE	1	0.597371268277257	2		651	85	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164707	36164708	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0063432-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	41	642	0	ENST00000300305.3:c.1167_1168insAG	p.Gln390SerfsTer205	p.Q390Sfs*205	ENST00000300305		389	-/AG	8/8	0.194965072866445	1	FACETS	0.776	0.662	0.896	0.776	0.662	0.896	INDETERMINATE	1	TRUE	0	0.597371268277257	1		642	124	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875994	76875994	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063432-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	15	159	0	ENST00000373344.5:c.5141A>G	p.Asp1714Gly	p.D1714G	ENST00000373344	NM_000489.3	1714	gAt/gGt	20/35	0.304196884265894	2	FACETS	1	0.807	1			1	INDETERMINATE	2	TRUE	NA	0.597371268277257	2		159	25	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0063433-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	61	404	2	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.711	0.617	0.811	0.711	0.617	0.811	SUBCLONAL	1	TRUE	1	0.541449434669515	2		406	317	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0063433-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	98	367	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.973	0.876	1	0.973	0.876	1	CLONAL	1	TRUE	1	0.541449434669515	2		367	372	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845935	156845935	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063433-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	265	835	0	ENST00000524377.1:c.1565G>T	p.Gly522Val	p.G522V	ENST00000524377	NM_002529.3	522	gGg/gTg	13/17	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.541449434669515	2		835	970	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984941	101984941	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063433-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	92	250	0	ENST00000282441.5:c.388G>T	p.Ala130Ser	p.A130S	ENST00000282441	NM_001130145.2	130	Gct/Tct	2/9	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.541449434669515	2		250	331	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641388	18641389	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1229278001	NA	P-0063433-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	119	463	0	ENST00000266497.5:c.2393dup	p.Asn798LysfsTer5	p.N798Kfs*5	ENST00000266497		796	cta/ctAa	17/31	1	2	FACETS	0.897	0.814	0.984	0.897	0.814	0.984	CLONAL	1	TRUE	1	0.541449434669515	2		463	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579316	7579317	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0063433-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	194	605	0	ENST00000269305.4:c.370dup	p.Cys124LeufsTer25	p.C124Lfs*25	ENST00000269305	NM_001126112.2	124	tgc/tTgc	4/11	0.541449434669515	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.541449434669515	1		605	496	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66518987	66518987	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063433-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	232	570	0	ENST00000358598.2:c.268G>A	p.Val90Met	p.V90M	ENST00000358598	NM_212471.2	90	Gtg/Atg	3/11	0.136461577150835	5	FACETS	0.973	0.91	1	0.487	0.455	0.519	INDETERMINATE	2	TRUE	1	0.541449434669515	5		570	798	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374918	45374918	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063433-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	166	536	0	ENST00000262160.6:c.925G>T	p.Glu309Ter	p.E309*	ENST00000262160	NM_005901.5	309	Gag/Tag	8/11	0.541449434669515	1	FACETS	0.97	0.899	1	0.97	0.899	1	CLONAL	1	TRUE	0	0.541449434669515	1		536	461	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276311	15276311	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754537422	NA	P-0063433-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	194	563	0	ENST00000263388.2:c.5683C>T	p.Arg1895Cys	p.R1895C	ENST00000263388	NM_000435.2	1895	Cgc/Tgc	31/33	0.541449434669515	2	FACETS	0.934	0.867	1	0.467	0.433	0.502	CLONAL	1	TRUE	0	0.541449434669515	2		563	767	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143409	30143409	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063433-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	136	544	0	ENST00000389048.3:c.117G>T	p.Gln39His	p.Q39H	ENST00000389048	NM_004304.4	39	caG/caT	1/29	1	2	FACETS	0.912	0.833	0.994	0.912	0.833	0.994	CLONAL	1	TRUE	1	0.541449434669515	2		544	551	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204006	142204006	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886058052	NA	P-0063433-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	157	451	0	ENST00000350721.4:c.6197G>A	p.Arg2066Gln	p.R2066Q	ENST00000350721	NM_001184.3	2066	cGg/cAg	36/47	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.541449434669515	2		451	575	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1962801	1962801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772470710	NA	P-0063433-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	205	582	2	ENST00000382891.5:c.3295G>A	p.Glu1099Lys	p.E1099K	ENST00000382891	NM_133335.3	1099	Gag/Aag	18/22	0.541449434669515	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.541449434669515	1		584	544	SUCCESS
APC	324	MSKCC	GRCh37	5	112154715	112154716	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0063433-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	120	435	0	ENST00000257430.4:c.988_989del	p.Met330ValfsTer9	p.M330Vfs*9	ENST00000257430	NM_000038.5	329	gAT/g	10/16	1	2	FACETS	0.841	0.763	0.923	0.841	0.763	0.923	CLONAL	1	TRUE	1	0.541449434669515	2		435	527	SUCCESS
APC	324	MSKCC	GRCh37	5	112175930	112175930	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063433-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	182	536	0	ENST00000257430.4:c.4639G>T	p.Glu1547Ter	p.E1547*	ENST00000257430	NM_000038.5	1547	Gaa/Taa	16/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.541449434669515	2		536	610	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358944	81358944	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063433-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	284	422	0	ENST00000222390.5:c.1017G>T	p.Met339Ile	p.M339I	ENST00000222390	NM_000601.4	339	atG/atT	8/18	0.541449434669515	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.541449434669515	3		422	653	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0063434-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	84	292	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.926	0.823	1	0.926	0.823	1	CLONAL	1	TRUE	1	0.47	2		292	386	SUCCESS
APC	324	MSKCC	GRCh37	5	112151245	112151246	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs1114167567	NA	P-0063434-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	109	366	0	ENST00000257430.4:c.893_894del	p.His298LeufsTer28	p.H298Lfs*28	ENST00000257430	NM_000038.5	296	agCAca/agca	9/16	1	2	FACETS	0.875	0.789	0.966	0.875	0.789	0.966	CLONAL	1	TRUE	1	0.47	2		366	530	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637121	176637121	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063434-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	154	530	0	ENST00000439151.2:c.1721G>T	p.Gly574Val	p.G574V	ENST00000439151	NM_022455.4	574	gGa/gTa	5/23	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.47	2		530	618	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599320	55599320	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913506	NA	P-0063435-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	57	383	0	ENST00000288135.5:c.2446G>C	p.Asp816His	p.D816H	ENST00000288135	NM_000222.2	816	Gac/Cac	17/21	0.23349884079005	1	FACETS	0.417	0.361	0.478	0.417	0.361	0.478	INDETERMINATE	1	TRUE	0	0.660713866046637	1		383	277	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0063436-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	16	662	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.273	0.201	0.36	0.273	0.201	0.36	SUBCLONAL	1	TRUE	1	0.27	2		662	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782144	NA	P-0063436-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	80	726	0	ENST00000269305.4:c.473G>C	p.Arg158Pro	p.R158P	ENST00000269305	NM_001126112.2	158	cGc/cCc	5/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.27	2		726	510	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40743933	40743933	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063436-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	53	670	0	ENST00000392038.2:c.774G>C	p.Glu258Asp	p.E258D	ENST00000392038	NM_001626.4	258	gaG/gaC	9/14	0.201787699675287	3	FACETS	0.787	0.671	0.915	0.394	0.335	0.458	CLONAL	1	TRUE	1	0.27	3		670	566	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55270215	55271237	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGCTGTCCCATCAAGGAAGACAGCTTCTTGCAGCGATACAGCTCAGACCCCACAGGCGCCTTGACTGAGGACAGCATAGACGACACCTTCCTCCCAGTGCCTGGTGAGTGGCTTGTCTGGAAACAGTCCTGCTCCTCAACCTCCTCGACCCACTCAGCAGCAGCCAGTCTCCAGTGTCCAAGCCAGGTGCTCCCTCCAGCATCTCCAGAGGGGGAAACAGTGGCAGATTTGCAGACACAGTGAAGGGCGTAAGGAGCAGATAAACACATGACCGAGCCTGCACAAGCTCTTTGTTGTGTCTGGTTGTTTGCTGTACCTCTGTTGTAAGAATGAATCTGCAAAATTTCTAGCTTATGAAGCAAATCACGGACATACACATCTGTGTGTGTGAGTGTTCATGATGTGTGTACATCTGTGTATGTGTGTGTGTGTATGTGTGTGTTTGTGACAGATTTGATCCCTGTTCTCTCTGCTGGCTCTATCTTGACCTGTGAAACGTATATTTAACTAATTAAATATTAGTTAATATTAATAAATTTTAAGCTTTATCCAGATACTCATAACCTGCTAACACACACACATATACACACACATACACATACACACATATACACACACCACACACATACACAGACACCACACACATACCATACACAGACACATACACATGCACACACATATACACACACACCTCAAATACATACACACCACACACACATACATGTATACACACATACACACACCACACATACACCACAAAAACCCCACACACATACACATATACACACCACACACACCACATACACACACGTATACACACATATATACACACATACACCATGCATACATACACACCACACATACATACAGACACACCACACACACGTACACACAACACACAACACAGACACGTACACACACTACAGACATGTATGCACACATACACACACACCACACATACATACACACAGACACATATACACTACACACACCATTACATACACACGTACACATACACCACA	AAGCTGTCCCATCAAGGAAGACAGCTTCTTGCAGCGATACAGCTCAGACCCCACAGGCGCCTTGACTGAGGACAGCATAGACGACACCTTCCTCCCAGTGCCTGGTGAGTGGCTTGTCTGGAAACAGTCCTGCTCCTCAACCTCCTCGACCCACTCAGCAGCAGCCAGTCTCCAGTGTCCAAGCCAGGTGCTCCCTCCAGCATCTCCAGAGGGGGAAACAGTGGCAGATTTGCAGACACAGTGAAGGGCGTAAGGAGCAGATAAACACATGACCGAGCCTGCACAAGCTCTTTGTTGTGTCTGGTTGTTTGCTGTACCTCTGTTGTAAGAATGAATCTGCAAAATTTCTAGCTTATGAAGCAAATCACGGACATACACATCTGTGTGTGTGAGTGTTCATGATGTGTGTACATCTGTGTATGTGTGTGTGTGTATGTGTGTGTTTGTGACAGATTTGATCCCTGTTCTCTCTGCTGGCTCTATCTTGACCTGTGAAACGTATATTTAACTAATTAAATATTAGTTAATATTAATAAATTTTAAGCTTTATCCAGATACTCATAACCTGCTAACACACACACATATACACACACATACACATACACACATATACACACACCACACACATACACAGACACCACACACATACCATACACAGACACATACACATGCACACACATATACACACACACCTCAAATACATACACACCACACACACATACATGTATACACACATACACACACCACACATACACCACAAAAACCCCACACACATACACATATACACACCACACACACCACATACACACACGTATACACACATATATACACACATACACCATGCATACATACACACCACACATACATACAGACACACCACACACACGTACACACAACACACAACACAGACACGTACACACACTACAGACATGTATGCACACATACACACACACCACACATACATACACACAGACACATATACACTACACACACCATTACATACACACGTACACATACACCACA	-	novel	NA	P-0063437-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	8	593	0	ENST00000275493.2:c.3168_3271+919del		p.X1056_splice	ENST00000275493	NM_005228.3	1056		27/28	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		593	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0063437-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	119	681	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.543716234680419	2	FACETS	0.968	0.898	1	0.968	0.898	1	CLONAL	2	TRUE	0	0.571668705541922	2		682	215	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0063437-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	109	470	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.567336194754618	2	FACETS	0.998	0.924	1	0.998	0.924	1	CLONAL	2	TRUE	0	0.571668705541922	2		470	191	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55270215	55271237	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGCTGTCCCATCAAGGAAGACAGCTTCTTGCAGCGATACAGCTCAGACCCCACAGGCGCCTTGACTGAGGACAGCATAGACGACACCTTCCTCCCAGTGCCTGGTGAGTGGCTTGTCTGGAAACAGTCCTGCTCCTCAACCTCCTCGACCCACTCAGCAGCAGCCAGTCTCCAGTGTCCAAGCCAGGTGCTCCCTCCAGCATCTCCAGAGGGGGAAACAGTGGCAGATTTGCAGACACAGTGAAGGGCGTAAGGAGCAGATAAACACATGACCGAGCCTGCACAAGCTCTTTGTTGTGTCTGGTTGTTTGCTGTACCTCTGTTGTAAGAATGAATCTGCAAAATTTCTAGCTTATGAAGCAAATCACGGACATACACATCTGTGTGTGTGAGTGTTCATGATGTGTGTACATCTGTGTATGTGTGTGTGTGTATGTGTGTGTTTGTGACAGATTTGATCCCTGTTCTCTCTGCTGGCTCTATCTTGACCTGTGAAACGTATATTTAACTAATTAAATATTAGTTAATATTAATAAATTTTAAGCTTTATCCAGATACTCATAACCTGCTAACACACACACATATACACACACATACACATACACACATATACACACACCACACACATACACAGACACCACACACATACCATACACAGACACATACACATGCACACACATATACACACACACCTCAAATACATACACACCACACACACATACATGTATACACACATACACACACCACACATACACCACAAAAACCCCACACACATACACATATACACACCACACACACCACATACACACACGTATACACACATATATACACACATACACCATGCATACATACACACCACACATACATACAGACACACCACACACACGTACACACAACACACAACACAGACACGTACACACACTACAGACATGTATGCACACATACACACACACCACACATACATACACACAGACACATATACACTACACACACCATTACATACACACGTACACATACACCACA	AAGCTGTCCCATCAAGGAAGACAGCTTCTTGCAGCGATACAGCTCAGACCCCACAGGCGCCTTGACTGAGGACAGCATAGACGACACCTTCCTCCCAGTGCCTGGTGAGTGGCTTGTCTGGAAACAGTCCTGCTCCTCAACCTCCTCGACCCACTCAGCAGCAGCCAGTCTCCAGTGTCCAAGCCAGGTGCTCCCTCCAGCATCTCCAGAGGGGGAAACAGTGGCAGATTTGCAGACACAGTGAAGGGCGTAAGGAGCAGATAAACACATGACCGAGCCTGCACAAGCTCTTTGTTGTGTCTGGTTGTTTGCTGTACCTCTGTTGTAAGAATGAATCTGCAAAATTTCTAGCTTATGAAGCAAATCACGGACATACACATCTGTGTGTGTGAGTGTTCATGATGTGTGTACATCTGTGTATGTGTGTGTGTGTATGTGTGTGTTTGTGACAGATTTGATCCCTGTTCTCTCTGCTGGCTCTATCTTGACCTGTGAAACGTATATTTAACTAATTAAATATTAGTTAATATTAATAAATTTTAAGCTTTATCCAGATACTCATAACCTGCTAACACACACACATATACACACACATACACATACACACATATACACACACCACACACATACACAGACACCACACACATACCATACACAGACACATACACATGCACACACATATACACACACACCTCAAATACATACACACCACACACACATACATGTATACACACATACACACACCACACATACACCACAAAAACCCCACACACATACACATATACACACCACACACACCACATACACACACGTATACACACATATATACACACATACACCATGCATACATACACACCACACATACATACAGACACACCACACACACGTACACACAACACACAACACAGACACGTACACACACTACAGACATGTATGCACACATACACACACACCACACATACATACACACAGACACATATACACTACACACACCATTACATACACACGTACACATACACCACA	-	novel	NA	P-0063437-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6385	2569	593	0	ENST00000275493.2:c.3168_3271+919del		p.X1056_splice	ENST00000275493	NM_005228.3	1056		27/28	0.571668705541922	98	FACETS	0.984	0.965	1	0.294	0.288	0.301	CLONAL	29	TRUE	1	0.571668705541922	98		593	8954	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998898	11998898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063437-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	101	369	0	ENST00000353533.5:c.400C>T	p.Arg134Trp	p.R134W	ENST00000353533	NM_003010.3	134	Cgg/Tgg	4/11	0.543716234680419	2	FACETS	0.993	0.915	1	0.993	0.915	1	CLONAL	2	TRUE	0	0.571668705541922	2		369	178	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914137	32914137	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs80358785	NA	P-0063437-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	16	463	0	ENST00000380152.3:c.5645C>A	p.Ser1882Ter	p.S1882*	ENST00000380152		1882	tCa/tAa	11/27	0.548834510994973	3	FACETS	0.267	0.197	0.35	0.133	0.098	0.175	SUBCLONAL	1	TRUE	1	0.571668705541922	3		463	270	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905432	11905432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34966596	NA	P-0063437-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	185	466	0	ENST00000396373.4:c.82G>A	p.Ala28Thr	p.A28T	ENST00000396373	NM_001987.4	28	Gct/Act	2/8	0.571668705541922	6	FACETS	1	0.985	1			1	CLONAL	2	TRUE	NA	0.571668705541922	6		466	569	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437592	56437592	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063437-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	231	563	0	ENST00000407977.2:c.870C>G	p.Cys290Trp	p.C290W	ENST00000407977		290	tgC/tgG	8/10	0.571668705541922	2	FACETS	0.935	0.902	0.967	1	0.995	1	CLONAL	3	TRUE	0	0.571668705541922	2		563	288	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0063439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	94	515	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.993	0.884	1	0.993	0.884	1	CLONAL	1	TRUE	1	0.29	2		515	653	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81960742	81960742	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	73	622	0	ENST00000359376.3:c.2473G>C	p.Glu825Gln	p.E825Q	ENST00000359376	NM_002661.3	825	Gag/Cag	23/33	0.219879472134757	3	FACETS	0.643	0.561	0.732	0.322	0.28	0.366	SUBCLONAL	1	TRUE	1	0.29	3		622	896	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404570	8404570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	129	468	0	ENST00000356435.5:c.4177G>A	p.Asp1393Asn	p.D1393N	ENST00000356435		1393	Gat/Aat	25/35	0.245984278225737	2	FACETS	0.762	0.693	0.833	0.762	0.693	0.833	SUBCLONAL	2	TRUE	0	0.29	2		468	584	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442077	52442077	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	108	536	0	ENST00000460680.1:c.272G>C	p.Cys91Ser	p.C91S	ENST00000460680	NM_004656.3	91	tGt/tCt	5/17	0.219879472134757	3	FACETS	0.963	0.863	1	0.481	0.431	0.534	CLONAL	1	TRUE	1	0.29	3		536	886	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097760	27097760	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	361	591	0	ENST00000324856.7:c.3349del	p.Ile1117SerfsTer44	p.I1117Sfs*44	ENST00000324856	NM_006015.4	1117	Atc/tc	12/20	0.287062416346204	3	FACETS	0.9	0.854	0.946	0.9	0.854	0.946	CLONAL	3	TRUE	0	0.29	3		591	1056	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858935	243858935	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	61	433	0	ENST00000263826.5:c.130G>C	p.Asp44His	p.D44H	ENST00000263826	NM_005465.4	44	Gat/Cat	2/13	0.219879472134757	3	FACETS	0.819	0.707	0.942	0.41	0.353	0.471	CLONAL	1	TRUE	1	0.29	3		433	588	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196068	67196096	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	GAGGGCGAGCCAGAGCTCAGCCCCGCGGT	GAGGGCGAGCCAGAGCTCAGCCCCGCGGT	-	novel	NA	P-0063439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	55	450	0	ENST00000312629.5:c.55_78+5del		p.X19_splice	ENST00000312629	NM_003952.2	19		1/15	0.259460341355341	2	FACETS	0.625	0.534	0.724	0.312	0.267	0.362	SUBCLONAL	1	TRUE	0	0.29	2		450	607	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425806	49425806	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	178	793	0	ENST00000301067.7:c.12682C>T	p.Gln4228Ter	p.Q4228*	ENST00000301067	NM_003482.3	4228	Cag/Tag	39/54	0.157580016077343	5	FACETS	0.807	0.743	0.874	0.538	0.495	0.583	INDETERMINATE	2	TRUE	2	0.29	5		793	1091	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647326	23647326	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs864622280	NA	P-0063439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	94	514	0	ENST00000261584.4:c.541G>C	p.Glu181Gln	p.E181Q	ENST00000261584	NM_024675.3	181	Gaa/Caa	4/13	1	2	FACETS	0.938	0.835	1	0.938	0.835	1	CLONAL	1	TRUE	1	0.29	2		514	691	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715946	52715946	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1404808367	NA	P-0063439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	80	649	0	ENST00000322088.6:c.511C>T	p.Arg171Trp	p.R171W	ENST00000322088	NM_014225.5	171	Cgg/Tgg	5/15	0.219879472134757	3	FACETS	0.671	0.589	0.759	0.335	0.294	0.38	SUBCLONAL	1	TRUE	1	0.29	3		649	942	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437690	52437690	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	201	706	0	ENST00000460680.1:c.1471G>T	p.Glu491Ter	p.E491*	ENST00000460680	NM_004656.3	491	Gag/Tag	13/17	0.219879472134757	3	FACETS	0.782	0.724	0.842	0.782	0.724	0.842	SUBCLONAL	2	TRUE	1	0.29	3		706	1015	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437861	52437861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	224	715	0	ENST00000460680.1:c.1300G>A	p.Asp434Asn	p.D434N	ENST00000460680	NM_004656.3	434	Gat/Aat	13/17	0.219879472134757	3	FACETS	0.915	0.852	0.979	0.915	0.852	0.979	CLONAL	2	TRUE	1	0.29	3		715	967	SUCCESS
REST	5978	MSKCC	GRCh37	4	57797074	57797074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	139	907	0	ENST00000309042.7:c.2050C>T	p.His684Tyr	p.H684Y	ENST00000309042	NM_005612.4	684	Cac/Tac	4/4	1	2	FACETS	0.769	0.698	0.844	0.769	0.698	0.844	SUBCLONAL	1	TRUE	1	0.29	2		907	1247	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157216	106157216	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	56	582	0	ENST00000380013.4:c.2117A>T	p.Gln706Leu	p.Q706L	ENST00000380013	NM_001127208.2	706	cAg/cTg	3/11	1	2	FACETS	0.453	0.387	0.525	0.453	0.387	0.525	SUBCLONAL	1	TRUE	1	0.29	2		582	853	SUCCESS
APC	324	MSKCC	GRCh37	5	112179132	112179132	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	59	563	0	ENST00000257430.4:c.7841A>G	p.Lys2614Arg	p.K2614R	ENST00000257430	NM_000038.5	2614	aAa/aGa	16/16	0.219879472134757	3	FACETS	0.669	0.575	0.772	0.335	0.287	0.386	SUBCLONAL	1	TRUE	1	0.29	3		563	696	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981359	68981359	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	76	355	0	ENST00000288368.4:c.1431C>A	p.Asp477Glu	p.D477E	ENST00000288368	NM_024870.2	477	gaC/gaA	12/40	0.191065343468075	4	FACETS	1	0.949	1	0.385	0.337	0.435	CLONAL	1	TRUE	1	0.29	4		355	586	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0063443-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	143	361	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.478114566531945	2	FACETS	0.908	0.83	0.99	0.454	0.415	0.495	CLONAL	1	TRUE	0	0.479204035286828	2		361	657	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183871	10183871	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs869025636	NA	P-0063443-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	156	453	0	ENST00000256474.2:c.340G>C	p.Gly114Arg	p.G114R	ENST00000256474	NM_000551.3	114	Ggt/Cgt	1/3	0.479204035286828	1	FACETS	0.998	0.921	1	0.998	0.921	1	CLONAL	1	TRUE	0	0.479204035286828	1		453	496	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0063444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	182	331	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.52949306060997	2		331	547	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653867	89653867	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0063444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	51	213	0	ENST00000371953.3:c.164+1G>A		p.X55_splice	ENST00000371953	NM_000314.4	55			0.274057738495458	1	FACETS	0.342	0.291	0.398	0.342	0.291	0.398	INDETERMINATE	1	TRUE	0	0.52949306060997	1		213	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578207	7578207	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	341	627	0	ENST00000269305.4:c.642del	p.His214GlnfsTer33	p.H214Qfs*33	ENST00000269305	NM_001126112.2	214	caT/ca	6/11	0.52949306060997	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.52949306060997	1		627	852	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295817	212295817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	161	384	0	ENST00000342788.4:c.2496G>A	p.Met832Ile	p.M832I	ENST00000342788	NM_005235.2	832	atG/atA	21/28	1	2	FACETS	0.949	0.873	1	0.949	0.873	1	CLONAL	1	TRUE	1	0.52949306060997	2		384	641	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0063445-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	391	683	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.745364655143577	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.745364655143577	1		683	589	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354163	15354163	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063445-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	247	388	1	ENST00000263377.2:c.2717C>G	p.Ala906Gly	p.A906G	ENST00000263377	NM_058243.2	906	gCc/gGc	14/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.745364655143577	2		389	581	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92404083	92404083	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063445-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	151	443	0	ENST00000265734.4:c.296A>G	p.Glu99Gly	p.E99G	ENST00000265734	NM_001259.6	99	gAa/gGa	3/8	1	2	FACETS	0.585	0.536	0.636	0.585	0.536	0.636	SUBCLONAL	1	TRUE	1	0.745364655143577	2		443	693	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0063446-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	124	547	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.378191260260472	4	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	2	0.378191260260472	4		548	440	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521481	8521481	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760428875	NA	P-0063446-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	120	592	0	ENST00000356435.5:c.757G>A	p.Val253Ile	p.V253I	ENST00000356435		253	Gtt/Att	9/35	0.371394215701348	2	FACETS	0.942	0.861	1	0.942	0.861	1	CLONAL	2	TRUE	0	0.378191260260472	2		592	337	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910349	29910349	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063446-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	40	1014	0	ENST00000376809.5:c.19C>T	p.Arg7Ter	p.R7*	ENST00000376809	NM_002116.7	7	Cga/Tga	1/8	0.378191260260472	3	FACETS	0.409	0.339	0.487	0.204	0.169	0.244	SUBCLONAL	1	TRUE	1	0.378191260260472	3		1014	615	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957488	175957488	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063446-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	136	487	0	ENST00000367669.3:c.1908C>G	p.Phe636Leu	p.F636L	ENST00000367669	NM_022457.5	636	ttC/ttG	17/20	0.365024881788724	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.378191260260472	3		487	392	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858313	27858313	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063446-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	81	873	0	ENST00000359303.2:c.258G>T	p.Gln86His	p.Q86H	ENST00000359303	NM_003535.2	86	caG/caT	1/1	0.378191260260472	3	FACETS	0.806	0.71	0.908	0.403	0.355	0.454	CLONAL	1	TRUE	1	0.378191260260472	3		873	632	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719196	190719196	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	TT	novel	NA	P-0063446-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	72	376	0	ENST00000441310.2:c.1198delinsTT	p.Gly400LeufsTer5	p.G400Lfs*5	ENST00000441310	NM_000534.4	400	Gga/TTga	9/13	0.365024881788724	3	FACETS	1	0.957	1	0.604	0.53	0.682	CLONAL	1	TRUE	1	0.378191260260472	3		376	375	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0063447-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	309	662	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.562818688239263	2		662	1040	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69143594	69143594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063447-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	78	335	0	ENST00000288368.4:c.4802C>T	p.Pro1601Leu	p.P1601L	ENST00000288368	NM_024870.2	1601	cCc/cTc	40/40	1	2	FACETS	0.853	0.756	0.955	0.853	0.756	0.955	CLONAL	1	FALSE	1	0.562818688239263	2		335	325	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443625	52443625	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0063447-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	216	604	0	ENST00000460680.1:c.68-1G>T		p.X23_splice	ENST00000460680	NM_004656.3	23			0.537898725675046	1	FACETS	0.788	0.736	0.842	0.788	0.736	0.842	SUBCLONAL	1	FALSE	0	0.562818688239263	1		604	700	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	188	523	0				ENST00000310581	NM_198253.2	-/1132			0.528932022264093	2	FACETS	0.751	0.708	0.794	0.751	0.708	0.794	SUBCLONAL	2	TRUE	0	0.749072642766802	2		523	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0063449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	198	558	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.429554349308986	3	FACETS	1	0.937	1	0.505	0.469	0.542	INDETERMINATE	1	TRUE	1	0.749072642766802	3		558	720	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0063449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	410	684	0	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.429554349308986	3	FACETS	0.965	0.925	1	0.965	0.925	1	INDETERMINATE	2	TRUE	1	0.749072642766802	3		684	780	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229229	123229229	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0063449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	108	190	0	ENST00000218089.9:c.3713C>G	p.Ser1238Ter	p.S1238*	ENST00000218089	NM_001042749.1	1238	tCa/tGa	34/35	1	1	FACETS	0.902	0.832	0.971	0.902	0.832	0.971	CLONAL	1	TRUE	0	0.749072642766802	1		190	200	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229561	5229561	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	76	576	0	ENST00000357368.4:c.2290G>C	p.Glu764Gln	p.E764Q	ENST00000357368	NM_002850.3	764	Gag/Cag	15/38	0.321085200003271	3	FACETS	0.641	0.565	0.723	0.321	0.282	0.362	INDETERMINATE	1	TRUE	1	0.749072642766802	3		576	435	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961363	41961363	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	148	521	0	ENST00000219905.7:c.271C>T	p.Arg91Ter	p.R91*	ENST00000219905	NM_001164273.1	91	Cga/Tga	2/24	0.546085257230201	3	FACETS	0.868	0.795	0.943	0.434	0.397	0.472	CLONAL	1	TRUE	1	0.749072642766802	3		521	626	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566491	139566491	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs557018245	NA	P-0063449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	28	618	0	ENST00000308874.7:c.750C>G	p.Ile250Met	p.I250M	ENST00000308874		250	atC/atG	9/10	0.495022336070999	2	FACETS	0.152	0.121	0.188	0.076	0.06	0.094	SUBCLONAL	1	TRUE	0	0.749072642766802	2		618	491	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120806003	120806003	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	170	652	0	ENST00000257552.2:c.174G>C	p.Lys58Asn	p.K58N	ENST00000257552	NM_002442.3	58	aaG/aaC	3/15	0.495022336070999	2	FACETS	0.74	0.684	0.799	0.37	0.342	0.4	SUBCLONAL	1	TRUE	0	0.749072642766802	2		652	613	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273152	115273152	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	130	510	0	ENST00000438362.2:c.1306G>T	p.Glu436Ter	p.E436*	ENST00000438362	NM_001242891.1	436	Gaa/Taa	11/20	0.60151657992608	4	FACETS	0.778	0.706	0.854	0.259	0.235	0.285	SUBCLONAL	1	TRUE	1	0.749072642766802	4		510	780	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117024	193117024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	110	326	0	ENST00000367435.3:c.757C>T	p.Leu253Phe	p.L253F	ENST00000367435	NM_024529.4	253	Ctt/Ttt	8/17	0.504047721353889	3	FACETS	0.834	0.753	0.919	0.417	0.376	0.46	CLONAL	1	TRUE	1	0.749072642766802	3		326	484	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231488800	231488800	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	112	493	0	ENST00000295050.7:c.1163C>T	p.Ser388Leu	p.S388L	ENST00000295050	NM_032018.5	388	tCa/tTa	5/5	0.504047721353889	3	FACETS	0.873	0.789	0.96	0.436	0.394	0.48	CLONAL	1	TRUE	1	0.749072642766802	3		493	471	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464400	464400	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	36	388	0	ENST00000399788.2:c.794G>C	p.Arg265Thr	p.R265T	ENST00000399788	NM_001042603.1	265	aGa/aCa	7/28	0.113626596902747	6	FACETS	0.522	0.429	0.626			1	INDETERMINATE	1	TRUE	NA	0.749072642766802	6		388	460	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041691	14041691	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1258424638	NA	P-0063449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	188	605	0	ENST00000311895.7:c.2238C>G	p.Ile746Met	p.I746M	ENST00000311895	NM_005236.2	746	atC/atG	11/11	0.356036295808985	3	FACETS	0.709	0.655	0.765	0.236	0.218	0.255	INDETERMINATE	1	TRUE	0	0.749072642766802	3		605	973	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86546612	86546612	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	198	616	0	ENST00000262426.4:c.1061C>G	p.Ser354Cys	p.S354C	ENST00000262426	NM_001451.2	354	tCt/tGt	2/2	0.718515048131787	2	FACETS	0.831	0.774	0.89	0.416	0.387	0.445	CLONAL	1	TRUE	0	0.749072642766802	2		616	636	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61308225	61308225	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1568164065	NA	P-0063449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	98	267	0	ENST00000341074.5:c.352G>A	p.Glu118Lys	p.E118K	ENST00000341074	NM_002974.2	118	Gaa/Aaa	5/8	0.504047721353889	3	FACETS	1	0.926	1	0.517	0.465	0.57	CLONAL	1	TRUE	1	0.749072642766802	3		267	348	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050400	13050400	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	118	523	0	ENST00000316448.5:c.352G>C	p.Asp118His	p.D118H	ENST00000316448	NM_004343.3	118	Gac/Cac	3/9	0.321085200003271	3	FACETS	0.518	0.467	0.572	0.259	0.233	0.286	INDETERMINATE	1	TRUE	1	0.749072642766802	3		523	836	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296171	15296171	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	210	732	0	ENST00000263388.2:c.2193G>C	p.Gln731His	p.Q731H	ENST00000263388	NM_000435.2	731	caG/caC	14/33	0.501621286882753	4	FACETS	0.957	0.888	1	0.478	0.444	0.514	CLONAL	1	TRUE	2	0.749072642766802	4		732	1025	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156732	106156732	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	177	569	1	ENST00000380013.4:c.1633G>C	p.Asp545His	p.D545H	ENST00000380013	NM_001127208.2	545	Gac/Cac	3/11	0.53363244974948	2	FACETS	0.69	0.638	0.744	0.345	0.319	0.372	SUBCLONAL	1	TRUE	0	0.749072642766802	2		570	685	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955554	90955554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	74	349	0	ENST00000265433.3:c.2111G>A	p.Gly704Glu	p.G704E	ENST00000265433	NM_002485.4	704	gGa/gAa	14/16	0.332250373812487	3	FACETS	0.734	0.646	0.827	0.367	0.323	0.414	INDETERMINATE	1	TRUE	1	0.749072642766802	3		349	370	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0063450-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	189	411	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.582022800761669	3	FACETS	0.911	0.854	0.969	0.911	0.854	0.969	CLONAL	2	FALSE	1	0.670501108053963	3		411	413	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216328	2216328	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063450-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	249	620	0	ENST00000398665.3:c.1972C>A	p.Gln658Lys	p.Q658K	ENST00000398665	NM_032482.2	658	Cag/Aag	20/28	0.670501108053963	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	FALSE	0	0.670501108053963	2		620	335	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574178	46574178	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs374587818	NA	P-0063450-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	76	514	0	ENST00000263734.3:c.193C>T	p.Arg65Ter	p.R65*	ENST00000263734	NM_001430.4	65	Cga/Tga	2/16	0.582022800761669	3	FACETS	0.67	0.589	0.755	0.335	0.294	0.378	SUBCLONAL	1	FALSE	1	0.670501108053963	3		514	452	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561887	55561887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	46	517	0	ENST00000288135.5:c.277G>A	p.Gly93Ser	p.G93S	ENST00000288135	NM_000222.2	93	Ggc/Agc	2/21	0.679576253295857	1	FACETS	0.202	0.17	0.237	0.202	0.17	0.237	SUBCLONAL	1	TRUE	0	0.679576253295857	1		517	443	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348319	89348319	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	235	713	0	ENST00000301030.4:c.4631A>G	p.Asp1544Gly	p.D1544G	ENST00000301030	NM_001256183.1	1544	gAc/gGc	9/13	0.679576253295857	1	FACETS	0.832	0.783	0.881	0.832	0.783	0.881	CLONAL	1	TRUE	0	0.679576253295857	1		713	549	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556068	29556075	+	frameshift_variant	Frame_Shift_Del	DEL	TTGTTAAG	TTGTTAAG	-	novel	NA	P-0063451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	143	387	0	ENST00000356175.3:c.2435_2442del	p.Ile812LysfsTer16	p.I812Kfs*16	ENST00000356175	NM_000267.3	812	aTTGTTAAG/a	21/57	0.679576253295857	1	FACETS	0.845	0.782	0.908	0.845	0.782	0.908	CLONAL	1	TRUE	0	0.679576253295857	1		387	329	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165518	47165519	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0063458-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	92	673	0	ENST00000409792.3:c.607_608del	p.Ser203IlefsTer33	p.S203Ifs*33	ENST00000409792	NM_014159.6	203	TCa/a	3/21	0.293194483687906	1	FACETS	0.594	0.527	0.666	0.594	0.527	0.666	SUBCLONAL	1	TRUE	0	0.293194483687906	1		673	902	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651528	52651529	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063458-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	57	430	0	ENST00000394830.3:c.1567dup	p.Met523AsnfsTer10	p.M523Nfs*10	ENST00000394830	NM_018313.4	523	atg/aAtg	15/30	0.293194483687906	1	FACETS	0.77	0.662	0.887	0.77	0.662	0.887	SUBCLONAL	1	TRUE	0	0.293194483687906	1		430	431	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045855	26045855	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063458-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1218	183	780	0	ENST00000540144.1:c.217C>G	p.Arg73Gly	p.R73G	ENST00000540144	NM_003531.2	73	Cga/Gga	1/1	1	2	FACETS	0.891	0.82	0.965	0.891	0.82	0.965	CLONAL	1	TRUE	1	0.293194483687906	2		780	1401	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0063461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	288	466	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	1	2	FACETS	0.933	0.885	0.982	0.933	0.885	0.982	CLONAL	1	TRUE	1	0.960136480176868	2		466	643	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101102	27101105	+	frameshift_variant	Frame_Shift_Del	DEL	GACC	GACC	-	novel	NA	P-0063461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	391	550	0	ENST00000324856.7:c.4385_4388del	p.Asp1462ValfsTer18	p.D1462Vfs*18	ENST00000324856	NM_006015.4	1462	GACCgt/gt	18/20	1	2	FACETS	0.997	0.954	1	0.997	0.954	1	CLONAL	1	TRUE	1	0.960136480176868	2		550	817	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0063462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	56	429	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	1	2	FACETS	0.547	0.468	0.633	0.547	0.468	0.633	SUBCLONAL	1	TRUE	1	0.341980353844371	2		429	599	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190656538	190656538	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0063462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	49	167	0	ENST00000441310.2:c.3G>A	p.Met1?	p.M1?	ENST00000441310	NM_000534.4	1	atG/atA	2/13	1	2	FACETS	0.668	0.567	0.779	0.668	0.567	0.779	SUBCLONAL	1	TRUE	1	0.341980353844371	2		167	429	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792245	33792245	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0063462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	18	245	0	ENST00000498907.2:c.1076G>C	p.Ter359SerextTer36	p.*359Sext*36	ENST00000498907	NM_004364.3	359	tGa/tCa	1/1	1	2	FACETS	0.332	0.25	0.43	0.332	0.25	0.43	SUBCLONAL	1	TRUE	1	0.341980353844371	2		245	317	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763871	76763871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	35	179	0	ENST00000373344.5:c.7437G>A	p.Met2479Ile	p.M2479I	ENST00000373344	NM_000489.3	2479	atG/atA	35/35	0.15315172763546	2	FACETS	0.747	0.615	0.894			1	INDETERMINATE	1	TRUE	NA	0.341980353844371	2		179	274	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471634	120471634	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs782319914	NA	P-0063462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	50	346	0	ENST00000256646.2:c.3857A>G	p.Asn1286Ser	p.N1286S	ENST00000256646	NM_024408.3	1286	aAt/aGt	23/34	1	2	FACETS	0.623	0.529	0.727	0.623	0.529	0.727	SUBCLONAL	1	TRUE	1	0.341980353844371	2		346	469	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098882	178098882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	52	228	0	ENST00000397062.3:c.163G>A	p.Glu55Lys	p.E55K	ENST00000397062	NM_006164.4	55	Gaa/Aaa	2/5	1	2	FACETS	0.618	0.527	0.718	0.618	0.527	0.718	SUBCLONAL	1	TRUE	1	0.341980353844371	2		228	492	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629057	14629057	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	26	341	0	ENST00000254322.2:c.105G>C	p.Lys35Asn	p.K35N	ENST00000254322	NM_006145.1	35	aaG/aaC	1/3	1	2	FACETS	0.457	0.362	0.565	0.457	0.362	0.565	SUBCLONAL	1	TRUE	1	0.341980353844371	2		341	333	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431792	49431808	+	frameshift_variant	Frame_Shift_Del	DEL	GGGAGCACAGATGCCAG	GGGAGCACAGATGCCAG	-	novel	NA	P-0063462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	62	447	0	ENST00000301067.7:c.9331_9347del	p.Leu3111Ter	p.L3111*	ENST00000301067	NM_003482.3	3111	CTGGCATCTGTGCTCCCt/t	34/54	1	2	FACETS	0.742	0.642	0.85	0.742	0.642	0.85	SUBCLONAL	1	TRUE	1	0.341980353844371	2		447	489	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657369	29657369	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	41	224	0	ENST00000356175.3:c.5602G>T	p.Glu1868Ter	p.E1868*	ENST00000356175	NM_000267.3	1868	Gag/Tag	38/57	1	2	FACETS	0.485	0.404	0.576	0.485	0.404	0.576	SUBCLONAL	1	TRUE	1	0.341980353844371	2		224	494	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58711330	58711330	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	28	184	0	ENST00000305921.3:c.818G>C	p.Arg273Thr	p.R273T	ENST00000305921	NM_003620.3	273	aGa/aCa	3/6	1	2	FACETS	0.389	0.31	0.479	0.389	0.31	0.479	SUBCLONAL	1	TRUE	1	0.341980353844371	2		184	421	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098975	178099189	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAGTATGTCAATCAAATCCATGTCCTATGTTTAAGACAAAAAAAGGAAGGAGAGAGCTCATGTTTTTTAAATGACAGATACCACATAAATTAATTCACATTATGCCACTGTTGATGGTGGGAAGTGGGGAGATTACAAATACAATCTAAATGAGAACACAGATCCAATGTTCTAGAAGAGCACAGTTAATTCCATTCAATGAATCTATTCATTA	AAAGTATGTCAATCAAATCCATGTCCTATGTTTAAGACAAAAAAAGGAAGGAGAGAGCTCATGTTTTTTAAATGACAGATACCACATAAATTAATTCACATTATGCCACTGTTGATGGTGGGAAGTGGGGAGATTACAAATACAATCTAAATGAGAACACAGATCCAATGTTCTAGAAGAGCACAGTTAATTCCATTCAATGAATCTATTCATTA	-	novel	NA	P-0063462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	28	183	0	ENST00000397062.3:c.46-190_70del		p.X16_splice	ENST00000397062	NM_006164.4	16		2/5	1	2	FACETS	0.351	0.28	0.432	0.351	0.28	0.432	SUBCLONAL	1	TRUE	1	0.341980353844371	2		183	467	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86676352	86676357	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	TACAGA	TACAGA	-	novel	NA	P-0063462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	37	167	0	ENST00000274376.6:c.2630_2635del	p.Leu877_Lys879delinsTer	p.L877_K879delins*	ENST00000274376	NM_002890.2	877	tTACAGAaa/taa	20/25	1	2	FACETS	0.459	0.378	0.55	0.459	0.378	0.55	SUBCLONAL	1	TRUE	1	0.341980353844371	2		167	471	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651663	48651663	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	37	192	0	ENST00000376670.3:c.829C>A	p.Pro277Thr	p.P277T	ENST00000376670	NM_002049.3	277	Ccc/Acc	5/6	0.15315172763546	2	FACETS	0.703	0.581	0.837			1	INDETERMINATE	1	TRUE	NA	0.341980353844371	2		192	308	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0063463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	678	521	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.60823266476247	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.60823266476247	3		521	916	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0063463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	181	400	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.60823266476247	2		400	535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578260	7578260	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786204041	NA	P-0063463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	62	579	0	ENST00000269305.4:c.589G>T	p.Val197Leu	p.V197L	ENST00000269305	NM_001126112.2	197	Gtg/Ttg	6/11	0.60823266476247	1	FACETS	0.264	0.228	0.303	0.264	0.228	0.303	SUBCLONAL	1	TRUE	0	0.60823266476247	1		579	538	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0063463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	578	466	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.60823266476247	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.60823266476247	3		466	769	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0063463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	413	453	1	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.946	0.909	0.982	1	0.997	1	CLONAL	2	TRUE	1	0.60823266476247	2		454	718	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	57	424	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	1	2	FACETS	0.287	0.246	0.332	0.287	0.246	0.332	SUBCLONAL	1	TRUE	1	0.60823266476247	2		424	653	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636818	8636818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146973770	NA	P-0063463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	40	369	0	ENST00000356435.5:c.91G>A	p.Val31Ile	p.V31I	ENST00000356435		31	Gtt/Att	2/35	1	2	FACETS	0.188	0.156	0.225	0.188	0.156	0.225	SUBCLONAL	1	TRUE	1	0.60823266476247	2		369	699	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256696	46256696	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768977330	NA	P-0063463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	55	315	0	ENST00000371998.3:c.752G>A	p.Arg251His	p.R251H	ENST00000371998		251	cGc/cAc	8/23	0.460341173311005	3	FACETS	0.388	0.331	0.45	0.194	0.165	0.225	SUBCLONAL	1	TRUE	1	0.60823266476247	3		315	608	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610695	52610695	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	169	390	0	ENST00000394830.3:c.3478C>T	p.Arg1160Ter	p.R1160*	ENST00000394830	NM_018313.4	1160	Cga/Tga	23/30	0.60823266476247	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.60823266476247	1		390	368	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165282	47165283	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	94	411	1	ENST00000409792.3:c.843dup	p.Glu282ArgfsTer9	p.E282Rfs*9	ENST00000409792	NM_014159.6	281	-/A	3/21	0.60823266476247	1	FACETS	0.552	0.494	0.612	0.552	0.494	0.612	SUBCLONAL	1	TRUE	0	0.60823266476247	1		412	390	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593397	48593397	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs377767355	NA	P-0063463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	26	414	0	ENST00000342988.3:c.1148T>A	p.Ile383Lys	p.I383K	ENST00000342988	NM_005359.5	383	aTa/aAa	10/12	0.259444240307499	1	FACETS	0.115	0.091	0.143	0.115	0.091	0.143	INDETERMINATE	1	TRUE	0	0.60823266476247	1		414	517	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992729	68992729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779079528	NA	P-0063463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	29	305	1	ENST00000288368.4:c.1694C>T	p.Ser565Leu	p.S565L	ENST00000288368	NM_024870.2	565	tCg/tTg	16/40	1	2	FACETS	0.215	0.172	0.264	0.215	0.172	0.264	SUBCLONAL	1	TRUE	1	0.60823266476247	2		306	444	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784121	9784121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	140	500	0	ENST00000377346.4:c.2689G>A	p.Asp897Asn	p.D897N	ENST00000377346	NM_005026.3	897	Gac/Aac	21/24	1	2	FACETS	0.809	0.74	0.881	0.809	0.74	0.881	CLONAL	1	TRUE	1	0.60823266476247	2		500	569	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608463	28608463	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	46	376	0	ENST00000241453.7:c.1679T>A	p.Leu560Gln	p.L560Q	ENST00000241453	NM_004119.2	560	cTg/cAg	13/24	1	2	FACETS	0.266	0.223	0.313	0.266	0.223	0.313	SUBCLONAL	1	TRUE	1	0.60823266476247	2		376	569	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446869	187446869	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	193	443	0	ENST00000232014.4:c.1324C>T	p.Gln442Ter	p.Q442*	ENST00000232014	NM_001130845.1	442	Caa/Taa	5/10	1	2	FACETS	0.89	0.826	0.956	0.89	0.826	0.956	CLONAL	1	TRUE	1	0.60823266476247	2		443	713	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818381	170818381	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	81	145	0	ENST00000296930.5:c.211C>T	p.Pro71Ser	p.P71S	ENST00000296930	NM_002520.6	71	Cca/Tca	3/11	1	2	FACETS	0.962	0.858	1	0.962	0.858	1	CLONAL	1	TRUE	1	0.60823266476247	2		145	277	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151181843	151181843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	33	281	0	ENST00000262187.5:c.172C>T	p.Leu58Phe	p.L58F	ENST00000262187	NM_005614.3	58	Ctt/Ttt	3/8	1	2	FACETS	0.186	0.151	0.226	0.186	0.151	0.226	SUBCLONAL	1	TRUE	1	0.60823266476247	2		281	584	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0063464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	72	213	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.189305447207355	2	FACETS	1	0.927	1	0.529	0.47	0.591	INDETERMINATE	1	TRUE	0	0.627093113361355	2		213	217	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0063464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	116	409	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	1	2	FACETS	0.847	0.768	0.928	0.847	0.768	0.928	CLONAL	1	TRUE	1	0.627093113361355	2		409	437	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998409	100998409	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	95	420	0	ENST00000325455.5:c.1393G>C	p.Ala465Pro	p.A465P	ENST00000325455	NM_001202474.3	465	Gcg/Ccg	1/8	1	2	FACETS	0.856	0.769	0.947	0.856	0.769	0.947	CLONAL	1	TRUE	1	0.627093113361355	2		420	354	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998427	100998427	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs767827820	NA	P-0063464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	112	437	0	ENST00000325455.5:c.1375G>C	p.Glu459Gln	p.E459Q	ENST00000325455	NM_001202474.3	459	Gag/Cag	1/8	1	2	FACETS	0.871	0.79	0.956	0.871	0.79	0.956	CLONAL	1	TRUE	1	0.627093113361355	2		437	410	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120066	70120066	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	101	480	0	ENST00000245479.2:c.1068del	p.Gln357ArgfsTer26	p.Q357Rfs*26	ENST00000245479	NM_000346.3	356	ccG/cc	3/3	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.627093113361355	2		480	322	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0063465-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	163	362	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.416681531997538	5	FACETS	1	0.982	1	0.796	0.736	0.857	CLONAL	2	TRUE	2	0.478652748110413	5		362	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0063465-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	233	514	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.458987457072689	2	FACETS	0.882	0.83	0.934	0.882	0.83	0.934	CLONAL	2	TRUE	0	0.478652748110413	2		514	552	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1036350	1036350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063465-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	93	419	1	ENST00000358495.3:c.428G>A	p.Arg143Lys	p.R143K	ENST00000358495	NM_134424.2	143	aGg/aAg	6/12	0.44522890926043	3	FACETS	0.832	0.741	0.928	0.416	0.37	0.464	CLONAL	1	TRUE	1	0.478652748110413	3		420	579	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736234	243736234	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063465-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	116	356	0	ENST00000263826.5:c.813T>A	p.Asp271Glu	p.D271E	ENST00000263826	NM_005465.4	271	gaT/gaA	8/13	0.44522890926043	3	FACETS	1	0.95	1	0.539	0.488	0.593	CLONAL	1	TRUE	1	0.478652748110413	3		356	557	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610164	10610164	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063465-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	119	513	0	ENST00000171111.5:c.546C>G	p.Ser182Arg	p.S182R	ENST00000171111	NM_203500.1	182	agC/agG	2/6	0.431956156701544	3	FACETS	0.929	0.84	1	0.465	0.42	0.512	CLONAL	1	TRUE	1	0.478652748110413	3		513	663	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231088	53231088	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063465-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	118	259	0	ENST00000375401.3:c.1814T>C	p.Phe605Ser	p.F605S	ENST00000375401	NM_004187.3	605	tTc/tCc	13/26	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.478652748110413	1		259	263	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0063477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	134	210	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.755694817918606	6	FACETS	1	0.952	1	0.422	0.387	0.459	CLONAL	2	TRUE	1	0.755694817918606	6		210	422	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0063477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	120	187	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.755694817918606	6	FACETS	0.894	0.813	0.978	0.358	0.325	0.392	CLONAL	2	TRUE	1	0.755694817918606	6		187	446	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160227	22160227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	190	504	0	ENST00000215832.6:c.404G>A	p.Arg135Lys	p.R135K	ENST00000215832	NM_002745.4	135	aGa/aAa	3/9	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.755694817918606	2		504	477	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513352	41513352	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	227	575	0	ENST00000263253.7:c.256C>T	p.Arg86Ter	p.R86*	ENST00000263253	NM_001429.3	86	Cga/Tga	2/31	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.755694817918606	2		575	554	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226388	2226388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs112052747	NA	P-0063477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	221	749	0	ENST00000398665.3:c.3868G>A	p.Ala1290Thr	p.A1290T	ENST00000398665	NM_032482.2	1290	Gct/Act	27/28	0.755694817918606	3	FACETS	0.996	0.929	1	0.498	0.464	0.533	CLONAL	1	TRUE	1	0.755694817918606	3		749	809	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356243	70356243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374390933	NA	P-0063477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	181	596	0	ENST00000374080.3:c.5138G>A	p.Arg1713Gln	p.R1713Q	ENST00000374080		1713	cGa/cAa	37/45	0.635077965036784	5	FACETS	1	0.958	1	0.352	0.325	0.381	CLONAL	1	TRUE	2	0.755694817918606	5		596	967	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438128	438128	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	171	527	0	ENST00000399788.2:c.1841A>G	p.Glu614Gly	p.E614G	ENST00000399788	NM_001042603.1	614	gAg/gGg	14/28	0.755694817918606	3	FACETS	0.896	0.827	0.968	0.448	0.413	0.484	CLONAL	1	TRUE	1	0.755694817918606	3		527	696	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	rs886039483	NA	P-0063478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	858	577	1	ENST00000269305.4:c.376T>A	p.Tyr126Asn	p.Y126N	ENST00000269305	NM_001126112.2	126	Tac/Aac	5/11	0.87565378358707	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.87565378358707	3		578	938	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226098	2226098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	120	671	2	ENST00000326181.6:c.1795G>A	p.Val599Met	p.V599M	ENST00000326181	NM_032271.2	599	Gtg/Atg	19/21	0.449218164636763	1	FACETS	0.344	0.312	0.377	0.344	0.312	0.377	INDETERMINATE	1	TRUE	0	0.87565378358707	1		673	448	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030465	49030501	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTCACTGTTTTATAAAAAAGGTTAGTAGATGATTAT	TTTCACTGTTTTATAAAAAAGGTTAGTAGATGATTAT	-	novel	NA	P-0063478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	211	395	0	ENST00000267163.4:c.1945_1960+21del		p.X649_splice	ENST00000267163	NM_000321.2	649		19/27	0.87565378358707	1	FACETS	0.928	0.887	0.967	0.928	0.887	0.967	CLONAL	1	TRUE	0	0.87565378358707	1		395	292	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465632	99465632	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	412	583	0	ENST00000268035.6:c.2457C>G	p.Asn819Lys	p.N819K	ENST00000268035	NM_000875.3	819	aaC/aaG	11/21	0.183818110283937	4	FACETS	1	0.994	1	1	0.994	1	INDETERMINATE	2	TRUE	2	0.87565378358707	4		583	743	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197840	123197840	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	72	354	0	ENST00000218089.9:c.1964G>T	p.Ser655Ile	p.S655I	ENST00000218089	NM_001042749.1	655	aGt/aTt	20/35	0.87565378358707	1	FACETS	0.797	0.727	0.864	0.797	0.727	0.864	SUBCLONAL	1	TRUE	0	0.87565378358707	1		354	116	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0063479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	87	540	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	1	2	FACETS	0.91	0.808	1	0.91	0.808	1	CLONAL	1	TRUE	1	0.352131055459094	2		540	543	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0063480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	177	331	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.925	0.861	0.99	0.925	0.861	0.99	CLONAL	1	TRUE	1	0.837216197803272	2		331	457	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0063480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	327	664	1	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.837216197803272	1	FACETS	0.973	0.937	1	0.973	0.937	1	CLONAL	1	TRUE	0	0.837216197803272	1		665	467	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247810	59247810	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	381	692	2	ENST00000371222.2:c.933del	p.Val312SerfsTer2	p.V312Sfs*2	ENST00000371222	NM_002228.3	311	aaA/aa	1/1	0.837216197803272	1	FACETS	0.998	0.965	1	0.998	0.965	1	CLONAL	1	TRUE	0	0.837216197803272	1		694	530	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63553989	63553990	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0063480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	324	666	1	ENST00000307078.5:c.748_749dup	p.Leu250PhefsTer7	p.L250Ffs*7	ENST00000307078	NM_004655.3	250	ttg/ttTTg	2/11	1	2	FACETS	0.888	0.841	0.934	0.888	0.841	0.934	CLONAL	1	TRUE	1	0.837216197803272	2		667	872	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916925	178916927	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0063480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	422	283	4	ENST00000263967.3:c.314_316del	p.Val105del	p.V105del	ENST00000263967	NM_006218.2	104	ccAGTa/cca	2/21	0.837216197803272	2	FACETS	0.984	0.96	1	0.984	0.96	1	CLONAL	2	TRUE	0	0.837216197803272	2		287	512	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627176	86627177	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0063480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	255	492	1	ENST00000274376.6:c.555dup	p.Leu186ThrfsTer2	p.L186Tfs*2	ENST00000274376	NM_002890.2	184	gga/ggAa	2/25	0.837216197803272	1	FACETS	0.989	0.949	1	0.989	0.949	1	CLONAL	1	TRUE	0	0.837216197803272	1		493	358	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0063481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	477	850	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.873825766583649	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.873825766583649	2		852	522	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899079	40899079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs951719751	NA	P-0063481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	283	413	0	ENST00000373198.4:c.2191G>A	p.Ala731Thr	p.A731T	ENST00000373198	NM_133170.3	731	Gcc/Acc	14/32	0.435027840346342	4	FACETS	1	0.988	1	1	0.988	1	INDETERMINATE	2	TRUE	2	0.873825766583649	4		413	539	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602335	10602335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	245	837	0	ENST00000171111.5:c.1243C>T	p.Arg415Cys	p.R415C	ENST00000171111	NM_203500.1	415	Cgc/Tgc	3/6	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.873825766583649	NA		837	551	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103717	47103717	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1205330893	NA	P-0063481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	88	633	0	ENST00000409792.3:c.6229C>T	p.Arg2077Ter	p.R2077*	ENST00000409792	NM_014159.6	2077	Cga/Tga	14/21	0.873825766583649	3	FACETS	0.345	0.305	0.388	0.172	0.152	0.194	SUBCLONAL	1	TRUE	1	0.873825766583649	3		633	839	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085842	16085842	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	128	640	0	ENST00000281043.3:c.1018G>T	p.Glu340Ter	p.E340*	ENST00000281043	NM_005378.4	340	Gag/Tag	3/3	0.456395949977073	3	FACETS	0.785	0.715	0.859	0.262	0.238	0.287	INDETERMINATE	1	TRUE	0	0.873825766583649	3		640	536	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61720187	61720389	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCTATACTCAACAATATATCAATCAAGAAAAAAATCGTTAGATCACTGAAATCATTAGTGTAGAAGCTTAGTTAAAAACAAACAAAACCAAAAAAACCACAAGCCAGCCATGTGTAGGGATTCATGCCTATAATTCCAACTATTCCGGAGGGCCGAGGCAAAAAGAACTGTTGTGGCCAGGAATTTGAGAGCAGCTTGAGCA	ACCTATACTCAACAATATATCAATCAAGAAAAAAATCGTTAGATCACTGAAATCATTAGTGTAGAAGCTTAGTTAAAAACAAACAAAACCAAAAAAACCACAAGCCAGCCATGTGTAGGGATTCATGCCTATAATTCCAACTATTCCGGAGGGCCGAGGCAAAAAGAACTGTTGTGGCCAGGAATTTGAGAGCAGCTTGAGCA	-	novel	NA	P-0063481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	49	370	0	ENST00000401558.2:c.1246-201_1247del		p.X416_splice	ENST00000401558	NM_003400.3	416		13/25	0.456395949977073	3	FACETS	0.473	0.402	0.55	0.158	0.134	0.184	INDETERMINATE	1	TRUE	0	0.873825766583649	3		370	341	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158215	47158262	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTAATATCTCGATGAGATTTATTCTTCTTTCTATTGGGTAAAATTTCA	TTAATATCTCGATGAGATTTATTCTTCTTTCTATTGGGTAAAATTTCA	-	novel	NA	P-0063481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	61	265	0	ENST00000409792.3:c.4455-18_4484del		p.X1485_splice	ENST00000409792	NM_014159.6	1485		4/21	0.873825766583649	3	FACETS	0.685	0.595	0.78	0.342	0.297	0.39	SUBCLONAL	1	TRUE	1	0.873825766583649	3		265	293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0063482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	60	721	0	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	FALSE	1	0.178090524588551	2		721	638	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050682	30050682	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	24	497	0	ENST00000338641.4:c.488del	p.Leu163TrpfsTer11	p.L163Wfs*11	ENST00000338641	NM_000268.3	162	Ttt/tt	5/16	1	2	FACETS	0.62	0.485	0.776	0.62	0.485	0.776	SUBCLONAL	1	FALSE	1	0.178090524588551	2		497	435	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016570	12016570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	16	422	0	ENST00000353533.5:c.706C>T	p.Leu236Phe	p.L236F	ENST00000353533	NM_003010.3	236	Ctt/Ttt	7/11	1	2	FACETS	0.665	0.492	0.873	0.665	0.492	0.873	SUBCLONAL	1	FALSE	1	0.178090524588551	2		422	270	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0063483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	94	619	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.546682028932885	1	FACETS	0.962	0.87	1	0.962	0.87	1	CLONAL	1	TRUE	0	0.550774932055974	1		619	257	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101099	41101099	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	40	579	0	ENST00000373198.4:c.1257C>A	p.Ser419Arg	p.S419R	ENST00000373198	NM_133170.3	419	agC/agA	8/32	0.550774932055974	6	FACETS	0.465	0.385	0.554	0.155	0.128	0.185	SUBCLONAL	1	TRUE	3	0.550774932055974	6		579	657	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020718	26020718	+	start_lost	Translation_Start_Site	SNP	A	A	T	rs148106225	NA	P-0063483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	87	534	0	ENST00000357647.3:c.1A>T	p.Met1?	p.M1?	ENST00000357647	NM_003529.2	1	Atg/Ttg	1/1	0.550774932055974	3	FACETS	1	0.947	1	0.367	0.327	0.409	CLONAL	1	TRUE	0	0.550774932055974	3		534	366	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0063484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	414	454	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.628738384955192	3	FACETS	0.965	0.933	0.996	0.965	0.933	0.996	CLONAL	3	TRUE	0	0.628738384955192	3		454	598	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186501404	186501404	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764605841	NA	P-0063484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	130	417	0	ENST00000323963.5:c.5C>G	p.Ser2Cys	p.S2C	ENST00000323963		2	tCt/tGt	1/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.628738384955192	2		417	369	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247830	59247836	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGTTC	CCTGTTC	-	novel	NA	P-0063484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	160	677	0	ENST00000371222.2:c.907_913del	p.Glu303TrpfsTer9	p.E303Wfs*9	ENST00000371222	NM_002228.3	303	GAACAGGtg/tg	1/1	0.60493776904136	4	FACETS	0.807	0.739	0.878			1	CLONAL	1	TRUE	NA	0.628738384955192	4		677	1027	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983188	149983200	+	frameshift_variant	Frame_Shift_Del	DEL	CAGACTGCTGTCT	CAGACTGCTGTCT	-	novel	NA	P-0063484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	117	536	0	ENST00000253339.5:c.3058_3070del	p.Arg1020LeufsTer34	p.R1020Lfs*34	ENST00000253339		1020	AGACAGCAGTCTGct/ct	7/7	1	2	FACETS	0.914	0.832	1	0.914	0.832	1	CLONAL	1	TRUE	1	0.628738384955192	2		536	407	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412899	63412899	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs781369600	NA	P-0063484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	156	687	2	ENST00000330258.3:c.268C>A	p.Leu90Ile	p.L90I	ENST00000330258	NM_152424.3	90	Ctc/Atc	2/2	0.628738384955192	1	FACETS	0.983	0.914	1	0.983	0.914	1	CLONAL	1	TRUE	0	0.628738384955192	1		689	346	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315472	30315472	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	79	427	0	ENST00000322652.5:c.1157A>G	p.His386Arg	p.H386R	ENST00000322652	NM_015355.2	386	cAt/cGt	10/16	1	2	FACETS	0.886	0.787	0.99	0.886	0.787	0.99	CLONAL	1	TRUE	1	0.59435983055412	2		427	300	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405246	139405246	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	115	547	0	ENST00000277541.6:c.2599G>T	p.Glu867Ter	p.E867*	ENST00000277541	NM_017617.3	867	Gag/Tag	17/34	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.59435983055412	2		547	321	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159101	24159101	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0063485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	88	550	0	ENST00000263121.7:c.773C>G	p.Ser258Ter	p.S258*	ENST00000263121	NM_003073.3	258	tCa/tGa	6/9	0.59435983055412	1	FACETS	0.864	0.778	0.952	0.864	0.778	0.952	CLONAL	1	TRUE	0	0.59435983055412	1		550	241	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228032	53228032	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	81	687	0	ENST00000375401.3:c.2282del	p.His761LeufsTer3	p.H761Lfs*3	ENST00000375401	NM_004187.3	761	cAt/ct	16/26	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.59435983055412	2		687	269	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0063486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	63	681	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.733	0.634	0.841	0.733	0.634	0.841	SUBCLONAL	1	TRUE	1	0.26	2		682	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578277	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs1555525902	NA	P-0063486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	25	855	0	ENST00000269305.4:c.572_574del	p.Pro191del	p.P191del	ENST00000269305	NM_001126112.2	191	cCTCag/cag	6/11	1	2	FACETS	0.263	0.206	0.329	0.263	0.206	0.329	SUBCLONAL	1	TRUE	1	0.26	2		855	731	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041563	47041563	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0063486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	86	383	0	ENST00000377604.3:c.1788T>G	p.Tyr596Ter	p.Y596*	ENST00000377604	NM_001204468.1	596	taT/taG	17/24	0.172174867142774	2	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.26	2		383	442	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238941	5238941	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs913402227	NA	P-0063486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	56	762	0	ENST00000357368.4:c.1838C>T	p.Thr613Met	p.T613M	ENST00000357368	NM_002850.3	613	aCg/aTg	13/38	1	2	FACETS	0.593	0.507	0.687	0.593	0.507	0.687	SUBCLONAL	1	TRUE	1	0.26	2		762	727	SUCCESS
APC	324	MSKCC	GRCh37	5	112173600	112173600	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060503310	NA	P-0063486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	35	500	0	ENST00000257430.4:c.2309C>G	p.Ser770Ter	p.S770*	ENST00000257430	NM_000038.5	770	tCa/tGa	16/16	1	2	FACETS	0.968	0.797	1	0.968	0.797	1	CLONAL	1	TRUE	1	0.26	2		500	278	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2097740	2097740	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1161055704	NA	P-0063486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	40	699	0	ENST00000219066.1:c.109G>A	p.Gly37Arg	p.G37R	ENST00000219066	NM_002528.5	37	Ggg/Agg	1/6	1	2	FACETS	0.476	0.394	0.567	0.476	0.394	0.567	SUBCLONAL	1	TRUE	1	0.26	2		699	647	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220651	2220651	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1226377975	NA	P-0063486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	41	774	0	ENST00000326181.6:c.268A>T	p.Ile90Phe	p.I90F	ENST00000326181	NM_032271.2	90	Atc/Ttc	5/21	1	2	FACETS	0.4	0.332	0.476	0.4	0.332	0.476	SUBCLONAL	1	TRUE	1	0.26	2		774	789	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0063487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	147	372	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.547966827792446	2		372	455	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	118	523	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.764	0.691	0.839	0.764	0.691	0.839	SUBCLONAL	1	TRUE	1	0.547966827792446	2		523	564	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979257	93979257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	149	439	0	ENST00000369303.4:c.1571G>A	p.Gly524Glu	p.G524E	ENST00000369303	NM_004440.3	524	gGa/gAa	7/17	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.547966827792446	2		439	544	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120269	94120269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	200	539	0	ENST00000369303.4:c.782G>A	p.Gly261Glu	p.G261E	ENST00000369303	NM_004440.3	261	gGa/gAa	3/17	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.547966827792446	2		539	716	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276662	115276662	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	165	448	0	ENST00000438362.2:c.797T>C	p.Leu266Ser	p.L266S	ENST00000438362	NM_001242891.1	266	tTa/tCa	8/20	0.547966827792446	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.547966827792446	1		448	407	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70442705	70442705	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	167	402	0	ENST00000373644.4:c.5027A>T	p.His1676Leu	p.H1676L	ENST00000373644	NM_030625.2	1676	cAc/cTc	10/12	0.547966827792446	1	FACETS	0.992	0.921	1	0.992	0.921	1	CLONAL	1	TRUE	0	0.547966827792446	1		402	446	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908230	28908230	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	93	427	0	ENST00000282397.4:c.2525T>C	p.Val842Ala	p.V842A	ENST00000282397	NM_002019.4	842	gTt/gCt	18/30	0.347213823874456	1	FACETS	0.445	0.396	0.496	0.445	0.396	0.496	SUBCLONAL	1	TRUE	0	0.547966827792446	1		427	554	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437858	52437858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	191	554	0	ENST00000460680.1:c.1303G>A	p.Gly435Arg	p.G435R	ENST00000460680	NM_004656.3	435	Ggg/Agg	13/17	0.547966827792446	1	FACETS	0.919	0.856	0.983	0.919	0.856	0.983	CLONAL	1	TRUE	0	0.547966827792446	1		554	551	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597435	52597450	+	frameshift_variant	Frame_Shift_Del	DEL	GCAAATTTAGCTTCTA	GCAAATTTAGCTTCTA	-	novel	NA	P-0063487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	156	465	0	ENST00000394830.3:c.3860_3875del	p.Leu1287ProfsTer3	p.L1287Pfs*3	ENST00000394830	NM_018313.4	1287	cTAGAAGCTAAATTTGCc/cc	25/30	0.547966827792446	1	FACETS	0.97	0.898	1	0.97	0.898	1	CLONAL	1	TRUE	0	0.547966827792446	1		465	426	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	17	583	2	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	0.449	0.335	0.585	0.449	0.335	0.585	SUBCLONAL	1	TRUE	1	0.26	2		585	291	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124503600	124503600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1385542313	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	13	497	0	ENST00000357628.3:c.350G>A	p.Arg117His	p.R117H	ENST00000357628	NM_015450.2	117	cGc/cAc	8/19	1	2	FACETS	0.397	0.283	0.536	0.397	0.283	0.536	SUBCLONAL	1	TRUE	1	0.26	2		497	252	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs1057519842	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	31	449	0	ENST00000274335.5:c.1727_1729del	p.Thr576del	p.T576del	ENST00000274335		575	aaGACg/aag	12/15	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.26	2		449	206	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975746	26975746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	35	518	0	ENST00000381527.3:c.1254G>A	p.Met418Ile	p.M418I	ENST00000381527	NM_001260.1	418	atG/atA	12/13	1	2	FACETS	0.955	0.786	1	0.955	0.786	1	CLONAL	1	TRUE	1	0.26	2		518	282	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	54	804	1	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	0.832	0.712	0.964	0.832	0.712	0.964	CLONAL	1	TRUE	1	0.26	2		805	499	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	34	399	0	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.26	2		399	207	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	25	488	2	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.743	0.587	0.92	0.743	0.587	0.92	CLONAL	1	TRUE	1	0.26	2		490	259	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521694	89521694	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs150555764	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	28	517	0	ENST00000336596.2:c.2771G>A	p.Trp924Ter	p.W924*	ENST00000336596	NM_005233.5	924	tGg/tAg	16/17	1	2	FACETS	0.585	0.468	0.719	0.585	0.468	0.719	SUBCLONAL	1	TRUE	1	0.26	2		517	368	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794441	42794441	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	62	704	0	ENST00000575354.2:c.1526del	p.Pro509HisfsTer14	p.P509Hfs*14	ENST00000575354	NM_015125.3	507	cgC/cg	10/20	0.112789664901118	3	FACETS	1	0.928	1	0.557	0.482	0.638	INDETERMINATE	1	TRUE	1	0.26	3		704	484	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	50	625	1	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.969	0.824	1	0.969	0.824	1	CLONAL	1	TRUE	1	0.26	2		626	397	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053347	37053348	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs63751653	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	20	403	0	ENST00000231790.2:c.588dup	p.Gln197ThrfsTer7	p.Q197Tfs*7	ENST00000231790	NM_000249.3	194	-/A	7/19	1	2	FACETS	0.62	0.475	0.789	0.62	0.475	0.789	SUBCLONAL	1	TRUE	1	0.26	2		403	248	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	58	594	1	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.978	0.842	1	0.978	0.842	1	CLONAL	1	TRUE	1	0.26	2		595	456	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274042	10274042	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184494228	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	32	731	1	ENST00000330684.3:c.227G>A	p.Arg76His	p.R76H	ENST00000330684	NM_001134407.1	76	cGc/cAc	2/13	1	2	FACETS	0.557	0.452	0.676	0.557	0.452	0.676	SUBCLONAL	1	TRUE	1	0.26	2		732	442	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100462	8100462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752779081	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	39	873	2	ENST00000346208.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000346208		146	Gcc/Acc	3/6	1	2	FACETS	0.625	0.518	0.745	0.625	0.518	0.745	SUBCLONAL	1	TRUE	1	0.26	2		875	480	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755426	39755427	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	38	801	2	ENST00000288319.7:c.1338dup	p.Ala447CysfsTer19	p.A447Cfs*19	ENST00000288319	NM_182918.3	446	-/T	10/10	1	2	FACETS	0.597	0.493	0.713	0.597	0.493	0.713	SUBCLONAL	1	TRUE	1	0.26	2		803	490	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405201	139405201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767886377	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	34	634	1	ENST00000277541.6:c.2644G>A	p.Ala882Thr	p.A882T	ENST00000277541	NM_017617.3	882	Gca/Aca	17/34	1	2	FACETS	0.615	0.503	0.742	0.615	0.503	0.742	SUBCLONAL	1	TRUE	1	0.26	2		635	425	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380350	14380350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	71	627	0	ENST00000256196.4:c.67G>A	p.Gly23Ser	p.G23S	ENST00000256196		23	Ggc/Agc	1/6	1	2	FACETS	0.815	0.717	0.92	1	0.978	1	CLONAL	2	TRUE	1	0.26	2		627	335	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725045	89725045	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	20	260	0	ENST00000371953.3:c.1028T>A	p.Val343Glu	p.V343E	ENST00000371953	NM_000314.4	343	gTg/gAg	9/9	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.26	2		260	108	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262581	39262581	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs397517180	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	59	400	0	ENST00000402219.2:c.925G>T	p.Asp309Tyr	p.D309Y	ENST00000402219	NM_005633.3	309	Gat/Tat	7/23	1	2	FACETS	0.893	0.777	1	1	0.977	1	CLONAL	2	TRUE	1	0.26	2		400	254	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857386	9857386	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754686222	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	30	642	0	ENST00000330684.3:c.4015A>G	p.Lys1339Glu	p.K1339E	ENST00000330684	NM_001134407.1	1339	Aaa/Gaa	13/13	1	2	FACETS	0.607	0.489	0.741	0.607	0.489	0.741	SUBCLONAL	1	TRUE	1	0.26	2		642	380	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128230352	128230352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530682321	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	35	483	0	ENST00000265960.3:c.1244C>T	p.Thr415Met	p.T415M	ENST00000265960	NM_001006617.1	415	aCg/aTg	10/12	1	2	FACETS	0.78	0.641	0.936	0.78	0.641	0.936	CLONAL	1	TRUE	1	0.26	2		483	345	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7141702	7141702	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1568440846	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	20	543	0	ENST00000302850.5:c.2668C>T	p.Arg890Ter	p.R890*	ENST00000302850	NM_000208.2	890	Cga/Tga	13/22	0.112789664901118	3	FACETS	0.498	0.38	0.636	0.249	0.19	0.318	INDETERMINATE	1	TRUE	1	0.26	3		543	349	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128419995	128419995	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1238730432	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	12	466	0	ENST00000265960.3:c.433C>T	p.Arg145Cys	p.R145C	ENST00000265960	NM_001006617.1	145	Cgc/Tgc	4/12	1	2	FACETS	0.42	0.295	0.573	0.42	0.295	0.573	SUBCLONAL	1	TRUE	1	0.26	2		466	220	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791339	42791339	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	61	745	0	ENST00000575354.2:c.404del	p.Pro135GlnfsTer70	p.P135Qfs*70	ENST00000575354	NM_015125.3	133	ggC/gg	3/20	0.112789664901118	3	FACETS	1	0.944	1	0.59	0.51	0.677	INDETERMINATE	1	TRUE	1	0.26	3		745	449	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631616	90631616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1174854555	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	38	727	0	ENST00000330062.3:c.653G>A	p.Gly218Asp	p.G218D	ENST00000330062	NM_002168.2	218	gGc/gAc	5/11	1	2	FACETS	0.549	0.454	0.657	0.549	0.454	0.657	SUBCLONAL	1	TRUE	1	0.26	2		727	532	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822005	72822005	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	45	769	0	ENST00000268489.5:c.10170del	p.Val3391CysfsTer94	p.V3391Cfs*94	ENST00000268489	NM_006885.3	3390	aaA/aa	10/10	1	2	FACETS	0.764	0.643	0.898	0.764	0.643	0.898	SUBCLONAL	1	TRUE	1	0.26	2		769	453	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424279	47424279	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	66	546	0	ENST00000404338.3:c.2347C>T	p.Arg783Ter	p.R783*	ENST00000404338	NM_004491.4	783	Cga/Tga	1/6	0.112789664901118	3	FACETS	0.982	0.86	1	0.982	0.86	1	INDETERMINATE	2	TRUE	1	0.26	3		546	292	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097616	27097616	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	34	565	2	ENST00000324856.7:c.3205A>G	p.Lys1069Glu	p.K1069E	ENST00000324856	NM_006015.4	1069	Aag/Gag	12/20	1	2	FACETS	0.651	0.532	0.784	0.651	0.532	0.784	SUBCLONAL	1	TRUE	1	0.26	2		567	402	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984366	201984369	+	frameshift_variant	Frame_Shift_Del	DEL	GGGT	GGGT	-	novel	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	105	646	0	ENST00000359651.3:c.1033_1036del	p.Val345MetfsTer101	p.V345Mfs*101	ENST00000359651		344	cGGGTg/cg	8/8	1	2	FACETS	0.831	0.748	0.918	1	0.985	1	CLONAL	2	TRUE	1	0.26	2		646	486	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845604	63845604	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	108	625	0	ENST00000279873.7:c.1343del	p.Ile448AsnfsTer31	p.I448Nfs*31	ENST00000279873	NM_032199.2	448	aTa/aa	9/10	1	2	FACETS	1	0.954	1	1	0.989	1	CLONAL	2	TRUE	1	0.26	2		625	381	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446375	70446375	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	22	648	0	ENST00000373644.4:c.5315C>T	p.Ala1772Val	p.A1772V	ENST00000373644	NM_030625.2	1772	gCa/gTa	11/12	1	2	FACETS	0.398	0.308	0.504	0.398	0.308	0.504	SUBCLONAL	1	TRUE	1	0.26	2		648	425	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120644	115120644	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	26	743	0	ENST00000257566.3:c.362C>A	p.Thr121Asn	p.T121N	ENST00000257566	NM_016569.3	121	aCc/aAc	1/8	1	2	FACETS	0.435	0.344	0.54	0.435	0.344	0.54	SUBCLONAL	1	TRUE	1	0.26	2		743	460	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95556978	95556978	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	31	492	0	ENST00000393063.1:c.5626G>T	p.Gly1876Trp	p.G1876W	ENST00000393063	NM_030621.3	1876	Ggg/Tgg	28/28	1	2	FACETS	0.615	0.497	0.747	0.615	0.497	0.747	SUBCLONAL	1	TRUE	1	0.26	2		492	388	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034970	42034971	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	37	595	0	ENST00000219905.7:c.4817dup	p.Leu1606PhefsTer15	p.L1606Ffs*15	ENST00000219905	NM_001164273.1	1604	-/T	15/24	1	2	FACETS	0.703	0.58	0.84	0.703	0.58	0.84	SUBCLONAL	1	TRUE	1	0.26	2		595	405	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223305	2223305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	36	754	1	ENST00000326181.6:c.917C>T	p.Ala306Val	p.A306V	ENST00000326181	NM_032271.2	306	gCc/gTc	10/21	1	2	FACETS	0.613	0.503	0.735	0.613	0.503	0.735	SUBCLONAL	1	TRUE	1	0.26	2		755	452	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993218	72993218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1384632006	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	45	632	0	ENST00000268489.5:c.827G>A	p.Gly276Asp	p.G276D	ENST00000268489	NM_006885.3	276	gGc/gAc	2/10	1	2	FACETS	0.834	0.702	0.98	0.834	0.702	0.98	CLONAL	1	TRUE	1	0.26	2		632	415	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216204	36216204	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	107	767	0	ENST00000222270.7:c.3612C>G	p.Cys1204Trp	p.C1204W	ENST00000222270	NM_014727.1	1204	tgC/tgG	11/37	0.112789664901118	3	FACETS	0.959	0.864	1	0.959	0.864	1	INDETERMINATE	2	TRUE	1	0.26	3		767	485	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47503709	47503712	+	frameshift_variant	Frame_Shift_Del	DEL	CAGA	CAGA	-	novel	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	93	684	0	ENST00000404338.3:c.4266_4269del	p.Thr1423SerfsTer375	p.T1423Sfs*375	ENST00000404338	NM_004491.4	1422	CAGAca/ca	6/6	0.112789664901118	3	FACETS	0.84	0.75	0.935	0.84	0.75	0.935	INDETERMINATE	2	TRUE	1	0.26	3		684	481	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103883	209103883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	28	453	0	ENST00000345146.2:c.1066G>A	p.Ala356Thr	p.A356T	ENST00000345146	NM_005896.2	356	Gca/Aca	9/10	1	2	FACETS	0.858	0.689	1	0.858	0.689	1	CLONAL	1	TRUE	1	0.26	2		453	251	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39690120	39690120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	38	515	0	ENST00000361337.2:c.145C>T	p.His49Tyr	p.H49Y	ENST00000361337	NM_003286.2	49	Cat/Tat	3/21	1	2	FACETS	0.943	0.782	1	0.943	0.782	1	CLONAL	1	TRUE	1	0.26	2		515	310	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277239	41277239	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	36	498	0	ENST00000349496.5:c.1708G>A	p.Val570Ile	p.V570I	ENST00000349496	NM_001904.3	570	Gtt/Att	11/15	1	2	FACETS	0.92	0.759	1	0.92	0.759	1	CLONAL	1	TRUE	1	0.26	2		498	301	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683417	182683417	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	27	342	0	ENST00000292782.4:c.128A>T	p.Asn43Ile	p.N43I	ENST00000292782	NM_020640.2	43	aAt/aTt	2/7	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.26	2		342	153	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189477	56189478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	14	535	0	ENST00000399503.3:c.4511dup	p.His1505AlafsTer18	p.H1505Afs*18	ENST00000399503	NM_005921.1	1503	-/A	20/20	1	2	FACETS	0.4	0.289	0.535	0.4	0.289	0.535	SUBCLONAL	1	TRUE	1	0.26	2		535	269	SUCCESS
APC	324	MSKCC	GRCh37	5	112162874	112162874	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs770649674	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	11	422	0	ENST00000257430.4:c.1478A>G	p.Tyr493Cys	p.Y493C	ENST00000257430	NM_000038.5	493	tAc/tGc	12/16	1	2	FACETS	0.465	0.321	0.643	0.465	0.321	0.643	SUBCLONAL	1	TRUE	1	0.26	2		422	182	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181995	32181995	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	46	638	0	ENST00000375023.3:c.2059G>T	p.Glu687Ter	p.E687*	ENST00000375023	NM_004557.3	687	Gag/Tag	13/30	1	2	FACETS	0.774	0.653	0.908	0.774	0.653	0.908	CLONAL	1	TRUE	1	0.26	2		638	457	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879529	151879529	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	36	612	1	ENST00000262189.6:c.5416A>G	p.Ile1806Val	p.I1806V	ENST00000262189	NM_170606.2	1806	Ata/Gta	36/59	1	2	FACETS	0.81	0.667	0.969	0.81	0.667	0.969	CLONAL	1	TRUE	1	0.26	2		613	342	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742076	145742076	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	45	657	0	ENST00000428558.2:c.427C>A	p.Pro143Thr	p.P143T	ENST00000428558	NM_004260.3	143	Cca/Aca	5/22	1	2	FACETS	0.906	0.763	1	0.906	0.763	1	CLONAL	1	TRUE	1	0.26	2		657	382	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0063493-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	36	504	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	0.258	0.212	0.31	0.258	0.212	0.31	SUBCLONAL	1	TRUE	1	0.619119441997651	2		504	450	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0063493-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	155	362	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.526199084478463	3	FACETS	0.854	0.791	0.917	0.854	0.791	0.917	CLONAL	2	TRUE	1	0.619119441997651	3		362	384	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747993	41748031	+	inframe_deletion	In_Frame_Del	DEL	GCCGCCGCTGCCGCTGCCGCCGCCGCCGCTGCCGCGGCC	GCCGCCGCTGCCGCTGCCGCCGCCGCCGCTGCCGCGGCC	-	rs757020181	NA	P-0063493-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	23	382	0	ENST00000226382.2:c.738_776del	p.Ala248_Ala260del	p.A248_A260del	ENST00000226382	NM_003924.3	246	gcGGCCGCGGCAGCGGCGGCGGCGGCAGCGGCAGCGGCGGCa/gca	3/3	0.226829585582158	1	FACETS	0.204	0.159	0.256	0.204	0.159	0.256	INDETERMINATE	1	TRUE	0	0.619119441997651	1		382	251	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371798	55371819	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCGGCCGCGCTGGGCCCCGA	AGGCGGCCGCGCTGGGCCCCGA	-	novel	NA	P-0063493-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	168	690	1	ENST00000297316.4:c.488_509del	p.Gln163ArgfsTer217	p.Q163Rfs*217	ENST00000297316	NM_022454.3	163	cAGGCGGCCGCGCTGGGCCCCGAg/cg	2/2	0.520626470743392	4	FACETS	1	0.981	1	0.4	0.368	0.433	CLONAL	1	TRUE	1	0.619119441997651	4		691	732	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442974	49442974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768072508	NA	P-0063493-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	214	550	0	ENST00000301067.7:c.3934C>T	p.Arg1312Cys	p.R1312C	ENST00000301067	NM_003482.3	1312	Cgc/Tgc	12/54	0.194379939824696	3	FACETS	1	0.992	1	0.727	0.679	0.775	INDETERMINATE	1	TRUE	1	0.619119441997651	3		550	623	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0063494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	251	547	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.699016733859664	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.699016733859664	1		548	438	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0063494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	51	393	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.405565341525508	3	FACETS	1	0.966	1	0.703	0.612	0.798	INDETERMINATE	1	TRUE	1	0.699016733859664	3		394	140	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777894	NA	P-0063494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	164	506	0	ENST00000361445.4:c.6644C>T	p.Ser2215Phe	p.S2215F	ENST00000361445	NM_004958.3	2215	tCt/tTt	47/58	0.699016733859664	1	FACETS	0.898	0.838	0.958	0.898	0.838	0.958	CLONAL	1	TRUE	0	0.699016733859664	1		506	340	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0063494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	258	664	1	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.469471701736506	3	FACETS	1	0.985	1	0.576	0.541	0.613	CLONAL	1	TRUE	1	0.699016733859664	3		665	864	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727453	66727453	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397516790	NA	P-0063494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	356	497	4	ENST00000307102.5:c.169A>G	p.Lys57Glu	p.K57E	ENST00000307102	NM_002755.3	57	Aag/Gag	2/11	0.654528597137737	2	FACETS	0.952	0.917	0.986	0.952	0.917	0.986	CLONAL	2	TRUE	0	0.699016733859664	2		501	535	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099403	157099432	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAGCAACAGCAG	CAGCAGCAGCAGCAGCAGCAGCAACAGCAG	-	novel	NA	P-0063494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	194	763	0	ENST00000346085.5:c.357_386del	p.Gln122_Gln131del	p.Q122_Q131del	ENST00000346085	NM_020732.3	114	CAGCAGCAGCAGCAGCAGCAGCAACAGCAG/-	1/20	1	2	FACETS	0.519	0.48	0.56	0.519	0.48	0.56	SUBCLONAL	1	TRUE	1	0.699016733859664	2		763	1069	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936103	178936103	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	73	300	1	ENST00000263967.3:c.1645G>C	p.Asp549His	p.D549H	ENST00000263967	NM_006218.2	549	Gat/Cat	10/21	0.405565341525508	3	FACETS	1	0.976	1	0.708	0.631	0.787	INDETERMINATE	1	TRUE	1	0.699016733859664	3		301	199	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710590	114710610	+	inframe_deletion	In_Frame_Del	DEL	CGAACAGGAGGAGAAGAGCTC	CGAACAGGAGGAGAAGAGCTC	-	novel	NA	P-0063494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	177	624	0	ENST00000543371.1:c.79_99del	p.Gln27_Glu33del	p.Q27_E33del	ENST00000543371	NM_001198531.1	25	ggCGAACAGGAGGAGAAGAGCTCc/ggc	1/14	1	2	FACETS	0.806	0.746	0.868	0.806	0.746	0.868	CLONAL	1	TRUE	1	0.699016733859664	2		624	628	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952101	76952101	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	15	355	0	ENST00000373344.5:c.334T>C	p.Ser112Pro	p.S112P	ENST00000373344	NM_000489.3	112	Tca/Cca	5/35	0.350183601585739	1	FACETS	0.245	0.181	0.32	0.245	0.181	0.32	INDETERMINATE	1	TRUE	0	0.699016733859664	1		355	114	SUCCESS
APC	324	MSKCC	GRCh37	5	112103081	112103082	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0063494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	98	350	0	ENST00000257430.4:c.421_422dup	p.Ser142GlyfsTer29	p.S142Gfs*29	ENST00000257430	NM_000038.5	139	aaa/aaAGa	4/16	0.469471701736506	3	FACETS	1	0.981	1	0.683	0.618	0.75	CLONAL	1	TRUE	1	0.699016733859664	3		350	277	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0063496-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	13	580	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		582	594	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0063508-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	606	511	3	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	0.292735107161636	5	FACETS	1	0.992	1			1	INDETERMINATE	3	TRUE	NA	0.738939425216932	5		514	1075	SUCCESS
ALB	213	MSKCC	GRCh37	4	74275141	74275141	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063508-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	162	329	2	ENST00000295897.4:c.552G>T	p.Arg184Ser	p.R184S	ENST00000295897	NM_000477.5	184	agG/agT	5/15	1	2	FACETS	0.966	0.894	1	0.966	0.894	1	CLONAL	1	TRUE	1	0.738939425216932	2		331	454	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106556	27106556	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063509-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	123	868	0	ENST00000324856.7:c.6167T>G	p.Leu2056Arg	p.L2056R	ENST00000324856	NM_006015.4	2056	cTc/cGc	20/20	1	2	FACETS	1	0.945	1	1	0.99	1	CLONAL	2	TRUE	1	0.12571656868064	2		868	917	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0063510-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	364	697	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.534608895027305	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.534608895027305	2		697	615	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152083	11152083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760654888	NA	P-0063510-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	158	704	1	ENST00000358026.2:c.4367C>T	p.Pro1456Leu	p.P1456L	ENST00000358026	NM_001128849.1	1456	cCg/cTg	31/36	0.534608895027305	3	FACETS	1	0.935	1	0.51	0.468	0.554	CLONAL	1	TRUE	1	0.534608895027305	3		705	734	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38960603	38960603	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063510-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	95	502	1	ENST00000357387.3:c.1748C>A	p.Pro583His	p.P583H	ENST00000357387	NM_152756.3	583	cCc/cAc	20/38	0.534608895027305	4	FACETS	0.732	0.652	0.818	0.244	0.217	0.273	SUBCLONAL	1	TRUE	1	0.534608895027305	4		503	745	SUCCESS
APC	324	MSKCC	GRCh37	5	112175205	112175205	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063510-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	323	562	0	ENST00000257430.4:c.3914del	p.Ala1305GlufsTer3	p.A1305Efs*3	ENST00000257430	NM_000038.5	1305	gCa/ga	16/16	0.507467626109093	3	FACETS	0.877	0.838	0.916	0.877	0.838	0.916	CLONAL	3	TRUE	0	0.534608895027305	3		562	582	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0063511-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	248	466	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.842304829178844	2		466	556	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123875223	123875223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202048118	NA	P-0063512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	43	207	0	ENST00000330479.4:c.179C>T	p.Pro60Leu	p.P60L	ENST00000330479	NM_020382.3	60	cCg/cTg	3/9	0.494000697481415	4	FACETS	1	0.881	1	0.351	0.296	0.411	CLONAL	1	FALSE	1	0.497290849492897	4		207	246	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292708	91292708	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	235	591	0	ENST00000355112.3:c.210C>A	p.Asp70Glu	p.D70E	ENST00000355112	NM_000057.2	70	gaC/gaA	3/22	0.498349655650695	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	FALSE	1	0.497290849492897	3		591	536	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627892	37627892	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	118	676	0	ENST00000447079.4:c.1811del	p.Pro604LeufsTer6	p.P604Lfs*6	ENST00000447079	NM_015083.1	603	Ccc/cc	2/14	0.479759732241614	4	FACETS	0.977	0.883	1	0.326	0.294	0.359	CLONAL	1	FALSE	1	0.497290849492897	4		676	727	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676292	37676293	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0063512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	276	493	0	ENST00000447079.4:c.3049_3050del	p.Ser1017ArgfsTer4	p.S1017Rfs*4	ENST00000447079	NM_015083.1	1016	cAG/c	11/14	0.479759732241614	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	3	FALSE	1	0.497290849492897	4		493	548	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0063513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	59	188	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.728183587754687	2	FACETS	0.988	0.904	1	0.988	0.904	1	CLONAL	2	FALSE	0	0.728183587754687	2		188	82	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944568	71944568	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0063513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	29	590	0	ENST00000298229.2:c.2122+2T>A		p.X708_splice	ENST00000298229	NM_001567.3	708			0.728183587754687	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	0	0.728183587754687	1		590	45	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259089	16259090	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0063514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	81	726	0	ENST00000375759.3:c.6354_6355insC	p.Val2119ArgfsTer4	p.V2119Rfs*4	ENST00000375759	NM_015001.2	2118	-/C	11/15	1	2	FACETS	0.939	0.836	1	0.939	0.836	1	CLONAL	1	TRUE	1	0.562021554296497	2		726	307	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133234479	133234479	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	62	445	0	ENST00000320574.5:c.3353C>T	p.Ser1118Phe	p.S1118F	ENST00000320574	NM_006231.2	1118	tCc/tTc	27/49	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.562021554296497	2		445	203	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063518-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	54	523	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.488257098692425	2		523	175	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0063518-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	195	660	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	0.488257098692425	1	FACETS	0.818	0.77	0.866	1	0.993	1	CLONAL	2	TRUE	0	0.488257098692425	1		660	369	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287235	38287235	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063518-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	166	609	0	ENST00000425967.3:c.422G>T	p.Gly141Val	p.G141V	ENST00000425967	NM_001174067.1	141	gGc/gTc	4/19	1	2	FACETS	0.87	0.809	0.931	1	0.992	1	CLONAL	2	TRUE	1	0.488257098692425	2		609	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0063519-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	219	619	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.810328890368262	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.810328890368262	1		619	299	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795012	42795012	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063519-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	136	629	0	ENST00000575354.2:c.2092G>T	p.Glu698Ter	p.E698*	ENST00000575354	NM_015125.3	698	Gag/Tag	10/20	NA	2	FACETS	0.987	0.91	1			1	INDETERMINATE	1	TRUE	NA	0.810328890368262	2		629	340	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795860	42795860	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063519-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	35	630	0	ENST00000575354.2:c.2849C>A	p.Ser950Ter	p.S950*	ENST00000575354	NM_015125.3	950	tCa/tAa	11/20	NA	2	FACETS	0.211	0.172	0.254			1	INDETERMINATE	1	TRUE	NA	0.810328890368262	2		630	410	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005678	150005678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063519-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	146	516	0	ENST00000253339.5:c.547G>A	p.Glu183Lys	p.E183K	ENST00000253339		183	Gaa/Aaa	3/7	0.810328890368262	1	FACETS	0.821	0.767	0.874	0.821	0.767	0.874	CLONAL	1	TRUE	0	0.810328890368262	1		516	261	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577571	7577571	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs765848205	NA	P-0063524-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	84	703	0	ENST00000269305.4:c.710T>A	p.Met237Lys	p.M237K	ENST00000269305	NM_001126112.2	237	aTg/aAg	7/11	0.215301773592207	1	FACETS	0.793	0.704	0.888	1	0.98	1	SUBCLONAL	2	TRUE	0	0.215301773592207	1		703	439	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566487	41566487	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063524-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	56	620	0	ENST00000263253.7:c.4364A>T	p.Gln1455Leu	p.Q1455L	ENST00000263253	NM_001429.3	1455	cAg/cTg	27/31	0.215301773592207	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.215301773592207	1		620	317	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371726	55371726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063524-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	35	880	0	ENST00000297316.4:c.416C>T	p.Pro139Leu	p.P139L	ENST00000297316	NM_022454.3	139	cCg/cTg	2/2	0.193232787609391	5	FACETS	0.722	0.59	0.87	0.18	0.147	0.218	SUBCLONAL	1	TRUE	1	0.215301773592207	5		880	596	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224148	39224148	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs765070830	NA	P-0063524-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	38	310	0	ENST00000402219.2:c.2996A>G	p.Asn999Ser	p.N999S	ENST00000402219	NM_005633.3	999	aAt/aGt	19/23	0.215301773592207	3	FACETS	1	0.951	1	0.729	0.606	0.865	CLONAL	1	TRUE	1	0.215301773592207	3		310	268	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440844	52440844	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0063524-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	41	751	0	ENST00000460680.1:c.659+1G>C		p.X220_splice	ENST00000460680	NM_004656.3	220			0.201858062132156	1	FACETS	0.581	0.483	0.69	0.581	0.483	0.69	SUBCLONAL	1	TRUE	0	0.215301773592207	1		751	585	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443859	52443873	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TGGGTCGCTCTCCAG	TGGGTCGCTCTCCAG	-	novel	NA	P-0063524-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	55	774	0	ENST00000460680.1:c.22_36del	p.Leu8_Pro12del	p.L8_P12del	ENST00000460680	NM_004656.3	8	CTGGAGAGCGACCCA/-	1/17	0.201858062132156	1	FACETS	0.998	0.855	1	0.998	0.855	1	CLONAL	1	TRUE	0	0.215301773592207	1		774	457	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55569945	55569945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063524-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	29	392	0	ENST00000288135.5:c.812G>A	p.Arg271His	p.R271H	ENST00000288135	NM_000222.2	271	cGt/cAt	5/21	0.21211742515296	1	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	0	0.215301773592207	1		392	225	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0063525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	127	348	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.370559406043804	2		348	541	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372518	55372518	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	171	590	0	ENST00000297316.4:c.1208G>T	p.Ser403Ile	p.S403I	ENST00000297316	NM_022454.3	403	aGc/aTc	2/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.370559406043804	2		590	822	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0063525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	88	118	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.370176895553762	2	FACETS	0.954	0.859	1	0.954	0.859	1	CLONAL	2	TRUE	0	0.370559406043804	2		118	249	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226309	2226309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	190	734	0	ENST00000326181.6:c.1922G>A	p.Arg641His	p.R641H	ENST00000326181	NM_032271.2	641	cGt/cAt	20/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.370559406043804	2		734	939	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341275	89341275	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	49	198	0	ENST00000301030.4:c.7660G>C	p.Ala2554Pro	p.A2554P	ENST00000301030	NM_001256183.1	2554	Gcc/Ccc	11/13	1	2	FACETS	0.945	0.806	1	0.945	0.806	1	CLONAL	1	TRUE	1	0.370559406043804	2		198	280	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591095	67591096	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAA	novel	NA	P-0063525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	120	382	0	ENST00000274335.5:c.1689_1691dup	p.Met563_Asn564insLys	p.M563_N564insK	ENST00000274335		563	atg/atGAAg	12/15	1	2	FACETS	0.838	0.757	0.923	0.838	0.757	0.923	CLONAL	1	TRUE	1	0.370559406043804	2		382	773	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0063526-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	33	331	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.384	0.312	0.464	0.384	0.312	0.464	SUBCLONAL	1	TRUE	1	0.406448733625586	2		331	423	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0063526-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	33	361	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.259	0.21	0.315	0.259	0.21	0.315	SUBCLONAL	1	TRUE	1	0.406448733625586	2		361	626	SUCCESS
APC	324	MSKCC	GRCh37	5	112116601	112116601	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs863225370	NA	P-0063526-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	47	284	0	ENST00000257430.4:c.645+1G>T		p.X215_splice	ENST00000257430	NM_000038.5	215			1	2	FACETS	0.517	0.437	0.606	0.517	0.437	0.606	SUBCLONAL	1	TRUE	1	0.406448733625586	2		284	447	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0063528-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	129	362	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.302362277115412	4	FACETS	1	0.979	1	0.804	0.738	0.87	CLONAL	2	TRUE	1	0.463238403237069	4		362	338	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578491	7578491	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1567553924	NA	P-0063528-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	172	527	0	ENST00000269305.4:c.439del	p.Val147LeufsTer23	p.V147Lfs*23	ENST00000269305	NM_001126112.2	147	Gtt/tt	5/11	0.463238403237069	1	FACETS	0.928	0.858	1	0.928	0.858	1	CLONAL	1	TRUE	0	0.463238403237069	1		527	615	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971066	21971100	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGCACCACCAGCGTGTCCAGGAAGCCCTCCCGG	GCAGCACCACCAGCGTGTCCAGGAAGCCCTCCCGG	-	novel	NA	P-0063528-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	78	559	0	ENST00000304494.5:c.258_292del	p.Arg87ProfsTer21	p.R87Pfs*21	ENST00000304494	NM_000077.4	86	gcCCGGGAGGGCTTCCTGGACACGCTGGTGGTGCTGCac/gcac	2/3	0.361072828374508	0	FACETS	0.458	0.404	0.514			1	SUBCLONAL	1	TRUE	0	0.463238403237069	0		559	395	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784210	43784210	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs767062977	NA	P-0063528-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	26	408	0	ENST00000382044.4:c.276C>A	p.Asn92Lys	p.N92K	ENST00000382044	NM_001141980.1	92	aaC/aaA	3/28	1	2	FACETS	0.24	0.19	0.299	0.24	0.19	0.299	SUBCLONAL	1	TRUE	1	0.463238403237069	2		408	467	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778422	3778424	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	rs754267405	NA	P-0063528-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	89	590	1	ENST00000262367.5:c.6624_6626del	p.Gln2216del	p.Q2216del	ENST00000262367	NM_004380.2	2208	caACAg/cag	31/31	0.236998974410502	1	FACETS	0.409	0.362	0.459	0.409	0.362	0.459	INDETERMINATE	1	TRUE	0	0.463238403237069	1		591	722	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264425	30264426	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCT	rs774288551	NA	P-0063528-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	99	540	0	ENST00000322652.5:c.175_177dup	p.Ser59dup	p.S59dup	ENST00000322652	NM_015355.2	59	gcc/gCCTcc	1/16	1	2	FACETS	0.717	0.641	0.797	0.717	0.641	0.797	SUBCLONAL	1	TRUE	1	0.463238403237069	2		540	596	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0063530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	79	331	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.106444966729753	3	FACETS	0.867	0.765	0.977	0.867	0.765	0.977	INDETERMINATE	2	TRUE	1	0.20001177336742	3		331	501	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0063530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	92	547	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.20001177336742	1	FACETS	0.897	0.796	1	0.897	0.796	1	CLONAL	1	TRUE	0	0.20001177336742	1		548	923	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974715	21974732	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCCCCCGCCTCCA	GCAGCGCCCCCGCCTCCA	-	novel	NA	P-0063530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	113	736	0	ENST00000304494.5:c.95_112del	p.Leu32_Leu37del	p.L32_L37del	ENST00000304494	NM_000077.4	32	cTGGAGGCGGGGGCGCTGCcc/ccc	1/3	0.20001177336742	1	FACETS	0.829	0.744	0.92	0.829	0.744	0.92	CLONAL	1	TRUE	0	0.20001177336742	1		736	1227	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028875	47028875	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0063530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	86	609	0	ENST00000377604.3:c.179C>G	p.Ser60Ter	p.S60*	ENST00000377604	NM_001204468.1	60	tCa/tGa	3/24	0.20001177336742	1	FACETS	0.89	0.786	1	0.89	0.786	1	CLONAL	1	TRUE	0	0.20001177336742	1		609	870	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0063531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	72	348	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.28	2		348	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519980	NA	P-0063531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	264	752	0	ENST00000269305.4:c.528C>G	p.Cys176Trp	p.C176W	ENST00000269305	NM_001126112.2	176	tgC/tgG	5/11	0.266171707819156	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.28	2		752	920	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	95	364	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.42	2		364	410	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913403	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	151	449	0	ENST00000349496.5:c.110C>A	p.Ser37Tyr	p.S37Y	ENST00000349496	NM_001904.3	37	tCt/tAt	3/15	1	2	FACETS	0.916	0.838	0.997	0.916	0.838	0.997	CLONAL	1	TRUE	1	0.42	2		449	785	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609994	43609994	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148935214	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	130	731	1	ENST00000355710.3:c.1946C>T	p.Ser649Leu	p.S649L	ENST00000355710	NM_020975.4	649	tCg/tTg	11/20	1	2	FACETS	0.591	0.535	0.65	0.591	0.535	0.65	SUBCLONAL	1	TRUE	1	0.42	2		732	1048	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047519	49047519	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1131690908	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	18	207	0	ENST00000267163.4:c.2513C>A	p.Ser838Ter	p.S838*	ENST00000267163	NM_000321.2	838	tCa/tAa	24/27	1	2	FACETS	0.316	0.238	0.409	0.316	0.238	0.409	SUBCLONAL	1	TRUE	1	0.42	2		207	271	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	14	393	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.327	0.236	0.436	0.327	0.236	0.436	SUBCLONAL	1	TRUE	1	0.42	2		394	204	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	93	383	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.42	2		383	418	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	148	458	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.42	2		458	699	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938229	76938229	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs191682105	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	107	446	0	ENST00000373344.5:c.2519G>T	p.Arg840Ile	p.R840I	ENST00000373344	NM_000489.3	840	aGa/aTa	9/35	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.42	2		446	476	SUCCESS
APC	324	MSKCC	GRCh37	5	112179011	112179011	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876659753	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	105	408	0	ENST00000257430.4:c.7720C>A	p.Leu2574Ile	p.L2574I	ENST00000257430	NM_000038.5	2574	Ctt/Att	16/16	1	2	FACETS	0.898	0.807	0.994	0.898	0.807	0.994	CLONAL	1	TRUE	1	0.42	2		408	557	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561352	9561352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773981325	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	57	510	0	ENST00000353224.5:c.430G>A	p.Glu144Lys	p.E144K	ENST00000353224	NM_177990.2	144	Gaa/Aaa	4/10	1	2	FACETS	0.327	0.28	0.379	0.327	0.28	0.379	SUBCLONAL	1	TRUE	1	0.42	2		510	829	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374245	138374245	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	57	375	0	ENST00000289153.2:c.3199G>T	p.Asp1067Tyr	p.D1067Y	ENST00000289153	NM_006219.2	1067	Gac/Tac	22/22	1	2	FACETS	0.452	0.387	0.522	0.452	0.387	0.522	SUBCLONAL	1	TRUE	1	0.42	2		375	601	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259486	16259486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759585687	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	75	650	0	ENST00000375759.3:c.6751G>A	p.Ala2251Thr	p.A2251T	ENST00000375759	NM_015001.2	2251	Gca/Aca	11/15	1	2	FACETS	0.352	0.307	0.4	0.352	0.307	0.4	SUBCLONAL	1	TRUE	1	0.42	2		650	1015	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332915	153332915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200698994	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	80	529	0	ENST00000281708.4:c.41G>A	p.Arg14Gln	p.R14Q	ENST00000281708	NM_033632.3	14	cGa/cAa	2/12	1	2	FACETS	0.453	0.398	0.512	0.453	0.398	0.512	SUBCLONAL	1	TRUE	1	0.42	2		529	841	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243859016	243859016	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	58	327	0	ENST00000263826.5:c.49G>T	p.Glu17Ter	p.E17*	ENST00000263826	NM_005465.4	17	Gaa/Taa	2/13	1	2	FACETS	0.874	0.756	1	0.874	0.756	1	CLONAL	1	TRUE	1	0.42	2		327	316	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200425	138200425	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	267	639	0	ENST00000237289.4:c.1843T>G	p.Phe615Val	p.F615V	ENST00000237289	NM_001270507.1	615	Ttt/Gtt	7/9	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.42	2		639	1149	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274880	142274880	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs372610600	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	98	368	0	ENST00000350721.4:c.2180C>A	p.Ser727Tyr	p.S727Y	ENST00000350721	NM_001184.3	727	tCt/tAt	10/47	1	2	FACETS	0.97	0.869	1	0.97	0.869	1	CLONAL	1	TRUE	1	0.42	2		368	481	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587777894	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	16	523	0	ENST00000361445.4:c.6644C>A	p.Ser2215Tyr	p.S2215Y	ENST00000361445	NM_004958.3	2215	tCt/tAt	47/58	1	2	FACETS	0.112	0.082	0.148	0.112	0.082	0.148	SUBCLONAL	1	TRUE	1	0.42	2		523	682	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178199	142178199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746049210	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	24	338	0	ENST00000350721.4:c.7219C>T	p.Arg2407Cys	p.R2407C	ENST00000350721	NM_001184.3	2407	Cgc/Tgc	43/47	1	2	FACETS	0.275	0.215	0.344	0.275	0.215	0.344	SUBCLONAL	1	TRUE	1	0.42	2		338	416	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	218	368	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	1	0.982	1	1	0.995	1	CLONAL	2	TRUE	1	0.42	2		368	468	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962930	2962930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349831751	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	83	571	0	ENST00000396946.4:c.1978C>T	p.Arg660Trp	p.R660W	ENST00000396946	NM_032415.4	660	Cgg/Tgg	16/25	1	2	FACETS	0.468	0.412	0.528	0.468	0.412	0.528	SUBCLONAL	1	TRUE	1	0.42	2		571	845	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956553	93956553	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1035177735	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	113	401	0	ENST00000369303.4:c.2683C>T	p.Arg895Ter	p.R895*	ENST00000369303	NM_004440.3	895	Cga/Tga	15/17	1	2	FACETS	0.946	0.854	1	0.946	0.854	1	CLONAL	1	TRUE	1	0.42	2		401	569	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346314	73346314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs575448022	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	66	335	0	ENST00000377767.4:c.1486G>A	p.Glu496Lys	p.E496K	ENST00000377767	NM_014953.3	496	Gaa/Aaa	10/21	1	2	FACETS	0.901	0.787	1	0.901	0.787	1	CLONAL	1	TRUE	1	0.42	2		335	349	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056286	180056286	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759344198	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	194	597	2	ENST00000261937.6:c.958C>T	p.Arg320Trp	p.R320W	ENST00000261937	NM_182925.4	320	Cgg/Tgg	7/30	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.42	2		599	851	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829806	76829806	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	96	357	0	ENST00000373344.5:c.6235C>T	p.Arg2079Ter	p.R2079*	ENST00000373344	NM_000489.3	2079	Cga/Tga	28/35	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.42	2		357	377	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550850	150550850	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	218	540	0	ENST00000369026.2:c.806C>A	p.Ser269Tyr	p.S269Y	ENST00000369026	NM_021960.4	269	tCt/tAt	2/3	1	2	FACETS	0.981	0.912	1	0.981	0.912	1	CLONAL	1	TRUE	1	0.42	2		540	1058	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027958	48027958	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1558666905	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	143	472	0	ENST00000234420.5:c.2836G>T	p.Glu946Ter	p.E946*	ENST00000234420	NM_000179.2	946	Gaa/Taa	4/10	1	2	FACETS	0.98	0.895	1	0.98	0.895	1	CLONAL	1	TRUE	1	0.42	2		472	695	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169373	99169373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1423422253	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	95	591	0	ENST00000074304.5:c.1303G>A	p.Ala435Thr	p.A435T	ENST00000074304	NM_001134224.1	435	Gca/Aca	15/26	1	2	FACETS	0.509	0.453	0.57	0.509	0.453	0.57	SUBCLONAL	1	TRUE	1	0.42	2		591	888	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450814	70450814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776722537	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	236	634	0	ENST00000373644.4:c.5654C>T	p.Ser1885Leu	p.S1885L	ENST00000373644	NM_030625.2	1885	tCg/tTg	12/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.42	2		634	896	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782130	135782130	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	85	272	0	ENST00000298552.3:c.1426G>T	p.Asp476Tyr	p.D476Y	ENST00000298552	NM_001162426.1	476	Gat/Tat	14/23	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.42	2		272	379	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198347	138198347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776397709	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	57	427	0	ENST00000237289.4:c.940G>A	p.Val314Ile	p.V314I	ENST00000237289	NM_001270507.1	314	Gtc/Atc	6/9	1	2	FACETS	0.37	0.317	0.429	0.37	0.317	0.429	SUBCLONAL	1	TRUE	1	0.42	2		427	733	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679798	88679798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774739739	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	50	417	0	ENST00000360948.2:c.665G>A	p.Arg222Gln	p.R222Q	ENST00000360948	NM_001012338.2	222	cGa/cAa	7/19	1	2	FACETS	0.38	0.322	0.444	0.38	0.322	0.444	SUBCLONAL	1	TRUE	1	0.42	2		417	627	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14303198	14303198	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	87	378	0	ENST00000256196.4:c.477G>T	p.Lys159Asn	p.K159N	ENST00000256196		159	aaG/aaT	5/6	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.42	2		378	340	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945066	151945066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138111015	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	24	253	0	ENST00000262189.6:c.2453C>T	p.Ser818Leu	p.S818L	ENST00000262189	NM_170606.2	818	tCa/tTa	14/59	1	2	FACETS	0.316	0.247	0.395	0.316	0.247	0.395	SUBCLONAL	1	TRUE	1	0.42	2		253	362	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912133	50912133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768773535	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	59	531	0	ENST00000440232.2:c.1867C>T	p.Arg623Trp	p.R623W	ENST00000440232	NM_002691.3	623	Cgg/Tgg	15/27	1	2	FACETS	0.342	0.293	0.396	0.342	0.293	0.396	SUBCLONAL	1	TRUE	1	0.42	2		531	821	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565858	55565858	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	63	343	0	ENST00000288135.5:c.682G>T	p.Glu228Ter	p.E228*	ENST00000288135	NM_000222.2	228	Gaa/Taa	4/21	1	2	FACETS	0.562	0.486	0.644	0.562	0.486	0.644	SUBCLONAL	1	TRUE	1	0.42	2		343	534	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260151	149260151	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1307297959	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	136	417	1	ENST00000360632.3:c.742C>T	p.Arg248Ter	p.R248*	ENST00000360632	NM_015472.4	248	Cga/Tga	4/7	1	2	FACETS	0.926	0.844	1	0.926	0.844	1	CLONAL	1	TRUE	1	0.42	2		418	699	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937338	76937338	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	39	356	0	ENST00000373344.5:c.3410G>T	p.Arg1137Ile	p.R1137I	ENST00000373344	NM_000489.3	1137	aGa/aTa	9/35	1	2	FACETS	0.45	0.373	0.535	0.45	0.373	0.535	SUBCLONAL	1	TRUE	1	0.42	2		356	413	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978732	70978732	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs751550241	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	120	406	0	ENST00000276594.2:c.921A>C	p.Glu307Asp	p.E307D	ENST00000276594	NM_024504.3	307	gaA/gaC	5/8	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.42	2		406	507	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740836	58740836	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs747668756	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	201	510	0	ENST00000305921.3:c.1741C>T	p.Arg581Ter	p.R581*	ENST00000305921	NM_003620.3	581	Cga/Tga	6/6	1	2	FACETS	0.994	0.921	1	0.994	0.921	1	CLONAL	1	TRUE	1	0.42	2		510	963	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342866	118342866	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148514018	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	162	477	1	ENST00000534358.1:c.992G>A	p.Arg331Gln	p.R331Q	ENST00000534358	NM_005933.3	331	cGg/cAg	3/36	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.42	2		478	766	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020771	112020771	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374907658	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	110	451	0	ENST00000368678.4:c.800C>T	p.Ser267Leu	p.S267L	ENST00000368678		267	tCg/tTg	8/13	1	2	FACETS	0.516	0.463	0.573	0.516	0.463	0.573	SUBCLONAL	1	TRUE	1	0.42	2		451	1015	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39317430	39317430	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	92	313	0	ENST00000373001.3:c.757-1G>T		p.X253_splice	ENST00000373001	NM_022157.3	253			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.42	2		313	378	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80021297	80021297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs963234468	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	87	328	0	ENST00000265081.6:c.1366G>A	p.Glu456Lys	p.E456K	ENST00000265081	NM_002439.4	456	Gaa/Aaa	9/24	1	2	FACETS	0.982	0.874	1	0.982	0.874	1	CLONAL	1	TRUE	1	0.42	2		328	422	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346631	81346631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	130	394	2	ENST00000222390.5:c.1322G>A	p.Arg441Gln	p.R441Q	ENST00000222390	NM_000601.4	441	cGa/cAa	11/18	1	2	FACETS	0.976	0.888	1	0.976	0.888	1	CLONAL	1	TRUE	1	0.42	2		396	634	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236109	108236109	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	157	468	0	ENST00000278616.4:c.9045G>T	p.Glu3015Asp	p.E3015D	ENST00000278616	NM_000051.3	3015	gaG/gaT	63/63	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.42	2		468	703	SUCCESS
APC	324	MSKCC	GRCh37	5	112179333	112179333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182456139	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	64	495	0	ENST00000257430.4:c.8042C>T	p.Pro2681Leu	p.P2681L	ENST00000257430	NM_000038.5	2681	cCg/cTg	16/16	1	2	FACETS	0.487	0.421	0.558	0.487	0.421	0.558	SUBCLONAL	1	TRUE	1	0.42	2		495	626	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850642	63850642	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	177	588	0	ENST00000279873.7:c.1420G>T	p.Glu474Ter	p.E474*	ENST00000279873	NM_032199.2	474	Gaa/Taa	10/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.42	2		588	711	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219468	133219468	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768741587	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	178	643	0	ENST00000320574.5:c.4666C>T	p.Arg1556Trp	p.R1556W	ENST00000320574	NM_006231.2	1556	Cgg/Tgg	36/49	1	2	FACETS	0.949	0.875	1	0.949	0.875	1	CLONAL	1	TRUE	1	0.42	2		643	893	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333925	70333925	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	76	520	0	ENST00000373644.4:c.1830G>T	p.Lys610Asn	p.K610N	ENST00000373644	NM_030625.2	610	aaG/aaT	2/12	1	2	FACETS	0.397	0.347	0.451	0.397	0.347	0.451	SUBCLONAL	1	TRUE	1	0.42	2		520	912	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953100	38953100	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	59	312	0	ENST00000357387.3:c.2884C>A	p.Leu962Ile	p.L962I	ENST00000357387	NM_152756.3	962	Ctt/Att	29/38	1	2	FACETS	0.824	0.713	0.943	0.824	0.713	0.943	CLONAL	1	TRUE	1	0.42	2		312	341	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939054	36939054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	75	661	0	ENST00000361632.4:c.655C>T	p.Leu219Phe	p.L219F	ENST00000361632		219	Ctt/Ttt	5/16	1	2	FACETS	0.409	0.358	0.465	0.409	0.358	0.465	SUBCLONAL	1	TRUE	1	0.42	2		661	873	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31431770	31431770	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs775775322	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	45	344	1	ENST00000344624.3:c.3058C>T	p.Arg1020Ter	p.R1020*	ENST00000344624		1020	Cga/Tga	23/33	1	2	FACETS	0.317	0.265	0.374	0.317	0.265	0.374	SUBCLONAL	1	TRUE	1	0.42	2		345	677	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43769884	43769884	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	57	365	0	ENST00000382044.4:c.862G>T	p.Glu288Ter	p.E288*	ENST00000382044	NM_001141980.1	288	Gaa/Taa	8/28	1	2	FACETS	0.401	0.343	0.464	0.401	0.343	0.464	SUBCLONAL	1	TRUE	1	0.42	2		365	677	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40856677	40856677	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs376492983	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	120	332	0	ENST00000428826.2:c.1960C>T	p.Arg654Ter	p.R654*	ENST00000428826		654	Cga/Tga	18/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.42	2		332	530	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120612	94120612	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	64	433	0	ENST00000369303.4:c.439G>T	p.Asp147Tyr	p.D147Y	ENST00000369303	NM_004440.3	147	Gac/Tac	3/17	1	2	FACETS	0.653	0.566	0.746	0.653	0.566	0.746	SUBCLONAL	1	TRUE	1	0.42	2		433	467	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830892	72830892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150923130	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	99	701	2	ENST00000268489.5:c.5689G>A	p.Glu1897Lys	p.E1897K	ENST00000268489	NM_006885.3	1897	Gag/Aag	9/10	1	2	FACETS	0.386	0.344	0.432	0.386	0.344	0.432	SUBCLONAL	1	TRUE	1	0.42	2		703	1220	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633383	3633383	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200178217	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	213	641	0	ENST00000294008.3:c.4868C>T	p.Ala1623Val	p.A1623V	ENST00000294008	NM_032444.2	1623	gCg/gTg	14/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.42	2		641	894	SUCCESS
AR	367	MSKCC	GRCh37	X	66942740	66942740	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852577	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	66	401	0	ENST00000374690.3:c.2521C>T	p.Arg841Cys	p.R841C	ENST00000374690	NM_000044.3	841	Cgt/Tgt	7/8	1	2	FACETS	0.516	0.448	0.59	0.516	0.448	0.59	SUBCLONAL	1	TRUE	1	0.42	2		401	609	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828084	72828084	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	187	518	0	ENST00000268489.5:c.8497G>A	p.Asp2833Asn	p.D2833N	ENST00000268489	NM_006885.3	2833	Gat/Aat	9/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.42	2		518	857	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353757	68353757	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs774910383	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	72	275	0	ENST00000487270.1:c.592G>T	p.Glu198Ter	p.E198*	ENST00000487270	NM_133509.3	198	Gaa/Taa	7/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.42	2		275	297	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937896	76937896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	129	440	0	ENST00000373344.5:c.2852C>T	p.Thr951Ile	p.T951I	ENST00000373344	NM_000489.3	951	aCc/aTc	9/35	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.42	2		440	613	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256657	16256657	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	133	537	0	ENST00000375759.3:c.3922A>C	p.Lys1308Gln	p.K1308Q	ENST00000375759	NM_015001.2	1308	Aaa/Caa	11/15	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.42	2		537	631	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855911	76855911	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	74	373	0	ENST00000373344.5:c.5689G>T	p.Glu1897Ter	p.E1897*	ENST00000373344	NM_000489.3	1897	Gaa/Taa	23/35	1	2	FACETS	0.935	0.823	1	0.935	0.823	1	CLONAL	1	TRUE	1	0.42	2		373	377	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424921	47424921	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	186	521	0	ENST00000404338.3:c.2989C>T	p.Arg997Ter	p.R997*	ENST00000404338	NM_004491.4	997	Cga/Tga	1/6	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.42	2		521	862	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2170448	2170448	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	55	341	0	ENST00000349721.2:c.4229C>A	p.Ser1410Tyr	p.S1410Y	ENST00000349721	NM_003070.3	1410	tCt/tAt	29/34	1	2	FACETS	0.445	0.38	0.515	0.445	0.38	0.515	SUBCLONAL	1	TRUE	1	0.42	2		341	589	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292526	15292526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	228	666	0	ENST00000263388.2:c.2653G>A	p.Ala885Thr	p.A885T	ENST00000263388	NM_000435.2	885	Gcc/Acc	17/33	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.42	2		666	936	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713506	30713506	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs886038794	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	73	625	0	ENST00000295754.5:c.831G>T	p.Lys277Asn	p.K277N	ENST00000295754	NM_003242.5	277	aaG/aaT	4/7	1	2	FACETS	0.437	0.382	0.497	0.437	0.382	0.497	SUBCLONAL	1	TRUE	1	0.42	2		625	795	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363634	40363634	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	51	413	0	ENST00000397332.2:c.595G>T	p.Glu199Ter	p.E199*	ENST00000397332	NM_001033082.2	199	Gaa/Taa	3/3	1	2	FACETS	0.346	0.294	0.405	0.346	0.294	0.405	SUBCLONAL	1	TRUE	1	0.42	2		413	701	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231488744	231488744	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	36	418	0	ENST00000295050.7:c.1107G>T	p.Gln369His	p.Q369H	ENST00000295050	NM_032018.5	369	caG/caT	5/5	1	2	FACETS	0.424	0.349	0.509	0.424	0.349	0.509	SUBCLONAL	1	TRUE	1	0.42	2		418	404	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124577	108124577	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	78	315	0	ENST00000278616.4:c.1935C>A	p.Phe645Leu	p.F645L	ENST00000278616	NM_000051.3	645	ttC/ttA	13/63	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.42	2		315	351	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151755	108151755	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1565441511	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	74	307	0	ENST00000278616.4:c.3436G>T	p.Glu1146Ter	p.E1146*	ENST00000278616	NM_000051.3	1146	Gaa/Taa	24/63	1	2	FACETS	0.94	0.828	1	0.94	0.828	1	CLONAL	1	TRUE	1	0.42	2		307	375	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427246	49427246	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	90	630	0	ENST00000301067.7:c.11242C>A	p.Leu3748Ile	p.L3748I	ENST00000301067	NM_003482.3	3748	Cta/Ata	39/54	1	2	FACETS	0.518	0.459	0.582	0.518	0.459	0.582	SUBCLONAL	1	TRUE	1	0.42	2		630	827	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891102	112891102	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	175	450	0	ENST00000351677.2:c.436G>T	p.Asp146Tyr	p.D146Y	ENST00000351677	NM_002834.3	146	Gat/Tat	4/16	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.42	2		450	827	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061696	38061696	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750947894	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	142	591	0	ENST00000250448.2:c.293C>T	p.Ala98Val	p.A98V	ENST00000250448	NM_004496.3	98	gCg/gTg	2/2	1	2	FACETS	0.828	0.755	0.904	0.828	0.755	0.904	CLONAL	1	TRUE	1	0.42	2		591	817	SUCCESS
SCG5	6447	MSKCC	GRCh37	15	32976829	32976829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	75	397	0	ENST00000300175.4:c.448C>T	p.Leu150Phe	p.L150F	ENST00000300175	NM_001144757.1	150	Ctc/Ttc	4/6	1	2	FACETS	0.475	0.416	0.539	0.475	0.416	0.539	SUBCLONAL	1	TRUE	1	0.42	2		397	752	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028595	42028595	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	68	565	0	ENST00000219905.7:c.4133C>A	p.Ser1378Tyr	p.S1378Y	ENST00000219905	NM_001164273.1	1378	tCt/tAt	13/24	1	2	FACETS	0.382	0.331	0.437	0.382	0.331	0.437	SUBCLONAL	1	TRUE	1	0.42	2		565	848	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676219	29676219	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1555536029	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	40	363	0	ENST00000356175.3:c.7208G>T	p.Arg2403Ile	p.R2403I	ENST00000356175	NM_000267.3	2403	aGa/aTa	48/57	1	2	FACETS	0.443	0.368	0.526	0.443	0.368	0.526	SUBCLONAL	1	TRUE	1	0.42	2		363	430	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245998	41245998	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	108	487	0	ENST00000357654.3:c.1550T>C	p.Phe517Ser	p.F517S	ENST00000357654	NM_007294.3	517	tTt/tCt	10/23	1	2	FACETS	0.965	0.869	1	0.965	0.869	1	CLONAL	1	TRUE	1	0.42	2		487	533	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211714	5211714	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs750656757	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	80	482	0	ENST00000357368.4:c.5121C>A	p.Phe1707Leu	p.F1707L	ENST00000357368	NM_002850.3	1707	ttC/ttA	33/38	1	2	FACETS	0.466	0.41	0.527	0.466	0.41	0.527	SUBCLONAL	1	TRUE	1	0.42	2		482	817	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210441	36210441	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	61	517	0	ENST00000222270.7:c.434G>A	p.Arg145Gln	p.R145Q	ENST00000222270	NM_014727.1	145	cGa/cAa	2/37	1	2	FACETS	0.296	0.254	0.341	0.296	0.254	0.341	SUBCLONAL	1	TRUE	1	0.42	2		517	982	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424672	47424672	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	161	504	0	ENST00000404338.3:c.2740G>T	p.Glu914Ter	p.E914*	ENST00000404338	NM_004491.4	914	Gaa/Taa	1/6	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.42	2		504	764	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631177	67631177	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	86	399	0	ENST00000272342.5:c.1363G>T	p.Glu455Ter	p.E455*	ENST00000272342	NM_019002.3	455	Gaa/Taa	5/6	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.42	2		399	319	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095653	178095653	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	72	488	0	ENST00000397062.3:c.1678T>G	p.Leu560Val	p.L560V	ENST00000397062	NM_006164.4	560	Tta/Gta	5/5	1	2	FACETS	0.543	0.475	0.617	0.543	0.475	0.617	SUBCLONAL	1	TRUE	1	0.42	2		488	631	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150041	202150041	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1329125753	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	77	528	0	ENST00000358485.4:c.1481+1G>T		p.X494_splice	ENST00000358485	NM_001080125.1	494			1	2	FACETS	0.45	0.395	0.511	0.45	0.395	0.511	SUBCLONAL	1	TRUE	1	0.42	2		528	814	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63965761	63965761	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	79	528	0	ENST00000398590.3:c.670T>G	p.Ser224Ala	p.S224A	ENST00000398590	NM_001177387.1	224	Tca/Gca	6/14	1	2	FACETS	0.399	0.349	0.451	0.399	0.349	0.451	SUBCLONAL	1	TRUE	1	0.42	2		528	944	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587123	189587123	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	66	377	0	ENST00000264731.3:c.1140G>T	p.Gln380His	p.Q380H	ENST00000264731	NM_003722.4	380	caG/caT	9/14	1	2	FACETS	0.577	0.501	0.659	0.577	0.501	0.659	SUBCLONAL	1	TRUE	1	0.42	2		377	545	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604263	189604263	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	56	541	0	ENST00000264731.3:c.1430C>A	p.Ser477Tyr	p.S477Y	ENST00000264731	NM_003722.4	477	tCt/tAt	11/14	1	2	FACETS	0.283	0.242	0.329	0.283	0.242	0.329	SUBCLONAL	1	TRUE	1	0.42	2		541	941	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168529	56168529	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	22	296	0	ENST00000399503.3:c.1485G>A	p.Trp495Ter	p.W495*	ENST00000399503	NM_005921.1	495	tgG/tgA	8/20	1	2	FACETS	0.239	0.185	0.303	0.239	0.185	0.303	SUBCLONAL	1	TRUE	1	0.42	2		296	438	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591080	67591080	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	120	387	0	ENST00000274335.5:c.1673A>C	p.Glu558Ala	p.E558A	ENST00000274335		558	gAa/gCa	12/15	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.42	2		387	540	SUCCESS
APC	324	MSKCC	GRCh37	5	112176411	112176411	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	50	396	0	ENST00000257430.4:c.5120C>T	p.Ser1707Phe	p.S1707F	ENST00000257430	NM_000038.5	1707	tCt/tTt	16/16	1	2	FACETS	0.414	0.351	0.484	0.414	0.351	0.484	SUBCLONAL	1	TRUE	1	0.42	2		396	575	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931381	131931381	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1388500583	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	133	407	0	ENST00000265335.6:c.2086G>T	p.Glu696Ter	p.E696*	ENST00000265335		696	Gaa/Taa	13/25	1	2	FACETS	0.902	0.821	0.988	0.902	0.821	0.988	CLONAL	1	TRUE	1	0.42	2		407	702	SUCCESS
MET	4233	MSKCC	GRCh37	7	116422095	116422095	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	100	339	0	ENST00000397752.3:c.3576G>T	p.Met1192Ile	p.M1192I	ENST00000397752	NM_000245.2	1192	atG/atT	18/21	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.42	2		339	438	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873909	151873909	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	86	474	0	ENST00000262189.6:c.8629C>A	p.Leu2877Ile	p.L2877I	ENST00000262189	NM_170606.2	2877	Cta/Ata	38/59	1	2	FACETS	0.604	0.534	0.679	0.604	0.534	0.679	SUBCLONAL	1	TRUE	1	0.42	2		474	678	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70971054	70971054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	132	399	0	ENST00000276594.2:c.1207G>A	p.Glu403Lys	p.E403K	ENST00000276594	NM_024504.3	403	Gaa/Aaa	6/8	1	2	FACETS	0.957	0.871	1	0.957	0.871	1	CLONAL	1	TRUE	1	0.42	2		399	657	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285802	87285802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	91	603	0	ENST00000277120.3:c.139G>A	p.Asp47Asn	p.D47N	ENST00000277120		47	Gac/Aac	2/19	1	2	FACETS	0.448	0.397	0.503	0.448	0.397	0.503	SUBCLONAL	1	TRUE	1	0.42	2		603	967	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045505	47045505	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	111	648	0	ENST00000377604.3:c.2472G>T	p.Lys824Asn	p.K824N	ENST00000377604	NM_001204468.1	824	aaG/aaT	22/24	1	2	FACETS	0.547	0.49	0.606	0.547	0.49	0.606	SUBCLONAL	1	TRUE	1	0.42	2		648	967	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615619	100615619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	84	509	0	ENST00000308731.7:c.713G>A	p.Gly238Asp	p.G238D	ENST00000308731	NM_000061.2	238	gGt/gAt	8/19	1	2	FACETS	0.54	0.476	0.608	0.54	0.476	0.608	SUBCLONAL	1	TRUE	1	0.42	2		509	741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0063535-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	227	662	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.317842706101287	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.317842706101287	2		662	632	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950926	32950926	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063535-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	117	394	0	ENST00000380152.3:c.8752G>A	p.Glu2918Lys	p.E2918K	ENST00000380152		2918	Gag/Aag	21/27	1	2	FACETS	0.756	0.685	0.83	1	0.985	1	SUBCLONAL	2	TRUE	1	0.317842706101287	2		394	487	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063535-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	118	232	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	0.234368600826656	2	FACETS	1	0.96	1			1	CLONAL	2	TRUE	NA	0.317842706101287	2		232	341	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996065	73996065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747735855	NA	P-0063535-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	49	571	0	ENST00000318443.5:c.799C>T	p.Arg267Cys	p.R267C	ENST00000318443	NM_001024736.1	267	Cgc/Tgc	5/10	1	2	FACETS	0.515	0.435	0.602	0.515	0.435	0.602	SUBCLONAL	1	TRUE	1	0.317842706101287	2		571	599	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652341	206652341	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063535-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	65	549	0	ENST00000367120.3:c.1048C>T	p.Gln350Ter	p.Q350*	ENST00000367120	NM_014002.3	350	Cag/Tag	10/22	1	2	FACETS	0.65	0.564	0.744	0.65	0.564	0.744	SUBCLONAL	1	TRUE	1	0.317842706101287	2		549	629	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414281	32414281	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063535-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	143	350	0	ENST00000332351.3:c.1270G>T	p.Asp424Tyr	p.D424Y	ENST00000332351	NM_024426.4	424	Gac/Tac	8/10	0.317842706101287	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.317842706101287	3		350	462	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124503533	124503533	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063535-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	125	350	0	ENST00000357628.3:c.417G>T	p.Trp139Cys	p.W139C	ENST00000357628	NM_015450.2	139	tgG/tgT	8/19	1	2	FACETS	0.753	0.685	0.825	1	0.986	1	SUBCLONAL	2	TRUE	1	0.317842706101287	2		350	522	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0063535-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	121	213	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.317842706101287	2	FACETS	0.981	0.895	1	0.981	0.895	1	CLONAL	2	TRUE	0	0.317842706101287	2		213	388	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884948	111884948	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063535-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	219	492	0	ENST00000341259.2:c.946G>C	p.Glu316Gln	p.E316Q	ENST00000341259	NM_005475.2	316	Gag/Cag	5/8	0.317842706101287	2	FACETS	0.984	0.92	1	0.984	0.92	1	CLONAL	2	TRUE	0	0.317842706101287	2		492	700	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225883	2225883	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063535-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	202	543	0	ENST00000326181.6:c.1675G>T	p.Gly559Cys	p.G559C	ENST00000326181	NM_032271.2	559	Ggt/Tgt	18/21	0.3037204705593	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.317842706101287	2		543	627	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858397	89858397	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1390701776	NA	P-0063535-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	192	481	0	ENST00000389301.3:c.1163G>T	p.Arg388Ile	p.R388I	ENST00000389301	NM_000135.2	388	aGa/aTa	13/43	0.3037204705593	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	0	0.317842706101287	2		481	601	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308347	15308347	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063535-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	93	458	0	ENST00000263388.2:c.161G>C	p.Arg54Pro	p.R54P	ENST00000263388	NM_000435.2	54	cGt/cCt	2/33	0.241063960093936	2	FACETS	1	0.969	1	0.62	0.553	0.69	CLONAL	1	TRUE	0	0.317842706101287	2		458	472	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293146	212293146	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063535-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	74	250	0	ENST00000342788.4:c.2706C>A	p.Asp902Glu	p.D902E	ENST00000342788	NM_005235.2	902	gaC/gaA	22/28	0.133237451829863	4	FACETS	1	0.975	1	0.736	0.647	0.831	INDETERMINATE	1	TRUE	2	0.317842706101287	4		250	417	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453639	138453639	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063535-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	41	291	0	ENST00000289153.2:c.809G>T	p.Arg270Leu	p.R270L	ENST00000289153	NM_006219.2	270	cGg/cTg	5/22	1	2	FACETS	0.588	0.49	0.696	0.588	0.49	0.696	SUBCLONAL	1	TRUE	1	0.317842706101287	2		291	439	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979618	55979618	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063535-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	103	306	0	ENST00000263923.4:c.829C>G	p.Leu277Val	p.L277V	ENST00000263923	NM_002253.2	277	Cta/Gta	7/30	1	2	FACETS	0.755	0.68	0.834	1	0.983	1	SUBCLONAL	2	TRUE	1	0.317842706101287	2		306	429	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449767	149449767	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063535-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	60	506	0	ENST00000286301.3:c.1297C>A	p.Gln433Lys	p.Q433K	ENST00000286301	NM_005211.3	433	Cag/Aag	9/22	1	2	FACETS	0.588	0.506	0.677	0.588	0.506	0.677	SUBCLONAL	1	TRUE	1	0.317842706101287	2		506	642	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188830	32188830	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063535-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	74	612	0	ENST00000375023.3:c.724G>T	p.Gly242Cys	p.G242C	ENST00000375023	NM_004557.3	242	Ggc/Tgc	4/30	1	2	FACETS	0.683	0.597	0.775	0.683	0.597	0.775	SUBCLONAL	1	TRUE	1	0.317842706101287	2		612	682	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739768	41739768	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0063535-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	125	485	0	ENST00000242208.4:c.205A>T	p.Lys69Ter	p.K69*	ENST00000242208	NM_002192.2	69	Aag/Tag	2/3	1	2	FACETS	0.818	0.745	0.894	1	0.988	1	CLONAL	2	TRUE	1	0.317842706101287	2		485	481	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27173238	27173238	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063535-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	109	414	0	ENST00000380036.4:c.779T>G	p.Phe260Cys	p.F260C	ENST00000380036	NM_000459.3	260	tTt/tGt	6/23	0.317842706101287	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.317842706101287	1		414	487	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27173346	27173346	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063535-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	98	397	0	ENST00000380036.4:c.887T>C	p.Leu296Pro	p.L296P	ENST00000380036	NM_000459.3	296	cTg/cCg	6/23	0.317842706101287	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.317842706101287	1		397	401	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0063545-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	57	452	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.13	2		452	872	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440372	52440372	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063545-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	48	605	0	ENST00000460680.1:c.680G>C	p.Arg227Pro	p.R227P	ENST00000460680	NM_004656.3	227	cGc/cCc	9/17	1	2	FACETS	0.869	0.732	1	0.869	0.732	1	CLONAL	1	TRUE	1	0.13	2		605	850	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971073	21971074	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0063545-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	67	618	0	ENST00000304494.5:c.284_285del	p.Val95GlyfsTer24	p.V95Gfs*24	ENST00000304494	NM_000077.4	95	gTG/g	2/3	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.13	2		618	761	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196743	123196755	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCCTTTAGGTGC	TTCCTTTAGGTGC	-	novel	NA	P-0063545-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	14	156	0	ENST00000218089.9:c.1639-7_1644del		p.X547_splice	ENST00000218089	NM_001042749.1	547		18/35	1	1	FACETS	0.857	0.62	1	0.857	0.62	1	CLONAL	1	TRUE	0	0.13	1		156	235	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063545-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	27	523	0				ENST00000310581	NM_198253.2	-/1132			0.16824270537797	3	FACETS	0.619	0.49	0.767	0.309	0.245	0.384	SUBCLONAL	1	TRUE	1	0.13	3		523	715	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878051	48878051	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0063545-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	18	0	0	ENST00000267163.4:c.3G>A	p.Met1?	p.M1?	ENST00000267163	NM_000321.2	1	atG/atA	1/27	1	2	FACETS	0.338	0.253	0.44	0.338	0.253	0.44	SUBCLONAL	1	TRUE	1	0.13	2		0	819	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0063556-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	693	454	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.688611069882554	7	FACETS	1	0.989	1	1	0.989	1	CLONAL	5	TRUE	2	0.688611069882554	7		454	1062	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186599	108186599	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876658415	NA	P-0063556-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	179	487	0	ENST00000278616.4:c.6056A>G	p.Tyr2019Cys	p.Y2019C	ENST00000278616	NM_000051.3	2019	tAt/tGt	41/63	0.646597876453605	2	FACETS	0.928	0.878	0.977	0.928	0.878	0.977	CLONAL	2	TRUE	0	0.688611069882554	2		487	280	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820605	3820605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147083140	NA	P-0063556-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	223	557	0	ENST00000262367.5:c.2846C>T	p.Pro949Leu	p.P949L	ENST00000262367	NM_004380.2	949	cCg/cTg	14/31	0.367713726824383	3	FACETS	0.907	0.854	0.96	0.605	0.569	0.64	INDETERMINATE	2	TRUE	0	0.688611069882554	3		557	480	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251200	115251200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063556-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	51	452	0	ENST00000369535.4:c.526G>T	p.Asp176Tyr	p.D176Y	ENST00000369535	NM_002524.4	176	Gat/Tat	5/7	0.35539437096151	2	FACETS	0.445	0.38	0.516	0.222	0.19	0.258	INDETERMINATE	1	TRUE	0	0.688611069882554	2		452	333	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445384	49445384	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1449494133	NA	P-0063556-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	69	809	1	ENST00000301067.7:c.2082G>T	p.Glu694Asp	p.E694D	ENST00000301067	NM_003482.3	694	gaG/gaT	10/54	0.688611069882554	3	FACETS	0.429	0.373	0.489	0.214	0.186	0.245	SUBCLONAL	1	TRUE	1	0.688611069882554	3		810	628	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117870627	117870629	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0063556-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	41	342	0	ENST00000297338.2:c.443_445del	p.Glu148del	p.E148del	ENST00000297338	NM_006265.2	148	gAAGtt/gtt	5/14	0.688611069882554	5	FACETS	0.532	0.443	0.631	0.106	0.088	0.127	SUBCLONAL	1	TRUE	0	0.688611069882554	5		342	455	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620386	43620386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1363037947	NA	P-0063556-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	127	586	0	ENST00000355710.3:c.2995G>A	p.Ala999Thr	p.A999T	ENST00000355710	NM_020975.4	999	Gcg/Acg	18/20	0.626745651379448	6	FACETS	1	0.962	1	0.224	0.202	0.246	CLONAL	1	TRUE	1	0.688611069882554	6		586	784	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144993	58144993	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063556-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	85	598	0	ENST00000257904.6:c.351C>G	p.Ile117Met	p.I117M	ENST00000257904	NM_000075.3	117	atC/atG	3/8	0.688611069882554	3	FACETS	0.539	0.477	0.605	0.269	0.238	0.303	SUBCLONAL	1	TRUE	1	0.688611069882554	3		598	616	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45854929	45854930	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1339015407	NA	P-0063556-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	49	494	0	ENST00000391945.4:c.2240_2241del	p.Glu747GlyfsTer26	p.E747Gfs*26	ENST00000391945	NM_000400.3	747	gAG/g	23/23	0.343882313991313	3	FACETS	0.497	0.422	0.579	0.166	0.14	0.193	INDETERMINATE	1	TRUE	0	0.688611069882554	3		494	385	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281179	46281179	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063556-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	41	561	0	ENST00000371998.3:c.3976G>T	p.Gly1326Cys	p.G1326C	ENST00000371998		1326	Ggt/Tgt	21/23	0.252787595919301	5	FACETS	0.548	0.456	0.649	0.183	0.152	0.217	INDETERMINATE	1	TRUE	2	0.688611069882554	5		561	442	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513299	106513299	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063556-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	53	497	0	ENST00000359195.3:c.2203C>G	p.Gln735Glu	p.Q735E	ENST00000359195	NM_002649.2	735	Caa/Gaa	4/11	0.688611069882554	2	FACETS	0.428	0.366	0.495	0.214	0.183	0.248	SUBCLONAL	1	TRUE	0	0.688611069882554	2		497	360	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040893	47040948	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCCTCCTTACAGGTCCCGAGGCCTCCCTAGAGCCTGGGGCCGACTCTGTGTCGAT	TCCCTCCTTACAGGTCCCGAGGCCTCCCTAGAGCCTGGGGCCGACTCTGTGTCGAT	-	novel	NA	P-0063556-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	127	346	0	ENST00000377604.3:c.1436-13_1478del		p.X479_splice	ENST00000377604	NM_001204468.1	479		14/24	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.688611069882554	1		346	201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	239	547	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.218956457048107	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.355992539410512	2		548	645	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	280	523	0				ENST00000310581	NM_198253.2	-/1132			0.355992539410512	5	FACETS	0.904	0.856	0.954			1	CLONAL	4	TRUE	NA	0.355992539410512	5		523	667	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1721920	1721920	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	125	679	0	ENST00000378609.4:c.613G>A	p.Asp205Asn	p.D205N	ENST00000378609	NM_002074.3	205	Gat/Aat	9/12	0.3451735239036	3	FACETS	1	0.937	1	0.349	0.315	0.384	CLONAL	1	TRUE	0	0.355992539410512	3		679	791	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28601351	28601351	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	116	693	0	ENST00000253063.3:c.1036G>C	p.Asp346His	p.D346H	ENST00000253063	NM_031459.4	346	Gac/Cac	8/10	0.3451735239036	3	FACETS	1	0.91	1	0.337	0.303	0.372	CLONAL	1	TRUE	0	0.355992539410512	3		693	760	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28601387	28601387	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	117	721	0	ENST00000253063.3:c.1072G>A	p.Glu358Lys	p.E358K	ENST00000253063	NM_031459.4	358	Gag/Aag	8/10	0.3451735239036	3	FACETS	0.957	0.863	1	0.319	0.287	0.353	CLONAL	1	TRUE	0	0.355992539410512	3		721	809	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363243	40363243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	79	770	0	ENST00000397332.2:c.986C>T	p.Ser329Leu	p.S329L	ENST00000397332	NM_001033082.2	329	tCg/tTg	3/3	0.3451735239036	3	FACETS	0.679	0.596	0.768	0.226	0.198	0.256	SUBCLONAL	1	TRUE	0	0.355992539410512	3		770	770	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366994	40366994	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	121	842	0	ENST00000397332.2:c.203C>G	p.Ser68Trp	p.S68W	ENST00000397332	NM_001033082.2	68	tCg/tGg	2/3	0.3451735239036	3	FACETS	0.9	0.812	0.992	0.3	0.27	0.331	CLONAL	1	TRUE	0	0.355992539410512	3		842	890	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335050	65335050	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	82	542	0	ENST00000342505.4:c.591C>G	p.Ile197Met	p.I197M	ENST00000342505	NM_002227.2	197	atC/atG	6/25	0.258203105543628	2	FACETS	0.835	0.737	0.938	0.417	0.368	0.469	CLONAL	1	TRUE	0	0.355992539410512	2		542	552	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729669	162729669	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	96	644	0	ENST00000367921.3:c.755C>A	p.Pro252His	p.P252H	ENST00000367921	NM_006182.2	252	cCc/cAc	8/18	0.355992539410512	5	FACETS	0.804	0.715	0.9	0.268	0.238	0.3	CLONAL	1	TRUE	2	0.355992539410512	5		644	1029	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983095	201983095	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	137	642	0	ENST00000359651.3:c.944G>T	p.Trp315Leu	p.W315L	ENST00000359651		315	tGg/tTg	7/8	0.355992539410512	2	FACETS	1	0.952	1	0.534	0.486	0.584	CLONAL	1	TRUE	0	0.355992539410512	2		642	721	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984354	201984355	+	missense_variant	Missense_Mutation	DNP	AG	AG	TA	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	177	600	0	ENST00000359651.3:c.1019_1020delinsTA	p.Glu340Val	p.E340V	ENST00000359651		340	gAG/gTA	8/8	0.355992539410512	2	FACETS	0.806	0.746	0.867	0.806	0.746	0.867	CLONAL	2	TRUE	0	0.355992539410512	2		600	617	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201691	67201691	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	131	895	0	ENST00000312629.5:c.992T>A	p.Met331Lys	p.M331K	ENST00000312629	NM_003952.2	331	aTg/aAg	12/15	0.355992539410512	3	FACETS	1	0.949	1	0.533	0.484	0.585	CLONAL	1	TRUE	1	0.355992539410512	3		895	813	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77091025	77091025	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	85	549	0	ENST00000356341.3:c.205G>C	p.Glu69Gln	p.E69Q	ENST00000356341	NM_002576.4	69	Gag/Cag	3/15	0.355992539410512	3	FACETS	0.989	0.876	1	0.494	0.438	0.555	CLONAL	1	TRUE	1	0.355992539410512	3		549	569	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933480	100933480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766277966	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	49	448	0	ENST00000325455.5:c.1910G>A	p.Arg637Gln	p.R637Q	ENST00000325455	NM_001202474.3	637	cGa/cAa	4/8	0.330135519899098	2	FACETS	0.793	0.675	0.923	0.397	0.337	0.462	CLONAL	1	TRUE	0	0.355992539410512	2		448	347	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102198836	102198836	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	75	476	0	ENST00000263464.3:c.1007C>A	p.Ala336Asp	p.A336D	ENST00000263464	NM_001165.4	336	gCc/gAc	4/9	0.330135519899098	2	FACETS	1	0.947	1	0.568	0.501	0.639	CLONAL	1	TRUE	0	0.355992539410512	2		476	371	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158432	108158432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	83	401	0	ENST00000278616.4:c.4099G>A	p.Asp1367Asn	p.D1367N	ENST00000278616	NM_000051.3	1367	Gac/Aac	27/63	0.330135519899098	2	FACETS	1	0.965	1	0.61	0.542	0.682	CLONAL	1	TRUE	0	0.355992539410512	2		401	382	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186751	108186751	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1448711296	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	113	613	0	ENST00000278616.4:c.6109G>A	p.Glu2037Lys	p.E2037K	ENST00000278616	NM_000051.3	2037	Gaa/Aaa	42/63	0.330135519899098	2	FACETS	1	0.969	1	0.59	0.533	0.65	CLONAL	1	TRUE	0	0.355992539410512	2		613	538	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343529	118343529	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	217	762	0	ENST00000534358.1:c.1660del	p.Gln554SerfsTer13	p.Q554Sfs*13	ENST00000534358	NM_005933.3	552	gCc/gc	3/36	0.330135519899098	2	FACETS	0.928	0.867	0.99	0.928	0.867	0.99	CLONAL	2	TRUE	0	0.355992539410512	2		762	657	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215725	133215725	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	32	594	0	ENST00000320574.5:c.5538G>C	p.Lys1846Asn	p.K1846N	ENST00000320574	NM_006231.2	1846	aaG/aaC	40/49	0.261738768305734	2	FACETS	0.363	0.294	0.441	0.182	0.147	0.221	SUBCLONAL	1	TRUE	0	0.355992539410512	2		594	495	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912039	32912039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	200	663	0	ENST00000380152.3:c.3547G>A	p.Glu1183Lys	p.E1183K	ENST00000380152		1183	Gaa/Aaa	11/27	0.355992539410512	3	FACETS	0.998	0.929	1	0.998	0.929	1	CLONAL	2	TRUE	1	0.355992539410512	3		663	663	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913908	32913908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	168	594	0	ENST00000380152.3:c.5416G>A	p.Glu1806Lys	p.E1806K	ENST00000380152		1806	Gaa/Aaa	11/27	0.355992539410512	3	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	1	0.355992539410512	3		594	545	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914187	32914187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371189402	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	139	582	0	ENST00000380152.3:c.5695G>A	p.Asp1899Asn	p.D1899N	ENST00000380152		1899	Gat/Aat	11/27	0.355992539410512	3	FACETS	0.881	0.807	0.958	0.881	0.807	0.958	CLONAL	2	TRUE	1	0.355992539410512	3		582	522	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914827	32914827	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	169	625	0	ENST00000380152.3:c.6335G>C	p.Arg2112Thr	p.R2112T	ENST00000380152		2112	aGa/aCa	11/27	0.355992539410512	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.355992539410512	3		625	493	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353742	68353742	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	59	420	0	ENST00000487270.1:c.577G>A	p.Glu193Lys	p.E193K	ENST00000487270	NM_133509.3	193	Gaa/Aaa	7/11	0.266061054307527	3	FACETS	0.936	0.808	1	0.468	0.404	0.538	CLONAL	1	TRUE	1	0.355992539410512	3		420	417	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636726	2636726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	124	733	0	ENST00000342085.4:c.1175C>T	p.Ser392Phe	p.S392F	ENST00000342085	NM_002613.4	392	tCc/tTc	11/14	0.355992539410512	3	FACETS	1	0.948	1	0.535	0.484	0.589	CLONAL	1	TRUE	1	0.355992539410512	3		733	767	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846048	68846048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61747631	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	83	655	0	ENST00000261769.5:c.1019C>T	p.Thr340Met	p.T340M	ENST00000261769	NM_004360.3	340	aCg/aTg	8/16	0.184199788363304	4	FACETS	0.948	0.837	1	0.474	0.418	0.534	INDETERMINATE	1	TRUE	2	0.355992539410512	4		655	667	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998913	11998913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1371329502	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	156	420	1	ENST00000353533.5:c.415G>A	p.Glu139Lys	p.E139K	ENST00000353533	NM_003010.3	139	Gaa/Aaa	4/11	0.218956457048107	2	FACETS	0.911	0.841	0.983	0.911	0.841	0.983	CLONAL	2	TRUE	0	0.355992539410512	2		421	481	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627509	37627509	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	218	590	0	ENST00000447079.4:c.1424C>G	p.Ser475Cys	p.S475C	ENST00000447079	NM_015083.1	475	tCt/tGt	2/14	0.355992539410512	5	FACETS	1	0.937	1	0.503	0.468	0.54	CLONAL	2	TRUE	1	0.355992539410512	5		590	933	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	495	589	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.355992539410512	5	FACETS	0.931	0.897	0.965	1	0.994	1	CLONAL	5	TRUE	1	0.355992539410512	5		589	916	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879592	37879592	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	324	763	0	ENST00000269571.5:c.1967C>T	p.Ser656Phe	p.S656F	ENST00000269571		656	tCt/tTt	17/27	0.355992539410512	5	FACETS	1	0.991	1	0.618	0.584	0.653	CLONAL	2	TRUE	1	0.355992539410512	5		763	1130	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883249	37883249	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	264	649	0	ENST00000269571.5:c.3152C>G	p.Ser1051Cys	p.S1051C	ENST00000269571		1051	tCt/tGt	25/27	0.355992539410512	5	FACETS	1	0.989	1	0.611	0.573	0.649	CLONAL	2	TRUE	1	0.355992539410512	5		649	931	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55754388	55754388	+	stop_lost	Nonstop_Mutation	SNP	G	G	T	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	60	422	0	ENST00000284073.2:c.986G>T	p.Ter329LeuextTer10	p.*329Lext*10	ENST00000284073	NM_138962.2	329	tGa/tTa	13/14	0.355992539410512	3	FACETS	0.744	0.641	0.855	0.248	0.213	0.285	SUBCLONAL	1	TRUE	0	0.355992539410512	3		422	534	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56413007	56413007	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	78	499	0	ENST00000348428.3:c.2021C>T	p.Ser674Leu	p.S674L	ENST00000348428	NM_006785.3	674	tCa/tTa	16/17	0.355992539410512	2	FACETS	1	0.887	1	0.503	0.443	0.566	CLONAL	1	TRUE	0	0.355992539410512	2		499	436	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61305078	61305078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1450083629	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	116	716	0	ENST00000341074.5:c.1048G>A	p.Val350Ile	p.V350I	ENST00000341074	NM_002974.2	350	Gta/Ata	8/8	0.355992539410512	2	FACETS	1	0.956	1	0.55	0.497	0.606	CLONAL	1	TRUE	0	0.355992539410512	2		716	592	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210435	2210435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866975812	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	84	677	2	ENST00000398665.3:c.1042G>A	p.Glu348Lys	p.E348K	ENST00000398665	NM_032482.2	348	Gag/Aag	13/28	0.3451735239036	3	FACETS	0.762	0.672	0.857	0.254	0.224	0.286	SUBCLONAL	1	TRUE	0	0.355992539410512	3		679	730	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274335	5274335	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	113	602	0	ENST00000357368.4:c.112G>C	p.Glu38Gln	p.E38Q	ENST00000357368	NM_002850.3	38	Gaa/Caa	3/38	0.3451735239036	3	FACETS	1	0.952	1	0.365	0.329	0.403	CLONAL	1	TRUE	0	0.355992539410512	3		602	683	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627485	14627485	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	88	510	0	ENST00000254322.2:c.585G>C	p.Lys195Asn	p.K195N	ENST00000254322	NM_006145.1	195	aaG/aaC	2/3	0.3451735239036	3	FACETS	0.845	0.749	0.948	0.282	0.249	0.316	CLONAL	1	TRUE	0	0.355992539410512	3		510	689	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627564	14627564	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	102	623	0	ENST00000254322.2:c.506G>C	p.Arg169Pro	p.R169P	ENST00000254322	NM_006145.1	169	cGa/cCa	2/3	0.3451735239036	3	FACETS	0.918	0.822	1	0.306	0.274	0.341	CLONAL	1	TRUE	0	0.355992539410512	3		623	735	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39214691	39214691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs727505383	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	71	383	0	ENST00000402219.2:c.3433G>A	p.Asp1145Asn	p.D1145N	ENST00000402219	NM_005633.3	1145	Gat/Aat	22/23	0.355992539410512	3	FACETS	1	0.926	1	0.54	0.473	0.612	CLONAL	1	TRUE	1	0.355992539410512	3		383	435	SUCCESS
REL	5966	MSKCC	GRCh37	2	61148963	61148963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	217	612	0	ENST00000295025.8:c.1153G>A	p.Glu385Lys	p.E385K	ENST00000295025	NM_002908.2	385	Gaa/Aaa	11/11	0.355992539410512	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.355992539410512	3		612	629	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721201	61721201	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	71	496	0	ENST00000401558.2:c.1073C>T	p.Ser358Phe	p.S358F	ENST00000401558	NM_003400.3	358	tCt/tTt	12/25	0.355992539410512	3	FACETS	0.977	0.855	1	0.488	0.427	0.554	CLONAL	1	TRUE	1	0.355992539410512	3		496	481	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439988	220439988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1341715949	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	188	791	0	ENST00000243786.2:c.841G>A	p.Val281Met	p.V281M	ENST00000243786	NM_002191.3	281	Gtg/Atg	2/2	0.355992539410512	3	FACETS	0.919	0.852	0.987	0.919	0.852	0.987	CLONAL	2	TRUE	1	0.355992539410512	3		791	677	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292768	62292768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140042227	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	45	705	0	ENST00000360203.5:c.220G>A	p.Glu74Lys	p.E74K	ENST00000360203	NM_001283009.1	74	Gag/Aag	3/35	0.184199788363304	4	FACETS	0.421	0.353	0.497	0.211	0.176	0.249	INDETERMINATE	1	TRUE	2	0.355992539410512	4		705	814	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143154	24143154	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	86	714	0	ENST00000263121.7:c.386G>C	p.Ser129Thr	p.S129T	ENST00000263121	NM_003073.3	129	aGc/aCc	4/9	0.355992539410512	4	FACETS	0.637	0.562	0.717	0.212	0.187	0.239	SUBCLONAL	1	TRUE	1	0.355992539410512	4		714	1029	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927376	49927376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561814812	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	124	829	0	ENST00000296474.3:c.3928G>A	p.Glu1310Lys	p.E1310K	ENST00000296474	NM_002447.2	1310	Gag/Aag	19/20	0.24435237441938	4	FACETS	1	0.963	1	0.566	0.511	0.623	CLONAL	1	TRUE	2	0.355992539410512	4		829	835	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448627	89448627	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	88	567	0	ENST00000336596.2:c.1591G>C	p.Asp531His	p.D531H	ENST00000336596	NM_005233.5	531	Gac/Cac	7/17	0.348994190044585	3	FACETS	0.989	0.877	1	0.494	0.438	0.554	CLONAL	1	TRUE	1	0.355992539410512	3		567	589	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177849	142177849	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	119	476	0	ENST00000350721.4:c.7454C>G	p.Ser2485Cys	p.S2485C	ENST00000350721	NM_001184.3	2485	tCt/tGt	44/47	0.186626059004849	5	FACETS	0.99	0.898	1	0.66	0.598	0.724	INDETERMINATE	2	TRUE	2	0.355992539410512	5		476	518	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532843	187532843	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	49	532	0	ENST00000441802.2:c.9550G>C	p.Glu3184Gln	p.E3184Q	ENST00000441802	NM_005245.3	3184	Gaa/Caa	14/27	0.258203105543628	2	FACETS	0.494	0.418	0.578	0.247	0.209	0.289	SUBCLONAL	1	TRUE	0	0.355992539410512	2		532	557	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31451748	31451748	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs768758559	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	56	375	1	ENST00000344624.3:c.2575-1G>T		p.X859_splice	ENST00000344624		859			0.355992539410512	6	FACETS	0.93	0.797	1	0.233	0.199	0.269	CLONAL	1	TRUE	2	0.355992539410512	6		376	579	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915159	131915159	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	74	396	0	ENST00000265335.6:c.516G>C	p.Leu172Phe	p.L172F	ENST00000265335		172	ttG/ttC	4/25	0.348994190044585	3	FACETS	1	0.947	1	0.571	0.502	0.645	CLONAL	1	TRUE	1	0.355992539410512	3		396	429	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176516682	176516682	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	74	484	0	ENST00000292408.4:c.79G>T	p.Glu27Ter	p.E27*	ENST00000292408	NM_213647.1	27	Gaa/Taa	2/18	1	2	FACETS	0.82	0.719	0.928	0.82	0.719	0.928	CLONAL	1	TRUE	1	0.355992539410512	2		484	507	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720911	176720911	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	106	679	0	ENST00000439151.2:c.6542C>G	p.Ser2181Cys	p.S2181C	ENST00000439151	NM_022455.4	2181	tCc/tGc	23/23	1	2	FACETS	0.859	0.771	0.953	0.859	0.771	0.953	CLONAL	1	TRUE	1	0.355992539410512	2		679	693	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721105	176721105	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	91	696	0	ENST00000439151.2:c.6736C>G	p.Gln2246Glu	p.Q2246E	ENST00000439151	NM_022455.4	2246	Cag/Gag	23/23	1	2	FACETS	0.683	0.607	0.766	0.683	0.607	0.766	SUBCLONAL	1	TRUE	1	0.355992539410512	2		696	748	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680064	30680065	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	124	781	0	ENST00000376406.3:c.1654_1655del	p.Asp552CysfsTer26	p.D552Cfs*26	ENST00000376406	NM_014641.2	552	GAt/t	5/15	0.266061054307527	3	FACETS	0.938	0.848	1	0.469	0.424	0.517	CLONAL	1	TRUE	1	0.355992539410512	3		781	875	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415567	152415567	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	94	593	0	ENST00000206249.3:c.1417G>A	p.Asp473Asn	p.D473N	ENST00000206249	NM_000125.3	473	Gac/Aac	7/8	1	2	FACETS	0.874	0.779	0.975	0.874	0.779	0.975	CLONAL	1	TRUE	1	0.355992539410512	2		593	604	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467631	50467631	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	71	570	0	ENST00000331340.3:c.866C>G	p.Ser289Cys	p.S289C	ENST00000331340	NM_006060.4	289	tCc/tGc	8/8	0.266061054307527	3	FACETS	0.809	0.706	0.919	0.404	0.353	0.46	CLONAL	1	TRUE	1	0.355992539410512	3		570	581	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481451	140481451	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs754904100	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	52	476	0	ENST00000288602.6:c.1357C>G	p.Pro453Ala	p.P453A	ENST00000288602	NM_004333.4	453	Cct/Gct	11/18	0.186626059004849	5	FACETS	0.767	0.653	0.893	0.256	0.217	0.298	INDETERMINATE	1	TRUE	2	0.355992539410512	5		476	584	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56882345	56882345	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	84	580	0	ENST00000519728.1:c.1043C>A	p.Ser348Tyr	p.S348Y	ENST00000519728	NM_002350.3	348	tCt/tAt	10/13	0.195442332008441	5	FACETS	1	0.889	1	0.336	0.296	0.378	INDETERMINATE	1	TRUE	2	0.355992539410512	5		580	719	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741168	145741168	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	116	713	0	ENST00000428558.2:c.1238C>A	p.Ala413Glu	p.A413E	ENST00000428558	NM_004260.3	413	gCa/gAa	6/22	0.195442332008441	5	FACETS	1	0.963	1	0.382	0.344	0.423	INDETERMINATE	1	TRUE	2	0.355992539410512	5		713	872	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771798	135771798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060503226	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	109	780	0	ENST00000298552.3:c.3319G>A	p.Asp1107Asn	p.D1107N	ENST00000298552	NM_001162426.1	1107	Gac/Aac	23/23	0.355992539410512	3	FACETS	1	0.93	1	0.522	0.469	0.578	CLONAL	1	TRUE	1	0.355992539410512	3		780	691	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772856	135772856	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	127	607	0	ENST00000298552.3:c.2767C>G	p.Leu923Val	p.L923V	ENST00000298552	NM_001162426.1	923	Ctt/Gtt	21/23	0.355992539410512	3	FACETS	1	0.973	1	0.598	0.542	0.656	CLONAL	1	TRUE	1	0.355992539410512	3		607	703	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040712	47040713	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	191	342	0	ENST00000377604.3:c.1349_1350del	p.Thr450ArgfsTer67	p.T450Rfs*67	ENST00000377604	NM_001204468.1	449	ggCAca/ggca	13/24	0.24151870164367	2	FACETS	0.975	0.917	1			1	CLONAL	3	TRUE	NA	0.355992539410512	2		342	367	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205158	123205158	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	23	242	0	ENST00000218089.9:c.2518G>C	p.Asp840His	p.D840H	ENST00000218089	NM_001042749.1	840	Gat/Cat	25/35	1	1	FACETS	0.681	0.536	0.845	0.681	0.536	0.845	SUBCLONAL	1	TRUE	0	0.355992539410512	1		242	156	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0063562-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	131	466	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	1	2	FACETS	0.988	0.911	1	0.988	0.911	1	CLONAL	1	TRUE	1	0.861057733726697	2		466	308	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913514	NA	P-0063562-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	126	452	0	ENST00000288135.5:c.2466T>G	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaG	17/21	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.861057733726697	2		452	284	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562637	21562637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758639228	NA	P-0063562-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	89	472	1	ENST00000382592.4:c.1282G>A	p.Ala428Thr	p.A428T	ENST00000382592	NM_014572.2	428	Gcc/Acc	4/8	1	2	FACETS	0.903	0.815	0.992	0.903	0.815	0.992	CLONAL	1	TRUE	1	0.861057733726697	2		473	229	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741951	40741951	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063562-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	31	850	0	ENST00000392038.2:c.1021T>C	p.Tyr341His	p.Y341H	ENST00000392038	NM_001626.4	341	Tac/Cac	11/14	1	2	FACETS	0.199	0.161	0.243	0.199	0.161	0.243	SUBCLONAL	1	TRUE	1	0.861057733726697	2		850	361	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0063563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	18	372	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.644	0.486	0.829	0.644	0.486	0.829	SUBCLONAL	1	TRUE	1	0.27	2		372	207	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	17	523	0				ENST00000310581	NM_198253.2	-/1132			0.141510009497048	1	FACETS	0.589	0.441	0.763	0.589	0.441	0.763	INDETERMINATE	1	TRUE	0	0.27	1		523	185	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790123	40790123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757562149	NA	P-0063563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	14	617	0	ENST00000373198.4:c.2608C>T	p.Arg870Cys	p.R870C	ENST00000373198	NM_133170.3	870	Cgc/Tgc	18/32	0.3	0	FACETS	0.297	0.214	0.397			1	SUBCLONAL	1	TRUE	0	0.27	0		617	255	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361128	70361128	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	24	450	0	ENST00000374080.3:c.6316C>T	p.Gln2106Ter	p.Q2106*	ENST00000374080		2106	Cag/Tag	43/45	1	1	FACETS	0.572	0.449	0.712	0.572	0.449	0.712	SUBCLONAL	1	TRUE	0	0.27	1		450	269	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	9	414	0	ENST00000371953.3:c.511C>G	p.Gln171Glu	p.Q171E	ENST00000371953	NM_000314.4	171	Cag/Gag	6/9	1	2	FACETS	0.294	0.194	0.421	0.294	0.194	0.421	SUBCLONAL	1	TRUE	1	0.27	2		414	227	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543943	41543952	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TCAACCCGGT	TCAACCCGGT	-	novel	NA	P-0063563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	21	490	0	ENST00000263253.7:c.2235_2241+3del		p.X745_splice	ENST00000263253	NM_001429.3	745		12/31	1	2	FACETS	0.542	0.418	0.687	0.542	0.418	0.687	SUBCLONAL	1	TRUE	1	0.27	2		490	287	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971163	21971164	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0063563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	15	643	0	ENST00000304494.5:c.194_195del	p.Leu65ProfsTer54	p.L65Pfs*54	ENST00000304494	NM_000077.4	65	cTC/c	2/3	0.141510009497048	1	FACETS	0.4	0.293	0.53	0.4	0.293	0.53	INDETERMINATE	1	TRUE	0	0.27	1		643	240	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0063564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	89	331	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.425225292856452	4	FACETS	1	0.972	1	0.641	0.572	0.713	CLONAL	1	FALSE	2	0.564630802895872	4		331	385	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0063564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	14	504	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	0.188998352529379	4	FACETS	0.22	0.158	0.295	0.073	0.052	0.099	INDETERMINATE	1	FALSE	1	0.564630802895872	4		504	353	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256780	133256780	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	35	384	0	ENST00000320574.5:c.314A>C	p.Tyr105Ser	p.Y105S	ENST00000320574	NM_006231.2	105	tAc/tCc	4/49	1	2	FACETS	0.477	0.393	0.57	0.477	0.393	0.57	SUBCLONAL	1	FALSE	1	0.564630802895872	2		384	260	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231736	66231736	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	62	307	0	ENST00000273854.3:c.1964C>A	p.Thr655Asn	p.T655N	ENST00000273854	NM_004439.5	655	aCc/aAc	11/18	0.119441749886639	5	FACETS	1	0.955	1	0.412	0.358	0.47	INDETERMINATE	1	FALSE	2	0.564630802895872	5		307	328	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0063564-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	58	331	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.888	0.766	1	0.888	0.766	1	CLONAL	1	TRUE	1	0.347450943039496	2		331	376	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0063564-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	58	504	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	0.209128410463341	1	FACETS	0.499	0.429	0.575	0.499	0.429	0.575	SUBCLONAL	1	TRUE	0	0.347450943039496	1		504	553	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256780	133256780	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063564-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	50	384	0	ENST00000320574.5:c.314A>C	p.Tyr105Ser	p.Y105S	ENST00000320574	NM_006231.2	105	tAc/tCc	4/49	0.209128410463341	1	FACETS	0.445	0.377	0.519	0.445	0.377	0.519	SUBCLONAL	1	TRUE	0	0.347450943039496	1		384	535	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231736	66231736	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063564-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	57	307	0	ENST00000273854.3:c.1964C>A	p.Thr655Asn	p.T655N	ENST00000273854	NM_004439.5	655	aCc/aAc	11/18	1	2	FACETS	0.833	0.717	0.958	0.833	0.717	0.958	CLONAL	1	TRUE	1	0.347450943039496	2		307	394	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443695	29443695	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs863225281	NA	P-0063575-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	269	575	0	ENST00000389048.3:c.3522C>A	p.Phe1174Leu	p.F1174L	ENST00000389048	NM_004304.4	1174	ttC/ttA	23/29	1	2	FACETS	0.927	0.873	0.982	0.927	0.873	0.982	CLONAL	1	TRUE	1	0.738001457802742	2		575	786	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0063592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	249	362	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.712502389857355	4	FACETS	0.999	0.942	1	0.999	0.942	1	CLONAL	2	TRUE	2	0.712502389857355	4		362	599	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206667312	206667312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781860835	NA	P-0063592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	123	474	2	ENST00000367120.3:c.2105G>A	p.Arg702His	p.R702H	ENST00000367120	NM_014002.3	702	cGc/cAc	21/22	0.712502389857355	4	FACETS	0.924	0.837	1	0.308	0.279	0.339	CLONAL	1	TRUE	1	0.712502389857355	4		476	640	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465943	69465943	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	317	563	0	ENST00000227507.2:c.781C>T	p.Gln261Ter	p.Q261*	ENST00000227507	NM_053056.2	261	Cag/Tag	5/5	0.712502389857355	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.712502389857355	4		563	753	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514098	69514098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762938267	NA	P-0063592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	155	553	0	ENST00000294312.3:c.583G>A	p.Asp195Asn	p.D195N	ENST00000294312	NM_005117.2	195	Gac/Aac	3/3	0.712502389857355	4	FACETS	0.988	0.906	1	0.494	0.453	0.537	CLONAL	1	TRUE	2	0.712502389857355	4		553	754	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180982	108180982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781963	NA	P-0063592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	152	315	0	ENST00000278616.4:c.5858C>T	p.Thr1953Ile	p.T1953I	ENST00000278616	NM_000051.3	1953	aCa/aTa	39/63	1	2	FACETS	0.985	0.91	1	0.985	0.91	1	CLONAL	1	TRUE	1	0.712502389857355	2		315	433	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778652	3778687	+	inframe_deletion	In_Frame_Del	DEL	GCCAGGCTGGGGTTGCATGCCGGGCTGGGACTGGAG	GCCAGGCTGGGGTTGCATGCCGGGCTGGGACTGGAG	-	rs761028983	NA	P-0063592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	109	592	0	ENST00000262367.5:c.6361_6396del	p.Leu2121_Gly2132del	p.L2121_G2132del	ENST00000262367	NM_004380.2	2121	CTCCAGTCCCAGCCCGGCATGCAACCCCAGCCTGGC/-	31/31	0.712502389857355	1	FACETS	0.788	0.721	0.855	0.788	0.721	0.855	SUBCLONAL	1	TRUE	0	0.712502389857355	1		592	250	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913315	NA	P-0063592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	428	555	0	ENST00000326873.7:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000326873	NM_000455.4	194	Gac/Tac	4/10	0.712502389857355	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	0	0.712502389857355	3		555	531	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439494	220439494	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	279	614	0	ENST00000243786.2:c.347G>T	p.Arg116Leu	p.R116L	ENST00000243786	NM_002191.3	116	cGg/cTg	2/2	0.712502389857355	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.712502389857355	2		614	363	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376760	31376760	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs754201724	NA	P-0063592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	242	464	0	ENST00000328111.2:c.755G>T	p.Arg252Leu	p.R252L	ENST00000328111	NM_006892.3	252	cGa/cTa	7/23	0.712502389857355	3	FACETS	0.972	0.92	1	0.972	0.92	1	CLONAL	2	TRUE	1	0.712502389857355	3		464	474	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967317	134967317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868241569	NA	P-0063592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	155	495	2	ENST00000398015.3:c.2656G>A	p.Ala886Thr	p.A886T	ENST00000398015	NM_004441.4	886	Gca/Aca	14/16	0.712502389857355	2	FACETS	1	0.933	1	0.505	0.466	0.544	CLONAL	1	TRUE	0	0.712502389857355	2		497	431	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202221	108202221	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	GT	novel	NA	P-0063592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	130	327	0	ENST00000278616.4:c.7566delinsGT	p.Leu2523PhefsTer4	p.L2523Ffs*4	ENST00000278616	NM_000051.3	2522	caA/caGT	51/63	1	2	FACETS	0.875	0.801	0.952	0.875	0.801	0.952	CLONAL	1	TRUE	1	0.712502389857355	2		327	417	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134170	41134170	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121578-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	272	488	0	ENST00000379561.5:c.1458G>T	p.Gln486His	p.Q486H	ENST00000379561	NM_002015.3	486	caG/caT	2/3	1	2	FACETS	0.993	0.941	1	0.993	0.941	1	CLONAL	1	NA	1	0.923585988446013	2		488	593	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644579	3644579	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121578-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	239	529	0	ENST00000294008.3:c.2035G>T	p.Ala679Ser	p.A679S	ENST00000294008	NM_032444.2	679	Gct/Tct	10/15	1	2	FACETS	0.96	0.905	1	0.96	0.905	1	CLONAL	1	NA	1	0.923585988446013	2		529	539	SUCCESS
AR	367	MSKCC	GRCh37	X	66931328	66931328	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0121578-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	78	494	0	ENST00000374690.3:c.1970C>G	p.Thr657Ser	p.T657S	ENST00000374690	NM_000044.3	657	aCc/aGc	4/8	1	2	FACETS	0.307	0.27	0.347	0.307	0.27	0.347	SUBCLONAL	1	NA	1	0.923585988446013	2		494	550	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0063594-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	24	600	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		600	455	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038830	47038831	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0063594-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	31	497	0	ENST00000377604.3:c.837_838delinsTT	p.Gln279_Gly280delinsHisTer	p.Q279_G280delinsH*	ENST00000377604	NM_001204468.1	279	caGGga/caTTga	9/24	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		497	566	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0063595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	71	728	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.852	0.746	0.967	0.852	0.746	0.967	CLONAL	1	TRUE	1	0.34	2		728	490	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0063595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	15	482	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.162	0.117	0.215	0.162	0.117	0.215	SUBCLONAL	1	TRUE	1	0.34	2		482	546	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0063595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	121	657	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.913	0.825	1	0.913	0.825	1	CLONAL	1	TRUE	1	0.34	2		657	780	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094488	27094488	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	97	570	0	ENST00000324856.7:c.3196C>T	p.Gln1066Ter	p.Q1066*	ENST00000324856	NM_006015.4	1066	Cag/Tag	11/20	1	2	FACETS	0.825	0.735	0.919	0.825	0.735	0.919	CLONAL	1	TRUE	1	0.34	2		570	692	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169221	119169221	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	128	588	0	ENST00000264033.4:c.2405G>A	p.Trp802Ter	p.W802*	ENST00000264033	NM_005188.3	802	tGg/tAg	15/16	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.34	2		588	745	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579415	7579415	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063596-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	278	692	0	ENST00000269305.4:c.272G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tGg/tAg	4/11	0.345500853458888	2	FACETS	0.939	0.884	0.994	0.939	0.884	0.994	CLONAL	2	TRUE	0	0.345500853458888	2		692	857	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001231	150001231	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063596-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	64	436	0	ENST00000253339.5:c.2373G>C	p.Met791Ile	p.M791I	ENST00000253339		791	atG/atC	4/7	0.167205728191416	3	FACETS	1	0.916	1	0.536	0.466	0.612	INDETERMINATE	1	TRUE	1	0.345500853458888	3		436	405	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622307	1623329	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTACCTGCCACGTAGAAGGGGGCGGGATAGGTGCTGCTGGGGGTCTTGGCGGACGGGTAGGCGGTGGCATCCCTGCCGTAGTCCTCACCTGAGCTGGGTGGGTACACCTGCGGGCGGGTGGGCGGTGGGGGGTGCAGTCAGGACGGAGGGACCACGATCAGCCCATGCACCTTGCCGGCCTCCTGTCCCCTCCTGGTAGCACATCTACCACCCCGTTTCCCTTCCCTGTAAAGCCACCCCCCTTTAGGTAAATCCCAGCCCCTGGCCAAGTTTGAGGTTCTTATGATGTCCTGGTCTCTCTCTCCTACTCCTTTTCCAGCCCCCACCTCCCGCCTCCCTGAACTTCTGACCTTTGTACTTGAGGACTTGGATCTGGCTCTGCCTACTAAACCTTTTTCCTCCTTAATCCAGAAAACTCCTATCGACCCATCAAAACCCCAGCTCCAACACCCCATCCCATCCTTCTCCCTTGTTCCCCAGCTGGAATCAATCTTCCAGTGCTGAGCTTCCCTTGGTCCCAGAGCAACATTCGTCCTTCACTAAAGTAACAGGAAGAGGGGTCTGTGAGTAGCGCCAGCTCTGACTGGTTGGCACTGCCTGGACTGTGGGGCTGGGGCCTGTTGGTAACGTCTGCTGCTGTGCTGGAGCGGGAAGTATGCTGGGTGGGCCTGATGTTGTAATAAACTGGGGGGCGGTTTCAGGGCAGAGAAAGTGCACCCTGGGGAAGGAGGGGAGTGAGTGATACTGTTGGGAGCAGAGCCTGACCACGCCTTTGGCCTGGGAAGTCAACCTGACTCTAACCCCGAACCCAGGCCTGTGGGGAGCTGGTCGGCTGGAGGGGTGAGGAGATGTATGCCCAGGGCTCTTGGGGCCAGCACAGGCACTGGGCAGAGGGTGGTTGGTGGCTACTGAGCCAGGGAATCGGCAAATTCCCTCTCCCTCCAGCGAGATGAGACCGCAGGAGTGTGGCACAGCAGCCTGGACCATCTGCGAGGCCTGGTAGGGAGGCAGGGATGCGGGGC	TGTACCTGCCACGTAGAAGGGGGCGGGATAGGTGCTGCTGGGGGTCTTGGCGGACGGGTAGGCGGTGGCATCCCTGCCGTAGTCCTCACCTGAGCTGGGTGGGTACACCTGCGGGCGGGTGGGCGGTGGGGGGTGCAGTCAGGACGGAGGGACCACGATCAGCCCATGCACCTTGCCGGCCTCCTGTCCCCTCCTGGTAGCACATCTACCACCCCGTTTCCCTTCCCTGTAAAGCCACCCCCCTTTAGGTAAATCCCAGCCCCTGGCCAAGTTTGAGGTTCTTATGATGTCCTGGTCTCTCTCTCCTACTCCTTTTCCAGCCCCCACCTCCCGCCTCCCTGAACTTCTGACCTTTGTACTTGAGGACTTGGATCTGGCTCTGCCTACTAAACCTTTTTCCTCCTTAATCCAGAAAACTCCTATCGACCCATCAAAACCCCAGCTCCAACACCCCATCCCATCCTTCTCCCTTGTTCCCCAGCTGGAATCAATCTTCCAGTGCTGAGCTTCCCTTGGTCCCAGAGCAACATTCGTCCTTCACTAAAGTAACAGGAAGAGGGGTCTGTGAGTAGCGCCAGCTCTGACTGGTTGGCACTGCCTGGACTGTGGGGCTGGGGCCTGTTGGTAACGTCTGCTGCTGTGCTGGAGCGGGAAGTATGCTGGGTGGGCCTGATGTTGTAATAAACTGGGGGGCGGTTTCAGGGCAGAGAAAGTGCACCCTGGGGAAGGAGGGGAGTGAGTGATACTGTTGGGAGCAGAGCCTGACCACGCCTTTGGCCTGGGAAGTCAACCTGACTCTAACCCCGAACCCAGGCCTGTGGGGAGCTGGTCGGCTGGAGGGGTGAGGAGATGTATGCCCAGGGCTCTTGGGGCCAGCACAGGCACTGGGCAGAGGGTGGTTGGTGGCTACTGAGCCAGGGAATCGGCAAATTCCCTCTCCCTCCAGCGAGATGAGACCGCAGGAGTGTGGCACAGCAGCCTGGACCATCTGCGAGGCCTGGTAGGGAGGCAGGGATGCGGGGC	-	novel	NA	P-0063596-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	67	639	0	ENST00000344749.5:c.549+621_652+5del		p.X183_splice	ENST00000344749	NM_001136139.2	183		9/19	0.33007847002013	2	FACETS	0.545	0.473	0.624	0.273	0.236	0.312	SUBCLONAL	1	TRUE	0	0.345500853458888	2		639	711	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0063597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	17	331	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.94	0.705	1	0.94	0.705	1	CLONAL	1	FALSE	1	0.219326829212663	2		331	165	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0063597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	125	654	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.219326829212663	2		654	922	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231488893	231488894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs567805129	NA	P-0063597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	29	417	0	ENST00000295050.7:c.1263dup	p.Ile422TyrfsTer11	p.I422Yfs*11	ENST00000295050	NM_032018.5	419	aat/aaTt	5/5	1	2	FACETS	0.561	0.45	0.689	0.561	0.45	0.689	SUBCLONAL	1	FALSE	1	0.219326829212663	2		417	471	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	18	372	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	0.846	0.648	1	1	0.923	1	CLONAL	2	FALSE	1	0.219326829212663	2		372	97	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247373	153247373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	63	406	0	ENST00000281708.4:c.1429G>A	p.Gly477Ser	p.G477S	ENST00000281708	NM_033632.3	477	Ggt/Agt	10/12	1	2	FACETS	0.747	0.645	0.858	0.747	0.645	0.858	SUBCLONAL	1	FALSE	1	0.219326829212663	2		406	769	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143043366	143043366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199940140	NA	P-0063597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	51	369	0	ENST00000262992.4:c.2050G>A	p.Val684Ile	p.V684I	ENST00000262992	NM_001101669.1	684	Gtt/Att	19/24	1	2	FACETS	0.975	0.83	1	0.975	0.83	1	CLONAL	1	FALSE	1	0.219326829212663	2		369	477	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495330	56495330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	89	579	0	ENST00000267101.3:c.3520G>A	p.Glu1174Lys	p.E1174K	ENST00000267101	NM_001982.3	1174	Gaa/Aaa	28/28	1	2	FACETS	0.706	0.624	0.795	0.706	0.624	0.795	SUBCLONAL	1	FALSE	1	0.219326829212663	2		579	1149	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579554	7579555	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CATCAAAT	novel	NA	P-0063597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	124	586	0	ENST00000269305.4:c.125_132dup	p.Leu45IlefsTer2	p.L45Ifs*2	ENST00000269305	NM_001126112.2	44	-/ATTTGATG	4/11	0.219326829212663	1	FACETS	0.898	0.811	0.991	0.898	0.811	0.991	CLONAL	1	FALSE	0	0.219326829212663	1		586	1121	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117940	70117941	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0063597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	264	571	0	ENST00000245479.2:c.410dup	p.Thr138AspfsTer114	p.T138Dfs*114	ENST00000245479	NM_000346.3	136	-/A	1/3	0.219326829212663	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	FALSE	0	0.219326829212663	2		571	1095	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604667	48604667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762118751	NA	P-0063597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	63	515	0	ENST00000342988.3:c.1489C>T	p.Arg497Cys	p.R497C	ENST00000342988	NM_005359.5	497	Cgc/Tgc	12/12	0.219326829212663	1	FACETS	0.611	0.527	0.703	0.611	0.527	0.703	SUBCLONAL	1	FALSE	0	0.219326829212663	1		515	837	SUCCESS
APC	324	MSKCC	GRCh37	5	112175770	112175771	+	frameshift_variant	Frame_Shift_Ins	INS	GG	GG	AGAAAGCAA	novel	NA	P-0063597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	83	499	0	ENST00000257430.4:c.4479_4480delinsAGAAAGCAA	p.Thr1496LysfsTer20	p.T1496Kfs*20	ENST00000257430	NM_000038.5	1493	acGGaa/acAGAAAGCAAaa	16/16	1	2	FACETS	0.945	0.833	1	0.945	0.833	1	CLONAL	1	FALSE	1	0.219326829212663	2		499	801	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0063598-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	160	515	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.741374022037458	2		515	387	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0063598-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	327	1119	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	0.159182090669241	3	FACETS	0.875	0.833	0.917	0.875	0.833	0.917	INDETERMINATE	2	TRUE	1	0.741374022037458	3		1120	691	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805540	1805540	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057517964	NA	P-0063598-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	264	472	0	ENST00000260795.2:c.1052C>G	p.Ser351Cys	p.S351C	ENST00000260795		351	tCt/tGt	7/17	0.159182090669241	3	FACETS	0.832	0.786	0.877	0.832	0.786	0.877	INDETERMINATE	2	TRUE	1	0.741374022037458	3		472	587	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983049	201983049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063598-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	319	573	0	ENST00000359651.3:c.898G>A	p.Glu300Lys	p.E300K	ENST00000359651		300	Gaa/Aaa	7/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.741374022037458	2		573	759	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652204	36652205	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0063598-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	209	491	0	ENST00000244741.5:c.328dup	p.His110ProfsTer19	p.H110Pfs*19	ENST00000244741	NM_000389.4	109	gac/gaCc	2/3	1	2	FACETS	0.946	0.884	1	0.946	0.884	1	CLONAL	1	TRUE	1	0.741374022037458	2		491	596	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265243	16265243	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063598-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	229	430	0	ENST00000375759.3:c.10735C>G	p.Leu3579Val	p.L3579V	ENST00000375759	NM_015001.2	3579	Ctg/Gtg	14/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.741374022037458	2		430	569	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984371	201984371	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063598-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	313	562	0	ENST00000359651.3:c.1036G>A	p.Asp346Asn	p.D346N	ENST00000359651		346	Gat/Aat	8/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.741374022037458	2		562	804	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966672	25966672	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0063598-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	272	539	0	ENST00000435504.4:c.2534C>G	p.Ser845Ter	p.S845*	ENST00000435504		845	tCa/tGa	13/13	0.657185679328139	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.741374022037458	1		539	417	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675482	30675482	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063598-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	275	620	0	ENST00000376406.3:c.2874G>C	p.Gln958His	p.Q958H	ENST00000376406	NM_014641.2	958	caG/caC	8/15	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.741374022037458	2		620	732	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0063599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	54	210	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.714	0.613	0.824	0.714	0.613	0.824	SUBCLONAL	1	TRUE	1	0.449958731578128	2		210	336	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0063599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	48	405	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.3	0.253	0.352	0.3	0.253	0.352	SUBCLONAL	1	TRUE	1	0.449958731578128	2		405	711	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0063599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	77	362	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.68	0.599	0.768	0.68	0.599	0.768	SUBCLONAL	1	TRUE	1	0.449958731578128	2		362	503	SUCCESS
APC	324	MSKCC	GRCh37	5	112155044	112155044	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	C	rs863225311	NA	P-0063599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	137	366	0	ENST00000257430.4:c.1312+3A>C		p.X438_splice	ENST00000257430	NM_000038.5	438			0.426612101698833	1	FACETS	0.965	0.884	1	0.965	0.884	1	CLONAL	1	TRUE	0	0.449958731578128	1		366	489	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965602	93965602	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	135	456	0	ENST00000369303.4:c.2326G>T	p.Asp776Tyr	p.D776Y	ENST00000369303	NM_004440.3	776	Gat/Tat	13/17	1	2	FACETS	0.969	0.884	1	0.969	0.884	1	CLONAL	1	TRUE	1	0.449958731578128	2		456	619	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870848	12870849	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0063599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	122	517	0	ENST00000228872.4:c.78dup	p.Ser27LeufsTer98	p.S27Lfs*98	ENST00000228872	NM_004064.3	25	-/C	1/3	1	2	FACETS	0.748	0.677	0.823	0.748	0.677	0.823	SUBCLONAL	1	TRUE	1	0.449958731578128	2		517	725	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0063608-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	332	514	0	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	0.35201674130718	3	FACETS	0.889	0.849	0.93	0.889	0.849	0.93	CLONAL	3	TRUE	0	0.481788706291605	3		514	641	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446849	49446849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1204392134	NA	P-0063608-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	193	654	0	ENST00000301067.7:c.961C>T	p.Arg321Trp	p.R321W	ENST00000301067	NM_003482.3	321	Cgg/Tgg	8/54	0.481788706291605	3	FACETS	1	0.975	1	0.374	0.346	0.403	CLONAL	1	TRUE	0	0.481788706291605	3		654	887	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438525	49438525	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0063608-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	100	521	0	ENST00000301067.7:c.4963+2T>G		p.X1655_splice	ENST00000301067	NM_003482.3	1655			0.481788706291605	3	FACETS	0.722	0.646	0.804	0.241	0.215	0.268	SUBCLONAL	1	TRUE	0	0.481788706291605	3		521	713	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56860257	56860257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301994322	NA	P-0063608-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	163	390	0	ENST00000519728.1:c.259G>A	p.Gly87Arg	p.G87R	ENST00000519728	NM_002350.3	87	Gga/Aga	4/13	0.481788706291605	4	FACETS	1	0.986	1	0.449	0.413	0.487	CLONAL	1	TRUE	1	0.481788706291605	4		390	744	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006056	22006056	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs921490761	NA	P-0063608-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	90	673	0	ENST00000276925.6:c.347C>T	p.Pro116Leu	p.P116L	ENST00000276925	NM_004936.3	116	cCc/cTc	2/2	0.481788706291605	5	FACETS	0.532	0.471	0.599	0.177	0.157	0.2	SUBCLONAL	1	TRUE	2	0.481788706291605	5		673	1209	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759595	133759595	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063608-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	97	706	0	ENST00000318560.5:c.1918G>T	p.Asp640Tyr	p.D640Y	ENST00000318560	NM_005157.4	640	Gac/Tac	11/11	0.457701717994989	3	FACETS	0.638	0.569	0.712	0.213	0.189	0.238	SUBCLONAL	1	TRUE	0	0.481788706291605	3		706	783	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579691	7579718	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTCCTTACCAGAACGTTGTTTTCAGGA	TGTCCTTACCAGAACGTTGTTTTCAGGA	-	novel	NA	P-0063609-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	413	400	0	ENST00000269305.4:c.78_96+9del		p.X26_splice	ENST00000269305	NM_001126112.2	26		3/11	0.666161142582506	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.662554570965131	2		400	585	SUCCESS
MTAP	4507	MSKCC	GRCh37	9	21818137	21818137	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063609-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	151	421	0	ENST00000380172.4:c.283T>C	p.Cys95Arg	p.C95R	ENST00000380172	NM_002451.3	95	Tgt/Cgt	4/8	1	2	FACETS	0.528	0.482	0.575	0.528	0.482	0.575	SUBCLONAL	1	TRUE	1	0.662554570965131	2		421	864	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0063610-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	135	372	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.34	2		372	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578393	7578393	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876660821	NA	P-0063611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	313	955	0	ENST00000269305.4:c.537T>G	p.His179Gln	p.H179Q	ENST00000269305	NM_001126112.2	179	caT/caG	5/11	0.433260612105039	2	FACETS	0.951	0.902	1	0.951	0.902	1	CLONAL	2	TRUE	0	0.433260612105039	2		955	760	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591270	67591270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1289880098	NA	P-0063611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	115	643	0	ENST00000274335.5:c.1768C>T	p.Arg590Trp	p.R590W	ENST00000274335		590	Cgg/Tgg	13/15	0.433758549905833	3	FACETS	0.921	0.831	1	0.461	0.415	0.509	CLONAL	1	TRUE	1	0.433260612105039	3		643	701	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624294	89624295	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0063611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	176	449	0	ENST00000371953.3:c.69dup	p.Asp24ArgfsTer20	p.D24Rfs*20	ENST00000371953	NM_000314.4	23	tta/ttAa	1/9	0.433260612105039	2	FACETS	0.974	0.908	1	0.974	0.908	1	CLONAL	2	TRUE	0	0.433260612105039	2		449	417	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665752	29665755	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1555535032	NA	P-0063611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	89	477	0	ENST00000356175.3:c.6789_6792del	p.Tyr2264ThrfsTer5	p.Y2264Tfs*5	ENST00000356175	NM_000267.3	2263	ACTTac/ac	45/57	0.433260612105039	2	FACETS	1	0.915	1	0.515	0.459	0.573	CLONAL	1	TRUE	0	0.433260612105039	2		477	399	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422101	81422103	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0063611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	127	761	0	ENST00000298171.2:c.78_80del	p.Pro28del	p.P28del	ENST00000298171	NM_000369.2	26	tCTCca/tca	1/10	0.433260612105039	2	FACETS	0.952	0.865	1	0.476	0.432	0.522	CLONAL	1	TRUE	0	0.433260612105039	2		761	616	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943612	17943612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	169	1029	0	ENST00000458235.1:c.2477C>T	p.Ser826Leu	p.S826L	ENST00000458235	NM_000215.3	826	tCa/tTa	18/24	0.433758549905833	4	FACETS	0.999	0.917	1	0.5	0.458	0.543	CLONAL	1	TRUE	2	0.433260612105039	4		1029	1119	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117639410	117639410	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	87	395	0	ENST00000368508.3:c.5946G>C	p.Leu1982Phe	p.L1982F	ENST00000368508	NM_002944.2	1982	ttG/ttC	37/43	0.433758549905833	2	FACETS	1	0.914	1	0.515	0.459	0.574	CLONAL	1	TRUE	0	0.433260612105039	2		395	390	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197457	27197457	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	260	700	0	ENST00000380036.4:c.1769A>G	p.Asn590Ser	p.N590S	ENST00000380036	NM_000459.3	590	aAt/aGt	12/23	0.386658263706212	3	FACETS	0.841	0.795	0.887	0.841	0.795	0.887	CLONAL	3	TRUE	0	0.433260612105039	3		700	579	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12043192	12043192	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063612-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	28	374	0	ENST00000353533.5:c.1077A>C	p.Lys359Asn	p.K359N	ENST00000353533	NM_003010.3	359	aaA/aaC	10/11	0.477642005062783	1	FACETS	0.29	0.233	0.356	0.29	0.233	0.356	SUBCLONAL	1	TRUE	0	0.551918660572659	1		374	253	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0063613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	105	210	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.555167496449576	4	FACETS	0.85	0.77	0.934	0.567	0.513	0.623	CLONAL	2	TRUE	1	0.555167496449576	4		210	346	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0063613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	200	213	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.555167496449576	3	FACETS	0.949	0.888	1	0.949	0.888	1	CLONAL	2	TRUE	1	0.555167496449576	3		213	485	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0063613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	379	654	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.555167496449576	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.555167496449576	3		654	833	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0063613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	627	469	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.555167496449576	4	FACETS	0.962	0.936	0.987	0.962	0.936	0.987	CLONAL	4	TRUE	0	0.555167496449576	4		472	913	SUCCESS
APC	324	MSKCC	GRCh37	5	112175766	112175766	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	184	612	0	ENST00000257430.4:c.4476del	p.Thr1493ArgfsTer14	p.T1493Rfs*14	ENST00000257430	NM_000038.5	1492	gCc/gc	16/16	0.555167496449576	3	FACETS	1	0.937	1	0.508	0.469	0.548	CLONAL	1	TRUE	1	0.555167496449576	3		612	834	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395615	31395615	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	190	798	0	ENST00000328111.2:c.2468G>A	p.Arg823His	p.R823H	ENST00000328111	NM_006892.3	823	cGt/cAt	23/23	0.546344920578323	4	FACETS	0.911	0.841	0.985	0.456	0.42	0.493	CLONAL	1	TRUE	2	0.555167496449576	4		798	1168	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720928	119720928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	218	434	0	ENST00000316626.5:c.247G>A	p.Ala83Thr	p.A83T	ENST00000316626		83	Gcc/Acc	2/12	0.555167496449576	3	FACETS	0.929	0.872	0.987	0.929	0.872	0.987	CLONAL	2	TRUE	1	0.555167496449576	3		434	540	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414922	56414922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	194	557	0	ENST00000348428.3:c.2323G>A	p.Asp775Asn	p.D775N	ENST00000348428	NM_006785.3	775	Gat/Aat	17/17	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.555167496449576	2		557	617	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468403	89468403	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063613-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	253	434	0	ENST00000336596.2:c.1937A>C	p.Lys646Thr	p.K646T	ENST00000336596	NM_005233.5	646	aAa/aCa	11/17	0.555167496449576	3	FACETS	0.897	0.845	0.95	0.897	0.845	0.95	CLONAL	2	TRUE	1	0.555167496449576	3		434	649	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50782608	50782608	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1313852039	NA	P-0063614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	203	706	0	ENST00000307179.4:c.2120A>G	p.Asp707Gly	p.D707G	ENST00000307179		707	gAt/gGt	14/20	0.739577441227137	3	FACETS	0.678	0.628	0.73	0.339	0.314	0.365	SUBCLONAL	1	TRUE	1	0.761080390418518	3		706	1086	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244954	41244956	+	inframe_deletion	In_Frame_Del	DEL	TTT	TTT	-	novel	NA	P-0063614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	136	722	0	ENST00000357654.3:c.2592_2594del	p.Lys865del	p.K865del	ENST00000357654	NM_007294.3	864	tcAAAg/tcg	10/23	0.269757896970432	2	FACETS	0.638	0.583	0.696	0.319	0.291	0.348	INDETERMINATE	1	TRUE	0	0.761080390418518	2		722	560	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0063615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	291	514	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.713271783847246	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.713271783847246	2		514	402	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0063615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	121	583	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.922	0.842	1	0.922	0.842	1	CLONAL	1	TRUE	1	0.713271783847246	2		584	368	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0063615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	86	383	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.713271783847246	1	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	0	0.713271783847246	1		383	155	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0063615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	156	429	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.713271783847246	3	FACETS	0.973	0.908	1	0.973	0.908	1	CLONAL	2	TRUE	1	0.713271783847246	3		429	305	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285327	212285327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143134749	NA	P-0063615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	118	453	0	ENST00000342788.4:c.2974C>T	p.Arg992Cys	p.R992C	ENST00000342788	NM_005235.2	992	Cgt/Tgt	25/28	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.713271783847246	2		453	317	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72994016	72994016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs12922687	NA	P-0063615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	191	670	0	ENST00000268489.5:c.29C>T	p.Ser10Leu	p.S10L	ENST00000268489	NM_006885.3	10	tCg/tTg	2/10	1	2	FACETS	0.963	0.897	1	0.963	0.897	1	CLONAL	1	TRUE	1	0.713271783847246	2		670	556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579717	7579717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs922736614	NA	P-0063615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	163	479	0	ENST00000269305.4:c.79C>T	p.Pro27Ser	p.P27S	ENST00000269305	NM_001126112.2	27	Cct/Tct	3/11	0.713271783847246	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.713271783847246	1		479	287	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17350532	17350532	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	334	464	0	ENST00000375499.3:c.578G>C	p.Ser193Thr	p.S193T	ENST00000375499	NM_003000.2	193	aGc/aCc	6/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.713271783847246	2		464	833	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134217	41134217	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750423870	NA	P-0063615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	161	711	0	ENST00000379561.5:c.1411C>T	p.Pro471Ser	p.P471S	ENST00000379561	NM_002015.3	471	Cct/Tct	2/3	0.270735249881592	1	FACETS	0.527	0.486	0.569	0.527	0.486	0.569	INDETERMINATE	1	TRUE	0	0.713271783847246	1		711	551	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260302	10260302	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	217	632	0	ENST00000340748.4:c.2365G>A	p.Gly789Arg	p.G789R	ENST00000340748		789	Ggg/Agg	25/40	1	2	FACETS	0.97	0.908	1	0.97	0.908	1	CLONAL	1	TRUE	1	0.713271783847246	2		632	627	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857889	9857889	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	197	722	0	ENST00000330684.3:c.3512C>T	p.Pro1171Leu	p.P1171L	ENST00000330684	NM_001134407.1	1171	cCc/cTc	13/13	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.713271783847246	2		722	543	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639611	3639611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1341974917	NA	P-0063615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	242	862	0	ENST00000294008.3:c.4028C>T	p.Pro1343Leu	p.P1343L	ENST00000294008	NM_032444.2	1343	cCt/cTt	12/15	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.713271783847246	2		862	675	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347221	70347221	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	219	304	0	ENST00000374080.3:c.2885C>T	p.Ser962Phe	p.S962F	ENST00000374080		962	tCc/tTc	21/45	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.713271783847246	1		304	311	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859281	151859281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	122	517	0	ENST00000262189.6:c.11381C>T	p.Pro3794Leu	p.P3794L	ENST00000262189	NM_170606.2	3794	cCt/cTt	43/59	0.713271783847246	3	FACETS	0.971	0.883	1	0.485	0.441	0.531	CLONAL	1	TRUE	1	0.713271783847246	3		517	478	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248519	212248519	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754829537	NA	P-0063615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	281	766	0	ENST00000342788.4:c.3748C>T	p.Arg1250Trp	p.R1250W	ENST00000342788	NM_005235.2	1250	Cgg/Tgg	28/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.713271783847246	2		766	749	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127710	64127710	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	199	584	0	ENST00000334205.4:c.203G>C	p.Arg68Pro	p.R68P	ENST00000334205	NM_003942.2	68	cGc/cCc	3/17	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.713271783847246	2		584	518	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416734	121416734	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	186	749	0	ENST00000257555.6:c.163G>A	p.Gly55Arg	p.G55R	ENST00000257555		55	Ggg/Agg	1/10	1	2	FACETS	0.907	0.843	0.973	0.907	0.843	0.973	CLONAL	1	TRUE	1	0.713271783847246	2		749	575	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022650	31022651	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0063615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	178	773	0	ENST00000375687.4:c.2135_2136delinsTT	p.Ala712Val	p.A712V	ENST00000375687	NM_015338.5	712	gCC/gTT	13/13	0.591331880549874	3	FACETS	0.847	0.782	0.915	0.424	0.391	0.458	CLONAL	1	TRUE	1	0.713271783847246	3		773	799	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008403	71008403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	152	530	0	ENST00000318789.4:c.2029G>A	p.Glu677Lys	p.E677K	ENST00000318789	NM_032682.5	677	Gag/Aag	21/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.713271783847246	2		530	402	SUCCESS
ALB	213	MSKCC	GRCh37	4	74276066	74276066	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	153	436	0	ENST00000295897.4:c.653C>T	p.Ala218Val	p.A218V	ENST00000295897	NM_000477.5	218	gCc/gTc	6/15	0.701715860749488	2	FACETS	0.879	0.827	0.93	0.879	0.827	0.93	CLONAL	2	TRUE	0	0.713271783847246	2		436	244	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38960061	38960061	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	61	422	0	ENST00000357387.3:c.1871A>G	p.Glu624Gly	p.E624G	ENST00000357387	NM_152756.3	624	gAa/gGa	21/38	1	2	FACETS	0.972	0.855	1	0.972	0.855	1	CLONAL	1	TRUE	1	0.713271783847246	2		422	176	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722089	176722089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	262	773	0	ENST00000439151.2:c.7720C>T	p.Pro2574Ser	p.P2574S	ENST00000439151	NM_022455.4	2574	Ccg/Tcg	23/23	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.713271783847246	2		773	684	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250784	26250784	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	246	838	0	ENST00000446824.2:c.50C>T	p.Pro17Leu	p.P17L	ENST00000446824	NM_021018.2	17	cCg/cTg	1/1	0.599281088402525	5	FACETS	1	0.944	1	0.338	0.315	0.362	CLONAL	1	TRUE	2	0.713271783847246	5		838	1409	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686994	37686994	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769197936	NA	P-0063616-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	35	648	0	ENST00000447079.4:c.3898G>A	p.Ala1300Thr	p.A1300T	ENST00000447079	NM_015083.1	1300	Gcc/Acc	14/14	0.499306468791697	1	FACETS	0.235	0.192	0.283	0.235	0.192	0.283	SUBCLONAL	1	TRUE	0	0.499306468791697	1		648	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0063617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	193	454	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.275138004134874	1	FACETS	1	0.963	1	1	0.963	1	INDETERMINATE	1	TRUE	0	0.498612037498048	1		454	554	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0063617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	52	362	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.753	0.646	0.868	0.753	0.646	0.868	SUBCLONAL	1	TRUE	1	0.498612037498048	2		362	277	SUCCESS
APC	324	MSKCC	GRCh37	5	112175153	112175153	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	60	650	1	ENST00000257430.4:c.3862G>T	p.Gly1288Ter	p.G1288*	ENST00000257430	NM_000038.5	1288	Gga/Tga	16/16	0.339407110333382	0	FACETS	0.391	0.339	0.446			1	SUBCLONAL	1	TRUE	0	0.498612037498048	0		651	309	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0063617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	32	893	1	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.275138004134874	1	FACETS	0.124	0.1	0.151	0.124	0.1	0.151	INDETERMINATE	1	TRUE	0	0.498612037498048	1		894	777	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912188	114912188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	68	441	1	ENST00000543371.1:c.1258C>T	p.Arg420Trp	p.R420W	ENST00000543371	NM_001198531.1	420	Cgg/Tgg	11/14	0.275138004134874	1	FACETS	0.396	0.345	0.451	0.396	0.345	0.451	INDETERMINATE	1	TRUE	0	0.498612037498048	1		442	517	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120258	70120259	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0063617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	235	850	0	ENST00000245479.2:c.1261dup	p.Ser421LysfsTer157	p.S421Kfs*157	ENST00000245479	NM_000346.3	420	-/A	3/3	0.275138004134874	1	FACETS	0.913	0.855	0.973	0.913	0.855	0.973	INDETERMINATE	1	TRUE	0	0.498612037498048	1		850	775	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591901	48591901	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	136	696	1	ENST00000342988.3:c.1064A>G	p.Asp355Gly	p.D355G	ENST00000342988	NM_005359.5	355	gAc/gGc	9/12	0.358926575775301	0	FACETS	0.615	0.563	0.668			1	SUBCLONAL	1	TRUE	0	0.498612037498048	0		697	445	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371691	225371691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	72	493	0	ENST00000264414.4:c.913C>T	p.Arg305Cys	p.R305C	ENST00000264414	NM_003590.4	305	Cgt/Tgt	7/16	NA	2	FACETS	1	0.933	1			1	INDETERMINATE	1	TRUE	NA	0.498612037498048	2		493	267	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77961221	77961221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs539815954	NA	P-0063617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	216	669	0	ENST00000361507.4:c.602G>A	p.Arg201Gln	p.R201Q	ENST00000361507	NM_080491.2	201	cGa/cAa	3/10	0.275138004134874	1	FACETS	0.939	0.876	1	0.939	0.876	1	INDETERMINATE	1	TRUE	0	0.498612037498048	1		669	693	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123788	11123788	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0063617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	99	618	0	ENST00000358026.2:c.2438C>G	p.Ser813Ter	p.S813*	ENST00000358026	NM_001128849.1	813	tCa/tGa	16/36	1	2	FACETS	0.63	0.563	0.701	0.63	0.563	0.701	SUBCLONAL	1	TRUE	1	0.498612037498048	2		618	630	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032764	30032768	+	frameshift_variant	Frame_Shift_Del	DEL	TTTGA	TTTGA	-	novel	NA	P-0063618-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	353	666	0	ENST00000338641.4:c.143_147del	p.Asp48GlyfsTer36	p.D48Gfs*36	ENST00000338641	NM_000268.3	47	TTTGAt/t	2/16	0.792002705597465	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.792002705597465	1		666	535	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973976	55973976	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063618-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	27	670	0	ENST00000263923.4:c.1340T>C	p.Val447Ala	p.V447A	ENST00000263923	NM_002253.2	447	gTc/gCc	10/30	0.792002705597465	1	FACETS	0.087	0.069	0.108	0.087	0.069	0.108	SUBCLONAL	1	TRUE	0	0.792002705597465	1		670	473	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063619-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	80	523	0				ENST00000310581	NM_198253.2	-/1132			0.401875845414973	1	FACETS	0.38	0.337	0.425	0.38	0.337	0.425	INDETERMINATE	1	TRUE	0	0.762095407826868	1		523	342	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857895	9857895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761399460	NA	P-0063619-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	165	784	0	ENST00000330684.3:c.3506G>A	p.Arg1169Gln	p.R1169Q	ENST00000330684	NM_001134407.1	1169	cGg/cAg	13/13	0.287466097665643	1	FACETS	0.45	0.415	0.487	0.45	0.415	0.487	INDETERMINATE	1	TRUE	0	0.762095407826868	1		784	595	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0063619-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	229	814	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	0.915	0.857	0.973	0.915	0.857	0.973	CLONAL	1	TRUE	1	0.762095407826868	2		814	657	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843243	128843243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173715127	NA	P-0063619-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	153	702	0	ENST00000249373.3:c.350G>A	p.Arg117His	p.R117H	ENST00000249373	NM_005631.4	117	cGc/cAc	2/12	0.265026398044464	3	FACETS	0.943	0.867	1	0.472	0.433	0.511	INDETERMINATE	1	TRUE	1	0.762095407826868	3		702	588	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655488	67655488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063619-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	131	502	0	ENST00000264010.4:c.1351G>A	p.Asp451Asn	p.D451N	ENST00000264010	NM_006565.3	451	Gat/Aat	7/12	0.287466097665643	1	FACETS	0.448	0.409	0.488	0.448	0.409	0.488	INDETERMINATE	1	TRUE	0	0.762095407826868	1		502	475	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984344	201984344	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063619-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	114	638	0	ENST00000359651.3:c.1009T>G	p.Tyr337Asp	p.Y337D	ENST00000359651		337	Tac/Gac	8/8	1	2	FACETS	0.633	0.573	0.695	0.633	0.573	0.695	SUBCLONAL	1	TRUE	1	0.762095407826868	2		638	473	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11027107	11027117	+	frameshift_variant	Frame_Shift_Del	DEL	ACGTCCACCTT	ACGTCCACCTT	-	novel	NA	P-0063619-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	164	605	0	ENST00000327064.4:c.872_882del	p.Asp291GlyfsTer6	p.D291Gfs*6	ENST00000327064	NM_199141.1	291	gACGTCCACCTT/g	7/16	1	2	FACETS	0.815	0.753	0.879	0.815	0.753	0.879	CLONAL	1	TRUE	1	0.762095407826868	2		605	528	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141645596	141645597	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0063619-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	61	472	0	ENST00000220592.5:c.9_10delinsTA	p.Gly4Arg	p.G4R	ENST00000220592	NM_012154.3	3	tcGGga/tcTAga	1/19	1	2	FACETS	0.443	0.384	0.507	0.443	0.384	0.507	SUBCLONAL	1	TRUE	1	0.762095407826868	2		472	361	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949024	44949025	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0063619-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	164	468	0	ENST00000377967.4:c.3587dup	p.Asn1196LysfsTer3	p.N1196Kfs*3	ENST00000377967	NM_021140.2	1195	-/A	25/29	0.482357612916512	1	FACETS	0.73	0.68	0.78	0.73	0.68	0.78	SUBCLONAL	1	TRUE	0	0.762095407826868	1		468	365	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0063624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	43	515	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.759	0.637	0.891	0.759	0.637	0.891	SUBCLONAL	1	TRUE	1	0.358782212828714	2		515	316	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0063624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	16	272	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.196	0.144	0.259	0.196	0.144	0.259	SUBCLONAL	1	TRUE	1	0.358782212828714	2		272	454	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0063624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	197	494	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.358782212828714	2	FACETS	0.818	0.761	0.877	0.818	0.761	0.877	CLONAL	2	TRUE	0	0.358782212828714	2		494	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0063624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	61	558	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.594	0.513	0.683	0.594	0.513	0.683	SUBCLONAL	1	TRUE	1	0.358782212828714	2		558	572	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440364	187440364	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1426858162	NA	P-0063624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	98	476	0	ENST00000232014.4:c.2003G>A	p.Arg668His	p.R668H	ENST00000232014	NM_001130845.1	668	cGt/cAt	10/10	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.358782212828714	2		476	511	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0063624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	134	589	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.358782212828714	2		589	639	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0063624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	13	482	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.132	0.093	0.179	0.132	0.093	0.179	SUBCLONAL	1	TRUE	1	0.358782212828714	2		482	551	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610695	52610695	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	55	390	0	ENST00000394830.3:c.3478C>T	p.Arg1160Ter	p.R1160*	ENST00000394830	NM_018313.4	1160	Cga/Tga	23/30	1	2	FACETS	0.604	0.517	0.698	0.604	0.517	0.698	SUBCLONAL	1	TRUE	1	0.358782212828714	2		390	508	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911144	40911144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776134993	NA	P-0063624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	22	281	0	ENST00000373198.4:c.2161C>T	p.Arg721Cys	p.R721C	ENST00000373198	NM_133170.3	721	Cgt/Tgt	13/32	1	2	FACETS	0.319	0.246	0.403	0.319	0.246	0.403	SUBCLONAL	1	TRUE	1	0.358782212828714	2		281	385	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795103	242795104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768249210	NA	P-0063624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	53	731	2	ENST00000334409.5:c.105dup	p.Thr36HisfsTer70	p.T36Hfs*70	ENST00000334409	NM_005018.2	35	-/C	2/5	1	2	FACETS	0.482	0.41	0.56	0.482	0.41	0.56	SUBCLONAL	1	TRUE	1	0.358782212828714	2		733	613	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971292	13971292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772105404	NA	P-0063624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	72	539	0	ENST00000405192.2:c.637C>T	p.Arg213Cys	p.R213C	ENST00000405192	NM_001163147.1	213	Cgc/Tgc	8/12	1	2	FACETS	0.664	0.581	0.755	0.664	0.581	0.755	SUBCLONAL	1	TRUE	1	0.358782212828714	2		539	604	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482607	56482607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs993665271	NA	P-0063624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	100	496	0	ENST00000267101.3:c.1064C>T	p.Thr355Ile	p.T355I	ENST00000267101	NM_001982.3	355	aCc/aTc	9/28	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.358782212828714	2		496	538	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683228	88683228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876658515	NA	P-0063624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	35	339	0	ENST00000372037.3:c.1438C>T	p.Arg480Trp	p.R480W	ENST00000372037	NM_004329.2	480	Cgg/Tgg	12/13	1	2	FACETS	0.469	0.384	0.564	0.469	0.384	0.564	SUBCLONAL	1	TRUE	1	0.358782212828714	2		339	416	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812466	43812466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1298113648	NA	P-0063624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	84	595	0	ENST00000372470.3:c.1169G>A	p.Arg390His	p.R390H	ENST00000372470	NM_005373.2	390	cGc/cAc	8/12	1	2	FACETS	0.787	0.696	0.884	0.787	0.696	0.884	SUBCLONAL	1	TRUE	1	0.358782212828714	2		595	595	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681410	88681410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780108	NA	P-0063624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	45	198	0	ENST00000372037.3:c.1300G>A	p.Gly434Ser	p.G434S	ENST00000372037	NM_004329.2	434	Ggc/Agc	11/13	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.358782212828714	2		198	247	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120351	70120352	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	101	686	0	ENST00000245479.2:c.1354dup	p.Tyr452LeufsTer126	p.Y452Lfs*126	ENST00000245479	NM_000346.3	451	-/T	3/3	1	2	FACETS	0.81	0.725	0.901	0.81	0.725	0.901	CLONAL	1	TRUE	1	0.358782212828714	2		686	695	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983117	201983118	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0063624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	49	575	0	ENST00000359651.3:c.968dup	p.Asn323LysfsTer148	p.N323Kfs*148	ENST00000359651		322	-/A	7/8	1	2	FACETS	0.429	0.363	0.503	0.429	0.363	0.503	SUBCLONAL	1	TRUE	1	0.358782212828714	2		575	636	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588203	69588203	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	112	513	0	ENST00000168712.1:c.495C>A	p.Asn165Lys	p.N165K	ENST00000168712	NM_002007.2	165	aaC/aaA	3/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.358782212828714	2		513	501	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811656	102811656	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	97	617	0	ENST00000307046.8:c.528del	p.Glu177SerfsTer25	p.E177Sfs*25	ENST00000307046	NM_001111285.1	176	aaA/aa	4/4	1	2	FACETS	0.755	0.673	0.842	0.755	0.673	0.842	SUBCLONAL	1	TRUE	1	0.358782212828714	2		617	716	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120354	70120354	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	78	681	1	ENST00000245479.2:c.1356C>A	p.Tyr452Ter	p.Y452*	ENST00000245479	NM_000346.3	452	taC/taA	3/3	1	2	FACETS	0.626	0.549	0.708	0.626	0.549	0.708	SUBCLONAL	1	TRUE	1	0.358782212828714	2		682	695	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967529	38967529	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	53	366	0	ENST00000357387.3:c.1061A>G	p.Asp354Gly	p.D354G	ENST00000357387	NM_152756.3	354	gAt/gGt	13/38	1	2	FACETS	0.522	0.445	0.607	0.522	0.445	0.607	SUBCLONAL	1	TRUE	1	0.358782212828714	2		366	566	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0063632-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	42	203	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	1	0.19	2		203	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0063632-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	79	849	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.19	2		849	789	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210876	133210876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201273415	NA	P-0063632-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	74	706	1	ENST00000320574.5:c.5900C>T	p.Ala1967Val	p.A1967V	ENST00000320574	NM_006231.2	1967	gCg/gTg	43/49	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.19	2		707	774	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041617	14041617	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs754771000	NA	P-0063632-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	44	574	0	ENST00000311895.7:c.2164A>G	p.Met722Val	p.M722V	ENST00000311895	NM_005236.2	722	Atg/Gtg	11/11	1	2	FACETS	0.729	0.611	0.861	0.729	0.611	0.861	SUBCLONAL	1	TRUE	1	0.19	2		574	635	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859668	151859668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063632-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	85	784	0	ENST00000262189.6:c.10994G>A	p.Gly3665Asp	p.G3665D	ENST00000262189	NM_170606.2	3665	gGc/gAc	43/59	0.142923522345622	3	FACETS	1	0.936	1	0.546	0.482	0.615	CLONAL	1	TRUE	1	0.19	3		784	897	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209595	98209595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746022197	NA	P-0063632-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	61	776	0	ENST00000331920.6:c.3943C>T	p.Pro1315Ser	p.P1315S	ENST00000331920	NM_000264.3	1315	Ccc/Tcc	23/24	1	2	FACETS	0.979	0.844	1	0.979	0.844	1	CLONAL	1	TRUE	1	0.19	2		776	656	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024614	31024614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147456014	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	43	674	0	ENST00000375687.4:c.4099G>A	p.Val1367Ile	p.V1367I	ENST00000375687	NM_015338.5	1367	Gtc/Atc	13/13	1	2	FACETS	0.809	0.677	0.956	0.809	0.677	0.956	CLONAL	1	TRUE	1	0.22	2		674	483	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542110	187542110	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	36	732	3	ENST00000441802.2:c.5630del	p.Pro1877LeufsTer20	p.P1877Lfs*20	ENST00000441802	NM_005245.3	1877	cCt/ct	10/27	1	2	FACETS	0.758	0.623	0.909	0.758	0.623	0.909	CLONAL	1	TRUE	1	0.22	2		735	432	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	37	228	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.22	2		228	267	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101099	27101099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	56	616	0	ENST00000324856.7:c.4381C>T	p.Arg1461Ter	p.R1461*	ENST00000324856	NM_006015.4	1461	Cga/Tga	18/20	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.22	2		616	444	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	46	796	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.899	0.758	1	0.899	0.758	1	CLONAL	1	TRUE	1	0.22	2		796	465	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308382	15308383	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs749829137	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	46	734	1	ENST00000263388.2:c.125dup	p.Cys43LeufsTer32	p.C43Lfs*32	ENST00000263388	NM_000435.2	42	cct/ccCt	2/33	1	2	FACETS	0.975	0.822	1	0.975	0.822	1	CLONAL	1	TRUE	1	0.22	2		735	429	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796883	42796883	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	58	1053	3	ENST00000575354.2:c.3347del	p.Pro1116GlnfsTer45	p.P1116Qfs*45	ENST00000575354	NM_015125.3	1114	gCc/gc	14/20	1	2	FACETS	0.947	0.814	1	0.947	0.814	1	CLONAL	1	TRUE	1	0.22	2		1056	557	SUCCESS
APC	324	MSKCC	GRCh37	5	112173647	112173647	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1165139414	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	34	298	0	ENST00000257430.4:c.2356C>T	p.Arg786Cys	p.R786C	ENST00000257430	NM_000038.5	786	Cgt/Tgt	16/16	1	2	FACETS	0.966	0.791	1	0.966	0.791	1	CLONAL	1	TRUE	1	0.22	2		298	320	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252817	10252817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187394074	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	48	674	0	ENST00000340748.4:c.3148G>A	p.Val1050Met	p.V1050M	ENST00000340748		1050	Gtg/Atg	29/40	1	2	FACETS	0.974	0.825	1	0.974	0.825	1	CLONAL	1	TRUE	1	0.22	2		674	448	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	45	896	1	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.747	0.627	0.879	0.747	0.627	0.879	SUBCLONAL	1	TRUE	1	0.22	2		897	548	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750529	128750531	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	31	754	0	ENST00000377970.2:c.68_70del	p.Thr23del	p.T23del	ENST00000377970	NM_002467.4	22	ttCACc/ttc	2/3	1	2	FACETS	0.623	0.504	0.759	0.623	0.504	0.759	SUBCLONAL	1	TRUE	1	0.22	2		754	452	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057788	27057788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748935625	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	59	924	0	ENST00000324856.7:c.1496C>T	p.Ser499Leu	p.S499L	ENST00000324856	NM_006015.4	499	tCg/tTg	3/20	1	2	FACETS	0.864	0.743	0.996	0.864	0.743	0.996	CLONAL	1	TRUE	1	0.22	2		924	621	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730335	133730335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	34	549	0	ENST00000318560.5:c.401G>A	p.Arg134His	p.R134H	ENST00000318560	NM_005157.4	134	cGc/cAc	3/11	1	2	FACETS	0.777	0.635	0.936	0.777	0.635	0.936	CLONAL	1	TRUE	1	0.22	2		549	398	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440866	52440866	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1220529268	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	53	741	0	ENST00000460680.1:c.638G>A	p.Arg213His	p.R213H	ENST00000460680	NM_004656.3	213	cGt/cAt	8/17	1	2	FACETS	0.966	0.824	1	0.966	0.824	1	CLONAL	1	TRUE	1	0.22	2		741	499	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119666150	119666150	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	22	171	0	ENST00000316626.5:c.331C>T	p.Arg111Ter	p.R111*	ENST00000316626		111	Cga/Tga	3/12	1	2	FACETS	0.935	0.728	1	0.935	0.728	1	CLONAL	1	TRUE	1	0.22	2		171	214	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842042	3842042	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783464	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	29	394	0	ENST00000262367.5:c.1270C>T	p.Arg424Ter	p.R424*	ENST00000262367	NM_004380.2	424	Cga/Tga	5/31	1	2	FACETS	0.707	0.567	0.865	0.707	0.567	0.865	SUBCLONAL	1	TRUE	1	0.22	2		394	373	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638614	176638614	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784098	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	37	574	0	ENST00000439151.2:c.3214C>T	p.Arg1072Ter	p.R1072*	ENST00000439151	NM_022455.4	1072	Cga/Tga	5/23	1	2	FACETS	0.71	0.585	0.849	0.71	0.585	0.849	SUBCLONAL	1	TRUE	1	0.22	2		574	474	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091782	29091782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373073383	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	46	296	0	ENST00000328354.6:c.1175C>T	p.Ala392Val	p.A392V	ENST00000328354	NM_007194.3	392	gCg/gTg	11/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.22	2		296	299	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288463	15288463	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	37	706	2	ENST00000263388.2:c.4276C>T	p.Arg1426Trp	p.R1426W	ENST00000263388	NM_000435.2	1426	Cgg/Tgg	24/33	1	2	FACETS	0.948	0.783	1	0.948	0.783	1	CLONAL	1	TRUE	1	0.22	2		708	355	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808261	99808261	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	10	131	0	ENST00000280892.6:c.428G>A	p.Arg143Gln	p.R143Q	ENST00000280892	NM_001130678.1	143	cGa/cAa	5/7	1	2	FACETS	0.538	0.365	0.755	0.538	0.365	0.755	SUBCLONAL	1	TRUE	1	0.22	2		131	169	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43733757	43733757	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	25	210	1	ENST00000382044.4:c.3065del	p.Asn1022MetfsTer20	p.N1022Mfs*20	ENST00000382044	NM_001141980.1	1022	aAt/at	15/28	1	2	FACETS	0.82	0.648	1	0.82	0.648	1	CLONAL	1	TRUE	1	0.22	2		211	277	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427950	49427950	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775632051	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	43	655	1	ENST00000301067.7:c.10640G>A	p.Arg3547His	p.R3547H	ENST00000301067	NM_003482.3	3547	cGc/cAc	38/54	1	2	FACETS	0.937	0.786	1	0.937	0.786	1	CLONAL	1	TRUE	1	0.22	2		656	417	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90960096	90960096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs962092255	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	18	126	0	ENST00000265433.3:c.1870C>T	p.Arg624Cys	p.R624C	ENST00000265433	NM_002485.4	624	Cgt/Tgt	12/16	1	2	FACETS	1	0.808	1	1	0.808	1	CLONAL	1	TRUE	1	0.22	2		126	152	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675204	176675204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144900277	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	46	570	0	ENST00000439151.2:c.4520C>T	p.Thr1507Met	p.T1507M	ENST00000439151	NM_022455.4	1507	aCg/aTg	11/23	1	2	FACETS	0.938	0.79	1	0.938	0.79	1	CLONAL	1	TRUE	1	0.22	2		570	446	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716302	52716302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	39	688	0	ENST00000322088.6:c.746G>A	p.Arg249His	p.R249H	ENST00000322088	NM_014225.5	249	cGc/cAc	6/15	1	2	FACETS	0.838	0.695	0.997	0.838	0.695	0.997	CLONAL	1	TRUE	1	0.22	2		688	423	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966987	25966987	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	39	794	0	ENST00000435504.4:c.2219C>T	p.Thr740Met	p.T740M	ENST00000435504		740	aCg/aTg	13/13	1	2	FACETS	0.808	0.67	0.961	0.808	0.67	0.961	CLONAL	1	TRUE	1	0.22	2		794	439	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703652	47703652	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779139	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	47	382	2	ENST00000233146.2:c.2152C>T	p.Gln718Ter	p.Q718*	ENST00000233146	NM_000251.2	718	Caa/Taa	13/16	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.22	2		384	399	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420688	49420688	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783695	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	56	757	0	ENST00000301067.7:c.15061C>T	p.Arg5021Ter	p.R5021*	ENST00000301067	NM_003482.3	5021	Cga/Tga	48/54	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.22	2		757	501	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27192559	27192559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766717660	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	24	455	0	ENST00000380036.4:c.1562G>A	p.Arg521His	p.R521H	ENST00000380036	NM_000459.3	521	cGt/cAt	11/23	1	2	FACETS	0.613	0.48	0.766	0.613	0.48	0.766	SUBCLONAL	1	TRUE	1	0.22	2		455	356	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454592	99454592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761469469	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	33	586	0	ENST00000268035.6:c.1511G>A	p.Arg504His	p.R504H	ENST00000268035	NM_000875.3	504	cGc/cAc	7/21	1	2	FACETS	0.815	0.665	0.984	0.815	0.665	0.984	CLONAL	1	TRUE	1	0.22	2		586	368	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21348256	21348256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777180	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	47	925	0	ENST00000215739.8:c.1397G>A	p.Arg466Gln	p.R466Q	ENST00000215739	NM_006767.3	466	cGg/cAg	13/21	1	2	FACETS	0.808	0.681	0.947	0.808	0.681	0.947	CLONAL	1	TRUE	1	0.22	2		925	529	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144146	11144146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	16	665	0	ENST00000358026.2:c.3727C>T	p.Arg1243Trp	p.R1243W	ENST00000358026	NM_001128849.1	1243	Cgg/Tgg	26/36	1	2	FACETS	0.313	0.23	0.412	0.313	0.23	0.412	SUBCLONAL	1	TRUE	1	0.22	2		665	465	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422128	47422128	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	44	568	0	ENST00000404338.3:c.196C>T	p.Arg66Ter	p.R66*	ENST00000404338	NM_004491.4	66	Cga/Tga	1/6	1	2	FACETS	0.851	0.714	1	0.851	0.714	1	CLONAL	1	TRUE	1	0.22	2		568	470	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70441164	70441164	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	17	145	0	ENST00000373644.4:c.4833C>A	p.Asn1611Lys	p.N1611K	ENST00000373644	NM_030625.2	1611	aaC/aaA	9/12	1	2	FACETS	0.805	0.603	1	0.805	0.603	1	CLONAL	1	TRUE	1	0.22	2		145	192	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307386	118307387	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	15	379	0	ENST00000534358.1:c.165dup	p.Ser56LeufsTer91	p.S56Lfs*91	ENST00000534358	NM_005933.3	53	-/C	1/36	1	2	FACETS	0.847	0.623	1	0.847	0.623	1	CLONAL	1	TRUE	1	0.22	2		379	161	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438081	110438081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	36	656	0	ENST00000375856.3:c.320C>T	p.Ala107Val	p.A107V	ENST00000375856	NM_003749.2	107	gCc/gTc	1/2	1	2	FACETS	0.843	0.694	1	0.843	0.694	1	CLONAL	1	TRUE	1	0.22	2		656	388	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346631	89346631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780905536	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	40	808	0	ENST00000301030.4:c.6319C>T	p.Arg2107Cys	p.R2107C	ENST00000301030	NM_001256183.1	2107	Cgc/Tgc	9/13	1	2	FACETS	0.832	0.692	0.988	0.832	0.692	0.988	CLONAL	1	TRUE	1	0.22	2		808	437	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553474	29553474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779546178	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	49	514	0	ENST00000356175.3:c.2023G>A	p.Gly675Arg	p.G675R	ENST00000356175	NM_000267.3	675	Gga/Aga	18/57	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.22	2		514	429	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41251839	41251839	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	47	287	1	ENST00000357654.3:c.500C>A	p.Thr167Lys	p.T167K	ENST00000357654	NM_007294.3	167	aCa/aAa	7/23	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.22	2		288	353	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350228	15350228	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199833998	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	26	771	0	ENST00000263377.2:c.3551C>T	p.Pro1184Leu	p.P1184L	ENST00000263377	NM_058243.2	1184	cCg/cTg	17/20	1	2	FACETS	0.508	0.402	0.631	0.508	0.402	0.631	SUBCLONAL	1	TRUE	1	0.22	2		771	465	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313457	30313457	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1225502237	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	26	525	1	ENST00000262643.3:c.1057G>A	p.Ala353Thr	p.A353T	ENST00000262643	NM_001238.2	353	Gct/Act	11/12	1	2	FACETS	0.559	0.442	0.693	0.559	0.442	0.693	SUBCLONAL	1	TRUE	1	0.22	2		526	423	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224009	36224009	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751221427	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	44	939	0	ENST00000222270.7:c.6559G>A	p.Ala2187Thr	p.A2187T	ENST00000222270	NM_014727.1	2187	Gcc/Acc	28/37	1	2	FACETS	0.787	0.66	0.928	0.787	0.66	0.928	CLONAL	1	TRUE	1	0.22	2		939	508	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735466	40735466	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	42	684	0	ENST00000373198.4:c.3407G>T	p.Arg1136Leu	p.R1136L	ENST00000373198	NM_133170.3	1136	cGt/cTt	25/32	0.3	1	FACETS	0.85	0.71	1	0.85	0.71	1	CLONAL	1	TRUE	0	0.22	1		684	400	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576509	67576509	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	25	217	0	ENST00000274335.5:c.788T>C	p.Val263Ala	p.V263A	ENST00000274335		263	gTa/gCa	5/15	1	2	FACETS	0.913	0.722	1	0.913	0.722	1	CLONAL	1	TRUE	1	0.22	2		217	249	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687040	176687041	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	33	606	0	ENST00000439151.2:c.5019_5020del	p.Phe1673LeufsTer12	p.F1673Lfs*12	ENST00000439151	NM_022455.4	1673	TTt/t	14/23	1	2	FACETS	0.662	0.539	0.801	0.662	0.539	0.801	SUBCLONAL	1	TRUE	1	0.22	2		606	453	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404554	8404554	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	22	241	0	ENST00000356435.5:c.4193T>G	p.Leu1398Arg	p.L1398R	ENST00000356435		1398	cTc/cGc	25/35	1	2	FACETS	1	0.812	1	1	0.812	1	CLONAL	1	TRUE	1	0.22	2		241	191	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485833	8485833	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1250425659	NA	P-0063633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	26	433	0	ENST00000356435.5:c.2984G>A	p.Arg995His	p.R995H	ENST00000356435		995	cGt/cAt	17/35	1	2	FACETS	0.712	0.564	0.881	0.712	0.564	0.881	SUBCLONAL	1	TRUE	1	0.22	2		433	332	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0063634-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	43	272	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.495	0.414	0.585	0.495	0.414	0.585	SUBCLONAL	1	TRUE	1	0.32	2		272	543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0063634-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	157	675	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.304255267907123	1	FACETS	0.855	0.783	0.931	0.855	0.783	0.931	CLONAL	1	TRUE	0	0.32	1		675	964	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287315	46287315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1565642121	NA	P-0063634-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	127	518	0	ENST00000334344.6:c.5260C>T	p.Arg1754Ter	p.R1754*	ENST00000334344	NM_152641.2	1754	Cga/Tga	19/21	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.32	2		518	763	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005326	29005326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371426326	NA	P-0063634-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	222	361	0	ENST00000282397.4:c.935G>A	p.Arg312His	p.R312H	ENST00000282397	NM_002019.4	312	cGt/cAt	7/30	0.304255267907123	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.32	3		361	761	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230686	46230691	+	inframe_deletion	In_Frame_Del	DEL	GTCTTC	GTCTTC	-	novel	NA	P-0063634-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	112	473	0	ENST00000334344.6:c.937_942del	p.Leu313_Arg314del	p.L313_R314del	ENST00000334344	NM_152641.2	312	tGTCTTCgt/tgt	8/21	1	2	FACETS	0.901	0.81	0.997	0.901	0.81	0.997	CLONAL	1	TRUE	1	0.32	2		473	777	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0063635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	57	482	0	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	0.231870054553013	2	FACETS	0.754	0.647	0.87	0.377	0.323	0.435	SUBCLONAL	1	TRUE	0	0.280069815455852	2		482	540	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589586	67589591	+	inframe_deletion	In_Frame_Del	DEL	ATGAAT	ATGAAT	-	novel	NA	P-0063635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	14	293	0	ENST00000274335.5:c.1351_1356del	p.Glu451_Tyr452del	p.E451_Y452del	ENST00000274335		450	cATGAATat/cat	10/15	1	2	FACETS	0.502	0.364	0.67	0.502	0.364	0.67	SUBCLONAL	1	TRUE	1	0.280069815455852	2		293	199	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691094	18691094	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs201586034	NA	P-0063635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	30	378	2	ENST00000266497.5:c.3205C>T	p.Arg1069Ter	p.R1069*	ENST00000266497		1069	Cga/Tga	23/31	0.0807334673078552	4	FACETS	0.554	0.446	0.677	0.277	0.223	0.339	INDETERMINATE	1	TRUE	2	0.280069815455852	4		380	495	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202995	16202995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200777699	NA	P-0063635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	83	694	0	ENST00000375759.3:c.703C>T	p.Arg235Trp	p.R235W	ENST00000375759	NM_015001.2	235	Cgg/Tgg	3/15	0.234205890882822	3	FACETS	0.878	0.774	0.989	0.439	0.387	0.495	CLONAL	1	TRUE	1	0.280069815455852	3		694	770	SUCCESS
APC	324	MSKCC	GRCh37	5	112174193	112174193	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	57	573	0	ENST00000257430.4:c.2902A>G	p.Ser968Gly	p.S968G	ENST00000257430	NM_000038.5	968	Agt/Ggt	16/16	1	2	FACETS	0.85	0.73	0.98	0.85	0.73	0.98	CLONAL	1	TRUE	1	0.280069815455852	2		573	479	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911267	29911268	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0063635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	71	324	0	ENST00000376809.5:c.568dup	p.Glu190GlyfsTer31	p.E190Gfs*31	ENST00000376809	NM_002116.7	189	gtg/gtGg	3/8	0.221307164423632	3	FACETS	1	0.973	1	0.482	0.422	0.545	CLONAL	1	TRUE	0	0.280069815455852	3		324	400	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649449	48650471	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	TGTGGGGTGGAAGGATTTCTGTGTCTGAGGACCCCTTCTGTCCTCGCAGGTTAATCCCCAGAGGCTCCATGGAGTTCCCTGGCCTGGGGTCCCTGGGGACCTCAGAGCCCCTCCCCCAGTTTGTGGATCCTGCTCTGGTGTCCTCCACACCAGAATCAGGGGTTTTCTTCCCCTCTGGGCCTGAGGGCTTGGATGCAGCAGCTTCCTCCACTGCCCCGAGCACAGCCACCGCTGCAGCTGCGGCACTGGCCTACTACAGGGACGCTGAGGCCTACAGACACTCCCCAGGTAACTCCATTGAGTGGCTGTCTTGGCATTGGCTGAGTGCTGTTGGGGTTGCCATGGAGATCCTTGGCTAGGTCAGAATACCACTGTGAGGATATCTCAGAAATGGCTGGAAGCTTCTCAAATGGATGTGCCGACCACTTTCCCTAGTTAAGTGCAGACCTGGGAATTCCAATGCTCCTCAACCTGCCATATTGGGGCGGCCACACTGAGAGGCAATACTGGAAGTATGTGGTGGTTGCCCTAGTTGTCGAGTGATCCGTGGAGCTCCAAATCCCAACAGTCATCCTCAAAAACCCACTTGGAAATGGTCAGAGGTTATTGCAGAGGCCACACTGACCAGTGGGGGTCAGGATCCAGGAAGCATCCAATGGCCAGCAGCTGTTCTGGTAGCCTGTGGAAAAGCTGGGAACTTGGCCACCATGTTGGGGGTGCTGGGAACCACTGCACCCTGACGTGCGCTGACCCTAGACTGATTTTGCCTCTTCTTTCCTCCATCCCTACCTGCCCCCAACAGTCTTTCAGGTGTACCCATTGCTCAACTGTATGGAGGGGATCCCAGGGGGCTCACCATATGCCGGCTGGGCCTACGGCAAGACGGGGCTCTACCCTGCCTCAACTGTGTGTCCCACCCGCGAGGACTCTCCTCCCCAGGCCGTGGAAGATCTGGATGGAAAAGGCAGCACCAGCTTCCTGGAGACTTTGAAGACAGAGCGGCTGAGCCCAGACCTCCTGACC	TGTGGGGTGGAAGGATTTCTGTGTCTGAGGACCCCTTCTGTCCTCGCAGGTTAATCCCCAGAGGCTCCATGGAGTTCCCTGGCCTGGGGTCCCTGGGGACCTCAGAGCCCCTCCCCCAGTTTGTGGATCCTGCTCTGGTGTCCTCCACACCAGAATCAGGGGTTTTCTTCCCCTCTGGGCCTGAGGGCTTGGATGCAGCAGCTTCCTCCACTGCCCCGAGCACAGCCACCGCTGCAGCTGCGGCACTGGCCTACTACAGGGACGCTGAGGCCTACAGACACTCCCCAGGTAACTCCATTGAGTGGCTGTCTTGGCATTGGCTGAGTGCTGTTGGGGTTGCCATGGAGATCCTTGGCTAGGTCAGAATACCACTGTGAGGATATCTCAGAAATGGCTGGAAGCTTCTCAAATGGATGTGCCGACCACTTTCCCTAGTTAAGTGCAGACCTGGGAATTCCAATGCTCCTCAACCTGCCATATTGGGGCGGCCACACTGAGAGGCAATACTGGAAGTATGTGGTGGTTGCCCTAGTTGTCGAGTGATCCGTGGAGCTCCAAATCCCAACAGTCATCCTCAAAAACCCACTTGGAAATGGTCAGAGGTTATTGCAGAGGCCACACTGACCAGTGGGGGTCAGGATCCAGGAAGCATCCAATGGCCAGCAGCTGTTCTGGTAGCCTGTGGAAAAGCTGGGAACTTGGCCACCATGTTGGGGGTGCTGGGAACCACTGCACCCTGACGTGCGCTGACCCTAGACTGATTTTGCCTCTTCTTTCCTCCATCCCTACCTGCCCCCAACAGTCTTTCAGGTGTACCCATTGCTCAACTGTATGGAGGGGATCCCAGGGGGCTCACCATATGCCGGCTGGGCCTACGGCAAGACGGGGCTCTACCCTGCCTCAACTGTGTGTCCCACCCGCGAGGACTCTCCTCCCCAGGCCGTGGAAGATCTGGATGGAAAAGGCAGCACCAGCTTCCTGGAGACTTTGAAGACAGAGCGGCTGAGCCCAGACCTCCTGACC	-	novel	NA	P-0063635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	48	303	0	ENST00000376670.3:c.-19-49_441del		p.X7_splice	ENST00000376670	NM_002049.3	7		2-3/6	0.235403177549352	2	FACETS	1	0.954	1	0.669	0.571	0.776	CLONAL	1	TRUE	0	0.280069815455852	2		303	256	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0063636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	95	728	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.392861917511771	2		728	458	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0063636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	105	211	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.958	0.872	1	1	0.989	1	CLONAL	2	TRUE	1	0.392861917511771	2		211	279	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0063636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	165	444	0	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	0.381903212936619	2	FACETS	0.913	0.846	0.981	0.913	0.846	0.981	CLONAL	2	TRUE	0	0.392861917511771	2		444	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0063636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	267	476	0	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.376212961977153	2	FACETS	0.999	0.943	1	0.999	0.943	1	CLONAL	2	TRUE	0	0.392861917511771	2		476	680	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467878	66467878	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	76	386	0	ENST00000273854.3:c.391A>G	p.Lys131Glu	p.K131E	ENST00000273854	NM_004439.5	131	Aaa/Gaa	3/18	1	2	FACETS	0.941	0.83	1	0.941	0.83	1	CLONAL	1	TRUE	1	0.392861917511771	2		386	411	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664669	138664669	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	84	451	0	ENST00000330315.3:c.896T>G	p.Leu299Arg	p.L299R	ENST00000330315	NM_023067.3	299	cTg/cGg	1/1	1	2	FACETS	0.988	0.877	1	0.988	0.877	1	CLONAL	1	TRUE	1	0.392861917511771	2		451	433	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416552	49416552	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	181	672	0	ENST00000301067.7:c.16159C>T	p.Gln5387Ter	p.Q5387*	ENST00000301067	NM_003482.3	5387	Cag/Tag	51/54	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.544635182527791	2		672	606	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852468	63852468	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0063637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	148	594	1	ENST00000279873.7:c.3246T>G	p.Tyr1082Ter	p.Y1082*	ENST00000279873	NM_032199.2	1082	taT/taG	10/10	1	2	FACETS	0.962	0.883	1	0.962	0.883	1	CLONAL	1	TRUE	1	0.544635182527791	2		595	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912656	NA	P-0063639-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	18	274	0	ENST00000269305.4:c.734G>C	p.Gly245Ala	p.G245A	ENST00000269305	NM_001126112.2	245	gGc/gCc	7/11	1	2	FACETS	0.416	0.312	0.539	0.416	0.312	0.539	SUBCLONAL	1	TRUE	1	0.19	2		274	456	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317600	163317601	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063639-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	25	274	0	ENST00000271452.3:c.996_997insT	p.Lys333Ter	p.K333*	ENST00000271452	NM_145697.2	332	-/T	12/14	1	2	FACETS	0.611	0.48	0.761	0.611	0.48	0.761	SUBCLONAL	1	TRUE	1	0.19	2		274	431	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811492	56811496	+	frameshift_variant	Frame_Shift_Del	DEL	GAGAT	GAGAT	-	novel	NA	P-0063639-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	31	180	0	ENST00000337432.4:c.1040_1044del	p.Arg347AsnfsTer44	p.R347Nfs*44	ENST00000337432	NM_058216.2	347	aGAGAT/a	9/9	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.19	2		180	293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0063640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	173	454	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.156797389076519	3	FACETS	0.877	0.808	0.949	0.585	0.539	0.633	INDETERMINATE	2	TRUE	0	0.28	3		454	803	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189364	99189364	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371978515	NA	P-0063640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	188	646	0	ENST00000074304.5:c.2620G>A	p.Val874Ile	p.V874I	ENST00000074304	NM_001134224.1	874	Gtc/Atc	24/26	0.250851066108592	3	FACETS	0.883	0.817	0.952	0.883	0.817	0.952	CLONAL	2	TRUE	1	0.28	3		646	867	SUCCESS
APC	324	MSKCC	GRCh37	5	112175750	112175751	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTTTATT	novel	NA	P-0063640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	137	698	0	ENST00000257430.4:c.4460_4466dup	p.Leu1489PhefsTer27	p.L1489Ffs*27	ENST00000257430	NM_000038.5	1487	act/aCTTTATTct	16/16	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.28	2		698	808	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0063658-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	10	600	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.435	0.293	0.614	0.435	0.293	0.614	SUBCLONAL	1	TRUE	1	0.13	2		600	354	SUCCESS
ATM	472	MSKCC	GRCh37	11	108154986	108154986	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063658-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	16	299	0	ENST00000278616.4:c.3779T>A	p.Val1260Glu	p.V1260E	ENST00000278616	NM_000051.3	1260	gTg/gAg	26/63	1	2	FACETS	1	0.758	1	1	0.758	1	CLONAL	1	TRUE	1	0.13	2		299	240	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46738374	46738374	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	80	677	0	ENST00000371975.4:c.1275G>C	p.Lys425Asn	p.K425N	ENST00000371975	NM_003579.3	425	aaG/aaC	12/18	1	2	FACETS	0.899	0.793	1	0.899	0.793	1	CLONAL	1	TRUE	1	0.32	2		677	556	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248385	59248385	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs370449022	NA	P-0063659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	71	829	0	ENST00000371222.2:c.358G>T	p.Glu120Ter	p.E120*	ENST00000371222	NM_002228.3	120	Gaa/Taa	1/1	1	2	FACETS	0.666	0.581	0.758	0.666	0.581	0.758	SUBCLONAL	1	TRUE	1	0.32	2		829	666	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913237	NA	P-0063659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	64	494	0	ENST00000369535.4:c.35G>C	p.Gly12Ala	p.G12A	ENST00000369535	NM_002524.4	12	gGt/gCt	2/7	1	2	FACETS	0.723	0.627	0.828	0.723	0.627	0.828	SUBCLONAL	1	TRUE	1	0.32	2		494	553	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120508147	120508147	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	55	552	0	ENST00000256646.2:c.1610C>A	p.Ser537Tyr	p.S537Y	ENST00000256646	NM_024408.3	537	tCc/tAc	10/34	1	2	FACETS	0.689	0.59	0.797	0.689	0.59	0.797	SUBCLONAL	1	TRUE	1	0.32	2		552	499	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650571	18650571	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	45	460	0	ENST00000266497.5:c.2782C>A	p.Gln928Lys	p.Q928K	ENST00000266497		928	Cag/Aag	20/31	0.28249716138779	1	FACETS	0.685	0.577	0.802	0.685	0.577	0.802	SUBCLONAL	1	TRUE	0	0.32	1		460	345	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245225	46245225	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs529386166	NA	P-0063659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	62	685	0	ENST00000334344.6:c.3319G>T	p.Ala1107Ser	p.A1107S	ENST00000334344	NM_152641.2	1107	Gca/Tca	15/21	0.169057449379719	3	FACETS	0.724	0.625	0.831	0.362	0.312	0.416	INDETERMINATE	1	TRUE	1	0.32	3		685	621	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202707	133202707	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0063659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	78	683	0	ENST00000320574.5:c.6527C>G	p.Ser2176Ter	p.S2176*	ENST00000320574	NM_006231.2	2176	tCa/tGa	46/49	1	2	FACETS	0.845	0.743	0.954	0.845	0.743	0.954	CLONAL	1	TRUE	1	0.32	2		683	577	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437157	110437157	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	28	413	0	ENST00000375856.3:c.1244A>T	p.Lys415Met	p.K415M	ENST00000375856	NM_003749.2	415	aAg/aTg	1/2	1	2	FACETS	0.473	0.378	0.581	0.473	0.378	0.581	SUBCLONAL	1	TRUE	1	0.32	2		413	370	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130215	2130215	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1265832990	NA	P-0063659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	64	835	0	ENST00000219476.3:c.3447C>G	p.Phe1149Leu	p.F1149L	ENST00000219476	NM_000548.3	1149	ttC/ttG	30/42	1	2	FACETS	0.621	0.537	0.712	0.621	0.537	0.712	SUBCLONAL	1	TRUE	1	0.32	2		835	644	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842735	68842735	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201511530	NA	P-0063659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	68	566	0	ENST00000261769.5:c.671G>A	p.Arg224His	p.R224H	ENST00000261769	NM_004360.3	224	cGc/cAc	5/16	1	2	FACETS	0.802	0.699	0.913	0.802	0.699	0.913	CLONAL	1	TRUE	1	0.32	2		566	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0063659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	16	431	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.12638420472325	3	FACETS	0.23	0.169	0.303	0.115	0.084	0.152	INDETERMINATE	1	TRUE	1	0.32	3		431	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577578	7577578	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	64	563	0	ENST00000269305.4:c.703A>G	p.Asn235Asp	p.N235D	ENST00000269305	NM_001126112.2	235	Aac/Gac	7/11	0.12638420472325	3	FACETS	0.841	0.728	0.962	0.42	0.364	0.481	INDETERMINATE	1	TRUE	1	0.32	3		563	552	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690489	33690489	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs898941876	NA	P-0063659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	55	687	0	ENST00000308377.4:c.338G>A	p.Gly113Asp	p.G113D	ENST00000308377	NM_152270.3	113	gGc/gAc	2/5	0.12638420472325	3	FACETS	0.718	0.615	0.832	0.359	0.307	0.416	INDETERMINATE	1	TRUE	1	0.32	3		687	555	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489452	40489452	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0063659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	33	532	0	ENST00000264657.5:c.797+1G>C		p.X266_splice	ENST00000264657	NM_139276.2	266			0.12638420472325	3	FACETS	0.455	0.37	0.551	0.227	0.185	0.276	INDETERMINATE	1	TRUE	1	0.32	3		532	526	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119783	70119783	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1196485591	NA	P-0063659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	53	610	0	ENST00000245479.2:c.785G>T	p.Gly262Val	p.G262V	ENST00000245479	NM_000346.3	262	gGg/gTg	3/3	0.12638420472325	3	FACETS	0.867	0.741	1	0.434	0.37	0.503	INDETERMINATE	1	TRUE	1	0.32	3		610	443	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732418	74732418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	43	732	0	ENST00000359995.5:c.491G>A	p.Arg164Lys	p.R164K	ENST00000359995	NM_001195427.1	164	aGa/aAa	2/3	0.12638420472325	3	FACETS	0.392	0.327	0.465	0.196	0.163	0.233	INDETERMINATE	1	TRUE	1	0.32	3		732	795	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220382	1220382	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	78	697	0	ENST00000326873.7:c.475C>T	p.Gln159Ter	p.Q159*	ENST00000326873	NM_000455.4	159	Cag/Tag	4/10	0.28249716138779	1	FACETS	0.662	0.582	0.747	0.662	0.582	0.747	SUBCLONAL	1	TRUE	0	0.32	1		697	619	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610126	10610126	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	74	704	0	ENST00000171111.5:c.584G>T	p.Gly195Val	p.G195V	ENST00000171111	NM_203500.1	195	gGc/gTc	2/6	0.28249716138779	1	FACETS	0.6	0.526	0.681	0.6	0.526	0.681	SUBCLONAL	1	TRUE	0	0.32	1		704	647	SUCCESS
ALK	238	MSKCC	GRCh37	2	29419727	29419727	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0063659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	25	494	0	ENST00000389048.3:c.4074-1G>A		p.X1358_splice	ENST00000389048	NM_004304.4	1358			1	2	FACETS	0.419	0.33	0.521	0.419	0.33	0.521	SUBCLONAL	1	TRUE	1	0.32	2		494	373	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010526	48010526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	33	714	0	ENST00000234420.5:c.154G>A	p.Glu52Lys	p.E52K	ENST00000234420	NM_000179.2	52	Gag/Aag	1/10	1	2	FACETS	0.351	0.285	0.426	0.351	0.285	0.426	SUBCLONAL	1	TRUE	1	0.32	2		714	587	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623229	52623229	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	55	524	1	ENST00000394830.3:c.2822C>A	p.Ser941Ter	p.S941*	ENST00000394830	NM_018313.4	941	tCa/tAa	19/30	1	2	FACETS	0.656	0.561	0.759	0.656	0.561	0.759	SUBCLONAL	1	TRUE	1	0.32	2		525	524	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955589	55955589	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	29	468	0	ENST00000263923.4:c.3356T>C	p.Leu1119Ser	p.L1119S	ENST00000263923	NM_002253.2	1119	tTg/tCg	25/30	1	2	FACETS	0.472	0.379	0.578	0.472	0.379	0.578	SUBCLONAL	1	TRUE	1	0.32	2		468	384	SUCCESS
APC	324	MSKCC	GRCh37	5	112175558	112175558	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	40	615	0	ENST00000257430.4:c.4267C>A	p.Leu1423Ile	p.L1423I	ENST00000257430	NM_000038.5	1423	Ctt/Att	16/16	1	2	FACETS	0.402	0.333	0.479	0.402	0.333	0.479	SUBCLONAL	1	TRUE	1	0.32	2		615	622	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20487009	20487009	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	26	482	0	ENST00000346618.3:c.974G>C	p.Arg325Thr	p.R325T	ENST00000346618	NM_001949.4	325	aGa/aCa	5/7	1	2	FACETS	0.374	0.295	0.464	0.374	0.295	0.464	SUBCLONAL	1	TRUE	1	0.32	2		482	435	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056650	26056650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	89	577	0	ENST00000343677.2:c.7G>A	p.Glu3Lys	p.E3K	ENST00000343677	NM_005319.3	3	Gag/Aag	1/1	0.3	3	FACETS	1	0.93	1	0.532	0.472	0.596	CLONAL	1	TRUE	1	0.32	3		577	606	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671278	30671278	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	37	772	0	ENST00000376406.3:c.5599G>T	p.Asp1867Tyr	p.D1867Y	ENST00000376406	NM_014641.2	1867	Gac/Tac	11/15	0.3	3	FACETS	0.399	0.328	0.479	0.2	0.164	0.24	SUBCLONAL	1	TRUE	1	0.32	3		772	672	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168711	32168711	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	128	710	0	ENST00000375023.3:c.4212C>A	p.Asp1404Glu	p.D1404E	ENST00000375023	NM_004557.3	1404	gaC/gaA	23/30	0.3	3	FACETS	0.762	0.693	0.834	0.762	0.693	0.834	SUBCLONAL	2	TRUE	1	0.32	3		710	609	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289023	33289023	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	125	841	0	ENST00000374542.5:c.529C>G	p.Gln177Glu	p.Q177E	ENST00000374542	NM_001141970.1	177	Cag/Gag	3/8	0.3	3	FACETS	1	0.958	1	0.553	0.5	0.608	CLONAL	1	TRUE	1	0.32	3		841	820	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956617	93956617	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	46	632	0	ENST00000369303.4:c.2619G>A	p.Trp873Ter	p.W873*	ENST00000369303	NM_004440.3	873	tgG/tgA	15/17	1	2	FACETS	0.607	0.511	0.712	0.607	0.511	0.712	SUBCLONAL	1	TRUE	1	0.32	2		632	474	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956676	93956676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465960814	NA	P-0063659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	24	518	0	ENST00000369303.4:c.2560C>T	p.Arg854Cys	p.R854C	ENST00000369303	NM_004440.3	854	Cgt/Tgt	15/17	1	2	FACETS	0.38	0.297	0.475	0.38	0.297	0.475	SUBCLONAL	1	TRUE	1	0.32	2		518	395	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56910981	56910981	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	52	552	0	ENST00000519728.1:c.1127C>G	p.Ser376Cys	p.S376C	ENST00000519728	NM_002350.3	376	tCc/tGc	11/13	1	2	FACETS	0.566	0.482	0.659	0.566	0.482	0.659	SUBCLONAL	1	TRUE	1	0.32	2		552	574	SUCCESS
PHF6	84295	MSKCC	GRCh37	X	133511724	133511724	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	20	425	0	ENST00000332070.3:c.77A>G	p.Lys26Arg	p.K26R	ENST00000332070	NM_032458.2	26	aAg/aGg	2/10	0.208287298524977	0	FACETS	0.25	0.191	0.319			1	SUBCLONAL	1	TRUE	0	0.32	0		425	340	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0063660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	323	818	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.293562817622781	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.293562817622781	2		818	936	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0063660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	141	949	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.293562817622781	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.293562817622781	1		950	733	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888075	81888075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780140339	NA	P-0063660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	66	469	0	ENST00000359376.3:c.220C>T	p.Arg74Cys	p.R74C	ENST00000359376	NM_002661.3	74	Cgc/Tgc	3/33	0.293562817622781	1	FACETS	0.868	0.756	0.989	0.868	0.756	0.989	CLONAL	1	TRUE	0	0.293562817622781	1		469	442	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353939	15353947	+	inframe_deletion	In_Frame_Del	DEL	GGGGTGGTG	GGGGTGGTG	-	rs758265124	NA	P-0063660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	46	283	0	ENST00000263377.2:c.2933_2941del	p.Pro978_Pro980del	p.P978_P980del	ENST00000263377	NM_058243.2	978	cCACCACCCCag/cag	14/20	0.293562817622781	1	FACETS	0.99	0.84	1	0.99	0.84	1	CLONAL	1	TRUE	0	0.293562817622781	1		283	270	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150916470	150916470	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0063660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	88	446	0	ENST00000271640.5:c.949+1G>A		p.X317_splice	ENST00000271640	NM_001145415.1	317			1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.293562817622781	2		446	509	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435029	18435029	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs577826082	NA	P-0063660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	100	414	0	ENST00000266497.5:c.14G>A	p.Trp5Ter	p.W5*	ENST00000266497		5	tGg/tAg	1/31	0.290886426708419	2	FACETS	0.954	0.86	1	0.954	0.86	1	CLONAL	2	TRUE	0	0.293562817622781	2		414	357	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243826	46243842	+	frameshift_variant	Frame_Shift_Del	DEL	TCATGGATCACAAACCA	TCATGGATCACAAACCA	-	novel	NA	P-0063660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	124	436	0	ENST00000334344.6:c.1921_1937del	p.His641ArgfsTer60	p.H641Rfs*60	ENST00000334344	NM_152641.2	640	ccTCATGGATCACAAACCAta/ccta	15/21	0.219082373203694	3	FACETS	1	0.918	1	0.673	0.612	0.736	CLONAL	2	TRUE	0	0.293562817622781	3		436	480	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220424	1220433	+	frameshift_variant	Frame_Shift_Del	DEL	GTGCACAAGG	GTGCACAAGG	-	novel	NA	P-0063660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	99	664	0	ENST00000326873.7:c.517_526del	p.Val173ThrfsTer111	p.V173Tfs*111	ENST00000326873	NM_000455.4	173	GTGCACAAGGac/ac	4/10	0.293562817622781	1	FACETS	0.924	0.826	1	0.924	0.826	1	CLONAL	1	TRUE	0	0.293562817622781	1		664	623	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928071	178928100	+	inframe_deletion	In_Frame_Del	DEL	ATGGATTAGAAGATTTGCTGAACCCTATTG	ATGGATTAGAAGATTTGCTGAACCCTATTG	-	novel	NA	P-0063660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	42	503	0	ENST00000263967.3:c.1349_1378del	p.His450_Gly460delinsArg	p.H450_G460delinsR	ENST00000263967	NM_006218.2	450	cATGGATTAGAAGATTTGCTGAACCCTATTGgt/cgt	8/21	1	2	FACETS	0.721	0.603	0.851	0.721	0.603	0.851	SUBCLONAL	1	TRUE	1	0.293562817622781	2		503	397	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	183	622	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.876	0.812	0.942	1	0.992	1	CLONAL	2	TRUE	1	0.32	2		626	653	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	43	348	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.664	0.556	0.782	0.664	0.556	0.782	SUBCLONAL	1	TRUE	1	0.32	2		348	405	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158465	26158467	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs766586530	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	107	666	0	ENST00000289316.2:c.73_75del	p.Lys25del	p.K25del	ENST00000289316	NM_138720.2	23	cAGAag/cag	1/2	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.32	2		666	642	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429978	78429978	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	83	562	0	ENST00000370768.2:c.901del	p.Ile301TyrfsTer22	p.I301Yfs*22	ENST00000370768	NM_003902.3	301	Ata/ta	11/20	1	2	FACETS	0.981	0.868	1	0.981	0.868	1	CLONAL	1	TRUE	1	0.32	2		562	529	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	65	399	0	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.951	0.828	1	0.951	0.828	1	CLONAL	1	TRUE	1	0.32	2		399	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780068	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	87	832	0	ENST00000269305.4:c.472C>T	p.Arg158Cys	p.R158C	ENST00000269305	NM_001126112.2	158	Cgc/Tgc	5/11	1	2	FACETS	0.796	0.705	0.894	0.796	0.705	0.894	SUBCLONAL	1	TRUE	1	0.32	2		832	683	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780069	9780069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762320758	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	79	970	0	ENST00000377346.4:c.1333G>A	p.Val445Ile	p.V445I	ENST00000377346	NM_005026.3	445	Gtc/Atc	10/24	1	2	FACETS	0.796	0.701	0.899	0.796	0.701	0.899	SUBCLONAL	1	TRUE	1	0.32	2		970	620	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22413313	22413313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1449280793	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	35	268	0	ENST00000344548.3:c.440G>A	p.Arg147His	p.R147H	ENST00000344548	NM_001039802.1	147	cGt/cAt	6/7	1	2	FACETS	0.999	0.825	1	0.999	0.825	1	CLONAL	1	TRUE	1	0.32	2		268	219	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105715	27105717	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs765246223	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	99	765	2	ENST00000324856.7:c.5334_5336del	p.Glu1780del	p.E1780del	ENST00000324856	NM_006015.4	1776	GAA/-	20/20	1	2	FACETS	0.971	0.868	1	0.971	0.868	1	CLONAL	1	TRUE	1	0.32	2		767	637	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805058	43805058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1339501124	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	89	714	0	ENST00000372470.3:c.508C>T	p.Arg170Cys	p.R170C	ENST00000372470	NM_005373.2	170	Cgc/Tgc	4/12	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.32	2		714	472	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812204	43812204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs751975712	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	81	782	0	ENST00000372470.3:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000372470	NM_005373.2	357	Cga/Tga	7/12	1	2	FACETS	0.938	0.828	1	0.938	0.828	1	CLONAL	1	TRUE	1	0.32	2		782	540	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247810	59247811	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	112	792	0	ENST00000371222.2:c.932_933del	p.Lys311SerfsTer6	p.K311Sfs*6	ENST00000371222	NM_002228.3	311	aAA/a	1/1	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.32	2		792	676	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468185	120468185	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	40	884	1	ENST00000256646.2:c.4254del	p.Ser1419AlafsTer8	p.S1419Afs*8	ENST00000256646	NM_024408.3	1418	ccC/cc	25/34	1	2	FACETS	0.359	0.297	0.428	0.359	0.297	0.428	SUBCLONAL	1	TRUE	1	0.32	2		885	697	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851285	156851285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778520978	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	82	762	0	ENST00000524377.1:c.2242C>T	p.Arg748Trp	p.R748W	ENST00000524377	NM_002529.3	748	Cgg/Tgg	17/17	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.32	2		762	456	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652477	206652477	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs781999092	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	78	716	0	ENST00000367120.3:c.1183+1G>A		p.X395_splice	ENST00000367120	NM_014002.3	395			1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.32	2		716	484	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612921	228612921	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779185305	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	97	1141	1	ENST00000366696.1:c.106G>A	p.Val36Met	p.V36M	ENST00000366696	NM_003493.2	36	Gtg/Atg	1/1	1	2	FACETS	0.805	0.718	0.898	0.805	0.718	0.898	CLONAL	1	TRUE	1	0.32	2		1142	753	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230472880	230472880	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767901578	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	52	621	0	ENST00000391860.1:c.704C>T	p.Thr235Met	p.T235M	ENST00000391860	NM_001258311.1	235	aCg/aTg	4/7	1	2	FACETS	0.694	0.592	0.807	0.694	0.592	0.807	SUBCLONAL	1	TRUE	1	0.32	2		621	468	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021816	246021816	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218705109	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	74	567	0	ENST00000388985.4:c.1058G>A	p.Arg353Gln	p.R353Q	ENST00000388985		353	cGg/cAg	10/12	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.32	2		567	448	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137748	64137748	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201085797	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	67	693	0	ENST00000334205.4:c.1849G>A	p.Gly617Arg	p.G617R	ENST00000334205	NM_003942.2	617	Ggg/Agg	15/17	1	2	FACETS	0.867	0.755	0.987	0.867	0.755	0.987	CLONAL	1	TRUE	1	0.32	2		693	483	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491390	18491390	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1377942847	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	66	394	0	ENST00000266497.5:c.1309del	p.Ile437TyrfsTer5	p.I437Yfs*5	ENST00000266497		435	Aaa/aa	8/31	1	2	FACETS	0.984	0.858	1	0.984	0.858	1	CLONAL	1	TRUE	1	0.32	2		394	419	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242662	46242662	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	52	426	0	ENST00000334344.6:c.1624C>T	p.Arg542Ter	p.R542*	ENST00000334344	NM_152641.2	542	Cga/Tga	13/21	1	2	FACETS	0.898	0.767	1	0.898	0.767	1	CLONAL	1	TRUE	1	0.32	2		426	362	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433995	49433995	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759516070	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	82	845	0	ENST00000301067.7:c.7558C>T	p.Arg2520Trp	p.R2520W	ENST00000301067	NM_003482.3	2520	Cgg/Tgg	31/54	1	2	FACETS	0.956	0.845	1	0.956	0.845	1	CLONAL	1	TRUE	1	0.32	2		845	536	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143249	58143249	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257383551	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	54	489	0	ENST00000257904.6:c.671G>A	p.Gly224Asp	p.G224D	ENST00000257904	NM_000075.3	224	gGc/gAc	6/8	1	2	FACETS	0.697	0.596	0.808	0.697	0.596	0.808	SUBCLONAL	1	TRUE	1	0.32	2		489	484	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589318	28589318	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1318196723	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	51	386	0	ENST00000241453.7:c.2729A>G	p.Gln910Arg	p.Q910R	ENST00000241453	NM_004119.2	910	cAg/cGg	22/24	1	2	FACETS	0.85	0.725	0.986	0.85	0.725	0.986	CLONAL	1	TRUE	1	0.32	2		386	375	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355832	73355832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs934539972	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	83	635	0	ENST00000377767.4:c.139G>A	p.Ala47Thr	p.A47T	ENST00000377767	NM_014953.3	47	Gcc/Acc	1/21	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.32	2		635	436	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435774	110435774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1428455100	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	81	716	1	ENST00000375856.3:c.2627G>A	p.Arg876His	p.R876H	ENST00000375856	NM_003749.2	876	cGc/cAc	1/2	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.32	2		717	439	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242073	105242075	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs768025881	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	69	737	5	ENST00000349310.3:c.349_351del	p.Glu117del	p.E117del	ENST00000349310	NM_001014432.1	117	GAG/-	6/15	1	2	FACETS	0.869	0.759	0.988	0.869	0.759	0.988	CLONAL	1	TRUE	1	0.32	2		742	496	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034744	42034744	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs752630480	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	29	533	0	ENST00000219905.7:c.4586C>T	p.Ala1529Val	p.A1529V	ENST00000219905	NM_001164273.1	1529	gCg/gTg	15/24	0.13485939235562	1	FACETS	0.314	0.251	0.385	0.314	0.251	0.385	INDETERMINATE	1	TRUE	0	0.32	1		533	485	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003771	45003772	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTCGCGCTACTCTCTCTTTC	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	31	726	0	ENST00000558401.1:c.28_47dup	p.Gly17SerfsTer34	p.G17Sfs*34	ENST00000558401	NM_004048.2	9	-/CTCGCGCTACTCTCTCTTTC	1/4	0.13485939235562	1	FACETS	0.345	0.278	0.42	0.345	0.278	0.42	INDETERMINATE	1	TRUE	0	0.32	1		726	472	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	360006	360006	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	62	678	0	ENST00000262320.3:c.1083G>T	p.Gln361His	p.Q361H	ENST00000262320	NM_003502.3	361	caG/caT	4/11	1	2	FACETS	0.784	0.679	0.899	0.784	0.679	0.899	SUBCLONAL	1	TRUE	1	0.32	2		678	494	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223532	2223532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	76	797	0	ENST00000326181.6:c.1063C>T	p.Arg355Trp	p.R355W	ENST00000326181	NM_032271.2	355	Cgg/Tgg	11/21	1	2	FACETS	0.798	0.701	0.903	0.798	0.701	0.903	CLONAL	1	TRUE	1	0.32	2		797	595	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639453	3639453	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376437029	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	96	787	0	ENST00000294008.3:c.4186G>A	p.Gly1396Arg	p.G1396R	ENST00000294008	NM_032444.2	1396	Gga/Aga	12/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.32	2		787	530	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639540	3639540	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs17136464	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	78	851	1	ENST00000294008.3:c.4099G>A	p.Ala1367Thr	p.A1367T	ENST00000294008	NM_032444.2	1367	Gcc/Acc	12/15	1	2	FACETS	0.811	0.713	0.916	0.811	0.713	0.916	CLONAL	1	TRUE	1	0.32	2		852	601	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639605	3639605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757202686	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	88	936	0	ENST00000294008.3:c.4034G>A	p.Arg1345His	p.R1345H	ENST00000294008	NM_032444.2	1345	cGt/cAt	12/15	1	2	FACETS	0.863	0.766	0.968	0.863	0.766	0.968	CLONAL	1	TRUE	1	0.32	2		936	637	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647564	3647564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377440877	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	74	717	0	ENST00000294008.3:c.1499C>T	p.Thr500Met	p.T500M	ENST00000294008	NM_032444.2	500	aCg/aTg	7/15	1	2	FACETS	0.936	0.822	1	0.936	0.822	1	CLONAL	1	TRUE	1	0.32	2		717	494	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786718	3786718	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567269945	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	33	637	0	ENST00000262367.5:c.4493G>A	p.Arg1498Gln	p.R1498Q	ENST00000262367	NM_004380.2	1498	cGa/cAa	27/31	1	2	FACETS	0.359	0.292	0.436	0.359	0.292	0.436	SUBCLONAL	1	TRUE	1	0.32	2		637	574	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993384	72993384	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	72	803	0	ENST00000268489.5:c.661C>A	p.Leu221Met	p.L221M	ENST00000268489	NM_006885.3	221	Ctg/Atg	2/10	1	2	FACETS	0.779	0.681	0.884	0.779	0.681	0.884	SUBCLONAL	1	TRUE	1	0.32	2		803	578	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993737	72993737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776936617	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	83	906	0	ENST00000268489.5:c.308G>A	p.Arg103His	p.R103H	ENST00000268489	NM_006885.3	103	cGc/cAc	2/10	1	2	FACETS	0.917	0.81	1	0.917	0.81	1	CLONAL	1	TRUE	1	0.32	2		906	566	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81927367	81927367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781016626	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	80	507	1	ENST00000359376.3:c.1040G>A	p.Arg347His	p.R347H	ENST00000359376	NM_002661.3	347	cGc/cAc	12/33	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.32	2		508	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397516435	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	87	849	0	ENST00000269305.4:c.586C>G	p.Arg196Gly	p.R196G	ENST00000269305	NM_001126112.2	196	Cga/Gga	6/11	1	2	FACETS	0.873	0.773	0.979	0.873	0.773	0.979	CLONAL	1	TRUE	1	0.32	2		849	623	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	10	466	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.127	0.085	0.18	0.127	0.085	0.18	SUBCLONAL	1	TRUE	1	0.32	2		466	491	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40860919	40860919	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	42	433	0	ENST00000428826.2:c.1509C>G	p.His503Gln	p.H503Q	ENST00000428826		503	caC/caG	14/21	1	2	FACETS	0.702	0.587	0.828	0.702	0.587	0.828	SUBCLONAL	1	TRUE	1	0.32	2		433	374	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246554	41246554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357176	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	52	727	0	ENST00000357654.3:c.994C>T	p.Arg332Trp	p.R332W	ENST00000357654	NM_007294.3	332	Cgg/Tgg	10/23	1	2	FACETS	0.572	0.487	0.666	0.572	0.487	0.666	SUBCLONAL	1	TRUE	1	0.32	2		727	568	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256182	41256182	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80357357	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	93	510	0	ENST00000357654.3:c.398G>A	p.Arg133His	p.R133H	ENST00000357654	NM_007294.3	133	cGt/cAt	6/23	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.32	2		510	495	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	181	793	2	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	1	2	FACETS	0.967	0.897	1	1	0.993	1	CLONAL	2	TRUE	1	0.32	2		795	585	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899218	78899218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201551267	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	110	690	2	ENST00000306801.3:c.2857G>A	p.Ala953Thr	p.A953T	ENST00000306801	NM_020761.2	953	Gcc/Acc	24/34	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.32	2		692	602	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584806	48584806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370176106	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	90	691	1	ENST00000342988.3:c.884C>T	p.Pro295Leu	p.P295L	ENST00000342988	NM_005359.5	295	cCg/cTg	7/12	1	2	FACETS	0.778	0.69	0.872	0.778	0.69	0.872	SUBCLONAL	1	TRUE	1	0.32	2		692	723	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5206811	5206811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200187372	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	28	720	2	ENST00000357368.4:c.5821G>A	p.Gly1941Arg	p.G1941R	ENST00000357368	NM_002850.3	1941	Gga/Aga	38/38	1	2	FACETS	0.369	0.294	0.455	0.369	0.294	0.455	SUBCLONAL	1	TRUE	1	0.32	2		722	474	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229346	5229346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761681941	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	88	771	0	ENST00000357368.4:c.2357C>T	p.Thr786Met	p.T786M	ENST00000357368	NM_002850.3	786	aCg/aTg	16/38	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.32	2		771	479	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6230627	6230627	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	69	711	0	ENST00000252674.7:c.374A>G	p.Asn125Ser	p.N125S	ENST00000252674	NM_005934.3	125	aAc/aGc	4/12	1	2	FACETS	0.763	0.665	0.869	0.763	0.665	0.869	SUBCLONAL	1	TRUE	1	0.32	2		711	565	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600462	10600462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	101	813	1	ENST00000171111.5:c.1393G>A	p.Val465Met	p.V465M	ENST00000171111	NM_203500.1	465	Gtg/Atg	4/6	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.32	2		814	592	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129635	11129635	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	75	640	0	ENST00000358026.2:c.2441C>T	p.Thr814Met	p.T814M	ENST00000358026	NM_001128849.1	814	aCg/aTg	17/36	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.32	2		640	466	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288687	15288687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	51	492	0	ENST00000263388.2:c.4052G>A	p.Arg1351His	p.R1351H	ENST00000263388	NM_000435.2	1351	cGc/cAc	24/33	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.32	2		492	289	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354052	15354052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753396296	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	42	470	0	ENST00000263377.2:c.2828C>T	p.Pro943Leu	p.P943L	ENST00000263377	NM_058243.2	943	cCg/cTg	14/20	1	2	FACETS	0.852	0.715	1	0.852	0.715	1	CLONAL	1	TRUE	1	0.32	2		470	308	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272121	18272121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	59	930	0	ENST00000222254.8:c.631C>T	p.Pro211Ser	p.P211S	ENST00000222254	NM_005027.3	211	Cca/Tca	6/16	1	2	FACETS	0.809	0.697	0.929	0.809	0.697	0.929	CLONAL	1	TRUE	1	0.32	2		930	456	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968250	18968250	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	54	606	0	ENST00000262803.5:c.2090G>A	p.Arg697His	p.R697H	ENST00000262803	NM_002911.3	697	cGc/cAc	15/24	1	2	FACETS	0.835	0.716	0.966	0.835	0.716	0.966	CLONAL	1	TRUE	1	0.32	2		606	404	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18975060	18975060	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	53	458	0	ENST00000262803.5:c.2857G>T	p.Gly953Cys	p.G953C	ENST00000262803	NM_002911.3	953	Ggc/Tgc	20/24	1	2	FACETS	0.798	0.682	0.924	0.798	0.682	0.924	CLONAL	1	TRUE	1	0.32	2		458	415	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256768	19256769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1202792889	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	46	730	1	ENST00000162023.5:c.944dup	p.Val316SerfsTer6	p.V316Sfs*6	ENST00000162023		315	cca/ccCa	13/13	1	2	FACETS	0.637	0.537	0.748	0.637	0.537	0.748	SUBCLONAL	1	TRUE	1	0.32	2		731	451	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792311	33792311	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760372994	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	60	596	0	ENST00000498907.2:c.1010C>T	p.Thr337Met	p.T337M	ENST00000498907	NM_004364.3	337	aCg/aTg	1/1	1	2	FACETS	0.822	0.71	0.944	0.822	0.71	0.944	CLONAL	1	TRUE	1	0.32	2		596	456	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214714	36214714	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	33	709	0	ENST00000222270.7:c.3145del	p.Ala1049ArgfsTer133	p.A1049Rfs*133	ENST00000222270	NM_014727.1	1047	cGg/cg	8/37	1	2	FACETS	0.481	0.391	0.582	0.481	0.391	0.582	SUBCLONAL	1	TRUE	1	0.32	2		709	429	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424653	47424653	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	53	660	0	ENST00000404338.3:c.2725del	p.Glu909ArgfsTer39	p.E909Rfs*39	ENST00000404338	NM_004491.4	907	gaG/ga	1/6	1	2	FACETS	0.59	0.503	0.686	0.59	0.503	0.686	SUBCLONAL	1	TRUE	1	0.32	2		660	561	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424841	47424841	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	61	770	0	ENST00000404338.3:c.2914del	p.Arg972GlyfsTer55	p.R972Gfs*55	ENST00000404338	NM_004491.4	970	tCc/tc	1/6	1	2	FACETS	0.651	0.561	0.748	0.651	0.561	0.748	SUBCLONAL	1	TRUE	1	0.32	2		770	586	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905596	50905596	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910905700	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	68	988	0	ENST00000440232.2:c.724G>A	p.Ala242Thr	p.A242T	ENST00000440232	NM_002691.3	242	Gcg/Acg	6/27	1	2	FACETS	0.762	0.663	0.868	0.762	0.663	0.868	SUBCLONAL	1	TRUE	1	0.32	2		988	558	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906370	50906370	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs749601227	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	25	813	2	ENST00000440232.2:c.1036del	p.Glu346SerfsTer47	p.E346Sfs*47	ENST00000440232	NM_002691.3	344	tGg/tg	9/27	1	2	FACETS	0.314	0.246	0.392	0.314	0.246	0.392	SUBCLONAL	1	TRUE	1	0.32	2		815	498	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690278	47690278	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	69	511	0	ENST00000233146.2:c.1495del	p.Ala499GlnfsTer27	p.A499Qfs*27	ENST00000233146	NM_000251.2	499	Gca/ca	9/16	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.32	2		511	430	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682810	190682810	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	47	406	3	ENST00000441310.2:c.492del	p.Lys164AsnfsTer6	p.K164Nfs*6	ENST00000441310	NM_000534.4	162	gcA/gc	5/13	1	2	FACETS	0.8	0.677	0.935	0.8	0.677	0.935	CLONAL	1	TRUE	1	0.32	2		409	367	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131393	202131393	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	38	607	0	ENST00000358485.4:c.361C>A	p.Leu121Met	p.L121M	ENST00000358485	NM_001080125.1	121	Ctg/Atg	2/9	1	2	FACETS	0.468	0.386	0.559	0.468	0.386	0.559	SUBCLONAL	1	TRUE	1	0.32	2		607	508	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150031	202150031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167464002	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	21	730	0	ENST00000358485.4:c.1472G>A	p.Arg491Gln	p.R491Q	ENST00000358485	NM_001080125.1	491	cGa/cAa	8/9	1	2	FACETS	0.226	0.173	0.288	0.226	0.173	0.288	SUBCLONAL	1	TRUE	1	0.32	2		730	582	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	33	704	9	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.376	0.305	0.455	0.376	0.305	0.455	SUBCLONAL	1	TRUE	1	0.32	2		713	549	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46252780	46252780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs181661523	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	38	401	0	ENST00000371998.3:c.209C>T	p.Ala70Val	p.A70V	ENST00000371998		70	gCg/gTg	4/23	1	2	FACETS	0.57	0.471	0.679	0.57	0.471	0.679	SUBCLONAL	1	TRUE	1	0.32	2		401	417	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292793	62292793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143461704	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	98	742	0	ENST00000360203.5:c.245C>T	p.Pro82Leu	p.P82L	ENST00000360203	NM_001283009.1	82	cCg/cTg	3/35	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.32	2		742	532	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29279900	29279904	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCC	GGCCC	-	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	45	547	0	ENST00000544604.2:c.149_153del	p.Pro50ArgfsTer57	p.P50Rfs*57	ENST00000544604	NM_001206998.1	49	gGGCCC/g	1/9	1	2	FACETS	0.922	0.779	1	0.922	0.779	1	CLONAL	1	TRUE	1	0.32	2		547	305	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29383127	29383127	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	105	710	0	ENST00000544604.2:c.364G>T	p.Gly122Ter	p.G122*	ENST00000544604	NM_001206998.1	122	Gga/Tga	2/9	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.32	2		710	579	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446630	29446630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1448914612	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	76	735	0	ENST00000544604.2:c.2461G>A	p.Gly821Arg	p.G821R	ENST00000544604	NM_001206998.1	821	Ggg/Agg	8/9	1	2	FACETS	0.99	0.871	1	0.99	0.871	1	CLONAL	1	TRUE	1	0.32	2		735	480	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	101	719	0	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.32	2		719	586	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390093	89390093	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	102	553	0	ENST00000336596.2:c.842T>C	p.Leu281Ser	p.L281S	ENST00000336596	NM_005233.5	281	tTg/tCg	4/17	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.32	2		553	538	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226864	142226864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758322712	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	82	577	0	ENST00000350721.4:c.4940G>A	p.Arg1647His	p.R1647H	ENST00000350721	NM_001184.3	1647	cGc/cAc	28/47	1	2	FACETS	0.965	0.853	1	0.965	0.853	1	CLONAL	1	TRUE	1	0.32	2		577	531	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952025	178952025	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	41	562	0	ENST00000263967.3:c.3080C>T	p.Ala1027Val	p.A1027V	ENST00000263967	NM_006218.2	1027	gCc/gTc	21/21	1	2	FACETS	0.505	0.421	0.6	0.505	0.421	0.6	SUBCLONAL	1	TRUE	1	0.32	2		562	507	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806170	1806170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576428377	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	81	780	0	ENST00000260795.2:c.1189C>T	p.Arg397Cys	p.R397C	ENST00000260795		397	Cgc/Tgc	8/17	1	2	FACETS	0.959	0.847	1	0.959	0.847	1	CLONAL	1	TRUE	1	0.32	2		780	528	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133805	55133805	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376626935	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	80	634	0	ENST00000257290.5:c.1018C>T	p.Arg340Trp	p.R340W	ENST00000257290	NM_006206.4	340	Cgg/Tgg	7/23	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.32	2		634	477	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961056	55961056	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1312670638	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	69	527	0	ENST00000263923.4:c.2884C>T	p.Arg962Cys	p.R962C	ENST00000263923	NM_002253.2	962	Cgc/Tgc	21/30	1	2	FACETS	0.908	0.793	1	0.908	0.793	1	CLONAL	1	TRUE	1	0.32	2		527	475	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196976	106196976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs556077207	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	67	615	0	ENST00000380013.4:c.5309C>T	p.Pro1770Leu	p.P1770L	ENST00000380013	NM_001127208.2	1770	cCg/cTg	11/11	1	2	FACETS	0.872	0.76	0.994	0.872	0.76	0.994	CLONAL	1	TRUE	1	0.32	2		615	480	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144336883	144336883	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377700737	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	64	467	0	ENST00000262995.4:c.326G>A	p.Arg109His	p.R109H	ENST00000262995	NM_207123.2	109	cGt/cAt	2/11	1	2	FACETS	0.939	0.816	1	0.939	0.816	1	CLONAL	1	TRUE	1	0.32	2		467	426	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254570	1254570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	69	614	1	ENST00000310581.5:c.3208G>A	p.Val1070Met	p.V1070M	ENST00000310581	NM_198253.2	1070	Gtg/Atg	15/16	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.32	2		615	406	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295969	1295969	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	106	1016	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.32	2		1016	639	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753011	57753012	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	104	680	6	ENST00000274289.3:c.1004dup	p.Leu335PhefsTer12	p.L335Ffs*12	ENST00000274289	NM_006622.3	335	ttg/ttTg	7/14	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.32	2		686	650	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659299	86659299	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771416114	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	52	459	0	ENST00000274376.6:c.1588G>A	p.Val530Ile	p.V530I	ENST00000274376	NM_002890.2	530	Gtt/Att	11/25	1	2	FACETS	0.772	0.659	0.896	0.772	0.659	0.896	SUBCLONAL	1	TRUE	1	0.32	2		459	421	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518080	176518080	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	47	730	0	ENST00000292408.4:c.578G>T	p.Gly193Val	p.G193V	ENST00000292408	NM_213647.1	193	gGg/gTg	5/18	1	2	FACETS	0.588	0.496	0.689	0.588	0.496	0.689	SUBCLONAL	1	TRUE	1	0.32	2		730	500	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043464	180043464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	79	723	0	ENST00000261937.6:c.3122G>A	p.Arg1041Gln	p.R1041Q	ENST00000261937	NM_182925.4	1041	cGg/cAg	23/30	1	2	FACETS	0.995	0.878	1	0.995	0.878	1	CLONAL	1	TRUE	1	0.32	2		723	496	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058747	180058748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755445139	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	56	751	1	ENST00000261937.6:c.89dup	p.Thr31AspfsTer15	p.T31Dfs*15	ENST00000261937	NM_182925.4	30	ccg/ccCg	2/30	1	2	FACETS	0.676	0.579	0.781	0.676	0.579	0.781	SUBCLONAL	1	TRUE	1	0.32	2		752	518	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910584	29910584	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	42	425	1	ENST00000376809.5:c.127del	p.Glu43SerfsTer34	p.E43Sfs*34	ENST00000376809	NM_002116.7	42	Ggg/gg	2/8	1	2	FACETS	0.955	0.802	1	0.955	0.802	1	CLONAL	1	TRUE	1	0.32	2		426	275	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31238888	31238888	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	17	463	0	ENST00000376228.5:c.581G>T	p.Arg194Ile	p.R194I	ENST00000376228	NM_002117.5	194	aGa/aTa	3/8	1	2	FACETS	0.321	0.239	0.419	0.321	0.239	0.419	SUBCLONAL	1	TRUE	1	0.32	2		463	331	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323982	31323982	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	15	162	0	ENST00000412585.2:c.581G>T	p.Arg194Ile	p.R194I	ENST00000412585	NM_005514.6	194	aGa/aTa	3/8	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.32	2		162	70	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405833	157405833	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1239063473	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	68	756	0	ENST00000346085.5:c.2075C>T	p.Thr692Met	p.T692M	ENST00000346085	NM_020732.3	692	aCg/aTg	6/20	1	2	FACETS	0.71	0.617	0.809	0.71	0.617	0.809	SUBCLONAL	1	TRUE	1	0.32	2		756	599	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781146	161781146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531247345	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	60	643	2	ENST00000366898.1:c.1259G>A	p.Arg420His	p.R420H	ENST00000366898	NM_004562.2	420	cGc/cAc	11/12	1	2	FACETS	0.668	0.576	0.769	0.668	0.576	0.769	SUBCLONAL	1	TRUE	1	0.32	2		645	561	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367243	50367244	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	42	607	0	ENST00000331340.3:c.56dup	p.Val20CysfsTer7	p.V20Cfs*7	ENST00000331340	NM_006060.4	17	agc/agCc	3/8	1	2	FACETS	0.512	0.427	0.606	0.512	0.427	0.606	SUBCLONAL	1	TRUE	1	0.32	2		607	513	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467747	50467747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	59	702	0	ENST00000331340.3:c.982C>T	p.Arg328Cys	p.R328C	ENST00000331340	NM_006060.4	328	Cgc/Tgc	8/8	1	2	FACETS	0.684	0.589	0.788	0.684	0.589	0.788	SUBCLONAL	1	TRUE	1	0.32	2		702	539	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523513	106523513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	75	496	0	ENST00000359195.3:c.2665G>A	p.Ala889Thr	p.A889T	ENST00000359195	NM_002649.2	889	Gcc/Acc	8/11	1	2	FACETS	0.866	0.761	0.98	0.866	0.761	0.98	CLONAL	1	TRUE	1	0.32	2		496	541	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524705	106524705	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1487014289	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	78	352	0	ENST00000359195.3:c.2866G>A	p.Glu956Lys	p.E956K	ENST00000359195	NM_002649.2	956	Gag/Aag	9/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.32	2		352	373	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852213	128852213	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376280244	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	88	805	0	ENST00000249373.3:c.2285G>A	p.Arg762His	p.R762H	ENST00000249373	NM_005631.4	762	cGc/cAc	12/12	0.13485939235562	1	FACETS	0.933	0.83	1	0.933	0.83	1	INDETERMINATE	1	TRUE	0	0.32	1		805	495	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482926	140482927	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	44	743	0	ENST00000288602.6:c.1207_1208dup	p.Ala404LeufsTer8	p.A404Lfs*8	ENST00000288602	NM_004333.4	403	cct/ccCCt	10/18	1	2	FACETS	0.351	0.293	0.415	0.351	0.293	0.415	SUBCLONAL	1	TRUE	1	0.32	2		743	784	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965417	68965417	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	76	568	0	ENST00000288368.4:c.1033del	p.Thr345HisfsTer13	p.T345Hfs*13	ENST00000288368	NM_024870.2	343	gcA/gc	9/40	1	2	FACETS	0.956	0.841	1	0.956	0.841	1	CLONAL	1	TRUE	1	0.32	2		568	497	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	37	686	1	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	1	2	FACETS	0.476	0.392	0.57	0.476	0.392	0.57	SUBCLONAL	1	TRUE	1	0.32	2		687	486	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2058452	2058452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	29	527	0	ENST00000349721.2:c.1509G>A	p.Met503Ile	p.M503I	ENST00000349721	NM_003070.3	503	atG/atA	8/34	1	2	FACETS	0.372	0.298	0.457	0.372	0.298	0.457	SUBCLONAL	1	TRUE	1	0.32	2		527	487	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97897654	97897654	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143181565	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	56	492	0	ENST00000289081.3:c.817G>A	p.Glu273Lys	p.E273K	ENST00000289081	NM_000136.2	273	Gaa/Aaa	8/15	1	2	FACETS	0.738	0.633	0.853	0.738	0.633	0.853	SUBCLONAL	1	TRUE	1	0.32	2		492	474	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98222017	98222017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	56	577	0	ENST00000331920.6:c.2752G>A	p.Ala918Thr	p.A918T	ENST00000331920	NM_000264.3	918	Gct/Act	17/24	1	2	FACETS	0.633	0.542	0.732	0.633	0.542	0.732	SUBCLONAL	1	TRUE	1	0.32	2		577	553	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738297	133738297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1394653602	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	29	712	1	ENST00000318560.5:c.697G>A	p.Asp233Asn	p.D233N	ENST00000318560	NM_005157.4	233	Gac/Aac	4/11	1	2	FACETS	0.346	0.277	0.425	0.346	0.277	0.425	SUBCLONAL	1	TRUE	1	0.32	2		713	524	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400080	139400080	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	107	904	0	ENST00000277541.6:c.4268T>G	p.Leu1423Arg	p.L1423R	ENST00000277541	NM_017617.3	1423	cTc/cGc	25/34	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.32	2		904	635	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412368	139412368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528033027	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	75	795	1	ENST00000277541.6:c.1277C>T	p.Ala426Val	p.A426V	ENST00000277541	NM_017617.3	426	gCg/gTg	8/34	1	2	FACETS	0.859	0.753	0.971	0.859	0.753	0.971	CLONAL	1	TRUE	1	0.32	2		796	546	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929340	44929340	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	100	389	0	ENST00000377967.4:c.2440T>G	p.Ser814Ala	p.S814A	ENST00000377967	NM_021140.2	814	Tct/Gct	17/29	1	1	FACETS	0.765	0.691	0.843	1	0.984	1	SUBCLONAL	2	TRUE	0	0.32	1		389	343	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347241	70347241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	59	302	0	ENST00000374080.3:c.2905C>T	p.Arg969Cys	p.R969C	ENST00000374080		969	Cgc/Tgc	21/45	1	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.32	1		302	262	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0063662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	39	348	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.716	0.595	0.849	0.716	0.595	0.849	SUBCLONAL	1	TRUE	1	0.332209034507145	2		348	328	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411678	63411678	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	90	343	0	ENST00000330258.3:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000330258	NM_152424.3	497	Cga/Tga	2/2	1	1	FACETS	0.953	0.861	1	1	0.987	1	CLONAL	2	TRUE	0	0.332209034507145	1		343	237	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981536	201981536	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	69	579	0	ENST00000359651.3:c.451del	p.Gln151ArgfsTer4	p.Q151Rfs*4	ENST00000359651		150	ttC/tt	3/8	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.332209034507145	2		579	363	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681453	88681453	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs766986283	NA	P-0063662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	42	396	0	ENST00000372037.3:c.1342+1G>A		p.X448_splice	ENST00000372037	NM_004329.2	448			1	2	FACETS	0.716	0.6	0.845	0.716	0.6	0.845	SUBCLONAL	1	TRUE	1	0.332209034507145	2		396	353	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251866	8251866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	90	793	0	ENST00000335790.3:c.211C>T	p.Leu71Phe	p.L71F	ENST00000335790	NM_002315.2	71	Ctc/Ttc	2/4	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.332209034507145	2		793	542	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435649	110435649	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1441639943	NA	P-0063662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	53	609	1	ENST00000375856.3:c.2752G>A	p.Glu918Lys	p.E918K	ENST00000375856	NM_003749.2	918	Gag/Aag	1/2	1	2	FACETS	0.906	0.776	1	0.906	0.776	1	CLONAL	1	TRUE	1	0.332209034507145	2		610	352	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457361	67457361	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906854	NA	P-0063662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	181	839	0	ENST00000327367.4:c.335C>T	p.Ala112Val	p.A112V	ENST00000327367	NM_005902.3	112	gCc/gTc	2/9	0.332209034507145	2	FACETS	0.958	0.889	1	0.958	0.889	1	CLONAL	2	TRUE	0	0.332209034507145	2		839	569	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788651	3788651	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	62	441	0	ENST00000262367.5:c.4303G>T	p.Asp1435Tyr	p.D1435Y	ENST00000262367	NM_004380.2	1435	Gat/Tat	26/31	1	2	FACETS	0.854	0.74	0.977	0.854	0.74	0.977	CLONAL	1	TRUE	1	0.332209034507145	2		441	437	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371777	45371777	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	67	549	0	ENST00000262160.6:c.1214T>A	p.Val405Asp	p.V405D	ENST00000262160	NM_005901.5	405	gTc/gAc	10/11	1	2	FACETS	0.915	0.797	1	0.915	0.797	1	CLONAL	1	TRUE	1	0.332209034507145	2		549	441	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375021	45375021	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	36	468	0	ENST00000262160.6:c.822G>A	p.Trp274Ter	p.W274*	ENST00000262160	NM_005901.5	274	tgG/tgA	8/11	1	2	FACETS	0.735	0.606	0.877	0.735	0.606	0.877	SUBCLONAL	1	TRUE	1	0.332209034507145	2		468	295	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266831	18266831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1011337615	NA	P-0063662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	65	711	0	ENST00000222254.8:c.142G>A	p.Glu48Lys	p.E48K	ENST00000222254	NM_005027.3	48	Gag/Aag	2/16	1	2	FACETS	0.945	0.823	1	0.945	0.823	1	CLONAL	1	TRUE	1	0.332209034507145	2		711	414	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735466	40735466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182388300	NA	P-0063662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	82	697	0	ENST00000373198.4:c.3407G>A	p.Arg1136His	p.R1136H	ENST00000373198	NM_133170.3	1136	cGt/cAt	25/32	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.332209034507145	2		697	458	SUCCESS
APC	324	MSKCC	GRCh37	5	112175799	112175799	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	139	557	0	ENST00000257430.4:c.4508C>A	p.Ser1503Ter	p.S1503*	ENST00000257430	NM_000038.5	1503	tCa/tAa	16/16	0.332209034507145	2	FACETS	0.912	0.836	0.989	0.912	0.836	0.989	CLONAL	2	TRUE	0	0.332209034507145	2		557	459	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468032	50468032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757907717	NA	P-0063662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	54	736	0	ENST00000331340.3:c.1267C>T	p.Arg423Cys	p.R423C	ENST00000331340	NM_006060.4	423	Cgc/Tgc	8/8	1	2	FACETS	0.588	0.502	0.682	0.588	0.502	0.682	SUBCLONAL	1	TRUE	1	0.332209034507145	2		736	553	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110251267	110251267	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	67	656	0	ENST00000374672.4:c.70G>A	p.Ala24Thr	p.A24T	ENST00000374672	NM_004235.4	24	Gcg/Acg	2/5	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.332209034507145	2		656	369	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0063664-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	10	103	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.776	0.527	1	0.776	0.527	1	CLONAL	1	TRUE	1	0.16	2		103	161	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0063664-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	9	118	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	1	2	FACETS	0.589	0.39	0.843	0.589	0.39	0.843	SUBCLONAL	1	TRUE	1	0.16	2		118	191	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562325	21562325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063664-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	39	694	0	ENST00000382592.4:c.1594G>A	p.Asp532Asn	p.D532N	ENST00000382592	NM_014572.2	532	Gac/Aac	4/8	1	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	TRUE	1	0.16	2		694	480	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150936141	150936141	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063664-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	33	626	0	ENST00000271640.5:c.3593G>A	p.Arg1198His	p.R1198H	ENST00000271640	NM_001145415.1	1198	cGc/cAc	20/22	1	2	FACETS	0.657	0.533	0.797	0.657	0.533	0.797	SUBCLONAL	1	TRUE	1	0.16	2		626	628	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438226	56438227	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0063664-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	46	624	0	ENST00000407977.2:c.766dup	p.Arg256ProfsTer3	p.R256Pfs*3	ENST00000407977		256	cgg/cCgg	7/10	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.16	2		624	477	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188982	142188982	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063664-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	28	260	0	ENST00000350721.4:c.6265C>G	p.Arg2089Gly	p.R2089G	ENST00000350721	NM_001184.3	2089	Cga/Gga	37/47	1	2	FACETS	0.909	0.727	1	0.909	0.727	1	CLONAL	1	TRUE	1	0.16	2		260	385	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259878	142259878	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0063664-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	41	389	0	ENST00000350721.4:c.3451-2A>G		p.X1151_splice	ENST00000350721	NM_001184.3	1151			1	2	FACETS	0.918	0.764	1	0.918	0.764	1	CLONAL	1	TRUE	1	0.16	2		389	558	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589539	67589562	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TCAAGTTGTCAAAGAAGATAATAT	TCAAGTTGTCAAAGAAGATAATAT	-	novel	NA	P-0063664-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	23	194	0	ENST00000274335.5:c.1303_1326del	p.Gln435_Ile442del	p.Q435_I442del	ENST00000274335		434	gaTCAAGTTGTCAAAGAAGATAATATt/gat	10/15	1	2	FACETS	0.916	0.714	1	0.916	0.714	1	CLONAL	1	TRUE	1	0.16	2		194	314	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0063665-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	45	626	0	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	1	2	FACETS	0.887	0.745	1	0.887	0.745	1	CLONAL	1	TRUE	1	0.20101697779229	2		626	505	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246550	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	TC	TC	CT	novel	NA	P-0063665-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	87	591	0	ENST00000349310.3:c.49_50delinsAG	p.Glu17Arg	p.E17R	ENST00000349310	NM_001014432.1	17	GAg/AGg	4/15	0.161340135717771	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	2	TRUE	0	0.20101697779229	2		591	423	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	275	622	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.927	0.875	0.979	1	0.995	1	CLONAL	2	TRUE	1	0.409297028404438	2		626	725	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	125	803	7	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.409297028404438	2		810	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	153	662	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.409297028404438	2		662	696	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	116	616	2	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.409297028404438	2		618	530	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279861	46279866	+	inframe_deletion	In_Frame_Del	DEL	CAGCAA	CAGCAA	-	rs748517056	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	41	704	5	ENST00000371998.3:c.3810_3815del	p.Gln1275_Gln1276del	p.Q1275_Q1276del	ENST00000371998		1263	CAGCAA/-	20/23	1	2	FACETS	0.303	0.252	0.361	0.303	0.252	0.361	SUBCLONAL	1	TRUE	1	0.409297028404438	2		709	661	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	116	795	2	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.729	0.657	0.805	0.729	0.657	0.805	SUBCLONAL	1	TRUE	1	0.409297028404438	2		797	778	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	74	358	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.969	0.854	1	0.969	0.854	1	CLONAL	1	TRUE	1	0.409297028404438	2		358	373	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219487	133219487	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	117	828	1	ENST00000320574.5:c.4647del	p.Lys1550AsnfsTer12	p.K1550Nfs*12	ENST00000320574	NM_006231.2	1549	ccC/cc	36/49	1	2	FACETS	0.913	0.825	1	0.913	0.825	1	CLONAL	1	TRUE	1	0.409297028404438	2		829	626	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542110	187542110	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	114	732	3	ENST00000441802.2:c.5630del	p.Pro1877LeufsTer20	p.P1877Lfs*20	ENST00000441802	NM_005245.3	1877	cCt/ct	10/27	1	2	FACETS	0.854	0.771	0.943	0.854	0.771	0.943	CLONAL	1	TRUE	1	0.409297028404438	2		735	652	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	20	188	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	0.555	0.427	0.703	0.555	0.427	0.703	SUBCLONAL	1	TRUE	1	0.409297028404438	2		188	176	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429978	78429978	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	123	562	0	ENST00000370768.2:c.901del	p.Ile301TyrfsTer22	p.I301Yfs*22	ENST00000370768	NM_003902.3	301	Ata/ta	11/20	1	2	FACETS	0.993	0.901	1	0.993	0.901	1	CLONAL	1	TRUE	1	0.409297028404438	2		562	605	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	140	517	2	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.409297028404438	2		519	646	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	142	786	3	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.409297028404438	2		789	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882019	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	32	806	0	ENST00000269305.4:c.455del	p.Pro152ArgfsTer18	p.P152Rfs*18	ENST00000269305	NM_001126112.2	152	cCg/cg	5/11	1	2	FACETS	0.214	0.172	0.26	0.214	0.172	0.26	SUBCLONAL	1	TRUE	1	0.409297028404438	2		806	732	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878127	48878127	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1276653645	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	81	817	0	ENST00000267163.4:c.83del	p.Pro28LeufsTer37	p.P28Lfs*37	ENST00000267163	NM_000321.2	27	Ccc/cc	1/27	1	2	FACETS	0.86	0.761	0.966	0.86	0.761	0.966	CLONAL	1	TRUE	1	0.409297028404438	2		817	460	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393656	139393656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196509879	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	139	786	0	ENST00000277541.6:c.5990C>T	p.Thr1997Met	p.T1997M	ENST00000277541	NM_017617.3	1997	aCg/aTg	32/34	1	2	FACETS	0.999	0.911	1	0.999	0.911	1	CLONAL	1	TRUE	1	0.409297028404438	2		786	680	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	147	554	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.409297028404438	2		554	667	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	144	597	0	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.409297028404438	2		597	675	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	77	483	1	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	1	2	FACETS	0.844	0.744	0.95	0.844	0.744	0.95	CLONAL	1	TRUE	1	0.409297028404438	2		484	446	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	112	728	0	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	1	2	FACETS	0.836	0.753	0.923	0.836	0.753	0.923	CLONAL	1	TRUE	1	0.409297028404438	2		728	655	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692779	89692779	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	71	373	0	ENST00000371953.3:c.263A>G	p.Tyr88Cys	p.Y88C	ENST00000371953	NM_000314.4	88	tAt/tGt	5/9	1	2	FACETS	0.994	0.874	1	0.994	0.874	1	CLONAL	1	TRUE	1	0.409297028404438	2		373	349	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505564	25505564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778149141	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	95	543	1	ENST00000264709.3:c.194C>T	p.Thr65Met	p.T65M	ENST00000264709	NM_175629.2	65	aCg/aTg	4/23	1	2	FACETS	0.852	0.761	0.948	0.852	0.761	0.948	CLONAL	1	TRUE	1	0.409297028404438	2		544	545	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084146	47084146	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	141	704	0	ENST00000409792.3:c.7143del	p.Ser2382LeufsTer29	p.S2382Lfs*29	ENST00000409792	NM_014159.6	2381	ccC/cc	17/21	1	2	FACETS	0.929	0.847	1	0.929	0.847	1	CLONAL	1	TRUE	1	0.409297028404438	2		704	742	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022332	31022332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778061	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	136	774	0	ENST00000375687.4:c.1817G>A	p.Arg606Gln	p.R606Q	ENST00000375687	NM_015338.5	606	cGg/cAg	13/13	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.409297028404438	2		774	635	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930904	39930904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	72	335	0	ENST00000378444.4:c.3037G>A	p.Ala1013Thr	p.A1013T	ENST00000378444	NM_001123385.1	1013	Gct/Act	5/15	1	2	FACETS	0.904	0.794	1	0.904	0.794	1	CLONAL	1	TRUE	1	0.409297028404438	2		335	389	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737578	145737578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558058260	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	139	1087	0	ENST00000428558.2:c.3185G>A	p.Arg1062Gln	p.R1062Q	ENST00000428558	NM_004260.3	1062	cGg/cAg	19/22	1	2	FACETS	0.974	0.889	1	0.974	0.889	1	CLONAL	1	TRUE	1	0.409297028404438	2		1087	697	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777933	3777933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1048314482	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	206	902	0	ENST00000262367.5:c.7115C>T	p.Ser2372Leu	p.S2372L	ENST00000262367	NM_004380.2	2372	tCg/tTg	31/31	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.409297028404438	2		902	793	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202351	138202351	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	95	703	1	ENST00000237289.4:c.2274del	p.Lys759SerfsTer57	p.K759Sfs*57	ENST00000237289	NM_001270507.1	756	gaC/ga	9/9	1	2	FACETS	0.816	0.728	0.909	0.816	0.728	0.909	CLONAL	1	TRUE	1	0.409297028404438	2		704	569	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353815	15353815	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780028668	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	52	307	0	ENST00000263377.2:c.3065C>T	p.Pro1022Leu	p.P1022L	ENST00000263377	NM_058243.2	1022	cCg/cTg	14/20	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.409297028404438	2		307	252	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429758	78429758	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	106	490	0	ENST00000370768.2:c.1030C>T	p.Arg344Ter	p.R344*	ENST00000370768	NM_003902.3	344	Cga/Tga	12/20	1	2	FACETS	0.918	0.826	1	0.918	0.826	1	CLONAL	1	TRUE	1	0.409297028404438	2		490	564	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867543	+	inframe_deletion	In_Frame_Del	DEL	GGCGGC	GGCGGC	-	rs11466445	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	32	456	0	ENST00000374994.4:c.73_78del	p.Ala25_Ala26del	p.A25_A26del	ENST00000374994	NM_004612.2	17	ctGGCGGCg/ctg	1/9	1	2	FACETS	0.501	0.408	0.606	0.501	0.408	0.606	SUBCLONAL	1	TRUE	1	0.409297028404438	2		456	312	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246532	41246532	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357569	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	116	677	4	ENST00000357654.3:c.1016del	p.Lys339ArgfsTer2	p.K339Rfs*2	ENST00000357654	NM_007294.3	339	aAg/ag	10/23	1	2	FACETS	0.926	0.837	1	0.926	0.837	1	CLONAL	1	TRUE	1	0.409297028404438	2		681	612	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832265	72832265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267604632	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	115	700	0	ENST00000268489.5:c.4316G>A	p.Arg1439Gln	p.R1439Q	ENST00000268489	NM_006885.3	1439	cGa/cAa	9/10	1	2	FACETS	0.957	0.865	1	0.957	0.865	1	CLONAL	1	TRUE	1	0.409297028404438	2		700	587	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264500	16264500	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1023242507	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	75	602	2	ENST00000375759.3:c.10703C>T	p.Thr3568Met	p.T3568M	ENST00000375759	NM_015001.2	3568	aCg/aTg	13/15	1	2	FACETS	0.795	0.699	0.898	0.795	0.699	0.898	SUBCLONAL	1	TRUE	1	0.409297028404438	2		604	461	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	86	399	0	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.8	0.71	0.897	0.8	0.71	0.897	SUBCLONAL	1	TRUE	1	0.409297028404438	2		399	525	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589015	67589016	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	27	519	0	ENST00000274335.5:c.1108_1109del	p.Leu370TyrfsTer8	p.L370Yfs*8	ENST00000274335		369	aCT/a	8/15	1	2	FACETS	0.249	0.197	0.308	0.249	0.197	0.308	SUBCLONAL	1	TRUE	1	0.409297028404438	2		519	530	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	71	872	1	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	0.594	0.519	0.675	0.594	0.519	0.675	SUBCLONAL	1	TRUE	1	0.409297028404438	2		873	584	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135247	2135247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769834772	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	109	642	0	ENST00000219476.3:c.4586G>A	p.Arg1529Gln	p.R1529Q	ENST00000219476	NM_000548.3	1529	cGg/cAg	36/42	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.409297028404438	2		642	484	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488362	20488362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	112	642	0	ENST00000346618.3:c.1018G>A	p.Ala340Thr	p.A340T	ENST00000346618	NM_001949.4	340	Gca/Aca	6/7	1	2	FACETS	0.955	0.862	1	0.955	0.862	1	CLONAL	1	TRUE	1	0.409297028404438	2		642	573	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937950	36937950	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368300579	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	107	865	0	ENST00000361632.4:c.886G>A	p.Gly296Arg	p.G296R	ENST00000361632		296	Ggg/Agg	7/16	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.409297028404438	2		865	514	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464445	25464445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768899154	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	75	606	0	ENST00000264709.3:c.2068G>A	p.Val690Ile	p.V690I	ENST00000264709	NM_175629.2	690	Gtc/Atc	17/23	1	2	FACETS	0.74	0.65	0.837	0.74	0.65	0.837	SUBCLONAL	1	TRUE	1	0.409297028404438	2		606	495	SUCCESS
APC	324	MSKCC	GRCh37	5	112178001	112178001	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1299714632	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	118	601	0	ENST00000257430.4:c.6710G>A	p.Arg2237Gln	p.R2237Q	ENST00000257430	NM_000038.5	2237	cGa/cAa	16/16	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.409297028404438	2		601	570	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357061	70357061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763700798	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	118	815	0	ENST00000374080.3:c.5576G>A	p.Arg1859His	p.R1859H	ENST00000374080		1859	cGt/cAt	39/45	1	2	FACETS	0.928	0.84	1	0.928	0.84	1	CLONAL	1	TRUE	1	0.409297028404438	2		815	621	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829701	72829701	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	144	718	0	ENST00000268489.5:c.6880C>T	p.Arg2294Ter	p.R2294*	ENST00000268489	NM_006885.3	2294	Cga/Tga	9/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.409297028404438	2		718	628	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693948	47693948	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs267607969	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	100	387	0	ENST00000233146.2:c.1661+1G>T		p.X554_splice	ENST00000233146	NM_000251.2	554			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.409297028404438	2		387	454	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266736	18266736	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1215895377	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	83	714	0	ENST00000222254.8:c.47G>A	p.Arg16His	p.R16H	ENST00000222254	NM_005027.3	16	cGc/cAc	2/16	1	2	FACETS	0.852	0.755	0.956	0.852	0.755	0.956	CLONAL	1	TRUE	1	0.409297028404438	2		714	476	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353767	40353767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760771231	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	152	663	2	ENST00000293328.3:c.2353G>A	p.Ala785Thr	p.A785T	ENST00000293328	NM_012448.3	785	Gca/Aca	19/19	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.409297028404438	2		665	691	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495745	56495746	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs762900471	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	78	654	0	ENST00000267101.3:c.3937_3938del	p.Leu1313ThrfsTer2	p.L1313Tfs*2	ENST00000267101	NM_001982.3	1312	aCT/a	28/28	1	2	FACETS	0.895	0.79	1	0.895	0.79	1	CLONAL	1	TRUE	1	0.409297028404438	2		654	426	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850866	128850866	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	118	584	0	ENST00000249373.3:c.1713G>T	p.Lys571Asn	p.K571N	ENST00000249373	NM_005631.4	571	aaG/aaT	10/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.409297028404438	2		584	503	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639155	3639155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777033175	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	129	910	0	ENST00000294008.3:c.4484C>T	p.Ala1495Val	p.A1495V	ENST00000294008	NM_032444.2	1495	gCg/gTg	12/15	1	2	FACETS	0.935	0.85	1	0.935	0.85	1	CLONAL	1	TRUE	1	0.409297028404438	2		910	674	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578260	7578260	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786204041	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	94	579	0	ENST00000269305.4:c.589G>T	p.Val197Leu	p.V197L	ENST00000269305	NM_001126112.2	197	Gtg/Ttg	6/11	1	2	FACETS	0.67	0.596	0.748	0.67	0.596	0.748	SUBCLONAL	1	TRUE	1	0.409297028404438	2		579	686	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591723	38591723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750686148	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	78	432	0	ENST00000299084.4:c.182G>A	p.Arg61His	p.R61H	ENST00000299084	NM_152594.2	61	cGt/cAt	2/7	1	2	FACETS	0.88	0.777	0.99	0.88	0.777	0.99	CLONAL	1	TRUE	1	0.409297028404438	2		432	433	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665047	138665047	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	22	586	0	ENST00000330315.3:c.518C>G	p.Ala173Gly	p.A173G	ENST00000330315	NM_023067.3	173	gCa/gGa	1/1	0.409297028404438	3	FACETS	0.357	0.276	0.451	0.178	0.138	0.226	SUBCLONAL	1	TRUE	1	0.409297028404438	3		586	363	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101364	27101364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	107	678	0	ENST00000324856.7:c.4646G>A	p.Gly1549Asp	p.G1549D	ENST00000324856	NM_006015.4	1549	gGc/gAc	18/20	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.409297028404438	2		678	512	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445020	89445020	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs925530491	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	114	621	0	ENST00000336596.2:c.1340G>A	p.Arg447Gln	p.R447Q	ENST00000336596	NM_005233.5	447	cGg/cAg	6/17	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.409297028404438	2		621	550	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865370	40865370	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1287970047	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	103	588	0	ENST00000428826.2:c.1061G>A	p.Arg354His	p.R354H	ENST00000428826		354	cGc/cAc	11/21	1	2	FACETS	0.889	0.798	0.986	0.889	0.798	0.986	CLONAL	1	TRUE	1	0.409297028404438	2		588	566	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166398	7166398	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767160876	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	116	596	0	ENST00000302850.5:c.1628C>T	p.Thr543Met	p.T543M	ENST00000302850	NM_000208.2	543	aCg/aTg	8/22	1	2	FACETS	0.923	0.834	1	0.923	0.834	1	CLONAL	1	TRUE	1	0.409297028404438	2		596	614	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324290	62324290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61736615	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	109	780	3	ENST00000360203.5:c.2785G>A	p.Ala929Thr	p.A929T	ENST00000360203	NM_001283009.1	929	Gcc/Acc	29/35	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.409297028404438	2		783	525	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77931369	77931369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769709400	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	113	721	1	ENST00000361507.4:c.1883G>A	p.Arg628His	p.R628H	ENST00000361507	NM_080491.2	628	cGc/cAc	9/10	1	2	FACETS	0.931	0.84	1	0.931	0.84	1	CLONAL	1	TRUE	1	0.409297028404438	2		722	593	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850894	63850894	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	38	796	1	ENST00000279873.7:c.1675del	p.Ala559ProfsTer70	p.A559Pfs*70	ENST00000279873	NM_032199.2	558	Ggg/gg	10/10	1	2	FACETS	0.302	0.249	0.362	0.302	0.249	0.362	SUBCLONAL	1	TRUE	1	0.409297028404438	2		797	615	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533520	533520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	168	886	0	ENST00000451590.1:c.383G>A	p.Arg128Gln	p.R128Q	ENST00000451590	NM_001130442.1	128	cGg/cAg	4/5	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.409297028404438	2		886	694	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47599133	47599133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771167882	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	155	721	0	ENST00000430070.2:c.467G>A	p.Arg156His	p.R156H	ENST00000430070	NM_018095.4	156	cGc/cAc	2/4	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.409297028404438	2		721	706	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119773	108119773	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	40	449	0	ENST00000278616.4:c.1179G>T	p.Trp393Cys	p.W393C	ENST00000278616	NM_000051.3	393	tgG/tgT	9/63	1	2	FACETS	0.401	0.332	0.476	0.401	0.332	0.476	SUBCLONAL	1	TRUE	1	0.409297028404438	2		449	488	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1022557	1022557	+	stop_lost	Nonstop_Mutation	SNP	T	T	A	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	48	436	0	ENST00000358495.3:c.1257A>T	p.Ter419TyrextTer42	p.*419Yext*42	ENST00000358495	NM_134424.2	419	taA/taT	12/12	1	2	FACETS	0.614	0.52	0.716	0.614	0.52	0.716	SUBCLONAL	1	TRUE	1	0.409297028404438	2		436	382	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110005	115110005	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773785943	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	107	680	0	ENST00000257566.3:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000257566	NM_016569.3	625	Cgc/Tgc	8/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.409297028404438	2		680	417	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675178	40675179	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	114	754	0	ENST00000249776.8:c.143_144del	p.Thr48SerfsTer36	p.T48Sfs*36	ENST00000249776	NM_033286.3	48	ACa/a	1/9	1	2	FACETS	0.988	0.892	1	0.988	0.892	1	CLONAL	1	TRUE	1	0.409297028404438	2		754	564	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303415	91303415	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	35	432	0	ENST00000355112.3:c.1126A>G	p.Met376Val	p.M376V	ENST00000355112	NM_000057.2	376	Atg/Gtg	6/22	1	2	FACETS	0.374	0.306	0.45	0.374	0.306	0.45	SUBCLONAL	1	TRUE	1	0.409297028404438	2		432	457	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899182	78899182	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200660726	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	90	681	0	ENST00000306801.3:c.2821G>A	p.Ala941Thr	p.A941T	ENST00000306801	NM_020761.2	941	Gcg/Acg	24/34	1	2	FACETS	0.729	0.648	0.816	0.729	0.648	0.816	SUBCLONAL	1	TRUE	1	0.409297028404438	2		681	603	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291169	10291169	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	211	944	0	ENST00000340748.4:c.302G>T	p.Arg101Leu	p.R101L	ENST00000340748		101	cGg/cTg	4/40	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.409297028404438	2		944	875	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600395	10600395	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	115	858	0	ENST00000171111.5:c.1460C>A	p.Ala487Asp	p.A487D	ENST00000171111	NM_203500.1	487	gCt/gAt	4/6	1	2	FACETS	0.772	0.696	0.852	0.772	0.696	0.852	SUBCLONAL	1	TRUE	1	0.409297028404438	2		858	728	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097624	11097625	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1165714406	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	41	703	0	ENST00000358026.2:c.810dup	p.Gly271ArgfsTer16	p.G271Rfs*16	ENST00000358026	NM_001128849.1	268	-/C	5/36	1	2	FACETS	0.353	0.294	0.42	0.353	0.294	0.42	SUBCLONAL	1	TRUE	1	0.409297028404438	2		703	567	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423517	47423517	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	127	685	0	ENST00000404338.3:c.1585C>T	p.Arg529Ter	p.R529*	ENST00000404338	NM_004491.4	529	Cga/Tga	1/6	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.409297028404438	2		685	580	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424085	47424086	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	121	667	0	ENST00000404338.3:c.2154dup	p.Gln719ThrfsTer8	p.Q719Tfs*8	ENST00000404338	NM_004491.4	718	ata/atAa	1/6	1	2	FACETS	0.908	0.822	0.999	0.908	0.822	0.999	CLONAL	1	TRUE	1	0.409297028404438	2		667	651	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637247	47637250	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	87	511	0	ENST00000233146.2:c.385_388del	p.Gln130LeufsTer43	p.Q130Lfs*43	ENST00000233146	NM_000251.2	127	aaTCTC/aa	3/16	1	2	FACETS	0.934	0.831	1	0.934	0.831	1	CLONAL	1	TRUE	1	0.409297028404438	2		511	455	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156091	99156091	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	117	656	0	ENST00000074304.5:c.771del	p.His257GlnfsTer7	p.H257Qfs*7	ENST00000074304	NM_001134224.1	257	caC/ca	10/26	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.409297028404438	2		656	487	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662074	227662074	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168013838	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	104	901	0	ENST00000305123.5:c.1381G>A	p.Glu461Lys	p.E461K	ENST00000305123	NM_005544.2	461	Gag/Aag	1/2	1	2	FACETS	0.901	0.809	0.998	0.901	0.809	0.998	CLONAL	1	TRUE	1	0.409297028404438	2		901	564	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161680	47161683	+	frameshift_variant	Frame_Shift_Del	DEL	TAAA	TAAA	-	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	70	448	0	ENST00000409792.3:c.4443_4446del	p.Tyr1481Ter	p.Y1481*	ENST00000409792	NM_014159.6	1481	taTTTA/ta	3/21	1	2	FACETS	0.907	0.795	1	0.907	0.795	1	CLONAL	1	TRUE	1	0.409297028404438	2		448	377	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196921	106196921	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	99	651	0	ENST00000380013.4:c.5258del	p.Asn1753MetfsTer10	p.N1753Mfs*10	ENST00000380013	NM_001127208.2	1752	Aaa/aa	11/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.409297028404438	2		651	426	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144381537	144381537	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1314151809	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	95	550	0	ENST00000262995.4:c.1795del	p.Arg599AspfsTer24	p.R599Dfs*24	ENST00000262995	NM_207123.2	597	tCc/tc	9/11	1	2	FACETS	0.771	0.688	0.86	0.771	0.688	0.86	SUBCLONAL	1	TRUE	1	0.409297028404438	2		550	602	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534437	187534437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768112959	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	112	645	0	ENST00000441802.2:c.9289G>A	p.Val3097Ile	p.V3097I	ENST00000441802	NM_005245.3	3097	Gtc/Atc	13/27	1	2	FACETS	0.962	0.868	1	0.962	0.868	1	CLONAL	1	TRUE	1	0.409297028404438	2		645	569	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31451644	31451644	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	76	367	0	ENST00000344624.3:c.2678T>C	p.Leu893Ser	p.L893S	ENST00000344624		893	tTg/tCg	18/33	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.409297028404438	2		367	356	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670952	30670952	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773668966	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	121	824	0	ENST00000376406.3:c.5794C>T	p.Arg1932Cys	p.R1932C	ENST00000376406	NM_014641.2	1932	Cgc/Tgc	12/15	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.409297028404438	2		824	574	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793564	89793567	+	frameshift_variant	Frame_Shift_Del	DEL	AAAC	AAAC	-	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	109	563	0	ENST00000336032.3:c.634_637del	p.Asn212AspfsTer10	p.N212Dfs*10	ENST00000336032	NM_006813.2	211	atAAAC/at	2/2	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.409297028404438	2		563	525	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778750	76778750	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	116	579	0	ENST00000373344.5:c.6829G>A	p.Glu2277Lys	p.E2277K	ENST00000373344	NM_000489.3	2277	Gag/Aag	31/35	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.409297028404438	2		579	545	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907612	76907613	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	72	511	0	ENST00000373344.5:c.4548dup	p.Leu1517IlefsTer8	p.L1517Ifs*8	ENST00000373344	NM_000489.3	1516	-/A	15/35	1	2	FACETS	0.675	0.591	0.766	0.675	0.591	0.766	SUBCLONAL	1	TRUE	1	0.409297028404438	2		511	521	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455266	29455266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1558629763	NA	P-0063666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	120	712	0	ENST00000389048.3:c.2536G>A	p.Gly846Ser	p.G846S	ENST00000389048	NM_004304.4	846	Ggc/Agc	15/29	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.409297028404438	2		712	567	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836642	89836642	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	48	546	0	ENST00000389301.3:c.2248G>C	p.Val750Leu	p.V750L	ENST00000389301	NM_000135.2	750	Gtg/Ctg	25/43	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.246059905649953	2		546	359	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057312	30057312	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	55	545	0	ENST00000338641.4:c.794C>A	p.Ser265Ter	p.S265*	ENST00000338641	NM_000268.3	265	tCg/tAg	8/16	0.246059905649953	1	FACETS	0.927	0.795	1	0.927	0.795	1	CLONAL	1	TRUE	0	0.246059905649953	1		545	423	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436387	52436388	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	35	576	0	ENST00000460680.1:c.2106dup	p.Gly703ArgfsTer14	p.G703Rfs*14	ENST00000460680	NM_004656.3	702	-/A	17/17	1	2	FACETS	0.668	0.547	0.803	0.668	0.547	0.803	SUBCLONAL	1	TRUE	1	0.246059905649953	2		576	426	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0063668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	80	331	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.392713086744991	3	FACETS	0.855	0.762	0.953	0.855	0.762	0.953	CLONAL	2	TRUE	1	0.407996991476875	3		331	276	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0063668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	36	393	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.392713086744991	3	FACETS	1	0.933	1	0.632	0.527	0.747	CLONAL	1	TRUE	1	0.407996991476875	3		394	168	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0063668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	79	654	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.407996991476875	2		654	339	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637555	52637555	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	43	439	0	ENST00000394830.3:c.2761C>T	p.Arg921Ter	p.R921*	ENST00000394830	NM_018313.4	921	Cga/Tga	18/30	0.392713086744991	3	FACETS	0.811	0.681	0.953	0.405	0.34	0.477	CLONAL	1	TRUE	1	0.407996991476875	3		439	313	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858210	9858210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756930722	NA	P-0063668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	52	675	0	ENST00000330684.3:c.3191C>T	p.Thr1064Met	p.T1064M	ENST00000330684	NM_001134407.1	1064	aCg/aTg	13/13	1	2	FACETS	0.763	0.653	0.883	0.763	0.653	0.883	SUBCLONAL	1	TRUE	1	0.407996991476875	2		675	334	SUCCESS
APC	324	MSKCC	GRCh37	5	112175969	112175969	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	72	618	0	ENST00000257430.4:c.4678G>T	p.Glu1560Ter	p.E1560*	ENST00000257430	NM_000038.5	1560	Gaa/Taa	16/16	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.407996991476875	2		618	352	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540974	187540974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752611276	NA	P-0063668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	76	805	0	ENST00000441802.2:c.6766G>A	p.Ala2256Thr	p.A2256T	ENST00000441802	NM_005245.3	2256	Gca/Aca	10/27	1	2	FACETS	0.988	0.872	1	0.988	0.872	1	CLONAL	1	TRUE	1	0.407996991476875	2		805	377	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711987	89711987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1085308053	NA	P-0063668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	44	388	0	ENST00000371953.3:c.605C>T	p.Thr202Ile	p.T202I	ENST00000371953	NM_000314.4	202	aCt/aTt	6/9	0.392713086744991	3	FACETS	0.958	0.809	1	0.479	0.404	0.561	CLONAL	1	TRUE	1	0.407996991476875	3		388	271	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1686080	1686080	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376387032	NA	P-0063668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	45	776	0	ENST00000378625.1:c.1181G>A	p.Arg394Gln	p.R394Q	ENST00000378625	NM_001198994.1	394	cGg/cAg	10/14	1	2	FACETS	0.755	0.638	0.883	0.755	0.638	0.883	SUBCLONAL	1	TRUE	1	0.407996991476875	2		776	292	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620355	43620355	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	48	684	1	ENST00000355710.3:c.2964G>A	p.Trp988Ter	p.W988*	ENST00000355710	NM_020975.4	988	tgG/tgA	18/20	0.392713086744991	3	FACETS	0.774	0.656	0.903	0.387	0.328	0.452	CLONAL	1	TRUE	1	0.407996991476875	3		685	366	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534436	63534437	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	67	789	0	ENST00000307078.5:c.1084dup	p.Met362AsnfsTer12	p.M362Nfs*12	ENST00000307078	NM_004655.3	362	atg/aAtg	5/11	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.407996991476875	2		789	309	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119765	70119766	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCGC	novel	NA	P-0063668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	30	574	0	ENST00000245479.2:c.768_771dup	p.Pro258AlafsTer39	p.P258Afs*39	ENST00000245479	NM_000346.3	256	ggg/ggGCGCg	3/3	1	2	FACETS	0.668	0.542	0.81	0.668	0.542	0.81	SUBCLONAL	1	TRUE	1	0.407996991476875	2		574	220	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs869320707	NA	P-0063669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	139	603	0	ENST00000397752.3:c.3028+1G>T		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.178392621399056	2	FACETS	0.934	0.853	1	0.934	0.853	1	CLONAL	2	TRUE	0	0.238796479966867	2		603	623	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53241019	53241019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	45	540	0	ENST00000375401.3:c.1192G>A	p.Gly398Ser	p.G398S	ENST00000375401	NM_004187.3	398	Ggc/Agc	9/26	1	2	FACETS	0.644	0.541	0.759	0.644	0.541	0.759	SUBCLONAL	1	TRUE	1	0.238796479966867	2		540	585	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0063670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	203	708	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	0.808258995222296	1	FACETS	0.975	0.927	1	0.975	0.927	1	CLONAL	1	TRUE	0	0.808258995222296	1		708	307	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0063671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	91	372	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.447664053304329	4	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	2	0.443661079231081	4		372	271	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0063671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	248	454	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.443661079231081	8	FACETS	1	0.977	1	0.902	0.864	0.94	CLONAL	7	TRUE	0	0.443661079231081	8		454	361	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591888	48591888	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519739	NA	P-0063671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	74	533	0	ENST00000342988.3:c.1051G>C	p.Asp351His	p.D351H	ENST00000342988	NM_005359.5	351	Gat/Cat	9/12	0.425395008504625	2	FACETS	0.772	0.688	0.86	0.772	0.688	0.86	SUBCLONAL	2	TRUE	0	0.443661079231081	2		533	216	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46277765	46277765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774124954	NA	P-0063671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	159	364	0	ENST00000371998.3:c.3563G>A	p.Arg1188Gln	p.R1188Q	ENST00000371998		1188	cGa/cAa	19/23	0.443661079231081	7	FACETS	0.984	0.914	1	0.787	0.731	0.844	CLONAL	4	TRUE	2	0.443661079231081	7		364	384	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29444454	29444454	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	86	456	0	ENST00000544604.2:c.994del	p.His332ThrfsTer7	p.H332Tfs*7	ENST00000544604	NM_001206998.1	330	tgC/tg	7/9	0.304860409355217	4	FACETS	1	0.966	1	0.59	0.531	0.651	CLONAL	2	TRUE	0	0.443661079231081	4		456	237	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942110	17942110	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	85	408	0	ENST00000458235.1:c.2905G>A	p.Gly969Ser	p.G969S	ENST00000458235	NM_000215.3	969	Ggc/Agc	21/24	0.443661079231081	7	FACETS	1	0.968	1	0.618	0.551	0.688	CLONAL	2	TRUE	3	0.443661079231081	7		408	327	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277583	142277593	+	frameshift_variant	Frame_Shift_Del	DEL	AATCTTCCAGG	AATCTTCCAGG	-	novel	NA	P-0063671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	68	309	0	ENST00000350721.4:c.1758_1768del	p.Leu587MetfsTer14	p.L587Mfs*14	ENST00000350721	NM_001184.3	586	atCCTGGAAGATTta/atta	8/47	0.447664053304329	4	FACETS	0.95	0.838	1	0.95	0.838	1	CLONAL	2	TRUE	2	0.443661079231081	4		309	233	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0063672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	573	771	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.765287369271293	2		771	689	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0063672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	300	748	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	0.702274209367963	3	FACETS	1	0.989	1	0.589	0.556	0.623	CLONAL	1	TRUE	1	0.765287369271293	3		752	920	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456569	138456569	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	143	295	0	ENST00000289153.2:c.781C>T	p.His261Tyr	p.H261Y	ENST00000289153	NM_006219.2	261	Cat/Tat	4/22	0.742317067046809	4	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	2	0.765287369271293	4		295	325	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164509	36164509	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	188	567	0	ENST00000300305.3:c.1366G>A	p.Glu456Lys	p.E456K	ENST00000300305		456	Gag/Aag	8/8	0.674430654657829	3	FACETS	0.996	0.924	1	0.498	0.462	0.535	CLONAL	1	TRUE	1	0.765287369271293	3		567	682	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938390	44938390	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0063672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	77	123	0	ENST00000377967.4:c.2939-1G>C		p.X980_splice	ENST00000377967	NM_021140.2	980			1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.765287369271293	1		123	88	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142950049	142950049	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs375588188	NA	P-0063672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	106	389	0	ENST00000262992.4:c.2661G>C	p.Glu887Asp	p.E887D	ENST00000262992	NM_001101669.1	887	gaG/gaC	24/24	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.765287369271293	2		389	269	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578445	7578446	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0063672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	581	679	0	ENST00000269305.4:c.484_485del	p.Ile162LeufsTer18	p.I162Lfs*18	ENST00000269305	NM_001126112.2	162	ATc/c	5/11	0.765287369271293	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.765287369271293	2		679	691	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55334146	55334146	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	211	392	0	ENST00000284073.2:c.43G>T	p.Asp15Tyr	p.D15Y	ENST00000284073	NM_138962.2	15	Gac/Tac	1/14	0.674430654657829	3	FACETS	0.948	0.895	1	0.948	0.895	1	CLONAL	2	TRUE	1	0.765287369271293	3		392	402	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440001	220440001	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	1411	639	0	ENST00000243786.2:c.854G>C	p.Ser285Thr	p.S285T	ENST00000243786	NM_002191.3	285	aGt/aCt	2/2	0.538802195476285	5	FACETS	1	0.998	1			1	CLONAL	5	TRUE	NA	0.765287369271293	5		639	1515	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29444473	29444473	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	468	527	0	ENST00000544604.2:c.1009A>T	p.Ile337Phe	p.I337F	ENST00000544604	NM_001206998.1	337	Atc/Ttc	7/9	0.765287369271293	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.765287369271293	3		527	779	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545057	41545066	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCGTATGC	CCTCGTATGC	-	novel	NA	P-0063672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	176	506	0	ENST00000263253.7:c.2257_2266del	p.Pro753AsnfsTer20	p.P753Nfs*20	ENST00000263253	NM_001429.3	753	CCTCGTATGCaa/aa	13/31	1	2	FACETS	0.989	0.92	1	0.989	0.92	1	CLONAL	1	TRUE	1	0.765287369271293	2		506	465	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498376	89498376	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	119	431	0	ENST00000336596.2:c.2348G>C	p.Gly783Ala	p.G783A	ENST00000336596	NM_005233.5	783	gGa/gCa	14/17	0.765287369271293	3	FACETS	0.979	0.891	1	0.49	0.445	0.536	CLONAL	1	TRUE	1	0.765287369271293	3		431	439	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920042	1920042	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	603	608	0	ENST00000382891.5:c.1102G>C	p.Glu368Gln	p.E368Q	ENST00000382891	NM_133335.3	368	Gag/Cag	5/22	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.765287369271293	2		608	739	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0063673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	136	473	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.303386129049677	4	FACETS	1	0.928	1	0.678	0.62	0.738	CLONAL	2	TRUE	1	0.353758113326204	4		473	512	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0063678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	154	393	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.661529235970253	6	FACETS	0.939	0.863	1	0.469	0.431	0.509	CLONAL	2	TRUE	2	0.661529235970253	6		394	576	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0063678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	372	340	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.632821446747952	3	FACETS	0.974	0.942	1	0.974	0.942	1	CLONAL	3	TRUE	0	0.661529235970253	3		340	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0063678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	393	449	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	NA	2	FACETS	1	0.968	1			1	INDETERMINATE	2	TRUE	NA	0.661529235970253	2		449	592	SUCCESS
AR	367	MSKCC	GRCh37	X	66766456	66766456	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	65	353	0	ENST00000374690.3:c.1468C>G	p.Leu490Val	p.L490V	ENST00000374690	NM_000044.3	490	Ctg/Gtg	1/8	0.661529235970253	3	FACETS	0.83	0.725	0.942	0.415	0.362	0.471	CLONAL	1	TRUE	1	0.661529235970253	3		353	315	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406167	70406167	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	158	528	0	ENST00000373644.4:c.3681G>T	p.Arg1227Ser	p.R1227S	ENST00000373644	NM_030625.2	1227	agG/agT	4/12	0.651447136297448	4	FACETS	0.988	0.907	1	0.329	0.302	0.358	CLONAL	1	TRUE	1	0.661529235970253	4		528	803	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954378	48954378	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1131690909	NA	P-0063678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	350	318	0	ENST00000267163.4:c.1498+1G>A		p.X500_splice	ENST00000267163	NM_000321.2	500			0.632821446747952	3	FACETS	0.978	0.945	1	0.978	0.945	1	CLONAL	3	TRUE	0	0.661529235970253	3		318	480	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125523710	125523710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	216	259	0	ENST00000428830.2:c.1303G>A	p.Asp435Asn	p.D435N	ENST00000428830	NM_001114121.2	435	Gat/Aat	12/14	0.661529235970253	3	FACETS	0.945	0.889	1	0.945	0.889	1	CLONAL	2	TRUE	1	0.661529235970253	3		259	460	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628554	90628554	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	140	590	0	ENST00000330062.3:c.1033G>C	p.Glu345Gln	p.E345Q	ENST00000330062	NM_002168.2	345	Gag/Cag	8/11	1	2	FACETS	0.96	0.882	1	0.96	0.882	1	CLONAL	1	TRUE	1	0.661529235970253	2		590	441	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969896	81969896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	287	553	0	ENST00000359376.3:c.2965G>A	p.Gly989Arg	p.G989R	ENST00000359376	NM_002661.3	989	Gga/Aga	27/33	0.646123602359751	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.661529235970253	2		553	427	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562694	29562694	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	115	391	1	ENST00000356175.3:c.3774G>C	p.Trp1258Cys	p.W1258C	ENST00000356175	NM_000267.3	1258	tgG/tgC	28/57	0.618804272643873	5	FACETS	1	0.951	1	0.272	0.245	0.3	CLONAL	1	TRUE	1	0.661529235970253	5		392	637	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40486012	40486012	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	148	505	0	ENST00000264657.5:c.853G>C	p.Glu285Gln	p.E285Q	ENST00000264657	NM_139276.2	285	Gag/Cag	9/24	0.476746646884069	3	FACETS	1	0.963	1	0.542	0.498	0.588	CLONAL	1	TRUE	1	0.661529235970253	3		505	549	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245955	41245955	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	121	455	0	ENST00000357654.3:c.1593G>A	p.Met531Ile	p.M531I	ENST00000357654	NM_007294.3	531	atG/atA	10/23	0.476746646884069	3	FACETS	0.86	0.78	0.944	0.43	0.39	0.472	CLONAL	1	TRUE	1	0.661529235970253	3		455	566	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961474	54961474	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	136	437	0	ENST00000312783.6:c.158del	p.Ser53PhefsTer40	p.S53Ffs*40	ENST00000312783	NM_198436.1	53	tCt/tt	4/10	0.661529235970253	6	FACETS	1	0.963	1	0.279	0.253	0.306	CLONAL	1	TRUE	2	0.661529235970253	6		437	857	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286164	66286164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1365668708	NA	P-0063678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	98	320	0	ENST00000273854.3:c.1522G>A	p.Glu508Lys	p.E508K	ENST00000273854	NM_004439.5	508	Gaa/Aaa	6/18	0.646123602359751	2	FACETS	0.847	0.762	0.934	0.423	0.381	0.467	CLONAL	1	TRUE	0	0.661529235970253	2		320	350	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158280	106158280	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	358	541	1	ENST00000380013.4:c.3181C>A	p.Pro1061Thr	p.P1061T	ENST00000380013	NM_001127208.2	1061	Cca/Aca	3/11	0.646123602359751	2	FACETS	0.935	0.898	0.971	0.935	0.898	0.971	CLONAL	2	TRUE	0	0.661529235970253	2		542	579	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053131	180053131	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	491	675	0	ENST00000261937.6:c.1238G>T	p.Ser413Ile	p.S413I	ENST00000261937	NM_182925.4	413	aGc/aTc	9/30	0.62260197448486	4	FACETS	0.946	0.92	0.971	0.946	0.92	0.971	CLONAL	4	TRUE	0	0.661529235970253	4		675	652	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13949264	13949264	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	128	357	0	ENST00000405192.2:c.864A>T	p.Lys288Asn	p.K288N	ENST00000405192	NM_001163147.1	288	aaA/aaT	9/12	0.661529235970253	4	FACETS	0.906	0.822	0.993	0.226	0.205	0.249	CLONAL	1	TRUE	0	0.661529235970253	4		357	710	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140454002	140454002	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057517915	NA	P-0063678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	437	323	0	ENST00000288602.6:c.1726G>T	p.Asp576Tyr	p.D576Y	ENST00000288602	NM_004333.4	576	Gac/Tac	14/18	0.661529235970253	4	FACETS	0.966	0.939	0.992	0.966	0.939	0.992	CLONAL	4	TRUE	0	0.661529235970253	4		323	568	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151948009	151948009	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	244	351	0	ENST00000262189.6:c.1664T>A	p.Met555Lys	p.M555K	ENST00000262189	NM_170606.2	555	aTg/aAg	12/59	0.56057237896398	4	FACETS	1	0.952	1			1	CLONAL	2	TRUE	NA	0.661529235970253	4		351	605	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141570554	141570554	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	158	552	0	ENST00000220592.5:c.574C>G	p.Leu192Val	p.L192V	ENST00000220592	NM_012154.3	192	Ctt/Gtt	5/19	0.646123602359751	2	FACETS	0.94	0.868	1	0.47	0.434	0.508	CLONAL	1	TRUE	0	0.661529235970253	2		552	508	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8525032	8525032	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	344	295	0	ENST00000356435.5:c.572C>A	p.Ala191Asp	p.A191D	ENST00000356435		191	gCc/gAc	7/35	0.637617609485126	4	FACETS	0.984	0.954	1	0.984	0.954	1	CLONAL	4	TRUE	0	0.661529235970253	4		295	439	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0063679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	26	728	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.668	0.528	0.83	0.668	0.528	0.83	SUBCLONAL	1	TRUE	1	0.15	2		728	519	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0063679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	26	322	0	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.15	2		322	290	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023071	27023080	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCCCCGCC	GGGCCCCGCC	-	novel	NA	P-0063679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	19	540	0	ENST00000324856.7:c.178_187del	p.Gly60TrpfsTer38	p.G60Wfs*38	ENST00000324856	NM_006015.4	59	gaGGGCCCCGCC/ga	1/20	1	2	FACETS	1	0.773	1	1	0.773	1	CLONAL	1	TRUE	1	0.15	2		540	249	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088680	27088680	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	33	544	0	ENST00000324856.7:c.2290del	p.Ser764ProfsTer69	p.S764Pfs*69	ENST00000324856	NM_006015.4	763	agT/ag	7/20	1	2	FACETS	0.845	0.687	1	0.845	0.687	1	CLONAL	1	TRUE	1	0.15	2		544	521	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654708	67654708	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0063679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	37	461	0	ENST00000264010.4:c.1195A>T	p.Arg399Ter	p.R399*	ENST00000264010	NM_006565.3	399	Aga/Tga	6/12	1	2	FACETS	0.977	0.805	1	0.977	0.805	1	CLONAL	1	TRUE	1	0.15	2		461	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587781702	NA	P-0063680-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	196	575	0	ENST00000269305.4:c.920-1G>C		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.61457692798388	1	FACETS	0.952	0.892	1	0.952	0.892	1	CLONAL	1	TRUE	0	0.621986197797882	1		575	456	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243482	41243482	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886040193	NA	P-0063680-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	317	457	0	ENST00000357654.3:c.4066C>T	p.Gln1356Ter	p.Q1356*	ENST00000357654	NM_007294.3	1356	Caa/Taa	10/23	NA	2	FACETS	0.933	0.893	0.974			1	INDETERMINATE	2	TRUE	NA	0.621986197797882	2		457	546	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400092	41400092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063680-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	109	388	0	ENST00000373198.4:c.667G>A	p.Asp223Asn	p.D223N	ENST00000373198	NM_133170.3	223	Gac/Aac	5/32	1	2	FACETS	0.863	0.781	0.949	0.863	0.781	0.949	CLONAL	1	TRUE	1	0.621986197797882	2		388	406	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949123	71949183	+	protein_altering_variant	In_Frame_Del	DEL	GCGAGGCAGGCATGAGTGCCTGGCTGCGGGCCATCGGCTTGGAGCGCTATGAGGAGGGCCT	GCGAGGCAGGCATGAGTGCCTGGCTGCGGGCCATCGGCTTGGAGCGCTATGAGGAGGGCCT	C	novel	NA	P-0063680-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	242	784	0	ENST00000298229.2:c.3590_3650delinsC	p.Gly1197_Leu1217delinsAla	p.G1197_L1217delinsA	ENST00000298229	NM_001567.3	1197	gGCGAGGCAGGCATGAGTGCCTGGCTGCGGGCCATCGGCTTGGAGCGCTATGAGGAGGGCCTg/gCg	27/28	0.621986197797882	2	FACETS	1	0.974	1	0.534	0.501	0.568	CLONAL	1	TRUE	0	0.621986197797882	2		784	729	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	149	331	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.998	0.921	1	0.998	0.921	1	CLONAL	1	TRUE	1	0.684574841511523	2		331	436	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	549	622	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.978	0.949	1	1	0.998	1	CLONAL	2	TRUE	1	0.684574841511523	2		626	820	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	218	728	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.684574841511523	2		728	603	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822586	72822586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	242	755	2	ENST00000268489.5:c.9589del	p.Gln3197SerfsTer44	p.Q3197Sfs*44	ENST00000268489	NM_006885.3	3197	Cag/ag	10/10	1	2	FACETS	0.875	0.82	0.932	0.875	0.82	0.932	CLONAL	1	TRUE	1	0.684574841511523	2		757	808	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	208	705	22	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	0.944	0.88	1	0.944	0.88	1	CLONAL	1	TRUE	1	0.684574841511523	2		727	644	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691872	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs79375991	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	392	500	18	ENST00000295754.5:c.383del	p.Lys128SerfsTer35	p.K128Sfs*35	ENST00000295754	NM_003242.5	125	gAa/ga	3/7	1	2	FACETS	0.842	0.809	0.875	1	0.997	1	CLONAL	2	TRUE	1	0.684574841511523	2		518	680	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	191	596	4	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	1	2	FACETS	0.924	0.859	0.99	0.924	0.859	0.99	CLONAL	1	TRUE	1	0.684574841511523	2		600	604	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	235	748	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.97	0.909	1	0.97	0.909	1	CLONAL	1	TRUE	1	0.684574841511523	2		752	708	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	188	399	0	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.911	0.846	0.977	0.911	0.846	0.977	CLONAL	1	TRUE	1	0.684574841511523	2		399	603	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9786991	9786993	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	190	501	0	ENST00000377346.4:c.3029_3031del	p.Glu1010del	p.E1010del	ENST00000377346	NM_005026.3	1008	GAG/-	24/24	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.684574841511523	2		501	537	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	192	725	1	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.952	0.886	1	0.952	0.886	1	CLONAL	1	TRUE	1	0.684574841511523	2		726	589	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023827	27023827	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	193	738	0	ENST00000324856.7:c.936del	p.Gly314AlafsTer49	p.G314Afs*49	ENST00000324856	NM_006015.4	311	taC/ta	1/20	1	2	FACETS	0.842	0.782	0.903	0.842	0.782	0.903	CLONAL	1	TRUE	1	0.684574841511523	2		738	670	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736511	85736511	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs387906351	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	234	471	12	ENST00000370580.1:c.136del	p.Ile46TyrfsTer24	p.I46Yfs*24	ENST00000370580	NM_003921.4	46	Ata/ta	2/3	1	2	FACETS	0.935	0.876	0.996	0.935	0.876	0.996	CLONAL	1	TRUE	1	0.684574841511523	2		483	731	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	207	319	0	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	1	2	FACETS	0.96	0.896	1	0.96	0.896	1	CLONAL	1	TRUE	1	0.684574841511523	2		319	630	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	94	264	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.684574841511523	2		264	252	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441816	49441816	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	139	519	0	ENST00000301067.7:c.4168del	p.Ala1390GlnfsTer27	p.A1390Qfs*27	ENST00000301067	NM_003482.3	1390	Gca/ca	14/54	1	2	FACETS	0.768	0.703	0.835	0.768	0.703	0.835	SUBCLONAL	1	TRUE	1	0.684574841511523	2		519	529	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445202	49445202	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776110112	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	275	875	0	ENST00000301067.7:c.2264G>A	p.Arg755Gln	p.R755Q	ENST00000301067	NM_003482.3	755	cGg/cAg	10/54	1	2	FACETS	0.997	0.939	1	0.997	0.939	1	CLONAL	1	TRUE	1	0.684574841511523	2		875	806	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	222	619	4	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.958	0.896	1	0.958	0.896	1	CLONAL	1	TRUE	1	0.684574841511523	2		623	677	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436831	110436831	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs745987317	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	243	795	0	ENST00000375856.3:c.1570A>G	p.Ile524Val	p.I524V	ENST00000375856	NM_003749.2	524	Atc/Gtc	1/2	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.684574841511523	2		795	705	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986880	36986880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1001194608	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	228	682	0	ENST00000354822.5:c.809G>A	p.Gly270Glu	p.G270E	ENST00000354822	NM_001079668.2	270	gGg/gAg	3/3	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.684574841511523	2		682	662	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052603	42052603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	217	542	2	ENST00000219905.7:c.7274G>A	p.Arg2425His	p.R2425H	ENST00000219905	NM_001164273.1	2425	cGc/cAc	20/24	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.684574841511523	2		544	628	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705500	43705501	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	193	584	0	ENST00000382044.4:c.5121_5122insA	p.Cys1708MetfsTer2	p.C1708Mfs*2	ENST00000382044	NM_001141980.1	1707	-/A	24/28	1	2	FACETS	0.974	0.907	1	0.974	0.907	1	CLONAL	1	TRUE	1	0.684574841511523	2		584	579	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51535079	51535079	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	203	516	0	ENST00000260433.2:c.31T>C	p.Tyr11His	p.Y11H	ENST00000260433		11	Tat/Cat	2/10	1	2	FACETS	0.99	0.924	1	0.99	0.924	1	CLONAL	1	TRUE	1	0.684574841511523	2		516	599	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347983	347983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760961378	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	265	834	2	ENST00000262320.3:c.1523del	p.Gly508ValfsTer197	p.G508Vfs*197	ENST00000262320	NM_003502.3	508	gGt/gt	6/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.684574841511523	2		836	770	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	360055	360055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	170	624	0	ENST00000262320.3:c.1034del	p.Pro345HisfsTer69	p.P345Hfs*69	ENST00000262320	NM_003502.3	345	cCa/ca	4/11	1	2	FACETS	0.951	0.881	1	0.951	0.881	1	CLONAL	1	TRUE	1	0.684574841511523	2		624	522	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226167	2226167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	194	780	0	ENST00000326181.6:c.1864G>A	p.Asp622Asn	p.D622N	ENST00000326181	NM_032271.2	622	Gac/Aac	19/21	1	2	FACETS	0.903	0.839	0.967	0.903	0.839	0.967	CLONAL	1	TRUE	1	0.684574841511523	2		780	628	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789629	3789629	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	189	580	1	ENST00000262367.5:c.4230del	p.Phe1410LeufsTer49	p.F1410Lfs*49	ENST00000262367	NM_004380.2	1410	ttT/tt	25/31	1	2	FACETS	0.928	0.863	0.995	0.928	0.863	0.995	CLONAL	1	TRUE	1	0.684574841511523	2		581	595	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807953	3807953	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755945995	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	207	543	0	ENST00000262367.5:c.3466G>A	p.Asp1156Asn	p.D1156N	ENST00000262367	NM_004380.2	1156	Gac/Aac	18/31	1	2	FACETS	0.958	0.894	1	0.958	0.894	1	CLONAL	1	TRUE	1	0.684574841511523	2		543	631	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846057	68846057	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	240	491	1	ENST00000261769.5:c.1028T>C	p.Leu343Pro	p.L343P	ENST00000261769	NM_004360.3	343	cTg/cCg	8/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.684574841511523	2		492	634	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864662	37864662	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1348253156	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	230	691	0	ENST00000269571.5:c.314C>T	p.Thr105Ile	p.T105I	ENST00000269571		105	aCc/aTc	3/27	1	2	FACETS	0.995	0.933	1	0.995	0.933	1	CLONAL	1	TRUE	1	0.684574841511523	2		691	675	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	253	715	3	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.991	0.931	1	0.991	0.931	1	CLONAL	1	TRUE	1	0.684574841511523	2		718	746	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617680	39617680	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	169	451	0	ENST00000262039.4:c.1869del	p.Phe623LeufsTer43	p.F623Lfs*43	ENST00000262039	NM_002647.2	622	Ttt/tt	17/25	0.684574841511523	3	FACETS	0.924	0.852	0.999	0.462	0.426	0.5	CLONAL	1	TRUE	1	0.684574841511523	3		451	717	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223060	1223060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746564972	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	248	637	0	ENST00000326873.7:c.997C>T	p.Arg333Cys	p.R333C	ENST00000326873	NM_000455.4	333	Cgc/Tgc	8/10	1	2	FACETS	0.998	0.938	1	0.998	0.938	1	CLONAL	1	TRUE	1	0.684574841511523	2		637	726	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6213975	6213976	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGG	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	65	628	0	ENST00000252674.7:c.1379_1381dup	p.Pro460dup	p.P460dup	ENST00000252674	NM_005934.3	460	cag/cCCCag	9/12	1	2	FACETS	0.393	0.341	0.449	0.393	0.341	0.449	SUBCLONAL	1	TRUE	1	0.684574841511523	2		628	483	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291084	10291084	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	335	1093	0	ENST00000340748.4:c.387del	p.Lys130AsnfsTer129	p.K130Nfs*129	ENST00000340748		129	ccC/cc	4/40	1	2	FACETS	0.845	0.799	0.892	0.845	0.799	0.892	CLONAL	1	TRUE	1	0.684574841511523	2		1093	1158	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257369	19257369	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs950872499	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	250	629	0	ENST00000162023.5:c.764C>T	p.Pro255Leu	p.P255L	ENST00000162023		255	cCc/cTc	11/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.684574841511523	2		629	646	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	250	737	2	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	1	2	FACETS	0.996	0.936	1	0.996	0.936	1	CLONAL	1	TRUE	1	0.684574841511523	2		739	733	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223857	36223858	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs754806477	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	243	893	0	ENST00000222270.7:c.6413dup	p.Ala2139GlyfsTer6	p.A2139Gfs*6	ENST00000222270	NM_014727.1	2136	ctc/ctCc	28/37	1	2	FACETS	0.891	0.835	0.948	0.891	0.835	0.948	CLONAL	1	TRUE	1	0.684574841511523	2		893	797	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42790929	42790929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	146	497	2	ENST00000575354.2:c.74C>T	p.Thr25Met	p.T25M	ENST00000575354	NM_015125.3	25	aCg/aTg	2/20	1	2	FACETS	0.908	0.835	0.982	0.908	0.835	0.982	CLONAL	1	TRUE	1	0.684574841511523	2		499	470	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989591	212989594	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	186	470	0	ENST00000342788.4:c.117_120del	p.Ser40ThrfsTer25	p.S40Tfs*25	ENST00000342788	NM_005235.2	39	ctCTCT/ct	2/28	1	2	FACETS	0.948	0.881	1	0.948	0.881	1	CLONAL	1	TRUE	1	0.684574841511523	2		470	573	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370741	225370741	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	197	402	0	ENST00000264414.4:c.1138C>A	p.Leu380Ile	p.L380I	ENST00000264414	NM_003590.4	380	Ctc/Atc	8/16	1	2	FACETS	0.969	0.903	1	0.969	0.903	1	CLONAL	1	TRUE	1	0.684574841511523	2		402	594	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385164	41385164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	156	514	2	ENST00000373198.4:c.797G>A	p.Arg266His	p.R266H	ENST00000373198	NM_133170.3	266	cGc/cAc	6/32	0.187870033492907	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.684574841511523	0		516	512	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21346659	21346659	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs767191322	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	45	519	0	ENST00000215739.8:c.1149+1G>A		p.X383_splice	ENST00000215739	NM_006767.3	383			1	2	FACETS	0.25	0.21	0.295	0.25	0.21	0.295	SUBCLONAL	1	TRUE	1	0.684574841511523	2		519	525	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413009	49413009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519953	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	251	476	0	ENST00000418115.1:c.14G>A	p.Arg5Gln	p.R5Q	ENST00000418115	NM_001664.2	5	cGg/cAg	2/5	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.684574841511523	2		476	582	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72873626	72873626	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	161	395	0	ENST00000325599.8:c.676del	p.Met226Ter	p.M226*	ENST00000325599	NM_018130.2	226	Atg/tg	6/11	1	2	FACETS	0.838	0.773	0.906	0.838	0.773	0.906	CLONAL	1	TRUE	1	0.684574841511523	2		395	561	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430936	181430936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	189	799	1	ENST00000325404.1:c.788C>T	p.Ala263Val	p.A263V	ENST00000325404	NM_003106.3	263	gCg/gTg	1/1	1	2	FACETS	0.805	0.747	0.865	0.805	0.747	0.865	CLONAL	1	TRUE	1	0.684574841511523	2		800	686	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	210	706	5	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	0.684574841511523	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.684574841511523	1		711	401	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152094	55152096	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	201	529	0	ENST00000257290.5:c.2529_2531del	p.Ile843del	p.I843del	ENST00000257290	NM_006206.4	842	gaCATc/gac	18/23	1	2	FACETS	0.92	0.857	0.985	0.92	0.857	0.985	CLONAL	1	TRUE	1	0.684574841511523	2		529	638	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156082	106156082	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	229	634	1	ENST00000380013.4:c.987del	p.Phe329LeufsTer18	p.F329Lfs*18	ENST00000380013	NM_001127208.2	328	gTt/gt	3/11	1	2	FACETS	0.91	0.852	0.97	0.91	0.852	0.97	CLONAL	1	TRUE	1	0.684574841511523	2		635	735	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244056	153244056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	251	608	0	ENST00000281708.4:c.2101G>A	p.Asp701Asn	p.D701N	ENST00000281708	NM_033632.3	701	Gac/Aac	12/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.684574841511523	2		608	694	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628340	187628340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536104649	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	299	676	0	ENST00000441802.2:c.2642G>A	p.Arg881His	p.R881H	ENST00000441802	NM_005245.3	881	cGc/cAc	2/27	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.684574841511523	2		676	872	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931452	131931452	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507178	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	203	432	18	ENST00000265335.6:c.2165del	p.Lys722ArgfsTer14	p.K722Rfs*14	ENST00000265335		719	ctA/ct	13/25	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.684574841511523	2		450	586	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520497	176520497	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145635664	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	242	697	0	ENST00000292408.4:c.1342G>A	p.Gly448Ser	p.G448S	ENST00000292408	NM_213647.1	448	Ggc/Agc	10/18	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.684574841511523	2		697	661	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777869	27777869	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	254	800	0	ENST00000369163.2:c.18G>C	p.Gln6His	p.Q6H	ENST00000369163	NM_003536.2	6	caG/caC	1/1	1	2	FACETS	0.954	0.896	1	0.954	0.896	1	CLONAL	1	TRUE	1	0.684574841511523	2		800	778	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671005	30671005	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1344945241	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	217	675	0	ENST00000376406.3:c.5741del	p.Gly1914GlufsTer57	p.G1914Efs*57	ENST00000376406	NM_014641.2	1914	gGa/ga	12/15	1	2	FACETS	0.916	0.856	0.978	0.916	0.856	0.978	CLONAL	1	TRUE	1	0.684574841511523	2		675	692	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172157	32172157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765990930	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	183	535	0	ENST00000375023.3:c.2875G>A	p.Gly959Ser	p.G959S	ENST00000375023	NM_004557.3	959	Ggc/Agc	19/30	1	2	FACETS	0.946	0.879	1	0.946	0.879	1	CLONAL	1	TRUE	1	0.684574841511523	2		535	565	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651904	36651904	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143419412	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	235	710	0	ENST00000244741.5:c.26G>A	p.Arg9His	p.R9H	ENST00000244741	NM_000389.4	9	cGt/cAt	2/3	1	2	FACETS	0.966	0.905	1	0.966	0.905	1	CLONAL	1	TRUE	1	0.684574841511523	2		710	711	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748498	43748498	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	231	555	0	ENST00000523873.1:c.456del	p.Lys152AsnfsTer22	p.K152Nfs*22	ENST00000523873		151	cAa/ca	6/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.684574841511523	2		555	654	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793716	89793716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754149624	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	229	510	1	ENST00000336032.3:c.785C>T	p.Ser262Leu	p.S262L	ENST00000336032	NM_006813.2	262	tCg/tTg	2/2	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.684574841511523	2		511	655	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	201	425	3	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.684574841511523	2		428	532	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151216588	151216588	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	48	194	0	ENST00000262187.5:c.10T>C	p.Ser4Pro	p.S4P	ENST00000262187	NM_005614.3	4	Tcc/Ccc	1/8	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.684574841511523	2		194	125	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277092	38277092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	186	535	0	ENST00000425967.3:c.1336C>T	p.His446Tyr	p.H446Y	ENST00000425967	NM_001174067.1	446	Cac/Tac	10/19	0.684574841511523	3	FACETS	0.964	0.892	1	0.482	0.446	0.519	CLONAL	1	TRUE	1	0.684574841511523	3		535	757	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950481	68950481	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	155	406	0	ENST00000288368.4:c.798del	p.Leu267PhefsTer16	p.L267Ffs*16	ENST00000288368	NM_024870.2	265	Ttt/tt	7/40	0.684574841511523	3	FACETS	0.921	0.846	0.999	0.46	0.423	0.5	CLONAL	1	TRUE	1	0.684574841511523	3		406	660	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965809	90965809	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	172	468	1	ENST00000265433.3:c.1508del	p.Asn503IlefsTer26	p.N503Ifs*26	ENST00000265433	NM_002485.4	503	aAt/at	11/16	0.684574841511523	3	FACETS	0.932	0.859	1	0.466	0.429	0.503	CLONAL	1	TRUE	1	0.684574841511523	3		469	724	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2186114	2186114	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1307331797	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	196	551	0	ENST00000349721.2:c.4480G>A	p.Val1494Ile	p.V1494I	ENST00000349721	NM_003070.3	1494	Gtc/Atc	32/34	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.684574841511523	2		551	543	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209616	98209617	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761353734	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	117	599	2	ENST00000331920.6:c.3921dup	p.Arg1308GlnfsTer17	p.R1308Qfs*17	ENST00000331920	NM_000264.3	1307	-/C	23/24	1	2	FACETS	0.629	0.57	0.692	0.629	0.57	0.692	SUBCLONAL	1	TRUE	1	0.684574841511523	2		601	543	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300040	137300040	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	160	529	5	ENST00000481739.1:c.331del	p.Leu111TrpfsTer57	p.L111Wfs*57	ENST00000481739	NM_002957.4	109	Ccc/cc	3/10	1	2	FACETS	0.88	0.812	0.95	0.88	0.812	0.95	CLONAL	1	TRUE	1	0.684574841511523	2		534	531	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923086	39923087	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	210	524	0	ENST00000378444.4:c.3621dup	p.Gln1208ThrfsTer8	p.Q1208Tfs*8	ENST00000378444	NM_001123385.1	1207	-/A	8/15	1	2	FACETS	0.983	0.918	1	0.983	0.918	1	CLONAL	1	TRUE	1	0.684574841511523	2		524	624	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47004904	47004904	+	intron_variant	Intron	SNP	G	G	A	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	300	971	1	ENST00000377604.3:c.-126+20G>A		p.*42*	ENST00000377604	NM_001204468.1	-/852			1	2	FACETS	0.88	0.83	0.931	0.88	0.83	0.931	CLONAL	1	TRUE	1	0.684574841511523	2		972	996	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361128	70361130	+	inframe_deletion	In_Frame_Del	DEL	CAG	CAG	-	rs1168018409	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	270	866	7	ENST00000374080.3:c.6327_6329del	p.Gln2115del	p.Q2115del	ENST00000374080		2106	CAG/-	43/45	1	2	FACETS	0.862	0.81	0.915	0.862	0.81	0.915	CLONAL	1	TRUE	1	0.684574841511523	2		873	915	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123026584	123026585	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	334	765	0	ENST00000355640.3:c.1061_1062del	p.Arg354AsnfsTer3	p.R354Nfs*3	ENST00000355640		354	AGa/a	5/7	1	2	FACETS	0.902	0.854	0.951	0.902	0.854	0.951	CLONAL	1	TRUE	1	0.684574841511523	2		765	1082	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821616	72821618	+	inframe_deletion	In_Frame_Del	DEL	CCA	CCA	-	rs766266415	NA	P-0063681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	105	574	20	ENST00000268489.5:c.10557_10559del	p.Gly3527del	p.G3527del	ENST00000268489	NM_006885.3	3519	ggTGGc/ggc	10/10	1	2	FACETS	0.549	0.493	0.608	0.549	0.493	0.608	SUBCLONAL	1	TRUE	1	0.684574841511523	2		594	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0063682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	331	662	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.697399205890281	2	FACETS	0.88	0.849	0.909	0.88	0.849	0.909	CLONAL	2	TRUE	0	0.839946154173558	2		662	448	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413560	32413560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28941778	NA	P-0063682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	305	479	1	ENST00000332351.3:c.1390G>A	p.Asp464Asn	p.D464N	ENST00000332351	NM_024426.4	464	Gac/Aac	9/10	0.665262962731359	4	FACETS	0.997	0.947	1	0.997	0.947	1	CLONAL	2	TRUE	2	0.839946154173558	4		480	670	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953759	48953759	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	106	233	0	ENST00000267163.4:c.1362C>A	p.Tyr454Ter	p.Y454*	ENST00000267163	NM_000321.2	454	taC/taA	14/27	0.703155583454204	2	FACETS	0.789	0.735	0.84	0.789	0.735	0.84	SUBCLONAL	2	TRUE	0	0.839946154173558	2		233	160	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61708394	61708394	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	103	339	0	ENST00000401558.2:c.2995A>T	p.Thr999Ser	p.T999S	ENST00000401558	NM_003400.3	999	Aca/Tca	24/25	0.724184784789186	3	FACETS	0.929	0.838	1	0.464	0.419	0.512	CLONAL	1	TRUE	1	0.839946154173558	3		339	375	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545969	41545974	+	inframe_deletion	In_Frame_Del	DEL	CCTGTT	CCTGTT	-	novel	NA	P-0063682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	686	690	0	ENST00000263253.7:c.2587_2592del	p.Val863_Pro864del	p.V863_P864del	ENST00000263253	NM_001429.3	862	CCTGTT/-	14/31	0.731111518651573	6	FACETS	0.878	0.851	0.905	0.878	0.851	0.905	CLONAL	4	TRUE	2	0.839946154173558	6		690	1246	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332730	153332730	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	458	650	1	ENST00000281708.4:c.226C>T	p.Gln76Ter	p.Q76*	ENST00000281708	NM_033632.3	76	Cag/Tag	2/12	0.700817264862026	3	FACETS	0.887	0.863	0.909	0.887	0.863	0.909	CLONAL	3	TRUE	0	0.839946154173558	3		651	582	SUCCESS
APC	324	MSKCC	GRCh37	5	112175476	112175476	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	449	512	0	ENST00000257430.4:c.4188del	p.Phe1396LeufsTer19	p.F1396Lfs*19	ENST00000257430	NM_000038.5	1395	agT/ag	16/16	0.7067821893932	3	FACETS	0.932	0.904	0.959	0.932	0.904	0.959	CLONAL	3	TRUE	0	0.7067821893932	3		512	615	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577115	7577115	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	365	564	1	ENST00000269305.4:c.823del	p.Cys275ValfsTer70	p.C275Vfs*70	ENST00000269305	NM_001126112.2	275	Tgt/gt	8/11	0.684684906671074	2	FACETS	0.974	0.94	1	0.974	0.94	1	CLONAL	2	TRUE	0	0.7067821893932	2		565	530	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749309	43749309	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	111	446	1	ENST00000382044.4:c.1497G>T	p.Glu499Asp	p.E499D	ENST00000382044	NM_001141980.1	499	gaG/gaT	12/28	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.7067821893932	2		447	303	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866576	78866576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	359	501	0	ENST00000306801.3:c.2149C>T	p.Leu717Phe	p.L717F	ENST00000306801	NM_020761.2	717	Ctt/Ttt	19/34	0.569202131370872	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.7067821893932	4		501	820	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	894924	894941	+	inframe_deletion	In_Frame_Del	DEL	AACCTGAGTGTTAGAAAG	AACCTGAGTGTTAGAAAG	-	novel	NA	P-0063683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	60	362	0	ENST00000166345.3:c.115_132del	p.Asn39_Lys44del	p.N39_K44del	ENST00000166345	NM_004237.3	39	AACCTGAGTGTTAGAAAG/-	2/13	0.656144330886129	3	FACETS	0.698	0.605	0.798	0.349	0.302	0.399	SUBCLONAL	1	TRUE	1	0.7067821893932	3		362	329	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109312007	109312007	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	50	372	0	ENST00000436639.2:c.1265T>C	p.Leu422Ser	p.L422S	ENST00000436639	NM_014454.2	422	tTg/tCg	8/10	0.684820131170459	3	FACETS	0.694	0.593	0.803	0.347	0.296	0.402	SUBCLONAL	1	TRUE	1	0.7067821893932	3		372	276	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	281	622	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.534094443310112	2		626	977	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	179	728	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.951	0.879	1	0.951	0.879	1	CLONAL	1	TRUE	1	0.534094443310112	2		728	705	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	167	440	7	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	1	2	FACETS	0.872	0.803	0.944	0.872	0.803	0.944	CLONAL	1	TRUE	1	0.534094443310112	2		447	717	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	148	469	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.866	0.793	0.941	0.866	0.793	0.941	CLONAL	1	TRUE	1	0.534094443310112	2		472	640	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	214	370	1	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.956	0.89	1	0.956	0.89	1	CLONAL	1	TRUE	1	0.534094443310112	2		371	838	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	198	507	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.534094443310112	2		507	734	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212381	5212381	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372226485	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	194	765	1	ENST00000357368.4:c.4736C>T	p.Pro1579Leu	p.P1579L	ENST00000357368	NM_002850.3	1579	cCg/cTg	31/38	1	2	FACETS	0.819	0.758	0.882	0.819	0.758	0.882	CLONAL	1	TRUE	1	0.534094443310112	2		766	887	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	229	715	3	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.944	0.881	1	0.944	0.881	1	CLONAL	1	TRUE	1	0.534094443310112	2		718	908	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	253	661	4	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	0.975	0.913	1	0.975	0.913	1	CLONAL	1	TRUE	1	0.534094443310112	2		665	972	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1023835002	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	420	559	0	ENST00000558401.1:c.1A>G	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Gtg	1/4	0.534094443310112	2	FACETS	0.989	0.95	1	0.989	0.95	1	CLONAL	2	TRUE	0	0.534094443310112	2		559	795	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308383	15308383	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	91	663	0	ENST00000263388.2:c.125del	p.Pro42LeufsTer194	p.P42Lfs*194	ENST00000263388	NM_000435.2	42	cCt/ct	2/33	1	2	FACETS	0.406	0.36	0.456	0.406	0.36	0.456	SUBCLONAL	1	TRUE	1	0.534094443310112	2		663	839	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973548	15973548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1000518180	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	224	522	1	ENST00000268712.3:c.4444C>T	p.Arg1482Trp	p.R1482W	ENST00000268712	NM_006311.3	1482	Cgg/Tgg	31/46	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.534094443310112	2		523	837	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440943	56440943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786205215	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	217	368	0	ENST00000407977.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000407977		132	Cga/Tga	4/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.534094443310112	2		368	792	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625251	69625251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782147248	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	213	593	0	ENST00000334134.2:c.542G>A	p.Arg181His	p.R181H	ENST00000334134	NM_005247.2	181	cGc/cAc	3/3	1	2	FACETS	0.966	0.899	1	0.966	0.899	1	CLONAL	1	TRUE	1	0.534094443310112	2		593	826	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023769	27023769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	194	647	0	ENST00000324856.7:c.879del	p.Thr294ProfsTer69	p.T294Pfs*69	ENST00000324856	NM_006015.4	292	aCc/ac	1/20	1	2	FACETS	0.945	0.876	1	0.945	0.876	1	CLONAL	1	TRUE	1	0.534094443310112	2		647	769	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753910	133753910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149852028	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	89	434	0	ENST00000318560.5:c.1379G>A	p.Arg460His	p.R460H	ENST00000318560	NM_005157.4	460	cGc/cAc	8/11	1	2	FACETS	0.505	0.448	0.566	0.505	0.448	0.566	SUBCLONAL	1	TRUE	1	0.534094443310112	2		434	660	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	206	574	8	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	0.869	0.807	0.933	0.869	0.807	0.933	CLONAL	1	TRUE	1	0.534094443310112	2		582	888	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852118	63852118	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	212	557	1	ENST00000279873.7:c.2901del	p.Lys967AsnfsTer15	p.K967Nfs*15	ENST00000279873	NM_032199.2	966	Aaa/aa	10/10	1	2	FACETS	0.927	0.863	0.994	0.927	0.863	0.994	CLONAL	1	TRUE	1	0.534094443310112	2		558	856	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118885	70118885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	285	704	0	ENST00000245479.2:c.457C>T	p.Pro153Ser	p.P153S	ENST00000245479	NM_000346.3	153	Ccc/Tcc	2/3	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.534094443310112	2		704	1065	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553249	106553249	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1415765117	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	256	696	0	ENST00000369096.4:c.1214C>T	p.Ser405Leu	p.S405L	ENST00000369096	NM_001198.3	405	tCg/tTg	5/7	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.534094443310112	2		696	952	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	207	631	0	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.534094443310112	2		631	747	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687472	37687472	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	218	652	1	ENST00000447079.4:c.4382del	p.Gly1461AlafsTer38	p.G1461Afs*38	ENST00000447079	NM_015083.1	1459	tGg/tg	14/14	1	2	FACETS	0.899	0.837	0.963	0.899	0.837	0.963	CLONAL	1	TRUE	1	0.534094443310112	2		653	908	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933400	39933400	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	217	699	0	ENST00000378444.4:c.1199del	p.Gly400AlafsTer42	p.G400Afs*42	ENST00000378444	NM_001123385.1	400	gGc/gc	4/15	1	2	FACETS	0.768	0.714	0.824	0.768	0.714	0.824	SUBCLONAL	1	TRUE	1	0.534094443310112	2		699	1058	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926270	112926270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918457	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	169	361	0	ENST00000351677.2:c.1403C>T	p.Thr468Met	p.T468M	ENST00000351677	NM_002834.3	468	aCg/aTg	12/16	1	2	FACETS	0.965	0.89	1	0.965	0.89	1	CLONAL	1	TRUE	1	0.534094443310112	2		361	656	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868176	45868176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559154781	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	203	582	0	ENST00000391945.4:c.514G>A	p.Ala172Thr	p.A172T	ENST00000391945	NM_000400.3	172	Gct/Act	7/23	1	2	FACETS	0.918	0.853	0.986	0.918	0.853	0.986	CLONAL	1	TRUE	1	0.534094443310112	2		582	828	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906603	32906603	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359777	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	49	465	2	ENST00000380152.3:c.994del	p.Ile332PhefsTer17	p.I332Ffs*17	ENST00000380152		330	Aaa/aa	10/27	1	2	FACETS	0.25	0.211	0.293	0.25	0.211	0.293	SUBCLONAL	1	TRUE	1	0.534094443310112	2		467	734	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448297	56448298	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1567880599	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	230	667	0	ENST00000407977.2:c.349dup	p.Arg117ProfsTer8	p.R117Pfs*8	ENST00000407977		117	cgc/cCgc	3/10	1	2	FACETS	0.94	0.878	1	0.94	0.878	1	CLONAL	1	TRUE	1	0.534094443310112	2		667	916	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137271	64137271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	220	607	2	ENST00000334205.4:c.1703C>T	p.Thr568Met	p.T568M	ENST00000334205	NM_003942.2	568	aCg/aTg	14/17	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.534094443310112	2		609	782	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981721	101981721	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555075353	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	68	631	1	ENST00000282441.5:c.147del	p.Ala50ProfsTer24	p.A50Pfs*24	ENST00000282441	NM_001130145.2	48	Ccc/cc	1/9	1	2	FACETS	0.357	0.31	0.408	0.357	0.31	0.408	SUBCLONAL	1	TRUE	1	0.534094443310112	2		632	713	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864776	37864776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs185670819	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	199	527	0	ENST00000269571.5:c.428G>A	p.Arg143Gln	p.R143Q	ENST00000269571		143	cGa/cAa	3/27	1	2	FACETS	0.948	0.88	1	0.948	0.88	1	CLONAL	1	TRUE	1	0.534094443310112	2		527	786	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922363	178922363	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	84	237	0	ENST00000263967.3:c.1132T>C	p.Cys378Arg	p.C378R	ENST00000263967	NM_006218.2	378	Tgt/Cgt	6/21	1	2	FACETS	0.95	0.847	1	0.95	0.847	1	CLONAL	1	TRUE	1	0.534094443310112	2		237	331	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	198	465	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.534094443310112	2		465	720	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261146	16261146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769982439	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	278	650	0	ENST00000375759.3:c.8411C>T	p.Ala2804Val	p.A2804V	ENST00000375759	NM_015001.2	2804	gCg/gTg	11/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.534094443310112	2		650	937	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105512	30105512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768104173	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	178	519	0	ENST00000331968.5:c.1174G>A	p.Ala392Thr	p.A392T	ENST00000331968	NM_002742.2	392	Gcc/Acc	7/18	1	2	FACETS	0.897	0.829	0.968	0.897	0.829	0.968	CLONAL	1	TRUE	1	0.534094443310112	2		519	743	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	218	953	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.812	0.755	0.871	0.812	0.755	0.871	CLONAL	1	TRUE	1	0.534094443310112	2		954	1005	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612358	1612358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770576452	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	219	660	0	ENST00000344749.5:c.1661G>A	p.Arg554Gln	p.R554Q	ENST00000344749	NM_001136139.2	554	cGg/cAg	18/19	1	2	FACETS	0.972	0.906	1	0.972	0.906	1	CLONAL	1	TRUE	1	0.534094443310112	2		660	844	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557846	187557848	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs764081811	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	93	575	0	ENST00000441802.2:c.3863_3865del	p.Ser1288del	p.S1288del	ENST00000441802	NM_005245.3	1288	tCCTac/tac	5/27	1	2	FACETS	0.387	0.344	0.434	0.387	0.344	0.434	SUBCLONAL	1	TRUE	1	0.534094443310112	2		575	899	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395677	31395677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1267164985	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	194	648	2	ENST00000328111.2:c.2530G>A	p.Ala844Thr	p.A844T	ENST00000328111	NM_006892.3	844	Gcc/Acc	23/23	1	2	FACETS	0.885	0.82	0.952	0.885	0.82	0.952	CLONAL	1	TRUE	1	0.534094443310112	2		650	821	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438688	49438688	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749039924	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	164	614	0	ENST00000301067.7:c.4802G>A	p.Arg1601His	p.R1601H	ENST00000301067	NM_003482.3	1601	cGt/cAt	19/54	1	2	FACETS	0.753	0.692	0.816	0.753	0.692	0.816	SUBCLONAL	1	TRUE	1	0.534094443310112	2		614	816	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210925	36210925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531663002	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	235	785	0	ENST00000222270.7:c.676C>T	p.Arg226Trp	p.R226W	ENST00000222270	NM_014727.1	226	Cgg/Tgg	3/37	1	2	FACETS	0.99	0.925	1	0.99	0.925	1	CLONAL	1	TRUE	1	0.534094443310112	2		785	889	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092947	29092947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881688	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	144	356	0	ENST00000328354.6:c.1037G>A	p.Arg346His	p.R346H	ENST00000328354	NM_007194.3	346	cGt/cAt	10/15	1	2	FACETS	0.999	0.916	1	0.999	0.916	1	CLONAL	1	TRUE	1	0.534094443310112	2		356	540	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244249	5244249	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	187	722	0	ENST00000357368.4:c.1233del	p.Ser414AlafsTer30	p.S414Afs*30	ENST00000357368	NM_002850.3	411	ggG/gg	11/38	1	2	FACETS	0.813	0.752	0.877	0.813	0.752	0.877	CLONAL	1	TRUE	1	0.534094443310112	2		722	861	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980293	201980293	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	119	551	0	ENST00000359651.3:c.33del	p.Phe11LeufsTer32	p.F11Lfs*32	ENST00000359651		10	aTt/at	1/8	1	2	FACETS	0.519	0.468	0.573	0.519	0.468	0.573	SUBCLONAL	1	TRUE	1	0.534094443310112	2		551	859	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200228	67200228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770979132	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	204	663	0	ENST00000312629.5:c.536C>T	p.Thr179Met	p.T179M	ENST00000312629	NM_003952.2	179	aCg/aTg	7/15	1	2	FACETS	0.889	0.826	0.955	0.889	0.826	0.955	CLONAL	1	TRUE	1	0.534094443310112	2		663	859	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40476850	40476850	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	98	592	0	ENST00000264657.5:c.1479del	p.Phe493LeufsTer16	p.F493Lfs*16	ENST00000264657	NM_139276.2	493	ttT/tt	17/24	1	2	FACETS	0.417	0.372	0.466	0.417	0.372	0.466	SUBCLONAL	1	TRUE	1	0.534094443310112	2		592	879	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480028	50480028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs759976916	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	195	562	0	ENST00000394963.4:c.262C>T	p.Arg88Ter	p.R88*	ENST00000394963	NM_003076.4	88	Cga/Tga	2/13	1	2	FACETS	0.963	0.894	1	0.963	0.894	1	CLONAL	1	TRUE	1	0.534094443310112	2		562	758	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798839	42798839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778649585	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	198	645	0	ENST00000575354.2:c.4411C>T	p.Arg1471Trp	p.R1471W	ENST00000575354	NM_015125.3	1471	Cgg/Tgg	19/20	1	2	FACETS	0.948	0.88	1	0.948	0.88	1	CLONAL	1	TRUE	1	0.534094443310112	2		645	782	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051105	13051105	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	109	626	0	ENST00000316448.5:c.541A>G	p.Thr181Ala	p.T181A	ENST00000316448	NM_004343.3	181	Acc/Gcc	5/9	1	2	FACETS	0.428	0.383	0.475	0.428	0.383	0.475	SUBCLONAL	1	TRUE	1	0.534094443310112	2		626	954	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794048	42794048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762143212	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	184	566	0	ENST00000575354.2:c.1409G>A	p.Arg470Gln	p.R470Q	ENST00000575354	NM_015125.3	470	cGg/cAg	9/20	1	2	FACETS	0.965	0.894	1	0.965	0.894	1	CLONAL	1	TRUE	1	0.534094443310112	2		566	714	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243675627	243675627	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	73	236	0	ENST00000263826.5:c.1353del	p.Lys451AsnfsTer55	p.K451Nfs*55	ENST00000263826	NM_005465.4	451	aaA/aa	12/13	1	2	FACETS	0.716	0.629	0.808	0.716	0.629	0.808	SUBCLONAL	1	TRUE	1	0.534094443310112	2		236	382	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956955	2956955	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	169	470	0	ENST00000396946.4:c.2672G>A	p.Arg891Gln	p.R891Q	ENST00000396946	NM_032415.4	891	cGa/cAa	20/25	1	2	FACETS	0.859	0.791	0.929	0.859	0.791	0.929	CLONAL	1	TRUE	1	0.534094443310112	2		470	737	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436084	51436084	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	159	476	0	ENST00000262662.1:c.49del	p.Asp17ThrfsTer2	p.D17Tfs*2	ENST00000262662		15	aGg/ag	3/4	1	2	FACETS	0.799	0.734	0.867	0.799	0.734	0.867	SUBCLONAL	1	TRUE	1	0.534094443310112	2		476	745	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851924	63851924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199637139	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	247	584	1	ENST00000279873.7:c.2702C>T	p.Thr901Met	p.T901M	ENST00000279873	NM_032199.2	901	aCg/aTg	10/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.534094443310112	2		585	827	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268687	46268687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	117	593	0	ENST00000371998.3:c.2972T>C	p.Met991Thr	p.M991T	ENST00000371998		991	aTg/aCg	16/23	1	2	FACETS	0.492	0.443	0.544	0.492	0.443	0.544	SUBCLONAL	1	TRUE	1	0.534094443310112	2		593	890	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025606	1025606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	210	692	1	ENST00000358495.3:c.769C>T	p.Arg257Trp	p.R257W	ENST00000358495	NM_134424.2	257	Cgg/Tgg	9/12	1	2	FACETS	0.901	0.838	0.966	0.901	0.838	0.966	CLONAL	1	TRUE	1	0.534094443310112	2		693	873	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235930	108235930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	175	496	0	ENST00000278616.4:c.8972G>A	p.Cys2991Tyr	p.C2991Y	ENST00000278616	NM_000051.3	2991	tGc/tAc	62/63	1	2	FACETS	0.817	0.754	0.883	0.817	0.754	0.883	CLONAL	1	TRUE	1	0.534094443310112	2		496	802	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141549424	141549424	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	187	443	0	ENST00000220592.5:c.2164G>A	p.Glu722Lys	p.E722K	ENST00000220592	NM_012154.3	722	Gag/Aag	16/19	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.534094443310112	2		443	666	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	90	488	2	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.467	0.414	0.523	0.467	0.414	0.523	SUBCLONAL	1	TRUE	1	0.534094443310112	2		490	722	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21341837	21341837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587777177	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	207	541	0	ENST00000215739.8:c.365C>T	p.Ser122Leu	p.S122L	ENST00000215739	NM_006767.3	122	tCg/tTg	4/21	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.534094443310112	2		541	757	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29439321	29439321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	197	477	0	ENST00000544604.2:c.536C>T	p.Pro179Leu	p.P179L	ENST00000544604	NM_001206998.1	179	cCg/cTg	4/9	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.534094443310112	2		477	701	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10794202	10794202	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	67	383	0	ENST00000361367.2:c.2580G>T	p.Gln860His	p.Q860H	ENST00000361367	NM_014633.3	860	caG/caT	20/25	1	2	FACETS	0.39	0.338	0.445	0.39	0.338	0.445	SUBCLONAL	1	TRUE	1	0.534094443310112	2		383	644	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115738	108115738	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	139	402	0	ENST00000278616.4:c.889del	p.Thr297ProfsTer23	p.T297Pfs*23	ENST00000278616	NM_000051.3	296	Aaa/aa	7/63	1	2	FACETS	0.986	0.902	1	0.986	0.902	1	CLONAL	1	TRUE	1	0.534094443310112	2		402	528	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112910817	112910817	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	114	346	0	ENST00000351677.2:c.830del	p.Asn277IlefsTer62	p.N277Ifs*62	ENST00000351677	NM_002834.3	276	Aaa/aa	7/16	1	2	FACETS	0.914	0.828	1	0.914	0.828	1	CLONAL	1	TRUE	1	0.534094443310112	2		346	467	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562640	21562640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs541484742	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	198	505	0	ENST00000382592.4:c.1279C>T	p.Pro427Ser	p.P427S	ENST00000382592	NM_014572.2	427	Ccc/Tcc	4/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.534094443310112	2		505	662	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908170	28908170	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	85	415	0	ENST00000282397.4:c.2585T>C	p.Met862Thr	p.M862T	ENST00000282397	NM_002019.4	862	aTg/aCg	18/30	1	2	FACETS	0.499	0.441	0.561	0.499	0.441	0.561	SUBCLONAL	1	TRUE	1	0.534094443310112	2		415	638	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518708	103518708	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201581850	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	137	428	1	ENST00000355739.4:c.2296G>A	p.Gly766Arg	p.G766R	ENST00000355739	NM_000123.3	766	Gga/Aga	10/15	1	2	FACETS	0.903	0.825	0.984	0.903	0.825	0.984	CLONAL	1	TRUE	1	0.534094443310112	2		429	568	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396708	30396708	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	106	356	0	ENST00000331968.5:c.11del	p.Pro4LeufsTer54	p.P4Lfs*54	ENST00000331968	NM_002742.2	4	cCt/ct	1/18	1	2	FACETS	0.869	0.783	0.958	0.869	0.783	0.958	CLONAL	1	TRUE	1	0.534094443310112	2		356	457	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023381	33023381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1332974507	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	235	607	0	ENST00000300177.4:c.490C>T	p.Pro164Ser	p.P164S	ENST00000300177	NM_001191322.1	164	Cct/Tct	2/2	0.534094443310112	2	FACETS	1	0.941	1	0.503	0.47	0.537	CLONAL	1	TRUE	0	0.534094443310112	2		607	874	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988607	41988607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	387	532	0	ENST00000219905.7:c.1399C>T	p.Pro467Ser	p.P467S	ENST00000219905	NM_001164273.1	467	Cca/Tca	3/24	0.534094443310112	2	FACETS	0.993	0.951	1	0.993	0.951	1	CLONAL	2	TRUE	0	0.534094443310112	2		532	730	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096262	2096262	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	111	492	0	ENST00000219066.1:c.245T>A	p.Leu82His	p.L82H	ENST00000219066	NM_002528.5	82	cTc/cAc	2/6	1	2	FACETS	0.582	0.524	0.644	0.582	0.524	0.644	SUBCLONAL	1	TRUE	1	0.534094443310112	2		492	714	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134304	2134304	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs560831385	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	256	741	0	ENST00000219476.3:c.4081C>T	p.Arg1361Ter	p.R1361*	ENST00000219476	NM_000548.3	1361	Cga/Tga	34/42	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.534094443310112	2		741	926	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647941	3647941	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377135500	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	218	588	2	ENST00000294008.3:c.1223G>A	p.Arg408Gln	p.R408Q	ENST00000294008	NM_032444.2	408	cGg/cAg	6/15	1	2	FACETS	0.998	0.93	1	0.998	0.93	1	CLONAL	1	TRUE	1	0.534094443310112	2		590	818	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50815179	50815179	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761903963	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	146	434	0	ENST00000398568.2:c.1532C>T	p.Thr511Met	p.T511M	ENST00000398568	NM_001042412.1	511	aCg/aTg	9/18	1	2	FACETS	0.85	0.778	0.925	0.85	0.778	0.925	CLONAL	1	TRUE	1	0.534094443310112	2		434	643	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845609	72845609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs190630040	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	201	672	1	ENST00000268489.5:c.3731C>T	p.Thr1244Met	p.T1244M	ENST00000268489	NM_006885.3	1244	aCg/aTg	7/10	1	2	FACETS	0.863	0.801	0.928	0.863	0.801	0.928	CLONAL	1	TRUE	1	0.534094443310112	2		673	872	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991560	72991560	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	95	646	0	ENST00000268489.5:c.2485A>T	p.Met829Leu	p.M829L	ENST00000268489	NM_006885.3	829	Atg/Ttg	2/10	1	2	FACETS	0.434	0.386	0.485	0.434	0.386	0.485	SUBCLONAL	1	TRUE	1	0.534094443310112	2		646	820	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357493	89357493	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	218	661	1	ENST00000301030.4:c.325T>C	p.Tyr109His	p.Y109H	ENST00000301030	NM_001256183.1	109	Tac/Cac	5/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.534094443310112	2		662	791	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110945	8110945	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	82	481	0	ENST00000585124.1:c.152-2A>G		p.X51_splice	ENST00000585124	NM_004217.3	51			1	2	FACETS	0.409	0.36	0.461	0.409	0.36	0.461	SUBCLONAL	1	TRUE	1	0.534094443310112	2		481	751	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120281	70120281	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	267	656	0	ENST00000245479.2:c.1283A>G	p.Tyr428Cys	p.Y428C	ENST00000245479	NM_000346.3	428	tAc/tGc	3/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.534094443310112	2		656	945	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101854	11101854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377549345	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	217	589	0	ENST00000358026.2:c.1274G>A	p.Arg425Gln	p.R425Q	ENST00000358026	NM_001128849.1	425	cGg/cAg	8/36	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.534094443310112	2		589	772	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105601	11105601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1286498410	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	199	573	0	ENST00000358026.2:c.1517C>T	p.Thr506Met	p.T506M	ENST00000358026	NM_001128849.1	506	aCg/aTg	9/36	1	2	FACETS	0.926	0.859	0.994	0.926	0.859	0.994	CLONAL	1	TRUE	1	0.534094443310112	2		573	805	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302979	15302979	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	276	809	0	ENST00000263388.2:c.471C>A	p.Ser157Arg	p.S157R	ENST00000263388	NM_000435.2	157	agC/agA	4/33	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.534094443310112	2		809	945	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726664	41726664	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	209	567	0	ENST00000301178.4:c.209T>G	p.Leu70Arg	p.L70R	ENST00000301178	NM_021913.4	70	cTt/cGt	2/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.534094443310112	2		567	752	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754531	42754531	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370521331	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	252	610	0	ENST00000222329.4:c.209G>A	p.Arg70His	p.R70H	ENST00000222329	NM_006494.2	70	cGc/cAc	2/4	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.534094443310112	2		610	854	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798412	42798412	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	85	548	0	ENST00000575354.2:c.4283A>C	p.Lys1428Thr	p.K1428T	ENST00000575354	NM_015125.3	1428	aAg/aCg	18/20	1	2	FACETS	0.405	0.357	0.456	0.405	0.357	0.456	SUBCLONAL	1	TRUE	1	0.534094443310112	2		548	786	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422973	47422973	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	215	572	0	ENST00000404338.3:c.1044del	p.Phe348LeufsTer8	p.F348Lfs*8	ENST00000404338	NM_004491.4	347	gcT/gc	1/6	1	2	FACETS	0.891	0.829	0.955	0.891	0.829	0.955	CLONAL	1	TRUE	1	0.534094443310112	2		572	904	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906429	50906429	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	235	664	1	ENST00000440232.2:c.1090C>A	p.Leu364Met	p.L364M	ENST00000440232	NM_002691.3	364	Ctg/Atg	9/27	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.534094443310112	2		665	824	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022368	26022368	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	93	411	0	ENST00000435504.4:c.289G>T	p.Gly97Cys	p.G97C	ENST00000435504		97	Ggt/Tgt	5/13	1	2	FACETS	0.505	0.449	0.565	0.505	0.449	0.565	SUBCLONAL	1	TRUE	1	0.534094443310112	2		411	689	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213165	39213165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881051	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	247	629	0	ENST00000402219.2:c.3802G>A	p.Gly1268Ser	p.G1268S	ENST00000402219	NM_005633.3	1268	Ggc/Agc	23/23	NA	2	FACETS	0.985	0.922	1			1	INDETERMINATE	1	TRUE	NA	0.534094443310112	2		629	939	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656920	47656921	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGGC	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	145	298	0	ENST00000233146.2:c.1119_1122dup	p.Thr375AlafsTer15	p.T375Afs*15	ENST00000233146	NM_000251.2	372	-/AGGC	7/16	1	2	FACETS	0.928	0.85	1	0.928	0.85	1	CLONAL	1	TRUE	1	0.534094443310112	2		298	585	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657037	47657037	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	190	410	0	ENST00000233146.2:c.1235del	p.Asn412IlefsTer26	p.N412Ifs*26	ENST00000233146	NM_000251.2	411	atA/at	7/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.534094443310112	2		410	686	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29444430	29444431	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	236	510	0	ENST00000544604.2:c.966_967insA	p.Trp323MetfsTer144	p.W323Mfs*144	ENST00000544604	NM_001206998.1	322	-/A	7/9	1	2	FACETS	0.996	0.931	1	0.996	0.931	1	CLONAL	1	TRUE	1	0.534094443310112	2		510	887	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098457	47098457	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	211	593	0	ENST00000409792.3:c.6817del	p.Trp2273GlyfsTer36	p.W2273Gfs*36	ENST00000409792	NM_014159.6	2273	Tgg/gg	15/21	1	2	FACETS	0.864	0.804	0.927	0.864	0.804	0.927	CLONAL	1	TRUE	1	0.534094443310112	2		593	914	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981465	63981465	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	59	785	0	ENST00000398590.3:c.1967C>A	p.Pro656His	p.P656H	ENST00000398590	NM_001177387.1	656	cCc/cAc	12/14	1	2	FACETS	0.224	0.192	0.26	0.224	0.192	0.26	SUBCLONAL	1	TRUE	1	0.534094443310112	2		785	985	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205847	128205847	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1576749993	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	89	538	0	ENST00000341105.2:c.28T>C	p.Trp10Arg	p.W10R	ENST00000341105	NM_032638.4	10	Tgg/Cgg	2/6	1	2	FACETS	0.478	0.424	0.536	0.478	0.424	0.536	SUBCLONAL	1	TRUE	1	0.534094443310112	2		538	697	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447176	187447176	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	106	633	0	ENST00000232014.4:c.1017C>A	p.Cys339Ter	p.C339*	ENST00000232014	NM_001130845.1	339	tgC/tgA	5/10	1	2	FACETS	0.445	0.399	0.495	0.445	0.399	0.495	SUBCLONAL	1	TRUE	1	0.534094443310112	2		633	891	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748020	41748020	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	102	288	1	ENST00000226382.2:c.749C>T	p.Ala250Val	p.A250V	ENST00000226382	NM_003924.3	250	gCg/gTg	3/3	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.534094443310112	2		289	300	SUCCESS
REST	5978	MSKCC	GRCh37	4	57777484	57777484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	246	631	2	ENST00000309042.7:c.680G>A	p.Arg227Gln	p.R227Q	ENST00000309042	NM_005612.4	227	cGa/cAa	2/4	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.534094443310112	2		633	898	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637165	176637165	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	123	560	0	ENST00000439151.2:c.1765T>G	p.Ser589Ala	p.S589A	ENST00000439151	NM_022455.4	589	Tct/Gct	5/23	1	2	FACETS	0.496	0.448	0.547	0.496	0.448	0.547	SUBCLONAL	1	TRUE	1	0.534094443310112	2		560	929	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821376	32821376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	145	692	2	ENST00000354258.4:c.218G>A	p.Arg73His	p.R73H	ENST00000354258	NM_000593.5	73	cGc/cAc	1/11	1	2	FACETS	0.576	0.525	0.63	0.576	0.525	0.63	SUBCLONAL	1	TRUE	1	0.534094443310112	2		694	942	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109319939	109319939	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	45	412	0	ENST00000436639.2:c.749A>C	p.Glu250Ala	p.E250A	ENST00000436639	NM_014454.2	250	gAg/gCg	5/10	1	2	FACETS	0.249	0.208	0.293	0.249	0.208	0.293	SUBCLONAL	1	TRUE	1	0.534094443310112	2		412	678	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686286	117686286	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	163	484	0	ENST00000368508.3:c.3055A>G	p.Thr1019Ala	p.T1019A	ENST00000368508	NM_002944.2	1019	Act/Gct	20/43	NA	2	FACETS	0.88	0.809	0.952			1	INDETERMINATE	1	TRUE	NA	0.534094443310112	2		484	694	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199748	138199748	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	239	651	0	ENST00000237289.4:c.1166C>T	p.Thr389Met	p.T389M	ENST00000237289	NM_001270507.1	389	aCg/aTg	7/9	1	2	FACETS	0.949	0.887	1	0.949	0.887	1	CLONAL	1	TRUE	1	0.534094443310112	2		651	943	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864443	162864443	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	47	453	0	ENST00000366898.1:c.70T>A	p.Phe24Ile	p.F24I	ENST00000366898	NM_004562.2	24	Ttc/Atc	2/12	1	2	FACETS	0.303	0.255	0.356	0.303	0.255	0.356	SUBCLONAL	1	TRUE	1	0.534094443310112	2		453	580	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397752	116397752	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	71	489	0	ENST00000397752.3:c.2026A>G	p.Thr676Ala	p.T676A	ENST00000397752	NM_000245.2	676	Act/Gct	8/21	1	2	FACETS	0.402	0.351	0.458	0.402	0.351	0.458	SUBCLONAL	1	TRUE	1	0.534094443310112	2		489	661	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878505	151878505	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	259	557	0	ENST00000262189.6:c.6440A>G	p.Gln2147Arg	p.Q2147R	ENST00000262189	NM_170606.2	2147	cAa/cGa	36/59	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.534094443310112	2		557	874	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737558	145737558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758648484	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	283	881	2	ENST00000428558.2:c.3205C>T	p.Arg1069Cys	p.R1069C	ENST00000428558	NM_004260.3	1069	Cgt/Tgt	19/22	1	2	FACETS	0.993	0.934	1	0.993	0.934	1	CLONAL	1	TRUE	1	0.534094443310112	2		883	1067	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215884	98215884	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1344231723	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	146	402	0	ENST00000331920.6:c.3325G>A	p.Gly1109Ser	p.G1109S	ENST00000331920	NM_000264.3	1109	Ggc/Agc	20/24	1	2	FACETS	0.996	0.914	1	0.996	0.914	1	CLONAL	1	TRUE	1	0.534094443310112	2		402	549	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139563037	139563037	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	244	643	0	ENST00000308874.7:c.112del	p.Asp38ThrfsTer159	p.D38Tfs*159	ENST00000308874		37	Ggg/gg	4/10	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.534094443310112	2		643	902	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932603	39932603	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	209	737	0	ENST00000378444.4:c.1996A>G	p.Ile666Val	p.I666V	ENST00000378444	NM_001123385.1	666	Att/Gtt	4/15	1	2	FACETS	0.748	0.694	0.804	0.748	0.694	0.804	SUBCLONAL	1	TRUE	1	0.534094443310112	2		737	1046	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	93	372	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.294366085833525	2		372	511	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	61	210	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.294366085833525	2		210	302	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	162	622	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.753	0.692	0.816	1	0.989	1	SUBCLONAL	2	TRUE	1	0.294366085833525	2		626	731	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	199	593	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.885	0.828	0.944	1	0.995	1	CLONAL	3	TRUE	1	0.294366085833525	2		593	509	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	109	399	0	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.294366085833525	2		399	581	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	138	953	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.294366085833525	2		954	681	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057937	27057937	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	75	827	0	ENST00000324856.7:c.1650del	p.Tyr551ThrfsTer68	p.Y551Tfs*68	ENST00000324856	NM_006015.4	549	Ccc/cc	3/20	1	2	FACETS	0.739	0.647	0.837	0.739	0.647	0.837	SUBCLONAL	1	TRUE	1	0.294366085833525	2		827	690	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803863	43803863	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs6087	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	133	593	0	ENST00000372470.3:c.173C>T	p.Ala58Val	p.A58V	ENST00000372470	NM_005373.2	58	gCg/gTg	2/12	1	2	FACETS	0.804	0.733	0.878	1	0.988	1	CLONAL	2	TRUE	1	0.294366085833525	2		593	562	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743579	46743579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144347182	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	48	663	0	ENST00000371975.4:c.1960C>T	p.Arg654Cys	p.R654C	ENST00000371975	NM_003579.3	654	Cgc/Tgc	17/18	1	2	FACETS	0.523	0.442	0.614	0.523	0.442	0.614	SUBCLONAL	1	TRUE	1	0.294366085833525	2		663	623	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149355	119149356	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATG	rs397507494	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	97	593	2	ENST00000264033.4:c.1380_1382dup	p.Asp460dup	p.D460dup	ENST00000264033	NM_005188.3	460	tat/tATGat	9/16	1	2	FACETS	0.999	0.891	1	0.999	0.891	1	CLONAL	1	TRUE	1	0.294366085833525	2		595	660	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230389	46230391	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	102	435	0	ENST00000334344.6:c.727_729del	p.Asp243del	p.D243del	ENST00000334344	NM_152641.2	241	gtTGAt/gtt	7/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.294366085833525	2		435	483	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435484	49435484	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	111	567	0	ENST00000301067.7:c.6188del	p.Lys2063ArgfsTer31	p.K2063Rfs*31	ENST00000301067	NM_003482.3	2063	aAg/ag	30/54	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.294366085833525	2		567	509	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514020	103514020	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	123	566	0	ENST00000355739.4:c.836G>T	p.Arg279Met	p.R279M	ENST00000355739	NM_000123.3	279	aGg/aTg	7/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.294366085833525	2		566	577	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293225	91293225	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs201722470	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	132	595	0	ENST00000355112.3:c.727A>G	p.Ile243Val	p.I243V	ENST00000355112	NM_000057.2	243	Att/Gtt	3/22	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.294366085833525	2		595	642	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354396	354396	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	34	504	0	ENST00000262320.3:c.1162T>G	p.Phe388Val	p.F388V	ENST00000262320	NM_003502.3	388	Ttc/Gtc	5/11	1	2	FACETS	0.414	0.337	0.5	0.414	0.337	0.5	SUBCLONAL	1	TRUE	1	0.294366085833525	2		504	558	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647622	3647622	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1265030199	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	47	744	0	ENST00000294008.3:c.1441C>T	p.Arg481Ter	p.R481*	ENST00000294008	NM_032444.2	481	Cga/Tga	7/15	1	2	FACETS	0.525	0.442	0.617	0.525	0.442	0.617	SUBCLONAL	1	TRUE	1	0.294366085833525	2		744	608	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646735	23646735	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	114	585	0	ENST00000261584.4:c.1132C>G	p.Pro378Ala	p.P378A	ENST00000261584	NM_024675.3	378	Cct/Gct	4/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.294366085833525	2		585	611	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	93	724	3	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.972	0.865	1	0.972	0.865	1	CLONAL	1	TRUE	1	0.294366085833525	2		727	650	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992965	72992965	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	130	675	0	ENST00000268489.5:c.1080del	p.Gly361AspfsTer35	p.G361Dfs*35	ENST00000268489	NM_006885.3	360	ccC/cc	2/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.294366085833525	2		675	625	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979987	7979987	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746723399	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	142	620	2	ENST00000319144.4:c.1350del	p.Leu451SerfsTer16	p.L451Sfs*16	ENST00000319144	NM_001139.2	450	ggG/gg	10/15	1	2	FACETS	0.813	0.744	0.885	1	0.989	1	CLONAL	2	TRUE	1	0.294366085833525	2		622	593	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679713	33679713	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	117	658	0	ENST00000308377.4:c.2368A>G	p.Thr790Ala	p.T790A	ENST00000308377	NM_152270.3	790	Acc/Gcc	5/5	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.294366085833525	2		658	701	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883780	37883780	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	135	804	0	ENST00000269571.5:c.3392T>C	p.Leu1131Pro	p.L1131P	ENST00000269571		1131	cTg/cCg	26/27	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.294366085833525	2		804	659	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40460269	40460269	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	107	549	0	ENST00000345506.4:c.1984del	p.Asp662ThrfsTer2	p.D662Tfs*2	ENST00000345506	NM_003152.3	660	ctG/ct	17/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.294366085833525	2		549	577	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492686	56492686	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	126	484	0	ENST00000407977.2:c.252+1G>A		p.X84_splice	ENST00000407977		84			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.294366085833525	2		484	577	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	124	709	3	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.294366085833525	2		712	672	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533152	63533152	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881399	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	118	583	0	ENST00000307078.5:c.1742G>A	p.Arg581His	p.R581H	ENST00000307078	NM_004655.3	581	cGc/cAc	7/11	1	2	FACETS	0.827	0.75	0.907	1	0.987	1	CLONAL	2	TRUE	1	0.294366085833525	2		583	485	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533939	63533940	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs771001164	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	94	604	0	ENST00000307078.5:c.1214_1215del	p.Glu405GlyfsTer56	p.E405Gfs*56	ENST00000307078	NM_004655.3	405	gAG/g	6/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.294366085833525	2		604	488	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152098	11152098	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1290442223	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	151	741	2	ENST00000358026.2:c.4382G>A	p.Arg1461His	p.R1461H	ENST00000358026	NM_001128849.1	1461	cGc/cAc	31/36	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.294366085833525	2		743	750	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298757	15298757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1354107566	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	116	556	0	ENST00000263388.2:c.1541C>T	p.Thr514Met	p.T514M	ENST00000263388	NM_000435.2	514	aCg/aTg	10/33	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.294366085833525	2		556	604	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656880	47656880	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	77	284	0	ENST00000233146.2:c.1077-1G>A		p.X359_splice	ENST00000233146	NM_000251.2	359			1	2	FACETS	0.754	0.667	0.846	1	0.977	1	SUBCLONAL	2	TRUE	1	0.294366085833525	2		284	347	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714424	40714424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747347462	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	112	581	0	ENST00000373198.4:c.3973G>A	p.Ala1325Thr	p.A1325T	ENST00000373198	NM_133170.3	1325	Gca/Aca	29/32	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.294366085833525	2		581	585	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29445208	29445209	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	113	630	0	ENST00000544604.2:c.1046_1047del	p.Val349GlyfsTer117	p.V349Gfs*117	ENST00000544604	NM_001206998.1	347	GTg/g	8/9	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.294366085833525	2		630	634	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572291	41572291	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs767060302	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	120	616	0	ENST00000263253.7:c.4820A>G	p.Asn1607Ser	p.N1607S	ENST00000263253	NM_001429.3	1607	aAc/aGc	30/31	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.294366085833525	2		616	644	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277972	41277972	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	134	592	0	ENST00000349496.5:c.1936T>C	p.Ser646Pro	p.S646P	ENST00000349496	NM_001904.3	646	Tct/Cct	12/15	1	2	FACETS	0.757	0.69	0.827	1	0.987	1	SUBCLONAL	2	TRUE	1	0.294366085833525	2		592	601	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801507	1801507	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	28	636	0	ENST00000260795.2:c.413A>T	p.Glu138Val	p.E138V	ENST00000260795		138	gAg/gTg	3/17	1	2	FACETS	0.368	0.293	0.454	0.368	0.293	0.454	SUBCLONAL	1	TRUE	1	0.294366085833525	2		636	517	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748321	41748321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	125	538	0	ENST00000226382.2:c.448C>T	p.Arg150Cys	p.R150C	ENST00000226382	NM_003924.3	150	Cgc/Tgc	3/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.294366085833525	2		538	586	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535424	66535424	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	89	559	1	ENST00000273854.3:c.37C>T	p.Arg13Trp	p.R13W	ENST00000273854	NM_004439.5	13	Cgg/Tgg	1/18	1	2	FACETS	0.864	0.773	0.96	1	0.984	1	CLONAL	2	TRUE	1	0.294366085833525	2		560	350	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	150	617	8	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.294366085833525	2		625	754	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323313	31323313	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	51	196	0	ENST00000412585.2:c.676A>G	p.Arg226Gly	p.R226G	ENST00000412585	NM_005514.6	226	Agg/Ggg	4/8	1	2	FACETS	0.984	0.851	1	1	0.976	1	CLONAL	2	TRUE	1	0.294366085833525	2		196	176	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64288917	64288917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755475012	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	108	403	0	ENST00000370651.3:c.313G>A	p.Val105Ile	p.V105I	ENST00000370651	NM_003463.4	105	Gtt/Att	4/6	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.294366085833525	2		403	551	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005515	150005515	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	120	731	2	ENST00000253339.5:c.710del	p.Pro237HisfsTer6	p.P237Hfs*6	ENST00000253339		237	cCa/ca	3/7	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.294366085833525	2		733	710	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129329	152129329	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	97	676	2	ENST00000206249.3:c.287del	p.Gly96ValfsTer13	p.G96Vfs*13	ENST00000206249	NM_000125.3	94	ctG/ct	1/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.294366085833525	2		678	480	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622284	162622284	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	98	477	0	ENST00000366898.1:c.413C>T	p.Ala138Val	p.A138V	ENST00000366898	NM_004562.2	138	gCa/gTa	4/12	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.294366085833525	2		477	541	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240761	55240761	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1231769201	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	155	758	0	ENST00000275493.2:c.2005C>T	p.Arg669Ter	p.R669*	ENST00000275493	NM_005228.3	669	Cga/Tga	17/28	1	2	FACETS	0.842	0.774	0.913	1	0.99	1	CLONAL	2	TRUE	1	0.294366085833525	2		758	625	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380988	116380988	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	50	482	0	ENST00000397752.3:c.1610A>G	p.Gln537Arg	p.Q537R	ENST00000397752	NM_000245.2	537	cAg/cGg	5/21	1	2	FACETS	0.5	0.424	0.585	0.5	0.424	0.585	SUBCLONAL	1	TRUE	1	0.294366085833525	2		482	679	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372093	55372093	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	105	757	2	ENST00000297316.4:c.788del	p.Pro263ArgfsTer124	p.P263Rfs*124	ENST00000297316	NM_022454.3	261	ggC/gg	2/2	0.232167241366332	4	FACETS	0.81	0.728	0.897	0.54	0.485	0.598	CLONAL	2	TRUE	1	0.294366085833525	4		759	570	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965666	90965666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	107	524	0	ENST00000265433.3:c.1651del	p.Arg551GlyfsTer8	p.R551Gfs*8	ENST00000265433	NM_002485.4	551	Agg/gg	11/16	0.232167241366332	4	FACETS	1	0.981	1	0.478	0.429	0.53	CLONAL	1	TRUE	1	0.294366085833525	4		524	656	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524978	8524978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	113	351	0	ENST00000356435.5:c.626C>T	p.Ala209Val	p.A209V	ENST00000356435		209	gCc/gTc	7/35	1	2	FACETS	0.776	0.701	0.853	1	0.985	1	SUBCLONAL	2	TRUE	1	0.294366085833525	2		351	495	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27173286	27173286	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	131	513	0	ENST00000380036.4:c.827C>A	p.Ser276Tyr	p.S276Y	ENST00000380036	NM_000459.3	276	tCt/tAt	6/23	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.294366085833525	2		513	671	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412494	80412494	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	160	526	0	ENST00000286548.4:c.547C>T	p.Arg183Ter	p.R183*	ENST00000286548	NM_002072.3	183	Cga/Tga	4/7	1	2	FACETS	0.762	0.701	0.827	1	0.989	1	SUBCLONAL	2	TRUE	1	0.294366085833525	2		526	713	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913510	39913513	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	ACAA	ACAA	-	novel	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	110	468	0	ENST00000378444.4:c.4815_4818del	p.Cys1606AsnfsTer11	p.C1606Nfs*11	ENST00000378444	NM_001123385.1	1605	gtTTGT/gt	13/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.294366085833525	2		468	570	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228289	53228289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	133	614	0	ENST00000375401.3:c.2113C>T	p.Arg705Cys	p.R705C	ENST00000375401	NM_004187.3	705	Cgc/Tgc	15/26	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.294366085833525	2		614	642	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763971	76763971	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	97	590	1	ENST00000373344.5:c.7337T>C	p.Met2446Thr	p.M2446T	ENST00000373344	NM_000489.3	2446	aTg/aCg	35/35	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.294366085833525	2		591	542	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	92	523	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.804	0.72	0.892	0.804	0.72	0.892	CLONAL	1	TRUE	1	0.616953454772786	2		523	371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0063686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	322	617	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.614901241852159	2	FACETS	0.956	0.915	0.996	0.956	0.915	0.996	CLONAL	2	TRUE	0	0.616953454772786	2		617	546	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717650	89717650	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs1057520900	NA	P-0063686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	180	396	0	ENST00000371953.3:c.675T>G	p.Tyr225Ter	p.Y225*	ENST00000371953	NM_000314.4	225	taT/taG	7/9	0.616953454772786	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.616953454772786	1		396	357	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435230	49435230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774739665	NA	P-0063686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	169	539	0	ENST00000301067.7:c.6323C>T	p.Pro2108Leu	p.P2108L	ENST00000301067	NM_003482.3	2108	cCg/cTg	31/54	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.616953454772786	2		539	531	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023696	27023696	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	40	557	0	ENST00000324856.7:c.802C>G	p.Gln268Glu	p.Q268E	ENST00000324856	NM_006015.4	268	Cag/Gag	1/20	1	2	FACETS	0.26	0.215	0.309	0.26	0.215	0.309	SUBCLONAL	1	TRUE	1	0.616953454772786	2		557	499	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518617	69518617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	138	513	0	ENST00000294312.3:c.28G>A	p.Val10Ile	p.V10I	ENST00000294312	NM_005117.2	10	Gta/Ata	1/3	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.616953454772786	2		513	410	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657044	45657044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768853378	NA	P-0063686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	164	507	0	ENST00000407780.3:c.112G>A	p.Ala38Thr	p.A38T	ENST00000407780	NM_001283052.1	38	Gct/Act	3/7	1	2	FACETS	0.907	0.837	0.98	0.907	0.837	0.98	CLONAL	1	TRUE	1	0.616953454772786	2		507	586	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335718	81335718	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	145	368	0	ENST00000222390.5:c.1642C>T	p.Leu548Phe	p.L548F	ENST00000222390	NM_000601.4	548	Ctt/Ttt	15/18	0.317180886932475	6	FACETS	1	0.981	1	0.421	0.384	0.46	INDETERMINATE	1	TRUE	3	0.616953454772786	6		368	831	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063687-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	119	523	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.77	0.703	0.84	0.77	0.703	0.84	SUBCLONAL	1	TRUE	1	0.853392820694988	2		523	362	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264457	16264457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063687-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	227	513	0	ENST00000375759.3:c.10660C>T	p.Arg3554Trp	p.R3554W	ENST00000375759	NM_015001.2	3554	Cgg/Tgg	13/15	1	2	FACETS	0.973	0.914	1	0.973	0.914	1	CLONAL	1	TRUE	1	0.853392820694988	2		513	547	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0063687-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	205	462	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.853392820694988	2		462	480	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512446	149512446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1291265658	NA	P-0063687-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	270	653	0	ENST00000261799.4:c.994C>T	p.Arg332Trp	p.R332W	ENST00000261799	NM_002609.3	332	Cgg/Tgg	7/23	1	2	FACETS	0.953	0.9	1	0.953	0.9	1	CLONAL	1	TRUE	1	0.853392820694988	2		653	664	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0063696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	68	452	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	0.955	0.831	1	0.955	0.831	1	CLONAL	1	FALSE	1	0.209325379547087	2		452	680	SUCCESS
APC	324	MSKCC	GRCh37	5	112175147	112175147	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	29	539	0	ENST00000257430.4:c.3856G>T	p.Glu1286Ter	p.E1286*	ENST00000257430	NM_000038.5	1286	Gaa/Taa	16/16	0.162286241951387	3	FACETS	1	0.813	1	0.667	0.542	0.805	CLONAL	2	FALSE	0	0.209325379547087	3		539	153	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727975	78727975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148973724	NA	P-0063696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	94	489	0	ENST00000306801.3:c.820G>A	p.Ala274Thr	p.A274T	ENST00000306801	NM_020761.2	274	Gcc/Acc	6/34	0.209325379547087	4	FACETS	1	0.969	1	0.419	0.372	0.469	CLONAL	1	FALSE	1	0.209325379547087	4		489	865	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222212	2222212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375286771	NA	P-0063696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	82	679	1	ENST00000326181.6:c.496G>A	p.Val166Ile	p.V166I	ENST00000326181	NM_032271.2	166	Gtc/Atc	8/21	0.147122614367901	3	FACETS	1	0.912	1	0.522	0.459	0.589	CLONAL	1	FALSE	1	0.209325379547087	3		680	829	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954976	2954976	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772829458	NA	P-0063696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	93	660	1	ENST00000396946.4:c.2734C>T	p.Arg912Trp	p.R912W	ENST00000396946	NM_032415.4	912	Cgg/Tgg	21/25	0.145466036972472	4	FACETS	0.939	0.833	1	0.47	0.416	0.527	CLONAL	1	FALSE	2	0.209325379547087	4		661	1144	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0063697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	381	699	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.714818746449904	2	FACETS	0.991	0.957	1	0.991	0.957	1	CLONAL	2	TRUE	0	0.714818746449904	2		699	538	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037430	12037430	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	159	638	0	ENST00000396373.4:c.1061A>G	p.Tyr354Cys	p.Y354C	ENST00000396373	NM_001987.4	354	tAc/tGc	6/8	0.714818746449904	3	FACETS	0.88	0.809	0.954	0.44	0.404	0.477	CLONAL	1	TRUE	1	0.714818746449904	3		638	686	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346157	89346158	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs878855327	NA	P-0063697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	8	721	0	ENST00000301030.4:c.6792dup	p.Ala2265ArgfsTer8	p.A2265Rfs*8	ENST00000301030	NM_001256183.1	2264	-/C	9/13	0.710499836755738	2	FACETS	0.059	0.037	0.087	0.029	0.018	0.044	SUBCLONAL	1	TRUE	0	0.714818746449904	2		721	380	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554626	29554626	+	splice_donor_variant	Splice_Site	SNP	T	T	G	rs876660826	NA	P-0063697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	192	392	0	ENST00000356175.3:c.2409+2T>G		p.X803_splice	ENST00000356175	NM_000267.3	803			0.712690878467558	2	FACETS	0.959	0.912	1	0.959	0.912	1	CLONAL	2	TRUE	0	0.714818746449904	2		392	280	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723443	52723443	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	190	423	0	ENST00000322088.6:c.1304G>A	p.Gly435Glu	p.G435E	ENST00000322088	NM_014225.5	435	gGa/gAa	11/15	0.714818746449904	3	FACETS	0.935	0.877	0.992	0.935	0.877	0.992	CLONAL	2	TRUE	1	0.714818746449904	3		423	386	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379396	225379396	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs775545593	NA	P-0063697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	73	387	0	ENST00000264414.4:c.472A>G	p.Arg158Gly	p.R158G	ENST00000264414	NM_003590.4	158	Agg/Ggg	4/16	1	2	FACETS	0.904	0.803	1	0.904	0.803	1	CLONAL	1	TRUE	1	0.714818746449904	2		387	226	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178227	56178227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	126	511	0	ENST00000399503.3:c.3200C>T	p.Pro1067Leu	p.P1067L	ENST00000399503	NM_005921.1	1067	cCa/cTa	14/20	0.714818746449904	2	FACETS	0.847	0.774	0.923	0.424	0.387	0.462	CLONAL	1	TRUE	0	0.714818746449904	2		511	416	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64286829	64286829	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	175	349	0	ENST00000370651.3:c.44A>G	p.Lys15Arg	p.K15R	ENST00000370651	NM_003463.4	15	aAg/aGg	2/6	0.61907080613724	4	FACETS	0.935	0.87	1	0.935	0.87	1	CLONAL	2	TRUE	2	0.714818746449904	4		349	449	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370969	55370969	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	117	525	0	ENST00000297316.4:c.271C>T	p.Pro91Ser	p.P91S	ENST00000297316	NM_022454.3	91	Cca/Tca	1/2	0.714818746449904	4	FACETS	1	0.906	1	0.334	0.302	0.367	CLONAL	1	TRUE	1	0.714818746449904	4		525	561	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371967	55371967	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	137	653	0	ENST00000297316.4:c.657G>T	p.Leu219Phe	p.L219F	ENST00000297316	NM_022454.3	219	ttG/ttT	2/2	0.714818746449904	4	FACETS	1	0.951	1	0.354	0.323	0.387	CLONAL	1	TRUE	1	0.714818746449904	4		653	619	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500814	8500814	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	165	527	0	ENST00000356435.5:c.2068C>A	p.His690Asn	p.H690N	ENST00000356435		690	Cat/Aat	13/35	0.714818746449904	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.714818746449904	1		527	291	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813059	76813059	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	195	231	0	ENST00000373344.5:c.6562C>T	p.Arg2188Ter	p.R2188*	ENST00000373344	NM_000489.3	2188	Cga/Tga	30/35	0.590882136736355	2	FACETS	1	0.99	1			1	CLONAL	2	TRUE	NA	0.714818746449904	2		231	246	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505122	149505122	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	220	538	0	ENST00000261799.4:c.1693del	p.Arg565AspfsTer4	p.R565Dfs*4	ENST00000261799	NM_002609.3	565	Cga/ga	12/23	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		538	680	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0063700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	172	213	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.502560482548323	10	FACETS	1	0.924	1	0.429	0.396	0.463	CLONAL	3	TRUE	3	0.502560482548323	10		213	686	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0063700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	271	728	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.502560482548323	5	FACETS	0.936	0.89	0.982	0.936	0.89	0.982	CLONAL	4	TRUE	1	0.502560482548323	5		728	505	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424930	47424930	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	90	647	0	ENST00000404338.3:c.2998A>G	p.Thr1000Ala	p.T1000A	ENST00000404338	NM_004491.4	1000	Aca/Gca	1/6	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.502560482548323	2		647	333	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0063701-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	28	331	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.931	0.748	1	0.931	0.748	1	CLONAL	1	TRUE	1	0.253758772759775	2		331	237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063701-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	44	486	0	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.253758772759775	2		486	300	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835781	68835781	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060501215	NA	P-0063701-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	37	446	1	ENST00000261769.5:c.377del	p.Pro126ArgfsTer89	p.P126Rfs*89	ENST00000261769	NM_004360.3	124	cgC/cg	3/16	1	2	FACETS	0.938	0.776	1	0.938	0.776	1	CLONAL	1	TRUE	1	0.253758772759775	2		447	311	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937355	32937355	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507952	NA	P-0063701-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	31	345	1	ENST00000380152.3:c.8021del	p.Lys2674ArgfsTer2	p.K2674Rfs*2	ENST00000380152		2672	atA/at	18/27	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.253758772759775	2		346	210	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999005	100999005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs766777673	NA	P-0063701-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	32	511	0	ENST00000325455.5:c.797C>A	p.Ala266Asp	p.A266D	ENST00000325455	NM_001202474.3	266	gCc/gAc	1/8	1	2	FACETS	0.717	0.582	0.868	0.717	0.582	0.868	SUBCLONAL	1	TRUE	1	0.253758772759775	2		511	352	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0063702-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	97	393	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.539135025422582	3	FACETS	1	0.981	1	0.695	0.629	0.763	CLONAL	1	TRUE	1	0.703707009612193	3		394	268	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247367	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747241612	NA	P-0063702-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	266	453	0	ENST00000281708.4:c.1435C>G	p.Arg479Gly	p.R479G	ENST00000281708	NM_033632.3	479	Cga/Gga	10/12	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.703707009612193	2		453	752	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323241	31323241	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063702-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	341	550	0	ENST00000412585.2:c.748C>T	p.Gln250Ter	p.Q250*	ENST00000412585	NM_005514.6	250	Cag/Tag	4/8	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.703707009612193	2		550	874	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637254	47637254	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060501989	NA	P-0063702-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	259	433	0	ENST00000233146.2:c.388C>T	p.Gln130Ter	p.Q130*	ENST00000233146	NM_000251.2	130	Cag/Tag	3/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.703707009612193	2		433	730	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317052	11317052	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063702-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	317	582	0	ENST00000361445.4:c.442G>C	p.Glu148Gln	p.E148Q	ENST00000361445	NM_004958.3	148	Gag/Cag	4/58	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.703707009612193	2		582	897	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743262	162743262	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063702-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	225	434	0	ENST00000367921.3:c.1732C>A	p.His578Asn	p.H578N	ENST00000367921	NM_006182.2	578	Cat/Aat	14/18	1	2	FACETS	0.978	0.916	1	0.978	0.916	1	CLONAL	1	TRUE	1	0.703707009612193	2		434	654	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799683	3799683	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063702-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	123	241	0	ENST00000262367.5:c.3781A>T	p.Thr1261Ser	p.T1261S	ENST00000262367	NM_004380.2	1261	Aca/Tca	21/31	0.703707009612193	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.703707009612193	1		241	202	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50143318	50143318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764597042	NA	P-0063702-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	236	530	0	ENST00000246792.3:c.38G>A	p.Arg13Gln	p.R13Q	ENST00000246792	NM_006270.3	13	cGg/cAg	1/6	0.703707009612193	3	FACETS	1	0.947	1	0.507	0.474	0.541	CLONAL	1	TRUE	1	0.703707009612193	3		530	894	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125413	47125413	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063702-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	274	603	0	ENST00000409792.3:c.5857G>C	p.Glu1953Gln	p.E1953Q	ENST00000409792	NM_014159.6	1953	Gaa/Caa	12/21	0.703707009612193	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.703707009612193	1		603	477	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443604	52443604	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063702-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	342	624	0	ENST00000460680.1:c.88G>T	p.Glu30Ter	p.E30*	ENST00000460680	NM_004656.3	30	Gag/Tag	3/17	0.703707009612193	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.703707009612193	1		624	598	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981450	63981450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063702-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	354	727	0	ENST00000398590.3:c.1952C>T	p.Ser651Leu	p.S651L	ENST00000398590	NM_001177387.1	651	tCa/tTa	12/14	0.703707009612193	1	FACETS	0.981	0.938	1	0.981	0.938	1	CLONAL	1	TRUE	0	0.703707009612193	1		727	665	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324616	31324616	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063702-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	333	771	0	ENST00000412585.2:c.192del	p.Ala65ArgfsTer12	p.A65Rfs*12	ENST00000412585	NM_005514.6	64	gcC/gc	2/8	1	2	FACETS	0.945	0.896	0.996	0.945	0.896	0.996	CLONAL	1	TRUE	1	0.703707009612193	2		771	1001	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACAACCCCC	rs397517115	NA	P-0063703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	30	665	0	ENST00000275493.2:c.2311_2319dup	p.Asn771_His773dup	p.N771_H773dup	ENST00000275493	NM_005228.3	771	gac/gACAACCCCCac	20/28	1	2	FACETS	0.87	0.701	1	0.87	0.701	1	CLONAL	1	TRUE	1	0.18	2		665	383	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	47	758	0	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	0.116731008586153	0	FACETS	1	0.906	1			1	CLONAL	1	TRUE	0	0.18	0		758	389	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	12	460	0	ENST00000347630.2:c.305T>C	p.Phe102Ser	p.F102S	ENST00000347630	NM_001007230.1	102	tTc/tCc	5/11	1	2	FACETS	0.281	0.196	0.386	0.281	0.196	0.386	SUBCLONAL	1	TRUE	1	0.18	2		460	475	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109918	115109918	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	40	667	0	ENST00000257566.3:c.1960A>G	p.Ser654Gly	p.S654G	ENST00000257566	NM_016569.3	654	Agt/Ggt	8/8	0.116731008586153	0	FACETS	0.834	0.693	0.99			1	CLONAL	1	TRUE	0	0.18	0		667	437	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445541	49445541	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	40	790	0	ENST00000301067.7:c.1925C>A	p.Ser642Ter	p.S642*	ENST00000301067	NM_003482.3	642	tCa/tAa	10/54	1	2	FACETS	0.985	0.819	1	0.985	0.819	1	CLONAL	1	TRUE	1	0.18	2		790	451	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69229639	69229639	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	44	436	0	ENST00000462284.1:c.715G>C	p.Gly239Arg	p.G239R	ENST00000462284	NM_002392.5	239	Ggt/Cgt	9/11	1	2	FACETS	0.978	0.82	1	0.978	0.82	1	CLONAL	1	TRUE	1	0.18	2		436	500	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811598	102811598	+	stop_lost	Nonstop_Mutation	SNP	A	A	C	rs202145836	NA	P-0063703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	29	496	0	ENST00000307046.8:c.586T>G	p.Ter196GlyextTer12	p.*196Gext*12	ENST00000307046	NM_001111285.1	196	Tga/Gga	4/4	1	2	FACETS	0.673	0.539	0.825	0.673	0.539	0.825	SUBCLONAL	1	TRUE	1	0.18	2		496	479	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636064	73636065	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0063703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	40	477	0	ENST00000377687.4:c.332dup	p.Tyr112ValfsTer2	p.Y112Vfs*2	ENST00000377687	NM_001730.3	109	-/A	2/4	0.116731008586153	3	FACETS	0.862	0.715	1	0.431	0.357	0.513	CLONAL	1	TRUE	1	0.18	3		477	562	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046249	128046249	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	39	552	0	ENST00000285398.2:c.1014T>G	p.Ile338Met	p.I338M	ENST00000285398	NM_000122.1	338	atT/atG	7/15	1	2	FACETS	0.93	0.771	1	0.93	0.771	1	CLONAL	1	TRUE	1	0.18	2		552	466	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652126	36652142	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGAGGCCGGGATGAG	GGCGAGGCCGGGATGAG	-	novel	NA	P-0063703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	46	664	0	ENST00000244741.5:c.248_264del	p.Arg83LeufsTer40	p.R83Lfs*40	ENST00000244741	NM_000389.4	83	cGGCGAGGCCGGGATGAG/c	2/3	1	2	FACETS	0.985	0.829	1	0.985	0.829	1	CLONAL	1	TRUE	1	0.18	2		664	519	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55272952	55272956	+	frameshift_variant	Frame_Shift_Del	DEL	ACATA	ACATA	-	novel	NA	P-0063703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	25	489	0	ENST00000275493.2:c.3276_3280del	p.Tyr1092Ter	p.Y1092*	ENST00000275493	NM_005228.3	1092	tACATA/t	28/28	0.19412321348928	0	FACETS	0.564	0.444	0.702			1	SUBCLONAL	1	TRUE	0	0.18	0		489	404	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371789	116371789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	44	377	0	ENST00000397752.3:c.1268C>T	p.Ala423Val	p.A423V	ENST00000397752	NM_000245.2	423	gCt/gTt	3/21	0.116731008586153	3	FACETS	1	0.919	1	0.579	0.486	0.682	CLONAL	1	TRUE	1	0.18	3		377	460	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172288	38172288	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	26	484	0	ENST00000317025.8:c.2119T>C	p.Cys707Arg	p.C707R	ENST00000317025	NM_023034.1	707	Tgt/Cgt	12/24	1	2	FACETS	0.621	0.491	0.771	0.621	0.491	0.771	SUBCLONAL	1	TRUE	1	0.18	2		484	465	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205166	38205166	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	22	409	0	ENST00000317025.8:c.524A>C	p.Asp175Ala	p.D175A	ENST00000317025	NM_023034.1	175	gAc/gCc	2/24	1	2	FACETS	0.593	0.459	0.75	0.593	0.459	0.75	SUBCLONAL	1	TRUE	1	0.18	2		409	412	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0063704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	163	473	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.410402382406941	6	FACETS	1	0.98	1	0.598	0.551	0.646	CLONAL	2	TRUE	2	0.410402382406941	6		473	605	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514495	NA	P-0063704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	42	688	0	ENST00000269305.4:c.542G>A	p.Arg181His	p.R181H	ENST00000269305	NM_001126112.2	181	cGc/cAc	5/11	0.286947956445531	3	FACETS	0.437	0.364	0.518			1	SUBCLONAL	1	TRUE	NA	0.410402382406941	3		688	565	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607565	43607565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1206969193	NA	P-0063704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	48	1015	0	ENST00000355710.3:c.1541G>A	p.Gly514Asp	p.G514D	ENST00000355710	NM_020975.4	514	gGc/gAc	8/20	0.272319823818369	4	FACETS	0.439	0.37	0.516	0.22	0.185	0.258	SUBCLONAL	1	TRUE	2	0.410402382406941	4		1015	751	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988508	41988508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	27	577	1	ENST00000219905.7:c.1300G>A	p.Asp434Asn	p.D434N	ENST00000219905	NM_001164273.1	434	Gac/Aac	3/24	1	2	FACETS	0.389	0.31	0.48	0.389	0.31	0.48	SUBCLONAL	1	TRUE	1	0.410402382406941	2		578	338	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437597	56437597	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	24	543	0	ENST00000407977.2:c.865del	p.Ser289ProfsTer130	p.S289Pfs*130	ENST00000407977		289	Tcc/cc	8/10	1	2	FACETS	0.274	0.214	0.343	0.274	0.214	0.343	SUBCLONAL	1	TRUE	1	0.410402382406941	2		543	427	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438277	56438278	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCA	novel	NA	P-0063704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	23	525	0	ENST00000407977.2:c.712_715dup	p.Ala239ValfsTer21	p.A239Vfs*21	ENST00000407977		239	gcc/gTGGGcc	7/10	1	2	FACETS	0.254	0.197	0.319	0.254	0.197	0.319	SUBCLONAL	1	TRUE	1	0.410402382406941	2		525	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0063707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	130	341	0	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.705435859305666	1	FACETS	0.943	0.875	1	0.943	0.875	1	CLONAL	1	TRUE	0	0.705435859305666	1		341	253	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537115	41537115	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853039	NA	P-0063707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	170	373	0	ENST00000263253.7:c.1942C>T	p.Arg648Ter	p.R648*	ENST00000263253	NM_001429.3	648	Cga/Tga	10/31	0.705435859305666	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.705435859305666	1		373	302	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046758	180046758	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	159	509	0	ENST00000261937.6:c.2554G>C	p.Gly852Arg	p.G852R	ENST00000261937	NM_182925.4	852	Ggc/Cgc	18/30	0.686975956554092	2	FACETS	1	0.943	1	0.511	0.473	0.55	CLONAL	1	TRUE	0	0.705435859305666	2		509	441	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556878	29556934	+	inframe_deletion	In_Frame_Del	DEL	AATTTGTAGAACAAACCATAGCTATAATGAAGAACTTGCTAGATAATCATACTGAAG	AATTTGTAGAACAAACCATAGCTATAATGAAGAACTTGCTAGATAATCATACTGAAG	-	novel	NA	P-0063707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	57	176	0	ENST00000356175.3:c.2876_2932del	p.Gln959_Gly978delinsArg	p.Q959_G978delinsR	ENST00000356175	NM_000267.3	959	cAATTTGTAGAACAAACCATAGCTATAATGAAGAACTTGCTAGATAATCATACTGAAGgc/cgc	22/57	0.705435859305666	1	FACETS	0.798	0.705	0.893	0.798	0.705	0.893	SUBCLONAL	1	TRUE	0	0.705435859305666	1		176	131	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042029	14042029	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063708-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	156	462	0	ENST00000311895.7:c.2576A>T	p.Asn859Ile	p.N859I	ENST00000311895	NM_005236.2	859	aAt/aTt	11/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.42229696632116	2		462	613	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813612	50813612	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	755	301	0	ENST00000398568.2:c.1166C>G	p.Ser389Cys	p.S389C	ENST00000398568	NM_001042412.1	389	tCt/tGt	8/18	0.577161665030124	8	FACETS	0.967	0.94	0.993			1	CLONAL	6	TRUE	NA	0.577161665030124	8		301	1232	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	114	523	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.914	0.836	0.994	0.914	0.836	0.994	CLONAL	1	TRUE	1	0.865921677782453	2		523	288	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0063710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	224	449	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.865921677782453	2		449	478	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401034	139401034	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	42	531	0	ENST00000277541.6:c.3959del	p.Gly1320AlafsTer125	p.G1320Afs*125	ENST00000277541	NM_017617.3	1320	gGc/gc	24/34	1	2	FACETS	0.175	0.146	0.208	0.175	0.146	0.208	SUBCLONAL	1	TRUE	1	0.865921677782453	2		531	553	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106658	27106658	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	17	623	0	ENST00000324856.7:c.6269A>G	p.His2090Arg	p.H2090R	ENST00000324856	NM_006015.4	2090	cAc/cGc	20/20	0.865921677782453	1	FACETS	0.072	0.053	0.094	0.072	0.053	0.094	SUBCLONAL	1	TRUE	0	0.865921677782453	1		623	311	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517415	157517415	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554234412	NA	P-0063710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	46	364	0	ENST00000346085.5:c.3979C>T	p.Gln1327Ter	p.Q1327*	ENST00000346085	NM_020732.3	1327	Cag/Tag	16/20	1	2	FACETS	0.291	0.246	0.341	0.291	0.246	0.341	SUBCLONAL	1	TRUE	1	0.865921677782453	2		364	365	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511302	157511302	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	84	504	0	ENST00000346085.5:c.3822del	p.Tyr1275MetfsTer11	p.Y1275Mfs*11	ENST00000346085	NM_020732.3	1274	Ccc/cc	15/20	1	2	FACETS	0.386	0.341	0.433	0.386	0.341	0.433	SUBCLONAL	1	TRUE	1	0.865921677782453	2		504	503	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412360	139412360	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587777736	NA	P-0063710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	36	599	0	ENST00000277541.6:c.1285T>C	p.Cys429Arg	p.C429R	ENST00000277541	NM_017617.3	429	Tgc/Cgc	8/34	1	2	FACETS	0.143	0.117	0.173	0.143	0.117	0.173	SUBCLONAL	1	TRUE	1	0.865921677782453	2		599	580	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413126	139413126	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	45	528	0	ENST00000277541.6:c.1016G>A	p.Cys339Tyr	p.C339Y	ENST00000277541	NM_017617.3	339	tGt/tAt	6/34	1	2	FACETS	0.18	0.151	0.213	0.18	0.151	0.213	SUBCLONAL	1	TRUE	1	0.865921677782453	2		528	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0063711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	83	850	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.234066380948961	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	0	0.234066380948961	1		852	525	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0063711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	92	454	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.157219079648542	3	FACETS	0.851	0.758	0.949	0.851	0.758	0.949	CLONAL	2	FALSE	1	0.234066380948961	3		454	516	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226568802	226568802	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	35	419	0	ENST00000366794.5:c.1267del	p.Ala423ProfsTer17	p.A423Pfs*17	ENST00000366794	NM_001618.3	423	Gcc/cc	9/23	1	2	FACETS	0.652	0.534	0.784	0.652	0.534	0.784	SUBCLONAL	1	FALSE	1	0.234066380948961	2		419	459	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982593	10982654	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACAGCCGTGAGTACGGGGCCCCGGGGCAGGCGCAGGGCCGGGGCTGCTCACGAGGCCGGCCC	ACAGCCGTGAGTACGGGGCCCCGGGGCAGGCGCAGGGCCGGGGCTGCTCACGAGGCCGGCCC	-	novel	NA	P-0063711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	47	586	0	ENST00000327064.4:c.215_220+56del		p.X72_splice	ENST00000327064	NM_199141.1	72		1/16	1	2	FACETS	0.786	0.663	0.921	0.786	0.663	0.921	CLONAL	1	FALSE	1	0.234066380948961	2		586	511	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584761	187584761	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	22	397	0	ENST00000441802.2:c.3272T>C	p.Ile1091Thr	p.I1091T	ENST00000441802	NM_005245.3	1091	aTa/aCa	3/27	1	2	FACETS	0.49	0.379	0.619	0.49	0.379	0.619	SUBCLONAL	1	FALSE	1	0.234066380948961	2		397	384	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335613	81335613	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	31	399	0	ENST00000222390.5:c.1747A>G	p.Lys583Glu	p.K583E	ENST00000222390	NM_000601.4	583	Aag/Gag	15/18	0.157219079648542	3	FACETS	0.759	0.614	0.923	0.379	0.307	0.462	CLONAL	1	FALSE	1	0.234066380948961	3		399	390	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0063712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	69	331	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.952	0.834	1	0.952	0.834	1	CLONAL	1	TRUE	1	0.407135240666426	2		331	356	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101099	27101099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	92	616	0	ENST00000324856.7:c.4381C>T	p.Arg1461Ter	p.R1461*	ENST00000324856	NM_006015.4	1461	Cga/Tga	18/20	1	2	FACETS	0.962	0.858	1	0.962	0.858	1	CLONAL	1	TRUE	1	0.407135240666426	2		616	470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578525	7578525	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519976	NA	P-0063712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	113	597	0	ENST00000269305.4:c.405C>G	p.Cys135Trp	p.C135W	ENST00000269305	NM_001126112.2	135	tgC/tgG	5/11	0.407135240666426	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.407135240666426	1		597	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0063713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	87	514	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.196631325741099	2	FACETS	0.82	0.729	0.917	0.82	0.729	0.917	CLONAL	2	TRUE	0	0.221022657674681	2		514	480	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255631	16255631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	81	513	0	ENST00000375759.3:c.2896C>T	p.Pro966Ser	p.P966S	ENST00000375759	NM_015001.2	966	Cct/Tct	11/15	0.210914589396219	3	FACETS	0.841	0.743	0.945	0.841	0.743	0.945	CLONAL	2	TRUE	1	0.221022657674681	3		513	484	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128657	64128657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	33	402	0	ENST00000334205.4:c.514G>A	p.Glu172Lys	p.E172K	ENST00000334205	NM_003942.2	172	Gag/Aag	5/17	1	2	FACETS	0.713	0.58	0.862	0.713	0.58	0.862	SUBCLONAL	1	TRUE	1	0.221022657674681	2		402	419	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627766	187627766	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	60	445	0	ENST00000441802.2:c.3216del	p.Ile1073LeufsTer12	p.I1073Lfs*12	ENST00000441802	NM_005245.3	1072	tcC/tc	2/27	0.206345850139309	3	FACETS	0.824	0.713	0.943	0.549	0.475	0.629	CLONAL	2	TRUE	0	0.221022657674681	3		445	366	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120257	94120257	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	27	465	1	ENST00000369303.4:c.794G>T	p.Cys265Phe	p.C265F	ENST00000369303	NM_004440.3	265	tGc/tTc	3/17	0.221022657674681	3	FACETS	0.643	0.511	0.794	0.321	0.255	0.397	SUBCLONAL	1	TRUE	1	0.221022657674681	3		466	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0063714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	72	547	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.265291659980005	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.26	1		548	430	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105616	11105616	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	44	575	0	ENST00000358026.2:c.1532C>G	p.Thr511Arg	p.T511R	ENST00000358026	NM_001128849.1	511	aCg/aGg	9/36	1	2	FACETS	0.522	0.437	0.617	0.522	0.437	0.617	SUBCLONAL	1	TRUE	1	0.26	2		575	648	SUCCESS
APC	324	MSKCC	GRCh37	5	112111429	112111429	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	24	228	0	ENST00000257430.4:c.526G>T	p.Glu176Ter	p.E176*	ENST00000257430	NM_000038.5	176	Gaa/Taa	5/16	1	2	FACETS	0.863	0.68	1	0.863	0.68	1	CLONAL	1	TRUE	1	0.26	2		228	214	SUCCESS
APC	324	MSKCC	GRCh37	5	112175387	112175397	+	frameshift_variant	Frame_Shift_Del	DEL	GCTCAGACACC	GCTCAGACACC	-	novel	NA	P-0063714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	74	516	0	ENST00000257430.4:c.4096_4106del	p.Ala1366GlnfsTer5	p.A1366Qfs*5	ENST00000257430	NM_000038.5	1366	GCTCAGACACCc/c	16/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.26	2		516	473	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	33	210	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.826	0.678	0.99	0.826	0.678	0.99	CLONAL	1	TRUE	1	0.380346514041065	2		210	210	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	32	622	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.284	0.229	0.345	0.284	0.229	0.345	SUBCLONAL	1	TRUE	1	0.380346514041065	2		626	593	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	33	565	4	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	0.380309902952945	2	FACETS	0.283	0.23	0.344	0.142	0.115	0.172	SUBCLONAL	1	TRUE	0	0.380346514041065	2		569	613	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	64	517	2	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	0.380309902952945	2	FACETS	0.591	0.512	0.677	0.296	0.256	0.339	SUBCLONAL	1	TRUE	0	0.380346514041065	2		519	569	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	40	425	3	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.449	0.373	0.534	0.449	0.373	0.534	SUBCLONAL	1	TRUE	1	0.380346514041065	2		428	468	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190321	32190321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1033015617	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	44	454	0	ENST00000375023.3:c.418C>T	p.Arg140Cys	p.R140C	ENST00000375023	NM_004557.3	140	Cgc/Tgc	3/30	1	2	FACETS	0.644	0.542	0.757	0.644	0.542	0.757	SUBCLONAL	1	TRUE	1	0.380346514041065	2		454	359	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165213	47165213	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	53	343	0	ENST00000409792.3:c.913del	p.Thr305GlnfsTer35	p.T305Qfs*35	ENST00000409792	NM_014159.6	305	Aca/ca	3/21	1	2	FACETS	0.693	0.593	0.803	0.693	0.593	0.803	SUBCLONAL	1	TRUE	1	0.380346514041065	2		343	402	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	186	347	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.380309902952945	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.380346514041065	2		347	469	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715450	117715450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	19	369	0	ENST00000368508.3:c.1039G>A	p.Ala347Thr	p.A347T	ENST00000368508	NM_002944.2	347	Gcg/Acg	10/43	1	2	FACETS	0.362	0.275	0.464	0.362	0.275	0.464	SUBCLONAL	1	TRUE	1	0.380346514041065	2		369	276	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692901	89692901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786204929	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	34	285	0	ENST00000371953.3:c.385G>A	p.Gly129Arg	p.G129R	ENST00000371953	NM_000314.4	129	Gga/Aga	5/9	1	2	FACETS	0.645	0.53	0.775	0.645	0.53	0.775	SUBCLONAL	1	TRUE	1	0.380346514041065	2		285	277	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720711	89720712	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	17	79	0	ENST00000371953.3:c.867dup	p.Val290SerfsTer8	p.V290Sfs*8	ENST00000371953	NM_000314.4	288	gaa/gAaa	8/9	1	2	FACETS	0.868	0.657	1	0.868	0.657	1	CLONAL	1	TRUE	1	0.380346514041065	2		79	103	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467464	66467464	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773032839	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	103	489	0	ENST00000273854.3:c.805G>A	p.Asp269Asn	p.D269N	ENST00000273854	NM_004439.5	269	Gat/Aat	3/18	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.380346514041065	2		489	536	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466027	69466035	+	inframe_deletion	In_Frame_Del	DEL	GACGTGCGG	GACGTGCGG	-	novel	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	95	545	0	ENST00000227507.2:c.871_879del	p.Arg291_Val293del	p.R291_V293del	ENST00000227507	NM_053056.2	289	GACGTGCGG/-	5/5	1	2	FACETS	0.927	0.828	1	0.927	0.828	1	CLONAL	1	TRUE	1	0.380346514041065	2		545	539	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626865	14626865	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	82	456	0	ENST00000254322.2:c.910del	p.Leu304SerfsTer17	p.L304Sfs*17	ENST00000254322	NM_006145.1	304	Ctc/tc	3/3	1	2	FACETS	0.741	0.654	0.834	0.741	0.654	0.834	SUBCLONAL	1	TRUE	1	0.380346514041065	2		456	582	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50815196	50815196	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	77	363	0	ENST00000398568.2:c.1549G>T	p.Gly517Cys	p.G517C	ENST00000398568	NM_001042412.1	517	Ggc/Tgc	9/18	1	2	FACETS	0.826	0.727	0.932	0.826	0.727	0.932	CLONAL	1	TRUE	1	0.380346514041065	2		363	490	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645904	67645904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266478000	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	86	395	0	ENST00000264010.4:c.832C>T	p.Arg278Cys	p.R278C	ENST00000264010	NM_006565.3	278	Cgt/Tgt	4/12	1	2	FACETS	0.875	0.776	0.98	0.875	0.776	0.98	CLONAL	1	TRUE	1	0.380346514041065	2		395	517	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681835	30681835	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs748098912	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	100	466	0	ENST00000376406.3:c.262A>G	p.Ile88Val	p.I88V	ENST00000376406	NM_014641.2	88	Atc/Gtc	3/15	1	2	FACETS	0.918	0.822	1	0.918	0.822	1	CLONAL	1	TRUE	1	0.380346514041065	2		466	573	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536260	41536260	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	60	318	0	ENST00000263253.7:c.1877G>A	p.Arg626Gln	p.R626Q	ENST00000263253	NM_001429.3	626	cGa/cAa	9/31	1	2	FACETS	0.789	0.682	0.904	0.789	0.682	0.904	CLONAL	1	TRUE	1	0.380346514041065	2		318	400	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219050	36219050	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1459799356	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	81	491	0	ENST00000222270.7:c.4549C>T	p.Arg1517Ter	p.R1517*	ENST00000222270	NM_014727.1	1517	Cga/Tga	19/37	1	2	FACETS	0.81	0.715	0.911	0.81	0.715	0.911	CLONAL	1	TRUE	1	0.380346514041065	2		491	526	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056345	27056345	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	119	437	0	ENST00000324856.7:c.1341T>A	p.Tyr447Ter	p.Y447*	ENST00000324856	NM_006015.4	447	taT/taA	2/20	0.380309902952945	2	FACETS	1	0.972	1	0.596	0.54	0.654	CLONAL	1	TRUE	0	0.380346514041065	2		437	525	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598279	28598279	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	27	533	0	ENST00000253063.3:c.251G>A	p.Gly84Asp	p.G84D	ENST00000253063	NM_031459.4	84	gGc/gAc	3/10	0.380309902952945	2	FACETS	0.276	0.219	0.341	0.138	0.109	0.171	SUBCLONAL	1	TRUE	0	0.380346514041065	2		533	515	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925494	114925494	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1193915978	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	62	472	0	ENST00000543371.1:c.1576del	p.Leu526TrpfsTer6	p.L526Wfs*6	ENST00000543371	NM_001198531.1	524	gaC/ga	14/14	1	2	FACETS	0.746	0.646	0.854	0.746	0.646	0.854	SUBCLONAL	1	TRUE	1	0.380346514041065	2		472	437	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434698	99434698	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	52	541	0	ENST00000268035.6:c.785C>A	p.Pro262His	p.P262H	ENST00000268035	NM_000875.3	262	cCt/cAt	3/21	1	2	FACETS	0.516	0.439	0.6	0.516	0.439	0.6	SUBCLONAL	1	TRUE	1	0.380346514041065	2		541	530	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662354	67662354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	112	520	0	ENST00000264010.4:c.1600C>T	p.Gln534Ter	p.Q534*	ENST00000264010	NM_006565.3	534	Cag/Tag	9/12	1	2	FACETS	0.944	0.851	1	0.944	0.851	1	CLONAL	1	TRUE	1	0.380346514041065	2		520	624	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829753	72829754	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	45	401	0	ENST00000268489.5:c.6827_6828del	p.Ser2276Ter	p.S2276*	ENST00000268489	NM_006885.3	2276	tCT/t	9/10	1	2	FACETS	0.524	0.44	0.615	0.524	0.44	0.615	SUBCLONAL	1	TRUE	1	0.380346514041065	2		401	452	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560113	29560113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370820478	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	56	464	0	ENST00000356175.3:c.3590C>T	p.Ala1197Val	p.A1197V	ENST00000356175	NM_000267.3	1197	gCa/gTa	27/57	1	2	FACETS	0.534	0.458	0.618	0.534	0.458	0.618	SUBCLONAL	1	TRUE	1	0.380346514041065	2		464	551	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858839	78858839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146011201	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	77	545	0	ENST00000306801.3:c.1874C>T	p.Thr625Met	p.T625M	ENST00000306801	NM_020761.2	625	aCg/aTg	17/34	1	2	FACETS	0.813	0.716	0.917	0.813	0.716	0.917	CLONAL	1	TRUE	1	0.380346514041065	2		545	498	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291778	15291778	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	94	521	0	ENST00000263388.2:c.2988G>T	p.Gln996His	p.Q996H	ENST00000263388	NM_000435.2	996	caG/caT	18/33	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.380346514041065	2		521	486	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229070	36229070	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	63	577	0	ENST00000222270.7:c.7850G>T	p.Arg2617Leu	p.R2617L	ENST00000222270	NM_014727.1	2617	cGg/cTg	36/37	1	2	FACETS	0.544	0.47	0.624	0.544	0.47	0.624	SUBCLONAL	1	TRUE	1	0.380346514041065	2		577	609	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794136	242794136	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	68	323	0	ENST00000334409.5:c.593-1G>T		p.X198_splice	ENST00000334409	NM_005018.2	198			1	2	FACETS	0.977	0.855	1	0.977	0.855	1	CLONAL	1	TRUE	1	0.380346514041065	2		323	366	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385018	31385042	+	frameshift_variant	Frame_Shift_Del	DEL	TGTATGATGACGATGGCTATCAGTC	TGTATGATGACGATGGCTATCAGTC	-	novel	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	45	406	0	ENST00000328111.2:c.1404_1428del	p.Met468IlefsTer114	p.M468Ifs*114	ENST00000328111	NM_006892.3	468	aTGTATGATGACGATGGCTATCAGTCt/at	14/23	1	2	FACETS	0.539	0.453	0.634	0.539	0.453	0.634	SUBCLONAL	1	TRUE	1	0.380346514041065	2		406	439	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980811	40980811	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	55	463	0	ENST00000373198.4:c.1675G>T	p.Gly559Trp	p.G559W	ENST00000373198	NM_133170.3	559	Ggg/Tgg	10/32	0.323442525321594	1	FACETS	0.462	0.395	0.535	0.462	0.395	0.535	SUBCLONAL	1	TRUE	0	0.380346514041065	1		463	507	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317438	1317438	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	81	362	0	ENST00000400841.2:c.627G>A	p.Trp209Ter	p.W209*	ENST00000400841		209	tgG/tgA	5/6	1	2	FACETS	0.972	0.861	1	0.972	0.861	1	CLONAL	1	TRUE	1	0.380346514041065	2		362	438	SUCCESS
AR	367	MSKCC	GRCh37	X	66937443	66937443	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	53	374	0	ENST00000374690.3:c.2297C>T	p.Ala766Val	p.A766V	ENST00000374690	NM_000044.3	766	gCc/gTc	5/8	1	2	FACETS	0.592	0.505	0.686	0.592	0.505	0.686	SUBCLONAL	1	TRUE	1	0.380346514041065	2		374	471	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118905	70118906	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0063717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	53	494	0	ENST00000245479.2:c.478dup	p.Arg160ProfsTer92	p.R160Pfs*92	ENST00000245479	NM_000346.3	159	-/C	2/3	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.16	2		494	641	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427734	49427734	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	40	488	0	ENST00000301067.7:c.10754del	p.Gln3585ArgfsTer73	p.Q3585Rfs*73	ENST00000301067	NM_003482.3	3585	cAg/cg	39/54	0.3	2	FACETS	0.975	0.809	1			1	CLONAL	1	TRUE	NA	0.16	2		488	513	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120362	70120363	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0063717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	33	431	0	ENST00000245479.2:c.1365_1366dup	p.Ala456GlyfsTer15	p.A456Gfs*15	ENST00000245479	NM_000346.3	455	gcg/gcGGg	3/3	1	2	FACETS	0.79	0.643	0.957	0.79	0.643	0.957	CLONAL	1	TRUE	1	0.16	2		431	522	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087525	27087536	+	frameshift_variant	Frame_Shift_Del	DEL	TTGGCTCTCCCG	TTGGCTCTCCCG	C	novel	NA	P-0063717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	45	474	0	ENST00000324856.7:c.2099_2110delinsC	p.Val700AlafsTer113	p.V700Afs*113	ENST00000324856	NM_006015.4	700	gTTGGCTCTCCCGcc/gCcc	5/20	1	2	FACETS	0.886	0.743	1	0.886	0.743	1	CLONAL	1	TRUE	1	0.16	2		474	635	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	174	768	0	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	0.52379565508533	3	FACETS	0.933	0.869	0.998	0.933	0.869	0.998	CLONAL	2	TRUE	1	0.565434961319614	3		768	423	SUCCESS
APC	324	MSKCC	GRCh37	5	112175419	112175419	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0063718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	221	742	0	ENST00000257430.4:c.4128T>A	p.Tyr1376Ter	p.Y1376*	ENST00000257430	NM_000038.5	1376	taT/taA	16/16	0.52379565508533	3	FACETS	0.973	0.915	1	0.973	0.915	1	CLONAL	2	TRUE	1	0.565434961319614	3		742	515	SUCCESS
APC	324	MSKCC	GRCh37	5	112175350	112175351	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	112	779	0	ENST00000257430.4:c.4063dup	p.Ser1355PhefsTer20	p.S1355Ffs*20	ENST00000257430	NM_000038.5	1353	-/T	16/16	0.52379565508533	3	FACETS	0.962	0.869	1	0.481	0.434	0.53	CLONAL	1	TRUE	1	0.565434961319614	3		779	528	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609849	117609849	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	66	753	0	ENST00000368508.3:c.6850G>A	p.Gly2284Ser	p.G2284S	ENST00000368508	NM_002944.2	2284	Ggt/Agt	43/43	0.532078939975615	4	FACETS	0.8	0.696	0.911	0.267	0.232	0.304	CLONAL	1	TRUE	1	0.565434961319614	4		753	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576857	7576858	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGGT	novel	NA	P-0063718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	215	976	0	ENST00000269305.4:c.985_988dup	p.Leu330HisfsTer8	p.L330Hfs*8	ENST00000269305	NM_001126112.2	330	ctt/cACCCtt	9/11	0.549233015434122	2	FACETS	0.89	0.84	0.941	0.89	0.84	0.941	CLONAL	2	TRUE	0	0.565434961319614	2		976	427	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874563	151874563	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	154	835	0	ENST00000262189.6:c.7975G>T	p.Glu2659Ter	p.E2659*	ENST00000262189	NM_170606.2	2659	Gaa/Taa	38/59	0.510581479268805	4	FACETS	0.921	0.85	0.994	0.921	0.85	0.994	CLONAL	2	TRUE	2	0.565434961319614	4		835	463	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254906	16254906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	182	892	1	ENST00000375759.3:c.2171G>A	p.Arg724Gln	p.R724Q	ENST00000375759	NM_015001.2	724	cGa/cAa	11/15	1	2	FACETS	0.788	0.728	0.85	0.788	0.728	0.85	SUBCLONAL	1	TRUE	1	0.565309445194777	2		893	817	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437548	110437548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	149	884	0	ENST00000375856.3:c.853G>A	p.Glu285Lys	p.E285K	ENST00000375856	NM_003749.2	285	Gag/Aag	1/2	0.211164934771801	3	FACETS	0.806	0.737	0.878	0.403	0.368	0.439	INDETERMINATE	1	TRUE	1	0.565309445194777	3		884	839	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856640	111856640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs899111445	NA	P-0063719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	119	751	0	ENST00000341259.2:c.691G>A	p.Asp231Asn	p.D231N	ENST00000341259	NM_005475.2	231	Gat/Aat	2/8	0.565309445194777	3	FACETS	0.742	0.67	0.817	0.371	0.335	0.409	SUBCLONAL	1	TRUE	1	0.565309445194777	3		751	728	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797313	135797313	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	174	807	0	ENST00000298552.3:c.556del	p.Ala186HisfsTer24	p.A186Hfs*24	ENST00000298552	NM_001162426.1	186	Gca/ca	7/23	0.565309445194777	1	FACETS	0.84	0.779	0.902	0.84	0.779	0.902	CLONAL	1	TRUE	0	0.565309445194777	1		807	526	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795073	242795073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1429395114	NA	P-0063719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	161	971	0	ENST00000334409.5:c.136G>A	p.Glu46Lys	p.E46K	ENST00000334409	NM_005018.2	46	Gaa/Aaa	2/5	0.243997249986079	1	FACETS	0.62	0.57	0.671	0.62	0.57	0.671	INDETERMINATE	1	TRUE	0	0.565309445194777	1		971	659	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857917	89857917	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	67	865	0	ENST00000389301.3:c.1253C>T	p.Ala418Val	p.A418V	ENST00000389301	NM_000135.2	418	gCa/gTa	14/43	0.14208473880895	3	FACETS	0.342	0.296	0.392	0.171	0.148	0.196	INDETERMINATE	1	TRUE	1	0.565309445194777	3		865	889	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17940958	17940958	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	90	871	0	ENST00000458235.1:c.3166G>A	p.Glu1056Lys	p.E1056K	ENST00000458235	NM_000215.3	1056	Gag/Aag	23/24	1	2	FACETS	0.57	0.506	0.637	0.57	0.506	0.637	SUBCLONAL	1	TRUE	1	0.565309445194777	2		871	559	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939856	49939856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781591594	NA	P-0063719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	170	884	0	ENST00000296474.3:c.1187G>A	p.Arg396Gln	p.R396Q	ENST00000296474	NM_002447.2	396	cGa/cAa	1/20	0.319448953073524	3	FACETS	0.988	0.91	1	0.494	0.455	0.535	INDETERMINATE	1	TRUE	1	0.565309445194777	3		884	781	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215276	123215276	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0063719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	103	195	0	ENST00000218089.9:c.2822C>G	p.Ser941Ter	p.S941*	ENST00000218089	NM_001042749.1	941	tCa/tGa	28/35	0.331526968516905	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.565309445194777	2		195	282	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120467995	120467995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	197	928	0	ENST00000256646.2:c.4444G>A	p.Glu1482Lys	p.E1482K	ENST00000256646	NM_024408.3	1482	Gag/Aag	25/34	1	2	FACETS	0.788	0.731	0.848	0.788	0.731	0.848	SUBCLONAL	1	TRUE	1	0.565309445194777	2		928	884	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490353	56490353	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	149	736	0	ENST00000267101.3:c.2122G>C	p.Glu708Gln	p.E708Q	ENST00000267101	NM_001982.3	708	Gag/Cag	18/28	0.565309445194777	3	FACETS	0.751	0.686	0.82	0.376	0.343	0.41	SUBCLONAL	1	TRUE	1	0.565309445194777	3		736	900	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981146	201981146	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	217	781	0	ENST00000359651.3:c.225G>A	p.Trp75Ter	p.W75*	ENST00000359651		75	tgG/tgA	2/8	1	2	FACETS	0.909	0.846	0.973	0.909	0.846	0.973	CLONAL	1	TRUE	1	0.565309445194777	2		781	845	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254800	16254800	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	190	774	0	ENST00000375759.3:c.2065G>A	p.Glu689Lys	p.E689K	ENST00000375759	NM_015001.2	689	Gaa/Aaa	11/15	1	2	FACETS	0.881	0.816	0.948	0.881	0.816	0.948	CLONAL	1	TRUE	1	0.565309445194777	2		774	763	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255100	16255100	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	195	966	0	ENST00000375759.3:c.2365G>A	p.Glu789Lys	p.E789K	ENST00000375759	NM_015001.2	789	Gaa/Aaa	11/15	1	2	FACETS	0.84	0.779	0.904	0.84	0.779	0.904	CLONAL	1	TRUE	1	0.565309445194777	2		966	821	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983145	201983145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	179	850	0	ENST00000359651.3:c.994G>A	p.Ala332Thr	p.A332T	ENST00000359651		332	Gcc/Acc	7/8	1	2	FACETS	0.75	0.692	0.811	0.75	0.692	0.811	SUBCLONAL	1	TRUE	1	0.565309445194777	2		850	844	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231488761	231488761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	120	641	0	ENST00000295050.7:c.1124C>A	p.Ser375Tyr	p.S375Y	ENST00000295050	NM_032018.5	375	tCt/tAt	5/5	1	2	FACETS	0.669	0.605	0.735	0.669	0.605	0.735	SUBCLONAL	1	TRUE	1	0.565309445194777	2		641	635	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114799795	114799795	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	71	479	0	ENST00000543371.1:c.462G>A	p.Met154Ile	p.M154I	ENST00000543371	NM_001198531.1	154	atG/atA	5/14	1	2	FACETS	0.494	0.432	0.561	0.494	0.432	0.561	SUBCLONAL	1	TRUE	1	0.565309445194777	2		479	508	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77991656	77991656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	171	737	0	ENST00000361507.4:c.367G>A	p.Glu123Lys	p.E123K	ENST00000361507	NM_080491.2	123	Gag/Aag	2/10	1	2	FACETS	0.779	0.717	0.842	0.779	0.717	0.842	SUBCLONAL	1	TRUE	1	0.565309445194777	2		737	777	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196160	108196160	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	136	614	0	ENST00000278616.4:c.6696G>C	p.Glu2232Asp	p.E2232D	ENST00000278616	NM_000051.3	2232	gaG/gaC	46/63	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.565309445194777	2		614	458	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490628	56490628	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	176	759	0	ENST00000267101.3:c.2272G>A	p.Asp758Asn	p.D758N	ENST00000267101	NM_001982.3	758	Gat/Aat	19/28	0.565309445194777	3	FACETS	0.873	0.804	0.944	0.436	0.402	0.472	CLONAL	1	TRUE	1	0.565309445194777	3		759	915	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143029	58143029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	355	967	0	ENST00000257904.6:c.755G>A	p.Arg252Lys	p.R252K	ENST00000257904	NM_000075.3	252	aGa/aAa	7/8	0.565309445194777	3	FACETS	1	0.995	1	0.722	0.684	0.76	CLONAL	1	TRUE	1	0.565309445194777	3		967	1116	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911073	32911073	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs773356478	NA	P-0063719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	117	595	0	ENST00000380152.3:c.2581C>T	p.Gln861Ter	p.Q861*	ENST00000380152		861	Caa/Taa	11/27	0.337193750808843	2	FACETS	0.963	0.875	1	0.481	0.437	0.527	INDETERMINATE	1	TRUE	0	0.565309445194777	2		595	430	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43730524	43730524	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	141	669	0	ENST00000382044.4:c.3189C>G	p.Ile1063Met	p.I1063M	ENST00000382044	NM_001141980.1	1063	atC/atG	16/28	1	2	FACETS	0.799	0.731	0.871	0.799	0.731	0.871	SUBCLONAL	1	TRUE	1	0.565309445194777	2		669	624	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50789307	50789307	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1233994254	NA	P-0063719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	140	609	0	ENST00000307179.4:c.2917A>G	p.Lys973Glu	p.K973E	ENST00000307179		973	Aaa/Gaa	18/20	1	2	FACETS	0.824	0.753	0.898	0.824	0.753	0.898	CLONAL	1	TRUE	1	0.565309445194777	2		609	601	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99452016	99452016	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	201	896	0	ENST00000268035.6:c.1350C>G	p.Phe450Leu	p.F450L	ENST00000268035	NM_000875.3	450	ttC/ttG	6/21	1	2	FACETS	0.827	0.767	0.888	0.827	0.767	0.888	CLONAL	1	TRUE	1	0.565309445194777	2		896	860	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085620	16085620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	147	714	0	ENST00000281043.3:c.796G>A	p.Glu266Lys	p.E266K	ENST00000281043	NM_005378.4	266	Gaa/Aaa	3/3	1	2	FACETS	0.839	0.769	0.912	0.839	0.769	0.912	CLONAL	1	TRUE	1	0.565309445194777	2		714	620	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420070	41420070	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	119	755	0	ENST00000373198.4:c.251C>G	p.Ser84Cys	p.S84C	ENST00000373198	NM_133170.3	84	tCt/tGt	3/32	0.324514923446356	5	FACETS	0.926	0.836	1	0.309	0.278	0.341	INDETERMINATE	1	TRUE	2	0.565309445194777	5		755	840	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147489	47147489	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	267	1233	0	ENST00000409792.3:c.4837G>T	p.Glu1613Ter	p.E1613*	ENST00000409792	NM_014159.6	1613	Gag/Tag	6/21	0.319448953073524	3	FACETS	1	0.951	1	0.509	0.476	0.542	INDETERMINATE	1	TRUE	1	0.565309445194777	3		1233	1191	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919302	178919302	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	78	431	0	ENST00000263967.3:c.787G>C	p.Glu263Gln	p.E263Q	ENST00000263967	NM_006218.2	263	Gaa/Caa	4/21	0.565309445194777	3	FACETS	0.611	0.538	0.69	0.306	0.269	0.345	SUBCLONAL	1	TRUE	1	0.565309445194777	3		431	579	SUCCESS
ALB	213	MSKCC	GRCh37	4	74282058	74282058	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	21	489	0	ENST00000295897.4:c.1277A>T	p.Lys426Ile	p.K426I	ENST00000295897	NM_000477.5	426	aAa/aTa	10/15	1	2	FACETS	0.186	0.143	0.237	0.186	0.143	0.237	SUBCLONAL	1	TRUE	1	0.565309445194777	2		489	399	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38960514	38960514	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	136	680	0	ENST00000357387.3:c.1837C>G	p.Leu613Val	p.L613V	ENST00000357387	NM_152756.3	613	Ctt/Gtt	20/38	1	2	FACETS	0.688	0.627	0.753	0.688	0.627	0.753	SUBCLONAL	1	TRUE	1	0.565309445194777	2		680	699	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982049	38982049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	128	687	0	ENST00000357387.3:c.673G>A	p.Glu225Lys	p.E225K	ENST00000357387	NM_152756.3	225	Gag/Aag	8/38	1	2	FACETS	0.757	0.688	0.829	0.757	0.688	0.829	SUBCLONAL	1	TRUE	1	0.565309445194777	2		687	598	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651859	36651873	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	GTATCTCTGCTGCAG	GTATCTCTGCTGCAG	-	novel	NA	P-0063719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	404	800	0	ENST00000244741.5:c.-5-14_-5del		p.X2_splice	ENST00000244741	NM_000389.4	2			NA	2	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.565309445194777	2		800	579	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696430	47696430	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063721-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	193	741	0	ENST00000347630.2:c.393G>C	p.Trp131Cys	p.W131C	ENST00000347630	NM_001007230.1	131	tgG/tgC	6/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.708806459720213	2		741	518	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705396	43705396	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063721-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	236	977	0	ENST00000382044.4:c.5226del	p.Met1743TrpfsTer67	p.M1743Wfs*67	ENST00000382044	NM_001141980.1	1742	acC/ac	24/28	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.708806459720213	2		977	657	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0063722-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	141	516	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.705495556626727	1	FACETS	0.955	0.889	1	0.955	0.889	1	CLONAL	1	TRUE	0	0.705495556626727	1		516	271	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439387	149439387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1392968737	NA	P-0063722-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	302	791	1	ENST00000286301.3:c.2008G>A	p.Asp670Asn	p.D670N	ENST00000286301	NM_005211.3	670	Gac/Aac	15/22	1	2	FACETS	0.963	0.91	1	0.963	0.91	1	CLONAL	1	TRUE	1	0.705495556626727	2		792	889	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888165	112888165	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507510	NA	P-0063722-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	163	691	0	ENST00000351677.2:c.181G>A	p.Asp61Asn	p.D61N	ENST00000351677	NM_002834.3	61	Gat/Aat	3/16	1	2	FACETS	0.913	0.844	0.984	0.913	0.844	0.984	CLONAL	1	TRUE	1	0.705495556626727	2		691	506	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550536	29550536	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1131691130	NA	P-0063722-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	104	528	0	ENST00000356175.3:c.1796G>A	p.Trp599Ter	p.W599*	ENST00000356175	NM_000267.3	599	tGg/tAg	16/57	1	2	FACETS	0.973	0.883	1	0.973	0.883	1	CLONAL	1	TRUE	1	0.705495556626727	2		528	303	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652976	29652979	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	rs1085307459	NA	P-0063722-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	242	805	0	ENST00000356175.3:c.4914_4917del	p.Lys1640GlyfsTer36	p.K1640Gfs*36	ENST00000356175	NM_000267.3	1637	ttTCTC/tt	36/57	1	2	FACETS	0.999	0.938	1	0.999	0.938	1	CLONAL	1	TRUE	1	0.705495556626727	2		805	687	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835878	151835879	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	novel	NA	P-0063722-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	202	647	0	ENST00000262189.6:c.14643+2dup		p.X4881_splice	ENST00000262189	NM_170606.2	4881			0.705495556626727	3	FACETS	1	0.96	1	0.523	0.486	0.561	CLONAL	1	TRUE	1	0.705495556626727	3		647	741	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295192	1295192	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0063722-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	57	690	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.305	0.261	0.352	0.305	0.261	0.352	SUBCLONAL	1	TRUE	1	0.705495556626727	2		690	530	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295192	1295192	+	upstream_gene_variant	5'Flank	INS	C	C	AGCGGAAAGGAAGGGGA	novel	NA	P-0063722-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	80	788	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.395	0.348	0.445	0.395	0.348	0.445	SUBCLONAL	1	TRUE	1	0.705495556626727	2		788	574	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	148	523	0				ENST00000310581	NM_198253.2	-/1132			0.664483271364912	3	FACETS	0.794	0.727	0.865	0.397	0.363	0.433	SUBCLONAL	1	TRUE	1	0.664483271364912	3		523	747	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941653	48941653	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0063723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	169	338	0	ENST00000267163.4:c.963C>G	p.Tyr321Ter	p.Y321*	ENST00000267163	NM_000321.2	321	taC/taG	10/27	0.647730468420565	2	FACETS	0.886	0.834	0.938	0.886	0.834	0.938	CLONAL	2	TRUE	0	0.664483271364912	2		338	287	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0063723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	292	998	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.661563938268157	3	FACETS	1	0.98	1	0.545	0.512	0.578	CLONAL	1	TRUE	1	0.664483271364912	3		998	1075	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs879253911	NA	P-0063723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	573	1127	0	ENST00000269305.4:c.538G>T	p.Glu180Ter	p.E180*	ENST00000269305	NM_001126112.2	180	Gag/Tag	5/11	0.661563938268157	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.664483271364912	3		1127	1106	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566478	41566478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	434	760	0	ENST00000263253.7:c.4355C>T	p.Pro1452Leu	p.P1452L	ENST00000263253	NM_001429.3	1452	cCt/cTt	27/31	0.649475287729822	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.664483271364912	2		760	623	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949801	151949801	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0063723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	328	607	1	ENST00000262189.6:c.1300-1G>C		p.X434_splice	ENST00000262189	NM_170606.2	434			0.661563938268157	3	FACETS	0.938	0.893	0.983	0.938	0.893	0.983	CLONAL	2	TRUE	1	0.664483271364912	3		608	701	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022258	26022258	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	182	777	0	ENST00000435504.4:c.399G>C	p.Arg133Ser	p.R133S	ENST00000435504		133	agG/agC	5/13	0.661563938268157	3	FACETS	0.835	0.771	0.902	0.418	0.385	0.451	CLONAL	1	TRUE	1	0.664483271364912	3		777	874	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307520	118307520	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0063723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	442	877	0	ENST00000534358.1:c.293C>G	p.Ser98Ter	p.S98*	ENST00000534358	NM_005933.3	98	tCa/tGa	1/36	0.664483271364912	3	FACETS	0.981	0.942	1	0.981	0.942	1	CLONAL	2	TRUE	1	0.664483271364912	3		877	903	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376124	118376124	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	241	1079	0	ENST00000534358.1:c.9517C>T	p.Gln3173Ter	p.Q3173*	ENST00000534358	NM_005933.3	3173	Caa/Taa	27/36	0.664483271364912	3	FACETS	0.887	0.828	0.947	0.443	0.414	0.474	CLONAL	1	TRUE	1	0.664483271364912	3		1079	1090	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73649963	73649963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	502	834	1	ENST00000377687.4:c.1313G>A	p.Cys438Tyr	p.C438Y	ENST00000377687	NM_001730.3	438	tGc/tAc	4/4	0.664483271364912	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.664483271364912	3		835	990	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953157	81953157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	231	855	0	ENST00000359376.3:c.2123C>T	p.Ala708Val	p.A708V	ENST00000359376	NM_002661.3	708	gCc/gTc	20/33	0.664483271364912	3	FACETS	0.994	0.928	1	0.497	0.464	0.531	CLONAL	1	TRUE	1	0.664483271364912	3		855	932	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649060	37649060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	217	710	1	ENST00000447079.4:c.2165G>A	p.Arg722His	p.R722H	ENST00000447079	NM_015083.1	722	cGc/cAc	4/14	0.478593293746856	4	FACETS	1	0.948	1	0.512	0.475	0.549	CLONAL	1	TRUE	2	0.664483271364912	4		711	1062	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022273	26022273	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	221	831	0	ENST00000435504.4:c.384G>C	p.Lys128Asn	p.K128N	ENST00000435504		128	aaG/aaC	5/13	0.661563938268157	3	FACETS	0.904	0.842	0.969	0.452	0.421	0.485	CLONAL	1	TRUE	1	0.664483271364912	3		831	980	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022330	26022330	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	249	807	0	ENST00000435504.4:c.327G>C	p.Gln109His	p.Q109H	ENST00000435504		109	caG/caC	5/13	0.661563938268157	3	FACETS	0.971	0.909	1	0.486	0.454	0.518	CLONAL	1	TRUE	1	0.664483271364912	3		807	1028	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022359	26022359	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	246	763	0	ENST00000435504.4:c.298G>A	p.Glu100Lys	p.E100K	ENST00000435504		100	Gaa/Aaa	5/13	0.661563938268157	3	FACETS	1	0.943	1	0.504	0.472	0.538	CLONAL	1	TRUE	1	0.664483271364912	3		763	978	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566550	41566550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	418	648	0	ENST00000263253.7:c.4427C>T	p.Ser1476Leu	p.S1476L	ENST00000263253	NM_001429.3	1476	tCa/tTa	27/31	0.649475287729822	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.664483271364912	2		648	625	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434135	12434135	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	206	731	0	ENST00000287820.6:c.503G>C	p.Arg168Thr	p.R168T	ENST00000287820	NM_015869.4	168	aGa/aCa	4/7	1	2	FACETS	0.975	0.909	1	0.975	0.909	1	CLONAL	1	TRUE	1	0.664483271364912	2		731	636	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753136	57753136	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063723-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	278	907	0	ENST00000274289.3:c.880del	p.Glu294LysfsTer17	p.E294Kfs*17	ENST00000274289	NM_006622.3	294	Gaa/aa	7/14	0.664483271364912	3	FACETS	0.959	0.9	1	0.479	0.45	0.51	CLONAL	1	TRUE	1	0.664483271364912	3		907	1163	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063723-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	122	523	0				ENST00000310581	NM_198253.2	-/1132			0.90896983591571	3	FACETS	0.755	0.686	0.828	0.378	0.343	0.414	SUBCLONAL	1	TRUE	1	0.90896983591571	3		523	517	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941653	48941653	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0063723-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	136	338	0	ENST00000267163.4:c.963C>G	p.Tyr321Ter	p.Y321*	ENST00000267163	NM_000321.2	321	taC/taG	10/27	0.90896983591571	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.90896983591571	2		338	147	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0063723-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	363	998	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.862654896353127	6	FACETS	0.994	0.943	1	0.497	0.471	0.523	CLONAL	2	TRUE	2	0.90896983591571	6		998	1132	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs879253911	NA	P-0063723-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	647	1127	0	ENST00000269305.4:c.538G>T	p.Glu180Ter	p.E180*	ENST00000269305	NM_001126112.2	180	Gag/Tag	5/11	0.862654896353127	6	FACETS	1	0.992	1	1	0.992	1	CLONAL	4	TRUE	2	0.90896983591571	6		1127	957	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566478	41566478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063723-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	476	760	0	ENST00000263253.7:c.4355C>T	p.Pro1452Leu	p.P1452L	ENST00000263253	NM_001429.3	1452	cCt/cTt	27/31	0.90896983591571	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.90896983591571	2		760	502	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949801	151949801	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0063723-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	264	607	1	ENST00000262189.6:c.1300-1G>C		p.X434_splice	ENST00000262189	NM_170606.2	434			0.615508157782575	4	FACETS	0.872	0.832	0.911	0.872	0.832	0.911	CLONAL	3	TRUE	1	0.90896983591571	4		608	424	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022258	26022258	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063723-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	187	777	0	ENST00000435504.4:c.399G>C	p.Arg133Ser	p.R133S	ENST00000435504		133	agG/agC	5/13	0.615508157782575	4	FACETS	1	0.988	1	0.434	0.403	0.466	CLONAL	1	TRUE	1	0.90896983591571	4		777	603	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307520	118307520	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0063723-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	449	877	0	ENST00000534358.1:c.293C>G	p.Ser98Ter	p.S98*	ENST00000534358	NM_005933.3	98	tCa/tGa	1/36	0.536395607455371	4	FACETS	0.859	0.828	0.889	0.859	0.828	0.889	INDETERMINATE	3	TRUE	1	0.90896983591571	4		877	732	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376124	118376124	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063723-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	282	1079	0	ENST00000534358.1:c.9517C>T	p.Gln3173Ter	p.Q3173*	ENST00000534358	NM_005933.3	3173	Caa/Taa	27/36	0.536395607455371	4	FACETS	1	0.992	1	0.441	0.415	0.467	INDETERMINATE	1	TRUE	1	0.90896983591571	4		1079	896	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73649963	73649963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063723-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	514	834	1	ENST00000377687.4:c.1313G>A	p.Cys438Tyr	p.C438Y	ENST00000377687	NM_001730.3	438	tGc/tAc	4/4	0.615508157782575	4	FACETS	0.916	0.887	0.944	0.916	0.887	0.944	CLONAL	3	TRUE	1	0.90896983591571	4		835	786	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953157	81953157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063723-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	214	855	0	ENST00000359376.3:c.2123C>T	p.Ala708Val	p.A708V	ENST00000359376	NM_002661.3	708	gCc/gTc	20/33	0.615508157782575	4	FACETS	1	0.988	1	0.427	0.398	0.456	CLONAL	1	TRUE	1	0.90896983591571	4		855	702	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649060	37649060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063723-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	227	710	1	ENST00000447079.4:c.2165G>A	p.Arg722His	p.R722H	ENST00000447079	NM_015083.1	722	cGc/cAc	4/14	0.570014986750895	6	FACETS	1	0.991	1	0.484	0.451	0.518	CLONAL	1	TRUE	3	0.90896983591571	6		711	970	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022273	26022273	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063723-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	214	831	0	ENST00000435504.4:c.384G>C	p.Lys128Asn	p.K128N	ENST00000435504		128	aaG/aaC	5/13	0.615508157782575	4	FACETS	1	0.989	1	0.427	0.399	0.457	CLONAL	1	TRUE	1	0.90896983591571	4		831	701	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022330	26022330	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063723-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	244	807	0	ENST00000435504.4:c.327G>C	p.Gln109His	p.Q109H	ENST00000435504		109	caG/caC	5/13	0.615508157782575	4	FACETS	1	0.99	1	0.432	0.405	0.46	CLONAL	1	TRUE	1	0.90896983591571	4		807	791	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022359	26022359	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063723-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	240	763	0	ENST00000435504.4:c.298G>A	p.Glu100Lys	p.E100K	ENST00000435504		100	Gaa/Aaa	5/13	0.615508157782575	4	FACETS	1	0.991	1	0.457	0.428	0.486	CLONAL	1	TRUE	1	0.90896983591571	4		763	736	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566550	41566550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063723-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	509	648	0	ENST00000263253.7:c.4427C>T	p.Ser1476Leu	p.S1476L	ENST00000263253	NM_001429.3	1476	tCa/tTa	27/31	0.90896983591571	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.90896983591571	2		648	532	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434135	12434135	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063723-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	158	731	0	ENST00000287820.6:c.503G>C	p.Arg168Thr	p.R168T	ENST00000287820	NM_015869.4	168	aGa/aCa	4/7	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.90896983591571	2		731	293	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753136	57753136	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063723-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	212	907	0	ENST00000274289.3:c.880del	p.Glu294LysfsTer17	p.E294Kfs*17	ENST00000274289	NM_006622.3	294	Gaa/aa	7/14	0.90896983591571	3	FACETS	1	0.958	1	0.517	0.483	0.552	CLONAL	1	TRUE	1	0.90896983591571	3		907	656	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0063724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	110	210	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.701971702749594	2		210	284	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0063724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	313	1119	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	0.949	0.897	1	0.949	0.897	1	CLONAL	1	TRUE	1	0.701971702749594	2		1120	940	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891277	101891277	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	540	711	0	ENST00000374994.4:c.238C>T	p.Arg80Ter	p.R80*	ENST00000374994	NM_004612.2	80	Cga/Tga	2/9	0.701971702749594	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.701971702749594	2		711	719	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059183	27059183	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1010301017	NA	P-0063724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	62	582	0	ENST00000324856.7:c.1820C>T	p.Ser607Leu	p.S607L	ENST00000324856	NM_006015.4	607	tCa/tTa	4/20	1	2	FACETS	0.321	0.277	0.368	0.321	0.277	0.368	SUBCLONAL	1	TRUE	1	0.701971702749594	2		582	551	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928839	44928839	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	177	548	0	ENST00000377967.4:c.1939C>T	p.Gln647Ter	p.Q647*	ENST00000377967	NM_021140.2	647	Cag/Tag	17/29	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.701971702749594	2		548	498	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418649	49418649	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0063724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	161	1040	0	ENST00000301067.7:c.15865A>T	p.Lys5289Ter	p.K5289*	ENST00000301067	NM_003482.3	5289	Aag/Tag	49/54	1	2	FACETS	0.527	0.483	0.572	0.527	0.483	0.572	SUBCLONAL	1	TRUE	1	0.701971702749594	2		1040	871	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133862	41133862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	589	872	0	ENST00000379561.5:c.1766G>A	p.Arg589Lys	p.R589K	ENST00000379561	NM_002015.3	589	aGa/aAa	2/3	0.701971702749594	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.701971702749594	3		872	1108	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928878	44928878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748170230	NA	P-0063724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	198	651	1	ENST00000377967.4:c.1978C>T	p.Leu660Phe	p.L660F	ENST00000377967	NM_021140.2	660	Ctc/Ttc	17/29	1	2	FACETS	0.939	0.875	1	0.939	0.875	1	CLONAL	1	TRUE	1	0.701971702749594	2		652	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0063725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	226	547	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.540560909427793	1	FACETS	0.983	0.921	1	0.983	0.921	1	CLONAL	1	TRUE	0	0.540560909427793	1		548	621	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0063725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	77	211	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.540560909427793	1	FACETS	0.686	0.608	0.768	0.686	0.608	0.768	SUBCLONAL	1	TRUE	0	0.540560909427793	1		211	303	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102199	27102199	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0063725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	95	628	0	ENST00000324856.7:c.5124+1G>T		p.X1708_splice	ENST00000324856	NM_006015.4	1708			0.429631156372835	1	FACETS	0.41	0.366	0.458	0.41	0.366	0.458	SUBCLONAL	1	TRUE	0	0.540560909427793	1		628	625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0063725-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	182	547	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.368158064876234	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.368158064876234	1		548	760	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0063725-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	72	211	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.368158064876234	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.368158064876234	1		211	294	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102199	27102199	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0063725-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	146	628	0	ENST00000324856.7:c.5124+1G>T		p.X1708_splice	ENST00000324856	NM_006015.4	1708			1	2	FACETS	0.918	0.838	1	0.918	0.838	1	CLONAL	1	TRUE	1	0.368158064876234	2		628	864	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0063728-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	288	916	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.569157410529316	1	FACETS	0.992	0.939	1	0.992	0.939	1	CLONAL	1	TRUE	0	0.590082702823719	1		916	694	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063731-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	91	523	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.79	0.706	0.878	0.79	0.706	0.878	SUBCLONAL	1	TRUE	1	0.573099420816116	2		523	402	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0063731-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	74	254	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	0.573099420816116	1	FACETS	0.908	0.81	1	0.908	0.81	1	CLONAL	1	TRUE	0	0.573099420816116	1		254	203	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0063731-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	174	363	0	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	0.554183852011944	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.573099420816116	1		363	407	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457640	67457640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs863223759	NA	P-0063731-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	362	449	0	ENST00000327367.4:c.455del	p.Pro152HisfsTer34	p.P152Hfs*34	ENST00000327367	NM_005902.3	150	ttC/tt	3/9	0.571501754148486	2	FACETS	0.961	0.921	1	0.961	0.921	1	CLONAL	2	TRUE	0	0.573099420816116	2		449	657	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933533	39933533	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063731-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	161	465	0	ENST00000378444.4:c.1066G>T	p.Glu356Ter	p.E356*	ENST00000378444	NM_001123385.1	356	Gag/Tag	4/15	1	2	FACETS	0.834	0.767	0.903	0.834	0.767	0.903	CLONAL	1	TRUE	1	0.573099420816116	2		465	674	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628433	86628437	+	frameshift_variant	Frame_Shift_Del	DEL	TTACT	TTACT	-	novel	NA	P-0063731-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	69	263	0	ENST00000274376.6:c.806_810del	p.Leu269ProfsTer11	p.L269Pfs*11	ENST00000274376	NM_002890.2	268	TTACTt/t	3/25	0.496781078037754	1	FACETS	0.924	0.821	1	0.924	0.821	1	CLONAL	1	TRUE	0	0.573099420816116	1		263	186	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867304	68867304	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063731-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	146	398	0	ENST00000261769.5:c.2551T>A	p.Ser851Thr	p.S851T	ENST00000261769	NM_004360.3	851	Tca/Aca	16/16	1	2	FACETS	0.995	0.914	1	0.995	0.914	1	CLONAL	1	TRUE	1	0.573099420816116	2		398	512	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961472	41961472	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063731-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	227	362	0	ENST00000219905.7:c.380T>G	p.Ile127Arg	p.I127R	ENST00000219905	NM_001164273.1	127	aTa/aGa	2/24	0.571501754148486	2	FACETS	0.89	0.841	0.939	0.89	0.841	0.939	CLONAL	2	TRUE	0	0.573099420816116	2		362	445	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670434	88670434	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs970508396	NA	P-0063731-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	222	247	0	ENST00000360948.2:c.1252C>A	p.Pro418Thr	p.P418T	ENST00000360948	NM_001012338.2	418	Cct/Act	11/19	NA	2	FACETS	0.956	0.905	1			1	INDETERMINATE	2	TRUE	NA	0.573099420816116	2		247	405	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678448	88678449	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0063731-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	237	405	0	ENST00000360948.2:c.1087dup	p.Leu363ProfsTer44	p.L363Pfs*44	ENST00000360948	NM_001012338.2	363	ctg/cCtg	9/19	NA	2	FACETS	0.862	0.814	0.909			1	INDETERMINATE	2	TRUE	NA	0.573099420816116	2		405	480	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483049	29483049	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063731-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	87	293	0	ENST00000356175.3:c.109G>T	p.Glu37Ter	p.E37*	ENST00000356175	NM_000267.3	37	Gag/Tag	2/57	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.573099420816116	2		293	291	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490366	29490366	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063731-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	87	303	0	ENST00000356175.3:c.452del	p.Asn151MetfsTer14	p.N151Mfs*14	ENST00000356175	NM_000267.3	151	Aat/at	4/57	1	2	FACETS	0.78	0.696	0.87	0.78	0.696	0.87	SUBCLONAL	1	TRUE	1	0.573099420816116	2		303	389	SUCCESS
ALB	213	MSKCC	GRCh37	4	74285356	74285356	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063731-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	183	250	0	ENST00000295897.4:c.1785G>T	p.Glu595Asp	p.E595D	ENST00000295897	NM_000477.5	595	gaG/gaT	13/15	0.574991814011055	3	FACETS	0.911	0.85	0.973	0.911	0.85	0.973	CLONAL	2	TRUE	1	0.573099420816116	3		250	451	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032526	47032526	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0063731-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	160	372	0	ENST00000377604.3:c.433-1G>T		p.X145_splice	ENST00000377604	NM_001204468.1	145			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.573099420816116	2		372	536	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426499	47426499	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063731-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	203	509	0	ENST00000377045.4:c.842G>T	p.Arg281Leu	p.R281L	ENST00000377045	NM_001654.4	281	cGg/cTg	9/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.573099420816116	2		509	652	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845332	42845332	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	AA	novel	NA	P-0063731-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	186	471	0	ENST00000398585.3:c.930delinsTT	p.His311SerfsTer30	p.H311Sfs*30	ENST00000398585	NM_001135099.1	310	ctG/ctTT	9/14	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.573099420816116	2		471	581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0063741-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	72	374	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	0.22759694744889	1	FACETS	0.931	0.814	1	0.931	0.814	1	CLONAL	1	TRUE	0	0.24	1		374	567	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0063741-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	46	282	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	0.795	0.67	0.934	0.795	0.67	0.934	CLONAL	1	TRUE	1	0.24	2		282	482	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584497	48584497	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063741-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	63	330	0	ENST00000342988.3:c.670C>T	p.Gln224Ter	p.Q224*	ENST00000342988	NM_005359.5	224	Cag/Tag	6/12	0.22759694744889	1	FACETS	0.86	0.745	0.986	0.86	0.745	0.986	CLONAL	1	TRUE	0	0.24	1		330	537	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2164215	2164215	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063741-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	76	374	0	ENST00000398665.3:c.32C>T	p.Ser11Leu	p.S11L	ENST00000398665	NM_032482.2	11	tCg/tTg	1/28	0.22759694744889	1	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	0	0.24	1		374	543	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433617	49433617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063741-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	84	565	0	ENST00000301067.7:c.7936G>A	p.Glu2646Lys	p.E2646K	ENST00000301067	NM_003482.3	2646	Gaa/Aaa	31/54	1	2	FACETS	0.814	0.718	0.917	0.814	0.718	0.917	CLONAL	1	TRUE	1	0.24	2		565	860	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169993035	169993035	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs370513574	NA	P-0063741-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	32	205	0	ENST00000295797.4:c.665C>G	p.Ser222Ter	p.S222*	ENST00000295797	NM_002740.5	222	tCa/tGa	8/18	0.403111997056238	3	FACETS	0.503	0.407	0.612	0.251	0.203	0.306	SUBCLONAL	1	TRUE	1	0.24	3		205	594	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577052	7577052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs672601296	NA	P-0063741-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	111	565	0	ENST00000269305.4:c.886C>T	p.His296Tyr	p.H296Y	ENST00000269305	NM_001126112.2	296	Cac/Tac	8/11	0.22759694744889	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.24	1		565	801	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137026	64137026	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063741-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	85	377	0	ENST00000334205.4:c.1537C>G	p.Leu513Val	p.L513V	ENST00000334205	NM_003942.2	513	Ctc/Gtc	13/17	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.24	2		377	618	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28886147	28886147	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063741-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	40	288	0	ENST00000282397.4:c.3475C>G	p.Gln1159Glu	p.Q1159E	ENST00000282397	NM_002019.4	1159	Caa/Gaa	26/30	1	2	FACETS	0.722	0.6	0.857	0.722	0.6	0.857	SUBCLONAL	1	TRUE	1	0.24	2		288	462	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610019	81610019	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063741-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	81	571	0	ENST00000298171.2:c.1617T>G	p.Cys539Trp	p.C539W	ENST00000298171	NM_000369.2	539	tgT/tgG	10/10	1	2	FACETS	0.788	0.693	0.89	0.788	0.693	0.89	SUBCLONAL	1	TRUE	1	0.24	2		571	857	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762157	43762157	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063741-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	102	386	0	ENST00000382044.4:c.1288G>C	p.Glu430Gln	p.E430Q	ENST00000382044	NM_001141980.1	430	Gag/Cag	11/28	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.24	2		386	715	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762193	43762193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063741-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	99	375	0	ENST00000382044.4:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000382044	NM_001141980.1	418	Gaa/Aaa	11/28	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.24	2		375	709	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163795	32163796	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0063741-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	72	471	0	ENST00000375023.3:c.5430dup	p.Asn1811Ter	p.N1811*	ENST00000375023	NM_004557.3	1810	-/T	30/30	1	2	FACETS	0.957	0.836	1	0.957	0.836	1	CLONAL	1	TRUE	1	0.24	2		471	627	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482862	140482862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063741-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	80	490	0	ENST00000288602.6:c.1273G>A	p.Glu425Lys	p.E425K	ENST00000288602	NM_004333.4	425	Gaa/Aaa	10/18	1	2	FACETS	0.751	0.66	0.849	0.751	0.66	0.849	SUBCLONAL	1	TRUE	1	0.24	2		490	888	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874792	151874793	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0063741-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	67	471	0	ENST00000262189.6:c.7745dup	p.Glu2583ArgfsTer5	p.E2583Rfs*5	ENST00000262189	NM_170606.2	2582	gta/gtTa	38/59	1	2	FACETS	0.749	0.65	0.857	0.749	0.65	0.857	SUBCLONAL	1	TRUE	1	0.24	2		471	745	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342596	87342596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063741-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	50	359	0	ENST00000277120.3:c.881C>T	p.Ser294Phe	p.S294F	ENST00000277120		294	tCt/tTt	9/19	0.22759694744889	1	FACETS	0.702	0.596	0.819	0.702	0.596	0.819	SUBCLONAL	1	TRUE	0	0.24	1		359	522	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0063742-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	581	454	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.534820359382926	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	0	0.534820359382926	3		454	917	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242478	55242478	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913229	NA	P-0063742-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	460	387	0	ENST00000275493.2:c.2248G>C	p.Ala750Pro	p.A750P	ENST00000275493	NM_005228.3	750	Gca/Cca	19/28	0.526853844359225	5	FACETS	0.994	0.953	1	0.994	0.953	1	CLONAL	3	TRUE	2	0.534820359382926	5		387	1040	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242474	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGA	GAATTAAGA	-	rs121913436	NA	P-0063742-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	441	392	0	ENST00000275493.2:c.2239_2247del	p.Leu747_Glu749del	p.L747_E749del	ENST00000275493	NM_005228.3	746	GAATTAAGA/-	19/28	0.526853844359225	5	FACETS	0.942	0.901	0.983	0.942	0.901	0.983	CLONAL	3	TRUE	2	0.534820359382926	5		392	1052	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43749814	43749814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752907384	NA	P-0063742-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1952	241	515	0	ENST00000523873.1:c.667C>T	p.Arg223Cys	p.R223C	ENST00000523873		223	Cgt/Tgt	7/8	0.534820359382926	7	FACETS	0.96	0.893	1			1	CLONAL	1	TRUE	NA	0.534820359382926	7		515	2193	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063743-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	28	523	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		523	476	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519896	NA	P-0063744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	288	536	0	ENST00000281708.4:c.1514G>A	p.Arg505His	p.R505H	ENST00000281708	NM_033632.3	505	cGc/cAc	10/12	0.37240535257527	6	FACETS	1	0.959	1			1	CLONAL	3	TRUE	NA	0.37240535257527	6		536	882	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0063744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	148	577	2	ENST00000257430.4:c.3919dup	p.Ile1307AsnfsTer8	p.I1307Nfs*8	ENST00000257430	NM_000038.5	1306	gaa/gAaa	16/16	0.376631077245109	3	FACETS	0.933	0.858	1	0.933	0.858	1	CLONAL	2	TRUE	1	0.37240535257527	3		579	505	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058536	69058536	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753703	NA	P-0063744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	73	428	0	ENST00000288368.4:c.4180C>T	p.Arg1394Trp	p.R1394W	ENST00000288368	NM_024870.2	1394	Cgg/Tgg	34/40	0.376631077245109	3	FACETS	1	0.965	1	0.637	0.561	0.718	CLONAL	1	TRUE	1	0.37240535257527	3		428	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578175	7578175	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0063744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	295	665	0	ENST00000269305.4:c.672+2T>C		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.255600446199979	5	FACETS	1	0.955	1	0.804	0.764	0.845	CLONAL	4	TRUE	0	0.37240535257527	5		665	614	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521694	89521694	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs150555764	NA	P-0063744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	48	517	0	ENST00000336596.2:c.2771G>A	p.Trp924Ter	p.W924*	ENST00000336596	NM_005233.5	924	tGg/tAg	16/17	0.344367305869222	1	FACETS	0.623	0.528	0.725	0.623	0.528	0.725	SUBCLONAL	1	TRUE	0	0.37240535257527	1		517	337	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119624616	119624616	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	211	474	0	ENST00000316626.5:c.799G>C	p.Val267Leu	p.V267L	ENST00000316626		267	Gta/Cta	7/12	0.376631077245109	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.37240535257527	3		474	556	SUCCESS
APC	324	MSKCC	GRCh37	5	112164571	112164574	+	frameshift_variant	Frame_Shift_Del	DEL	AGGA	AGGA	-	novel	NA	P-0063744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	47	391	0	ENST00000257430.4:c.1646_1649del	p.Arg549IlefsTer8	p.R549Ifs*8	ENST00000257430	NM_000038.5	549	AGGAat/at	14/16	0.376631077245109	3	FACETS	0.784	0.663	0.916	0.392	0.331	0.458	CLONAL	1	TRUE	1	0.37240535257527	3		391	382	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557628	95557628	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063757-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	23	438	0	ENST00000393063.1:c.5439G>T	p.Glu1813Asp	p.E1813D	ENST00000393063	NM_030621.3	1813	gaG/gaT	26/28	0.520286963387115	6	FACETS	0.52	0.406	0.651	0.173	0.135	0.217	INDETERMINATE	1	TRUE	3	0.867972053950304	6		438	279	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577543	7577543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1019340046	NA	P-0063758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	22	403	0	ENST00000269305.4:c.738G>A	p.Met246Ile	p.M246I	ENST00000269305	NM_001126112.2	246	atG/atA	7/11	1	2	FACETS	0.264	0.203	0.335	0.264	0.203	0.335	SUBCLONAL	1	TRUE	1	0.23	2		403	725	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0063759-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	278	681	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.468788518678641	3	FACETS	0.864	0.823	0.904	0.864	0.823	0.904	CLONAL	3	TRUE	0	0.557663587397315	3		682	492	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243869	46243869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1368116171	NA	P-0063759-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	259	424	0	ENST00000334344.6:c.1963G>A	p.Val655Ile	p.V655I	ENST00000334344	NM_152641.2	655	Gtt/Att	15/21	0.376956668860681	6	FACETS	0.959	0.904	1	0.959	0.904	1	CLONAL	3	TRUE	3	0.557663587397315	6		424	683	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058895	42058895	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063759-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	278	377	0	ENST00000219905.7:c.8615G>C	p.Arg2872Thr	p.R2872T	ENST00000219905	NM_001164273.1	2872	aGa/aCa	24/24	0.557663587397315	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.557663587397315	4		377	716	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243892	53243892	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063759-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	209	360	0	ENST00000375401.3:c.1101del	p.Cys368AlafsTer62	p.C368Afs*62	ENST00000375401	NM_004187.3	367	cgG/cg	8/26	0.557663587397315	4	FACETS	0.943	0.881	1	0.943	0.881	1	CLONAL	2	TRUE	2	0.557663587397315	4		360	619	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0063760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	103	210	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.98	0.891	1	0.98	0.891	1	CLONAL	1	TRUE	1	0.787617572813241	2		210	267	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	135	523	0				ENST00000310581	NM_198253.2	-/1132			0.456132533912873	1	FACETS	0.732	0.678	0.786	0.732	0.678	0.786	INDETERMINATE	1	TRUE	0	0.787617572813241	1		523	284	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612028	189612028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs900140738	NA	P-0063760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	205	442	0	ENST00000264731.3:c.1780C>T	p.Arg594Ter	p.R594*	ENST00000264731	NM_003722.4	594	Cga/Tga	14/14	1	2	FACETS	0.893	0.834	0.953	0.893	0.834	0.953	CLONAL	1	TRUE	1	0.787617572813241	2		442	583	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0063760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	267	589	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.787617572813241	2		589	664	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0063760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	202	465	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	0.926	0.865	0.988	0.926	0.865	0.988	CLONAL	1	TRUE	1	0.787617572813241	2		465	554	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0063760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	264	464	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.781833394000585	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.787617572813241	1		464	397	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577599	7577599	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	8	339	0	ENST00000269305.4:c.682G>C	p.Asp228His	p.D228H	ENST00000269305	NM_001126112.2	228	Gac/Cac	7/11	0.781833394000585	1	FACETS	0.036	0.023	0.053	0.036	0.023	0.053	SUBCLONAL	1	TRUE	0	0.787617572813241	1		339	342	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200477	138200477	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	230	393	0	ENST00000237289.4:c.1895G>C	p.Arg632Thr	p.R632T	ENST00000237289	NM_001270507.1	632	aGa/aCa	7/9	0.739204827399217	3	FACETS	0.897	0.837	0.958	0.448	0.418	0.479	CLONAL	1	TRUE	1	0.787617572813241	3		393	908	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057947	27057948	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0063760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	601	553	0	ENST00000324856.7:c.1656dup	p.Gln553ThrfsTer70	p.Q553Tfs*70	ENST00000324856	NM_006015.4	552	tca/tcAa	3/20	0.787617572813241	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.787617572813241	2		553	702	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223707	36223707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1468457510	NA	P-0063760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	362	630	0	ENST00000222270.7:c.6257C>T	p.Ser2086Leu	p.S2086L	ENST00000222270	NM_014727.1	2086	tCg/tTg	28/37	0.396279568798349	3	FACETS	0.835	0.797	0.873	0.835	0.797	0.873	INDETERMINATE	2	TRUE	1	0.787617572813241	3		630	767	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376454	118376454	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	303	443	0	ENST00000534358.1:c.9847C>T	p.Arg3283Ter	p.R3283*	ENST00000534358	NM_005933.3	3283	Cga/Tga	27/36	0.781833394000585	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.787617572813241	1		443	425	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878049	48878049	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0063760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	199	394	0	ENST00000267163.4:c.1A>G	p.Met1?	p.M1?	ENST00000267163	NM_000321.2	1	Atg/Gtg	1/27	0.787617572813241	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.787617572813241	1		394	287	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920702	100920702	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	163	275	0	ENST00000325455.5:c.2446G>C	p.Glu816Gln	p.E816Q	ENST00000325455	NM_001202474.3	816	Gaa/Caa	6/8	0.787617572813241	2	FACETS	0.813	0.752	0.876	0.407	0.376	0.438	CLONAL	1	TRUE	0	0.787617572813241	2		275	509	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203603	108203603	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	138	267	0	ENST00000278616.4:c.7903G>C	p.Ala2635Pro	p.A2635P	ENST00000278616	NM_000051.3	2635	Gcc/Ccc	53/63	0.781833394000585	1	FACETS	0.953	0.892	1	0.953	0.892	1	CLONAL	1	TRUE	0	0.787617572813241	1		267	223	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203623	108203623	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	130	263	0	ENST00000278616.4:c.7923G>C	p.Gln2641His	p.Q2641H	ENST00000278616	NM_000051.3	2641	caG/caC	53/63	0.781833394000585	1	FACETS	0.939	0.878	1	0.939	0.878	1	CLONAL	1	TRUE	0	0.787617572813241	1		263	213	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422458	47422458	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	249	440	0	ENST00000404338.3:c.526G>A	p.Asp176Asn	p.D176N	ENST00000404338	NM_004491.4	176	Gac/Aac	1/6	0.574465705975147	1	FACETS	0.805	0.763	0.847	0.805	0.763	0.847	CLONAL	1	TRUE	0	0.787617572813241	1		440	476	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50143292	50143292	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754976061	NA	P-0063760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	66	370	0	ENST00000246792.3:c.64G>A	p.Gly22Arg	p.G22R	ENST00000246792	NM_006270.3	22	Ggg/Agg	1/6	0.108910573684898	5	FACETS	0.835	0.727	0.951			1	INDETERMINATE	1	TRUE	NA	0.787617572813241	5		370	438	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90949264	90949264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746479577	NA	P-0063760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	110	193	0	ENST00000265433.3:c.2224G>A	p.Asp742Asn	p.D742N	ENST00000265433	NM_002485.4	742	Gat/Aat	15/16	1	2	FACETS	0.947	0.863	1	0.947	0.863	1	CLONAL	1	TRUE	1	0.787617572813241	2		193	295	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0063761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	417	338	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.766754097895037	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.766754097895037	2		338	540	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200024	123200024	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0063761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	146	58	0	ENST00000218089.9:c.2097-1G>A		p.X699_splice	ENST00000218089	NM_001042749.1	699			0.748199442714547	2	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.766754097895037	2		58	161	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678572	88678572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1161765368	NA	P-0063761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	225	350	0	ENST00000360948.2:c.964G>A	p.Glu322Lys	p.E322K	ENST00000360948	NM_001012338.2	322	Gag/Aag	9/19	0.320688998732882	6	FACETS	1	0.973	1	0.536	0.501	0.571	INDETERMINATE	2	TRUE	2	0.766754097895037	6		350	694	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023348	27023348	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	320	321	0	ENST00000324856.7:c.454C>T	p.Gln152Ter	p.Q152*	ENST00000324856	NM_006015.4	152	Caa/Taa	1/20	0.320688998732882	6	FACETS	0.883	0.842	0.923	0.883	0.842	0.923	INDETERMINATE	4	TRUE	2	0.766754097895037	6		321	599	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11273467	11273467	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	95	284	0	ENST00000361445.4:c.3274G>A	p.Val1092Ile	p.V1092I	ENST00000361445	NM_004958.3	1092	Gtc/Atc	21/58	0.766754097895037	4	FACETS	0.671	0.598	0.749	0.224	0.199	0.25	SUBCLONAL	1	TRUE	1	0.766754097895037	4		284	652	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724439	162724439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1280	99	382	0	ENST00000367921.3:c.211G>A	p.Ala71Thr	p.A71T	ENST00000367921	NM_006182.2	71	Gcc/Acc	5/18	0.766754097895037	6	FACETS	0.474	0.422	0.531			1	SUBCLONAL	1	TRUE	NA	0.766754097895037	6		382	1379	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220464	133220464	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	369	324	0	ENST00000320574.5:c.4249G>C	p.Glu1417Gln	p.E1417Q	ENST00000320574	NM_006231.2	1417	Gag/Cag	33/49	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.766754097895037	2		324	469	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569771	95569771	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	391	377	0	ENST00000393063.1:c.3962C>G	p.Ser1321Cys	p.S1321C	ENST00000393063	NM_030621.3	1321	tCc/tGc	22/28	0.766754097895037	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.766754097895037	2		377	472	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437616	110437616	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063762-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	166	510	0	ENST00000375856.3:c.785C>T	p.Ser262Leu	p.S262L	ENST00000375856	NM_003749.2	262	tCg/tTg	1/2	0.249665205612873	1	FACETS	0.928	0.855	1	0.928	0.855	1	CLONAL	1	TRUE	0	0.414193493430298	1		510	685	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400932	72400932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063762-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	93	442	0	ENST00000357731.5:c.239C>T	p.Ala80Val	p.A80V	ENST00000357731	NM_173808.2	80	gCg/gTg	2/7	1	2	FACETS	0.668	0.594	0.747	0.668	0.594	0.747	SUBCLONAL	1	TRUE	1	0.414193493430298	2		442	672	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349223	89349223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063762-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	126	467	0	ENST00000301030.4:c.3727G>A	p.Glu1243Lys	p.E1243K	ENST00000301030	NM_001256183.1	1243	Gaa/Aaa	9/13	1	2	FACETS	0.73	0.66	0.802	0.73	0.66	0.802	SUBCLONAL	1	TRUE	1	0.414193493430298	2		467	834	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4384870	4385337	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGAGCGTCGCGGAGCTGCCGCGGCTGCTGCGCACTTCTCCGACTCCCCGTTTTGGAGCTGTAGTTCACCCCCTTTTATAGGATCCCTGGGAATACCAAAGCACTGATGGGCTATTCTGATTCACTCCAGTTTCCTCATCTTTGTTCTTTATTCTTATCACGCATTCTGGTCCCCTCCCCCTCCCACAAAAAAAAATTAATTTTTTTTGTTTCGATAGATTACGCTTTTTTATTCTTTTTCTCTTTTGCTGATGCTATGCTCTCCACCCCCGCCCCCCAACCCTTTCCCACTCCCATTATAGGTCTGTGAGGAACAGAAGTGCGAAGAAGAGGTCTTCCCTCTGGCCATGAATTACCTGGACCGTTTCTTGGCTGGGGTCCCGACTCCGAAGTCCCATCTGCAACTCCTGGGTGCTGTCTGCATGTTCCTGGCCTCCAAACTCAAAGAGACCAGCCCGCTGACCGCGGA	GGAGCGTCGCGGAGCTGCCGCGGCTGCTGCGCACTTCTCCGACTCCCCGTTTTGGAGCTGTAGTTCACCCCCTTTTATAGGATCCCTGGGAATACCAAAGCACTGATGGGCTATTCTGATTCACTCCAGTTTCCTCATCTTTGTTCTTTATTCTTATCACGCATTCTGGTCCCCTCCCCCTCCCACAAAAAAAAATTAATTTTTTTTGTTTCGATAGATTACGCTTTTTTATTCTTTTTCTCTTTTGCTGATGCTATGCTCTCCACCCCCGCCCCCCAACCCTTTCCCACTCCCATTATAGGTCTGTGAGGAACAGAAGTGCGAAGAAGAGGTCTTCCCTCTGGCCATGAATTACCTGGACCGTTTCTTGGCTGGGGTCCCGACTCCGAAGTCCCATCTGCAACTCCTGGGTGCTGTCTGCATGTTCCTGGCCTCCAAACTCAAAGAGACCAGCCCGCTGACCGCGGA	-	novel	NA	P-0063762-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	74	9	0	ENST00000261254.3:c.196-300_363del		p.X66_splice	ENST00000261254	NM_001759.3	66		2/5	0.350498324486633	2	FACETS		NA	1	1	0.99	1	NA	5	TRUE	0	0.414193493430298	2		9	79	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438495	52438518	+	inframe_deletion	In_Frame_Del	DEL	GTCATCCTCCTCGTCATCCTCATA	GTCATCCTCCTCGTCATCCTCATA	-	rs1429624602	NA	P-0063762-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	227	432	0	ENST00000460680.1:c.1201_1224del	p.Tyr401_Asp408del	p.Y401_D408del	ENST00000460680	NM_004656.3	401	TATGAGGATGACGAGGAGGATGAC/-	12/17	0.350498324486633	2	FACETS	1	0.992	1	0.724	0.677	0.772	CLONAL	1	TRUE	0	0.414193493430298	2		432	757	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982114	93982114	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0063762-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	132	379	0	ENST00000369303.4:c.1351A>T	p.Lys451Ter	p.K451*	ENST00000369303	NM_004440.3	451	Aag/Tag	6/17	0.338636614848977	1	FACETS	0.873	0.795	0.954	0.873	0.795	0.954	CLONAL	1	TRUE	0	0.414193493430298	1		379	579	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322661	109322661	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063762-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	147	355	0	ENST00000436639.2:c.376A>G	p.Met126Val	p.M126V	ENST00000436639	NM_014454.2	126	Atg/Gtg	3/10	0.338636614848977	1	FACETS	0.929	0.851	1	0.929	0.851	1	CLONAL	1	TRUE	0	0.414193493430298	1		355	606	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0063763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	34	362	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.180101926769787	2		362	357	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911535	101911535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113605875	NA	P-0063763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	33	295	0	ENST00000374994.4:c.1460G>A	p.Arg487Gln	p.R487Q	ENST00000374994	NM_004612.2	487	cGg/cAg	9/9	1	2	FACETS	0.856	0.697	1	0.856	0.697	1	CLONAL	1	TRUE	1	0.180101926769787	2		295	428	SUCCESS
APC	324	MSKCC	GRCh37	5	112175952	112175952	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587783031	NA	P-0063763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	110	409	0	ENST00000257430.4:c.4666del	p.Thr1556LeufsTer9	p.T1556Lfs*9	ENST00000257430	NM_000038.5	1554	gAa/ga	16/16	0.167200650245102	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	0	0.180101926769787	2		409	588	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718671	190718671	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768246348	NA	P-0063763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	19	198	0	ENST00000441310.2:c.829C>T	p.Arg277Ter	p.R277*	ENST00000441310	NM_000534.4	277	Cga/Tga	8/13	1	2	FACETS	0.639	0.485	0.821	0.639	0.485	0.821	SUBCLONAL	1	TRUE	1	0.180101926769787	2		198	330	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411798	63411798	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	65	475	0	ENST00000330258.3:c.1369C>T	p.Gln457Ter	p.Q457*	ENST00000330258	NM_152424.3	457	Cag/Tag	2/2	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.180101926769787	2		475	643	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261745	16261745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	69	576	0	ENST00000375759.3:c.9010G>A	p.Gly3004Arg	p.G3004R	ENST00000375759	NM_015001.2	3004	Ggg/Agg	11/15	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.180101926769787	2		576	765	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303688	65303688	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1374324844	NA	P-0063763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	50	343	0	ENST00000342505.4:c.3067G>A	p.Gly1023Ser	p.G1023S	ENST00000342505	NM_002227.2	1023	Ggt/Agt	22/25	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.180101926769787	2		343	501	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111417	56111417	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1450698465	NA	P-0063763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	43	437	0	ENST00000399503.3:c.17G>T	p.Gly6Val	p.G6V	ENST00000399503	NM_005921.1	6	gGg/gTg	1/20	1	2	FACETS	0.845	0.706	0.999	0.845	0.706	0.999	CLONAL	1	TRUE	1	0.180101926769787	2		437	565	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	66	372	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.806	0.705	0.915	1	0.976	1	CLONAL	2	TRUE	1	0.24	2		372	341	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	69	350	0	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	0.885	0.77	1	0.885	0.77	1	CLONAL	1	TRUE	1	0.24	2		350	650	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467590	66467590	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746706656	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	43	268	0	ENST00000273854.3:c.679C>T	p.Arg227Cys	p.R227C	ENST00000273854	NM_004439.5	227	Cgt/Tgt	3/18	1	2	FACETS	0.898	0.753	1	0.898	0.753	1	CLONAL	1	TRUE	1	0.24	2		268	399	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	63	748	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.872	0.754	1	0.872	0.754	1	CLONAL	1	TRUE	1	0.24	2		752	602	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	63	370	1	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.904	0.782	1	0.904	0.782	1	CLONAL	1	TRUE	1	0.24	2		371	581	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	39	319	0	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	1	2	FACETS	0.729	0.604	0.868	0.729	0.604	0.868	SUBCLONAL	1	TRUE	1	0.24	2		319	446	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440943	56440943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786205215	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	63	368	0	ENST00000407977.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000407977		132	Cga/Tga	4/10	1	2	FACETS	0.904	0.782	1	0.904	0.782	1	CLONAL	1	TRUE	1	0.24	2		368	581	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231783	36231783	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057519748	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	70	389	0	ENST00000300305.3:c.601C>T	p.Arg201Ter	p.R201*	ENST00000300305		201	Cga/Tga	5/8	1	2	FACETS	0.864	0.753	0.984	0.864	0.753	0.984	CLONAL	1	TRUE	1	0.24	2		389	675	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339111	65339111	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	79	351	2	ENST00000342505.4:c.425del	p.Lys142ArgfsTer26	p.K142Rfs*26	ENST00000342505	NM_002227.2	142	aAg/ag	5/25	1	2	FACETS	0.955	0.84	1	0.955	0.84	1	CLONAL	1	TRUE	1	0.24	2		353	689	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747084	40747084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762809890	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	43	297	0	ENST00000373198.4:c.2998G>A	p.Ala1000Thr	p.A1000T	ENST00000373198	NM_133170.3	1000	Gcc/Acc	22/32	0.3	1	FACETS	0.883	0.741	1	0.883	0.741	1	CLONAL	1	TRUE	0	0.24	1		297	357	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835780	68835781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	30	317	0	ENST00000261769.5:c.377dup	p.Pro127AlafsTer41	p.P127Afs*41	ENST00000261769	NM_004360.3	124	cgc/cgCc	3/16	1	2	FACETS	0.425	0.341	0.521	0.425	0.341	0.521	SUBCLONAL	1	TRUE	1	0.24	2		317	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780068	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	60	832	0	ENST00000269305.4:c.472C>T	p.Arg158Cys	p.R158C	ENST00000269305	NM_001126112.2	158	Cgc/Tgc	5/11	1	2	FACETS	0.826	0.712	0.951	0.826	0.712	0.951	CLONAL	1	TRUE	1	0.24	2		832	605	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535450	66535450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	39	222	0	ENST00000273854.3:c.11C>T	p.Ser4Leu	p.S4L	ENST00000273854	NM_004439.5	4	tCg/tTg	1/18	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.24	2		222	295	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047906	180047906	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	50	429	0	ENST00000261937.6:c.2269G>A	p.Val757Ile	p.V757I	ENST00000261937	NM_182925.4	757	Gtc/Atc	15/30	1	2	FACETS	0.822	0.698	0.958	0.822	0.698	0.958	CLONAL	1	TRUE	1	0.24	2		429	507	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	55	332	2	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	0.883	0.756	1	0.883	0.756	1	CLONAL	1	TRUE	1	0.24	2		334	519	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533932	63533932	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749846538	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	53	385	0	ENST00000307078.5:c.1222G>A	p.Glu408Lys	p.E408K	ENST00000307078	NM_004655.3	408	Gag/Aag	6/11	1	2	FACETS	0.851	0.726	0.988	0.851	0.726	0.988	CLONAL	1	TRUE	1	0.24	2		385	519	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395287	139395287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs545259523	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	52	291	1	ENST00000277541.6:c.5651C>T	p.Pro1884Leu	p.P1884L	ENST00000277541	NM_017617.3	1884	cCg/cTg	31/34	0.182825341571071	3	FACETS	0.916	0.78	1	0.458	0.39	0.533	CLONAL	1	TRUE	1	0.24	3		292	530	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993013	72993014	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	46	333	0	ENST00000268489.5:c.1031dup	p.Asn344LysfsTer13	p.N344Kfs*13	ENST00000268489	NM_006885.3	344	aac/aaAc	2/10	1	2	FACETS	0.913	0.77	1	0.913	0.77	1	CLONAL	1	TRUE	1	0.24	2		333	420	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760714	133760714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755821709	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	129	370	0	ENST00000318560.5:c.3037C>T	p.Arg1013Trp	p.R1013W	ENST00000318560	NM_005157.4	1013	Cgg/Tgg	11/11	0.182825341571071	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.24	3		370	528	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119910	70119910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1297203260	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	52	330	0	ENST00000245479.2:c.916del	p.Val306CysfsTer77	p.V306Cfs*77	ENST00000245479	NM_000346.3	304	ccG/cc	3/3	1	2	FACETS	0.932	0.794	1	0.932	0.794	1	CLONAL	1	TRUE	1	0.24	2		330	465	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263974	104263974	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776579	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	39	272	1	ENST00000369902.3:c.71del	p.Pro24ArgfsTer72	p.P24Rfs*72	ENST00000369902	NM_016169.3	22	gCc/gc	1/12	1	2	FACETS	0.768	0.637	0.914	0.768	0.637	0.914	CLONAL	1	TRUE	1	0.24	2		273	423	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127709	64127709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	63	333	0	ENST00000334205.4:c.202C>T	p.Arg68Cys	p.R68C	ENST00000334205	NM_003942.2	68	Cgc/Tgc	3/17	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.24	2		333	503	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324496	31324496	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs2308559	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	19	195	2	ENST00000412585.2:c.312C>A	p.Asn104Lys	p.N104K	ENST00000412585	NM_005514.6	104	aaC/aaA	2/8	1	2	FACETS	0.458	0.347	0.588	0.458	0.347	0.588	SUBCLONAL	1	TRUE	1	0.24	2		197	346	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873702	35873702	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	35	248	0	ENST00000303115.3:c.658T>C	p.Trp220Arg	p.W220R	ENST00000303115	NM_002185.3	220	Tgg/Cgg	5/8	1	2	FACETS	0.826	0.678	0.992	0.826	0.678	0.992	CLONAL	1	TRUE	1	0.24	2		248	353	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs753143066	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	32	219	2	ENST00000295797.4:c.826dup	p.Thr276AsnfsTer16	p.T276Nfs*16	ENST00000295797	NM_002740.5	273	tta/ttAa	9/18	1	2	FACETS	0.823	0.669	0.996	0.823	0.669	0.996	CLONAL	1	TRUE	1	0.24	2		221	324	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209593	98209593	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	50	337	0	ENST00000331920.6:c.3945del	p.Tyr1316ThrfsTer56	p.Y1316Tfs*56	ENST00000331920	NM_000264.3	1315	ccC/cc	23/24	0.182825341571071	3	FACETS	0.897	0.762	1	0.449	0.381	0.524	CLONAL	1	TRUE	1	0.24	3		337	520	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	44	388	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	0.739	0.62	0.871	0.739	0.62	0.871	SUBCLONAL	1	TRUE	1	0.24	2		388	496	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948586	71948586	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	50	453	0	ENST00000298229.2:c.3302del	p.Pro1101GlnfsTer30	p.P1101Qfs*30	ENST00000298229	NM_001567.3	1100	Ccc/cc	26/28	1	2	FACETS	0.739	0.626	0.862	0.739	0.626	0.862	SUBCLONAL	1	TRUE	1	0.24	2		453	564	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856434	111856434	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs776317487	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	60	392	2	ENST00000341259.2:c.489del	p.Thr165ProfsTer32	p.T165Pfs*32	ENST00000341259	NM_005475.2	162	gCc/gc	2/8	1	2	FACETS	0.859	0.74	0.989	0.859	0.74	0.989	CLONAL	1	TRUE	1	0.24	2		394	582	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754054	42754055	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	63	349	0	ENST00000222329.4:c.297dup	p.Lys100GlufsTer21	p.K100Efs*21	ENST00000222329	NM_006494.2	99	-/G	3/4	1	2	FACETS	0.991	0.858	1	0.991	0.858	1	CLONAL	1	TRUE	1	0.24	2		349	530	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426444	47426444	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1439786171	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	45	413	0	ENST00000377045.4:c.787G>A	p.Val263Met	p.V263M	ENST00000377045	NM_001654.4	263	Gtg/Atg	9/16	0.156992049745742	1	FACETS	0.562	0.472	0.662	0.562	0.472	0.662	SUBCLONAL	1	TRUE	0	0.24	1		413	587	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31493321	31493322	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1330233722	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	39	240	0	ENST00000344624.3:c.1834dup	p.Leu612ProfsTer8	p.L612Pfs*8	ENST00000344624		612	ctg/cCtg	10/33	1	2	FACETS	0.893	0.742	1	0.893	0.742	1	CLONAL	1	TRUE	1	0.24	2		240	364	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578401	7578401	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs147002414	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	70	395	0	ENST00000269305.4:c.529C>A	p.Pro177Thr	p.P177T	ENST00000269305	NM_001126112.2	177	Ccc/Acc	5/11	1	2	FACETS	0.967	0.844	1	0.967	0.844	1	CLONAL	1	TRUE	1	0.24	2		395	603	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139804439	139804439	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199507094	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	51	271	0	ENST00000247668.2:c.596G>T	p.Arg199Leu	p.R199L	ENST00000247668	NM_021138.3	199	cGg/cTg	6/11	0.182825341571071	3	FACETS	0.905	0.769	1	0.452	0.384	0.527	CLONAL	1	TRUE	1	0.24	3		271	526	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484236	57484236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1027670523	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	48	272	0	ENST00000371085.3:c.550G>A	p.Val184Met	p.V184M	ENST00000371085	NM_000516.4	184	Gtg/Atg	7/13	1	2	FACETS	0.911	0.771	1	0.911	0.771	1	CLONAL	1	TRUE	1	0.24	2		272	439	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745295	43745295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs933893718	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	61	366	0	ENST00000523873.1:c.208G>A	p.Glu70Lys	p.E70K	ENST00000523873		70	Gag/Aag	3/8	1	2	FACETS	0.919	0.793	1	0.919	0.793	1	CLONAL	1	TRUE	1	0.24	2		366	553	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468195	120468195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758275919	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	74	470	0	ENST00000256646.2:c.4244C>T	p.Thr1415Met	p.T1415M	ENST00000256646	NM_024408.3	1415	aCg/aTg	25/34	1	2	FACETS	0.952	0.833	1	0.952	0.833	1	CLONAL	1	TRUE	1	0.24	2		470	648	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604776	48604776	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs377767382	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	62	305	0	ENST00000342988.3:c.1598T>G	p.Leu533Arg	p.L533R	ENST00000342988	NM_005359.5	533	cTc/cGc	12/12	0.156992049745742	1	FACETS	0.984	0.852	1	0.984	0.852	1	CLONAL	1	TRUE	0	0.24	1		305	462	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609002	43609003	+	splice_acceptor_variant	Splice_Site	INS	-	-	G	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	61	453	0	ENST00000355710.3:c.1763dup		p.X588_splice	ENST00000355710	NM_020975.4	588			1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.24	2		453	488	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50733661	50733661	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1567603601	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	27	184	0	ENST00000307179.4:c.226del	p.Arg76AspfsTer36	p.R76Dfs*36	ENST00000307179		74	Aaa/aa	3/20	1	2	FACETS	0.76	0.606	0.935	0.76	0.606	0.935	CLONAL	1	TRUE	1	0.24	2		184	296	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434174	49434174	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774358086	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	40	426	0	ENST00000301067.7:c.7379G>A	p.Arg2460His	p.R2460H	ENST00000301067	NM_003482.3	2460	cGt/cAt	31/54	0.182825341571071	3	FACETS	0.588	0.487	0.7	0.294	0.243	0.35	SUBCLONAL	1	TRUE	1	0.24	3		426	635	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683698	162683698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs552077922	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	42	293	0	ENST00000366898.1:c.271G>A	p.Ala91Thr	p.A91T	ENST00000366898	NM_004562.2	91	Gcg/Acg	3/12	1	2	FACETS	0.787	0.657	0.93	0.787	0.657	0.93	CLONAL	1	TRUE	1	0.24	2		293	445	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294235	11294235	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs746242022	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	46	317	1	ENST00000361445.4:c.2296del	p.Arg766AspfsTer11	p.R766Dfs*11	ENST00000361445	NM_004958.3	766	Cga/ga	14/58	1	2	FACETS	0.799	0.673	0.937	0.799	0.673	0.937	CLONAL	1	TRUE	1	0.24	2		318	480	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202780	16202780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	46	326	0	ENST00000375759.3:c.488G>A	p.Arg163Lys	p.R163K	ENST00000375759	NM_015001.2	163	aGa/aAa	3/15	1	2	FACETS	0.702	0.591	0.825	0.702	0.591	0.825	SUBCLONAL	1	TRUE	1	0.24	2		326	546	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797333	45797333	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	67	465	0	ENST00000450313.1:c.1186G>T	p.Gly396Cys	p.G396C	ENST00000450313	NM_012222.2	396	Ggt/Tgt	12/16	1	2	FACETS	0.866	0.752	0.989	0.866	0.752	0.989	CLONAL	1	TRUE	1	0.24	2		465	645	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612887	228612891	+	frameshift_variant	Frame_Shift_Del	DEL	ACCGT	ACCGT	-	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	75	539	0	ENST00000366696.1:c.136_140del	p.Thr46GlyfsTer13	p.T46Gfs*13	ENST00000366696	NM_003493.2	46	ACGGTg/g	1/1	1	2	FACETS	0.827	0.724	0.938	0.827	0.724	0.938	CLONAL	1	TRUE	1	0.24	2		539	756	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518529	69518529	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	59	316	0	ENST00000294312.3:c.116del	p.Gly39AlafsTer107	p.G39Afs*107	ENST00000294312	NM_005117.2	39	gGc/gc	1/3	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.24	2		316	393	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94209523	94209523	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	22	182	0	ENST00000323929.3:c.591del	p.Val198Ter	p.V198*	ENST00000323929	NM_005591.3	197	aaA/aa	7/20	1	2	FACETS	0.857	0.667	1	0.857	0.667	1	CLONAL	1	TRUE	1	0.24	2		182	214	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442499	49442500	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCA	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	29	269	0	ENST00000301067.7:c.4071_4073dup	p.Asp1358dup	p.D1358dup	ENST00000301067	NM_003482.3	1358	gac/gaTGAc	13/54	0.182825341571071	3	FACETS	0.596	0.478	0.731	0.298	0.239	0.366	SUBCLONAL	1	TRUE	1	0.24	3		269	454	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954223	32954223	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	51	252	2	ENST00000380152.3:c.9197A>G	p.Gln3066Arg	p.Q3066R	ENST00000380152		3066	cAg/cGg	24/27	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.24	2		254	371	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295058	91295058	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	29	212	0	ENST00000355112.3:c.841C>T	p.His281Tyr	p.H281Y	ENST00000355112	NM_000057.2	281	Cat/Tat	4/22	1	2	FACETS	0.744	0.598	0.909	0.744	0.598	0.909	CLONAL	1	TRUE	1	0.24	2		212	325	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662391	67662391	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	50	320	0	ENST00000264010.4:c.1637A>G	p.His546Arg	p.H546R	ENST00000264010	NM_006565.3	546	cAc/cGc	9/12	1	2	FACETS	0.779	0.661	0.909	0.779	0.661	0.909	CLONAL	1	TRUE	1	0.24	2		320	535	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350895	89350896	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	31	282	0	ENST00000301030.4:c.2054_2055del	p.Lys685SerfsTer10	p.K685Sfs*10	ENST00000301030	NM_001256183.1	685	aAA/a	9/13	1	2	FACETS	0.594	0.48	0.723	0.594	0.48	0.723	SUBCLONAL	1	TRUE	1	0.24	2		282	435	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16046996	16046996	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	33	188	0	ENST00000268712.3:c.1097del	p.Gly366GlufsTer37	p.G366Efs*37	ENST00000268712	NM_006311.3	366	gGa/ga	11/46	1	2	FACETS	0.741	0.604	0.895	0.741	0.604	0.895	SUBCLONAL	1	TRUE	1	0.24	2		188	371	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40461423	40461423	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	63	372	0	ENST00000345506.4:c.2143G>T	p.Gly715Cys	p.G715C	ENST00000345506	NM_003152.3	715	Ggc/Tgc	19/20	1	2	FACETS	0.861	0.744	0.987	0.861	0.744	0.987	CLONAL	1	TRUE	1	0.24	2		372	610	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440930	56440930	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	47	373	0	ENST00000407977.2:c.407C>A	p.Ala136Asp	p.A136D	ENST00000407977		136	gCt/gAt	4/10	1	2	FACETS	0.673	0.567	0.79	0.673	0.567	0.79	SUBCLONAL	1	TRUE	1	0.24	2		373	582	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1620997	1620997	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	53	440	0	ENST00000344749.5:c.1063A>G	p.Thr355Ala	p.T355A	ENST00000344749	NM_001136139.2	355	Acc/Gcc	13/19	1	2	FACETS	0.684	0.582	0.795	0.684	0.582	0.795	SUBCLONAL	1	TRUE	1	0.24	2		440	646	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2193748	2193748	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	62	341	0	ENST00000398665.3:c.554T>A	p.Val185Asp	p.V185D	ENST00000398665	NM_032482.2	185	gTc/gAc	6/28	1	2	FACETS	0.997	0.863	1	0.997	0.863	1	CLONAL	1	TRUE	1	0.24	2		341	518	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098500	11098500	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371214327	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	62	391	1	ENST00000358026.2:c.1018G>A	p.Ala340Thr	p.A340T	ENST00000358026	NM_001128849.1	340	Gcg/Acg	6/36	1	2	FACETS	0.966	0.835	1	0.966	0.835	1	CLONAL	1	TRUE	1	0.24	2		392	535	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144150	11144150	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502060	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	50	308	0	ENST00000358026.2:c.3731G>A	p.Arg1244His	p.R1244H	ENST00000358026	NM_001128849.1	1244	cGc/cAc	26/36	1	2	FACETS	0.82	0.696	0.956	0.82	0.696	0.956	CLONAL	1	TRUE	1	0.24	2		308	508	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794665	42794665	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200040001	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	53	333	1	ENST00000575354.2:c.1745C>T	p.Ala582Val	p.A582V	ENST00000575354	NM_015125.3	582	gCg/gTg	10/20	1	2	FACETS	0.866	0.739	1	0.866	0.739	1	CLONAL	1	TRUE	1	0.24	2		334	510	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422555	47422555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324543011	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	45	320	0	ENST00000404338.3:c.623G>A	p.Arg208Gln	p.R208Q	ENST00000404338	NM_004491.4	208	cGg/cAg	1/6	1	2	FACETS	0.708	0.594	0.833	0.708	0.594	0.833	SUBCLONAL	1	TRUE	1	0.24	2		320	530	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422569	47422569	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	55	306	1	ENST00000404338.3:c.637G>A	p.Ala213Thr	p.A213T	ENST00000404338	NM_004491.4	213	Gca/Aca	1/6	1	2	FACETS	0.926	0.793	1	0.926	0.793	1	CLONAL	1	TRUE	1	0.24	2		307	495	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288989	212288989	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	39	238	0	ENST00000342788.4:c.2757del	p.Lys919AsnfsTer15	p.K919Nfs*15	ENST00000342788	NM_005235.2	919	aaA/aa	23/28	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.24	2		238	300	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660313	227660313	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	45	302	0	ENST00000305123.5:c.3142C>T	p.Gln1048Ter	p.Q1048*	ENST00000305123	NM_005544.2	1048	Caa/Taa	1/2	1	2	FACETS	0.775	0.651	0.911	0.775	0.651	0.911	CLONAL	1	TRUE	1	0.24	2		302	484	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721173	39721173	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1360819731	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	52	260	0	ENST00000361337.2:c.676G>A	p.Val226Ile	p.V226I	ENST00000361337	NM_003286.2	226	Gta/Ata	9/21	1	2	FACETS	0.888	0.757	1	0.888	0.757	1	CLONAL	1	TRUE	1	0.24	2		260	488	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264868	46264868	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	46	308	0	ENST00000371998.3:c.1738G>A	p.Val580Met	p.V580M	ENST00000371998		580	Gtg/Atg	12/23	1	2	FACETS	0.863	0.728	1	0.863	0.728	1	CLONAL	1	TRUE	1	0.24	2		308	444	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446022	29446022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572878226	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	46	288	0	ENST00000544604.2:c.1853G>A	p.Arg618Gln	p.R618Q	ENST00000544604	NM_001206998.1	618	cGg/cAg	8/9	1	2	FACETS	0.908	0.766	1	0.908	0.766	1	CLONAL	1	TRUE	1	0.24	2		288	422	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1918715	1918715	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	55	247	0	ENST00000382891.5:c.878T>C	p.Leu293Ser	p.L293S	ENST00000382891	NM_133335.3	293	tTa/tCa	4/22	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.24	2		247	384	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	231115	231115	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	39	128	0	ENST00000264932.6:c.895G>T	p.Gly299Cys	p.G299C	ENST00000264932	NM_004168.2	299	Ggc/Tgc	7/15	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.24	2		128	281	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512430	149512430	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	56	375	0	ENST00000261799.4:c.1010A>C	p.Gln337Pro	p.Q337P	ENST00000261799	NM_002609.3	337	cAg/cCg	7/23	1	2	FACETS	0.784	0.672	0.908	0.784	0.672	0.908	CLONAL	1	TRUE	1	0.24	2		375	595	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816829	32816829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	48	235	0	ENST00000354258.4:c.1495G>A	p.Val499Ile	p.V499I	ENST00000354258	NM_000593.5	499	Gta/Ata	6/11	1	2	FACETS	0.684	0.577	0.801	0.684	0.577	0.801	SUBCLONAL	1	TRUE	1	0.24	2		235	585	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687237	117687237	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	42	253	0	ENST00000368508.3:c.2812+2T>C		p.X938_splice	ENST00000368508	NM_002944.2	938			0.156992049745742	1	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	0	0.24	1		253	290	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402747	139402747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531420022	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	66	373	0	ENST00000277541.6:c.3262G>A	p.Gly1088Ser	p.G1088S	ENST00000277541	NM_017617.3	1088	Ggc/Agc	20/34	0.182825341571071	3	FACETS	0.964	0.837	1	0.482	0.418	0.551	CLONAL	1	TRUE	1	0.24	3		373	639	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922979	44922979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs931403834	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	46	347	1	ENST00000377967.4:c.1840G>A	p.Ala614Thr	p.A614T	ENST00000377967	NM_021140.2	614	Gca/Aca	16/29	0.156992049745742	1	FACETS	0.603	0.508	0.709	0.603	0.508	0.709	SUBCLONAL	1	TRUE	0	0.24	1		348	559	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020179	123020179	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1229008261	NA	P-0063764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	62	323	0	ENST00000355640.3:c.667C>T	p.His223Tyr	p.H223Y	ENST00000355640		223	Cac/Tac	2/7	0.156992049745742	1	FACETS	0.949	0.822	1	0.949	0.822	1	CLONAL	1	TRUE	0	0.24	1		323	479	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	164	523	0				ENST00000310581	NM_198253.2	-/1132			0.253102189350721	3	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	FALSE	1	0.253102189350721	3		523	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0063765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	127	681	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	FALSE	NA	0.253102189350721	2		682	734	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044901	47044901	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	135	356	0	ENST00000377604.3:c.2227G>T	p.Glu743Ter	p.E743*	ENST00000377604	NM_001204468.1	743	Gag/Tag	20/24	1	1	FACETS	0.919	0.84	1	1	0.99	1	CLONAL	2	FALSE	0	0.253102189350721	1		356	507	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434817	110434817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	67	543	0	ENST00000375856.3:c.3584G>A	p.Gly1195Glu	p.G1195E	ENST00000375856	NM_003749.2	1195	gGa/gAa	1/2	0.253102189350721	2	FACETS	0.59	0.511	0.675	0.295	0.255	0.338	SUBCLONAL	1	FALSE	0	0.253102189350721	2		543	898	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481397	140481397	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913376	NA	P-0063765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	70	248	0	ENST00000288602.6:c.1411G>T	p.Val471Phe	p.V471F	ENST00000288602	NM_004333.4	471	Gtc/Ttc	11/18	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.253102189350721	2		248	415	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031880	10031880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765104792	NA	P-0063765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	49	456	0	ENST00000330684.3:c.943G>A	p.Glu315Lys	p.E315K	ENST00000330684	NM_001134407.1	315	Gag/Aag	3/13	0.253102189350721	1	FACETS	0.591	0.5	0.691	0.591	0.5	0.691	SUBCLONAL	1	FALSE	0	0.253102189350721	1		456	572	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739128	40739128	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0063765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	39	372	0	ENST00000373198.4:c.3157-1G>A		p.X1053_splice	ENST00000373198	NM_133170.3	1053			NA	2	FACETS	0.46	0.38	0.549			1	INDETERMINATE	1	FALSE	NA	0.253102189350721	2		372	670	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459900	99459900	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0063765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	42	314	0	ENST00000268035.6:c.1997-1G>C		p.X666_splice	ENST00000268035	NM_000875.3	666			0.160196577046965	2	FACETS	0.684	0.571	0.81	0.342	0.285	0.405	SUBCLONAL	1	FALSE	0	0.253102189350721	2		314	485	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713794	30713794	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	153	554	0	ENST00000295754.5:c.1119G>T	p.Met373Ile	p.M373I	ENST00000295754	NM_003242.5	373	atG/atT	4/7	0.253102189350721	3	FACETS	1	0.987	1	0.726	0.664	0.791	CLONAL	1	FALSE	1	0.253102189350721	3		554	938	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045134	47045134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782351435	NA	P-0063765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	106	241	0	ENST00000377604.3:c.2375G>A	p.Arg792Gln	p.R792Q	ENST00000377604	NM_001204468.1	792	cGg/cAg	21/24	1	1	FACETS	0.757	0.682	0.836	1	0.983	1	SUBCLONAL	2	FALSE	0	0.253102189350721	1		241	483	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454613	99454613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs33958176	NA	P-0063766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	154	442	2	ENST00000268035.6:c.1532G>A	p.Arg511Gln	p.R511Q	ENST00000268035	NM_000875.3	511	cGg/cAg	7/21	0.595986463632218	1	FACETS	0.757	0.699	0.818	0.757	0.699	0.818	SUBCLONAL	1	FALSE	0	0.595986463632218	1		444	479	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243840	41243840	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs28897687	NA	P-0063766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	202	415	0	ENST00000357654.3:c.3708T>G	p.Asn1236Lys	p.N1236K	ENST00000357654	NM_007294.3	1236	aaT/aaG	10/23	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.595986463632218	2		415	518	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607376	46607471	+	inframe_deletion	In_Frame_Del	DEL	ATGAGCTGGACTTGGAGACACTGGCACCCTATATCCCCATGGACGGGGAAGACTTCCAGCTAAGCCCCATCTGCCCCGAGGAGCGGCTCTTGGCGG	ATGAGCTGGACTTGGAGACACTGGCACCCTATATCCCCATGGACGGGGAAGACTTCCAGCTAAGCCCCATCTGCCCCGAGGAGCGGCTCTTGGCGG	-	novel	NA	P-0063766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	186	452	0	ENST00000263734.3:c.1566_1661del	p.Asn522_Glu554delinsLys	p.N522_E554delinsK	ENST00000263734	NM_001430.4	522	aATGAGCTGGACTTGGAGACACTGGCACCCTATATCCCCATGGACGGGGAAGACTTCCAGCTAAGCCCCATCTGCCCCGAGGAGCGGCTCTTGGCGGag/aag	12/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.595986463632218	2		452	577	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0063791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	32	362	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.227371040479373	4	FACETS	1	0.886	1	0.738	0.607	0.882	CLONAL	2	TRUE	1	0.227371040479373	4		362	156	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0063791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	135	561	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	0.227371040479373	5	FACETS	0.923	0.843	1			1	CLONAL	3	TRUE	NA	0.227371040479373	5		561	575	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680572	30680572	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	90	471	0	ENST00000376406.3:c.1147G>T	p.Gly383Cys	p.G383C	ENST00000376406	NM_014641.2	383	Ggc/Tgc	5/15	0.227371040479373	5	FACETS	0.832	0.739	0.931	0.555	0.492	0.621	CLONAL	2	TRUE	2	0.227371040479373	5		471	638	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441431	52441431	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	79	600	0	ENST00000460680.1:c.421C>A	p.His141Asn	p.H141N	ENST00000460680	NM_004656.3	141	Cat/Aat	6/17	0.10926903344081	4	FACETS	1	0.952	1	0.583	0.512	0.659	INDETERMINATE	1	TRUE	2	0.227371040479373	4		600	732	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434734	110434734	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	73	489	0	ENST00000375856.3:c.3667G>T	p.Gly1223Cys	p.G1223C	ENST00000375856	NM_003749.2	1223	Ggt/Tgt	1/2	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.227371040479373	2		489	519	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968256	2968256	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	87	428	0	ENST00000396946.4:c.1730A>G	p.Tyr577Cys	p.Y577C	ENST00000396946	NM_032415.4	577	tAc/tGc	13/25	0.192351836561504	4	FACETS	0.972	0.864	1	0.972	0.864	1	CLONAL	2	TRUE	2	0.227371040479373	4		428	483	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760205	133760205	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	49	472	0	ENST00000318560.5:c.2528G>C	p.Gly843Ala	p.G843A	ENST00000318560	NM_005157.4	843	gGg/gCg	11/11	0.10926903344081	4	FACETS	1	0.955	1	0.678	0.576	0.79	INDETERMINATE	1	TRUE	2	0.227371040479373	4		472	390	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405202	139405206	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGT	GCCGT	-	novel	NA	P-0063791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	65	496	0	ENST00000277541.6:c.2639_2643del	p.His880ArgfsTer62	p.H880Rfs*62	ENST00000277541	NM_017617.3	880	cACGGC/c	17/34	0.10926903344081	4	FACETS	1	0.968	1	0.702	0.609	0.802	INDETERMINATE	1	TRUE	2	0.227371040479373	4		496	500	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18943053	18943053	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063793-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	254	651	0	ENST00000262803.5:c.35C>T	p.Thr12Ile	p.T12I	ENST00000262803	NM_002911.3	12	aCt/aTt	1/24	0.121634982055641	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.922043455695514	0		651	530	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881440	111881440	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063793-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	245	455	0	ENST00000393256.3:c.118C>T	p.Pro40Ser	p.P40S	ENST00000393256	NM_006538.4	40	Cca/Tca	2/4	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	FALSE	NA	0.922043455695514	2		455	482	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979563	2979563	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0063793-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	38	361	0	ENST00000396946.4:c.685-1G>C		p.X229_splice	ENST00000396946	NM_032415.4	229			0.153821996973887	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.922043455695514	0		361	277	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851150	151851150	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063793-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	39	475	0	ENST00000262189.6:c.12221G>T	p.Gly4074Val	p.G4074V	ENST00000262189	NM_170606.2	4074	gGt/gTt	48/59	0.66776516565956	1	FACETS	0.121	0.1	0.145	0.121	0.1	0.145	SUBCLONAL	1	FALSE	0	0.922043455695514	1		475	376	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	250	523	0				ENST00000310581	NM_198253.2	-/1132			0.325073700390741	6	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	3	0.325073700390741	6		523	755	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	216	232	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	0.302100834090991	2	FACETS	1	0.95	1			1	CLONAL	3	TRUE	NA	0.325073700390741	2		232	439	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481403	140481403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913357	NA	P-0063794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	68	279	0	ENST00000288602.6:c.1405G>A	p.Gly469Arg	p.G469R	ENST00000288602	NM_004333.4	469	Gga/Aga	11/18	0.190177567649392	5	FACETS	1	0.933	1	0.372	0.323	0.424	INDETERMINATE	1	TRUE	2	0.325073700390741	5		279	558	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0063794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	116	589	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.325073700390741	5	FACETS	1	0.972	1	0.305	0.274	0.338	CLONAL	1	TRUE	1	0.325073700390741	5		589	870	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936983	48936983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690863	NA	P-0063794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	147	305	0	ENST00000267163.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000267163	NM_000321.2	251	Cga/Tga	8/27	0.190177567649392	5	FACETS	1	0.94	1	0.688	0.63	0.748	INDETERMINATE	2	TRUE	2	0.325073700390741	5		305	652	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107135	27107136	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0063794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	215	585	0	ENST00000324856.7:c.6747dup	p.Glu2250ArgfsTer28	p.E2250Rfs*28	ENST00000324856	NM_006015.4	2249	tca/tcAa	20/20	0.304461179097799	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.325073700390741	3		585	737	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860556	45860556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	105	524	0	ENST00000391945.4:c.1451C>T	p.Thr484Met	p.T484M	ENST00000391945	NM_000400.3	484	aCg/aTg	15/23	0.304461179097799	3	FACETS	1	0.927	1	0.522	0.467	0.579	CLONAL	1	TRUE	1	0.325073700390741	3		524	720	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197847	66197847	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0063794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	45	282	0	ENST00000273854.3:c.2853-1G>A		p.X951_splice	ENST00000273854	NM_004439.5	951			0.304461179097799	3	FACETS	0.732	0.615	0.86	0.366	0.307	0.43	SUBCLONAL	1	TRUE	1	0.325073700390741	3		282	440	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978556	70978556	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	181	429	0	ENST00000276594.2:c.1097A>G	p.Tyr366Cys	p.Y366C	ENST00000276594	NM_024504.3	366	tAt/tGt	5/8	0.190177567649392	5	FACETS	1	0.957	1	0.702	0.648	0.757	INDETERMINATE	2	TRUE	2	0.325073700390741	5		429	787	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597846	43597846	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	285	543	0	ENST00000355710.3:c.394C>G	p.Leu132Val	p.L132V	ENST00000355710	NM_020975.4	132	Ctt/Gtt	3/20	0.325073700390741	5	FACETS	0.907	0.854	0.961	0.907	0.854	0.961	CLONAL	3	TRUE	2	0.325073700390741	5		543	959	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732461	74732461	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	100	515	0	ENST00000359995.5:c.448C>T	p.Arg150Trp	p.R150W	ENST00000359995	NM_001195427.1	150	Cgg/Tgg	2/3	0.325073700390741	5	FACETS	0.981	0.875	1	0.245	0.218	0.274	CLONAL	1	TRUE	1	0.325073700390741	5		515	933	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261437	16261437	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	109	538	0	ENST00000375759.3:c.8702C>G	p.Ser2901Cys	p.S2901C	ENST00000375759	NM_015001.2	2901	tCt/tGt	11/15	0.304461179097799	3	FACETS	1	0.95	1	0.547	0.491	0.606	CLONAL	1	TRUE	1	0.325073700390741	3		538	713	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335048	65335048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	71	370	0	ENST00000342505.4:c.593C>T	p.Ser198Leu	p.S198L	ENST00000342505	NM_002227.2	198	tCa/tTa	6/25	0.299329603448115	4	FACETS	0.802	0.699	0.913	0.267	0.233	0.305	CLONAL	1	TRUE	1	0.325073700390741	4		370	722	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600484	43600484	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	286	542	0	ENST00000355710.3:c.710A>G	p.Tyr237Cys	p.Y237C	ENST00000355710	NM_020975.4	237	tAc/tGc	4/20	0.325073700390741	5	FACETS	0.936	0.882	0.992	0.936	0.882	0.992	CLONAL	3	TRUE	2	0.325073700390741	5		542	932	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865639	57865639	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	99	584	0	ENST00000228682.2:c.3116C>G	p.Ser1039Cys	p.S1039C	ENST00000228682	NM_005269.2	1039	tCt/tGt	12/12	0.304461179097799	3	FACETS	0.866	0.772	0.965	0.433	0.386	0.483	CLONAL	1	TRUE	1	0.325073700390741	3		584	818	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910863	32910863	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	78	396	0	ENST00000380152.3:c.2371T>G	p.Ser791Ala	p.S791A	ENST00000380152		791	Tca/Gca	11/27	0.251666395517999	3	FACETS	0.906	0.796	1	0.453	0.398	0.512	CLONAL	1	TRUE	1	0.325073700390741	3		396	616	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910887	32910887	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0063794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	72	410	0	ENST00000380152.3:c.2395A>T	p.Lys799Ter	p.K799*	ENST00000380152		799	Aaa/Taa	11/27	0.251666395517999	3	FACETS	0.833	0.728	0.947	0.417	0.364	0.474	CLONAL	1	TRUE	1	0.325073700390741	3		410	618	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878089	48878114	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCTGCCGCCGCGGAACCCCCGGCA	CCGCTGCCGCCGCGGAACCCCCGGCA	-	novel	NA	P-0063794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	146	509	1	ENST00000267163.4:c.45_70del	p.Glu19ProfsTer3	p.E19Pfs*3	ENST00000267163	NM_000321.2	14	gCCGCTGCCGCCGCGGAACCCCCGGCA/g	1/27	0.190177567649392	5	FACETS	0.892	0.815	0.972	0.595	0.543	0.648	INDETERMINATE	2	TRUE	2	0.325073700390741	5		510	749	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122868	2122868	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	101	408	0	ENST00000219476.3:c.2239C>G	p.Leu747Val	p.L747V	ENST00000219476	NM_000548.3	747	Ctg/Gtg	21/42	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.325073700390741	2		408	559	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40460195	40460195	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0063794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	73	393	0	ENST00000345506.4:c.1907-1G>A		p.X636_splice	ENST00000345506	NM_003152.3	636			0.325073700390741	5	FACETS	0.892	0.779	1	0.223	0.194	0.254	CLONAL	1	TRUE	1	0.325073700390741	5		393	749	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56338916	56338916	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	58	372	0	ENST00000348428.3:c.41C>A	p.Ser14Ter	p.S14*	ENST00000348428	NM_006785.3	14	tCg/tAg	1/17	0.304461179097799	3	FACETS	0.947	0.816	1	0.474	0.408	0.545	CLONAL	1	TRUE	1	0.325073700390741	3		372	438	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735374	204735374	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	97	533	0	ENST00000302823.3:c.175G>C	p.Glu59Gln	p.E59Q	ENST00000302823	NM_005214.4	59	Gag/Cag	2/4	0.325073700390741	2	FACETS	0.925	0.826	1	0.463	0.413	0.516	CLONAL	1	TRUE	0	0.325073700390741	2		533	645	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54956502	54956502	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	144	315	0	ENST00000312783.6:c.692A>G	p.Gln231Arg	p.Q231R	ENST00000312783	NM_198436.1	231	cAg/cGg	7/10	0.325073700390741	5	FACETS	0.981	0.897	1	0.654	0.598	0.712	CLONAL	2	TRUE	2	0.325073700390741	5		315	672	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226836	142226836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	98	352	0	ENST00000350721.4:c.4968G>A	p.Met1656Ile	p.M1656I	ENST00000350721	NM_001184.3	1656	atG/atA	28/47	0.325073700390741	7	FACETS	1	0.965	1			1	CLONAL	1	TRUE	NA	0.325073700390741	7		352	906	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184658	185184658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369470313	NA	P-0063794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	240	425	0	ENST00000265026.3:c.1550G>A	p.Arg517Gln	p.R517Q	ENST00000265026	NM_004721.4	517	cGa/cAa	10/14	0.325073700390741	6	FACETS	0.837	0.782	0.894	0.628	0.587	0.67	CLONAL	3	TRUE	2	0.325073700390741	6		425	970	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393153	393153	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1218231557	NA	P-0063794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	154	393	0	ENST00000380956.4:c.1A>G	p.Met1?	p.M1?	ENST00000380956	NM_001195286.1	1	Atg/Gtg	2/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.325073700390741	NA		393	615	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874026	151874026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	203	423	0	ENST00000262189.6:c.8512G>A	p.Glu2838Lys	p.E2838K	ENST00000262189	NM_170606.2	2838	Gaa/Aaa	38/59	0.190177567649392	5	FACETS	1	0.975	1	0.74	0.687	0.794	INDETERMINATE	2	TRUE	2	0.325073700390741	5		423	837	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56854446	56854446	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	65	309	0	ENST00000519728.1:c.28G>C	p.Asp10His	p.D10H	ENST00000519728	NM_002350.3	10	Gac/Cac	2/13	0.190177567649392	5	FACETS	1	0.869	1	0.334	0.289	0.382	INDETERMINATE	1	TRUE	2	0.325073700390741	5		309	594	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855279	76855279	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	49	171	0	ENST00000373344.5:c.5708A>G	p.Asp1903Gly	p.D1903G	ENST00000373344	NM_000489.3	1903	gAt/gGt	24/35	0.325073700390741	3	FACETS	1	0.915	1			1	CLONAL	1	TRUE	NA	0.325073700390741	3		171	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0063795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	308	850	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.732623633732821	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.732623633732821	2		852	392	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974792	21974792	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs141798398	NA	P-0063795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	182	576	0	ENST00000304494.5:c.35C>A	p.Ser12Ter	p.S12*	ENST00000304494	NM_000077.4	12	tCg/tAg	1/3	0.724887685715892	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.732623633732821	2		576	231	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259192	16259192	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	297	610	0	ENST00000375759.3:c.6457G>T	p.Val2153Leu	p.V2153L	ENST00000375759	NM_015001.2	2153	Gtg/Ttg	11/15	0.732623633732821	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.732623633732821	3		610	509	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416114	49416114	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	203	409	0	ENST00000301067.7:c.16361G>T	p.Arg5454Leu	p.R5454L	ENST00000301067	NM_003482.3	5454	cGa/cTa	52/54	0.732623633732821	3	FACETS	0.932	0.878	0.987	0.932	0.878	0.987	CLONAL	2	TRUE	1	0.732623633732821	3		409	406	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38801856	38801856	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	163	390	0	ENST00000348513.6:c.23C>A	p.Ala8Asp	p.A8D	ENST00000348513	NM_003079.4	8	gCc/gAc	3/11	0.732623633732821	4	FACETS	0.943	0.875	1	0.943	0.875	1	CLONAL	2	TRUE	2	0.732623633732821	4		390	409	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481624	40481624	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	140	482	0	ENST00000264657.5:c.1181T>A	p.Met394Lys	p.M394K	ENST00000264657	NM_139276.2	394	aTg/aAg	13/24	0.732623633732821	4	FACETS	0.89	0.812	0.972	0.445	0.406	0.486	CLONAL	1	TRUE	2	0.732623633732821	4		482	744	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645782	215645782	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	92	508	0	ENST00000260947.4:c.816del	p.Phe272LeufsTer4	p.F272Lfs*4	ENST00000260947	NM_000465.2	272	ttT/tt	4/11	0.732623633732821	3	FACETS	0.889	0.796	0.987	0.444	0.398	0.494	CLONAL	1	TRUE	1	0.732623633732821	3		508	386	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521704	89521704	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	248	439	0	ENST00000336596.2:c.2781C>A	p.His927Gln	p.H927Q	ENST00000336596	NM_005233.5	927	caC/caA	16/17	0.732623633732821	2	FACETS	0.978	0.938	1	0.978	0.938	1	CLONAL	2	TRUE	0	0.732623633732821	2		439	346	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674344	86674344	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	147	316	0	ENST00000274376.6:c.2476C>T	p.Gln826Ter	p.Q826*	ENST00000274376	NM_002890.2	826	Cag/Tag	18/25	0.724887685715892	2	FACETS	0.96	0.908	1	0.96	0.908	1	CLONAL	2	TRUE	0	0.732623633732821	2		316	209	SUCCESS
MTAP	4507	MSKCC	GRCh37	9	21838002	21838002	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	233	344	0	ENST00000380172.4:c.443C>G	p.Thr148Arg	p.T148R	ENST00000380172	NM_002451.3	148	aCg/aGg	5/8	0.724887685715892	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.732623633732821	2		344	306	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0063796-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	188	362	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.679410814295524	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.679410814295524	3		362	350	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376748	118376748	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs782638810	NA	P-0063796-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	175	561	0	ENST00000534358.1:c.10141A>G	p.Ile3381Val	p.I3381V	ENST00000534358	NM_005933.3	3381	Ata/Gta	27/36	0.679410814295524	3	FACETS	1	0.978	1	0.573	0.53	0.617	CLONAL	1	TRUE	1	0.679410814295524	3		561	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0063797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	216	406	1	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.485013999283778	2	FACETS	0.972	0.915	1	0.972	0.915	1	CLONAL	2	TRUE	0	0.485013999283778	2		407	458	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0063797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	169	362	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.485013999283778	3	FACETS	0.991	0.921	1	0.991	0.921	1	CLONAL	2	TRUE	1	0.485013999283778	3		362	437	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0063797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	230	451	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	0.485013999283778	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.485013999283778	3		451	560	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0063797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	152	520	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	0.485013999283778	3	FACETS	1	0.968	1	0.557	0.51	0.606	CLONAL	1	TRUE	1	0.485013999283778	3		520	699	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426795	212426795	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	60	476	0	ENST00000342788.4:c.2320A>C	p.Ser774Arg	p.S774R	ENST00000342788	NM_005235.2	774	Agt/Cgt	20/28	0.277952475406219	5	FACETS	0.654	0.562	0.753	0.218	0.187	0.251	INDETERMINATE	1	TRUE	2	0.485013999283778	5		476	654	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101064	41101064	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	122	512	0	ENST00000373198.4:c.1292A>C	p.Asn431Thr	p.N431T	ENST00000373198	NM_133170.3	431	aAc/aCc	8/32	0.221913368665311	6	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.485013999283778	6		512	860	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211120	2211120	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	198	521	2	ENST00000398665.3:c.1374C>G	p.Ser458Arg	p.S458R	ENST00000398665	NM_032482.2	458	agC/agG	15/28	0.277952475406219	5	FACETS	0.908	0.843	0.975	0.605	0.562	0.65	INDETERMINATE	2	TRUE	2	0.485013999283778	5		523	777	SUCCESS
AR	367	MSKCC	GRCh37	X	66765950	66765950	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	142	536	0	ENST00000374690.3:c.962A>G	p.Glu321Gly	p.E321G	ENST00000374690	NM_000044.3	321	gAa/gGa	1/8	0.309702206602448	4	FACETS	1	0.962	1	0.55	0.501	0.6	CLONAL	1	TRUE	2	0.485013999283778	4		536	791	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0063798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	1241	454	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.40239376037942	14	FACETS	0.963	0.946	0.98	0.963	0.946	0.98	CLONAL	13	TRUE	1	0.40239376037942	14		454	1682	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0063798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	350	608	0	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	0.388328726741867	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	0	0.40239376037942	3		608	684	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809764	36809764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	223	472	0	ENST00000373129.3:c.841G>A	p.Glu281Lys	p.E281K	ENST00000373129	NM_032017.1	281	Gag/Aag	9/12	0.399785048105303	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.40239376037942	4		472	686	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647030	23647030	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1220937122	NA	P-0063798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	278	486	0	ENST00000261584.4:c.837A>T	p.Lys279Asn	p.K279N	ENST00000261584	NM_024675.3	279	aaA/aaT	4/13	0.40239376037942	6	FACETS	0.968	0.912	1			1	CLONAL	3	TRUE	NA	0.40239376037942	6		486	859	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281649	142281649	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1216297780	NA	P-0063798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	114	407	0	ENST00000350721.4:c.595A>G	p.Met199Val	p.M199V	ENST00000350721	NM_001184.3	199	Atg/Gtg	4/47	0.24683858272752	3	FACETS	1	0.982	1	0.464	0.42	0.51	CLONAL	1	TRUE	0	0.40239376037942	3		407	489	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981471	70981471	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs766778802	NA	P-0063798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	168	526	0	ENST00000276594.2:c.625G>T	p.Val209Phe	p.V209F	ENST00000276594	NM_024504.3	209	Gtc/Ttc	2/8	0.405233545265425	4	FACETS	1	0.986	1	0.443	0.407	0.48	CLONAL	1	TRUE	1	0.40239376037942	4		526	882	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777894	NA	P-0063799-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	118	506	0	ENST00000361445.4:c.6644C>T	p.Ser2215Phe	p.S2215F	ENST00000361445	NM_004958.3	2215	tCt/tTt	47/58	0.259117430569014	2	FACETS	0.751	0.682	0.824	0.751	0.682	0.824	SUBCLONAL	2	TRUE	0	0.334162613740995	2		506	470	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0063799-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	145	467	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.334162613740995	9	FACETS	0.987	0.9	1			1	CLONAL	2	TRUE	NA	0.334162613740995	9		467	954	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780071	NA	P-0063799-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	220	779	0	ENST00000269305.4:c.580C>T	p.Leu194Phe	p.L194F	ENST00000269305	NM_001126112.2	194	Ctt/Ttt	6/11	0.323865654633168	2	FACETS	0.96	0.897	1	0.96	0.897	1	CLONAL	2	TRUE	0	0.334162613740995	2		779	686	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778031	3778032	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGGG	novel	NA	P-0063799-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	149	716	0	ENST00000262367.5:c.7013_7016dup	p.Ser2340ProfsTer2	p.S2340Pfs*2	ENST00000262367	NM_004380.2	2339	ctt/ctCCCTt	31/31	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.334162613740995	2		716	878	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618451	37618459	+	inframe_deletion	In_Frame_Del	DEL	AAGCGGCAT	AAGCGGCAT	-	novel	NA	P-0063799-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	47	711	0	ENST00000447079.4:c.130_138del	p.Arg44_Lys46del	p.R44_K46del	ENST00000447079	NM_015083.1	43	AAGCGGCAT/-	1/14	0.259117430569014	2	FACETS	0.376	0.316	0.442	0.188	0.158	0.221	SUBCLONAL	1	TRUE	0	0.334162613740995	2		711	749	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11027130	11027130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063799-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	257	586	0	ENST00000327064.4:c.895G>A	p.Asp299Asn	p.D299N	ENST00000327064	NM_199141.1	299	Gat/Aat	7/16	0.323865654633168	2	FACETS	0.911	0.861	0.961	1	0.993	1	CLONAL	3	TRUE	0	0.334162613740995	2		586	563	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0063800-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	75	362	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.931	0.821	1	0.931	0.821	1	CLONAL	1	TRUE	1	0.448861997733325	2		362	359	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022592	31022592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs373221034	NA	P-0063800-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	140	597	0	ENST00000375687.4:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000375687	NM_015338.5	693	Cga/Tga	13/13	0.448861997733325	4	FACETS	0.74	0.672	0.812	0.247	0.224	0.271	SUBCLONAL	1	TRUE	1	0.448861997733325	4		597	1221	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326683	62326683	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs368747623	NA	P-0063800-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	153	611	1	ENST00000360203.5:c.3502C>T	p.Pro1168Ser	p.P1168S	ENST00000360203	NM_001283009.1	1168	Ccc/Tcc	34/35	0.448861997733325	4	FACETS	0.769	0.702	0.84	0.256	0.234	0.28	SUBCLONAL	1	TRUE	1	0.448861997733325	4		612	1284	SUCCESS
APC	324	MSKCC	GRCh37	5	112175645	112175646	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063800-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	145	537	0	ENST00000257430.4:c.4355dup	p.Pro1453ThrfsTer2	p.P1453Tfs*2	ENST00000257430	NM_000038.5	1452	gta/gTta	16/16	1	2	FACETS	0.858	0.784	0.936	0.858	0.784	0.936	CLONAL	1	TRUE	1	0.448861997733325	2		537	753	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2047238	2047238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063800-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	97	207	0	ENST00000349721.2:c.800C>T	p.Pro267Leu	p.P267L	ENST00000349721	NM_003070.3	267	cCg/cTg	5/34	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.448861997733325	2		207	347	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411872	63411873	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0063800-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	192	659	0	ENST00000330258.3:c.1293_1294dup	p.Gly432GlufsTer18	p.G432Efs*18	ENST00000330258	NM_152424.3	432	ggc/gAGgc	2/2	1	2	FACETS	0.995	0.921	1	0.995	0.921	1	CLONAL	1	TRUE	1	0.448861997733325	2		659	860	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061240	38061240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063802-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	696	570	0	ENST00000250448.2:c.749C>T	p.Ser250Phe	p.S250F	ENST00000250448	NM_004496.3	250	tCc/tTc	2/2	0.534311809316928	7	FACETS	1	0.978	1			1	CLONAL	5	FALSE	NA	0.534311809316928	7		570	1205	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615164	43615164	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063802-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	104	613	0	ENST00000355710.3:c.2578C>T	p.Gln860Ter	p.Q860*	ENST00000355710	NM_020975.4	860	Cag/Tag	14/20	0.540309722501254	1	FACETS	0.686	0.618	0.756	0.686	0.618	0.756	SUBCLONAL	1	FALSE	0	0.534311809316928	1		613	416	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186591	108186591	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063802-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	154	403	0	ENST00000278616.4:c.6048T>G	p.Asp2016Glu	p.D2016E	ENST00000278616	NM_000051.3	2016	gaT/gaG	41/63	0.540309722501254	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	0	0.534311809316928	1		403	302	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0063803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	36	331	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.847	0.698	1	0.847	0.698	1	CLONAL	1	TRUE	1	0.261510938751746	2		331	325	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0063803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	61	728	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.826	0.713	0.949	0.826	0.713	0.949	CLONAL	1	TRUE	1	0.261510938751746	2		728	565	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094384	27094429	+	frameshift_variant	Frame_Shift_Del	DEL	CTGAGGAGAAGGCCATGGGCATGACAAATCTGCCTGCTGTGGGTAG	CTGAGGAGAAGGCCATGGGCATGACAAATCTGCCTGCTGTGGGTAG	-	novel	NA	P-0063803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	71	459	0	ENST00000324856.7:c.3092_3137del	p.Thr1031ArgfsTer13	p.T1031Rfs*13	ENST00000324856	NM_006015.4	1031	aCTGAGGAGAAGGCCATGGGCATGACAAATCTGCCTGCTGTGGGTAGg/ag	11/20	1	2	FACETS	0.869	0.758	0.988	0.869	0.758	0.988	CLONAL	1	TRUE	1	0.261510938751746	2		459	625	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	88	565	4	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.86	0.761	0.965	0.86	0.761	0.965	CLONAL	1	TRUE	1	0.261510938751746	2		569	783	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809340	243809340	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0063803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	41	337	0	ENST00000263826.5:c.285-1G>A		p.X95_splice	ENST00000263826	NM_005465.4	95			1	2	FACETS	0.871	0.727	1	0.871	0.727	1	CLONAL	1	TRUE	1	0.261510938751746	2		337	360	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0063803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	96	284	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.223192394662529	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	0	0.261510938751746	2		285	354	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10796810	10796811	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1564972898	NA	P-0063803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	58	401	1	ENST00000361367.2:c.2949dup	p.Arg984ThrfsTer35	p.R984Tfs*35	ENST00000361367	NM_014633.3	981	cca/ccAa	23/25	1	2	FACETS	0.885	0.762	1	0.885	0.762	1	CLONAL	1	TRUE	1	0.261510938751746	2		402	501	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466025	69466026	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGACGTGCGGGA	novel	NA	P-0063803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	57	586	0	ENST00000227507.2:c.866_877dup	p.Asp289_Asp292dup	p.D289_D292dup	ENST00000227507	NM_053056.2	289	acc/acCGACGTGCGGGAc	5/5	1	2	FACETS	0.627	0.537	0.726	0.627	0.537	0.726	SUBCLONAL	1	TRUE	1	0.261510938751746	2		586	695	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121791	2121792	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs137854144	NA	P-0063803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	45	484	0	ENST00000219476.3:c.1959_1960del	p.Gly654LeufsTer2	p.G654Lfs*2	ENST00000219476	NM_000548.3	651	ccAGag/ccag	19/42	1	2	FACETS	0.636	0.534	0.749	0.636	0.534	0.749	SUBCLONAL	1	TRUE	1	0.261510938751746	2		484	541	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644874	67644874	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	69	514	0	ENST00000264010.4:c.143del	p.Gly48ValfsTer14	p.G48Vfs*14	ENST00000264010	NM_006565.3	47	Ggg/gg	3/12	1	2	FACETS	0.632	0.549	0.722	0.632	0.549	0.722	SUBCLONAL	1	TRUE	1	0.261510938751746	2		514	835	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645019	67645025	+	frameshift_variant	Frame_Shift_Del	DEL	TTATAAC	TTATAAC	-	novel	NA	P-0063803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	99	483	0	ENST00000264010.4:c.286_292del	p.Ile96TyrfsTer4	p.I96Yfs*4	ENST00000264010	NM_006565.3	95	aTTATAACt/at	3/12	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.261510938751746	2		483	736	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272266	15272266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1363323415	NA	P-0063803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	69	601	0	ENST00000263388.2:c.6173C>T	p.Ser2058Leu	p.S2058L	ENST00000263388	NM_000435.2	2058	tCg/tTg	33/33	1	2	FACETS	0.854	0.744	0.973	0.854	0.744	0.973	CLONAL	1	TRUE	1	0.261510938751746	2		601	618	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0063803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	56	567	3	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.566	0.484	0.656	0.566	0.484	0.656	SUBCLONAL	1	TRUE	1	0.261510938751746	2		570	757	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024614	31024614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147456014	NA	P-0063803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	69	674	0	ENST00000375687.4:c.4099G>A	p.Val1367Ile	p.V1367I	ENST00000375687	NM_015338.5	1367	Gtc/Atc	13/13	1	2	FACETS	0.709	0.617	0.809	0.709	0.617	0.809	SUBCLONAL	1	TRUE	1	0.261510938751746	2		674	744	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002728	37002728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	70	535	0	ENST00000358127.4:c.521C>T	p.Ser174Leu	p.S174L	ENST00000358127	NM_001280556.1	174	tCg/tTg	5/10	1	2	FACETS	0.903	0.788	1	0.903	0.788	1	CLONAL	1	TRUE	1	0.261510938751746	2		535	593	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435198	49435199	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755159728	NA	P-0063804-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	98	508	1	ENST00000301067.7:c.6354dup	p.Ala2119ArgfsTer36	p.A2119Rfs*36	ENST00000301067	NM_003482.3	2118	-/C	31/54	1	2	FACETS	0.613	0.55	0.678	0.613	0.55	0.678	SUBCLONAL	1	TRUE	1	0.784143330091999	2		509	408	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9928001	9928001	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs777029084	NA	P-0063804-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	189	441	0	ENST00000330684.3:c.1738A>G	p.Ser580Gly	p.S580G	ENST00000330684	NM_001134407.1	580	Agc/Ggc	8/13	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.784143330091999	2		441	463	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822166	72822166	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063804-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	266	652	0	ENST00000268489.5:c.10009G>A	p.Gly3337Ser	p.G3337S	ENST00000268489	NM_006885.3	3337	Ggc/Agc	10/10	0.784143330091999	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.784143330091999	1		652	404	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948467	54948467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063804-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	229	352	0	ENST00000312783.6:c.851C>T	p.Ser284Phe	p.S284F	ENST00000312783	NM_198436.1	284	tCc/tTc	8/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.784143330091999	2		352	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0063805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	186	409	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	0.252272543688872	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	1	0.252174899823019	4		409	562	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602856	10602856	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	49	545	0	ENST00000171111.5:c.722G>T	p.Cys241Phe	p.C241F	ENST00000171111	NM_203500.1	241	tGc/tTc	3/6	0.160836548597161	2	FACETS	0.69	0.584	0.807	0.345	0.292	0.404	SUBCLONAL	1	TRUE	0	0.252174899823019	2		545	563	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200877	67200877	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	69	565	0	ENST00000312629.5:c.870del	p.Tyr291ThrfsTer14	p.Y291Tfs*14	ENST00000312629	NM_003952.2	289	Ccc/cc	10/15	0.252272543688872	3	FACETS	0.955	0.832	1	0.478	0.416	0.545	CLONAL	1	TRUE	1	0.252174899823019	3		565	645	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212381	5212381	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372226485	NA	P-0063805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	101	765	1	ENST00000357368.4:c.4736C>T	p.Pro1579Leu	p.P1579L	ENST00000357368	NM_002850.3	1579	cCg/cTg	31/38	0.160836548597161	2	FACETS	0.852	0.765	0.943	0.852	0.765	0.943	CLONAL	2	TRUE	0	0.252174899823019	2		766	470	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073424	8073424	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	49	444	0	ENST00000377482.5:c.1235G>A	p.Arg412Lys	p.R412K	ENST00000377482	NM_018948.3	412	aGg/aAg	4/4	0.06092210319974	3	FACETS	0.779	0.659	0.91	0.389	0.329	0.455	INDETERMINATE	1	TRUE	1	0.252174899823019	3		444	562	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885650	23885650	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	100	584	0	ENST00000374561.5:c.268G>T	p.Gly90Ter	p.G90*	ENST00000374561	NM_002167.4	90	Gga/Tga	1/3	0.0815951160541779	4	FACETS	0.811	0.726	0.902	0.811	0.726	0.902	INDETERMINATE	2	TRUE	2	0.252174899823019	4		584	612	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123246892	123246892	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	36	424	0	ENST00000358487.5:c.2033G>C	p.Arg678Thr	p.R678T	ENST00000358487	NM_000141.4	678	aGa/aCa	15/18	0.111995293441651	4	FACETS	0.676	0.555	0.812	0.338	0.277	0.406	INDETERMINATE	1	TRUE	2	0.252174899823019	4		424	529	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589663	69589663	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	155	830	0	ENST00000168712.1:c.190C>G	p.Pro64Ala	p.P64A	ENST00000168712	NM_002007.2	64	Ccc/Gcc	1/3	0.252272543688872	3	FACETS	0.965	0.886	1	0.965	0.886	1	CLONAL	2	TRUE	1	0.252174899823019	3		830	717	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427509	49427510	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0063805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	103	528	0	ENST00000301067.7:c.10978_10979delinsTT	p.Gly3660Leu	p.G3660L	ENST00000301067	NM_003482.3	3660	GGg/TTg	39/54	0.252174899823019	5	FACETS	0.891	0.798	0.988	0.594	0.532	0.659	CLONAL	2	TRUE	2	0.252174899823019	5		528	632	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435018	110435018	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1255377313	NA	P-0063805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	45	557	0	ENST00000375856.3:c.3383A>C	p.Asp1128Ala	p.D1128A	ENST00000375856	NM_003749.2	1128	gAc/gCc	1/2	0.252272543688872	3	FACETS	0.65	0.546	0.766	0.325	0.273	0.383	SUBCLONAL	1	TRUE	1	0.252174899823019	3		557	618	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968651	55968651	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	144	381	0	ENST00000263923.4:c.2012G>T	p.Gly671Val	p.G671V	ENST00000263923	NM_002253.2	671	gGa/gTa	14/30	0.252272543688872	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.252174899823019	3		381	592	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968660	55968660	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	132	374	0	ENST00000263923.4:c.2003C>A	p.Thr668Lys	p.T668K	ENST00000263923	NM_002253.2	668	aCg/aAg	14/30	0.252272543688872	3	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	1	0.252174899823019	3		374	577	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048572	180048572	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs774487220	NA	P-0063805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	82	573	0	ENST00000261937.6:c.1990C>A	p.His664Asn	p.H664N	ENST00000261937	NM_182925.4	664	Cac/Aac	13/30	0.232728740284481	2	FACETS	1	0.963	1	0.612	0.541	0.688	CLONAL	1	TRUE	0	0.252174899823019	2		573	531	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30668291	30668291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	46	392	1	ENST00000376406.3:c.6221C>T	p.Ala2074Val	p.A2074V	ENST00000376406	NM_014641.2	2074	gCc/gTc	15/15	0.0815951160541779	4	FACETS	0.942	0.794	1	0.471	0.397	0.553	INDETERMINATE	1	TRUE	2	0.252174899823019	4		393	485	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971102	21971102	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	148	445	0	ENST00000304494.5:c.256G>C	p.Ala86Pro	p.A86P	ENST00000304494	NM_000077.4	86	Gcc/Ccc	2/3	0.232728740284481	2	FACETS	0.854	0.787	0.924	1	0.984	1	CLONAL	3	TRUE	0	0.252174899823019	2		445	458	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139780992	139780992	+	splice_region_variant,5_prime_UTR_variant	Splice_Region	DEL	G	G	-	novel	NA	P-0063805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	26	148	0	ENST00000247668.2:c.-29+1del		p.X10_splice	ENST00000247668	NM_021138.3	10		1/11	0.232728740284481	2	FACETS	1	0.932	1	0.726	0.582	0.886	CLONAL	1	TRUE	0	0.252174899823019	2		148	142	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245105	53245105	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	54	271	0	ENST00000375401.3:c.835G>T	p.Gly279Trp	p.G279W	ENST00000375401	NM_004187.3	279	Ggg/Tgg	7/26	0.252174899823019	2	FACETS	1	0.924	1			1	CLONAL	1	TRUE	NA	0.252174899823019	2		271	381	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410881	63410881	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	109	244	0	ENST00000330258.3:c.2286A>T	p.Glu762Asp	p.E762D	ENST00000330258	NM_152424.3	762	gaA/gaT	2/2	0.252174899823019	2	FACETS	1	0.976	1			1	CLONAL	2	TRUE	NA	0.252174899823019	2		244	350	SUCCESS
PHF6	84295	MSKCC	GRCh37	X	133547973	133547973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs794727878	NA	P-0063805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	33	154	0	ENST00000332070.3:c.706G>A	p.Ala236Thr	p.A236T	ENST00000332070	NM_032458.2	236	Gca/Aca	7/10	0.252174899823019	2	FACETS	1	0.839	1			1	CLONAL	1	TRUE	NA	0.252174899823019	2		154	255	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161990431	161990433	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	AGG	AGG	TT	novel	NA	P-0063805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	28	421	0	ENST00000366898.1:c.887_889delinsAA	p.Ser296Ter	p.S296*	ENST00000366898	NM_004562.2	296	tCCTtg/tAAtg	8/12	0.0815951160541779	4	FACETS	0.529	0.421	0.651	0.264	0.21	0.326	INDETERMINATE	1	TRUE	2	0.252174899823019	4		421	526	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0063807-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	565	404	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	0.901681546026347	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.910012832551223	2		404	619	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053312	37053312	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063807-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	417	342	0	ENST00000231790.2:c.547T>C	p.Tyr183His	p.Y183H	ENST00000231790	NM_000249.3	183	Tat/Cat	7/19	0.910012832551223	2	FACETS	0.998	0.98	1	0.998	0.98	1	CLONAL	2	TRUE	0	0.910012832551223	2		342	459	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968206	68968206	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063807-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	199	289	0	ENST00000288368.4:c.1235G>T	p.Gly412Val	p.G412V	ENST00000288368	NM_024870.2	412	gGa/gTa	10/40	1	2	FACETS	0.972	0.911	1	0.972	0.911	1	CLONAL	1	TRUE	1	0.910012832551223	2		289	450	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217909	2217909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1230117726	NA	P-0063808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	141	439	0	ENST00000398665.3:c.2683G>A	p.Glu895Lys	p.E895K	ENST00000398665	NM_032482.2	895	Gag/Aag	22/28	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.399216290575288	2		439	637	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468219	120468219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395144495	NA	P-0063808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	180	596	0	ENST00000256646.2:c.4220C>T	p.Ser1407Leu	p.S1407L	ENST00000256646	NM_024408.3	1407	tCg/tTg	25/34	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.399216290575288	2		596	887	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904977	101904977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223833	NA	P-0063808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	190	372	0	ENST00000374994.4:c.965G>A	p.Gly322Asp	p.G322D	ENST00000374994	NM_004612.2	322	gGt/gAt	5/9	0.351845511901102	2	FACETS	0.946	0.883	1	0.946	0.883	1	CLONAL	2	TRUE	0	0.399216290575288	2		372	503	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94211976	94211976	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs147771140	NA	P-0063808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	113	403	0	ENST00000323929.3:c.469A>G	p.Met157Val	p.M157V	ENST00000323929	NM_005591.3	157	Atg/Gtg	6/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.399216290575288	2		403	409	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436659	52436659	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	135	516	0	ENST00000460680.1:c.2015A>G	p.Asp672Gly	p.D672G	ENST00000460680	NM_004656.3	672	gAt/gGt	16/17	0.399216290575288	1	FACETS	0.925	0.844	1	0.925	0.844	1	CLONAL	1	TRUE	0	0.399216290575288	1		516	585	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919097	178919097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1182102297	NA	P-0063808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	35	259	0	ENST00000263967.3:c.582C>G	p.Ile194Met	p.I194M	ENST00000263967	NM_006218.2	194	atC/atG	4/21	0.252369581730322	4	FACETS	0.375	0.306	0.453	0.188	0.153	0.227	SUBCLONAL	1	TRUE	2	0.399216290575288	4		259	654	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347852	128347852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	48	344	0	ENST00000265960.3:c.653G>A	p.Gly218Glu	p.G218E	ENST00000265960	NM_001006617.1	218	gGa/gAa	5/12	0.351845511901102	2	FACETS	0.412	0.348	0.483	0.206	0.174	0.242	SUBCLONAL	1	TRUE	0	0.399216290575288	2		344	584	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0063809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	134	515	0				ENST00000310581	NM_198253.2	-/1132			0.395480396080119	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.395480396080119	3		515	364	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0063809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	68	372	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.395480396080119	2		372	309	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248552	59248552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	81	614	0	ENST00000371222.2:c.191C>T	p.Pro64Leu	p.P64L	ENST00000371222	NM_002228.3	64	cCc/cTc	1/1	1	2	FACETS	0.877	0.776	0.985	0.877	0.776	0.985	CLONAL	1	TRUE	1	0.395480396080119	2		614	467	SUCCESS
EED	8726	MSKCC	GRCh37	11	85966300	85966300	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745786094	NA	P-0063809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	56	300	0	ENST00000263360.6:c.397C>T	p.Arg133Trp	p.R133W	ENST00000263360	NM_003797.3	133	Cgg/Tgg	4/12	1	2	FACETS	0.914	0.788	1	0.914	0.788	1	CLONAL	1	TRUE	1	0.395480396080119	2		300	310	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155775	119155775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	86	563	0	ENST00000264033.4:c.1528C>T	p.Pro510Ser	p.P510S	ENST00000264033	NM_005188.3	510	Ccc/Tcc	10/16	1	2	FACETS	0.937	0.833	1	0.937	0.833	1	CLONAL	1	TRUE	1	0.395480396080119	2		563	464	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800901	18800901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767127006	NA	P-0063809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	56	358	0	ENST00000266497.5:c.4277G>A	p.Arg1426Gln	p.R1426Q	ENST00000266497		1426	cGa/cAa	31/31	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.395480396080119	2		358	271	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443637	49443637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	75	579	0	ENST00000301067.7:c.3734C>T	p.Ser1245Phe	p.S1245F	ENST00000301067	NM_003482.3	1245	tCt/tTt	11/54	1	2	FACETS	0.912	0.803	1	0.912	0.803	1	CLONAL	1	TRUE	1	0.395480396080119	2		579	416	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257809	133257809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1565981653	NA	P-0063809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	125	465	0	ENST00000320574.5:c.119G>A	p.Trp40Ter	p.W40*	ENST00000320574	NM_006231.2	40	tGg/tAg	2/49	0.351021814554741	5	FACETS	0.887	0.805	0.971			1	CLONAL	2	TRUE	NA	0.395480396080119	5		465	568	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001417	29001417	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	67	484	0	ENST00000282397.4:c.1315C>T	p.Pro439Ser	p.P439S	ENST00000282397	NM_002019.4	439	Cca/Tca	10/30	1	2	FACETS	0.913	0.798	1	0.913	0.798	1	CLONAL	1	TRUE	1	0.395480396080119	2		484	371	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028604	42028605	+	missense_variant	Missense_Mutation	DNP	AG	AG	GA	novel	NA	P-0063809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	69	537	0	ENST00000219905.7:c.4142_4143delinsGA	p.Lys1381Arg	p.K1381R	ENST00000219905	NM_001164273.1	1381	aAG/aGA	13/24	1	2	FACETS	0.875	0.765	0.992	0.875	0.765	0.992	CLONAL	1	TRUE	1	0.395480396080119	2		537	399	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857016	9857016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	79	347	0	ENST00000330684.3:c.4385C>T	p.Ser1462Phe	p.S1462F	ENST00000330684	NM_001134407.1	1462	tCt/tTt	13/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.395480396080119	2		347	327	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857379	9857379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	77	554	1	ENST00000330684.3:c.4022G>A	p.Ser1341Asn	p.S1341N	ENST00000330684	NM_001134407.1	1341	aGc/aAc	13/13	1	2	FACETS	0.943	0.832	1	0.943	0.832	1	CLONAL	1	TRUE	1	0.395480396080119	2		555	413	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288684	15288685	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	A	novel	NA	P-0063809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	71	475	0	ENST00000263388.2:c.4054_4055delinsT	p.Pro1352SerfsTer68	p.P1352Sfs*68	ENST00000263388	NM_000435.2	1352	CCc/Tc	24/33	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.395480396080119	2		475	308	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965771	18965771	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	79	605	0	ENST00000262803.5:c.1349T>G	p.Val450Gly	p.V450G	ENST00000262803	NM_002911.3	450	gTg/gGg	10/24	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.395480396080119	2		605	373	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728783	190728783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	67	388	0	ENST00000441310.2:c.2171C>T	p.Pro724Leu	p.P724L	ENST00000441310	NM_000534.4	724	cCt/cTt	10/13	1	2	FACETS	0.853	0.745	0.97	0.853	0.745	0.97	CLONAL	1	TRUE	1	0.395480396080119	2		388	397	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426789	212426789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	64	469	0	ENST00000342788.4:c.2326G>A	p.Asp776Asn	p.D776N	ENST00000342788	NM_005235.2	776	Gat/Aat	20/28	1	2	FACETS	0.946	0.825	1	0.946	0.825	1	CLONAL	1	TRUE	1	0.395480396080119	2		469	342	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944413	40944413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867675509	NA	P-0063809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	127	494	0	ENST00000373198.4:c.2089C>T	p.Pro697Ser	p.P697S	ENST00000373198	NM_133170.3	697	Ccc/Tcc	12/32	1	2	FACETS	0.765	0.699	0.833	1	0.987	1	SUBCLONAL	2	TRUE	1	0.395480396080119	2		494	420	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526942	31526942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752554295	NA	P-0063809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	68	477	0	ENST00000344624.3:c.98C>T	p.Ser33Phe	p.S33F	ENST00000344624		33	tCc/tTc	2/33	0.395480396080119	3	FACETS	0.913	0.797	1	0.457	0.398	0.519	CLONAL	1	TRUE	1	0.395480396080119	3		477	451	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671480	30671480	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	70	628	0	ENST00000376406.3:c.5480C>G	p.Pro1827Arg	p.P1827R	ENST00000376406	NM_014641.2	1827	cCc/cGc	10/15	0.395480396080119	3	FACETS	0.876	0.766	0.995	0.438	0.383	0.498	CLONAL	1	TRUE	1	0.395480396080119	3		628	484	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686887	117686887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	38	364	0	ENST00000368508.3:c.2830C>T	p.Pro944Ser	p.P944S	ENST00000368508	NM_002944.2	944	Cct/Tct	19/43	1	2	FACETS	0.658	0.546	0.782	0.658	0.546	0.782	SUBCLONAL	1	TRUE	1	0.395480396080119	2		364	292	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704661	117704661	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs745689107	NA	P-0063809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	53	350	0	ENST00000368508.3:c.2315A>C	p.Gln772Pro	p.Q772P	ENST00000368508	NM_002944.2	772	cAg/cCg	16/43	1	2	FACETS	0.921	0.791	1	0.921	0.791	1	CLONAL	1	TRUE	1	0.395480396080119	2		350	291	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509072	106509072	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372885634	NA	P-0063809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	67	635	0	ENST00000359195.3:c.1066G>A	p.Asp356Asn	p.D356N	ENST00000359195	NM_002649.2	356	Gac/Aac	2/11	1	2	FACETS	0.887	0.775	1	0.887	0.775	1	CLONAL	1	TRUE	1	0.395480396080119	2		635	382	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513378	106513378	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290751197	NA	P-0063809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	67	426	0	ENST00000359195.3:c.2282C>T	p.Ser761Phe	p.S761F	ENST00000359195	NM_002649.2	761	tCc/tTc	4/11	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.395480396080119	2		426	338	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031678	69031678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	65	379	0	ENST00000288368.4:c.3433C>T	p.Pro1145Ser	p.P1145S	ENST00000288368	NM_024870.2	1145	Ccc/Tcc	28/40	1	2	FACETS	0.939	0.819	1	0.939	0.819	1	CLONAL	1	TRUE	1	0.395480396080119	2		379	350	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471007	8471007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764232627	NA	P-0063809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	54	376	0	ENST00000356435.5:c.3492G>A	p.Met1164Ile	p.M1164I	ENST00000356435		1164	atG/atA	20/35	0.395480396080119	1	FACETS	0.921	0.795	1	0.921	0.795	1	CLONAL	1	TRUE	0	0.395480396080119	1		376	238	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485773	8485773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	48	392	0	ENST00000356435.5:c.3044C>T	p.Pro1015Leu	p.P1015L	ENST00000356435		1015	cCt/cTt	17/35	0.395480396080119	1	FACETS	0.955	0.817	1	0.955	0.817	1	CLONAL	1	TRUE	0	0.395480396080119	1		392	204	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135800978	135800978	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	49	343	0	ENST00000298552.3:c.359T>G	p.Leu120Arg	p.L120R	ENST00000298552	NM_001162426.1	120	cTc/cGc	5/23	0.395480396080119	1	FACETS	0.683	0.582	0.793	0.683	0.582	0.793	SUBCLONAL	1	TRUE	0	0.395480396080119	1		343	291	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0063810-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	208	699	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.374072317518867	2	FACETS	0.782	0.732	0.832	0.782	0.732	0.832	SUBCLONAL	2	TRUE	0	0.510744495004951	2		699	521	SUCCESS
APC	324	MSKCC	GRCh37	5	112175351	112175352	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0063810-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	158	390	0	ENST00000257430.4:c.4062_4063del	p.Ser1355PhefsTer19	p.S1355Ffs*19	ENST00000257430	NM_000038.5	1354	TTt/t	16/16	0.385436364355041	3	FACETS	0.753	0.694	0.813	0.753	0.694	0.813	SUBCLONAL	2	TRUE	1	0.510744495004951	3		390	516	SUCCESS
APC	324	MSKCC	GRCh37	5	112173835	112173838	+	frameshift_variant	Frame_Shift_Del	DEL	AGAT	AGAT	-	rs398123118	NA	P-0063810-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	68	385	0	ENST00000257430.4:c.2547_2550del	p.Asp849GlufsTer11	p.D849Efs*11	ENST00000257430	NM_000038.5	848	aaAGAT/aa	16/16	0.385436364355041	3	FACETS	0.705	0.615	0.802	0.353	0.307	0.401	SUBCLONAL	1	TRUE	1	0.510744495004951	3		385	474	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0063813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	260	728	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.462695056382759	3	FACETS	0.924	0.878	0.97	0.924	0.878	0.97	INDETERMINATE	2	TRUE	1	0.822046785403429	3		728	483	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0063813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	172	362	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.127041969379372	4	FACETS	0.978	0.925	1			1	INDETERMINATE	3	TRUE	NA	0.822046785403429	4		362	260	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0063813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	190	427	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.822046785403429	2		427	453	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107180	27107180	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0063813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	279	465	0	ENST00000324856.7:c.6791C>G	p.Ser2264Ter	p.S2264*	ENST00000324856	NM_006015.4	2264	tCa/tGa	20/20	0.791159803293233	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.822046785403429	1		465	367	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642823	3642823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1221651354	NA	P-0063813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	47	365	0	ENST00000294008.3:c.2204C>T	p.Thr735Ile	p.T735I	ENST00000294008	NM_032444.2	735	aCc/aTc	11/15	0.410955019828429	2	FACETS	0.303	0.256	0.355	0.152	0.128	0.178	INDETERMINATE	1	TRUE	0	0.822046785403429	2		365	377	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120691	94120691	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	75	343	0	ENST00000369303.4:c.360G>T	p.Lys120Asn	p.K120N	ENST00000369303	NM_004440.3	120	aaG/aaT	3/17	0.501970851798324	1	FACETS	0.315	0.278	0.355	0.315	0.278	0.355	SUBCLONAL	1	TRUE	0	0.822046785403429	1		343	341	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528696	157528696	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	181	419	0	ENST00000346085.5:c.6424del	p.Asp2142ThrfsTer3	p.D2142Tfs*3	ENST00000346085	NM_020732.3	2141	Ggg/gg	20/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.822046785403429	2		419	428	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	58	457	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	0.962	0.827	1	0.962	0.827	1	CLONAL	1	TRUE	1	0.230050540220166	2		457	524	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	106	593	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.823	0.74	0.91	1	0.985	1	CLONAL	2	TRUE	1	0.230050540220166	2		593	560	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	51	387	0	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	1	2	FACETS	0.854	0.726	0.995	0.854	0.726	0.995	CLONAL	1	TRUE	1	0.230050540220166	2		387	519	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276316	15276316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372834264	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	54	420	0	ENST00000263388.2:c.5678G>A	p.Arg1893Gln	p.R1893Q	ENST00000263388	NM_000435.2	1893	cGa/cAa	31/33	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.230050540220166	2		420	403	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256769	19256769	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	38	418	2	ENST00000162023.5:c.944del	p.Pro315GlnfsTer?	p.P315Qfs*?	ENST00000162023		315	cCa/ca	13/13	1	2	FACETS	0.733	0.606	0.874	0.733	0.606	0.874	SUBCLONAL	1	TRUE	1	0.230050540220166	2		420	451	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	80	400	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	0.229289939944994	2	FACETS	0.803	0.71	0.902	0.803	0.71	0.902	CLONAL	2	TRUE	0	0.230050540220166	2		400	433	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	37	477	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.755	0.623	0.903	0.755	0.623	0.903	CLONAL	1	TRUE	1	0.230050540220166	2		477	426	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245587	41245587	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357522	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	40	392	1	ENST00000357654.3:c.1961del	p.Lys654SerfsTer47	p.K654Sfs*47	ENST00000357654	NM_007294.3	654	aAg/ag	10/23	0.224936129352954	3	FACETS	0.746	0.619	0.887	0.373	0.309	0.444	SUBCLONAL	1	TRUE	1	0.230050540220166	3		393	520	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	62	804	1	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	0.199575688454113	1	FACETS	0.91	0.787	1	0.91	0.787	1	CLONAL	1	TRUE	0	0.230050540220166	1		805	524	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219487	133219487	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	27	828	1	ENST00000320574.5:c.4647del	p.Lys1550AsnfsTer12	p.K1550Nfs*12	ENST00000320574	NM_006231.2	1549	ccC/cc	36/49	0.229289939944994	2	FACETS	0.487	0.387	0.602	0.243	0.193	0.301	SUBCLONAL	1	TRUE	0	0.230050540220166	2		829	482	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258894	16258894	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs779191752	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	66	454	0	ENST00000375759.3:c.6159C>A	p.Asn2053Lys	p.N2053K	ENST00000375759	NM_015001.2	2053	aaC/aaA	11/15	1	2	FACETS	0.989	0.859	1	0.989	0.859	1	CLONAL	1	TRUE	1	0.230050540220166	2		454	580	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542110	187542110	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	54	732	3	ENST00000441802.2:c.5630del	p.Pro1877LeufsTer20	p.P1877Lfs*20	ENST00000441802	NM_005245.3	1877	cCt/ct	10/27	1	2	FACETS	0.921	0.787	1	0.921	0.787	1	CLONAL	1	TRUE	1	0.230050540220166	2		735	510	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745617	162745617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759124429	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	60	335	0	ENST00000367921.3:c.2032G>A	p.Asp678Asn	p.D678N	ENST00000367921	NM_006182.2	678	Gat/Aat	15/18	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.230050540220166	2		335	444	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151290	202151290	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	23	296	0	ENST00000358485.4:c.1596del	p.Lys532AsnfsTer73	p.K532Nfs*73	ENST00000358485	NM_001080125.1	530	agA/ag	9/9	1	2	FACETS	0.595	0.464	0.747	0.595	0.464	0.747	SUBCLONAL	1	TRUE	1	0.230050540220166	2		296	336	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535430	66535430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	47	365	0	ENST00000273854.3:c.31C>T	p.Arg11Cys	p.R11C	ENST00000273854	NM_004439.5	11	Cgc/Tgc	1/18	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.230050540220166	2		365	360	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347608	89347608	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	50	455	0	ENST00000301030.4:c.5342G>T	p.Arg1781Met	p.R1781M	ENST00000301030	NM_001256183.1	1781	aGg/aTg	9/13	1	2	FACETS	0.937	0.796	1	0.937	0.796	1	CLONAL	1	TRUE	1	0.230050540220166	2		455	464	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322590	30322590	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	80	320	0	ENST00000322652.5:c.1603C>T	p.Arg535Ter	p.R535*	ENST00000322652	NM_015355.2	535	Cga/Tga	14/16	0.224936129352954	3	FACETS	0.999	0.885	1	0.999	0.885	1	CLONAL	2	TRUE	1	0.230050540220166	3		320	388	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438491	52438491	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	42	344	1	ENST00000460680.1:c.1228C>T	p.Gln410Ter	p.Q410*	ENST00000460680	NM_004656.3	410	Cag/Tag	12/17	1	2	FACETS	0.913	0.763	1	0.913	0.763	1	CLONAL	1	TRUE	1	0.230050540220166	2		345	400	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391982	139391982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751048658	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	37	396	0	ENST00000277541.6:c.6209G>A	p.Arg2070Gln	p.R2070Q	ENST00000277541	NM_017617.3	2070	cGg/cAg	34/34	1	2	FACETS	0.794	0.655	0.949	0.794	0.655	0.949	CLONAL	1	TRUE	1	0.230050540220166	2		396	405	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637631	23637631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45476495	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	41	359	0	ENST00000261584.4:c.2674G>A	p.Glu892Lys	p.E892K	ENST00000261584	NM_024675.3	892	Gaa/Aaa	7/13	1	2	FACETS	0.827	0.689	0.98	0.827	0.689	0.98	CLONAL	1	TRUE	1	0.230050540220166	2		359	431	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	44	444	1	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	NA	2	FACETS	0.787	0.66	0.928			1	INDETERMINATE	1	TRUE	NA	0.230050540220166	2		445	486	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863054	56863054	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1266824391	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	40	355	2	ENST00000519728.1:c.327del	p.Glu110LysfsTer15	p.E110Kfs*15	ENST00000519728	NM_002350.3	107	acA/ac	5/13	1	2	FACETS	0.836	0.695	0.992	0.836	0.695	0.992	CLONAL	1	TRUE	1	0.230050540220166	2		357	416	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753149	42753151	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs199960550	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	69	539	4	ENST00000222329.4:c.1113_1115del	p.Ser373del	p.S373del	ENST00000222329	NM_006494.2	371	tcTTCc/tcc	4/4	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.230050540220166	2		543	547	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517326	157517326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371538726	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	24	224	0	ENST00000346085.5:c.3890C>T	p.Thr1297Met	p.T1297M	ENST00000346085	NM_020732.3	1297	aCg/aTg	16/20	1	2	FACETS	0.693	0.544	0.865	0.693	0.544	0.865	SUBCLONAL	1	TRUE	1	0.230050540220166	2		224	301	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338617	70338617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	32	314	0	ENST00000374080.3:c.13G>A	p.Gly5Arg	p.G5R	ENST00000374080		5	Ggg/Agg	1/45	1	2	FACETS	0.811	0.659	0.982	0.811	0.659	0.982	CLONAL	1	TRUE	1	0.230050540220166	2		314	343	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609689	46609689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147672406	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	48	410	0	ENST00000263734.3:c.2413G>A	p.Ala805Thr	p.A805T	ENST00000263734	NM_001430.4	805	Gcc/Acc	15/16	1	2	FACETS	0.911	0.771	1	0.911	0.771	1	CLONAL	1	TRUE	1	0.230050540220166	2		410	458	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120378	94120378	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	68	427	0	ENST00000369303.4:c.673T>C	p.Ser225Pro	p.S225P	ENST00000369303	NM_004440.3	225	Tcc/Ccc	3/17	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.230050540220166	2		427	497	SUCCESS
AR	367	MSKCC	GRCh37	X	66766384	66766384	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	25	347	0	ENST00000374690.3:c.1396G>A	p.Gly466Ser	p.G466S	ENST00000374690	NM_000044.3	466	Ggc/Agc	1/8	1	2	FACETS	0.757	0.598	0.94	0.757	0.598	0.94	CLONAL	1	TRUE	1	0.230050540220166	2		347	287	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983105	201983106	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	61	388	0	ENST00000359651.3:c.959dup	p.Asn321GlufsTer150	p.N321Efs*150	ENST00000359651		318	-/A	7/8	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.230050540220166	2		388	484	SUCCESS
AR	367	MSKCC	GRCh37	X	66766121	66766121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	66	525	0	ENST00000374690.3:c.1133C>T	p.Pro378Leu	p.P378L	ENST00000374690	NM_000044.3	378	cCg/cTg	1/8	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.230050540220166	2		525	465	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981832	63981832	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	49	495	5	ENST00000398590.3:c.2340del	p.Thr781ProfsTer11	p.T781Pfs*11	ENST00000398590	NM_001177387.1	778	ggC/gg	12/14	1	2	FACETS	0.751	0.636	0.878	0.751	0.636	0.878	SUBCLONAL	1	TRUE	1	0.230050540220166	2		500	567	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	46	507	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.93	0.784	1	0.93	0.784	1	CLONAL	1	TRUE	1	0.230050540220166	2		507	430	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777673	9777673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	56	434	0	ENST00000377346.4:c.1009G>A	p.Glu337Lys	p.E337K	ENST00000377346	NM_005026.3	337	Gag/Aag	8/24	1	2	FACETS	0.887	0.76	1	0.887	0.76	1	CLONAL	1	TRUE	1	0.230050540220166	2		434	549	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21336681	21336681	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587777613	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	50	491	1	ENST00000215739.8:c.27del	p.Gln10ArgfsTer15	p.Q10Rfs*15	ENST00000215739	NM_006767.3	7	acG/ac	1/21	1	2	FACETS	0.902	0.766	1	0.902	0.766	1	CLONAL	1	TRUE	1	0.230050540220166	2		492	482	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158465	26158467	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs766586530	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	39	666	0	ENST00000289316.2:c.73_75del	p.Lys25del	p.K25del	ENST00000289316	NM_138720.2	23	cAGAag/cag	1/2	1	2	FACETS	0.665	0.551	0.792	0.665	0.551	0.792	SUBCLONAL	1	TRUE	1	0.230050540220166	2		666	510	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1696692	1696692	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764966748	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	51	344	0	ENST00000378625.1:c.154G>A	p.Ala52Thr	p.A52T	ENST00000378625	NM_001198994.1	52	Gcc/Acc	2/14	1	2	FACETS	0.999	0.85	1	0.999	0.85	1	CLONAL	1	TRUE	1	0.230050540220166	2		344	444	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36823902	36823902	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	52	337	0	ENST00000373129.3:c.280T>C	p.Tyr94His	p.Y94H	ENST00000373129	NM_032017.1	94	Tac/Cac	5/12	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.230050540220166	2		337	411	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589842	69589842	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	68	691	0	ENST00000168712.1:c.11C>A	p.Pro4His	p.P4H	ENST00000168712	NM_002007.2	4	cCc/cAc	1/3	1	2	FACETS	0.971	0.845	1	0.971	0.845	1	CLONAL	1	TRUE	1	0.230050540220166	2		691	609	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77931370	77931370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374012460	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	43	398	0	ENST00000361507.4:c.1882C>T	p.Arg628Cys	p.R628C	ENST00000361507	NM_080491.2	628	Cgc/Tgc	9/10	1	2	FACETS	0.807	0.676	0.953	0.807	0.676	0.953	CLONAL	1	TRUE	1	0.230050540220166	2		398	463	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50782631	50782631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	64	409	0	ENST00000307179.4:c.2143C>T	p.Arg715Cys	p.R715C	ENST00000307179		715	Cgc/Tgc	14/20	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.230050540220166	2		409	492	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81927342	81927342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	30	295	0	ENST00000359376.3:c.1015G>A	p.Glu339Lys	p.E339K	ENST00000359376	NM_002661.3	339	Gag/Aag	12/33	1	2	FACETS	0.844	0.682	1	0.844	0.682	1	CLONAL	1	TRUE	1	0.230050540220166	2		295	309	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661949	29661950	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs863224835	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	105	332	0	ENST00000356175.3:c.5844_5845del	p.Arg1949SerfsTer6	p.R1949Sfs*6	ENST00000356175	NM_000267.3	1948	cAA/c	39/57	0.224936129352954	3	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	TRUE	1	0.230050540220166	3		332	494	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618542	37618544	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	novel	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	86	484	0	ENST00000447079.4:c.223_225del	p.Asp75del	p.D75del	ENST00000447079	NM_015083.1	73	tATGat/tat	1/14	0.224936129352954	3	FACETS	1	0.974	1	0.686	0.607	0.769	CLONAL	1	TRUE	1	0.230050540220166	3		484	608	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858205	40858205	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	56	316	0	ENST00000428826.2:c.1661-2A>G		p.X554_splice	ENST00000428826		554			0.224936129352954	3	FACETS	1	0.943	1	0.6	0.515	0.693	CLONAL	1	TRUE	1	0.230050540220166	3		316	452	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55704620	55704620	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758155590	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	89	329	0	ENST00000284073.2:c.683G>A	p.Arg228His	p.R228H	ENST00000284073	NM_138962.2	228	cGt/cAt	10/14	0.224936129352954	3	FACETS	1	0.921	1	1	0.921	1	CLONAL	2	TRUE	1	0.230050540220166	3		329	415	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732349	74732354	+	inframe_deletion	In_Frame_Del	DEL	GACCGG	GACCGG	-	novel	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	70	406	0	ENST00000359995.5:c.555_560del	p.Arg190_Ser191del	p.R190_S191del	ENST00000359995	NM_001195427.1	185	tcCCGGTCt/tct	2/3	0.224936129352954	3	FACETS	1	0.916	1	0.533	0.465	0.608	CLONAL	1	TRUE	1	0.230050540220166	3		406	636	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131437	202131440	+	frameshift_variant	Frame_Shift_Del	DEL	TACC	TACC	-	novel	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	40	361	0	ENST00000358485.4:c.411_414del	p.Tyr137Ter	p.Y137*	ENST00000358485	NM_001080125.1	135	atTACC/at	2/9	1	2	FACETS	0.74	0.615	0.879	0.74	0.615	0.879	SUBCLONAL	1	TRUE	1	0.230050540220166	2		361	470	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022752	31022752	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764844021	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	60	459	0	ENST00000375687.4:c.2237C>T	p.Ala746Val	p.A746V	ENST00000375687	NM_015338.5	746	gCc/gTc	13/13	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.230050540220166	2		459	518	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050315	37050316	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	rs63751101	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	45	301	0	ENST00000231790.2:c.468_469del	p.Phe156LeufsTer15	p.F156Lfs*15	ENST00000231790	NM_000249.3	155	cTT/c	6/19	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.230050540220166	2		301	331	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155983	106155983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756732317	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	53	429	0	ENST00000380013.4:c.884C>T	p.Ala295Val	p.A295V	ENST00000380013	NM_001127208.2	295	gCc/gTc	3/11	1	2	FACETS	0.793	0.676	0.921	0.793	0.676	0.921	CLONAL	1	TRUE	1	0.230050540220166	2		429	581	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534558	140534558	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	53	343	0	ENST00000288602.6:c.355A>G	p.Thr119Ala	p.T119A	ENST00000288602	NM_004333.4	119	Acc/Gcc	3/18	0.229289939944994	2	FACETS	0.958	0.818	1	0.479	0.409	0.556	CLONAL	1	TRUE	0	0.230050540220166	2		343	481	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009288	69009288	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	44	328	0	ENST00000288368.4:c.2405A>G	p.Asp802Gly	p.D802G	ENST00000288368	NM_024870.2	802	gAt/gGt	22/40	1	2	FACETS	0.922	0.774	1	0.922	0.774	1	CLONAL	1	TRUE	1	0.230050540220166	2		328	415	SUCCESS
MTAP	4507	MSKCC	GRCh37	9	21818185	21818185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	39	290	0	ENST00000380172.4:c.331G>A	p.Asp111Asn	p.D111N	ENST00000380172	NM_002451.3	111	Gat/Aat	4/8	1	2	FACETS	1	0.834	1	1	0.834	1	CLONAL	1	TRUE	1	0.230050540220166	2		290	338	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400245	139400245	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779086531	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	59	462	0	ENST00000277541.6:c.4103G>A	p.Arg1368His	p.R1368H	ENST00000277541	NM_017617.3	1368	cGc/cAc	25/34	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.230050540220166	2		462	493	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916522	39916522	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	62	357	0	ENST00000378444.4:c.4481A>G	p.Asp1494Gly	p.D1494G	ENST00000378444	NM_001123385.1	1494	gAc/gGc	11/15	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.230050540220166	2		357	448	SUCCESS
AR	367	MSKCC	GRCh37	X	66766372	66766372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	18	303	0	ENST00000374690.3:c.1384G>A	p.Gly462Ser	p.G462S	ENST00000374690	NM_000044.3	462	Ggc/Agc	1/8	1	2	FACETS	0.626	0.472	0.808	0.626	0.472	0.808	SUBCLONAL	1	TRUE	1	0.230050540220166	2		303	250	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0063815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	126	681	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.293112234949206	2	FACETS	0.934	0.852	1	0.934	0.852	1	CLONAL	2	TRUE	0	0.299140442415636	2		682	451	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0063815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	191	473	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.299140442415636	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	1	0.299140442415636	4		473	506	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345073	73345073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765260071	NA	P-0063815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	16	288	0	ENST00000377767.4:c.1724C>T	p.Thr575Met	p.T575M	ENST00000377767	NM_014953.3	575	aCg/aTg	13/21	0.299140442415636	1	FACETS	0.319	0.236	0.419	0.319	0.236	0.419	SUBCLONAL	1	TRUE	0	0.299140442415636	1		288	285	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054027	42054027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1384151590	NA	P-0063815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	17	274	0	ENST00000219905.7:c.7489C>T	p.Arg2497Trp	p.R2497W	ENST00000219905	NM_001164273.1	2497	Cgg/Tgg	21/24	0.200471359141652	3	FACETS	0.42	0.313	0.548	0.14	0.104	0.183	SUBCLONAL	1	TRUE	0	0.299140442415636	3		274	311	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440729	56440729	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	111	428	0	ENST00000407977.2:c.489G>C	p.Leu163Phe	p.L163F	ENST00000407977		163	ttG/ttC	5/10	0.299140442415636	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.299140442415636	1		428	513	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31238074	31238075	+	missense_variant	Missense_Mutation	DNP	CT	CT	AC	novel	NA	P-0063815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	14	17	0	ENST00000376228.5:c.807_808delinsGT	p.Ala270Ser	p.A270S	ENST00000376228	NM_002117.5	269	gcAGct/gcGTct	4/8	0.150082605678085	3	FACETS	0.944	0.718	1	0.944	0.718	1	INDETERMINATE	3	TRUE	0	0.299140442415636	3		17	38	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813523	32813523	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	31	327	0	ENST00000354258.4:c.2260del	p.Arg754AlafsTer105	p.R754Afs*105	ENST00000354258	NM_000593.5	754	Cgc/gc	11/11	0.150082605678085	3	FACETS	0.624	0.505	0.758	0.208	0.168	0.253	INDETERMINATE	1	TRUE	0	0.299140442415636	3		327	382	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0063816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	191	728	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.989	0.924	1	0.989	0.924	1	CLONAL	1	TRUE	1	0.84	2		728	460	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755707	57755707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746929950	NA	P-0063816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	208	482	0	ENST00000274289.3:c.80G>A	p.Gly27Glu	p.G27E	ENST00000274289	NM_006622.3	27	gGa/gAa	1/14	1	2	FACETS	0.931	0.872	0.991	0.931	0.872	0.991	CLONAL	1	TRUE	1	0.84	2		482	532	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0063816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	290	601	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	0.0938517189791355	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.84	0		601	668	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186629	108186629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224575	NA	P-0063816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	134	420	0	ENST00000278616.4:c.6086C>T	p.Pro2029Leu	p.P2029L	ENST00000278616	NM_000051.3	2029	cCc/cTc	41/63	1	2	FACETS	0.812	0.745	0.88	0.812	0.745	0.88	CLONAL	1	TRUE	1	0.84	2		420	393	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50821744	50821744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	116	258	0	ENST00000398568.2:c.2080G>A	p.Glu694Lys	p.E694K	ENST00000398568	NM_001042412.1	694	Gaa/Aaa	13/18	1	2	FACETS	0.943	0.863	1	0.943	0.863	1	CLONAL	1	TRUE	1	0.84	2		258	293	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225365205	225365205	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0063816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	226	320	0	ENST00000264414.4:c.1486-1G>A		p.X496_splice	ENST00000264414	NM_003590.4	496			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.84	2		320	529	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200069	123200070	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACTCTTGAAAACTGGAATCGAAAATGGAGACATGCCTGAGC	novel	NA	P-0063816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	13	153	0	ENST00000218089.9:c.2143_2183dup	p.Gln728HisfsTer3	p.Q728Hfs*3	ENST00000218089	NM_001042749.1	714	aaa/aaACTCTTGAAAACTGGAATCGAAAATGGAGACATGCCTGAGCa	22/35	1	1	FACETS	0.117	0.084	0.158	0.117	0.084	0.158	SUBCLONAL	1	TRUE	0	0.84	1		153	153	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465390	99465390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145300307	NA	P-0063837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	53	549	0	ENST00000268035.6:c.2215C>T	p.Arg739Trp	p.R739W	ENST00000268035	NM_000875.3	739	Cgg/Tgg	11/21	0.514052904222104	3	FACETS	1	0.883	1	0.512	0.442	0.587	CLONAL	1	TRUE	1	0.645412516746241	3		549	212	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7590694	7590694	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0063837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	234	593	1	ENST00000269305.4:c.-29+1G>A		p.X10_splice	ENST00000269305	NM_001126112.2	10			0.645412516746241	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.645412516746241	2		594	354	SUCCESS
APC	324	MSKCC	GRCh37	5	112175351	112175355	+	frameshift_variant	Frame_Shift_Del	DEL	TTTTC	TTTTC	-	novel	NA	P-0063837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	94	618	0	ENST00000257430.4:c.4062_4066del	p.Ser1355ArgfsTer18	p.S1355Rfs*18	ENST00000257430	NM_000038.5	1354	TTTTCt/t	16/16	0.645412516746241	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.645412516746241	2		618	138	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0063841-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	112	372	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		372	375	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587777894	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	59	523	0	ENST00000361445.4:c.6644C>A	p.Ser2215Tyr	p.S2215Y	ENST00000361445	NM_004958.3	2215	tCt/tAt	47/58	1	2	FACETS	0.973	0.852	1	0.973	0.852	1	CLONAL	1	TRUE	1	0.645000712039148	2		523	188	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850642	63850642	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	44	588	0	ENST00000279873.7:c.1420G>T	p.Glu474Ter	p.E474*	ENST00000279873	NM_032199.2	474	Gaa/Taa	10/10	1	2	FACETS	0.812	0.692	0.94	0.812	0.692	0.94	CLONAL	1	TRUE	1	0.645000712039148	2		588	168	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	32	445	0	ENST00000263967.3:c.333G>T	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaT	2/21	1	2	FACETS	0.91	0.756	1	0.91	0.756	1	CLONAL	1	TRUE	1	0.645000712039148	2		445	109	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	26	544	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	0.666	0.536	0.81	0.666	0.536	0.81	SUBCLONAL	1	TRUE	1	0.645000712039148	2		544	121	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478786	56478786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324972550	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	51	465	1	ENST00000267101.3:c.242G>A	p.Arg81Gln	p.R81Q	ENST00000267101	NM_001982.3	81	cGa/cAa	3/28	1	2	FACETS	0.925	0.8	1	0.925	0.8	1	CLONAL	1	TRUE	1	0.645000712039148	2		466	171	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641904	12641904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752713997	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	53	592	0	ENST00000251849.4:c.845G>A	p.Arg282Gln	p.R282Q	ENST00000251849	NM_002880.3	282	cGa/cAa	8/17	1	2	FACETS	0.939	0.815	1	0.939	0.815	1	CLONAL	1	TRUE	1	0.645000712039148	2		592	175	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098419	108098419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587779858	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	30	354	1	ENST00000278616.4:c.68G>A	p.Arg23Gln	p.R23Q	ENST00000278616	NM_000051.3	23	cGa/cAa	2/63	1	2	FACETS	0.838	0.69	0.998	0.838	0.69	0.998	CLONAL	1	TRUE	1	0.645000712039148	2		355	111	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	35	768	0	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	1	2	FACETS	0.786	0.656	0.927	0.786	0.656	0.927	CLONAL	1	TRUE	1	0.645000712039148	2		768	138	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665697	86665697	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	25	357	0	ENST00000274376.6:c.1678G>T	p.Glu560Ter	p.E560*	ENST00000274376	NM_002890.2	560	Gaa/Taa	12/25	1	2	FACETS	0.663	0.531	0.808	0.663	0.531	0.808	SUBCLONAL	1	TRUE	1	0.645000712039148	2		357	117	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570366	87570366	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	64	716	0	ENST00000277120.3:c.2106G>T	p.Glu702Asp	p.E702D	ENST00000277120		702	gaG/gaT	17/19	1	2	FACETS	0.794	0.695	0.898	0.794	0.695	0.898	SUBCLONAL	1	TRUE	1	0.645000712039148	2		716	250	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342954	225342954	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	36	395	0	ENST00000264414.4:c.2138C>A	p.Ser713Tyr	p.S713Y	ENST00000264414	NM_003590.4	713	tCt/tAt	15/16	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.645000712039148	2		395	107	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270162	198270162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	43	432	0	ENST00000335508.6:c.1274G>A	p.Arg425Gln	p.R425Q	ENST00000335508	NM_012433.2	425	cGa/cAa	10/25	1	2	FACETS	0.901	0.768	1	0.901	0.768	1	CLONAL	1	TRUE	1	0.645000712039148	2		432	148	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131412	202131412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339962485	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	33	561	0	ENST00000358485.4:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000358485	NM_001080125.1	127	cGa/cAa	2/9	1	2	FACETS	0.747	0.619	0.886	0.747	0.619	0.886	SUBCLONAL	1	TRUE	1	0.645000712039148	2		561	137	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698180	47698180	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63751411	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	24	327	0	ENST00000233146.2:c.1738G>T	p.Glu580Ter	p.E580*	ENST00000233146	NM_000251.2	580	Gaa/Taa	11/16	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.645000712039148	2		327	70	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642538	117642538	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	56	570	0	ENST00000368508.3:c.5661G>T	p.Lys1887Asn	p.K1887N	ENST00000368508	NM_002944.2	1887	aaG/aaT	35/43	1	2	FACETS	0.86	0.747	0.978	0.86	0.747	0.978	CLONAL	1	TRUE	1	0.645000712039148	2		570	202	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249847	133249847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	50	582	0	ENST00000320574.5:c.1376C>T	p.Ser459Phe	p.S459F	ENST00000320574	NM_006231.2	459	tCt/tTt	14/49	1	2	FACETS	0.923	0.797	1	0.923	0.797	1	CLONAL	1	TRUE	1	0.645000712039148	2		582	168	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467500	66467500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757521167	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	87	666	0	ENST00000273854.3:c.769G>A	p.Glu257Lys	p.E257K	ENST00000273854	NM_004439.5	257	Gaa/Aaa	3/18	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.645000712039148	2		666	269	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908873	101908873	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200595614	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	53	517	0	ENST00000374994.4:c.1237C>T	p.Arg413Ter	p.R413*	ENST00000374994	NM_004612.2	413	Cga/Tga	7/9	1	2	FACETS	0.814	0.704	0.93	0.814	0.704	0.93	CLONAL	1	TRUE	1	0.645000712039148	2		517	202	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587161	189587161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173679499	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	40	487	0	ENST00000264731.3:c.1178G>A	p.Arg393Gln	p.R393Q	ENST00000264731	NM_003722.4	393	cGa/cAa	9/14	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.645000712039148	2		487	124	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250046	53250046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1569282235	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	47	627	0	ENST00000375401.3:c.203G>A	p.Arg68Gln	p.R68Q	ENST00000375401	NM_004187.3	68	cGa/cAa	2/26	0.182132112744013	1	FACETS	0.472	0.403	0.547	0.472	0.403	0.547	INDETERMINATE	1	TRUE	0	0.645000712039148	1		627	209	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578253	28578253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144397269	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	54	590	0	ENST00000241453.7:c.2918G>A	p.Arg973Gln	p.R973Q	ENST00000241453	NM_004119.2	973	cGa/cAa	24/24	1	2	FACETS	0.713	0.615	0.816	0.713	0.615	0.816	SUBCLONAL	1	TRUE	1	0.645000712039148	2		590	235	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565543	41565543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	25	362	0	ENST00000263253.7:c.4209C>A	p.Phe1403Leu	p.F1403L	ENST00000263253	NM_001429.3	1403	ttC/ttA	26/31	1	2	FACETS	0.753	0.605	0.914	0.753	0.605	0.914	CLONAL	1	TRUE	1	0.645000712039148	2		362	103	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454670	99454670	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs780247189	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	38	578	0	ENST00000268035.6:c.1589C>T	p.Ala530Val	p.A530V	ENST00000268035	NM_000875.3	530	gCa/gTa	7/21	1	2	FACETS	0.662	0.554	0.779	0.662	0.554	0.779	SUBCLONAL	1	TRUE	1	0.645000712039148	2		578	178	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692940	89692940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746152219	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	31	516	0	ENST00000371953.3:c.424C>T	p.Arg142Trp	p.R142W	ENST00000371953	NM_000314.4	142	Cgg/Tgg	5/9	1	2	FACETS	0.645	0.529	0.772	0.645	0.529	0.772	SUBCLONAL	1	TRUE	1	0.645000712039148	2		516	149	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554452	63554452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	67	764	0	ENST00000307078.5:c.287G>A	p.Arg96Gln	p.R96Q	ENST00000307078	NM_004655.3	96	cGa/cAa	2/11	1	2	FACETS	0.923	0.814	1	0.923	0.814	1	CLONAL	1	TRUE	1	0.645000712039148	2		764	225	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796804	135796804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223799508	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	15	489	0	ENST00000298552.3:c.683G>A	p.Arg228Gln	p.R228Q	ENST00000298552	NM_001162426.1	228	cGa/cAa	8/23	1	2	FACETS	0.375	0.277	0.491	0.375	0.277	0.491	SUBCLONAL	1	TRUE	1	0.645000712039148	2		489	124	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541679	187541679	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs185406112	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	70	720	0	ENST00000441802.2:c.6061C>T	p.Arg2021Cys	p.R2021C	ENST00000441802	NM_005245.3	2021	Cgc/Tgc	10/27	1	2	FACETS	0.786	0.693	0.885	0.786	0.693	0.885	SUBCLONAL	1	TRUE	1	0.645000712039148	2		720	276	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910556	29910556	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	47	718	0	ENST00000376809.5:c.96C>A	p.Phe32Leu	p.F32L	ENST00000376809	NM_002116.7	32	ttC/ttA	2/8	1	2	FACETS	0.618	0.526	0.716	0.618	0.526	0.716	SUBCLONAL	1	TRUE	1	0.645000712039148	2		718	236	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584747	187584747	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1358297166	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	69	606	0	ENST00000441802.2:c.3286C>T	p.Arg1096Ter	p.R1096*	ENST00000441802	NM_005245.3	1096	Cga/Tga	3/27	1	2	FACETS	0.859	0.758	0.966	0.859	0.758	0.966	CLONAL	1	TRUE	1	0.645000712039148	2		606	249	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754304	57754304	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	49	510	0	ENST00000274289.3:c.547C>T	p.Arg183Ter	p.R183*	ENST00000274289	NM_006622.3	183	Cga/Tga	4/14	1	2	FACETS	0.849	0.73	0.974	0.849	0.73	0.974	CLONAL	1	TRUE	1	0.645000712039148	2		510	179	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692811	89692811	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	17	205	0	ENST00000371953.3:c.295G>T	p.Glu99Ter	p.E99*	ENST00000371953	NM_000314.4	99	Gaa/Taa	5/9	1	2	FACETS	0.976	0.756	1	0.976	0.756	1	CLONAL	1	TRUE	1	0.645000712039148	2		205	54	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193181526	193181526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	22	374	0	ENST00000367435.3:c.1073G>A	p.Arg358Gln	p.R358Q	ENST00000367435	NM_024529.4	358	cGa/cAa	13/17	1	2	FACETS	0.875	0.697	1	0.875	0.697	1	CLONAL	1	TRUE	1	0.645000712039148	2		374	78	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953214	81953214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369516453	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	81	603	0	ENST00000359376.3:c.2180G>A	p.Arg727Gln	p.R727Q	ENST00000359376	NM_002661.3	727	cGa/cAa	20/33	1	2	FACETS	0.863	0.769	0.962	0.863	0.769	0.962	CLONAL	1	TRUE	1	0.645000712039148	2		603	291	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832852	3832852	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	70	615	0	ENST00000262367.5:c.1406C>A	p.Ser469Tyr	p.S469Y	ENST00000262367	NM_004380.2	469	tCt/tAt	6/31	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.645000712039148	2		615	197	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131421	202131421	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	35	568	0	ENST00000358485.4:c.389G>T	p.Arg130Ile	p.R130I	ENST00000358485	NM_001080125.1	130	aGa/aTa	2/9	1	2	FACETS	0.748	0.624	0.884	0.748	0.624	0.884	SUBCLONAL	1	TRUE	1	0.645000712039148	2		568	145	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852659	63852659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1349220963	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	53	717	0	ENST00000279873.7:c.3437C>T	p.Ala1146Val	p.A1146V	ENST00000279873	NM_032199.2	1146	gCg/gTg	10/10	1	2	FACETS	0.806	0.697	0.921	0.806	0.697	0.921	CLONAL	1	TRUE	1	0.645000712039148	2		717	204	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515335	103515335	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	41	535	0	ENST00000355739.4:c.1836G>T	p.Glu612Asp	p.E612D	ENST00000355739	NM_000123.3	612	gaG/gaT	8/15	1	2	FACETS	0.883	0.75	1	0.883	0.75	1	CLONAL	1	TRUE	1	0.645000712039148	2		535	144	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468517	89468517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372257039	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	37	480	0	ENST00000336596.2:c.2051G>A	p.Arg684Gln	p.R684Q	ENST00000336596	NM_005233.5	684	cGa/cAa	11/17	1	2	FACETS	0.883	0.743	1	0.883	0.743	1	CLONAL	1	TRUE	1	0.645000712039148	2		480	130	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640169	3640169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769688259	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	55	635	0	ENST00000294008.3:c.3470C>T	p.Ser1157Leu	p.S1157L	ENST00000294008	NM_032444.2	1157	tCg/tTg	12/15	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.645000712039148	2		635	168	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696399	47696399	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	43	574	0	ENST00000347630.2:c.424C>A	p.Leu142Ile	p.L142I	ENST00000347630	NM_001007230.1	142	Ctt/Att	6/11	1	2	FACETS	0.813	0.691	0.943	0.813	0.691	0.943	CLONAL	1	TRUE	1	0.645000712039148	2		574	164	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520088	106520088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1484305297	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	30	364	0	ENST00000359195.3:c.2516G>A	p.Arg839His	p.R839H	ENST00000359195	NM_002649.2	839	cGc/cAc	6/11	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.645000712039148	2		364	90	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917610	151917610	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	11	319	0	ENST00000262189.6:c.3710G>A	p.Arg1237Gln	p.R1237Q	ENST00000262189	NM_170606.2	1237	cGa/cAa	23/59	1	2	FACETS	0.559	0.395	0.754	0.559	0.395	0.754	SUBCLONAL	1	TRUE	1	0.645000712039148	2		319	61	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288290	21288290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1260646700	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	77	759	0	ENST00000354336.3:c.535G>A	p.Glu179Lys	p.E179K	ENST00000354336	NM_005207.3	179	Gaa/Aaa	2/3	1	2	FACETS	0.94	0.837	1	0.94	0.837	1	CLONAL	1	TRUE	1	0.645000712039148	2		759	254	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349196	15349196	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	47	487	0	ENST00000263377.2:c.4081C>A	p.Leu1361Ile	p.L1361I	ENST00000263377	NM_058243.2	1361	Ctt/Att	20/20	1	2	FACETS	0.946	0.814	1	0.946	0.814	1	CLONAL	1	TRUE	1	0.645000712039148	2		487	154	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31466354	31466354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376262500	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	47	494	0	ENST00000344624.3:c.2401C>T	p.Arg801Cys	p.R801C	ENST00000344624		801	Cgc/Tgc	16/33	1	2	FACETS	0.928	0.798	1	0.928	0.798	1	CLONAL	1	TRUE	1	0.645000712039148	2		494	157	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389407	8389407	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	33	421	0	ENST00000356435.5:c.4211G>T	p.Gly1404Val	p.G1404V	ENST00000356435		1404	gGg/gTg	26/35	1	2	FACETS	0.832	0.691	0.983	0.832	0.691	0.983	CLONAL	1	TRUE	1	0.645000712039148	2		421	123	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79960969	79960969	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1472947441	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	24	458	0	ENST00000265081.6:c.366G>T	p.Lys122Asn	p.K122N	ENST00000265081	NM_002439.4	122	aaG/aaT	3/24	1	2	FACETS	0.752	0.602	0.916	0.752	0.602	0.916	CLONAL	1	TRUE	1	0.645000712039148	2		458	99	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978930	25978930	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	41	368	0	ENST00000435504.4:c.993C>A	p.Phe331Leu	p.F331L	ENST00000435504		331	ttC/ttA	10/13	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.645000712039148	2		368	114	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214058	36214058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1385766471	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	73	718	1	ENST00000222270.7:c.2884C>T	p.Arg962Cys	p.R962C	ENST00000222270	NM_014727.1	962	Cgc/Tgc	6/37	1	2	FACETS	0.947	0.84	1	0.947	0.84	1	CLONAL	1	TRUE	1	0.645000712039148	2		719	239	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777951	3777951	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1338620715	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	106	964	0	ENST00000262367.5:c.7097G>A	p.Arg2366Gln	p.R2366Q	ENST00000262367	NM_004380.2	2366	cGg/cAg	31/31	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.645000712039148	2		964	317	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612035	189612035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773237715	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	80	684	0	ENST00000264731.3:c.1787C>T	p.Ala596Val	p.A596V	ENST00000264731	NM_003722.4	596	gCg/gTg	14/14	1	2	FACETS	0.926	0.825	1	0.926	0.825	1	CLONAL	1	TRUE	1	0.645000712039148	2		684	268	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542870	187542870	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	21	440	0	ENST00000441802.2:c.4870G>T	p.Glu1624Ter	p.E1624*	ENST00000441802	NM_005245.3	1624	Gaa/Taa	10/27	1	2	FACETS	0.804	0.635	0.99	0.804	0.635	0.99	CLONAL	1	TRUE	1	0.645000712039148	2		440	81	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30682823	30682823	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	42	531	0	ENST00000376406.3:c.130G>T	p.Glu44Ter	p.E44*	ENST00000376406	NM_014641.2	44	Gaa/Taa	2/15	1	2	FACETS	0.696	0.589	0.812	0.696	0.589	0.812	SUBCLONAL	1	TRUE	1	0.645000712039148	2		531	187	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545817	106545817	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	23	433	0	ENST00000359195.3:c.3294G>T	p.Glu1098Asp	p.E1098D	ENST00000359195	NM_002649.2	1098	gaG/gaT	11/11	1	2	FACETS	0.767	0.611	0.938	0.767	0.611	0.938	CLONAL	1	TRUE	1	0.645000712039148	2		433	93	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645372	67645372	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1220590499	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	45	674	0	ENST00000264010.4:c.637C>T	p.Arg213Cys	p.R213C	ENST00000264010	NM_006565.3	213	Cgt/Tgt	3/12	1	2	FACETS	0.738	0.629	0.856	0.738	0.629	0.856	SUBCLONAL	1	TRUE	1	0.645000712039148	2		674	189	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438156	56438156	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs141997049	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	60	672	0	ENST00000407977.2:c.837C>A	p.Phe279Leu	p.F279L	ENST00000407977		279	ttC/ttA	7/10	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.645000712039148	2		672	174	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256264	16256264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1409348994	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	45	673	0	ENST00000375759.3:c.3529C>T	p.Arg1177Cys	p.R1177C	ENST00000375759	NM_015001.2	1177	Cgt/Tgt	11/15	1	2	FACETS	0.708	0.603	0.822	0.708	0.603	0.822	SUBCLONAL	1	TRUE	1	0.645000712039148	2		673	197	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874231	151874231	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	17	511	0	ENST00000262189.6:c.8307G>T	p.Lys2769Asn	p.K2769N	ENST00000262189	NM_170606.2	2769	aaG/aaT	38/59	1	2	FACETS	0.676	0.516	0.857	0.676	0.516	0.857	SUBCLONAL	1	TRUE	1	0.645000712039148	2		511	78	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218086	108218086	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	30	257	0	ENST00000278616.4:c.8665G>T	p.Asp2889Tyr	p.D2889Y	ENST00000278616	NM_000051.3	2889	Gat/Tat	59/63	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.645000712039148	2		257	89	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	28	380	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.851	0.696	1	0.851	0.696	1	CLONAL	1	TRUE	1	0.645000712039148	2		380	102	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087958	27087958	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	66	573	0	ENST00000324856.7:c.2245G>A	p.Asp749Asn	p.D749N	ENST00000324856	NM_006015.4	749	Gat/Aat	6/20	1	2	FACETS	0.898	0.79	1	0.898	0.79	1	CLONAL	1	TRUE	1	0.645000712039148	2		573	228	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39321394	39321394	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	50	522	0	ENST00000373001.3:c.627A>T	p.Glu209Asp	p.E209D	ENST00000373001	NM_022157.3	209	gaA/gaT	3/7	1	2	FACETS	0.975	0.844	1	0.975	0.844	1	CLONAL	1	TRUE	1	0.645000712039148	2		522	159	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218865	193218865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	22	413	0	ENST00000367435.3:c.1423G>A	p.Ala475Thr	p.A475T	ENST00000367435	NM_024529.4	475	Gcc/Acc	16/17	1	2	FACETS	0.689	0.544	0.85	0.689	0.544	0.85	SUBCLONAL	1	TRUE	1	0.645000712039148	2		413	99	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10786114	10786114	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	43	484	1	ENST00000361367.2:c.1433T>C	p.Leu478Ser	p.L478S	ENST00000361367	NM_014633.3	478	tTg/tCg	12/25	1	2	FACETS	0.988	0.845	1	0.988	0.845	1	CLONAL	1	TRUE	1	0.645000712039148	2		485	135	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178692	108178692	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	36	434	0	ENST00000278616.4:c.5743T>G	p.Tyr1915Asp	p.Y1915D	ENST00000278616	NM_000051.3	1915	Tac/Gac	38/63	1	2	FACETS	0.775	0.648	0.912	0.775	0.648	0.912	CLONAL	1	TRUE	1	0.645000712039148	2		434	144	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362018	118362018	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	41	528	0	ENST00000534358.1:c.4804C>A	p.Leu1602Ile	p.L1602I	ENST00000534358	NM_005933.3	1602	Ctt/Att	14/36	1	2	FACETS	0.826	0.7	0.96	0.826	0.7	0.96	CLONAL	1	TRUE	1	0.645000712039148	2		528	154	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446851	18446851	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	19	201	0	ENST00000266497.5:c.936A>T	p.Lys312Asn	p.K312N	ENST00000266497		312	aaA/aaT	4/31	1	2	FACETS	0.669	0.519	0.839	0.669	0.519	0.839	SUBCLONAL	1	TRUE	1	0.645000712039148	2		201	88	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431376	121431376	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	68	675	0	ENST00000257555.6:c.580C>A	p.Leu194Ile	p.L194I	ENST00000257555		194	Cta/Ata	3/10	1	2	FACETS	0.929	0.82	1	0.929	0.82	1	CLONAL	1	TRUE	1	0.645000712039148	2		675	227	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623666	28623666	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	30	538	0	ENST00000241453.7:c.891C>A	p.Tyr297Ter	p.Y297*	ENST00000241453	NM_004119.2	297	taC/taA	8/24	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.645000712039148	2		538	87	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915216	32915216	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	34	525	0	ENST00000380152.3:c.6724G>T	p.Asp2242Tyr	p.D2242Y	ENST00000380152		2242	Gat/Tat	11/27	1	2	FACETS	0.824	0.686	0.972	0.824	0.686	0.972	CLONAL	1	TRUE	1	0.645000712039148	2		525	128	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95583017	95583017	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886037672	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	23	454	0	ENST00000393063.1:c.1525C>T	p.Arg509Ter	p.R509*	ENST00000393063	NM_030621.3	509	Cga/Tga	11/28	1	2	FACETS	0.767	0.611	0.938	0.767	0.611	0.938	CLONAL	1	TRUE	1	0.645000712039148	2		454	93	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42057083	42057083	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	35	521	0	ENST00000219905.7:c.7745-1G>T		p.X2582_splice	ENST00000219905	NM_001164273.1	2582			1	2	FACETS	0.631	0.523	0.748	0.631	0.523	0.748	SUBCLONAL	1	TRUE	1	0.645000712039148	2		521	172	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990470	81990470	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	56	679	0	ENST00000359376.3:c.3741G>T	p.Glu1247Asp	p.E1247D	ENST00000359376	NM_002661.3	1247	gaG/gaT	32/33	1	2	FACETS	0.819	0.711	0.933	0.819	0.711	0.933	CLONAL	1	TRUE	1	0.645000712039148	2		679	212	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684326	29684326	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201367	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	39	451	0	ENST00000356175.3:c.7846C>T	p.Arg2616Ter	p.R2616*	ENST00000356175	NM_000267.3	2616	Cga/Tga	53/57	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.645000712039148	2		451	118	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679748	33679748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs541914273	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	40	701	0	ENST00000308377.4:c.2333G>A	p.Arg778Gln	p.R778Q	ENST00000308377	NM_152270.3	778	cGa/cAa	5/5	1	2	FACETS	0.816	0.69	0.951	0.816	0.69	0.951	CLONAL	1	TRUE	1	0.645000712039148	2		701	152	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414956	56414956	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	56	541	0	ENST00000348428.3:c.2357T>G	p.Phe786Cys	p.F786C	ENST00000348428	NM_006785.3	786	tTt/tGt	17/17	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.645000712039148	2		541	151	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754024	42754024	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	68	739	0	ENST00000222329.4:c.328A>T	p.Lys110Ter	p.K110*	ENST00000222329	NM_006494.2	110	Aaa/Taa	3/4	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.645000712039148	2		739	207	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899084	40899084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1359501262	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	131	419	0	ENST00000373198.4:c.2186G>A	p.Gly729Asp	p.G729D	ENST00000373198	NM_133170.3	729	gGc/gAc	14/32	0.645000712039148	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.645000712039148	3		419	240	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944495	40944495	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	198	719	0	ENST00000373198.4:c.2007G>T	p.Lys669Asn	p.K669N	ENST00000373198	NM_133170.3	669	aaG/aaT	12/32	0.645000712039148	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.645000712039148	3		719	380	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385137	41385137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	49	584	0	ENST00000373198.4:c.824C>T	p.Ser275Phe	p.S275F	ENST00000373198	NM_133170.3	275	tCt/tTt	6/32	0.645000712039148	3	FACETS	0.584	0.497	0.679	0.292	0.248	0.34	SUBCLONAL	1	TRUE	1	0.645000712039148	3		584	344	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054240	30054240	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	60	506	0	ENST00000338641.4:c.662A>C	p.Tyr221Ser	p.Y221S	ENST00000338641	NM_000268.3	221	tAc/tCc	7/16	1	2	FACETS	0.944	0.827	1	0.944	0.827	1	CLONAL	1	TRUE	1	0.645000712039148	2		506	197	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720982	119720982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	54	470	0	ENST00000316626.5:c.193G>T	p.Gly65Ter	p.G65*	ENST00000316626		65	Gga/Tga	2/12	1	2	FACETS	0.968	0.842	1	0.968	0.842	1	CLONAL	1	TRUE	1	0.645000712039148	2		470	173	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977957	134977957	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	47	519	0	ENST00000398015.3:c.2950G>T	p.Ala984Ser	p.A984S	ENST00000398015	NM_004441.4	984	Gca/Tca	16/16	1	2	FACETS	0.889	0.763	1	0.889	0.763	1	CLONAL	1	TRUE	1	0.645000712039148	2		519	164	SUCCESS
ATR	545	MSKCC	GRCh37	3	142232357	142232357	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	27	410	0	ENST00000350721.4:c.4627G>T	p.Glu1543Ter	p.E1543*	ENST00000350721	NM_001184.3	1543	Gaa/Taa	26/47	1	2	FACETS	0.775	0.63	0.934	0.775	0.63	0.934	CLONAL	1	TRUE	1	0.645000712039148	2		410	108	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917676	178917676	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	18	290	0	ENST00000263967.3:c.551A>C	p.Lys184Thr	p.K184T	ENST00000263967	NM_006218.2	184	aAa/aCa	3/21	1	2	FACETS	0.786	0.608	0.984	0.786	0.608	0.984	CLONAL	1	TRUE	1	0.645000712039148	2		290	71	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161361	185161361	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	45	477	0	ENST00000265026.3:c.788T>A	p.Ile263Asn	p.I263N	ENST00000265026	NM_004721.4	263	aTt/aAt	4/14	1	2	FACETS	0.856	0.732	0.988	0.856	0.732	0.988	CLONAL	1	TRUE	1	0.645000712039148	2		477	163	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979587	55979587	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	43	470	0	ENST00000263923.4:c.860A>C	p.Lys287Thr	p.K287T	ENST00000263923	NM_002253.2	287	aAa/aCa	7/30	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.645000712039148	2		470	132	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155122	106155122	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1266451196	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	68	630	0	ENST00000380013.4:c.23A>T	p.His8Leu	p.H8L	ENST00000380013	NM_001127208.2	8	cAt/cTt	3/11	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.645000712039148	2		630	201	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751140	57751140	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	41	487	0	ENST00000274289.3:c.1727C>A	p.Ser576Tyr	p.S576Y	ENST00000274289	NM_006622.3	576	tCt/tAt	12/14	1	2	FACETS	0.908	0.772	1	0.908	0.772	1	CLONAL	1	TRUE	1	0.645000712039148	2		487	140	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771187	161771187	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	63	544	0	ENST00000366898.1:c.1342A>G	p.Asn448Asp	p.N448D	ENST00000366898	NM_004562.2	448	Aac/Gac	12/12	1	2	FACETS	0.944	0.829	1	0.944	0.829	1	CLONAL	1	TRUE	1	0.645000712039148	2		544	207	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2966415	2966415	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	56	452	0	ENST00000396946.4:c.1765G>T	p.Glu589Ter	p.E589*	ENST00000396946	NM_032415.4	589	Gaa/Taa	14/25	1	2	FACETS	0.998	0.871	1	0.998	0.871	1	CLONAL	1	TRUE	1	0.645000712039148	2		452	174	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6036966	6036966	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	15	434	0	ENST00000265849.7:c.794A>C	p.Asn265Thr	p.N265T	ENST00000265849	NM_000535.5	265	aAt/aCt	7/15	1	2	FACETS	0.328	0.241	0.43	0.328	0.241	0.43	SUBCLONAL	1	TRUE	1	0.645000712039148	2		434	142	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151866290	151866290	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	18	314	0	ENST00000262189.6:c.9498T>A	p.Asn3166Lys	p.N3166K	ENST00000262189	NM_170606.2	3166	aaT/aaA	41/59	1	2	FACETS	0.607	0.465	0.767	0.607	0.465	0.767	SUBCLONAL	1	TRUE	1	0.645000712039148	2		314	92	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080231	5080231	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	20	352	0	ENST00000381652.3:c.2134C>A	p.Leu712Ile	p.L712I	ENST00000381652	NM_004972.3	712	Ctt/Att	17/25	1	2	FACETS	0.827	0.65	1	0.827	0.65	1	CLONAL	1	TRUE	1	0.645000712039148	2		352	75	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912178	127912178	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	30	436	0	ENST00000373547.4:c.692A>G	p.Lys231Arg	p.K231R	ENST00000373547	NM_002721.4	231	aAa/aGa	7/7	1	2	FACETS	0.809	0.665	0.964	0.809	0.665	0.964	CLONAL	1	TRUE	1	0.645000712039148	2		436	115	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820625	44820625	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	21	315	0	ENST00000377967.4:c.322G>T	p.Asp108Tyr	p.D108Y	ENST00000377967	NM_021140.2	108	Gat/Tat	3/29	0.182132112744013	1	FACETS	0.588	0.466	0.722	0.588	0.466	0.722	INDETERMINATE	1	TRUE	0	0.645000712039148	1		315	75	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225121	53225121	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	58	632	0	ENST00000375401.3:c.3097A>T	p.Ile1033Phe	p.I1033F	ENST00000375401	NM_004187.3	1033	Att/Ttt	20/26	0.182132112744013	1	FACETS	0.659	0.576	0.745	0.659	0.576	0.745	INDETERMINATE	1	TRUE	0	0.645000712039148	1		632	185	SUCCESS
AR	367	MSKCC	GRCh37	X	66905900	66905900	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	24	486	0	ENST00000374690.3:c.1817A>C	p.Lys606Thr	p.K606T	ENST00000374690	NM_000044.3	606	aAa/aCa	3/8	0.182132112744013	1	FACETS	0.567	0.455	0.688	0.567	0.455	0.688	INDETERMINATE	1	TRUE	0	0.645000712039148	1		486	89	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76919026	76919026	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	24	425	0	ENST00000373344.5:c.3965C>A	p.Ser1322Tyr	p.S1322Y	ENST00000373344	NM_000489.3	1322	tCt/tAt	12/35	0.182132112744013	1	FACETS	0.586	0.472	0.711	0.586	0.472	0.711	INDETERMINATE	1	TRUE	0	0.645000712039148	1		425	86	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205029	123205029	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	32	376	0	ENST00000218089.9:c.2389A>G	p.Ile797Val	p.I797V	ENST00000218089	NM_001042749.1	797	Atc/Gtc	25/35	0.182132112744013	1	FACETS	0.622	0.517	0.735	0.622	0.517	0.735	INDETERMINATE	1	TRUE	0	0.645000712039148	1		376	108	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231434	46231434	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063844-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	84	463	0	ENST00000334344.6:c.1274T>C	p.Leu425Pro	p.L425P	ENST00000334344	NM_152641.2	425	cTc/cCc	10/21	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.380134126472716	2		463	410	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061208	38061229	+	frameshift_variant	Frame_Shift_Del	DEL	GCAAGTAGCAGCCGTTCTCGAA	GCAAGTAGCAGCCGTTCTCGAA	-	novel	NA	P-0063844-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	233	678	0	ENST00000250448.2:c.760_781del	p.Phe254AlafsTer60	p.F254Afs*60	ENST00000250448	NM_004496.3	254	TTCGAGAACGGCTGCTACTTGCgc/gc	2/2	1	2	FACETS	0.812	0.76	0.865	1	0.993	1	CLONAL	2	TRUE	1	0.380134126472716	2		678	755	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061274	38061282	+	inframe_deletion	In_Frame_Del	DEL	CCGGCTTGT	CCGGCTTGT	-	novel	NA	P-0063844-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	108	695	0	ENST00000250448.2:c.707_715del	p.Asp236_Pro238del	p.D236_P238del	ENST00000250448	NM_004496.3	236	gACAAGCCGGgc/ggc	2/2	1	2	FACETS	0.71	0.637	0.788	0.71	0.637	0.788	SUBCLONAL	1	TRUE	1	0.380134126472716	2		695	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0063850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	78	623	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.15	2		623	882	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412905	49412905	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519951	NA	P-0063850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	27	690	0	ENST00000418115.1:c.118G>C	p.Glu40Gln	p.E40Q	ENST00000418115	NM_001664.2	40	Gag/Cag	2/5	1	2	FACETS	0.366	0.29	0.455	0.366	0.29	0.455	SUBCLONAL	1	TRUE	1	0.15	2		690	983	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857304	68857304	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	42	507	0	ENST00000261769.5:c.1939C>T	p.Gln647Ter	p.Q647*	ENST00000261769	NM_004360.3	647	Caa/Taa	13/16	1	2	FACETS	0.714	0.595	0.848	0.714	0.595	0.848	SUBCLONAL	1	TRUE	1	0.15	2		507	784	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0063851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	56	393	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.803	0.692	0.922	1	0.971	1	CLONAL	2	TRUE	1	0.22	2		394	317	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0063851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	124	771	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.978	0.882	1	0.978	0.882	1	CLONAL	1	TRUE	1	0.22	2		771	1153	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938447	44938447	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	78	537	0	ENST00000377967.4:c.2995G>T	p.Glu999Ter	p.E999*	ENST00000377967	NM_021140.2	999	Gaa/Taa	20/29	0.274083287363637	3	FACETS	1	0.943	1			1	CLONAL	1	TRUE	NA	0.22	3		537	698	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651906	36651906	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	166	903	0	ENST00000244741.5:c.28C>T	p.Gln10Ter	p.Q10*	ENST00000244741	NM_000389.4	10	Cag/Tag	2/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.22	2		903	1140	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38793825	38793825	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0063851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	52	640	0	ENST00000348513.6:c.157-1G>A		p.X53_splice	ENST00000348513	NM_003079.4	53			1	2	FACETS	0.605	0.513	0.705	0.605	0.513	0.705	SUBCLONAL	1	TRUE	1	0.22	2		640	782	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966758	18966758	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	53	898	0	ENST00000262803.5:c.1569C>G	p.Ser523Arg	p.S523R	ENST00000262803	NM_002911.3	523	agC/agG	12/24	1	2	FACETS	0.494	0.419	0.576	0.494	0.419	0.576	SUBCLONAL	1	TRUE	1	0.22	2		898	976	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0063855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	144	547	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.371655958972277	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.371655958972277	1		548	511	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0063855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	73	210	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.371655958972277	2		210	380	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0063855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	90	600	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.371655958972277	2		600	453	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0063855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	97	451	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.852	0.76	0.948	0.852	0.76	0.948	CLONAL	1	TRUE	1	0.371655958972277	2		451	613	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175481	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0063855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	153	678	0	ENST00000257430.4:c.4192_4193del	p.Arg1399PhefsTer9	p.R1399Ffs*9	ENST00000257430	NM_000038.5	1397	GAg/g	16/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.371655958972277	2		678	760	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106073	27106074	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0063855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	164	841	0	ENST00000324856.7:c.5688dup	p.Pro1897AlafsTer4	p.P1897Afs*4	ENST00000324856	NM_006015.4	1895	gag/gaGg	20/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.371655958972277	2		841	840	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112544	115112544	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746953122	NA	P-0063855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	112	704	0	ENST00000257566.3:c.1196C>T	p.Thr399Met	p.T399M	ENST00000257566	NM_016569.3	399	aCg/aTg	7/8	1	2	FACETS	0.967	0.872	1	0.967	0.872	1	CLONAL	1	TRUE	1	0.371655958972277	2		704	623	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643760	38643760	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	142	584	0	ENST00000299084.4:c.1230G>C	p.Leu410Phe	p.L410F	ENST00000299084	NM_152594.2	410	ttG/ttC	7/7	1	2	FACETS	0.995	0.908	1	0.995	0.908	1	CLONAL	1	TRUE	1	0.371655958972277	2		584	768	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287797	33287797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1340601101	NA	P-0063855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	142	726	0	ENST00000374542.5:c.1456G>A	p.Ala486Thr	p.A486T	ENST00000374542	NM_001141970.1	486	Gca/Aca	5/8	1	2	FACETS	0.926	0.844	1	0.926	0.844	1	CLONAL	1	TRUE	1	0.371655958972277	2		726	825	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140777	37140778	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGT	novel	NA	P-0063855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	146	684	0	ENST00000373509.5:c.615_618dup	p.Tyr207SerfsTer3	p.Y207Sfs*3	ENST00000373509	NM_002648.3	205	cga/cGAGTga	5/6	1	2	FACETS	0.874	0.797	0.954	0.874	0.797	0.954	CLONAL	1	TRUE	1	0.371655958972277	2		684	899	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0063856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	73	515	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.892	0.791	0.998	1	0.986	1	CLONAL	3	TRUE	1	0.22	2		515	248	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099364	27099364	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	53	576	0	ENST00000324856.7:c.3601A>C	p.Lys1201Gln	p.K1201Q	ENST00000324856	NM_006015.4	1201	Aag/Cag	14/20	1	2	FACETS	0.795	0.677	0.924	0.795	0.677	0.924	CLONAL	1	TRUE	1	0.22	2		576	606	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10795653	10795653	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	42	484	0	ENST00000361367.2:c.2822G>C	p.Ser941Thr	p.S941T	ENST00000361367	NM_014633.3	941	aGt/aCt	22/25	1	2	FACETS	0.576	0.48	0.683	0.576	0.48	0.683	SUBCLONAL	1	TRUE	1	0.22	2		484	663	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427647	49427647	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs758877211	NA	P-0063856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	57	586	0	ENST00000301067.7:c.10841C>A	p.Ser3614Ter	p.S3614*	ENST00000301067	NM_003482.3	3614	tCa/tAa	39/54	0.105753551322932	3	FACETS	1	0.926	1	0.562	0.482	0.648	INDETERMINATE	1	TRUE	1	0.22	3		586	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0063856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	84	916	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	1	2	FACETS	0.771	0.683	0.865	1	0.979	1	SUBCLONAL	2	TRUE	1	0.22	2		916	495	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276869	15276869	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	58	657	0	ENST00000263388.2:c.5396G>T	p.Cys1799Phe	p.C1799F	ENST00000263388	NM_000435.2	1799	tGt/tTt	30/33	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.22	2		657	468	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212417	36212417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1319017297	NA	P-0063856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	57	584	0	ENST00000222270.7:c.2168G>A	p.Gly723Glu	p.G723E	ENST00000222270	NM_014727.1	723	gGg/gAg	3/37	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.22	2		584	514	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711173	61711173	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	47	330	0	ENST00000401558.2:c.2576G>T	p.Cys859Phe	p.C859F	ENST00000401558	NM_003400.3	859	tGt/tTt	21/25	1	2	FACETS	0.909	0.768	1	0.909	0.768	1	CLONAL	1	TRUE	1	0.22	2		330	470	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098807	178098807	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	77	459	0	ENST00000397062.3:c.238A>C	p.Thr80Pro	p.T80P	ENST00000397062	NM_006164.4	80	Aca/Cca	2/5	0.105753551322932	3	FACETS	0.995	0.872	1	0.497	0.436	0.564	INDETERMINATE	1	TRUE	1	0.22	3		459	781	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660985	227660985	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	34	569	0	ENST00000305123.5:c.2470A>G	p.Arg824Gly	p.R824G	ENST00000305123	NM_005544.2	824	Agg/Ggg	1/2	1	2	FACETS	0.604	0.492	0.729	0.604	0.492	0.729	SUBCLONAL	1	TRUE	1	0.22	2		569	512	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638036	176638036	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	70	520	0	ENST00000439151.2:c.2636C>G	p.Ser879Cys	p.S879C	ENST00000439151	NM_022455.4	879	tCt/tGt	5/23	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.22	2		520	467	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323187	31323187	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	67	768	0	ENST00000412585.2:c.802T>C	p.Trp268Arg	p.W268R	ENST00000412585	NM_005514.6	268	Tgg/Cgg	4/8	0.105753551322932	3	FACETS	0.911	0.791	1	0.456	0.395	0.521	INDETERMINATE	1	TRUE	1	0.22	3		768	742	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522045	157522045	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	71	616	0	ENST00000346085.5:c.4317G>C	p.Gln1439His	p.Q1439H	ENST00000346085	NM_020732.3	1439	caG/caC	18/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.22	2		616	549	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971000	21971000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	191	640	0	ENST00000304494.5:c.358G>T	p.Glu120Ter	p.E120*	ENST00000304494	NM_000077.4	120	Gag/Tag	2/3	0.183641933945763	2	FACETS	0.9	0.836	0.966	1	0.989	1	CLONAL	3	TRUE	0	0.22	2		640	643	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413258	139413267	+	frameshift_variant	Frame_Shift_Del	DEL	TCCTCGGTAC	TCCTCGGTAC	-	novel	NA	P-0063856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	10	430	0	ENST00000277541.6:c.875_884del	p.Cys292LeufsTer7	p.C292Lfs*7	ENST00000277541	NM_017617.3	292	tGTACCGAGGAt/tt	6/34	0.3	1	FACETS	0.235	0.158	0.331	0.235	0.158	0.331	SUBCLONAL	1	TRUE	0	0.22	1		430	345	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0063893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	136	393	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.727224127076746	4	FACETS	0.902	0.831	0.974	0.451	0.415	0.487	CLONAL	2	TRUE	0	0.760431705113253	4		394	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0063893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	598	511	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.760431705113253	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.760431705113253	3		511	712	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373188	118373193	+	inframe_deletion	In_Frame_Del	DEL	GCTCCA	GCTCCA	-	novel	NA	P-0063893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	560	453	0	ENST00000534358.1:c.6582_6587del	p.Ser2195_Arg2196del	p.S2195_R2196del	ENST00000534358	NM_005933.3	2194	gGCTCCAgg/ggg	27/36	0.743827467308863	3	FACETS	0.969	0.947	0.991	0.969	0.947	0.991	CLONAL	3	TRUE	0	0.760431705113253	3		453	699	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176684035	176684035	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	80	379	0	ENST00000439151.2:c.4849G>A	p.Glu1617Lys	p.E1617K	ENST00000439151	NM_022455.4	1617	Gaa/Aaa	13/23	0.174268556858563	2	FACETS	0.959	0.856	1	0.959	0.856	1	INDETERMINATE	2	TRUE	0	0.33511680490918	2		379	249	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112035607	112035607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764943142	NA	P-0063894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	33	311	0	ENST00000368678.4:c.287G>A	p.Arg96Gln	p.R96Q	ENST00000368678		96	cGg/cAg	4/13	0.33511680490918	1	FACETS	0.937	0.772	1	0.937	0.772	1	CLONAL	1	TRUE	0	0.33511680490918	1		311	175	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617454	43617454	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1175933358	NA	P-0063894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	73	370	0	ENST00000355710.3:c.2791C>A	p.Gln931Lys	p.Q931K	ENST00000355710	NM_020975.4	931	Caa/Aaa	16/20	1	2	FACETS	0.923	0.819	1	1	0.983	1	CLONAL	2	TRUE	1	0.33511680490918	2		370	236	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541636	120541636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	48	479	0	ENST00000229340.5:c.221C>T	p.Thr74Ile	p.T74I	ENST00000229340	NM_006861.6	74	aCc/aTc	3/6	0.33511680490918	1	FACETS	0.672	0.57	0.783	0.672	0.57	0.783	SUBCLONAL	1	TRUE	0	0.33511680490918	1		479	355	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351079	89351079	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	123	487	0	ENST00000301030.4:c.1871A>G	p.Lys624Arg	p.K624R	ENST00000301030	NM_001256183.1	624	aAg/aGg	9/13	0.33511680490918	1	FACETS	1	0.976	1	1	0.992	1	CLONAL	2	TRUE	0	0.33511680490918	1		487	265	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446603	29446603	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758750767	NA	P-0063894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	44	391	0	ENST00000544604.2:c.2434G>A	p.Glu812Lys	p.E812K	ENST00000544604	NM_001206998.1	812	Gag/Aag	8/9	1	2	FACETS	0.931	0.786	1	0.931	0.786	1	CLONAL	1	TRUE	1	0.33511680490918	2		391	282	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0063895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	180	622	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.532	0.491	0.575	0.532	0.491	0.575	SUBCLONAL	1	TRUE	1	0.826887276841894	2		626	818	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0063895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	270	748	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.999	0.944	1	0.999	0.944	1	CLONAL	1	TRUE	1	0.826887276841894	2		752	654	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0063895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	106	319	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.442112263141967	2	FACETS	1	0.943	1	0.521	0.476	0.567	INDETERMINATE	1	TRUE	0	0.826887276841894	2		319	246	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	100	464	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.385	0.344	0.428	0.385	0.344	0.428	SUBCLONAL	1	TRUE	1	0.826887276841894	2		464	629	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947827	178947827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	80	180	0	ENST00000263967.3:c.2702G>T	p.Cys901Phe	p.C901F	ENST00000263967	NM_006218.2	901	tGt/tTt	19/21	1	2	FACETS	0.559	0.496	0.626	0.559	0.496	0.626	SUBCLONAL	1	TRUE	1	0.826887276841894	2		180	346	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560514	65560514	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	134	344	0	ENST00000358664.4:c.83A>G	p.His28Arg	p.H28R	ENST00000358664	NM_002382.4	28	cAt/cGt	3/5	1	2	FACETS	0.627	0.573	0.683	0.627	0.573	0.683	SUBCLONAL	1	TRUE	1	0.826887276841894	2		344	517	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900288	101900288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111854391	NA	P-0063895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	104	200	0	ENST00000374994.4:c.722C>T	p.Ser241Leu	p.S241L	ENST00000374994	NM_004612.2	241	tCg/tTg	4/9	1	2	FACETS	0.621	0.56	0.685	0.621	0.56	0.685	SUBCLONAL	1	TRUE	1	0.826887276841894	2		200	405	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699369	47699369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	65	162	0	ENST00000347630.2:c.139G>A	p.Glu47Lys	p.E47K	ENST00000347630	NM_001007230.1	47	Gaa/Aaa	4/11	1	2	FACETS	0.45	0.393	0.512	0.45	0.393	0.512	SUBCLONAL	1	TRUE	1	0.826887276841894	2		162	349	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0063895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	18	156	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	0.179	0.135	0.231	0.179	0.135	0.231	SUBCLONAL	1	TRUE	1	0.826887276841894	2		156	243	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239957	98239957	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	104	426	0	ENST00000331920.6:c.1375C>G	p.Arg459Gly	p.R459G	ENST00000331920	NM_000264.3	459	Cgc/Ggc	10/24	1	2	FACETS	0.509	0.458	0.563	0.509	0.458	0.563	SUBCLONAL	1	TRUE	1	0.826887276841894	2		426	494	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275422	115275422	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	89	199	0	ENST00000438362.2:c.991G>T	p.Gly331Ter	p.G331*	ENST00000438362	NM_001242891.1	331	Gga/Tga	10/20	1	2	FACETS	0.486	0.433	0.542	0.486	0.433	0.542	SUBCLONAL	1	TRUE	1	0.826887276841894	2		199	443	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30946591	30946592	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGA	rs752094508	NA	P-0063895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	63	303	0	ENST00000375687.4:c.25_27dup	p.Lys9dup	p.K9dup	ENST00000375687	NM_015338.5	9	cag/cAGAag	1/13	1	2	FACETS	0.437	0.38	0.498	0.437	0.38	0.498	SUBCLONAL	1	TRUE	1	0.826887276841894	2		303	349	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15809081	15809083	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0063895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	30	347	0	ENST00000307771.7:c.70_72del	p.Lys24del	p.K24del	ENST00000307771	NM_005089.3	22	ctGAAg/ctg	2/11	1	2	FACETS	0.174	0.14	0.213	0.174	0.14	0.213	SUBCLONAL	1	TRUE	1	0.826887276841894	2		347	417	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267836	7267836	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	125	472	0	ENST00000302850.5:c.172G>T	p.Gly58Ter	p.G58*	ENST00000302850	NM_000208.2	58	Gga/Tga	2/22	1	2	FACETS	0.513	0.466	0.563	0.513	0.466	0.563	SUBCLONAL	1	TRUE	1	0.826887276841894	2		472	589	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47491205	47491277	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCCAGTTCCTGCTCCTAAGACCCTGCCTGTTTCTCCTCAGGACTGAGCACGGAAGGCATCTACCGGGTCAGC	CTCCAGTTCCTGCTCCTAAGACCCTGCCTGTTTCTCCTCAGGACTGAGCACGGAAGGCATCTACCGGGTCAGC	-	novel	NA	P-0063895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	61	342	0	ENST00000404338.3:c.3827-41_3858del		p.X1276_splice	ENST00000404338	NM_004491.4	1276		3/6	1	2	FACETS	0.403	0.349	0.461	0.403	0.349	0.461	SUBCLONAL	1	TRUE	1	0.826887276841894	2		342	366	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900139	101900139	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0063895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	63	143	0	ENST00000374994.4:c.575-2A>G		p.X192_splice	ENST00000374994	NM_004612.2	192			1	2	FACETS	0.586	0.512	0.664	0.586	0.512	0.664	SUBCLONAL	1	TRUE	1	0.826887276841894	2		143	260	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820331	139820331	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	33	606	0	ENST00000247668.2:c.1484T>C	p.Ile495Thr	p.I495T	ENST00000247668	NM_021138.3	495	aTt/aCt	11/11	1	2	FACETS	0.144	0.116	0.174	0.144	0.116	0.174	SUBCLONAL	1	TRUE	1	0.826887276841894	2		606	556	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094277	27094278	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	CAGAAAT	novel	NA	P-0063895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	104	335	0	ENST00000324856.7:c.2989-2_2993dup		p.X997_splice	ENST00000324856	NM_006015.4	997			1	2	FACETS	0.561	0.506	0.62	0.561	0.506	0.62	SUBCLONAL	1	TRUE	1	0.826887276841894	2		335	448	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051598	30051598	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	183	419	0	ENST00000338641.4:c.532C>T	p.Gln178Ter	p.Q178*	ENST00000338641	NM_000268.3	178	Cag/Tag	6/16	0.524169529628487	2	FACETS	0.844	0.789	0.899	0.844	0.789	0.899	CLONAL	2	TRUE	0	0.52651116624029	2		419	412	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0063897-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	76	451	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	0.250652169034563	3	FACETS	0.975	0.86	1	0.487	0.43	0.548	INDETERMINATE	1	TRUE	1	0.521578762580218	3		451	377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063897-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	165	382	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.449807743212897	2	FACETS	0.896	0.836	0.957	0.896	0.836	0.957	CLONAL	2	TRUE	0	0.521578762580218	2		382	353	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006897	47006897	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063897-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	135	236	0	ENST00000377604.3:c.17G>A	p.Arg6His	p.R6H	ENST00000377604	NM_001204468.1	6	cGt/cAt	2/24	0.281560418664409	2	FACETS	1	0.978	1			1	INDETERMINATE	2	TRUE	NA	0.521578762580218	2		236	232	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912173	114912173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063897-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	92	370	0	ENST00000543371.1:c.1243C>T	p.Pro415Ser	p.P415S	ENST00000543371	NM_001198531.1	415	Ccc/Tcc	11/14	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.521578762580218	2		370	339	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89851272	89851272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377637236	NA	P-0063897-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	60	364	0	ENST00000389301.3:c.1460G>A	p.Arg487Gln	p.R487Q	ENST00000389301	NM_000135.2	487	cGg/cAg	15/43	0.463548995477616	4	FACETS	0.743	0.642	0.854	0.372	0.321	0.427	SUBCLONAL	1	TRUE	2	0.521578762580218	4		364	471	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331962	81331962	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs201768315	NA	P-0063897-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	154	358	0	ENST00000222390.5:c.2122C>T	p.Arg708Ter	p.R708*	ENST00000222390	NM_000601.4	708	Cga/Tga	18/18	0.521578762580218	4	FACETS	0.859	0.791	0.929	0.859	0.791	0.929	CLONAL	2	TRUE	2	0.521578762580218	4		358	523	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976742	2976742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1225008718	NA	P-0063897-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	42	536	0	ENST00000396946.4:c.1270C>T	p.Arg424Trp	p.R424W	ENST00000396946	NM_032415.4	424	Cgg/Tgg	9/25	0.346813882521827	5	FACETS	0.504	0.42	0.598	0.168	0.14	0.2	SUBCLONAL	1	TRUE	2	0.521578762580218	5		536	569	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128849189	128849189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17710891	NA	P-0063897-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	43	442	0	ENST00000249373.3:c.1417G>A	p.Asp473Asn	p.D473N	ENST00000249373	NM_005631.4	473	Gac/Aac	8/12	0.521578762580218	4	FACETS	0.414	0.346	0.49	0.207	0.173	0.245	SUBCLONAL	1	TRUE	2	0.521578762580218	4		442	606	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	68	586	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.926	0.821	1	0.926	0.821	1	CLONAL	1	TRUE	1	0.764799163977736	2		586	192	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	159	705	22	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.764799163977736	2		727	345	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519505	137519506	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs780346130	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	63	651	2	ENST00000367739.4:c.1132_1133del	p.Ser378PhefsTer6	p.S378Ffs*6	ENST00000367739	NM_000416.2	378	AGt/t	7/7	1	2	FACETS	0.832	0.732	0.937	0.832	0.732	0.937	CLONAL	1	TRUE	1	0.764799163977736	2		653	198	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	31	358	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	0.764799163977736	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.764799163977736	1		358	42	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111579	56111579	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	118	526	0	ENST00000399503.3:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000399503	NM_005921.1	60	cGg/cAg	1/20	1	2	FACETS	0.877	0.8	0.956	0.877	0.8	0.956	CLONAL	1	TRUE	1	0.764799163977736	2		526	352	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67459125	67459125	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	82	296	0	ENST00000327367.4:c.545del	p.Pro182LeufsTer4	p.P182Lfs*4	ENST00000327367	NM_005902.3	181	Ccc/cc	4/9	1	2	FACETS	0.979	0.879	1	0.979	0.879	1	CLONAL	1	TRUE	1	0.764799163977736	2		296	219	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112064	115112064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757023811	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	147	648	1	ENST00000257566.3:c.1676C>T	p.Thr559Met	p.T559M	ENST00000257566	NM_016569.3	559	aCg/aTg	7/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.764799163977736	2		649	355	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822585	72822586	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs764626362	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	91	618	1	ENST00000268489.5:c.9589dup	p.Gln3197ProfsTer42	p.Q3197Pfs*42	ENST00000268489	NM_006885.3	3197	cag/cCag	10/10	0.764799163977736	3	FACETS	0.635	0.566	0.709	0.318	0.283	0.355	SUBCLONAL	1	TRUE	1	0.764799163977736	3		619	518	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	178	440	7	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	0.702489726767294	4	FACETS	0.997	0.931	1	0.997	0.931	1	CLONAL	2	TRUE	2	0.764799163977736	4		447	412	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	31	99	0	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	0.764799163977736	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.764799163977736	1		99	40	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391404	139391404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770022692	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	131	659	0	ENST00000277541.6:c.6787C>T	p.Arg2263Trp	p.R2263W	ENST00000277541	NM_017617.3	2263	Cgg/Tgg	34/34	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.764799163977736	2		659	338	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	166	469	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.987	0.94	1	1	0.994	1	CLONAL	2	TRUE	1	0.764799163977736	2		472	220	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	43	216	3	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.764799163977736	2		219	101	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729607	41729607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	160	542	0	ENST00000242208.4:c.922C>T	p.Arg308Cys	p.R308C	ENST00000242208	NM_002192.2	308	Cgt/Tgt	3/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.764799163977736	2		542	377	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	21	370	1	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	0.764799163977736	2	FACETS	0.157	0.121	0.2	0.079	0.06	0.1	SUBCLONAL	1	TRUE	0	0.764799163977736	2		371	349	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40761117	40761117	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	120	396	0	ENST00000392038.2:c.235C>T	p.Gln79Ter	p.Q79*	ENST00000392038	NM_001626.4	79	Cag/Tag	4/14	1	2	FACETS	0.945	0.865	1	0.945	0.865	1	CLONAL	1	TRUE	1	0.764799163977736	2		396	332	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936262	78936262	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs777396934	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	104	356	0	ENST00000306801.3:c.3694G>A	p.Val1232Ile	p.V1232I	ENST00000306801	NM_020761.2	1232	Gtc/Atc	32/34	0.764799163977736	2	FACETS	1	0.969	1	0.569	0.519	0.619	CLONAL	1	TRUE	0	0.764799163977736	2		356	239	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644524	3644524	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs554989399	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	123	451	0	ENST00000294008.3:c.2090C>T	p.Thr697Met	p.T697M	ENST00000294008	NM_032444.2	697	aCg/aTg	10/15	1	2	FACETS	0.978	0.896	1	0.978	0.896	1	CLONAL	1	TRUE	1	0.764799163977736	2		451	329	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431759	49431759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1359665754	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	134	535	1	ENST00000301067.7:c.9380G>A	p.Arg3127His	p.R3127H	ENST00000301067	NM_003482.3	3127	cGc/cAc	34/54	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.764799163977736	2		536	331	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960943	15960943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs575750270	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	72	209	0	ENST00000268712.3:c.6277G>A	p.Val2093Met	p.V2093M	ENST00000268712	NM_006311.3	2093	Gtg/Atg	40/46	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.764799163977736	2		209	176	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115277091	115277091	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754952923	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	47	165	0	ENST00000438362.2:c.692G>A	p.Arg231His	p.R231H	ENST00000438362	NM_001242891.1	231	cGc/cAc	7/20	1	2	FACETS	0.938	0.812	1	0.938	0.812	1	CLONAL	1	TRUE	1	0.764799163977736	2		165	131	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651903	36651903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752557277	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	139	584	0	ENST00000244741.5:c.25C>T	p.Arg9Cys	p.R9C	ENST00000244741	NM_000389.4	9	Cgt/Tgt	2/3	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.764799163977736	2		584	356	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424840	47424841	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1365296949	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	128	410	0	ENST00000404338.3:c.2914dup	p.Arg972ProfsTer40	p.R972Pfs*40	ENST00000404338	NM_004491.4	970	tcc/tCcc	1/6	1	2	FACETS	0.959	0.88	1	0.959	0.88	1	CLONAL	1	TRUE	1	0.764799163977736	2		410	349	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231488893	231488894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs567805129	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	62	417	0	ENST00000295050.7:c.1263dup	p.Ile422TyrfsTer11	p.I422Yfs*11	ENST00000295050	NM_032018.5	419	aat/aaTt	5/5	0.764799163977736	3	FACETS	0.83	0.739	0.922	0.83	0.739	0.922	CLONAL	2	TRUE	1	0.764799163977736	3		417	135	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367532	40367532	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	221	886	1	ENST00000397332.2:c.29C>T	p.Ala10Val	p.A10V	ENST00000397332	NM_001033082.2	10	gCc/gTc	1/3	0.764799163977736	3	FACETS	1	0.977	1	0.549	0.512	0.586	CLONAL	1	TRUE	1	0.764799163977736	3		887	728	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190703	108190704	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	29	78	0	ENST00000278616.4:c.6371dup	p.Tyr2124Ter	p.Y2124*	ENST00000278616	NM_000051.3	2124	tac/tAac	44/63	0.764799163977736	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	0	0.764799163977736	2		78	36	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211112	2211112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1010982338	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	132	573	0	ENST00000398665.3:c.1366C>A	p.Pro456Thr	p.P456T	ENST00000398665	NM_032482.2	456	Cct/Act	15/28	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.764799163977736	2		573	320	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169374	99169374	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	93	393	0	ENST00000074304.5:c.1304C>T	p.Ala435Val	p.A435V	ENST00000074304	NM_001134224.1	435	gCa/gTa	15/26	1	2	FACETS	0.816	0.735	0.901	0.816	0.735	0.901	CLONAL	1	TRUE	1	0.764799163977736	2		393	298	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29442730	29442730	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	113	357	0	ENST00000544604.2:c.771G>T	p.Gln257His	p.Q257H	ENST00000544604	NM_001206998.1	257	caG/caT	6/9	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.764799163977736	2		357	267	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	908106	908106	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	98	382	0	ENST00000166345.3:c.676G>T	p.Gly226Cys	p.G226C	ENST00000166345	NM_004237.3	226	Ggc/Tgc	8/13	0.764799163977736	3	FACETS	0.952	0.857	1	0.476	0.428	0.526	CLONAL	1	TRUE	1	0.764799163977736	3		382	372	SUCCESS
APC	324	MSKCC	GRCh37	5	112174587	112174587	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	72	220	0	ENST00000257430.4:c.3298del	p.Ser1100LeufsTer26	p.S1100Lfs*26	ENST00000257430	NM_000038.5	1099	gTt/gt	16/16	1	2	FACETS	0.986	0.879	1	0.986	0.879	1	CLONAL	1	TRUE	1	0.764799163977736	2		220	191	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124491938	124491938	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770779418	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	21	103	0	ENST00000357628.3:c.937G>A	p.Asp313Asn	p.D313N	ENST00000357628	NM_015450.2	313	Gac/Aac	11/19	1	2	FACETS	0.886	0.707	1	0.886	0.707	1	CLONAL	1	TRUE	1	0.764799163977736	2		103	62	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206629	27206629	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	63	185	0	ENST00000380036.4:c.2414G>T	p.Arg805Met	p.R805M	ENST00000380036	NM_000459.3	805	aGg/aTg	15/23	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.764799163977736	2		185	153	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76949316	76949316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1569540314	NA	P-0063898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	25	46	0	ENST00000373344.5:c.481G>A	p.Gly161Arg	p.G161R	ENST00000373344	NM_000489.3	161	Gga/Aga	6/35	1	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.764799163977736	1		46	31	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459897	149459897	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063899-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	67	554	0	ENST00000286301.3:c.310C>T	p.Pro104Ser	p.P104S	ENST00000286301	NM_005211.3	104	Cct/Tct	4/22	0.0944614233287576	6	FACETS	1	0.919	1			1	INDETERMINATE	1	TRUE	NA	0.419924312069322	6		554	545	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0063901-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	8	210	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.134225729594343	3	FACETS	0.585	0.376	0.857	0.293	0.188	0.429	SUBCLONAL	1	TRUE	1	0.13	3		210	224	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063901-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	18	362	0	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	0.134225729594343	3	FACETS	0.728	0.547	0.943	0.364	0.273	0.472	CLONAL	1	TRUE	1	0.13	3		362	405	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87338594	87338594	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063901-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	40	333	0	ENST00000277120.3:c.690G>A	p.Trp230Ter	p.W230*	ENST00000277120		230	tgG/tgA	7/19	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.13	2		333	427	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872219	45872219	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	281	651	0	ENST00000391945.4:c.215A>G	p.Tyr72Cys	p.Y72C	ENST00000391945	NM_000400.3	72	tAc/tGc	4/23	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.750391738387156	2		651	677	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974695	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	154	672	1	ENST00000304494.5:c.132C>A	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	taC/taA	1/3	0.750391738387156	1	FACETS	0.641	0.593	0.69	0.641	0.593	0.69	SUBCLONAL	1	TRUE	0	0.750391738387156	1		673	400	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533552	533552	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	575	718	0	ENST00000451590.1:c.351G>C	p.Lys117Asn	p.K117N	ENST00000451590	NM_001130442.1	117	aaG/aaC	4/5	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.750391738387156	2		718	716	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041686	42041686	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs777793672	NA	P-0063906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	257	608	0	ENST00000219905.7:c.5881C>G	p.Gln1961Glu	p.Q1961E	ENST00000219905	NM_001164273.1	1961	Cag/Gag	17/24	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.750391738387156	2		608	634	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712546	43712546	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	230	604	0	ENST00000382044.4:c.4638C>G	p.Asp1546Glu	p.D1546E	ENST00000382044	NM_001141980.1	1546	gaC/gaG	21/28	1	2	FACETS	0.943	0.884	1	0.943	0.884	1	CLONAL	1	TRUE	1	0.750391738387156	2		604	650	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162094	22162094	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	200	469	0	ENST00000215832.6:c.161A>G	p.Lys54Arg	p.K54R	ENST00000215832	NM_002745.4	54	aAg/aGg	2/9	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.750391738387156	2		469	519	SUCCESS
MTAP	4507	MSKCC	GRCh37	9	21837905	21837905	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0063906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	172	323	0	ENST00000380172.4:c.348-2A>G		p.X116_splice	ENST00000380172	NM_002451.3	116			0.750391738387156	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.750391738387156	1		323	236	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0063908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	217	998	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.435731044579308	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.4567162446001	2		998	473	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947585	48947585	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	76	159	0	ENST00000267163.4:c.1172C>A	p.Ser391Ter	p.S391*	ENST00000267163	NM_000321.2	391	tCa/tAa	12/27	0.427356358490175	3	FACETS	1	0.946	1	0.725	0.65	0.802	CLONAL	2	TRUE	0	0.4567162446001	3		159	188	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899066	40899066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199994862	NA	P-0063908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	112	257	0	ENST00000373198.4:c.2204C>T	p.Pro735Leu	p.P735L	ENST00000373198	NM_133170.3	735	cCg/cTg	14/32	0.395064735380096	3	FACETS	0.933	0.85	1	0.933	0.85	1	CLONAL	2	TRUE	1	0.4567162446001	3		257	323	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539216	187539216	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	97	528	0	ENST00000441802.2:c.8524G>T	p.Gly2842Cys	p.G2842C	ENST00000441802	NM_005245.3	2842	Ggc/Tgc	10/27	0.363736857515429	3	FACETS	0.819	0.731	0.912	0.41	0.365	0.456	CLONAL	1	TRUE	1	0.4567162446001	3		528	637	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743277	162743277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	68	348	0	ENST00000367921.3:c.1747G>A	p.Glu583Lys	p.E583K	ENST00000367921	NM_006182.2	583	Gag/Aag	14/18	0.391143918509168	4	FACETS	0.869	0.758	0.989	0.29	0.252	0.33	CLONAL	1	TRUE	1	0.4567162446001	4		348	499	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44920659	44920659	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	56	115	0	ENST00000377967.4:c.1420T>A	p.Leu474Ile	p.L474I	ENST00000377967	NM_021140.2	474	Tta/Ata	14/29	1	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.4567162446001	1		115	139	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169359	11169359	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	55	358	0	ENST00000361445.4:c.7516G>C	p.Asp2506His	p.D2506H	ENST00000361445	NM_004958.3	2506	Gat/Cat	56/58	0.395064735380096	3	FACETS	0.72	0.617	0.831	0.36	0.308	0.416	SUBCLONAL	1	TRUE	1	0.4567162446001	3		358	411	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975746	26975746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	267	518	0	ENST00000381527.3:c.1254G>A	p.Met418Ile	p.M418I	ENST00000381527	NM_001260.1	418	atG/atA	12/13	0.427356358490175	3	FACETS	0.948	0.901	0.995	0.948	0.901	0.995	CLONAL	3	TRUE	0	0.4567162446001	3		518	505	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150922953	150922954	+	missense_variant	Missense_Mutation	DNP	GC	GC	CT	novel	NA	P-0063908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	52	467	1	ENST00000271640.5:c.1600_1601delinsCT	p.Ala534Leu	p.A534L	ENST00000271640	NM_001145415.1	534	GCc/CTc	13/22	0.391143918509168	4	FACETS	0.604	0.514	0.703	0.201	0.171	0.235	SUBCLONAL	1	TRUE	1	0.4567162446001	4		468	549	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975458	26975458	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	220	396	0	ENST00000381527.3:c.1084G>A	p.Glu362Lys	p.E362K	ENST00000381527	NM_001260.1	362	Gaa/Aaa	11/13	0.427356358490175	3	FACETS	0.899	0.848	0.949	0.899	0.848	0.949	CLONAL	3	TRUE	0	0.4567162446001	3		396	439	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975666	26975666	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	349	506	0	ENST00000381527.3:c.1174G>C	p.Asp392His	p.D392H	ENST00000381527	NM_001260.1	392	Gac/Cac	12/13	0.427356358490175	3	FACETS	0.957	0.915	0.998	0.957	0.915	0.998	CLONAL	3	TRUE	0	0.4567162446001	3		506	654	SUCCESS
APC	324	MSKCC	GRCh37	5	112173863	112173863	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	78	406	0	ENST00000257430.4:c.2572A>T	p.Ile858Phe	p.I858F	ENST00000257430	NM_000038.5	858	Att/Ttt	16/16	0.405454054310472	3	FACETS	0.86	0.758	0.969	0.43	0.379	0.485	CLONAL	1	TRUE	1	0.4567162446001	3		406	488	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287175	33287175	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	130	489	0	ENST00000374542.5:c.1922C>T	p.Ser641Leu	p.S641L	ENST00000374542	NM_001141970.1	641	tCa/tTa	6/8	0.395064735380096	3	FACETS	1	0.985	1	0.715	0.652	0.78	CLONAL	1	TRUE	1	0.4567162446001	3		489	489	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929003	44929004	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0063908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	80	188	0	ENST00000377967.4:c.2103_2104insG	p.His702AlafsTer28	p.H702Afs*28	ENST00000377967	NM_021140.2	701	-/G	17/29	1	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.4567162446001	1		188	208	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123199746	123199746	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	26	109	0	ENST00000218089.9:c.2046del	p.Asp682GlufsTer10	p.D682Efs*10	ENST00000218089	NM_001042749.1	682	gaT/ga	21/35	1	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.4567162446001	1		109	70	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	122	402	0	ENST00000425967.3:c.1731C>G	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaG	13/19	0.523513591187877	1	FACETS	0.722	0.673	0.769	0.722	0.673	0.769	INDETERMINATE	1	TRUE	0	0.923495972086682	1		402	197	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891466	76891466	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	66	130	0	ENST00000373344.5:c.4639G>T	p.Glu1547Ter	p.E1547*	ENST00000373344	NM_000489.3	1547	Gaa/Taa	16/35	1	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.923495972086682	1		130	74	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0063910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	89	272	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.226302194956231	3	FACETS	1	0.933	1	1	0.933	1	CLONAL	3	FALSE	0	0.226302194956231	3		272	278	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0063910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	67	558	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.170255725300714	2	FACETS	1	0.969	1	0.697	0.607	0.792	CLONAL	1	FALSE	0	0.226302194956231	2		558	425	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099382	157099408	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCTAAACCAGTTCCAGCAG	CAGCAGCAGCTAAACCAGTTCCAGCAG	-	rs1244866216	NA	P-0063910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	28	164	0	ENST00000346085.5:c.329_355del	p.Leu110_Gln118del	p.L110_Q118del	ENST00000346085	NM_020732.3	107	CAGCAGCAGCTAAACCAGTTCCAGCAG/-	1/20	1	2	FACETS	0.472	0.376	0.582	0.472	0.376	0.582	SUBCLONAL	1	FALSE	1	0.226302194956231	2		164	524	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943645	17943645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200579386	NA	P-0063911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	169	709	0	ENST00000458235.1:c.2444C>T	p.Thr815Met	p.T815M	ENST00000458235	NM_000215.3	815	aCg/aTg	18/24	0.696578159900591	3	FACETS	0.925	0.853	1	0.463	0.426	0.5	CLONAL	1	TRUE	1	0.696578159900591	3		709	707	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919257	48919258	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	33	97	0	ENST00000267163.4:c.423dup	p.Thr142TyrfsTer4	p.T142Yfs*4	ENST00000267163	NM_000321.2	141	agt/agTt	4/27	0.696578159900591	1	FACETS	0.679	0.57	0.792	0.679	0.57	0.792	SUBCLONAL	1	TRUE	0	0.696578159900591	1		97	91	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394385	162394385	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	72	492	0	ENST00000366898.1:c.683del	p.Leu228ArgfsTer31	p.L228Rfs*31	ENST00000366898	NM_004562.2	228	cTg/cg	6/12	0.291805509766135	1	FACETS	0.376	0.331	0.425	0.376	0.331	0.425	INDETERMINATE	1	TRUE	0	0.696578159900591	1		492	358	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481857	56481857	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519817	NA	P-0063912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	400	464	0	ENST00000267101.3:c.785C>A	p.Pro262His	p.P262H	ENST00000267101	NM_001982.3	262	cCt/cAt	7/28	0.381515248495634	3	FACETS	0.915	0.877	0.953	0.915	0.877	0.953	CLONAL	3	TRUE	0	0.460663400835393	3		464	778	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978892	25978892	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0063912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	99	282	0	ENST00000435504.4:c.1031C>G	p.Ser344Ter	p.S344*	ENST00000435504		344	tCa/tGa	10/13	0.235510917909067	5	FACETS	0.893	0.803	0.987	0.595	0.535	0.658	INDETERMINATE	2	TRUE	2	0.460663400835393	5		282	407	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262096	10262096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	107	399	0	ENST00000340748.4:c.2195C>T	p.Ser732Phe	p.S732F	ENST00000340748		732	tCt/tTt	23/40	0.235510917909067	5	FACETS	0.963	0.863	1	0.321	0.287	0.356	INDETERMINATE	1	TRUE	2	0.460663400835393	5		399	816	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274965	142274965	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	97	240	0	ENST00000350721.4:c.2095G>A	p.Asp699Asn	p.D699N	ENST00000350721	NM_001184.3	699	Gat/Aat	10/47	0.235510917909067	5	FACETS	1	0.981	1	0.492	0.441	0.547	INDETERMINATE	1	TRUE	2	0.460663400835393	5		240	482	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106279	27106279	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	276	609	0	ENST00000324856.7:c.5890G>T	p.Glu1964Ter	p.E1964*	ENST00000324856	NM_006015.4	1964	Gag/Tag	20/20	0.287301176285977	2	FACETS	0.773	0.729	0.818	0.773	0.729	0.818	SUBCLONAL	2	TRUE	0	0.460663400835393	2		609	775	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022340	26022340	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0063912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	180	429	0	ENST00000435504.4:c.317C>G	p.Ser106Ter	p.S106*	ENST00000435504		106	tCa/tGa	5/13	0.235510917909067	5	FACETS	0.955	0.883	1	0.637	0.589	0.686	INDETERMINATE	2	TRUE	2	0.460663400835393	5		429	692	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248085	98248085	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	329	409	0	ENST00000331920.6:c.466C>T	p.Gln156Ter	p.Q156*	ENST00000331920	NM_000264.3	156	Caa/Taa	3/24	0.460663400835393	3	FACETS	0.87	0.83	0.911	0.87	0.83	0.911	CLONAL	3	TRUE	0	0.460663400835393	3		409	673	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236107	108236107	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	260	443	0	ENST00000278616.4:c.9043G>A	p.Glu3015Lys	p.E3015K	ENST00000278616	NM_000051.3	3015	Gag/Aag	63/63	0.374949248548038	2	FACETS	0.896	0.846	0.947	0.896	0.846	0.947	CLONAL	2	TRUE	0	0.460663400835393	2		443	630	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941101	36941101	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	248	503	0	ENST00000361632.4:c.238G>C	p.Asp80His	p.D80H	ENST00000361632		80	Gat/Cat	3/16	0.287301176285977	2	FACETS	1	0.992	1	0.713	0.669	0.758	CLONAL	1	TRUE	0	0.460663400835393	2		503	755	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163315573	163315573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	110	296	0	ENST00000271452.3:c.913G>A	p.Asp305Asn	p.D305N	ENST00000271452	NM_145697.2	305	Gat/Aat	11/14	0.460663400835393	5	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.460663400835393	5		296	558	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317727	163317727	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	93	219	0	ENST00000271452.3:c.1123G>C	p.Glu375Gln	p.E375Q	ENST00000271452	NM_145697.2	375	Gag/Cag	12/14	0.460663400835393	5	FACETS	1	0.974	1			1	CLONAL	1	TRUE	NA	0.460663400835393	5		219	519	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318796	163318796	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	101	308	1	ENST00000271452.3:c.1186C>T	p.Gln396Ter	p.Q396*	ENST00000271452	NM_145697.2	396	Caa/Taa	13/14	0.460663400835393	5	FACETS	1	0.948	1			1	CLONAL	1	TRUE	NA	0.460663400835393	5		309	676	SUCCESS
FH	2271	MSKCC	GRCh37	1	241683007	241683007	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	101	385	0	ENST00000366560.3:c.16C>G	p.Arg6Gly	p.R6G	ENST00000366560	NM_000143.3	6	Cgg/Ggg	1/10	0.116932117651803	5	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.460663400835393	5		385	608	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829527	72829527	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	126	497	0	ENST00000268489.5:c.7054del	p.Tyr2352ThrfsTer24	p.Y2352Tfs*24	ENST00000268489	NM_006885.3	2352	Tac/ac	9/10	0.343987428772887	4	FACETS	0.944	0.855	1	0.472	0.427	0.52	CLONAL	1	TRUE	2	0.460663400835393	4		497	846	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630648	158630648	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	140	336	0	ENST00000263640.3:c.595C>G	p.Leu199Val	p.L199V	ENST00000263640	NM_001105.4	199	Ctg/Gtg	6/11	0.450547664393227	3	FACETS	1	0.987	1	0.743	0.681	0.808	CLONAL	1	TRUE	1	0.460663400835393	3		336	503	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187560900	187560900	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	124	290	0	ENST00000441802.2:c.3618del	p.Glu1206AspfsTer8	p.E1206Dfs*8	ENST00000441802	NM_005245.3	1206	gaA/ga	4/27	0.366039748865567	2	FACETS	0.806	0.739	0.875	0.806	0.739	0.875	CLONAL	2	TRUE	0	0.460663400835393	2		290	334	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295168	1295169	+	upstream_gene_variant	5'Flank	DNP	CG	CG	TC	novel	NA	P-0063912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	125	471	0				ENST00000310581	NM_198253.2	-/1132			0.450547664393227	3	FACETS	0.853	0.772	0.938	0.426	0.386	0.469	CLONAL	1	TRUE	1	0.460663400835393	3		471	783	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739896	41739896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755619740	NA	P-0063912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	181	446	0	ENST00000242208.4:c.77C>T	p.Ser26Phe	p.S26F	ENST00000242208	NM_002192.2	26	tCc/tTc	2/3	0.460663400835393	3	FACETS	0.825	0.765	0.886	0.825	0.765	0.886	CLONAL	2	TRUE	1	0.460663400835393	3		446	586	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2088583	2088583	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1554624100	NA	P-0063912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	108	221	0	ENST00000349721.2:c.2853G>C	p.Lys951Asn	p.K951N	ENST00000349721	NM_003070.3	951	aaG/aaC	19/34	0.402327220471683	4	FACETS	0.852	0.771	0.937			1	CLONAL	2	TRUE	NA	0.460663400835393	4		221	402	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942782	44942782	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs766711516	NA	P-0063912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	152	146	0	ENST00000377967.4:c.3362A>G	p.His1121Arg	p.H1121R	ENST00000377967	NM_021140.2	1121	cAt/cGt	23/29	0.347016225314941	2	FACETS	1	0.987	1			1	CLONAL	2	TRUE	NA	0.460663400835393	2		146	265	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039379	47039379	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	246	245	0	ENST00000377604.3:c.1002A>G	p.Ile334Met	p.I334M	ENST00000377604	NM_001204468.1	334	atA/atG	10/24	0.347016225314941	2	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.460663400835393	2		245	458	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0063913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	200	331	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.60648436976096	5	FACETS	0.907	0.851	0.964	0.907	0.851	0.964	CLONAL	3	FALSE	2	0.640291576090181	5		331	450	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0063913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	30	420	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	0.312665222563735	5	FACETS	0.329	0.264	0.402	0.11	0.088	0.134	INDETERMINATE	1	FALSE	2	0.640291576090181	5		420	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0063913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	255	413	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.587804995325827	3	FACETS	0.987	0.947	1	0.987	0.947	1	CLONAL	3	FALSE	0	0.640291576090181	3		413	355	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212761	27212761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	68	485	0	ENST00000380036.4:c.2743C>A	p.Arg915Ser	p.R915S	ENST00000380036	NM_000459.3	915	Cgc/Agc	17/23	0.346376885194159	4	FACETS	0.712	0.621	0.811	0.356	0.31	0.406	INDETERMINATE	1	FALSE	2	0.640291576090181	4		485	489	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0063914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	195	331	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.414630780775077	4	FACETS	0.94	0.879	1	0.94	0.879	1	CLONAL	3	TRUE	1	0.414630780775077	4		331	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0063914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	368	850	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.414630780775077	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.414630780775077	2		852	823	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008324	29008324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770377283	NA	P-0063914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	107	384	0	ENST00000282397.4:c.547C>T	p.Arg183Cys	p.R183C	ENST00000282397	NM_002019.4	183	Cgc/Tgc	5/30	0.322690028908664	3	FACETS	1	0.916	1	0.511	0.459	0.565	CLONAL	1	TRUE	1	0.414630780775077	3		384	610	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337651	73337651	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs745945890	NA	P-0063914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	126	310	0	ENST00000377767.4:c.2065C>T	p.Arg689Ter	p.R689*	ENST00000377767	NM_014953.3	689	Cga/Tga	16/21	0.322690028908664	3	FACETS	1	0.971	1	0.586	0.532	0.643	CLONAL	1	TRUE	1	0.414630780775077	3		310	626	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891615	151891615	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	171	287	0	ENST00000262189.6:c.4417C>T	p.Gln1473Ter	p.Q1473*	ENST00000262189	NM_170606.2	1473	Cag/Tag	29/59	0.343008906539859	4	FACETS	0.955	0.883	1	0.955	0.883	1	CLONAL	2	TRUE	2	0.414630780775077	4		287	611	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593485	48593485	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	236	367	0	ENST00000342988.3:c.1236C>A	p.Tyr412Ter	p.Y412*	ENST00000342988	NM_005359.5	412	taC/taA	10/12	0.414630780775077	2	FACETS	0.92	0.864	0.976	0.92	0.864	0.976	CLONAL	2	TRUE	0	0.414630780775077	2		367	619	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183872	10183872	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs730882032	NA	P-0063915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	104	507	0	ENST00000256474.2:c.340+1G>T		p.X114_splice	ENST00000256474	NM_000551.3	114			0.152303901084758	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	2	TRUE	0	0.152303901084758	2		507	657	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948568	71948568	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	105	706	0	ENST00000298229.2:c.3280C>A	p.His1094Asn	p.H1094N	ENST00000298229	NM_001567.3	1094	Cat/Aat	26/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.152303901084758	2		706	924	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246114	46246114	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	63	503	0	ENST00000334344.6:c.4208A>G	p.Gln1403Arg	p.Q1403R	ENST00000334344	NM_152641.2	1403	cAg/cGg	15/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.152303901084758	2		503	672	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423082	47423086	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGA	GAAGA	-	novel	NA	P-0063915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	60	556	0	ENST00000404338.3:c.1152_1156del	p.Glu384AspfsTer10	p.E384Dfs*10	ENST00000404338	NM_004491.4	384	GAAGAg/g	1/6	1	2	FACETS	0.979	0.842	1	0.979	0.842	1	CLONAL	1	TRUE	1	0.152303901084758	2		556	805	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038223	30038223	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0063915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	53	376	0	ENST00000338641.4:c.396C>G	p.Tyr132Ter	p.Y132*	ENST00000338641	NM_000268.3	132	taC/taG	4/16	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.152303901084758	2		376	592	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439854	52439855	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0063915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	105	497	0	ENST00000460680.1:c.856_857dup	p.Ala288GlnfsTer48	p.A288Qfs*48	ENST00000460680	NM_004656.3	286	aag/aaAAg	10/17	0.152303901084758	2	FACETS	0.866	0.776	0.962	0.866	0.776	0.962	CLONAL	2	TRUE	0	0.152303901084758	2		497	796	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046460	30046460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150599710	NA	P-0063916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	147	485	0	ENST00000331968.5:c.2723G>A	p.Arg908His	p.R908H	ENST00000331968	NM_002742.2	908	cGt/cAt	18/18	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.484479848115031	2		485	542	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716271	52716271	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	142	634	0	ENST00000322088.6:c.715G>C	p.Asp239His	p.D239H	ENST00000322088	NM_014225.5	239	Gat/Cat	6/15	1	2	FACETS	0.945	0.865	1	0.945	0.865	1	CLONAL	1	TRUE	1	0.484479848115031	2		634	620	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442512	52442512	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1319729011	NA	P-0063916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	149	491	0	ENST00000460680.1:c.233A>G	p.Asn78Ser	p.N78S	ENST00000460680	NM_004656.3	78	aAt/aGt	4/17	0.46611802412943	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.484479848115031	1		491	433	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564694	86564710	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGCCCCCTTTGGGGG	CCTGCCCCCTTTGGGGG	-	novel	NA	P-0063916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	166	818	0	ENST00000274376.6:c.427_443del	p.Leu143GlyfsTer9	p.L143Gfs*9	ENST00000274376	NM_002890.2	142	taCCTGCCCCCTTTGGGGGcg/tacg	1/25	0.46611802412943	1	FACETS	0.894	0.825	0.964	0.894	0.825	0.964	CLONAL	1	TRUE	0	0.484479848115031	1		818	581	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0063917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	64	340	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.965	0.85	1	0.965	0.85	1	CLONAL	1	TRUE	1	0.66	2		340	201	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0063917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	157	299	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	1	2	FACETS	0.979	0.904	1	0.979	0.904	1	CLONAL	1	TRUE	1	0.66	2		299	486	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374361	81374361	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1476385169	NA	P-0063917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	137	287	0	ENST00000222390.5:c.701G>A	p.Arg234His	p.R234H	ENST00000222390	NM_000601.4	234	cGc/cAc	6/18	1	2	FACETS	0.87	0.797	0.946	0.87	0.797	0.946	CLONAL	1	TRUE	1	0.66	2		287	477	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37628870	37628870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748613308	NA	P-0063917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	192	417	1	ENST00000249071.6:c.196C>T	p.Arg66Cys	p.R66C	ENST00000249071	NM_002872.4	66	Cgt/Tgt	3/7	1	2	FACETS	0.931	0.865	0.998	0.931	0.865	0.998	CLONAL	1	TRUE	1	0.66	2		418	625	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649940	88649940	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	141	291	0	ENST00000372037.3:c.189C>G	p.Cys63Trp	p.C63W	ENST00000372037	NM_004329.2	63	tgC/tgG	4/13	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.66	2		291	420	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55704608	55704608	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765095480	NA	P-0063917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	167	355	0	ENST00000284073.2:c.671C>T	p.Ala224Val	p.A224V	ENST00000284073	NM_138962.2	224	gCg/gTg	10/14	1	2	FACETS	0.932	0.862	1	0.932	0.862	1	CLONAL	1	TRUE	1	0.66	2		355	543	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158416	26158416	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	231	497	0	ENST00000289316.2:c.19T>C	p.Ser7Pro	p.S7P	ENST00000289316	NM_138720.2	7	Tct/Cct	1/2	1	2	FACETS	0.966	0.904	1	0.966	0.904	1	CLONAL	1	TRUE	1	0.66	2		497	725	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0063925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	140	623	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.469644282685177	2	FACETS	0.901	0.833	0.97	0.901	0.833	0.97	CLONAL	2	TRUE	0	0.469644282685177	2		623	331	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347903	347903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376143198	NA	P-0063925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	218	426	1	ENST00000262320.3:c.1603G>A	p.Val535Ile	p.V535I	ENST00000262320	NM_003502.3	535	Gtc/Atc	6/11	0.469239770275194	4	FACETS	0.855	0.797	0.914	0.855	0.797	0.914	CLONAL	2	TRUE	2	0.469644282685177	4		427	798	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352462	73352462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768054707	NA	P-0063925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	107	308	0	ENST00000377767.4:c.443C>T	p.Ala148Val	p.A148V	ENST00000377767	NM_014953.3	148	gCg/gTg	3/21	0.450042071883077	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.469644282685177	1		308	316	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28644741	28644741	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	32	253	0	ENST00000241453.7:c.52del	p.Ser18LeufsTer3	p.S18Lfs*3	ENST00000241453	NM_004119.2	18	Tct/ct	2/24	0.149732794990169	3	FACETS	0.501	0.407	0.606	0.25	0.203	0.303	INDETERMINATE	1	TRUE	1	0.469644282685177	3		253	336	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656965	45656965	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	195	370	0	ENST00000407780.3:c.191C>T	p.Thr64Ile	p.T64I	ENST00000407780	NM_001283052.1	64	aCc/aTc	3/7	0.418532207398941	3	FACETS	0.903	0.841	0.965	0.903	0.841	0.965	CLONAL	2	TRUE	1	0.469644282685177	3		370	568	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046838	180047674	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGAGCCCCGTGCAGAGGTCCAGGAGGACAGGCCTGGCAGCAGGAGGAGCGTGGGGAGCCACAGCGGGAAGACAAGGAGAGGTGGACAGGAGGCCGCGCATCCTCCCGGGTAGGTGTGACAGATACACCCTGCTCAGGGTGGCAGCAGGTGACCTCAGGGAGCCTGGGAACTGGGGACCCTGGCTGAGGTTCTAGGTACCCACGCCCACAGGGACAGGTCAGGCCAGGCGGAACTTCCTGGTGCAAGTTTTGAAAATGGAGGGATTCAGGCACTCCGGCCTGCAGCAGGTGGGTCGGGCAGGAGGTGTGGGTTGGGCAGGCTGGTGCTGGCCTCACCCAGGTGCAGCCGCTCTCGGGGGAATTCCCACTGGCTGGCATCGTAGGACAGGTATTCGCATTGCTCCTCCAGAGGCACCTCCCCGGGGTCCATGATGATGGACAGGTAGCCCGTCTTGATGTCTGCGTGGGCCGGCTGCGGGGAGGGGACAGGGAGGAGTGGGGCAGCTCACTGATTTGGCCATACCACTGTGGCTTGGGCAGAACTTTGCCCAGGACAGATGGCACTTCCTGCGGGGTTCTCAGTCAAGGAGGGGACAGAAAAAAAGACAGACAACCTCTGCGGGGTTGGAGCCCAGCGTGAAGGGCAGGGAGGCTTCCCAGGAAACAAGGCTGCCAGGTGAACTAGGGCGGGCACCTTATTCTTTATCTTAGGGGCGGCCAGGGTGGGGAAGGCCTGAGAGAGACTCCATCAGGAGCGGGGAGGGACACTCACCCTCCTCATGTTACAGAAGATGAGGAGGAGGAGGACCCAGAAGAAGACAGCGATGACGCCGGTACC	GGAGCCCCGTGCAGAGGTCCAGGAGGACAGGCCTGGCAGCAGGAGGAGCGTGGGGAGCCACAGCGGGAAGACAAGGAGAGGTGGACAGGAGGCCGCGCATCCTCCCGGGTAGGTGTGACAGATACACCCTGCTCAGGGTGGCAGCAGGTGACCTCAGGGAGCCTGGGAACTGGGGACCCTGGCTGAGGTTCTAGGTACCCACGCCCACAGGGACAGGTCAGGCCAGGCGGAACTTCCTGGTGCAAGTTTTGAAAATGGAGGGATTCAGGCACTCCGGCCTGCAGCAGGTGGGTCGGGCAGGAGGTGTGGGTTGGGCAGGCTGGTGCTGGCCTCACCCAGGTGCAGCCGCTCTCGGGGGAATTCCCACTGGCTGGCATCGTAGGACAGGTATTCGCATTGCTCCTCCAGAGGCACCTCCCCGGGGTCCATGATGATGGACAGGTAGCCCGTCTTGATGTCTGCGTGGGCCGGCTGCGGGGAGGGGACAGGGAGGAGTGGGGCAGCTCACTGATTTGGCCATACCACTGTGGCTTGGGCAGAACTTTGCCCAGGACAGATGGCACTTCCTGCGGGGTTCTCAGTCAAGGAGGGGACAGAAAAAAAGACAGACAACCTCTGCGGGGTTGGAGCCCAGCGTGAAGGGCAGGGAGGCTTCCCAGGAAACAAGGCTGCCAGGTGAACTAGGGCGGGCACCTTATTCTTTATCTTAGGGGCGGCCAGGGTGGGGAAGGCCTGAGAGAGACTCCATCAGGAGCGGGGAGGGACACTCACCCTCCTCATGTTACAGAAGATGAGGAGGAGGAGGACCCAGAAGAAGACAGCGATGACGCCGGTACC	-	novel	NA	P-0063925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	66	216	0	ENST00000261937.6:c.2341_2543-69del		p.X781_splice	ENST00000261937	NM_182925.4	781		16-17/30	0.469644282685177	5	FACETS	0.954	0.83	1	0.318	0.276	0.363	CLONAL	1	TRUE	2	0.469644282685177	5		216	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0063926-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	410	850	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.749823704453924	2	FACETS	0.894	0.865	0.922	0.894	0.865	0.922	CLONAL	2	TRUE	0	0.797523970397585	2		852	575	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105761	27105761	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0063926-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	29	502	0	ENST00000324856.7:c.5372C>G	p.Ser1791Ter	p.S1791*	ENST00000324856	NM_006015.4	1791	tCa/tGa	20/20	0.567249069902426	1	FACETS	0.079	0.063	0.098	0.079	0.063	0.098	SUBCLONAL	1	TRUE	0	0.797523970397585	1		502	552	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305354	39305354	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063926-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	34	307	0	ENST00000373001.3:c.1071C>A	p.His357Gln	p.H357Q	ENST00000373001	NM_022157.3	357	caC/caA	7/7	0.567249069902426	1	FACETS	0.094	0.076	0.114	0.094	0.076	0.114	SUBCLONAL	1	TRUE	0	0.797523970397585	1		307	544	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690802	89690802	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1114167621	NA	P-0063926-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	128	154	0	ENST00000371953.3:c.210-1G>A		p.X70_splice	ENST00000371953	NM_000314.4	70			0.749823704453924	2	FACETS	0.877	0.825	0.926	0.877	0.825	0.926	CLONAL	2	TRUE	0	0.797523970397585	2		154	183	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917731	94917731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063926-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	114	258	0	ENST00000536441.1:c.790G>A	p.Ala264Thr	p.A264T	ENST00000536441	NM_144665.3	264	Gcc/Acc	6/10	0.759743100294099	2	FACETS	0.853	0.778	0.931	0.427	0.389	0.466	CLONAL	1	TRUE	0	0.797523970397585	2		258	335	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119781	70119781	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1274036689	NA	P-0063926-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	302	379	0	ENST00000245479.2:c.788del	p.Gly263AlafsTer16	p.G263Afs*16	ENST00000245479	NM_000346.3	261	gaG/ga	3/3	0.749823704453924	2	FACETS	0.956	0.923	0.988	0.956	0.923	0.988	CLONAL	2	TRUE	0	0.797523970397585	2		379	396	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67632376	67632376	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063926-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	19	271	0	ENST00000272342.5:c.2562G>C	p.Glu854Asp	p.E854D	ENST00000272342	NM_019002.3	854	gaG/gaC	5/6	0.797523970397585	1	FACETS	0.108	0.082	0.139	0.108	0.082	0.139	SUBCLONAL	1	TRUE	0	0.797523970397585	1		271	265	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266492	198266492	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063926-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	42	260	0	ENST00000335508.6:c.2344G>C	p.Glu782Gln	p.E782Q	ENST00000335508	NM_012433.2	782	Gag/Cag	16/25	0.797523970397585	1	FACETS	0.189	0.158	0.223	0.189	0.158	0.223	SUBCLONAL	1	TRUE	0	0.797523970397585	1		260	335	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46275925	46275925	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063926-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	45	359	0	ENST00000371998.3:c.3361C>G	p.Pro1121Ala	p.P1121A	ENST00000371998		1121	Cca/Gca	18/23	0.3426535859377	3	FACETS	0.206	0.172	0.243	0.103	0.086	0.122	INDETERMINATE	1	TRUE	1	0.797523970397585	3		359	767	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163784	47163785	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063926-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	155	319	0	ENST00000409792.3:c.2341dup	p.Thr781AsnfsTer20	p.T781Nfs*20	ENST00000409792	NM_014159.6	781	acg/aAcg	3/21	0.797523970397585	1	FACETS	0.644	0.598	0.691	0.644	0.598	0.691	SUBCLONAL	1	TRUE	0	0.797523970397585	1		319	363	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590660	189590660	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063926-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	33	318	0	ENST00000264731.3:c.1225G>A	p.Glu409Lys	p.E409K	ENST00000264731	NM_003722.4	409	Gag/Aag	10/14	0.332107616621144	1	FACETS	0.1	0.081	0.121	0.1	0.081	0.121	INDETERMINATE	1	TRUE	0	0.797523970397585	1		318	498	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196571	106196571	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063926-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	50	381	0	ENST00000380013.4:c.4904G>C	p.Gly1635Ala	p.G1635A	ENST00000380013	NM_001127208.2	1635	gGa/gCa	11/11	0.797523970397585	1	FACETS	0.201	0.17	0.233	0.201	0.17	0.233	SUBCLONAL	1	TRUE	0	0.797523970397585	1		381	376	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280308	1280308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151121796	NA	P-0063926-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	182	453	0	ENST00000310581.5:c.1915G>A	p.Val639Ile	p.V639I	ENST00000310581	NM_198253.2	639	Gtc/Atc	4/16	0.44745011005427	3	FACETS	0.761	0.703	0.821	0.38	0.351	0.411	INDETERMINATE	1	TRUE	1	0.797523970397585	3		453	839	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504315	149504315	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063926-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	30	274	0	ENST00000261799.4:c.1887G>C	p.Met629Ile	p.M629I	ENST00000261799	NM_002609.3	629	atG/atC	13/23	0.716163927254379	1	FACETS	0.141	0.114	0.173	0.141	0.114	0.173	SUBCLONAL	1	TRUE	0	0.797523970397585	1		274	320	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624413	140624422	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCGGCGCC	CGCCGGCGCC	-	novel	NA	P-0063926-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	223	265	0	ENST00000288602.6:c.82_91del	p.Gly28ProfsTer23	p.G28Pfs*23	ENST00000288602	NM_004333.4	28	GGCGCCGGCGcc/cc	1/18	0.317254784323351	2	FACETS	0.764	0.726	0.802	0.764	0.726	0.802	INDETERMINATE	2	TRUE	0	0.797523970397585	2		265	366	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090832	5090832	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063926-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	47	270	0	ENST00000381652.3:c.2980G>C	p.Asp994His	p.D994H	ENST00000381652	NM_004972.3	994	Gat/Cat	22/25	1	2	FACETS	0.255	0.215	0.299	0.255	0.215	0.299	SUBCLONAL	1	TRUE	1	0.797523970397585	2		270	462	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0063928-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	53	331	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.773	0.664	0.891	1	0.968	1	SUBCLONAL	2	TRUE	1	0.23	2		331	298	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0063928-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	34	453	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.976	0.8	1	0.976	0.8	1	CLONAL	1	TRUE	1	0.23	2		453	303	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17743036	17743036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063928-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	35	638	0	ENST00000250003.3:c.944C>T	p.Pro315Leu	p.P315L	ENST00000250003	NM_002478.4	315	cCg/cTg	3/3	1	2	FACETS	0.643	0.527	0.774	0.643	0.527	0.774	SUBCLONAL	1	TRUE	1	0.23	2		638	473	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123692	11123692	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063928-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	51	535	0	ENST00000358026.2:c.2342T>C	p.Met781Thr	p.M781T	ENST00000358026	NM_001128849.1	781	aTg/aCg	16/36	1	2	FACETS	0.926	0.788	1	0.926	0.788	1	CLONAL	1	TRUE	1	0.23	2		535	479	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056181	27056181	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	210	455	0	ENST00000324856.7:c.1177C>T	p.Gln393Ter	p.Q393*	ENST00000324856	NM_006015.4	393	Cag/Tag	2/20	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.715609256632039	2		455	441	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	84	523	0				ENST00000310581	NM_198253.2	-/1132			0.432928263335547	5	FACETS	0.958	0.859	1	0.639	0.572	0.708	CLONAL	2	TRUE	2	0.715609256632039	5		523	254	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271831	15271831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779902629	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	188	842	0	ENST00000263388.2:c.6608C>T	p.Ser2203Phe	p.S2203F	ENST00000263388	NM_000435.2	2203	tCc/tTc	33/33	0.258530526141651	3	FACETS	0.876	0.821	0.932	0.876	0.821	0.932	INDETERMINATE	2	TRUE	1	0.715609256632039	3		842	407	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074431	8074431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1231758887	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	68	425	0	ENST00000377482.5:c.228G>A	p.Met76Ile	p.M76I	ENST00000377482	NM_018948.3	76	atG/atA	4/4	0.266281854889008	3	FACETS	0.717	0.627	0.812	0.358	0.313	0.406	INDETERMINATE	1	TRUE	1	0.715609256632039	3		425	360	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259714	11259714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	28	462	0	ENST00000361445.4:c.3991G>A	p.Glu1331Lys	p.E1331K	ENST00000361445	NM_004958.3	1331	Gaa/Aaa	27/58	0.541897497507236	1	FACETS	0.173	0.138	0.212	0.173	0.138	0.212	SUBCLONAL	1	TRUE	0	0.715609256632039	1		462	291	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023667	27023667	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	106	657	0	ENST00000324856.7:c.773C>T	p.Ser258Phe	p.S258F	ENST00000324856	NM_006015.4	258	tCc/tTc	1/20	NA	2	FACETS	1	0.924	1			1	INDETERMINATE	1	TRUE	NA	0.715609256632039	2		657	291	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46597517	46597517	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	54	297	0	ENST00000262741.5:c.106+2T>A		p.X36_splice	ENST00000262741	NM_003629.3	36			1	2	FACETS	0.576	0.496	0.662	0.576	0.496	0.662	SUBCLONAL	1	TRUE	1	0.715609256632039	2		297	262	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699376	117699376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771030019	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	94	500	0	ENST00000369458.3:c.265G>A	p.Glu89Lys	p.E89K	ENST00000369458	NM_024626.3	89	Gag/Aag	3/6	0.137737741889326	4	FACETS	0.767	0.683	0.855	0.256	0.227	0.285	INDETERMINATE	1	TRUE	1	0.715609256632039	4		500	588	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150915462	150915462	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	68	377	0	ENST00000271640.5:c.808G>C	p.Asp270His	p.D270H	ENST00000271640	NM_001145415.1	270	Gat/Cat	7/22	0.579163399967209	4	FACETS	0.684	0.596	0.778	0.228	0.198	0.26	SUBCLONAL	1	TRUE	1	0.715609256632039	4		377	477	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150935062	150935062	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	27	388	0	ENST00000271640.5:c.3159-1G>C		p.X1053_splice	ENST00000271640	NM_001145415.1	1053			0.579163399967209	4	FACETS	0.29	0.23	0.358	0.097	0.076	0.12	SUBCLONAL	1	TRUE	1	0.715609256632039	4		388	447	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163313556	163313556	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	79	197	0	ENST00000271452.3:c.703G>C	p.Glu235Gln	p.E235Q	ENST00000271452	NM_145697.2	235	Gaa/Caa	10/14	0.715609256632039	7	FACETS	0.933	0.821	1			1	CLONAL	1	TRUE	NA	0.715609256632039	7		197	660	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175942	176175942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs964768927	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	27	549	0	ENST00000367669.3:c.173C>T	p.Ser58Leu	p.S58L	ENST00000367669	NM_022457.5	58	tCg/tTg	1/20	1	2	FACETS	0.29	0.231	0.357	0.29	0.231	0.357	SUBCLONAL	1	TRUE	1	0.715609256632039	2		549	260	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112767392	112767392	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	78	305	0	ENST00000369452.4:c.1265C>G	p.Ser422Cys	p.S422C	ENST00000369452	NM_007373.3	422	tCt/tGt	6/9	0.715609256632039	1	FACETS	0.711	0.638	0.786	0.711	0.638	0.786	SUBCLONAL	1	TRUE	0	0.715609256632039	1		305	197	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10785047	10785047	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	20	351	0	ENST00000361367.2:c.919G>C	p.Glu307Gln	p.E307Q	ENST00000361367	NM_014633.3	307	Gag/Cag	8/25	0.220102496538705	2	FACETS	0.209	0.16	0.267	0.105	0.08	0.134	INDETERMINATE	1	TRUE	0	0.715609256632039	2		351	267	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204756	94204756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	16	319	0	ENST00000323929.3:c.829G>A	p.Gly277Arg	p.G277R	ENST00000323929	NM_005591.3	277	Gga/Aga	8/20	1	2	FACETS	0.192	0.142	0.252	0.192	0.142	0.252	SUBCLONAL	1	TRUE	1	0.715609256632039	2		319	233	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402050	402050	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	41	533	1	ENST00000399788.2:c.4741G>A	p.Glu1581Lys	p.E1581K	ENST00000399788	NM_001042603.1	1581	Gaa/Aaa	27/28	NA	2	FACETS	0.242	0.201	0.288			1	INDETERMINATE	1	TRUE	NA	0.715609256632039	2		534	473	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123647	46123647	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	64	525	0	ENST00000334344.6:c.28C>G	p.Pro10Ala	p.P10A	ENST00000334344	NM_152641.2	10	Ccg/Gcg	1/21	0.30720658586607	3	FACETS	0.656	0.571	0.748	0.328	0.285	0.374	INDETERMINATE	1	TRUE	1	0.715609256632039	3		525	370	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230637	46230637	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	43	423	0	ENST00000334344.6:c.886C>G	p.Leu296Val	p.L296V	ENST00000334344	NM_152641.2	296	Ctt/Gtt	8/21	0.30720658586607	3	FACETS	0.442	0.371	0.521	0.221	0.185	0.261	INDETERMINATE	1	TRUE	1	0.715609256632039	3		423	369	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245204	46245204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	47	565	0	ENST00000334344.6:c.3298C>T	p.Gln1100Ter	p.Q1100*	ENST00000334344	NM_152641.2	1100	Cag/Tag	15/21	0.30720658586607	3	FACETS	0.363	0.306	0.425	0.181	0.153	0.213	INDETERMINATE	1	TRUE	1	0.715609256632039	3		565	492	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245965	46245965	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	41	471	0	ENST00000334344.6:c.4059G>C	p.Leu1353Phe	p.L1353F	ENST00000334344	NM_152641.2	1353	ttG/ttC	15/21	0.30720658586607	3	FACETS	0.448	0.374	0.53	0.224	0.187	0.265	INDETERMINATE	1	TRUE	1	0.715609256632039	3		471	347	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856388	111856388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479678654	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	28	751	0	ENST00000341259.2:c.439C>T	p.Arg147Cys	p.R147C	ENST00000341259	NM_005475.2	147	Cgc/Tgc	2/8	1	2	FACETS	0.257	0.206	0.316	0.257	0.206	0.316	SUBCLONAL	1	TRUE	1	0.715609256632039	2		751	304	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257765	133257765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	85	438	0	ENST00000320574.5:c.163G>A	p.Glu55Lys	p.E55K	ENST00000320574	NM_006231.2	55	Gag/Aag	2/49	1	2	FACETS	0.716	0.638	0.797	0.716	0.638	0.797	SUBCLONAL	1	TRUE	1	0.715609256632039	2		438	332	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941639	48941639	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	64	151	0	ENST00000267163.4:c.949C>G	p.Leu317Val	p.L317V	ENST00000267163	NM_000321.2	317	Ctt/Gtt	10/27	0.715609256632039	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.715609256632039	1		151	88	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941720	48941720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	52	168	0	ENST00000267163.4:c.1030C>T	p.Gln344Ter	p.Q344*	ENST00000267163	NM_000321.2	344	Cag/Tag	10/27	0.715609256632039	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.715609256632039	1		168	74	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557590	95557590	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	80	475	0	ENST00000393063.1:c.5477C>T	p.Ser1826Leu	p.S1826L	ENST00000393063	NM_030621.3	1826	tCa/tTa	26/28	0.258530526141651	3	FACETS	0.73	0.646	0.819	0.365	0.323	0.41	INDETERMINATE	1	TRUE	1	0.715609256632039	3		475	416	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292680	91292680	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1060500644	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	40	357	0	ENST00000355112.3:c.182G>C	p.Arg61Thr	p.R61T	ENST00000355112	NM_000057.2	61	aGa/aCa	3/22	0.334656224898153	2	FACETS	0.442	0.369	0.521	0.221	0.184	0.261	INDETERMINATE	1	TRUE	0	0.715609256632039	2		357	253	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293138	91293138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	68	466	0	ENST00000355112.3:c.640G>A	p.Glu214Lys	p.E214K	ENST00000355112	NM_000057.2	214	Gaa/Aaa	3/22	0.334656224898153	2	FACETS	0.552	0.484	0.626	0.276	0.242	0.313	INDETERMINATE	1	TRUE	0	0.715609256632039	2		466	344	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500658	99500658	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	69	505	0	ENST00000268035.6:c.4091C>G	p.Ser1364Cys	p.S1364C	ENST00000268035	NM_000875.3	1364	tCt/tGt	21/21	0.334656224898153	2	FACETS	0.597	0.524	0.675	0.299	0.262	0.338	INDETERMINATE	1	TRUE	0	0.715609256632039	2		505	323	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639732	3639732	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	34	643	0	ENST00000294008.3:c.3907G>C	p.Glu1303Gln	p.E1303Q	ENST00000294008	NM_032444.2	1303	Gaa/Caa	12/15	0.370379156980565	2	FACETS	0.287	0.235	0.346	0.144	0.117	0.173	INDETERMINATE	1	TRUE	0	0.715609256632039	2		643	331	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640107	3640107	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	32	512	0	ENST00000294008.3:c.3532G>T	p.Glu1178Ter	p.E1178*	ENST00000294008	NM_032444.2	1178	Gaa/Taa	12/15	0.370379156980565	2	FACETS	0.304	0.247	0.368	0.152	0.123	0.184	INDETERMINATE	1	TRUE	0	0.715609256632039	2		512	294	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779720	3779720	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	29	619	0	ENST00000262367.5:c.5328C>G	p.Ile1776Met	p.I1776M	ENST00000262367	NM_004380.2	1776	atC/atG	31/31	0.370379156980565	2	FACETS	0.277	0.222	0.338	0.138	0.111	0.169	INDETERMINATE	1	TRUE	0	0.715609256632039	2		619	293	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781326	3781332	+	protein_altering_variant	In_Frame_Del	DEL	GAGGAGA	GAGGAGA	AAGG	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	31	654	1	ENST00000262367.5:c.5033_5039delinsCCTT	p.Phe1678_Ser1680delinsSerPhe	p.F1678_S1680delinsSF	ENST00000262367	NM_004380.2	1678	tTCTCCTCc/tCCTTc	30/31	0.370379156980565	2	FACETS	0.273	0.221	0.332	0.137	0.11	0.166	INDETERMINATE	1	TRUE	0	0.715609256632039	2		655	317	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781410	3781410	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	37	569	0	ENST00000262367.5:c.4955C>G	p.Pro1652Arg	p.P1652R	ENST00000262367	NM_004380.2	1652	cCc/cGc	30/31	0.370379156980565	2	FACETS	0.299	0.247	0.357	0.149	0.123	0.179	INDETERMINATE	1	TRUE	0	0.715609256632039	2		569	346	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3794922	3794922	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555475250	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	30	327	0	ENST00000262367.5:c.3955C>T	p.Arg1319Ter	p.R1319*	ENST00000262367	NM_004380.2	1319	Cga/Tga	23/31	0.370379156980565	2	FACETS	0.272	0.22	0.332	0.136	0.11	0.166	INDETERMINATE	1	TRUE	0	0.715609256632039	2		327	308	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831465	72831465	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371601618	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	236	586	0	ENST00000268489.5:c.5116G>C	p.Glu1706Gln	p.E1706Q	ENST00000268489	NM_006885.3	1706	Gag/Cag	9/10	0.559742639186757	5	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.715609256632039	5		586	591	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351326	89351326	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	85	616	0	ENST00000301030.4:c.1624C>G	p.His542Asp	p.H542D	ENST00000301030	NM_001256183.1	542	Cac/Gac	9/13	0.220102496538705	2	FACETS	0.625	0.556	0.698	0.313	0.278	0.349	INDETERMINATE	1	TRUE	0	0.715609256632039	2		616	380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576886	7576886	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	140	572	0	ENST00000269305.4:c.960G>T	p.Lys320Asn	p.K320N	ENST00000269305	NM_001126112.2	320	aaG/aaT	9/11	0.099923232400585	4	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.715609256632039	4		572	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	309	338	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.099923232400585	4	FACETS	0.952	0.922	0.981			1	INDETERMINATE	4	TRUE	NA	0.715609256632039	4		338	389	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044536	12044536	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	63	336	0	ENST00000353533.5:c.1159C>G	p.Gln387Glu	p.Q387E	ENST00000353533	NM_003010.3	387	Caa/Gaa	11/11	0.715609256632039	1	FACETS	0.377	0.328	0.429	0.377	0.328	0.429	SUBCLONAL	1	TRUE	0	0.715609256632039	1		336	300	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16001793	16001793	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	54	312	0	ENST00000268712.3:c.2708C>G	p.Ser903Ter	p.S903*	ENST00000268712	NM_006311.3	903	tCa/tGa	21/46	0.715609256632039	1	FACETS	0.371	0.32	0.427	0.371	0.32	0.427	SUBCLONAL	1	TRUE	0	0.715609256632039	1		312	261	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38504597	38504597	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	71	489	0	ENST00000254066.5:c.208G>A	p.Glu70Lys	p.E70K	ENST00000254066	NM_000964.3	70	Gag/Aag	3/9	1	2	FACETS	0.554	0.487	0.626	0.554	0.487	0.626	SUBCLONAL	1	TRUE	1	0.715609256632039	2		489	358	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511642	38511642	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	32	541	0	ENST00000254066.5:c.1140G>C	p.Lys380Asn	p.K380N	ENST00000254066	NM_000964.3	380	aaG/aaC	8/9	1	2	FACETS	0.284	0.231	0.344	0.284	0.231	0.344	SUBCLONAL	1	TRUE	1	0.715609256632039	2		541	315	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246748	41246748	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs80357392	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	28	441	0	ENST00000357654.3:c.800C>G	p.Ser267Ter	p.S267*	ENST00000357654	NM_007294.3	267	tCa/tGa	10/23	1	2	FACETS	0.201	0.16	0.247	0.201	0.16	0.247	SUBCLONAL	1	TRUE	1	0.715609256632039	2		441	390	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55704655	55704655	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	32	379	0	ENST00000284073.2:c.718C>G	p.Gln240Glu	p.Q240E	ENST00000284073	NM_138962.2	240	Cag/Gag	10/14	1	2	FACETS	0.262	0.212	0.317	0.262	0.212	0.317	SUBCLONAL	1	TRUE	1	0.715609256632039	2		379	342	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774109	56774109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194019460	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	199	410	0	ENST00000337432.4:c.460G>A	p.Glu154Lys	p.E154K	ENST00000337432	NM_058216.2	154	Gaa/Aaa	3/9	1	2	FACETS	0.756	0.712	0.799	1	0.993	1	SUBCLONAL	2	TRUE	1	0.715609256632039	2		410	368	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39644771	39644771	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	40	285	0	ENST00000262039.4:c.2500G>C	p.Glu834Gln	p.E834Q	ENST00000262039	NM_002647.2	834	Gaa/Caa	23/25	0.334656224898153	2	FACETS	0.559	0.469	0.656	0.279	0.234	0.328	INDETERMINATE	1	TRUE	0	0.715609256632039	2		285	200	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56412904	56412904	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	45	258	0	ENST00000348428.3:c.1918G>C	p.Asp640His	p.D640H	ENST00000348428	NM_006785.3	640	Gat/Cat	16/17	0.334656224898153	2	FACETS	0.68	0.579	0.788	0.34	0.289	0.394	INDETERMINATE	1	TRUE	0	0.715609256632039	2		258	185	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223277	5223277	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	61	595	0	ENST00000357368.4:c.2526G>C	p.Gln842His	p.Q842H	ENST00000357368	NM_002850.3	842	caG/caC	18/38	0.220102496538705	2	FACETS	0.622	0.542	0.708	0.311	0.271	0.354	INDETERMINATE	1	TRUE	0	0.715609256632039	2		595	274	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271663	15271663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	178	740	0	ENST00000263388.2:c.6776C>T	p.Ser2259Leu	p.S2259L	ENST00000263388	NM_000435.2	2259	tCa/tTa	33/33	0.258530526141651	3	FACETS	0.884	0.827	0.942	0.884	0.827	0.942	INDETERMINATE	2	TRUE	1	0.715609256632039	3		740	382	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227710	36227710	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	147	586	0	ENST00000222270.7:c.7279G>C	p.Glu2427Gln	p.E2427Q	ENST00000222270	NM_014727.1	2427	Gag/Cag	31/37	0.258530526141651	3	FACETS	1	0.987	1	0.679	0.626	0.733	INDETERMINATE	1	TRUE	1	0.715609256632039	3		586	411	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422215	47422215	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	45	472	0	ENST00000404338.3:c.283G>C	p.Glu95Gln	p.E95Q	ENST00000404338	NM_004491.4	95	Gag/Cag	1/6	0.258530526141651	3	FACETS	0.478	0.403	0.561	0.239	0.201	0.281	INDETERMINATE	1	TRUE	1	0.715609256632039	3		472	357	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143341	30143341	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	97	558	0	ENST00000389048.3:c.185C>A	p.Ser62Ter	p.S62*	ENST00000389048	NM_004304.4	62	tCg/tAg	1/29	0.258530526141651	3	FACETS	1	0.982	1	0.711	0.644	0.779	INDETERMINATE	1	TRUE	1	0.715609256632039	3		558	259	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149332	61149332	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	62	537	0	ENST00000295025.8:c.1522G>C	p.Glu508Gln	p.E508Q	ENST00000295025	NM_002908.2	508	Gag/Cag	11/11	0.258530526141651	3	FACETS	0.646	0.561	0.738	0.323	0.28	0.369	INDETERMINATE	1	TRUE	1	0.715609256632039	3		537	364	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288578	198288578	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	29	324	0	ENST00000335508.6:c.149G>C	p.Arg50Thr	p.R50T	ENST00000335508	NM_012433.2	50	aGa/aCa	2/25	0.258530526141651	3	FACETS	0.338	0.271	0.413	0.169	0.135	0.207	INDETERMINATE	1	TRUE	1	0.715609256632039	3		324	326	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141586	202141586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760898260	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	125	355	0	ENST00000358485.4:c.874C>T	p.Arg292Trp	p.R292W	ENST00000358485	NM_001080125.1	292	Cgg/Tgg	7/9	0.258530526141651	3	FACETS	1	0.979	1	0.614	0.562	0.669	INDETERMINATE	1	TRUE	1	0.715609256632039	3		355	386	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022899	31022899	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	64	608	0	ENST00000375687.4:c.2384C>G	p.Ser795Cys	p.S795C	ENST00000375687	NM_015338.5	795	tCc/tGc	13/13	0.302664424636314	5	FACETS	0.784	0.68	0.896	0.261	0.226	0.299	INDETERMINATE	1	TRUE	2	0.715609256632039	5		608	473	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743889	40743889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	69	361	0	ENST00000373198.4:c.3106G>A	p.Glu1036Lys	p.E1036K	ENST00000373198	NM_133170.3	1036	Gaa/Aaa	23/32	0.302664424636314	5	FACETS	0.985	0.862	1	0.328	0.287	0.373	INDETERMINATE	1	TRUE	2	0.715609256632039	5		361	406	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478783	57478783	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	256	492	0	ENST00000371085.3:c.369G>C	p.Glu123Asp	p.E123D	ENST00000371085	NM_000516.4	123	gaG/gaC	5/13	0.302664424636314	5	FACETS	1	0.988	1	0.778	0.733	0.822	INDETERMINATE	2	TRUE	2	0.715609256632039	5		492	636	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21351636	21351636	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	17	477	0	ENST00000215739.8:c.2522G>C	p.Ter841SerextTer61	p.*841Sext*61	ENST00000215739	NM_006767.3	841	tGa/tCa	21/21	0.715609256632039	1	FACETS	0.138	0.103	0.18	0.138	0.103	0.18	SUBCLONAL	1	TRUE	0	0.715609256632039	1		477	221	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568527	41568527	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	42	326	0	ENST00000263253.7:c.4477G>C	p.Asp1493His	p.D1493H	ENST00000263253	NM_001429.3	1493	Gat/Cat	28/31	0.715609256632039	1	FACETS	0.433	0.367	0.505	0.433	0.367	0.505	SUBCLONAL	1	TRUE	0	0.715609256632039	1		326	174	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568590	41568590	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	70	415	0	ENST00000263253.7:c.4540G>C	p.Glu1514Gln	p.E1514Q	ENST00000263253	NM_001429.3	1514	Gaa/Caa	28/31	0.715609256632039	1	FACETS	0.493	0.435	0.554	0.493	0.435	0.554	SUBCLONAL	1	TRUE	0	0.715609256632039	1		415	255	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421262	12421262	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141797536	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	30	463	0	ENST00000287820.6:c.142G>A	p.Val48Met	p.V48M	ENST00000287820	NM_015869.4	48	Gtg/Atg	2/7	0.180359473556399	3	FACETS	0.241	0.194	0.295	0.08	0.064	0.099	INDETERMINATE	1	TRUE	0	0.715609256632039	3		463	472	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434133	12434133	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs149064546	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	178	335	0	ENST00000287820.6:c.501C>G	p.Ile167Met	p.I167M	ENST00000287820	NM_015869.4	167	atC/atG	4/7	0.180359473556399	3	FACETS	0.965	0.905	1	0.643	0.603	0.684	INDETERMINATE	2	TRUE	0	0.715609256632039	3		335	350	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662984	52662984	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	21	332	0	ENST00000394830.3:c.1369G>C	p.Glu457Gln	p.E457Q	ENST00000394830	NM_018313.4	457	Gaa/Caa	13/30	0.180359473556399	3	FACETS	0.268	0.206	0.34	0.089	0.068	0.114	INDETERMINATE	1	TRUE	0	0.715609256632039	3		332	297	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967163	134967163	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	114	449	0	ENST00000398015.3:c.2502C>G	p.Ile834Met	p.I834M	ENST00000398015	NM_004441.4	834	atC/atG	14/16	0.180359473556399	3	FACETS	1	0.975	1	0.402	0.365	0.439	INDETERMINATE	1	TRUE	0	0.715609256632039	3		449	359	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430786	181430786	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	128	721	0	ENST00000325404.1:c.638C>G	p.Ser213Trp	p.S213W	ENST00000325404	NM_003106.3	213	tCg/tGg	1/1	0.180359473556399	3	FACETS	1	0.976	1	0.395	0.361	0.43	INDETERMINATE	1	TRUE	0	0.715609256632039	3		721	410	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185169163	185169163	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879126131	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	63	339	0	ENST00000265026.3:c.1258G>A	p.Glu420Lys	p.E420K	ENST00000265026	NM_004721.4	420	Gaa/Aaa	7/14	0.180359473556399	3	FACETS	0.714	0.621	0.813	0.238	0.207	0.271	INDETERMINATE	1	TRUE	0	0.715609256632039	3		339	335	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190894	185190894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555365583	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	57	578	0	ENST00000265026.3:c.1775G>A	p.Arg592Gln	p.R592Q	ENST00000265026	NM_004721.4	592	cGa/cAa	11/14	0.180359473556399	3	FACETS	0.4	0.343	0.462	0.133	0.114	0.154	INDETERMINATE	1	TRUE	0	0.715609256632039	3		578	541	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565907	55565907	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	23	326	0	ENST00000288135.5:c.731C>G	p.Ser244Ter	p.S244*	ENST00000288135	NM_000222.2	244	tCa/tGa	4/21	0.258530526141651	3	FACETS	0.338	0.264	0.424	0.169	0.132	0.212	INDETERMINATE	1	TRUE	1	0.715609256632039	3		326	258	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573263	55573263	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	43	218	0	ENST00000288135.5:c.926-1G>C		p.X309_splice	ENST00000288135	NM_000222.2	309			0.258530526141651	3	FACETS	1	0.889	1	0.526	0.448	0.61	INDETERMINATE	1	TRUE	1	0.715609256632039	3		218	155	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467733	66467733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	94	459	1	ENST00000273854.3:c.536C>T	p.Ala179Val	p.A179V	ENST00000273854	NM_004439.5	179	gCc/gTc	3/18	0.258530526141651	3	FACETS	1	0.932	1	0.525	0.471	0.58	INDETERMINATE	1	TRUE	1	0.715609256632039	3		460	340	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157513	106157513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	145	420	0	ENST00000380013.4:c.2414G>A	p.Gly805Glu	p.G805E	ENST00000380013	NM_001127208.2	805	gGa/gAa	3/11	0.258530526141651	3	FACETS	0.829	0.768	0.89	0.829	0.768	0.89	INDETERMINATE	2	TRUE	1	0.715609256632039	3		420	332	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539579	187539579	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	43	481	0	ENST00000441802.2:c.8161G>C	p.Glu2721Gln	p.E2721Q	ENST00000441802	NM_005245.3	2721	Gag/Cag	10/27	0.258530526141651	3	FACETS	0.452	0.379	0.532	0.226	0.189	0.266	INDETERMINATE	1	TRUE	1	0.715609256632039	3		481	361	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131926991	131926991	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	45	320	0	ENST00000265335.6:c.1528G>C	p.Glu510Gln	p.E510Q	ENST00000265335		510	Gaa/Caa	10/25	0.715609256632039	1	FACETS	0.398	0.338	0.462	0.398	0.338	0.462	SUBCLONAL	1	TRUE	0	0.715609256632039	1		320	203	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170814997	170814997	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	22	184	0	ENST00000296930.5:c.45G>C	p.Gln15His	p.Q15H	ENST00000296930	NM_002520.6	15	caG/caC	1/11	0.715609256632039	1	FACETS	0.387	0.305	0.478	0.387	0.305	0.478	SUBCLONAL	1	TRUE	0	0.715609256632039	1		184	102	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056218	26056218	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	166	613	0	ENST00000343677.2:c.439C>G	p.Pro147Ala	p.P147A	ENST00000343677	NM_005319.3	147	Ccg/Gcg	1/1	0.715609256632039	3	FACETS	1	0.959	1	0.529	0.488	0.572	CLONAL	1	TRUE	1	0.715609256632039	3		613	595	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190532	32190532	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	55	658	0	ENST00000375023.3:c.207G>C	p.Gln69His	p.Q69H	ENST00000375023	NM_004557.3	69	caG/caC	3/30	1	2	FACETS	0.425	0.365	0.49	0.425	0.365	0.49	SUBCLONAL	1	TRUE	1	0.715609256632039	2		658	362	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288194	33288194	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs375524506	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	136	580	0	ENST00000374542.5:c.1214C>G	p.Ser405Cys	p.S405C	ENST00000374542	NM_001141970.1	405	tCt/tGt	4/8	1	2	FACETS	0.982	0.903	1	0.982	0.903	1	CLONAL	1	TRUE	1	0.715609256632039	2		580	387	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652129	36652129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34916193	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	72	607	0	ENST00000244741.5:c.251G>A	p.Arg84Gln	p.R84Q	ENST00000244741	NM_000389.4	84	cGa/cAa	2/3	1	2	FACETS	0.551	0.484	0.622	0.551	0.484	0.622	SUBCLONAL	1	TRUE	1	0.715609256632039	2		607	365	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979369	93979369	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	148	311	0	ENST00000369303.4:c.1459G>C	p.Glu487Gln	p.E487Q	ENST00000369303	NM_004440.3	487	Gaa/Caa	7/17	0.220102496538705	2	FACETS	0.848	0.795	0.899	0.848	0.795	0.899	INDETERMINATE	2	TRUE	0	0.715609256632039	2		311	244	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845606	128845606	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	172	479	0	ENST00000249373.3:c.903G>C	p.Met301Ile	p.M301I	ENST00000249373	NM_005631.4	301	atG/atC	4/12	0.139137585883859	5	FACETS	0.835	0.778	0.892	0.835	0.778	0.892	INDETERMINATE	3	TRUE	2	0.715609256632039	5		479	398	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434567	140434567	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	44	251	0	ENST00000288602.6:c.2131C>T	p.Leu711Phe	p.L711F	ENST00000288602	NM_004333.4	711	Ctc/Ttc	18/18	0.139137585883859	5	FACETS	0.644	0.541	0.757	0.215	0.18	0.253	INDETERMINATE	1	TRUE	2	0.715609256632039	5		251	396	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172198	38172198	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs753382312	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	70	391	0	ENST00000317025.8:c.2209G>C	p.Asp737His	p.D737H	ENST00000317025	NM_023034.1	737	Gat/Cat	12/24	NA	2	FACETS	0.368	0.321	0.418			1	INDETERMINATE	1	TRUE	NA	0.715609256632039	2		391	532	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205065	38205065	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	180	379	0	ENST00000317025.8:c.625G>C	p.Glu209Gln	p.E209Q	ENST00000317025	NM_023034.1	209	Gaa/Caa	2/24	NA	2	FACETS	0.984	0.915	1			1	INDETERMINATE	1	TRUE	NA	0.715609256632039	2		379	511	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271737	38271737	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	206	639	0	ENST00000425967.3:c.2212G>C	p.Glu738Gln	p.E738Q	ENST00000425967	NM_001174067.1	738	Gag/Cag	17/19	NA	2	FACETS	0.991	0.926	1			1	INDETERMINATE	1	TRUE	NA	0.715609256632039	2		639	581	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90995054	90995054	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	48	339	0	ENST00000265433.3:c.67G>C	p.Glu23Gln	p.E23Q	ENST00000265433	NM_002485.4	23	Gag/Cag	2/16	1	2	FACETS	0.537	0.457	0.622	0.537	0.457	0.622	SUBCLONAL	1	TRUE	1	0.715609256632039	2		339	250	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741148	145741148	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	47	546	1	ENST00000428558.2:c.1258G>A	p.Ala420Thr	p.A420T	ENST00000428558	NM_004260.3	420	Gca/Aca	6/22	NA	2	FACETS	0.381	0.322	0.445			1	INDETERMINATE	1	TRUE	NA	0.715609256632039	2		547	345	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2186210	2186210	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	44	450	0	ENST00000349721.2:c.4576G>C	p.Glu1526Gln	p.E1526Q	ENST00000349721	NM_003070.3	1526	Gaa/Caa	32/34	0.258530526141651	3	FACETS	0.435	0.365	0.511	0.217	0.182	0.256	INDETERMINATE	1	TRUE	1	0.715609256632039	3		450	384	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158002	27158002	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	34	565	0	ENST00000380036.4:c.226C>G	p.Gln76Glu	p.Q76E	ENST00000380036	NM_000459.3	76	Caa/Gaa	2/23	0.258530526141651	3	FACETS	0.297	0.243	0.359	0.149	0.121	0.18	INDETERMINATE	1	TRUE	1	0.715609256632039	3		565	434	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293602	137293602	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	34	728	0	ENST00000481739.1:c.153C>G	p.Ile51Met	p.I51M	ENST00000481739	NM_002957.4	51	atC/atG	2/10	0.258530526141651	3	FACETS	0.361	0.295	0.435	0.181	0.147	0.218	INDETERMINATE	1	TRUE	1	0.715609256632039	3		728	357	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396305	139396305	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	147	670	0	ENST00000277541.6:c.5533C>T	p.Gln1845Ter	p.Q1845*	ENST00000277541	NM_017617.3	1845	Cag/Tag	30/34	0.258530526141651	3	FACETS	0.806	0.747	0.866	0.806	0.747	0.866	INDETERMINATE	2	TRUE	1	0.715609256632039	3		670	346	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222244	53222244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	82	572	0	ENST00000375401.3:c.4588G>A	p.Glu1530Lys	p.E1530K	ENST00000375401	NM_004187.3	1530	Gaa/Aaa	26/26	0.71542315335547	3	FACETS	0.685	0.607	0.769	0.343	0.303	0.385	SUBCLONAL	1	TRUE	1	0.715609256632039	3		572	454	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222642	53222642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	89	556	0	ENST00000375401.3:c.4294G>A	p.Glu1432Lys	p.E1432K	ENST00000375401	NM_004187.3	1432	Gag/Aag	25/26	0.71542315335547	3	FACETS	0.771	0.687	0.86	0.386	0.343	0.43	SUBCLONAL	1	TRUE	1	0.715609256632039	3		556	438	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222976	53222976	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	85	498	0	ENST00000375401.3:c.4096G>A	p.Glu1366Lys	p.E1366K	ENST00000375401	NM_004187.3	1366	Gag/Aag	24/26	0.71542315335547	3	FACETS	0.735	0.652	0.822	0.367	0.326	0.411	SUBCLONAL	1	TRUE	1	0.715609256632039	3		498	439	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223431	53223431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	107	565	0	ENST00000375401.3:c.3928G>A	p.Glu1310Lys	p.E1310K	ENST00000375401	NM_004187.3	1310	Gag/Aag	23/26	0.71542315335547	3	FACETS	0.846	0.763	0.933	0.423	0.381	0.467	CLONAL	1	TRUE	1	0.715609256632039	3		565	480	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223533	53223533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	83	591	0	ENST00000375401.3:c.3826G>A	p.Glu1276Lys	p.E1276K	ENST00000375401	NM_004187.3	1276	Gag/Aag	23/26	0.71542315335547	3	FACETS	0.746	0.662	0.836	0.373	0.331	0.418	SUBCLONAL	1	TRUE	1	0.715609256632039	3		591	422	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225190	53225190	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	TTT	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	91	554	0	ENST00000375401.3:c.3028delinsAAA	p.Glu1010LysfsTer46	p.E1010Kfs*46	ENST00000375401	NM_004187.3	1010	Gaa/AAAaa	20/26	0.71542315335547	3	FACETS	0.629	0.56	0.703	0.315	0.28	0.352	SUBCLONAL	1	TRUE	1	0.715609256632039	3		554	549	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226018	53226018	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	114	638	0	ENST00000375401.3:c.2831G>A	p.Arg944Lys	p.R944K	ENST00000375401	NM_004187.3	944	aGg/aAg	19/26	0.71542315335547	3	FACETS	0.791	0.715	0.871	0.395	0.357	0.436	SUBCLONAL	1	TRUE	1	0.715609256632039	3		638	547	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226100	53226100	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	78	547	0	ENST00000375401.3:c.2749G>A	p.Glu917Lys	p.E917K	ENST00000375401	NM_004187.3	917	Gag/Aag	19/26	0.71542315335547	3	FACETS	0.731	0.646	0.822	0.365	0.323	0.411	SUBCLONAL	1	TRUE	1	0.715609256632039	3		547	405	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226924	53226999	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCCTCATCAGCACTCCAAGCGTCCTCACCTTGACATCCCCAATCTGGTGCATGGCGCAAGGCAGGTTGTTCATCT	TCCCTCATCAGCACTCCAAGCGTCCTCACCTTGACATCCCCAATCTGGTGCATGGCGCAAGGCAGGTTGTTCATCT	AAGG	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	74	365	2	ENST00000375401.3:c.2576_2622+29delinsCCTT		p.X859_splice	ENST00000375401	NM_004187.3	859		18/26	0.71542315335547	3	FACETS	0.658	0.578	0.743	0.329	0.289	0.372	SUBCLONAL	1	TRUE	1	0.715609256632039	3		367	427	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019826	123019826	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	157	382	0	ENST00000355640.3:c.314C>G	p.Ser105Cys	p.S105C	ENST00000355640		105	tCt/tGt	2/7	0.71542315335547	3	FACETS	1	0.988	1	0.685	0.633	0.737	CLONAL	1	TRUE	1	0.715609256632039	3		382	435	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0063969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	290	494	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.590877869834053	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.590877869834053	2		494	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0063969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	573	619	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.590877869834053	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	0	0.590877869834053	3		619	834	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086010	16086010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	316	485	0	ENST00000281043.3:c.1186G>A	p.Asp396Asn	p.D396N	ENST00000281043	NM_005378.4	396	Gac/Aac	3/3	0.590877869834053	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.590877869834053	3		485	680	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	282	402	0	ENST00000425967.3:c.1731C>G	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaG	13/19	0.558180253369409	5	FACETS	1	0.953	1	0.675	0.636	0.715	CLONAL	2	TRUE	2	0.590877869834053	5		402	889	SUCCESS
APC	324	MSKCC	GRCh37	5	112173531	112173531	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs773020689	NA	P-0063969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	329	503	0	ENST00000257430.4:c.2240C>G	p.Ser747Ter	p.S747*	ENST00000257430	NM_000038.5	747	tCa/tGa	16/16	0.590877869834053	2	FACETS	0.975	0.933	1	0.975	0.933	1	CLONAL	2	TRUE	0	0.590877869834053	2		503	571	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937046	48937046	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0063969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	256	355	0	ENST00000267163.4:c.814A>T	p.Arg272Ter	p.R272*	ENST00000267163	NM_000321.2	272	Aga/Tga	8/27	0.590877869834053	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.590877869834053	2		355	426	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417469	139417469	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	201	695	0	ENST00000277541.6:c.575G>A	p.Gly192Glu	p.G192E	ENST00000277541	NM_017617.3	192	gGa/gAa	4/34	0.588422692978469	3	FACETS	1	0.942	1	0.509	0.472	0.547	CLONAL	1	TRUE	1	0.590877869834053	3		695	866	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0063969-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	242	494	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.803508323246618	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.814719132302362	2		494	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0063969-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	512	619	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.814719132302362	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.814719132302362	3		619	574	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086010	16086010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063969-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	293	485	0	ENST00000281043.3:c.1186G>A	p.Asp396Asn	p.D396N	ENST00000281043	NM_005378.4	396	Gac/Aac	3/3	0.626667525692706	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.814719132302362	3		485	490	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063969-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	242	402	0	ENST00000425967.3:c.1731C>G	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaG	13/19	0.814719132302362	5	FACETS	1	0.949	1	0.674	0.633	0.715	CLONAL	2	TRUE	2	0.814719132302362	5		402	653	SUCCESS
APC	324	MSKCC	GRCh37	5	112173531	112173531	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs773020689	NA	P-0063969-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	186	503	0	ENST00000257430.4:c.2240C>G	p.Ser747Ter	p.S747*	ENST00000257430	NM_000038.5	747	tCa/tGa	16/16	0.803508323246618	2	FACETS	0.963	0.923	1	0.963	0.923	1	CLONAL	2	TRUE	0	0.814719132302362	2		503	237	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937046	48937046	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0063969-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	159	355	0	ENST00000267163.4:c.814A>T	p.Arg272Ter	p.R272*	ENST00000267163	NM_000321.2	272	Aga/Tga	8/27	0.803508323246618	2	FACETS	0.957	0.913	0.998	0.957	0.913	0.998	CLONAL	2	TRUE	0	0.814719132302362	2		355	204	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417469	139417469	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063969-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	129	695	0	ENST00000277541.6:c.575G>A	p.Gly192Glu	p.G192E	ENST00000277541	NM_017617.3	192	gGa/gAa	4/34	0.508798168064091	3	FACETS	1	0.964	1	0.549	0.502	0.597	CLONAL	1	TRUE	1	0.814719132302362	3		695	406	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0063970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	101	728	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.256237622939999	4	FACETS	0.982	0.884	1	0.982	0.884	1	CLONAL	2	TRUE	2	0.341491002149575	4		728	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0063970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	162	667	1	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	0.341491002149575	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.341491002149575	2		668	436	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538897	23538897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1200957711	NA	P-0063970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	79	498	0	ENST00000380871.4:c.542G>A	p.Arg181Gln	p.R181Q	ENST00000380871	NM_006167.3	181	cGa/cAa	2/2	0.341491002149575	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.341491002149575	1		498	305	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178098	56178098	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	63	475	0	ENST00000399503.3:c.3071A>C	p.Lys1024Thr	p.K1024T	ENST00000399503	NM_005921.1	1024	aAg/aCg	14/20	1	2	FACETS	0.909	0.789	1	0.909	0.789	1	CLONAL	1	TRUE	1	0.341491002149575	2		475	406	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752789	57752789	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	55	439	0	ENST00000274289.3:c.1139G>C	p.Arg380Thr	p.R380T	ENST00000274289	NM_006622.3	380	aGa/aCa	8/14	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.341491002149575	2		439	297	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604763	48604764	+	inframe_insertion	In_Frame_Ins	INS	-	-	TAC	novel	NA	P-0063971-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	33	539	0	ENST00000342988.3:c.1586_1588dup	p.Leu529dup	p.L529dup	ENST00000342988	NM_005359.5	529	tta/tTACta	12/12	1	2	FACETS	0.498	0.405	0.603	0.498	0.405	0.603	SUBCLONAL	1	FALSE	1	0.274811718241702	2		539	482	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861474	152861474	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs782031283	NA	P-0063971-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	41	232	0	ENST00000406277.2:c.278A>G	p.Asn93Ser	p.N93S	ENST00000406277	NM_152274.4	93	aAt/aGt	4/7	0.227882005175715		FACETS		0.954	1				CLONAL	1	FALSE	NA	0.274811718241702	2		232	210	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0063972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	344	850	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.638106074373968	3	FACETS	0.926	0.882	0.97	0.926	0.882	0.97	CLONAL	2	TRUE	1	0.638106074373968	3		852	768	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0063972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	312	301	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.603872233282498	2	FACETS	0.966	0.926	1	0.966	0.926	1	CLONAL	2	TRUE	0	0.638106074373968	2		301	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0063972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	200	626	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.638106074373968	3	FACETS	0.932	0.865	1	0.466	0.432	0.501	CLONAL	1	TRUE	1	0.638106074373968	3		626	887	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562982	21562982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	156	655	0	ENST00000382592.4:c.937G>A	p.Val313Met	p.V313M	ENST00000382592	NM_014572.2	313	Gtg/Atg	4/8	0.579099853272461	5	FACETS	0.972	0.889	1	0.324	0.296	0.353	CLONAL	1	TRUE	2	0.638106074373968	5		655	985	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450883	70450883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	149	650	0	ENST00000373644.4:c.5723C>T	p.Ala1908Val	p.A1908V	ENST00000373644	NM_030625.2	1908	gCt/gTt	12/12	1	2	FACETS	0.884	0.813	0.958	0.884	0.813	0.958	CLONAL	1	TRUE	1	0.638106074373968	2		650	528	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114905759	114905770	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTCTTTGTAGG	CTTCTTTGTAGG	-	novel	NA	P-0063972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	93	294	0	ENST00000543371.1:c.789-10_790del		p.X263_splice	ENST00000543371	NM_001198531.1	263		8/14	1	2	FACETS	0.965	0.869	1	0.965	0.869	1	CLONAL	1	TRUE	1	0.638106074373968	2		294	302	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374865	45374920	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTACCGTGGCATTTCGGTTAACATTGGAGAGTAAACCTAAGCAGAACCTCTCTG	TTCTACCGTGGCATTTCGGTTAACATTGGAGAGTAAACCTAAGCAGAACCTCTCTG	-	novel	NA	P-0063972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	73	435	0	ENST00000262160.6:c.923_978del	p.Ser308TyrfsTer22	p.S308Yfs*22	ENST00000262160	NM_005901.5	308	tCAGAGAGGTTCTGCTTAGGTTTACTCTCCAATGTTAACCGAAATGCCACGGTAGAA/t	8/11	0.638106074373968	1	FACETS	0.728	0.648	0.811	0.728	0.648	0.811	SUBCLONAL	1	TRUE	0	0.638106074373968	1		435	214	SUCCESS
ALB	213	MSKCC	GRCh37	4	74285973	74285974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs75000326	NA	P-0063972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	61	316	0	ENST00000295897.4:c.1794dup	p.Leu599ThrfsTer30	p.L599Tfs*30	ENST00000295897	NM_000477.5	596	-/A	14/15	1	2	FACETS	0.966	0.847	1	0.966	0.847	1	CLONAL	1	TRUE	1	0.638106074373968	2		316	198	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	163	523	0				ENST00000310581	NM_198253.2	-/1132			0.444415152114277	3	FACETS	0.803	0.749	0.858	0.803	0.749	0.858	INDETERMINATE	2	TRUE	1	0.839986857409293	3		523	343	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372394	55372394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	94	542	0	ENST00000297316.4:c.1084G>A	p.Glu362Lys	p.E362K	ENST00000297316	NM_022454.3	362	Gaa/Aaa	2/2	0.430519716162741	4	FACETS	0.632	0.562	0.705	0.158	0.14	0.177	INDETERMINATE	1	TRUE	0	0.839986857409293	4		542	652	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658469	117658469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	225	362	0	ENST00000368508.3:c.5114C>T	p.Ser1705Leu	p.S1705L	ENST00000368508	NM_002944.2	1705	tCa/tTa	31/43	0.839986857409293	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.839986857409293	1		362	293	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027385	48027385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	204	454	0	ENST00000234420.5:c.2263G>A	p.Glu755Lys	p.E755K	ENST00000234420	NM_000179.2	755	Gaa/Aaa	4/10	0.345636952265409	3	FACETS	1	0.991	1	0.68	0.637	0.724	INDETERMINATE	1	TRUE	1	0.839986857409293	3		454	507	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862887	9862887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868222927	NA	P-0063973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	236	421	0	ENST00000330684.3:c.2416G>A	p.Glu806Lys	p.E806K	ENST00000330684	NM_001134407.1	806	Gag/Aag	12/13	0.81265553687801	2	FACETS	0.927	0.892	0.96	0.927	0.892	0.96	CLONAL	2	TRUE	0	0.839986857409293	2		421	303	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525066	9525066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	156	441	0	ENST00000353224.5:c.1819C>T	p.Pro607Ser	p.P607S	ENST00000353224	NM_177990.2	607	Ccc/Tcc	8/10	1	2	FACETS	0.929	0.86	0.998	0.929	0.86	0.998	CLONAL	1	TRUE	1	0.839986857409293	2		441	400	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857869	9857869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	286	543	0	ENST00000330684.3:c.3532C>T	p.Leu1178Phe	p.L1178F	ENST00000330684	NM_001134407.1	1178	Ctt/Ttt	13/13	0.81265553687801	2	FACETS	0.97	0.94	0.999	0.97	0.94	0.999	CLONAL	2	TRUE	0	0.839986857409293	2		543	351	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279549	123279549	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	183	561	0	ENST00000358487.5:c.883G>A	p.Glu295Lys	p.E295K	ENST00000358487	NM_000141.4	295	Gaa/Aaa	7/18	0.427709176695749	1	FACETS	0.687	0.644	0.73	0.687	0.644	0.73	INDETERMINATE	1	TRUE	0	0.839986857409293	1		561	368	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246027122	246027122	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	211	425	0	ENST00000388985.4:c.880G>A	p.Glu294Lys	p.E294K	ENST00000388985		294	Gaa/Aaa	9/12	0.428541534018352	4	FACETS	0.84	0.787	0.895	0.84	0.787	0.895	INDETERMINATE	2	TRUE	2	0.839986857409293	4		425	550	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400143	41400143	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	159	423	0	ENST00000373198.4:c.616G>A	p.Gly206Arg	p.G206R	ENST00000373198	NM_133170.3	206	Ggg/Agg	5/32	1	2	FACETS	0.956	0.887	1	0.956	0.887	1	CLONAL	1	TRUE	1	0.839986857409293	2		423	396	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95579443	95579443	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs878855246	NA	P-0063973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	224	366	0	ENST00000393063.1:c.2026C>T	p.Arg676Ter	p.R676*	ENST00000393063	NM_030621.3	676	Cga/Tga	13/28	0.428541534018352	4	FACETS	0.977	0.92	1	0.977	0.92	1	INDETERMINATE	2	TRUE	2	0.839986857409293	4		366	502	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099976	27099976	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0063973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	274	675	0	ENST00000324856.7:c.3855T>G	p.Tyr1285Ter	p.Y1285*	ENST00000324856	NM_006015.4	1285	taT/taG	15/20	0.4815946320007	3	FACETS	1	0.992	1	0.658	0.621	0.695	INDETERMINATE	1	TRUE	1	0.839986857409293	3		675	704	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148891	119148891	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs267606706	NA	P-0063973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	126	362	0	ENST00000264033.4:c.1111T>A	p.Tyr371Asn	p.Y371N	ENST00000264033	NM_005188.3	371	Tac/Aac	8/16	0.839986857409293	1	FACETS	0.916	0.859	0.971	0.916	0.859	0.971	CLONAL	1	TRUE	0	0.839986857409293	1		362	190	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18747456	18747456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	115	317	0	ENST00000266497.5:c.3917C>T	p.Ser1306Phe	p.S1306F	ENST00000266497		1306	tCt/tTt	28/31	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.839986857409293	2		317	270	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042709	42042709	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	209	556	0	ENST00000219905.7:c.6904G>A	p.Glu2302Lys	p.E2302K	ENST00000219905	NM_001164273.1	2302	Gaa/Aaa	17/24	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.839986857409293	2		556	487	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784489	43784489	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	216	455	0	ENST00000382044.4:c.185C>T	p.Pro62Leu	p.P62L	ENST00000382044	NM_001141980.1	62	cCt/cTt	2/28	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.839986857409293	2		455	490	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032051	10032051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	270	458	0	ENST00000330684.3:c.772C>T	p.Pro258Ser	p.P258S	ENST00000330684	NM_001134407.1	258	Ccc/Tcc	3/13	0.81265553687801	2	FACETS	0.965	0.934	0.995	0.965	0.934	0.995	CLONAL	2	TRUE	0	0.839986857409293	2		458	333	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559101	29559101	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202023	NA	P-0063973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	32	132	0	ENST00000356175.3:c.3208C>T	p.Gln1070Ter	p.Q1070*	ENST00000356175	NM_000267.3	1070	Cag/Tag	25/57	0.839986857409293	1	FACETS	0.85	0.738	0.957	0.85	0.738	0.957	CLONAL	1	TRUE	0	0.839986857409293	1		132	52	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144131	11144131	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs756044034	NA	P-0063973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	170	474	0	ENST00000358026.2:c.3712T>C	p.Ser1238Pro	p.S1238P	ENST00000358026	NM_001128849.1	1238	Tcc/Ccc	26/36	0.427709176695749	1	FACETS	0.705	0.66	0.75	0.705	0.66	0.75	INDETERMINATE	1	TRUE	0	0.839986857409293	1		474	333	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266738	18266738	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868385898	NA	P-0063973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	190	550	0	ENST00000222254.8:c.49C>T	p.Arg17Trp	p.R17W	ENST00000222254	NM_005027.3	17	Cgg/Tgg	2/16	0.427709176695749	1	FACETS	0.745	0.702	0.789	0.745	0.702	0.789	INDETERMINATE	1	TRUE	0	0.839986857409293	1		550	352	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748919	41748919	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	205	500	0	ENST00000301178.4:c.1444G>A	p.Gly482Arg	p.G482R	ENST00000301178	NM_021913.4	482	Gga/Aga	11/20	0.427709176695749	1	FACETS	0.821	0.777	0.864	0.821	0.777	0.864	INDETERMINATE	1	TRUE	0	0.839986857409293	1		500	345	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690274	47690275	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0063973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	295	395	0	ENST00000233146.2:c.1491_1492del	p.Ile497MetfsTer15	p.I497Mfs*15	ENST00000233146	NM_000251.2	497	atAAgt/atgt	9/16	0.345636952265409	3	FACETS	0.932	0.889	0.975	0.932	0.889	0.975	INDETERMINATE	2	TRUE	1	0.839986857409293	3		395	535	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143261	24143261	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	213	612	0	ENST00000263121.7:c.493C>T	p.Pro165Ser	p.P165S	ENST00000263121	NM_003073.3	165	Ccc/Tcc	4/9	0.421395686789999	1	FACETS	0.699	0.659	0.739	0.699	0.659	0.739	INDETERMINATE	1	TRUE	0	0.839986857409293	1		612	421	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149452906	149452906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	262	494	0	ENST00000286301.3:c.1040C>T	p.Pro347Leu	p.P347L	ENST00000286301	NM_005211.3	347	cCt/cTt	7/22	0.807994758608702	2	FACETS	0.951	0.918	0.981	0.951	0.918	0.981	CLONAL	2	TRUE	0	0.839986857409293	2		494	328	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673595	30673595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1284900880	NA	P-0063973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	350	606	0	ENST00000376406.3:c.3365C>T	p.Ser1122Phe	p.S1122F	ENST00000376406	NM_014641.2	1122	tCt/tTt	10/15	0.444415152114277	3	FACETS	0.984	0.944	1	0.984	0.944	1	INDETERMINATE	2	TRUE	1	0.839986857409293	3		606	601	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524677	137524677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	160	358	0	ENST00000367739.4:c.692C>T	p.Ser231Leu	p.S231L	ENST00000367739	NM_000416.2	231	tCa/tTa	5/7	0.839986857409293	1	FACETS	0.944	0.893	0.993	0.944	0.893	0.993	CLONAL	1	TRUE	0	0.839986857409293	1		358	234	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411045	63411045	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	205	278	0	ENST00000330258.3:c.2122A>G	p.Thr708Ala	p.T708A	ENST00000330258	NM_152424.3	708	Acc/Gcc	2/2	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.839986857409293	1		278	242	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0063974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	60	372	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.142803779639628	5	FACETS	0.961	0.844	1	1	0.972	1	CLONAL	6	FALSE	1	0.142803779639628	5		372	177	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0063974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	14	210	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.142803779639628	7	FACETS	1	0.825	1	0.475	0.347	0.627	CLONAL	2	FALSE	2	0.142803779639628	7		210	112	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0063974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	36	494	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.142803779639628	6	FACETS	0.994	0.829	1	0.994	0.829	1	CLONAL	4	FALSE	2	0.142803779639628	6		494	163	SUCCESS
APC	324	MSKCC	GRCh37	5	112175675	112175676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0063974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	39	537	0	ENST00000257430.4:c.4393_4394dup	p.Ser1465ArgfsTer9	p.S1465Rfs*9	ENST00000257430	NM_000038.5	1462	aag/aAGag	16/16	0.142803779639628	6	FACETS	0.9	0.755	1	0.9	0.755	1	CLONAL	4	FALSE	2	0.142803779639628	6		537	195	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653864	89653865	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	AACT	novel	NA	P-0063974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	30	329	0	ENST00000371953.3:c.163_164insACTA	p.Arg55AsnfsTer2	p.R55Nfs*2	ENST00000371953	NM_000314.4	54	-/AACT	2/9	0.142803779639628	6	FACETS	0.923	0.759	1	1	0.901	1	CLONAL	5	FALSE	2	0.142803779639628	6		329	117	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911934	32911934	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	38	480	0	ENST00000380152.3:c.3442C>A	p.Gln1148Lys	p.Q1148K	ENST00000380152		1148	Cag/Aag	11/27	0.142803779639628	9	FACETS	0.988	0.825	1	0.659	0.55	0.777	CLONAL	4	FALSE	3	0.142803779639628	9		480	202	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968195	18968195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764657446	NA	P-0063974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	90	511	0	ENST00000262803.5:c.2035G>A	p.Gly679Arg	p.G679R	ENST00000262803	NM_002911.3	679	Ggg/Agg	15/24	0.142803779639628	7	FACETS	0.951	0.857	1	1	0.978	1	CLONAL	7	FALSE	2	0.142803779639628	7		511	257	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968141	68968141	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	16	409	0	ENST00000288368.4:c.1170C>A	p.Cys390Ter	p.C390*	ENST00000288368	NM_024870.2	390	tgC/tgA	10/40	0.142803779639628	1	FACETS	1	0.825	1	1	0.932	1	CLONAL	2	FALSE	0	0.142803779639628	1		409	92	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868894	117868894	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	11	332	0	ENST00000297338.2:c.805A>T	p.Asn269Tyr	p.N269Y	ENST00000297338	NM_006265.2	269	Aat/Tat	7/14	0.142803779639628	10	FACETS	1	0.803	1	0.177	0.122	0.246	CLONAL	1	FALSE	3	0.142803779639628	10		332	195	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	27	331	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.13131280564153	3	FACETS	0.826	0.669	0.999	0.413	0.334	0.5	INDETERMINATE	1	TRUE	1	0.74	3		331	121	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	28	298	0	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	0.934	0.771	1	0.934	0.771	1	CLONAL	1	TRUE	1	0.74	2		298	81	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	49	712	3	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.616	0.528	0.711	0.616	0.528	0.711	SUBCLONAL	1	TRUE	1	0.74	2		715	215	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	34	339	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.729	0.608	0.86	0.729	0.608	0.86	SUBCLONAL	1	TRUE	1	0.74	2		339	126	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	33	334	1	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.74	2		335	84	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	35	387	0	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	1	2	FACETS	0.681	0.568	0.802	0.681	0.568	0.802	SUBCLONAL	1	TRUE	1	0.74	2		387	139	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	100	428	0	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.74	2		428	262	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624275	89624275	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204910	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	47	249	0	ENST00000371953.3:c.49C>T	p.Gln17Ter	p.Q17*	ENST00000371953	NM_000314.4	17	Caa/Taa	1/9	0.13131280564153	3	FACETS	1	0.947	1	0.608	0.525	0.696	INDETERMINATE	1	TRUE	1	0.74	3		249	143	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106861	27106861	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	154	638	0	ENST00000324856.7:c.6472C>T	p.Arg2158Ter	p.R2158*	ENST00000324856	NM_006015.4	2158	Cga/Tga	20/20	1	2	FACETS	0.996	0.921	1	0.996	0.921	1	CLONAL	1	TRUE	1	0.74	2		638	418	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	96	434	5	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	1	2	FACETS	0.837	0.755	0.922	0.837	0.755	0.922	CLONAL	1	TRUE	1	0.74	2		439	310	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306996	65306997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	65	486	4	ENST00000342505.4:c.2580dup	p.Pro861ThrfsTer4	p.P861Tfs*4	ENST00000342505	NM_002227.2	860	-/A	19/25	1	2	FACETS	0.791	0.696	0.891	0.791	0.696	0.891	SUBCLONAL	1	TRUE	1	0.74	2		490	222	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099430	27099430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1227227387	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	60	514	0	ENST00000324856.7:c.3667C>T	p.Arg1223Cys	p.R1223C	ENST00000324856	NM_006015.4	1223	Cgc/Tgc	14/20	1	2	FACETS	0.881	0.773	0.994	0.881	0.773	0.994	CLONAL	1	TRUE	1	0.74	2		514	184	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720650	89720650	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1257124719	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	14	127	0	ENST00000371953.3:c.802-1G>A		p.X268_splice	ENST00000371953	NM_000314.4	268			0.13131280564153	3	FACETS	0.798	0.591	1	0.399	0.295	0.517	INDETERMINATE	1	TRUE	1	0.74	3		127	65	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519505	137519506	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs780346130	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	65	651	2	ENST00000367739.4:c.1132_1133del	p.Ser378PhefsTer6	p.S378Ffs*6	ENST00000367739	NM_000416.2	378	AGt/t	7/7	1	2	FACETS	0.761	0.668	0.857	0.761	0.668	0.857	SUBCLONAL	1	TRUE	1	0.74	2		653	231	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962529	100962529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767360879	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	61	347	0	ENST00000325455.5:c.1868G>A	p.Arg623His	p.R623H	ENST00000325455	NM_001202474.3	623	cGc/cAc	3/8	1	2	FACETS	0.97	0.855	1	0.97	0.855	1	CLONAL	1	TRUE	1	0.74	2		347	170	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391716	139391716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371742334	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	116	580	1	ENST00000277541.6:c.6475C>T	p.Arg2159Cys	p.R2159C	ENST00000277541	NM_017617.3	2159	Cgc/Tgc	34/34	1	2	FACETS	0.998	0.912	1	0.998	0.912	1	CLONAL	1	TRUE	1	0.74	2		581	314	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102199	27102199	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	48	404	0	ENST00000324856.7:c.5124+1G>A		p.X1708_splice	ENST00000324856	NM_006015.4	1708			1	2	FACETS	0.701	0.602	0.807	0.701	0.602	0.807	SUBCLONAL	1	TRUE	1	0.74	2		404	185	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748399150	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	143	442	2	ENST00000220592.5:c.1806del	p.Ala603ProfsTer92	p.A603Pfs*92	ENST00000220592	NM_012154.3	602	ccC/cc	14/19	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.74	2		444	376	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983970	2983970	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776851359	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	107	523	0	ENST00000396946.4:c.560G>A	p.Arg187Gln	p.R187Q	ENST00000396946	NM_032415.4	187	cGg/cAg	5/25	1	2	FACETS	0.93	0.845	1	0.93	0.845	1	CLONAL	1	TRUE	1	0.74	2		523	311	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392087	81392088	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	53	277	0	ENST00000222390.5:c.189dup	p.Val64SerfsTer9	p.V64Sfs*9	ENST00000222390	NM_000601.4	63	-/A	2/18	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.74	2		277	140	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821610	72821618	+	inframe_deletion	In_Frame_Del	DEL	CCGCCGCCA	CCGCCGCCA	-	rs760306096	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	98	528	9	ENST00000268489.5:c.10557_10565del	p.Gly3525_Gly3527del	p.G3525_G3527del	ENST00000268489	NM_006885.3	3519	ggTGGCGGCGGc/ggc	10/10	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.74	2		537	253	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855832	45855832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761085729	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	25	571	0	ENST00000391945.4:c.1978G>A	p.Ala660Thr	p.A660T	ENST00000391945	NM_000400.3	660	Gcg/Acg	21/23	0.13131280564153	3	FACETS	0.225	0.177	0.281	0.113	0.088	0.141	INDETERMINATE	1	TRUE	1	0.74	3		571	411	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28980032	28980032	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	30	298	0	ENST00000282397.4:c.1437-1G>A		p.X479_splice	ENST00000282397	NM_002019.4	479			1	2	FACETS	0.633	0.519	0.758	0.633	0.519	0.758	SUBCLONAL	1	TRUE	1	0.74	2		298	128	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28886237	28886237	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	65	350	0	ENST00000282397.4:c.3387-2A>G		p.X1129_splice	ENST00000282397	NM_002019.4	1129			1	2	FACETS	0.965	0.854	1	0.965	0.854	1	CLONAL	1	TRUE	1	0.74	2		350	182	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656567	3656567	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762475814	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	52	516	0	ENST00000294008.3:c.668G>A	p.Arg223His	p.R223H	ENST00000294008	NM_032444.2	223	cGt/cAt	3/15	1	2	FACETS	0.289	0.246	0.336	0.289	0.246	0.336	SUBCLONAL	1	TRUE	1	0.74	2		516	487	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123599	108123600	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	41	273	0	ENST00000278616.4:c.1859_1860del	p.Cys620Ter	p.C620*	ENST00000278616	NM_000051.3	620	TGt/t	12/63	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.74	2		273	105	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276357	115276357	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	28	318	0	ENST00000438362.2:c.971del	p.Asn324ThrfsTer15	p.N324Tfs*15	ENST00000438362	NM_001242891.1	324	aAc/ac	9/20	1	2	FACETS	0.797	0.653	0.951	0.797	0.653	0.951	CLONAL	1	TRUE	1	0.74	2		318	95	SUCCESS
BTK	695	MSKCC	GRCh37	X	100629548	100629549	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs886041148	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	58	393	0	ENST00000308731.7:c.215dup	p.Asn72LysfsTer13	p.N72Kfs*13	ENST00000308731	NM_000061.2	72	aat/aaAt	3/19	1	2	FACETS	0.95	0.834	1	0.95	0.834	1	CLONAL	1	TRUE	1	0.74	2		393	165	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246794	41246794	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs273902786	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	80	429	0	ENST00000357654.3:c.754C>T	p.Arg252Cys	p.R252C	ENST00000357654	NM_007294.3	252	Cgt/Tgt	10/23	1	2	FACETS	0.952	0.853	1	0.952	0.853	1	CLONAL	1	TRUE	1	0.74	2		429	227	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264305	16264307	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGA	AGA	-	novel	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	66	467	0	ENST00000375759.3:c.10510_10512del		p.X3504_splice	ENST00000375759	NM_015001.2	3504		13/15	1	2	FACETS	0.874	0.772	0.981	0.874	0.772	0.981	CLONAL	1	TRUE	1	0.74	2		467	204	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165653	118165653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763834209	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	165	568	1	ENST00000369448.3:c.163G>A	p.Val55Ile	p.V55I	ENST00000369448	NM_017709.3	55	Gtc/Atc	2/2	1	2	FACETS	0.995	0.923	1	0.995	0.923	1	CLONAL	1	TRUE	1	0.74	2		569	448	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231487219	231487219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	87	442	0	ENST00000295050.7:c.620G>A	p.Gly207Asp	p.G207D	ENST00000295050	NM_032018.5	207	gGc/gAc	4/5	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.74	2		442	233	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466024	69466035	+	inframe_deletion	In_Frame_Del	DEL	ACCGACGTGCGG	ACCGACGTGCGG	-	novel	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	142	578	0	ENST00000227507.2:c.862_873del	p.Thr288_Arg291del	p.T288_R291del	ENST00000227507	NM_053056.2	288	ACCGACGTGCGG/-	5/5	1	2	FACETS	0.857	0.787	0.928	0.857	0.787	0.928	CLONAL	1	TRUE	1	0.74	2		578	448	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949368	71949370	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	122	600	0	ENST00000298229.2:c.3750_3752del	p.Leu1251del	p.L1251del	ENST00000298229	NM_001567.3	1250	CTT/-	28/28	1	2	FACETS	0.913	0.835	0.994	0.913	0.835	0.994	CLONAL	1	TRUE	1	0.74	2		600	361	SUCCESS
ATM	472	MSKCC	GRCh37	11	108225572	108225572	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	50	328	0	ENST00000278616.4:c.8821T>A	p.Ser2941Thr	p.S2941T	ENST00000278616	NM_000051.3	2941	Tct/Act	61/63	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.74	2		328	101	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95595947	95595947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	50	325	0	ENST00000393063.1:c.596G>A	p.Cys199Tyr	p.C199Y	ENST00000393063	NM_030621.3	199	tGt/tAt	7/28	1	2	FACETS	0.994	0.864	1	0.994	0.864	1	CLONAL	1	TRUE	1	0.74	2		325	136	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349114	89349115	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	111	479	0	ENST00000301030.4:c.3835dup	p.Ser1279LysfsTer4	p.S1279Kfs*4	ENST00000301030	NM_001256183.1	1279	agc/aAgc	9/13	1	2	FACETS	0.932	0.848	1	0.932	0.848	1	CLONAL	1	TRUE	1	0.74	2		479	322	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349382	89349382	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	199	540	1	ENST00000301030.4:c.3568del	p.Ala1190LeufsTer128	p.A1190Lfs*128	ENST00000301030	NM_001256183.1	1190	Gct/ct	9/13	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.74	2		541	509	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976485	7976485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	111	428	0	ENST00000319144.4:c.1907G>A	p.Ser636Asn	p.S636N	ENST00000319144	NM_001139.2	636	aGc/aAc	14/15	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.74	2		428	295	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995181	15995181	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	72	385	0	ENST00000268712.3:c.3012G>T	p.Trp1004Cys	p.W1004C	ENST00000268712	NM_006311.3	1004	tgG/tgT	22/46	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.74	2		385	172	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587388	29587388	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	29	310	0	ENST00000356175.3:c.4373del	p.Phe1458SerfsTer4	p.F1458Sfs*4	ENST00000356175	NM_000267.3	1457	Ttt/tt	33/57	1	2	FACETS	0.754	0.619	0.899	0.754	0.619	0.899	SUBCLONAL	1	TRUE	1	0.74	2		310	104	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703565	47703565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	60	441	0	ENST00000233146.2:c.2065G>A	p.Ala689Thr	p.A689T	ENST00000233146	NM_000251.2	689	Gcc/Acc	13/16	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.74	2		441	158	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400300	225400300	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	24	295	0	ENST00000264414.4:c.323C>A	p.Ala108Asp	p.A108D	ENST00000264414	NM_003590.4	108	gCt/gAt	3/16	1	2	FACETS	0.801	0.646	0.968	0.801	0.646	0.968	CLONAL	1	TRUE	1	0.74	2		295	81	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21348225	21348225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs565109294	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	147	576	0	ENST00000215739.8:c.1366G>A	p.Val456Met	p.V456M	ENST00000215739	NM_006767.3	456	Gtg/Atg	13/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.74	2		576	352	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564853	41564853	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	87	462	1	ENST00000263253.7:c.4154G>A	p.Cys1385Tyr	p.C1385Y	ENST00000263253	NM_001429.3	1385	tGc/tAc	25/31	1	2	FACETS	0.98	0.882	1	0.98	0.882	1	CLONAL	1	TRUE	1	0.74	2		463	240	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713202	30713202	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	87	459	0	ENST00000295754.5:c.527T>C	p.Leu176Pro	p.L176P	ENST00000295754	NM_003242.5	176	cTg/cCg	4/7	1	2	FACETS	0.771	0.69	0.855	0.771	0.69	0.855	SUBCLONAL	1	TRUE	1	0.74	2		459	305	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032285	26032285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1275976747	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	125	463	0	ENST00000244661.2:c.4G>T	p.Ala2Ser	p.A2S	ENST00000244661	NM_003537.3	2	Gct/Tct	1/1	1	2	FACETS	0.871	0.796	0.948	0.871	0.796	0.948	CLONAL	1	TRUE	1	0.74	2		463	388	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508713	106508713	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	28	514	0	ENST00000359195.3:c.707C>A	p.Ser236Ter	p.S236*	ENST00000359195	NM_002649.2	236	tCa/tAa	2/11	1	2	FACETS	0.195	0.155	0.24	0.195	0.155	0.24	SUBCLONAL	1	TRUE	1	0.74	2		514	388	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738148	133738148	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	93	342	0	ENST00000318560.5:c.550-2A>G		p.X184_splice	ENST00000318560	NM_005157.4	184			1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.74	2		342	249	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753835	133753835	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	66	388	0	ENST00000318560.5:c.1304A>G	p.Tyr435Cys	p.Y435C	ENST00000318560	NM_005157.4	435	tAt/tGt	8/11	1	2	FACETS	0.959	0.849	1	0.959	0.849	1	CLONAL	1	TRUE	1	0.74	2		388	186	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135777028	135777028	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	70	342	0	ENST00000298552.3:c.2450C>T	p.Ala817Val	p.A817V	ENST00000298552	NM_001162426.1	817	gCc/gTc	19/23	1	2	FACETS	0.86	0.762	0.962	0.86	0.762	0.962	CLONAL	1	TRUE	1	0.74	2		342	220	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	64	523	0				ENST00000310581	NM_198253.2	-/1132			0.527982813797101	1	FACETS	0.625	0.546	0.708	0.625	0.546	0.708	SUBCLONAL	1	TRUE	0	0.535726750354888	1		523	280	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0063976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	1920	771	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.535726750354888	13	FACETS	1	0.995	1			1	CLONAL	12	TRUE	NA	0.535726750354888	13		771	2323	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944298	206944298	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	176	628	0	ENST00000423557.1:c.332C>T	p.Ser111Phe	p.S111F	ENST00000423557	NM_000572.2	111	tCc/tTc	3/5	1	2	FACETS	0.862	0.796	0.931	0.862	0.796	0.931	CLONAL	1	TRUE	1	0.535726750354888	2		628	762	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129384	2129385	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0063976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	136	582	0	ENST00000219476.3:c.3240dup	p.Leu1081ThrfsTer87	p.L1081Tfs*87	ENST00000219476	NM_000548.3	1080	tta/ttAa	28/42	1	2	FACETS	0.823	0.751	0.898	0.823	0.751	0.898	CLONAL	1	TRUE	1	0.535726750354888	2		582	617	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216536	7216537	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0063976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	196	671	0	ENST00000380728.2:c.798dup	p.Asp267ArgfsTer?	p.D267Rfs*?	ENST00000380728		266	-/C	9/11	0.510850801881628	1	FACETS	0.979	0.914	1	0.979	0.914	1	CLONAL	1	TRUE	0	0.535726750354888	1		671	547	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206732	36206733	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0063976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	371	591	0	ENST00000300305.3:c.779_780del	p.Asn260ThrfsTer339	p.N260Tfs*339	ENST00000300305		260	aAC/a	6/8	0.535726750354888	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.535726750354888	2		591	676	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916945	178916945	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	65	358	0	ENST00000263967.3:c.332A>T	p.Lys111Met	p.K111M	ENST00000263967	NM_006218.2	111	aAg/aTg	2/21	1	2	FACETS	0.879	0.77	0.995	0.879	0.77	0.995	CLONAL	1	TRUE	1	0.535726750354888	2		358	276	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	900616	900616	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	105	469	0	ENST00000166345.3:c.396C>G	p.Phe132Leu	p.F132L	ENST00000166345	NM_004237.3	132	ttC/ttG	4/13	0.527982813797101	1	FACETS	0.654	0.589	0.721	0.654	0.589	0.721	SUBCLONAL	1	TRUE	0	0.535726750354888	1		469	439	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151919145	151919145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	61	341	0	ENST00000262189.6:c.3440C>T	p.Ser1147Phe	p.S1147F	ENST00000262189	NM_170606.2	1147	tCc/tTc	22/59	1	2	FACETS	0.957	0.836	1	0.957	0.836	1	CLONAL	1	TRUE	1	0.535726750354888	2		341	238	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772852	135772852	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	120	532	0	ENST00000298552.3:c.2771del	p.Leu924TrpfsTer7	p.L924Wfs*7	ENST00000298552	NM_001162426.1	924	tTg/tg	21/23	0.535726750354888	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.535726750354888	1		532	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0063977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	71	619	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.706	0.616	0.804	0.706	0.616	0.804	SUBCLONAL	1	TRUE	1	0.3	2		619	670	SUCCESS
APC	324	MSKCC	GRCh37	5	112176017	112176017	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554086134	NA	P-0063977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	47	571	0	ENST00000257430.4:c.4726G>T	p.Glu1576Ter	p.E1576*	ENST00000257430	NM_000038.5	1576	Gaa/Taa	16/16	1	2	FACETS	0.599	0.505	0.703	0.599	0.505	0.703	SUBCLONAL	1	TRUE	1	0.3	2		571	523	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370346	40370346	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs753213429	NA	P-0063977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	110	654	0	ENST00000293328.3:c.992C>T	p.Thr331Met	p.T331M	ENST00000293328	NM_012448.3	331	aCg/aTg	9/19	0.0828113775937456	3	FACETS	1	0.966	1	0.585	0.526	0.647	INDETERMINATE	1	TRUE	1	0.3	3		654	721	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0063978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	59	187	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.346064699031345	4	FACETS	1	0.911	1	0.269	0.232	0.309	CLONAL	1	TRUE	0	0.352492336554333	4		187	421	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0063978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	67	393	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.346064699031345	4	FACETS	1	0.95	1	0.296	0.258	0.337	CLONAL	1	TRUE	0	0.352492336554333	4		394	434	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520017	NA	P-0063978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	196	664	0	ENST00000326873.7:c.647C>T	p.Ser216Phe	p.S216F	ENST00000326873	NM_000455.4	216	tCc/tTc	5/10	1	2	FACETS	0.867	0.801	0.937	0.867	0.801	0.937	CLONAL	1	TRUE	1	0.352492336554333	2		664	1282	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308348	15308348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555730189	NA	P-0063978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	202	614	0	ENST00000263388.2:c.160C>T	p.Arg54Cys	p.R54C	ENST00000263388	NM_000435.2	54	Cgt/Tgt	2/33	1	2	FACETS	0.979	0.906	1	0.979	0.906	1	CLONAL	1	TRUE	1	0.352492336554333	2		614	1171	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220485	1220485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	199	656	0	ENST00000326873.7:c.578C>T	p.Ser193Phe	p.S193F	ENST00000326873	NM_000455.4	193	tCc/tTc	4/10	1	2	FACETS	0.921	0.852	0.993	0.921	0.852	0.993	CLONAL	1	TRUE	1	0.352492336554333	2		656	1226	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687547	37687547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	168	559	0	ENST00000447079.4:c.4451G>A	p.Arg1484Lys	p.R1484K	ENST00000447079	NM_015083.1	1484	aGa/aAa	14/14	1	2	FACETS	0.963	0.884	1	0.963	0.884	1	CLONAL	1	TRUE	1	0.352492336554333	2		559	990	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099262	4099262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730880523	NA	P-0063978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	108	614	0	ENST00000262948.5:c.856G>A	p.Gly286Arg	p.G286R	ENST00000262948	NM_030662.3	286	Ggg/Agg	7/11	1	2	FACETS	0.553	0.495	0.615	0.553	0.495	0.615	SUBCLONAL	1	TRUE	1	0.352492336554333	2		614	1108	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972626	25972626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	166	528	0	ENST00000435504.4:c.1799C>T	p.Ser600Leu	p.S600L	ENST00000435504		600	tCa/tTa	12/13	1	2	FACETS	0.868	0.796	0.943	0.868	0.796	0.943	CLONAL	1	TRUE	1	0.352492336554333	2		528	1085	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205028	123205028	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	79	360	0	ENST00000218089.9:c.2388G>T	p.Met796Ile	p.M796I	ENST00000218089	NM_001042749.1	796	atG/atT	25/35	1	2	FACETS	0.977	0.862	1	0.977	0.862	1	CLONAL	1	TRUE	1	0.352492336554333	2		360	459	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288763	11288763	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	138	580	0	ENST00000361445.4:c.2992C>T	p.Leu998Phe	p.L998F	ENST00000361445	NM_004958.3	998	Ctt/Ttt	19/58	1	2	FACETS	0.826	0.751	0.905	0.826	0.751	0.905	CLONAL	1	TRUE	1	0.352492336554333	2		580	948	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001927	29001927	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	110	405	0	ENST00000282397.4:c.1238A>G	p.Asn413Ser	p.N413S	ENST00000282397	NM_002019.4	413	aAt/aGt	9/30	1	2	FACETS	0.949	0.854	1	0.949	0.854	1	CLONAL	1	TRUE	1	0.352492336554333	2		405	658	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960967	15960967	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	119	466	0	ENST00000268712.3:c.6253C>A	p.Pro2085Thr	p.P2085T	ENST00000268712	NM_006311.3	2085	Cct/Act	40/46	1	2	FACETS	0.832	0.75	0.917	0.832	0.75	0.917	CLONAL	1	TRUE	1	0.352492336554333	2		466	812	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110184	3110184	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	174	469	0	ENST00000078429.4:c.174G>C	p.Gln58His	p.Q58H	ENST00000078429	NM_002067.2	58	caG/caC	2/7	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.352492336554333	2		469	934	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836271	151836546	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTGCGGGCCCTCCTGTGAGCGTCGCGTCAATCACATGGTCGTTATCCATGCGGAACATGTACACACCACGGTTCTGAGGGAAAAGTCAGTCAGTAAGTCATCAATGTCGACCTGAAACTCCCCTCTGTGTTCCTATCCACACCAGGAGGACTCAGTCGAAACTGAACGGAACGGCAGCCTGATCATCCTTACTGTGGATATTCTATTAGGCACAGATGACATTTACATGGCACGAATGGAAAGCATGGAATCAGTAGGTTGTGTGTGAAGCCAGG	CTTGCGGGCCCTCCTGTGAGCGTCGCGTCAATCACATGGTCGTTATCCATGCGGAACATGTACACACCACGGTTCTGAGGGAAAAGTCAGTCAGTAAGTCATCAATGTCGACCTGAAACTCCCCTCTGTGTTCCTATCCACACCAGGAGGACTCAGTCGAAACTGAACGGAACGGCAGCCTGATCATCCTTACTGTGGATATTCTATTAGGCACAGATGACATTTACATGGCACGAATGGAAAGCATGGAATCAGTAGGTTGTGTGTGAAGCCAGG	-	novel	NA	P-0063978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	138	467	0	ENST00000262189.6:c.14461-202_14534del		p.X4821_splice	ENST00000262189	NM_170606.2	4821		57/59	0.232517807602577	2	FACETS	1	0.934	1	0.515	0.469	0.563	CLONAL	1	TRUE	0	0.352492336554333	2		467	760	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89842156	89842156	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs983221015	NA	P-0064021-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	366	285	0	ENST00000389301.3:c.1894C>G	p.Pro632Ala	p.P632A	ENST00000389301	NM_000135.2	632	Cca/Gca	21/43	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		285	823	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	67	523	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.897	0.781	1	0.897	0.781	1	CLONAL	1	TRUE	1	0.325606186300826	2		523	459	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864432	57864432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200606293	NA	P-0064026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	111	650	0	ENST00000228682.2:c.1909C>T	p.Arg637Trp	p.R637W	ENST00000228682	NM_005269.2	637	Cgg/Tgg	12/12	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.325606186300826	2		650	641	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630604	187630605	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0064026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	61	628	2	ENST00000441802.2:c.377dup	p.Asn126LysfsTer3	p.N126Kfs*3	ENST00000441802	NM_005245.3	126	aat/aaAt	2/27	1	2	FACETS	0.784	0.677	0.899	0.784	0.677	0.899	SUBCLONAL	1	TRUE	1	0.325606186300826	2		630	478	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519920	NA	P-0064026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	57	349	0	ENST00000397062.3:c.85G>A	p.Asp29Asn	p.D29N	ENST00000397062	NM_006164.4	29	Gat/Aat	2/5	1	2	FACETS	0.862	0.742	0.993	0.862	0.742	0.993	CLONAL	1	TRUE	1	0.325606186300826	2		349	406	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0064026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	100	682	0	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.325606186300826	2		682	522	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510755	120510755	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	76	580	0	ENST00000256646.2:c.1209C>G	p.Cys403Trp	p.C403W	ENST00000256646	NM_024408.3	403	tgC/tgG	7/34	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.325606186300826	2		580	454	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679878	33679878	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	84	622	0	ENST00000308377.4:c.2203G>T	p.Asp735Tyr	p.D735Y	ENST00000308377	NM_152270.3	735	Gat/Tat	5/5	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.325606186300826	2		622	481	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245973	41245980	+	frameshift_variant	Frame_Shift_Del	DEL	AACTGCCA	AACTGCCA	-	novel	NA	P-0064026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	59	506	0	ENST00000357654.3:c.1568_1575del	p.Leu523SerfsTer5	p.L523Sfs*5	ENST00000357654	NM_007294.3	523	tTGGCAGTT/t	10/23	1	2	FACETS	0.924	0.799	1	0.924	0.799	1	CLONAL	1	TRUE	1	0.325606186300826	2		506	392	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29445841	29445841	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200735359	NA	P-0064026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	105	607	0	ENST00000544604.2:c.1672G>A	p.Gly558Ser	p.G558S	ENST00000544604	NM_001206998.1	558	Ggc/Agc	8/9	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.325606186300826	2		607	506	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521141	187521141	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	77	642	0	ENST00000441802.2:c.12014T>A	p.Val4005Glu	p.V4005E	ENST00000441802	NM_005245.3	4005	gTa/gAa	22/27	1	2	FACETS	0.944	0.831	1	0.944	0.831	1	CLONAL	1	TRUE	1	0.325606186300826	2		642	501	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524129	187524129	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	82	574	0	ENST00000441802.2:c.11410G>T	p.Glu3804Ter	p.E3804*	ENST00000441802	NM_005245.3	3804	Gaa/Taa	20/27	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.325606186300826	2		574	475	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540329	187540329	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	80	632	0	ENST00000441802.2:c.7411G>C	p.Val2471Leu	p.V2471L	ENST00000441802	NM_005245.3	2471	Gtt/Ctt	10/27	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.325606186300826	2		632	479	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459466	50459466	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	57	518	0	ENST00000331340.3:c.755A>T	p.Asp252Val	p.D252V	ENST00000331340	NM_006060.4	252	gAc/gTc	7/8	1	2	FACETS	0.836	0.719	0.962	0.836	0.719	0.962	CLONAL	1	TRUE	1	0.325606186300826	2		518	419	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126437	5126437	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	38	455	0	ENST00000381652.3:c.3282C>A	p.Cys1094Ter	p.C1094*	ENST00000381652	NM_004972.3	1094	tgC/tgA	24/25	0.325606186300826	4	FACETS	0.711	0.588	0.849	0.237	0.196	0.283	SUBCLONAL	1	TRUE	1	0.325606186300826	4		455	435	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401045	139401045	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	103	650	0	ENST00000277541.6:c.3948C>A	p.Cys1316Ter	p.C1316*	ENST00000277541	NM_017617.3	1316	tgC/tgA	24/34	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.325606186300826	2		650	548	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44911047	44911047	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	62	368	0	ENST00000377967.4:c.748G>T	p.Gly250Cys	p.G250C	ENST00000377967	NM_021140.2	250	Ggt/Tgt	9/29	1	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.325606186300826	1		368	264	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0064027-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	176	681	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.210033728453323	2	FACETS	0.787	0.725	0.852	0.787	0.725	0.852	SUBCLONAL	2	TRUE	0	0.23465861560731	2		682	953	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591115	67591123	+	inframe_deletion	In_Frame_Del	DEL	CTTATCCAG	CTTATCCAG	-	novel	NA	P-0064027-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	140	335	0	ENST00000274335.5:c.1710_1718del	p.Ile571_Leu573del	p.I571_L573del	ENST00000274335		570	CTTATCCAG/-	12/15	0.210033728453323	2	FACETS	0.907	0.828	0.989	0.907	0.828	0.989	CLONAL	2	TRUE	0	0.23465861560731	2		335	658	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625363	69625363	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1242191483	NA	P-0064027-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	80	567	0	ENST00000334134.2:c.430C>T	p.Arg144Cys	p.R144C	ENST00000334134	NM_005247.2	144	Cgc/Tgc	3/3	1	2	FACETS	0.81	0.712	0.915	0.81	0.712	0.915	CLONAL	1	TRUE	1	0.23465861560731	2		567	842	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912127	114912127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064027-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	112	408	0	ENST00000543371.1:c.1197C>A	p.Tyr399Ter	p.Y399*	ENST00000543371	NM_001198531.1	399	taC/taA	11/14	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.23465861560731	2		408	902	SUCCESS
AR	367	MSKCC	GRCh37	X	66931340	66931340	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064027-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	86	519	0	ENST00000374690.3:c.1982C>A	p.Thr661Lys	p.T661K	ENST00000374690	NM_000044.3	661	aCa/aAa	4/8	0.213752724855105	3	FACETS	0.836	0.738	0.941	0.418	0.369	0.471	CLONAL	1	TRUE	1	0.23465861560731	3		519	980	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937694	76937694	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1184990999	NA	P-0064028-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	83	528	0	ENST00000373344.5:c.3054G>T	p.Lys1018Asn	p.K1018N	ENST00000373344	NM_000489.3	1018	aaG/aaT	9/35	1	2	FACETS	0.378	0.333	0.426	0.378	0.333	0.426	SUBCLONAL	1	TRUE	1	0.56	2		528	785	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022913	27022938	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGCCGCCGCCAGCAGCCTGGGCAA	CCCGCCGCCGCCAGCAGCCTGGGCAA	-	rs797045262	NA	P-0064029-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	209	531	0	ENST00000324856.7:c.31_56del	p.Ser11AlafsTer91	p.S11Afs*91	ENST00000324856	NM_006015.4	7	CCCGCCGCCGCCAGCAGCCTGGGCAAc/c	1/20	0.628690689039202	2	FACETS	1	0.993	1	0.746	0.701	0.791	CLONAL	1	TRUE	0	0.629638603638945	2		531	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0064029-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	360	604	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	0.629638603638945	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.629638603638945	2		604	556	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415628	49415628	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064029-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	270	468	0	ENST00000301067.7:c.16549G>C	p.Glu5517Gln	p.E5517Q	ENST00000301067	NM_003482.3	5517	Gag/Cag	54/54	0.280683566668476	5	FACETS	0.878	0.83	0.927			1	INDETERMINATE	3	TRUE	NA	0.629638603638945	5		468	633	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974770	21974770	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064029-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	323	568	0	ENST00000304494.5:c.57del	p.Ala20ArgfsTer6	p.A20Rfs*6	ENST00000304494	NM_000077.4	19	gcC/gc	1/3	0.628690689039202	2	FACETS	0.936	0.896	0.976	0.936	0.896	0.976	CLONAL	2	TRUE	0	0.629638603638945	2		568	548	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18747471	18747471	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs368190625	NA	P-0064029-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	34	298	0	ENST00000266497.5:c.3932A>G	p.Gln1311Arg	p.Q1311R	ENST00000266497		1311	cAa/cGa	28/31	0.629638603638945	3	FACETS	0.477	0.39	0.573	0.238	0.195	0.287	SUBCLONAL	1	TRUE	1	0.629638603638945	3		298	298	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544854	86544854	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064029-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	135	537	0	ENST00000262426.4:c.679G>T	p.Gly227Cys	p.G227C	ENST00000262426	NM_001451.2	227	Ggc/Tgc	1/2	1	2	FACETS	0.877	0.802	0.954	0.877	0.802	0.954	CLONAL	1	TRUE	1	0.629638603638945	2		537	489	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665503	138665503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064029-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	302	416	2	ENST00000330315.3:c.62G>A	p.Gly21Asp	p.G21D	ENST00000330315	NM_023067.3	21	gGt/gAt	1/1	0.629638603638945	6	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	3	0.629638603638945	6		418	683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064029-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	31	617	0	ENST00000269305.4:c.528C>A	p.Cys176Ter	p.C176*	ENST00000269305	NM_001126112.2	176	tgC/tgA	5/11	0.257631408449246	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		617	486	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713341	40713341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1305277749	NA	P-0064029-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	19	628	1	ENST00000373198.4:c.4174C>T	p.Arg1392Cys	p.R1392C	ENST00000373198	NM_133170.3	1392	Cgt/Tgt	30/32	0.337966816399283	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		629	296	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128201179	128201179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064029-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	51	525	0	ENST00000265960.3:c.1556C>T	p.Ser519Phe	p.S519F	ENST00000265960	NM_001006617.1	519	tCc/tTc	12/12	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		525	305	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418406	139418406	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1348892740	NA	P-0064029-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	38	502	0	ENST00000277541.6:c.166C>T	p.Arg56Ter	p.R56*	ENST00000277541	NM_017617.3	56	Cga/Tga	3/34	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		502	305	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198273	185198273	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064029-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	52	505	0	ENST00000265026.3:c.2755C>G	p.Gln919Glu	p.Q919E	ENST00000265026	NM_004721.4	919	Cag/Gag	13/14	0.162060347061184	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		505	486	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831081	72831081	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064029-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	20	540	0	ENST00000268489.5:c.5500G>A	p.Asp1834Asn	p.D1834N	ENST00000268489	NM_006885.3	1834	Gat/Aat	9/10	0.162060347061184	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		540	261	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265067	5265067	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064029-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	13	587	0	ENST00000357368.4:c.520C>T	p.Pro174Ser	p.P174S	ENST00000357368	NM_002850.3	174	Cct/Tct	5/38	0.162060347061184	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		587	237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0064030-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	510	454	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.838754233309892	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.83941982724935	2		454	606	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106662	27106662	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064030-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	594	702	0	ENST00000324856.7:c.6273G>A	p.Trp2091Ter	p.W2091*	ENST00000324856	NM_006015.4	2091	tgG/tgA	20/20	1	2	FACETS	0.969	0.948	0.99	1	0.998	1	CLONAL	2	TRUE	1	0.83941982724935	2		702	730	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0064030-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	341	470	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.83941982724935	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.83941982724935	1		470	439	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967226	134967226	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064030-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	296	622	0	ENST00000398015.3:c.2565G>T	p.Gln855His	p.Q855H	ENST00000398015	NM_004441.4	855	caG/caT	14/16	NA	2	FACETS	0.861	0.814	0.909			1	INDETERMINATE	1	TRUE	NA	0.83941982724935	2		622	819	SUCCESS
ALB	213	MSKCC	GRCh37	4	74285256	74285256	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1336744235	NA	P-0064030-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	121	494	0	ENST00000295897.4:c.1685A>G	p.Lys562Arg	p.K562R	ENST00000295897	NM_000477.5	562	aAg/aGg	13/15	0.569460967522594	1	FACETS	0.312	0.283	0.343	0.312	0.283	0.343	SUBCLONAL	1	TRUE	0	0.83941982724935	1		494	536	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974744	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAGCAGCGCCCGCA	CCTCCAGCAGCGCCCGCA	-	novel	NA	P-0064030-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	349	656	0	ENST00000304494.5:c.83_100del	p.Val28_Glu33del	p.V28_E33del	ENST00000304494	NM_000077.4	28	gTGCGGGCGCTGCTGGAGGcg/gcg	1/3	0.83941982724935	1	FACETS	0.971	0.936	1	0.971	0.936	1	CLONAL	1	TRUE	0	0.83941982724935	1		656	497	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	136	523	0				ENST00000310581	NM_198253.2	-/1132			0.195955122277922	3	FACETS	1	0.942	1	0.686	0.631	0.743	INDETERMINATE	2	TRUE	0	0.427746884939802	3		523	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0064031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	193	666	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.427746884939802	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.427746884939802	1		666	633	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374305	138374305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	80	427	0	ENST00000289153.2:c.3139G>A	p.Glu1047Lys	p.E1047K	ENST00000289153	NM_006219.2	1047	Gag/Aag	22/22	0.315227786246517	1	FACETS	0.546	0.481	0.615	0.546	0.481	0.615	SUBCLONAL	1	TRUE	0	0.427746884939802	1		427	539	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140165	50140165	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	293	555	0	ENST00000246792.3:c.260A>T	p.Gln87Leu	p.Q87L	ENST00000246792	NM_006270.3	87	cAg/cTg	3/6	0.427746884939802	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.427746884939802	2		555	668	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518254	187518254	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	161	495	0	ENST00000441802.2:c.12440G>T	p.Gly4147Val	p.G4147V	ENST00000441802	NM_005245.3	4147	gGc/gTc	25/27	0.315227786246517	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.427746884939802	1		495	591	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929479	81929479	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	109	509	0	ENST00000359376.3:c.1140C>G	p.Ile380Met	p.I380M	ENST00000359376	NM_002661.3	380	atC/atG	13/33	1	2	FACETS	0.795	0.715	0.879	0.795	0.715	0.879	SUBCLONAL	1	TRUE	1	0.427746884939802	2		509	641	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858399	89858399	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	154	542	0	ENST00000389301.3:c.1161G>C	p.Gln387His	p.Q387H	ENST00000389301	NM_000135.2	387	caG/caC	13/43	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.427746884939802	2		542	670	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485448	57485448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	153	454	0	ENST00000371085.3:c.1030G>A	p.Glu344Lys	p.E344K	ENST00000371085	NM_000516.4	344	Gag/Aag	12/13	1	2	FACETS	0.964	0.884	1	0.964	0.884	1	CLONAL	1	TRUE	1	0.427746884939802	2		454	742	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038233	30038233	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	172	385	0	ENST00000338641.4:c.406G>A	p.Glu136Lys	p.E136K	ENST00000338641	NM_000268.3	136	Gag/Aag	4/16	0.427746884939802	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.427746884939802	1		385	559	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599209	28599209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	68	590	0	ENST00000253063.3:c.655G>A	p.Glu219Lys	p.E219K	ENST00000253063	NM_031459.4	219	Gag/Aag	5/10	0.315227786246517	1	FACETS	0.436	0.38	0.497	0.436	0.38	0.497	SUBCLONAL	1	TRUE	0	0.427746884939802	1		590	573	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858800	9858800	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs768337205	NA	P-0064031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	125	403	0	ENST00000330684.3:c.2601C>G	p.Ile867Met	p.I867M	ENST00000330684	NM_001134407.1	867	atC/atG	13/13	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.427746884939802	2		403	532	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206646576	206646576	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	55	472	0	ENST00000367120.3:c.6G>T	p.Gln2His	p.Q2H	ENST00000367120	NM_014002.3	2	caG/caT	3/22	0.315227786246517	1	FACETS	0.429	0.367	0.497	0.429	0.367	0.497	SUBCLONAL	1	TRUE	0	0.427746884939802	1		472	471	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94906420	94906420	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0064031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	78	326	0	ENST00000536441.1:c.1478G>C	p.Ter493SerextTer18	p.*493Sext*18	ENST00000536441	NM_144665.3	493	tGa/tCa	10/10	0.315227786246517	1	FACETS	0.841	0.745	0.942	0.841	0.745	0.942	CLONAL	1	TRUE	0	0.427746884939802	1		326	341	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110007	115110007	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	97	501	0	ENST00000257566.3:c.1871A>T	p.His624Leu	p.H624L	ENST00000257566	NM_016569.3	624	cAc/cTc	8/8	0.252646882180399	1	FACETS	0.851	0.763	0.943	0.851	0.763	0.943	INDETERMINATE	1	TRUE	0	0.427746884939802	1		501	419	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120802538	120802538	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	64	355	0	ENST00000257552.2:c.288C>A	p.Phe96Leu	p.F96L	ENST00000257552	NM_002442.3	96	ttC/ttA	5/15	0.252646882180399	1	FACETS	0.488	0.423	0.558	0.488	0.423	0.558	INDETERMINATE	1	TRUE	0	0.427746884939802	1		355	482	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219271	133219271	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	126	511	0	ENST00000320574.5:c.4773G>T	p.Trp1591Cys	p.W1591C	ENST00000320574	NM_006231.2	1591	tgG/tgT	37/49	0.252646882180399	1	FACETS	0.815	0.741	0.893	0.815	0.741	0.893	INDETERMINATE	1	TRUE	0	0.427746884939802	1		511	568	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562475	21562475	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751975912	NA	P-0064031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	60	495	0	ENST00000382592.4:c.1444G>A	p.Glu482Lys	p.E482K	ENST00000382592	NM_014572.2	482	Gag/Aag	4/8	0.351232247845366	1	FACETS	0.554	0.479	0.635	0.554	0.479	0.635	SUBCLONAL	1	TRUE	0	0.427746884939802	1		495	398	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33681019	33681019	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	105	441	0	ENST00000308377.4:c.1258C>A	p.His420Asn	p.H420N	ENST00000308377	NM_152270.3	420	Cac/Aac	4/5	1	2	FACETS	0.874	0.785	0.967	0.874	0.785	0.967	CLONAL	1	TRUE	1	0.427746884939802	2		441	562	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629670	187629670	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	91	477	0	ENST00000441802.2:c.1312G>T	p.Val438Leu	p.V438L	ENST00000441802	NM_005245.3	438	Gta/Tta	2/27	0.315227786246517	1	FACETS	0.513	0.456	0.574	0.513	0.456	0.574	SUBCLONAL	1	TRUE	0	0.427746884939802	1		477	652	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20487032	20487032	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs868668550	NA	P-0064031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	99	330	0	ENST00000346618.3:c.997G>A	p.Glu333Lys	p.E333K	ENST00000346618	NM_001949.4	333	Gag/Aag	5/7	0.427746884939802	2	FACETS	1	0.897	1	0.5	0.448	0.554	CLONAL	1	TRUE	0	0.427746884939802	2		330	463	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38157014	38157014	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	115	422	0	ENST00000317025.8:c.2706G>A	p.Met902Ile	p.M902I	ENST00000317025	NM_023034.1	902	atG/atA	15/24	0.427746884939802	1	FACETS	0.983	0.892	1	0.983	0.892	1	CLONAL	1	TRUE	0	0.427746884939802	1		422	430	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341449	70341449	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	160	506	0	ENST00000374080.3:c.884G>T	p.Arg295Leu	p.R295L	ENST00000374080		295	cGc/cTc	7/45	0.351232247845366	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.427746884939802	1		506	572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0064032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	213	409	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	0.466544709558174	1	FACETS	0.959	0.894	1	0.959	0.894	1	CLONAL	1	TRUE	0	0.466544709558174	1		409	730	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120846	94120846	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1300929218	NA	P-0064032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	165	591	0	ENST00000369303.4:c.205C>T	p.Arg69Ter	p.R69*	ENST00000369303	NM_004440.3	69	Cga/Tga	3/17	1	2	FACETS	0.821	0.754	0.89	0.821	0.754	0.89	CLONAL	1	TRUE	1	0.466544709558174	2		591	862	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977129	85977131	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	novel	NA	P-0064032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	105	359	0	ENST00000263360.6:c.733_735del	p.Asp245del	p.D245del	ENST00000263360	NM_003797.3	244	tATGat/tat	8/12	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.466544709558174	2		359	430	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989538	85989538	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	149	432	0	ENST00000263360.6:c.1297A>G	p.Ser433Gly	p.S433G	ENST00000263360	NM_003797.3	433	Agt/Ggt	12/12	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.466544709558174	2		432	616	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027184	49027184	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0064032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	157	508	0	ENST00000267163.4:c.1751del	p.Asp584ValfsTer27	p.D584Vfs*27	ENST00000267163	NM_000321.2	584	gAt/gt	18/27	0.466544709558174	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.466544709558174	1		508	489	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856136	151856136	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	204	609	0	ENST00000262189.6:c.11482C>T	p.Gln3828Ter	p.Q3828*	ENST00000262189	NM_170606.2	3828	Caa/Taa	44/59	0.352859088032388	2	FACETS	0.926	0.859	0.996	0.463	0.429	0.498	CLONAL	1	TRUE	0	0.466544709558174	2		609	944	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793244	139793244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	169	602	0	ENST00000247668.2:c.52G>A	p.Gly18Ser	p.G18S	ENST00000247668	NM_021138.3	18	Ggc/Agc	2/11	1	2	FACETS	0.906	0.834	0.98	0.906	0.834	0.98	CLONAL	1	TRUE	1	0.466544709558174	2		602	800	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	152	331	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.48520267719892	1	FACETS	0.927	0.853	1	0.927	0.853	1	CLONAL	1	TRUE	0	0.48520267719892	1		331	512	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602487	10602488	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0064033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	196	649	0	ENST00000171111.5:c.1090_1091delinsCT	p.Gly364Leu	p.G364L	ENST00000171111	NM_203500.1	364	GGc/CTc	3/6	0.48520267719892	1	FACETS	0.874	0.812	0.938	0.874	0.812	0.938	CLONAL	1	TRUE	0	0.48520267719892	1		649	700	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132634	11132635	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0064033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	229	514	0	ENST00000358026.2:c.2854dup	p.Glu952GlyfsTer7	p.E952Gfs*7	ENST00000358026	NM_001128849.1	950	-/G	19/36	0.48520267719892	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.48520267719892	1		514	656	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239598	53239598	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	206	506	0	ENST00000375401.3:c.1744C>G	p.Pro582Ala	p.P582A	ENST00000375401	NM_004187.3	582	Cca/Gca	12/26	1	2	FACETS	0.979	0.91	1	0.979	0.91	1	CLONAL	1	TRUE	1	0.48520267719892	2		506	867	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349190	70349190	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	277	621	0	ENST00000374080.3:c.3602C>T	p.Ser1201Phe	p.S1201F	ENST00000374080		1201	tCc/tTc	26/45	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.48520267719892	2		621	1059	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938791	76938791	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	231	432	0	ENST00000373344.5:c.1957C>A	p.Leu653Ile	p.L653I	ENST00000373344	NM_000489.3	653	Ctt/Att	9/35	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.48520267719892	2		432	872	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064034-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	235	331	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.249827084531862	3	FACETS	0.889	0.84	0.939	0.889	0.84	0.939	INDETERMINATE	3	TRUE	0	0.442903754019398	3		331	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0064034-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	340	525	0	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	0.442903754019398	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.442903754019398	2		525	639	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913385	NA	P-0064034-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	239	649	1	ENST00000304494.5:c.247C>G	p.His83Asp	p.H83D	ENST00000304494	NM_000077.4	83	Cac/Gac	2/3	0.442903754019398	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.442903754019398	1		650	614	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965472	68965472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200682883	NA	P-0064034-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	141	549	1	ENST00000288368.4:c.1084C>T	p.Arg362Trp	p.R362W	ENST00000288368	NM_024870.2	362	Cgg/Tgg	9/40	0.139104680400751	5	FACETS	0.901	0.824	0.981	0.451	0.412	0.491	INDETERMINATE	2	TRUE	1	0.442903754019398	5		550	588	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182292	38182292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1353791431	NA	P-0064035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	80	1178	0	ENST00000396334.3:c.728G>A	p.Ser243Asn	p.S243N	ENST00000396334	NM_002468.4	243	aGc/aAc	4/5	0.124758521742201	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.910142028636135	0		1178	182	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100998	41100998	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772057709	NA	P-0064035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	137	1758	1	ENST00000373198.4:c.1358G>A	p.Arg453His	p.R453H	ENST00000373198	NM_133170.3	453	cGc/cAc	8/32	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.910142028636135	2		1759	278	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003764	45003764	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0064035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	132	1021	0	ENST00000558401.1:c.20T>G	p.Leu7Ter	p.L7*	ENST00000558401	NM_004048.2	7	tTa/tGa	1/4	0.910142028636135	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.910142028636135	2		1021	142	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937230	76937230	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	116	217	0	ENST00000373344.5:c.3518C>A	p.Ser1173Ter	p.S1173*	ENST00000373344	NM_000489.3	1173	tCa/tAa	9/35	0.720998401509775	0	FACETS		NA	1			1	NA	1	TRUE	NA	0.910142028636135	0		217	125	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736474	85736474	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	231	698	2	ENST00000370580.1:c.173G>T	p.Arg58Leu	p.R58L	ENST00000370580	NM_003921.4	58	cGa/cTa	2/3	0.910142028636135	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.910142028636135	2		700	249	SUCCESS
BLM	641	MSKCC	GRCh37	15	91306195	91306195	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs772230310	NA	P-0064035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	217	527	0	ENST00000355112.3:c.1883-1G>A		p.X628_splice	ENST00000355112	NM_000057.2	628			0.910142028636135	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.910142028636135	2		527	238	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797252	42797252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762633949	NA	P-0064035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	92	1880	2	ENST00000575354.2:c.3614G>A	p.Arg1205Gln	p.R1205Q	ENST00000575354	NM_015125.3	1205	cGg/cAg	15/20	0.181483095000243	1	FACETS	0.535	0.486	0.584	0.535	0.486	0.584	INDETERMINATE	1	TRUE	0	0.910142028636135	1		1882	206	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541472	187541472	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	155	1392	4	ENST00000441802.2:c.6268G>A	p.Val2090Ile	p.V2090I	ENST00000441802	NM_005245.3	2090	Gtt/Att	10/27	0.910142028636135	1	FACETS	0.573	0.533	0.613	0.573	0.533	0.613	SUBCLONAL	1	TRUE	0	0.910142028636135	1		1396	324	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200443	138200444	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0064035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	88	1158	0	ENST00000237289.4:c.1861_1862del	p.Lys621GlyfsTer50	p.K621Gfs*50	ENST00000237289	NM_001270507.1	621	AAg/g	7/9	0.910142028636135	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.910142028636135	1		1158	96	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106512992	106512992	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	121	880	0	ENST00000359195.3:c.2006T>G	p.Phe669Cys	p.F669C	ENST00000359195	NM_002649.2	669	tTt/tGt	3/11	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.910142028636135	2		880	264	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981584	70981584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	144	1499	0	ENST00000276594.2:c.512C>T	p.Pro171Leu	p.P171L	ENST00000276594	NM_024504.3	171	cCt/cTt	2/8	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.910142028636135	2		1499	315	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0064036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	683	473	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.802543697607828	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	1	0.830789800999773	4		473	992	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0064036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	803	617	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.830789800999773	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.830789800999773	3		617	894	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138567	55138567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	48	486	0	ENST00000257290.5:c.1244C>T	p.Ser415Leu	p.S415L	ENST00000257290	NM_006206.4	415	tCa/tTa	9/23	1	2	FACETS	0.207	0.174	0.242	0.207	0.174	0.242	SUBCLONAL	1	TRUE	1	0.830789800999773	2		486	559	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735351	204735351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759766975	NA	P-0064036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	249	636	0	ENST00000302823.3:c.152G>A	p.Arg51Gln	p.R51Q	ENST00000302823	NM_005214.4	51	cGa/cAa	2/4	0.830789800999773	3	FACETS	0.833	0.78	0.889	0.417	0.39	0.445	CLONAL	1	TRUE	1	0.830789800999773	3		636	1018	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262364	39262364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	195	442	0	ENST00000402219.2:c.1063G>A	p.Glu355Lys	p.E355K	ENST00000402219	NM_005633.3	355	Gaa/Aaa	8/23	0.830789800999773	3	FACETS	0.772	0.715	0.83	0.386	0.357	0.415	SUBCLONAL	1	TRUE	1	0.830789800999773	3		442	861	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864663	68864663	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773560075	NA	P-0064036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	36	471	0	ENST00000288368.4:c.34G>A	p.Glu12Lys	p.E12K	ENST00000288368	NM_024870.2	12	Gag/Aag	1/40	1	2	FACETS	0.178	0.146	0.214	0.178	0.146	0.214	SUBCLONAL	1	TRUE	1	0.830789800999773	2		471	486	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748898	41748898	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1307122843	NA	P-0064036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	97	702	0	ENST00000301178.4:c.1423C>T	p.Arg475Ter	p.R475*	ENST00000301178	NM_021913.4	475	Cga/Tga	11/20	0.830789800999773	3	FACETS	0.286	0.254	0.32	0.143	0.127	0.16	SUBCLONAL	1	TRUE	1	0.830789800999773	3		702	1156	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315393	30315393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146306622	NA	P-0064036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	52	592	0	ENST00000322652.5:c.1078C>T	p.Arg360Cys	p.R360C	ENST00000322652	NM_015355.2	360	Cgt/Tgt	10/16	0.830789800999773	3	FACETS	0.192	0.163	0.225	0.064	0.054	0.075	SUBCLONAL	1	TRUE	0	0.830789800999773	3		592	921	SUCCESS
MAD2L2	10459	MSKCC	GRCh37	1	11736130	11736130	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	232	631	0	ENST00000235310.3:c.400G>A	p.Asp134Asn	p.D134N	ENST00000235310		134	Gat/Aat	8/11	0.830789800999773	2	FACETS	0.811	0.76	0.863	0.405	0.38	0.432	CLONAL	1	TRUE	0	0.830789800999773	2		631	689	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115252327	115252327	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	170	489	0	ENST00000369535.4:c.313G>A	p.Asp105Asn	p.D105N	ENST00000369535	NM_002524.4	105	Gac/Aac	4/7	0.830789800999773	2	FACETS	0.715	0.662	0.771	0.358	0.331	0.386	SUBCLONAL	1	TRUE	0	0.830789800999773	2		489	572	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195490	102195490	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	61	662	0	ENST00000263464.3:c.250G>C	p.Glu84Gln	p.E84Q	ENST00000263464	NM_001165.4	84	Gaa/Caa	2/9	0.830789800999773	3	FACETS	0.183	0.157	0.211	0.091	0.078	0.106	SUBCLONAL	1	TRUE	1	0.830789800999773	3		662	1137	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123889486	123889486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61955123	NA	P-0064036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	120	212	0	ENST00000330479.4:c.713G>A	p.Arg238Gln	p.R238Q	ENST00000330479	NM_020382.3	238	cGg/cAg	7/9	0.830789800999773	2	FACETS	1	0.976	1	0.578	0.533	0.623	CLONAL	1	TRUE	0	0.830789800999773	2		212	250	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993813	72993813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	317	825	0	ENST00000268489.5:c.232G>A	p.Glu78Lys	p.E78K	ENST00000268489	NM_006885.3	78	Gag/Aag	2/10	0.829562412635676	3	FACETS	1	0.969	1	0.345	0.326	0.365	CLONAL	1	TRUE	0	0.830789800999773	3		825	1043	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727114	41727114	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	252	622	0	ENST00000301178.4:c.372G>C	p.Gln124His	p.Q124H	ENST00000301178	NM_021913.4	124	caG/caC	3/20	0.830789800999773	3	FACETS	0.853	0.798	0.909	0.426	0.399	0.455	CLONAL	1	TRUE	1	0.830789800999773	3		622	1007	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719518	190719518	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0064036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	189	523	0	ENST00000441310.2:c.1520C>G	p.Ser507Ter	p.S507*	ENST00000441310	NM_000534.4	507	tCa/tGa	9/13	1	2	FACETS	0.779	0.724	0.835	0.779	0.724	0.835	SUBCLONAL	1	TRUE	1	0.830789800999773	2		523	584	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293997	1293997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1440	276	825	0	ENST00000310581.5:c.1004C>T	p.Ser335Leu	p.S335L	ENST00000310581	NM_198253.2	335	tCa/tTa	2/16	0.773330721408534	5	FACETS	0.87	0.814	0.928			1	CLONAL	1	TRUE	NA	0.830789800999773	5		825	1716	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637460	176637460	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1493	276	535	0	ENST00000439151.2:c.2060C>G	p.Ser687Cys	p.S687C	ENST00000439151	NM_022455.4	687	tCt/tGt	5/23	0.830789800999773	6	FACETS	1	0.935	1	0.2	0.187	0.214	CLONAL	1	TRUE	1	0.830789800999773	6		535	1769	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415043	109415043	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	245	544	0	ENST00000436639.2:c.234C>G	p.Phe78Leu	p.F78L	ENST00000436639	NM_014454.2	78	ttC/ttG	1/10	1	2	FACETS	0.84	0.789	0.892	0.84	0.789	0.892	CLONAL	1	TRUE	1	0.830789800999773	2		544	702	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0064037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	71	348	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.928	0.81	1	0.928	0.81	1	CLONAL	1	TRUE	1	0.232480239741612	2		348	658	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0064037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	152	494	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.177359747063506	2	FACETS	1	0.98	1	0.624	0.57	0.681	CLONAL	1	TRUE	0	0.232480239741612	2		494	1048	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0064037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	196	681	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.232480239741612	2		681	1273	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169377	11169377	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519916	NA	P-0064037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	139	417	0	ENST00000361445.4:c.7498A>T	p.Ile2500Phe	p.I2500F	ENST00000361445	NM_004958.3	2500	Att/Ttt	56/58	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.232480239741612	2		417	865	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487556	38487556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1234	77	594	0	ENST00000254066.5:c.86C>T	p.Pro29Leu	p.P29L	ENST00000254066	NM_000964.3	29	cCc/cTc	2/9	1	2	FACETS	0.505	0.442	0.574	0.505	0.442	0.574	SUBCLONAL	1	TRUE	1	0.232480239741612	2		594	1311	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141557661	141557661	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759579021	NA	P-0064037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	84	593	0	ENST00000220592.5:c.1654G>A	p.Val552Met	p.V552M	ENST00000220592	NM_012154.3	552	Gtg/Atg	13/19	1	2	FACETS	0.613	0.54	0.693	0.613	0.54	0.693	SUBCLONAL	1	TRUE	1	0.232480239741612	2		593	1178	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250842	153250842	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	47	344	0	ENST00000281708.4:c.1218G>A	p.Trp406Ter	p.W406*	ENST00000281708	NM_033632.3	406	tgG/tgA	8/12	0.232480239741612	1	FACETS	0.599	0.504	0.703	0.599	0.504	0.703	SUBCLONAL	1	TRUE	0	0.232480239741612	1		344	597	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357078	70357078	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587778438	NA	P-0064037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	116	690	0	ENST00000374080.3:c.5593A>G	p.Met1865Val	p.M1865V	ENST00000374080		1865	Atg/Gtg	39/45	1	2	FACETS	0.831	0.747	0.92	0.831	0.747	0.92	CLONAL	1	TRUE	1	0.232480239741612	2		690	1201	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508437	106508437	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	104	563	0	ENST00000359195.3:c.431C>T	p.Ser144Phe	p.S144F	ENST00000359195	NM_002649.2	144	tCc/tTc	2/11	1	2	FACETS	0.913	0.816	1	0.913	0.816	1	CLONAL	1	TRUE	1	0.232480239741612	2		563	980	SUCCESS
APC	324	MSKCC	GRCh37	5	112175765	112175770	+	frameshift_variant	Frame_Shift_Del	DEL	GCCACG	GCCACG	CCACA	novel	NA	P-0064037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	123	574	1	ENST00000257430.4:c.4474_4479delinsCCACA	p.Ala1492ProfsTer15	p.A1492Pfs*15	ENST00000257430	NM_000038.5	1492	GCCACG/CCACA	16/16	0.232480239741612	1	FACETS	0.947	0.856	1	0.947	0.856	1	CLONAL	1	TRUE	0	0.232480239741612	1		575	987	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	170	523	0				ENST00000310581	NM_198253.2	-/1132			0.39018805225667	3	FACETS	0.859	0.794	0.927	0.859	0.794	0.927	CLONAL	2	TRUE	1	0.39018805225667	3		523	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0064038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	159	850	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.39018805225667	2		852	713	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0064038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	141	998	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.978	0.892	1	0.978	0.892	1	CLONAL	1	TRUE	1	0.39018805225667	2		998	739	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955550	48955550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913304	NA	P-0064038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	166	365	0	ENST00000267163.4:c.1666C>T	p.Arg556Ter	p.R556*	ENST00000267163	NM_000321.2	556	Cga/Tga	17/27	0.39018805225667	3	FACETS	0.968	0.896	1	0.968	0.896	1	CLONAL	2	TRUE	1	0.39018805225667	3		365	525	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412884	49412884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	124	473	0	ENST00000418115.1:c.139G>A	p.Glu47Lys	p.E47K	ENST00000418115	NM_001664.2	47	Gag/Aag	2/5	0.39018805225667	3	FACETS	1	0.934	1	0.52	0.47	0.571	CLONAL	1	TRUE	1	0.39018805225667	3		473	731	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929157	44929157	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	96	452	0	ENST00000377967.4:c.2257C>T	p.Gln753Ter	p.Q753*	ENST00000377967	NM_021140.2	753	Cag/Tag	17/29	1	2	FACETS	0.851	0.76	0.948	0.851	0.76	0.948	CLONAL	1	TRUE	1	0.39018805225667	2		452	578	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390302	56390302	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	106	376	0	ENST00000348428.3:c.1041G>C	p.Leu347Phe	p.L347F	ENST00000348428	NM_006785.3	347	ttG/ttC	10/17	1	2	FACETS	0.988	0.889	1	0.988	0.889	1	CLONAL	1	TRUE	1	0.39018805225667	2		376	550	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923102	48923102	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	66	289	0	ENST00000267163.4:c.550G>T	p.Glu184Ter	p.E184*	ENST00000267163	NM_000321.2	184	Gaa/Taa	6/27	0.39018805225667	3	FACETS	0.909	0.791	1	0.454	0.395	0.518	CLONAL	1	TRUE	1	0.39018805225667	3		289	445	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257971	16257971	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444111349	NA	P-0064038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	150	696	0	ENST00000375759.3:c.5236G>A	p.Glu1746Lys	p.E1746K	ENST00000375759	NM_015001.2	1746	Gag/Aag	11/15	0.39018805225667	3	FACETS	1	0.956	1	0.535	0.489	0.584	CLONAL	1	TRUE	1	0.39018805225667	3		696	858	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205038	123205038	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	60	399	0	ENST00000218089.9:c.2398C>T	p.His800Tyr	p.H800Y	ENST00000218089	NM_001042749.1	800	Cat/Tat	25/35	0.39018805225667	3	FACETS	0.705	0.608	0.811	0.353	0.304	0.406	SUBCLONAL	1	TRUE	1	0.39018805225667	3		399	521	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478815	56478815	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	212	491	1	ENST00000267101.3:c.271A>C	p.Met91Leu	p.M91L	ENST00000267101	NM_001982.3	91	Atg/Ctg	3/28	0.39018805225667	3	FACETS	0.99	0.924	1	0.99	0.924	1	CLONAL	2	TRUE	1	0.39018805225667	3		492	656	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239889	41239889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1290398156	NA	P-0064038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	89	400	0	ENST00000379561.5:c.461C>T	p.Ser154Leu	p.S154L	ENST00000379561	NM_002015.3	154	tCg/tTg	1/3	0.39018805225667	3	FACETS	0.937	0.832	1	0.468	0.416	0.524	CLONAL	1	TRUE	1	0.39018805225667	3		400	582	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390450	56390450	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	101	381	0	ENST00000348428.3:c.1189G>T	p.Glu397Ter	p.E397*	ENST00000348428	NM_006785.3	397	Gag/Tag	10/17	1	2	FACETS	0.91	0.815	1	0.91	0.815	1	CLONAL	1	TRUE	1	0.39018805225667	2		381	569	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67626348	67626349	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0064038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	97	384	0	ENST00000272342.5:c.272dup	p.Ser92PhefsTer6	p.S92Ffs*6	ENST00000272342	NM_019002.3	91	tct/tCct	2/6	0.39018805225667	3	FACETS	0.928	0.829	1	0.464	0.414	0.517	CLONAL	1	TRUE	1	0.39018805225667	3		384	640	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851773	134851773	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	122	650	0	ENST00000398015.3:c.1179C>G	p.Ile393Met	p.I393M	ENST00000398015	NM_004441.4	393	atC/atG	5/16	0.362185483825173	4	FACETS	0.936	0.845	1	0.468	0.422	0.516	CLONAL	1	TRUE	2	0.39018805225667	4		650	929	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	615	523	0				ENST00000310581	NM_198253.2	-/1132			0.730558317242767	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.730558317242767	3		523	1098	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0064039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	440	558	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.730558317242767	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.730558317242767	1		558	723	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721760	176721760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587784216	NA	P-0064039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	409	643	0	ENST00000439151.2:c.7391G>A	p.Arg2464His	p.R2464H	ENST00000439151	NM_022455.4	2464	cGc/cAc	23/23	0.730558317242767	3	FACETS	0.977	0.929	1	0.489	0.464	0.514	CLONAL	1	TRUE	1	0.730558317242767	3		643	1564	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0064040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	371	597	0	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	0.630006043802808	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.630006043802808	2		597	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0064041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	146	514	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.331433356569228	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.331433356569228	1		514	681	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602764	10602764	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	143	627	2	ENST00000171111.5:c.814C>T	p.Arg272Cys	p.R272C	ENST00000171111	NM_203500.1	272	Cgc/Tgc	3/6	0.331433356569228	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.331433356569228	1		629	661	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945084	151945084	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	22	334	0	ENST00000262189.6:c.2435T>G	p.Met812Arg	p.M812R	ENST00000262189	NM_170606.2	812	aTg/aGg	14/59	0.296337993696954	3	FACETS	0.366	0.283	0.463	0.183	0.141	0.232	SUBCLONAL	1	TRUE	1	0.331433356569228	3		334	423	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486248	8486248	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768330226	NA	P-0064041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	201	582	1	ENST00000356435.5:c.2569C>A	p.Arg857Ser	p.R857S	ENST00000356435		857	Cgt/Agt	17/35	0.331433356569228	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.331433356569228	1		583	702	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123688	11123688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	133	522	0	ENST00000358026.2:c.2338G>A	p.Glu780Lys	p.E780K	ENST00000358026	NM_001128849.1	780	Gag/Aag	16/36	0.331433356569228	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.331433356569228	1		522	615	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302855	15302855	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	135	642	0	ENST00000263388.2:c.595G>T	p.Val199Leu	p.V199L	ENST00000263388	NM_000435.2	199	Gtg/Ttg	4/33	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.331433356569228	2		642	801	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198263223	198263223	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	92	401	0	ENST00000335508.6:c.3096A>T	p.Gln1032His	p.Q1032H	ENST00000335508	NM_012433.2	1032	caA/caT	21/25	0.331433356569228	1	FACETS	0.957	0.854	1	0.957	0.854	1	CLONAL	1	TRUE	0	0.331433356569228	1		401	484	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422987	12422987	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	107	419	0	ENST00000287820.6:c.477C>A	p.Cys159Ter	p.C159*	ENST00000287820	NM_015869.4	159	tgC/tgA	3/7	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.331433356569228	2		419	557	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748296	41748296	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	92	559	0	ENST00000226382.2:c.473G>T	p.Arg158Leu	p.R158L	ENST00000226382	NM_003924.3	158	cGc/cTc	3/3	1	2	FACETS	0.866	0.77	0.968	0.866	0.77	0.968	CLONAL	1	TRUE	1	0.331433356569228	2		559	641	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673527	30673528	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0064041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	162	841	0	ENST00000376406.3:c.3432_3433delinsTT	p.Gln1144_Ala1145delinsHisSer	p.Q1144_A1145delinsHS	ENST00000376406	NM_014641.2	1144	caGGcc/caTTcc	10/15	1	2	FACETS	0.969	0.888	1	0.969	0.888	1	CLONAL	1	TRUE	1	0.331433356569228	2		841	1009	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434586	110434586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1566411917	NA	P-0064043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	452	647	0	ENST00000375856.3:c.3815C>T	p.Pro1272Leu	p.P1272L	ENST00000375856	NM_003749.2	1272	cCg/cTg	1/2	0.591082253788075	5	FACETS	1	0.99	1	0.749	0.715	0.783	CLONAL	2	TRUE	2	0.586699215470422	5		647	1289	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105238591	105238700	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CCTGAGGTGAGGGCGAGTGTGTGGGAAATCTGGCGAGCGTGCCACGTGCATGCGTGAGTGTGGATATGTGGGGAGCATGCGTGCGCGTGAATATGCGGGGAGCAGCCGCA	CCTGAGGTGAGGGCGAGTGTGTGGGAAATCTGGCGAGCGTGCCACGTGCATGCGTGAGTGTGGATATGTGGGGAGCATGCGTGCGCGTGAATATGCGGGGAGCAGCCGCA	-	novel	NA	P-0064043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	41	250	0	ENST00000349310.3:c.1260+2_1260+111del		p.X420_splice	ENST00000349310	NM_001014432.1	420			0.327427539046459	3	FACETS	0.509	0.425	0.602	0.255	0.212	0.301	INDETERMINATE	1	TRUE	1	0.586699215470422	3		250	355	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098465	2098672	+	splice_acceptor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	GGGAGTGTGGGAGGAAAGGTTATGCCCACCAGAGACCCAGGGTCCTGACGGCTGGAGGTCCGCAGTGGGGAAGGTGGGCAGAGGTGTTGCTCAGATGTCCCCATTCCTGTTTCGTTTGCACAGAGGGGTTTTCTGGTGCGTCCTGGTCCACCATGGCCAAACCAACAAGCAAAGATTCAGGCTTGAAGGAGAAGTTTAAGATTCTGTT	GGGAGTGTGGGAGGAAAGGTTATGCCCACCAGAGACCCAGGGTCCTGACGGCTGGAGGTCCGCAGTGGGGAAGGTGGGCAGAGGTGTTGCTCAGATGTCCCCATTCCTGTTTCGTTTGCACAGAGGGGTTTTCTGGTGCGTCCTGGTCCACCATGGCCAAACCAACAAGCAAAGATTCAGGCTTGAAGGAGAAGTTTAAGATTCTGTT	-	novel	NA	P-0064043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	183	178	0	ENST00000219476.3:c.-29-119_60del		p.X10_splice	ENST00000219476	NM_000548.3	10		2/42	0.567890861569461	1	FACETS	0.813	0.772	0.853	1	0.994	1	CLONAL	2	TRUE	0	0.586699215470422	1		178	271	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900645	3900645	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	669	608	0	ENST00000262367.5:c.451del	p.Leu151Ter	p.L151*	ENST00000262367	NM_004380.2	151	Ctg/tg	2/31	0.451284502412426	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.586699215470422	3		608	942	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519986	NA	P-0064043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	765	545	0	ENST00000269305.4:c.809T>G	p.Phe270Cys	p.F270C	ENST00000269305	NM_001126112.2	270	tTt/tGt	8/11	0.556309990731278	4	FACETS	1	0.989	1			1	CLONAL	4	TRUE	NA	0.586699215470422	4		545	1017	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342988	225342988	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	157	442	0	ENST00000264414.4:c.2104G>T	p.Glu702Ter	p.E702*	ENST00000264414	NM_003590.4	702	Gag/Tag	15/16	0.591082253788075	3	FACETS	0.951	0.873	1	0.475	0.436	0.516	CLONAL	1	TRUE	1	0.586699215470422	3		442	728	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0064044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	517	482	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.654462911462917	3	FACETS	0.997	0.959	1	0.664	0.639	0.689	CLONAL	2	TRUE	0	0.654462911462917	3		482	1052	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751036	128751036	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3300	230	581	0	ENST00000377970.2:c.573G>C	p.Leu191Phe	p.L191F	ENST00000377970	NM_002467.4	191	ttG/ttC	2/3	0.654462911462917	11	FACETS	0.786	0.727	0.846	0.131	0.121	0.141	SUBCLONAL	1	TRUE	5	0.654462911462917	11		581	3530	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022909	27022940	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCCCCGCCGCCGCCAGCAGCCTGGGCAACC	CGCCCCCGCCGCCGCCAGCAGCCTGGGCAACC	-	novel	NA	P-0064044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	216	515	0	ENST00000324856.7:c.19_50del	p.Pro7AlafsTer93	p.P7Afs*93	ENST00000324856	NM_006015.4	5	gtCGCCCCCGCCGCCGCCAGCAGCCTGGGCAACCcg/gtcg	1/20	1	2	FACETS	0.787	0.733	0.842	0.787	0.733	0.842	SUBCLONAL	1	TRUE	1	0.654462911462917	2		515	839	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404932	70404932	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	272	523	0	ENST00000373644.4:c.2446C>A	p.Leu816Ile	p.L816I	ENST00000373644	NM_030625.2	816	Ctc/Atc	4/12	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.654462911462917	2		523	783	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238146	133238146	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	239	554	0	ENST00000320574.5:c.2831C>A	p.Ala944Asp	p.A944D	ENST00000320574	NM_006231.2	944	gCc/gAc	24/49	1	2	FACETS	0.894	0.837	0.952	0.894	0.837	0.952	CLONAL	1	TRUE	1	0.654462911462917	2		554	817	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292941	91292941	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0064044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	245	536	0	ENST00000355112.3:c.443T>G	p.Leu148Ter	p.L148*	ENST00000355112	NM_000057.2	148	tTa/tGa	3/22	1	2	FACETS	0.937	0.879	0.997	0.937	0.879	0.997	CLONAL	1	TRUE	1	0.654462911462917	2		536	799	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164886	36164886	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	122	670	0	ENST00000300305.3:c.989T>C	p.Phe330Ser	p.F330S	ENST00000300305		330	tTc/tCc	8/8	1	2	FACETS	0.416	0.376	0.459	0.416	0.376	0.459	SUBCLONAL	1	TRUE	1	0.654462911462917	2		670	896	SUCCESS
APC	324	MSKCC	GRCh37	5	112173656	112173656	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs398123117	NA	P-0064044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	252	477	0	ENST00000257430.4:c.2365C>G	p.Gln789Glu	p.Q789E	ENST00000257430	NM_000038.5	789	Cag/Gag	16/16	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.654462911462917	2		477	757	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	121	523	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.842	0.769	0.917	1	0.988	1	CLONAL	2	TRUE	1	0.397063546755007	2		523	362	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240193	41240193	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1350774254	NA	P-0064045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	95	466	0	ENST00000379561.5:c.157G>A	p.Asp53Asn	p.D53N	ENST00000379561	NM_002015.3	53	Gac/Aac	1/3	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.397063546755007	2		466	359	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619153	37619153	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	240	519	0	ENST00000447079.4:c.833del	p.Pro278LeufsTer60	p.P278Lfs*60	ENST00000447079	NM_015083.1	277	Ccc/cc	1/14	1	2	FACETS	0.814	0.763	0.865	1	0.994	1	CLONAL	2	TRUE	1	0.397063546755007	2		519	743	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	133	331	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.246513724293425	4	FACETS	0.873	0.799	0.949	0.873	0.799	0.949	CLONAL	3	TRUE	1	0.29	4		331	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0064049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	66	949	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.601	0.521	0.689	0.601	0.521	0.689	SUBCLONAL	1	TRUE	1	0.29	2		950	757	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0064049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	100	504	1	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	1	2	FACETS	0.953	0.851	1	0.953	0.851	1	CLONAL	1	TRUE	1	0.29	2		505	724	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604750	48604750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	133	436	2	ENST00000342988.3:c.1572G>T	p.Trp524Cys	p.W524C	ENST00000342988	NM_005359.5	524	tgG/tgT	12/12	0.293146807995455	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.29	1		438	608	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664393	29664394	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAGCAAGTTTTG	novel	NA	P-0064049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	37	202	1	ENST00000356175.3:c.6374_6385dup	p.Lys2125_Leu2128dup	p.K2125_L2128dup	ENST00000356175	NM_000267.3	2125	-/AAGCAAGTTTTG	42/57	1	2	FACETS	0.684	0.565	0.817	0.684	0.565	0.817	SUBCLONAL	1	TRUE	1	0.29	2		203	373	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374995	45374995	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	115	222	0	ENST00000262160.6:c.848del	p.Asn283IlefsTer17	p.N283Ifs*17	ENST00000262160	NM_005901.5	283	aAt/at	8/11	0.293146807995455	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.29	1		222	519	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419875	41419875	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	109	563	3	ENST00000373198.4:c.446C>A	p.Ala149Glu	p.A149E	ENST00000373198	NM_133170.3	149	gCa/gAa	3/32	0.299705774305972	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.29	1		566	633	SUCCESS
APC	324	MSKCC	GRCh37	5	112173623	112173627	+	frameshift_variant	Frame_Shift_Del	DEL	AATTT	AATTT	-	novel	NA	P-0064049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	53	252	2	ENST00000257430.4:c.2334_2338del	p.Asn778LysfsTer8	p.N778Kfs*8	ENST00000257430	NM_000038.5	778	AATTTa/a	16/16	1	2	FACETS	0.768	0.656	0.891	0.768	0.656	0.891	SUBCLONAL	1	TRUE	1	0.29	2		254	476	SUCCESS
APC	324	MSKCC	GRCh37	5	112175774	112175775	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0064049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	40	380	1	ENST00000257430.4:c.4483_4484del	p.Ser1495TyrfsTer18	p.S1495Yfs*18	ENST00000257430	NM_000038.5	1495	AGt/t	16/16	1	2	FACETS	0.465	0.386	0.554	0.465	0.386	0.554	SUBCLONAL	1	TRUE	1	0.29	2		381	593	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0064052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	72	485	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	1	2	FACETS	0.963	0.844	1	0.963	0.844	1	CLONAL	1	TRUE	1	0.34	2		485	440	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0064052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	21	623	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.26	0.199	0.331	0.26	0.199	0.331	SUBCLONAL	1	TRUE	1	0.34	2		623	475	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0064052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	72	518	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	1	2	FACETS	0.799	0.699	0.906	0.799	0.699	0.906	CLONAL	1	TRUE	1	0.34	2		518	530	SUCCESS
APC	324	MSKCC	GRCh37	5	112163677	112163677	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0064052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	109	342	0	ENST00000257430.4:c.1600A>T	p.Lys534Ter	p.K534*	ENST00000257430	NM_000038.5	534	Aaa/Taa	13/16	1	2	FACETS	0.913	0.829	1	1	0.988	1	CLONAL	2	TRUE	1	0.34	2		342	351	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519896	NA	P-0064052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	21	536	0	ENST00000281708.4:c.1514G>A	p.Arg505His	p.R505H	ENST00000281708	NM_033632.3	505	cGc/cAc	10/12	1	2	FACETS	0.238	0.182	0.303	0.238	0.182	0.303	SUBCLONAL	1	TRUE	1	0.34	2		536	520	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0064052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	40	254	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.694	0.578	0.822	0.694	0.578	0.822	SUBCLONAL	1	TRUE	1	0.34	2		254	339	SUCCESS
APC	324	MSKCC	GRCh37	5	112175754	112175755	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0064052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	91	574	0	ENST00000257430.4:c.4464_4465del	p.Leu1488PhefsTer25	p.L1488Ffs*25	ENST00000257430	NM_000038.5	1488	tTA/t	16/16	1	2	FACETS	0.915	0.814	1	0.915	0.814	1	CLONAL	1	TRUE	1	0.34	2		574	585	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119694	70119694	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	50	551	0	ENST00000245479.2:c.698del	p.Gly233AlafsTer20	p.G233Afs*20	ENST00000245479	NM_000346.3	232	caG/ca	3/3	1	2	FACETS	0.549	0.465	0.64	0.549	0.465	0.64	SUBCLONAL	1	TRUE	1	0.34	2		551	536	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435273	110435273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775912180	NA	P-0064052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	57	768	1	ENST00000375856.3:c.3128G>A	p.Arg1043His	p.R1043H	ENST00000375856	NM_003749.2	1043	cGc/cAc	1/2	0.3	5	FACETS	0.541	0.462	0.627	0.18	0.154	0.209	SUBCLONAL	1	TRUE	2	0.34	5		769	936	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911481	101911481	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	31	437	0	ENST00000374994.4:c.1406A>C	p.Lys469Thr	p.K469T	ENST00000374994	NM_004612.2	469	aAa/aCa	9/9	0.132777588240433	5	FACETS	0.592	0.478	0.721	0.197	0.159	0.241	INDETERMINATE	1	TRUE	2	0.34	5		437	465	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380282	25380282	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	38	443	0	ENST00000311936.3:c.176C>G	p.Ala59Gly	p.A59G	ENST00000311936	NM_004985.3	59	gCa/gGa	3/5	1	2	FACETS	0.562	0.465	0.67	0.562	0.465	0.67	SUBCLONAL	1	TRUE	1	0.34	2		443	398	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150923275	150923275	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs760870314	NA	P-0064052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	75	581	0	ENST00000271640.5:c.1922T>C	p.Ile641Thr	p.I641T	ENST00000271640	NM_001145415.1	641	aTa/aCa	13/22	1	2	FACETS	0.812	0.713	0.919	0.812	0.713	0.919	CLONAL	1	TRUE	1	0.34	2		581	543	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981547	201981548	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0064052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	37	546	0	ENST00000359651.3:c.463_464dup	p.Asp155GlufsTer100	p.D155Efs*100	ENST00000359651		154	cta/ctAGa	3/8	1	2	FACETS	0.448	0.369	0.536	0.448	0.369	0.536	SUBCLONAL	1	TRUE	1	0.34	2		546	486	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10792071	10792071	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	41	549	0	ENST00000361367.2:c.2264T>G	p.Phe755Cys	p.F755C	ENST00000361367	NM_014633.3	755	tTt/tGt	18/25	1	2	FACETS	0.51	0.425	0.605	0.51	0.425	0.605	SUBCLONAL	1	TRUE	1	0.34	2		549	473	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398262	25398262	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913538	NA	P-0064052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	10	295	0	ENST00000311936.3:c.57G>T	p.Leu19Phe	p.L19F	ENST00000311936	NM_004985.3	19	ttG/ttT	2/5	1	2	FACETS	0.187	0.126	0.265	0.187	0.126	0.265	SUBCLONAL	1	TRUE	1	0.34	2		295	314	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584726	48584726	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	50	563	0	ENST00000342988.3:c.804G>A	p.Trp268Ter	p.W268*	ENST00000342988	NM_005359.5	268	tgG/tgA	7/12	0.224232233035831	0	FACETS	0.445	0.378	0.519			1	SUBCLONAL	1	TRUE	0	0.34	0		563	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0064053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	85	454	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.159213293404548	2	FACETS	1	0.965	1	0.615	0.545	0.691	CLONAL	1	FALSE	0	0.242341787708801	2		454	570	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0064053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	36	586	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.987	0.815	1	0.987	0.815	1	CLONAL	1	FALSE	1	0.242341787708801	2		586	301	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094856	11094856	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	53	667	0	ENST00000358026.2:c.29G>T	p.Gly10Val	p.G10V	ENST00000358026	NM_001128849.1	10	gGa/gTa	2/36	1	2	FACETS	0.714	0.608	0.829	0.714	0.608	0.829	SUBCLONAL	1	FALSE	1	0.242341787708801	2		667	613	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998635	100998635	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	TT	novel	NA	P-0064053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	97	897	0	ENST00000325455.5:c.1167delinsAA	p.Glu390ArgfsTer184	p.E390Rfs*184	ENST00000325455	NM_001202474.3	389	gaG/gaAA	1/8	0.159213293404548	2	FACETS	1	0.966	1	0.603	0.538	0.672	CLONAL	1	FALSE	0	0.242341787708801	2		897	664	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0064055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	449	622	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.971	1	1	0.997	1	CLONAL	2	TRUE	1	0.539520573921211	2		626	823	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088788	27088788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	145	613	0	ENST00000324856.7:c.2402del	p.Gly801ValfsTer32	p.G801Vfs*32	ENST00000324856	NM_006015.4	799	caG/ca	7/20	1	2	FACETS	0.941	0.863	1	0.941	0.863	1	CLONAL	1	TRUE	1	0.539520573921211	2		613	571	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0064055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	126	803	7	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	0.539520573921211	3	FACETS	0.724	0.656	0.796	0.362	0.328	0.398	SUBCLONAL	1	TRUE	1	0.539520573921211	3		810	819	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443599	52443601	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0064055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	156	703	0	ENST00000460680.1:c.91_93del	p.Glu31del	p.E31del	ENST00000460680	NM_004656.3	31	GAG/-	3/17	1	2	FACETS	0.891	0.819	0.966	0.891	0.819	0.966	CLONAL	1	TRUE	1	0.539520573921211	2		703	649	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932085	39932085	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	207	409	0	ENST00000378444.4:c.2514del	p.Lys839SerfsTer17	p.K839Sfs*17	ENST00000378444	NM_001123385.1	838	ccC/cc	4/15	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.539520573921211	1		409	381	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	207	350	0	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.539520573921211	2		350	728	SUCCESS
APC	324	MSKCC	GRCh37	5	112177653	112177653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	127	366	0	ENST00000257430.4:c.6362C>T	p.Ala2121Val	p.A2121V	ENST00000257430	NM_000038.5	2121	gCt/gTt	16/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.539520573921211	2		366	386	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960038	134960038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1346978629	NA	P-0064055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	163	545	0	ENST00000398015.3:c.2395C>T	p.Arg799Cys	p.R799C	ENST00000398015	NM_004441.4	799	Cgc/Tgc	13/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.539520573921211	2		545	584	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106937	27106937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1470694207	NA	P-0064055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	224	763	0	ENST00000324856.7:c.6548G>A	p.Arg2183His	p.R2183H	ENST00000324856	NM_006015.4	2183	cGt/cAt	20/20	1	2	FACETS	0.986	0.92	1	0.986	0.92	1	CLONAL	1	TRUE	1	0.539520573921211	2		763	842	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919514	78919514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149834841	NA	P-0064055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	157	621	0	ENST00000306801.3:c.3073G>A	p.Val1025Ile	p.V1025I	ENST00000306801	NM_020761.2	1025	Gtc/Atc	26/34	1	2	FACETS	0.978	0.9	1	0.978	0.9	1	CLONAL	1	TRUE	1	0.539520573921211	2		621	595	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214675	5214675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1274728310	NA	P-0064055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	201	859	1	ENST00000357368.4:c.4391C>T	p.Thr1464Met	p.T1464M	ENST00000357368	NM_002850.3	1464	aCg/aTg	29/38	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.539520573921211	2		860	656	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602443	10602443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1321752702	NA	P-0064055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	212	896	0	ENST00000171111.5:c.1135G>A	p.Gly379Ser	p.G379S	ENST00000171111	NM_203500.1	379	Ggc/Agc	3/6	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.539520573921211	2		896	715	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294361	1294361	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	59	840	0	ENST00000310581.5:c.640del	p.Leu214TrpfsTer137	p.L214Wfs*137	ENST00000310581	NM_198253.2	214	Ctg/tg	2/16	1	2	FACETS	0.337	0.289	0.389	0.337	0.289	0.389	SUBCLONAL	1	TRUE	1	0.539520573921211	2		840	649	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640238	3640238	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	162	608	0	ENST00000294008.3:c.3401C>A	p.Ser1134Ter	p.S1134*	ENST00000294008	NM_032444.2	1134	tCg/tAg	12/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.539520573921211	2		608	528	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0064055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	86	348	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.539520573921211	3	FACETS	1	0.906	1	0.51	0.454	0.569	CLONAL	1	TRUE	1	0.539520573921211	3		348	397	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63976489	63976489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs74823804	NA	P-0064055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	170	507	0	ENST00000398590.3:c.1636G>A	p.Ala546Thr	p.A546T	ENST00000398590	NM_001177387.1	546	Gcc/Acc	11/14	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.539520573921211	2		507	553	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589749	69589749	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	294	1229	0	ENST00000168712.1:c.104C>A	p.Pro35His	p.P35H	ENST00000168712	NM_002007.2	35	cCc/cAc	1/3	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.539520573921211	2		1229	908	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150289	108150290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0064055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	80	294	0	ENST00000278616.4:c.3360dup	p.Glu1121Ter	p.E1121*	ENST00000278616	NM_000051.3	1119	gct/gcTt	23/63	1	2	FACETS	0.957	0.85	1	0.957	0.85	1	CLONAL	1	TRUE	1	0.539520573921211	2		294	310	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125523651	125523653	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	novel	NA	P-0064055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	10	222	0	ENST00000428830.2:c.1248_1250del	p.Thr417del	p.T417del	ENST00000428830	NM_001114121.2	415	tCAAca/tca	12/14	1	2	FACETS	0.207	0.14	0.291	0.207	0.14	0.291	SUBCLONAL	1	TRUE	1	0.539520573921211	2		222	179	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489547	56489547	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	185	488	0	ENST00000267101.3:c.2012T>A	p.Ile671Asn	p.I671N	ENST00000267101	NM_001982.3	671	aTt/aAt	17/28	0.539520573921211	3	FACETS	1	0.96	1	0.528	0.488	0.57	CLONAL	1	TRUE	1	0.539520573921211	3		488	824	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219172	133219172	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs754982151	NA	P-0064055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	180	792	0	ENST00000320574.5:c.4872G>A	p.Trp1624Ter	p.W1624*	ENST00000320574	NM_006231.2	1624	tgG/tgA	37/49	0.539520573921211	3	FACETS	1	0.954	1	0.522	0.482	0.564	CLONAL	1	TRUE	1	0.539520573921211	3		792	811	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254622	10254622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	167	558	0	ENST00000340748.4:c.2888C>T	p.Pro963Leu	p.P963L	ENST00000340748		963	cCc/cTc	28/40	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.539520573921211	2		558	526	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30682855	30682855	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769500971	NA	P-0064055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	175	432	0	ENST00000376406.3:c.98G>A	p.Arg33Gln	p.R33Q	ENST00000376406	NM_014641.2	33	cGg/cAg	2/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.539520573921211	2		432	605	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163276	32163567	+	frameshift_variant	Frame_Shift_Del	DEL	CAAGTTGAGGTGATCCCCGCTCCGGGGACGGAGTAAGGCAAGGAGGCGGGATCGGAATGTTGGAGGCAGAACCGCAAGCTCCCAGGGCCACCCAATCACAGGGCCAGTCATCCGTTGAGACCCTGCCTCCGCGCCCGGCAGCCACTCCGTATCTTCCTCGCATTATCGCAGGGTTGGGCCGAGGCCCGCGCATGCCTGCAGAAAACCTACGGCCGCGAGGGGTCGGGCCTCCTCCTGCTCCTACTCCCGAGAGGCTCCGGCAATGAGAATAGGCCCCGCCCCCCCGCGCAGC	CAAGTTGAGGTGATCCCCGCTCCGGGGACGGAGTAAGGCAAGGAGGCGGGATCGGAATGTTGGAGGCAGAACCGCAAGCTCCCAGGGCCACCCAATCACAGGGCCAGTCATCCGTTGAGACCCTGCCTCCGCGCCCGGCAGCCACTCCGTATCTTCCTCGCATTATCGCAGGGTTGGGCCGAGGCCCGCGCATGCCTGCAGAAAACCTACGGCCGCGAGGGGTCGGGCCTCCTCCTGCTCCTACTCCCGAGAGGCTCCGGCAATGAGAATAGGCCCCGCCCCCCCGCGCAGC	-	novel	NA	P-0064055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	126	714	0	ENST00000375023.3:c.5659_5950del	p.Ala1887ThrfsTer12	p.A1887Tfs*12	ENST00000375023	NM_004557.3	1887	GCTGCGCGGGGGGGCGGGGCCTATTCTCATTGCCGGAGCCTCTCGGGAGTAGGAGCAGGAGGAGGCCCGACCCCTCGCGGCCGTAGGTTTTCTGCAGGCATGCGCGGGCCTCGGCCCAACCCTGCGATAATGCGAGGAAGATACGGAGTGGCTGCCGGGCGCGGAGGCAGGGTCTCAACGGATGACTGGCCCTGTGATTGGGTGGCCCTGGGAGCTTGCGGTTCTGCCTCCAACATTCCGATCCCGCCTCCTTGCCTTACTCCGTCCCCGGAGCGGGGATCACCTCAACTTGac/ac	30/30	1	2	FACETS	0.752	0.683	0.825	0.752	0.683	0.825	SUBCLONAL	1	TRUE	1	0.539520573921211	2		714	621	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412291	139412291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559403480	NA	P-0064055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	243	785	0	ENST00000277541.6:c.1354G>A	p.Asp452Asn	p.D452N	ENST00000277541	NM_017617.3	452	Gac/Aac	8/34	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.539520573921211	2		785	706	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0064066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	530	413	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.869360251617017	2	FACETS	0.992	0.972	1	0.992	0.972	1	CLONAL	2	TRUE	0	0.871532859717809	2		413	613	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592245	29592245	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs1295045178	NA	P-0064066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	389	236	0	ENST00000356175.3:c.4662-2A>T		p.X1554_splice	ENST00000356175	NM_000267.3	1554			0.869360251617017	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.871532859717809	2		236	436	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21336860	21336860	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs1338433423	NA	P-0064066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	28	541	0	ENST00000215739.8:c.200G>C	p.Arg67Pro	p.R67P	ENST00000215739	NM_006767.3	67	cGg/cCg	1/21	0.871532859717809	1	FACETS	0.082	0.065	0.101	0.082	0.065	0.101	SUBCLONAL	1	TRUE	0	0.871532859717809	1		541	444	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12632370	12632370	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs368676608	NA	P-0064066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	444	492	0	ENST00000251849.4:c.1297C>G	p.Leu433Val	p.L433V	ENST00000251849	NM_002880.3	433	Ctg/Gtg	12/17	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.871532859717809	2		492	865	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178708	32178708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	451	364	1	ENST00000375023.3:c.2686G>A	p.Asp896Asn	p.D896N	ENST00000375023	NM_004557.3	896	Gac/Aac	18/30	0.817718533023904	3	FACETS	0.974	0.939	1	0.974	0.939	1	CLONAL	2	TRUE	1	0.871532859717809	3		365	763	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064067-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	44	331	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.926	0.782	1	0.926	0.782	1	CLONAL	1	TRUE	1	0.344154731384682	2		331	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0064067-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	64	623	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.344154731384682	1	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	0	0.344154731384682	1		623	302	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0064067-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	46	378	0	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	1	2	FACETS	0.823	0.696	0.961	0.823	0.696	0.961	CLONAL	1	TRUE	1	0.344154731384682	2		378	325	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591909	48591909	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121912576	NA	P-0064067-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	81	452	0	ENST00000342988.3:c.1072G>T	p.Gly358Ter	p.G358*	ENST00000342988	NM_005359.5	358	Gga/Tga	9/12	0.344154731384682	1	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	0	0.344154731384682	1		452	382	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0064068-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	78	728	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.761	0.673	0.856	0.761	0.673	0.856	SUBCLONAL	1	TRUE	1	0.509706707684853	2		728	402	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860667	151860667	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0064068-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	217	569	0	ENST00000262189.6:c.9995T>A	p.Leu3332Ter	p.L3332*	ENST00000262189	NM_170606.2	3332	tTa/tAa	43/59	0.484472963325277	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.509706707684853	3		569	518	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055756	152055756	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1283285486	NA	P-0064068-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	93	254	0	ENST00000262189.6:c.166C>T	p.Arg56Ter	p.R56*	ENST00000262189	NM_170606.2	56	Cga/Tga	2/59	0.484472963325277	3	FACETS	1	0.95	1	0.553	0.495	0.614	CLONAL	1	TRUE	1	0.509706707684853	3		254	414	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961567	54961567	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064068-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	79	350	0	ENST00000312783.6:c.65C>A	p.Pro22Gln	p.P22Q	ENST00000312783	NM_198436.1	22	cCa/cAa	4/10	0.135919279232659	6	FACETS	1	0.977	1	0.498	0.44	0.56	INDETERMINATE	1	TRUE	3	0.509706707684853	6		350	419	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064069-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	81	331	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.411485498688002	2		331	321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0064069-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	106	351	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.336859843162074	1	FACETS	0.941	0.849	1	0.941	0.849	1	CLONAL	1	TRUE	0	0.411485498688002	1		351	435	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064070-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	52	331	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.226571568999086	2		331	373	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589650	69589651	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0064070-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	40	869	0	ENST00000168712.1:c.202dup	p.Ala68GlyfsTer87	p.A68Gfs*87	ENST00000168712	NM_002007.2	68	gcc/gGcc	1/3	1	2	FACETS	0.468	0.387	0.558	0.468	0.387	0.558	SUBCLONAL	1	TRUE	1	0.226571568999086	2		869	755	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999387	100999387	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064070-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	39	489	0	ENST00000325455.5:c.415T>A	p.Ser139Thr	p.S139T	ENST00000325455	NM_001202474.3	139	Tct/Act	1/8	1	2	FACETS	0.587	0.486	0.701	0.587	0.486	0.701	SUBCLONAL	1	TRUE	1	0.226571568999086	2		489	586	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153513	108153513	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064070-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	22	220	0	ENST00000278616.4:c.3653T>G	p.Val1218Gly	p.V1218G	ENST00000278616	NM_000051.3	1218	gTt/gGt	25/63	1	2	FACETS	0.511	0.395	0.646	0.511	0.395	0.646	SUBCLONAL	1	TRUE	1	0.226571568999086	2		220	380	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926255	112926255	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064070-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	57	306	0	ENST00000351677.2:c.1388T>C	p.Ile463Thr	p.I463T	ENST00000351677	NM_002834.3	463	aTt/aCt	12/16	0.226571568999086	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.226571568999086	1		306	382	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562339	21562339	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064070-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	74	521	0	ENST00000382592.4:c.1580A>T	p.Lys527Met	p.K527M	ENST00000382592	NM_014572.2	527	aAg/aTg	4/8	0.226571568999086	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.226571568999086	1		521	539	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251265	99251265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760481311	NA	P-0064070-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	61	495	0	ENST00000268035.6:c.569C>T	p.Pro190Leu	p.P190L	ENST00000268035	NM_000875.3	190	cCg/cTg	2/21	0.226571568999086	3	FACETS	0.973	0.839	1	0.487	0.419	0.56	CLONAL	1	TRUE	1	0.226571568999086	3		495	616	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0064070-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	53	465	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.109871850427162	1	FACETS	0.885	0.755	1	0.885	0.755	1	INDETERMINATE	1	TRUE	0	0.226571568999086	1		465	469	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604755	48604755	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064070-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	60	448	0	ENST00000342988.3:c.1577A>T	p.Glu526Val	p.E526V	ENST00000342988	NM_005359.5	526	gAa/gTa	12/12	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.226571568999086	2		448	491	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422113	47422113	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064070-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	117	391	0	ENST00000404338.3:c.181A>C	p.Ser61Arg	p.S61R	ENST00000404338	NM_004491.4	61	Agt/Cgt	1/6	0.190580466391908	3	FACETS	0.893	0.807	0.983	0.893	0.807	0.983	CLONAL	2	TRUE	1	0.226571568999086	3		391	644	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467442	25467442	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064070-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	65	504	0	ENST00000264709.3:c.1634A>C	p.Glu545Ala	p.E545A	ENST00000264709	NM_175629.2	545	gAg/gCg	14/23	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.226571568999086	2		504	570	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37640175	37640175	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064070-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	50	527	0	ENST00000249071.6:c.14A>C	p.Lys5Thr	p.K5T	ENST00000249071	NM_002872.4	5	aAg/aCg	1/7	1	2	FACETS	0.742	0.629	0.866	0.742	0.629	0.866	SUBCLONAL	1	TRUE	1	0.226571568999086	2		527	595	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878227	151878227	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0064070-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	57	511	0	ENST00000262189.6:c.6718A>T	p.Arg2240Ter	p.R2240*	ENST00000262189	NM_170606.2	2240	Aga/Tga	36/59	1	2	FACETS	0.871	0.747	1	0.871	0.747	1	CLONAL	1	TRUE	1	0.226571568999086	2		511	578	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0064070-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	68	525	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.226571568999086	1	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	0	0.226571568999086	1		525	527	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448270	56448270	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0064071-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	150	430	0	ENST00000407977.2:c.375+2T>C		p.X125_splice	ENST00000407977		125			0.194862968424536	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.194862968424536	2		430	651	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340168	116340168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761768345	NA	P-0064071-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	57	332	0	ENST00000397752.3:c.1030G>A	p.Gly344Arg	p.G344R	ENST00000397752	NM_000245.2	344	Ggg/Agg	2/21	0.194862968424536	3	FACETS	1	0.934	1	0.577	0.495	0.667	CLONAL	1	TRUE	1	0.194862968424536	3		332	556	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867068	45867068	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064071-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	60	410	0	ENST00000391945.4:c.1051C>T	p.Gln351Ter	p.Q351*	ENST00000391945	NM_000400.3	351	Cag/Tag	11/23	0.17958789833558	4	FACETS	1	0.914	1			1	CLONAL	1	TRUE	NA	0.194862968424536	4		410	678	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7590693	7590693	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0064071-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	101	414	0	ENST00000269305.4:c.-29+2T>G		p.X10_splice	ENST00000269305	NM_001126112.2	10			0.194862968424536	2	FACETS	0.955	0.856	1	0.955	0.856	1	CLONAL	2	TRUE	0	0.194862968424536	2		414	543	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591931	+	frameshift_variant	Frame_Shift_Del	DEL	GCTTTTGTTTGGG	GCTTTTGTTTGGG	-	novel	NA	P-0064071-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	111	328	0	ENST00000342988.3:c.1082_1094del	p.Arg361LeufsTer19	p.R361Lfs*19	ENST00000342988	NM_005359.5	361	cGCTTTTGTTTGGGt/ct	9/12	0.194862968424536	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	0	0.194862968424536	2		328	535	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262523	10262523	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064071-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	82	318	0	ENST00000340748.4:c.1972G>C	p.Val658Leu	p.V658L	ENST00000340748		658	Gtg/Ctg	22/40	0.167644235379399	4	FACETS	0.923	0.815	1	0.923	0.815	1	CLONAL	2	TRUE	2	0.194862968424536	4		318	545	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069622	69069622	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs762016096	NA	P-0064071-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	49	241	0	ENST00000288368.4:c.4297A>G	p.Ile1433Val	p.I1433V	ENST00000288368	NM_024870.2	1433	Ata/Gta	35/40	0.194862968424536	8	FACETS	0.76	0.644	0.889	0.253	0.214	0.297	SUBCLONAL	2	TRUE	2	0.194862968424536	8		241	524	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994234	21994234	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064072-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	188	468	2	ENST00000579755.1:c.97del	p.Glu33SerfsTer15	p.E33Sfs*15	ENST00000579755		33	Gag/ag	1/3	0.871257540738471				NA	1				NA	1	TRUE	0	0.879743774232256	0		470	278	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593650	55593651	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCAACACAACTTCCTTATGATCACAAATGGGAGTTT	novel	NA	P-0064072-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	365	440	0	ENST00000288135.5:c.1719_1754dup	p.Thr574_Pro585dup	p.T574_P585dup	ENST00000288135	NM_000222.2	574	-/CCAACACAACTTCCTTATGATCACAAATGGGAGTTT	11/21	0.879743774232256	3	FACETS	1	0.992	1	0.4	0.38	0.42	CLONAL	1	TRUE	0	0.879743774232256	3		440	996	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005449	42005449	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064072-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	182	565	1	ENST00000219905.7:c.3185C>A	p.Ala1062Asp	p.A1062D	ENST00000219905	NM_001164273.1	1062	gCt/gAt	9/24	0.879743774232256	1	FACETS	0.526	0.49	0.561	0.526	0.49	0.561	SUBCLONAL	1	TRUE	0	0.879743774232256	1		566	441	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064073-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	106	331	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.874	0.792	0.96	0.874	0.792	0.96	CLONAL	1	TRUE	1	0.688886642770896	2		331	352	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0064073-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	143	586	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.744	0.682	0.809	0.744	0.682	0.809	SUBCLONAL	1	TRUE	1	0.688886642770896	2		586	558	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0064073-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	23	362	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.19	0.147	0.239	0.19	0.147	0.239	SUBCLONAL	1	TRUE	1	0.688886642770896	2		362	352	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196849	108196849	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064073-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	354	282	0	ENST00000278616.4:c.6872G>A	p.Trp2291Ter	p.W2291*	ENST00000278616	NM_000051.3	2291	tGg/tAg	47/63	0.686066360603048	2	FACETS	0.966	0.93	1	0.966	0.93	1	CLONAL	2	TRUE	0	0.688886642770896	2		282	532	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513784	41513785	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGGGAGG	novel	NA	P-0064073-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	206	325	0	ENST00000263253.7:c.689_695dup	p.Gln233GlyfsTer13	p.Q233Gfs*13	ENST00000263253	NM_001429.3	230	atg/aTGGGAGGtg	2/31	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.688886642770896	2		325	576	SUCCESS
APC	324	MSKCC	GRCh37	5	112173844	112173844	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064073-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	199	394	0	ENST00000257430.4:c.2555del	p.Leu852TrpfsTer9	p.L852Wfs*9	ENST00000257430	NM_000038.5	851	agT/ag	16/16	1	2	FACETS	0.958	0.893	1	0.958	0.893	1	CLONAL	1	TRUE	1	0.688886642770896	2		394	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519998	NA	P-0064083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	211	747	0	ENST00000269305.4:c.581T>C	p.Leu194Pro	p.L194P	ENST00000269305	NM_001126112.2	194	cTt/cCt	6/11	0.318107202993271	2	FACETS	0.928	0.867	0.989	0.928	0.867	0.989	CLONAL	2	TRUE	0	0.380367838052002	2		747	598	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087366	27087366	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	85	470	0	ENST00000324856.7:c.1940A>T	p.Asp647Val	p.D647V	ENST00000324856	NM_006015.4	647	gAt/gTt	5/20	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.380367838052002	2		470	447	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459031	120459031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587650529	NA	P-0064083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	103	629	1	ENST00000256646.2:c.6314G>A	p.Arg2105Gln	p.R2105Q	ENST00000256646	NM_024408.3	2105	cGg/cAg	34/34	0.163560555343542	3	FACETS	1	0.963	1	0.579	0.519	0.641	INDETERMINATE	1	TRUE	1	0.380367838052002	3		630	557	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436388	49436388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	142	550	0	ENST00000301067.7:c.5823G>A	p.Met1941Ile	p.M1941I	ENST00000301067	NM_003482.3	1941	atG/atA	27/54	0.318107202993271	2	FACETS	1	0.987	1	0.712	0.653	0.774	CLONAL	1	TRUE	0	0.380367838052002	2		550	524	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870985	12870986	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1555085549	NA	P-0064084-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	54	706	0	ENST00000228872.4:c.215dup	p.Lys73GlnfsTer52	p.K73Qfs*52	ENST00000228872	NM_004064.3	71	gag/gaGg	1/3	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.14	2		706	703	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118940	70118941	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0064084-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	42	792	0	ENST00000245479.2:c.514dup	p.Tyr172LeufsTer80	p.Y172Lfs*80	ENST00000245479	NM_000346.3	171	gat/gaTt	2/3	1	2	FACETS	0.768	0.639	0.912	0.768	0.639	0.912	CLONAL	1	TRUE	1	0.14	2		792	781	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0064084-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	14	465	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	1	2	FACETS	0.362	0.26	0.487	0.362	0.26	0.487	SUBCLONAL	1	TRUE	1	0.14	2		465	552	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713813	30713838	+	protein_altering_variant	In_Frame_Del	DEL	CTCAAGAGCTCCAATATCCTCGTGAA	CTCAAGAGCTCCAATATCCTCGTGAA	TC	novel	NA	P-0064084-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	36	753	1	ENST00000295754.5:c.1138_1163delinsTC	p.Leu380_Lys388delinsSer	p.L380_K388delinsS	ENST00000295754	NM_003242.5	380	CTCAAGAGCTCCAATATCCTCGTGAAg/TCg	4/7	1	2	FACETS	0.708	0.58	0.853	0.708	0.58	0.853	SUBCLONAL	1	TRUE	1	0.14	2		754	726	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925316	114925317	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs745872748	NA	P-0064085-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	176	350	11	ENST00000543371.1:c.1403dup	p.Cys469ValfsTer8	p.C469Vfs*8	ENST00000543371	NM_001198531.1	465	aga/agAa	14/14	0.550353664411346	3	FACETS	1	0.99	1	0.734	0.681	0.789	CLONAL	1	TRUE	1	0.591499210753412	3		361	525	SUCCESS
APC	324	MSKCC	GRCh37	5	112175193	112175193	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1064794042	NA	P-0064085-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	263	367	0	ENST00000257430.4:c.3904del	p.Leu1302CysfsTer3	p.L1302Cfs*3	ENST00000257430	NM_000038.5	1301	aCc/ac	16/16	0.535596940843709	2	FACETS	0.952	0.906	0.998	0.952	0.906	0.998	CLONAL	2	TRUE	0	0.591499210753412	2		367	467	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467590	66467590	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746706656	NA	P-0064085-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	122	268	0	ENST00000273854.3:c.679C>T	p.Arg227Cys	p.R227C	ENST00000273854	NM_004439.5	227	Cgt/Tgt	3/18	1	2	FACETS	0.938	0.854	1	0.938	0.854	1	CLONAL	1	TRUE	1	0.591499210753412	2		268	440	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0064085-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	179	312	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.550353664411346	3	FACETS	0.916	0.855	0.979	0.916	0.855	0.979	CLONAL	2	TRUE	1	0.591499210753412	3		312	428	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0064086-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	283	764	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.748843104275732	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.770872340251526	1		764	418	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0064086-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4703	580	521	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.770872340251526	24	FACETS	0.9	0.859	0.943	0.117	0.112	0.123	CLONAL	3	TRUE	1	0.770872340251526	24		521	5283	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624290	89624290	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660420	NA	P-0064086-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	105	274	0	ENST00000371953.3:c.64G>T	p.Asp22Tyr	p.D22Y	ENST00000371953	NM_000314.4	22	Gac/Tac	1/9	0.166858901184044	3	FACETS	1	0.964	1	0.378	0.342	0.415	INDETERMINATE	1	TRUE	0	0.770872340251526	3		274	333	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720874	89720891	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTCAGTTAAATTAAAC	AGGTCAGTTAAATTAAAC	-	novel	NA	P-0064086-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	21	155	0	ENST00000371953.3:c.1026_1026+17del		p.X342_splice	ENST00000371953	NM_000314.4	342		8/9	0.166858901184044	3	FACETS	0.645	0.504	0.805	0.215	0.168	0.269	INDETERMINATE	1	TRUE	0	0.770872340251526	3		155	117	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639559	47639559	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064086-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	102	282	0	ENST00000233146.2:c.652C>G	p.Gln218Glu	p.Q218E	ENST00000233146	NM_000251.2	218	Caa/Gaa	4/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.770872340251526	2		282	227	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434181	12434182	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064086-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	43	413	0	ENST00000287820.6:c.556dup	p.Ser186LysfsTer2	p.S186Kfs*2	ENST00000287820	NM_015869.4	183	-/A	4/7	0.353406349214141	2	FACETS	0.297	0.249	0.351	0.149	0.124	0.176	INDETERMINATE	1	TRUE	0	0.770872340251526	2		413	375	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913492	NA	P-0064087-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	67	257	0	ENST00000286548.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000286548	NM_002072.3	209	cAa/cTa	5/7	0.368563372478786	1	FACETS	0.693	0.612	0.778	0.693	0.612	0.778	INDETERMINATE	1	TRUE	0	0.626171282177018	1		257	212	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064088-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	15	523	0				ENST00000310581	NM_198253.2	-/1132			0.322472122464983	1	FACETS	0.422	0.309	0.556	0.422	0.309	0.556	SUBCLONAL	1	TRUE	0	0.322472122464983	1		523	185	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555526101	NA	P-0064088-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	100	630	0	ENST00000269305.4:c.497C>G	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tGa	5/11	1	2	FACETS	0.781	0.703	0.863	1	0.984	1	SUBCLONAL	2	TRUE	1	0.322472122464983	2		630	397	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212851	94212851	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs368403414	NA	P-0064088-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	17	367	0	ENST00000323929.3:c.391G>T	p.Asp131Tyr	p.D131Y	ENST00000323929	NM_005591.3	131	Gat/Tat	5/20	1	2	FACETS	0.322	0.24	0.42	0.322	0.24	0.42	SUBCLONAL	1	TRUE	1	0.322472122464983	2		367	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0064090-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	540	485	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.51731519801163	4	FACETS	0.958	0.928	0.987	0.958	0.928	0.987	CLONAL	4	TRUE	0	0.518116545460693	4		485	826	SUCCESS
FH	2271	MSKCC	GRCh37	1	241676941	241676941	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064090-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	89	0	0	ENST00000366560.3:c.340C>G	p.Pro114Ala	p.P114A	ENST00000366560	NM_000143.3	114	Cca/Gca	3/10	0.51731519801163	2	FACETS	0.936	0.837	1	0.468	0.418	0.521	CLONAL	1	TRUE	0	0.518116545460693	2		0	367	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872905	35872905	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064090-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	126	0	0	ENST00000216797.5:c.327C>A	p.Asn109Lys	p.N109K	ENST00000216797	NM_020529.2	109	aaC/aaA	2/6	0.43102820620257	4	FACETS	0.952	0.862	1	0.476	0.431	0.523	CLONAL	1	TRUE	2	0.518116545460693	4		0	776	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661966	29661966	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064090-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	96	0	0	ENST00000356175.3:c.5860C>G	p.Leu1954Val	p.L1954V	ENST00000356175	NM_000267.3	1954	Ctt/Gtt	39/57	0.51731519801163	3	FACETS	0.839	0.75	0.934	0.42	0.375	0.467	CLONAL	1	TRUE	1	0.518116545460693	3		0	556	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664497	29664497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1212510392	NA	P-0064090-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	121	0	0	ENST00000356175.3:c.6476C>T	p.Ser2159Phe	p.S2159F	ENST00000356175	NM_000267.3	2159	tCc/tTc	42/57	0.51731519801163	3	FACETS	0.945	0.856	1	0.473	0.428	0.52	CLONAL	1	TRUE	1	0.518116545460693	3		0	622	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983018	149983018	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064090-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	89	0	0	ENST00000253339.5:c.3240C>A	p.Phe1080Leu	p.F1080L	ENST00000253339		1080	ttC/ttA	7/7	1	2	FACETS	0.883	0.788	0.983	0.883	0.788	0.983	CLONAL	1	TRUE	1	0.518116545460693	2		0	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0064090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	57	485	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.163279519079212	2	FACETS	0.817	0.704	0.939	0.817	0.704	0.939	CLONAL	2	TRUE	0	0.190579920444004	2		485	366	SUCCESS
FH	2271	MSKCC	GRCh37	1	241676941	241676941	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	12	0	0	ENST00000366560.3:c.340C>G	p.Pro114Ala	p.P114A	ENST00000366560	NM_000143.3	114	Cca/Gca	3/10	1	2	FACETS	0.465	0.326	0.636	0.465	0.326	0.636	SUBCLONAL	1	TRUE	1	0.190579920444004	2		0	271	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872905	35872905	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	16	0	0	ENST00000216797.5:c.327C>A	p.Asn109Lys	p.N109K	ENST00000216797	NM_020529.2	109	aaC/aaA	2/6	1	2	FACETS	0.477	0.352	0.627	0.477	0.352	0.627	SUBCLONAL	1	TRUE	1	0.190579920444004	2		0	352	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661966	29661966	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	10	0	0	ENST00000356175.3:c.5860C>G	p.Leu1954Val	p.L1954V	ENST00000356175	NM_000267.3	1954	Ctt/Gtt	39/57	1	2	FACETS	0.309	0.208	0.436	0.309	0.208	0.436	SUBCLONAL	1	TRUE	1	0.190579920444004	2		0	340	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664497	29664497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1212510392	NA	P-0064090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	13	0	0	ENST00000356175.3:c.6476C>T	p.Ser2159Phe	p.S2159F	ENST00000356175	NM_000267.3	2159	tCc/tTc	42/57	1	2	FACETS	0.404	0.287	0.547	0.404	0.287	0.547	SUBCLONAL	1	TRUE	1	0.190579920444004	2		0	338	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983018	149983018	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	12	0	0	ENST00000253339.5:c.3240C>A	p.Phe1080Leu	p.F1080L	ENST00000253339		1080	ttC/ttA	7/7	1	2	FACETS	0.45	0.315	0.616	0.45	0.315	0.616	SUBCLONAL	1	TRUE	1	0.190579920444004	2		0	280	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101402	27101402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	34	254	0	ENST00000324856.7:c.4689del	p.Met1564Ter	p.M1564*	ENST00000324856	NM_006015.4	1562	Ccc/cc	18/20	0.258392717149508	1	FACETS	1	0.838	1	1	0.838	1	CLONAL	1	TRUE	0	0.258392717149508	1		254	225	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593405	48593405	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	59	320	0	ENST00000342988.3:c.1156G>C	p.Gly386Arg	p.G386R	ENST00000342988	NM_005359.5	386	Ggt/Cgt	10/12	0.258392717149508	1	FACETS	0.927	0.8	1	0.927	0.8	1	CLONAL	1	TRUE	0	0.258392717149508	1		320	429	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481403	140481403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913357	NA	P-0064091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	30	279	0	ENST00000288602.6:c.1405G>A	p.Gly469Arg	p.G469R	ENST00000288602	NM_004333.4	469	Gga/Aga	11/18	1	2	FACETS	0.751	0.607	0.915	0.751	0.607	0.915	CLONAL	1	TRUE	1	0.258392717149508	2		279	309	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591247	67591247	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0064091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	10	359	0	ENST00000274335.5:c.1746-1G>C		p.X582_splice	ENST00000274335		582			1	2	FACETS	0.167	0.112	0.236	0.167	0.112	0.236	SUBCLONAL	1	TRUE	1	0.258392717149508	2		359	464	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878106	48878128	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCCGGCACCGCCGCCGCCGCC	CCCCCGGCACCGCCGCCGCCGCC	-	novel	NA	P-0064091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	42	570	0	ENST00000267163.4:c.61_83del	p.Pro21SerfsTer2	p.P21Sfs*2	ENST00000267163	NM_000321.2	20	CCCCCGGCACCGCCGCCGCCGCCc/c	1/27	1	2	FACETS	0.645	0.538	0.764	0.645	0.538	0.764	SUBCLONAL	1	TRUE	1	0.258392717149508	2		570	504	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50773873	50773873	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs975531155	NA	P-0064091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	56	454	0	ENST00000307179.4:c.1414C>G	p.Leu472Val	p.L472V	ENST00000307179		472	Cta/Gta	11/20	1	2	FACETS	0.822	0.705	0.951	0.822	0.705	0.951	CLONAL	1	TRUE	1	0.258392717149508	2		454	527	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325726	30325726	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	25	287	0	ENST00000322652.5:c.1924A>C	p.Asn642His	p.N642H	ENST00000322652	NM_015355.2	642	Aat/Cat	16/16	1	2	FACETS	0.614	0.485	0.763	0.614	0.485	0.763	SUBCLONAL	1	TRUE	1	0.258392717149508	2		287	315	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185169123	185169123	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	47	355	0	ENST00000265026.3:c.1220del	p.Leu407Ter	p.L407*	ENST00000265026	NM_004721.4	406	caT/ca	7/14	0.148562600401128	3	FACETS	0.893	0.754	1	0.447	0.377	0.523	INDETERMINATE	1	TRUE	1	0.258392717149508	3		355	460	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	911966	911966	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	41	402	0	ENST00000166345.3:c.875A>G	p.Asn292Ser	p.N292S	ENST00000166345	NM_004237.3	292	aAt/aGt	10/13	1	2	FACETS	0.697	0.581	0.827	0.697	0.581	0.827	SUBCLONAL	1	TRUE	1	0.258392717149508	2		402	455	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495486	149495486	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	39	540	0	ENST00000261799.4:c.3161C>A	p.Thr1054Asn	p.T1054N	ENST00000261799	NM_002609.3	1054	aCc/aAc	23/23	1	2	FACETS	0.59	0.488	0.703	0.59	0.488	0.703	SUBCLONAL	1	TRUE	1	0.258392717149508	2		540	512	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868477	117868477	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1485628801	NA	P-0064091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	30	370	0	ENST00000297338.2:c.865A>G	p.Thr289Ala	p.T289A	ENST00000297338	NM_006265.2	289	Acc/Gcc	8/14	0.222000306948927	4	FACETS	0.542	0.436	0.663	0.181	0.145	0.221	SUBCLONAL	1	TRUE	1	0.258392717149508	4		370	539	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647348	23647348	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	32	376	0	ENST00000261584.4:c.519del	p.Arg175AspfsTer2	p.R175Dfs*2	ENST00000261584	NM_024675.3	173	ggG/gg	4/13	1	2	FACETS	0.733	0.596	0.887	0.733	0.596	0.887	SUBCLONAL	1	TRUE	1	0.258392717149508	2		376	338	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845887	156845889	+	protein_altering_variant	In_Frame_Ins	INS	AGC	AGC	CCTGGA	novel	NA	P-0064091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	39	638	0	ENST00000524377.1:c.1517_1519delinsCCTGGA	p.Lys506_Arg507delinsThrTrpSer	p.K506_R507delinsTWS	ENST00000524377	NM_002529.3	506	aAGCgc/aCCTGGAgc	13/17	1	2	FACETS	0.48	0.397	0.573	0.48	0.397	0.573	SUBCLONAL	1	TRUE	1	0.258392717149508	2		638	629	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0064093-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	151	850	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.378052202212849	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.404198746983309	1		852	582	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs80338963	NA	P-0064093-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	125	478	0	ENST00000342988.3:c.1081C>G	p.Arg361Gly	p.R361G	ENST00000342988	NM_005359.5	361	Cgc/Ggc	9/12	0.404198746983309	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.404198746983309	1		478	447	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193252	11193252	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064093-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	120	480	0	ENST00000361445.4:c.5249G>A	p.Cys1750Tyr	p.C1750Y	ENST00000361445	NM_004958.3	1750	tGc/tAc	38/58	0.404198746983309	9	FACETS	1	0.962	1			1	CLONAL	1	TRUE	NA	0.404198746983309	9		480	1260	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087404	27087419	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGTGAGCACATCAG	GGAGTGAGCACATCAG	-	novel	NA	P-0064093-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	111	528	0	ENST00000324856.7:c.1981_1996del	p.Val661PhefsTer76	p.V661Ffs*76	ENST00000324856	NM_006015.4	660	GGAGTGAGCACATCAGgg/gg	5/20	0.404198746983309	1	FACETS	0.891	0.805	0.981	0.891	0.805	0.981	CLONAL	1	TRUE	0	0.404198746983309	1		528	492	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797180	45797180	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0064093-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	153	691	0	ENST00000450313.1:c.1235C>G	p.Ser412Ter	p.S412*	ENST00000450313	NM_012222.2	412	tCa/tGa	13/16	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.404198746983309	2		691	697	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937496	32937507	+	inframe_deletion	In_Frame_Del	DEL	TGAACTTACAGA	TGAACTTACAGA	-	novel	NA	P-0064093-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	120	480	0	ENST00000380152.3:c.8159_8170del	p.Glu2720_Asp2723del	p.E2720_D2723del	ENST00000380152		2719	atTGAACTTACAGAt/att	18/27	0.404198746983309	1	FACETS	0.987	0.897	1	0.987	0.897	1	CLONAL	1	TRUE	0	0.404198746983309	1		480	480	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946288	81946288	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064093-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	89	543	0	ENST00000359376.3:c.2021G>C	p.Arg674Pro	p.R674P	ENST00000359376	NM_002661.3	674	cGa/cCa	19/33	0.404198746983309	1	FACETS	0.819	0.73	0.913	0.819	0.73	0.913	CLONAL	1	TRUE	0	0.404198746983309	1		543	429	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11957762	11958273	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAATTTTTCAGATTCTTCACTCTGTTGTTTATATTCATTAAAATGAGGGAAAACGATATTTATTAAACTGAGGGCATTAAGTATAACACTGAACAGATGGTAATATTTTTAGAATTTTTCAGTATATCTACTGAGATAATTGATTTTTATAATAGTATTTTCACTTGCAAAAGTATTAACTTCCCTGAATAATGGAAACTTGAAGTGATAGCATTCTATCTATTGTATCATAGCCTAGTGAATGATTTGTAGTTAGTAACAACTTTAGATTATTTTATTTTTTCTTAGTTTAAGAAATTCCTCATTGCCTTTCAAAATATTGTCCTATATTAACTGTTTGTTAAAGCAAGTTCTCTTGCCTTTTGGTGTGACTTTCTTATGCCCTCAGAATAGTACCTGTTTTGTAGTACTTGAAACTTTTACTTTTTATTTGTTATTTCTCAGGTAAACGCAAAGCACTGAAGTTGAATTTTGCAAATCCACCTTTCAAATCTACAGCAAGGTTTACTCTG	AAATTTTTCAGATTCTTCACTCTGTTGTTTATATTCATTAAAATGAGGGAAAACGATATTTATTAAACTGAGGGCATTAAGTATAACACTGAACAGATGGTAATATTTTTAGAATTTTTCAGTATATCTACTGAGATAATTGATTTTTATAATAGTATTTTCACTTGCAAAAGTATTAACTTCCCTGAATAATGGAAACTTGAAGTGATAGCATTCTATCTATTGTATCATAGCCTAGTGAATGATTTGTAGTTAGTAACAACTTTAGATTATTTTATTTTTTCTTAGTTTAAGAAATTCCTCATTGCCTTTCAAAATATTGTCCTATATTAACTGTTTGTTAAAGCAAGTTCTCTTGCCTTTTGGTGTGACTTTCTTATGCCCTCAGAATAGTACCTGTTTTGTAGTACTTGAAACTTTTACTTTTTATTTGTTATTTCTCAGGTAAACGCAAAGCACTGAAGTTGAATTTTGCAAATCCACCTTTCAAATCTACAGCAAGGTTTACTCTG	-	novel	NA	P-0064093-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3	33	5	0	ENST00000353533.5:c.116-442_185del		p.X39_splice	ENST00000353533	NM_003010.3	39		2/11	0.378052202212849	1	FACETS		NA	1	1	0.978	1	NA	4	TRUE	0	0.404198746983309	1		5	36	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931860	68931860	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064093-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	101	413	0	ENST00000288368.4:c.290C>A	p.Pro97His	p.P97H	ENST00000288368	NM_024870.2	97	cCc/cAc	3/40	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.404198746983309	2		413	484	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064094-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	82	523	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.796	0.707	0.89	0.796	0.707	0.89	SUBCLONAL	1	TRUE	1	0.5723353797462	2		523	360	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023903	27023904	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0064094-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	243	575	0	ENST00000324856.7:c.1015dup	p.Ala339GlyfsTer61	p.A339Gfs*61	ENST00000324856	NM_006015.4	337	tgg/tGgg	1/20	0.267735128110935	2	FACETS	1	0.993	1	0.742	0.699	0.785	INDETERMINATE	1	TRUE	0	0.5723353797462	2		575	572	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123044	5123044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064094-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	100	412	0	ENST00000381652.3:c.3100G>A	p.Ala1034Thr	p.A1034T	ENST00000381652	NM_004972.3	1034	Gcc/Acc	23/25	0.305047841801074	1	FACETS	0.624	0.561	0.689	0.624	0.561	0.689	INDETERMINATE	1	TRUE	0	0.5723353797462	1		412	400	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982331	201982332	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0064094-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	85	664	0	ENST00000359651.3:c.715dup	p.Asp239GlyfsTer62	p.D239Gfs*62	ENST00000359651		237	aag/aaGg	6/8	0.5723353797462	2	FACETS	0.43	0.38	0.484	0.215	0.19	0.242	SUBCLONAL	1	TRUE	0	0.5723353797462	2		664	691	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265452	198265452	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064094-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	126	314	0	ENST00000335508.6:c.2705A>G	p.Glu902Gly	p.E902G	ENST00000335508	NM_012433.2	902	gAa/gGa	18/25	0.290332891781217	3	FACETS	0.789	0.722	0.857	0.789	0.722	0.857	INDETERMINATE	2	TRUE	1	0.5723353797462	3		314	359	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150923259	150923259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1454215279	NA	P-0064094-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	251	560	0	ENST00000271640.5:c.1906C>T	p.Arg636Trp	p.R636W	ENST00000271640	NM_001145415.1	636	Cgg/Tgg	13/22	0.528254296249138	3	FACETS	1	0.993	1	0.493	0.463	0.524	CLONAL	1	TRUE	0	0.5723353797462	3		560	763	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981472	201981473	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0064094-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	246	545	0	ENST00000359651.3:c.388dup	p.Ser130PhefsTer5	p.S130Ffs*5	ENST00000359651		129	act/acTt	3/8	0.5723353797462	2	FACETS	0.774	0.731	0.818	0.774	0.731	0.818	SUBCLONAL	2	TRUE	0	0.5723353797462	2		545	555	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627279	14627280	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0064094-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	182	707	0	ENST00000254322.2:c.790dup	p.Glu264GlyfsTer54	p.E264Gfs*54	ENST00000254322	NM_006145.1	264	gag/gGag	2/3	1	2	FACETS	0.817	0.756	0.881	0.817	0.756	0.881	CLONAL	1	TRUE	1	0.5723353797462	2		707	778	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759767	133759782	+	frameshift_variant	Frame_Shift_Del	DEL	GCCTAGCCACCGGCGA	GCCTAGCCACCGGCGA	-	novel	NA	P-0064094-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	82	587	0	ENST00000318560.5:c.2091_2106del	p.Leu698ArgfsTer73	p.L698Rfs*73	ENST00000318560	NM_005157.4	697	cGCCTAGCCACCGGCGAg/cg	11/11	0.5723353797462	1	FACETS	0.523	0.464	0.586	0.523	0.464	0.586	SUBCLONAL	1	TRUE	0	0.5723353797462	1		587	391	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0064095-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	99	383	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.526832444020359	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.526832444020359	2		383	162	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372518	55372518	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064095-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	185	590	0	ENST00000297316.4:c.1208G>T	p.Ser403Ile	p.S403I	ENST00000297316	NM_022454.3	403	aGc/aTc	2/2	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.526832444020359	2		590	550	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268984	142268984	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558627427	NA	P-0064095-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	18	253	0	ENST00000350721.4:c.2966G>A	p.Arg989His	p.R989H	ENST00000350721	NM_001184.3	989	cGt/cAt	14/47	1	2	FACETS	0.251	0.189	0.325	0.251	0.189	0.325	SUBCLONAL	1	TRUE	1	0.526832444020359	2		253	272	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50791164	50791164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766802045	NA	P-0064095-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	75	452	0	ENST00000307179.4:c.3236G>A	p.Arg1079Gln	p.R1079Q	ENST00000307179		1079	cGg/cAg	20/20	1	2	FACETS	0.765	0.675	0.862	0.765	0.675	0.862	SUBCLONAL	1	TRUE	1	0.526832444020359	2		452	372	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539605	187539605	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0064095-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	84	478	0	ENST00000441802.2:c.8135del	p.Val2712GlyfsTer11	p.V2712Gfs*11	ENST00000441802	NM_005245.3	2712	gTg/gg	10/27	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.526832444020359	2		478	299	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593240	67593252	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GGTGGACGGCGAA	GGTGGACGGCGAA	-	novel	NA	P-0064095-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	92	431	0	ENST00000274335.5:c.1987_1999del	p.Val663Ter	p.V663*	ENST00000274335		662	gtGGTGGACGGCGAA/gt	15/15	1	2	FACETS	0.838	0.749	0.931	0.838	0.749	0.931	CLONAL	1	TRUE	1	0.526832444020359	2		431	417	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184067	123184067	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064095-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	62	392	0	ENST00000218089.9:c.925A>G	p.Ile309Val	p.I309V	ENST00000218089	NM_001042749.1	309	Att/Gtt	11/35	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.526832444020359	2		392	216	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0064098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	141	616	2	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.384228333044532	3	FACETS	0.994	0.906	1			1	CLONAL	1	TRUE	NA	0.405012088596652	3		618	842	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163512	47163512	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	97	383	0	ENST00000409792.3:c.2614C>T	p.Gln872Ter	p.Q872*	ENST00000409792	NM_014159.6	872	Caa/Taa	3/21	1	2	FACETS	0.882	0.789	0.981	0.882	0.789	0.981	CLONAL	1	TRUE	1	0.405012088596652	2		383	543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0064098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	148	462	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.405012088596652	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.405012088596652	1		462	582	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663350	29663350	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs1555534596	NA	P-0064098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	88	265	0	ENST00000356175.3:c.5944-1G>C		p.X1982_splice	ENST00000356175	NM_000267.3	1982			0.405012088596652	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.405012088596652	1		265	335	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0064099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	220	541	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	0.865046348370686	3	FACETS	0.932	0.869	0.996	0.466	0.434	0.498	CLONAL	1	TRUE	1	0.865046348370686	3		541	782	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964532	70964532	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	235	499	0	ENST00000276594.2:c.1496C>G	p.Thr499Arg	p.T499R	ENST00000276594	NM_024504.3	499	aCa/aGa	8/8	0.865046348370686	4	FACETS	0.915	0.854	0.979	0.458	0.427	0.49	CLONAL	1	TRUE	2	0.865046348370686	4		499	1107	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2088540	2088540	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	50	286	0	ENST00000349721.2:c.2810G>A	p.Arg937His	p.R937H	ENST00000349721	NM_003070.3	937	cGt/cAt	19/34	0.865046348370686	3	FACETS	1	0.917	1	0.541	0.469	0.617	CLONAL	1	TRUE	1	0.865046348370686	3		286	153	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437777	52437804	+	frameshift_variant	Frame_Shift_Del	DEL	GAATTGAGAGGTCCTTCTGGGACTCTTT	GAATTGAGAGGTCCTTCTGGGACTCTTT	-	novel	NA	P-0064100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	88	537	0	ENST00000460680.1:c.1357_1384del	p.Lys453LeufsTer109	p.K453Lfs*109	ENST00000460680	NM_004656.3	453	AAAGAGTCCCAGAAGGACCTCTCAATTCct/ct	13/17	0.33383900313799	1	FACETS	0.81	0.72	0.905	0.81	0.72	0.905	CLONAL	1	TRUE	0	0.353013389740219	1		537	507	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958831	38958831	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	82	414	0	ENST00000357387.3:c.2281G>T	p.Asp761Tyr	p.D761Y	ENST00000357387	NM_152756.3	761	Gat/Tat	23/38	1	2	FACETS	0.997	0.882	1	0.997	0.882	1	CLONAL	1	TRUE	1	0.353013389740219	2		414	466	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064101-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	111	523	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.887	0.803	0.975	0.887	0.803	0.975	CLONAL	1	TRUE	1	0.567293784461715	2		523	441	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46215221	46215222	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTATTTGGAGAAGAATGGAAAGAGAAGACTGATAGAGACTTCGTTAAGG	novel	NA	P-0064101-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	32	145	0	ENST00000334344.6:c.658_705+2dup		p.T219fs	ENST00000334344	NM_152641.2	219	act/acTGTATTTGGAGAAGAATGGAAAGAGAAGACTGATAGAGACTTCGTTAAGGt	6/21	1	2	FACETS	0.508	0.415	0.612	0.508	0.415	0.612	SUBCLONAL	1	TRUE	1	0.567293784461715	2		145	222	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058920	42058920	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064101-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	204	524	1	ENST00000219905.7:c.8640G>C	p.Leu2880Phe	p.L2880F	ENST00000219905	NM_001164273.1	2880	ttG/ttC	24/24	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.567293784461715	2		525	709	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0064102-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	276	728	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.918096007226232	2		728	545	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463307	25463307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757211277	NA	P-0064102-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	258	662	0	ENST00000264709.3:c.2186G>A	p.Arg729Gln	p.R729Q	ENST00000264709	NM_175629.2	729	cGg/cAg	19/23	1	2	FACETS	0.986	0.932	1	0.986	0.932	1	CLONAL	1	TRUE	1	0.918096007226232	2		662	570	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225518	26225518	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064102-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	58	928	0	ENST00000360408.1:c.136A>C	p.Thr46Pro	p.T46P	ENST00000360408	NM_003532.2	46	Acc/Ccc	1/1	1	2	FACETS	0.135	0.115	0.156	0.135	0.115	0.156	SUBCLONAL	1	TRUE	1	0.918096007226232	2		928	937	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0064103-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	218	648	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.360653046786489	3	FACETS	0.887	0.827	0.949	0.887	0.827	0.949	CLONAL	2	TRUE	1	0.360653046786489	3		648	804	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033865	49033865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369755801	NA	P-0064103-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	103	457	0	ENST00000267163.4:c.2002C>T	p.Arg668Cys	p.R668C	ENST00000267163	NM_000321.2	668	Cgc/Tgc	20/27	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.360653046786489	2		457	524	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758762	41758762	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064103-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	67	625	0	ENST00000301178.4:c.1816C>T	p.Gln606Ter	p.Q606*	ENST00000301178	NM_021913.4	606	Cag/Tag	16/20	1	2	FACETS	0.624	0.543	0.713	0.624	0.543	0.713	SUBCLONAL	1	TRUE	1	0.360653046786489	2		625	595	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0064104-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	52	362	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.998	0.862	1	1	0.977	1	CLONAL	2	TRUE	1	0.27	2		362	193	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	532733	532733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778400	NA	P-0064104-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	85	412	0	ENST00000451590.1:c.473C>T	p.Thr158Met	p.T158M	ENST00000451590	NM_001130442.1	158	aCg/aTg	5/5	1	2	FACETS	0.846	0.753	0.944	1	0.983	1	CLONAL	2	TRUE	1	0.27	2		412	372	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235809	108235809	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1555151205	NA	P-0064104-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	47	366	0	ENST00000278616.4:c.8851G>A	p.Val2951Ile	p.V2951I	ENST00000278616	NM_000051.3	2951	Gtc/Atc	62/63	0.3	0	FACETS	1	0.943	1			1	CLONAL	1	TRUE	0	0.27	0		366	207	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795053	42795053	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064104-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	99	613	0	ENST00000575354.2:c.2133G>C	p.Met711Ile	p.M711I	ENST00000575354	NM_015125.3	711	atG/atC	10/20	1	2	FACETS	0.797	0.715	0.883	1	0.984	1	SUBCLONAL	2	TRUE	1	0.27	2		613	460	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0064104-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	129	580	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.279302273649885	3	FACETS	0.902	0.825	0.98	1	0.984	1	CLONAL	3	TRUE	1	0.27	3		582	401	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117632201	117632201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779401784	NA	P-0064104-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	54	337	0	ENST00000368508.3:c.6215G>A	p.Arg2072Gln	p.R2072Q	ENST00000368508	NM_002944.2	2072	cGg/cAg	39/43	0.3	1	FACETS	1	0.952	1	1	0.981	1	CLONAL	2	TRUE	0	0.27	1		337	145	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0064106-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	55	391	2	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	1	2	FACETS	0.524	0.448	0.607	0.524	0.448	0.607	SUBCLONAL	1	TRUE	1	0.381664031935838	2		393	550	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0064107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	9	420	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.391	0.258	0.562	0.391	0.258	0.562	SUBCLONAL	1	TRUE	1	0.15	2		420	307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0064107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	20	662	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.768	0.587	0.981	0.768	0.587	0.981	CLONAL	1	TRUE	1	0.15	2		662	347	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974715	21974732	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCCCCCGCCTCCA	GCAGCGCCCCCGCCTCCA	-	novel	NA	P-0064107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	14	736	0	ENST00000304494.5:c.95_112del	p.Leu32_Leu37del	p.L32_L37del	ENST00000304494	NM_000077.4	32	cTGGAGGCGGGGGCGCTGCcc/ccc	1/3	1	2	FACETS	0.49	0.353	0.657	0.49	0.353	0.657	SUBCLONAL	1	TRUE	1	0.15	2		736	381	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814798	139814798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201857326	NA	P-0064107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	24	577	0	ENST00000247668.2:c.791C>T	p.Ala264Val	p.A264V	ENST00000247668	NM_021138.3	264	gCg/gTg	8/11	1	2	FACETS	0.764	0.598	0.956	0.764	0.598	0.956	CLONAL	1	TRUE	1	0.15	2		577	419	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023217	27023218	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0064107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	26	477	0	ENST00000324856.7:c.326dup	p.Arg110Ter	p.R110*	ENST00000324856	NM_006015.4	108	ggc/ggCc	1/20	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.15	2		477	290	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842466	68842491	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCAGGTAGAGAAAGAAGTTCTCTGT	TTCAGGTAGAGAAAGAAGTTCTCTGT	-	novel	NA	P-0064107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	22	440	0	ENST00000261769.5:c.530_531+24del		p.X177_splice	ENST00000261769	NM_004360.3	177		4/16	1	2	FACETS	0.984	0.764	1	0.984	0.764	1	CLONAL	1	TRUE	1	0.15	2		440	298	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732958	30732958	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	43	532	0	ENST00000295754.5:c.1571A>G	p.Asp524Gly	p.D524G	ENST00000295754	NM_003242.5	524	gAc/gGc	7/7	1	2	FACETS	0.904	0.76	1	1	0.967	1	CLONAL	2	TRUE	1	0.15	2		532	317	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151868416	151868432	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATAAAAGGGAACCTGTC	ATAAAAGGGAACCTGTC	TT	novel	NA	P-0064107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	11	396	1	ENST00000262189.6:c.9375-5_9386delinsAA		p.X3125_splice	ENST00000262189	NM_170606.2	3125		40/59	1	2	FACETS	0.702	0.485	0.971	0.702	0.485	0.971	CLONAL	1	TRUE	1	0.15	2		397	209	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0064108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	30	454	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.238	0.191	0.291	0.238	0.191	0.291	SUBCLONAL	1	TRUE	1	0.45	2		454	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578242	7578242	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882003	NA	P-0064108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	21	567	0	ENST00000269305.4:c.607G>T	p.Val203Leu	p.V203L	ENST00000269305	NM_001126112.2	203	Gtg/Ttg	6/11	1	2	FACETS	0.154	0.118	0.196	0.154	0.118	0.196	SUBCLONAL	1	TRUE	1	0.45	2		567	607	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508824	106508824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226994105	NA	P-0064109-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	123	526	1	ENST00000359195.3:c.818G>A	p.Arg273His	p.R273H	ENST00000359195	NM_002649.2	273	cGc/cAc	2/11	0.459805257484814	3	FACETS	0.954	0.864	1	0.477	0.432	0.524	CLONAL	1	TRUE	1	0.459805257484814	3		527	690	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0064109-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	224	368	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.459805257484814	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.459805257484814	2		368	449	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307243	118307243	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555138451	NA	P-0064110-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	16	310	0	ENST00000534358.1:c.16C>T	p.Arg6Trp	p.R6W	ENST00000534358	NM_005933.3	6	Cgg/Tgg	1/36	0.486830227892604	1	FACETS	0.284	0.211	0.371	0.284	0.211	0.371	SUBCLONAL	1	TRUE	0	0.486830227892604	1		310	175	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061087	38061087	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064110-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	83	553	0	ENST00000250448.2:c.902C>G	p.Ser301Cys	p.S301C	ENST00000250448	NM_004496.3	301	tCt/tGt	2/2	1	2	FACETS	0.932	0.828	1	0.932	0.828	1	CLONAL	1	TRUE	1	0.486830227892604	2		553	366	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061189	38061191	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	novel	NA	P-0064110-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	111	565	0	ENST00000250448.2:c.798_800del	p.Phe266_Lys267delinsLeu	p.F266_K267delinsL	ENST00000250448	NM_004496.3	266	ttCAAg/ttg	2/2	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.486830227892604	2		565	404	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0064118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	137	494	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.470847108271326	1	FACETS	0.919	0.842	0.999	0.919	0.842	0.999	CLONAL	1	TRUE	0	0.48466864744438	1		494	466	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0064118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	183	362	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.48466864744438	3	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	1	0.48466864744438	3		362	469	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0064118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	153	551	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.48466864744438	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.48466864744438	1		551	436	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482425	56482425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	305	544	0	ENST00000267101.3:c.973G>A	p.Gly325Arg	p.G325R	ENST00000267101	NM_001982.3	325	Gga/Aga	8/28	0.48466864744438	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	1	0.48466864744438	3		544	781	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216546	108216546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529296539	NA	P-0064118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	101	392	0	ENST00000278616.4:c.8495G>A	p.Arg2832His	p.R2832H	ENST00000278616	NM_000051.3	2832	cGt/cAt	58/63	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.48466864744438	2		392	411	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721532	176721532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373116626	NA	P-0064118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	175	582	0	ENST00000439151.2:c.7163C>T	p.Pro2388Leu	p.P2388L	ENST00000439151	NM_022455.4	2388	cCg/cTg	23/23	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.48466864744438	2		582	671	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0064118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	12	533	0	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	0.48466864744438	1	FACETS	0.087	0.061	0.12	0.087	0.061	0.12	SUBCLONAL	1	TRUE	0	0.48466864744438	1		533	430	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411678	63411678	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	164	343	0	ENST00000330258.3:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000330258	NM_152424.3	497	Cga/Tga	2/2	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.48466864744438	1		343	359	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211118	36211118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200835025	NA	P-0064118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	166	669	1	ENST00000222270.7:c.869G>A	p.Arg290His	p.R290H	ENST00000222270	NM_014727.1	290	cGt/cAt	3/37	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.48466864744438	2		670	661	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981536	201981536	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	245	579	0	ENST00000359651.3:c.451del	p.Gln151ArgfsTer4	p.Q151Rfs*4	ENST00000359651		150	ttC/tt	3/8	0.139309784971259	5	FACETS	0.919	0.865	0.974			1	INDETERMINATE	3	TRUE	NA	0.48466864744438	5		579	633	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205764	108205766	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs1565540828	NA	P-0064118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	95	382	0	ENST00000278616.4:c.8082_8084del	p.Gly2695del	p.G2695del	ENST00000278616	NM_000051.3	2693	gcAGGa/gca	55/63	1	2	FACETS	0.992	0.89	1	0.992	0.89	1	CLONAL	1	TRUE	1	0.48466864744438	2		382	395	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972354	32972354	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	165	508	2	ENST00000380152.3:c.9704C>A	p.Ala3235Asp	p.A3235D	ENST00000380152		3235	gCc/gAc	27/27	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.48466864744438	2		510	565	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421239	12421239	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064118-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	113	484	0	ENST00000287820.6:c.119C>A	p.Pro40His	p.P40H	ENST00000287820	NM_015869.4	40	cCc/cAc	2/7	1	2	FACETS	0.916	0.828	1	0.916	0.828	1	CLONAL	1	TRUE	1	0.48466864744438	2		484	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587782272	NA	P-0064119-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	412	372	0	ENST00000269305.4:c.994-1G>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.752198012591087	5	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	2	0.820406969474153	5		372	722	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0064119-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	425	568	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.752198012591087	5	FACETS	1	0.985	1	0.711	0.679	0.744	CLONAL	2	TRUE	2	0.820406969474153	5		568	1083	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0064119-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	512	380	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.820406969474153	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.820406969474153	3		380	570	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717777	89717777	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0064120-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	56	300	0	ENST00000371953.3:c.801+1G>T		p.X267_splice	ENST00000371953	NM_000314.4	267			1	2	FACETS	0.84	0.723	0.967	0.84	0.723	0.967	CLONAL	1	TRUE	1	0.374505414613632	2		300	356	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624296	89624296	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs786201995	NA	P-0064120-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	93	326	0	ENST00000371953.3:c.70G>C	p.Asp24His	p.D24H	ENST00000371953	NM_000314.4	24	Gac/Cac	1/9	1	2	FACETS	0.963	0.859	1	0.963	0.859	1	CLONAL	1	TRUE	1	0.374505414613632	2		326	516	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0064120-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	114	487	0	ENST00000349496.5:c.101G>A	p.Gly34Glu	p.G34E	ENST00000349496	NM_001904.3	34	gGa/gAa	3/15	1	2	FACETS	0.918	0.828	1	0.918	0.828	1	CLONAL	1	TRUE	1	0.374505414613632	2		487	663	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105715	27105715	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064120-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	144	652	0	ENST00000324856.7:c.5326G>T	p.Glu1776Ter	p.E1776*	ENST00000324856	NM_006015.4	1776	Gaa/Taa	20/20	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.374505414613632	2		652	752	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591135	67591135	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064120-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	231	489	1	ENST00000274335.5:c.1728del	p.Arg577GlufsTer5	p.R577Efs*5	ENST00000274335		576	acG/ac	12/15	0.374505414613632	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.374505414613632	2		490	609	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502271	157502271	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs387907141	NA	P-0064120-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	134	587	0	ENST00000346085.5:c.3304C>T	p.Arg1102Ter	p.R1102*	ENST00000346085	NM_020732.3	1102	Cga/Tga	12/20	1	2	FACETS	0.993	0.903	1	0.993	0.903	1	CLONAL	1	TRUE	1	0.374505414613632	2		587	721	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0064120-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	59	339	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.854	0.738	0.979	0.854	0.738	0.979	CLONAL	1	TRUE	1	0.374505414613632	2		339	369	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056193	27056193	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064120-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	110	590	0	ENST00000324856.7:c.1191del	p.Thr398LeufsTer35	p.T398Lfs*35	ENST00000324856	NM_006015.4	397	Ggg/gg	2/20	1	2	FACETS	0.829	0.745	0.917	0.829	0.745	0.917	CLONAL	1	TRUE	1	0.374505414613632	2		590	709	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609058	43609058	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064120-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	167	762	0	ENST00000355710.3:c.1814G>C	p.Gly605Ala	p.G605A	ENST00000355710	NM_020975.4	605	gGc/gCc	10/20	1	2	FACETS	0.973	0.894	1	0.973	0.894	1	CLONAL	1	TRUE	1	0.374505414613632	2		762	917	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466017	69466025	+	inframe_deletion	In_Frame_Del	DEL	CACACCCAC	CACACCCAC	-	novel	NA	P-0064120-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	143	685	2	ENST00000227507.2:c.856_864del	p.Thr286_Thr288del	p.T286_T288del	ENST00000227507	NM_053056.2	285	tgCACACCCACc/tgc	5/5	1	2	FACETS	0.989	0.903	1	0.989	0.903	1	CLONAL	1	TRUE	1	0.374505414613632	2		687	772	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435767	110435767	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs778386128	NA	P-0064120-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	120	573	0	ENST00000375856.3:c.2634G>C	p.Glu878Asp	p.E878D	ENST00000375856	NM_003749.2	878	gaG/gaC	1/2	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.374505414613632	2		573	634	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645415	67645416	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0064120-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	132	565	0	ENST00000264010.4:c.684dup	p.Glu229Ter	p.E229*	ENST00000264010	NM_006565.3	227	gat/gaTt	3/12	1	2	FACETS	0.95	0.863	1	0.95	0.863	1	CLONAL	1	TRUE	1	0.374505414613632	2		565	742	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245823	5245823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064120-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	49	532	0	ENST00000357368.4:c.952G>A	p.Gly318Ser	p.G318S	ENST00000357368	NM_002850.3	318	Ggc/Agc	10/38	1	2	FACETS	0.369	0.312	0.432	0.369	0.312	0.432	SUBCLONAL	1	TRUE	1	0.374505414613632	2		532	709	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861534	152861534	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782228548	NA	P-0064120-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	113	516	0	ENST00000406277.2:c.218C>T	p.Ser73Phe	p.S73F	ENST00000406277	NM_152274.4	73	tCt/tTt	4/7	1		FACETS		0.882	1				CLONAL	1	TRUE	1	0.374505414613632	2		516	617	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0064121-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	164	301	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.287548612963922	2	FACETS	0.909	0.838	0.982	0.909	0.838	0.982	CLONAL	2	TRUE	0	0.289687754648873	2		301	623	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249510	153249510	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1157879635	NA	P-0064121-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	83	458	0	ENST00000281708.4:c.1268G>T	p.Gly423Val	p.G423V	ENST00000281708	NM_033632.3	423	gGa/gTa	9/12	1	2	FACETS	0.929	0.82	1	0.929	0.82	1	CLONAL	1	TRUE	1	0.289687754648873	2		458	617	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205765	108205765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555127157	NA	P-0064121-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	57	446	0	ENST00000278616.4:c.8080G>A	p.Gly2694Arg	p.G2694R	ENST00000278616	NM_000051.3	2694	Gga/Aga	55/63	1	2	FACETS	0.758	0.651	0.875	0.758	0.651	0.875	SUBCLONAL	1	TRUE	1	0.289687754648873	2		446	519	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597990	43597990	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs76449634	NA	P-0064121-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	89	724	1	ENST00000355710.3:c.538C>T	p.Arg180Ter	p.R180*	ENST00000355710	NM_020975.4	180	Cga/Tga	3/20	1	2	FACETS	0.774	0.685	0.868	0.774	0.685	0.868	SUBCLONAL	1	TRUE	1	0.289687754648873	2		725	794	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0064121-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	55	340	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.289687754648873	2		340	347	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032463	12032463	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064121-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	71	424	0	ENST00000353533.5:c.899T>G	p.Leu300Trp	p.L300W	ENST00000353533	NM_003010.3	300	tTg/tGg	9/11	0.283487080263617	1	FACETS	0.964	0.844	1	0.964	0.844	1	CLONAL	1	TRUE	0	0.289687754648873	1		424	435	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93973599	93973599	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064121-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	39	337	0	ENST00000369303.4:c.1777G>T	p.Asp593Tyr	p.D593Y	ENST00000369303	NM_004440.3	593	Gat/Tat	9/17	1	2	FACETS	0.962	0.801	1	0.962	0.801	1	CLONAL	1	TRUE	1	0.289687754648873	2		337	280	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0064122-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	256	558	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.262693058397548	3	FACETS	1	0.965	1	0.692	0.65	0.734	CLONAL	2	TRUE	0	0.392534332083098	3		558	752	SUCCESS
APC	324	MSKCC	GRCh37	5	112175273	112175273	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123121	NA	P-0064122-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	167	549	0	ENST00000257430.4:c.3982C>T	p.Gln1328Ter	p.Q1328*	ENST00000257430	NM_000038.5	1328	Cag/Tag	16/16	0.296859662286766	2	FACETS	1	0.989	1	0.744	0.687	0.802	CLONAL	1	TRUE	0	0.392534332083098	2		549	572	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0064122-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	97	785	0	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	1	2	FACETS	0.53	0.472	0.593	0.53	0.472	0.593	SUBCLONAL	1	TRUE	1	0.392534332083098	2		785	932	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973094	25973094	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064122-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	53	653	0	ENST00000435504.4:c.1331A>T	p.Lys444Ile	p.K444I	ENST00000435504		444	aAa/aTa	12/13	0.362408611237351	4	FACETS	0.406	0.345	0.474	0.135	0.115	0.158	SUBCLONAL	1	TRUE	1	0.392534332083098	4		653	926	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0064123-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	85	515	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.996	0.892	1	0.996	0.892	1	CLONAL	1	TRUE	1	0.616321097668703	2		515	277	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644679	134644679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773064927	NA	P-0064123-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	146	438	0	ENST00000398015.3:c.80C>T	p.Thr27Met	p.T27M	ENST00000398015	NM_004441.4	27	aCg/aTg	2/16	0.226345350013641	3	FACETS	1	0.987	1	0.706	0.65	0.763	INDETERMINATE	1	TRUE	1	0.616321097668703	3		438	439	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189322	99189322	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759626940	NA	P-0064123-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	126	513	0	ENST00000074304.5:c.2578C>T	p.Arg860Trp	p.R860W	ENST00000074304	NM_001134224.1	860	Cgg/Tgg	24/26	1	2	FACETS	0.964	0.881	1	0.964	0.881	1	CLONAL	1	TRUE	1	0.616321097668703	2		513	424	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591054	67591056	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0064123-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	104	390	0	ENST00000274335.5:c.1651_1653del	p.Lys551del	p.K551del	ENST00000274335		549	ttGAAg/ttg	12/15	0.588003049678393	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.616321097668703	1		390	231	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509809	187509809	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1552691	NA	P-0064123-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	186	535	0	ENST00000441802.2:c.13704C>A	p.Asp4568Glu	p.D4568E	ENST00000441802	NM_005245.3	4568	gaC/gaA	27/27	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.616321097668703	2		535	548	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064124-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	136	331	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.593225565003358	3	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	1	0.593225565003358	3		331	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0064124-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	290	558	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.575240656969184	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.593225565003358	2		558	470	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0064124-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	46	404	2	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.593225565003358	3	FACETS	0.742	0.629	0.865	0.371	0.314	0.433	SUBCLONAL	1	TRUE	1	0.593225565003358	3		406	271	SUCCESS
APC	324	MSKCC	GRCh37	5	112175153	112175153	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064124-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	192	650	1	ENST00000257430.4:c.3862G>T	p.Gly1288Ter	p.G1288*	ENST00000257430	NM_000038.5	1288	Gga/Tga	16/16	0.593225565003358	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.593225565003358	3		651	380	SUCCESS
AR	367	MSKCC	GRCh37	X	66765778	66765778	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064124-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	123	636	0	ENST00000374690.3:c.790C>T	p.Arg264Trp	p.R264W	ENST00000374690	NM_000044.3	264	Cgg/Tgg	1/8	0.593225565003358	3	FACETS	0.971	0.881	1	0.485	0.44	0.532	CLONAL	1	TRUE	1	0.593225565003358	3		636	554	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068302	30068302	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064124-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	62	295	0	ENST00000331968.5:c.2097T>A	p.Phe699Leu	p.F699L	ENST00000331968	NM_002742.2	699	ttT/ttA	15/18	1	2	FACETS	0.986	0.865	1	0.986	0.865	1	CLONAL	1	TRUE	1	0.593225565003358	2		295	212	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40991027	40991027	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064124-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	106	371	0	ENST00000267868.3:c.71C>T	p.Pro24Leu	p.P24L	ENST00000267868	NM_002875.4	24	cCc/cTc	2/10	1	2	FACETS	0.987	0.894	1	0.987	0.894	1	CLONAL	1	TRUE	1	0.593225565003358	2		371	362	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119752	70119753	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0064124-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	97	362	0	ENST00000245479.2:c.755_756dup	p.Lys253Ter	p.K253*	ENST00000245479	NM_000346.3	252	ctg/cTGtg	3/3	0.571059440564029	3	FACETS	0.97	0.87	1	0.485	0.435	0.538	CLONAL	1	TRUE	1	0.593225565003358	3		362	437	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	44	362	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.862	0.729	1	0.862	0.729	1	CLONAL	1	TRUE	1	0.42701505626656	2		362	239	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491381	2491381	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs551576039	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	119	626	0	ENST00000355716.4:c.424G>A	p.Ala142Thr	p.A142T	ENST00000355716	NM_003820.2	142	Gcc/Acc	4/8	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.42701505626656	2		626	537	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230561421	230561421	+	5_prime_UTR_variant	5'UTR	SNP	G	G	A	novel	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	160	854	0	ENST00000391860.1:c.-92C>T		p.*31*	ENST00000391860	NM_001258311.1	-/409		1/7	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.42701505626656	2		854	611	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100728	8100728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs771019738	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	57	524	3	ENST00000346208.3:c.708del	p.Ser237AlafsTer28	p.S237Afs*28	ENST00000346208		234	ttC/tt	3/6	1	2	FACETS	0.553	0.475	0.638	0.553	0.475	0.638	SUBCLONAL	1	TRUE	1	0.42701505626656	2		527	483	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601830	43601830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34682185	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	129	528	0	ENST00000355710.3:c.874G>A	p.Val292Met	p.V292M	ENST00000355710	NM_020975.4	292	Gtg/Atg	5/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.42701505626656	2		528	523	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936122	71936122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	110	504	0	ENST00000298229.2:c.94G>A	p.Glu32Lys	p.E32K	ENST00000298229	NM_001567.3	32	Gag/Aag	1/28	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.42701505626656	2		504	366	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197307	94197308	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	41	288	0	ENST00000323929.3:c.1196dup	p.Arg400GlnfsTer3	p.R400Qfs*3	ENST00000323929	NM_005591.3	399	ttc/ttTc	11/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.42701505626656	2		288	140	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201141	108201141	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	109	432	0	ENST00000278616.4:c.7508T>C	p.Met2503Thr	p.M2503T	ENST00000278616	NM_000051.3	2503	aTg/aCg	50/63	1	2	FACETS	0.842	0.767	0.92	1	0.987	1	CLONAL	2	TRUE	1	0.42701505626656	2		432	303	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	159	605	0	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.42701505626656	2		605	605	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426760	49426760	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	37	726	0	ENST00000301067.7:c.11728C>T	p.Gln3910Ter	p.Q3910*	ENST00000301067	NM_003482.3	3910	Cag/Tag	39/54	1	2	FACETS	0.248	0.204	0.298	0.248	0.204	0.298	SUBCLONAL	1	TRUE	1	0.42701505626656	2		726	698	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578215	28578216	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	141	499	0	ENST00000241453.7:c.2955_2956del	p.Pro986AlafsTer27	p.P986Afs*27	ENST00000241453	NM_004119.2	985	tcTCcg/tccg	24/24	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.42701505626656	2		499	521	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239933	41239933	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	61	355	0	ENST00000379561.5:c.417del	p.Ala140ProfsTer193	p.A140Pfs*193	ENST00000379561	NM_002015.3	139	ccC/cc	1/3	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.42701505626656	2		355	284	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	126	583	2	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.42701505626656	2		585	420	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	123	593	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.42701505626656	2		593	476	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	27	587	1	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	0.25	0.198	0.309	0.25	0.198	0.309	SUBCLONAL	1	TRUE	1	0.42701505626656	2		588	506	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822586	72822586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	139	755	2	ENST00000268489.5:c.9589del	p.Gln3197SerfsTer44	p.Q3197Sfs*44	ENST00000268489	NM_006885.3	3197	Cag/ag	10/10	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.42701505626656	2		757	605	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349914	89349916	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs761762028	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	13	627	0	ENST00000301030.4:c.3034_3036del	p.Lys1012del	p.K1012del	ENST00000301030	NM_001256183.1	1012	AAG/-	9/13	1	2	FACETS	0.1	0.071	0.137	0.1	0.071	0.137	SUBCLONAL	1	TRUE	1	0.42701505626656	2		627	606	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222431	2222431	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370815654	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	150	612	3	ENST00000398665.3:c.3263G>A	p.Arg1088Gln	p.R1088Q	ENST00000398665	NM_032482.2	1088	cGg/cAg	24/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.42701505626656	2		615	543	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18958581	18958581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	88	365	1	ENST00000262803.5:c.400G>A	p.Val134Met	p.V134M	ENST00000262803	NM_002911.3	134	Gtg/Atg	3/24	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.42701505626656	2		366	376	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36208925	36208926	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCGGCGGCG	novel	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	29	324	0	ENST00000222270.7:c.15_24dup	p.Ser9GlyfsTer110	p.S9Gfs*110	ENST00000222270	NM_014727.1	2	gcg/gcGGCGGCGGCGg	1/37	1	2	FACETS	0.629	0.508	0.764	0.629	0.508	0.764	SUBCLONAL	1	TRUE	1	0.42701505626656	2		324	216	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219736	36219736	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	106	641	0	ENST00000222270.7:c.4633C>T	p.Gln1545Ter	p.Q1545*	ENST00000222270	NM_014727.1	1545	Cag/Tag	20/37	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.42701505626656	2		641	493	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905055	50905055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	51	471	2	ENST00000440232.2:c.342del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	113	Ggg/gg	4/27	1	2	FACETS	0.545	0.464	0.634	0.545	0.464	0.634	SUBCLONAL	1	TRUE	1	0.42701505626656	2		473	438	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906466	50906466	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1231801192	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	44	527	0	ENST00000440232.2:c.1127A>T	p.Asp376Val	p.D376V	ENST00000440232	NM_002691.3	376	gAc/gTc	9/27	1	2	FACETS	0.454	0.381	0.535	0.454	0.381	0.535	SUBCLONAL	1	TRUE	1	0.42701505626656	2		527	454	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101089	26101089	+	start_lost	Translation_Start_Site	SNP	C	C	T	rs1559535727	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	88	388	0	ENST00000435504.4:c.3G>A	p.Met1?	p.M1?	ENST00000435504		1	atG/atA	1/13	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.42701505626656	2		388	368	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	145	559	8	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.42701505626656	2		567	530	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	179	705	22	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.42701505626656	2		727	601	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691872	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs79375991	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	177	500	18	ENST00000295754.5:c.383del	p.Lys128SerfsTer35	p.K128Sfs*35	ENST00000295754	NM_003242.5	125	gAa/ga	3/7	1	2	FACETS	1	0.979	1	1	0.994	1	CLONAL	2	TRUE	1	0.42701505626656	2		518	374	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070349	37070349	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs63750855	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	28	494	1	ENST00000231790.2:c.1489del	p.Arg497GlyfsTer11	p.R497Gfs*11	ENST00000231790	NM_000249.3	495	aCc/ac	13/19	1	2	FACETS	0.3	0.239	0.37	0.3	0.239	0.37	SUBCLONAL	1	TRUE	1	0.42701505626656	2		495	437	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940067	49940067	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	144	619	0	ENST00000296474.3:c.976T>G	p.Ser326Ala	p.S326A	ENST00000296474	NM_002447.2	326	Tcc/Gcc	1/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.42701505626656	2		619	600	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178158	142178158	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	56	334	1	ENST00000350721.4:c.7260del	p.Lys2420AsnfsTer22	p.K2420Nfs*22	ENST00000350721	NM_001184.3	2420	aaA/aa	43/47	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.42701505626656	2		335	240	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169988218	169988218	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	120	352	0	ENST00000295797.4:c.460T>A	p.Cys154Ser	p.C154S	ENST00000295797	NM_002740.5	154	Tgt/Agt	6/18	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.42701505626656	2		352	411	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	48	367	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.781	0.675	0.892	1	0.969	1	SUBCLONAL	2	TRUE	1	0.42701505626656	2		367	144	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749509	41749509	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	110	394	0	ENST00000226382.2:c.286C>T	p.Arg96Cys	p.R96C	ENST00000226382	NM_003924.3	96	Cgc/Tgc	2/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.42701505626656	2		394	391	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542861	187542861	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1340793072	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	75	395	0	ENST00000441802.2:c.4879C>T	p.Arg1627Ter	p.R1627*	ENST00000441802	NM_005245.3	1627	Cga/Tga	10/27	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.42701505626656	2		395	288	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294903	1294903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	127	528	2	ENST00000310581.5:c.202G>A	p.Ala68Thr	p.A68T	ENST00000310581	NM_198253.2	68	Gcc/Acc	1/16	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.42701505626656	2		530	415	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589576	67589576	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1289537429	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	35	168	0	ENST00000274335.5:c.1344del	p.Lys448AsnfsTer32	p.K448Nfs*32	ENST00000274335		447	Aaa/aa	10/15	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.42701505626656	2		168	119	SUCCESS
APC	324	MSKCC	GRCh37	5	112175435	112175435	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	65	444	0	ENST00000257430.4:c.4144C>G	p.Leu1382Val	p.L1382V	ENST00000257430	NM_000038.5	1382	Ctc/Gtc	16/16	1	2	FACETS	0.632	0.549	0.721	0.632	0.549	0.721	SUBCLONAL	1	TRUE	1	0.42701505626656	2		444	482	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497223	149497223	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	46	473	0	ENST00000261799.4:c.3095T>G	p.Val1032Gly	p.V1032G	ENST00000261799	NM_002609.3	1032	gTt/gGt	22/23	1	2	FACETS	0.468	0.395	0.55	0.468	0.395	0.55	SUBCLONAL	1	TRUE	1	0.42701505626656	2		473	460	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522696	176522696	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369266328	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	68	620	0	ENST00000292408.4:c.1793G>A	p.Arg598Gln	p.R598Q	ENST00000292408	NM_213647.1	598	cGa/cAa	13/18	1	2	FACETS	0.547	0.476	0.624	0.547	0.476	0.624	SUBCLONAL	1	TRUE	1	0.42701505626656	2		620	582	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722306	176722307	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs587784219	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	74	634	0	ENST00000439151.2:c.7939_7940del	p.Gln2647ValfsTer35	p.Q2647Vfs*35	ENST00000439151	NM_022455.4	2646	gCA/g	23/23	1	2	FACETS	0.59	0.517	0.669	0.59	0.517	0.669	SUBCLONAL	1	TRUE	1	0.42701505626656	2		634	587	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	123	596	4	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.42701505626656	2		600	503	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129192	152129192	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	58	559	0	ENST00000206249.3:c.147del	p.Ala50ProfsTer59	p.A50Pfs*59	ENST00000206249	NM_000125.3	49	Ccc/cc	1/8	1	2	FACETS	0.464	0.398	0.535	0.464	0.398	0.535	SUBCLONAL	1	TRUE	1	0.42701505626656	2		559	586	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	117	543	1	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.42701505626656	2		544	473	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514998	148515000	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs775039041	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	103	403	2	ENST00000320356.2:c.1209_1211del	p.Glu404del	p.E404del	ENST00000320356	NM_004456.4	403	gaAGAg/gag	10/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.42701505626656	2		405	405	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738230	145738232	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CCT	CCT	-	rs755113079	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	149	651	0	ENST00000428558.2:c.2753_2755del	p.Glu918del	p.E918del	ENST00000428558	NM_004260.3	918	gAGGcc/gcc	16/22	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.42701505626656	2		651	575	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741503	145741503	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	162	667	0	ENST00000428558.2:c.1000G>T	p.Glu334Ter	p.E334*	ENST00000428558	NM_004260.3	334	Gag/Tag	5/22	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.42701505626656	2		667	552	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412095	63412095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852217	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	136	588	1	ENST00000330258.3:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000330258	NM_152424.3	358	Cga/Tga	2/2	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.42701505626656	2		589	508	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279861	46279866	+	inframe_deletion	In_Frame_Del	DEL	CAGCAA	CAGCAA	-	rs748517056	NA	P-0064125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	55	704	5	ENST00000371998.3:c.3810_3815del	p.Gln1275_Gln1276del	p.Q1275_Q1276del	ENST00000371998		1263	CAGCAA/-	20/23	1	2	FACETS	0.437	0.373	0.506	0.437	0.373	0.506	SUBCLONAL	1	TRUE	1	0.42701505626656	2		709	590	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593596	55593652	+	inframe_deletion	In_Frame_Del	DEL	AGTACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCC	AGTACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCC	-	novel	NA	P-0064129-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	61	369	0	ENST00000288135.5:c.1663_1719del	p.Val555_Pro573del	p.V555_P573del	ENST00000288135	NM_000222.2	554	gaAGTACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCCa/gaa	11/21	0.352186773597711	3	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	FALSE	1	0.352186773597711	3		369	182	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0064131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	246	441	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.371802531554161	2	FACETS	0.955	0.9	1	0.955	0.9	1	CLONAL	2	TRUE	0	0.425084155699646	2		441	606	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220693	1220693	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	113	573	0	ENST00000326873.7:c.711C>A	p.Asp237Glu	p.D237E	ENST00000326873	NM_000455.4	237	gaC/gaA	5/10	0.425084155699646	1	FACETS	0.829	0.75	0.912	0.829	0.75	0.912	CLONAL	1	TRUE	0	0.425084155699646	1		573	505	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0064132-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	106	600	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.276572811787766	2	FACETS	0.99	0.896	1	0.99	0.896	1	CLONAL	2	TRUE	0	0.288537305605285	2		600	371	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089685	27089685	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064132-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	102	599	0	ENST00000324856.7:c.2641del	p.Ser881GlnfsTer10	p.S881Qfs*10	ENST00000324856	NM_006015.4	881	Tca/ca	8/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.288537305605285	2		599	516	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068269	30068287	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTGGTTTGAGGTCACAG	TTCTGGTTTGAGGTCACAG	-	novel	NA	P-0064132-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	51	364	0	ENST00000331968.5:c.2112_2130del	p.His704GlnfsTer5	p.H704Qfs*5	ENST00000331968	NM_002742.2	704	caCTGTGACCTCAAACCAGAA/ca	15/18	1	2	FACETS	0.879	0.749	1	0.879	0.749	1	CLONAL	1	TRUE	1	0.288537305605285	2		364	402	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100046	30100046	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064132-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	66	554	0	ENST00000331968.5:c.1574G>T	p.Gly525Val	p.G525V	ENST00000331968	NM_002742.2	525	gGt/gTt	10/18	1	2	FACETS	0.945	0.822	1	0.945	0.822	1	CLONAL	1	TRUE	1	0.288537305605285	2		554	484	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458333	12458333	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064132-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	65	487	0	ENST00000287820.6:c.950C>G	p.Ser317Cys	p.S317C	ENST00000287820	NM_015869.4	317	tCc/tGc	6/7	1	2	FACETS	0.813	0.706	0.93	0.813	0.706	0.93	CLONAL	1	TRUE	1	0.288537305605285	2		487	554	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922364	178922364	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397514565	NA	P-0064132-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	29	218	0	ENST00000263967.3:c.1133G>A	p.Cys378Tyr	p.C378Y	ENST00000263967	NM_006218.2	378	tGt/tAt	6/21	1	2	FACETS	0.77	0.621	0.939	0.77	0.621	0.939	CLONAL	1	TRUE	1	0.288537305605285	2		218	261	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197788	66197788	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0064132-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	60	435	0	ENST00000273854.3:c.2911G>T	p.Gly971Cys	p.G971C	ENST00000273854	NM_004439.5	971	Ggt/Tgt	17/18	1	2	FACETS	0.849	0.732	0.975	0.849	0.732	0.975	CLONAL	1	TRUE	1	0.288537305605285	2		435	490	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460476	149460476	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs752543190	NA	P-0064132-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	53	642	0	ENST00000286301.3:c.161C>A	p.Pro54Gln	p.P54Q	ENST00000286301	NM_005211.3	54	cCa/cAa	3/22	0.280252872525537	1	FACETS	0.602	0.514	0.699	0.602	0.514	0.699	SUBCLONAL	1	TRUE	0	0.288537305605285	1		642	522	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959178	2959178	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064132-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	63	483	0	ENST00000396946.4:c.2338C>A	p.Leu780Met	p.L780M	ENST00000396946	NM_032415.4	780	Ctg/Atg	18/25	1	2	FACETS	0.975	0.845	1	0.975	0.845	1	CLONAL	1	TRUE	1	0.288537305605285	2		483	448	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245084	53245084	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064132-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	72	556	0	ENST00000375401.3:c.856A>T	p.Thr286Ser	p.T286S	ENST00000375401	NM_004187.3	286	Aca/Tca	7/26	1	2	FACETS	0.977	0.855	1	0.977	0.855	1	CLONAL	1	TRUE	1	0.288537305605285	2		556	511	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412473	63412473	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064132-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	66	621	0	ENST00000330258.3:c.694C>T	p.Gln232Ter	p.Q232*	ENST00000330258	NM_152424.3	232	Caa/Taa	2/2	1	2	FACETS	0.945	0.822	1	0.945	0.822	1	CLONAL	1	TRUE	1	0.288537305605285	2		621	484	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	316	515	0				ENST00000310581	NM_198253.2	-/1132			0.180566308329731	5	FACETS	0.972	0.924	1	1	0.993	1	INDETERMINATE	4	TRUE	2	0.354755848556034	5		515	702	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	144	372	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.354755848556034	1	FACETS	1	0.945	1	1	0.992	1	CLONAL	2	TRUE	0	0.354755848556034	1		372	326	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	84	583	1				ENST00000310581	NM_198253.2	-/1132			0.180566308329731	5	FACETS	1	0.942	1	0.369	0.326	0.416	INDETERMINATE	1	TRUE	2	0.354755848556034	5		584	655	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678455	88678455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	104	617	0	ENST00000360948.2:c.1081G>A	p.Gly361Ser	p.G361S	ENST00000360948	NM_001012338.2	361	Ggc/Agc	9/19	1	2	FACETS	0.923	0.828	1	0.923	0.828	1	CLONAL	1	TRUE	1	0.354755848556034	2		617	635	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274554	198274554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	131	534	0	ENST00000335508.6:c.844G>A	p.Gly282Arg	p.G282R	ENST00000335508	NM_012433.2	282	Gga/Aga	7/25	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.354755848556034	2		534	730	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658412	117658412	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	59	576	0	ENST00000368508.3:c.5171C>T	p.Ser1724Leu	p.S1724L	ENST00000368508	NM_002944.2	1724	tCa/tTa	31/43	0.354755848556034	1	FACETS	0.874	0.757	1	0.874	0.757	1	CLONAL	1	TRUE	0	0.354755848556034	1		576	313	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521384	8521384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777779009	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	186	509	0	ENST00000356435.5:c.854G>A	p.Gly285Glu	p.G285E	ENST00000356435		285	gGa/gAa	9/35	0.354755848556034	0	FACETS	0.692	0.652	0.731			1	SUBCLONAL	3	TRUE	0	0.354755848556034	0		509	326	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952292	17952292	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	94	592	0	ENST00000458235.1:c.1048C>T	p.Arg350Trp	p.R350W	ENST00000458235	NM_000215.3	350	Cgg/Tgg	8/24	0.354755848556034	1	FACETS	0.954	0.853	1	0.954	0.853	1	CLONAL	1	TRUE	0	0.354755848556034	1		592	457	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061148	38061148	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1300427032	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	114	691	0	ENST00000250448.2:c.841G>A	p.Gly281Arg	p.G281R	ENST00000250448	NM_004496.3	281	Gga/Aga	2/2	0.354755848556034	1	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	0	0.354755848556034	1		691	522	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804407	46804407	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	155	516	0	ENST00000290295.7:c.602-2A>C		p.X201_splice	ENST00000290295	NM_006361.5	201			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.354755848556034	2		516	664	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55960990	55960990	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	86	412	0	ENST00000263923.4:c.2950A>T	p.Ser984Cys	p.S984C	ENST00000263923	NM_002253.2	984	Agt/Tgt	21/30	1	2	FACETS	0.954	0.847	1	0.954	0.847	1	CLONAL	1	TRUE	1	0.354755848556034	2		412	508	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674236	117674236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	89	519	0	ENST00000368508.3:c.4238G>A	p.Gly1413Glu	p.G1413E	ENST00000368508	NM_002944.2	1413	gGa/gAa	26/43	0.354755848556034	1	FACETS	0.869	0.774	0.97	0.869	0.774	0.97	CLONAL	1	TRUE	0	0.354755848556034	1		519	475	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098623	2098623	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	127	499	0	ENST00000219476.3:c.7A>G	p.Lys3Glu	p.K3E	ENST00000219476	NM_000548.3	3	Aaa/Gaa	2/42	1	2	FACETS	0.975	0.885	1	0.975	0.885	1	CLONAL	1	TRUE	1	0.354755848556034	2		499	734	SUCCESS
BTK	695	MSKCC	GRCh37	X	100604935	100604935	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	64	365	0	ENST00000308731.7:c.1918G>T	p.Glu640Ter	p.E640*	ENST00000308731	NM_000061.2	640	Gag/Tag	19/19	0.354755848556034	1	FACETS	0.865	0.754	0.985	0.865	0.754	0.985	CLONAL	1	TRUE	0	0.354755848556034	1		365	343	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915661	112915661	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	85	476	0	ENST00000351677.2:c.934C>T	p.Pro312Ser	p.P312S	ENST00000351677	NM_002834.3	312	Cct/Tct	9/16	1	2	FACETS	0.927	0.822	1	0.927	0.822	1	CLONAL	1	TRUE	1	0.354755848556034	2		476	517	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609798	117609798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	93	507	0	ENST00000368508.3:c.6901G>A	p.Gly2301Ser	p.G2301S	ENST00000368508	NM_002944.2	2301	Ggt/Agt	43/43	0.354755848556034	1	FACETS	0.851	0.759	0.948	0.851	0.759	0.948	CLONAL	1	TRUE	0	0.354755848556034	1		507	507	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069607	69069607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	48	333	0	ENST00000288368.4:c.4282G>A	p.Glu1428Lys	p.E1428K	ENST00000288368	NM_024870.2	1428	Gaa/Aaa	35/40	0.354755848556034	3	FACETS	0.94	0.798	1	0.47	0.399	0.548	CLONAL	1	TRUE	1	0.354755848556034	3		333	339	SUCCESS
BTK	695	MSKCC	GRCh37	X	100612502	100612502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	35	472	0	ENST00000308731.7:c.1172G>A	p.Gly391Glu	p.G391E	ENST00000308731	NM_000061.2	391	gGa/gAa	13/19	0.354755848556034	1	FACETS	0.337	0.276	0.406	0.337	0.276	0.406	SUBCLONAL	1	TRUE	0	0.354755848556034	1		472	481	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343409	118343409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	388	591	0	ENST00000534358.1:c.1535C>T	p.Pro512Leu	p.P512L	ENST00000534358	NM_005933.3	512	cCa/cTa	3/36	0.354755848556034	3	FACETS	0.976	0.932	1	1	0.996	1	CLONAL	3	TRUE	1	0.354755848556034	3		591	880	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434009	49434010	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	229	736	0	ENST00000301067.7:c.7543_7544delinsTT	p.Pro2515Phe	p.P2515F	ENST00000301067	NM_003482.3	2515	CCc/TTc	31/54	1	2	FACETS	0.881	0.824	0.939	1	0.994	1	CLONAL	2	TRUE	1	0.354755848556034	2		736	733	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445773	49445773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	207	883	0	ENST00000301067.7:c.1693C>T	p.Pro565Ser	p.P565S	ENST00000301067	NM_003482.3	565	Ccg/Tcg	10/54	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.354755848556034	2		883	1107	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912283	32912283	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	59	414	0	ENST00000380152.3:c.3791A>G	p.Lys1264Arg	p.K1264R	ENST00000380152		1264	aAa/aGa	11/27	1	2	FACETS	0.934	0.808	1	0.934	0.808	1	CLONAL	1	TRUE	1	0.354755848556034	2		414	356	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73649890	73649890	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	93	495	0	ENST00000377687.4:c.1240T>G	p.Phe414Val	p.F414V	ENST00000377687	NM_001730.3	414	Ttc/Gtc	4/4	1	2	FACETS	0.902	0.804	1	0.902	0.804	1	CLONAL	1	TRUE	1	0.354755848556034	2		495	581	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	364655	364655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	207	509	0	ENST00000262320.3:c.907C>T	p.Pro303Ser	p.P303S	ENST00000262320	NM_003502.3	303	Ccc/Tcc	3/11	1	2	FACETS	0.992	0.927	1	1	0.994	1	CLONAL	2	TRUE	1	0.354755848556034	2		509	588	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61306495	61306495	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	163	448	0	ENST00000341074.5:c.692T>A	p.Val231Asp	p.V231D	ENST00000341074	NM_002974.2	231	gTc/gAc	7/8	1	2	FACETS	1	0.96	1	1	0.993	1	CLONAL	2	TRUE	1	0.354755848556034	2		448	436	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110574	4110574	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs267607230	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	144	648	0	ENST00000262948.5:c.383C>G	p.Pro128Arg	p.P128R	ENST00000262948	NM_030662.3	128	cCg/cGg	3/11	0.354755848556034	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.354755848556034	1		648	650	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265078	5265078	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	138	656	0	ENST00000357368.4:c.509A>C	p.Lys170Thr	p.K170T	ENST00000357368	NM_002850.3	170	aAg/aCg	5/38	0.354755848556034	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.354755848556034	1		656	606	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101825	11101825	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	122	526	0	ENST00000358026.2:c.1246-1G>A		p.X416_splice	ENST00000358026	NM_001128849.1	416			0.354755848556034	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.354755848556034	1		526	473	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798765	42798765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	210	516	0	ENST00000575354.2:c.4337C>T	p.Ala1446Val	p.A1446V	ENST00000575354	NM_015125.3	1446	gCc/gTc	19/20	1	2	FACETS	1	0.961	1	1	0.994	1	CLONAL	2	TRUE	1	0.354755848556034	2		516	570	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268704	46268704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	137	640	0	ENST00000371998.3:c.2989C>T	p.Pro997Ser	p.P997S	ENST00000371998		997	Ccc/Tcc	16/23	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.354755848556034	2		640	770	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63967873	63967873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	132	441	0	ENST00000398590.3:c.764C>T	p.Ser255Phe	p.S255F	ENST00000398590	NM_001177387.1	255	tCt/tTt	7/14	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.354755848556034	2		441	614	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532879	187532879	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	90	462	0	ENST00000441802.2:c.9514T>C	p.Phe3172Leu	p.F3172L	ENST00000441802	NM_005245.3	3172	Ttc/Ctc	14/27	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.354755848556034	2		462	453	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1296236	1296236	+	upstream_gene_variant	5'Flank	SNP	T	T	C	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	344	649	0				ENST00000310581	NM_198253.2	-/1132			0.180566308329731	5	FACETS	1	0.98	1	1	0.98	1	INDETERMINATE	3	TRUE	2	0.354755848556034	5		649	932	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149450078	149450078	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	110	605	0	ENST00000286301.3:c.1139C>T	p.Ser380Phe	p.S380F	ENST00000286301	NM_005211.3	380	tCc/tTc	8/22	0.354755848556034	1	FACETS	0.943	0.85	1	0.943	0.85	1	CLONAL	1	TRUE	0	0.354755848556034	1		605	541	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637787	176637787	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	120	582	0	ENST00000439151.2:c.2387A>T	p.Glu796Val	p.E796V	ENST00000439151	NM_022455.4	796	gAa/gTa	5/23	0.354755848556034	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.354755848556034	1		582	524	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178599	32178599	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs766572091	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	268	616	0	ENST00000375023.3:c.2795A>G	p.Asn932Ser	p.N932S	ENST00000375023	NM_004557.3	932	aAc/aGc	18/30	1	2	FACETS	1	0.976	1	1	0.995	1	CLONAL	2	TRUE	1	0.354755848556034	2		616	710	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382254	152382254	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	71	373	0	ENST00000206249.3:c.1364A>T	p.Asn455Ile	p.N455I	ENST00000206249	NM_000125.3	455	aAt/aTt	6/8	1	2	FACETS	0.949	0.831	1	0.949	0.831	1	CLONAL	1	TRUE	1	0.354755848556034	2		373	422	SUCCESS
MET	4233	MSKCC	GRCh37	7	116417504	116417504	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	49	352	0	ENST00000397752.3:c.3321T>G	p.Cys1107Trp	p.C1107W	ENST00000397752	NM_000245.2	1107	tgT/tgG	16/21	0.354755848556034	1	FACETS	0.82	0.7	0.951	0.82	0.7	0.951	CLONAL	1	TRUE	0	0.354755848556034	1		352	277	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981596	70981596	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775250906	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	148	717	0	ENST00000276594.2:c.500C>T	p.Ser167Phe	p.S167F	ENST00000276594	NM_024504.3	167	tCc/tTc	2/8	0.354755848556034	3	FACETS	1	0.974	1	0.583	0.533	0.636	CLONAL	1	TRUE	1	0.354755848556034	3		717	842	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2039774	2039774	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	163	740	0	ENST00000349721.2:c.664C>T	p.Gln222Ter	p.Q222*	ENST00000349721	NM_003070.3	222	Caa/Taa	4/34	0.354755848556034	0	FACETS	1	0.96	1			1	CLONAL	1	TRUE	0	0.354755848556034	0		740	559	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759625	133759625	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	126	714	0	ENST00000318560.5:c.1948C>T	p.Pro650Ser	p.P650S	ENST00000318560	NM_005157.4	650	Ccc/Tcc	11/11	0.354755848556034	1	FACETS	0.979	0.889	1	0.979	0.889	1	CLONAL	1	TRUE	0	0.354755848556034	1		714	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579344	7579345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0064142-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	139	575	0	ENST00000269305.4:c.342dup	p.His115AlafsTer34	p.H115Afs*34	ENST00000269305	NM_001126112.2	114	-/G	4/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		575	548	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725059	89725059	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0064142-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	75	201	0	ENST00000371953.3:c.1042A>C	p.Thr348Pro	p.T348P	ENST00000371953	NM_000314.4	348	Aca/Cca	9/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		201	266	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244095	46244095	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064142-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	130	502	0	ENST00000334344.6:c.2189T>C	p.Val730Ala	p.V730A	ENST00000334344	NM_152641.2	730	gTt/gCt	15/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		502	708	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248998	55248999	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCAGCG	rs727504263	NA	P-0064143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	49	530	0	ENST00000275493.2:c.2300_2308dup	p.Ala767_Val769dup	p.A767_V769dup	ENST00000275493	NM_005228.3	767	atg/aTGGCCAGCGtg	20/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		530	301	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0064153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	80	210	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.650954513038693	3	FACETS	1	0.934	1	0.536	0.476	0.598	CLONAL	1	TRUE	1	0.650954513038693	3		210	304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0064153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	126	427	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	0.650954513038693	1	FACETS	0.967	0.893	1	0.967	0.893	1	CLONAL	1	TRUE	0	0.650954513038693	1		427	270	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857311	68857312	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0064153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	93	312	0	ENST00000261769.5:c.1947dup	p.Ile650TyrfsTer13	p.I650Yfs*13	ENST00000261769	NM_004360.3	649	tct/tcTt	13/16	0.650954513038693	1	FACETS	0.949	0.864	1	0.949	0.864	1	CLONAL	1	TRUE	0	0.650954513038693	1		312	203	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247516	123247516	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519795	NA	P-0064153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	97	315	0	ENST00000358487.5:c.1975A>G	p.Lys659Glu	p.K659E	ENST00000358487	NM_000141.4	659	Aag/Gag	14/18	0.650954513038693	3	FACETS	0.772	0.69	0.857	0.386	0.345	0.429	SUBCLONAL	1	TRUE	1	0.650954513038693	3		315	512	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256215	123256215	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121918506	NA	P-0064153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	45	446	0	ENST00000358487.5:c.1694A>C	p.Glu565Ala	p.E565A	ENST00000358487	NM_000141.4	565	gAg/gCg	13/18	0.650954513038693	3	FACETS	0.299	0.251	0.353	0.15	0.125	0.177	SUBCLONAL	1	TRUE	1	0.650954513038693	3		446	612	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150902552	150902552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	47	361	0	ENST00000271640.5:c.370G>A	p.Glu124Lys	p.E124K	ENST00000271640	NM_001145415.1	124	Gag/Aag	3/22	0.537089033255536	4	FACETS	0.361	0.304	0.424	0.18	0.151	0.212	SUBCLONAL	1	TRUE	2	0.650954513038693	4		361	661	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47599342	47599344	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0064153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	293	457	0	ENST00000430070.2:c.256_258del	p.Phe86del	p.F86del	ENST00000430070	NM_018095.4	86	TTC/-	2/4	0.59950755199491	4	FACETS	0.897	0.848	0.948	0.897	0.848	0.948	CLONAL	2	TRUE	2	0.650954513038693	4		457	828	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114235	115114285	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTCATCAAACACCCTCATGGACTGCAGGGTGAGCTGTTTTCTGTGGCAGA	TTTCATCAAACACCCTCATGGACTGCAGGGTGAGCTGTTTTCTGTGGCAGA	-	novel	NA	P-0064153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	242	372	0	ENST00000257566.3:c.942-10_982del		p.X314_splice	ENST00000257566	NM_016569.3	314		6/8	0.650954513038693	2	FACETS	0.994	0.948	1	0.994	0.948	1	CLONAL	2	TRUE	0	0.650954513038693	2		372	374	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544591	86544591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs672601295	NA	P-0064153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	117	587	0	ENST00000262426.4:c.416G>A	p.Arg139Gln	p.R139Q	ENST00000262426	NM_001451.2	139	cGg/cAg	1/2	0.650954513038693	1	FACETS	0.567	0.515	0.621	0.567	0.515	0.621	SUBCLONAL	1	TRUE	0	0.650954513038693	1		587	428	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512065	148512065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	42	404	0	ENST00000320356.2:c.1613C>T	p.Ser538Leu	p.S538L	ENST00000320356	NM_004456.4	538	tCg/tTg	14/20	0.59950755199491	4	FACETS	0.314	0.261	0.373	0.157	0.13	0.187	SUBCLONAL	1	TRUE	2	0.650954513038693	4		404	679	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0064155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	102	454	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.230928096709877	2	FACETS	0.94	0.845	1	0.94	0.845	1	CLONAL	2	TRUE	0	0.236532366601798	2		454	459	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0064155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	94	549	0				ENST00000310581	NM_198253.2	-/1132			0.236532366601798	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.236532366601798	3		549	369	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796966	57796966	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs569722591	NA	P-0064155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	74	665	0	ENST00000309042.7:c.1942C>T	p.Pro648Ser	p.P648S	ENST00000309042	NM_005612.4	648	Cct/Tct	4/4	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.236532366601798	2		665	591	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0064156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	303	405	0	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	0.707985236427488	4	FACETS	0.987	0.935	1	0.987	0.935	1	CLONAL	2	TRUE	2	0.726226380611753	4		405	730	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0064156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	359	416	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.136210732489073	3	FACETS	0.985	0.956	1			1	INDETERMINATE	3	TRUE	NA	0.726226380611753	3		416	456	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311640	30311640	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4382	506	284	0	ENST00000262643.3:c.494C>T	p.Thr165Ile	p.T165I	ENST00000262643	NM_001238.2	165	aCc/aTc	7/12	0.726226380611753	27	FACETS	0.958	0.91	1			1	CLONAL	3	TRUE	NA	0.726226380611753	27		284	4888	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55219035	55219035	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	169	484	0	ENST00000275493.2:c.608G>A	p.Gly203Glu	p.G203E	ENST00000275493	NM_005228.3	203	gGa/gAa	5/28	0.728300200695224	3	FACETS	0.944	0.871	1	0.472	0.435	0.51	CLONAL	1	TRUE	1	0.726226380611753	3		484	672	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045682	47045682	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	162	634	0	ENST00000377604.3:c.2563G>C	p.Gly855Arg	p.G855R	ENST00000377604	NM_001204468.1	855	Ggg/Cgg	23/24	0.449706882152352	3	FACETS	0.842	0.775	0.913	0.281	0.258	0.305	CLONAL	1	TRUE	0	0.726226380611753	3		634	722	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61713087	61713087	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0064157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	57	344	0	ENST00000401558.2:c.2324del	p.Asn775IlefsTer32	p.N775Ifs*32	ENST00000401558	NM_003400.3	775	aAt/at	20/25	1	2	FACETS	0.953	0.82	1	0.953	0.82	1	CLONAL	1	TRUE	1	0.27	2		344	443	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538866	23538867	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0064157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	82	507	0	ENST00000380871.4:c.572dup	p.Leu191PhefsTer25	p.L191Ffs*25	ENST00000380871	NM_006167.3	191	ttg/ttTg	2/2	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.27	2		507	469	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	59	523	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.889	1	1	0.984	1	CLONAL	3	TRUE	1	0.155598704950729	2		523	247	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0064160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	15	187	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.155598704950729	3	FACETS	0.855	0.626	1	0.428	0.313	0.566	CLONAL	1	TRUE	1	0.155598704950729	3		187	243	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405971	49405971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	210	342	0	ENST00000418115.1:c.167C>T	p.Ala56Val	p.A56V	ENST00000418115	NM_001664.2	56	gCt/gTt	3/5	0.155598704950729	3	FACETS	0.974	0.913	1	1	0.995	1	CLONAL	6	TRUE	1	0.155598704950729	3		342	498	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105872	27105872	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0064160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	135	478	0	ENST00000324856.7:c.5483C>G	p.Ser1828Ter	p.S1828*	ENST00000324856	NM_006015.4	1828	tCa/tGa	20/20	1	2	FACETS	0.925	0.847	1	1	0.993	1	CLONAL	4	TRUE	1	0.155598704950729	2		478	469	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43699633	43699633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763713800	NA	P-0064160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	20	410	0	ENST00000382044.4:c.5882G>A	p.Arg1961Lys	p.R1961K	ENST00000382044	NM_001141980.1	1961	aGa/aAa	28/28	0.155598704950729	1	FACETS	0.672	0.513	0.858	0.672	0.513	0.858	SUBCLONAL	1	TRUE	0	0.155598704950729	1		410	353	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0064160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	18	272	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.851	0.641	1	0.851	0.641	1	CLONAL	1	TRUE	1	0.155598704950729	2		272	272	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416811	416811	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0064160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	130	441	1	ENST00000399788.2:c.3739C>T	p.Gln1247Ter	p.Q1247*	ENST00000399788	NM_001042603.1	1247	Cag/Tag	23/28	1	2	FACETS	1	0.967	1	1	0.993	1	CLONAL	3	TRUE	1	0.155598704950729	2		442	497	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445167	49445188	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCAGCCTGCGGAGATAGGTG	CCTCAGCCTGCGGAGATAGGTG	-	novel	NA	P-0064160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	51	604	0	ENST00000301067.7:c.2278_2299del	p.His760SerfsTer163	p.H760Sfs*163	ENST00000301067	NM_003482.3	760	CACCTATCTCCGCAGGCTGAGGag/ag	10/54	0.155598704950729	2	FACETS	1	0.924	1	0.573	0.487	0.668	CLONAL	1	TRUE	0	0.155598704950729	2		604	572	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133889	41133889	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	134	427	0	ENST00000379561.5:c.1739C>A	p.Ser580Tyr	p.S580Y	ENST00000379561	NM_002015.3	580	tCc/tAc	2/3	1	2	FACETS	1	0.971	1	1	0.993	1	CLONAL	3	TRUE	1	0.155598704950729	2		427	503	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436271	110436272	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCCCCGCA	rs1305776458	NA	P-0064160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	50	563	0	ENST00000375856.3:c.2121_2129dup	p.Gly709_Ala711dup	p.G709_A711dup	ENST00000375856	NM_003749.2	709	cca/ccTGCGGGGCCa	1/2	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.155598704950729	2		563	468	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423085	47423085	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	116	409	0	ENST00000404338.3:c.1153G>T	p.Glu385Ter	p.E385*	ENST00000404338	NM_004491.4	385	Gag/Tag	1/6	1	2	FACETS	1	0.921	1	1	0.991	1	CLONAL	3	TRUE	1	0.155598704950729	2		409	488	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423967	47423967	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	123	414	0	ENST00000404338.3:c.2035G>C	p.Glu679Gln	p.E679Q	ENST00000404338	NM_004491.4	679	Gag/Cag	1/6	1	2	FACETS	1	0.966	1	1	0.992	1	CLONAL	3	TRUE	1	0.155598704950729	2		414	467	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521477	8521477	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1470492346	NA	P-0064160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	129	386	0	ENST00000356435.5:c.761A>G	p.Asn254Ser	p.N254S	ENST00000356435		254	aAt/aGt	9/35	1	2	FACETS	0.878	0.802	0.958	1	0.993	1	CLONAL	4	TRUE	1	0.155598704950729	2		386	472	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0064194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	91	393	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.663548010797058	3	FACETS	1	0.956	1	0.562	0.504	0.623	CLONAL	1	TRUE	1	0.663548010797058	3		394	325	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0064194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	164	312	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.663548010797058	2		312	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0064194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	331	683	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.663548010797058	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.663548010797058	1		683	647	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0064194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	266	563	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	0.927	0.871	0.984	0.927	0.871	0.984	CLONAL	1	TRUE	1	0.663548010797058	2		563	865	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0064194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	266	654	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.663548010797058	2		654	750	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022592	31022592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs373221034	NA	P-0064194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	220	597	0	ENST00000375687.4:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000375687	NM_015338.5	693	Cga/Tga	13/13	1	2	FACETS	0.884	0.825	0.944	0.884	0.825	0.944	CLONAL	1	TRUE	1	0.663548010797058	2		597	750	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120818	115120818	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	247	629	0	ENST00000257566.3:c.188C>T	p.Pro63Leu	p.P63L	ENST00000257566	NM_016569.3	63	cCg/cTg	1/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.663548010797058	2		629	712	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579349	7579349	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1567555667	NA	P-0064197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	221	500	0	ENST00000269305.4:c.338T>G	p.Phe113Cys	p.F113C	ENST00000269305	NM_001126112.2	113	tTc/tGc	4/11	0.488286748177314	2	FACETS	0.944	0.889	0.999	0.944	0.889	0.999	CLONAL	2	FALSE	0	0.492752000003719	2		500	475	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031883	26031884	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs758780418	NA	P-0064197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	213	661	0	ENST00000244661.2:c.405_406del	p.Arg135SerfsTer12	p.R135Sfs*12	ENST00000244661	NM_003537.3	135	agAGcg/agcg	1/1	0.492615725218169	4	FACETS	0.96	0.896	1	0.96	0.896	1	CLONAL	2	FALSE	2	0.492752000003719	4		661	672	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21346027	21346027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139823732	NA	P-0064197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	212	582	0	ENST00000215739.8:c.902G>A	p.Gly301Asp	p.G301D	ENST00000215739	NM_006767.3	301	gGt/gAt	9/21	0.492615725218169	3	FACETS	0.956	0.895	1	0.956	0.895	1	CLONAL	2	FALSE	1	0.492752000003719	3		582	561	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437168	110437212	+	inframe_deletion	In_Frame_Del	DEL	GCCGCCGCAGCCGCCGCTCAGGGTGTGCGAGCGGCTCAGGGGCGC	GCCGCCGCAGCCGCCGCTCAGGGTGTGCGAGCGGCTCAGGGGCGC	-	novel	NA	P-0064197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	50	285	0	ENST00000375856.3:c.1189_1233del	p.Ala397_Gly411del	p.A397_G411del	ENST00000375856	NM_003749.2	397	GCGCCCCTGAGCCGCTCGCACACCCTGAGCGGCGGCTGCGGCGGC/-	1/2	0.492615725218169	3	FACETS	0.884	0.756	1	0.442	0.378	0.512	CLONAL	1	FALSE	1	0.492752000003719	3		285	286	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56872976	56872976	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0064197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	136	272	0	ENST00000308159.5:c.2131T>A	p.Phe711Ile	p.F711I	ENST00000308159	NM_014669.4	711	Ttt/Att	19/22	0.488286748177314	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	FALSE	0	0.492752000003719	2		272	276	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775415	39775434	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGGGGAGCTTACTCTCTCT	AGGGGGAGCTTACTCTCTCT	TAGTG	novel	NA	P-0064197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	92	505	1	ENST00000288319.7:c.586_592+13delinsCACTA		p.X196_splice	ENST00000288319	NM_182918.3	196		4/10	0.492615725218169	2	FACETS	0.924	0.827	1	0.462	0.413	0.514	CLONAL	1	FALSE	0	0.492752000003719	2		506	404	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0064198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	103	372	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.588864014145348	2		372	259	SUCCESS
APC	324	MSKCC	GRCh37	5	112175153	112175153	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0064198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	46	650	1	ENST00000257430.4:c.3862G>T	p.Gly1288Ter	p.G1288*	ENST00000257430	NM_000038.5	1288	Gga/Tga	16/16	1	2	FACETS	0.858	0.734	0.992	0.858	0.734	0.992	CLONAL	1	TRUE	1	0.588864014145348	2		651	182	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0064198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	44	203	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.588864014145348	2		203	137	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0064198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	114	681	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.571803178407708	1	FACETS	0.99	0.906	1	0.99	0.906	1	CLONAL	1	TRUE	0	0.588864014145348	1		682	276	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861870	57861870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764631331	NA	P-0064198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	106	628	0	ENST00000228682.2:c.1171G>A	p.Ala391Thr	p.A391T	ENST00000228682	NM_005269.2	391	Gcc/Acc	10/12	1	2	FACETS	0.868	0.783	0.955	0.868	0.783	0.955	CLONAL	1	TRUE	1	0.588864014145348	2		628	415	SUCCESS
APC	324	MSKCC	GRCh37	5	112175938	112175941	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	novel	NA	P-0064198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	60	524	0	ENST00000257430.4:c.4648_4651del	p.Glu1550LysfsTer14	p.E1550Kfs*14	ENST00000257430	NM_000038.5	1549	caAGAG/ca	16/16	1	2	FACETS	0.796	0.693	0.906	0.796	0.693	0.906	CLONAL	1	TRUE	1	0.588864014145348	2		524	256	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	181	331	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.198182588819993	5	FACETS	0.911	0.85	0.974	0.911	0.85	0.974	INDETERMINATE	3	TRUE	2	0.537403114021905	5		331	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0064199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	347	675	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.537403114021905	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.537403114021905	2		675	585	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971066	21971103	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGCACCACCAGCGTGTCCAGGAAGCCCTCCCGGGCA	GCAGCACCACCAGCGTGTCCAGGAAGCCCTCCCGGGCA	-	novel	NA	P-0064199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	223	563	0	ENST00000304494.5:c.255_292del	p.Ala86ProfsTer21	p.A86Pfs*21	ENST00000304494	NM_000077.4	85	gcTGCCCGGGAGGGCTTCCTGGACACGCTGGTGGTGCTGCac/gcac	2/3	0.537403114021905	2	FACETS	0.976	0.923	1	0.976	0.923	1	CLONAL	2	TRUE	0	0.537403114021905	2		563	425	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0064222-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	64	523	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.51	2		523	249	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0064222-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	108	405	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.901	0.813	0.993	0.901	0.813	0.993	CLONAL	1	TRUE	1	0.51	2		405	470	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148726	20148726	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0064222-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	35	215	0	ENST00000379607.5:c.338-1G>T		p.X113_splice	ENST00000379607	NM_001412.3	113			1	2	FACETS	0.758	0.629	0.9	0.758	0.629	0.9	SUBCLONAL	1	TRUE	1	0.51	2		215	181	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0064282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	435	406	1	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.350096445702979	5	FACETS	0.952	0.915	0.989			1	CLONAL	5	TRUE	NA	0.350096445702979	5		407	796	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197716	123197716	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	46	165	0	ENST00000218089.9:c.1840C>T	p.Arg614Ter	p.R614*	ENST00000218089	NM_001042749.1	614	Cga/Tga	20/35	0.332858451196888	1	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	0	0.350096445702979	1		165	203	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163853	47163853	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0064282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	92	245	0	ENST00000409792.3:c.2273A>G	p.Asp758Gly	p.D758G	ENST00000409792	NM_014159.6	758	gAt/gGt	3/21	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.350096445702979	2		245	479	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751565	57751565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	47	324	0	ENST00000274289.3:c.1426G>A	p.Ala476Thr	p.A476T	ENST00000274289	NM_006622.3	476	Gca/Aca	11/14	0.266582869872041	2	FACETS	0.461	0.388	0.541	0.23	0.194	0.271	SUBCLONAL	1	TRUE	0	0.350096445702979	2		324	583	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651103	206651103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	119	755	0	ENST00000367120.3:c.713C>T	p.Thr238Ile	p.T238I	ENST00000367120	NM_014002.3	238	aCc/aTc	8/22	0.184837380677792	2	FACETS	1	0.933	1	0.52	0.47	0.572	INDETERMINATE	1	TRUE	0	0.350096445702979	2		755	654	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796297	42796297	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	57	678	0	ENST00000575354.2:c.2946C>G	p.Ser982Arg	p.S982R	ENST00000575354	NM_015125.3	982	agC/agG	12/20	0.132130869576858	3	FACETS	0.457	0.391	0.53	0.229	0.195	0.265	INDETERMINATE	1	TRUE	1	0.350096445702979	3		678	837	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67632404	67632404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1676184787	NA	P-0064282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	13	160	0	ENST00000272342.5:c.2590G>A	p.Glu864Lys	p.E864K	ENST00000272342	NM_019002.3	864	Gag/Aag	5/6	1	2	FACETS	0.326	0.232	0.44	0.326	0.232	0.44	SUBCLONAL	1	TRUE	1	0.350096445702979	2		160	228	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584567	189584571	+	frameshift_variant	Frame_Shift_Del	DEL	TACCT	TACCT	-	novel	NA	P-0064282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	110	285	0	ENST00000264731.3:c.865_869del	p.Pro289Ter	p.P289*	ENST00000264731	NM_003722.4	288	gTACCT/g	6/14	0.350096445702979	3	FACETS	1	0.972	1	0.61	0.549	0.674	CLONAL	1	TRUE	1	0.350096445702979	3		285	605	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243532	46243533	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATGT	novel	NA	P-0064285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	20	294	0	ENST00000334344.6:c.1888_1891dup	p.Ser631CysfsTer77	p.S631Cfs*77	ENST00000334344	NM_152641.2	629	gat/gATGTat	14/21	1	2	FACETS	0.424	0.324	0.541	0.424	0.324	0.541	SUBCLONAL	1	TRUE	1	0.287718898874558	2		294	328	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285807	46285807	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0064319-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	30	814	0	ENST00000334344.6:c.5075C>G	p.Ser1692Ter	p.S1692*	ENST00000334344	NM_152641.2	1692	tCa/tGa	18/21	1	2	FACETS	0.46	0.372	0.558	0.46	0.372	0.558	SUBCLONAL	1	FALSE	1	0.543751013440453	2		814	240	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056181	27056181	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0064319-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	115	455	0	ENST00000324856.7:c.1177C>T	p.Gln393Ter	p.Q393*	ENST00000324856	NM_006015.4	393	Cag/Tag	2/20	1	2	FACETS	0.583	0.526	0.644	0.583	0.526	0.644	SUBCLONAL	1	FALSE	1	0.543751013440453	2		455	725	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	364577	364577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754764999	NA	P-0064319-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	175	1139	2	ENST00000262320.3:c.985G>A	p.Asp329Asn	p.D329N	ENST00000262320	NM_003502.3	329	Gat/Aat	3/11	1	2	FACETS	0.567	0.521	0.615	0.567	0.521	0.615	SUBCLONAL	1	FALSE	1	0.543751013440453	2		1141	1135	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439357	149439357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0064319-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	47	1152	0	ENST00000286301.3:c.2038G>A	p.Glu680Lys	p.E680K	ENST00000286301	NM_005211.3	680	Gag/Aag	15/22	1	2	FACETS	0.191	0.16	0.225	0.191	0.16	0.225	SUBCLONAL	1	FALSE	1	0.543751013440453	2		1152	907	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439405	149439405	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0064319-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	48	1016	0	ENST00000286301.3:c.1990G>C	p.Glu664Gln	p.E664Q	ENST00000286301	NM_005211.3	664	Gag/Cag	15/22	1	2	FACETS	0.223	0.187	0.262	0.223	0.187	0.262	SUBCLONAL	1	FALSE	1	0.543751013440453	2		1016	793	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936168	71936168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064319-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	193	1029	0	ENST00000298229.2:c.140G>A	p.Arg47Gln	p.R47Q	ENST00000298229	NM_001567.3	47	cGa/cAa	1/28	0.421591208389519	1	FACETS	0.596	0.552	0.642	0.596	0.552	0.642	SUBCLONAL	1	FALSE	0	0.543751013440453	1		1029	867	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913430	28913430	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064319-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	19	588	0	ENST00000282397.4:c.2363C>G	p.Ser788Cys	p.S788C	ENST00000282397	NM_002019.4	788	tCt/tGt	17/30	0.543751013440453	1	FACETS	0.578	0.448	0.725	0.578	0.448	0.725	SUBCLONAL	1	FALSE	0	0.543751013440453	1		588	88	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640028	3640028	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064319-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	39	1062	1	ENST00000294008.3:c.3611C>A	p.Ser1204Tyr	p.S1204Y	ENST00000294008	NM_032444.2	1204	tCc/tAc	12/15	1	2	FACETS	0.207	0.171	0.248	0.207	0.171	0.248	SUBCLONAL	1	FALSE	1	0.543751013440453	2		1063	693	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585383	29585383	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691072	NA	P-0064319-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	17	803	0	ENST00000356175.3:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000356175	NM_000267.3	1378	Cag/Tag	31/57	0.521448941121574	1	FACETS	0.364	0.274	0.468	0.364	0.274	0.468	SUBCLONAL	1	FALSE	0	0.543751013440453	1		803	125	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21345936	21345936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064319-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	242	1231	0	ENST00000215739.8:c.811G>A	p.Glu271Lys	p.E271K	ENST00000215739	NM_006767.3	271	Gaa/Aaa	9/21	1	2	FACETS	0.936	0.875	0.999	0.936	0.875	0.999	CLONAL	1	FALSE	1	0.543751013440453	2		1231	951	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245376	153245376	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0064319-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	24	568	0	ENST00000281708.4:c.1815C>G	p.Ile605Met	p.I605M	ENST00000281708	NM_033632.3	605	atC/atG	11/12	0.543751013440453	1	FACETS	0.73	0.587	0.886	0.73	0.587	0.886	SUBCLONAL	1	FALSE	0	0.543751013440453	1		568	88	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526898	31526898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0064319-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	121	898	0	ENST00000344624.3:c.142C>T	p.Pro48Ser	p.P48S	ENST00000344624		48	Cct/Tct	2/33	1	2	FACETS	0.676	0.612	0.744	0.676	0.612	0.744	SUBCLONAL	1	FALSE	1	0.543751013440453	2		898	658	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045880	180045880	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0064319-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	204	1263	0	ENST00000261937.6:c.2891T>C	p.Val964Ala	p.V964A	ENST00000261937	NM_182925.4	964	gTg/gCg	21/30	1	2	FACETS	0.788	0.731	0.847	0.788	0.731	0.847	SUBCLONAL	1	FALSE	1	0.543751013440453	2		1263	952	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0064320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	98	457	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.3	2		457	531	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0064320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	50	331	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.929	0.791	1	0.929	0.791	1	CLONAL	1	TRUE	1	0.3	2		331	359	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492837	56492841	+	frameshift_variant	Frame_Shift_Del	DEL	TGCTG	TGCTG	-	novel	NA	P-0064320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	37	770	0	ENST00000407977.2:c.98_102del	p.Ala33GlyfsTer5	p.A33Gfs*5	ENST00000407977		33	gCAGCA/g	2/10	1	2	FACETS	0.34	0.279	0.409	0.34	0.279	0.409	SUBCLONAL	1	TRUE	1	0.3	2		770	725	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39647451	39647451	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0064320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	104	598	0	ENST00000262039.4:c.2623G>T	p.Val875Leu	p.V875L	ENST00000262039	NM_002647.2	875	Gtg/Ttg	24/25	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.3	2		598	677	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63661920	63661921	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTCGGCTCACCC	novel	NA	P-0000012-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	87	316	0	ENST00000279873.7:c.35_36insCGTCGGCTCACC	p.Val9_Pro12dup	p.V9_P12dup	ENST00000279873	NM_032199.2	9	-/GTCGGCTCACCC	2/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		316	518	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154374	2154374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000012-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	249	925	0	ENST00000434045.2:c.554G>T	p.Gly185Val	p.G185V	ENST00000434045	NM_001127598.1	185	gGc/gTc	5/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		925	1000	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495564	56495564	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000012-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	37	601	0	ENST00000267101.3:c.3754G>A	p.Ala1252Thr	p.A1252T	ENST00000267101	NM_001982.3	1252	Gca/Aca	28/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		601	638	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509541	29509541	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1567826623	NA	P-0000012-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	222	482	0	ENST00000356175.3:c.746T>C	p.Leu249Pro	p.L249P	ENST00000356175	NM_000267.3	249	cTa/cCa	8/57	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		482	588	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566486	41566486	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000012-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	39	451	0	ENST00000263253.7:c.4363C>G	p.Gln1455Glu	p.Q1455E	ENST00000263253	NM_001429.3	1455	Cag/Gag	27/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		451	685	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201749	66201749	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000012-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	152	576	0	ENST00000273854.3:c.2753A>T	p.Glu918Val	p.E918V	ENST00000273854	NM_004439.5	918	gAg/gTg	16/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		576	691	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467494	66467494	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000012-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	47	408	0	ENST00000273854.3:c.775T>C	p.Ser259Pro	p.S259P	ENST00000273854	NM_004439.5	259	Tca/Cca	3/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		408	402	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403458	139403458	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000012-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1192	248	1102	0	ENST00000277541.6:c.3035G>T	p.Gly1012Val	p.G1012V	ENST00000277541	NM_017617.3	1012	gGc/gTc	19/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1102	1440	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345208	70345208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000012-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	176	713	0	ENST00000374080.3:c.2234C>T	p.Ser745Leu	p.S745L	ENST00000374080		745	tCa/tTa	16/45	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		713	789	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0000025-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	231	577	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		579	438	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225060	NA	P-0000025-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	185	553	0	ENST00000263967.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000263967	NM_006218.2	104	cCa/cTa	2/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		553	688	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725066	89725066	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000025-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	52	205	0	ENST00000371953.3:c.1049C>G	p.Thr350Arg	p.T350R	ENST00000371953	NM_000314.4	350	aCa/aGa	9/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		205	185	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47004894	47004894	+	intron_variant	Intron	SNP	G	G	C	novel	NA	P-0000025-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	138	627	0	ENST00000377604.3:c.-126+10G>C		p.*42*	ENST00000377604	NM_001204468.1	-/163			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		627	721	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196832	123196832	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000025-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	76	501	0	ENST00000218089.9:c.1719G>C	p.Gln573His	p.Q573H	ENST00000218089	NM_001042749.1	573	caG/caC	18/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		501	569	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870953	12870953	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000121-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	146	418	0	ENST00000228872.4:c.180G>T	p.Trp60Cys	p.W60C	ENST00000228872	NM_004064.3	60	tgG/tgT	1/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		418	848	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579310	7579310	+	splice_donor_variant	Splice_Site	SNP	A	A	C	rs1555526469	NA	P-0000121-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	104	319	0	ENST00000269305.4:c.375+2T>G		p.X125_splice	ENST00000269305	NM_001126112.2	125			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		319	439	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619172	37619172	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000121-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1483	402	434	0	ENST00000447079.4:c.848C>A	p.Ser283Ter	p.S283*	ENST00000447079	NM_015083.1	283	tCg/tAg	1/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		434	1885	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0000219-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	66	368	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.0629920615897628	3	FACETS	1	0.958	1	0.631	0.549	0.719	INDETERMINATE	1	TRUE	1	0.246415213624766	3		368	477	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481433	140481433	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000219-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	84	448	0	ENST00000288602.6:c.1375G>T	p.Val459Leu	p.V459L	ENST00000288602	NM_004333.4	459	Gtg/Ttg	11/18	0.0629920615897628	3	FACETS	1	0.964	1	0.615	0.543	0.691	INDETERMINATE	1	TRUE	1	0.246415213624766	3		448	623	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857875	9857875	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000219-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	41	605	0	ENST00000330684.3:c.3526G>A	p.Glu1176Lys	p.E1176K	ENST00000330684	NM_001134407.1	1176	Gag/Aag	13/13	0.168614311048288	3	FACETS	0.532	0.442	0.633	0.266	0.221	0.317	SUBCLONAL	1	TRUE	1	0.246415213624766	3		605	702	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604755	48604755	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0000219-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	79	351	0	ENST00000342988.3:c.1579del	p.Ile527PhefsTer10	p.I527Ffs*10	ENST00000342988	NM_005359.5	526	gAa/ga	12/12	0.246415213624766	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.246415213624766	1		351	389	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076931	41076932	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0000219-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	37	519	0	ENST00000373198.4:c.1488dup	p.Pro497AlafsTer3	p.P497Afs*3	ENST00000373198	NM_133170.3	496	-/G	9/32	1	2	FACETS	0.477	0.392	0.572	0.477	0.392	0.572	SUBCLONAL	1	TRUE	1	0.246415213624766	2		519	630	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359448	118359462	+	frameshift_variant	Frame_Shift_Del	DEL	TTGTGGAAGGCAACA	TTGTGGAAGGCAACA	G	novel	NA	P-0000219-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	29	364	0	ENST00000534358.1:c.4452_4466delinsG	p.Cys1485SerfsTer10	p.C1485Sfs*10	ENST00000534358	NM_005933.3	1484	gtTTGTGGAAGGCAACAt/gtGt	11/36	1	2	FACETS	0.521	0.417	0.639	0.521	0.417	0.639	SUBCLONAL	1	TRUE	1	0.246415213624766	2		364	452	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0002421-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	164	462	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.19037860430901	3	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	FALSE	1	0.19037860430901	3		462	922	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579336	7579336	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002421-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	69	205	0	ENST00000269305.4:c.351del	p.Thr118GlnfsTer5	p.T118Qfs*5	ENST00000269305	NM_001126112.2	117	ggG/gg	4/11	0.19037860430901	6	FACETS	0.826	0.719	0.941			1	CLONAL	2	FALSE	NA	0.19037860430901	6		205	606	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837985	156837985	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002421-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	104	258	0	ENST00000524377.1:c.518A>T	p.Gln173Leu	p.Q173L	ENST00000524377	NM_002529.3	173	cAg/cTg	5/17	0.19037860430901	6	FACETS	1	0.938	1	0.533	0.478	0.592	CLONAL	2	FALSE	2	0.19037860430901	6		258	707	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176085798	176085798	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002421-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	70	327	0	ENST00000367669.3:c.988G>T	p.Glu330Ter	p.E330*	ENST00000367669	NM_022457.5	330	Gaa/Taa	9/20	0.19037860430901	3	FACETS	0.734	0.638	0.839	0.367	0.319	0.42	SUBCLONAL	1	FALSE	1	0.19037860430901	3		327	1097	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119666120	119666120	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002421-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	152	345	0	ENST00000316626.5:c.361G>T	p.Glu121Ter	p.E121*	ENST00000316626		121	Gag/Tag	3/12	1	2	FACETS	0.937	0.857	1	1	0.991	1	CLONAL	2	FALSE	1	0.19037860430901	2		345	852	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212048	142212048	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002421-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	92	405	0	ENST00000350721.4:c.6004G>T	p.Ala2002Ser	p.A2002S	ENST00000350721	NM_001184.3	2002	Gct/Tct	35/47	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	FALSE	1	0.19037860430901	2		405	914	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043483	180043483	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002421-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	46	161	0	ENST00000261937.6:c.3103C>A	p.His1035Asn	p.H1035N	ENST00000261937	NM_182925.4	1035	Cac/Aac	23/30	0.19037860430901	1	FACETS	0.965	0.814	1	0.965	0.814	1	CLONAL	1	FALSE	0	0.19037860430901	1		161	453	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047947	180047947	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002421-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	41	258	0	ENST00000261937.6:c.2228C>A	p.Ala743Glu	p.A743E	ENST00000261937	NM_182925.4	743	gCg/gAg	15/30	0.19037860430901	1	FACETS	0.664	0.552	0.789	0.664	0.552	0.789	SUBCLONAL	1	FALSE	0	0.19037860430901	1		258	587	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332804	152332804	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002421-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	83	455	0	ENST00000206249.3:c.1110G>T	p.Leu370Phe	p.L370F	ENST00000206249	NM_000125.3	370	ttG/ttT	5/8	0.144479754368673	0	FACETS	0.838	0.739	0.946			1	CLONAL	1	FALSE	0	0.19037860430901	0		455	842	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509012	106509012	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002421-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	137	193	0	ENST00000359195.3:c.1006C>A	p.His336Asn	p.H336N	ENST00000359195	NM_002649.2	336	Cat/Aat	2/11	NA	2	FACETS	0.954	0.873	1			1	INDETERMINATE	3	FALSE	NA	0.19037860430901	2		193	503	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5078436	5078436	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002421-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	122	233	0	ENST00000381652.3:c.2123C>A	p.Pro708Gln	p.P708Q	ENST00000381652	NM_004972.3	708	cCa/cAa	16/25	NA	2	FACETS	1	0.923	1			1	INDETERMINATE	2	FALSE	NA	0.19037860430901	2		233	628	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396757	139396757	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002421-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	50	165	0	ENST00000277541.6:c.5351G>T	p.Arg1784Leu	p.R1784L	ENST00000277541	NM_017617.3	1784	cGg/cTg	28/34	0.19037860430901	5	FACETS	1	0.925	1	0.385	0.326	0.449	CLONAL	1	FALSE	2	0.19037860430901	5		165	585	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121599	108121599	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002421-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	174	365	0	ENST00000278616.4:c.1407G>C	p.Arg469Ser	p.R469S	ENST00000278616	NM_000051.3	469	agG/agC	10/63	0.19037860430901	5	FACETS	0.97	0.891	1	0.647	0.594	0.702	CLONAL	2	FALSE	2	0.19037860430901	5		365	1211	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225522	133225522	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002421-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	52	245	1	ENST00000320574.5:c.4142A>G	p.Tyr1381Cys	p.Y1381C	ENST00000320574	NM_006231.2	1381	tAt/tGt	32/49	0.19037860430901	5	FACETS	0.892	0.758	1	0.223	0.189	0.261	CLONAL	1	FALSE	1	0.19037860430901	5		246	787	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244501	41244501	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002421-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	254	300	0	ENST00000357654.3:c.3047A>T	p.Asn1016Ile	p.N1016I	ENST00000357654	NM_007294.3	1016	aAt/aTt	10/23	0.19037860430901	7	FACETS	0.912	0.853	0.972			1	CLONAL	4	FALSE	NA	0.19037860430901	7		300	1080	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291100	10291101	+	missense_variant	Missense_Mutation	DNP	TC	TC	CA	novel	NA	P-0002421-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	68	223	0	ENST00000340748.4:c.370_371delinsTG	p.Asp124Cys	p.D124C	ENST00000340748		124	GAt/TGt	4/40	0.19037860430901	3	FACETS	1	0.931	1	0.556	0.483	0.636	CLONAL	1	FALSE	1	0.19037860430901	3		223	703	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602257	10602257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002421-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	133	163	0	ENST00000171111.5:c.1321G>T	p.Glu441Ter	p.E441*	ENST00000171111	NM_203500.1	441	Gag/Tag	3/6	0.19037860430901	3	FACETS	0.961	0.877	1	1	0.986	1	CLONAL	3	FALSE	1	0.19037860430901	3		163	531	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113812	11113812	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002421-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	131	167	0	ENST00000358026.2:c.1920G>T	p.Glu640Asp	p.E640D	ENST00000358026	NM_001128849.1	640	gaG/gaT	12/36	0.19037860430901	3	FACETS	0.842	0.766	0.92	1	0.979	1	CLONAL	3	FALSE	1	0.19037860430901	3		167	597	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52709219	52709219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1313754779	NA	P-0002421-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	105	205	0	ENST00000322088.6:c.173C>T	p.Thr58Ile	p.T58I	ENST00000322088	NM_014225.5	58	aCc/aTc	3/15	0.19037860430901	3	FACETS	0.954	0.856	1	0.954	0.856	1	CLONAL	2	FALSE	1	0.19037860430901	3		205	633	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561142	9561142	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002421-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	108	346	0	ENST00000353224.5:c.640G>T	p.Asp214Tyr	p.D214Y	ENST00000353224	NM_177990.2	214	Gac/Tac	4/10	1	2	FACETS	0.899	0.808	0.995	1	0.987	1	CLONAL	2	FALSE	1	0.19037860430901	2		346	631	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306615	41306615	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002421-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	52	329	0	ENST00000373198.4:c.1044del	p.Trp348CysfsTer49	p.W348Cfs*49	ENST00000373198	NM_133170.3	348	tgG/tg	7/32	0.183473754916082	1	FACETS	0.719	0.611	0.838	0.719	0.611	0.838	SUBCLONAL	1	FALSE	0	0.19037860430901	1		329	687	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207201	1207203	+	splice_donor_variant,coding_sequence_variant	Splice_Site	TNP	AAG	AAG	GAT	novel	NA	P-0002421-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	75	112	0	ENST00000326873.7:c.289_290+1delinsGAT		p.X97_splice	ENST00000326873	NM_000455.4	97		1/10	0.19037860430901	3	FACETS	1	0.913	1	1	0.913	1	CLONAL	2	FALSE	1	0.19037860430901	3		112	413	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018264	48018264	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0002615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	32	507	0	ENST00000234420.5:c.457+2T>G		p.X153_splice	ENST00000234420	NM_000179.2	153			0.286985223836487	4	FACETS	0.939	0.761	1	0.47	0.38	0.571	CLONAL	1	TRUE	2	0.16	4		507	494	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183776	10183777	+	missense_variant	Missense_Mutation	DNP	GC	GC	CT	novel	NA	P-0002615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	22	0	0	ENST00000256474.2:c.245_246delinsCT	p.Arg82Pro	p.R82P	ENST00000256474	NM_000551.3	82	cGC/cCT	1/3	1	2	FACETS	0.424	0.327	0.537	0.424	0.327	0.537	SUBCLONAL	1	TRUE	1	0.16	2		0	649	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508709	38508709	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	28	544	0	ENST00000254066.5:c.757A>G	p.Thr253Ala	p.T253A	ENST00000254066	NM_000964.3	253	Acc/Gcc	6/9	0.286985223836487	4	FACETS	0.725	0.578	0.894	0.363	0.289	0.447	SUBCLONAL	1	TRUE	2	0.16	4		544	560	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438456	52438469	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGCTGGGCTGACC	AAGCTGGGCTGACC	-	novel	NA	P-0002615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	28	590	0	ENST00000460680.1:c.1250_1250+13del		p.X417_splice	ENST00000460680	NM_004656.3	417		12/17	0.198723353158869	3	FACETS	0.754	0.602	0.929	0.377	0.301	0.465	CLONAL	1	TRUE	1	0.16	3		590	501	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1685639	1685639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780824098	NA	P-0002615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	41	826	0	ENST00000378625.1:c.1387G>A	p.Val463Met	p.V463M	ENST00000378625	NM_001198994.1	463	Gtg/Atg	12/14	0.198723353158869	3	FACETS	0.887	0.738	1	0.444	0.369	0.527	CLONAL	1	TRUE	1	0.16	3		826	624	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43738996	43738996	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	39	715	0	ENST00000523873.1:c.13C>G	p.Leu5Val	p.L5V	ENST00000523873		5	Ctg/Gtg	1/8	0.286985223836487	4	FACETS	0.927	0.767	1	0.464	0.383	0.553	CLONAL	1	TRUE	2	0.16	4		715	610	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003408-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	55	343	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.942	0.827	1	0.942	0.827	1	CLONAL	1	TRUE	1	0.828026133842056	2		343	141	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0003408-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	109	473	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.805	0.732	0.881	0.805	0.732	0.881	CLONAL	1	TRUE	1	0.828026133842056	2		473	327	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105604	27105604	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758075735	NA	P-0003408-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	191	372	0	ENST00000324856.7:c.5215C>T	p.Pro1739Ser	p.P1739S	ENST00000324856	NM_006015.4	1739	Cca/Tca	20/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.828026133842056	2		372	431	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938412	44938412	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003408-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	147	128	0	ENST00000377967.4:c.2960A>G	p.Lys987Arg	p.K987R	ENST00000377967	NM_021140.2	987	aAa/aGa	20/29	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.828026133842056	1		128	180	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651893	36651894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0003408-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	205	336	0	ENST00000244741.5:c.19dup	p.Asp7GlyfsTer29	p.D7Gfs*29	ENST00000244741	NM_000389.4	5	-/G	2/3	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.828026133842056	2		336	470	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436054	49436054	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0003408-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	114	276	0	ENST00000301067.7:c.5927C>G	p.Ser1976Ter	p.S1976*	ENST00000301067	NM_003482.3	1976	tCa/tGa	28/54	1	2	FACETS	0.883	0.806	0.961	0.883	0.806	0.961	CLONAL	1	TRUE	1	0.828026133842056	2		276	312	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	154	205	0				ENST00000310581	NM_198253.2	-/1132			0.272283637784848	5	FACETS	1	0.94	1	1	0.94	1	CLONAL	4	TRUE	1	0.39	5		205	310	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	32	190	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.39	2		190	137	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650109	93650109	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	51	689	2	ENST00000375746.1:c.1660G>A	p.Asp554Asn	p.D554N	ENST00000375746	NM_001174167.1	554	Gat/Aat	12/14	1	2	FACETS	0.722	0.616	0.838	0.722	0.616	0.838	SUBCLONAL	1	TRUE	1	0.39	2		691	362	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480341	56480341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	74	561	0	ENST00000267101.3:c.448G>A	p.Glu150Lys	p.E150K	ENST00000267101	NM_001982.3	150	Gag/Aag	4/28	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.39	2		561	363	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363243	40363243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	67	657	0	ENST00000397332.2:c.986C>T	p.Ser329Leu	p.S329L	ENST00000397332	NM_001033082.2	329	tCg/tTg	3/3	1	2	FACETS	0.902	0.788	1	0.902	0.788	1	CLONAL	1	TRUE	1	0.39	2		657	381	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567800	226567800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1389888337	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	79	795	0	ENST00000366794.5:c.1366G>A	p.Glu456Lys	p.E456K	ENST00000366794	NM_001618.3	456	Gag/Aag	10/23	1	2	FACETS	0.919	0.811	1	0.919	0.811	1	CLONAL	1	TRUE	1	0.39	2		795	441	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645639	215645639	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	48	737	0	ENST00000260947.4:c.959G>A	p.Gly320Glu	p.G320E	ENST00000260947	NM_000465.2	320	gGa/gAa	4/11	1	2	FACETS	0.711	0.604	0.829	0.711	0.604	0.829	SUBCLONAL	1	TRUE	1	0.39	2		737	346	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053566	37053566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	70	699	0	ENST00000231790.2:c.653C>T	p.Ser218Phe	p.S218F	ENST00000231790	NM_000249.3	218	tCc/tTc	8/19	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.39	2		699	345	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125533	47125533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	59	575	0	ENST00000409792.3:c.5737G>A	p.Glu1913Lys	p.E1913K	ENST00000409792	NM_014159.6	1913	Gaa/Aaa	12/21	1	2	FACETS	0.917	0.794	1	0.917	0.794	1	CLONAL	1	TRUE	1	0.39	2		575	330	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157491	106157491	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777279382	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	33	409	0	ENST00000380013.4:c.2392G>A	p.Glu798Lys	p.E798K	ENST00000380013	NM_001127208.2	798	Gag/Aag	3/11	1	2	FACETS	0.664	0.543	0.798	0.664	0.543	0.798	SUBCLONAL	1	TRUE	1	0.39	2		409	255	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876382	35876382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1283489708	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	73	670	0	ENST00000303115.3:c.1174G>A	p.Glu392Lys	p.E392K	ENST00000303115	NM_002185.3	392	Gag/Aag	8/8	1	2	FACETS	0.998	0.878	1	0.998	0.878	1	CLONAL	1	TRUE	1	0.39	2		670	375	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562804	176562804	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771968592	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	82	647	0	ENST00000439151.2:c.700G>A	p.Glu234Lys	p.E234K	ENST00000439151	NM_022455.4	234	Gaa/Aaa	2/23	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.39	2		647	391	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638668	176638668	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	93	773	0	ENST00000439151.2:c.3268C>A	p.Pro1090Thr	p.P1090T	ENST00000439151	NM_022455.4	1090	Ccc/Acc	5/23	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.39	2		773	349	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502163	157502163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	68	490	0	ENST00000346085.5:c.3196G>A	p.Glu1066Lys	p.E1066K	ENST00000346085	NM_020732.3	1066	Gag/Aag	12/20	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.39	2		490	322	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750924	128750924	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	58	603	0	ENST00000377970.2:c.461C>T	p.Ser154Leu	p.S154L	ENST00000377970	NM_002467.4	154	tCg/tTg	2/3	0.3	3	FACETS	0.875	0.755	1	0.438	0.377	0.503	CLONAL	1	TRUE	1	0.39	3		603	406	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430541	80430541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	20	656	0	ENST00000286548.4:c.467C>T	p.Ser156Phe	p.S156F	ENST00000286548	NM_002072.3	156	tCt/tTt	3/7	1	2	FACETS	0.493	0.378	0.626	0.493	0.378	0.626	SUBCLONAL	1	TRUE	1	0.39	2		656	208	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904914	101904914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	52	496	0	ENST00000374994.4:c.902G>A	p.Gly301Glu	p.G301E	ENST00000374994	NM_004612.2	301	gGa/gAa	5/9	1	2	FACETS	0.855	0.732	0.988	0.855	0.732	0.988	CLONAL	1	TRUE	1	0.39	2		496	312	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759700	133759700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	63	682	0	ENST00000318560.5:c.2023G>A	p.Glu675Lys	p.E675K	ENST00000318560	NM_005157.4	675	Gag/Aag	11/11	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.39	2		682	279	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623699	43623699	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	68	635	0	ENST00000355710.3:c.3327G>T	p.Met1109Ile	p.M1109I	ENST00000355710	NM_020975.4	1109	atG/atT	20/20	1	2	FACETS	0.899	0.786	1	0.899	0.786	1	CLONAL	1	TRUE	1	0.39	2		635	388	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285666	46285666	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	59	595	0	ENST00000334344.6:c.5026C>T	p.Gln1676Ter	p.Q1676*	ENST00000334344	NM_152641.2	1676	Cag/Tag	17/21	1	2	FACETS	0.867	0.75	0.993	0.867	0.75	0.993	CLONAL	1	TRUE	1	0.39	2		595	349	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611388	28611388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	67	663	0	ENST00000241453.7:c.1243G>A	p.Glu415Lys	p.E415K	ENST00000241453	NM_004119.2	415	Gaa/Aaa	10/24	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.39	2		663	323	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988856	41988856	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	63	560	0	ENST00000219905.7:c.1648C>T	p.Gln550Ter	p.Q550*	ENST00000219905	NM_001164273.1	550	Cag/Tag	3/24	1	2	FACETS	0.964	0.84	1	0.964	0.84	1	CLONAL	1	TRUE	1	0.39	2		560	335	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619264	23619264	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs864622138	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	77	597	0	ENST00000261584.4:c.3271C>T	p.Gln1091Ter	p.Q1091*	ENST00000261584	NM_024675.3	1091	Cag/Tag	12/13	1	2	FACETS	0.97	0.856	1	0.97	0.856	1	CLONAL	1	TRUE	1	0.39	2		597	407	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56792478	56792478	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	57	589	0	ENST00000308159.5:c.208G>A	p.Asp70Asn	p.D70N	ENST00000308159	NM_014669.4	70	Gac/Aac	3/22	1	2	FACETS	0.786	0.677	0.903	0.786	0.677	0.903	CLONAL	1	TRUE	1	0.39	2		589	372	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828205	72828205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	65	771	2	ENST00000268489.5:c.8376G>A	p.Met2792Ile	p.M2792I	ENST00000268489	NM_006885.3	2792	atG/atA	9/10	1	2	FACETS	0.958	0.836	1	0.958	0.836	1	CLONAL	1	TRUE	1	0.39	2		773	348	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993237	72993237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567606533	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	83	898	3	ENST00000268489.5:c.808G>A	p.Asp270Asn	p.D270N	ENST00000268489	NM_006885.3	270	Gat/Aat	2/10	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.39	2		901	420	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619289	37619289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	47	469	0	ENST00000447079.4:c.965G>A	p.Arg322Gln	p.R322Q	ENST00000447079	NM_015083.1	322	cGa/cAa	1/14	1	2	FACETS	0.739	0.627	0.862	0.739	0.627	0.862	SUBCLONAL	1	TRUE	1	0.39	2		469	326	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40478160	40478160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	70	610	0	ENST00000264657.5:c.1339C>T	p.His447Tyr	p.H447Y	ENST00000264657	NM_139276.2	447	Cac/Tac	15/24	1	2	FACETS	0.889	0.778	1	0.889	0.778	1	CLONAL	1	TRUE	1	0.39	2		610	404	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677792	47677792	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	60	512	0	ENST00000347630.2:c.1073C>T	p.Ser358Leu	p.S358L	ENST00000347630	NM_001007230.1	358	tCa/tTa	11/11	1	2	FACETS	0.91	0.789	1	0.91	0.789	1	CLONAL	1	TRUE	1	0.39	2		512	338	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267597	7267597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	99	822	0	ENST00000302850.5:c.411G>A	p.Met137Ile	p.M137I	ENST00000302850	NM_000208.2	137	atG/atA	2/22	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.39	2		822	440	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952217	17952217	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	76	727	0	ENST00000458235.1:c.1123C>T	p.Gln375Ter	p.Q375*	ENST00000458235	NM_000215.3	375	Cag/Tag	8/24	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.39	2		727	387	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953330	17953330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	70	709	0	ENST00000458235.1:c.656G>A	p.Arg219Lys	p.R219K	ENST00000458235	NM_000215.3	219	aGa/aAa	6/24	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.39	2		709	356	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871992	45871992	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	61	617	0	ENST00000391945.4:c.256G>C	p.Glu86Gln	p.E86Q	ENST00000391945	NM_000400.3	86	Gag/Cag	5/23	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.39	2		617	302	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206804	36206804	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	71	617	0	ENST00000300305.3:c.708G>A	p.Met236Ile	p.M236I	ENST00000300305		236	atG/atA	6/8	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.39	2		617	360	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175881	24175881	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	52	463	0	ENST00000263121.7:c.1109G>C	p.Arg370Thr	p.R370T	ENST00000263121	NM_003073.3	370	aGg/aCg	8/9	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.39	2		463	243	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106297	27106303	+	frameshift_variant	Frame_Shift_Del	DEL	CTTCTGG	CTTCTGG	-	novel	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	67	763	0	ENST00000324856.7:c.5908_5914del	p.Leu1970ThrfsTer43	p.L1970Tfs*43	ENST00000324856	NM_006015.4	1970	CTTCTGGac/ac	20/20	1	2	FACETS	0.855	0.746	0.971	0.855	0.746	0.971	CLONAL	1	TRUE	1	0.39	2		763	402	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	86	876	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.39	2		876	396	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252682	133252682	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	33	585	0	ENST00000320574.5:c.1018G>C	p.Glu340Gln	p.E340Q	ENST00000320574	NM_006231.2	340	Gag/Cag	10/49	0.3	1	FACETS	0.476	0.389	0.574	0.476	0.389	0.574	SUBCLONAL	1	TRUE	0	0.39	1		585	286	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788674	3788674	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	52	377	0	ENST00000262367.5:c.4281-1G>A		p.X1427_splice	ENST00000262367	NM_004380.2	1427			1	2	FACETS	0.841	0.72	0.972	0.841	0.72	0.972	CLONAL	1	TRUE	1	0.39	2		377	317	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11019805	11019805	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	55	554	0	ENST00000327064.4:c.480G>C	p.Gln160His	p.Q160H	ENST00000327064	NM_199141.1	160	caG/caC	4/16	1	2	FACETS	0.81	0.697	0.934	0.81	0.697	0.934	CLONAL	1	TRUE	1	0.39	2		554	348	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265452	198265452	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	24	682	0	ENST00000335508.6:c.2705A>G	p.Glu902Gly	p.E902G	ENST00000335508	NM_012433.2	902	gAa/gGa	18/25	1	2	FACETS	0.468	0.368	0.583	0.468	0.368	0.583	SUBCLONAL	1	TRUE	1	0.39	2		682	263	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004983-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	151	343	0				ENST00000310581	NM_198253.2	-/1132			0.65214827397308	4	FACETS	0.962	0.902	1	0.962	0.902	1	CLONAL	3	TRUE	1	0.70076895535157	4		343	254	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651917	36651917	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs756319938	NA	P-0004983-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	168	929	0	ENST00000244741.5:c.39C>A	p.Cys13Ter	p.C13*	ENST00000244741	NM_000389.4	13	tgC/tgA	2/3	1	2	FACETS	0.979	0.907	1	0.979	0.907	1	CLONAL	1	TRUE	1	0.70076895535157	2		929	490	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790170	40790170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373191879	NA	P-0004983-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	114	844	0	ENST00000373198.4:c.2561G>A	p.Arg854His	p.R854H	ENST00000373198	NM_133170.3	854	cGc/cAc	18/32	1	2	FACETS	0.896	0.815	0.98	0.896	0.815	0.98	CLONAL	1	TRUE	1	0.70076895535157	2		844	363	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894230	NA	P-0004983-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	267	851	0	ENST00000451590.1:c.35G>A	p.Gly12Asp	p.G12D	ENST00000451590	NM_001130442.1	12	gGc/gAc	2/5	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.70076895535157	2		851	520	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11027110	11027110	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004983-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	138	739	0	ENST00000327064.4:c.875T>C	p.Val292Ala	p.V292A	ENST00000327064	NM_199141.1	292	gTc/gCc	7/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.70076895535157	2		739	345	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131468	202131468	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004983-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	139	714	0	ENST00000358485.4:c.436G>T	p.Glu146Ter	p.E146*	ENST00000358485	NM_001080125.1	146	Gaa/Taa	2/9	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.70076895535157	2		714	379	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626386	12626389	+	frameshift_variant	Frame_Shift_Del	DEL	CAGT	CAGT	-	novel	NA	P-0004983-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	126	814	0	ENST00000251849.4:c.1760_1763del	p.Asp587ValfsTer2	p.D587Vfs*2	ENST00000251849	NM_002880.3	587	gACTGt/gt	16/17	1	2	FACETS	0.951	0.871	1	0.951	0.871	1	CLONAL	1	TRUE	1	0.70076895535157	2		814	378	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55963891	55963891	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004983-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	121	575	0	ENST00000263923.4:c.2552C>G	p.Ala851Gly	p.A851G	ENST00000263923	NM_002253.2	851	gCa/gGa	18/30	0.198881704654517	1	FACETS	0.583	0.531	0.636	0.583	0.531	0.636	INDETERMINATE	1	TRUE	0	0.70076895535157	1		575	385	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0005543-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	16	418	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	0.911	0.674	1	0.911	0.674	1	CLONAL	1	TRUE	1	0.14	2		418	251	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0005543-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	43	1004	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	1	2	FACETS	0.978	0.817	1	0.978	0.817	1	CLONAL	1	TRUE	1	0.14	2		1004	628	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220640	1220640	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690940	NA	P-0005543-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	33	1133	0	ENST00000326873.7:c.658C>T	p.Gln220Ter	p.Q220*	ENST00000326873	NM_000455.4	220	Cag/Tag	5/10	0.133882682996489	0	FACETS	0.656	0.533	0.796			1	SUBCLONAL	1	TRUE	0	0.14	0		1133	618	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508577	106508577	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005543-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	30	671	0	ENST00000359195.3:c.571C>A	p.Arg191Ser	p.R191S	ENST00000359195	NM_002649.2	191	Cgc/Agc	2/11	1	2	FACETS	0.884	0.711	1	0.884	0.711	1	CLONAL	1	TRUE	1	0.14	2		671	485	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610078	43610078	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536038262	NA	P-0005543-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	36	1064	0	ENST00000355710.3:c.2030G>A	p.Arg677Gln	p.R677Q	ENST00000355710	NM_020975.4	677	cGg/cAg	11/20	0.133882682996489	1	FACETS	0.859	0.705	1	0.859	0.705	1	CLONAL	1	TRUE	0	0.14	1		1064	557	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148516697	148516697	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0005543-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	20	568	0	ENST00000320356.2:c.990C>G	p.Tyr330Ter	p.Y330*	ENST00000320356	NM_004456.4	330	taC/taG	9/20	1	2	FACETS	0.823	0.629	1	0.823	0.629	1	CLONAL	1	TRUE	1	0.14	2		568	347	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63662078	63662079	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005543-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	47	768	1	ENST00000279873.7:c.182_183insT	p.Trp61CysfsTer14	p.W61Cfs*14	ENST00000279873	NM_032199.2	61	tgg/tgTg	2/10	0.3	4	FACETS	1	0.86	1			1	CLONAL	1	TRUE	NA	0.14	4		769	748	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645109	67645109	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005543-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	31	885	0	ENST00000264010.4:c.374C>G	p.Pro125Arg	p.P125R	ENST00000264010	NM_006565.3	125	cCt/cGt	3/12	1	2	FACETS	0.831	0.671	1	0.831	0.671	1	CLONAL	1	TRUE	1	0.14	2		885	533	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905970	50905970	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005543-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	35	1051	0	ENST00000440232.2:c.942C>G	p.Ser314Arg	p.S314R	ENST00000440232	NM_002691.3	314	agC/agG	8/27	0.0912050244497961	0	FACETS	0.811	0.664	0.977			1	CLONAL	1	TRUE	0	0.14	0		1051	530	SUCCESS
APC	324	MSKCC	GRCh37	5	112175594	112175594	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1454804146	NA	P-0005543-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	37	817	0	ENST00000257430.4:c.4303A>G	p.Arg1435Gly	p.R1435G	ENST00000257430	NM_000038.5	1435	Aga/Gga	16/16	1	2	FACETS	1	0.835	1	1	0.835	1	CLONAL	1	TRUE	1	0.14	2		817	521	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0006189-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	117	408	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	0.823	0.744	0.905	0.823	0.744	0.905	CLONAL	1	TRUE	1	0.489471909727969	2		408	581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0006189-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	156	662	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.489471909727969	1	FACETS	0.882	0.812	0.954	0.882	0.812	0.954	CLONAL	1	TRUE	0	0.489471909727969	1		662	546	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29107974	29107974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121908702	NA	P-0006189-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	91	340	0	ENST00000328354.6:c.715G>A	p.Glu239Lys	p.E239K	ENST00000328354	NM_007194.3	239	Gag/Aag	6/15	0.489471909727969	1	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	0	0.489471909727969	1		340	280	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15952173	15952182	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTGCGCCC	CTCTGCGCCC	-	novel	NA	P-0006189-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	118	393	0	ENST00000268712.3:c.6513_6522del	p.Arg2171SerfsTer15	p.R2171Sfs*15	ENST00000268712	NM_006311.3	2171	agGGGCGCAGAG/ag	41/46	0.489471909727969	1	FACETS	0.843	0.766	0.923	0.843	0.766	0.923	CLONAL	1	TRUE	0	0.489471909727969	1		393	432	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089741	27089741	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006189-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	170	545	0	ENST00000324856.7:c.2697del	p.Ala900ProfsTer19	p.A900Pfs*19	ENST00000324856	NM_006015.4	899	gtC/gt	8/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.489471909727969	2		545	669	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244435	46244438	+	frameshift_variant	Frame_Shift_Del	DEL	AGAT	AGAT	-	novel	NA	P-0006189-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	153	519	0	ENST00000334344.6:c.2530_2533del	p.Asp844LeufsTer4	p.D844Lfs*4	ENST00000334344	NM_152641.2	843	caAGAT/ca	15/21	0.483445695016794	2	FACETS	0.992	0.911	1	0.496	0.455	0.539	CLONAL	1	TRUE	0	0.489471909727969	2		519	630	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742438	145742438	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006189-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	171	491	0	ENST00000428558.2:c.350T>C	p.Leu117Pro	p.L117P	ENST00000428558	NM_004260.3	117	cTg/cCg	4/22	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.489471909727969	2		491	618	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0006280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	203	698	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.340508869896117	3	FACETS	0.9	0.84	0.962	0.9	0.84	0.962	CLONAL	2	TRUE	1	0.460051099261095	3		698	603	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082299	16082299	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs958489598	NA	P-0006280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	135	214	2	ENST00000281043.3:c.113G>A	p.Gly38Asp	p.G38D	ENST00000281043	NM_005378.4	38	gGc/gAc	2/3	1	2	FACETS	0.756	0.695	0.819	1	0.988	1	SUBCLONAL	2	TRUE	1	0.460051099261095	2		216	388	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793305	242793305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	64	203	0	ENST00000334409.5:c.772G>A	p.Gly258Ser	p.G258S	ENST00000334409	NM_005018.2	258	Ggc/Agc	5/5	0.441533837301893	1	FACETS	0.83	0.727	0.94	0.83	0.727	0.94	CLONAL	1	TRUE	0	0.460051099261095	1		203	258	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497225	149497225	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	38	206	0	ENST00000261799.4:c.3093G>C	p.Glu1031Asp	p.E1031D	ENST00000261799	NM_002609.3	1031	gaG/gaC	22/23	1	2	FACETS	0.438	0.363	0.522	0.438	0.363	0.522	SUBCLONAL	1	TRUE	1	0.460051099261095	2		206	377	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575491	64575491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376872829	NA	P-0006280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	88	235	3	ENST00000312049.6:c.526G>A	p.Ala176Thr	p.A176T	ENST00000312049	NM_130799.2	176	Gcc/Acc	3/10	0.41194657312667	1	FACETS	0.735	0.655	0.819	0.735	0.655	0.819	SUBCLONAL	1	TRUE	0	0.460051099261095	1		238	401	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153445	108153445	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	119	107	1	ENST00000278616.4:c.3585G>T	p.Glu1195Asp	p.E1195D	ENST00000278616	NM_000051.3	1195	gaG/gaT	25/63	0.333049875284687	1	FACETS	0.853	0.775	0.935	0.853	0.775	0.935	CLONAL	1	TRUE	0	0.460051099261095	1		108	467	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205082	123205083	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	278	242	1	ENST00000218089.9:c.2443dup	p.Tyr815LeufsTer4	p.Y815Lfs*4	ENST00000218089	NM_001042749.1	814	-/T	25/35	0.279636390088282	1	FACETS	0.954	0.898	1	0.954	0.898	1	CLONAL	1	TRUE	0	0.460051099261095	1		243	975	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919281	48919282	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	156	146	1	ENST00000267163.4:c.448dup	p.Arg150LysfsTer7	p.R150Kfs*7	ENST00000267163	NM_000321.2	149	tca/tcAa	4/27	0.460051099261095	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.460051099261095	1		147	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577551	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0006280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	116	203	1	ENST00000269305.4:c.730_731delinsTT	p.Gly244Phe	p.G244F	ENST00000269305	NM_001126112.2	244	GGc/TTc	7/11	0.460051099261095	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.460051099261095	1		204	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	359	801	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	0.965	0.924	1			1	INDETERMINATE	2	TRUE	NA	0.562073430412027	2		804	662	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289259	33289260	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	207	431	0	ENST00000374542.5:c.292_293del	p.Leu98ValfsTer13	p.L98Vfs*13	ENST00000374542	NM_001141970.1	98	CTg/g	3/8	0.562073430412027	3	FACETS	0.95	0.882	1	0.475	0.441	0.511	CLONAL	1	TRUE	1	0.562073430412027	3		431	993	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736296	243736296	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	369	533	0	ENST00000263826.5:c.751T>A	p.Tyr251Asn	p.Y251N	ENST00000263826	NM_005465.4	251	Tat/Aat	8/13	0.516900198262152	4	FACETS	0.97	0.922	1			1	CLONAL	2	TRUE	NA	0.562073430412027	4		533	1057	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795120	242795120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1412459900	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	136	313	0	ENST00000334409.5:c.89G>A	p.Arg30Lys	p.R30K	ENST00000334409	NM_005018.2	30	aGg/aAg	2/5	0.306924033008529	4	FACETS	1	0.955	1			1	INDETERMINATE	1	TRUE	NA	0.562073430412027	4		313	702	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670255	134670255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	609	400	0	ENST00000398015.3:c.166C>A	p.Arg56Ser	p.R56S	ENST00000398015	NM_004441.4	56	Cgc/Agc	3/16	0.562073430412027	5	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	2	0.562073430412027	5		400	1315	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851685	134851685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377348490	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	603	394	0	ENST00000398015.3:c.1091G>A	p.Arg364Gln	p.R364Q	ENST00000398015	NM_004441.4	364	cGg/cAg	5/16	0.562073430412027	5	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	2	0.562073430412027	5		394	1192	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502609	149502609	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	203	207	0	ENST00000261799.4:c.2179C>T	p.Pro727Ser	p.P727S	ENST00000261799	NM_002609.3	727	Ccc/Tcc	15/23	0.562073430412027	2	FACETS	0.989	0.934	1	0.989	0.934	1	CLONAL	2	TRUE	0	0.562073430412027	2		207	365	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393209	393209	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	175	435	0	ENST00000380956.4:c.57C>A	p.Cys19Ter	p.C19*	ENST00000380956	NM_001195286.1	19	tgC/tgA	2/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.562073430412027	NA		435	850	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286823	33286823	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs143737807	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	342	329	0	ENST00000374542.5:c.2114G>T	p.Arg705Leu	p.R705L	ENST00000374542	NM_001141970.1	705	cGg/cTg	7/8	0.562073430412027	3	FACETS	0.999	0.951	1	0.999	0.951	1	CLONAL	2	TRUE	1	0.562073430412027	3		329	780	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066637	94066637	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	658	709	2	ENST00000369303.4:c.1122G>T	p.Trp374Cys	p.W374C	ENST00000369303	NM_004440.3	374	tgG/tgT	5/17	0.562073430412027	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.562073430412027	2		711	1145	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729690	41729690	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1517	327	669	0	ENST00000242208.4:c.839G>C	p.Gly280Ala	p.G280A	ENST00000242208	NM_002192.2	280	gGa/gCa	3/3	0.562073430412027	4	FACETS	0.986	0.928	1	0.329	0.309	0.349	CLONAL	1	TRUE	1	0.562073430412027	4		669	1844	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55087040	55087040	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	211	244	0	ENST00000275493.2:c.70G>T	p.Ala24Ser	p.A24S	ENST00000275493	NM_005228.3	24	Gct/Tct	1/28	0.562073430412027	4	FACETS	0.882	0.823	0.942	0.588	0.548	0.628	CLONAL	2	TRUE	1	0.562073430412027	4		244	665	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967783	90967783	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	89	191	0	ENST00000265433.3:c.1125G>T	p.Trp375Cys	p.W375C	ENST00000265433	NM_002485.4	375	tgG/tgT	10/16	0.296064141715154	5	FACETS	0.935	0.838	1	0.624	0.559	0.691	INDETERMINATE	2	TRUE	2	0.562073430412027	5		191	312	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983459	90983459	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	191	328	0	ENST00000265433.3:c.644G>T	p.Arg215Leu	p.R215L	ENST00000265433	NM_002485.4	215	cGg/cTg	6/16	0.296064141715154	5	FACETS	0.943	0.876	1	0.629	0.584	0.675	INDETERMINATE	2	TRUE	2	0.562073430412027	5		328	664	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90995084	90995084	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	168	210	0	ENST00000265433.3:c.38-1G>T		p.X13_splice	ENST00000265433	NM_002485.4	13			0.296064141715154	5	FACETS	1	0.945	1	0.684	0.633	0.737	INDETERMINATE	2	TRUE	2	0.562073430412027	5		210	537	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465608	8465608	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	149	530	0	ENST00000356435.5:c.3572A>G	p.Tyr1191Cys	p.Y1191C	ENST00000356435		1191	tAt/tGt	21/35	1	2	FACETS	0.916	0.84	0.994	0.916	0.84	0.994	CLONAL	1	TRUE	1	0.562073430412027	2		530	579	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521321	8521321	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	138	342	2	ENST00000356435.5:c.917C>A	p.Ser306Ter	p.S306*	ENST00000356435		306	tCa/tAa	9/35	1	2	FACETS	0.916	0.838	0.997	0.916	0.838	0.997	CLONAL	1	TRUE	1	0.562073430412027	2		344	536	SUCCESS
RET	5979	MSKCC	GRCh37	10	43602011	43602011	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	273	371	0	ENST00000355710.3:c.1055A>C	p.His352Pro	p.H352P	ENST00000355710	NM_020975.4	352	cAt/cCt	5/20	0.296064141715154	5	FACETS	1	0.941	1	0.667	0.627	0.707	INDETERMINATE	2	TRUE	2	0.562073430412027	5		371	895	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852370	63852370	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	331	435	0	ENST00000279873.7:c.3148G>T	p.Glu1050Ter	p.E1050*	ENST00000279873	NM_032199.2	1050	Gag/Tag	10/10	0.296064141715154	5	FACETS	1	0.971	1	0.692	0.655	0.73	INDETERMINATE	2	TRUE	2	0.562073430412027	5		435	1045	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156635	2156635	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	620	569	0	ENST00000434045.2:c.287C>A	p.Thr96Asn	p.T96N	ENST00000434045	NM_001127598.1	96	aCc/aAc	3/5	0.562073430412027	3	FACETS	0.964	0.936	0.992	0.964	0.936	0.992	CLONAL	3	TRUE	0	0.562073430412027	3		569	977	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230370	46230370	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	678	322	1	ENST00000334344.6:c.706-2A>T		p.X236_splice	ENST00000334344	NM_152641.2	236			0.562073430412027	4	FACETS	0.945	0.92	0.969	0.945	0.92	0.969	CLONAL	4	TRUE	0	0.562073430412027	4		323	997	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555662	21555662	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	267	509	0	ENST00000382592.4:c.2608G>T	p.Ala870Ser	p.A870S	ENST00000382592	NM_014572.2	870	Gca/Tca	6/8	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.562073430412027	2		509	887	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589378	28589378	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	209	421	0	ENST00000241453.7:c.2669C>A	p.Pro890His	p.P890H	ENST00000241453	NM_004119.2	890	cCt/cAt	22/24	0.562073430412027	3	FACETS	0.851	0.789	0.915	0.425	0.394	0.458	CLONAL	1	TRUE	1	0.562073430412027	3		421	1120	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592650	28592650	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	231	644	0	ENST00000241453.7:c.2495T>A	p.Leu832Ter	p.L832*	ENST00000241453	NM_004119.2	832	tTg/tAg	20/24	0.562073430412027	3	FACETS	0.82	0.763	0.879	0.41	0.381	0.44	CLONAL	1	TRUE	1	0.562073430412027	3		644	1284	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041743	42041743	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	682	758	1	ENST00000219905.7:c.5938G>T	p.Glu1980Ter	p.E1980*	ENST00000219905	NM_001164273.1	1980	Gaa/Taa	17/24	0.562073430412027	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.562073430412027	2		759	1149	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483917	88483917	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	451	477	0	ENST00000360948.2:c.1653G>T	p.Lys551Asn	p.K551N	ENST00000360948	NM_001012338.2	551	aaG/aaT	14/19	0.562073430412027	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.562073430412027	2		477	802	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647685	2647685	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	270	539	1	ENST00000342085.4:c.1588G>T	p.Gly530Trp	p.G530W	ENST00000342085	NM_002613.4	530	Ggg/Tgg	14/14	0.432949360130103	3	FACETS	1	0.977	1	0.541	0.507	0.576	CLONAL	1	TRUE	1	0.562073430412027	3		540	1137	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857922	9857922	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	368	366	0	ENST00000330684.3:c.3479A>C	p.Lys1160Thr	p.K1160T	ENST00000330684	NM_001134407.1	1160	aAg/aCg	13/13	0.432949360130103	3	FACETS	0.905	0.861	0.949	0.905	0.861	0.949	CLONAL	2	TRUE	1	0.562073430412027	3		366	927	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020435	14020435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	159	322	0	ENST00000311895.7:c.406G>A	p.Ala136Thr	p.A136T	ENST00000311895	NM_005236.2	136	Gcc/Acc	3/11	0.432949360130103	3	FACETS	0.911	0.836	0.989	0.455	0.418	0.495	CLONAL	1	TRUE	1	0.562073430412027	3		322	796	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821181	72821181	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	342	575	0	ENST00000268489.5:c.10994A>T	p.Asp3665Val	p.D3665V	ENST00000268489	NM_006885.3	3665	gAc/gTc	10/10	0.509303294898547	3	FACETS	1	0.986	1	0.56	0.529	0.592	CLONAL	1	TRUE	1	0.562073430412027	3		575	1391	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998899	11998899	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	108	338	0	ENST00000353533.5:c.401G>T	p.Arg134Leu	p.R134L	ENST00000353533	NM_003010.3	134	cGg/cTg	4/11	0.501552254848399	1	FACETS	0.912	0.83	0.996	0.912	0.83	0.996	CLONAL	1	TRUE	0	0.562073430412027	1		338	303	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40379566	40379566	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1663	376	891	0	ENST00000293328.3:c.266A>T	p.His89Leu	p.H89L	ENST00000293328	NM_012448.3	89	cAc/cTc	3/19	0.545765498706442	4	FACETS	1	0.964	1	0.342	0.323	0.361	CLONAL	1	TRUE	1	0.562073430412027	4		891	2039	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453366	40453366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	967	744	0	ENST00000345506.4:c.1063C>A	p.Leu355Met	p.L355M	ENST00000345506	NM_003152.3	355	Ctg/Atg	10/20	0.545765498706442	4	FACETS	0.985	0.959	1	0.985	0.959	1	CLONAL	3	TRUE	1	0.562073430412027	4		744	1818	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625631	1625631	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	482	553	0	ENST00000344749.5:c.443A>T	p.Gln148Leu	p.Q148L	ENST00000344749	NM_001136139.2	148	cAg/cTg	7/19	0.562073430412027	2	FACETS	0.974	0.939	1	0.974	0.939	1	CLONAL	2	TRUE	0	0.562073430412027	2		553	880	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953337	17953337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202167678	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	385	444	0	ENST00000458235.1:c.649G>A	p.Val217Met	p.V217M	ENST00000458235	NM_000215.3	217	Gtg/Atg	6/24	0.562073430412027	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.562073430412027	2		444	665	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726687	41726687	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	271	504	0	ENST00000301178.4:c.232C>A	p.Leu78Ile	p.L78I	ENST00000301178	NM_021913.4	78	Ctc/Atc	2/20	0.562073430412027	3	FACETS	1	0.98	1	0.552	0.518	0.588	CLONAL	1	TRUE	1	0.562073430412027	3		504	1118	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50916773	50916773	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	272	461	1	ENST00000440232.2:c.2245G>T	p.Ala749Ser	p.A749S	ENST00000440232	NM_002691.3	749	Gcc/Tcc	18/27	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.562073430412027	2		462	856	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031269	36031269	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	214	427	0	ENST00000358208.4:c.1388G>T	p.Arg463Leu	p.R463L	ENST00000358208		463	cGg/cTg	11/12	0.562073430412027	3	FACETS	0.967	0.898	1	0.483	0.449	0.519	CLONAL	1	TRUE	1	0.562073430412027	3		427	1009	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922875	39922875	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1381182530	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	377	509	0	ENST00000378444.4:c.3833G>C	p.Ser1278Thr	p.S1278T	ENST00000378444	NM_001123385.1	1278	aGt/aCt	8/15	0.436655726010034	4	FACETS	0.791	0.75	0.832			1	SUBCLONAL	2	TRUE	NA	0.562073430412027	4		509	1325	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930322	39930322	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	446	631	2	ENST00000378444.4:c.3142C>A	p.Pro1048Thr	p.P1048T	ENST00000378444	NM_001123385.1	1048	Cca/Aca	6/15	0.436655726010034	4	FACETS	0.906	0.864	0.948			1	CLONAL	2	TRUE	NA	0.562073430412027	4		633	1368	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934052	39934052	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	433	552	0	ENST00000378444.4:c.547G>T	p.Gly183Cys	p.G183C	ENST00000378444	NM_001123385.1	183	Ggt/Tgt	4/15	0.436655726010034	4	FACETS	0.832	0.793	0.872			1	CLONAL	2	TRUE	NA	0.562073430412027	4		552	1446	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922878	44922878	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs987956112	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	606	574	0	ENST00000377967.4:c.1739G>T	p.Ser580Ile	p.S580I	ENST00000377967	NM_021140.2	580	aGc/aTc	16/29	0.436655726010034	4	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.562073430412027	4		574	1553	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528126	29528127	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	301	365	0	ENST00000356175.3:c.1135dup	p.Cys379LeufsTer17	p.C379Lfs*17	ENST00000356175	NM_000267.3	378	-/T	10/57	0.432949360130103	3	FACETS	0.836	0.797	0.874	1	0.993	1	CLONAL	3	TRUE	1	0.562073430412027	3		365	547	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532710	187532710	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1010116749	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	415	496	0	ENST00000441802.2:c.9683del	p.Pro3228LeufsTer42	p.P3228Lfs*42	ENST00000441802	NM_005245.3	3228	cCt/ct	14/27	0.562073430412027	2	FACETS	0.914	0.876	0.951	0.914	0.876	0.951	CLONAL	2	TRUE	0	0.562073430412027	2		496	808	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106670	27106671	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	T	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	372	311	1	ENST00000324856.7:c.6281_6282delinsT	p.Cys2094PhefsTer41	p.C2094Ffs*41	ENST00000324856	NM_006015.4	2094	tGC/tT	20/20	0.296064141715154	5	FACETS	0.844	0.804	0.886	0.844	0.804	0.886	INDETERMINATE	3	TRUE	2	0.562073430412027	5		312	963	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94209494	94209495	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0006713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	533	473	0	ENST00000323929.3:c.619_620delinsTT	p.Glu207Leu	p.E207L	ENST00000323929	NM_005591.3	207	GAg/TTg	7/20	0.562073430412027	3	FACETS	0.956	0.926	0.986	0.956	0.926	0.986	CLONAL	3	TRUE	0	0.562073430412027	3		473	847	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006713-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	54	1032	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.858	0.734	0.994	0.858	0.734	0.994	CLONAL	1	TRUE	1	0.27	2		1032	466	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913315	NA	P-0006713-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	79	360	0	ENST00000326873.7:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000326873	NM_000455.4	194	Gac/Tac	4/10	0.230452803292025	1	FACETS	0.855	0.753	0.965	0.855	0.753	0.965	CLONAL	1	TRUE	0	0.27	1		360	592	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4095426	4095426	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006713-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	86	392	0	ENST00000262948.5:c.1006G>T	p.Gly336Cys	p.G336C	ENST00000262948	NM_030662.3	336	Ggt/Tgt	9/11	0.230452803292025	1	FACETS	0.936	0.829	1	0.936	0.829	1	CLONAL	1	TRUE	0	0.27	1		392	589	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600424	10600424	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006713-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	73	452	0	ENST00000171111.5:c.1431del	p.Phe478LeufsTer22	p.F478Lfs*22	ENST00000171111	NM_203500.1	477	ggC/gg	4/6	0.230452803292025	1	FACETS	0.651	0.569	0.74	0.651	0.569	0.74	SUBCLONAL	1	TRUE	0	0.27	1		452	718	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792017	42792017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007009-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	648	553	0	ENST00000575354.2:c.821G>A	p.Arg274Gln	p.R274Q	ENST00000575354	NM_015125.3	274	cGa/cAa	6/20	0.813378316512028	2	FACETS	0.916	0.894	0.937	0.916	0.894	0.937	CLONAL	2	TRUE	0	0.830448542277811	2		553	852	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243050	105243051	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCAGCGGATGATGAAGGTGTTGGGCCGGG	novel	NA	P-0007009-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	453	560	0	ENST00000349310.3:c.203_232dup	p.Pro68_Cys77dup	p.P68_C77dup	ENST00000349310	NM_001014432.1	68	ctg/cCCCGGCCCAACACCTTCATCATCCGCTGCCtg	5/15	0.546078778261424	4	FACETS	1	0.994	1	0.435	0.415	0.456	CLONAL	1	TRUE	1	0.830448542277811	4		560	1530	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0007418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	231	462	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.312262018640805	3	FACETS	0.931	0.875	0.987	1	0.992	1	CLONAL	3	TRUE	1	0.348095255596554	3		462	558	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032069	26032069	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	187	637	0	ENST00000244661.2:c.220G>C	p.Glu74Gln	p.E74Q	ENST00000244661	NM_003537.3	74	Gaa/Caa	1/1	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.348095255596554	2		637	975	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944720	206944720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	63	190	0	ENST00000423557.1:c.206C>T	p.Ser69Phe	p.S69F	ENST00000423557	NM_000572.2	69	tCc/tTc	2/5	0.348095255596554	7	FACETS	1	0.896	1	0.174	0.15	0.2	CLONAL	1	TRUE	1	0.348095255596554	7		190	649	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086073	16086073	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	132	223	0	ENST00000281043.3:c.1249G>C	p.Ala417Pro	p.A417P	ENST00000281043	NM_005378.4	417	Gcc/Ccc	3/3	0.312262018640805	3	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	1	0.348095255596554	3		223	433	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457222	89457222	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	115	256	0	ENST00000336596.2:c.1703G>C	p.Cys568Ser	p.C568S	ENST00000336596	NM_005233.5	568	tGt/tCt	9/17	0.348095255596554	5	FACETS	0.921	0.833	1			1	CLONAL	2	TRUE	NA	0.348095255596554	5		256	546	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956693	93956693	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	200	448	0	ENST00000369303.4:c.2543C>G	p.Ala848Gly	p.A848G	ENST00000369303	NM_004440.3	848	gCa/gGa	15/17	0.305287484437739	0	FACETS	0.834	0.782	0.887			1	CLONAL	2	TRUE	0	0.348095255596554	0		448	449	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852183	63852183	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	69	292	0	ENST00000279873.7:c.2961G>T	p.Arg987Ser	p.R987S	ENST00000279873	NM_032199.2	987	agG/agT	10/10	0.347314622973095	1	FACETS	0.969	0.85	1	0.969	0.85	1	CLONAL	1	TRUE	0	0.348095255596554	1		292	338	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444938	49444938	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	104	131	0	ENST00000301067.7:c.2528C>T	p.Ser843Phe	p.S843F	ENST00000301067	NM_003482.3	843	tCc/tTc	10/54	0.204887212352889	5	FACETS	0.975	0.884	1	0.975	0.884	1	INDETERMINATE	3	TRUE	2	0.348095255596554	5		131	311	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117417	115117417	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	96	264	0	ENST00000257566.3:c.757C>A	p.His253Asn	p.H253N	ENST00000257566	NM_016569.3	253	Cac/Aac	4/8	0.312262018640805	3	FACETS	0.845	0.759	0.936	0.845	0.759	0.936	CLONAL	2	TRUE	1	0.348095255596554	3		264	383	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2218080	2218080	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	252	378	1	ENST00000326181.6:c.142G>T	p.Asp48Tyr	p.D48Y	ENST00000326181	NM_032271.2	48	Gac/Tac	4/21	0.347738299148189	4	FACETS	1	0.979	1			1	CLONAL	2	TRUE	NA	0.348095255596554	4		379	888	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733244	40733244	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	39	206	0	ENST00000373198.4:c.3562C>T	p.Gln1188Ter	p.Q1188*	ENST00000373198	NM_133170.3	1188	Cag/Tag	26/32	NA	2	FACETS	0.616	0.511	0.731			1	INDETERMINATE	1	TRUE	NA	0.348095255596554	2		206	364	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20153891	20153891	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	62	255	0	ENST00000379607.5:c.169A>G	p.Arg57Gly	p.R57G	ENST00000379607	NM_001412.3	57	Agg/Ggg	3/7	0.348095255596554	1	FACETS	0.937	0.815	1	0.937	0.815	1	CLONAL	1	TRUE	0	0.348095255596554	1		255	314	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649664	48649664	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	98	448	0	ENST00000376670.3:c.148C>A	p.Pro50Thr	p.P50T	ENST00000376670	NM_002049.3	50	Ccg/Acg	2/6	0.348095255596554	1	FACETS	0.919	0.823	1	0.919	0.823	1	CLONAL	1	TRUE	0	0.348095255596554	1		448	506	SUCCESS
AR	367	MSKCC	GRCh37	X	66937377	66937377	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs137852600	NA	P-0007418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	94	444	0	ENST00000374690.3:c.2231G>T	p.Gly744Val	p.G744V	ENST00000374690	NM_000044.3	744	gGg/gTg	5/8	0.348095255596554	1	FACETS	0.848	0.757	0.945	0.848	0.757	0.945	CLONAL	1	TRUE	0	0.348095255596554	1		444	526	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445045	89445045	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	133	317	0	ENST00000336596.2:c.1365del	p.Leu455PhefsTer33	p.L455Ffs*33	ENST00000336596	NM_005233.5	455	ttG/tt	6/17	0.348095255596554	5	FACETS	0.802	0.729	0.878			1	CLONAL	2	TRUE	NA	0.348095255596554	5		317	725	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161325	55161326	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0007418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	41	241	0	ENST00000257290.5:c.3156_3157delinsTT	p.Gly1053Cys	p.G1053C	ENST00000257290	NM_006206.4	1052	acGGgt/acTTgt	23/23	0.347314622973095	1	FACETS	0.71	0.595	0.837	0.71	0.595	0.837	SUBCLONAL	1	TRUE	0	0.348095255596554	1		241	274	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414241	32414242	+	missense_variant	Missense_Mutation	DNP	TG	TG	CT	novel	NA	P-0007418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	154	357	0	ENST00000332351.3:c.1309_1310delinsAG	p.Gln437Arg	p.Q437R	ENST00000332351	NM_024426.4	437	CAg/AGg	8/10	0.288600336566046	3	FACETS	0.827	0.76	0.897			1	CLONAL	2	TRUE	NA	0.348095255596554	3		357	628	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0007966-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	236	473	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.945	0.891	1	0.945	0.891	1	CLONAL	1	TRUE	1	0.924826485911524	2		473	540	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651292	52651292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007966-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	337	563	0	ENST00000394830.3:c.1804G>A	p.Glu602Lys	p.E602K	ENST00000394830	NM_018313.4	602	Gag/Aag	15/30	1	2	FACETS	0.981	0.934	1	0.981	0.934	1	CLONAL	1	TRUE	1	0.924826485911524	2		563	743	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246498752	246498752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1306095883	NA	P-0007966-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	383	662	0	ENST00000388985.4:c.253C>T	p.Arg85Trp	p.R85W	ENST00000388985		85	Cgg/Tgg	3/12	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.924826485911524	2		662	822	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859827	151859827	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007966-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	210	468	0	ENST00000262189.6:c.10835del	p.Arg3612LysfsTer18	p.R3612Kfs*18	ENST00000262189	NM_170606.2	3612	aGa/aa	43/59	1	2	FACETS	0.867	0.812	0.922	0.867	0.812	0.922	CLONAL	1	TRUE	1	0.924826485911524	2		468	524	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007064	152007064	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0007966-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	298	420	0	ENST00000262189.6:c.836C>G	p.Ser279Ter	p.S279*	ENST00000262189	NM_170606.2	279	tCa/tGa	6/59	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.924826485911524	2		420	638	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0010077-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	220	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.385276742666943	1	FACETS	0.74	0.695	0.785	0.74	0.695	0.785	INDETERMINATE	1	TRUE	0	0.734076395461854	1		434	513	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0010077-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	160	419	0	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	0.385276742666943	1	FACETS	0.637	0.59	0.685	0.637	0.59	0.685	INDETERMINATE	1	TRUE	0	0.734076395461854	1		419	433	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061450	38061450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010077-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	180	568	1	ENST00000250448.2:c.539C>T	p.Thr180Ile	p.T180I	ENST00000250448	NM_004496.3	180	aCc/aTc	2/2	0.385276742666943	1	FACETS	0.416	0.384	0.448	0.416	0.384	0.448	INDETERMINATE	1	TRUE	0	0.734076395461854	1		569	747	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404767	404767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010077-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	242	557	0	ENST00000399788.2:c.4427C>T	p.Ser1476Phe	p.S1476F	ENST00000399788	NM_001042603.1	1476	tCt/tTt	26/28	NA	2	FACETS	0.984	0.925	1			1	INDETERMINATE	1	TRUE	NA	0.734076395461854	2		557	670	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720342	43720342	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1220444634	NA	P-0010077-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	281	581	0	ENST00000382044.4:c.3700C>T	p.Gln1234Ter	p.Q1234*	ENST00000382044	NM_001141980.1	1234	Cag/Tag	18/28	0.734076395461854	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.734076395461854	1		581	480	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348337	89348337	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010077-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	252	911	0	ENST00000301030.4:c.4613C>G	p.Ala1538Gly	p.A1538G	ENST00000301030	NM_001256183.1	1538	gCa/gGa	9/13	0.734076395461854	1	FACETS	0.981	0.933	1	0.981	0.933	1	CLONAL	1	TRUE	0	0.734076395461854	1		911	443	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160644	56160644	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010077-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	248	375	0	ENST00000399503.3:c.919del	p.Arg307ValfsTer5	p.R307Vfs*5	ENST00000399503	NM_005921.1	306	cgC/cg	4/20	0.305598707327231	3	FACETS	1	0.992	1	0.697	0.655	0.739	INDETERMINATE	1	TRUE	1	0.734076395461854	3		375	663	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178466	56178466	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010077-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	237	392	0	ENST00000399503.3:c.3439del	p.Val1147Ter	p.V1147*	ENST00000399503	NM_005921.1	1147	Gta/ta	14/20	0.305598707327231	3	FACETS	1	0.993	1	0.748	0.704	0.793	INDETERMINATE	1	TRUE	1	0.734076395461854	3		392	590	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158441	108158441	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	108	289	0	ENST00000278616.4:c.4109+1del		p.G1370fs	ENST00000278616	NM_000051.3	1370	Ggg/gg	27/63	1	2	FACETS	0.992	0.897	1	0.992	0.897	1	CLONAL	1	TRUE	1	0.532576224398445	2		289	409	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966040	25966040	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367562789	NA	P-0010180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	200	622	0	ENST00000435504.4:c.3166G>A	p.Glu1056Lys	p.E1056K	ENST00000435504		1056	Gaa/Aaa	13/13	1	2	FACETS	0.954	0.886	1	0.954	0.886	1	CLONAL	1	TRUE	1	0.532576224398445	2		622	787	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2119506	2119506	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs759746608	NA	P-0010180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	113	422	0	ENST00000349721.2:c.3733C>T	p.Arg1245Ter	p.R1245*	ENST00000349721	NM_003070.3	1245	Cga/Tga	26/34	1	2	FACETS	0.893	0.808	0.982	0.893	0.808	0.982	CLONAL	1	TRUE	1	0.532576224398445	2		422	475	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010363-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	10	387	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		387	302	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0010472-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	48	205	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.25	2		205	363	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589586	67589591	+	inframe_deletion	In_Frame_Del	DEL	ATGAAT	ATGAAT	-	novel	NA	P-0010472-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	27	296	0	ENST00000274335.5:c.1351_1356del	p.Glu451_Tyr452del	p.E451_Y452del	ENST00000274335		450	cATGAATat/cat	10/15	1	2	FACETS	0.722	0.576	0.889	0.722	0.576	0.889	SUBCLONAL	1	TRUE	1	0.25	2		296	299	SUCCESS
AR	367	MSKCC	GRCh37	X	66943532	66943532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143040492	NA	P-0010472-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	56	558	0	ENST00000374690.3:c.2612C>T	p.Ala871Val	p.A871V	ENST00000374690	NM_000044.3	871	gCg/gTg	8/8	1	2	FACETS	0.786	0.673	0.909	0.786	0.673	0.909	CLONAL	1	TRUE	1	0.25	2		558	570	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813023	89813023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142833057	NA	P-0010472-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	35	647	0	ENST00000389301.3:c.3482C>T	p.Thr1161Met	p.T1161M	ENST00000389301	NM_000135.2	1161	aCg/aTg	35/43	1	2	FACETS	0.524	0.429	0.632	0.524	0.429	0.632	SUBCLONAL	1	TRUE	1	0.25	2		647	534	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619937	21619937	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010472-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	38	711	0	ENST00000382592.4:c.229T>A	p.Leu77Met	p.L77M	ENST00000382592	NM_014572.2	77	Ttg/Atg	2/8	1	2	FACETS	0.441	0.363	0.528	0.441	0.363	0.528	SUBCLONAL	1	TRUE	1	0.25	2		711	690	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522789	67522789	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010472-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	82	634	0	ENST00000274335.5:c.287del	p.Pro96LeufsTer18	p.P96Lfs*18	ENST00000274335		96	Cct/ct	1/15	1	2	FACETS	0.965	0.851	1	0.965	0.851	1	CLONAL	1	TRUE	1	0.25	2		634	680	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	113	343	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.468216876932365	2		343	442	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	152	446	1	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.192440137529007	3	FACETS	0.869	0.802	0.938	0.869	0.802	0.938	INDETERMINATE	2	TRUE	1	0.468216876932365	3		447	461	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	164	542	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.192440137529007	3	FACETS	1	0.978	1	0.585	0.538	0.634	INDETERMINATE	1	TRUE	1	0.468216876932365	3		542	739	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	42	733	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.185	0.153	0.22	0.185	0.153	0.22	SUBCLONAL	1	TRUE	1	0.468216876932365	2		733	970	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060925	38060925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1388855660	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	133	599	0	ENST00000250448.2:c.1064C>T	p.Ser355Leu	p.S355L	ENST00000250448	NM_004496.3	355	tCa/tTa	2/2	1	2	FACETS	0.995	0.907	1	0.995	0.907	1	CLONAL	1	TRUE	1	0.468216876932365	2		599	571	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101186	27101186	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	401	750	0	ENST00000324856.7:c.4468G>A	p.Glu1490Lys	p.E1490K	ENST00000324856	NM_006015.4	1490	Gag/Aag	18/20	0.468216876932365	3	FACETS	0.976	0.93	1	0.976	0.93	1	CLONAL	2	TRUE	1	0.468216876932365	3		750	1083	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685536	29685536	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1131691074	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	127	478	0	ENST00000356175.3:c.7946C>A	p.Ser2649Ter	p.S2649*	ENST00000356175	NM_000267.3	2649	tCa/tAa	54/57	1	2	FACETS	0.854	0.776	0.936	0.854	0.776	0.936	CLONAL	1	TRUE	1	0.468216876932365	2		478	635	SUCCESS
H3C13	653604	MSKCC	GRCh37	1	149784830	149784830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	100	225	0	ENST00000331491.1:c.407C>T	p.Ala136Val	p.A136V	ENST00000331491	NM_001123375.2	136	gCc/gTc	1/1	0.468216876932365	3	FACETS	1	0.972	1	0.619	0.556	0.684	CLONAL	1	TRUE	1	0.468216876932365	3		225	426	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045930	26045930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	356	533	0	ENST00000540144.1:c.292G>A	p.Glu98Lys	p.E98K	ENST00000540144	NM_003531.2	98	Gag/Aag	1/1	0.468216876932365	3	FACETS	0.852	0.814	0.891	0.852	0.814	0.891	CLONAL	3	TRUE	0	0.468216876932365	3		533	734	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100384	27100384	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	272	591	1	ENST00000324856.7:c.4096C>T	p.Gln1366Ter	p.Q1366*	ENST00000324856	NM_006015.4	1366	Cag/Tag	17/20	0.468216876932365	3	FACETS	0.863	0.812	0.914	0.863	0.812	0.914	CLONAL	2	TRUE	1	0.468216876932365	3		592	831	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101181	27101181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	408	737	0	ENST00000324856.7:c.4463C>T	p.Ser1488Leu	p.S1488L	ENST00000324856	NM_006015.4	1488	tCa/tTa	18/20	0.468216876932365	3	FACETS	0.982	0.937	1	0.982	0.937	1	CLONAL	2	TRUE	1	0.468216876932365	3		737	1095	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550857	150550857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	208	554	0	ENST00000369026.2:c.799C>T	p.Leu267Phe	p.L267F	ENST00000369026	NM_021960.4	267	Ctc/Ttc	2/3	0.468216876932365	3	FACETS	1	0.976	1	0.557	0.517	0.599	CLONAL	1	TRUE	1	0.468216876932365	3		554	984	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265468	198265468	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	124	494	0	ENST00000335508.6:c.2689C>G	p.Leu897Val	p.L897V	ENST00000335508	NM_012433.2	897	Ctt/Gtt	18/25	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.468216876932365	2		494	465	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55987340	55987340	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	106	462	0	ENST00000263923.4:c.85C>G	p.Leu29Val	p.L29V	ENST00000263923	NM_002253.2	29	Ctt/Gtt	2/30	1	2	FACETS	0.982	0.885	1	0.982	0.885	1	CLONAL	1	TRUE	1	0.468216876932365	2		462	461	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495394	149495394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	95	855	0	ENST00000261799.4:c.3253G>A	p.Glu1085Lys	p.E1085K	ENST00000261799	NM_002609.3	1085	Gag/Aag	23/23	0.26086761888784	1	FACETS	0.33	0.293	0.37	0.33	0.293	0.37	INDETERMINATE	1	TRUE	0	0.468216876932365	1		855	941	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999192	100999192	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	223	834	3	ENST00000325455.5:c.610C>A	p.His204Asn	p.H204N	ENST00000325455	NM_001202474.3	204	Cac/Aac	1/8	0.468216876932365	2	FACETS	1	0.978	1	0.556	0.519	0.595	CLONAL	1	TRUE	0	0.468216876932365	2		837	856	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199839	108199839	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	172	316	0	ENST00000278616.4:c.7181C>G	p.Ser2394Ter	p.S2394*	ENST00000278616	NM_000051.3	2394	tCa/tGa	49/63	0.468216876932365	2	FACETS	0.967	0.902	1	0.967	0.902	1	CLONAL	2	TRUE	0	0.468216876932365	2		316	380	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253212	133253212	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	304	670	0	ENST00000320574.5:c.829G>C	p.Glu277Gln	p.E277Q	ENST00000320574	NM_006231.2	277	Gag/Cag	9/49	0.260028809180023	3	FACETS	0.821	0.775	0.868	0.821	0.775	0.868	INDETERMINATE	2	TRUE	1	0.468216876932365	3		670	976	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422137	81422137	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	175	612	0	ENST00000298171.2:c.113G>C	p.Arg38Thr	p.R38T	ENST00000298171	NM_000369.2	38	aGa/aCa	1/10	1	2	FACETS	0.994	0.917	1	0.994	0.917	1	CLONAL	1	TRUE	1	0.468216876932365	2		612	752	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988785	41988785	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	157	574	0	ENST00000219905.7:c.1577C>G	p.Ser526Ter	p.S526*	ENST00000219905	NM_001164273.1	526	tCa/tGa	3/24	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.468216876932365	2		574	653	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99473513	99473513	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	68	326	0	ENST00000268035.6:c.2935G>C	p.Glu979Gln	p.E979Q	ENST00000268035	NM_000875.3	979	Gag/Cag	15/21	1	2	FACETS	0.663	0.579	0.754	0.663	0.579	0.754	SUBCLONAL	1	TRUE	1	0.468216876932365	2		326	438	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226298	2226298	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	487	830	0	ENST00000326181.6:c.1911G>C	p.Gln637His	p.Q637H	ENST00000326181	NM_032271.2	637	caG/caC	20/21	0.468216876932365	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.468216876932365	2		830	1026	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650719	67650719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1131691283	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	305	773	0	ENST00000264010.4:c.1024C>T	p.Arg342Cys	p.R342C	ENST00000264010	NM_006565.3	342	Cgt/Tgt	5/12	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.468216876932365	2		773	1091	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829005	72829005	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	296	784	0	ENST00000268489.5:c.7576C>T	p.Gln2526Ter	p.Q2526*	ENST00000268489	NM_006885.3	2526	Cag/Tag	9/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.468216876932365	2		784	1059	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831165	72831165	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	207	608	0	ENST00000268489.5:c.5416G>C	p.Glu1806Gln	p.E1806Q	ENST00000268489	NM_006885.3	1806	Gag/Cag	9/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.468216876932365	2		608	766	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831659	72831659	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	88	695	0	ENST00000268489.5:c.4922A>G	p.Asn1641Ser	p.N1641S	ENST00000268489	NM_006885.3	1641	aAc/aGc	9/10	1	2	FACETS	0.429	0.379	0.482	0.429	0.379	0.482	SUBCLONAL	1	TRUE	1	0.468216876932365	2		695	877	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350674	89350674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	310	934	0	ENST00000301030.4:c.2276G>A	p.Arg759Lys	p.R759K	ENST00000301030	NM_001256183.1	759	aGa/aAa	9/13	0.17816994941946	2	FACETS	1	0.993	1	0.676	0.638	0.714	INDETERMINATE	1	TRUE	0	0.468216876932365	2		934	980	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89869695	89869695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	273	699	0	ENST00000389301.3:c.764G>A	p.Arg255Lys	p.R255K	ENST00000389301	NM_000135.2	255	aGa/aAa	8/43	0.17816994941946	2	FACETS	1	0.991	1	0.648	0.609	0.687	INDETERMINATE	1	TRUE	0	0.468216876932365	2		699	900	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761214	59761214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1490736110	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	200	746	0	ENST00000259008.2:c.3193G>A	p.Gly1065Arg	p.G1065R	ENST00000259008	NM_032043.2	1065	Gga/Aga	20/20	1	2	FACETS	0.958	0.888	1	0.958	0.888	1	CLONAL	1	TRUE	1	0.468216876932365	2		746	892	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213956	2213956	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371142941	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	84	715	0	ENST00000398665.3:c.1768C>T	p.Arg590Cys	p.R590C	ENST00000398665	NM_032482.2	590	Cgc/Tgc	18/28	1	2	FACETS	0.384	0.338	0.433	0.384	0.338	0.433	SUBCLONAL	1	TRUE	1	0.468216876932365	2		715	935	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274178	18274178	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	172	729	0	ENST00000222254.8:c.1396G>C	p.Glu466Gln	p.E466Q	ENST00000222254	NM_005027.3	466	Gag/Cag	11/16	1	2	FACETS	0.775	0.713	0.84	0.775	0.713	0.84	SUBCLONAL	1	TRUE	1	0.468216876932365	2		729	948	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44894227	44894227	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	120	466	0	ENST00000377967.4:c.616G>T	p.Glu206Ter	p.E206*	ENST00000377967	NM_021140.2	206	Gaa/Taa	7/29	0.26086761888784	1	FACETS	0.946	0.861	1	0.946	0.861	1	INDETERMINATE	1	TRUE	0	0.468216876932365	1		466	415	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776973	76776973	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	21	473	0	ENST00000373344.5:c.6979C>G	p.Leu2327Val	p.L2327V	ENST00000373344	NM_000489.3	2327	Ctc/Gtc	33/35	0.223876014395189	0	FACETS	0.116	0.089	0.148			1	INDETERMINATE	1	TRUE	0	0.468216876932365	0		473	411	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276289	15276301	+	frameshift_variant	Frame_Shift_Del	DEL	CGGGCATCCAAGT	CGGGCATCCAAGT	-	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	72	752	0	ENST00000263388.2:c.5693_5705del	p.Asp1898AlafsTer9	p.D1898Afs*9	ENST00000263388	NM_000435.2	1898	gACTTGGATGCCCGc/gc	31/33	1	2	FACETS	0.314	0.274	0.359	0.314	0.274	0.359	SUBCLONAL	1	TRUE	1	0.468216876932365	2		752	978	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468080	50468080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	36	627	0	ENST00000331340.3:c.1315C>T	p.Arg439Cys	p.R439C	ENST00000331340	NM_006060.4	439	Cgc/Tgc	8/8	0.324661084054904	2	FACETS	0.228	0.187	0.275	0.114	0.093	0.138	SUBCLONAL	1	TRUE	0	0.468216876932365	2		627	674	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163848	32163848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1210630301	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	127	607	0	ENST00000375023.3:c.5378G>A	p.Arg1793Gln	p.R1793Q	ENST00000375023	NM_004557.3	1793	cGa/cAa	30/30	0.17816994941946	2	FACETS	0.695	0.629	0.763	0.347	0.314	0.382	INDETERMINATE	1	TRUE	0	0.468216876932365	2		607	781	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224149	98224149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531947455	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	43	331	0	ENST00000331920.6:c.2692G>A	p.Asp898Asn	p.D898N	ENST00000331920	NM_000264.3	898	Gac/Aac	16/24	0.468216876932365	2	FACETS	0.398	0.333	0.471	0.199	0.166	0.236	SUBCLONAL	1	TRUE	0	0.468216876932365	2		331	461	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441477	52441477	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	87	462	0	ENST00000460680.1:c.376-1G>A		p.X126_splice	ENST00000460680	NM_004656.3	126			1	2	FACETS	0.636	0.564	0.713	0.636	0.564	0.713	SUBCLONAL	1	TRUE	1	0.468216876932365	2		462	584	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116170	67116170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761036715	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	220	615	0	ENST00000412916.2:c.454G>A	p.Glu152Lys	p.E152K	ENST00000412916		152	Gaa/Aaa	5/6	1	2	FACETS	0.992	0.924	1	0.992	0.924	1	CLONAL	1	TRUE	1	0.468216876932365	2		615	947	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748747	43748747	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	221	879	0	ENST00000382044.4:c.2059G>T	p.Glu687Ter	p.E687*	ENST00000382044	NM_001141980.1	687	Gaa/Taa	12/28	1	2	FACETS	0.912	0.849	0.978	0.912	0.849	0.978	CLONAL	1	TRUE	1	0.468216876932365	2		879	1035	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402485	139402485	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1212292354	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	95	881	0	ENST00000277541.6:c.3432C>G	p.Asp1144Glu	p.D1144E	ENST00000277541	NM_017617.3	1144	gaC/gaG	21/34	0.468216876932365	2	FACETS	0.328	0.291	0.368	0.164	0.145	0.184	SUBCLONAL	1	TRUE	0	0.468216876932365	2		881	1236	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288765	33288765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761608312	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	51	599	1	ENST00000374542.5:c.787C>T	p.Arg263Cys	p.R263C	ENST00000374542	NM_001141970.1	263	Cgc/Tgc	3/8	1	2	FACETS	0.294	0.249	0.344	0.294	0.249	0.344	SUBCLONAL	1	TRUE	1	0.468216876932365	2		600	740	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708465	43708465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	88	723	0	ENST00000382044.4:c.4831G>A	p.Glu1611Lys	p.E1611K	ENST00000382044	NM_001141980.1	1611	Gaa/Aaa	22/28	1	2	FACETS	0.431	0.381	0.484	0.431	0.381	0.484	SUBCLONAL	1	TRUE	1	0.468216876932365	2		723	873	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493685	56493685	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	149	636	0	ENST00000267101.3:c.3001G>C	p.Glu1001Gln	p.E1001Q	ENST00000267101	NM_001982.3	1001	Gag/Cag	25/28	0.149622248319979	5	FACETS	1	0.974	1	0.388	0.354	0.424	INDETERMINATE	1	TRUE	2	0.468216876932365	5		636	930	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375392	118375392	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	127	429	0	ENST00000534358.1:c.8785G>T	p.Glu2929Ter	p.E2929*	ENST00000534358	NM_005933.3	2929	Gag/Tag	27/36	0.468216876932365	2	FACETS	1	0.969	1	0.569	0.518	0.621	CLONAL	1	TRUE	0	0.468216876932365	2		429	477	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493730	56493730	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	167	711	0	ENST00000267101.3:c.3046G>C	p.Glu1016Gln	p.E1016Q	ENST00000267101	NM_001982.3	1016	Gaa/Caa	25/28	0.149622248319979	5	FACETS	1	0.974	1	0.383	0.352	0.417	INDETERMINATE	1	TRUE	2	0.468216876932365	5		711	1056	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926284	112926284	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	68	515	0	ENST00000351677.2:c.1417G>T	p.Asp473Tyr	p.D473Y	ENST00000351677	NM_002834.3	473	Gat/Tat	12/16	0.149622248319979	5	FACETS	0.498	0.432	0.571	0.166	0.144	0.191	INDETERMINATE	1	TRUE	2	0.468216876932365	5		515	992	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28963977	28963977	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	42	426	1	ENST00000282397.4:c.1925A>G	p.Tyr642Cys	p.Y642C	ENST00000282397	NM_002019.4	642	tAc/tGc	13/30	1	2	FACETS	0.306	0.254	0.363	0.306	0.254	0.363	SUBCLONAL	1	TRUE	1	0.468216876932365	2		427	587	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244038	5244038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771439798	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	75	878	0	ENST00000357368.4:c.1444G>A	p.Asp482Asn	p.D482N	ENST00000357368	NM_002850.3	482	Gac/Aac	11/38	1	2	FACETS	0.294	0.257	0.335	0.294	0.257	0.335	SUBCLONAL	1	TRUE	1	0.468216876932365	2		878	1089	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911525	134911525	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	72	649	0	ENST00000398015.3:c.1990G>T	p.Asp664Tyr	p.D664Y	ENST00000398015	NM_004441.4	664	Gac/Tac	11/16	0.192440137529007	3	FACETS	0.399	0.348	0.455	0.2	0.174	0.228	INDETERMINATE	1	TRUE	1	0.468216876932365	3		649	951	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158626	26158626	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	26	249	0	ENST00000289316.2:c.229G>T	p.Glu77Ter	p.E77*	ENST00000289316	NM_138720.2	77	Gag/Tag	1/2	0.468216876932365	3	FACETS	0.348	0.275	0.431	0.116	0.091	0.144	SUBCLONAL	1	TRUE	0	0.468216876932365	3		249	394	SUCCESS
AR	367	MSKCC	GRCh37	X	66765406	66765406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1214854933	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	44	767	0	ENST00000374690.3:c.418G>A	p.Ala140Thr	p.A140T	ENST00000374690	NM_000044.3	140	Gcc/Acc	1/8	0.223876014395189	0	FACETS	0.129	0.108	0.153			1	INDETERMINATE	1	TRUE	0	0.468216876932365	0		767	772	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945136	151945136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1443491328	NA	P-0010531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	18	211	0	ENST00000262189.6:c.2383G>A	p.Asp795Asn	p.D795N	ENST00000262189	NM_170606.2	795	Gac/Aac	14/59	0.324661084054904	2	FACETS	0.386	0.292	0.497	0.193	0.146	0.249	SUBCLONAL	1	TRUE	0	0.468216876932365	2		211	199	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0012098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	685	616	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	2	FALSE	NA	0.591465304604521	2		616	1048	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087578	27087578	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	49	519	1	ENST00000324856.7:c.2152G>T	p.Ala718Ser	p.A718S	ENST00000324856	NM_006015.4	718	Gca/Tca	5/20	0.351106557889734	4	FACETS	0.288	0.243	0.338	0.072	0.06	0.085	INDETERMINATE	1	FALSE	0	0.591465304604521	4		520	915	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796587	42796587	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1826	102	612	2	ENST00000575354.2:c.3144C>A	p.Ser1048Arg	p.S1048R	ENST00000575354	NM_015125.3	1048	agC/agA	13/20	0.591465304604521	6	FACETS	0.391	0.347	0.437			1	SUBCLONAL	1	FALSE	NA	0.591465304604521	6		614	1928	SUCCESS
ATR	545	MSKCC	GRCh37	3	142232351	142232351	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	28	370	0	ENST00000350721.4:c.4633C>T	p.Gln1545Ter	p.Q1545*	ENST00000350721	NM_001184.3	1545	Cag/Tag	26/47	0.601678430696029	3	FACETS	0.501	0.402	0.612	0.167	0.134	0.204	SUBCLONAL	1	FALSE	0	0.591465304604521	3		370	245	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242482	+	protein_altering_variant	In_Frame_Del	DEL	GGAATTAAGAGAAGCAAC	GGAATTAAGAGAAGCAAC	AAT	novel	NA	P-0012098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	194	380	1	ENST00000275493.2:c.2235_2252delinsAAT	p.Glu746_Thr751delinsIle	p.E746_T751delinsI	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCAACa/aaAATa	19/28	0.591465304604521	7	FACETS	0.92	0.852	0.99			1	CLONAL	2	FALSE	NA	0.591465304604521	7		381	884	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012663-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	53	343	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.386386386461617	2		343	228	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0012663-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	67	473	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.671	0.584	0.765	0.671	0.584	0.765	SUBCLONAL	1	TRUE	1	0.386386386461617	2		473	517	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179050	123179050	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012663-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	107	400	0	ENST00000218089.9:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000218089	NM_001042749.1	167	Cag/Tag	8/35	1	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.386386386461617	1		400	323	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057788	27057788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748935625	NA	P-0012663-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	177	869	0	ENST00000324856.7:c.1496C>T	p.Ser499Leu	p.S499L	ENST00000324856	NM_006015.4	499	tCg/tTg	3/20	1	2	FACETS	0.819	0.754	0.888	0.819	0.754	0.888	CLONAL	1	TRUE	1	0.386386386461617	2		869	1118	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087360	27087360	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012663-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	106	523	0	ENST00000324856.7:c.1934C>A	p.Ser645Ter	p.S645*	ENST00000324856	NM_006015.4	645	tCa/tAa	5/20	1	2	FACETS	0.795	0.713	0.882	0.795	0.713	0.882	SUBCLONAL	1	TRUE	1	0.386386386461617	2		523	690	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738853	145738853	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012663-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	112	875	0	ENST00000428558.2:c.2212A>G	p.Lys738Glu	p.K738E	ENST00000428558	NM_004260.3	738	Aaa/Gaa	14/22	1	2	FACETS	0.681	0.612	0.754	0.681	0.612	0.754	SUBCLONAL	1	TRUE	1	0.386386386461617	2		875	851	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691139	18691139	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012663-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	101	576	0	ENST00000266497.5:c.3250G>C	p.Glu1084Gln	p.E1084Q	ENST00000266497		1084	Gag/Cag	23/31	1	2	FACETS	0.935	0.838	1	0.935	0.838	1	CLONAL	1	TRUE	1	0.386386386461617	2		576	559	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246543	46246543	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012663-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	80	295	0	ENST00000334344.6:c.4637A>G	p.Asn1546Ser	p.N1546S	ENST00000334344	NM_152641.2	1546	aAt/aGt	15/21	0.103589322276366	3	FACETS	1	0.913	1	0.52	0.459	0.585	INDETERMINATE	1	TRUE	1	0.386386386461617	3		295	475	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41962061	41962061	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012663-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	73	567	1	ENST00000219905.7:c.969G>C	p.Lys323Asn	p.K323N	ENST00000219905	NM_001164273.1	323	aaG/aaC	2/24	1	2	FACETS	0.568	0.497	0.645	0.568	0.497	0.645	SUBCLONAL	1	TRUE	1	0.386386386461617	2		568	665	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820624	3820624	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012663-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	128	795	1	ENST00000262367.5:c.2827C>T	p.Gln943Ter	p.Q943*	ENST00000262367	NM_004380.2	943	Cag/Tag	14/31	0.117892029231656	3	FACETS	0.821	0.743	0.903	0.274	0.247	0.301	INDETERMINATE	1	TRUE	0	0.386386386461617	3		796	963	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900873	3900873	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012663-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	262	728	0	ENST00000262367.5:c.223C>T	p.Arg75Ter	p.R75*	ENST00000262367	NM_004380.2	75	Cga/Tga	2/31	0.117892029231656	3	FACETS	0.801	0.751	0.852	0.534	0.501	0.568	INDETERMINATE	2	TRUE	0	0.386386386461617	3		728	1010	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038729	47038729	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0012663-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	119	361	0	ENST00000377604.3:c.736A>T	p.Lys246Ter	p.K246*	ENST00000377604	NM_001204468.1	246	Aag/Tag	9/24	1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.386386386461617	1		361	390	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0012663-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	79	391	0	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	1	2	FACETS	0.794	0.7	0.894	0.794	0.7	0.894	SUBCLONAL	1	TRUE	1	0.386386386461617	2		391	515	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246027140	246027140	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326631387	NA	P-0012663-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	101	652	3	ENST00000388985.4:c.862G>A	p.Glu288Lys	p.E288K	ENST00000388985		288	Gaa/Aaa	9/12	1	2	FACETS	0.7	0.625	0.779	0.7	0.625	0.779	SUBCLONAL	1	TRUE	1	0.386386386461617	2		655	747	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127933423	127933423	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012663-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	44	592	0	ENST00000373547.4:c.112G>C	p.Glu38Gln	p.E38Q	ENST00000373547	NM_002721.4	38	Gag/Cag	2/7	0.386386386461617	1	FACETS	0.279	0.233	0.33	0.279	0.233	0.33	SUBCLONAL	1	TRUE	0	0.386386386461617	1		592	658	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0012739-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	142	462	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.507049114440262	2		462	457	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0012739-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	102	308	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.507049114440262	2		308	328	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039347	47039347	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012739-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	166	330	0	ENST00000377604.3:c.970G>C	p.Ala324Pro	p.A324P	ENST00000377604	NM_001204468.1	324	Gcg/Ccg	10/24	1	1	FACETS	0.908	0.856	0.96	1	0.993	1	CLONAL	2	TRUE	0	0.507049114440262	1		330	269	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713421	40713421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199947379	NA	P-0012739-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	45	541	1	ENST00000373198.4:c.4094C>T	p.Thr1365Met	p.T1365M	ENST00000373198	NM_133170.3	1365	aCg/aTg	30/32	1	2	FACETS	0.401	0.337	0.471	0.401	0.337	0.471	SUBCLONAL	1	TRUE	1	0.507049114440262	2		542	443	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741708	17741708	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012739-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	102	434	0	ENST00000250003.3:c.379G>A	p.Glu127Lys	p.E127K	ENST00000250003	NM_002478.4	127	Gag/Aag	1/3	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.507049114440262	2		434	353	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256114	133256114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs993340577	NA	P-0012739-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	119	476	0	ENST00000320574.5:c.547G>A	p.Ala183Thr	p.A183T	ENST00000320574	NM_006231.2	183	Gcc/Acc	6/49	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.507049114440262	2		476	458	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281575	49281575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012739-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	170	726	0	ENST00000282018.3:c.622G>A	p.Val208Met	p.V208M	ENST00000282018	NM_020377.2	208	Gtg/Atg	1/1	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.507049114440262	2		726	611	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336064	73336064	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012739-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	52	226	0	ENST00000377767.4:c.2339G>T	p.Arg780Ile	p.R780I	ENST00000377767	NM_014953.3	780	aGa/aTa	17/21	1	2	FACETS	0.771	0.662	0.889	0.771	0.662	0.889	SUBCLONAL	1	TRUE	1	0.507049114440262	2		226	266	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291807	15291807	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012739-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	142	606	0	ENST00000263388.2:c.2959A>T	p.Thr987Ser	p.T987S	ENST00000263388	NM_000435.2	987	Acc/Tcc	18/33	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.507049114440262	2		606	513	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523287	9523287	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012739-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	110	533	0	ENST00000353224.5:c.1950G>C	p.Gln650His	p.Q650H	ENST00000353224	NM_177990.2	650	caG/caC	9/10	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.507049114440262	2		533	398	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178942576	178942576	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012739-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	56	344	0	ENST00000263967.3:c.2383C>G	p.Gln795Glu	p.Q795E	ENST00000263967	NM_006218.2	795	Cag/Gag	16/21	1	2	FACETS	0.604	0.519	0.695	0.604	0.519	0.695	SUBCLONAL	1	TRUE	1	0.507049114440262	2		344	366	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747939	41747939	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012739-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	65	328	0	ENST00000226382.2:c.830C>G	p.Pro277Arg	p.P277R	ENST00000226382	NM_003924.3	277	cCc/cGc	3/3	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.507049114440262	2		328	218	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515170	148515170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1427041861	NA	P-0012739-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	117	308	0	ENST00000320356.2:c.1039C>T	p.Arg347Trp	p.R347W	ENST00000320356	NM_004456.4	347	Cgg/Tgg	10/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.507049114440262	2		308	336	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500931	8500931	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012739-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	147	454	0	ENST00000356435.5:c.1951G>T	p.Ala651Ser	p.A651S	ENST00000356435		651	Gca/Tca	13/35	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.507049114440262	2		454	461	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856515	111856515	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1195675821	NA	P-0012836-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	30	251	0	ENST00000341259.2:c.566G>A	p.Arg189Gln	p.R189Q	ENST00000341259	NM_005475.2	189	cGg/cAg	2/8	0.338089532740516	2	FACETS	1	0.865	1	0.538	0.438	0.648	CLONAL	1	TRUE	0	0.338089532740516	2		251	165	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849417	68849417	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0012836-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	83	501	0	ENST00000261769.5:c.1321-1G>A		p.X441_splice	ENST00000261769	NM_004360.3	441			0.338089532740516	1	FACETS	0.85	0.762	0.941	1	0.984	1	CLONAL	2	TRUE	0	0.338089532740516	1		501	240	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024145	31024145	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012836-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	54	574	0	ENST00000375687.4:c.3630T>A	p.Phe1210Leu	p.F1210L	ENST00000375687	NM_015338.5	1210	ttT/ttA	13/13	0.144500682118248	4	FACETS	1	0.925	1	0.562	0.482	0.65	INDETERMINATE	1	TRUE	2	0.338089532740516	4		574	380	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670430	134670430	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012836-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	42	448	0	ENST00000398015.3:c.341A>T	p.Tyr114Phe	p.Y114F	ENST00000398015	NM_004441.4	114	tAc/tTc	3/16	0.224151581836276	2	FACETS	0.91	0.765	1	0.455	0.382	0.535	CLONAL	1	TRUE	0	0.338089532740516	2		448	273	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575679	55575679	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012836-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	44	359	0	ENST00000288135.5:c.1205C>G	p.Ala402Gly	p.A402G	ENST00000288135	NM_000222.2	402	gCc/gGc	7/21	0.0151202058243864	3	FACETS	1	0.887	1			1	INDETERMINATE	1	TRUE	NA	0.338089532740516	3		359	286	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372206	55372206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	67	88	0	ENST00000297316.4:c.896C>T	p.Ala299Val	p.A299V	ENST00000297316	NM_022454.3	299	gCg/gTg	2/2	0.745311766439103	11	FACETS	1	0.937	1	0.126	0.109	0.145	CLONAL	1	TRUE	2	0.745311766439103	11		88	689	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856520	45856520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751318902	NA	P-0013299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1362	180	503	1	ENST00000391945.4:c.1738G>A	p.Ala580Thr	p.A580T	ENST00000391945	NM_000400.3	580	Gcc/Acc	18/23	0.745311766439103	6	FACETS	0.78	0.717	0.847			1	SUBCLONAL	1	TRUE	NA	0.745311766439103	6		504	1542	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905098	50905098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	169	510	0	ENST00000440232.2:c.380C>T	p.Ala127Val	p.A127V	ENST00000440232	NM_002691.3	127	gCc/gTc	4/27	0.3261615454008	6	FACETS	0.979	0.898	1			1	INDETERMINATE	1	TRUE	NA	0.745311766439103	6		510	1154	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579524	7579540	+	frameshift_variant	Frame_Shift_Del	DEL	TGAACCATTGTTCAATA	TGAACCATTGTTCAATA	-	novel	NA	P-0013299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	355	471	1	ENST00000269305.4:c.147_163del	p.Ile50Ter	p.I50*	ENST00000269305	NM_001126112.2	49	gaTATTGAACAATGGTTCAct/gact	4/11	NA	2	FACETS	0.843	0.81	0.875			1	INDETERMINATE	2	TRUE	NA	0.745311766439103	2		472	565	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649444	23649444	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	47	177	0	ENST00000261584.4:c.55G>C	p.Glu19Gln	p.E19Q	ENST00000261584	NM_024675.3	19	Gag/Cag	2/13	0.337834253646659	6	FACETS	0.801	0.678	0.937	0.267	0.226	0.313	INDETERMINATE	1	TRUE	3	0.745311766439103	6		177	392	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727943	78727943	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	57	343	0	ENST00000306801.3:c.788T>G	p.Phe263Cys	p.F263C	ENST00000306801	NM_020761.2	263	tTc/tGc	6/34	0.537662660628435	6	FACETS	0.52	0.445	0.602	0.173	0.148	0.201	SUBCLONAL	1	TRUE	3	0.745311766439103	6		343	733	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0014282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	754	190	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.637218419079679	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	1	0.637218419079679	4		190	1232	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999203	100999330	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGCCGGGAGCAGCAGCTGCCGGGCTGGTGACAGGCCCCGGGGCAGCACTTTATGGGCAGCTGCCGTCCCGGAGCTGTCTCCAACCTTGCACCCGGACCGGCTCATGAGCGGGGACAACACCCGCTG	GAGGCCGGGAGCAGCAGCTGCCGGGCTGGTGACAGGCCCCGGGGCAGCACTTTATGGGCAGCTGCCGTCCCGGAGCTGTCTCCAACCTTGCACCCGGACCGGCTCATGAGCGGGGACAACACCCGCTG	-	novel	NA	P-0014282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	344	666	0	ENST00000325455.5:c.472_599del	p.Gln158Ter	p.Q158*	ENST00000325455	NM_001202474.3	158	CAGCGGGTGTTGTCCCCGCTCATGAGCCGGTCCGGGTGCAAGGTTGGAGACAGCTCCGGGACGGCAGCTGCCCATAAAGTGCTGCCCCGGGGCCTGTCACCAGCCCGGCAGCTGCTGCTCCCGGCCTCt/t	1/8	0.277499356650778	3	FACETS	0.888	0.845	0.931	0.888	0.845	0.931	INDETERMINATE	2	TRUE	1	0.637218419079679	3		666	802	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593652	55593653	+	inframe_insertion	In_Frame_Ins	INS	-	-	AACACAACTTCCTTATGATCACAAATGGGAGTTTCCCAG	novel	NA	P-0014722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	75	513	0	ENST00000288135.5:c.1721_1759dup	p.Thr574_Arg586dup	p.T574_R586dup	ENST00000288135	NM_000222.2	574	cca/ccAACACAACTTCCTTATGATCACAAATGGGAGTTTCCCAGa	11/21	1	2	FACETS	0.416	0.364	0.471	0.416	0.364	0.471	SUBCLONAL	1	TRUE	1	0.57207792824632	2		513	631	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0015590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	26	289	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	0.176787212622158	3	FACETS	0.959	0.762	1	0.479	0.381	0.591	CLONAL	1	TRUE	1	0.246611256182432	3		289	247	SUCCESS
CBL	867	MSKCC	GRCh37	11	119145657	119145657	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	39	278	0	ENST00000264033.4:c.863C>G	p.Pro288Arg	p.P288R	ENST00000264033	NM_005188.3	288	cCt/cGt	5/16	0.246611256182432	3	FACETS	1	0.937	1	0.641	0.534	0.759	CLONAL	1	TRUE	1	0.246611256182432	3		278	277	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968900	32968900	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs397508047	NA	P-0015590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	17	348	0	ENST00000380152.3:c.9331G>T	p.Glu3111Ter	p.E3111*	ENST00000380152		3111	Gag/Tag	25/27	0.175037562047644	2	FACETS	0.624	0.466	0.81	0.312	0.233	0.405	SUBCLONAL	1	TRUE	0	0.246611256182432	2		348	221	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476251	88476251	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	25	396	0	ENST00000360948.2:c.1881G>T	p.Lys627Asn	p.K627N	ENST00000360948	NM_001012338.2	627	aaG/aaT	15/19	0.246611256182432	2	FACETS	0.714	0.564	0.886	0.357	0.282	0.443	SUBCLONAL	1	TRUE	0	0.246611256182432	2		396	284	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412889	63412889	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	41	702	0	ENST00000330258.3:c.278G>T	p.Ser93Ile	p.S93I	ENST00000330258	NM_152424.3	93	aGc/aTc	2/2	0.246611256182432	1	FACETS	0.765	0.638	0.905	0.765	0.638	0.905	CLONAL	1	TRUE	0	0.246611256182432	1		702	381	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412033	116412046	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTCCAGAAGGTA	TTTTCCAGAAGGTA	G	novel	NA	P-0015590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	179	769	0	ENST00000397752.3:c.3018_3028+3delinsG		p.X1006_splice	ENST00000397752	NM_000245.2	1006		14/21	0.183426066537275	3	FACETS	1	0.947	1	1	0.947	1	CLONAL	3	TRUE	0	0.246611256182432	3		769	531	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877802	151877802	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	45	309	0	ENST00000262189.6:c.7143G>C	p.Leu2381Phe	p.L2381F	ENST00000262189	NM_170606.2	2381	ttG/ttC	36/59	0.183426066537275	3	FACETS	1	0.884	1	0.697	0.593	0.809	CLONAL	2	TRUE	0	0.246611256182432	3		309	196	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744512	41744512	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	36	529	0	ENST00000301178.4:c.1132G>C	p.Glu378Gln	p.E378Q	ENST00000301178	NM_021913.4	378	Gag/Cag	8/20	0.246611256182432	3	FACETS	0.814	0.669	0.975	0.407	0.334	0.488	CLONAL	1	TRUE	1	0.246611256182432	3		529	403	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	279	1032	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.171164182728145	2	FACETS	0.912	0.858	0.968	1	0.992	1	CLONAL	3	TRUE	0	0.202842535933111	2		1032	1005	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0016138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	177	557	1	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	0.176421021453221	0	FACETS	1	0.984	1			1	CLONAL	1	TRUE	0	0.202842535933111	0		558	1100	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977992	131977992	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	132	405	0	ENST00000265335.6:c.3875A>G	p.Asn1292Ser	p.N1292S	ENST00000265335		1292	aAc/aGc	25/25	1	2	FACETS	0.762	0.692	0.836	1	0.986	1	SUBCLONAL	2	TRUE	1	0.202842535933111	2		405	854	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740581	58740581	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs35491690	NA	P-0016138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	334	494	0	ENST00000305921.3:c.1486A>G	p.Ile496Val	p.I496V	ENST00000305921	NM_003620.3	496	Att/Gtt	6/6	0.178956325389097	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	1	0.202842535933111	4		494	1251	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932770	49932770	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	210	543	0	ENST00000296474.3:c.3101G>C	p.Cys1034Ser	p.C1034S	ENST00000296474	NM_002447.2	1034	tGt/tCt	14/20	0.165979121828961	2	FACETS	0.799	0.741	0.861	0.799	0.741	0.861	SUBCLONAL	2	TRUE	0	0.202842535933111	2		543	1295	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430773	181430774	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0016138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	252	510	0	ENST00000325404.1:c.627dup	p.Met210HisfsTer100	p.M210Hfs*100	ENST00000325404	NM_003106.3	209	tcc/tCcc	1/1	0.165979121828961	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.202842535933111	2		510	1108	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0016350-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	142	698	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.303178184534231	5	FACETS	0.785	0.716	0.857	0.523	0.477	0.571	SUBCLONAL	2	TRUE	2	0.366000438142506	5		698	766	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578528	7578528	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016350-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	307	723	1	ENST00000269305.4:c.402T>A	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	ttT/ttA	5/11	0.345294096178003	3	FACETS	1	0.987	1	0.76	0.719	0.802	CLONAL	2	TRUE	0	0.366000438142506	3		724	870	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215252	142215252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016350-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	147	447	0	ENST00000350721.4:c.5849C>T	p.Ser1950Leu	p.S1950L	ENST00000350721	NM_001184.3	1950	tCa/tTa	34/47	0.180551691247438	2	FACETS	1	0.987	1	0.725	0.665	0.787	INDETERMINATE	1	TRUE	0	0.366000438142506	2		447	554	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382150	152382150	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016350-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	101	374	0	ENST00000206249.3:c.1260del	p.Met421TrpfsTer17	p.M421Wfs*17	ENST00000206249	NM_000125.3	420	ggC/gg	6/8	0.366000438142506	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.366000438142506	1		374	375	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	130	1032	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.236516649312679	2		1032	971	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0017037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	81	380	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.236516649312679	1	FACETS	0.891	0.785	1	0.891	0.785	1	CLONAL	1	TRUE	0	0.236516649312679	1		380	678	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217330	11217330	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	119	535	0	ENST00000361445.4:c.4348T>G	p.Tyr1450Asp	p.Y1450D	ENST00000361445	NM_004958.3	1450	Tat/Gat	30/58	0.236516649312679	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.236516649312679	1		535	858	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153536	108153536	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs370974808	NA	P-0017037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	99	459	0	ENST00000278616.4:c.3676G>C	p.Asp1226His	p.D1226H	ENST00000278616	NM_000051.3	1226	Gat/Cat	25/63	1	2	FACETS	0.944	0.841	1	0.944	0.841	1	CLONAL	1	TRUE	1	0.236516649312679	2		459	887	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211024	36211024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	115	684	1	ENST00000222270.7:c.775G>A	p.Val259Met	p.V259M	ENST00000222270	NM_014727.1	259	Gtg/Atg	3/37	1	2	FACETS	0.895	0.805	0.992	0.895	0.805	0.992	CLONAL	1	TRUE	1	0.236516649312679	2		685	1086	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798127	42798127	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	88	468	0	ENST00000575354.2:c.4081del	p.Glu1361SerfsTer54	p.E1361Sfs*54	ENST00000575354	NM_015125.3	1361	Gag/ag	17/20	1	2	FACETS	0.936	0.829	1	0.936	0.829	1	CLONAL	1	TRUE	1	0.236516649312679	2		468	795	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440025	220440025	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	129	790	2	ENST00000243786.2:c.878G>A	p.Gly293Asp	p.G293D	ENST00000243786	NM_002191.3	293	gGt/gAt	2/2	0.23566386756816	2	FACETS	0.909	0.822	1	0.455	0.411	0.501	CLONAL	1	TRUE	0	0.236516649312679	2		792	1200	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265630	41266188	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCAGTCTGGCTGAGATCCCCCTGCTTTCCTCTCTCCCTGCTTACTTGTCAGGCTACCTTTTGCTCCATTTTCTGCTCACTCCTCCTAATGGCTTGGTGAAATAGCAAACAAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGT	CCAGTCTGGCTGAGATCCCCCTGCTTTCCTCTCTCCCTGCTTACTTGTCAGGCTACCTTTTGCTCCATTTTCTGCTCACTCCTCCTAATGGCTTGGTGAAATAGCAAACAAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGT	-	novel	NA	P-0017037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	188	261	0	ENST00000349496.5:c.13+60_187del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.23566386756816	2	FACETS	0.853	0.792	0.916	1	0.987	1	CLONAL	3	TRUE	0	0.236516649312679	2		261	621	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71019884	71019884	+	splice_region_variant,intron_variant	Splice_Region	SNP	T	T	G	novel	NA	P-0017037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	40	229	0	ENST00000318789.4:c.1722+3A>C		p.X574_splice	ENST00000318789	NM_032682.5	574			1	2	FACETS	0.717	0.595	0.852	0.717	0.595	0.852	SUBCLONAL	1	TRUE	1	0.236516649312679	2		229	472	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732826	44732837	+	inframe_deletion	In_Frame_Del	DEL	CCGCCGCCGCTG	CCGCCGCCGCTG	-	rs749062014	NA	P-0017037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	71	273	0	ENST00000377967.4:c.40_51del	p.Ala14_Ala17del	p.A14_A17del	ENST00000377967	NM_021140.2	10	aCCGCCGCCGCTGcc/acc	1/29	1	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.236516649312679	1		273	403	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291782	15291782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs940948912	NA	P-0017158-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	69	743	0	ENST00000263388.2:c.2984C>T	p.Pro995Leu	p.P995L	ENST00000263388	NM_000435.2	995	cCg/cTg	18/33	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		743	1040	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77048425	77048425	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017158-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	47	500	0	ENST00000356341.3:c.1160A>T	p.His387Leu	p.H387L	ENST00000356341	NM_002576.4	387	cAc/cTc	12/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		500	857	SUCCESS
ATM	472	MSKCC	GRCh37	11	108128305	108128305	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017158-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	79	387	0	ENST00000278616.4:c.2348G>T	p.Cys783Phe	p.C783F	ENST00000278616	NM_000051.3	783	tGt/tTt	15/63	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		387	844	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343622	118343622	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017158-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	58	491	0	ENST00000534358.1:c.1748C>G	p.Pro583Arg	p.P583R	ENST00000534358	NM_005933.3	583	cCt/cGt	3/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		491	927	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118888	115118888	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017158-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	47	434	0	ENST00000257566.3:c.453A>T	p.Leu151Phe	p.L151F	ENST00000257566	NM_016569.3	151	ttA/ttT	2/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		434	774	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873491	45873491	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0017158-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	44	403	0	ENST00000391945.4:c.6-1G>T		p.X2_splice	ENST00000391945	NM_000400.3	2			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		403	632	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564654	55564654	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017158-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	38	480	0	ENST00000288135.5:c.542G>T	p.Arg181Leu	p.R181L	ENST00000288135	NM_000222.2	181	cGg/cTg	3/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		480	757	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874275	151874275	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017158-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	51	423	0	ENST00000262189.6:c.8263G>C	p.Asp2755His	p.D2755H	ENST00000262189	NM_170606.2	2755	Gat/Cat	38/59	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		423	701	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937038	76937038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1557136793	NA	P-0017158-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	22	246	0	ENST00000373344.5:c.3710C>T	p.Ser1237Leu	p.S1237L	ENST00000373344	NM_000489.3	1237	tCa/tTa	9/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		246	370	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0017166-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	29	698	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.180030590484916	5	FACETS	1	0.824	1	0.679	0.55	0.822	CLONAL	2	TRUE	2	0.212225470849241	5		698	177	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0017166-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	14	801	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.212088819031135	1	FACETS	0.698	0.506	0.928	0.698	0.506	0.928	SUBCLONAL	1	TRUE	0	0.212225470849241	1		804	169	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468065	50468065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749084924	NA	P-0017166-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	12	527	0	ENST00000331340.3:c.1300G>A	p.Ala434Thr	p.A434T	ENST00000331340	NM_006060.4	434	Gcc/Acc	8/8	0.180030590484916	5	FACETS	1	0.747	1	0.355	0.25	0.482	CLONAL	1	TRUE	2	0.212225470849241	5		527	140	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640896	3640920	+	frameshift_variant	Frame_Shift_Del	DEL	CATCTCTTCCTGGCTCCAACGGCTC	CATCTCTTCCTGGCTCCAACGGCTC	-	novel	NA	P-0017310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	305	632	0	ENST00000294008.3:c.2719_2743del	p.Glu907ArgfsTer86	p.E907Rfs*86	ENST00000294008	NM_032444.2	907	GAGCCGTTGGAGCCAGGAAGAGATGag/ag	12/15	0.206997044422628	5	FACETS	0.938	0.886	0.992	0.938	0.886	0.992	CLONAL	3	TRUE	2	0.31587952138246	5		632	1011	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217695	7217695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	128	477	0	ENST00000380728.2:c.232G>A	p.Ala78Thr	p.A78T	ENST00000380728		78	Gct/Act	4/11	NA	2	FACETS	0.87	0.793	0.949			1	INDETERMINATE	2	TRUE	NA	0.31587952138246	2		477	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578254	7578311	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTCCACTCGGATAAGATGCTGAGGAGGGGCCAGACCTAAGAGCAATCAGTGAGGAAT	CTTCCACTCGGATAAGATGCTGAGGAGGGGCCAGACCTAAGAGCAATCAGTGAGGAAT	-	novel	NA	P-0017310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	159	561	0	ENST00000269305.4:c.560-22_595del		p.X187_splice	ENST00000269305	NM_001126112.2	187		6/11	NA	2	FACETS	0.937	0.865	1			1	INDETERMINATE	2	TRUE	NA	0.31587952138246	2		561	537	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856064	68856081	+	frameshift_variant	Frame_Shift_Del	DEL	TCCCTTCACAGCAGAACT	TCCCTTCACAGCAGAACT	C	novel	NA	P-0017310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	204	505	0	ENST00000261769.5:c.1872_1889delinsC	p.Pro625AsnfsTer32	p.P625Nfs*32	ENST00000261769	NM_004360.3	624	tcTCCCTTCACAGCAGAACTa/tcCa	12/16	0.303912992141519	3	FACETS	0.841	0.785	0.898	0.841	0.785	0.898	CLONAL	3	TRUE	0	0.31587952138246	3		505	593	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0017435-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	106	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.468961648504761	3	FACETS	0.866	0.787	0.947	0.866	0.787	0.947	CLONAL	2	TRUE	1	0.504364040769645	3		434	304	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017435-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	92	567	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.468961648504761	3	FACETS	0.894	0.797	0.997	0.447	0.398	0.499	CLONAL	1	TRUE	1	0.504364040769645	3		567	511	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427579	72427579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1424267110	NA	P-0017435-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	53	298	0	ENST00000477973.2:c.911C>T	p.Thr304Met	p.T304M	ENST00000477973	NM_012234.5	304	aCg/aTg	4/4	0.468961648504761	3	FACETS	1	0.877	1	0.51	0.439	0.587	CLONAL	1	TRUE	1	0.504364040769645	3		298	258	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171608	36171618	+	frameshift_variant	Frame_Shift_Del	DEL	ACTGGAAAGTT	ACTGGAAAGTT	-	novel	NA	P-0017435-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	94	251	0	ENST00000300305.3:c.947_957del	p.Glu316AlafsTer280	p.E316Afs*280	ENST00000300305		316	gAACTTTCCAGT/g	7/8	0.468961648504761	3	FACETS	0.922	0.834	1	0.922	0.834	1	CLONAL	2	TRUE	1	0.504364040769645	3		251	253	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231810	36231810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017435-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	103	642	0	ENST00000300305.3:c.574G>A	p.Ala192Thr	p.A192T	ENST00000300305		192	Gcc/Acc	5/8	0.468961648504761	3	FACETS	0.902	0.809	1	0.451	0.404	0.5	CLONAL	1	TRUE	1	0.504364040769645	3		642	567	SUCCESS
ATM	472	MSKCC	GRCh37	11	108159734	108159737	+	frameshift_variant	Frame_Shift_Del	DEL	TTTT	TTTT	-	novel	NA	P-0017435-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	52	537	0	ENST00000278616.4:c.4140_4143del	p.Phe1381HisfsTer4	p.F1381Hfs*4	ENST00000278616	NM_000051.3	1380	caTTTT/ca	28/63	0.496492932468744	2	FACETS	0.614	0.525	0.71	0.307	0.262	0.355	SUBCLONAL	1	TRUE	0	0.504364040769645	2		537	336	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610201	81610201	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs371436408	NA	P-0017435-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	73	411	0	ENST00000298171.2:c.1799G>C	p.Cys600Ser	p.C600S	ENST00000298171	NM_000369.2	600	tGt/tCt	10/10	0.495039763241386	4	FACETS	0.951	0.834	1	0.475	0.417	0.538	CLONAL	1	TRUE	2	0.504364040769645	4		411	458	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130415	29130415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs537051622	NA	P-0017435-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	93	508	0	ENST00000328354.6:c.295C>T	p.Leu99Phe	p.L99F	ENST00000328354	NM_007194.3	99	Ctt/Ttt	2/15	1	2	FACETS	0.968	0.867	1	0.968	0.867	1	CLONAL	1	TRUE	1	0.504364040769645	2		508	381	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542780	187542780	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533979319	NA	P-0017435-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	77	454	0	ENST00000441802.2:c.4960C>T	p.Arg1654Cys	p.R1654C	ENST00000441802	NM_005245.3	1654	Cgt/Tgt	10/27	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.504364040769645	2		454	295	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0018300-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	65	502	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.182301687059816	2		502	712	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143350346	143350346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483862322	NA	P-0018300-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	30	209	0	ENST00000262992.4:c.116C>T	p.Pro39Leu	p.P39L	ENST00000262992	NM_001101669.1	39	cCg/cTg	3/24	0.182301687059816	3	FACETS	0.863	0.701	1	0.863	0.701	1	CLONAL	2	TRUE	1	0.182301687059816	3		209	208	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287568	33287568	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018300-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	68	480	0	ENST00000374542.5:c.1529C>G	p.Pro510Arg	p.P510R	ENST00000374542	NM_001141970.1	510	cCt/cGt	6/8	1	2	FACETS	0.924	0.803	1	0.924	0.803	1	CLONAL	1	TRUE	1	0.182301687059816	2		480	807	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841842	151841842	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018300-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	43	274	0	ENST00000262189.6:c.14299del	p.Thr4767LeufsTer43	p.T4767Lfs*43	ENST00000262189	NM_170606.2	4767	Act/ct	55/59	1	2	FACETS	0.997	0.835	1	0.997	0.835	1	CLONAL	1	TRUE	1	0.182301687059816	2		274	473	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0018453-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	23	557	3	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	1	2	FACETS	0.395	0.306	0.498	0.395	0.306	0.498	SUBCLONAL	1	FALSE	1	0.172531432129435	2		560	675	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249091	55249091	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519861	NA	P-0018453-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	34	736	0	ENST00000275493.2:c.2389T>A	p.Cys797Ser	p.C797S	ENST00000275493	NM_005228.3	797	Tgc/Agc	20/28	1	2	FACETS	0.58	0.473	0.702	0.58	0.473	0.702	SUBCLONAL	1	FALSE	1	0.172531432129435	2		736	679	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497323	149497323	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1561984776	NA	P-0018453-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	77	594	0	ENST00000261799.4:c.2995C>T	p.Arg999Ter	p.R999*	ENST00000261799	NM_002609.3	999	Cga/Tga	22/23	0.170010436714398	3	FACETS	1	0.972	1	0.702	0.616	0.794	CLONAL	1	FALSE	1	0.172531432129435	3		594	691	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138627	11138627	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0018453-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	42	508	0	ENST00000358026.2:c.3382+1G>A		p.X1128_splice	ENST00000358026	NM_001128849.1	1128			1	2	FACETS	0.957	0.798	1	0.957	0.798	1	CLONAL	1	FALSE	1	0.172531432129435	2		508	509	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242486	+	frameshift_variant	Frame_Shift_Del	DEL	TTAAGAGAAGCAACATCT	TTAAGAGAAGCAACATCT	GCAA	novel	NA	P-0018453-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	81	531	1	ENST00000275493.2:c.2239_2256delinsGCAA	p.Leu747AlafsTer11	p.L747Afs*11	ENST00000275493	NM_005228.3	747	TTAAGAGAAGCAACATCT/GCAA	19/28	1	2	FACETS	0.873	0.77	0.982	1	0.982	1	CLONAL	2	FALSE	1	0.172531432129435	2		532	538	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400868	72400868	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	37	395	0	ENST00000357731.5:c.303C>A	p.Tyr101Ter	p.Y101*	ENST00000357731	NM_173808.2	101	taC/taA	2/7	0.765006549741322	1	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	0	0.765006549741322	1		395	57	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124499135	124499135	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018636-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	29	359	0	ENST00000357628.3:c.578C>T	p.Ser193Phe	p.S193F	ENST00000357628	NM_015450.2	193	tCt/tTt	9/19	0.722470076721242	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.765006549741322	1		359	40	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0018681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	528	479	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.57819365282827	7	FACETS	1	0.991	1	0.824	0.791	0.858	CLONAL	3	TRUE	3	0.57819365282827	7		479	1355	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0018681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	107	308	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.57819365282827	3	FACETS	0.986	0.889	1	0.493	0.444	0.544	CLONAL	1	TRUE	1	0.57819365282827	3		308	484	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0018681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	131	338	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	1	2	FACETS	0.952	0.87	1	0.952	0.87	1	CLONAL	1	TRUE	1	0.57819365282827	2		338	476	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525914	41525914	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs773503228	NA	P-0018681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	73	448	1	ENST00000263253.7:c.1189C>T	p.Arg397Ter	p.R397*	ENST00000263253	NM_001429.3	397	Cga/Tga	5/31	0.29114067975536	6	FACETS	0.87	0.761	0.987			1	INDETERMINATE	1	TRUE	NA	0.57819365282827	6		449	626	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145561	24145561	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	54	460	0	ENST00000263121.7:c.580G>C	p.Glu194Gln	p.E194Q	ENST00000263121	NM_003073.3	194	Gag/Cag	5/9	0.184143537870506	5	FACETS	0.418	0.356	0.487			1	INDETERMINATE	1	TRUE	NA	0.57819365282827	5		460	834	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981586	101981586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1319669560	NA	P-0018681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	31	252	0	ENST00000282441.5:c.7C>T	p.Pro3Ser	p.P3S	ENST00000282441	NM_001130145.2	3	Ccc/Tcc	1/9	0.57819365282827	4	FACETS	0.279	0.225	0.34	0.093	0.075	0.114	SUBCLONAL	1	TRUE	1	0.57819365282827	4		252	607	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250728	26250728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	45	230	0	ENST00000446824.2:c.106G>A	p.Val36Met	p.V36M	ENST00000446824	NM_021018.2	36	Gtg/Atg	1/1	0.57819365282827	3	FACETS	0.43	0.361	0.505	0.215	0.18	0.253	SUBCLONAL	1	TRUE	1	0.57819365282827	3		230	467	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958195	2958195	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1443	169	442	0	ENST00000396946.4:c.2537T>G	p.Leu846Arg	p.L846R	ENST00000396946	NM_032415.4	846	cTg/cGg	19/25	0.57819365282827	8	FACETS	0.992	0.908	1	0.198	0.181	0.216	CLONAL	1	TRUE	3	0.57819365282827	8		442	1612	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611083	100611083	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	291	587	1	ENST00000308731.7:c.1523C>A	p.Ala508Asp	p.A508D	ENST00000308731	NM_000061.2	508	gCc/gAc	15/19	0.57819365282827	3	FACETS	1	0.988	1	0.588	0.553	0.624	CLONAL	1	TRUE	1	0.57819365282827	3		588	1103	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0019459-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	13	557	3	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	1	2	FACETS	0.042	0.029	0.057	0.042	0.029	0.057	SUBCLONAL	1	TRUE	1	0.763162818127827	2		560	817	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0019459-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	158	292	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.95	0.879	1	0.95	0.879	1	CLONAL	1	TRUE	1	0.763162818127827	2		292	436	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241722	55241722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1051753269	NA	P-0019459-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	280	523	2	ENST00000275493.2:c.2170G>A	p.Gly724Ser	p.G724S	ENST00000275493	NM_005228.3	724	Ggc/Agc	18/28	1	2	FACETS	0.971	0.916	1	0.971	0.916	1	CLONAL	1	TRUE	1	0.763162818127827	2		525	756	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0019459-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	188	510	1	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	1	2	FACETS	0.715	0.663	0.769	0.715	0.663	0.769	SUBCLONAL	1	TRUE	1	0.763162818127827	2		511	689	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366883	40366883	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019459-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	293	499	4	ENST00000397332.2:c.314C>A	p.Ser105Tyr	p.S105Y	ENST00000397332	NM_001033082.2	105	tCc/tAc	2/3	1	2	FACETS	0.931	0.879	0.983	0.931	0.879	0.983	CLONAL	1	TRUE	1	0.763162818127827	2		503	825	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357753	70357753	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019459-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	392	404	1	ENST00000374080.3:c.6004C>T	p.Gln2002Ter	p.Q2002*	ENST00000374080		2002	Cag/Tag	41/45	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.763162818127827	1		405	527	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0020940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	248	809	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.422051034081718	1	FACETS	0.934	0.874	0.995	0.934	0.874	0.995	CLONAL	1	TRUE	0	0.439234969280173	1		809	944	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520114	9520114	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	121	546	0	ENST00000353224.5:c.2155C>T	p.His719Tyr	p.H719Y	ENST00000353224	NM_177990.2	719	Cac/Tac	10/10	0.161975797125382	3	FACETS	1	0.985	1	0.492	0.448	0.539	INDETERMINATE	1	TRUE	0	0.439234969280173	3		546	455	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602334	10602334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1379198956	NA	P-0020940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	248	1150	1	ENST00000171111.5:c.1244G>A	p.Arg415His	p.R415H	ENST00000171111	NM_203500.1	415	cGc/cAc	3/6	0.422051034081718	1	FACETS	0.871	0.815	0.929	0.871	0.815	0.929	CLONAL	1	TRUE	0	0.439234969280173	1		1151	1012	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792245	33792245	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0020940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1437	255	850	0	ENST00000498907.2:c.1076G>C	p.Ter359SerextTer36	p.*359Sext*36	ENST00000498907	NM_004364.3	359	tGa/tCa	1/1	0.439234969280173	8	FACETS	0.795	0.742	0.851			1	SUBCLONAL	2	TRUE	NA	0.439234969280173	8		850	1692	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906633	32906633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	43	554	0	ENST00000380152.3:c.1018G>A	p.Glu340Lys	p.E340K	ENST00000380152		340	Gaa/Aaa	10/27	0.29860069369026	2	FACETS	0.539	0.452	0.635	0.27	0.226	0.318	SUBCLONAL	1	TRUE	0	0.439234969280173	2		554	363	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17355105	17355105	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	39	721	0	ENST00000375499.3:c.413A>T	p.Asp138Val	p.D138V	ENST00000375499	NM_003000.2	138	gAt/gTt	4/8	0.161694123014878	2	FACETS	0.287	0.237	0.343	0.144	0.118	0.172	INDETERMINATE	1	TRUE	0	0.439234969280173	2		721	618	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332109	70332109	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	23	256	0	ENST00000373644.4:c.14G>T	p.Arg5Leu	p.R5L	ENST00000373644	NM_030625.2	5	cGc/cTc	2/12	1	2	FACETS	0.487	0.381	0.608	0.487	0.381	0.608	SUBCLONAL	1	TRUE	1	0.439234969280173	2		256	215	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742480	17742480	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	134	984	0	ENST00000250003.3:c.662G>T	p.Arg221Leu	p.R221L	ENST00000250003	NM_002478.4	221	cGg/cTg	2/3	0.30531924254062	0	FACETS	0.526	0.479	0.575			1	SUBCLONAL	1	TRUE	0	0.439234969280173	0		984	651	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398099	4398099	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	166	835	0	ENST00000261254.3:c.663C>A	p.Ser221Arg	p.S221R	ENST00000261254	NM_001759.3	221	agC/agA	4/5	0.431733678393441	4	FACETS	1	0.967	1	0.367	0.337	0.399	CLONAL	1	TRUE	1	0.439234969280173	4		835	988	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235935	133235935	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	148	831	0	ENST00000320574.5:c.3221T>C	p.Leu1074Pro	p.L1074P	ENST00000320574	NM_006231.2	1074	cTg/cCg	26/49	0.439234969280173	1	FACETS	0.841	0.771	0.914	0.841	0.771	0.914	CLONAL	1	TRUE	0	0.439234969280173	1		831	625	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907112	32907112	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	66	662	0	ENST00000380152.3:c.1497G>C	p.Gln499His	p.Q499H	ENST00000380152		499	caG/caC	10/27	0.29860069369026	2	FACETS	0.71	0.619	0.809	0.355	0.309	0.405	SUBCLONAL	1	TRUE	0	0.439234969280173	2		662	423	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937070	48937070	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	72	430	1	ENST00000267163.4:c.838G>T	p.Glu280Ter	p.E280*	ENST00000267163	NM_000321.2	280	Gaa/Taa	8/27	0.29860069369026	2	FACETS	1	0.967	1	0.635	0.562	0.712	CLONAL	1	TRUE	0	0.439234969280173	2		431	258	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782879	66782879	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	63	783	0	ENST00000307102.5:c.1108G>C	p.Asp370His	p.D370H	ENST00000307102	NM_002755.3	370	Gat/Cat	11/11	0.422051034081718	1	FACETS	0.332	0.286	0.381	0.332	0.286	0.381	SUBCLONAL	1	TRUE	0	0.439234969280173	1		783	675	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67459186	67459186	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	180	764	0	ENST00000327367.4:c.602A>T	p.Asp201Val	p.D201V	ENST00000327367	NM_005902.3	201	gAc/gTc	4/9	0.422051034081718	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.439234969280173	1		764	610	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476397	88476397	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	35	762	0	ENST00000360948.2:c.1735C>A	p.Leu579Met	p.L579M	ENST00000360948	NM_001012338.2	579	Ctg/Atg	15/19	0.422051034081718	1	FACETS	0.223	0.182	0.269	0.223	0.182	0.269	SUBCLONAL	1	TRUE	0	0.439234969280173	1		762	557	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652196	3652196	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	88	1198	0	ENST00000294008.3:c.873G>T	p.Lys291Asn	p.K291N	ENST00000294008	NM_032444.2	291	aaG/aaT	4/15	0.161694123014878	2	FACETS	0.374	0.331	0.422	0.187	0.165	0.211	INDETERMINATE	1	TRUE	0	0.439234969280173	2		1198	1070	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817750	3817750	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1397325627	NA	P-0020940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	58	920	0	ENST00000262367.5:c.3221C>T	p.Ser1074Leu	p.S1074L	ENST00000262367	NM_004380.2	1074	tCa/tTa	16/31	0.161694123014878	2	FACETS	0.341	0.292	0.394	0.17	0.146	0.197	INDETERMINATE	1	TRUE	0	0.439234969280173	2		920	775	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821632	72821632	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	12	124	0	ENST00000268489.5:c.10543G>T	p.Gly3515Cys	p.G3515C	ENST00000268489	NM_006885.3	3515	Ggc/Tgc	10/10	0.161694123014878	2	FACETS	0.536	0.38	0.723	0.268	0.19	0.362	INDETERMINATE	1	TRUE	0	0.439234969280173	2		124	102	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512371	38512371	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1449127199	NA	P-0020940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	83	880	0	ENST00000254066.5:c.1282G>T	p.Gly428Trp	p.G428W	ENST00000254066	NM_000964.3	428	Ggg/Tgg	9/9	1	2	FACETS	0.488	0.43	0.551	0.488	0.43	0.551	SUBCLONAL	1	TRUE	1	0.439234969280173	2		880	774	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698159	47698159	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	45	649	0	ENST00000233146.2:c.1717G>T	p.Ala573Ser	p.A573S	ENST00000233146	NM_000251.2	573	Gcc/Tcc	11/16	1	2	FACETS	0.446	0.375	0.525	0.446	0.375	0.525	SUBCLONAL	1	TRUE	1	0.439234969280173	2		649	459	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272248	21272248	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	36	565	0	ENST00000354336.3:c.26C>G	p.Ser9Trp	p.S9W	ENST00000354336	NM_005207.3	9	tCg/tGg	1/3	0.114077953627441	4	FACETS	0.382	0.313	0.46	0.191	0.156	0.23	INDETERMINATE	1	TRUE	2	0.439234969280173	4		565	617	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99812476	99812476	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	98	506	0	ENST00000280892.6:c.193C>G	p.Leu65Val	p.L65V	ENST00000280892	NM_001130678.1	65	Ctc/Gtc	3/7	0.439234969280173	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	0	0.439234969280173	1		506	345	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295436	1295436	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0020940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	24	107	0				ENST00000310581	NM_198253.2	-/1132			0.114077953627441	4	FACETS	0.925	0.745	1	0.925	0.745	1	INDETERMINATE	2	TRUE	2	0.439234969280173	4		107	85	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160622	56160622	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1561188463	NA	P-0020940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	58	488	0	ENST00000399503.3:c.896A>G	p.Tyr299Cys	p.Y299C	ENST00000399503	NM_005921.1	299	tAt/tGt	4/20	0.407130548563436	1	FACETS	0.528	0.456	0.607	0.528	0.456	0.607	SUBCLONAL	1	TRUE	0	0.439234969280173	1		488	390	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592161	67592161	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	25	319	0	ENST00000274335.5:c.1977C>A	p.Cys659Ter	p.C659*	ENST00000274335		659	tgC/tgA	14/15	0.407130548563436	1	FACETS	0.353	0.278	0.437	0.353	0.278	0.437	SUBCLONAL	1	TRUE	0	0.439234969280173	1		319	252	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250597	26250597	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	57	822	0	ENST00000446824.2:c.237C>G	p.Phe79Leu	p.F79L	ENST00000446824	NM_021018.2	79	ttC/ttG	1/1	1	2	FACETS	0.365	0.312	0.423	0.365	0.312	0.423	SUBCLONAL	1	TRUE	1	0.439234969280173	2		822	711	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200021	138200021	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	121	573	0	ENST00000237289.4:c.1439G>T	p.Ser480Ile	p.S480I	ENST00000237289	NM_001270507.1	480	aGc/aTc	7/9	0.407891390629264	1	FACETS	0.855	0.776	0.937	0.855	0.776	0.937	CLONAL	1	TRUE	0	0.439234969280173	1		573	503	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981331	68981331	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	40	653	0	ENST00000288368.4:c.1403C>T	p.Thr468Ile	p.T468I	ENST00000288368	NM_024870.2	468	aCa/aTa	12/40	1	2	FACETS	0.445	0.37	0.529	0.445	0.37	0.529	SUBCLONAL	1	TRUE	1	0.439234969280173	2		653	409	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993107	90993107	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	64	463	0	ENST00000265433.3:c.335C>A	p.Pro112His	p.P112H	ENST00000265433	NM_002485.4	112	cCt/cAt	4/16	1	2	FACETS	0.85	0.74	0.967	0.85	0.74	0.967	CLONAL	1	TRUE	1	0.439234969280173	2		463	343	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499787	8499787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	70	805	1	ENST00000356435.5:c.2182G>A	p.Val728Ile	p.V728I	ENST00000356435		728	Gtt/Att	14/35	0.37085550817642	1	FACETS	0.378	0.329	0.431	0.378	0.329	0.431	SUBCLONAL	1	TRUE	0	0.439234969280173	1		806	658	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232124	98232124	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	34	668	0	ENST00000331920.6:c.1818G>T	p.Arg606Ser	p.R606S	ENST00000331920	NM_000264.3	606	agG/agT	13/24	0.37085550817642	1	FACETS	0.19	0.154	0.23	0.19	0.154	0.23	SUBCLONAL	1	TRUE	0	0.439234969280173	1		668	636	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0021044-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	327	557	3	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.465910478398513	5	FACETS	1	0.975	1	0.781	0.743	0.82	CLONAL	3	TRUE	1	0.465910478398513	5		560	763	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971177	21971177	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913382	NA	P-0021044-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	108	433	0	ENST00000304494.5:c.181G>T	p.Glu61Ter	p.E61*	ENST00000304494	NM_000077.4	61	Gag/Tag	2/3	0.465910478398513	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.465910478398513	1		433	347	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0021044-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	291	348	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.465910478398513	5	FACETS	1	0.989	1	0.858	0.815	0.902	CLONAL	3	TRUE	1	0.465910478398513	5		348	618	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921555	178921555	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021044-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	77	209	0	ENST00000263967.3:c.1037T>A	p.Val346Glu	p.V346E	ENST00000263967	NM_006218.2	346	gTa/gAa	5/21	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.465910478398513	2		209	276	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044898	47044898	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021044-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	267	632	0	ENST00000377604.3:c.2224C>T	p.Gln742Ter	p.Q742*	ENST00000377604	NM_001204468.1	742	Cag/Tag	20/24	0.440602418638685	4	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	2	0.465910478398513	4		632	837	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249091	55249091	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519861	NA	P-0021044-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	207	736	0	ENST00000275493.2:c.2389T>A	p.Cys797Ser	p.C797S	ENST00000275493	NM_005228.3	797	Tgc/Agc	20/28	0.465910478398513	5	FACETS	1	0.952	1	0.514	0.479	0.551	CLONAL	2	TRUE	1	0.465910478398513	5		736	734	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001317	150001317	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021044-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	28	385	0	ENST00000253339.5:c.2287G>T	p.Glu763Ter	p.E763*	ENST00000253339		763	Gaa/Taa	4/7	0.465910478398513	2	FACETS	0.259	0.206	0.319	0.13	0.103	0.16	SUBCLONAL	1	TRUE	0	0.465910478398513	2		385	464	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137092	64137092	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0021044-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	84	388	0	ENST00000334205.4:c.1602+1G>T		p.X534_splice	ENST00000334205	NM_003942.2	534			0.465910478398513	3	FACETS	0.909	0.806	1	0.455	0.403	0.51	CLONAL	1	TRUE	1	0.465910478398513	3		388	489	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885896	59885896	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021044-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	89	377	0	ENST00000259008.2:c.850G>T	p.Val284Phe	p.V284F	ENST00000259008	NM_032043.2	284	Gtc/Ttc	7/20	0.465910478398513	3	FACETS	0.816	0.725	0.913	0.408	0.362	0.457	CLONAL	1	TRUE	1	0.465910478398513	3		377	577	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611919	100611919	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021044-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	191	326	0	ENST00000308731.7:c.1202A>T	p.Asp401Val	p.D401V	ENST00000308731	NM_000061.2	401	gAc/gTc	14/19	0.465910478398513	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.465910478398513	3		326	485	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346620	81346620	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021044-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	107	353	0	ENST00000222390.5:c.1333G>T	p.Asp445Tyr	p.D445Y	ENST00000222390	NM_000601.4	445	Gat/Tat	11/18	0.465910478398513	5	FACETS	1	0.957	1	0.281	0.252	0.312	CLONAL	1	TRUE	1	0.465910478398513	5		353	694	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291801	15291801	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021124-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	424	752	0	ENST00000263388.2:c.2965C>A	p.Leu989Ile	p.L989I	ENST00000263388	NM_000435.2	989	Ctc/Atc	18/33	0.508104502053181	4	FACETS	0.982	0.936	1	0.982	0.936	1	CLONAL	2	TRUE	2	0.53657060902964	4		752	1237	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059136	47059136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021124-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	145	565	0	ENST00000409792.3:c.7525G>A	p.Ala2509Thr	p.A2509T	ENST00000409792	NM_014159.6	2509	Gct/Act	20/21	0.53535162090824	2	FACETS	0.924	0.847	1	0.462	0.423	0.502	CLONAL	1	TRUE	0	0.53657060902964	2		565	585	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563527	87563528	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0021124-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	141	556	0	ENST00000277120.3:c.1915_1916delinsTT	p.Gly639Leu	p.G639L	ENST00000277120		639	GGg/TTg	16/19	0.53657060902964	3	FACETS	0.848	0.773	0.926	0.424	0.386	0.463	CLONAL	1	TRUE	1	0.53657060902964	3		556	786	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225223	53225223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021124-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	86	359	0	ENST00000375401.3:c.2995C>T	p.Pro999Ser	p.P999S	ENST00000375401	NM_004187.3	999	Cca/Tca	20/26	0.490175468341851	2	FACETS	0.583	0.517	0.653			1	SUBCLONAL	1	TRUE	NA	0.53657060902964	2		359	550	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	322	1032	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.542199719351617	2		1032	1048	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0021575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	384	905	3	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.542199719351617	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.542199719351617	1		908	942	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089705	27089706	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1286891446	NA	P-0021575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	289	769	0	ENST00000324856.7:c.2666dup	p.Met890HisfsTer46	p.M890Hfs*46	ENST00000324856	NM_006015.4	887	-/G	8/20	0.542199719351617	1	FACETS	0.933	0.881	0.986	0.933	0.881	0.986	CLONAL	1	TRUE	0	0.542199719351617	1		769	833	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873003	134873003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	248	750	0	ENST00000398015.3:c.1307C>T	p.Thr436Ile	p.T436I	ENST00000398015	NM_004441.4	436	aCc/aTc	6/16	0.512792349801459	3	FACETS	0.922	0.861	0.985	0.307	0.287	0.329	CLONAL	1	TRUE	0	0.542199719351617	3		750	1261	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291431	11291431	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	300	796	1	ENST00000361445.4:c.2575A>G	p.Arg859Gly	p.R859G	ENST00000361445	NM_004958.3	859	Agg/Ggg	17/58	1	2	FACETS	0.992	0.935	1	0.992	0.935	1	CLONAL	1	TRUE	1	0.542199719351617	2		797	1115	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446261	187446261	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs535108808	NA	P-0021575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	847	873	0	ENST00000232014.4:c.1427C>T	p.Thr476Met	p.T476M	ENST00000232014	NM_001130845.1	476	aCg/aTg	6/10	0.512792349801459	3	FACETS	0.972	0.947	0.996	0.972	0.947	0.996	CLONAL	3	TRUE	0	0.542199719351617	3		873	1362	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38632026	38632026	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0021785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	227	974	0	ENST00000299084.4:c.512C>G	p.Ser171Ter	p.S171*	ENST00000299084	NM_152594.2	171	tCa/tGa	5/7	1	2	FACETS	0.846	0.805	0.887	1	0.995	1	CLONAL	2	TRUE	1	0.733007159346039	2		974	366	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577554	7577554	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	367	931	0	ENST00000269305.4:c.727del	p.Met243TrpfsTer4	p.M243Wfs*4	ENST00000269305	NM_001126112.2	243	Atg/tg	7/11	0.662013992182978	2	FACETS	0.967	0.933	0.999	0.967	0.933	0.999	CLONAL	2	TRUE	0	0.733007159346039	2		931	518	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	138	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.378987510019911	2		434	697	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061185	38061202	+	inframe_deletion	In_Frame_Del	DEL	GCACTTGAAGCGCTTCTG	GCACTTGAAGCGCTTCTG	-	novel	NA	P-0021788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	124	518	0	ENST00000250448.2:c.787_804del	p.Gln263_Cys268del	p.Q263_C268del	ENST00000250448	NM_004496.3	263	CAGAAGCGCTTCAAGTGC/-	2/2	1	2	FACETS	0.854	0.773	0.94	0.854	0.773	0.94	CLONAL	1	TRUE	1	0.378987510019911	2		518	766	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734012	58734012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753470217	NA	P-0021788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	168	556	0	ENST00000305921.3:c.1070G>A	p.Arg357His	p.R357H	ENST00000305921	NM_003620.3	357	cGc/cAc	5/6	1	2	FACETS	0.987	0.908	1	0.987	0.908	1	CLONAL	1	TRUE	1	0.378987510019911	2		556	898	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497878	25497878	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	219	718	0	ENST00000264709.3:c.571C>T	p.Gln191Ter	p.Q191*	ENST00000264709	NM_175629.2	191	Cag/Tag	6/23	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.378987510019911	2		718	1049	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0021791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	167	809	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.444399842661676	2	FACETS	0.824	0.764	0.884	0.824	0.764	0.884	CLONAL	2	TRUE	0	0.448562269674621	2		809	452	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717735	89717739	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGT	AAAGT	-	rs606231169	NA	P-0021791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	136	525	0	ENST00000371953.3:c.761_765del	p.Lys254ArgfsTer42	p.K254Rfs*42	ENST00000371953	NM_000314.4	254	AAAGTa/a	7/9	0.444801929425323	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.448562269674621	2		525	290	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855835	45855835	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	132	794	1	ENST00000391945.4:c.1975del	p.His659ThrfsTer50	p.H659Tfs*50	ENST00000391945	NM_000400.3	659	Cac/ac	21/23	0.0755142354744507	6	FACETS	1	0.971	1	0.766	0.7	0.834	INDETERMINATE	2	TRUE	3	0.448562269674621	6		795	486	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268860	115268860	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	204	662	0	ENST00000438362.2:c.1750C>G	p.His584Asp	p.H584D	ENST00000438362	NM_001242891.1	584	Cat/Gat	14/20	1	2	FACETS	0.868	0.806	0.931	0.868	0.806	0.931	CLONAL	1	TRUE	1	0.562389726759314	2		662	836	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526522	66526522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	185	541	1	ENST00000358598.2:c.1078G>A	p.Gly360Ser	p.G360S	ENST00000358598	NM_212471.2	360	Ggc/Agc	11/11	0.562389726759314	4	FACETS	0.905	0.834	0.979	0.302	0.278	0.327	CLONAL	1	TRUE	1	0.562389726759314	4		542	1136	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890256	72890256	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	213	698	0	ENST00000325599.8:c.426G>C	p.Leu142Phe	p.L142F	ENST00000325599	NM_018130.2	142	ttG/ttC	4/11	0.537560192289907	1	FACETS	0.89	0.832	0.949	0.89	0.832	0.949	CLONAL	1	TRUE	0	0.562389726759314	1		698	612	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1978262	1978262	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	375	762	0	ENST00000382891.5:c.3682C>T	p.Arg1228Cys	p.R1228C	ENST00000382891	NM_133335.3	1228	Cgc/Tgc	21/22	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.562389726759314	2		762	1236	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045901	26045901	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	232	635	0	ENST00000540144.1:c.263C>G	p.Ser88Cys	p.S88C	ENST00000540144	NM_003531.2	88	tCt/tGt	1/1	0.562389726759314	1	FACETS	0.974	0.915	1	0.974	0.915	1	CLONAL	1	TRUE	0	0.562389726759314	1		635	609	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517990	8517990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	231	588	2	ENST00000356435.5:c.1401G>A	p.Met467Ile	p.M467I	ENST00000356435		467	atG/atA	10/35	0.548362599599177	3	FACETS	1	0.982	1	0.571	0.533	0.611	CLONAL	1	TRUE	1	0.562389726759314	3		590	921	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0021842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	352	709	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	0.816191644536737	1	FACETS	0.865	0.83	0.9	0.865	0.83	0.9	CLONAL	1	TRUE	0	0.816191644536737	1		710	590	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	16	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.411361821004894	1	FACETS	0.042	0.03	0.055	0.042	0.03	0.055	INDETERMINATE	1	TRUE	0	0.816191644536737	1		434	558	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0021842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	940	727	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.504414842909166	3	FACETS	1	0.998	1			1	CLONAL	2	TRUE	NA	0.816191644536737	3		727	1359	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	145	604	2	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	0.411361821004894	1	FACETS	0.292	0.266	0.318	0.292	0.266	0.318	INDETERMINATE	1	TRUE	0	0.816191644536737	1		606	721	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0021842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	191	774	14	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	0.411361821004894	1	FACETS	0.342	0.316	0.368	0.342	0.316	0.368	INDETERMINATE	1	TRUE	0	0.816191644536737	1		788	811	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	126	396	0	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	0.816191644536737	1	FACETS	0.444	0.405	0.483	0.444	0.405	0.483	SUBCLONAL	1	TRUE	0	0.816191644536737	1		396	412	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525104	9525104	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	343	619	3	ENST00000353224.5:c.1781C>T	p.Ser594Phe	p.S594F	ENST00000353224	NM_177990.2	594	tCc/tTc	8/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.816191644536737	2		622	811	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405968	157405968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	216	646	1	ENST00000346085.5:c.2210C>T	p.Pro737Leu	p.P737L	ENST00000346085	NM_020732.3	737	cCc/cTc	6/20	0.314324691256913	1	FACETS	0.387	0.36	0.414	0.387	0.36	0.414	INDETERMINATE	1	TRUE	0	0.816191644536737	1		647	810	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0021842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	211	323	2				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.816191644536737	2		325	379	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42851110	42851110	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	143	589	0	ENST00000398585.3:c.783del	p.Lys261AsnfsTer19	p.K261Nfs*19	ENST00000398585	NM_001135099.1	261	aaA/aa	7/14	0.405752896988248	2	FACETS	0.42	0.383	0.459	0.21	0.191	0.23	INDETERMINATE	1	TRUE	0	0.816191644536737	2		589	834	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809763	36809763	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	235	764	0	ENST00000373129.3:c.842A>C	p.Glu281Ala	p.E281A	ENST00000373129	NM_032017.1	281	gAg/gCg	9/12	0.411361821004894	1	FACETS	0.428	0.4	0.457	0.428	0.4	0.457	INDETERMINATE	1	TRUE	0	0.816191644536737	1		764	796	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885538	111885538	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	229	780	1	ENST00000341259.2:c.1315C>T	p.His439Tyr	p.H439Y	ENST00000341259	NM_005475.2	439	Cac/Tac	7/8	0.411361821004894	1	FACETS	0.363	0.339	0.389	0.363	0.339	0.389	INDETERMINATE	1	TRUE	0	0.816191644536737	1		781	914	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437122	110437122	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	52	114	0	ENST00000375856.3:c.1279C>A	p.His427Asn	p.H427N	ENST00000375856	NM_003749.2	427	Cac/Aac	1/2	1	2	FACETS	0.644	0.556	0.737	0.644	0.556	0.737	SUBCLONAL	1	TRUE	1	0.816191644536737	2		114	198	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761252	59761252	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	200	802	2	ENST00000259008.2:c.3155A>G	p.Lys1052Arg	p.K1052R	ENST00000259008	NM_032043.2	1052	aAa/aGa	20/20	0.782278480184339	2	FACETS	0.537	0.498	0.578	0.269	0.249	0.289	SUBCLONAL	1	TRUE	0	0.816191644536737	2		804	912	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289701	15289701	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	81	842	0	ENST00000263388.2:c.3770A>G	p.His1257Arg	p.H1257R	ENST00000263388	NM_000435.2	1257	cAt/cGt	23/33	0.35668462058989	1	FACETS	0.108	0.095	0.123	0.108	0.095	0.123	INDETERMINATE	1	TRUE	0	0.816191644536737	1		842	1085	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416137	29416137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	173	598	2	ENST00000389048.3:c.4816G>A	p.Asp1606Asn	p.D1606N	ENST00000389048	NM_004304.4	1606	Gat/Aat	29/29	0.411361821004894	1	FACETS	0.362	0.334	0.391	0.362	0.334	0.391	INDETERMINATE	1	TRUE	0	0.816191644536737	1		600	694	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663295	227663295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753900721	NA	P-0021842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	156	576	2	ENST00000305123.5:c.160C>T	p.Arg54Trp	p.R54W	ENST00000305123	NM_005544.2	54	Cgg/Tgg	1/2	0.411361821004894	1	FACETS	0.34	0.312	0.369	0.34	0.312	0.369	INDETERMINATE	1	TRUE	0	0.816191644536737	1		578	665	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590669	189590669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	339	552	0	ENST00000264731.3:c.1234G>A	p.Glu412Lys	p.E412K	ENST00000264731	NM_003722.4	412	Gaa/Aaa	10/14	0.314324691256913	1	FACETS	0.708	0.676	0.741	0.708	0.676	0.741	INDETERMINATE	1	TRUE	0	0.816191644536737	1		552	694	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248153	59248154	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGGCC	novel	NA	P-0022184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	17	92	0	ENST00000371222.2:c.585_589dup	p.Phe197TrpfsTer31	p.F197Wfs*31	ENST00000371222	NM_002228.3	197	ttt/tGGCCTtt	1/1	1	2	FACETS	0.522	0.392	0.676	0.522	0.392	0.676	SUBCLONAL	1	TRUE	1	0.371903995584172	2		92	175	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019410	42019410	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs528009988	NA	P-0022184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	90	586	0	ENST00000219905.7:c.3463C>T	p.Arg1155Ter	p.R1155*	ENST00000219905	NM_001164273.1	1155	Cga/Tga	10/24	1	2	FACETS	0.958	0.853	1	0.958	0.853	1	CLONAL	1	TRUE	1	0.371903995584172	2		586	505	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272263	18272263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1255802241	NA	P-0022184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	16	16	0	ENST00000222254.8:c.773C>T	p.Pro258Leu	p.P258L	ENST00000222254	NM_005027.3	258	cCg/cTg	6/16	1	2	FACETS	0.812	0.622	1	1	0.916	1	CLONAL	2	TRUE	1	0.371903995584172	2		16	53	SUCCESS
APC	324	MSKCC	GRCh37	5	112175180	112175180	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	16	288	0	ENST00000257430.4:c.3889G>C	p.Asp1297His	p.D1297H	ENST00000257430	NM_000038.5	1297	Gat/Cat	16/16	1	2	FACETS	0.418	0.309	0.546	0.418	0.309	0.546	SUBCLONAL	1	TRUE	1	0.371903995584172	2		288	206	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0022198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	3034	698	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.210489159838539	32	FACETS	1	0.993	1			1	CLONAL	31	TRUE	NA	0.210489159838539	32		698	3848	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411902	116411902	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0022198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3060	496	849	0	ENST00000397752.3:c.2888-1G>A		p.X963_splice	ENST00000397752	NM_000245.2	963			0.210489159838539	21	FACETS	0.994	0.945	1			1	CLONAL	4	TRUE	NA	0.210489159838539	21		849	3556	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857449	57857449	+	splice_region_variant,5_prime_UTR_variant	Splice_Region	SNP	G	G	C	novel	NA	P-0022198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	123	627	0	ENST00000228682.2:c.-26G>C		p.X9_splice	ENST00000228682	NM_005269.2	9		2/12	0.210489159838539	3	FACETS	1	0.978	1	0.651	0.588	0.718	CLONAL	1	TRUE	1	0.210489159838539	3		627	992	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988529	41988529	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	72	632	0	ENST00000219905.7:c.1321C>G	p.Leu441Val	p.L441V	ENST00000219905	NM_001164273.1	441	Cta/Gta	3/24	1	2	FACETS	0.764	0.666	0.87	0.764	0.666	0.87	SUBCLONAL	1	TRUE	1	0.210489159838539	2		632	896	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411914	116411914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3034	492	831	1	ENST00000397752.3:c.2899G>A	p.Glu967Lys	p.E967K	ENST00000397752	NM_000245.2	967	Gaa/Aaa	14/21	0.210489159838539	21	FACETS	0.994	0.945	1			1	CLONAL	4	TRUE	NA	0.210489159838539	21		832	3526	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500902	8500902	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	83	615	1	ENST00000356435.5:c.1980C>A	p.His660Gln	p.H660Q	ENST00000356435		660	caC/caA	13/35	0.210489159838539	1	FACETS	0.946	0.834	1	0.946	0.834	1	CLONAL	1	TRUE	0	0.210489159838539	1		616	746	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248067	110248067	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	91	620	0	ENST00000374672.4:c.1405G>C	p.Asp469His	p.D469H	ENST00000374672	NM_004235.4	469	Gac/Cac	5/5	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.210489159838539	2		620	850	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0022198-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	2016	698	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.365801419628745	24	FACETS	1	0.991	1	1	0.991	1	CLONAL	21	TRUE	3	0.365801419628745	24		698	2622	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500902	8500902	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022198-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	32	615	1	ENST00000356435.5:c.1980C>A	p.His660Gln	p.H660Q	ENST00000356435		660	caC/caA	13/35	0.365801419628745	1	FACETS	0.274	0.222	0.333	0.274	0.222	0.333	SUBCLONAL	1	TRUE	0	0.365801419628745	1		616	522	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0022731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	622	462	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.477190799139056	3	FACETS	0.981	0.95	1	0.981	0.95	1	CLONAL	3	TRUE	0	0.477190799139056	3		462	1097	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1023835002	NA	P-0022731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	155	440	0	ENST00000558401.1:c.1A>G	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Gtg	1/4	0.257938158500219	1	FACETS	0.628	0.575	0.683	0.628	0.575	0.683	INDETERMINATE	1	TRUE	0	0.477190799139056	1		440	788	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0022731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	229	270	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	0.226131181426981	3	FACETS	1	0.97	1	0.701	0.659	0.744	INDETERMINATE	2	TRUE	0	0.477190799139056	3		270	565	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846325	156846325	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	333	713	0	ENST00000524377.1:c.1766T>C	p.Phe589Ser	p.F589S	ENST00000524377	NM_002529.3	589	tTt/tCt	14/17	1	2	FACETS	0.973	0.918	1	0.973	0.918	1	CLONAL	1	TRUE	1	0.477190799139056	2		713	1434	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861939	57861939	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	192	478	0	ENST00000228682.2:c.1242del	p.Lys415ArgfsTer15	p.K415Rfs*15	ENST00000228682	NM_005269.2	414	Ccc/cc	10/12	1	2	FACETS	0.879	0.814	0.948	0.879	0.814	0.948	CLONAL	1	TRUE	1	0.477190799139056	2		478	915	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29002024	29002024	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	100	492	0	ENST00000282397.4:c.1141G>T	p.Ala381Ser	p.A381S	ENST00000282397	NM_002019.4	381	Gct/Tct	9/30	0.257938158500219	1	FACETS	0.454	0.405	0.505	0.454	0.405	0.505	INDETERMINATE	1	TRUE	0	0.477190799139056	1		492	703	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217107	66217107	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	135	374	0	ENST00000273854.3:c.2508G>T	p.Arg836Ser	p.R836S	ENST00000273854	NM_004439.5	836	agG/agT	14/18	1	2	FACETS	0.907	0.827	0.99	0.907	0.827	0.99	CLONAL	1	TRUE	1	0.477190799139056	2		374	624	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532804	187532804	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	207	581	0	ENST00000441802.2:c.9589C>A	p.Leu3197Ile	p.L3197I	ENST00000441802	NM_005245.3	3197	Ctc/Atc	14/27	1	2	FACETS	0.873	0.81	0.938	0.873	0.81	0.938	CLONAL	1	TRUE	1	0.477190799139056	2		581	994	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046334	69046334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	474	471	0	ENST00000288368.4:c.3807G>T	p.Gln1269His	p.Q1269H	ENST00000288368	NM_024870.2	1269	caG/caT	32/40	0.447801316074082	4	FACETS	0.893	0.857	0.93	0.893	0.857	0.93	CLONAL	3	TRUE	1	0.477190799139056	4		471	1095	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0023100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	246	698	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.39538549382413	5	FACETS	1	0.97	1	0.707	0.662	0.754	CLONAL	2	TRUE	2	0.39538549382413	5		698	934	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0023100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	532	898	0	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	0.39538549382413	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	4	TRUE	0	0.39538549382413	4		898	904	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154241	2154242	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755455183	NA	P-0023100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	101	879	3	ENST00000434045.2:c.686dup	p.Glu230ArgfsTer50	p.E230Rfs*50	ENST00000434045	NM_001127598.1	229	cca/ccCa	5/5	0.39538549382413	4	FACETS	0.947	0.846	1	0.473	0.423	0.527	CLONAL	1	TRUE	2	0.39538549382413	4		882	753	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422697	47422697	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	178	788	0	ENST00000377045.4:c.169G>C	p.Asp57His	p.D57H	ENST00000377045	NM_001654.4	57	Gac/Cac	3/16	0.39538549382413	4	FACETS	0.781	0.721	0.844	0.521	0.481	0.563	SUBCLONAL	2	TRUE	1	0.39538549382413	4		788	804	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711962	89711962	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	52	583	0	ENST00000371953.3:c.580T>G	p.Leu194Val	p.L194V	ENST00000371953	NM_000314.4	194	Ttg/Gtg	6/9	0.39538549382413	3	FACETS	1	0.865	1	0.505	0.432	0.584	CLONAL	1	TRUE	1	0.39538549382413	3		583	312	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042482	16042482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	20	717	0	ENST00000268712.3:c.1192C>T	p.Arg398Trp	p.R398W	ENST00000268712	NM_006311.3	398	Cgg/Tgg	12/46	0.39538549382413	4	FACETS	0.388	0.296	0.496	0.194	0.148	0.248	SUBCLONAL	1	TRUE	2	0.39538549382413	4		717	364	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090530	71090530	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	45	606	0	ENST00000318789.4:c.818C>G	p.Pro273Arg	p.P273R	ENST00000318789	NM_032682.5	273	cCa/cGa	11/21	0.39538549382413	3	FACETS	0.562	0.472	0.661			1	SUBCLONAL	1	TRUE	NA	0.39538549382413	3		606	485	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930345	39930345	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	88	813	0	ENST00000378444.4:c.3119A>C	p.Asp1040Ala	p.D1040A	ENST00000378444	NM_001123385.1	1040	gAc/gCc	6/15	0.165934948068079	2	FACETS	0.805	0.715	0.901	0.402	0.357	0.451	INDETERMINATE	1	TRUE	0	0.39538549382413	2		813	553	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424269	47424269	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	191	853	1	ENST00000377045.4:c.274G>A	p.Glu92Lys	p.E92K	ENST00000377045	NM_001654.4	92	Gaa/Aaa	4/16	0.39538549382413	4	FACETS	0.853	0.791	0.918	0.569	0.527	0.612	CLONAL	2	TRUE	1	0.39538549382413	4		854	790	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424669	47424669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	185	863	2	ENST00000377045.4:c.477G>T	p.Gln159His	p.Q159H	ENST00000377045	NM_001654.4	159	caG/caT	6/16	0.39538549382413	4	FACETS	0.777	0.718	0.838	0.518	0.479	0.559	SUBCLONAL	2	TRUE	1	0.39538549382413	4		865	840	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424682	47424682	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	184	882	0	ENST00000377045.4:c.490G>A	p.Gly164Ser	p.G164S	ENST00000377045	NM_001654.4	164	Ggc/Agc	6/16	0.39538549382413	4	FACETS	1	0.99	1	0.498	0.459	0.537	CLONAL	1	TRUE	1	0.39538549382413	4		882	870	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0023321-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	250	592	1	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.4562955865305	2	FACETS	0.806	0.759	0.854	0.806	0.759	0.854	CLONAL	2	TRUE	0	0.470700950420427	2		593	659	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173715	108173716	+	missense_variant	Missense_Mutation	DNP	AC	AC	CA	novel	NA	P-0023321-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	77	444	1	ENST00000278616.4:c.5455_5456delinsCA	p.Thr1819Gln	p.T1819Q	ENST00000278616	NM_000051.3	1819	ACa/CAa	36/63	0.4562955865305	2	FACETS	0.982	0.87	1	0.491	0.435	0.551	CLONAL	1	TRUE	0	0.470700950420427	2		445	333	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46215243	46215264	+	frameshift_variant	Frame_Shift_Del	DEL	AGAGAAGACTGATAGAGACTTC	AGAGAAGACTGATAGAGACTTC	-	novel	NA	P-0023321-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	19	298	0	ENST00000334344.6:c.678_699del	p.Glu227LeufsTer58	p.E227Lfs*58	ENST00000334344	NM_152641.2	226	aaAGAGAAGACTGATAGAGACTTC/aa	6/21	0.4562955865305	2	FACETS	0.332	0.252	0.426	0.166	0.126	0.213	SUBCLONAL	1	TRUE	0	0.470700950420427	2		298	243	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061540	38061540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023321-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	157	263	3	ENST00000250448.2:c.449G>A	p.Arg150His	p.R150H	ENST00000250448	NM_004496.3	150	cGc/cAc	2/2	0.471412797649701	3	FACETS	0.89	0.822	0.959			1	CLONAL	2	TRUE	NA	0.470700950420427	3		266	463	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750750	39750750	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023321-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	119	516	0	ENST00000361337.2:c.2150G>C	p.Gly717Ala	p.G717A	ENST00000361337	NM_003286.2	717	gGa/gCa	20/21	0.4562955865305	2	FACETS	0.989	0.898	1	0.495	0.449	0.543	CLONAL	1	TRUE	0	0.470700950420427	2		516	511	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748554	43748554	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023321-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	128	434	0	ENST00000523873.1:c.508C>G	p.Arg170Gly	p.R170G	ENST00000523873		170	Cgc/Ggc	6/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.470700950420427	2		434	445	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993681	90993681	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786202085	NA	P-0023321-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	183	439	0	ENST00000265433.3:c.242A>G	p.Glu81Gly	p.E81G	ENST00000265433	NM_002485.4	81	gAa/gGa	3/16	0.338398165345102	4	FACETS	0.77	0.712	0.829	0.77	0.712	0.829	SUBCLONAL	2	TRUE	2	0.470700950420427	4		439	743	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0023357-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	61	178	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.55620826348284	3	FACETS	0.891	0.788	0.998	0.891	0.788	0.998	CLONAL	2	TRUE	1	0.557332260489021	3		178	157	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0023357-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	63	169	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	0.55620826348284	3	FACETS	0.921	0.816	1	0.921	0.816	1	CLONAL	2	TRUE	1	0.557332260489021	3		169	157	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226174	2226174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023357-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	80	425	0	ENST00000326181.6:c.1871C>T	p.Ser624Phe	p.S624F	ENST00000326181	NM_032271.2	624	tCc/tTc	19/21	0.378079208109597	5	FACETS	0.841	0.754	0.929	0.841	0.754	0.929	CLONAL	3	TRUE	2	0.557332260489021	5		425	209	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252880	36252880	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023357-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	93	241	1	ENST00000300305.3:c.482T>A	p.Leu161His	p.L161H	ENST00000300305		161	cTc/cAc	4/8	0.428848459600257	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.557332260489021	4		242	218	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827262	72827262	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023357-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	82	370	0	ENST00000268489.5:c.9319C>T	p.Gln3107Ter	p.Q3107*	ENST00000268489	NM_006885.3	3107	Cag/Tag	9/10	0.556267240031229	2	FACETS	0.886	0.804	0.969	0.886	0.804	0.969	CLONAL	2	TRUE	0	0.557332260489021	2		370	166	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217458	7217458	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023357-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	62	390	0	ENST00000380728.2:c.338C>A	p.Ser113Ter	p.S113*	ENST00000380728		113	tCa/tAa	5/11	0.557332260489021	2	FACETS	0.951	0.853	1	0.951	0.853	1	CLONAL	2	TRUE	0	0.557332260489021	2		390	117	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100041	157100055	+	inframe_deletion	In_Frame_Del	DEL	AGGAGGAGCAGGAGC	AGGAGGAGCAGGAGC	-	rs773423003	NA	P-0023357-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	13	506	0	ENST00000346085.5:c.993_1007del	p.Gly333_Gly337del	p.G333_G337del	ENST00000346085	NM_020732.3	326	ggAGGAGGAGCAGGAGCa/gga	1/20	0.55620826348284	3	FACETS	0.414	0.297	0.556	0.207	0.148	0.278	SUBCLONAL	1	TRUE	1	0.557332260489021	3		506	144	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849652	68849652	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023357-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	80	334	0	ENST00000261769.5:c.1555C>T	p.Gln519Ter	p.Q519*	ENST00000261769	NM_004360.3	519	Cag/Tag	10/16	0.556267240031229	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	0	0.557332260489021	2		334	141	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016559	12016559	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023357-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	68	236	0	ENST00000353533.5:c.695C>T	p.Pro232Leu	p.P232L	ENST00000353533	NM_003010.3	232	cCt/cTt	7/11	0.557332260489021	2	FACETS	0.891	0.8	0.981	0.891	0.8	0.981	CLONAL	2	TRUE	0	0.557332260489021	2		236	137	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348485	56348485	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023357-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	10	336	0	ENST00000348428.3:c.297del	p.Gly100ValfsTer7	p.G100Vfs*7	ENST00000348428	NM_006785.3	98	gAa/ga	2/17	0.556267240031229	2	FACETS	0.18	0.122	0.254	0.09	0.061	0.127	SUBCLONAL	1	TRUE	0	0.557332260489021	2		336	199	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118339493	118339493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782605513	NA	P-0023357-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	35	219	0	ENST00000534358.1:c.436G>A	p.Glu146Lys	p.E146K	ENST00000534358	NM_005933.3	146	Gag/Aag	2/36	0.55620826348284	3	FACETS	0.945	0.784	1	0.472	0.392	0.56	CLONAL	1	TRUE	1	0.557332260489021	3		219	170	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911982	32911982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023357-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	65	307	0	ENST00000380152.3:c.3490C>T	p.Leu1164Phe	p.L1164F	ENST00000380152		1164	Ctt/Ttt	11/27	0.425814049980923	3	FACETS	0.877	0.778	0.98	0.877	0.778	0.98	CLONAL	2	TRUE	1	0.557332260489021	3		307	170	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978815	13978815	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023357-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	115	243	0	ENST00000405192.2:c.292G>C	p.Glu98Gln	p.E98Q	ENST00000405192	NM_001163147.1	98	Gaa/Caa	6/12	0.558213272599527	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	2	0.557332260489021	4		243	298	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44733219	44733219	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023357-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	88	275	0	ENST00000377967.4:c.211G>C	p.Ala71Pro	p.A71P	ENST00000377967	NM_021140.2	71	Gcc/Ccc	2/29	0.378079208109597	5	FACETS	0.899	0.813	0.987	0.899	0.813	0.987	CLONAL	3	TRUE	2	0.557332260489021	5		275	215	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223070	41223070	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023357-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	14	369	0	ENST00000357654.3:c.4861G>A	p.Asp1621Asn	p.D1621N	ENST00000357654	NM_007294.3	1621	Gat/Aat	15/23	0.557332260489021	2	FACETS	0.235	0.17	0.313	0.117	0.085	0.157	SUBCLONAL	1	TRUE	0	0.557332260489021	2		369	214	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29440871	29440871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372884606	NA	P-0023357-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	24	255	0	ENST00000544604.2:c.737G>A	p.Arg246His	p.R246H	ENST00000544604	NM_001206998.1	246	cGc/cAc	5/9	0.558213272599527	4	FACETS	0.667	0.526	0.828	0.334	0.263	0.414	SUBCLONAL	1	TRUE	2	0.557332260489021	4		255	201	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	543	1032	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.307480940439004	6	FACETS	0.973	0.937	1	0.973	0.937	1	CLONAL	5	TRUE	1	0.307480940439004	6		1032	1172	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579522	7579522	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	261	1134	1	ENST00000269305.4:c.165del	p.Glu56LysfsTer67	p.E56Kfs*67	ENST00000269305	NM_001126112.2	55	acT/ac	4/11	0.307480940439004	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.307480940439004	2		1135	705	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620615	52620616	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TTAA	novel	NA	P-0023478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	227	884	0	ENST00000394830.3:c.3134_3137dup	p.Lys1046AsnfsTer2	p.K1046Nfs*2	ENST00000394830	NM_018313.4	1046	aag/aaTTAAg	21/30	0.307480940439004	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.307480940439004	2		884	656	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0024196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	111	704	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	0.2502288742154	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.2502288742154	1		704	759	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321727	62321729	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs771771098	NA	P-0024196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	44	697	0	ENST00000360203.5:c.2351_2353del	p.Phe784del	p.F784del	ENST00000360203	NM_001283009.1	782	ccCTTc/ccc	26/35	NA	2	FACETS	0.463	0.387	0.547			1	INDETERMINATE	1	TRUE	NA	0.2502288742154	2		697	760	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589014	67589015	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0024196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	52	288	0	ENST00000274335.5:c.1105_1106insAT	p.Thr369AsnfsTer5	p.T369Nfs*5	ENST00000274335		369	act/aATct	8/15	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.2502288742154	2		288	343	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589575	67589613	+	inframe_deletion	In_Frame_Del	DEL	GAAAAAATTACATGAATATAACACTCAGTTTCAAGAAAA	GAAAAAATTACATGAATATAACACTCAGTTTCAAGAAAA	-	novel	NA	P-0024196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	20	299	0	ENST00000274335.5:c.1338_1376del	p.Lys447_Lys459del	p.K447_K459del	ENST00000274335		446	ggGAAAAAATTACATGAATATAACACTCAGTTTCAAGAAAAa/gga	10/15	1	2	FACETS	0.423	0.323	0.541	0.423	0.323	0.541	SUBCLONAL	1	TRUE	1	0.2502288742154	2		299	378	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005283	150005284	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0024196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	64	511	0	ENST00000253339.5:c.941_942del	p.Asn314ThrfsTer7	p.N314Tfs*7	ENST00000253339		314	aAT/a	3/7	1	2	FACETS	0.776	0.672	0.89	0.776	0.672	0.89	SUBCLONAL	1	TRUE	1	0.2502288742154	2		511	659	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350000	70350000	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	35	602	0	ENST00000374080.3:c.3983A>T	p.His1328Leu	p.H1328L	ENST00000374080		1328	cAt/cTt	28/45	1	2	FACETS	0.402	0.328	0.485	0.402	0.328	0.485	SUBCLONAL	1	TRUE	1	0.2502288742154	2		602	696	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0024348-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	375	448	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	1	2	FACETS	0.969	0.926	1	0.969	0.926	1	CLONAL	1	TRUE	1	0.955060366653113	2		448	810	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599341	55599341	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519761	NA	P-0024348-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	325	414	0	ENST00000288135.5:c.2467T>G	p.Tyr823Asp	p.Y823D	ENST00000288135	NM_000222.2	823	Tat/Gat	17/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.955060366653113	2		414	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578242	7578242	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882003	NA	P-0024572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	46	1037	1	ENST00000269305.4:c.607G>T	p.Val203Leu	p.V203L	ENST00000269305	NM_001126112.2	203	Gtg/Ttg	6/11	1	2	FACETS	0.47	0.395	0.553	0.47	0.395	0.553	SUBCLONAL	1	TRUE	1	0.324015470197263	2		1038	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0024801-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	939	792	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.838493332984086	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.839929526248249	2		792	1094	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038260	30038260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1185977513	NA	P-0024801-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	300	485	0	ENST00000338641.4:c.433G>A	p.Ala145Thr	p.A145T	ENST00000338641	NM_000268.3	145	Gcc/Acc	4/16	1	2	FACETS	0.979	0.927	1	0.979	0.927	1	CLONAL	1	TRUE	1	0.839929526248249	2		485	730	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16062142	16062142	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1391561740	NA	P-0024801-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1711	294	503	0	ENST00000268712.3:c.664C>G	p.Pro222Ala	p.P222A	ENST00000268712	NM_006311.3	222	Ccc/Gcc	6/46	0.839929526248249	7	FACETS	1	0.976	1	0.155	0.144	0.165	CLONAL	1	TRUE	0	0.839929526248249	7		503	2005	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278122	15278122	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024801-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	666	570	0	ENST00000263388.2:c.5300C>G	p.Ala1767Gly	p.A1767G	ENST00000263388	NM_000435.2	1767	gCa/gGa	29/33	0.838493332984086	4	FACETS	0.999	0.965	1	0.666	0.643	0.689	CLONAL	2	TRUE	1	0.839929526248249	4		570	1461	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22123583	22123583	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024801-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	445	434	0	ENST00000215832.6:c.993del	p.Phe331LeufsTer16	p.F331Lfs*16	ENST00000215832	NM_002745.4	331	ttC/tt	8/9	0.838493332984086	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.839929526248249	3		434	735	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592115	55592115	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024801-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	212	423	0	ENST00000288135.5:c.1439C>G	p.Ser480Cys	p.S480C	ENST00000288135	NM_000222.2	480	tCt/tGt	9/21	0.776912956893894	3	FACETS	1	0.965	1	0.526	0.491	0.563	CLONAL	1	TRUE	1	0.839929526248249	3		423	681	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177789	56177789	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024801-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	253	567	0	ENST00000399503.3:c.2762G>T	p.Ser921Ile	p.S921I	ENST00000399503	NM_005921.1	921	aGt/aTt	14/20	NA	2	FACETS	0.988	0.932	1			1	INDETERMINATE	1	TRUE	NA	0.839929526248249	2		567	610	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006851	47006851	+	5_prime_UTR_variant	5'UTR	SNP	C	C	A	novel	NA	P-0024801-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	218	566	1	ENST00000377604.3:c.-30C>A		p.*10*	ENST00000377604	NM_001204468.1	-/852		2/24	NA	2	FACETS	0.597	0.556	0.64			1	INDETERMINATE	1	TRUE	NA	0.839929526248249	2		567	869	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546833	9546833	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024845-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	78	644	0	ENST00000353224.5:c.1189del	p.Thr397ArgfsTer5	p.T397Rfs*5	ENST00000353224	NM_177990.2	397	Acg/cg	5/10	1	2	FACETS	0.693	0.61	0.783	0.693	0.61	0.783	SUBCLONAL	1	TRUE	1	0.394648517679337	2		644	570	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0025080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	180	241	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.983	0.91	1	0.983	0.91	1	CLONAL	1	TRUE	1	0.577822664920679	2		241	634	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361255	66361255	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	30	259	0	ENST00000273854.3:c.917G>A	p.Arg306Lys	p.R306K	ENST00000273854	NM_004439.5	306	aGa/aAa	4/18	1	2	FACETS	0.202	0.162	0.247	0.202	0.162	0.247	SUBCLONAL	1	TRUE	1	0.577822664920679	2		259	514	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189412	56189412	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	180	566	0	ENST00000399503.3:c.4444C>T	p.Arg1482Ter	p.R1482*	ENST00000399503	NM_005921.1	1482	Cga/Tga	20/20	1	2	FACETS	0.666	0.614	0.72	0.666	0.614	0.72	SUBCLONAL	1	TRUE	1	0.577822664920679	2		566	935	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830976	72830976	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	202	451	0	ENST00000268489.5:c.5605C>T	p.Gln1869Ter	p.Q1869*	ENST00000268489	NM_006885.3	1869	Cag/Tag	9/10	1	2	FACETS	0.96	0.893	1	0.96	0.893	1	CLONAL	1	TRUE	1	0.577822664920679	2		451	728	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229292	36229292	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	66	628	0	ENST00000222270.7:c.7982C>G	p.Ser2661Cys	p.S2661C	ENST00000222270	NM_014727.1	2661	tCt/tGt	37/37	1	2	FACETS	0.224	0.193	0.257	0.224	0.193	0.257	SUBCLONAL	1	TRUE	1	0.577822664920679	2		628	1021	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0025080-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	71	241	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.898	0.797	1	0.898	0.797	1	CLONAL	1	FALSE	1	0.756759326246681	2		241	209	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361255	66361255	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025080-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	104	259	0	ENST00000273854.3:c.917G>A	p.Arg306Lys	p.R306K	ENST00000273854	NM_004439.5	306	aGa/aAa	4/18	0.448000929658122	3	FACETS	1	0.985	1			1	INDETERMINATE	1	FALSE	NA	0.756759326246681	3		259	259	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830976	72830976	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025080-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	188	451	0	ENST00000268489.5:c.5605C>T	p.Gln1869Ter	p.Q1869*	ENST00000268489	NM_006885.3	1869	Cag/Tag	9/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.756759326246681	2		451	446	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140500172	140500172	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025080-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	321	771	0	ENST00000288602.6:c.970G>A	p.Asp324Asn	p.D324N	ENST00000288602	NM_004333.4	324	Gac/Aac	7/18	1	2	FACETS	0.931	0.882	0.981	0.931	0.882	0.981	CLONAL	1	FALSE	1	0.756759326246681	2		771	911	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799129	42799129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139613152	NA	P-0025139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	306	687	0	ENST00000575354.2:c.4613C>T	p.Pro1538Leu	p.P1538L	ENST00000575354	NM_015125.3	1538	cCg/cTg	20/20	0.73186486037118	1	FACETS	0.975	0.931	1	0.975	0.931	1	CLONAL	1	TRUE	0	0.73186486037118	1		687	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579702	7579702	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	287	587	0	ENST00000269305.4:c.94del	p.Leu32CysfsTer12	p.L32Cfs*12	ENST00000269305	NM_001126112.2	32	Ctg/tg	3/11	0.730531375009315	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.73186486037118	1		587	494	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642558	117642558	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0025139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	298	719	0	ENST00000368508.3:c.5642-1G>T		p.X1881_splice	ENST00000368508	NM_002944.2	1881			1	2	FACETS	0.957	0.904	1	0.957	0.904	1	CLONAL	1	TRUE	1	0.73186486037118	2		719	851	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870472	40870472	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs923918969	NA	P-0025139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	57	686	1	ENST00000428826.2:c.931C>T	p.Pro311Ser	p.P311S	ENST00000428826		311	Cct/Tct	9/21	0.730531375009315	1	FACETS	0.168	0.144	0.195	0.168	0.144	0.195	SUBCLONAL	1	TRUE	0	0.73186486037118	1		687	587	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490980	56490980	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs931676601	NA	P-0025199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	291	454	0	ENST00000267101.3:c.2426A>G	p.Gln809Arg	p.Q809R	ENST00000267101	NM_001982.3	809	cAg/cGg	20/28	1	2	FACETS	0.984	0.931	1	0.984	0.931	1	CLONAL	1	TRUE	1	0.789795010733733	2		454	749	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015315	176015315	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0025199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	26	381	1	ENST00000367669.3:c.1421+2T>C		p.X474_splice	ENST00000367669	NM_022457.5	474			0.789795010733733	3	FACETS	0.201	0.158	0.249	0.1	0.079	0.125	SUBCLONAL	1	TRUE	1	0.789795010733733	3		382	458	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489535	56489535	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	299	489	0	ENST00000267101.3:c.2000G>T	p.Arg667Leu	p.R667L	ENST00000267101	NM_001982.3	667	cGt/cTt	17/28	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.789795010733733	2		489	749	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976742	2976742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1225008718	NA	P-0025199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	351	609	1	ENST00000396946.4:c.1270C>T	p.Arg424Trp	p.R424W	ENST00000396946	NM_032415.4	424	Cgg/Tgg	9/25	0.789795010733733	3	FACETS	1	0.966	1	0.513	0.485	0.541	CLONAL	1	TRUE	1	0.789795010733733	3		610	1209	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	38	204	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.422698292332868	2		204	171	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	12	213	0	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	1	2	FACETS	0.332	0.234	0.452	0.332	0.234	0.452	SUBCLONAL	1	TRUE	1	0.422698292332868	2		213	171	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	16	163	1	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.433	0.321	0.565	0.433	0.321	0.565	SUBCLONAL	1	TRUE	1	0.422698292332868	2		164	175	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600392	10600392	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	97	433	1	ENST00000171111.5:c.1463A>T	p.Glu488Val	p.E488V	ENST00000171111	NM_203500.1	488	gAg/gTg	4/6	0.422698292332868	1	FACETS	0.868	0.779	0.962	0.868	0.779	0.962	CLONAL	1	TRUE	0	0.422698292332868	1		434	417	SUCCESS
APC	324	MSKCC	GRCh37	5	112102932	112102932	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554069710	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	23	179	0	ENST00000257430.4:c.271del	p.Met91CysfsTer34	p.M91Cfs*34	ENST00000257430	NM_000038.5	89	tcA/tc	4/16	0.422698292332868	1	FACETS	0.867	0.69	1	0.867	0.69	1	CLONAL	1	TRUE	0	0.422698292332868	1		179	99	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426737	47426737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200106543	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	60	321	1	ENST00000377045.4:c.982C>T	p.Arg328Trp	p.R328W	ENST00000377045	NM_001654.4	328	Cgg/Tgg	10/16	0.20557996342577	1	FACETS	0.754	0.655	0.86	0.754	0.655	0.86	INDETERMINATE	1	TRUE	0	0.422698292332868	1		322	297	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300040	137300040	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	33	486	3	ENST00000481739.1:c.331del	p.Leu111TrpfsTer57	p.L111Wfs*57	ENST00000481739	NM_002957.4	109	Ccc/cc	3/10	1	2	FACETS	0.298	0.242	0.361	0.298	0.242	0.361	SUBCLONAL	1	TRUE	1	0.422698292332868	2		489	524	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927443	245927443	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	47	269	0	ENST00000388985.4:c.1085del	p.Phe362SerfsTer12	p.F362Sfs*12	ENST00000388985		362	tTc/tc	11/12	0.422698292332868	3	FACETS	0.692	0.586	0.81	0.346	0.293	0.405	SUBCLONAL	1	TRUE	1	0.422698292332868	3		269	389	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300076	137300076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373515948	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	65	493	2	ENST00000481739.1:c.361G>A	p.Ala121Thr	p.A121T	ENST00000481739	NM_002957.4	121	Gcc/Acc	3/10	1	2	FACETS	0.601	0.521	0.686	0.601	0.521	0.686	SUBCLONAL	1	TRUE	1	0.422698292332868	2		495	512	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704499	117704499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	20	132	0	ENST00000368508.3:c.2477C>T	p.Pro826Leu	p.P826L	ENST00000368508	NM_002944.2	826	cCt/cTt	16/43	1	2	FACETS	0.644	0.497	0.812	0.644	0.497	0.812	SUBCLONAL	1	TRUE	1	0.422698292332868	2		132	147	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109769	115109769	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	102	496	1	ENST00000257566.3:c.2109del	p.Met704CysfsTer185	p.M704Cfs*185	ENST00000257566	NM_016569.3	703	tcC/tc	8/8	1	2	FACETS	0.956	0.858	1	0.956	0.858	1	CLONAL	1	TRUE	1	0.422698292332868	2		497	505	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097022	11097044	+	protein_altering_variant	In_Frame_Del	DEL	ATTTAACCAGAACCAGCTGCACC	ATTTAACCAGAACCAGCTGCACC	GCACG	novel	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	72	498	2	ENST00000358026.2:c.513_535delinsGCACG	p.Phe172_Gln179delinsHisGlu	p.F172_Q179delinsHE	ENST00000358026	NM_001128849.1	171	ccATTTAACCAGAACCAGCTGCACCag/ccGCACGag	4/36	0.422698292332868	1	FACETS	0.768	0.675	0.866	0.768	0.675	0.866	SUBCLONAL	1	TRUE	0	0.422698292332868	1		500	350	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815712	32815712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1374606443	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	74	370	0	ENST00000354258.4:c.1904G>A	p.Arg635His	p.R635H	ENST00000354258	NM_000593.5	635	cGc/cAc	8/11	1	2	FACETS	0.9	0.792	1	0.9	0.792	1	CLONAL	1	TRUE	1	0.422698292332868	2		370	389	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409042	139409042	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	83	533	0	ENST00000277541.6:c.2127C>G	p.His709Gln	p.H709Q	ENST00000277541	NM_017617.3	709	caC/caG	13/34	1	2	FACETS	0.806	0.714	0.905	0.806	0.714	0.905	CLONAL	1	TRUE	1	0.422698292332868	2		533	487	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262463	16262463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	30	113	0	ENST00000375759.3:c.9728C>T	p.Pro3243Leu	p.P3243L	ENST00000375759	NM_015001.2	3243	cCc/cTc	11/15	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.422698292332868	2		113	136	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78425922	78425923	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	26	176	0	ENST00000370768.2:c.1522dup	p.Gln508ProfsTer17	p.Q508Pfs*17	ENST00000370768	NM_003902.3	508	cag/cCag	16/20	1	2	FACETS	0.586	0.467	0.721	0.586	0.467	0.721	SUBCLONAL	1	TRUE	1	0.422698292332868	2		176	210	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981887	201981887	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	43	468	0	ENST00000359651.3:c.598G>T	p.Gly200Trp	p.G200W	ENST00000359651		200	Ggg/Tgg	4/8	0.422698292332868	3	FACETS	0.377	0.315	0.447	0.189	0.157	0.224	SUBCLONAL	1	TRUE	1	0.422698292332868	3		468	653	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575147	64575147	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886039414	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	31	222	0	ENST00000312049.6:c.660G>A	p.Trp220Ter	p.W220*	ENST00000312049	NM_130799.2	220	tgG/tgA	4/10	1	2	FACETS	0.638	0.519	0.771	0.638	0.519	0.771	SUBCLONAL	1	TRUE	1	0.422698292332868	2		222	230	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643682	38643682	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	44	281	0	ENST00000299084.4:c.1152G>T	p.Glu384Asp	p.E384D	ENST00000299084	NM_152594.2	384	gaG/gaT	7/7	1	2	FACETS	0.738	0.623	0.864	0.738	0.623	0.864	SUBCLONAL	1	TRUE	1	0.422698292332868	2		281	282	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984856	9984856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	58	233	0	ENST00000330684.3:c.1109G>A	p.Arg370Gln	p.R370Q	ENST00000330684	NM_001134407.1	370	cGg/cAg	4/13	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.422698292332868	2		233	273	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654633	67654633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	50	193	2	ENST00000264010.4:c.1120A>G	p.Thr374Ala	p.T374A	ENST00000264010	NM_006565.3	374	Act/Gct	6/12	1	2	FACETS	0.943	0.807	1	0.943	0.807	1	CLONAL	1	TRUE	1	0.422698292332868	2		195	251	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942073	81942073	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	19	285	0	ENST00000359376.3:c.1610T>C	p.Val537Ala	p.V537A	ENST00000359376	NM_002661.3	537	gTg/gCg	17/33	1	2	FACETS	0.281	0.213	0.361	0.281	0.213	0.361	SUBCLONAL	1	TRUE	1	0.422698292332868	2		285	320	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765802	41765802	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	34	170	0	ENST00000301178.4:c.2678G>T	p.Gly893Val	p.G893V	ENST00000301178	NM_021913.4	893	gGt/gTt	20/20	0.370739713519183	3	FACETS	0.701	0.575	0.841	0.35	0.287	0.421	SUBCLONAL	1	TRUE	1	0.422698292332868	3		170	278	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288989	212288989	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	26	205	0	ENST00000342788.4:c.2757A>C	p.Lys919Asn	p.K919N	ENST00000342788	NM_005235.2	919	aaA/aaC	23/28	1	2	FACETS	0.764	0.611	0.935	0.764	0.611	0.935	CLONAL	1	TRUE	1	0.422698292332868	2		205	161	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513480	41513480	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1244840343	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	24	283	0	ENST00000263253.7:c.384G>T	p.Gln128His	p.Q128H	ENST00000263253	NM_001429.3	128	caG/caT	2/31	1	2	FACETS	0.369	0.289	0.46	0.369	0.289	0.46	SUBCLONAL	1	TRUE	1	0.422698292332868	2		283	308	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55974007	55974007	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	68	313	0	ENST00000263923.4:c.1309T>C	p.Tyr437His	p.Y437H	ENST00000263923	NM_002253.2	437	Tac/Cac	10/30	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.422698292332868	2		313	284	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911200	29911200	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs199474540	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	26	283	0	ENST00000376809.5:c.499A>C	p.Thr167Pro	p.T167P	ENST00000376809	NM_002116.7	167	Acc/Ccc	3/8	1	2	FACETS	0.508	0.404	0.627	0.508	0.404	0.627	SUBCLONAL	1	TRUE	1	0.422698292332868	2		283	242	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508284	106508284	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	27	134	0	ENST00000359195.3:c.278C>A	p.Pro93Gln	p.P93Q	ENST00000359195	NM_002649.2	93	cCg/cAg	2/11	1	2	FACETS	0.687	0.551	0.839	0.687	0.551	0.839	SUBCLONAL	1	TRUE	1	0.422698292332868	2		134	186	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395457	116395458	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	47	208	0	ENST00000397752.3:c.1752_1753del	p.Cys584TrpfsTer10	p.C584Wfs*10	ENST00000397752	NM_000245.2	584	TGt/t	6/21	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.422698292332868	2		208	209	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5055689	5055689	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	19	147	0	ENST00000381652.3:c.960del	p.Pro321LeufsTer22	p.P321Lfs*22	ENST00000381652	NM_004972.3	319	gaT/ga	8/25	0.422698292332868	1	FACETS	0.945	0.736	1	0.945	0.736	1	CLONAL	1	TRUE	0	0.422698292332868	1		147	75	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912238	97912238	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	58	245	0	ENST00000289081.3:c.653A>C	p.Glu218Ala	p.E218A	ENST00000289081	NM_000136.2	218	gAg/gCg	7/15	1	2	FACETS	0.924	0.8	1	0.924	0.8	1	CLONAL	1	TRUE	1	0.422698292332868	2		245	297	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321300	1321300	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	51	254	0	ENST00000400841.2:c.455A>T	p.Tyr152Phe	p.Y152F	ENST00000400841		152	tAc/tTc	4/6	0.20557996342577	1	FACETS	0.735	0.63	0.848	0.735	0.63	0.848	INDETERMINATE	1	TRUE	0	0.422698292332868	1		254	259	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426421	47426421	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	52	357	0	ENST00000377045.4:c.764G>T	p.Arg255Leu	p.R255L	ENST00000377045	NM_001654.4	255	cGg/cTg	9/16	0.20557996342577	1	FACETS	0.574	0.491	0.664	0.574	0.491	0.664	INDETERMINATE	1	TRUE	0	0.422698292332868	1		357	338	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617634	100617634	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	41	357	0	ENST00000308731.7:c.435C>G	p.Cys145Trp	p.C145W	ENST00000308731	NM_000061.2	145	tgC/tgG	6/19	0.20557996342577	1	FACETS	0.533	0.446	0.629	0.533	0.446	0.629	INDETERMINATE	1	TRUE	0	0.422698292332868	1		357	287	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220506	123220506	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	40	280	0	ENST00000218089.9:c.3163G>T	p.Asp1055Tyr	p.D1055Y	ENST00000218089	NM_001042749.1	1055	Gac/Tac	30/35	0.20557996342577	1	FACETS	0.535	0.447	0.632	0.535	0.447	0.632	INDETERMINATE	1	TRUE	0	0.422698292332868	1		280	279	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198261042	198261042	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	44	283	0	ENST00000335508.6:c.3277G>A	p.Val1093Ile	p.V1093I	ENST00000335508	NM_012433.2	1093	Gta/Ata	23/25	0.229599541584186	3	FACETS	0.592	0.497	0.698	0.296	0.248	0.349	INDETERMINATE	1	TRUE	1	0.401764269655412	3		283	444	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980808	40980808	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	141	506	0	ENST00000373198.4:c.1678A>G	p.Thr560Ala	p.T560A	ENST00000373198	NM_133170.3	560	Acc/Gcc	10/32	0.130452526296071	3	FACETS	1	0.985	1	0.69	0.631	0.751	INDETERMINATE	1	TRUE	1	0.401764269655412	3		506	611	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0025958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	1504	871	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.599618892508387	5	FACETS	1	0.996	1			1	CLONAL	5	TRUE	NA	0.666049205667626	5		871	1766	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291371	11291371	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	174	640	0	ENST00000361445.4:c.2635G>A	p.Gly879Ser	p.G879S	ENST00000361445	NM_004958.3	879	Ggt/Agt	17/58	0.211838721903063	4	FACETS	1	0.968	1	0.546	0.503	0.59	INDETERMINATE	1	TRUE	2	0.666049205667626	4		640	797	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255068	16255068	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	132	550	0	ENST00000375759.3:c.2333A>T	p.Asp778Val	p.D778V	ENST00000375759	NM_015001.2	778	gAc/gTc	11/15	0.211838721903063	4	FACETS	1	0.927	1	0.51	0.464	0.559	INDETERMINATE	1	TRUE	2	0.666049205667626	4		550	647	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919101	178919101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs541134560	NA	P-0026300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	56	104	0	ENST00000263967.3:c.586G>A	p.Val196Ile	p.V196I	ENST00000263967	NM_006218.2	196	Gta/Ata	4/21	0.579780179094349	4	FACETS	0.807	0.694	0.93	0.269	0.231	0.31	CLONAL	1	TRUE	1	0.579780179094349	4		104	378	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526648	106526648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	110	188	0	ENST00000359195.3:c.2941G>A	p.Glu981Lys	p.E981K	ENST00000359195	NM_002649.2	981	Gag/Aag	10/11	0.252664635623639	4	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.579780179094349	4		188	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0026300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	146	287	0	ENST00000269305.4:c.560-2A>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.579780179094349	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.579780179094349	1		287	351	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511645	46511645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	322	332	0	ENST00000262741.5:c.1132G>A	p.Gly378Ser	p.G378S	ENST00000262741	NM_003629.3	378	Ggt/Agt	9/10	0.564156031540979	2	FACETS	0.983	0.94	1	0.983	0.94	1	CLONAL	2	TRUE	0	0.579780179094349	2		332	565	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418679	49418696	+	inframe_deletion	In_Frame_Del	DEL	CAGCCTCTTTTCTCATGG	CAGCCTCTTTTCTCATGG	-	novel	NA	P-0026300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	116	270	0	ENST00000301067.7:c.15818_15835del	p.Ala5273_Ala5278del	p.A5273_A5278del	ENST00000301067	NM_003482.3	5273	gCCATGAGAAAAGAGGCTGac/gac	49/54	1	2	FACETS	0.808	0.732	0.888	0.808	0.732	0.888	CLONAL	1	TRUE	1	0.579780179094349	2		270	495	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778390	3778390	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	186	403	0	ENST00000262367.5:c.6658G>T	p.Gly2220Cys	p.G2220C	ENST00000262367	NM_004380.2	2220	Ggc/Tgc	31/31	0.579780179094349	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.579780179094349	1		403	436	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246871	41246871	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1376262238	NA	P-0026300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	68	120	0	ENST00000357654.3:c.677G>A	p.Cys226Tyr	p.C226Y	ENST00000357654	NM_007294.3	226	tGt/tAt	10/23	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.579780179094349	2		120	214	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414877	56414877	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	157	281	0	ENST00000348428.3:c.2278G>T	p.Val760Phe	p.V760F	ENST00000348428	NM_006785.3	760	Gtt/Ttt	17/17	0.579780179094349	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.579780179094349	1		281	374	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281213	46281213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148634537	NA	P-0026300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	137	254	0	ENST00000371998.3:c.4010C>T	p.Ser1337Leu	p.S1337L	ENST00000371998		1337	tCg/tTg	21/23	1	2	FACETS	0.974	0.892	1	0.974	0.892	1	CLONAL	1	TRUE	1	0.579780179094349	2		254	485	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31483733	31483733	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	54	111	0	ENST00000344624.3:c.1999C>G	p.Pro667Ala	p.P667A	ENST00000344624		667	Cct/Gct	13/33	0.579780179094349	7	FACETS	0.918	0.785	1	0.153	0.13	0.178	CLONAL	1	TRUE	1	0.579780179094349	7		111	497	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509244	106509244	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	120	294	0	ENST00000359195.3:c.1238G>C	p.Trp413Ser	p.W413S	ENST00000359195	NM_002649.2	413	tGg/tCg	2/11	0.252664635623639	4	FACETS	0.922	0.834	1			1	INDETERMINATE	1	TRUE	NA	0.579780179094349	4		294	709	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340239	116340239	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	80	164	0	ENST00000397752.3:c.1101C>G	p.Ile367Met	p.I367M	ENST00000397752	NM_000245.2	367	atC/atG	2/21	0.252664635623639	4	FACETS	1	0.944	1			1	INDETERMINATE	1	TRUE	NA	0.579780179094349	4		164	392	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0026361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	178	241	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.75784107274807	2		241	426	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441989	52441990	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0026361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	142	250	0	ENST00000460680.1:c.359dup	p.Ser123GlnfsTer3	p.S123Qfs*3	ENST00000460680	NM_004656.3	120	aag/aaAg	5/17	1	2	FACETS	0.844	0.776	0.914	0.844	0.776	0.914	CLONAL	1	TRUE	1	0.75784107274807	2		250	444	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123199741	123199741	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	97	197	1	ENST00000218089.9:c.2041G>T	p.Glu681Ter	p.E681*	ENST00000218089	NM_001042749.1	681	Gaa/Taa	21/35	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.75784107274807	2		198	245	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0026361-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	209	586	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.652696793624075	1	FACETS	0.992	0.933	1	0.992	0.933	1	CLONAL	1	TRUE	0	0.652696793624075	1		586	435	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670125	29670125	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026361-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	80	383	0	ENST00000356175.3:c.7098C>A	p.Asn2366Lys	p.N2366K	ENST00000356175	NM_000267.3	2366	aaC/aaA	47/57	0.652696793624075	1	FACETS	0.409	0.362	0.459	0.409	0.362	0.459	SUBCLONAL	1	TRUE	0	0.652696793624075	1		383	404	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685595	29685599	+	frameshift_variant	Frame_Shift_Del	DEL	TACCA	TACCA	-	novel	NA	P-0026361-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	140	443	0	ENST00000356175.3:c.8006_8010del	p.Tyr2669Ter	p.Y2669*	ENST00000356175	NM_000267.3	2669	TACCAt/t	54/57	0.652696793624075	1	FACETS	0.733	0.675	0.793	0.733	0.675	0.793	SUBCLONAL	1	TRUE	0	0.652696793624075	1		443	394	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0026481-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	83	556	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.809273089779141	2		556	197	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953730	48953730	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs3092891	NA	P-0026481-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	73	151	0	ENST00000267163.4:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000267163	NM_000321.2	445	Cga/Tga	14/27	0.809273089779141	1	FACETS	0.846	0.769	0.921	0.846	0.769	0.921	CLONAL	1	TRUE	0	0.809273089779141	1		151	127	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101235	27101235	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026481-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	213	459	0	ENST00000324856.7:c.4517del	p.Tyr1506LeufsTer21	p.Y1506Lfs*21	ENST00000324856	NM_006015.4	1506	tAt/tt	18/20	1	2	FACETS	0.84	0.785	0.896	0.84	0.785	0.896	CLONAL	1	TRUE	1	0.809273089779141	2		459	627	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845755	68845756	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0026481-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	149	320	0	ENST00000261769.5:c.1003dup	p.Arg335ProfsTer15	p.R335Pfs*15	ENST00000261769	NM_004360.3	334	gac/gaCc	7/16	0.809273089779141	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.809273089779141	1		320	217	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180499	56180499	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0026481-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	120	259	0	ENST00000399503.3:c.3828T>A	p.Tyr1276Ter	p.Y1276*	ENST00000399503	NM_005921.1	1276	taT/taA	16/20	0.809273089779141	3	FACETS	0.989	0.901	1	0.495	0.45	0.541	CLONAL	1	TRUE	1	0.809273089779141	3		259	421	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181875	56181875	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026481-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	240	214	0	ENST00000399503.3:c.4099C>G	p.His1367Asp	p.H1367D	ENST00000399503	NM_005921.1	1367	Cac/Gac	17/20	0.809273089779141	3	FACETS	0.973	0.924	1	0.973	0.924	1	CLONAL	2	TRUE	1	0.809273089779141	3		214	428	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026481-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	150	456	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	1	2	FACETS	0.658	0.605	0.714	0.658	0.605	0.714	SUBCLONAL	1	TRUE	1	0.809273089779141	2		456	563	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945402	151945403	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0026481-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	42	236	0	ENST00000262189.6:c.2116dup	p.Ser706LysfsTer7	p.S706Kfs*7	ENST00000262189	NM_170606.2	706	agt/aAgt	14/59	1	2	FACETS	0.32	0.268	0.378	0.32	0.268	0.378	SUBCLONAL	1	TRUE	1	0.809273089779141	2		236	324	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0026540-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	79	556	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.646076020767771	2		556	216	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174909	56174909	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026540-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	181	500	0	ENST00000399503.3:c.2070del	p.Lys690AsnfsTer35	p.K690Nfs*35	ENST00000399503	NM_005921.1	690	Aaa/aa	11/20	0.646076020767771	3	FACETS	0.978	0.904	1	0.489	0.452	0.527	CLONAL	1	TRUE	1	0.646076020767771	3		500	758	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178245	56178246	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026540-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	421	600	0	ENST00000399503.3:c.3221dup	p.Asp1075ArgfsTer6	p.D1075Rfs*6	ENST00000399503	NM_005921.1	1073	cag/caGg	14/20	0.646076020767771	3	FACETS	0.928	0.888	0.968	0.928	0.888	0.968	CLONAL	2	TRUE	1	0.646076020767771	3		600	929	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026540-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	121	761	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.412618498159133	1	FACETS	0.43	0.389	0.472	0.43	0.389	0.472	SUBCLONAL	1	TRUE	0	0.646076020767771	1		761	590	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878175	151878175	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026540-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	398	792	0	ENST00000262189.6:c.6770del	p.Arg2257GlnfsTer10	p.R2257Qfs*10	ENST00000262189	NM_170606.2	2257	cGa/ca	36/59	0.328525740817763	3	FACETS	0.838	0.799	0.876	0.838	0.799	0.876	INDETERMINATE	2	TRUE	1	0.646076020767771	3		792	973	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164586	36164586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253570532	NA	P-0026906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	23	362	0	ENST00000300305.3:c.1289C>T	p.Pro430Leu	p.P430L	ENST00000300305		430	cCg/cTg	8/8	0.8869121559082	1	FACETS	0.084	0.065	0.106	0.084	0.065	0.106	SUBCLONAL	1	TRUE	0	0.89	1		362	341	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115279467	115279467	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	492	545	0	ENST00000438362.2:c.550del	p.Tyr184IlefsTer2	p.Y184Ifs*2	ENST00000438362	NM_001242891.1	184	Tat/at	6/20	0.8869121559082	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.89	1		545	598	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039146	49039146	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1060503083	NA	P-0026906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	223	283	0	ENST00000267163.4:c.2224G>T	p.Val742Phe	p.V742F	ENST00000267163	NM_000321.2	742	Gtt/Ttt	22/27	0.8869121559082	1	FACETS	0.959	0.921	0.995	0.959	0.921	0.995	CLONAL	1	TRUE	0	0.89	1		283	290	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593598	55593645	+	inframe_deletion	In_Frame_Del	DEL	TACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACA	TACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACA	-	novel	NA	P-0026906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	273	472	0	ENST00000288135.5:c.1666_1713del	p.Gln556_Ile571del	p.Q556_I571del	ENST00000288135	NM_000222.2	555	gTACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACAta/gta	11/21	1	2	FACETS	0.756	0.712	0.801	0.756	0.712	0.801	SUBCLONAL	1	TRUE	1	0.89	2		472	811	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	146	1032	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.952	0.872	1	1	0.993	1	CLONAL	3	FALSE	1	0.16304095626171	2		1032	627	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0028062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	108	556	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.972	1	1	0.99	1	CLONAL	2	FALSE	1	0.16304095626171	2		556	541	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0028062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	51	450	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.88	0.746	1	0.88	0.746	1	CLONAL	1	FALSE	1	0.16304095626171	2		451	711	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0028062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	143	393	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.911	0.833	0.992	1	0.993	1	CLONAL	3	FALSE	1	0.16304095626171	2		393	642	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0028062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	114	469	2	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.16304095626171	1	FACETS	0.953	0.859	1	1	0.988	1	CLONAL	2	FALSE	0	0.16304095626171	1		471	674	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0028062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	176	402	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.965	1	1	0.994	1	CLONAL	3	FALSE	1	0.16304095626171	2		403	671	SUCCESS
APC	324	MSKCC	GRCh37	5	112154942	112154942	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779780	NA	P-0028062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	240	592	0	ENST00000257430.4:c.1213C>T	p.Arg405Ter	p.R405*	ENST00000257430	NM_000038.5	405	Cga/Tga	10/16	1	2	FACETS	1	0.962	1	1	0.996	1	CLONAL	3	FALSE	1	0.16304095626171	2		592	942	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711368	114711368	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0028062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	16	184	0	ENST00000543371.1:c.381+2T>G		p.X127_splice	ENST00000543371	NM_001198531.1	127			0.16304095626171	1	FACETS	0.757	0.56	0.992	0.757	0.56	0.992	CLONAL	1	FALSE	0	0.16304095626171	1		184	238	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863266	57863266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149950420	NA	P-0028062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	75	542	0	ENST00000228682.2:c.1361C>T	p.Pro454Leu	p.P454L	ENST00000228682	NM_005269.2	454	cCg/cTg	11/12	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.16304095626171	2		542	766	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115111969	115111969	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0028062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	93	587	0	ENST00000257566.3:c.1770+1G>C		p.X590_splice	ENST00000257566	NM_016569.3	590			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.16304095626171	2		587	853	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923807	72923807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766702555	NA	P-0028062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	67	529	0	ENST00000268489.5:c.3271G>A	p.Val1091Ile	p.V1091I	ENST00000268489	NM_006885.3	1091	Gtt/Att	4/10	1	2	FACETS	0.924	0.802	1	0.924	0.802	1	CLONAL	1	FALSE	1	0.16304095626171	2		529	889	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267215	41267215	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	143	418	0	ENST00000349496.5:c.799G>A	p.Glu267Lys	p.E267K	ENST00000349496	NM_001904.3	267	Gaa/Aaa	6/15	1	2	FACETS	1	0.978	1	1	0.992	1	CLONAL	2	FALSE	1	0.16304095626171	2		418	723	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242845	142242845	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	57	478	0	ENST00000350721.4:c.4142T>C	p.Phe1381Ser	p.F1381S	ENST00000350721	NM_001184.3	1381	tTt/tCt	22/47	1	2	FACETS	0.982	0.841	1	0.982	0.841	1	CLONAL	1	FALSE	1	0.16304095626171	2		478	712	SUCCESS
APC	324	MSKCC	GRCh37	5	112174119	112174120	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	129	379	0	ENST00000257430.4:c.2831dup	p.Asn944LysfsTer2	p.N944Kfs*2	ENST00000257430	NM_000038.5	943	tca/tcAa	16/16	1	2	FACETS	0.902	0.82	0.986	1	0.992	1	CLONAL	3	FALSE	1	0.16304095626171	2		379	585	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	103	567	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.405947014002495	8	FACETS	0.898	0.801	1			1	CLONAL	1	TRUE	NA	0.405947014002495	8		567	1253	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0028072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	201	563	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.405947014002495	2	FACETS	0.958	0.896	1	0.958	0.896	1	CLONAL	2	TRUE	0	0.405947014002495	2		563	517	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271208	26271208	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	118	315	0	ENST00000305910.3:c.405A>T	p.Arg135Ser	p.R135S	ENST00000305910	NM_003534.2	135	agA/agT	1/1	0.405947014002495	3	FACETS	1	0.974	1	0.774	0.709	0.841	CLONAL	2	TRUE	0	0.405947014002495	3		315	301	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252973	36252974	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0028072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	326	413	0	ENST00000300305.3:c.388_389del	p.Val130HisfsTer7	p.V130Hfs*7	ENST00000300305		130	GTc/c	4/8	0.367813256380843	5	FACETS	0.904	0.864	0.942			1	CLONAL	5	TRUE	NA	0.405947014002495	5		413	572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0028511-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	117	532	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	0.546871975240384	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.546871975240384	1		532	286	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028777-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	168	343	0				ENST00000310581	NM_198253.2	-/1132			0.414425091638419	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.535136281283045	1		343	455	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0028777-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	278	473	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA	2	FACETS	0.835	0.791	0.88			1	INDETERMINATE	2	TRUE	NA	0.535136281283045	2		473	622	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0028777-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	234	538	0	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	0.492893181010953	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.535136281283045	1		538	588	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281802	46281802	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs769002244	NA	P-0028777-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	230	582	0	ENST00000371998.3:c.4249A>G	p.Met1417Val	p.M1417V	ENST00000371998		1417	Atg/Gtg	22/23	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.535136281283045	2		582	710	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573052	41573052	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028777-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	482	705	0	ENST00000263253.7:c.5337C>A	p.Cys1779Ter	p.C1779*	ENST00000263253	NM_001429.3	1779	tgC/tgA	31/31	0.127665245697508	3	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.535136281283045	3		705	1094	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0028902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	116	387	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.789	0.716	0.865	0.789	0.716	0.865	SUBCLONAL	1	TRUE	1	0.669997667876116	2		387	439	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123788	11123788	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1064795105	NA	P-0028902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	206	438	0	ENST00000358026.2:c.2438C>T	p.Ser813Leu	p.S813L	ENST00000358026	NM_001128849.1	813	tCa/tTa	16/36	0.669997667876116	1	FACETS	0.962	0.905	1	0.962	0.905	1	CLONAL	1	TRUE	0	0.669997667876116	1		438	425	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098959	178098959	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519921	NA	P-0028902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	117	233	0	ENST00000397062.3:c.86A>G	p.Asp29Gly	p.D29G	ENST00000397062	NM_006164.4	29	gAt/gGt	2/5	1	2	FACETS	0.978	0.892	1	0.978	0.892	1	CLONAL	1	TRUE	1	0.669997667876116	2		233	357	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223104	1223109	+	inframe_deletion	In_Frame_Del	DEL	GGACGA	GGACGA	-	rs762810203	NA	P-0028902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	347	573	0	ENST00000326873.7:c.1051_1056del	p.Glu351_Asp352del	p.E351_D352del	ENST00000326873	NM_000455.4	347	gcGGACGAg/gcg	8/10	0.669997667876116	1	FACETS	0.984	0.939	1	0.984	0.939	1	CLONAL	1	TRUE	0	0.669997667876116	1		573	700	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65349014	65349014	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	206	323	0	ENST00000342505.4:c.151G>T	p.Gly51Cys	p.G51C	ENST00000342505	NM_002227.2	51	Ggc/Tgc	3/25	1	2	FACETS	0.965	0.901	1	0.965	0.901	1	CLONAL	1	TRUE	1	0.669997667876116	2		323	637	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834528	156834528	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1405	323	692	3	ENST00000524377.1:c.296T>A	p.Val99Glu	p.V99E	ENST00000524377	NM_002529.3	99	gTg/gAg	3/17	0.646714582425095	4	FACETS	0.932	0.877	0.988	0.311	0.292	0.33	CLONAL	1	TRUE	1	0.669997667876116	4		695	1728	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646738	23646738	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs929474806	NA	P-0028902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	247	563	0	ENST00000261584.4:c.1129C>T	p.Gln377Ter	p.Q377*	ENST00000261584	NM_024675.3	377	Caa/Taa	4/13	1	2	FACETS	0.982	0.922	1	0.982	0.922	1	CLONAL	1	TRUE	1	0.669997667876116	2		563	751	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350861	89350861	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	44	729	0	ENST00000301030.4:c.2089G>C	p.Glu697Gln	p.E697Q	ENST00000301030	NM_001256183.1	697	Gaa/Caa	9/13	1	2	FACETS	0.154	0.129	0.183	0.154	0.129	0.183	SUBCLONAL	1	TRUE	1	0.669997667876116	2		729	851	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220697	1221719	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGTCGGCTGGGGTCACCCTGTAAGTGCCCCGCCCCCCCGGGCACTCACCACACGCACACTCCGAGGGGCCTCTGCGTCTTGGGCAGCTGCCGGCCTGTGGGCGCAGGGCGTGGCCACCGGCCCAGACCCTCTCTGGCCACAGCCGCTAGGGGGTGCTTACTTTATGGAAATGTAACTCATACGGCAGATGGTGGTTCACCCGTGTGAAGTGCAGCCTGGCCCGTCAGGGATCTTCACAGAGTGGCACGGCCGACCCTCCTCCCAGAGCCCCACAGGGAAGCTGGGCGGGTGACAGCAGCTCCAGGCCCCTTCCCCGGGTGGGTCCAGAGGACACTCCCCTCCTACCCCGTAGCCTCCACTAGTGGAAGGTGGTGAAGACAGAGGTGTCCTTGAGTCCACAGGGCCTCTGGTCCAGCAGCCACGGGACGCCTCTGTCCCTGGGGTAGAGCTGGGGCTCCTAGGGCGTCAACCACCTTGACTGACCACGCCTTTCTTCCCTCCCCTCGAAATGAAGCTACAACATCACCACGGGTCTGTACCCCTTCGAAGGGGACAACATCTACAAGTTGTTTGAGAACATCGGGAAGGGGAGCTACGCCATCCCGGGCGACTGTGGCCCCCCGCTCTCTGACCTGCTGAAAGGTGGGAGCCTCATCCCTCTGCCCGCAGCCCCAGGGAGGCGGGGCTTTTGTGCAGAAATGTAGGGTTGGGGGTGTCAGGTGGGGGGCTATTGGCCCCGAGACCCCAGCAGGCATTGAGAGGACTGAGTGGAGAGGCCGACCTCCCCGCAGGGCCTGGTTTGCCAGGTCCCTCAGCTCCACCCTGCTTCTGGGCCCTGTTCACCCTCCGAACTCCCACCCCAGAGGGCAGTGCTGCCCTGCGCCTCCCCCAGCCCCACCCTCGGGGGCTCCCTGGCTTGCAGGGTCTGTCAGGGTTGTCCTGCTGCACTTCCTACGCATGGCAGCAGGTGGCACTGGCCGTCCGTCCATCTGCCCAGTGGCCTTGGGAGAACGGAACCGCCC	TGGTCGGCTGGGGTCACCCTGTAAGTGCCCCGCCCCCCCGGGCACTCACCACACGCACACTCCGAGGGGCCTCTGCGTCTTGGGCAGCTGCCGGCCTGTGGGCGCAGGGCGTGGCCACCGGCCCAGACCCTCTCTGGCCACAGCCGCTAGGGGGTGCTTACTTTATGGAAATGTAACTCATACGGCAGATGGTGGTTCACCCGTGTGAAGTGCAGCCTGGCCCGTCAGGGATCTTCACAGAGTGGCACGGCCGACCCTCCTCCCAGAGCCCCACAGGGAAGCTGGGCGGGTGACAGCAGCTCCAGGCCCCTTCCCCGGGTGGGTCCAGAGGACACTCCCCTCCTACCCCGTAGCCTCCACTAGTGGAAGGTGGTGAAGACAGAGGTGTCCTTGAGTCCACAGGGCCTCTGGTCCAGCAGCCACGGGACGCCTCTGTCCCTGGGGTAGAGCTGGGGCTCCTAGGGCGTCAACCACCTTGACTGACCACGCCTTTCTTCCCTCCCCTCGAAATGAAGCTACAACATCACCACGGGTCTGTACCCCTTCGAAGGGGACAACATCTACAAGTTGTTTGAGAACATCGGGAAGGGGAGCTACGCCATCCCGGGCGACTGTGGCCCCCCGCTCTCTGACCTGCTGAAAGGTGGGAGCCTCATCCCTCTGCCCGCAGCCCCAGGGAGGCGGGGCTTTTGTGCAGAAATGTAGGGTTGGGGGTGTCAGGTGGGGGGCTATTGGCCCCGAGACCCCAGCAGGCATTGAGAGGACTGAGTGGAGAGGCCGACCTCCCCGCAGGGCCTGGTTTGCCAGGTCCCTCAGCTCCACCCTGCTTCTGGGCCCTGTTCACCCTCCGAACTCCCACCCCAGAGGGCAGTGCTGCCCTGCGCCTCCCCCAGCCCCACCCTCGGGGGCTCCCTGGCTTGCAGGGTCTGTCAGGGTTGTCCTGCTGCACTTCCTACGCATGGCAGCAGGTGGCACTGGCCGTCCGTCCATCTGCCCAGTGGCCTTGGGAGAACGGAACCGCCC	-	novel	NA	P-0028902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	339	657	0	ENST00000326873.7:c.718_863-226del		p.X240_splice	ENST00000326873	NM_000455.4	240		5-6/10	0.669997667876116	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.669997667876116	1		657	669	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713411	40713411	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	261	544	1	ENST00000373198.4:c.4104del	p.Lys1369SerfsTer30	p.K1369Sfs*30	ENST00000373198	NM_133170.3	1368	tcC/tc	30/32	1	2	FACETS	0.922	0.866	0.979	0.922	0.866	0.979	CLONAL	1	TRUE	1	0.669997667876116	2		545	845	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37622806	37622806	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	696	653	0	ENST00000249071.6:c.486G>C	p.Gln162His	p.Q162H	ENST00000249071	NM_002872.4	162	caG/caC	6/7	0.221446277468091	5	FACETS	0.995	0.963	1			1	INDETERMINATE	3	TRUE	NA	0.669997667876116	5		653	1395	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670844	134670844	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	176	314	0	ENST00000398015.3:c.755G>T	p.Arg252Leu	p.R252L	ENST00000398015	NM_004441.4	252	cGa/cTa	3/16	1	2	FACETS	0.977	0.906	1	0.977	0.906	1	CLONAL	1	TRUE	1	0.669997667876116	2		314	538	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467690	66467690	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	140	276	1	ENST00000273854.3:c.579G>T	p.Met193Ile	p.M193I	ENST00000273854	NM_004439.5	193	atG/atT	3/18	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.669997667876116	2		277	417	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003194	143003194	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	159	346	1	ENST00000262992.4:c.2632T>A	p.Cys878Ser	p.C878S	ENST00000262992	NM_001101669.1	878	Tgc/Agc	23/24	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.669997667876116	2		347	446	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441973	6441973	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	369	664	0	ENST00000356142.4:c.532G>A	p.Ala178Thr	p.A178T	ENST00000356142	NM_018890.3	178	Gcg/Acg	7/7	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.669997667876116	2		664	1082	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0028945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	63	698	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.982	0.848	1	0.982	0.848	1	CLONAL	1	TRUE	1	0.15	2		698	855	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579361	7579361	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	68	861	0	ENST00000269305.4:c.326T>A	p.Phe109Tyr	p.F109Y	ENST00000269305	NM_001126112.2	109	tTc/tAc	4/11	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.15	2		861	875	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0028960-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	37	241	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		241	512	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0028960-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	14	378	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		378	380	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192065	108192065	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1317619286	NA	P-0028960-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	34	616	0	ENST00000278616.4:c.6490G>C	p.Glu2164Gln	p.E2164Q	ENST00000278616	NM_000051.3	2164	Gag/Cag	45/63	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		616	826	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555014	106555014	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373847038	NA	P-0028960-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	30	498	1	ENST00000369096.4:c.2131G>A	p.Ala711Thr	p.A711T	ENST00000369096	NM_001198.3	711	Gct/Act	7/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		499	549	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720732	89720732	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028960-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	10	138	0	ENST00000371953.3:c.883del	p.Leu295TyrfsTer12	p.L295Yfs*12	ENST00000371953	NM_000314.4	295	Cta/ta	8/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		138	155	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118875	115118876	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AATGTCC	novel	NA	P-0028960-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	48	553	0	ENST00000257566.3:c.459_465dup	p.Ile156GlyfsTer6	p.I156Gfs*6	ENST00000257566	NM_016569.3	155	-/GGACATT	2/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		553	614	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863692	68863698	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	ATTGATG	ATTGATG	-	novel	NA	P-0028960-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	48	426	0	ENST00000261769.5:c.2432_2438del	p.Ile811LysfsTer3	p.I811Kfs*3	ENST00000261769	NM_004360.3	811	ATTGATGaa/aa	15/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		426	438	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71050209	71050209	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028960-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	29	372	1	ENST00000318789.4:c.976C>T	p.His326Tyr	p.H326Y	ENST00000318789	NM_032682.5	326	Cat/Tat	13/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		373	463	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557287	187557287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028960-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	67	641	0	ENST00000441802.2:c.4075G>A	p.Glu1359Lys	p.E1359K	ENST00000441802	NM_005245.3	1359	Gaa/Aaa	6/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		641	812	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38949923	38949923	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028960-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	32	482	0	ENST00000357387.3:c.4027C>A	p.Pro1343Thr	p.P1343T	ENST00000357387	NM_152756.3	1343	Cca/Aca	31/38	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		482	601	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068390	16068390	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029140-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	34	62	0	ENST00000268712.3:c.521C>A	p.Ser174Ter	p.S174*	ENST00000268712	NM_006311.3	174	tCa/tAa	5/46	0.565885321520159	1	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	0	0.713677929672982	1		62	60	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244467	41244467	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029140-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	354	790	0	ENST00000357654.3:c.3081C>G	p.Ser1027Arg	p.S1027R	ENST00000357654	NM_007294.3	1027	agC/agG	10/23	0.713677929672982	3	FACETS	0.979	0.926	1	0.489	0.463	0.517	CLONAL	1	TRUE	1	0.713677929672982	3		790	1375	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386571	81386571	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs969488858	NA	P-0029140-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	302	790	1	ENST00000222390.5:c.416C>T	p.Thr139Ile	p.T139I	ENST00000222390	NM_000601.4	139	aCa/aTa	4/18	1	2	FACETS	0.974	0.921	1	0.974	0.921	1	CLONAL	1	TRUE	1	0.713677929672982	2		791	869	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717699	89717701	+	frameshift_variant	Frame_Shift_Del	DEL	GAG	GAG	T	novel	NA	P-0029365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	153	383	0	ENST00000371953.3:c.724_726delinsT	p.Glu242PhefsTer10	p.E242Ffs*10	ENST00000371953	NM_000314.4	242	GAG/T	7/9	0.495552333149049	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.495552333149049	1		383	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs760043106	NA	P-0029455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	290	474	0	ENST00000269305.4:c.584T>A	p.Ile195Asn	p.I195N	ENST00000269305	NM_001126112.2	195	aTc/aAc	6/11	0.752790342271397	2	FACETS	0.965	0.934	0.994	0.965	0.934	0.994	CLONAL	2	TRUE	0	0.835073107767902	2		474	360	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0029455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	115	284	0	ENST00000288602.6:c.1397G>T	p.Gly466Val	p.G466V	ENST00000288602	NM_004333.4	466	gGa/gTa	11/18	0.835073107767902	4	FACETS	0.825	0.745	0.909	0.275	0.248	0.303	CLONAL	1	TRUE	1	0.835073107767902	4		284	613	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272206	15272206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765403158	NA	P-0029455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	83	394	1	ENST00000263388.2:c.6233G>A	p.Arg2078Gln	p.R2078Q	ENST00000263388	NM_000435.2	2078	cGg/cAg	33/33	0.529139252607992	4	FACETS	0.646	0.571	0.726			1	SUBCLONAL	1	TRUE	NA	0.835073107767902	4		395	565	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033889	49033889	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	151	302	0	ENST00000267163.4:c.2027del	p.Leu676Ter	p.L676*	ENST00000267163	NM_000321.2	676	Tta/ta	20/27	0.835073107767902	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.835073107767902	1		302	200	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420203	88420203	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	145	325	0	ENST00000360948.2:c.2483G>C	p.Gly828Ala	p.G828A	ENST00000360948	NM_001012338.2	828	gGg/gCg	19/19	0.449516780782102	1	FACETS	0.816	0.763	0.867	0.816	0.763	0.867	INDETERMINATE	1	TRUE	0	0.835073107767902	1		325	248	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774732	73774732	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	43	121	0	ENST00000254810.4:c.355A>T	p.Thr119Ser	p.T119S	ENST00000254810	NM_005324.3	119	Acc/Tcc	4/4	1	2	FACETS	0.972	0.839	1	0.972	0.839	1	CLONAL	1	TRUE	1	0.835073107767902	2		121	106	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273255	198273255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	81	364	0	ENST00000335508.6:c.955G>T	p.Gly319Cys	p.G319C	ENST00000335508	NM_012433.2	319	Ggt/Tgt	8/25	0.432700920941368	3	FACETS	0.676	0.598	0.758			1	INDETERMINATE	1	TRUE	NA	0.835073107767902	3		364	407	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660923	227660923	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	91	451	0	ENST00000305123.5:c.2532G>C	p.Lys844Asn	p.K844N	ENST00000305123	NM_005544.2	844	aaG/aaC	1/2	0.392923332192857	2	FACETS	0.495	0.442	0.552	0.248	0.221	0.276	INDETERMINATE	1	TRUE	0	0.835073107767902	2		451	440	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662388	227662388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	80	372	1	ENST00000305123.5:c.1067C>T	p.Ala356Val	p.A356V	ENST00000305123	NM_005544.2	356	gCc/gTc	1/2	0.392923332192857	2	FACETS	0.455	0.402	0.511	0.228	0.201	0.256	INDETERMINATE	1	TRUE	0	0.835073107767902	2		373	421	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871316	35871316	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0029455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	113	233	4	ENST00000303115.3:c.537+1G>T		p.X179_splice	ENST00000303115	NM_002185.3	179			0.835073107767902	6	FACETS	1	0.98	1	0.339	0.306	0.374	CLONAL	1	TRUE	2	0.835073107767902	6		237	533	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164726	32164726	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	195	458	0	ENST00000375023.3:c.5176G>T	p.Asp1726Tyr	p.D1726Y	ENST00000375023	NM_004557.3	1726	Gac/Tac	28/30	1	2	FACETS	0.928	0.867	0.991	0.928	0.867	0.991	CLONAL	1	TRUE	1	0.835073107767902	2		458	503	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168689	32168689	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	210	546	1	ENST00000375023.3:c.4234C>A	p.Leu1412Ile	p.L1412I	ENST00000375023	NM_004557.3	1412	Ctt/Att	23/30	1	2	FACETS	0.964	0.903	1	0.964	0.903	1	CLONAL	1	TRUE	1	0.835073107767902	2		547	522	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370780	55370780	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	348	278	0	ENST00000297316.4:c.82G>T	p.Gly28Cys	p.G28C	ENST00000297316	NM_022454.3	28	Ggc/Tgc	1/2	0.746865615184702	3	FACETS	1	0.995	1	0.82	0.792	0.848	CLONAL	2	TRUE	0	0.835073107767902	3		278	480	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70355087	70355087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	106	543	0	ENST00000374080.3:c.5009C>T	p.Ser1670Phe	p.S1670F	ENST00000374080		1670	tCc/tTc	36/45	0.449516780782102	1	FACETS	0.336	0.303	0.371	0.336	0.303	0.371	INDETERMINATE	1	TRUE	0	0.835073107767902	1		543	440	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907844	76907844	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0029455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	19	102	0	ENST00000373344.5:c.4318-1G>T		p.X1440_splice	ENST00000373344	NM_000489.3	1440			0.449516780782102	1	FACETS	0.408	0.319	0.505	0.408	0.319	0.505	INDETERMINATE	1	TRUE	0	0.835073107767902	1		102	65	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445208	49445234	+	inframe_deletion	In_Frame_Del	DEL	GACAGGTGCGGCTCCTCAGGCCGGGGT	GACAGGTGCGGCTCCTCAGGCCGGGGT	-	rs398123736	NA	P-0029455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	38	584	0	ENST00000301067.7:c.2232_2258del	p.Arg755_Pro763del	p.R755_P763del	ENST00000301067	NM_003482.3	744	tcACCCCGGCCTGAGGAGCCGCACCTGTCc/tcc	10/54	1	2	FACETS	0.177	0.146	0.212	0.177	0.146	0.212	SUBCLONAL	1	TRUE	1	0.835073107767902	2		584	515	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30303565	30303565	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	11	32	0	ENST00000322652.5:c.849A>T	p.Arg283Ser	p.R283S	ENST00000322652	NM_015355.2	283	agA/agT	8/16	0.417257534001723	4	FACETS	1	0.785	1			1	INDETERMINATE	1	TRUE	NA	0.835073107767902	4		32	43	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303421	91303421	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	31	212	0	ENST00000355112.3:c.1132C>A	p.His378Asn	p.H378N	ENST00000355112	NM_000057.2	378	Cac/Aac	6/22	NA	2	FACETS	0.166	0.134	0.203			1	INDETERMINATE	1	TRUE	NA	0.801763879730495	2		212	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0029514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	500	265	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	NA	2	FACETS	0.985	0.96	1			1	INDETERMINATE	2	TRUE	NA	0.801763879730495	2		265	633	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387681	17387681	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs896271183	NA	P-0029514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	264	357	0	ENST00000359435.4:c.749A>G	p.Asn250Ser	p.N250S	ENST00000359435	NM_001033549.1	250	aAt/aGt	8/9	0.649203835314273	3	FACETS	0.934	0.876	0.993			1	CLONAL	1	TRUE	NA	0.801763879730495	3		357	988	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441623	6441623	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	253	292	0	ENST00000356142.4:c.470C>G	p.Thr157Ser	p.T157S	ENST00000356142	NM_018890.3	157	aCc/aGc	6/7	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.801763879730495	2		292	613	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755988	133755988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463481185	NA	P-0029514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	249	272	1	ENST00000318560.5:c.1615G>A	p.Ala539Thr	p.A539T	ENST00000318560	NM_005157.4	539	Gca/Aca	10/11	NA	2	FACETS	1	0.95	1			1	INDETERMINATE	1	TRUE	NA	0.801763879730495	2		273	616	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0029526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	48	462	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.659	0.557	0.772	0.659	0.557	0.772	SUBCLONAL	1	TRUE	1	0.267293278237609	2		462	545	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0029526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	50	522	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.561	0.475	0.656	0.561	0.475	0.656	SUBCLONAL	1	TRUE	1	0.267293278237609	2		522	667	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023644	27023662	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGCCTCCCTCCTCCAGC	GCCGCCTCCCTCCTCCAGC	-	novel	NA	P-0029526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	27	409	0	ENST00000324856.7:c.753_771del	p.Ser254ProfsTer103	p.S254Pfs*103	ENST00000324856	NM_006015.4	250	aaGCCGCCTCCCTCCTCCAGC/aa	1/20	1	2	FACETS	0.378	0.299	0.467	0.378	0.299	0.467	SUBCLONAL	1	TRUE	1	0.267293278237609	2		409	535	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186749	108186749	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	35	494	0	ENST00000278616.4:c.6107A>C	p.Tyr2036Ser	p.Y2036S	ENST00000278616	NM_000051.3	2036	tAt/tCt	42/63	1	2	FACETS	0.422	0.345	0.51	0.422	0.345	0.51	SUBCLONAL	1	TRUE	1	0.267293278237609	2		494	620	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298737	46298737	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	43	341	1	ENST00000334344.6:c.5384A>G	p.Asn1795Ser	p.N1795S	ENST00000334344	NM_152641.2	1795	aAt/aGt	21/21	1	2	FACETS	0.633	0.53	0.748	0.633	0.53	0.748	SUBCLONAL	1	TRUE	1	0.267293278237609	2		342	508	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646419	23646419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057520736	NA	P-0029526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	35	516	0	ENST00000261584.4:c.1448C>T	p.Ser483Leu	p.S483L	ENST00000261584	NM_024675.3	483	tCa/tTa	4/13	1	2	FACETS	0.375	0.306	0.453	0.375	0.306	0.453	SUBCLONAL	1	TRUE	1	0.267293278237609	2		516	698	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56367676	56367676	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs560703292	NA	P-0029526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	24	246	0	ENST00000348428.3:c.502C>A	p.Pro168Thr	p.P168T	ENST00000348428	NM_006785.3	168	Cca/Aca	4/17	1	2	FACETS	0.563	0.442	0.703	0.563	0.442	0.703	SUBCLONAL	1	TRUE	1	0.267293278237609	2		246	319	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272066	15272066	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	54	624	1	ENST00000263388.2:c.6373G>T	p.Gly2125Trp	p.G2125W	ENST00000263388	NM_000435.2	2125	Ggg/Tgg	33/33	1	2	FACETS	0.575	0.49	0.668	0.575	0.49	0.668	SUBCLONAL	1	TRUE	1	0.267293278237609	2		625	703	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945910	17945910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201000040	NA	P-0029526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	75	702	3	ENST00000458235.1:c.2029G>A	p.Ala677Thr	p.A677T	ENST00000458235	NM_000215.3	677	Gct/Act	15/24	1	2	FACETS	0.64	0.559	0.727	0.64	0.559	0.727	SUBCLONAL	1	TRUE	1	0.267293278237609	2		705	877	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917793	29917793	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs149145987	NA	P-0029526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	53	601	0	ENST00000389048.3:c.875G>T	p.Arg292Leu	p.R292L	ENST00000389048	NM_004304.4	292	cGc/cTc	3/29	1	2	FACETS	0.499	0.425	0.582	0.499	0.425	0.582	SUBCLONAL	1	TRUE	1	0.267293278237609	2		601	794	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380989	116380989	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	54	536	0	ENST00000397752.3:c.1611G>C	p.Gln537His	p.Q537H	ENST00000397752	NM_000245.2	537	caG/caC	5/21	1	2	FACETS	0.547	0.466	0.636	0.547	0.466	0.636	SUBCLONAL	1	TRUE	1	0.267293278237609	2		536	739	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128419986	128419986	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	61	703	0	ENST00000265960.3:c.442C>T	p.Gln148Ter	p.Q148*	ENST00000265960	NM_001006617.1	148	Cag/Tag	4/12	1	2	FACETS	0.523	0.45	0.603	0.523	0.45	0.603	SUBCLONAL	1	TRUE	1	0.267293278237609	2		703	872	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044965	47044965	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	81	370	0	ENST00000377604.3:c.2291G>T	p.Cys764Phe	p.C764F	ENST00000377604	NM_001204468.1	764	tGc/tTc	20/24	1	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.267293278237609	1		370	464	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356282	70356282	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030044-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	409	368	0	ENST00000374080.3:c.5177A>G	p.Tyr1726Cys	p.Y1726C	ENST00000374080		1726	tAc/tGc	37/45	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.81	1		368	501	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0030053-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	425	698	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.860290579373528	4	FACETS	0.955	0.914	0.996	0.955	0.914	0.996	CLONAL	2	TRUE	2	0.872209722873053	4		698	955	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0030053-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	80	556	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.872209722873053	4	FACETS	0.918	0.814	1	0.23	0.203	0.258	CLONAL	1	TRUE	0	0.872209722873053	4		556	374	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591888	48591888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519739	NA	P-0030053-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	225	580	0	ENST00000342988.3:c.1051G>A	p.Asp351Asn	p.D351N	ENST00000342988	NM_005359.5	351	Gat/Aat	9/12	0.872209722873053	1	FACETS	0.951	0.911	0.989	0.951	0.911	0.989	CLONAL	1	TRUE	0	0.872209722873053	1		580	306	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998756	100998756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749674024	NA	P-0030053-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	293	635	0	ENST00000325455.5:c.1046C>T	p.Ser349Leu	p.S349L	ENST00000325455	NM_001202474.3	349	tCg/tTg	1/8	0.872209722873053	3	FACETS	1	0.964	1	0.515	0.485	0.545	CLONAL	1	TRUE	1	0.872209722873053	3		635	937	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259442	55259442	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397517127	NA	P-0030053-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	401	469	0	ENST00000275493.2:c.2500G>T	p.Val834Leu	p.V834L	ENST00000275493	NM_005228.3	834	Gtg/Ttg	21/28	0.860290579373528	4	FACETS	0.963	0.92	1	0.963	0.92	1	CLONAL	2	TRUE	2	0.872209722873053	4		469	894	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0030053-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	645	731	0	ENST00000269305.4:c.559+1G>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.872209722873053	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.872209722873053	2		731	732	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246498703	246498703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030053-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	180	406	0	ENST00000388985.4:c.302C>T	p.Ser101Phe	p.S101F	ENST00000388985		101	tCc/tTc	3/12	0.866068255969605	3	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.872209722873053	3		406	524	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550938	150550938	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030053-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	261	536	0	ENST00000369026.2:c.718G>A	p.Glu240Lys	p.E240K	ENST00000369026	NM_021960.4	240	Gaa/Aaa	2/3	0.872209722873053	5	FACETS	1	0.956	1	0.206	0.192	0.22	CLONAL	1	TRUE	0	0.872209722873053	5		536	1344	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942698	48942701	+	frameshift_variant	Frame_Shift_Del	DEL	TTGA	TTGA	-	novel	NA	P-0030053-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	204	282	0	ENST00000267163.4:c.1086_1089del	p.Asp363LysfsTer3	p.D363Kfs*3	ENST00000267163	NM_000321.2	362	cTTGAt/ct	11/27	0.872209722873053	2	FACETS	0.995	0.963	1	0.995	0.963	1	CLONAL	2	TRUE	0	0.872209722873053	2		282	235	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17117161	17117161	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030053-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	254	567	0	ENST00000285071.4:c.1548G>C	p.Lys516Asn	p.K516N	ENST00000285071	NM_144997.5	516	aaG/aaC	14/14	0.872209722873053	2	FACETS	1	0.982	1	0.543	0.514	0.573	CLONAL	1	TRUE	0	0.872209722873053	2		567	536	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753376	57753376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030053-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	183	475	0	ENST00000274289.3:c.748G>A	p.Glu250Lys	p.E250K	ENST00000274289	NM_006622.3	250	Gaa/Aaa	6/14	0.872209722873053	5	FACETS	0.908	0.837	0.982	0.303	0.279	0.328	CLONAL	1	TRUE	2	0.872209722873053	5		475	1067	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500777	149500777	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030053-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	244	539	0	ENST00000261799.4:c.2453C>A	p.Ala818Asp	p.A818D	ENST00000261799	NM_002609.3	818	gCc/gAc	17/23	0.872209722873053	3	FACETS	1	0.951	1	0.339	0.318	0.361	CLONAL	1	TRUE	0	0.872209722873053	3		539	790	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520432	176520432	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030053-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	245	588	0	ENST00000292408.4:c.1277G>T	p.Gly426Val	p.G426V	ENST00000292408	NM_213647.1	426	gGc/gTc	10/18	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.872209722873053	2		588	523	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6442022	6442022	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030053-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	176	113	0	ENST00000356142.4:c.581C>G	p.Ala194Gly	p.A194G	ENST00000356142	NM_018890.3	194	gCa/gGa	7/7	0.860290579373528	4	FACETS	0.893	0.843	0.942	1	0.991	1	CLONAL	3	TRUE	2	0.872209722873053	4		113	282	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030053-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	193	467	0	ENST00000263967.3:c.3012G>C	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atC	21/21	0.872209722873053	4	FACETS	1	0.937	1	0.253	0.234	0.272	CLONAL	1	TRUE	0	0.872209722873053	4		467	819	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222460	39222460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1194032302	NA	P-0030053-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	239	578	0	ENST00000402219.2:c.3150G>A	p.Met1050Ile	p.M1050I	ENST00000402219	NM_005633.3	1050	atG/atA	20/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.872209722873053	2		578	523	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348691	118348691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030053-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	165	380	0	ENST00000534358.1:c.3344C>T	p.Ser1115Leu	p.S1115L	ENST00000534358	NM_005933.3	1115	tCa/tTa	5/36	0.872209722873053	3	FACETS	0.979	0.904	1	0.49	0.452	0.528	CLONAL	1	TRUE	1	0.872209722873053	3		380	555	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983116	7983116	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886690058	NA	P-0030053-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	229	488	0	ENST00000319144.4:c.898G>A	p.Glu300Lys	p.E300K	ENST00000319144	NM_001139.2	300	Gag/Aag	7/15	0.872209722873053	2	FACETS	1	0.962	1	0.514	0.484	0.544	CLONAL	1	TRUE	0	0.872209722873053	2		488	511	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070832	30070832	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030053-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	208	545	0	ENST00000338641.4:c.1348G>C	p.Glu450Gln	p.E450Q	ENST00000338641	NM_000268.3	450	Gag/Cag	13/16	0.872209722873053	2	FACETS	0.998	0.936	1	0.499	0.468	0.53	CLONAL	1	TRUE	0	0.872209722873053	2		545	478	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080270	5080270	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030053-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	174	414	0	ENST00000381652.3:c.2173G>C	p.Glu725Gln	p.E725Q	ENST00000381652	NM_004972.3	725	Gaa/Caa	17/25	0.872209722873053	3	FACETS	1	0.984	1	0.402	0.373	0.431	CLONAL	1	TRUE	0	0.872209722873053	3		414	475	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69039620	69039620	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030279-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	49	232	0	ENST00000288368.4:c.3732G>T	p.Lys1244Asn	p.K1244N	ENST00000288368	NM_024870.2	1244	aaG/aaT	31/40	1	2	FACETS	0.377	0.321	0.438	0.377	0.321	0.438	SUBCLONAL	1	TRUE	1	0.866920804462245	2		232	300	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829701	72829701	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030279-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	51	665	0	ENST00000268489.5:c.6880C>T	p.Arg2294Ter	p.R2294*	ENST00000268489	NM_006885.3	2294	Cga/Tga	9/10	0.866920804462245	1	FACETS	0.171	0.146	0.199	0.171	0.146	0.199	SUBCLONAL	1	TRUE	0	0.866920804462245	1		665	389	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729964	39729964	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030279-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	360	514	0	ENST00000361337.2:c.1279A>C	p.Ile427Leu	p.I427L	ENST00000361337	NM_003286.2	427	Atc/Ctc	13/21	0.866920804462245	3	FACETS	1	0.98	1	0.532	0.505	0.56	CLONAL	1	TRUE	1	0.866920804462245	3		514	1119	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953772	55953772	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0030279-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	293	515	0	ENST00000263923.4:c.3662+2T>C		p.X1221_splice	ENST00000263923	NM_002253.2	1221			1	2	FACETS	0.926	0.876	0.976	0.926	0.876	0.976	CLONAL	1	TRUE	1	0.866920804462245	2		515	730	SUCCESS
ALB	213	MSKCC	GRCh37	4	74270099	74270099	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030279-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	241	432	0	ENST00000295897.4:c.55A>T	p.Arg19Trp	p.R19W	ENST00000295897	NM_000477.5	19	Agg/Tgg	1/15	1	2	FACETS	0.998	0.941	1	0.998	0.941	1	CLONAL	1	TRUE	1	0.866920804462245	2		432	557	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956734	68956734	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030279-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	187	388	0	ENST00000288368.4:c.852C>G	p.Asn284Lys	p.N284K	ENST00000288368	NM_024870.2	284	aaC/aaG	8/40	1	2	FACETS	0.879	0.819	0.939	0.879	0.819	0.939	CLONAL	1	TRUE	1	0.866920804462245	2		388	491	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260046	19260046	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	95	625	2	ENST00000162023.5:c.247G>A	p.Asp83Asn	p.D83N	ENST00000162023		83	Gac/Aac	7/13	1	2	FACETS	0.671	0.597	0.749	0.671	0.597	0.749	SUBCLONAL	1	TRUE	1	0.4	2		627	708	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672758	86672758	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1204340475	NA	P-0032909-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	152	457	0	ENST00000274376.6:c.2245C>T	p.Arg749Ter	p.R749*	ENST00000274376	NM_002890.2	749	Cga/Tga	17/25	1	2	FACETS	0.609	0.558	0.661	0.609	0.558	0.661	SUBCLONAL	1	TRUE	1	0.760330030226541	2		457	657	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245498	46245498	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs757713971	NA	P-0032909-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	200	619	0	ENST00000334344.6:c.3592C>G	p.Pro1198Ala	p.P1198A	ENST00000334344	NM_152641.2	1198	Cca/Gca	15/21	0.560840200346196	1	FACETS	0.583	0.544	0.623	0.583	0.544	0.623	SUBCLONAL	1	TRUE	0	0.760330030226541	1		619	559	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435317	56435317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200066146	NA	P-0033436-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	248	657	0	ENST00000407977.2:c.1820C>T	p.Ser607Leu	p.S607L	ENST00000407977		607	tCg/tTg	9/10	0.391650854367965	5	FACETS	0.953	0.896	1	0.953	0.896	1	CLONAL	3	TRUE	2	0.391650854367965	5		657	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0033436-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	210	611	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.391650854367965	4	FACETS	0.906	0.848	0.965	0.906	0.848	0.965	CLONAL	3	TRUE	1	0.391650854367965	4		611	549	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444987	49444987	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033436-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	167	658	0	ENST00000301067.7:c.2479del	p.Gln827AsnfsTer103	p.Q827Nfs*103	ENST00000301067	NM_003482.3	827	Caa/aa	10/54	0.237237608587714	3	FACETS	0.946	0.875	1	0.631	0.583	0.68	CLONAL	2	TRUE	0	0.391650854367965	3		658	539	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923606	39923606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777165878	NA	P-0033436-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	62	480	0	ENST00000378444.4:c.3485G>A	p.Arg1162His	p.R1162H	ENST00000378444	NM_001123385.1	1162	cGc/cAc	7/15	NA	2	FACETS	0.849	0.737	0.969			1	INDETERMINATE	1	TRUE	NA	0.391650854367965	2		480	373	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982529	10982529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1163340108	NA	P-0033436-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	142	626	0	ENST00000327064.4:c.151G>A	p.Ala51Thr	p.A51T	ENST00000327064	NM_199141.1	51	Gcg/Acg	1/16	0.391650854367965	4	FACETS	0.911	0.834	0.99	0.911	0.834	0.99	CLONAL	2	TRUE	2	0.391650854367965	4		626	554	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638273	176638273	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0033436-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	172	573	0	ENST00000439151.2:c.2873C>G	p.Ser958Ter	p.S958*	ENST00000439151	NM_022455.4	958	tCa/tGa	5/23	0.184359099013027	4	FACETS	1	0.925	1	1	0.925	1	INDETERMINATE	2	TRUE	2	0.391650854367965	4		573	611	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880071	151880071	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033436-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	123	418	0	ENST00000262189.6:c.5253G>A	p.Trp1751Ter	p.W1751*	ENST00000262189	NM_170606.2	1751	tgG/tgA	35/59	0.391650854367965	5	FACETS	0.991	0.901	1	0.661	0.601	0.723	CLONAL	2	TRUE	2	0.391650854367965	5		418	503	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0034623-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	94	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.288760246990193	3	FACETS	1	0.976	1	0.682	0.609	0.76	CLONAL	1	TRUE	1	0.288760246990193	3		434	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579487	7579487	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034623-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	92	879	0	ENST00000269305.4:c.200del	p.Pro67GlnfsTer56	p.P67Qfs*56	ENST00000269305	NM_001126112.2	67	cCa/ca	4/11	NA	2	FACETS	0.735	0.652	0.824			1	INDETERMINATE	1	TRUE	NA	0.288760246990193	2		879	867	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162722958	162722958	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034623-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	74	516	0	ENST00000367921.3:c.156G>A	p.Trp52Ter	p.W52*	ENST00000367921	NM_006182.2	52	tgG/tgA	4/18	1	2	FACETS	0.703	0.615	0.798	0.703	0.615	0.798	SUBCLONAL	1	TRUE	1	0.288760246990193	2		516	729	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575700	55575700	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1219033476	NA	P-0035267-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	55	328	0	ENST00000288135.5:c.1226T>C	p.Val409Ala	p.V409A	ENST00000288135	NM_000222.2	409	gTg/gCg	7/21	0.6565882486104	3	FACETS	0.901	0.779	1	0.45	0.389	0.516	CLONAL	1	TRUE	1	0.6565882486104	3		328	247	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512270	38512270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866777491	NA	P-0035267-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	74	457	0	ENST00000254066.5:c.1181G>A	p.Arg394Gln	p.R394Q	ENST00000254066	NM_000964.3	394	cGg/cAg	9/9	0.460359158744321	4	FACETS	0.993	0.875	1	0.497	0.437	0.56	CLONAL	1	TRUE	2	0.6565882486104	4		457	376	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099981	157099982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCGGC	rs587779747	NA	P-0035267-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	104	677	0	ENST00000346085.5:c.939_944dup	p.Gly318_Gly319dup	p.G318_G319dup	ENST00000346085	NM_020732.3	318	-/GGCGGC	1/20	0.6565882486104	2	FACETS	1	0.964	1	0.562	0.51	0.614	CLONAL	1	TRUE	0	0.6565882486104	2		677	282	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155196	55155196	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036106-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	77	630	0	ENST00000257290.5:c.2795G>T	p.Cys932Phe	p.C932F	ENST00000257290	NM_006206.4	932	tGc/tTc	21/23	0.663380933526347	3	FACETS	0.377	0.331	0.428	0.189	0.165	0.214	SUBCLONAL	1	TRUE	1	0.663380933526347	3		630	819	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748014	41748014	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1475701090	NA	P-0036106-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	92	312	0	ENST00000226382.2:c.755C>T	p.Ala252Val	p.A252V	ENST00000226382	NM_003924.3	252	gCg/gTg	3/3	0.663380933526347	3	FACETS	1	0.954	1	0.556	0.499	0.616	CLONAL	1	TRUE	1	0.663380933526347	3		312	332	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157256690	157256690	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1477561038	NA	P-0036106-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	35	369	0	ENST00000346085.5:c.2017G>C	p.Glu673Gln	p.E673Q	ENST00000346085	NM_020732.3	673	Gaa/Caa	5/20	1	2	FACETS	0.251	0.206	0.302	0.251	0.206	0.302	SUBCLONAL	1	TRUE	1	0.663380933526347	2		369	420	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0039408-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	328	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.347295048939409	6	FACETS	0.921	0.877	0.965	0.921	0.877	0.965	CLONAL	5	TRUE	1	0.347295048939409	6		434	695	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0039408-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	141	443	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.347295048939409	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.347295048939409	2		443	371	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242475	55242475	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057520037	NA	P-0039408-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	56	344	0	ENST00000275493.2:c.2245G>C	p.Glu749Gln	p.E749Q	ENST00000275493	NM_005228.3	749	Gaa/Caa	19/28	0.235961433696249	4	FACETS	1	0.957	1	0.652	0.562	0.75	CLONAL	1	TRUE	2	0.347295048939409	4		344	333	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4123815	4123815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039408-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	75	308	0	ENST00000262948.5:c.58G>A	p.Glu20Lys	p.E20K	ENST00000262948	NM_030662.3	20	Gag/Aag	1/11	0.330984293283498	3	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	1	0.347295048939409	3		308	233	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518640	69518640	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039408-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	30	322	1	ENST00000294312.3:c.5G>A	p.Arg2Gln	p.R2Q	ENST00000294312	NM_005117.2	2	cGg/cAg	1/3	0.235961433696249	4	FACETS	1	0.848	1	0.527	0.427	0.638	CLONAL	1	TRUE	2	0.347295048939409	4		323	221	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0042173-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	54	686	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.605166637878584	4	FACETS	1	0.921	1	0.534	0.468	0.601	CLONAL	2	TRUE	0	0.599582631184018	4		686	135	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912664	NA	P-0042173-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	52	458	0	ENST00000269305.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000269305	NM_001126112.2	337	cGc/cAc	10/11	0.605166637878584	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.599582631184018	2		458	78	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056321	27056321	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042173-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	43	640	0	ENST00000324856.7:c.1317G>C	p.Gln439His	p.Q439H	ENST00000324856	NM_006015.4	439	caG/caC	2/20	0.218546279759891	1	FACETS	1	0.945	1	1	0.945	1	INDETERMINATE	1	TRUE	0	0.599582631184018	1		640	86	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823904	3823904	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042173-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	36	636	0	ENST00000262367.5:c.2311C>T	p.Gln771Ter	p.Q771*	ENST00000262367	NM_004380.2	771	Cag/Tag	13/31	0.605166637878584	3	FACETS	1	0.93	1	0.61	0.511	0.715	CLONAL	1	TRUE	1	0.599582631184018	3		636	128	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40740990	40740990	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042173-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	31	669	0	ENST00000392038.2:c.1328T>G	p.Phe443Cys	p.F443C	ENST00000392038	NM_001626.4	443	tTt/tGt	13/14	0.549601186536402	5	FACETS	1	0.946	1	0.492	0.405	0.588	CLONAL	1	TRUE	2	0.599582631184018	5		669	133	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002814	69002814	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042173-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	14	398	0	ENST00000288368.4:c.2114G>T	p.Gly705Val	p.G705V	ENST00000288368	NM_024870.2	705	gGa/gTa	20/40	0.599582631184018	5	FACETS	0.878	0.643	1	0.293	0.214	0.386	CLONAL	1	TRUE	2	0.599582631184018	5		398	101	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0043339-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	465	241	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.740293249514778	5	FACETS	0.997	0.966	1	0.997	0.966	1	CLONAL	4	TRUE	1	0.740293249514778	5		241	665	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0043339-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	852	855	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.740293249514778	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	4	TRUE	0	0.740293249514778	4		857	980	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711918	89711918	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043339-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	196	289	0	ENST00000371953.3:c.536G>T	p.Ser179Ile	p.S179I	ENST00000371953	NM_000314.4	179	aGc/aTc	6/9	0.740293249514778	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.740293249514778	2		289	258	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100282	8100282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043339-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	173	733	0	ENST00000346208.3:c.256C>T	p.Arg86Cys	p.R86C	ENST00000346208		86	Cgc/Tgc	3/6	0.740293249514778	2	FACETS	0.926	0.859	0.994	0.463	0.429	0.497	CLONAL	1	TRUE	0	0.740293249514778	2		733	505	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2104085	2104085	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043339-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	112	554	0	ENST00000349721.2:c.3208C>G	p.Leu1070Val	p.L1070V	ENST00000349721	NM_003070.3	1070	Ctg/Gtg	23/34	NA	2	FACETS	0.556	0.502	0.613			1	INDETERMINATE	1	TRUE	NA	0.740293249514778	2		554	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0043364-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	207	809	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.335201830671708	2	FACETS	0.897	0.837	0.958	0.897	0.837	0.958	CLONAL	2	TRUE	0	0.367026207902314	2		809	629	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0043364-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	242	402	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.342798810065722	3	FACETS	0.883	0.832	0.935	0.883	0.832	0.935	CLONAL	3	TRUE	0	0.367026207902314	3		402	589	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0043364-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	34	190	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.367026207902314	3	FACETS	0.847	0.695	1	0.423	0.347	0.508	CLONAL	1	TRUE	1	0.367026207902314	3		190	259	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672177	30672177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762832250	NA	P-0043364-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1205	214	1004	0	ENST00000376406.3:c.4783C>T	p.Arg1595Trp	p.R1595W	ENST00000376406	NM_014641.2	1595	Cgg/Tgg	10/15	0.367026207902314	3	FACETS	0.973	0.901	1	0.486	0.45	0.524	CLONAL	1	TRUE	1	0.367026207902314	3		1004	1419	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110332	3110332	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0043364-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	295	488	0	ENST00000078429.4:c.321+1G>A		p.X107_splice	ENST00000078429	NM_002067.2	107			0.342798810065722	3	FACETS	0.866	0.82	0.913	0.866	0.82	0.913	CLONAL	3	TRUE	0	0.367026207902314	3		488	732	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729442	41729442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043364-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	66	556	0	ENST00000242208.4:c.1087G>A	p.Gly363Arg	p.G363R	ENST00000242208	NM_002192.2	363	Ggg/Agg	3/3	0.367026207902314	4	FACETS	0.577	0.5	0.661	0.192	0.166	0.221	SUBCLONAL	1	TRUE	1	0.367026207902314	4		556	852	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	93	1032	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.184671941569061	4	FACETS	1	0.969	1	1	0.969	1	INDETERMINATE	2	FALSE	2	0.48561437254752	4		1032	242	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578245	7578610	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCAAATTTCCTTCCACTCGGATAAGATGCTGAGGAGGGGCCAGACCTAAGAGCAATCAGTGAGGAATCAGAGGCCTGGGGACCCTGGGCAACCAGCCCTGTCGTCTCTCCAGCCCCAGCTGCTCACCATCGCTATCTGAGCAGCGCTCATGGTGGGGGCAGCGCCTCACAACCTCCGTCATGTGCTGTGACTGCTTGTAGATGGCCATGGCGCGGACGCGGGTGCCGGGCGGGGGTGTGGAATCAACCCACAGCTGCACAGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAA	GCAAATTTCCTTCCACTCGGATAAGATGCTGAGGAGGGGCCAGACCTAAGAGCAATCAGTGAGGAATCAGAGGCCTGGGGACCCTGGGCAACCAGCCCTGTCGTCTCTCCAGCCCCAGCTGCTCACCATCGCTATCTGAGCAGCGCTCATGGTGGGGGCAGCGCCTCACAACCTCCGTCATGTGCTGTGACTGCTTGTAGATGGCCATGGCGCGGACGCGGGTGCCGGGCGGGGGTGTGGAATCAACCCACAGCTGCACAGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAA	-	novel	NA	P-0044659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	151	714	0	ENST00000269305.4:c.376-56_604del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5-6/11	0.285926787794638	1	FACETS	0.762	0.699	0.827	0.762	0.699	0.827	INDETERMINATE	1	FALSE	0	0.48561437254752	1		714	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0045016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	241	440	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.857042003539766	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.857042003539766	1		440	309	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44520605	44520605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	80	388	1	ENST00000291552.4:c.157C>T	p.Arg53Cys	p.R53C	ENST00000291552	NM_006758.2	53	Cgt/Tgt	3/8	1	2	FACETS	0.373	0.329	0.42	0.373	0.329	0.42	SUBCLONAL	1	TRUE	1	0.857042003539766	2		389	501	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803562	43803562	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	257	686	1	ENST00000372470.3:c.43C>A	p.Leu15Met	p.L15M	ENST00000372470	NM_005373.2	15	Ctg/Atg	1/12	0.431727285829851	1	FACETS	0.806	0.768	0.844	0.806	0.768	0.844	INDETERMINATE	1	TRUE	0	0.857042003539766	1		687	425	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039215	49039215	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	147	388	0	ENST00000267163.4:c.2296del	p.Thr766GlnfsTer44	p.T766Qfs*44	ENST00000267163	NM_000321.2	765	Aaa/aa	22/27	0.857042003539766	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.857042003539766	1		388	180	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138609	2138609	+	stop_lost	Nonstop_Mutation	SNP	T	T	A	rs1567135442	NA	P-0045016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	232	474	0	ENST00000219476.3:c.5422T>A	p.Ter1808ArgextTer19	p.*1808Rext*19	ENST00000219476	NM_000548.3	1808	Tga/Aga	42/42	0.857042003539766	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.857042003539766	1		474	286	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31493328	31493328	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	191	386	0	ENST00000344624.3:c.1828G>T	p.Ala610Ser	p.A610S	ENST00000344624		610	Gcc/Tcc	10/33	0.857042003539766	3	FACETS	1	0.93	1	0.501	0.465	0.537	CLONAL	1	TRUE	1	0.857042003539766	3		386	636	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659861	88659861	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	45	214	0	ENST00000372037.3:c.508T>C	p.Phe170Leu	p.F170L	ENST00000372037	NM_004329.2	170	Ttc/Ctc	7/13	0.857042003539766	1	FACETS	0.48	0.414	0.549	0.48	0.414	0.549	SUBCLONAL	1	TRUE	0	0.857042003539766	1		214	125	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544806	86544806	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	186	531	0	ENST00000262426.4:c.631C>G	p.His211Asp	p.H211D	ENST00000262426	NM_001451.2	211	Cac/Gac	1/2	0.857042003539766	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.857042003539766	1		531	232	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664556	29664556	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	26	478	0	ENST00000356175.3:c.6535A>G	p.Thr2179Ala	p.T2179A	ENST00000356175	NM_000267.3	2179	Aca/Gca	42/57	1	2	FACETS	0.118	0.092	0.146	0.118	0.092	0.146	SUBCLONAL	1	TRUE	1	0.857042003539766	2		478	516	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11022860	11022860	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	32	544	1	ENST00000327064.4:c.559A>T	p.Ile187Phe	p.I187F	ENST00000327064	NM_199141.1	187	Atc/Ttc	5/16	1	2	FACETS	0.14	0.113	0.171	0.14	0.113	0.171	SUBCLONAL	1	TRUE	1	0.857042003539766	2		545	533	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170755	99170755	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	201	425	0	ENST00000074304.5:c.1384T>C	p.Cys462Arg	p.C462R	ENST00000074304	NM_001134224.1	462	Tgc/Cgc	16/26	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.857042003539766	2		425	416	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515130	31515130	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	213	470	0	ENST00000344624.3:c.1255G>C	p.Glu419Gln	p.E419Q	ENST00000344624		419	Gaa/Caa	5/33	0.857042003539766	3	FACETS	0.973	0.907	1	0.486	0.453	0.52	CLONAL	1	TRUE	1	0.857042003539766	3		470	730	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777856	27777856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778245917	NA	P-0045016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	92	584	0	ENST00000369163.2:c.5C>T	p.Ala2Val	p.A2V	ENST00000369163	NM_003536.2	2	gCg/gTg	1/1	0.150865866539467	5	FACETS	0.768	0.683	0.858	0.256	0.227	0.286	INDETERMINATE	1	TRUE	2	0.857042003539766	5		584	639	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027156	49027159	+	frameshift_variant	Frame_Shift_Del	DEL	CAAT	CAAT	-	novel	NA	P-0046319-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	58	423	0	ENST00000267163.4:c.1726_1729del	p.Ser576ArgfsTer34	p.S576Rfs*34	ENST00000267163	NM_000321.2	575	CAATca/ca	18/27	0.288939867359259	2	FACETS	0.923	0.814	1	1	0.97	1	CLONAL	3	TRUE	0	0.288939867359259	2		423	145	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39321543	39321543	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046319-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	26	500	1	ENST00000373001.3:c.478A>C	p.Thr160Pro	p.T160P	ENST00000373001	NM_022157.3	160	Act/Cct	3/7	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.288939867359259	2		501	140	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628736	187628736	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs369161430	NA	P-0046319-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	22	677	0	ENST00000441802.2:c.2246A>G	p.Asn749Ser	p.N749S	ENST00000441802	NM_005245.3	749	aAt/aGt	2/27	0.238269720341519	0	FACETS	0.727	0.569	0.906			1	CLONAL	1	TRUE	0	0.288939867359259	0		677	149	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931610	39931610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046319-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	29	282	0	ENST00000378444.4:c.2989del	p.Ala997HisfsTer24	p.A997Hfs*24	ENST00000378444	NM_001123385.1	997	Gca/ca	4/15	1	1	FACETS	1	0.924	1	1	0.966	1	CLONAL	2	TRUE	0	0.288939867359259	1		282	71	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042147	6042147	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046319-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	14	558	0	ENST00000265849.7:c.474C>G	p.Ser158Arg	p.S158R	ENST00000265849	NM_000535.5	158	agC/agG	5/15	0.288939867359259	3	FACETS	0.581	0.421	0.773	0.29	0.21	0.387	SUBCLONAL	1	TRUE	1	0.288939867359259	3		558	191	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046437-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	19	0	0	ENST00000269305.4:c.329del	p.Arg110LeufsTer13	p.R110Lfs*13	ENST00000269305	NM_001126112.2	110	cGt/ct	4/11	1	2	FACETS	0.473	0.357	0.611	0.473	0.357	0.611	SUBCLONAL	1	TRUE	1	0.09	2		0	893	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151871270	151871270	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046437-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	11	0	0	ENST00000262189.6:c.9320T>C	p.Ile3107Thr	p.I3107T	ENST00000262189	NM_170606.2	3107	aTa/aCa	39/59	1	2	FACETS	0.445	0.306	0.621	0.445	0.306	0.621	SUBCLONAL	1	TRUE	1	0.09	2		0	549	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0046712-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	40	629	0	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	1	2	FACETS	0.496	0.41	0.592	0.496	0.41	0.592	SUBCLONAL	1	TRUE	1	0.16	2		629	1009	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0046712-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	83	448	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.16	2		448	693	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0046712-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	120	839	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.16	2		839	1237	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724439	162724439	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046712-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	162	770	0	ENST00000367921.3:c.211G>T	p.Ala71Ser	p.A71S	ENST00000367921	NM_006182.2	71	Gcc/Tcc	5/18	0.145461544963036	3	FACETS	0.91	0.833	0.99	0.91	0.833	0.99	CLONAL	2	TRUE	1	0.16	3		770	1202	SUCCESS
ATM	472	MSKCC	GRCh37	11	108138070	108138070	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0046712-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	66	396	0	ENST00000278616.4:c.2638+1G>A		p.X880_splice	ENST00000278616	NM_000051.3	880			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.16	2		396	577	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945792	17945792	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046712-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	137	735	0	ENST00000458235.1:c.2068T>A	p.Trp690Arg	p.W690R	ENST00000458235	NM_000215.3	690	Tgg/Agg	16/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.16	2		735	1214	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347910	73347910	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs375756603	NA	P-0048073-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	141	545	0	ENST00000377767.4:c.1151G>T	p.Arg384Leu	p.R384L	ENST00000377767	NM_014953.3	384	cGc/cTc	8/21	1	2	FACETS	0.954	0.88	1	0.954	0.88	1	CLONAL	1	TRUE	1	0.807706163420538	2		545	366	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518112	8518112	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048073-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	33	685	0	ENST00000356435.5:c.1279C>G	p.Arg427Gly	p.R427G	ENST00000356435		427	Cga/Gga	10/35	1	2	FACETS	0.166	0.135	0.202	0.166	0.135	0.202	SUBCLONAL	1	TRUE	1	0.807706163420538	2		685	491	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0049295-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	37	205	0				ENST00000310581	NM_198253.2	-/1132			0.205093997213192	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.205093997213192	1		205	277	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0049295-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	54	805	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.205093997213192	1	FACETS	0.704	0.601	0.818	0.704	0.601	0.818	SUBCLONAL	1	TRUE	0	0.205093997213192	1		805	671	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572508	64572508	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs1114167509	NA	P-0049295-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	66	1077	0	ENST00000312049.6:c.1348C>T	p.Gln450Ter	p.Q450*	ENST00000312049	NM_130799.2	450	Cag/Tag	9/10	0.205093997213192	1	FACETS	0.785	0.68	0.898	0.785	0.68	0.898	SUBCLONAL	1	TRUE	0	0.205093997213192	1		1077	736	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852149	128852149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049295-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	55	887	1	ENST00000249373.3:c.2221C>T	p.Pro741Ser	p.P741S	ENST00000249373	NM_005631.4	741	Ccc/Tcc	12/12	0.205093997213192	1	FACETS	0.94	0.805	1	0.94	0.805	1	CLONAL	1	TRUE	0	0.205093997213192	1		888	512	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2081946	2081946	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049295-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	59	585	0	ENST00000349721.2:c.2299A>C	p.Met767Leu	p.M767L	ENST00000349721	NM_003070.3	767	Atg/Ctg	15/34	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.205093997213192	2		585	550	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950928	32950928	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	105	485	0	ENST00000380152.3:c.8754+1del		p.E2918fs	ENST00000380152		2918	gaG/ga	21/27	0.92925280756474	1	FACETS	0.189	0.17	0.21	0.189	0.17	0.21	SUBCLONAL	1	TRUE	0	0.92925280756474	1		485	639	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436207	110436207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	150	799	0	ENST00000375856.3:c.2194C>T	p.Pro732Ser	p.P732S	ENST00000375856	NM_003749.2	732	Ccc/Tcc	1/2	0.92925280756474	1	FACETS	0.191	0.174	0.209	0.191	0.174	0.209	SUBCLONAL	1	TRUE	0	0.92925280756474	1		799	904	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183838	10183838	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1561	149	671	0	ENST00000256474.2:c.307C>T	p.Pro103Ser	p.P103S	ENST00000256474	NM_000551.3	103	Cct/Tct	1/3	1	2	FACETS	0.188	0.17	0.206	0.188	0.17	0.206	SUBCLONAL	1	TRUE	1	0.92925280756474	2		671	1710	SUCCESS
APC	324	MSKCC	GRCh37	5	112103082	112103083	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1554069850	NA	P-0049616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	42	360	0	ENST00000257430.4:c.421_422del	p.Arg141ValfsTer6	p.R141Vfs*6	ENST00000257430	NM_000038.5	139	aaAGag/aaag	4/16	0.493151577457158	1	FACETS	0.09	0.075	0.107	0.09	0.075	0.107	INDETERMINATE	1	TRUE	0	0.92925280756474	1		360	537	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2969663	2969663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	128	665	0	ENST00000396946.4:c.1616G>A	p.Cys539Tyr	p.C539Y	ENST00000396946	NM_032415.4	539	tGc/tAc	12/25	0.618078315315446	1	FACETS	0.158	0.143	0.174	0.158	0.143	0.174	SUBCLONAL	1	TRUE	0	0.92925280756474	1		665	934	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911572	101911572	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	101	457	0	ENST00000374994.4:c.1497A>T	p.Glu499Asp	p.E499D	ENST00000374994	NM_004612.2	499	gaA/gaT	9/9	0.43296311438572	1	FACETS	0.151	0.135	0.169	0.151	0.135	0.169	INDETERMINATE	1	TRUE	0	0.92925280756474	1		457	770	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391118	139391118	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	158	897	0	ENST00000277541.6:c.7073C>A	p.Ala2358Asp	p.A2358D	ENST00000277541	NM_017617.3	2358	gCc/gAc	34/34	0.618078315315446	1	FACETS	0.138	0.126	0.151	0.138	0.126	0.151	SUBCLONAL	1	TRUE	0	0.92925280756474	1		897	1321	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0051230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	39	368	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.181261363556819	2		368	404	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913283	NA	P-0051230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	56	301	0	ENST00000263967.3:c.3129G>T	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atT	21/21	0.155170793140562	2	FACETS	0.919	0.792	1	0.919	0.792	1	CLONAL	2	TRUE	0	0.181261363556819	2		301	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs28934577	NA	P-0051230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	67	461	0	ENST00000269305.4:c.770T>G	p.Leu257Arg	p.L257R	ENST00000269305	NM_001126112.2	257	cTg/cGg	7/11	0.155170793140562	2	FACETS	1	0.969	1	0.709	0.617	0.809	CLONAL	1	TRUE	0	0.181261363556819	2		461	521	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913385	NA	P-0051230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	81	633	0	ENST00000304494.5:c.247C>G	p.His83Asp	p.H83D	ENST00000304494	NM_000077.4	83	Cac/Gac	2/3	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.181261363556819	2		633	630	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0051230-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	47	368	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.125423668712637	3	FACETS	0.903	0.763	1	0.451	0.381	0.528	INDETERMINATE	1	TRUE	1	0.28	3		368	424	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913283	NA	P-0051230-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	51	301	0	ENST00000263967.3:c.3129G>T	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atT	21/21	1	2	FACETS	0.915	0.78	1	0.915	0.78	1	CLONAL	1	TRUE	1	0.28	2		301	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs28934577	NA	P-0051230-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	43	461	0	ENST00000269305.4:c.770T>G	p.Leu257Arg	p.L257R	ENST00000269305	NM_001126112.2	257	cTg/cGg	7/11	1	2	FACETS	0.689	0.577	0.813	0.689	0.577	0.813	SUBCLONAL	1	TRUE	1	0.28	2		461	446	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913385	NA	P-0051230-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	64	633	0	ENST00000304494.5:c.247C>G	p.His83Asp	p.H83D	ENST00000304494	NM_000077.4	83	Cac/Gac	2/3	1	2	FACETS	0.9	0.78	1	0.9	0.78	1	CLONAL	1	TRUE	1	0.28	2		633	508	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0051230-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	77	368	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.168999076650761	3	FACETS	1	0.974	1	0.706	0.623	0.794	INDETERMINATE	1	TRUE	1	0.315842395919739	3		368	400	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913283	NA	P-0051230-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	126	301	0	ENST00000263967.3:c.3129G>T	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atT	21/21	0.267069631831429	2	FACETS	0.892	0.814	0.974	0.892	0.814	0.974	CLONAL	2	TRUE	0	0.315842395919739	2		301	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs28934577	NA	P-0051230-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	88	461	0	ENST00000269305.4:c.770T>G	p.Leu257Arg	p.L257R	ENST00000269305	NM_001126112.2	257	cTg/cGg	7/11	NA	2	FACETS	0.759	0.678	0.845			1	INDETERMINATE	2	TRUE	NA	0.315842395919739	2		461	367	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913385	NA	P-0051230-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	116	633	0	ENST00000304494.5:c.247C>G	p.His83Asp	p.H83D	ENST00000304494	NM_000077.4	83	Cac/Gac	2/3	0.315842395919739	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.315842395919739	1		633	431	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0051341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	261	484	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.606999251404636	3	FACETS	0.816	0.769	0.863	0.544	0.513	0.576	CLONAL	2	TRUE	0	0.620932808009512	3		484	675	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0051341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	319	502	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.620932808009512	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.620932808009512	1		502	645	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562927	176562927	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs754265807	NA	P-0051341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	99	416	0	ENST00000439151.2:c.823A>C	p.Asn275His	p.N275H	ENST00000439151	NM_022455.4	275	Aat/Cat	2/23	0.379083847540076	1	FACETS	0.442	0.396	0.49	0.442	0.396	0.49	SUBCLONAL	1	TRUE	0	0.620932808009512	1		416	498	SUCCESS
APC	324	MSKCC	GRCh37	5	112176017	112176017	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554086134	NA	P-0051341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	79	494	0	ENST00000257430.4:c.4726G>T	p.Glu1576Ter	p.E1576*	ENST00000257430	NM_000038.5	1576	Gaa/Taa	16/16	0.379083847540076	1	FACETS	0.398	0.351	0.448	0.398	0.351	0.448	SUBCLONAL	1	TRUE	0	0.620932808009512	1		494	441	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093363	30093363	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	42	164	0	ENST00000331968.5:c.1900C>G	p.Leu634Val	p.L634V	ENST00000331968	NM_002742.2	634	Cta/Gta	13/18	0.313155341186725	3	FACETS	0.589	0.494	0.693	0.196	0.164	0.231	INDETERMINATE	1	TRUE	0	0.620932808009512	3		164	301	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539014	187539014	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	115	720	0	ENST00000441802.2:c.8726C>A	p.Thr2909Asn	p.T2909N	ENST00000441802	NM_005245.3	2909	aCc/aAc	10/27	0.303236576406543	2	FACETS	0.456	0.41	0.504	0.228	0.205	0.252	INDETERMINATE	1	TRUE	0	0.620932808009512	2		720	813	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533779	533779	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	143	830	0	ENST00000451590.1:c.277A>T	p.Ile93Phe	p.I93F	ENST00000451590	NM_001130442.1	93	Atc/Ttc	3/5	0.620932808009512	1	FACETS	0.394	0.359	0.431	0.394	0.359	0.431	SUBCLONAL	1	TRUE	0	0.620932808009512	1		830	806	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727445	66727445	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	37	648	0	ENST00000307102.5:c.161T>C	p.Leu54Pro	p.L54P	ENST00000307102	NM_002755.3	54	cTt/cCt	2/11	0.620932808009512	1	FACETS	0.151	0.123	0.181	0.151	0.123	0.181	SUBCLONAL	1	TRUE	0	0.620932808009512	1		648	546	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592293	29592293	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	53	194	0	ENST00000356175.3:c.4708A>C	p.Ser1570Arg	p.S1570R	ENST00000356175	NM_000267.3	1570	Agt/Cgt	35/57	1	2	FACETS	0.542	0.465	0.625	0.542	0.465	0.625	SUBCLONAL	1	TRUE	1	0.620932808009512	2		194	315	SUCCESS
YES1	7525	MSKCC	GRCh37	18	742983	742983	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4314	1031	188	0	ENST00000314574.4:c.995T>G	p.Leu332Arg	p.L332R	ENST00000314574	NM_005433.3	332	cTt/cGt	8/12	0.620932808009512	42	FACETS	1	0.988	1			1	CLONAL	8	TRUE	NA	0.620932808009512	42		188	5345	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735461	204735461	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	144	811	0	ENST00000302823.3:c.262A>C	p.Thr88Pro	p.T88P	ENST00000302823	NM_005214.4	88	Acc/Ccc	2/4	1	2	FACETS	0.537	0.49	0.587	0.537	0.49	0.587	SUBCLONAL	1	TRUE	1	0.620932808009512	2		811	863	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612141	189612141	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	61	794	0	ENST00000264731.3:c.1893T>G	p.Ser631Arg	p.S631R	ENST00000264731	NM_003722.4	631	agT/agG	14/14	0.349682045917086	1	FACETS	0.157	0.135	0.182	0.157	0.135	0.182	INDETERMINATE	1	TRUE	0	0.620932808009512	1		794	862	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681073	30681073	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	120	753	0	ENST00000376406.3:c.646T>G	p.Leu216Val	p.L216V	ENST00000376406	NM_014641.2	216	Ttg/Gtg	5/15	0.313155341186725	3	FACETS	0.558	0.503	0.616	0.186	0.167	0.206	INDETERMINATE	1	TRUE	0	0.620932808009512	3		753	908	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0051534-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	70	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.417667219317097	6	FACETS	0.903	0.8	1	0.678	0.6	0.759	CLONAL	3	TRUE	2	0.417667219317097	6		434	227	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054544	13054544	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051534-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	26	565	0	ENST00000316448.5:c.1071G>A	p.Met357Ile	p.M357I	ENST00000316448	NM_004343.3	357	atG/atA	9/9	0.417667219317097	1	FACETS	0.719	0.577	0.877	0.719	0.577	0.877	SUBCLONAL	1	TRUE	0	0.417667219317097	1		565	137	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037492	12037492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051534-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	25	446	0	ENST00000396373.4:c.1123G>A	p.Gly375Arg	p.G375R	ENST00000396373	NM_001987.4	375	Gga/Aga	6/8	0.266663691405048	4	FACETS	0.948	0.753	1	0.316	0.251	0.39	CLONAL	1	TRUE	1	0.417667219317097	4		446	179	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411878	116411894	+	intron_variant	Intron	DEL	GCTCTTTCTTTCTCTCT	GCTCTTTCTTTCTCTCT	-	novel	NA	P-0051534-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	313	603	0	ENST00000397752.3:c.2888-24_2888-8del		p.*963*	ENST00000397752	NM_000245.2	-/1390			0.417667219317097	4	FACETS	0.93	0.894	0.965	1	0.993	1	CLONAL	5	TRUE	0	0.417667219317097	4		603	457	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271280	1271280	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200119385	NA	P-0051534-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	28	334	0	ENST00000310581.5:c.2422G>A	p.Val808Ile	p.V808I	ENST00000310581	NM_198253.2	808	Gtc/Atc	8/16	0.417667219317097	10	FACETS	1	0.907	1	0.208	0.166	0.255	CLONAL	1	TRUE	4	0.417667219317097	10		334	287	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032195	26032195	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs972497745	NA	P-0051534-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	91	641	0	ENST00000244661.2:c.94G>T	p.Ala32Ser	p.A32S	ENST00000244661	NM_003537.3	32	Gct/Tct	1/1	0.417667219317097	4	FACETS	0.862	0.779	0.947	0.862	0.779	0.947	CLONAL	3	TRUE	1	0.417667219317097	4		641	239	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0052103-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	69	350	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.448031814258263	2		350	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0052103-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	188	699	0	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	0.448031814258263	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.448031814258263	1		699	604	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748003	41748003	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052103-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	162	491	0	ENST00000226382.2:c.766G>T	p.Ala256Ser	p.A256S	ENST00000226382	NM_003924.3	256	Gca/Tca	3/3	0.245710615328452	1	FACETS	1	0.98	1	1	0.98	1	INDETERMINATE	1	TRUE	0	0.448031814258263	1		491	478	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343252	118343252	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052103-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	195	530	0	ENST00000534358.1:c.1378G>C	p.Glu460Gln	p.E460Q	ENST00000534358	NM_005933.3	460	Gaa/Caa	3/36	0.448031814258263	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.448031814258263	1		530	548	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304411	91304411	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052103-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	47	506	0	ENST00000355112.3:c.1808C>T	p.Ala603Val	p.A603V	ENST00000355112	NM_000057.2	603	gCc/gTc	7/22	1	2	FACETS	0.495	0.418	0.579	0.495	0.418	0.579	SUBCLONAL	1	TRUE	1	0.448031814258263	2		506	424	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422636	47422636	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052103-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	107	522	0	ENST00000404338.3:c.704A>T	p.Asn235Ile	p.N235I	ENST00000404338	NM_004491.4	235	aAc/aTc	1/6	0.297090512231704	3	FACETS	0.835	0.75	0.926	0.418	0.375	0.463	CLONAL	1	TRUE	1	0.448031814258263	3		522	700	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	49	343	0				ENST00000310581	NM_198253.2	-/1132			0.194570865195311	3	FACETS	0.778	0.663	0.903	0.259	0.221	0.301	INDETERMINATE	1	TRUE	0	0.529054778371311	3		343	301	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0052341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	98	538	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.408227328929825	1	FACETS	0.984	0.891	1	0.984	0.891	1	CLONAL	1	TRUE	0	0.529054778371311	1		538	277	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056244	27056244	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	143	704	0	ENST00000324856.7:c.1240G>T	p.Gly414Ter	p.G414*	ENST00000324856	NM_006015.4	414	Gga/Tga	2/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.529054778371311	2		704	404	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098794	47098794	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	112	647	0	ENST00000409792.3:c.6480del	p.His2161IlefsTer87	p.H2161Ifs*87	ENST00000409792	NM_014159.6	2160	ccG/cc	15/21	1	2	FACETS	0.954	0.863	1	0.954	0.863	1	CLONAL	1	TRUE	1	0.529054778371311	2		647	444	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165608	47165608	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0052341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	117	637	0	ENST00000409792.3:c.518T>A	p.Leu173Ter	p.L173*	ENST00000409792	NM_014159.6	173	tTa/tAa	3/21	1	2	FACETS	0.908	0.823	0.997	0.908	0.823	0.997	CLONAL	1	TRUE	1	0.529054778371311	2		637	487	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538254	187538254	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1204335133	NA	P-0052341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	31	364	0	ENST00000441802.2:c.8980C>G	p.Leu2994Val	p.L2994V	ENST00000441802	NM_005245.3	2994	Ctt/Gtt	11/27	0.408227328929825	1	FACETS	0.634	0.521	0.757	0.634	0.521	0.757	SUBCLONAL	1	TRUE	0	0.529054778371311	1		364	136	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629978	187629978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	69	592	0	ENST00000441802.2:c.1004C>T	p.Thr335Ile	p.T335I	ENST00000441802	NM_005245.3	335	aCa/aTa	2/27	0.408227328929825	1	FACETS	0.601	0.528	0.68	0.601	0.528	0.68	SUBCLONAL	1	TRUE	0	0.529054778371311	1		592	319	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120625	115120642	+	frameshift_variant	Frame_Shift_Del	DEL	CTTGGTAATGACCATCTC	CTTGGTAATGACCATCTC	T	novel	NA	P-0052341-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	102	578	0	ENST00000257566.3:c.364_381delinsA	p.Glu122IlefsTer10	p.E122Ifs*10	ENST00000257566	NM_016569.3	122	GAGATGGTCATTACCAAG/A	1/8	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.529054778371311	2		578	369	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0052439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	681	178	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.653733336332752	11	FACETS	0.98	0.948	1			1	CLONAL	6	TRUE	NA	0.653733336332752	11		178	1397	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115955	8115956	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0052439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	480	622	0	ENST00000346208.3:c.1305dup	p.Ser436LeufsTer71	p.S436Lfs*71	ENST00000346208		434	cac/caCc	6/6	0.621558585533158	4	FACETS	0.97	0.929	1	0.97	0.929	1	CLONAL	2	TRUE	2	0.653733336332752	4		622	1252	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830695	72830695	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	253	549	0	ENST00000268489.5:c.5886G>C	p.Glu1962Asp	p.E1962D	ENST00000268489	NM_006885.3	1962	gaG/gaC	9/10	0.653733336332752	3	FACETS	1	0.966	1	0.523	0.49	0.557	CLONAL	1	TRUE	1	0.653733336332752	3		549	982	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772013	135772013	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	567	653	0	ENST00000298552.3:c.3104G>T	p.Gly1035Val	p.G1035V	ENST00000298552	NM_001162426.1	1035	gGt/gTt	23/23	0.653733336332752	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.653733336332752	3		653	1130	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650445	48650445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	296	701	0	ENST00000376670.3:c.415G>A	p.Glu139Lys	p.E139K	ENST00000376670	NM_002049.3	139	Gag/Aag	3/6	0.653733336332752	3	FACETS	1	0.979	1	0.54	0.509	0.573	CLONAL	1	TRUE	1	0.653733336332752	3		701	1112	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939789	76939789	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs201301590	NA	P-0052682-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	27	419	0	ENST00000373344.5:c.959C>G	p.Thr320Ser	p.T320S	ENST00000373344	NM_000489.3	320	aCt/aGt	9/35	0.289520684911864	1	FACETS	0.229	0.184	0.281	0.229	0.184	0.281	INDETERMINATE	1	TRUE	0	0.760228548593155	1		419	192	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0053369-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	129	462	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.815	0.742	0.891	0.815	0.742	0.891	CLONAL	1	TRUE	1	0.556386316401374	2		462	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0053369-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	345	776	1	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.539810640452043	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.556386316401374	1		777	846	SUCCESS
APC	324	MSKCC	GRCh37	5	112173848	112173848	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053369-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	219	563	0	ENST00000257430.4:c.2557G>T	p.Glu853Ter	p.E853*	ENST00000257430	NM_000038.5	853	Gag/Tag	16/16	0.556386316401374	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.556386316401374	1		563	544	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239351	105239351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1168658858	NA	P-0053369-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	343	770	1	ENST00000349310.3:c.1036C>T	p.Arg346Cys	p.R346C	ENST00000349310	NM_001014432.1	346	Cgc/Tgc	12/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.556386316401374	2		771	1167	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38616990	38616990	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053369-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	109	335	0	ENST00000299084.4:c.403G>T	p.Glu135Ter	p.E135*	ENST00000299084	NM_152594.2	135	Gaa/Taa	4/7	1	2	FACETS	0.953	0.863	1	0.953	0.863	1	CLONAL	1	TRUE	1	0.556386316401374	2		335	411	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779037	3779037	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053369-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	302	743	0	ENST00000262367.5:c.6011G>T	p.Arg2004Leu	p.R2004L	ENST00000262367	NM_004380.2	2004	cGa/cTa	31/31	1	2	FACETS	0.992	0.935	1	0.992	0.935	1	CLONAL	1	TRUE	1	0.556386316401374	2		743	1094	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965200	81965200	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053369-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	258	648	0	ENST00000359376.3:c.2680G>T	p.Glu894Ter	p.E894*	ENST00000359376	NM_002661.3	894	Gag/Tag	25/33	0.119068938747659	0	FACETS	0.458	0.43	0.487			1	INDETERMINATE	1	TRUE	0	0.556386316401374	0		648	898	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41251818	41251818	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1567806035	NA	P-0053369-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	215	488	0	ENST00000357654.3:c.521A>C	p.Gln174Pro	p.Q174P	ENST00000357654	NM_007294.3	174	cAa/cCa	7/23	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.556386316401374	2		488	725	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530023	212530071	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCCCTTGGCCAGCAAGAATGCTTACCCTTGGGTGCAGTTTGGATGGCAT	GCCCTTGGCCAGCAAGAATGCTTACCCTTGGGTGCAGTTTGGATGGCAT	-	novel	NA	P-0053369-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	155	454	0	ENST00000342788.4:c.1848_1871+25del		p.X616_splice	ENST00000342788	NM_005235.2	616		15/28	1	2	FACETS	0.897	0.825	0.973	0.897	0.825	0.973	CLONAL	1	TRUE	1	0.556386316401374	2		454	621	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119595278	119595278	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053369-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	154	407	0	ENST00000316626.5:c.891G>T	p.Lys297Asn	p.K297N	ENST00000316626		297	aaG/aaT	8/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.556386316401374	2		407	506	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555015	106555015	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053369-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	265	673	1	ENST00000369096.4:c.2132C>T	p.Ala711Val	p.A711V	ENST00000369096	NM_001198.3	711	gCt/gTt	7/7	0.556386316401374	1	FACETS	0.963	0.908	1	0.963	0.908	1	CLONAL	1	TRUE	0	0.556386316401374	1		674	714	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124487002	124487002	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053369-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	202	306	0	ENST00000357628.3:c.1000G>T	p.Ala334Ser	p.A334S	ENST00000357628	NM_015450.2	334	Gct/Tct	12/19	0.552433285663423	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.556386316401374	2		306	355	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0053399-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	247	575	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.554500715783734	2		575	891	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782664	NA	P-0053399-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	196	462	0	ENST00000269305.4:c.711G>C	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atC	7/11	0.541101033900589	1	FACETS	0.906	0.845	0.969	0.906	0.845	0.969	CLONAL	1	TRUE	0	0.554500715783734	1		462	564	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971292	13971292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772105404	NA	P-0053399-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	227	548	0	ENST00000405192.2:c.637C>T	p.Arg213Cys	p.R213C	ENST00000405192	NM_001163147.1	213	Cgc/Tgc	8/12	0.554500715783734	3	FACETS	0.976	0.909	1	0.488	0.454	0.523	CLONAL	1	TRUE	1	0.554500715783734	3		548	1071	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39311610	39311610	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0053399-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	124	216	0	ENST00000373001.3:c.1048+1G>A		p.X350_splice	ENST00000373001	NM_022157.3	350			1	2	FACETS	0.985	0.898	1	0.985	0.898	1	CLONAL	1	TRUE	1	0.554500715783734	2		216	454	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913376	28913376	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053399-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	356	465	0	ENST00000282397.4:c.2417T>C	p.Leu806Ser	p.L806S	ENST00000282397	NM_002019.4	806	tTg/tCg	17/30	0.481480162108116	4	FACETS	0.888	0.842	0.935	0.888	0.842	0.935	CLONAL	2	TRUE	2	0.554500715783734	4		465	1124	SUCCESS
APC	324	MSKCC	GRCh37	5	112173495	112173496	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0053399-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	187	548	0	ENST00000257430.4:c.2205dup	p.Lys736GlufsTer20	p.K736Efs*20	ENST00000257430	NM_000038.5	735	gcg/gcGg	16/16	1	2	FACETS	0.924	0.856	0.994	0.924	0.856	0.994	CLONAL	1	TRUE	1	0.554500715783734	2		548	730	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0053399-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	124	358	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.92	0.838	1	0.92	0.838	1	CLONAL	1	TRUE	1	0.554500715783734	2		358	486	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654789	29654793	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	novel	NA	P-0053399-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	258	586	0	ENST00000356175.3:c.5479_5483del	p.Lys1827CysfsTer12	p.K1827Cfs*12	ENST00000356175	NM_000267.3	1826	ccAAAAGat/ccat	37/57	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.554500715783734	2		586	907	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002752	37002752	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053399-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	48	536	0	ENST00000358127.4:c.497A>G	p.Gln166Arg	p.Q166R	ENST00000358127	NM_001280556.1	166	cAg/cGg	5/10	1	2	FACETS	0.228	0.192	0.268	0.228	0.192	0.268	SUBCLONAL	1	TRUE	1	0.554500715783734	2		536	760	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0053648-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	53	387	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.85	0.727	0.984	0.85	0.727	0.984	CLONAL	1	TRUE	1	0.310248332973334	2		387	402	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0053648-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	93	308	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.310248332973334	2		308	594	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0053648-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	155	662	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.310248332973334	1	FACETS	0.908	0.831	0.988	0.908	0.831	0.988	CLONAL	1	TRUE	0	0.310248332973334	1		662	930	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584513	48584514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs377767334	NA	P-0053648-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	129	499	0	ENST00000342988.3:c.692dup	p.Ser232GlnfsTer3	p.S232Qfs*3	ENST00000342988	NM_005359.5	229	ctg/ctGg	6/12	0.310248332973334	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.310248332973334	1		499	629	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971000	21971000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054725-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	135	890	0	ENST00000304494.5:c.358G>T	p.Glu120Ter	p.E120*	ENST00000304494	NM_000077.4	120	Gag/Tag	2/3	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.363977188675067	2		890	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057519990	NA	P-0054725-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	94	609	0	ENST00000269305.4:c.796G>T	p.Gly266Ter	p.G266*	ENST00000269305	NM_001126112.2	266	Gga/Tga	8/11	0.363977188675067	1	FACETS	0.901	0.805	1	0.901	0.805	1	CLONAL	1	TRUE	0	0.363977188675067	1		609	469	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981167	201981168	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054725-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	141	696	0	ENST00000359651.3:c.248dup	p.Asn83LysfsTer9	p.N83Kfs*9	ENST00000359651		82	-/A	2/8	0.175539155393661	2	FACETS	1	0.986	1	0.703	0.644	0.765	INDETERMINATE	1	TRUE	0	0.363977188675067	2		696	551	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003500	57003500	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0121606-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	166	812	0	ENST00000257254.3:c.979G>C	p.Gly327Arg	p.G327R	ENST00000257254		327	Ggc/Cgc	1/2	0.479403320884745	1	FACETS	0.42	0.389	0.452	0.42	0.389	0.452	INDETERMINATE	1	NA	0	0.918893451144133	1		812	465	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371753	118371753	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0121606-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	131	530	0	ENST00000534358.1:c.6210T>G	p.Tyr2070Ter	p.Y2070*	ENST00000534358	NM_005933.3	2070	taT/taG	25/36	0.918893451144133	1	FACETS	0.496	0.457	0.535	0.496	0.457	0.535	SUBCLONAL	1	NA	0	0.918893451144133	1		530	311	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107960	30107960	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0121606-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	152	620	0	ENST00000331968.5:c.847G>C	p.Val283Leu	p.V283L	ENST00000331968	NM_002742.2	283	Gtg/Ctg	5/18	0.444948779088367	3	FACETS	0.559	0.511	0.609	0.279	0.255	0.305	INDETERMINATE	1	NA	1	0.918893451144133	3		620	864	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81954875	81954875	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0121606-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	159	623	0	ENST00000359376.3:c.2307+1G>A		p.X769_splice	ENST00000359376	NM_002661.3	769			1	2	FACETS	0.535	0.492	0.58	0.535	0.492	0.58	SUBCLONAL	1	NA	1	0.918893451144133	2		623	647	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0055343-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	46	178	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.2	2		178	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579444	7579444	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055343-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	121	768	0	ENST00000269305.4:c.243del	p.Pro82ArgfsTer41	p.P82Rfs*41	ENST00000269305	NM_001126112.2	81	acA/ac	4/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.2	2		768	862	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724513	724513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055343-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	12	154	0	ENST00000314574.4:c.1543G>A	p.Glu515Lys	p.E515K	ENST00000314574	NM_005433.3	515	Gaa/Aaa	12/12	1	2	FACETS	0.615	0.433	0.839	0.615	0.433	0.839	SUBCLONAL	1	TRUE	1	0.2	2		154	195	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178147	56178148	+	stop_gained	Nonsense_Mutation	DNP	TA	TA	CT	novel	NA	P-0055343-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	189	536	0	ENST00000399503.3:c.3120_3121delinsCT	p.Lys1041Ter	p.K1041*	ENST00000399503	NM_005921.1	1040	gaTAaa/gaCTaa	14/20	0.2989908022608	4	FACETS	0.984	0.912	1	0.984	0.912	1	CLONAL	3	TRUE	1	0.2	4		536	768	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860394	151860395	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055343-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	158	582	0	ENST00000262189.6:c.10267dup	p.Arg3423LysfsTer18	p.R3423Kfs*18	ENST00000262189	NM_170606.2	3423	aga/aAga	43/59	0.232544371029755	4	FACETS	1	0.928	1			1	CLONAL	2	TRUE	NA	0.2	4		582	935	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0055424-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	13	556	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.845	0.608	1	0.845	0.608	1	CLONAL	1	TRUE	1	0.27	2		556	114	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0055424-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	24	380	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.27	2		380	139	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055424-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	21	567	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.301813524251073	1	FACETS	0.65	0.503	0.82	0.65	0.503	0.82	SUBCLONAL	1	TRUE	0	0.27	1		567	207	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042539	42042539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055424-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	47	615	2	ENST00000219905.7:c.6734G>A	p.Ser2245Asn	p.S2245N	ENST00000219905	NM_001164273.1	2245	aGt/aAt	17/24	0.155804822654015	1	FACETS	1	0.955	1	1	0.955	1	INDETERMINATE	1	TRUE	0	0.27	1		617	223	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023258	27023258	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055679-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	197	672	1	ENST00000324856.7:c.365del	p.Gly122AlafsTer110	p.G122Afs*110	ENST00000324856	NM_006015.4	122	Ggc/gc	1/20	0.740572591805182	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.737503392002049	1		673	264	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100459	8100459	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055679-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1251	379	1210	0	ENST00000346208.3:c.433C>T	p.His145Tyr	p.H145Y	ENST00000346208		145	Cac/Tac	3/6	0.740572591805182	4	FACETS	1	0.984	1	0.365	0.346	0.385	CLONAL	1	TRUE	1	0.737503392002049	4		1210	1630	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986848	36986848	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055679-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	238	797	0	ENST00000354822.5:c.841C>G	p.Gln281Glu	p.Q281E	ENST00000354822	NM_001079668.2	281	Cag/Gag	3/3	0.705557993291019	3	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.737503392002049	3		797	814	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519920	NA	P-0055679-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	207	486	0	ENST00000397062.3:c.85G>T	p.Asp29Tyr	p.D29Y	ENST00000397062	NM_006164.4	29	Gat/Tat	2/5	0.174550382284067	3	FACETS	0.789	0.74	0.839	0.789	0.74	0.839	INDETERMINATE	2	TRUE	1	0.737503392002049	3		486	487	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0056523-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	119	479	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.403205150684448	4	FACETS	0.831	0.754	0.91	0.831	0.754	0.91	CLONAL	2	TRUE	2	0.435719133699004	4		479	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0056523-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	125	545	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.367761484253043	2	FACETS	0.782	0.715	0.85	0.782	0.715	0.85	SUBCLONAL	2	TRUE	0	0.435719133699004	2		545	367	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842284	151842284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056523-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	35	671	1	ENST00000262189.6:c.14128C>T	p.Arg4710Cys	p.R4710C	ENST00000262189	NM_170606.2	4710	Cgt/Tgt	54/59	0.131085846083788	5	FACETS	0.46	0.376	0.554			1	INDETERMINATE	1	TRUE	NA	0.435719133699004	5		672	578	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778773	3778773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056523-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	80	886	0	ENST00000262367.5:c.6275C>T	p.Ser2092Leu	p.S2092L	ENST00000262367	NM_004380.2	2092	tCa/tTa	31/31	0.419819402604729	3	FACETS	0.891	0.786	1	0.297	0.262	0.334	CLONAL	1	TRUE	0	0.435719133699004	3		886	502	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256466	16256466	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056523-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	29	681	0	ENST00000375759.3:c.3731A>T	p.Asn1244Ile	p.N1244I	ENST00000375759	NM_015001.2	1244	aAt/aTt	11/15	0.235019335491203	1	FACETS	0.279	0.224	0.342	0.279	0.224	0.342	INDETERMINATE	1	TRUE	0	0.435719133699004	1		681	373	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805171	43805171	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056523-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	39	766	0	ENST00000372470.3:c.621C>A	p.Asp207Glu	p.D207E	ENST00000372470	NM_005373.2	207	gaC/gaA	4/12	0.287956865502051	2	FACETS	0.44	0.365	0.523	0.22	0.182	0.262	SUBCLONAL	1	TRUE	0	0.435719133699004	2		766	407	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003408	42003408	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056523-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	49	686	0	ENST00000219905.7:c.2945G>T	p.Gly982Val	p.G982V	ENST00000219905	NM_001164273.1	982	gGa/gTa	8/24	0.279943978543033	1	FACETS	0.514	0.437	0.598	0.514	0.437	0.598	SUBCLONAL	1	TRUE	0	0.435719133699004	1		686	342	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0056888-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	135	698	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.311096189870939	3	FACETS	0.827	0.755	0.903	0.827	0.755	0.903	CLONAL	2	TRUE	1	0.311096189870939	3		698	606	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0056888-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	158	557	3	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.311096189870939	3	FACETS	0.848	0.779	0.92	0.848	0.779	0.92	CLONAL	2	TRUE	1	0.311096189870939	3		560	692	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163374	108163374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056888-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	30	277	0	ENST00000278616.4:c.4465C>A	p.Arg1489Ser	p.R1489S	ENST00000278616	NM_000051.3	1489	Cgt/Agt	30/63	1	2	FACETS	0.509	0.41	0.621	0.509	0.41	0.621	SUBCLONAL	1	TRUE	1	0.311096189870939	2		277	379	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560374	95560374	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056888-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	53	325	0	ENST00000393063.1:c.5215C>G	p.Leu1739Val	p.L1739V	ENST00000393063	NM_030621.3	1739	Ctg/Gtg	25/28	1	2	FACETS	0.667	0.569	0.774	0.667	0.569	0.774	SUBCLONAL	1	TRUE	1	0.311096189870939	2		325	511	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942159	17942175	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCCAGGTCGCGGT	GGCGGCCAGGTCGCGGT	-	novel	NA	P-0056888-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	33	380	0	ENST00000458235.1:c.2840_2856del	p.His947ProfsTer15	p.H947Pfs*15	ENST00000458235	NM_000215.3	947	cACCGCGACCTGGCCGCC/c	21/24	1	2	FACETS	0.439	0.357	0.532	0.439	0.357	0.532	SUBCLONAL	1	TRUE	1	0.311096189870939	2		380	483	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058109-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	10	343	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.352	0.237	0.495	0.352	0.237	0.495	SUBCLONAL	1	TRUE	1	0.23316597307058	2		343	244	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0058109-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	75	508	0	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	0.229346032835779	3	FACETS	1	0.973	1	0.714	0.627	0.807	CLONAL	1	TRUE	1	0.23316597307058	3		508	503	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075194	16075194	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058109-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	80	524	0	ENST00000268712.3:c.358C>T	p.Gln120Ter	p.Q120*	ENST00000268712	NM_006311.3	120	Cag/Tag	4/46	0.229346032835779	3	FACETS	1	0.97	1	0.663	0.584	0.747	CLONAL	1	TRUE	1	0.23316597307058	3		524	578	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682991	241682991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226883651	NA	P-0058109-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	31	444	0	ENST00000366560.3:c.32C>T	p.Ser11Leu	p.S11L	ENST00000366560	NM_000143.3	11	tCg/tTg	1/10	1	2	FACETS	0.799	0.647	0.969	0.799	0.647	0.969	CLONAL	1	TRUE	1	0.23316597307058	2		444	333	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023050	27023051	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0058109-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	22	462	0	ENST00000324856.7:c.157dup	p.Ala53GlyfsTer58	p.A53Gfs*58	ENST00000324856	NM_006015.4	52	-/G	1/20	1	2	FACETS	0.642	0.498	0.809	0.642	0.498	0.809	SUBCLONAL	1	TRUE	1	0.23316597307058	2		462	294	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411583	116411583	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058109-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	20	0	0	ENST00000397752.3:c.2762G>C	p.Gly921Ala	p.G921A	ENST00000397752	NM_000245.2	921	gGa/gCa	13/21	1	2	FACETS	0.34	0.259	0.436	0.34	0.259	0.436	SUBCLONAL	1	TRUE	1	0.23316597307058	2		0	504	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843359	128843359	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs749414966	NA	P-0058109-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	23	480	0	ENST00000249373.3:c.466A>G	p.Ile156Val	p.I156V	ENST00000249373	NM_005631.4	156	Atc/Gtc	2/12	1	2	FACETS	0.486	0.378	0.611	0.486	0.378	0.611	SUBCLONAL	1	TRUE	1	0.23316597307058	2		480	406	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0058424-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	161	205	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.83705216166615	2		205	354	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158132	27158132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773256013	NA	P-0058424-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	156	616	0	ENST00000380036.4:c.356G>A	p.Arg119His	p.R119H	ENST00000380036	NM_000459.3	119	cGt/cAt	2/23	1	2	FACETS	0.485	0.444	0.527	0.485	0.444	0.527	SUBCLONAL	1	TRUE	1	0.83705216166615	2		616	769	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646270	3646270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780697002	NA	P-0058424-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	101	646	0	ENST00000294008.3:c.1808C>T	p.Ser603Leu	p.S603L	ENST00000294008	NM_032444.2	603	tCg/tTg	8/15	1	2	FACETS	0.46	0.412	0.51	0.46	0.412	0.51	SUBCLONAL	1	TRUE	1	0.83705216166615	2		646	525	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982405	201982405	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058424-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	288	694	0	ENST00000359651.3:c.784del	p.Glu262ArgfsTer32	p.E262Rfs*32	ENST00000359651		262	Gag/ag	6/8	0.481527531655237	3	FACETS	1	0.987	1	0.577	0.544	0.61	INDETERMINATE	1	TRUE	1	0.83705216166615	3		694	846	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533455	533455	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs1064796999	NA	P-0058424-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	552	889	0	ENST00000451590.1:c.448C>T	p.Gln150Ter	p.Q150*	ENST00000451590	NM_001130442.1	150	Cag/Tag	4/5	0.793354320521817	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.83705216166615	2		889	651	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894230	NA	P-0058424-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	439	671	0	ENST00000451590.1:c.35G>C	p.Gly12Ala	p.G12A	ENST00000451590	NM_001130442.1	12	gGc/gCc	2/5	0.793354320521817	2	FACETS	0.954	0.928	0.978	0.954	0.928	0.978	CLONAL	2	TRUE	0	0.83705216166615	2		671	550	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38157033	38157033	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0058424-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	166	549	0	ENST00000317025.8:c.2687C>G	p.Ser896Ter	p.S896*	ENST00000317025	NM_023034.1	896	tCa/tGa	15/24	0.83705216166615	3	FACETS	0.855	0.788	0.924	0.428	0.394	0.462	CLONAL	1	TRUE	1	0.83705216166615	3		549	658	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312439	91312439	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058689-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	28	233	0	ENST00000355112.3:c.2384A>C	p.Asp795Ala	p.D795A	ENST00000355112	NM_000057.2	795	gAt/gCt	11/22	1	2	FACETS	0.994	0.826	1	1	0.961	1	CLONAL	2	TRUE	1	0.396652365167681	2		233	71	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0058720-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	205	489	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.942	0.877	1	0.942	0.877	1	CLONAL	1	TRUE	1	0.651831067070648	2		489	668	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143021	47143021	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058720-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	120	291	0	ENST00000409792.3:c.4942G>T	p.Val1648Phe	p.V1648F	ENST00000409792	NM_014159.6	1648	Gtt/Ttt	8/21	1	2	FACETS	0.959	0.874	1	0.959	0.874	1	CLONAL	1	TRUE	1	0.651831067070648	2		291	384	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165123	47165123	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0058720-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	123	407	0	ENST00000409792.3:c.1003A>T	p.Arg335Ter	p.R335*	ENST00000409792	NM_014159.6	335	Aga/Tga	3/21	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.651831067070648	2		407	376	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357418	70357419	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0058720-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	199	667	0	ENST00000374080.3:c.5760dup	p.Met1921HisfsTer130	p.M1921Hfs*130	ENST00000374080		1920	ggc/ggCc	40/45	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.651831067070648	2		667	541	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971266	15971278	+	frameshift_variant	Frame_Shift_Del	DEL	CCGATAAACCTCG	CCGATAAACCTCG	-	novel	NA	P-0059442-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	211	637	0	ENST00000268712.3:c.4671_4683del	p.Glu1558AlafsTer53	p.E1558Afs*53	ENST00000268712	NM_006311.3	1557	ggCGAGGTTTATCGG/gg	32/46	0.806004881184132	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.806004881184132	2		637	252	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164744	32164744	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059442-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	621	620	0	ENST00000375023.3:c.5158C>A	p.Leu1720Met	p.L1720M	ENST00000375023	NM_004557.3	1720	Ctg/Atg	28/30	0.806004881184132	6	FACETS	1	0.976	1	1	0.997	1	CLONAL	5	TRUE	2	0.806004881184132	6		620	805	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059630-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	117	343	0				ENST00000310581	NM_198253.2	-/1132			0.327121517614855	1	FACETS	0.746	0.676	0.819	0.746	0.676	0.819	SUBCLONAL	1	TRUE	0	0.487158613846319	1		343	487	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913233	NA	P-0059630-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	361	1010	0	ENST00000451590.1:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000451590	NM_001130442.1	61	cAg/cTg	3/5	0.487158613846319	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.487158613846319	1		1010	853	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781324	3781326	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs587783502	NA	P-0059630-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	100	934	0	ENST00000262367.5:c.5039_5041del	p.Ser1680del	p.S1680del	ENST00000262367	NM_004380.2	1680	tCCTtg/ttg	30/31	0.288743049012894	1	FACETS	0.452	0.404	0.503	0.452	0.404	0.503	INDETERMINATE	1	TRUE	0	0.487158613846319	1		934	687	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477806	140477806	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs180177039	NA	P-0059630-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	166	312	0	ENST00000288602.6:c.1502A>T	p.Glu501Val	p.E501V	ENST00000288602	NM_004333.4	501	gAa/gTa	12/18	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.487158613846319	2		312	602	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059654-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	97	343	0				ENST00000310581	NM_198253.2	-/1132			0.210854266763614	4	FACETS	0.948	0.853	1	0.948	0.853	1	CLONAL	3	TRUE	1	0.236235302011953	4		343	357	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936983	48936983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690863	NA	P-0059654-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	127	523	0	ENST00000267163.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000267163	NM_000321.2	251	Cga/Tga	8/27	0.117895372765996	3	FACETS	0.843	0.765	0.925	0.843	0.765	0.925	INDETERMINATE	2	TRUE	1	0.236235302011953	3		523	713	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0059654-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	193	592	1	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.209857874338209	3	FACETS	0.949	0.882	1	0.949	0.882	1	CLONAL	3	TRUE	0	0.236235302011953	3		593	642	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102067	27102067	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0059654-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	164	756	1	ENST00000324856.7:c.4994-1G>A		p.X1665_splice	ENST00000324856	NM_006015.4	1665			0.0807600365351235	4	FACETS	1	0.968	1	1	0.968	1	INDETERMINATE	2	TRUE	2	0.236235302011953	4		757	780	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881523	48881523	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059654-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	78	459	0	ENST00000267163.4:c.245C>A	p.Ser82Ter	p.S82*	ENST00000267163	NM_000321.2	82	tCa/tAa	2/27	0.117895372765996	3	FACETS	1	0.948	1	0.573	0.504	0.648	INDETERMINATE	1	TRUE	1	0.236235302011953	3		459	644	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940373	13940373	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059654-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	73	442	0	ENST00000405192.2:c.1133T>C	p.Ile378Thr	p.I378T	ENST00000405192	NM_001163147.1	378	aTt/aCt	11/12	0.117895372765996	3	FACETS	1	0.96	1	0.621	0.544	0.705	INDETERMINATE	1	TRUE	1	0.236235302011953	3		442	556	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195192	123195192	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0059654-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	100	220	0	ENST00000218089.9:c.1534+1G>A		p.X512_splice	ENST00000218089	NM_001042749.1	512			0.214001088460952	2	FACETS	1	0.941	1			1	CLONAL	3	TRUE	NA	0.236235302011953	2		220	269	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791351	42791360	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCCGGCTG	GCCCCGGCTG	-	novel	NA	P-0059654-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	39	891	0	ENST00000575354.2:c.412_421del	p.Pro138ThrfsTer64	p.P138Tfs*64	ENST00000575354	NM_015125.3	137	gaGCCCCGGCTG/ga	3/20	1	2	FACETS	0.445	0.368	0.532	0.445	0.368	0.532	SUBCLONAL	1	TRUE	1	0.236235302011953	2		891	742	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676249	29676250	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0059767-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	20	132	0	ENST00000356175.3:c.7240_7241del	p.Ser2414ArgfsTer12	p.S2414Rfs*12	ENST00000356175	NM_000267.3	2413	cAG/c	48/57	0.192396339535716	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		132	91	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	81	497	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.709	0.626	0.797	0.709	0.626	0.797	SUBCLONAL	1	TRUE	1	0.459959992235688	2		499	497	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	79	302	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.459959992235688	2		306	311	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	199	815	0	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.898	0.84	0.956	1	0.993	1	CLONAL	2	TRUE	1	0.459959992235688	2		815	482	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115252203	115252203	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	79	421	0	ENST00000369535.4:c.437C>T	p.Ala146Val	p.A146V	ENST00000369535	NM_002524.4	146	gCc/gTc	4/7	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.459959992235688	2		421	334	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612920	228612920	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs372584075	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	134	1035	0	ENST00000366696.1:c.107T>C	p.Val36Ala	p.V36A	ENST00000366696	NM_003493.2	36	gTg/gCg	1/1	1	2	FACETS	0.89	0.81	0.973	0.89	0.81	0.973	CLONAL	1	TRUE	1	0.459959992235688	2		1035	655	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88677065	88677065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765530074	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	37	307	0	ENST00000372037.3:c.850C>T	p.Arg284Cys	p.R284C	ENST00000372037	NM_004329.2	284	Cgc/Tgc	9/13	1	2	FACETS	0.696	0.578	0.826	0.696	0.578	0.826	SUBCLONAL	1	TRUE	1	0.459959992235688	2		307	231	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10789627	10789627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751781919	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	111	537	0	ENST00000361367.2:c.1879C>T	p.Arg627Cys	p.R627C	ENST00000361367	NM_014633.3	627	Cgt/Tgt	15/25	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.459959992235688	2		537	420	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948747	71948748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760925109	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	91	850	7	ENST00000298229.2:c.3466dup	p.Arg1156ProfsTer59	p.R1156Pfs*59	ENST00000298229	NM_001567.3	1153	-/C	26/28	1	2	FACETS	0.979	0.875	1	0.979	0.875	1	CLONAL	1	TRUE	1	0.459959992235688	2		857	404	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs770248150	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	121	385	0	ENST00000311936.3:c.351A>T	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaT	4/5	0.459959992235688	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.459959992235688	3		385	302	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433773	49433773	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs35050033	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	80	775	1	ENST00000301067.7:c.7780del	p.Leu2594TrpfsTer97	p.L2594Wfs*97	ENST00000301067	NM_003482.3	2594	Ctg/tg	31/54	0.459959992235688	3	FACETS	0.877	0.774	0.986	0.438	0.387	0.493	CLONAL	1	TRUE	1	0.459959992235688	3		776	488	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434005	49434005	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	89	778	0	ENST00000301067.7:c.7548del	p.Asn2517IlefsTer26	p.N2517Ifs*26	ENST00000301067	NM_003482.3	2516	ccC/cc	31/54	0.459959992235688	3	FACETS	0.939	0.835	1	0.469	0.417	0.525	CLONAL	1	TRUE	1	0.459959992235688	3		778	507	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	118	825	3	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	0.459959992235688	3	FACETS	0.971	0.878	1	0.485	0.439	0.535	CLONAL	1	TRUE	1	0.459959992235688	3		828	650	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705401	43705401	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	96	654	0	ENST00000382044.4:c.5221C>A	p.Leu1741Ile	p.L1741I	ENST00000382044	NM_001141980.1	1741	Ctt/Att	24/28	1	2	FACETS	0.962	0.862	1	0.962	0.862	1	CLONAL	1	TRUE	1	0.459959992235688	2		654	434	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727430	66727430	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910099707	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	67	444	0	ENST00000307102.5:c.146G>A	p.Arg49His	p.R49H	ENST00000307102	NM_002755.3	49	cGc/cAc	2/11	1	2	FACETS	0.759	0.662	0.862	0.759	0.662	0.862	SUBCLONAL	1	TRUE	1	0.459959992235688	2		444	384	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129596	2129596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781782	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	98	613	1	ENST00000219476.3:c.3323C>T	p.Ala1108Val	p.A1108V	ENST00000219476	NM_000548.3	1108	gCg/gTg	29/42	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.459959992235688	2		614	410	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781402	3781402	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	98	682	1	ENST00000262367.5:c.4963del	p.Leu1655CysfsTer89	p.L1655Cfs*89	ENST00000262367	NM_004380.2	1655	Ctg/tg	30/31	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.459959992235688	2		683	413	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857074	9857075	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	69	478	0	ENST00000330684.3:c.4326dup	p.Arg1443GlnfsTer9	p.R1443Qfs*9	ENST00000330684	NM_001134407.1	1442	-/C	13/13	1	2	FACETS	0.965	0.847	1	0.965	0.847	1	CLONAL	1	TRUE	1	0.459959992235688	2		478	311	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029546	14029546	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	79	453	0	ENST00000311895.7:c.1757C>G	p.Thr586Ser	p.T586S	ENST00000311895	NM_005236.2	586	aCc/aGc	8/11	1	2	FACETS	0.909	0.804	1	0.909	0.804	1	CLONAL	1	TRUE	1	0.459959992235688	2		453	378	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56867247	56867247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	27	512	1	ENST00000308159.5:c.1466C>T	p.Ala489Val	p.A489V	ENST00000308159	NM_014669.4	489	gCt/gTt	13/22	1	2	FACETS	0.301	0.239	0.372	0.301	0.239	0.372	SUBCLONAL	1	TRUE	1	0.459959992235688	2		513	390	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829266	72829266	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	91	620	1	ENST00000268489.5:c.7315C>T	p.Gln2439Ter	p.Q2439*	ENST00000268489	NM_006885.3	2439	Cag/Tag	9/10	1	2	FACETS	0.885	0.79	0.986	0.885	0.79	0.986	CLONAL	1	TRUE	1	0.459959992235688	2		621	447	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38792680	38792680	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	50	333	0	ENST00000348513.6:c.336del	p.Lys112AsnfsTer5	p.K112Nfs*5	ENST00000348513	NM_003079.4	112	aaA/aa	6/11	1	2	FACETS	0.91	0.78	1	0.91	0.78	1	CLONAL	1	TRUE	1	0.459959992235688	2		333	239	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	83	513	0	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	0.991	0.881	1	0.991	0.881	1	CLONAL	1	TRUE	1	0.459959992235688	2		513	364	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	128	691	0	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.459959992235688	2		691	552	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66524000	66524000	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	48	335	0	ENST00000358598.2:c.728G>A	p.Arg243Gln	p.R243Q	ENST00000358598	NM_212471.2	243	cGg/cAg	8/11	1	2	FACETS	0.884	0.755	1	0.884	0.755	1	CLONAL	1	TRUE	1	0.459959992235688	2		335	236	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619821	1619821	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	105	693	0	ENST00000344749.5:c.1125del	p.Gly376ValfsTer18	p.G376Vfs*18	ENST00000344749	NM_001136139.2	375	ccC/cc	14/19	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.459959992235688	2		693	418	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231336	5231336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776822913	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	98	720	0	ENST00000357368.4:c.2140C>T	p.Arg714Cys	p.R714C	ENST00000357368	NM_002850.3	714	Cgc/Tgc	14/38	1	2	FACETS	0.975	0.875	1	0.975	0.875	1	CLONAL	1	TRUE	1	0.459959992235688	2		720	437	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117348	7117348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753193407	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	87	637	0	ENST00000302850.5:c.3868C>T	p.Leu1290Phe	p.L1290F	ENST00000302850	NM_000208.2	1290	Ctc/Ttc	22/22	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.459959992235688	2		637	349	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626865	14626865	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	131	614	1	ENST00000254322.2:c.910del	p.Leu304SerfsTer17	p.L304Sfs*17	ENST00000254322	NM_006145.1	304	Ctc/tc	3/3	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.459959992235688	2		615	524	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349666	15349666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200976853	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	50	728	3	ENST00000263377.2:c.3908C>T	p.Ala1303Val	p.A1303V	ENST00000263377	NM_058243.2	1303	gCg/gTg	19/20	1	2	FACETS	0.636	0.542	0.738	0.636	0.542	0.738	SUBCLONAL	1	TRUE	1	0.459959992235688	2		731	342	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	114	731	3	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	1	2	FACETS	0.915	0.827	1	0.915	0.827	1	CLONAL	1	TRUE	1	0.459959992235688	2		734	542	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	112	816	2	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.951	0.859	1	0.951	0.859	1	CLONAL	1	TRUE	1	0.459959992235688	2		818	512	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743988	41743988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776310618	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	89	871	0	ENST00000301178.4:c.923G>A	p.Arg308His	p.R308H	ENST00000301178	NM_021913.4	308	cGc/cAc	7/20	1	2	FACETS	0.93	0.83	1	0.93	0.83	1	CLONAL	1	TRUE	1	0.459959992235688	2		871	416	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744385	41744385	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	85	594	0	ENST00000301178.4:c.1010del	p.Pro337LeufsTer29	p.P337Lfs*29	ENST00000301178	NM_021913.4	335	ggC/gg	8/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.459959992235688	2		594	325	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383725	42383725	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	79	507	0	ENST00000221972.3:c.498+2T>C		p.X166_splice	ENST00000221972	NM_021601.3	166			1	2	FACETS	0.981	0.87	1	0.981	0.87	1	CLONAL	1	TRUE	1	0.459959992235688	2		507	350	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791587	42791587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767502801	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	111	750	0	ENST00000575354.2:c.568C>T	p.Arg190Cys	p.R190C	ENST00000575354	NM_015125.3	190	Cgc/Tgc	4/20	1	2	FACETS	0.999	0.903	1	0.999	0.903	1	CLONAL	1	TRUE	1	0.459959992235688	2		750	483	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799060	42799060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	70	662	0	ENST00000575354.2:c.4544G>A	p.Arg1515His	p.R1515H	ENST00000575354	NM_015125.3	1515	cGc/cAc	20/20	1	2	FACETS	0.862	0.757	0.975	0.862	0.757	0.975	CLONAL	1	TRUE	1	0.459959992235688	2		662	353	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912075	50912077	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs398122386	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	93	637	0	ENST00000440232.2:c.1812_1814del	p.Ser605del	p.S605del	ENST00000440232	NM_002691.3	603	ttCTCc/ttc	15/27	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.459959992235688	2		637	390	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918194	50918194	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	77	660	1	ENST00000440232.2:c.2515del	p.Leu839SerfsTer49	p.L839Sfs*49	ENST00000440232	NM_002691.3	837	tgC/tg	20/27	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.459959992235688	2		661	317	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661664	227661664	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs761880048	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	94	759	8	ENST00000305123.5:c.1791del	p.His598ThrfsTer38	p.H598Tfs*38	ENST00000305123	NM_005544.2	597	ggG/gg	1/2	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.459959992235688	2		767	366	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573312	41573312	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763290593	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	31	936	0	ENST00000263253.7:c.5597C>T	p.Pro1866Leu	p.P1866L	ENST00000263253	NM_001429.3	1866	cCg/cTg	31/31	1	2	FACETS	0.264	0.213	0.322	0.264	0.213	0.322	SUBCLONAL	1	TRUE	1	0.459959992235688	2		936	511	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090077	37090077	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	130	417	0	ENST00000231790.2:c.1967del	p.Phe656SerfsTer5	p.F656Sfs*5	ENST00000231790	NM_000249.3	656	Ttc/tc	17/19	0.421635182217751	2	FACETS	0.981	0.906	1	0.981	0.906	1	CLONAL	2	TRUE	0	0.459959992235688	2		417	288	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	148	458	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.421635182217751	2	FACETS	0.872	0.807	0.938	0.872	0.807	0.938	CLONAL	2	TRUE	0	0.459959992235688	2		458	369	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49726045	49726045	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	18	209	0	ENST00000449682.2:c.80G>T	p.Cys27Phe	p.C27F	ENST00000449682	NM_020998.3	27	tGc/tTc	1/18	1	2	FACETS	0.824	0.631	1	0.824	0.631	1	CLONAL	1	TRUE	1	0.459959992235688	2		209	95	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935108	49935108	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760946033	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	68	684	0	ENST00000296474.3:c.1891C>T	p.Arg631Trp	p.R631W	ENST00000296474	NM_002447.2	631	Cgg/Tgg	6/20	1	2	FACETS	0.706	0.616	0.802	0.706	0.616	0.802	SUBCLONAL	1	TRUE	1	0.459959992235688	2		684	419	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52677265	52677265	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	74	439	0	ENST00000394830.3:c.994C>A	p.Arg332Ser	p.R332S	ENST00000394830	NM_018313.4	332	Cgt/Agt	10/30	1	2	FACETS	0.804	0.708	0.907	0.804	0.708	0.907	CLONAL	1	TRUE	1	0.459959992235688	2		439	400	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs753143066	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	51	389	2	ENST00000295797.4:c.826dup	p.Thr276AsnfsTer16	p.T276Nfs*16	ENST00000295797	NM_002740.5	273	tta/ttAa	9/18	1	2	FACETS	0.682	0.583	0.79	0.682	0.583	0.79	SUBCLONAL	1	TRUE	1	0.459959992235688	2		391	325	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	82	455	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.459959992235688	2		455	329	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952138	178952138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	51	405	1	ENST00000263967.3:c.3193C>T	p.His1065Tyr	p.H1065Y	ENST00000263967	NM_006218.2	1065	Cat/Tat	21/21	1	2	FACETS	0.86	0.737	0.992	0.86	0.737	0.992	CLONAL	1	TRUE	1	0.459959992235688	2		406	258	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957419	1957419	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	92	488	1	ENST00000382891.5:c.2523del		p.X841_splice	ENST00000382891	NM_133335.3	841			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.459959992235688	2		489	317	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874637	35874637	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	70	441	3	ENST00000303115.3:c.799del	p.Arg267GlyfsTer28	p.R267Gfs*28	ENST00000303115	NM_002185.3	265	Aaa/aa	6/8	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.459959992235688	2		444	299	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79968087	79968087	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs186924833	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	50	389	0	ENST00000265081.6:c.817T>C	p.Tyr273His	p.Y273H	ENST00000265081	NM_002439.4	273	Tat/Cat	5/24	1	2	FACETS	0.898	0.77	1	0.898	0.77	1	CLONAL	1	TRUE	1	0.459959992235688	2		389	242	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502734	149502734	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200986052	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	106	591	0	ENST00000261799.4:c.2054G>A	p.Arg685His	p.R685H	ENST00000261799	NM_002609.3	685	cGc/cAc	15/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.459959992235688	2		591	390	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	106	704	2	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.857	0.771	0.947	0.857	0.771	0.947	CLONAL	1	TRUE	1	0.459959992235688	2		706	538	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395883	395883	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	72	596	0	ENST00000380956.4:c.440C>A	p.Ser147Tyr	p.S147Y	ENST00000380956	NM_001195286.1	147	tCc/tAc	4/9	1	2	FACETS	0.874	0.769	0.987	0.874	0.769	0.987	CLONAL	1	TRUE	1	0.459959992235688	2		596	358	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32191695	32191695	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	27	516	0	ENST00000375023.3:c.11del	p.Pro4LeufsTer39	p.P4Lfs*39	ENST00000375023	NM_004557.3	4	cCt/ct	1/30	1	2	FACETS	0.405	0.323	0.498	0.405	0.323	0.498	SUBCLONAL	1	TRUE	1	0.459959992235688	2		516	290	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803005	32803005	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	102	564	0	ENST00000374899.4:c.871C>T	p.Arg291Ter	p.R291*	ENST00000374899	NM_018833.2	291	Cga/Tga	5/12	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.459959992235688	2		564	429	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803531	32803531	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1372620501	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	87	558	0	ENST00000374899.4:c.628C>T	p.Arg210Ter	p.R210*	ENST00000374899	NM_018833.2	210	Cga/Tga	4/12	1	2	FACETS	0.958	0.853	1	0.958	0.853	1	CLONAL	1	TRUE	1	0.459959992235688	2		558	395	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	92	747	2	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	0.875	0.781	0.974	0.875	0.781	0.974	CLONAL	1	TRUE	1	0.459959992235688	2		749	457	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714408	117714409	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	25	399	0	ENST00000368508.3:c.1240dup	p.Ile414AsnfsTer4	p.I414Nfs*4	ENST00000368508	NM_002944.2	414	att/aAtt	11/43	1	2	FACETS	0.477	0.377	0.59	0.477	0.377	0.59	SUBCLONAL	1	TRUE	1	0.459959992235688	2		399	228	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	104	531	0	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.987	0.889	1	0.987	0.889	1	CLONAL	1	TRUE	1	0.459959992235688	2		531	458	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508856	106508856	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376958957	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	91	655	0	ENST00000359195.3:c.850G>A	p.Glu284Lys	p.E284K	ENST00000359195	NM_002649.2	284	Gaa/Aaa	2/11	1	2	FACETS	0.855	0.762	0.952	0.855	0.762	0.952	CLONAL	1	TRUE	1	0.459959992235688	2		655	463	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845165	128845165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200359079	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	78	637	0	ENST00000249373.3:c.659C>T	p.Pro220Leu	p.P220L	ENST00000249373	NM_005631.4	220	cCg/cTg	3/12	1	2	FACETS	0.835	0.738	0.939	0.835	0.738	0.939	CLONAL	1	TRUE	1	0.459959992235688	2		637	406	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146945	38146945	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	70	380	0	ENST00000317025.8:c.3197del	p.Asn1066ThrfsTer16	p.N1066Tfs*16	ENST00000317025	NM_023034.1	1066	aAc/ac	18/24	1	2	FACETS	0.877	0.77	0.991	0.877	0.77	0.991	CLONAL	1	TRUE	1	0.459959992235688	2		380	347	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	62	343	1	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	1	2	FACETS	0.998	0.871	1	0.998	0.871	1	CLONAL	1	TRUE	1	0.459959992235688	2		344	270	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737820	145737820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs36023964	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	103	772	1	ENST00000428558.2:c.3010C>T	p.Arg1004Trp	p.R1004W	ENST00000428558	NM_004260.3	1004	Cgg/Tgg	18/22	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.459959992235688	2		773	381	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321002	137321002	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	114	641	0	ENST00000481739.1:c.959T>C	p.Val320Ala	p.V320A	ENST00000481739	NM_002957.4	320	gTg/gCg	7/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.459959992235688	2		641	406	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923000	44923000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139486036	NA	P-0060180-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	104	290	0	ENST00000377967.4:c.1861C>T	p.Arg621Cys	p.R621C	ENST00000377967	NM_021140.2	621	Cgc/Tgc	16/29	1	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.459959992235688	1		290	244	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0060389-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	60	358	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.449292946382798	2		358	262	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0060389-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	135	577	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.317661462452347	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.449292946382798	1		579	464	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0060389-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	13	665	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.449292946382798	1	FACETS	0.147	0.104	0.199	0.147	0.104	0.199	SUBCLONAL	1	TRUE	0	0.449292946382798	1		665	305	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0060389-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	63	393	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.362078934080196	1	FACETS	0.426	0.369	0.488	0.426	0.369	0.488	SUBCLONAL	1	TRUE	0	0.449292946382798	1		393	510	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0060389-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	56	465	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.317661462452347	1	FACETS	0.42	0.36	0.485	0.42	0.36	0.485	SUBCLONAL	1	TRUE	0	0.449292946382798	1		465	460	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953038	2953038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747530675	NA	P-0060389-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	62	589	0	ENST00000396946.4:c.2902G>A	p.Ala968Thr	p.A968T	ENST00000396946	NM_032415.4	968	Gcc/Acc	22/25	0.259817659695709	3	FACETS	0.583	0.503	0.669	0.291	0.251	0.335	INDETERMINATE	1	TRUE	1	0.449292946382798	3		589	580	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411246	63411246	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060389-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	185	344	0	ENST00000330258.3:c.1921C>T	p.Arg641Ter	p.R641*	ENST00000330258	NM_152424.3	641	Cga/Tga	2/2	0.403883052849033	2	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.449292946382798	2		344	331	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2090156	2090156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148474733	NA	P-0060389-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	66	662	1	ENST00000219066.1:c.793G>A	p.Ala265Thr	p.A265T	ENST00000219066	NM_002528.5	265	Gcc/Acc	5/6	0.22559282021626	2	FACETS	0.47	0.408	0.538	0.235	0.204	0.269	INDETERMINATE	1	TRUE	0	0.449292946382798	2		663	625	SUCCESS
APC	324	MSKCC	GRCh37	5	112174154	112174154	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060389-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	66	269	0	ENST00000257430.4:c.2863G>T	p.Glu955Ter	p.E955*	ENST00000257430	NM_000038.5	955	Gaa/Taa	16/16	0.362078934080196	1	FACETS	0.911	0.801	1	0.911	0.801	1	CLONAL	1	TRUE	0	0.449292946382798	1		269	250	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10267151	10267151	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1181209213	NA	P-0060389-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	160	392	0	ENST00000340748.4:c.1267G>A	p.Asp423Asn	p.D423N	ENST00000340748		423	Gac/Aac	17/40	0.449292946382798	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.449292946382798	1		392	433	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541547	187541547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1165941519	NA	P-0060389-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	148	560	0	ENST00000441802.2:c.6193G>A	p.Val2065Ile	p.V2065I	ENST00000441802	NM_005245.3	2065	Gtt/Att	10/27	0.362078934080196	1	FACETS	0.969	0.891	1	0.969	0.891	1	CLONAL	1	TRUE	0	0.449292946382798	1		560	527	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788627	3788627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060389-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	50	330	0	ENST00000262367.5:c.4327C>T	p.Arg1443Cys	p.R1443C	ENST00000262367	NM_004380.2	1443	Cgt/Tgt	26/31	0.22559282021626	2	FACETS	0.519	0.441	0.604	0.259	0.22	0.302	INDETERMINATE	1	TRUE	0	0.449292946382798	2		330	429	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738353	190738353	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060389-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	59	190	0	ENST00000441310.2:c.2605A>G	p.Arg869Gly	p.R869G	ENST00000441310	NM_000534.4	869	Aga/Gga	12/13	1	2	FACETS	0.922	0.8	1	0.922	0.8	1	CLONAL	1	TRUE	1	0.449292946382798	2		190	285	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498486	89498486	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060389-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	34	366	0	ENST00000336596.2:c.2458T>G	p.Tyr820Asp	p.Y820D	ENST00000336596	NM_005233.5	820	Tat/Gat	14/17	1	2	FACETS	0.358	0.292	0.432	0.358	0.292	0.432	SUBCLONAL	1	TRUE	1	0.449292946382798	2		366	423	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068003	94068003	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060389-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	20	327	0	ENST00000369303.4:c.959C>G	p.Pro320Arg	p.P320R	ENST00000369303	NM_004440.3	320	cCa/cGa	4/17	0.362078934080196	1	FACETS	0.202	0.154	0.259	0.202	0.154	0.259	SUBCLONAL	1	TRUE	0	0.449292946382798	1		327	341	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0060681-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	53	792	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	0.495	0.421	0.576	0.495	0.421	0.576	SUBCLONAL	1	TRUE	1	0.26	2		792	824	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842437	68842472	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TGAAAAAGGCCCATTTCCTAAAAACCTGGTTCAGGT	TGAAAAAGGCCCATTTCCTAAAAACCTGGTTCAGGT	-	novel	NA	P-0060681-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	42	446	0	ENST00000261769.5:c.498_531+2del		p.X166_splice	ENST00000261769	NM_004360.3	166		4/16	1	2	FACETS	0.597	0.498	0.707	0.597	0.498	0.707	SUBCLONAL	1	TRUE	1	0.26	2		446	541	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845763	68845763	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0060681-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	34	528	0	ENST00000261769.5:c.1008+1G>A		p.X336_splice	ENST00000261769	NM_004360.3	336			1	2	FACETS	0.466	0.38	0.564	0.466	0.38	0.564	SUBCLONAL	1	TRUE	1	0.26	2		528	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0060707-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	47	776	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	1	2	FACETS	0.635	0.538	0.742	0.635	0.538	0.742	SUBCLONAL	1	FALSE	1	0.428946304430268	2		776	345	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342932	118342932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060707-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	17	544	0	ENST00000534358.1:c.1058G>A	p.Arg353Gln	p.R353Q	ENST00000534358	NM_005933.3	353	cGa/cAa	3/36	1	2	FACETS	0.294	0.219	0.382	0.294	0.219	0.382	SUBCLONAL	1	FALSE	1	0.428946304430268	2		544	270	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445223	29445223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060707-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	38	602	0	ENST00000389048.3:c.3502G>A	p.Ala1168Thr	p.A1168T	ENST00000389048	NM_004304.4	1168	Gcc/Acc	22/29	1	2	FACETS	0.609	0.505	0.723	0.609	0.505	0.723	SUBCLONAL	1	FALSE	1	0.428946304430268	2		602	291	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411964	116411965	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0060707-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	98	718	0	ENST00000397752.3:c.2950dup	p.Val984GlyfsTer16	p.V984Gfs*16	ENST00000397752	NM_000245.2	983	-/G	14/21	0.428946304430268	3	FACETS	1	0.981	1	0.715	0.643	0.791	CLONAL	1	FALSE	1	0.428946304430268	3		718	388	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342946	118342946	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060707-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	18	555	0	ENST00000534358.1:c.1072G>C	p.Val358Leu	p.V358L	ENST00000534358	NM_005933.3	358	Gtt/Ctt	3/36	1	2	FACETS	0.33	0.249	0.427	0.33	0.249	0.427	SUBCLONAL	1	FALSE	1	0.428946304430268	2		555	254	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295726	1295726	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs577225323	NA	P-0060707-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	21	789	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.314	0.241	0.398	0.314	0.241	0.398	SUBCLONAL	1	FALSE	1	0.428946304430268	2		789	312	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0061022-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	119	462	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.484028504025418	3	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	TRUE	1	0.484028504025418	3		462	303	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266709	198266709	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061022-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	193	478	0	ENST00000335508.6:c.2223G>C	p.Lys741Asn	p.K741N	ENST00000335508	NM_012433.2	741	aaG/aaC	15/25	0.433287634137125	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	2	0.484028504025418	4		478	574	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188140	108188140	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587779855	NA	P-0061022-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	295	372	0	ENST00000278616.4:c.6239A>G	p.Tyr2080Cys	p.Y2080C	ENST00000278616	NM_000051.3	2080	tAt/tGt	43/63	0.484028504025418	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	4	TRUE	0	0.484028504025418	4		372	445	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837937	156837937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141021604	NA	P-0061022-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	165	766	0	ENST00000524377.1:c.470G>A	p.Arg157His	p.R157H	ENST00000524377	NM_002529.3	157	cGc/cAc	5/17	0.484028504025418	6	FACETS	1	0.944	1	0.208	0.19	0.227	CLONAL	1	TRUE	1	0.484028504025418	6		766	1291	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371613	225371613	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061022-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	139	443	0	ENST00000264414.4:c.991G>T	p.Glu331Ter	p.E331*	ENST00000264414	NM_003590.4	331	Gaa/Taa	7/16	0.433287634137125	4	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	2	0.484028504025418	4		443	422	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912617	32912617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061022-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	86	456	0	ENST00000380152.3:c.4127del	p.Gly1376GlufsTer12	p.G1376Efs*12	ENST00000380152		1375	gaG/ga	11/27	0.484028504025418	3	FACETS	0.929	0.825	1	0.465	0.412	0.52	CLONAL	1	TRUE	1	0.484028504025418	3		456	475	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145719	11145719	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061022-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	296	823	0	ENST00000358026.2:c.4081G>T	p.Glu1361Ter	p.E1361*	ENST00000358026	NM_001128849.1	1361	Gag/Tag	29/36	0.484028504025418	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	1	0.484028504025418	3		823	754	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528615	89528615	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061022-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	188	461	0	ENST00000336596.2:c.2915T>C	p.Leu972Pro	p.L972P	ENST00000336596	NM_005233.5	972	cTa/cCa	17/17	0.484028504025418	6	FACETS	0.896	0.829	0.966			1	CLONAL	2	TRUE	NA	0.484028504025418	6		461	853	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149450084	149450084	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061022-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	149	681	0	ENST00000286301.3:c.1133G>T	p.Arg378Leu	p.R378L	ENST00000286301	NM_005211.3	378	cGc/cTc	8/22	0.484028504025418	3	FACETS	1	0.951	1	0.528	0.483	0.575	CLONAL	1	TRUE	1	0.484028504025418	3		681	724	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444377	50444377	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061022-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	317	704	0	ENST00000331340.3:c.307G>T	p.Ala103Ser	p.A103S	ENST00000331340	NM_006060.4	103	Gct/Tct	4/8	0.433287634137125	4	FACETS	0.992	0.938	1	0.992	0.938	1	CLONAL	2	TRUE	2	0.484028504025418	4		704	980	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	74	330	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.550798674256252	3	FACETS	0.987	0.905	1	0.987	0.905	1	CLONAL	3	TRUE	0	0.568210178362518	3		330	113	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120791147	120791147	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	14	405	0	ENST00000257552.2:c.688C>T	p.Arg230Trp	p.R230W	ENST00000257552	NM_002442.3	230	Cgg/Tgg	10/15	0.44423959675168	3	FACETS	0.355	0.257	0.473	0.178	0.128	0.237	SUBCLONAL	1	TRUE	1	0.568210178362518	3		405	178	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31511274	31511275	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	23	256	0	ENST00000344624.3:c.1299dup	p.Thr434TyrfsTer7	p.T434Yfs*7	ENST00000344624		433	-/T	6/33	1	2	FACETS	0.786	0.625	0.965	0.786	0.625	0.965	CLONAL	1	TRUE	1	0.568210178362518	2		256	103	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061317-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	217	343	0				ENST00000310581	NM_198253.2	-/1132			0.759219304189366	3	FACETS	0.945	0.893	0.997	0.945	0.893	0.997	CLONAL	2	TRUE	1	0.791524879230054	3		343	405	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555054	106555054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061317-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	213	598	0	ENST00000369096.4:c.2171C>T	p.Thr724Ile	p.T724I	ENST00000369096	NM_001198.3	724	aCc/aTc	7/7	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.791524879230054	2		598	504	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47613717	47613717	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061317-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	25	150	0	ENST00000263735.4:c.910G>A	p.Glu304Lys	p.E304K	ENST00000263735	NM_002354.2	304	Gag/Aag	9/9	1	2	FACETS	0.752	0.609	0.906	0.752	0.609	0.906	CLONAL	1	TRUE	1	0.791524879230054	2		150	84	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101176	41101176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370385649	NA	P-0061317-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	221	534	0	ENST00000373198.4:c.1180G>A	p.Glu394Lys	p.E394K	ENST00000373198	NM_133170.3	394	Gaa/Aaa	8/32	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.791524879230054	2		534	522	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750596	41750596	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061317-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	150	407	0	ENST00000226382.2:c.32C>T	p.Ser11Phe	p.S11F	ENST00000226382	NM_003924.3	11	tCc/tTc	1/3	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.791524879230054	2		407	350	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169036	32169036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745902446	NA	P-0061317-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	221	531	0	ENST00000375023.3:c.3997C>T	p.Arg1333Cys	p.R1333C	ENST00000375023	NM_004557.3	1333	Cgt/Tgt	22/30	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.791524879230054	2		531	545	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714445	117714445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1307627482	NA	P-0061317-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	71	315	0	ENST00000368508.3:c.1204G>A	p.Glu402Lys	p.E402K	ENST00000368508	NM_002944.2	402	Gaa/Aaa	11/43	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.791524879230054	2		315	169	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857205	9857205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061317-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	212	544	0	ENST00000330684.3:c.4196G>A	p.Ser1399Asn	p.S1399N	ENST00000330684	NM_001134407.1	1399	aGc/aAc	13/13	1	2	FACETS	0.996	0.933	1	0.996	0.933	1	CLONAL	1	TRUE	1	0.791524879230054	2		544	538	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514319	149514319	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061317-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	179	532	0	ENST00000261799.4:c.625C>T	p.Leu209Phe	p.L209F	ENST00000261799	NM_002609.3	209	Ctc/Ttc	4/23	0.791524879230054	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.791524879230054	1		532	260	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230468764	230468764	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1327319064	NA	P-0061317-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	190	521	0	ENST00000391860.1:c.754C>T	p.Arg252Cys	p.R252C	ENST00000391860	NM_001258311.1	252	Cgc/Tgc	5/7	0.783457970610861	3	FACETS	0.959	0.889	1	0.479	0.444	0.515	CLONAL	1	TRUE	1	0.791524879230054	3		521	699	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276976	123276976	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061317-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	167	441	0	ENST00000358487.5:c.941C>T	p.Ala314Val	p.A314V	ENST00000358487	NM_000141.4	314	gCc/gTc	8/18	1	2	FACETS	0.993	0.923	1	0.993	0.923	1	CLONAL	1	TRUE	1	0.791524879230054	2		441	425	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533882	533883	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0061317-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	224	642	0	ENST00000451590.1:c.173_174delinsTT	p.Thr58Ile	p.T58I	ENST00000451590	NM_001130442.1	58	aCC/aTT	3/5	1	2	FACETS	0.92	0.863	0.979	0.92	0.863	0.979	CLONAL	1	TRUE	1	0.791524879230054	2		642	615	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201511	67201511	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061317-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	291	706	0	ENST00000312629.5:c.952G>A	p.Asp318Asn	p.D318N	ENST00000312629	NM_003952.2	318	Gat/Aat	11/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.791524879230054	2		706	676	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102094426	102094426	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs955087272	NA	P-0061317-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	141	401	0	ENST00000282441.5:c.1106G>A	p.Gly369Glu	p.G369E	ENST00000282441	NM_001130145.2	369	gGg/gAg	7/9	0.791524879230054	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.791524879230054	1		401	210	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435028	110435028	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061317-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	212	752	0	ENST00000375856.3:c.3373C>T	p.Gln1125Ter	p.Q1125*	ENST00000375856	NM_003749.2	1125	Cag/Tag	1/2	1	2	FACETS	0.893	0.835	0.952	0.893	0.835	0.952	CLONAL	1	TRUE	1	0.791524879230054	2		752	600	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652920	29652920	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061317-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	125	400	0	ENST00000356175.3:c.4855G>T	p.Glu1619Ter	p.E1619*	ENST00000356175	NM_000267.3	1619	Gaa/Taa	36/57	0.791524879230054	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.791524879230054	1		400	181	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33689997	33689997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061317-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	122	445	0	ENST00000308377.4:c.830C>T	p.Ala277Val	p.A277V	ENST00000308377	NM_152270.3	277	gCc/gTc	2/5	0.791524879230054	1	FACETS	0.904	0.842	0.966	0.904	0.842	0.966	CLONAL	1	TRUE	0	0.791524879230054	1		445	206	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619072	37619073	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0061317-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	181	608	0	ENST00000447079.4:c.748_749delinsTT	p.Pro250Phe	p.P250F	ENST00000447079	NM_015083.1	250	CCc/TTc	1/14	0.791524879230054	1	FACETS	0.963	0.911	1	0.963	0.911	1	CLONAL	1	TRUE	0	0.791524879230054	1		608	287	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38793825	38793825	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0061317-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	161	361	0	ENST00000348513.6:c.157-1G>A		p.X53_splice	ENST00000348513	NM_003079.4	53			0.791524879230054	1	FACETS	0.987	0.931	1	0.987	0.931	1	CLONAL	1	TRUE	0	0.791524879230054	1		361	249	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284957	15284957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061317-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	275	555	0	ENST00000263388.2:c.4658C>T	p.Ala1553Val	p.A1553V	ENST00000263388	NM_000435.2	1553	gCc/gTc	25/33	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.791524879230054	2		555	595	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594071	158594071	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061317-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	141	412	0	ENST00000263640.3:c.1502C>T	p.Ser501Phe	p.S501F	ENST00000263640	NM_001105.4	501	tCc/tTc	11/11	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.791524879230054	2		412	345	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737497	204737497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061317-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	67	396	0	ENST00000302823.3:c.634G>A	p.Glu212Lys	p.E212K	ENST00000302823	NM_005214.4	212	Gaa/Aaa	4/4	1	2	FACETS	0.763	0.673	0.857	0.763	0.673	0.857	SUBCLONAL	1	TRUE	1	0.791524879230054	2		396	222	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710541	40710541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770678610	NA	P-0061317-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	161	442	0	ENST00000373198.4:c.4310C>T	p.Ser1437Phe	p.S1437F	ENST00000373198	NM_133170.3	1437	tCc/tTc	31/32	1	2	FACETS	0.929	0.861	0.998	0.929	0.861	0.998	CLONAL	1	TRUE	1	0.791524879230054	2		442	438	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49929236	49929236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061317-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	187	460	1	ENST00000296474.3:c.3307G>A	p.Asp1103Asn	p.D1103N	ENST00000296474	NM_002447.2	1103	Gac/Aac	15/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.791524879230054	2		461	471	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972933	55972933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061317-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	71	302	0	ENST00000263923.4:c.1457G>A	p.Arg486Lys	p.R486K	ENST00000263923	NM_002253.2	486	aGa/aAa	11/30	0.791524879230054	4	FACETS	0.965	0.849	1	0.322	0.283	0.363	CLONAL	1	TRUE	1	0.791524879230054	4		302	333	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803494	32803494	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1252311955	NA	P-0061317-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	238	414	0	ENST00000374899.4:c.665A>G	p.Asn222Ser	p.N222S	ENST00000374899	NM_018833.2	222	aAc/aGc	4/12	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.791524879230054	2		414	535	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952954	2952954	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061317-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	204	490	0	ENST00000396946.4:c.2986G>A	p.Gly996Arg	p.G996R	ENST00000396946	NM_032415.4	996	Gga/Aga	22/25	0.783457970610861	3	FACETS	0.99	0.921	1	0.495	0.46	0.53	CLONAL	1	TRUE	1	0.791524879230054	3		490	727	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229228	55229228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061317-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	365	588	0	ENST00000275493.2:c.1535C>T	p.Pro512Leu	p.P512L	ENST00000275493	NM_005228.3	512	cCc/cTc	13/28	0.783457970610861	3	FACETS	0.938	0.898	0.978	0.938	0.898	0.978	CLONAL	2	TRUE	1	0.791524879230054	3		588	686	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319915	8319915	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061317-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	144	402	0	ENST00000356435.5:c.5586A>T	p.Glu1862Asp	p.E1862D	ENST00000356435		1862	gaA/gaT	34/35	0.791524879230054	1	FACETS	0.995	0.936	1	0.995	0.936	1	CLONAL	1	TRUE	0	0.791524879230054	1		402	221	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354699	70354699	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0061317-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	200	479	0	ENST00000374080.3:c.4863+1G>A		p.X1621_splice	ENST00000374080		1621			1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.791524879230054	2		479	492	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123159710	123159710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061317-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	52	187	0	ENST00000218089.9:c.65C>T	p.Ser22Phe	p.S22F	ENST00000218089	NM_001042749.1	22	tCt/tTt	4/35	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.791524879230054	2		187	113	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143353	30143355	+	missense_variant	Missense_Mutation	TNP	AAG	AAG	GGA	novel	NA	P-0061317-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	185	544	0	ENST00000389048.3:c.171_173delinsTCC	p.Phe58Pro	p.F58P	ENST00000389048	NM_004304.4	57	gaCTTc/gaTCCc	1/29	1	2	FACETS	0.956	0.891	1	0.956	0.891	1	CLONAL	1	TRUE	1	0.791524879230054	2		544	489	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555731	21555732	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061445-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	198	792	0	ENST00000382592.4:c.2538dup	p.Asn847Ter	p.N847*	ENST00000382592	NM_014572.2	846	-/T	6/8	0.475698885468168	2	FACETS	0.984	0.924	1	0.984	0.924	1	CLONAL	2	TRUE	0	0.475698885468168	2		792	423	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443613	52443613	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061445-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	185	801	1	ENST00000460680.1:c.79del	p.Val27CysfsTer45	p.V27Cfs*45	ENST00000460680	NM_004656.3	27	Gtg/tg	3/17	0.475698885468168	2	FACETS	0.866	0.809	0.924	0.866	0.809	0.924	CLONAL	2	TRUE	0	0.475698885468168	2		802	449	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007811	45007811	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0061445-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	27	641	0	ENST00000558401.1:c.258C>G	p.Tyr86Ter	p.Y86*	ENST00000558401	NM_004048.2	86	taC/taG	2/4	0.475698885468168	2	FACETS	0.458	0.365	0.562	0.229	0.182	0.281	SUBCLONAL	1	TRUE	0	0.475698885468168	2		641	248	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615584	100615584	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061445-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	36	318	0	ENST00000308731.7:c.748C>G	p.Pro250Ala	p.P250A	ENST00000308731	NM_000061.2	250	Cca/Gca	8/19	0.290480691217313	2	FACETS	0.587	0.485	0.699			1	SUBCLONAL	1	TRUE	NA	0.475698885468168	2		318	258	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841431	156841431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061445-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	350	804	0	ENST00000524377.1:c.734C>T	p.Pro245Leu	p.P245L	ENST00000524377	NM_002529.3	245	cCa/cTa	7/17	0.475698885468168	6	FACETS	0.955	0.91	0.999	0.955	0.91	0.999	CLONAL	4	TRUE	2	0.475698885468168	6		804	752	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623093	52623093	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061445-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	28	586	0	ENST00000394830.3:c.2958T>A	p.Asp986Glu	p.D986E	ENST00000394830	NM_018313.4	986	gaT/gaA	19/30	0.475698885468168	2	FACETS	0.381	0.305	0.467	0.19	0.152	0.234	SUBCLONAL	1	TRUE	0	0.475698885468168	2		586	309	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005091	150005092	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061445-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	399	860	0	ENST00000253339.5:c.1133dup	p.Thr379AspfsTer4	p.T379Dfs*4	ENST00000253339		378	ctg/ctTg	3/7	0.468168723250493	4	FACETS	0.982	0.947	1	0.982	0.947	1	CLONAL	4	TRUE	0	0.475698885468168	4		860	630	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463242	25463242	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	34	533	0	ENST00000264709.3:c.2251T>G	p.Phe751Val	p.F751V	ENST00000264709	NM_175629.2	751	Ttc/Gtc	19/23	0.368292845077696	3	FACETS	0.334	0.272	0.405	0.167	0.136	0.203	SUBCLONAL	1	TRUE	1	0.368292845077696	3		533	654	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438750	49438750	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0061564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	36	416	1	ENST00000301067.7:c.4742-2A>G		p.X1581_splice	ENST00000301067	NM_003482.3	1581			0.368292845077696	6	FACETS	0.489	0.401	0.589	0.122	0.1	0.148	SUBCLONAL	1	TRUE	2	0.368292845077696	6		417	694	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910983	32910983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507287	NA	P-0061564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	23	387	0	ENST00000380152.3:c.2491G>A	p.Val831Ile	p.V831I	ENST00000380152		831	Gtt/Att	11/27	0.27883021646152	3	FACETS	0.34	0.264	0.428	0.113	0.088	0.143	SUBCLONAL	1	TRUE	0	0.368292845077696	3		387	435	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805534	46805534	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	254	615	0	ENST00000290295.7:c.422C>A	p.Ala141Asp	p.A141D	ENST00000290295	NM_006361.5	141	gCc/gAc	1/2	0.351566872700175	4	FACETS	0.923	0.875	0.972	0.923	0.875	0.972	CLONAL	4	TRUE	0	0.368292845077696	4		615	511	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061628-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	14	343	0				ENST00000310581	NM_198253.2	-/1132			0.143641950838002	0	FACETS	0.954	0.714	1			1	CLONAL	2	TRUE	0	0.230560440472605	0		343	49	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0061628-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	400	1085	0	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.230560440472605	39	FACETS	0.99	0.966	1	1	0.992	1	CLONAL	39	TRUE	2	0.230560440472605	39		1085	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0061666-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	545	706	1	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.665195624001021	2	FACETS	0.982	0.952	1	0.982	0.952	1	CLONAL	2	TRUE	0	0.665195624001021	2		707	834	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828768	3828768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061666-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	39	495	0	ENST00000262367.5:c.1874G>A	p.Arg625His	p.R625H	ENST00000262367	NM_004380.2	625	cGc/cAc	9/31	0.665195624001021	1	FACETS	0.176	0.145	0.21	0.176	0.145	0.21	SUBCLONAL	1	TRUE	0	0.665195624001021	1		495	445	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858476	57858476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199685332	NA	P-0061666-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	206	544	0	ENST00000228682.2:c.214C>T	p.Arg72Trp	p.R72W	ENST00000228682	NM_005269.2	72	Cgg/Tgg	4/12	0.665195624001021	1	FACETS	0.919	0.863	0.975	0.919	0.863	0.975	CLONAL	1	TRUE	0	0.665195624001021	1		544	450	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845969	156845974	+	inframe_deletion	In_Frame_Del	DEL	GCCTGA	GCCTGA	-	novel	NA	P-0061666-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	172	605	0	ENST00000524377.1:c.1601_1606del	p.Pro534_Glu535del	p.P534_E535del	ENST00000524377	NM_002529.3	533	ctGCCTGAg/ctg	13/17	0.62829204488989	5	FACETS	0.802	0.736	0.871	0.201	0.184	0.218	CLONAL	1	TRUE	1	0.665195624001021	5		605	1288	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431635	6431635	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061666-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	94	247	0	ENST00000356142.4:c.188A>C	p.Asp63Ala	p.D63A	ENST00000356142	NM_018890.3	63	gAt/gCt	3/7	0.665195624001021	1	FACETS	0.831	0.754	0.909	0.831	0.754	0.909	CLONAL	1	TRUE	0	0.665195624001021	1		247	227	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0061752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	118	809	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.764	0.689	0.842	1	0.985	1	SUBCLONAL	2	TRUE	1	0.20966631018474	2		809	737	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437274	220437274	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs980893896	NA	P-0061752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	38	649	0	ENST00000243786.2:c.178C>T	p.Arg60Ter	p.R60*	ENST00000243786	NM_002191.3	60	Cga/Tga	1/2	0.172265513848924	2	FACETS	0.538	0.443	0.644	0.269	0.221	0.322	SUBCLONAL	1	TRUE	0	0.20966631018474	2		649	674	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731659	47731659	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	40	616	0	ENST00000449228.1:c.133C>G	p.Pro45Ala	p.P45A	ENST00000449228	NM_001127240.2	45	Ccc/Gcc	2/4	0.20966631018474	3	FACETS	0.54	0.447	0.644	0.27	0.223	0.322	SUBCLONAL	1	TRUE	1	0.20966631018474	3		616	781	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0061782-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	52	612	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			1	2	FACETS	0.752	0.64	0.876	0.752	0.64	0.876	SUBCLONAL	1	TRUE	1	0.23	2		612	601	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2161878	2161878	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764576819	NA	P-0061782-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	14	0	0	ENST00000349721.2:c.4174G>A	p.Asp1392Asn	p.D1392N	ENST00000349721	NM_003070.3	1392	Gat/Aat	28/34	1	2	FACETS	0.238	0.171	0.32	0.238	0.171	0.32	SUBCLONAL	1	TRUE	1	0.23	2		0	511	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149290701	149290701	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061782-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	20	0	0	ENST00000360632.3:c.518G>T	p.Ser173Ile	p.S173I	ENST00000360632	NM_015472.4	173	aGt/aTt	3/7	1	2	FACETS	0.409	0.312	0.524	0.409	0.312	0.524	SUBCLONAL	1	TRUE	1	0.23	2		0	425	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038466	180038466	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061782-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	12	0	0	ENST00000261937.6:c.3551T>C	p.Val1184Ala	p.V1184A	ENST00000261937	NM_182925.4	1184	gTc/gCc	27/30	0.3	1	FACETS	0.188	0.131	0.259	0.188	0.131	0.259	SUBCLONAL	1	TRUE	0	0.23	1		0	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764146326	NA	P-0061817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	167	540	2	ENST00000269305.4:c.841G>T	p.Asp281Tyr	p.D281Y	ENST00000269305	NM_001126112.2	281	Gac/Tac	8/11	0.227619690765195	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.236084469053885	2		542	628	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242486	+	inframe_deletion	In_Frame_Del	DEL	TTAAGAGAAGCAACATCT	TTAAGAGAAGCAACATCT	-	rs121913440	NA	P-0061817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	236	415	0	ENST00000275493.2:c.2239_2256del	p.Leu747_Ser752del	p.L747_S752del	ENST00000275493	NM_005228.3	747	TTAAGAGAAGCAACATCT/-	19/28	0.236084469053885	8	FACETS	1	0.94	1	1	0.94	1	CLONAL	5	TRUE	3	0.236084469053885	8		415	682	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249007	55249007	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs147149347	NA	P-0061817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	307	589	0	ENST00000275493.2:c.2305G>C	p.Val769Leu	p.V769L	ENST00000275493	NM_005228.3	769	Gtg/Ctg	20/28	0.236084469053885	8	FACETS	0.916	0.865	0.968	0.916	0.865	0.968	CLONAL	5	TRUE	3	0.236084469053885	8		589	970	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664873	138664902	+	inframe_deletion	In_Frame_Del	DEL	GCCGCAGCTGCTGCAGCCGCTGCGGCTGCC	GCCGCAGCTGCTGCAGCCGCTGCGGCTGCC	-	rs764243782	NA	P-0061817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	25	403	0	ENST00000330315.3:c.663_692del	p.Ala225_Ala234del	p.A225_A234del	ENST00000330315	NM_023067.3	221	gcGGCAGCCGCAGCGGCTGCAGCAGCTGCGGCt/gct	1/1	0.236084469053885	3	FACETS	0.562	0.443	0.701	0.281	0.221	0.351	SUBCLONAL	1	TRUE	1	0.236084469053885	3		403	421	SUCCESS
AR	367	MSKCC	GRCh37	X	66764991	66764992	+	stop_gained,start_lost	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0061817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	168	525	0	ENST00000374690.3:c.3_4delinsTT	p.MetGlu1_?2	p.ME1_?2	ENST00000374690	NM_000044.3	1	atGGaa/atTTaa	1/8	0.236084469053885	5	FACETS	0.994	0.918	1	0.994	0.918	1	CLONAL	3	TRUE	2	0.236084469053885	5		525	646	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33689779	33689779	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	109	505	0	ENST00000308377.4:c.1048A>C	p.Met350Leu	p.M350L	ENST00000308377	NM_152270.3	350	Atg/Ctg	2/5	0.222023906685527	4	FACETS	0.852	0.766	0.943	0.852	0.766	0.943	CLONAL	2	TRUE	2	0.236084469053885	4		505	670	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061875-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	57	482	0	ENST00000425967.3:c.1731C>G	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaG	13/19	0.189139628649043	3	FACETS	0.909	0.783	1	0.606	0.522	0.696	CLONAL	2	TRUE	0	0.189139628649043	3		482	363	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41818303	41818303	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1328218770	NA	P-0061875-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	30	1115	0	ENST00000373198.4:c.71G>T	p.Arg24Leu	p.R24L	ENST00000373198	NM_133170.3	24	cGg/cTg	1/32	1	2	FACETS	0.64	0.514	0.782	0.64	0.514	0.782	SUBCLONAL	1	TRUE	1	0.189139628649043	2		1115	496	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0061952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	136	491	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	0.369648366261867	4	FACETS	0.901	0.823	0.983	0.901	0.823	0.983	CLONAL	2	TRUE	2	0.369648366261867	4		491	559	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510573	38510573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	69	461	0	ENST00000254066.5:c.827G>A	p.Arg276Gln	p.R276Q	ENST00000254066	NM_000964.3	276	cGg/cAg	7/9	0.369648366261867	16	FACETS	1	0.949	1			1	CLONAL	1	TRUE	NA	0.369648366261867	16		461	1120	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801726	3801726	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs587783483	NA	P-0061952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	73	440	0	ENST00000262367.5:c.3779+1G>A		p.X1260_splice	ENST00000262367	NM_004380.2	1260			0.310426090203613	5	FACETS	1	0.94	1	0.375	0.328	0.425	CLONAL	1	TRUE	2	0.369648366261867	5		440	546	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619279	23619279	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587776527	NA	P-0061952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	99	412	0	ENST00000261584.4:c.3256C>T	p.Arg1086Ter	p.R1086*	ENST00000261584	NM_024675.3	1086	Cga/Tga	12/13	0.310426090203613	5	FACETS	0.878	0.788	0.974	0.586	0.525	0.649	CLONAL	2	TRUE	2	0.369648366261867	5		412	474	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920347	50920347	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs201139477	NA	P-0061952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	148	520	0	ENST00000440232.2:c.3113A>G	p.Gln1038Arg	p.Q1038R	ENST00000440232	NM_002691.3	1038	cAg/cGg	25/27	0.369648366261867	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.369648366261867	3		520	445	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753387	57753387	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	155	447	0	ENST00000274289.3:c.737A>C	p.Tyr246Ser	p.Y246S	ENST00000274289	NM_006622.3	246	tAt/tCt	6/14	0.369648366261867	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	2	0.369648366261867	4		447	522	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048658	180048658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753863393	NA	P-0061952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	152	649	0	ENST00000261937.6:c.1904C>T	p.Thr635Met	p.T635M	ENST00000261937	NM_182925.4	635	aCg/aTg	13/30	0.352311529570192	4	FACETS	0.969	0.891	1	0.969	0.891	1	CLONAL	2	TRUE	2	0.369648366261867	4		649	581	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738165	133738165	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1174294624	NA	P-0061952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	65	416	0	ENST00000318560.5:c.565G>A	p.Glu189Lys	p.E189K	ENST00000318560	NM_005157.4	189	Gag/Aag	4/11	0.369648366261867	3	FACETS	1	0.952	1	0.4	0.349	0.455	CLONAL	1	TRUE	0	0.369648366261867	3		416	347	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061953-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	62	343	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.628	0.543	0.721	0.628	0.543	0.721	SUBCLONAL	1	TRUE	1	0.361393054177634	2		343	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0061953-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	190	622	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.228904753932108	2	FACETS	0.882	0.82	0.946	0.882	0.82	0.946	CLONAL	2	TRUE	0	0.361393054177634	2		622	596	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940780	71940780	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1415696831	NA	P-0062021-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	41	584	0	ENST00000298229.2:c.827C>G	p.Ser276Ter	p.S276*	ENST00000298229	NM_001567.3	276	tCa/tGa	7/28	1	2	FACETS	0.895	0.747	1	0.895	0.747	1	CLONAL	1	FALSE	1	0.244356546130516	2		584	375	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039501	49039501	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0062021-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	10	338	0	ENST00000267163.4:c.2486C>G	p.Ser829Ter	p.S829*	ENST00000267163	NM_000321.2	829	tCa/tGa	23/27	0.144486468381968	0	FACETS	0.476	0.324	0.665			1	INDETERMINATE	1	FALSE	0	0.244356546130516	0		338	130	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821842	72821842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062021-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	36	509	0	ENST00000268489.5:c.10333G>A	p.Glu3445Lys	p.E3445K	ENST00000268489	NM_006885.3	3445	Gaa/Aaa	10/10	0.244356546130516	1	FACETS	0.611	0.503	0.733	0.611	0.503	0.733	SUBCLONAL	1	FALSE	0	0.244356546130516	1		509	423	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0062117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	175	462	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.518945317046736	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.518945317046736	3		462	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0062117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	312	851	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.518945317046736	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.518945317046736	2		851	531	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602493	10602493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	252	792	1	ENST00000171111.5:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000171111	NM_203500.1	362	cGg/cAg	3/6	0.518945317046736	2	FACETS	0.989	0.937	1	0.989	0.937	1	CLONAL	2	TRUE	0	0.518945317046736	2		793	491	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911278	29911278	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199474570	NA	P-0062117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	130	684	0	ENST00000376809.5:c.577C>T	p.Arg193Cys	p.R193C	ENST00000376809	NM_002116.7	193	Cgc/Tgc	3/8	0.518945317046736	3	FACETS	1	0.979	1	0.624	0.569	0.681	CLONAL	1	TRUE	1	0.518945317046736	3		684	506	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209358	98209358	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1297685477	NA	P-0062117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	112	679	0	ENST00000331920.6:c.4180C>T	p.Arg1394Ter	p.R1394*	ENST00000331920	NM_000264.3	1394	Cga/Tga	23/24	0.518945317046736	3	FACETS	1	0.904	1	0.501	0.452	0.552	CLONAL	1	TRUE	1	0.518945317046736	3		679	543	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105721	27105721	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	199	675	0	ENST00000324856.7:c.5332G>T	p.Glu1778Ter	p.E1778*	ENST00000324856	NM_006015.4	1778	Gaa/Taa	20/20	0.331168109939024	3	FACETS	0.824	0.768	0.881	0.824	0.768	0.881	CLONAL	2	TRUE	1	0.518945317046736	3		675	586	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641046	117641046	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	124	555	0	ENST00000368508.3:c.5925C>G	p.Ile1975Met	p.I1975M	ENST00000368508	NM_002944.2	1975	atC/atG	36/43	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.518945317046736	2		555	416	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026281	48026281	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	217	628	0	ENST00000234420.5:c.1159G>T	p.Asp387Tyr	p.D387Y	ENST00000234420	NM_000179.2	387	Gat/Tat	4/10	0.518945317046736	3	FACETS	0.984	0.924	1	0.984	0.924	1	CLONAL	2	TRUE	1	0.518945317046736	3		628	535	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910680	32910680	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0062117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	233	548	0	ENST00000380152.3:c.2188A>T	p.Lys730Ter	p.K730*	ENST00000380152		730	Aaa/Taa	11/27	0.518945317046736	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.518945317046736	2		548	435	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589827	69589827	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	307	1204	0	ENST00000168712.1:c.26T>A	p.Val9Glu	p.V9E	ENST00000168712	NM_002007.2	9	gTa/gAa	1/3	0.152761780590641	6	FACETS	1	0.991	1	0.824	0.778	0.871	INDETERMINATE	2	TRUE	3	0.518945317046736	6		1204	975	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939784	71939784	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	131	758	1	ENST00000298229.2:c.411G>C	p.Glu137Asp	p.E137D	ENST00000298229	NM_001567.3	137	gaG/gaC	4/28	0.518945317046736	5	FACETS	0.991	0.899	1	0.33	0.299	0.363	CLONAL	1	TRUE	2	0.518945317046736	5		759	906	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877353	28877353	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	221	556	0	ENST00000282397.4:c.3968C>A	p.Pro1323Gln	p.P1323Q	ENST00000282397	NM_002019.4	1323	cCg/cAg	30/30	0.518945317046736	2	FACETS	0.934	0.88	0.988	0.934	0.88	0.988	CLONAL	2	TRUE	0	0.518945317046736	2		556	456	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610121	81610121	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	118	748	0	ENST00000298171.2:c.1719C>A	p.Asp573Glu	p.D573E	ENST00000298171	NM_000369.2	573	gaC/gaA	10/10	1	2	FACETS	0.883	0.8	0.969	0.883	0.8	0.969	CLONAL	1	TRUE	1	0.518945317046736	2		748	515	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054049	42054049	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0062117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	117	358	0	ENST00000219905.7:c.7510+1G>A		p.X2504_splice	ENST00000219905	NM_001164273.1	2504			0.518945317046736	2	FACETS	0.913	0.84	0.985	0.913	0.84	0.985	CLONAL	2	TRUE	0	0.518945317046736	2		358	247	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923360	9923360	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	200	626	0	ENST00000330684.3:c.1927G>T	p.Ala643Ser	p.A643S	ENST00000330684	NM_001134407.1	643	Gct/Tct	9/13	0.518945317046736	3	FACETS	0.965	0.903	1	0.965	0.903	1	CLONAL	2	TRUE	1	0.518945317046736	3		626	503	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39644771	39644771	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	133	390	0	ENST00000262039.4:c.2500G>C	p.Glu834Gln	p.E834Q	ENST00000262039	NM_002647.2	834	Gaa/Caa	23/25	0.518945317046736	2	FACETS	0.909	0.841	0.977	0.909	0.841	0.977	CLONAL	2	TRUE	0	0.518945317046736	2		390	282	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145406	61145406	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	76	370	0	ENST00000295025.8:c.616C>G	p.Leu206Val	p.L206V	ENST00000295025	NM_002908.2	206	Cta/Gta	6/11	0.518945317046736	3	FACETS	0.866	0.763	0.976	0.433	0.381	0.488	CLONAL	1	TRUE	1	0.518945317046736	3		370	426	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610559	215610559	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1357185397	NA	P-0062117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	215	463	0	ENST00000260947.4:c.1697G>A	p.Arg566Lys	p.R566K	ENST00000260947	NM_000465.2	566	aGg/aAg	8/11	0.0859136756735959	4	FACETS	1	0.982	1	1	0.982	1	INDETERMINATE	2	TRUE	2	0.518945317046736	4		463	560	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660940	227660940	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	180	729	0	ENST00000305123.5:c.2515C>A	p.Pro839Thr	p.P839T	ENST00000305123	NM_005544.2	839	Ccc/Acc	1/2	0.0859136756735959	4	FACETS	1	0.964	1	1	0.964	1	INDETERMINATE	2	TRUE	2	0.518945317046736	4		729	499	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125288	47125288	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	257	586	0	ENST00000409792.3:c.5982G>C	p.Arg1994Ser	p.R1994S	ENST00000409792	NM_014159.6	1994	agG/agC	12/21	0.518945317046736	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.518945317046736	2		586	459	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940798	49940798	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	290	754	0	ENST00000296474.3:c.245G>T	p.Gly82Val	p.G82V	ENST00000296474	NM_002447.2	82	gGg/gTg	1/20	0.518945317046736	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.518945317046736	2		754	524	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197450	26197450	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	150	866	0	ENST00000356476.2:c.29A>G	p.Lys10Arg	p.K10R	ENST00000356476		10	aAg/aGg	1/1	0.518945317046736	3	FACETS	1	0.959	1	0.539	0.493	0.586	CLONAL	1	TRUE	1	0.518945317046736	3		866	676	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910371	29910371	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	154	905	0	ENST00000376809.5:c.41C>G	p.Ser14Trp	p.S14W	ENST00000376809	NM_002116.7	14	tCg/tGg	1/8	0.518945317046736	3	FACETS	1	0.972	1	0.565	0.518	0.613	CLONAL	1	TRUE	1	0.518945317046736	3		905	662	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534575	140534575	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	232	570	0	ENST00000288602.6:c.338G>C	p.Ser113Thr	p.S113T	ENST00000288602	NM_004333.4	113	aGc/aCc	3/18	0.518945317046736	3	FACETS	0.798	0.747	0.849			1	SUBCLONAL	2	TRUE	NA	0.518945317046736	3		570	706	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421847	49421848	+	frameshift_variant	Frame_Shift_Ins	INS	TG	TG	ATA	novel	NA	P-0062117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	128	804	1	ENST00000301067.7:c.14459_14460delinsTAT	p.Pro4820LeufsTer2	p.P4820Lfs*2	ENST00000301067	NM_003482.3	4820	cCA/cTAT	46/54	0.518945317046736	2	FACETS	1	0.936	1	0.516	0.47	0.563	CLONAL	1	TRUE	0	0.518945317046736	2		805	478	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944206	206944258	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTATTTTGGGGGCAGCTGCAAGGGAAAAAACTGATCTGCTACTTACACAGCGC	GTATTTTGGGGGCAGCTGCAAGGGAAAAAACTGATCTGCTACTTACACAGCGC	CA	novel	NA	P-0062117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	93	496	0	ENST00000423557.1:c.372_378+46delinsTG		p.X124_splice	ENST00000423557	NM_000572.2	124		3/5	0.152761780590641	6	FACETS	1	0.979	1	0.477	0.426	0.532	INDETERMINATE	1	TRUE	3	0.518945317046736	6		496	510	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	22	606	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.350442036523917	2	FACETS	0.277	0.214	0.35	0.138	0.107	0.175	SUBCLONAL	1	TRUE	0	0.394220915577097	2		606	403	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546931	9546931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs562732119	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	51	603	0	ENST00000353224.5:c.1091C>T	p.Ser364Leu	p.S364L	ENST00000353224	NM_177990.2	364	tCg/tTg	5/10	1	2	FACETS	0.491	0.417	0.572	0.491	0.417	0.572	SUBCLONAL	1	TRUE	1	0.394220915577097	2		603	527	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524966	187524966	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	44	545	0	ENST00000441802.2:c.10714C>T	p.Gln3572Ter	p.Q3572*	ENST00000441802	NM_005245.3	3572	Cag/Tag	19/27	1	2	FACETS	0.603	0.507	0.709	0.603	0.507	0.709	SUBCLONAL	1	TRUE	1	0.394220915577097	2		545	370	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346252	89346252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs570265865	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	129	747	0	ENST00000301030.4:c.6698G>A	p.Gly2233Glu	p.G2233E	ENST00000301030	NM_001256183.1	2233	gGg/gAg	9/13	0.394220915577097	1	FACETS	0.966	0.88	1	0.966	0.88	1	CLONAL	1	TRUE	0	0.394220915577097	1		747	544	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169355	11169355	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	29	363	0	ENST00000361445.4:c.7520A>G	p.Lys2507Arg	p.K2507R	ENST00000361445	NM_004958.3	2507	aAg/aGg	56/58	1	2	FACETS	0.598	0.482	0.729	0.598	0.482	0.729	SUBCLONAL	1	TRUE	1	0.394220915577097	2		363	246	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641508	23641508	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370360082	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	39	506	0	ENST00000261584.4:c.1967C>T	p.Pro656Leu	p.P656L	ENST00000261584	NM_024675.3	656	cCa/cTa	5/13	1	2	FACETS	0.779	0.65	0.921	0.779	0.65	0.921	CLONAL	1	TRUE	1	0.394220915577097	2		506	254	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678977	117678977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1052987141	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	34	320	0	ENST00000368508.3:c.3844C>T	p.Pro1282Ser	p.P1282S	ENST00000368508	NM_002944.2	1282	Cct/Tct	24/43	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.394220915577097	2		320	123	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739024	145739024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371818842	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	128	796	0	ENST00000428558.2:c.2131G>A	p.Glu711Lys	p.E711K	ENST00000428558	NM_004260.3	711	Gag/Aag	13/22	1	2	FACETS	0.894	0.812	0.982	0.894	0.812	0.982	CLONAL	1	TRUE	1	0.394220915577097	2		796	726	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490458	20490458	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	60	495	0	ENST00000346618.3:c.1195C>T	p.Pro399Ser	p.P399S	ENST00000346618	NM_001949.4	399	Cct/Tct	7/7	1	2	FACETS	0.744	0.643	0.853	0.744	0.643	0.853	SUBCLONAL	1	TRUE	1	0.394220915577097	2		495	409	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542313	187542313	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	27	553	0	ENST00000441802.2:c.5427T>A	p.Tyr1809Ter	p.Y1809*	ENST00000441802	NM_005245.3	1809	taT/taA	10/27	1	2	FACETS	0.527	0.42	0.647	0.527	0.42	0.647	SUBCLONAL	1	TRUE	1	0.394220915577097	2		553	260	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557873	187557873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	41	678	0	ENST00000441802.2:c.3838G>A	p.Asp1280Asn	p.D1280N	ENST00000441802	NM_005245.3	1280	Gat/Aat	5/27	1	2	FACETS	0.363	0.302	0.431	0.363	0.302	0.431	SUBCLONAL	1	TRUE	1	0.394220915577097	2		678	573	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324513	31324513	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs41541213	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	109	910	0	ENST00000412585.2:c.295C>T	p.Arg99Ter	p.R99*	ENST00000412585	NM_005514.6	99	Cga/Tga	2/8	1	2	FACETS	0.755	0.679	0.837	0.755	0.679	0.837	SUBCLONAL	1	TRUE	1	0.394220915577097	2		910	732	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17949200	17949200	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	38	528	0	ENST00000458235.1:c.1442-1G>A		p.X481_splice	ENST00000458235	NM_000215.3	481			1	2	FACETS	0.387	0.32	0.463	0.387	0.32	0.463	SUBCLONAL	1	TRUE	1	0.394220915577097	2		528	498	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976771	2976771	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	107	578	0	ENST00000396946.4:c.1241A>G	p.Asn414Ser	p.N414S	ENST00000396946	NM_032415.4	414	aAc/aGc	9/25	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.394220915577097	2		578	533	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10796824	10796824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	52	490	0	ENST00000361367.2:c.2956C>T	p.Pro986Ser	p.P986S	ENST00000361367	NM_014633.3	986	Cca/Tca	23/25	1	2	FACETS	0.817	0.699	0.944	0.817	0.699	0.944	CLONAL	1	TRUE	1	0.394220915577097	2		490	323	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12043960	12043960	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	78	387	0	ENST00000396373.4:c.1339del	p.Tyr447ThrfsTer31	p.Y447Tfs*31	ENST00000396373	NM_001987.4	447	Tac/ac	8/8	1	2	FACETS	0.847	0.747	0.954	0.847	0.747	0.954	CLONAL	1	TRUE	1	0.394220915577097	2		387	467	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864658	57864659	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	93	739	0	ENST00000228682.2:c.2135_2136delinsTT	p.Ser712Phe	p.S712F	ENST00000228682	NM_005269.2	712	tCC/tTT	12/12	1	2	FACETS	0.821	0.731	0.915	0.821	0.731	0.915	CLONAL	1	TRUE	1	0.394220915577097	2		739	575	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562052	21562053	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	24	517	1	ENST00000382592.4:c.1866_1867delinsTT	p.Arg623Trp	p.R623W	ENST00000382592	NM_014572.2	622	aaCCgg/aaTTgg	4/8	1	2	FACETS	0.256	0.2	0.321	0.256	0.2	0.321	SUBCLONAL	1	TRUE	1	0.394220915577097	2		518	475	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726667	88726667	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs761119703	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	35	412	0	ENST00000360948.2:c.377A>G	p.Asn126Ser	p.N126S	ENST00000360948	NM_001012338.2	126	aAc/aGc	4/19	1	2	FACETS	0.393	0.322	0.473	0.393	0.322	0.473	SUBCLONAL	1	TRUE	1	0.394220915577097	2		412	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579314	7579315	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	TG	TG	GC	novel	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	147	538	1	ENST00000269305.4:c.372_373delinsGC	p.Cys124_Thr125delinsTrpPro	p.C124_T125delinsWP	ENST00000269305	NM_001126112.2	124	tgCAcg/tgGCcg	4/11	0.350442036523917	2	FACETS	0.829	0.763	0.896	0.829	0.763	0.896	CLONAL	2	TRUE	0	0.394220915577097	2		539	450	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223033	1223033	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs549474196	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	29	654	0	ENST00000326873.7:c.970C>T	p.Pro324Ser	p.P324S	ENST00000326873	NM_000455.4	324	Ccg/Tcg	8/10	1	2	FACETS	0.259	0.207	0.318	0.259	0.207	0.318	SUBCLONAL	1	TRUE	1	0.394220915577097	2		654	569	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212092	5212092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	31	700	0	ENST00000357368.4:c.4939G>A	p.Glu1647Lys	p.E1647K	ENST00000357368	NM_002850.3	1647	Gag/Aag	32/38	1	2	FACETS	0.26	0.209	0.317	0.26	0.209	0.317	SUBCLONAL	1	TRUE	1	0.394220915577097	2		700	605	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470515	25470515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	135	566	0	ENST00000264709.3:c.959G>A	p.Arg320Gln	p.R320Q	ENST00000264709	NM_175629.2	320	cGa/cAa	8/23	1	2	FACETS	0.985	0.897	1	0.985	0.897	1	CLONAL	1	TRUE	1	0.394220915577097	2		566	695	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159016	24159017	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	75	534	0	ENST00000263121.7:c.688_689delinsTT	p.Pro230Leu	p.P230L	ENST00000263121	NM_003073.3	230	CCg/TTg	6/9	1	2	FACETS	0.691	0.606	0.781	0.691	0.606	0.781	SUBCLONAL	1	TRUE	1	0.394220915577097	2		534	551	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185195145	185195145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	95	354	0	ENST00000265026.3:c.2462G>A	p.Gly821Glu	p.G821E	ENST00000265026	NM_004721.4	821	gGg/gAg	12/14	0.394220915577097	3	FACETS	0.91	0.819	1	0.91	0.819	1	CLONAL	2	TRUE	1	0.394220915577097	3		354	317	SUCCESS
REST	5978	MSKCC	GRCh37	4	57777022	57777022	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	99	549	1	ENST00000309042.7:c.218T>C	p.Met73Thr	p.M73T	ENST00000309042	NM_005612.4	73	aTg/aCg	2/4	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.394220915577097	2		550	463	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627761	187627761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	34	529	0	ENST00000441802.2:c.3221G>A	p.Arg1074Lys	p.R1074K	ENST00000441802	NM_005245.3	1074	aGa/aAa	2/27	1	2	FACETS	0.486	0.397	0.585	0.486	0.397	0.585	SUBCLONAL	1	TRUE	1	0.394220915577097	2		529	355	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288879	33288879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	108	578	0	ENST00000374542.5:c.673G>A	p.Glu225Lys	p.E225K	ENST00000374542	NM_001141970.1	225	Gag/Aag	3/8	1	2	FACETS	0.994	0.896	1	0.994	0.896	1	CLONAL	1	TRUE	1	0.394220915577097	2		578	551	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662471	117662471	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370393953	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	26	499	0	ENST00000368508.3:c.4906C>T	p.Leu1636Phe	p.L1636F	ENST00000368508	NM_002944.2	1636	Ctt/Ttt	30/43	1	2	FACETS	0.498	0.395	0.614	0.498	0.395	0.614	SUBCLONAL	1	TRUE	1	0.394220915577097	2		499	265	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200060	138200060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	154	715	1	ENST00000237289.4:c.1478G>A	p.Gly493Glu	p.G493E	ENST00000237289	NM_001270507.1	493	gGa/gAa	7/9	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.394220915577097	2		716	765	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287353	38287353	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1309311395	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	90	701	0	ENST00000425967.3:c.304G>A	p.Asp102Asn	p.D102N	ENST00000425967	NM_001174067.1	102	Gac/Aac	4/19	1	2	FACETS	0.783	0.696	0.876	0.783	0.696	0.876	SUBCLONAL	1	TRUE	1	0.394220915577097	2		701	583	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069584	69069584	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	20	317	0	ENST00000288368.4:c.4259A>G	p.Tyr1420Cys	p.Y1420C	ENST00000288368	NM_024870.2	1420	tAc/tGc	35/40	1	2	FACETS	0.583	0.449	0.738	0.583	0.449	0.738	SUBCLONAL	1	TRUE	1	0.394220915577097	2		317	174	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141570513	141570514	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	52	586	0	ENST00000220592.5:c.614_615delinsTT	p.Ser205Phe	p.S205F	ENST00000220592	NM_012154.3	205	tCC/tTT	5/19	1	2	FACETS	0.45	0.383	0.524	0.45	0.383	0.524	SUBCLONAL	1	TRUE	1	0.394220915577097	2		586	586	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413994	139413994	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	34	573	0	ENST00000277541.6:c.766del	p.Glu256LysfsTer21	p.E256Kfs*21	ENST00000277541	NM_017617.3	256	Gaa/aa	5/34	0.158599104225873	2	FACETS	0.318	0.259	0.385	0.159	0.129	0.193	INDETERMINATE	1	TRUE	0	0.394220915577097	2		573	542	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615560	100615560	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	103	515	0	ENST00000308731.7:c.772A>T	p.Asn258Tyr	p.N258Y	ENST00000308731	NM_000061.2	258	Aat/Tat	8/19	1	2	FACETS	0.901	0.808	0.999	0.901	0.808	0.999	CLONAL	1	TRUE	1	0.394220915577097	2		515	580	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412665	139412667	+	missense_variant	Missense_Mutation	TNP	ATT	ATT	TTC	novel	NA	P-0062117-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	37	684	0	ENST00000277541.6:c.1177_1179delinsGAA	p.Asn393Glu	p.N393E	ENST00000277541	NM_017617.3	393	AAT/GAA	7/34	0.158599104225873	2	FACETS	0.303	0.249	0.364	0.152	0.124	0.182	INDETERMINATE	1	TRUE	0	0.394220915577097	2		684	619	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	140	519	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.973	0.891	1	0.973	0.891	1	CLONAL	1	TRUE	1	0.545269519507064	2		520	528	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	72	759	0	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.557	0.488	0.631	0.557	0.488	0.631	SUBCLONAL	1	TRUE	1	0.545269519507064	2		759	474	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	60	497	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.379	0.326	0.436	0.379	0.326	0.436	SUBCLONAL	1	TRUE	1	0.545269519507064	2		499	581	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	58	302	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.498	0.429	0.573	0.498	0.429	0.573	SUBCLONAL	1	TRUE	1	0.545269519507064	2		306	427	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	58	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.498	0.429	0.573	0.498	0.429	0.573	SUBCLONAL	1	TRUE	1	0.545269519507064	2		434	427	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	91	816	2	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.596	0.53	0.666	0.596	0.53	0.666	SUBCLONAL	1	TRUE	1	0.545269519507064	2		818	560	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	68	560	7	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.613	0.535	0.696	0.613	0.535	0.696	SUBCLONAL	1	TRUE	1	0.545269519507064	2		567	407	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	109	555	2	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.795	0.717	0.877	0.795	0.717	0.877	SUBCLONAL	1	TRUE	1	0.545269519507064	2		557	503	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954198	48954198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123331	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	15	113	0	ENST00000267163.4:c.1399C>T	p.Arg467Ter	p.R467*	ENST00000267163	NM_000321.2	467	Cga/Tga	15/27	1	2	FACETS	0.408	0.3	0.534	0.408	0.3	0.534	SUBCLONAL	1	TRUE	1	0.545269519507064	2		113	135	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	70	615	0	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	1	2	FACETS	0.613	0.536	0.695	0.613	0.536	0.695	SUBCLONAL	1	TRUE	1	0.545269519507064	2		615	419	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1268741	1268741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060503009	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	40	452	0	ENST00000310581.5:c.2476G>A	p.Val826Ile	p.V826I	ENST00000310581	NM_198253.2	826	Gtc/Atc	9/16	1	2	FACETS	0.406	0.338	0.482	0.406	0.338	0.482	SUBCLONAL	1	TRUE	1	0.545269519507064	2		452	361	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	50	599	2	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	1	2	FACETS	0.476	0.405	0.554	0.476	0.405	0.554	SUBCLONAL	1	TRUE	1	0.545269519507064	2		601	385	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	42	383	3	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	1	2	FACETS	0.494	0.414	0.582	0.494	0.414	0.582	SUBCLONAL	1	TRUE	1	0.545269519507064	2		386	312	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	52	469	2	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.49	0.419	0.568	0.49	0.419	0.568	SUBCLONAL	1	TRUE	1	0.545269519507064	2		471	389	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796882	42796883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761345552	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	95	756	0	ENST00000575354.2:c.3347dup	p.Ser1117LysfsTer34	p.S1117Kfs*34	ENST00000575354	NM_015125.3	1114	gcc/gCcc	14/20	1	2	FACETS	0.679	0.607	0.756	0.679	0.607	0.756	SUBCLONAL	1	TRUE	1	0.545269519507064	2		756	513	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	99	659	0	ENST00000269571.5:c.829G>T	p.Asp277Tyr	p.D277Y	ENST00000269571		277	Gac/Tac	7/27	1	2	FACETS	0.635	0.568	0.706	0.635	0.568	0.706	SUBCLONAL	1	TRUE	1	0.545269519507064	2		659	572	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434413	140434413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775889922	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	90	385	0	ENST00000288602.6:c.2285C>T	p.Ala762Val	p.A762V	ENST00000288602	NM_004333.4	762	gCg/gTg	18/18	0.239563907430401	3	FACETS	0.721	0.64	0.806	0.36	0.32	0.403	INDETERMINATE	1	TRUE	1	0.545269519507064	3		385	583	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	34	553	2	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	0.507	0.416	0.607	0.507	0.416	0.607	SUBCLONAL	1	TRUE	1	0.545269519507064	2		555	246	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781375	3781375	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	70	547	0	ENST00000262367.5:c.4990C>T	p.Arg1664Cys	p.R1664C	ENST00000262367	NM_004380.2	1664	Cgc/Tgc	30/31	1	2	FACETS	0.55	0.481	0.624	0.55	0.481	0.624	SUBCLONAL	1	TRUE	1	0.545269519507064	2		547	467	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217557	142217557	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1268253442	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	24	304	1	ENST00000350721.4:c.5440del	p.Arg1814GlufsTer10	p.R1814Efs*10	ENST00000350721	NM_001184.3	1814	Aga/ga	32/47	1	2	FACETS	0.246	0.192	0.308	0.246	0.192	0.308	SUBCLONAL	1	TRUE	1	0.545269519507064	2		305	358	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099468	157099470	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	rs1429292576	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	55	711	0	ENST00000346085.5:c.413_415del	p.Asn138del	p.N138del	ENST00000346085	NM_020732.3	135	tcCAAc/tcc	1/20	1	2	FACETS	0.469	0.402	0.542	0.469	0.402	0.542	SUBCLONAL	1	TRUE	1	0.545269519507064	2		711	430	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041037	112041037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761032788	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	79	547	1	ENST00000368678.4:c.218C>T	p.Thr73Met	p.T73M	ENST00000368678		73	aCg/aTg	3/13	1	2	FACETS	0.554	0.488	0.624	0.554	0.488	0.624	SUBCLONAL	1	TRUE	1	0.545269519507064	2		548	523	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	68	620	3	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	1	2	FACETS	0.345	0.299	0.394	0.345	0.299	0.394	SUBCLONAL	1	TRUE	1	0.545269519507064	2		623	724	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	51	612	1	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	1	2	FACETS	0.358	0.304	0.417	0.358	0.304	0.417	SUBCLONAL	1	TRUE	1	0.545269519507064	2		613	523	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443512	49443512	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	69	597	0	ENST00000301067.7:c.3859del	p.Glu1287ArgfsTer43	p.E1287Rfs*43	ENST00000301067	NM_003482.3	1287	Gag/ag	11/54	1	2	FACETS	0.507	0.442	0.577	0.507	0.442	0.577	SUBCLONAL	1	TRUE	1	0.545269519507064	2		597	499	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125473	7125473	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913144	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	73	647	0	ENST00000302850.5:c.3079C>T	p.Arg1027Ter	p.R1027*	ENST00000302850	NM_000208.2	1027	Cga/Tga	17/22	1	2	FACETS	0.475	0.415	0.538	0.475	0.415	0.538	SUBCLONAL	1	TRUE	1	0.545269519507064	2		647	564	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131436	17131436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	68	606	0	ENST00000285071.4:c.16G>A	p.Ala6Thr	p.A6T	ENST00000285071	NM_144997.5	6	Gct/Act	4/14	1	2	FACETS	0.557	0.486	0.633	0.557	0.486	0.633	SUBCLONAL	1	TRUE	1	0.545269519507064	2		606	448	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800903	120800903	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748469666	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	81	535	0	ENST00000257552.2:c.345del	p.Leu116CysfsTer3	p.L116Cfs*3	ENST00000257552	NM_002442.3	115	ggG/gg	6/15	1	2	FACETS	0.521	0.46	0.587	0.521	0.46	0.587	SUBCLONAL	1	TRUE	1	0.545269519507064	2		535	570	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190811	106190811	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	95	357	0	ENST00000380013.4:c.4089G>T	p.Lys1363Asn	p.K1363N	ENST00000380013	NM_001127208.2	1363	aaG/aaT	9/11	1	2	FACETS	0.697	0.623	0.775	0.697	0.623	0.775	SUBCLONAL	1	TRUE	1	0.545269519507064	2		357	500	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743754	46743754	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs368105178	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	67	705	0	ENST00000371975.4:c.2044C>T	p.Arg682Ter	p.R682*	ENST00000371975	NM_003579.3	682	Cga/Tga	18/18	1	2	FACETS	0.466	0.406	0.532	0.466	0.406	0.532	SUBCLONAL	1	TRUE	1	0.545269519507064	2		705	527	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134638	2134638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	92	753	0	ENST00000219476.3:c.4415G>A	p.Gly1472Asp	p.G1472D	ENST00000219476	NM_000548.3	1472	gGc/gAc	34/42	1	2	FACETS	0.674	0.601	0.751	0.674	0.601	0.751	SUBCLONAL	1	TRUE	1	0.545269519507064	2		753	501	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44520604	44520604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	71	468	0	ENST00000291552.4:c.158G>A	p.Arg53His	p.R53H	ENST00000291552	NM_006758.2	53	cGt/cAt	3/8	1	2	FACETS	0.49	0.429	0.557	0.49	0.429	0.557	SUBCLONAL	1	TRUE	1	0.545269519507064	2		468	531	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981832	63981832	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	59	569	1	ENST00000398590.3:c.2340del	p.Thr781ProfsTer11	p.T781Pfs*11	ENST00000398590	NM_001177387.1	778	ggC/gg	12/14	1	2	FACETS	0.422	0.363	0.486	0.422	0.363	0.486	SUBCLONAL	1	TRUE	1	0.545269519507064	2		570	513	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1687734	1687734	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	72	529	2	ENST00000378625.1:c.983del	p.Gly328GlufsTer30	p.G328Efs*30	ENST00000378625	NM_001198994.1	328	gGa/ga	8/14	1	2	FACETS	0.522	0.457	0.592	0.522	0.457	0.592	SUBCLONAL	1	TRUE	1	0.545269519507064	2		531	506	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22412931	22412931	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	46	288	0	ENST00000344548.3:c.179-1G>A		p.X60_splice	ENST00000344548	NM_001039802.1	60			1	2	FACETS	0.548	0.464	0.64	0.548	0.464	0.64	SUBCLONAL	1	TRUE	1	0.545269519507064	2		288	308	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748122	72748122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	75	479	2	ENST00000357731.5:c.56C>T	p.Ala19Val	p.A19V	ENST00000357731	NM_173808.2	19	gCg/gTg	1/7	1	2	FACETS	0.601	0.528	0.678	0.601	0.528	0.678	SUBCLONAL	1	TRUE	1	0.545269519507064	2		481	458	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480012	120480012	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	89	528	1	ENST00000256646.2:c.3415del	p.Leu1139TrpfsTer68	p.L1139Wfs*68	ENST00000256646	NM_024408.3	1139	Ctg/tg	21/34	1	2	FACETS	0.606	0.538	0.677	0.606	0.538	0.677	SUBCLONAL	1	TRUE	1	0.545269519507064	2		529	539	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392633	118392633	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	60	491	0	ENST00000534358.1:c.11665C>T	p.Arg3889Ter	p.R3889*	ENST00000534358	NM_005933.3	3889	Cga/Tga	36/36	1	2	FACETS	0.523	0.452	0.6	0.523	0.452	0.6	SUBCLONAL	1	TRUE	1	0.545269519507064	2		491	421	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873677	35873677	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	47	441	0	ENST00000216797.5:c.174G>T	p.Glu58Asp	p.E58D	ENST00000216797	NM_020529.2	58	gaG/gaT	1/6	1	2	FACETS	0.567	0.481	0.661	0.567	0.481	0.661	SUBCLONAL	1	TRUE	1	0.545269519507064	2		441	304	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781422	3781422	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	63	562	0	ENST00000262367.5:c.4943C>A	p.Pro1648His	p.P1648H	ENST00000262367	NM_004380.2	1648	cCc/cAc	30/31	1	2	FACETS	0.489	0.423	0.559	0.489	0.423	0.559	SUBCLONAL	1	TRUE	1	0.545269519507064	2		562	473	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17117131	17117131	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	79	568	0	ENST00000285071.4:c.1578T>A	p.Ser526Arg	p.S526R	ENST00000285071	NM_144997.5	526	agT/agA	14/14	1	2	FACETS	0.653	0.576	0.734	0.653	0.576	0.734	SUBCLONAL	1	TRUE	1	0.545269519507064	2		568	444	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821856	59821856	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	59	346	0	ENST00000259008.2:c.2194A>G	p.Lys732Glu	p.K732E	ENST00000259008	NM_032043.2	732	Aaa/Gaa	15/20	1	2	FACETS	0.598	0.517	0.685	0.598	0.517	0.685	SUBCLONAL	1	TRUE	1	0.545269519507064	2		346	362	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226257	2226257	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	58	693	0	ENST00000398665.3:c.3737del	p.Ser1246CysfsTer81	p.S1246Cfs*81	ENST00000398665	NM_032482.2	1246	tCg/tg	27/28	1	2	FACETS	0.523	0.45	0.601	0.523	0.45	0.601	SUBCLONAL	1	TRUE	1	0.545269519507064	2		693	407	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753265	42753265	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	72	741	0	ENST00000222329.4:c.999C>A	p.His333Gln	p.H333Q	ENST00000222329	NM_006494.2	333	caC/caA	4/4	1	2	FACETS	0.513	0.449	0.582	0.513	0.449	0.582	SUBCLONAL	1	TRUE	1	0.545269519507064	2		741	515	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163265	47163265	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	66	480	0	ENST00000409792.3:c.2861T>C	p.Leu954Ser	p.L954S	ENST00000409792	NM_014159.6	954	tTa/tCa	3/21	1	2	FACETS	0.515	0.448	0.587	0.515	0.448	0.587	SUBCLONAL	1	TRUE	1	0.545269519507064	2		480	470	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430308	181430308	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	47	383	0	ENST00000325404.1:c.160G>A	p.Gly54Arg	p.G54R	ENST00000325404	NM_003106.3	54	Ggg/Agg	1/1	1	2	FACETS	0.813	0.694	0.941	0.813	0.694	0.941	CLONAL	1	TRUE	1	0.545269519507064	2		383	212	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781128	135781128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	78	594	0	ENST00000298552.3:c.1837C>T	p.Pro613Ser	p.P613S	ENST00000298552	NM_001162426.1	613	Cca/Tca	15/23	1	2	FACETS	0.583	0.513	0.657	0.583	0.513	0.657	SUBCLONAL	1	TRUE	1	0.545269519507064	2		594	491	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224142	53224142	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062121-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	50	282	0	ENST00000375401.3:c.3409G>A	p.Ala1137Thr	p.A1137T	ENST00000375401	NM_004187.3	1137	Gcg/Acg	22/26	1	1	FACETS	0.626	0.538	0.721	0.626	0.538	0.721	SUBCLONAL	1	TRUE	0	0.545269519507064	1		282	213	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0062147-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	156	629	0	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	0.289970747360918	3	FACETS	0.995	0.915	1	0.995	0.915	1	CLONAL	2	TRUE	1	0.289970747360918	3		629	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934571	NA	P-0062147-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	219	360	0	ENST00000269305.4:c.747G>C	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agC	7/11	0.289970747360918	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	1	0.289970747360918	4		360	588	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406124	70406124	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062147-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	79	401	0	ENST00000373644.4:c.3640del	p.Ser1214LeufsTer29	p.S1214Lfs*29	ENST00000373644	NM_030625.2	1213	aTt/at	4/12	0.204597102204235	4	FACETS	0.754	0.666	0.849			1	SUBCLONAL	2	TRUE	NA	0.289970747360918	4		401	466	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426566	49426577	+	inframe_deletion	In_Frame_Del	DEL	CTGCTGCTGTTG	CTGCTGCTGTTG	-	rs1390609183	NA	P-0062147-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	158	716	0	ENST00000301067.7:c.11911_11922del	p.Gln3971_Gln3974del	p.Q3971_Q3974del	ENST00000301067	NM_003482.3	3971	CAACAGCAGCAG/-	39/54	0.289970747360918	3	FACETS	1	0.988	1	0.743	0.681	0.807	CLONAL	1	TRUE	1	0.289970747360918	3		716	840	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646875	23646875	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062147-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	117	405	4	ENST00000261584.4:c.992A>G	p.Glu331Gly	p.E331G	ENST00000261584	NM_024675.3	331	gAa/gGa	4/13	0.27061864259949	3	FACETS	0.856	0.775	0.94	0.856	0.775	0.94	CLONAL	2	TRUE	1	0.289970747360918	3		409	540	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61325866	61325866	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0062147-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	44	254	0	ENST00000283752.5:c.352-2A>T		p.X118_splice	ENST00000283752	NM_006919.2	118			1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.289970747360918	2		254	267	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641460	47641460	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062147-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	117	331	0	ENST00000233146.2:c.845A>T	p.Asp282Val	p.D282V	ENST00000233146	NM_000251.2	282	gAt/gTt	5/16	0.211265687746822	5	FACETS	1	0.96	1	0.739	0.67	0.812	CLONAL	2	TRUE	2	0.289970747360918	5		331	522	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878394	151878394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062147-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	96	481	0	ENST00000262189.6:c.6551C>T	p.Ser2184Phe	p.S2184F	ENST00000262189	NM_170606.2	2184	tCt/tTt	36/59	0.289970747360918	5	FACETS	1	0.953	1	0.282	0.251	0.316	CLONAL	1	TRUE	1	0.289970747360918	5		481	841	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17349159	17349159	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs186768244	NA	P-0062195-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	114	437	0	ENST00000375499.3:c.709C>G	p.Pro237Ala	p.P237A	ENST00000375499	NM_003000.2	237	Cca/Gca	7/8	1	2	FACETS	0.987	0.887	1	0.987	0.887	1	CLONAL	1	TRUE	1	0.24	2		437	963	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000090	30000091	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACTC	novel	NA	P-0062195-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	115	395	1	ENST00000338641.4:c.103_104insACTC	p.Phe35TyrfsTer15	p.F35Yfs*15	ENST00000338641	NM_000268.3	35	ttc/tACTCtc	1/16	0.3	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.24	1		396	826	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163715	47163715	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062195-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	113	462	0	ENST00000409792.3:c.2411del	p.Leu804CysfsTer14	p.L804Cfs*14	ENST00000409792	NM_014159.6	804	tTg/tg	3/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.24	2		462	746	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150900410	150900411	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGGTGGCTCACGTTGACCAACTCTTTGATGATGCATCC	novel	NA	P-0062195-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	73	521	0	ENST00000271640.5:c.226_260+3dup		p.E74fs	ENST00000271640	NM_001145415.1	74	gag/gAGGTGGCTCACGTTGACCAACTCTTTGATGATGCATCCag	2/22	1	2	FACETS	0.517	0.45	0.589	0.517	0.45	0.589	SUBCLONAL	1	TRUE	1	0.24	2		521	1177	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0062211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	413	387	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.822099585866765	7	FACETS	1	0.973	1			1	CLONAL	4	TRUE	NA	0.822099585866765	7		387	755	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974765	21974765	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1329324238	NA	P-0062211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	388	0	0	ENST00000304494.5:c.62C>A	p.Ala21Asp	p.A21D	ENST00000304494	NM_000077.4	21	gCc/gAc	1/3	0.8121240197642	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.822099585866765	2		0	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0062211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	565	506	0	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.822366734793411	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	4	TRUE	0	0.822099585866765	4		506	624	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946782	17946782	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	342	0	0	ENST00000458235.1:c.1865G>T	p.Ser622Ile	p.S622I	ENST00000458235	NM_000215.3	622	aGc/aTc	14/24	0.818426122917589	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.822099585866765	2		0	391	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0062211-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	19	387	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.122	0.092	0.158	0.122	0.092	0.158	SUBCLONAL	1	TRUE	1	0.700143719396955	2		387	444	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974765	21974765	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1329324238	NA	P-0062211-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	35	0	0	ENST00000304494.5:c.62C>A	p.Ala21Asp	p.A21D	ENST00000304494	NM_000077.4	21	gCc/gAc	1/3	0.214728445822862	1	FACETS	0.061	0.049	0.074	0.061	0.049	0.074	INDETERMINATE	1	TRUE	0	0.700143719396955	1		0	1062	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0062211-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	34	506	0	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	0.097	0.078	0.118	0.097	0.078	0.118	SUBCLONAL	1	TRUE	1	0.700143719396955	2		506	1002	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946782	17946782	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062211-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	32	0	0	ENST00000458235.1:c.1865G>T	p.Ser622Ile	p.S622I	ENST00000458235	NM_000215.3	622	aGc/aTc	14/24	1	2	FACETS	0.085	0.068	0.104	0.085	0.068	0.104	SUBCLONAL	1	TRUE	1	0.700143719396955	2		0	1079	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577466	64577466	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062211-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	396	549	0	ENST00000312049.6:c.116T>G	p.Leu39Trp	p.L39W	ENST00000312049	NM_130799.2	39	tTg/tGg	2/10	0.700143719396955	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.700143719396955	1		549	720	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939651	76939651	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062211-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	201	180	0	ENST00000373344.5:c.1097T>G	p.Met366Arg	p.M366R	ENST00000373344	NM_000489.3	366	aTg/aGg	9/35	0.700143719396955	1	FACETS	0.866	0.813	0.919	0.866	0.813	0.919	CLONAL	1	TRUE	0	0.700143719396955	1		180	431	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221236	1221236	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062271-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	133	633	0	ENST00000326873.7:c.762del	p.Phe255SerfsTer32	p.F255Sfs*32	ENST00000326873	NM_000455.4	253	taC/ta	6/10	0.194904010720988	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	0	0.194904010720988	1		633	1056	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0062288-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	129	462	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.208119486254995	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	FALSE	0	0.233087903810431	2		462	501	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51514666	51514666	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062288-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	69	556	0	ENST00000260433.2:c.508A>G	p.Thr170Ala	p.T170A	ENST00000260433		170	Aca/Gca	5/10	1	2	FACETS	0.872	0.759	0.994	0.872	0.759	0.994	CLONAL	1	FALSE	1	0.233087903810431	2		556	679	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579374	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1060501195	NA	P-0062288-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	148	566	0	ENST00000269305.4:c.313G>C	p.Gly105Arg	p.G105R	ENST00000269305	NM_001126112.2	105	Ggc/Cgc	4/11	0.233087903810431	1	FACETS	0.962	0.883	1	1	0.991	1	CLONAL	2	FALSE	0	0.233087903810431	1		566	583	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22142619	22142619	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062288-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	41	361	0	ENST00000215832.6:c.783G>T	p.Arg261Ser	p.R261S	ENST00000215832	NM_002745.4	261	agG/agT	6/9	0.233087903810431	3	FACETS	0.769	0.64	0.912	0.384	0.32	0.456	CLONAL	1	FALSE	1	0.233087903810431	3		361	511	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564807	41564807	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062288-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	78	545	0	ENST00000263253.7:c.4108G>C	p.Asp1370His	p.D1370H	ENST00000263253	NM_001429.3	1370	Gac/Cac	25/31	0.233087903810431	3	FACETS	1	0.91	1	0.522	0.458	0.59	CLONAL	1	FALSE	1	0.233087903810431	3		545	716	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125356	47125356	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062288-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	146	587	0	ENST00000409792.3:c.5914G>T	p.Glu1972Ter	p.E1972*	ENST00000409792	NM_014159.6	1972	Gaa/Taa	12/21	0.198879725560596	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	FALSE	2	0.233087903810431	4		587	720	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665213	138665213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062288-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	58	515	0	ENST00000330315.3:c.352G>A	p.Glu118Lys	p.E118K	ENST00000330315	NM_023067.3	118	Gag/Aag	1/1	0.221816012868562	3	FACETS	1	0.94	1	0.589	0.506	0.678	CLONAL	1	FALSE	1	0.233087903810431	3		515	472	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749470	41749470	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062288-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	45	328	0	ENST00000226382.2:c.325C>A	p.Gln109Lys	p.Q109K	ENST00000226382	NM_003924.3	109	Cag/Aag	2/3	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	FALSE	1	0.233087903810431	2		328	316	SUCCESS
APC	324	MSKCC	GRCh37	5	112176624	112176624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs952662066	NA	P-0062288-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	150	501	0	ENST00000257430.4:c.5333C>T	p.Pro1778Leu	p.P1778L	ENST00000257430	NM_000038.5	1778	cCt/cTt	16/16	0.206943996195215	5	FACETS	1	0.975	1	0.78	0.714	0.849	CLONAL	2	FALSE	2	0.233087903810431	5		501	742	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662440	117662440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1046359018	NA	P-0062288-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	73	459	0	ENST00000368508.3:c.4937C>T	p.Thr1646Ile	p.T1646I	ENST00000368508	NM_002944.2	1646	aCa/aTa	30/43	0.221261664566995	3	FACETS	0.935	0.817	1	0.467	0.408	0.532	CLONAL	1	FALSE	1	0.233087903810431	3		459	748	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507420	8507420	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062288-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	70	461	0	ENST00000356435.5:c.1558C>G	p.Leu520Val	p.L520V	ENST00000356435		520	Cta/Gta	11/35	0.149806005112945	4	FACETS	0.928	0.808	1	0.464	0.404	0.529	CLONAL	1	FALSE	2	0.233087903810431	4		461	798	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974732	21974732	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs878853650	NA	P-0062288-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	200	612	0	ENST00000304494.5:c.95T>C	p.Leu32Pro	p.L32P	ENST00000304494	NM_000077.4	32	cTg/cCg	1/3	0.149806005112945	4	FACETS	0.97	0.902	1	1	0.991	1	CLONAL	3	FALSE	2	0.233087903810431	4		612	727	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932729	39932729	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062288-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	110	654	1	ENST00000378444.4:c.1870C>A	p.Pro624Thr	p.P624T	ENST00000378444	NM_001123385.1	624	Ccg/Acg	4/15	1	2	FACETS	0.779	0.701	0.86	1	0.984	1	SUBCLONAL	2	FALSE	1	0.233087903810431	2		655	606	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041242	47041242	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062288-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	145	626	0	ENST00000377604.3:c.1672del	p.Gln558ArgfsTer146	p.Q558Rfs*146	ENST00000377604	NM_001204468.1	557	gCc/gc	15/24	1	2	FACETS	0.898	0.821	0.978	1	0.99	1	CLONAL	2	FALSE	1	0.233087903810431	2		626	693	SUCCESS
AR	367	MSKCC	GRCh37	X	66765957	66765957	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062288-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	39	573	0	ENST00000374690.3:c.969G>C	p.Glu323Asp	p.E323D	ENST00000374690	NM_000044.3	323	gaG/gaC	1/8	1	2	FACETS	0.588	0.487	0.702	0.588	0.487	0.702	SUBCLONAL	1	FALSE	1	0.233087903810431	2		573	569	SUCCESS
AR	367	MSKCC	GRCh37	X	66931304	66931304	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062288-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	75	574	0	ENST00000374690.3:c.1946C>G	p.Thr649Ser	p.T649S	ENST00000374690	NM_000044.3	649	aCc/aGc	4/8	1	2	FACETS	0.874	0.766	0.992	0.874	0.766	0.992	CLONAL	1	FALSE	1	0.233087903810431	2		574	736	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0062303-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	185	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.183230002538009	3	FACETS	1	0.984	1	0.806	0.748	0.866	CLONAL	2	TRUE	0	0.291106111623034	3		434	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0062303-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	179	608	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.291106111623034	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	0	0.291106111623034	2		608	613	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118709	115118709	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs756408358	NA	P-0062303-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	203	510	0	ENST00000257566.3:c.632A>C	p.Asn211Thr	p.N211T	ENST00000257566	NM_016569.3	211	aAc/aCc	2/8	0.289393267649159	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.291106111623034	3		510	731	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121571	108121571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781841	NA	P-0062303-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	176	461	0	ENST00000278616.4:c.1379C>T	p.Thr460Met	p.T460M	ENST00000278616	NM_000051.3	460	aCg/aTg	10/63	0.291106111623034	2	FACETS	0.972	0.9	1	0.972	0.9	1	CLONAL	2	TRUE	0	0.291106111623034	2		461	622	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0062304-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	1930	368	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.613883202746793	22	FACETS	1	0.997	1	0.974	0.965	0.984	CLONAL	20	TRUE	1	0.613883202746793	22		368	2194	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0062304-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	193	818	1	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.569748051092831	2	FACETS	0.823	0.773	0.873	0.823	0.773	0.873	CLONAL	2	TRUE	0	0.613883202746793	2		819	382	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076719	72076719	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062304-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	38	685	0	ENST00000357731.5:c.778G>T	p.Gly260Ter	p.G260*	ENST00000357731	NM_173808.2	260	Gga/Tga	5/7	0.518580210134821	3	FACETS	0.327	0.27	0.391	0.109	0.09	0.131	SUBCLONAL	1	TRUE	0	0.613883202746793	3		685	495	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602488	10602488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062304-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	220	866	0	ENST00000171111.5:c.1090G>A	p.Gly364Ser	p.G364S	ENST00000171111	NM_203500.1	364	Ggc/Agc	3/6	0.613883202746793	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.613883202746793	1		866	363	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399966	139399966	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062304-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	47	879	0	ENST00000277541.6:c.4382A>T	p.Lys1461Met	p.K1461M	ENST00000277541	NM_017617.3	1461	aAg/aTg	25/34	0.613883202746793	1	FACETS	0.304	0.257	0.355	0.304	0.257	0.355	SUBCLONAL	1	TRUE	0	0.613883202746793	1		879	349	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0062347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	146	462	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.315373155352343	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.31663411777082	2		462	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0062347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	174	898	0	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	0.315373155352343	2	FACETS	0.939	0.87	1	0.939	0.87	1	CLONAL	2	TRUE	0	0.31663411777082	2		898	585	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584572	48584572	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	214	634	0	ENST00000342988.3:c.745C>T	p.Gln249Ter	p.Q249*	ENST00000342988	NM_005359.5	249	Cag/Tag	6/12	0.315373155352343	2	FACETS	0.975	0.91	1	0.975	0.91	1	CLONAL	2	TRUE	0	0.31663411777082	2		634	693	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955394	48955394	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886043247	NA	P-0062347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	136	396	1	ENST00000267163.4:c.1510C>T	p.Gln504Ter	p.Q504*	ENST00000267163	NM_000321.2	504	Cag/Tag	17/27	0.315373155352343	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	0	0.31663411777082	2		397	424	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217267	66217267	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs199801676	NA	P-0062347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	202	594	0	ENST00000273854.3:c.2348G>T	p.Gly783Val	p.G783V	ENST00000273854	NM_004439.5	783	gGt/gTt	14/18	0.31663411777082	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	2	0.31663411777082	4		594	793	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713385	40713385	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	228	807	0	ENST00000373198.4:c.4130G>T	p.Arg1377Leu	p.R1377L	ENST00000373198	NM_133170.3	1377	cGa/cTa	30/32	0.270050718608651	4	FACETS	0.937	0.873	1	0.937	0.873	1	CLONAL	2	TRUE	2	0.31663411777082	4		807	1012	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203684	94203684	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	171	496	0	ENST00000323929.3:c.970G>C	p.Asp324His	p.D324H	ENST00000323929	NM_005591.3	324	Gat/Cat	9/20	0.31663411777082	4	FACETS	0.99	0.913	1	0.99	0.913	1	CLONAL	2	TRUE	2	0.31663411777082	4		496	718	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0062347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	254	771	1	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	0.31663411777082	4	FACETS	0.978	0.915	1	0.978	0.915	1	CLONAL	2	TRUE	2	0.31663411777082	4		772	1080	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52729052	52729052	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	317	811	0	ENST00000322088.6:c.1744G>T	p.Ala582Ser	p.A582S	ENST00000322088	NM_014225.5	582	Gct/Tct	14/15	0.307779245953636	3	FACETS	0.989	0.938	1	0.989	0.938	1	CLONAL	3	TRUE	0	0.31663411777082	3		811	782	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114290	143114290	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	140	431	0	ENST00000262992.4:c.1131G>C	p.Lys377Asn	p.K377N	ENST00000262992	NM_001101669.1	377	aaG/aaC	13/24	0.31663411777082	4	FACETS	0.859	0.784	0.937	0.859	0.784	0.937	CLONAL	2	TRUE	2	0.31663411777082	4		431	678	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871172	35871172	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	88	460	0	ENST00000303115.3:c.394C>A	p.Pro132Thr	p.P132T	ENST00000303115	NM_002185.3	132	Cct/Act	4/8	0.309630081097725	3	FACETS	1	0.938	1	0.543	0.482	0.608	CLONAL	1	TRUE	1	0.31663411777082	3		460	593	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057672	180057672	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	107	730	0	ENST00000261937.6:c.283G>C	p.Val95Leu	p.V95L	ENST00000261937	NM_182925.4	95	Gtg/Ctg	3/30	0.31663411777082	3	FACETS	0.991	0.889	1	0.495	0.444	0.55	CLONAL	1	TRUE	1	0.31663411777082	3		730	790	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805573	32805573	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	257	806	0	ENST00000374899.4:c.438G>C	p.Arg146Ser	p.R146S	ENST00000374899	NM_018833.2	146	agG/agC	2/12	0.31663411777082	4	FACETS	0.996	0.933	1	0.996	0.933	1	CLONAL	2	TRUE	2	0.31663411777082	4		806	1073	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964484	93964484	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	170	500	1	ENST00000369303.4:c.2413C>A	p.Pro805Thr	p.P805T	ENST00000369303	NM_004440.3	805	Ccc/Acc	14/17	0.315373155352343	2	FACETS	0.95	0.879	1	0.95	0.879	1	CLONAL	2	TRUE	0	0.31663411777082	2		501	565	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124511062	124511062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	154	443	0	ENST00000357628.3:c.158C>T	p.Thr53Ile	p.T53I	ENST00000357628	NM_015450.2	53	aCa/aTa	7/19	0.31663411777082	4	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	2	0.31663411777082	4		443	610	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971038	21971038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370823171	NA	P-0062347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	177	756	0	ENST00000304494.5:c.320G>A	p.Arg107His	p.R107H	ENST00000304494	NM_000077.4	107	cGc/cAc	2/3	0.31663411777082	3	FACETS	1	0.988	1	0.705	0.649	0.762	CLONAL	1	TRUE	1	0.31663411777082	3		756	919	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239927	98239927	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1438523462	NA	P-0062347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	353	600	0	ENST00000331920.6:c.1405G>T	p.Val469Leu	p.V469L	ENST00000331920	NM_000264.3	469	Gtg/Ttg	10/24	0.31663411777082	5	FACETS	0.962	0.915	1	0.962	0.915	1	CLONAL	4	TRUE	1	0.31663411777082	5		600	855	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413030	63413030	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	54	778	0	ENST00000330258.3:c.137C>A	p.Ser46Ter	p.S46*	ENST00000330258	NM_152424.3	46	tCa/tAa	2/2	1	2	FACETS	0.478	0.408	0.556	0.478	0.408	0.556	SUBCLONAL	1	TRUE	1	0.31663411777082	2		778	713	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034505	123034505	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	22	292	0	ENST00000355640.3:c.1262G>T	p.Ser421Ile	p.S421I	ENST00000355640		421	aGt/aTt	6/7	0.31663411777082	3	FACETS	0.368	0.285	0.466	0.184	0.142	0.233	SUBCLONAL	1	TRUE	1	0.31663411777082	3		292	437	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877451	40877451	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062412-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	52	434	0	ENST00000373198.4:c.2245C>A	p.Gln749Lys	p.Q749K	ENST00000373198	NM_133170.3	749	Cag/Aag	15/32	0.263059821043469	3	FACETS	0.58	0.494	0.675	0.29	0.247	0.338	SUBCLONAL	1	TRUE	1	0.36107001659731	3		434	586	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395636	45395636	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	49	309	0	ENST00000262160.6:c.498C>G	p.His166Gln	p.H166Q	ENST00000262160	NM_005901.5	166	caC/caG	4/11	0.339944713223861	3	FACETS	0.798	0.677	0.93	0.399	0.338	0.465	CLONAL	1	TRUE	1	0.346361554514155	3		309	416	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907837	76907837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	30	126	0	ENST00000373344.5:c.4324del	p.Ser1442LeufsTer48	p.S1442Lfs*48	ENST00000373344	NM_000489.3	1442	Tct/ct	15/35	1	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	0	0.346361554514155	1		126	120	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0062484-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	399	828	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.283607239649811	6	FACETS	0.906	0.862	0.95	0.906	0.862	0.95	CLONAL	4	FALSE	2	0.283607239649811	6		828	1217	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106861	27106861	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062484-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	196	788	0	ENST00000324856.7:c.6472C>T	p.Arg2158Ter	p.R2158*	ENST00000324856	NM_006015.4	2158	Cga/Tga	20/20	0.20193253692118	3	FACETS	1	0.961	1	0.702	0.652	0.754	CLONAL	2	FALSE	0	0.283607239649811	3		788	749	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025621	1025621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763842232	NA	P-0062484-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	197	851	0	ENST00000358495.3:c.754G>A	p.Glu252Lys	p.E252K	ENST00000358495	NM_134424.2	252	Gag/Aag	9/12	0.283607239649811	5	FACETS	1	0.963	1			1	CLONAL	2	FALSE	NA	0.283607239649811	5		851	933	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180964	108180964	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062484-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	101	306	0	ENST00000278616.4:c.5840C>G	p.Ser1947Cys	p.S1947C	ENST00000278616	NM_000051.3	1947	tCt/tGt	39/63	0.274253305470939	2	FACETS	0.968	0.873	1	0.968	0.873	1	CLONAL	2	FALSE	0	0.283607239649811	2		306	368	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839755	27839764	+	frameshift_variant	Frame_Shift_Del	DEL	AATGGCGCAC	AATGGCGCAC	-	novel	NA	P-0062484-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	227	827	0	ENST00000328488.2:c.330_339del	p.Cys111ThrfsTer?	p.C111Tfs*?	ENST00000328488	NM_003533.2	110	ctGTGCGCCATT/ct	1/1	0.091668618267178	6	FACETS	1	0.982	1	0.77	0.717	0.825	INDETERMINATE	2	FALSE	3	0.283607239649811	6		827	1086	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221325	1221325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062484-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	40	794	0	ENST00000326873.7:c.848C>T	p.Ser283Phe	p.S283F	ENST00000326873	NM_000455.4	283	tCt/tTt	6/10	0.20193253692118	3	FACETS	0.435	0.36	0.519	0.145	0.12	0.173	SUBCLONAL	1	FALSE	0	0.283607239649811	3		794	740	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401529	401529	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062484-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	36	703	0	ENST00000380956.4:c.851C>G	p.Ala284Gly	p.A284G	ENST00000380956	NM_001195286.1	284	gCc/gGc	7/9	1	2	FACETS	0.422	0.346	0.507	0.422	0.346	0.507	SUBCLONAL	1	FALSE	1	0.283607239649811	2		703	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0062522-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	226	809	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.518779059518015	1	FACETS	0.982	0.92	1	0.982	0.92	1	CLONAL	1	TRUE	0	0.518779059518015	1		809	657	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0062522-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	186	665	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.518779059518015	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.518779059518015	1		665	494	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102094392	102094392	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062522-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	177	444	0	ENST00000282441.5:c.1072G>C	p.Asp358His	p.D358H	ENST00000282441	NM_001130145.2	358	Gat/Cat	7/9	1	2	FACETS	0.996	0.921	1	0.996	0.921	1	CLONAL	1	TRUE	1	0.518779059518015	2		444	685	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239364	105239364	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062522-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	274	808	0	ENST00000349310.3:c.1023G>C	p.Glu341Asp	p.E341D	ENST00000349310	NM_001014432.1	341	gaG/gaC	12/15	0.518779059518015	1	FACETS	0.914	0.86	0.969	0.914	0.86	0.969	CLONAL	1	TRUE	0	0.518779059518015	1		808	856	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99175950	99175950	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1347504780	NA	P-0062522-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	151	456	0	ENST00000074304.5:c.1862C>G	p.Ser621Cys	p.S621C	ENST00000074304	NM_001134224.1	621	tCc/tGc	18/26	1	2	FACETS	0.904	0.829	0.982	0.904	0.829	0.982	CLONAL	1	TRUE	1	0.518779059518015	2		456	644	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172165	32172165	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs762922977	NA	P-0062522-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	230	508	0	ENST00000375023.3:c.2867G>A	p.Cys956Tyr	p.C956Y	ENST00000375023	NM_004557.3	956	tGt/tAt	19/30	1	2	FACETS	0.957	0.893	1	0.957	0.893	1	CLONAL	1	TRUE	1	0.518779059518015	2		508	927	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293508	137293508	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062522-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	217	688	0	ENST00000481739.1:c.59C>A	p.Thr20Asn	p.T20N	ENST00000481739	NM_002957.4	20	aCc/aAc	2/10	1	2	FACETS	0.953	0.887	1	0.953	0.887	1	CLONAL	1	TRUE	1	0.518779059518015	2		688	878	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31239460	31239460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1065385	NA	P-0062529-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	144	738	0	ENST00000376228.5:c.259G>A	p.Glu87Lys	p.E87K	ENST00000376228	NM_002117.5	87	Gag/Aag	2/8	1	2	FACETS	0.878	0.808	0.95	0.878	0.808	0.95	CLONAL	1	TRUE	1	0.752000112195371	2		738	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578220	+	inframe_deletion	In_Frame_Del	DEL	TATGTCGAAAAGTGT	TATGTCGAAAAGTGT	-	novel	NA	P-0062529-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	72	590	0	ENST00000269305.4:c.629_643del	p.Asn210_His214del	p.N210_H214del	ENST00000269305	NM_001126112.2	210	aACACTTTTCGACATAgt/agt	6/11	0.457019671588731	1	FACETS	0.31	0.272	0.351	0.31	0.272	0.351	SUBCLONAL	1	TRUE	0	0.752000112195371	1		590	385	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58733985	58733985	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062529-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	233	389	0	ENST00000305921.3:c.1043A>G	p.Lys348Arg	p.K348R	ENST00000305921	NM_003620.3	348	aAa/aGa	5/6	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.752000112195371	2		389	568	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37061892	37061892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881739	NA	P-0062529-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	52	433	0	ENST00000231790.2:c.976G>A	p.Val326Met	p.V326M	ENST00000231790	NM_000249.3	326	Gtg/Atg	11/19	1	2	FACETS	0.224	0.19	0.261	0.224	0.19	0.261	SUBCLONAL	1	TRUE	1	0.752000112195371	2		433	617	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0062547-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	811	698	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.498015019618261	8	FACETS	1	0.992	1	1	0.992	1	CLONAL	6	TRUE	2	0.498015019618261	8		698	1297	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210075	55210075	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062547-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	750	402	0	ENST00000275493.2:c.185T>G	p.Leu62Arg	p.L62R	ENST00000275493	NM_005228.3	62	cTt/cGt	2/28	0.498015019618261	8	FACETS	1	0.993	1	1	0.993	1	CLONAL	6	TRUE	2	0.498015019618261	8		402	1181	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891188	101891188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062547-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	208	369	0	ENST00000374994.4:c.149C>T	p.Thr50Ile	p.T50I	ENST00000374994	NM_004612.2	50	aCa/aTa	2/9	0.498765704357638	2	FACETS	0.914	0.859	0.97	0.914	0.859	0.97	CLONAL	2	TRUE	0	0.498015019618261	2		369	457	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720826	89720826	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062547-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	79	162	0	ENST00000371953.3:c.977A>G	p.Asp326Gly	p.D326G	ENST00000371953	NM_000314.4	326	gAc/gGc	8/9	0.498765704357638	2	FACETS	0.922	0.833	1	0.922	0.833	1	CLONAL	2	TRUE	0	0.498015019618261	2		162	172	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720679	89720679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123329	NA	P-0062547-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	74	111	0	ENST00000371953.3:c.830C>T	p.Thr277Ile	p.T277I	ENST00000371953	NM_000314.4	277	aCa/aTa	8/9	0.498765704357638	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	2	TRUE	0	0.498015019618261	2		111	146	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3824616	3824616	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062547-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	136	471	0	ENST00000262367.5:c.2237C>T	p.Pro746Leu	p.P746L	ENST00000262367	NM_004380.2	746	cCa/cTa	12/31	0.498765704357638	3	FACETS	0.976	0.889	1	0.488	0.444	0.534	CLONAL	1	TRUE	1	0.498015019618261	3		471	699	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578385	7578385	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1567552584	NA	P-0062547-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	290	531	0	ENST00000269305.4:c.545del	p.Cys182SerfsTer65	p.C182Sfs*65	ENST00000269305	NM_001126112.2	182	tGc/tc	5/11	0.46338585009092	2	FACETS	0.903	0.856	0.95	0.903	0.856	0.95	CLONAL	2	TRUE	0	0.498015019618261	2		531	645	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076788	72076788	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs754424709	NA	P-0062547-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	145	541	0	ENST00000357731.5:c.709C>A	p.Pro237Thr	p.P237T	ENST00000357731	NM_173808.2	237	Ccc/Acc	5/7	0.498765704357638	3	FACETS	1	0.951	1	0.529	0.484	0.577	CLONAL	1	TRUE	1	0.498015019618261	3		541	687	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900087	151900087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062547-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	75	411	0	ENST00000262189.6:c.4024G>A	p.Glu1342Lys	p.E1342K	ENST00000262189	NM_170606.2	1342	Gaa/Aaa	26/59	0.452848437387769	3	FACETS	0.855	0.752	0.965	0.427	0.376	0.483	CLONAL	1	TRUE	1	0.498015019618261	3		411	440	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0062602-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	576	698	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.273449057021856	5	FACETS	1	0.989	1	0.845	0.816	0.874	CLONAL	4	TRUE	0	0.386150263017158	5		698	1115	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259439	55259439	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs397517126	NA	P-0062602-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	479	447	0	ENST00000275493.2:c.2497T>G	p.Leu833Val	p.L833V	ENST00000275493	NM_005228.3	833	Ttg/Gtg	21/28	0.273449057021856	5	FACETS	0.985	0.947	1	0.788	0.757	0.819	CLONAL	4	TRUE	0	0.386150263017158	5		447	994	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970901	21970901	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs45476696	NA	P-0062602-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	376	600	0	ENST00000304494.5:c.457G>A	p.Asp153Asn	p.D153N	ENST00000304494	NM_000077.4	153	Gac/Aac	2/3	0.386019968028292	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.386150263017158	3		600	1079	SUCCESS
ATR	545	MSKCC	GRCh37	3	142222283	142222283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062602-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	65	208	0	ENST00000350721.4:c.5209C>T	p.His1737Tyr	p.H1737Y	ENST00000350721	NM_001184.3	1737	Cat/Tat	30/47	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.386150263017158	2		208	321	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955465	48955465	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062602-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	109	181	0	ENST00000267163.4:c.1585del	p.Tyr529ThrfsTer3	p.Y529Tfs*3	ENST00000267163	NM_000321.2	527	gaT/ga	17/27	0.374904153319452	3	FACETS	1	0.961	1	0.736	0.67	0.804	CLONAL	2	TRUE	0	0.386150263017158	3		181	305	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361119	70361119	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062602-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	209	767	0	ENST00000374080.3:c.6307C>T	p.Gln2103Ter	p.Q2103*	ENST00000374080		2103	Caa/Taa	43/45	0.386150263017158	1	FACETS	0.96	0.892	1	0.96	0.892	1	CLONAL	1	TRUE	0	0.386150263017158	1		767	910	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	348	554	10	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	0.885	0.84	0.931	0.885	0.84	0.931	CLONAL	1	TRUE	1	0.796430805790489	2		564	987	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	356	809	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.796430805790489	2		809	809	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	862	749	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.973	0.954	0.992	1	0.999	1	CLONAL	2	TRUE	1	0.796430805790489	2		754	1112	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	422	241	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.796430805790489	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.796430805790489	3		241	734	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15821896	15821896	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	224	435	1	ENST00000307771.7:c.294del	p.Lys98AsnfsTer10	p.K98Nfs*10	ENST00000307771	NM_005089.3	97	Aaa/aa	4/11	NA	2	FACETS	0.845	0.791	0.9			1	INDETERMINATE	1	TRUE	NA	0.796430805790489	2		436	666	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687472	37687472	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	271	616	1	ENST00000447079.4:c.4382del	p.Gly1461AlafsTer38	p.G1461Afs*38	ENST00000447079	NM_015083.1	1459	tGg/tg	14/14	1	2	FACETS	0.737	0.692	0.782	0.737	0.692	0.782	SUBCLONAL	1	TRUE	1	0.796430805790489	2		617	924	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190824	11190824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868040471	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	337	517	0	ENST00000361445.4:c.5375C>T	p.Ala1792Val	p.A1792V	ENST00000361445	NM_004958.3	1792	gCg/gTg	39/58	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.796430805790489	2		517	789	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22404976	22404976	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	10	71	0	ENST00000344548.3:c.5A>G	p.Gln2Arg	p.Q2R	ENST00000344548	NM_001039802.1	2	cAg/cGg	3/7	1	2	FACETS	0.249	0.169	0.346	0.249	0.169	0.346	SUBCLONAL	1	TRUE	1	0.796430805790489	2		71	101	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957459	175957459	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	250	437	0	ENST00000367669.3:c.1937T>C	p.Val646Ala	p.V646A	ENST00000367669	NM_022457.5	646	gTa/gCa	17/20	1	2	FACETS	0.967	0.911	1	0.967	0.911	1	CLONAL	1	TRUE	1	0.796430805790489	2		437	649	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206646650	206646650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553384304	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	305	455	0	ENST00000367120.3:c.80G>A	p.Arg27His	p.R27H	ENST00000367120	NM_014002.3	27	cGc/cAc	3/22	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.796430805790489	2		455	732	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450940	70450940	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	335	598	0	ENST00000373644.4:c.5780C>A	p.Ser1927Tyr	p.S1927Y	ENST00000373644	NM_030625.2	1927	tCc/tAc	12/12	1	2	FACETS	0.956	0.907	1	0.956	0.907	1	CLONAL	1	TRUE	1	0.796430805790489	2		598	880	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154241	2154242	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755455183	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	128	879	3	ENST00000434045.2:c.686dup	p.Glu230ArgfsTer50	p.E230Rfs*50	ENST00000434045	NM_001127598.1	229	cca/ccCa	5/5	1	2	FACETS	0.392	0.355	0.431	0.392	0.355	0.431	SUBCLONAL	1	TRUE	1	0.796430805790489	2		882	819	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942229	71942229	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770428487	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	376	549	0	ENST00000298229.2:c.1493G>A	p.Arg498His	p.R498H	ENST00000298229	NM_001567.3	498	cGc/cAc	12/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.796430805790489	2		549	891	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998492	100998492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	313	601	1	ENST00000325455.5:c.1310C>T	p.Ala437Val	p.A437V	ENST00000325455	NM_001202474.3	437	gCg/gTg	1/8	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.796430805790489	2		602	726	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121531	108121531	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779815	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	299	477	0	ENST00000278616.4:c.1339C>T	p.Arg447Ter	p.R447*	ENST00000278616	NM_000051.3	447	Cga/Tga	10/63	1	2	FACETS	0.961	0.91	1	0.961	0.91	1	CLONAL	1	TRUE	1	0.796430805790489	2		477	781	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203563	108203563	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	174	383	0	ENST00000278616.4:c.7863G>T	p.Glu2621Asp	p.E2621D	ENST00000278616	NM_000051.3	2621	gaG/gaT	53/63	1	2	FACETS	0.969	0.901	1	0.969	0.901	1	CLONAL	1	TRUE	1	0.796430805790489	2		383	451	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426849	49426850	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	360	616	0	ENST00000301067.7:c.11638_11639del	p.Leu3880AspfsTer131	p.L3880Dfs*131	ENST00000301067	NM_003482.3	3880	CTg/g	39/54	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.796430805790489	2		616	903	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435297	110435302	+	inframe_deletion	In_Frame_Del	DEL	GGCGGT	GGCGGT	-	rs761851705	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	209	737	0	ENST00000375856.3:c.3099_3104del	p.Pro1035_Pro1036del	p.P1035_P1036del	ENST00000375856	NM_003749.2	1033	ccACCGCCg/ccg	1/2	1	2	FACETS	0.628	0.584	0.673	0.628	0.584	0.673	SUBCLONAL	1	TRUE	1	0.796430805790489	2		737	836	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	333	577	2	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	0.958	0.909	1	0.958	0.909	1	CLONAL	1	TRUE	1	0.796430805790489	2		579	873	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779210	3779211	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs587783507	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	122	518	1	ENST00000262367.5:c.5837dup	p.Pro1947ThrfsTer19	p.P1947Tfs*19	ENST00000262367	NM_004380.2	1946	cca/ccCa	31/31	1	2	FACETS	0.486	0.44	0.534	0.486	0.44	0.534	SUBCLONAL	1	TRUE	1	0.796430805790489	2		519	630	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821344	72821344	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	211	428	1	ENST00000268489.5:c.10831del	p.His3611ThrfsTer83	p.H3611Tfs*83	ENST00000268489	NM_006885.3	3611	Cac/ac	10/10	1	2	FACETS	0.895	0.837	0.954	0.895	0.837	0.954	CLONAL	1	TRUE	1	0.796430805790489	2		429	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577138	7577138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780075	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	299	571	0	ENST00000269305.4:c.800G>A	p.Arg267Gln	p.R267Q	ENST00000269305	NM_001126112.2	267	cGg/cAg	8/11	1	2	FACETS	0.971	0.919	1	0.971	0.919	1	CLONAL	1	TRUE	1	0.796430805790489	2		571	773	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687019	37687019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	373	587	0	ENST00000447079.4:c.3923C>A	p.Pro1308His	p.P1308H	ENST00000447079	NM_015083.1	1308	cCt/cAt	14/14	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.796430805790489	2		587	854	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007443	62007443	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	337	624	0	ENST00000392795.3:c.424C>T	p.Arg142Ter	p.R142*	ENST00000392795	NM_001039933.1	142	Cga/Tga	3/6	1	2	FACETS	0.994	0.945	1	0.994	0.945	1	CLONAL	1	TRUE	1	0.796430805790489	2		624	851	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533732	63533733	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGG	rs570443161	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	314	760	1	ENST00000307078.5:c.1419_1421dup	p.His474dup	p.H474dup	ENST00000307078	NM_004655.3	474	cat/caCCAt	6/11	1	2	FACETS	0.741	0.7	0.783	0.741	0.7	0.783	SUBCLONAL	1	TRUE	1	0.796430805790489	2		761	1064	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219399	5219399	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	351	640	0	ENST00000357368.4:c.3845G>T	p.Gly1282Val	p.G1282V	ENST00000357368	NM_002850.3	1282	gGg/gTg	23/38	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.796430805790489	2		640	868	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246447	10246447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747467776	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	249	401	0	ENST00000340748.4:c.4690C>T	p.Arg1564Trp	p.R1564W	ENST00000340748		1564	Cgg/Tgg	38/40	1	2	FACETS	0.947	0.892	1	0.947	0.892	1	CLONAL	1	TRUE	1	0.796430805790489	2		401	660	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10283839	10283839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758190156	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	308	470	0	ENST00000340748.4:c.647C>T	p.Pro216Leu	p.P216L	ENST00000340748		216	cCg/cTg	8/40	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.796430805790489	2		470	728	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085728	16085728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144939456	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	360	537	0	ENST00000281043.3:c.904C>T	p.Arg302Cys	p.R302C	ENST00000281043	NM_005378.4	302	Cgt/Tgt	3/3	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.796430805790489	2		537	806	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972671	25972671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	218	585	0	ENST00000435504.4:c.1754C>A	p.Pro585Gln	p.P585Q	ENST00000435504		585	cCa/cAa	12/13	1	2	FACETS	0.566	0.527	0.607	0.566	0.527	0.607	SUBCLONAL	1	TRUE	1	0.796430805790489	2		585	967	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714369	40714369	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs775489787	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	644	505	1	ENST00000373198.4:c.4028G>A	p.Arg1343Gln	p.R1343Q	ENST00000373198	NM_133170.3	1343	cGg/cAg	29/32	0.796430805790489	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.796430805790489	3		506	1099	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458339	12458339	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	364	534	0	ENST00000287820.6:c.956A>T	p.Glu319Val	p.E319V	ENST00000287820	NM_015869.4	319	gAg/gTg	6/7	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.796430805790489	2		534	863	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715600	30715600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	276	516	0	ENST00000295754.5:c.1258G>A	p.Gly420Arg	p.G420R	ENST00000295754	NM_003242.5	420	Gga/Aga	5/7	1	2	FACETS	0.979	0.925	1	0.979	0.925	1	CLONAL	1	TRUE	1	0.796430805790489	2		516	708	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670340	134670340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415689583	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	343	486	0	ENST00000398015.3:c.251G>A	p.Arg84His	p.R84H	ENST00000398015	NM_004441.4	84	cGc/cAc	3/16	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.796430805790489	2		486	781	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138376566	138376566	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	259	350	0	ENST00000289153.2:c.2908C>T	p.Gln970Ter	p.Q970*	ENST00000289153	NM_006219.2	970	Caa/Taa	20/22	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.796430805790489	2		350	585	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440364	187440364	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1426858162	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	306	460	0	ENST00000232014.4:c.2003G>A	p.Arg668His	p.R668H	ENST00000232014	NM_001130845.1	668	cGt/cAt	10/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.796430805790489	2		460	709	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271211	153271212	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	77	302	0	ENST00000281708.4:c.566_567del	p.Lys189SerfsTer66	p.K189Sfs*66	ENST00000281708	NM_033632.3	189	aAA/a	3/12	1	2	FACETS	0.93	0.832	1	0.93	0.832	1	CLONAL	1	TRUE	1	0.796430805790489	2		302	208	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	165	213	0	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	1	2	FACETS	0.899	0.833	0.966	0.899	0.833	0.966	CLONAL	1	TRUE	1	0.796430805790489	2		213	461	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177584	56177584	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368201444	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	333	525	2	ENST00000399503.3:c.2557C>T	p.Arg853Cys	p.R853C	ENST00000399503	NM_005921.1	853	Cgt/Tgt	14/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.796430805790489	2		527	788	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753379	57753380	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	239	485	0	ENST00000274289.3:c.744_745del	p.Pro249Ter	p.P249*	ENST00000274289	NM_006622.3	248	tcTCct/tcct	6/14	1	2	FACETS	0.96	0.903	1	0.96	0.903	1	CLONAL	1	TRUE	1	0.796430805790489	2		485	625	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753914	57753916	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	249	394	0	ENST00000274289.3:c.708_710del	p.Arg238del	p.R238del	ENST00000274289	NM_006622.3	236	agAAGg/agg	5/14	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.796430805790489	2		394	618	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120759	94120759	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	320	558	0	ENST00000369303.4:c.292A>T	p.Ile98Phe	p.I98F	ENST00000369303	NM_004440.3	98	Att/Ttt	3/17	1	2	FACETS	0.971	0.92	1	0.971	0.92	1	CLONAL	1	TRUE	1	0.796430805790489	2		558	828	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450363	50450363	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1441542459	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	327	507	0	ENST00000331340.3:c.547C>T	p.Arg183Cys	p.R183C	ENST00000331340	NM_006060.4	183	Cgc/Tgc	5/8	0.796430805790489	3	FACETS	1	0.979	1	0.534	0.504	0.563	CLONAL	1	TRUE	1	0.796430805790489	3		507	1076	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090496	5090496	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs750978665	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	123	329	0	ENST00000381652.3:c.2812C>T	p.Arg938Ter	p.R938*	ENST00000381652	NM_004972.3	938	Cga/Tga	21/25	1	2	FACETS	0.95	0.871	1	0.95	0.871	1	CLONAL	1	TRUE	1	0.796430805790489	2		329	325	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006222	22006222	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752675430	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	361	663	0	ENST00000276925.6:c.181G>A	p.Val61Met	p.V61M	ENST00000276925	NM_004936.3	61	Gtg/Atg	2/2	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.796430805790489	2		663	849	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840613	36840613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756710542	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	331	485	0	ENST00000358127.4:c.1120G>A	p.Ala374Thr	p.A374T	ENST00000358127	NM_001280556.1	374	Gct/Act	10/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.796430805790489	2		485	750	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776925	76776925	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	157	364	0	ENST00000373344.5:c.7027A>G	p.Thr2343Ala	p.T2343A	ENST00000373344	NM_000489.3	2343	Aca/Gca	33/35	1	2	FACETS	0.917	0.849	0.987	0.917	0.849	0.987	CLONAL	1	TRUE	1	0.796430805790489	2		364	430	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279861	46279866	+	inframe_deletion	In_Frame_Del	DEL	CAGCAA	CAGCAA	-	rs748517056	NA	P-0062603-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	145	707	0	ENST00000371998.3:c.3810_3815del	p.Gln1275_Gln1276del	p.Q1275_Q1276del	ENST00000371998		1263	CAGCAA/-	20/23	0.796430805790489	3	FACETS	0.384	0.349	0.421	0.192	0.174	0.211	SUBCLONAL	1	TRUE	1	0.796430805790489	3		707	1325	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0062605-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	32	1032	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.89	0.734	1	0.89	0.734	1	CLONAL	1	TRUE	1	0.492306421356628	2		1032	146	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431942	49431943	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0062605-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	149	652	1	ENST00000301067.7:c.9196_9197del	p.Phe3066GlnfsTer2	p.F3066Qfs*2	ENST00000301067	NM_003482.3	3066	TTc/c	34/54	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.492306421356628	2		653	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0062605-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	110	654	0	ENST00000269305.4:c.915dup	p.Arg306AlafsTer31	p.R306Afs*31	ENST00000269305	NM_001126112.2	305	-/G	8/11	0.463028782926885	1	FACETS	0.877	0.795	0.962	0.877	0.795	0.962	CLONAL	1	TRUE	0	0.492306421356628	1		654	384	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216590	108216590	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062613-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	70	419	0	ENST00000278616.4:c.8539G>T	p.Glu2847Ter	p.E2847*	ENST00000278616	NM_000051.3	2847	Gag/Tag	58/63	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.757817480301658	2		419	175	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47643527	47643527	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062613-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	75	418	0	ENST00000233146.2:c.1035G>T	p.Trp345Cys	p.W345C	ENST00000233146	NM_000251.2	345	tgG/tgT	6/16	0.757817480301658	3	FACETS	0.913	0.808	1	0.456	0.404	0.512	CLONAL	1	TRUE	1	0.757817480301658	3		418	299	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149048	61149048	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062613-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	228	702	0	ENST00000295025.8:c.1238C>A	p.Ser413Ter	p.S413*	ENST00000295025	NM_002908.2	413	tCa/tAa	11/11	0.757817480301658	3	FACETS	1	0.947	1	0.508	0.474	0.542	CLONAL	1	TRUE	1	0.757817480301658	3		702	817	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309073	137309073	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062613-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	345	739	1	ENST00000481739.1:c.680A>T	p.Asn227Ile	p.N227I	ENST00000481739	NM_002957.4	227	aAc/aTc	5/10	0.757817480301658	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.757817480301658	2		740	431	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417315	139417315	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062613-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	321	735	0	ENST00000277541.6:c.729T>G	p.Cys243Trp	p.C243W	ENST00000277541	NM_017617.3	243	tgT/tgG	4/34	0.757817480301658	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.757817480301658	2		735	412	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	102	343	0				ENST00000310581	NM_198253.2	-/1132			0.251376236893784	5	FACETS	1	0.915	1	0.761	0.687	0.839	CLONAL	3	TRUE	1	0.251376236893784	5		343	367	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692932	89692932	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	517	335	0	ENST00000371953.3:c.416T>C	p.Leu139Ser	p.L139S	ENST00000371953	NM_000314.4	139	tTa/tCa	5/9	0.251376236893784	5	FACETS	1	0.994	1	1	0.998	1	CLONAL	9	TRUE	0	0.251376236893784	5		335	605	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589607	67589607	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	243	251	0	ENST00000274335.5:c.1370A>C	p.Gln457Pro	p.Q457P	ENST00000274335		457	cAa/cCa	10/15	0.251376236893784	5	FACETS	0.939	0.893	0.984	1	0.995	1	CLONAL	7	TRUE	1	0.251376236893784	5		251	405	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692964	89692964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	481	310	0	ENST00000371953.3:c.448G>A	p.Glu150Lys	p.E150K	ENST00000371953	NM_000314.4	150	Gag/Aag	5/9	0.251376236893784	5	FACETS	1	0.992	1	1	0.998	1	CLONAL	9	TRUE	0	0.251376236893784	5		310	568	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003535	57003535	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	C	C	T	rs760732461	NA	P-0062630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	181	565	1	ENST00000257254.3:c.944G>A	p.Arg315His	p.R315H	ENST00000257254		315	cGc/cAc	1/2	1	2	FACETS	1	0.979	1	1	0.995	1	CLONAL	3	TRUE	1	0.251376236893784	2		566	428	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415124	109415127	+	frameshift_variant	Frame_Shift_Del	DEL	GTCT	GTCT	-	novel	NA	P-0062630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	206	439	0	ENST00000436639.2:c.150_153del	p.Asp51GlyfsTer11	p.D51Gfs*11	ENST00000436639	NM_014454.2	50	tcAGAC/tc	1/10	1	2	FACETS	1	0.981	1	1	0.995	1	CLONAL	3	TRUE	1	0.251376236893784	2		439	489	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410631	63410631	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	132	502	0	ENST00000330258.3:c.2536T>A	p.Tyr846Asn	p.Y846N	ENST00000330258	NM_152424.3	846	Tat/Aat	2/2	0.251376236893784	1	FACETS	1	0.962	1	1	0.991	1	CLONAL	2	TRUE	0	0.251376236893784	1		502	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578262	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs483352697	NA	P-0062707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	364	700	0	ENST00000269305.4:c.587G>C	p.Arg196Pro	p.R196P	ENST00000269305	NM_001126112.2	196	cGa/cCa	6/11	0.209156852461928	2	FACETS	0.859	0.813	0.905	1	0.993	1	CLONAL	3	TRUE	0	0.209156852461928	2		700	1351	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149280	119149280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs991981291	NA	P-0062707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	236	579	0	ENST00000264033.4:c.1288G>A	p.Val430Met	p.V430M	ENST00000264033	NM_005188.3	430	Gtg/Atg	9/16	0.209156852461928	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.209156852461928	3		579	1065	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486193	99486193	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374121578	NA	P-0062707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	126	581	0	ENST00000268035.6:c.3499C>T	p.Arg1167Trp	p.R1167W	ENST00000268035	NM_000875.3	1167	Cgg/Tgg	19/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.209156852461928	2		581	993	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0062707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	170	536	2	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	0.209156852461928	3	FACETS	0.909	0.835	0.985	0.909	0.835	0.985	CLONAL	2	TRUE	1	0.209156852461928	3		538	988	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647164	23647164	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	112	585	0	ENST00000261584.4:c.703A>G	p.Thr235Ala	p.T235A	ENST00000261584	NM_024675.3	235	Aca/Gca	4/13	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.209156852461928	2		585	1049	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546122	29546122	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs894292181	NA	P-0062707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	116	508	0	ENST00000356175.3:c.1627C>T	p.Gln543Ter	p.Q543*	ENST00000356175	NM_000267.3	543	Cag/Tag	14/57	0.209156852461928	3	FACETS	1	0.955	1	0.555	0.499	0.615	CLONAL	1	TRUE	1	0.209156852461928	3		508	1103	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223177	41223177	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	235	609	0	ENST00000357654.3:c.4754C>G	p.Pro1585Arg	p.P1585R	ENST00000357654	NM_007294.3	1585	cCa/cGa	15/23	0.209156852461928	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.209156852461928	3		609	1156	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006601	62006601	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	253	566	0	ENST00000392795.3:c.678C>A	p.His226Gln	p.H226Q	ENST00000392795	NM_001039933.1	226	caC/caA	6/6	0.209156852461928	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.209156852461928	3		566	1090	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248759	212248759	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	92	516	0	ENST00000342788.4:c.3508C>G	p.Pro1170Ala	p.P1170A	ENST00000342788	NM_005235.2	1170	Cct/Gct	28/28	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.209156852461928	2		516	827	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124499166	124499166	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	103	371	0	ENST00000357628.3:c.547G>T	p.Val183Leu	p.V183L	ENST00000357628	NM_015450.2	183	Gta/Tta	9/19	0.208074202629539	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.209156852461928	1		371	600	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829012	128829012	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	127	395	0	ENST00000249373.3:c.20C>A	p.Ala7Glu	p.A7E	ENST00000249373	NM_005631.4	7	gCg/gAg	1/12	0.0966573353771085	3	FACETS	0.924	0.838	1	0.924	0.838	1	INDETERMINATE	2	TRUE	1	0.209156852461928	3		395	726	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0062725-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	344	1102	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.423755136752134	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.423755136752134	1		1102	1048	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440912	52440912	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1553645720	NA	P-0062725-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	214	926	0	ENST00000460680.1:c.592G>T	p.Glu198Ter	p.E198*	ENST00000460680	NM_004656.3	198	Gag/Tag	8/17	0.423755136752134	1	FACETS	0.891	0.829	0.955	0.891	0.829	0.955	CLONAL	1	TRUE	0	0.423755136752134	1		926	893	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615555	43615555	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062725-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	217	907	0	ENST00000355710.3:c.2636del	p.Asn879ThrfsTer4	p.N879Tfs*4	ENST00000355710	NM_020975.4	878	agA/ag	15/20	1	2	FACETS	0.954	0.887	1	0.954	0.887	1	CLONAL	1	TRUE	1	0.423755136752134	2		907	1073	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628400	86628400	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062725-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	158	610	0	ENST00000274376.6:c.769A>C	p.Ser257Arg	p.S257R	ENST00000274376	NM_002890.2	257	Agt/Cgt	3/25	0.406896826474707	3	FACETS	1	0.941	1	0.516	0.473	0.562	CLONAL	1	TRUE	1	0.423755136752134	3		610	875	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051363	13051363	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062725-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	73	1013	0	ENST00000316448.5:c.711C>A	p.Asp237Glu	p.D237E	ENST00000316448	NM_004343.3	237	gaC/gaA	6/9	1	2	FACETS	0.269	0.234	0.307	0.269	0.234	0.307	SUBCLONAL	1	TRUE	1	0.423755136752134	2		1013	1281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0062725-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	223	1102	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.438767681144795	1	FACETS	0.872	0.813	0.932	0.872	0.813	0.932	CLONAL	1	FALSE	0	0.470845230309532	1		1102	831	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440912	52440912	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1553645720	NA	P-0062725-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	186	926	0	ENST00000460680.1:c.592G>T	p.Glu198Ter	p.E198*	ENST00000460680	NM_004656.3	198	Gag/Tag	8/17	0.470845230309532	1	FACETS	0.801	0.742	0.863	0.801	0.742	0.863	CLONAL	1	FALSE	0	0.470845230309532	1		926	754	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615555	43615555	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062725-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	132	907	0	ENST00000355710.3:c.2636del	p.Asn879ThrfsTer4	p.N879Tfs*4	ENST00000355710	NM_020975.4	878	agA/ag	15/20	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.470845230309532	NA		907	892	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628400	86628400	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062725-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	98	610	0	ENST00000274376.6:c.769A>C	p.Ser257Arg	p.S257R	ENST00000274376	NM_002890.2	257	Agt/Cgt	3/25	0.470845230309532	1	FACETS	0.648	0.581	0.719	0.648	0.581	0.719	SUBCLONAL	1	FALSE	0	0.470845230309532	1		610	491	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0062744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	74	597	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.842	0.74	0.951	0.842	0.74	0.951	CLONAL	1	TRUE	1	0.398657163823663	2		597	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0062744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	320	801	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.344722422162159	2	FACETS	0.874	0.828	0.922	0.874	0.828	0.922	CLONAL	2	TRUE	0	0.398657163823663	2		804	918	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	18	551	0	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	1	2	FACETS	0.499	0.377	0.641	0.499	0.377	0.641	SUBCLONAL	1	TRUE	1	0.398657163823663	2		551	181	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670658	134670658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771145808	NA	P-0062744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	97	662	2	ENST00000398015.3:c.569G>A	p.Arg190His	p.R190H	ENST00000398015	NM_004441.4	190	cGt/cAt	3/16	1	2	FACETS	0.858	0.767	0.955	0.858	0.767	0.955	CLONAL	1	TRUE	1	0.398657163823663	2		664	567	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851741	134851741	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	132	776	0	ENST00000398015.3:c.1147C>A	p.Gln383Lys	p.Q383K	ENST00000398015	NM_004441.4	383	Cag/Aag	5/16	1	2	FACETS	0.939	0.854	1	0.939	0.854	1	CLONAL	1	TRUE	1	0.398657163823663	2		776	705	SUCCESS
APC	324	MSKCC	GRCh37	5	112128147	112128148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0062744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	15	322	0	ENST00000257430.4:c.652dup	p.Ile218AsnfsTer34	p.I218Nfs*34	ENST00000257430	NM_000038.5	217	aga/agAa	7/16	1	2	FACETS	0.627	0.463	0.82	0.627	0.463	0.82	SUBCLONAL	1	TRUE	1	0.398657163823663	2		322	120	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0062748-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	120	159	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.447181032162924	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.447181032162924	2		159	246	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521504	46521504	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062748-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	36	118	0	ENST00000262741.5:c.904C>G	p.Leu302Val	p.L302V	ENST00000262741	NM_003629.3	302	Ctg/Gtg	7/10	0.447181032162924	4	FACETS	1	0.877	1	0.358	0.296	0.426	CLONAL	1	TRUE	1	0.447181032162924	4		118	217	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478851	56478851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146486757	NA	P-0062748-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	10	169	0	ENST00000267101.3:c.307C>T	p.Arg103Cys	p.R103C	ENST00000267101	NM_001982.3	103	Cgc/Tgc	3/28	0.447181032162924	5	FACETS	0.161	0.108	0.228	0.04	0.027	0.057	SUBCLONAL	1	TRUE	1	0.447181032162924	5		169	464	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524129	187524129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375766862	NA	P-0062748-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	12	193	0	ENST00000441802.2:c.11410G>A	p.Glu3804Lys	p.E3804K	ENST00000441802	NM_005245.3	3804	Gaa/Aaa	20/27	0.447181032162924	1	FACETS	0.177	0.124	0.243	0.177	0.124	0.243	SUBCLONAL	1	TRUE	0	0.447181032162924	1		193	235	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150923847	150923848	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0062748-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	33	165	0	ENST00000271640.5:c.2223_2224del	p.Ala742LeufsTer20	p.A742Lfs*20	ENST00000271640	NM_001145415.1	740	aaGTgt/aagt	14/22	0.447181032162924	4	FACETS	0.645	0.527	0.778	0.215	0.175	0.26	SUBCLONAL	1	TRUE	1	0.447181032162924	4		165	331	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332547	70332547	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062748-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	21	138	0	ENST00000373644.4:c.452A>G	p.Lys151Arg	p.K151R	ENST00000373644	NM_030625.2	151	aAg/aGg	2/12	0.233410380405172	2	FACETS	0.854	0.668	1	0.427	0.334	0.532	INDETERMINATE	1	TRUE	0	0.447181032162924	2		138	110	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233055	69233055	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062748-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	64	130	0	ENST00000462284.1:c.920A>C	p.Asp307Ala	p.D307A	ENST00000462284	NM_002392.5	307	gAc/gCc	11/11	0.447181032162924	3	FACETS	0.796	0.699	0.897	0.531	0.466	0.598	SUBCLONAL	2	TRUE	0	0.447181032162924	3		130	220	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910761	32910761	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs886040420	NA	P-0062748-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	84	155	0	ENST00000380152.3:c.2272del	p.Ser758ValfsTer14	p.S758Vfs*14	ENST00000380152		757	Aaa/aa	11/27	0.447181032162924	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	3	TRUE	0	0.447181032162924	3		155	143	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383128	42383128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs557160710	NA	P-0062748-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	40	179	0	ENST00000221972.3:c.148G>A	p.Ala50Thr	p.A50T	ENST00000221972	NM_021601.3	50	Gcc/Acc	2/5	0.447181032162924	3	FACETS	0.471	0.391	0.56	0.235	0.195	0.28	SUBCLONAL	1	TRUE	1	0.447181032162924	3		179	465	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42788888	42788888	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062748-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	77	161	0	ENST00000575354.2:c.32C>G	p.Ala11Gly	p.A11G	ENST00000575354	NM_015125.3	11	gCg/gGg	1/20	0.447181032162924	3	FACETS	0.67	0.588	0.758	0.335	0.294	0.379	SUBCLONAL	1	TRUE	1	0.447181032162924	3		161	629	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467088	25467089	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCA	novel	NA	P-0062748-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	164	214	0	ENST00000264709.3:c.1784_1786dup	p.Leu595dup	p.L595dup	ENST00000264709	NM_175629.2	595	cgg/cTGCgg	15/23	0.368711028791269	4	FACETS	1	0.987	1	0.461	0.424	0.5	CLONAL	1	TRUE	1	0.447181032162924	4		214	767	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165638	185165646	+	inframe_deletion	In_Frame_Del	DEL	AGTGACAAA	AGTGACAAA	-	novel	NA	P-0062748-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	25	136	0	ENST00000265026.3:c.916_924del	p.Asp306_Ser308del	p.D306_S308del	ENST00000265026	NM_004721.4	305	AGTGACAAA/-	5/14	0.359742128841695	5	FACETS	0.719	0.568	0.891	0.144	0.113	0.179	SUBCLONAL	1	TRUE	0	0.447181032162924	5		136	260	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573984	7573984	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	60	458	0	ENST00000269305.4:c.1043T>C	p.Leu348Ser	p.L348S	ENST00000269305	NM_001126112.2	348	tTg/tCg	10/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.510726129022081	2		458	199	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601244	28601244	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062749-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	12	495	0	ENST00000241453.7:c.2188C>A	p.Gln730Lys	p.Q730K	ENST00000241453	NM_004119.2	730	Caa/Aaa	17/24	0.449682754752494	0	FACETS	0.237	0.168	0.32			1	SUBCLONAL	1	TRUE	0	0.510726129022081	0		495	97	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0062750-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	309	710	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.325919401637319	2	FACETS	0.988	0.935	1	0.988	0.935	1	CLONAL	2	TRUE	0	0.346631088353909	2		710	902	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342613	87342613	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062750-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	133	602	0	ENST00000277120.3:c.898C>A	p.His300Asn	p.H300N	ENST00000277120		300	Cac/Aac	9/19	0.343337215945399	2	FACETS	1	0.915	1	0.504	0.457	0.552	CLONAL	1	TRUE	0	0.346631088353909	2		602	762	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0062751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	114	539	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.559145403263885	2		539	323	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723359	49723359	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	50	371	0	ENST00000449682.2:c.1184C>A	p.Thr395Lys	p.T395K	ENST00000449682	NM_020998.3	395	aCg/aAg	10/18	1	2	FACETS	0.68	0.582	0.786	0.68	0.582	0.786	SUBCLONAL	1	TRUE	1	0.559145403263885	2		371	263	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0062752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	347	662	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.390108230907593	3	FACETS	0.974	0.923	1	0.974	0.923	1	CLONAL	2	TRUE	1	0.390108230907593	3		662	1091	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0062752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	44	693	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	1	2	FACETS	0.195	0.162	0.231	0.195	0.162	0.231	SUBCLONAL	1	TRUE	1	0.390108230907593	2		693	1159	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416493	29416493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1182539285	NA	P-0062752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	225	720	0	ENST00000389048.3:c.4460C>T	p.Ser1487Leu	p.S1487L	ENST00000389048	NM_004304.4	1487	tCg/tTg	29/29	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.390108230907593	2		720	1087	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247384	153247384	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0062752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	151	468	0	ENST00000281708.4:c.1419-1G>A		p.X473_splice	ENST00000281708	NM_033632.3	473			1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.390108230907593	2		468	771	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548892	29548892	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	28	277	0	ENST00000356175.3:c.1666G>C	p.Asp556His	p.D556H	ENST00000356175	NM_000267.3	556	Gat/Cat	15/57	1	2	FACETS	0.997	0.808	1	0.997	0.808	1	CLONAL	1	TRUE	1	0.390108230907593	2		277	144	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581288	48581289	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGCTCT	novel	NA	P-0062752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	178	589	0	ENST00000342988.3:c.593_599dup	p.Leu201SerfsTer7	p.L201Sfs*7	ENST00000342988	NM_005359.5	198	cca/cCAGCTCTca	5/12	0.390108230907593	1	FACETS	0.863	0.796	0.933	0.863	0.796	0.933	CLONAL	1	TRUE	0	0.390108230907593	1		589	851	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062753-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	19	343	0				ENST00000310581	NM_198253.2	-/1132			0.396652241799136	1	FACETS	0.505	0.388	0.639	0.505	0.388	0.639	SUBCLONAL	1	FALSE	0	0.483427473779257	1		343	118	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189847	11189847	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062753-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	61	509	0	ENST00000361445.4:c.5662T>A	p.Phe1888Ile	p.F1888I	ENST00000361445	NM_004958.3	1888	Ttc/Atc	40/58	0.321311114344133	0	FACETS	0.519	0.453	0.59			1	SUBCLONAL	1	FALSE	0	0.483427473779257	0		509	251	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374878	45374878	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs765635449	NA	P-0062753-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	35	466	0	ENST00000262160.6:c.965A>G	p.Asn322Ser	p.N322S	ENST00000262160	NM_005901.5	322	aAt/aGt	8/11	0.483427473779257	1	FACETS	0.737	0.614	0.871	0.737	0.614	0.871	SUBCLONAL	1	FALSE	0	0.483427473779257	1		466	149	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188232	10188233	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0062753-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	122	392	0	ENST00000256474.2:c.376dup	p.Asp126GlyfsTer6	p.D126Gfs*6	ENST00000256474	NM_000551.3	125	-/G	2/3	0.359365880381883	2	FACETS	1	0.986	1	0.717	0.656	0.78	CLONAL	1	FALSE	0	0.483427473779257	2		392	352	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436644	52436663	+	frameshift_variant	Frame_Shift_Del	DEL	GTGCAGATGAACTCATCGTA	GTGCAGATGAACTCATCGTA	-	novel	NA	P-0062753-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	79	621	0	ENST00000460680.1:c.2011_2030del	p.Tyr671LeufsTer39	p.Y671Lfs*39	ENST00000460680	NM_004656.3	671	TACGATGAGTTCATCTGCACc/c	16/17	0.359365880381883	2	FACETS	1	0.961	1	0.592	0.527	0.66	CLONAL	1	FALSE	0	0.483427473779257	2		621	276	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584479	187584480	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0062753-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	54	399	0	ENST00000441802.2:c.3553_3554del	p.Gly1185IlefsTer7	p.G1185Ifs*7	ENST00000441802	NM_005245.3	1185	GGa/a	3/27	0.145713975978426	0	FACETS	0.691	0.602	0.785			1	INDETERMINATE	1	FALSE	0	0.483427473779257	0		399	167	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2182220	2182220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062753-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	54	391	0	ENST00000349721.2:c.4439C>A	p.Thr1480Lys	p.T1480K	ENST00000349721	NM_003070.3	1480	aCg/aAg	31/34	1	2	FACETS	0.869	0.749	0.998	0.869	0.749	0.998	CLONAL	1	FALSE	1	0.483427473779257	2		391	257	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	19	915	1	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	0.091	0.068	0.118	0.091	0.068	0.118	SUBCLONAL	1	TRUE	1	0.446255240122078	2		916	933	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188218	10188218	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	161	361	0	ENST00000256474.2:c.361G>T	p.Asp121Tyr	p.D121Y	ENST00000256474	NM_000551.3	121	Gat/Tat	2/3	0.446255240122078	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.446255240122078	1		361	470	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871147	12871148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0062754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	199	654	0	ENST00000228872.4:c.375dup	p.Glu126Ter	p.E126*	ENST00000228872	NM_004064.3	125	tct/tcTt	1/3	1	2	FACETS	0.982	0.911	1	0.982	0.911	1	CLONAL	1	TRUE	1	0.446255240122078	2		654	908	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619280	37619280	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	218	696	0	ENST00000447079.4:c.956A>T	p.Tyr319Phe	p.Y319F	ENST00000447079	NM_015083.1	319	tAc/tTc	1/14	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.446255240122078	2		696	918	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250231	39250232	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATT	novel	NA	P-0062754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	111	163	0	ENST00000402219.2:c.1335_1337dup	p.Ile445dup	p.I445dup	ENST00000402219	NM_005633.3	445	atg/atAATg	10/23	0.125449546180101	4	FACETS	1	0.98	1	0.679	0.612	0.748	INDETERMINATE	1	TRUE	2	0.446255240122078	4		163	530	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525915	41525930	+	frameshift_variant	Frame_Shift_Del	DEL	GACAAATCATTTCACA	GACAAATCATTTCACA	-	novel	NA	P-0062754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	79	180	0	ENST00000263253.7:c.1190_1205del	p.Arg397ProfsTer29	p.R397Pfs*29	ENST00000263253	NM_001429.3	397	cGACAAATCATTTCACAc/cc	5/31	1	2	FACETS	0.827	0.731	0.93	0.827	0.731	0.93	CLONAL	1	TRUE	1	0.446255240122078	2		180	428	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610609	52610610	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0062754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	116	222	0	ENST00000394830.3:c.3563_3564del	p.Lys1188ArgfsTer6	p.K1188Rfs*6	ENST00000394830	NM_018313.4	1188	aAA/a	23/30	0.446255240122078	1	FACETS	0.944	0.857	1	0.944	0.857	1	CLONAL	1	TRUE	0	0.446255240122078	1		222	428	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	218483	218484	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0062754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	155	603	0	ENST00000264932.6:c.17dup	p.Leu7ProfsTer32	p.L7Pfs*32	ENST00000264932	NM_004168.2	5	cgg/cGgg	1/15	1	2	FACETS	0.937	0.86	1	0.937	0.86	1	CLONAL	1	TRUE	1	0.446255240122078	2		603	741	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618715	37618716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0062755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	26	787	1	ENST00000447079.4:c.397dup	p.Ser133LysfsTer24	p.S133Kfs*24	ENST00000447079	NM_015083.1	131	gaa/gAaa	1/14	1	2	FACETS	0.934	0.74	1	0.934	0.74	1	CLONAL	1	TRUE	1	0.15	2		788	371	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515369	149515369	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754766440	NA	P-0062755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	36	759	1	ENST00000261799.4:c.113C>T	p.Pro38Leu	p.P38L	ENST00000261799	NM_002609.3	38	cCg/cTg	3/23	1	2	FACETS	0.874	0.718	1	0.874	0.718	1	CLONAL	1	TRUE	1	0.15	2		760	549	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878081	48878112	+	frameshift_variant	Frame_Shift_Del	DEL	CACCGCCGCCGCTGCCGCCGCGGAACCCCCGG	CACCGCCGCCGCTGCCGCCGCGGAACCCCCGG	-	novel	NA	P-0062763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	240	690	0	ENST00000267163.4:c.45_76del	p.Ala17ProfsTer3	p.A17Pfs*3	ENST00000267163	NM_000321.2	11	gcCACCGCCGCCGCTGCCGCCGCGGAACCCCCGGca/gcca	1/27	0.595687394496839	5	FACETS	0.912	0.87	0.953			1	CLONAL	4	TRUE	NA	0.771331182827165	5		690	368	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727501	88727501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147992979	NA	P-0062763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	44	589	0	ENST00000360948.2:c.278C>T	p.Thr93Met	p.T93M	ENST00000360948	NM_001012338.2	93	aCg/aTg	3/19	1	2	FACETS	0.652	0.555	0.756	0.652	0.555	0.756	SUBCLONAL	1	TRUE	1	0.771331182827165	2		589	175	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265133	46265133	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	121	558	0	ENST00000371998.3:c.2003C>G	p.Ser668Cys	p.S668C	ENST00000371998		668	tCc/tGc	12/23	0.269198697607869	4	FACETS	0.914	0.838	0.991	0.914	0.838	0.991	INDETERMINATE	2	TRUE	2	0.771331182827165	4		558	304	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652571	48652571	+	stop_lost	Nonstop_Mutation	SNP	A	A	C	novel	NA	P-0062763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	23	552	0	ENST00000376670.3:c.1242A>C	p.Ter414CysextTer41	p.*414Cext*41	ENST00000376670	NM_002049.3	414	tgA/tgC	6/6	NA	2	FACETS	0.426	0.336	0.528			1	INDETERMINATE	1	TRUE	NA	0.771331182827165	2		552	140	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	19	190	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.877	0.67	1	0.877	0.67	1	CLONAL	1	TRUE	1	0.270912856062338	2		190	160	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	112	544	3	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.855	0.768	0.948	0.855	0.768	0.948	CLONAL	1	TRUE	1	0.270912856062338	2		547	967	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	119	555	2	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.887	0.8	0.98	0.887	0.8	0.98	CLONAL	1	TRUE	1	0.270912856062338	2		557	990	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981832	63981832	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	50	569	1	ENST00000398590.3:c.2340del	p.Thr781ProfsTer11	p.T781Pfs*11	ENST00000398590	NM_001177387.1	778	ggC/gg	12/14	1	2	FACETS	0.384	0.324	0.45	0.384	0.324	0.45	SUBCLONAL	1	TRUE	1	0.270912856062338	2		570	962	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515036	103515036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775996769	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	108	524	0	ENST00000355739.4:c.1537G>A	p.Ala513Thr	p.A513T	ENST00000355739	NM_000123.3	513	Gca/Aca	8/15	1	2	FACETS	0.968	0.868	1	0.968	0.868	1	CLONAL	1	TRUE	1	0.270912856062338	2		524	824	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	54	337	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.270912856062338	1	FACETS	0.751	0.642	0.869	0.751	0.642	0.869	SUBCLONAL	1	TRUE	0	0.270912856062338	1		337	459	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214604	5214604	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs116515629	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	125	545	0	ENST00000357368.4:c.4462G>A	p.Val1488Ile	p.V1488I	ENST00000357368	NM_002850.3	1488	Gtc/Atc	29/38	1	2	FACETS	0.988	0.893	1	0.988	0.893	1	CLONAL	1	TRUE	1	0.270912856062338	2		545	934	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921551	178921551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	34	290	0	ENST00000263967.3:c.1033A>G	p.Asn345Asp	p.N345D	ENST00000263967	NM_006218.2	345	Aat/Gat	5/21	1	2	FACETS	0.562	0.458	0.677	0.562	0.458	0.677	SUBCLONAL	1	TRUE	1	0.270912856062338	2		290	447	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	62	438	0	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	0.598	0.515	0.687	0.598	0.515	0.687	SUBCLONAL	1	TRUE	1	0.270912856062338	2		438	766	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135777085	135777085	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1331635112	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	72	308	0	ENST00000298552.3:c.2393C>T	p.Thr798Met	p.T798M	ENST00000298552	NM_001162426.1	798	aCg/aTg	19/23	1	2	FACETS	0.855	0.747	0.971	0.855	0.747	0.971	CLONAL	1	TRUE	1	0.270912856062338	2		308	622	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866321	42866321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766047137	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	136	566	0	ENST00000398585.3:c.311C>T	p.Thr104Met	p.T104M	ENST00000398585	NM_001135099.1	104	aCg/aTg	3/14	1	2	FACETS	0.999	0.907	1	0.999	0.907	1	CLONAL	1	TRUE	1	0.270912856062338	2		566	1005	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905055	50905055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	92	488	0	ENST00000440232.2:c.342del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	113	Ggg/gg	4/27	1	2	FACETS	0.891	0.792	0.998	0.891	0.792	0.998	CLONAL	1	TRUE	1	0.270912856062338	2		488	762	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905504	50905504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373192520	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	126	601	0	ENST00000440232.2:c.632G>A	p.Arg211His	p.R211H	ENST00000440232	NM_002691.3	211	cGc/cAc	6/27	1	2	FACETS	0.92	0.832	1	0.92	0.832	1	CLONAL	1	TRUE	1	0.270912856062338	2		601	1011	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007825	45007825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	100	430	0	ENST00000558401.1:c.276del	p.Thr93LeufsTer10	p.T93Lfs*10	ENST00000558401	NM_004048.2	91	aCc/ac	2/4	1	2	FACETS	0.846	0.754	0.943	0.846	0.754	0.943	CLONAL	1	TRUE	1	0.270912856062338	2		430	873	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198852	67198852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs185889430	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	131	423	0	ENST00000312629.5:c.323G>A	p.Arg108His	p.R108H	ENST00000312629	NM_003952.2	108	cGc/cAc	5/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.270912856062338	2		423	828	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799059	42799059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	123	545	0	ENST00000575354.2:c.4543C>T	p.Arg1515Cys	p.R1515C	ENST00000575354	NM_015125.3	1515	Cgc/Tgc	20/20	1	2	FACETS	0.987	0.892	1	0.987	0.892	1	CLONAL	1	TRUE	1	0.270912856062338	2		545	920	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508082	106508082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	85	484	0	ENST00000359195.3:c.76C>T	p.Arg26Cys	p.R26C	ENST00000359195	NM_002649.2	26	Cgc/Tgc	2/11	1	2	FACETS	0.81	0.715	0.911	0.81	0.715	0.911	CLONAL	1	TRUE	1	0.270912856062338	2		484	775	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442567	52442567	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1253151209	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	104	456	0	ENST00000460680.1:c.178C>T	p.Arg60Ter	p.R60*	ENST00000460680	NM_004656.3	60	Cga/Tga	4/17	1	2	FACETS	0.916	0.82	1	0.916	0.82	1	CLONAL	1	TRUE	1	0.270912856062338	2		456	838	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920404	114920404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	208	417	0	ENST00000543371.1:c.1345G>A	p.Ala449Thr	p.A449T	ENST00000543371	NM_001198531.1	449	Gca/Aca	13/14	0.234396358547674	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.270912856062338	2		417	729	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138111	2138111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139779505	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	115	639	0	ENST00000219476.3:c.5131G>A	p.Val1711Met	p.V1711M	ENST00000219476	NM_000548.3	1711	Gtg/Atg	40/42	1	2	FACETS	0.799	0.718	0.884	0.799	0.718	0.884	SUBCLONAL	1	TRUE	1	0.270912856062338	2		639	1063	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152566	56152566	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	122	483	0	ENST00000399503.3:c.622C>T	p.Arg208Ter	p.R208*	ENST00000399503	NM_005921.1	208	Cga/Tga	2/20	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.270912856062338	2		483	867	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281360	49281360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201503697	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	104	466	0	ENST00000282018.3:c.407G>A	p.Arg136His	p.R136H	ENST00000282018	NM_020377.2	136	cGt/cAt	1/1	1	2	FACETS	0.909	0.813	1	0.909	0.813	1	CLONAL	1	TRUE	1	0.270912856062338	2		466	845	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375316	15375316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200264318	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	104	496	0	ENST00000263377.2:c.1111G>A	p.Ala371Thr	p.A371T	ENST00000263377	NM_058243.2	371	Gcc/Acc	6/20	1	2	FACETS	0.862	0.771	0.959	0.862	0.771	0.959	CLONAL	1	TRUE	1	0.270912856062338	2		496	891	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492694	56492694	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	59	456	0	ENST00000407977.2:c.245T>C	p.Leu82Ser	p.L82S	ENST00000407977		82	tTa/tCa	2/10	1	2	FACETS	0.682	0.586	0.786	0.682	0.586	0.786	SUBCLONAL	1	TRUE	1	0.270912856062338	2		456	639	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007729	45007729	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	87	467	0	ENST00000558401.1:c.176T>G	p.Leu59Ter	p.L59*	ENST00000558401	NM_004048.2	59	tTa/tGa	2/4	1	2	FACETS	0.766	0.677	0.861	0.766	0.677	0.861	SUBCLONAL	1	TRUE	1	0.270912856062338	2		467	839	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242885	142242885	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1194388677	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	79	409	0	ENST00000350721.4:c.4102C>T	p.Arg1368Ter	p.R1368*	ENST00000350721	NM_001184.3	1368	Cga/Tga	22/47	1	2	FACETS	0.842	0.74	0.951	0.842	0.74	0.951	CLONAL	1	TRUE	1	0.270912856062338	2		409	693	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249994	39249994	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	68	373	0	ENST00000402219.2:c.1575A>G	p.Ile525Met	p.I525M	ENST00000402219	NM_005633.3	525	atA/atG	10/23	1	2	FACETS	0.776	0.675	0.885	0.776	0.675	0.885	SUBCLONAL	1	TRUE	1	0.270912856062338	2		373	647	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741906	40741906	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568518786	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	125	602	0	ENST00000392038.2:c.1066G>A	p.Glu356Lys	p.E356K	ENST00000392038	NM_001626.4	356	Gag/Aag	11/14	1	2	FACETS	0.982	0.888	1	0.982	0.888	1	CLONAL	1	TRUE	1	0.270912856062338	2		602	940	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257169	19257169	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	95	377	0	ENST00000162023.5:c.794C>A	p.Pro265Gln	p.P265Q	ENST00000162023		265	cCg/cAg	12/13	1	2	FACETS	0.892	0.794	0.997	0.892	0.794	0.997	CLONAL	1	TRUE	1	0.270912856062338	2		377	786	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651187	45651187	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs749300015	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	113	523	0	ENST00000407780.3:c.838C>T	p.Arg280Ter	p.R280*	ENST00000407780	NM_001283052.1	280	Cga/Tga	5/7	1	2	FACETS	0.954	0.858	1	0.954	0.858	1	CLONAL	1	TRUE	1	0.270912856062338	2		523	874	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932702	39932702	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	107	586	0	ENST00000378444.4:c.1897C>A	p.Leu633Ile	p.L633I	ENST00000378444	NM_001123385.1	633	Ctt/Att	4/15	1	2	FACETS	0.859	0.769	0.954	0.859	0.769	0.954	CLONAL	1	TRUE	1	0.270912856062338	2		586	920	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741184	40741184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781260194	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	107	478	1	ENST00000392038.2:c.1249G>A	p.Val417Met	p.V417M	ENST00000392038	NM_001626.4	417	Gtg/Atg	12/14	1	2	FACETS	0.999	0.896	1	0.999	0.896	1	CLONAL	1	TRUE	1	0.270912856062338	2		479	791	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228789	36228789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	125	614	0	ENST00000222270.7:c.7688C>T	p.Ala2563Val	p.A2563V	ENST00000222270	NM_014727.1	2563	gCc/gTc	35/37	1	2	FACETS	0.873	0.789	0.962	0.873	0.789	0.962	CLONAL	1	TRUE	1	0.270912856062338	2		614	1057	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794779	120794779	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768324684	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	136	519	0	ENST00000257552.2:c.578C>T	p.Thr193Met	p.T193M	ENST00000257552	NM_002442.3	193	aCg/aTg	9/15	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.270912856062338	2		519	918	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615776	1615776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs182482393	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	137	506	0	ENST00000344749.5:c.1495C>T	p.Arg499Trp	p.R499W	ENST00000344749	NM_001136139.2	499	Cgg/Tgg	17/19	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.270912856062338	2		506	930	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	43	237	0	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	0.718	0.601	0.847	0.718	0.601	0.847	SUBCLONAL	1	TRUE	1	0.270912856062338	2		237	442	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21348931	21348931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372417941	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	52	580	1	ENST00000215739.8:c.1700G>A	p.Arg567His	p.R567H	ENST00000215739	NM_006767.3	567	cGc/cAc	15/21	1	2	FACETS	0.381	0.323	0.445	0.381	0.323	0.445	SUBCLONAL	1	TRUE	1	0.270912856062338	2		581	1008	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205092	38205092	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	38	402	2	ENST00000317025.8:c.598del	p.Ser200AlafsTer20	p.S200Afs*20	ENST00000317025	NM_023034.1	200	Agc/gc	2/24	1	2	FACETS	0.535	0.442	0.64	0.535	0.442	0.64	SUBCLONAL	1	TRUE	1	0.270912856062338	2		404	524	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533881	533881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs727503093	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	118	550	1	ENST00000451590.1:c.175G>A	p.Ala59Thr	p.A59T	ENST00000451590	NM_001130442.1	59	Gcc/Acc	3/5	1	2	FACETS	0.847	0.763	0.937	0.847	0.763	0.937	CLONAL	1	TRUE	1	0.270912856062338	2		551	1028	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005279	29005279	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	38	331	0	ENST00000282397.4:c.982A>G	p.Ile328Val	p.I328V	ENST00000282397	NM_002019.4	328	Ata/Gta	7/30	1	2	FACETS	0.543	0.448	0.649	0.543	0.448	0.649	SUBCLONAL	1	TRUE	1	0.270912856062338	2		331	517	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2214004	2214004	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	89	562	0	ENST00000326181.6:c.81+2T>C		p.X27_splice	ENST00000326181	NM_032271.2	27			1	2	FACETS	0.68	0.602	0.764	0.68	0.602	0.764	SUBCLONAL	1	TRUE	1	0.270912856062338	2		562	966	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89871769	89871769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	84	396	0	ENST00000389301.3:c.628C>T	p.Leu210Phe	p.L210F	ENST00000389301	NM_000135.2	210	Ctc/Ttc	7/43	1	2	FACETS	0.737	0.65	0.831	0.737	0.65	0.831	SUBCLONAL	1	TRUE	1	0.270912856062338	2		396	841	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650949	37650949	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	58	365	0	ENST00000447079.4:c.2419+2T>C		p.X807_splice	ENST00000447079	NM_015083.1	807			1	2	FACETS	0.632	0.542	0.73	0.632	0.542	0.73	SUBCLONAL	1	TRUE	1	0.270912856062338	2		365	678	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6213772	6213772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758763739	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	102	476	2	ENST00000252674.7:c.1444C>T	p.Pro482Ser	p.P482S	ENST00000252674	NM_005934.3	482	Cct/Tct	10/12	1	2	FACETS	0.861	0.769	0.958	0.861	0.769	0.958	CLONAL	1	TRUE	1	0.270912856062338	2		478	875	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252756	10252756	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	76	487	0	ENST00000340748.4:c.3209A>G	p.Glu1070Gly	p.E1070G	ENST00000340748		1070	gAg/gGg	29/40	1	2	FACETS	0.602	0.527	0.683	0.602	0.527	0.683	SUBCLONAL	1	TRUE	1	0.270912856062338	2		487	932	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375046	31375046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1457500486	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	91	483	0	ENST00000328111.2:c.443G>A	p.Arg148Gln	p.R148Q	ENST00000328111	NM_006892.3	148	cGg/cAg	6/23	1	2	FACETS	0.814	0.722	0.913	0.814	0.722	0.913	CLONAL	1	TRUE	1	0.270912856062338	2		483	825	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164776	36164776	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	136	658	0	ENST00000300305.3:c.1099G>A	p.Gly367Ser	p.G367S	ENST00000300305		367	Ggc/Agc	8/8	1	2	FACETS	0.966	0.877	1	0.966	0.877	1	CLONAL	1	TRUE	1	0.270912856062338	2		658	1039	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383900	84383900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775345294	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	46	411	0	ENST00000321945.7:c.952G>A	p.Asp318Asn	p.D318N	ENST00000321945	NM_139076.2	318	Gat/Aat	9/9	1	2	FACETS	0.593	0.498	0.697	0.593	0.498	0.697	SUBCLONAL	1	TRUE	1	0.270912856062338	2		411	573	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31238245	31238245	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	26	262	0	ENST00000376228.5:c.637G>T	p.Val213Leu	p.V213L	ENST00000376228	NM_002117.5	213	Gtg/Ttg	4/8	0.235912973229637	2	FACETS	0.37	0.292	0.46	0.185	0.146	0.23	SUBCLONAL	1	TRUE	0	0.270912856062338	2		262	519	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411460	63411460	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	125	587	0	ENST00000330258.3:c.1707G>T	p.Leu569Phe	p.L569F	ENST00000330258	NM_152424.3	569	ttG/ttT	2/2	1	2	FACETS	0.972	0.879	1	0.972	0.879	1	CLONAL	1	TRUE	1	0.270912856062338	2		587	949	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360685	70360685	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	123	495	0	ENST00000374080.3:c.6245A>G	p.Gln2082Arg	p.Q2082R	ENST00000374080		2082	cAg/cGg	42/45	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.270912856062338	2		495	890	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760096	133760096	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062768-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	29	404	0	ENST00000318560.5:c.2419G>T	p.Gly807Cys	p.G807C	ENST00000318560	NM_005157.4	807	Ggc/Tgc	11/11	1	2	FACETS	0.209	0.167	0.256	0.209	0.167	0.256	SUBCLONAL	1	TRUE	1	0.796253161731437	2		404	349	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0062778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	12	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.243702099400461	3	FACETS	0.146	0.102	0.202	0.073	0.051	0.101	INDETERMINATE	1	TRUE	1	0.4167777052443	3		434	475	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579395	7579395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	253	663	0	ENST00000269305.4:c.292C>T	p.Pro98Ser	p.P98S	ENST00000269305	NM_001126112.2	98	Cct/Tct	4/11	0.354879823876928	2	FACETS	0.806	0.758	0.856	0.806	0.758	0.856	CLONAL	2	TRUE	0	0.4167777052443	2		663	753	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604699	48604699	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	160	548	0	ENST00000342988.3:c.1521A>T	p.Lys507Asn	p.K507N	ENST00000342988	NM_005359.5	507	aaA/aaT	12/12	0.353362821570125	2	FACETS	1	0.987	1	0.681	0.627	0.736	CLONAL	1	TRUE	0	0.4167777052443	2		548	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577592	7577592	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	171	523	0	ENST00000269305.4:c.689C>T	p.Thr230Ile	p.T230I	ENST00000269305	NM_001126112.2	230	aCc/aTc	7/11	0.354879823876928	2	FACETS	0.784	0.727	0.844	0.784	0.727	0.844	SUBCLONAL	2	TRUE	0	0.4167777052443	2		523	523	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977855	134977855	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1354688627	NA	P-0062778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	68	419	0	ENST00000398015.3:c.2848G>A	p.Asp950Asn	p.D950N	ENST00000398015	NM_004441.4	950	Gac/Aac	16/16	0.243702099400461	3	FACETS	0.867	0.756	0.985	0.433	0.378	0.493	INDETERMINATE	1	TRUE	1	0.4167777052443	3		419	455	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230468758	230468758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748504542	NA	P-0062778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	321	626	0	ENST00000391860.1:c.760C>T	p.Arg254Trp	p.R254W	ENST00000391860	NM_001258311.1	254	Cgg/Tgg	5/7	0.4167777052443	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.4167777052443	3		626	794	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432767	49432767	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	75	548	0	ENST00000301067.7:c.8372T>C	p.Leu2791Pro	p.L2791P	ENST00000301067	NM_003482.3	2791	cTg/cCg	34/54	0.4167777052443	3	FACETS	0.625	0.547	0.709	0.312	0.273	0.355	SUBCLONAL	1	TRUE	1	0.4167777052443	3		548	696	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793303	33793304	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAGTC	novel	NA	P-0062778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	161	435	0	ENST00000498907.2:c.13_17dup	p.Phe6LeufsTer12	p.F6Lfs*12	ENST00000498907	NM_004364.3	6	ttc/ttGACTTc	1/1	0.4167777052443	5	FACETS	1	0.988	1	0.488	0.448	0.531	CLONAL	1	TRUE	2	0.4167777052443	5		435	857	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578207	7578207	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062780-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	298	570	0	ENST00000269305.4:c.642del	p.His214GlnfsTer33	p.H214Qfs*33	ENST00000269305	NM_001126112.2	214	caT/ca	6/11	0.792539338471523	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	0	0.792539338471523	1		570	419	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589599	67589604	+	inframe_deletion	In_Frame_Del	DEL	TCAGTT	TCAGTT	-	novel	NA	P-0062782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	18	182	0	ENST00000274335.5:c.1365_1370del	p.Phe456_Gln457del	p.F456_Q457del	ENST00000274335		454	acTCAGTTt/act	10/15	1	2	FACETS	0.777	0.595	0.985	0.777	0.595	0.985	CLONAL	1	TRUE	1	0.47257619883477	2		182	98	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630626	158630626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912678	NA	P-0062782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	78	466	0	ENST00000263640.3:c.617G>A	p.Arg206His	p.R206H	ENST00000263640	NM_001105.4	206	cGc/cAc	6/11	1	2	FACETS	0.768	0.678	0.864	0.768	0.678	0.864	SUBCLONAL	1	TRUE	1	0.47257619883477	2		466	430	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720858	89720858	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1564568660	NA	P-0062782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	70	116	0	ENST00000371953.3:c.1012del	p.Ser338LeufsTer6	p.S338Lfs*6	ENST00000371953	NM_000314.4	337	Ttt/tt	8/9	0.445628353397877	3	FACETS	0.918	0.828	1	0.918	0.828	1	CLONAL	3	TRUE	0	0.47257619883477	3		116	133	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057848	27057848	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	171	739	0	ENST00000324856.7:c.1558del	p.Gln520SerfsTer99	p.Q520Sfs*99	ENST00000324856	NM_006015.4	519	tCc/tc	3/20	1	2	FACETS	0.898	0.827	0.972	0.898	0.827	0.972	CLONAL	1	TRUE	1	0.47257619883477	2		739	806	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247569	123247569	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519047	NA	P-0062782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	288	379	0	ENST00000358487.5:c.1922A>G	p.Lys641Arg	p.K641R	ENST00000358487	NM_000141.4	641	aAa/aGa	14/18	0.445628353397877	3	FACETS	0.902	0.858	0.946	0.902	0.858	0.946	CLONAL	3	TRUE	0	0.47257619883477	3		379	557	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087891	27087912	+	frameshift_variant	Frame_Shift_Del	DEL	TCGGCCACCCAGTGGCCAGTCG	TCGGCCACCCAGTGGCCAGTCG	-	novel	NA	P-0062782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	75	544	0	ENST00000324856.7:c.2178_2199del	p.Arg727ThrfsTer8	p.R727Tfs*8	ENST00000324856	NM_006015.4	726	ccTCGGCCACCCAGTGGCCAGTCG/cc	6/20	1	2	FACETS	0.546	0.479	0.619	0.546	0.479	0.619	SUBCLONAL	1	TRUE	1	0.47257619883477	2		544	581	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0062783-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	26	462	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.709	0.562	0.876	0.709	0.562	0.876	SUBCLONAL	1	TRUE	1	0.238930392667192	2		462	307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0062784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	406	809	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.753483688341599	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.753483688341599	2		809	504	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0062784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	346	488	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.753483688341599	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.753483688341599	2		488	441	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0062784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	293	597	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.739960179096352	4	FACETS	0.958	0.907	1	0.958	0.907	1	CLONAL	2	TRUE	2	0.753483688341599	4		597	712	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0062784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	167	446	1	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.497571014572299	3	FACETS	0.954	0.893	1	0.954	0.893	1	CLONAL	2	TRUE	1	0.753483688341599	3		447	320	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733279	40733279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201275244	NA	P-0062784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	363	590	0	ENST00000373198.4:c.3527G>A	p.Arg1176His	p.R1176H	ENST00000373198	NM_133170.3	1176	cGt/cAt	26/32	0.571863662706773	6	FACETS	1	0.979	1			1	CLONAL	2	TRUE	NA	0.753483688341599	6		590	1139	SUCCESS
APC	324	MSKCC	GRCh37	5	112163696	112163697	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1131691555	NA	P-0062784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	192	297	0	ENST00000257430.4:c.1620dup	p.Gln541ThrfsTer19	p.Q541Tfs*19	ENST00000257430	NM_000038.5	540	tta/ttAa	13/16	0.739960179096352	4	FACETS	0.868	0.809	0.927	0.868	0.809	0.927	CLONAL	2	TRUE	2	0.753483688341599	4		297	515	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739761	41739762	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCT	novel	NA	P-0062784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	266	593	0	ENST00000242208.4:c.209_211dup	p.Lys70dup	p.K70dup	ENST00000242208	NM_002192.2	70	aga/aAGAga	2/3	0.672260335574979	4	FACETS	0.777	0.731	0.823	0.777	0.731	0.823	SUBCLONAL	2	TRUE	2	0.753483688341599	4		593	797	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099989	27099989	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0062786-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	83	760	0	ENST00000324856.7:c.3866+2T>C		p.X1289_splice	ENST00000324856	NM_006015.4	1289			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		760	1206	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847381	68847407	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTTTGAAAACAGCAAAGGTTTGTATG	ATTTTGAAAACAGCAAAGGTTTGTATG	-	novel	NA	P-0062786-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	40	459	0	ENST00000261769.5:c.1303_1320+9del		p.X435_splice	ENST00000261769	NM_004360.3	435		9/16	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		459	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0062787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	195	776	1	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.268141905843163	3	FACETS	0.821	0.76	0.885	0.821	0.76	0.885	CLONAL	2	TRUE	1	0.268141905843163	3		777	1004	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928060	178928086	+	inframe_deletion	In_Frame_Del	DEL	GCCAGTACCTCATGGATTAGAAGATTT	GCCAGTACCTCATGGATTAGAAGATTT	-	novel	NA	P-0062787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	16	439	0	ENST00000263967.3:c.1340_1366del	p.Pro447_Leu455del	p.P447_L455del	ENST00000263967	NM_006218.2	446	tgGCCAGTACCTCATGGATTAGAAGATTTg/tgg	8/21	0.253864169058163	3	FACETS	0.231	0.17	0.305	0.115	0.085	0.153	SUBCLONAL	1	TRUE	1	0.268141905843163	3		439	586	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740824	145740824	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	85	698	0	ENST00000428558.2:c.1276G>C	p.Asp426His	p.D426H	ENST00000428558	NM_004260.3	426	Gat/Cat	7/22	0.253864169058163	3	FACETS	0.72	0.635	0.812	0.36	0.317	0.406	SUBCLONAL	1	TRUE	1	0.268141905843163	3		698	998	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992158	11992165	+	frameshift_variant	Frame_Shift_Del	DEL	ACAGCAAC	ACAGCAAC	-	novel	NA	P-0062787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	40	535	0	ENST00000396373.4:c.250_257del	p.Ser84ValfsTer2	p.S84Vfs*2	ENST00000396373	NM_001987.4	83	gACAGCAAC/g	3/8	0.0623328022833101	3	FACETS	0.427	0.353	0.509	0.213	0.176	0.255	INDETERMINATE	1	TRUE	1	0.268141905843163	3		535	793	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267845	46267845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	45	509	0	ENST00000371998.3:c.2606C>T	p.Pro869Leu	p.P869L	ENST00000371998		869	cCa/cTa	14/23	0.135503309763755	3	FACETS	0.478	0.4	0.564	0.239	0.2	0.282	INDETERMINATE	1	TRUE	1	0.268141905843163	3		509	797	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878118	151878118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1445885320	NA	P-0062787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	178	709	0	ENST00000262189.6:c.6827C>T	p.Pro2276Leu	p.P2276L	ENST00000262189	NM_170606.2	2276	cCt/cTt	36/59	0.253864169058163	3	FACETS	1	0.989	1	0.75	0.691	0.812	CLONAL	1	TRUE	1	0.268141905843163	3		709	1004	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945496	151945496	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	32	401	0	ENST00000262189.6:c.2023A>T	p.Thr675Ser	p.T675S	ENST00000262189	NM_170606.2	675	Aca/Tca	14/59	0.253864169058163	3	FACETS	0.447	0.361	0.543	0.223	0.18	0.272	SUBCLONAL	1	TRUE	1	0.268141905843163	3		401	606	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0062788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	62	387	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.135178014828717	2	FACETS	0.82	0.711	0.937	0.82	0.711	0.937	CLONAL	2	TRUE	0	0.188194306289181	2		387	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579419	7579420	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs587783062	NA	P-0062788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	68	730	0	ENST00000269305.4:c.267dup	p.Ser90LeufsTer59	p.S90Lfs*59	ENST00000269305	NM_001126112.2	89	-/C	4/11	0.135178014828717	2	FACETS	0.958	0.833	1	0.479	0.416	0.548	CLONAL	1	TRUE	0	0.188194306289181	2		730	754	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891137	101891137	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1554698880	NA	P-0062788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	40	323	0	ENST00000374994.4:c.98C>T	p.Ala33Val	p.A33V	ENST00000374994	NM_004612.2	33	gCg/gTg	2/9	0.188194306289181	1	FACETS	0.784	0.651	0.932	0.784	0.651	0.932	CLONAL	1	TRUE	0	0.188194306289181	1		323	491	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0062789-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	156	387	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.73669209423293	2		387	422	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0062789-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	371	462	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.70568827841228	3	FACETS	0.938	0.908	0.966	0.938	0.908	0.966	CLONAL	3	TRUE	0	0.73669209423293	3		462	490	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120031	70120031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062789-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	280	791	3	ENST00000245479.2:c.1037del	p.Pro346ArgfsTer37	p.P346Rfs*37	ENST00000245479	NM_000346.3	345	Ccc/cc	3/3	1	2	FACETS	0.982	0.927	1	0.982	0.927	1	CLONAL	1	TRUE	1	0.73669209423293	2		794	774	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103346	2103346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777459404	NA	P-0062789-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	43	515	0	ENST00000219476.3:c.229G>A	p.Ala77Thr	p.A77T	ENST00000219476	NM_000548.3	77	Gca/Aca	4/42	1	2	FACETS	0.197	0.164	0.233	0.197	0.164	0.233	SUBCLONAL	1	TRUE	1	0.73669209423293	2		515	594	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216397	2216397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1386157480	NA	P-0062789-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	349	887	0	ENST00000398665.3:c.2041C>T	p.Arg681Cys	p.R681C	ENST00000398665	NM_032482.2	681	Cgc/Tgc	20/28	1	2	FACETS	0.971	0.922	1	0.971	0.922	1	CLONAL	1	TRUE	1	0.73669209423293	2		887	976	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062789-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	140	363	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.73669209423293	2		363	379	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106465	27106465	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062789-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	423	821	0	ENST00000324856.7:c.6076C>T	p.Gln2026Ter	p.Q2026*	ENST00000324856	NM_006015.4	2026	Cag/Tag	20/20	1	2	FACETS	0.945	0.901	0.99	0.945	0.901	0.99	CLONAL	1	TRUE	1	0.73669209423293	2		821	1215	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968829	15968829	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062789-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	291	643	0	ENST00000268712.3:c.4921C>T	p.Pro1641Ser	p.P1641S	ENST00000268712	NM_006311.3	1641	Cca/Tca	33/46	1	2	FACETS	0.934	0.882	0.987	0.934	0.882	0.987	CLONAL	1	TRUE	1	0.73669209423293	2		643	846	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466018	69466018	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062789-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	384	890	0	ENST00000227507.2:c.856A>G	p.Thr286Ala	p.T286A	ENST00000227507	NM_053056.2	286	Aca/Gca	5/5	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.73669209423293	2		890	1037	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2492097	2492097	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs772088410	NA	P-0062789-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	183	745	0	ENST00000355716.4:c.500del	p.Pro167ArgfsTer23	p.P167Rfs*23	ENST00000355716	NM_003820.2	165	tgC/tg	5/8	1	2	FACETS	0.587	0.542	0.633	0.587	0.542	0.633	SUBCLONAL	1	TRUE	1	0.73669209423293	2		745	847	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250162	39250162	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062789-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	212	538	0	ENST00000402219.2:c.1407T>G	p.Ile469Met	p.I469M	ENST00000402219	NM_005633.3	469	atT/atG	10/23	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.73669209423293	2		538	533	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216189	36216189	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062789-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	53	884	0	ENST00000222270.7:c.3602del	p.Pro1201ArgfsTer154	p.P1201Rfs*154	ENST00000222270	NM_014727.1	1199	ggC/gg	11/37	1	2	FACETS	0.147	0.125	0.172	0.147	0.125	0.172	SUBCLONAL	1	TRUE	1	0.73669209423293	2		884	976	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856434	111856434	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs776317487	NA	P-0062789-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	346	884	5	ENST00000341259.2:c.489del	p.Thr165ProfsTer32	p.T165Pfs*32	ENST00000341259	NM_005475.2	162	gCc/gc	2/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.73669209423293	2		889	883	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143552	108143552	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769857066	NA	P-0062789-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	99	475	0	ENST00000278616.4:c.3257G>A	p.Arg1086His	p.R1086H	ENST00000278616	NM_000051.3	1086	cGc/cAc	22/63	1	2	FACETS	0.629	0.565	0.697	0.629	0.565	0.697	SUBCLONAL	1	TRUE	1	0.73669209423293	2		475	427	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442816	442816	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0062789-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	291	606	0	ENST00000399788.2:c.1491-1G>A		p.X497_splice	ENST00000399788	NM_001042603.1	497			1	2	FACETS	0.999	0.944	1	0.999	0.944	1	CLONAL	1	TRUE	1	0.73669209423293	2		606	791	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023305	27023306	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0062789-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	210	652	0	ENST00000324856.7:c.412_413del	p.Ala139ArgfsTer260	p.A139Rfs*260	ENST00000324856	NM_006015.4	137	caCTca/caca	1/20	1	2	FACETS	0.905	0.845	0.966	0.905	0.845	0.966	CLONAL	1	TRUE	1	0.73669209423293	2		652	630	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10794726	10794726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1397467879	NA	P-0062789-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	142	604	2	ENST00000361367.2:c.2633G>A	p.Arg878Gln	p.R878Q	ENST00000361367	NM_014633.3	878	cGg/cAg	21/25	1	2	FACETS	0.674	0.617	0.733	0.674	0.617	0.733	SUBCLONAL	1	TRUE	1	0.73669209423293	2		606	572	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465988	69465990	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs753296543	NA	P-0062789-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	321	983	10	ENST00000227507.2:c.839_841del	p.Glu280del	p.E280del	ENST00000227507	NM_053056.2	276	GAG/-	5/5	1	2	FACETS	0.8	0.756	0.845	0.8	0.756	0.845	SUBCLONAL	1	TRUE	1	0.73669209423293	2		993	1089	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350003	89350003	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062789-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	87	878	2	ENST00000301030.4:c.2947A>G	p.Ser983Gly	p.S983G	ENST00000301030	NM_001256183.1	983	Agt/Ggt	9/13	1	2	FACETS	0.196	0.172	0.221	0.196	0.172	0.221	SUBCLONAL	1	TRUE	1	0.73669209423293	2		880	1208	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097625	11097625	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062789-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	308	806	0	ENST00000358026.2:c.810del	p.Met272CysfsTer31	p.M272Cfs*31	ENST00000358026	NM_001128849.1	269	Ccc/cc	5/36	1	2	FACETS	0.864	0.816	0.913	0.864	0.816	0.913	CLONAL	1	TRUE	1	0.73669209423293	2		806	968	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098425	11098425	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062789-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	325	702	1	ENST00000358026.2:c.947del	p.Pro316LeufsTer10	p.P316Lfs*10	ENST00000358026	NM_001128849.1	315	Ccc/cc	6/36	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.73669209423293	2		703	849	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162312	47162312	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062789-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	302	785	0	ENST00000409792.3:c.3814C>A	p.Gln1272Lys	p.Q1272K	ENST00000409792	NM_014159.6	1272	Cag/Aag	3/21	1	2	FACETS	0.863	0.815	0.912	0.863	0.815	0.912	CLONAL	1	TRUE	1	0.73669209423293	2		785	950	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589585	67589587	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	novel	NA	P-0062789-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	44	295	0	ENST00000274335.5:c.1348_1350del	p.His450del	p.H450del	ENST00000274335		450	CAT/-	10/15	1	2	FACETS	0.866	0.742	0.996	0.866	0.742	0.996	CLONAL	1	TRUE	1	0.73669209423293	2		295	138	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917782	29917782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56077855	NA	P-0062792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	197	712	1	ENST00000389048.3:c.886G>A	p.Glu296Lys	p.E296K	ENST00000389048	NM_004304.4	296	Gag/Aag	3/29	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.554402370876641	2		713	688	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041182	47041182	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	32	377	0	ENST00000377604.3:c.1610C>T	p.Ser537Phe	p.S537F	ENST00000377604	NM_001204468.1	537	tCt/tTt	15/24	0.537383260043805	2	FACETS	0.19	0.153	0.231			1	SUBCLONAL	1	TRUE	NA	0.554402370876641	2		377	609	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0062793-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	132	711	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.773242845634159	2		711	270	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833925	44833925	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062793-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3	73	123	0	ENST00000377967.4:c.349C>T	p.Gln117Ter	p.Q117*	ENST00000377967	NM_021140.2	117	Cag/Tag	4/29	1	1	FACETS		NA	1	1	0.989	1	NA	2	TRUE	0	0.773242845634159	1		123	76	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41558784	41558784	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0062793-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	0	232	330	0	ENST00000263253.7:c.3728+1G>T		p.X1243_splice	ENST00000263253	NM_001429.3	1243			0.773242845634159	2	FACETS		NA	1	1	0.997	1	NA	3	TRUE	0	0.773242845634159	2		330	232	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175870	24175871	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0062793-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	21	625	0	ENST00000263121.7:c.1099dup	p.Asp367GlyfsTer78	p.D367Gfs*78	ENST00000263121	NM_003073.3	366	-/G	8/9	1	2	FACETS	0.169	0.129	0.214	0.169	0.129	0.214	SUBCLONAL	1	TRUE	1	0.773242845634159	2		625	322	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160488	108160488	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730881369	NA	P-0062793-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	91	333	0	ENST00000278616.4:c.4396C>G	p.Arg1466Gly	p.R1466G	ENST00000278616	NM_000051.3	1466	Cga/Gga	29/63	1	2	FACETS	0.916	0.826	1	0.916	0.826	1	CLONAL	1	TRUE	1	0.773242845634159	2		333	257	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426673	49426673	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062793-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	167	911	1	ENST00000301067.7:c.11815C>T	p.Gln3939Ter	p.Q3939*	ENST00000301067	NM_003482.3	3939	Cag/Tag	39/54	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.773242845634159	2		912	418	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200942	108200942	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1565529213	NA	P-0062793-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	118	420	0	ENST00000278616.4:c.7309T>C	p.Tyr2437His	p.Y2437H	ENST00000278616	NM_000051.3	2437	Tac/Cac	50/63	1	2	FACETS	0.957	0.875	1	0.957	0.875	1	CLONAL	1	TRUE	1	0.773242845634159	2		420	319	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441785	49441785	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062793-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	138	564	0	ENST00000301067.7:c.4199G>T	p.Cys1400Phe	p.C1400F	ENST00000301067	NM_003482.3	1400	tGc/tTc	14/54	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.773242845634159	2		564	302	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138575	11138575	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062793-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	170	598	0	ENST00000358026.2:c.3331A>G	p.Ile1111Val	p.I1111V	ENST00000358026	NM_001128849.1	1111	Atc/Gtc	24/36	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.773242845634159	2		598	373	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021715	31021715	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062793-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	161	583	0	ENST00000375687.4:c.1714del	p.Ile572SerfsTer131	p.I572Sfs*131	ENST00000375687	NM_015338.5	572	Atc/tc	12/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.773242845634159	2		583	341	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877145	151877146	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0062793-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	129	580	0	ENST00000262189.6:c.7215_7216del	p.Lys2406GlyfsTer23	p.K2406Gfs*23	ENST00000262189	NM_170606.2	2405	gaGAag/gaag	37/59	1	2	FACETS	0.914	0.838	0.992	0.914	0.838	0.992	CLONAL	1	TRUE	1	0.773242845634159	2		580	365	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044976	47044976	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062793-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	25	429	0	ENST00000377604.3:c.2302T>A	p.Phe768Ile	p.F768I	ENST00000377604	NM_001204468.1	768	Ttc/Atc	20/24	1	1	FACETS	0.264	0.21	0.325	0.264	0.21	0.325	SUBCLONAL	1	TRUE	0	0.773242845634159	1		429	150	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855976	76855976	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062793-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	20	240	0	ENST00000373344.5:c.5624A>G	p.Asp1875Gly	p.D1875G	ENST00000373344	NM_000489.3	1875	gAt/gGt	23/35	1	1	FACETS	0.188	0.144	0.238	0.188	0.144	0.238	SUBCLONAL	1	TRUE	0	0.773242845634159	1		240	169	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0062794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	236	809	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.530248570956765	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.530248570956765	1		809	624	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251754	212251754	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	188	697	0	ENST00000342788.4:c.3305T>G	p.Phe1102Cys	p.F1102C	ENST00000342788	NM_005235.2	1102	tTt/tGt	27/28	1	2	FACETS	0.915	0.847	0.985	0.915	0.847	0.985	CLONAL	1	TRUE	1	0.530248570956765	2		697	775	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793483	18793483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603405	NA	P-0062794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	94	372	0	ENST00000266497.5:c.4180G>A	p.Glu1394Lys	p.E1394K	ENST00000266497		1394	Gaa/Aaa	30/31	0.518242606871859	2	FACETS	1	0.934	1	0.526	0.472	0.582	CLONAL	1	TRUE	0	0.530248570956765	2		372	337	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357501	89357501	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779404022	NA	P-0062794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	249	730	0	ENST00000301030.4:c.317G>A	p.Arg106Gln	p.R106Q	ENST00000301030	NM_001256183.1	106	cGa/cAa	5/13	0.530248570956765	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.530248570956765	1		730	626	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891678	28891678	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776861138	NA	P-0062794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	187	507	0	ENST00000282397.4:c.3343G>A	p.Glu1115Lys	p.E1115K	ENST00000282397	NM_002019.4	1115	Gaa/Aaa	25/30	0.510968077952763	3	FACETS	1	0.934	1	0.505	0.467	0.545	CLONAL	1	TRUE	1	0.530248570956765	3		507	883	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804286	43804286	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	260	768	0	ENST00000372470.3:c.286C>A	p.Pro96Thr	p.P96T	ENST00000372470	NM_005373.2	96	Cca/Aca	3/12	0.530248570956765	2	FACETS	1	0.983	1	0.562	0.527	0.597	CLONAL	1	TRUE	0	0.530248570956765	2		768	873	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122667	108122667	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	125	439	0	ENST00000278616.4:c.1711T>C	p.Ser571Pro	p.S571P	ENST00000278616	NM_000051.3	571	Tct/Cct	11/63	0.530248570956765	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.530248570956765	1		439	317	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90627572	90627572	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	459	623	0	ENST00000330062.3:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000330062	NM_002168.2	429	Gag/Tag	11/11	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.530248570956765	2		623	800	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564139	139564139	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	211	586	0	ENST00000308874.7:c.279G>T	p.Lys93Asn	p.K93N	ENST00000308874		93	aaG/aaT	5/10	0.530248570956765	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.530248570956765	1		586	570	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350005	70350005	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	207	346	0	ENST00000374080.3:c.3988C>G	p.Leu1330Val	p.L1330V	ENST00000374080		1330	Ctg/Gtg	28/45	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.530248570956765	1		346	419	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20487030	20487030	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs983370060	NA	P-0062795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	81	397	0	ENST00000346618.3:c.995T>C	p.Ile332Thr	p.I332T	ENST00000346618	NM_001949.4	332	aTa/aCa	5/7	1	2	FACETS	0.936	0.841	1	1	0.989	1	CLONAL	4	FALSE	1	0.206007544797107	2		397	210	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772950	135772951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs118203724	NA	P-0062796-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	51	423	0	ENST00000298552.3:c.2672dup	p.Asn891LysfsTer13	p.N891Kfs*13	ENST00000298552	NM_001162426.1	891	aac/aaAc	21/23	0.67005071758793	1	FACETS	0.589	0.509	0.672	0.589	0.509	0.672	SUBCLONAL	1	TRUE	0	0.67005071758793	1		423	172	SUCCESS
ALB	213	MSKCC	GRCh37	4	74272395	74272395	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062796-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	111	356	0	ENST00000295897.4:c.187del	p.His63MetfsTer2	p.H63Mfs*2	ENST00000295897	NM_000477.5	63	Cat/at	3/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.67005071758793	2		356	230	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0062797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	223	772	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.33547056619861	2	FACETS	0.851	0.796	0.908	0.851	0.796	0.908	CLONAL	2	TRUE	0	0.369936622270295	2		772	708	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225896	2225896	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	123	814	1	ENST00000326181.6:c.1688A>G	p.Tyr563Cys	p.Y563C	ENST00000326181	NM_032271.2	563	tAc/tGc	18/21	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.369936622270295	2		815	596	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021329	31021329	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	83	775	0	ENST00000375687.4:c.1329del	p.Ser444GlnfsTer18	p.S444Qfs*18	ENST00000375687	NM_015338.5	443	gCc/gc	12/13	1	2	FACETS	0.699	0.617	0.787	0.699	0.617	0.787	SUBCLONAL	1	TRUE	1	0.369936622270295	2		775	642	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0062798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	414	205	0				ENST00000310581	NM_198253.2	-/1132			0.484281609626869	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	1	0.484281609626869	4		205	794	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0062798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	83	190	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.484281609626869	3	FACETS	0.887	0.795	0.982	0.887	0.795	0.982	CLONAL	2	TRUE	1	0.484281609626869	3		190	240	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149961	202149962	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs587776665	NA	P-0062798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	206	854	0	ENST00000358485.4:c.1405_1406del	p.Val469PhefsTer28	p.V469Ffs*28	ENST00000358485	NM_001080125.1	468	TGt/t	8/9	1	2	FACETS	0.993	0.922	1	0.993	0.922	1	CLONAL	1	TRUE	1	0.484281609626869	2		854	857	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323141	31323141	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	242	1022	0	ENST00000412585.2:c.848G>A	p.Cys283Tyr	p.C283Y	ENST00000412585	NM_005514.6	283	tGc/tAc	4/8	1	2	FACETS	0.999	0.934	1	0.999	0.934	1	CLONAL	1	TRUE	1	0.484281609626869	2		1022	1000	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633481	3633481	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	194	763	0	ENST00000294008.3:c.4770G>T	p.Gln1590His	p.Q1590H	ENST00000294008	NM_032444.2	1590	caG/caT	14/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.484281609626869	2		763	753	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29120965	29120966	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0062798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	70	288	0	ENST00000328354.6:c.591dup	p.Val198SerfsTer6	p.V198Sfs*6	ENST00000328354	NM_007194.3	197	-/A	4/15	1	2	FACETS	0.831	0.729	0.939	0.831	0.729	0.939	CLONAL	1	TRUE	1	0.484281609626869	2		288	348	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121031	29121031	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs876661085	NA	P-0062798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	109	367	0	ENST00000328354.6:c.526G>C	p.Gly176Arg	p.G176R	ENST00000328354	NM_007194.3	176	Ggg/Cgg	4/15	1	2	FACETS	0.964	0.87	1	0.964	0.87	1	CLONAL	1	TRUE	1	0.484281609626869	2		367	467	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540029	187540029	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0062798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	172	676	0	ENST00000441802.2:c.7711A>T	p.Lys2571Ter	p.K2571*	ENST00000441802	NM_005245.3	2571	Aag/Tag	10/27	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.484281609626869	2		676	673	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323338	31323338	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	102	315	0	ENST00000412585.2:c.651del	p.Ile218SerfsTer8	p.I218Sfs*8	ENST00000412585	NM_005514.6	217	ccC/cc	4/8	1	2	FACETS	0.977	0.88	1	0.977	0.88	1	CLONAL	1	TRUE	1	0.484281609626869	2		315	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0062799-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	158	506	0	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.756333697629817	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.756333697629817	1		506	199	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404796	404796	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062799-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	160	519	0	ENST00000399788.2:c.4398G>T	p.Trp1466Cys	p.W1466C	ENST00000399788	NM_001042603.1	1466	tgG/tgT	26/28	0.756333697629817	2	FACETS	1	0.981	1	0.58	0.539	0.621	CLONAL	1	TRUE	0	0.756333697629817	2		519	365	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95556913	95556921	+	inframe_deletion	In_Frame_Del	DEL	GTAACTTCG	GTAACTTCG	-	novel	NA	P-0062799-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	54	272	0	ENST00000393063.1:c.5683_5691del	p.Ser1896_Arg1898del	p.S1896_R1898del	ENST00000393063	NM_030621.3	1895	CGAAGTTAC/-	28/28	0.24807805846876	4	FACETS	0.842	0.736	0.951	0.842	0.736	0.951	INDETERMINATE	2	TRUE	2	0.756333697629817	4		272	149	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790428	3790428	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062799-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	155	549	0	ENST00000262367.5:c.4105G>T	p.Val1369Leu	p.V1369L	ENST00000262367	NM_004380.2	1369	Gtg/Ttg	24/31	0.24807805846876	4	FACETS	0.791	0.731	0.853	0.791	0.731	0.853	INDETERMINATE	2	TRUE	2	0.756333697629817	4		549	455	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032046	10032046	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062799-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	13	568	0	ENST00000330684.3:c.777C>G	p.Ser259Arg	p.S259R	ENST00000330684	NM_001134407.1	259	agC/agG	3/13	0.24807805846876	4	FACETS	0.234	0.166	0.317	0.117	0.083	0.159	INDETERMINATE	1	TRUE	2	0.756333697629817	4		568	258	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116228	209116228	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062799-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	148	260	0	ENST00000345146.2:c.48T>A	p.Asp16Glu	p.D16E	ENST00000345146	NM_005896.2	16	gaT/gaA	3/10	0.756333697629817	2	FACETS	1	0.991	1	0.75	0.701	0.798	CLONAL	1	TRUE	0	0.756333697629817	2		260	261	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524445	44524445	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062799-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	99	314	0	ENST00000291552.4:c.112A>C	p.Asn38His	p.N38H	ENST00000291552	NM_006758.2	38	Aat/Cat	2/8	0.756333697629817	2	FACETS	0.893	0.808	0.981	0.447	0.404	0.491	CLONAL	1	TRUE	0	0.756333697629817	2		314	293	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933713	49933713	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062799-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	207	845	0	ENST00000296474.3:c.2564C>G	p.Pro855Arg	p.P855R	ENST00000296474	NM_002447.2	855	cCt/cGt	10/20	0.756333697629817	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.756333697629817	1		845	260	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403209	116403209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062799-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	85	225	0	ENST00000397752.3:c.2470G>A	p.Asp824Asn	p.D824N	ENST00000397752	NM_000245.2	824	Gat/Aat	11/21	0.53675878797063	6	FACETS	1	0.957	1	0.565	0.507	0.625	CLONAL	2	TRUE	2	0.756333697629817	6		225	250	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341630	70341630	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062799-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	146	695	0	ENST00000374080.3:c.1065C>A	p.His355Gln	p.H355Q	ENST00000374080		355	caC/caA	7/45	1	2	FACETS	0.995	0.919	1	0.995	0.919	1	CLONAL	1	TRUE	1	0.756333697629817	2		695	388	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0062801-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	152	358	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.324284605429301	3	FACETS	1	0.975	1	0.753	0.696	0.811	CLONAL	2	TRUE	0	0.399693425671752	3		358	404	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589813	28589813	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062801-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	622	514	2	ENST00000241453.7:c.2567C>G	p.Ala856Gly	p.A856G	ENST00000241453	NM_004119.2	856	gCc/gGc	21/24	0.399693425671752	6	FACETS	1	0.985	1	1	0.985	1	CLONAL	5	TRUE	1	0.399693425671752	6		516	1088	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639986	3639986	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062801-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	161	754	0	ENST00000294008.3:c.3653A>G	p.Asp1218Gly	p.D1218G	ENST00000294008	NM_032444.2	1218	gAt/gGt	12/15	0.343436480362082	3	FACETS	0.864	0.791	0.94	0.432	0.395	0.47	CLONAL	1	TRUE	1	0.399693425671752	3		754	1119	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857020	9857020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555481892	NA	P-0062801-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	60	391	0	ENST00000330684.3:c.4381G>A	p.Glu1461Lys	p.E1461K	ENST00000330684	NM_001134407.1	1461	Gaa/Aaa	13/13	0.343436480362082	3	FACETS	0.775	0.669	0.889	0.387	0.334	0.445	SUBCLONAL	1	TRUE	1	0.399693425671752	3		391	465	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614790	23614790	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062801-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	66	319	0	ENST00000261584.4:c.3551A>G	p.His1184Arg	p.H1184R	ENST00000261584	NM_024675.3	1184	cAc/cGc	13/13	0.343436480362082	3	FACETS	0.93	0.81	1	0.465	0.405	0.53	CLONAL	1	TRUE	1	0.399693425671752	3		319	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577516	7577527	+	inframe_deletion	In_Frame_Del	DEL	GATGATGGTGAG	GATGATGGTGAG	-	novel	NA	P-0062801-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	271	610	0	ENST00000269305.4:c.754_765del	p.Leu252_Ile255del	p.L252_I255del	ENST00000269305	NM_001126112.2	252	CTCACCATCATC/-	7/11	0.363576037884284	2	FACETS	0.879	0.829	0.931	0.879	0.829	0.931	CLONAL	2	TRUE	0	0.399693425671752	2		610	771	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5260824	5260824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774744361	NA	P-0062801-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	121	579	0	ENST00000357368.4:c.587C>T	p.Pro196Leu	p.P196L	ENST00000357368	NM_002850.3	196	cCg/cTg	7/38	0.112516653086451	0	FACETS	0.533	0.482	0.586			1	INDETERMINATE	1	TRUE	0	0.399693425671752	0		579	682	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957566	1957566	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062801-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	70	550	0	ENST00000382891.5:c.2665G>C	p.Gly889Arg	p.G889R	ENST00000382891	NM_133335.3	889	Ggg/Cgg	14/22	0.362178890485946	2	FACETS	0.527	0.459	0.6	0.263	0.229	0.3	SUBCLONAL	1	TRUE	0	0.399693425671752	2		550	665	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852215	128852215	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs765830913	NA	P-0062801-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1152	189	791	0	ENST00000249373.3:c.2287C>T	p.Arg763Ter	p.R763*	ENST00000249373	NM_005631.4	763	Cga/Tga	12/12	0.36235990007258	4	FACETS	0.987	0.91	1	0.329	0.303	0.356	CLONAL	1	TRUE	1	0.399693425671752	4		791	1341	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119459	193119459	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062802-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	329	495	0	ENST00000367435.3:c.854C>G	p.Pro285Arg	p.P285R	ENST00000367435	NM_024529.4	285	cCt/cGt	9/17	0.491017949804434	3	FACETS	0.856	0.817	0.894	0.856	0.817	0.894	INDETERMINATE	2	TRUE	1	0.916127955165788	3		495	612	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120502048	120502048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1352414422	NA	P-0062802-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	234	601	0	ENST00000256646.2:c.1993C>T	p.Arg665Cys	p.R665C	ENST00000256646	NM_024408.3	665	Cgc/Tgc	12/34	0.491017949804434	3	FACETS	0.858	0.813	0.903	0.858	0.813	0.903	INDETERMINATE	2	TRUE	1	0.916127955165788	3		601	434	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250506	110250506	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062802-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	191	610	0	ENST00000374672.4:c.169G>T	p.Val57Leu	p.V57L	ENST00000374672	NM_004235.4	57	Gtg/Ttg	3/5	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.916127955165788	2		610	403	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0062803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	84	1032	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.558001384068773	4	FACETS	0.829	0.743	0.919	0.829	0.743	0.919	CLONAL	2	TRUE	2	0.626235826827538	4		1032	263	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743988	41743988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776310618	NA	P-0062803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	222	871	0	ENST00000301178.4:c.923G>A	p.Arg308His	p.R308H	ENST00000301178	NM_021913.4	308	cGc/cAc	7/20	0.558001384068773	4	FACETS	0.931	0.872	0.991	0.931	0.872	0.991	CLONAL	2	TRUE	2	0.626235826827538	4		871	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0062803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	408	860	2	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.609058814315142	3	FACETS	0.917	0.885	0.948	0.917	0.885	0.948	CLONAL	3	TRUE	0	0.626235826827538	3		862	622	SUCCESS
APC	324	MSKCC	GRCh37	5	112175561	112175561	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	115	668	1	ENST00000257430.4:c.4271del	p.Pro1424GlnfsTer49	p.P1424Qfs*49	ENST00000257430	NM_000038.5	1424	Cca/ca	16/16	0.626235826827538	1	FACETS	0.952	0.873	1	0.952	0.873	1	CLONAL	1	TRUE	0	0.626235826827538	1		669	265	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604668	48604668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	146	573	0	ENST00000342988.3:c.1490G>A	p.Arg497His	p.R497H	ENST00000342988	NM_005359.5	497	cGc/cAc	12/12	0.626235826827538	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.626235826827538	1		573	275	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005338	150005338	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	189	763	0	ENST00000253339.5:c.887G>A	p.Trp296Ter	p.W296*	ENST00000253339		296	tGg/tAg	3/7	0.622905137466042	3	FACETS	0.889	0.831	0.947	0.889	0.831	0.947	CLONAL	2	TRUE	1	0.626235826827538	3		763	446	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945574	151945574	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	58	81	0	ENST00000262189.6:c.1945G>A	p.Val649Met	p.V649M	ENST00000262189	NM_170606.2	649	Gtg/Atg	14/59	0.626235826827538	4	FACETS	1	0.961	1	1	0.982	1	CLONAL	3	TRUE	2	0.626235826827538	4		81	89	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0062806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	83	387	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.156898839425518	4	FACETS	0.842	0.749	0.94	0.842	0.749	0.94	CLONAL	3	TRUE	1	0.231843584711304	4		387	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0062806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	73	528	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.231843584711304	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	0	0.231843584711304	1		528	532	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106851	27106852	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0062806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	83	835	0	ENST00000324856.7:c.6462_6463del	p.Leu2155GlnfsTer2	p.L2155Qfs*2	ENST00000324856	NM_006015.4	2154	ttCCtc/tttc	20/20	0.231843584711304	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.231843584711304	1		835	614	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575185	48575186	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0062806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	40	375	0	ENST00000342988.3:c.383_384del	p.Val128GlufsTer14	p.V128Efs*14	ENST00000342988	NM_005359.5	127	TGt/t	3/12	0.231843584711304	1	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	0	0.231843584711304	1		375	280	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0062807-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	63	438	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	0.871	0.754	0.998	0.871	0.754	0.998	CLONAL	1	TRUE	1	0.271432531740507	2		438	533	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120114	70120115	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGTGC	novel	NA	P-0062807-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	351	744	1	ENST00000245479.2:c.1117_1118insGTGCC	p.Pro373ArgfsTer12	p.P373Rfs*12	ENST00000245479	NM_000346.3	372	-/CGTGC	3/3	0.267504700093587	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.271432531740507	2		745	1281	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131240	202131240	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062807-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	165	527	4	ENST00000358485.4:c.208G>T	p.Gly70Trp	p.G70W	ENST00000358485	NM_001080125.1	70	Ggg/Tgg	2/9	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.271432531740507	2		531	977	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131267	202131267	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062807-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	175	593	4	ENST00000358485.4:c.235G>T	p.Ala79Ser	p.A79S	ENST00000358485	NM_001080125.1	79	Gcc/Tcc	2/9	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.271432531740507	2		597	1080	SUCCESS
APC	324	MSKCC	GRCh37	5	112175340	112175342	+	frameshift_variant	Frame_Shift_Del	DEL	AAG	AAG	T	novel	NA	P-0062807-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	94	537	0	ENST00000257430.4:c.4049_4051delinsT	p.Lys1350IlefsTer3	p.K1350Ifs*3	ENST00000257430	NM_000038.5	1350	aAAGct/aTct	16/16	1	2	FACETS	0.732	0.65	0.82	0.732	0.65	0.82	SUBCLONAL	1	TRUE	1	0.271432531740507	2		537	946	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581282	48581283	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	C	novel	NA	P-0062807-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	56	642	0	ENST00000342988.3:c.586_587delinsC	p.Ser196ProfsTer6	p.S196Pfs*6	ENST00000342988	NM_005359.5	196	AGc/Cc	5/12	0.271432531740507	1	FACETS	0.394	0.337	0.458	0.394	0.337	0.458	SUBCLONAL	1	TRUE	0	0.271432531740507	1		642	904	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86676366	86676366	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	52	324	0	ENST00000274376.6:c.2644C>T	p.Gln882Ter	p.Q882*	ENST00000274376	NM_002890.2	882	Cag/Tag	20/25	1	2	FACETS	0.367	0.312	0.427	0.367	0.312	0.427	SUBCLONAL	1	TRUE	1	0.508053109205114	2		324	558	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910797	29910797	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs41559912	NA	P-0062808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	95	646	0	ENST00000376809.5:c.337G>T	p.Glu113Ter	p.E113*	ENST00000376809	NM_002116.7	113	Gag/Tag	2/8	0.508053109205114	1	FACETS	0.334	0.297	0.373	0.334	0.297	0.373	SUBCLONAL	1	TRUE	0	0.508053109205114	1		646	836	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245357	153245357	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	280	294	0	ENST00000281708.4:c.1834C>T	p.Gln612Ter	p.Q612*	ENST00000281708	NM_033632.3	612	Cag/Tag	11/12	0.508053109205114	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.508053109205114	2		294	473	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645064	86645064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	38	349	0	ENST00000274376.6:c.1136C>T	p.Ser379Leu	p.S379L	ENST00000274376	NM_002890.2	379	tCa/tTa	8/25	1	2	FACETS	0.259	0.214	0.31	0.259	0.214	0.31	SUBCLONAL	1	TRUE	1	0.508053109205114	2		349	577	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912276	29912276	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0062808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	134	592	0	ENST00000376809.5:c.896-1G>A		p.X299_splice	ENST00000376809	NM_002116.7	299			0.508053109205114	1	FACETS	0.622	0.566	0.68	0.622	0.566	0.68	SUBCLONAL	1	TRUE	0	0.508053109205114	1		592	633	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782184	135782184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	41	353	0	ENST00000298552.3:c.1372G>A	p.Asp458Asn	p.D458N	ENST00000298552	NM_001162426.1	458	Gat/Aat	14/23	0.322803707976968	3	FACETS	0.285	0.237	0.34	0.143	0.118	0.17	SUBCLONAL	1	TRUE	1	0.508053109205114	3		353	709	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412437	63412437	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	130	615	0	ENST00000330258.3:c.730G>A	p.Glu244Lys	p.E244K	ENST00000330258	NM_152424.3	244	Gaa/Aaa	2/2	0.264012583434993	3	FACETS	0.598	0.541	0.657	0.299	0.27	0.329	INDETERMINATE	1	TRUE	1	0.508053109205114	3		615	1074	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0062809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	282	546	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.962	0.911	1	0.962	0.911	1	CLONAL	1	TRUE	1	0.913023704435887	2		546	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0062809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	253	679	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	0.913023704435887	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.913023704435887	1		679	300	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372252	55372253	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0062809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	298	958	0	ENST00000297316.4:c.944dup	p.Gln316AlafsTer49	p.Q316Afs*49	ENST00000297316	NM_022454.3	314	-/C	2/2	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.913023704435887	2		958	644	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546417	46546417	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	79	388	0	ENST00000262741.5:c.112C>G	p.Pro38Ala	p.P38A	ENST00000262741	NM_003629.3	38	Cca/Gca	2/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.506251184258583	2		388	285	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692918	89692918	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	60	456	0	ENST00000371953.3:c.402G>A	p.Met134Ile	p.M134I	ENST00000371953	NM_000314.4	134	atG/atA	5/9	1	2	FACETS	0.76	0.659	0.868	0.76	0.659	0.868	SUBCLONAL	1	TRUE	1	0.506251184258583	2		456	312	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692928	89692928	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	69	493	0	ENST00000371953.3:c.412T>G	p.Tyr138Asp	p.Y138D	ENST00000371953	NM_000314.4	138	Tat/Gat	5/9	1	2	FACETS	0.804	0.705	0.909	0.804	0.705	0.909	CLONAL	1	TRUE	1	0.506251184258583	2		493	339	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342573	118342573	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	98	527	0	ENST00000534358.1:c.699C>G	p.Ile233Met	p.I233M	ENST00000534358	NM_005933.3	233	atC/atG	3/36	0.506251184258583	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.506251184258583	1		527	286	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342656	118342656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	96	519	0	ENST00000534358.1:c.782C>T	p.Ser261Phe	p.S261F	ENST00000534358	NM_005933.3	261	tCt/tTt	3/36	0.506251184258583	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.506251184258583	1		519	246	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799172	88799172	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	60	515	0	ENST00000360948.2:c.213C>G	p.Ile71Met	p.I71M	ENST00000360948	NM_001012338.2	71	atC/atG	2/19	NA	2	FACETS	1	0.92	1			1	INDETERMINATE	1	TRUE	NA	0.506251184258583	2		515	221	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821265	72821265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	86	610	0	ENST00000268489.5:c.10910C>T	p.Ser3637Leu	p.S3637L	ENST00000268489	NM_006885.3	3637	tCa/tTa	10/10	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.506251184258583	2		610	320	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350822	15350822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200902225	NA	P-0062811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	74	507	0	ENST00000263377.2:c.3181G>A	p.Glu1061Lys	p.E1061K	ENST00000263377	NM_058243.2	1061	Gaa/Aaa	15/20	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.506251184258583	2		507	265	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945254	54945254	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0062811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	23	403	0	ENST00000312783.6:c.1172C>G	p.Ser391Ter	p.S391*	ENST00000312783	NM_198436.1	391	tCa/tGa	10/10	1	2	FACETS	0.516	0.405	0.642	0.516	0.405	0.642	SUBCLONAL	1	TRUE	1	0.506251184258583	2		403	176	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324031	31324031	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	64	622	0	ENST00000412585.2:c.532G>T	p.Glu178Ter	p.E178*	ENST00000412585	NM_005514.6	178	Gag/Tag	3/8	1	2	FACETS	0.961	0.841	1	0.961	0.841	1	CLONAL	1	TRUE	1	0.506251184258583	2		622	263	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324621	31324621	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs41563012	NA	P-0062811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	43	557	0	ENST00000412585.2:c.187G>T	p.Asp63Tyr	p.D63Y	ENST00000412585	NM_005514.6	63	Gac/Tac	2/8	1	2	FACETS	0.629	0.53	0.738	0.629	0.53	0.738	SUBCLONAL	1	TRUE	1	0.506251184258583	2		557	270	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324681	31324681	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs137854653	NA	P-0062811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	58	540	0	ENST00000412585.2:c.127G>T	p.Glu43Ter	p.E43*	ENST00000412585	NM_005514.6	43	Gag/Tag	2/8	1	2	FACETS	0.875	0.759	0.998	0.875	0.759	0.998	CLONAL	1	TRUE	1	0.506251184258583	2		540	262	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324721	31324721	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	14	200	0	ENST00000412585.2:c.87G>C	p.Met29Ile	p.M29I	ENST00000412585	NM_005514.6	29	atG/atC	2/8	1	2	FACETS	0.658	0.484	0.862	0.658	0.484	0.862	SUBCLONAL	1	TRUE	1	0.506251184258583	2		200	84	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945679	151945679	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	51	307	0	ENST00000262189.6:c.1840G>T	p.Glu614Ter	p.E614*	ENST00000262189	NM_170606.2	614	Gaa/Taa	14/59	1	2	FACETS	0.924	0.795	1	0.924	0.795	1	CLONAL	1	TRUE	1	0.506251184258583	2		307	218	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0062813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	57	1032	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.95	0.819	1	0.95	0.819	1	CLONAL	1	TRUE	1	0.334217739679705	2		1032	359	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0062813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	114	563	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	0.334217739679705	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.334217739679705	1		563	505	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0062817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	19	462	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.641	0.487	0.821	0.641	0.487	0.821	SUBCLONAL	1	TRUE	1	0.24	2		462	247	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300039	137300040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755912201	NA	P-0062817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	10	441	1	ENST00000481739.1:c.331dup	p.Leu111ProfsTer70	p.L111Pfs*70	ENST00000481739	NM_002957.4	108	-/C	3/10	1	2	FACETS	0.563	0.382	0.789	0.563	0.382	0.789	SUBCLONAL	1	TRUE	1	0.24	2		442	148	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	11	343	0				ENST00000310581	NM_198253.2	-/1132			0.164577951741988	0	FACETS	0.882	0.618	1			1	CLONAL	1	TRUE	0	0.24	0		343	79	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0062817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	42	488	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.978	0.819	1	0.978	0.819	1	CLONAL	1	TRUE	1	0.24	2		488	358	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119822	108119822	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	54	393	0	ENST00000278616.4:c.1228G>C	p.Val410Leu	p.V410L	ENST00000278616	NM_000051.3	410	Gtg/Ctg	9/63	0.209559767090117	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.24	1		393	331	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861799	57861799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	20	557	0	ENST00000228682.2:c.1100C>A	p.Pro367His	p.P367H	ENST00000228682	NM_005269.2	367	cCt/cAt	10/12	1	2	FACETS	0.779	0.598	0.989	0.779	0.598	0.989	CLONAL	1	TRUE	1	0.24	2		557	214	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109974	115109974	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	17	560	0	ENST00000257566.3:c.1904G>T	p.Arg635Leu	p.R635L	ENST00000257566	NM_016569.3	635	cGc/cTc	8/8	1	2	FACETS	0.897	0.673	1	0.897	0.673	1	CLONAL	1	TRUE	1	0.24	2		560	158	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239324	105239324	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	26	735	0	ENST00000349310.3:c.1063G>C	p.Glu355Gln	p.E355Q	ENST00000349310	NM_001014432.1	355	Gag/Cag	12/15	1	2	FACETS	1	0.83	1	1	0.83	1	CLONAL	1	TRUE	1	0.24	2		735	207	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732517	74732517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	36	565	0	ENST00000359995.5:c.392G>A	p.Arg131Gln	p.R131Q	ENST00000359995	NM_001195427.1	131	cGg/cAg	2/3	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.24	2		565	231	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39542597	39542597	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	39	434	0	ENST00000262039.4:c.401G>T	p.Gly134Val	p.G134V	ENST00000262039	NM_002647.2	134	gGc/gTc	3/25	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.24	2		434	311	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219355	1219356	+	missense_variant	Missense_Mutation	DNP	TG	TG	AT	novel	NA	P-0062817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	36	511	0	ENST00000326873.7:c.407_408delinsAT	p.Met136Asn	p.M136N	ENST00000326873	NM_000455.4	136	aTG/aAT	3/10	0.288750921900462	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.24	1		511	184	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170431	11170431	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	15	445	0	ENST00000358026.2:c.4734C>G	p.Ile1578Met	p.I1578M	ENST00000358026	NM_001128849.1	1578	atC/atG	34/36	0.288750921900462	1	FACETS	0.738	0.543	0.97	0.738	0.543	0.97	CLONAL	1	TRUE	0	0.24	1		445	149	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46277781	46277781	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	29	438	0	ENST00000371998.3:c.3579G>C	p.Leu1193Phe	p.L1193F	ENST00000371998		1193	ttG/ttC	19/23	1	2	FACETS	1	0.831	1	1	0.831	1	CLONAL	1	TRUE	1	0.24	2		438	234	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41489064	41489064	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0062817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	28	309	0	ENST00000263253.7:c.56C>G	p.Ser19Ter	p.S19*	ENST00000263253	NM_001429.3	19	tCa/tGa	1/31	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.24	2		309	200	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067120	143067120	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	30	457	0	ENST00000262992.4:c.1593C>A	p.Ser531Arg	p.S531R	ENST00000262992	NM_001101669.1	531	agC/agA	16/24	1	2	FACETS	0.947	0.766	1	0.947	0.766	1	CLONAL	1	TRUE	1	0.24	2		457	264	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332721	153332721	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	33	645	0	ENST00000281708.4:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000281708	NM_033632.3	79	Gaa/Caa	2/12	1	2	FACETS	0.851	0.695	1	0.851	0.695	1	CLONAL	1	TRUE	1	0.24	2		645	323	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005302	150005302	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	50	712	0	ENST00000253339.5:c.923C>G	p.Ser308Cys	p.S308C	ENST00000253339		308	tCc/tGc	3/7	0.3	3	FACETS	0.901	0.771	1	0.901	0.771	1	CLONAL	2	TRUE	1	0.24	3		712	259	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335706	81335706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	24	446	0	ENST00000222390.5:c.1654G>A	p.Asp552Asn	p.D552N	ENST00000222390	NM_000601.4	552	Gat/Aat	15/18	0.191336547994024	3	FACETS	0.727	0.571	0.907	0.364	0.285	0.454	CLONAL	1	TRUE	1	0.24	3		446	308	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477853	140477853	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs180177036	NA	P-0062817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	20	457	0	ENST00000288602.6:c.1455G>C	p.Leu485Phe	p.L485F	ENST00000288602	NM_004333.4	485	ttG/ttC	12/18	0.191336547994024	3	FACETS	0.674	0.516	0.859	0.337	0.258	0.43	SUBCLONAL	1	TRUE	1	0.24	3		457	277	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842278	151842278	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	27	605	0	ENST00000262189.6:c.14134G>C	p.Glu4712Gln	p.E4712Q	ENST00000262189	NM_170606.2	4712	Gaa/Caa	54/59	0.191336547994024	3	FACETS	0.829	0.661	1	0.414	0.33	0.51	CLONAL	1	TRUE	1	0.24	3		605	304	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884435	151884435	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	41	473	0	ENST00000262189.6:c.4920G>C	p.Glu1640Asp	p.E1640D	ENST00000262189	NM_170606.2	1640	gaG/gaC	33/59	0.191336547994024	3	FACETS	1	0.871	1	0.526	0.439	0.622	CLONAL	1	TRUE	1	0.24	3		473	364	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864525	56864525	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs868430124	NA	P-0062817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	17	428	0	ENST00000519728.1:c.488G>A	p.Gly163Glu	p.G163E	ENST00000519728	NM_002350.3	163	gGa/gAa	7/13	1	2	FACETS	0.723	0.541	0.937	0.723	0.541	0.937	CLONAL	1	TRUE	1	0.24	2		428	196	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980596	70980596	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	20	628	0	ENST00000276594.2:c.781G>T	p.Gly261Cys	p.G261C	ENST00000276594	NM_024504.3	261	Ggt/Tgt	4/8	1	2	FACETS	0.62	0.474	0.789	0.62	0.474	0.789	SUBCLONAL	1	TRUE	1	0.24	2		628	269	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213589	27213589	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	20	390	0	ENST00000380036.4:c.2985G>C	p.Lys995Asn	p.K995N	ENST00000380036	NM_000459.3	995	aaG/aaC	18/23	0.234236170544649	3	FACETS	0.911	0.699	1	0.304	0.233	0.386	CLONAL	1	TRUE	0	0.24	3		390	205	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038828	47038828	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062817-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	18	229	0	ENST00000377604.3:c.835C>T	p.Gln279Ter	p.Q279*	ENST00000377604	NM_001204468.1	279	Cag/Tag	9/24	1	1	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	0	0.24	1		229	90	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0062818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	409	869	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		869	1174	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740278	46740296	+	frameshift_variant	Frame_Shift_Del	DEL	CCGGCTGGTCATGTTTGAC	CCGGCTGGTCATGTTTGAC	-	novel	NA	P-0062818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	149	647	0	ENST00000371975.4:c.1760_1778del	p.Arg587LeufsTer49	p.R587Lfs*49	ENST00000371975	NM_003579.3	586	aaCCGGCTGGTCATGTTTGAC/aa	16/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		647	1070	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95595900	95595900	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	48	498	0	ENST00000393063.1:c.643G>T	p.Asp215Tyr	p.D215Y	ENST00000393063	NM_030621.3	215	Gat/Tat	7/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		498	464	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007672	45007672	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0062818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	62	712	0	ENST00000558401.1:c.119C>G	p.Ser40Ter	p.S40*	ENST00000558401	NM_004048.2	40	tCa/tGa	2/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		712	688	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59820424	59820424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	259	610	0	ENST00000259008.2:c.2329C>A	p.Arg777Ser	p.R777S	ENST00000259008	NM_032043.2	777	Cgt/Agt	16/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		610	1003	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226488	1226488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	175	725	2	ENST00000326873.7:c.1144C>T	p.Gln382Ter	p.Q382*	ENST00000326873	NM_000455.4	382	Cag/Tag	9/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		727	935	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572890	41572890	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1198	88	843	0	ENST00000263253.7:c.5175G>C	p.Gln1725His	p.Q1725H	ENST00000263253	NM_001429.3	1725	caG/caC	31/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		843	1286	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081687	143081687	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200589366	NA	P-0062818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	67	525	0	ENST00000262992.4:c.1387G>A	p.Asp463Asn	p.D463N	ENST00000262992	NM_001101669.1	463	Gat/Aat	15/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		525	599	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31451639	31451639	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0062818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	82	348	0	ENST00000344624.3:c.2682+1G>T		p.X894_splice	ENST00000344624		894			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		348	783	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031919	26031919	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1270004025	NA	P-0062818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1338	98	961	0	ENST00000244661.2:c.370G>C	p.Asp124His	p.D124H	ENST00000244661	NM_003537.3	124	Gac/Cac	1/1	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		961	1436	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33290651	33290651	+	5_prime_UTR_variant	5'UTR	SNP	C	C	G	novel	NA	P-0062818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	53	402	0	ENST00000374542.5:c.-65G>C		p.*22*	ENST00000374542	NM_001141970.1	-/740		1/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		402	593	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388026	81388026	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	69	347	0	ENST00000222390.5:c.349G>C	p.Asp117His	p.D117H	ENST00000222390	NM_000601.4	117	Gac/Cac	3/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		347	325	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508921	106508921	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	146	740	0	ENST00000359195.3:c.916del	p.Val306TyrfsTer10	p.V306Yfs*10	ENST00000359195	NM_002649.2	305	gtG/gt	2/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		740	1162	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971194	21971194	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs561034503	NA	P-0062818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	495	782	0	ENST00000304494.5:c.164G>T	p.Gly55Val	p.G55V	ENST00000304494	NM_000077.4	55	gGc/gTc	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		782	1065	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062824-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	85	343	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.149957452504836	2		343	891	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0062824-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	54	557	1	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	1	2	FACETS	0.731	0.622	0.851	0.731	0.622	0.851	SUBCLONAL	1	TRUE	1	0.149957452504836	2		558	985	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404589	8404589	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0062824-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	42	352	0	ENST00000356435.5:c.4158C>G	p.Tyr1386Ter	p.Y1386*	ENST00000356435		1386	taC/taG	25/35	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.149957452504836	2		352	443	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143191873	143191873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062824-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	35	344	0	ENST00000262992.4:c.558G>T	p.Met186Ile	p.M186I	ENST00000262992	NM_001101669.1	186	atG/atT	8/24	1	2	FACETS	0.724	0.592	0.873	0.724	0.592	0.873	SUBCLONAL	1	TRUE	1	0.149957452504836	2		344	645	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201828	66201828	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062824-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	54	418	0	ENST00000273854.3:c.2674G>T	p.Glu892Ter	p.E892*	ENST00000273854	NM_004439.5	892	Gag/Tag	16/18	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.149957452504836	2		418	719	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781291	9781291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369950232	NA	P-0062824-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	75	430	0	ENST00000377346.4:c.1796C>T	p.Ser599Leu	p.S599L	ENST00000377346	NM_005026.3	599	tCg/tTg	14/24	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.149957452504836	2		430	853	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103291	119103291	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062824-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	45	461	0	ENST00000264033.4:c.329G>T	p.Gly110Val	p.G110V	ENST00000264033	NM_005188.3	110	gGa/gTa	2/16	1	2	FACETS	0.864	0.724	1	0.864	0.724	1	CLONAL	1	TRUE	1	0.149957452504836	2		461	695	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398286	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0062824-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	53	253	0	ENST00000311936.3:c.33_34delinsCT	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	11	gcTGgt/gcCTgt	2/5	0.149957452504836	2	FACETS	0.844	0.721	0.977	0.844	0.721	0.977	CLONAL	2	TRUE	0	0.149957452504836	2		253	419	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004738	16004738	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062824-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	46	507	0	ENST00000268712.3:c.2516A>G	p.Asp839Gly	p.D839G	ENST00000268712	NM_006311.3	839	gAt/gGt	20/46	1	2	FACETS	0.738	0.62	0.87	0.738	0.62	0.87	SUBCLONAL	1	TRUE	1	0.149957452504836	2		507	831	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387637	17387637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766641020	NA	P-0062824-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	69	530	0	ENST00000359435.4:c.705G>A	p.Met235Ile	p.M235I	ENST00000359435	NM_001033549.1	235	atG/atA	8/9	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.149957452504836	2		530	841	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55124963	55124963	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062824-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	54	376	0	ENST00000257290.5:c.28G>T	p.Val10Phe	p.V10F	ENST00000257290	NM_006206.4	10	Gtc/Ttc	2/23	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.149957452504836	2		376	677	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968173	55968173	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062824-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	41	319	0	ENST00000263923.4:c.2157C>A	p.Asn719Lys	p.N719K	ENST00000263923	NM_002253.2	719	aaC/aaA	15/30	1	2	FACETS	0.991	0.824	1	0.991	0.824	1	CLONAL	1	TRUE	1	0.149957452504836	2		319	552	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100253	157100253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1235258455	NA	P-0062824-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	69	394	0	ENST00000346085.5:c.1190C>T	p.Ser397Leu	p.S397L	ENST00000346085	NM_020732.3	397	tCg/tTg	1/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.149957452504836	2		394	765	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372699	81372700	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0062824-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	110	416	0	ENST00000222390.5:c.834_835delinsAA	p.Arg279Ser	p.R279S	ENST00000222390	NM_000601.4	278	acCCgc/acAAgc	7/18	0.149957452504836	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	2	TRUE	0	0.149957452504836	2		416	727	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8338951	8338951	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062824-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	42	367	0	ENST00000356435.5:c.5350C>A	p.Leu1784Ile	p.L1784I	ENST00000356435		1784	Cta/Ata	32/35	1	2	FACETS	0.99	0.825	1	0.99	0.825	1	CLONAL	1	TRUE	1	0.149957452504836	2		367	566	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500842	8500842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062824-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	74	478	0	ENST00000356435.5:c.2040G>T	p.Trp680Cys	p.W680C	ENST00000356435		680	tgG/tgT	13/35	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.149957452504836	2		478	851	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971056	21971056	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062824-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	96	554	0	ENST00000304494.5:c.302G>T	p.Gly101Val	p.G101V	ENST00000304494	NM_000077.4	101	gGg/gTg	2/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.149957452504836	2		554	973	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832709	3832709	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062836-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	336	639	20	ENST00000262367.5:c.1549C>T	p.Gln517Ter	p.Q517*	ENST00000262367	NM_004380.2	517	Cag/Tag	6/31	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.866118415970057	2		659	744	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412898	49412898	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519954	NA	P-0062836-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	283	606	7	ENST00000418115.1:c.125A>G	p.Tyr42Cys	p.Y42C	ENST00000418115	NM_001664.2	42	tAt/tGt	2/5	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.866118415970057	2		613	630	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100357	27100357	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062836-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	399	776	21	ENST00000324856.7:c.4069C>T	p.Gln1357Ter	p.Q1357*	ENST00000324856	NM_006015.4	1357	Cag/Tag	17/20	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.866118415970057	2		797	793	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260193	16260194	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0062836-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	382	893	18	ENST00000375759.3:c.7464dup	p.Ile2489AspfsTer9	p.I2489Dfs*9	ENST00000375759	NM_015001.2	2486	-/G	11/15	1	2	FACETS	0.991	0.946	1	0.991	0.946	1	CLONAL	1	TRUE	1	0.866118415970057	2		911	890	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740581	145740581	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062836-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	398	1014	8	ENST00000428558.2:c.1436A>T	p.Gln479Leu	p.Q479L	ENST00000428558	NM_004260.3	479	cAa/cTa	8/22	0.866118415970057	3	FACETS	1	0.98	1	0.529	0.502	0.555	CLONAL	1	TRUE	1	0.866118415970057	3		1022	1246	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390896	139390897	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCCCT	novel	NA	P-0062836-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	430	997	2	ENST00000277541.6:c.7294_7295insAGGGA	p.Ser2432LysfsTer5	p.S2432Kfs*5	ENST00000277541	NM_017617.3	2432	agc/aAGGGAgc	34/34	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.866118415970057	2		999	992	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397639	139397639	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062836-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	394	812	4	ENST00000277541.6:c.5162T>A	p.Val1721Glu	p.V1721E	ENST00000277541	NM_017617.3	1721	gTg/gAg	27/34	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.866118415970057	2		816	840	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593667	55593669	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	rs1060502543	NA	P-0062837-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	200	567	0	ENST00000288135.5:c.1735_1737del	p.Asp579del	p.D579del	ENST00000288135	NM_000222.2	578	tATGat/tat	11/21	1	2	FACETS	0.995	0.932	1	0.995	0.932	1	CLONAL	1	TRUE	1	0.864590391418167	2		567	465	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0062838-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	54	387	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.282614468557983	1	FACETS	0.646	0.563	0.733	0.646	0.563	0.733	INDETERMINATE	1	TRUE	0	0.678088024709506	1		387	163	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0062838-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	141	489	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.678088024709506	2		489	416	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25362797	25362798	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0062838-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	15	274	0	ENST00000311936.3:c.498_499del	p.His166GlnfsTer9	p.H166Qfs*9	ENST00000311936	NM_004985.3	166	caTAaa/caaa	5/5	0.282614468557983	1	FACETS	0.178	0.131	0.235	0.178	0.131	0.235	INDETERMINATE	1	TRUE	0	0.678088024709506	1		274	164	SUCCESS
MTAP	4507	MSKCC	GRCh37	9	21816752	21816752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062838-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	90	238	0	ENST00000380172.4:c.160G>A	p.Asp54Asn	p.D54N	ENST00000380172	NM_002451.3	54	Gat/Aat	3/8	0.609930460424796	2	FACETS	0.935	0.863	1	0.935	0.863	1	CLONAL	2	TRUE	0	0.678088024709506	2		238	142	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932018	39932018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367736022	NA	P-0062838-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	142	556	0	ENST00000378444.4:c.2581C>T	p.Arg861Cys	p.R861C	ENST00000378444	NM_001123385.1	861	Cgc/Tgc	4/15	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.678088024709506	2		556	404	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039278	47039278	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0062838-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	138	655	0	ENST00000377604.3:c.902-1G>A		p.X301_splice	ENST00000377604	NM_001204468.1	301			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.678088024709506	2		655	372	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0062839-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	54	387	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.885	0.761	1	1	0.974	1	CLONAL	2	TRUE	1	0.2	2		387	305	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0062839-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	38	706	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	1	2	FACETS	0.654	0.54	0.782	0.654	0.54	0.782	SUBCLONAL	1	TRUE	1	0.2	2		706	581	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027316	48027316	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63751127	NA	P-0062839-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	42	584	0	ENST00000234420.5:c.2194C>T	p.Arg732Ter	p.R732*	ENST00000234420	NM_000179.2	732	Cga/Tga	4/10	1	2	FACETS	0.811	0.677	0.96	0.811	0.677	0.96	CLONAL	1	TRUE	1	0.2	2		584	518	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0062841-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	16	387	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.591	0.436	0.777	0.591	0.436	0.777	SUBCLONAL	1	TRUE	1	0.15	2		387	361	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0062841-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	35	662	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.839	0.687	1	0.839	0.687	1	CLONAL	1	TRUE	1	0.15	2		662	556	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0062841-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	62	665	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.15	2		665	626	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0062842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	31	446	1	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.644	0.524	0.779	0.644	0.524	0.779	SUBCLONAL	1	TRUE	1	0.401158721837825	2		447	240	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0062842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	175	507	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.330358607872488	2	FACETS	1	0.987	1	0.661	0.611	0.713	CLONAL	1	TRUE	0	0.401158721837825	2		507	660	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0062842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	158	546	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.894	0.819	0.972	0.894	0.819	0.972	CLONAL	1	TRUE	1	0.401158721837825	2		546	881	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578535	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0062842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	152	650	0	ENST00000269305.4:c.395dup	p.Met133AspfsTer16	p.M133Dfs*16	ENST00000269305	NM_001126112.2	132	aag/aaAg	5/11	0.367812945301141	1	FACETS	0.796	0.729	0.866	0.796	0.729	0.866	SUBCLONAL	1	TRUE	0	0.401158721837825	1		650	761	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32899248	32899248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375125172	NA	P-0062842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	54	334	0	ENST00000380152.3:c.352C>T	p.Arg118Cys	p.R118C	ENST00000380152		118	Cgc/Tgc	4/27	1	2	FACETS	0.598	0.512	0.693	0.598	0.512	0.693	SUBCLONAL	1	TRUE	1	0.401158721837825	2		334	450	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866533	117866533	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	73	402	0	ENST00000297338.2:c.1112A>C	p.Lys371Thr	p.K371T	ENST00000297338	NM_006265.2	371	aAa/aCa	9/14	1	2	FACETS	0.757	0.663	0.856	0.757	0.663	0.856	SUBCLONAL	1	TRUE	1	0.401158721837825	2		402	481	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992181	72992181	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	57	751	0	ENST00000268489.5:c.1864C>T	p.His622Tyr	p.H622Y	ENST00000268489	NM_006885.3	622	Cac/Tac	2/10	0.354454531842645	3	FACETS	0.317	0.27	0.368	0.158	0.135	0.184	SUBCLONAL	1	TRUE	1	0.401158721837825	3		751	1077	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0062850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	175	380	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.764093330677973	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.764093330677973	3		380	199	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0062850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	58	682	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.755456738462211	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.764093330677973	1		682	83	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0062850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	54	289	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.764093330677973	2		289	137	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419923	+	missense_variant	Missense_Mutation	DNP	TA	TA	AG	novel	NA	P-0062850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	76	713	2	ENST00000206249.3:c.1609_1610delinsAG	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	TAt/AGt	8/8	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.764093330677973	2		715	170	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512279	38512279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	34	611	0	ENST00000254066.5:c.1190C>T	p.Thr397Met	p.T397M	ENST00000254066	NM_000964.3	397	aCg/aTg	9/9	1	2	FACETS	0.712	0.593	0.839	0.712	0.593	0.839	SUBCLONAL	1	TRUE	1	0.764093330677973	2		611	125	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11168338	11168338	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	47	528	0	ENST00000361445.4:c.7534G>C	p.Asp2512His	p.D2512H	ENST00000361445	NM_004958.3	2512	Gac/Cac	57/58	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.764093330677973	2		528	102	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11297967	11298063	+	frameshift_variant	Frame_Shift_Del	DEL	GTGCAGATGGCCAGCTCCCGGATCTCAAACACCTGGTCATTCAGAGCCACAAACAAGGCCTGCAAGTTCTCCGCCTGGGCCAGGTGTGCATCAAAGC	GTGCAGATGGCCAGCTCCCGGATCTCAAACACCTGGTCATTCAGAGCCACAAACAAGGCCTGCAAGTTCTCCGCCTGGGCCAGGTGTGCATCAAAGC	-	novel	NA	P-0062850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	68	727	0	ENST00000361445.4:c.2045_2141del	p.Arg682LeufsTer8	p.R682Lfs*8	ENST00000361445	NM_004958.3	682	cGCTTTGATGCACACCTGGCCCAGGCGGAGAACTTGCAGGCCTTGTTTGTGGCTCTGAATGACCAGGTGTTTGAGATCCGGGAGCTGGCCATCTGCACt/ct	13/58	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.764093330677973	2		727	154	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679505	33679505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1328037924	NA	P-0062850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	18	406	0	ENST00000308377.4:c.2576G>A	p.Gly859Asp	p.G859D	ENST00000308377	NM_152270.3	859	gGc/gAc	5/5	1	2	FACETS	0.812	0.633	1	0.812	0.633	1	CLONAL	1	TRUE	1	0.764093330677973	2		406	58	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0062851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	128	1032	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.986	0.902	1	0.986	0.902	1	CLONAL	1	TRUE	1	0.651019009698881	2		1032	399	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0062851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	213	476	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.651019009698881	2		476	624	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0062851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	243	664	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	1	2	FACETS	0.964	0.904	1	0.964	0.904	1	CLONAL	1	TRUE	1	0.651019009698881	2		664	774	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457308	67457308	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	314	854	2	ENST00000327367.4:c.282G>A	p.Trp94Ter	p.W94*	ENST00000327367	NM_005902.3	94	tgG/tgA	2/9	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.651019009698881	2		856	889	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195401	102195401	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	237	531	0	ENST00000263464.3:c.161G>T	p.Gly54Val	p.G54V	ENST00000263464	NM_001165.4	54	gGt/gTt	2/9	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.651019009698881	2		531	679	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422992	45422993	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0062851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	36	591	0	ENST00000262160.6:c.135_136del	p.Leu48GlyfsTer12	p.L48Gfs*12	ENST00000262160	NM_005901.5	45	gtGAaa/gtaa	2/11	0.651019009698881	1	FACETS	0.153	0.126	0.185	0.153	0.126	0.185	SUBCLONAL	1	TRUE	0	0.651019009698881	1		591	486	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729985	39729985	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	52	405	0	ENST00000361337.2:c.1300C>T	p.Arg434Ter	p.R434*	ENST00000361337	NM_003286.2	434	Cga/Tga	13/21	0.651019009698881	3	FACETS	0.275	0.233	0.321	0.137	0.116	0.161	SUBCLONAL	1	TRUE	1	0.651019009698881	3		405	771	SUCCESS
APC	324	MSKCC	GRCh37	5	112155034	112155035	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AATCC	novel	NA	P-0062851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	162	432	0	ENST00000257430.4:c.1308_1312dup	p.Met438IlefsTer18	p.M438Ifs*18	ENST00000257430	NM_000038.5	435	-/AATCC	10/16	1	2	FACETS	0.897	0.828	0.968	0.897	0.828	0.968	CLONAL	1	TRUE	1	0.651019009698881	2		432	555	SUCCESS
APC	324	MSKCC	GRCh37	5	112173338	112173338	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	160	463	0	ENST00000257430.4:c.2047A>C	p.Thr683Pro	p.T683P	ENST00000257430	NM_000038.5	683	Act/Cct	16/16	1	2	FACETS	0.886	0.817	0.957	0.886	0.817	0.957	CLONAL	1	TRUE	1	0.651019009698881	2		463	555	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062852-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	138	343	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.816	0.749	0.885	0.816	0.749	0.885	CLONAL	1	TRUE	1	0.779684168605337	2		343	434	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961058	55961058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199904772	NA	P-0062852-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	232	545	0	ENST00000263923.4:c.2882G>A	p.Arg961Gln	p.R961Q	ENST00000263923	NM_002253.2	961	cGg/cAg	21/30	1	2	FACETS	0.999	0.938	1	0.999	0.938	1	CLONAL	1	TRUE	1	0.779684168605337	2		545	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0062853-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	299	586	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.74505810624589	3	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.914806538177749	3		586	711	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131161	55131161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062853-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	835	420	0	ENST00000257290.5:c.704G>A	p.Cys235Tyr	p.C235Y	ENST00000257290	NM_006206.4	235	tGt/tAt	5/23	0.697531665081462	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	1	0.914806538177749	4		420	1156	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579321	7579322	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs587780067	NA	P-0062853-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	336	592	1	ENST00000269305.4:c.365_366del	p.Val122AspfsTer26	p.V122Dfs*26	ENST00000269305	NM_001126112.2	122	gTG/g	4/11	0.74505810624589	3	FACETS	1	0.995	1			1	CLONAL	1	TRUE	NA	0.914806538177749	3		593	754	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252155	226252155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553260624	NA	P-0062853-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	221	263	0	ENST00000366813.1:c.103G>A	p.Gly35Arg	p.G35R	ENST00000366813		35	Ggg/Agg	1/3	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.914806538177749	2		263	447	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814193	76814194	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0062853-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	428	174	0	ENST00000373344.5:c.6450_6451del	p.Arg2150SerfsTer8	p.R2150Sfs*8	ENST00000373344	NM_000489.3	2150	agAGtt/agtt	29/35	0.708581020289679	2	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.914806538177749	2		174	456	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446064	49446064	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062854-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	391	1014	0	ENST00000301067.7:c.1402del	p.Ser468HisfsTer462	p.S468Hfs*462	ENST00000301067	NM_003482.3	468	Tca/ca	10/54	1	2	FACETS	0.867	0.823	0.912	0.867	0.823	0.912	CLONAL	1	TRUE	1	0.646806973898557	2		1014	1394	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000101	30000101	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062854-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	198	476	0	ENST00000338641.4:c.114G>C	p.Glu38Asp	p.E38D	ENST00000338641	NM_000268.3	38	gaG/gaC	1/16	0.646806973898557	1	FACETS	0.957	0.897	1	0.957	0.897	1	CLONAL	1	TRUE	0	0.646806973898557	1		476	433	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971162	21971162	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062854-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	286	711	0	ENST00000304494.5:c.196del	p.His66ThrfsTer80	p.H66Tfs*80	ENST00000304494	NM_000077.4	66	Cac/ac	2/3	0.646806973898557	1	FACETS	0.957	0.908	1	0.957	0.908	1	CLONAL	1	TRUE	0	0.646806973898557	1		711	625	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937661	44937661	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062854-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	77	226	0	ENST00000377967.4:c.2849A>G	p.Asp950Gly	p.D950G	ENST00000377967	NM_021140.2	950	gAt/gGt	19/29	0.359672598473102	1	FACETS	0.463	0.409	0.52	0.463	0.409	0.52	INDETERMINATE	1	TRUE	0	0.646806973898557	1		226	348	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0062855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	70	241	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.252215513969498	2		241	519	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105568	27105568	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	295	456	0	ENST00000324856.7:c.5179A>T	p.Ile1727Phe	p.I1727F	ENST00000324856	NM_006015.4	1727	Atc/Ttc	20/20	0.835221094427599	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.836842172370339	2		456	328	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46527665	46527665	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776150263	NA	P-0062856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	95	295	0	ENST00000262741.5:c.700G>A	p.Glu234Lys	p.E234K	ENST00000262741	NM_003629.3	234	Gaa/Aaa	6/10	0.558673373996374	5	FACETS	0.769	0.691	0.849	0.513	0.461	0.566	SUBCLONAL	2	TRUE	2	0.836842172370339	5		295	333	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23625371	23625386	+	frameshift_variant	Frame_Shift_Del	DEL	TCAATGTGCATCTTTT	TCAATGTGCATCTTTT	-	novel	NA	P-0062856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	67	333	0	ENST00000261584.4:c.3140_3155del	p.Lys1047MetfsTer23	p.K1047Mfs*23	ENST00000261584	NM_024675.3	1047	aAAAAGATGCACATTGAt/at	11/13	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.836842172370339	2		333	160	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0062856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	349	618	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.837755751987317	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.836842172370339	2		618	392	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61324516	61324516	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	35	267	0	ENST00000283752.5:c.600T>A	p.Phe200Leu	p.F200L	ENST00000283752	NM_006919.2	200	ttT/ttA	6/8	1	2	FACETS	0.62	0.517	0.73	0.62	0.517	0.73	SUBCLONAL	1	TRUE	1	0.836842172370339	2		267	135	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216452	36216452	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1210523879	NA	P-0062856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	148	604	0	ENST00000222270.7:c.3715C>T	p.Gln1239Ter	p.Q1239*	ENST00000222270	NM_014727.1	1239	Cag/Tag	12/37	0.535479004942141	4	FACETS	1	0.984	1	0.429	0.394	0.465	CLONAL	1	TRUE	1	0.836842172370339	4		604	505	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786842	135786842	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	142	420	0	ENST00000298552.3:c.1027C>T	p.Gln343Ter	p.Q343*	ENST00000298552	NM_001162426.1	343	Caa/Taa	10/23	1	2	FACETS	0.935	0.863	1	0.935	0.863	1	CLONAL	1	TRUE	1	0.836842172370339	2		420	363	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0062857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	165	746	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.443228351471961	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.443228351471961	1		746	494	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0062857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	76	438	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.386890728056758	2	FACETS	1	0.972	1	0.662	0.588	0.739	CLONAL	1	TRUE	0	0.443228351471961	2		438	259	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317099	11317099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201093943	NA	P-0062857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	34	681	0	ENST00000361445.4:c.395G>A	p.Arg132His	p.R132H	ENST00000361445	NM_004958.3	132	cGt/cAt	4/58	0.41136463691809	2	FACETS	0.289	0.235	0.349	0.144	0.117	0.175	SUBCLONAL	1	TRUE	0	0.443228351471961	2		681	531	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912149	114912149	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	185	490	0	ENST00000543371.1:c.1219C>T	p.Arg407Ter	p.R407*	ENST00000543371	NM_001198531.1	407	Cga/Tga	11/14	0.173539428145517	2	FACETS	0.774	0.72	0.83	0.774	0.72	0.83	INDETERMINATE	2	TRUE	0	0.443228351471961	2		490	539	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919631	28919631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200840674	NA	P-0062857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	45	527	0	ENST00000282397.4:c.2306C>T	p.Ala769Val	p.A769V	ENST00000282397	NM_002019.4	769	gCg/gTg	16/30	0.301628141362439	4	FACETS	0.435	0.364	0.513	0.217	0.182	0.257	SUBCLONAL	1	TRUE	2	0.443228351471961	4		527	674	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870487	40870487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770125478	NA	P-0062857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	56	597	0	ENST00000428826.2:c.916G>A	p.Asp306Asn	p.D306N	ENST00000428826		306	Gac/Aac	9/21	1	2	FACETS	0.428	0.367	0.496	0.428	0.367	0.496	SUBCLONAL	1	TRUE	1	0.443228351471961	2		597	590	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639987	3639987	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	75	682	0	ENST00000294008.3:c.3652G>A	p.Asp1218Asn	p.D1218N	ENST00000294008	NM_032444.2	1218	Gat/Aat	12/15	0.443228351471961	3	FACETS	0.742	0.651	0.84	0.371	0.325	0.42	SUBCLONAL	1	TRUE	1	0.443228351471961	3		682	557	SUCCESS
APC	324	MSKCC	GRCh37	5	112177578	112177578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	114	514	0	ENST00000257430.4:c.6287C>T	p.Ser2096Leu	p.S2096L	ENST00000257430	NM_000038.5	2096	tCa/tTa	16/16	0.386890728056758	2	FACETS	1	0.985	1	0.731	0.665	0.798	CLONAL	1	TRUE	0	0.443228351471961	2		514	352	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243047	105243048	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCAGGCAGCGGATGATGAAGGTGTTGGGCCGGGGCC	novel	NA	P-0062858-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	150	632	0	ENST00000349310.3:c.200_235dup	p.Arg67_Leu78dup	p.R67_L78dup	ENST00000349310	NM_001014432.1	67	cag/cGGCCCCGGCCCAACACCTTCATCATCCGCTGCCTGCag	5/15	0.516740280584078	4	FACETS	1	0.98	1	0.615	0.564	0.669	CLONAL	1	TRUE	2	0.562691157159549	4		632	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578283	+	inframe_deletion	In_Frame_Del	DEL	CCACTCGGATAAGATGCTGAGGAGGGG	CCACTCGGATAAGATGCTGAGGAGGGG	-	novel	NA	P-0062858-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	247	790	0	ENST00000269305.4:c.566_592del	p.Ala189_Val197del	p.A189_V197del	ENST00000269305	NM_001126112.2	189	gCCCCTCCTCAGCATCTTATCCGAGTGGaa/gaa	6/11	0.562691157159549	2	FACETS	0.969	0.919	1	0.969	0.919	1	CLONAL	2	TRUE	0	0.562691157159549	2		790	453	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424532	47424532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1321474185	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	137	847	0	ENST00000377045.4:c.452G>A	p.Arg151His	p.R151H	ENST00000377045	NM_001654.4	151	cGc/cAc	5/16	0.443637943653337	0	FACETS	0.514	0.468	0.561			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		847	669	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052603	42052603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	93	746	0	ENST00000219905.7:c.7274G>A	p.Arg2425His	p.R2425H	ENST00000219905	NM_001164273.1	2425	cGc/cAc	20/24	0.443637943653337	0	FACETS	0.258	0.229	0.29			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		746	903	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	82	517	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.443637943653337	0	FACETS	0.492	0.436	0.552			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		517	418	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776003	9776003	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	132	986	1	ENST00000377346.4:c.467A>G	p.Gln156Arg	p.Q156R	ENST00000377346	NM_005026.3	156	cAg/cGg	5/24	0.443637943653337	0	FACETS	0.515	0.468	0.563			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		987	643	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782113	9782113	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	112	854	0	ENST00000377346.4:c.2136G>T	p.Lys712Asn	p.K712N	ENST00000377346	NM_005026.3	712	aaG/aaT	17/24	0.443637943653337	0	FACETS	0.46	0.414	0.508			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		854	611	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784418	9784418	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	131	759	0	ENST00000377346.4:c.2803A>G	p.Thr935Ala	p.T935A	ENST00000377346	NM_005026.3	935	Acc/Gcc	22/24	0.443637943653337	0	FACETS	0.513	0.466	0.561			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		759	641	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190723	11190723	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	178	1042	0	ENST00000361445.4:c.5476A>G	p.Thr1826Ala	p.T1826A	ENST00000361445	NM_004958.3	1826	Acc/Gcc	39/58	0.443637943653337	0	FACETS	0.568	0.524	0.613			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1042	786	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11205032	11205032	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	32	644	0	ENST00000361445.4:c.4757C>T	p.Ala1586Val	p.A1586V	ENST00000361445	NM_004958.3	1586	gCa/gTa	33/58	0.443637943653337	0	FACETS	0.141	0.113	0.171			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		644	571	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317015	11317015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759750826	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	42	855	2	ENST00000361445.4:c.479G>A	p.Arg160His	p.R160H	ENST00000361445	NM_004958.3	160	cGc/cAc	4/58	0.443637943653337	0	FACETS	0.155	0.129	0.184			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		857	679	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16235818	16235818	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	119	533	0	ENST00000375759.3:c.884G>A	p.Ser295Asn	p.S295N	ENST00000375759	NM_015001.2	295	aGt/aAt	4/15	0.443637943653337	0	FACETS	0.485	0.438	0.533			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		533	616	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255402	16255402	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	158	804	0	ENST00000375759.3:c.2667G>T	p.Lys889Asn	p.K889N	ENST00000375759	NM_015001.2	889	aaG/aaT	11/15	0.443637943653337	0	FACETS	0.55	0.505	0.597			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		804	721	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023528	27023528	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	129	751	0	ENST00000324856.7:c.634T>C	p.Tyr212His	p.Y212H	ENST00000324856	NM_006015.4	212	Tac/Cac	1/20	0.443637943653337	0	FACETS	0.631	0.575	0.689			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		751	513	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023556	27023556	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	133	715	0	ENST00000324856.7:c.662C>A	p.Ala221Asp	p.A221D	ENST00000324856	NM_006015.4	221	gCc/gAc	1/20	0.443637943653337	0	FACETS	0.684	0.625	0.745			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		715	488	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089734	27089734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	203	903	0	ENST00000324856.7:c.2690C>T	p.Thr897Ile	p.T897I	ENST00000324856	NM_006015.4	897	aCt/aTt	8/20	0.443637943653337	0	FACETS	0.618	0.574	0.663			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		903	824	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100175	27100176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	187	1075	0	ENST00000324856.7:c.3977dup	p.Gln1327AlafsTer11	p.Q1327Afs*11	ENST00000324856	NM_006015.4	1324	tac/taCc	16/20	0.443637943653337	0	FACETS	0.554	0.512	0.597			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1075	847	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28607258	28607258	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1438624951	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	151	816	0	ENST00000253063.3:c.1388G>A	p.Arg463His	p.R463H	ENST00000253063	NM_031459.4	463	cGc/cAc	10/10	0.443637943653337	0	FACETS	0.55	0.504	0.598			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		816	689	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809788	36809788	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	150	875	0	ENST00000373129.3:c.817C>T	p.Pro273Ser	p.P273S	ENST00000373129	NM_032017.1	273	Ccc/Tcc	9/12	0.443637943653337	0	FACETS	0.64	0.587	0.694			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		875	588	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36814357	36814357	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	167	848	2	ENST00000373129.3:c.683A>G	p.Asp228Gly	p.D228G	ENST00000373129	NM_032017.1	228	gAc/gGc	8/12	0.443637943653337	0	FACETS	0.527	0.485	0.571			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		850	795	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932265	36932265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	181	1000	0	ENST00000361632.4:c.2204C>T	p.Ala735Val	p.A735V	ENST00000361632		735	gCa/gTa	16/16	0.443637943653337	0	FACETS	0.621	0.574	0.669			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1000	731	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935432	36935432	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	142	790	0	ENST00000361632.4:c.1295T>C	p.Leu432Pro	p.L432P	ENST00000361632		432	cTg/cCg	10/16	0.443637943653337	0	FACETS	0.567	0.518	0.618			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		790	628	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39321569	39321569	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	97	391	2	ENST00000373001.3:c.452T>C	p.Met151Thr	p.M151T	ENST00000373001	NM_022157.3	151	aTg/aCg	3/7	0.443637943653337	0	FACETS	0.579	0.52	0.642			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		393	420	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322727	39322727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764801643	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	92	485	0	ENST00000373001.3:c.265G>A	p.Glu89Lys	p.E89K	ENST00000373001	NM_022157.3	89	Gag/Aag	2/7	0.443637943653337	0	FACETS	0.539	0.482	0.6			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		485	428	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546383	46546383	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	44	597	0	ENST00000262741.5:c.146T>C	p.Val49Ala	p.V49A	ENST00000262741	NM_003629.3	49	gTt/gCt	2/10	0.443637943653337	0	FACETS	0.208	0.174	0.245			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		597	531	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726526	46726526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761573792	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	158	915	0	ENST00000371975.4:c.605G>A	p.Arg202His	p.R202H	ENST00000371975	NM_003579.3	202	cGc/cAc	7/18	0.443637943653337	0	FACETS	0.522	0.479	0.567			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		915	759	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301137	65301137	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	158	589	0	ENST00000342505.4:c.3311T>C	p.Leu1104Pro	p.L1104P	ENST00000342505	NM_002227.2	1104	cTt/cCt	24/25	0.443637943653337	0	FACETS	0.52	0.477	0.565			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		589	762	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344833	65344833	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	91	602	0	ENST00000342505.4:c.206-2A>G		p.X69_splice	ENST00000342505	NM_002227.2	69			0.443637943653337	0	FACETS	0.426	0.379	0.476			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		602	536	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076708	72076708	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	118	660	0	ENST00000357731.5:c.788+1G>A		p.X263_splice	ENST00000357731	NM_173808.2	263			0.443637943653337	0	FACETS	0.485	0.439	0.534			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		660	610	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78425905	78425905	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	66	820	0	ENST00000370768.2:c.1540T>A	p.Tyr514Asn	p.Y514N	ENST00000370768	NM_003902.3	514	Tat/Aat	16/20	0.443637943653337	0	FACETS	0.219	0.189	0.251			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		820	757	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733372	85733372	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	144	640	0	ENST00000370580.1:c.640A>G	p.Thr214Ala	p.T214A	ENST00000370580	NM_003921.4	214	Act/Gct	3/3	0.443637943653337	0	FACETS	0.591	0.541	0.643			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		640	611	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263225	115263225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	138	700	0	ENST00000438362.2:c.2125G>A	p.Ala709Thr	p.A709T	ENST00000438362	NM_001242891.1	709	Gca/Aca	17/20	0.443637943653337	0	FACETS	0.565	0.515	0.616			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		700	613	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263231	115263231	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	139	694	0	ENST00000438362.2:c.2119C>T	p.Gln707Ter	p.Q707*	ENST00000438362	NM_001242891.1	707	Caa/Taa	17/20	0.443637943653337	0	FACETS	0.557	0.508	0.607			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		694	626	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275325	115275325	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	110	600	0	ENST00000438362.2:c.1088G>T	p.Arg363Met	p.R363M	ENST00000438362	NM_001242891.1	363	aGg/aTg	10/20	0.443637943653337	0	FACETS	0.541	0.488	0.597			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		600	510	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471731	120471731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	169	847	2	ENST00000256646.2:c.3760C>T	p.Pro1254Ser	p.P1254S	ENST00000256646	NM_024408.3	1254	Cct/Tct	23/34	0.443637943653337	0	FACETS	0.536	0.493	0.58			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		849	791	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510137	120510137	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	139	814	0	ENST00000256646.2:c.1372A>G	p.Asn458Asp	p.N458D	ENST00000256646	NM_024408.3	458	Aat/Gat	8/34	0.443637943653337	0	FACETS	0.489	0.446	0.534			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		814	713	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150913833	150913833	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	101	485	0	ENST00000271640.5:c.476A>G	p.Lys159Arg	p.K159R	ENST00000271640	NM_001145415.1	159	aAg/aGg	5/22	0.443637943653337	0	FACETS	0.531	0.477	0.588			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		485	477	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150919401	150919401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377752861	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	129	663	0	ENST00000271640.5:c.1180C>T	p.Arg394Trp	p.R394W	ENST00000271640	NM_001145415.1	394	Cgg/Tgg	10/22	0.443637943653337	0	FACETS	0.556	0.506	0.608			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		663	582	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150933350	150933350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759691820	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	148	1023	0	ENST00000271640.5:c.2812G>A	p.Gly938Arg	p.G938R	ENST00000271640	NM_001145415.1	938	Gga/Aga	16/22	0.443637943653337	0	FACETS	0.476	0.435	0.519			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1023	780	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150933600	150933600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150892641	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	166	834	0	ENST00000271640.5:c.3062C>T	p.Ala1021Val	p.A1021V	ENST00000271640	NM_001145415.1	1021	gCt/gTt	16/22	0.443637943653337	0	FACETS	0.66	0.608	0.713			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		834	631	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731122	162731122	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	187	907	1	ENST00000367921.3:c.977A>T	p.Asp326Val	p.D326V	ENST00000367921	NM_006182.2	326	gAc/gTc	9/18	0.443637943653337	0	FACETS	0.558	0.516	0.601			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		908	841	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741879	162741879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	144	793	0	ENST00000367921.3:c.1570G>A	p.Ala524Thr	p.A524T	ENST00000367921	NM_006182.2	524	Gct/Act	13/18	0.443637943653337	0	FACETS	0.564	0.516	0.615			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		793	640	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745470	162745470	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	90	604	0	ENST00000367921.3:c.1885A>G	p.Met629Val	p.M629V	ENST00000367921	NM_006182.2	629	Atg/Gtg	15/18	0.443637943653337	0	FACETS	0.504	0.449	0.562			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		604	448	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163298020	163298020	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	47	314	0	ENST00000271452.3:c.201G>A	p.Met67Ile	p.M67I	ENST00000271452	NM_145697.2	67	atG/atA	4/14	0.443637943653337	0	FACETS	0.515	0.439	0.597			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		314	229	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163298076	163298076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	52	349	0	ENST00000271452.3:c.257G>A	p.Ser86Asn	p.S86N	ENST00000271452	NM_145697.2	86	aGc/aAc	4/14	0.443637943653337	0	FACETS	0.504	0.432	0.58			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		349	259	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176133027	176133027	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	51	253	0	ENST00000367669.3:c.566T>C	p.Val189Ala	p.V189A	ENST00000367669	NM_022457.5	189	gTg/gCg	4/20	0.443637943653337	0	FACETS	0.479	0.41	0.553			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		253	267	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648217	206648217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149591181	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	115	803	0	ENST00000367120.3:c.238C>T	p.Arg80Trp	p.R80W	ENST00000367120	NM_014002.3	80	Cgg/Tgg	5/22	0.443637943653337	0	FACETS	0.501	0.452	0.552			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		803	576	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206665043	206665043	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	167	783	0	ENST00000367120.3:c.1796A>G	p.Lys599Arg	p.K599R	ENST00000367120	NM_014002.3	599	aAg/aGg	18/22	0.443637943653337	0	FACETS	0.553	0.509	0.599			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		783	757	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666671	206666671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	136	827	0	ENST00000367120.3:c.2005G>A	p.Ala669Thr	p.A669T	ENST00000367120	NM_014002.3	669	Gct/Act	20/22	0.443637943653337	0	FACETS	0.492	0.448	0.538			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		827	694	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666712	206666712	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	135	704	0	ENST00000367120.3:c.2045+1G>A		p.X682_splice	ENST00000367120	NM_014002.3	682			0.443637943653337	0	FACETS	0.551	0.502	0.601			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		704	615	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555934	226555934	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs920832776	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	117	711	0	ENST00000366794.5:c.2243A>G	p.Lys748Arg	p.K748R	ENST00000366794	NM_001618.3	748	aAg/aGg	16/23	0.443637943653337	0	FACETS	0.476	0.43	0.525			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		711	616	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570752	226570752	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	154	863	0	ENST00000366794.5:c.1144T>A	p.Ser382Thr	p.S382T	ENST00000366794	NM_001618.3	382	Tcc/Acc	8/23	0.443637943653337	0	FACETS	0.49	0.448	0.533			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		863	789	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667384	241667384	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	144	692	0	ENST00000366560.3:c.1066T>A	p.Leu356Met	p.L356M	ENST00000366560	NM_000143.3	356	Ttg/Atg	7/10	0.443637943653337	0	FACETS	0.588	0.538	0.64			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		692	614	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667545	241667545	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	78	388	0	ENST00000366560.3:c.905G>A	p.Gly302Asp	p.G302D	ENST00000366560	NM_000143.3	302	gGc/gAc	7/10	0.443637943653337	0	FACETS	0.458	0.404	0.516			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		388	427	SUCCESS
FH	2271	MSKCC	GRCh37	1	241671961	241671961	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	89	451	0	ENST00000366560.3:c.680A>G	p.Gln227Arg	p.Q227R	ENST00000366560	NM_000143.3	227	cAg/cGg	5/10	0.443637943653337	0	FACETS	0.638	0.57	0.709			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		451	350	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100525	8100525	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	98	1036	0	ENST00000346208.3:c.499C>A	p.Leu167Met	p.L167M	ENST00000346208		167	Ctg/Atg	3/6	0.443637943653337	0	FACETS	0.386	0.344	0.43			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1036	637	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100727	8100727	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	117	873	0	ENST00000346208.3:c.701T>C	p.Phe234Ser	p.F234S	ENST00000346208		234	tTc/tCc	3/6	0.443637943653337	0	FACETS	0.495	0.447	0.545			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		873	593	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106097	8106097	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	138	682	0	ENST00000346208.3:c.917G>A	p.Arg306Lys	p.R306K	ENST00000346208		306	aGg/aAg	4/6	0.443637943653337	0	FACETS	0.577	0.527	0.629			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		682	600	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609990	43609990	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs77711105	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	179	1156	0	ENST00000355710.3:c.1942G>A	p.Val648Ile	p.V648I	ENST00000355710	NM_020975.4	648	Gtc/Atc	11/20	0.443637943653337	0	FACETS	0.554	0.511	0.598			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1156	811	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851758	63851758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	136	891	0	ENST00000279873.7:c.2536C>T	p.His846Tyr	p.H846Y	ENST00000279873	NM_032199.2	846	Cac/Tac	10/10	0.443637943653337	0	FACETS	0.5	0.456	0.547			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		891	682	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332957	70332957	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	30	714	0	ENST00000373644.4:c.862G>T	p.Asp288Tyr	p.D288Y	ENST00000373644	NM_030625.2	288	Gat/Tat	2/12	0.443637943653337	0	FACETS	0.129	0.103	0.158			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		714	585	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685315	89685315	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1554897280	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	27	105	0	ENST00000371953.3:c.209+1G>A		p.X70_splice	ENST00000371953	NM_000314.4	70			0.443637943653337	0	FACETS	0.351	0.281	0.429			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		105	193	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711927	89711928	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554900593	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	62	419	0	ENST00000371953.3:c.548dup	p.Asn184GlufsTer6	p.N184Efs*6	ENST00000371953	NM_000314.4	182	tta/ttAa	6/9	0.443637943653337	0	FACETS	0.51	0.444	0.581			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		419	305	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279675	123279675	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	168	790	0	ENST00000358487.5:c.757C>G	p.Pro253Ala	p.P253A	ENST00000358487	NM_000141.4	253	Cct/Gct	7/18	0.443637943653337	0	FACETS	0.545	0.502	0.59			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		790	773	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156636	2156636	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	119	992	0	ENST00000434045.2:c.286A>T	p.Thr96Ser	p.T96S	ENST00000434045	NM_001127598.1	96	Acc/Tcc	3/5	0.443637943653337	0	FACETS	0.442	0.399	0.487			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		992	675	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10777246	10777246	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	69	470	0	ENST00000361367.2:c.406T>A	p.Cys136Ser	p.C136S	ENST00000361367	NM_014633.3	136	Tgc/Agc	4/25	0.443637943653337	0	FACETS	0.459	0.402	0.52			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		470	377	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10778295	10778295	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	78	284	0	ENST00000361367.2:c.503-1G>T		p.X168_splice	ENST00000361367	NM_014633.3	168			0.443637943653337	0	FACETS	0.557	0.493	0.625			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		284	351	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316397	14316397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782457908	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	70	512	0	ENST00000256196.4:c.208G>A	p.Ala70Thr	p.A70T	ENST00000256196		70	Gca/Aca	3/6	0.443637943653337	0	FACETS	0.5	0.439	0.566			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		512	351	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741457	17741457	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1283272430	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	118	798	0	ENST00000250003.3:c.128T>C	p.Phe43Ser	p.F43S	ENST00000250003	NM_002478.4	43	tTc/tCc	1/3	0.443637943653337	0	FACETS	0.564	0.511	0.619			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		798	525	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741691	17741691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	108	897	0	ENST00000250003.3:c.362G>A	p.Arg121His	p.R121H	ENST00000250003	NM_002478.4	121	cGc/cAc	1/3	0.443637943653337	0	FACETS	0.518	0.466	0.572			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		897	523	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741835	17741835	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	34	687	0	ENST00000250003.3:c.506C>T	p.Ala169Val	p.A169V	ENST00000250003	NM_002478.4	169	gCc/gTc	1/3	0.443637943653337	0	FACETS	0.216	0.176	0.26			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		687	395	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741858	17741858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	98	668	0	ENST00000250003.3:c.529G>A	p.Ala177Thr	p.A177T	ENST00000250003	NM_002478.4	177	Gcc/Acc	1/3	0.443637943653337	0	FACETS	0.687	0.618	0.758			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		668	358	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421529	32421529	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	45	839	0	ENST00000332351.3:c.1063A>G	p.Arg355Gly	p.R355G	ENST00000332351	NM_024426.4	355	Aga/Gga	6/10	0.443637943653337	0	FACETS	0.16	0.134	0.189			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		839	705	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47594577	47594577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	175	949	0	ENST00000430070.2:c.1510G>A	p.Ala504Thr	p.A504T	ENST00000430070	NM_018095.4	504	Gcc/Acc	4/4	0.443637943653337	0	FACETS	0.595	0.549	0.642			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		949	738	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132833	64132833	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1447050686	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	164	928	0	ENST00000334205.4:c.967C>T	p.Arg323Cys	p.R323C	ENST00000334205	NM_003942.2	323	Cgc/Tgc	9/17	0.443637943653337	0	FACETS	0.55	0.506	0.596			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		928	748	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575123	64575123	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	179	931	0	ENST00000312049.6:c.684G>A	p.Met228Ile	p.M228I	ENST00000312049	NM_130799.2	228	atG/atA	4/10	0.443637943653337	0	FACETS	0.599	0.554	0.647			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		931	749	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625080	69625080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782166974	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	83	667	0	ENST00000334134.2:c.713C>T	p.Ala238Val	p.A238V	ENST00000334134	NM_005247.2	238	gCg/gTg	3/3	0.443637943653337	0	FACETS	0.44	0.39	0.494			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		667	473	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936080	71936080	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	21	659	0	ENST00000298229.2:c.52G>C	p.Ala18Pro	p.A18P	ENST00000298229	NM_001567.3	18	Gcc/Ccc	1/28	0.443637943653337	0	FACETS	0.153	0.117	0.194			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		659	345	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194122	94194122	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587781439	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	65	274	0	ENST00000323929.3:c.1306T>C	p.Tyr436His	p.Y436H	ENST00000323929	NM_005591.3	436	Tac/Cac	12/20	0.443637943653337	0	FACETS	0.471	0.411	0.536			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		274	346	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94923106	94923106	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	63	439	1	ENST00000536441.1:c.362G>A	p.Cys121Tyr	p.C121Y	ENST00000536441	NM_144665.3	121	tGt/tAt	4/10	0.443637943653337	0	FACETS	0.472	0.41	0.537			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		440	335	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998402	100998402	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	40	742	0	ENST00000325455.5:c.1400G>A	p.Gly467Asp	p.G467D	ENST00000325455	NM_001202474.3	467	gGc/gAc	1/8	0.443637943653337	0	FACETS	0.245	0.204	0.291			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		742	409	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998543	100998543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	129	895	0	ENST00000325455.5:c.1259G>A	p.Gly420Glu	p.G420E	ENST00000325455	NM_001202474.3	420	gGg/gAg	1/8	0.443637943653337	0	FACETS	0.559	0.508	0.611			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		895	579	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102098229	102098229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	106	534	0	ENST00000282441.5:c.1193C>T	p.Thr398Ile	p.T398I	ENST00000282441	NM_001130145.2	398	aCa/aTa	8/9	0.443637943653337	0	FACETS	0.483	0.434	0.534			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		534	551	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206871	102206871	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	76	427	0	ENST00000263464.3:c.1499T>C	p.Leu500Ser	p.L500S	ENST00000263464	NM_001165.4	500	tTa/tCa	7/9	0.443637943653337	0	FACETS	0.462	0.407	0.52			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		427	413	SUCCESS
ATM	472	MSKCC	GRCh37	11	108128328	108128328	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555075814	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	53	259	0	ENST00000278616.4:c.2371A>G	p.Thr791Ala	p.T791A	ENST00000278616	NM_000051.3	791	Acc/Gcc	15/63	0.443637943653337	0	FACETS	0.465	0.399	0.536			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		259	286	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160528	108160528	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	107	315	0	ENST00000278616.4:c.4436G>T	p.Arg1479Met	p.R1479M	ENST00000278616	NM_000051.3	1479	aGg/aTg	29/63	0.443637943653337	0	FACETS	0.731	0.662	0.803			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		315	367	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172405	108172405	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	83	451	0	ENST00000278616.4:c.5208T>A	p.Cys1736Ter	p.C1736*	ENST00000278616	NM_000051.3	1736	tgT/tgA	35/63	0.443637943653337	0	FACETS	0.588	0.523	0.657			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		451	354	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111957645	111957645	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs104894310	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	148	603	1	ENST00000375549.3:c.14G>A	p.Trp5Ter	p.W5*	ENST00000375549	NM_003002.3	5	tGg/tAg	1/4	0.443637943653337	0	FACETS	0.669	0.614	0.726			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		604	555	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373980	118373980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1367628820	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	102	775	0	ENST00000534358.1:c.7373G>A	p.Gly2458Asp	p.G2458D	ENST00000534358	NM_005933.3	2458	gGt/gAt	27/36	0.443637943653337	0	FACETS	0.451	0.404	0.501			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		775	567	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118391564	118391565	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	105	505	0	ENST00000534358.1:c.11483dup	p.Thr3829AspfsTer3	p.T3829Dfs*3	ENST00000534358	NM_005933.3	3826	tta/ttAa	34/36	0.443637943653337	0	FACETS	0.529	0.476	0.585			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		505	498	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142506	119142506	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	114	548	0	ENST00000264033.4:c.505T>G	p.Phe169Val	p.F169V	ENST00000264033	NM_005188.3	169	Ttt/Gtt	3/16	0.443637943653337	0	FACETS	0.594	0.538	0.653			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		548	481	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155909	119155909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	176	906	1	ENST00000264033.4:c.1574G>A	p.Gly525Asp	p.G525D	ENST00000264033	NM_005188.3	525	gGc/gAc	11/16	0.443637943653337	0	FACETS	0.563	0.519	0.608			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		907	784	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406317	406318	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	63	609	2	ENST00000399788.2:c.4123dup	p.Cys1375LeufsTer2	p.C1375Lfs*2	ENST00000399788	NM_001042603.1	1375	tgt/tTgt	25/28	0.443637943653337	0	FACETS	0.294	0.254	0.337			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		611	538	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398119	4398119	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	109	615	2	ENST00000261254.3:c.683T>C	p.Leu228Pro	p.L228P	ENST00000261254	NM_001759.3	228	cTg/cCg	4/5	0.443637943653337	0	FACETS	0.517	0.466	0.571			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		617	529	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409159	4409159	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753881524	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	140	744	0	ENST00000261254.3:c.854G>A	p.Arg285Gln	p.R285Q	ENST00000261254	NM_001759.3	285	cGg/cAg	5/5	0.443637943653337	0	FACETS	0.528	0.482	0.576			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		744	665	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21643223	21643223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1065751	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	95	441	0	ENST00000421138.2:c.304G>A	p.Val102Ile	p.V102I	ENST00000421138		102	Gta/Ata	5/16	0.443637943653337	0	FACETS	0.605	0.542	0.67			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		441	394	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233172	46233172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376273452	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	104	556	0	ENST00000334344.6:c.1391C>T	p.Ala464Val	p.A464V	ENST00000334344	NM_152641.2	464	gCg/gTg	11/21	0.443637943653337	0	FACETS	0.473	0.425	0.524			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		556	551	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243385	46243385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	88	501	0	ENST00000334344.6:c.1738G>A	p.Val580Met	p.V580M	ENST00000334344	NM_152641.2	580	Gtg/Atg	14/21	0.443637943653337	0	FACETS	0.495	0.44	0.553			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		501	446	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287215	46287216	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	58	814	0	ENST00000334344.6:c.5165dup	p.Thr1723HisfsTer6	p.T1723Hfs*6	ENST00000334344	NM_152641.2	1720	-/G	19/21	0.443637943653337	0	FACETS	0.19	0.162	0.22			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		814	767	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426618	49426618	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	181	1114	0	ENST00000301067.7:c.11870A>G	p.Gln3957Arg	p.Q3957R	ENST00000301067	NM_003482.3	3957	cAg/cGg	39/54	0.443637943653337	0	FACETS	0.481	0.443	0.52			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1114	944	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427534	49427534	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	143	829	0	ENST00000301067.7:c.10954G>A	p.Ala3652Thr	p.A3652T	ENST00000301067	NM_003482.3	3652	Gcc/Acc	39/54	0.443637943653337	0	FACETS	0.612	0.56	0.666			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		829	586	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432416	49432416	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	177	1023	0	ENST00000301067.7:c.8723C>A	p.Pro2908His	p.P2908H	ENST00000301067	NM_003482.3	2908	cCt/cAt	34/54	0.443637943653337	0	FACETS	0.538	0.496	0.582			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1023	825	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434946	49434946	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	38	942	0	ENST00000301067.7:c.6607A>G	p.Thr2203Ala	p.T2203A	ENST00000301067	NM_003482.3	2203	Acg/Gcg	31/54	0.443637943653337	0	FACETS	0.168	0.139	0.202			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		942	566	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436006	49436006	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	107	862	0	ENST00000301067.7:c.5975A>T	p.Glu1992Val	p.E1992V	ENST00000301067	NM_003482.3	1992	gAg/gTg	28/54	0.443637943653337	0	FACETS	0.468	0.421	0.518			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		862	573	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439721	49439721	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs762474552	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	140	651	0	ENST00000301067.7:c.4723A>G	p.Met1575Val	p.M1575V	ENST00000301067	NM_003482.3	1575	Atg/Gtg	18/54	0.443637943653337	0	FACETS	0.579	0.529	0.632			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		651	606	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443923	49443923	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	123	932	0	ENST00000301067.7:c.3448G>T	p.Gly1150Cys	p.G1150C	ENST00000301067	NM_003482.3	1150	Ggc/Tgc	11/54	0.443637943653337	0	FACETS	0.473	0.429	0.52			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		932	652	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445425	49445425	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	176	1309	0	ENST00000301067.7:c.2041T>A	p.Ser681Thr	p.S681T	ENST00000301067	NM_003482.3	681	Tcc/Acc	10/54	0.443637943653337	0	FACETS	0.522	0.481	0.565			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1309	845	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446365	49446365	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	156	952	0	ENST00000301067.7:c.1240T>C	p.Cys414Arg	p.C414R	ENST00000301067	NM_003482.3	414	Tgt/Cgt	9/54	0.443637943653337	0	FACETS	0.523	0.48	0.568			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		952	748	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482363	56482363	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	129	676	0	ENST00000267101.3:c.911C>T	p.Ala304Val	p.A304V	ENST00000267101	NM_001982.3	304	gCc/gTc	8/28	0.443637943653337	0	FACETS	0.526	0.478	0.576			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		676	615	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487277	56487277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035001455	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	130	677	0	ENST00000267101.3:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000267101	NM_001982.3	475	Cgg/Tgg	12/28	0.443637943653337	0	FACETS	0.537	0.489	0.588			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		677	607	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495535	56495535	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	178	1018	3	ENST00000267101.3:c.3725C>A	p.Pro1242Gln	p.P1242Q	ENST00000267101	NM_001982.3	1242	cCa/cAa	28/28	0.443637943653337	0	FACETS	0.575	0.531	0.621			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1021	776	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864585	57864585	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1356844630	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	148	965	0	ENST00000228682.2:c.2062C>T	p.Gln688Ter	p.Q688*	ENST00000228682	NM_005269.2	688	Cag/Tag	12/12	0.443637943653337	0	FACETS	0.551	0.504	0.599			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		965	674	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865392	57865392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	133	955	0	ENST00000228682.2:c.2869C>T	p.Pro957Ser	p.P957S	ENST00000228682	NM_005269.2	957	Ccc/Tcc	12/12	0.443637943653337	0	FACETS	0.493	0.448	0.539			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		955	677	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865518	57865518	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	181	1037	0	ENST00000228682.2:c.2995T>C	p.Tyr999His	p.Y999H	ENST00000228682	NM_005269.2	999	Tat/Cat	12/12	0.443637943653337	0	FACETS	0.581	0.537	0.627			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1037	781	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69203031	69203031	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	103	578	0	ENST00000462284.1:c.58G>A	p.Val20Ile	p.V20I	ENST00000462284	NM_002392.5	20	Gta/Ata	2/11	0.443637943653337	0	FACETS	0.488	0.438	0.541			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		578	529	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69229754	69229754	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	60	342	0	ENST00000462284.1:c.830A>G	p.Glu277Gly	p.E277G	ENST00000462284	NM_002392.5	277	gAa/gGa	9/11	0.443637943653337	0	FACETS	0.455	0.394	0.52			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		342	331	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69230450	69230450	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	87	303	0	ENST00000462284.1:c.841-2A>G		p.X281_splice	ENST00000462284	NM_002392.5	281			0.443637943653337	0	FACETS	0.657	0.587	0.731			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		303	332	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117324	115117324	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	101	564	0	ENST00000257566.3:c.850T>C	p.Tyr284His	p.Y284H	ENST00000257566	NM_016569.3	284	Tac/Cac	4/8	0.443637943653337	0	FACETS	0.485	0.435	0.538			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		564	522	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117359	115117359	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	112	633	0	ENST00000257566.3:c.815T>C	p.Leu272Ser	p.L272S	ENST00000257566	NM_016569.3	272	tTg/tCg	4/8	0.443637943653337	0	FACETS	0.514	0.463	0.566			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		633	547	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120546259	120546259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	28	544	0	ENST00000229340.5:c.65G>A	p.Ser22Asn	p.S22N	ENST00000229340	NM_006861.6	22	aGc/aAc	2/6	0.443637943653337	0	FACETS	0.133	0.106	0.165			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		544	527	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416675	121416675	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	125	691	0	ENST00000257555.6:c.104C>A	p.Pro35His	p.P35H	ENST00000257555		35	cCc/cAc	1/10	0.443637943653337	0	FACETS	0.589	0.536	0.645			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		691	532	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209049	133209049	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	124	780	0	ENST00000320574.5:c.6182A>G	p.Gln2061Arg	p.Q2061R	ENST00000320574	NM_006231.2	2061	cAg/cGg	45/49	0.443637943653337	0	FACETS	0.567	0.514	0.621			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		780	549	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210876	133210876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201273415	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	125	865	0	ENST00000320574.5:c.5900C>T	p.Ala1967Val	p.A1967V	ENST00000320574	NM_006231.2	1967	gCg/gTg	43/49	0.443637943653337	0	FACETS	0.474	0.429	0.52			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		865	662	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549071	21549071	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	115	695	0	ENST00000382592.4:c.3205T>C	p.Ser1069Pro	p.S1069P	ENST00000382592	NM_014572.2	1069	Tca/Cca	8/8	0.443637943653337	0	FACETS	0.528	0.477	0.582			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		695	546	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557740	21557740	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	38	818	6	ENST00000382592.4:c.2105del	p.Lys702ArgfsTer4	p.K702Rfs*4	ENST00000382592	NM_014572.2	702	aAg/ag	5/8	0.443637943653337	0	FACETS	0.133	0.109	0.159			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		824	719	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563033	21563033	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	52	1001	0	ENST00000382592.4:c.886G>A	p.Gly296Arg	p.G296R	ENST00000382592	NM_014572.2	296	Gga/Aga	4/8	0.443637943653337	0	FACETS	0.208	0.177	0.243			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1001	626	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923221	26923221	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	104	507	0	ENST00000381527.3:c.217C>T	p.Leu73Phe	p.L73F	ENST00000381527	NM_001260.1	73	Ctt/Ttt	3/13	0.443637943653337	0	FACETS	0.556	0.5	0.615			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		507	469	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914975	32914975	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	55	406	0	ENST00000380152.3:c.6483C>G	p.Asp2161Glu	p.D2161E	ENST00000380152		2161	gaC/gaG	11/27	0.443637943653337	0	FACETS	0.434	0.373	0.499			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		406	318	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945188	32945188	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	81	397	0	ENST00000380152.3:c.8583A>T	p.Arg2861Ser	p.R2861S	ENST00000380152		2861	agA/agT	20/27	0.443637943653337	0	FACETS	0.494	0.438	0.554			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		397	411	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134141	41134141	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	157	885	0	ENST00000379561.5:c.1487T>A	p.Val496Asp	p.V496D	ENST00000379561	NM_002015.3	496	gTc/gAc	2/3	0.443637943653337	0	FACETS	0.536	0.492	0.583			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		885	734	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881450	48881450	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	27	288	0	ENST00000267163.4:c.172A>T	p.Thr58Ser	p.T58S	ENST00000267163	NM_000321.2	58	Act/Tct	2/27	0.443637943653337	0	FACETS	0.217	0.173	0.268			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		288	312	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281106	49281106	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs996333793	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	98	623	0	ENST00000282018.3:c.153G>T	p.Trp51Cys	p.W51C	ENST00000282018	NM_020377.2	51	tgG/tgT	1/1	0.443637943653337	0	FACETS	0.621	0.558	0.687			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		623	396	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636791	73636791	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	183	838	1	ENST00000377687.4:c.1054C>T	p.Gln352Ter	p.Q352*	ENST00000377687	NM_001730.3	352	Caa/Taa	2/4	0.443637943653337	0	FACETS	0.552	0.51	0.596			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		839	831	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504500	103504500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	89	461	0	ENST00000355739.4:c.121G>A	p.Gly41Arg	p.G41R	ENST00000355739	NM_000123.3	41	Gga/Aga	2/15	0.443637943653337	0	FACETS	0.554	0.494	0.617			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		461	403	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519063	103519063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	161	741	0	ENST00000355739.4:c.2401G>A	p.Asp801Asn	p.D801N	ENST00000355739	NM_000123.3	801	Gat/Aat	11/15	0.443637943653337	0	FACETS	0.673	0.62	0.728			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		741	600	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434725	110434725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369041453	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	123	949	0	ENST00000375856.3:c.3676G>A	p.Gly1226Arg	p.G1226R	ENST00000375856	NM_003749.2	1226	Ggg/Agg	1/2	0.443637943653337	0	FACETS	0.522	0.473	0.573			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		949	591	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435136	110435136	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs780127725	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	148	879	0	ENST00000375856.3:c.3265G>C	p.Ala1089Pro	p.A1089P	ENST00000375856	NM_003749.2	1089	Gcc/Ccc	1/2	0.443637943653337	0	FACETS	0.626	0.574	0.68			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		879	593	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435574	110435574	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	102	774	0	ENST00000375856.3:c.2827G>A	p.Ala943Thr	p.A943T	ENST00000375856	NM_003749.2	943	Gcc/Acc	1/2	0.443637943653337	0	FACETS	0.555	0.499	0.614			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		774	461	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437996	110437996	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	101	575	0	ENST00000375856.3:c.405G>A	p.Trp135Ter	p.W135*	ENST00000375856	NM_003749.2	135	tgG/tgA	1/2	0.443637943653337	0	FACETS	0.574	0.516	0.635			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		575	441	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093425	30093425	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	51	242	0	ENST00000331968.5:c.1838T>A	p.Ile613Asn	p.I613N	ENST00000331968	NM_002742.2	613	aTc/aAc	13/18	0.443637943653337	0	FACETS	0.476	0.407	0.549			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		242	269	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872918	35872918	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1314076146	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	137	676	0	ENST00000216797.5:c.314A>G	p.Asn105Ser	p.N105S	ENST00000216797	NM_020529.2	105	aAc/aGc	2/6	0.443637943653337	0	FACETS	0.562	0.513	0.614			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		676	611	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986553	36986553	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	126	874	0	ENST00000354822.5:c.1136A>G	p.His379Arg	p.H379R	ENST00000354822	NM_001079668.2	379	cAc/cGc	3/3	0.443637943653337	0	FACETS	0.58	0.527	0.635			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		874	545	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987181	36987181	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	154	816	0	ENST00000354822.5:c.508A>G	p.Met170Val	p.M170V	ENST00000354822	NM_001079668.2	170	Atg/Gtg	3/3	0.443637943653337	0	FACETS	0.679	0.624	0.735			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		816	569	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610320	81610320	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	110	818	0	ENST00000298171.2:c.1918A>T	p.Ile640Phe	p.I640F	ENST00000298171	NM_000369.2	640	Atc/Ttc	10/10	0.443637943653337	0	FACETS	0.439	0.395	0.486			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		818	628	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105236683	105236683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	68	787	0	ENST00000349310.3:c.1438G>A	p.Ala480Thr	p.A480T	ENST00000349310	NM_001014432.1	480	Gcc/Acc	15/15	0.443637943653337	0	FACETS	0.241	0.209	0.275			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		787	709	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022986	33022986	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	137	815	0	ENST00000300177.4:c.95C>A	p.Ala32Asp	p.A32D	ENST00000300177	NM_001191322.1	32	gCc/gAc	2/2	0.443637943653337	0	FACETS	0.588	0.537	0.642			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		815	584	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41011040	41011040	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1440531742	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	153	643	0	ENST00000267868.3:c.473T>C	p.Met158Thr	p.M158T	ENST00000267868	NM_002875.4	158	aTg/aCg	6/10	0.443637943653337	0	FACETS	0.581	0.533	0.63			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		643	661	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042317	42042317	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	142	756	0	ENST00000219905.7:c.6512G>T	p.Arg2171Met	p.R2171M	ENST00000219905	NM_001164273.1	2171	aGg/aTg	17/24	0.443637943653337	0	FACETS	0.557	0.509	0.607			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		756	639	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058378	42058378	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs536098547	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	126	680	0	ENST00000219905.7:c.8098A>G	p.Arg2700Gly	p.R2700G	ENST00000219905	NM_001164273.1	2700	Aga/Gga	24/24	0.443637943653337	0	FACETS	0.62	0.564	0.678			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		680	510	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708009	43708009	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	140	577	0	ENST00000382044.4:c.4874-2A>G		p.X1625_splice	ENST00000382044	NM_001141980.1	1625			0.443637943653337	0	FACETS	0.579	0.529	0.632			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		577	606	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748134	43748134	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	80	699	1	ENST00000382044.4:c.2672A>G	p.Lys891Arg	p.K891R	ENST00000382044	NM_001141980.1	891	aAg/aGg	12/28	0.443637943653337	0	FACETS	0.292	0.256	0.33			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		700	688	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762174	43762174	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs776812022	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	147	685	0	ENST00000382044.4:c.1271A>C	p.Asn424Thr	p.N424T	ENST00000382044	NM_001141980.1	424	aAc/aCc	11/28	0.443637943653337	0	FACETS	0.584	0.535	0.635			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		685	631	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51514705	51514705	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	80	723	0	ENST00000260433.2:c.469C>T	p.Leu157Phe	p.L157F	ENST00000260433		157	Ctt/Ttt	5/10	0.443637943653337	0	FACETS	0.264	0.232	0.299			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		723	760	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727514	66727514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	130	677	0	ENST00000307102.5:c.230G>A	p.Gly77Asp	p.G77D	ENST00000307102	NM_002755.3	77	gGc/gAc	2/11	0.443637943653337	0	FACETS	0.48	0.436	0.526			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		677	679	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678509	88678509	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373935634	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	116	773	0	ENST00000360948.2:c.1027C>T	p.Arg343Trp	p.R343W	ENST00000360948	NM_001012338.2	343	Cgg/Tgg	9/19	0.443637943653337	0	FACETS	0.547	0.495	0.601			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		773	532	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628520	90628520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1237752648	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	147	836	0	ENST00000330062.3:c.1067G>A	p.Arg356Gln	p.R356Q	ENST00000330062	NM_002168.2	356	cGg/cAg	8/11	0.443637943653337	0	FACETS	0.609	0.558	0.662			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		836	605	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293240	91293240	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs558524280	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	113	634	0	ENST00000355112.3:c.742A>G	p.Ile248Val	p.I248V	ENST00000355112	NM_000057.2	248	Ata/Gta	3/22	0.443637943653337	0	FACETS	0.514	0.464	0.567			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		634	551	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303853	91303853	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	98	531	0	ENST00000355112.3:c.1250A>G	p.Asn417Ser	p.N417S	ENST00000355112	NM_000057.2	417	aAt/aGt	7/22	0.443637943653337	0	FACETS	0.495	0.443	0.549			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		531	497	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	97	705	11	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	0.443637943653337	0	FACETS	0.48	0.429	0.533			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		716	507	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304164	91304164	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	124	663	0	ENST00000355112.3:c.1561C>A	p.Pro521Thr	p.P521T	ENST00000355112	NM_000057.2	521	Cca/Aca	7/22	0.443637943653337	0	FACETS	0.632	0.575	0.692			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		663	492	SUCCESS
BLM	641	MSKCC	GRCh37	15	91306226	91306226	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	100	440	0	ENST00000355112.3:c.1913A>T	p.Asn638Ile	p.N638I	ENST00000355112	NM_000057.2	638	aAt/aTt	8/22	0.443637943653337	0	FACETS	0.581	0.522	0.642			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		440	432	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465477	99465477	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	163	752	0	ENST00000268035.6:c.2302C>T	p.Pro768Ser	p.P768S	ENST00000268035	NM_000875.3	768	Ccg/Tcg	11/21	0.443637943653337	0	FACETS	0.575	0.529	0.623			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		752	711	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500612	99500612	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs774314535	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	38	848	0	ENST00000268035.6:c.4045A>G	p.Met1349Val	p.M1349V	ENST00000268035	NM_000875.3	1349	Atg/Gtg	21/21	0.443637943653337	0	FACETS	0.149	0.122	0.178			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		848	641	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112996	2112996	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45494392	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	117	655	3	ENST00000219476.3:c.1385G>A	p.Arg462His	p.R462H	ENST00000219476	NM_000548.3	462	cGc/cAc	14/42	0.443637943653337	0	FACETS	0.59	0.535	0.648			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		658	497	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129148	2129148	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45517280	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	162	906	0	ENST00000219476.3:c.3082G>A	p.Asp1028Asn	p.D1028N	ENST00000219476	NM_000548.3	1028	Gac/Aac	27/42	0.443637943653337	0	FACETS	0.56	0.515	0.608			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		906	725	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2588117	2588117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1284780606	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	165	1069	0	ENST00000342085.4:c.4G>A	p.Ala2Thr	p.A2T	ENST00000342085	NM_002613.4	2	Gcc/Acc	1/14	0.443637943653337	0	FACETS	0.565	0.519	0.612			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1069	733	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807905	3807905	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	146	751	0	ENST00000262367.5:c.3514T>C	p.Ser1172Pro	p.S1172P	ENST00000262367	NM_004380.2	1172	Tcc/Ccc	18/31	0.443637943653337	0	FACETS	0.566	0.518	0.616			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		751	647	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820989	3820989	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	95	538	0	ENST00000262367.5:c.2464-2A>G		p.X822_splice	ENST00000262367	NM_004380.2	822			0.443637943653337	0	FACETS	0.55	0.493	0.611			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		538	433	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832804	3832804	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs746188366	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	155	888	0	ENST00000262367.5:c.1454A>G	p.Tyr485Cys	p.Y485C	ENST00000262367	NM_004380.2	485	tAt/tGt	6/31	0.443637943653337	0	FACETS	0.553	0.507	0.601			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		888	703	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857217	9857217	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199696775	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	161	936	1	ENST00000330684.3:c.4184C>T	p.Ala1395Val	p.A1395V	ENST00000330684	NM_001134407.1	1395	gCg/gTg	13/13	0.443637943653337	0	FACETS	0.543	0.499	0.59			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		937	743	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029098	14029098	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	138	661	0	ENST00000311895.7:c.1309A>G	p.Arg437Gly	p.R437G	ENST00000311895	NM_005236.2	437	Agg/Ggg	8/11	0.443637943653337	0	FACETS	0.595	0.543	0.648			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		661	582	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647095	23647095	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	100	715	0	ENST00000261584.4:c.772A>G	p.Ser258Gly	p.S258G	ENST00000261584	NM_024675.3	258	Agt/Ggt	4/13	0.443637943653337	0	FACETS	0.501	0.449	0.555			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		715	501	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50784042	50784042	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778620114	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	120	732	0	ENST00000398568.2:c.433G>A	p.Val145Ile	p.V145I	ENST00000398568	NM_001042412.1	145	Gtt/Att	3/18	0.443637943653337	0	FACETS	0.48	0.434	0.528			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		732	627	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813833	50813833	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	133	733	0	ENST00000398568.2:c.1387A>G	p.Asn463Asp	p.N463D	ENST00000398568	NM_001042412.1	463	Aac/Gac	8/18	0.443637943653337	0	FACETS	0.518	0.471	0.567			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		733	644	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56857716	56857716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370111038	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	160	733	0	ENST00000308159.5:c.752G>A	p.Arg251His	p.R251H	ENST00000308159	NM_014669.4	251	cGc/cAc	8/22	0.443637943653337	0	FACETS	0.561	0.516	0.609			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		733	715	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645905	67645905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779012125	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	146	629	0	ENST00000264010.4:c.833G>A	p.Arg278His	p.R278H	ENST00000264010	NM_006565.3	278	cGt/cAt	4/12	0.443637943653337	0	FACETS	0.521	0.476	0.568			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		629	703	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822303	72822303	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	46	1062	0	ENST00000268489.5:c.9872T>C	p.Leu3291Pro	p.L3291P	ENST00000268489	NM_006885.3	3291	cTg/cCg	10/10	0.443637943653337	0	FACETS	0.141	0.118	0.167			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1062	816	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830234	72830234	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	141	842	0	ENST00000268489.5:c.6347del	p.Pro2116ArgfsTer60	p.P2116Rfs*60	ENST00000268489	NM_006885.3	2116	cCg/cg	9/10	0.443637943653337	0	FACETS	0.559	0.51	0.609			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		842	633	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992119	72992119	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	170	1033	0	ENST00000268489.5:c.1926C>A	p.Cys642Ter	p.C642*	ENST00000268489	NM_006885.3	642	tgC/tgA	2/10	0.443637943653337	0	FACETS	0.587	0.541	0.635			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1033	726	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992348	72992348	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	145	882	0	ENST00000268489.5:c.1697G>A	p.Arg566Lys	p.R566K	ENST00000268489	NM_006885.3	566	aGg/aAg	2/10	0.443637943653337	0	FACETS	0.497	0.454	0.542			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		882	732	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81962231	81962231	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	107	534	0	ENST00000359376.3:c.2581+2T>C		p.X861_splice	ENST00000359376	NM_002661.3	861			0.443637943653337	0	FACETS	0.521	0.469	0.576			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		534	515	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86546656	86546656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	124	822	0	ENST00000262426.4:c.1105G>A	p.Val369Ile	p.V369I	ENST00000262426	NM_001451.2	369	Gtc/Atc	2/2	0.443637943653337	0	FACETS	0.506	0.459	0.555			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		822	615	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347332	89347332	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	166	993	0	ENST00000301030.4:c.5618T>C	p.Val1873Ala	p.V1873A	ENST00000301030	NM_001256183.1	1873	gTc/gCc	9/13	0.443637943653337	0	FACETS	0.575	0.529	0.623			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		993	724	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348776	89348776	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	155	885	0	ENST00000301030.4:c.4174T>C	p.Tyr1392His	p.Y1392H	ENST00000301030	NM_001256183.1	1392	Tac/Cac	9/13	0.443637943653337	0	FACETS	0.536	0.492	0.583			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		885	725	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349432	89349432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	149	960	0	ENST00000301030.4:c.3518C>T	p.Pro1173Leu	p.P1173L	ENST00000301030	NM_001256183.1	1173	cCt/cTt	9/13	0.443637943653337	0	FACETS	0.523	0.479	0.57			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		960	714	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357487	89357487	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	127	935	0	ENST00000301030.4:c.331C>T	p.Leu111Phe	p.L111F	ENST00000301030	NM_001256183.1	111	Ctc/Ttc	5/13	0.443637943653337	0	FACETS	0.511	0.464	0.561			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		935	623	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89811466	89811466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	134	719	0	ENST00000389301.3:c.3527G>A	p.Ser1176Asn	p.S1176N	ENST00000389301	NM_000135.2	1176	aGc/aAc	36/43	0.443637943653337	0	FACETS	0.536	0.488	0.586			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		719	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577563	7577563	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1567549584	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	112	679	0	ENST00000269305.4:c.718A>G	p.Ser240Gly	p.S240G	ENST00000269305	NM_001126112.2	240	Agt/Ggt	7/11	0.443637943653337	0	FACETS	0.461	0.415	0.508			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		679	610	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976198	7976198	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1274525093	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	32	748	1	ENST00000319144.4:c.1997G>A	p.Arg666His	p.R666H	ENST00000319144	NM_001139.2	666	cGc/cAc	15/15	0.443637943653337	0	FACETS	0.131	0.105	0.159			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		749	615	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984241	7984241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	134	798	0	ENST00000319144.4:c.488G>A	p.Arg163His	p.R163H	ENST00000319144	NM_001139.2	163	cGc/cAc	4/15	0.443637943653337	0	FACETS	0.507	0.461	0.555			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		798	663	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965428	15965428	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	129	660	0	ENST00000268712.3:c.5378T>C	p.Leu1793Pro	p.L1793P	ENST00000268712	NM_006311.3	1793	cTa/cCa	36/46	0.443637943653337	0	FACETS	0.585	0.533	0.64			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		660	553	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971252	15971252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs118021690	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	168	764	0	ENST00000268712.3:c.4697C>T	p.Thr1566Met	p.T1566M	ENST00000268712	NM_006311.3	1566	aCg/aTg	32/46	0.443637943653337	0	FACETS	0.584	0.538	0.631			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		764	722	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971361	15971361	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	165	702	0	ENST00000268712.3:c.4588C>A	p.Pro1530Thr	p.P1530T	ENST00000268712	NM_006311.3	1530	Cca/Aca	32/46	0.443637943653337	0	FACETS	0.585	0.539	0.634			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		702	707	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075154	16075154	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	63	647	1	ENST00000268712.3:c.398T>C	p.Leu133Pro	p.L133P	ENST00000268712	NM_006311.3	133	cTg/cCg	4/46	0.443637943653337	0	FACETS	0.2	0.173	0.231			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		648	789	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17117171	17117171	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	124	727	1	ENST00000285071.4:c.1539-1G>A		p.X513_splice	ENST00000285071	NM_144997.5	513			0.443637943653337	0	FACETS	0.534	0.485	0.586			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		728	582	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118522	17118522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	164	908	0	ENST00000285071.4:c.1409G>A	p.Gly470Glu	p.G470E	ENST00000285071	NM_144997.5	470	gGg/gAg	12/14	0.443637943653337	0	FACETS	0.601	0.554	0.651			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		908	684	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661955	29661955	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	98	577	0	ENST00000356175.3:c.5849T>A	p.Val1950Asp	p.V1950D	ENST00000356175	NM_000267.3	1950	gTt/gAt	39/57	0.443637943653337	0	FACETS	0.523	0.469	0.58			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		577	470	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685985	29685985	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	69	334	0	ENST00000356175.3:c.8051-2A>G		p.X2684_splice	ENST00000356175	NM_000267.3	2684			0.443637943653337	0	FACETS	0.523	0.459	0.591			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		334	331	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690006	33690006	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	114	708	0	ENST00000308377.4:c.821T>C	p.Ile274Thr	p.I274T	ENST00000308377	NM_152270.3	274	aTa/aCa	2/5	0.443637943653337	0	FACETS	0.496	0.448	0.547			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		708	576	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646866	37646866	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141353560	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	134	515	0	ENST00000447079.4:c.1988G>A	p.Arg663His	p.R663H	ENST00000447079	NM_015083.1	663	cGt/cAt	3/14	0.443637943653337	0	FACETS	0.557	0.508	0.609			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		515	603	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879595	37879595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	192	953	0	ENST00000269571.5:c.1970C>T	p.Ala657Val	p.A657V	ENST00000269571		657	gCg/gTg	17/27	0.443637943653337	0	FACETS	0.596	0.552	0.641			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		953	808	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510644	38510644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	149	911	0	ENST00000254066.5:c.898G>A	p.Ala300Thr	p.A300T	ENST00000254066	NM_000964.3	300	Gct/Act	7/9	0.443637943653337	0	FACETS	0.529	0.484	0.576			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		911	706	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354370	40354370	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	173	1079	0	ENST00000293328.3:c.2225T>C	p.Met742Thr	p.M742T	ENST00000293328	NM_012448.3	742	aTg/aCg	18/19	0.443637943653337	0	FACETS	0.576	0.531	0.623			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1079	753	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453295	40453295	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1363166765	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	138	913	0	ENST00000345506.4:c.992C>T	p.Thr331Ile	p.T331I	ENST00000345506	NM_003152.3	331	aCa/aTa	10/20	0.443637943653337	0	FACETS	0.479	0.436	0.523			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		913	723	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453436	40453436	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	106	868	0	ENST00000345506.4:c.1133A>G	p.Gln378Arg	p.Q378R	ENST00000345506	NM_003152.3	378	cAg/cGg	10/20	0.443637943653337	0	FACETS	0.409	0.367	0.454			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		868	650	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481576	40481576	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	19	805	0	ENST00000264657.5:c.1229A>T	p.His410Leu	p.H410L	ENST00000264657	NM_139276.2	410	cAc/cTc	13/24	0.443637943653337	0	FACETS	0.069	0.052	0.09			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		805	688	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870501	40870501	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768296055	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	183	771	0	ENST00000428826.2:c.902G>A	p.Arg301His	p.R301H	ENST00000428826		301	cGc/cAc	9/21	0.443637943653337	0	FACETS	0.637	0.59	0.687			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		771	720	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805612	46805612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764401781	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	127	913	0	ENST00000290295.7:c.344C>T	p.Thr115Met	p.T115M	ENST00000290295	NM_006361.5	115	aCg/aTg	1/2	0.443637943653337	0	FACETS	0.538	0.489	0.589			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		913	592	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752465	55752465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1382332810	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	119	664	0	ENST00000284073.2:c.923C>T	p.Ser308Leu	p.S308L	ENST00000284073	NM_138962.2	308	tCg/tTg	12/14	0.443637943653337	0	FACETS	0.504	0.456	0.554			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		664	592	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752474	55752474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	32	645	0	ENST00000284073.2:c.932G>A	p.Gly311Asp	p.G311D	ENST00000284073	NM_138962.2	311	gGc/gAc	12/14	0.443637943653337	0	FACETS	0.136	0.11	0.166			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		645	591	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755128667	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	46	1141	1	ENST00000407977.2:c.1976dup	p.Pro660SerfsTer87	p.P660Sfs*87	ENST00000407977		659	ggt/ggGt	9/10	0.443637943653337	0	FACETS	0.134	0.112	0.158			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1142	864	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857759	59857759	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs745367580	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	81	296	0	ENST00000259008.2:c.1798T>C	p.Phe600Leu	p.F600L	ENST00000259008	NM_032043.2	600	Ttt/Ctt	13/20	0.443637943653337	0	FACETS	0.606	0.539	0.678			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		296	335	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62008719	62008719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	143	768	0	ENST00000392795.3:c.97G>A	p.Glu33Lys	p.E33K	ENST00000392795	NM_001039933.1	33	Gag/Aag	2/6	0.443637943653337	0	FACETS	0.618	0.566	0.673			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		768	580	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533649	63533649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	152	902	0	ENST00000307078.5:c.1505G>A	p.Gly502Asp	p.G502D	ENST00000307078	NM_004655.3	502	gGc/gAc	6/11	0.443637943653337	0	FACETS	0.557	0.511	0.606			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		902	684	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899222	78899222	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150835528	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	166	812	1	ENST00000306801.3:c.2861C>T	p.Thr954Met	p.T954M	ENST00000306801	NM_020761.2	954	aCg/aTg	24/34	0.443637943653337	0	FACETS	0.555	0.511	0.601			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		813	750	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919572	78919572	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	181	658	0	ENST00000306801.3:c.3131A>G	p.Asp1044Gly	p.D1044G	ENST00000306801	NM_020761.2	1044	gAc/gGc	26/34	0.443637943653337	0	FACETS	0.725	0.672	0.78			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		658	626	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923339	78923339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1441841406	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	37	739	0	ENST00000306801.3:c.3362C>T	p.Thr1121Met	p.T1121M	ENST00000306801	NM_020761.2	1121	aCg/aTg	28/34	0.443637943653337	0	FACETS	0.151	0.124	0.182			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		739	613	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637930	39637930	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs200046143	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	120	563	0	ENST00000262039.4:c.2347A>G	p.Met783Val	p.M783V	ENST00000262039	NM_002647.2	783	Atg/Gtg	22/25	0.443637943653337	0	FACETS	0.55	0.499	0.604			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		563	547	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395736	45395736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	125	603	0	ENST00000262160.6:c.398G>A	p.Arg133His	p.R133H	ENST00000262160	NM_005901.5	133	cGc/cAc	4/11	0.443637943653337	0	FACETS	0.561	0.509	0.615			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		603	559	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591862	48591862	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	111	706	1	ENST00000342988.3:c.1025C>A	p.Pro342His	p.P342H	ENST00000342988	NM_005359.5	342	cCt/cAt	9/12	0.443637943653337	0	FACETS	0.469	0.422	0.518			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		707	594	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414638	56414638	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1369941741	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	68	386	0	ENST00000348428.3:c.2039A>G	p.Glu680Gly	p.E680G	ENST00000348428	NM_006785.3	680	gAa/gGa	17/17	0.443637943653337	0	FACETS	0.614	0.539	0.692			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		386	278	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220667	1220667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	134	846	0	ENST00000326873.7:c.685G>A	p.Asp229Asn	p.D229N	ENST00000326873	NM_000455.4	229	Gac/Aac	5/10	0.443637943653337	0	FACETS	0.564	0.514	0.616			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		846	596	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625691	1625691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	130	785	0	ENST00000344749.5:c.383G>A	p.Gly128Asp	p.G128D	ENST00000344749	NM_001136139.2	128	gGc/gAc	7/19	0.443637943653337	0	FACETS	0.535	0.486	0.585			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		785	610	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226323	2226323	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	155	1005	0	ENST00000398665.3:c.3803G>A	p.Ser1268Asn	p.S1268N	ENST00000398665	NM_032482.2	1268	aGc/aAc	27/28	0.443637943653337	0	FACETS	0.548	0.502	0.595			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1005	710	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226633	2226633	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	196	1094	0	ENST00000398665.3:c.4113G>T	p.Arg1371Ser	p.R1371S	ENST00000398665	NM_032482.2	1371	agG/agT	27/28	0.443637943653337	0	FACETS	0.605	0.561	0.651			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1094	812	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3114962	3114962	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	36	826	0	ENST00000078429.4:c.497G>A	p.Arg166His	p.R166H	ENST00000078429	NM_002067.2	166	cGc/cAc	4/7	0.443637943653337	0	FACETS	0.143	0.117	0.172			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		826	632	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119316	3119316	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	132	856	0	ENST00000078429.4:c.848T>C	p.Ile283Thr	p.I283T	ENST00000078429	NM_002067.2	283	aTc/aCc	6/7	0.443637943653337	0	FACETS	0.53	0.482	0.579			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		856	625	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119346	3119346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	135	812	0	ENST00000078429.4:c.878C>T	p.Pro293Leu	p.P293L	ENST00000078429	NM_002067.2	293	cCc/cTc	6/7	0.443637943653337	0	FACETS	0.554	0.505	0.605			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		812	611	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3120989	3120989	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	122	733	0	ENST00000078429.4:c.892C>T	p.Pro298Ser	p.P298S	ENST00000078429	NM_002067.2	298	Ccc/Tcc	7/7	0.443637943653337	0	FACETS	0.56	0.508	0.615			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		733	546	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121050	3121050	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	111	816	0	ENST00000078429.4:c.953C>T	p.Pro318Leu	p.P318L	ENST00000078429	NM_002067.2	318	cCc/cTc	7/7	0.443637943653337	0	FACETS	0.424	0.381	0.469			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		816	657	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121139	3121139	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	130	757	0	ENST00000078429.4:c.1042A>G	p.Ile348Val	p.I348V	ENST00000078429	NM_002067.2	348	Atc/Gtc	7/7	0.443637943653337	0	FACETS	0.489	0.444	0.536			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		757	667	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101031	4101031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375843855	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	102	644	0	ENST00000262948.5:c.691C>T	p.Arg231Cys	p.R231C	ENST00000262948	NM_030662.3	231	Cgc/Tgc	6/11	0.443637943653337	0	FACETS	0.543	0.488	0.601			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		644	471	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220122	5220122	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	132	881	0	ENST00000357368.4:c.3593A>G	p.His1198Arg	p.H1198R	ENST00000357368	NM_002850.3	1198	cAc/cGc	22/38	0.443637943653337	0	FACETS	0.547	0.498	0.598			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		881	605	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220126	5220126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781134304	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	127	866	0	ENST00000357368.4:c.3589C>T	p.Arg1197Trp	p.R1197W	ENST00000357368	NM_002850.3	1197	Cgg/Tgg	22/38	0.443637943653337	0	FACETS	0.524	0.476	0.574			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		866	608	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6222248	6222248	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	175	1112	0	ENST00000252674.7:c.994G>T	p.Asp332Tyr	p.D332Y	ENST00000252674	NM_005934.3	332	Gac/Tac	6/12	0.443637943653337	0	FACETS	0.539	0.497	0.583			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1112	814	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247808	10247808	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	82	938	0	ENST00000340748.4:c.4394G>A	p.Gly1465Asp	p.G1465D	ENST00000340748		1465	gGc/gAc	36/40	0.443637943653337	0	FACETS	0.274	0.241	0.309			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		938	751	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291142	10291142	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	232	1273	0	ENST00000340748.4:c.329G>A	p.Gly110Glu	p.G110E	ENST00000340748		110	gGg/gAg	4/40	0.443637943653337	0	FACETS	0.539	0.502	0.577			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1273	1079	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597482	10597482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	128	590	0	ENST00000171111.5:c.1721G>A	p.Gly574Asp	p.G574D	ENST00000171111	NM_203500.1	574	gGt/gAt	6/6	0.443637943653337	0	FACETS	0.554	0.504	0.607			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		590	579	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610075	10610075	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	62	695	0	ENST00000171111.5:c.635G>A	p.Gly212Glu	p.G212E	ENST00000171111	NM_203500.1	212	gGg/gAg	2/6	0.443637943653337	0	FACETS	0.254	0.219	0.292			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		695	613	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132474	11132474	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	176	958	1	ENST00000358026.2:c.2690T>C	p.Leu897Pro	p.L897P	ENST00000358026	NM_001128849.1	897	cTc/cCc	19/36	0.443637943653337	0	FACETS	0.619	0.572	0.668			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		959	713	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144534	11144534	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	32	641	0	ENST00000358026.2:c.3866C>T	p.Pro1289Leu	p.P1289L	ENST00000358026	NM_001128849.1	1289	cCt/cTt	27/36	0.443637943653337	0	FACETS	0.14	0.113	0.17			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		641	575	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145708	11145708	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	132	864	0	ENST00000358026.2:c.4070T>C	p.Leu1357Pro	p.L1357P	ENST00000358026	NM_001128849.1	1357	cTg/cCg	29/36	0.443637943653337	0	FACETS	0.481	0.437	0.526			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		864	689	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051063	13051063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	154	877	0	ENST00000316448.5:c.499G>A	p.Glu167Lys	p.E167K	ENST00000316448	NM_004343.3	167	Gag/Aag	5/9	0.443637943653337	0	FACETS	0.541	0.496	0.588			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		877	714	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278205	15278205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	134	708	0	ENST00000263388.2:c.5217G>A	p.Met1739Ile	p.M1739I	ENST00000263388	NM_000435.2	1739	atG/atA	29/33	0.443637943653337	0	FACETS	0.555	0.505	0.606			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		708	606	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281359	15281359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769347071	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	143	968	0	ENST00000263388.2:c.4897C>T	p.Pro1633Ser	p.P1633S	ENST00000263388	NM_000435.2	1633	Ccg/Tcg	27/33	0.443637943653337	0	FACETS	0.559	0.511	0.609			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		968	642	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288682	15288682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	69	642	0	ENST00000263388.2:c.4057G>A	p.Ala1353Thr	p.A1353T	ENST00000263388	NM_000435.2	1353	Gcg/Acg	24/33	0.443637943653337	0	FACETS	0.595	0.523	0.671			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		642	291	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302292	15302292	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767905805	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	121	808	0	ENST00000263388.2:c.979G>A	p.Ala327Thr	p.A327T	ENST00000263388	NM_000435.2	327	Gcc/Acc	6/33	0.443637943653337	0	FACETS	0.494	0.448	0.543			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		808	614	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302432	15302432	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	151	974	0	ENST00000263388.2:c.839T>C	p.Leu280Pro	p.L280P	ENST00000263388	NM_000435.2	280	cTg/cCg	6/33	0.443637943653337	0	FACETS	0.576	0.528	0.625			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		974	658	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355087	15355087	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1339893752	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	36	824	0	ENST00000263377.2:c.2536A>G	p.Ser846Gly	p.S846G	ENST00000263377	NM_058243.2	846	Agc/Ggc	13/20	0.443637943653337	0	FACETS	0.132	0.108	0.159			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		824	683	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379773	17379773	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	137	914	0	ENST00000359435.4:c.158G>T	p.Gly53Val	p.G53V	ENST00000359435	NM_001033549.1	53	gGt/gTt	2/9	0.443637943653337	0	FACETS	0.535	0.488	0.585			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		914	642	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387303	17387303	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	149	752	1	ENST00000359435.4:c.570-1G>A		p.X190_splice	ENST00000359435	NM_001033549.1	190			0.443637943653337	0	FACETS	0.602	0.552	0.654			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		753	621	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954241	17954241	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	159	845	0	ENST00000458235.1:c.368A>T	p.Asp123Val	p.D123V	ENST00000458235	NM_000215.3	123	gAt/gTt	4/24	0.443637943653337	0	FACETS	0.574	0.527	0.622			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		845	695	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212702	36212702	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	140	816	0	ENST00000222270.7:c.2453T>C	p.Met818Thr	p.M818T	ENST00000222270	NM_014727.1	818	aTg/aCg	3/37	0.443637943653337	0	FACETS	0.506	0.462	0.552			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		816	694	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216678	36216678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	134	866	0	ENST00000222270.7:c.3844C>T	p.Pro1282Ser	p.P1282S	ENST00000222270	NM_014727.1	1282	Ccc/Tcc	13/37	0.443637943653337	0	FACETS	0.475	0.432	0.52			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		866	708	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40747901	40747901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	150	842	0	ENST00000392038.2:c.517G>A	p.Ala173Thr	p.A173T	ENST00000392038	NM_001626.4	173	Gcc/Acc	6/14	0.443637943653337	0	FACETS	0.537	0.491	0.584			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		842	701	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383102	42383102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	30	658	0	ENST00000221972.3:c.122C>T	p.Ser41Leu	p.S41L	ENST00000221972	NM_021601.3	41	tCa/tTa	2/5	0.443637943653337	0	FACETS	0.174	0.14	0.213			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		658	432	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753143	42753143	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	163	1175	0	ENST00000222329.4:c.1121C>A	p.Pro374Gln	p.P374Q	ENST00000222329	NM_006494.2	374	cCa/cAa	4/4	0.443637943653337	0	FACETS	0.522	0.48	0.566			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1175	783	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753837	42753837	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs368169058	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	166	1005	0	ENST00000222329.4:c.427C>A	p.Arg143Ser	p.R143S	ENST00000222329	NM_006494.2	143	Cgc/Agc	4/4	0.443637943653337	0	FACETS	0.532	0.49	0.577			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1005	782	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42759136	42759136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	92	634	0	ENST00000222329.4:c.16G>A	p.Asp6Asn	p.D6N	ENST00000222329	NM_006494.2	6	Gac/Aac	1/4	0.443637943653337	0	FACETS	0.474	0.422	0.528			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		634	487	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794644	42794644	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	122	861	0	ENST00000575354.2:c.1724C>T	p.Pro575Leu	p.P575L	ENST00000575354	NM_015125.3	575	cCc/cTc	10/20	0.443637943653337	0	FACETS	0.549	0.498	0.603			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		861	557	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795112	42795112	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	147	886	0	ENST00000575354.2:c.2192A>G	p.Asp731Gly	p.D731G	ENST00000575354	NM_015125.3	731	gAc/gGc	10/20	0.443637943653337	0	FACETS	0.569	0.521	0.619			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		886	648	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797976	42797976	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	43	1148	0	ENST00000575354.2:c.4028A>T	p.Asp1343Val	p.D1343V	ENST00000575354	NM_015125.3	1343	gAc/gTc	16/20	0.443637943653337	0	FACETS	0.135	0.112	0.16			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1148	801	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425075	47425076	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	154	790	0	ENST00000404338.3:c.3147dup	p.Glu1050Ter	p.E1050*	ENST00000404338	NM_004491.4	1048	cat/caTt	1/6	0.443637943653337	0	FACETS	0.538	0.493	0.585			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		790	718	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47503665	47503665	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	150	858	0	ENST00000404338.3:c.4220C>T	p.Pro1407Leu	p.P1407L	ENST00000404338	NM_004491.4	1407	cCt/cTt	6/6	0.443637943653337	0	FACETS	0.502	0.459	0.546			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		858	750	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731662	47731662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	111	765	0	ENST00000449228.1:c.130C>T	p.Leu44Phe	p.L44F	ENST00000449228	NM_001127240.2	44	Ctc/Ttc	2/4	0.443637943653337	0	FACETS	0.555	0.501	0.611			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		765	502	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905980	50905980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775232133	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	148	974	0	ENST00000440232.2:c.952G>A	p.Glu318Lys	p.E318K	ENST00000440232	NM_002691.3	318	Gag/Aag	8/27	0.443637943653337	0	FACETS	0.621	0.569	0.674			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		974	598	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920465	50920465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779208942	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	121	851	0	ENST00000440232.2:c.3157C>T	p.Arg1053Cys	p.R1053C	ENST00000440232	NM_002691.3	1053	Cgc/Tgc	26/27	0.443637943653337	0	FACETS	0.626	0.568	0.685			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		851	485	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52709300	52709300	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	144	624	0	ENST00000322088.6:c.254A>G	p.Tyr85Cys	p.Y85C	ENST00000322088	NM_014225.5	85	tAc/tGc	3/15	0.443637943653337	0	FACETS	0.502	0.458	0.547			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		624	720	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714579	52714579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113545781	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	137	852	0	ENST00000322088.6:c.337C>T	p.Arg113Trp	p.R113W	ENST00000322088	NM_014225.5	113	Cgg/Tgg	4/15	0.443637943653337	0	FACETS	0.545	0.497	0.595			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		852	631	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719903	52719903	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	141	778	0	ENST00000322088.6:c.1115A>G	p.Gln372Arg	p.Q372R	ENST00000322088	NM_014225.5	372	cAg/cGg	9/15	0.443637943653337	0	FACETS	0.515	0.47	0.562			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		778	687	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505471	25505471	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771499883	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	107	774	0	ENST00000264709.3:c.287G>A	p.Arg96Gln	p.R96Q	ENST00000264709	NM_175629.2	96	cGg/cAg	4/23	0.443637943653337	0	FACETS	0.484	0.436	0.536			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		774	554	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965592	25965592	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	154	798	0	ENST00000435504.4:c.3614C>T	p.Ala1205Val	p.A1205V	ENST00000435504		1205	gCt/gTt	13/13	0.443637943653337	0	FACETS	0.511	0.468	0.556			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		798	756	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449856	29449856	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs776287213	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	154	1039	0	ENST00000389048.3:c.2999A>G	p.Glu1000Gly	p.E1000G	ENST00000389048	NM_004304.4	1000	gAa/gGa	18/29	0.443637943653337	0	FACETS	0.506	0.463	0.55			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1039	764	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143324	30143324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	112	775	0	ENST00000389048.3:c.202G>A	p.Ala68Thr	p.A68T	ENST00000389048	NM_004304.4	68	Gcc/Acc	1/29	0.443637943653337	0	FACETS	0.638	0.578	0.702			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		775	440	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249797	39249797	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	96	474	0	ENST00000402219.2:c.1772A>T	p.Asn591Ile	p.N591I	ENST00000402219	NM_005633.3	591	aAc/aTc	10/23	0.443637943653337	0	FACETS	0.647	0.581	0.716			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		474	372	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023188	48023188	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	140	670	0	ENST00000234420.5:c.613G>T	p.Glu205Ter	p.E205*	ENST00000234420	NM_000179.2	205	Gaa/Taa	3/10	0.443637943653337	0	FACETS	0.524	0.478	0.572			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		670	670	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025939	48025939	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587779948	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	155	933	0	ENST00000234420.5:c.817G>A	p.Gly273Arg	p.G273R	ENST00000234420	NM_000179.2	273	Gga/Aga	4/10	0.443637943653337	0	FACETS	0.534	0.49	0.58			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		933	728	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147580	61147580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	77	375	0	ENST00000295025.8:c.985C>T	p.Pro329Ser	p.P329S	ENST00000295025	NM_002908.2	329	Ccc/Tcc	9/11	0.443637943653337	0	FACETS	0.539	0.477	0.606			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		375	358	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631924	67631924	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	72	636	0	ENST00000272342.5:c.2110A>T	p.Thr704Ser	p.T704S	ENST00000272342	NM_019002.3	704	Aca/Tca	5/6	0.443637943653337	0	FACETS	0.417	0.366	0.472			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		636	433	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047052	128047052	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	130	752	0	ENST00000285398.2:c.683G>A	p.Gly228Asp	p.G228D	ENST00000285398	NM_000122.1	228	gGt/gAt	6/15	0.443637943653337	0	FACETS	0.561	0.511	0.614			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		752	581	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872602	136872602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1379060376	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	150	801	0	ENST00000241393.3:c.896C>T	p.Pro299Leu	p.P299L	ENST00000241393	NM_003467.2	299	cCc/cTc	2/2	0.443637943653337	0	FACETS	0.464	0.424	0.506			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		801	811	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736118	204736118	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	51	717	0	ENST00000302823.3:c.475G>A	p.Asp159Asn	p.D159N	ENST00000302823	NM_005214.4	159	Gat/Aat	3/4	0.443637943653337	0	FACETS	0.177	0.15	0.207			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		717	722	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663420	227663420	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	111	680	0	ENST00000305123.5:c.35A>T	p.Asp12Val	p.D12V	ENST00000305123	NM_005544.2	12	gAc/gTc	1/2	0.443637943653337	0	FACETS	0.573	0.517	0.631			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		680	486	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793251	242793251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1025628936	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	140	848	0	ENST00000334409.5:c.826C>T	p.Pro276Ser	p.P276S	ENST00000334409	NM_005018.2	276	Cca/Tca	5/5	0.443637943653337	0	FACETS	0.633	0.579	0.689			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		848	555	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024147	31024147	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	160	912	0	ENST00000375687.4:c.3632A>T	p.Asp1211Val	p.D1211V	ENST00000375687	NM_015338.5	1211	gAc/gTc	13/13	0.443637943653337	0	FACETS	0.606	0.557	0.657			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		912	662	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385044	31385044	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	122	712	0	ENST00000328111.2:c.1429T>C	p.Tyr477His	p.Y477H	ENST00000328111	NM_006892.3	477	Tac/Cac	14/23	0.443637943653337	0	FACETS	0.514	0.466	0.565			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		712	595	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728870	39728870	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	64	627	0	ENST00000361337.2:c.1150A>G	p.Ile384Val	p.I384V	ENST00000361337	NM_003286.2	384	Atc/Gtc	12/21	0.443637943653337	0	FACETS	0.277	0.24	0.318			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		627	579	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739100	40739100	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1158638222	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	114	676	0	ENST00000373198.4:c.3184C>T	p.Arg1062Cys	p.R1062C	ENST00000373198	NM_133170.3	1062	Cgc/Tgc	24/32	0.443637943653337	0	FACETS	0.611	0.553	0.671			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		676	468	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385216	41385216	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	125	659	1	ENST00000373198.4:c.745T>C	p.Ser249Pro	p.S249P	ENST00000373198	NM_133170.3	249	Tca/Cca	6/32	0.443637943653337	0	FACETS	0.532	0.483	0.584			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		660	589	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326490	62326490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263144885	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	132	1041	1	ENST00000360203.5:c.3415C>T	p.Pro1139Ser	p.P1139S	ENST00000360203	NM_001283009.1	1139	Ccc/Tcc	33/35	0.443637943653337	0	FACETS	0.483	0.439	0.529			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1042	686	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164514	36164514	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	103	888	0	ENST00000300305.3:c.1361A>T	p.Glu454Val	p.E454V	ENST00000300305		454	gAg/gTg	8/8	0.443637943653337	0	FACETS	0.456	0.409	0.506			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		888	566	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164574	36164574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs748885850	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	86	857	0	ENST00000300305.3:c.1301A>G	p.Asn434Ser	p.N434S	ENST00000300305		434	aAc/aGc	8/8	0.443637943653337	0	FACETS	0.402	0.357	0.451			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		857	536	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164727	36164727	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	161	1068	1	ENST00000300305.3:c.1148C>T	p.Pro383Leu	p.P383L	ENST00000300305		383	cCg/cTg	8/8	0.443637943653337	0	FACETS	0.57	0.524	0.617			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1069	709	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171606	36171606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761688033	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	147	723	0	ENST00000300305.3:c.959G>A	p.Arg320Gln	p.R320Q	ENST00000300305		320	cGa/cAa	7/8	0.443637943653337	0	FACETS	0.517	0.473	0.563			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		723	713	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36421184	36421184	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1248488974	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	152	809	0	ENST00000300305.3:c.13A>G	p.Ser5Gly	p.S5G	ENST00000300305		5	Agc/Ggc	1/8	0.443637943653337	0	FACETS	0.493	0.451	0.536			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		809	774	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845300	42845300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	133	881	0	ENST00000398585.3:c.962C>T	p.Ser321Phe	p.S321F	ENST00000398585	NM_001135099.1	321	tCc/tTc	9/14	0.443637943653337	0	FACETS	0.541	0.492	0.591			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		881	617	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651283	45651283	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	46	781	0	ENST00000407780.3:c.742A>G	p.Ser248Gly	p.S248G	ENST00000407780	NM_001283052.1	248	Agt/Ggt	5/7	0.443637943653337	0	FACETS	0.153	0.128	0.181			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		781	752	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655431	45655431	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	138	844	0	ENST00000407780.3:c.421C>G	p.Pro141Ala	p.P141A	ENST00000407780	NM_001283052.1	141	Ccc/Gcc	4/7	0.443637943653337	0	FACETS	0.506	0.461	0.553			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		844	684	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288353	21288353	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	178	897	0	ENST00000354336.3:c.598A>G	p.Ile200Val	p.I200V	ENST00000354336	NM_005207.3	200	Atc/Gtc	2/3	0.443637943653337	0	FACETS	0.635	0.587	0.685			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		897	703	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21348454	21348454	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	124	1091	0	ENST00000215739.8:c.1511C>T	p.Ala504Val	p.A504V	ENST00000215739	NM_006767.3	504	gCc/gTc	14/21	0.443637943653337	0	FACETS	0.481	0.436	0.529			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1091	646	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145582	24145582	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555877286	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	154	822	1	ENST00000263121.7:c.601C>T	p.Arg201Ter	p.R201*	ENST00000263121	NM_003073.3	201	Cga/Tga	5/9	0.443637943653337	0	FACETS	0.543	0.498	0.59			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		823	711	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29083926	29083926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781710	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	37	283	0	ENST00000328354.6:c.1591G>A	p.Glu531Lys	p.E531K	ENST00000328354	NM_007194.3	531	Gag/Aag	15/15	0.443637943653337	0	FACETS	0.304	0.251	0.363			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		283	305	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29279945	29279945	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	150	910	0	ENST00000544604.2:c.191T>C	p.Val64Ala	p.V64A	ENST00000544604	NM_001206998.1	64	gTg/gCg	1/9	0.443637943653337	0	FACETS	0.549	0.503	0.597			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		910	685	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29439317	29439317	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	142	656	0	ENST00000544604.2:c.532A>G	p.Arg178Gly	p.R178G	ENST00000544604	NM_001206998.1	178	Agg/Ggg	4/9	0.443637943653337	0	FACETS	0.529	0.483	0.577			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		656	673	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29440792	29440792	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	135	687	0	ENST00000544604.2:c.658G>A	p.Gly220Arg	p.G220R	ENST00000544604	NM_001206998.1	220	Ggg/Agg	5/9	0.443637943653337	0	FACETS	0.527	0.48	0.576			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		687	642	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069342	30069342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	160	885	2	ENST00000338641.4:c.1207G>A	p.Ala403Thr	p.A403T	ENST00000338641	NM_000268.3	403	Gca/Aca	12/16	0.443637943653337	0	FACETS	0.561	0.516	0.609			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		887	715	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069403	30069403	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	185	843	0	ENST00000338641.4:c.1268A>G	p.Lys423Arg	p.K423R	ENST00000338641	NM_000268.3	423	aAg/aGg	12/16	0.443637943653337	0	FACETS	0.648	0.6	0.698			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		843	716	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30090740	30090740	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	99	543	0	ENST00000338641.4:c.1738-1G>A		p.X580_splice	ENST00000338641	NM_000268.3	580			0.443637943653337	0	FACETS	0.497	0.445	0.551			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		543	500	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447386	12447386	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	116	651	0	ENST00000287820.6:c.625A>G	p.Arg209Gly	p.R209G	ENST00000287820	NM_015869.4	209	Agg/Ggg	5/7	0.443637943653337	0	FACETS	0.48	0.434	0.529			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		651	606	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053539	37053539	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs150478207	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	115	613	0	ENST00000231790.2:c.626A>G	p.Asn209Ser	p.N209S	ENST00000231790	NM_000249.3	209	aAt/aGt	8/19	0.443637943653337	0	FACETS	0.585	0.53	0.643			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		613	493	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067472	37067472	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs63751293	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	142	814	0	ENST00000231790.2:c.1383G>T	p.Lys461Asn	p.K461N	ENST00000231790	NM_000249.3	461	aaG/aaT	12/19	0.443637943653337	0	FACETS	0.537	0.491	0.586			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		814	663	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277888	41277888	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	133	729	0	ENST00000349496.5:c.1852C>A	p.Leu618Ile	p.L618I	ENST00000349496	NM_001904.3	618	Ctc/Atc	12/15	0.443637943653337	0	FACETS	0.55	0.501	0.601			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		729	607	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162093	47162093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1252087914	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	126	655	0	ENST00000409792.3:c.4033G>A	p.Asp1345Asn	p.D1345N	ENST00000409792	NM_014159.6	1345	Gat/Aat	3/21	0.443637943653337	0	FACETS	0.621	0.565	0.679			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		655	509	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162857	47162857	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772606528	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	100	574	0	ENST00000409792.3:c.3269G>A	p.Ser1090Asn	p.S1090N	ENST00000409792	NM_014159.6	1090	aGc/aAc	3/21	0.443637943653337	0	FACETS	0.486	0.436	0.539			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		574	516	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163091	47163091	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	88	563	0	ENST00000409792.3:c.3035G>T	p.Ser1012Ile	p.S1012I	ENST00000409792	NM_014159.6	1012	aGt/aTt	3/21	0.443637943653337	0	FACETS	0.488	0.434	0.545			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		563	452	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165283	47165283	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	94	461	0	ENST00000409792.3:c.843del	p.Glu282LysfsTer19	p.E282Kfs*19	ENST00000409792	NM_014159.6	281	aaA/aa	3/21	0.443637943653337	0	FACETS	0.509	0.455	0.566			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		461	463	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723122	49723122	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	96	584	0	ENST00000449682.2:c.1294T>C	p.Phe432Leu	p.F432L	ENST00000449682	NM_020998.3	432	Ttc/Ctc	11/18	0.443637943653337	0	FACETS	0.596	0.535	0.66			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		584	404	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935571	49935571	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	159	984	0	ENST00000296474.3:c.1793C>A	p.Pro598His	p.P598H	ENST00000296474	NM_002447.2	598	cCt/cAt	5/20	0.443637943653337	0	FACETS	0.537	0.493	0.583			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		984	743	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437183	52437183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866649101	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	56	834	0	ENST00000460680.1:c.1861C>T	p.Pro621Ser	p.P621S	ENST00000460680	NM_004656.3	621	Ccc/Tcc	14/17	0.443637943653337	0	FACETS	0.208	0.177	0.241			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		834	676	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651400	52651400	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	85	574	0	ENST00000394830.3:c.1696A>G	p.Met566Val	p.M566V	ENST00000394830	NM_018313.4	566	Atg/Gtg	15/30	0.443637943653337	0	FACETS	0.528	0.469	0.59			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		574	404	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52692256	52692256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765525545	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	111	517	0	ENST00000394830.3:c.604C>T	p.Arg202Cys	p.R202C	ENST00000394830	NM_018313.4	202	Cgt/Tgt	6/30	0.443637943653337	0	FACETS	0.55	0.497	0.606			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		517	506	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63965680	63965680	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	177	750	0	ENST00000398590.3:c.589G>T	p.Gly197Ter	p.G197*	ENST00000398590	NM_001177387.1	197	Gga/Tga	6/14	0.443637943653337	0	FACETS	0.608	0.562	0.656			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		750	730	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014260	70014260	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	171	831	0	ENST00000394351.3:c.1121T>C	p.Leu374Pro	p.L374P	ENST00000394351	NM_000248.3	374	cTg/cCg	9/9	0.443637943653337	0	FACETS	0.577	0.532	0.624			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		831	743	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008492	71008492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	149	737	0	ENST00000318789.4:c.1940G>A	p.Gly647Glu	p.G647E	ENST00000318789	NM_032682.5	647	gGg/gAg	21/21	0.443637943653337	0	FACETS	0.503	0.46	0.548			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		737	743	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037144	71037144	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	176	704	4	ENST00000318789.4:c.1146+1G>A		p.X382_splice	ENST00000318789	NM_032682.5	382			0.443637943653337	0	FACETS	0.563	0.519	0.608			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		708	784	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427717	72427717	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	174	715	0	ENST00000477973.2:c.773T>C	p.Ile258Thr	p.I258T	ENST00000477973	NM_012234.5	258	aTt/aCt	4/4	0.443637943653337	0	FACETS	0.651	0.602	0.703			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		715	670	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495729	72495729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	175	645	0	ENST00000477973.2:c.343G>A	p.Asp115Asn	p.D115N	ENST00000477973	NM_012234.5	115	Gat/Aat	1/4	0.443637943653337	0	FACETS	0.589	0.544	0.636			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		645	745	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799661	72799661	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	116	736	1	ENST00000325599.8:c.1508T>C	p.Leu503Pro	p.L503P	ENST00000325599	NM_018130.2	503	cTt/cCt	11/11	0.443637943653337	0	FACETS	0.513	0.464	0.565			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		737	567	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456442	89456442	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	90	548	0	ENST00000336596.2:c.1618A>G	p.Ser540Gly	p.S540G	ENST00000336596	NM_005233.5	540	Agc/Ggc	8/17	0.443637943653337	0	FACETS	0.502	0.447	0.559			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		548	450	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374322	138374322	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	110	585	0	ENST00000289153.2:c.3122T>C	p.Phe1041Ser	p.F1041S	ENST00000289153	NM_006219.2	1041	tTt/tCt	22/22	0.443637943653337	0	FACETS	0.521	0.469	0.574			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		585	530	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664819	138664819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	78	597	1	ENST00000330315.3:c.746C>T	p.Ala249Val	p.A249V	ENST00000330315	NM_023067.3	249	gCg/gTg	1/1	0.443637943653337	0	FACETS	0.485	0.429	0.546			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		598	403	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176537	142176537	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	72	531	0	ENST00000350721.4:c.7564G>T	p.Gly2522Ter	p.G2522*	ENST00000350721	NM_001184.3	2522	Gga/Tga	45/47	0.443637943653337	0	FACETS	0.431	0.378	0.488			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		531	419	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281112	142281112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	110	508	1	ENST00000350721.4:c.1132G>A	p.Ala378Thr	p.A378T	ENST00000350721	NM_001184.3	378	Gct/Act	4/47	0.443637943653337	0	FACETS	0.551	0.497	0.607			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		509	501	SUCCESS
ATR	545	MSKCC	GRCh37	3	142284981	142284981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	103	556	1	ENST00000350721.4:c.274G>A	p.Ala92Thr	p.A92T	ENST00000350721	NM_001184.3	92	Gcc/Acc	3/47	0.443637943653337	0	FACETS	0.478	0.429	0.529			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		557	541	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149290785	149290785	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	97	431	0	ENST00000360632.3:c.434A>G	p.His145Arg	p.H145R	ENST00000360632	NM_015472.4	145	cAc/cGc	3/7	0.443637943653337	0	FACETS	0.53	0.475	0.588			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		431	459	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374664	149374664	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	111	606	0	ENST00000360632.3:c.430A>G	p.Asn144Asp	p.N144D	ENST00000360632	NM_015472.4	144	Aat/Gat	2/7	0.443637943653337	0	FACETS	0.605	0.547	0.666			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		606	460	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	74	446	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	0.443637943653337	0	FACETS	0.495	0.436	0.558			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		446	375	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919083	178919083	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	74	339	0	ENST00000263967.3:c.568A>G	p.Ile190Val	p.I190V	ENST00000263967	NM_006218.2	190	Ata/Gta	4/21	0.443637943653337	0	FACETS	0.5	0.44	0.564			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		339	371	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430462	181430462	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	159	942	0	ENST00000325404.1:c.314A>G	p.His105Arg	p.H105R	ENST00000325404	NM_003106.3	105	cAc/cGc	1/1	0.443637943653337	0	FACETS	0.642	0.591	0.695			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		942	621	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503837	186503837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	93	474	1	ENST00000323963.5:c.514C>T	p.Leu172Phe	p.L172F	ENST00000323963		172	Ctt/Ttt	5/11	0.443637943653337	0	FACETS	0.527	0.47	0.586			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		475	443	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504969	186504969	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	67	574	1	ENST00000323963.5:c.825G>T	p.Gln275His	p.Q275H	ENST00000323963		275	caG/caT	8/11	0.443637943653337	0	FACETS	0.246	0.214	0.282			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		575	682	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189349345	189349345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	106	570	0	ENST00000264731.3:c.41G>A	p.Cys14Tyr	p.C14Y	ENST00000264731	NM_003722.4	14	tGc/tAc	1/14	0.443637943653337	0	FACETS	0.428	0.384	0.474			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		570	621	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582066	189582066	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	127	757	0	ENST00000264731.3:c.625T>C	p.Cys209Arg	p.C209R	ENST00000264731	NM_003722.4	209	Tgc/Cgc	5/14	0.443637943653337	0	FACETS	0.504	0.458	0.553			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		757	632	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590763	189590763	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	154	834	0	ENST00000264731.3:c.1328A>G	p.His443Arg	p.H443R	ENST00000264731	NM_003722.4	443	cAc/cGc	10/14	0.443637943653337	0	FACETS	0.504	0.462	0.548			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		834	766	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902415	1902415	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	144	671	0	ENST00000382891.5:c.34G>A	p.Val12Ile	p.V12I	ENST00000382891	NM_133335.3	12	Gtt/Att	2/22	0.443637943653337	0	FACETS	0.626	0.573	0.681			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		671	577	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1956987	1956987	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	191	890	2	ENST00000382891.5:c.2438G>A	p.Cys813Tyr	p.C813Y	ENST00000382891	NM_133335.3	813	tGc/tAc	13/22	0.443637943653337	0	FACETS	0.636	0.59	0.684			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		892	753	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749502	41749502	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1577560359	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	117	679	0	ENST00000226382.2:c.293A>G	p.Gln98Arg	p.Q98R	ENST00000226382	NM_003924.3	98	cAg/cGg	2/3	0.443637943653337	0	FACETS	0.526	0.476	0.578			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		679	558	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973986	55973986	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	153	765	0	ENST00000263923.4:c.1330A>T	p.Thr444Ser	p.T444S	ENST00000263923	NM_002253.2	444	Aca/Tca	10/30	0.443637943653337	0	FACETS	0.537	0.493	0.584			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		765	714	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981157	55981157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	65	511	0	ENST00000263923.4:c.542G>A	p.Ser181Asn	p.S181N	ENST00000263923	NM_002253.2	181	aGc/aAc	5/30	0.443637943653337	0	FACETS	0.438	0.382	0.499			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		511	372	SUCCESS
ALB	213	MSKCC	GRCh37	4	74275138	74275138	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	93	554	1	ENST00000295897.4:c.549A>C	p.Lys183Asn	p.K183N	ENST00000295897	NM_000477.5	183	aaA/aaC	5/15	0.443637943653337	0	FACETS	0.529	0.473	0.588			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		555	441	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155929	106155929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	174	853	0	ENST00000380013.4:c.830C>T	p.Ala277Val	p.A277V	ENST00000380013	NM_001127208.2	277	gCa/gTa	3/11	0.443637943653337	0	FACETS	0.568	0.524	0.614			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		853	768	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156915	106156915	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	183	811	0	ENST00000380013.4:c.1816A>G	p.Thr606Ala	p.T606A	ENST00000380013	NM_001127208.2	606	Act/Gct	3/11	0.443637943653337	0	FACETS	0.619	0.573	0.667			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		811	741	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106194036	106194036	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	129	631	0	ENST00000380013.4:c.4498A>T	p.Lys1500Ter	p.K1500*	ENST00000380013	NM_001127208.2	1500	Aaa/Taa	10/11	0.443637943653337	0	FACETS	0.519	0.472	0.569			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		631	623	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197572	106197572	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	171	737	2	ENST00000380013.4:c.5905A>G	p.Lys1969Glu	p.K1969E	ENST00000380013	NM_001127208.2	1969	Aag/Gag	11/11	0.443637943653337	0	FACETS	0.593	0.547	0.641			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		739	723	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007341	143007341	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	81	344	0	ENST00000262992.4:c.2443T>A	p.Ser815Thr	p.S815T	ENST00000262992	NM_001101669.1	815	Tcc/Acc	22/24	0.443637943653337	0	FACETS	0.599	0.532	0.67			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		344	339	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541093	187541093	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1403621739	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	144	809	0	ENST00000441802.2:c.6647A>G	p.Tyr2216Cys	p.Y2216C	ENST00000441802	NM_005245.3	2216	tAc/tGc	10/27	0.443637943653337	0	FACETS	0.553	0.506	0.602			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		809	653	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	256473	256473	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	141	618	0	ENST00000264932.6:c.1933A>T	p.Ile645Phe	p.I645F	ENST00000264932	NM_004168.2	645	Atc/Ttc	15/15	0.443637943653337	0	FACETS	0.549	0.502	0.599			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		618	644	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278868	1278868	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	154	886	0	ENST00000310581.5:c.2174T>A	p.Leu725His	p.L725H	ENST00000310581	NM_198253.2	725	cTc/cAc	6/16	0.443637943653337	0	FACETS	0.557	0.511	0.605			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		886	693	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293830	1293830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	161	1099	0	ENST00000310581.5:c.1171C>T	p.Pro391Ser	p.P391S	ENST00000310581	NM_198253.2	391	Ccc/Tcc	2/16	0.443637943653337	0	FACETS	0.59	0.542	0.639			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1099	685	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1296435	1296435	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	37	274	0				ENST00000310581	NM_198253.2	-/1132			0.443637943653337	0	FACETS	0.603	0.505	0.708			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		274	154	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526427	31526427	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	131	750	1	ENST00000344624.3:c.613A>G	p.Arg205Gly	p.R205G	ENST00000344624		205	Aga/Gga	2/33	0.443637943653337	0	FACETS	0.534	0.486	0.585			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		751	615	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111821	56111821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773710793	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	70	659	0	ENST00000399503.3:c.421G>A	p.Ala141Thr	p.A141T	ENST00000399503	NM_005921.1	141	Gcc/Acc	1/20	0.443637943653337	0	FACETS	0.578	0.508	0.651			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		659	304	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152521	56152521	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	176	658	0	ENST00000399503.3:c.577T>C	p.Cys193Arg	p.C193R	ENST00000399503	NM_005921.1	193	Tgt/Cgt	2/20	0.443637943653337	0	FACETS	0.574	0.53	0.62			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		658	769	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161176	56161176	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	81	415	0	ENST00000399503.3:c.1045T>C	p.Cys349Arg	p.C349R	ENST00000399503	NM_005921.1	349	Tgt/Cgt	5/20	0.443637943653337	0	FACETS	0.543	0.482	0.608			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		415	374	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161260	56161260	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	26	393	1	ENST00000399503.3:c.1129A>T	p.Arg377Ter	p.R377*	ENST00000399503	NM_005921.1	377	Aga/Tga	5/20	0.443637943653337	0	FACETS	0.228	0.181	0.282			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		394	286	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161733	56161733	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	98	513	0	ENST00000399503.3:c.1230G>C	p.Lys410Asn	p.K410N	ENST00000399503	NM_005921.1	410	aaG/aaC	6/20	0.443637943653337	0	FACETS	0.544	0.488	0.603			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		513	452	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177836	56177836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	177	830	0	ENST00000399503.3:c.2809G>A	p.Gly937Arg	p.G937R	ENST00000399503	NM_005921.1	937	Gga/Aga	14/20	0.443637943653337	0	FACETS	0.588	0.543	0.635			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		830	755	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569216	67569216	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	125	578	0	ENST00000274335.5:c.335-2A>T		p.X112_splice	ENST00000274335		112			0.443637943653337	0	FACETS	0.517	0.469	0.567			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		578	607	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86667938	86667938	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	97	520	0	ENST00000274376.6:c.1702T>C	p.Trp568Arg	p.W568R	ENST00000274376	NM_002890.2	568	Tgg/Cgg	13/25	0.443637943653337	0	FACETS	0.555	0.498	0.616			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		520	438	SUCCESS
APC	324	MSKCC	GRCh37	5	112173488	112173488	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	96	680	0	ENST00000257430.4:c.2197A>G	p.Arg733Gly	p.R733G	ENST00000257430	NM_000038.5	733	Agg/Ggg	16/16	0.443637943653337	0	FACETS	0.435	0.389	0.485			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		680	553	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973815	131973815	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	106	513	0	ENST00000265335.6:c.3518T>C	p.Val1173Ala	p.V1173A	ENST00000265335		1173	gTa/gCa	23/25	0.443637943653337	0	FACETS	0.525	0.473	0.581			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		513	506	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149440482	149440482	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	114	689	0	ENST00000286301.3:c.1912A>G	p.Ser638Gly	p.S638G	ENST00000286301	NM_005211.3	638	Agc/Ggc	14/22	0.443637943653337	0	FACETS	0.543	0.49	0.597			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		689	527	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149452891	149452891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	134	771	0	ENST00000286301.3:c.1055C>T	p.Ala352Val	p.A352V	ENST00000286301	NM_005211.3	352	gCt/gTt	7/22	0.443637943653337	0	FACETS	0.519	0.473	0.568			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		771	647	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460572	149460572	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	145	832	0	ENST00000286301.3:c.65T>C	p.Val22Ala	p.V22A	ENST00000286301	NM_005211.3	22	gTg/gCg	3/22	0.443637943653337	0	FACETS	0.58	0.531	0.631			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		832	627	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512373	149512373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774697563	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	200	1034	0	ENST00000261799.4:c.1067C>T	p.Thr356Ile	p.T356I	ENST00000261799	NM_002609.3	356	aCc/aTc	7/23	0.443637943653337	0	FACETS	0.592	0.549	0.637			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1034	847	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523645	176523645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	152	1054	0	ENST00000292408.4:c.2056G>A	p.Gly686Arg	p.G686R	ENST00000292408	NM_213647.1	686	Ggg/Agg	16/18	0.443637943653337	0	FACETS	0.597	0.547	0.648			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1054	639	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638654	176638654	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	153	753	0	ENST00000439151.2:c.3254C>A	p.Pro1085His	p.P1085H	ENST00000439151	NM_022455.4	1085	cCt/cAt	5/23	0.443637943653337	0	FACETS	0.544	0.498	0.591			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		753	706	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721559	176721559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	172	886	0	ENST00000439151.2:c.7190G>A	p.Ser2397Asn	p.S2397N	ENST00000439151	NM_022455.4	2397	aGt/aAt	23/23	0.443637943653337	0	FACETS	0.53	0.488	0.574			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		886	814	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722191	176722191	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	151	980	0	ENST00000439151.2:c.7822G>A	p.Ala2608Thr	p.A2608T	ENST00000439151	NM_022455.4	2608	Gcc/Acc	23/23	0.443637943653337	0	FACETS	0.555	0.508	0.603			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		980	683	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043464	180043464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	155	780	0	ENST00000261937.6:c.3122G>A	p.Arg1041Gln	p.R1041Q	ENST00000261937	NM_182925.4	1041	cGg/cAg	23/30	0.443637943653337	0	FACETS	0.573	0.525	0.622			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		780	679	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393340	393340	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	96	671	0	ENST00000380956.4:c.188A>G	p.Asn63Ser	p.N63S	ENST00000380956	NM_001195286.1	63	aAc/aGc	2/9	0.443637943653337	0	FACETS	0.587	0.527	0.651			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		671	410	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020940	26020940	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	208	1104	0	ENST00000357647.3:c.223A>T	p.Ile75Phe	p.I75F	ENST00000357647	NM_003529.2	75	Att/Ttt	1/1	0.443637943653337	0	FACETS	0.584	0.543	0.627			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1104	893	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032267	26032267	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	34	844	0	ENST00000244661.2:c.22G>A	p.Ala8Thr	p.A8T	ENST00000244661	NM_003537.3	8	Gct/Act	1/1	0.443637943653337	0	FACETS	0.126	0.102	0.153			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		844	677	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056197	26056197	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs548795634	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	192	925	0	ENST00000343677.2:c.460A>G	p.Thr154Ala	p.T154A	ENST00000343677	NM_005319.3	154	Aca/Gca	1/1	0.443637943653337	0	FACETS	0.6	0.556	0.645			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		925	803	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250758	26250758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	199	1009	0	ENST00000446824.2:c.76G>A	p.Ala26Thr	p.A26T	ENST00000446824	NM_021018.2	26	Gct/Act	1/1	0.443637943653337	0	FACETS	0.572	0.531	0.616			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1009	872	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911237	29911237	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs78674188	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	177	656	0	ENST00000376809.5:c.536A>G	p.Gln179Arg	p.Q179R	ENST00000376809	NM_002116.7	179	cAg/cGg	3/8	0.443637943653337	0	FACETS	0.963	0.896	1			1	CLONAL	1	FALSE	0	0.443637943653337	0		656	461	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675957	30675957	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1003687322	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	167	857	0	ENST00000376406.3:c.2399T>C	p.Met800Thr	p.M800T	ENST00000376406	NM_014641.2	800	aTg/aCg	8/15	0.443637943653337	0	FACETS	0.568	0.522	0.614			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		857	738	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679936	30679936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	165	1010	0	ENST00000376406.3:c.1783G>A	p.Val595Ile	p.V595I	ENST00000376406	NM_014641.2	595	Gta/Ata	5/15	0.443637943653337	0	FACETS	0.602	0.555	0.652			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1010	687	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31238202	31238202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	11	275	0	ENST00000376228.5:c.680G>A	p.Cys227Tyr	p.C227Y	ENST00000376228	NM_002117.5	227	tGc/tAc	4/8	0.443637943653337	0	FACETS	0.135	0.093	0.187			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		275	205	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163378	32163378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	143	882	0	ENST00000375023.3:c.5848C>T	p.Pro1950Ser	p.P1950S	ENST00000375023	NM_004557.3	1950	Ccc/Tcc	30/30	0.443637943653337	0	FACETS	0.552	0.504	0.601			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		882	650	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171946	32171946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1427973750	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	139	760	0	ENST00000375023.3:c.3086C>T	p.Ala1029Val	p.A1029V	ENST00000375023	NM_004557.3	1029	gCc/gTc	19/30	0.443637943653337	0	FACETS	0.569	0.519	0.62			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		760	613	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180293	32180293	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	183	901	0	ENST00000375023.3:c.2638A>T	p.Asn880Tyr	p.N880Y	ENST00000375023	NM_004557.3	880	Aac/Tac	17/30	0.443637943653337	0	FACETS	0.626	0.579	0.675			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		901	733	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288657	33288657	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1213838920	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	135	763	1	ENST00000374542.5:c.895C>T	p.Arg299Ter	p.R299*	ENST00000374542	NM_001141970.1	299	Cga/Tga	3/8	0.443637943653337	0	FACETS	0.551	0.503	0.602			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		764	614	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288785	33288785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765273333	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	39	852	0	ENST00000374542.5:c.767G>A	p.Arg256His	p.R256H	ENST00000374542	NM_001141970.1	256	cGc/cAc	3/8	0.443637943653337	0	FACETS	0.152	0.125	0.182			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		852	644	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289681	33289681	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	138	652	0	ENST00000374542.5:c.22A>G	p.Ile8Val	p.I8V	ENST00000374542	NM_001141970.1	8	Atc/Gtc	2/8	0.443637943653337	0	FACETS	0.647	0.592	0.704			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		652	535	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652320	36652320	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	133	656	0	ENST00000244741.5:c.442A>G	p.Thr148Ala	p.T148A	ENST00000244741	NM_000389.4	148	Aca/Gca	2/3	0.443637943653337	0	FACETS	0.649	0.593	0.708			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		656	514	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37141788	37141788	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	137	698	0	ENST00000373509.5:c.863C>T	p.Pro288Leu	p.P288L	ENST00000373509	NM_002648.3	288	cCa/cTa	6/6	0.443637943653337	0	FACETS	0.525	0.479	0.574			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		698	654	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554349	106554349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	138	736	0	ENST00000369096.4:c.1877C>T	p.Thr626Met	p.T626M	ENST00000369096	NM_001198.3	626	aCg/aTg	6/7	0.443637943653337	0	FACETS	0.497	0.453	0.543			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		736	697	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630005	117630005	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	98	572	0	ENST00000368508.3:c.6521T>C	p.Val2174Ala	p.V2174A	ENST00000368508	NM_002944.2	2174	gTg/gCg	41/43	0.443637943653337	0	FACETS	0.562	0.505	0.623			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		572	437	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679042	117679042	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	71	405	0	ENST00000368508.3:c.3779T>C	p.Val1260Ala	p.V1260A	ENST00000368508	NM_002944.2	1260	gTg/gCg	24/43	0.443637943653337	0	FACETS	0.484	0.425	0.547			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		405	368	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725441	117725441	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	82	449	0	ENST00000368508.3:c.438+2T>C		p.X146_splice	ENST00000368508	NM_002944.2	146			0.443637943653337	0	FACETS	0.562	0.499	0.629			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		449	366	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150022928	150022928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	66	470	0	ENST00000253339.5:c.335C>T	p.Ala112Val	p.A112V	ENST00000253339		112	gCt/gTt	1/7	0.443637943653337	0	FACETS	0.413	0.36	0.47			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		470	401	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415537	152415537	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519714	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	53	720	0	ENST00000206249.3:c.1387T>C	p.Ser463Pro	p.S463P	ENST00000206249	NM_000125.3	463	Tcc/Ccc	7/8	0.443637943653337	0	FACETS	0.236	0.201	0.274			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		720	564	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157495251	157495251	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	181	625	0	ENST00000346085.5:c.3135G>T	p.Lys1045Asn	p.K1045N	ENST00000346085	NM_020732.3	1045	aaG/aaT	11/20	0.443637943653337	0	FACETS	0.654	0.605	0.705			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		625	694	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527427	157527427	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	108	756	0	ENST00000346085.5:c.5152A>G	p.Lys1718Glu	p.K1718E	ENST00000346085	NM_020732.3	1718	Aag/Gag	20/20	0.443637943653337	0	FACETS	0.398	0.358	0.441			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		756	680	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969905	161969905	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	118	609	0	ENST00000366898.1:c.1064G>C	p.Gly355Ala	p.G355A	ENST00000366898	NM_004562.2	355	gGc/gCc	9/12	0.443637943653337	0	FACETS	0.561	0.508	0.616			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		609	528	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962788	2962788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201948130	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	96	585	0	ENST00000396946.4:c.2120G>A	p.Arg707His	p.R707H	ENST00000396946	NM_032415.4	707	cGt/cAt	16/25	0.443637943653337	0	FACETS	0.63	0.566	0.698			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		585	382	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6029554	6029554	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	82	390	0	ENST00000265849.7:c.1021A>G	p.Arg341Gly	p.R341G	ENST00000265849	NM_000535.5	341	Agg/Ggg	10/15	0.443637943653337	0	FACETS	0.55	0.488	0.615			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		390	374	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350165	81350165	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	64	259	0	ENST00000222390.5:c.1169-2A>G		p.X390_splice	ENST00000222390	NM_000601.4	390			0.443637943653337	0	FACETS	0.577	0.505	0.655			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		259	278	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508676	106508676	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	129	779	0	ENST00000359195.3:c.670A>G	p.Ile224Val	p.I224V	ENST00000359195	NM_002649.2	224	Att/Gtt	2/11	0.443637943653337	0	FACETS	0.479	0.435	0.525			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		779	676	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509847	106509847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	33	723	0	ENST00000359195.3:c.1841G>A	p.Arg614Lys	p.R614K	ENST00000359195	NM_002649.2	614	aGg/aAg	2/11	0.443637943653337	0	FACETS	0.141	0.114	0.172			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		723	586	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340234	116340234	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	89	624	0	ENST00000397752.3:c.1096C>T	p.Pro366Ser	p.P366S	ENST00000397752	NM_000245.2	366	Cct/Tct	2/21	0.443637943653337	0	FACETS	0.399	0.355	0.447			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		624	559	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124465341	124465341	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	62	320	0	ENST00000357628.3:c.1757T>A	p.Ile586Asn	p.I586N	ENST00000357628	NM_015450.2	586	aTc/aAc	18/19	0.443637943653337	0	FACETS	0.589	0.514	0.669			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		320	264	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124493048	124493048	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	70	435	0	ENST00000357628.3:c.847T>A	p.Ser283Thr	p.S283T	ENST00000357628	NM_015450.2	283	Tct/Act	10/19	0.443637943653337	0	FACETS	0.513	0.45	0.58			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		435	342	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846153	128846153	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	72	959	0	ENST00000249373.3:c.1083C>G	p.His361Gln	p.H361Q	ENST00000249373	NM_005631.4	361	caC/caG	5/12	0.443637943653337	0	FACETS	0.23	0.2	0.262			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		959	785	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851889	128851889	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	124	804	0	ENST00000249373.3:c.1961T>C	p.Leu654Pro	p.L654P	ENST00000249373	NM_005631.4	654	cTg/cCg	12/12	0.443637943653337	0	FACETS	0.499	0.453	0.548			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		804	623	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494126	140494126	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	127	655	0	ENST00000288602.6:c.1122A>G	p.Ile374Met	p.I374M	ENST00000288602	NM_004333.4	374	atA/atG	8/18	0.443637943653337	0	FACETS	0.481	0.437	0.528			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		655	662	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525882	148525882	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	91	557	0	ENST00000320356.2:c.575A>T	p.Asp192Val	p.D192V	ENST00000320356	NM_004456.4	192	gAt/gTt	6/20	0.443637943653337	0	FACETS	0.504	0.449	0.561			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		557	453	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860280	151860280	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	36	864	0	ENST00000262189.6:c.10382A>T	p.Asp3461Val	p.D3461V	ENST00000262189	NM_170606.2	3461	gAt/gTt	43/59	0.443637943653337	0	FACETS	0.131	0.107	0.158			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		864	691	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874620	151874620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	145	872	0	ENST00000262189.6:c.7918C>T	p.His2640Tyr	p.H2640Y	ENST00000262189	NM_170606.2	2640	Cat/Tat	38/59	0.443637943653337	0	FACETS	0.514	0.469	0.56			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		872	708	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29195991	29195991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775693732	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	153	844	0	ENST00000240100.2:c.607C>T	p.Leu203Phe	p.L203F	ENST00000240100	NM_001394.6	203	Ctc/Ttc	3/4	0.443637943653337	1	FACETS	0.804	0.737	0.872	0.804	0.737	0.872	CLONAL	1	FALSE	0	0.443637943653337	1		844	668	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372532	55372532	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	122	756	0	ENST00000297316.4:c.1222T>C	p.Tyr408His	p.Y408H	ENST00000297316	NM_022454.3	408	Tac/Cac	2/2	0.443637943653337	0	FACETS	0.49	0.443	0.538			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		756	625	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56854501	56854501	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	93	471	0	ENST00000519728.1:c.83A>T	p.Glu28Val	p.E28V	ENST00000519728	NM_002350.3	28	gAa/gTa	2/13	0.443637943653337	0	FACETS	0.546	0.488	0.607			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		471	427	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56910992	56910992	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	67	561	0	ENST00000519728.1:c.1138A>G	p.Met380Val	p.M380V	ENST00000519728	NM_002350.3	380	Atg/Gtg	11/13	0.443637943653337	0	FACETS	0.266	0.231	0.304			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		561	631	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965415	68965415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1419877039	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	95	523	3	ENST00000288368.4:c.1027G>A	p.Ala343Thr	p.A343T	ENST00000288368	NM_024870.2	343	Gca/Aca	9/40	0.443637943653337	0	FACETS	0.593	0.531	0.657			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		526	402	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005937	69005937	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	85	505	0	ENST00000288368.4:c.2348C>T	p.Ala783Val	p.A783V	ENST00000288368	NM_024870.2	783	gCt/gTt	21/40	0.443637943653337	0	FACETS	0.524	0.466	0.585			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		505	407	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69012049	69012049	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	83	344	0	ENST00000288368.4:c.2686C>A	p.Leu896Ile	p.L896I	ENST00000288368	NM_024870.2	896	Cta/Ata	23/40	0.443637943653337	0	FACETS	0.575	0.511	0.643			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		344	362	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020374	69020374	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	110	517	0	ENST00000288368.4:c.2746C>T	p.Pro916Ser	p.P916S	ENST00000288368	NM_024870.2	916	Cct/Tct	24/40	0.443637943653337	0	FACETS	0.559	0.504	0.616			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		517	494	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136860	69136860	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs371954703	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	132	598	0	ENST00000288368.4:c.4774A>G	p.Arg1592Gly	p.R1592G	ENST00000288368	NM_024870.2	1592	Agg/Ggg	39/40	0.443637943653337	0	FACETS	0.593	0.541	0.648			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		598	558	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980488	70980488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267601982	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	152	729	1	ENST00000276594.2:c.889G>A	p.Gly297Arg	p.G297R	ENST00000276594	NM_024504.3	297	Gga/Aga	4/8	0.443637943653337	0	FACETS	0.564	0.517	0.613			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		730	676	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551294	141551294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	174	821	0	ENST00000220592.5:c.2003G>A	p.Arg668His	p.R668H	ENST00000220592	NM_012154.3	668	cGc/cAc	15/19	0.443637943653337	0	FACETS	0.573	0.529	0.62			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		821	761	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741827	145741827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	170	998	0	ENST00000428558.2:c.676G>A	p.Ala226Thr	p.A226T	ENST00000428558	NM_004260.3	226	Gct/Act	5/22	0.443637943653337	0	FACETS	0.616	0.568	0.666			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		998	692	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2039894	2039894	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	142	864	0	ENST00000349721.2:c.784C>G	p.Pro262Ala	p.P262A	ENST00000349721	NM_003070.3	262	Cca/Gca	4/34	0.443637943653337	0	FACETS	0.466	0.425	0.509			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		864	764	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2047283	2047283	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	30	160	0	ENST00000349721.2:c.845C>T	p.Ala282Val	p.A282V	ENST00000349721	NM_003070.3	282	gCg/gTg	5/34	0.443637943653337	0	FACETS	0.697	0.574	0.829			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		160	108	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5029881	5029881	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	48	378	0	ENST00000381652.3:c.325A>G	p.Arg109Gly	p.R109G	ENST00000381652	NM_004972.3	109	Agg/Ggg	4/25	0.443637943653337	0	FACETS	0.474	0.404	0.55			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		378	254	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066725	5066725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	65	301	0	ENST00000381652.3:c.1262G>A	p.Gly421Glu	p.G421E	ENST00000381652	NM_004972.3	421	gGa/gAa	10/25	0.443637943653337	0	FACETS	0.549	0.48	0.622			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		301	297	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066731	5066731	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1011666024	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	68	306	0	ENST00000381652.3:c.1268A>G	p.Tyr423Cys	p.Y423C	ENST00000381652	NM_004972.3	423	tAt/tGt	10/25	0.443637943653337	0	FACETS	0.569	0.499	0.642			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		306	300	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5078388	5078388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	77	436	0	ENST00000381652.3:c.2075C>T	p.Pro692Leu	p.P692L	ENST00000381652	NM_004972.3	692	cCt/cTt	16/25	0.443637943653337	0	FACETS	0.508	0.449	0.571			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		436	380	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089842	5089842	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	81	612	0	ENST00000381652.3:c.2740A>G	p.Lys914Glu	p.K914E	ENST00000381652	NM_004972.3	914	Aag/Gag	20/25	0.443637943653337	0	FACETS	0.398	0.351	0.447			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		612	511	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484239	8484239	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	125	612	0	ENST00000356435.5:c.3293G>T	p.Arg1098Met	p.R1098M	ENST00000356435		1098	aGg/aTg	19/35	0.443637943653337	0	FACETS	0.509	0.462	0.558			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		612	616	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500873	8500873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770452187	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	121	772	0	ENST00000356435.5:c.2009C>T	p.Thr670Ile	p.T670I	ENST00000356435		670	aCc/aTc	13/35	0.443637943653337	0	FACETS	0.556	0.504	0.61			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		772	546	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27205005	27205005	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1174230775	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	148	643	0	ENST00000380036.4:c.2306T>C	p.Ile769Thr	p.I769T	ENST00000380036	NM_000459.3	769	aTa/aCa	14/23	0.443637943653337	0	FACETS	0.584	0.535	0.635			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		643	636	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966697	36966697	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	115	681	0	ENST00000358127.4:c.629A>T	p.Asn210Ile	p.N210I	ENST00000358127	NM_001280556.1	210	aAc/aTc	6/10	0.443637943653337	0	FACETS	0.539	0.487	0.593			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		681	535	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342845	87342845	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs146616471	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	124	666	0	ENST00000277120.3:c.1130A>G	p.His377Arg	p.H377R	ENST00000277120		377	cAc/cGc	9/19	0.443637943653337	0	FACETS	0.537	0.487	0.589			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		666	579	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93636496	93636496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	124	598	0	ENST00000375746.1:c.926C>T	p.Ala309Val	p.A309V	ENST00000375746	NM_001174167.1	309	gCc/gTc	8/14	0.443637943653337	0	FACETS	0.515	0.467	0.565			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		598	604	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637014	93637014	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	39	777	0	ENST00000375746.1:c.1064C>A	p.Pro355His	p.P355H	ENST00000375746	NM_001174167.1	355	cCc/cAc	9/14	0.443637943653337	0	FACETS	0.133	0.109	0.159			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		777	736	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637132	93637132	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	36	525	0	ENST00000375746.1:c.1181+1G>A		p.X394_splice	ENST00000375746	NM_001174167.1	394			0.443637943653337	0	FACETS	0.195	0.16	0.234			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		525	464	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639897	93639897	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	141	631	0	ENST00000375746.1:c.1226A>G	p.Asn409Ser	p.N409S	ENST00000375746	NM_001174167.1	409	aAt/aGt	10/14	0.443637943653337	0	FACETS	0.554	0.506	0.604			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		631	638	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93657860	93657860	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	150	707	0	ENST00000375746.1:c.1886A>T	p.Tyr629Phe	p.Y629F	ENST00000375746	NM_001174167.1	629	tAc/tTc	14/14	0.443637943653337	0	FACETS	0.561	0.514	0.61			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		707	671	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97897637	97897637	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	82	463	0	ENST00000289081.3:c.834T>A	p.Asp278Glu	p.D278E	ENST00000289081	NM_000136.2	278	gaT/gaA	8/15	0.443637943653337	0	FACETS	0.514	0.456	0.576			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		463	400	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97897764	97897764	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	100	522	0	ENST00000289081.3:c.707T>C	p.Met236Thr	p.M236T	ENST00000289081	NM_000136.2	236	aTg/aCg	8/15	0.443637943653337	0	FACETS	0.495	0.443	0.549			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		522	507	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98009741	98009741	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	81	346	0	ENST00000289081.3:c.223T>C	p.Cys75Arg	p.C75R	ENST00000289081	NM_000136.2	75	Tgt/Cgt	3/15	0.443637943653337	0	FACETS	0.567	0.504	0.635			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		346	358	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98011515	98011515	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	138	638	0	ENST00000289081.3:c.59C>T	p.Ser20Phe	p.S20F	ENST00000289081	NM_000136.2	20	tCt/tTt	2/15	0.443637943653337	0	FACETS	0.584	0.533	0.636			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		638	593	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231298	98231298	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs756263511	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	176	967	0	ENST00000331920.6:c.1985T>C	p.Val662Ala	p.V662A	ENST00000331920	NM_000264.3	662	gTc/gCc	14/24	0.443637943653337	0	FACETS	0.533	0.491	0.576			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		967	828	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900198	101900198	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	44	558	0	ENST00000374994.4:c.632T>C	p.Ile211Thr	p.I211T	ENST00000374994	NM_004612.2	211	aTt/aCt	4/9	0.443637943653337	0	FACETS	0.207	0.173	0.245			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		558	532	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133748264	133748264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	126	634	0	ENST00000318560.5:c.925C>T	p.Pro309Ser	p.P309S	ENST00000318560	NM_005157.4	309	Ccc/Tcc	6/11	0.443637943653337	0	FACETS	0.573	0.52	0.627			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		634	552	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760343	133760343	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	123	867	0	ENST00000318560.5:c.2666A>G	p.Lys889Arg	p.K889R	ENST00000318560	NM_005157.4	889	aAg/aGg	11/11	0.443637943653337	0	FACETS	0.583	0.53	0.639			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		867	529	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760934	133760934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	107	753	0	ENST00000318560.5:c.3257C>T	p.Ala1086Val	p.A1086V	ENST00000318560	NM_005157.4	1086	gCc/gTc	11/11	0.443637943653337	0	FACETS	0.477	0.429	0.527			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		753	563	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797354	135797354	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	156	638	0	ENST00000298552.3:c.515T>C	p.Val172Ala	p.V172A	ENST00000298552	NM_001162426.1	172	gTg/gCg	7/23	0.443637943653337	0	FACETS	0.565	0.519	0.614			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		638	692	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396829	139396829	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1009338178	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	104	782	0	ENST00000277541.6:c.5279G>A	p.Arg1760His	p.R1760H	ENST00000277541	NM_017617.3	1760	cGc/cAc	28/34	0.443637943653337	0	FACETS	0.445	0.399	0.494			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		782	586	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402508	139402508	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	136	899	0	ENST00000277541.6:c.3409T>C	p.Tyr1137His	p.Y1137H	ENST00000277541	NM_017617.3	1137	Tac/Cac	21/34	0.443637943653337	0	FACETS	0.539	0.491	0.589			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		899	633	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139408961	139408961	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	113	808	0	ENST00000277541.6:c.2207+1G>A		p.X736_splice	ENST00000277541	NM_017617.3	736			0.443637943653337	0	FACETS	0.484	0.436	0.533			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		808	586	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409082	139409082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1385662021	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	175	981	1	ENST00000277541.6:c.2087G>A	p.Gly696Asp	p.G696D	ENST00000277541	NM_017617.3	696	gGc/gAc	13/34	0.443637943653337	0	FACETS	0.612	0.565	0.661			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		982	717	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412669	139412669	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	38	961	0	ENST00000277541.6:c.1175T>C	p.Val392Ala	p.V392A	ENST00000277541	NM_017617.3	392	gTc/gCc	7/34	0.443637943653337	0	FACETS	0.128	0.105	0.154			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		961	745	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413270	139413270	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	31	646	0	ENST00000277541.6:c.872A>G	p.Tyr291Cys	p.Y291C	ENST00000277541	NM_017617.3	291	tAc/tGc	6/34	0.443637943653337	0	FACETS	0.138	0.111	0.169			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		646	563	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417521	139417521	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	154	947	0	ENST00000277541.6:c.523T>C	p.Cys175Arg	p.C175R	ENST00000277541	NM_017617.3	175	Tgc/Cgc	4/34	0.443637943653337	0	FACETS	0.577	0.53	0.627			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		947	669	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139804421	139804421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	134	632	0	ENST00000247668.2:c.578G>A	p.Gly193Asp	p.G193D	ENST00000247668	NM_021138.3	193	gGc/gAc	6/11	0.443637943653337	0	FACETS	0.59	0.538	0.644			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		632	570	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814830	139814830	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	188	944	0	ENST00000247668.2:c.823C>A	p.Leu275Met	p.L275M	ENST00000247668	NM_021138.3	275	Ctg/Atg	8/11	0.443637943653337	0	FACETS	0.631	0.585	0.679			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		944	747	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932028	39932028	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	120	762	1	ENST00000378444.4:c.2571G>T	p.Glu857Asp	p.E857D	ENST00000378444	NM_001123385.1	857	gaG/gaT	4/15	0.443637943653337	0	FACETS	0.441	0.399	0.486			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		763	682	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932653	39932653	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	176	1064	0	ENST00000378444.4:c.1946C>A	p.Pro649Gln	p.P649Q	ENST00000378444	NM_001123385.1	649	cCa/cAa	4/15	0.443637943653337	0	FACETS	0.605	0.558	0.653			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1064	730	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922874	44922874	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	149	867	3	ENST00000377967.4:c.1735T>C	p.Cys579Arg	p.C579R	ENST00000377967	NM_021140.2	579	Tgt/Cgt	16/29	0.443637943653337	0	FACETS	0.552	0.505	0.6			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		870	677	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039870	47039870	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	113	660	0	ENST00000377604.3:c.1213A>G	p.Thr405Ala	p.T405A	ENST00000377604	NM_001204468.1	405	Act/Gct	12/24	0.443637943653337	0	FACETS	0.668	0.606	0.734			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		660	424	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426738	47426738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766305105	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	140	880	0	ENST00000377045.4:c.983G>A	p.Arg328Gln	p.R328Q	ENST00000377045	NM_001654.4	328	cGg/cAg	10/16	0.443637943653337	0	FACETS	0.495	0.452	0.541			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		880	709	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428238	47428238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754803899	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	167	862	1	ENST00000377045.4:c.1198C>T	p.Arg400Cys	p.R400C	ENST00000377045	NM_001654.4	400	Cgc/Tgc	11/16	0.443637943653337	0	FACETS	0.571	0.525	0.618			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		863	734	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650326	48650326	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	169	1040	0	ENST00000376670.3:c.296G>A	p.Gly99Asp	p.G99D	ENST00000376670	NM_002049.3	99	gGc/gAc	3/6	0.443637943653337	0	FACETS	0.6	0.553	0.648			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1040	707	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225934	53225934	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	131	848	0	ENST00000375401.3:c.2915A>G	p.Glu972Gly	p.E972G	ENST00000375401	NM_004187.3	972	gAg/gGg	19/26	0.443637943653337	0	FACETS	0.485	0.44	0.531			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		848	678	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409898	63409898	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	160	964	1	ENST00000330258.3:c.3269T>A	p.Val1090Asp	p.V1090D	ENST00000330258	NM_152424.3	1090	gTc/gAc	2/2	0.443637943653337	0	FACETS	0.55	0.506	0.597			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		965	729	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410180	63410180	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	32	945	0	ENST00000330258.3:c.2987T>C	p.Ile996Thr	p.I996T	ENST00000330258	NM_152424.3	996	aTa/aCa	2/2	0.443637943653337	0	FACETS	0.145	0.117	0.176			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		945	555	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410390	63410390	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	138	1060	0	ENST00000330258.3:c.2777A>G	p.Glu926Gly	p.E926G	ENST00000330258	NM_152424.3	926	gAa/gGa	2/2	0.443637943653337	0	FACETS	0.524	0.478	0.573			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		1060	660	SUCCESS
AR	367	MSKCC	GRCh37	X	66766175	66766175	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	145	900	1	ENST00000374690.3:c.1187G>A	p.Gly396Asp	p.G396D	ENST00000374690	NM_000044.3	396	gGc/gAc	1/8	0.443637943653337	0	FACETS	0.605	0.554	0.658			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		901	601	SUCCESS
AR	367	MSKCC	GRCh37	X	66766582	66766582	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	143	764	0	ENST00000374690.3:c.1594T>A	p.Ser532Thr	p.S532T	ENST00000374690	NM_000044.3	532	Tcc/Acc	1/8	0.443637943653337	0	FACETS	0.561	0.513	0.611			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		764	639	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357772	70357772	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	151	890	0	ENST00000374080.3:c.6023A>G	p.His2008Arg	p.H2008R	ENST00000374080		2008	cAt/cGt	41/45	0.443637943653337	0	FACETS	0.548	0.502	0.596			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		890	691	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938753	76938753	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	112	598	0	ENST00000373344.5:c.1995G>C	p.Arg665Ser	p.R665S	ENST00000373344	NM_000489.3	665	agG/agC	9/35	0.443637943653337	0	FACETS	0.638	0.578	0.702			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		598	440	SUCCESS
BTK	695	MSKCC	GRCh37	X	100609666	100609666	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	114	584	0	ENST00000308731.7:c.1583T>C	p.Leu528Ser	p.L528S	ENST00000308731	NM_000061.2	528	tTg/tCg	16/19	0.443637943653337	0	FACETS	0.493	0.445	0.543			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		584	580	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202418	123202418	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	34	185	0	ENST00000218089.9:c.2270A>T	p.Asp757Val	p.D757V	ENST00000218089	NM_001042749.1	757	gAc/gTc	24/35	0.443637943653337	0	FACETS	0.416	0.343	0.497			1	SUBCLONAL	1	FALSE	0	0.443637943653337	0		185	205	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750454	57750454	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062866-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	282	497	0	ENST00000274289.3:c.2014C>T	p.Arg672Ter	p.R672*	ENST00000274289	NM_006622.3	672	Cga/Tga	14/14	0.307816465630341	5	FACETS	0.85	0.803	0.898	0.85	0.803	0.898	INDETERMINATE	3	TRUE	2	0.529669165250484	5		497	749	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375249	31375249	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062866-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	99	648	0	ENST00000328111.2:c.646G>A	p.Glu216Lys	p.E216K	ENST00000328111	NM_006892.3	216	Gag/Aag	6/23	0.359609379753666	4	FACETS	0.688	0.614	0.767	0.344	0.307	0.384	SUBCLONAL	1	TRUE	2	0.529669165250484	4		648	831	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41904348	41904348	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062866-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	166	657	0	ENST00000372991.4:c.660G>A	p.Met220Ile	p.M220I	ENST00000372991	NM_001760.3	220	atG/atA	4/5	0.307816465630341	5	FACETS	1	0.987	1	0.456	0.419	0.495	INDETERMINATE	1	TRUE	2	0.529669165250484	5		657	822	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	42	343	0				ENST00000310581	NM_198253.2	-/1132			0.0526357044489296	3	FACETS	1	0.893	1	0.545	0.456	0.643	INDETERMINATE	1	TRUE	1	0.231204145220924	3		343	372	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	145	689	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	1	0.958	1	1	0.992	1	CLONAL	2	TRUE	1	0.231204145220924	2		689	585	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115284194	115284194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	39	429	0	ENST00000438362.2:c.92C>T	p.Ser31Leu	p.S31L	ENST00000438362	NM_001242891.1	31	tCa/tTa	2/20	0.231204145220924	3	FACETS	0.591	0.489	0.705	0.295	0.244	0.353	SUBCLONAL	1	TRUE	1	0.231204145220924	3		429	637	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458899	120458899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	172	675	0	ENST00000256646.2:c.6446C>T	p.Ser2149Phe	p.S2149F	ENST00000256646	NM_024408.3	2149	tCc/tTc	34/34	0.231204145220924	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.231204145220924	3		675	695	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466287	120466288	+	missense_variant	Missense_Mutation	DNP	GG	GG	TA	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	119	500	0	ENST00000256646.2:c.4831_4832delinsTA	p.Pro1611Tyr	p.P1611Y	ENST00000256646	NM_024408.3	1611	CCt/TAt	26/34	0.231204145220924	3	FACETS	0.797	0.72	0.879	0.797	0.72	0.879	SUBCLONAL	2	TRUE	1	0.231204145220924	3		500	720	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480632	120480632	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	48	455	0	ENST00000256646.2:c.3185C>T	p.Thr1062Ile	p.T1062I	ENST00000256646	NM_024408.3	1062	aCc/aTc	20/34	0.231204145220924	3	FACETS	0.638	0.538	0.749	0.319	0.269	0.375	SUBCLONAL	1	TRUE	1	0.231204145220924	3		455	726	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150933182	150933182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	73	691	0	ENST00000271640.5:c.2644G>A	p.Gly882Ser	p.G882S	ENST00000271640	NM_001145415.1	882	Ggt/Agt	16/22	1	2	FACETS	0.849	0.742	0.965	0.849	0.742	0.965	CLONAL	1	TRUE	1	0.231204145220924	2		691	744	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175708	176175708	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	57	537	0	ENST00000367669.3:c.407G>A	p.Cys136Tyr	p.C136Y	ENST00000367669	NM_022457.5	136	tGc/tAc	1/20	1	2	FACETS	0.925	0.794	1	0.925	0.794	1	CLONAL	1	TRUE	1	0.231204145220924	2		537	533	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604568	43604568	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	123	571	0	ENST00000355710.3:c.1153G>A	p.Gly385Arg	p.G385R	ENST00000355710	NM_020975.4	385	Gga/Aga	6/20	0.0526357044489296	3	FACETS	0.783	0.708	0.862	0.783	0.708	0.862	INDETERMINATE	2	TRUE	1	0.231204145220924	3		571	758	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47595054	47595054	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1457096443	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	110	655	0	ENST00000430070.2:c.1033A>C	p.Lys345Gln	p.K345Q	ENST00000430070	NM_018095.4	345	Aaa/Caa	4/4	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.231204145220924	2		655	685	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137784	64137784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	58	657	0	ENST00000334205.4:c.1885C>T	p.Arg629Cys	p.R629C	ENST00000334205	NM_003942.2	629	Cgc/Tgc	15/17	1	2	FACETS	0.775	0.666	0.895	0.775	0.666	0.895	SUBCLONAL	1	TRUE	1	0.231204145220924	2		657	647	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650562	18650562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	78	378	0	ENST00000266497.5:c.2773G>A	p.Asp925Asn	p.D925N	ENST00000266497		925	Gat/Aat	20/31	0.231204145220924	2	FACETS	0.865	0.765	0.972	0.865	0.765	0.972	CLONAL	2	TRUE	0	0.231204145220924	2		378	390	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622508	28622508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	46	385	0	ENST00000241453.7:c.1109C>T	p.Ser370Phe	p.S370F	ENST00000241453	NM_004119.2	370	tCt/tTt	9/24	1	2	FACETS	0.831	0.7	0.975	0.831	0.7	0.975	CLONAL	1	TRUE	1	0.231204145220924	2		385	479	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912711	32912711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	40	387	0	ENST00000380152.3:c.4219G>A	p.Glu1407Lys	p.E1407K	ENST00000380152		1407	Gaa/Aaa	11/27	1	2	FACETS	0.698	0.579	0.829	0.698	0.579	0.829	SUBCLONAL	1	TRUE	1	0.231204145220924	2		387	496	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913252	32913252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555283930	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	49	458	0	ENST00000380152.3:c.4760C>T	p.Ala1587Val	p.A1587V	ENST00000380152		1587	gCt/gTt	11/27	1	2	FACETS	0.766	0.649	0.896	0.766	0.649	0.896	SUBCLONAL	1	TRUE	1	0.231204145220924	2		458	553	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107739	30107739	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778680785	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	58	440	0	ENST00000331968.5:c.941C>T	p.Pro314Leu	p.P314L	ENST00000331968	NM_002742.2	314	cCg/cTg	6/18	1	2	FACETS	0.736	0.631	0.85	0.736	0.631	0.85	SUBCLONAL	1	TRUE	1	0.231204145220924	2		440	682	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779646	3779646	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	60	769	0	ENST00000262367.5:c.5402T>G	p.Val1801Gly	p.V1801G	ENST00000262367	NM_004380.2	1801	gTg/gGg	31/31	1	2	FACETS	0.73	0.628	0.841	0.73	0.628	0.841	SUBCLONAL	1	TRUE	1	0.231204145220924	2		769	711	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857376	9857376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	60	612	0	ENST00000330684.3:c.4025C>T	p.Ser1342Phe	p.S1342F	ENST00000330684	NM_001134407.1	1342	tCc/tTc	13/13	1	2	FACETS	0.974	0.84	1	0.974	0.84	1	CLONAL	1	TRUE	1	0.231204145220924	2		612	533	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858517	9858517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765370528	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	44	601	0	ENST00000330684.3:c.2884G>A	p.Glu962Lys	p.E962K	ENST00000330684	NM_001134407.1	962	Gaa/Aaa	13/13	1	2	FACETS	0.74	0.621	0.873	0.74	0.621	0.873	SUBCLONAL	1	TRUE	1	0.231204145220924	2		601	514	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821854	72821854	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	69	683	0	ENST00000268489.5:c.10321G>A	p.Glu3441Lys	p.E3441K	ENST00000268489	NM_006885.3	3441	Gag/Aag	10/10	1	2	FACETS	0.838	0.729	0.956	0.838	0.729	0.956	CLONAL	1	TRUE	1	0.231204145220924	2		683	712	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831073	72831073	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	58	593	0	ENST00000268489.5:c.5508G>C	p.Lys1836Asn	p.K1836N	ENST00000268489	NM_006885.3	1836	aaG/aaC	9/10	1	2	FACETS	0.775	0.666	0.895	0.775	0.666	0.895	SUBCLONAL	1	TRUE	1	0.231204145220924	2		593	647	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845827	72845827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	99	684	0	ENST00000268489.5:c.3640G>A	p.Ala1214Thr	p.A1214T	ENST00000268489	NM_006885.3	1214	Gct/Act	6/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.231204145220924	2		684	672	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993003	72993003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	78	617	0	ENST00000268489.5:c.1042C>T	p.Gln348Ter	p.Q348*	ENST00000268489	NM_006885.3	348	Caa/Taa	2/10	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.231204145220924	2		617	675	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957117	81957117	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	41	577	0	ENST00000359376.3:c.2335G>A	p.Asp779Asn	p.D779N	ENST00000359376	NM_002661.3	779	Gac/Aac	22/33	1	2	FACETS	0.697	0.58	0.827	0.697	0.58	0.827	SUBCLONAL	1	TRUE	1	0.231204145220924	2		577	509	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346822	89346822	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253174351	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	40	587	0	ENST00000301030.4:c.6128C>T	p.Ala2043Val	p.A2043V	ENST00000301030	NM_001256183.1	2043	gCc/gTc	9/13	1	2	FACETS	0.715	0.594	0.85	0.715	0.594	0.85	SUBCLONAL	1	TRUE	1	0.231204145220924	2		587	484	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831420	89831420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	53	633	0	ENST00000389301.3:c.2656G>A	p.Glu886Lys	p.E886K	ENST00000389301	NM_000135.2	886	Gag/Aag	28/43	1	2	FACETS	0.649	0.553	0.756	0.649	0.553	0.756	SUBCLONAL	1	TRUE	1	0.231204145220924	2		633	706	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579529	7579529	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658483	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	278	777	0	ENST00000269305.4:c.158G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tGg/tAg	4/11	0.231204145220924	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	0	0.231204145220924	3		777	854	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989441	7989441	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	224	691	0	ENST00000319144.4:c.245G>A	p.Trp82Ter	p.W82*	ENST00000319144	NM_001139.2	82	tGg/tAg	2/15	0.231204145220924	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.231204145220924	3		691	633	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676149	29676149	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	96	353	0	ENST00000356175.3:c.7139del	p.Pro2380LeufsTer17	p.P2380Lfs*17	ENST00000356175	NM_000267.3	2380	Cct/ct	48/57	0.186283681630977	2	FACETS	0.802	0.717	0.891	0.802	0.717	0.891	CLONAL	2	TRUE	0	0.231204145220924	2		353	518	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40476776	40476776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765182656	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	129	648	0	ENST00000264657.5:c.1553G>A	p.Arg518Gln	p.R518Q	ENST00000264657	NM_139276.2	518	cGa/cAa	17/24	0.186283681630977	2	FACETS	0.896	0.814	0.981	0.896	0.814	0.981	CLONAL	2	TRUE	0	0.231204145220924	2		648	623	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489816	40489816	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	156	635	0	ENST00000264657.5:c.610G>A	p.Glu204Lys	p.E204K	ENST00000264657	NM_139276.2	204	Gaa/Aaa	7/24	0.186283681630977	2	FACETS	0.922	0.846	1	0.922	0.846	1	CLONAL	2	TRUE	0	0.231204145220924	2		635	732	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530109	63530109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793454	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	47	507	0	ENST00000307078.5:c.2326C>T	p.Pro776Ser	p.P776S	ENST00000307078	NM_004655.3	776	Cca/Tca	10/11	0.0398153272033968	3	FACETS	0.673	0.567	0.791	0.336	0.283	0.396	INDETERMINATE	1	TRUE	1	0.231204145220924	3		507	674	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220671	1220671	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555738440	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	106	589	0	ENST00000326873.7:c.689C>T	p.Thr230Ile	p.T230I	ENST00000326873	NM_000455.4	230	aCc/aTc	5/10	0.0398153272033968	3	FACETS	1	0.98	1	0.708	0.635	0.786	INDETERMINATE	1	TRUE	1	0.231204145220924	3		589	722	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611804	1611804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1343124101	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	140	554	0	ENST00000344749.5:c.1858G>A	p.Glu620Lys	p.E620K	ENST00000344749	NM_001136139.2	620	Gag/Aag	19/19	0.0398153272033968	3	FACETS	0.838	0.764	0.916	0.838	0.764	0.916	INDETERMINATE	2	TRUE	1	0.231204145220924	3		554	806	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121160	3121160	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	112	525	0	ENST00000078429.4:c.1063G>T	p.Glu355Ter	p.E355*	ENST00000078429	NM_002067.2	355	Gag/Tag	7/7	0.0398153272033968	3	FACETS	1	0.982	1	0.719	0.646	0.795	INDETERMINATE	1	TRUE	1	0.231204145220924	3		525	752	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210584	5210584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	111	643	1	ENST00000357368.4:c.5383C>T	p.Pro1795Ser	p.P1795S	ENST00000357368	NM_002850.3	1795	Ccg/Tcg	35/38	0.0398153272033968	3	FACETS	1	0.981	1	0.704	0.633	0.779	INDETERMINATE	1	TRUE	1	0.231204145220924	3		644	761	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247916	10247916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1442538027	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	129	652	0	ENST00000340748.4:c.4286C>T	p.Pro1429Leu	p.P1429L	ENST00000340748		1429	cCc/cTc	36/40	0.0398153272033968	3	FACETS	0.802	0.728	0.88	0.802	0.728	0.88	INDETERMINATE	2	TRUE	1	0.231204145220924	3		652	776	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250743	10250743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	91	585	0	ENST00000340748.4:c.3737C>T	p.Ser1246Phe	p.S1246F	ENST00000340748		1246	tCt/tTt	32/40	0.0398153272033968	3	FACETS	1	0.973	1	0.659	0.586	0.738	INDETERMINATE	1	TRUE	1	0.231204145220924	3		585	666	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10271061	10271061	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	72	392	0	ENST00000340748.4:c.994C>T	p.Pro332Ser	p.P332S	ENST00000340748		332	Cca/Tca	13/40	0.0398153272033968	3	FACETS	1	0.963	1	0.64	0.56	0.726	INDETERMINATE	1	TRUE	1	0.231204145220924	3		392	543	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971135	18971135	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1195464113	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	118	548	0	ENST00000262803.5:c.2188C>T	p.Arg730Cys	p.R730C	ENST00000262803	NM_002911.3	730	Cgt/Tgt	16/24	0.0398153272033968	3	FACETS	0.861	0.778	0.949	0.861	0.778	0.949	INDETERMINATE	2	TRUE	1	0.231204145220924	3		548	661	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213968	36213968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	52	713	0	ENST00000222270.7:c.2794C>T	p.Pro932Ser	p.P932S	ENST00000222270	NM_014727.1	932	Cct/Tct	6/37	0.0398153272033968	3	FACETS	0.648	0.551	0.756	0.324	0.275	0.378	INDETERMINATE	1	TRUE	1	0.231204145220924	3		713	774	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214368	36214368	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	124	507	0	ENST00000222270.7:c.3022A>T	p.Ile1008Leu	p.I1008L	ENST00000222270	NM_014727.1	1008	Ata/Tta	7/37	0.0398153272033968	3	FACETS	0.815	0.738	0.896	0.815	0.738	0.896	INDETERMINATE	2	TRUE	1	0.231204145220924	3		507	734	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905936	50905936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	109	712	0	ENST00000440232.2:c.908C>T	p.Pro303Leu	p.P303L	ENST00000440232	NM_002691.3	303	cCa/cTa	8/27	0.0398153272033968	3	FACETS	1	0.98	1	0.693	0.622	0.768	INDETERMINATE	1	TRUE	1	0.231204145220924	3		712	759	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909451	50909451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	121	653	0	ENST00000440232.2:c.1255C>T	p.Pro419Ser	p.P419S	ENST00000440232	NM_002691.3	419	Cct/Tct	11/27	0.0398153272033968	3	FACETS	0.791	0.715	0.871	0.791	0.715	0.871	INDETERMINATE	2	TRUE	1	0.231204145220924	3		653	738	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082848	16082848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779590223	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	25	448	0	ENST00000281043.3:c.662C>T	p.Ser221Leu	p.S221L	ENST00000281043	NM_005378.4	221	tCg/tTg	2/3	1	2	FACETS	0.728	0.575	0.904	0.728	0.575	0.904	CLONAL	1	TRUE	1	0.231204145220924	2		448	297	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466824	25466824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	53	690	0	ENST00000264709.3:c.1879C>T	p.Pro627Ser	p.P627S	ENST00000264709	NM_175629.2	627	Cca/Tca	16/23	1	2	FACETS	0.659	0.561	0.766	0.659	0.561	0.766	SUBCLONAL	1	TRUE	1	0.231204145220924	2		690	696	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570084	212570084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1366336180	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	86	401	0	ENST00000342788.4:c.1157C>T	p.Pro386Leu	p.P386L	ENST00000342788	NM_005235.2	386	cCa/cTa	10/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.231204145220924	2		401	547	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306568	41306568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	107	463	0	ENST00000373198.4:c.1091G>A	p.Arg364Gln	p.R364Q	ENST00000373198	NM_133170.3	364	cGa/cAa	7/32	1	2	FACETS	0.897	0.808	0.99	1	0.987	1	CLONAL	2	TRUE	1	0.231204145220924	2		463	516	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46266468	46266468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	57	376	1	ENST00000371998.3:c.2453C>T	p.Ser818Phe	p.S818F	ENST00000371998		818	tCc/tTc	13/23	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.231204145220924	2		377	459	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478776	57478776	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	106	601	0	ENST00000371085.3:c.362A>T	p.Asn121Ile	p.N121I	ENST00000371085	NM_000516.4	121	aAc/aTc	5/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.231204145220924	2		601	760	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319075	62319075	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	68	799	0	ENST00000360203.5:c.1433C>T	p.Thr478Ile	p.T478I	ENST00000360203	NM_001283009.1	478	aCc/aTc	17/35	1	2	FACETS	0.762	0.662	0.871	0.762	0.662	0.871	SUBCLONAL	1	TRUE	1	0.231204145220924	2		799	772	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45649946	45649946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	34	583	0	ENST00000407780.3:c.889G>A	p.Glu297Lys	p.E297K	ENST00000407780	NM_001283052.1	297	Gag/Aag	6/7	0.231204145220924	1	FACETS	0.393	0.32	0.476	0.393	0.32	0.476	SUBCLONAL	1	TRUE	0	0.231204145220924	1		583	662	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499337	89499337	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	117	505	0	ENST00000336596.2:c.2507C>T	p.Ala836Val	p.A836V	ENST00000336596	NM_005233.5	836	gCt/gTt	15/17	1	2	FACETS	0.755	0.682	0.832	1	0.984	1	SUBCLONAL	2	TRUE	1	0.231204145220924	2		505	670	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670289	134670289	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs778421975	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	55	503	0	ENST00000398015.3:c.200A>G	p.Asn67Ser	p.N67S	ENST00000398015	NM_004441.4	67	aAc/aGc	3/16	1	2	FACETS	0.917	0.785	1	0.917	0.785	1	CLONAL	1	TRUE	1	0.231204145220924	2		503	519	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178942576	178942576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	37	352	0	ENST00000263967.3:c.2383C>T	p.Gln795Ter	p.Q795*	ENST00000263967	NM_006218.2	795	Cag/Tag	16/21	1	2	FACETS	0.76	0.627	0.909	0.76	0.627	0.909	CLONAL	1	TRUE	1	0.231204145220924	2		352	421	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607171	189607171	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	51	655	0	ENST00000264731.3:c.1550A>T	p.Asn517Ile	p.N517I	ENST00000264731	NM_003722.4	517	aAt/aTt	12/14	1	2	FACETS	0.834	0.709	0.971	0.834	0.709	0.971	CLONAL	1	TRUE	1	0.231204145220924	2		655	529	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913514	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	22	370	0	ENST00000288135.5:c.2466T>A	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaA	17/21	0.231204145220924	1	FACETS	0.407	0.314	0.514	0.407	0.314	0.514	SUBCLONAL	1	TRUE	0	0.231204145220924	1		370	414	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55960992	55960992	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	27	397	0	ENST00000263923.4:c.2948T>G	p.Leu983Arg	p.L983R	ENST00000263923	NM_002253.2	983	cTc/cGc	21/30	0.231204145220924	1	FACETS	0.5	0.397	0.618	0.5	0.397	0.618	SUBCLONAL	1	TRUE	0	0.231204145220924	1		397	413	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964331	55964331	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866577501	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	50	424	0	ENST00000263923.4:c.2482G>A	p.Glu828Lys	p.E828K	ENST00000263923	NM_002253.2	828	Gaa/Aaa	17/30	0.231204145220924	1	FACETS	0.839	0.713	0.977	0.839	0.713	0.977	CLONAL	1	TRUE	0	0.231204145220924	1		424	456	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968610	55968610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374980446	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	39	462	0	ENST00000263923.4:c.2053G>A	p.Glu685Lys	p.E685K	ENST00000263923	NM_002253.2	685	Gaa/Aaa	14/30	0.231204145220924	1	FACETS	0.54	0.446	0.644	0.54	0.446	0.644	SUBCLONAL	1	TRUE	0	0.231204145220924	1		462	553	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196445	106196445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	51	625	0	ENST00000380013.4:c.4778G>A	p.Ser1593Asn	p.S1593N	ENST00000380013	NM_001127208.2	1593	aGc/aAc	11/11	0.231204145220924	1	FACETS	0.644	0.547	0.751	0.644	0.547	0.751	SUBCLONAL	1	TRUE	0	0.231204145220924	1		625	606	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144359553	144359553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	67	594	0	ENST00000262995.4:c.995C>T	p.Ser332Leu	p.S332L	ENST00000262995	NM_207123.2	332	tCa/tTa	4/11	0.231204145220924	1	FACETS	0.89	0.774	1	0.89	0.774	1	CLONAL	1	TRUE	0	0.231204145220924	1		594	576	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541856	187541856	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	79	598	0	ENST00000441802.2:c.5884C>T	p.Leu1962Phe	p.L1962F	ENST00000441802	NM_005245.3	1962	Ctt/Ttt	10/27	0.231204145220924	1	FACETS	0.86	0.756	0.971	0.86	0.756	0.971	CLONAL	1	TRUE	0	0.231204145220924	1		598	703	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31521302	31521302	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	89	397	0	ENST00000344624.3:c.875del	p.His292ProfsTer60	p.H292Pfs*60	ENST00000344624		292	cAc/cc	3/33	0.0526357044489296	3	FACETS	1	0.975	1	0.683	0.606	0.765	INDETERMINATE	1	TRUE	1	0.231204145220924	3		397	629	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874581	35874581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	45	444	0	ENST00000303115.3:c.737G>A	p.Ser246Asn	p.S246N	ENST00000303115	NM_002185.3	246	aGc/aAc	6/8	0.0526357044489296	3	FACETS	0.686	0.576	0.809	0.343	0.288	0.405	INDETERMINATE	1	TRUE	1	0.231204145220924	3		444	633	SUCCESS
APC	324	MSKCC	GRCh37	5	112179285	112179285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	99	463	0	ENST00000257430.4:c.7994C>T	p.Pro2665Leu	p.P2665L	ENST00000257430	NM_000038.5	2665	cCc/cTc	16/16	0.186283681630977	2	FACETS	0.89	0.798	0.987	0.89	0.798	0.987	CLONAL	2	TRUE	0	0.231204145220924	2		463	481	SUCCESS
APC	324	MSKCC	GRCh37	5	112179452	112179452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782312	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	101	536	0	ENST00000257430.4:c.8161C>T	p.Arg2721Cys	p.R2721C	ENST00000257430	NM_000038.5	2721	Cgc/Tgc	16/16	0.186283681630977	2	FACETS	1	0.981	1	0.74	0.663	0.822	CLONAL	1	TRUE	0	0.231204145220924	2		536	590	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911159	29911159	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	35	282	0	ENST00000376809.5:c.458A>T	p.Asp153Val	p.D153V	ENST00000376809	NM_002116.7	153	gAc/gTc	3/8	0.0814580592584908	4	FACETS	1	0.9	1	0.573	0.471	0.688	INDETERMINATE	1	TRUE	2	0.231204145220924	4		282	325	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982059	93982059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	160	473	0	ENST00000369303.4:c.1406C>T	p.Pro469Leu	p.P469L	ENST00000369303	NM_004440.3	469	cCc/cTc	6/17	0.0814580592584908	4	FACETS	0.961	0.886	1	1	0.988	1	INDETERMINATE	3	TRUE	2	0.231204145220924	4		473	591	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631302	117631302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138376257	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	85	416	0	ENST00000368508.3:c.6376C>T	p.Arg2126Trp	p.R2126W	ENST00000368508	NM_002944.2	2126	Cgg/Tgg	40/43	0.0814580592584908	4	FACETS	1	0.977	1	0.738	0.653	0.829	INDETERMINATE	1	TRUE	2	0.231204145220924	4		416	613	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662706	117662706	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	88	496	0	ENST00000368508.3:c.4759C>T	p.Pro1587Ser	p.P1587S	ENST00000368508	NM_002944.2	1587	Cct/Tct	29/43	0.0814580592584908	4	FACETS	1	0.973	1	0.668	0.592	0.75	INDETERMINATE	1	TRUE	2	0.231204145220924	4		496	701	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700229	117700229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	102	393	0	ENST00000368508.3:c.2590G>A	p.Gly864Arg	p.G864R	ENST00000368508	NM_002944.2	864	Gga/Aga	17/43	0.0814580592584908	4	FACETS	1	0.953	1	1	0.953	1	INDETERMINATE	2	TRUE	2	0.231204145220924	4		393	492	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517377	157517377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	114	405	0	ENST00000346085.5:c.3941C>T	p.Pro1314Leu	p.P1314L	ENST00000346085	NM_020732.3	1314	cCc/cTc	16/20	0.0814580592584908	4	FACETS	0.959	0.865	1	0.959	0.865	1	INDETERMINATE	2	TRUE	2	0.231204145220924	4		405	633	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528391	157528391	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	138	685	0	ENST00000346085.5:c.6116C>T	p.Ala2039Val	p.A2039V	ENST00000346085	NM_020732.3	2039	gCt/gTt	20/20	0.0814580592584908	4	FACETS	0.919	0.836	1	0.919	0.836	1	INDETERMINATE	2	TRUE	2	0.231204145220924	4		685	800	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2957001	2957001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	112	491	0	ENST00000396946.4:c.2626G>A	p.Glu876Lys	p.E876K	ENST00000396946	NM_032415.4	876	Gaa/Aaa	20/25	1	2	FACETS	0.765	0.69	0.845	1	0.984	1	SUBCLONAL	2	TRUE	1	0.231204145220924	2		491	633	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959135	2959135	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	64	640	0	ENST00000396946.4:c.2381C>T	p.Ser794Phe	p.S794F	ENST00000396946	NM_032415.4	794	tCc/tTc	18/25	1	2	FACETS	0.906	0.785	1	0.906	0.785	1	CLONAL	1	TRUE	1	0.231204145220924	2		640	611	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963988	2963988	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755527825	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	96	642	0	ENST00000396946.4:c.1819G>A	p.Glu607Lys	p.E607K	ENST00000396946	NM_032415.4	607	Gaa/Aaa	15/25	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.231204145220924	2		642	587	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950406	68950406	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	75	397	0	ENST00000288368.4:c.718A>T	p.Thr240Ser	p.T240S	ENST00000288368	NM_024870.2	240	Act/Tct	7/40	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.231204145220924	2		397	517	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989689	68989689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1428676809	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	55	440	0	ENST00000288368.4:c.1627G>A	p.Gly543Arg	p.G543R	ENST00000288368	NM_024870.2	543	Gga/Aga	15/40	1	2	FACETS	0.906	0.776	1	0.906	0.776	1	CLONAL	1	TRUE	1	0.231204145220924	2		440	525	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989705	68989705	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	51	415	0	ENST00000288368.4:c.1642+1G>C		p.X548_splice	ENST00000288368	NM_024870.2	548			1	2	FACETS	0.947	0.806	1	0.947	0.806	1	CLONAL	1	TRUE	1	0.231204145220924	2		415	466	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995569	68995569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775560862	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	26	348	0	ENST00000288368.4:c.1973C>T	p.Ser658Leu	p.S658L	ENST00000288368	NM_024870.2	658	tCg/tTg	18/40	1	2	FACETS	0.522	0.413	0.647	0.522	0.413	0.647	SUBCLONAL	1	TRUE	1	0.231204145220924	2		348	431	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542698	141542698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	51	536	0	ENST00000220592.5:c.2288C>T	p.Ser763Leu	p.S763L	ENST00000220592	NM_012154.3	763	tCg/tTg	18/19	1	2	FACETS	0.755	0.642	0.881	0.755	0.642	0.881	SUBCLONAL	1	TRUE	1	0.231204145220924	2		536	584	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534834	5534834	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	63	614	0	ENST00000397747.3:c.145C>T	p.His49Tyr	p.H49Y	ENST00000397747	NM_025239.3	49	Cat/Tat	3/7	1	2	FACETS	0.743	0.642	0.854	0.743	0.642	0.854	SUBCLONAL	1	TRUE	1	0.231204145220924	2		614	733	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486134	8486134	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	117	610	0	ENST00000356435.5:c.2683C>T	p.Leu895Phe	p.L895F	ENST00000356435		895	Ctc/Ttc	17/35	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.231204145220924	2		610	689	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518238	8518238	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	91	458	0	ENST00000356435.5:c.1153C>T	p.Pro385Ser	p.P385S	ENST00000356435		385	Ccc/Tcc	10/35	1	2	FACETS	0.757	0.674	0.845	1	0.98	1	SUBCLONAL	2	TRUE	1	0.231204145220924	2		458	520	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411447	63411447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754938624	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	139	374	0	ENST00000330258.3:c.1720C>T	p.Arg574Trp	p.R574W	ENST00000330258	NM_152424.3	574	Cgg/Tgg	2/2	0.195521618281516	2	FACETS	0.973	0.894	1			1	CLONAL	3	TRUE	NA	0.231204145220924	2		374	412	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617550	100617551	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	TC	TC	CT	novel	NA	P-0062867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	96	270	2	ENST00000308731.7:c.518_519delinsAG	p.Gly173Glu	p.G173E	ENST00000308731	NM_000061.2	173	gGA/gAG	6/19	0.195521618281516	2	FACETS	1	0.971	1			1	CLONAL	2	TRUE	NA	0.231204145220924	2		272	341	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0062868-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	109	597	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.220955970705841	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.280486466966596	1		597	586	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0062868-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	248	1041	1	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.258953400985073	2	FACETS	0.951	0.89	1	0.951	0.89	1	CLONAL	2	TRUE	0	0.280486466966596	2		1042	930	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622081	43622081	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062868-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	57	826	0	ENST00000355710.3:c.3098T>A	p.Leu1033His	p.L1033H	ENST00000355710	NM_020975.4	1033	cTc/cAc	19/20	0.258863148417409	3	FACETS	0.571	0.488	0.661	0.285	0.244	0.331	SUBCLONAL	1	TRUE	1	0.280486466966596	3		826	812	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120883	115120887	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGA	GAAGA	-	novel	NA	P-0062868-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	130	942	0	ENST00000257566.3:c.119_123del	p.Phe40SerfsTer69	p.F40Sfs*69	ENST00000257566	NM_016569.3	40	tTCTTC/t	1/8	0.100047680198236	5	FACETS	0.79	0.716	0.867	0.526	0.477	0.578	INDETERMINATE	2	TRUE	2	0.280486466966596	5		942	834	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913153	32913153	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876661225	NA	P-0062868-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	146	654	0	ENST00000380152.3:c.4661G>C	p.Ser1554Thr	p.S1554T	ENST00000380152		1554	aGt/aCt	11/27	0.20450061704228	4	FACETS	0.982	0.898	1	0.982	0.898	1	CLONAL	2	TRUE	2	0.280486466966596	4		654	679	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961985	41961985	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062868-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	65	781	0	ENST00000219905.7:c.893A>G	p.Gln298Arg	p.Q298R	ENST00000219905	NM_001164273.1	298	cAg/cGg	2/24	0.258863148417409	3	FACETS	0.712	0.617	0.816	0.356	0.308	0.408	SUBCLONAL	1	TRUE	1	0.280486466966596	3		781	742	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940880	49940880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062868-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	104	1055	0	ENST00000296474.3:c.163G>A	p.Val55Ile	p.V55I	ENST00000296474	NM_002447.2	55	Gta/Ata	1/20	0.251778299932805	3	FACETS	0.863	0.771	0.961	0.431	0.385	0.481	CLONAL	1	TRUE	1	0.280486466966596	3		1055	980	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680727	30680727	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062868-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	104	896	0	ENST00000376406.3:c.992C>G	p.Thr331Ser	p.T331S	ENST00000376406	NM_014641.2	331	aCt/aGt	5/15	0.251778299932805	3	FACETS	0.974	0.871	1	0.487	0.435	0.542	CLONAL	1	TRUE	1	0.280486466966596	3		896	868	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161990395	161990395	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1168877682	NA	P-0062868-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	44	615	0	ENST00000366898.1:c.925G>T	p.Glu309Ter	p.E309*	ENST00000366898	NM_004562.2	309	Gaa/Taa	8/12	0.251778299932805	3	FACETS	0.562	0.47	0.663	0.281	0.235	0.332	SUBCLONAL	1	TRUE	1	0.280486466966596	3		615	637	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595340	141595340	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062868-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	66	902	0	ENST00000220592.5:c.93T>A	p.Phe31Leu	p.F31L	ENST00000220592	NM_012154.3	31	ttT/ttA	2/19	0.22090307986271	4	FACETS	0.583	0.504	0.669	0.194	0.168	0.223	SUBCLONAL	1	TRUE	1	0.280486466966596	4		902	1034	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402536	139402536	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062868-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	80	944	0	ENST00000277541.6:c.3381C>A	p.Asn1127Lys	p.N1127K	ENST00000277541	NM_017617.3	1127	aaC/aaA	21/34	1	2	FACETS	0.716	0.629	0.809	0.716	0.629	0.809	SUBCLONAL	1	TRUE	1	0.280486466966596	2		944	797	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355276	15355276	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062868-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	25	512	0	ENST00000263377.2:c.2347C>A	p.Pro783Thr	p.P783T	ENST00000263377	NM_058243.2	783	Ccc/Acc	13/20	0.251778299932805	3	FACETS	0.517	0.407	0.644	0.259	0.203	0.322	SUBCLONAL	1	TRUE	1	0.280486466966596	3		512	393	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062872-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	137	343	0				ENST00000310581	NM_198253.2	-/1132			0.215948057231363	2	FACETS	0.91	0.834	0.988	0.91	0.834	0.988	CLONAL	2	TRUE	0	0.332341925302521	2		343	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578493	7578493	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1206165503	NA	P-0062872-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	271	843	0	ENST00000269305.4:c.437G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tGg/tAg	5/11	0.101873963678419	4	FACETS	1	0.967	1			1	INDETERMINATE	2	TRUE	NA	0.332341925302521	4		843	1039	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670679	134670679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369940583	NA	P-0062872-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	49	722	0	ENST00000398015.3:c.590C>T	p.Pro197Leu	p.P197L	ENST00000398015	NM_004441.4	197	cCc/cTc	3/16	0.332341925302521	0	FACETS	0.38	0.322	0.444			1	SUBCLONAL	1	TRUE	0	0.332341925302521	0		722	518	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796949	45796949	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062872-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	94	791	0	ENST00000450313.1:c.1381G>T	p.Glu461Ter	p.E461*	ENST00000450313	NM_012222.2	461	Gaa/Taa	14/16	0.0452449783202533	4	FACETS	0.76	0.675	0.851	0.38	0.337	0.426	INDETERMINATE	1	TRUE	2	0.332341925302521	4		791	992	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027209	49027210	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0062872-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	132	458	0	ENST00000267163.4:c.1776_1777del	p.Asn593SerfsTer6	p.N593Sfs*6	ENST00000267163	NM_000321.2	592	ctTAat/ctat	18/27	0.262414969688907	3	FACETS	1	0.969	1	0.748	0.685	0.812	CLONAL	2	TRUE	0	0.332341925302521	3		458	413	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040949	42040952	+	frameshift_variant	Frame_Shift_Del	DEL	CTGT	CTGT	-	novel	NA	P-0062872-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	98	779	0	ENST00000219905.7:c.5329_5332del	p.Val1777GlnfsTer21	p.V1777Qfs*21	ENST00000219905	NM_001164273.1	1776	cCTGTc/cc	16/24	0.225549235027386	3	FACETS	0.704	0.627	0.787	0.235	0.209	0.263	SUBCLONAL	1	TRUE	0	0.332341925302521	3		779	977	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964324	55964324	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062872-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	46	502	0	ENST00000263923.4:c.2489C>T	p.Pro830Leu	p.P830L	ENST00000263923	NM_002253.2	830	cCc/cTc	17/30	0.332341925302521	1	FACETS	0.455	0.383	0.535	0.455	0.383	0.535	SUBCLONAL	1	TRUE	0	0.332341925302521	1		502	507	SUCCESS
REST	5978	MSKCC	GRCh37	4	57785951	57785951	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0062872-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	33	344	1	ENST00000309042.7:c.899-2A>G		p.X300_splice	ENST00000309042	NM_005612.4	300			0.332341925302521	1	FACETS	0.607	0.496	0.73	0.607	0.496	0.73	SUBCLONAL	1	TRUE	0	0.332341925302521	1		345	273	SUCCESS
APC	324	MSKCC	GRCh37	5	112178501	112178501	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062872-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	29	569	0	ENST00000257430.4:c.7210A>G	p.Met2404Val	p.M2404V	ENST00000257430	NM_000038.5	2404	Atg/Gtg	16/16	1	2	FACETS	0.446	0.358	0.547	0.446	0.358	0.547	SUBCLONAL	1	TRUE	1	0.332341925302521	2		569	391	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004216	150004216	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062872-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	46	336	0	ENST00000253339.5:c.2009G>C	p.Arg670Pro	p.R670P	ENST00000253339		670	cGg/cCg	3/7	0.172580371341344	3	FACETS	0.933	0.789	1	0.467	0.394	0.546	INDETERMINATE	1	TRUE	1	0.332341925302521	3		336	346	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038783	47038783	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062872-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	68	742	0	ENST00000377604.3:c.790G>C	p.Glu264Gln	p.E264Q	ENST00000377604	NM_001204468.1	264	Gag/Cag	9/24	1	2	FACETS	0.595	0.517	0.679	0.595	0.517	0.679	SUBCLONAL	1	TRUE	1	0.332341925302521	2		742	688	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057936	27057937	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1415146710	NA	P-0062873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	137	1007	1	ENST00000324856.7:c.1650dup	p.Tyr551LeufsTer72	p.Y551Lfs*72	ENST00000324856	NM_006015.4	548	-/C	3/20	1	2	FACETS	0.818	0.75	0.888	0.818	0.75	0.888	CLONAL	1	TRUE	1	0.76316618707129	2		1008	439	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154872	2154872	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	154	856	0	ENST00000434045.2:c.349C>A	p.Arg117Ser	p.R117S	ENST00000434045	NM_001127598.1	117	Cgt/Agt	4/5	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.76316618707129	2		856	393	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543274	65543274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201312694	NA	P-0062873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	131	711	1	ENST00000358664.4:c.403G>A	p.Asp135Asn	p.D135N	ENST00000358664	NM_002382.4	135	Gat/Aat	5/5	1	2	FACETS	0.946	0.868	1	0.946	0.868	1	CLONAL	1	TRUE	1	0.76316618707129	2		712	363	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	161	343	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.826	0.761	0.894	0.826	0.761	0.894	CLONAL	1	TRUE	1	0.625452748545078	2		343	623	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972029	55972029	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55716939	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	231	560	0	ENST00000263923.4:c.1615G>A	p.Gly539Arg	p.G539R	ENST00000263923	NM_002253.2	539	Gga/Aga	12/30	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.625452748545078	2		560	700	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578464	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	335	854	0	ENST00000269305.4:c.466C>G	p.Arg156Gly	p.R156G	ENST00000269305	NM_001126112.2	156	Cgc/Ggc	5/11	1	2	FACETS	0.995	0.942	1	0.995	0.942	1	CLONAL	1	TRUE	1	0.625452748545078	2		854	1077	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799167	42799167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	189	606	0	ENST00000575354.2:c.4651C>T	p.Pro1551Ser	p.P1551S	ENST00000575354	NM_015125.3	1551	Ccc/Tcc	20/20	1	2	FACETS	0.923	0.857	0.991	0.923	0.857	0.991	CLONAL	1	TRUE	1	0.625452748545078	2		606	655	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467675	50467675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759124417	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	183	674	0	ENST00000331340.3:c.910G>A	p.Glu304Lys	p.E304K	ENST00000331340	NM_006060.4	304	Gaa/Aaa	8/8	0.625452748545078	3	FACETS	0.762	0.703	0.824	0.381	0.351	0.412	SUBCLONAL	1	TRUE	1	0.625452748545078	3		674	1008	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453179	140453179	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913340	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	319	400	0	ENST00000288602.6:c.1756G>A	p.Glu586Lys	p.E586K	ENST00000288602	NM_004333.4	586	Gaa/Aaa	15/18	0.625452748545078	3	FACETS	0.998	0.95	1	0.998	0.95	1	CLONAL	2	TRUE	1	0.625452748545078	3		400	671	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663611	117663611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202169003	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	147	332	0	ENST00000368508.3:c.4621G>A	p.Glu1541Lys	p.E1541K	ENST00000368508	NM_002944.2	1541	Gaa/Aaa	28/43	0.625452748545078	1	FACETS	0.97	0.9	1	0.97	0.9	1	CLONAL	1	TRUE	0	0.625452748545078	1		332	333	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923318	9923318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867335598	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	231	589	0	ENST00000330684.3:c.1969G>A	p.Glu657Lys	p.E657K	ENST00000330684	NM_001134407.1	657	Gaa/Aaa	9/13	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.625452748545078	2		589	696	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134123	41134123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751383976	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	137	796	0	ENST00000379561.5:c.1505C>T	p.Ser502Leu	p.S502L	ENST00000379561	NM_002015.3	502	tCg/tTg	2/3	0.340916316979455	1	FACETS	0.372	0.338	0.408	0.372	0.338	0.408	INDETERMINATE	1	TRUE	0	0.625452748545078	1		796	809	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972909	55972909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	162	353	0	ENST00000263923.4:c.1481G>A	p.Gly494Glu	p.G494E	ENST00000263923	NM_002253.2	494	gGa/gAa	11/30	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.625452748545078	2		353	507	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741395	145741395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368979398	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	378	967	0	ENST00000428558.2:c.1108C>T	p.Arg370Cys	p.R370C	ENST00000428558	NM_004260.3	370	Cgt/Tgt	5/22	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.625452748545078	2		967	1178	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197443	106197443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1452689450	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	222	596	0	ENST00000380013.4:c.5776C>T	p.Arg1926Cys	p.R1926C	ENST00000380013	NM_001127208.2	1926	Cgt/Tgt	11/11	1	2	FACETS	0.974	0.91	1	0.974	0.91	1	CLONAL	1	TRUE	1	0.625452748545078	2		596	729	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023751	31023751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	277	768	0	ENST00000375687.4:c.3236C>T	p.Ser1079Phe	p.S1079F	ENST00000375687	NM_015338.5	1079	tCc/tTc	13/13	1	2	FACETS	0.884	0.831	0.938	0.884	0.831	0.938	CLONAL	1	TRUE	1	0.625452748545078	2		768	1002	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858359	9858359	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1306036000	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	269	752	0	ENST00000330684.3:c.3042G>A	p.Trp1014Ter	p.W1014*	ENST00000330684	NM_001134407.1	1014	tgG/tgA	13/13	1	2	FACETS	0.905	0.851	0.962	0.905	0.851	0.962	CLONAL	1	TRUE	1	0.625452748545078	2		752	950	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	154	761	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	0.284094072709531	0	FACETS	0.264	0.242	0.287			1	INDETERMINATE	1	TRUE	0	0.625452748545078	0		761	698	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743501	46743503	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs746553748	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	231	643	0	ENST00000371975.4:c.1885_1887del	p.Glu629del	p.E629del	ENST00000371975	NM_003579.3	628	GAG/-	17/18	1	2	FACETS	0.837	0.782	0.895	0.837	0.782	0.895	CLONAL	1	TRUE	1	0.625452748545078	2		643	882	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959121	2959121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778152	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	261	725	0	ENST00000396946.4:c.2395G>A	p.Asp799Asn	p.D799N	ENST00000396946	NM_032415.4	799	Gat/Aat	18/25	0.625452748545078	3	FACETS	0.94	0.88	1	0.47	0.44	0.501	CLONAL	1	TRUE	1	0.625452748545078	3		725	1166	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932312	39932312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780348147	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	348	452	0	ENST00000378444.4:c.2287C>T	p.Arg763Trp	p.R763W	ENST00000378444	NM_001123385.1	763	Cgg/Tgg	4/15	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.625452748545078	1		452	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577540	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	rs1555525498	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	209	606	0	ENST00000269305.4:c.741_742delinsTT	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	247	aaCCgg/aaTTgg	7/11	1	2	FACETS	0.829	0.771	0.889	0.829	0.771	0.889	CLONAL	1	TRUE	1	0.625452748545078	2		606	806	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288221	21288221	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	286	725	0	ENST00000354336.3:c.466C>T	p.Pro156Ser	p.P156S	ENST00000354336	NM_005207.3	156	Cct/Tct	2/3	1	2	FACETS	0.942	0.887	0.998	0.942	0.887	0.998	CLONAL	1	TRUE	1	0.625452748545078	2		725	971	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088718	27088718	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	258	682	0	ENST00000324856.7:c.2327C>T	p.Pro776Leu	p.P776L	ENST00000324856	NM_006015.4	776	cCt/cTt	7/20	1	2	FACETS	0.853	0.8	0.908	0.853	0.8	0.908	CLONAL	1	TRUE	1	0.625452748545078	2		682	967	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69143588	69143588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150821816	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	171	473	0	ENST00000288368.4:c.4796C>T	p.Pro1599Leu	p.P1599L	ENST00000288368	NM_024870.2	1599	cCa/cTa	40/40	1	2	FACETS	0.846	0.782	0.913	0.846	0.782	0.913	CLONAL	1	TRUE	1	0.625452748545078	2		473	646	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169024	32169024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	359	927	0	ENST00000375023.3:c.4009G>A	p.Asp1337Asn	p.D1337N	ENST00000375023	NM_004557.3	1337	Gac/Aac	22/30	1	2	FACETS	0.99	0.939	1	0.99	0.939	1	CLONAL	1	TRUE	1	0.625452748545078	2		927	1159	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721132	176721132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	317	804	0	ENST00000439151.2:c.6763C>T	p.Pro2255Ser	p.P2255S	ENST00000439151	NM_022455.4	2255	Cct/Tct	23/23	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.625452748545078	2		804	857	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180841	106180841	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1315871913	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	211	478	0	ENST00000380013.4:c.3869C>T	p.Ser1290Leu	p.S1290L	ENST00000380013	NM_001127208.2	1290	tCa/tTa	7/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.625452748545078	2		478	650	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639605	47639605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	164	357	0	ENST00000233146.2:c.698C>T	p.Ser233Phe	p.S233F	ENST00000233146	NM_000251.2	233	tCc/tTc	4/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.625452748545078	2		357	457	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522771	67522771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141974044	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	229	681	0	ENST00000274335.5:c.268C>T	p.Arg90Trp	p.R90W	ENST00000274335		90	Cgg/Tgg	1/15	1	2	FACETS	0.83	0.775	0.887	0.83	0.775	0.887	CLONAL	1	TRUE	1	0.625452748545078	2		681	882	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342713	118342713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	261	639	0	ENST00000534358.1:c.839C>T	p.Pro280Leu	p.P280L	ENST00000534358	NM_005933.3	280	cCt/cTt	3/36	0.625452748545078	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.625452748545078	1		639	563	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791308	42791308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573059625	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	295	847	0	ENST00000575354.2:c.368C>T	p.Pro123Leu	p.P123L	ENST00000575354	NM_015125.3	123	cCg/cTg	3/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.625452748545078	2		847	872	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187546	32187546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	446	815	0	ENST00000375023.3:c.1333C>T	p.Pro445Ser	p.P445S	ENST00000375023	NM_004557.3	445	Ccc/Tcc	8/30	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.625452748545078	2		815	1206	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798418	32798418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776413811	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	348	812	0	ENST00000374899.4:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000374899	NM_018833.2	480	Cgc/Tgc	8/12	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.625452748545078	2		812	1110	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541901	187541901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751134485	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	299	773	0	ENST00000441802.2:c.5839C>T	p.Arg1947Cys	p.R1947C	ENST00000441802	NM_005245.3	1947	Cgc/Tgc	10/27	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.625452748545078	2		773	955	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609793	81609793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	345	873	0	ENST00000298171.2:c.1391G>A	p.Gly464Glu	p.G464E	ENST00000298171	NM_000369.2	464	gGg/gAg	10/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.625452748545078	2		873	1054	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120479958	120479958	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	287	727	0	ENST00000256646.2:c.3469C>T	p.Pro1157Ser	p.P1157S	ENST00000256646	NM_024408.3	1157	Ccc/Tcc	21/34	1	2	FACETS	0.884	0.832	0.938	0.884	0.832	0.938	CLONAL	1	TRUE	1	0.625452748545078	2		727	1038	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150916413	150916413	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	185	490	0	ENST00000271640.5:c.893A>G	p.Asp298Gly	p.D298G	ENST00000271640	NM_001145415.1	298	gAt/gGt	8/22	1	2	FACETS	0.924	0.857	0.993	0.924	0.857	0.993	CLONAL	1	TRUE	1	0.625452748545078	2		490	640	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692927	89692927	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	215	576	0	ENST00000371953.3:c.411del	p.Tyr138IlefsTer9	p.Y138Ifs*9	ENST00000371953	NM_000314.4	137	gcA/gc	5/9	0.625452748545078	1	FACETS	0.925	0.868	0.982	0.925	0.868	0.982	CLONAL	1	TRUE	0	0.625452748545078	1		576	511	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742808	17742808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	263	618	0	ENST00000250003.3:c.716G>A	p.Arg239Lys	p.R239K	ENST00000250003	NM_002478.4	239	aGg/aAg	3/3	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.625452748545078	2		618	713	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003546	57003546	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	304	866	1	ENST00000257254.3:c.933T>G	p.Phe311Leu	p.F311L	ENST00000257254		311	ttT/ttG	1/2	1	2	FACETS	0.926	0.873	0.98	0.926	0.873	0.98	CLONAL	1	TRUE	1	0.625452748545078	2		867	1050	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57004081	57004081	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	C	C	T	rs776670797	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	326	834	0	ENST00000257254.3:c.398G>A	p.Arg133Lys	p.R133K	ENST00000257254		133	aGg/aAg	1/2	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.625452748545078	2		834	972	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57004327	57004327	+	stop_gained,NMD_transcript_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	288	766	0	ENST00000257254.3:c.152G>A	p.Trp51Ter	p.W51*	ENST00000257254		51	tGg/tAg	1/2	1	2	FACETS	0.996	0.938	1	0.996	0.938	1	CLONAL	1	TRUE	1	0.625452748545078	2		766	925	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544080	18544080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	172	444	0	ENST00000266497.5:c.1897G>A	p.Glu633Lys	p.E633K	ENST00000266497		633	Gag/Aag	13/31	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.625452748545078	2		444	543	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25362794	25362794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	155	399	0	ENST00000311936.3:c.502G>A	p.Glu168Lys	p.E168K	ENST00000311936	NM_004985.3	168	Gaa/Aaa	5/5	1	2	FACETS	0.964	0.889	1	0.964	0.889	1	CLONAL	1	TRUE	1	0.625452748545078	2		399	514	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611340	28611340	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	61	376	0	ENST00000241453.7:c.1291T>C	p.Phe431Leu	p.F431L	ENST00000241453	NM_004119.2	431	Ttc/Ctc	10/24	0.340916316979455	1	FACETS	0.285	0.246	0.327	0.285	0.246	0.327	INDETERMINATE	1	TRUE	0	0.625452748545078	1		376	471	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51504608	51504608	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1317925758	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	131	634	0	ENST00000260433.2:c.1172G>A	p.Gly391Glu	p.G391E	ENST00000260433		391	gGg/gAg	9/10	0.284094072709531	0	FACETS	0.292	0.266	0.319			1	INDETERMINATE	1	TRUE	0	0.625452748545078	0		634	537	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354482	91354483	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	151	719	0	ENST00000355112.3:c.3922_3923delinsAA	p.Gly1308Lys	p.G1308K	ENST00000355112	NM_000057.2	1308	GGa/AAa	21/22	0.284094072709531	0	FACETS	0.284	0.26	0.309			1	INDETERMINATE	1	TRUE	0	0.625452748545078	0		719	637	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641008	23641008	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555460320	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	280	712	0	ENST00000261584.4:c.2467C>T	p.Leu823Phe	p.L823F	ENST00000261584	NM_024675.3	823	Ctc/Ttc	5/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.625452748545078	2		712	794	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782220	56782220	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	227	515	0	ENST00000308159.5:c.61G>A	p.Glu21Lys	p.E21K	ENST00000308159	NM_014669.4	21	Gag/Aag	2/22	1	2	FACETS	0.988	0.924	1	0.988	0.924	1	CLONAL	1	TRUE	1	0.625452748545078	2		515	735	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950288	15950288	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1387701604	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	215	542	0	ENST00000268712.3:c.6656C>T	p.Ser2219Phe	p.S2219F	ENST00000268712	NM_006311.3	2219	tCt/tTt	42/46	1	2	FACETS	0.905	0.843	0.967	0.905	0.843	0.967	CLONAL	1	TRUE	1	0.625452748545078	2		542	760	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15952158	15952158	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	74	525	0	ENST00000268712.3:c.6536+1G>A		p.X2179_splice	ENST00000268712	NM_006311.3	2179			1	2	FACETS	0.303	0.265	0.345	0.303	0.265	0.345	SUBCLONAL	1	TRUE	1	0.625452748545078	2		525	780	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560179	29560179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	298	565	0	ENST00000356175.3:c.3656G>A	p.Gly1219Glu	p.G1219E	ENST00000356175	NM_000267.3	1219	gGa/gAa	27/57	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.625452748545078	2		565	891	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652931	29652932	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	237	557	1	ENST00000356175.3:c.4866_4867delinsAA	p.Asp1623Asn	p.D1623N	ENST00000356175	NM_000267.3	1622	gtGGac/gtAAac	36/57	1	2	FACETS	0.907	0.848	0.966	0.907	0.848	0.966	CLONAL	1	TRUE	1	0.625452748545078	2		558	836	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652932	29652932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	237	558	0	ENST00000356175.3:c.4867G>A	p.Asp1623Asn	p.D1623N	ENST00000356175	NM_000267.3	1623	Gac/Aac	36/57	1	2	FACETS	0.907	0.848	0.966	0.907	0.848	0.966	CLONAL	1	TRUE	1	0.625452748545078	2		558	836	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683993	29683993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	198	519	0	ENST00000356175.3:c.7691C>T	p.Ser2564Phe	p.S2564F	ENST00000356175	NM_000267.3	2564	tCc/tTc	52/57	1	2	FACETS	0.964	0.897	1	0.964	0.897	1	CLONAL	1	TRUE	1	0.625452748545078	2		519	657	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224553	36224553	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1468595921	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	368	848	0	ENST00000222270.7:c.7015C>T	p.Arg2339Trp	p.R2339W	ENST00000222270	NM_014727.1	2339	Cgg/Tgg	29/37	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.625452748545078	2		848	1019	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982407	25982407	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	175	482	0	ENST00000435504.4:c.883C>G	p.Leu295Val	p.L295V	ENST00000435504		295	Ctt/Gtt	9/13	1	2	FACETS	0.89	0.823	0.958	0.89	0.823	0.958	CLONAL	1	TRUE	1	0.625452748545078	2		482	629	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606980	47606980	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755757555	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	160	507	0	ENST00000263735.4:c.730C>T	p.Pro244Ser	p.P244S	ENST00000263735	NM_002354.2	244	Cct/Tct	7/9	1	2	FACETS	0.816	0.751	0.883	0.816	0.751	0.883	CLONAL	1	TRUE	1	0.625452748545078	2		507	627	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47643498	47643498	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63751062	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	171	485	0	ENST00000233146.2:c.1006C>T	p.Pro336Ser	p.P336S	ENST00000233146	NM_000251.2	336	Cct/Tct	6/16	1	2	FACETS	0.862	0.797	0.93	0.862	0.797	0.93	CLONAL	1	TRUE	1	0.625452748545078	2		485	634	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99175940	99175940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200856510	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	188	517	0	ENST00000074304.5:c.1852C>T	p.Pro618Ser	p.P618S	ENST00000074304	NM_001134224.1	618	Cct/Tct	18/26	1	2	FACETS	0.939	0.872	1	0.939	0.872	1	CLONAL	1	TRUE	1	0.625452748545078	2		517	640	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872806	136872807	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	181	884	0	ENST00000241393.3:c.691_692delinsAA	p.Gly231Asn	p.G231N	ENST00000241393	NM_003467.2	231	GGc/AAc	2/2	1	2	FACETS	0.633	0.584	0.684	0.633	0.584	0.684	SUBCLONAL	1	TRUE	1	0.625452748545078	2		884	914	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561249	9561249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	256	715	0	ENST00000353224.5:c.533G>A	p.Gly178Glu	p.G178E	ENST00000353224	NM_177990.2	178	gGg/gAg	4/10	1	2	FACETS	0.973	0.914	1	0.973	0.914	1	CLONAL	1	TRUE	1	0.625452748545078	2		715	841	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944632	40944632	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	226	524	0	ENST00000373198.4:c.1870T>C	p.Tyr624His	p.Y624H	ENST00000373198	NM_133170.3	624	Tat/Cat	12/32	1	2	FACETS	0.979	0.916	1	0.979	0.916	1	CLONAL	1	TRUE	1	0.625452748545078	2		524	738	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076895	41076895	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	224	478	0	ENST00000373198.4:c.1525C>A	p.Pro509Thr	p.P509T	ENST00000373198	NM_133170.3	509	Ccc/Acc	9/32	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.625452748545078	2		478	647	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164666	47164666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	253	552	0	ENST00000409792.3:c.1460C>T	p.Ser487Phe	p.S487F	ENST00000409792	NM_014159.6	487	tCc/tTc	3/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.625452748545078	2		552	769	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799511	72799511	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	242	662	0	ENST00000325599.8:c.1658C>T	p.Ser553Phe	p.S553F	ENST00000325599	NM_018130.2	553	tCt/tTt	11/11	0.625452748545078	3	FACETS	0.963	0.899	1	0.481	0.449	0.514	CLONAL	1	TRUE	1	0.625452748545078	3		662	1055	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480508	89480508	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	203	463	0	ENST00000336596.2:c.2345G>C	p.Arg782Thr	p.R782T	ENST00000336596	NM_005233.5	782	aGa/aCa	13/17	0.625452748545078	3	FACETS	1	0.956	1	0.52	0.482	0.558	CLONAL	1	TRUE	1	0.625452748545078	3		463	820	SUCCESS
ALB	213	MSKCC	GRCh37	4	74279255	74279255	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	261	617	0	ENST00000295897.4:c.962A>C	p.Glu321Ala	p.E321A	ENST00000295897	NM_000477.5	321	gAg/gCg	8/15	1	2	FACETS	0.974	0.915	1	0.974	0.915	1	CLONAL	1	TRUE	1	0.625452748545078	2		617	857	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950717	38950717	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	218	532	0	ENST00000357387.3:c.3233C>T	p.Pro1078Leu	p.P1078L	ENST00000357387	NM_152756.3	1078	cCc/cTc	31/38	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.625452748545078	2		532	639	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178120	56178120	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	221	601	0	ENST00000399503.3:c.3093A>C	p.Arg1031Ser	p.R1031S	ENST00000399503	NM_005921.1	1031	agA/agC	14/20	1	2	FACETS	0.84	0.784	0.899	0.84	0.784	0.899	CLONAL	1	TRUE	1	0.625452748545078	2		601	841	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439377	149439377	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	306	732	0	ENST00000286301.3:c.2018A>G	p.Asn673Ser	p.N673S	ENST00000286301	NM_005211.3	673	aAc/aGc	15/22	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.625452748545078	2		732	825	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225622	26225622	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	433	1025	0	ENST00000360408.1:c.240G>C	p.Lys80Asn	p.K80N	ENST00000360408	NM_003532.2	80	aaG/aaC	1/1	1	2	FACETS	0.982	0.936	1	0.982	0.936	1	CLONAL	1	TRUE	1	0.625452748545078	2		1025	1410	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166245	32166246	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	327	701	0	ENST00000375023.3:c.4708_4709delinsTT	p.Pro1570Phe	p.P1570F	ENST00000375023	NM_004557.3	1570	CCc/TTc	26/30	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.625452748545078	2		701	1011	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983236	149983236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374498548	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	257	581	0	ENST00000253339.5:c.3022C>T	p.Pro1008Ser	p.P1008S	ENST00000253339		1008	Cca/Tca	7/7	0.625452748545078	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.625452748545078	1		581	539	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450382	50450382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	302	710	0	ENST00000331340.3:c.566C>T	p.Thr189Ile	p.T189I	ENST00000331340	NM_006060.4	189	aCt/aTt	5/8	0.625452748545078	3	FACETS	1	0.988	1	0.59	0.556	0.624	CLONAL	1	TRUE	1	0.625452748545078	3		710	1075	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124467288	124467288	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	157	356	0	ENST00000357628.3:c.1666G>A	p.Glu556Lys	p.E556K	ENST00000357628	NM_015450.2	556	Gaa/Aaa	17/19	0.625452748545078	3	FACETS	0.955	0.877	1	0.478	0.438	0.518	CLONAL	1	TRUE	1	0.625452748545078	3		356	690	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851403	151851403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	250	660	0	ENST00000262189.6:c.12088G>A	p.Glu4030Lys	p.E4030K	ENST00000262189	NM_170606.2	4030	Gaa/Aaa	47/59	0.625452748545078	3	FACETS	0.961	0.899	1	0.481	0.449	0.513	CLONAL	1	TRUE	1	0.625452748545078	3		660	1092	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372352	55372352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	345	946	0	ENST00000297316.4:c.1042C>T	p.Pro348Ser	p.P348S	ENST00000297316	NM_022454.3	348	Ccc/Tcc	2/2	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.625452748545078	2		946	1052	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982036	70982036	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	282	691	0	ENST00000276594.2:c.60G>T	p.Glu20Asp	p.E20D	ENST00000276594	NM_024504.3	20	gaG/gaT	2/8	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.625452748545078	2		691	876	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248103	110248103	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	244	523	0	ENST00000374672.4:c.1369C>T	p.Gln457Ter	p.Q457*	ENST00000374672	NM_004235.4	457	Cag/Tag	5/5	0.625452748545078	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.625452748545078	1		523	519	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929155	44929155	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	264	354	0	ENST00000377967.4:c.2255A>T	p.His752Leu	p.H752L	ENST00000377967	NM_021140.2	752	cAt/cTt	17/29	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.625452748545078	1		354	404	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966761	44966761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	208	241	0	ENST00000377967.4:c.3985C>T	p.His1329Tyr	p.H1329Y	ENST00000377967	NM_021140.2	1329	Cat/Tat	27/29	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.625452748545078	1		241	351	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457687	67457689	+	missense_variant	Missense_Mutation	TNP	TCC	TCC	ACT	novel	NA	P-0062874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	156	848	0	ENST00000327367.4:c.497_499delinsACT	p.Phe166_Pro167delinsTyrSer	p.F166_P167delinsYS	ENST00000327367	NM_005902.3	166	tTCCcc/tACTcc	3/9	0.284094072709531	0	FACETS	0.258	0.236	0.281			1	INDETERMINATE	1	TRUE	0	0.625452748545078	0		848	724	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266729	198266729	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0121591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	114	432	0	ENST00000335508.6:c.2203A>G	p.Ile735Val	p.I735V	ENST00000335508	NM_012433.2	735	Atc/Gtc	15/25	1	2	FACETS	0.964	0.871	1	0.964	0.871	1	CLONAL	1	NA	1	0.401471617938252	2		432	589	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176978	56176980	+	inframe_deletion	In_Frame_Del	DEL	AAT	AAT	-	novel	NA	P-0121591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	96	445	0	ENST00000399503.3:c.2248_2250del	p.Asn750del	p.N750del	ENST00000399503	NM_005921.1	750	AAT/-	13/20	1	2	FACETS	0.825	0.736	0.918	0.825	0.736	0.918	CLONAL	1	NA	1	0.401471617938252	2		445	580	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679970	30679970	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	33	782	0	ENST00000376406.3:c.1749G>T	p.Glu583Asp	p.E583D	ENST00000376406	NM_014641.2	583	gaG/gaT	5/15	1	2	FACETS	0.282	0.229	0.342	0.282	0.229	0.342	SUBCLONAL	1	NA	1	0.401471617938252	2		782	583	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56832447	56832447	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	89	422	0	ENST00000308159.5:c.357G>C	p.Lys119Asn	p.K119N	ENST00000308159	NM_014669.4	119	aaG/aaC	4/22	1	2	FACETS	0.975	0.87	1	0.975	0.87	1	CLONAL	1	TRUE	1	0.446212041102746	2		422	409	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191507	10191507	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs5030821	NA	P-0062876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	128	592	1	ENST00000256474.2:c.500G>T	p.Arg167Leu	p.R167L	ENST00000256474	NM_000551.3	167	cGg/cTg	3/3	0.446212041102746	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.446212041102746	1		593	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574013	7574013	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062877-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	181	586	0	ENST00000269305.4:c.1014del	p.Phe338LeufsTer7	p.F338Lfs*7	ENST00000269305	NM_001126112.2	338	ttC/tt	10/11	0.429410496354595	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.429410496354595	1		586	528	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922291	100922291	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062877-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	69	334	0	ENST00000325455.5:c.2221A>C	p.Asn741His	p.N741H	ENST00000325455	NM_001202474.3	741	Aac/Cac	5/8	1	2	FACETS	0.794	0.694	0.9	0.794	0.694	0.9	SUBCLONAL	1	TRUE	1	0.429410496354595	2		334	405	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498438	89498438	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062877-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	172	571	0	ENST00000336596.2:c.2410G>C	p.Ala804Pro	p.A804P	ENST00000336596	NM_005233.5	804	Gcc/Ccc	14/17	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.429410496354595	2		571	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0062902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	364	818	1	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.847135342308229	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	FALSE	0	0.840193390290289	2		819	416	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0062902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	223	425	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	0.847135342308229	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	FALSE	0	0.840193390290289	2		425	256	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770824	59770824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45572934	NA	P-0062902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	172	419	0	ENST00000259008.2:c.2542C>T	p.Arg848Cys	p.R848C	ENST00000259008	NM_032043.2	848	Cgc/Tgc	18/20	0.847135342308229	3	FACETS	1	0.953	1	0.675	0.636	0.714	CLONAL	2	FALSE	0	0.840193390290289	3		419	287	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678598	88678598	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	236	564	0	ENST00000360948.2:c.938C>A	p.Pro313His	p.P313H	ENST00000360948	NM_001012338.2	313	cCt/cAt	9/19	0.847135342308229	3	FACETS	1	0.961	1	0.675	0.641	0.708	CLONAL	2	FALSE	0	0.840193390290289	3		564	394	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206753	102206753	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	108	443	0	ENST00000263464.3:c.1381G>T	p.Val461Leu	p.V461L	ENST00000263464	NM_001165.4	461	Gta/Tta	7/9	0.695760622934174	4	FACETS	0.962	0.867	1	0.321	0.289	0.354	CLONAL	1	FALSE	1	0.840193390290289	4		443	492	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786753	3786753	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	148	528	0	ENST00000262367.5:c.4458C>A	p.Cys1486Ter	p.C1486*	ENST00000262367	NM_004380.2	1486	tgC/tgA	27/31	0.847135342308229	2	FACETS	1	0.959	1	0.524	0.486	0.563	CLONAL	1	FALSE	0	0.840193390290289	2		528	336	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061537	38061537	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	95	610	0	ENST00000250448.2:c.452G>C	p.Ser151Thr	p.S151T	ENST00000250448	NM_004496.3	151	aGc/aCc	2/2	0.823144480315001	4	FACETS	0.993	0.89	1	0.497	0.445	0.551	CLONAL	1	FALSE	2	0.840193390290289	4		610	419	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79974812	79974812	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	51	479	0	ENST00000265081.6:c.1240C>G	p.Leu414Val	p.L414V	ENST00000265081	NM_002439.4	414	Cta/Gta	8/24	0.831792221961996	4	FACETS	0.331	0.281	0.386	0.11	0.093	0.129	SUBCLONAL	1	FALSE	1	0.840193390290289	4		479	675	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497299	149497299	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	145	556	0	ENST00000261799.4:c.3019G>T	p.Val1007Phe	p.V1007F	ENST00000261799	NM_002609.3	1007	Gtc/Ttc	22/23	0.847135342308229	5	FACETS	1	0.976	1	0.393	0.359	0.428	CLONAL	1	FALSE	2	0.840193390290289	5		556	662	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8523518	8523518	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	152	486	0	ENST00000356435.5:c.686G>C	p.Arg229Pro	p.R229P	ENST00000356435		229	cGa/cCa	8/35	0.768405187416417	5	FACETS	0.974	0.891	1	0.325	0.297	0.354	CLONAL	1	FALSE	2	0.840193390290289	5		486	840	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156753	2156760	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	TTGGTGTC	TTGGTGTC	A	novel	NA	P-0062902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	124	711	0	ENST00000434045.2:c.163-1_169delinsT		p.X55_splice	ENST00000434045	NM_001127598.1	55		3/5	0.847135342308229		FACETS		0.855	1				CLONAL	1	FALSE	1	0.840193390290289	3		711	447	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0062903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	475	464	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	0.768080186522474	6	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	3	0.768080186522474	6		464	996	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	333	583	0	ENST00000322088.6:c.767C>A	p.Ser256Tyr	p.S256Y	ENST00000322088	NM_014225.5	256	tCc/tAc	6/15	0.72862770916059	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.768080186522474	4		583	698	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578525	7578525	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519976	NA	P-0062903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	391	589	0	ENST00000269305.4:c.405C>G	p.Cys135Trp	p.C135W	ENST00000269305	NM_001126112.2	135	tgC/tgG	5/11	0.772776348894462	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.768080186522474	2		589	470	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532696	187532696	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200230570	NA	P-0062903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	181	553	0	ENST00000441802.2:c.9697C>T	p.Arg3233Cys	p.R3233C	ENST00000441802	NM_005245.3	3233	Cgt/Tgt	14/27	0.772776348894462	2	FACETS	1	0.967	1	0.53	0.494	0.566	CLONAL	1	TRUE	0	0.768080186522474	2		553	445	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	53	343	0				ENST00000310581	NM_198253.2	-/1132			0.267081512607556	1	FACETS	0.967	0.837	1	0.967	0.837	1	CLONAL	1	TRUE	0	0.440744576141686	1		343	194	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720679	89720679	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs398123329	NA	P-0062904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	13	80	3	ENST00000371953.3:c.830C>A	p.Thr277Lys	p.T277K	ENST00000371953	NM_000314.4	277	aCa/aAa	8/9	0.440744576141686	1	FACETS	0.852	0.655	1	1	0.915	1	CLONAL	2	TRUE	0	0.440744576141686	1		83	27	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032264	10032264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751692867	NA	P-0062904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	102	568	0	ENST00000330684.3:c.559G>A	p.Val187Ile	p.V187I	ENST00000330684	NM_001134407.1	187	Gtc/Atc	3/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.440744576141686	2		568	369	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268793	98268793	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	118	654	0	ENST00000331920.6:c.290A>C	p.Asn97Thr	p.N97T	ENST00000331920	NM_000264.3	97	aAc/aCc	2/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.440744576141686	2		654	368	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557630	95557630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	71	641	0	ENST00000393063.1:c.5437G>A	p.Glu1813Lys	p.E1813K	ENST00000393063	NM_030621.3	1813	Gag/Aag	26/28	0.344852783598825	3	FACETS	0.774	0.684	0.868	0.774	0.684	0.868	SUBCLONAL	2	TRUE	1	0.440744576141686	3		641	254	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0062905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	555	622	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.843	0.821	0.864	1	0.998	1	CLONAL	3	TRUE	1	0.595372537080749	2		622	737	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0062905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	209	513	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.595372537080749	2		513	654	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431437	121431437	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	271	652	0	ENST00000257555.6:c.641T>A	p.Leu214Gln	p.L214Q	ENST00000257555		214	cTg/cAg	3/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.595372537080749	2		652	710	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938009	76938009	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	278	274	0	ENST00000373344.5:c.2739del	p.Ala914GlnfsTer56	p.A914Qfs*56	ENST00000373344	NM_000489.3	913	caA/ca	9/35	1	1	FACETS	0.79	0.757	0.822	1	0.996	1	SUBCLONAL	2	TRUE	0	0.595372537080749	1		274	415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0062906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	235	801	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.954	0.893	1	0.954	0.893	1	CLONAL	1	TRUE	1	0.624211761893603	2		804	789	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0062906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	231	552	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.624211761893603	2		552	736	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883726	37883726	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	266	929	0	ENST00000269571.5:c.3338G>A	p.Ser1113Asn	p.S1113N	ENST00000269571		1113	aGt/aAt	26/27	1	2	FACETS	0.953	0.896	1	0.953	0.896	1	CLONAL	1	TRUE	1	0.624211761893603	2		929	894	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547177	106547177	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	251	645	0	ENST00000369096.4:c.414del	p.Tyr139IlefsTer24	p.Y139Ifs*24	ENST00000369096	NM_001198.3	138	atC/at	4/7	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.624211761893603	2		645	767	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0062907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	88	1032	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.245388461080852	3	FACETS	1	0.975	1	0.688	0.611	0.771	CLONAL	1	TRUE	1	0.245388461080852	3		1032	585	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	100	915	1	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	0.879	0.784	0.981	0.879	0.784	0.981	CLONAL	1	TRUE	1	0.245388461080852	2		916	927	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781504	NA	P-0062907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	173	787	0	ENST00000269305.4:c.314G>T	p.Gly105Val	p.G105V	ENST00000269305	NM_001126112.2	105	gGc/gTc	4/11	0.211418602157112	2	FACETS	0.756	0.695	0.818	0.756	0.695	0.818	SUBCLONAL	2	TRUE	0	0.245388461080852	2		787	933	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508490	106508490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	58	585	0	ENST00000359195.3:c.484G>A	p.Val162Ile	p.V162I	ENST00000359195	NM_002649.2	162	Gtc/Atc	2/11	0.229381147300706	4	FACETS	0.738	0.632	0.853	0.369	0.316	0.427	SUBCLONAL	1	TRUE	2	0.245388461080852	4		585	798	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956164	55956164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780209077	NA	P-0062907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	61	489	0	ENST00000263923.4:c.3151C>T	p.Arg1051Trp	p.R1051W	ENST00000263923	NM_002253.2	1051	Cgg/Tgg	23/30	1	2	FACETS	0.734	0.633	0.845	0.734	0.633	0.845	SUBCLONAL	1	TRUE	1	0.245388461080852	2		489	677	SUCCESS
APC	324	MSKCC	GRCh37	5	112154907	112154907	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1114167545	NA	P-0062907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	230	646	0	ENST00000257430.4:c.1178C>G	p.Ser393Ter	p.S393*	ENST00000257430	NM_000038.5	393	tCa/tGa	10/16	0.245388461080852	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.245388461080852	2		646	871	SUCCESS
APC	324	MSKCC	GRCh37	5	112175925	112175925	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs863225356	NA	P-0062907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	267	486	0	ENST00000257430.4:c.4634C>A	p.Ser1545Ter	p.S1545*	ENST00000257430	NM_000038.5	1545	tCa/tAa	16/16	0.245388461080852	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.245388461080852	2		486	935	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989346	7989346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397514526	NA	P-0062907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	155	660	0	ENST00000319144.4:c.340C>T	p.Arg114Trp	p.R114W	ENST00000319144	NM_001139.2	114	Cgg/Tgg	2/15	0.211418602157112	2	FACETS	0.892	0.819	0.969	0.892	0.819	0.969	CLONAL	2	TRUE	0	0.245388461080852	2		660	708	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003509	42003509	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	137	531	1	ENST00000219905.7:c.3046C>T	p.Arg1016Ter	p.R1016*	ENST00000219905	NM_001164273.1	1016	Cga/Tga	8/24	0.229381147300706	4	FACETS	0.82	0.746	0.898	0.82	0.746	0.898	CLONAL	2	TRUE	2	0.245388461080852	4		532	848	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0062908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	142	785	4	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.25526349229742	2		789	977	SUCCESS
APC	324	MSKCC	GRCh37	5	112175411	112175411	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	119	622	3	ENST00000257430.4:c.4120G>T	p.Glu1374Ter	p.E1374*	ENST00000257430	NM_000038.5	1374	Gaa/Taa	16/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.25526349229742	2		625	729	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119875	70119875	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	108	754	1	ENST00000245479.2:c.877G>T	p.Glu293Ter	p.E293*	ENST00000245479	NM_000346.3	293	Gag/Tag	3/3	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.25526349229742	2		755	840	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0062909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	482	462	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.603270341022393	4	FACETS	0.975	0.947	1	0.975	0.947	1	CLONAL	4	TRUE	0	0.603270341022393	4		462	657	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0062909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	361	855	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.603270341022393	2	FACETS	0.984	0.945	1	0.984	0.945	1	CLONAL	2	TRUE	0	0.603270341022393	2		857	608	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448600	89448600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759973751	NA	P-0062909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	352	688	0	ENST00000336596.2:c.1564C>T	p.Arg522Cys	p.R522C	ENST00000336596	NM_005233.5	522	Cgc/Tgc	7/17	0.536919672370006	3	FACETS	0.98	0.934	1	0.98	0.934	1	CLONAL	2	TRUE	1	0.603270341022393	3		688	775	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211624	36211624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs574808075	NA	P-0062909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	266	629	0	ENST00000222270.7:c.1375C>T	p.Pro459Ser	p.P459S	ENST00000222270	NM_014727.1	459	Cct/Tct	3/37	0.579938222846472	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.603270341022393	4		629	645	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597400	10597401	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0062909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	265	630	0	ENST00000171111.5:c.1802_1803delinsTT	p.Arg601Leu	p.R601L	ENST00000171111	NM_203500.1	601	cGG/cTT	6/6	0.603270341022393	2	FACETS	0.929	0.883	0.974	0.929	0.883	0.974	CLONAL	2	TRUE	0	0.603270341022393	2		630	473	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073636	8073637	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0062909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	212	722	0	ENST00000377482.5:c.1022dup	p.Tyr341Ter	p.Y341*	ENST00000377482	NM_018948.3	341	tac/taAc	4/4	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.603270341022393	2		722	647	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465031	120465031	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	148	559	0	ENST00000256646.2:c.5041C>A	p.Leu1681Ile	p.L1681I	ENST00000256646	NM_024408.3	1681	Ctc/Atc	28/34	0.603270341022393	3	FACETS	0.852	0.779	0.927	0.426	0.389	0.464	CLONAL	1	TRUE	1	0.603270341022393	3		559	750	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949104	71949104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	346	859	0	ENST00000298229.2:c.3573del	p.Arg1192GlyfsTer10	p.R1192Gfs*10	ENST00000298229	NM_001567.3	1191	Ggg/gg	27/28	0.603270341022393	5	FACETS	0.954	0.904	1	0.636	0.602	0.671	CLONAL	2	TRUE	2	0.603270341022393	5		859	1145	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984911	101984911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1591100315	NA	P-0062909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	439	472	0	ENST00000282441.5:c.358C>T	p.Pro120Ser	p.P120S	ENST00000282441	NM_001130145.2	120	Cca/Tca	2/9	0.603270341022393	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.603270341022393	3		472	593	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864565	56864565	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	128	576	0	ENST00000308159.5:c.1053G>T	p.Trp351Cys	p.W351C	ENST00000308159	NM_014669.4	351	tgG/tgT	10/22	1	2	FACETS	0.873	0.796	0.953	0.873	0.796	0.953	CLONAL	1	TRUE	1	0.603270341022393	2		576	486	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308048	30308048	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	277	535	0	ENST00000262643.3:c.187del	p.Asp63ThrfsTer12	p.D63Tfs*12	ENST00000262643	NM_001238.2	62	tGg/tg	5/12	0.579938222846472	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.603270341022393	4		535	711	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959043	2959044	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0062909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	397	625	0	ENST00000396946.4:c.2472_2473delinsAA	p.Asp824_His825delinsGluAsn	p.D824_H825delinsEN	ENST00000396946	NM_032415.4	824	gaCCat/gaAAat	18/25	0.493477701191231	5	FACETS	0.956	0.914	0.999			1	CLONAL	3	TRUE	NA	0.603270341022393	5		625	874	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6438334	6438334	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	259	392	0	ENST00000356142.4:c.267A>C	p.Lys89Asn	p.K89N	ENST00000356142	NM_018890.3	89	aaA/aaC	4/7	0.603270341022393	6	FACETS	1	0.978	1	0.543	0.509	0.577	CLONAL	2	TRUE	2	0.603270341022393	6		392	873	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69000045	69000045	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs772254176	NA	P-0062909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	233	551	0	ENST00000288368.4:c.2113+1G>T		p.X705_splice	ENST00000288368	NM_024870.2	705			0.578109228599908	3	FACETS	0.856	0.805	0.909	0.856	0.805	0.909	CLONAL	2	TRUE	1	0.603270341022393	3		551	587	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518148	8518148	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1308	269	564	0	ENST00000356435.5:c.1243C>G	p.Gln415Glu	p.Q415E	ENST00000356435		415	Caa/Gaa	10/35	0.603270341022393	8	FACETS	0.794	0.743	0.848			1	SUBCLONAL	2	TRUE	NA	0.603270341022393	8		564	1577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0062910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	21	502	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	1	2	FACETS	0.616	0.473	0.784	0.616	0.473	0.784	SUBCLONAL	1	TRUE	1	0.14	2		502	487	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280037	18280037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772782368	NA	P-0062910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	27	513	0	ENST00000222254.8:c.2120C>T	p.Ala707Val	p.A707V	ENST00000222254	NM_005027.3	707	gCg/gTg	16/16	1	2	FACETS	1	0.801	1	1	0.801	1	CLONAL	1	TRUE	1	0.14	2		513	383	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464381	464381	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	34	425	0	ENST00000399788.2:c.813del	p.Arg271SerfsTer9	p.R271Sfs*9	ENST00000399788	NM_001042603.1	271	agG/ag	7/28	0.165690771194911	3	FACETS	0.769	0.626	0.93	0.384	0.313	0.465	CLONAL	1	TRUE	1	0.14	3		425	676	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443794	18443794	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	38	390	0	ENST00000266497.5:c.767G>T	p.Arg256Ile	p.R256I	ENST00000266497		256	aGa/aTa	3/31	0.165690771194911	3	FACETS	1	0.836	1	0.507	0.418	0.606	CLONAL	1	TRUE	1	0.14	3		390	573	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719923	18719923	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	43	360	0	ENST00000266497.5:c.3820C>A	p.His1274Asn	p.H1274N	ENST00000266497		1274	Cac/Aac	27/31	0.165690771194911	3	FACETS	1	0.917	1	0.582	0.486	0.688	CLONAL	1	TRUE	1	0.14	3		360	565	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233280	46233280	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0062910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	53	462	0	ENST00000334344.6:c.1498+1G>T		p.X500_splice	ENST00000334344	NM_152641.2	500			0.165690771194911	3	FACETS	1	0.957	1	0.68	0.579	0.79	CLONAL	1	TRUE	1	0.14	3		462	596	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36217171	36217171	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	99	505	0	ENST00000222270.7:c.3920G>T	p.Gly1307Val	p.G1307V	ENST00000222270	NM_014727.1	1307	gGg/gTg	14/37	0.165690771194911	3	FACETS	0.858	0.767	0.954	1	0.974	1	CLONAL	3	TRUE	1	0.14	3		505	588	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47440666	47440666	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0062910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	67	336	0	ENST00000404338.3:c.3826+1G>T		p.X1276_splice	ENST00000404338	NM_004491.4	1276			0.165690771194911	3	FACETS	1	0.907	1	1	0.907	1	CLONAL	2	TRUE	1	0.14	3		336	487	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965136	25965136	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	31	610	0	ENST00000435504.4:c.4070T>A	p.Val1357Asp	p.V1357D	ENST00000435504		1357	gTc/gAc	13/13	1	2	FACETS	0.721	0.582	0.88	0.721	0.582	0.88	SUBCLONAL	1	TRUE	1	0.14	2		610	614	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250463	110250463	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	37	537	0	ENST00000374672.4:c.212C>A	p.Ala71Asp	p.A71D	ENST00000374672	NM_004235.4	71	gCc/gAc	3/5	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.14	2		537	466	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070577	67070578	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0062912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	241	485	0	ENST00000412916.2:c.207dup	p.Pro70SerfsTer13	p.P70Sfs*13	ENST00000412916		67	-/T	3/6	0.529661351970912	1	FACETS	0.944	0.886	1	0.944	0.886	1	CLONAL	1	TRUE	0	0.529661351970912	1		485	709	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880998	37880998	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs144434331	NA	P-0062912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	259	604	0	ENST00000269571.5:c.2327G>T	p.Gly776Val	p.G776V	ENST00000269571		776	gGt/gTt	20/27	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.529661351970912	2		604	943	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061316	38061316	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	234	586	0	ENST00000250448.2:c.673A>C	p.Asn225His	p.N225H	ENST00000250448	NM_004496.3	225	Aat/Cat	2/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.529661351970912	2		586	824	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846085	68846085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	229	481	0	ENST00000261769.5:c.1056del	p.Glu353ArgfsTer3	p.E353Rfs*3	ENST00000261769	NM_004360.3	352	ggT/gg	8/16	0.529661351970912	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.529661351970912	1		481	598	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534289	187534290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0062912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	205	523	0	ENST00000441802.2:c.9435_9436dup	p.Arg3146LysfsTer12	p.R3146Kfs*12	ENST00000441802	NM_005245.3	3146	aga/aAAga	13/27	1	2	FACETS	0.901	0.837	0.967	0.901	0.837	0.967	CLONAL	1	TRUE	1	0.529661351970912	2		523	859	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0062913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	178	190	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.354676519855205	5	FACETS	1	0.981	1	0.859	0.801	0.917	CLONAL	3	TRUE	1	0.394934966460942	5		190	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0062913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	345	746	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.379819692576961	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.394934966460942	2		746	813	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs149680468	NA	P-0062913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	202	651	0	ENST00000281708.4:c.1513C>A	p.Arg505Ser	p.R505S	ENST00000281708	NM_033632.3	505	Cgc/Agc	10/12	0.282271149212134	1	FACETS	0.967	0.898	1	0.967	0.898	1	CLONAL	1	TRUE	0	0.394934966460942	1		651	849	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345240	73345240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	111	619	0	ENST00000377767.4:c.1649C>T	p.Ser550Phe	p.S550F	ENST00000377767	NM_014953.3	550	tCc/tTc	12/21	0.161077878061799	0	FACETS	0.655	0.591	0.722			1	INDETERMINATE	1	TRUE	0	0.394934966460942	0		619	519	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427885	49427885	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	39	620	0	ENST00000301067.7:c.10705del	p.Glu3569SerfsTer89	p.E3569Sfs*89	ENST00000301067	NM_003482.3	3569	Gag/ag	38/54	1	2	FACETS	0.287	0.237	0.344	0.287	0.237	0.344	SUBCLONAL	1	TRUE	1	0.394934966460942	2		620	687	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347614	89347614	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	102	687	0	ENST00000301030.4:c.5336C>A	p.Pro1779His	p.P1779H	ENST00000301030	NM_001256183.1	1779	cCt/cAt	9/13	0.394934966460942	1	FACETS	0.622	0.556	0.691	0.622	0.556	0.691	SUBCLONAL	1	TRUE	0	0.394934966460942	1		687	667	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0062914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	59	1032	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.825	0.71	0.949	0.825	0.71	0.949	CLONAL	1	TRUE	1	0.27	2		1032	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0062914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	98	1022	0	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	0.265909864936603	1	FACETS	0.823	0.734	0.918	0.823	0.734	0.918	CLONAL	1	TRUE	0	0.27	1		1022	763	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696747	47696747	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	74	589	0	ENST00000347630.2:c.201G>C	p.Trp67Cys	p.W67C	ENST00000347630	NM_001007230.1	67	tgG/tgC	5/11	1	2	FACETS	0.772	0.675	0.876	0.772	0.675	0.876	SUBCLONAL	1	TRUE	1	0.27	2		589	710	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47108598	47108598	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	67	312	0	ENST00000409792.3:c.6071G>C	p.Arg2024Pro	p.R2024P	ENST00000409792	NM_014159.6	2024	cGa/cCa	13/21	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.27	2		312	392	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0062915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	23	241	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.465	0.361	0.587	0.465	0.361	0.587	SUBCLONAL	1	TRUE	1	0.14	2		241	706	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0062915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	56	450	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.14	2		451	751	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820792	3820792	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	53	852	0	ENST00000262367.5:c.2659C>A	p.Gln887Lys	p.Q887K	ENST00000262367	NM_004380.2	887	Cag/Aag	14/31	1	2	FACETS	0.844	0.718	0.984	0.844	0.718	0.984	CLONAL	1	TRUE	1	0.14	2		852	897	SUCCESS
APC	324	MSKCC	GRCh37	5	112175720	112175720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	58	690	0	ENST00000257430.4:c.4429C>T	p.Gln1477Ter	p.Q1477*	ENST00000257430	NM_000038.5	1477	Cag/Tag	16/16	1	2	FACETS	0.939	0.805	1	0.939	0.805	1	CLONAL	1	TRUE	1	0.14	2		690	882	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625228	69625228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868995912	NA	P-0062915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	47	786	2	ENST00000334134.2:c.565G>A	p.Glu189Lys	p.E189K	ENST00000334134	NM_005247.2	189	Gag/Aag	3/3	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.14	2		788	644	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844182	68844182	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	57	669	0	ENST00000261769.5:c.770A>T	p.Asp257Val	p.D257V	ENST00000261769	NM_004360.3	257	gAc/gTc	6/16	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.14	2		669	811	SUCCESS
APC	324	MSKCC	GRCh37	5	112173582	112173582	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0062915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	43	652	0	ENST00000257430.4:c.2291T>G	p.Leu764Ter	p.L764*	ENST00000257430	NM_000038.5	764	tTa/tGa	16/16	1	2	FACETS	0.819	0.684	0.97	0.819	0.684	0.97	CLONAL	1	TRUE	1	0.14	2		652	750	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541738	120541738	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	38	780	0	ENST00000229340.5:c.119C>T	p.Thr40Met	p.T40M	ENST00000229340	NM_006861.6	40	aCg/aTg	3/6	1	2	FACETS	0.807	0.665	0.966	0.807	0.665	0.966	CLONAL	1	TRUE	1	0.14	2		780	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0062916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	152	809	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.533632869364181	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.533632869364181	1		809	395	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0062916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	184	665	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.533632869364181	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.533632869364181	1		665	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0062916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	9	705	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.533632869364181	1	FACETS	0.063	0.041	0.091	0.063	0.041	0.091	SUBCLONAL	1	TRUE	0	0.533632869364181	1		705	395	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763246	59763246	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	140	522	0	ENST00000259008.2:c.2856T>G	p.Ile952Met	p.I952M	ENST00000259008	NM_032043.2	952	atT/atG	19/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.533632869364181	2		522	454	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368235	45368235	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	25	534	0	ENST00000262160.6:c.1367T>A	p.Met456Lys	p.M456K	ENST00000262160	NM_005901.5	456	aTg/aAg	11/11	0.533632869364181	1	FACETS	0.178	0.139	0.221	0.178	0.139	0.221	SUBCLONAL	1	TRUE	0	0.533632869364181	1		534	387	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80083460	80083460	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	106	494	0	ENST00000265081.6:c.2512G>A	p.Ala838Thr	p.A838T	ENST00000265081	NM_002439.4	838	Gcc/Acc	18/24	0.513670665181547	1	FACETS	0.745	0.673	0.82	0.745	0.673	0.82	SUBCLONAL	1	TRUE	0	0.533632869364181	1		494	391	SUCCESS
APC	324	MSKCC	GRCh37	5	112175184	112175185	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0062916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	155	525	0	ENST00000257430.4:c.3894_3895dup	p.Ala1299ValfsTer7	p.A1299Vfs*7	ENST00000257430	NM_000038.5	1298	tct/tcTGt	16/16	0.513670665181547	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.533632869364181	1		525	418	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352327	70352327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	188	353	0	ENST00000374080.3:c.4354G>A	p.Glu1452Lys	p.E1452K	ENST00000374080		1452	Gag/Aag	31/45	1	1	FACETS	0.802	0.757	0.847	1	0.993	1	CLONAL	2	TRUE	0	0.533632869364181	1		353	322	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0062917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	672	541	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.78559215728607	3	FACETS	0.971	0.942	1			1	CLONAL	2	TRUE	NA	0.883781178957221	3		541	1129	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589602	67589604	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	novel	NA	P-0062917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	310	324	0	ENST00000274335.5:c.1365_1367del	p.Gln455_Phe456delinsHis	p.Q455_F456delinsH	ENST00000274335		455	caGTTt/cat	10/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.883781178957221	2		324	644	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502394	186502409	+	frameshift_variant	Frame_Shift_Del	DEL	TTTAAAGGAGTCTCTC	TTTAAAGGAGTCTCTC	-	novel	NA	P-0062917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	165	545	0	ENST00000323963.5:c.117_132del	p.Leu40PhefsTer29	p.L40Ffs*29	ENST00000323963		39	aaTTTAAAGGAGTCTCTC/aa	3/11	0.442151941998137	1	FACETS	0.322	0.297	0.349	0.322	0.297	0.349	INDETERMINATE	1	TRUE	0	0.883781178957221	1		545	647	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	132	555	2	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	0.31814451565012	2	FACETS	0.922	0.839	1	0.461	0.419	0.504	CLONAL	1	TRUE	0	0.460447358324117	2		557	622	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0062918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	154	647	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.460447358324117	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.460447358324117	1		647	420	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46611675	46611675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1327397090	NA	P-0062918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	121	696	0	ENST00000263734.3:c.2489C>T	p.Ser830Leu	p.S830L	ENST00000263734	NM_001430.4	830	tCa/tTa	16/16	1	2	FACETS	0.889	0.806	0.977	0.889	0.806	0.977	CLONAL	1	TRUE	1	0.460447358324117	2		696	591	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022238	31022238	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs747847938	NA	P-0062918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	141	531	0	ENST00000375687.4:c.1723C>T	p.Gln575Ter	p.Q575*	ENST00000375687	NM_015338.5	575	Caa/Taa	13/13	0.387172318849229	3	FACETS	1	0.985	1	0.689	0.63	0.749	CLONAL	1	TRUE	1	0.460447358324117	3		531	547	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249007	+	missense_variant	Missense_Mutation	TNP	GCG	GCG	TCA	novel	NA	P-0062918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	451	680	0	ENST00000275493.2:c.2303_2305delinsTCA	p.Ser768_Val769delinsIleMet	p.S768_V769delinsIM	ENST00000275493	NM_005228.3	768	aGCGtg/aTCAtg	20/28	0.441081010039025	5	FACETS	0.978	0.94	1	0.978	0.94	1	CLONAL	4	TRUE	1	0.460447358324117	5		680	847	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0062919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	39	1032	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.998	0.829	1	0.998	0.829	1	CLONAL	1	TRUE	1	0.21	2		1032	372	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0062919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	16	556	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.627	0.464	0.822	0.627	0.464	0.822	SUBCLONAL	1	TRUE	1	0.21	2		556	243	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0062919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	57	665	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.873	0.748	1	0.873	0.748	1	CLONAL	1	TRUE	1	0.21	2		665	622	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902658	1902658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761663126	NA	P-0062919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	52	850	0	ENST00000382891.5:c.277G>A	p.Ala93Thr	p.A93T	ENST00000382891	NM_133335.3	93	Gca/Aca	2/22	1	2	FACETS	0.555	0.471	0.648	0.555	0.471	0.648	SUBCLONAL	1	TRUE	1	0.21	2		850	892	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230590	46230590	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	65	693	0	ENST00000334344.6:c.839A>G	p.Asp280Gly	p.D280G	ENST00000334344	NM_152641.2	280	gAt/gGt	8/21	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.21	2		693	605	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430303	181430303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	75	435	0	ENST00000325404.1:c.155C>T	p.Ser52Phe	p.S52F	ENST00000325404	NM_003106.3	52	tCc/tTc	1/1	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.392317310637105	2		435	276	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061238	38061239	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGAGTCCGGGTGCAGCGTCCAGTA	novel	NA	P-0062920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	216	783	0	ENST00000250448.2:c.727_750dup	p.Tyr243_Ser250dup	p.Y243_S250dup	ENST00000250448	NM_004496.3	243	-/TACTGGACGCTGCACCCGGACTCC	2/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.392317310637105	2		783	948	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929161	32929162	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs397507899	NA	P-0062920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	13	558	0	ENST00000380152.3:c.7177dup	p.Met2393AsnfsTer19	p.M2393Nfs*19	ENST00000380152		2391	gaa/gAaa	14/27	0.392317310637105	1	FACETS	0.301	0.215	0.405	0.301	0.215	0.405	SUBCLONAL	1	TRUE	0	0.392317310637105	1		558	177	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033492	48033492	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs972387746	NA	P-0062920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	35	643	0	ENST00000234420.5:c.3796C>T	p.His1266Tyr	p.H1266Y	ENST00000234420	NM_000179.2	1266	Cat/Tat	8/10	1	2	FACETS	0.572	0.47	0.685	0.572	0.47	0.685	SUBCLONAL	1	TRUE	1	0.392317310637105	2		643	312	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44920663	44920663	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	50	166	0	ENST00000377967.4:c.1424del	p.Gln475ArgfsTer13	p.Q475Rfs*13	ENST00000377967	NM_021140.2	475	cAg/cg	14/29	0.296576431451348	2	FACETS	1	0.961	1			1	CLONAL	2	TRUE	NA	0.392317310637105	2		166	102	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692790	89692790	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554898067	NA	P-0062921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	121	358	0	ENST00000371953.3:c.274G>T	p.Asp92Tyr	p.D92Y	ENST00000371953	NM_000314.4	92	Gac/Tac	5/9	0.747960482508045	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.747960482508045	1		358	195	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	164	442	0	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.747960482508045	2		442	407	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376563	118376563	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	299	770	0	ENST00000534358.1:c.9956C>T	p.Thr3319Ile	p.T3319I	ENST00000534358	NM_005933.3	3319	aCa/aTa	27/36	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.747960482508045	2		770	783	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796835	42796835	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	316	892	0	ENST00000575354.2:c.3293G>T	p.Gly1098Val	p.G1098V	ENST00000575354	NM_015125.3	1098	gGc/gTc	14/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.747960482508045	2		892	816	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183813	10183821	+	inframe_deletion	In_Frame_Del	DEL	GCCGCAGCC	GCCGCAGCC	-	novel	NA	P-0062921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	208	701	0	ENST00000256474.2:c.282_290del	p.Glu94_Pro97delinsAsp	p.E94_P97delinsD	ENST00000256474	NM_000551.3	94	gaGCCGCAGCCc/gac	1/3	0.747960482508045	1	FACETS	0.924	0.872	0.974	0.924	0.872	0.974	CLONAL	1	TRUE	0	0.747960482508045	1		701	377	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52661288	52661288	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0062921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	203	573	0	ENST00000394830.3:c.1541+1G>T		p.X514_splice	ENST00000394830	NM_018313.4	514			0.747960482508045	1	FACETS	0.901	0.85	0.952	0.901	0.85	0.952	CLONAL	1	TRUE	0	0.747960482508045	1		573	377	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928070	178928099	+	frameshift_variant	Frame_Shift_Del	DEL	CATGGATTAGAAGATTTGCTGAACCCTATT	CATGGATTAGAAGATTTGCTGAACCCTATT	GAAC	novel	NA	P-0062921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	166	590	2	ENST00000263967.3:c.1348_1377delinsGAAC	p.His450GlufsTer10	p.H450Efs*10	ENST00000263967	NM_006218.2	450	CATGGATTAGAAGATTTGCTGAACCCTATT/GAAC	8/21	0.747960482508045	1	FACETS	0.952	0.894	1	0.952	0.894	1	CLONAL	1	TRUE	0	0.747960482508045	1		592	292	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0062922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	220	586	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.414517761120615	2	FACETS	0.941	0.883	1	0.941	0.883	1	CLONAL	2	TRUE	0	0.414517761120615	2		586	564	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0062922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	102	622	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.414517761120615	2		622	469	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0062922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	89	591	1	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	1	2	FACETS	0.868	0.772	0.969	0.868	0.772	0.969	CLONAL	1	TRUE	1	0.414517761120615	2		592	495	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119041	70119041	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0062922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	299	828	0	ENST00000245479.2:c.613A>T	p.Lys205Ter	p.K205*	ENST00000245479	NM_000346.3	205	Aag/Tag	2/3	0.398147485507944	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.414517761120615	2		828	683	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0062923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	114	698	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.526	0.473	0.582	0.526	0.473	0.582	SUBCLONAL	1	TRUE	1	0.540297566735348	2		698	802	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0062923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	147	557	3	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	1	2	FACETS	0.654	0.597	0.713	0.654	0.597	0.713	SUBCLONAL	1	TRUE	1	0.540297566735348	2		560	832	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044472	47044472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556781457	NA	P-0062923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	99	711	0	ENST00000377604.3:c.1969C>T	p.Arg657Cys	p.R657C	ENST00000377604	NM_001204468.1	657	Cgc/Tgc	18/24	1	2	FACETS	0.46	0.41	0.513	0.46	0.41	0.513	SUBCLONAL	1	TRUE	1	0.540297566735348	2		711	797	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414250	32414250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121907901	NA	P-0062923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	45	661	0	ENST00000332351.3:c.1301G>A	p.Arg434His	p.R434H	ENST00000332351	NM_024426.4	434	cGt/cAt	8/10	1	2	FACETS	0.202	0.169	0.238	0.202	0.169	0.238	SUBCLONAL	1	TRUE	1	0.540297566735348	2		661	826	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449580	32449580	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	33	649	0	ENST00000332351.3:c.794C>G	p.Pro265Arg	p.P265R	ENST00000332351	NM_024426.4	265	cCc/cGc	3/10	1	2	FACETS	0.198	0.161	0.241	0.198	0.161	0.241	SUBCLONAL	1	TRUE	1	0.540297566735348	2		649	616	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0062930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	8	398	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.336	0.215	0.494	0.336	0.215	0.494	SUBCLONAL	1	TRUE	1	0.13	2		398	366	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562233	21562234	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0062930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	19	609	0	ENST00000382592.4:c.1685_1686insT	p.Lys562AsnfsTer9	p.K562Nfs*9	ENST00000382592	NM_014572.2	562	aag/aaTg	4/8	1	2	FACETS	0.433	0.327	0.559	0.433	0.327	0.559	SUBCLONAL	1	TRUE	1	0.13	2		609	675	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681707	78681707	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	12	429	0	ENST00000306801.3:c.415C>T	p.Arg139Cys	p.R139C	ENST00000306801	NM_020761.2	139	Cgc/Tgc	4/34	1	2	FACETS	0.318	0.222	0.437	0.318	0.222	0.437	SUBCLONAL	1	TRUE	1	0.13	2		429	581	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114580	73114580	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	19	336	0	ENST00000356692.5:c.961G>A	p.Glu321Lys	p.E321K	ENST00000356692		321	Gaa/Aaa	9/9	1	2	FACETS	0.784	0.594	1	0.784	0.594	1	CLONAL	1	TRUE	1	0.13	2		336	373	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913283	NA	P-0062930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	18	301	0	ENST00000263967.3:c.3129G>T	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atT	21/21	1	2	FACETS	0.519	0.389	0.673	0.519	0.389	0.673	SUBCLONAL	1	TRUE	1	0.13	2		301	534	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131895051	131895051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370769989	NA	P-0062930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	12	261	0	ENST00000265335.6:c.205G>A	p.Asp69Asn	p.D69N	ENST00000265335		69	Gat/Aat	2/25	1	2	FACETS	0.613	0.43	0.84	0.613	0.43	0.84	SUBCLONAL	1	TRUE	1	0.13	2		261	301	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0062931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	225	710	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.463146214952316	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.483325178370246	1		710	582	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480354	56480354	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	133	574	0	ENST00000267101.3:c.461A>G	p.Lys154Arg	p.K154R	ENST00000267101	NM_001982.3	154	aAg/aGg	4/28	0.24032791055791	1	FACETS	0.736	0.671	0.804	0.736	0.671	0.804	INDETERMINATE	1	TRUE	0	0.483325178370246	1		574	567	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105592	11105592	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	62	666	0	ENST00000358026.2:c.1508C>T	p.Ala503Val	p.A503V	ENST00000358026	NM_001128849.1	503	gCa/gTa	9/36	0.483325178370246	1	FACETS	0.351	0.303	0.403	0.351	0.303	0.403	SUBCLONAL	1	TRUE	0	0.483325178370246	1		666	554	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792915	33792915	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1172993204	NA	P-0062931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	74	381	0	ENST00000498907.2:c.406G>T	p.Ala136Ser	p.A136S	ENST00000498907	NM_004364.3	136	Gcc/Tcc	1/1	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.483325178370246	2		381	257	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0062932-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	97	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.586949095518599	2		434	320	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0062932-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	120	801	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.56763033204842	1	FACETS	0.963	0.883	1	0.963	0.883	1	CLONAL	1	TRUE	0	0.586949095518599	1		804	300	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653782	89653782	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs886041877	NA	P-0062932-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	54	308	0	ENST00000371953.3:c.80A>G	p.Tyr27Cys	p.Y27C	ENST00000371953	NM_000314.4	27	tAt/tGt	2/9	0.567125919317561	1	FACETS	0.929	0.814	1	0.929	0.814	1	CLONAL	1	TRUE	0	0.586949095518599	1		308	140	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679007	117679007	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062932-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	79	377	0	ENST00000368508.3:c.3814A>C	p.Asn1272His	p.N1272H	ENST00000368508	NM_002944.2	1272	Aat/Cat	24/43	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.586949095518599	2		377	233	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880113	151880114	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0062932-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	103	475	0	ENST00000262189.6:c.5210_5211del	p.Lys1737ArgfsTer11	p.K1737Rfs*11	ENST00000262189	NM_170606.2	1737	aAA/a	35/59	0.567125919317561	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.586949095518599	1		475	218	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0062933-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	380	380	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.331908936347967	6	FACETS	1	0.989	1	0.834	0.795	0.872	CLONAL	3	TRUE	2	0.522694007207476	6		380	892	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845890	156845890	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750477154	NA	P-0062933-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1270	115	818	0	ENST00000524377.1:c.1520G>A	p.Arg507His	p.R507H	ENST00000524377	NM_002529.3	507	cGc/cAc	13/17	0.522694007207476	5	FACETS	0.567	0.509	0.629	0.189	0.169	0.21	SUBCLONAL	1	TRUE	2	0.522694007207476	5		818	1385	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0062933-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	462	724	2	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	0.49867530596545	4	FACETS	0.893	0.856	0.929	0.893	0.856	0.929	CLONAL	3	TRUE	1	0.522694007207476	4		726	1005	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061124	38061201	+	protein_altering_variant	In_Frame_Del	DEL	CCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCT	CCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCT	GAA	novel	NA	P-0062933-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	317	627	2	ENST00000250448.2:c.788_865delinsTTC	p.Gln263_Gly289delinsLeuArg	p.Q263_G289delinsLR	ENST00000250448	NM_004496.3	263	cAGAAGCGCTTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGGCGCCAAGGgc/cTTCgc	2/2	0.331908936347967	6	FACETS	1	0.987	1	0.573	0.541	0.605	CLONAL	2	TRUE	2	0.522694007207476	6		629	1083	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0062933-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	275	538	0	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	0.373269887108033	3	FACETS	1	0.987	1	0.75	0.711	0.789	CLONAL	2	TRUE	0	0.522694007207476	3		538	590	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936697	49936697	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0062933-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	349	629	0	ENST00000296474.3:c.1231-1G>T		p.X411_splice	ENST00000296474	NM_002447.2	411			0.522694007207476	3	FACETS	0.968	0.921	1	0.968	0.921	1	CLONAL	2	TRUE	1	0.522694007207476	3		629	870	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247492	71247492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062933-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	103	471	0	ENST00000318789.4:c.41C>T	p.Ser14Leu	p.S14L	ENST00000318789	NM_032682.5	14	tCa/tTa	6/21	0.522694007207476	3	FACETS	0.658	0.588	0.731	0.329	0.294	0.366	SUBCLONAL	1	TRUE	1	0.522694007207476	3		471	756	SUCCESS
APC	324	MSKCC	GRCh37	5	112174604	112174604	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768454793	NA	P-0062933-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	95	553	0	ENST00000257430.4:c.3313C>T	p.Arg1105Trp	p.R1105W	ENST00000257430	NM_000038.5	1105	Cgg/Tgg	16/16	0.522694007207476	5	FACETS	0.62	0.551	0.694	0.207	0.183	0.232	SUBCLONAL	1	TRUE	2	0.522694007207476	5		553	1046	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665388	176665388	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062933-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	181	543	0	ENST00000439151.2:c.4072C>T	p.Gln1358Ter	p.Q1358*	ENST00000439151	NM_022455.4	1358	Cag/Tag	7/23	0.522694007207476	5	FACETS	1	0.981	1	0.402	0.37	0.435	CLONAL	1	TRUE	2	0.522694007207476	5		543	1025	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0062934-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	427	520	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	0.912435395333176	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.912435395333176	3		520	675	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636893	176636893	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1353450334	NA	P-0062934-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1625	167	647	0	ENST00000439151.2:c.1493G>A	p.Arg498Gln	p.R498Q	ENST00000439151	NM_022455.4	498	cGa/cAa	5/23	0.912435395333176	7	FACETS	0.67	0.613	0.73	0.112	0.102	0.122	SUBCLONAL	1	TRUE	1	0.912435395333176	7		647	1792	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0062935-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	20	538	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	1	2	FACETS	0.366	0.279	0.468	0.366	0.279	0.468	SUBCLONAL	1	TRUE	1	0.305184903468037	2		538	358	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221930	98221930	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs768039033	NA	P-0062935-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	21	625	0	ENST00000331920.6:c.2839G>C	p.Glu947Gln	p.E947Q	ENST00000331920	NM_000264.3	947	Gaa/Caa	17/24	1	2	FACETS	0.374	0.287	0.475	0.374	0.287	0.475	SUBCLONAL	1	TRUE	1	0.305184903468037	2		625	368	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424098	49424099	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CATCCTTGGGGTGCTCCCCCAGCTCTTCAGATGGGGTGACGCCATTCAC	novel	NA	P-0062935-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	26	510	0	ENST00000301067.7:c.13915_13963dup	p.Ala4655GlyfsTer8	p.A4655Gfs*8	ENST00000301067	NM_003482.3	4655	gct/gGTGAATGGCGTCACCCCATCTGAAGAGCTGGGGGAGCACCCCAAGGATGct	42/54	1	2	FACETS	0.373	0.295	0.463	0.373	0.295	0.463	SUBCLONAL	1	TRUE	1	0.305184903468037	2		510	457	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686312	117686312	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062935-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	53	505	1	ENST00000368508.3:c.3029C>A	p.Pro1010His	p.P1010H	ENST00000368508	NM_002944.2	1010	cCt/cAt	20/43	0.305184903468037	1	FACETS	0.827	0.717	0.942	1	0.973	1	CLONAL	2	TRUE	0	0.305184903468037	1		506	178	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	115	343	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.871	0.794	0.951	0.871	0.794	0.951	CLONAL	1	TRUE	1	0.783171866182511	2		343	337	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220274	55220274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23322	521	467	0	ENST00000275493.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000275493	NM_005228.3	222	Cgc/Tgc	6/28	0.783171866182511	44	FACETS	0.974	0.924	1	0.022	0.021	0.024	CLONAL	1	TRUE	0	0.783171866182511	44		467	23843	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220295	55220295	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16356	7128	454	0	ENST00000275493.2:c.685A>T	p.Ser229Cys	p.S229C	ENST00000275493	NM_005228.3	229	Agt/Tgt	6/28	0.783171866182511	44	FACETS	0.966	0.954	0.978	0.307	0.303	0.311	CLONAL	14	TRUE	0	0.783171866182511	44		454	23484	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625078	69625078	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	64	608	0	ENST00000334134.2:c.715C>T	p.His239Tyr	p.H239Y	ENST00000334134	NM_005247.2	239	Cac/Tac	3/3	0.749357739950741	1	FACETS	0.314	0.273	0.357	0.314	0.273	0.357	SUBCLONAL	1	TRUE	0	0.783171866182511	1		608	317	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250962	10250962	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772419584	NA	P-0062938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	161	558	1	ENST00000340748.4:c.3518C>T	p.Ala1173Val	p.A1173V	ENST00000340748		1173	gCg/gTg	32/40	0.31704716379445	2	FACETS	0.627	0.577	0.679	0.313	0.288	0.34	INDETERMINATE	1	TRUE	0	0.783171866182511	2		559	656	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313190	30313190	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	67	604	0	ENST00000262643.3:c.884C>A	p.Pro295His	p.P295H	ENST00000262643	NM_001238.2	295	cCt/cAt	10/12	0.248328616949066	3	FACETS	0.375	0.325	0.429	0.125	0.108	0.143	INDETERMINATE	1	TRUE	0	0.783171866182511	3		604	635	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468481	89468481	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	269	536	0	ENST00000336596.2:c.2015G>A	p.Ser672Asn	p.S672N	ENST00000336596	NM_005233.5	672	aGc/aAc	11/17	1	2	FACETS	0.915	0.862	0.968	0.915	0.862	0.968	CLONAL	1	TRUE	1	0.783171866182511	2		536	751	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508718	106508718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149432307	NA	P-0062938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	242	728	0	ENST00000359195.3:c.712G>A	p.Asp238Asn	p.D238N	ENST00000359195	NM_002649.2	238	Gac/Aac	2/11	0.783171866182511	3	FACETS	0.901	0.843	0.962	0.451	0.421	0.481	CLONAL	1	TRUE	1	0.783171866182511	3		728	954	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857640	78857640	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	121	531	0	ENST00000306801.3:c.1710C>A	p.His570Gln	p.H570Q	ENST00000306801	NM_020761.2	570	caC/caA	16/34	0.70575964614463	4	FACETS	0.779	0.712	0.849	0.779	0.712	0.849	SUBCLONAL	2	TRUE	2	0.747636098645452	4		531	363	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025963	48025963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1229666565	NA	P-0062952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	242	621	0	ENST00000234420.5:c.841G>A	p.Gly281Arg	p.G281R	ENST00000234420	NM_000179.2	281	Gga/Aga	4/10	0.464722595287696	5	FACETS	0.997	0.945	1	0.997	0.945	1	CLONAL	3	TRUE	2	0.747636098645452	5		621	459	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26978094	26978094	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1160704856	NA	P-0062954-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	116	375	0	ENST00000381527.3:c.1271G>A	p.Arg424His	p.R424H	ENST00000381527	NM_001260.1	424	cGt/cAt	13/13	0.221227806630667	2	FACETS	0.669	0.606	0.736	0.335	0.303	0.368	INDETERMINATE	1	TRUE	0	0.663974468342517	2		375	522	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857912	89857912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760352719	NA	P-0062954-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	118	550	0	ENST00000389301.3:c.1258G>A	p.Glu420Lys	p.E420K	ENST00000389301	NM_000135.2	420	Gag/Aag	14/43	1	2	FACETS	0.58	0.524	0.638	0.58	0.524	0.638	SUBCLONAL	1	TRUE	1	0.663974468342517	2		550	613	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741483	17741483	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062954-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	80	475	0	ENST00000250003.3:c.154C>A	p.His52Asn	p.H52N	ENST00000250003	NM_002478.4	52	Cac/Aac	1/3	0.268158252520226	1	FACETS	0.282	0.249	0.319	0.282	0.249	0.319	INDETERMINATE	1	TRUE	0	0.663974468342517	1		475	570	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607632	46607632	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062954-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	91	578	1	ENST00000263734.3:c.1821C>G	p.Ile607Met	p.I607M	ENST00000263734	NM_001430.4	607	atC/atG	12/16	0.278630489654647	3	FACETS	0.472	0.419	0.529	0.236	0.209	0.265	INDETERMINATE	1	TRUE	1	0.663974468342517	3		579	773	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0062956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	215	457	0	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	0.97	0.911	1	0.97	0.911	1	CLONAL	1	TRUE	1	0.88859712151311	2		457	499	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243444	46243444	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	152	304	0	ENST00000334344.6:c.1800del	p.Lys600AsnfsTer47	p.K600Nfs*47	ENST00000334344	NM_152641.2	599	gtA/gt	14/21	0.88859712151311	1	FACETS	0.932	0.885	0.976	0.932	0.885	0.976	CLONAL	1	TRUE	0	0.88859712151311	1		304	204	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782177	NA	P-0062957-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	191	516	0	ENST00000269305.4:c.644G>A	p.Ser215Asn	p.S215N	ENST00000269305	NM_001126112.2	215	aGt/aAt	6/11	0.43443359745707	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.495592110393207	1		516	526	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051652	30051652	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062957-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	26	293	0	ENST00000338641.4:c.586C>G	p.Arg196Gly	p.R196G	ENST00000338641	NM_000268.3	196	Cga/Gga	6/16	0.254245997673509	1	FACETS	0.263	0.208	0.325	0.263	0.208	0.325	INDETERMINATE	1	TRUE	0	0.495592110393207	1		293	300	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459532	50459532	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062957-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	102	389	0	ENST00000331340.3:c.821G>T	p.Arg274Leu	p.R274L	ENST00000331340	NM_006060.4	274	cGt/cTt	7/8	1	2	FACETS	0.997	0.898	1	0.997	0.898	1	CLONAL	1	TRUE	1	0.495592110393207	2		389	413	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265389	10265389	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062957-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	71	570	0	ENST00000340748.4:c.1657C>A	p.His553Asn	p.H553N	ENST00000340748		553	Cac/Aac	20/40	0.254245997673509	1	FACETS	0.413	0.361	0.469	0.413	0.361	0.469	INDETERMINATE	1	TRUE	0	0.495592110393207	1		570	522	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	149	343	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.779	0.719	0.84	0.779	0.719	0.84	SUBCLONAL	1	TRUE	1	0.930597279890293	2		343	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578397	7578397	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1555526004	NA	P-0062958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	787	489	0	ENST00000269305.4:c.533A>C	p.His178Pro	p.H178P	ENST00000269305	NM_001126112.2	178	cAc/cCc	5/11	0.930597279890293	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.930597279890293	2		489	833	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0062960-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	82	1032	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.197082271077875	2	FACETS	1	0.971	1	0.665	0.589	0.747	CLONAL	1	TRUE	0	0.258886467670288	2		1032	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0062960-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	195	577	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.258886467670288	1	FACETS	0.862	0.8	0.926	1	0.992	1	CLONAL	2	TRUE	0	0.258886467670288	1		579	761	SUCCESS
APC	324	MSKCC	GRCh37	5	112163677	112163677	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0062960-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	121	442	0	ENST00000257430.4:c.1600A>T	p.Lys534Ter	p.K534*	ENST00000257430	NM_000038.5	534	Aaa/Taa	13/16	0.258886467670288	1	FACETS	0.848	0.77	0.928	1	0.988	1	CLONAL	2	TRUE	0	0.258886467670288	1		442	480	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0062960-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	88	756	0	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	0.258886467670288	1	FACETS	0.7	0.62	0.787	0.7	0.62	0.787	SUBCLONAL	1	TRUE	0	0.258886467670288	1		756	845	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715747	18715747	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062960-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	213	692	0	ENST00000266497.5:c.3578C>G	p.Pro1193Arg	p.P1193R	ENST00000266497		1193	cCt/cGt	25/31	0.197082271077875	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.258886467670288	2		692	766	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832580	72832580	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062960-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	41	652	0	ENST00000268489.5:c.4001C>T	p.Pro1334Leu	p.P1334L	ENST00000268489	NM_006885.3	1334	cCa/cTa	9/10	1	2	FACETS	0.399	0.331	0.475	0.399	0.331	0.475	SUBCLONAL	1	TRUE	1	0.258886467670288	2		652	794	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094931	11094931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs563079629	NA	P-0062960-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	170	764	0	ENST00000358026.2:c.104C>T	p.Ser35Leu	p.S35L	ENST00000358026	NM_001128849.1	35	tCg/tTg	2/36	1	2	FACETS	0.824	0.759	0.892	1	0.991	1	CLONAL	2	TRUE	1	0.258886467670288	2		764	797	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622164	162622164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062960-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	79	683	0	ENST00000366898.1:c.533A>T	p.Gln178Leu	p.Q178L	ENST00000366898	NM_004562.2	178	cAg/cTg	4/12	1	2	FACETS	0.668	0.586	0.756	0.668	0.586	0.756	SUBCLONAL	1	TRUE	1	0.258886467670288	2		683	914	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947539	48947539	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1131690892	NA	P-0062961-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	119	419	0	ENST00000267163.4:c.1128-2A>G		p.X376_splice	ENST00000267163	NM_000321.2	376			0.465126376374002	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.465126376374002	1		419	314	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748012	72748019	+	frameshift_variant	Frame_Shift_Del	DEL	CCGTGTCC	CCGTGTCC	-	novel	NA	P-0062961-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	191	828	0	ENST00000357731.5:c.159_166del	p.Asp54GlyfsTer3	p.D54Gfs*3	ENST00000357731	NM_173808.2	53	ggGGACACGGcg/ggcg	1/7	0.464019288310854	1	FACETS	0.996	0.925	1	0.996	0.925	1	CLONAL	1	TRUE	0	0.465126376374002	1		828	633	SUCCESS
RET	5979	MSKCC	GRCh37	10	43598063	43598063	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062961-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	150	822	0	ENST00000355710.3:c.611A>T	p.Tyr204Phe	p.Y204F	ENST00000355710	NM_020975.4	204	tAc/tTc	3/20	0.176733017144262	0	FACETS	0.631	0.579	0.684			1	INDETERMINATE	1	TRUE	0	0.465126376374002	0		822	547	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543383	65543399	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TAAAAGGCAACCAAGGG	TAAAAGGCAACCAAGGG	-	novel	NA	P-0062961-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	215	723	0	ENST00000358664.4:c.296-18_296-2del		p.X99_splice	ENST00000358664	NM_002382.4	99			0.465126376374002	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.465126376374002	1		723	599	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772278	68772279	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0062961-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	176	665	0	ENST00000261769.5:c.129dup	p.Arg44AlafsTer15	p.R44Afs*15	ENST00000261769	NM_004360.3	43	cgg/cGgg	2/16	0.465126376374002	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.465126376374002	1		665	430	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21346027	21346027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139823732	NA	P-0062961-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	156	948	1	ENST00000215739.8:c.902G>A	p.Gly301Asp	p.G301D	ENST00000215739	NM_006767.3	301	gGt/gAt	9/21	0.465126376374002	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.465126376374002	1		949	454	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983046	111983046	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062961-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	221	869	1	ENST00000368678.4:c.1501A>G	p.Lys501Glu	p.K501E	ENST00000368678		501	Aaa/Gaa	13/13	0.180853077776363	3	FACETS	1	0.989	1	0.657	0.612	0.703	INDETERMINATE	1	TRUE	1	0.465126376374002	3		870	892	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593664	55593665	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTATGATCAAAATGA	novel	NA	P-0062962-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	225	614	0	ENST00000288135.5:c.1739_1740insAAATGATTATGATCA	p.Asp579_His580insGlnAsnAspTyrAsp	p.D579_H580insQNDYD	ENST00000288135	NM_000222.2	577	cct/ccTTATGATCAAAATGAt	11/21	1	2	FACETS	0.681	0.636	0.726	0.681	0.636	0.726	SUBCLONAL	1	TRUE	1	0.887554173155195	2		614	745	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891445	76891445	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0062964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	104	382	0	ENST00000373344.5:c.4660A>T	p.Arg1554Ter	p.R1554*	ENST00000373344	NM_000489.3	1554	Aga/Tga	16/35	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.904230844115037	2		382	160	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7590694	7590694	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0062964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	884	569	1	ENST00000269305.4:c.-29+1G>A		p.X10_splice	ENST00000269305	NM_001126112.2	10			0.901075655587729	5	FACETS	1	0.996	1	1	0.996	1	CLONAL	5	TRUE	0	0.904230844115037	5		570	914	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51535057	51535057	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	194	543	0	ENST00000260433.2:c.53C>G	p.Pro18Arg	p.P18R	ENST00000260433		18	cCt/cGt	2/10	0.904230844115037	4	FACETS	1	0.974	1	0.551	0.511	0.592	CLONAL	1	TRUE	2	0.904230844115037	4		543	741	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111689	56111689	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	483	543	0	ENST00000399503.3:c.289G>C	p.Asp97His	p.D97H	ENST00000399503	NM_005921.1	97	Gac/Cac	1/20	0.904230844115037	6	FACETS	1	0.989	1	1	0.989	1	CLONAL	4	TRUE	2	0.904230844115037	6		543	718	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509436	106509436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200175951	NA	P-0062983-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	246	492	0	ENST00000359195.3:c.1430G>A	p.Arg477His	p.R477H	ENST00000359195	NM_002649.2	477	cGt/cAt	2/11	1	2	FACETS	0.964	0.906	1	0.964	0.906	1	CLONAL	1	TRUE	1	0.726828338217237	2		492	702	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720857	89720857	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062983-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	61	117	0	ENST00000371953.3:c.1008C>A	p.Tyr336Ter	p.Y336*	ENST00000371953	NM_000314.4	336	taC/taA	8/9	0.685021343920018	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.726828338217237	1		117	93	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849592	68849593	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0062983-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	292	502	0	ENST00000261769.5:c.1496_1497del	p.Phe499TrpfsTer37	p.F499Wfs*37	ENST00000261769	NM_004360.3	499	TTt/t	10/16	0.685021343920018	1	FACETS	0.944	0.899	0.988	0.944	0.899	0.988	CLONAL	1	TRUE	0	0.726828338217237	1		502	542	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458258	120458258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371357549	NA	P-0062983-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	345	710	0	ENST00000256646.2:c.7087G>A	p.Gly2363Arg	p.G2363R	ENST00000256646	NM_024408.3	2363	Ggg/Agg	34/34	1	2	FACETS	0.945	0.896	0.994	0.945	0.896	0.994	CLONAL	1	TRUE	1	0.726828338217237	2		710	1005	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670060	29670060	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062983-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	151	282	0	ENST00000356175.3:c.7033C>A	p.Pro2345Thr	p.P2345T	ENST00000356175	NM_000267.3	2345	Cct/Act	47/57	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.726828338217237	2		282	392	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852108	63852108	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	141	759	2	ENST00000279873.7:c.2886G>C	p.Met962Ile	p.M962I	ENST00000279873	NM_032199.2	962	atG/atC	10/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.282197770384149	2		761	895	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039379	49039413	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTTACAAGTTTCCTAGTTCACCCTTACGGATTC	CCCTTACAAGTTTCCTAGTTCACCCTTACGGATTC	-	novel	NA	P-0062988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	70	651	2	ENST00000267163.4:c.2365_2399del	p.Pro789TrpfsTer14	p.P789Wfs*14	ENST00000267163	NM_000321.2	788	agCCCTTACAAGTTTCCTAGTTCACCCTTACGGATTCct/agct	23/27	0.282197770384149	1	FACETS	0.719	0.627	0.818	0.719	0.627	0.818	SUBCLONAL	1	TRUE	0	0.282197770384149	1		653	593	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0062988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	139	712	0	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.282197770384149	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.282197770384149	1		712	694	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266860	18266860	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	126	699	5	ENST00000222254.8:c.171G>T	p.Met57Ile	p.M57I	ENST00000222254	NM_005027.3	57	atG/atT	2/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.282197770384149	2		704	740	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641128	117641128	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	99	824	3	ENST00000368508.3:c.5843G>T	p.Arg1948Leu	p.R1948L	ENST00000368508	NM_002944.2	1948	cGt/cTt	36/43	1	2	FACETS	0.768	0.685	0.858	0.768	0.685	0.858	SUBCLONAL	1	TRUE	1	0.282197770384149	2		827	913	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939461	68939461	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	24	431	0	ENST00000288368.4:c.446G>A	p.Cys149Tyr	p.C149Y	ENST00000288368	NM_024870.2	149	tGc/tAc	5/40	0.282197770384149	3	FACETS	0.714	0.561	0.889	0.357	0.28	0.445	SUBCLONAL	1	TRUE	1	0.282197770384149	3		431	272	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97869397	97869397	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	162	792	6	ENST00000289081.3:c.1484T>A	p.Leu495Gln	p.L495Q	ENST00000289081	NM_000136.2	495	cTg/cAg	14/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.282197770384149	2		798	910	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0062990-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	214	710	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.421299840202987	3	FACETS	0.91	0.859	0.96	0.91	0.859	0.96	CLONAL	3	TRUE	0	0.480168193649399	3		710	405	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87322806	87322806	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144037140	NA	P-0062990-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	51	314	0	ENST00000277120.3:c.407G>A	p.Arg136His	p.R136H	ENST00000277120		136	cGt/cAt	5/19	0.435076496947303	2	FACETS	0.814	0.698	0.939	0.407	0.349	0.47	CLONAL	1	TRUE	0	0.480168193649399	2		314	261	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242483	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACA	AATTAAGAGAAGCAACA	CT	novel	NA	P-0062990-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	102	363	0	ENST00000275493.2:c.2237_2253delinsCT	p.Glu746_Thr751delinsAla	p.E746_T751delinsA	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACA/gCT	19/28	0.264295085245646	6	FACETS	1	0.963	1	0.761	0.686	0.838	INDETERMINATE	2	TRUE	3	0.480168193649399	6		363	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0062999-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	70	860	2	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.292661760029793	1	FACETS	0.975	0.853	1	0.975	0.853	1	CLONAL	1	TRUE	0	0.291479172806679	1		862	421	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589529	69589529	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	138	839	0	ENST00000168712.1:c.324C>A	p.His108Gln	p.H108Q	ENST00000168712	NM_002007.2	108	caC/caA	1/3	0.346319053544903	3	FACETS	0.602	0.548	0.658	0.301	0.274	0.329	INDETERMINATE	1	TRUE	1	0.82	3		839	789	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55154981	55154981	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	44	522	0	ENST00000257290.5:c.2690C>A	p.Pro897His	p.P897H	ENST00000257290	NM_006206.4	897	cCc/cAc	20/23	1	2	FACETS	0.192	0.16	0.226	0.192	0.16	0.226	SUBCLONAL	1	TRUE	1	0.82	2		522	560	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597401	10597401	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	57	508	0	ENST00000171111.5:c.1802G>C	p.Arg601Pro	p.R601P	ENST00000171111	NM_203500.1	601	cGg/cCg	6/6	1	2	FACETS	0.246	0.211	0.285	0.246	0.211	0.285	SUBCLONAL	1	TRUE	1	0.82	2		508	565	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55704604	55704604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757147876	NA	P-0063012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	25	432	0	ENST00000284073.2:c.667G>A	p.Val223Met	p.V223M	ENST00000284073	NM_138962.2	223	Gtg/Atg	10/14	1	2	FACETS	0.123	0.096	0.154	0.123	0.096	0.154	SUBCLONAL	1	TRUE	1	0.82	2		432	496	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097795	8097795	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	58	630	0	ENST00000346208.3:c.177C>A	p.His59Gln	p.H59Q	ENST00000346208		59	caC/caA	2/6	0.0956799387028695	3	FACETS	0.316	0.271	0.365	0.158	0.135	0.183	INDETERMINATE	1	TRUE	1	0.82	3		630	632	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637573	52637573	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	39	382	0	ENST00000394830.3:c.2743G>T	p.Glu915Ter	p.E915*	ENST00000394830	NM_018313.4	915	Gag/Tag	18/30	1	2	FACETS	0.211	0.174	0.251	0.211	0.174	0.251	SUBCLONAL	1	TRUE	1	0.82	2		382	451	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197829	66197829	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	19	415	0	ENST00000273854.3:c.2870C>G	p.Ala957Gly	p.A957G	ENST00000273854	NM_004439.5	957	gCa/gGa	17/18	1	2	FACETS	0.127	0.096	0.164	0.127	0.096	0.164	SUBCLONAL	1	TRUE	1	0.82	2		415	364	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157495150	157495150	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	36	477	0	ENST00000346085.5:c.3034G>T	p.Gly1012Cys	p.G1012C	ENST00000346085	NM_020732.3	1012	Ggt/Tgt	11/20	1	2	FACETS	0.166	0.136	0.2	0.166	0.136	0.2	SUBCLONAL	1	TRUE	1	0.82	2		477	528	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729775	41729775	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1378762087	NA	P-0063012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	56	539	0	ENST00000242208.4:c.754G>T	p.Ala252Ser	p.A252S	ENST00000242208	NM_002192.2	252	Gcc/Tcc	3/3	1	2	FACETS	0.227	0.194	0.263	0.227	0.194	0.263	SUBCLONAL	1	TRUE	1	0.82	2		539	602	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0063013-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	40	387	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.231646441160052	2		387	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0063013-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	76	551	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.231646441160052	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.231646441160052	1		551	446	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969354	44969354	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063013-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	50	435	0	ENST00000377967.4:c.4037del	p.Asn1346MetfsTer10	p.N1346Mfs*10	ENST00000377967	NM_021140.2	1346	Aat/at	28/29	0.231646441160052	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.231646441160052	1		435	339	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735466	40735466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182388300	NA	P-0063014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	122	530	0	ENST00000373198.4:c.3407G>A	p.Arg1136His	p.R1136H	ENST00000373198	NM_133170.3	1136	cGt/cAt	25/32	0.263890157089125	3	FACETS	0.887	0.804	0.974	0.887	0.804	0.974	CLONAL	2	TRUE	1	0.263890157089125	3		530	590	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0063014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	60	273	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.263890157089125	2		273	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579505	7579505	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	168	683	0	ENST00000269305.4:c.182del	p.Asp61ValfsTer62	p.D61Vfs*62	ENST00000269305	NM_001126112.2	61	gAt/gt	4/11	0.174885989583725	2	FACETS	0.945	0.871	1	0.945	0.871	1	CLONAL	2	TRUE	0	0.263890157089125	2		683	674	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281344	49281344	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202077345	NA	P-0063014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	38	565	0	ENST00000282018.3:c.391G>A	p.Val131Met	p.V131M	ENST00000282018	NM_020377.2	131	Gtg/Atg	1/1	1	2	FACETS	0.456	0.376	0.546	0.456	0.376	0.546	SUBCLONAL	1	TRUE	1	0.263890157089125	2		565	631	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190717454	190717455	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	93	392	0	ENST00000441310.2:c.776dup	p.Ile260HisfsTer46	p.I260Hfs*46	ENST00000441310	NM_000534.4	258	agt/agTt	7/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.263890157089125	2		392	538	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55991433	55991433	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs375186728	NA	P-0063014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	24	435	0	ENST00000263923.4:c.28G>T	p.Ala10Ser	p.A10S	ENST00000263923	NM_002253.2	10	Gcc/Tcc	1/30	0.214137429314297	2	FACETS	0.421	0.329	0.527	0.211	0.164	0.264	SUBCLONAL	1	TRUE	0	0.263890157089125	2		435	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863224499	NA	P-0063015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	719	521	0	ENST00000269305.4:c.672+1G>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.89990696762047	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.905482196227307	2		521	765	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18943204	18943204	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	115	264	0	ENST00000262803.5:c.188del	p.Gly63AlafsTer31	p.G63Afs*31	ENST00000262803	NM_002911.3	62	ccG/cc	1/24	1	2	FACETS	0.898	0.822	0.975	0.898	0.822	0.975	CLONAL	1	TRUE	1	0.905482196227307	2		264	283	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509868	187509868	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371451914	NA	P-0063015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	207	539	1	ENST00000441802.2:c.13645G>A	p.Val4549Met	p.V4549M	ENST00000441802	NM_005245.3	4549	Gtg/Atg	27/27	1	2	FACETS	0.589	0.548	0.632	0.589	0.548	0.632	SUBCLONAL	1	TRUE	1	0.905482196227307	2		540	776	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074237	39074237	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	418	417	0	ENST00000357387.3:c.73A>C	p.Asn25His	p.N25H	ENST00000357387	NM_152756.3	25	Aac/Cac	2/38	0.88243901929012	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.905482196227307	3		417	647	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	44	586	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.926	0.776	1	0.926	0.776	1	CLONAL	1	TRUE	1	0.168168165169184	2		586	565	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88677065	88677065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765530074	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	49	307	0	ENST00000372037.3:c.850C>T	p.Arg284Cys	p.R284C	ENST00000372037	NM_004329.2	284	Cgc/Tgc	9/13	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.168168165169184	2		307	393	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	102	546	3	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	0.168168165169184	2	FACETS	0.808	0.722	0.898	0.808	0.722	0.898	CLONAL	2	TRUE	0	0.168168165169184	2		549	751	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	56	477	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.168168165169184	2		477	592	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	65	568	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.168168165169184	2		568	657	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097751	27097751	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	105	576	0	ENST00000324856.7:c.3344del	p.Pro1115GlnfsTer46	p.P1115Qfs*46	ENST00000324856	NM_006015.4	1114	Ccc/cc	12/20	0.168168165169184	2	FACETS	0.943	0.846	1	0.943	0.846	1	CLONAL	2	TRUE	0	0.168168165169184	2		576	662	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609094	43609094	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	75	747	0	ENST00000355710.3:c.1850A>T	p.Lys617Met	p.K617M	ENST00000355710	NM_020975.4	617	aAg/aTg	10/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.168168165169184	2		747	763	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717621	89717621	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1554825160	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	43	363	0	ENST00000371953.3:c.646del	p.Val216TrpfsTer5	p.V216Wfs*5	ENST00000371953	NM_000314.4	216	Gtg/tg	7/9	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.168168165169184	2		363	477	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	50	427	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.168168165169184	2		427	565	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200086	67200086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377609182	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	56	500	0	ENST00000312629.5:c.473C>T	p.Thr158Met	p.T158M	ENST00000312629	NM_003952.2	158	aCg/aTg	6/15	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.168168165169184	2		500	568	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941843	71941843	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514511	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	43	508	0	ENST00000298229.2:c.1201C>T	p.Arg401Trp	p.R401W	ENST00000298229	NM_001567.3	401	Cgg/Tgg	11/28	1	2	FACETS	0.935	0.782	1	0.935	0.782	1	CLONAL	1	TRUE	1	0.168168165169184	2		508	547	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943379	71943379	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1165709765	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	62	616	0	ENST00000298229.2:c.1711C>T	p.Arg571Trp	p.R571W	ENST00000298229	NM_001567.3	571	Cgg/Tgg	14/28	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.168168165169184	2		616	699	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94910931	94910931	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1166940410	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	47	414	0	ENST00000536441.1:c.1199T>C	p.Met400Thr	p.M400T	ENST00000536441	NM_144665.3	400	aTg/aCg	8/10	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.168168165169184	2		414	485	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	35	370	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.907	0.743	1	0.907	0.743	1	CLONAL	1	TRUE	1	0.168168165169184	2		370	459	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343855	118343855	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458634194	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	82	646	0	ENST00000534358.1:c.1981G>A	p.Val661Ile	p.V661I	ENST00000534358	NM_005933.3	661	Gtt/Att	3/36	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.168168165169184	2		646	792	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926270	112926270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918457	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	49	399	0	ENST00000351677.2:c.1403C>T	p.Thr468Met	p.T468M	ENST00000351677	NM_002834.3	468	aCg/aTg	12/16	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.168168165169184	2		399	513	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794732	120794732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276733276	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	59	568	0	ENST00000257552.2:c.625G>A	p.Ala209Thr	p.A209T	ENST00000257552	NM_002442.3	209	Gcc/Acc	9/15	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.168168165169184	2		568	666	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50769067	50769067	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763116964	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	46	402	0	ENST00000307179.4:c.871C>T	p.Arg291Cys	p.R291C	ENST00000307179		291	Cgc/Tgc	9/20	1	2	FACETS	0.918	0.772	1	0.918	0.772	1	CLONAL	1	TRUE	1	0.168168165169184	2		402	596	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346912	89346912	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745685018	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	65	649	0	ENST00000301030.4:c.6038C>T	p.Ala2013Val	p.A2013V	ENST00000301030	NM_001256183.1	2013	gCg/gTg	9/13	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.168168165169184	2		649	531	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357066	89357066	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	61	642	0	ENST00000301030.4:c.568G>A	p.Glu190Lys	p.E190K	ENST00000301030	NM_001256183.1	190	Gag/Aag	6/13	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.168168165169184	2		642	660	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984848	11984848	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	31	372	0	ENST00000353533.5:c.393+1G>A		p.X131_splice	ENST00000353533	NM_003010.3	131			1	2	FACETS	0.807	0.652	0.982	0.807	0.652	0.982	CLONAL	1	TRUE	1	0.168168165169184	2		372	457	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40460306	40460306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	66	560	0	ENST00000345506.4:c.2017C>T	p.Arg673Cys	p.R673C	ENST00000345506	NM_003152.3	673	Cgc/Tgc	17/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.168168165169184	2		560	615	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39600627	39600627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774620242	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	58	399	1	ENST00000262039.4:c.1442C>T	p.Ser481Leu	p.S481L	ENST00000262039	NM_002647.2	481	tCg/tTg	13/25	1	2	FACETS	0.793	0.683	0.912	1	0.971	1	CLONAL	2	TRUE	1	0.168168165169184	2		400	435	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231557	5231557	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150939732	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	42	445	0	ENST00000357368.4:c.1919G>A	p.Arg640His	p.R640H	ENST00000357368	NM_002850.3	640	cGc/cAc	14/38	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.168168165169184	2		445	428	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221277	36221277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1391848136	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	72	676	0	ENST00000222270.7:c.5111G>A	p.Arg1704His	p.R1704H	ENST00000222270	NM_014727.1	1704	cGc/cAc	24/37	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.168168165169184	2		676	695	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224505	36224505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs942168751	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	66	674	0	ENST00000222270.7:c.6967C>T	p.Arg2323Cys	p.R2323C	ENST00000222270	NM_014727.1	2323	Cgt/Tgt	29/37	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.168168165169184	2		674	677	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424397	47424397	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	60	625	0	ENST00000404338.3:c.2465T>C	p.Leu822Pro	p.L822P	ENST00000404338	NM_004491.4	822	cTt/cCt	1/6	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.168168165169184	2		625	660	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918729	50918729	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367680864	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	47	483	2	ENST00000440232.2:c.2599G>A	p.Val867Ile	p.V867I	ENST00000440232	NM_002691.3	867	Gtc/Atc	21/27	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.168168165169184	2		485	510	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	44	518	5	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	TRUE	1	0.168168165169184	2		523	520	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966853	25966853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201533674	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	82	732	0	ENST00000435504.4:c.2353G>A	p.Val785Ile	p.V785I	ENST00000435504		785	Gtc/Atc	13/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.168168165169184	2		732	765	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583310	46583310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770783327	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	75	495	0	ENST00000263734.3:c.238G>A	p.Glu80Lys	p.E80K	ENST00000263734	NM_001430.4	80	Gaa/Aaa	3/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.168168165169184	2		495	621	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670789	134670789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368276671	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	64	543	1	ENST00000398015.3:c.700G>A	p.Val234Met	p.V234M	ENST00000398015	NM_004441.4	234	Gtg/Atg	3/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.168168165169184	2		544	599	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144381543	144381543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	73	509	0	ENST00000262995.4:c.1796G>A	p.Arg599Gln	p.R599Q	ENST00000262995	NM_207123.2	599	cGa/cAa	9/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.168168165169184	2		509	649	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279521	1279521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1353891039	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	64	520	0	ENST00000310581.5:c.2015G>A	p.Arg672His	p.R672H	ENST00000310581	NM_198253.2	672	cGc/cAc	5/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.168168165169184	2		520	511	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	40	451	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	0.868	0.721	1	0.868	0.721	1	CLONAL	1	TRUE	1	0.168168165169184	2		451	548	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589582	67589582	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	36	341	0	ENST00000274335.5:c.1346del	p.Leu449TyrfsTer31	p.L449Yfs*31	ENST00000274335		449	Tta/ta	10/15	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.168168165169184	2		341	406	SUCCESS
APC	324	MSKCC	GRCh37	5	112179453	112179453	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780606	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	66	578	0	ENST00000257430.4:c.8162G>A	p.Arg2721His	p.R2721H	ENST00000257430	NM_000038.5	2721	cGc/cAc	16/16	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.168168165169184	2		578	695	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117632202	117632202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139881304	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	44	367	1	ENST00000368508.3:c.6214C>T	p.Arg2072Trp	p.R2072W	ENST00000368508	NM_002944.2	2072	Cgg/Tgg	39/43	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.168168165169184	2		368	489	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411576	116411576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759522148	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	60	446	0	ENST00000397752.3:c.2755G>A	p.Val919Ile	p.V919I	ENST00000397752	NM_000245.2	919	Gtc/Atc	13/21	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.168168165169184	2		446	583	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325704	87325704	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	53	422	0	ENST00000277120.3:c.581G>A	p.Cys194Tyr	p.C194Y	ENST00000277120		194	tGt/tAt	6/19	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.168168165169184	2		422	491	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570254	87570254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747525829	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	61	625	1	ENST00000277120.3:c.1994C>T	p.Thr665Met	p.T665M	ENST00000277120		665	aCg/aTg	17/19	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.168168165169184	2		626	579	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127911983	127911983	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	74	487	0	ENST00000373547.4:c.887C>A	p.Pro296His	p.P296H	ENST00000373547	NM_002721.4	296	cCt/cAt	7/7	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.168168165169184	2		487	609	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776176	135776176	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	69	560	0	ENST00000298552.3:c.2551C>T	p.Gln851Ter	p.Q851*	ENST00000298552	NM_001162426.1	851	Cag/Tag	20/23	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.168168165169184	2		560	682	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223853	53223853	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	71	649	0	ENST00000375401.3:c.3506C>T	p.Ser1169Leu	p.S1169L	ENST00000375401	NM_004187.3	1169	tCg/tTg	23/26	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.168168165169184	2		649	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0063017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	84	423	0	ENST00000269305.4:c.838A>T	p.Arg280Ter	p.R280*	ENST00000269305	NM_001126112.2	280	Aga/Tga	8/11	0.34378353570854	1	FACETS	0.907	0.805	1	0.907	0.805	1	CLONAL	1	TRUE	0	0.34378353570854	1		423	446	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950660	38950660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759204549	NA	P-0063017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	44	385	1	ENST00000357387.3:c.3290G>A	p.Arg1097His	p.R1097H	ENST00000357387	NM_152756.3	1097	cGt/cAt	31/38	0.34378353570854	3	FACETS	0.437	0.366	0.517	0.219	0.183	0.259	SUBCLONAL	1	TRUE	1	0.34378353570854	3		386	686	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40747863	40747863	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	66	358	0	ENST00000392038.2:c.555G>C	p.Lys185Asn	p.K185N	ENST00000392038	NM_001626.4	185	aaG/aaC	6/14	0.34378353570854	1	FACETS	0.862	0.752	0.979	0.862	0.752	0.979	CLONAL	1	TRUE	0	0.34378353570854	1		358	369	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	27	343	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.836	0.674	1	0.836	0.674	1	CLONAL	1	TRUE	1	0.454838265764556	2		343	142	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0063018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	212	622	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.454838265764556	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.454838265764556	2		622	392	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711950	89711950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	57	369	2	ENST00000371953.3:c.568C>T	p.Pro190Ser	p.P190S	ENST00000371953	NM_000314.4	190	Cca/Tca	6/9	0.454838265764556	1	FACETS	0.88	0.765	1	0.88	0.765	1	CLONAL	1	TRUE	0	0.454838265764556	1		371	220	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638557	176638557	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	51	621	0	ENST00000439151.2:c.3157A>G	p.Lys1053Glu	p.K1053E	ENST00000439151	NM_022455.4	1053	Aaa/Gaa	5/23	1	2	FACETS	0.402	0.341	0.469	0.402	0.341	0.469	SUBCLONAL	1	TRUE	1	0.454838265764556	2		621	558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0063019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	188	809	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.573219559072328	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.573219559072328	1		809	420	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56411728	56411728	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0063019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	26	276	0	ENST00000348428.3:c.1911+1G>C		p.X637_splice	ENST00000348428	NM_006785.3	637			0.573219559072328	5	FACETS	0.659	0.524	0.813	0.22	0.174	0.271	SUBCLONAL	1	TRUE	2	0.573219559072328	5		276	256	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719615	61719615	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	62	390	0	ENST00000401558.2:c.1568A>G	p.Asp523Gly	p.D523G	ENST00000401558	NM_003400.3	523	gAt/gGt	15/25	0.551891489218959	3	FACETS	1	0.896	1	0.515	0.449	0.586	CLONAL	1	TRUE	1	0.573219559072328	3		390	270	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775614	39775616	+	inframe_deletion	In_Frame_Del	DEL	TAC	TAC	-	novel	NA	P-0063019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	171	519	0	ENST00000288319.7:c.404_406del	p.Ser135del	p.S135del	ENST00000288319	NM_182918.3	135	aGTAca/aca	4/10	0.573219559072328	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.573219559072328	1		519	405	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42861490	42861490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1350156643	NA	P-0063019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	165	416	0	ENST00000398585.3:c.380C>T	p.Thr127Ile	p.T127I	ENST00000398585	NM_001135099.1	127	aCc/aTc	4/14	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.573219559072328	2		416	527	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845727	151845727	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	153	516	1	ENST00000262189.6:c.13285C>A	p.His4429Asn	p.H4429N	ENST00000262189	NM_170606.2	4429	Cac/Aac	52/59	0.54437754324421	2	FACETS	0.958	0.882	1	0.479	0.441	0.519	CLONAL	1	TRUE	0	0.573219559072328	2		517	557	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752711	128752711	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	164	438	0	ENST00000377970.2:c.872G>T	p.Arg291Met	p.R291M	ENST00000377970	NM_002467.4	291	aGg/aTg	3/3	0.551891489218959	3	FACETS	0.955	0.878	1	0.477	0.439	0.518	CLONAL	1	TRUE	1	0.573219559072328	3		438	771	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0063022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	324	869	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	0.629638529530468	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.622693497770919	2		869	476	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851544	63851544	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063022-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	31	602	0	ENST00000279873.7:c.2322G>C	p.Lys774Asn	p.K774N	ENST00000279873	NM_032199.2	774	aaG/aaC	10/10	0.629638529530468	1	FACETS	0.181	0.146	0.22	0.181	0.146	0.22	SUBCLONAL	1	TRUE	0	0.622693497770919	1		602	379	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0063023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	58	556	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.643	0.559	0.733	0.643	0.559	0.733	SUBCLONAL	1	TRUE	1	0.730050091451026	2		556	247	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	73	567	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	0.526	0.463	0.594	0.526	0.463	0.594	SUBCLONAL	1	TRUE	1	0.730050091451026	2		567	380	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519886	NA	P-0063023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	92	636	0	ENST00000349496.5:c.97T>C	p.Ser33Pro	p.S33P	ENST00000349496	NM_001904.3	33	Tct/Cct	3/15	1	2	FACETS	0.51	0.455	0.569	0.51	0.455	0.569	SUBCLONAL	1	TRUE	1	0.730050091451026	2		636	494	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0063023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	13	749	0	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	1	2	FACETS	0.079	0.055	0.107	0.079	0.055	0.107	SUBCLONAL	1	TRUE	1	0.730050091451026	2		749	453	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023652	27023653	+	frameshift_variant	Frame_Shift_Ins	INS	CC	CC	GGA	novel	NA	P-0063023-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	47	650	1	ENST00000324856.7:c.758_759delinsGGA	p.Pro253ArgfsTer147	p.P253Rfs*147	ENST00000324856	NM_006015.4	253	cCC/cGGA	1/20	1	2	FACETS	0.515	0.438	0.598	0.515	0.438	0.598	SUBCLONAL	1	TRUE	1	0.730050091451026	2		651	250	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988433	41988433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063024-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	274	685	2	ENST00000219905.7:c.1225G>A	p.Glu409Lys	p.E409K	ENST00000219905	NM_001164273.1	409	Gaa/Aaa	3/24	1	2	FACETS	0.978	0.925	1	0.978	0.925	1	CLONAL	1	TRUE	1	0.859405150726475	2		687	652	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632279	215632279	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063024-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	245	666	2	ENST00000260947.4:c.1495C>T	p.His499Tyr	p.H499Y	ENST00000260947	NM_000465.2	499	Cac/Tac	6/11	0.859405150726475	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.859405150726475	1		668	304	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844139	68844139	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063024-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	272	884	0	ENST00000261769.5:c.727G>C	p.Glu243Gln	p.E243Q	ENST00000261769	NM_004360.3	243	Gag/Cag	6/16	0.817326279093784	4	FACETS	0.894	0.838	0.953	0.298	0.279	0.318	CLONAL	1	TRUE	1	0.859405150726475	4		884	1316	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149290705	149290705	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063024-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	144	508	0	ENST00000360632.3:c.514G>C	p.Val172Leu	p.V172L	ENST00000360632	NM_015472.4	172	Gtc/Ctc	3/7	0.218181935658642	4	FACETS	0.84	0.767	0.916	0.42	0.383	0.458	INDETERMINATE	1	TRUE	2	0.859405150726475	4		508	742	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873749	151873749	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0063024-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	1123	934	0	ENST00000262189.6:c.8789C>G	p.Ser2930Ter	p.S2930*	ENST00000262189	NM_170606.2	2930	tCa/tGa	38/59	0.859405150726475	4	FACETS	1	0.996	1	1	0.996	1	CLONAL	4	TRUE	0	0.859405150726475	4		934	1202	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905960	50905960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777944185	NA	P-0063024-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	292	1066	0	ENST00000440232.2:c.932G>A	p.Arg311His	p.R311H	ENST00000440232	NM_002691.3	311	cGc/cAc	8/27	0.56153040124172	1	FACETS	0.658	0.625	0.691	0.658	0.625	0.691	SUBCLONAL	1	TRUE	0	0.859405150726475	1		1066	589	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781374	3781374	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063024-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	767	976	1	ENST00000262367.5:c.4991G>A	p.Arg1664His	p.R1664H	ENST00000262367	NM_004380.2	1664	cGc/cAc	30/31	0.859405150726475	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.859405150726475	2		977	857	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670591	134670591	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063024-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	288	626	0	ENST00000398015.3:c.502C>G	p.Leu168Val	p.L168V	ENST00000398015	NM_004441.4	168	Ctt/Gtt	3/16	1	2	FACETS	0.941	0.891	0.992	0.941	0.891	0.992	CLONAL	1	TRUE	1	0.859405150726475	2		626	712	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486041	8486041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063024-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	302	655	0	ENST00000356435.5:c.2776C>T	p.His926Tyr	p.H926Y	ENST00000356435		926	Cac/Tac	17/35	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.859405150726475	2		655	699	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532590	187532590	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063024-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	267	492	0	ENST00000441802.2:c.9803C>A	p.Ser3268Ter	p.S3268*	ENST00000441802	NM_005245.3	3268	tCa/tAa	14/27	1	2	FACETS	0.999	0.944	1	0.999	0.944	1	CLONAL	1	TRUE	1	0.859405150726475	2		492	622	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243859016	243859016	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063024-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	194	479	0	ENST00000263826.5:c.49G>C	p.Glu17Gln	p.E17Q	ENST00000263826	NM_005465.4	17	Gaa/Caa	2/13	0.852955297824881	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.859405150726475	1		479	251	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575049	64575049	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs386134259	NA	P-0063024-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	662	801	1	ENST00000312049.6:c.758C>A	p.Ser253Ter	p.S253*	ENST00000312049	NM_130799.2	253	tCg/tAg	4/10	0.859405150726475	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.859405150726475	3		802	1057	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343756	118343756	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063024-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	244	714	0	ENST00000534358.1:c.1882G>A	p.Glu628Lys	p.E628K	ENST00000534358	NM_005933.3	628	Gag/Aag	3/36	1	2	FACETS	0.838	0.787	0.889	0.838	0.787	0.889	CLONAL	1	TRUE	1	0.859405150726475	2		714	678	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427273	49427273	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063024-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	321	710	0	ENST00000301067.7:c.11215C>T	p.Gln3739Ter	p.Q3739*	ENST00000301067	NM_003482.3	3739	Cag/Tag	39/54	1	2	FACETS	0.971	0.922	1	0.971	0.922	1	CLONAL	1	TRUE	1	0.859405150726475	2		710	769	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432335	49432335	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0063024-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	385	1234	0	ENST00000301067.7:c.8804C>G	p.Ser2935Ter	p.S2935*	ENST00000301067	NM_003482.3	2935	tCa/tGa	34/54	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.859405150726475	2		1234	892	SUCCESS
ALK	238	MSKCC	GRCh37	2	29419654	29419654	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063024-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	238	466	0	ENST00000389048.3:c.4146G>C	p.Arg1382Ser	p.R1382S	ENST00000389048	NM_004304.4	1382	agG/agC	28/29	1	2	FACETS	0.952	0.896	1	0.952	0.896	1	CLONAL	1	TRUE	1	0.859405150726475	2		466	582	SUCCESS
ATR	545	MSKCC	GRCh37	3	142234275	142234275	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063024-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	237	404	1	ENST00000350721.4:c.4465G>C	p.Glu1489Gln	p.E1489Q	ENST00000350721	NM_001184.3	1489	Gaa/Caa	25/47	0.218181935658642	4	FACETS	1	0.971	1	1	0.971	1	INDETERMINATE	2	TRUE	2	0.859405150726475	4		405	491	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707627	176707628	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0063024-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	565	762	0	ENST00000439151.2:c.5684_5685delinsTT	p.Cys1895Phe	p.C1895F	ENST00000439151	NM_022455.4	1895	tGC/tTT	18/23	0.859405150726475	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.859405150726475	2		762	656	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450358	50450358	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063024-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	143	930	1	ENST00000331340.3:c.542C>A	p.Ala181Asp	p.A181D	ENST00000331340	NM_006060.4	181	gCc/gAc	5/8	0.491081522997305	1	FACETS	0.357	0.327	0.389	0.357	0.327	0.389	INDETERMINATE	1	TRUE	0	0.859405150726475	1		931	531	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336335	80336335	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063024-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	289	742	0	ENST00000286548.4:c.984C>G	p.Phe328Leu	p.F328L	ENST00000286548	NM_002072.3	328	ttC/ttG	7/7	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.859405150726475	2		742	616	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650832	93650832	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063024-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	245	604	0	ENST00000375746.1:c.1758G>C	p.Glu586Asp	p.E586D	ENST00000375746	NM_001174167.1	586	gaG/gaC	13/14	1	2	FACETS	0.932	0.877	0.987	0.932	0.877	0.987	CLONAL	1	TRUE	1	0.859405150726475	2		604	612	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934094	39934094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063024-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	237	832	0	ENST00000378444.4:c.505G>A	p.Asp169Asn	p.D169N	ENST00000378444	NM_001123385.1	169	Gac/Aac	4/15	0.478536524526441	3	FACETS	0.803	0.75	0.858	0.401	0.375	0.429	INDETERMINATE	1	TRUE	1	0.859405150726475	3		832	982	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045930	26045930	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063024-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	384	811	0	ENST00000540144.1:c.292G>C	p.Glu98Gln	p.E98Q	ENST00000540144	NM_003531.2	98	Gag/Cag	1/1	0.218181935658642	4	FACETS	0.886	0.845	0.927	0.886	0.845	0.927	INDETERMINATE	2	TRUE	2	0.859405150726475	4		811	938	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880867	28880867	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	112	589	0	ENST00000282397.4:c.3763C>G	p.Leu1255Val	p.L1255V	ENST00000282397	NM_002019.4	1255	Ctg/Gtg	29/30	0.341699317521829	1	FACETS	0.652	0.589	0.717	0.652	0.589	0.717	SUBCLONAL	1	TRUE	0	0.533768517203514	1		589	472	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871110	35871462	+	splice_acceptor_variant,coding_sequence_variant,3_prime_UTR_variant,intron_variant	Splice_Site	DEL	GGATATAAGTACACCCTTTAAATTTTTTCTTCTTTTTTCTTTTTTTAGAAAAATAAAACTTTTTTTTTGTACAAATATACAAGTCCATGTTCTTTCAGCCCCTTTGCGCTCATAACGTCAGACGCTGGCCTCCAAACACACAGTCATCATAGGGCAGCTGAAAACAAGGGGAAAAAAGACACGTTAAGCTTCCGGAGCGGAGCTCTGCCAAGCTACCGGGATGGGGAGGCCACTACTGGAAATAACTCTTGGACTCCATTCTCCATAGCCCAAATATAATGAACTTTACAGGCTGAGAGAGTTTGCCTTTAATGCTTCTCTTTAAAAAAAGAGGGGGGGCAGGTACATTCTTG	GGATATAAGTACACCCTTTAAATTTTTTCTTCTTTTTTCTTTTTTTAGAAAAATAAAACTTTTTTTTTGTACAAATATACAAGTCCATGTTCTTTCAGCCCCTTTGCGCTCATAACGTCAGACGCTGGCCTCCAAACACACAGTCATCATAGGGCAGCTGAAAACAAGGGGAAAAAAGACACGTTAAGCTTCCGGAGCGGAGCTCTGCCAAGCTACCGGGATGGGGAGGCCACTACTGGAAATAACTCTTGGACTCCATTCTCCATAGCCCAAATATAATGAACTTTACAGGCTGAGAGAGTTTGCCTTTAATGCTTCTCTTTAAAAAAAGAGGGGGGGCAGGTACATTCTTG	-	novel	NA	P-0063025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	21	95	0	ENST00000216797.5:c.906+138_*109del		p.X302_splice	ENST00000216797	NM_020529.2	302		6/6	1	2	FACETS	0.735	0.576	0.915	0.735	0.576	0.915	CLONAL	1	TRUE	1	0.533768517203514	2		95	107	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221599	2221601	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0063025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	123	629	0	ENST00000326181.6:c.469_471del	p.Lys157del	p.K157del	ENST00000326181	NM_032271.2	156	ttGAAg/ttg	7/21	1	2	FACETS	0.989	0.9	1	0.989	0.9	1	CLONAL	1	TRUE	1	0.533768517203514	2		629	466	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900698	3900698	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	166	694	0	ENST00000262367.5:c.398del	p.Leu133ArgfsTer19	p.L133Rfs*19	ENST00000262367	NM_004380.2	133	cTg/cg	2/31	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.533768517203514	2		694	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7590692	7590715	+	splice_donor_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	TACCCAATCCAGGGAAGCGTGTCA	TACCCAATCCAGGGAAGCGTGTCA	-	novel	NA	P-0063025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	168	532	0	ENST00000269305.4:c.-49_-29+3del		p.X17_splice	ENST00000269305	NM_001126112.2	17		1/11	0.518613310784741	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.533768517203514	1		532	441	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384958	17384958	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	119	618	0	ENST00000359435.4:c.508C>G	p.Leu170Val	p.L170V	ENST00000359435	NM_001033549.1	170	Ctc/Gtc	5/9	1	2	FACETS	0.925	0.84	1	0.925	0.84	1	CLONAL	1	TRUE	1	0.533768517203514	2		618	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0063026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	48	801	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.485856550052771	1	FACETS	0.878	0.758	1	0.878	0.758	1	CLONAL	1	TRUE	0	0.534091922811527	1		804	150	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513371	106513371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765080806	NA	P-0063026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	24	347	0	ENST00000359195.3:c.2275G>A	p.Val759Ile	p.V759I	ENST00000359195	NM_002649.2	759	Gtc/Atc	4/11	0.3266331608309	1	FACETS	0.578	0.461	0.708	0.578	0.461	0.708	SUBCLONAL	1	TRUE	0	0.534091922811527	1		347	114	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004349	150004349	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	37	399	0	ENST00000253339.5:c.1876C>T	p.Arg626Ter	p.R626*	ENST00000253339		626	Cga/Tga	3/7	0.206976954236687	1	FACETS	0.923	0.781	1	0.923	0.781	1	INDETERMINATE	1	TRUE	0	0.534091922811527	1		399	110	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220333	98220333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138458710	NA	P-0063026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	61	416	0	ENST00000331920.6:c.3130G>A	p.Ala1044Thr	p.A1044T	ENST00000331920	NM_000264.3	1044	Gct/Act	18/24	0.258722793843541	1	FACETS	0.821	0.719	0.927	0.821	0.719	0.927	INDETERMINATE	1	TRUE	0	0.534091922811527	1		416	204	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323193	31323193	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	54	616	0	ENST00000412585.2:c.796C>T	p.Gln266Ter	p.Q266*	ENST00000412585	NM_005514.6	266	Cag/Tag	4/8	0.206976954236687	1	FACETS	0.524	0.451	0.602	0.524	0.451	0.602	INDETERMINATE	1	TRUE	0	0.534091922811527	1		616	283	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980318	201980319	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	67	508	0	ENST00000359651.3:c.55dup	p.Tyr19LeufsTer21	p.Y19Lfs*21	ENST00000359651		18	-/T	1/8	0.206976954236687	1	FACETS	0.821	0.724	0.922	0.821	0.724	0.922	INDETERMINATE	1	TRUE	0	0.534091922811527	1		508	224	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102874097	102874097	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	50	297	0	ENST00000307046.8:c.63G>T	p.Lys21Asn	p.K21N	ENST00000307046	NM_001111285.1	21	aaG/aaT	1/4	1	2	FACETS	0.814	0.713	0.917	1	0.974	1	CLONAL	2	TRUE	1	0.534091922811527	2		297	115	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489465	40489465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451984094	NA	P-0063026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	30	431	1	ENST00000264657.5:c.785G>A	p.Arg262Gln	p.R262Q	ENST00000264657	NM_139276.2	262	cGg/cAg	8/24	0.512272553411805	2	FACETS	0.677	0.551	0.815	0.338	0.275	0.408	SUBCLONAL	1	TRUE	0	0.534091922811527	2		432	166	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670634	134670634	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	26	505	0	ENST00000398015.3:c.545C>A	p.Ala182Asp	p.A182D	ENST00000398015	NM_004441.4	182	gCc/gAc	3/16	0.211647184250237	0	FACETS	0.44	0.356	0.532			1	INDETERMINATE	1	TRUE	0	0.534091922811527	0		505	103	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0063032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	184	329	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	0.585739787733806	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	1	0.585739787733806	4		329	309	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029169	26029169	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	193	403	0	ENST00000435504.4:c.181del	p.His61ThrfsTer23	p.H61Tfs*23	ENST00000435504		61	Cac/ac	4/13	0.444459285284803	4	FACETS	1	0.981	1	0.814	0.769	0.857	CLONAL	3	TRUE	0	0.585739787733806	4		403	321	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958866	55958866	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs892780242	NA	P-0063032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	267	351	0	ENST00000263923.4:c.2987A>G	p.Tyr996Cys	p.Y996C	ENST00000263923	NM_002253.2	996	tAt/tGt	22/30	0.585739787733806	5	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	2	0.585739787733806	5		351	494	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0063033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	50	387	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.871	0.742	1	0.871	0.742	1	CLONAL	1	TRUE	1	0.325117085564691	2		387	353	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856403	111856403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749162265	NA	P-0063033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	133	509	0	ENST00000341259.2:c.454G>A	p.Gly152Arg	p.G152R	ENST00000341259	NM_005475.2	152	Ggg/Agg	2/8	1	2	FACETS	0.92	0.835	1	0.92	0.835	1	CLONAL	1	TRUE	1	0.325117085564691	2		509	889	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633146	3633146	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	134	551	0	ENST00000294008.3:c.5105C>A	p.Ser1702Tyr	p.S1702Y	ENST00000294008	NM_032444.2	1702	tCc/tAc	14/15	1	2	FACETS	0.904	0.821	0.991	0.904	0.821	0.991	CLONAL	1	TRUE	1	0.325117085564691	2		551	912	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578266	+	missense_variant	Missense_Mutation	DNP	AT	AT	GC	novel	NA	P-0063033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	140	641	1	ENST00000269305.4:c.583_584delinsGC	p.Ile195Ala	p.I195A	ENST00000269305	NM_001126112.2	195	ATc/GCc	6/11	0.28930327080481	1	FACETS	0.886	0.807	0.969	0.886	0.807	0.969	CLONAL	1	TRUE	0	0.325117085564691	1		642	814	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149864	99149864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199762176	NA	P-0063033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	93	376	0	ENST00000074304.5:c.176C>T	p.Ser59Leu	p.S59L	ENST00000074304	NM_001134224.1	59	tCg/tTg	5/26	1	2	FACETS	0.834	0.742	0.932	0.834	0.742	0.932	CLONAL	1	TRUE	1	0.325117085564691	2		376	686	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0063035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	1126	855	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.57062080176803	6	FACETS	1	0.999	1			1	CLONAL	6	TRUE	NA	0.9029578269196	6		857	1140	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715880	61715880	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	150	411	0	ENST00000401558.2:c.2049A>T	p.Glu683Asp	p.E683D	ENST00000401558	NM_003400.3	683	gaA/gaT	18/25	0.9029578269196	3	FACETS	0.97	0.893	1	0.485	0.446	0.525	CLONAL	1	TRUE	1	0.9029578269196	3		411	497	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0063036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	62	387	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.9	0.782	1	0.9	0.782	1	CLONAL	1	TRUE	1	0.422757761810081	2		387	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0063036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	190	801	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.422757761810081	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.422757761810081	1		804	654	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	121	468	0	ENST00000267101.3:c.310G>C	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ctg	3/28	1	2	FACETS	0.919	0.832	1	0.919	0.832	1	CLONAL	1	TRUE	1	0.422757761810081	2		468	623	SUCCESS
APC	324	MSKCC	GRCh37	5	112175273	112175273	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123121	NA	P-0063036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	368	528	0	ENST00000257430.4:c.3982C>T	p.Gln1328Ter	p.Q1328*	ENST00000257430	NM_000038.5	1328	Cag/Tag	16/16	0.422757761810081	3	FACETS	0.985	0.942	1	0.985	0.942	1	CLONAL	3	TRUE	0	0.422757761810081	3		528	714	SUCCESS
AR	367	MSKCC	GRCh37	X	66766441	66766441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	70	359	2	ENST00000374690.3:c.1453C>T	p.Arg485Trp	p.R485W	ENST00000374690	NM_000044.3	485	Cgg/Tgg	1/8	1	2	FACETS	0.843	0.738	0.954	0.843	0.738	0.954	CLONAL	1	TRUE	1	0.422757761810081	2		361	393	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959063	2959063	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41497250	NA	P-0063036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	524	569	0	ENST00000396946.4:c.2453G>A	p.Arg818Gln	p.R818Q	ENST00000396946	NM_032415.4	818	cGg/cAg	18/25	0.422757761810081	5	FACETS	0.959	0.924	0.995	0.959	0.924	0.995	CLONAL	4	TRUE	1	0.422757761810081	5		569	1056	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391014	139391014	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	160	688	0	ENST00000277541.6:c.7177C>T	p.Gln2393Ter	p.Q2393*	ENST00000277541	NM_017617.3	2393	Cag/Tag	34/34	1	2	FACETS	0.949	0.871	1	0.949	0.871	1	CLONAL	1	TRUE	1	0.422757761810081	2		688	798	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423553	88423553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	160	441	0	ENST00000360948.2:c.2282G>A	p.Trp761Ter	p.W761*	ENST00000360948	NM_001012338.2	761	tGg/tAg	18/19	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.422757761810081	2		441	639	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678200	58678201	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0063036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	137	609	1	ENST00000305921.3:c.425_426delinsAT	p.Ile142Asn	p.I142N	ENST00000305921	NM_003620.3	142	aTC/aAT	1/6	1	2	FACETS	0.921	0.839	1	0.921	0.839	1	CLONAL	1	TRUE	1	0.422757761810081	2		610	704	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31401578	31401579	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	rs772793274	NA	P-0063036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	105	347	0	ENST00000344624.3:c.4085_4086del	p.Gln1362ArgfsTer6	p.Q1362Rfs*6	ENST00000344624		1362	cAA/c	33/33	1	2	FACETS	0.991	0.892	1	0.991	0.892	1	CLONAL	1	TRUE	1	0.422757761810081	2		347	501	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932288	39932288	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs755710383	NA	P-0063036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	151	608	0	ENST00000378444.4:c.2311A>G	p.Ser771Gly	p.S771G	ENST00000378444	NM_001123385.1	771	Agc/Ggc	4/15	1	2	FACETS	0.918	0.84	0.999	0.918	0.84	0.999	CLONAL	1	TRUE	1	0.422757761810081	2		608	778	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0063037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	97	1032	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.191430035285001	3	FACETS	0.889	0.803	0.977	0.592	0.535	0.651	INDETERMINATE	2	FALSE	0	0.469689622247784	3		1032	287	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0063037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	125	343	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.956	0.868	1	0.956	0.868	1	CLONAL	1	FALSE	1	0.469689622247784	2		343	557	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441821	49441822	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CG	novel	NA	P-0063037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	305	477	0	ENST00000301067.7:c.4162_4163insCG	p.Arg1388ProfsTer30	p.R1388Pfs*30	ENST00000301067	NM_003482.3	1388	cgg/cCGgg	14/54	0.191430035285001	3	FACETS	0.913	0.863	0.964	0.609	0.575	0.643	INDETERMINATE	2	FALSE	0	0.469689622247784	3		477	878	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347141	347141	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	133	503	0	ENST00000262320.3:c.1870G>A	p.Glu624Lys	p.E624K	ENST00000262320	NM_003502.3	624	Gag/Aag	7/11	0.469689622247784	3	FACETS	0.8	0.726	0.878	0.4	0.363	0.439	SUBCLONAL	1	FALSE	1	0.469689622247784	3		503	874	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956783	68956783	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	36	373	0	ENST00000288368.4:c.901A>C	p.Asn301His	p.N301H	ENST00000288368	NM_024870.2	301	Aac/Cac	8/40	1	2	FACETS	0.257	0.211	0.31	0.257	0.211	0.31	SUBCLONAL	1	FALSE	1	0.469689622247784	2		373	596	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	209	343	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.912	0.853	0.973	0.912	0.853	0.973	CLONAL	1	TRUE	1	0.78469256469518	2		343	584	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0063038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	284	513	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.78469256469518	2		513	671	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480352	89480352	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	35	418	0	ENST00000336596.2:c.2189T>G	p.Ile730Arg	p.I730R	ENST00000336596	NM_005233.5	730	aTa/aGa	13/17	1	2	FACETS	0.132	0.107	0.16	0.132	0.107	0.16	SUBCLONAL	1	TRUE	1	0.78469256469518	2		418	676	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798872	42798886	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GGCTTCTTCCCGTCA	GGCTTCTTCCCGTCA	-	novel	NA	P-0063038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	136	613	0	ENST00000575354.2:c.4446_4459+1del		p.GFFPSdel	ENST00000575354	NM_015125.3	1482	GGCTTCTTCCCGTCA/-	19/20	0.78469256469518	1	FACETS	0.431	0.394	0.469	0.431	0.394	0.469	SUBCLONAL	1	TRUE	0	0.78469256469518	1		613	489	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0063039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	20	241	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.862	0.66	1	0.862	0.66	1	CLONAL	1	TRUE	1	0.16	2		241	290	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0063039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	24	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.716	0.561	0.896	0.716	0.561	0.896	SUBCLONAL	1	TRUE	1	0.16	2		434	419	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0063040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	87	387	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.303570828800913	3	FACETS	0.767	0.685	0.852	0.767	0.685	0.852	SUBCLONAL	2	TRUE	1	0.42940381248751	3		387	321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0063040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	140	746	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.308146741845078	2	FACETS	1	0.984	1	0.656	0.601	0.713	CLONAL	1	TRUE	0	0.42940381248751	2		746	497	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0063040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	27	304	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.495	0.395	0.608	0.495	0.395	0.608	SUBCLONAL	1	TRUE	1	0.42940381248751	2		304	254	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	45	361	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	0.678	0.573	0.794	0.678	0.573	0.794	SUBCLONAL	1	TRUE	1	0.42940381248751	2		361	309	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160392	99160392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377398401	NA	P-0063040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	140	533	0	ENST00000074304.5:c.871C>T	p.Arg291Trp	p.R291W	ENST00000074304	NM_001134224.1	291	Cgg/Tgg	11/26	0.26793215339824	5	FACETS	0.838	0.765	0.913	0.558	0.51	0.609	CLONAL	2	TRUE	2	0.42940381248751	5		533	640	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229441	36229441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	34	543	0	ENST00000222270.7:c.8131C>T	p.Arg2711Cys	p.R2711C	ENST00000222270	NM_014727.1	2711	Cgt/Tgt	37/37	0.361104117679937	3	FACETS	0.41	0.335	0.495	0.205	0.167	0.248	SUBCLONAL	1	TRUE	1	0.42940381248751	3		543	469	SUCCESS
APC	324	MSKCC	GRCh37	5	112175630	112175630	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	84	543	0	ENST00000257430.4:c.4339del	p.Gln1447LysfsTer26	p.Q1447Kfs*26	ENST00000257430	NM_000038.5	1447	Caa/aa	16/16	1	2	FACETS	0.757	0.67	0.849	0.757	0.67	0.849	SUBCLONAL	1	TRUE	1	0.42940381248751	2		543	517	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203809	94203809	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0063040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	79	323	0	ENST00000323929.3:c.846-1G>A		p.X282_splice	ENST00000323929	NM_005591.3	282			0.320472033160108	6	FACETS	0.775	0.685	0.872	0.388	0.342	0.436	SUBCLONAL	2	TRUE	2	0.42940381248751	6		323	441	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443837	18443837	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	29	346	0	ENST00000266497.5:c.810G>T	p.Lys270Asn	p.K270N	ENST00000266497		270	aaG/aaT	3/31	0.303570828800913	3	FACETS	0.47	0.377	0.575	0.235	0.188	0.288	SUBCLONAL	1	TRUE	1	0.42940381248751	3		346	349	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0063041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	160	204	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.211068911926647	3	FACETS	1	0.975	1	1	0.991	1	CLONAL	3	TRUE	1	0.211068911926647	3		204	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	170	670	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.211068911926647	1	FACETS	0.803	0.739	0.87	1	0.99	1	CLONAL	2	TRUE	0	0.211068911926647	1		670	897	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0063041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	72	350	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.211068911926647	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.211068911926647	1		350	472	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354007	15354008	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0063041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	31	240	3	ENST00000263377.2:c.2872dup	p.Leu958ProfsTer135	p.L958Pfs*135	ENST00000263377	NM_058243.2	958	ctg/cCtg	14/20	1	2	FACETS	0.807	0.653	0.981	0.807	0.653	0.981	CLONAL	1	TRUE	1	0.211068911926647	2		243	364	SUCCESS
APC	324	MSKCC	GRCh37	5	112175160	112175161	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0063041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	88	434	0	ENST00000257430.4:c.3869_3870del	p.Asn1290ThrfsTer10	p.N1290Tfs*10	ENST00000257430	NM_000038.5	1290	aAT/a	16/16	0.211068911926647	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.211068911926647	1		434	690	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760580	133760580	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	184	657	0	ENST00000318560.5:c.2903C>A	p.Ser968Tyr	p.S968Y	ENST00000318560	NM_005157.4	968	tCc/tAc	11/11	1	2	FACETS	0.798	0.736	0.863	1	0.991	1	SUBCLONAL	2	TRUE	1	0.211068911926647	2		657	1092	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0063042-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	101	462	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.157282276769918	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.204281603082561	4		462	500	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0063042-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	24	556	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.204281603082561	1	FACETS	1	0.792	1	1	0.792	1	CLONAL	1	TRUE	0	0.204281603082561	1		556	210	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0063042-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	70	529	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.159148111804264	1	FACETS	0.713	0.62	0.814	0.713	0.62	0.814	SUBCLONAL	1	TRUE	0	0.204281603082561	1		529	863	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248525	59248525	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063042-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	76	584	0	ENST00000371222.2:c.218C>A	p.Ser73Ter	p.S73*	ENST00000371222	NM_002228.3	73	tCg/tAg	1/1	0.159148111804264	1	FACETS	0.622	0.544	0.707	0.622	0.544	0.707	SUBCLONAL	1	TRUE	0	0.204281603082561	1		584	1074	SUCCESS
APC	324	MSKCC	GRCh37	5	112175773	112175774	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0063042-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	79	490	0	ENST00000257430.4:c.4483_4484dup	p.Ser1495ArgfsTer13	p.S1495Rfs*13	ENST00000257430	NM_000038.5	1494	-/AG	16/16	0.159148111804264	1	FACETS	0.782	0.686	0.885	0.782	0.686	0.885	SUBCLONAL	1	TRUE	0	0.204281603082561	1		490	888	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869580	117869580	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063042-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	50	364	0	ENST00000297338.2:c.614A>T	p.Lys205Ile	p.K205I	ENST00000297338	NM_006265.2	205	aAa/aTa	6/14	1	2	FACETS	0.854	0.724	0.997	0.854	0.724	0.997	CLONAL	1	TRUE	1	0.204281603082561	2		364	573	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882918	89883052	+	splice_donor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	CTCCCGCGGCCTGCCGCGCCCACCTACCCAGCAGCTCGGCCCAGGCCCTCCGGCGGCCCCCTGGGTCCTGGCCCGAGGCGGAGTTCGGGACCCACGAGTCGGACATGGCCTTGGCGCCTACAGCCCCGGCGGCGG	CTCCCGCGGCCTGCCGCGCCCACCTACCCAGCAGCTCGGCCCAGGCCCTCCGGCGGCCCCCTGGGTCCTGGCCCGAGGCGGAGTTCGGGACCCACGAGTCGGACATGGCCTTGGCGCCTACAGCCCCGGCGGCGG	-	novel	NA	P-0063043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	76	391	0	ENST00000389301.3:c.-29_79+27del		p.X10_splice	ENST00000389301	NM_000135.2	10		1/43	0.692248200611293	4	FACETS	0.287	0.25	0.326	0.143	0.125	0.163	SUBCLONAL	1	TRUE	2	0.762077254636567	4		391	1226	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579399	+	frameshift_variant	Frame_Shift_Del	DEL	GGGAAGGGACA	GGGAAGGGACA	-	novel	NA	P-0063043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	945	730	0	ENST00000269305.4:c.288_298del	p.Val97GlufsTer48	p.V97Efs*48	ENST00000269305	NM_001126112.2	96	tcTGTCCCTTCCCag/tcag	4/11	0.764178774456956	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.762077254636567	2		730	1122	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711208	61711218	+	frameshift_variant	Frame_Shift_Del	DEL	GTTCGTTCTAT	GTTCGTTCTAT	-	novel	NA	P-0063043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	60	421	0	ENST00000401558.2:c.2531_2541del	p.His844LeufsTer25	p.H844Lfs*25	ENST00000401558	NM_003400.3	844	cATAGAACGAAC/c	21/25	0.762077254636567	6	FACETS	0.724	0.624	0.833			1	SUBCLONAL	1	TRUE	NA	0.762077254636567	6		421	549	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202989	27202989	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	290	532	0	ENST00000380036.4:c.2081T>G	p.Ile694Ser	p.I694S	ENST00000380036	NM_000459.3	694	aTc/aGc	13/23	0.602308114113978	4	FACETS	1	0.986	1	0.386	0.363	0.41	CLONAL	1	TRUE	1	0.762077254636567	4		532	1157	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0063051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	418	801	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.776630278748926	2	FACETS	0.983	0.957	1	0.983	0.957	1	CLONAL	2	TRUE	0	0.818954272621478	2		804	519	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604790	48604790	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1568211615	NA	P-0063051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	433	608	0	ENST00000342988.3:c.1612G>T	p.Glu538Ter	p.E538*	ENST00000342988	NM_005359.5	538	Gaa/Taa	12/12	0.781461415235387	3	FACETS	0.957	0.934	0.979	0.957	0.934	0.979	CLONAL	3	TRUE	0	0.818954272621478	3		608	519	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0063051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	165	507	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.818954272621478	2		507	397	SUCCESS
APC	324	MSKCC	GRCh37	5	112174268	112174268	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0063051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	115	665	0	ENST00000257430.4:c.2977A>T	p.Lys993Ter	p.K993*	ENST00000257430	NM_000038.5	993	Aag/Tag	16/16	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.818954272621478	2		665	278	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120311	70120311	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0063051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	424	760	2	ENST00000245479.2:c.1313C>G	p.Ser438Ter	p.S438*	ENST00000245479	NM_000346.3	438	tCa/tGa	3/3	NA	2	FACETS	0.979	0.953	1			1	INDETERMINATE	2	TRUE	NA	0.818954272621478	2		762	529	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967029	18967029	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	290	510	1	ENST00000262803.5:c.1744G>A	p.Asp582Asn	p.D582N	ENST00000262803	NM_002911.3	582	Gac/Aac	13/24	0.782584147730039	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.818954272621478	3		511	492	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878663	151878663	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0063051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	197	747	0	ENST00000262189.6:c.6282T>G	p.Tyr2094Ter	p.Y2094*	ENST00000262189	NM_170606.2	2094	taT/taG	36/59	0.787628208188728	4	FACETS	1	0.946	1	0.342	0.316	0.368	CLONAL	1	TRUE	1	0.818954272621478	4		747	854	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044470	47044470	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	330	658	0	ENST00000377604.3:c.1967A>G	p.Glu656Gly	p.E656G	ENST00000377604	NM_001204468.1	656	gAa/gGa	18/24	0.791400559344445	2	FACETS	0.897	0.866	0.927	0.897	0.866	0.927	CLONAL	2	TRUE	0	0.818954272621478	2		658	449	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0063052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	93	462	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.327711507463844	3	FACETS	0.879	0.788	0.975	0.879	0.788	0.975	CLONAL	2	TRUE	1	0.328300793048969	3		462	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934874	NA	P-0063052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	90	624	0	ENST00000269305.4:c.451C>A	p.Pro151Thr	p.P151T	ENST00000269305	NM_001126112.2	151	Ccc/Acc	5/11	0.328300793048969	1	FACETS	0.983	0.876	1	0.983	0.876	1	CLONAL	1	TRUE	0	0.328300793048969	1		624	466	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0063052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	47	308	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.69	0.583	0.807	0.69	0.583	0.807	SUBCLONAL	1	TRUE	1	0.328300793048969	2		308	415	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971206	21971206	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	86	540	0	ENST00000304494.5:c.152T>A	p.Val51Asp	p.V51D	ENST00000304494	NM_000077.4	51	gTc/gAc	2/3	0.328300793048969	1	FACETS	0.958	0.851	1	0.958	0.851	1	CLONAL	1	TRUE	0	0.328300793048969	1		540	457	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103499	77103501	+	inframe_deletion	In_Frame_Del	DEL	TAG	TAG	-	novel	NA	P-0063052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	39	520	0	ENST00000356341.3:c.65_67del	p.Thr22del	p.T22del	ENST00000356341	NM_002576.4	22	aCTAtg/atg	2/15	1	2	FACETS	0.39	0.322	0.466	0.39	0.322	0.466	SUBCLONAL	1	TRUE	1	0.328300793048969	2		520	609	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131895053	131895053	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	31	290	0	ENST00000265335.6:c.207T>A	p.Asp69Glu	p.D69E	ENST00000265335		69	gaT/gaA	2/25	1	2	FACETS	0.818	0.665	0.988	0.818	0.665	0.988	CLONAL	1	TRUE	1	0.328300793048969	2		290	231	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45854906	45854906	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0121471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	202	546	2	ENST00000391945.4:c.2264A>G	p.Gln755Arg	p.Q755R	ENST00000391945	NM_000400.3	755	cAg/cGg	23/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	NA	1	0.923970590512033	2		548	414	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923342	9923342	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397514557	NA	P-0063054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	42	572	0	ENST00000330684.3:c.1945C>G	p.Leu649Val	p.L649V	ENST00000330684	NM_001134407.1	649	Ctg/Gtg	9/13	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.218810047391667	2		572	267	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121575	2121575	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	29	629	0	ENST00000219476.3:c.1904A>T	p.Asp635Val	p.D635V	ENST00000219476	NM_000548.3	635	gAt/gTt	18/42	1	2	FACETS	0.753	0.605	0.921	0.753	0.605	0.921	CLONAL	1	TRUE	1	0.218810047391667	2		629	352	SUCCESS
APC	324	MSKCC	GRCh37	5	112170789	112170790	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs387906233	NA	P-0063054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	23	549	0	ENST00000257430.4:c.1885_1886insA	p.Leu629TyrfsTer5	p.L629Yfs*5	ENST00000257430	NM_000038.5	629	tta/tAta	15/16	0.218810047391667	1	FACETS	0.931	0.73	1	0.931	0.73	1	CLONAL	1	TRUE	0	0.218810047391667	1		549	201	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0063055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	38	479	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	0.673	0.556	0.803	0.673	0.556	0.803	SUBCLONAL	1	TRUE	1	0.23785177304797	2		479	475	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165122	47165122	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	66	422	0	ENST00000409792.3:c.1004G>T	p.Arg335Ile	p.R335I	ENST00000409792	NM_014159.6	335	aGa/aTa	3/21	1	2	FACETS	0.908	0.788	1	0.908	0.788	1	CLONAL	1	TRUE	1	0.23785177304797	2		422	611	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357726	70357726	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	63	797	0	ENST00000374080.3:c.5977C>T	p.Gln1993Ter	p.Q1993*	ENST00000374080		1993	Cag/Tag	41/45	1	2	FACETS	0.961	0.832	1	0.961	0.832	1	CLONAL	1	TRUE	1	0.23785177304797	2		797	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587781525	NA	P-0063056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	129	640	0	ENST00000269305.4:c.842A>G	p.Asp281Gly	p.D281G	ENST00000269305	NM_001126112.2	281	gAc/gGc	8/11	0.331387846037714	5	FACETS	1	0.958	1	1	0.958	1	CLONAL	3	FALSE	2	0.404627645640899	5		640	321	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0063056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	61	515	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	0.331387846037714	5	FACETS	1	0.953	1	0.796	0.697	0.899	CLONAL	2	FALSE	2	0.404627645640899	5		515	203	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579381	7579381	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	52	692	0	ENST00000269305.4:c.306del	p.Tyr103ThrfsTer20	p.Y103Tfs*20	ENST00000269305	NM_001126112.2	102	acC/ac	4/11	0.331387846037714	5	FACETS	1	0.966	1	0.495	0.425	0.571	CLONAL	1	FALSE	2	0.404627645640899	5		692	278	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523517	106523517	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	83	464	0	ENST00000359195.3:c.2669A>C	p.Lys890Thr	p.K890T	ENST00000359195	NM_002649.2	890	aAa/aCa	8/11	0.404627645640899	5	FACETS	0.872	0.781	0.966	0.872	0.781	0.966	CLONAL	3	FALSE	2	0.404627645640899	5		464	252	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18649086	18649086	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	21	409	0	ENST00000266497.5:c.2761A>C	p.Lys921Gln	p.K921Q	ENST00000266497		921	Aag/Cag	19/31	0.348307502046354	4	FACETS	1	0.922	1	0.496	0.389	0.615	CLONAL	1	FALSE	1	0.404627645640899	4		409	98	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059315	42059315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567118489	NA	P-0063056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	26	722	1	ENST00000219905.7:c.9035C>T	p.Pro3012Leu	p.P3012L	ENST00000219905	NM_001164273.1	3012	cCt/cTt	24/24	1	2	FACETS	0.981	0.789	1	0.981	0.789	1	CLONAL	1	FALSE	1	0.404627645640899	2		723	131	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063057-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	62	343	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		343	209	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0063058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	840	387	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.7224569896893	27	FACETS	1	0.992	1	1	0.992	1	CLONAL	25	TRUE	2	0.7224569896893	27		387	925	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	142	343	0				ENST00000310581	NM_198253.2	-/1132			0.7224569896893	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.7224569896893	2		343	171	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0063058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	159	589	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.7224569896893	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.7224569896893	2		589	203	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910398	29910398	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	60	799	0	ENST00000376809.5:c.68G>A	p.Trp23Ter	p.W23*	ENST00000376809	NM_002116.7	23	tGg/tAg	1/8	0.329674232681334	2	FACETS	0.427	0.369	0.489	0.213	0.184	0.245	INDETERMINATE	1	TRUE	0	0.7224569896893	2		799	389	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494891	56494891	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	147	529	0	ENST00000267101.3:c.3248C>G	p.Ser1083Cys	p.S1083C	ENST00000267101	NM_001982.3	1083	tCt/tGt	27/28	0.111073510151811	4	FACETS	0.856	0.799	0.913			1	INDETERMINATE	3	TRUE	NA	0.7224569896893	4		529	273	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818189	32818189	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777683307	NA	P-0063058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	136	534	0	ENST00000354258.4:c.1336G>A	p.Glu446Lys	p.E446K	ENST00000354258	NM_000593.5	446	Gaa/Aaa	5/11	0.329674232681334	2	FACETS	1	0.99	1	0.744	0.692	0.795	INDETERMINATE	1	TRUE	0	0.7224569896893	2		534	253	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162413	47162413	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	44	499	0	ENST00000409792.3:c.3713C>G	p.Ser1238Cys	p.S1238C	ENST00000409792	NM_014159.6	1238	tCt/tGt	3/21	0.295742614207247	4	FACETS	0.82	0.704	0.94	0.82	0.704	0.94	INDETERMINATE	2	TRUE	2	0.7224569896893	4		499	128	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570055	95570055	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	88	594	0	ENST00000393063.1:c.3678G>C	p.Glu1226Asp	p.E1226D	ENST00000393063	NM_030621.3	1226	gaG/gaC	22/28	0.403543793471811	6	FACETS	1	0.955	1	1	0.955	1	INDETERMINATE	3	TRUE	3	0.7224569896893	6		594	183	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12043173	12043173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	14	296	0	ENST00000353533.5:c.1058C>T	p.Ser353Phe	p.S353F	ENST00000353533	NM_003010.3	353	tCc/tTc	10/11	0.7224569896893	2	FACETS	0.451	0.331	0.591	0.225	0.165	0.296	SUBCLONAL	1	TRUE	0	0.7224569896893	2		296	86	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973025	25973025	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0063058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	31	558	0	ENST00000435504.4:c.1400C>G	p.Ser467Ter	p.S467*	ENST00000435504		467	tCa/tGa	12/13	0.419185564567823	2	FACETS	0.631	0.519	0.754	0.316	0.259	0.377	INDETERMINATE	1	TRUE	0	0.7224569896893	2		558	136	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288578	198288578	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	16	473	0	ENST00000335508.6:c.149G>C	p.Arg50Thr	p.R50T	ENST00000335508	NM_012433.2	50	aGa/aCa	2/25	0.474284110508559	1	FACETS	0.318	0.239	0.409	0.318	0.239	0.409	SUBCLONAL	1	TRUE	0	0.7224569896893	1		473	89	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162569	47162569	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1346882059	NA	P-0063058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	51	477	0	ENST00000409792.3:c.3557C>T	p.Ser1186Leu	p.S1186L	ENST00000409792	NM_014159.6	1186	tCa/tTa	3/21	0.295742614207247	4	FACETS	1	0.887	1	1	0.887	1	INDETERMINATE	2	TRUE	2	0.7224569896893	4		477	120	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163239	47163239	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	48	550	0	ENST00000409792.3:c.2887C>G	p.Gln963Glu	p.Q963E	ENST00000409792	NM_014159.6	963	Caa/Gaa	3/21	0.295742614207247	4	FACETS	0.923	0.802	1	0.923	0.802	1	INDETERMINATE	2	TRUE	2	0.7224569896893	4		550	124	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509814	187509814	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	42	663	0	ENST00000441802.2:c.13699G>C	p.Gly4567Arg	p.G4567R	ENST00000441802	NM_005245.3	4567	Ggg/Cgg	27/27	0.380958959381837	1	FACETS	0.41	0.347	0.478	0.41	0.347	0.478	INDETERMINATE	1	TRUE	0	0.7224569896893	1		663	181	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542710	187542710	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	47	577	0	ENST00000441802.2:c.5030G>T	p.Ser1677Ile	p.S1677I	ENST00000441802	NM_005245.3	1677	aGt/aTt	10/27	0.380958959381837	1	FACETS	0.807	0.705	0.91	0.807	0.705	0.91	INDETERMINATE	1	TRUE	0	0.7224569896893	1		577	103	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021033	26021033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	123	718	0	ENST00000357647.3:c.316G>A	p.Glu106Lys	p.E106K	ENST00000357647	NM_003529.2	106	Gag/Aag	1/1	0.329674232681334	2	FACETS	0.996	0.912	1	0.498	0.456	0.541	INDETERMINATE	1	TRUE	0	0.7224569896893	2		718	342	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739916	41739916	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	100	527	0	ENST00000242208.4:c.57G>T	p.Arg19Ser	p.R19S	ENST00000242208	NM_002192.2	19	agG/agT	2/3	0.295742614207247	4	FACETS	0.87	0.789	0.953	0.87	0.789	0.953	INDETERMINATE	2	TRUE	2	0.7224569896893	4		527	274	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141569556	141569556	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	31	446	0	ENST00000220592.5:c.728T>G	p.Ile243Ser	p.I243S	ENST00000220592	NM_012154.3	243	aTt/aGt	6/19	0.7224569896893	5	FACETS	0.791	0.644	0.956	0.264	0.214	0.319	CLONAL	1	TRUE	2	0.7224569896893	5		446	226	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209555	98209555	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	55	608	0	ENST00000331920.6:c.3983A>T	p.Glu1328Val	p.E1328V	ENST00000331920	NM_000264.3	1328	gAa/gTa	23/24	0.320128545922127	3	FACETS	1	0.946	1	0.39	0.34	0.443	INDETERMINATE	1	TRUE	0	0.7224569896893	3		608	177	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038865	47038865	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	93	408	0	ENST00000377604.3:c.872C>A	p.Ser291Ter	p.S291*	ENST00000377604	NM_001204468.1	291	tCg/tAg	9/24	0.7224569896893	3	FACETS	0.885	0.806	0.964	0.885	0.806	0.964	CLONAL	2	TRUE	1	0.7224569896893	3		408	198	SUCCESS
AR	367	MSKCC	GRCh37	X	66765191	66765191	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	12	480	4	ENST00000374690.3:c.203A>C	p.Gln68Pro	p.Q68P	ENST00000374690	NM_000044.3	68	cAg/cCg	1/8	0.7224569896893	3	FACETS	0.191	0.134	0.261	0.095	0.067	0.131	SUBCLONAL	1	TRUE	1	0.7224569896893	3		484	237	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115873	8115874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0063059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	242	664	0	ENST00000346208.3:c.1220dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tCcg	6/6	1	2	FACETS	0.977	0.917	1	0.977	0.917	1	CLONAL	1	TRUE	1	0.676469369388068	2		664	732	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811768	102811768	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	270	604	0	ENST00000307046.8:c.416C>G	p.Ser139Cys	p.S139C	ENST00000307046	NM_001111285.1	139	tCt/tGt	4/4	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.676469369388068	2		604	740	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912177	32912178	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0063059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	190	427	0	ENST00000380152.3:c.3687_3688dup	p.Ser1230PhefsTer10	p.S1230Ffs*10	ENST00000380152		1229	gtt/gTTtt	11/27	0.676469369388068	1	FACETS	0.994	0.934	1	0.994	0.934	1	CLONAL	1	TRUE	0	0.676469369388068	1		427	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574014	7574014	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1064796401	NA	P-0063059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	183	452	0	ENST00000269305.4:c.1013T>G	p.Phe338Cys	p.F338C	ENST00000269305	NM_001126112.2	338	tTc/tGc	10/11	0.674050812987641	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.676469369388068	1		452	357	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819719	170819719	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	117	206	0	ENST00000296930.5:c.358G>C	p.Glu120Gln	p.E120Q	ENST00000296930	NM_002520.6	120	Gag/Cag	5/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.676469369388068	2		206	306	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430782	47430782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	178	644	0	ENST00000377045.4:c.1747G>A	p.Glu583Lys	p.E583K	ENST00000377045	NM_001654.4	583	Gaa/Aaa	16/16	1	2	FACETS	0.91	0.844	0.979	0.91	0.844	0.979	CLONAL	1	TRUE	1	0.676469369388068	2		644	578	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0063096-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	63	117	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.807054928609631	1	FACETS	0.941	0.854	1	0.941	0.854	1	CLONAL	1	TRUE	0	0.807054928609631	1		117	99	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063096-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	191	343	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.755	0.702	0.81	0.755	0.702	0.81	SUBCLONAL	1	TRUE	1	0.807054928609631	2		343	627	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211805	123211805	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0063096-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	449	512	0	ENST00000218089.9:c.2674-2A>C		p.X892_splice	ENST00000218089	NM_001042749.1	892			1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.807054928609631	2		512	1035	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858044	152858044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557026036	NA	P-0063096-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	391	416	0	ENST00000406277.2:c.571G>A	p.Val191Met	p.V191M	ENST00000406277	NM_152274.4	191	Gtg/Atg	6/7	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.807054928609631	2		416	951	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	98	343	0				ENST00000310581	NM_198253.2	-/1132			0.177491011078964	0	FACETS	0.467	0.418	0.519			1	INDETERMINATE	1	TRUE	0	0.457205127850693	0		343	498	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0063098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	140	416	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	1	2	FACETS	0.925	0.845	1	0.925	0.845	1	CLONAL	1	TRUE	1	0.457205127850693	2		416	662	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556707	41556707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	145	456	0	ENST00000263253.7:c.3652G>A	p.Asp1218Asn	p.D1218N	ENST00000263253	NM_001429.3	1218	Gac/Aac	20/31	1	2	FACETS	0.934	0.854	1	0.934	0.854	1	CLONAL	1	TRUE	1	0.457205127850693	2		456	679	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0063098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	423	457	0	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	0.457205127850693	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.457205127850693	2		457	824	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942708	44942708	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	112	316	0	ENST00000377967.4:c.3288G>A	p.Trp1096Ter	p.W1096*	ENST00000377967	NM_021140.2	1096	tgG/tgA	23/29	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.457205127850693	2		316	356	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226551650	226551650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	139	488	0	ENST00000366794.5:c.2780G>A	p.Gly927Glu	p.G927E	ENST00000366794	NM_001618.3	927	gGa/gAa	20/23	1	2	FACETS	0.817	0.745	0.893	0.817	0.745	0.893	CLONAL	1	TRUE	1	0.457205127850693	2		488	744	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636639	73636639	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	224	656	0	ENST00000377687.4:c.902C>T	p.Pro301Leu	p.P301L	ENST00000377687	NM_001730.3	301	cCc/cTc	2/4	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.457205127850693	2		656	977	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044889	47044889	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	221	745	0	ENST00000377604.3:c.2215G>T	p.Glu739Ter	p.E739*	ENST00000377604	NM_001204468.1	739	Gag/Tag	20/24	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.457205127850693	2		745	916	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0063099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	136	441	1	ENST00000269305.4:c.97-1G>A		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.283900581845646	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.283900581845646	1		442	714	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61306969	61306969	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	121	385	0	ENST00000341074.5:c.511G>A	p.Asp171Asn	p.D171N	ENST00000341074	NM_002974.2	171	Gat/Aat	6/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.283900581845646	2		385	668	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484406	57484406	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	132	412	0	ENST00000371085.3:c.587A>T	p.Asp196Val	p.D196V	ENST00000371085	NM_000516.4	196	gAc/gTc	8/13	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.283900581845646	2		412	803	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578558	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTACTGT	AGTACTGT	-	novel	NA	P-0063124-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	216	643	0	ENST00000269305.4:c.376-4_379del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	0.462429022822967	3	FACETS	0.982	0.931	1	0.982	0.931	1	CLONAL	3	FALSE	0	0.511423804271335	3		643	360	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950708	79950709	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCAGCGGCC	rs758960105	NA	P-0063124-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	47	474	0	ENST00000265081.6:c.178_186dup	p.Ala60_Ala62dup	p.A60_A62dup	ENST00000265081	NM_002439.4	60	-/GCAGCGGCC	1/24	0.484340190489679	2	FACETS	0.753	0.641	0.874	0.377	0.32	0.437	SUBCLONAL	1	FALSE	0	0.511423804271335	2		474	244	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980398	201980399	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0063124-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	481	766	0	ENST00000359651.3:c.135dup	p.Asn46GlnfsTer46	p.N46Qfs*46	ENST00000359651		45	agc/agCc	1/8	0.511423804271335	12	FACETS	0.934	0.895	0.973			1	CLONAL	6	FALSE	NA	0.511423804271335	12		766	1194	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	175	343	0				ENST00000310581	NM_198253.2	-/1132			0.565954052330185	3	FACETS	0.946	0.888	1	0.946	0.888	1	CLONAL	2	TRUE	1	0.799279550888891	3		343	324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0063125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	204	600	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.332301848197203	3	FACETS	0.954	0.887	1	0.477	0.443	0.511	INDETERMINATE	1	TRUE	1	0.799279550888891	3		600	749	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936983	48936983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690863	NA	P-0063125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	245	523	0	ENST00000267163.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000267163	NM_000321.2	251	Cga/Tga	8/27	0.799279550888891	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.799279550888891	1		523	326	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611219	100611219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781792640	NA	P-0063125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	241	188	0	ENST00000308731.7:c.1387G>A	p.Val463Ile	p.V463I	ENST00000308731	NM_000061.2	463	Gtc/Atc	15/19	0.799279550888891	2	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.799279550888891	2		188	281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577590	7577591	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0063125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	300	415	0	ENST00000269305.4:c.690dup	p.Thr231HisfsTer9	p.T231Hfs*9	ENST00000269305	NM_001126112.2	230	-/C	7/11	0.332301848197203	3	FACETS	0.945	0.901	0.989	0.945	0.901	0.989	INDETERMINATE	2	TRUE	1	0.799279550888891	3		415	556	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2114357	2114390	+	frameshift_variant	Frame_Shift_Del	DEL	CAGTTGCTGGTGGACCTGGCAGAGGGCTGCCACA	CAGTTGCTGGTGGACCTGGCAGAGGGCTGCCACA	-	novel	NA	P-0063125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	192	614	0	ENST00000219476.3:c.1530_1563del	p.Gln510HisfsTer14	p.Q510Hfs*14	ENST00000219476	NM_000548.3	510	CAGTTGCTGGTGGACCTGGCAGAGGGCTGCCACAca/ca	15/42	0.799279550888891	3	FACETS	0.716	0.662	0.772	0.358	0.331	0.386	SUBCLONAL	1	TRUE	1	0.799279550888891	3		614	939	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198283290	198283442	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTAGGATCAGGGGTTTTCCCTCCTGCAGAAAAGAACAGCAACAGGAAAAAGAGTACAATAAATAAAAAATAAGCAGGTTCAACTGATTTATCTGCCCTGCTCTAAATATTATGTTATTCCATAATCATTTAAATTATTTTTTGATGGAAAAC	TTTAGGATCAGGGGTTTTCCCTCCTGCAGAAAAGAACAGCAACAGGAAAAAGAGTACAATAAATAAAAAATAAGCAGGTTCAACTGATTTATCTGCCCTGCTCTAAATATTATGTTATTCCATAATCATTTAAATTATTTTTTGATGGAAAAC	-	novel	NA	P-0063125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	51	327	0	ENST00000335508.6:c.416-130_438del		p.X139_splice	ENST00000335508	NM_012433.2	139		5/25	1	2	FACETS	0.408	0.348	0.472	0.408	0.348	0.472	SUBCLONAL	1	TRUE	1	0.799279550888891	2		327	313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0063126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	270	809	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.819541725444361	1	FACETS	0.967	0.927	1	0.967	0.927	1	CLONAL	1	TRUE	0	0.819541725444361	1		809	402	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593253	67593253	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	223	553	0	ENST00000274335.5:c.1999G>C	p.Val667Leu	p.V667L	ENST00000274335		667	Gta/Cta	15/15	0.819541725444361	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.819541725444361	1		553	314	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634755	158634755	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	113	694	0	ENST00000263640.3:c.431T>G	p.Val144Gly	p.V144G	ENST00000263640	NM_001105.4	144	gTt/gGt	5/11	0.819541725444361	1	FACETS	0.44	0.4	0.482	0.44	0.4	0.482	SUBCLONAL	1	TRUE	0	0.819541725444361	1		694	370	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872004	35872005	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACCAAAAGCTCCACGATGCCTCTATCCATGGCT	novel	NA	P-0063126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	64	709	0	ENST00000216797.5:c.608_609insAGCCATGGATAGAGGCATCGTGGAGCTTTTGGT	p.Val203_Ser204insAlaMetAspArgGlyIleValGluLeuLeuVal	p.V203_S204insAMDRGIVELLV	ENST00000216797	NM_020529.2	203	gtg/gtAGCCATGGATAGAGGCATCGTGGAGCTTTTGGTg	4/6	0.819541725444361	1	FACETS	0.135	0.116	0.155	0.135	0.116	0.155	SUBCLONAL	1	TRUE	0	0.819541725444361	1		709	685	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872015	35872015	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	70	706	0	ENST00000216797.5:c.598G>T	p.Glu200Ter	p.E200*	ENST00000216797	NM_020529.2	200	Gag/Tag	4/6	0.819541725444361	1	FACETS	0.166	0.145	0.19	0.166	0.145	0.19	SUBCLONAL	1	TRUE	0	0.819541725444361	1		706	606	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274185	10274215	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCGCCGCCGCGCTCGGCGCCGGACCGCGC	CTCCGCCGCCGCGCTCGGCGCCGGACCGCGC	-	novel	NA	P-0063126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	184	596	0	ENST00000330684.3:c.54_84del	p.Trp18Ter	p.W18*	ENST00000330684	NM_001134407.1	18	tgGCGCGGTCCGGCGCCGAGCGCGGCGGCGGAG/tg	2/13	1	2	FACETS	0.865	0.805	0.927	0.865	0.805	0.927	CLONAL	1	TRUE	1	0.819541725444361	2		596	519	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40761149	40761149	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	229	578	0	ENST00000392038.2:c.203C>G	p.Pro68Arg	p.P68R	ENST00000392038	NM_001626.4	68	cCg/cGg	4/14	1	2	FACETS	0.996	0.936	1	0.996	0.936	1	CLONAL	1	TRUE	1	0.819541725444361	2		578	561	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61709631	61709631	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	102	327	0	ENST00000401558.2:c.2856G>T	p.Leu952Phe	p.L952F	ENST00000401558	NM_003400.3	952	ttG/ttT	23/25	1	2	FACETS	0.988	0.899	1	0.988	0.899	1	CLONAL	1	TRUE	1	0.819541725444361	2		327	252	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495383	149495383	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	239	760	0	ENST00000261799.4:c.3264G>T	p.Gln1088His	p.Q1088H	ENST00000261799	NM_002609.3	1088	caG/caT	23/23	0.819541725444361	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.819541725444361	1		760	317	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0063127-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	63	292	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.118753588047	4	FACETS	1	0.896	1	1	0.983	1	INDETERMINATE	4	FALSE	2	0.272166947551939	4		292	146	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0063128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	229	727	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.582748838506758	2		727	583	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324926	31324926	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063133-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	189	914	0	ENST00000412585.2:c.10A>G	p.Met4Val	p.M4V	ENST00000412585	NM_005514.6	4	Atg/Gtg	1/8	1	2	FACETS	0.955	0.889	1	0.955	0.889	1	CLONAL	1	TRUE	1	0.732983831226273	2		914	540	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938409	44938409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063133-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	88	87	0	ENST00000377967.4:c.2957C>T	p.Thr986Ile	p.T986I	ENST00000377967	NM_021140.2	986	aCt/aTt	20/29	1	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.732983831226273	1		87	138	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063134-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	126	329	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.320618113970412	2	FACETS	0.771	0.705	0.84	0.771	0.705	0.84	SUBCLONAL	2	TRUE	0	0.410477078913902	2		329	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0063134-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	267	809	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	0.327790176536269	2	FACETS	0.849	0.8	0.899	0.849	0.8	0.899	CLONAL	2	TRUE	0	0.410477078913902	2		809	766	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0063134-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	82	420	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.32256998603469	3	FACETS	0.922	0.815	1	0.461	0.407	0.519	CLONAL	1	TRUE	1	0.410477078913902	3		420	522	SUCCESS
APC	324	MSKCC	GRCh37	5	112175761	112175761	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063134-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	171	592	0	ENST00000257430.4:c.4473del	p.Phe1491LeufsTer16	p.F1491Lfs*16	ENST00000257430	NM_000038.5	1490	caT/ca	16/16	0.32256998603469	3	FACETS	1	0.989	1	0.739	0.682	0.799	CLONAL	1	TRUE	1	0.410477078913902	3		592	679	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727442	66727442	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063134-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	196	501	0	ENST00000307102.5:c.158T>G	p.Phe53Cys	p.F53C	ENST00000307102	NM_002755.3	53	tTt/tGt	2/11	0.327790176536269	2	FACETS	0.828	0.771	0.885	0.828	0.771	0.885	CLONAL	2	TRUE	0	0.410477078913902	2		501	577	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174404	11174404	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063134-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	181	458	0	ENST00000361445.4:c.7271A>C	p.Asp2424Ala	p.D2424A	ENST00000361445	NM_004958.3	2424	gAc/gCc	53/58	0.327790176536269	2	FACETS	0.837	0.778	0.897	0.837	0.778	0.897	CLONAL	2	TRUE	0	0.410477078913902	2		458	527	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554238	29554238	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063134-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	127	454	1	ENST00000356175.3:c.2254A>G	p.Arg752Gly	p.R752G	ENST00000356175	NM_000267.3	752	Aga/Gga	19/57	0.328198978491484	3	FACETS	0.78	0.711	0.852	0.52	0.474	0.568	SUBCLONAL	2	TRUE	0	0.410477078913902	3		455	478	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0063135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	67	440	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.223348839920462	1	FACETS	0.957	0.832	1	0.957	0.832	1	CLONAL	1	TRUE	0	0.223348839920462	1		440	557	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608282	28608282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773466203	NA	P-0063135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	43	626	1	ENST00000241453.7:c.1774G>A	p.Val592Ile	p.V592I	ENST00000241453	NM_004119.2	592	Gtt/Att	14/24	1	2	FACETS	0.904	0.757	1	0.904	0.757	1	CLONAL	1	TRUE	1	0.223348839920462	2		627	426	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696598	47696598	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	63	696	0	ENST00000347630.2:c.350T>C	p.Met117Thr	p.M117T	ENST00000347630	NM_001007230.1	117	aTg/aCg	5/11	0.108867653382346	3	FACETS	1	0.938	1	0.574	0.497	0.658	INDETERMINATE	1	TRUE	1	0.223348839920462	3		696	546	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs149680468	NA	P-0063135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	193	651	0	ENST00000281708.4:c.1513C>A	p.Arg505Ser	p.R505S	ENST00000281708	NM_033632.3	505	Cgc/Agc	10/12	0.223348839920462	3	FACETS	0.855	0.793	0.919	1	0.987	1	CLONAL	3	TRUE	1	0.223348839920462	3		651	749	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247920	59247920	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	87	1008	0	ENST00000371222.2:c.823G>A	p.Glu275Lys	p.E275K	ENST00000371222	NM_002228.3	275	Gag/Aag	1/1	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.223348839920462	2		1008	718	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672833	86672833	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	38	553	0	ENST00000274376.6:c.2320A>T	p.Asn774Tyr	p.N774Y	ENST00000274376	NM_002890.2	774	Aat/Tat	17/25	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.223348839920462	2		553	317	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0063136-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	32	496	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.11	2		496	516	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0063136-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	25	350	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.788	1	1	0.788	1	CLONAL	1	TRUE	1	0.11	2		350	454	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591861	48591861	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063136-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	35	573	0	ENST00000342988.3:c.1025del	p.Pro342LeufsTer42	p.P342Lfs*42	ENST00000342988	NM_005359.5	342	Cct/ct	9/12	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.11	2		573	605	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971129	21971129	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063136-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	27	781	0	ENST00000304494.5:c.229A>T	p.Thr77Ser	p.T77S	ENST00000304494	NM_000077.4	77	Act/Tct	2/3	1	2	FACETS	0.912	0.724	1	0.912	0.724	1	CLONAL	1	TRUE	1	0.11	2		781	538	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461101	120461101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs312262796	NA	P-0063137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	132	617	0	ENST00000256646.2:c.5857C>T	p.Arg1953Cys	p.R1953C	ENST00000256646	NM_024408.3	1953	Cgc/Tgc	32/34	1	2	FACETS	0.789	0.719	0.863	0.789	0.719	0.863	SUBCLONAL	1	TRUE	1	0.536917470326061	2		617	623	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051060	180051060	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs768956955	NA	P-0063137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	178	584	0	ENST00000261937.6:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000261937	NM_182925.4	475	Cgg/Tgg	11/30	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.536917470326061	2		584	533	SUCCESS
BLM	641	MSKCC	GRCh37	15	91333879	91333879	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	124	362	1	ENST00000355112.3:c.2824G>T	p.Val942Phe	p.V942F	ENST00000355112	NM_000057.2	942	Gtt/Ttt	15/22	1	2	FACETS	0.968	0.882	1	0.968	0.882	1	CLONAL	1	TRUE	1	0.536917470326061	2		363	477	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0063138-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	26	350	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		350	331	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591135	67591149	+	inframe_deletion	In_Frame_Del	DEL	GAGAGACCAATACTT	GAGAGACCAATACTT	-	novel	NA	P-0063139-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	143	515	0	ENST00000274335.5:c.1730_1744del	p.Arg577_Leu581del	p.R577_L581del	ENST00000274335		576	acGAGAGACCAATACTTg/acg	12/15	1	2	FACETS	0.775	0.711	0.842	1	0.988	1	SUBCLONAL	2	TRUE	1	0.354137908095788	2		515	521	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057811	27057817	+	frameshift_variant	Frame_Shift_Del	DEL	CAACCAC	CAACCAC	-	novel	NA	P-0063139-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	215	941	0	ENST00000324856.7:c.1521_1527del	p.Gln507HisfsTer110	p.Q507Hfs*110	ENST00000324856	NM_006015.4	507	CAACCACca/ca	3/20	1	2	FACETS	0.819	0.764	0.876	1	0.993	1	CLONAL	2	TRUE	1	0.354137908095788	2		941	741	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106363	27106363	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063139-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	240	699	0	ENST00000324856.7:c.5974T>C	p.Ser1992Pro	p.S1992P	ENST00000324856	NM_006015.4	1992	Tca/Cca	20/20	1	2	FACETS	0.971	0.911	1	1	0.995	1	CLONAL	2	TRUE	1	0.354137908095788	2		699	698	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919657	50919657	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063139-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	114	729	0	ENST00000440232.2:c.2825C>A	p.Pro942Gln	p.P942Q	ENST00000440232	NM_002691.3	942	cCg/cAg	23/27	0.351803523002082	2	FACETS	0.965	0.87	1	0.483	0.435	0.533	CLONAL	1	TRUE	0	0.354137908095788	2		729	667	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106861	27106861	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063140-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	33	788	0	ENST00000324856.7:c.6472C>T	p.Arg2158Ter	p.R2158*	ENST00000324856	NM_006015.4	2158	Cga/Tga	20/20	1	2	FACETS	0.23	0.186	0.28	0.23	0.186	0.28	SUBCLONAL	1	TRUE	1	0.29	2		788	989	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577529	7577529	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs730882027	NA	P-0063141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	256	679	0	ENST00000269305.4:c.752T>G	p.Ile251Ser	p.I251S	ENST00000269305	NM_001126112.2	251	aTc/aGc	7/11	0.450725070900633	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.450725070900633	2		679	553	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426431	49426432	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0063141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	381	856	0	ENST00000301067.7:c.12056dup	p.Leu4020ProfsTer20	p.L4020Pfs*20	ENST00000301067	NM_003482.3	4019	ctc/ctTc	39/54	0.450725070900633	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.450725070900633	3		856	911	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861486	152861486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	117	592	0	ENST00000406277.2:c.266G>A	p.Arg89His	p.R89H	ENST00000406277	NM_152274.4	89	cGt/cAt	4/7	0.450725070900633		FACETS		0.956	1				CLONAL	1	TRUE	0	0.450725070900633	2		592	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0063142-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	176	502	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.312436430725252	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.312436430725252	1		502	918	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183787	10183787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123481	NA	P-0063142-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	151	654	0	ENST00000256474.2:c.256C>T	p.Pro86Ser	p.P86S	ENST00000256474	NM_000551.3	86	Ccc/Tcc	1/3	0.312436430725252	1	FACETS	0.912	0.834	0.994	0.912	0.834	0.994	CLONAL	1	TRUE	0	0.312436430725252	1		654	894	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164760	47164760	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063142-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	67	630	0	ENST00000409792.3:c.1366C>T	p.Arg456Ter	p.R456*	ENST00000409792	NM_014159.6	456	Cga/Tga	3/21	0.312436430725252	1	FACETS	0.549	0.477	0.628	0.549	0.477	0.628	SUBCLONAL	1	TRUE	0	0.312436430725252	1		630	659	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808005	1808005	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063142-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	161	1088	0	ENST00000260795.2:c.1981A>G	p.Met661Val	p.M661V	ENST00000260795		661	Atg/Gtg	14/17	1	2	FACETS	0.82	0.75	0.893	0.82	0.75	0.893	CLONAL	1	TRUE	1	0.312436430725252	2		1088	1257	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011194	12011194	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	16	251	0	ENST00000353533.5:c.601C>T	p.Pro201Ser	p.P201S	ENST00000353533	NM_003010.3	201	Cca/Tca	5/11	1	2	FACETS	0.549	0.408	0.715	0.549	0.408	0.715	SUBCLONAL	1	TRUE	1	0.388589431574078	2		251	150	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188207	10188207	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1559428056	NA	P-0063143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	70	475	0	ENST00000256474.2:c.350G>A	p.Trp117Ter	p.W117*	ENST00000256474	NM_000551.3	117	tGg/tAg	2/3	0.388589431574078	1	FACETS	0.899	0.79	1	0.899	0.79	1	CLONAL	1	TRUE	0	0.388589431574078	1		475	323	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162634	47162635	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	33	513	0	ENST00000409792.3:c.3491dup	p.Ser1165GlufsTer2	p.S1165Efs*2	ENST00000409792	NM_014159.6	1164	cag/caAg	3/21	0.388589431574078	1	FACETS	0.522	0.427	0.628	0.522	0.427	0.628	SUBCLONAL	1	TRUE	0	0.388589431574078	1		513	262	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352397	143352397	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	61	383	0	ENST00000262992.4:c.16G>C	p.Glu6Gln	p.E6Q	ENST00000262992	NM_001101669.1	6	Gaa/Caa	2/24	1	2	FACETS	0.994	0.863	1	0.994	0.863	1	CLONAL	1	TRUE	1	0.388589431574078	2		383	316	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	77	343	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.914	0.816	1	0.914	0.816	1	CLONAL	1	TRUE	1	0.773279841894662	2		343	218	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0063144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	13	839	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.190917348746942	1	FACETS	0.042	0.03	0.058	0.042	0.03	0.058	INDETERMINATE	1	TRUE	0	0.773279841894662	1		839	487	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916614	178916614	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0063144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	134	379	1	ENST00000263967.3:c.1A>G	p.Met1?	p.M1?	ENST00000263967	NM_006218.2	1	Atg/Gtg	2/21	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.773279841894662	2		380	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578470	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGGG	novel	NA	P-0063144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	211	871	0	ENST00000269305.4:c.457_460dup	p.Gly154AlafsTer28	p.G154Afs*28	ENST00000269305	NM_001126112.2	154	ggc/gCCCGgc	5/11	0.190917348746942	1	FACETS	0.673	0.632	0.716	0.673	0.632	0.716	INDETERMINATE	1	TRUE	0	0.773279841894662	1		871	497	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692920	89692920	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	129	457	0	ENST00000371953.3:c.404T>G	p.Ile135Arg	p.I135R	ENST00000371953	NM_000314.4	135	aTa/aGa	5/9	0.773279841894662	1	FACETS	0.886	0.824	0.947	0.886	0.824	0.947	CLONAL	1	TRUE	0	0.773279841894662	1		457	231	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947567	48947567	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs878853947	NA	P-0063144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	94	227	0	ENST00000267163.4:c.1154T>G	p.Leu385Ter	p.L385*	ENST00000267163	NM_000321.2	385	tTa/tGa	12/27	0.773279841894662	1	FACETS	0.938	0.864	1	0.938	0.864	1	CLONAL	1	TRUE	0	0.773279841894662	1		227	159	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586070	29586070	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	92	231	0	ENST00000356175.3:c.4290T>G	p.Asn1430Lys	p.N1430K	ENST00000356175	NM_000267.3	1430	aaT/aaG	32/57	NA	2	FACETS	1	0.919	1			1	INDETERMINATE	1	TRUE	NA	0.773279841894662	2		231	234	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0063148-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	27	398	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.491	0.39	0.606	0.491	0.39	0.606	SUBCLONAL	1	TRUE	1	0.28	2		398	393	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0063148-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	30	350	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.516	0.416	0.631	0.516	0.416	0.631	SUBCLONAL	1	TRUE	1	0.28	2		350	415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0063148-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	47	465	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.505	0.425	0.593	0.505	0.425	0.593	SUBCLONAL	1	TRUE	1	0.28	2		465	665	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578192	7578192	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063148-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	47	757	0	ENST00000269305.4:c.657del	p.Tyr220MetfsTer27	p.Y220Mfs*27	ENST00000269305	NM_001126112.2	219	ccC/cc	6/11	1	2	FACETS	0.433	0.364	0.51	0.433	0.364	0.51	SUBCLONAL	1	TRUE	1	0.28	2		757	775	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579190	7579354	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAAAACACTGACAGGAAGCCAAAGGGTGAAGAGGAATCCCAAAGTTCCAAACAAAAGAAATGCAGGGGGATACGGCCAGGCATTGAAGTCTCATGGAAGCCAGCCCCTCAGGGCAACTGACCGTGCAAGTCACAGACTTGGCTGTCCCAGAATGCAAGAAGCCC	AAAAAACACTGACAGGAAGCCAAAGGGTGAAGAGGAATCCCAAAGTTCCAAACAAAAGAAATGCAGGGGGATACGGCCAGGCATTGAAGTCTCATGGAAGCCAGCCCCTCAGGGCAACTGACCGTGCAAGTCACAGACTTGGCTGTCCCAGAATGCAAGAAGCCC	-	novel	NA	P-0063149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	149	205	0	ENST00000269305.4:c.333_375+122del		p.X111_splice	ENST00000269305	NM_001126112.2	111		4/11	0.739854694744502	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.739854694744502	1		205	170	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402599	20402613	+	inframe_deletion	In_Frame_Del	DEL	GCCGCCGCCGCCGCT	GCCGCCGCCGCCGCT	-	rs1202094234	NA	P-0063149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	109	759	0	ENST00000346618.3:c.145_159del	p.Ala49_Ala53del	p.A49_A53del	ENST00000346618	NM_001949.4	46	GCCGCCGCCGCCGCT/-	1/7	1	2	FACETS	0.859	0.78	0.941	0.859	0.78	0.941	CLONAL	1	TRUE	1	0.739854694744502	2		759	343	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0063150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	57	241	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.349038088915126	3	FACETS	0.942	0.811	1	0.471	0.405	0.542	CLONAL	1	TRUE	1	0.36862451736138	3		241	389	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0063150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	123	665	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.36862451736138	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.36862451736138	1		665	477	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609994	43609994	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148935214	NA	P-0063150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	222	865	0	ENST00000355710.3:c.1946C>T	p.Ser649Leu	p.S649L	ENST00000355710	NM_020975.4	649	tCg/tTg	11/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.36862451736138	2		865	1131	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094347	27094347	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	198	640	0	ENST00000324856.7:c.3055G>T	p.Glu1019Ter	p.E1019*	ENST00000324856	NM_006015.4	1019	Gag/Tag	11/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.36862451736138	2		640	756	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582193	189582193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1198643405	NA	P-0063150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	75	608	1	ENST00000264731.3:c.752G>A	p.Arg251His	p.R251H	ENST00000264731	NM_003722.4	251	cGt/cAt	5/14	1	2	FACETS	0.667	0.585	0.756	0.667	0.585	0.756	SUBCLONAL	1	TRUE	1	0.36862451736138	2		609	610	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986800	36986800	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	151	615	0	ENST00000354822.5:c.889G>A	p.Gly297Ser	p.G297S	ENST00000354822	NM_001079668.2	297	Ggc/Agc	3/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.36862451736138	2		615	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579396	7579397	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0063150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	334	805	0	ENST00000269305.4:c.290_291insG	p.Ser99PhefsTer50	p.S99Ffs*50	ENST00000269305	NM_001126112.2	97	gtc/gtGc	4/11	0.314318074770615	2	FACETS	0.95	0.9	1	0.95	0.9	1	CLONAL	2	TRUE	0	0.36862451736138	2		805	954	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492814	56492815	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0063150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	198	646	0	ENST00000407977.2:c.124_125insT	p.Ala42ValfsTer33	p.A42Vfs*33	ENST00000407977		42	gca/gTca	2/10	0.36862451736138	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.36862451736138	1		646	708	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	110	343	0				ENST00000310581	NM_198253.2	-/1132			0.647716831257029	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.647716831257029	1		343	228	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947827	178947827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	189	498	0	ENST00000263967.3:c.2702G>T	p.Cys901Phe	p.C901F	ENST00000263967	NM_006218.2	901	tGt/tTt	19/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.647716831257029	2		498	517	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0063151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	178	571	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	0.948	0.878	1	0.948	0.878	1	CLONAL	1	TRUE	1	0.647716831257029	2		571	580	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888166	112888166	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121918461	NA	P-0063151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	167	573	0	ENST00000351677.2:c.182A>T	p.Asp61Val	p.D61V	ENST00000351677	NM_002834.3	61	gAt/gTt	3/16	1	2	FACETS	0.944	0.873	1	0.944	0.873	1	CLONAL	1	TRUE	1	0.647716831257029	2		573	546	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560030	29560030	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	216	621	0	ENST00000356175.3:c.3507C>A	p.Tyr1169Ter	p.Y1169*	ENST00000356175	NM_000267.3	1169	taC/taA	27/57	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.647716831257029	2		621	635	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663492	29663492	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0063151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	155	463	0	ENST00000356175.3:c.6084+1G>T		p.X2028_splice	ENST00000356175	NM_000267.3	2028			1	2	FACETS	0.872	0.803	0.943	0.872	0.803	0.943	CLONAL	1	TRUE	1	0.647716831257029	2		463	549	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125622	47125623	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	187	705	0	ENST00000409792.3:c.5647dup	p.Ile1883AsnfsTer4	p.I1883Nfs*4	ENST00000409792	NM_014159.6	1883	att/aAtt	12/21	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.647716831257029	2		705	576	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90996762	90996762	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	122	486	0	ENST00000265433.3:c.28C>T	p.Pro10Ser	p.P10S	ENST00000265433	NM_002485.4	10	Ccg/Tcg	1/16	1	2	FACETS	0.923	0.842	1	0.923	0.842	1	CLONAL	1	TRUE	1	0.647716831257029	2		486	408	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	123	343	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.991	0.899	1	0.991	0.899	1	CLONAL	1	TRUE	1	0.416295844909125	2		343	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572986	7572986	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555524156	NA	P-0063153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	161	626	1	ENST00000269305.4:c.1123C>T	p.Gln375Ter	p.Q375*	ENST00000269305	NM_001126112.2	375	Cag/Tag	11/11	1	2	FACETS	0.946	0.868	1	0.946	0.868	1	CLONAL	1	TRUE	1	0.416295844909125	2		627	818	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577560	7577560	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520002	NA	P-0063153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	173	525	0	ENST00000269305.4:c.721T>G	p.Ser241Ala	p.S241A	ENST00000269305	NM_001126112.2	241	Tcc/Gcc	7/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.416295844909125	2		525	742	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	359972	359972	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0063153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	144	574	0	ENST00000262320.3:c.1116+1G>A		p.X372_splice	ENST00000262320	NM_003502.3	372			0.416295844909125	1	FACETS	0.963	0.882	1	0.963	0.882	1	CLONAL	1	TRUE	0	0.416295844909125	1		574	569	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150931665	150931666	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	128	480	0	ENST00000271640.5:c.2343dup	p.Asn782Ter	p.N782*	ENST00000271640	NM_001145415.1	781	tgt/tgTt	15/22	1	2	FACETS	0.904	0.821	0.992	0.904	0.821	0.992	CLONAL	1	TRUE	1	0.416295844909125	2		480	680	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448488	49448488	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	213	749	4	ENST00000301067.7:c.223A>T	p.Ser75Cys	p.S75C	ENST00000301067	NM_003482.3	75	Agt/Tgt	3/54	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.416295844909125	2		753	976	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644887	67644887	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	92	750	0	ENST00000264010.4:c.152T>G	p.Val51Gly	p.V51G	ENST00000264010	NM_006565.3	51	gTc/gGc	3/12	1	2	FACETS	0.499	0.442	0.559	0.499	0.442	0.559	SUBCLONAL	1	TRUE	1	0.416295844909125	2		750	886	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47061309	47061332	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	CTGTCTTGGGCTTTTTCGAGGCCT	CTGTCTTGGGCTTTTTCGAGGCCT	-	novel	NA	P-0063153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	135	602	0	ENST00000409792.3:c.7351-2_7372del		p.X2451_splice	ENST00000409792	NM_014159.6	2451		19/21	1	2	FACETS	0.882	0.803	0.966	0.882	0.803	0.966	CLONAL	1	TRUE	1	0.416295844909125	2		602	735	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705380	43705380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	84	844	0	ENST00000382044.4:c.5242G>A	p.Asp1748Asn	p.D1748N	ENST00000382044	NM_001141980.1	1748	Gac/Aac	24/28	1	2	FACETS	0.851	0.751	0.959	0.851	0.751	0.959	CLONAL	1	TRUE	1	0.257639016792725	2		844	766	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0063154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	88	611	1	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.941	0.833	1	0.941	0.833	1	CLONAL	1	TRUE	1	0.257639016792725	2		612	726	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519938	NA	P-0063154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	40	434	0	ENST00000263967.3:c.1034A>C	p.Asn345Thr	p.N345T	ENST00000263967	NM_006218.2	345	aAt/aCt	5/21	1	2	FACETS	0.911	0.759	1	0.911	0.759	1	CLONAL	1	TRUE	1	0.257639016792725	2		434	341	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143330	108143330	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555085890	NA	P-0063154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	65	482	0	ENST00000278616.4:c.3149T>C	p.Leu1050Pro	p.L1050P	ENST00000278616	NM_000051.3	1050	cTt/cCt	21/63	0.257639016792725	1	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	0	0.257639016792725	1		482	421	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023440	27023440	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	105	693	0	ENST00000324856.7:c.546del	p.Ala183ArgfsTer49	p.A183Rfs*49	ENST00000324856	NM_006015.4	182	gcA/gc	1/20	0.257639016792725	2	FACETS	0.943	0.851	1	0.943	0.851	1	CLONAL	2	TRUE	0	0.257639016792725	2		693	432	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161308	55161308	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	71	614	0	ENST00000257290.5:c.3139G>T	p.Glu1047Ter	p.E1047*	ENST00000257290	NM_006206.4	1047	Gag/Tag	23/23	1	2	FACETS	0.868	0.758	0.987	0.868	0.758	0.987	CLONAL	1	TRUE	1	0.257639016792725	2		614	635	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193181562	193181562	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	53	421	0	ENST00000367435.3:c.1109C>G	p.Ser370Cys	p.S370C	ENST00000367435	NM_024529.4	370	tCt/tGt	13/17	0.257639016792725	2	FACETS	0.847	0.723	0.982	0.423	0.361	0.491	CLONAL	1	TRUE	0	0.257639016792725	2		421	486	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582879	95582879	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	86	592	0	ENST00000393063.1:c.1663G>T	p.Ala555Ser	p.A555S	ENST00000393063	NM_030621.3	555	Gca/Tca	11/28	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.257639016792725	2		592	544	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705451	43705451	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	79	826	0	ENST00000382044.4:c.5171G>C	p.Arg1724Thr	p.R1724T	ENST00000382044	NM_001141980.1	1724	aGa/aCa	24/28	1	2	FACETS	0.935	0.822	1	0.935	0.822	1	CLONAL	1	TRUE	1	0.257639016792725	2		826	656	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100442	2100442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	86	605	0	ENST00000219476.3:c.180G>A	p.Met60Ile	p.M60I	ENST00000219476	NM_000548.3	60	atG/atA	3/42	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.257639016792725	2		605	623	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811548	56811548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782449	NA	P-0063154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	253	458	0	ENST00000337432.4:c.1096C>T	p.Arg366Trp	p.R366W	ENST00000337432	NM_058216.2	366	Cgg/Tgg	9/9	0.257639016792725	4	FACETS	0.954	0.899	1	0.954	0.899	1	CLONAL	4	TRUE	0	0.257639016792725	4		458	647	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299893	15299893	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	88	835	0	ENST00000263388.2:c.1285G>C	p.Glu429Gln	p.E429Q	ENST00000263388	NM_000435.2	429	Gag/Cag	8/33	1	2	FACETS	0.968	0.857	1	0.968	0.857	1	CLONAL	1	TRUE	1	0.257639016792725	2		835	706	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978935	25978935	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	122	466	0	ENST00000435504.4:c.988G>C	p.Glu330Gln	p.E330Q	ENST00000435504		330	Gaa/Caa	10/13	0.241892470884711	3	FACETS	1	0.952	1	0.716	0.65	0.784	CLONAL	2	TRUE	0	0.257639016792725	3		466	498	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21350043	21350043	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	97	851	0	ENST00000215739.8:c.1951C>G	p.Leu651Val	p.L651V	ENST00000215739	NM_006767.3	651	Ctg/Gtg	17/21	0.0713596821201459	4	FACETS	1	0.966	1	0.606	0.54	0.677	INDETERMINATE	1	TRUE	2	0.257639016792725	4		851	781	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446903	29446903	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs199737518	NA	P-0063154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	73	665	0	ENST00000544604.2:c.2734C>G	p.Gln912Glu	p.Q912E	ENST00000544604	NM_001206998.1	912	Cag/Gag	8/9	0.0713596821201459	4	FACETS	0.962	0.84	1	0.481	0.42	0.547	INDETERMINATE	1	TRUE	2	0.257639016792725	4		665	741	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031930	26031930	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	96	959	0	ENST00000244661.2:c.359T>C	p.Ile120Thr	p.I120T	ENST00000244661	NM_003537.3	120	aTt/aCt	1/1	1	2	FACETS	0.913	0.813	1	0.913	0.813	1	CLONAL	1	TRUE	1	0.257639016792725	2		959	816	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851222	151851222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	73	520	0	ENST00000262189.6:c.12149C>T	p.Ser4050Leu	p.S4050L	ENST00000262189	NM_170606.2	4050	tCa/tTa	48/59	0.216215464339226	3	FACETS	1	0.876	1	0.501	0.438	0.568	CLONAL	1	TRUE	1	0.257639016792725	3		520	639	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888868	76888868	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	75	474	0	ENST00000373344.5:c.4961C>G	p.Ser1654Cys	p.S1654C	ENST00000373344	NM_000489.3	1654	tCt/tGt	19/35	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.257639016792725	2		474	504	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	131	519	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	NA	2	FACETS	0.735	0.67	0.801			1	INDETERMINATE	1	TRUE	NA	0.709131754538682	2		520	503	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	506	749	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.921	0.892	0.949	1	0.998	1	CLONAL	2	TRUE	1	0.709131754538682	2		754	775	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	130	605	0	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.857	0.784	0.932	0.857	0.784	0.932	CLONAL	1	TRUE	1	0.709131754538682	2		605	428	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	152	497	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.699	0.642	0.759	0.699	0.642	0.759	SUBCLONAL	1	TRUE	1	0.709131754538682	2		499	613	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	153	605	2	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.895	0.825	0.967	0.895	0.825	0.967	CLONAL	1	TRUE	1	0.709131754538682	2		607	482	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	173	302	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.787	0.739	0.834	1	0.992	1	SUBCLONAL	2	TRUE	1	0.709131754538682	2		306	310	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	111	241	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.96	0.874	1	0.96	0.874	1	CLONAL	1	TRUE	1	0.709131754538682	2		241	326	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	208	704	2	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.998	0.932	1	0.998	0.932	1	CLONAL	1	TRUE	1	0.709131754538682	2		706	588	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	84	304	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.936	0.839	1	0.936	0.839	1	CLONAL	1	TRUE	1	0.709131754538682	2		304	253	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	176	665	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.709131754538682	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.709131754538682	1		665	306	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	250	929	2	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	0.201382764525544	1	FACETS	0.612	0.574	0.65	0.612	0.574	0.65	INDETERMINATE	1	TRUE	0	0.709131754538682	1		931	744	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	110	430	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.709131754538682	2		430	292	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804953	43804953	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	229	560	1	ENST00000372470.3:c.408del	p.Ser137ValfsTer29	p.S137Vfs*29	ENST00000372470	NM_005373.2	135	Ccc/cc	4/12	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.709131754538682	2		561	560	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953855	55953856	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	135	549	0	ENST00000263923.4:c.3580_3581del	p.Leu1194AlafsTer15	p.L1194Afs*15	ENST00000263923	NM_002253.2	1194	CTg/g	27/30	1	2	FACETS	0.885	0.812	0.961	0.885	0.812	0.961	CLONAL	1	TRUE	1	0.709131754538682	2		549	430	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406043	70406043	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	147	568	1	ENST00000373644.4:c.3557T>C	p.Ile1186Thr	p.I1186T	ENST00000373644	NM_030625.2	1186	aTa/aCa	4/12	1	2	FACETS	0.938	0.864	1	0.938	0.864	1	CLONAL	1	TRUE	1	0.709131754538682	2		569	442	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	39	726	4	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	NA	2	FACETS	0.198	0.164	0.237			1	INDETERMINATE	1	TRUE	NA	0.709131754538682	2		730	555	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339111	65339111	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	62	685	6	ENST00000342505.4:c.425del	p.Lys142ArgfsTer26	p.K142Rfs*26	ENST00000342505	NM_002227.2	142	aAg/ag	5/25	NA	2	FACETS	0.35	0.302	0.401			1	INDETERMINATE	1	TRUE	NA	0.709131754538682	2		691	500	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	92	416	2	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.859	0.773	0.949	0.859	0.773	0.949	CLONAL	1	TRUE	1	0.709131754538682	2		418	302	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005365	150005365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs918439730	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	258	771	0	ENST00000253339.5:c.860G>A	p.Arg287Gln	p.R287Q	ENST00000253339		287	cGa/cAa	3/7	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.709131754538682	2		771	676	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610612	10610612	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	49	731	0	ENST00000171111.5:c.98A>G	p.Tyr33Cys	p.Y33C	ENST00000171111	NM_203500.1	33	tAc/tGc	2/6	1	2	FACETS	0.207	0.175	0.243	0.207	0.175	0.243	SUBCLONAL	1	TRUE	1	0.709131754538682	2		731	668	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923086	39923087	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	185	639	0	ENST00000378444.4:c.3621dup	p.Gln1208ThrfsTer8	p.Q1208Tfs*8	ENST00000378444	NM_001123385.1	1207	-/A	8/15	NA	2	FACETS	0.818	0.759	0.879			1	INDETERMINATE	1	TRUE	NA	0.709131754538682	2		639	638	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	64	544	3	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.284	0.245	0.326	0.284	0.245	0.326	SUBCLONAL	1	TRUE	1	0.709131754538682	2		547	636	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845588	63845588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774238244	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	168	558	0	ENST00000279873.7:c.1327C>T	p.Arg443Cys	p.R443C	ENST00000279873	NM_032199.2	443	Cgc/Tgc	9/10	1	2	FACETS	0.881	0.815	0.948	0.881	0.815	0.948	CLONAL	1	TRUE	1	0.709131754538682	2		558	538	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852118	63852118	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	187	736	0	ENST00000279873.7:c.2901del	p.Lys967AsnfsTer15	p.K967Nfs*15	ENST00000279873	NM_032199.2	966	Aaa/aa	10/10	1	2	FACETS	0.949	0.882	1	0.949	0.882	1	CLONAL	1	TRUE	1	0.709131754538682	2		736	556	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	164	536	2	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	0.709131754538682	3	FACETS	1	0.975	1	0.565	0.522	0.61	CLONAL	1	TRUE	1	0.709131754538682	3		538	554	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229301	123229301	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	16	383	0	ENST00000218089.9:c.3783+2T>C		p.X1261_splice	ENST00000218089	NM_001042749.1	1261			0.201382764525544	1	FACETS	0.094	0.069	0.124	0.094	0.069	0.124	INDETERMINATE	1	TRUE	0	0.709131754538682	1		383	309	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370236	40370236	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs761761205	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	131	691	12	ENST00000293328.3:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000293328	NM_012448.3	368	Cag/ag	9/19	1	2	FACETS	0.726	0.662	0.792	0.726	0.662	0.792	SUBCLONAL	1	TRUE	1	0.709131754538682	2		703	509	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981861	101981863	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	210	695	0	ENST00000282441.5:c.286_288del	p.Phe96del	p.F96del	ENST00000282441	NM_001130145.2	94	tcCTTc/tcc	1/9	1	2	FACETS	0.931	0.87	0.994	0.931	0.87	0.994	CLONAL	1	TRUE	1	0.709131754538682	2		695	636	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	175	695	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.851	0.788	0.916	0.851	0.788	0.916	CLONAL	1	TRUE	1	0.709131754538682	2		695	580	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687472	37687472	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	203	616	1	ENST00000447079.4:c.4382del	p.Gly1461AlafsTer38	p.G1461Afs*38	ENST00000447079	NM_015083.1	1459	tGg/tg	14/14	1	2	FACETS	0.897	0.836	0.96	0.897	0.836	0.96	CLONAL	1	TRUE	1	0.709131754538682	2		617	638	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5225777	5225777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751437578	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	196	605	0	ENST00000357368.4:c.2455G>A	p.Ala819Thr	p.A819T	ENST00000357368	NM_002850.3	819	Gct/Act	17/38	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.709131754538682	2		605	495	SUCCESS
ATM	472	MSKCC	GRCh37	11	108213958	108213959	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs775899653	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	138	491	0	ENST00000278616.4:c.8283_8284del	p.Gln2762AlafsTer6	p.Q2762Afs*6	ENST00000278616	NM_000051.3	2760	CTc/c	57/63	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.709131754538682	2		491	384	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627730	14627730	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	253	852	0	ENST00000254322.2:c.340A>G	p.Thr114Ala	p.T114A	ENST00000254322	NM_006145.1	114	Acc/Gcc	2/3	1	2	FACETS	0.914	0.858	0.97	0.914	0.858	0.97	CLONAL	1	TRUE	1	0.709131754538682	2		852	781	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911460	134911460	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768101201	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	26	667	0	ENST00000398015.3:c.1925G>A	p.Gly642Asp	p.G642D	ENST00000398015	NM_004441.4	642	gGc/gAc	11/16	NA	2	FACETS	0.145	0.115	0.181			1	INDETERMINATE	1	TRUE	NA	0.709131754538682	2		667	504	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938543	44938543	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	109	417	0	ENST00000377967.4:c.3091A>G	p.Thr1031Ala	p.T1031A	ENST00000377967	NM_021140.2	1031	Aca/Gca	20/29	NA	2	FACETS	0.881	0.799	0.965			1	INDETERMINATE	1	TRUE	NA	0.709131754538682	2		417	349	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120031	70120031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	193	791	3	ENST00000245479.2:c.1037del	p.Pro346ArgfsTer37	p.P346Rfs*37	ENST00000245479	NM_000346.3	345	Ccc/cc	3/3	1	2	FACETS	0.986	0.919	1	0.986	0.919	1	CLONAL	1	TRUE	1	0.709131754538682	2		794	552	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954643	17954643	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	217	777	1	ENST00000458235.1:c.251del	p.Pro84ArgfsTer63	p.P84Rfs*63	ENST00000458235	NM_000215.3	84	cCg/cg	3/24	1	2	FACETS	0.936	0.875	0.998	0.936	0.875	0.998	CLONAL	1	TRUE	1	0.709131754538682	2		778	654	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740171	162740171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs189206909	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	187	718	1	ENST00000367921.3:c.1373G>A	p.Arg458His	p.R458H	ENST00000367921	NM_006182.2	458	cGc/cAc	12/18	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.709131754538682	2		719	515	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346157	89346158	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs878855327	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	159	800	1	ENST00000301030.4:c.6792dup	p.Ala2265ArgfsTer8	p.A2265Rfs*8	ENST00000301030	NM_001256183.1	2264	-/C	9/13	1	2	FACETS	0.76	0.7	0.822	0.76	0.7	0.822	SUBCLONAL	1	TRUE	1	0.709131754538682	2		801	590	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533556	63533556	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147716924	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	231	764	0	ENST00000307078.5:c.1598C>T	p.Ala533Val	p.A533V	ENST00000307078	NM_004655.3	533	gCg/gTg	6/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.709131754538682	2		764	577	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656917	45656917	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	217	700	0	ENST00000407780.3:c.239A>G	p.Tyr80Cys	p.Y80C	ENST00000407780	NM_001283052.1	80	tAc/tGc	3/7	1	2	FACETS	0.929	0.868	0.991	0.929	0.868	0.991	CLONAL	1	TRUE	1	0.709131754538682	2		700	659	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649561	48649561	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	171	704	0	ENST00000376670.3:c.49del	p.Gln17SerfsTer120	p.Q17Sfs*120	ENST00000376670	NM_002049.3	15	ctC/ct	2/6	0.201382764525544	1	FACETS	0.614	0.569	0.66	0.614	0.569	0.66	INDETERMINATE	1	TRUE	0	0.709131754538682	1		704	507	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25458619	25458619	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs746967478	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	130	561	0	ENST00000264709.3:c.2554A>G	p.Met852Val	p.M852V	ENST00000264709	NM_175629.2	852	Atg/Gtg	22/23	1	2	FACETS	0.802	0.733	0.874	0.802	0.733	0.874	CLONAL	1	TRUE	1	0.709131754538682	2		561	457	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942053	71942053	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	58	831	2	ENST00000298229.2:c.1322del	p.Asn441ThrfsTer2	p.N441Tfs*2	ENST00000298229	NM_001567.3	439	ccA/cc	12/28	1	2	FACETS	0.238	0.204	0.276	0.238	0.204	0.276	SUBCLONAL	1	TRUE	1	0.709131754538682	2		833	686	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733329	85733329	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1052221974	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	122	497	0	ENST00000370580.1:c.683G>A	p.Arg228His	p.R228H	ENST00000370580	NM_003921.4	228	cGt/cAt	3/3	1	2	FACETS	0.967	0.884	1	0.967	0.884	1	CLONAL	1	TRUE	1	0.709131754538682	2		497	356	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	242	756	4	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.709131754538682	2		760	654	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871757	12871757	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	159	537	0	ENST00000228872.4:c.476-2A>G		p.X159_splice	ENST00000228872	NM_004064.3	159			NA	2	FACETS	0.881	0.813	0.951			1	INDETERMINATE	1	TRUE	NA	0.709131754538682	2		537	509	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392634	118392634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555053677	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	168	572	1	ENST00000534358.1:c.11666G>A	p.Arg3889Gln	p.R3889Q	ENST00000534358	NM_005933.3	3889	cGa/cAa	36/36	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.709131754538682	2		573	460	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156541	55156541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368266633	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	136	563	0	ENST00000257290.5:c.2942G>A	p.Arg981His	p.R981H	ENST00000257290	NM_006206.4	981	cGt/cAt	22/23	1	2	FACETS	0.854	0.783	0.928	0.854	0.783	0.928	CLONAL	1	TRUE	1	0.709131754538682	2		563	449	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	248	847	2	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.984	0.924	1	0.984	0.924	1	CLONAL	1	TRUE	1	0.709131754538682	2		849	711	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266175	198266175	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	17	442	1	ENST00000335508.6:c.2445del	p.Phe815LeufsTer19	p.F815Lfs*19	ENST00000335508	NM_012433.2	815	ttT/tt	17/25	1	2	FACETS	0.193	0.144	0.252	0.193	0.144	0.252	SUBCLONAL	1	TRUE	1	0.709131754538682	2		443	248	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639273	3639273	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760286353	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	207	737	0	ENST00000294008.3:c.4366C>T	p.Arg1456Cys	p.R1456C	ENST00000294008	NM_032444.2	1456	Cgc/Tgc	12/15	1	2	FACETS	0.921	0.859	0.984	0.921	0.859	0.984	CLONAL	1	TRUE	1	0.709131754538682	2		737	634	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38631981	38631981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1255149646	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	18	414	2	ENST00000299084.4:c.471del	p.Gln158SerfsTer16	p.Q158Sfs*16	ENST00000299084	NM_152594.2	156	cTt/ct	5/7	1	2	FACETS	0.144	0.108	0.187	0.144	0.108	0.187	SUBCLONAL	1	TRUE	1	0.709131754538682	2		416	353	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821353	72821353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	114	456	2	ENST00000268489.5:c.10822G>A	p.Ala3608Thr	p.A3608T	ENST00000268489	NM_006885.3	3608	Gct/Act	10/10	1	2	FACETS	0.999	0.911	1	0.999	0.911	1	CLONAL	1	TRUE	1	0.709131754538682	2		458	322	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15975514	15975514	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	35	427	0	ENST00000268712.3:c.3840del	p.Ser1281ValfsTer16	p.S1281Vfs*16	ENST00000268712	NM_006311.3	1280	ggG/gg	29/46	1	2	FACETS	0.268	0.22	0.322	0.268	0.22	0.322	SUBCLONAL	1	TRUE	1	0.709131754538682	2		427	368	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143021	58143021	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778188	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	84	695	0	ENST00000257904.6:c.763C>T	p.Arg255Cys	p.R255C	ENST00000257904	NM_000075.3	255	Cgc/Tgc	7/8	1	2	FACETS	0.34	0.3	0.383	0.34	0.3	0.383	SUBCLONAL	1	TRUE	1	0.709131754538682	2		695	697	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634731	158634731	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748791232	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	197	641	1	ENST00000263640.3:c.455G>A	p.Arg152His	p.R152H	ENST00000263640	NM_001105.4	152	cGc/cAc	5/11	1	2	FACETS	0.975	0.909	1	0.975	0.909	1	CLONAL	1	TRUE	1	0.709131754538682	2		642	570	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248692	212248692	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	174	680	0	ENST00000342788.4:c.3575C>T	p.Ser1192Phe	p.S1192F	ENST00000342788	NM_005235.2	1192	tCc/tTc	28/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.709131754538682	2		680	431	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549454	187549454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201060026	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	227	646	0	ENST00000441802.2:c.4664C>T	p.Thr1555Met	p.T1555M	ENST00000441802	NM_005245.3	1555	aCg/aTg	9/27	0.709131754538682	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.709131754538682	1		646	386	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242073	105242075	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs768025881	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	169	697	6	ENST00000349310.3:c.349_351del	p.Glu117del	p.E117del	ENST00000349310	NM_001014432.1	117	GAG/-	6/15	1	2	FACETS	0.856	0.791	0.922	0.856	0.791	0.922	CLONAL	1	TRUE	1	0.709131754538682	2		703	557	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164451	36164451	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	123	480	0	ENST00000300305.3:c.1424C>A	p.Ala475Asp	p.A475D	ENST00000300305		475	gCc/gAc	8/8	1	2	FACETS	0.913	0.834	0.994	0.913	0.834	0.994	CLONAL	1	TRUE	1	0.709131754538682	2		480	380	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778977	3778977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745551441	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	146	854	0	ENST00000262367.5:c.6071C>T	p.Ala2024Val	p.A2024V	ENST00000262367	NM_004380.2	2024	gCg/gTg	31/31	1	2	FACETS	0.616	0.564	0.671	0.616	0.564	0.671	SUBCLONAL	1	TRUE	1	0.709131754538682	2		854	668	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462662	29462662	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762395127	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	203	667	2	ENST00000389048.3:c.2239G>A	p.Gly747Arg	p.G747R	ENST00000389048	NM_004304.4	747	Ggg/Agg	13/29	1	2	FACETS	0.922	0.86	0.986	0.922	0.86	0.986	CLONAL	1	TRUE	1	0.709131754538682	2		669	621	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288852	33288852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767991311	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	210	651	0	ENST00000374542.5:c.700C>T	p.Arg234Cys	p.R234C	ENST00000374542	NM_001141970.1	234	Cgc/Tgc	3/8	1	2	FACETS	0.927	0.865	0.99	0.927	0.865	0.99	CLONAL	1	TRUE	1	0.709131754538682	2		651	639	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251265	99251265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760481311	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	105	671	1	ENST00000268035.6:c.569C>T	p.Pro190Leu	p.P190L	ENST00000268035	NM_000875.3	190	cCg/cTg	2/21	1	2	FACETS	0.5	0.449	0.554	0.5	0.449	0.554	SUBCLONAL	1	TRUE	1	0.709131754538682	2		672	592	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16097805	16097805	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	147	497	0	ENST00000268712.3:c.79T>C	p.Tyr27His	p.Y27H	ENST00000268712	NM_006311.3	27	Tat/Cat	2/46	1	2	FACETS	0.839	0.772	0.909	0.839	0.772	0.909	CLONAL	1	TRUE	1	0.709131754538682	2		497	494	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599964	10599964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1364007421	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	226	687	0	ENST00000171111.5:c.1612G>A	p.Asp538Asn	p.D538N	ENST00000171111	NM_203500.1	538	Gat/Aat	5/6	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.709131754538682	2		687	633	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1749278	1749279	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	132	465	0	ENST00000378609.4:c.93_94del	p.Gln32AspfsTer46	p.Q32Dfs*46	ENST00000378609	NM_002074.3	31	tcTCag/tcag	4/12	1	2	FACETS	0.91	0.834	0.989	0.91	0.834	0.989	CLONAL	1	TRUE	1	0.709131754538682	2		465	409	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691872	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs79375991	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	258	548	30	ENST00000295754.5:c.383del	p.Lys128SerfsTer35	p.K128Sfs*35	ENST00000295754	NM_003242.5	125	gAa/ga	3/7	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.709131754538682	2		578	559	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538820	23538820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753524833	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	185	581	0	ENST00000380871.4:c.619C>T	p.Arg207Trp	p.R207W	ENST00000380871	NM_006167.3	207	Cgg/Tgg	2/2	0.709131754538682	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.709131754538682	1		581	324	SUCCESS
AR	367	MSKCC	GRCh37	X	66766357	66766362	+	inframe_deletion	In_Frame_Del	DEL	GGCGGC	GGCGGC	-	rs746853821	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	23	336	2	ENST00000374690.3:c.1415_1420del	p.Gly472_Gly473del	p.G472_G473del	ENST00000374690	NM_000044.3	457	GGCGGC/-	1/8	0.201382764525544	1	FACETS	0.193	0.151	0.241	0.193	0.151	0.241	INDETERMINATE	1	TRUE	0	0.709131754538682	1		338	217	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303219	11303219	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	40	671	0	ENST00000361445.4:c.1364T>C	p.Val455Ala	p.V455A	ENST00000361445	NM_004958.3	455	gTg/gCg	9/58	1	2	FACETS	0.181	0.15	0.216	0.181	0.15	0.216	SUBCLONAL	1	TRUE	1	0.709131754538682	2		671	624	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106855	27106855	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1191962249	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	231	796	0	ENST00000324856.7:c.6466A>G	p.Ser2156Gly	p.S2156G	ENST00000324856	NM_006015.4	2156	Agt/Ggt	20/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.709131754538682	2		796	635	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797873	45797873	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	42	803	0	ENST00000450313.1:c.898T>C	p.Cys300Arg	p.C300R	ENST00000450313	NM_012222.2	300	Tgc/Cgc	10/16	1	2	FACETS	0.158	0.131	0.187	0.158	0.131	0.187	SUBCLONAL	1	TRUE	1	0.709131754538682	2		803	752	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332604	65332604	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs914598730	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	25	571	0	ENST00000342505.4:c.935A>G	p.Tyr312Cys	p.Y312C	ENST00000342505	NM_002227.2	312	tAc/tGc	7/25	NA	2	FACETS	0.158	0.124	0.197			1	INDETERMINATE	1	TRUE	NA	0.709131754538682	2		571	446	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332808	65332808	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	129	487	0	ENST00000342505.4:c.731del	p.Phe244SerfsTer5	p.F244Sfs*5	ENST00000342505	NM_002227.2	244	tTc/tc	7/25	NA	2	FACETS	0.957	0.877	1			1	INDETERMINATE	1	TRUE	NA	0.709131754538682	2		487	380	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446293	70446293	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	87	678	0	ENST00000373644.4:c.5233A>G	p.Thr1745Ala	p.T1745A	ENST00000373644	NM_030625.2	1745	Acg/Gcg	11/12	1	2	FACETS	0.391	0.346	0.438	0.391	0.346	0.438	SUBCLONAL	1	TRUE	1	0.709131754538682	2		678	628	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534225	534225	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	150	595	0	ENST00000451590.1:c.98A>G	p.Asp33Gly	p.D33G	ENST00000451590	NM_001130442.1	33	gAc/gGc	2/5	1	2	FACETS	0.807	0.742	0.874	0.807	0.742	0.874	CLONAL	1	TRUE	1	0.709131754538682	2		595	524	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936038	71936038	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	164	515	0	ENST00000298229.2:c.10G>A	p.Ala4Thr	p.A4T	ENST00000298229	NM_001567.3	4	Gcc/Acc	1/28	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.709131754538682	2		515	432	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942602	71942602	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	45	559	0	ENST00000298229.2:c.1558A>C	p.Asn520His	p.N520H	ENST00000298229	NM_001567.3	520	Aac/Cac	13/28	1	2	FACETS	0.23	0.193	0.272	0.23	0.193	0.272	SUBCLONAL	1	TRUE	1	0.709131754538682	2		559	551	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163389	108163389	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	114	507	0	ENST00000278616.4:c.4480T>A	p.Cys1494Ser	p.C1494S	ENST00000278616	NM_000051.3	1494	Tgt/Agt	30/63	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.709131754538682	2		507	314	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380238	25380238	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs770020203	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	116	454	0	ENST00000311936.3:c.220A>G	p.Thr74Ala	p.T74A	ENST00000311936	NM_004985.3	74	Act/Gct	3/5	1	2	FACETS	0.911	0.83	0.995	0.911	0.83	0.995	CLONAL	1	TRUE	1	0.709131754538682	2		454	359	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380267	25380267	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	133	493	0	ENST00000311936.3:c.191A>G	p.Tyr64Cys	p.Y64C	ENST00000311936	NM_004985.3	64	tAc/tGc	3/5	1	2	FACETS	0.95	0.871	1	0.95	0.871	1	CLONAL	1	TRUE	1	0.709131754538682	2		493	395	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420996	49420996	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	40	631	0	ENST00000301067.7:c.14753del	p.Pro4918LeufsTer77	p.P4918Lfs*77	ENST00000301067	NM_003482.3	4918	cCt/ct	48/54	1	2	FACETS	0.2	0.165	0.238	0.2	0.165	0.238	SUBCLONAL	1	TRUE	1	0.709131754538682	2		631	565	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444888	49444888	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	71	898	0	ENST00000301067.7:c.2578C>A	p.Leu860Met	p.L860M	ENST00000301067	NM_003482.3	860	Ctg/Atg	10/54	1	2	FACETS	0.271	0.236	0.309	0.271	0.236	0.309	SUBCLONAL	1	TRUE	1	0.709131754538682	2		898	738	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445484	49445484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769580238	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	48	864	1	ENST00000301067.7:c.1982G>A	p.Arg661His	p.R661H	ENST00000301067	NM_003482.3	661	cGc/cAc	10/54	1	2	FACETS	0.195	0.164	0.229	0.195	0.164	0.229	SUBCLONAL	1	TRUE	1	0.709131754538682	2		865	696	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489493	56489493	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	153	555	0	ENST00000267101.3:c.1958T>C	p.Val653Ala	p.V653A	ENST00000267101	NM_001982.3	653	gTa/gCa	17/28	1	2	FACETS	0.908	0.838	0.981	0.908	0.838	0.981	CLONAL	1	TRUE	1	0.709131754538682	2		555	475	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856610	111856610	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	28	638	0	ENST00000341259.2:c.661A>G	p.Arg221Gly	p.R221G	ENST00000341259	NM_005475.2	221	Agg/Ggg	2/8	1	2	FACETS	0.154	0.122	0.19	0.154	0.122	0.19	SUBCLONAL	1	TRUE	1	0.709131754538682	2		638	513	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794791	120794791	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	206	614	0	ENST00000257552.2:c.566T>C	p.Val189Ala	p.V189A	ENST00000257552	NM_002442.3	189	gTg/gCg	9/15	1	2	FACETS	0.905	0.844	0.967	0.905	0.844	0.967	CLONAL	1	TRUE	1	0.709131754538682	2		614	642	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245468	133245468	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377657524	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	200	673	0	ENST00000320574.5:c.1852G>A	p.Glu618Lys	p.E618K	ENST00000320574	NM_006231.2	618	Gag/Aag	17/49	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.709131754538682	2		673	549	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873824	35873824	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	179	519	0	ENST00000216797.5:c.27G>T	p.Gln9His	p.Q9H	ENST00000216797	NM_020529.2	9	caG/caT	1/6	1	2	FACETS	0.903	0.838	0.97	0.903	0.838	0.97	CLONAL	1	TRUE	1	0.709131754538682	2		519	559	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	69061215	69061215	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	102	341	0	ENST00000487270.1:c.1050C>A	p.Cys350Ter	p.C350*	ENST00000487270	NM_133509.3	350	tgC/tgA	11/11	1	2	FACETS	0.934	0.846	1	0.934	0.846	1	CLONAL	1	TRUE	1	0.709131754538682	2		341	308	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95597849	95597849	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	24	432	0	ENST00000393063.1:c.435C>A	p.His145Gln	p.H145Q	ENST00000393063	NM_030621.3	145	caC/caA	5/28	1	2	FACETS	0.185	0.145	0.232	0.185	0.145	0.232	SUBCLONAL	1	TRUE	1	0.709131754538682	2		432	366	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239339	105239341	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	253	862	1	ENST00000349310.3:c.1046_1048del	p.Phe349del	p.F349del	ENST00000349310	NM_001014432.1	349	tTCTac/tac	12/15	1	2	FACETS	0.984	0.925	1	0.984	0.925	1	CLONAL	1	TRUE	1	0.709131754538682	2		863	725	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041441	42041441	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	222	667	0	ENST00000219905.7:c.5636T>C	p.Val1879Ala	p.V1879A	ENST00000219905	NM_001164273.1	1879	gTt/gCt	17/24	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.709131754538682	2		667	588	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347072	347072	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	158	482	0	ENST00000262320.3:c.1939C>A	p.Arg647Ser	p.R647S	ENST00000262320	NM_003502.3	647	Cgc/Agc	7/11	1	2	FACETS	0.919	0.849	0.991	0.919	0.849	0.991	CLONAL	1	TRUE	1	0.709131754538682	2		482	485	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096190	2096190	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	56	587	0	ENST00000219066.1:c.317A>C	p.Lys106Thr	p.K106T	ENST00000219066	NM_002528.5	106	aAg/aCg	2/6	1	2	FACETS	0.278	0.237	0.321	0.278	0.237	0.321	SUBCLONAL	1	TRUE	1	0.709131754538682	2		587	569	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642733	3642733	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	173	632	0	ENST00000294008.3:c.2294G>T	p.Gly765Val	p.G765V	ENST00000294008	NM_032444.2	765	gGc/gTc	11/15	1	2	FACETS	0.859	0.795	0.925	0.859	0.795	0.925	CLONAL	1	TRUE	1	0.709131754538682	2		632	568	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026108	14026108	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs775161827	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	61	429	0	ENST00000311895.7:c.1068A>C	p.Lys356Asn	p.K356N	ENST00000311895	NM_005236.2	356	aaA/aaC	6/11	1	2	FACETS	0.642	0.559	0.73	0.642	0.559	0.73	SUBCLONAL	1	TRUE	1	0.709131754538682	2		429	268	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29422365	29422365	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	35	460	0	ENST00000356175.3:c.38T>C	p.Val13Ala	p.V13A	ENST00000356175	NM_000267.3	13	gTg/gCg	1/57	1	2	FACETS	0.216	0.177	0.261	0.216	0.177	0.261	SUBCLONAL	1	TRUE	1	0.709131754538682	2		460	456	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867629	78867629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	205	711	0	ENST00000306801.3:c.2365C>T	p.Arg789Cys	p.R789C	ENST00000306801	NM_020761.2	789	Cgc/Tgc	20/34	1	2	FACETS	0.948	0.885	1	0.948	0.885	1	CLONAL	1	TRUE	1	0.709131754538682	2		711	610	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756689	756689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	177	638	0	ENST00000314574.4:c.139G>A	p.Ala47Thr	p.A47T	ENST00000314574	NM_005433.3	47	Gca/Aca	2/12	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.709131754538682	2		638	487	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2206754	2206754	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	25	531	0	ENST00000398665.3:c.814T>A	p.Phe272Ile	p.F272I	ENST00000398665	NM_032482.2	272	Ttt/Att	10/28	1	2	FACETS	0.141	0.11	0.176	0.141	0.11	0.176	SUBCLONAL	1	TRUE	1	0.709131754538682	2		531	500	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6213975	6213976	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs772076449	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	110	671	0	ENST00000252674.7:c.1381dup	p.Gln461ProfsTer23	p.Q461Pfs*23	ENST00000252674	NM_005934.3	461	cag/cCag	9/12	1	2	FACETS	0.613	0.553	0.676	0.613	0.553	0.676	SUBCLONAL	1	TRUE	1	0.709131754538682	2		671	506	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132219	7132219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	198	691	2	ENST00000302850.5:c.2792C>T	p.Ala931Val	p.A931V	ENST00000302850	NM_000208.2	931	gCg/gTg	14/22	1	2	FACETS	0.934	0.87	0.999	0.934	0.87	0.999	CLONAL	1	TRUE	1	0.709131754538682	2		693	598	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354014	15354014	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1175491600	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	72	249	0	ENST00000263377.2:c.2866C>G	p.Pro956Ala	p.P956A	ENST00000263377	NM_058243.2	956	Ccc/Gcc	14/20	1	2	FACETS	0.995	0.886	1	0.995	0.886	1	CLONAL	1	TRUE	1	0.709131754538682	2		249	204	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367010	15367010	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	57	546	0	ENST00000263377.2:c.1616A>G	p.Lys539Arg	p.K539R	ENST00000263377	NM_058243.2	539	aAg/aGg	9/20	1	2	FACETS	0.294	0.252	0.34	0.294	0.252	0.34	SUBCLONAL	1	TRUE	1	0.709131754538682	2		546	546	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976890	18976890	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	207	575	1	ENST00000262803.5:c.3275A>G	p.Asp1092Gly	p.D1092G	ENST00000262803	NM_002911.3	1092	gAc/gGc	23/24	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.709131754538682	2		576	573	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211298	36211298	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	197	774	0	ENST00000222270.7:c.1049G>T	p.Gly350Val	p.G350V	ENST00000222270	NM_014727.1	350	gGg/gTg	3/37	1	2	FACETS	0.798	0.742	0.856	0.798	0.742	0.856	SUBCLONAL	1	TRUE	1	0.709131754538682	2		774	696	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223671	36223671	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368981212	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	234	862	0	ENST00000222270.7:c.6221C>T	p.Ala2074Val	p.A2074V	ENST00000222270	NM_014727.1	2074	gCg/gTg	28/37	1	2	FACETS	0.928	0.87	0.988	0.928	0.87	0.988	CLONAL	1	TRUE	1	0.709131754538682	2		862	711	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727865	41727865	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774284669	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	187	670	0	ENST00000301178.4:c.490G>A	p.Gly164Arg	p.G164R	ENST00000301178	NM_021913.4	164	Gga/Aga	4/20	1	2	FACETS	0.961	0.894	1	0.961	0.894	1	CLONAL	1	TRUE	1	0.709131754538682	2		670	549	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45864812	45864815	+	frameshift_variant	Frame_Shift_Del	DEL	AGTT	AGTT	-	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	250	747	0	ENST00000391945.4:c.1204_1207del	p.Asn402LeufsTer81	p.N402Lfs*81	ENST00000391945	NM_000400.3	402	AACTtt/tt	12/23	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.709131754538682	2		747	664	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867574	45867574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs755766334	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	75	877	0	ENST00000391945.4:c.734A>G	p.Asp245Gly	p.D245G	ENST00000391945	NM_000400.3	245	gAc/gGc	9/23	1	2	FACETS	0.322	0.282	0.365	0.322	0.282	0.365	SUBCLONAL	1	TRUE	1	0.709131754538682	2		877	657	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422638	47422638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	57	607	1	ENST00000404338.3:c.706G>A	p.Val236Met	p.V236M	ENST00000404338	NM_004491.4	236	Gtg/Atg	1/6	1	2	FACETS	0.295	0.253	0.341	0.295	0.253	0.341	SUBCLONAL	1	TRUE	1	0.709131754538682	2		608	545	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641436	47641436	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	137	361	0	ENST00000233146.2:c.821T>G	p.Ile274Ser	p.I274S	ENST00000233146	NM_000251.2	274	aTc/aGc	5/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.709131754538682	2		361	308	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721133	61721133	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs753951461	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	147	521	0	ENST00000401558.2:c.1141T>C	p.Tyr381His	p.Y381H	ENST00000401558	NM_003400.3	381	Tat/Cat	12/25	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.709131754538682	2		521	362	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096034	178096034	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	220	691	0	ENST00000397062.3:c.1297A>G	p.Ser433Gly	p.S433G	ENST00000397062	NM_006164.4	433	Agt/Ggt	5/5	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.709131754538682	2		691	615	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267716	198267716	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	18	466	0	ENST00000335508.6:c.1763A>G	p.Tyr588Cys	p.Y588C	ENST00000335508	NM_012433.2	588	tAt/tGt	13/25	1	2	FACETS	0.185	0.139	0.239	0.185	0.139	0.239	SUBCLONAL	1	TRUE	1	0.709131754538682	2		466	275	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403247	213403247	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	28	602	0	ENST00000342788.4:c.8C>A	p.Pro3Gln	p.P3Q	ENST00000342788	NM_005235.2	3	cCg/cAg	1/28	1	2	FACETS	0.154	0.123	0.19	0.154	0.123	0.19	SUBCLONAL	1	TRUE	1	0.709131754538682	2		602	512	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29279824	29279825	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	134	160	0	ENST00000544604.2:c.70_71insT	p.Arg24LeufsTer85	p.R24Lfs*85	ENST00000544604	NM_001206998.1	24	cgc/cTgc	1/9	0.708909515299255	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.709131754538682	2		160	156	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732924	30732924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	187	557	0	ENST00000295754.5:c.1537G>A	p.Val513Met	p.V513M	ENST00000295754	NM_003242.5	513	Gtg/Atg	7/7	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.709131754538682	2		557	525	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042480	37042480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63751069	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	13	390	0	ENST00000231790.2:c.242C>T	p.Thr81Ile	p.T81I	ENST00000231790	NM_000249.3	81	aCt/aTt	3/19	1	2	FACETS	0.144	0.102	0.195	0.144	0.102	0.195	SUBCLONAL	1	TRUE	1	0.709131754538682	2		390	255	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49399942	49399942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1420305556	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	202	546	0	ENST00000418115.1:c.395C>T	p.Ala132Val	p.A132V	ENST00000418115	NM_001664.2	132	gCc/gTc	4/5	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.709131754538682	2		546	566	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63982080	63982080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	53	726	0	ENST00000398590.3:c.2582C>T	p.Ala861Val	p.A861V	ENST00000398590	NM_001177387.1	861	gCc/gTc	12/14	1	2	FACETS	0.241	0.205	0.281	0.241	0.205	0.281	SUBCLONAL	1	TRUE	1	0.709131754538682	2		726	620	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63985181	63985181	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	44	592	0	ENST00000398590.3:c.2787del	p.Phe929LeufsTer30	p.F929Lfs*30	ENST00000398590	NM_001177387.1	928	acT/ac	14/14	1	2	FACETS	0.253	0.212	0.299	0.253	0.212	0.299	SUBCLONAL	1	TRUE	1	0.709131754538682	2		592	490	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200784	128200784	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	149	538	0	ENST00000341105.2:c.1021G>T	p.Ala341Ser	p.A341S	ENST00000341105	NM_032638.4	341	Gcc/Tcc	5/6	1	2	FACETS	0.926	0.853	1	0.926	0.853	1	CLONAL	1	TRUE	1	0.709131754538682	2		538	454	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204800	128204800	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	183	705	1	ENST00000341105.2:c.641A>G	p.Gln214Arg	p.Q214R	ENST00000341105	NM_032638.4	214	cAg/cGg	3/6	1	2	FACETS	0.944	0.877	1	0.944	0.877	1	CLONAL	1	TRUE	1	0.709131754538682	2		706	547	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138431115	138431115	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	43	370	1	ENST00000289153.2:c.1334T>C	p.Val445Ala	p.V445A	ENST00000289153	NM_006219.2	445	gTt/gCt	8/22	1	2	FACETS	0.507	0.428	0.594	0.507	0.428	0.594	SUBCLONAL	1	TRUE	1	0.709131754538682	2		371	239	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446919	187446919	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	58	826	0	ENST00000232014.4:c.1274T>C	p.Leu425Pro	p.L425P	ENST00000232014	NM_001130845.1	425	cTc/cCc	5/10	1	2	FACETS	0.237	0.203	0.274	0.237	0.203	0.274	SUBCLONAL	1	TRUE	1	0.709131754538682	2		826	691	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55524237	55524237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747253141	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	153	683	0	ENST00000288135.5:c.56G>A	p.Arg19His	p.R19H	ENST00000288135	NM_000222.2	19	cGc/cAc	1/21	1	2	FACETS	0.928	0.856	1	0.928	0.856	1	CLONAL	1	TRUE	1	0.709131754538682	2		683	465	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796907	57796907	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	36	813	0	ENST00000309042.7:c.1883T>C	p.Val628Ala	p.V628A	ENST00000309042	NM_005612.4	628	gTg/gCg	4/4	1	2	FACETS	0.162	0.133	0.196	0.162	0.133	0.196	SUBCLONAL	1	TRUE	1	0.709131754538682	2		813	625	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352337	143352337	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	135	411	0	ENST00000262992.4:c.76del	p.Asp26ThrfsTer34	p.D26Tfs*34	ENST00000262992	NM_001101669.1	26	Gac/ac	2/24	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.709131754538682	2		411	371	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144336649	144336649	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	132	407	0	ENST00000262995.4:c.92T>C	p.Phe31Ser	p.F31S	ENST00000262995	NM_207123.2	31	tTc/tCc	2/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.709131754538682	2		407	302	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1296374	1296374	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	19	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.167	0.126	0.215	0.167	0.126	0.215	SUBCLONAL	1	TRUE	1	0.709131754538682	2		429	321	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564497	86564497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	228	758	0	ENST00000274376.6:c.229G>A	p.Val77Met	p.V77M	ENST00000274376	NM_002890.2	77	Gtg/Atg	1/25	1	2	FACETS	0.868	0.812	0.925	0.868	0.812	0.925	CLONAL	1	TRUE	1	0.709131754538682	2		758	741	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672795	86672795	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	27	489	0	ENST00000274376.6:c.2282T>C	p.Leu761Pro	p.L761P	ENST00000274376	NM_002890.2	761	cTt/cCt	17/25	1	2	FACETS	0.216	0.171	0.266	0.216	0.171	0.266	SUBCLONAL	1	TRUE	1	0.709131754538682	2		489	353	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973792	131973792	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	41	370	0	ENST00000265335.6:c.3495A>G	p.Ile1165Met	p.I1165M	ENST00000265335		1165	atA/atG	23/25	1	2	FACETS	0.361	0.302	0.427	0.361	0.302	0.427	SUBCLONAL	1	TRUE	1	0.709131754538682	2		370	320	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439426	149439426	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	183	522	0	ENST00000286301.3:c.1970-1G>T		p.X657_splice	ENST00000286301	NM_005211.3	657			1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.709131754538682	2		522	509	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523182	176523182	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	248	849	0	ENST00000292408.4:c.1944+2T>C		p.X648_splice	ENST00000292408	NM_213647.1	648			1	2	FACETS	0.982	0.923	1	0.982	0.923	1	CLONAL	1	TRUE	1	0.709131754538682	2		849	712	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039597	180039597	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	192	631	0	ENST00000261937.6:c.3446T>C	p.Leu1149Pro	p.L1149P	ENST00000261937	NM_182925.4	1149	cTg/cCg	26/30	0.143072484847172	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.709131754538682	0		631	458	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401714	401714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1400777715	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	270	915	0	ENST00000380956.4:c.1036C>T	p.Arg346Trp	p.R346W	ENST00000380956	NM_001195286.1	346	Cgg/Tgg	7/9	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.709131754538682	2		915	689	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187497	32187497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780911923	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	273	818	0	ENST00000375023.3:c.1382G>A	p.Cys461Tyr	p.C461Y	ENST00000375023	NM_004557.3	461	tGc/tAc	8/30	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.709131754538682	2		818	715	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37141833	37141833	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	213	637	0	ENST00000373509.5:c.908A>G	p.His303Arg	p.H303R	ENST00000373509	NM_002648.3	303	cAc/cGc	6/6	1	2	FACETS	0.993	0.929	1	0.993	0.929	1	CLONAL	1	TRUE	1	0.709131754538682	2		637	605	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129255	152129255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	171	672	0	ENST00000206249.3:c.208G>A	p.Ala70Thr	p.A70T	ENST00000206249	NM_000125.3	70	Gcg/Acg	1/8	1	2	FACETS	0.984	0.913	1	0.984	0.913	1	CLONAL	1	TRUE	1	0.709131754538682	2		672	490	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522329	157522329	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	42	803	0	ENST00000346085.5:c.4601G>T	p.Arg1534Leu	p.R1534L	ENST00000346085	NM_020732.3	1534	cGc/cTc	18/20	1	2	FACETS	0.162	0.134	0.192	0.162	0.134	0.192	SUBCLONAL	1	TRUE	1	0.709131754538682	2		803	733	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249008	55249008	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	32	705	0	ENST00000275493.2:c.2306T>C	p.Val769Ala	p.V769A	ENST00000275493	NM_005228.3	769	gTg/gCg	20/28	1	2	FACETS	0.145	0.117	0.177	0.145	0.117	0.177	SUBCLONAL	1	TRUE	1	0.709131754538682	2		705	623	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508670	106508670	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	26	599	0	ENST00000359195.3:c.664A>G	p.Ile222Val	p.I222V	ENST00000359195	NM_002649.2	222	Atc/Gtc	2/11	1	2	FACETS	0.144	0.113	0.179	0.144	0.113	0.179	SUBCLONAL	1	TRUE	1	0.709131754538682	2		599	511	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124532409	124532409	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	12	303	0	ENST00000357628.3:c.35C>T	p.Thr12Ile	p.T12I	ENST00000357628	NM_015450.2	12	aCa/aTa	6/19	1	2	FACETS	0.237	0.167	0.322	0.237	0.167	0.322	SUBCLONAL	1	TRUE	1	0.709131754538682	2		303	143	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859422	151859422	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	195	705	0	ENST00000262189.6:c.11240A>G	p.Asn3747Ser	p.N3747S	ENST00000262189	NM_170606.2	3747	aAc/aGc	43/59	1	2	FACETS	0.902	0.839	0.966	0.902	0.839	0.966	CLONAL	1	TRUE	1	0.709131754538682	2		705	610	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945040	151945040	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	33	323	0	ENST00000262189.6:c.2479A>G	p.Lys827Glu	p.K827E	ENST00000262189	NM_170606.2	827	Aaa/Gaa	14/59	1	2	FACETS	0.378	0.31	0.455	0.378	0.31	0.455	SUBCLONAL	1	TRUE	1	0.709131754538682	2		323	246	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020519	69020519	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781428016	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	129	467	0	ENST00000288368.4:c.2891G>A	p.Ser964Asn	p.S964N	ENST00000288368	NM_024870.2	964	aGc/aAc	24/40	0.709131754538682	3	FACETS	0.998	0.91	1	0.499	0.455	0.545	CLONAL	1	TRUE	1	0.709131754538682	3		467	494	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104648	69104648	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	178	598	0	ENST00000288368.4:c.4492T>G	p.Cys1498Gly	p.C1498G	ENST00000288368	NM_024870.2	1498	Tgt/Ggt	37/40	0.709131754538682	3	FACETS	1	0.959	1	0.527	0.488	0.568	CLONAL	1	TRUE	1	0.709131754538682	3		598	645	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739313	145739313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	222	679	0	ENST00000428558.2:c.2057A>G	p.Gln686Arg	p.Q686R	ENST00000428558	NM_004260.3	686	cAg/cGg	12/22	0.702518780714677	3	FACETS	1	0.95	1	0.511	0.476	0.546	CLONAL	1	TRUE	1	0.709131754538682	3		679	830	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742434	145742434	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs544163984	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	436	719	0	ENST00000428558.2:c.354G>T	p.Gln118His	p.Q118H	ENST00000428558	NM_004260.3	118	caG/caT	4/22	0.702518780714677	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.709131754538682	3		719	795	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2039826	2039826	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs752254994	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	35	776	1	ENST00000349721.2:c.716C>A	p.Pro239Gln	p.P239Q	ENST00000349721	NM_003070.3	239	cCg/cAg	4/34	1	2	FACETS	0.142	0.116	0.172	0.142	0.116	0.172	SUBCLONAL	1	TRUE	1	0.709131754538682	2		777	694	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404579	8404579	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	112	453	0	ENST00000356435.5:c.4168A>G	p.Ile1390Val	p.I1390V	ENST00000356435		1390	Atc/Gtc	25/35	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.709131754538682	2		453	282	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202905	27202905	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	129	578	0	ENST00000380036.4:c.1997C>A	p.Ser666Tyr	p.S666Y	ENST00000380036	NM_000459.3	666	tCt/tAt	13/23	1	2	FACETS	0.943	0.864	1	0.943	0.864	1	CLONAL	1	TRUE	1	0.709131754538682	2		578	386	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409450	80409450	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	69	228	0	ENST00000286548.4:c.664A>G	p.Asn222Asp	p.N222D	ENST00000286548	NM_002072.3	222	Aat/Gat	5/7	0.180338985062098	6	FACETS	1	0.931	1			1	INDETERMINATE	2	TRUE	NA	0.709131754538682	6		228	219	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923154	39923154	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	29	616	0	ENST00000378444.4:c.3554A>G	p.Asp1185Gly	p.D1185G	ENST00000378444	NM_001123385.1	1185	gAc/gGc	8/15	NA	2	FACETS	0.152	0.122	0.187			1	INDETERMINATE	1	TRUE	NA	0.709131754538682	2		616	537	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034519	123034519	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	93	265	0	ENST00000355640.3:c.1276T>A	p.Ser426Thr	p.S426T	ENST00000355640		426	Tca/Aca	6/7	0.201382764525544	1	FACETS	0.739	0.67	0.81	0.739	0.67	0.81	INDETERMINATE	1	TRUE	0	0.709131754538682	1		265	229	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858068	152858068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	219	695	0	ENST00000406277.2:c.547C>T	p.Arg183Cys	p.R183C	ENST00000406277	NM_152274.4	183	Cgc/Tgc	6/7	0.201382764525544	1	FACETS	0.764	0.717	0.811	0.764	0.717	0.811	INDETERMINATE	1	TRUE	0	0.709131754538682	1		695	522	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636943	158636943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1403278698	NA	P-0063156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	41	757	0	ENST00000263640.3:c.237G>A	p.Met79Ile	p.M79I	ENST00000263640	NM_001105.4	79	atG/atA	4/11	0.393673863389163	3	FACETS	0.31	0.258	0.368	0.155	0.129	0.184	INDETERMINATE	1	TRUE	1	0.77695556833723	3		757	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0063157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	391	600	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.481030052186025	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.486958642502185	2		600	751	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0063157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	319	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.445667481003291	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	3	TRUE	1	0.486958642502185	4		434	640	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937095	48937095	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0063157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	64	210	0	ENST00000267163.4:c.861+2T>G		p.X287_splice	ENST00000267163	NM_000321.2	287			0.486958642502185	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	2	TRUE	0	0.486958642502185	2		210	127	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	78128726	78128726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	173	863	0	ENST00000361507.4:c.41G>A	p.Arg14Lys	p.R14K	ENST00000361507	NM_080491.2	14	aGg/aAg	1/10	0.232961566340281	4	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.486958642502185	4		863	936	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829005	72829007	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs1304517616	NA	P-0063157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	166	803	1	ENST00000268489.5:c.7574_7576del	p.Pro2525del	p.P2525del	ENST00000268489	NM_006885.3	2525	cCTCag/cag	9/10	NA	2	FACETS	0.968	0.892	1			1	INDETERMINATE	1	TRUE	NA	0.486958642502185	2		804	704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0063198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	50	582	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.3	1	FACETS	0.519	0.44	0.606	0.519	0.44	0.606	SUBCLONAL	1	TRUE	0	0.31	1		582	525	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	65	559	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	1	2	FACETS	0.615	0.533	0.704	0.615	0.533	0.704	SUBCLONAL	1	TRUE	1	0.31	2		559	682	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696462	47696462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	61	532	0	ENST00000347630.2:c.361C>T	p.Arg121Trp	p.R121W	ENST00000347630	NM_001007230.1	121	Cgg/Tgg	6/11	1	2	FACETS	0.633	0.545	0.728	0.633	0.545	0.728	SUBCLONAL	1	TRUE	1	0.31	2		532	622	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631434	117631434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	25	358	0	ENST00000368508.3:c.6244G>A	p.Ala2082Thr	p.A2082T	ENST00000368508	NM_002944.2	2082	Gct/Act	40/43	1	2	FACETS	0.284	0.223	0.355	0.284	0.223	0.355	SUBCLONAL	1	TRUE	1	0.385591652453139	2		358	456	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0063199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	43	315	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.471	0.394	0.556	0.471	0.394	0.556	SUBCLONAL	1	TRUE	1	0.385591652453139	2		315	474	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404742	404742	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	90	492	0	ENST00000399788.2:c.4452G>T	p.Met1484Ile	p.M1484I	ENST00000399788	NM_001042603.1	1484	atG/atT	26/28	1	2	FACETS	0.629	0.558	0.705	0.629	0.558	0.705	SUBCLONAL	1	TRUE	1	0.385591652453139	2		492	742	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420540	49420541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0063199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	47	638	0	ENST00000301067.7:c.15208dup	p.Tyr5070LeufsTer2	p.Y5070Lfs*2	ENST00000301067	NM_003482.3	5070	tat/tTat	48/54	1	2	FACETS	0.279	0.234	0.328	0.279	0.234	0.328	SUBCLONAL	1	TRUE	1	0.385591652453139	2		638	875	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005695	42005695	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0063199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	37	462	0	ENST00000219905.7:c.3430+1G>A		p.X1144_splice	ENST00000219905	NM_001164273.1	1144			1	2	FACETS	0.333	0.274	0.4	0.333	0.274	0.4	SUBCLONAL	1	TRUE	1	0.385591652453139	2		462	576	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142955	30142955	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	47	640	1	ENST00000389048.3:c.571C>A	p.Pro191Thr	p.P191T	ENST00000389048	NM_004304.4	191	Ccc/Acc	1/29	1	2	FACETS	0.29	0.243	0.341	0.29	0.243	0.341	SUBCLONAL	1	TRUE	1	0.385591652453139	2		641	842	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636772	176636772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	73	510	0	ENST00000439151.2:c.1372G>A	p.Glu458Lys	p.E458K	ENST00000439151	NM_022455.4	458	Gaa/Aaa	5/23	1	2	FACETS	0.488	0.426	0.555	0.488	0.426	0.555	SUBCLONAL	1	TRUE	1	0.385591652453139	2		510	776	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386512	81386512	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	25	345	0	ENST00000222390.5:c.475G>T	p.Glu159Ter	p.E159*	ENST00000222390	NM_000601.4	159	Gaa/Taa	4/18	1	2	FACETS	0.259	0.204	0.324	0.259	0.204	0.324	SUBCLONAL	1	TRUE	1	0.385591652453139	2		345	500	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509348	106509348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	56	592	0	ENST00000359195.3:c.1342G>T	p.Glu448Ter	p.E448*	ENST00000359195	NM_002649.2	448	Gag/Tag	2/11	1	2	FACETS	0.343	0.292	0.398	0.343	0.292	0.398	SUBCLONAL	1	TRUE	1	0.385591652453139	2		592	848	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0063200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	157	586	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.602392089222153	1	FACETS	0.977	0.907	1	0.977	0.907	1	CLONAL	1	TRUE	0	0.602392089222153	1		586	373	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0063200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	161	464	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	0.975	0.9	1	0.975	0.9	1	CLONAL	1	TRUE	1	0.602392089222153	2		464	548	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692910	89692910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	126	401	1	ENST00000371953.3:c.394G>A	p.Gly132Ser	p.G132S	ENST00000371953	NM_000314.4	132	Ggt/Agt	5/9	1	2	FACETS	0.773	0.703	0.846	0.773	0.703	0.846	SUBCLONAL	1	TRUE	1	0.602392089222153	2		402	541	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338671	70338671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	153	422	0	ENST00000374080.3:c.67G>T	p.Asp23Tyr	p.D23Y	ENST00000374080		23	Gat/Tat	1/45	0.196565862789454	1	FACETS	0.879	0.813	0.946	0.879	0.813	0.946	INDETERMINATE	1	TRUE	0	0.602392089222153	1		422	404	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023952	27023952	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	120	392	0	ENST00000324856.7:c.1060del	p.Gln354AsnfsTer9	p.Q354Nfs*9	ENST00000324856	NM_006015.4	353	gCc/gc	1/20	0.602392089222153	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.602392089222153	1		392	237	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981516	70981516	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	44	568	0	ENST00000276594.2:c.580C>T	p.Arg194Trp	p.R194W	ENST00000276594	NM_024504.3	194	Cgg/Tgg	2/8	0.352823166861608	3	FACETS	0.271	0.226	0.32	0.135	0.113	0.16	INDETERMINATE	1	TRUE	1	0.602392089222153	3		568	702	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624242	89624242	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	66	153	0	ENST00000371953.3:c.18del	p.Glu7ArgfsTer17	p.E7Rfs*17	ENST00000371953	NM_000314.4	6	Aaa/aa	1/9	1	2	FACETS	0.996	0.878	1	0.996	0.878	1	CLONAL	1	TRUE	1	0.602392089222153	2		153	220	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546126	41546126	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	29	567	0	ENST00000263253.7:c.2741C>T	p.Pro914Leu	p.P914L	ENST00000263253	NM_001429.3	914	cCt/cTt	14/31	0.602392089222153	1	FACETS	0.13	0.104	0.16	0.13	0.104	0.16	SUBCLONAL	1	TRUE	0	0.602392089222153	1		567	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0063201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	83	479	0	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		479	551	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0063202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	201	462	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.31368644591758	5	FACETS	0.992	0.925	1	0.992	0.925	1	CLONAL	3	TRUE	2	0.31368644591758	5		462	633	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0063202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	21	190	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.298220640245689	4	FACETS	0.435	0.334	0.553	0.145	0.111	0.185	SUBCLONAL	1	TRUE	1	0.31368644591758	4		190	404	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1620984	1620984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772853413	NA	P-0063202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	114	773	0	ENST00000344749.5:c.1076C>T	p.Ser359Phe	p.S359F	ENST00000344749	NM_001136139.2	359	tCc/tTc	13/19	0.31368644591758	2	FACETS	0.964	0.868	1	0.482	0.434	0.533	CLONAL	1	TRUE	0	0.31368644591758	2		773	754	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65569055	65569055	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0063202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	107	454	0	ENST00000358664.4:c.3G>A	p.Met1?	p.M1?	ENST00000358664	NM_002382.4	1	atG/atA	1/5	0.31368644591758	3	FACETS	0.999	0.903	1	0.999	0.903	1	CLONAL	2	TRUE	1	0.31368644591758	3		454	395	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066630	94066630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	80	593	0	ENST00000369303.4:c.1129G>A	p.Gly377Ser	p.G377S	ENST00000369303	NM_004440.3	377	Ggc/Agc	5/17	1	2	FACETS	0.917	0.809	1	0.917	0.809	1	CLONAL	1	TRUE	1	0.31368644591758	2		593	556	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798163	32798163	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	179	632	0	ENST00000374899.4:c.1516G>T	p.Gly506Trp	p.G506W	ENST00000374899	NM_018833.2	506	Ggg/Tgg	9/12	0.263315762897629	4	FACETS	0.974	0.899	1	0.974	0.899	1	CLONAL	2	TRUE	2	0.31368644591758	4		632	770	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206624	108206624	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	149	500	0	ENST00000278616.4:c.8204G>T	p.Cys2735Phe	p.C2735F	ENST00000278616	NM_000051.3	2735	tGt/tTt	56/63	0.284495435766966	2	FACETS	0.928	0.853	1	0.928	0.853	1	CLONAL	2	TRUE	0	0.31368644591758	2		500	512	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2202753	2202753	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	173	546	0	ENST00000398665.3:c.762G>T	p.Lys254Asn	p.K254N	ENST00000398665	NM_032482.2	254	aaG/aaT	9/28	0.31368644591758	2	FACETS	0.987	0.914	1	0.987	0.914	1	CLONAL	2	TRUE	0	0.31368644591758	2		546	559	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793420	42793420	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	77	699	0	ENST00000575354.2:c.1222G>T	p.Gly408Cys	p.G408C	ENST00000575354	NM_015125.3	408	Ggt/Tgt	8/20	0.31368644591758	3	FACETS	0.9	0.791	1	0.45	0.395	0.509	CLONAL	1	TRUE	1	0.31368644591758	3		699	631	SUCCESS
ALK	238	MSKCC	GRCh37	2	29450460	29450460	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	124	755	0	ENST00000389048.3:c.2894T>A	p.Leu965Gln	p.L965Q	ENST00000389048	NM_004304.4	965	cTg/cAg	17/29	0.31368644591758	4	FACETS	1	0.949	1	0.359	0.324	0.396	CLONAL	1	TRUE	1	0.31368644591758	4		755	965	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248576	212248576	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	66	683	0	ENST00000342788.4:c.3691G>C	p.Glu1231Gln	p.E1231Q	ENST00000342788	NM_005235.2	1231	Gag/Cag	28/28	0.31368644591758	3	FACETS	0.573	0.496	0.657	0.287	0.248	0.329	SUBCLONAL	1	TRUE	1	0.31368644591758	3		683	849	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560994	9560994	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	75	619	0	ENST00000353224.5:c.788A>T	p.Asp263Val	p.D263V	ENST00000353224	NM_177990.2	263	gAc/gTc	4/10	0.294930686304292	3	FACETS	0.972	0.853	1	0.486	0.426	0.55	CLONAL	1	TRUE	1	0.31368644591758	3		619	569	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295262	1295262	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0063202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	274	473	0				ENST00000310581	NM_198253.2	-/1132			0.31368644591758	7	FACETS	1	0.959	1	1	0.959	1	CLONAL	5	TRUE	2	0.31368644591758	7		473	614	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206848	162206848	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	78	531	0	ENST00000366898.1:c.827A>G	p.Gln276Arg	p.Q276R	ENST00000366898	NM_004562.2	276	cAg/cGg	7/12	1	2	FACETS	0.893	0.786	1	0.893	0.786	1	CLONAL	1	TRUE	1	0.31368644591758	2		531	557	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207468	29207468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	163	409	0	ENST00000240100.2:c.328G>A	p.Glu110Lys	p.E110K	ENST00000240100	NM_001394.6	110	Gag/Aag	1/4	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	2	TRUE	NA	0.31368644591758	2		409	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782620	NA	P-0063203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	294	653	0	ENST00000269305.4:c.427G>A	p.Val143Met	p.V143M	ENST00000269305	NM_001126112.2	143	Gtg/Atg	5/11	0.651689260047773	2	FACETS	0.983	0.941	1	0.983	0.941	1	CLONAL	2	TRUE	0	0.651689260047773	2		653	459	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0063203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	91	359	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	0.651689260047773	1	FACETS	0.856	0.775	0.938	0.856	0.775	0.938	CLONAL	1	TRUE	0	0.651689260047773	1		359	220	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0063203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	409	440	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.651689260047773	5	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	2	0.651689260047773	5		440	781	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631120	67631120	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	207	546	0	ENST00000272342.5:c.1306G>T	p.Ala436Ser	p.A436S	ENST00000272342	NM_019002.3	436	Gcc/Tcc	5/6	0.494478643129569	4	FACETS	0.822	0.767	0.879	0.822	0.767	0.879	CLONAL	2	TRUE	2	0.651689260047773	4		546	638	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0063204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	74	1032	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.261688575865902	4	FACETS	0.996	0.88	1	0.996	0.88	1	CLONAL	2	TRUE	2	0.311083711472931	4		1032	313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0063204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	72	586	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.274950489009699	2	FACETS	0.956	0.847	1	0.956	0.847	1	CLONAL	2	TRUE	0	0.311083711472931	2		586	242	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955550	48955550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913304	NA	P-0063204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	78	370	0	ENST00000267163.4:c.1666C>T	p.Arg556Ter	p.R556*	ENST00000267163	NM_000321.2	556	Cga/Tga	17/27	0.274950489009699	2	FACETS	0.943	0.839	1	0.943	0.839	1	CLONAL	2	TRUE	0	0.311083711472931	2		370	266	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0063206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	150	704	0	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	0.614858869422409	1	FACETS	0.899	0.832	0.967	0.899	0.832	0.967	CLONAL	1	TRUE	0	0.614858869422409	1		704	376	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591924	48591924	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs377767348	NA	P-0063206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	121	530	0	ENST00000342988.3:c.1087T>C	p.Cys363Arg	p.C363R	ENST00000342988	NM_005359.5	363	Tgt/Cgt	9/12	0.614858869422409	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.614858869422409	1		530	264	SUCCESS
APC	324	MSKCC	GRCh37	5	112175174	112175174	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	104	539	0	ENST00000257430.4:c.3883G>T	p.Glu1295Ter	p.E1295*	ENST00000257430	NM_000038.5	1295	Gaa/Taa	16/16	1	2	FACETS	0.978	0.885	1	0.978	0.885	1	CLONAL	1	TRUE	1	0.614858869422409	2		539	346	SUCCESS
APC	324	MSKCC	GRCh37	5	112175153	112175153	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	99	542	0	ENST00000257430.4:c.3863del	p.Gly1288AspfsTer17	p.G1288Dfs*17	ENST00000257430	NM_000038.5	1288	Gga/ga	16/16	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.614858869422409	2		542	319	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515167	31515169	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs760849334	NA	P-0063206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	97	549	2	ENST00000344624.3:c.1216_1218del	p.Glu406del	p.E406del	ENST00000344624		406	GAA/-	5/33	1	2	FACETS	0.837	0.752	0.926	0.837	0.752	0.926	CLONAL	1	TRUE	1	0.614858869422409	2		551	377	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156840	106156840	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560827535	NA	P-0063206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	121	653	0	ENST00000380013.4:c.1741C>T	p.Arg581Cys	p.R581C	ENST00000380013	NM_001127208.2	581	Cgt/Tgt	3/11	1	2	FACETS	0.977	0.89	1	0.977	0.89	1	CLONAL	1	TRUE	1	0.614858869422409	2		653	403	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932254	36932254	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	147	682	0	ENST00000361632.4:c.2215C>T	p.Gln739Ter	p.Q739*	ENST00000361632		739	Cag/Tag	16/16	1	2	FACETS	0.889	0.816	0.964	0.889	0.816	0.964	CLONAL	1	TRUE	1	0.614858869422409	2		682	538	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663652	29663652	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0063206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	55	381	0	ENST00000356175.3:c.6085-1G>A		p.X2029_splice	ENST00000356175	NM_000267.3	2029			0.614858869422409	1	FACETS	0.843	0.739	0.951	0.843	0.739	0.951	CLONAL	1	TRUE	0	0.614858869422409	1		381	147	SUCCESS
FH	2271	MSKCC	GRCh37	1	241671911	241671911	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	44	279	0	ENST00000366560.3:c.730C>G	p.Leu244Val	p.L244V	ENST00000366560	NM_000143.3	244	Ctt/Gtt	5/10	0.283910305214188	4	FACETS	0.95	0.798	1	0.317	0.266	0.373	CLONAL	1	TRUE	1	0.283910305214188	4		279	419	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041099	29041099	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	66	434	0	ENST00000282397.4:c.329T>A	p.Leu110Gln	p.L110Q	ENST00000282397	NM_002019.4	110	cTa/cAa	3/30	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.283910305214188	2		434	435	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562618	95562618	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	104	543	0	ENST00000393063.1:c.4639G>T	p.Asp1547Tyr	p.D1547Y	ENST00000393063	NM_030621.3	1547	Gac/Tac	24/28	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.283910305214188	2		543	615	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410931	31410931	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1289997268	NA	P-0063217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	69	510	0	ENST00000344624.3:c.3589C>T	p.Gln1197Ter	p.Q1197*	ENST00000344624		1197	Cag/Tag	28/33	0.242944760869045	4	FACETS	0.911	0.793	1	0.456	0.396	0.52	CLONAL	1	TRUE	2	0.283910305214188	4		510	685	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249006	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGTGGACAACCCCCA	rs1554350367	NA	P-0063217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	79	465	0	ENST00000275493.2:c.2308_2322dup	p.Asp770_Val774dup	p.D770_V774dup	ENST00000275493	NM_005228.3	770	agc/agCGTGGACAACCCCCAc	20/28	0.27688662940755	3	FACETS	1	0.955	1	0.587	0.517	0.662	CLONAL	1	TRUE	1	0.283910305214188	3		465	541	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249073	55249073	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	122	539	0	ENST00000275493.2:c.2371C>G	p.Gln791Glu	p.Q791E	ENST00000275493	NM_005228.3	791	Cag/Gag	20/28	0.27688662940755	3	FACETS	0.966	0.878	1	0.966	0.878	1	CLONAL	2	TRUE	1	0.283910305214188	3		539	508	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0063218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	53	418	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.154373373275394	3	FACETS	0.957	0.819	1	0.957	0.819	1	CLONAL	2	TRUE	1	0.16	3		418	374	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0063218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	46	546	3	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	0.141859886051569	1	FACETS	0.797	0.67	0.938	0.797	0.67	0.938	CLONAL	1	TRUE	0	0.16	1		549	664	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037474	12037474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	47	554	0	ENST00000396373.4:c.1105C>T	p.Arg369Trp	p.R369W	ENST00000396373	NM_001987.4	369	Cgg/Tgg	6/8	0.141859886051569	1	FACETS	0.865	0.729	1	0.865	0.729	1	CLONAL	1	TRUE	0	0.16	1		554	625	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089123	37089125	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs63751247	NA	P-0063218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	47	438	0	ENST00000231790.2:c.1852_1854del	p.Lys618del	p.K618del	ENST00000231790	NM_000249.3	615	ctGAAg/ctg	16/19	0.141859886051569	1	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	0	0.16	1		438	537	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465048	120465048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372916164	NA	P-0063218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	44	546	1	ENST00000256646.2:c.5024G>A	p.Arg1675His	p.R1675H	ENST00000256646	NM_024408.3	1675	cGc/cAc	28/34	0.141859886051569	1	FACETS	0.902	0.756	1	0.902	0.756	1	CLONAL	1	TRUE	0	0.16	1		547	561	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647490	3647490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143831403	NA	P-0063218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	33	658	0	ENST00000294008.3:c.1573C>T	p.Arg525Cys	p.R525C	ENST00000294008	NM_032444.2	525	Cgc/Tgc	7/15	1	2	FACETS	0.725	0.589	0.879	0.725	0.589	0.879	SUBCLONAL	1	TRUE	1	0.16	2		658	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577520	7577520	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	28	511	0	ENST00000269305.4:c.761T>C	p.Ile254Thr	p.I254T	ENST00000269305	NM_001126112.2	254	aTc/aCc	7/11	1	2	FACETS	0.763	0.609	0.939	0.763	0.609	0.939	CLONAL	1	TRUE	1	0.16	2		511	459	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247536	123247536	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	45	377	0	ENST00000358487.5:c.1955A>G	p.Asn652Ser	p.N652S	ENST00000358487	NM_000141.4	652	aAc/aGc	14/18	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.16	2		377	515	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198480	108198480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	30	306	0	ENST00000278616.4:c.7084G>A	p.Glu2362Lys	p.E2362K	ENST00000278616	NM_000051.3	2362	Gaa/Aaa	48/63	1	2	FACETS	0.949	0.765	1	0.949	0.765	1	CLONAL	1	TRUE	1	0.16	2		306	395	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	495113	495113	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	37	325	0	ENST00000399788.2:c.193G>T	p.Val65Leu	p.V65L	ENST00000399788	NM_001042603.1	65	Gta/Tta	2/28	0.141859886051569	1	FACETS	0.99	0.816	1	0.99	0.816	1	CLONAL	1	TRUE	0	0.16	1		325	430	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40993269	40993269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866677917	NA	P-0063218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	26	348	0	ENST00000267868.3:c.95G>A	p.Gly32Asp	p.G32D	ENST00000267868	NM_002875.4	32	gGc/gAc	3/10	1	2	FACETS	0.689	0.544	0.855	0.689	0.544	0.855	SUBCLONAL	1	TRUE	1	0.16	2		348	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577515	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587781433	NA	P-0063218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	29	533	0	ENST00000269305.4:c.766A>G	p.Thr256Ala	p.T256A	ENST00000269305	NM_001126112.2	256	Aca/Gca	7/11	1	2	FACETS	0.785	0.629	0.962	0.785	0.629	0.962	CLONAL	1	TRUE	1	0.16	2		533	462	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125256	47125256	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	51	486	0	ENST00000409792.3:c.6014T>G	p.Ile2005Arg	p.I2005R	ENST00000409792	NM_014159.6	2005	aTa/aGa	12/21	0.141859886051569	1	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	0	0.16	1		486	552	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120889	94120889	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0063218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	23	425	0	ENST00000369303.4:c.163-1G>A		p.X55_splice	ENST00000369303	NM_004440.3	55			0.141859886051569	1	FACETS	0.625	0.487	0.786	0.625	0.487	0.786	SUBCLONAL	1	TRUE	0	0.16	1		425	423	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859851	151859851	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	45	686	0	ENST00000262189.6:c.10811del	p.Lys3604ArgfsTer26	p.K3604Rfs*26	ENST00000262189	NM_170606.2	3604	aAg/ag	43/59	0.154373373275394	3	FACETS	0.782	0.655	0.923	0.391	0.327	0.462	CLONAL	1	TRUE	1	0.16	3		686	777	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285761	87285761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063218-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	36	726	0	ENST00000277120.3:c.98C>A	p.Pro33His	p.P33H	ENST00000277120		33	cCc/cAc	2/19	1	2	FACETS	0.771	0.632	0.926	0.771	0.632	0.926	CLONAL	1	TRUE	1	0.16	2		726	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0063219-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	82	577	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.668	0.59	0.751	0.668	0.59	0.751	SUBCLONAL	1	TRUE	1	0.457348669162206	2		579	537	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	35	549	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	1	2	FACETS	0.275	0.225	0.331	0.275	0.225	0.331	SUBCLONAL	1	TRUE	1	0.484452022673547	2		549	526	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10286275	10286275	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	39	381	0	ENST00000340748.4:c.541C>G	p.Gln181Glu	p.Q181E	ENST00000340748		181	Cag/Gag	6/40	1	2	FACETS	0.325	0.269	0.388	0.325	0.269	0.388	SUBCLONAL	1	TRUE	1	0.484452022673547	2		381	495	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024649	14024649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202243691	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	35	344	0	ENST00000311895.7:c.875G>A	p.Arg292Gln	p.R292Q	ENST00000311895	NM_005236.2	292	cGa/cAa	5/11	1	2	FACETS	0.355	0.291	0.427	0.355	0.291	0.427	SUBCLONAL	1	TRUE	1	0.484452022673547	2		344	407	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374305	138374305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	36	436	0	ENST00000289153.2:c.3139G>A	p.Glu1047Lys	p.E1047K	ENST00000289153	NM_006219.2	1047	Gag/Aag	22/22	1	2	FACETS	0.262	0.214	0.315	0.262	0.214	0.315	SUBCLONAL	1	TRUE	1	0.484452022673547	2		436	568	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680215	30680215	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	63	637	0	ENST00000376406.3:c.1504G>C	p.Asp502His	p.D502H	ENST00000376406	NM_014641.2	502	Gat/Cat	5/15	1	2	FACETS	0.389	0.336	0.447	0.389	0.336	0.447	SUBCLONAL	1	TRUE	1	0.484452022673547	2		637	668	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545864	41545864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	49	636	0	ENST00000263253.7:c.2479C>T	p.Leu827Phe	p.L827F	ENST00000263253	NM_001429.3	827	Ctt/Ttt	14/31	1	2	FACETS	0.284	0.239	0.333	0.284	0.239	0.333	SUBCLONAL	1	TRUE	1	0.484452022673547	2		636	713	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680634	30680634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1438361788	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	52	557	0	ENST00000376406.3:c.1085G>A	p.Gly362Glu	p.G362E	ENST00000376406	NM_014641.2	362	gGa/gAa	5/15	1	2	FACETS	0.402	0.342	0.468	0.402	0.342	0.468	SUBCLONAL	1	TRUE	1	0.484452022673547	2		557	534	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547996	41547996	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	31	477	0	ENST00000263253.7:c.2977C>T	p.Gln993Ter	p.Q993*	ENST00000263253	NM_001429.3	993	Cag/Tag	15/31	1	2	FACETS	0.239	0.192	0.291	0.239	0.192	0.291	SUBCLONAL	1	TRUE	1	0.484452022673547	2		477	536	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545883	41545883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	52	678	0	ENST00000263253.7:c.2498C>T	p.Ser833Leu	p.S833L	ENST00000263253	NM_001429.3	833	tCg/tTg	14/31	1	2	FACETS	0.284	0.241	0.331	0.284	0.241	0.331	SUBCLONAL	1	TRUE	1	0.484452022673547	2		678	756	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101225	27101225	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	53	617	0	ENST00000324856.7:c.4507G>C	p.Asp1503His	p.D1503H	ENST00000324856	NM_006015.4	1503	Gac/Cac	18/20	1	2	FACETS	0.347	0.295	0.403	0.347	0.295	0.403	SUBCLONAL	1	TRUE	1	0.484452022673547	2		617	631	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374308	138374308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	34	438	0	ENST00000289153.2:c.3136G>A	p.Asp1046Asn	p.D1046N	ENST00000289153	NM_006219.2	1046	Gat/Aat	22/22	1	2	FACETS	0.249	0.203	0.301	0.249	0.203	0.301	SUBCLONAL	1	TRUE	1	0.484452022673547	2		438	564	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965421	18965421	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	31	419	0	ENST00000262803.5:c.1168G>C	p.Glu390Gln	p.E390Q	ENST00000262803	NM_002911.3	390	Gag/Cag	9/24	1	2	FACETS	0.292	0.236	0.356	0.292	0.236	0.356	SUBCLONAL	1	TRUE	1	0.484452022673547	2		419	438	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543909	41543909	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	47	461	0	ENST00000263253.7:c.2200C>T	p.Gln734Ter	p.Q734*	ENST00000263253	NM_001429.3	734	Cag/Tag	12/31	1	2	FACETS	0.287	0.241	0.338	0.287	0.241	0.338	SUBCLONAL	1	TRUE	1	0.484452022673547	2		461	676	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849501	89849501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501886	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	56	568	0	ENST00000389301.3:c.1480C>T	p.Leu494Phe	p.L494F	ENST00000389301	NM_000135.2	494	Ctc/Ttc	16/43	1	2	FACETS	0.387	0.331	0.448	0.387	0.331	0.448	SUBCLONAL	1	TRUE	1	0.484452022673547	2		568	598	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660490	67660490	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	32	343	0	ENST00000264010.4:c.1390G>C	p.Glu464Gln	p.E464Q	ENST00000264010	NM_006565.3	464	Gag/Cag	8/12	1	2	FACETS	0.285	0.231	0.346	0.285	0.231	0.346	SUBCLONAL	1	TRUE	1	0.484452022673547	2		343	464	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045806	180045806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1051985552	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	54	636	0	ENST00000261937.6:c.2965G>A	p.Glu989Lys	p.E989K	ENST00000261937	NM_182925.4	989	Gag/Aag	21/30	1	2	FACETS	0.411	0.35	0.476	0.411	0.35	0.476	SUBCLONAL	1	TRUE	1	0.484452022673547	2		636	543	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711983	89711983	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554900638	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	76	288	0	ENST00000371953.3:c.601G>T	p.Glu201Ter	p.E201*	ENST00000371953	NM_000314.4	201	Gaa/Taa	6/9	0.484452022673547	1	FACETS	0.874	0.776	0.977	0.874	0.776	0.977	CLONAL	1	TRUE	0	0.484452022673547	1		288	272	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545781	41545781	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	40	489	0	ENST00000263253.7:c.2396C>T	p.Ser799Phe	p.S799F	ENST00000263253	NM_001429.3	799	tCt/tTt	14/31	1	2	FACETS	0.282	0.234	0.336	0.282	0.234	0.336	SUBCLONAL	1	TRUE	1	0.484452022673547	2		489	585	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143452	108143452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	50	433	0	ENST00000278616.4:c.3157G>A	p.Asp1053Asn	p.D1053N	ENST00000278616	NM_000051.3	1053	Gat/Aat	22/63	1	2	FACETS	0.389	0.33	0.454	0.389	0.33	0.454	SUBCLONAL	1	TRUE	1	0.484452022673547	2		433	531	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705380	43705380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	50	844	0	ENST00000382044.4:c.5242G>A	p.Asp1748Asn	p.D1748N	ENST00000382044	NM_001141980.1	1748	Gac/Aac	24/28	1	2	FACETS	0.335	0.284	0.392	0.335	0.284	0.392	SUBCLONAL	1	TRUE	1	0.484452022673547	2		844	616	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264349	16264349	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	41	502	0	ENST00000375759.3:c.10552G>T	p.Asp3518Tyr	p.D3518Y	ENST00000375759	NM_015001.2	3518	Gac/Tac	13/15	1	2	FACETS	0.362	0.302	0.43	0.362	0.302	0.43	SUBCLONAL	1	TRUE	1	0.484452022673547	2		502	467	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531782	46531782	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	32	356	0	ENST00000262741.5:c.565C>T	p.Gln189Ter	p.Q189*	ENST00000262741	NM_003629.3	189	Cag/Tag	5/10	1	2	FACETS	0.297	0.24	0.361	0.297	0.24	0.361	SUBCLONAL	1	TRUE	1	0.484452022673547	2		356	445	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745472	162745472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	99	457	0	ENST00000367921.3:c.1887G>A	p.Met629Ile	p.M629I	ENST00000367921	NM_006182.2	629	atG/atA	15/18	0.484452022673547	3	FACETS	0.891	0.797	0.99	0.445	0.398	0.495	CLONAL	1	TRUE	1	0.484452022673547	3		457	570	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246490507	246490507	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	41	387	0	ENST00000388985.4:c.527C>G	p.Ala176Gly	p.A176G	ENST00000388985		176	gCa/gGa	5/12	0.484452022673547	3	FACETS	0.368	0.306	0.438	0.184	0.153	0.219	SUBCLONAL	1	TRUE	1	0.484452022673547	3		387	571	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274822	123274822	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	39	510	0	ENST00000358487.5:c.1096G>C	p.Glu366Gln	p.E366Q	ENST00000358487	NM_000141.4	366	Gaa/Caa	9/18	0.484452022673547	1	FACETS	0.292	0.242	0.348	0.292	0.242	0.348	SUBCLONAL	1	TRUE	0	0.484452022673547	1		510	418	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456807	32456807	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	38	523	0	ENST00000332351.3:c.85G>C	p.Glu29Gln	p.E29Q	ENST00000332351	NM_024426.4	29	Gag/Cag	1/10	1	2	FACETS	0.401	0.332	0.478	0.401	0.332	0.478	SUBCLONAL	1	TRUE	1	0.484452022673547	2		523	391	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948409	71948409	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	55	751	0	ENST00000298229.2:c.3121G>A	p.Asp1041Asn	p.D1041N	ENST00000298229	NM_001567.3	1041	Gat/Aat	26/28	1	2	FACETS	0.389	0.332	0.451	0.389	0.332	0.451	SUBCLONAL	1	TRUE	1	0.484452022673547	2		751	584	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427177	49427177	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs747132864	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	43	741	0	ENST00000301067.7:c.11311C>A	p.Pro3771Thr	p.P3771T	ENST00000301067	NM_003482.3	3771	Ccc/Acc	39/54	0.12663556913452	3	FACETS	0.337	0.281	0.399	0.169	0.14	0.2	INDETERMINATE	1	TRUE	1	0.484452022673547	3		741	654	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118700	115118700	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	42	550	0	ENST00000257566.3:c.641C>G	p.Ser214Ter	p.S214*	ENST00000257566	NM_016569.3	214	tCa/tGa	2/8	0.12663556913452	3	FACETS	0.3	0.249	0.356	0.15	0.124	0.178	INDETERMINATE	1	TRUE	1	0.484452022673547	3		550	719	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519149	103519149	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	105	394	0	ENST00000355739.4:c.2487del	p.Asn829LysfsTer4	p.N829Kfs*4	ENST00000355739	NM_000123.3	829	aaC/aa	11/15	1	2	FACETS	0.883	0.795	0.975	0.883	0.795	0.975	CLONAL	1	TRUE	1	0.484452022673547	2		394	491	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060661	38060661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1484270927	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	72	859	0	ENST00000250448.2:c.1328C>T	p.Ser443Leu	p.S443L	ENST00000250448	NM_004496.3	443	tCg/tTg	2/2	1	2	FACETS	0.366	0.319	0.417	0.366	0.319	0.417	SUBCLONAL	1	TRUE	1	0.484452022673547	2		859	812	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831846	72831846	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780546363	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	46	636	0	ENST00000268489.5:c.4735G>A	p.Glu1579Lys	p.E1579K	ENST00000268489	NM_006885.3	1579	Gaa/Aaa	9/10	1	2	FACETS	0.259	0.218	0.306	0.259	0.218	0.306	SUBCLONAL	1	TRUE	1	0.484452022673547	2		636	732	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095023	11095023	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	36	639	0	ENST00000358026.2:c.196C>G	p.Gln66Glu	p.Q66E	ENST00000358026	NM_001128849.1	66	Cag/Gag	2/36	1	2	FACETS	0.283	0.232	0.34	0.283	0.232	0.34	SUBCLONAL	1	TRUE	1	0.484452022673547	2		639	525	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136986	11136986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	32	378	1	ENST00000358026.2:c.3179C>T	p.Ser1060Phe	p.S1060F	ENST00000358026	NM_001128849.1	1060	tCc/tTc	23/36	1	2	FACETS	0.309	0.251	0.376	0.309	0.251	0.376	SUBCLONAL	1	TRUE	1	0.484452022673547	2		379	427	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250176	39250176	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	30	430	0	ENST00000402219.2:c.1393G>C	p.Asp465His	p.D465H	ENST00000402219	NM_005633.3	465	Gat/Cat	10/23	1	2	FACETS	0.269	0.216	0.329	0.269	0.216	0.329	SUBCLONAL	1	TRUE	1	0.484452022673547	2		430	461	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024801	31024801	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	42	675	1	ENST00000375687.4:c.4286C>G	p.Ser1429Cys	p.S1429C	ENST00000375687	NM_015338.5	1429	tCt/tGt	13/13	1	2	FACETS	0.281	0.234	0.333	0.281	0.234	0.333	SUBCLONAL	1	TRUE	1	0.484452022673547	2		676	617	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42851186	42851186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	36	342	0	ENST00000398585.3:c.707G>A	p.Gly236Glu	p.G236E	ENST00000398585	NM_001135099.1	236	gGa/gAa	7/14	1	2	FACETS	0.301	0.247	0.362	0.301	0.247	0.362	SUBCLONAL	1	TRUE	1	0.484452022673547	2		342	494	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543930	41543930	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	40	486	0	ENST00000263253.7:c.2221C>G	p.Gln741Glu	p.Q741E	ENST00000263253	NM_001429.3	741	Caa/Gaa	12/31	1	2	FACETS	0.241	0.199	0.288	0.241	0.199	0.288	SUBCLONAL	1	TRUE	1	0.484452022673547	2		486	685	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545099	41545099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	40	484	0	ENST00000263253.7:c.2299C>T	p.Gln767Ter	p.Q767*	ENST00000263253	NM_001429.3	767	Cag/Tag	13/31	1	2	FACETS	0.25	0.207	0.298	0.25	0.207	0.298	SUBCLONAL	1	TRUE	1	0.484452022673547	2		484	661	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545105	41545105	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	41	484	0	ENST00000263253.7:c.2305C>T	p.Gln769Ter	p.Q769*	ENST00000263253	NM_001429.3	769	Cag/Tag	13/31	1	2	FACETS	0.26	0.216	0.309	0.26	0.216	0.309	SUBCLONAL	1	TRUE	1	0.484452022673547	2		484	651	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545775	41545775	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	38	476	0	ENST00000263253.7:c.2390C>A	p.Ser797Tyr	p.S797Y	ENST00000263253	NM_001429.3	797	tCt/tAt	14/31	1	2	FACETS	0.279	0.23	0.334	0.279	0.23	0.334	SUBCLONAL	1	TRUE	1	0.484452022673547	2		476	562	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546047	41546047	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	52	711	0	ENST00000263253.7:c.2662C>A	p.Pro888Thr	p.P888T	ENST00000263253	NM_001429.3	888	Cca/Aca	14/31	1	2	FACETS	0.299	0.254	0.349	0.299	0.254	0.349	SUBCLONAL	1	TRUE	1	0.484452022673547	2		711	717	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553182	41553182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	25	401	0	ENST00000263253.7:c.3271G>A	p.Asp1091Asn	p.D1091N	ENST00000263253	NM_001429.3	1091	Gat/Aat	18/31	1	2	FACETS	0.258	0.203	0.322	0.258	0.203	0.322	SUBCLONAL	1	TRUE	1	0.484452022673547	2		401	400	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553234	41553234	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	35	440	0	ENST00000263253.7:c.3323C>A	p.Thr1108Asn	p.T1108N	ENST00000263253	NM_001429.3	1108	aCt/aAt	18/31	1	2	FACETS	0.294	0.241	0.355	0.294	0.241	0.355	SUBCLONAL	1	TRUE	1	0.484452022673547	2		440	491	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119562162	119562162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	37	418	0	ENST00000316626.5:c.1174C>T	p.Pro392Ser	p.P392S	ENST00000316626		392	Cct/Tct	11/12	1	2	FACETS	0.258	0.212	0.31	0.258	0.212	0.31	SUBCLONAL	1	TRUE	1	0.484452022673547	2		418	591	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1952892	1952892	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	36	589	0	ENST00000382891.5:c.1975G>C	p.Glu659Gln	p.E659Q	ENST00000382891	NM_133335.3	659	Gag/Cag	10/22	1	2	FACETS	0.243	0.199	0.292	0.243	0.199	0.292	SUBCLONAL	1	TRUE	1	0.484452022673547	2		589	612	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177833	56177833	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	46	582	0	ENST00000399503.3:c.2806G>C	p.Val936Leu	p.V936L	ENST00000399503	NM_005921.1	936	Gta/Cta	14/20	1	2	FACETS	0.284	0.239	0.335	0.284	0.239	0.335	SUBCLONAL	1	TRUE	1	0.484452022673547	2		582	668	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687278	117687278	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	43	469	0	ENST00000368508.3:c.2773C>T	p.Gln925Ter	p.Q925*	ENST00000368508	NM_002944.2	925	Cag/Tag	18/43	1	2	FACETS	0.323	0.27	0.383	0.323	0.27	0.383	SUBCLONAL	1	TRUE	1	0.484452022673547	2		469	549	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161990397	161990397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	77	406	0	ENST00000366898.1:c.923G>A	p.Gly308Glu	p.G308E	ENST00000366898	NM_004562.2	308	gGa/gAa	8/12	1	2	FACETS	0.641	0.564	0.723	0.641	0.564	0.723	SUBCLONAL	1	TRUE	1	0.484452022673547	2		406	496	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739822	41739822	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	56	552	0	ENST00000242208.4:c.151C>G	p.Gln51Glu	p.Q51E	ENST00000242208	NM_002192.2	51	Cag/Gag	2/3	1	2	FACETS	0.425	0.364	0.492	0.425	0.364	0.492	SUBCLONAL	1	TRUE	1	0.484452022673547	2		552	544	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050695	69050695	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	25	277	0	ENST00000288368.4:c.4030G>C	p.Asp1344His	p.D1344H	ENST00000288368	NM_024870.2	1344	Gat/Cat	33/40	1	2	FACETS	0.292	0.229	0.363	0.292	0.229	0.363	SUBCLONAL	1	TRUE	1	0.484452022673547	2		277	354	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771690	135771690	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs574823234	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	46	538	0	ENST00000298552.3:c.3427C>G	p.Pro1143Ala	p.P1143A	ENST00000298552	NM_001162426.1	1143	Ccg/Gcg	23/23	0.484452022673547	1	FACETS	0.268	0.226	0.316	0.268	0.226	0.316	SUBCLONAL	1	TRUE	0	0.484452022673547	1		538	536	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891409	76891409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063220-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	21	260	0	ENST00000373344.5:c.4696G>A	p.Asp1566Asn	p.D1566N	ENST00000373344	NM_000489.3	1566	Gat/Aat	16/35	1	2	FACETS	0.239	0.183	0.304	0.239	0.183	0.304	SUBCLONAL	1	TRUE	1	0.484452022673547	2		260	363	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578464	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	118	798	0	ENST00000269305.4:c.466del	p.Arg156AlafsTer14	p.R156Afs*14	ENST00000269305	NM_001126112.2	156	Cgc/gc	5/11	0.250879152979247	2	FACETS	1	0.977	1	0.635	0.574	0.698	CLONAL	1	TRUE	0	0.323371501033511	2		798	575	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526152	189526152	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751300168	NA	P-0063221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	92	820	0	ENST00000264731.3:c.416C>T	p.Ala139Val	p.A139V	ENST00000264731	NM_003722.4	139	gCg/gTg	4/14	0.12172934978813	5	FACETS	1	0.918	1	0.347	0.308	0.389	INDETERMINATE	1	TRUE	2	0.323371501033511	5		820	811	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953730	48953730	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs3092891	NA	P-0063221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	48	151	0	ENST00000267163.4:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000267163	NM_000321.2	445	Cga/Tga	14/27	0.250879152979247	2	FACETS	1	0.962	1	0.721	0.617	0.832	CLONAL	1	TRUE	0	0.323371501033511	2		151	206	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741618	17741618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1425797546	NA	P-0063221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	70	687	0	ENST00000250003.3:c.289G>A	p.Ala97Thr	p.A97T	ENST00000250003	NM_002478.4	97	Gcc/Acc	1/3	0.228222421450573	3	FACETS	0.933	0.815	1	0.467	0.407	0.531	CLONAL	1	TRUE	1	0.323371501033511	3		687	539	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420989	49420989	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	94	650	1	ENST00000301067.7:c.14760del	p.Leu4921TrpfsTer74	p.L4921Wfs*74	ENST00000301067	NM_003482.3	4920	ccC/cc	48/54	0.12172934978813	5	FACETS	1	0.98	1	0.489	0.436	0.546	INDETERMINATE	1	TRUE	2	0.323371501033511	5		651	588	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112565	115112565	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	151	721	0	ENST00000257566.3:c.1175C>A	p.Ala392Glu	p.A392E	ENST00000257566	NM_016569.3	392	gCg/gAg	7/8	0.193295150386814	3	FACETS	0.816	0.748	0.886	0.816	0.748	0.886	INDETERMINATE	2	TRUE	1	0.323371501033511	3		721	665	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434509	121434509	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	62	632	0	ENST00000257555.6:c.1273A>T	p.Thr425Ser	p.T425S	ENST00000257555		425	Acg/Tcg	6/10	0.193295150386814	3	FACETS	0.637	0.55	0.733	0.319	0.275	0.367	INDETERMINATE	1	TRUE	1	0.323371501033511	3		632	699	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618896	37618896	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	100	881	0	ENST00000447079.4:c.572A>T	p.Lys191Met	p.K191M	ENST00000447079	NM_015083.1	191	aAg/aTg	1/14	0.228222421450573	3	FACETS	0.963	0.86	1	0.482	0.43	0.536	CLONAL	1	TRUE	1	0.323371501033511	3		881	746	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67637139	67637139	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	24	385	0	ENST00000272342.5:c.2750C>G	p.Ser917Cys	p.S917C	ENST00000272342	NM_019002.3	917	tCt/tGt	6/6	0.175214255645878	4	FACETS	0.624	0.489	0.778	0.312	0.244	0.389	INDETERMINATE	1	TRUE	2	0.323371501033511	4		385	315	SUCCESS
ATR	545	MSKCC	GRCh37	3	142297540	142297541	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0063221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	59	368	0	ENST00000350721.4:c.6_7delinsAA	p.Glu3Lys	p.E3K	ENST00000350721	NM_001184.3	2	ggGGaa/ggAAaa	1/47	0.12172934978813	5	FACETS	1	0.952	1	0.414	0.357	0.476	INDETERMINATE	1	TRUE	2	0.323371501033511	5		368	436	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919273	178919273	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	24	392	0	ENST00000263967.3:c.758A>C	p.Lys253Thr	p.K253T	ENST00000263967	NM_006218.2	253	aAa/aCa	4/21	0.12172934978813	5	FACETS	0.544	0.426	0.681	0.181	0.142	0.227	INDETERMINATE	1	TRUE	2	0.323371501033511	5		392	405	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151643	55151643	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	41	346	0	ENST00000257290.5:c.2429C>G	p.Ala810Gly	p.A810G	ENST00000257290	NM_006206.4	810	gCt/gGt	17/23	0.228222421450573	3	FACETS	0.798	0.666	0.944	0.399	0.333	0.472	CLONAL	1	TRUE	1	0.323371501033511	3		346	369	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754243	57754243	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	34	517	0	ENST00000274289.3:c.608A>G	p.His203Arg	p.H203R	ENST00000274289	NM_006622.3	203	cAc/cGc	4/14	0.262046335192302	1	FACETS	0.411	0.335	0.496	0.411	0.335	0.496	SUBCLONAL	1	TRUE	0	0.323371501033511	1		517	429	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89791153	89791153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	65	527	0	ENST00000336032.3:c.540G>T	p.Glu180Asp	p.E180D	ENST00000336032	NM_006813.2	180	gaG/gaT	1/2	1	2	FACETS	0.731	0.634	0.836	0.731	0.634	0.836	SUBCLONAL	1	TRUE	1	0.323371501033511	2		527	550	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715886	117715886	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	63	410	0	ENST00000368508.3:c.872A>G	p.Gln291Arg	p.Q291R	ENST00000368508	NM_002944.2	291	cAg/cGg	9/43	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.323371501033511	2		410	367	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965680	90965680	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1360502904	NA	P-0063221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	83	480	0	ENST00000265433.3:c.1637G>C	p.Arg546Thr	p.R546T	ENST00000265433	NM_002485.4	546	aGa/aCa	11/16	0.323371501033511	5	FACETS	1	0.938	1	0.366	0.322	0.412	CLONAL	1	TRUE	2	0.323371501033511	5		480	695	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028852	47028852	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	106	360	0	ENST00000377604.3:c.158del	p.Gly53AlafsTer81	p.G53Afs*81	ENST00000377604	NM_001204468.1	52	gaG/ga	3/24	0.200666864105987	2	FACETS	1	0.963	1			1	CLONAL	2	TRUE	NA	0.323371501033511	2		360	294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0063222-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	177	582	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.212413672663481	1	FACETS	1	0.985	1	1	0.994	1	CLONAL	2	FALSE	0	0.212413672663481	1		582	600	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150936207	150936207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063222-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	162	713	0	ENST00000271640.5:c.3659G>A	p.Arg1220His	p.R1220H	ENST00000271640	NM_001145415.1	1220	cGc/cAc	20/22	1	2	FACETS	1	0.942	1	1	0.992	1	CLONAL	2	FALSE	1	0.212413672663481	2		713	740	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717610	89717610	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063222-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	38	361	1	ENST00000371953.3:c.635A>C	p.Asn212Thr	p.N212T	ENST00000371953	NM_000314.4	212	aAt/aCt	7/9	0.212413672663481	1	FACETS	0.922	0.764	1	0.922	0.764	1	CLONAL	1	FALSE	0	0.212413672663481	1		362	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0063223-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	266	619	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.592777510702819	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.5923540637258	2		619	403	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38506151	38506151	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063223-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	177	581	0	ENST00000254066.5:c.443G>T	p.Cys148Phe	p.C148F	ENST00000254066	NM_000964.3	148	tGc/tTc	4/9	0.592777510702819	3	FACETS	1	0.948	1	0.344	0.318	0.372	CLONAL	1	TRUE	0	0.5923540637258	3		581	750	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421327	12421327	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063223-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	319	506	0	ENST00000287820.6:c.207C>A	p.Asp69Glu	p.D69E	ENST00000287820	NM_015869.4	69	gaC/gaA	2/7	0.592777510702819	4	FACETS	1	0.991	1	0.783	0.744	0.822	CLONAL	2	TRUE	1	0.5923540637258	4		506	730	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0063224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	71	556	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.649802168264801	2		556	206	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857481	68857481	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	159	381	1	ENST00000261769.5:c.2116C>T	p.Gln706Ter	p.Q706*	ENST00000261769	NM_004360.3	706	Caa/Taa	13/16	0.649802168264801	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.649802168264801	1		382	310	SUCCESS
APC	324	MSKCC	GRCh37	5	112174466	112174466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253882360	NA	P-0063224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	154	457	0	ENST00000257430.4:c.3175G>A	p.Glu1059Lys	p.E1059K	ENST00000257430	NM_000038.5	1059	Gaa/Aaa	16/16	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.649802168264801	2		457	457	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448406	49448406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368471915	NA	P-0063224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	205	648	0	ENST00000301067.7:c.305G>A	p.Ser102Asn	p.S102N	ENST00000301067	NM_003482.3	102	aGc/aAc	3/54	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.649802168264801	2		648	619	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27016077	27016077	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194974108	NA	P-0063224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	40	461	0	ENST00000335756.4:c.353G>A	p.Arg118Gln	p.R118Q	ENST00000335756	NM_001809.3	118	cGa/cAa	4/5	1	2	FACETS	0.242	0.201	0.289	0.242	0.201	0.289	SUBCLONAL	1	TRUE	1	0.649802168264801	2		461	508	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305325	65305325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	191	554	0	ENST00000342505.4:c.2803G>A	p.Glu935Lys	p.E935K	ENST00000342505	NM_002227.2	935	Gag/Aag	20/25	0.649802168264801	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.649802168264801	1		554	373	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247875	59247875	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	240	742	0	ENST00000371222.2:c.868C>T	p.Gln290Ter	p.Q290*	ENST00000371222	NM_002228.3	290	Cag/Tag	1/1	0.649802168264801	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.649802168264801	1		742	491	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237716	133237716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	194	546	0	ENST00000320574.5:c.2899G>A	p.Glu967Lys	p.E967K	ENST00000320574	NM_006231.2	967	Gag/Aag	25/49	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.649802168264801	2		546	578	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060674	38060674	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	319	893	0	ENST00000250448.2:c.1315C>G	p.Leu439Val	p.L439V	ENST00000250448	NM_004496.3	439	Cta/Gta	2/2	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.649802168264801	2		893	894	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060743	38060743	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	262	842	0	ENST00000250448.2:c.1246G>C	p.Asp416His	p.D416H	ENST00000250448	NM_004496.3	416	Gac/Cac	2/2	1	2	FACETS	0.992	0.933	1	0.992	0.933	1	CLONAL	1	TRUE	1	0.649802168264801	2		842	813	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061495	38061495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	143	637	1	ENST00000250448.2:c.494G>A	p.Ser165Asn	p.S165N	ENST00000250448	NM_004496.3	165	aGc/aAc	2/2	1	2	FACETS	0.915	0.84	0.992	0.915	0.84	0.992	CLONAL	1	TRUE	1	0.649802168264801	2		638	481	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122902	2122902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45517223	NA	P-0063224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	174	508	0	ENST00000219476.3:c.2273C>T	p.Ser758Phe	p.S758F	ENST00000219476	NM_000548.3	758	tCc/tTc	21/42	1	2	FACETS	0.965	0.894	1	0.965	0.894	1	CLONAL	1	TRUE	1	0.649802168264801	2		508	555	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55729514	55729514	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	205	508	0	ENST00000284073.2:c.782G>C	p.Arg261Thr	p.R261T	ENST00000284073	NM_138962.2	261	aGa/aCa	11/14	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.649802168264801	2		508	608	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796900	78796900	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	181	416	0	ENST00000306801.3:c.1013G>C	p.Arg338Thr	p.R338T	ENST00000306801	NM_020761.2	338	aGa/aCa	9/34	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.649802168264801	2		416	541	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39537650	39537650	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	130	466	0	ENST00000262039.4:c.184C>T	p.Gln62Ter	p.Q62*	ENST00000262039	NM_002647.2	62	Caa/Taa	2/25	1	2	FACETS	0.889	0.813	0.968	0.889	0.813	0.968	CLONAL	1	TRUE	1	0.649802168264801	2		466	450	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267374	7267374	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	168	509	0	ENST00000302850.5:c.634C>G	p.His212Asp	p.H212D	ENST00000302850	NM_000208.2	212	Cat/Gat	2/22	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.649802168264801	2		509	507	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212599	36212606	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCTGTC	CCGCTGTC	-	novel	NA	P-0063224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	243	779	0	ENST00000222270.7:c.2350_2357del	p.Pro784TrpfsTer59	p.P784Wfs*59	ENST00000222270	NM_014727.1	784	CCGCTGTCt/t	3/37	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.649802168264801	2		779	715	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022379	31022379	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	227	726	0	ENST00000375687.4:c.1864C>G	p.Leu622Val	p.L622V	ENST00000375687	NM_015338.5	622	Ctg/Gtg	13/13	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.649802168264801	2		726	682	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755640	39755640	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	199	697	0	ENST00000288319.7:c.1125G>T	p.Lys375Asn	p.K375N	ENST00000288319	NM_182918.3	375	aaG/aaT	10/10	1	2	FACETS	0.935	0.87	1	0.935	0.87	1	CLONAL	1	TRUE	1	0.649802168264801	2		697	655	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226809	142226809	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	118	275	0	ENST00000350721.4:c.4995G>C	p.Lys1665Asn	p.K1665N	ENST00000350721	NM_001184.3	1665	aaG/aaC	28/47	1	2	FACETS	0.924	0.841	1	0.924	0.841	1	CLONAL	1	TRUE	1	0.649802168264801	2		275	393	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38966783	38966783	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0063224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	119	294	0	ENST00000357387.3:c.1259C>G	p.Ser420Ter	p.S420*	ENST00000357387	NM_152756.3	420	tCa/tGa	15/38	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.649802168264801	2		294	352	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177993	56177993	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	197	632	0	ENST00000399503.3:c.2966C>G	p.Ser989Cys	p.S989C	ENST00000399503	NM_005921.1	989	tCt/tGt	14/20	1	2	FACETS	0.986	0.918	1	0.986	0.918	1	CLONAL	1	TRUE	1	0.649802168264801	2		632	615	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158610	26158610	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	105	327	0	ENST00000289316.2:c.213C>G	p.Phe71Leu	p.F71L	ENST00000289316	NM_138720.2	71	ttC/ttG	1/2	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.649802168264801	2		327	313	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673671	30673671	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs756847561	NA	P-0063224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	269	758	0	ENST00000376406.3:c.3289G>C	p.Glu1097Gln	p.E1097Q	ENST00000376406	NM_014641.2	1097	Gag/Cag	10/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.649802168264801	2		758	754	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380076	116380076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1391853762	NA	P-0063224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	175	470	0	ENST00000397752.3:c.1465G>A	p.Glu489Lys	p.E489K	ENST00000397752	NM_000245.2	489	Gaa/Aaa	4/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.649802168264801	2		470	511	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205466	38205466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3419	184	509	0	ENST00000317025.8:c.224C>T	p.Ser75Leu	p.S75L	ENST00000317025	NM_023034.1	75	tCa/tTa	2/24	0.649802168264801	18	FACETS	0.974	0.894	1			1	CLONAL	1	TRUE	NA	0.649802168264801	18		509	3603	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93636961	93636961	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs762311925	NA	P-0063224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	172	540	0	ENST00000375746.1:c.1011G>C	p.Gln337His	p.Q337H	ENST00000375746	NM_001174167.1	337	caG/caC	9/14	1	2	FACETS	0.927	0.858	0.998	0.927	0.858	0.998	CLONAL	1	TRUE	1	0.649802168264801	2		540	571	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615098	100615098	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	128	327	0	ENST00000308731.7:c.817G>C	p.Glu273Gln	p.E273Q	ENST00000308731	NM_000061.2	273	Gaa/Caa	9/19	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.649802168264801	2		327	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0063225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	169	558	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.352639132447772	2	FACETS	0.867	0.802	0.934	0.867	0.802	0.934	CLONAL	2	TRUE	0	0.355572231080883	2		558	548	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89335056	89335056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	74	380	2	ENST00000301030.4:c.7822C>T	p.Arg2608Trp	p.R2608W	ENST00000301030	NM_001256183.1	2608	Cgg/Tgg	13/13	0.355572231080883	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.355572231080883	1		382	328	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805488	1805488	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373496046	NA	P-0063225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	41	494	0	ENST00000260795.2:c.1000G>A	p.Ala334Thr	p.A334T	ENST00000260795		334	Gcc/Acc	7/17	1	2	FACETS	0.445	0.37	0.528	0.445	0.37	0.528	SUBCLONAL	1	TRUE	1	0.355572231080883	2		494	518	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	13	556	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.177853325726289	3	FACETS	0.788	0.563	1	0.394	0.281	0.531	CLONAL	1	TRUE	1	0.177853325726289	3		556	202	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	45	343	0				ENST00000310581	NM_198253.2	-/1132			0.177853325726289	4	FACETS	1	0.862	1	1	0.862	1	CLONAL	2	TRUE	2	0.177853325726289	4		343	292	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	30	397	0	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	1	2	FACETS	0.907	0.731	1	0.907	0.731	1	CLONAL	1	TRUE	1	0.177853325726289	2		397	372	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969327	44969327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	67	181	0	ENST00000377967.4:c.4009G>A	p.Glu1337Lys	p.E1337K	ENST00000377967	NM_021140.2	1337	Gag/Aag	28/29	0.177853325726289	3	FACETS	1	0.938	1			1	CLONAL	4	TRUE	NA	0.177853325726289	3		181	188	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727843	78727843	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	59	462	0	ENST00000306801.3:c.688C>G	p.Gln230Glu	p.Q230E	ENST00000306801	NM_020761.2	230	Cag/Gag	6/34	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.177853325726289	2		462	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577543	7577543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	81	493	0	ENST00000269305.4:c.738G>T	p.Met246Ile	p.M246I	ENST00000269305	NM_001126112.2	246	atG/atT	7/11	0.176446305499972	2	FACETS	0.867	0.77	0.97	1	0.971	1	CLONAL	3	TRUE	0	0.177853325726289	2		493	350	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178943812	178943812	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	35	329	0	ENST00000263967.3:c.2479C>G	p.Gln827Glu	p.Q827E	ENST00000263967	NM_006218.2	827	Caa/Gaa	17/21	0.177853325726289	3	FACETS	1	0.941	1	0.696	0.572	0.834	CLONAL	1	TRUE	1	0.177853325726289	3		329	308	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875616	56875616	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	35	425	0	ENST00000308159.5:c.2221-1G>T		p.X741_splice	ENST00000308159	NM_014669.4	741			1	2	FACETS	0.884	0.725	1	0.884	0.725	1	CLONAL	1	TRUE	1	0.177853325726289	2		425	445	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196477	106196477	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	45	629	0	ENST00000380013.4:c.4810G>A	p.Ala1604Thr	p.A1604T	ENST00000380013	NM_001127208.2	1604	Gct/Act	11/11	1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	1	0.177853325726289	2		629	496	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650671	67650671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	91	432	0	ENST00000264010.4:c.976G>A	p.Asp326Asn	p.D326N	ENST00000264010	NM_006565.3	326	Gac/Aac	5/12	1	2	FACETS	1	0.911	1	1	0.986	1	CLONAL	2	TRUE	1	0.177853325726289	2		432	499	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176619016	176619016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1309337861	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	69	356	0	ENST00000439151.2:c.1059G>A	p.Met353Ile	p.M353I	ENST00000439151	NM_022455.4	353	atG/atA	3/23	0.177853325726289	3	FACETS	0.93	0.817	1	0.93	0.817	1	CLONAL	3	TRUE	0	0.177853325726289	3		356	303	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948824	17948824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747854515	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	42	641	0	ENST00000458235.1:c.1618C>T	p.Arg540Cys	p.R540C	ENST00000458235	NM_000215.3	540	Cgc/Tgc	12/24	0.177853325726289	3	FACETS	0.947	0.79	1	0.474	0.395	0.561	CLONAL	1	TRUE	1	0.177853325726289	3		641	543	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534978	5534978	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201840318	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1863	189	603	0	ENST00000397747.3:c.289G>A	p.Glu97Lys	p.E97K	ENST00000397747	NM_025239.3	97	Gaa/Aaa	3/7	0.177853325726289	28	FACETS	1	0.975	1	0.127	0.116	0.138	CLONAL	3	TRUE	1	0.177853325726289	28		603	2052	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295052	91295052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	31	341	0	ENST00000355112.3:c.835G>A	p.Glu279Lys	p.E279K	ENST00000355112	NM_000057.2	279	Gaa/Aaa	4/22	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.177853325726289	2		341	319	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873157	71873157	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	38	464	0	ENST00000357731.5:c.1037T>G	p.Phe346Cys	p.F346C	ENST00000357731	NM_173808.2	346	tTc/tGc	7/7	0.177853325726289	3	FACETS	1	0.86	1	0.523	0.432	0.624	CLONAL	1	TRUE	1	0.177853325726289	3		464	445	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102098217	102098217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	27	390	0	ENST00000282441.5:c.1181G>A	p.Arg394Gln	p.R394Q	ENST00000282441	NM_001130145.2	394	cGa/cAa	8/9	0.177853325726289	3	FACETS	0.961	0.765	1	0.32	0.255	0.395	CLONAL	1	TRUE	0	0.177853325726289	3		390	344	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598203	28598203	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	51	609	0	ENST00000253063.3:c.175G>A	p.Glu59Lys	p.E59K	ENST00000253063	NM_031459.4	59	Gag/Aag	3/10	0.177853325726289	3	FACETS	1	0.942	1	0.615	0.523	0.716	CLONAL	1	TRUE	1	0.177853325726289	3		609	508	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556674	41556674	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	46	521	0	ENST00000263253.7:c.3619G>C	p.Glu1207Gln	p.E1207Q	ENST00000263253	NM_001429.3	1207	Gag/Cag	20/31	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.177853325726289	2		521	486	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791024	42791024	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	157	708	0	ENST00000575354.2:c.169G>C	p.Glu57Gln	p.E57Q	ENST00000575354	NM_015125.3	57	Gag/Cag	2/20	0.177853325726289	2	FACETS	1	0.955	1	1	0.99	1	CLONAL	3	TRUE	0	0.177853325726289	2		708	559	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162923	47162923	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	80	576	0	ENST00000409792.3:c.3203C>G	p.Ser1068Cys	p.S1068C	ENST00000409792	NM_014159.6	1068	tCt/tGt	3/21	0.177853325726289	3	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	1	0.177853325726289	3		576	446	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212212	5212212	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	45	706	0	ENST00000357368.4:c.4819G>C	p.Glu1607Gln	p.E1607Q	ENST00000357368	NM_002850.3	1607	Gag/Cag	32/38	0.177853325726289	1	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	0	0.177853325726289	1		706	445	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291078	11291078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	46	627	0	ENST00000361445.4:c.2683G>A	p.Asp895Asn	p.D895N	ENST00000361445	NM_004958.3	895	Gat/Aat	18/58	0.177853325726289	1	FACETS	0.948	0.799	1	0.948	0.799	1	CLONAL	1	TRUE	0	0.177853325726289	1		627	497	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638258	176638258	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	43	654	0	ENST00000439151.2:c.2858C>G	p.Ser953Cys	p.S953C	ENST00000439151	NM_022455.4	953	tCt/tGt	5/23	0.177853325726289	3	FACETS	1	0.857	1	0.342	0.286	0.404	CLONAL	1	TRUE	0	0.177853325726289	3		654	513	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434539	140434539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	41	411	0	ENST00000288602.6:c.2159C>T	p.Ser720Leu	p.S720L	ENST00000288602	NM_004333.4	720	tCa/tTa	18/18	0.177853325726289	5	FACETS	0.861	0.716	1	0.215	0.179	0.256	CLONAL	1	TRUE	1	0.177853325726289	5		411	678	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266519	115266519	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	47	424	0	ENST00000438362.2:c.1996G>C	p.Glu666Gln	p.E666Q	ENST00000438362	NM_001242891.1	666	Gag/Cag	16/20	0.177853325726289	3	FACETS	1	0.959	1	0.725	0.613	0.848	CLONAL	1	TRUE	1	0.177853325726289	3		424	397	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497832	120497832	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	101	603	0	ENST00000256646.2:c.2050G>C	p.Asp684His	p.D684H	ENST00000256646	NM_024408.3	684	Gat/Cat	13/34	0.177853325726289	3	FACETS	1	0.896	1	1	0.896	1	CLONAL	2	TRUE	1	0.177853325726289	3		603	618	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119762	108119762	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	74	387	0	ENST00000278616.4:c.1168G>C	p.Glu390Gln	p.E390Q	ENST00000278616	NM_000051.3	390	Gaa/Caa	9/63	0.177853325726289	3	FACETS	1	0.957	1	0.799	0.704	0.901	CLONAL	2	TRUE	0	0.177853325726289	3		387	378	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196791	108196791	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	93	343	0	ENST00000278616.4:c.6814G>C	p.Glu2272Gln	p.E2272Q	ENST00000278616	NM_000051.3	2272	Gaa/Caa	47/63	0.177853325726289	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	3	TRUE	0	0.177853325726289	3		343	329	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416554	49416554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	63	691	0	ENST00000301067.7:c.16157C>T	p.Ser5386Phe	p.S5386F	ENST00000301067	NM_003482.3	5386	tCt/tTt	51/54	0.177853325726289	6	FACETS	1	0.969	1	0.372	0.321	0.427	CLONAL	1	TRUE	2	0.177853325726289	6		691	646	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432609	49432609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	144	741	0	ENST00000301067.7:c.8530G>A	p.Glu2844Lys	p.E2844K	ENST00000301067	NM_003482.3	2844	Gaa/Aaa	34/54	0.177853325726289	6	FACETS	0.938	0.859	1	0.938	0.859	1	CLONAL	4	TRUE	2	0.177853325726289	6		741	585	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73633589	73633589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	41	321	0	ENST00000377687.4:c.124G>A	p.Asp42Asn	p.D42N	ENST00000377687	NM_001730.3	42	Gac/Aac	1/4	0.177853325726289	5	FACETS	0.901	0.754	1	0.451	0.377	0.532	CLONAL	2	TRUE	1	0.177853325726289	5		321	324	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527837	103527837	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	54	563	0	ENST00000355739.4:c.3145G>C	p.Asp1049His	p.D1049H	ENST00000355739	NM_000123.3	1049	Gat/Cat	15/15	0.177853325726289	5	FACETS	1	0.955	1	0.331	0.282	0.384	CLONAL	1	TRUE	1	0.177853325726289	5		563	581	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989159	41989159	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1159081612	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	82	516	0	ENST00000219905.7:c.1951C>T	p.Pro651Ser	p.P651S	ENST00000219905	NM_001164273.1	651	Cca/Tca	3/24	1	2	FACETS	1	0.93	1	1	0.985	1	CLONAL	2	TRUE	1	0.177853325726289	2		516	431	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019477	42019477	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	44	532	0	ENST00000219905.7:c.3530C>G	p.Pro1177Arg	p.P1177R	ENST00000219905	NM_001164273.1	1177	cCt/cGt	10/24	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.177853325726289	2		532	478	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66735655	66735655	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	26	321	0	ENST00000307102.5:c.476G>T	p.Gly159Val	p.G159V	ENST00000307102	NM_002755.3	159	gGa/gTa	4/11	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.177853325726289	2		321	241	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74005274	74005274	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	25	375	0	ENST00000318443.5:c.1583-1G>A		p.X528_splice	ENST00000318443	NM_001024736.1	528			1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.177853325726289	2		375	245	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2111990	2111990	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	111	708	0	ENST00000219476.3:c.1238G>C	p.Arg413Thr	p.R413T	ENST00000219476	NM_000548.3	413	aGa/aCa	12/42	0.177853325726289	4	FACETS	0.904	0.816	0.997	1	0.98	1	CLONAL	3	TRUE	2	0.177853325726289	4		708	542	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273984	10273984	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	78	720	0	ENST00000330684.3:c.285C>G	p.Ile95Met	p.I95M	ENST00000330684	NM_001134407.1	95	atC/atG	2/13	0.177853325726289	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	2	0.177853325726289	4		720	426	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782077	56782192	+	splice_acceptor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	CAGATTCAGGCAGTGTTTGAAACCTGTCTTTCCCTTGATTTAGATCTTTTCATTTTTTCTCCCATCTAGGATCTGCATCTCCAATGGATACTGAGGGGTTTGGTGAGCTCCTTCAG	CAGATTCAGGCAGTGTTTGAAACCTGTCTTTCCCTTGATTTAGATCTTTTCATTTTTTCTCCCATCTAGGATCTGCATCTCCAATGGATACTGAGGGGTTTGGTGAGCTCCTTCAG	-	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	22	197	0	ENST00000308159.5:c.-14-67_35del		p.X5_splice	ENST00000308159	NM_014669.4	5		2/22	1	2	FACETS	1	0.803	1	1	0.946	1	CLONAL	2	TRUE	1	0.177853325726289	2		197	121	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346327	89346327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	30	744	0	ENST00000301030.4:c.6623C>T	p.Ser2208Leu	p.S2208L	ENST00000301030	NM_001256183.1	2208	tCa/tTa	9/13	1	2	FACETS	0.922	0.743	1	0.922	0.743	1	CLONAL	1	TRUE	1	0.177853325726289	2		744	366	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816161	89816161	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	50	538	0	ENST00000389301.3:c.3216G>C	p.Gln1072His	p.Q1072H	ENST00000389301	NM_000135.2	1072	caG/caC	32/43	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.177853325726289	2		538	431	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78829313	78829313	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	68	446	0	ENST00000306801.3:c.1364G>A	p.Arg455Lys	p.R455K	ENST00000306801	NM_020761.2	455	aGa/aAa	12/34	1	2	FACETS	0.787	0.686	0.895	1	0.975	1	SUBCLONAL	2	TRUE	1	0.177853325726289	2		446	486	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690201	47690201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63751403	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	24	392	0	ENST00000233146.2:c.1418C>T	p.Ser473Leu	p.S473L	ENST00000233146	NM_000251.2	473	tCa/tTa	9/16	0.177853325726289	3	FACETS	0.913	0.716	1	0.456	0.358	0.57	CLONAL	1	TRUE	1	0.177853325726289	3		392	322	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631048	67631048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	51	525	0	ENST00000272342.5:c.1234G>A	p.Asp412Asn	p.D412N	ENST00000272342	NM_019002.3	412	Gat/Aat	5/6	0.177853325726289	4	FACETS	0.946	0.807	1	0.473	0.403	0.549	CLONAL	2	TRUE	0	0.177853325726289	4		525	357	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543863	41543863	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	50	403	0	ENST00000263253.7:c.2154G>A	p.Met718Ile	p.M718I	ENST00000263253	NM_001429.3	718	atG/atA	12/31	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.177853325726289	2		403	423	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556659	41556661	+	frameshift_variant	Frame_Shift_Del	DEL	GAG	GAG	AA	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	47	535	0	ENST00000263253.7:c.3604_3606delinsAA	p.Glu1202LysfsTer25	p.E1202Kfs*25	ENST00000263253	NM_001429.3	1202	GAG/AA	20/31	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.177853325726289	2		535	504	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41560064	41560064	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	45	366	0	ENST00000263253.7:c.3736G>C	p.Glu1246Gln	p.E1246Q	ENST00000263253	NM_001429.3	1246	Gaa/Caa	22/31	1	2	FACETS	0.806	0.68	0.943	1	0.964	1	CLONAL	2	TRUE	1	0.177853325726289	2		366	314	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12393144	12393144	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	31	426	0	ENST00000287820.6:c.53C>G	p.Thr18Ser	p.T18S	ENST00000287820	NM_015869.4	18	aCt/aGt	1/7	0.177853325726289	5	FACETS	0.751	0.606	0.916	0.188	0.151	0.229	CLONAL	1	TRUE	1	0.177853325726289	5		426	588	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089049	37089049	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	53	480	0	ENST00000231790.2:c.1771G>C	p.Asp591His	p.D591H	ENST00000231790	NM_000249.3	591	Gat/Cat	16/19	0.177853325726289	3	FACETS	1	0.945	1	0.618	0.527	0.718	CLONAL	1	TRUE	1	0.177853325726289	3		480	525	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651289	52651289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	58	513	0	ENST00000394830.3:c.1807G>A	p.Glu603Lys	p.E603K	ENST00000394830	NM_018313.4	603	Gag/Aag	15/30	0.177853325726289	3	FACETS	1	0.943	1	0.598	0.513	0.69	CLONAL	1	TRUE	1	0.177853325726289	3		513	594	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668633	52668633	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	66	329	0	ENST00000394830.3:c.1286C>G	p.Ser429Ter	p.S429*	ENST00000394830	NM_018313.4	429	tCa/tGa	12/30	0.177853325726289	3	FACETS	0.839	0.734	0.952	1	0.96	1	CLONAL	3	TRUE	1	0.177853325726289	3		329	321	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63898308	63898308	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs993137587	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	56	426	0	ENST00000398590.3:c.34G>A	p.Glu12Lys	p.E12K	ENST00000398590	NM_001177387.1	12	Gag/Aag	3/14	0.177853325726289	3	FACETS	1	0.964	1	0.717	0.615	0.828	CLONAL	1	TRUE	1	0.177853325726289	3		426	478	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446229	187446229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	48	624	0	ENST00000232014.4:c.1459G>A	p.Glu487Lys	p.E487K	ENST00000232014	NM_001130845.1	487	Gag/Aag	6/10	0.177853325726289	3	FACETS	0.936	0.79	1	0.468	0.395	0.549	CLONAL	1	TRUE	1	0.177853325726289	3		624	628	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295497	1295497	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	48	955	0				ENST00000310581	NM_198253.2	-/1132			0.177853325726289	4	FACETS	0.832	0.705	0.971	0.832	0.705	0.971	CLONAL	2	TRUE	2	0.177853325726289	4		955	382	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31485068	31485068	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	25	285	0	ENST00000344624.3:c.1916A>G	p.Asn639Ser	p.N639S	ENST00000344624		639	aAt/aGt	12/33	0.177853325726289	4	FACETS	1	0.917	1	0.684	0.541	0.847	CLONAL	1	TRUE	2	0.177853325726289	4		285	242	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564761	86564761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	57	765	0	ENST00000274376.6:c.493G>A	p.Glu165Lys	p.E165K	ENST00000274376	NM_002890.2	165	Gag/Aag	1/25	0.177853325726289	4	FACETS	1	0.936	1	0.583	0.5	0.675	CLONAL	1	TRUE	2	0.177853325726289	4		765	647	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048564	180048564	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	53	750	0	ENST00000261937.6:c.1998C>G	p.His666Gln	p.H666Q	ENST00000261937	NM_182925.4	666	caC/caG	13/30	0.177853325726289	3	FACETS	0.966	0.828	1	0.644	0.552	0.744	CLONAL	2	TRUE	0	0.177853325726289	3		750	336	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777972	27777972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	683	1015	0	ENST00000369163.2:c.121C>T	p.Arg41Cys	p.R41C	ENST00000369163	NM_003536.2	41	Cgc/Tgc	1/1	0.177853325726289	13	FACETS	0.966	0.934	0.998	0.885	0.856	0.915	CLONAL	11	TRUE	1	0.177853325726289	13		1015	1430	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962810	2962810	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1444062424	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	38	521	0	ENST00000396946.4:c.2098C>G	p.Leu700Val	p.L700V	ENST00000396946	NM_032415.4	700	Ctg/Gtg	16/25	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.177853325726289	2		521	289	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6029485	6029485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	64	305	0	ENST00000265849.7:c.1090G>A	p.Asp364Asn	p.D364N	ENST00000265849	NM_000535.5	364	Gat/Aat	10/15	1	2	FACETS	1	0.957	1	1	0.983	1	CLONAL	2	TRUE	1	0.177853325726289	2		305	291	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971276	13971276	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1213895329	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	49	606	0	ENST00000405192.2:c.653C>G	p.Pro218Arg	p.P218R	ENST00000405192	NM_001163147.1	218	cCa/cGa	8/12	0.177853325726289	10	FACETS	0.998	0.842	1	0.111	0.093	0.13	CLONAL	1	TRUE	1	0.177853325726289	10		606	945	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249094	55249094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	32	634	0	ENST00000275493.2:c.2392C>T	p.Leu798Phe	p.L798F	ENST00000275493	NM_005228.3	798	Ctc/Ttc	20/28	1	2	FACETS	0.857	0.695	1	0.857	0.695	1	CLONAL	1	TRUE	1	0.177853325726289	2		634	420	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852236	128852236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	42	781	0	ENST00000249373.3:c.2308C>T	p.His770Tyr	p.H770Y	ENST00000249373	NM_005631.4	770	Cac/Tac	12/12	0.177853325726289	5	FACETS	1	0.915	1	0.29	0.242	0.344	CLONAL	1	TRUE	1	0.177853325726289	5		781	516	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123098	5123098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	55	402	0	ENST00000381652.3:c.3154G>A	p.Glu1052Lys	p.E1052K	ENST00000381652	NM_004972.3	1052	Gag/Aag	23/25	0.177853325726289	28	FACETS	0.941	0.802	1	0.07	0.059	0.081	CLONAL	2	TRUE	1	0.177853325726289	28		402	1089	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932159	39932159	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	84	316	0	ENST00000378444.4:c.2440G>C	p.Asp814His	p.D814H	ENST00000378444	NM_001123385.1	814	Gat/Cat	4/15	0.177853325726289	3	FACETS	0.985	0.883	1			1	CLONAL	4	TRUE	NA	0.177853325726289	3		316	261	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556659	41556659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	47	525	0	ENST00000263253.7:c.3604del	p.Glu1202ArgfsTer25	p.E1202Rfs*25	ENST00000263253	NM_001429.3	1202	Gag/ag	20/31	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.177853325726289	2		525	502	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0063232-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	28	1032	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.727	0.583	0.889	0.727	0.583	0.889	SUBCLONAL	1	TRUE	1	0.294137140431646	2		1032	262	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0063232-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	61	359	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.294137140431646	2		359	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs267605076	NA	P-0063232-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	63	662	0	ENST00000269305.4:c.672G>T	p.Glu224Asp	p.E224D	ENST00000269305	NM_001126112.2	224	gaG/gaT	6/11	0.258940869446066	1	FACETS	0.812	0.704	0.928	0.812	0.704	0.928	CLONAL	1	TRUE	0	0.294137140431646	1		662	450	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048632	180048632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063232-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	37	670	0	ENST00000261937.6:c.1930G>A	p.Ala644Thr	p.A644T	ENST00000261937	NM_182925.4	644	Gcg/Acg	13/30	0.294137140431646	1	FACETS	0.633	0.523	0.755	0.633	0.523	0.755	SUBCLONAL	1	TRUE	0	0.294137140431646	1		670	339	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526071	189526071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063232-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	73	592	1	ENST00000264731.3:c.335C>T	p.Thr112Met	p.T112M	ENST00000264731	NM_003722.4	112	aCg/aTg	4/14	1	2	FACETS	0.859	0.752	0.974	0.859	0.752	0.974	CLONAL	1	TRUE	1	0.294137140431646	2		593	578	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332108	70332108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140156594	NA	P-0063232-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	26	412	0	ENST00000373644.4:c.13C>T	p.Arg5Cys	p.R5C	ENST00000373644	NM_030625.2	5	Cgc/Tgc	2/12	0.258940869446066	1	FACETS	0.548	0.435	0.677	0.548	0.435	0.677	SUBCLONAL	1	TRUE	0	0.294137140431646	1		412	275	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586086	29586086	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs878853893	NA	P-0063232-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	20	245	0	ENST00000356175.3:c.4306A>G	p.Lys1436Glu	p.K1436E	ENST00000356175	NM_000267.3	1436	Aaa/Gaa	32/57	0.258940869446066	1	FACETS	0.589	0.452	0.747	0.589	0.452	0.747	SUBCLONAL	1	TRUE	0	0.294137140431646	1		245	197	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011106	12011106	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0063232-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	44	297	0	ENST00000353533.5:c.515del		p.X172_splice	ENST00000353533	NM_003010.3	172			0.258940869446066	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.294137140431646	1		297	203	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0063235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	55	178	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.254831117419616	2	FACETS	0.874	0.755	1	0.874	0.755	1	CLONAL	2	TRUE	0	0.254831117419616	2		178	247	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0063235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	38	155	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	0.254831117419616	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	2	TRUE	0	0.254831117419616	2		155	144	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0063235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	94	460	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.254831117419616	2		460	671	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0063236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	98	556	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.33971604356116	5	FACETS	1	0.957	1	1	0.957	1	CLONAL	3	TRUE	2	0.33971604356116	5		556	264	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606150	81606150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373712078	NA	P-0063236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	212	531	0	ENST00000298171.2:c.820C>T	p.Arg274Trp	p.R274W	ENST00000298171	NM_000369.2	274	Cgg/Tgg	9/10	0.332994566810863	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	2	0.33971604356116	4		531	799	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806119	1806119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931614	NA	P-0063236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	18	626	0	ENST00000260795.2:c.1138G>A	p.Gly380Arg	p.G380R	ENST00000260795		380	Ggg/Agg	8/17	0.239318557770483	4	FACETS	0.158	0.118	0.206	0.079	0.059	0.103	SUBCLONAL	1	TRUE	2	0.33971604356116	4		626	896	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011144	12011144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	74	293	0	ENST00000353533.5:c.551C>T	p.Ser184Leu	p.S184L	ENST00000353533	NM_003010.3	184	tCg/tTg	5/11	0.33971604356116	2	FACETS	0.784	0.694	0.878	0.784	0.694	0.878	SUBCLONAL	2	TRUE	0	0.33971604356116	2		293	278	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938932	178938932	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	87	150	0	ENST00000263967.3:c.2174A>G	p.Asp725Gly	p.D725G	ENST00000263967	NM_006218.2	725	gAt/gGt	14/21	0.33971604356116	5	FACETS	0.901	0.808	0.998	0.901	0.808	0.998	CLONAL	3	TRUE	2	0.33971604356116	5		150	286	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971154	21971154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	112	719	0	ENST00000579755.1:c.247G>A	p.Gly83Arg	p.G83R	ENST00000579755		83	Gga/Aga	2/3	0.338852790975471	3	FACETS	0.918	0.825	1	0.459	0.412	0.509	CLONAL	1	TRUE	1	0.33971604356116	3		719	840	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803416	1803416	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368831528	NA	P-0063236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	304	833	0	ENST00000260795.2:c.685G>A	p.Val229Ile	p.V229I	ENST00000260795		229	Gtc/Atc	5/17	0.239318557770483	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.33971604356116	4		833	1104	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110073	115110073	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	233	498	0	ENST00000257566.3:c.1805del	p.Pro602LeufsTer30	p.P602Lfs*30	ENST00000257566	NM_016569.3	602	cCt/ct	8/8	0.332994566810863	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.33971604356116	4		498	841	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561756	55561756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376469897	NA	P-0063236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	156	503	0	ENST00000288135.5:c.146G>A	p.Arg49His	p.R49H	ENST00000288135	NM_000222.2	49	cGc/cAc	2/21	0.239318557770483	4	FACETS	0.927	0.851	1	0.927	0.851	1	CLONAL	2	TRUE	2	0.33971604356116	4		503	664	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73342975	73342975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757306363	NA	P-0063236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	111	308	0	ENST00000377767.4:c.1831C>T	p.Arg611Cys	p.R611C	ENST00000377767	NM_014953.3	611	Cgt/Tgt	14/21	0.283340161908507	4	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	2	0.33971604356116	4		308	419	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885287	111885287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs953911126	NA	P-0063236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	192	626	0	ENST00000341259.2:c.1175G>A	p.Arg392Gln	p.R392Q	ENST00000341259	NM_005475.2	392	cGg/cAg	6/8	0.332994566810863	4	FACETS	0.934	0.865	1	0.934	0.865	1	CLONAL	2	TRUE	2	0.33971604356116	4		626	811	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106074	8106075	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0063236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	99	608	0	ENST00000346208.3:c.898dup	p.Leu300ProfsTer3	p.L300Pfs*3	ENST00000346208		298	-/C	4/6	0.283340161908507	4	FACETS	0.892	0.796	0.996	0.446	0.398	0.498	CLONAL	1	TRUE	2	0.33971604356116	4		608	875	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99181187	99181187	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	207	577	0	ENST00000074304.5:c.2128G>A	p.Gly710Arg	p.G710R	ENST00000074304	NM_001134224.1	710	Ggg/Agg	20/26	0.332994566810863	4	FACETS	0.982	0.913	1	0.982	0.913	1	CLONAL	2	TRUE	2	0.33971604356116	4		577	831	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217617	7217617	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	209	579	0	ENST00000380728.2:c.310del	p.Glu104AsnfsTer5	p.E104Nfs*5	ENST00000380728		104	Gaa/aa	4/11	0.33971604356116	2	FACETS	0.945	0.882	1	0.945	0.882	1	CLONAL	2	TRUE	0	0.33971604356116	2		579	651	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441520	40441520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	71	566	0	ENST00000345506.4:c.91C>T	p.Arg31Trp	p.R31W	ENST00000345506	NM_003152.3	31	Cgg/Tgg	3/20	0.332994566810863	4	FACETS	0.612	0.533	0.698	0.306	0.266	0.349	SUBCLONAL	1	TRUE	2	0.33971604356116	4		566	915	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554671	63554671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	142	724	0	ENST00000307078.5:c.68G>A	p.Arg23Gln	p.R23Q	ENST00000307078	NM_004655.3	23	cGg/cAg	2/11	0.332994566810863	4	FACETS	1	0.937	1	0.519	0.472	0.569	CLONAL	1	TRUE	2	0.33971604356116	4		724	1079	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937485	178937485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303751906	NA	P-0063236-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	103	202	0	ENST00000263967.3:c.1873G>A	p.Asp625Asn	p.D625N	ENST00000263967	NM_006218.2	625	Gat/Aat	12/21	0.33971604356116	5	FACETS	1	0.931	1	1	0.931	1	CLONAL	3	TRUE	2	0.33971604356116	5		202	296	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0063237-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	10	387	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.819	1	1	0.819	1	CLONAL	1	TRUE	1	0.29	2		387	53	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0063237-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	56	450	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.168108278820421	3	FACETS	1	0.919	1	0.551	0.474	0.636	INDETERMINATE	1	TRUE	1	0.29	3		451	401	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260212	10260212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063237-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	80	604	0	ENST00000340748.4:c.2455G>A	p.Glu819Lys	p.E819K	ENST00000340748		819	Gaa/Aaa	25/40	0.168108278820421	3	FACETS	1	0.924	1	0.533	0.469	0.601	INDETERMINATE	1	TRUE	1	0.29	3		604	593	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796222	45796222	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144111588	NA	P-0063237-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	18	383	0	ENST00000450313.1:c.1484G>A	p.Arg495His	p.R495H	ENST00000450313	NM_012222.2	495	cGt/cAt	15/16	1	2	FACETS	0.359	0.269	0.465	0.359	0.269	0.465	SUBCLONAL	1	TRUE	1	0.29	2		383	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0063271-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	91	577	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.3	1	FACETS	0.72	0.639	0.806	0.72	0.639	0.806	SUBCLONAL	1	TRUE	0	0.31	1		579	689	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410525	63410525	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372769953	NA	P-0063271-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	119	415	0	ENST00000330258.3:c.2642G>A	p.Arg881Gln	p.R881Q	ENST00000330258	NM_152424.3	881	cGa/cAa	2/2	0.203129760021212	2	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.31	2		415	622	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851339	156851339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760974854	NA	P-0063271-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	115	719	2	ENST00000524377.1:c.2296C>T	p.Arg766Trp	p.R766W	ENST00000524377	NM_002529.3	766	Cgg/Tgg	17/17	1	2	FACETS	0.844	0.76	0.933	0.844	0.76	0.933	CLONAL	1	TRUE	1	0.31	2		721	879	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123875	46123896	+	frameshift_variant	Frame_Shift_Del	DEL	TCACGGTCTCTACACCAGAGTC	TCACGGTCTCTACACCAGAGTC	-	novel	NA	P-0063271-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	203	695	0	ENST00000334344.6:c.141_162del	p.His48LeufsTer3	p.H48Lfs*3	ENST00000334344	NM_152641.2	47	ctTCACGGTCTCTACACCAGAGTC/ct	2/21	0.263506638078383	2	FACETS	1	0.991	1	0.746	0.692	0.801	CLONAL	1	TRUE	0	0.31	2		695	878	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248584	212248584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063271-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	102	700	0	ENST00000342788.4:c.3683C>T	p.Ser1228Leu	p.S1228L	ENST00000342788	NM_005235.2	1228	tCa/tTa	28/28	0.263506638078383	2	FACETS	0.725	0.647	0.807	0.362	0.323	0.404	SUBCLONAL	1	TRUE	0	0.31	2		700	908	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380276	+	missense_variant	Missense_Mutation	DNP	TT	TT	GC	novel	NA	P-0063272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	76	447	0	ENST00000311936.3:c.182_183delinsGC	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAA/cGC	3/5	1	2	FACETS	0.802	0.708	0.902	0.802	0.708	0.902	CLONAL	1	TRUE	1	0.493518716418532	2		447	384	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	397	343	0				ENST00000310581	NM_198253.2	-/1132			0.547043265841886	5	FACETS	0.9	0.863	0.936	0.9	0.863	0.936	CLONAL	4	TRUE	1	0.547043265841886	5		343	734	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	123	582	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	1	2	FACETS	0.615	0.557	0.677	0.615	0.557	0.677	SUBCLONAL	1	TRUE	1	0.547043265841886	2		582	731	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	32	190	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.629	0.515	0.754	0.629	0.515	0.754	SUBCLONAL	1	TRUE	1	0.547043265841886	2		190	186	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	225	443	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.547043265841886	2		443	647	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	21	557	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	1	2	FACETS	0.129	0.098	0.164	0.129	0.098	0.164	SUBCLONAL	1	TRUE	1	0.547043265841886	2		557	597	SUCCESS
MET	4233	MSKCC	GRCh37	7	116409781	116409781	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	62	396	0	ENST00000397752.3:c.2666C>G	p.Ser889Cys	p.S889C	ENST00000397752	NM_000245.2	889	tCt/tGt	12/21	0.545594240363931	2	FACETS	0.606	0.526	0.692	0.303	0.263	0.346	SUBCLONAL	1	TRUE	0	0.547043265841886	2		396	374	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	13	517	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.11	0.078	0.15	0.11	0.078	0.15	SUBCLONAL	1	TRUE	1	0.547043265841886	2		517	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577077	7577077	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs748891343	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	234	642	0	ENST00000269305.4:c.861G>C	p.Glu287Asp	p.E287D	ENST00000269305	NM_001126112.2	287	gaG/gaC	8/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.547043265841886	2		642	673	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868953	117868953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	51	276	0	ENST00000297338.2:c.746C>T	p.Ser249Phe	p.S249F	ENST00000297338	NM_006265.2	249	tCt/tTt	7/14	0.125546713302658	3	FACETS	0.726	0.62	0.841	0.242	0.206	0.281	INDETERMINATE	1	TRUE	0	0.547043265841886	3		276	327	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230827	53230827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	176	316	0	ENST00000375401.3:c.1966G>A	p.Glu656Lys	p.E656K	ENST00000375401	NM_004187.3	656	Gag/Aag	14/26	1	1	FACETS	0.754	0.709	0.798	1	0.992	1	SUBCLONAL	2	TRUE	0	0.547043265841886	1		316	310	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023895	27023895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	91	651	0	ENST00000324856.7:c.1001C>T	p.Ser334Leu	p.S334L	ENST00000324856	NM_006015.4	334	tCg/tTg	1/20	NA	2	FACETS	0.56	0.498	0.626			1	INDETERMINATE	1	TRUE	NA	0.547043265841886	2		651	594	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456273	32456273	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	65	578	0	ENST00000332351.3:c.619G>A	p.Glu207Lys	p.E207K	ENST00000332351	NM_024426.4	207	Gag/Aag	1/10	0.282750524217539	1	FACETS	0.281	0.243	0.322	0.281	0.243	0.322	INDETERMINATE	1	TRUE	0	0.547043265841886	1		578	614	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435749	116435749	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	64	470	0	ENST00000397752.3:c.3839G>A	p.Gly1280Glu	p.G1280E	ENST00000397752	NM_000245.2	1280	gGa/gAa	20/21	0.545594240363931	2	FACETS	0.476	0.412	0.544	0.238	0.206	0.272	SUBCLONAL	1	TRUE	0	0.547043265841886	2		470	492	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001359	150001359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747544430	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	91	520	0	ENST00000253339.5:c.2245C>T	p.His749Tyr	p.H749Y	ENST00000253339		749	Cat/Tat	4/7	0.282750524217539	1	FACETS	0.421	0.374	0.471	0.421	0.374	0.471	INDETERMINATE	1	TRUE	0	0.547043265841886	1		520	574	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55960978	55960978	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	45	395	0	ENST00000263923.4:c.2962G>T	p.Glu988Ter	p.E988*	ENST00000263923	NM_002253.2	988	Gaa/Taa	21/30	1	2	FACETS	0.404	0.34	0.475	0.404	0.34	0.475	SUBCLONAL	1	TRUE	1	0.547043265841886	2		395	407	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418607	49418607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs980258889	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	179	673	0	ENST00000301067.7:c.15907C>T	p.Arg5303Cys	p.R5303C	ENST00000301067	NM_003482.3	5303	Cgc/Tgc	49/54	1	2	FACETS	0.978	0.905	1	0.978	0.905	1	CLONAL	1	TRUE	1	0.547043265841886	2		673	669	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131945035	131945035	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	55	325	0	ENST00000265335.6:c.2983G>A	p.Glu995Lys	p.E995K	ENST00000265335		995	Gaa/Aaa	19/25	0.282750524217539	1	FACETS	0.425	0.365	0.489	0.425	0.365	0.489	INDETERMINATE	1	TRUE	0	0.547043265841886	1		325	344	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342446	118342446	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	79	468	0	ENST00000534358.1:c.572C>G	p.Ser191Ter	p.S191*	ENST00000534358	NM_005933.3	191	tCa/tGa	3/36	0.282750524217539	1	FACETS	0.407	0.358	0.458	0.407	0.358	0.458	INDETERMINATE	1	TRUE	0	0.547043265841886	1		468	516	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112910775	112910775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	113	317	0	ENST00000351677.2:c.784C>T	p.Leu262Phe	p.L262F	ENST00000351677	NM_002834.3	262	Ctc/Ttc	7/16	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.547043265841886	2		317	407	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553365	41553365	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	71	512	0	ENST00000263253.7:c.3454G>A	p.Glu1152Lys	p.E1152K	ENST00000263253	NM_001429.3	1152	Gaa/Aaa	18/31	0.170678419803775	3	FACETS	0.597	0.521	0.678	0.298	0.26	0.339	INDETERMINATE	1	TRUE	1	0.547043265841886	3		512	554	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324565	62324565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369716125	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	178	750	1	ENST00000360203.5:c.2921G>A	p.Arg974Gln	p.R974Q	ENST00000360203	NM_001283009.1	974	cGa/cAa	30/35	0.268155286987632	3	FACETS	1	0.94	1	0.51	0.471	0.551	INDETERMINATE	1	TRUE	1	0.547043265841886	3		751	812	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202978	16202978	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139125517	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	76	560	0	ENST00000375759.3:c.686G>A	p.Arg229Gln	p.R229Q	ENST00000375759	NM_015001.2	229	cGa/cAa	3/15	1	2	FACETS	0.502	0.441	0.568	0.502	0.441	0.568	SUBCLONAL	1	TRUE	1	0.547043265841886	2		560	553	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202992	16202992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	75	552	0	ENST00000375759.3:c.700G>A	p.Glu234Lys	p.E234K	ENST00000375759	NM_015001.2	234	Gag/Aag	3/15	1	2	FACETS	0.504	0.442	0.57	0.504	0.442	0.57	SUBCLONAL	1	TRUE	1	0.547043265841886	2		552	544	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711968	89711968	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	31	296	0	ENST00000371953.3:c.586C>A	p.His196Asn	p.H196N	ENST00000371953	NM_000314.4	196	Cac/Aac	6/9	0.146089321433373	0	FACETS	0.173	0.14	0.21			1	INDETERMINATE	1	TRUE	0	0.547043265841886	0		296	297	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664873	29664873	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	48	421	0	ENST00000356175.3:c.6616G>C	p.Asp2206His	p.D2206H	ENST00000356175	NM_000267.3	2206	Gac/Cac	43/57	0.17713134051343	4	FACETS	0.514	0.434	0.602	0.257	0.217	0.301	INDETERMINATE	1	TRUE	2	0.547043265841886	4		421	528	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2220191	2220191	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	82	620	0	ENST00000398665.3:c.2776G>T	p.Gly926Trp	p.G926W	ENST00000398665	NM_032482.2	926	Ggg/Tgg	23/28	1	2	FACETS	0.487	0.429	0.548	0.487	0.429	0.548	SUBCLONAL	1	TRUE	1	0.547043265841886	2		620	616	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284980	15284980	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	139	564	0	ENST00000263388.2:c.4635C>G	p.Phe1545Leu	p.F1545L	ENST00000263388	NM_000435.2	1545	ttC/ttG	25/33	1	2	FACETS	0.861	0.787	0.939	0.861	0.787	0.939	CLONAL	1	TRUE	1	0.547043265841886	2		564	590	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366988	15366988	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs761158744	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	34	541	0	ENST00000263377.2:c.1638G>C	p.Lys546Asn	p.K546N	ENST00000263377	NM_058243.2	546	aaG/aaC	9/20	1	2	FACETS	0.237	0.193	0.286	0.237	0.193	0.286	SUBCLONAL	1	TRUE	1	0.547043265841886	2		541	525	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18958636	18958636	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	129	355	0	ENST00000262803.5:c.455C>G	p.Ser152Cys	p.S152C	ENST00000262803	NM_002911.3	152	tCt/tGt	3/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.547043265841886	2		355	421	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965964	25965964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	73	586	0	ENST00000435504.4:c.3242C>T	p.Ser1081Leu	p.S1081L	ENST00000435504		1081	tCa/tTa	13/13	0.350048383510446	3	FACETS	0.511	0.447	0.581	0.256	0.223	0.291	SUBCLONAL	1	TRUE	1	0.547043265841886	3		586	665	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630740	67630740	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	30	461	0	ENST00000272342.5:c.926G>C	p.Ser309Thr	p.S309T	ENST00000272342	NM_019002.3	309	aGt/aCt	5/6	0.170678419803775	3	FACETS	0.254	0.204	0.312	0.127	0.102	0.156	INDETERMINATE	1	TRUE	1	0.547043265841886	3		461	549	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149290732	149290732	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	69	426	0	ENST00000360632.3:c.487C>G	p.Leu163Val	p.L163V	ENST00000360632	NM_015472.4	163	Ctg/Gtg	3/7	1	2	FACETS	0.495	0.431	0.563	0.495	0.431	0.563	SUBCLONAL	1	TRUE	1	0.547043265841886	2		426	510	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287361	33287361	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395619684	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	193	666	0	ENST00000374542.5:c.1736C>T	p.Pro579Leu	p.P579L	ENST00000374542	NM_001141970.1	579	cCt/cTt	6/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.547043265841886	2		666	606	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394413	162394413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	56	461	0	ENST00000366898.1:c.655G>A	p.Asp219Asn	p.D219N	ENST00000366898	NM_004562.2	219	Gac/Aac	6/12	0.282750524217539	1	FACETS	0.343	0.294	0.396	0.343	0.294	0.396	INDETERMINATE	1	TRUE	0	0.547043265841886	1		461	434	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851451	151851451	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	59	509	0	ENST00000262189.6:c.12040G>C	p.Glu4014Gln	p.E4014Q	ENST00000262189	NM_170606.2	4014	Gaa/Caa	47/59	0.350048383510446	3	FACETS	0.402	0.345	0.464	0.201	0.172	0.232	SUBCLONAL	1	TRUE	1	0.547043265841886	3		509	684	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372115	55372115	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	106	691	0	ENST00000297316.4:c.805C>G	p.Pro269Ala	p.P269A	ENST00000297316	NM_022454.3	269	Ccc/Gcc	2/2	1	2	FACETS	0.554	0.497	0.614	0.554	0.497	0.614	SUBCLONAL	1	TRUE	1	0.547043265841886	2		691	700	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336266	80336266	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	58	497	0	ENST00000286548.4:c.1053G>C	p.Leu351Phe	p.L351F	ENST00000286548	NM_002072.3	351	ttG/ttC	7/7	0.547043265841886	1	FACETS	0.464	0.401	0.532	0.464	0.401	0.532	SUBCLONAL	1	TRUE	0	0.547043265841886	1		497	332	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230857	53230857	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	178	309	0	ENST00000375401.3:c.1936G>T	p.Glu646Ter	p.E646*	ENST00000375401	NM_004187.3	646	Gag/Tag	14/26	1	1	FACETS	0.758	0.713	0.802	1	0.992	1	SUBCLONAL	2	TRUE	0	0.547043265841886	1		309	312	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0063276-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	51	652	0	ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	4/10	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.18	2		652	526	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0063277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	196	387	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.265083040376489	4	FACETS	0.923	0.862	0.985	0.923	0.862	0.985	CLONAL	3	TRUE	1	0.372044401696051	4		387	522	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0063277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	22	665	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.372044401696051	1	FACETS	0.183	0.141	0.232	0.183	0.141	0.232	SUBCLONAL	1	TRUE	0	0.372044401696051	1		665	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0063277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	359	735	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.369435913151378	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.372044401696051	2		735	866	SUCCESS
APC	324	MSKCC	GRCh37	5	112175788	112175788	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	123	664	0	ENST00000257430.4:c.4497del	p.Ser1501LeufsTer6	p.S1501Lfs*6	ENST00000257430	NM_000038.5	1499	ggA/gg	16/16	1	2	FACETS	0.968	0.877	1	0.968	0.877	1	CLONAL	1	TRUE	1	0.372044401696051	2		664	683	SUCCESS
APC	324	MSKCC	GRCh37	5	112174759	112174762	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs786203020	NA	P-0063277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	119	576	0	ENST00000257430.4:c.3471_3474del	p.Glu1157AspfsTer7	p.E1157Dfs*7	ENST00000257430	NM_000038.5	1156	gaAGAG/ga	16/16	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.372044401696051	2		576	633	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412647	63412648	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0063277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	271	291	0	ENST00000330258.3:c.519dup	p.Ser174Ter	p.S174*	ENST00000330258	NM_152424.3	173	-/T	2/2	0.372044401696051	2	FACETS	0.967	0.92	1			1	CLONAL	3	TRUE	NA	0.372044401696051	2		291	502	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492582	50492582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	46	502	0	ENST00000394963.4:c.1478G>A	p.Arg493Gln	p.R493Q	ENST00000394963	NM_003076.4	493	cGa/cAa	12/13	0.351848577619796	3	FACETS	0.44	0.37	0.518	0.22	0.185	0.259	SUBCLONAL	1	TRUE	1	0.372044401696051	3		502	666	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625390	69625390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs574433541	NA	P-0063277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	130	632	0	ENST00000334134.2:c.403C>T	p.Arg135Trp	p.R135W	ENST00000334134	NM_005247.2	135	Cgg/Tgg	3/3	0.371855889025714	2	FACETS	0.947	0.86	1	0.473	0.43	0.519	CLONAL	1	TRUE	0	0.372044401696051	2		632	738	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434243	49434243	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	180	866	0	ENST00000301067.7:c.7310del	p.Pro2437HisfsTer48	p.P2437Hfs*48	ENST00000301067	NM_003482.3	2437	cCa/ca	31/54	0.351848577619796	3	FACETS	1	0.956	1	0.527	0.486	0.571	CLONAL	1	TRUE	1	0.372044401696051	3		866	1088	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628619	187628619	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	178	706	0	ENST00000441802.2:c.2363A>G	p.Tyr788Cys	p.Y788C	ENST00000441802	NM_005245.3	788	tAc/tGc	2/27	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.372044401696051	2		706	797	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123040897	123040897	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	48	172	0	ENST00000355640.3:c.1360A>G	p.Met454Val	p.M454V	ENST00000355640		454	Atg/Gtg	7/7	0.372044401696051	2	FACETS	0.918	0.782	1			1	CLONAL	1	TRUE	NA	0.372044401696051	2		172	281	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0063278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	226	689	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.106297929673899	5	FACETS	1	0.985	1	0.594	0.555	0.634	INDETERMINATE	2	TRUE	1	0.391038371915296	5		689	772	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508374	106508374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200423506	NA	P-0063278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	274	788	0	ENST00000359195.3:c.368G>A	p.Arg123His	p.R123H	ENST00000359195	NM_002649.2	123	cGc/cAc	2/11	0.330140713863053	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.391038371915296	4		788	830	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0063278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	268	1021	0	ENST00000269305.4:c.560-1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.316570149980869	2	FACETS	0.839	0.789	0.889	0.839	0.789	0.889	CLONAL	2	TRUE	0	0.391038371915296	2		1021	817	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517326	157517326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371538726	NA	P-0063278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	38	489	0	ENST00000346085.5:c.3890C>T	p.Thr1297Met	p.T1297M	ENST00000346085	NM_020732.3	1297	aCg/aTg	16/20	0.106297929673899	5	FACETS	0.615	0.508	0.735	0.154	0.127	0.184	INDETERMINATE	1	TRUE	1	0.391038371915296	5		489	501	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448422	49448422	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs375614893	NA	P-0063278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	99	844	0	ENST00000301067.7:c.289G>T	p.Val97Leu	p.V97L	ENST00000301067	NM_003482.3	97	Gtg/Ttg	3/54	0.372833589244533	4	FACETS	0.628	0.559	0.702	0.314	0.279	0.351	SUBCLONAL	1	TRUE	2	0.391038371915296	4		844	1121	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046276	180046276	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	71	506	0	ENST00000261937.6:c.2738T>A	p.Leu913His	p.L913H	ENST00000261937	NM_182925.4	913	cTc/cAc	19/30	1	2	FACETS	0.702	0.614	0.797	0.702	0.614	0.797	SUBCLONAL	1	TRUE	1	0.391038371915296	2		506	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0063279-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	266	443	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.420746104288723	2	FACETS	0.989	0.935	1	0.989	0.935	1	CLONAL	2	TRUE	0	0.420746104288723	2		443	639	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0063279-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	85	308	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.971	0.863	1	0.971	0.863	1	CLONAL	1	TRUE	1	0.420746104288723	2		308	416	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0063279-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	130	477	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	0.395255058272831	4	FACETS	1	0.96	1	0.368	0.334	0.404	CLONAL	1	TRUE	1	0.420746104288723	4		477	795	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813078	89813078	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs61753269	NA	P-0063279-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	126	738	0	ENST00000389301.3:c.3427C>G	p.Leu1143Val	p.L1143V	ENST00000389301	NM_000135.2	1143	Ctg/Gtg	35/43	0.420746104288723	3	FACETS	1	0.951	1	0.537	0.487	0.59	CLONAL	1	TRUE	1	0.420746104288723	3		738	675	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218444	1218445	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0063279-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	357	754	0	ENST00000326873.7:c.320dup	p.His107GlnfsTer56	p.H107Qfs*56	ENST00000326873	NM_000455.4	107	cac/cAac	2/10	0.414790402501708	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	0	0.420746104288723	3		754	672	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600012	10600013	+	missense_variant	Missense_Mutation	DNP	CA	CA	GG	novel	NA	P-0063279-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	238	835	1	ENST00000171111.5:c.1563_1564delinsCC	p.Ala522Pro	p.A522P	ENST00000171111	NM_203500.1	521	gcTGct/gcCCct	5/6	0.420746104288723	2	FACETS	0.938	0.882	0.995	0.938	0.882	0.995	CLONAL	2	TRUE	0	0.420746104288723	2		836	603	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965928	25965928	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0063279-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	147	741	0	ENST00000435504.4:c.3278C>G	p.Ser1093Ter	p.S1093*	ENST00000435504		1093	tCa/tGa	13/13	0.420746104288723	3	FACETS	1	0.958	1	0.54	0.493	0.589	CLONAL	1	TRUE	1	0.420746104288723	3		741	783	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267699	198267699	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063279-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	242	435	0	ENST00000335508.6:c.1780C>G	p.Arg594Gly	p.R594G	ENST00000335508	NM_012433.2	594	Cga/Gga	13/25	0.420746104288723	5	FACETS	0.874	0.82	0.928	0.874	0.82	0.928	CLONAL	3	TRUE	2	0.420746104288723	5		435	716	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508750	106508750	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063279-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	178	757	0	ENST00000359195.3:c.744C>A	p.Phe248Leu	p.F248L	ENST00000359195	NM_002649.2	248	ttC/ttA	2/11	0.258800452028777	4	FACETS	1	0.988	1	0.71	0.655	0.767	CLONAL	1	TRUE	2	0.420746104288723	4		757	847	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160423	108160426	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	novel	NA	P-0063281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	47	386	0	ENST00000278616.4:c.4335_4338del	p.Phe1445LeufsTer5	p.F1445Lfs*5	ENST00000278616	NM_000051.3	1444	cTGTTt/ct	29/63	0.838045315729882	1	FACETS	0.973	0.877	1	0.973	0.877	1	CLONAL	1	TRUE	0	0.838045315729882	1		386	67	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99809081	99809081	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	49	370	0	ENST00000280892.6:c.304T>C	p.Ser102Pro	p.S102P	ENST00000280892	NM_001130678.1	102	Tct/Cct	4/7	0.15384224631338	4	FACETS	0.874	0.761	0.99	0.874	0.761	0.99	INDETERMINATE	2	TRUE	2	0.838045315729882	4		370	123	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929559	44929559	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	127	272	0	ENST00000377967.4:c.2659G>T	p.Val887Leu	p.V887L	ENST00000377967	NM_021140.2	887	Gtg/Ttg	17/29	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.838045315729882	1		272	136	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199744	138199744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	41	849	0	ENST00000237289.4:c.1162G>A	p.Glu388Lys	p.E388K	ENST00000237289	NM_001270507.1	388	Gaa/Aaa	7/9	0.266169217014409	2	FACETS	0.455	0.378	0.54	0.227	0.189	0.27	SUBCLONAL	1	TRUE	0	0.294164536118916	2		849	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0063282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	122	502	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.261059460733608	2	FACETS	0.91	0.828	0.995	0.91	0.828	0.995	CLONAL	2	TRUE	0	0.294164536118916	2		502	456	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665015	138665015	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	59	532	0	ENST00000330315.3:c.550G>A	p.Asp184Asn	p.D184N	ENST00000330315	NM_023067.3	184	Gac/Aac	1/1	0.294164536118916	5	FACETS	0.992	0.853	1	0.331	0.284	0.381	CLONAL	1	TRUE	2	0.294164536118916	5		532	583	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157256700	157256700	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0063282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	30	460	0	ENST00000346085.5:c.2027C>G	p.Ser676Ter	p.S676*	ENST00000346085	NM_020732.3	676	tCa/tGa	5/20	0.294557892804527	3	FACETS	0.447	0.36	0.547	0.149	0.12	0.183	SUBCLONAL	1	TRUE	0	0.294164536118916	3		460	523	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445051	89445051	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	354	665	0	ENST00000336596.2:c.1371G>T	p.Trp457Cys	p.W457C	ENST00000336596	NM_005233.5	457	tgG/tgT	6/17	0.294164536118916	8	FACETS	1	0.984	1	0.867	0.823	0.912	CLONAL	4	TRUE	3	0.294164536118916	8		665	1045	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164124	32164124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773802121	NA	P-0063282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	356	704	0	ENST00000375023.3:c.5275G>A	p.Asp1759Asn	p.D1759N	ENST00000375023	NM_004557.3	1759	Gat/Aat	29/30	0.294164536118916	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	4	TRUE	0	0.294164536118916	4		704	771	SUCCESS
AR	367	MSKCC	GRCh37	X	66765955	66765955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1021234843	NA	P-0063282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	42	423	0	ENST00000374690.3:c.967G>A	p.Glu323Lys	p.E323K	ENST00000374690	NM_000044.3	323	Gag/Aag	1/8	0.235851268555129	2	FACETS	0.67	0.56	0.792			1	SUBCLONAL	1	TRUE	NA	0.294164536118916	2		423	426	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513238	44513238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	80	404	1	ENST00000291552.4:c.697G>A	p.Asp233Asn	p.D233N	ENST00000291552	NM_006758.2	233	Gat/Aat	8/8	0.293661309225337	3	FACETS	0.845	0.749	0.947	0.845	0.749	0.947	CLONAL	2	TRUE	1	0.294164536118916	3		405	369	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112919968	112919968	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	81	273	0	ENST00000351677.2:c.1183G>T	p.Asp395Tyr	p.D395Y	ENST00000351677	NM_002834.3	395	Gac/Tac	10/16	0.294557892804527	4	FACETS	0.834	0.743	0.928	0.834	0.743	0.928	CLONAL	3	TRUE	1	0.294164536118916	4		273	285	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184818	32184818	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	53	718	0	ENST00000375023.3:c.1765G>C	p.Glu589Gln	p.E589Q	ENST00000375023	NM_004557.3	589	Gag/Cag	11/30	0.294164536118916	4	FACETS	0.554	0.471	0.645	0.138	0.117	0.162	SUBCLONAL	1	TRUE	0	0.294164536118916	4		718	842	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17345397	17345397	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	32	468	0	ENST00000375499.3:c.822G>T	p.Lys274Asn	p.K274N	ENST00000375499	NM_003000.2	274	aaG/aaT	8/8	0.169095638148898	5	FACETS	0.708	0.574	0.859	0.177	0.143	0.215	INDETERMINATE	1	TRUE	1	0.294164536118916	5		468	443	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231487251	231487251	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	49	624	0	ENST00000295050.7:c.652T>G	p.Tyr218Asp	p.Y218D	ENST00000295050	NM_032018.5	218	Tac/Gac	4/5	0.294164536118916	4	FACETS	0.644	0.545	0.755	0.161	0.136	0.189	SUBCLONAL	1	TRUE	0	0.294164536118916	4		624	669	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851740	63851740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	261	836	0	ENST00000279873.7:c.2518C>T	p.Leu840Phe	p.L840F	ENST00000279873	NM_032199.2	840	Ctc/Ttc	10/10	0.263868175414034	3	FACETS	0.89	0.838	0.944	0.89	0.838	0.944	CLONAL	3	TRUE	0	0.294164536118916	3		836	762	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066739	77066739	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	195	587	0	ENST00000356341.3:c.746C>A	p.Ser249Tyr	p.S249Y	ENST00000356341	NM_002576.4	249	tCt/tAt	7/15	0.293419112695266	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.294164536118916	4		587	713	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243532	46243532	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	170	507	0	ENST00000334344.6:c.1885G>T	p.Asp629Tyr	p.D629Y	ENST00000334344	NM_152641.2	629	Gat/Tat	14/21	0.294557892804527	4	FACETS	0.872	0.806	0.939	0.872	0.806	0.939	CLONAL	3	TRUE	1	0.294164536118916	4		507	572	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562952	95562952	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1566756652	NA	P-0063282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	117	654	0	ENST00000393063.1:c.4305G>T	p.Glu1435Asp	p.E1435D	ENST00000393063	NM_030621.3	1435	gaG/gaT	24/28	0.294164536118916	5	FACETS	1	0.981	1	0.46	0.415	0.509	CLONAL	1	TRUE	2	0.294164536118916	5		654	830	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66777487	66777487	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	47	762	0	ENST00000307102.5:c.853G>A	p.Glu285Lys	p.E285K	ENST00000307102	NM_002755.3	285	Gag/Aag	7/11	0.263868175414034	3	FACETS	0.508	0.428	0.598	0.169	0.142	0.2	SUBCLONAL	1	TRUE	0	0.294164536118916	3		762	721	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639432	3639433	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0063282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	316	872	0	ENST00000294008.3:c.4206_4207delinsTT	p.Gln1402_Glu1403delinsHisTer	p.Q1402_E1403delinsH*	ENST00000294008	NM_032444.2	1402	caGGag/caTTag	12/15	0.294557892804527	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	0	0.294164536118916	3		872	788	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602726	10602726	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	197	806	0	ENST00000171111.5:c.852G>T	p.Gln284His	p.Q284H	ENST00000171111	NM_203500.1	284	caG/caT	3/6	0.294557892804527	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.294164536118916	2		806	633	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796881	42796881	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	305	976	0	ENST00000575354.2:c.3339G>T	p.Gln1113His	p.Q1113H	ENST00000575354	NM_015125.3	1113	caG/caT	14/20	0.263868175414034	3	FACETS	0.941	0.89	0.992	0.941	0.89	0.992	CLONAL	3	TRUE	0	0.294164536118916	3		976	843	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906838	50906838	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	65	548	0	ENST00000440232.2:c.1226G>T	p.Arg409Leu	p.R409L	ENST00000440232	NM_002691.3	409	cGg/cTg	10/27	0.263868175414034	3	FACETS	0.913	0.793	1	0.304	0.264	0.348	CLONAL	1	TRUE	0	0.294164536118916	3		548	555	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917880	29917880	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	118	620	0	ENST00000389048.3:c.788G>T	p.Gly263Val	p.G263V	ENST00000389048	NM_004304.4	263	gGt/gTt	3/29	0.25554003747104	4	FACETS	0.886	0.802	0.974	0.886	0.802	0.974	CLONAL	2	TRUE	2	0.294164536118916	4		620	586	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919402	96919883	+	splice_acceptor_variant,coding_sequence_variant,3_prime_UTR_variant,intron_variant	Splice_Site	DEL	GGCAGAGTCTCTCCTGGGGAAGGTTTGGAGAAGATGGTCAGGATCCTACCAGTGAGGCCTGCTGGGGAAAGGAGCTCCTCTGGGTGCGAGAGGAGCTGCAGAGTTGAGGGAGGGGCTGCCGAGGAAGAGAGCCCAGGGCTGGCATTAGGGTGTGTAAGCAGGGGGTGGCTGGAACTGGTTGATGACCTCATATTCCGCCGGGTAGGGCTCGTTCTCTTCCATCTCTGAGAGCAGCTCCAGCGCCTGCTCCTCTTCCTCTGTGGGGTAGTGGCGCAGGAGGTTGGCTGCCGTGGCCAGGATTGAGGCTCCACCAGCTCCTGCCACCAGGTAGAAGCTAACGGCGAAGGTGACATAGACCTGGGATCCATGGTACTTCTTATGCTGCTGCTGCTGGGCCAAGATGAGTTCAGAAGCCCAATAAGAAAAGCCAATGACGGTGGCACACTGCAGAACTAGGAGACAGAGGGACAGCACAGAAGGGG	GGCAGAGTCTCTCCTGGGGAAGGTTTGGAGAAGATGGTCAGGATCCTACCAGTGAGGCCTGCTGGGGAAAGGAGCTCCTCTGGGTGCGAGAGGAGCTGCAGAGTTGAGGGAGGGGCTGCCGAGGAAGAGAGCCCAGGGCTGGCATTAGGGTGTGTAAGCAGGGGGTGGCTGGAACTGGTTGATGACCTCATATTCCGCCGGGTAGGGCTCGTTCTCTTCCATCTCTGAGAGCAGCTCCAGCGCCTGCTCCTCTTCCTCTGTGGGGTAGTGGCGCAGGAGGTTGGCTGCCGTGGCCAGGATTGAGGCTCCACCAGCTCCTGCCACCAGGTAGAAGCTAACGGCGAAGGTGACATAGACCTGGGATCCATGGTACTTCTTATGCTGCTGCTGCTGGGCCAAGATGAGTTCAGAAGCCCAATAAGAAAAGCCAATGACGGTGGCACACTGCAGAACTAGGAGACAGAGGGACAGCACAGAAGGGG	-	novel	NA	P-0063282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	46	218	0	ENST00000258439.3:c.410-30_*144del		p.X137_splice	ENST00000258439	NM_001193304.2	137		4/4	0.25554003747104	4	FACETS	0.982	0.837	1	0.982	0.837	1	CLONAL	2	TRUE	2	0.294164536118916	4		218	206	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561313	9561313	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	68	700	0	ENST00000353224.5:c.469G>T	p.Asp157Tyr	p.D157Y	ENST00000353224	NM_177990.2	157	Gat/Tat	4/10	0.294557892804527	3	FACETS	0.959	0.835	1	0.479	0.417	0.547	CLONAL	1	TRUE	1	0.294164536118916	3		700	553	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100921	41100921	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	205	742	0	ENST00000373198.4:c.1435C>A	p.Gln479Lys	p.Q479K	ENST00000373198	NM_133170.3	479	Cag/Aag	8/32	0.293419112695266	4	FACETS	0.844	0.786	0.904	1	0.987	1	CLONAL	3	TRUE	2	0.294164536118916	4		742	712	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500850	149500850	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	226	622	0	ENST00000261799.4:c.2380G>C	p.Glu794Gln	p.E794Q	ENST00000261799	NM_002609.3	794	Gag/Cag	17/23	0.294557892804527	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.294164536118916	3		622	729	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157256625	157256625	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	39	540	0	ENST00000346085.5:c.1952C>G	p.Thr651Ser	p.T651S	ENST00000346085	NM_020732.3	651	aCt/aGt	5/20	0.294557892804527	3	FACETS	0.555	0.459	0.662	0.185	0.153	0.221	SUBCLONAL	1	TRUE	0	0.294164536118916	3		540	548	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81340818	81340818	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	221	269	0	ENST00000222390.5:c.1423C>A	p.Pro475Thr	p.P475T	ENST00000222390	NM_000601.4	475	Cct/Act	12/18	0.294164536118916	9	FACETS	1	0.978	1	1	0.978	1	CLONAL	6	TRUE	3	0.294164536118916	9		269	471	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411605	63411605	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	195	430	0	ENST00000330258.3:c.1562G>C	p.Gly521Ala	p.G521A	ENST00000330258	NM_152424.3	521	gGa/gCa	2/2	0.235851268555129	2	FACETS	1	0.975	1			1	CLONAL	3	TRUE	NA	0.294164536118916	2		430	412	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411915	63411915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372775016	NA	P-0063282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	31	459	0	ENST00000330258.3:c.1252C>T	p.Arg418Trp	p.R418W	ENST00000330258	NM_152424.3	418	Cgg/Tgg	2/2	0.235851268555129	2	FACETS	0.419	0.338	0.511			1	SUBCLONAL	1	TRUE	NA	0.294164536118916	2		459	503	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76953083	76953083	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	11	182	0	ENST00000373344.5:c.230C>T	p.Ser77Leu	p.S77L	ENST00000373344	NM_000489.3	77	tCa/tTa	4/35	0.235851268555129	2	FACETS	0.39	0.269	0.539			1	SUBCLONAL	1	TRUE	NA	0.294164536118916	2		182	192	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617161	100617161	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	179	299	0	ENST00000308731.7:c.588G>T	p.Gln196His	p.Q196H	ENST00000308731	NM_000061.2	196	caG/caT	7/19	0.235851268555129	2	FACETS	1	0.985	1			1	CLONAL	3	TRUE	NA	0.294164536118916	2		299	349	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0063288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	24	727	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.658	0.514	0.825	0.658	0.514	0.825	SUBCLONAL	1	TRUE	1	0.12	2		727	608	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808651	1808651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752294041	NA	P-0063288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	35	696	1	ENST00000260795.2:c.2264C>T	p.Thr755Met	p.T755M	ENST00000260795		755	aCg/aTg	16/17	1	2	FACETS	0.972	0.795	1	0.972	0.795	1	CLONAL	1	TRUE	1	0.12	2		697	600	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0063289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	163	393	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.467613785805319	2		393	665	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0063289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	121	622	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.467613785805319	2		622	507	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779129	135779129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	109	462	0	ENST00000298552.3:c.2117G>A	p.Arg706His	p.R706H	ENST00000298552	NM_001162426.1	706	cGt/cAt	17/23	1	2	FACETS	0.822	0.741	0.908	0.822	0.741	0.908	CLONAL	1	TRUE	1	0.467613785805319	2		462	567	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42050032	42050032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	74	226	0	ENST00000219905.7:c.7186C>T	p.Arg2396Ter	p.R2396*	ENST00000219905	NM_001164273.1	2396	Cga/Tga	19/24	0.467613785805319	1	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	0	0.467613785805319	1		226	241	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0063289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	172	528	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.467613785805319	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.467613785805319	1		528	480	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371728	55371728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	36	526	0	ENST00000297316.4:c.418C>T	p.Arg140Trp	p.R140W	ENST00000297316	NM_022454.3	140	Cgg/Tgg	2/2	0.13665972537002	4	FACETS	0.393	0.322	0.473	0.196	0.161	0.237	INDETERMINATE	1	TRUE	2	0.467613785805319	4		526	575	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986757	36986757	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	125	450	0	ENST00000354822.5:c.932G>T	p.Ser311Ile	p.S311I	ENST00000354822	NM_001079668.2	311	aGc/aTc	3/3	0.467613785805319	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.467613785805319	1		450	358	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007692	45007693	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	62	481	0	ENST00000558401.1:c.140dup	p.Ser48ValfsTer9	p.S48Vfs*9	ENST00000558401	NM_004048.2	47	gtg/gTtg	2/4	0.467613785805319	1	FACETS	0.509	0.441	0.582	0.509	0.441	0.582	SUBCLONAL	1	TRUE	0	0.467613785805319	1		481	399	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798399	42798399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	208	482	0	ENST00000575354.2:c.4270C>T	p.Pro1424Ser	p.P1424S	ENST00000575354	NM_015125.3	1424	Ccc/Tcc	18/20	1	2	FACETS	0.77	0.719	0.821	1	0.992	1	SUBCLONAL	2	TRUE	1	0.467613785805319	2		482	578	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462553	29462553	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748009427	NA	P-0063289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	61	477	0	ENST00000389048.3:c.2348G>A	p.Cys783Tyr	p.C783Y	ENST00000389048	NM_004304.4	783	tGc/tAc	13/29	1	2	FACETS	0.54	0.467	0.62	0.54	0.467	0.62	SUBCLONAL	1	TRUE	1	0.467613785805319	2		477	483	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2033051	2033051	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs374114848	NA	P-0063289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	26	430	0	ENST00000349721.2:c.325C>G	p.Pro109Ala	p.P109A	ENST00000349721	NM_003070.3	109	Ccc/Gcc	3/34	0.367547667901543	1	FACETS	0.181	0.143	0.225	0.181	0.143	0.225	SUBCLONAL	1	TRUE	0	0.467613785805319	1		430	470	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453139	+	missense_variant	Missense_Mutation	ONP	ACTG	ACTG	TCTC	novel	NA	P-0063289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	106	314	0	ENST00000288602.6:c.1796_1799delinsGAGA	p.Thr599_Val600delinsArgGlu	p.T599_V600delinsRE	ENST00000288602	NM_004333.4	599	aCAGTg/aGAGAg	15/18	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.467613785805319	2		314	418	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0063291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	77	1032	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.341711698849815	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.341711698849815	1		1032	360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0063291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	172	801	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.341711698849815	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.341711698849815	1		804	720	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0063291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	127	665	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.341711698849815	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.341711698849815	1		665	553	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188188	32188188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370312303	NA	P-0063291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	152	680	0	ENST00000375023.3:c.1153C>T	p.Arg385Cys	p.R385C	ENST00000375023	NM_004557.3	385	Cgc/Tgc	6/30	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.341711698849815	2		680	804	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974744	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAGCAGCGCCCGCA	CCTCCAGCAGCGCCCGCA	-	novel	NA	P-0063291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	112	656	0	ENST00000304494.5:c.83_100del	p.Val28_Glu33del	p.V28_E33del	ENST00000304494	NM_000077.4	28	gTGCGGGCGCTGCTGGAGGcg/gcg	1/3	0.341711698849815	1	FACETS	0.969	0.874	1	0.969	0.874	1	CLONAL	1	TRUE	0	0.341711698849815	1		656	561	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923274	78923274	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	113	443	0	ENST00000306801.3:c.3297T>A	p.Phe1099Leu	p.F1099L	ENST00000306801	NM_020761.2	1099	ttT/ttA	28/34	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.341711698849815	2		443	603	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0063292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	72	1032	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.856	0.753	0.966	0.856	0.753	0.966	CLONAL	1	TRUE	1	0.460745462702836	2		1032	365	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0063292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	141	665	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.460745462702836	1	FACETS	0.911	0.835	0.99	0.911	0.835	0.99	CLONAL	1	TRUE	0	0.460745462702836	1		665	517	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200951	108200951	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1565529306	NA	P-0063292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	274	332	0	ENST00000278616.4:c.7318A>G	p.Lys2440Glu	p.K2440E	ENST00000278616	NM_000051.3	2440	Aag/Gag	50/63	0.460745462702836	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.460745462702836	2		332	576	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120181	70120182	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CG	novel	NA	P-0063292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	157	563	0	ENST00000245479.2:c.1185_1186dup	p.His396ArgfsTer8	p.H396Rfs*8	ENST00000245479	NM_000346.3	395	acg/aCGcg	3/3	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.460745462702836	2		563	480	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714370	40714370	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs956451753	NA	P-0063292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	91	465	1	ENST00000373198.4:c.4027C>T	p.Arg1343Trp	p.R1343W	ENST00000373198	NM_133170.3	1343	Cgg/Tgg	29/32	0.138062147176704	3	FACETS	0.903	0.804	1	0.301	0.268	0.336	INDETERMINATE	1	TRUE	0	0.460745462702836	3		466	538	SUCCESS
APC	324	MSKCC	GRCh37	5	112175147	112175147	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	261	413	0	ENST00000257430.4:c.3856G>T	p.Glu1286Ter	p.E1286*	ENST00000257430	NM_000038.5	1286	Gaa/Taa	16/16	0.456390939977491	2	FACETS	0.954	0.901	1	0.954	0.901	1	CLONAL	2	TRUE	0	0.460745462702836	2		413	594	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27172679	27172679	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	281	398	0	ENST00000380036.4:c.694G>T	p.Val232Phe	p.V232F	ENST00000380036	NM_000459.3	232	Gtc/Ttc	5/23	0.421084504235929	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.460745462702836	3		398	739	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7126637	7126637	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	181	380	0	ENST00000302850.5:c.2971C>G	p.Leu991Val	p.L991V	ENST00000302850	NM_000208.2	991	Ctt/Gtt	16/22	0.399018020301658	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.452206254032438	1		380	570	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038274	30038274	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	180	338	0	ENST00000338641.4:c.447+1del		p.K149fs	ENST00000338641	NM_000268.3	149	aaG/aa	4/16	0.452206254032438	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.452206254032438	1		338	580	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572273	41572273	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	113	473	0	ENST00000263253.7:c.4802T>C	p.Ile1601Thr	p.I1601T	ENST00000263253	NM_001429.3	1601	aTt/aCt	30/31	1	2	FACETS	0.73	0.657	0.806	0.73	0.657	0.806	SUBCLONAL	1	TRUE	1	0.452206254032438	2		473	685	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268879	98268879	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	93	390	0	ENST00000331920.6:c.204del	p.Lys69ArgfsTer11	p.K69Rfs*11	ENST00000331920	NM_000264.3	68	ggG/gg	2/24	0.226544890360277	1	FACETS	0.506	0.45	0.565	0.506	0.45	0.565	INDETERMINATE	1	TRUE	0	0.452206254032438	1		390	629	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0063295-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	94	1032	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.504489558105758	2		1032	361	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0063295-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	282	597	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.504489558105758	2	FACETS	0.902	0.855	0.949	0.902	0.855	0.949	CLONAL	2	TRUE	0	0.504489558105758	2		597	620	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0063295-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	201	801	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.504489558105758	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.504489558105758	1		804	571	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482425	56482425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063295-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	179	600	0	ENST00000267101.3:c.973G>A	p.Gly325Arg	p.G325R	ENST00000267101	NM_001982.3	325	Gga/Aga	8/28	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.504489558105758	2		600	708	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0063295-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	187	531	0	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	0.504489558105758	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.504489558105758	1		531	488	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857512	9857512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1431125566	NA	P-0063295-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	142	607	0	ENST00000330684.3:c.3889G>A	p.Asp1297Asn	p.D1297N	ENST00000330684	NM_001134407.1	1297	Gac/Aac	13/13	1	2	FACETS	0.949	0.869	1	0.949	0.869	1	CLONAL	1	TRUE	1	0.504489558105758	2		607	593	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591976	48591976	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063295-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	106	433	0	ENST00000342988.3:c.1139G>T	p.Arg380Met	p.R380M	ENST00000342988	NM_005359.5	380	aGg/aTg	9/12	0.504489558105758	1	FACETS	0.677	0.61	0.747	0.677	0.61	0.747	SUBCLONAL	1	TRUE	0	0.504489558105758	1		433	464	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692792	89692792	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs779530981	NA	P-0063296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	105	202	0	ENST00000371953.3:c.276C>A	p.Asp92Glu	p.D92E	ENST00000371953	NM_000314.4	92	gaC/gaA	5/9	0.5497552138624	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.5497552138624	1		202	246	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150022944	150022944	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	134	360	0	ENST00000253339.5:c.319C>T	p.Gln107Ter	p.Q107*	ENST00000253339		107	Caa/Taa	1/7	0.5497552138624	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.5497552138624	1		360	338	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393638	139393638	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	163	572	0	ENST00000277541.6:c.6008C>A	p.Ala2003Asp	p.A2003D	ENST00000277541	NM_017617.3	2003	gCc/gAc	32/34	0.315946661929663	1	FACETS	0.822	0.76	0.886	0.822	0.76	0.886	INDETERMINATE	1	TRUE	0	0.5497552138624	1		572	523	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0063300-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	71	1032	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.79	0.693	0.893	0.79	0.693	0.893	SUBCLONAL	1	FALSE	1	0.471919037150663	2		1032	381	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0063300-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	94	450	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.777	0.693	0.865	0.777	0.693	0.865	SUBCLONAL	1	FALSE	1	0.471919037150663	2		451	513	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063300-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	260	403	0	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	0.304867267281123	3	FACETS	1	0.988	1	0.776	0.733	0.819	CLONAL	2	FALSE	0	0.471919037150663	3		403	585	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401880	139401880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1272399533	NA	P-0063300-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	119	442	0	ENST00000277541.6:c.3520G>A	p.Gly1174Ser	p.G1174S	ENST00000277541	NM_017617.3	1174	Ggc/Agc	22/34	1	2	FACETS	0.927	0.84	1	0.927	0.84	1	CLONAL	1	FALSE	1	0.471919037150663	2		442	544	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0063301-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	107	462	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.584841309870541	2		462	315	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0063301-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	165	568	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.584841309870541	2		568	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520006	NA	P-0063301-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	186	449	0	ENST00000269305.4:c.821T>C	p.Val274Ala	p.V274A	ENST00000269305	NM_001126112.2	274	gTt/gCt	8/11	0.584841309870541	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.584841309870541	1		449	444	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693001	89693001	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063301-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	99	340	0	ENST00000371953.3:c.485A>T	p.Asp162Val	p.D162V	ENST00000371953	NM_000314.4	162	gAc/gTc	5/9	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.584841309870541	2		340	296	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685270	89685271	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063301-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	57	224	0	ENST00000371953.3:c.170dup	p.Leu57PhefsTer6	p.L57Ffs*6	ENST00000371953	NM_000314.4	55	-/T	3/9	1	2	FACETS	0.859	0.746	0.978	0.859	0.746	0.978	CLONAL	1	TRUE	1	0.584841309870541	2		224	227	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426742	49426742	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063301-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	158	519	0	ENST00000301067.7:c.11746C>T	p.Gln3916Ter	p.Q3916*	ENST00000301067	NM_003482.3	3916	Cag/Tag	39/54	1	2	FACETS	0.848	0.78	0.919	0.848	0.78	0.919	CLONAL	1	TRUE	1	0.584841309870541	2		519	637	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544908	86544908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754304579	NA	P-0063301-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	124	402	1	ENST00000262426.4:c.733G>A	p.Ala245Thr	p.A245T	ENST00000262426	NM_001451.2	245	Gcc/Acc	1/2	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.584841309870541	2		403	376	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152499	56152500	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGGG	novel	NA	P-0063301-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	159	406	0	ENST00000399503.3:c.558_561dup	p.Lys188GlyfsTer21	p.K188Gfs*21	ENST00000399503	NM_005921.1	185	-/AGGG	2/20	1	2	FACETS	0.98	0.903	1	0.98	0.903	1	CLONAL	1	TRUE	1	0.584841309870541	2		406	555	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0063302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	71	387	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.219704489619816	3	FACETS	0.758	0.666	0.856	0.758	0.666	0.856	SUBCLONAL	2	TRUE	1	0.309124338353681	3		387	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0063302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	91	586	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.232018467625392	2	FACETS	1	0.966	1	0.606	0.54	0.676	CLONAL	1	TRUE	0	0.309124338353681	2		586	486	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830339	72830339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	115	540	0	ENST00000268489.5:c.6242C>T	p.Pro2081Leu	p.P2081L	ENST00000268489	NM_006885.3	2081	cCa/cTa	9/10	0.211753154367794	3	FACETS	0.875	0.792	0.961	0.875	0.792	0.961	CLONAL	2	TRUE	1	0.309124338353681	3		540	491	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150936836	150936836	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	103	366	0	ENST00000271640.5:c.3874del	p.Ter1292ArgfsTer26	p.*1292Rfs*26	ENST00000271640	NM_001145415.1	1291	cTt/ct	22/22	0.218304607412299	5	FACETS	0.876	0.786	0.97	0.584	0.524	0.647	CLONAL	2	TRUE	2	0.309124338353681	5		366	557	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015393	176015393	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	69	250	0	ENST00000367669.3:c.1345G>C	p.Glu449Gln	p.E449Q	ENST00000367669	NM_022457.5	449	Gaa/Caa	12/20	0.218304607412299	5	FACETS	1	0.88	1	0.668	0.586	0.755	CLONAL	2	TRUE	2	0.309124338353681	5		250	326	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10797095	10797095	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs758927093	NA	P-0063302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	109	303	0	ENST00000361367.2:c.3010A>T	p.Met1004Leu	p.M1004L	ENST00000361367	NM_014633.3	1004	Atg/Ttg	24/25	0.211753154367794	3	FACETS	0.891	0.805	0.981	0.891	0.805	0.981	CLONAL	2	TRUE	1	0.309124338353681	3		303	457	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657111	215657111	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs750878896	NA	P-0063302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	96	324	0	ENST00000260947.4:c.274A>G	p.Ile92Val	p.I92V	ENST00000260947	NM_000465.2	92	Ata/Gta	3/11	0.219704489619816	3	FACETS	1	0.976	1	0.668	0.597	0.743	CLONAL	1	TRUE	1	0.309124338353681	3		324	537	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081560	143081560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	107	404	0	ENST00000262992.4:c.1514G>A	p.Arg505Lys	p.R505K	ENST00000262992	NM_001101669.1	505	aGa/aAa	15/24	0.219704489619816	3	FACETS	1	0.983	1	0.75	0.675	0.828	CLONAL	1	TRUE	1	0.309124338353681	3		404	533	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141569568	141569568	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	92	413	0	ENST00000220592.5:c.716A>G	p.Asp239Gly	p.D239G	ENST00000220592	NM_012154.3	239	gAt/gGt	6/19	0.138727913471238	3	FACETS	0.774	0.691	0.861	0.516	0.461	0.574	INDETERMINATE	2	TRUE	0	0.309124338353681	3		413	444	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0063303-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	97	541	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.369022495809447	3	FACETS	0.903	0.814	0.995	0.903	0.814	0.995	CLONAL	2	TRUE	1	0.391751739932084	3		541	328	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0063303-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	51	205	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.391751739932084	2		205	228	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245040	46245040	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063303-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	57	535	0	ENST00000334344.6:c.3134C>A	p.Ser1045Ter	p.S1045*	ENST00000334344	NM_152641.2	1045	tCg/tAg	15/21	1	2	FACETS	0.813	0.701	0.934	0.813	0.701	0.934	CLONAL	1	TRUE	1	0.391751739932084	2		535	358	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002844	69002844	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063303-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	43	303	0	ENST00000288368.4:c.2144C>A	p.Pro715His	p.P715H	ENST00000288368	NM_024870.2	715	cCt/cAt	20/40	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.391751739932084	2		303	209	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687614	29687614	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	356	309	0	ENST00000356175.3:c.8207C>G	p.Thr2736Ser	p.T2736S	ENST00000356175	NM_000267.3	2736	aCt/aGt	56/57	0.798538693279934	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	2	0.798538693279934	4		309	799	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056704	180056704	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063305-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	247	391	0	ENST00000261937.6:c.808G>T	p.Gly270Trp	p.G270W	ENST00000261937	NM_182925.4	270	Ggg/Tgg	6/30	0.111794863582406	4	FACETS	1	0.985	1	1	0.985	1	INDETERMINATE	2	TRUE	2	0.732069353017627	4		391	521	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572011	64572011	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063305-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	402	479	0	ENST00000312049.6:c.1628C>A	p.Ser543Ter	p.S543*	ENST00000312049	NM_130799.2	543	tCa/tAa	10/10	0.730397046478253	2	FACETS	0.977	0.946	1	0.977	0.946	1	CLONAL	2	TRUE	0	0.732069353017627	2		479	562	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138052	2138052	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs397515110	NA	P-0063305-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	370	504	0	ENST00000219476.3:c.5072T>C	p.Met1691Thr	p.M1691T	ENST00000219476	NM_000548.3	1691	aTg/aCg	40/42	0.730397046478253	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.732069353017627	2		504	486	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028639	12028639	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	129	401	0	ENST00000353533.5:c.842G>A	p.Arg281Gln	p.R281Q	ENST00000353533	NM_003010.3	281	cGa/cAa	8/11	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.765566992140376	2		401	335	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375998	118375998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150804738	NA	P-0063306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	61	568	0	ENST00000534358.1:c.9391G>A	p.Gly3131Ser	p.G3131S	ENST00000534358	NM_005933.3	3131	Ggt/Agt	27/36	0.765566992140376	2	FACETS	0.298	0.257	0.343	0.149	0.128	0.172	SUBCLONAL	1	TRUE	0	0.765566992140376	2		568	534	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115690	108115711	+	frameshift_variant	Frame_Shift_Del	DEL	ATTGAATTATTTCAACTGCAAA	ATTGAATTATTTCAACTGCAAA	-	novel	NA	P-0063306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	269	331	0	ENST00000278616.4:c.838_859del	p.Ile280PhefsTer33	p.I280Ffs*33	ENST00000278616	NM_000051.3	280	ATTGAATTATTTCAACTGCAAAtt/tt	7/63	0.765566992140376	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.765566992140376	2		331	351	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443818	49443818	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783712	NA	P-0063306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	197	586	1	ENST00000301067.7:c.3553C>T	p.Gln1185Ter	p.Q1185*	ENST00000301067	NM_003482.3	1185	Cag/Tag	11/54	0.765566992140376	4	FACETS	0.942	0.872	1	0.314	0.29	0.338	CLONAL	1	TRUE	1	0.765566992140376	4		587	965	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657562	37657562	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	44	457	0	ENST00000447079.4:c.2479G>C	p.Gly827Arg	p.G827R	ENST00000447079	NM_015083.1	827	Ggt/Cgt	6/14	0.752439419616042	4	FACETS	0.29	0.243	0.343	0.097	0.081	0.115	SUBCLONAL	1	TRUE	1	0.765566992140376	4		457	699	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26055927	26056160	+	coding_sequence_variant,3_prime_UTR_variant	In_Frame_Del	DEL	CAGATAGTAAAGAAATTATCCAGCTCTTTTATTGAGATCAGTGGTGGCTCTGAAAAGAGCCTTTTGGGTTTTAGAAGTAGGCGTTCGCCTATTTCTTCTTGGGCGCCGCCTTCTTAGGCTTGACAACCTTGGGCTTAGCGGCCTTGGGCTTCACAGCCTTAGCAGCACTTTTGGCAGCTTTCTTGGGCTTCGCAACCTTGGCCTTCTTTGGGCTCTTAGCCACTTTCTTGGTTA	CAGATAGTAAAGAAATTATCCAGCTCTTTTATTGAGATCAGTGGTGGCTCTGAAAAGAGCCTTTTGGGTTTTAGAAGTAGGCGTTCGCCTATTTCTTCTTGGGCGCCGCCTTCTTAGGCTTGACAACCTTGGGCTTAGCGGCCTTGGGCTTCACAGCCTTAGCAGCACTTTTGGCAGCTTTCTTGGGCTTCGCAACCTTGGCCTTCTTTGGGCTCTTAGCCACTTTCTTGGTTA	-	novel	NA	P-0063306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	79	162	0				ENST00000343677	NM_005319.3	166		1/1	0.666038499332357	5	FACETS	1	0.942	1	0.369	0.326	0.414	CLONAL	1	TRUE	2	0.765566992140376	5		162	401	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2039475	2039475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	29	401	0	ENST00000349721.2:c.365C>T	p.Ser122Leu	p.S122L	ENST00000349721	NM_003070.3	122	tCa/tTa	4/34	0.765566992140376	3	FACETS	0.227	0.182	0.279	0.114	0.091	0.14	SUBCLONAL	1	TRUE	1	0.765566992140376	3		401	461	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913492	NA	P-0063316-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	117	227	0	ENST00000286548.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000286548	NM_002072.3	209	cAa/cTa	5/7	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.876099275040441	2		227	252	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159752	20159752	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063316-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	164	266	0	ENST00000379607.5:c.7A>C	p.Lys3Gln	p.K3Q	ENST00000379607	NM_001412.3	3	Aag/Cag	1/7	0.834780261510335	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.876099275040441	1		266	193	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0063317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	203	577	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.317490097392694	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.319359566576527	2		579	546	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40991041	40991041	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	131	345	0	ENST00000267868.3:c.85G>C	p.Glu29Gln	p.E29Q	ENST00000267868	NM_002875.4	29	Gag/Cag	2/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.319359566576527	2		345	574	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396277	139396277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878855028	NA	P-0063317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	151	579	0	ENST00000277541.6:c.5561G>A	p.Arg1854His	p.R1854H	ENST00000277541	NM_017617.3	1854	cGc/cAc	30/34	1	2	FACETS	0.771	0.708	0.837	1	0.989	1	SUBCLONAL	2	TRUE	1	0.319359566576527	2		579	613	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231488432	231488432	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	49	445	0	ENST00000295050.7:c.797del	p.Leu266TyrfsTer7	p.L266Yfs*7	ENST00000295050	NM_032018.5	265	aaT/aa	5/5	0.235621871715075	4	FACETS	0.529	0.447	0.62	0.265	0.223	0.31	SUBCLONAL	1	TRUE	2	0.319359566576527	4		445	765	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999023	100999023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756847705	NA	P-0063317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	165	550	0	ENST00000325455.5:c.779C>T	p.Ala260Val	p.A260V	ENST00000325455	NM_001202474.3	260	gCg/gTg	1/8	0.235621871715075	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.319359566576527	4		550	588	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225645	26225645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	209	732	0	ENST00000360408.1:c.263C>T	p.Ser88Phe	p.S88F	ENST00000360408	NM_003532.2	88	tCc/tTc	1/1	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.319359566576527	2		732	1232	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923098	39923098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	32	271	0	ENST00000378444.4:c.3610C>T	p.His1204Tyr	p.H1204Y	ENST00000378444	NM_001123385.1	1204	Cat/Tat	8/15	1	1	FACETS	0.503	0.409	0.609	0.503	0.409	0.609	SUBCLONAL	1	TRUE	0	0.319359566576527	1		271	335	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0063318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	143	205	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.348717119731349	2		205	663	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020768	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs926053251	NA	P-0063318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	73	530	1	ENST00000358127.4:c.77T>G	p.Val26Gly	p.V26G	ENST00000358127	NM_001280556.1	26	gTt/gGt	2/10	0.273252825449566	3	FACETS	0.457	0.398	0.52	0.228	0.199	0.26	SUBCLONAL	1	TRUE	1	0.348717119731349	3		531	1077	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878116	48878116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	260	656	0	ENST00000267163.4:c.68C>T	p.Pro23Leu	p.P23L	ENST00000267163	NM_000321.2	23	cCg/cTg	1/27	0.284221611369623	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.348717119731349	1		656	1067	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249012	55249013	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGTTA	novel	NA	P-0063318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	317	621	0	ENST00000275493.2:c.2310_2311insGGGTTA	p.Asp770_Asn771insGlyLeu	p.D770_N771insGL	ENST00000275493	NM_005228.3	770	-/GGGTTA	20/28	0.348717119731349	2	FACETS	0.984	0.931	1	0.984	0.931	1	CLONAL	2	TRUE	0	0.348717119731349	2		621	924	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759904	63759904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	83	566	0	ENST00000279873.7:c.557G>A	p.Arg186Gln	p.R186Q	ENST00000279873	NM_032199.2	186	cGg/cAg	4/10	1	2	FACETS	0.484	0.426	0.546	0.484	0.426	0.546	SUBCLONAL	1	TRUE	1	0.348717119731349	2		566	984	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288732	11288732	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	159	562	0	ENST00000361445.4:c.3023T>C	p.Ile1008Thr	p.I1008T	ENST00000361445	NM_004958.3	1008	aTc/aCc	19/58	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.348717119731349	2		562	890	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944567	32944567	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	100	390	0	ENST00000380152.3:c.8360G>C	p.Arg2787Pro	p.R2787P	ENST00000380152		2787	cGc/cCc	19/27	0.284221611369623	1	FACETS	0.877	0.786	0.973	0.877	0.786	0.973	CLONAL	1	TRUE	0	0.348717119731349	1		390	540	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574361	41574361	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1333876461	NA	P-0063318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	293	738	0	ENST00000263253.7:c.6646G>A	p.Gly2216Arg	p.G2216R	ENST00000263253	NM_001429.3	2216	Gga/Aga	31/31	0.215704703316143	3	FACETS	0.931	0.877	0.986			1	CLONAL	2	TRUE	NA	0.348717119731349	3		738	1060	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045118	47045118	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	300	427	1	ENST00000377604.3:c.2359A>G	p.Asn787Asp	p.N787D	ENST00000377604	NM_001204468.1	787	Aac/Gac	21/24	0.348717119731349	2	FACETS	0.846	0.803	0.889			1	CLONAL	3	TRUE	NA	0.348717119731349	2		428	678	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405969	49405969	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063319-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	48	414	0	ENST00000418115.1:c.169T>G	p.Leu57Val	p.L57V	ENST00000418115	NM_001664.2	57	Ttg/Gtg	3/5	1	2	FACETS	0.789	0.665	0.926	0.789	0.665	0.926	CLONAL	1	TRUE	1	0.15	2		414	811	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733220	40733220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063319-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	42	420	0	ENST00000373198.4:c.3586G>A	p.Asp1196Asn	p.D1196N	ENST00000373198	NM_133170.3	1196	Gat/Aat	26/32	0.3	1	FACETS	0.719	0.599	0.854	0.719	0.599	0.854	SUBCLONAL	1	TRUE	0	0.15	1		420	720	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0063320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	178	689	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.587783862555287	2		689	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0063320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	226	746	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.587783862555287	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.587783862555287	1		746	537	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0063320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	602	572	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.587783862555287	5	FACETS	0.91	0.881	0.939	0.91	0.881	0.939	CLONAL	4	TRUE	1	0.587783862555287	5		572	1059	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575671	48575671	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0063320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	11	181	0	ENST00000342988.3:c.431C>G	p.Ser144Ter	p.S144*	ENST00000342988	NM_005359.5	144	tCa/tGa	4/12	0.587783862555287	1	FACETS	0.14	0.096	0.194	0.14	0.096	0.194	SUBCLONAL	1	TRUE	0	0.587783862555287	1		181	189	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881426	37881426	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	786	630	0	ENST00000269571.5:c.2618A>G	p.Asp873Gly	p.D873G	ENST00000269571		873	gAc/gGc	21/27	0.587783862555287	5	FACETS	0.995	0.969	1	0.995	0.969	1	CLONAL	4	TRUE	1	0.587783862555287	5		630	1264	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491184	120491184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587730290	NA	P-0063320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	177	502	0	ENST00000256646.2:c.2605C>T	p.Arg869Trp	p.R869W	ENST00000256646	NM_024408.3	869	Cgg/Tgg	17/34	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.587783862555287	2		502	546	SUCCESS
APC	324	MSKCC	GRCh37	5	112175991	112175991	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	135	438	0	ENST00000257430.4:c.4700del	p.Ser1567Ter	p.S1567*	ENST00000257430	NM_000038.5	1567	tCa/ta	16/16	0.587783862555287	1	FACETS	0.921	0.848	0.996	0.921	0.848	0.996	CLONAL	1	TRUE	0	0.587783862555287	1		438	352	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021497	42021497	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	87	538	0	ENST00000219905.7:c.3793C>T	p.Gln1265Ter	p.Q1265*	ENST00000219905	NM_001164273.1	1265	Cag/Tag	11/24	0.410472797072284	1	FACETS	0.407	0.362	0.456	0.407	0.362	0.456	SUBCLONAL	1	TRUE	0	0.587783862555287	1		538	513	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451152	70451152	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	208	580	0	ENST00000373644.4:c.5992G>A	p.Glu1998Lys	p.E1998K	ENST00000373644	NM_030625.2	1998	Gag/Aag	12/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.587783862555287	2		580	637	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223613	53223613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	40	572	2	ENST00000375401.3:c.3746G>A	p.Arg1249His	p.R1249H	ENST00000375401	NM_004187.3	1249	cGc/cAc	23/26	1	2	FACETS	0.265	0.22	0.316	0.265	0.22	0.316	SUBCLONAL	1	TRUE	1	0.587783862555287	2		574	513	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0063321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	214	577	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.229091747988425	2	FACETS	0.906	0.844	0.971	0.906	0.844	0.971	CLONAL	2	TRUE	0	0.271665028718153	2		577	869	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662128	227662128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775603579	NA	P-0063321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	55	667	0	ENST00000305123.5:c.1327C>T	p.Arg443Cys	p.R443C	ENST00000305123	NM_005544.2	443	Cgc/Tgc	1/2	1	2	FACETS	0.368	0.313	0.428	0.368	0.313	0.428	SUBCLONAL	1	TRUE	1	0.271665028718153	2		667	1100	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114633	73114633	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	72	309	0	ENST00000356692.5:c.1014G>C	p.Glu338Asp	p.E338D	ENST00000356692		338	gaG/gaC	9/9	0.23740784235833	3	FACETS	1	0.941	1	0.566	0.495	0.642	CLONAL	1	TRUE	1	0.271665028718153	3		309	532	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534425	187534425	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	112	559	0	ENST00000441802.2:c.9301G>A	p.Asp3101Asn	p.D3101N	ENST00000441802	NM_005245.3	3101	Gat/Aat	13/27	0.267465820532492	4	FACETS	1	0.934	1	0.351	0.315	0.39	CLONAL	1	TRUE	1	0.271665028718153	4		559	995	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680259	30680259	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	110	567	0	ENST00000376406.3:c.1460del	p.Lys487ArgfsTer52	p.K487Rfs*52	ENST00000376406	NM_014641.2	487	aAg/ag	5/15	0.218174125406997	5	FACETS	0.966	0.865	1	0.322	0.288	0.358	CLONAL	1	TRUE	2	0.271665028718153	5		567	1180	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524647	137524647	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371465030	NA	P-0063321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	61	307	0	ENST00000367739.4:c.722G>A	p.Ser241Asn	p.S241N	ENST00000367739	NM_000416.2	241	aGc/aAc	5/7	0.163547237718859	4	FACETS	1	0.912	1	0.538	0.464	0.618	CLONAL	1	TRUE	2	0.271665028718153	4		307	531	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730117	41730117	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	182	461	0	ENST00000242208.4:c.412T>G	p.Phe138Val	p.F138V	ENST00000242208	NM_002192.2	138	Ttc/Gtc	3/3	0.23740784235833	3	FACETS	0.893	0.825	0.964	0.893	0.825	0.964	CLONAL	2	TRUE	1	0.271665028718153	3		461	852	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424430	47424430	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	192	615	0	ENST00000377045.4:c.350A>T	p.Lys117Met	p.K117M	ENST00000377045	NM_001654.4	117	aAg/aTg	5/16	0.23740784235833	3	FACETS	0.792	0.732	0.854	0.792	0.732	0.854	SUBCLONAL	2	TRUE	1	0.271665028718153	3		615	1014	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913381	NA	P-0063322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	52	520	0	ENST00000304494.5:c.322G>A	p.Asp108Asn	p.D108N	ENST00000304494	NM_000077.4	108	Gat/Aat	2/3	0.233707577919617	1	FACETS	0.925	0.789	1	0.925	0.789	1	CLONAL	1	TRUE	0	0.233707577919617	1		520	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578513	7578513	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	148	571	0	ENST00000269305.4:c.417G>C	p.Lys139Asn	p.K139N	ENST00000269305	NM_001126112.2	139	aaG/aaC	5/11	1	2	FACETS	0.951	0.871	1	1	0.991	1	CLONAL	2	TRUE	1	0.233707577919617	2		571	666	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682877	190682877	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	15	255	0	ENST00000441310.2:c.553G>C	p.Asp185His	p.D185H	ENST00000441310	NM_000534.4	185	Gac/Cac	5/13	1	2	FACETS	0.444	0.324	0.589	0.444	0.324	0.589	SUBCLONAL	1	TRUE	1	0.233707577919617	2		255	289	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244517	46244517	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	112	542	0	ENST00000334344.6:c.2611C>T	p.Gln871Ter	p.Q871*	ENST00000334344	NM_152641.2	871	Cag/Tag	15/21	0.0903521732920363	3	FACETS	0.825	0.743	0.911	0.825	0.743	0.911	INDETERMINATE	2	TRUE	1	0.233707577919617	3		542	649	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633171	3633171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218491919	NA	P-0063322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	40	600	0	ENST00000294008.3:c.5080G>A	p.Ala1694Thr	p.A1694T	ENST00000294008	NM_032444.2	1694	Gcc/Acc	14/15	NA	3	FACETS	0.554	0.459	0.66			1	INDETERMINATE	1	TRUE	NA	0.233707577919617	3		600	690	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916851	178916851	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	52	344	0	ENST00000263967.3:c.238G>A	p.Glu80Lys	p.E80K	ENST00000263967	NM_006218.2	80	Gaa/Aaa	2/21	0.0903521732920363	3	FACETS	1	0.908	1	0.545	0.464	0.633	INDETERMINATE	1	TRUE	1	0.233707577919617	3		344	456	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288529	15288529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	66	388	0	ENST00000263388.2:c.4210G>A	p.Glu1404Lys	p.E1404K	ENST00000263388	NM_000435.2	1404	Gag/Aag	24/33	0.0903521732920363	3	FACETS	1	0.972	1	0.749	0.653	0.853	INDETERMINATE	1	TRUE	1	0.233707577919617	3		388	421	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40497642	40497642	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408283351	NA	P-0063322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	37	404	0	ENST00000264657.5:c.307C>T	p.Arg103Trp	p.R103W	ENST00000264657	NM_139276.2	103	Cgg/Tgg	4/24	0.20685659214881	3	FACETS	0.491	0.404	0.59	0.246	0.202	0.295	SUBCLONAL	1	TRUE	1	0.233707577919617	3		404	720	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733044	74733044	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	100	479	0	ENST00000359995.5:c.199G>C	p.Asp67His	p.D67H	ENST00000359995	NM_001195427.1	67	Gac/Cac	1/3	0.20685659214881	3	FACETS	0.885	0.793	0.982	0.885	0.793	0.982	CLONAL	2	TRUE	1	0.233707577919617	3		479	540	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433827	49433827	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	108	647	0	ENST00000301067.7:c.7726C>T	p.Gln2576Ter	p.Q2576*	ENST00000301067	NM_003482.3	2576	Caa/Taa	31/54	0.0903521732920363	3	FACETS	0.782	0.703	0.866	0.782	0.703	0.866	INDETERMINATE	2	TRUE	1	0.233707577919617	3		647	660	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217458	7217458	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0063322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	127	540	0	ENST00000380728.2:c.338C>G	p.Ser113Ter	p.S113*	ENST00000380728		113	tCa/tGa	5/11	1	2	FACETS	0.848	0.77	0.929	1	0.988	1	CLONAL	2	TRUE	1	0.233707577919617	2		540	641	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699486	117699486	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	37	434	0	ENST00000369458.3:c.155G>C	p.Gly52Ala	p.G52A	ENST00000369458	NM_024626.3	52	gGa/gCa	3/6	0.0434447727716256	4	FACETS	0.669	0.55	0.802	0.334	0.275	0.401	INDETERMINATE	1	TRUE	2	0.233707577919617	4		434	584	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333537	70333537	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0063322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	100	502	0	ENST00000373644.4:c.1442C>G	p.Ser481Ter	p.S481*	ENST00000373644	NM_030625.2	481	tCa/tGa	2/12	0.20685659214881	3	FACETS	0.9	0.807	0.998	0.9	0.807	0.998	CLONAL	2	TRUE	1	0.233707577919617	3		502	531	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023267	1023267	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	84	454	0	ENST00000358495.3:c.988G>C	p.Glu330Gln	p.E330Q	ENST00000358495	NM_134424.2	330	Gaa/Caa	11/12	0.0903521732920363	3	FACETS	1	0.955	1	0.583	0.514	0.656	INDETERMINATE	1	TRUE	1	0.233707577919617	3		454	689	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570395	95570395	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	130	386	0	ENST00000393063.1:c.3338C>G	p.Ser1113Cys	p.S1113C	ENST00000393063	NM_030621.3	1113	tCc/tGc	22/28	0.188652513595866	4	FACETS	0.997	0.911	1	0.748	0.683	0.815	CLONAL	3	TRUE	0	0.233707577919617	4		386	459	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81973601	81973601	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	47	480	0	ENST00000359376.3:c.3418G>C	p.Asp1140His	p.D1140H	ENST00000359376	NM_002661.3	1140	Gat/Cat	30/33	0.0434447727716256	4	FACETS	0.621	0.522	0.73	0.311	0.261	0.365	INDETERMINATE	1	TRUE	2	0.233707577919617	4		480	799	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622311	1622312	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AG	novel	NA	P-0063322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	120	594	0	ENST00000344749.5:c.652_652+1delinsCT		p.X218_splice	ENST00000344749	NM_001136139.2	218		9/19	0.0903521732920363	3	FACETS	1	0.984	1	0.732	0.661	0.807	INDETERMINATE	1	TRUE	1	0.233707577919617	3		594	783	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795012	42795012	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	130	598	0	ENST00000575354.2:c.2092G>T	p.Glu698Ter	p.E698*	ENST00000575354	NM_015125.3	698	Gag/Tag	10/20	0.0903521732920363	3	FACETS	0.9	0.818	0.987	0.9	0.818	0.987	INDETERMINATE	2	TRUE	1	0.233707577919617	3		598	690	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190742094	190742094	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	19	332	0	ENST00000441310.2:c.2731G>C	p.Glu911Gln	p.E911Q	ENST00000441310	NM_000534.4	911	Gaa/Caa	13/13	1	2	FACETS	0.481	0.365	0.618	0.481	0.365	0.618	SUBCLONAL	1	TRUE	1	0.233707577919617	2		332	338	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663414	227663414	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752822640	NA	P-0063322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	29	429	0	ENST00000305123.5:c.41G>A	p.Arg14His	p.R14H	ENST00000305123	NM_005544.2	14	cGc/cAc	1/2	1	2	FACETS	0.538	0.431	0.66	0.538	0.431	0.66	SUBCLONAL	1	TRUE	1	0.233707577919617	2		429	461	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022398	31022398	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1600585859	NA	P-0063322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	125	635	0	ENST00000375687.4:c.1883G>C	p.Arg628Thr	p.R628T	ENST00000375687	NM_015338.5	628	aGa/aCa	13/13	0.0846426158020706	3	FACETS	0.798	0.722	0.877	0.798	0.722	0.877	INDETERMINATE	2	TRUE	1	0.233707577919617	3		635	749	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72891506	72891506	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	56	466	0	ENST00000325599.8:c.256G>C	p.Glu86Gln	p.E86Q	ENST00000325599	NM_018130.2	86	Gag/Cag	3/11	0.0903521732920363	3	FACETS	0.781	0.668	0.905	0.391	0.334	0.453	INDETERMINATE	1	TRUE	1	0.233707577919617	3		466	685	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937470	76937471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	20	223	0	ENST00000373344.5:c.3277dup	p.Arg1093LysfsTer19	p.R1093Kfs*19	ENST00000373344	NM_000489.3	1093	agg/aAgg	9/35	0.233707577919617	2	FACETS	0.582	0.445	0.742			1	SUBCLONAL	1	TRUE	NA	0.233707577919617	2		223	294	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182927	123182927	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	31	99	0	ENST00000218089.9:c.892C>G	p.Arg298Gly	p.R298G	ENST00000218089	NM_001042749.1	298	Cgt/Ggt	10/35	1	1	FACETS	0.901	0.742	1	1	0.958	1	CLONAL	2	TRUE	0	0.233707577919617	1		99	130	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0063323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	113	418	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.112890300549882	3	FACETS	1	0.979	1	0.654	0.592	0.719	INDETERMINATE	1	TRUE	1	0.47	3		418	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0063323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	126	589	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.283793201150492	0	FACETS	0.556	0.506	0.608			1	SUBCLONAL	1	TRUE	0	0.47	0		589	511	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241679	55241681	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	rs397517086	NA	P-0063325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	9	525	0	ENST00000275493.2:c.2127_2129del	p.Glu709_Thr710delinsAsp	p.E709_T710delinsD	ENST00000275493	NM_005228.3	709	gaAACt/gat	18/28	0.125213928847381	4	FACETS	1	0.814	1	0.665	0.454	0.915	INDETERMINATE	1	TRUE	2	0.474919024466346	4		525	42	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0063326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	221	241	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.396417389647671	1	FACETS	0.694	0.653	0.734	0.694	0.653	0.734	INDETERMINATE	1	TRUE	0	0.80604712975412	1		241	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	147	274	0	ENST00000269305.4:c.503A>C	p.His168Pro	p.H168P	ENST00000269305	NM_001126112.2	168	cAc/cCc	5/11	0.201427598775388	2	FACETS	0.848	0.777	0.92	1	0.983	1	CLONAL	3	TRUE	0	0.201427598775388	2		274	574	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291533	15291533	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	121	214	1	ENST00000263388.2:c.3101A>G	p.Asp1034Gly	p.D1034G	ENST00000263388	NM_000435.2	1034	gAc/gGc	19/33	0.201427598775388	3	FACETS	0.889	0.807	0.974	1	0.981	1	CLONAL	3	TRUE	1	0.201427598775388	3		215	496	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726704	41726704	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	111	196	0	ENST00000301178.4:c.249G>C	p.Gln83His	p.Q83H	ENST00000301178	NM_021913.4	83	caG/caC	2/20	0.201427598775388	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.201427598775388	3		196	508	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659322	86659322	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0063327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	82	136	0	ENST00000274376.6:c.1610+1G>C		p.X537_splice	ENST00000274376	NM_002890.2	537			0.201427598775388	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	2	TRUE	0	0.201427598775388	2		136	389	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0063328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	460	521	0	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	0.614876178853678	2	FACETS	0.98	0.946	1	0.98	0.946	1	CLONAL	2	TRUE	0	0.614876178853678	2		521	763	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231238	98231238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1366288601	NA	P-0063328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	158	644	0	ENST00000331920.6:c.2045G>A	p.Arg682His	p.R682H	ENST00000331920	NM_000264.3	682	cGc/cAc	14/24	1	2	FACETS	0.56	0.513	0.609	0.56	0.513	0.609	SUBCLONAL	1	TRUE	1	0.614876178853678	2		644	918	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857680	9857680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303700994	NA	P-0063328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	133	624	1	ENST00000330684.3:c.3721C>T	p.Arg1241Trp	p.R1241W	ENST00000330684	NM_001134407.1	1241	Cgg/Tgg	13/13	1	2	FACETS	0.456	0.414	0.501	0.456	0.414	0.501	SUBCLONAL	1	TRUE	1	0.614876178853678	2		625	948	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0063328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	504	529	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.614876178853678	2	FACETS	0.967	0.934	0.999	0.967	0.934	0.999	CLONAL	2	TRUE	0	0.614876178853678	2		529	848	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056053	26056067	+	inframe_deletion	In_Frame_Del	DEL	CCTTGGGCTTAGCGG	CCTTGGGCTTAGCGG	-	rs756916945	NA	P-0063328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	42	536	0	ENST00000343677.2:c.590_604del	p.Ala197_Lys201del	p.A197_K201del	ENST00000343677	NM_005319.3	197	gCCGCTAAGCCCAAGGtt/gtt	1/1	1	2	FACETS	0.192	0.16	0.229	0.192	0.16	0.229	SUBCLONAL	1	TRUE	1	0.614876178853678	2		536	710	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951899	178951899	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	125	325	0	ENST00000263967.3:c.2954A>C	p.Tyr985Ser	p.Y985S	ENST00000263967	NM_006218.2	985	tAc/tCc	21/21	1	2	FACETS	0.935	0.853	1	0.935	0.853	1	CLONAL	1	TRUE	1	0.614876178853678	2		325	435	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855249	76855249	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0063328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	29	281	0	ENST00000373344.5:c.5738C>G	p.Ser1913Ter	p.S1913*	ENST00000373344	NM_000489.3	1913	tCa/tGa	24/35	1	2	FACETS	0.263	0.211	0.322	0.263	0.211	0.322	SUBCLONAL	1	TRUE	1	0.614876178853678	2		281	359	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913351	NA	P-0063329-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	37	278	0	ENST00000288602.6:c.1397G>C	p.Gly466Ala	p.G466A	ENST00000288602	NM_004333.4	466	gGa/gCa	11/18	1	2	FACETS	0.533	0.438	0.639	0.533	0.438	0.639	SUBCLONAL	1	TRUE	1	0.245484928744435	2		278	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578528	7578528	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063329-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	146	468	0	ENST00000269305.4:c.402T>G	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	ttT/ttG	5/11	0.236094403911092	2	FACETS	1	0.987	1	0.746	0.682	0.814	CLONAL	1	TRUE	0	0.245484928744435	2		468	797	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073971	8073971	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063329-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	38	458	0	ENST00000377482.5:c.688G>T	p.Gly230Ter	p.G230*	ENST00000377482	NM_018948.3	230	Gga/Tga	4/4	1	2	FACETS	0.444	0.366	0.532	0.444	0.366	0.532	SUBCLONAL	1	TRUE	1	0.245484928744435	2		458	697	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094699	2094699	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs781629683	NA	P-0063329-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	52	387	0	ENST00000219066.1:c.481G>T	p.Val161Leu	p.V161L	ENST00000219066	NM_002528.5	161	Gtg/Ttg	3/6	1	2	FACETS	0.524	0.445	0.612	0.524	0.445	0.612	SUBCLONAL	1	TRUE	1	0.245484928744435	2		387	808	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40742249	40742250	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0063329-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	48	424	0	ENST00000392038.2:c.874_875del	p.Thr292Ter	p.T292*	ENST00000392038	NM_001626.4	292	ACt/t	10/14	1	2	FACETS	0.536	0.452	0.63	0.536	0.452	0.63	SUBCLONAL	1	TRUE	1	0.245484928744435	2		424	729	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609575	46609575	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063329-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	42	467	0	ENST00000263734.3:c.2299C>T	p.Gln767Ter	p.Q767*	ENST00000263734	NM_001430.4	767	Caa/Taa	15/16	1	2	FACETS	0.467	0.388	0.554	0.467	0.388	0.554	SUBCLONAL	1	TRUE	1	0.245484928744435	2		467	733	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916543	39916543	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063329-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	32	324	0	ENST00000378444.4:c.4460T>A	p.Ile1487Asn	p.I1487N	ENST00000378444	NM_001123385.1	1487	aTt/aAt	11/15	1	2	FACETS	0.413	0.334	0.503	0.413	0.334	0.503	SUBCLONAL	1	TRUE	1	0.245484928744435	2		324	631	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0063330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	48	556	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.925	0.786	1	0.925	0.786	1	CLONAL	1	TRUE	1	0.335994387839752	2		556	309	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0063330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	10	175	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.199	0.134	0.281	0.199	0.134	0.281	SUBCLONAL	1	TRUE	1	0.335994387839752	2		175	299	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs869025608	NA	P-0063330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	115	426	0	ENST00000307102.5:c.171G>T	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaT	2/11	1	2	FACETS	0.879	0.792	0.971	0.879	0.792	0.971	CLONAL	1	TRUE	1	0.335994387839752	2		426	779	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900288	101900288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111854391	NA	P-0063330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	131	408	0	ENST00000374994.4:c.722C>T	p.Ser241Leu	p.S241L	ENST00000374994	NM_004612.2	241	tCg/tTg	4/9	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.335994387839752	2		408	755	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579408	7579460	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTG	CAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTG	-	rs1555526610	NA	P-0063330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	207	635	0	ENST00000269305.4:c.227_279del	p.Ala76ValfsTer55	p.A76Vfs*55	ENST00000269305	NM_001126112.2	76	gCACCAGCAGCTCCTACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTG/g	4/11	0.325882973969441	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.335994387839752	1		635	928	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110251306	110251306	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	116	441	0	ENST00000374672.4:c.31G>T	p.Ala11Ser	p.A11S	ENST00000374672	NM_004235.4	11	Gct/Tct	2/5	1	2	FACETS	0.941	0.848	1	0.941	0.848	1	CLONAL	1	TRUE	1	0.335994387839752	2		441	734	SUCCESS
APC	324	MSKCC	GRCh37	5	112175789	112175789	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	125	503	0	ENST00000257430.4:c.4501del	p.Ser1501LeufsTer6	p.S1501Lfs*6	ENST00000257430	NM_000038.5	1500	Ttt/tt	16/16	1	2	FACETS	0.936	0.847	1	0.936	0.847	1	CLONAL	1	TRUE	1	0.335994387839752	2		503	795	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920422	114920422	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	133	389	0	ENST00000543371.1:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000543371	NM_001198531.1	455	Cga/Tga	13/14	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.335994387839752	2		389	729	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729115	66729115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504819	NA	P-0063330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	116	521	0	ENST00000307102.5:c.323G>A	p.Arg108Gln	p.R108Q	ENST00000307102	NM_002755.3	108	cGg/cAg	3/11	1	2	FACETS	0.757	0.682	0.837	0.757	0.682	0.837	SUBCLONAL	1	TRUE	1	0.335994387839752	2		521	912	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2185889	2185889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	161	398	0	ENST00000398665.3:c.161C>T	p.Ala54Val	p.A54V	ENST00000398665	NM_032482.2	54	gCt/gTt	3/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.335994387839752	2		398	785	SUCCESS
APC	324	MSKCC	GRCh37	5	112174149	112174150	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATTAGAAT	novel	NA	P-0063330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	69	417	0	ENST00000257430.4:c.2860_2867dup	p.Lys957Ter	p.K957*	ENST00000257430	NM_000038.5	953	aaa/aaATTAGAATa	16/16	1	2	FACETS	0.708	0.617	0.806	0.708	0.617	0.806	SUBCLONAL	1	TRUE	1	0.335994387839752	2		417	580	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519746	176519746	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1472541408	NA	P-0063330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	137	563	0	ENST00000292408.4:c.1018G>A	p.Gly340Ser	p.G340S	ENST00000292408	NM_213647.1	340	Ggc/Agc	8/18	1	2	FACETS	0.979	0.891	1	0.979	0.891	1	CLONAL	1	TRUE	1	0.335994387839752	2		563	833	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158642	26158642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	13	133	0	ENST00000289316.2:c.245C>T	p.Ala82Val	p.A82V	ENST00000289316	NM_138720.2	82	gCg/gTg	1/2	0.325882973969441	1	FACETS	0.294	0.209	0.397	0.294	0.209	0.397	SUBCLONAL	1	TRUE	0	0.335994387839752	1		133	219	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	17	343	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	0.534	0.398	0.696	0.534	0.398	0.696	SUBCLONAL	1	TRUE	0	0.18	1		343	322	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0063369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	31	711	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	0.605	0.488	0.738	0.605	0.488	0.738	SUBCLONAL	1	TRUE	1	0.18	2		711	569	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057835	27057835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	56	920	0	ENST00000324856.7:c.1543C>T	p.Gln515Ter	p.Q515*	ENST00000324856	NM_006015.4	515	Cag/Tag	3/20	0.33385186229987	4	FACETS	0.811	0.693	0.941	0.406	0.346	0.471	CLONAL	1	TRUE	2	0.18	4		920	905	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191755	123191759	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAA	GAAAA	-	novel	NA	P-0063369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	15	361	0	ENST00000218089.9:c.1347_1351del	p.Arg451LysfsTer10	p.R451Kfs*10	ENST00000218089	NM_001042749.1	448	atGAAAAga/atga	15/35	1	2	FACETS	1	0.787	1	1	0.787	1	CLONAL	1	TRUE	1	0.18	2		361	154	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832751	3832751	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	51	826	0	ENST00000262367.5:c.1507C>T	p.Gln503Ter	p.Q503*	ENST00000262367	NM_004380.2	503	Cag/Tag	6/31	0.269052095255277	4	FACETS	1	0.855	1	0.504	0.427	0.588	CLONAL	1	TRUE	2	0.18	4		826	664	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640791	3640791	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	55	832	0	ENST00000294008.3:c.2848G>C	p.Glu950Gln	p.E950Q	ENST00000294008	NM_032444.2	950	Gag/Cag	12/15	0.269052095255277	4	FACETS	1	0.954	1	0.653	0.559	0.756	CLONAL	1	TRUE	2	0.18	4		832	552	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295181	1295181	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1195843544	NA	P-0063369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	37	684	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	0	0.18	1		684	352	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981805	201981806	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0063369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	54	890	0	ENST00000359651.3:c.518dup	p.Gln174SerfsTer22	p.Q174Sfs*22	ENST00000359651		172	-/G	4/8	0.152839952238929	4	FACETS	1	0.951	1	0.64	0.547	0.742	CLONAL	1	TRUE	2	0.18	4		890	553	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640704	3640704	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	51	948	0	ENST00000294008.3:c.2935G>C	p.Asp979His	p.D979H	ENST00000294008	NM_032444.2	979	Gat/Cat	12/15	0.269052095255277	4	FACETS	1	0.927	1	0.579	0.492	0.675	CLONAL	1	TRUE	2	0.18	4		948	577	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085928	16085928	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	38	684	0	ENST00000281043.3:c.1104G>C	p.Lys368Asn	p.K368N	ENST00000281043	NM_005378.4	368	aaG/aaC	3/3	0.152839952238929	3	FACETS	1	0.911	1	0.584	0.483	0.696	CLONAL	1	TRUE	1	0.18	3		684	394	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982350	25982350	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0063369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	19	469	0	ENST00000435504.4:c.939+1G>A		p.X313_splice	ENST00000435504		313			0.152839952238929	3	FACETS	0.819	0.622	1	0.409	0.311	0.525	CLONAL	1	TRUE	1	0.18	3		469	281	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21336764	21336764	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs775067152	NA	P-0063369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	34	844	0	ENST00000215739.8:c.104C>A	p.Ser35Ter	p.S35*	ENST00000215739	NM_006767.3	35	tCg/tAg	1/21	0.269052095255277	4	FACETS	0.792	0.646	0.957	0.396	0.323	0.479	CLONAL	1	TRUE	2	0.18	4		844	563	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21336817	21336817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329142115	NA	P-0063369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	41	852	0	ENST00000215739.8:c.157C>T	p.Arg53Cys	p.R53C	ENST00000215739	NM_006767.3	53	Cgc/Tgc	1/21	0.269052095255277	4	FACETS	0.83	0.69	0.986	0.415	0.345	0.493	CLONAL	1	TRUE	2	0.18	4		852	648	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21336838	21336838	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	42	864	0	ENST00000215739.8:c.178T>C	p.Cys60Arg	p.C60R	ENST00000215739	NM_006767.3	60	Tgc/Cgc	1/21	0.269052095255277	4	FACETS	0.838	0.698	0.994	0.419	0.349	0.497	CLONAL	1	TRUE	2	0.18	4		864	657	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913100	44913112	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGGAGATAAAG	CTGGGAGATAAAG	-	novel	NA	P-0063369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	13	418	0	ENST00000377967.4:c.776_788del	p.Leu259ProfsTer62	p.L259Pfs*62	ENST00000377967	NM_021140.2	259	CTGGGAGATAAAGcc/cc	10/29	0.210090161405366	4	FACETS	0.937	0.67	1	0.468	0.335	0.63	CLONAL	1	TRUE	2	0.18	4		418	182	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	68	343	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.874	0.764	0.992	0.874	0.764	0.992	CLONAL	1	FALSE	1	0.393772665034673	2		343	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0063370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	43	595	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	1	2	FACETS	0.436	0.364	0.515	0.436	0.364	0.515	SUBCLONAL	1	FALSE	1	0.393772665034673	2		595	501	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934874	NA	P-0063370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	196	624	0	ENST00000269305.4:c.451C>A	p.Pro151Thr	p.P151T	ENST00000269305	NM_001126112.2	151	Ccc/Acc	5/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.393772665034673	2		624	715	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0063370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	26	361	0	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	0.377914524113615	1	FACETS	0.93	0.75	1	0.93	0.75	1	CLONAL	1	FALSE	0	0.393772665034673	1		361	114	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729866	39729866	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs990347811	NA	P-0063370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	59	584	0	ENST00000361337.2:c.1181C>T	p.Ser394Phe	p.S394F	ENST00000361337	NM_003286.2	394	tCt/tTt	13/21	0.115428675738488	0	FACETS	0.584	0.506	0.668			1	INDETERMINATE	1	FALSE	0	0.393772665034673	0		584	311	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111429	56111429	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	112	777	0	ENST00000399503.3:c.29C>A	p.Ser10Ter	p.S10*	ENST00000399503	NM_005921.1	10	tCg/tAg	1/20	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	FALSE	1	0.393772665034673	2		777	549	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871990	45871990	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	72	558	0	ENST00000391945.4:c.258G>T	p.Glu86Asp	p.E86D	ENST00000391945	NM_000400.3	86	gaG/gaT	5/23	1	2	FACETS	0.875	0.768	0.989	0.875	0.768	0.989	CLONAL	1	FALSE	1	0.393772665034673	2		558	418	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150034	202150034	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	92	734	0	ENST00000358485.4:c.1475G>A	p.Cys492Tyr	p.C492Y	ENST00000358485	NM_001080125.1	492	tGt/tAt	8/9	0.377914524113615	1	FACETS	0.97	0.868	1	0.97	0.868	1	CLONAL	1	FALSE	0	0.393772665034673	1		734	387	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105610	27105610	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	83	616	0	ENST00000324856.7:c.5221C>T	p.Gln1741Ter	p.Q1741*	ENST00000324856	NM_006015.4	1741	Cag/Tag	20/20	1	2	FACETS	0.907	0.803	1	0.907	0.803	1	CLONAL	1	FALSE	1	0.393772665034673	2		616	465	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231483666	231483666	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	56	445	0	ENST00000295050.7:c.445A>T	p.Ile149Leu	p.I149L	ENST00000295050	NM_032018.5	149	Ata/Tta	3/5	0.170877442822022	3	FACETS	1	0.952	1	0.621	0.537	0.712	INDETERMINATE	1	FALSE	1	0.393772665034673	3		445	274	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14021986	14021986	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs779737289	NA	P-0063370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	66	464	0	ENST00000311895.7:c.686T>C	p.Ile229Thr	p.I229T	ENST00000311895	NM_005236.2	229	aTa/aCa	4/11	0.393772665034673	3	FACETS	1	0.895	1	1	0.895	1	CLONAL	2	FALSE	1	0.393772665034673	3		464	198	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618965	37618965	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	126	777	0	ENST00000447079.4:c.641A>T	p.Asp214Val	p.D214V	ENST00000447079	NM_015083.1	214	gAc/gTc	1/14	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	FALSE	1	0.393772665034673	2		777	616	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761205	59761205	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	35	606	0	ENST00000259008.2:c.3202C>G	p.Pro1068Ala	p.P1068A	ENST00000259008	NM_032043.2	1068	Cct/Gct	20/20	1	2	FACETS	0.684	0.563	0.817	0.684	0.563	0.817	SUBCLONAL	1	FALSE	1	0.393772665034673	2		606	260	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953201	17953208	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGCCCC	AGGGCCCC	-	novel	NA	P-0063370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	118	708	0	ENST00000458235.1:c.778_785del	p.Gly260TrpfsTer14	p.G260Wfs*14	ENST00000458235	NM_000215.3	260	GGGGCCCTt/t	6/24	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.393772665034673	2		708	543	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251942	153251942	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	25	539	0	ENST00000281708.4:c.1064A>G	p.Tyr355Cys	p.Y355C	ENST00000281708	NM_033632.3	355	tAc/tGc	7/12	1	2	FACETS	0.686	0.545	0.846	0.686	0.545	0.846	SUBCLONAL	1	FALSE	1	0.393772665034673	2		539	185	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100233	157100269	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCAAGGCGGCCGCCGGCTCGGCGGCGGGGGGCTTC	CAGCAAGGCGGCCGCCGGCTCGGCGGCGGGGGGCTTC	-	novel	NA	P-0063370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	28	548	0	ENST00000346085.5:c.1174_1210del	p.Lys392AlafsTer26	p.K392Afs*26	ENST00000346085	NM_020732.3	390	ctCAGCAAGGCGGCCGCCGGCTCGGCGGCGGGGGGCTTC/ct	1/20	1	2	FACETS	0.311	0.248	0.383	0.311	0.248	0.383	SUBCLONAL	1	FALSE	1	0.393772665034673	2		548	457	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373384	118373428	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGCAAAACACTTCCACCTCTTCAAATTTGCAAAGGACAGTGGT	AGGGCAAAACACTTCCACCTCTTCAAATTTGCAAAGGACAGTGGT	G	novel	NA	P-0063370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	53	676	0	ENST00000534358.1:c.6777_6821delinsG	p.Gly2260TyrfsTer5	p.G2260Yfs*5	ENST00000534358	NM_005933.3	2259	ttAGGGCAAAACACTTCCACCTCTTCAAATTTGCAAAGGACAGTGGTt/ttGt	27/36	1	2	FACETS	0.726	0.621	0.839	0.726	0.621	0.839	SUBCLONAL	1	FALSE	1	0.393772665034673	2		676	371	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0063371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	118	525	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.862	0.778	0.95	0.862	0.778	0.95	CLONAL	1	TRUE	1	0.378592949324965	2		525	723	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633229	12633229	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs368807126	NA	P-0063371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	78	565	0	ENST00000251849.4:c.1171A>T	p.Arg391Trp	p.R391W	ENST00000251849	NM_002880.3	391	Agg/Tgg	11/17	1	2	FACETS	0.561	0.492	0.634	0.561	0.492	0.634	SUBCLONAL	1	TRUE	1	0.378592949324965	2		565	735	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236188	108236188	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	111	592	0	ENST00000278616.4:c.9124C>A	p.Pro3042Thr	p.P3042T	ENST00000278616	NM_000051.3	3042	Ccc/Acc	63/63	1	2	FACETS	0.714	0.642	0.791	0.714	0.642	0.791	SUBCLONAL	1	TRUE	1	0.378592949324965	2		592	821	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578448	7578448	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1064795691	NA	P-0063372-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	91	662	0	ENST00000269305.4:c.482C>A	p.Ala161Asp	p.A161D	ENST00000269305	NM_001126112.2	161	gCc/gAc	5/11	0.356493206964692	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.356493206964692	1		662	399	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432435	49432435	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063372-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	89	641	0	ENST00000301067.7:c.8704C>T	p.Gln2902Ter	p.Q2902*	ENST00000301067	NM_003482.3	2902	Cag/Tag	34/54	0.356493206964692	1	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	0	0.356493206964692	1		641	409	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428488	78428488	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063372-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	33	310	0	ENST00000370768.2:c.1311C>A	p.Asp437Glu	p.D437E	ENST00000370768	NM_003902.3	437	gaC/gaA	14/20	1	2	FACETS	0.759	0.621	0.912	0.759	0.621	0.912	CLONAL	1	TRUE	1	0.356493206964692	2		310	244	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262635	39262635	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063372-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	32	271	0	ENST00000402219.2:c.871G>T	p.Ala291Ser	p.A291S	ENST00000402219	NM_005633.3	291	Gca/Tca	7/23	1	2	FACETS	0.816	0.667	0.982	0.816	0.667	0.982	CLONAL	1	TRUE	1	0.356493206964692	2		271	220	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896362	151896362	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0063372-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	85	258	0	ENST00000262189.6:c.4273+2T>A		p.X1425_splice	ENST00000262189	NM_170606.2	1425			0.356493206964692	3	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	1	0.356493206964692	3		258	262	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62320910	62320910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367688683	NA	P-0063374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	30	823	0	ENST00000360203.5:c.1934G>A	p.Gly645Asp	p.G645D	ENST00000360203	NM_001283009.1	645	gGc/gAc	23/35	0.224854936950826	1	FACETS	0.798	0.646	0.969	0.798	0.646	0.969	CLONAL	1	FALSE	0	0.256036389354913	1		823	256	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681136	117681136	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	40	394	0	ENST00000368508.3:c.3484A>T	p.Asn1162Tyr	p.N1162Y	ENST00000368508	NM_002944.2	1162	Aac/Tac	23/43	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.256036389354913	2		394	209	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947865	178947865	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776932	NA	P-0063375-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	50	504	0	ENST00000263967.3:c.2740G>A	p.Gly914Arg	p.G914R	ENST00000263967	NM_006218.2	914	Gga/Aga	19/21	1	2	FACETS	0.698	0.593	0.812	0.698	0.593	0.812	SUBCLONAL	1	TRUE	1	0.32	2		504	448	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445601	49445601	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063375-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	92	1030	0	ENST00000301067.7:c.1865A>C	p.Glu622Ala	p.E622A	ENST00000301067	NM_003482.3	622	gAg/gCg	10/54	1	2	FACETS	0.649	0.576	0.727	0.649	0.576	0.727	SUBCLONAL	1	TRUE	1	0.32	2		1030	886	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576890	7576906	+	frameshift_variant	Frame_Shift_Del	DEL	TTTGGCTGGGGAGAGGA	TTTGGCTGGGGAGAGGA	-	novel	NA	P-0063375-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	98	758	0	ENST00000269305.4:c.940_956del	p.Ser314GlufsTer17	p.S314Efs*17	ENST00000269305	NM_001126112.2	314	TCCTCTCCCCAGCCAAAg/g	9/11	0.3	1	FACETS	0.716	0.638	0.798	0.716	0.638	0.798	SUBCLONAL	1	TRUE	0	0.32	1		758	719	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372356	55372356	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1194638628	NA	P-0063375-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	103	810	0	ENST00000297316.4:c.1046G>T	p.Ser349Ile	p.S349I	ENST00000297316	NM_022454.3	349	aGt/aTt	2/2	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.32	2		810	642	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024679	11024679	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063376-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	156	668	0	ENST00000327064.4:c.796G>A	p.Glu266Lys	p.E266K	ENST00000327064	NM_199141.1	266	Gag/Aag	6/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.587463480292245	2		668	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574002	7574007	+	inframe_deletion	In_Frame_Del	DEL	CGGAAC	CGGAAC	-	novel	NA	P-0063376-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	107	597	0	ENST00000269305.4:c.1020_1025del	p.Met340_Arg342delinsIle	p.M340_R342delinsI	ENST00000269305	NM_001126112.2	340	atGTTCCGa/ata	10/11	1	2	FACETS	0.75	0.676	0.827	0.75	0.676	0.827	SUBCLONAL	1	TRUE	1	0.587463480292245	2		597	486	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120053	70120053	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063376-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	182	698	0	ENST00000245479.2:c.1058del	p.Pro353ArgfsTer30	p.P353Rfs*30	ENST00000245479	NM_000346.3	352	gCc/gc	3/3	0.303947328386153	1	FACETS	1	0.946	1	1	0.946	1	INDETERMINATE	1	TRUE	0	0.587463480292245	1		698	431	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275630	41275630	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063376-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	201	625	0	ENST00000349496.5:c.1525G>T	p.Ala509Ser	p.A509S	ENST00000349496	NM_001904.3	509	Gct/Tct	10/15	0.303947328386153	1	FACETS	0.942	0.881	1	0.942	0.881	1	INDETERMINATE	1	TRUE	0	0.587463480292245	1		625	513	SUCCESS
APC	324	MSKCC	GRCh37	5	112174048	112174048	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs863225331	NA	P-0063376-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	190	626	0	ENST00000257430.4:c.2759del	p.Asn920MetfsTer35	p.N920Mfs*35	ENST00000257430	NM_000038.5	919	agA/ag	16/16	0.303947328386153	1	FACETS	0.77	0.716	0.826	0.77	0.716	0.826	INDETERMINATE	1	TRUE	0	0.587463480292245	1		626	593	SUCCESS
APC	324	MSKCC	GRCh37	5	112175217	112175218	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0063376-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	92	629	0	ENST00000257430.4:c.3928_3929del	p.Lys1310AspfsTer4	p.K1310Dfs*4	ENST00000257430	NM_000038.5	1309	gAA/g	16/16	0.303947328386153	1	FACETS	0.389	0.347	0.435	0.389	0.347	0.435	INDETERMINATE	1	TRUE	0	0.587463480292245	1		629	568	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241952	133241952	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	8256	564	0	ENST00000320574.5:c.2404G>C	p.Asp802His	p.D802H	ENST00000320574	NM_006231.2	802	Gac/Cac	21/49	1	2	FACETS	0.965	0.962	0.969			1	CLONAL	2	TRUE	1	0.968481730478443	2		564	8830	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509206	106509206	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	214	626	0	ENST00000359195.3:c.1200C>A	p.Ser400Arg	p.S400R	ENST00000359195	NM_002649.2	400	agC/agA	2/11	1	2	FACETS	0.648	0.605	0.692	0.648	0.605	0.692	SUBCLONAL	1	TRUE	1	0.968481730478443	2		626	682	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063378-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	117	343	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.762	0.691	0.836	0.762	0.691	0.836	SUBCLONAL	1	TRUE	1	0.64500832208367	2		343	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0063378-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	66	459	0	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.626051084490551	1	FACETS	0.26	0.226	0.297	0.26	0.226	0.297	SUBCLONAL	1	TRUE	0	0.64500832208367	1		459	533	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258035	123258035	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs763017169	NA	P-0063378-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	120	364	0	ENST00000358487.5:c.1646A>G	p.Asn549Ser	p.N549S	ENST00000358487	NM_000141.4	549	aAt/aGt	12/18	0.541320347972885	1	FACETS	0.662	0.603	0.722	0.662	0.603	0.722	SUBCLONAL	1	TRUE	0	0.64500832208367	1		364	381	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0063380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	252	473	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.79	2		473	618	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294970	1294971	+	missense_variant	Missense_Mutation	DNP	CG	CG	TT	novel	NA	P-0063380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	191	711	0	ENST00000310581.5:c.134_135delinsAA	p.Ala45Glu	p.A45E	ENST00000310581	NM_198253.2	45	gCG/gAA	1/16	1	2	FACETS	0.995	0.929	1	0.995	0.929	1	CLONAL	1	TRUE	1	0.79	2		711	486	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224542	123224542	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0063380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	239	324	0	ENST00000218089.9:c.3395T>G	p.Leu1132Ter	p.L1132*	ENST00000218089	NM_001042749.1	1132	tTa/tGa	31/35	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.79	1		324	316	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833924	44833925	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0063380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	83	146	0	ENST00000377967.4:c.349_350dup	p.Gln117HisfsTer64	p.Q117Hfs*64	ENST00000377967	NM_021140.2	116	-/CA	4/29	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.79	1		146	102	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933360	100933360	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	175	454	0	ENST00000325455.5:c.2030C>G	p.Pro677Arg	p.P677R	ENST00000325455	NM_001202474.3	677	cCa/cGa	4/8	0.379980332910466	4	FACETS	0.809	0.748	0.872	0.809	0.748	0.872	CLONAL	2	FALSE	2	0.504754561535618	4		454	645	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56432308	56432309	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGC	novel	NA	P-0063381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	269	388	0	ENST00000407977.2:c.2344_2347dup	p.Val783GlyfsTer101	p.V783Gfs*101	ENST00000407977		783	gtg/gGCTGtg	10/10	0.410389999353371	3	FACETS	1	0.988	1	0.765	0.724	0.805	CLONAL	2	FALSE	0	0.504754561535618	3		388	582	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	C	C	TA	novel	NA	P-0063381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	238	583	0	ENST00000269305.4:c.811delinsTA	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/TAag	8/11	0.413559649232269	2	FACETS	1	0.992	1	0.688	0.646	0.732	CLONAL	1	FALSE	0	0.504754561535618	2		583	685	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589586	67589591	+	inframe_deletion	In_Frame_Del	DEL	ATGAAT	ATGAAT	-	novel	NA	P-0063383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	17	296	0	ENST00000274335.5:c.1351_1356del	p.Glu451_Tyr452del	p.E451_Y452del	ENST00000274335		450	cATGAATat/cat	10/15	1	2	FACETS	0.825	0.618	1	0.825	0.618	1	CLONAL	1	TRUE	1	0.2	2		296	206	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0063383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	18	484	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	0.291	0.218	0.378	0.291	0.218	0.378	SUBCLONAL	1	TRUE	1	0.2	2		484	619	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121913370	NA	P-0063383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	26	361	0	ENST00000288602.6:c.1742A>G	p.Asn581Ser	p.N581S	ENST00000288602	NM_004333.4	581	aAt/aGt	15/18	1	2	FACETS	0.836	0.663	1	0.836	0.663	1	CLONAL	1	TRUE	1	0.2	2		361	311	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720806	89720806	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167682	NA	P-0063383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	15	156	0	ENST00000371953.3:c.959del	p.Leu320Ter	p.L320*	ENST00000371953	NM_000314.4	319	acT/ac	8/9	1	2	FACETS	1	0.821	1	1	0.821	1	CLONAL	1	TRUE	1	0.2	2		156	130	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0063384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	15	464	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.63	0.459	0.838	0.63	0.459	0.838	SUBCLONAL	1	TRUE	1	0.1	2		464	476	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0063384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	8	398	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.429	0.275	0.63	0.429	0.275	0.63	SUBCLONAL	1	TRUE	1	0.1	2		398	373	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0063384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	24	609	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	1	2	FACETS	0.728	0.569	0.914	0.728	0.569	0.914	CLONAL	1	TRUE	1	0.1	2		609	659	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974702	21974702	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	8	788	0	ENST00000304494.5:c.125del	p.Asn42IlefsTer11	p.N42Ifs*11	ENST00000304494	NM_000077.4	42	aAt/at	1/3	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		788	369	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0063386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	24	387	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.753	0.59	0.941	0.753	0.59	0.941	CLONAL	1	TRUE	1	0.17	2		387	375	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0063386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	30	380	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.68	0.547	0.832	0.68	0.547	0.832	SUBCLONAL	1	TRUE	1	0.17	2		380	519	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0063386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	57	662	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.17	2		662	614	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593466	48593466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064796102	NA	P-0063386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	49	469	0	ENST00000342988.3:c.1217C>T	p.Ala406Val	p.A406V	ENST00000342988	NM_005359.5	406	gCg/gTg	10/12	1	2	FACETS	0.953	0.806	1	0.953	0.806	1	CLONAL	1	TRUE	1	0.17	2		469	605	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624559	93624559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	40	625	1	ENST00000375746.1:c.650G>A	p.Arg217His	p.R217H	ENST00000375746	NM_001174167.1	217	cGc/cAc	4/14	1	2	FACETS	0.851	0.706	1	0.851	0.706	1	CLONAL	1	TRUE	1	0.17	2		626	553	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513266	44513267	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCGCCGCCACCTCCA	novel	NA	P-0063386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	19	686	0	ENST00000291552.4:c.654_668dup	p.Gly219_Gly223dup	p.G219_G223dup	ENST00000291552	NM_006758.2	219	gga/ggTGGAGGTGGCGGCGGa	8/8	1	2	FACETS	0.386	0.292	0.498	0.386	0.292	0.498	SUBCLONAL	1	TRUE	1	0.17	2		686	579	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098533	108098533	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs55861249	NA	P-0063387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	94	190	0	ENST00000278616.4:c.103C>T	p.Arg35Ter	p.R35*	ENST00000278616	NM_000051.3	35	Cga/Tga	3/63	0.475214343773188	2	FACETS	0.755	0.682	0.83	0.755	0.682	0.83	SUBCLONAL	2	TRUE	0	0.475214343773188	2		190	262	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726698	88726698	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375475747	NA	P-0063387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	331	497	0	ENST00000360948.2:c.346C>T	p.Arg116Trp	p.R116W	ENST00000360948	NM_001012338.2	116	Cgg/Tgg	4/19	0.472475905228577	3	FACETS	0.942	0.9	0.984	0.942	0.9	0.984	CLONAL	3	TRUE	0	0.475214343773188	3		497	610	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864653	56864653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759824481	NA	P-0063387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	349	292	0	ENST00000519728.1:c.616G>A	p.Asp206Asn	p.D206N	ENST00000519728	NM_002350.3	206	Gac/Aac	7/13	0.475214343773188	7	FACETS	0.937	0.895	0.979	0.937	0.895	0.979	CLONAL	5	TRUE	2	0.475214343773188	7		292	686	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428573	78428573	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	24	279	0	ENST00000370768.2:c.1226G>T	p.Arg409Ile	p.R409I	ENST00000370768	NM_003902.3	409	aGa/aTa	14/20	0.471214187428575	2	FACETS	0.217	0.169	0.272	0.108	0.084	0.136	SUBCLONAL	1	TRUE	0	0.475214343773188	2		279	466	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634395	23634395	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	80	366	0	ENST00000261584.4:c.2891G>C	p.Gly964Ala	p.G964A	ENST00000261584	NM_024675.3	964	gGa/gCa	9/13	0.40004186409849	3	FACETS	0.918	0.811	1	0.459	0.405	0.516	CLONAL	1	TRUE	1	0.475214343773188	3		366	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579535	7579536	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CAATATC	novel	NA	P-0063387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	316	725	0	ENST00000269305.4:c.145_151dup	p.Glu51GlyfsTer3	p.E51Gfs*3	ENST00000269305	NM_001126112.2	51	gaa/gGATATTGaa	4/11	0.107234497797437	3	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.475214343773188	3		725	690	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252976	36252977	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0063387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	124	506	0	ENST00000300305.3:c.385dup	p.Leu129ProfsTer9	p.L129Pfs*9	ENST00000300305		129	ctg/cCtg	4/8	1	2	FACETS	0.972	0.883	1	0.972	0.883	1	CLONAL	1	TRUE	1	0.475214343773188	2		506	537	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189418	56189420	+	inframe_deletion	In_Frame_Del	DEL	GTG	GTG	-	novel	NA	P-0063387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	105	557	0	ENST00000399503.3:c.4451_4453del	p.Val1484del	p.V1484del	ENST00000399503	NM_005921.1	1484	GTG/-	20/20	0.40004186409849	3	FACETS	0.888	0.797	0.984	0.444	0.398	0.492	CLONAL	1	TRUE	1	0.475214343773188	3		557	616	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0063388-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	72	539	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.23	2		539	507	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161447	2161447	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063388-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	73	559	1	ENST00000434045.2:c.80A>T	p.Asp27Val	p.D27V	ENST00000434045	NM_001127598.1	27	gAc/gTc	2/5	1	2	FACETS	0.874	0.764	0.994	0.874	0.764	0.994	CLONAL	1	TRUE	1	0.23	2		560	726	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498351	29498351	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063388-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	38	518	0	ENST00000389048.3:c.1829A>G	p.Gln610Arg	p.Q610R	ENST00000389048	NM_004304.4	610	cAg/cGg	10/29	1	2	FACETS	0.595	0.491	0.712	0.595	0.491	0.712	SUBCLONAL	1	TRUE	1	0.23	2		518	555	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063390-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	140	343	0				ENST00000310581	NM_198253.2	-/1132			0.403734643419817	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.403734643419817	2		343	316	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509436	106509436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200175951	NA	P-0063390-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	117	492	0	ENST00000359195.3:c.1430G>A	p.Arg477His	p.R477H	ENST00000359195	NM_002649.2	477	cGt/cAt	2/11	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.403734643419817	2		492	579	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219050	36219050	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1459799356	NA	P-0063390-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	129	504	1	ENST00000222270.7:c.4549C>T	p.Arg1517Ter	p.R1517*	ENST00000222270	NM_014727.1	1517	Cga/Tga	19/37	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.403734643419817	2		505	568	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220199	36220199	+	splice_donor_variant	Splice_Site	SNP	T	T	G	rs1599688046	NA	P-0063390-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	123	515	0	ENST00000222270.7:c.4917+2T>G		p.X1639_splice	ENST00000222270	NM_014727.1	1639			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.403734643419817	2		515	570	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412328	139412328	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063390-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	213	525	0	ENST00000277541.6:c.1317del	p.Gln439HisfsTer192	p.Q439Hfs*192	ENST00000277541	NM_017617.3	439	caG/ca	8/34	0.378904802890935	2	FACETS	0.957	0.897	1	0.957	0.897	1	CLONAL	2	TRUE	0	0.403734643419817	2		525	551	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240749	53240750	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0063390-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	103	187	0	ENST00000375401.3:c.1330dup	p.Ile444AsnfsTer14	p.I444Nfs*14	ENST00000375401	NM_004187.3	444	atc/aAtc	10/26	1	1	FACETS	0.863	0.788	0.939	1	0.988	1	CLONAL	2	TRUE	0	0.403734643419817	1		187	236	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0063391-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	61	572	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.864	0.746	0.991	1	0.975	1	CLONAL	2	TRUE	1	0.146555665277102	2		572	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579350	7579350	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587781642	NA	P-0063391-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	65	581	0	ENST00000269305.4:c.337T>G	p.Phe113Val	p.F113V	ENST00000269305	NM_001126112.2	113	Ttc/Gtc	4/11	1	2	FACETS	0.832	0.722	0.951	1	0.975	1	CLONAL	2	TRUE	1	0.146555665277102	2		581	533	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	76	343	0				ENST00000310581	NM_198253.2	-/1132			0.655593638296071	3	FACETS	0.797	0.719	0.875	0.797	0.719	0.875	SUBCLONAL	2	TRUE	1	0.865069753466344	3		343	158	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913407	NA	P-0063392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	175	383	0	ENST00000349496.5:c.133T>G	p.Ser45Ala	p.S45A	ENST00000349496	NM_001904.3	45	Tct/Gct	3/15	0.83756404223193	2	FACETS	0.92	0.881	0.956	0.92	0.881	0.956	CLONAL	2	TRUE	0	0.865069753466344	2		383	220	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600330	10600330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	80	531	0	ENST00000171111.5:c.1525G>A	p.Gly509Arg	p.G509R	ENST00000171111	NM_203500.1	509	Ggg/Agg	4/6	1	2	FACETS	0.902	0.81	0.996	0.902	0.81	0.996	CLONAL	1	TRUE	1	0.865069753466344	2		531	205	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602645	10602680	+	inframe_deletion	In_Frame_Del	DEL	GTGCAGGGTGAGCTCCTCGAAGATCTTGACCAGGTA	GTGCAGGGTGAGCTCCTCGAAGATCTTGACCAGGTA	-	novel	NA	P-0063392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	72	538	0	ENST00000171111.5:c.898_933del	p.Tyr300_His311del	p.Y300_H311del	ENST00000171111	NM_203500.1	300	TACCTGGTCAAGATCTTCGAGGAGCTCACCCTGCAC/-	3/6	1	2	FACETS	0.841	0.749	0.936	0.841	0.749	0.936	CLONAL	1	TRUE	1	0.865069753466344	2		538	198	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247756	59247756	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	27	475	0	ENST00000371222.2:c.987A>T	p.Gln329His	p.Q329H	ENST00000371222	NM_002228.3	329	caA/caT	1/1	1	2	FACETS	0.26	0.206	0.322	0.26	0.206	0.322	SUBCLONAL	1	TRUE	1	0.389034154652797	2		475	533	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651448	52651448	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	85	326	0	ENST00000394830.3:c.1648C>A	p.Pro550Thr	p.P550T	ENST00000394830	NM_018313.4	550	Cca/Aca	15/30	0.389034154652797	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.389034154652797	1		326	253	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197730	66197730	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	20	348	0	ENST00000273854.3:c.2969G>A	p.Gly990Glu	p.G990E	ENST00000273854	NM_004439.5	990	gGa/gAa	17/18	1	2	FACETS	0.3	0.229	0.383	0.3	0.229	0.383	SUBCLONAL	1	TRUE	1	0.389034154652797	2		348	343	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442591	52442594	+	missense_variant	Missense_Mutation	ONP	ATTT	ATTT	CTTC	novel	NA	P-0063394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	58	430	0	ENST00000460680.1:c.151_154delinsGAAG	p.Lys51_Trp52delinsGluGly	p.K51_W52delinsEG	ENST00000460680	NM_004656.3	51	AAATgg/GAAGgg	4/17	0.389034154652797	1	FACETS	0.575	0.495	0.661	0.575	0.495	0.661	SUBCLONAL	1	TRUE	0	0.389034154652797	1		430	418	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191526	10191527	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	T	novel	NA	P-0063394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	106	408	0	ENST00000256474.2:c.519_520delinsT	p.Glu173AspfsTer29	p.E173Dfs*29	ENST00000256474	NM_000551.3	173	gaGAat/gaTat	3/3	0.389034154652797	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.389034154652797	1		408	413	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777894	NA	P-0063395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	64	333	0	ENST00000361445.4:c.6644C>T	p.Ser2215Phe	p.S2215F	ENST00000361445	NM_004958.3	2215	tCt/tTt	47/58	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		333	553	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063397-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	134	406	0	ENST00000267101.3:c.850G>C	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Cga	7/28	1	2	FACETS	0.976	0.888	1	0.976	0.888	1	CLONAL	1	TRUE	1	0.380930455196868	2		406	721	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057302	30057302	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315496	NA	P-0063397-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	97	436	0	ENST00000338641.4:c.784C>T	p.Arg262Ter	p.R262*	ENST00000338641	NM_000268.3	262	Cga/Tga	8/16	0.361317844506054	1	FACETS	0.73	0.652	0.812	0.73	0.652	0.812	SUBCLONAL	1	TRUE	0	0.380930455196868	1		436	565	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0063398-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	37	205	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.975	0.802	1	0.975	0.802	1	CLONAL	1	TRUE	1	0.13	2		205	584	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0063398-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	26	473	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.526	0.415	0.655	0.526	0.415	0.655	SUBCLONAL	1	TRUE	1	0.13	2		473	760	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0063398-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	32	457	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	1	2	FACETS	0.864	0.7	1	0.864	0.7	1	CLONAL	1	TRUE	1	0.13	2		457	570	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165518	47165518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063398-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	49	775	0	ENST00000409792.3:c.608C>T	p.Ser203Leu	p.S203L	ENST00000409792	NM_014159.6	203	tCa/tTa	3/21	1	2	FACETS	0.8	0.675	0.939	0.8	0.675	0.939	CLONAL	1	TRUE	1	0.13	2		775	942	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922749	44922749	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0063398-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	48	291	0	ENST00000377967.4:c.1610C>G	p.Ser537Ter	p.S537*	ENST00000377967	NM_021140.2	537	tCa/tGa	16/29	1	1	FACETS	0.954	0.809	1	1	0.972	1	CLONAL	2	TRUE	0	0.13	1		291	362	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258079	16258079	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063398-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	41	634	0	ENST00000375759.3:c.5344G>T	p.Asp1782Tyr	p.D1782Y	ENST00000375759	NM_015001.2	1782	Gat/Tat	11/15	1	2	FACETS	0.778	0.646	0.926	0.778	0.646	0.926	CLONAL	1	TRUE	1	0.13	2		634	811	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445197	49445197	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063398-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	66	886	0	ENST00000301067.7:c.2269G>T	p.Glu757Ter	p.E757*	ENST00000301067	NM_003482.3	757	Gag/Tag	10/54	1	2	FACETS	0.897	0.776	1	0.897	0.776	1	CLONAL	1	TRUE	1	0.13	2		886	1132	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175850	24175850	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063398-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	41	596	0	ENST00000263121.7:c.1078G>T	p.Glu360Ter	p.E360*	ENST00000263121	NM_003073.3	360	Gag/Tag	8/9	1	2	FACETS	0.846	0.702	1	0.846	0.702	1	CLONAL	1	TRUE	1	0.13	2		596	746	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877172	151877172	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063398-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	41	517	2	ENST00000262189.6:c.7189C>T	p.Gln2397Ter	p.Q2397*	ENST00000262189	NM_170606.2	2397	Cag/Tag	37/59	1	2	FACETS	0.872	0.725	1	0.872	0.725	1	CLONAL	1	TRUE	1	0.13	2		519	723	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651980	36651983	+	frameshift_variant	Frame_Shift_Del	DEL	TGAT	TGAT	CC	novel	NA	P-0063398-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	44	700	0	ENST00000244741.5:c.102_105delinsCC	p.Asp35ArgfsTer12	p.D35Rfs*12	ENST00000244741	NM_000389.4	34	tgTGAT/tgCC	2/3	1	2	FACETS	0.783	0.654	0.926	0.783	0.654	0.926	CLONAL	1	TRUE	1	0.13	2		700	865	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0063401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	165	678	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.258733592875865	5	FACETS	1	0.967	1	0.731	0.672	0.793	CLONAL	2	TRUE	2	0.258733592875865	5		678	807	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1567555907	NA	P-0063401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	196	731	0	ENST00000269305.4:c.314del	p.Gly105AlafsTer18	p.G105Afs*18	ENST00000269305	NM_001126112.2	105	gGc/gc	4/11	0.258581884391869	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	0	0.258733592875865	2		731	747	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953019	2953019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750407488	NA	P-0063401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	88	579	0	ENST00000396946.4:c.2921G>A	p.Arg974His	p.R974H	ENST00000396946	NM_032415.4	974	cGc/cAc	22/25	1	2	FACETS	0.903	0.8	1	0.903	0.8	1	CLONAL	1	TRUE	1	0.258733592875865	2		579	753	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374909	149374909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	48	650	0	ENST00000360632.3:c.185C>T	p.Ser62Leu	p.S62L	ENST00000360632	NM_015472.4	62	tCg/tTg	2/7	0.258733592875865	5	FACETS	0.768	0.648	0.9	0.256	0.216	0.3	SUBCLONAL	1	TRUE	2	0.258733592875865	5		650	671	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390569	139390569	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	75	691	0	ENST00000277541.6:c.7622C>T	p.Thr2541Ile	p.T2541I	ENST00000277541	NM_017617.3	2541	aCc/aTc	34/34	0.206562867157654	3	FACETS	0.882	0.773	1	0.441	0.386	0.501	CLONAL	1	TRUE	1	0.258733592875865	3		691	742	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263783	16263783	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	95	768	0	ENST00000375759.3:c.10152G>C	p.Lys3384Asn	p.K3384N	ENST00000375759	NM_015001.2	3384	aaG/aaC	12/15	0.138812303380868	4	FACETS	0.919	0.816	1	0.459	0.408	0.515	INDETERMINATE	1	TRUE	2	0.258733592875865	4		768	1006	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092799	27092799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	32	546	0	ENST00000324856.7:c.2820G>A	p.Met940Ile	p.M940I	ENST00000324856	NM_006015.4	940	atG/atA	9/20	0.138812303380868	4	FACETS	0.567	0.459	0.689	0.284	0.229	0.345	INDETERMINATE	1	TRUE	2	0.258733592875865	4		546	549	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092967	27092967	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	68	604	1	ENST00000324856.7:c.2898G>C	p.Glu966Asp	p.E966D	ENST00000324856	NM_006015.4	966	gaG/gaC	10/20	0.138812303380868	4	FACETS	0.974	0.847	1	0.487	0.423	0.556	INDETERMINATE	1	TRUE	2	0.258733592875865	4		605	679	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434449	49434449	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	78	805	0	ENST00000301067.7:c.7104C>G	p.Ile2368Met	p.I2368M	ENST00000301067	NM_003482.3	2368	atC/atG	31/54	0.206562867157654	3	FACETS	0.82	0.72	0.929	0.41	0.36	0.465	CLONAL	1	TRUE	1	0.258733592875865	3		805	830	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251536	251536	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063401-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	66	415	0	ENST00000264932.6:c.1747G>C	p.Glu583Gln	p.E583Q	ENST00000264932	NM_004168.2	583	Gag/Cag	13/15	0.138812303380868	4	FACETS	1	0.94	1	0.574	0.499	0.656	INDETERMINATE	1	TRUE	2	0.258733592875865	4		415	559	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	149	709	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.765	0.7	0.832	1	0.988	1	SUBCLONAL	2	TRUE	1	0.28	2		710	696	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	93	749	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.757	0.672	0.848	0.757	0.672	0.848	SUBCLONAL	1	TRUE	1	0.28	2		754	877	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	49	605	2	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.28	2		607	327	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	37	361	0	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	0.298412351372131	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.28	1		361	170	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	43	439	0	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	0.718	0.601	0.846	0.718	0.601	0.846	SUBCLONAL	1	TRUE	1	0.28	2		439	428	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578277	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs1555525902	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	65	786	0	ENST00000269305.4:c.572_574del	p.Pro191del	p.P191del	ENST00000269305	NM_001126112.2	191	cCTCag/cag	6/11	1	2	FACETS	0.664	0.575	0.761	0.664	0.575	0.761	SUBCLONAL	1	TRUE	1	0.28	2		786	699	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	43	304	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	0.212561179468855	3	FACETS	0.907	0.769	1	0.907	0.769	1	CLONAL	2	TRUE	1	0.28	3		304	193	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465373	120465373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	74	641	0	ENST00000256646.2:c.4888C>T	p.Arg1630Cys	p.R1630C	ENST00000256646	NM_024408.3	1630	Cgc/Tgc	27/34	1	2	FACETS	0.826	0.723	0.937	0.826	0.723	0.937	CLONAL	1	TRUE	1	0.28	2		641	640	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101099	27101099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	74	620	0	ENST00000324856.7:c.4381C>T	p.Arg1461Ter	p.R1461*	ENST00000324856	NM_006015.4	1461	Cga/Tga	18/20	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.28	2		620	524	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220644	1220644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1167609100	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	99	620	0	ENST00000326873.7:c.662C>T	p.Pro221Leu	p.P221L	ENST00000326873	NM_000455.4	221	cCg/cTg	5/10	0.112618266625665	4	FACETS	1	0.978	1	0.699	0.625	0.778	INDETERMINATE	1	TRUE	2	0.28	4		620	647	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	39	713	1	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.5	0.414	0.597	0.5	0.414	0.597	SUBCLONAL	1	TRUE	1	0.28	2		714	557	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	62	560	7	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.651	0.562	0.749	0.651	0.562	0.749	SUBCLONAL	1	TRUE	1	0.28	2		567	680	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921786	111921786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1466732626	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	117	447	0	ENST00000393256.3:c.575G>A	p.Arg192His	p.R192H	ENST00000393256	NM_006538.4	192	cGc/cAc	4/4	0.299152815452936	2	FACETS	0.885	0.803	0.971	0.885	0.803	0.971	CLONAL	2	TRUE	0	0.28	2		447	472	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835780	68835781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	51	575	1	ENST00000261769.5:c.377dup	p.Pro127AlafsTer41	p.P127Afs*41	ENST00000261769	NM_004360.3	124	cgc/cgCc	3/16	1	2	FACETS	0.505	0.428	0.59	0.505	0.428	0.59	SUBCLONAL	1	TRUE	1	0.28	2		576	721	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849887	156849887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759190964	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	77	507	0	ENST00000524377.1:c.2143G>A	p.Val715Met	p.V715M	ENST00000524377	NM_002529.3	715	Gtg/Atg	16/17	1	2	FACETS	0.816	0.716	0.923	0.816	0.716	0.923	CLONAL	1	TRUE	1	0.28	2		507	674	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	86	510	0	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.28	2		510	607	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	73	691	1	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.708	0.619	0.805	0.708	0.619	0.805	SUBCLONAL	1	TRUE	1	0.28	2		692	736	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs397518442	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	100	652	0	ENST00000326873.7:c.650del	p.Pro217ArgfsTer70	p.P217Rfs*70	ENST00000326873	NM_000455.4	216	tCc/tc	5/10	0.112618266625665	4	FACETS	1	0.976	1	0.671	0.6	0.747	INDETERMINATE	1	TRUE	2	0.28	4		652	681	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938230	76938230	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	14	472	4	ENST00000373344.5:c.2518del	p.Arg840GlufsTer29	p.R840Efs*29	ENST00000373344	NM_000489.3	840	Aga/ga	9/35	1	2	FACETS	0.42	0.303	0.561	0.42	0.303	0.561	SUBCLONAL	1	TRUE	1	0.28	2		476	238	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806180	1806181	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760502257	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	36	719	2	ENST00000260795.2:c.1206dup	p.Lys403GlnfsTer93	p.K403Qfs*93	ENST00000260795		400	agc/agCc	8/17	1	2	FACETS	0.375	0.307	0.451	0.375	0.307	0.451	SUBCLONAL	1	TRUE	1	0.28	2		721	686	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639588	47639588	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63749897	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	15	326	0	ENST00000233146.2:c.687del	p.Ala230LeufsTer16	p.A230Lfs*16	ENST00000233146	NM_000251.2	227	agA/ag	4/16	0.203090401250928	2	FACETS	0.489	0.358	0.646	0.245	0.179	0.323	SUBCLONAL	1	TRUE	0	0.28	2		326	219	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521525	46521525	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	46	463	3	ENST00000262741.5:c.883del	p.Met295Ter	p.M295*	ENST00000262741	NM_003629.3	295	Atg/tg	7/10	1	2	FACETS	0.936	0.791	1	0.936	0.791	1	CLONAL	1	TRUE	1	0.28	2		466	351	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15821896	15821896	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	17	435	1	ENST00000307771.7:c.294del	p.Lys98AsnfsTer10	p.K98Nfs*10	ENST00000307771	NM_005089.3	97	Aaa/aa	4/11	1	2	FACETS	0.369	0.275	0.481	0.369	0.275	0.481	SUBCLONAL	1	TRUE	1	0.28	2		436	329	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828024	72828024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200701402	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	72	579	0	ENST00000268489.5:c.8557G>A	p.Ala2853Thr	p.A2853T	ENST00000268489	NM_006885.3	2853	Gca/Aca	9/10	1	2	FACETS	0.757	0.661	0.861	0.757	0.661	0.861	SUBCLONAL	1	TRUE	1	0.28	2		579	679	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380346	14380346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	76	568	0	ENST00000256196.4:c.71G>A	p.Gly24Asp	p.G24D	ENST00000256196		24	gGc/gAc	1/6	1	2	FACETS	0.985	0.866	1	0.985	0.866	1	CLONAL	1	TRUE	1	0.28	2		568	551	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46251055	46251055	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs140235515	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	21	373	0	ENST00000371998.3:c.64T>C	p.Cys22Arg	p.C22R	ENST00000371998		22	Tgt/Cgt	3/23	1	2	FACETS	0.595	0.459	0.753	0.595	0.459	0.753	SUBCLONAL	1	TRUE	1	0.28	2		373	252	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936277	78936277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1476697249	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	35	533	0	ENST00000306801.3:c.3709C>T	p.Arg1237Cys	p.R1237C	ENST00000306801	NM_020761.2	1237	Cgc/Tgc	32/34	1	2	FACETS	0.496	0.406	0.597	0.496	0.406	0.597	SUBCLONAL	1	TRUE	1	0.28	2		533	504	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	42	643	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.735	0.615	0.869	0.735	0.615	0.869	SUBCLONAL	1	TRUE	1	0.28	2		643	408	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790090	40790090	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	59	636	1	ENST00000373198.4:c.2641del	p.Arg881GlyfsTer20	p.R881Gfs*20	ENST00000373198	NM_133170.3	881	Cgg/gg	18/32	1	2	FACETS	0.649	0.558	0.749	0.649	0.558	0.749	SUBCLONAL	1	TRUE	1	0.28	2		637	649	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356452	70356454	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	40	745	0	ENST00000374080.3:c.5353_5355del	p.Lys1785del	p.K1785del	ENST00000374080		1783	AAG/-	37/45	1	2	FACETS	0.392	0.325	0.468	0.392	0.325	0.468	SUBCLONAL	1	TRUE	1	0.28	2		745	728	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748399150	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	35	592	5	ENST00000220592.5:c.1806del	p.Ala603ProfsTer92	p.A603Pfs*92	ENST00000220592	NM_012154.3	602	ccC/cc	14/19	1	2	FACETS	0.373	0.304	0.45	0.373	0.304	0.45	SUBCLONAL	1	TRUE	1	0.28	2		597	671	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431665	6431665	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	40	361	0	ENST00000356142.4:c.218C>T	p.Pro73Leu	p.P73L	ENST00000356142	NM_018890.3	73	cCg/cTg	3/7	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.28	2		361	227	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27098991	27098991	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs375417370	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	38	597	0	ENST00000324856.7:c.3407C>T	p.Ala1136Val	p.A1136V	ENST00000324856	NM_006015.4	1136	gCg/gTg	13/20	1	2	FACETS	0.443	0.365	0.53	0.443	0.365	0.53	SUBCLONAL	1	TRUE	1	0.28	2		597	613	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980293	201980293	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	60	581	0	ENST00000359651.3:c.33del	p.Phe11LeufsTer32	p.F11Lfs*32	ENST00000359651		10	aTt/at	1/8	1	2	FACETS	0.713	0.614	0.821	0.713	0.614	0.821	SUBCLONAL	1	TRUE	1	0.28	2		581	601	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67646012	67646013	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	56	508	0	ENST00000264010.4:c.950_951dup	p.Gly318GlnfsTer16	p.G318Qfs*16	ENST00000264010	NM_006565.3	314	aac/aACac	4/12	1	2	FACETS	0.768	0.658	0.887	0.768	0.658	0.887	SUBCLONAL	1	TRUE	1	0.28	2		508	521	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665096	138665096	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs758370933	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	40	540	0	ENST00000330315.3:c.469C>G	p.Pro157Ala	p.P157A	ENST00000330315	NM_023067.3	157	Ccc/Gcc	1/1	0.299152815452936	3	FACETS	0.595	0.494	0.709	0.298	0.247	0.355	SUBCLONAL	1	TRUE	1	0.28	3		540	547	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137283	64137283	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	96	646	0	ENST00000334205.4:c.1715C>T	p.Thr572Met	p.T572M	ENST00000334205	NM_003942.2	572	aCg/aTg	14/17	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.28	2		646	684	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823928	3823928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768288810	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	39	468	0	ENST00000262367.5:c.2287G>A	p.Ala763Thr	p.A763T	ENST00000262367	NM_004380.2	763	Gcc/Acc	13/31	1	2	FACETS	0.522	0.432	0.622	0.522	0.432	0.622	SUBCLONAL	1	TRUE	1	0.28	2		468	534	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830233	72830234	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	87	692	0	ENST00000268489.5:c.6347dup	p.Gln2117AlafsTer39	p.Q2117Afs*39	ENST00000268489	NM_006885.3	2116	ccg/ccCg	9/10	1	2	FACETS	0.907	0.803	1	0.907	0.803	1	CLONAL	1	TRUE	1	0.28	2		692	685	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528016	157528016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751391187	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	153	707	1	ENST00000346085.5:c.5741G>A	p.Arg1914Gln	p.R1914Q	ENST00000346085	NM_020732.3	1914	cGg/cAg	20/20	0.190035346017026	2	FACETS	1	0.988	1	0.74	0.678	0.805	CLONAL	1	TRUE	0	0.28	2		708	738	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509583	106509583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749714535	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	131	676	0	ENST00000359195.3:c.1577C>T	p.Pro526Leu	p.P526L	ENST00000359195	NM_002649.2	526	cCg/cTg	2/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.28	2		676	696	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658505	3658505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778404827	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	82	621	0	ENST00000294008.3:c.461G>A	p.Arg154Gln	p.R154Q	ENST00000294008	NM_032444.2	154	cGg/cAg	2/15	1	2	FACETS	0.897	0.791	1	0.897	0.791	1	CLONAL	1	TRUE	1	0.28	2		621	653	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442539	52442539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572063023	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	30	536	0	ENST00000460680.1:c.206C>T	p.Thr69Met	p.T69M	ENST00000460680	NM_004656.3	69	aCg/aTg	4/17	1	2	FACETS	0.368	0.296	0.451	0.368	0.296	0.451	SUBCLONAL	1	TRUE	1	0.28	2		536	582	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31431727	31431727	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1003588847	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	66	414	0	ENST00000344624.3:c.3101C>T	p.Ser1034Leu	p.S1034L	ENST00000344624		1034	tCg/tTg	23/33	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.28	2		414	343	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50481242	50481242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	101	534	0	ENST00000394963.4:c.628C>T	p.Arg210Trp	p.R210W	ENST00000394963	NM_003076.4	210	Cgg/Tgg	5/13	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.28	2		534	679	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518431	69518431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	17	393	0	ENST00000294312.3:c.214C>T	p.Arg72Trp	p.R72W	ENST00000294312	NM_005117.2	72	Cgg/Tgg	1/3	1	2	FACETS	0.426	0.318	0.555	0.426	0.318	0.555	SUBCLONAL	1	TRUE	1	0.28	2		393	285	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845268	42845268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372563970	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	88	499	1	ENST00000398585.3:c.994G>A	p.Ala332Thr	p.A332T	ENST00000398585	NM_001135099.1	332	Gcc/Acc	9/14	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.28	2		500	588	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572092	64572093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767319284	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	92	748	2	ENST00000312049.6:c.1546dup	p.Arg516ProfsTer15	p.R516Pfs*15	ENST00000312049	NM_130799.2	516	cgg/cCgg	10/10	1	2	FACETS	0.971	0.863	1	0.971	0.863	1	CLONAL	1	TRUE	1	0.28	2		750	677	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1747235	1747235	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	44	495	0	ENST00000378609.4:c.163C>A	p.Leu55Met	p.L55M	ENST00000378609	NM_002074.3	55	Ctg/Atg	5/12	1	2	FACETS	0.485	0.406	0.573	0.485	0.406	0.573	SUBCLONAL	1	TRUE	1	0.28	2		495	648	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073607	8073608	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	39	615	0	ENST00000377482.5:c.1051_1052del	p.Ser351LeufsTer4	p.S351Lfs*4	ENST00000377482	NM_018948.3	351	AGc/c	4/4	1	2	FACETS	0.453	0.374	0.541	0.453	0.374	0.541	SUBCLONAL	1	TRUE	1	0.28	2		615	615	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074151	8074152	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CA	CA	-	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	83	661	0	ENST00000377482.5:c.507_508del	p.Cys169Ter	p.C169*	ENST00000377482	NM_018948.3	169	tgTGag/tgag	4/4	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.28	2		661	567	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257582	16257582	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	45	655	0	ENST00000375759.3:c.4847A>G	p.His1616Arg	p.H1616R	ENST00000375759	NM_015001.2	1616	cAt/cGt	11/15	1	2	FACETS	0.706	0.594	0.83	0.706	0.594	0.83	SUBCLONAL	1	TRUE	1	0.28	2		655	455	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262286	16262286	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	53	676	0	ENST00000375759.3:c.9551A>G	p.Tyr3184Cys	p.Y3184C	ENST00000375759	NM_015001.2	3184	tAc/tGc	11/15	1	2	FACETS	0.607	0.517	0.705	0.607	0.517	0.705	SUBCLONAL	1	TRUE	1	0.28	2		676	624	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273217	115273217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773033036	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	46	511	1	ENST00000438362.2:c.1241G>A	p.Arg414His	p.R414H	ENST00000438362	NM_001242891.1	414	cGt/cAt	11/20	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.28	2		512	306	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47599319	47599319	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	36	627	0	ENST00000430070.2:c.281T>C	p.Leu94Pro	p.L94P	ENST00000430070	NM_018095.4	94	cTg/cCg	2/4	1	2	FACETS	0.411	0.337	0.495	0.411	0.337	0.495	SUBCLONAL	1	TRUE	1	0.28	2		627	625	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102033248	102033248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867350713	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	95	611	0	ENST00000282441.5:c.634G>A	p.Val212Ile	p.V212I	ENST00000282441	NM_001130145.2	212	Gtc/Atc	3/9	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.28	2		611	678	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344815	118344815	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	63	634	0	ENST00000534358.1:c.2941C>A	p.Pro981Thr	p.P981T	ENST00000534358	NM_005933.3	981	Cca/Aca	3/36	1	2	FACETS	0.814	0.704	0.932	0.814	0.704	0.932	CLONAL	1	TRUE	1	0.28	2		634	553	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442797	442797	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	76	502	0	ENST00000399788.2:c.1509G>C	p.Trp503Cys	p.W503C	ENST00000399788	NM_001042603.1	503	tgG/tgC	12/28	1	2	FACETS	0.952	0.836	1	0.952	0.836	1	CLONAL	1	TRUE	1	0.28	2		502	570	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006418	12006418	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	46	587	1	ENST00000396373.4:c.391del	p.Ser131HisfsTer78	p.S131Hfs*78	ENST00000396373	NM_001987.4	129	cTt/ct	4/8	1	2	FACETS	0.656	0.552	0.77	0.656	0.552	0.77	SUBCLONAL	1	TRUE	1	0.28	2		588	501	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25362833	25362835	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	14	307	0	ENST00000311936.3:c.461_463del	p.Asp154del	p.D154del	ENST00000311936	NM_004985.3	154	gATGcc/gcc	5/5	1	2	FACETS	0.781	0.569	1	0.781	0.569	1	CLONAL	1	TRUE	1	0.28	2		307	128	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669575	88669575	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	70	399	0	ENST00000360948.2:c.1323del	p.Phe441LeufsTer12	p.F441Lfs*12	ENST00000360948	NM_001012338.2	441	ttT/tt	12/19	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.28	2		399	443	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865828	56865828	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	53	408	0	ENST00000308159.5:c.1160A>G	p.Lys387Arg	p.K387R	ENST00000308159	NM_014669.4	387	aAg/aGg	11/22	1	2	FACETS	0.713	0.608	0.828	0.713	0.608	0.828	SUBCLONAL	1	TRUE	1	0.28	2		408	531	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346707	89346707	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	87	732	1	ENST00000301030.4:c.6243del	p.Glu2082SerfsTer5	p.E2082Sfs*5	ENST00000301030	NM_001256183.1	2081	ccC/cc	9/13	1	2	FACETS	0.939	0.831	1	0.939	0.831	1	CLONAL	1	TRUE	1	0.28	2		733	662	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216962	7216962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	37	590	0	ENST00000380728.2:c.559G>A	p.Ala187Thr	p.A187T	ENST00000380728		187	Gcc/Acc	7/11	1	2	FACETS	0.44	0.362	0.528	0.44	0.362	0.528	SUBCLONAL	1	TRUE	1	0.28	2		590	601	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679917	33679917	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1399121008	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	40	635	0	ENST00000308377.4:c.2164T>C	p.Tyr722His	p.Y722H	ENST00000308377	NM_152270.3	722	Tat/Cat	5/5	1	2	FACETS	0.507	0.42	0.603	0.507	0.42	0.603	SUBCLONAL	1	TRUE	1	0.28	2		635	564	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510698	38510698	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1484574802	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	48	592	0	ENST00000254066.5:c.955del	p.Leu319TrpfsTer41	p.L319Wfs*41	ENST00000254066	NM_000964.3	318	Ccc/cc	7/9	1	2	FACETS	0.501	0.422	0.587	0.501	0.422	0.587	SUBCLONAL	1	TRUE	1	0.28	2		592	685	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533877	63533877	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	39	710	0	ENST00000307078.5:c.1277T>C	p.Leu426Pro	p.L426P	ENST00000307078	NM_004655.3	426	cTg/cCg	6/11	1	2	FACETS	0.457	0.378	0.546	0.457	0.378	0.546	SUBCLONAL	1	TRUE	1	0.28	2		710	609	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573655	48573655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	30	488	0	ENST00000342988.3:c.239G>A	p.Gly80Glu	p.G80E	ENST00000342988	NM_005359.5	80	gGg/gAg	2/12	1	2	FACETS	0.965	0.783	1	0.965	0.783	1	CLONAL	1	TRUE	1	0.28	2		488	222	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119324	3119324	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	41	627	0	ENST00000078429.4:c.856T>C	p.Ser286Pro	p.S286P	ENST00000078429	NM_002067.2	286	Tcg/Ccg	6/7	0.112618266625665	4	FACETS	0.531	0.441	0.632	0.265	0.22	0.316	INDETERMINATE	1	TRUE	2	0.28	4		627	706	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267760	7267760	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	37	533	0	ENST00000302850.5:c.248T>C	p.Met83Thr	p.M83T	ENST00000302850	NM_000208.2	83	aTg/aCg	2/22	0.112618266625665	4	FACETS	0.611	0.503	0.732	0.305	0.251	0.366	INDETERMINATE	1	TRUE	2	0.28	4		533	554	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098392	11098392	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	44	684	0	ENST00000358026.2:c.914del	p.Pro305ArgfsTer21	p.P305Rfs*21	ENST00000358026	NM_001128849.1	304	Ccc/cc	6/36	0.112618266625665	4	FACETS	0.566	0.473	0.669	0.283	0.236	0.335	INDETERMINATE	1	TRUE	2	0.28	4		684	711	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123788	11123788	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1064795105	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	79	438	0	ENST00000358026.2:c.2438C>T	p.Ser813Leu	p.S813L	ENST00000358026	NM_001128849.1	813	tCa/tTa	16/36	0.112618266625665	4	FACETS	1	0.959	1	0.605	0.532	0.683	INDETERMINATE	1	TRUE	2	0.28	4		438	597	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753144	42753144	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	105	889	0	ENST00000222329.4:c.1120C>A	p.Pro374Thr	p.P374T	ENST00000222329	NM_006494.2	374	Cca/Aca	4/4	0.112618266625665	4	FACETS	1	0.929	1	0.525	0.469	0.584	INDETERMINATE	1	TRUE	2	0.28	4		889	915	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867040	45867040	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	37	596	0	ENST00000391945.4:c.1079G>A	p.Gly360Asp	p.G360D	ENST00000391945	NM_000400.3	360	gGc/gAc	11/23	0.112618266625665	4	FACETS	0.53	0.436	0.636	0.265	0.218	0.318	INDETERMINATE	1	TRUE	2	0.28	4		596	638	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464577	25464577	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	38	499	0	ENST00000264709.3:c.1937-1G>T		p.X646_splice	ENST00000264709	NM_175629.2	646			0.203090401250928	2	FACETS	0.404	0.333	0.484	0.202	0.166	0.242	SUBCLONAL	1	TRUE	0	0.28	2		499	672	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966390	25966390	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	35	576	0	ENST00000435504.4:c.2816C>G	p.Thr939Ser	p.T939S	ENST00000435504		939	aCt/aGt	13/13	0.203090401250928	2	FACETS	0.46	0.376	0.554	0.23	0.188	0.277	SUBCLONAL	1	TRUE	0	0.28	2		576	544	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583344	46583344	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1181746327	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	46	516	0	ENST00000263734.3:c.272A>G	p.Tyr91Cys	p.Y91C	ENST00000263734	NM_001430.4	91	tAc/tGc	3/16	0.203090401250928	2	FACETS	0.533	0.448	0.628	0.267	0.224	0.314	SUBCLONAL	1	TRUE	0	0.28	2		516	616	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656887	47656887	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	50	255	0	ENST00000233146.2:c.1085del	p.Leu362Ter	p.L362*	ENST00000233146	NM_000251.2	361	aaT/aa	7/16	0.203090401250928	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	2	TRUE	0	0.28	2		255	166	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656963	47656967	+	frameshift_variant	Frame_Shift_Del	DEL	CTTAA	CTTAA	-	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	20	340	0	ENST00000233146.2:c.1160_1164del	p.Leu387ProfsTer28	p.L387Pfs*28	ENST00000233146	NM_000251.2	387	CTTAAc/c	7/16	0.203090401250928	2	FACETS	0.523	0.4	0.667	0.262	0.2	0.334	SUBCLONAL	1	TRUE	0	0.28	2		340	273	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346763	225346763	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	14	383	0	ENST00000264414.4:c.1875A>C	p.Arg625Ser	p.R625S	ENST00000264414	NM_003590.4	625	agA/agC	14/16	0.299152815452936	2	FACETS	0.5	0.362	0.666	0.25	0.181	0.333	SUBCLONAL	1	TRUE	0	0.28	2		383	200	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63898291	63898291	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	33	567	0	ENST00000398590.3:c.17C>T	p.Ala6Val	p.A6V	ENST00000398590	NM_001177387.1	6	gCg/gTg	3/14	1	2	FACETS	0.392	0.318	0.475	0.392	0.318	0.475	SUBCLONAL	1	TRUE	1	0.28	2		567	602	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749527	41749527	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs528408156	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	41	439	0	ENST00000226382.2:c.268G>T	p.Gly90Cys	p.G90C	ENST00000226382	NM_003924.3	90	Ggc/Tgc	2/3	1	2	FACETS	0.538	0.448	0.639	0.538	0.448	0.639	SUBCLONAL	1	TRUE	1	0.28	2		439	544	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796517	57796517	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	21	515	0	ENST00000309042.7:c.1493A>G	p.Glu498Gly	p.E498G	ENST00000309042	NM_005612.4	498	gAg/gGg	4/4	1	2	FACETS	0.595	0.459	0.753	0.595	0.459	0.753	SUBCLONAL	1	TRUE	1	0.28	2		515	252	SUCCESS
ALB	213	MSKCC	GRCh37	4	74283352	74283352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1216671531	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	38	360	0	ENST00000295897.4:c.1394C>T	p.Pro465Leu	p.P465L	ENST00000295897	NM_000477.5	465	cCt/cTt	11/15	1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	1	0.28	2		360	266	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176719055	176719055	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	39	557	0	ENST00000439151.2:c.6359A>C	p.Glu2120Ala	p.E2120A	ENST00000439151	NM_022455.4	2120	gAg/gCg	22/23	1	2	FACETS	0.372	0.307	0.445	0.372	0.307	0.445	SUBCLONAL	1	TRUE	1	0.28	2		557	749	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040011	180040011	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	91	646	0	ENST00000261937.6:c.3431T>C	p.Ile1144Thr	p.I1144T	ENST00000261937	NM_182925.4	1144	aTa/aCa	25/30	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.28	2		646	593	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877199	151877199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	50	469	1	ENST00000262189.6:c.7162C>T	p.Arg2388Cys	p.R2388C	ENST00000262189	NM_170606.2	2388	Cgt/Tgt	37/59	1	2	FACETS	0.682	0.578	0.795	0.682	0.578	0.795	SUBCLONAL	1	TRUE	1	0.28	2		470	524	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2123720	2123720	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	64	455	0	ENST00000349721.2:c.3764G>A	p.Arg1255Gln	p.R1255Q	ENST00000349721	NM_003070.3	1255	cGg/cAg	27/34	1	2	FACETS	0.825	0.715	0.944	0.825	0.715	0.944	CLONAL	1	TRUE	1	0.28	2		455	554	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815581	139815581	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	39	671	1	ENST00000247668.2:c.1052A>G	p.Asp351Gly	p.D351G	ENST00000247668	NM_021138.3	351	gAt/gGt	9/11	1	2	FACETS	0.427	0.353	0.51	0.427	0.353	0.51	SUBCLONAL	1	TRUE	1	0.28	2		672	652	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345219	70345219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	84	556	1	ENST00000374080.3:c.2245G>A	p.Glu749Lys	p.E749K	ENST00000374080		749	Gag/Aag	16/45	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.28	2		557	581	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0063403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	144	204	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.4451285832973	3	FACETS	0.774	0.714	0.836	0.774	0.714	0.836	SUBCLONAL	2	TRUE	1	0.611730665370843	3		204	397	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0063403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	1906	851	1	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.611730665370843	10	FACETS	0.977	0.962	0.992	0.977	0.962	0.992	CLONAL	8	TRUE	2	0.611730665370843	10		852	2748	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0063403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	1681	828	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.611730665370843	10	FACETS	0.964	0.948	0.98	0.964	0.948	0.98	CLONAL	8	TRUE	2	0.611730665370843	10		828	2456	SUCCESS
APC	324	MSKCC	GRCh37	5	112175606	112175606	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	403	626	0	ENST00000257430.4:c.4316del	p.Pro1439LeufsTer34	p.P1439Lfs*34	ENST00000257430	NM_000038.5	1439	Cct/ct	16/16	0.508618465855225	3	FACETS	1	0.993	1	0.775	0.744	0.806	CLONAL	2	TRUE	0	0.611730665370843	3		626	740	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0063403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	300	580	0	ENST00000269305.4:c.376-1G>C		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.477844643051148	2	FACETS	0.812	0.772	0.852	0.812	0.772	0.852	CLONAL	2	TRUE	0	0.611730665370843	2		580	604	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488249	56488249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	187	592	0	ENST00000267101.3:c.1768C>T	p.Pro590Ser	p.P590S	ENST00000267101	NM_001982.3	590	Ccc/Tcc	15/28	0.4451285832973	3	FACETS	0.971	0.899	1	0.486	0.449	0.524	CLONAL	1	TRUE	1	0.611730665370843	3		592	822	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467916	50467916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1372604802	NA	P-0063403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	182	633	0	ENST00000331340.3:c.1151C>T	p.Ser384Leu	p.S384L	ENST00000331340	NM_006060.4	384	tCg/tTg	8/8	0.4451285832973	3	FACETS	0.948	0.876	1	0.474	0.438	0.511	CLONAL	1	TRUE	1	0.611730665370843	3		633	820	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372146	55372146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	484	770	2	ENST00000297316.4:c.836C>T	p.Ala279Val	p.A279V	ENST00000297316	NM_022454.3	279	gCg/gTg	2/2	0.530825526952102	4	FACETS	0.874	0.84	0.907	0.874	0.84	0.907	CLONAL	3	TRUE	1	0.611730665370843	4		772	973	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052603	42052603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	294	746	0	ENST00000219905.7:c.7274G>A	p.Arg2425His	p.R2425H	ENST00000219905	NM_001164273.1	2425	cGc/cAc	20/24	0.508155986958357	3	FACETS	0.803	0.759	0.847	0.803	0.759	0.847	CLONAL	2	TRUE	1	0.611730665370843	3		746	782	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526574	31526574	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	159	454	0	ENST00000344624.3:c.466C>G	p.Pro156Ala	p.P156A	ENST00000344624		156	Ccc/Gcc	2/33	0.443927755361323	4	FACETS	1	0.978	1	0.592	0.544	0.642	CLONAL	1	TRUE	2	0.611730665370843	4		454	708	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593604	55593609	+	inframe_deletion	In_Frame_Del	DEL	GGAAGG	GGAAGG	-	novel	NA	P-0063404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	358	455	0	ENST00000288135.5:c.1670_1675del	p.Trp557_Val559delinsPhe	p.W557_V559delinsF	ENST00000288135	NM_000222.2	557	tGGAAGGtt/ttt	11/21	0.742902759916798	3	FACETS	0.97	0.941	0.998	0.97	0.941	0.998	CLONAL	3	FALSE	0	0.742902759916798	3		455	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577063	7577085	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTTGCGGAGATTCTCTTCCTC	TTCTTGCGGAGATTCTCTTCCTC	-	novel	NA	P-0063405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	237	640	0	ENST00000269305.4:c.853_875del	p.Glu285ArgfsTer13	p.E285Rfs*13	ENST00000269305	NM_001126112.2	285	GAGGAAGAGAATCTCCGCAAGAAa/a	8/11	0.539181315160091	1	FACETS	0.996	0.939	1	0.996	0.939	1	CLONAL	1	TRUE	0	0.622189827652027	1		640	527	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306553	41306553	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	159	408	0	ENST00000373198.4:c.1106G>T	p.Gly369Val	p.G369V	ENST00000373198	NM_133170.3	369	gGt/gTt	7/32	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.622189827652027	2		408	511	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813074	76813074	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	126	370	0	ENST00000373344.5:c.6547C>T	p.Gln2183Ter	p.Q2183*	ENST00000373344	NM_000489.3	2183	Cag/Tag	30/35	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.622189827652027	2		370	370	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0063407-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	285	462	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.481730216197823	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	4	TRUE	0	0.490038426125271	4		462	425	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0063407-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	96	279	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.479436922897305	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	1	0.490038426125271	3		279	228	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063407-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	91	543	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	1	2	FACETS	0.756	0.674	0.844	0.756	0.674	0.844	SUBCLONAL	1	TRUE	1	0.490038426125271	2		543	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578509	7578509	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519978	NA	P-0063407-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	287	721	0	ENST00000269305.4:c.421T>G	p.Cys141Gly	p.C141G	ENST00000269305	NM_001126112.2	141	Tgc/Ggc	5/11	0.490038426125271	2	FACETS	0.973	0.924	1	0.973	0.924	1	CLONAL	2	TRUE	0	0.490038426125271	2		721	602	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55130023	55130023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063407-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	124	664	0	ENST00000257290.5:c.557C>T	p.Pro186Leu	p.P186L	ENST00000257290	NM_006206.4	186	cCc/cTc	4/23	0.378125074539255	3	FACETS	1	0.929	1	0.514	0.466	0.564	CLONAL	1	TRUE	1	0.490038426125271	3		664	613	SUCCESS
APC	324	MSKCC	GRCh37	5	112170787	112170788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs863224817	NA	P-0063407-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	142	516	0	ENST00000257430.4:c.1886dup	p.Leu629PhefsTer5	p.L629Ffs*5	ENST00000257430	NM_000038.5	628	act/acTt	15/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.490038426125271	2		516	504	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0063408-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	142	488	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.512956931784239	2		488	525	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0063408-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	170	522	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	0.512956931784239	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.512956931784239	1		522	459	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226066	53226066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556837402	NA	P-0063408-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	189	590	0	ENST00000375401.3:c.2783C>T	p.Ala928Val	p.A928V	ENST00000375401	NM_004187.3	928	gCg/gTg	19/26	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.512956931784239	2		590	709	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063408-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	126	439	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.813	0.739	0.891	0.813	0.739	0.891	CLONAL	1	TRUE	1	0.512956931784239	2		439	604	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0063408-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	84	446	1	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.512956931784239	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.512956931784239	2		447	146	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579314	7579322	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TGCAAGTCA	TGCAAGTCA	-	novel	NA	P-0063408-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	214	467	0	ENST00000269305.4:c.365_373del	p.Val122_Thr125delinsAla	p.V122_T125delinsA	ENST00000269305	NM_001126112.2	122	gTGACTTGCAcg/gcg	4/11	0.512956931784239	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.512956931784239	1		467	510	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117939	70117939	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063408-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	351	586	0	ENST00000245479.2:c.407G>C	p.Ser136Thr	p.S136T	ENST00000245479	NM_000346.3	136	aGc/aCc	1/3	0.512956931784239	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.512956931784239	2		586	621	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629703	187629703	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs756850240	NA	P-0063408-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	148	496	1	ENST00000441802.2:c.1279A>G	p.Lys427Glu	p.K427E	ENST00000441802	NM_005245.3	427	Aaa/Gaa	2/27	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.512956931784239	2		497	556	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104588	69104588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143014630	NA	P-0063408-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	124	409	0	ENST00000288368.4:c.4432G>A	p.Ala1478Thr	p.A1478T	ENST00000288368	NM_024870.2	1478	Gct/Act	37/40	0.512956931784239	3	FACETS	0.923	0.837	1	0.462	0.418	0.507	CLONAL	1	TRUE	1	0.512956931784239	3		409	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0063409-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	119	801	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.20916986923412	2		804	780	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0063409-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	34	851	1	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.364	0.296	0.441	0.364	0.296	0.441	SUBCLONAL	1	TRUE	1	0.20916986923412	2		852	893	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0063409-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	54	448	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	0.20916986923412	3	FACETS	1	0.885	1	0.521	0.445	0.605	CLONAL	1	TRUE	1	0.20916986923412	3		448	547	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835596	68835596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587783047	NA	P-0063409-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	110	538	1	ENST00000261769.5:c.187C>T	p.Arg63Ter	p.R63*	ENST00000261769	NM_004360.3	63	Cga/Tga	3/16	0.157885697115165	2	FACETS	0.804	0.724	0.889	0.804	0.724	0.889	CLONAL	2	TRUE	0	0.20916986923412	2		539	654	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440741	56440741	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063409-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	149	748	1	ENST00000407977.2:c.477G>A	p.Trp159Ter	p.W159*	ENST00000407977		159	tgG/tgA	5/10	1	2	FACETS	0.877	0.802	0.956	1	0.99	1	CLONAL	2	TRUE	1	0.20916986923412	2		749	812	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442723	442723	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063409-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	88	552	0	ENST00000399788.2:c.1583C>A	p.Ser528Tyr	p.S528Y	ENST00000399788	NM_001042603.1	528	tCc/tAc	12/28	0.0683861688403695	4	FACETS	1	0.961	1	0.602	0.533	0.677	INDETERMINATE	1	TRUE	2	0.20916986923412	4		552	845	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713506	30713506	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs886038794	NA	P-0063409-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	77	648	0	ENST00000295754.5:c.831G>T	p.Lys277Asn	p.K277N	ENST00000295754	NM_003242.5	277	aaG/aaT	4/7	1	2	FACETS	0.934	0.819	1	0.934	0.819	1	CLONAL	1	TRUE	1	0.20916986923412	2		648	788	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169122	32169122	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063409-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	58	683	0	ENST00000375023.3:c.3911G>T	p.Ser1304Ile	p.S1304I	ENST00000375023	NM_004557.3	1304	aGc/aTc	22/30	1	2	FACETS	0.838	0.719	0.967	0.838	0.719	0.967	CLONAL	1	TRUE	1	0.20916986923412	2		683	662	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0063423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	8	556	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.135689087222995	4	FACETS	0.201	0.128	0.295	0.1	0.064	0.148	INDETERMINATE	1	TRUE	2	0.329091512234068	4		556	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0063423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	85	513	0	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.159678327606687	2	FACETS	1	0.97	1	0.636	0.565	0.711	INDETERMINATE	1	TRUE	0	0.329091512234068	2		513	406	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696453	47696453	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	42	415	0	ENST00000347630.2:c.370A>G	p.Arg124Gly	p.R124G	ENST00000347630	NM_001007230.1	124	Agg/Ggg	6/11	1	2	FACETS	0.445	0.371	0.528	0.445	0.371	0.528	SUBCLONAL	1	TRUE	1	0.329091512234068	2		415	573	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435948	116435948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	71	426	0	ENST00000397752.3:c.3943G>A	p.Val1315Ile	p.V1315I	ENST00000397752	NM_000245.2	1315	Gta/Ata	21/21	0.190097364723789	2	FACETS	0.985	0.863	1	0.493	0.431	0.558	INDETERMINATE	1	TRUE	0	0.329091512234068	2		426	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0063527-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	488	785	4	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	0.800422007521929	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.800422007521929	1		789	689	SUCCESS
APC	324	MSKCC	GRCh37	5	112175746	112175746	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063527-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	352	631	0	ENST00000257430.4:c.4455del	p.Asp1486IlefsTer21	p.D1486Ifs*21	ENST00000257430	NM_000038.5	1485	gcT/gc	16/16	0.800422007521929	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.800422007521929	1		631	526	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045869	26045869	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063527-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	581	889	0	ENST00000540144.1:c.231G>C	p.Gln77His	p.Q77H	ENST00000540144	NM_003531.2	77	caG/caC	1/1	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.800422007521929	2		889	1374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578491	7578491	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1567553924	NA	P-0063528-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	67	762	0	ENST00000269305.4:c.439del	p.Val147LeufsTer23	p.V147Lfs*23	ENST00000269305	NM_001126112.2	147	Gtt/tt	5/11	1	2	FACETS	0.398	0.344	0.456	0.398	0.344	0.456	SUBCLONAL	1	TRUE	1	0.349645434827128	2		762	964	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971066	21971100	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGCACCACCAGCGTGTCCAGGAAGCCCTCCCGG	GCAGCACCACCAGCGTGTCCAGGAAGCCCTCCCGG	-	novel	NA	P-0063528-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	23	0	0	ENST00000304494.5:c.258_292del	p.Arg87ProfsTer21	p.R87Pfs*21	ENST00000304494	NM_000077.4	86	gcCCGGGAGGGCTTCCTGGACACGCTGGTGGTGCTGCac/gcac	2/3	1	2	FACETS	0.175	0.135	0.221	0.175	0.135	0.221	SUBCLONAL	1	TRUE	1	0.349645434827128	2		0	753	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0063528-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	115	387	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.349645434827128	3	FACETS	1	0.981	1	0.69	0.624	0.76	CLONAL	1	TRUE	1	0.349645434827128	3		387	560	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784210	43784210	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs767062977	NA	P-0063528-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	18	0	0	ENST00000382044.4:c.276C>A	p.Asn92Lys	p.N92K	ENST00000382044	NM_001141980.1	92	aaC/aaA	3/28	1	2	FACETS	0.145	0.108	0.189	0.145	0.108	0.189	SUBCLONAL	1	TRUE	1	0.349645434827128	2		0	709	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778422	3778424	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	rs754267405	NA	P-0063528-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	32	0	0	ENST00000262367.5:c.6624_6626del	p.Gln2216del	p.Q2216del	ENST00000262367	NM_004380.2	2208	caACAg/cag	31/31	1	2	FACETS	0.173	0.139	0.212	0.173	0.139	0.212	SUBCLONAL	1	TRUE	1	0.349645434827128	2		0	1057	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264425	30264426	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCT	rs774288551	NA	P-0063528-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	22	0	0	ENST00000322652.5:c.175_177dup	p.Ser59dup	p.S59dup	ENST00000322652	NM_015355.2	59	gcc/gCCTcc	1/16	1	2	FACETS	0.118	0.09	0.15	0.118	0.09	0.15	SUBCLONAL	1	TRUE	1	0.349645434827128	2		0	1067	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577112	7577113	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACAAACACGCACCTCAA	novel	NA	P-0063529-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	94	523	0	ENST00000269305.4:c.809_825dup	p.Ala276LeufsTer75	p.A276Lfs*75	ENST00000269305	NM_001126112.2	275	-/TTGAGGTGCGTGTTTGT	8/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.205229680017253	2		523	775	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1696718	1696718	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	297	592	0	ENST00000378625.1:c.128A>G	p.Lys43Arg	p.K43R	ENST00000378625	NM_001198994.1	43	aAg/aGg	2/14	0.433298342890756	5	FACETS	0.883	0.83	0.937	0.353	0.332	0.375	CLONAL	2	TRUE	0	0.433298342890756	5		592	1281	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303751	65303751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	336	450	0	ENST00000342505.4:c.3004C>T	p.Arg1002Trp	p.R1002W	ENST00000342505	NM_002227.2	1002	Cgg/Tgg	22/25	0.392697805883794	3	FACETS	0.924	0.881	0.966	0.924	0.881	0.966	CLONAL	3	TRUE	0	0.433298342890756	3		450	681	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	324	519	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	0.392697805883794	3	FACETS	1	0.99	1	0.775	0.735	0.814	CLONAL	2	TRUE	0	0.433298342890756	3		520	783	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050355	176050355	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	249	411	0	ENST00000367669.3:c.1210T>C	p.Ser404Pro	p.S404P	ENST00000367669	NM_022457.5	404	Tca/Cca	11/20	0.392697805883794	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.433298342890756	3		411	415	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665764	241665764	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	282	395	0	ENST00000366560.3:c.1215G>T	p.Leu405Phe	p.L405F	ENST00000366560	NM_000143.3	405	ttG/ttT	8/10	0.392697805883794	3	FACETS	0.939	0.892	0.986	0.939	0.892	0.986	CLONAL	3	TRUE	0	0.433298342890756	3		395	562	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653814	89653814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780004	NA	P-0063532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	105	302	0	ENST00000371953.3:c.112C>T	p.Pro38Ser	p.P38S	ENST00000371953	NM_000314.4	38	Cct/Tct	2/9	0.392697805883794	3	FACETS	1	0.947	1	1	0.947	1	CLONAL	3	TRUE	0	0.433298342890756	3		302	190	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144723	119144723	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs376182596	NA	P-0063532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	242	457	0	ENST00000264033.4:c.736C>T	p.Arg246Ter	p.R246*	ENST00000264033	NM_005188.3	246	Cga/Tga	4/16	0.392697805883794	3	FACETS	0.913	0.863	0.963	0.913	0.863	0.963	CLONAL	3	TRUE	0	0.433298342890756	3		457	496	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431665	431665	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs754467075	NA	P-0063532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	313	418	0	ENST00000399788.2:c.2344C>T	p.Arg782Ter	p.R782*	ENST00000399788	NM_001042603.1	782	Cga/Tga	17/28	0.392697805883794	3	FACETS	0.959	0.914	1	0.959	0.914	1	CLONAL	3	TRUE	0	0.433298342890756	3		418	611	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439846	49439846	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0063532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	402	622	1	ENST00000301067.7:c.4693+2T>C		p.X1565_splice	ENST00000301067	NM_003482.3	1565			0.392697805883794	3	FACETS	0.865	0.827	0.903	0.865	0.827	0.903	CLONAL	3	TRUE	0	0.433298342890756	3		623	870	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123889615	123889615	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	295	366	0	ENST00000330479.4:c.842C>A	p.Thr281Asn	p.T281N	ENST00000330479	NM_020382.3	281	aCc/aAc	7/9	0.392697805883794	3	FACETS	0.914	0.869	0.96	0.914	0.869	0.96	CLONAL	3	TRUE	0	0.433298342890756	3		366	604	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919213	48919214	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TA	TA	-	novel	NA	P-0063532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	39	209	0	ENST00000267163.4:c.381-3_381-2del		p.X127_splice	ENST00000267163	NM_000321.2	127			0.433298342890756	1	FACETS	0.783	0.673	0.896	1	0.965	1	SUBCLONAL	2	TRUE	0	0.433298342890756	1		209	90	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543201	65543201	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	364	483	0	ENST00000358664.4:c.476C>G	p.Ala159Gly	p.A159G	ENST00000358664	NM_002382.4	159	gCc/gGc	5/5	0.406305593780016	3	FACETS	0.948	0.906	0.989	0.948	0.906	0.989	CLONAL	3	TRUE	0	0.433298342890756	3		483	719	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988382	41988382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774833703	NA	P-0063532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	53	470	0	ENST00000219905.7:c.1174G>A	p.Glu392Lys	p.E392K	ENST00000219905	NM_001164273.1	392	Gaa/Aaa	3/24	0.373708181105524	3	FACETS	0.436	0.371	0.507	0.145	0.123	0.169	SUBCLONAL	1	TRUE	0	0.433298342890756	3		470	683	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119757	17119757	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	381	633	0	ENST00000285071.4:c.1237T>C	p.Tyr413His	p.Y413H	ENST00000285071	NM_144997.5	413	Tat/Cat	11/14	0.433298342890756	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.433298342890756	2		633	820	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657383	29657384	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0063532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	35	481	0	ENST00000356175.3:c.5619_5620del	p.Glu1873AspfsTer18	p.E1873Dfs*18	ENST00000356175	NM_000267.3	1872	ctAGag/ctag	38/57	0.433298342890756	2	FACETS	0.312	0.255	0.376	0.156	0.127	0.188	SUBCLONAL	1	TRUE	0	0.433298342890756	2		481	518	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78797007	78797007	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	561	554	0	ENST00000306801.3:c.1120T>C	p.Tyr374His	p.Y374H	ENST00000306801	NM_020761.2	374	Tac/Cac	9/34	0.433298342890756	4	FACETS	0.934	0.903	0.965	0.934	0.903	0.965	CLONAL	4	TRUE	0	0.433298342890756	4		554	993	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798218	42798218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568528562	NA	P-0063532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	419	779	0	ENST00000575354.2:c.4172G>A	p.Arg1391His	p.R1391H	ENST00000575354	NM_015125.3	1391	cGc/cAc	17/20	0.392697805883794	3	FACETS	1	0.993	1	0.804	0.769	0.84	CLONAL	2	TRUE	0	0.433298342890756	3		779	975	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026324	48026324	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	337	524	1	ENST00000234420.5:c.1202A>T	p.Asp401Val	p.D401V	ENST00000234420	NM_000179.2	401	gAt/gTt	4/10	0.371834326987002	3	FACETS	0.892	0.85	0.934	0.892	0.85	0.934	CLONAL	3	TRUE	0	0.433298342890756	3		525	707	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0063532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	449	554	10	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	0.371834326987002	3	FACETS	1	0.994	1	0.821	0.786	0.856	CLONAL	2	TRUE	0	0.433298342890756	3		564	1024	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21304060	21304060	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	439	481	0	ENST00000354336.3:c.839A>G	p.Asn280Ser	p.N280S	ENST00000354336	NM_005207.3	280	aAc/aGc	3/3	0.433298342890756	7	FACETS	0.907	0.864	0.951	0.389	0.37	0.408	CLONAL	3	TRUE	0	0.433298342890756	7		481	1551	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513352	41513352	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	52	584	1	ENST00000263253.7:c.256C>T	p.Arg86Ter	p.R86*	ENST00000263253	NM_001429.3	86	Cga/Tga	2/31	0.373708181105524	3	FACETS	0.401	0.341	0.468	0.134	0.113	0.156	SUBCLONAL	1	TRUE	0	0.433298342890756	3		585	728	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960081	134960081	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	472	598	0	ENST00000398015.3:c.2438T>C	p.Val813Ala	p.V813A	ENST00000398015	NM_004441.4	813	gTc/gCc	13/16	0.433298342890756	3	FACETS	0.97	0.933	1	0.97	0.933	1	CLONAL	3	TRUE	0	0.433298342890756	3		598	911	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515435	149515435	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	296	549	0	ENST00000261799.4:c.47T>C	p.Leu16Pro	p.L16P	ENST00000261799	NM_002609.3	16	cTg/cCg	3/23	0.373708181105524	3	FACETS	1	0.991	1	0.809	0.767	0.851	CLONAL	2	TRUE	0	0.433298342890756	3		549	685	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566297	141566297	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	298	580	1	ENST00000220592.5:c.1115C>T	p.Ala372Val	p.A372V	ENST00000220592	NM_012154.3	372	gCg/gTg	9/19	0.167621976581176	6	FACETS	0.834	0.786	0.883	0.834	0.786	0.883	INDETERMINATE	3	TRUE	3	0.433298342890756	6		581	1026	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248123	110248123	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	322	484	0	ENST00000374672.4:c.1349A>G	p.His450Arg	p.H450R	ENST00000374672	NM_004235.4	450	cAc/cGc	5/5	0.373708181105524	3	FACETS	1	0.989	1	0.768	0.729	0.807	CLONAL	2	TRUE	0	0.433298342890756	3		484	785	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0063533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	67	462	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.979	0.855	1	0.979	0.855	1	CLONAL	1	FALSE	1	0.35566682394498	2		462	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579472	7579473	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	C	novel	NA	P-0063533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	129	867	0	ENST00000269305.4:c.214_215delinsG	p.Pro72AlafsTer51	p.P72Afs*51	ENST00000269305	NM_001126112.2	72	CCc/Gc	4/11	0.35566682394498	1	FACETS	0.831	0.754	0.911	0.831	0.754	0.911	CLONAL	1	FALSE	0	0.35566682394498	1		867	718	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0063533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	61	502	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.294455231655252	0	FACETS	0.391	0.337	0.45			1	SUBCLONAL	1	FALSE	0	0.35566682394498	0		502	565	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971106	21971123	+	inframe_deletion	In_Frame_Del	DEL	GTCGTGCACGGGTCGGGT	GTCGTGCACGGGTCGGGT	-	novel	NA	P-0063533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	30	666	0	ENST00000304494.5:c.235_252del	p.Thr79_Asp84del	p.T79_D84del	ENST00000304494	NM_000077.4	79	ACCCGACCCGTGCACGAC/-	2/3	0.35566682394498	1	FACETS	0.281	0.226	0.344	0.281	0.226	0.344	SUBCLONAL	1	FALSE	0	0.35566682394498	1		666	494	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0063541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	266	698	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.217502229467596	6	FACETS	0.913	0.86	0.967	0.913	0.86	0.967	CLONAL	5	TRUE	1	0.217502229467596	6		698	769	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576857	7576857	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063541-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	115	684	0	ENST00000269305.4:c.989T>G	p.Leu330Arg	p.L330R	ENST00000269305	NM_001126112.2	330	cTt/cGt	9/11	0.182748157422953	2	FACETS	0.838	0.756	0.924	0.838	0.756	0.924	CLONAL	2	TRUE	0	0.217502229467596	2		684	631	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16248742	16248742	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0063578-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	92	371	0	ENST00000375759.3:c.1750-2A>G		p.X584_splice	ENST00000375759	NM_015001.2	584			0.187689204147311	2	FACETS	1	0.931	1	1	0.931	1	INDETERMINATE	2	TRUE	0	0.324963922863422	2		371	272	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491681	120491681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063578-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	67	568	0	ENST00000256646.2:c.2548G>A	p.Glu850Lys	p.E850K	ENST00000256646	NM_024408.3	850	Gag/Aag	16/34	0.324963922863422	3	FACETS	0.893	0.777	1	0.446	0.388	0.509	CLONAL	1	TRUE	1	0.324963922863422	3		568	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0063578-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	159	809	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.322887907200662	2	FACETS	0.943	0.87	1	0.943	0.87	1	CLONAL	2	TRUE	0	0.324963922863422	2		809	519	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47607000	47607000	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0063578-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	93	515	0	ENST00000263735.4:c.750T>G	p.Tyr250Ter	p.Y250*	ENST00000263735	NM_002354.2	250	taT/taG	7/9	0.324963922863422	5	FACETS	1	0.976	1	0.341	0.303	0.381	CLONAL	1	TRUE	1	0.324963922863422	5		515	625	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0063578-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	46	556	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.324963922863422	3	FACETS	0.974	0.834	1	0.974	0.834	1	CLONAL	2	TRUE	1	0.324963922863422	3		556	169	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0063579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	198	539	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	0.384036233019381	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.384036233019381	1		539	650	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552783	18552783	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0063579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	38	559	0	ENST00000266497.5:c.2192+2T>A		p.X731_splice	ENST00000266497		731			0.365614607778996	1	FACETS	0.302	0.249	0.361	0.302	0.249	0.361	SUBCLONAL	1	TRUE	0	0.384036233019381	1		559	530	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439373	149439373	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	213	689	0	ENST00000286301.3:c.2022T>G	p.Phe674Leu	p.F674L	ENST00000286301	NM_005211.3	674	ttT/ttG	15/22	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.384036233019381	2		689	924	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139440192	139440192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	235	1039	0	ENST00000277541.6:c.47C>T	p.Ala16Val	p.A16V	ENST00000277541	NM_017617.3	16	gCg/gTg	1/34	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.384036233019381	2		1039	1089	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279605	123279605	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063580-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	471	810	0	ENST00000358487.5:c.827T>G	p.Phe276Cys	p.F276C	ENST00000358487	NM_000141.4	276	tTt/tGt	7/18	0.30033618271194	1	FACETS	0.775	0.742	0.809	0.775	0.742	0.809	INDETERMINATE	1	TRUE	0	0.668860959333017	1		810	1209	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	95	556	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.875	0.788	0.965	0.875	0.788	0.965	CLONAL	1	TRUE	1	0.689515120744271	2		556	315	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778972	9778972	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1214315014	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	302	576	0	ENST00000377346.4:c.1241C>T	p.Ala414Val	p.A414V	ENST00000377346	NM_005026.3	414	gCg/gTg	9/24	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.689515120744271	2		576	845	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023827	27023827	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1033394068	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	342	613	0	ENST00000324856.7:c.933C>G	p.Tyr311Ter	p.Y311*	ENST00000324856	NM_006015.4	311	taC/taG	1/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.689515120744271	2		613	973	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058500	72058500	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1428865181	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	269	535	0	ENST00000357731.5:c.940C>T	p.Pro314Ser	p.P314S	ENST00000357731	NM_173808.2	314	Cct/Tct	6/7	1	2	FACETS	0.956	0.9	1	0.956	0.9	1	CLONAL	1	TRUE	1	0.689515120744271	2		535	816	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733513	85733513	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs387906350	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	308	609	5	ENST00000370580.1:c.499del	p.Ser167LeufsTer6	p.S167Lfs*6	ENST00000370580	NM_003921.4	167	Tct/ct	3/3	1	2	FACETS	0.869	0.82	0.919	0.869	0.82	0.919	CLONAL	1	TRUE	1	0.689515120744271	2		614	1028	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161310401	161310401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760572684	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	249	425	0	ENST00000367975.2:c.197C>T	p.Ala66Val	p.A66V	ENST00000367975	NM_003001.3	66	gCg/gTg	4/6	1	2	FACETS	0.96	0.902	1	0.96	0.902	1	CLONAL	1	TRUE	1	0.689515120744271	2		425	752	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692888	89692889	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	179	277	0	ENST00000371953.3:c.375dup	p.Ala126SerfsTer54	p.A126Sfs*54	ENST00000371953	NM_000314.4	124	-/A	5/9	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.689515120744271	2		277	512	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	45	117	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.64	0.544	0.743	0.64	0.544	0.743	SUBCLONAL	1	TRUE	1	0.689515120744271	2		117	204	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900984	114900984	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778855667	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	367	632	1	ENST00000543371.1:c.598del	p.Leu200SerfsTer25	p.L200Sfs*25	ENST00000543371	NM_001198531.1	198	caC/ca	6/14	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.689515120744271	2		633	1049	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456749	32456749	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	274	638	0	ENST00000332351.3:c.143C>T	p.Ala48Val	p.A48V	ENST00000332351	NM_024426.4	48	gCc/gTc	1/10	1	2	FACETS	0.981	0.924	1	0.981	0.924	1	CLONAL	1	TRUE	1	0.689515120744271	2		638	810	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456802	32456802	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1056503917	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	256	548	0	ENST00000332351.3:c.90G>T	p.Gln30His	p.Q30H	ENST00000332351	NM_024426.4	30	caG/caT	1/10	1	2	FACETS	0.999	0.94	1	0.999	0.94	1	CLONAL	1	TRUE	1	0.689515120744271	2		548	743	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202543	67202543	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	358	743	0	ENST00000312629.5:c.1352T>C	p.Leu451Pro	p.L451P	ENST00000312629	NM_003952.2	451	cTg/cCg	15/15	1	2	FACETS	0.888	0.841	0.934	0.888	0.841	0.934	CLONAL	1	TRUE	1	0.689515120744271	2		743	1170	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	362	709	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.895	0.849	0.942	0.895	0.849	0.942	CLONAL	1	TRUE	1	0.689515120744271	2		710	1173	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111959690	111959690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200255724	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	172	267	0	ENST00000375549.3:c.269C>T	p.Ala90Val	p.A90V	ENST00000375549	NM_003002.3	90	gCg/gTg	3/4	1	2	FACETS	0.984	0.913	1	0.984	0.913	1	CLONAL	1	TRUE	1	0.689515120744271	2		267	507	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435658	18435658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143896492	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	259	532	0	ENST00000266497.5:c.643G>A	p.Gly215Arg	p.G215R	ENST00000266497		215	Gga/Aga	1/31	1	2	FACETS	0.914	0.859	0.97	0.914	0.859	0.97	CLONAL	1	TRUE	1	0.689515120744271	2		532	822	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425776	49425776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123714	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	402	661	0	ENST00000301067.7:c.12712C>T	p.Arg4238Cys	p.R4238C	ENST00000301067	NM_003482.3	4238	Cgc/Tgc	39/54	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.689515120744271	2		661	1091	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434683	110434683	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771644657	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	134	653	0	ENST00000375856.3:c.3718C>T	p.Arg1240Cys	p.R1240C	ENST00000375856	NM_003749.2	1240	Cgc/Tgc	1/2	1	2	FACETS	0.415	0.377	0.456	0.415	0.377	0.456	SUBCLONAL	1	TRUE	1	0.689515120744271	2		653	936	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058513	42058513	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	285	585	0	ENST00000219905.7:c.8237del	p.Lys2746ArgfsTer6	p.K2746Rfs*6	ENST00000219905	NM_001164273.1	2745	Aaa/aa	24/24	1	2	FACETS	0.893	0.841	0.946	0.893	0.841	0.946	CLONAL	1	TRUE	1	0.689515120744271	2		585	926	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633501	3633501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560866356	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	313	557	0	ENST00000294008.3:c.4750C>T	p.Arg1584Cys	p.R1584C	ENST00000294008	NM_032444.2	1584	Cgc/Tgc	14/15	1	2	FACETS	0.991	0.938	1	0.991	0.938	1	CLONAL	1	TRUE	1	0.689515120744271	2		557	916	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832810	3832810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	352	596	0	ENST00000262367.5:c.1448G>A	p.Arg483Gln	p.R483Q	ENST00000262367	NM_004380.2	483	cGa/cAa	6/31	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.689515120744271	2		596	967	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821875	72821875	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	396	724	0	ENST00000268489.5:c.10300del	p.Leu3434SerfsTer51	p.L3434Sfs*51	ENST00000268489	NM_006885.3	3434	Ctc/tc	10/10	1	2	FACETS	0.971	0.924	1	0.971	0.924	1	CLONAL	1	TRUE	1	0.689515120744271	2		724	1183	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350468	89350468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	318	549	0	ENST00000301030.4:c.2482G>A	p.Asp828Asn	p.D828N	ENST00000301030	NM_001256183.1	828	Gac/Aac	9/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.689515120744271	2		549	877	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831470	89831470	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	292	591	0	ENST00000389301.3:c.2606A>G	p.Gln869Arg	p.Q869R	ENST00000389301	NM_000135.2	869	cAg/cGg	28/43	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.689515120744271	2		591	823	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33680060	33680060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202123744	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	187	365	0	ENST00000308377.4:c.2021G>A	p.Arg674His	p.R674H	ENST00000308377	NM_152270.3	674	cGt/cAt	5/5	1	2	FACETS	0.997	0.928	1	0.997	0.928	1	CLONAL	1	TRUE	1	0.689515120744271	2		365	544	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	393	749	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.884	0.84	0.929	0.884	0.84	0.929	CLONAL	1	TRUE	1	0.689515120744271	2		754	1289	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899272	78899272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368064754	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	340	639	0	ENST00000306801.3:c.2911G>A	p.Val971Ile	p.V971I	ENST00000306801	NM_020761.2	971	Gtc/Atc	24/34	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.689515120744271	2		639	930	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621185	1621185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1159477032	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	306	594	0	ENST00000344749.5:c.961C>T	p.Arg321Ter	p.R321*	ENST00000344749	NM_001136139.2	321	Cga/Tga	12/19	1	2	FACETS	0.93	0.879	0.983	0.93	0.879	0.983	CLONAL	1	TRUE	1	0.689515120744271	2		594	954	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213888	2213888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1470399067	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	362	715	0	ENST00000398665.3:c.1700C>T	p.Ala567Val	p.A567V	ENST00000398665	NM_032482.2	567	gCg/gTg	18/28	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.689515120744271	2		715	1040	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	283	605	0	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.954	0.9	1	0.954	0.9	1	CLONAL	1	TRUE	1	0.689515120744271	2		605	860	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276765	15276765	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	418	669	0	ENST00000263388.2:c.5500del	p.Arg1834GlyfsTer77	p.R1834Gfs*77	ENST00000263388	NM_000435.2	1834	Cgg/gg	30/33	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.689515120744271	2		669	1148	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224111	36224111	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	273	390	0	ENST00000222270.7:c.6666del	p.Thr2223ProfsTer38	p.T2223Pfs*38	ENST00000222270	NM_014727.1	2221	Ccc/cc	28/37	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.689515120744271	2		390	686	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	706	759	0	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.868	0.843	0.892	1	0.998	1	CLONAL	2	TRUE	1	0.689515120744271	2		759	1180	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222520	39222520	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	224	467	1	ENST00000402219.2:c.3090del	p.Lys1030AsnfsTer6	p.K1030Nfs*6	ENST00000402219	NM_005633.3	1030	aaA/aa	20/23	1	2	FACETS	0.852	0.795	0.909	0.852	0.795	0.909	CLONAL	1	TRUE	1	0.689515120744271	2		468	763	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	277	497	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	0.689515120744271	1	FACETS	0.746	0.704	0.788	0.746	0.704	0.788	SUBCLONAL	1	TRUE	0	0.689515120744271	1		499	706	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030670	48030670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750253	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	363	627	0	ENST00000234420.5:c.3284G>A	p.Arg1095His	p.R1095H	ENST00000234420	NM_000179.2	1095	cGc/cAc	5/10	0.689515120744271	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.689515120744271	1		627	683	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630566	67630567	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	258	518	0	ENST00000272342.5:c.758dup	p.Pro254AlafsTer13	p.P254Afs*13	ENST00000272342	NM_019002.3	251	aca/acAa	5/6	1	2	FACETS	0.978	0.92	1	0.978	0.92	1	CLONAL	1	TRUE	1	0.689515120744271	2		518	765	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979281	40979281	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	307	523	0	ENST00000373198.4:c.1852G>T	p.Gly618Ter	p.G618*	ENST00000373198	NM_133170.3	618	Gga/Tga	11/32	1	2	FACETS	0.982	0.928	1	0.982	0.928	1	CLONAL	1	TRUE	1	0.689515120744271	2		523	907	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101118	41101118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751886972	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	326	603	0	ENST00000373198.4:c.1238C>T	p.Ala413Val	p.A413V	ENST00000373198	NM_133170.3	413	gCg/gTg	8/32	1	2	FACETS	0.984	0.932	1	0.984	0.932	1	CLONAL	1	TRUE	1	0.689515120744271	2		603	961	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852412	42852412	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	389	580	0	ENST00000398585.3:c.674T>C	p.Met225Thr	p.M225T	ENST00000398585	NM_001135099.1	225	aTg/aCg	6/14	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.689515120744271	2		580	1020	SUCCESS
NF2	4771	MSKCC	GRCh37	22	29999997	29999997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	238	434	0	ENST00000338641.4:c.10G>A	p.Ala4Thr	p.A4T	ENST00000338641	NM_000268.3	4	Gcc/Acc	1/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.689515120744271	2		434	669	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434182	12434182	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776687	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	247	524	3	ENST00000287820.6:c.556del	p.Ser186ValfsTer47	p.S186Vfs*47	ENST00000287820	NM_015869.4	184	Aaa/aa	4/7	1	2	FACETS	0.816	0.764	0.869	0.816	0.764	0.869	CLONAL	1	TRUE	1	0.689515120744271	2		527	878	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713381	30713381	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	402	694	0	ENST00000295754.5:c.706A>G	p.Asn236Asp	p.N236D	ENST00000295754	NM_003242.5	236	Aac/Gac	4/7	1	2	FACETS	0.964	0.918	1	0.964	0.918	1	CLONAL	1	TRUE	1	0.689515120744271	2		694	1209	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72842115	72842115	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs577488660	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	289	477	0	ENST00000325599.8:c.1133T>C	p.Leu378Pro	p.L378P	ENST00000325599	NM_018130.2	378	cTg/cCg	10/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.689515120744271	2		477	768	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155638	106155638	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	313	582	0	ENST00000380013.4:c.539A>G	p.Gln180Arg	p.Q180R	ENST00000380013	NM_001127208.2	180	cAg/cGg	3/11	1	2	FACETS	0.994	0.941	1	0.994	0.941	1	CLONAL	1	TRUE	1	0.689515120744271	2		582	913	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525604	187525604	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	318	571	0	ENST00000441802.2:c.10475A>G	p.Asn3492Ser	p.N3492S	ENST00000441802	NM_005245.3	3492	aAc/aGc	18/27	1	2	FACETS	0.968	0.916	1	0.968	0.916	1	CLONAL	1	TRUE	1	0.689515120744271	2		571	953	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294328	1294328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	360	726	0	ENST00000310581.5:c.673G>A	p.Gly225Arg	p.G225R	ENST00000310581	NM_198253.2	225	Ggg/Agg	2/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.689515120744271	2		726	1043	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31504714	31504714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1225717985	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	287	495	0	ENST00000344624.3:c.1616G>A	p.Ser539Asn	p.S539N	ENST00000344624		539	aGc/aAc	8/33	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.689515120744271	2		495	831	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	339	605	2	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.945	0.896	0.996	0.945	0.896	0.996	CLONAL	1	TRUE	1	0.689515120744271	2		607	1040	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576370	67576370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540361957	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	245	428	0	ENST00000274335.5:c.649G>A	p.Glu217Lys	p.E217K	ENST00000274335		217	Gaa/Aaa	5/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.689515120744271	2		428	671	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	241	302	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.882	0.826	0.938	0.882	0.826	0.938	CLONAL	1	TRUE	1	0.689515120744271	2		306	793	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562414	176562414	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	337	684	0	ENST00000439151.2:c.310G>A	p.Asp104Asn	p.D104N	ENST00000439151	NM_022455.4	104	Gat/Aat	2/23	1	2	FACETS	0.933	0.883	0.983	0.933	0.883	0.983	CLONAL	1	TRUE	1	0.689515120744271	2		684	1048	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748539	43748539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367571103	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	347	671	2	ENST00000523873.1:c.493G>A	p.Val165Met	p.V165M	ENST00000523873		165	Gtg/Atg	6/8	1	2	FACETS	0.961	0.912	1	0.961	0.912	1	CLONAL	1	TRUE	1	0.689515120744271	2		673	1047	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64290025	64290025	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	262	417	0	ENST00000370651.3:c.468G>A	p.Met156Ile	p.M156I	ENST00000370651	NM_003463.4	156	atG/atA	6/6	1	2	FACETS	0.966	0.908	1	0.966	0.908	1	CLONAL	1	TRUE	1	0.689515120744271	2		417	787	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508733	106508733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1207051578	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	392	668	0	ENST00000359195.3:c.727G>A	p.Ala243Thr	p.A243T	ENST00000359195	NM_002649.2	243	Gcc/Acc	2/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.689515120744271	2		668	1099	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	343	665	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	0.907	0.859	0.956	0.907	0.859	0.956	CLONAL	1	TRUE	1	0.689515120744271	2		665	1097	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151919110	151919110	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	198	350	0	ENST00000262189.6:c.3475A>T	p.Ile1159Phe	p.I1159F	ENST00000262189	NM_170606.2	1159	Att/Ttt	22/59	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.689515120744271	2		350	500	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981483	70981483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	351	669	1	ENST00000276594.2:c.613G>A	p.Val205Ile	p.V205I	ENST00000276594	NM_024504.3	205	Gtt/Att	2/8	1	2	FACETS	0.995	0.944	1	0.995	0.944	1	CLONAL	1	TRUE	1	0.689515120744271	2		670	1023	SUCCESS
MTAP	4507	MSKCC	GRCh37	9	21854739	21854739	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147028761	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	323	557	0	ENST00000380172.4:c.560G>A	p.Arg187His	p.R187H	ENST00000380172	NM_002451.3	187	cGc/cAc	6/8	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.689515120744271	2		557	926	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300039	137300040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755912201	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	267	441	1	ENST00000481739.1:c.331dup	p.Leu111ProfsTer70	p.L111Pfs*70	ENST00000481739	NM_002957.4	108	-/C	3/10	1	2	FACETS	0.906	0.852	0.961	0.906	0.852	0.961	CLONAL	1	TRUE	1	0.689515120744271	2		442	855	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650816	48650816	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1557020321	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	350	425	0	ENST00000376670.3:c.685G>A	p.Gly229Ser	p.G229S	ENST00000376670	NM_002049.3	229	Ggc/Agc	4/6	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.689515120744271	1		425	568	SUCCESS
AR	367	MSKCC	GRCh37	X	66943606	66943606	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	353	268	0	ENST00000374690.3:c.2686A>T	p.Met896Leu	p.M896L	ENST00000374690	NM_000044.3	896	Atg/Ttg	8/8	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.689515120744271	1		268	504	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042403	42042403	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	92	521	0	ENST00000219905.7:c.6598C>T	p.Gln2200Ter	p.Q2200*	ENST00000219905	NM_001164273.1	2200	Cag/Tag	17/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.2	2		521	739	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974748	21974748	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1554656411	NA	P-0063587-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	134	588	0	ENST00000304494.5:c.79G>T	p.Glu27Ter	p.E27*	ENST00000304494	NM_000077.4	27	Gag/Tag	1/3	0.476152527137171	2	FACETS	0.954	0.882	1	0.954	0.882	1	CLONAL	2	TRUE	0	0.476152527137171	2		588	295	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720711	89720712	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0063587-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	33	77	0	ENST00000371953.3:c.867dup	p.Val290SerfsTer8	p.V290Sfs*8	ENST00000371953	NM_000314.4	288	gaa/gAaa	8/9	0.458697805921022	3	FACETS	0.908	0.779	1	0.908	0.779	1	CLONAL	3	TRUE	0	0.476152527137171	3		77	63	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100111	27100111	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0063587-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	198	684	0	ENST00000324856.7:c.3910del	p.Ala1304ProfsTer177	p.A1304Pfs*177	ENST00000324856	NM_006015.4	1303	Ggg/gg	16/20	0.453645324564333	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	1	0.476152527137171	3		684	503	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729640	41729640	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063587-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	101	601	0	ENST00000242208.4:c.889G>A	p.Ala297Thr	p.A297T	ENST00000242208	NM_002192.2	297	Gcc/Acc	3/3	0.453645324564333	3	FACETS	1	0.952	1	0.551	0.494	0.61	CLONAL	1	TRUE	1	0.476152527137171	3		601	477	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494587	2494587	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs556584527	NA	P-0063587-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	147	525	0	ENST00000355716.4:c.727C>T	p.Arg243Trp	p.R243W	ENST00000355716	NM_003820.2	243	Cgg/Tgg	8/8	0.453645324564333	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.476152527137171	3		525	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578535	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTG	novel	NA	P-0063587-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	155	475	0	ENST00000269305.4:c.393_395dup	p.Asn131dup	p.N131dup	ENST00000269305	NM_001126112.2	131	aag/aaCAAg	5/11	0.476152527137171	2	FACETS	0.82	0.76	0.881	0.82	0.76	0.881	CLONAL	2	TRUE	0	0.476152527137171	2		475	397	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29686011	29686011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1170836879	NA	P-0063587-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	97	272	0	ENST00000356175.3:c.8075G>A	p.Arg2692Gln	p.R2692Q	ENST00000356175	NM_000267.3	2692	cGg/cAg	55/57	0.476152527137171	4	FACETS	0.925	0.834	1	0.925	0.834	1	CLONAL	2	TRUE	2	0.476152527137171	4		272	325	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78865606	78865606	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063587-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	63	442	0	ENST00000306801.3:c.2070G>C	p.Lys690Asn	p.K690N	ENST00000306801	NM_020761.2	690	aaG/aaC	18/34	0.476152527137171	5	FACETS	0.98	0.849	1	0.327	0.283	0.374	CLONAL	1	TRUE	2	0.476152527137171	5		442	463	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825424	134825424	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063587-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	96	441	0	ENST00000398015.3:c.940C>A	p.Pro314Thr	p.P314T	ENST00000398015	NM_004441.4	314	Cct/Act	4/16	0.476152527137171	3	FACETS	1	0.968	1	0.603	0.541	0.668	CLONAL	1	TRUE	1	0.476152527137171	3		441	414	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589610	67589615	+	inframe_deletion	In_Frame_Del	DEL	AAAAAA	AAAAAA	-	novel	NA	P-0063587-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	92	244	0	ENST00000274335.5:c.1373_1378del	p.Glu458_Ser460delinsGly	p.E458_S460delinsG	ENST00000274335		458	gAAAAAAgt/ggt	10/15	0.476152527137171	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.476152527137171	2		244	165	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512619	148512619	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063587-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	68	336	0	ENST00000320356.2:c.1525A>G	p.Arg509Gly	p.R509G	ENST00000320356	NM_004456.4	509	Aga/Gga	13/20	0.453645324564333	3	FACETS	1	0.904	1	0.519	0.454	0.587	CLONAL	1	TRUE	1	0.476152527137171	3		336	341	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679595	86679595	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0063588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	45	223	0	ENST00000274376.6:c.2756C>G	p.Ser919Ter	p.S919*	ENST00000274376	NM_002890.2	919	tCa/tGa	21/25	0.309544192377823	1	FACETS	0.934	0.791	1	0.934	0.791	1	CLONAL	1	TRUE	0	0.309544192377823	1		223	263	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711903	89711903	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs864622341	NA	P-0063588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	78	299	0	ENST00000371953.3:c.521A>G	p.Tyr174Cys	p.Y174C	ENST00000371953	NM_000314.4	174	tAt/tGt	6/9	0.309544192377823	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.309544192377823	1		299	367	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348161	89348161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	164	454	0	ENST00000301030.4:c.4789C>T	p.Arg1597Cys	p.R1597C	ENST00000301030	NM_001256183.1	1597	Cgc/Tgc	9/13	0.309544192377823	2	FACETS	1	0.953	1	0.528	0.484	0.574	CLONAL	1	TRUE	0	0.309544192377823	2		454	1003	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11206841	11206841	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	143	373	0	ENST00000361445.4:c.4578G>T	p.Trp1526Cys	p.W1526C	ENST00000361445	NM_004958.3	1526	tgG/tgT	32/58	0.309544192377823	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.309544192377823	1		373	636	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230486751	230486751	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	131	421	0	ENST00000391860.1:c.502T>A	p.Phe168Ile	p.F168I	ENST00000391860	NM_001258311.1	168	Ttc/Atc	3/7	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.309544192377823	2		421	844	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577508	64577508	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1462138625	NA	P-0063588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	155	450	0	ENST00000312049.6:c.74C>T	p.Ala25Val	p.A25V	ENST00000312049	NM_130799.2	25	gCc/gTc	2/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.309544192377823	2		450	810	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118698	115118698	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	167	445	0	ENST00000257566.3:c.643G>T	p.Asp215Tyr	p.D215Y	ENST00000257566	NM_016569.3	215	Gac/Tac	2/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.309544192377823	2		445	966	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515276	103515276	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	117	406	0	ENST00000355739.4:c.1777C>A	p.Pro593Thr	p.P593T	ENST00000355739	NM_000123.3	593	Cct/Act	8/15	0.187232380241678	3	FACETS	0.961	0.866	1	0.481	0.433	0.531	CLONAL	1	TRUE	1	0.309544192377823	3		406	908	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690616	33690616	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	176	423	0	ENST00000308377.4:c.211G>C	p.Val71Leu	p.V71L	ENST00000308377	NM_152270.3	71	Gtg/Ctg	2/5	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.309544192377823	2		423	1063	SUCCESS
ATR	545	MSKCC	GRCh37	3	142185372	142185372	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	67	236	0	ENST00000350721.4:c.6691G>T	p.Asp2231Tyr	p.D2231Y	ENST00000350721	NM_001184.3	2231	Gat/Tat	40/47	0.309544192377823	4	FACETS	1	0.923	1	0.713	0.626	0.805	CLONAL	2	TRUE	1	0.309544192377823	4		236	265	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272750	142272750	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	27	273	0	ENST00000350721.4:c.2449G>C	p.Asp817His	p.D817H	ENST00000350721	NM_001184.3	817	Gac/Cac	11/47	0.309544192377823	4	FACETS	0.684	0.545	0.843	0.228	0.181	0.281	SUBCLONAL	1	TRUE	1	0.309544192377823	4		273	334	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356203	66356203	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	157	443	0	ENST00000273854.3:c.1294C>G	p.Leu432Val	p.L432V	ENST00000273854	NM_004439.5	432	Ctc/Gtc	5/18	0.309544192377823	3	FACETS	0.953	0.871	1	0.477	0.435	0.52	CLONAL	1	TRUE	1	0.309544192377823	3		443	1229	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92244413	92244506	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	GGTGTTCTCCGCAGGATCAGCTTAAGGCGGCTGCTGAGGCCTCAGGCTGTATTCAGCTCCGAGGTGTTCTGGCTGGGCGGCAGGTGGGAATCCA	GGTGTTCTCCGCAGGATCAGCTTAAGGCGGCTGCTGAGGCCTCAGGCTGTATTCAGCTCCGAGGTGTTCTGGCTGGGCGGCAGGTGGGAATCCA	-	novel	NA	P-0063588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	33	276	0	ENST00000265734.4:c.929_*41del		p.*310*	ENST00000265734	NM_001259.6	310		8/8	0.309544192377823	1	FACETS	0.32	0.259	0.388	0.32	0.259	0.388	SUBCLONAL	1	TRUE	0	0.309544192377823	1		276	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782620	NA	P-0063589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	81	653	0	ENST00000269305.4:c.427G>A	p.Val143Met	p.V143M	ENST00000269305	NM_001126112.2	143	Gtg/Atg	5/11	0.247428660711484	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.247428660711484	1		653	505	SUCCESS
APC	324	MSKCC	GRCh37	5	112128142	112128142	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0063589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	48	214	0	ENST00000257430.4:c.646-1G>A		p.X216_splice	ENST00000257430	NM_000038.5	216			1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.247428660711484	2		214	350	SUCCESS
APC	324	MSKCC	GRCh37	5	112173560	112173561	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0063589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	71	396	0	ENST00000257430.4:c.2274dup	p.Ala759SerfsTer16	p.A759Sfs*16	ENST00000257430	NM_000038.5	757	caa/cAaa	16/16	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.247428660711484	2		396	514	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375080	118375080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	31	503	0	ENST00000534358.1:c.8473G>A	p.Asp2825Asn	p.D2825N	ENST00000534358	NM_005933.3	2825	Gac/Aac	27/36	1	2	FACETS	0.404	0.326	0.493	0.404	0.326	0.493	SUBCLONAL	1	TRUE	1	0.247428660711484	2		503	620	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141453	11141453	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	58	437	0	ENST00000358026.2:c.3430G>A	p.Glu1144Lys	p.E1144K	ENST00000358026	NM_001128849.1	1144	Gag/Aag	25/36	1	2	FACETS	0.997	0.859	1	0.997	0.859	1	CLONAL	1	TRUE	1	0.247428660711484	2		437	470	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0063590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	79	629	0	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	0.871911956313519	4	FACETS	0.824	0.728	0.925	0.412	0.364	0.463	CLONAL	1	TRUE	2	0.891545416005535	4		629	407	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219878	133219878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	205	540	0	ENST00000320574.5:c.4483G>A	p.Ala1495Thr	p.A1495T	ENST00000320574	NM_006231.2	1495	Gcc/Acc	35/49	0.831716474947969	3	FACETS	1	0.969	1			1	CLONAL	2	TRUE	NA	0.891545416005535	3		540	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578403	+	missense_variant	Missense_Mutation	DNP	GC	GC	AG	novel	NA	P-0063590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	206	608	2	ENST00000269305.4:c.527_528delinsCT	p.Cys176Ser	p.C176S	ENST00000269305	NM_001126112.2	176	tGC/tCT	5/11	NA	2	FACETS	0.975	0.944	1			1	INDETERMINATE	2	TRUE	NA	0.891545416005535	2		610	237	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39240631	39240631	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	82	285	0	ENST00000402219.2:c.2137C>G	p.Arg713Gly	p.R713G	ENST00000402219	NM_005633.3	713	Cga/Gga	13/23	0.891545416005535	3	FACETS	1	0.955	1	0.561	0.503	0.621	CLONAL	1	TRUE	1	0.891545416005535	3		285	237	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702528	52702528	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	124	250	0	ENST00000394830.3:c.370A>C	p.Lys124Gln	p.K124Q	ENST00000394830	NM_018313.4	124	Aag/Cag	4/30	0.871911956313519	4	FACETS	0.946	0.872	1	0.946	0.872	1	CLONAL	2	TRUE	2	0.891545416005535	4		250	278	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929164	44929165	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0063590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	171	203	0	ENST00000377967.4:c.2266dup	p.Ala756GlyfsTer8	p.A756Gfs*8	ENST00000377967	NM_021140.2	755	acg/acGg	17/29	0.891545416005535	2	FACETS	0.974	0.939	1			1	CLONAL	2	TRUE	NA	0.891545416005535	2		203	197	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875892	76875892	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	79	156	0	ENST00000373344.5:c.5243G>T	p.Gly1748Val	p.G1748V	ENST00000373344	NM_000489.3	1748	gGa/gTa	20/35	0.891545416005535	2	FACETS	0.974	0.877	1			1	CLONAL	1	TRUE	NA	0.891545416005535	2		156	182	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875898	76875898	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	81	161	0	ENST00000373344.5:c.5237T>C	p.Leu1746Ser	p.L1746S	ENST00000373344	NM_000489.3	1746	tTa/tCa	20/35	0.891545416005535	2	FACETS	0.946	0.853	1			1	CLONAL	1	TRUE	NA	0.891545416005535	2		161	192	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0063591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	19	223	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	0.854	0.666	1	0.854	0.666	1	CLONAL	1	TRUE	1	0.626732087809702	2		223	71	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413565	32413565	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121907903	NA	P-0063591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	95	413	0	ENST00000332351.3:c.1385G>A	p.Arg462Gln	p.R462Q	ENST00000332351	NM_024426.4	462	cGg/cAg	9/10	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.626732087809702	2		413	299	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438527	52438527	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	147	459	0	ENST00000460680.1:c.1192G>T	p.Glu398Ter	p.E398*	ENST00000460680	NM_004656.3	398	Gag/Tag	12/17	0.626732087809702	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.626732087809702	1		459	248	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0063607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	87	698	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.205359403551467	3	FACETS	0.871	0.772	0.976	0.871	0.772	0.976	CLONAL	2	TRUE	1	0.18	3		698	605	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241678	55241678	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517085	NA	P-0063607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	99	591	0	ENST00000275493.2:c.2126A>C	p.Glu709Ala	p.E709A	ENST00000275493	NM_005228.3	709	gAa/gCa	18/28	0.205359403551467	3	FACETS	0.956	0.855	1	0.956	0.855	1	CLONAL	2	TRUE	1	0.18	3		591	627	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400754	56400754	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	39	376	0	ENST00000348428.3:c.1348C>G	p.Gln450Glu	p.Q450E	ENST00000348428	NM_006785.3	450	Caa/Gaa	11/17	1	2	FACETS	0.989	0.82	1	0.989	0.82	1	CLONAL	1	TRUE	1	0.18	2		376	438	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341735	8341735	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063607-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	50	481	0	ENST00000356435.5:c.4905A>G	p.Ile1635Met	p.I1635M	ENST00000356435		1635	atA/atG	29/35	0.284789153585247	1	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	0	0.18	1		481	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0063620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	216	809	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.492638824309212	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.492638824309212	1		809	645	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937072	36937072	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	86	492	0	ENST00000361632.4:c.1247C>A	p.Thr416Asn	p.T416N	ENST00000361632		416	aCc/aAc	9/16	1	2	FACETS	0.365	0.322	0.411	0.365	0.322	0.411	SUBCLONAL	1	TRUE	1	0.492638824309212	2		492	957	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222439	2222439	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	215	592	1	ENST00000398665.3:c.3271C>T	p.Arg1091Ter	p.R1091*	ENST00000398665	NM_032482.2	1091	Cga/Tga	24/28	0.492638824309212	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.492638824309212	1		593	632	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124467322	124467322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	30	316	0	ENST00000357628.3:c.1632G>A	p.Met544Ile	p.M544I	ENST00000357628	NM_015450.2	544	atG/atA	17/19	1	2	FACETS	0.21	0.168	0.257	0.21	0.168	0.257	SUBCLONAL	1	TRUE	1	0.492638824309212	2		316	580	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	99	343	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.838	0.749	0.931	0.838	0.749	0.931	CLONAL	1	TRUE	1	0.391339958812456	2		343	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0063621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	170	600	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.391339958812456	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.391339958812456	1		600	692	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0063621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	161	486	0	ENST00000349496.5:c.101G>A	p.Gly34Glu	p.G34E	ENST00000349496	NM_001904.3	34	gGa/gAa	3/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.391339958812456	2		486	763	SUCCESS
ATR	545	MSKCC	GRCh37	3	142234278	142234278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	108	338	0	ENST00000350721.4:c.4462G>A	p.Ala1488Thr	p.A1488T	ENST00000350721	NM_001184.3	1488	Gca/Aca	25/47	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.391339958812456	2		338	505	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967940	93967940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs953493697	NA	P-0063621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	125	396	0	ENST00000369303.4:c.1987G>A	p.Ala663Thr	p.A663T	ENST00000369303	NM_004440.3	663	Gcc/Acc	11/17	1	2	FACETS	0.994	0.901	1	0.994	0.901	1	CLONAL	1	TRUE	1	0.391339958812456	2		396	643	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652130	36652132	+	frameshift_variant	Frame_Shift_Del	DEL	AGG	AGG	C	novel	NA	P-0063621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	349	664	2	ENST00000244741.5:c.252_254delinsC	p.Gly85ProfsTer3	p.G85Pfs*3	ENST00000244741	NM_000389.4	84	cgAGGc/cgCc	2/3	0.377959396322231	3	FACETS	0.997	0.946	1	0.997	0.946	1	CLONAL	2	TRUE	1	0.391339958812456	3		666	1069	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0063622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	106	241	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		241	404	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0063622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	132	488	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		488	465	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0063623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	414	739	1	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	0.374052928099808	4	FACETS	1	0.994	1	0.653	0.621	0.685	INDETERMINATE	1	TRUE	2	0.847439092325355	4		740	1382	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271999	15271999	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs897705605	NA	P-0063623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	360	751	0	ENST00000263388.2:c.6440G>A	p.Gly2147Asp	p.G2147D	ENST00000263388	NM_000435.2	2147	gGt/gAt	33/33	0.262136811168621	1	FACETS	0.523	0.497	0.549	0.523	0.497	0.549	INDETERMINATE	1	TRUE	0	0.847439092325355	1		751	936	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352489	89352489	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	363	597	0	ENST00000301030.4:c.850T>G	p.Leu284Val	p.L284V	ENST00000301030	NM_001256183.1	284	Tta/Gta	8/13	0.38988319083511	1	FACETS	0.691	0.661	0.722	0.691	0.661	0.722	INDETERMINATE	1	TRUE	0	0.847439092325355	1		597	714	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661949	29661949	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	500	476	0	ENST00000356175.3:c.5845del	p.Arg1949GlufsTer9	p.R1949Efs*9	ENST00000356175	NM_000267.3	1948	cAa/ca	39/57	0.827622486350159	2	FACETS	0.975	0.953	0.997	0.975	0.953	0.997	CLONAL	2	TRUE	0	0.847439092325355	2		476	605	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066778	5066778	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	20	320	0	ENST00000381652.3:c.1315T>A	p.Phe439Ile	p.F439I	ENST00000381652	NM_004972.3	439	Ttt/Att	10/25	0.847439092325355	1	FACETS	0.136	0.104	0.173	0.136	0.104	0.173	SUBCLONAL	1	TRUE	0	0.847439092325355	1		320	200	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521280	8521280	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	28	436	0	ENST00000356435.5:c.958A>C	p.Lys320Gln	p.K320Q	ENST00000356435		320	Aaa/Caa	9/35	0.847439092325355	1	FACETS	0.109	0.087	0.134	0.109	0.087	0.134	SUBCLONAL	1	TRUE	0	0.847439092325355	1		436	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876659675	NA	P-0063625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	351	438	0	ENST00000269305.4:c.764T>A	p.Ile255Asn	p.I255N	ENST00000269305	NM_001126112.2	255	aTc/aAc	7/11	0.564128512614258	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.564128512614258	2		438	545	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21340185	21340185	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0063625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	132	404	0	ENST00000215739.8:c.319A>T	p.Arg107Trp	p.R107W	ENST00000215739	NM_006767.3	107	Agg/Tgg	3/21	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.564128512614258	2		404	438	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0063626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	121	502	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.362881659209236	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	0	0.362881659209236	1		502	462	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0063626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	137	241	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.362881659209236	4	FACETS	0.909	0.831	0.991	0.909	0.831	0.991	CLONAL	2	FALSE	2	0.362881659209236	4		241	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782177	NA	P-0063626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	244	516	0	ENST00000269305.4:c.644G>A	p.Ser215Asn	p.S215N	ENST00000269305	NM_001126112.2	215	aGt/aAt	6/11	0.329093046532091	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	FALSE	0	0.362881659209236	2		516	653	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028432	42028432	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1317629679	NA	P-0063626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	111	509	0	ENST00000219905.7:c.3970A>G	p.Met1324Val	p.M1324V	ENST00000219905	NM_001164273.1	1324	Atg/Gtg	13/24	0.147743442484171	4	FACETS	1	0.983	1	0.726	0.655	0.801	INDETERMINATE	1	FALSE	2	0.362881659209236	4		509	574	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212011	94212011	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	106	380	0	ENST00000323929.3:c.434G>A	p.Ser145Asn	p.S145N	ENST00000323929	NM_005591.3	145	aGt/aAt	6/20	0.273954563826113	3	FACETS	0.88	0.796	0.969	0.88	0.796	0.969	CLONAL	2	FALSE	1	0.362881659209236	3		380	392	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436034	56436035	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0063626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	257	820	0	ENST00000407977.2:c.1101_1102dup	p.Arg368LeufsTer52	p.R368Lfs*52	ENST00000407977		368	cgg/cTCgg	9/10	0.329093046532091	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	FALSE	0	0.362881659209236	2		820	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579368	7579368	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0063627-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	120	731	0	ENST00000269305.4:c.319T>G	p.Tyr107Asp	p.Y107D	ENST00000269305	NM_001126112.2	107	Tac/Gac	4/11	0.298825580836404	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	0	0.31	1		731	651	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0063627-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	46	204	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.843	0.712	0.986	0.843	0.712	0.986	CLONAL	1	TRUE	1	0.31	2		204	352	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221969	1221993	+	frameshift_variant	Frame_Shift_Del	DEL	CCAAGAGGTTCTCCATCCGGCAGAT	CCAAGAGGTTCTCCATCCGGCAGAT	-	novel	NA	P-0063627-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	58	452	0	ENST00000326873.7:c.886_910del	p.Lys296GlyfsTer32	p.K296Gfs*32	ENST00000326873	NM_000455.4	295	gCCAAGAGGTTCTCCATCCGGCAGATc/gc	7/10	0.298825580836404	1	FACETS	0.677	0.583	0.78	0.677	0.583	0.78	SUBCLONAL	1	TRUE	0	0.31	1		452	467	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0063628-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	19	1032	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.949	0.721	1	0.949	0.721	1	CLONAL	1	TRUE	1	0.15	2		1032	267	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0063628-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	30	450	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.609	0.489	0.746	0.609	0.489	0.746	SUBCLONAL	1	TRUE	1	0.15	2		451	657	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041690	47041991	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGAAGGAGAAGCACAAGACCAAGACAGCTCAACAGGTGAACACCAGGGTCCAGCAGTCACTGGCTGGCTGTGTGGTGTCTTCCAGCAACGGCACTCTGTCAGCTCTTGCCCTCTCCTGCCAAGGGAGATGGCGGGCAGGTGTGGATGTGGGCAGTGACTGCTTAGCAGACCATGCTCTTGCCCCAGCTCTGCTCTTTGCTGAATGGCCTTGAGCCAGAGCAGTCTCCTCAGTGTGTGGCAGGGTTGCCCAACTCCAGGAGGTGGCTTGTGCCATCCGAGTGAGCCCTGTCAGGTGTCTTCT	AAGAAGGAGAAGCACAAGACCAAGACAGCTCAACAGGTGAACACCAGGGTCCAGCAGTCACTGGCTGGCTGTGTGGTGTCTTCCAGCAACGGCACTCTGTCAGCTCTTGCCCTCTCCTGCCAAGGGAGATGGCGGGCAGGTGTGGATGTGGGCAGTGACTGCTTAGCAGACCATGCTCTTGCCCCAGCTCTGCTCTTTGCTGAATGGCCTTGAGCCAGAGCAGTCTCCTCAGTGTGTGGCAGGGTTGCCCAACTCCAGGAGGTGGCTTGTGCCATCCGAGTGAGCCCTGTCAGGTGTCTTCT	-	novel	NA	P-0063628-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	28	315	0	ENST00000377604.3:c.1915_1950+266del		p.X639_splice	ENST00000377604	NM_001204468.1	639		17/24	1	1	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	0	0.15	1		315	287	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0063629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	478	532	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.721945285021773	2	FACETS	0.967	0.938	0.995	0.967	0.938	0.995	CLONAL	2	TRUE	0	0.741073048625331	2		532	667	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509857	106509857	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0063629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	372	468	1	ENST00000359195.3:c.1851G>T	p.Trp617Cys	p.W617C	ENST00000359195	NM_002649.2	617	tgG/tgT	2/11	0.389309176709362	3	FACETS	0.887	0.847	0.926	0.887	0.847	0.926	INDETERMINATE	2	TRUE	1	0.741073048625331	3		469	776	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10244378	10244892	+	splice_donor_variant,splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTGAAGGGAAATAAAAGGAAAAGTCACTCTGGGGAACACGCCCGGTGTCACGCCACTTGACAGGCGAGTAACAGACATGGACCATCAGGAAACATTAACGTACTGATGTTAACAGCTGACCCAATAAGTGGCAGAGTGCTAAGGGAACGTTCACGGAGACTGAACACTCCTCAAACGGTCCCCAGAGGGTTCTAGACCCAGAGGCTCAAGTGAGCAGCTGAGGCAGGTGCCTGCTGAGCCAAATTCACCGAGCAGGAGTGAGGGAAACGGCCCCAGGGCCAGCCCAGCAGCCAACCTGACCAAAGGCCTGCTGTGTGCAGCACGCCTGCTCTAAGCACTTGACACGTGCAACTCACTCAATCCTCACAGCAGCCCCTTGAGAAAGATGGGGCCACGAACGTGGGTAGGTGACCCGCCTGAGTCCCAGAGCCCAAAACGGTGGCCAGCAACTGCCCCCACATGTACCCCCAGAGGGCAGTCAGGCCCCAGAGGAAGCCTGGCCCACCCCACCATAC	CTGAAGGGAAATAAAAGGAAAAGTCACTCTGGGGAACACGCCCGGTGTCACGCCACTTGACAGGCGAGTAACAGACATGGACCATCAGGAAACATTAACGTACTGATGTTAACAGCTGACCCAATAAGTGGCAGAGTGCTAAGGGAACGTTCACGGAGACTGAACACTCCTCAAACGGTCCCCAGAGGGTTCTAGACCCAGAGGCTCAAGTGAGCAGCTGAGGCAGGTGCCTGCTGAGCCAAATTCACCGAGCAGGAGTGAGGGAAACGGCCCCAGGGCCAGCCCAGCAGCCAACCTGACCAAAGGCCTGCTGTGTGCAGCACGCCTGCTCTAAGCACTTGACACGTGCAACTCACTCAATCCTCACAGCAGCCCCTTGAGAAAGATGGGGCCACGAACGTGGGTAGGTGACCCGCCTGAGTCCCAGAGCCCAAAACGGTGGCCAGCAACTGCCCCCACATGTACCCCCAGAGGGCAGTCAGGCCCCAGAGGAAGCCTGGCCCACCCCACCATAC	-	novel	NA	P-0063629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	252	370	0	ENST00000340748.4:c.4816+1_4817-1del		p.X1606_splice	ENST00000340748		1606			0.736145018913689	4	FACETS	1	0.936	1			1	CLONAL	1	TRUE	NA	0.741073048625331	4		370	1182	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144722	58144722	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	141	757	0	ENST00000257904.6:c.506T>C	p.Met169Thr	p.M169T	ENST00000257904	NM_000075.3	169	aTg/aCg	4/8	0.389309176709362	3	FACETS	0.392	0.356	0.43	0.196	0.178	0.215	INDETERMINATE	1	TRUE	1	0.741073048625331	3		757	1331	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449745	149449745	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	369	653	0	ENST00000286301.3:c.1319G>T	p.Arg440Met	p.R440M	ENST00000286301	NM_005211.3	440	aGg/aTg	9/22	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.741073048625331	2		653	941	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983965	2983965	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0063629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	213	521	0	ENST00000396946.4:c.565A>C	p.Ser189Arg	p.S189R	ENST00000396946	NM_032415.4	189	Agc/Cgc	5/25	0.389309176709362	3	FACETS	0.811	0.754	0.871	0.406	0.377	0.436	INDETERMINATE	1	TRUE	1	0.741073048625331	3		521	971	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971125	21971125	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1554654118	NA	P-0063629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	449	643	0	ENST00000304494.5:c.233T>C	p.Leu78Pro	p.L78P	ENST00000304494	NM_000077.4	78	cTc/cCc	2/3	0.741073048625331	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.741073048625331	1		643	665	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0063630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	460	582	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.690237595607057	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.690237595607057	1		582	820	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0063631-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	81	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.862658224394619	2		434	173	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0063631-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	179	541	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.862658224394619	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.862658224394619	2		541	207	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939504	76939504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063631-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	47	214	0	ENST00000373344.5:c.1244C>T	p.Ser415Phe	p.S415F	ENST00000373344	NM_000489.3	415	tCc/tTc	9/35	1	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.862658224394619	1		214	53	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0063631-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	250	205	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.862658224394619	2		205	442	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738621	145738621	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501371	NA	P-0063631-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	431	617	0	ENST00000428558.2:c.2443C>T	p.His815Tyr	p.H815Y	ENST00000428558	NM_004260.3	815	Cac/Tac	15/22	0.856874944888815	3	FACETS	0.783	0.751	0.816	0.522	0.5	0.544	SUBCLONAL	2	TRUE	0	0.862658224394619	3		617	913	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942724	44942724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1453322733	NA	P-0063644-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	33	197	0	ENST00000377967.4:c.3304G>A	p.Glu1102Lys	p.E1102K	ENST00000377967	NM_021140.2	1102	Gag/Aag	23/29	1	1	FACETS	0.856	0.701	1	1	0.955	1	CLONAL	2	TRUE	0	0.151676940680397	1		197	235	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101054	27101054	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063644-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	55	645	0	ENST00000324856.7:c.4336C>T	p.Arg1446Ter	p.R1446*	ENST00000324856	NM_006015.4	1446	Cga/Tga	18/20	1	2	FACETS	0.932	0.796	1	0.932	0.796	1	CLONAL	1	TRUE	1	0.151676940680397	2		645	778	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167794	185167794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063644-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	54	488	0	ENST00000265026.3:c.1117C>T	p.Pro373Ser	p.P373S	ENST00000265026	NM_004721.4	373	Cca/Tca	6/14	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.151676940680397	2		488	619	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412008	63412008	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0063644-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	28	376	0	ENST00000330258.3:c.1159G>T	p.Glu387Ter	p.E387*	ENST00000330258	NM_152424.3	387	Gag/Tag	2/2	1	1	FACETS	0.758	0.605	0.933	0.758	0.605	0.933	CLONAL	1	TRUE	0	0.151676940680397	1		376	450	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119759	70119778	+	frameshift_variant	Frame_Shift_Del	DEL	GAGAGGGGCGCCCCTTGCCA	GAGAGGGGCGCCCCTTGCCA	-	novel	NA	P-0063644-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	34	509	0	ENST00000245479.2:c.764_783del	p.Glu255GlyfsTer34	p.E255Gfs*34	ENST00000245479	NM_000346.3	254	cGAGAGGGGCGCCCCTTGCCA/c	3/3	1	2	FACETS	0.833	0.68	1	0.833	0.68	1	CLONAL	1	TRUE	1	0.151676940680397	2		509	538	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591901	48591901	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063644-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	58	590	0	ENST00000342988.3:c.1064A>G	p.Asp355Gly	p.D355G	ENST00000342988	NM_005359.5	355	gAc/gGc	9/12	0.151676940680397	1	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	0	0.151676940680397	1		590	681	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847393	68847407	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCAAAGGTTTGTATG	GCAAAGGTTTGTATG	-	novel	NA	P-0063644-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	40	513	0	ENST00000261769.5:c.1316_1320+10del		p.X439_splice	ENST00000261769	NM_004360.3	439		9/16	0.151676940680397	1	FACETS	0.803	0.666	0.956	0.803	0.666	0.956	CLONAL	1	TRUE	0	0.151676940680397	1		513	607	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641405	18641405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs553015066	NA	P-0063644-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	47	399	0	ENST00000266497.5:c.2404G>A	p.Glu802Lys	p.E802K	ENST00000266497		802	Gaa/Aaa	17/31	1	2	FACETS	0.982	0.828	1	0.982	0.828	1	CLONAL	1	TRUE	1	0.151676940680397	2		399	631	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119061	70119062	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0063644-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	59	742	0	ENST00000245479.2:c.635dup	p.His213ThrfsTer39	p.H213Tfs*39	ENST00000245479	NM_000346.3	211	-/C	2/3	1	2	FACETS	0.969	0.832	1	0.969	0.832	1	CLONAL	1	TRUE	1	0.151676940680397	2		742	803	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248998	55248999	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCAGCG	rs727504263	NA	P-0063645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	122	648	0	ENST00000275493.2:c.2300_2308dup	p.Ala767_Val769dup	p.A767_V769dup	ENST00000275493	NM_005228.3	767	atg/aTGGCCAGCGtg	20/28	1	2	FACETS	0.77	0.697	0.847	0.77	0.697	0.847	SUBCLONAL	1	TRUE	1	0.459367094296513	2		648	690	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031880	10031880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765104792	NA	P-0063645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	152	565	0	ENST00000330684.3:c.943G>A	p.Glu315Lys	p.E315K	ENST00000330684	NM_001134407.1	315	Gag/Aag	3/13	0.424104720435974	3	FACETS	0.961	0.879	1	0.48	0.439	0.523	CLONAL	1	TRUE	1	0.459367094296513	3		565	847	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112352	115112352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1247378046	NA	P-0063645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	189	671	0	ENST00000257566.3:c.1388C>T	p.Ala463Val	p.A463V	ENST00000257566	NM_016569.3	463	gCg/gTg	7/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.459367094296513	2		671	659	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150936801	150936801	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0063645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	361	633	0	ENST00000271640.5:c.3837T>A	p.Cys1279Ter	p.C1279*	ENST00000271640	NM_001145415.1	1279	tgT/tgA	22/22	0.434338793301737	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.459367094296513	2		633	781	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328385	137328391	+	frameshift_variant	Frame_Shift_Del	DEL	CTTCAAG	CTTCAAG	-	novel	NA	P-0063645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	164	597	0	ENST00000481739.1:c.1316_1322del	p.Phe439SerfsTer21	p.F439Sfs*21	ENST00000481739	NM_002957.4	438	ttCTTCAAG/tt	10/10	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.459367094296513	2		597	711	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	41	343	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.28311520383886	2		343	253	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0063646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	57	434	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.945	0.813	1	0.945	0.813	1	CLONAL	1	TRUE	1	0.28311520383886	2		434	426	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057811	27057811	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	86	814	0	ENST00000324856.7:c.1519C>T	p.Gln507Ter	p.Q507*	ENST00000324856	NM_006015.4	507	Caa/Taa	3/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.28311520383886	2		814	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578415	7578416	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCTCCGTCATGTGCTGTGACTGCTTGTAGATGG	novel	NA	P-0063646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	21	769	0	ENST00000269305.4:c.482_514dup	p.Ala161_Glu171dup	p.A161_E171dup	ENST00000269305	NM_001126112.2	161	gtt/gCCATCTACAAGCAGTCACAGCACATGACGGAGGtt	5/11	1	2	FACETS	0.267	0.204	0.34	0.267	0.204	0.34	SUBCLONAL	1	TRUE	1	0.28311520383886	2		769	556	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576778	67576778	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	57	346	0	ENST00000274335.5:c.860T>A	p.Ile287Lys	p.I287K	ENST00000274335		287	aTa/aAa	6/15	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.28311520383886	2		346	347	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0063647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	27	343	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.937	0.744	1	0.937	0.744	1	CLONAL	1	TRUE	1	0.11	2		343	524	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0063647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	31	479	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	0.947	0.764	1	0.947	0.764	1	CLONAL	1	TRUE	1	0.11	2		479	595	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63985107	63985142	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCCCCTCTTTTTTGAAAGCCAAAGGCACGTCCCTG	ACCCCCTCTTTTTTGAAAGCCAAAGGCACGTCCCTG	-	novel	NA	P-0063647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	33	492	0	ENST00000398590.3:c.2729-17_2747del		p.X910_splice	ENST00000398590	NM_001177387.1	910		14/14	1	2	FACETS	0.987	0.802	1	0.987	0.802	1	CLONAL	1	TRUE	1	0.11	2		492	608	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0063648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	32	462	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.18	2		462	302	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970924	70970924	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	36	591	0	ENST00000276594.2:c.1337G>C	p.Arg446Pro	p.R446P	ENST00000276594	NM_024504.3	446	cGg/cCg	6/8	1	2	FACETS	0.666	0.546	0.8	0.666	0.546	0.8	SUBCLONAL	1	TRUE	1	0.18	2		591	601	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332988	70332988	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	39	680	0	ENST00000373644.4:c.893C>A	p.Pro298His	p.P298H	ENST00000373644	NM_030625.2	298	cCc/cAc	2/12	1	2	FACETS	0.794	0.657	0.946	0.794	0.657	0.946	CLONAL	1	TRUE	1	0.18	2		680	546	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444022	49444022	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	49	796	0	ENST00000301067.7:c.3349G>C	p.Gly1117Arg	p.G1117R	ENST00000301067	NM_003482.3	1117	Ggc/Cgc	11/54	1	2	FACETS	0.95	0.804	1	0.95	0.804	1	CLONAL	1	TRUE	1	0.18	2		796	573	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544748	+	frameshift_variant	Frame_Shift_Ins	INS	CG	CG	AGA	novel	NA	P-0063648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	44	564	0	ENST00000358664.4:c.178_179delinsTCT	p.Arg60SerfsTer27	p.R60Sfs*27	ENST00000358664	NM_002382.4	60	CGg/TCTg	4/5	1	2	FACETS	0.964	0.809	1	0.964	0.809	1	CLONAL	1	TRUE	1	0.18	2		564	507	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0063648-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	104	387	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.536069252803852	5	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.5784211006947	5		387	452	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0063648-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	21	589	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	0.144	0.11	0.184	0.144	0.11	0.184	SUBCLONAL	1	TRUE	1	0.5784211006947	2		589	503	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218459	1218459	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0063648-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	169	583	1	ENST00000326873.7:c.334C>T	p.Gln112Ter	p.Q112*	ENST00000326873	NM_000455.4	112	Cag/Tag	2/10	0.5784211006947	1	FACETS	0.769	0.726	0.812	1	0.993	1	SUBCLONAL	2	TRUE	0	0.5784211006947	1		584	270	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203580	108203580	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs767670019	NA	P-0063648-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	111	407	0	ENST00000278616.4:c.7880A>G	p.Tyr2627Cys	p.Y2627C	ENST00000278616	NM_000051.3	2627	tAt/tGt	53/63	0.562179357214175	2	FACETS	0.936	0.865	1	0.936	0.865	1	CLONAL	2	TRUE	0	0.5784211006947	2		407	205	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196441	106196441	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063648-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	43	725	0	ENST00000380013.4:c.4774A>G	p.Thr1592Ala	p.T1592A	ENST00000380013	NM_001127208.2	1592	Acc/Gcc	11/11	1	2	FACETS	0.448	0.376	0.527	0.448	0.376	0.527	SUBCLONAL	1	TRUE	1	0.5784211006947	2		725	332	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0063649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	14	556	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.577	0.418	0.77	0.577	0.418	0.77	SUBCLONAL	1	TRUE	1	0.237719372281926	2		556	204	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0063649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	53	241	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.989	0.845	1	0.989	0.845	1	CLONAL	1	TRUE	1	0.237719372281926	2		241	451	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161888	47161891	+	frameshift_variant	Frame_Shift_Del	DEL	CTCT	CTCT	-	rs771527963	NA	P-0063649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	43	586	0	ENST00000409792.3:c.4235_4238del	p.Glu1412ValfsTer19	p.E1412Vfs*19	ENST00000409792	NM_014159.6	1412	gAGAGt/gt	3/21	1	2	FACETS	0.651	0.544	0.769	0.651	0.544	0.769	SUBCLONAL	1	TRUE	1	0.237719372281926	2		586	556	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165169	47165169	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0063649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	24	481	0	ENST00000409792.3:c.957del	p.Gly320ValfsTer20	p.G320Vfs*20	ENST00000409792	NM_014159.6	319	ctT/ct	3/21	1	2	FACETS	0.579	0.453	0.723	0.579	0.453	0.723	SUBCLONAL	1	TRUE	1	0.237719372281926	2		481	349	SUCCESS
APC	324	MSKCC	GRCh37	5	112173354	112173354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0063649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	30	537	0	ENST00000257430.4:c.2063C>T	p.Ser688Leu	p.S688L	ENST00000257430	NM_000038.5	688	tCa/tTa	16/16	1	2	FACETS	0.591	0.476	0.722	0.591	0.476	0.722	SUBCLONAL	1	TRUE	1	0.237719372281926	2		537	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0063650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	203	552	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.319346935704704	2	FACETS	0.895	0.834	0.957	0.895	0.834	0.957	CLONAL	2	TRUE	0	0.360557669193772	2		552	629	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0063650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	289	597	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.360557669193772	3	FACETS	1	0.991	1	0.818	0.773	0.864	CLONAL	2	TRUE	0	0.360557669193772	3		597	771	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424532	47424532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1321474185	NA	P-0063650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	84	847	0	ENST00000377045.4:c.452G>A	p.Arg151His	p.R151H	ENST00000377045	NM_001654.4	151	cGc/cAc	5/16	0.360557669193772	3	FACETS	0.937	0.829	1			1	CLONAL	1	TRUE	NA	0.360557669193772	3		847	587	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245453	153245453	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0063650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	405	568	1	ENST00000281708.4:c.1738C>T	p.His580Tyr	p.H580Y	ENST00000281708	NM_033632.3	580	Cac/Tac	11/12	0.319139868300238	4	FACETS	0.936	0.897	0.976	0.936	0.897	0.976	CLONAL	4	TRUE	0	0.360557669193772	4		569	816	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336624	81336624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771437724	NA	P-0063650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	121	451	0	ENST00000222390.5:c.1598G>A	p.Arg533Gln	p.R533Q	ENST00000222390	NM_000601.4	533	cGa/cAa	14/18	0.183771153687235	4	FACETS	0.801	0.726	0.879	0.801	0.726	0.879	INDETERMINATE	2	TRUE	2	0.360557669193772	4		451	570	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843333	128843333	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0063650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	86	754	0	ENST00000249373.3:c.440G>C	p.Cys147Ser	p.C147S	ENST00000249373	NM_005631.4	147	tGc/tCc	2/12	0.286321727619853	3	FACETS	0.713	0.63	0.802	0.356	0.315	0.401	SUBCLONAL	1	TRUE	1	0.360557669193772	3		754	790	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0063651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	322	586	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.462594514870137	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.462594514870137	2		586	695	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941729	48941730	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0063651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	75	204	0	ENST00000267163.4:c.1040_1041del	p.Ser347TyrfsTer5	p.S347Yfs*5	ENST00000267163	NM_000321.2	347	TCt/t	10/27	0.458193777196662	2	FACETS	0.881	0.79	0.975	0.881	0.79	0.975	CLONAL	2	TRUE	0	0.462594514870137	2		204	184	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102918	71102918	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs148369068	NA	P-0063651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	53	519	0	ENST00000318789.4:c.289G>C	p.Val97Leu	p.V97L	ENST00000318789	NM_032682.5	97	Gtg/Ctg	8/21	0.462594514870137	2	FACETS	0.421	0.359	0.489	0.211	0.179	0.245	SUBCLONAL	1	TRUE	0	0.462594514870137	2		519	544	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714408	117714408	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs770589705	NA	P-0063651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	222	426	0	ENST00000368508.3:c.1241T>C	p.Ile414Thr	p.I414T	ENST00000368508	NM_002944.2	414	aTt/aCt	11/43	0.215150986652674	3	FACETS	1	0.956	1	0.683	0.64	0.726	INDETERMINATE	2	TRUE	0	0.462594514870137	3		426	577	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464574	25464577	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	ONP	GCCC	GCCC	CCCA	novel	NA	P-0063651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	191	528	0	ENST00000264709.3:c.1937-1_1939delinsTGGG		p.X646_splice	ENST00000264709	NM_175629.2	646		17/23	0.219772605705306	3	FACETS	1	0.989	1	0.704	0.653	0.757	INDETERMINATE	1	TRUE	1	0.462594514870137	3		528	722	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121528	193121528	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0063652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	74	318	0	ENST00000367435.3:c.926T>C	p.Ile309Thr	p.I309T	ENST00000367435	NM_024529.4	309	aTt/aCt	10/17	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		318	132	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124503463	124503463	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	41	560	0	ENST00000357628.3:c.487G>T	p.Asp163Tyr	p.D163Y	ENST00000357628	NM_015450.2	163	Gac/Tac	8/19	1	2	FACETS	0.676	0.563	0.801	0.676	0.563	0.801	SUBCLONAL	1	TRUE	1	0.250253681155792	2		560	485	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274745	123274745	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	53	600	0	ENST00000358487.5:c.1173G>T	p.Met391Ile	p.M391I	ENST00000358487	NM_000141.4	391	atG/atT	9/18	1	2	FACETS	0.789	0.673	0.916	0.789	0.673	0.916	CLONAL	1	TRUE	1	0.250253681155792	2		600	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577111	7577112	+	missense_variant	Missense_Mutation	DNP	GC	GC	TA	novel	NA	P-0063653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	99	637	0	ENST00000269305.4:c.826_827delinsTA	p.Ala276Tyr	p.A276Y	ENST00000269305	NM_001126112.2	276	GCc/TAc	8/11	0.175373255579709	2	FACETS	1	0.979	1	0.698	0.624	0.775	CLONAL	1	TRUE	0	0.250253681155792	2		637	567	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527560	29527560	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs747241884	NA	P-0063653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	36	445	0	ENST00000356175.3:c.1009G>T	p.Glu337Ter	p.E337*	ENST00000356175	NM_000267.3	337	Gaa/Taa	9/57	1	2	FACETS	0.725	0.596	0.868	0.725	0.596	0.868	SUBCLONAL	1	TRUE	1	0.250253681155792	2		445	397	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559158	29559158	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0063653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	28	247	0	ENST00000356175.3:c.3265G>T	p.Glu1089Ter	p.E1089*	ENST00000356175	NM_000267.3	1089	Gaa/Taa	25/57	1	2	FACETS	0.627	0.501	0.77	0.627	0.501	0.77	SUBCLONAL	1	TRUE	1	0.250253681155792	2		247	357	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78617533	78617533	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0063653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	36	627	0	ENST00000306801.3:c.271C>G	p.Leu91Val	p.L91V	ENST00000306801	NM_020761.2	91	Ctg/Gtg	3/34	1	2	FACETS	0.602	0.494	0.723	0.602	0.494	0.723	SUBCLONAL	1	TRUE	1	0.250253681155792	2		627	478	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86648993	86648993	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0063653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	39	396	0	ENST00000274376.6:c.1273C>A	p.His425Asn	p.H425N	ENST00000274376	NM_002890.2	425	Cac/Aac	9/25	0.250253681155792	1	FACETS	0.888	0.739	1	0.888	0.739	1	CLONAL	1	TRUE	0	0.250253681155792	1		396	307	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776369	76776369	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0063653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	49	513	0	ENST00000373344.5:c.7097A>T	p.Glu2366Val	p.E2366V	ENST00000373344	NM_000489.3	2366	gAg/gTg	34/35	0.250253681155792	1	FACETS	0.902	0.766	1	0.902	0.766	1	CLONAL	1	TRUE	0	0.250253681155792	1		513	380	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0063663-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	34	698	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.477	0.389	0.577	0.477	0.389	0.577	SUBCLONAL	1	TRUE	1	0.253002824285938	2		698	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0063663-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	91	878	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	1	2	FACETS	0.996	0.885	1	0.996	0.885	1	CLONAL	1	TRUE	1	0.253002824285938	2		878	722	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259502	55259502	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0063663-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	36	581	0	ENST00000275493.2:c.2560A>G	p.Thr854Ala	p.T854A	ENST00000275493	NM_005228.3	854	Aca/Gca	21/28	1	2	FACETS	0.47	0.385	0.565	0.47	0.385	0.565	SUBCLONAL	1	TRUE	1	0.253002824285938	2		581	606	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0000370-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	59	575	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		575	97	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129430	64129430	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000370-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	21	424	0	ENST00000334205.4:c.862G>T	p.Gly288Trp	p.G288W	ENST00000334205	NM_003942.2	288	Ggg/Tgg	8/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		424	62	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736308	243736308	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754990008	NA	P-0000370-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	10	364	0	ENST00000263826.5:c.739C>T	p.Arg247Cys	p.R247C	ENST00000263826	NM_005465.4	247	Cgc/Tgc	8/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		364	67	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420300	88420300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000370-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	20	311	0	ENST00000360948.2:c.2386C>T	p.Pro796Ser	p.P796S	ENST00000360948	NM_001012338.2	796	Ccc/Tcc	19/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		311	55	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0000370-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	12	543	0	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		543	33	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983761	15983761	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs752731748	NA	P-0000370-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	25	326	0	ENST00000268712.3:c.3361G>T	p.Gly1121Cys	p.G1121C	ENST00000268712	NM_006311.3	1121	Ggt/Tgt	25/46	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		326	74	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76931740	76931740	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000370-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	34	662	0	ENST00000373344.5:c.3790G>T	p.Asp1264Tyr	p.D1264Y	ENST00000373344	NM_000489.3	1264	Gac/Tac	10/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		662	99	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211898	123211898	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000370-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	23	598	0	ENST00000218089.9:c.2765G>T	p.Ser922Ile	p.S922I	ENST00000218089	NM_001042749.1	922	aGt/aTt	27/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		598	97	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221787	55221788	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0000370-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	31	418	0	ENST00000275493.2:c.831_832delinsTT	p.Met277_Asp278delinsIleTyr	p.M277_D278delinsIY	ENST00000275493	NM_005228.3	277	atGGat/atTTat	7/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		418	57	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0000416-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	55	632	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		632	710	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867546	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs11466445	NA	P-0000416-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	28	3	0	ENST00000374994.4:c.70_78del	p.Ala24_Ala26del	p.A24_A26del	ENST00000374994	NM_004612.2	17	ctGGCGGCGGCg/ctg	1/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		3	82	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411928	116411928	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000416-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	25	350	0	ENST00000397752.3:c.2913C>A	p.Tyr971Ter	p.Y971*	ENST00000397752	NM_000245.2	971	taC/taA	14/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		350	235	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0000825-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	388	869	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.247182379577011	2	FACETS	0.99	0.943	1	1	0.995	1	CLONAL	3	TRUE	0	0.247182379577011	2		869	1057	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682974	241682974	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs755886213	NA	P-0000825-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	56	480	0	ENST00000366560.3:c.49G>C	p.Ala17Pro	p.A17P	ENST00000366560	NM_000143.3	17	Gct/Cct	1/10	0.24467332076168	3	FACETS	0.97	0.831	1	0.485	0.415	0.561	CLONAL	1	TRUE	1	0.247182379577011	3		480	525	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668681	52668681	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0000825-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	169	533	0	ENST00000394830.3:c.1238C>G	p.Ser413Ter	p.S413*	ENST00000394830	NM_018313.4	413	tCa/tGa	12/30	0.247182379577011	2	FACETS	0.904	0.833	0.978	0.904	0.833	0.978	CLONAL	2	TRUE	0	0.247182379577011	2		533	756	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799628	72799628	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000825-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	67	619	0	ENST00000325599.8:c.1541C>G	p.Ala514Gly	p.A514G	ENST00000325599	NM_018130.2	514	gCc/gGc	11/11	0.247182379577011	2	FACETS	0.813	0.706	0.929	0.406	0.353	0.465	CLONAL	1	TRUE	0	0.247182379577011	2		619	667	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100324	8100324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs904307886	NA	P-0000825-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	209	779	1	ENST00000346208.3:c.298G>A	p.Gly100Ser	p.G100S	ENST00000346208		100	Ggc/Agc	3/6	1	2	FACETS	1	0.938	1	1	0.994	1	CLONAL	2	TRUE	1	0.247182379577011	2		780	838	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109968	115109968	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000825-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	83	817	0	ENST00000257566.3:c.1910G>T	p.Arg637Leu	p.R637L	ENST00000257566	NM_016569.3	637	cGg/cTg	8/8	0.24467332076168	3	FACETS	0.954	0.841	1	0.477	0.42	0.538	CLONAL	1	TRUE	1	0.247182379577011	3		817	791	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911271	32911271	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786201837	NA	P-0000825-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	132	666	0	ENST00000380152.3:c.2779A>G	p.Met927Val	p.M927V	ENST00000380152		927	Atg/Gtg	11/27	0.247182379577011	2	FACETS	1	0.98	1	0.647	0.587	0.709	CLONAL	1	TRUE	0	0.247182379577011	2		666	826	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526445	66526445	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000825-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	139	433	0	ENST00000358598.2:c.1001C>T	p.Pro334Leu	p.P334L	ENST00000358598	NM_212471.2	334	cCt/cTt	11/11	0.24467332076168	3	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	1	0.247182379577011	3		433	604	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221215	1221215	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs137853083	NA	P-0000825-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	171	739	0	ENST00000326873.7:c.738C>G	p.Tyr246Ter	p.Y246*	ENST00000326873	NM_000455.4	246	taC/taG	6/10	0.247182379577011	2	FACETS	0.882	0.813	0.954	0.882	0.813	0.954	CLONAL	2	TRUE	0	0.247182379577011	2		739	784	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610466	10610466	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000825-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	167	695	0	ENST00000171111.5:c.244C>T	p.Gln82Ter	p.Q82*	ENST00000171111	NM_203500.1	82	Cag/Tag	2/6	0.247182379577011	2	FACETS	0.981	0.904	1	0.981	0.904	1	CLONAL	2	TRUE	0	0.247182379577011	2		695	689	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755657	39755657	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000825-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	166	672	0	ENST00000288319.7:c.1108C>G	p.Arg370Gly	p.R370G	ENST00000288319	NM_182918.3	370	Cgt/Ggt	10/10	0.247182379577011	2	FACETS	0.983	0.906	1	0.983	0.906	1	CLONAL	2	TRUE	0	0.247182379577011	2		672	683	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11205075	11205075	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000825-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	157	649	0	ENST00000361445.4:c.4714del	p.Asp1572MetfsTer4	p.D1572Mfs*4	ENST00000361445	NM_004958.3	1572	Gat/at	33/58	0.24467332076168	3	FACETS	0.922	0.846	1	0.922	0.846	1	CLONAL	2	TRUE	1	0.247182379577011	3		649	774	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129327	152129328	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000825-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	47	595	0	ENST00000206249.3:c.281dup	p.Leu100ThrfsTer57	p.L100Tfs*57	ENST00000206249	NM_000125.3	94	ctg/cTtg	1/8	1	2	FACETS	0.719	0.606	0.843	0.719	0.606	0.843	SUBCLONAL	1	TRUE	1	0.247182379577011	2		595	529	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262229	115262229	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000825-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	86	446	0	ENST00000438362.2:c.2325G>C	p.Lys775Asn	p.K775N	ENST00000438362	NM_001242891.1	775	aaG/aaC	18/20	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.247182379577011	2		446	690	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420529	49420529	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000825-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	94	669	0	ENST00000301067.7:c.15220G>T	p.Gly5074Cys	p.G5074C	ENST00000301067	NM_003482.3	5074	Ggc/Tgc	48/54	0.24467332076168	3	FACETS	1	0.94	1	0.544	0.483	0.608	CLONAL	1	TRUE	1	0.247182379577011	3		669	786	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019273	31019273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000825-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	65	480	0	ENST00000375687.4:c.868G>A	p.Glu290Lys	p.E290K	ENST00000375687	NM_015338.5	290	Gaa/Aaa	9/13	0.247182379577011	2	FACETS	0.954	0.828	1	0.477	0.414	0.546	CLONAL	1	TRUE	0	0.247182379577011	2		480	551	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066686	94066686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000825-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	64	591	0	ENST00000369303.4:c.1073G>A	p.Gly358Glu	p.G358E	ENST00000369303	NM_004440.3	358	gGg/gAg	5/17	1	2	FACETS	0.837	0.724	0.958	0.837	0.724	0.958	CLONAL	1	TRUE	1	0.247182379577011	2		591	619	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041058	112041058	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000825-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	57	530	0	ENST00000368678.4:c.197G>T	p.Gly66Val	p.G66V	ENST00000368678		66	gGt/gTt	3/13	1	2	FACETS	0.857	0.736	0.99	0.857	0.736	0.99	CLONAL	1	TRUE	1	0.247182379577011	2		530	538	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627729	187627729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758545401	NA	P-0000840-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	96	380	0	ENST00000441802.2:c.3253G>A	p.Gly1085Ser	p.G1085S	ENST00000441802	NM_005245.3	1085	Ggt/Agt	2/27	0.509020472575056	3	FACETS	0.736	0.656	0.82	0.368	0.328	0.41	SUBCLONAL	1	TRUE	1	0.509020472575056	3		380	643	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127712	2127712	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000840-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	72	212	0	ENST00000219476.3:c.2951A>T	p.Glu984Val	p.E984V	ENST00000219476	NM_000548.3	984	gAa/gTa	26/42	0.509020472575056	3	FACETS	1	0.954	1	0.586	0.516	0.659	CLONAL	1	TRUE	1	0.509020472575056	3		212	303	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158451	106158451	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000968-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	171	450	0	ENST00000380013.4:c.3352A>G	p.Asn1118Asp	p.N1118D	ENST00000380013	NM_001127208.2	1118	Aat/Gat	3/11	1	2	FACETS	0.981	0.911	1	0.981	0.911	1	CLONAL	1	FALSE	1	0.776602124516405	2		450	449	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412493	80412493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514698	NA	P-0000968-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	219	555	0	ENST00000286548.4:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000286548	NM_002072.3	183	cGa/cAa	4/7	0.430548413558854	1	FACETS	0.791	0.746	0.836	0.791	0.746	0.836	INDETERMINATE	1	FALSE	0	0.776602124516405	1		555	436	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396497	396497	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000968-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	187	549	0	ENST00000262320.3:c.529A>T	p.Ile177Phe	p.I177F	ENST00000262320	NM_003502.3	177	Atc/Ttc	2/11	1	2	FACETS	0.923	0.859	0.987	0.923	0.859	0.987	CLONAL	1	FALSE	1	0.776602124516405	2		549	522	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001018-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	33	320	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.532	0.433	0.645	0.532	0.433	0.645	SUBCLONAL	1	TRUE	1	0.251003465911404	2		321	494	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0001018-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	36	304	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.767	0.631	0.918	0.767	0.631	0.918	CLONAL	1	TRUE	1	0.251003465911404	2		304	374	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045667	47045667	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1556782537	NA	P-0001018-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	122	627	0	ENST00000377604.3:c.2548C>T	p.Gln850Ter	p.Q850*	ENST00000377604	NM_001204468.1	850	Cag/Tag	23/24	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.251003465911404	2		627	811	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567546196	NA	P-0001683-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	123	378	0	ENST00000269305.4:c.949del	p.Gln317SerfsTer28	p.Q317Sfs*28	ENST00000269305	NM_001126112.2	317	Cag/ag	9/11	0.381637403196072	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.381637403196072	1		378	503	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233146	46233146	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001683-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	174	365	0	ENST00000334344.6:c.1365G>C	p.Gln455His	p.Q455H	ENST00000334344	NM_152641.2	455	caG/caC	11/21	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.381637403196072	2		365	850	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218393	69218393	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001683-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	176	489	0	ENST00000462284.1:c.485C>G	p.Pro162Arg	p.P162R	ENST00000462284	NM_002392.5	162	cCa/cGa	7/11	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.381637403196072	2		489	905	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244391	41244391	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001683-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	147	479	0	ENST00000357654.3:c.3157G>A	p.Glu1053Lys	p.E1053K	ENST00000357654	NM_007294.3	1053	Gaa/Aaa	10/23	1	2	FACETS	0.906	0.828	0.989	0.906	0.828	0.989	CLONAL	1	TRUE	1	0.381637403196072	2		479	850	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367818	15367818	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1385204010	NA	P-0001683-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	28	342	0	ENST00000263377.2:c.1508C>G	p.Ser503Cys	p.S503C	ENST00000263377	NM_058243.2	503	tCt/tGt	8/20	0.304919079568855	1	FACETS	0.26	0.207	0.321	0.26	0.207	0.321	SUBCLONAL	1	TRUE	0	0.381637403196072	1		342	456	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526239	189526239	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002233-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	427	396	0	ENST00000264731.3:c.503A>G	p.Asn168Ser	p.N168S	ENST00000264731	NM_003722.4	168	aAc/aGc	4/14	0.948742572889015	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.948742572889015	1		396	468	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287185	33287185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002233-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	474	475	0	ENST00000374542.5:c.1912C>T	p.Gln638Ter	p.Q638*	ENST00000374542	NM_001141970.1	638	Caa/Taa	6/8	0.948742572889015	1	FACETS	0.999	0.98	1	0.999	0.98	1	CLONAL	1	TRUE	0	0.948742572889015	1		475	526	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134987	41134987	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002233-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	258	240	0	ENST00000379561.5:c.641G>T	p.Arg214Leu	p.R214L	ENST00000379561	NM_002015.3	214	cGt/cTt	2/3	0.948742572889015	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.948742572889015	1		240	281	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003412-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	56	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.568	0.487	0.657	0.568	0.487	0.657	SUBCLONAL	1	TRUE	1	0.37	2		452	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs267605076	NA	P-0003412-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	56	375	0	ENST00000269305.4:c.672G>T	p.Glu224Asp	p.E224D	ENST00000269305	NM_001126112.2	224	gaG/gaT	6/11	0.235618478457302	1	FACETS	0.703	0.605	0.809	0.703	0.605	0.809	SUBCLONAL	1	TRUE	0	0.37	1		375	351	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0003438-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	83	83	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.66222901379316	2		83	207	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0003438-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	206	276	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.969	0.92	1	1	0.995	1	CLONAL	2	TRUE	1	0.66222901379316	2		276	321	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102839	71102839	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003438-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	126	225	0	ENST00000318789.4:c.368C>T	p.Pro123Leu	p.P123L	ENST00000318789	NM_032682.5	123	cCt/cTt	8/21	1	2	FACETS	0.928	0.848	1	0.928	0.848	1	CLONAL	1	TRUE	1	0.66222901379316	2		225	410	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920378	114920378	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003438-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	195	293	0	ENST00000543371.1:c.1319A>T	p.Asp440Val	p.D440V	ENST00000543371	NM_001198531.1	440	gAt/gTt	13/14	1	2	FACETS	0.941	0.875	1	0.941	0.875	1	CLONAL	1	TRUE	1	0.66222901379316	2		293	626	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742921	17742921	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs769178698	NA	P-0003438-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	143	360	0	ENST00000250003.3:c.829G>C	p.Glu277Gln	p.E277Q	ENST00000250003	NM_002478.4	277	Gag/Cag	3/3	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.66222901379316	2		360	393	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179197	123179197	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003438-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	68	167	0	ENST00000218089.9:c.646C>T	p.Arg216Ter	p.R216*	ENST00000218089	NM_001042749.1	216	Cga/Tga	8/35	1	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.66222901379316	1		167	113	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087530	27087531	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0003438-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	300	485	0	ENST00000324856.7:c.2105dup	p.Pro703SerfsTer114	p.P703Sfs*114	ENST00000324856	NM_006015.4	702	tct/tCct	5/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.66222901379316	2		485	804	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444494	49444494	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0003438-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	215	427	0	ENST00000301067.7:c.2877C>G	p.Tyr959Ter	p.Y959*	ENST00000301067	NM_003482.3	959	taC/taG	11/54	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.66222901379316	2		427	627	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	161	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.939	0.862	1	0.939	0.862	1	CLONAL	1	TRUE	1	0.39	2		452	879	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951964	178951964	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	136	511	0	ENST00000263967.3:c.3019G>C	p.Gly1007Arg	p.G1007R	ENST00000263967	NM_006218.2	1007	Ggc/Cgc	21/21	1	2	FACETS	0.732	0.665	0.803	0.732	0.665	0.803	SUBCLONAL	1	TRUE	1	0.39	2		511	953	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089777	27089777	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0004934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	40	156	0	ENST00000324856.7:c.2732+1G>T		p.X911_splice	ENST00000324856	NM_006015.4	911			1	2	FACETS	0.725	0.605	0.856	0.725	0.605	0.856	SUBCLONAL	1	TRUE	1	0.39	2		156	283	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128030508	128030508	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	181	676	1	ENST00000285398.2:c.1760G>T	p.Gly587Val	p.G587V	ENST00000285398	NM_000122.1	587	gGg/gTg	11/15	1	2	FACETS	0.946	0.872	1	0.946	0.872	1	CLONAL	1	TRUE	1	0.39	2		677	981	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729974	30729974	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs397516840	NA	P-0004934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	151	336	0	ENST00000295754.5:c.1495G>T	p.Glu499Ter	p.E499*	ENST00000295754	NM_003242.5	499	Gaa/Taa	6/7	1	2	FACETS	0.948	0.867	1	0.948	0.867	1	CLONAL	1	TRUE	1	0.39	2		336	817	SUCCESS
APC	324	MSKCC	GRCh37	5	112174366	112174366	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	145	381	0	ENST00000257430.4:c.3075A>G	p.Ile1025Met	p.I1025M	ENST00000257430	NM_000038.5	1025	atA/atG	16/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.39	2		381	711	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372753	81372753	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	151	521	0	ENST00000222390.5:c.781C>A	p.Arg261Ser	p.R261S	ENST00000222390	NM_000601.4	261	Cgc/Agc	7/18	1	2	FACETS	0.844	0.771	0.92	0.844	0.771	0.92	CLONAL	1	TRUE	1	0.39	2		521	918	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553649	29553649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	295	483	0	ENST00000356175.3:c.2198C>T	p.Pro733Leu	p.P733L	ENST00000356175	NM_000267.3	733	cCc/cTc	18/57	0.3	3	FACETS	0.878	0.828	0.93	0.878	0.828	0.93	CLONAL	2	TRUE	1	0.39	3		483	1029	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123701	11123701	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	161	540	0	ENST00000358026.2:c.2351G>T	p.Gly784Val	p.G784V	ENST00000358026	NM_001128849.1	784	gGg/gTg	16/36	1	2	FACETS	0.968	0.888	1	0.968	0.888	1	CLONAL	1	TRUE	1	0.39	2		540	853	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525905	41525905	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	159	445	3	ENST00000263253.7:c.1180G>T	p.Ala394Ser	p.A394S	ENST00000263253	NM_001429.3	394	Gca/Tca	5/31	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.39	2		448	772	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032560	47032560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	174	695	0	ENST00000377604.3:c.466G>A	p.Ala156Thr	p.A156T	ENST00000377604	NM_001204468.1	156	Gca/Aca	5/24	1	2	FACETS	0.813	0.747	0.881	0.813	0.747	0.881	CLONAL	1	TRUE	1	0.39	2		695	1098	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044892	47044892	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	210	732	1	ENST00000377604.3:c.2218G>T	p.Glu740Ter	p.E740*	ENST00000377604	NM_001204468.1	740	Gag/Tag	20/24	1	2	FACETS	0.99	0.918	1	0.99	0.918	1	CLONAL	1	TRUE	1	0.39	2		733	1088	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422704	47422704	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	206	708	0	ENST00000377045.4:c.176G>T	p.Cys59Phe	p.C59F	ENST00000377045	NM_001654.4	59	tGt/tTt	3/16	1	2	FACETS	0.863	0.799	0.929	0.863	0.799	0.929	CLONAL	1	TRUE	1	0.39	2		708	1224	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890099	76890099	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004934-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	210	687	0	ENST00000373344.5:c.4795G>A	p.Gly1599Ser	p.G1599S	ENST00000373344	NM_000489.3	1599	Ggt/Agt	17/35	1	2	FACETS	0.91	0.844	0.979	0.91	0.844	0.979	CLONAL	1	TRUE	1	0.39	2		687	1183	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0005436-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	218	692	1	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.435429140394167	1	FACETS	0.886	0.826	0.947	0.886	0.826	0.947	CLONAL	1	TRUE	0	0.481205388610385	1		693	777	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434891	56434891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005436-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	263	720	0	ENST00000407977.2:c.2246C>T	p.Ser749Phe	p.S749F	ENST00000407977		749	tCt/tTt	9/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.481205388610385	2		720	1013	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27220134	27220138	+	frameshift_variant	Frame_Shift_Del	DEL	ATGAT	ATGAT	-	novel	NA	P-0005436-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	71	481	0	ENST00000380036.4:c.3191_3195del	p.Asp1064GlyfsTer4	p.D1064Gfs*4	ENST00000380036	NM_000459.3	1064	gATGAT/g	21/23	0.266516363737229	1	FACETS	0.375	0.328	0.427	0.375	0.328	0.427	INDETERMINATE	1	TRUE	0	0.481205388610385	1		481	597	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0005467-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	291	346	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.724172811756651	4	FACETS	0.946	0.916	0.976	0.946	0.916	0.976	CLONAL	4	TRUE	0	0.724172811756651	4		346	366	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675071	40675071	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005467-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	205	707	0	ENST00000249776.8:c.35T>G	p.Val12Gly	p.V12G	ENST00000249776	NM_033286.3	12	gTt/gGt	1/9	0.724172811756651	3	FACETS	0.979	0.91	1	0.326	0.303	0.35	CLONAL	1	TRUE	0	0.724172811756651	3		707	788	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128970	64128972	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	novel	NA	P-0005467-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	141	558	0	ENST00000334205.4:c.601_603del	p.Ile201del	p.I201del	ENST00000334205	NM_003942.2	200	acCATc/acc	6/17	0.724172811756651	3	FACETS	0.857	0.783	0.934	0.428	0.391	0.467	CLONAL	1	TRUE	1	0.724172811756651	3		558	619	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	98	320	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.757574009501653	2		321	256	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	222	864	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.757574009501653	2		864	573	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994138	21994138	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	95	566	0	ENST00000579755.1:c.193G>A	p.Gly65Ser	p.G65S	ENST00000579755		65	Ggt/Agt	1/3	1				0.631	0.777				SUBCLONAL	1	TRUE	1	0.757574009501653	2		566	357	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791728	42791728	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	132	764	0	ENST00000575354.2:c.614A>G	p.Asn205Ser	p.N205S	ENST00000575354	NM_015125.3	205	aAt/aGt	5/20	0.757574009501653	1	FACETS	0.668	0.615	0.722	0.668	0.615	0.722	SUBCLONAL	1	TRUE	0	0.757574009501653	1		764	324	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332811	70332811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	130	579	0	ENST00000373644.4:c.716C>T	p.Ser239Phe	p.S239F	ENST00000373644	NM_030625.2	239	tCc/tTc	2/12	1	2	FACETS	0.798	0.73	0.869	0.798	0.73	0.869	SUBCLONAL	1	TRUE	1	0.757574009501653	2		579	430	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760616	133760616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	128	774	0	ENST00000318560.5:c.2939C>T	p.Pro980Leu	p.P980L	ENST00000318560	NM_005157.4	980	cCc/cTc	11/11	1	2	FACETS	0.612	0.557	0.67	0.612	0.557	0.67	SUBCLONAL	1	TRUE	1	0.757574009501653	2		774	552	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18576896	18576896	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs753453484	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	111	475	0	ENST00000266497.5:c.2304G>A	p.Trp768Ter	p.W768*	ENST00000266497		768	tgG/tgA	16/31	1	2	FACETS	0.779	0.707	0.854	0.779	0.707	0.854	SUBCLONAL	1	TRUE	1	0.757574009501653	2		475	376	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680827	30680827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	110	690	0	ENST00000376406.3:c.892G>A	p.Asp298Asn	p.D298N	ENST00000376406	NM_014641.2	298	Gac/Aac	5/15	1	2	FACETS	0.626	0.565	0.689	0.626	0.565	0.689	SUBCLONAL	1	TRUE	1	0.757574009501653	2		690	464	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551928	150551928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	120	718	1	ENST00000369026.2:c.79G>A	p.Gly27Ser	p.G27S	ENST00000369026	NM_021960.4	27	Ggc/Agc	1/3	1	2	FACETS	0.74	0.673	0.809	0.74	0.673	0.809	SUBCLONAL	1	TRUE	1	0.757574009501653	2		719	428	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699363	47699363	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	80	488	0	ENST00000347630.2:c.145G>A	p.Gly49Ser	p.G49S	ENST00000347630	NM_001007230.1	49	Ggt/Agt	4/11	1	2	FACETS	0.627	0.556	0.701	0.627	0.556	0.701	SUBCLONAL	1	TRUE	1	0.757574009501653	2		488	337	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917802	29917802	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs112782816	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	108	621	0	ENST00000389048.3:c.866C>T	p.Ser289Phe	p.S289F	ENST00000389048	NM_004304.4	289	tCc/tTc	3/29	1	2	FACETS	0.68	0.615	0.749	0.68	0.615	0.749	SUBCLONAL	1	TRUE	1	0.757574009501653	2		621	419	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797810	42797810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	131	774	0	ENST00000575354.2:c.3862G>A	p.Glu1288Lys	p.E1288K	ENST00000575354	NM_015125.3	1288	Gag/Aag	16/20	0.757574009501653	1	FACETS	0.695	0.641	0.75	0.695	0.641	0.75	SUBCLONAL	1	TRUE	0	0.757574009501653	1		774	309	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937839	36937839	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	128	783	0	ENST00000361632.4:c.997G>T	p.Ala333Ser	p.A333S	ENST00000361632		333	Gcc/Tcc	7/16	0.757574009501653	1	FACETS	0.707	0.651	0.763	0.707	0.651	0.763	SUBCLONAL	1	TRUE	0	0.757574009501653	1		783	297	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206943221	206943221	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	102	590	0	ENST00000423557.1:c.397G>A	p.Glu133Lys	p.E133K	ENST00000423557	NM_000572.2	133	Gaa/Aaa	4/5	1	2	FACETS	0.675	0.608	0.745	0.675	0.608	0.745	SUBCLONAL	1	TRUE	1	0.757574009501653	2		590	399	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230561467	230561467	+	5_prime_UTR_variant	5'UTR	SNP	G	G	A	rs960793940	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	147	899	0	ENST00000391860.1:c.-138C>T		p.*46*	ENST00000391860	NM_001258311.1	-/409		1/7	1	2	FACETS	0.778	0.715	0.843	0.778	0.715	0.843	SUBCLONAL	1	TRUE	1	0.757574009501653	2		899	499	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10800258	10800258	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	139	644	0	ENST00000361367.2:c.3128C>T	p.Ser1043Leu	p.S1043L	ENST00000361367	NM_014633.3	1043	tCa/tTa	25/25	1	2	FACETS	0.696	0.637	0.758	0.696	0.637	0.758	SUBCLONAL	1	TRUE	1	0.757574009501653	2		644	527	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47594724	47594724	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	125	768	0	ENST00000430070.2:c.1363G>A	p.Asp455Asn	p.D455N	ENST00000430070	NM_018095.4	455	Gac/Aac	4/4	1	2	FACETS	0.637	0.579	0.697	0.637	0.579	0.697	SUBCLONAL	1	TRUE	1	0.757574009501653	2		768	518	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426949	49426949	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	139	761	0	ENST00000301067.7:c.11539C>T	p.Leu3847Phe	p.L3847F	ENST00000301067	NM_003482.3	3847	Ctt/Ttt	39/54	1	2	FACETS	0.734	0.672	0.798	0.734	0.672	0.798	SUBCLONAL	1	TRUE	1	0.757574009501653	2		761	500	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437697	49437697	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	160	729	0	ENST00000301067.7:c.5273G>A	p.Gly1758Glu	p.G1758E	ENST00000301067	NM_003482.3	1758	gGg/gAg	22/54	1	2	FACETS	0.794	0.733	0.857	0.794	0.733	0.857	SUBCLONAL	1	TRUE	1	0.757574009501653	2		729	532	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219159	133219159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	120	657	0	ENST00000320574.5:c.4885G>A	p.Ala1629Thr	p.A1629T	ENST00000320574	NM_006231.2	1629	Gcc/Acc	37/49	1	2	FACETS	0.645	0.586	0.707	0.645	0.586	0.707	SUBCLONAL	1	TRUE	1	0.757574009501653	2		657	491	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30095689	30095689	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	59	305	0	ENST00000331968.5:c.1798+1G>A		p.X600_splice	ENST00000331968	NM_002742.2	600			1	2	FACETS	0.683	0.595	0.776	0.683	0.595	0.776	SUBCLONAL	1	TRUE	1	0.757574009501653	2		305	228	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41962063	41962063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	108	597	0	ENST00000219905.7:c.971C>T	p.Thr324Ile	p.T324I	ENST00000219905	NM_001164273.1	324	aCt/aTt	2/24	1	2	FACETS	0.669	0.605	0.737	0.669	0.605	0.737	SUBCLONAL	1	TRUE	1	0.757574009501653	2		597	426	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50774218	50774218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	134	570	0	ENST00000307179.4:c.1759G>A	p.Asp587Asn	p.D587N	ENST00000307179		587	Gat/Aat	11/20	1	2	FACETS	0.795	0.728	0.864	0.795	0.728	0.864	SUBCLONAL	1	TRUE	1	0.757574009501653	2		570	445	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472520	88472520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	119	692	0	ENST00000360948.2:c.2035G>A	p.Asp679Asn	p.D679N	ENST00000360948	NM_001012338.2	679	Gac/Aac	16/19	1	2	FACETS	0.632	0.573	0.693	0.632	0.573	0.693	SUBCLONAL	1	TRUE	1	0.757574009501653	2		692	497	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30302718	30302718	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	32	256	0	ENST00000322652.5:c.809C>T	p.Thr270Ile	p.T270I	ENST00000322652	NM_015355.2	270	aCc/aTc	7/16	1	2	FACETS	0.538	0.442	0.643	0.538	0.442	0.643	SUBCLONAL	1	TRUE	1	0.757574009501653	2		256	157	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33434407	33434407	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	101	601	0	ENST00000345365.6:c.323G>A	p.Gly108Asp	p.G108D	ENST00000345365	NM_002878.3	108	gGc/gAc	4/10	1	2	FACETS	0.627	0.564	0.694	0.627	0.564	0.694	SUBCLONAL	1	TRUE	1	0.757574009501653	2		601	425	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508207	38508207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	130	650	0	ENST00000254066.5:c.515C>T	p.Pro172Leu	p.P172L	ENST00000254066	NM_000964.3	172	cCc/cTc	5/9	1	2	FACETS	0.724	0.661	0.789	0.724	0.661	0.789	SUBCLONAL	1	TRUE	1	0.757574009501653	2		650	474	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244910	41244910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	115	628	0	ENST00000357654.3:c.2638G>A	p.Glu880Lys	p.E880K	ENST00000357654	NM_007294.3	880	Gag/Aag	10/23	1	2	FACETS	0.669	0.606	0.734	0.669	0.606	0.734	SUBCLONAL	1	TRUE	1	0.757574009501653	2		628	454	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350503	15350503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	101	538	0	ENST00000263377.2:c.3412G>A	p.Glu1138Lys	p.E1138K	ENST00000263377	NM_058243.2	1138	Gag/Aag	16/20	1	2	FACETS	0.751	0.678	0.827	0.751	0.678	0.827	SUBCLONAL	1	TRUE	1	0.757574009501653	2		538	355	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965058	25965058	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	112	631	0	ENST00000435504.4:c.4148C>T	p.Pro1383Leu	p.P1383L	ENST00000435504		1383	cCt/cTt	13/13	1	2	FACETS	0.646	0.584	0.71	0.646	0.584	0.71	SUBCLONAL	1	TRUE	1	0.757574009501653	2		631	458	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21344699	21344699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	95	652	0	ENST00000215739.8:c.676C>T	p.Pro226Ser	p.P226S	ENST00000215739	NM_006767.3	226	Cca/Tca	8/21	1	2	FACETS	0.56	0.501	0.622	0.56	0.501	0.622	SUBCLONAL	1	TRUE	1	0.757574009501653	2		652	448	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713892	30713892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748480163	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	158	675	0	ENST00000295754.5:c.1217C>T	p.Pro406Leu	p.P406L	ENST00000295754	NM_003242.5	406	cCt/cTt	4/7	1	2	FACETS	0.799	0.737	0.863	0.799	0.737	0.863	SUBCLONAL	1	TRUE	1	0.757574009501653	2		675	522	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919107	178919107	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	79	487	0	ENST00000263967.3:c.592G>A	p.Val198Ile	p.V198I	ENST00000263967	NM_006218.2	198	Gtt/Att	4/21	1	2	FACETS	0.664	0.59	0.743	0.664	0.59	0.743	SUBCLONAL	1	TRUE	1	0.757574009501653	2		487	314	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039582	180039582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	116	655	0	ENST00000261937.6:c.3461G>A	p.Gly1154Glu	p.G1154E	ENST00000261937	NM_182925.4	1154	gGa/gAa	26/30	1	2	FACETS	0.787	0.716	0.861	0.787	0.716	0.861	SUBCLONAL	1	TRUE	1	0.757574009501653	2		655	389	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288609	33288609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	95	644	0	ENST00000374542.5:c.943G>A	p.Asp315Asn	p.D315N	ENST00000374542	NM_001141970.1	315	Gat/Aat	3/8	1	2	FACETS	0.615	0.551	0.682	0.615	0.551	0.682	SUBCLONAL	1	TRUE	1	0.757574009501653	2		644	408	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624374	140624374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	71	522	0	ENST00000288602.6:c.130C>T	p.Pro44Ser	p.P44S	ENST00000288602	NM_004333.4	44	Ccg/Tcg	1/18	1	2	FACETS	0.718	0.634	0.806	0.718	0.634	0.806	SUBCLONAL	1	TRUE	1	0.757574009501653	2		522	261	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194694	29194694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329754886	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	117	739	0	ENST00000240100.2:c.1034G>A	p.Ser345Asn	p.S345N	ENST00000240100	NM_001394.6	345	aGc/aAc	4/4	1	2	FACETS	0.72	0.654	0.789	0.72	0.654	0.789	SUBCLONAL	1	TRUE	1	0.757574009501653	2		739	429	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730404	133730404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	88	550	0	ENST00000318560.5:c.470G>A	p.Ser157Asn	p.S157N	ENST00000318560	NM_005157.4	157	aGt/aAt	3/11	1	2	FACETS	0.63	0.562	0.701	0.63	0.562	0.701	SUBCLONAL	1	TRUE	1	0.757574009501653	2		550	369	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932072	39932072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	146	355	0	ENST00000378444.4:c.2527G>A	p.Glu843Lys	p.E843K	ENST00000378444	NM_001123385.1	843	Gag/Aag	4/15	1	1	FACETS	0.788	0.732	0.844	0.788	0.732	0.844	SUBCLONAL	1	TRUE	0	0.757574009501653	1		355	304	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019663	123019663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005616-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	151	299	0	ENST00000355640.3:c.151G>A	p.Gly51Arg	p.G51R	ENST00000355640		51	Ggg/Agg	2/7	1	1	FACETS	0.884	0.826	0.942	0.884	0.826	0.942	CLONAL	1	TRUE	0	0.757574009501653	1		299	280	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	370	320	1				ENST00000310581	NM_198253.2	-/1132			0.620159350890442	8	FACETS	0.995	0.964	1	0.995	0.964	1	CLONAL	7	TRUE	1	0.620159350890442	8		321	490	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218052	108218052	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1064794840	NA	P-0005916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	48	340	0	ENST00000278616.4:c.8631G>C	p.Leu2877Phe	p.L2877F	ENST00000278616	NM_000051.3	2877	ttG/ttC	59/63	0.166419247966314	4	FACETS	1	0.958	1			1	INDETERMINATE	1	TRUE	NA	0.620159350890442	4		340	186	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0005916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	547	423	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.620159350890442	4	FACETS	1	0.996	1	1	0.996	1	CLONAL	4	TRUE	0	0.620159350890442	4		423	658	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525099	9525099	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	113	339	0	ENST00000353224.5:c.1786G>C	p.Glu596Gln	p.E596Q	ENST00000353224	NM_177990.2	596	Gag/Cag	8/10	0.394894412020822	5	FACETS	1	0.948	1	0.706	0.643	0.771	CLONAL	2	TRUE	2	0.620159350890442	5		339	332	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900206	101900206	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs727503470	NA	P-0005916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	119	315	0	ENST00000374994.4:c.640G>T	p.Gly214Cys	p.G214C	ENST00000374994	NM_004612.2	214	Ggt/Tgt	4/9	0.620159350890442	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.620159350890442	2		315	175	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057826	27057826	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	386	631	1	ENST00000324856.7:c.1534C>T	p.Gln512Ter	p.Q512*	ENST00000324856	NM_006015.4	512	Cag/Tag	3/20	0.620159350890442	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.620159350890442	2		632	512	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199803	108199803	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	73	219	0	ENST00000278616.4:c.7145G>T	p.Gly2382Val	p.G2382V	ENST00000278616	NM_000051.3	2382	gGa/gTa	49/63	0.166419247966314	4	FACETS	1	0.956	1			1	INDETERMINATE	2	TRUE	NA	0.620159350890442	4		219	169	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199922	108199922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1163371592	NA	P-0005916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	50	172	0	ENST00000278616.4:c.7264G>A	p.Glu2422Lys	p.E2422K	ENST00000278616	NM_000051.3	2422	Gag/Aag	49/63	0.166419247966314	4	FACETS	1	0.939	1			1	INDETERMINATE	2	TRUE	NA	0.620159350890442	4		172	116	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201074	108201074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	116	385	0	ENST00000278616.4:c.7441G>A	p.Asp2481Asn	p.D2481N	ENST00000278616	NM_000051.3	2481	Gat/Aat	50/63	0.166419247966314	4	FACETS	0.845	0.779	0.912			1	INDETERMINATE	3	TRUE	NA	0.620159350890442	4		385	239	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201142	108201142	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	95	330	0	ENST00000278616.4:c.7509G>C	p.Met2503Ile	p.M2503I	ENST00000278616	NM_000051.3	2503	atG/atC	50/63	0.166419247966314	4	FACETS	1	0.969	1			1	INDETERMINATE	2	TRUE	NA	0.620159350890442	4		330	215	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202172	108202172	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1555123920	NA	P-0005916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	59	277	0	ENST00000278616.4:c.7517G>A	p.Arg2506Lys	p.R2506K	ENST00000278616	NM_000051.3	2506	aGa/aAa	51/63	0.166419247966314	4	FACETS	1	0.961	1			1	INDETERMINATE	2	TRUE	NA	0.620159350890442	4		277	128	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202232	108202232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659323	NA	P-0005916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	80	410	0	ENST00000278616.4:c.7577G>A	p.Arg2526Lys	p.R2526K	ENST00000278616	NM_000051.3	2526	aGa/aAa	51/63	0.166419247966314	4	FACETS	0.876	0.795	0.958			1	INDETERMINATE	3	TRUE	NA	0.620159350890442	4		410	159	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110704	2110704	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	282	472	0	ENST00000219476.3:c.1009G>C	p.Glu337Gln	p.E337Q	ENST00000219476	NM_000548.3	337	Gag/Cag	11/42	0.620159350890442	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.620159350890442	2		472	425	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110736	2110736	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	284	484	0	ENST00000219476.3:c.1041G>C	p.Lys347Asn	p.K347N	ENST00000219476	NM_000548.3	347	aaG/aaC	11/42	0.620159350890442	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.620159350890442	2		484	414	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40747957	40747957	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	122	416	0	ENST00000392038.2:c.461A>G	p.Tyr154Cys	p.Y154C	ENST00000392038	NM_001626.4	154	tAt/tGt	6/14	0.620159350890442	3	FACETS	1	0.914	1	0.503	0.457	0.552	CLONAL	1	TRUE	1	0.620159350890442	3		416	512	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295001	1295001	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	43	31	0	ENST00000310581.5:c.104G>T	p.Gly35Val	p.G35V	ENST00000310581	NM_198253.2	35	gGc/gTc	1/16	0.620159350890442	8	FACETS	0.833	0.703	0.975	0.238	0.201	0.279	CLONAL	2	TRUE	1	0.620159350890442	8		31	238	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433643	149433643	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	113	409	0	ENST00000286301.3:c.2908C>T	p.Gln970Ter	p.Q970*	ENST00000286301	NM_005211.3	970	Cag/Tag	22/22	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.620159350890442	2		409	344	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540213	23540213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	95	206	0	ENST00000380871.4:c.190G>A	p.Gly64Arg	p.G64R	ENST00000380871	NM_006167.3	64	Gga/Aga	1/2	0.620159350890442	2	FACETS	1	0.983	1	0.712	0.648	0.778	CLONAL	1	TRUE	0	0.620159350890442	2		206	215	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797300	135797300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs118203401	NA	P-0005916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	218	204	0	ENST00000298552.3:c.569del	p.Arg190ProfsTer20	p.R190Pfs*20	ENST00000298552	NM_001162426.1	190	cGc/cc	7/23	0.620159350890442	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	4	TRUE	0	0.620159350890442	4		204	284	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0006280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	183	575	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.232764031324085	3	FACETS	0.906	0.836	0.979	0.906	0.836	0.979	CLONAL	2	TRUE	1	0.232764031324085	3		575	969	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082299	16082299	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs958489598	NA	P-0006280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	129	1014	1	ENST00000281043.3:c.113G>A	p.Gly38Asp	p.G38D	ENST00000281043	NM_005378.4	38	gGc/gAc	2/3	1	2	FACETS	0.986	0.892	1	0.986	0.892	1	CLONAL	1	TRUE	1	0.232764031324085	2		1015	1124	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793305	242793305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	130	1134	1	ENST00000334409.5:c.772G>A	p.Gly258Ser	p.G258S	ENST00000334409	NM_005018.2	258	Ggc/Agc	5/5	1	2	FACETS	0.982	0.889	1	0.982	0.889	1	CLONAL	1	TRUE	1	0.232764031324085	2		1135	1137	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577551	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0006280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	80	716	1	ENST00000269305.4:c.730_731delinsTT	p.Gly244Phe	p.G244F	ENST00000269305	NM_001126112.2	244	GGc/TTc	7/11	0.232764031324085	1	FACETS	0.811	0.713	0.916	0.811	0.713	0.916	CLONAL	1	TRUE	0	0.232764031324085	1		717	749	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090083	37090083	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	173	314	0	ENST00000231790.2:c.1972C>G	p.Leu658Val	p.L658V	ENST00000231790	NM_000249.3	658	Ctt/Gtt	17/19	1	2	FACETS	0.964	0.887	1	0.964	0.887	1	CLONAL	1	TRUE	1	0.346424879597452	2		314	1036	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936069	49936069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	222	393	0	ENST00000296474.3:c.1601G>A	p.Gly534Glu	p.G534E	ENST00000296474	NM_002447.2	534	gGg/gAg	4/20	1	2	FACETS	0.938	0.871	1	0.938	0.871	1	CLONAL	1	TRUE	1	0.346424879597452	2		393	1367	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0007092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	699	499	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.815533189525135	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.815380452521743	1		501	925	SUCCESS
APC	324	MSKCC	GRCh37	5	112174784	112174784	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0007092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	216	311	0	ENST00000257430.4:c.3493A>T	p.Lys1165Ter	p.K1165*	ENST00000257430	NM_000038.5	1165	Aaa/Taa	16/16	0.423924913189467	1	FACETS	0.742	0.7	0.784	0.742	0.7	0.784	INDETERMINATE	1	TRUE	0	0.815380452521743	1		311	423	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0007092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	185	426	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.815533189525135	1	FACETS	0.905	0.856	0.953	0.905	0.856	0.953	CLONAL	1	TRUE	0	0.815380452521743	1		426	297	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0007092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	94	258	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.423924913189467	1	FACETS	0.338	0.302	0.375	0.338	0.302	0.375	INDETERMINATE	1	TRUE	0	0.815380452521743	1		258	404	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298126	15298126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201118034	NA	P-0007092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	373	393	1	ENST00000263388.2:c.1630C>T	p.Arg544Cys	p.R544C	ENST00000263388	NM_000435.2	544	Cgc/Tgc	11/33	1	2	FACETS	0.915	0.871	0.96	0.915	0.871	0.96	CLONAL	1	TRUE	1	0.815380452521743	2		394	1000	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775464	39775464	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1384526747	NA	P-0007092-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	479	358	1	ENST00000288319.7:c.556G>A	p.Asp186Asn	p.D186N	ENST00000288319	NM_182918.3	186	Gac/Aac	4/10	0.414729218062205	1	FACETS	0.763	0.734	0.792	0.763	0.734	0.792	INDETERMINATE	1	TRUE	0	0.815380452521743	1		359	912	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACAACCCCC	rs397517115	NA	P-0010333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	487	264	0	ENST00000275493.2:c.2311_2319dup	p.Asn771_His773dup	p.N771_H773dup	ENST00000275493	NM_005228.3	771	gac/gACAACCCCCac	20/28	0.791873084257269	4	FACETS	0.844	0.814	0.875			1	CLONAL	3	TRUE	NA	0.791873084257269	4		264	870	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884464	151884464	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	82	474	0	ENST00000262189.6:c.4891A>T	p.Asn1631Tyr	p.N1631Y	ENST00000262189	NM_170606.2	1631	Aat/Tat	33/59	1	2	FACETS	0.326	0.287	0.368	0.326	0.287	0.368	SUBCLONAL	1	TRUE	1	0.791873084257269	2		474	635	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0010363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	43	207	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.937	0.788	1	0.937	0.788	1	CLONAL	1	TRUE	1	0.3	2		207	306	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	63	369	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.766	0.663	0.878	0.766	0.663	0.878	SUBCLONAL	1	TRUE	1	0.3	2		369	548	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0010363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	73	243	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.826	0.723	0.937	0.826	0.723	0.937	CLONAL	1	TRUE	1	0.3	2		243	589	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0010363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	65	229	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	1	2	FACETS	0.679	0.589	0.778	0.679	0.589	0.778	SUBCLONAL	1	TRUE	1	0.3	2		229	638	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982141	93982141	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0010363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	89	294	0	ENST00000369303.4:c.1325-1G>T		p.X442_splice	ENST00000369303	NM_004440.3	442			1	2	FACETS	0.937	0.832	1	0.937	0.832	1	CLONAL	1	TRUE	1	0.3	2		294	633	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119823	70119823	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010363-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	99	302	0	ENST00000245479.2:c.825del	p.Ile275MetfsTer4	p.I275Mfs*4	ENST00000245479	NM_000346.3	275	atC/at	3/3	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.3	2		302	635	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0012251-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	2314	346	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.349450716734636	19	FACETS	0.983	0.97	0.996			1	CLONAL	17	TRUE	NA	0.349450716734636	19		346	3146	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0012251-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	220	513	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.218371892988883	2	FACETS	1	0.992	1	0.746	0.695	0.798	CLONAL	1	TRUE	0	0.349450716734636	2		513	844	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197791	66197791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012251-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	96	728	0	ENST00000273854.3:c.2908G>A	p.Val970Ile	p.V970I	ENST00000273854	NM_004439.5	970	Gta/Ata	17/18	0.349450716734636	1	FACETS	0.463	0.412	0.518	0.463	0.412	0.518	SUBCLONAL	1	TRUE	0	0.349450716734636	1		728	979	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0014833-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	111	405	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.170750728963973	4	FACETS	0.782	0.704	0.865	0.782	0.704	0.865	SUBCLONAL	2	FALSE	2	0.255758087143484	4		405	697	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28929495	NA	P-0014833-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	102	530	0	ENST00000275493.2:c.2155G>T	p.Gly719Cys	p.G719C	ENST00000275493	NM_005228.3	719	Ggc/Tgc	18/28	0.170750728963973	4	FACETS	1	0.974	1	0.65	0.581	0.724	CLONAL	1	FALSE	2	0.255758087143484	4		530	770	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0014833-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	72	732	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	1	2	FACETS	0.572	0.498	0.652	0.572	0.498	0.652	SUBCLONAL	1	FALSE	1	0.255758087143484	2		732	984	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014833-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	112	781	0	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	1	2	FACETS	0.815	0.732	0.905	0.815	0.732	0.905	CLONAL	1	FALSE	1	0.255758087143484	2		781	1074	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456893	149456893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3829986	NA	P-0014833-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	45	537	1	ENST00000286301.3:c.835G>A	p.Val279Met	p.V279M	ENST00000286301	NM_005211.3	279	Gtg/Atg	6/22	1	2	FACETS	0.464	0.388	0.547	0.464	0.388	0.547	SUBCLONAL	1	FALSE	1	0.255758087143484	2		538	759	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612623	228612623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1277450211	NA	P-0014833-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	45	510	0	ENST00000366696.1:c.404G>A	p.Arg135Gln	p.R135Q	ENST00000366696	NM_003493.2	135	cGg/cAg	1/1	0.257040390567943	3	FACETS	0.537	0.45	0.634	0.269	0.225	0.317	SUBCLONAL	1	FALSE	1	0.255758087143484	3		510	739	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917504	178917504	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014833-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	23	243	0	ENST00000263967.3:c.379G>C	p.Glu127Gln	p.E127Q	ENST00000263967	NM_006218.2	127	Gaa/Caa	3/21	1	2	FACETS	0.52	0.405	0.653	0.52	0.405	0.653	SUBCLONAL	1	FALSE	1	0.255758087143484	2		243	346	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404185	139404185	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014833-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	65	568	0	ENST00000277541.6:c.2969G>T	p.Ser990Ile	p.S990I	ENST00000277541	NM_017617.3	990	aGc/aTc	18/34	1	2	FACETS	0.681	0.59	0.781	0.681	0.59	0.781	SUBCLONAL	1	FALSE	1	0.255758087143484	2		568	746	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519934	NA	P-0014932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	180	453	0	ENST00000263967.3:c.333G>C	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaC	2/21	0.482303705572181	5	FACETS	0.914	0.845	0.984	0.609	0.563	0.656	CLONAL	2	TRUE	2	0.482303705572181	5		453	704	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456400	40456400	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	130	615	0	ENST00000345506.4:c.1210G>C	p.Glu404Gln	p.E404Q	ENST00000345506	NM_003152.3	404	Gag/Cag	11/20	0.482303705572181	3	FACETS	0.81	0.735	0.889	0.405	0.367	0.445	CLONAL	1	TRUE	1	0.482303705572181	3		615	826	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78519452	78519452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	129	601	0	ENST00000306801.3:c.23C>T	p.Ser8Leu	p.S8L	ENST00000306801	NM_020761.2	8	tCg/tTg	1/34	0.482303705572181	5	FACETS	0.936	0.848	1	0.312	0.282	0.343	CLONAL	1	TRUE	2	0.482303705572181	5		601	985	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881512	111881530	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGCCCCACCTGCCAGCC	CTGGCCCCACCTGCCAGCC	-	novel	NA	P-0014932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	81	495	0	ENST00000393256.3:c.197_215del	p.Pro66LeufsTer12	p.P66Lfs*12	ENST00000393256	NM_006538.4	64	CTGGCCCCACCTGCCAGCCct/ct	2/4	0.482303705572181	3	FACETS	0.682	0.602	0.769	0.341	0.301	0.385	SUBCLONAL	1	TRUE	1	0.482303705572181	3		495	611	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265052	198265052	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	104	381	0	ENST00000335508.6:c.2825A>G	p.Asn942Ser	p.N942S	ENST00000335508	NM_012433.2	942	aAc/aGc	19/25	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.482303705572181	2		381	407	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39708783	39708783	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	101	414	0	ENST00000361337.2:c.394G>T	p.Asp132Tyr	p.D132Y	ENST00000361337	NM_003286.2	132	Gat/Tat	6/21	0.482303705572181	4	FACETS	1	0.898	1	0.501	0.449	0.557	CLONAL	1	TRUE	2	0.482303705572181	4		414	619	SUCCESS
AR	367	MSKCC	GRCh37	X	66863103	66863103	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	140	260	0	ENST00000374690.3:c.1622A>T	p.Glu541Val	p.E541V	ENST00000374690	NM_000044.3	541	gAg/gTg	2/8	0.435937623180784	2	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.482303705572181	2		260	419	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242470	+	missense_variant	Missense_Mutation	ONP	GGAATT	GGAATT	AATTCC	novel	NA	P-0014932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	804	677	0	ENST00000275493.2:c.2235_2240inv	p.Glu746_Leu747delinsIlePro	p.E746_L747delinsIP	ENST00000275493	NM_005228.3	745	aaGGAATTa/aaAATTCCa	19/28	0.482303705572181	8	FACETS	0.96	0.933	0.986			1	CLONAL	6	TRUE	NA	0.482303705572181	8		677	1417	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0015665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	188	304	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.546724075728598	3	FACETS	0.905	0.844	0.966	0.905	0.844	0.966	CLONAL	2	TRUE	1	0.546704628075206	3		304	484	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	111	331	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.545772834397472	2	FACETS	0.812	0.744	0.881	0.812	0.744	0.881	CLONAL	2	TRUE	0	0.546704628075206	2		331	250	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520000	NA	P-0015665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	644	843	0	ENST00000269305.4:c.452C>A	p.Pro151His	p.P151H	ENST00000269305	NM_001126112.2	151	cCc/cAc	5/11	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.546704628075206	2		843	1069	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143044	30143044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	339	833	0	ENST00000389048.3:c.482C>T	p.Ala161Val	p.A161V	ENST00000389048	NM_004304.4	161	gCg/gTg	1/29	0.546724075728598	3	FACETS	1	0.983	1	0.548	0.517	0.579	CLONAL	1	TRUE	1	0.546704628075206	3		833	1442	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26970485	26970485	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	62	299	0	ENST00000381527.3:c.854G>A	p.Arg285Lys	p.R285K	ENST00000381527	NM_001260.1	285	aGa/aAa	8/13	0.546724075728598	4	FACETS	1	0.878	1	0.337	0.292	0.385	CLONAL	1	TRUE	1	0.546704628075206	4		299	347	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007620	45007620	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0015665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	29	205	0	ENST00000558401.1:c.68del		p.X23_splice	ENST00000558401	NM_004048.2	23			1	2	FACETS	0.786	0.641	0.945	0.786	0.641	0.945	CLONAL	1	TRUE	1	0.546704628075206	2		205	135	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996194	73996194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759425133	NA	P-0015665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	200	610	0	ENST00000318443.5:c.928C>T	p.Arg310Cys	p.R310C	ENST00000318443	NM_001024736.1	310	Cgc/Tgc	5/10	1	2	FACETS	0.902	0.838	0.969	0.902	0.838	0.969	CLONAL	1	TRUE	1	0.546704628075206	2		610	811	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238989	5238989	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1294241597	NA	P-0015665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	273	620	2	ENST00000357368.4:c.1790G>A	p.Arg597His	p.R597H	ENST00000357368	NM_002850.3	597	cGc/cAc	13/38	0.546724075728598	3	FACETS	1	0.988	1	0.599	0.562	0.637	CLONAL	1	TRUE	1	0.546704628075206	3		622	1061	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001359	150001359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747544430	NA	P-0015665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	72	625	1	ENST00000253339.5:c.2245C>T	p.His749Tyr	p.H749Y	ENST00000253339		749	Cat/Tat	4/7	0.49377307876486	4	FACETS	0.634	0.553	0.72	0.211	0.184	0.24	SUBCLONAL	1	TRUE	1	0.546704628075206	4		626	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0017938-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1416	103	707	2	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		709	1519	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465558	8465558	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1400992051	NA	P-0017938-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	12	733	0	ENST00000356435.5:c.3622G>A	p.Asp1208Asn	p.D1208N	ENST00000356435		1208	Gac/Aac	21/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		733	223	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576257	88576257	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017938-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	43	340	0	ENST00000360948.2:c.1416T>A	p.Ser472Arg	p.S472R	ENST00000360948	NM_001012338.2	472	agT/agA	13/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		340	680	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662352	67662352	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017938-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	89	588	0	ENST00000264010.4:c.1598G>C	p.Arg533Pro	p.R533P	ENST00000264010	NM_006565.3	533	cGc/cCc	9/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		588	1166	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677331	29677332	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017938-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	58	400	0	ENST00000356175.3:c.7390dup	p.Tyr2464LeufsTer2	p.Y2464Lfs*2	ENST00000356175	NM_000267.3	2463	-/T	49/57	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		400	387	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085729	16085729	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017938-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1263	67	727	0	ENST00000281043.3:c.905G>T	p.Arg302Leu	p.R302L	ENST00000281043	NM_005378.4	302	cGt/cTt	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		727	1330	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61717882	61717883	+	missense_variant	Missense_Mutation	DNP	GT	GT	AA	novel	NA	P-0017938-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	63	696	1	ENST00000401558.2:c.1916_1917delinsTT	p.Tyr639Phe	p.Y639F	ENST00000401558	NM_003400.3	639	tAC/tTT	17/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		697	1084	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525724	187525724	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017938-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	47	314	0	ENST00000441802.2:c.10355A>C	p.Asn3452Thr	p.N3452T	ENST00000441802	NM_005245.3	3452	aAt/aCt	18/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		314	525	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86686619	86686619	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017938-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	20	497	0	ENST00000274376.6:c.3063C>G	p.His1021Gln	p.H1021Q	ENST00000274376	NM_002890.2	1021	caC/caG	25/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		497	214	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347866	128347866	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017938-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	55	631	0	ENST00000265960.3:c.639G>C	p.Gln213His	p.Q213H	ENST00000265960	NM_001006617.1	213	caG/caC	5/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		631	953	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932465	39932465	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017938-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	65	712	0	ENST00000378444.4:c.2134G>T	p.Glu712Ter	p.E712*	ENST00000378444	NM_001123385.1	712	Gag/Tag	4/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		712	1085	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0018245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	287	749	0	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	0.242766432294045	3	FACETS	0.903	0.851	0.955	0.903	0.851	0.955	CLONAL	3	TRUE	0	0.272011693811003	3		749	885	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727451	66727451	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519729	NA	P-0018245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	256	522	0	ENST00000307102.5:c.167A>C	p.Gln56Pro	p.Q56P	ENST00000307102	NM_002755.3	56	cAg/cCg	2/11	0.242766432294045	3	FACETS	0.938	0.882	0.995	0.938	0.882	0.995	CLONAL	3	TRUE	0	0.272011693811003	3		522	760	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602617	10602617	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	271	639	0	ENST00000171111.5:c.961G>C	p.Ala321Pro	p.A321P	ENST00000171111	NM_203500.1	321	Gcg/Ccg	3/6	0.272011693811003	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.272011693811003	2		639	903	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543210	65543210	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876659544	NA	P-0018245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	31	319	0	ENST00000358664.4:c.467G>A	p.Arg156Gln	p.R156Q	ENST00000358664	NM_002382.4	156	cGg/cAg	5/5	0.272011693811003	3	FACETS	0.577	0.466	0.702	0.288	0.233	0.351	SUBCLONAL	1	TRUE	1	0.272011693811003	3		319	449	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876461	35876461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1426	237	872	0	ENST00000303115.3:c.1253C>T	p.Pro418Leu	p.P418L	ENST00000303115	NM_002185.3	418	cCa/cTa	8/8	0.272011693811003	7	FACETS	0.88	0.819	0.944			1	CLONAL	2	TRUE	NA	0.272011693811003	7		872	1663	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248409	59248409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184098204	NA	P-0018245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	28	408	2	ENST00000371222.2:c.334G>A	p.Glu112Lys	p.E112K	ENST00000371222	NM_002228.3	112	Gag/Aag	1/1	0.272011693811003	3	FACETS	0.456	0.363	0.562	0.228	0.181	0.281	SUBCLONAL	1	TRUE	1	0.272011693811003	3		410	513	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056591	26056591	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	84	283	0	ENST00000343677.2:c.66G>C	p.Lys22Asn	p.K22N	ENST00000343677	NM_005319.3	22	aaG/aaC	1/1	0.205586753030692	5	FACETS	0.893	0.791	1	0.595	0.527	0.667	CLONAL	2	TRUE	2	0.272011693811003	5		283	487	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999201	100999201	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	54	769	0	ENST00000325455.5:c.601G>C	p.Glu201Gln	p.E201Q	ENST00000325455	NM_001202474.3	201	Gag/Cag	1/8	0.253018920315877	3	FACETS	0.489	0.416	0.569	0.245	0.208	0.285	SUBCLONAL	1	TRUE	1	0.272011693811003	3		769	922	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609780	28609780	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	290	742	1	ENST00000241453.7:c.1449G>T	p.Trp483Cys	p.W483C	ENST00000241453	NM_004119.2	483	tgG/tgT	12/24	0.272011693811003	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.272011693811003	2		743	993	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303747	91304239	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAACTACAGATTTGCTTTTGTGGCCTACCAGAGTAAACTACTTATATTTAATACGTTGTTCTCTTTTCTCTCTTCAGAAGGAAACTTCTAACGGAAGTAGATTTTAATAAAAGTGATGCCAGTCTTCTTGGCTCATTGTGGAGATACAGGCCTGATTCACTTGATGGCCCTATGGAGGGTGATTCCTGCCCTACAGGGAATTCTATGAAGGAGTTAAATTTTTCACACCTTCCCTCAAATTCTGTTTCTCCTGGGGACTGTTTACTGACTACCACCCTAGGAAAGACAGGATTCTCTGCCACCAGGAAGAATCTTTTTGAAAGGCCTTTATTCAATACCCATTTACAGAAGTCCTTTGTAAGTAGCAACTGGGCTGAAACACCAAGACTAGGAAAAAAAAATGAAAGCTCTTATTTCCCAGGAAATGTTCTCACAAGCACTGCTGTGAAAGATCAGAATAAACATACTGCTTCAATAAATGACTTAGAAAGAG	AAACTACAGATTTGCTTTTGTGGCCTACCAGAGTAAACTACTTATATTTAATACGTTGTTCTCTTTTCTCTCTTCAGAAGGAAACTTCTAACGGAAGTAGATTTTAATAAAAGTGATGCCAGTCTTCTTGGCTCATTGTGGAGATACAGGCCTGATTCACTTGATGGCCCTATGGAGGGTGATTCCTGCCCTACAGGGAATTCTATGAAGGAGTTAAATTTTTCACACCTTCCCTCAAATTCTGTTTCTCCTGGGGACTGTTTACTGACTACCACCCTAGGAAAGACAGGATTCTCTGCCACCAGGAAGAATCTTTTTGAAAGGCCTTTATTCAATACCCATTTACAGAAGTCCTTTGTAAGTAGCAACTGGGCTGAAACACCAAGACTAGGAAAAAAAAATGAAAGCTCTTATTTCCCAGGAAATGTTCTCACAAGCACTGCTGTGAAAGATCAGAATAAACATACTGCTTCAATAAATGACTTAGAAAGAG	-	novel	NA	P-0018245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	72	121	0	ENST00000355112.3:c.1221-73_1640del		p.X407_splice	ENST00000355112	NM_000057.2	407		7/22	0.242766432294045	3	FACETS	0.983	0.875	1	0.983	0.875	1	CLONAL	3	TRUE	0	0.272011693811003	3		121	204	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351727	89351727	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0018245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	170	885	0	ENST00000301030.4:c.1223C>G	p.Ser408Ter	p.S408*	ENST00000301030	NM_001256183.1	408	tCa/tGa	9/13	0.245553809847541	3	FACETS	1	0.974	1	0.572	0.525	0.622	CLONAL	1	TRUE	1	0.272011693811003	3		885	1241	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223769	36223769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1618	86	884	0	ENST00000222270.7:c.6319G>A	p.Glu2107Lys	p.E2107K	ENST00000222270	NM_014727.1	2107	Gag/Aag	28/37	0.272011693811003	6	FACETS	0.573	0.504	0.647			1	SUBCLONAL	1	TRUE	NA	0.272011693811003	6		884	1704	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794670	42794670	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	82	707	0	ENST00000575354.2:c.1750C>A	p.Pro584Thr	p.P584T	ENST00000575354	NM_015125.3	584	Cct/Act	10/20	0.272011693811003	3	FACETS	0.669	0.588	0.756			1	SUBCLONAL	1	TRUE	NA	0.272011693811003	3		707	1024	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606700	29606700	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775514690	NA	P-0018245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	203	735	1	ENST00000389048.3:c.1180G>A	p.Gly394Arg	p.G394R	ENST00000389048	NM_004304.4	394	Ggg/Agg	5/29	0.200395678873664	4	FACETS	0.916	0.849	0.986	0.916	0.849	0.986	CLONAL	2	TRUE	2	0.272011693811003	4		736	1036	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61710172	61710172	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	180	722	0	ENST00000401558.2:c.2732C>G	p.Ala911Gly	p.A911G	ENST00000401558	NM_003400.3	911	gCt/gGt	22/25	0.200395678873664	4	FACETS	1	0.989	1	0.75	0.69	0.812	CLONAL	1	TRUE	2	0.272011693811003	4		722	1123	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095541	178095541	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	68	554	0	ENST00000397062.3:c.1790G>C	p.Ser597Thr	p.S597T	ENST00000397062	NM_006164.4	597	aGt/aCt	5/5	0.200395678873664	4	FACETS	0.748	0.65	0.855	0.374	0.325	0.428	SUBCLONAL	1	TRUE	2	0.272011693811003	4		554	850	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483931	212483931	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs182073178	NA	P-0018245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	87	883	1	ENST00000342788.4:c.2272G>T	p.Gly758Cys	p.G758C	ENST00000342788	NM_005235.2	758	Ggt/Tgt	19/28	0.200395678873664	4	FACETS	0.691	0.609	0.778	0.345	0.304	0.389	SUBCLONAL	1	TRUE	2	0.272011693811003	4		884	1178	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158117	47158117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	63	828	0	ENST00000409792.3:c.4582G>A	p.Glu1528Lys	p.E1528K	ENST00000409792	NM_014159.6	1528	Gaa/Aaa	4/21	0.272011693811003	2	FACETS	0.44	0.379	0.507	0.22	0.189	0.254	SUBCLONAL	1	TRUE	0	0.272011693811003	2		828	1053	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045777	26045777	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	152	402	2	ENST00000540144.1:c.139G>A	p.Val47Met	p.V47M	ENST00000540144	NM_003531.2	47	Gtg/Atg	1/1	0.205586753030692	5	FACETS	0.849	0.779	0.921	0.849	0.779	0.921	CLONAL	3	TRUE	2	0.272011693811003	5		404	618	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056570	26056571	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCAG	novel	NA	P-0018245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	104	323	0	ENST00000343677.2:c.83_86dup	p.Gly30TrpfsTer6	p.G30Wfs*6	ENST00000343677	NM_005319.3	29	ggg/ggCTGGg	1/1	0.205586753030692	5	FACETS	1	0.935	1	0.702	0.631	0.777	CLONAL	2	TRUE	2	0.272011693811003	5		323	511	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967617	90967617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	51	554	0	ENST00000265433.3:c.1291C>T	p.Leu431Phe	p.L431F	ENST00000265433	NM_002485.4	431	Ctt/Ttt	10/16	0.205586753030692	5	FACETS	0.581	0.492	0.679	0.194	0.164	0.227	SUBCLONAL	1	TRUE	2	0.272011693811003	5		554	909	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492907	8492907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	222	691	1	ENST00000356435.5:c.2422G>A	p.Asp808Asn	p.D808N	ENST00000356435		808	Gat/Aat	16/35	0.261852704500436	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.272011693811003	2		692	804	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428194	47428194	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	113	813	0	ENST00000377045.4:c.1154del	p.Cys385LeufsTer59	p.C385Lfs*59	ENST00000377045	NM_001654.4	385	tGt/tt	11/16	0.22727871285562	4	FACETS	0.922	0.828	1			1	CLONAL	1	TRUE	NA	0.272011693811003	4		813	1146	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0018300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	134	776	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.240141925349451	2		777	999	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143350346	143350346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483862322	NA	P-0018300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	20	287	0	ENST00000262992.4:c.116C>T	p.Pro39Leu	p.P39L	ENST00000262992	NM_001101669.1	39	cCg/cTg	3/24	1	2	FACETS	0.552	0.422	0.703	0.552	0.422	0.703	SUBCLONAL	1	TRUE	1	0.240141925349451	2		287	302	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287568	33287568	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	83	563	0	ENST00000374542.5:c.1529C>G	p.Pro510Arg	p.P510R	ENST00000374542	NM_001141970.1	510	cCt/cGt	6/8	1	2	FACETS	0.907	0.8	1	0.907	0.8	1	CLONAL	1	TRUE	1	0.240141925349451	2		563	762	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841842	151841842	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	64	331	0	ENST00000262189.6:c.14299del	p.Thr4767LeufsTer43	p.T4767Lfs*43	ENST00000262189	NM_170606.2	4767	Act/ct	55/59	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.240141925349451	2		331	517	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0018916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1235	50	575	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.501657789936806	3	FACETS	0.194	0.164	0.228	0.097	0.082	0.114	SUBCLONAL	1	TRUE	1	0.501657789936806	3		575	1285	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0018916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	119	594	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	1	2	FACETS	0.473	0.426	0.523	0.473	0.426	0.523	SUBCLONAL	1	TRUE	1	0.501657789936806	2		594	1003	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0019070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	197	422	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.436105784133734	2		422	853	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956183	55956183	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	234	854	0	ENST00000263923.4:c.3132C>G	p.Ile1044Met	p.I1044M	ENST00000263923	NM_002253.2	1044	atC/atG	23/30	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.436105784133734	2		854	999	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197257	106197257	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	52	374	0	ENST00000380013.4:c.5590G>C	p.Val1864Leu	p.V1864L	ENST00000380013	NM_001127208.2	1864	Gtg/Ctg	11/11	1	2	FACETS	0.516	0.44	0.6	0.516	0.44	0.6	SUBCLONAL	1	TRUE	1	0.436105784133734	2		374	462	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0019303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	180	346	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.301530271928478	3	FACETS	0.757	0.699	0.819	0.757	0.699	0.819	SUBCLONAL	2	TRUE	1	0.301530271928478	3		346	907	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1555525429	NA	P-0019303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	184	630	0	ENST00000269305.4:c.782+1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.282322967653556	2	FACETS	0.914	0.847	0.982	0.914	0.847	0.982	CLONAL	2	TRUE	0	0.301530271928478	2		630	668	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604749	48604749	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	95	470	0	ENST00000342988.3:c.1571G>A	p.Trp524Ter	p.W524*	ENST00000342988	NM_005359.5	524	tGg/tAg	12/12	0.301530271928478	1	FACETS	0.826	0.736	0.921	0.826	0.736	0.921	CLONAL	1	TRUE	0	0.301530271928478	1		470	648	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120497	94120497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	37	404	0	ENST00000369303.4:c.554C>T	p.Ala185Val	p.A185V	ENST00000369303	NM_004440.3	185	gCc/gTc	3/17	1	2	FACETS	0.59	0.487	0.705	0.59	0.487	0.705	SUBCLONAL	1	TRUE	1	0.301530271928478	2		404	416	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0019303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	131	346	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.421708690883468	3	FACETS	1	0.963	1	0.556	0.505	0.609	CLONAL	1	TRUE	1	0.422326503405564	3		346	676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1555525429	NA	P-0019303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	286	630	0	ENST00000269305.4:c.782+1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.309310618844226	2	FACETS	0.763	0.72	0.808	0.763	0.72	0.808	SUBCLONAL	2	TRUE	0	0.422326503405564	2		630	887	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604749	48604749	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	127	470	0	ENST00000342988.3:c.1571G>A	p.Trp524Ter	p.W524*	ENST00000342988	NM_005359.5	524	tGg/tAg	12/12	0.422326503405564	1	FACETS	0.938	0.854	1	0.938	0.854	1	CLONAL	1	TRUE	0	0.422326503405564	1		470	506	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120497	94120497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	57	404	0	ENST00000369303.4:c.554C>T	p.Ala185Val	p.A185V	ENST00000369303	NM_004440.3	185	gCc/gTc	3/17	1	2	FACETS	0.613	0.527	0.707	0.613	0.527	0.707	SUBCLONAL	1	TRUE	1	0.422326503405564	2		404	440	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587520	29587520	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	41	416	0	ENST00000356175.3:c.4501C>G	p.Leu1501Val	p.L1501V	ENST00000356175	NM_000267.3	1501	Ctt/Gtt	33/57	0.422326503405564	3	FACETS	0.389	0.323	0.462			1	SUBCLONAL	1	TRUE	NA	0.422326503405564	3		416	605	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913400	NA	P-0019459-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	129	61	0	ENST00000349496.5:c.98C>A	p.Ser33Tyr	p.S33Y	ENST00000349496	NM_001904.3	33	tCt/tAt	3/15	1	2	FACETS	0.684	0.623	0.747	0.684	0.623	0.747	SUBCLONAL	1	TRUE	1	0.724179107092902	2		61	521	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0019459-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	54	384	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.282	0.241	0.327	0.282	0.241	0.327	SUBCLONAL	1	TRUE	1	0.724179107092902	2		384	529	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241722	55241722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1051753269	NA	P-0019459-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	429	129	0	ENST00000275493.2:c.2170G>A	p.Gly724Ser	p.G724S	ENST00000275493	NM_005228.3	724	Ggc/Agc	18/28	0.701546793257305	3	FACETS	0.902	0.864	0.939	0.902	0.864	0.939	CLONAL	2	TRUE	1	0.724179107092902	3		129	895	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366883	40366883	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019459-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	327	177	0	ENST00000397332.2:c.314C>A	p.Ser105Tyr	p.S105Y	ENST00000397332	NM_001033082.2	105	tCc/tAc	2/3	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.724179107092902	2		177	770	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357753	70357753	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019459-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	346	151	1	ENST00000374080.3:c.6004C>T	p.Gln2002Ter	p.Q2002*	ENST00000374080		2002	Cag/Tag	41/45	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.724179107092902	1		152	500	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0019459-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	230	102	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	0.701546793257305	3	FACETS	1	0.991	1	0.678	0.636	0.721	CLONAL	1	TRUE	1	0.724179107092902	3		102	638	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0019687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	243	426	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.550715840854188	2		426	838	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0019687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	22	506	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.124	0.096	0.158	0.124	0.096	0.158	SUBCLONAL	1	TRUE	1	0.550715840854188	2		506	642	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222987	1222987	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	356	403	0	ENST00000326873.7:c.924G>T	p.Trp308Cys	p.W308C	ENST00000326873	NM_000455.4	308	tgG/tgT	8/10	0.54307480434848	2	FACETS	0.953	0.912	0.995	0.953	0.912	0.995	CLONAL	2	TRUE	0	0.550715840854188	2		403	678	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260210	16260210	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	176	345	0	ENST00000375759.3:c.7475A>T	p.Gln2492Leu	p.Q2492L	ENST00000375759	NM_015001.2	2492	cAg/cTg	11/15	0.550715840854188	1	FACETS	0.959	0.891	1	0.959	0.891	1	CLONAL	1	TRUE	0	0.550715840854188	1		345	483	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004233	29004233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778277302	NA	P-0019687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	172	337	0	ENST00000282397.4:c.1060C>T	p.Arg354Trp	p.R354W	ENST00000282397	NM_002019.4	354	Cgg/Tgg	8/30	0.550715840854188	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.550715840854188	1		337	451	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900635	32900635	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs81002849	NA	P-0019687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	137	333	0	ENST00000380152.3:c.517-1G>T		p.X173_splice	ENST00000380152		173			0.550715840854188	1	FACETS	0.982	0.905	1	0.982	0.905	1	CLONAL	1	TRUE	0	0.550715840854188	1		333	367	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107930	30107930	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	199	415	1	ENST00000331968.5:c.877G>T	p.Gly293Trp	p.G293W	ENST00000331968	NM_002742.2	293	Ggg/Tgg	5/18	1	2	FACETS	0.888	0.824	0.954	0.888	0.824	0.954	CLONAL	1	TRUE	1	0.550715840854188	2		416	814	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133048	30133048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	160	381	0	ENST00000331968.5:c.553C>T	p.His185Tyr	p.H185Y	ENST00000331968	NM_002742.2	185	Cat/Tat	4/18	1	2	FACETS	0.867	0.798	0.939	0.867	0.798	0.939	CLONAL	1	TRUE	1	0.550715840854188	2		381	670	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872484	35872484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771984394	NA	P-0019687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	169	367	0	ENST00000216797.5:c.419G>A	p.Arg140Gln	p.R140Q	ENST00000216797	NM_020529.2	140	cGa/cAa	3/6	1	2	FACETS	0.886	0.817	0.957	0.886	0.817	0.957	CLONAL	1	TRUE	1	0.550715840854188	2		367	693	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226294	2226294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	233	497	0	ENST00000326181.6:c.1907C>T	p.Thr636Met	p.T636M	ENST00000326181	NM_032271.2	636	aCg/aTg	20/21	1	2	FACETS	0.949	0.886	1	0.949	0.886	1	CLONAL	1	TRUE	1	0.550715840854188	2		497	892	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684353	29684353	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	197	493	0	ENST00000356175.3:c.7873G>T	p.Ala2625Ser	p.A2625S	ENST00000356175	NM_000267.3	2625	Gcc/Tcc	53/57	1	2	FACETS	0.915	0.849	0.983	0.915	0.849	0.983	CLONAL	1	TRUE	1	0.550715840854188	2		493	782	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40457721	40457721	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0019687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	151	341	0	ENST00000345506.4:c.1473+1G>T		p.X491_splice	ENST00000345506	NM_003152.3	491			1	2	FACETS	0.82	0.751	0.891	0.82	0.751	0.891	CLONAL	1	TRUE	1	0.550715840854188	2		341	669	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40871178	40871178	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	236	532	0	ENST00000428826.2:c.712A>C	p.Ser238Arg	p.S238R	ENST00000428826		238	Agt/Cgt	8/21	1	2	FACETS	0.959	0.896	1	0.959	0.896	1	CLONAL	1	TRUE	1	0.550715840854188	2		532	894	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897376	78897376	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	423	495	0	ENST00000306801.3:c.2711G>T	p.Gly904Val	p.G904V	ENST00000306801	NM_020761.2	904	gGc/gTc	23/34	0.5502625350039	3	FACETS	0.942	0.9	0.984	0.942	0.9	0.984	CLONAL	2	TRUE	1	0.550715840854188	3		495	1040	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573474	48573474	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1568202971	NA	P-0019687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	130	253	0	ENST00000342988.3:c.58G>T	p.Val20Leu	p.V20L	ENST00000342988	NM_005359.5	20	Gtg/Ttg	2/12	0.530540839771473	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.550715840854188	1		253	310	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602584	10602584	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1208201314	NA	P-0019687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	440	475	0	ENST00000171111.5:c.994G>T	p.Gly332Cys	p.G332C	ENST00000171111	NM_203500.1	332	Ggc/Tgc	3/6	0.54307480434848	2	FACETS	0.991	0.953	1	0.991	0.953	1	CLONAL	2	TRUE	0	0.550715840854188	2		475	806	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113759	11113759	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	459	513	0	ENST00000358026.2:c.1867G>T	p.Glu623Ter	p.E623*	ENST00000358026	NM_001128849.1	623	Gag/Tag	12/36	0.54307480434848	2	FACETS	0.925	0.889	0.961	0.925	0.889	0.961	CLONAL	2	TRUE	0	0.550715840854188	2		513	901	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905539	50905539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	283	494	0	ENST00000440232.2:c.667G>T	p.Ala223Ser	p.A223S	ENST00000440232	NM_002691.3	223	Gcc/Tcc	6/27	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.550715840854188	2		494	961	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872801	136872801	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1419294193	NA	P-0019687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	159	294	0	ENST00000241393.3:c.697C>A	p.Gln233Lys	p.Q233K	ENST00000241393	NM_003467.2	233	Cag/Aag	2/2	1	2	FACETS	0.975	0.898	1	0.975	0.898	1	CLONAL	1	TRUE	1	0.550715840854188	2		294	592	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728630	190728630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770849733	NA	P-0019687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	197	446	0	ENST00000441310.2:c.2018C>T	p.Ser673Phe	p.S673F	ENST00000441310	NM_000534.4	673	tCt/tTt	10/13	1	2	FACETS	0.883	0.819	0.949	0.883	0.819	0.949	CLONAL	1	TRUE	1	0.550715840854188	2		446	810	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059226	47059226	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	109	320	0	ENST00000409792.3:c.7435T>A	p.Ser2479Thr	p.S2479T	ENST00000409792	NM_014159.6	2479	Tcc/Acc	20/21	1	2	FACETS	0.711	0.64	0.785	0.711	0.64	0.785	SUBCLONAL	1	TRUE	1	0.550715840854188	2		320	557	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147551	47147551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	219	405	0	ENST00000409792.3:c.4775G>A	p.Arg1592Gln	p.R1592Q	ENST00000409792	NM_014159.6	1592	cGa/cAa	6/21	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.550715840854188	2		405	740	SUCCESS
ATR	545	MSKCC	GRCh37	3	142234270	142234270	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	309	475	0	ENST00000350721.4:c.4470G>T	p.Trp1490Cys	p.W1490C	ENST00000350721	NM_001184.3	1490	tgG/tgT	25/47	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.550715840854188	2		475	971	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584686	187584686	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	208	446	0	ENST00000441802.2:c.3347T>C	p.Val1116Ala	p.V1116A	ENST00000441802	NM_005245.3	1116	gTc/gCc	3/27	1	2	FACETS	0.868	0.807	0.932	0.868	0.807	0.932	CLONAL	1	TRUE	1	0.550715840854188	2		446	870	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189003	32189003	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	213	496	0	ENST00000375023.3:c.551C>G	p.Pro184Arg	p.P184R	ENST00000375023	NM_004557.3	184	cCg/cGg	4/30	1	2	FACETS	0.882	0.821	0.945	0.882	0.821	0.945	CLONAL	1	TRUE	1	0.550715840854188	2		496	877	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729968	41729968	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	210	528	1	ENST00000242208.4:c.561C>A	p.Asp187Glu	p.D187E	ENST00000242208	NM_002192.2	187	gaC/gaA	3/3	1	2	FACETS	0.88	0.818	0.943	0.88	0.818	0.943	CLONAL	1	TRUE	1	0.550715840854188	2		529	867	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273447	38273447	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	362	817	0	ENST00000425967.3:c.1888G>T	p.Asp630Tyr	p.D630Y	ENST00000425967	NM_001174067.1	630	Gac/Tac	14/19	0.550715840854188	1	FACETS	0.976	0.928	1	0.976	0.928	1	CLONAL	1	TRUE	0	0.550715840854188	1		817	976	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636752	8636752	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	178	410	0	ENST00000356435.5:c.157C>A	p.Pro53Thr	p.P53T	ENST00000356435		53	Cct/Act	2/35	0.550715840854188	1	FACETS	0.958	0.891	1	0.958	0.891	1	CLONAL	1	TRUE	0	0.550715840854188	1		410	489	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137326013	137326014	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0019687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	273	541	0	ENST00000481739.1:c.1201_1202delinsTT	p.Glu401Leu	p.E401L	ENST00000481739	NM_002957.4	401	GAg/TTg	9/10	0.550715840854188	3	FACETS	0.974	0.913	1	0.487	0.456	0.519	CLONAL	1	TRUE	1	0.550715840854188	3		541	1298	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941979	44941979	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	203	387	0	ENST00000377967.4:c.3229G>C	p.Gly1077Arg	p.G1077R	ENST00000377967	NM_021140.2	1077	Gga/Cga	22/29	1	2	FACETS	0.942	0.875	1	0.942	0.875	1	CLONAL	1	TRUE	1	0.550715840854188	2		387	783	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223000	53223000	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	256	543	0	ENST00000375401.3:c.4072A>G	p.Thr1358Ala	p.T1358A	ENST00000375401	NM_004187.3	1358	Acc/Gcc	24/26	1	2	FACETS	0.904	0.847	0.963	0.904	0.847	0.963	CLONAL	1	TRUE	1	0.550715840854188	2		543	1028	SUCCESS
AR	367	MSKCC	GRCh37	X	66943605	66943605	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	276	496	2	ENST00000374690.3:c.2685G>T	p.Met895Ile	p.M895I	ENST00000374690	NM_000044.3	895	atG/atT	8/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.550715840854188	2		498	961	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019961-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	176	369	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.460174363932154	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	2	0.460174363932154	4		369	530	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219381	1219381	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019961-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	365	796	0	ENST00000326873.7:c.433G>T	p.Glu145Ter	p.E145*	ENST00000326873	NM_000455.4	145	Gag/Tag	3/10	0.460174363932154	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.460174363932154	2		796	776	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239812	105239812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1390179436	NA	P-0019961-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	378	918	0	ENST00000349310.3:c.808G>A	p.Val270Met	p.V270M	ENST00000349310	NM_001014432.1	270	Gtg/Atg	10/15	0.370732834619768	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.460174363932154	4		918	1172	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623218	52623218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1402934247	NA	P-0019961-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	329	676	0	ENST00000394830.3:c.2833C>T	p.Arg945Cys	p.R945C	ENST00000394830	NM_018313.4	945	Cgc/Tgc	19/30	0.460174363932154	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.460174363932154	2		676	653	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623229	52623229	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0019961-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	322	670	0	ENST00000394830.3:c.2822C>G	p.Ser941Ter	p.S941*	ENST00000394830	NM_018313.4	941	tCa/tGa	19/30	0.460174363932154	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.460174363932154	2		670	629	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15809088	15809088	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019961-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	128	634	0	ENST00000307771.7:c.73G>T	p.Glu25Ter	p.E25*	ENST00000307771	NM_005089.3	25	Gag/Tag	2/11	0.20734552569938	3	FACETS	1	0.924	1	0.34	0.308	0.373	INDETERMINATE	1	TRUE	0	0.460174363932154	3		634	671	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428185	47428185	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019961-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	115	780	0	ENST00000377045.4:c.1145C>T	p.Thr382Ile	p.T382I	ENST00000377045	NM_001654.4	382	aCa/aTa	11/16	NA	2	FACETS	0.653	0.589	0.722			1	INDETERMINATE	1	TRUE	NA	0.460174363932154	2		780	765	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722179	176722179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772882533	NA	P-0019961-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	159	933	1	ENST00000439151.2:c.7810G>A	p.Gly2604Arg	p.G2604R	ENST00000439151	NM_022455.4	2604	Ggg/Agg	23/23	0.421997235388056	4	FACETS	0.939	0.859	1	0.469	0.429	0.511	CLONAL	1	TRUE	2	0.460174363932154	4		934	1075	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442569	52442569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1298276806	NA	P-0020619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	22	696	1	ENST00000460680.1:c.176G>A	p.Arg59Gln	p.R59Q	ENST00000460680	NM_004656.3	59	cGg/cAg	4/17	0.206389056034766	4	FACETS	0.756	0.591	0.946	0.756	0.591	0.946	CLONAL	2	TRUE	2	0.206389056034766	4		697	170	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835794	68835794	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	25	728	0	ENST00000261769.5:c.385C>T	p.Gln129Ter	p.Q129*	ENST00000261769	NM_004360.3	129	Cag/Tag	3/16	0.206389056034766	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.206389056034766	1		728	170	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49449082	49449082	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	26	898	0	ENST00000301067.7:c.26A>G	p.Glu9Gly	p.E9G	ENST00000301067	NM_003482.3	9	gAg/gGg	1/54	0.206389056034766	5	FACETS	1	0.914	1	0.66	0.524	0.814	CLONAL	1	TRUE	3	0.206389056034766	5		898	250	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032250	42032250	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0020619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	19	835	1	ENST00000219905.7:c.4435-1G>A		p.X1479_splice	ENST00000219905	NM_001164273.1	1479			1	2	FACETS	0.79	0.601	1	0.79	0.601	1	CLONAL	1	TRUE	1	0.206389056034766	2		836	233	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713236	43713236	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	13	1071	0	ENST00000382044.4:c.4237A>G	p.Thr1413Ala	p.T1413A	ENST00000382044	NM_001141980.1	1413	Acc/Gcc	20/28	1	2	FACETS	0.594	0.424	0.801	0.594	0.424	0.801	SUBCLONAL	1	TRUE	1	0.206389056034766	2		1071	212	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0021839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	284	743	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.307434010174904	3	FACETS	0.812	0.763	0.862	0.812	0.763	0.862	CLONAL	2	TRUE	1	0.386424407901175	3		743	1080	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0021839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	15	752	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.386424407901175	1	FACETS	0.091	0.066	0.121	0.091	0.066	0.121	SUBCLONAL	1	TRUE	0	0.386424407901175	1		752	691	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571891	64571891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	88	1041	0	ENST00000312049.6:c.1748C>T	p.Ser583Leu	p.S583L	ENST00000312049	NM_130799.2	583	tCg/tTg	10/10	1	2	FACETS	0.378	0.333	0.426	0.378	0.333	0.426	SUBCLONAL	1	TRUE	1	0.386424407901175	2		1041	1205	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47604179	47604183	+	frameshift_variant	Frame_Shift_Del	DEL	GTTAT	GTTAT	C	novel	NA	P-0021839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	127	646	0	ENST00000263735.4:c.518_522delinsC	p.Arg173ProfsTer36	p.R173Pfs*36	ENST00000263735	NM_002354.2	173	cGTTAT/cC	5/9	1	2	FACETS	0.757	0.686	0.833	0.757	0.686	0.833	SUBCLONAL	1	TRUE	1	0.386424407901175	2		646	868	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0023456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	549	575	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.382139167957582	6	FACETS	1	0.979	1	1	0.979	1	CLONAL	4	TRUE	2	0.382139167957582	6		575	1237	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044550	47044550	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	149	458	0	ENST00000377604.3:c.2047G>T	p.Glu683Ter	p.E683*	ENST00000377604	NM_001204468.1	683	Gag/Tag	18/24	1	1	FACETS	0.799	0.738	0.86	1	0.99	1	SUBCLONAL	2	TRUE	0	0.382139167957582	1		458	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0023456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	385	797	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.382139167957582	3	FACETS	0.947	0.904	0.989	0.947	0.904	0.989	CLONAL	3	TRUE	0	0.382139167957582	3		797	845	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820846	36820846	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs770651057	NA	P-0023456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	349	683	2	ENST00000373129.3:c.531C>G	p.Ile177Met	p.I177M	ENST00000373129	NM_032017.1	177	atC/atG	6/12	0.349909598849497	4	FACETS	0.892	0.848	0.938	0.892	0.848	0.938	CLONAL	3	TRUE	1	0.382139167957582	4		685	943	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207775	102207775	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	326	612	0	ENST00000263464.3:c.1757G>C	p.Arg586Thr	p.R586T	ENST00000263464	NM_001165.4	586	aGa/aCa	9/9	0.382139167957582	5	FACETS	0.989	0.937	1	0.989	0.937	1	CLONAL	3	TRUE	2	0.382139167957582	5		612	905	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0023702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	176	872	0	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	0.504084049944974	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.705107348970483	2		872	237	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493708	56493709	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTAGAC	rs755187499	NA	P-0023702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	134	726	0	ENST00000267101.3:c.3037_3042dup	p.Asp1014_Leu1015dup	p.D1014_L1015dup	ENST00000267101	NM_001982.3	1014	-/CTAGAC	25/28	0.705107348970483	7	FACETS	0.896	0.829	0.964			1	CLONAL	4	TRUE	NA	0.705107348970483	7		726	293	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733184	74733184	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1469	228	824	0	ENST00000359995.5:c.59A>G	p.Asn20Ser	p.N20S	ENST00000359995	NM_001195427.1	20	aAc/aGc	1/3	0.705107348970483	16	FACETS	1	0.978	1			1	CLONAL	2	TRUE	NA	0.705107348970483	16		824	1697	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39623731	39623731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	29	708	0	ENST00000262039.4:c.2138G>A	p.Gly713Glu	p.G713E	ENST00000262039	NM_002647.2	713	gGg/gAg	20/25	0.705107348970483	5	FACETS	0.951	0.771	1	0.238	0.192	0.288	CLONAL	1	TRUE	1	0.705107348970483	5		708	178	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50143354	50143355	+	start_lost	Translation_Start_Site	DNP	AT	AT	GA	novel	NA	P-0023702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	45	46	0	ENST00000246792.3:c.1_2delinsTC	p.Met1?	p.M1?	ENST00000246792	NM_006270.3	1	ATg/TCg	1/6	0.705107348970483	7	FACETS	0.926	0.798	1	0.694	0.598	0.794	CLONAL	3	TRUE	3	0.705107348970483	7		46	127	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024257-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	340	320	1				ENST00000310581	NM_198253.2	-/1132			0.482261086071764	2	FACETS	1	0.996	1	0.712	0.685	0.738	INDETERMINATE	1	TRUE	0	0.946208703600177	2		321	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0024257-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	701	432	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.997	1	1	0.998	1	CLONAL	2	TRUE	1	0.946208703600177	2		432	726	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652134	36652135	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0024257-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	677	628	0	ENST00000244741.5:c.259dup	p.Asp87GlyfsTer2	p.D87Gfs*2	ENST00000244741	NM_000389.4	86	cgg/cGgg	2/3	NA	2	FACETS	0.933	0.917	0.947			1	INDETERMINATE	2	TRUE	NA	0.946208703600177	2		628	767	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112509	115112509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264716771	NA	P-0024257-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	277	595	1	ENST00000257566.3:c.1231G>A	p.Ala411Thr	p.A411T	ENST00000257566	NM_016569.3	411	Gcg/Acg	7/8	0.469281539082925	2	FACETS	0.548	0.514	0.582	0.274	0.257	0.291	INDETERMINATE	1	TRUE	0	0.946208703600177	2		596	1069	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348239	348239	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770548875	NA	P-0024257-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	271	689	0	ENST00000262320.3:c.1267G>A	p.Glu423Lys	p.E423K	ENST00000262320	NM_003502.3	423	Gag/Aag	6/11	0.508105895662361	1	FACETS	0.357	0.335	0.378	0.357	0.335	0.378	INDETERMINATE	1	TRUE	0	0.946208703600177	1		689	846	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057811	27057811	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024257-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1300	343	744	0	ENST00000324856.7:c.1519C>T	p.Gln507Ter	p.Q507*	ENST00000324856	NM_006015.4	507	Caa/Taa	3/20	0.467591538541044	3	FACETS	0.65	0.613	0.688	0.217	0.204	0.23	INDETERMINATE	1	TRUE	0	0.946208703600177	3		744	1643	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305328	65305328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024257-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	207	479	0	ENST00000342505.4:c.2800C>T	p.His934Tyr	p.H934Y	ENST00000342505	NM_002227.2	934	Cat/Tat	20/25	0.467591538541044	3	FACETS	0.597	0.553	0.642	0.199	0.184	0.214	INDETERMINATE	1	TRUE	0	0.946208703600177	3		479	1080	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941638	48941641	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	rs1566194323	NA	P-0024257-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	219	187	0	ENST00000267163.4:c.951_954del	p.Ser318AsnfsTer13	p.S318Nfs*13	ENST00000267163	NM_000321.2	316	aaTCTT/aa	10/27	0.946208703600177	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.946208703600177	2		187	226	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234309	39234309	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397517159	NA	P-0024257-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	121	299	0	ENST00000402219.2:c.2536G>A	p.Glu846Lys	p.E846K	ENST00000402219	NM_005633.3	846	Gaa/Aaa	16/23	0.508105895662361	1	FACETS	0.388	0.355	0.423	0.388	0.355	0.423	INDETERMINATE	1	TRUE	0	0.946208703600177	1		299	347	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627173	37627173	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0024257-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	111	364	0	ENST00000447079.4:c.1088C>G	p.Ser363Ter	p.S363*	ENST00000447079	NM_015083.1	363	tCa/tGa	2/14	0.515331839263216	3	FACETS	0.505	0.455	0.559	0.253	0.227	0.28	INDETERMINATE	1	TRUE	1	0.946208703600177	3		364	684	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992781	68992781	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024257-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	301	505	0	ENST00000288368.4:c.1746C>A	p.Asp582Glu	p.D582E	ENST00000288368	NM_024870.2	582	gaC/gaA	16/40	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.946208703600177	2		505	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0024556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	178	590	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		590	868	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0024556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	142	337	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		337	476	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0024556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	155	694	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		694	938	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563132	21563132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	174	452	0	ENST00000382592.4:c.787G>A	p.Glu263Lys	p.E263K	ENST00000382592	NM_014572.2	263	Gaa/Aaa	4/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		452	845	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385104	31385104	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs757998715	NA	P-0024556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	136	555	0	ENST00000328111.2:c.1489C>T	p.Arg497Trp	p.R497W	ENST00000328111	NM_006892.3	497	Cgg/Tgg	14/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		555	835	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864302	151864302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	204	579	0	ENST00000262189.6:c.9679C>T	p.Pro3227Ser	p.P3227S	ENST00000262189	NM_170606.2	3227	Cca/Tca	42/59	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		579	1030	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153709	55153709	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0025040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	61	474	0	ENST00000257290.5:c.2674+1G>T		p.X892_splice	ENST00000257290	NM_006206.4	892			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		474	350	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	42	319	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.61	2		319	123	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	129	441	2	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.61	2		443	395	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	210	797	3	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.984	0.917	1	0.984	0.917	1	CLONAL	1	TRUE	1	0.61	2		800	700	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	55	384	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.478	0.411	0.552	0.478	0.411	0.552	SUBCLONAL	1	TRUE	1	0.61	2		384	377	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	35	726	1	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	2	FACETS	0.164	0.134	0.198	0.164	0.134	0.198	SUBCLONAL	1	TRUE	1	0.61	2		727	699	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	186	441	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.61	2		441	460	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	318	485	5	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.972	1	1	0.997	1	CLONAL	2	TRUE	1	0.61	2		490	512	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552144	29552144	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	12	360	0	ENST00000356175.3:c.1882del	p.Tyr628ThrfsTer3	p.Y628Tfs*3	ENST00000356175	NM_000267.3	626	cTt/ct	17/57	1	2	FACETS	0.266	0.187	0.362	0.266	0.187	0.362	SUBCLONAL	1	TRUE	1	0.61	2		360	148	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	120	547	4	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.603	0.545	0.663	0.603	0.545	0.663	SUBCLONAL	1	TRUE	1	0.61	2		551	653	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589610	67589612	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	94	402	0	ENST00000274335.5:c.1376_1378del	p.Lys459del	p.K459del	ENST00000274335		458	gAAAaa/gaa	10/15	1	2	FACETS	0.966	0.869	1	0.966	0.869	1	CLONAL	1	TRUE	1	0.61	2		402	319	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	87	511	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.696	0.619	0.776	0.696	0.619	0.776	SUBCLONAL	1	TRUE	1	0.61	2		512	410	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755128667	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	160	721	3	ENST00000407977.2:c.1976dup	p.Pro660SerfsTer87	p.P660Sfs*87	ENST00000407977		659	ggt/ggGt	9/10	1	2	FACETS	0.825	0.759	0.893	0.825	0.759	0.893	CLONAL	1	TRUE	1	0.61	2		724	636	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	40	498	4	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.388	0.323	0.46	0.388	0.323	0.46	SUBCLONAL	1	TRUE	1	0.61	2		502	338	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850705	63850705	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs201178069	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	28	447	0	ENST00000279873.7:c.1489del	p.Ile497Ter	p.I497*	ENST00000279873	NM_032199.2	495	Aaa/aa	10/10	1	2	FACETS	0.237	0.189	0.292	0.237	0.189	0.292	SUBCLONAL	1	TRUE	1	0.61	2		447	387	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332109	70332109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777837034	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	53	193	1	ENST00000373644.4:c.14G>A	p.Arg5His	p.R5H	ENST00000373644	NM_030625.2	5	cGc/cAc	2/12	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.61	2		194	172	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055897	180055897	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	35	539	2	ENST00000261937.6:c.1088del	p.Pro363ArgfsTer27	p.P363Rfs*27	ENST00000261937	NM_182925.4	363	cCg/cg	8/30	1	2	FACETS	0.215	0.176	0.259	0.215	0.176	0.259	SUBCLONAL	1	TRUE	1	0.61	2		541	534	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527697	157527697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745372243	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	209	658	0	ENST00000346085.5:c.5422C>T	p.Arg1808Cys	p.R1808C	ENST00000346085	NM_020732.3	1808	Cgt/Tgt	20/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.61	2		658	683	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	172	642	1	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.885	0.818	0.955	0.885	0.818	0.955	CLONAL	1	TRUE	1	0.61	2		643	637	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794441	42794441	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	312	997	2	ENST00000575354.2:c.1526del	p.Pro509HisfsTer14	p.P509Hfs*14	ENST00000575354	NM_015125.3	507	cgC/cg	10/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.61	2		999	994	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	225	782	2	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	0.904	0.844	0.966	0.904	0.844	0.966	CLONAL	1	TRUE	1	0.61	2		784	816	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460476	149460476	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	54	784	0	ENST00000286301.3:c.161del	p.Pro54HisfsTer58	p.P54Hfs*58	ENST00000286301	NM_005211.3	54	cCa/ca	3/22	1	2	FACETS	0.242	0.206	0.282	0.242	0.206	0.282	SUBCLONAL	1	TRUE	1	0.61	2		784	731	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699374	47699374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	42	591	1	ENST00000347630.2:c.134G>T	p.Arg45Leu	p.R45L	ENST00000347630	NM_001007230.1	45	cGg/cTg	4/11	1	2	FACETS	0.312	0.26	0.369	0.312	0.26	0.369	SUBCLONAL	1	TRUE	1	0.61	2		592	442	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178258	56178258	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	63	397	0	ENST00000399503.3:c.3236del	p.Asn1079IlefsTer3	p.N1079Ifs*3	ENST00000399503	NM_005921.1	1077	tcA/tc	14/20	1	2	FACETS	0.816	0.714	0.925	0.816	0.714	0.925	CLONAL	1	TRUE	1	0.61	2		397	253	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216380	7216380	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	212	689	2	ENST00000380728.2:c.868del	p.Gln290SerfsTer55	p.Q290Sfs*55	ENST00000380728		290	Cag/ag	10/11	1	2	FACETS	0.888	0.827	0.95	0.888	0.827	0.95	CLONAL	1	TRUE	1	0.61	2		691	783	SUCCESS
APC	324	MSKCC	GRCh37	5	112174643	112174643	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs140493115	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	21	462	0	ENST00000257430.4:c.3352A>G	p.Asn1118Asp	p.N1118D	ENST00000257430	NM_000038.5	1118	Aat/Gat	16/16	1	2	FACETS	0.235	0.181	0.298	0.235	0.181	0.298	SUBCLONAL	1	TRUE	1	0.61	2		462	293	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779703	3779703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	75	696	1	ENST00000262367.5:c.5345C>T	p.Ala1782Val	p.A1782V	ENST00000262367	NM_004380.2	1782	gCg/gTg	31/31	1	2	FACETS	0.428	0.376	0.485	0.428	0.376	0.485	SUBCLONAL	1	TRUE	1	0.61	2		697	574	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962530	100962530	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752817186	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	179	700	0	ENST00000325455.5:c.1867C>T	p.Arg623Cys	p.R623C	ENST00000325455	NM_001202474.3	623	Cgc/Tgc	3/8	1	2	FACETS	0.995	0.922	1	0.995	0.922	1	CLONAL	1	TRUE	1	0.61	2		700	590	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106534448	106534448	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	131	346	0	ENST00000369096.4:c.24del	p.Lys8AsnfsTer17	p.K8Nfs*17	ENST00000369096	NM_001198.3	7	gAa/ga	1/7	1	2	FACETS	0.985	0.901	1	0.985	0.901	1	CLONAL	1	TRUE	1	0.61	2		346	436	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458435	120458436	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs771237928	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	40	623	0	ENST00000256646.2:c.6909dup	p.Ile2304HisfsTer9	p.I2304Hfs*9	ENST00000256646	NM_024408.3	2303	-/C	34/34	1	2	FACETS	0.242	0.201	0.289	0.242	0.201	0.289	SUBCLONAL	1	TRUE	1	0.61	2		623	541	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667423	241667423	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913122	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	198	633	2	ENST00000366560.3:c.1027C>T	p.Arg343Ter	p.R343*	ENST00000366560	NM_000143.3	343	Cga/Tga	7/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.61	2		635	612	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752695	42752695	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1366176199	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	76	698	1	ENST00000222329.4:c.1569del	p.Leu525SerfsTer6	p.L525Sfs*6	ENST00000222329	NM_006494.2	523	ggG/gg	4/4	1	2	FACETS	0.411	0.361	0.465	0.411	0.361	0.465	SUBCLONAL	1	TRUE	1	0.61	2		699	606	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	271	933	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.989	0.931	1	0.989	0.931	1	CLONAL	1	TRUE	1	0.61	2		934	898	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178673	56178675	+	inframe_deletion	In_Frame_Del	DEL	ATC	ATC	-	rs758576258	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	69	282	0	ENST00000399503.3:c.3651_3653del	p.Ile1219del	p.I1219del	ENST00000399503	NM_005921.1	1216	ATC/-	14/20	1	2	FACETS	0.975	0.862	1	0.975	0.862	1	CLONAL	1	TRUE	1	0.61	2		282	232	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412563	116412563	+	intron_variant	Intron	DEL	A	A	-	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	207	1172	1	ENST00000397752.3:c.3028+526del		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.965	0.899	1	0.965	0.899	1	CLONAL	1	TRUE	1	0.61	2		1173	703	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81927337	81927337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1164040767	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	56	750	1	ENST00000359376.3:c.1010G>A	p.Arg337Gln	p.R337Q	ENST00000359376	NM_002661.3	337	cGg/cAg	12/33	1	2	FACETS	0.202	0.172	0.235	0.202	0.172	0.235	SUBCLONAL	1	TRUE	1	0.61	2		751	909	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372259	55372264	+	inframe_deletion	In_Frame_Del	DEL	CACCAG	CACCAG	-	rs564144826	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	38	460	0	ENST00000297316.4:c.972_977del	p.Gln324_His325del	p.Q324_H325del	ENST00000297316	NM_022454.3	317	CACCAG/-	2/2	1	2	FACETS	0.247	0.203	0.295	0.247	0.203	0.295	SUBCLONAL	1	TRUE	1	0.61	2		460	505	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865315	57865316	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs747342182	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	223	862	0	ENST00000228682.2:c.2798dup	p.Ser934PhefsTer4	p.S934Ffs*4	ENST00000228682	NM_005269.2	931	ctg/ctGg	12/12	1	2	FACETS	0.911	0.85	0.973	0.911	0.85	0.973	CLONAL	1	TRUE	1	0.61	2		862	803	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569793	95569793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	47	360	0	ENST00000393063.1:c.3940C>T	p.Arg1314Trp	p.R1314W	ENST00000393063	NM_030621.3	1314	Cgg/Tgg	22/28	1	2	FACETS	0.5	0.424	0.583	0.5	0.424	0.583	SUBCLONAL	1	TRUE	1	0.61	2		360	308	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128307	30128307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762464616	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	262	749	1	ENST00000263025.4:c.925C>T	p.Arg309Trp	p.R309W	ENST00000263025	NM_002746.2	309	Cgg/Tgg	7/9	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.61	2		750	771	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829486	72829487	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	68	698	0	ENST00000268489.5:c.7094dup	p.Asn2365LysfsTer2	p.N2365Kfs*2	ENST00000268489	NM_006885.3	2365	aat/aaAt	9/10	1	2	FACETS	0.328	0.285	0.375	0.328	0.285	0.375	SUBCLONAL	1	TRUE	1	0.61	2		698	680	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866357	37866357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	229	694	0	ENST00000269571.5:c.662C>T	p.Ala221Val	p.A221V	ENST00000269571		221	gCc/gTc	6/27	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.61	2		694	643	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291077	10291077	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs748783652	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	265	721	0	ENST00000340748.4:c.394C>A	p.Leu132Ile	p.L132I	ENST00000340748		132	Ctt/Att	4/40	1	2	FACETS	0.969	0.91	1	0.969	0.91	1	CLONAL	1	TRUE	1	0.61	2		721	897	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754054	42754055	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	111	764	0	ENST00000222329.4:c.297dup	p.Lys100GlufsTer21	p.K100Efs*21	ENST00000222329	NM_006494.2	99	-/G	3/4	1	2	FACETS	0.481	0.433	0.533	0.481	0.433	0.533	SUBCLONAL	1	TRUE	1	0.61	2		764	756	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754580	42754580	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	53	820	0	ENST00000222329.4:c.160del	p.Glu54AsnfsTer23	p.E54Nfs*23	ENST00000222329	NM_006494.2	54	Gaa/aa	2/4	1	2	FACETS	0.222	0.188	0.259	0.222	0.188	0.259	SUBCLONAL	1	TRUE	1	0.61	2		820	783	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617544	158617544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	67	533	0	ENST00000263640.3:c.1112G>A	p.Gly371Glu	p.G371E	ENST00000263640	NM_001105.4	371	gGg/gAg	9/11	1	2	FACETS	0.357	0.31	0.407	0.357	0.31	0.407	SUBCLONAL	1	TRUE	1	0.61	2		533	616	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021425	31021425	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	157	581	0	ENST00000375687.4:c.1424A>G	p.Asp475Gly	p.D475G	ENST00000375687	NM_015338.5	475	gAc/gGc	12/13	1	2	FACETS	0.939	0.865	1	0.939	0.865	1	CLONAL	1	TRUE	1	0.61	2		581	548	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645765	12645765	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	40	421	0	ENST00000251849.4:c.704C>A	p.Pro235His	p.P235H	ENST00000251849	NM_002880.3	235	cCt/cAt	7/17	1	2	FACETS	0.309	0.256	0.367	0.309	0.256	0.367	SUBCLONAL	1	TRUE	1	0.61	2		421	425	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37061800	37061801	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	rs63751620	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	168	553	0	ENST00000231790.2:c.887dup	p.Leu296PhefsTer11	p.L296Ffs*11	ENST00000231790	NM_000249.3	295	agt/agTt		1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.61	2		553	506	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55143627	55143627	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	131	466	0	ENST00000257290.5:c.1859C>A	p.Pro620His	p.P620H	ENST00000257290	NM_006206.4	620	cCt/cAt	13/23	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.61	2		466	421	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158107	106158107	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	93	385	0	ENST00000380013.4:c.3008G>A	p.Trp1003Ter	p.W1003*	ENST00000380013	NM_001127208.2	1003	tGg/tAg	3/11	1	2	FACETS	0.977	0.879	1	0.977	0.879	1	CLONAL	1	TRUE	1	0.61	2		385	312	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197418	106197418	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	43	372	0	ENST00000380013.4:c.5751G>T	p.Trp1917Cys	p.W1917C	ENST00000380013	NM_001127208.2	1917	tgG/tgT	11/11	1	2	FACETS	0.493	0.415	0.579	0.493	0.415	0.579	SUBCLONAL	1	TRUE	1	0.61	2		372	286	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541630	187541630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371538987	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	141	418	0	ENST00000441802.2:c.6110C>T	p.Thr2037Met	p.T2037M	ENST00000441802	NM_005245.3	2037	aCg/aTg	10/27	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.61	2		418	422	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293734	1293734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	53	877	0	ENST00000310581.5:c.1267G>A	p.Ala423Thr	p.A423T	ENST00000310581	NM_198253.2	423	Gcc/Acc	2/16	1	2	FACETS	0.225	0.191	0.262	0.225	0.191	0.262	SUBCLONAL	1	TRUE	1	0.61	2		877	774	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637615	176637615	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	45	631	0	ENST00000439151.2:c.2215G>A	p.Val739Ile	p.V739I	ENST00000439151	NM_022455.4	739	Gtt/Att	5/23	1	2	FACETS	0.237	0.199	0.28	0.237	0.199	0.28	SUBCLONAL	1	TRUE	1	0.61	2		631	622	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058751	180058751	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	271	759	0	ENST00000261937.6:c.86C>A	p.Pro29His	p.P29H	ENST00000261937	NM_182925.4	29	cCc/cAc	2/30	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.61	2		759	831	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505503	157505503	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	47	444	0	ENST00000346085.5:c.3488del	p.Pro1163ArgfsTer48	p.P1163Rfs*48	ENST00000346085	NM_020732.3	1162	Ccc/cc	13/20	1	2	FACETS	0.355	0.3	0.416	0.355	0.3	0.416	SUBCLONAL	1	TRUE	1	0.61	2		444	434	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38314976	38314976	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	69	915	0	ENST00000425967.3:c.88T>C	p.Cys30Arg	p.C30R	ENST00000425967	NM_001174067.1	30	Tgc/Cgc	3/19	1	2	FACETS	0.256	0.222	0.292	0.256	0.222	0.292	SUBCLONAL	1	TRUE	1	0.61	2		915	885	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371002	55371002	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	217	586	0	ENST00000297316.4:c.304C>A	p.Leu102Met	p.L102M	ENST00000297316	NM_022454.3	102	Ctg/Atg	1/2	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.61	2		586	633	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141567214	141567214	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	55	833	0	ENST00000220592.5:c.1000C>T	p.Gln334Ter	p.Q334*	ENST00000220592	NM_012154.3	334	Cag/Tag	8/19	1	2	FACETS	0.189	0.161	0.22	0.189	0.161	0.22	SUBCLONAL	1	TRUE	1	0.61	2		833	954	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248058	110248058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755781036	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	94	605	1	ENST00000374672.4:c.1414G>A	p.Ala472Thr	p.A472T	ENST00000374672	NM_004235.4	472	Gcc/Acc	5/5	1	2	FACETS	0.463	0.412	0.518	0.463	0.412	0.518	SUBCLONAL	1	TRUE	1	0.61	2		606	665	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200273	123200273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	36	620	0	ENST00000218089.9:c.2252G>A	p.Ser751Asn	p.S751N	ENST00000218089	NM_001042749.1	751	aGc/aAc	23/35	1	2	FACETS	0.27	0.222	0.324	0.27	0.222	0.324	SUBCLONAL	1	TRUE	1	0.61	2		620	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0025573-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	394	603	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.670305250394064	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.680610493442078	2		604	571	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612352	1612352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748738693	NA	P-0025573-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	90	804	0	ENST00000344749.5:c.1667G>A	p.Arg556Gln	p.R556Q	ENST00000344749	NM_001136139.2	556	cGg/cAg	18/19	0.526722299895015	2	FACETS	0.27	0.239	0.304	0.135	0.119	0.152	SUBCLONAL	1	TRUE	0	0.680610493442078	2		804	979	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378663	25378663	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025573-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	80	395	0	ENST00000311936.3:c.335T>C	p.Val112Ala	p.V112A	ENST00000311936	NM_004985.3	112	gTc/gCc	4/5	0.229872087638307	2	FACETS	0.66	0.585	0.739	0.33	0.292	0.37	INDETERMINATE	1	TRUE	0	0.680610493442078	2		395	356	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431269	49431270	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0025573-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	234	502	0	ENST00000301067.7:c.9869dup	p.Ala3292CysfsTer9	p.A3292Cfs*9	ENST00000301067	NM_003482.3	3290	ggc/ggGc	34/54	0.322990585198496	1	FACETS	1	0.992	1	1	0.992	1	INDETERMINATE	1	TRUE	0	0.680610493442078	1		502	372	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900792	3900792	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025573-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	537	534	0	ENST00000262367.5:c.304C>T	p.Gln102Ter	p.Q102*	ENST00000262367	NM_004380.2	102	Cag/Tag	2/31	0.680610493442078	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.680610493442078	3		534	679	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242884	142242884	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs868817417	NA	P-0025573-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	262	496	0	ENST00000350721.4:c.4103G>T	p.Arg1368Leu	p.R1368L	ENST00000350721	NM_001184.3	1368	cGa/cTa	22/47	0.498845952223406	6	FACETS	0.903	0.846	0.96	0.451	0.423	0.48	CLONAL	2	TRUE	2	0.680610493442078	6		496	1007	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56854511	56854511	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025573-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	222	417	0	ENST00000519728.1:c.93T>G	p.Ile31Met	p.I31M	ENST00000519728	NM_002350.3	31	atT/atG	2/13	0.680610493442078	3	FACETS	0.928	0.875	0.982	0.928	0.875	0.982	CLONAL	2	TRUE	1	0.680610493442078	3		417	471	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0025714-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	72	426	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.734	0.642	0.833	0.734	0.642	0.833	SUBCLONAL	1	TRUE	1	0.343152958710571	2		426	572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs786202525	NA	P-0025714-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	59	494	0	ENST00000269305.4:c.532del	p.His178ThrfsTer69	p.H178Tfs*69	ENST00000269305	NM_001126112.2	178	Cac/ac	5/11	0.270203628492522	1	FACETS	0.877	0.759	1	0.877	0.759	1	CLONAL	1	TRUE	0	0.343152958710571	1		494	325	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143132	30143132	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1262491330	NA	P-0025714-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	38	514	0	ENST00000389048.3:c.394G>T	p.Val132Leu	p.V132L	ENST00000389048	NM_004304.4	132	Gtg/Ttg	1/29	0.340566740150218	3	FACETS	0.808	0.67	0.961			1	CLONAL	1	TRUE	NA	0.343152958710571	3		514	321	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944167	71944167	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025714-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	55	451	1	ENST00000298229.2:c.2002del	p.Arg668GlyfsTer90	p.R668Gfs*90	ENST00000298229	NM_001567.3	667	tCc/tc	17/28	0.112996945914713	0	FACETS	0.545	0.468	0.629			1	INDETERMINATE	1	TRUE	0	0.343152958710571	0		452	386	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274696	198274696	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025714-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	50	383	0	ENST00000335508.6:c.702G>T	p.Glu234Asp	p.E234D	ENST00000335508	NM_012433.2	234	gaG/gaT	7/25	1	2	FACETS	0.6	0.509	0.699	0.6	0.509	0.699	SUBCLONAL	1	TRUE	1	0.343152958710571	2		383	486	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89478261	89478261	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025714-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	86	393	0	ENST00000336596.2:c.2080C>A	p.Pro694Thr	p.P694T	ENST00000336596	NM_005233.5	694	Cca/Aca	12/17	1	2	FACETS	0.771	0.682	0.866	0.771	0.682	0.866	SUBCLONAL	1	TRUE	1	0.343152958710571	2		393	650	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953054	2953055	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0025714-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	42	590	1	ENST00000396946.4:c.2885_2886delinsAT	p.Pro962His	p.P962H	ENST00000396946	NM_032415.4	962	cCC/cAT	22/25	1	2	FACETS	0.604	0.505	0.714	0.604	0.505	0.714	SUBCLONAL	1	TRUE	1	0.343152958710571	2		591	405	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959184	2959184	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025714-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	65	561	0	ENST00000396946.4:c.2332A>T	p.Ile778Phe	p.I778F	ENST00000396946	NM_032415.4	778	Atc/Ttc	18/25	1	2	FACETS	0.863	0.751	0.984	0.863	0.751	0.984	CLONAL	1	TRUE	1	0.343152958710571	2		561	439	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0026022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	488	575	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.430815997063632	6	FACETS	0.935	0.894	0.977	0.935	0.894	0.977	CLONAL	3	TRUE	3	0.430815997063632	6		575	1503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0026022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	294	432	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.430815997063632	2	FACETS	0.873	0.825	0.921	0.873	0.825	0.921	CLONAL	2	TRUE	0	0.430815997063632	2		432	782	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873020	136873020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147198552	NA	P-0026022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	47	331	1	ENST00000241393.3:c.478G>A	p.Val160Ile	p.V160I	ENST00000241393	NM_003467.2	160	Gtc/Atc	2/2	0.222025872494422	2	FACETS	0.433	0.365	0.508	0.216	0.182	0.254	INDETERMINATE	1	TRUE	0	0.430815997063632	2		332	504	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883184	37883186	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0026022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	59	595	0	ENST00000269571.5:c.3092_3094del	p.Phe1031del	p.F1031del	ENST00000269571		1029	ggCTTc/ggc	25/27	0.410554527499334	3	FACETS	0.324	0.278	0.375	0.162	0.139	0.188	SUBCLONAL	1	TRUE	1	0.430815997063632	3		595	1027	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940366	49940366	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770141981	NA	P-0026022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	80	567	0	ENST00000296474.3:c.677C>T	p.Ser226Leu	p.S226L	ENST00000296474	NM_002447.2	226	tCg/tTg	1/20	0.25345271477133	1	FACETS	0.392	0.345	0.443	0.392	0.345	0.443	INDETERMINATE	1	TRUE	0	0.430815997063632	1		567	743	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	93	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.258754631738134	2		452	540	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971082	21971083	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0026112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	91	183	0	ENST00000304494.5:c.275dup	p.Asp92GlufsTer28	p.D92Efs*28	ENST00000304494	NM_000077.4	92	gac/gaAc	2/3	0.190957216055997	2	FACETS	0.833	0.744	0.927	0.833	0.744	0.927	CLONAL	2	TRUE	0	0.258754631738134	2		183	422	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0026525-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	41	407	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	1	2	FACETS	0.78	0.649	0.927	0.78	0.649	0.927	CLONAL	1	TRUE	1	0.19	2		407	553	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015094	37015094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026525-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	43	529	0	ENST00000358127.4:c.310C>T	p.Arg104Cys	p.R104C	ENST00000358127	NM_001280556.1	104	Cgc/Tgc	3/10	1	2	FACETS	0.667	0.556	0.789	0.667	0.556	0.789	SUBCLONAL	1	TRUE	1	0.19	2		529	679	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578517	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs750600586	NA	P-0026525-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	134	569	0	ENST00000269305.4:c.413C>A	p.Ala138Asp	p.A138D	ENST00000269305	NM_001126112.2	138	gCc/gAc	5/11	0.173346023199483	2	FACETS	0.974	0.886	1	0.974	0.886	1	CLONAL	2	TRUE	0	0.19	2		569	724	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038783	47038783	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026525-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	56	240	0	ENST00000377604.3:c.790G>T	p.Glu264Ter	p.E264*	ENST00000377604	NM_001204468.1	264	Gag/Tag	9/24	1	1	FACETS	0.847	0.73	0.972	1	0.973	1	CLONAL	2	TRUE	0	0.19	1		240	315	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458078	120458078	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026525-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	59	642	0	ENST00000256646.2:c.7267G>T	p.Asp2423Tyr	p.D2423Y	ENST00000256646	NM_024408.3	2423	Gac/Tac	34/34	1	2	FACETS	0.848	0.729	0.979	0.848	0.729	0.979	CLONAL	1	TRUE	1	0.19	2		642	732	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866539	117866542	+	missense_variant	Missense_Mutation	ONP	ACTC	ACTC	TCTA	novel	NA	P-0026525-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	53	417	0	ENST00000297338.2:c.1103_1106delinsTAGA	p.Gly368_Val369delinsValGlu	p.G368_V369delinsVE	ENST00000297338	NM_006265.2	368	gGAGTa/gTAGAa	9/14	0.25494785022583	3	FACETS	1	0.908	1	0.544	0.464	0.633	CLONAL	1	TRUE	1	0.19	3		417	561	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087429	27087430	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	T	novel	NA	P-0026525-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	50	560	0	ENST00000324856.7:c.2003_2004delinsT	p.Ser668IlefsTer74	p.S668Ifs*74	ENST00000324856	NM_006015.4	668	aGC/aT	5/20	1	2	FACETS	0.793	0.671	0.926	0.793	0.671	0.926	CLONAL	1	TRUE	1	0.19	2		560	664	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0026724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	348	590	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.343967007774173	3	FACETS	1	0.992	1	0.797	0.761	0.834	CLONAL	2	TRUE	0	0.503851656816165	3		590	723	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404587	8404587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	161	373	0	ENST00000356435.5:c.4160C>T	p.Ala1387Val	p.A1387V	ENST00000356435		1387	gCg/gTg	25/35	0.498460540544261	4	FACETS	0.9	0.831	0.971	0.9	0.831	0.971	CLONAL	2	TRUE	2	0.503851656816165	4		373	534	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097270	11097270	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0026724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	523	623	0	ENST00000358026.2:c.760+1G>A		p.X254_splice	ENST00000358026	NM_001128849.1	254			0.503851656816165	4	FACETS	0.988	0.958	1	0.988	0.958	1	CLONAL	4	TRUE	0	0.503851656816165	4		623	790	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741574	17741574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1371486239	NA	P-0026724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	143	490	1	ENST00000250003.3:c.245G>A	p.Arg82His	p.R82H	ENST00000250003	NM_002478.4	82	cGc/cAc	1/3	0.498460540544261	4	FACETS	1	0.978	1	0.611	0.558	0.666	CLONAL	1	TRUE	2	0.503851656816165	4		491	699	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771536	112771536	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	147	557	0	ENST00000369452.4:c.1709A>C	p.Gln570Pro	p.Q570P	ENST00000369452	NM_007373.3	570	cAg/cCg	9/9	0.466198299593907	3	FACETS	1	0.972	1	0.571	0.523	0.621	CLONAL	1	TRUE	1	0.503851656816165	3		557	640	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249832	39249832	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	197	635	0	ENST00000402219.2:c.1737G>C	p.Glu579Asp	p.E579D	ENST00000402219	NM_005633.3	579	gaG/gaC	10/23	0.503851656816165	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.503851656816165	3		635	433	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930086	68930086	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	89	373	0	ENST00000288368.4:c.147C>A	p.Phe49Leu	p.F49L	ENST00000288368	NM_024870.2	49	ttC/ttA	2/40	0.503851656816165	6	FACETS	0.848	0.751	0.952	0.212	0.187	0.238	CLONAL	1	TRUE	2	0.503851656816165	6		373	836	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0027199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	276	674	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.410787157247051	4	FACETS	1	0.983	1	0.282	0.264	0.3	INDETERMINATE	1	TRUE	0	0.82148862706298	4		674	1085	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0027199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	551	346	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.410787157247051	4	FACETS	0.954	0.925	0.982	0.715	0.693	0.737	INDETERMINATE	3	TRUE	0	0.82148862706298	4		346	854	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0027199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	473	590	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.786745617010683	2	FACETS	0.953	0.928	0.977	0.953	0.928	0.977	CLONAL	2	TRUE	0	0.82148862706298	2		590	604	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908238	41908238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	198	661	1	ENST00000372991.4:c.284G>A	p.Arg95Gln	p.R95Q	ENST00000372991	NM_001760.3	95	cGa/cAa	2/5	1	2	FACETS	0.518	0.48	0.558	0.518	0.48	0.558	SUBCLONAL	1	TRUE	1	0.82148862706298	2		662	930	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459558	50459558	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	99	292	0	ENST00000331340.3:c.847C>A	p.Leu283Ile	p.L283I	ENST00000331340	NM_006060.4	283	Ctt/Att	7/8	0.410787157247051	4	FACETS	0.594	0.53	0.662	0.149	0.132	0.166	INDETERMINATE	1	TRUE	0	0.82148862706298	4		292	739	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647436	3647436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377148341	NA	P-0027199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1376	168	547	0	ENST00000294008.3:c.1627G>A	p.Glu543Lys	p.E543K	ENST00000294008	NM_032444.2	543	Gag/Aag	7/15	0.761121279687289	4	FACETS	0.483	0.442	0.525			1	SUBCLONAL	1	TRUE	NA	0.82148862706298	4		547	1544	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363282	40363282	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	160	462	0	ENST00000397332.2:c.947A>C	p.His316Pro	p.H316P	ENST00000397332	NM_001033082.2	316	cAc/cCc	3/3	1	2	FACETS	0.497	0.456	0.539	0.497	0.456	0.539	SUBCLONAL	1	TRUE	1	0.82148862706298	2		462	784	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574711	95574711	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	109	424	0	ENST00000393063.1:c.2386G>C	p.Glu796Gln	p.E796Q	ENST00000393063	NM_030621.3	796	Gaa/Caa	16/28	0.730927502225198	5	FACETS	0.46	0.412	0.512			1	SUBCLONAL	1	TRUE	NA	0.82148862706298	5		424	1287	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0027257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	58	476	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.161827579198067	2		476	517	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346419	152346419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	29	341	0	ENST00000359321.1:c.151G>A	p.Gly51Arg	p.G51R	ENST00000359321	NM_005431.1	51	Gga/Aga	3/3	1	2	FACETS	0.815	0.653	0.998	0.815	0.653	0.998	CLONAL	1	TRUE	1	0.161827579198067	2		341	440	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554566	29554566	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	52	316	1	ENST00000356175.3:c.2351G>A	p.Trp784Ter	p.W784*	ENST00000356175	NM_000267.3	784	tGg/tAg	20/57	1	2	FACETS	1	0.862	1	1	0.976	1	CLONAL	2	TRUE	1	0.161827579198067	2		317	319	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325346	1325346	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	40	454	0	ENST00000400841.2:c.329G>T	p.Ser110Ile	p.S110I	ENST00000400841		110	aGt/aTt	3/6	1	1	FACETS	0.814	0.676	0.969	0.814	0.676	0.969	CLONAL	1	TRUE	0	0.161827579198067	1		454	558	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0027833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	61	422	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.683	0.588	0.786	0.683	0.588	0.786	SUBCLONAL	1	FALSE	1	0.266339596908115	2		422	671	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0027833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	55	207	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.655	0.559	0.759	0.655	0.559	0.759	SUBCLONAL	1	FALSE	1	0.266339596908115	2		207	631	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0027833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	66	637	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	0.776	0.673	0.887	0.776	0.673	0.887	SUBCLONAL	1	FALSE	1	0.266339596908115	2		637	639	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133889	41133889	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	39	363	0	ENST00000379561.5:c.1739C>T	p.Ser580Phe	p.S580F	ENST00000379561	NM_002015.3	580	tCc/tTc	2/3	1	2	FACETS	0.775	0.643	0.921	0.775	0.643	0.921	CLONAL	1	FALSE	1	0.266339596908115	2		363	378	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971138	21971138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760640852	NA	P-0027833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	46	346	0	ENST00000304494.5:c.220G>A	p.Asp74Asn	p.D74N	ENST00000304494	NM_000077.4	74	Gac/Aac	2/3	1	2	FACETS	0.921	0.778	1	0.921	0.778	1	CLONAL	1	FALSE	1	0.266339596908115	2		346	375	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518442	204518442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140091735	NA	P-0027833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	36	375	0	ENST00000367182.3:c.1105C>T	p.Pro369Ser	p.P369S	ENST00000367182	NM_001278516.1	369	Cct/Tct	11/11	0.194120036506084	3	FACETS	0.687	0.564	0.824	0.343	0.282	0.412	SUBCLONAL	1	FALSE	1	0.266339596908115	3		375	446	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876977	151876977	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	48	367	1	ENST00000262189.6:c.7384C>T	p.Gln2462Ter	p.Q2462*	ENST00000262189	NM_170606.2	2462	Cag/Tag	37/59	1	2	FACETS	0.846	0.716	0.988	0.846	0.716	0.988	CLONAL	1	FALSE	1	0.266339596908115	2		368	426	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585383	29585383	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691072	NA	P-0027833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	38	502	0	ENST00000356175.3:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000356175	NM_000267.3	1378	Cag/Tag	31/57	1	2	FACETS	0.414	0.341	0.495	0.414	0.341	0.495	SUBCLONAL	1	FALSE	1	0.266339596908115	2		502	690	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431937	49431937	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	85	811	0	ENST00000301067.7:c.9202G>T	p.Glu3068Ter	p.E3068*	ENST00000301067	NM_003482.3	3068	Gag/Tag	34/54	1	2	FACETS	0.829	0.732	0.933	0.829	0.732	0.933	CLONAL	1	FALSE	1	0.266339596908115	2		811	770	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134301	2134301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397514997	NA	P-0027833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	57	781	0	ENST00000219476.3:c.4078G>A	p.Glu1360Lys	p.E1360K	ENST00000219476	NM_000548.3	1360	Gag/Aag	34/42	0.115147106945228	3	FACETS	0.58	0.496	0.672			1	INDETERMINATE	1	FALSE	NA	0.266339596908115	3		781	836	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11019846	11019846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	65	636	0	ENST00000327064.4:c.521G>A	p.Arg174His	p.R174H	ENST00000327064	NM_199141.1	174	cGc/cAc	4/16	1	2	FACETS	0.718	0.622	0.822	0.718	0.622	0.822	SUBCLONAL	1	FALSE	1	0.266339596908115	2		636	680	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244997	46244997	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs868082376	NA	P-0028081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	301	575	1	ENST00000334344.6:c.3091C>T	p.Gln1031Ter	p.Q1031*	ENST00000334344	NM_152641.2	1031	Cag/Tag	15/21	0.639333269987205	2	FACETS	0.981	0.94	1	0.981	0.94	1	CLONAL	2	TRUE	0	0.649744939299798	2		576	472	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771344	68771344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555509646	NA	P-0028081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	103	263	0	ENST00000261769.5:c.26C>T	p.Ser9Leu	p.S9L	ENST00000261769	NM_004360.3	9	tCg/tTg	1/16	0.348302017539674	3	FACETS	1	0.976	1	0.633	0.572	0.695	INDETERMINATE	1	TRUE	1	0.649744939299798	3		263	332	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609036	43609036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	179	567	0	ENST00000355710.3:c.1792G>A	p.Glu598Lys	p.E598K	ENST00000355710	NM_020975.4	598	Gag/Aag	10/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.649744939299798	2		567	461	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479261	50479261	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	242	421	1	ENST00000394963.4:c.110del	p.Pro37LeufsTer33	p.P37Lfs*33	ENST00000394963	NM_003076.4	37	Cct/ct	1/13	0.639333269987205	2	FACETS	0.945	0.9	0.99	0.945	0.9	0.99	CLONAL	2	TRUE	0	0.649744939299798	2		422	394	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346307	89346307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1259405084	NA	P-0028081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	150	352	0	ENST00000301030.4:c.6643G>A	p.Val2215Met	p.V2215M	ENST00000301030	NM_001256183.1	2215	Gtg/Atg	9/13	0.348302017539674	3	FACETS	0.836	0.774	0.898	0.836	0.774	0.898	INDETERMINATE	2	TRUE	1	0.649744939299798	3		352	366	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350309	89350309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	210	677	0	ENST00000301030.4:c.2641G>A	p.Val881Met	p.V881M	ENST00000301030	NM_001256183.1	881	Gtg/Atg	9/13	0.348302017539674	3	FACETS	1	0.98	1	0.569	0.53	0.61	INDETERMINATE	1	TRUE	1	0.649744939299798	3		677	752	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556332	29556332	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	148	409	0	ENST00000356175.3:c.2699C>G	p.Ser900Cys	p.S900C	ENST00000356175	NM_000267.3	900	tCc/tGc	21/57	0.348302017539674	3	FACETS	1	0.975	1	0.575	0.528	0.623	INDETERMINATE	1	TRUE	1	0.649744939299798	3		409	525	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180553	56180553	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	152	367	0	ENST00000399503.3:c.3882G>C	p.Glu1294Asp	p.E1294D	ENST00000399503	NM_005921.1	1294	gaG/gaC	16/20	0.365221996917339	5	FACETS	1	0.984	1	0.439	0.402	0.477	INDETERMINATE	1	TRUE	2	0.649744939299798	5		367	702	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395555	116395555	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	219	446	0	ENST00000397752.3:c.1848G>C	p.Glu616Asp	p.E616D	ENST00000397752	NM_000245.2	616	gaG/gaC	6/21	0.348302017539674	3	FACETS	0.793	0.744	0.843	0.793	0.744	0.843	INDETERMINATE	2	TRUE	1	0.649744939299798	3		446	563	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896520	151896520	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	186	263	0	ENST00000262189.6:c.4117C>G	p.Leu1373Val	p.L1373V	ENST00000262189	NM_170606.2	1373	Cta/Gta	27/59	0.348302017539674	3	FACETS	0.958	0.897	1	0.958	0.897	1	INDETERMINATE	2	TRUE	1	0.649744939299798	3		263	396	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481403	140481403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913357	NA	P-0028083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	153	408	0	ENST00000288602.6:c.1405G>A	p.Gly469Arg	p.G469R	ENST00000288602	NM_004333.4	469	Gga/Aga	11/18	1	2	FACETS	0.967	0.892	1	0.967	0.892	1	CLONAL	1	TRUE	1	0.648300509532646	2		408	488	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104386985	104386985	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	303	361	0	ENST00000369902.3:c.1350G>C	p.Leu450Phe	p.L450F	ENST00000369902	NM_016169.3	450	ttG/ttC	11/12	0.26556905044769	3	FACETS	0.924	0.877	0.971	0.924	0.877	0.971	INDETERMINATE	2	TRUE	1	0.648300509532646	3		361	670	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0028108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	339	422	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.55502767311091	5	FACETS	0.944	0.895	0.995	0.63	0.596	0.664	CLONAL	2	TRUE	2	0.693519003901543	5		422	1056	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0028108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	415	432	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.693519003901543	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.693519003901543	2		432	596	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0028108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	126	278	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.693519003901543	3	FACETS	1	0.931	1	0.513	0.467	0.56	CLONAL	1	TRUE	1	0.693519003901543	3		278	477	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604673	48604673	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060500738	NA	P-0028108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	288	312	0	ENST00000342988.3:c.1495T>C	p.Cys499Arg	p.C499R	ENST00000342988	NM_005359.5	499	Tgc/Cgc	12/12	0.693519003901543	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.693519003901543	2		312	411	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453987	140453987	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs180177040	NA	P-0028108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	111	216	0	ENST00000288602.6:c.1741A>C	p.Asn581His	p.N581H	ENST00000288602	NM_004333.4	581	Aat/Cat	14/18	0.693519003901543	3	FACETS	1	0.923	1	0.511	0.462	0.561	CLONAL	1	TRUE	1	0.693519003901543	3		216	422	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94922987	94922987	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	204	507	1	ENST00000536441.1:c.481C>A	p.Leu161Met	p.L161M	ENST00000536441	NM_144665.3	161	Ctg/Atg	4/10	0.693519003901543	3	FACETS	1	0.95	1	0.513	0.477	0.55	CLONAL	1	TRUE	1	0.693519003901543	3		508	772	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748584	40748584	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	57	354	0	ENST00000373198.4:c.2932G>A	p.Ala978Thr	p.A978T	ENST00000373198	NM_133170.3	978	Gcg/Acg	21/32	0.490472789300568	4	FACETS	0.428	0.366	0.495			1	SUBCLONAL	1	TRUE	NA	0.693519003901543	4		354	651	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620600	52620600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	406	513	0	ENST00000394830.3:c.3153G>A	p.Trp1051Ter	p.W1051*	ENST00000394830	NM_018313.4	1051	tgG/tgA	21/30	0.693519003901543	2	FACETS	0.989	0.956	1	0.989	0.956	1	CLONAL	2	TRUE	0	0.693519003901543	2		513	592	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964505	93964505	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs770305987	NA	P-0028108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	147	450	0	ENST00000369303.4:c.2392A>C	p.Ile798Leu	p.I798L	ENST00000369303	NM_004440.3	798	Att/Ctt	14/17	NA	2	FACETS	0.625	0.572	0.681			1	INDETERMINATE	1	TRUE	NA	0.693519003901543	2		450	678	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939192	76939192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	250	285	0	ENST00000373344.5:c.1556C>T	p.Ser519Phe	p.S519F	ENST00000373344	NM_000489.3	519	tCt/tTt	9/35	0.612543979567636	2	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.693519003901543	2		285	674	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	34	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.683	0.556	0.826	0.683	0.556	0.826	SUBCLONAL	1	TRUE	1	0.15	2		452	664	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587782289	NA	P-0028536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	58	569	0	ENST00000269305.4:c.706T>G	p.Tyr236Asp	p.Y236D	ENST00000269305	NM_001126112.2	236	Tac/Gac	7/11	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.15	2		569	747	SUCCESS
BTK	695	MSKCC	GRCh37	X	100609634	100609634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	44	462	0	ENST00000308731.7:c.1615G>A	p.Asp539Asn	p.D539N	ENST00000308731	NM_000061.2	539	Gat/Aat	16/19	1	2	FACETS	0.736	0.615	0.871	0.736	0.615	0.871	SUBCLONAL	1	TRUE	1	0.15	2		462	797	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560115	29560115	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	33	379	0	ENST00000356175.3:c.3592G>A	p.Glu1198Lys	p.E1198K	ENST00000356175	NM_000267.3	1198	Gaa/Aaa	27/57	1	2	FACETS	0.835	0.679	1	0.835	0.679	1	CLONAL	1	TRUE	1	0.15	2		379	527	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0028723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	356	426	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.285901471667857	4	FACETS	0.903	0.863	0.944	1	0.99	1	CLONAL	5	TRUE	0	0.285901471667857	4		426	709	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0028723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	172	590	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.272903124495331	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.285901471667857	2		590	557	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797429	45797429	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151316420	NA	P-0028723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	80	726	1	ENST00000450313.1:c.1090C>T	p.Arg364Cys	p.R364C	ENST00000450313	NM_012222.2	364	Cgc/Tgc	12/16	1	2	FACETS	0.994	0.876	1	0.994	0.876	1	CLONAL	1	TRUE	1	0.285901471667857	2		727	563	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195614	102195614	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	60	405	0	ENST00000263464.3:c.374T>A	p.Leu125His	p.L125H	ENST00000263464	NM_001165.4	125	cTt/cAt	2/9	0.249729897261616	3	FACETS	0.9	0.776	1	0.45	0.388	0.518	CLONAL	1	TRUE	1	0.285901471667857	3		405	533	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373764	118373764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	51	358	0	ENST00000534358.1:c.7157C>T	p.Thr2386Ile	p.T2386I	ENST00000534358	NM_005933.3	2386	aCa/aTa	27/36	0.249729897261616	3	FACETS	0.927	0.789	1	0.463	0.394	0.539	CLONAL	1	TRUE	1	0.285901471667857	3		358	440	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230550	46230550	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	134	310	0	ENST00000334344.6:c.799G>T	p.Glu267Ter	p.E267*	ENST00000334344	NM_152641.2	267	Gag/Tag	8/21	0.0439839574035688	3	FACETS	1	0.97	1			1	INDETERMINATE	2	TRUE	NA	0.285901471667857	3		310	472	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233721	133233721	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0028723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	99	305	0	ENST00000320574.5:c.3582+1G>T		p.X1194_splice	ENST00000320574	NM_006231.2	1194			0.282713249674491	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	0	0.285901471667857	2		305	329	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313391	30313391	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1280438075	NA	P-0028723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	170	606	0	ENST00000262643.3:c.991A>T	p.Met331Leu	p.M331L	ENST00000262643	NM_001238.2	331	Atg/Ttg	11/12	0.194961384392749	5	FACETS	1	0.98	1	0.792	0.73	0.856	CLONAL	2	TRUE	2	0.285901471667857	5		606	715	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500473	149500473	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	199	521	0	ENST00000261799.4:c.2564C>A	p.Ser855Ter	p.S855*	ENST00000261799	NM_002609.3	855	tCg/tAg	18/23	0.285901471667857	3	FACETS	0.914	0.853	0.977	0.914	0.853	0.977	CLONAL	3	TRUE	0	0.285901471667857	3		521	580	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636204	87636204	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	51	412	0	ENST00000277120.3:c.2369G>T	p.Arg790Leu	p.R790L	ENST00000277120		790	cGa/cTa	19/19	0.276621540335483	3	FACETS	1	0.866	1	0.508	0.433	0.591	CLONAL	1	TRUE	1	0.285901471667857	3		412	401	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137325976	137325976	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	158	688	0	ENST00000481739.1:c.1164G>T	p.Glu388Asp	p.E388D	ENST00000481739	NM_002957.4	388	gaG/gaT	9/10	0.276621540335483	3	FACETS	0.908	0.834	0.984	0.908	0.834	0.984	CLONAL	2	TRUE	1	0.285901471667857	3		688	696	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040621	47040621	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	115	222	0	ENST00000377604.3:c.1257del	p.Gly420ValfsTer65	p.G420Vfs*65	ENST00000377604	NM_001204468.1	419	cAa/ca	13/24	0.285901471667857	2	FACETS	0.982	0.9	1			1	CLONAL	3	TRUE	NA	0.285901471667857	2		222	273	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239728	53239728	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	145	296	0	ENST00000375401.3:c.1614del	p.Ser539HisfsTer10	p.S539Hfs*10	ENST00000375401	NM_004187.3	538	ccC/cc	12/26	0.285901471667857	2	FACETS	0.887	0.819	0.957			1	CLONAL	3	TRUE	NA	0.285901471667857	2		296	381	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0028723-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	93	673	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.56353846512348	2		673	318	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562657	29562660	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs1064794276	NA	P-0028723-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	118	447	0	ENST00000356175.3:c.3739_3742del	p.Phe1247IlefsTer18	p.F1247Ifs*18	ENST00000356175	NM_000267.3	1246	cTGTTt/ct	28/57	0.56353846512348	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.56353846512348	1		447	296	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0028723-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	57	211	1	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	1	2	FACETS	0.809	0.701	0.924	0.809	0.701	0.924	CLONAL	1	TRUE	1	0.56353846512348	2		212	250	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973597	15973597	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028723-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	200	774	0	ENST00000268712.3:c.4395A>C	p.Glu1465Asp	p.E1465D	ENST00000268712	NM_006311.3	1465	gaA/gaC	31/46	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.56353846512348	2		774	674	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0028917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	710	552	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.0947633213752395	5	FACETS	1	0.996	1			1	INDETERMINATE	4	TRUE	NA	0.555270576246734	5		552	1046	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120572	2120572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934872	NA	P-0028917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	229	799	1	ENST00000219476.3:c.1832G>A	p.Arg611Gln	p.R611Q	ENST00000219476	NM_000548.3	611	cGg/cAg	17/42	0.555270576246734	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.555270576246734	1		800	595	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0028996-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	73	778	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.150579253163323	1	FACETS	0.644	0.562	0.732	0.644	0.562	0.732	SUBCLONAL	1	TRUE	0	0.246104791626852	1		778	808	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121541	2121541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334081822	NA	P-0028996-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	113	712	1	ENST00000219476.3:c.1870G>A	p.Asp624Asn	p.D624N	ENST00000219476	NM_000548.3	624	Gac/Aac	18/42	0.246104791626852	3	FACETS	0.899	0.807	0.997	0.45	0.403	0.499	CLONAL	1	TRUE	1	0.246104791626852	3		713	1147	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0029203-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	39	664	1	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	1	2	FACETS	0.828	0.688	0.984	0.828	0.688	0.984	CLONAL	1	TRUE	1	0.255311336915163	2		665	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579346	7579346	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs781724995	NA	P-0029203-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	67	678	0	ENST00000269305.4:c.341T>A	p.Leu114Ter	p.L114*	ENST00000269305	NM_001126112.2	114	tTg/tAg	4/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.255311336915163	2		678	385	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440542	49440542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773033619	NA	P-0029203-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	33	806	0	ENST00000301067.7:c.4268G>A	p.Arg1423His	p.R1423H	ENST00000301067	NM_003482.3	1423	cGt/cAt	15/54	0.168412359709275	3	FACETS	0.623	0.507	0.754	0.311	0.253	0.377	SUBCLONAL	1	TRUE	1	0.255311336915163	3		806	468	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349935	15349935	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029203-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	30	691	0	ENST00000263377.2:c.3717G>C	p.Lys1239Asn	p.K1239N	ENST00000263377	NM_058243.2	1239	aaG/aaC	18/20	1	2	FACETS	0.679	0.548	0.828	0.679	0.548	0.828	SUBCLONAL	1	TRUE	1	0.255311336915163	2		691	346	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982382	25982382	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029203-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	21	307	0	ENST00000435504.4:c.908T>G	p.Leu303Arg	p.L303R	ENST00000435504		303	cTg/cGg	9/13	0.168412359709275	3	FACETS	0.606	0.467	0.769	0.303	0.233	0.385	SUBCLONAL	1	TRUE	1	0.255311336915163	3		307	306	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098958	178098963	+	inframe_deletion	In_Frame_Del	DEL	ATCTAT	ATCTAT	-	novel	NA	P-0029203-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	17	332	0	ENST00000397062.3:c.82_87del	p.Ile28_Asp29del	p.I28_D29del	ENST00000397062	NM_006164.4	28	ATAGAT/-	2/5	0.134730699388153	3	FACETS	0.521	0.389	0.679	0.174	0.129	0.227	INDETERMINATE	1	TRUE	0	0.255311336915163	3		332	288	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670856	134670856	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029203-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	28	362	0	ENST00000398015.3:c.767A>T	p.Lys256Met	p.K256M	ENST00000398015	NM_004441.4	256	aAg/aTg	3/16	0.178803738132081	2	FACETS	0.837	0.672	1	0.419	0.336	0.512	CLONAL	1	TRUE	0	0.255311336915163	2		362	262	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131895052	131895052	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029203-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	11	288	0	ENST00000265335.6:c.206A>G	p.Asp69Gly	p.D69G	ENST00000265335		69	gAt/gGt	2/25	0.134730699388153	3	FACETS	0.498	0.344	0.689	0.166	0.114	0.23	INDETERMINATE	1	TRUE	0	0.255311336915163	3		288	195	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415090	116415090	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029203-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	35	624	0	ENST00000397752.3:c.3184C>G	p.Leu1062Val	p.L1062V	ENST00000397752	NM_000245.2	1062	Ctg/Gtg	15/21	0.201361521903363	3	FACETS	0.677	0.554	0.814	0.338	0.277	0.407	SUBCLONAL	1	TRUE	1	0.255311336915163	3		624	457	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829178	128829178	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029203-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	15	258	0	ENST00000249373.3:c.186C>A	p.Ser62Arg	p.S62R	ENST00000249373	NM_005631.4	62	agC/agA	1/12	0.201361521903363	3	FACETS	0.914	0.673	1	0.457	0.336	0.6	CLONAL	1	TRUE	1	0.255311336915163	3		258	145	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0029225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	513	575	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.304845053107693	8	FACETS	1	0.99	1	0.868	0.835	0.901	INDETERMINATE	4	TRUE	3	0.68	8		575	1057	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176710828	176710828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587784177	NA	P-0029225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	106	454	0	ENST00000439151.2:c.6050G>A	p.Arg2017Gln	p.R2017Q	ENST00000439151	NM_022455.4	2017	cGg/cAg	20/23	0.304399875810819	4	FACETS	1	0.974	1	0.415	0.374	0.457	INDETERMINATE	1	TRUE	1	0.68	4		454	421	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21304066	21304066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444326760	NA	P-0029225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	205	668	0	ENST00000354336.3:c.845G>A	p.Arg282His	p.R282H	ENST00000354336	NM_005207.3	282	cGc/cAc	3/3	0.304845053107693	4	FACETS	1	0.985	1	0.406	0.377	0.436	INDETERMINATE	1	TRUE	1	0.68	4		668	832	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829569	72829569	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	151	594	0	ENST00000268489.5:c.7012C>T	p.Gln2338Ter	p.Q2338*	ENST00000268489	NM_006885.3	2338	Cag/Tag	9/10	0.181125195585193	3	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.68	3		594	461	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130286	11130287	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCCT	novel	NA	P-0029225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	153	571	2	ENST00000358026.2:c.2526_2530dup	p.Phe844TrpfsTer16	p.F844Wfs*16	ENST00000358026	NM_001128849.1	842	cgg/cgGGCCTg	18/36	0.304399875810819	4	FACETS	1	0.977	1	0.393	0.36	0.426	INDETERMINATE	1	TRUE	1	0.68	4		573	642	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638440	176638440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	192	673	2	ENST00000439151.2:c.3040G>A	p.Asp1014Asn	p.D1014N	ENST00000439151	NM_022455.4	1014	Gac/Aac	5/23	0.304399875810819	4	FACETS	1	0.984	1	0.406	0.376	0.437	INDETERMINATE	1	TRUE	1	0.68	4		675	778	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039864	47039865	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0029225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	423	799	1	ENST00000377604.3:c.1209dup	p.Ser404GlnfsTer39	p.S404Qfs*39	ENST00000377604	NM_001204468.1	403	gcc/gCcc	12/24	0.304845053107693	2	FACETS	0.9	0.867	0.933	0.9	0.867	0.933	INDETERMINATE	2	TRUE	0	0.68	2		800	691	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	205	369	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		369	1210	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366608	118366608	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	108	416	0	ENST00000534358.1:c.5557A>T	p.Ser1853Cys	p.S1853C	ENST00000534358	NM_005933.3	1853	Agt/Tgt	19/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		416	801	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207200	1207201	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0029545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	186	816	0	ENST00000326873.7:c.289_290dup	p.Glu98ArgfsTer6	p.E98Rfs*6	ENST00000326873	NM_000455.4	96	-/AA	1/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		816	1228	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594246	55594246	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	120	411	0	ENST00000288135.5:c.1949A>C	p.His650Pro	p.H650P	ENST00000288135	NM_000222.2	650	cAc/cCc	13/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		411	939	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460492	149460492	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	216	828	0	ENST00000286301.3:c.145G>T	p.Glu49Ter	p.E49*	ENST00000286301	NM_005211.3	49	Gaa/Taa	3/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		828	1339	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673648	30673648	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	174	709	0	ENST00000376406.3:c.3312G>T	p.Lys1104Asn	p.K1104N	ENST00000376406	NM_014641.2	1104	aaG/aaT	10/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		709	1236	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404577	8404577	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	116	326	0	ENST00000356435.5:c.4170C>G	p.Ile1390Met	p.I1390M	ENST00000356435		1390	atC/atG	25/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		326	717	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0030471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	84	346	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.163409971895368	3	FACETS	1	0.93	1	0.539	0.475	0.608	CLONAL	1	TRUE	1	0.188410573256242	3		346	905	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057520000	NA	P-0030471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	160	690	0	ENST00000269305.4:c.452C>G	p.Pro151Arg	p.P151R	ENST00000269305	NM_001126112.2	151	cCc/cGc	5/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.188410573256242	2		690	1133	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061099	38061099	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs577631417	NA	P-0030471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	13	60	0	ENST00000250448.2:c.890C>A	p.Pro297His	p.P297H	ENST00000250448	NM_004496.3	297	cCc/cAc	2/2	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.188410573256242	2		60	97	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0030797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	62	674	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.284426838424799	3	FACETS	0.694	0.598	0.798	0.347	0.299	0.399	SUBCLONAL	1	TRUE	1	0.27	3		674	751	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0030797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	96	557	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.27	2		557	696	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0030797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	100	346	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.284426838424799	3	FACETS	1	0.935	1	0.533	0.476	0.594	CLONAL	1	TRUE	1	0.27	3		346	789	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0030797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	461	557	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.381300706957462	3	FACETS	0.988	0.952	1			1	CLONAL	3	TRUE	NA	0.474646848185688	3		557	811	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0030797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	203	346	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.433637349473997	5	FACETS	1	0.985	1			1	CLONAL	2	TRUE	NA	0.474646848185688	5		346	614	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371801	55371801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746536924	NA	P-0030797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	64	174	0	ENST00000297316.4:c.491C>T	p.Ala164Val	p.A164V	ENST00000297316	NM_022454.3	164	gCg/gTg	2/2	0.0780753037306456	3	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.474646848185688	3		174	241	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413742	138413742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769082299	NA	P-0031396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	46	472	0	ENST00000289153.2:c.1778C>T	p.Ala593Val	p.A593V	ENST00000289153	NM_006219.2	593	gCg/gTg	12/22	1	2	FACETS	0.804	0.677	0.945	0.804	0.677	0.945	CLONAL	1	TRUE	1	0.22	2		472	520	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025952	1025952	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	42	550	0	ENST00000358495.3:c.578G>C	p.Arg193Thr	p.R193T	ENST00000358495	NM_134424.2	193	aGa/aCa	8/12	0.107108933102263	0	FACETS	0.718	0.6	0.848			1	INDETERMINATE	1	TRUE	0	0.22	0		550	415	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923408	36923408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs79813621	NA	P-0031396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	55	858	2	ENST00000358127.4:c.854C>T	p.Thr285Ile	p.T285I	ENST00000358127	NM_001280556.1	285	aCc/aTc	7/10	1	2	FACETS	0.967	0.828	1	0.967	0.828	1	CLONAL	1	TRUE	1	0.22	2		860	517	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456453	189456453	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	57	300	0	ENST00000264731.3:c.214A>G	p.Ile72Val	p.I72V	ENST00000264731	NM_003722.4	72	Att/Gtt	3/14	1	2	FACETS	0.698	0.599	0.805	0.698	0.599	0.805	SUBCLONAL	1	TRUE	1	0.31	2		300	527	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031651-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	55	320	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.718	0.618	0.826	0.718	0.618	0.826	SUBCLONAL	1	TRUE	1	0.502137656028961	2		321	305	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0031651-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	283	432	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.298048350874809	3	FACETS	0.9	0.85	0.952	0.6	0.567	0.635	INDETERMINATE	2	TRUE	0	0.502137656028961	3		432	783	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974721	21974721	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031651-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	99	302	0	ENST00000304494.5:c.106del	p.Ala36ArgfsTer17	p.A36Rfs*17	ENST00000304494	NM_000077.4	36	Gcg/cg	1/3	0.451970300043147	1	FACETS	0.849	0.765	0.936	0.849	0.765	0.936	CLONAL	1	TRUE	0	0.502137656028961	1		302	348	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249456	153249456	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031651-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	29	505	1	ENST00000281708.4:c.1322G>T	p.Arg441Leu	p.R441L	ENST00000281708	NM_033632.3	441	cGg/cTg	9/12	1	2	FACETS	0.217	0.173	0.266	0.217	0.173	0.266	SUBCLONAL	1	TRUE	1	0.502137656028961	2		506	533	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012199	16012199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031651-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	107	429	0	ENST00000268712.3:c.2083G>A	p.Asp695Asn	p.D695N	ENST00000268712	NM_006311.3	695	Gat/Aat	19/46	0.298048350874809	3	FACETS	1	0.98	1	0.447	0.404	0.491	INDETERMINATE	1	TRUE	0	0.502137656028961	3		429	398	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623605	43623605	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs762952212	NA	P-0031651-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	87	430	0	ENST00000355710.3:c.3233C>G	p.Thr1078Arg	p.T1078R	ENST00000355710	NM_020975.4	1078	aCg/aGg	20/20	0.231456303850406	1	FACETS	0.611	0.543	0.682	0.611	0.543	0.682	INDETERMINATE	1	TRUE	0	0.502137656028961	1		430	425	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427025	49427026	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031651-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	55	449	0	ENST00000301067.7:c.11462dup	p.His3824SerfsTer188	p.H3824Sfs*188	ENST00000301067	NM_003482.3	3821	cag/caAg	39/54	0.106433660061721	4	FACETS	0.971	0.835	1	0.485	0.417	0.559	INDETERMINATE	1	TRUE	2	0.502137656028961	4		449	339	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357153	89357153	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031651-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	104	634	0	ENST00000301030.4:c.481G>T	p.Val161Leu	p.V161L	ENST00000301030	NM_001256183.1	161	Gtg/Ttg	6/13	1	2	FACETS	0.507	0.454	0.564	0.507	0.454	0.564	SUBCLONAL	1	TRUE	1	0.502137656028961	2		634	817	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18958579	18958579	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031651-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	87	551	0	ENST00000262803.5:c.398G>T	p.Cys133Phe	p.C133F	ENST00000262803	NM_002911.3	133	tGc/tTc	3/24	1	2	FACETS	0.532	0.471	0.597	0.532	0.471	0.597	SUBCLONAL	1	TRUE	1	0.502137656028961	2		551	651	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189379	99189379	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031651-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	47	531	0	ENST00000074304.5:c.2635C>G	p.Gln879Glu	p.Q879E	ENST00000074304	NM_001134224.1	879	Caa/Gaa	24/26	1	2	FACETS	0.28	0.235	0.329	0.28	0.235	0.329	SUBCLONAL	1	TRUE	1	0.502137656028961	2		531	669	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527587	41527587	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031651-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	257	402	0	ENST00000263253.7:c.1478A>T	p.Asn493Ile	p.N493I	ENST00000263253	NM_001429.3	493	aAt/aTt	6/31	0.502137656028961	2	FACETS	0.807	0.761	0.854	0.807	0.761	0.854	CLONAL	2	TRUE	0	0.502137656028961	2		402	634	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437788	52438596	+	splice_acceptor_variant,splice_donor_variant,frameshift_variant,stop_lost,intron_variant	Splice_Site	DEL	TCCTTCTGGGACTCTTTGAGCTTCTCAGCCAAGACGTTGATGGTGTTGGGCTGCAGCACTGACAGTTGCCCATCAGCAGAACCGCTCAATGCCCCTGGCTTCCCTGTTCCCTTCCCCTTATACCTGTGGGGCCCGAGAAGATGTGAAGCAAGGGAACGGGCCAGGTGACCATACCCAGCAGTACCCAGAATGGCTTAAATACATCCCGACCTCCAGGGGCTGACCCTAAAACTCCTTATACTTGGTCCAAGCAACTTGAACTAGCCATGCTAAGCCTGGCATCAAGTTCTGACAGCTGCAGCCAAGTGTCCTCAAAAGACACTTCCTCTATTCCAGCCATCCCACTCCTGGCCTTTTGCCAATGCCCTGTGTTCCAGCAAAGCTGCCTCCCCACCACCCACATCTCCTCCATCCCTGCCCCAACCAATCCTTCAAGGCCTGGCTAAAAGGCCACTTCCAATAGGACATGATATAAGCTTACGTGCTCAGCCTTACCCCCCAGCCCACCAAAAACTTCCTGGGGACCTGGGGTCAGCCCCATCATGCCAGCCTCCCCCAGGGCCCCAAACTCCGCAGGTGCTCAACATTATCTGCTGCAGGGCATTCTCAGACACAGACTGAGATATTCAGGATGGGATCCGAAGCACCTAGAACCTGGTAGCCTTAGAAAGCTGGGCTGACCTAAGGGCAGAGTTGGTGTTCTGCACGTCATCCTCCTCGTCATCCTCATAGTCATCCTCATCATCTGAGTACTGCTGGGGTGGGCGGACTGGAACTCGGCTGCGGCCCACACCTGCCGCCAGGTCTTC	TCCTTCTGGGACTCTTTGAGCTTCTCAGCCAAGACGTTGATGGTGTTGGGCTGCAGCACTGACAGTTGCCCATCAGCAGAACCGCTCAATGCCCCTGGCTTCCCTGTTCCCTTCCCCTTATACCTGTGGGGCCCGAGAAGATGTGAAGCAAGGGAACGGGCCAGGTGACCATACCCAGCAGTACCCAGAATGGCTTAAATACATCCCGACCTCCAGGGGCTGACCCTAAAACTCCTTATACTTGGTCCAAGCAACTTGAACTAGCCATGCTAAGCCTGGCATCAAGTTCTGACAGCTGCAGCCAAGTGTCCTCAAAAGACACTTCCTCTATTCCAGCCATCCCACTCCTGGCCTTTTGCCAATGCCCTGTGTTCCAGCAAAGCTGCCTCCCCACCACCCACATCTCCTCCATCCCTGCCCCAACCAATCCTTCAAGGCCTGGCTAAAAGGCCACTTCCAATAGGACATGATATAAGCTTACGTGCTCAGCCTTACCCCCCAGCCCACCAAAAACTTCCTGGGGACCTGGGGTCAGCCCCATCATGCCAGCCTCCCCCAGGGCCCCAAACTCCGCAGGTGCTCAACATTATCTGCTGCAGGGCATTCTCAGACACAGACTGAGATATTCAGGATGGGATCCGAAGCACCTAGAACCTGGTAGCCTTAGAAAGCTGGGCTGACCTAAGGGCAGAGTTGGTGTTCTGCACGTCATCCTCCTCGTCATCCTCATAGTCATCCTCATCATCTGAGTACTGCTGGGGTGGGCGGACTGGAACTCGGCTGCGGCCCACACCTGCCGCCAGGTCTTC	-	novel	NA	P-0031651-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	62	651	0	ENST00000460680.1:c.1123_1373del		p.X375_splice	ENST00000460680	NM_004656.3	375	GAAGACCTGGCGGCAGGTGTGGGCCGCAGCCGAGTTCCAGTCCGCCCACCCCAGCAGTACTCAGATGATGAGGATGACTATGAGGATGACGAGGAGGATGACGTGCAGAACACCAACTCTGCCCTTAGGTCAGCCCAGCTTTCTAAGGCTACCAGGTTCTAGGTGCTTCGGATCCCATCCTGAATATCTCAGTCTGTGTCTGAGAATGCCCTGCAGCAGATAATGTTGAGCACCTGCGGAGTTTGGGGCCCTGGGGGAGGCTGGCATGATGGGGCTGACCCCAGGTCCCCAGGAAGTTTTTGGTGGGCTGGGGGGTAAGGCTGAGCACGTAAGCTTATATCATGTCCTATTGGAAGTGGCCTTTTAGCCAGGCCTTGAAGGATTGGTTGGGGCAGGGATGGAGGAGATGTGGGTGGTGGGGAGGCAGCTTTGCTGGAACACAGGGCATTGGCAAAAGGCCAGGAGTGGGATGGCTGGAATAGAGGAAGTGTCTTTTGAGGACACTTGGCTGCAGCTGTCAGAACTTGATGCCAGGCTTAGCATGGCTAGTTCAAGTTGCTTGGACCAAGTATAAGGAGTTTTAGGGTCAGCCCCTGGAGGTCGGGATGTATTTAAGCCATTCTGGGTACTGCTGGGTATGGTCACCTGGCCCGTTCCCTTGCTTCACATCTTCTCGGGCCCCACAGGTATAAGGGGAAGGGAACAGGGAAGCCAGGGGCATTGAGCGGTTCTGCTGATGGGCAACTGTCAGTGCTGCAGCCCAACACCATCAACGTCTTGGCTGAGAAGCTCAAAGAGTCCCAGAAGGAc/c	12-13/17	0.265281741801309	2	FACETS	0.468	0.404	0.537	0.234	0.202	0.269	INDETERMINATE	1	TRUE	0	0.502137656028961	2		651	528	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696660	176696660	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031651-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	102	334	0	ENST00000439151.2:c.5361G>A	p.Met1787Ile	p.M1787I	ENST00000439151	NM_022455.4	1787	atG/atA	16/23	NA	2	FACETS	0.897	0.807	0.992			1	INDETERMINATE	1	TRUE	NA	0.502137656028961	2		334	453	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287945	33287945	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031651-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	233	471	0	ENST00000374542.5:c.1308T>A	p.Asp436Glu	p.D436E	ENST00000374542	NM_001141970.1	436	gaT/gaA	5/8	0.502137656028961	5	FACETS	0.938	0.877	1	0.626	0.584	0.668	CLONAL	2	TRUE	2	0.502137656028961	5		471	867	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710999	117710999	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031651-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	38	241	1	ENST00000368508.3:c.1273del	p.Tyr425ThrfsTer3	p.Y425Tfs*3	ENST00000368508	NM_002944.2	425	Tac/ac	12/43	0.265281741801309	2	FACETS	1	0.873	1	0.522	0.439	0.611	INDETERMINATE	1	TRUE	0	0.502137656028961	2		242	145	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197827	66197827	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031651-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	18	307	0	ENST00000273854.3:c.2872del	p.Glu958AsnfsTer5	p.E958Nfs*5	ENST00000273854	NM_004439.5	958	Gaa/aa	17/18	1	2	FACETS	0.348	0.263	0.448	0.348	0.263	0.448	SUBCLONAL	1	TRUE	1	0.502137656028961	2		307	206	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0031660-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	118	756	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.308817486540792	1	FACETS	0.814	0.734	0.898	0.814	0.734	0.898	CLONAL	1	FALSE	0	0.308817486540792	1		756	794	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031660-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	136	320	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.308817486540792	2		321	680	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777933	3777933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1048314482	NA	P-0031660-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	176	899	0	ENST00000262367.5:c.7115C>T	p.Ser2372Leu	p.S2372L	ENST00000262367	NM_004380.2	2372	tCg/tTg	31/31	1	2	FACETS	0.823	0.756	0.893	0.823	0.756	0.893	CLONAL	1	FALSE	1	0.308817486540792	2		899	1385	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828304	72828304	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs2229288	NA	P-0031660-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	68	468	1	ENST00000268489.5:c.8277G>T	p.Gln2759His	p.Q2759H	ENST00000268489	NM_006885.3	2759	caG/caT	9/10	1	2	FACETS	0.713	0.62	0.813	0.713	0.62	0.813	SUBCLONAL	1	FALSE	1	0.308817486540792	2		469	618	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40709529	40709529	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031660-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	98	474	0	ENST00000373198.4:c.4373G>T	p.Ser1458Ile	p.S1458I	ENST00000373198	NM_133170.3	1458	aGc/aTc	32/32	1	2	FACETS	0.865	0.771	0.964	0.865	0.771	0.964	CLONAL	1	FALSE	1	0.308817486540792	2		474	734	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176719109	176719109	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031660-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	72	249	0	ENST00000439151.2:c.6413G>T	p.Cys2138Phe	p.C2138F	ENST00000439151	NM_022455.4	2138	tGc/tTc	22/23	0.180668397045994	2	FACETS	1	0.968	1	0.662	0.582	0.747	INDETERMINATE	1	FALSE	0	0.308817486540792	2		249	352	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431117	49431117	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	28	572	0	ENST00000301067.7:c.10022A>C	p.Gln3341Pro	p.Q3341P	ENST00000301067	NM_003482.3	3341	cAa/cCa	34/54	0.206267713037915	4	FACETS	0.563	0.449	0.693	0.281	0.224	0.347	SUBCLONAL	1	FALSE	2	0.225439891029859	4		572	541	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803108	1803108	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	45	666	0	ENST00000260795.2:c.460A>G	p.Thr154Ala	p.T154A	ENST00000260795		154	Aca/Gca	4/17	0.157234792133236	2	FACETS	0.599	0.503	0.707	0.3	0.251	0.354	SUBCLONAL	1	FALSE	0	0.225439891029859	2		666	666	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	327	320	1				ENST00000310581	NM_198253.2	-/1132			0.233720328868573	12	FACETS	1	0.98	1			1	CLONAL	8	TRUE	NA	0.233720328868573	12		321	720	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665213	138665213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	211	793	0	ENST00000330315.3:c.352G>A	p.Glu118Lys	p.E118K	ENST00000330315	NM_023067.3	118	Gag/Aag	1/1	0.194464633614165	4	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	2	0.233720328868573	4		793	1103	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077427	30077427	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0031770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	53	224	0	ENST00000338641.4:c.1575-1G>C		p.X525_splice	ENST00000338641	NM_000268.3	525			0.219465725968633	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	0	0.233720328868573	2		224	195	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579321	7579322	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs587780067	NA	P-0031770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	172	470	0	ENST00000269305.4:c.365_366del	p.Val122AspfsTer26	p.V122Dfs*26	ENST00000269305	NM_001126112.2	122	gTG/g	4/11	0.21674883737881	3	FACETS	0.95	0.879	1	0.95	0.879	1	CLONAL	3	TRUE	0	0.233720328868573	3		470	577	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109321750	109321750	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	69	610	0	ENST00000436639.2:c.673G>C	p.Glu225Gln	p.E225Q	ENST00000436639	NM_014454.2	225	Gaa/Caa	4/10	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.233720328868573	2		610	573	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100227	30100227	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	93	291	0	ENST00000331968.5:c.1393G>A	p.Glu465Lys	p.E465K	ENST00000331968	NM_002742.2	465	Gaa/Aaa	10/18	0.21674883737881	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	3	TRUE	0	0.233720328868573	3		291	278	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644703	134644703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536029159	NA	P-0031770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	106	445	0	ENST00000398015.3:c.104C>T	p.Thr35Met	p.T35M	ENST00000398015	NM_004441.4	35	aCg/aTg	2/16	0.233720328868573	3	FACETS	1	0.915	1	1	0.915	1	CLONAL	2	TRUE	1	0.233720328868573	3		445	498	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430411	78430411	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	65	353	0	ENST00000370768.2:c.757G>C	p.Glu253Gln	p.E253Q	ENST00000370768	NM_003902.3	253	Gag/Cag	10/20	0.191229458095028	3	FACETS	0.953	0.832	1	0.953	0.832	1	CLONAL	2	TRUE	1	0.233720328868573	3		353	326	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843736	156843736	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	129	849	0	ENST00000524377.1:c.1162G>C	p.Glu388Gln	p.E388Q	ENST00000524377	NM_002529.3	388	Gag/Cag	8/17	0.233683666560054	5	FACETS	1	0.983	1	0.28	0.253	0.309	CLONAL	1	TRUE	0	0.233720328868573	5		849	1064	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440437	49440458	+	frameshift_variant	Frame_Shift_Del	DEL	TCCAGGCAGTATGTGTGGTAGC	TCCAGGCAGTATGTGTGGTAGC	-	novel	NA	P-0031770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	103	621	0	ENST00000301067.7:c.4352_4373del	p.Ser1451ThrfsTer48	p.S1451Tfs*48	ENST00000301067	NM_003482.3	1451	aGCTACCACACATACTGCCTGGAc/ac	15/54	0.200595057718332	3	FACETS	1	0.981	1	0.73	0.654	0.811	CLONAL	1	TRUE	1	0.233720328868573	3		621	674	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602352	28602352	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	86	377	0	ENST00000241453.7:c.2016G>C	p.Glu672Asp	p.E672D	ENST00000241453	NM_004119.2	672	gaG/gaC	16/24	0.233720328868573	3	FACETS	0.958	0.852	1	0.958	0.852	1	CLONAL	2	TRUE	1	0.233720328868573	3		377	429	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849269	89849269	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	206	511	0	ENST00000389301.3:c.1624G>C	p.Glu542Gln	p.E542Q	ENST00000389301	NM_000135.2	542	Gag/Cag	17/43	0.233412964937711	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	TRUE	0	0.233720328868573	3		511	610	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639605	47639605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	46	475	0	ENST00000233146.2:c.698C>T	p.Ser233Phe	p.S233F	ENST00000233146	NM_000251.2	233	tCc/tTc	4/16	0.191229458095028	3	FACETS	0.984	0.829	1	0.492	0.414	0.577	CLONAL	1	TRUE	1	0.233720328868573	3		475	447	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198272790	198272790	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	176	452	0	ENST00000335508.6:c.1171G>C	p.Glu391Gln	p.E391Q	ENST00000335508	NM_012433.2	391	Gaa/Caa	9/25	0.233720328868573	3	FACETS	0.984	0.912	1	1	0.99	1	CLONAL	3	TRUE	1	0.233720328868573	3		452	570	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149243881	149243881	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	86	494	0	ENST00000360632.3:c.937G>C	p.Asp313His	p.D313H	ENST00000360632	NM_015472.4	313	Gac/Cac	6/7	0.194464633614165	4	FACETS	0.865	0.767	0.969	0.865	0.767	0.969	CLONAL	2	TRUE	2	0.233720328868573	4		494	525	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356169	66356169	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	63	407	0	ENST00000273854.3:c.1328C>A	p.Ala443Glu	p.A443E	ENST00000273854	NM_004439.5	443	gCa/gAa	5/18	0.191229458095028	3	FACETS	0.756	0.657	0.864	0.756	0.657	0.864	SUBCLONAL	2	TRUE	1	0.233720328868573	3		407	398	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630186	187630186	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760240029	NA	P-0031770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	48	457	0	ENST00000441802.2:c.796G>A	p.Glu266Lys	p.E266K	ENST00000441802	NM_005245.3	266	Gaa/Aaa	2/27	0.219465725968633	2	FACETS	0.992	0.84	1	0.496	0.42	0.579	CLONAL	1	TRUE	0	0.233720328868573	2		457	414	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164190	32164191	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0031770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	36	320	0	ENST00000375023.3:c.5208_5209del	p.Leu1738AlafsTer22	p.L1738Afs*22	ENST00000375023	NM_004557.3	1736	acTGcg/accg	29/30	0.233720328868573	3	FACETS	0.884	0.728	1	0.442	0.364	0.53	CLONAL	1	TRUE	1	0.233720328868573	3		320	389	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356494	70356494	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	68	301	0	ENST00000374080.3:c.5389A>G	p.Thr1797Ala	p.T1797A	ENST00000374080		1797	Acc/Gcc	37/45	0.192878364046464	2	FACETS	0.764	0.668	0.866			1	SUBCLONAL	2	TRUE	NA	0.233720328868573	2		301	381	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	130	320	1				ENST00000310581	NM_198253.2	-/1132			0.270315422021476	3	FACETS	1	0.912	1	1	0.912	1	CLONAL	2	TRUE	1	0.275084453279871	3		321	537	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584629	187584629	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1479462211	NA	P-0031912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	108	454	0	ENST00000441802.2:c.3404A>G	p.Asn1135Ser	p.N1135S	ENST00000441802	NM_005245.3	1135	aAt/aGt	3/27	0.273927264402168	3	FACETS	1	0.974	1	0.42	0.377	0.465	CLONAL	1	TRUE	0	0.275084453279871	3		454	709	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910647	29910647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	158	734	0	ENST00000376809.5:c.187G>A	p.Asp63Asn	p.D63N	ENST00000376809	NM_002116.7	63	Gac/Aac	2/8	0.203886572528619	5	FACETS	1	0.981	1	0.421	0.384	0.459	CLONAL	1	TRUE	2	0.275084453279871	5		734	1286	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032594	47032594	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	202	322	0	ENST00000377604.3:c.500del	p.Ser167Ter	p.S167*	ENST00000377604	NM_001204468.1	167	tCa/ta	5/24	0.232967709395872	2	FACETS	0.888	0.83	0.948			1	CLONAL	3	TRUE	NA	0.275084453279871	2		322	551	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405181	70405181	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	82	331	0	ENST00000373644.4:c.2695C>G	p.Gln899Glu	p.Q899E	ENST00000373644	NM_030625.2	899	Caa/Gaa	4/12	0.275084453279871	3	FACETS	1	0.969	1	0.65	0.574	0.73	CLONAL	1	TRUE	1	0.275084453279871	3		331	522	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514296	69514296	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	93	581	0	ENST00000294312.3:c.385G>C	p.Asp129His	p.D129H	ENST00000294312	NM_005117.2	129	Gat/Cat	3/3	0.270315422021476	3	FACETS	0.904	0.803	1	0.452	0.401	0.506	CLONAL	1	TRUE	1	0.275084453279871	3		581	851	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94926629	94926629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	37	443	0	ENST00000536441.1:c.136G>A	p.Glu46Lys	p.E46K	ENST00000536441	NM_144665.3	46	Gag/Aag	2/10	0.270315422021476	3	FACETS	0.592	0.487	0.709	0.296	0.243	0.355	SUBCLONAL	1	TRUE	1	0.275084453279871	3		443	517	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112919983	112919983	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	172	562	0	ENST00000351677.2:c.1198G>A	p.Glu400Lys	p.E400K	ENST00000351677	NM_002834.3	400	Gaa/Aaa	10/16	0.203886572528619	5	FACETS	1	0.921	1	0.667	0.614	0.722	CLONAL	2	TRUE	2	0.275084453279871	5		562	883	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557711	21557711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	117	588	0	ENST00000382592.4:c.2134C>T	p.His712Tyr	p.H712Y	ENST00000382592	NM_014572.2	712	Cac/Tac	5/8	0.141767789280913	3	FACETS	0.918	0.826	1	0.306	0.275	0.339	INDETERMINATE	1	TRUE	0	0.275084453279871	3		588	1054	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646384	23646384	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	80	548	0	ENST00000261584.4:c.1483G>A	p.Glu495Lys	p.E495K	ENST00000261584	NM_024675.3	495	Gaa/Aaa	4/13	0.275084453279871	3	FACETS	0.814	0.715	0.92	0.407	0.357	0.46	CLONAL	1	TRUE	1	0.275084453279871	3		548	813	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541604	29541604	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1060500331	NA	P-0031912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	25	122	0	ENST00000356175.3:c.1527+1G>T		p.X509_splice	ENST00000356175	NM_000267.3	509			NA	2	FACETS	1	0.931	1			1	INDETERMINATE	1	TRUE	NA	0.275084453279871	2		122	124	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248530	212248530	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	201	561	0	ENST00000342788.4:c.3737G>T	p.Ser1246Ile	p.S1246I	ENST00000342788	NM_005235.2	1246	aGc/aTc	28/28	0.270315422021476	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.275084453279871	3		561	809	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502843	186502843	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	83	389	0	ENST00000323963.5:c.301G>T	p.Glu101Ter	p.E101*	ENST00000323963		101	Gag/Tag	4/11	0.264651049432144	4	FACETS	0.974	0.859	1	0.325	0.286	0.366	CLONAL	1	TRUE	1	0.275084453279871	4		389	790	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509975	187509975	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	89	344	0	ENST00000441802.2:c.13538G>C	p.Arg4513Thr	p.R4513T	ENST00000441802	NM_005245.3	4513	aGa/aCa	27/27	0.273927264402168	3	FACETS	1	0.97	1	0.427	0.379	0.479	CLONAL	1	TRUE	0	0.275084453279871	3		344	574	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178032	56178032	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	56	283	0	ENST00000399503.3:c.3005C>G	p.Ser1002Cys	p.S1002C	ENST00000399503	NM_005921.1	1002	tCt/tGt	14/20	0.270315422021476	3	FACETS	1	0.881	1	0.515	0.442	0.594	CLONAL	1	TRUE	1	0.275084453279871	3		283	450	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979221	93979221	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	26	229	0	ENST00000369303.4:c.1607A>T	p.Glu536Val	p.E536V	ENST00000369303	NM_004440.3	536	gAg/gTg	7/17	0.270315422021476	3	FACETS	1	0.849	1	0.54	0.431	0.664	CLONAL	1	TRUE	1	0.275084453279871	3		229	199	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987322	2987322	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs758661288	NA	P-0031912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	81	594	0	ENST00000396946.4:c.107A>G	p.Tyr36Cys	p.Y36C	ENST00000396946	NM_032415.4	36	tAt/tGt	3/25	0.264651049432144	4	FACETS	0.589	0.517	0.667	0.196	0.172	0.223	SUBCLONAL	1	TRUE	1	0.275084453279871	4		594	1274	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576922	7576922	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	1300	590	0	ENST00000269305.4:c.924del	p.Asn310ThrfsTer35	p.N310Tfs*35	ENST00000269305	NM_001126112.2	308	ctG/ct	9/11	0.0823408818120681	5	FACETS	0.947	0.934	0.959			1	INDETERMINATE	5	TRUE	NA	0.788147531069107	5		590	1521	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0032016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	233	426	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.243901737564963	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	2	0.309761401856811	4		426	936	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076937	41076937	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	90	523	0	ENST00000373198.4:c.1483G>A	p.Gly495Arg	p.G495R	ENST00000373198	NM_133170.3	495	Ggg/Agg	9/32	1	2	FACETS	0.692	0.613	0.776	0.692	0.613	0.776	SUBCLONAL	1	TRUE	1	0.309761401856811	2		523	840	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607569	43607570	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0032016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	344	805	2	ENST00000355710.3:c.1545_1546delinsAA	p.Cys515_Pro516delinsTer	p.C515_P516delins*	ENST00000355710	NM_020975.4	515	tgCCcc/tgAAcc	8/20	0.309761401856811	2	FACETS	0.805	0.761	0.851	0.805	0.761	0.851	CLONAL	2	TRUE	0	0.309761401856811	2		807	1379	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588156	69588156	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1215	109	664	0	ENST00000168712.1:c.542T>C	p.Leu181Pro	p.L181P	ENST00000168712	NM_002007.2	181	cTg/cCg	3/3	1	2	FACETS	0.532	0.476	0.591	0.532	0.476	0.591	SUBCLONAL	1	TRUE	1	0.309761401856811	2		664	1324	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625156	69625156	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	106	713	0	ENST00000334134.2:c.637C>A	p.Gln213Lys	p.Q213K	ENST00000334134	NM_005247.2	213	Cag/Aag	3/3	1	2	FACETS	0.516	0.461	0.575	0.516	0.461	0.575	SUBCLONAL	1	TRUE	1	0.309761401856811	2		713	1326	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121641	108121673	+	inframe_deletion	In_Frame_Del	DEL	CTGGAATAAAATTTGGTGTATTACCTTTCGTGG	CTGGAATAAAATTTGGTGTATTACCTTTCGTGG	-	novel	NA	P-0032016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	154	507	0	ENST00000278616.4:c.1449_1481del	p.Trp484_Gly494del	p.W484_G494del	ENST00000278616	NM_000051.3	483	ctCTGGAATAAAATTTGGTGTATTACCTTTCGTGGt/ctt	10/63	0.254085186004363	2	FACETS	0.764	0.701	0.829	0.764	0.701	0.829	SUBCLONAL	2	TRUE	0	0.309761401856811	2		507	651	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371784	118371784	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	151	436	0	ENST00000534358.1:c.6241G>T	p.Val2081Phe	p.V2081F	ENST00000534358	NM_005933.3	2081	Gtc/Ttc	25/36	0.254085186004363	2	FACETS	1	0.986	1	0.689	0.632	0.75	CLONAL	1	TRUE	0	0.309761401856811	2		436	707	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394791	394791	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	282	566	0	ENST00000399788.2:c.4904G>A	p.Trp1635Ter	p.W1635*	ENST00000399788	NM_001042603.1	1635	tGg/tAg	28/28	0.309761401856811	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.309761401856811	2		566	861	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444039	49444039	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	94	600	0	ENST00000301067.7:c.3332C>G	p.Ala1111Gly	p.A1111G	ENST00000301067	NM_003482.3	1111	gCc/gGc	11/54	0.243901737564963	4	FACETS	0.646	0.573	0.724	0.323	0.286	0.362	SUBCLONAL	1	TRUE	2	0.309761401856811	4		600	1231	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001309	29001309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	99	333	0	ENST00000282397.4:c.1423C>T	p.His475Tyr	p.H475Y	ENST00000282397	NM_002019.4	475	Cat/Tat	10/30	0.226063026741997	2	FACETS	0.78	0.701	0.862	0.78	0.701	0.862	SUBCLONAL	2	TRUE	0	0.309761401856811	2		333	410	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322632	30322633	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0032016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	131	568	0	ENST00000322652.5:c.1645_1646delinsTT	p.Gly549Leu	p.G549L	ENST00000322652	NM_015355.2	549	GGg/TTg	14/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.309761401856811	2		568	767	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313457	30313457	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	218	572	0	ENST00000262643.3:c.1057G>C	p.Ala353Pro	p.A353P	ENST00000262643	NM_001238.2	353	Gct/Cct	11/12	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.309761401856811	2		572	1118	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416347	29416347	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752701859	NA	P-0032016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	450	821	0	ENST00000389048.3:c.4606G>A	p.Glu1536Lys	p.E1536K	ENST00000389048	NM_004304.4	1536	Gag/Aag	29/29	0.14368586557678	3	FACETS	1	0.978	1	0.695	0.662	0.729	INDETERMINATE	2	TRUE	0	0.309761401856811	3		821	1609	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661796	227661796	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	97	814	0	ENST00000305123.5:c.1659G>T	p.Glu553Asp	p.E553D	ENST00000305123	NM_005544.2	553	gaG/gaT	1/2	1	2	FACETS	0.506	0.449	0.566	0.506	0.449	0.566	SUBCLONAL	1	TRUE	1	0.309761401856811	2		814	1238	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721114	39721114	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	75	435	0	ENST00000361337.2:c.617G>T	p.Trp206Leu	p.W206L	ENST00000361337	NM_003286.2	206	tGg/tTg	9/21	1	2	FACETS	0.667	0.584	0.757	0.667	0.584	0.757	SUBCLONAL	1	TRUE	1	0.309761401856811	2		435	726	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101136	41101136	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	105	614	0	ENST00000373198.4:c.1220G>T	p.Trp407Leu	p.W407L	ENST00000373198	NM_133170.3	407	tGg/tTg	8/32	1	2	FACETS	0.651	0.582	0.724	0.651	0.582	0.724	SUBCLONAL	1	TRUE	1	0.309761401856811	2		614	1042	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081569	143081569	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	75	584	0	ENST00000262992.4:c.1505del	p.Pro502GlnfsTer2	p.P502Qfs*2	ENST00000262992	NM_001101669.1	502	cCa/ca	15/24	1	2	FACETS	0.576	0.503	0.654	0.576	0.503	0.654	SUBCLONAL	1	TRUE	1	0.309761401856811	2		584	841	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201827	152201827	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	153	380	0	ENST00000206249.3:c.681C>G	p.Cys227Trp	p.C227W	ENST00000206249	NM_000125.3	227	tgC/tgG	3/8	0.254085186004363	2	FACETS	0.779	0.715	0.845	0.779	0.715	0.845	SUBCLONAL	2	TRUE	0	0.309761401856811	2		380	634	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622188	162622188	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	172	461	0	ENST00000366898.1:c.509G>T	p.Arg170Met	p.R170M	ENST00000366898	NM_004562.2	170	aGg/aTg	4/12	0.254085186004363	2	FACETS	0.767	0.707	0.829	0.767	0.707	0.829	SUBCLONAL	2	TRUE	0	0.309761401856811	2		461	724	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729536	41729536	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	168	624	0	ENST00000242208.4:c.993G>T	p.Lys331Asn	p.K331N	ENST00000242208	NM_002192.2	331	aaG/aaT	3/3	0.155852246452487	4	FACETS	1	0.981	1	0.619	0.568	0.672	INDETERMINATE	1	TRUE	2	0.309761401856811	4		624	1148	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273078	55273078	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs865825533	NA	P-0032016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	207	542	0	ENST00000275493.2:c.3401G>T	p.Gly1134Val	p.G1134V	ENST00000275493	NM_005228.3	1134	gGc/gTc	28/28	0.155852246452487	4	FACETS	1	0.99	1	0.72	0.667	0.775	INDETERMINATE	1	TRUE	2	0.309761401856811	4		542	1216	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334819	81334819	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	134	494	0	ENST00000222390.5:c.1897C>A	p.His633Asn	p.H633N	ENST00000222390	NM_000601.4	633	Cat/Aat	17/18	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.309761401856811	2		494	734	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879262	151879262	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	87	489	0	ENST00000262189.6:c.5683A>T	p.Met1895Leu	p.M1895L	ENST00000262189	NM_170606.2	1895	Atg/Ttg	36/59	1	2	FACETS	0.666	0.589	0.749	0.666	0.589	0.749	SUBCLONAL	1	TRUE	1	0.309761401856811	2		489	843	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992980	68992980	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs1181417548	NA	P-0032016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	67	340	0	ENST00000288368.4:c.1786-1G>C		p.X596_splice	ENST00000288368	NM_024870.2	596			1	2	FACETS	0.979	0.853	1	0.979	0.853	1	CLONAL	1	TRUE	1	0.309761401856811	2		340	442	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1315015	1315015	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0032016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	106	583	0	ENST00000400841.2:c.647-1G>A		p.X216_splice	ENST00000400841		216			0.226063026741997	2	FACETS	0.671	0.6	0.746	0.335	0.3	0.373	SUBCLONAL	1	TRUE	0	0.309761401856811	2		583	1020	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954299	48954299	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs1395304450	NA	P-0032028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	19	349	0	ENST00000267163.4:c.1422-2A>T		p.X474_splice	ENST00000267163	NM_000321.2	474			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		349	358	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274356	5274356	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0032028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	11	410	0	ENST00000357368.4:c.92-1G>T		p.X31_splice	ENST00000357368	NM_002850.3	31			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		410	172	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950561	38950561	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201384226	NA	P-0032095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	81	622	0	ENST00000357387.3:c.3389G>A	p.Arg1130Gln	p.R1130Q	ENST00000357387	NM_152756.3	1130	cGa/cAa	31/38	1	2	FACETS	0.44	0.387	0.497	0.44	0.387	0.497	SUBCLONAL	1	TRUE	1	0.412003774407064	2		622	894	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917736	29917736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150966028	NA	P-0032095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	83	722	0	ENST00000389048.3:c.932G>A	p.Arg311His	p.R311H	ENST00000389048	NM_004304.4	311	cGt/cAt	3/29	1	2	FACETS	0.415	0.365	0.469	0.415	0.365	0.469	SUBCLONAL	1	TRUE	1	0.412003774407064	2		722	971	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142111	108142111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	72	473	0	ENST00000278616.4:c.3055C>T	p.Leu1019Phe	p.L1019F	ENST00000278616	NM_000051.3	1019	Ctt/Ttt	20/63	0.261544451691012	1	FACETS	0.374	0.326	0.425	0.374	0.326	0.425	SUBCLONAL	1	TRUE	0	0.412003774407064	1		473	743	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392854	118392866	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCGCCAAGAAA	TGGCGCCAAGAAA	-	novel	NA	P-0032095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	128	456	0	ENST00000534358.1:c.11888_11900del	p.Gly3963AlafsTer5	p.G3963Afs*5	ENST00000534358	NM_005933.3	3962	tgTGGCGCCAAGAAA/tg	36/36	1	2	FACETS	0.886	0.805	0.972	0.886	0.805	0.972	CLONAL	1	TRUE	1	0.412003774407064	2		456	701	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420450	49420450	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	67	683	0	ENST00000301067.7:c.15299C>A	p.Ala5100Asp	p.A5100D	ENST00000301067	NM_003482.3	5100	gCc/gAc	48/54	1	2	FACETS	0.316	0.273	0.362	0.316	0.273	0.362	SUBCLONAL	1	TRUE	1	0.412003774407064	2		683	1030	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579543	7579573	+	frameshift_variant	Frame_Shift_Del	DEL	GTCCGGGGACAGCATCAAATCATCCATTGCT	GTCCGGGGACAGCATCAAATCATCCATTGCT	-	novel	NA	P-0032095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	326	841	0	ENST00000269305.4:c.114_144del	p.Ala39IlefsTer74	p.A39Ifs*74	ENST00000269305	NM_001126112.2	38	caAGCAATGGATGATTTGATGCTGTCCCCGGAC/ca	4/11	0.320032131705487	2	FACETS	1	0.994	1	0.748	0.707	0.789	CLONAL	1	TRUE	0	0.412003774407064	2		841	1058	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223469	2223469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1462122341	NA	P-0032095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	31	330	0	ENST00000398665.3:c.3580G>A	p.Glu1194Lys	p.E1194K	ENST00000398665	NM_032482.2	1194	Gag/Aag	25/28	0.261544451691012	1	FACETS	0.294	0.238	0.358	0.294	0.238	0.358	SUBCLONAL	1	TRUE	0	0.412003774407064	1		330	406	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030841	69030841	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	53	426	1	ENST00000288368.4:c.3383A>T	p.Gln1128Leu	p.Q1128L	ENST00000288368	NM_024870.2	1128	cAg/cTg	27/40	1	2	FACETS	0.397	0.338	0.462	0.397	0.338	0.462	SUBCLONAL	1	TRUE	1	0.412003774407064	2		427	648	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413989	139413990	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	105	811	0	ENST00000277541.6:c.770dup	p.Asn257LysfsTer74	p.N257Kfs*74	ENST00000277541	NM_017617.3	257	aat/aaAt	5/34	0.261544451691012	1	FACETS	0.385	0.344	0.429	0.385	0.344	0.429	SUBCLONAL	1	TRUE	0	0.412003774407064	1		811	1051	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0032136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	14	674	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.113488302827329	4	FACETS	0.243	0.175	0.327	0.081	0.058	0.109	INDETERMINATE	1	TRUE	1	0.317080768607841	4		674	478	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0032136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	82	575	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.113488302827329	4	FACETS	1	0.968	1	0.426	0.376	0.479	INDETERMINATE	1	TRUE	1	0.317080768607841	4		575	533	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449727	8449727	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs772305581	NA	P-0032136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	32	607	0	ENST00000356435.5:c.3986C>T	p.Pro1329Leu	p.P1329L	ENST00000356435		1329	cCg/cTg	23/35	0.221813856380623	2	FACETS	0.35	0.284	0.426	0.175	0.142	0.213	SUBCLONAL	1	TRUE	0	0.317080768607841	2		607	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577052	7577053	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	131	813	0	ENST00000269305.4:c.885dup	p.His296SerfsTer10	p.H296Sfs*10	ENST00000269305	NM_001126112.2	295	-/T	8/11	0.317080768607841	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.317080768607841	1		813	634	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156092	99156092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1247349502	NA	P-0032136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	30	674	0	ENST00000074304.5:c.772G>A	p.Val258Met	p.V258M	ENST00000074304	NM_001134224.1	258	Gtg/Atg	10/26	0.112287573435944	5	FACETS	0.619	0.498	0.757	0.155	0.124	0.19	INDETERMINATE	1	TRUE	1	0.317080768607841	5		674	451	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99181157	99181157	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1236305078	NA	P-0032136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	30	720	0	ENST00000074304.5:c.2098G>A	p.Asp700Asn	p.D700N	ENST00000074304	NM_001134224.1	700	Gac/Aac	20/26	0.112287573435944	5	FACETS	0.556	0.447	0.68	0.139	0.111	0.17	INDETERMINATE	1	TRUE	1	0.317080768607841	5		720	502	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30668370	30668370	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	57	574	0	ENST00000376406.3:c.6142C>G	p.His2048Asp	p.H2048D	ENST00000376406	NM_014641.2	2048	Cat/Gat	15/15	0.317080768607841	3	FACETS	0.783	0.672	0.904	0.391	0.336	0.452	CLONAL	1	TRUE	1	0.317080768607841	3		574	532	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0032252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	13	515	2	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	0.083	0.058	0.112	0.083	0.058	0.112	SUBCLONAL	1	TRUE	1	0.922264710525025	2		517	341	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0032252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	115	328	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	0.327504531125517	3	FACETS	1	0.987	1	0.741	0.681	0.801	INDETERMINATE	1	TRUE	1	0.922264710525025	3		328	246	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466000	69466000	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10866	598	618	0	ENST00000227507.2:c.838G>A	p.Glu280Lys	p.E280K	ENST00000227507	NM_053056.2	280	Gag/Aag	5/5	0.922264710525025	30	FACETS	0.787	0.75	0.825			1	SUBCLONAL	2	TRUE	NA	0.922264710525025	30		618	11464	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965011	15965011	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	36	570	0	ENST00000268712.3:c.5585A>G	p.Glu1862Gly	p.E1862G	ENST00000268712	NM_006311.3	1862	gAa/gGa	37/46	1	2	FACETS	0.125	0.102	0.151	0.125	0.102	0.151	SUBCLONAL	1	TRUE	1	0.922264710525025	2		570	623	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278114	41278114	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	70	553	0	ENST00000349496.5:c.1990G>A	p.Glu664Lys	p.E664K	ENST00000349496	NM_001904.3	664	Gag/Aag	13/15	0.327504531125517	3	FACETS	0.403	0.352	0.459	0.202	0.176	0.23	INDETERMINATE	1	TRUE	1	0.922264710525025	3		553	550	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162609	47162609	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	166	408	0	ENST00000409792.3:c.3517C>T	p.His1173Tyr	p.H1173Y	ENST00000409792	NM_014159.6	1173	Cat/Tat	3/21	0.327504531125517	3	FACETS	1	0.987	1	0.638	0.593	0.684	INDETERMINATE	1	TRUE	1	0.922264710525025	3		408	412	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71019939	71019942	+	frameshift_variant	Frame_Shift_Del	DEL	TTAA	TTAA	-	novel	NA	P-0032252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	106	171	0	ENST00000318789.4:c.1667_1670del	p.Ile556LysfsTer42	p.I556Kfs*42	ENST00000318789	NM_032682.5	556	aTTAAa/aa	19/21	0.327504531125517	3	FACETS	0.875	0.807	0.942	0.875	0.807	0.942	INDETERMINATE	2	TRUE	1	0.922264710525025	3		171	192	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938406	44938406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	172	197	0	ENST00000377967.4:c.2954C>T	p.Ser985Phe	p.S985F	ENST00000377967	NM_021140.2	985	tCt/tTt	20/29	0.446810744459385	2	FACETS	1	0.975	1			1	INDETERMINATE	2	TRUE	NA	0.922264710525025	2		197	186	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0032253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	88	674	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.253308732328951	5	FACETS	0.901	0.801	1	0.36	0.32	0.404	CLONAL	2	FALSE	0	0.253308732328951	5		674	532	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0032253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	291	575	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.253308732328951	5	FACETS	1	0.961	1	1	0.992	1	CLONAL	6	FALSE	0	0.253308732328951	5		575	524	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0032253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	112	319	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.253630791619957	4	FACETS	1	0.952	1			1	CLONAL	4	FALSE	NA	0.253308732328951	4		319	262	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0032253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	107	264	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.225196278930308	5	FACETS	0.928	0.843	1	1	0.976	1	CLONAL	4	FALSE	2	0.253308732328951	5		264	314	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120733	115120733	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	128	506	0	ENST00000257566.3:c.273G>C	p.Lys91Asn	p.K91N	ENST00000257566	NM_016569.3	91	aaG/aaC	1/8	0.217691093541016	3	FACETS	1	0.967	1	0.752	0.685	0.821	CLONAL	2	FALSE	0	0.253308732328951	3		506	505	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123873988	123873988	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	10	27	0	ENST00000330479.4:c.19A>T	p.Met7Leu	p.M7L	ENST00000330479	NM_020382.3	7	Atg/Ttg	2/9	0.217691093541016	3	FACETS	1	0.848	1	0.494	0.341	0.677	CLONAL	1	FALSE	0	0.253308732328951	3		27	60	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132583	11132583	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	203	586	0	ENST00000358026.2:c.2799C>G	p.Phe933Leu	p.F933L	ENST00000358026	NM_001128849.1	933	ttC/ttG	19/36	0.253308732328951	7	FACETS	1	0.981	1			1	CLONAL	3	FALSE	NA	0.253308732328951	7		586	754	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044942	47044942	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1556781926	NA	P-0032253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	419	370	0	ENST00000377604.3:c.2268G>A	p.Trp756Ter	p.W756*	ENST00000377604	NM_001204468.1	756	tgG/tgA	20/24	0.253308732328951	6	FACETS	1	0.991	1			1	CLONAL	9	FALSE	NA	0.253308732328951	6		370	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0032254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	174	646	7	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.363073919995155	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.363073919995155	1		653	708	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653028	29653028	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756450772	NA	P-0032254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	119	412	2	ENST00000356175.3:c.4963G>A	p.Ala1655Thr	p.A1655T	ENST00000356175	NM_000267.3	1655	Gca/Aca	36/57	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.363073919995155	2		414	627	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048787	180048787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	197	770	2	ENST00000261937.6:c.1775G>A	p.Arg592His	p.R592H	ENST00000261937	NM_182925.4	592	cGc/cAc	13/30	NA	2	FACETS	0.968	0.895	1			1	INDETERMINATE	1	TRUE	NA	0.363073919995155	2		772	1121	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980416	201980417	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0032254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	148	529	0	ENST00000359651.3:c.154dup	p.Glu52GlyfsTer40	p.E52Gfs*40	ENST00000359651		51	ttg/ttGg	1/8	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.363073919995155	2		529	772	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849069	156849069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750168062	NA	P-0032259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1276	86	772	2	ENST00000524377.1:c.1961G>A	p.Arg654His	p.R654H	ENST00000524377	NM_002529.3	654	cGc/cAc	15/17	1	2	FACETS	0.238	0.209	0.269	0.238	0.209	0.269	SUBCLONAL	1	TRUE	1	0.530566839552822	2		774	1362	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488657	212488657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374970657	NA	P-0032263-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	133	466	0	ENST00000342788.4:c.2192C>T	p.Thr731Met	p.T731M	ENST00000342788	NM_005235.2	731	aCg/aTg	18/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		466	542	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115559	108115559	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032263-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	142	596	0	ENST00000278616.4:c.707T>G	p.Leu236Arg	p.L236R	ENST00000278616	NM_000051.3	236	cTt/cGt	7/63	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		596	468	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443866	52443866	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032263-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	224	715	0	ENST00000460680.1:c.29G>A	p.Ser10Asn	p.S10N	ENST00000460680	NM_004656.3	10	aGc/aAc	1/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		715	731	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782144	NA	P-0032265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	141	743	0	ENST00000269305.4:c.473G>C	p.Arg158Pro	p.R158P	ENST00000269305	NM_001126112.2	158	cGc/cCc	5/11	0.167967835299929	2	FACETS	1	0.986	1	0.737	0.671	0.806	CLONAL	1	TRUE	0	0.219844647304117	2		743	870	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564530	86564530	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	47	492	0	ENST00000274376.6:c.266del	p.Gly89GlufsTer7	p.G89Efs*7	ENST00000274376	NM_002890.2	88	Ggg/gg	1/25	1	2	FACETS	0.683	0.575	0.802	0.683	0.575	0.802	SUBCLONAL	1	TRUE	1	0.219844647304117	2		492	626	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197365	106197365	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	45	291	0	ENST00000380013.4:c.5698G>T	p.Val1900Phe	p.V1900F	ENST00000380013	NM_001127208.2	1900	Gtc/Ttc	11/11	0.219844647304117	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	0	0.219844647304117	1		291	326	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610615	10610615	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	84	537	0	ENST00000171111.5:c.95T>G	p.Met32Arg	p.M32R	ENST00000171111	NM_203500.1	32	aTg/aGg	2/6	1	2	FACETS	0.948	0.836	1	0.948	0.836	1	CLONAL	1	TRUE	1	0.219844647304117	2		537	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0032267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	231	646	7	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.347539931189246	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.347539931189246	2		653	651	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0032267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	181	430	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.243030633118641	2	FACETS	0.77	0.713	0.83	0.77	0.713	0.83	SUBCLONAL	2	TRUE	0	0.347539931189246	2		431	676	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0032267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	92	455	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.347539931189246	1	FACETS	0.974	0.87	1	0.974	0.87	1	CLONAL	1	TRUE	0	0.347539931189246	1		455	449	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0032267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	66	327	1	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.347539931189246	2		328	373	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627398	37627398	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	142	522	3	ENST00000447079.4:c.1313A>T	p.Lys438Met	p.K438M	ENST00000447079	NM_015083.1	438	aAg/aTg	2/14	0.347539931189246	2	FACETS	1	0.971	1	0.572	0.522	0.624	CLONAL	1	TRUE	0	0.347539931189246	2		525	714	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213964	2213964	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	121	544	0	ENST00000326181.6:c.43G>T	p.Gly15Trp	p.G15W	ENST00000326181	NM_032271.2	15	Ggg/Tgg	2/21	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.347539931189246	2		544	694	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	231041	231041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	111	532	0	ENST00000264932.6:c.821G>A	p.Gly274Asp	p.G274D	ENST00000264932	NM_004168.2	274	gGc/gAc	7/15	0.347539931189246	3	FACETS	0.933	0.838	1	0.466	0.419	0.517	CLONAL	1	TRUE	1	0.347539931189246	3		532	804	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0032270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	31	403	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.685	0.553	0.836	0.685	0.553	0.836	SUBCLONAL	1	TRUE	1	0.15	2		403	603	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913355	NA	P-0032270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	55	356	0	ENST00000288602.6:c.1406G>T	p.Gly469Val	p.G469V	ENST00000288602	NM_004333.4	469	gGa/gTa	11/18	1	2	FACETS	0.804	0.689	0.929	1	0.97	1	CLONAL	2	TRUE	1	0.15	2		356	456	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372755	81372755	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	22	294	0	ENST00000222390.5:c.779G>A	p.Cys260Tyr	p.C260Y	ENST00000222390	NM_000601.4	260	tGc/tAc	7/18	1	2	FACETS	0.758	0.587	0.957	0.758	0.587	0.957	CLONAL	1	TRUE	1	0.15	2		294	387	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221975	1221975	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	45	596	0	ENST00000326873.7:c.890G>T	p.Arg297Met	p.R297M	ENST00000326873	NM_000455.4	297	aGg/aTg	7/10	1	2	FACETS	0.799	0.67	0.943	0.799	0.67	0.943	CLONAL	1	TRUE	1	0.15	2		596	751	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955100	55955100	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs376432705	NA	P-0032270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	32	357	0	ENST00000263923.4:c.3445C>G	p.Gln1149Glu	p.Q1149E	ENST00000263923	NM_002253.2	1149	Cag/Gag	26/30	1	2	FACETS	0.773	0.626	0.94	0.773	0.626	0.94	CLONAL	1	TRUE	1	0.15	2		357	552	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	256	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.534804107600707	2	FACETS	0.991	0.94	1	0.991	0.94	1	CLONAL	2	TRUE	0	0.534804107600707	2		452	483	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410571	63410571	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	176	387	0	ENST00000330258.3:c.2596G>T	p.Val866Leu	p.V866L	ENST00000330258	NM_152424.3	866	Gtg/Ttg	2/2	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.534804107600707	1		387	345	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057519990	NA	P-0032274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	317	512	1	ENST00000269305.4:c.796G>T	p.Gly266Ter	p.G266*	ENST00000269305	NM_001126112.2	266	Gga/Tga	8/11	0.534804107600707	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.534804107600707	2		513	593	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109764	115109764	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	188	666	0	ENST00000257566.3:c.2114C>T	p.Ser705Phe	p.S705F	ENST00000257566	NM_016569.3	705	tCc/tTc	8/8	0.534804107600707	2	FACETS	0.987	0.915	1	0.494	0.457	0.531	CLONAL	1	TRUE	0	0.534804107600707	2		666	712	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518660	204518660	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	163	294	0	ENST00000367182.3:c.1323G>C	p.Glu441Asp	p.E441D	ENST00000367182	NM_001278516.1	441	gaG/gaC	11/11	0.197388329289876	3	FACETS	1	0.938	1	0.672	0.625	0.72	INDETERMINATE	2	TRUE	0	0.534804107600707	3		294	383	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294250	11294250	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	306	509	1	ENST00000361445.4:c.2281G>T	p.Val761Phe	p.V761F	ENST00000361445	NM_004958.3	761	Gtc/Ttc	14/58	0.520900678607774	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.534804107600707	2		510	533	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999756	100999756	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	285	649	0	ENST00000325455.5:c.46G>T	p.Gly16Cys	p.G16C	ENST00000325455	NM_001202474.3	16	Ggc/Tgc	1/8	0.534804107600707	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.534804107600707	2		649	531	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45864839	45864839	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	292	914	0	ENST00000391945.4:c.1180T>C	p.Phe394Leu	p.F394L	ENST00000391945	NM_000400.3	394	Ttc/Ctc	12/23	0.534804107600707	1	FACETS	0.905	0.854	0.957	0.905	0.854	0.957	CLONAL	1	TRUE	0	0.534804107600707	1		914	884	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794846	242794846	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	220	628	0	ENST00000334409.5:c.363C>A	p.Tyr121Ter	p.Y121*	ENST00000334409	NM_005018.2	121	taC/taA	2/5	0.534804107600707	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.534804107600707	1		628	475	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185195135	185195135	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	75	236	0	ENST00000265026.3:c.2452G>C	p.Glu818Gln	p.E818Q	ENST00000265026	NM_004721.4	818	Gag/Cag	12/14	0.534804107600707	2	FACETS	0.896	0.792	1	0.448	0.396	0.503	CLONAL	1	TRUE	0	0.534804107600707	2		236	313	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730074	41730074	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs377167564	NA	P-0032274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	215	437	0	ENST00000242208.4:c.455G>T	p.Arg152Leu	p.R152L	ENST00000242208	NM_002192.2	152	cGt/cTt	3/3	0.534804107600707	3	FACETS	0.923	0.865	0.982	0.923	0.865	0.982	CLONAL	2	TRUE	1	0.534804107600707	3		437	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0032275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	235	590	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.268999176837577	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.286007871872319	2		590	768	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347909	347909	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	158	1041	0	ENST00000262320.3:c.1597C>T	p.Arg533Ter	p.R533*	ENST00000262320	NM_003502.3	533	Cga/Tga	6/11	0.286007871872319	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.286007871872319	1		1041	913	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971053	21971053	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs137854598	NA	P-0032275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	137	294	1	ENST00000304494.5:c.305C>A	p.Ala102Glu	p.A102E	ENST00000304494	NM_000077.4	102	gCg/gAg	2/3	0.286007871872319	1	FACETS	1	0.926	1	1	0.991	1	CLONAL	2	TRUE	0	0.286007871872319	1		295	407	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426795	212426795	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	65	368	0	ENST00000342788.4:c.2320A>G	p.Ser774Gly	p.S774G	ENST00000342788	NM_005235.2	774	Agt/Ggt	20/28	0.194535810809179	3	FACETS	1	0.933	1	0.56	0.486	0.639	CLONAL	1	TRUE	1	0.286007871872319	3		368	464	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729816	41729816	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	35	383	0	ENST00000242208.4:c.713T>C	p.Leu238Pro	p.L238P	ENST00000242208	NM_002192.2	238	cTg/cCg	3/3	0.286007871872319	4	FACETS	0.603	0.493	0.726	0.301	0.246	0.363	SUBCLONAL	1	TRUE	2	0.286007871872319	4		383	522	SUCCESS
AR	367	MSKCC	GRCh37	X	66863135	66863135	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	168	328	0	ENST00000374690.3:c.1654T>C	p.Tyr552His	p.Y552H	ENST00000374690	NM_000044.3	552	Tat/Cat	2/8	0.189044063747376	2	FACETS	1	0.944	1			1	CLONAL	3	TRUE	NA	0.286007871872319	2		328	386	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913400	NA	P-0032277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	54	61	0	ENST00000349496.5:c.98C>A	p.Ser33Tyr	p.S33Y	ENST00000349496	NM_001904.3	33	tCt/tAt	3/15	1	2	FACETS	0.848	0.727	0.98	0.848	0.727	0.98	CLONAL	1	TRUE	1	0.33	2		61	386	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0032277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	105	508	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.896	0.804	0.995	0.896	0.804	0.995	CLONAL	1	TRUE	1	0.33	2		508	710	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750683	128750683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	75	467	0	ENST00000377970.2:c.220C>T	p.Pro74Ser	p.P74S	ENST00000377970	NM_002467.4	74	Ccg/Tcg	2/3	1	2	FACETS	0.922	0.81	1	0.922	0.81	1	CLONAL	1	TRUE	1	0.33	2		467	493	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0032277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	174	643	1	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.992	0.912	1	0.992	0.912	1	CLONAL	1	TRUE	1	0.33	2		644	1063	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0032277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	89	454	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.33	2		454	507	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058072	27058072	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	73	338	0	ENST00000324856.7:c.1780C>T	p.Gln594Ter	p.Q594*	ENST00000324856	NM_006015.4	594	Cag/Tag	3/20	1	2	FACETS	0.924	0.81	1	0.924	0.81	1	CLONAL	1	TRUE	1	0.33	2		338	479	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591129	67591130	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0032277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	25	204	0	ENST00000274335.5:c.1723_1724del	p.Lys575AspfsTer26	p.K575Dfs*26	ENST00000274335		574	agAAag/agag	12/15	1	2	FACETS	0.53	0.418	0.658	0.53	0.418	0.658	SUBCLONAL	1	TRUE	1	0.33	2		204	286	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717748	89717749	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0032277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	71	317	0	ENST00000371953.3:c.775dup	p.His259ProfsTer39	p.H259Pfs*39	ENST00000371953	NM_000314.4	258	ttc/ttCc	7/9	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.33	2		317	429	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136259	2136259	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs397515173	NA	P-0032277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	116	553	0	ENST00000219476.3:c.4730del	p.Gly1577AlafsTer8	p.G1577Afs*8	ENST00000219476	NM_000548.3	1576	acG/ac	37/42	1	2	FACETS	0.873	0.787	0.965	0.873	0.787	0.965	CLONAL	1	TRUE	1	0.33	2		553	805	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352697	NA	P-0032281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	20	615	0	ENST00000269305.4:c.587G>A	p.Arg196Gln	p.R196Q	ENST00000269305	NM_001126112.2	196	cGa/cAa	6/11	0.73826459481735	1	FACETS	0.074	0.056	0.095	0.074	0.056	0.095	SUBCLONAL	1	TRUE	0	0.73826459481735	1		615	463	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913255	NA	P-0032281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	640	680	0	ENST00000369535.4:c.183A>C	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caC	3/7	0.73826459481735	2	FACETS	0.976	0.951	1	0.976	0.951	1	CLONAL	2	TRUE	0	0.73826459481735	2		680	888	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	189	836	0	ENST00000269305.4:c.434T>G	p.Leu145Arg	p.L145R	ENST00000269305	NM_001126112.2	145	cTg/cGg	5/11	0.30251900038486	1	FACETS	0.975	0.9	1	0.975	0.9	1	CLONAL	1	TRUE	0	0.31	1		836	1057	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509596	29509596	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1064794273	NA	P-0032286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	93	525	0	ENST00000356175.3:c.801G>A	p.Trp267Ter	p.W267*	ENST00000356175	NM_000267.3	267	tgG/tgA	8/57	0.30251900038486	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.31	1		525	476	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884997	111884997	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	77	518	0	ENST00000341259.2:c.998del	p.Gly333AlafsTer40	p.G333Afs*40	ENST00000341259	NM_005475.2	332	aGg/ag	5/8	0.30251900038486	1	FACETS	0.649	0.57	0.734	0.649	0.57	0.734	SUBCLONAL	1	TRUE	0	0.31	1		518	647	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645120	86645120	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1210180190	NA	P-0032286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	54	294	0	ENST00000274376.6:c.1192C>T	p.Arg398Ter	p.R398*	ENST00000274376	NM_002890.2	398	Cga/Tga	8/25	0.30251900038486	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.31	1		294	228	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998283	100998283	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	31	122	0	ENST00000325455.5:c.1519G>A	p.Ala507Thr	p.A507T	ENST00000325455	NM_001202474.3	507	Gcg/Acg	1/8	1	2	FACETS	0.98	0.799	1	0.98	0.799	1	CLONAL	1	TRUE	1	0.31	2		122	204	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778591	3778591	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs370693698	NA	P-0032286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	223	655	0	ENST00000262367.5:c.6457G>T	p.Gly2153Cys	p.G2153C	ENST00000262367	NM_004380.2	2153	Ggt/Tgt	31/31	0.183014889888159	2	FACETS	0.823	0.767	0.88	0.823	0.767	0.88	INDETERMINATE	2	TRUE	0	0.31	2		655	874	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965658	93965658	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751194338	NA	P-0032286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	31	429	0	ENST00000369303.4:c.2270G>A	p.Arg757Lys	p.R757K	ENST00000369303	NM_004440.3	757	aGg/aAg	13/17	0.30251900038486	1	FACETS	0.335	0.27	0.409	0.335	0.27	0.409	SUBCLONAL	1	TRUE	0	0.31	1		429	504	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129345	152129345	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1362946000	NA	P-0032286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	65	456	0	ENST00000206249.3:c.298C>G	p.Leu100Val	p.L100V	ENST00000206249	NM_000125.3	100	Ctc/Gtc	1/8	0.30251900038486	1	FACETS	0.535	0.464	0.613	0.535	0.464	0.613	SUBCLONAL	1	TRUE	0	0.31	1		456	662	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864418	162864418	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	33	406	0	ENST00000366898.1:c.95A>T	p.Lys32Met	p.K32M	ENST00000366898	NM_004562.2	32	aAg/aTg	2/12	0.30251900038486	1	FACETS	0.304	0.247	0.369	0.304	0.247	0.369	SUBCLONAL	1	TRUE	0	0.31	1		406	592	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636815	8636815	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	90	397	0	ENST00000356435.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000356435		32	Gat/Tat	2/35	0.30251900038486	1	FACETS	0.856	0.761	0.957	0.856	0.761	0.957	CLONAL	1	TRUE	0	0.31	1		397	573	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0032292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	15	422	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.233	0.17	0.309	0.233	0.17	0.309	SUBCLONAL	1	TRUE	1	0.361758641814319	2		422	356	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0032292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	28	207	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.511	0.409	0.627	0.511	0.409	0.627	SUBCLONAL	1	TRUE	1	0.361758641814319	2		207	303	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624296	89624296	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs786201995	NA	P-0032292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	20	842	0	ENST00000371953.3:c.70G>C	p.Asp24His	p.D24H	ENST00000371953	NM_000314.4	24	Gac/Cac	1/9	0.361758641814319	1	FACETS	0.243	0.186	0.311	0.243	0.186	0.311	SUBCLONAL	1	TRUE	0	0.361758641814319	1		842	372	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141557668	141557668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	42	1324	0	ENST00000220592.5:c.1647G>A	p.Met549Ile	p.M549I	ENST00000220592	NM_012154.3	549	atG/atA	13/19	0.361758641814319	1	FACETS	0.394	0.329	0.466	0.394	0.329	0.466	SUBCLONAL	1	TRUE	0	0.361758641814319	1		1324	483	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61706065	61706065	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	24	885	1	ENST00000401558.2:c.3106G>T	p.Glu1036Ter	p.E1036*	ENST00000401558	NM_003400.3	1036	Gaa/Taa	25/25	1	2	FACETS	0.305	0.238	0.382	0.305	0.238	0.382	SUBCLONAL	1	TRUE	1	0.361758641814319	2		886	435	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61706089	61706089	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	21	770	0	ENST00000401558.2:c.3082G>T	p.Glu1028Ter	p.E1028*	ENST00000401558	NM_003400.3	1028	Gaa/Taa	25/25	1	2	FACETS	0.313	0.24	0.398	0.313	0.24	0.398	SUBCLONAL	1	TRUE	1	0.361758641814319	2		770	371	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165233	47165233	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	56	744	0	ENST00000409792.3:c.893T>C	p.Ile298Thr	p.I298T	ENST00000409792	NM_014159.6	298	aTt/aCt	3/21	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.361758641814319	2		744	273	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165702	185165702	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	32	579	0	ENST00000265026.3:c.977G>C	p.Arg326Pro	p.R326P	ENST00000265026	NM_004721.4	326	cGg/cCg	5/14	1	2	FACETS	0.675	0.55	0.815	0.675	0.55	0.815	SUBCLONAL	1	TRUE	1	0.361758641814319	2		579	262	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383891	84383891	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	43	1187	0	ENST00000321945.7:c.961G>T	p.Asp321Tyr	p.D321Y	ENST00000321945	NM_139076.2	321	Gac/Tac	9/9	1	2	FACETS	0.54	0.452	0.638	0.54	0.452	0.638	SUBCLONAL	1	TRUE	1	0.361758641814319	2		1187	440	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040958	47040977	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTCGCGCCCAGCCTGGTG	CTCTCGCGCCCAGCCTGGTG	-	novel	NA	P-0032292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	81	743	0	ENST00000377604.3:c.1490_1509del	p.Ser497CysfsTer14	p.S497Cfs*14	ENST00000377604	NM_001204468.1	496	ttCTCTCGCGCCCAGCCTGGTGct/ttct	14/24	1	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.361758641814319	1		743	311	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050864	49050864	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886042935	NA	P-0032293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	137	298	0	ENST00000267163.4:c.2548C>T	p.Gln850Ter	p.Q850*	ENST00000267163	NM_000321.2	850	Cag/Tag	25/27	0.850923865431646	2	FACETS	0.967	0.925	1	0.967	0.925	1	CLONAL	2	TRUE	0	0.863880298310097	2		298	164	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509421	106509421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751167601	NA	P-0032293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	217	591	1	ENST00000359195.3:c.1415G>A	p.Arg472His	p.R472H	ENST00000359195	NM_002649.2	472	cGt/cAt	2/11	0.863880298310097	5	FACETS	0.833	0.778	0.89	0.556	0.519	0.593	CLONAL	2	TRUE	2	0.863880298310097	5		592	692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0032293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	846	744	1	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.810766089679358	3	FACETS	0.956	0.941	0.97	0.956	0.941	0.97	CLONAL	3	TRUE	0	0.863880298310097	3		745	978	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484028	50484028	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	322	567	0	ENST00000394963.4:c.878C>T	p.Pro293Leu	p.P293L	ENST00000394963	NM_003076.4	293	cCc/cTc	8/13	0.528897341492075	5	FACETS	0.94	0.891	0.991	0.627	0.594	0.661	CLONAL	2	TRUE	2	0.863880298310097	5		567	910	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646686	23646686	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	310	607	0	ENST00000261584.4:c.1181A>G	p.His394Arg	p.H394R	ENST00000261584	NM_024675.3	394	cAt/cGt	4/13	0.367010701048576	5	FACETS	0.868	0.826	0.91	0.868	0.826	0.91	INDETERMINATE	3	TRUE	2	0.863880298310097	5		607	633	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289985	15289985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	562	817	0	ENST00000263388.2:c.3569G>C	p.Arg1190Pro	p.R1190P	ENST00000263388	NM_000435.2	1190	cGc/cCc	22/33	0.855396541151161	4	FACETS	0.917	0.882	0.952	0.917	0.882	0.952	CLONAL	2	TRUE	2	0.863880298310097	4		817	1322	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587168	189587169	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0032293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	95	451	0	ENST00000264731.3:c.1185_1186delinsAA	p.Pro396Thr	p.P396T	ENST00000264731	NM_003722.4	395	tcCCca/tcAAca	9/14	0.785920934530491	5	FACETS	0.897	0.801	0.999	0.299	0.267	0.333	CLONAL	1	TRUE	2	0.863880298310097	5		451	563	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989641	68989641	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199776134	NA	P-0032293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	135	504	1	ENST00000288368.4:c.1579C>T	p.Arg527Cys	p.R527C	ENST00000288368	NM_024870.2	527	Cgc/Tgc	15/40	0.863880298310097	3	FACETS	0.627	0.57	0.686	0.313	0.285	0.343	SUBCLONAL	1	TRUE	1	0.863880298310097	3		505	714	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389273	8389273	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	159	702	1	ENST00000356435.5:c.4345G>A	p.Ala1449Thr	p.A1449T	ENST00000356435		1449	Gcc/Acc	26/35	0.373053685364861	6	FACETS	1	0.985	1	0.219	0.201	0.238	INDETERMINATE	1	TRUE	0	0.863880298310097	6		703	764	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412345	139412345	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	220	677	0	ENST00000277541.6:c.1300G>T	p.Gly434Cys	p.G434C	ENST00000277541	NM_017617.3	434	Ggc/Tgc	8/34	0.368553243038241	2	FACETS	0.645	0.601	0.689	0.322	0.3	0.345	INDETERMINATE	1	TRUE	0	0.863880298310097	2		677	790	SUCCESS
AR	367	MSKCC	GRCh37	X	66863212	66863212	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0032293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	268	526	0	ENST00000374690.3:c.1731T>A	p.Cys577Ter	p.C577*	ENST00000374690	NM_000044.3	577	tgT/tgA	2/8	0.863880298310097	5	FACETS	1	0.951	1	0.673	0.634	0.711	CLONAL	2	TRUE	2	0.863880298310097	5		526	706	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020181	123020195	+	inframe_deletion	In_Frame_Del	DEL	CTTTCCTAATTGCTT	CTTTCCTAATTGCTT	-	novel	NA	P-0032293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	81	714	0	ENST00000355640.3:c.673_687del	p.Pro225_Phe229del	p.P225_F229del	ENST00000355640		223	caCTTTCCTAATTGCTTc/cac	2/7	0.863880298310097	5	FACETS	0.406	0.356	0.459	0.135	0.118	0.153	SUBCLONAL	1	TRUE	2	0.863880298310097	5		714	1061	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0032296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	104	756	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.229827067083044	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.229827067083044	1		756	767	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0032296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	46	648	1	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.226195786859804	2	FACETS	1	0.939	1	0.616	0.521	0.72	CLONAL	1	TRUE	0	0.229827067083044	2		649	325	SUCCESS
APC	324	MSKCC	GRCh37	5	112174835	112174835	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0032296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	31	255	0	ENST00000257430.4:c.3544A>T	p.Lys1182Ter	p.K1182*	ENST00000257430	NM_000038.5	1182	Aaa/Taa	16/16	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.229827067083044	2		255	250	SUCCESS
APC	324	MSKCC	GRCh37	5	112154963	112154963	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660802	NA	P-0032296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	99	711	1	ENST00000257430.4:c.1234C>T	p.Gln412Ter	p.Q412*	ENST00000257430	NM_000038.5	412	Cag/Tag	10/16	1	2	FACETS	0.962	0.857	1	0.962	0.857	1	CLONAL	1	TRUE	1	0.229827067083044	2		712	896	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041266	47041266	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0032296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	150	951	0	ENST00000377604.3:c.1693+1G>A		p.X565_splice	ENST00000377604	NM_001204468.1	565			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.229827067083044	2		951	1085	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573642	48573642	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0032296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	25	459	0	ENST00000342988.3:c.226A>T	p.Arg76Ter	p.R76*	ENST00000342988	NM_005359.5	76	Aga/Tga	2/12	0.229827067083044	1	FACETS	0.761	0.602	0.943	0.761	0.602	0.943	CLONAL	1	TRUE	0	0.229827067083044	1		459	253	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730132	41730132	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	68	373	0	ENST00000242208.4:c.397A>G	p.Arg133Gly	p.R133G	ENST00000242208	NM_002192.2	133	Agg/Ggg	3/3	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.229827067083044	2		373	454	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239877	98239884	+	frameshift_variant	Frame_Shift_Del	DEL	CAGTCCTG	CAGTCCTG	-	novel	NA	P-0032297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	209	555	0	ENST00000331920.6:c.1448_1455del	p.Ala483GlyfsTer11	p.A483Gfs*11	ENST00000331920	NM_000264.3	483	gCAGGACTG/g	10/24	0.943171733188393	1	FACETS	0.937	0.904	0.967	0.937	0.904	0.967	CLONAL	1	TRUE	0	0.943171733188393	1		555	250	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	54	320	1				ENST00000310581	NM_198253.2	-/1132			0.149042556298987	3	FACETS	1	0.956	1			1	INDETERMINATE	1	TRUE	NA	0.309218060304515	3		321	310	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0032337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	111	304	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.295601632523037	5	FACETS	1	0.932	1	0.694	0.626	0.764	CLONAL	2	TRUE	2	0.309218060304515	5		304	505	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0032337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	87	556	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.260421748848211	2	FACETS	1	0.954	1	0.571	0.507	0.639	CLONAL	1	TRUE	0	0.309218060304515	2		556	493	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0032337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	49	328	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	0.260421748848211	2	FACETS	0.804	0.683	0.937	0.402	0.341	0.469	CLONAL	1	TRUE	0	0.309218060304515	2		328	394	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61705957	61705957	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	novel	NA	P-0032337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	86	395	0	ENST00000401558.2:c.3214T>C	p.Ter1072GlnextTer27	p.*1072Qext*27	ENST00000401558	NM_003400.3	1072	Taa/Caa	25/25	0.309218060304515	3	FACETS	1	0.954	1	0.575	0.51	0.645	CLONAL	1	TRUE	1	0.309218060304515	3		395	558	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0032345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	126	405	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.182824112805509	3	FACETS	1	0.973	1	0.601	0.544	0.661	INDETERMINATE	1	TRUE	1	0.31	3		405	781	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241711	55241711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	128	442	0	ENST00000275493.2:c.2159C>T	p.Ser720Phe	p.S720F	ENST00000275493	NM_005228.3	720	tCc/tTc	18/28	0.182824112805509	3	FACETS	1	0.972	1	0.593	0.538	0.652	INDETERMINATE	1	TRUE	1	0.31	3		442	804	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	65	304	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.33	2		304	387	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	171	479	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.88	0.814	0.948	1	0.992	1	CLONAL	2	TRUE	1	0.33	2		483	589	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440129	99440129	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	36	302	0	ENST00000268035.6:c.1101del	p.Asn368IlefsTer17	p.N368Ifs*17	ENST00000268035	NM_000875.3	366	cGg/cg	4/21	1	2	FACETS	0.515	0.423	0.617	0.515	0.423	0.617	SUBCLONAL	1	TRUE	1	0.33	2		302	424	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103755	47103756	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	108	492	0	ENST00000409792.3:c.6190_6191del	p.Asp2064ProfsTer8	p.D2064Pfs*8	ENST00000409792	NM_014159.6	2064	GAc/c	14/21	1	2	FACETS	0.893	0.802	0.99	0.893	0.802	0.99	CLONAL	1	TRUE	1	0.33	2		492	733	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389135	31389135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1165118132	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	48	467	2	ENST00000328111.2:c.2048G>A	p.Arg683His	p.R683H	ENST00000328111	NM_006892.3	683	cGc/cAc	19/23	1	2	FACETS	0.462	0.39	0.541	0.462	0.39	0.541	SUBCLONAL	1	TRUE	1	0.33	2		469	630	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	71	279	0	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.33	2		279	381	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536164	106536164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	48	297	0	ENST00000369096.4:c.131C>T	p.Ala44Val	p.A44V	ENST00000369096	NM_001198.3	44	gCg/gTg	2/7	1	2	FACETS	0.628	0.532	0.735	0.628	0.532	0.735	SUBCLONAL	1	TRUE	1	0.33	2		297	463	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744385	41744385	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	28	454	0	ENST00000301178.4:c.1010del	p.Pro337LeufsTer29	p.P337Lfs*29	ENST00000301178	NM_021913.4	335	ggC/gg	8/20	1	2	FACETS	0.388	0.31	0.478	0.388	0.31	0.478	SUBCLONAL	1	TRUE	1	0.33	2		454	437	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526151	189526151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	75	455	0	ENST00000264731.3:c.415G>A	p.Ala139Thr	p.A139T	ENST00000264731	NM_003722.4	139	Gcg/Acg	4/14	1	2	FACETS	0.736	0.645	0.833	0.736	0.645	0.833	SUBCLONAL	1	TRUE	1	0.33	2		455	618	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968266	2968266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773909937	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	45	562	0	ENST00000396946.4:c.1720G>A	p.Val574Ile	p.V574I	ENST00000396946	NM_032415.4	574	Gtc/Atc	13/25	1	2	FACETS	0.396	0.332	0.468	0.396	0.332	0.468	SUBCLONAL	1	TRUE	1	0.33	2		562	688	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434791	99434791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	80	466	0	ENST00000268035.6:c.878C>T	p.Ser293Phe	p.S293F	ENST00000268035	NM_000875.3	293	tCc/tTc	3/21	1	2	FACETS	0.869	0.766	0.979	0.869	0.766	0.979	CLONAL	1	TRUE	1	0.33	2		466	558	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505418	25505418	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	54	451	0	ENST00000264709.3:c.340del	p.Ala114ProfsTer48	p.A114Pfs*48	ENST00000264709	NM_175629.2	114	Gcc/cc	4/23	1	2	FACETS	0.747	0.639	0.865	0.747	0.639	0.865	SUBCLONAL	1	TRUE	1	0.33	2		451	438	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161939	47161939	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	49	339	0	ENST00000409792.3:c.4187del	p.Asn1396MetfsTer16	p.N1396Mfs*16	ENST00000409792	NM_014159.6	1396	aAt/at	3/21	1	2	FACETS	0.633	0.537	0.739	0.633	0.537	0.739	SUBCLONAL	1	TRUE	1	0.33	2		339	469	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604628	55604628	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs139000082	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	97	433	0	ENST00000288135.5:c.2836C>T	p.Arg946Ter	p.R946*	ENST00000288135	NM_000222.2	946	Cga/Tga	21/21	1	2	FACETS	0.942	0.841	1	0.942	0.841	1	CLONAL	1	TRUE	1	0.33	2		433	624	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582302	119582302	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	50	356	1	ENST00000316626.5:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000316626		367	Cga/Tga	10/12	1	2	FACETS	0.458	0.388	0.536	0.458	0.388	0.536	SUBCLONAL	1	TRUE	1	0.33	2		357	661	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138915	64138915	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	77	354	0	ENST00000334205.4:c.2287del	p.Arg763AlafsTer21	p.R763Afs*21	ENST00000334205	NM_003942.2	761	gCc/gc	17/17	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.33	2		354	372	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232137	98232137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1382474804	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	87	286	0	ENST00000331920.6:c.1805G>A	p.Arg602Gln	p.R602Q	ENST00000331920	NM_000264.3	602	cGa/cAa	13/24	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.33	2		286	517	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020769	37020769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	43	392	0	ENST00000358127.4:c.76del	p.Val26PhefsTer3	p.V26Ffs*3	ENST00000358127	NM_001280556.1	26	Gtt/tt	2/10	1	2	FACETS	0.535	0.448	0.632	0.535	0.448	0.632	SUBCLONAL	1	TRUE	1	0.33	2		392	487	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987027	36987027	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	103	373	0	ENST00000354822.5:c.662G>A	p.Arg221His	p.R221H	ENST00000354822	NM_001079668.2	221	cGc/cAc	3/3	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.33	2		373	519	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933013	39933013	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	140	298	0	ENST00000378444.4:c.1586del	p.Asn529ThrfsTer60	p.N529Tfs*60	ENST00000378444	NM_001123385.1	529	aAc/ac	4/15	1	1	FACETS	0.856	0.787	0.926	1	0.99	1	CLONAL	2	TRUE	0	0.33	1		298	414	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610567	10610567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	125	632	0	ENST00000171111.5:c.143G>A	p.Gly48Asp	p.G48D	ENST00000171111	NM_203500.1	48	gGc/gAc	2/6	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.33	2		632	698	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405201	139405201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767886377	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	50	566	1	ENST00000277541.6:c.2644G>A	p.Ala882Thr	p.A882T	ENST00000277541	NM_017617.3	882	Gca/Aca	17/34	1	2	FACETS	0.483	0.409	0.565	0.483	0.409	0.565	SUBCLONAL	1	TRUE	1	0.33	2		567	627	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555686	21555686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194403560	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	54	505	0	ENST00000382592.4:c.2584C>T	p.Arg862Trp	p.R862W	ENST00000382592	NM_014572.2	862	Cgg/Tgg	6/8	1	2	FACETS	0.488	0.416	0.567	0.488	0.416	0.567	SUBCLONAL	1	TRUE	1	0.33	2		505	671	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432067	121432067	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555212014	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	162	559	0	ENST00000257555.6:c.814C>T	p.Arg272Cys	p.R272C	ENST00000257555		272	Cgc/Tgc	4/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.33	2		559	718	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857680	9857680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303700994	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	89	381	0	ENST00000330684.3:c.3721C>T	p.Arg1241Trp	p.R1241W	ENST00000330684	NM_001134407.1	1241	Cgg/Tgg	13/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.33	2		381	470	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952006	178952006	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	35	338	0	ENST00000263967.3:c.3061T>A	p.Tyr1021Asn	p.Y1021N	ENST00000263967	NM_006218.2	1021	Tac/Aac	21/21	1	2	FACETS	0.436	0.357	0.526	0.436	0.357	0.526	SUBCLONAL	1	TRUE	1	0.33	2		338	486	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29083913	29083913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544216926	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	14	142	0	ENST00000328354.6:c.1604G>A	p.Arg535His	p.R535H	ENST00000328354	NM_007194.3	535	cGc/cAc	15/15	1	2	FACETS	0.505	0.366	0.672	0.505	0.366	0.672	SUBCLONAL	1	TRUE	1	0.33	2		142	168	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434074	49434074	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	38	452	1	ENST00000301067.7:c.7479del	p.Phe2494SerfsTer49	p.F2494Sfs*49	ENST00000301067	NM_003482.3	2493	ggG/gg	31/54	1	2	FACETS	0.444	0.366	0.53	0.444	0.366	0.53	SUBCLONAL	1	TRUE	1	0.33	2		453	519	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793054	33793056	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs747773004	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	61	199	0	ENST00000498907.2:c.265_267del	p.Glu89del	p.E89del	ENST00000498907	NM_004364.3	89	GAG/-	1/1	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.33	2		199	275	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	71	455	2	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.33	2		457	418	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664900	138664900	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	12	144	0	ENST00000330315.3:c.665C>T	p.Ala222Val	p.A222V	ENST00000330315	NM_023067.3	222	gCa/gTa	1/1	1	2	FACETS	0.373	0.262	0.509	0.373	0.262	0.509	SUBCLONAL	1	TRUE	1	0.33	2		144	195	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309069	137309069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756234164	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	69	633	1	ENST00000481739.1:c.676G>A	p.Ala226Thr	p.A226T	ENST00000481739	NM_002957.4	226	Gcc/Acc	5/10	1	2	FACETS	0.55	0.478	0.628	0.55	0.478	0.628	SUBCLONAL	1	TRUE	1	0.33	2		634	760	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426973	49426973	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1565778024	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	135	413	1	ENST00000301067.7:c.11515del	p.Gln3839SerfsTer42	p.Q3839Sfs*42	ENST00000301067	NM_003482.3	3839	Cag/ag	39/54	1	2	FACETS	0.775	0.708	0.844	1	0.988	1	SUBCLONAL	2	TRUE	1	0.33	2		414	528	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662637	227662637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755496379	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	86	493	2	ENST00000305123.5:c.818C>T	p.Ser273Leu	p.S273L	ENST00000305123	NM_005544.2	273	tCg/tTg	1/2	1	2	FACETS	0.958	0.85	1	0.958	0.85	1	CLONAL	1	TRUE	1	0.33	2		495	544	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430482	181430482	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	40	408	1	ENST00000325404.1:c.337del	p.Arg113GlyfsTer8	p.R113Gfs*8	ENST00000325404	NM_003106.3	112	Ccc/cc	1/1	1	2	FACETS	0.404	0.335	0.481	0.404	0.335	0.481	SUBCLONAL	1	TRUE	1	0.33	2		409	600	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157191	106157191	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	67	365	0	ENST00000380013.4:c.2092G>T	p.Val698Leu	p.V698L	ENST00000380013	NM_001127208.2	698	Gtg/Ttg	3/11	1	2	FACETS	0.908	0.792	1	0.908	0.792	1	CLONAL	1	TRUE	1	0.33	2		365	447	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015053	27015053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151098324	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	58	331	1	ENST00000335756.4:c.155G>A	p.Arg52Gln	p.R52Q	ENST00000335756	NM_001809.3	52	cGa/cAa	2/5	1	2	FACETS	0.725	0.624	0.835	0.725	0.624	0.835	SUBCLONAL	1	TRUE	1	0.33	2		332	485	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437222	220437223	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1286117855	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	58	623	0	ENST00000243786.2:c.132dup	p.Ala45ArgfsTer29	p.A45Rfs*29	ENST00000243786	NM_002191.3	42	-/C	1/2	1	2	FACETS	0.507	0.435	0.586	0.507	0.435	0.586	SUBCLONAL	1	TRUE	1	0.33	2		623	693	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100072	27100072	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	44	510	0	ENST00000324856.7:c.3868A>G	p.Thr1290Ala	p.T1290A	ENST00000324856	NM_006015.4	1290	Acg/Gcg	16/20	1	2	FACETS	0.45	0.376	0.531	0.45	0.376	0.531	SUBCLONAL	1	TRUE	1	0.33	2		510	593	SUCCESS
FH	2271	MSKCC	GRCh37	1	241661204	241661204	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	41	513	0	ENST00000366560.3:c.1457C>T	p.Ala486Val	p.A486V	ENST00000366560	NM_000143.3	486	gCt/gTt	10/10	1	2	FACETS	0.348	0.288	0.414	0.348	0.288	0.414	SUBCLONAL	1	TRUE	1	0.33	2		513	715	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620336	43620336	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs368550200	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	26	321	0	ENST00000355710.3:c.2945G>T	p.Arg982Leu	p.R982L	ENST00000355710	NM_020975.4	982	cGc/cTc	18/20	1	2	FACETS	0.403	0.319	0.5	0.403	0.319	0.5	SUBCLONAL	1	TRUE	1	0.33	2		321	391	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63700116	63700117	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	24	182	0	ENST00000279873.7:c.451_452insA	p.Leu151HisfsTer47	p.L151Hfs*47	ENST00000279873	NM_032199.2	151	cta/cAta	3/10	1	2	FACETS	0.509	0.399	0.634	0.509	0.399	0.634	SUBCLONAL	1	TRUE	1	0.33	2		182	286	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419129	419129	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	58	230	0	ENST00000399788.2:c.3218T>C	p.Val1073Ala	p.V1073A	ENST00000399788	NM_001042603.1	1073	gTg/gCg	22/28	0.3	2	FACETS	0.999	0.862	1			1	CLONAL	1	TRUE	NA	0.33	2		230	352	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230592	46230592	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs762692646	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	48	423	0	ENST00000334344.6:c.841A>G	p.Ile281Val	p.I281V	ENST00000334344	NM_152641.2	281	Att/Gtt	8/21	1	2	FACETS	0.481	0.406	0.564	0.481	0.406	0.564	SUBCLONAL	1	TRUE	1	0.33	2		423	605	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562215	21562215	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	148	708	2	ENST00000382592.4:c.1704G>T	p.Lys568Asn	p.K568N	ENST00000382592	NM_014572.2	568	aaG/aaT	4/8	1	2	FACETS	0.967	0.882	1	0.967	0.882	1	CLONAL	1	TRUE	1	0.33	2		710	928	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923282	26923282	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	30	326	0	ENST00000381527.3:c.278T>G	p.Val93Gly	p.V93G	ENST00000381527	NM_001260.1	93	gTg/gGg	3/13	1	2	FACETS	0.361	0.29	0.442	0.361	0.29	0.442	SUBCLONAL	1	TRUE	1	0.33	2		326	503	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347433	91347433	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	67	302	0	ENST00000355112.3:c.3600del	p.Lys1200AsnfsTer5	p.K1200Nfs*5	ENST00000355112	NM_000057.2	1199	Aaa/aa	19/22	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.33	2		302	400	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346712	89346712	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778852816	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	41	355	1	ENST00000301030.4:c.6238G>T	p.Ala2080Ser	p.A2080S	ENST00000301030	NM_001256183.1	2080	Gcc/Tcc	9/13	1	2	FACETS	0.627	0.523	0.743	0.627	0.523	0.743	SUBCLONAL	1	TRUE	1	0.33	2		356	396	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38504610	38504610	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	42	544	2	ENST00000254066.5:c.221G>T	p.Ser74Ile	p.S74I	ENST00000254066	NM_000964.3	74	aGc/aTc	3/9	1	2	FACETS	0.383	0.319	0.455	0.383	0.319	0.455	SUBCLONAL	1	TRUE	1	0.33	2		546	664	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796099	78796099	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	54	299	0	ENST00000306801.3:c.991+1del		p.R330fs	ENST00000306801	NM_020761.2	330	cGg/cg	8/34	1	2	FACETS	0.82	0.703	0.948	0.82	0.703	0.948	CLONAL	1	TRUE	1	0.33	2		299	399	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599916	10599916	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs946921406	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	88	538	0	ENST00000171111.5:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000171111	NM_203500.1	554	Cga/Tga	5/6	1	2	FACETS	0.787	0.697	0.882	0.787	0.697	0.882	SUBCLONAL	1	TRUE	1	0.33	2		538	678	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353843	15353843	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1325249458	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	62	402	0	ENST00000263377.2:c.3037C>T	p.Pro1013Ser	p.P1013S	ENST00000263377	NM_058243.2	1013	Cca/Tca	14/20	1	2	FACETS	0.963	0.836	1	0.963	0.836	1	CLONAL	1	TRUE	1	0.33	2		402	390	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961573	18961573	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	41	444	0	ENST00000262803.5:c.706C>T	p.Arg236Cys	p.R236C	ENST00000262803	NM_002911.3	236	Cgc/Tgc	5/24	1	2	FACETS	0.44	0.366	0.522	0.44	0.366	0.522	SUBCLONAL	1	TRUE	1	0.33	2		444	565	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223827	36223827	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	132	640	0	ENST00000222270.7:c.6377A>G	p.Asp2126Gly	p.D2126G	ENST00000222270	NM_014727.1	2126	gAt/gGt	28/37	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.33	2		640	706	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224183	36224183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771130237	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	48	526	0	ENST00000222270.7:c.6733G>A	p.Val2245Met	p.V2245M	ENST00000222270	NM_014727.1	2245	Gtg/Atg	28/37	1	2	FACETS	0.527	0.445	0.617	0.527	0.445	0.617	SUBCLONAL	1	TRUE	1	0.33	2		526	552	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867026	45867026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751177434	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	33	411	0	ENST00000391945.4:c.1093G>A	p.Val365Met	p.V365M	ENST00000391945	NM_000400.3	365	Gtg/Atg	11/23	1	2	FACETS	0.451	0.367	0.546	0.451	0.367	0.546	SUBCLONAL	1	TRUE	1	0.33	2		411	443	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085884	16085884	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	78	360	1	ENST00000281043.3:c.1060G>T	p.Ala354Ser	p.A354S	ENST00000281043	NM_005378.4	354	Gcg/Tcg	3/3	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.33	2		361	429	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46602969	46602969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs574490008	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	35	526	1	ENST00000263734.3:c.1027G>A	p.Val343Ile	p.V343I	ENST00000263734	NM_001430.4	343	Gtc/Atc	8/16	1	2	FACETS	0.341	0.279	0.411	0.341	0.279	0.411	SUBCLONAL	1	TRUE	1	0.33	2		527	622	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182159	99182159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	107	421	0	ENST00000074304.5:c.2224G>A	p.Val742Met	p.V742M	ENST00000074304	NM_001134224.1	742	Gtg/Atg	21/26	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.33	2		421	611	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728874	39728874	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	37	211	0	ENST00000361337.2:c.1154A>T	p.Asn385Ile	p.N385I	ENST00000361337	NM_003286.2	385	aAc/aTc	12/21	1	2	FACETS	0.723	0.598	0.862	0.723	0.598	0.862	SUBCLONAL	1	TRUE	1	0.33	2		211	310	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090468	37090468	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	25	292	0	ENST00000231790.2:c.2063A>C	p.Lys688Thr	p.K688T	ENST00000231790	NM_000249.3	688	aAg/aCg	18/19	1	2	FACETS	0.306	0.24	0.382	0.306	0.24	0.382	SUBCLONAL	1	TRUE	1	0.33	2		292	495	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933163	49933163	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200766923	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	32	375	1	ENST00000296474.3:c.2947C>T	p.Arg983Trp	p.R983W	ENST00000296474	NM_002447.2	983	Cgg/Tgg	12/20	1	2	FACETS	0.495	0.402	0.6	0.495	0.402	0.6	SUBCLONAL	1	TRUE	1	0.33	2		376	392	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480435	89480435	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	86	352	0	ENST00000336596.2:c.2272T>G	p.Leu758Val	p.L758V	ENST00000336596	NM_005233.5	758	Ttg/Gtg	13/17	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.33	2		352	514	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825367	134825367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	96	312	0	ENST00000398015.3:c.883G>A	p.Ala295Thr	p.A295T	ENST00000398015	NM_004441.4	295	Gca/Aca	4/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.33	2		312	512	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683447	182683447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	80	357	0	ENST00000292782.4:c.98del	p.Asn33MetfsTer5	p.N33Mfs*5	ENST00000292782	NM_020640.2	33	aAt/at	2/7	1	2	FACETS	0.931	0.821	1	0.931	0.821	1	CLONAL	1	TRUE	1	0.33	2		357	521	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961772	55961772	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762955301	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	32	411	0	ENST00000263923.4:c.2789G>A	p.Ser930Asn	p.S930N	ENST00000263923	NM_002253.2	930	aGc/aAc	20/30	1	2	FACETS	0.384	0.311	0.467	0.384	0.311	0.467	SUBCLONAL	1	TRUE	1	0.33	2		411	505	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526249	31526249	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs541810066	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	74	640	0	ENST00000344624.3:c.791G>A	p.Arg264Gln	p.R264Q	ENST00000344624		264	cGg/cAg	2/33	1	2	FACETS	0.513	0.448	0.583	0.513	0.448	0.583	SUBCLONAL	1	TRUE	1	0.33	2		640	874	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970940	79970940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	31	383	0	ENST00000265081.6:c.1166G>A	p.Gly389Asp	p.G389D	ENST00000265081	NM_002439.4	389	gGc/gAc	7/24	1	2	FACETS	0.315	0.254	0.385	0.315	0.254	0.385	SUBCLONAL	1	TRUE	1	0.33	2		383	596	SUCCESS
APC	324	MSKCC	GRCh37	5	112174659	112174659	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	52	289	0	ENST00000257430.4:c.3371del	p.Asn1124MetfsTer2	p.N1124Mfs*2	ENST00000257430	NM_000038.5	1123	cAa/ca	16/16	1	2	FACETS	0.821	0.701	0.951	0.821	0.701	0.951	CLONAL	1	TRUE	1	0.33	2		289	384	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031981	26031982	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTA	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	51	353	0	ENST00000244661.2:c.305_307dup	p.Val102dup	p.V102dup	ENST00000244661	NM_003537.3	102	ggg/gTAGgg	1/1	1	2	FACETS	0.779	0.664	0.904	0.779	0.664	0.904	CLONAL	1	TRUE	1	0.33	2		353	397	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858200	27858200	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	86	424	0	ENST00000359303.2:c.371A>G	p.Asp124Gly	p.D124G	ENST00000359303	NM_003535.2	124	gAc/gGc	1/1	1	2	FACETS	0.939	0.833	1	0.939	0.833	1	CLONAL	1	TRUE	1	0.33	2		424	555	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680383	30680383	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	64	470	0	ENST00000376406.3:c.1336C>T	p.Gln446Ter	p.Q446*	ENST00000376406	NM_014641.2	446	Caa/Taa	5/15	1	2	FACETS	0.565	0.488	0.648	0.565	0.488	0.648	SUBCLONAL	1	TRUE	1	0.33	2		470	687	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201853	152201853	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	42	304	0	ENST00000206249.3:c.707G>A	p.Ser236Asn	p.S236N	ENST00000206249	NM_000125.3	236	aGc/aAc	3/8	1	2	FACETS	0.543	0.453	0.642	0.543	0.453	0.642	SUBCLONAL	1	TRUE	1	0.33	2		304	469	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194657	29194657	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	112	584	0	ENST00000240100.2:c.1071del	p.Ala358ProfsTer65	p.A358Pfs*65	ENST00000240100	NM_001394.6	357	ccC/cc	4/4	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.33	2		584	643	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231299	98231299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1332668908	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	81	608	0	ENST00000331920.6:c.1984G>A	p.Val662Ile	p.V662I	ENST00000331920	NM_000264.3	662	Gtc/Atc	14/24	1	2	FACETS	0.567	0.498	0.641	0.567	0.498	0.641	SUBCLONAL	1	TRUE	1	0.33	2		608	866	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240773	53240773	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	50	292	0	ENST00000375401.3:c.1307T>C	p.Val436Ala	p.V436A	ENST00000375401	NM_004187.3	436	gTg/gCg	10/26	1	1	FACETS	0.677	0.576	0.786	0.677	0.576	0.786	SUBCLONAL	1	TRUE	0	0.33	1		292	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0032349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	120	532	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.309142568712888	1	FACETS	0.962	0.87	1	0.962	0.87	1	CLONAL	1	TRUE	0	0.309142568712888	1		533	682	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0032349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	116	346	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.235055292072615	4	FACETS	1	0.907	1	0.667	0.604	0.733	CLONAL	2	TRUE	1	0.309142568712888	4		346	491	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97873861	97873861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	61	486	0	ENST00000289081.3:c.1213G>A	p.Glu405Lys	p.E405K	ENST00000289081	NM_000136.2	405	Gag/Aag	13/15	1	2	FACETS	0.629	0.543	0.724	0.629	0.543	0.724	SUBCLONAL	1	TRUE	1	0.309142568712888	2		486	627	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480590	50480590	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	27	351	0	ENST00000394963.4:c.460G>C	p.Glu154Gln	p.E154Q	ENST00000394963	NM_003076.4	154	Gaa/Caa	4/13	0.309142568712888	1	FACETS	0.306	0.243	0.379	0.306	0.243	0.379	SUBCLONAL	1	TRUE	0	0.309142568712888	1		351	482	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0032359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	385	583	1	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.688915493802641	2		584	1092	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	33	320	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.754	0.617	0.908	0.754	0.617	0.908	CLONAL	1	TRUE	1	0.317045472913863	2		321	276	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843365	128843365	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748690872	NA	P-0032362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	100	550	0	ENST00000249373.3:c.472G>A	p.Glu158Lys	p.E158K	ENST00000249373	NM_005631.4	158	Gag/Aag	2/12	0.289456416065566	4	FACETS	0.999	0.891	1	0.499	0.445	0.557	CLONAL	1	TRUE	2	0.317045472913863	4		550	832	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527570	29527571	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1555610905	NA	P-0032362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	66	498	0	ENST00000356175.3:c.1020dup	p.Val341CysfsTer12	p.V341Cfs*12	ENST00000356175	NM_000267.3	340	tct/tcTt	9/57	1	2	FACETS	0.625	0.542	0.715	0.625	0.542	0.715	SUBCLONAL	1	TRUE	1	0.317045472913863	2		498	666	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225685	26225685	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs748039771	NA	P-0032362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	97	445	0	ENST00000360408.1:c.303G>C	p.Leu101Phe	p.L101F	ENST00000360408	NM_003532.2	101	ttG/ttC	1/1	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.317045472913863	2		445	557	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0032902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	103	310	0	ENST00000311936.3:c.34_35delinsTT	p.Gly12Phe	p.G12F	ENST00000311936	NM_004985.3	12	GGt/TTt	2/5	1	2	FACETS	0.835	0.747	0.927	0.835	0.747	0.927	CLONAL	1	TRUE	1	0.357734630214464	2		310	690	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088723	27088723	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	77	446	0	ENST00000324856.7:c.2332G>T	p.Gly778Ter	p.G778*	ENST00000324856	NM_006015.4	778	Gga/Tga	7/20	1	2	FACETS	0.533	0.467	0.604	0.533	0.467	0.604	SUBCLONAL	1	TRUE	1	0.357734630214464	2		446	808	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121619	108121619	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	66	402	0	ENST00000278616.4:c.1430del	p.Lys477SerfsTer5	p.K477Sfs*5	ENST00000278616	NM_000051.3	476	cAa/ca	10/63	1	2	FACETS	0.621	0.539	0.71	0.621	0.539	0.71	SUBCLONAL	1	TRUE	1	0.357734630214464	2		402	594	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456268	32456268	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs775333473	NA	P-0032902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	74	500	0	ENST00000332351.3:c.624C>A	p.Ser208Arg	p.S208R	ENST00000332351	NM_024426.4	208	agC/agA	1/10	1	2	FACETS	0.539	0.471	0.612	0.539	0.471	0.612	SUBCLONAL	1	TRUE	1	0.357734630214464	2		500	768	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427425	427425	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	49	494	0	ENST00000399788.2:c.2744A>T	p.Gln915Leu	p.Q915L	ENST00000399788	NM_001042603.1	915	cAa/cTa	19/28	1	2	FACETS	0.352	0.297	0.413	0.352	0.297	0.413	SUBCLONAL	1	TRUE	1	0.357734630214464	2		494	778	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170477	11170477	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	88	452	0	ENST00000358026.2:c.4780C>T	p.Gln1594Ter	p.Q1594*	ENST00000358026	NM_001128849.1	1594	Cag/Tag	34/36	1	2	FACETS	0.706	0.625	0.792	0.706	0.625	0.792	SUBCLONAL	1	TRUE	1	0.357734630214464	2		452	697	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509086	106509086	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs556212355	NA	P-0032902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	61	368	1	ENST00000359195.3:c.1080G>T	p.Lys360Asn	p.K360N	ENST00000359195	NM_002649.2	360	aaG/aaT	2/11	0.113028221631747	4	FACETS	0.707	0.609	0.813	0.353	0.304	0.407	INDETERMINATE	1	TRUE	2	0.357734630214464	4		369	655	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981484	70981484	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	45	612	0	ENST00000276594.2:c.612C>A	p.Phe204Leu	p.F204L	ENST00000276594	NM_024504.3	204	ttC/ttA	2/8	1	2	FACETS	0.305	0.255	0.36	0.305	0.255	0.36	SUBCLONAL	1	TRUE	1	0.357734630214464	2		612	826	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0033326-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	224	557	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.557540056470947	2	FACETS	0.854	0.808	0.901	0.854	0.808	0.901	CLONAL	2	TRUE	0	0.621423739838343	2		557	422	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919556	78919556	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368881284	NA	P-0033326-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	76	386	0	ENST00000306801.3:c.3115G>A	p.Ala1039Thr	p.A1039T	ENST00000306801	NM_020761.2	1039	Gcc/Acc	26/34	0.368485295038562	5	FACETS	0.856	0.752	0.968	0.285	0.25	0.323	INDETERMINATE	1	TRUE	2	0.621423739838343	5		386	552	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103378	119103378	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033326-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	25	419	0	ENST00000264033.4:c.416G>T	p.Arg139Ile	p.R139I	ENST00000264033	NM_005188.3	139	aGa/aTa	2/16	0.621423739838343	3	FACETS	0.781	0.624	0.956	0.391	0.312	0.479	CLONAL	1	TRUE	1	0.621423739838343	3		419	135	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265144	5265144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769916725	NA	P-0033326-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	152	663	0	ENST00000357368.4:c.443G>A	p.Arg148Gln	p.R148Q	ENST00000357368	NM_002850.3	148	cGg/cAg	5/38	1	2	FACETS	0.914	0.841	0.99	0.914	0.841	0.99	CLONAL	1	TRUE	1	0.621423739838343	2		663	535	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718761	190718761	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033326-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	33	397	0	ENST00000441310.2:c.919G>C	p.Asp307His	p.D307H	ENST00000441310	NM_000534.4	307	Gat/Cat	8/13	0.621423739838343	3	FACETS	0.941	0.778	1	0.314	0.259	0.373	CLONAL	1	TRUE	0	0.621423739838343	3		397	148	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974725	21974742	+	inframe_deletion	In_Frame_Del	DEL	CGCCTCCAGCAGCGCCCG	CGCCTCCAGCAGCGCCCG	-	novel	NA	P-0033326-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	86	280	0	ENST00000304494.5:c.85_102del	p.Arg29_Ala34del	p.R29_A34del	ENST00000304494	NM_000077.4	29	CGGGCGCTGCTGGAGGCG/-	1/3	0.565309846591234	2	FACETS	1	0.979	1	0.675	0.61	0.741	CLONAL	1	TRUE	0	0.621423739838343	2		280	205	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89355066	89355066	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033326-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	120	519	0	ENST00000301030.4:c.614T>A	p.Leu205Gln	p.L205Q	ENST00000301030	NM_001256183.1	205	cTg/cAg	7/13	0.601029043511294	5	FACETS	1	0.971	1	0.396	0.358	0.436	CLONAL	1	TRUE	2	0.621423739838343	5		519	628	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0033335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	291	431	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.527985513549485	4	FACETS	0.948	0.911	0.984	0.948	0.911	0.984	CLONAL	4	TRUE	0	0.578012399936532	4		432	419	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905405	11905405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	203	455	0	ENST00000396373.4:c.55C>T	p.Pro19Ser	p.P19S	ENST00000396373	NM_001987.4	19	Cct/Tct	2/8	0.578012399936532	11	FACETS	1	0.938	1	0.575	0.536	0.615	CLONAL	4	TRUE	4	0.578012399936532	11		455	628	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0033569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	641	646	7	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.537853717154242	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.54697460670238	2		653	1151	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534717	18534717	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	214	412	0	ENST00000266497.5:c.1775C>G	p.Ser592Cys	p.S592C	ENST00000266497		592	tCt/tGt	12/31	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.54697460670238	2		412	778	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001245	150001245	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	160	558	0	ENST00000253339.5:c.2359G>C	p.Gly787Arg	p.G787R	ENST00000253339		787	Ggg/Cgg	4/7	1	2	FACETS	0.89	0.819	0.964	0.89	0.819	0.964	CLONAL	1	TRUE	1	0.54697460670238	2		558	657	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050644	30050644	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0033569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	367	324	1	ENST00000338641.4:c.448-2A>G		p.X150_splice	ENST00000338641	NM_000268.3	150			0.511765481156251	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.54697460670238	2		325	634	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70412311	70412311	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	111	261	0	ENST00000373644.4:c.4421A>T	p.Lys1474Ile	p.K1474I	ENST00000373644	NM_030625.2	1474	aAa/aTa	6/12	0.4124793908986	1	FACETS	0.764	0.693	0.838	0.764	0.693	0.838	SUBCLONAL	1	TRUE	0	0.54697460670238	1		261	386	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625392	69625392	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1554980371	NA	P-0033569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	332	720	0	ENST00000334134.2:c.401A>G	p.Tyr134Cys	p.Y134C	ENST00000334134	NM_005247.2	134	tAc/tGc	3/3	0.374267861638518	1	FACETS	0.977	0.926	1	0.977	0.926	1	CLONAL	1	TRUE	0	0.54697460670238	1		720	903	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038864	12038864	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	52	211	0	ENST00000396373.4:c.1157G>A	p.Arg386Lys	p.R386K	ENST00000396373	NM_001987.4	386	aGa/aAa	7/8	0.374267861638518	1	FACETS	0.371	0.317	0.43	0.371	0.317	0.43	SUBCLONAL	1	TRUE	0	0.54697460670238	1		211	372	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108783	2108783	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	393	770	0	ENST00000219476.3:c.884C>A	p.Ala295Asp	p.A295D	ENST00000219476	NM_000548.3	295	gCc/gAc	10/42	0.54697460670238	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.54697460670238	1		770	925	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638659	176638659	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	314	612	0	ENST00000439151.2:c.3261del	p.Glu1088ArgfsTer6	p.E1088Rfs*6	ENST00000439151	NM_022455.4	1087	Aaa/aa	5/23	0.54697460670238	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.54697460670238	1		612	818	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864634	56864634	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	93	536	0	ENST00000519728.1:c.597C>G	p.Ile199Met	p.I199M	ENST00000519728	NM_002350.3	199	atC/atG	7/13	1	2	FACETS	0.366	0.324	0.41	0.366	0.324	0.41	SUBCLONAL	1	TRUE	1	0.54697460670238	2		536	930	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117874144	117874144	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	113	413	0	ENST00000297338.2:c.310G>C	p.Ala104Pro	p.A104P	ENST00000297338	NM_006265.2	104	Gct/Cct	4/14	1	2	FACETS	0.877	0.794	0.964	0.877	0.794	0.964	CLONAL	1	TRUE	1	0.54697460670238	2		413	471	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572649	141572649	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	296	464	1	ENST00000220592.5:c.421C>T	p.Gln141Ter	p.Q141*	ENST00000220592	NM_012154.3	141	Cag/Tag	4/19	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.54697460670238	2		465	959	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175769	176175774	+	inframe_deletion	In_Frame_Del	DEL	GGAGAG	GGAGAG	-	novel	NA	P-0033979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	30	388	0	ENST00000367669.3:c.341_346del	p.Pro114_Leu115del	p.P114_L115del	ENST00000367669	NM_022457.5	114	cCTCTCCtc/ctc	1/20	1	2	FACETS	1	0.838	1	1	0.838	1	CLONAL	1	TRUE	1	0.1	2		388	572	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0034062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	959	575	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.333978155543356	11	FACETS	1	0.99	1	1	0.99	1	CLONAL	9	TRUE	2	0.333978155543356	11		575	1554	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0034062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	220	776	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.333978155543356	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.333978155543356	2		777	649	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0034062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	210	779	2	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.333978155543356	2		781	956	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552152	29552152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199474738	NA	P-0034062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	26	260	0	ENST00000356175.3:c.1885G>A	p.Gly629Arg	p.G629R	ENST00000356175	NM_000267.3	629	Ggg/Agg	17/57	0.333978155543356	2	FACETS	0.895	0.728	1	0.895	0.728	1	CLONAL	2	TRUE	0	0.333978155543356	2		260	87	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589591	67589592	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATA	novel	NA	P-0034062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	28	212	0	ENST00000274335.5:c.1356_1358dup	p.Asn453dup	p.N453dup	ENST00000274335		453	tat/tATAat	10/15	0.333978155543356	5	FACETS	0.865	0.709	1	0.865	0.709	1	CLONAL	3	TRUE	2	0.333978155543356	5		212	97	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0034125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	84	422	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.828	0.733	0.929	0.828	0.733	0.929	CLONAL	1	TRUE	1	0.385966988201478	2		422	526	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221243	1221243	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1057520606	NA	P-0034125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	102	415	1	ENST00000326873.7:c.766G>T	p.Glu256Ter	p.E256*	ENST00000326873	NM_000455.4	256	Gaa/Taa	6/10	0.385966988201478	1	FACETS	0.925	0.832	1	0.925	0.832	1	CLONAL	1	TRUE	0	0.385966988201478	1		416	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0034130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	35	885	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	1	0.827	1	1	0.827	1	CLONAL	1	TRUE	1	0.15	2		885	462	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662224	227662224	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	31	575	1	ENST00000305123.5:c.1231C>T	p.Arg411Ter	p.R411*	ENST00000305123	NM_005544.2	411	Cga/Tga	1/2	1	2	FACETS	0.715	0.577	0.872	0.715	0.577	0.872	SUBCLONAL	1	TRUE	1	0.15	2		576	578	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519920	NA	P-0034130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	17	288	0	ENST00000397062.3:c.85G>A	p.Asp29Asn	p.D29N	ENST00000397062	NM_006164.4	29	Gat/Aat	2/5	1	2	FACETS	0.724	0.54	0.943	0.724	0.54	0.943	CLONAL	1	TRUE	1	0.15	2		288	313	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719187	190719187	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	17	333	0	ENST00000441310.2:c.1189G>A	p.Asp397Asn	p.D397N	ENST00000441310	NM_000534.4	397	Gat/Aat	9/13	1	2	FACETS	0.793	0.591	1	0.793	0.591	1	CLONAL	1	TRUE	1	0.15	2		333	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0034259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	675	688	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	1	2	FACETS	0.93	0.911	0.948	1	0.998	1	CLONAL	2	FALSE	1	0.872590693089791	2		688	832	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954189	48954189	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	104	210	0	ENST00000267163.4:c.1390G>T	p.Glu464Ter	p.E464*	ENST00000267163	NM_000321.2	464	Gaa/Taa	15/27	0.872590693089791	2	FACETS	1	0.981	1	0.624	0.575	0.673	CLONAL	1	FALSE	0	0.872590693089791	2		210	191	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226579978	226579978	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	211	428	0	ENST00000366794.5:c.324G>C	p.Lys108Asn	p.K108N	ENST00000366794	NM_001618.3	108	aaG/aaC	3/23	1	2	FACETS	0.666	0.621	0.713	0.666	0.621	0.713	SUBCLONAL	1	FALSE	1	0.872590693089791	2		428	726	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102198850	102198850	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	150	295	0	ENST00000263464.3:c.1021C>G	p.Leu341Val	p.L341V	ENST00000263464	NM_001165.4	341	Cta/Gta	4/9	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.872590693089791	2		295	326	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858551	9858551	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	78	469	0	ENST00000330684.3:c.2850G>T	p.Gln950His	p.Q950H	ENST00000330684	NM_001134407.1	950	caG/caT	13/13	NA	2	FACETS	0.295	0.259	0.334			1	INDETERMINATE	1	FALSE	NA	0.872590693089791	2		469	606	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214893	36214893	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	445	516	1	ENST00000222270.7:c.3319A>T	p.Thr1107Ser	p.T1107S	ENST00000222270	NM_014727.1	1107	Acc/Tcc	8/37	0.872590693089791	3	FACETS	1	0.974	1	0.515	0.491	0.54	CLONAL	1	FALSE	1	0.872590693089791	3		517	1422	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037197	71037197	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	320	299	0	ENST00000318789.4:c.1094T>C	p.Met365Thr	p.M365T	ENST00000318789	NM_032682.5	365	aTg/aCg	14/21	0.872590693089791	1	FACETS	0.929	0.896	0.961	0.929	0.896	0.961	CLONAL	1	FALSE	0	0.872590693089791	1		299	445	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341693	8341693	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	276	425	0	ENST00000356435.5:c.4947G>C	p.Lys1649Asn	p.K1649N	ENST00000356435		1649	aaG/aaC	29/35	0.300132219625388	4	FACETS	0.904	0.855	0.954	0.452	0.427	0.477	INDETERMINATE	2	FALSE	0	0.872590693089791	4		425	655	SUCCESS
AR	367	MSKCC	GRCh37	X	66937342	66937342	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	659	439	0	ENST00000374690.3:c.2196C>A	p.Asp732Glu	p.D732E	ENST00000374690	NM_000044.3	732	gaC/gaA	5/8	0.563404211971539	4	FACETS	1	0.997	1			1	CLONAL	2	FALSE	NA	0.872590693089791	4		439	1145	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0034323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	65	207	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.351734784262814	3	FACETS	0.997	0.877	1	0.997	0.877	1	CLONAL	2	FALSE	1	0.351734784262814	3		207	218	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	11	374	0	ENST00000263967.3:c.3129G>C	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atC	21/21	0.351734784262814	3	FACETS	0.657	0.457	0.9	0.328	0.228	0.45	SUBCLONAL	1	FALSE	1	0.351734784262814	3		374	112	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207510	29207510	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	53	468	2	ENST00000240100.2:c.286C>T	p.Arg96Cys	p.R96C	ENST00000240100	NM_001394.6	96	Cgc/Tgc	1/4	0.351734784262814	3	FACETS	1	0.939	1	0.394	0.338	0.454	CLONAL	1	FALSE	0	0.351734784262814	3		470	300	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0034516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	982	442	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.773471245863706	9	FACETS	1	0.989	1	1	0.989	1	CLONAL	8	TRUE	1	0.773471245863706	9		442	1169	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521483	46521483	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs968243629	NA	P-0034516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	231	568	1	ENST00000262741.5:c.925C>T	p.Arg309Ter	p.R309*	ENST00000262741	NM_003629.3	309	Cga/Tga	7/10	0.773471245863706	3	FACETS	0.94	0.878	1	0.47	0.439	0.502	CLONAL	1	TRUE	1	0.773471245863706	3		569	881	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578519	7578520	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0034516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	1053	913	0	ENST00000269305.4:c.410_411del	p.Leu137ArgfsTer11	p.L137Rfs*11	ENST00000269305	NM_001126112.2	137	cTG/c	5/11	0.773471245863706	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.773471245863706	3		913	1230	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097197	11097197	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760294422	NA	P-0034516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	191	618	1	ENST00000358026.2:c.688C>T	p.Pro230Ser	p.P230S	ENST00000358026	NM_001128849.1	230	Ccc/Tcc	4/36	0.773471245863706	2	FACETS	0.935	0.872	1	0.468	0.436	0.5	CLONAL	1	TRUE	0	0.773471245863706	2		619	528	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522371	157522375	+	frameshift_variant	Frame_Shift_Del	DEL	ATCAC	ATCAC	-	novel	NA	P-0034516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	470	749	0	ENST00000346085.5:c.4646_4650del	p.His1549LeufsTer85	p.H1549Lfs*85	ENST00000346085	NM_020732.3	1548	aATCAC/a	18/20	0.773471245863706	3	FACETS	0.903	0.868	0.938	0.903	0.868	0.938	CLONAL	2	TRUE	1	0.773471245863706	3		749	933	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506210	148506210	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	190	488	1	ENST00000320356.2:c.2148del	p.Phe716LeufsTer24	p.F716Lfs*24	ENST00000320356	NM_004456.4	716	ttT/tt	19/20	0.773471245863706	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.773471245863706	1		489	291	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389236	8389236	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0034516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	150	525	0	ENST00000356435.5:c.4382C>G	p.Ser1461Ter	p.S1461*	ENST00000356435		1461	tCa/tGa	26/35	0.773471245863706	2	FACETS	0.923	0.853	0.996	0.462	0.426	0.498	CLONAL	1	TRUE	0	0.773471245863706	2		525	420	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514290	69514290	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	66	662	0	ENST00000294312.3:c.391T>C	p.Tyr131His	p.Y131H	ENST00000294312	NM_005117.2	131	Tac/Cac	3/3	0.773471245863706	27	FACETS	1	0.918	1			1	CLONAL	2	TRUE	NA	0.773471245863706	27		662	840	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0034575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	97	426	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.237145334437536	3	FACETS	1	0.977	1	0.687	0.614	0.764	CLONAL	1	TRUE	1	0.287987992870728	3		426	561	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220494	1220494	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519858	NA	P-0034575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	158	611	0	ENST00000326873.7:c.587G>T	p.Gly196Val	p.G196V	ENST00000326873	NM_000455.4	196	gGc/gTc	4/10	0.238919912317989	2	FACETS	1	0.988	1	0.732	0.671	0.794	CLONAL	1	TRUE	0	0.287987992870728	2		611	750	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562870	21562870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1047262994	NA	P-0034575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	86	632	0	ENST00000382592.4:c.1049C>T	p.Pro350Leu	p.P350L	ENST00000382592	NM_014572.2	350	cCc/cTc	4/8	1	2	FACETS	0.738	0.652	0.83	0.738	0.652	0.83	SUBCLONAL	1	TRUE	1	0.287987992870728	2		632	809	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156541	55156541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368266633	NA	P-0034575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	174	464	0	ENST00000257290.5:c.2942G>A	p.Arg981His	p.R981H	ENST00000257290	NM_006206.4	981	cGt/cAt	22/23	0.287987992870728	2	FACETS	0.906	0.837	0.977	0.906	0.837	0.977	CLONAL	2	TRUE	0	0.287987992870728	2		464	667	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651135	206651135	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	183	603	0	ENST00000367120.3:c.745G>T	p.Ala249Ser	p.A249S	ENST00000367120	NM_014002.3	249	Gcc/Tcc	8/22	0.287987992870728	3	FACETS	1	0.988	1	0.687	0.633	0.743	CLONAL	1	TRUE	1	0.287987992870728	3		603	1058	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483892	88483892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	81	602	0	ENST00000360948.2:c.1678C>T	p.Leu560Phe	p.L560F	ENST00000360948	NM_001012338.2	560	Ctc/Ttc	14/19	1	2	FACETS	0.583	0.512	0.659	0.583	0.512	0.659	SUBCLONAL	1	TRUE	1	0.287987992870728	2		602	965	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205780	108205780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	59	340	0	ENST00000278616.4:c.8095C>T	p.Pro2699Ser	p.P2699S	ENST00000278616	NM_000051.3	2699	Cca/Tca	55/63	0.218434952808394	2	FACETS	1	0.938	1	0.577	0.499	0.661	CLONAL	1	TRUE	0	0.287987992870728	2		340	355	SUCCESS
ATM	472	MSKCC	GRCh37	11	108213948	108213948	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0034575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	29	231	1	ENST00000278616.4:c.8269-1G>T		p.X2757_splice	ENST00000278616	NM_000051.3	2757			0.218434952808394	2	FACETS	0.516	0.414	0.633	0.258	0.207	0.317	SUBCLONAL	1	TRUE	0	0.287987992870728	2		232	390	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563023	21563023	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	119	590	1	ENST00000382592.4:c.896G>T	p.Gly299Val	p.G299V	ENST00000382592	NM_014572.2	299	gGc/gTc	4/8	1	2	FACETS	0.955	0.862	1	0.955	0.862	1	CLONAL	1	TRUE	1	0.287987992870728	2		591	865	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443649	29443649	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs747661585	NA	P-0034575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	204	506	0	ENST00000389048.3:c.3568C>A	p.Leu1190Met	p.L1190M	ENST00000389048	NM_004304.4	1190	Ctg/Atg	23/29	0.197517286080912	3	FACETS	0.847	0.785	0.91	0.847	0.785	0.91	CLONAL	2	TRUE	1	0.287987992870728	3		506	957	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825432	134825432	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	81	403	0	ENST00000398015.3:c.948A>C	p.Glu316Asp	p.E316D	ENST00000398015	NM_004441.4	316	gaA/gaC	4/16	0.167397267548585	2	FACETS	0.925	0.816	1	0.463	0.408	0.521	INDETERMINATE	1	TRUE	0	0.287987992870728	2		403	608	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948752	55948753	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0034575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	121	528	0	ENST00000263923.4:c.3712dup	p.Thr1238AsnfsTer3	p.T1238Nfs*3	ENST00000263923	NM_002253.2	1238	aca/aAca	28/30	0.287987992870728	2	FACETS	1	0.981	1	0.675	0.612	0.742	CLONAL	1	TRUE	0	0.287987992870728	2		528	622	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439365	149439365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	99	623	0	ENST00000286301.3:c.2030G>A	p.Arg677Lys	p.R677K	ENST00000286301	NM_005211.3	677	aGg/aAg	15/22	1	2	FACETS	0.748	0.667	0.835	0.748	0.667	0.835	SUBCLONAL	1	TRUE	1	0.287987992870728	2		623	919	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099502	157099502	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1256347904	NA	P-0034575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	51	217	0	ENST00000346085.5:c.439G>T	p.Ala147Ser	p.A147S	ENST00000346085	NM_020732.3	147	Gcg/Tcg	1/20	1	2	FACETS	0.918	0.782	1	0.918	0.782	1	CLONAL	1	TRUE	1	0.287987992870728	2		217	386	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371681	55371681	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	163	559	0	ENST00000297316.4:c.371T>A	p.Leu124Gln	p.L124Q	ENST00000297316	NM_022454.3	124	cTg/cAg	2/2	0.135439403960015	4	FACETS	0.926	0.851	1	0.926	0.851	1	INDETERMINATE	2	TRUE	2	0.287987992870728	4		559	787	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518235	8518235	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs765808310	NA	P-0034575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	102	314	0	ENST00000356435.5:c.1156T>C	p.Tyr386His	p.Y386H	ENST00000356435		386	Tac/Cac	10/35	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.287987992870728	2		314	591	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138944	64138944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	22	329	0	ENST00000334205.4:c.2311C>T	p.Pro771Ser	p.P771S	ENST00000334205	NM_003942.2	771	Ccc/Tcc	17/17	1	2	FACETS	0.849	0.658	1	0.849	0.658	1	CLONAL	1	TRUE	1	0.14	2		329	370	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414400	6414400	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	15	200	0	ENST00000356142.4:c.34G>A	p.Gly12Arg	p.G12R	ENST00000356142	NM_018890.3	12	Gga/Aga	1/7	1	2	FACETS	0.785	0.574	1	0.785	0.574	1	CLONAL	1	TRUE	1	0.14	2		200	273	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772605	135772605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	35	515	0	ENST00000298552.3:c.2941G>A	p.Glu981Lys	p.E981K	ENST00000298552	NM_001162426.1	981	Gaa/Aaa	22/23	1	2	FACETS	0.741	0.605	0.894	0.741	0.605	0.894	SUBCLONAL	1	TRUE	1	0.14	2		515	675	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994410	25994410	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0034592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	20	277	0	ENST00000435504.4:c.404-1G>A		p.X135_splice	ENST00000435504		135			1	2	FACETS	0.733	0.559	0.936	0.733	0.559	0.936	CLONAL	1	TRUE	1	0.14	2		277	390	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631608	119631608	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1289744832	NA	P-0034592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	19	288	0	ENST00000316626.5:c.658C>T	p.Arg220Trp	p.R220W	ENST00000316626		220	Cgg/Tgg	6/12	1	2	FACETS	0.714	0.541	0.919	0.714	0.541	0.919	CLONAL	1	TRUE	1	0.14	2		288	380	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241948	39241948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	25	216	0	ENST00000402219.2:c.1898C>T	p.Ser633Phe	p.S633F	ENST00000402219	NM_005633.3	633	tCc/tTc	11/23	1	2	FACETS	0.717	0.564	0.894	0.717	0.564	0.894	SUBCLONAL	1	TRUE	1	0.14	2		216	498	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739832	46739832	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	33	391	0	ENST00000371975.4:c.1634del	p.Gly545AlafsTer12	p.G545Afs*12	ENST00000371975	NM_003579.3	545	Ggc/gc	15/18	1	2	FACETS	0.878	0.714	1	0.878	0.714	1	CLONAL	1	TRUE	1	0.14	2		391	537	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43733733	43733733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269254041	NA	P-0034592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	37	350	0	ENST00000382044.4:c.3089C>T	p.Ser1030Phe	p.S1030F	ENST00000382044	NM_001141980.1	1030	tCt/tTt	15/28	1	2	FACETS	0.743	0.611	0.892	0.743	0.611	0.892	SUBCLONAL	1	TRUE	1	0.14	2		350	711	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779205	3779206	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0034592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	28	453	1	ENST00000262367.5:c.5842_5843delinsTT	p.Pro1948Leu	p.P1948L	ENST00000262367	NM_004380.2	1948	CCg/TTg	31/31	1	2	FACETS	0.789	0.629	0.972	0.789	0.629	0.972	CLONAL	1	TRUE	1	0.14	2		454	507	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292729	62292729	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	64	527	0	ENST00000360203.5:c.181G>A	p.Glu61Lys	p.E61K	ENST00000360203	NM_001283009.1	61	Gaa/Aaa	3/35	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.14	2		527	641	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326496	62326497	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0034592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	47	816	0	ENST00000360203.5:c.3421_3422delinsTT	p.Pro1141Leu	p.P1141L	ENST00000360203	NM_001283009.1	1141	CCg/TTg	33/35	1	2	FACETS	0.73	0.614	0.859	0.73	0.614	0.859	SUBCLONAL	1	TRUE	1	0.14	2		816	920	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130478	29130478	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555932341	NA	P-0034592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	60	558	0	ENST00000328354.6:c.232C>T	p.Gln78Ter	p.Q78*	ENST00000328354	NM_007194.3	78	Caa/Taa	2/15	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.14	2		558	755	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37628861	37628863	+	missense_variant	Missense_Mutation	TNP	GCC	GCC	TTT	novel	NA	P-0034592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	42	654	2	ENST00000249071.6:c.203_205delinsAAA	p.Arg68_Pro69delinsGlnThr	p.R68_P69delinsQT	ENST00000249071	NM_002872.4	68	cGGCcg/cAAAcg	3/7	1	2	FACETS	0.733	0.61	0.87	0.733	0.61	0.87	SUBCLONAL	1	TRUE	1	0.14	2		656	819	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930267	39930267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	43	688	1	ENST00000378444.4:c.3197C>T	p.Thr1066Ile	p.T1066I	ENST00000378444	NM_001123385.1	1066	aCc/aTc	6/15	1	2	FACETS	0.733	0.611	0.869	0.733	0.611	0.869	SUBCLONAL	1	TRUE	1	0.14	2		689	838	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0034861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	166	522	0	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.463799694444967	2		522	701	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	57	186	1	ENST00000257430.4:c.3919dup	p.Ile1307AsnfsTer8	p.I1307Nfs*8	ENST00000257430	NM_000038.5	1306	gaa/gAaa	16/16	0.463799694444967	1	FACETS	0.963	0.84	1	0.963	0.84	1	CLONAL	1	TRUE	0	0.463799694444967	1		187	196	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0034861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	151	641	0	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.463799694444967	2		641	639	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0034861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	91	344	0	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	1	2	FACETS	0.939	0.839	1	0.939	0.839	1	CLONAL	1	TRUE	1	0.463799694444967	2		344	418	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910880	114910881	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0034861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	95	318	0	ENST00000543371.1:c.999_1000del	p.Ser334LysfsTer21	p.S334Kfs*21	ENST00000543371	NM_001198531.1	333	agTTca/agca	9/14	1	2	FACETS	0.916	0.82	1	0.916	0.82	1	CLONAL	1	TRUE	1	0.463799694444967	2		318	447	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061531	38061538	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCGGCT	GCGCGGCT	-	novel	NA	P-0034861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	73	324	0	ENST00000250448.2:c.451_458del	p.Ser151GlyfsTer73	p.S151Gfs*73	ENST00000250448	NM_004496.3	151	AGCCGCGCg/g	2/2	1	2	FACETS	0.87	0.765	0.98	0.87	0.765	0.98	CLONAL	1	TRUE	1	0.463799694444967	2		324	362	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2185888	2185888	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	131	477	0	ENST00000398665.3:c.160G>T	p.Ala54Ser	p.A54S	ENST00000398665	NM_032482.2	54	Gct/Tct	3/28	0.463319421733058	3	FACETS	0.871	0.791	0.955	0.435	0.395	0.478	CLONAL	1	TRUE	1	0.463799694444967	3		477	799	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713867	30713867	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	118	434	0	ENST00000295754.5:c.1192T>A	p.Phe398Ile	p.F398I	ENST00000295754	NM_003242.5	398	Ttt/Att	4/7	0.463799694444967	1	FACETS	0.841	0.763	0.921	0.841	0.763	0.921	CLONAL	1	TRUE	0	0.463799694444967	1		434	465	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468452	89468452	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	95	214	0	ENST00000336596.2:c.1986G>T	p.Lys662Asn	p.K662N	ENST00000336596	NM_005233.5	662	aaG/aaT	11/17	0.45586713142711	2	FACETS	0.898	0.816	0.982	0.898	0.816	0.982	CLONAL	2	TRUE	0	0.463799694444967	2		214	228	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671913	30671913	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	153	559	0	ENST00000376406.3:c.5047A>C	p.Thr1683Pro	p.T1683P	ENST00000376406	NM_014641.2	1683	Aca/Cca	10/15	0.463319421733058	3	FACETS	0.984	0.901	1	0.492	0.45	0.536	CLONAL	1	TRUE	1	0.463799694444967	3		559	826	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970971	21970971	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035603-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	49	577	3	ENST00000304494.5:c.387C>A	p.Tyr129Ter	p.Y129*	ENST00000304494	NM_000077.4	129	taC/taA	2/3	1	2	FACETS	0.212	0.179	0.249	0.212	0.179	0.249	SUBCLONAL	1	TRUE	1	0.76623807158849	2		580	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0035774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	240	499	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.557447609969624	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.557447609969624	1		501	619	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936995	48936995	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778842	NA	P-0035774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	134	426	0	ENST00000267163.4:c.763C>T	p.Arg255Ter	p.R255*	ENST00000267163	NM_000321.2	255	Cga/Tga	8/27	0.557447609969624	1	FACETS	0.95	0.874	1	0.95	0.874	1	CLONAL	1	TRUE	0	0.557447609969624	1		426	365	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910371	29910372	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0035774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	88	800	0	ENST00000376809.5:c.46dup	p.Ala16GlyfsTer83	p.A16Gfs*83	ENST00000376809	NM_002116.7	14	tcg/tcGg	1/8	0.272810967841431	1	FACETS	0.333	0.295	0.374	0.333	0.295	0.374	INDETERMINATE	1	TRUE	0	0.557447609969624	1		800	683	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556370	29556370	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	147	654	0	ENST00000356175.3:c.2737A>G	p.Ile913Val	p.I913V	ENST00000356175	NM_000267.3	913	Ata/Gta	21/57	0.272810967841431	1	FACETS	0.566	0.518	0.616	0.566	0.518	0.616	INDETERMINATE	1	TRUE	0	0.557447609969624	1		654	672	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411887	116411888	+	intron_variant	Intron	INS	-	-	AG	novel	NA	P-0035774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	1972	1087	0	ENST00000397752.3:c.2888-16_2888-15insAG		p.*963*	ENST00000397752	NM_000245.2	-/1390			0.557447609969624	6	FACETS	1	0.99	1			1	CLONAL	6	TRUE	NA	0.557447609969624	6		1087	2486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0035792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	531	776	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.728292703191958	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.728292703191958	1		777	799	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879604	37879604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196929947	NA	P-0035792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	655	715	2	ENST00000269571.5:c.1979G>A	p.Gly660Asp	p.G660D	ENST00000269571		660	gGc/gAc	17/27	0.728292703191958	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.728292703191958	1		717	953	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40747938	40747938	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1384	881	769	0	ENST00000392038.2:c.480G>T	p.Lys160Asn	p.K160N	ENST00000392038	NM_001626.4	160	aaG/aaT	6/14	0.728292703191958	4	FACETS	0.923	0.894	0.952	0.923	0.894	0.952	CLONAL	2	TRUE	2	0.728292703191958	4		769	2265	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249007	55249008	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGACAGCA	novel	NA	P-0035792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	406	516	0	ENST00000275493.2:c.2311_2312insGCATGGACA	p.Asp770_Asn771insSerMetAsp	p.D770_N771insSMD	ENST00000275493	NM_005228.3	769	gtg/gTGGACAGCAtg	20/28	0.357852964276565	6	FACETS	1	0.978	1	0.523	0.497	0.549	INDETERMINATE	2	TRUE	2	0.728292703191958	6		516	1309	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5462965	5462965	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	68	277	0	ENST00000381577.3:c.526A>T	p.Ser176Cys	p.S176C	ENST00000381577	NM_014143.3	176	Agt/Tgt	4/7	1	2	FACETS	0.468	0.409	0.531	0.468	0.409	0.531	SUBCLONAL	1	TRUE	1	0.728292703191958	2		277	399	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953729	48953729	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0035896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	16	290	0	ENST00000267163.4:c.1333-1G>A		p.X445_splice	ENST00000267163	NM_000321.2	445			0.249279265707084	1	FACETS	0.77	0.573	1	0.77	0.573	1	CLONAL	1	TRUE	0	0.249279265707084	1		290	146	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412033	116412058	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTCCAGAAGGTATATTTCAGTTTA	TTTTCCAGAAGGTATATTTCAGTTTA	-	novel	NA	P-0035896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	90	944	0	ENST00000397752.3:c.3020_3028+17del		p.X1007_splice	ENST00000397752	NM_000245.2	1007		14/21	0.185261473042838	2	FACETS	0.916	0.819	1	0.916	0.819	1	CLONAL	2	TRUE	0	0.249279265707084	2		944	394	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373870	118373870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	20	365	0	ENST00000534358.1:c.7263G>A	p.Met2421Ile	p.M2421I	ENST00000534358	NM_005933.3	2421	atG/atA	27/36	1	2	FACETS	0.698	0.535	0.887	0.698	0.535	0.887	SUBCLONAL	1	TRUE	1	0.249279265707084	2		365	230	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441370	149441370	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	71	828	0	ENST00000286301.3:c.1669G>T	p.Glu557Ter	p.E557*	ENST00000286301	NM_005211.3	557	Gag/Tag	12/22	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.249279265707084	2		828	381	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017516	112017516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	26	552	0	ENST00000368678.4:c.997G>A	p.Glu333Lys	p.E333K	ENST00000368678		333	Gag/Aag	9/13	1	2	FACETS	0.658	0.522	0.814	0.658	0.522	0.814	SUBCLONAL	1	TRUE	1	0.249279265707084	2		552	317	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0036281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	79	351	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.438872355337099	2		351	321	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600382	10600382	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	295	663	0	ENST00000171111.5:c.1473C>A	p.Tyr491Ter	p.Y491*	ENST00000171111	NM_203500.1	491	taC/taA	4/6	0.438872355337099	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.438872355337099	2		663	644	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009108	27009108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	45	125	0	ENST00000335756.4:c.44G>A	p.Arg15Lys	p.R15K	ENST00000335756	NM_001809.3	15	aGg/aAg	1/5	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.438872355337099	2		125	143	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281279	49281279	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	137	738	0	ENST00000282018.3:c.326T>A	p.Leu109Gln	p.L109Q	ENST00000282018	NM_020377.2	109	cTg/cAg	1/1	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.438872355337099	2		738	578	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865364	40865364	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs776879514	NA	P-0036281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	124	594	0	ENST00000428826.2:c.1067A>G	p.Lys356Arg	p.K356R	ENST00000428826		356	aAg/aGg	11/21	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.438872355337099	2		594	545	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106975	11106975	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	222	542	0	ENST00000358026.2:c.1680C>A	p.Tyr560Ter	p.Y560*	ENST00000358026	NM_001128849.1	560	taC/taA	10/36	0.438872355337099	2	FACETS	0.954	0.897	1	0.954	0.897	1	CLONAL	2	TRUE	0	0.438872355337099	2		542	530	SUCCESS
ATR	545	MSKCC	GRCh37	3	142180928	142180928	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0036281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	66	298	0	ENST00000350721.4:c.7046T>G	p.Leu2349Ter	p.L2349*	ENST00000350721	NM_001184.3	2349	tTa/tGa	42/47	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.438872355337099	2		298	252	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938516	76938516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	72	565	0	ENST00000373344.5:c.2232G>A	p.Met744Ile	p.M744I	ENST00000373344	NM_000489.3	744	atG/atA	9/35	1	2	FACETS	0.857	0.753	0.968	0.857	0.753	0.968	CLONAL	1	TRUE	1	0.438872355337099	2		565	383	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	101	320	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.758	0.68	0.839	1	0.982	1	SUBCLONAL	2	TRUE	1	0.271486846878032	2		321	491	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0036667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	65	506	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.89	0.772	1	0.89	0.772	1	CLONAL	1	TRUE	1	0.271486846878032	2		506	538	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0036667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	24	368	1	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	1	2	FACETS	0.393	0.307	0.492	0.393	0.307	0.492	SUBCLONAL	1	TRUE	1	0.271486846878032	2		369	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0036667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	101	549	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	1	2	FACETS	0.904	0.808	1	0.904	0.808	1	CLONAL	1	TRUE	1	0.271486846878032	2		549	823	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057988	27057988	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	51	557	0	ENST00000324856.7:c.1696C>T	p.Gln566Ter	p.Q566*	ENST00000324856	NM_006015.4	566	Cag/Tag	3/20	1	2	FACETS	0.441	0.373	0.515	0.441	0.373	0.515	SUBCLONAL	1	TRUE	1	0.271486846878032	2		557	852	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682381	37682381	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	40	530	0	ENST00000447079.4:c.3572C>T	p.Ser1191Leu	p.S1191L	ENST00000447079	NM_015083.1	1191	tCa/tTa	13/14	1	2	FACETS	0.37	0.306	0.441	0.37	0.306	0.441	SUBCLONAL	1	TRUE	1	0.271486846878032	2		530	797	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398220	25398220	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	89	409	0	ENST00000311936.3:c.99T>A	p.Asp33Glu	p.D33E	ENST00000311936	NM_004985.3	33	gaT/gaA	2/5	NA	2	FACETS	1	0.958	1			1	INDETERMINATE	1	TRUE	NA	0.271486846878032	2		409	563	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022238	31022238	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs747847938	NA	P-0036667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	22	240	0	ENST00000375687.4:c.1723C>T	p.Gln575Ter	p.Q575*	ENST00000375687	NM_015338.5	575	Caa/Taa	13/13	1	2	FACETS	0.39	0.301	0.493	0.39	0.301	0.493	SUBCLONAL	1	TRUE	1	0.271486846878032	2		240	416	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737350	145737350	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs35101495	NA	P-0036667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1300	69	761	0	ENST00000428558.2:c.3337G>C	p.Gly1113Arg	p.G1113R	ENST00000428558	NM_004260.3	1113	Ggg/Cgg	20/22	0.212063230527286	3	FACETS	0.422	0.365	0.483	0.211	0.182	0.242	SUBCLONAL	1	TRUE	1	0.271486846878032	3		761	1369	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895689	28895689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	109	508	0	ENST00000282397.4:c.3085C>T	p.Leu1029Phe	p.L1029F	ENST00000282397	NM_002019.4	1029	Ctt/Ttt	23/30	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.271486846878032	2		508	787	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394052	31394052	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	46	371	1	ENST00000328111.2:c.2339C>T	p.Ser780Leu	p.S780L	ENST00000328111	NM_006892.3	780	tCg/tTg	22/23	1	2	FACETS	0.577	0.485	0.679	0.577	0.485	0.679	SUBCLONAL	1	TRUE	1	0.271486846878032	2		372	587	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278101	18278101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1056224197	NA	P-0036667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	115	641	1	ENST00000222254.8:c.1721G>A	p.Arg574Gln	p.R574Q	ENST00000222254	NM_005027.3	574	cGa/cAa	13/16	1	2	FACETS	0.784	0.704	0.868	0.784	0.704	0.868	SUBCLONAL	1	TRUE	1	0.271486846878032	2		642	1081	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057874	27057874	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	71	676	0	ENST00000324856.7:c.1582C>G	p.Gln528Glu	p.Q528E	ENST00000324856	NM_006015.4	528	Cag/Gag	3/20	1	2	FACETS	0.516	0.449	0.589	0.516	0.449	0.589	SUBCLONAL	1	TRUE	1	0.271486846878032	2		676	1013	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462990	120462990	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	89	501	0	ENST00000256646.2:c.5341G>C	p.Asp1781His	p.D1781H	ENST00000256646	NM_024408.3	1781	Gat/Cat	30/34	1	2	FACETS	0.966	0.856	1	0.966	0.856	1	CLONAL	1	TRUE	1	0.271486846878032	2		501	679	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819179	3819179	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	64	444	0	ENST00000262367.5:c.3056C>G	p.Ser1019Cys	p.S1019C	ENST00000262367	NM_004380.2	1019	tCt/tGt	15/31	1	2	FACETS	0.63	0.545	0.723	0.63	0.545	0.723	SUBCLONAL	1	TRUE	1	0.271486846878032	2		444	748	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475130	40475130	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193922720	NA	P-0036667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	54	576	0	ENST00000264657.5:c.1780G>A	p.Glu594Lys	p.E594K	ENST00000264657	NM_139276.2	594	Gag/Aag	20/24	1	2	FACETS	0.419	0.356	0.488	0.419	0.356	0.488	SUBCLONAL	1	TRUE	1	0.271486846878032	2		576	950	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40871125	40871125	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	41	435	0	ENST00000428826.2:c.765G>C	p.Glu255Asp	p.E255D	ENST00000428826		255	gaG/gaC	8/21	1	2	FACETS	0.426	0.354	0.507	0.426	0.354	0.507	SUBCLONAL	1	TRUE	1	0.271486846878032	2		435	709	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216637	2216637	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1318769899	NA	P-0036667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	61	706	0	ENST00000398665.3:c.2281G>C	p.Glu761Gln	p.E761Q	ENST00000398665	NM_032482.2	761	Gag/Cag	20/28	1	2	FACETS	0.394	0.338	0.454	0.394	0.338	0.454	SUBCLONAL	1	TRUE	1	0.271486846878032	2		706	1142	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163282	32163282	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1310	193	794	0	ENST00000375023.3:c.5944C>T	p.Gln1982Ter	p.Q1982*	ENST00000375023	NM_004557.3	1982	Caa/Taa	30/30	0.107222811051711	3	FACETS	1	0.963	1	0.537	0.495	0.581	INDETERMINATE	1	TRUE	1	0.271486846878032	3		794	1503	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035217	6035217	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782898	NA	P-0036667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	93	400	0	ENST00000265849.7:c.851C>T	p.Ser284Leu	p.S284L	ENST00000265849	NM_000535.5	284	tCa/tTa	8/15	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.271486846878032	2		400	675	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346431	152346431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	59	274	1	ENST00000359321.1:c.139C>T	p.His47Tyr	p.H47Y	ENST00000359321	NM_005431.1	47	Cat/Tat	3/3	1	2	FACETS	0.718	0.618	0.828	0.718	0.618	0.828	SUBCLONAL	1	TRUE	1	0.271486846878032	2		275	605	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56882350	56882350	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	79	571	0	ENST00000519728.1:c.1048C>T	p.Gln350Ter	p.Q350*	ENST00000519728	NM_002350.3	350	Cag/Tag	10/13	0.212063230527286	3	FACETS	0.666	0.584	0.754	0.333	0.292	0.377	SUBCLONAL	1	TRUE	1	0.271486846878032	3		571	993	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240351	98240351	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	77	383	0	ENST00000331920.6:c.1333G>T	p.Gly445Cys	p.G445C	ENST00000331920	NM_000264.3	445	Ggc/Tgc	9/24	1	2	FACETS	0.978	0.86	1	0.978	0.86	1	CLONAL	1	TRUE	1	0.271486846878032	2		383	580	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764146326	NA	P-0036792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	539	777	1	ENST00000269305.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000269305	NM_001126112.2	281	Gac/Aac	8/11	0.811378214504029	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.811378214504029	2		778	660	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242442	55242443	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTAAAATTCCCGTCGCTA	novel	NA	P-0036792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1434	1775	462	2	ENST00000275493.2:c.2214_2231dup	p.Ile740_Lys745dup	p.I740_K745dup	ENST00000275493	NM_005228.3	740	gtt/gTTAAAATTCCCGTCGCTAtt	19/28	0.811378214504029	16	FACETS	1	0.989	1			1	CLONAL	9	TRUE	NA	0.811378214504029	16		464	3209	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200617	67200617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	195	705	3	ENST00000312629.5:c.728G>A	p.Arg243His	p.R243H	ENST00000312629	NM_003952.2	243	cGc/cAc	9/15	0.398005685486992	2	FACETS	0.93	0.868	0.993	0.465	0.434	0.497	INDETERMINATE	1	TRUE	0	0.811378214504029	2		708	517	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0036915-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	123	506	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.22986253482724	4	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	2	0.274469676905978	4		506	546	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717609	89717609	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs876661024	NA	P-0036915-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	125	374	0	ENST00000371953.3:c.635-1G>C		p.X212_splice	ENST00000371953	NM_000314.4	212			0.273385606241184	2	FACETS	0.994	0.906	1	0.994	0.906	1	CLONAL	2	TRUE	0	0.274469676905978	2		374	458	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028883	47028883	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036915-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	110	693	0	ENST00000377604.3:c.187G>T	p.Glu63Ter	p.E63*	ENST00000377604	NM_001204468.1	63	Gag/Tag	3/24	0.169513564736474	3	FACETS	1	0.941	1			1	CLONAL	1	TRUE	NA	0.274469676905978	3		693	853	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65569015	65569036	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACTCACGTCGCTCTCCACCTC	GACTCACGTCGCTCTCCACCTC	-	novel	NA	P-0036915-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	86	540	0	ENST00000358664.4:c.22_36+7del		p.X8_splice	ENST00000358664	NM_002382.4	8		1/5	0.274469676905978	2	FACETS	0.868	0.768	0.975	0.434	0.384	0.488	CLONAL	1	TRUE	0	0.274469676905978	2		540	722	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955452	48955452	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0036915-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	91	350	0	ENST00000267163.4:c.1568T>G	p.Leu523Ter	p.L523*	ENST00000267163	NM_000321.2	523	tTa/tGa	17/27	0.273385606241184	2	FACETS	0.839	0.75	0.933	0.839	0.75	0.933	CLONAL	2	TRUE	0	0.274469676905978	2		350	395	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0036932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	144	524	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	0.909	0.832	0.988	0.909	0.832	0.988	CLONAL	1	TRUE	1	0.546551889391901	2		524	580	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527627	41527627	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	94	339	0	ENST00000263253.7:c.1518G>T	p.Met506Ile	p.M506I	ENST00000263253	NM_001429.3	506	atG/atT	6/31	1	2	FACETS	0.948	0.85	1	0.948	0.85	1	CLONAL	1	TRUE	1	0.546551889391901	2		339	363	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800869	120800869	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	133	730	0	ENST00000257552.2:c.379C>T	p.Gln127Ter	p.Q127*	ENST00000257552	NM_002442.3	127	Caa/Taa	6/15	0.399343305924988	3	FACETS	0.766	0.695	0.841	0.383	0.347	0.421	SUBCLONAL	1	TRUE	1	0.43523940174034	3		730	971	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257231	133257231	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	164	701	0	ENST00000320574.5:c.247G>C	p.Asp83His	p.D83H	ENST00000320574	NM_006231.2	83	Gat/Cat	3/49	0.399343305924988	3	FACETS	0.923	0.847	1	0.462	0.423	0.502	CLONAL	1	TRUE	1	0.43523940174034	3		701	994	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929403	32929404	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs80359650	NA	P-0037031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	173	735	0	ENST00000380152.3:c.7414_7415del	p.Lys2472ValfsTer2	p.K2472Vfs*2	ENST00000380152		2471	acAAag/acag	14/27	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.43523940174034	2		735	783	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023345	33023345	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	170	809	0	ENST00000300177.4:c.454A>G	p.Met152Val	p.M152V	ENST00000300177	NM_001191322.1	152	Atg/Gtg	2/2	1	2	FACETS	0.854	0.785	0.925	0.854	0.785	0.925	CLONAL	1	TRUE	1	0.43523940174034	2		809	915	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169150	32169150	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1341686766	NA	P-0037031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	119	666	0	ENST00000375023.3:c.3883C>A	p.Pro1295Thr	p.P1295T	ENST00000375023	NM_004557.3	1295	Ccc/Acc	22/30	0.43523940174034	3	FACETS	0.769	0.693	0.849	0.384	0.346	0.425	SUBCLONAL	1	TRUE	1	0.43523940174034	3		666	866	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0037068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	51	426	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.207754019163076	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.689626470232304	0		426	193	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0037068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	392	560	0	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	0.689626470232304	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.689626470232304	1		560	727	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608282	28608282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773466203	NA	P-0037068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	98	470	2	ENST00000241453.7:c.1774G>A	p.Val592Ile	p.V592I	ENST00000241453	NM_004119.2	592	Gtt/Att	14/24	0.309692916347668	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.689626470232304	0		472	223	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097630	27097630	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	224	359	0	ENST00000324856.7:c.3219G>A	p.Trp1073Ter	p.W1073*	ENST00000324856	NM_006015.4	1073	tgG/tgA	12/20	0.321200774114916	3	FACETS	1	0.983	1	0.575	0.537	0.614	INDETERMINATE	1	TRUE	1	0.689626470232304	3		359	760	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279524	1279524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774381540	NA	P-0037068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	125	570	0	ENST00000310581.5:c.2012G>A	p.Arg671Gln	p.R671Q	ENST00000310581	NM_198253.2	671	cGg/cAg	5/16	1	2	FACETS	0.387	0.35	0.426	0.387	0.35	0.426	SUBCLONAL	1	TRUE	1	0.689626470232304	2		570	937	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295106	91295106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	38	381	1	ENST00000355112.3:c.889G>A	p.Asp297Asn	p.D297N	ENST00000355112	NM_000057.2	297	Gat/Aat	4/22	0.682563419535183	2	FACETS	0.656	0.55	0.771	0.328	0.275	0.386	SUBCLONAL	1	TRUE	0	0.689626470232304	2		382	168	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270187	198270187	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	55	256	0	ENST00000335508.6:c.1249C>T	p.Pro417Ser	p.P417S	ENST00000335508	NM_012433.2	417	Cct/Tct	10/25	0.184144934370434	2	FACETS	0.67	0.58	0.767	0.335	0.29	0.384	INDETERMINATE	1	TRUE	0	0.689626470232304	2		256	238	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260782	16260782	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	236	406	0	ENST00000375759.3:c.8047G>T	p.Val2683Leu	p.V2683L	ENST00000375759	NM_015001.2	2683	Gtg/Ttg	11/15	0.321200774114916	3	FACETS	1	0.99	1	0.652	0.611	0.694	INDETERMINATE	1	TRUE	1	0.689626470232304	3		406	706	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163822	72163822	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	20	269	0	ENST00000357731.5:c.536C>A	p.Ala179Glu	p.A179E	ENST00000357731	NM_173808.2	179	gCa/gAa	4/7	1	2	FACETS	0.817	0.643	1	0.817	0.643	1	CLONAL	1	TRUE	1	0.689626470232304	2		269	71	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865136	57865136	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	421	657	0	ENST00000228682.2:c.2613T>A	p.Asp871Glu	p.D871E	ENST00000228682	NM_005269.2	871	gaT/gaA	12/12	0.224595041004537	4	FACETS	0.85	0.811	0.891	0.85	0.811	0.891	INDETERMINATE	2	TRUE	2	0.689626470232304	4		657	1213	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597579	28597579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1268548071	NA	P-0037068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	61	558	0	ENST00000241453.7:c.2326G>A	p.Glu776Lys	p.E776K	ENST00000241453	NM_004119.2	776	Gaa/Aaa	19/24	0.309692916347668	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.689626470232304	0		558	313	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678455	88678455	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	234	532	0	ENST00000360948.2:c.1081G>C	p.Gly361Arg	p.G361R	ENST00000360948	NM_001012338.2	361	Ggc/Cgc	9/19	0.682563419535183	2	FACETS	0.953	0.893	1	0.477	0.446	0.507	CLONAL	1	TRUE	0	0.689626470232304	2		532	712	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586097	29586115	+	frameshift_variant	Frame_Shift_Del	DEL	TATGCGGCCTTTCAATGAT	TATGCGGCCTTTCAATGAT	-	novel	NA	P-0037068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	37	469	0	ENST00000356175.3:c.4318_4336del	p.Met1440LeufsTer2	p.M1440Lfs*2	ENST00000356175	NM_000267.3	1439	caTATGCGGCCTTTCAATGAT/ca	32/57	0.675946416212926	3	FACETS	1	0.873	1	0.523	0.439	0.613	CLONAL	1	TRUE	1	0.689626470232304	3		469	138	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56412949	56412949	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	60	353	0	ENST00000348428.3:c.1963G>T	p.Gly655Cys	p.G655C	ENST00000348428	NM_006785.3	655	Ggc/Tgc	16/17	0.689626470232304	1	FACETS	0.905	0.805	1	0.905	0.805	1	CLONAL	1	TRUE	0	0.689626470232304	1		353	126	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728826	190728826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	31	356	0	ENST00000441310.2:c.2214G>A	p.Met738Ile	p.M738I	ENST00000441310	NM_000534.4	738	atG/atA	10/13	0.184144934370434	2	FACETS	0.731	0.602	0.87	0.365	0.301	0.435	INDETERMINATE	1	TRUE	0	0.689626470232304	2		356	123	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632319	215632322	+	frameshift_variant	Frame_Shift_Del	DEL	TGCC	TGCC	-	novel	NA	P-0037068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	209	433	0	ENST00000260947.4:c.1452_1455del	p.Lys484AsnfsTer3	p.K484Nfs*3	ENST00000260947	NM_000465.2	484	aaGGCA/aa	6/11	0.689626470232304	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.689626470232304	1		433	362	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794824	242794824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	265	440	0	ENST00000334409.5:c.385G>A	p.Ala129Thr	p.A129T	ENST00000334409	NM_005018.2	129	Gcc/Acc	2/5	0.689626470232304	1	FACETS	0.836	0.791	0.882	0.836	0.791	0.882	CLONAL	1	TRUE	0	0.689626470232304	1		440	602	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468453	89468453	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	41	238	0	ENST00000336596.2:c.1987C>A	p.Gln663Lys	p.Q663K	ENST00000336596	NM_005233.5	663	Cag/Aag	11/17	1	2	FACETS	0.881	0.749	1	0.881	0.749	1	CLONAL	1	TRUE	1	0.689626470232304	2		238	135	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157903	106157903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775589418	NA	P-0037068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	216	277	0	ENST00000380013.4:c.2804G>A	p.Gly935Glu	p.G935E	ENST00000380013	NM_001127208.2	935	gGa/gAa	3/11	0.155629674634203	3	FACETS	1	0.978	1	0.713	0.674	0.751	INDETERMINATE	2	TRUE	0	0.689626470232304	3		277	394	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874118	151874118	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	72	530	0	ENST00000262189.6:c.8420C>G	p.Ser2807Cys	p.S2807C	ENST00000262189	NM_170606.2	2807	tCt/tGt	38/59	0.689626470232304	3	FACETS	0.859	0.756	0.967	0.429	0.378	0.484	CLONAL	1	TRUE	1	0.689626470232304	3		530	327	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151947941	151947941	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	45	416	0	ENST00000262189.6:c.1732G>C	p.Asp578His	p.D578H	ENST00000262189	NM_170606.2	578	Gat/Cat	12/59	0.689626470232304	3	FACETS	1	0.883	1	0.519	0.443	0.6	CLONAL	1	TRUE	1	0.689626470232304	3		416	169	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371626	55371626	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	435	404	0	ENST00000297316.4:c.316T>A	p.Trp106Arg	p.W106R	ENST00000297316	NM_022454.3	106	Tgg/Agg	2/2	0.219932560958408	2	FACETS	1	0.996	1	0.711	0.682	0.74	INDETERMINATE	1	TRUE	0	0.689626470232304	2		404	887	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117875449	117875449	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	38	440	0	ENST00000297338.2:c.194G>T	p.Arg65Leu	p.R65L	ENST00000297338	NM_006265.2	65	cGa/cTa	3/14	0.689626470232304	4	FACETS	0.733	0.61	0.869	0.367	0.305	0.435	SUBCLONAL	1	TRUE	2	0.689626470232304	4		440	254	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740600	145740600	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587778654	NA	P-0037068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1693	423	508	0	ENST00000428558.2:c.1417C>G	p.Leu473Val	p.L473V	ENST00000428558	NM_004260.3	473	Ctg/Gtg	8/22	0.689626470232304	4	FACETS	0.98	0.93	1	0.49	0.465	0.516	CLONAL	1	TRUE	2	0.689626470232304	4		508	2116	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761387	59761387	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs886053214	NA	P-0037089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	196	216	0	ENST00000259008.2:c.3020C>A	p.Ser1007Tyr	p.S1007Y	ENST00000259008	NM_032043.2	1007	tCt/tAt	20/20	0.801691887438415	3	FACETS	0.91	0.844	0.977	0.455	0.422	0.489	CLONAL	1	TRUE	1	0.801691887438415	3		216	753	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0037091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	493	556	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.924500683967458	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.924500683967458	1		556	526	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566521	41566521	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	219	276	1	ENST00000263253.7:c.4398G>T	p.Trp1466Cys	p.W1466C	ENST00000263253	NM_001429.3	1466	tgG/tgT	27/31	1	2	FACETS	0.946	0.889	1	0.946	0.889	1	CLONAL	1	TRUE	1	0.924500683967458	2		277	501	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954221	48954221	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0037091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	196	162	0	ENST00000267163.4:c.1421+1G>A		p.X474_splice	ENST00000267163	NM_000321.2	474			0.924500683967458	2	FACETS	0.995	0.969	1	0.995	0.969	1	CLONAL	2	TRUE	0	0.924500683967458	2		162	213	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466428	120466428	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	353	519	0	ENST00000256646.2:c.4691G>T	p.Ser1564Ile	p.S1564I	ENST00000256646	NM_024408.3	1564	aGc/aTc	26/34	1	2	FACETS	0.955	0.91	1	0.955	0.91	1	CLONAL	1	TRUE	1	0.924500683967458	2		519	800	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141561	202141561	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	245	307	0	ENST00000358485.4:c.849A>T	p.Lys283Asn	p.K283N	ENST00000358485	NM_001080125.1	283	aaA/aaT	7/9	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.924500683967458	2		307	503	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687049	176687049	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	323	452	0	ENST00000439151.2:c.5026G>T	p.Ala1676Ser	p.A1676S	ENST00000439151	NM_022455.4	1676	Gct/Tct	14/23	0.924500683967458	1	FACETS	0.87	0.84	0.898	0.87	0.84	0.898	CLONAL	1	TRUE	0	0.924500683967458	1		452	432	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815771	32815771	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	409	600	0	ENST00000354258.4:c.1845C>A	p.Tyr615Ter	p.Y615*	ENST00000354258	NM_000593.5	615	taC/taA	8/11	1	2	FACETS	0.936	0.895	0.978	0.936	0.895	0.978	CLONAL	1	TRUE	1	0.924500683967458	2		600	945	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192423	138192423	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs533720482	NA	P-0037091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	160	230	0	ENST00000237289.4:c.59A>G	p.Lys20Arg	p.K20R	ENST00000237289	NM_001270507.1	20	aAg/aGg	2/9	1	2	FACETS	0.943	0.877	1	0.943	0.877	1	CLONAL	1	TRUE	1	0.924500683967458	2		230	367	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184075	123184075	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	510	418	0	ENST00000218089.9:c.933G>C	p.Glu311Asp	p.E311D	ENST00000218089	NM_001042749.1	311	gaG/gaC	11/35	0.924500683967458	3	FACETS	0.924	0.892	0.955	0.924	0.892	0.955	CLONAL	2	TRUE	1	0.924500683967458	3		418	873	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0037118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	499	566	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.83	0.798	0.862	1	0.997	1	CLONAL	2	TRUE	1	0.574707175462336	2		566	1046	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372379	55372379	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	235	734	0	ENST00000297316.4:c.1069G>A	p.Glu357Lys	p.E357K	ENST00000297316	NM_022454.3	357	Gag/Aag	2/2	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.574707175462336	2		734	816	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499372	89499372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	133	344	0	ENST00000336596.2:c.2542G>A	p.Asp848Asn	p.D848N	ENST00000336596	NM_005233.5	848	Gac/Aac	15/17	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.574707175462336	2		344	443	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384656	31384656	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	175	603	0	ENST00000328111.2:c.1358G>T	p.Gly453Val	p.G453V	ENST00000328111	NM_006892.3	453	gGg/gTg	13/23	1	2	FACETS	0.905	0.836	0.976	0.905	0.836	0.976	CLONAL	1	TRUE	1	0.574707175462336	2		603	673	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651181	206651181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	131	715	0	ENST00000367120.3:c.791C>T	p.Pro264Leu	p.P264L	ENST00000367120	NM_014002.3	264	cCc/cTc	8/22	0.161273103691763	2	FACETS	0.59	0.535	0.647	0.295	0.267	0.324	INDETERMINATE	1	TRUE	0	0.574707175462336	2		715	773	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0037118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	127	673	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.574707175462336	2		673	441	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675131	40675131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745844593	NA	P-0037118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	270	720	0	ENST00000249776.8:c.95G>A	p.Arg32Gln	p.R32Q	ENST00000249776	NM_033286.3	32	cGg/cAg	1/9	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.574707175462336	2		720	865	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246518373	246518373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1007512650	NA	P-0037118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	123	439	0	ENST00000388985.4:c.188C>T	p.Ser63Phe	p.S63F	ENST00000388985		63	tCt/tTt	2/12	0.161273103691763	2	FACETS	0.719	0.652	0.789	0.36	0.326	0.395	INDETERMINATE	1	TRUE	0	0.574707175462336	2		439	595	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295176	91295176	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	133	296	0	ENST00000355112.3:c.959G>A	p.Ser320Asn	p.S320N	ENST00000355112	NM_000057.2	320	aGt/aAt	4/22	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.574707175462336	2		296	451	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857097	9857098	+	missense_variant	Missense_Mutation	DNP	TT	TT	CC	novel	NA	P-0037118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	84	286	0	ENST00000330684.3:c.4303_4304delinsGG	p.Lys1435Gly	p.K1435G	ENST00000330684	NM_001134407.1	1435	AAg/GGg	13/13	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.574707175462336	2		286	277	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984936	9984937	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0037118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	127	463	0	ENST00000330684.3:c.1028_1029delinsAA	p.Trp343Ter	p.W343*	ENST00000330684	NM_001134407.1	343	tGG/tAA	4/13	1	2	FACETS	0.843	0.768	0.922	0.843	0.768	0.922	CLONAL	1	TRUE	1	0.574707175462336	2		463	524	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645490	67645490	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	95	213	0	ENST00000264010.4:c.755C>T	p.Pro252Leu	p.P252L	ENST00000264010	NM_006565.3	252	cCa/cTa	3/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.574707175462336	2		213	279	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626955	14626955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763247276	NA	P-0037118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	213	617	1	ENST00000254322.2:c.820C>T	p.Pro274Ser	p.P274S	ENST00000254322	NM_006145.1	274	Ccc/Tcc	3/3	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.574707175462336	2		618	726	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264964	46264964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	133	383	0	ENST00000371998.3:c.1834C>T	p.Pro612Ser	p.P612S	ENST00000371998		612	Cct/Tct	12/23	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.574707175462336	2		383	443	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547841	41547841	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	95	365	0	ENST00000263253.7:c.2822C>T	p.Ser941Phe	p.S941F	ENST00000263253	NM_001429.3	941	tCc/tTc	15/31	1	2	FACETS	0.827	0.741	0.916	0.827	0.741	0.916	CLONAL	1	TRUE	1	0.574707175462336	2		365	400	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937004	178937004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	151	459	0	ENST00000263967.3:c.1685C>T	p.Pro562Leu	p.P562L	ENST00000263967	NM_006218.2	562	cCc/cTc	11/21	1	2	FACETS	0.824	0.756	0.894	0.824	0.756	0.894	CLONAL	1	TRUE	1	0.574707175462336	2		459	638	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679034	117679034	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	178	503	0	ENST00000368508.3:c.3787C>T	p.Pro1263Ser	p.P1263S	ENST00000368508	NM_002944.2	1263	Ccc/Tcc	24/43	1	2	FACETS	0.98	0.907	1	0.98	0.907	1	CLONAL	1	TRUE	1	0.574707175462336	2		503	632	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028041	69028041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	116	429	0	ENST00000288368.4:c.3200G>A	p.Gly1067Asp	p.G1067D	ENST00000288368	NM_024870.2	1067	gGc/gAc	26/40	1	2	FACETS	0.874	0.792	0.959	0.874	0.792	0.959	CLONAL	1	TRUE	1	0.574707175462336	2		429	462	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21968229	21968229	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0037118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	128	278	0	ENST00000304494.5:c.470G>C	p.Ter157SerextTer13	p.*157Sext*13	ENST00000304494	NM_000077.4	157	tGa/tCa	3/3	0.541810922968262	0	FACETS	0.694	0.641	0.747			1	SUBCLONAL	1	TRUE	0	0.574707175462336	0		278	273	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458580	120458580	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	68	436	0	ENST00000256646.2:c.6765C>A	p.Asn2255Lys	p.N2255K	ENST00000256646	NM_024408.3	2255	aaC/aaA	34/34	0.235169260232426	3	FACETS	0.296	0.257	0.339	0.148	0.128	0.17	INDETERMINATE	1	TRUE	1	0.711064501705288	3		436	875	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	1404	549	0	ENST00000269305.4:c.396del	p.Met133CysfsTer37	p.M133Cfs*37	ENST00000269305	NM_001126112.2	132	aaG/aa	5/11	0.692734242631754	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.711064501705288	3		549	1745	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161970036	161970036	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0037150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	271	399	0	ENST00000366898.1:c.934-1G>A		p.X312_splice	ENST00000366898	NM_004562.2	312			1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.711064501705288	2		399	754	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900296	101900296	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	47	301	0	ENST00000374994.4:c.730C>A	p.Arg244Ser	p.R244S	ENST00000374994	NM_004612.2	244	Cgt/Agt	4/9	1	2	FACETS	0.275	0.232	0.323	0.275	0.232	0.323	SUBCLONAL	1	TRUE	1	0.711064501705288	2		301	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0037154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	579	555	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	1	2	FACETS	0.97	0.945	0.994	1	0.998	1	CLONAL	2	TRUE	1	0.771339958840535	2		555	774	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851709	134851709	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373296912	NA	P-0037154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	225	406	2	ENST00000398015.3:c.1115G>A	p.Arg372His	p.R372H	ENST00000398015	NM_004441.4	372	cGc/cAc	5/16	0.747450657143529	2	FACETS	1	0.991	1	0.631	0.595	0.667	CLONAL	1	TRUE	0	0.771339958840535	2		408	462	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981151	201981151	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	308	630	0	ENST00000359651.3:c.230G>T	p.Ser77Ile	p.S77I	ENST00000359651		77	aGc/aTc	2/8	0.122199715581755	4	FACETS	1	0.994	1	0.478	0.451	0.505	INDETERMINATE	1	TRUE	1	0.771339958840535	4		630	987	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339033	225339033	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	184	444	0	ENST00000264414.4:c.2236G>C	p.Glu746Gln	p.E746Q	ENST00000264414	NM_003590.4	746	Gaa/Caa	16/16	0.343729308225478	4	FACETS	0.905	0.844	0.967	0.452	0.422	0.484	INDETERMINATE	2	TRUE	0	0.771339958840535	4		444	467	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0037197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	180	426	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA	2	FACETS	0.788	0.729	0.849			1	INDETERMINATE	2	TRUE	NA	0.32	2		426	714	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143350344	143350344	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	32	257	0	ENST00000262992.4:c.118C>T	p.Gln40Ter	p.Q40*	ENST00000262992	NM_001101669.1	40	Cag/Tag	3/24	1	2	FACETS	0.629	0.512	0.761	0.629	0.512	0.761	SUBCLONAL	1	TRUE	1	0.32	2		257	318	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962554	100962554	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	109	609	0	ENST00000325455.5:c.1843C>A	p.Arg615Ser	p.R615S	ENST00000325455	NM_001202474.3	615	Cgc/Agc	3/8	1	2	FACETS	0.845	0.759	0.937	0.845	0.759	0.937	CLONAL	1	TRUE	1	0.32	2		609	806	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281035	49281035	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	98	672	0	ENST00000282018.3:c.82A>T	p.Ser28Cys	p.S28C	ENST00000282018	NM_020377.2	28	Agc/Tgc	1/1	1	2	FACETS	0.804	0.717	0.896	0.804	0.717	0.896	CLONAL	1	TRUE	1	0.32	2		672	762	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544726	65544726	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	86	655	0	ENST00000358664.4:c.200C>G	p.Ala67Gly	p.A67G	ENST00000358664	NM_002382.4	67	gCc/gGc	4/5	1	2	FACETS	0.691	0.611	0.777	0.691	0.611	0.777	SUBCLONAL	1	TRUE	1	0.32	2		655	778	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024552	31024552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	128	673	0	ENST00000375687.4:c.4037C>T	p.Ser1346Phe	p.S1346F	ENST00000375687	NM_015338.5	1346	tCt/tTt	13/13	1	2	FACETS	0.93	0.843	1	0.93	0.843	1	CLONAL	1	TRUE	1	0.32	2		673	860	SUCCESS
APC	324	MSKCC	GRCh37	5	112102988	112102988	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	89	479	4	ENST00000257430.4:c.323G>T	p.Gly108Val	p.G108V	ENST00000257430	NM_000038.5	108	gGa/gTa	4/16	1	2	FACETS	0.907	0.806	1	0.907	0.806	1	CLONAL	1	TRUE	1	0.32	2		483	613	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508963	106508963	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	64	412	0	ENST00000359195.3:c.957G>T	p.Arg319Ser	p.R319S	ENST00000359195	NM_002649.2	319	agG/agT	2/11	1	2	FACETS	0.749	0.649	0.857	0.749	0.649	0.857	SUBCLONAL	1	TRUE	1	0.32	2		412	534	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5563181	5563182	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0037197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	63	447	0	ENST00000397747.3:c.787dup	p.Thr263AsnfsTer21	p.T263Nfs*21	ENST00000397747	NM_025239.3	262	-/A	6/7	1	2	FACETS	0.635	0.549	0.729	0.635	0.549	0.729	SUBCLONAL	1	TRUE	1	0.32	2		447	620	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759812	133759812	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs766513552	NA	P-0037197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	126	622	0	ENST00000318560.5:c.2135G>T	p.Arg712Leu	p.R712L	ENST00000318560	NM_005157.4	712	cGc/cTc	11/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.32	2		622	668	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69456259	69456259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	79	703	1	ENST00000227507.2:c.178G>A	p.Val60Ile	p.V60I	ENST00000227507	NM_053056.2	60	Gtc/Atc	1/5	0.179476982829903	2	FACETS	0.581	0.51	0.658	0.291	0.255	0.329	INDETERMINATE	1	TRUE	0	0.321676154222228	2		704	845	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396623	396623	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	69	914	0	ENST00000262320.3:c.403G>T	p.Glu135Ter	p.E135*	ENST00000262320	NM_003502.3	135	Gag/Tag	2/11	0.287330347557375	1	FACETS	0.398	0.346	0.455	0.398	0.346	0.455	SUBCLONAL	1	TRUE	0	0.321676154222228	1		914	904	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578529	7578529	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs780442292	NA	P-0037229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	294	1132	0	ENST00000269305.4:c.401T>G	p.Phe134Cys	p.F134C	ENST00000269305	NM_001126112.2	134	tTt/tGt	5/11	0.226826134032768	2	FACETS	0.818	0.77	0.868	0.818	0.77	0.868	CLONAL	2	TRUE	0	0.321676154222228	2		1132	1117	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991668	25991668	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	80	741	0	ENST00000435504.4:c.574C>A	p.Gln192Lys	p.Q192K	ENST00000435504		192	Cag/Aag	7/13	0.287330347557375	1	FACETS	0.519	0.456	0.587	0.519	0.456	0.587	SUBCLONAL	1	TRUE	0	0.321676154222228	1		741	804	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495650	72495650	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	36	445	0	ENST00000477973.2:c.422C>T	p.Thr141Ile	p.T141I	ENST00000477973	NM_012234.5	141	aCc/aTc	1/4	0.321676154222228	1	FACETS	0.404	0.332	0.485	0.404	0.332	0.485	SUBCLONAL	1	TRUE	0	0.321676154222228	1		445	465	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197339	26197339	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	35	525	0	ENST00000356476.2:c.140T>C	p.Val47Ala	p.V47A	ENST00000356476		47	gTg/gCg	1/1	0.273356417465248	3	FACETS	0.465	0.38	0.561	0.155	0.126	0.187	SUBCLONAL	1	TRUE	0	0.321676154222228	3		525	543	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518130	8518130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	224	641	1	ENST00000356435.5:c.1261C>A	p.Pro421Thr	p.P421T	ENST00000356435		421	Ccg/Acg	10/35	0.174563375584033	3	FACETS	1	0.974	1	0.72	0.673	0.769	INDETERMINATE	2	TRUE	0	0.321676154222228	3		642	748	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0037229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	306	732	2	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.174563375584033	3	FACETS	0.863	0.816	0.91	0.863	0.816	0.91	INDETERMINATE	3	TRUE	0	0.321676154222228	3		734	853	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0037230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	288	575	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.672259676587531	1	FACETS	0.672	0.641	0.702	0.672	0.641	0.702	SUBCLONAL	1	TRUE	0	0.941555302201935	1		575	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579316	7579317	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0037230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	439	584	1	ENST00000269305.4:c.369_370dup	p.Cys124PhefsTer47	p.C124Ffs*47	ENST00000269305	NM_001126112.2	124	tgc/tTTgc	4/11	0.941555302201935	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.941555302201935	1		585	492	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672477	30672477	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	403	868	0	ENST00000376406.3:c.4483G>C	p.Glu1495Gln	p.E1495Q	ENST00000376406	NM_014641.2	1495	Gag/Cag	10/15	1	2	FACETS	0.945	0.903	0.987	0.945	0.903	0.987	CLONAL	1	TRUE	1	0.941555302201935	2		868	906	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021770	69021770	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	234	607	0	ENST00000288368.4:c.3059del	p.Leu1020Ter	p.L1020*	ENST00000288368	NM_024870.2	1020	Tta/ta	25/40	1	2	FACETS	0.578	0.54	0.617	0.578	0.54	0.617	SUBCLONAL	1	TRUE	1	0.941555302201935	2		607	860	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28929495	NA	P-0037235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	123	530	0	ENST00000275493.2:c.2155G>T	p.Gly719Cys	p.G719C	ENST00000275493	NM_005228.3	719	Ggc/Tgc	18/28	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.28	2		530	778	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0037235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	110	332	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.28	2		332	552	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0037235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	175	305	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	0.29316635993667	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.28	2		305	534	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426931	70426931	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	61	362	0	ENST00000373644.4:c.4591G>T	p.Asp1531Tyr	p.D1531Y	ENST00000373644	NM_030625.2	1531	Gac/Tac	7/12	1	2	FACETS	0.824	0.711	0.946	0.824	0.711	0.946	CLONAL	1	TRUE	1	0.28	2		362	529	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252963	36252963	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	92	327	0	ENST00000300305.3:c.399G>T	p.Met133Ile	p.M133I	ENST00000300305		133	atG/atT	4/8	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.28	2		327	582	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259647	89259647	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	54	257	0	ENST00000336596.2:c.791A>T	p.Glu264Val	p.E264V	ENST00000336596	NM_005233.5	264	gAa/gTa	3/17	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.28	2		257	375	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629954	187629954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	138	567	1	ENST00000441802.2:c.1028C>T	p.Thr343Ile	p.T343I	ENST00000441802	NM_005245.3	343	aCt/aTt	2/27	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.28	2		568	826	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515579	31515579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1405504265	NA	P-0037235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	65	257	0	ENST00000344624.3:c.1040C>T	p.Pro347Leu	p.P347L	ENST00000344624		347	cCc/cTc	4/33	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.28	2		257	409	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040716	47040716	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	127	533	0	ENST00000377604.3:c.1351G>T	p.Glu451Ter	p.E451*	ENST00000377604	NM_001204468.1	451	Gag/Tag	13/24	0.296816604136582	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.28	1		533	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0037244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	349	749	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.468923261092446	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.468923261092446	2		749	727	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524543	176524543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	309	730	0	ENST00000292408.4:c.2275C>A	p.Leu759Met	p.L759M	ENST00000292408	NM_213647.1	759	Ctg/Atg	18/18	0.391971709786725	4	FACETS	0.937	0.885	0.991			1	CLONAL	2	TRUE	NA	0.468923261092446	4		730	1033	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699217	117699217	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	203	408	0	ENST00000369458.3:c.424A>G	p.Asn142Asp	p.N142D	ENST00000369458	NM_024626.3	142	Aac/Gac	3/6	0.238742461827656	3	FACETS	1	0.945	1	0.675	0.631	0.719	INDETERMINATE	2	TRUE	0	0.468923261092446	3		408	528	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319317	11319317	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	189	581	0	ENST00000361445.4:c.150G>T	p.Met50Ile	p.M50I	ENST00000361445	NM_004958.3	50	atG/atT	2/58	0.231796929553814	5	FACETS	0.92	0.853	0.99	0.614	0.568	0.66	INDETERMINATE	2	TRUE	2	0.468923261092446	5		581	746	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814550	43814550	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	812	362	0	ENST00000372470.3:c.1345C>G	p.Leu449Val	p.L449V	ENST00000372470	NM_005373.2	449	Ctg/Gtg	9/12	0.468923261092446	10	FACETS	0.987	0.96	1			1	CLONAL	7	TRUE	NA	0.468923261092446	10		362	1441	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112767302	112767302	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	112	519	0	ENST00000369452.4:c.1175C>T	p.Thr392Ile	p.T392I	ENST00000369452	NM_007373.3	392	aCa/aTa	6/9	0.28257171560385	4	FACETS	0.786	0.706	0.87	0.393	0.353	0.435	SUBCLONAL	1	TRUE	2	0.468923261092446	4		519	893	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108083	30108083	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	308	491	0	ENST00000331968.5:c.724G>A	p.Gly242Ser	p.G242S	ENST00000331968	NM_002742.2	242	Ggt/Agt	5/18	0.102348521689459	6	FACETS	1	0.986	1			1	INDETERMINATE	3	TRUE	NA	0.468923261092446	6		491	761	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81558909	81558909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	196	477	0	ENST00000298171.2:c.502C>A	p.Pro168Thr	p.P168T	ENST00000298171	NM_000369.2	168	Cct/Act	6/10	0.175270547813365	5	FACETS	1	0.98	1	0.568	0.528	0.608	INDETERMINATE	2	TRUE	1	0.468923261092446	5		477	627	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971220	15971220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	160	403	0	ENST00000268712.3:c.4729G>T	p.Ala1577Ser	p.A1577S	ENST00000268712	NM_006311.3	1577	Gct/Tct	32/46	0.228536259867562	5	FACETS	1	0.966	1	0.723	0.667	0.781	INDETERMINATE	2	TRUE	2	0.468923261092446	5		403	536	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78938122	78938122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	189	498	1	ENST00000306801.3:c.4000G>A	p.Val1334Ile	p.V1334I	ENST00000306801	NM_020761.2	1334	Gtc/Atc	34/34	0.18033033783522	4	FACETS	0.81	0.751	0.871	0.81	0.751	0.871	INDETERMINATE	2	TRUE	2	0.468923261092446	4		499	731	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917770	29917770	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	208	611	1	ENST00000389048.3:c.898C>A	p.Gln300Lys	p.Q300K	ENST00000389048	NM_004304.4	300	Cag/Aag	3/29	0.245736920349422	3	FACETS	0.808	0.753	0.864	0.808	0.753	0.864	INDETERMINATE	2	TRUE	1	0.468923261092446	3		612	678	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024392	31024392	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	360	588	1	ENST00000375687.4:c.3877G>T	p.Asp1293Tyr	p.D1293Y	ENST00000375687	NM_015338.5	1293	Gat/Tat	13/13	0.175270547813365	5	FACETS	1	0.982	1	0.795	0.758	0.833	INDETERMINATE	3	TRUE	1	0.468923261092446	5		589	822	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204075	142204075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	444	600	0	ENST00000350721.4:c.6128C>T	p.Ala2043Val	p.A2043V	ENST00000350721	NM_001184.3	2043	gCc/gTc	36/47	0.40398958402025	5	FACETS	0.972	0.93	1	0.972	0.93	1	CLONAL	3	TRUE	2	0.468923261092446	5		600	1106	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612166	189612166	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	413	528	0	ENST00000264731.3:c.1918G>C	p.Asp640His	p.D640H	ENST00000264731	NM_003722.4	640	Gat/Cat	14/14	0.40398958402025	5	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	2	0.468923261092446	5		528	946	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356171	66356171	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	269	615	0	ENST00000273854.3:c.1326G>T	p.Glu442Asp	p.E442D	ENST00000273854	NM_004439.5	442	gaG/gaT	5/18	0.175270547813365	5	FACETS	1	0.954	1	0.757	0.716	0.8	INDETERMINATE	3	TRUE	1	0.468923261092446	5		615	645	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143033817	143033817	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	159	398	0	ENST00000262992.4:c.2154G>T	p.Glu718Asp	p.E718D	ENST00000262992	NM_001101669.1	718	gaG/gaT	20/24	0.175270547813365	5	FACETS	1	0.964	1	0.538	0.496	0.581	INDETERMINATE	2	TRUE	1	0.468923261092446	5		398	537	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851950	128851950	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1289445585	NA	P-0037244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	258	596	0	ENST00000249373.3:c.2022G>C	p.Lys674Asn	p.K674N	ENST00000249373	NM_005631.4	674	aaG/aaC	12/12	0.418427544679029	4	FACETS	0.989	0.929	1	0.989	0.929	1	CLONAL	2	TRUE	2	0.468923261092446	4		596	817	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492882	8492882	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	142	549	0	ENST00000356435.5:c.2447T>C	p.Leu816Pro	p.L816P	ENST00000356435		816	cTg/cCg	16/35	0.468923261092446	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.468923261092446	1		549	454	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006896	47006896	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	83	605	0	ENST00000377604.3:c.16C>T	p.Arg6Cys	p.R6C	ENST00000377604	NM_001204468.1	6	Cgt/Tgt	2/24	0.468923261092446	1	FACETS	0.425	0.375	0.478	0.425	0.375	0.478	SUBCLONAL	1	TRUE	0	0.468923261092446	1		605	638	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347963	70347963	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	70	523	0	ENST00000374080.3:c.3202C>A	p.Pro1068Thr	p.P1068T	ENST00000374080		1068	Ccc/Acc	22/45	0.347324182302005	2	FACETS	0.468	0.408	0.533	0.234	0.204	0.267	SUBCLONAL	1	TRUE	0	0.468923261092446	2		523	638	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96930956	96931040	+	protein_altering_variant	In_Frame_Del	DEL	TGCAACCAGGCGGGCTCGGCGAGGGCAGTGCACAGCGCCGTGATAGACAGGGCGCCAGGCAGGGCCGAGGCCAGGCTACGCTCCG	TGCAACCAGGCGGGCTCGGCGAGGGCAGTGCACAGCGCCGTGATAGACAGGGCGCCAGGCAGGGCCGAGGCCAGGCTACGCTCCG	A	novel	NA	P-0037244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	146	560	0	ENST00000258439.3:c.80_164delinsT	p.Pro27_His55delinsLeu	p.P27_H55delinsL	ENST00000258439	NM_001193304.2	27	cCGGAGCGTAGCCTGGCCTCGGCCCTGCCTGGCGCCCTGTCTATCACGGCGCTGTGCACTGCCCTCGCCGAGCCCGCCTGGTTGCAc/cTc	2/4	0.245736920349422	3	FACETS	1	0.983	1	0.641	0.587	0.696	INDETERMINATE	1	TRUE	1	0.468923261092446	3		560	600	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0037258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	25	426	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.183693594454083	NA		426	277	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0037280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	162	354	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.531426909450928	2	FACETS	0.956	0.893	1	0.956	0.893	1	CLONAL	2	TRUE	0	0.531426909450928	2		354	319	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0037289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	143	251	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	1	2	FACETS	0.997	0.918	1	0.997	0.918	1	CLONAL	1	TRUE	1	0.686405799456244	2		251	418	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003746	45003746	+	start_lost	Translation_Start_Site	SNP	T	T	C	rs1057519879	NA	P-0037289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	307	583	0	ENST00000558401.1:c.2T>C	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	aTg/aCg	1/4	0.686405799456244	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.686405799456244	1		583	586	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0037289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	59	781	5	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	1	2	FACETS	0.162	0.139	0.188	0.162	0.139	0.188	SUBCLONAL	1	TRUE	1	0.686405799456244	2		786	1058	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713617	52713618	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0037289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	480	514	0	ENST00000394830.3:c.110_111del	p.Arg37ThrfsTer15	p.R37Tfs*15	ENST00000394830	NM_018313.4	37	aGA/a	2/30	0.640902823200137	2	FACETS	0.934	0.903	0.964	0.934	0.903	0.964	CLONAL	2	TRUE	0	0.686405799456244	2		514	749	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505112	149505112	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	288	697	0	ENST00000261799.4:c.1703T>A	p.Val568Glu	p.V568E	ENST00000261799	NM_002609.3	568	gTg/gAg	12/23	0.213809072752025	1	FACETS	0.68	0.642	0.718	0.68	0.642	0.718	INDETERMINATE	1	TRUE	0	0.686405799456244	1		697	811	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77043912	77043912	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	441	702	0	ENST00000356341.3:c.1414G>T	p.Ala472Ser	p.A472S	ENST00000356341	NM_002576.4	472	Gcc/Tcc	14/15	0.460234302544803	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.545368926718351	4		702	1153	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	213	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.460234302544803	4	FACETS	0.856	0.799	0.915	0.856	0.799	0.915	CLONAL	2	TRUE	2	0.545368926718351	4		452	705	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632402	3632402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750340019	NA	P-0037297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	324	1030	1	ENST00000294008.3:c.5446G>A	p.Glu1816Lys	p.E1816K	ENST00000294008	NM_032444.2	1816	Gag/Aag	15/15	0.530087637363598	3	FACETS	1	0.97	1	0.521	0.491	0.552	CLONAL	1	TRUE	1	0.545368926718351	3		1031	1450	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220703	1220704	+	missense_variant	Missense_Mutation	DNP	GC	GC	TA	novel	NA	P-0037297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	417	665	1	ENST00000326873.7:c.721_722delinsTA	p.Ala241Tyr	p.A241Y	ENST00000326873	NM_000455.4	241	GCt/TAt	5/10	0.545368926718351	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.545368926718351	2		666	729	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602637	10602644	+	frameshift_variant	Frame_Shift_Del	DEL	GTGGGCTT	GTGGGCTT	-	novel	NA	P-0037297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	487	792	1	ENST00000171111.5:c.934_941del	p.Lys312AlafsTer35	p.K312Afs*35	ENST00000171111	NM_203500.1	312	AAGCCCACg/g	3/6	0.545368926718351	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.545368926718351	2		793	852	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427675	72427675	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	365	550	0	ENST00000477973.2:c.815C>T	p.Ser272Phe	p.S272F	ENST00000477973	NM_012234.5	272	tCc/tTc	4/4	0.545368926718351	3	FACETS	0.996	0.949	1	0.996	0.949	1	CLONAL	2	TRUE	1	0.545368926718351	3		550	855	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0037299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	31	251	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	1	2	FACETS	0.348	0.28	0.424	0.348	0.28	0.424	SUBCLONAL	1	TRUE	1	0.307385869890532	2		251	580	SUCCESS
APC	324	MSKCC	GRCh37	5	112174784	112174784	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0037299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	27	311	0	ENST00000257430.4:c.3493A>T	p.Lys1165Ter	p.K1165*	ENST00000257430	NM_000038.5	1165	Aaa/Taa	16/16	1	2	FACETS	0.381	0.303	0.471	0.381	0.303	0.471	SUBCLONAL	1	TRUE	1	0.307385869890532	2		311	461	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139302	108139302	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3218708	NA	P-0037299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	50	836	1	ENST00000278616.4:c.2804C>T	p.Thr935Met	p.T935M	ENST00000278616	NM_000051.3	935	aCg/aTg	18/63	1	2	FACETS	0.365	0.309	0.428	0.365	0.309	0.428	SUBCLONAL	1	TRUE	1	0.307385869890532	2		837	891	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214046	36214046	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	65	901	2	ENST00000222270.7:c.2872G>A	p.Gly958Ser	p.G958S	ENST00000222270	NM_014727.1	958	Ggc/Agc	6/37	1	2	FACETS	0.459	0.396	0.527	0.459	0.396	0.527	SUBCLONAL	1	TRUE	1	0.307385869890532	2		903	922	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263340	115263340	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0037299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	47	697	0	ENST00000438362.2:c.2012-2A>C		p.X671_splice	ENST00000438362	NM_001242891.1	671			1	2	FACETS	0.39	0.328	0.459	0.39	0.328	0.459	SUBCLONAL	1	TRUE	1	0.307385869890532	2		697	784	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119734	70119734	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	46	723	1	ENST00000245479.2:c.736C>T	p.Gln246Ter	p.Q246*	ENST00000245479	NM_000346.3	246	Cag/Tag	3/3	1	2	FACETS	0.399	0.334	0.47	0.399	0.334	0.47	SUBCLONAL	1	TRUE	1	0.307385869890532	2		724	751	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259278	89259278	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	49	604	1	ENST00000336596.2:c.422C>A	p.Thr141Lys	p.T141K	ENST00000336596	NM_005233.5	141	aCa/aAa	3/17	1	2	FACETS	0.47	0.397	0.551	0.47	0.397	0.551	SUBCLONAL	1	TRUE	1	0.307385869890532	2		605	678	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0037313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	187	566	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.898	0.832	0.968	0.898	0.832	0.968	CLONAL	1	TRUE	1	0.526274670446431	2		566	791	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0037313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	68	673	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.526274670446431	2		673	247	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0037313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	92	236	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.526274670446431	2		236	320	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0037313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	104	309	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.526274670446431	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	0	0.526274670446431	1		309	291	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955063	55955063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	111	360	0	ENST00000263923.4:c.3482G>A	p.Gly1161Glu	p.G1161E	ENST00000263923	NM_002253.2	1161	gGa/gAa	26/30	1	2	FACETS	0.803	0.725	0.886	0.803	0.725	0.886	CLONAL	1	TRUE	1	0.526274670446431	2		360	525	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612184	189612184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	130	478	0	ENST00000264731.3:c.1936C>T	p.Leu646Phe	p.L646F	ENST00000264731	NM_003722.4	646	Ctc/Ttc	14/14	1	2	FACETS	0.873	0.795	0.954	0.873	0.795	0.954	CLONAL	1	TRUE	1	0.526274670446431	2		478	566	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939479	68939479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778971988	NA	P-0037313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	230	330	0	ENST00000288368.4:c.464G>A	p.Arg155Gln	p.R155Q	ENST00000288368	NM_024870.2	155	cGg/cAg	5/40	0.491621267200653	3	FACETS	0.947	0.89	1	0.947	0.89	1	CLONAL	2	TRUE	1	0.526274670446431	3		330	583	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197079	26197079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	118	299	0	ENST00000356476.2:c.400G>A	p.Glu134Lys	p.E134K	ENST00000356476		134	Gag/Aag	1/1	0.526274670446431	4	FACETS	0.996	0.9	1	0.332	0.3	0.366	CLONAL	1	TRUE	1	0.526274670446431	4		299	687	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821823	72821823	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	129	465	1	ENST00000268489.5:c.10352C>T	p.Ser3451Phe	p.S3451F	ENST00000268489	NM_006885.3	3451	tCc/tTc	10/10	1	2	FACETS	0.857	0.78	0.937	0.857	0.78	0.937	CLONAL	1	TRUE	1	0.526274670446431	2		466	572	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546653	9546653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	128	421	0	ENST00000353224.5:c.1369G>A	p.Glu457Lys	p.E457K	ENST00000353224	NM_177990.2	457	Gaa/Aaa	5/10	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.526274670446431	2		421	470	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102094470	102094470	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	144	340	0	ENST00000282441.5:c.1150C>T	p.Pro384Ser	p.P384S	ENST00000282441	NM_001130145.2	384	Cct/Tct	7/9	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.526274670446431	2		340	479	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374366	118374366	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	99	305	0	ENST00000534358.1:c.7759C>T	p.Gln2587Ter	p.Q2587*	ENST00000534358	NM_005933.3	2587	Caa/Taa	27/36	1	2	FACETS	0.936	0.842	1	0.936	0.842	1	CLONAL	1	TRUE	1	0.526274670446431	2		305	402	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571547	95571547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	132	334	0	ENST00000393063.1:c.3130C>T	p.Pro1044Ser	p.P1044S	ENST00000393063	NM_030621.3	1044	Cca/Tca	21/28	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.526274670446431	2		334	477	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032062	10032062	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	138	533	0	ENST00000330684.3:c.761T>A	p.Phe254Tyr	p.F254Y	ENST00000330684	NM_001134407.1	254	tTc/tAc	3/13	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.526274670446431	2		533	500	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822507	72822507	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	157	580	0	ENST00000268489.5:c.9668A>G	p.Gln3223Arg	p.Q3223R	ENST00000268489	NM_006885.3	3223	cAg/cGg	10/10	1	2	FACETS	0.876	0.805	0.95	0.876	0.805	0.95	CLONAL	1	TRUE	1	0.526274670446431	2		580	681	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515295	149515295	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	127	501	0	ENST00000261799.4:c.187G>A	p.Glu63Lys	p.E63K	ENST00000261799	NM_002609.3	63	Gaa/Aaa	3/23	1	2	FACETS	0.899	0.818	0.983	0.899	0.818	0.983	CLONAL	1	TRUE	1	0.526274670446431	2		501	537	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0037322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	136	369	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.365407521367734	2		369	502	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588933	67588933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	27	204	0	ENST00000274335.5:c.1024G>A	p.Glu342Lys	p.E342K	ENST00000274335		342	Gaa/Aaa	8/15	0.263418854927818	4	FACETS	0.593	0.472	0.732	0.297	0.236	0.366	SUBCLONAL	1	TRUE	2	0.365407521367734	4		204	340	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39537699	39537699	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	62	316	0	ENST00000262039.4:c.233A>G	p.Tyr78Cys	p.Y78C	ENST00000262039	NM_002647.2	78	tAc/tGc	2/25	1	2	FACETS	0.922	0.801	1	0.922	0.801	1	CLONAL	1	TRUE	1	0.365407521367734	2		316	368	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151932982	151932982	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs772146328	NA	P-0037322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	17	34	0	ENST00000262189.6:c.2689C>T	p.Arg897Ter	p.R897*	ENST00000262189	NM_170606.2	897	Cga/Tga	16/59	0.117092154157691	3	FACETS	0.902	0.695	1	0.902	0.695	1	INDETERMINATE	2	TRUE	1	0.365407521367734	3		34	61	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918769	32918769	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs730881550	NA	P-0037322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	28	179	0	ENST00000380152.3:c.6916G>T	p.Ala2306Ser	p.A2306S	ENST00000380152		2306	Gct/Tct	12/27	1	2	FACETS	0.655	0.526	0.8	0.655	0.526	0.8	SUBCLONAL	1	TRUE	1	0.365407521367734	2		179	234	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138677	55138677	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	86	374	0	ENST00000257290.5:c.1354G>C	p.Asp452His	p.D452H	ENST00000257290	NM_006206.4	452	Gat/Cat	9/23	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.365407521367734	2		374	402	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243778453	243778453	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	36	336	0	ENST00000263826.5:c.572C>G	p.Ala191Gly	p.A191G	ENST00000263826	NM_005465.4	191	gCa/gGa	6/13	0.355921434840331	3	FACETS	0.646	0.531	0.773	0.323	0.265	0.387	SUBCLONAL	1	TRUE	1	0.365407521367734	3		336	361	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200626	67200626	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	210	607	0	ENST00000312629.5:c.737A>T	p.His246Leu	p.H246L	ENST00000312629	NM_003952.2	246	cAc/cTc	9/15	0.117092154157691	3	FACETS	0.845	0.787	0.906	0.845	0.787	0.906	INDETERMINATE	2	TRUE	1	0.365407521367734	3		607	804	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589847	69589848	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0037322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	10	21	0	ENST00000168712.1:c.5_6delinsTT	p.Ser2Phe	p.S2F	ENST00000168712	NM_002007.2	2	tCG/tTT	1/3	0.117092154157691	3	FACETS	1	0.799	1	1	0.799	1	INDETERMINATE	2	TRUE	1	0.365407521367734	3		21	28	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911310	32911310	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs80358532	NA	P-0037322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	70	395	0	ENST00000380152.3:c.2818C>T	p.Gln940Ter	p.Q940*	ENST00000380152		940	Caa/Taa	11/27	1	2	FACETS	0.923	0.808	1	0.923	0.808	1	CLONAL	1	TRUE	1	0.365407521367734	2		395	415	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038693	14038693	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587777943	NA	P-0037322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	52	249	0	ENST00000311895.7:c.2017+1G>A		p.X673_splice	ENST00000311895	NM_005236.2	673			1	2	FACETS	0.924	0.792	1	0.924	0.792	1	CLONAL	1	TRUE	1	0.365407521367734	2		249	308	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993425	72993425	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	310	705	0	ENST00000268489.5:c.620G>C	p.Trp207Ser	p.W207S	ENST00000268489	NM_006885.3	207	tGg/tCg	2/10	0.365407521367734	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.365407521367734	2		705	836	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40872297	40872297	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1296856855	NA	P-0037322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	168	577	0	ENST00000428826.2:c.658A>G	p.Ile220Val	p.I220V	ENST00000428826		220	Att/Gtt	7/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.365407521367734	2		577	875	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288979	212288979	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	77	486	0	ENST00000342788.4:c.2767G>C	p.Gly923Arg	p.G923R	ENST00000342788	NM_005235.2	923	Gga/Cga	23/28	1	2	FACETS	0.937	0.825	1	0.937	0.825	1	CLONAL	1	TRUE	1	0.365407521367734	2		486	450	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023963	31023963	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	209	534	0	ENST00000375687.4:c.3448G>T	p.Gly1150Ter	p.G1150*	ENST00000375687	NM_015338.5	1150	Gga/Tga	13/13	0.25224304566964	3	FACETS	0.98	0.914	1	0.98	0.914	1	CLONAL	2	TRUE	1	0.365407521367734	3		534	690	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568585	41568599	+	protein_altering_variant	In_Frame_Del	DEL	TTCTGGAAGAAAGCA	TTCTGGAAGAAAGCA	CTC	novel	NA	P-0037322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	56	448	1	ENST00000263253.7:c.4535_4549delinsCTC	p.Val1512_Ile1517delinsAlaLeu	p.V1512_I1517delinsAL	ENST00000263253	NM_001429.3	1512	gTTCTGGAAGAAAGCAtt/gCTCtt	28/31	1	2	FACETS	0.563	0.483	0.652	0.563	0.483	0.652	SUBCLONAL	1	TRUE	1	0.365407521367734	2		449	544	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499412	89499412	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	67	385	0	ENST00000336596.2:c.2582G>A	p.Trp861Ter	p.W861*	ENST00000336596	NM_005233.5	861	tGg/tAg	15/17	1	2	FACETS	0.725	0.631	0.826	0.725	0.631	0.826	SUBCLONAL	1	TRUE	1	0.365407521367734	2		385	506	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499420	89499420	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	71	411	0	ENST00000336596.2:c.2590G>A	p.Asp864Asn	p.D864N	ENST00000336596	NM_005233.5	864	Gac/Aac	15/17	1	2	FACETS	0.747	0.653	0.848	0.747	0.653	0.848	SUBCLONAL	1	TRUE	1	0.365407521367734	2		411	520	SUCCESS
ATR	545	MSKCC	GRCh37	3	142241641	142241641	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	24	448	0	ENST00000350721.4:c.4195G>T	p.Glu1399Ter	p.E1399*	ENST00000350721	NM_001184.3	1399	Gag/Tag	23/47	1	2	FACETS	0.3	0.234	0.376	0.3	0.234	0.376	SUBCLONAL	1	TRUE	1	0.365407521367734	2		448	438	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217175	66217175	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	94	387	0	ENST00000273854.3:c.2440T>G	p.Cys814Gly	p.C814G	ENST00000273854	NM_004439.5	814	Tgc/Ggc	14/18	1	2	FACETS	0.895	0.798	0.998	0.895	0.798	0.998	CLONAL	1	TRUE	1	0.365407521367734	2		387	575	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138389	37138389	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	112	392	0	ENST00000373509.5:c.38G>T	p.Arg13Leu	p.R13L	ENST00000373509	NM_002648.3	13	cGc/cTc	1/6	0.25381382476392	4	FACETS	1	0.966	1	0.389	0.35	0.43	CLONAL	1	TRUE	1	0.365407521367734	4		392	717	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978652	70978652	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	139	600	0	ENST00000276594.2:c.1001C>A	p.Pro334His	p.P334H	ENST00000276594	NM_024504.3	334	cCc/cAc	5/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.365407521367734	2		600	708	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570247	87570247	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	72	330	0	ENST00000277120.3:c.1987G>T	p.Glu663Ter	p.E663*	ENST00000277120		663	Gaa/Taa	17/19	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.365407521367734	2		330	374	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209628	98209628	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	84	470	0	ENST00000331920.6:c.3910A>T	p.Arg1304Trp	p.R1304W	ENST00000331920	NM_000264.3	1304	Agg/Tgg	23/24	1	2	FACETS	0.907	0.803	1	0.907	0.803	1	CLONAL	1	TRUE	1	0.365407521367734	2		470	507	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248205	110248205	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	66	320	0	ENST00000374672.4:c.1267G>T	p.Glu423Ter	p.E423*	ENST00000374672	NM_004235.4	423	Gag/Tag	5/5	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.365407521367734	2		320	323	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357595	70357608	+	frameshift_variant	Frame_Shift_Del	DEL	CTCATGTGGGATTG	CTCATGTGGGATTG	-	novel	NA	P-0037322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	56	717	0	ENST00000374080.3:c.5847_5860del	p.His1950AlafsTer96	p.H1950Afs*96	ENST00000374080		1949	tCTCATGTGGGATTG/t	41/45	0.365407521367734	1	FACETS	0.374	0.32	0.433	0.374	0.32	0.433	SUBCLONAL	1	TRUE	0	0.365407521367734	1		717	670	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0037336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	324	566	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.99	0.941	1	0.99	0.941	1	CLONAL	1	TRUE	1	0.872546766029244	2		566	750	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0037336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	309	673	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.872546766029244	2		673	632	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	295	534	0	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	1	2	FACETS	0.958	0.907	1	0.958	0.907	1	CLONAL	1	TRUE	1	0.872546766029244	2		534	706	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875645	35875645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201449880	NA	P-0037336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	174	358	0	ENST00000303115.3:c.832G>A	p.Asp278Asn	p.D278N	ENST00000303115	NM_002185.3	278	Gat/Aat	7/8	1	2	FACETS	0.915	0.851	0.979	0.915	0.851	0.979	CLONAL	1	TRUE	1	0.872546766029244	2		358	436	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101031	4101031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375843855	NA	P-0037336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	230	496	0	ENST00000262948.5:c.691C>T	p.Arg231Cys	p.R231C	ENST00000262948	NM_030662.3	231	Cgc/Tgc	6/11	1	2	FACETS	0.873	0.819	0.927	0.873	0.819	0.927	CLONAL	1	TRUE	1	0.872546766029244	2		496	604	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729162	66729162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519732	NA	P-0037336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	348	654	1	ENST00000307102.5:c.370C>T	p.Pro124Ser	p.P124S	ENST00000307102	NM_002755.3	124	Ccg/Tcg	3/11	1	2	FACETS	0.899	0.855	0.944	0.899	0.855	0.944	CLONAL	1	TRUE	1	0.872546766029244	2		655	887	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245450	153245450	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	244	635	1	ENST00000281708.4:c.1741C>T	p.Gln581Ter	p.Q581*	ENST00000281708	NM_033632.3	581	Cag/Tag	11/12	1	2	FACETS	0.86	0.809	0.913	0.86	0.809	0.913	CLONAL	1	TRUE	1	0.872546766029244	2		636	650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578541	7578541	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	352	840	0	ENST00000269305.4:c.389T>G	p.Leu130Arg	p.L130R	ENST00000269305	NM_001126112.2	130	cTc/cGc	5/11	0.553892039796243	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.553892039796243	2		840	595	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221084	5221084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371881792	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	63	653	2	ENST00000357368.4:c.3382G>A	p.Val1128Ile	p.V1128I	ENST00000357368	NM_002850.3	1128	Gtc/Atc	20/38	0.553892039796243	2	FACETS	0.533	0.462	0.609	0.266	0.231	0.305	SUBCLONAL	1	TRUE	0	0.553892039796243	2		655	427	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115443	115115443	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	264	649	0	ENST00000257566.3:c.883G>A	p.Asp295Asn	p.D295N	ENST00000257566	NM_016569.3	295	Gac/Aac	5/8	0.496627986928987	3	FACETS	0.944	0.891	0.997	0.944	0.891	0.997	CLONAL	2	TRUE	1	0.553892039796243	3		649	645	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730919	40730919	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	192	490	1	ENST00000373198.4:c.3616C>T	p.Pro1206Ser	p.P1206S	ENST00000373198	NM_133170.3	1206	Ccc/Tcc	27/32	0.553892039796243	4	FACETS	1	0.99	1			1	CLONAL	1	TRUE	NA	0.553892039796243	4		491	733	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142942	30142942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1442742511	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	153	784	1	ENST00000389048.3:c.584C>T	p.Ala195Val	p.A195V	ENST00000389048	NM_004304.4	195	gCg/gTg	1/29	0.170019006910037	3	FACETS	1	0.949	1			1	INDETERMINATE	1	TRUE	NA	0.553892039796243	3		785	674	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933824	36933824	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	111	538	0	ENST00000361632.4:c.1577-2A>T		p.X526_splice	ENST00000361632		526			0.553892039796243	3	FACETS	0.904	0.815	0.998	0.452	0.407	0.499	CLONAL	1	TRUE	1	0.553892039796243	3		538	566	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18439800	18439800	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	196	350	0	ENST00000266497.5:c.698A>T	p.Gln233Leu	p.Q233L	ENST00000266497		233	cAg/cTg	2/31	0.521327446210159	4	FACETS	0.94	0.876	1	0.94	0.876	1	CLONAL	2	TRUE	2	0.553892039796243	4		350	585	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433955	49433955	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	229	730	0	ENST00000301067.7:c.7598C>G	p.Pro2533Arg	p.P2533R	ENST00000301067	NM_003482.3	2533	cCc/cGc	31/54	0.521327446210159	4	FACETS	0.938	0.878	0.999	0.938	0.878	0.999	CLONAL	2	TRUE	2	0.553892039796243	4		730	685	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118767	115118767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768160499	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	251	632	0	ENST00000257566.3:c.574G>A	p.Ala192Thr	p.A192T	ENST00000257566	NM_016569.3	192	Gct/Act	2/8	0.496627986928987	3	FACETS	0.991	0.935	1	0.991	0.935	1	CLONAL	2	TRUE	1	0.553892039796243	3		632	584	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118925	115118925	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	77	309	0	ENST00000257566.3:c.416G>C	p.Arg139Thr	p.R139T	ENST00000257566	NM_016569.3	139	aGa/aCa	2/8	0.496627986928987	3	FACETS	1	0.894	1	0.506	0.447	0.568	CLONAL	1	TRUE	1	0.553892039796243	3		309	351	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422071	81422071	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	417	429	0	ENST00000298171.2:c.47C>A	p.Pro16His	p.P16H	ENST00000298171	NM_000369.2	16	cCc/cAc	1/10	0.553892039796243	5	FACETS	0.954	0.924	0.983	1	0.995	1	CLONAL	5	TRUE	1	0.553892039796243	5		429	578	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961517	41961517	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	238	683	0	ENST00000219905.7:c.425G>T	p.Trp142Leu	p.W142L	ENST00000219905	NM_001164273.1	142	tGg/tTg	2/24	0.299802352211144	4	FACETS	0.935	0.877	0.994	0.935	0.877	0.994	INDETERMINATE	2	TRUE	2	0.553892039796243	4		683	714	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245112	41245112	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	405	823	0	ENST00000357654.3:c.2436G>T	p.Lys812Asn	p.K812N	ENST00000357654	NM_007294.3	812	aaG/aaT	10/23	0.464666183605301	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.553892039796243	4		823	1093	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745856	745945	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCTGGGTGAAAAATAAATACTTTCACTATATCTTTCTCAAAATACTGCCCCAAGAAATTTTATACTTATACTAATATAACAATATTCAT	ACCTGGGTGAAAAATAAATACTTTCACTATATCTTTCTCAAAATACTGCCCCAAGAAATTTTATACTTATACTAATATAACAATATTCAT	-	novel	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	76	525	0	ENST00000314574.4:c.574+3_576del		p.X192_splice	ENST00000314574	NM_005433.3	192		6/12	0.553892039796243	6	FACETS	0.533	0.466	0.605			1	SUBCLONAL	1	TRUE	NA	0.553892039796243	6		525	1086	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134261	11134262	+	missense_variant	Missense_Mutation	DNP	TG	TG	CT	novel	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	338	566	1	ENST00000358026.2:c.2927_2928delinsCT	p.Leu976Ser	p.L976S	ENST00000358026	NM_001128849.1	976	tTG/tCT	20/36	0.553892039796243	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	0	0.553892039796243	3		567	510	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298045	15298045	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	487	909	1	ENST00000263388.2:c.1711G>T	p.Ala571Ser	p.A571S	ENST00000263388	NM_000435.2	571	Gct/Tct	11/33	0.553892039796243	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	0	0.553892039796243	3		910	728	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463508	25463509	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	78	466	2	ENST00000264709.3:c.2173_2173+1delinsTT		p.X725_splice	ENST00000264709	NM_175629.2	725		18/23	0.553892039796243	3	FACETS	0.814	0.718	0.916	0.407	0.359	0.458	CLONAL	1	TRUE	1	0.553892039796243	3		468	442	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972641	25972641	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	224	482	0	ENST00000435504.4:c.1784A>T	p.Gln595Leu	p.Q595L	ENST00000435504		595	cAg/cTg	12/13	0.553892039796243	3	FACETS	0.911	0.855	0.967	0.911	0.855	0.967	CLONAL	2	TRUE	1	0.553892039796243	3		482	567	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866303	42866303	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	63	562	0	ENST00000398585.3:c.329C>T	p.Ser110Phe	p.S110F	ENST00000398585	NM_001135099.1	110	tCc/tTc	3/14	0.521327446210159	4	FACETS	0.481	0.415	0.553	0.24	0.207	0.277	SUBCLONAL	1	TRUE	2	0.553892039796243	4		562	735	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175889	24176325	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTACCCCTGGCCCTGTGGTCCTGGGCTCTGCCCACAGGCACCTGGCTTTCCAGGCAGAGGCAGGGCCATTGCCTTTCCCAGTCTCCCATGGTCTCTGAGACAGAGTACCTCTAGTGCTGCTAGAGGCAGGCAGGCTTCTGGGTGATAAGGCCCCATCCAAACGCCAGGGTATGTTTCCCTGCATGGAACAAACATAATTCCTCAGGCTGAGGGTCTGACCACAGCCCAGATCCAGGTTTTGGGGTCCCTGGAGTGATGAGCAGGGCCTGAGTGGCAGACAGGCGAGGCTGAGAGAAGGCTGGGTCTGACCCTGCTGGGGGCCCACATCCTGCCTCTGTTCCCACCCCTACACTTGGCTGCCCTGTAGAGCCTTGGGAAGGGCAGCGCCCAGGCTGGGAGCTGGCCCCGACTCATTGCCCTCCCCACTCCTCTTCC	AGGTACCCCTGGCCCTGTGGTCCTGGGCTCTGCCCACAGGCACCTGGCTTTCCAGGCAGAGGCAGGGCCATTGCCTTTCCCAGTCTCCCATGGTCTCTGAGACAGAGTACCTCTAGTGCTGCTAGAGGCAGGCAGGCTTCTGGGTGATAAGGCCCCATCCAAACGCCAGGGTATGTTTCCCTGCATGGAACAAACATAATTCCTCAGGCTGAGGGTCTGACCACAGCCCAGATCCAGGTTTTGGGGTCCCTGGAGTGATGAGCAGGGCCTGAGTGGCAGACAGGCGAGGCTGAGAGAAGGCTGGGTCTGACCCTGCTGGGGGCCCACATCCTGCCTCTGTTCCCACCCCTACACTTGGCTGCCCTGTAGAGCCTTGGGAAGGGCAGCGCCCAGGCTGGGAGCTGGCCCCGACTCATTGCCCTCCCCACTCCTCTTCC	-	novel	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	126	388	0	ENST00000263121.7:c.1118+2_1119del		p.X373_splice	ENST00000263121	NM_003073.3	373		8/9	0.553892039796243	3	FACETS	1	0.971	1	0.58	0.528	0.634	CLONAL	1	TRUE	1	0.553892039796243	3		388	501	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41521941	41521941	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	272	579	0	ENST00000263253.7:c.803G>T	p.Ser268Ile	p.S268I	ENST00000263253	NM_001429.3	268	aGt/aTt	3/31	0.553892039796243	4	FACETS	0.934	0.88	0.989			1	CLONAL	2	TRUE	NA	0.553892039796243	4		579	817	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670852	134670852	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	167	378	0	ENST00000398015.3:c.763T>A	p.Cys255Ser	p.C255S	ENST00000398015	NM_004441.4	255	Tgc/Agc	3/16	0.386197029176936	4	FACETS	0.984	0.912	1	0.984	0.912	1	CLONAL	2	TRUE	2	0.553892039796243	4		378	476	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549739	187549739	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	216	455	0	ENST00000441802.2:c.4502G>T	p.Ser1501Ile	p.S1501I	ENST00000441802	NM_005245.3	1501	aGt/aTt	8/27	0.553892039796243	3	FACETS	0.971	0.911	1	0.971	0.911	1	CLONAL	2	TRUE	1	0.553892039796243	3		455	513	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629371	187629371	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	153	662	0	ENST00000441802.2:c.1611G>T	p.Arg537Ser	p.R537S	ENST00000441802	NM_005245.3	537	agG/agT	2/27	0.553892039796243	3	FACETS	0.887	0.813	0.965	0.444	0.406	0.483	CLONAL	1	TRUE	1	0.553892039796243	3		662	795	SUCCESS
APC	324	MSKCC	GRCh37	5	112170733	112170733	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs756090401	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	366	601	0	ENST00000257430.4:c.1829A>G	p.Asp610Gly	p.D610G	ENST00000257430	NM_000038.5	610	gAt/gGt	15/16	0.54580105944612	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.553892039796243	2		601	615	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512494	149512494	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs41287112	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	148	347	0	ENST00000261799.4:c.946G>T	p.Val316Leu	p.V316L	ENST00000261799	NM_002609.3	316	Gtg/Ttg	7/23	0.553892039796243	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.553892039796243	2		347	262	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058749	180058749	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	248	651	0	ENST00000261937.6:c.88C>A	p.Pro30Thr	p.P30T	ENST00000261937	NM_182925.4	30	Ccg/Acg	2/30	0.553892039796243	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.553892039796243	2		651	417	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679980	30679980	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	222	537	0	ENST00000376406.3:c.1739A>G	p.Asp580Gly	p.D580G	ENST00000376406	NM_014641.2	580	gAt/gGt	5/15	0.464666183605301	4	FACETS	0.942	0.882	1	0.942	0.882	1	CLONAL	2	TRUE	2	0.553892039796243	4		537	661	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680438	30680438	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	263	604	1	ENST00000376406.3:c.1281G>T	p.Trp427Cys	p.W427C	ENST00000376406	NM_014641.2	427	tgG/tgT	5/15	0.464666183605301	4	FACETS	0.957	0.901	1	0.957	0.901	1	CLONAL	2	TRUE	2	0.553892039796243	4		605	771	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55231508	55231508	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	139	479	0	ENST00000275493.2:c.1714A>G	p.Thr572Ala	p.T572A	ENST00000275493	NM_005228.3	572	Aca/Gca	14/28	0.553892039796243	3	FACETS	1	0.98	1	0.621	0.569	0.675	CLONAL	1	TRUE	1	0.553892039796243	3		479	516	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248993	55248993	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	225	520	0	ENST00000275493.2:c.2291A>T	p.Tyr764Phe	p.Y764F	ENST00000275493	NM_005228.3	764	tAc/tTc	20/28	0.553892039796243	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.553892039796243	3		520	467	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392150	81392150	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	196	363	0	ENST00000222390.5:c.127A>T	p.Lys43Ter	p.K43*	ENST00000222390	NM_000601.4	43	Aaa/Taa	2/18	0.553892039796243	3	FACETS	0.974	0.911	1	0.974	0.911	1	CLONAL	2	TRUE	1	0.553892039796243	3		363	464	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372148	55372148	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	381	596	0	ENST00000297316.4:c.838G>T	p.Gly280Cys	p.G280C	ENST00000297316	NM_022454.3	280	Ggt/Tgt	2/2	0.553892039796243	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	1	0.553892039796243	4		596	629	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942864	68942864	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	509	569	0	ENST00000288368.4:c.676G>C	p.Glu226Gln	p.E226Q	ENST00000288368	NM_024870.2	226	Gaa/Caa	6/40	0.553892039796243	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	1	0.553892039796243	4		569	850	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989636	68989636	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	104	479	0	ENST00000288368.4:c.1574A>T	p.Asp525Val	p.D525V	ENST00000288368	NM_024870.2	525	gAt/gTt	15/40	0.553892039796243	4	FACETS	0.771	0.69	0.856	0.257	0.23	0.286	SUBCLONAL	1	TRUE	1	0.553892039796243	4		479	757	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949988	44949988	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	121	201	0	ENST00000377967.4:c.3757G>T	p.Val1253Leu	p.V1253L	ENST00000377967	NM_021140.2	1253	Gtg/Ttg	26/29	0.170019006910037	2	FACETS	0.993	0.921	1			1	INDETERMINATE	2	TRUE	NA	0.553892039796243	2		201	220	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340819	70340819	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0037338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	181	214	0	ENST00000374080.3:c.554-2A>G		p.X185_splice	ENST00000374080		185			0.456694584702358	2	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.553892039796243	2		214	264	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572161	64572161	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	206	682	1	ENST00000312049.6:c.1478del	p.Pro493ArgfsTer66	p.P493Rfs*66	ENST00000312049	NM_130799.2	493	cCg/cg	10/10	0.783396172376277	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.783396172376277	1		683	318	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226066	53226066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556837402	NA	P-0037352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	258	874	0	ENST00000375401.3:c.2783C>T	p.Ala928Val	p.A928V	ENST00000375401	NM_004187.3	928	gCg/gTg	19/26	0.535796791391434	1	FACETS	0.844	0.801	0.886	0.844	0.801	0.886	CLONAL	1	TRUE	0	0.783396172376277	1		874	475	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210482	5210482	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs147647579	NA	P-0037352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	160	573	0	ENST00000357368.4:c.5485C>T	p.Arg1829Trp	p.R1829W	ENST00000357368	NM_002850.3	1829	Cgg/Tgg	35/38	0.314575466578378	1	FACETS	0.645	0.599	0.692	0.645	0.599	0.692	INDETERMINATE	1	TRUE	0	0.783396172376277	1		573	385	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602754	10602754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	301	893	0	ENST00000171111.5:c.824C>T	p.Ser275Leu	p.S275L	ENST00000171111	NM_203500.1	275	tCg/tTg	3/6	0.314575466578378	1	FACETS	0.724	0.687	0.76	0.724	0.687	0.76	INDETERMINATE	1	TRUE	0	0.783396172376277	1		893	646	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609105	43609105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1228204486	NA	P-0037352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	113	746	0	ENST00000355710.3:c.1861G>A	p.Glu621Lys	p.E621K	ENST00000355710	NM_020975.4	621	Gag/Aag	10/20	0.783396172376277	1	FACETS	0.537	0.489	0.586	0.537	0.489	0.586	SUBCLONAL	1	TRUE	0	0.783396172376277	1		746	327	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259043	16259043	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	81	481	1	ENST00000375759.3:c.6313del	p.Ala2105LeufsTer33	p.A2105Lfs*33	ENST00000375759	NM_015001.2	2103	aGg/ag	11/15	0.783396172376277	2	FACETS	0.525	0.465	0.588	0.262	0.232	0.294	SUBCLONAL	1	TRUE	0	0.783396172376277	2		482	394	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020751	37020751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	98	531	0	ENST00000358127.4:c.94C>T	p.Pro32Ser	p.P32S	ENST00000358127	NM_001280556.1	32	Cca/Tca	2/10	0.453782201767016	1	FACETS	0.399	0.359	0.442	0.399	0.359	0.442	INDETERMINATE	1	TRUE	0	0.783396172376277	1		531	381	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61709534	61709534	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	177	374	0	ENST00000401558.2:c.2953G>A	p.Ala985Thr	p.A985T	ENST00000401558	NM_003400.3	985	Gcc/Acc	23/25	0.783396172376277	1	FACETS	0.958	0.904	1	0.958	0.904	1	CLONAL	1	TRUE	0	0.783396172376277	1		374	287	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651978	36651979	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0037352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	257	717	0	ENST00000244741.5:c.102_103del	p.Cys34Ter	p.C34*	ENST00000244741	NM_000389.4	34	TGt/t	2/3	0.783396172376277	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.783396172376277	1		717	368	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106093	8106093	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	65	426	0	ENST00000346208.3:c.913C>T	p.Arg305Ter	p.R305*	ENST00000346208		305	Cga/Tga	4/6	0.783396172376277	1	FACETS	0.47	0.413	0.529	0.47	0.413	0.529	SUBCLONAL	1	TRUE	0	0.783396172376277	1		426	215	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118391539	118391539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782283493	NA	P-0037352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	165	394	1	ENST00000534358.1:c.11452C>T	p.Pro3818Ser	p.P3818S	ENST00000534358	NM_005933.3	3818	Cca/Tca	34/36	0.783396172376277	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.783396172376277	1		395	234	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18649065	18649065	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	81	456	1	ENST00000266497.5:c.2744del	p.Asn915ThrfsTer24	p.N915Tfs*24	ENST00000266497		914	Aaa/aa	19/31	0.383426293040377	1	FACETS	0.304	0.269	0.341	0.304	0.269	0.341	INDETERMINATE	1	TRUE	0	0.783396172376277	1		457	414	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715638	18715638	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs752088371	NA	P-0037352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	54	281	0	ENST00000266497.5:c.3469A>G	p.Lys1157Glu	p.K1157E	ENST00000266497		1157	Aaa/Gaa	25/31	0.383426293040377	1	FACETS	0.385	0.332	0.44	0.385	0.332	0.44	INDETERMINATE	1	TRUE	0	0.783396172376277	1		281	218	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246297	46246297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770601353	NA	P-0037352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	171	396	0	ENST00000334344.6:c.4391G>A	p.Arg1464His	p.R1464H	ENST00000334344	NM_152641.2	1464	cGc/cAc	15/21	1	2	FACETS	0.999	0.929	1	0.999	0.929	1	CLONAL	1	TRUE	1	0.783396172376277	2		396	437	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435914	110435914	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	95	726	1	ENST00000375856.3:c.2487del	p.Val830TrpfsTer36	p.V830Wfs*36	ENST00000375856	NM_003749.2	829	ccC/cc	1/2	0.264924666531133	2	FACETS	0.589	0.527	0.653	0.294	0.263	0.327	INDETERMINATE	1	TRUE	0	0.783396172376277	2		727	412	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830417	72830417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144401383	NA	P-0037352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	15	403	0	ENST00000268489.5:c.6164C>T	p.Pro2055Leu	p.P2055L	ENST00000268489	NM_006885.3	2055	cCg/cTg	9/10	0.783396172376277	1	FACETS	0.155	0.114	0.204	0.155	0.114	0.204	SUBCLONAL	1	TRUE	0	0.783396172376277	1		403	150	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484270	57484270	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	83	481	0	ENST00000371085.3:c.584A>G	p.Gln195Arg	p.Q195R	ENST00000371085	NM_000516.4	195	cAg/cGg	7/13	0.434412197123982	1	FACETS	0.35	0.311	0.392	0.35	0.311	0.392	INDETERMINATE	1	TRUE	0	0.783396172376277	1		481	368	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442498	52442498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	60	372	2	ENST00000460680.1:c.247G>A	p.Ala83Thr	p.A83T	ENST00000460680	NM_004656.3	83	Gcc/Acc	4/17	0.783396172376277	1	FACETS	0.368	0.32	0.419	0.368	0.32	0.419	SUBCLONAL	1	TRUE	0	0.783396172376277	1		374	253	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911522	134911522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778136807	NA	P-0037352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	175	528	0	ENST00000398015.3:c.1987C>T	p.Arg663Trp	p.R663W	ENST00000398015	NM_004441.4	663	Cgg/Tgg	11/16	0.783396172376277	1	FACETS	0.957	0.903	1	0.957	0.903	1	CLONAL	1	TRUE	0	0.783396172376277	1		528	284	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196846	106196846	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	144	451	0	ENST00000380013.4:c.5179C>T	p.His1727Tyr	p.H1727Y	ENST00000380013	NM_001127208.2	1727	Cat/Tat	11/11	0.383426293040377	1	FACETS	0.719	0.667	0.771	0.719	0.667	0.771	INDETERMINATE	1	TRUE	0	0.783396172376277	1		451	311	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449615	149449615	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	73	651	0	ENST00000286301.3:c.1331C>A	p.Ala444Asp	p.A444D	ENST00000286301	NM_005211.3	444	gCc/gAc	10/22	0.244210068578759	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.783396172376277	0		651	459	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046674	180046674	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	87	846	0	ENST00000261937.6:c.2638del	p.Met880CysfsTer2	p.M880Cfs*2	ENST00000261937	NM_182925.4	880	Atg/tg	18/30	0.242378941892063	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.783396172376277	0		846	457	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982050	93982050	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1232168679	NA	P-0037352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	101	539	0	ENST00000369303.4:c.1415T>C	p.Val472Ala	p.V472A	ENST00000369303	NM_004440.3	472	gTc/gCc	6/17	0.783396172376277	1	FACETS	0.446	0.402	0.491	0.446	0.402	0.491	SUBCLONAL	1	TRUE	0	0.783396172376277	1		539	352	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069936	5069938	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1216770146	NA	P-0037352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	54	338	0	ENST00000381652.3:c.1527_1529del	p.Leu510del	p.L510del	ENST00000381652	NM_004972.3	509	CTT/-	12/25	0.453782201767016	1	FACETS	0.307	0.264	0.353	0.307	0.264	0.353	INDETERMINATE	1	TRUE	0	0.783396172376277	1		338	273	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76812920	76812920	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0037352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	97	699	0	ENST00000373344.5:c.6699+2T>C		p.X2233_splice	ENST00000373344	NM_000489.3	2233			0.492945284775047	0	FACETS		NA	1			1	NA	1	TRUE	0	0.783396172376277	0		699	302	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	29	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.704	0.564	0.864	0.704	0.564	0.864	SUBCLONAL	1	TRUE	1	0.16	2		452	515	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0037394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	40	449	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	1	2	FACETS	0.882	0.732	1	0.882	0.732	1	CLONAL	1	TRUE	1	0.16	2		449	567	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201959	102201960	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0037394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	15	166	1	ENST00000263464.3:c.1311_1312delinsAA	p.Glu438Lys	p.E438K	ENST00000263464	NM_001165.4	437	gaGGaa/gaAAaa	6/9	1	2	FACETS	1	0.759	1	1	0.759	1	CLONAL	1	TRUE	1	0.16	2		167	181	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434297	49434297	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	47	664	0	ENST00000301067.7:c.7256C>T	p.Ser2419Phe	p.S2419F	ENST00000301067	NM_003482.3	2419	tCc/tTc	31/54	1	2	FACETS	0.752	0.633	0.885	0.752	0.633	0.885	SUBCLONAL	1	TRUE	1	0.16	2		664	781	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532671	63532671	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	27	455	0	ENST00000307078.5:c.1908T>A	p.Ser636Arg	p.S636R	ENST00000307078	NM_004655.3	636	agT/agA	8/11	1	2	FACETS	0.715	0.568	0.884	0.715	0.568	0.884	SUBCLONAL	1	TRUE	1	0.16	2		455	472	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584717	48584717	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	19	322	0	ENST00000342988.3:c.795del	p.Thr266ProfsTer70	p.T266Pfs*70	ENST00000342988	NM_005359.5	265	acT/ac	7/12	1	2	FACETS	0.656	0.497	0.843	0.656	0.497	0.843	SUBCLONAL	1	TRUE	1	0.16	2		322	362	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402742	139402742	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	39	594	1	ENST00000277541.6:c.3267G>A	p.Trp1089Ter	p.W1089*	ENST00000277541	NM_017617.3	1089	tgG/tgA	20/34	1	2	FACETS	0.893	0.739	1	0.893	0.739	1	CLONAL	1	TRUE	1	0.16	2		595	546	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220450	123220450	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	23	235	0	ENST00000218089.9:c.3107A>C	p.Asp1036Ala	p.D1036A	ENST00000218089	NM_001042749.1	1036	gAt/gCt	30/35	0.3	2	FACETS	0.882	0.688	1	0.441	0.344	0.553	CLONAL	1	TRUE	0	0.16	2		235	326	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0037413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	47	405	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.3	4	FACETS	0.514	0.432	0.604	0.171	0.144	0.202	SUBCLONAL	1	FALSE	1	0.3	4		405	793	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782177	NA	P-0037413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	37	780	0	ENST00000269305.4:c.644G>A	p.Ser215Asn	p.S215N	ENST00000269305	NM_001126112.2	215	aGt/aAt	6/11	1	2	FACETS	0.375	0.308	0.451	0.375	0.308	0.451	SUBCLONAL	1	FALSE	1	0.3	2		780	657	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020294	123020301	+	frameshift_variant	Frame_Shift_Del	DEL	CCATGGCA	CCATGGCA	-	novel	NA	P-0037413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	31	511	0	ENST00000355640.3:c.782_789del	p.Ser261Ter	p.S261*	ENST00000355640		261	tCCATGGCA/t	2/7	0.3	1	FACETS	0.31	0.25	0.379	0.31	0.25	0.379	SUBCLONAL	1	FALSE	0	0.3	1		511	566	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	56	320	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.149666824641079	2		321	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0037420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	50	431	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.648	0.548	0.759	0.648	0.548	0.759	SUBCLONAL	1	FALSE	1	0.149666824641079	2		432	1031	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0037420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	88	646	7	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	FALSE	1	0.149666824641079	2		653	1149	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637644	23637644	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	56	593	0	ENST00000261584.4:c.2661C>G	p.Ile887Met	p.I887M	ENST00000261584	NM_024675.3	887	atC/atG	7/13	1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	FALSE	1	0.149666824641079	2		593	748	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974693	21974694	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTA	novel	NA	P-0037420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	70	391	0	ENST00000304494.5:c.133_134insTAG	p.Tyr44_Gly45insVal	p.Y44_G45insV	ENST00000304494	NM_000077.4	45	ggt/gTAGgt	1/3	0.149666824641079	1	FACETS	0.751	0.655	0.855	1	0.973	1	SUBCLONAL	2	FALSE	0	0.149666824641079	1		391	576	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	73	320	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.51	2		321	286	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0037428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	117	304	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.51	2		304	355	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858116	40858116	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	165	652	0	ENST00000428826.2:c.1748C>G	p.Pro583Arg	p.P583R	ENST00000428826		583	cCt/cGt	16/21	1	2	FACETS	0.718	0.659	0.779	0.718	0.659	0.779	SUBCLONAL	1	TRUE	1	0.51	2		652	901	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	51	320	1				ENST00000310581	NM_198253.2	-/1132			0.15324165537278	3	FACETS	1	0.958	1	0.673	0.577	0.775	INDETERMINATE	1	TRUE	1	0.359235258433447	3		321	249	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0037459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	238	532	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.217360279275667	2	FACETS	0.986	0.926	1	0.986	0.926	1	CLONAL	2	TRUE	0	0.359235258433447	2		533	672	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0037459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	203	546	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.227100801104544	5	FACETS	1	0.981	1	0.769	0.715	0.824	CLONAL	2	TRUE	2	0.359235258433447	5		546	754	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125513776	125513776	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	53	538	0	ENST00000428830.2:c.904C>G	p.Pro302Ala	p.P302A	ENST00000428830	NM_001114121.2	302	Cca/Gca	9/14	0.359235258433447	2	FACETS	0.588	0.501	0.682	0.294	0.25	0.341	SUBCLONAL	1	TRUE	0	0.359235258433447	2		538	502	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249028	55249028	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1275022697	NA	P-0037459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	156	473	0	ENST00000275493.2:c.2326C>T	p.Arg776Cys	p.R776C	ENST00000275493	NM_005228.3	776	Cgc/Tgc	20/28	0.227100801104544	5	FACETS	1	0.968	1	0.735	0.676	0.796	CLONAL	2	TRUE	2	0.359235258433447	5		473	606	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464501	25464501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	155	570	2	ENST00000264709.3:c.2012C>T	p.Thr671Met	p.T671M	ENST00000264709	NM_175629.2	671	aCg/aTg	17/23	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.359235258433447	2		572	580	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588868	69588868	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	49	573	3	ENST00000168712.1:c.368G>A	p.Arg123Gln	p.R123Q	ENST00000168712	NM_002007.2	123	cGg/cAg	2/3	0.359235258433447	2	FACETS	0.662	0.562	0.772	0.331	0.281	0.386	SUBCLONAL	1	TRUE	0	0.359235258433447	2		576	412	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117383	115117383	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1418098778	NA	P-0037459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	126	404	0	ENST00000257566.3:c.791C>T	p.Pro264Leu	p.P264L	ENST00000257566	NM_016569.3	264	cCt/cTt	4/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.359235258433447	2		404	468	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878176	48878196	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCTCGTCAGGTGAGCGAGCA	CTCTCGTCAGGTGAGCGAGCA	TGT	novel	NA	P-0037459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	13	90	1	ENST00000267163.4:c.128_137+11delinsTGT		p.X43_splice	ENST00000267163	NM_000321.2	43		1/27	0.359235258433447	2	FACETS	0.754	0.544	1	0.377	0.272	0.501	CLONAL	1	TRUE	0	0.359235258433447	2		91	96	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133810	2133810	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs878854099	NA	P-0037459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	65	442	0	ENST00000219476.3:c.3998A>G	p.Tyr1333Cys	p.Y1333C	ENST00000219476	NM_000548.3	1333	tAc/tGc	33/42	1	2	FACETS	0.844	0.734	0.962	0.844	0.734	0.962	CLONAL	1	TRUE	1	0.359235258433447	2		442	429	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55270220	55270220	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	268	629	2	ENST00000275493.2:c.3173G>T	p.Cys1058Phe	p.C1058F	ENST00000275493	NM_005228.3	1058	tGt/tTt	27/28	0.227100801104544	5	FACETS	1	0.99	1	0.833	0.783	0.884	CLONAL	2	TRUE	2	0.359235258433447	5		631	919	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0037496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	91	673	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.558788038290254	NA		673	265	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562675	29562679	+	frameshift_variant	Frame_Shift_Del	DEL	TACTC	TACTC	-	novel	NA	P-0037496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	198	517	0	ENST00000356175.3:c.3758_3762del	p.Leu1253ProfsTer9	p.L1253Pfs*9	ENST00000356175	NM_000267.3	1252	tTACTC/t	28/57	0.558788038290254	1	FACETS	0.879	0.819	0.94	0.879	0.819	0.94	CLONAL	1	TRUE	0	0.558788038290254	1		517	581	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508470	106508470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1463222028	NA	P-0037496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	83	217	0	ENST00000359195.3:c.464C>T	p.Thr155Met	p.T155M	ENST00000359195	NM_002649.2	155	aCg/aTg	2/11	0.558788038290254	3	FACETS	0.845	0.749	0.947	0.422	0.374	0.474	CLONAL	1	TRUE	1	0.558788038290254	3		217	450	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653851	89653851	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1554893824	NA	P-0037496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	152	367	0	ENST00000371953.3:c.149T>C	p.Ile50Thr	p.I50T	ENST00000371953	NM_000314.4	50	aTt/aCt	2/9	0.558788038290254	1	FACETS	0.94	0.869	1	0.94	0.869	1	CLONAL	1	TRUE	0	0.558788038290254	1		367	417	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880101	151880101	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	217	446	0	ENST00000262189.6:c.5223G>T	p.Lys1741Asn	p.K1741N	ENST00000262189	NM_170606.2	1741	aaG/aaT	35/59	0.558788038290254	3	FACETS	0.966	0.898	1	0.483	0.449	0.518	CLONAL	1	TRUE	1	0.558788038290254	3		446	1029	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577567	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1567549651	NA	P-0037497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	338	485	0	ENST00000269305.4:c.714dup	p.Asn239Ter	p.N239*	ENST00000269305	NM_001126112.2	238	-/T	7/11	0.38944987117213	2	FACETS	1	0.994	1	0.692	0.657	0.728	CLONAL	1	TRUE	0	0.532986267509399	2		485	916	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471007	25471007	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	85	554	0	ENST00000264709.3:c.754G>A	p.Asp252Asn	p.D252N	ENST00000264709	NM_175629.2	252	Gac/Aac	7/23	0.399609707943016	2	FACETS	0.327	0.288	0.369	0.163	0.144	0.185	SUBCLONAL	1	TRUE	0	0.532986267509399	2		554	976	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680745	30680745	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	140	532	0	ENST00000376406.3:c.974G>A	p.Gly325Asp	p.G325D	ENST00000376406	NM_014641.2	325	gGc/gAc	5/15	0.388474058640544	2	FACETS	0.674	0.614	0.736	0.337	0.307	0.368	SUBCLONAL	1	TRUE	0	0.532986267509399	2		532	780	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411982	116411991	+	missense_variant	Missense_Mutation	ONP	AAGCCCAACT	AAGCCCAACT	GGCAGTCCAA	novel	NA	P-0037497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	1034	653	2	ENST00000397752.3:c.2967_2976delinsGGCAGTCCAA	p.Ser990_Thr992delinsAlaValGln	p.S990_T992delinsAVQ	ENST00000397752	NM_000245.2	989	gtAAGCCCAACT/gtGGCAGTCCAA	14/21	0.532986267509399	6	FACETS	1	0.993	1	0.843	0.822	0.864	CLONAL	4	TRUE	1	0.532986267509399	6		655	1902	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346304	70346315	+	inframe_deletion	In_Frame_Del	DEL	CATCAGTGGCCT	CATCAGTGGCCT	-	novel	NA	P-0037497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	289	642	0	ENST00000374080.3:c.2659_2670del	p.Ser887_Ile890del	p.S887_I890del	ENST00000374080		885	agCATCAGTGGCCTc/agc	19/45	0.121552031795785	5	FACETS	0.802	0.753	0.851	0.534	0.502	0.568	INDETERMINATE	2	TRUE	2	0.532986267509399	5		642	1217	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	119	320	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.815	0.753	0.878	1	0.989	1	CLONAL	2	TRUE	1	0.608048277110594	2		321	240	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0037512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	538	515	2	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	0.278807402802872	4	FACETS	1	0.992	1			1	INDETERMINATE	3	TRUE	NA	0.608048277110594	4		517	878	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0037512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	231	506	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.608048277110594	2		506	529	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141515	11141515	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	263	597	0	ENST00000358026.2:c.3492C>A	p.Asn1164Lys	p.N1164K	ENST00000358026	NM_001128849.1	1164	aaC/aaA	25/36	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.608048277110594	2		597	798	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719914	52719914	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1247831715	NA	P-0037512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	103	488	0	ENST00000322088.6:c.1126G>A	p.Glu376Lys	p.E376K	ENST00000322088	NM_014225.5	376	Gag/Aag	9/15	1	2	FACETS	0.506	0.453	0.562	0.506	0.453	0.562	SUBCLONAL	1	TRUE	1	0.608048277110594	2		488	670	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417337	139417337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs537766290	NA	P-0037512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	62	538	1	ENST00000277541.6:c.707C>T	p.Thr236Met	p.T236M	ENST00000277541	NM_017617.3	236	aCg/aTg	4/34	0.608048277110594	1	FACETS	0.357	0.309	0.408	0.357	0.309	0.408	SUBCLONAL	1	TRUE	0	0.608048277110594	1		539	398	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772950	135772951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs118203724	NA	P-0037512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	148	407	0	ENST00000298552.3:c.2672dup	p.Asn891LysfsTer13	p.N891Kfs*13	ENST00000298552	NM_001162426.1	891	aac/aaAc	21/23	0.608048277110594	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.608048277110594	1		407	304	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738518	145738518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368611522	NA	P-0037512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	247	527	0	ENST00000428558.2:c.2467G>A	p.Glu823Lys	p.E823K	ENST00000428558	NM_004260.3	823	Gaa/Aaa	16/22	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.608048277110594	2		527	757	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200023	123200023	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0037512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	115	134	0	ENST00000218089.9:c.2097-2A>G		p.X699_splice	ENST00000218089	NM_001042749.1	699			1	1	FACETS	0.975	0.931	1	1	0.993	1	CLONAL	2	TRUE	0	0.608048277110594	1		134	135	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328382	137328382	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	278	755	0	ENST00000481739.1:c.1311C>G	p.Phe437Leu	p.F437L	ENST00000481739	NM_002957.4	437	ttC/ttG	10/10	0.608048277110594	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.608048277110594	1		755	572	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741517	17741517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	188	402	0	ENST00000250003.3:c.188C>T	p.Ser63Leu	p.S63L	ENST00000250003	NM_002478.4	63	tCg/tTg	1/3	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.608048277110594	2		402	610	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845239	89845239	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	79	415	0	ENST00000389301.3:c.1796C>G	p.Ser599Cys	p.S599C	ENST00000389301	NM_000135.2	599	tCc/tGc	20/43	1	2	FACETS	0.435	0.383	0.491	0.435	0.383	0.491	SUBCLONAL	1	TRUE	1	0.608048277110594	2		415	597	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845385	89845385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	91	493	1	ENST00000389301.3:c.1742C>T	p.Ser581Phe	p.S581F	ENST00000389301	NM_000135.2	581	tCc/tTc	19/43	1	2	FACETS	0.419	0.372	0.47	0.419	0.372	0.47	SUBCLONAL	1	TRUE	1	0.608048277110594	2		494	714	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143033717	143033717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	149	384	0	ENST00000262992.4:c.2254G>A	p.Glu752Lys	p.E752K	ENST00000262992	NM_001101669.1	752	Gaa/Aaa	20/24	1	2	FACETS	0.925	0.85	1	0.925	0.85	1	CLONAL	1	TRUE	1	0.608048277110594	2		384	530	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870204	44870210	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGAATGC	AGAATGC	GA	novel	NA	P-0037512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	192	259	1	ENST00000377967.4:c.385-2_389delinsGA		p.X129_splice	ENST00000377967	NM_021140.2	129		5/29	1	1	FACETS	0.931	0.895	0.964	1	0.995	1	CLONAL	2	TRUE	0	0.608048277110594	1		260	236	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870210	44870210	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	192	258	0	ENST00000377967.4:c.389C>A	p.Ala130Asp	p.A130D	ENST00000377967	NM_021140.2	130	gCt/gAt	5/29	1	1	FACETS	0.968	0.934	0.999	1	0.995	1	CLONAL	2	TRUE	0	0.608048277110594	1		258	227	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0037518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	59	346	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	0.552	0.475	0.637	0.552	0.475	0.637	SUBCLONAL	1	TRUE	1	0.354363950403778	2		346	603	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593621	55593662	+	inframe_deletion	In_Frame_Del	DEL	ATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTT	ATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTT	-	novel	NA	P-0037522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	159	415	0	ENST00000288135.5:c.1687_1728del	p.Ile563_Leu576del	p.I563_L576del	ENST00000288135	NM_000222.2	563	ATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTT/-	11/21	1	2	FACETS	0.963	0.888	1	0.963	0.888	1	CLONAL	1	TRUE	1	0.588687085197896	2		415	561	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0037532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	47	506	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.48775292010317	3	FACETS	0.416	0.351	0.489	0.208	0.175	0.245	SUBCLONAL	1	TRUE	1	0.48775292010317	3		506	576	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435798	110435798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1240854451	NA	P-0037532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	90	345	1	ENST00000375856.3:c.2603C>T	p.Ser868Leu	p.S868L	ENST00000375856	NM_003749.2	868	tCg/tTg	1/2	0.479681976681192	5	FACETS	1	0.922	1	0.262	0.232	0.293	CLONAL	1	TRUE	1	0.48775292010317	5		346	610	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0037532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	202	430	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.48775292010317	2		431	645	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367257	50367257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1245618829	NA	P-0037532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	66	344	2	ENST00000331340.3:c.64G>A	p.Asp22Asn	p.D22N	ENST00000331340	NM_006060.4	22	Gat/Aat	3/8	0.48775292010317	3	FACETS	0.729	0.634	0.831	0.364	0.317	0.416	SUBCLONAL	1	TRUE	1	0.48775292010317	3		346	462	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992720	68992720	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs182978151	NA	P-0037532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	220	573	1	ENST00000288368.4:c.1685G>A	p.Arg562His	p.R562H	ENST00000288368	NM_024870.2	562	cGt/cAt	16/40	0.48775292010317	3	FACETS	0.877	0.82	0.934	0.877	0.82	0.934	CLONAL	2	TRUE	1	0.48775292010317	3		574	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577057	7577058	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0037532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	427	679	1	ENST00000269305.4:c.880dup	p.Glu294GlyfsTer12	p.E294Gfs*12	ENST00000269305	NM_001126112.2	294	gag/gGag	8/11	0.48775292010317	2	FACETS	0.969	0.929	1	0.969	0.929	1	CLONAL	2	TRUE	0	0.48775292010317	2		680	903	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15984012	15984012	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	33	414	0	ENST00000268712.3:c.3207T>G	p.His1069Gln	p.H1069Q	ENST00000268712	NM_006311.3	1069	caT/caG	24/46	0.48775292010317	2	FACETS	0.239	0.194	0.29	0.12	0.097	0.145	SUBCLONAL	1	TRUE	0	0.48775292010317	2		414	566	SUCCESS
APC	324	MSKCC	GRCh37	5	112175217	112175217	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	183	240	0	ENST00000257430.4:c.3929del	p.Lys1310ArgfsTer11	p.K1310Rfs*11	ENST00000257430	NM_000038.5	1309	gAa/ga	16/16	0.48775292010317	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.48775292010317	2		240	342	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0037549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	46	422	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.483	0.405	0.569	0.483	0.405	0.569	SUBCLONAL	1	TRUE	1	0.229308222675191	2		422	831	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149973	202149973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1272714323	NA	P-0037549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	108	676	0	ENST00000358485.4:c.1414C>T	p.Arg472Ter	p.R472*	ENST00000358485	NM_001080125.1	472	Cga/Tga	8/9	1	2	FACETS	0.966	0.866	1	0.966	0.866	1	CLONAL	1	TRUE	1	0.229308222675191	2		676	975	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95598872	95598872	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770567567	NA	P-0037549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	104	437	0	ENST00000393063.1:c.287C>T	p.Thr96Met	p.T96M	ENST00000393063	NM_030621.3	96	aCg/aTg	4/28	0.229308222675191	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.229308222675191	1		437	718	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161310413	161310413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	530	571	1	ENST00000367975.2:c.209G>A	p.Cys70Tyr	p.C70Y	ENST00000367975	NM_003001.3	70	tGc/tAc	4/6	0.436182025368929	4	FACETS	0.958	0.921	0.996	0.958	0.921	0.996	CLONAL	3	TRUE	1	0.436182025368929	4		572	1214	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622086	43622086	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	76	558	0	ENST00000355710.3:c.3103G>A	p.Glu1035Lys	p.E1035K	ENST00000355710	NM_020975.4	1035	Gag/Aag	19/20	0.436182025368929	3	FACETS	0.423	0.37	0.48	0.211	0.185	0.24	SUBCLONAL	1	TRUE	1	0.436182025368929	3		558	1004	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148904	119148904	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	137	432	0	ENST00000264033.4:c.1124G>T	p.Gly375Val	p.G375V	ENST00000264033	NM_005188.3	375	gGc/gTc	8/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.436182025368929	2		432	569	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445359	49445359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1363389206	NA	P-0037552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	248	841	0	ENST00000301067.7:c.2107G>A	p.Glu703Lys	p.E703K	ENST00000301067	NM_003482.3	703	Gag/Aag	10/54	NA	2	FACETS	0.933	0.871	0.997			1	INDETERMINATE	1	TRUE	NA	0.436182025368929	2		841	1219	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437424	121437424	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	121	586	0	ENST00000257555.6:c.1762C>G	p.Pro588Ala	p.P588A	ENST00000257555		588	Ccc/Gcc	9/10	0.436182025368929	3	FACETS	0.692	0.625	0.764	0.346	0.312	0.382	SUBCLONAL	1	TRUE	1	0.436182025368929	3		586	976	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133821	41133821	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	412	489	1	ENST00000379561.5:c.1807G>A	p.Asp603Asn	p.D603N	ENST00000379561	NM_002015.3	603	Gat/Aat	2/3	0.436182025368929	3	FACETS	0.987	0.947	1	0.987	0.947	1	CLONAL	3	TRUE	0	0.436182025368929	3		490	777	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73334666	73334666	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0037552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	283	444	0	ENST00000377767.4:c.2793+1G>T		p.X931_splice	ENST00000377767	NM_014953.3	931			0.436182025368929	3	FACETS	0.912	0.866	0.958	0.912	0.866	0.958	CLONAL	3	TRUE	0	0.436182025368929	3		444	578	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821988	72821989	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs752028320	NA	P-0037552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	44	422	0	ENST00000268489.5:c.10184_10186dup	p.Gln3395dup	p.Q3395dup	ENST00000268489	NM_006885.3	3395	ccc/cAGCcc	10/10	0.376887538093014	2	FACETS	0.374	0.313	0.441	0.187	0.156	0.221	SUBCLONAL	1	TRUE	0	0.436182025368929	2		422	540	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81891919	81891919	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	163	673	0	ENST00000359376.3:c.389A>T	p.His130Leu	p.H130L	ENST00000359376	NM_002661.3	130	cAc/cTc	4/33	0.376887538093014	2	FACETS	1	0.94	1	0.513	0.472	0.556	CLONAL	1	TRUE	0	0.436182025368929	2		673	728	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0037552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	588	713	0	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	0.42295932084004	3	FACETS	0.967	0.934	1	0.967	0.934	1	CLONAL	3	TRUE	0	0.436182025368929	3		713	1132	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511593	38511593	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	221	627	1	ENST00000254066.5:c.1091G>T	p.Arg364Leu	p.R364L	ENST00000254066	NM_000964.3	364	cGg/cTg	8/9	0.294480243283198	3	FACETS	1	0.976	1	0.369	0.343	0.396	CLONAL	1	TRUE	0	0.436182025368929	3		628	1114	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369415	40369415	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	129	841	0	ENST00000293328.3:c.1237A>T	p.Ser413Cys	p.S413C	ENST00000293328	NM_012448.3	413	Agt/Tgt	10/19	0.294480243283198	3	FACETS	0.564	0.51	0.622	0.188	0.17	0.208	SUBCLONAL	1	TRUE	0	0.436182025368929	3		841	1277	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42790944	42790944	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	582	678	0	ENST00000575354.2:c.89G>T	p.Arg30Leu	p.R30L	ENST00000575354	NM_015125.3	30	cGc/cTc	2/20	0.378678312159961	3	FACETS	0.927	0.894	0.959	0.927	0.894	0.959	CLONAL	3	TRUE	0	0.436182025368929	3		678	1169	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967276	134967276	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	313	633	0	ENST00000398015.3:c.2615C>G	p.Ala872Gly	p.A872G	ENST00000398015	NM_004441.4	872	gCg/gGg	14/16	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.436182025368929	2		633	1012	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1255449	1255449	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	80	746	0	ENST00000310581.5:c.3110C>T	p.Ser1037Phe	p.S1037F	ENST00000310581	NM_198253.2	1037	tCt/tTt	14/16	0.359460330689064	4	FACETS	0.443	0.389	0.503	0.222	0.194	0.252	SUBCLONAL	1	TRUE	2	0.436182025368929	4		746	1188	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547265	106547277	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCGGGAGCAAA	CCCCGGGAGCAAA	-	novel	NA	P-0037552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	133	469	0	ENST00000369096.4:c.502_514del	p.Pro168ThrfsTer9	p.P168Tfs*9	ENST00000369096	NM_001198.3	168	CCCCGGGAGCAAAac/ac	4/7	1	2	FACETS	0.875	0.796	0.958	0.875	0.796	0.958	CLONAL	1	TRUE	1	0.436182025368929	2		469	697	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518067	8518067	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	246	615	0	ENST00000356435.5:c.1324G>T	p.Glu442Ter	p.E442*	ENST00000356435		442	Gaa/Taa	10/35	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.436182025368929	2		615	961	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98241428	98241428	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	289	453	0	ENST00000331920.6:c.1069G>C	p.Ala357Pro	p.A357P	ENST00000331920	NM_000264.3	357	Gcc/Ccc	8/24	0.429936617356513	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.436182025368929	2		453	639	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76856028	76856028	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	111	313	0	ENST00000373344.5:c.5572G>T	p.Gly1858Cys	p.G1858C	ENST00000373344	NM_000489.3	1858	Ggc/Tgc	23/35	1	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.436182025368929	1		313	283	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191493	10191493	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs5030622	NA	P-0037555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	76	539	0	ENST00000256474.2:c.486C>G	p.Cys162Trp	p.C162W	ENST00000256474	NM_000551.3	162	tgC/tgG	3/3	0.514760812905359	1	FACETS	0.742	0.659	0.83	0.742	0.659	0.83	SUBCLONAL	1	TRUE	0	0.54985253542221	1		539	270	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163421	47163422	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0037555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	68	528	0	ENST00000409792.3:c.2704dup	p.Glu902GlyfsTer14	p.E902Gfs*14	ENST00000409792	NM_014159.6	902	gag/gGag	3/21	0.514760812905359	1	FACETS	0.754	0.664	0.847	0.754	0.664	0.847	SUBCLONAL	1	TRUE	0	0.54985253542221	1		528	238	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702630	52702631	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0037555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	124	540	0	ENST00000394830.3:c.267_268del	p.Gln90AlafsTer3	p.Q90Afs*3	ENST00000394830	NM_018313.4	89	tcTCag/tcag	4/30	0.514760812905359	1	FACETS	0.94	0.861	1	0.94	0.861	1	CLONAL	1	TRUE	0	0.54985253542221	1		540	348	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681910	30681910	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	130	551	0	ENST00000376406.3:c.187T>C	p.Ser63Pro	p.S63P	ENST00000376406	NM_014641.2	63	Tct/Cct	3/15	0.128281208229758	5	FACETS	0.851	0.776	0.929	0.567	0.517	0.619	INDETERMINATE	2	TRUE	2	0.54985253542221	5		551	507	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851867	128851867	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs34545616	NA	P-0037555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	67	698	0	ENST00000249373.3:c.1939C>A	p.Pro647Thr	p.P647T	ENST00000249373	NM_005631.4	647	Ccc/Acc	12/12	0.54985253542221	3	FACETS	0.721	0.629	0.82	0.36	0.314	0.41	SUBCLONAL	1	TRUE	1	0.54985253542221	3		698	431	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223403	53223410	+	frameshift_variant	Frame_Shift_Del	DEL	GGTTCAGC	GGTTCAGC	-	novel	NA	P-0037555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	78	403	0	ENST00000375401.3:c.3949_3956del	p.Ala1317Ter	p.A1317*	ENST00000375401	NM_004187.3	1317	GCTGAACCt/t	23/26	1	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.54985253542221	1		403	178	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015419	176015419	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	174	588	0	ENST00000367669.3:c.1319G>T	p.Gly440Val	p.G440V	ENST00000367669	NM_022457.5	440	gGa/gTa	12/20	0.674647558052461	3	FACETS	1	0.969	1	0.544	0.503	0.587	CLONAL	1	TRUE	1	0.674647558052461	3		588	634	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573830	64573830	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0037556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	176	603	0	ENST00000312049.6:c.923C>G	p.Ser308Ter	p.S308*	ENST00000312049	NM_130799.2	308	tCa/tGa	7/10	0.616322313621957	1	FACETS	0.867	0.809	0.925	0.867	0.809	0.925	CLONAL	1	TRUE	0	0.674647558052461	1		603	399	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220451	1220453	+	inframe_deletion	In_Frame_Del	DEL	CTG	CTG	-	novel	NA	P-0037556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	236	751	0	ENST00000326873.7:c.549_551del	p.Leu184del	p.L184del	ENST00000326873	NM_000455.4	182	CTG/-	4/10	0.674647558052461	1	FACETS	0.978	0.925	1	0.978	0.925	1	CLONAL	1	TRUE	0	0.674647558052461	1		751	474	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600531	10600531	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0037556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	144	526	0	ENST00000171111.5:c.1326-2A>T		p.X442_splice	ENST00000171111	NM_203500.1	442			0.674647558052461	1	FACETS	0.943	0.876	1	0.943	0.876	1	CLONAL	1	TRUE	0	0.674647558052461	1		526	300	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233660	233660	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	58	191	0	ENST00000264932.6:c.964C>G	p.Gln322Glu	p.Q322E	ENST00000264932	NM_004168.2	322	Caa/Gaa	8/15	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.674647558052461	2		191	171	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820905	32820905	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	289	838	0	ENST00000354258.4:c.689G>A	p.Gly230Glu	p.G230E	ENST00000354258	NM_000593.5	230	gGa/gAa	1/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.674647558052461	2		838	782	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140487374	140487374	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	228	642	0	ENST00000288602.6:c.1151G>C	p.Arg384Thr	p.R384T	ENST00000288602	NM_004333.4	384	aGa/aCa	9/18	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.674647558052461	2		642	642	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317479	1317479	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	224	783	0	ENST00000400841.2:c.586C>A	p.Pro196Thr	p.P196T	ENST00000400841		196	Cca/Aca	5/6	1	1	FACETS	0.661	0.618	0.704	0.661	0.618	0.704	SUBCLONAL	1	TRUE	0	0.674647558052461	1		783	666	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52663027	52663028	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TATTCTTGATTCTTCAGTT	novel	NA	P-0037557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	92	439	0	ENST00000394830.3:c.1307_1325dup	p.Tyr442Ter	p.Y442*	ENST00000394830	NM_018313.4	442	tat/taAACTGAAGAATCAAGAATAt	13/30	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	NA	NA		439	539	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579487	7579487	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	361	624	1	ENST00000269305.4:c.200del	p.Pro67GlnfsTer56	p.P67Qfs*56	ENST00000269305	NM_001126112.2	67	cCa/ca	4/11	0.257742578311592	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	3	TRUE	0	0.257742578311592	3		625	1034	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220371	1220371	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0037575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	238	353	0	ENST00000326873.7:c.465-1G>C		p.X155_splice	ENST00000326873	NM_000455.4	155			0.257742578311592	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.257742578311592	2		353	816	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207771	29207771	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	381	584	0	ENST00000240100.2:c.25G>A	p.Glu9Lys	p.E9K	ENST00000240100	NM_001394.6	9	Gag/Aag	1/4	0.257742578311592	2	FACETS	0.893	0.85	0.938	1	0.994	1	CLONAL	3	TRUE	0	0.257742578311592	2		584	1103	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226574132	226574133	+	missense_variant	Missense_Mutation	DNP	GT	GT	AA	novel	NA	P-0037575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	129	431	2	ENST00000366794.5:c.728_729delinsTT	p.Asp243Val	p.D243V	ENST00000366794	NM_001618.3	243	gAC/gTT	6/23	0.241471483268349	3	FACETS	0.891	0.81	0.976	0.891	0.81	0.976	CLONAL	2	TRUE	1	0.257742578311592	3		433	634	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434911	49434912	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCGCCCAGCATCGGGGGCT	novel	NA	P-0037575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	45	439	0	ENST00000301067.7:c.6623_6641dup	p.Ser2215AlafsTer34	p.S2215Afs*34	ENST00000301067	NM_003482.3	2214	gcc/gcAGCCCCCGATGCTGGGCGCc	31/54	0.25131663024386	3	FACETS	0.493	0.413	0.582	0.247	0.206	0.291	SUBCLONAL	1	TRUE	1	0.257742578311592	3		439	799	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133236026	133236026	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	184	445	0	ENST00000320574.5:c.3130G>T	p.Glu1044Ter	p.E1044*	ENST00000320574	NM_006231.2	1044	Gaa/Taa	26/49	0.257742578311592	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.257742578311592	3		445	732	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992753	72992753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	103	470	0	ENST00000268489.5:c.1292C>T	p.Ser431Leu	p.S431L	ENST00000268489	NM_006885.3	431	tCa/tTa	2/10	0.16625323044617	5	FACETS	1	0.972	1	0.422	0.377	0.47	CLONAL	1	TRUE	2	0.257742578311592	5		470	876	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170519	11170519	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	277	526	1	ENST00000358026.2:c.4822G>T	p.Glu1608Ter	p.E1608*	ENST00000358026	NM_001128849.1	1608	Gag/Tag	34/36	0.257742578311592	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.257742578311592	2		527	882	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912480	50912480	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	242	596	0	ENST00000440232.2:c.1994G>T	p.Ser665Ile	p.S665I	ENST00000440232	NM_002691.3	665	aGt/aTt	16/27	0.241471483268349	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.257742578311592	3		596	926	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213798	66213798	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	93	325	0	ENST00000273854.3:c.2632C>A	p.Pro878Thr	p.P878T	ENST00000273854	NM_004439.5	878	Ccc/Acc	15/18	0.257742578311592	3	FACETS	0.792	0.707	0.883	0.792	0.707	0.883	SUBCLONAL	2	TRUE	1	0.257742578311592	3		325	514	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523544	106523544	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	77	170	0	ENST00000359195.3:c.2696C>A	p.Thr899Lys	p.T899K	ENST00000359195	NM_002649.2	899	aCg/aAg	8/11	0.257742578311592	2	FACETS	0.951	0.843	1	0.951	0.843	1	CLONAL	2	TRUE	0	0.257742578311592	2		170	314	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499828	8499828	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	141	358	0	ENST00000356435.5:c.2141C>A	p.Pro714His	p.P714H	ENST00000356435		714	cCt/cAt	14/35	0.257742578311592	2	FACETS	0.894	0.817	0.974	0.894	0.817	0.974	CLONAL	2	TRUE	0	0.257742578311592	2		358	612	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974805	21974818	+	frameshift_variant	Frame_Shift_Del	DEL	TGCTCCCCGCCGCC	TGCTCCCCGCCGCC	GCTCGCG	novel	NA	P-0037575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	114	123	1	ENST00000304494.5:c.9_22delinsCGCGAGC	p.Ala5SerfsTer19	p.A5Sfs*19	ENST00000304494	NM_000077.4	3	ccGGCGGCGGGGAGCAgc/ccCGCGAGCgc	1/3	0.257742578311592	2	FACETS	0.993	0.907	1	1	0.986	1	CLONAL	3	TRUE	0	0.257742578311592	2		124	297	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0037600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	126	369	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.401860871035781	4	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.795623888462721	4		369	457	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0037600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	12	407	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	0.401860871035781	4	FACETS	0.093	0.065	0.129			1	INDETERMINATE	1	TRUE	NA	0.795623888462721	4		407	581	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0037600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	150	575	0	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	0.104334278988967	4	FACETS	0.754	0.695	0.814	0.754	0.695	0.814	INDETERMINATE	2	TRUE	2	0.795623888462721	4		575	449	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438503	52438503	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	332	647	0	ENST00000460680.1:c.1216G>T	p.Glu406Ter	p.E406*	ENST00000460680	NM_004656.3	406	Gag/Tag	12/17	0.873656341604103	1	FACETS	0.933	0.9	0.964	0.933	0.9	0.964	CLONAL	1	TRUE	0	0.873656341604103	1		647	459	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118926	70118926	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	52	515	1	ENST00000245479.2:c.498G>T	p.Lys166Asn	p.K166N	ENST00000245479	NM_000346.3	166	aaG/aaT	2/3	0.311194853273591	3	FACETS	1	0.936	1	0.584	0.501	0.673	CLONAL	1	FALSE	1	0.396681308254687	3		516	269	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713648	30713648	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	14	356	1	ENST00000295754.5:c.973A>C	p.Thr325Pro	p.T325P	ENST00000295754	NM_003242.5	325	Acc/Ccc	4/7	0.311194853273591	3	FACETS	0.711	0.518	0.939	0.355	0.259	0.47	CLONAL	1	FALSE	1	0.396681308254687	3		357	119	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168719	56168719	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	22	354	0	ENST00000399503.3:c.1573del	p.Gln525SerfsTer32	p.Q525Sfs*32	ENST00000399503	NM_005921.1	525	Cag/ag	9/20	0.396681308254687	4	FACETS	0.759	0.591	0.952	0.38	0.295	0.476	CLONAL	1	FALSE	2	0.396681308254687	4		354	204	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0037639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	253	778	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	NA	2	FACETS	0.988	0.925	1			1	INDETERMINATE	2	TRUE	NA	0.229979949127264	2		778	1113	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720317	43720317	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1449770187	NA	P-0037639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	223	602	0	ENST00000382044.4:c.3725A>G	p.His1242Arg	p.H1242R	ENST00000382044	NM_001141980.1	1242	cAt/cGt	18/28	0.229979949127264	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.229979949127264	2		602	879	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682382	52682383	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0037639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	45	237	0	ENST00000394830.3:c.790_791insGG	p.Glu264GlyfsTer20	p.E264Gfs*20	ENST00000394830	NM_018313.4	264	gag/gGGag	8/30	0.229979949127264	1	FACETS	0.763	0.642	0.897	0.763	0.642	0.897	SUBCLONAL	1	TRUE	0	0.229979949127264	1		237	454	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0037651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	534	426	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.454718011954973	6	FACETS	1	0.992	1	1	0.997	1	CLONAL	5	TRUE	2	0.454718011954973	6		426	841	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156719	20156719	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	147	422	0	ENST00000379607.5:c.38G>C	p.Arg13Pro	p.R13P	ENST00000379607	NM_001412.3	13	cGc/cCc	2/7	0.122996050124071	6	FACETS	1	0.971	1	0.752	0.69	0.816	INDETERMINATE	2	TRUE	3	0.454718011954973	6		422	547	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133523	55133523	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	56	404	0	ENST00000257290.5:c.827C>A	p.Thr276Lys	p.T276K	ENST00000257290	NM_006206.4	276	aCg/aAg	6/23	1	2	FACETS	0.844	0.728	0.968	0.844	0.728	0.968	CLONAL	1	TRUE	1	0.454718011954973	2		404	292	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148875	119148876	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AT	novel	NA	P-0037651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	54	228	0	ENST00000264033.4:c.1096-1_1096delinsAT		p.X366_splice	ENST00000264033	NM_005188.3	366		8/16	0.433870603193154	3	FACETS	0.81	0.704	0.921	0.81	0.704	0.921	CLONAL	2	TRUE	1	0.454718011954973	3		228	180	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219509	133219509	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	152	635	2	ENST00000320574.5:c.4625del	p.Gly1542AlafsTer20	p.G1542Afs*20	ENST00000320574	NM_006231.2	1542	gGc/gc	36/49	0.410811545364299	4	FACETS	0.93	0.856	1	0.93	0.856	1	CLONAL	2	TRUE	2	0.454718011954973	4		637	523	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592610	28592610	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	50	348	0	ENST00000241453.7:c.2535G>T	p.Arg845Ser	p.R845S	ENST00000241453	NM_004119.2	845	agG/agT	20/24	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.454718011954973	2		348	201	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127598	2127598	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0037651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	61	424	0	ENST00000219476.3:c.2838-1G>T		p.X946_splice	ENST00000219476	NM_000548.3	946			1	2	FACETS	0.986	0.859	1	0.986	0.859	1	CLONAL	1	TRUE	1	0.454718011954973	2		424	272	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274317	5274317	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	62	494	1	ENST00000357368.4:c.130G>T	p.Gly44Cys	p.G44C	ENST00000357368	NM_002850.3	44	Ggc/Tgc	3/38	1	2	FACETS	0.894	0.778	1	0.894	0.778	1	CLONAL	1	TRUE	1	0.454718011954973	2		495	305	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149243836	149243836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	86	548	1	ENST00000360632.3:c.982G>A	p.Glu328Lys	p.E328K	ENST00000360632	NM_015472.4	328	Gag/Aag	6/7	0.433870603193154	3	FACETS	0.971	0.862	1	0.486	0.431	0.544	CLONAL	1	TRUE	1	0.454718011954973	3		549	478	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820851	32820851	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	74	663	0	ENST00000354258.4:c.743C>T	p.Ser248Leu	p.S248L	ENST00000354258	NM_000593.5	248	tCg/tTg	1/11	1	2	FACETS	0.784	0.69	0.885	0.784	0.69	0.885	SUBCLONAL	1	TRUE	1	0.454718011954973	2		663	415	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984079	2984079	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	44	433	0	ENST00000396946.4:c.451G>T	p.Glu151Ter	p.E151*	ENST00000396946	NM_032415.4	151	Gag/Tag	5/25	1	2	FACETS	0.765	0.646	0.894	0.765	0.646	0.894	SUBCLONAL	1	TRUE	1	0.454718011954973	2		433	253	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033265	69033265	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1227610892	NA	P-0037651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	126	367	0	ENST00000288368.4:c.3705C>A	p.Asn1235Lys	p.N1235K	ENST00000288368	NM_024870.2	1235	aaC/aaA	30/40	0.433870603193154	3	FACETS	0.883	0.808	0.961	0.883	0.808	0.961	CLONAL	2	TRUE	1	0.454718011954973	3		367	385	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938153	76938153	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	176	639	1	ENST00000373344.5:c.2595C>A	p.His865Gln	p.H865Q	ENST00000373344	NM_000489.3	865	caC/caA	9/35	0.122996050124071	6	FACETS	1	0.956	1	0.699	0.646	0.754	INDETERMINATE	2	TRUE	3	0.454718011954973	6		640	705	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939102	76939102	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	127	558	0	ENST00000373344.5:c.1646G>T	p.Ser549Ile	p.S549I	ENST00000373344	NM_000489.3	549	aGc/aTc	9/35	0.122996050124071	6	FACETS	1	0.971	1	0.77	0.702	0.84	INDETERMINATE	2	TRUE	3	0.454718011954973	6		558	462	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76949315	76949315	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	120	409	0	ENST00000373344.5:c.482del	p.Gly161GlufsTer9	p.G161Efs*9	ENST00000373344	NM_000489.3	161	gGa/ga	6/35	0.122996050124071	6	FACETS	0.951	0.862	1	0.634	0.575	0.696	INDETERMINATE	2	TRUE	3	0.454718011954973	6		409	530	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0037672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	8	354	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	1	2	FACETS	0.231	0.149	0.338	0.231	0.149	0.338	SUBCLONAL	1	TRUE	1	0.4	2		354	173	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776975	135776975	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0037672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	23	344	0	ENST00000298552.3:c.2502+1G>A		p.X834_splice	ENST00000298552	NM_001162426.1	834			1	2	FACETS	0.324	0.252	0.407	0.324	0.252	0.407	SUBCLONAL	1	TRUE	1	0.4	2		344	355	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0037674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	129	544	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	1	2	FACETS	0.794	0.719	0.873	0.794	0.719	0.873	SUBCLONAL	1	TRUE	1	0.338256763242613	2		544	961	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577579	7577579	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	98	461	0	ENST00000269305.4:c.702C>A	p.Tyr234Ter	p.Y234*	ENST00000269305	NM_001126112.2	234	taC/taA	7/11	0.338256763242613	1	FACETS	0.756	0.675	0.841	0.756	0.675	0.841	SUBCLONAL	1	TRUE	0	0.338256763242613	1		461	637	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257797	16257797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	25	331	0	ENST00000375759.3:c.5062G>A	p.Glu1688Lys	p.E1688K	ENST00000375759	NM_015001.2	1688	Gaa/Aaa	11/15	NA	2	FACETS	0.308	0.242	0.384			1	INDETERMINATE	1	TRUE	NA	0.338256763242613	2		331	480	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257803	16257803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	26	321	0	ENST00000375759.3:c.5068G>A	p.Ala1690Thr	p.A1690T	ENST00000375759	NM_015001.2	1690	Gct/Act	11/15	NA	2	FACETS	0.314	0.248	0.391			1	INDETERMINATE	1	TRUE	NA	0.338256763242613	2		321	489	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068981	30068981	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	34	385	0	ENST00000331968.5:c.1948G>C	p.Glu650Gln	p.E650Q	ENST00000331968	NM_002742.2	650	Gag/Cag	14/18	1	2	FACETS	0.308	0.251	0.373	0.308	0.251	0.373	SUBCLONAL	1	TRUE	1	0.338256763242613	2		385	652	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661792	227661792	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	129	580	0	ENST00000305123.5:c.1663A>G	p.Met555Val	p.M555V	ENST00000305123	NM_005544.2	555	Atg/Gtg	1/2	0.289248338870022	1	FACETS	0.835	0.758	0.916	0.835	0.758	0.916	CLONAL	1	TRUE	0	0.338256763242613	1		580	759	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62325780	62325781	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0037674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	107	419	1	ENST00000360203.5:c.3048_3049delinsTT	p.Asp1017Tyr	p.D1017Y	ENST00000360203	NM_001283009.1	1016	ctGGac/ctTTac	31/35	1	2	FACETS	0.909	0.816	1	0.909	0.816	1	CLONAL	1	TRUE	1	0.338256763242613	2		420	696	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801128	1801128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1333699127	NA	P-0037674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	195	715	2	ENST00000260795.2:c.257G>A	p.Arg86His	p.R86H	ENST00000260795		86	cGt/cAt	2/17	0.325798602817654	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.338256763242613	1		717	901	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163576	32163576	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	63	312	0	ENST00000375023.3:c.5650G>T	p.Val1884Leu	p.V1884L	ENST00000375023	NM_004557.3	1884	Gta/Tta	30/30	1	2	FACETS	0.828	0.718	0.946	0.828	0.718	0.946	CLONAL	1	TRUE	1	0.338256763242613	2		312	450	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38139065	38139065	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	847	480	1	ENST00000317025.8:c.3538G>A	p.Asp1180Asn	p.D1180N	ENST00000317025	NM_023034.1	1180	Gat/Aat	20/24	0.338256763242613	15	FACETS	1	0.989	1			1	CLONAL	10	TRUE	NA	0.338256763242613	15		481	1549	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38139086	38139086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	690	421	0	ENST00000317025.8:c.3517G>A	p.Glu1173Lys	p.E1173K	ENST00000317025	NM_023034.1	1173	Gaa/Aaa	20/24	0.338256763242613	15	FACETS	1	0.975	1			1	CLONAL	10	TRUE	NA	0.338256763242613	15		421	1295	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0037771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	289	426	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.979	1	1	0.996	1	CLONAL	2	TRUE	1	0.310470900730991	2		426	865	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204681	108204681	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs745775382	NA	P-0037771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	94	181	0	ENST00000278616.4:c.7996A>G	p.Thr2666Ala	p.T2666A	ENST00000278616	NM_000051.3	2666	Act/Gct	54/63	0.310470900730991	2	FACETS	0.967	0.871	1	0.967	0.871	1	CLONAL	2	TRUE	0	0.310470900730991	2		181	313	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659952	227659952	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	50	695	0	ENST00000305123.5:c.3503G>T	p.Gly1168Val	p.G1168V	ENST00000305123	NM_005544.2	1168	gGg/gTg	1/2	NA	2	FACETS	0.349	0.295	0.409			1	INDETERMINATE	1	TRUE	NA	0.310470900730991	2		695	923	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11168338	11168338	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	69	368	0	ENST00000361445.4:c.7534G>T	p.Asp2512Tyr	p.D2512Y	ENST00000361445	NM_004958.3	2512	Gac/Tac	57/58	0.27809946812606	1	FACETS	0.731	0.637	0.831	0.731	0.637	0.831	SUBCLONAL	1	TRUE	0	0.310470900730991	1		368	514	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837895	156837895	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0037771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	215	674	0	ENST00000524377.1:c.429-1G>T		p.X143_splice	ENST00000524377	NM_002529.3	143			0.246210173288272	3	FACETS	0.813	0.756	0.872	0.813	0.756	0.872	CLONAL	2	TRUE	1	0.310470900730991	3		674	984	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417937	32417937	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	119	575	0	ENST00000332351.3:c.1115C>A	p.Pro372His	p.P372H	ENST00000332351	NM_024426.4	372	cCt/cAt	7/10	0.27809946812606	1	FACETS	0.858	0.775	0.945	0.858	0.775	0.945	CLONAL	1	TRUE	0	0.310470900730991	1		575	755	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562368	95562368	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs368343829	NA	P-0037771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	44	438	0	ENST00000393063.1:c.4889G>T	p.Arg1630Leu	p.R1630L	ENST00000393063	NM_030621.3	1630	cGc/cTc	24/28	1	2	FACETS	0.481	0.403	0.568	0.481	0.403	0.568	SUBCLONAL	1	TRUE	1	0.310470900730991	2		438	589	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361138	66361138	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	61	370	0	ENST00000273854.3:c.1034G>T	p.Arg345Ile	p.R345I	ENST00000273854	NM_004439.5	345	aGa/aTa	4/18	1	2	FACETS	0.728	0.628	0.836	0.728	0.628	0.836	SUBCLONAL	1	TRUE	1	0.310470900730991	2		370	540	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20487005	20487005	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs951556755	NA	P-0037771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	131	375	0	ENST00000346618.3:c.970A>G	p.Thr324Ala	p.T324A	ENST00000346618	NM_001949.4	324	Aca/Gca	5/7	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.310470900730991	2		375	631	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650029	93650029	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0037771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	52	434	0	ENST00000375746.1:c.1582-2A>T		p.X528_splice	ENST00000375746	NM_001174167.1	528			1	2	FACETS	0.57	0.485	0.663	0.57	0.485	0.663	SUBCLONAL	1	TRUE	1	0.310470900730991	2		434	588	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0037774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	21	310	0	ENST00000311936.3:c.34_35delinsTT	p.Gly12Phe	p.G12F	ENST00000311936	NM_004985.3	12	GGt/TTt	2/5	1	2	FACETS	0.503	0.386	0.64	0.503	0.386	0.64	SUBCLONAL	1	TRUE	1	0.15	2		310	557	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0037774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	44	667	0	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.128834253432728	1	FACETS	0.884	0.74	1	0.884	0.74	1	CLONAL	1	TRUE	0	0.15	1		667	614	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602580	10602580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	60	737	2	ENST00000171111.5:c.998G>A	p.Gly333Asp	p.G333D	ENST00000171111	NM_203500.1	333	gGc/gAc	3/6	0.128834253432728	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.15	1		739	684	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118700	11118700	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0037774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	39	613	0	ENST00000358026.2:c.2123+1G>C		p.X708_splice	ENST00000358026	NM_001128849.1	708			0.128834253432728	1	FACETS	0.85	0.703	1	0.85	0.703	1	CLONAL	1	TRUE	0	0.15	1		613	566	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662721	227662721	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	48	767	1	ENST00000305123.5:c.734T>A	p.Val245Glu	p.V245E	ENST00000305123	NM_005544.2	245	gTg/gAg	1/2	1	2	FACETS	0.851	0.718	0.999	0.851	0.718	0.999	CLONAL	1	TRUE	1	0.15	2		768	752	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675578	86675578	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	26	326	0	ENST00000274376.6:c.2514T>A	p.Asn838Lys	p.N838K	ENST00000274376	NM_002890.2	838	aaT/aaA	19/25	1	2	FACETS	0.963	0.763	1	0.963	0.763	1	CLONAL	1	TRUE	1	0.15	2		326	360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0037901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	9	1096	1	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.535102378809471	1	FACETS	0.061	0.04	0.088	0.061	0.04	0.088	SUBCLONAL	1	TRUE	0	0.535102378809471	1		1097	403	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865500	57865500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	209	553	1	ENST00000228682.2:c.2977C>T	p.Pro993Ser	p.P993S	ENST00000228682	NM_005269.2	993	Ccc/Tcc	12/12	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.535102378809471	2		554	728	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519183	103519183	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	101	255	0	ENST00000355739.4:c.2521C>G	p.His841Asp	p.H841D	ENST00000355739	NM_000123.3	841	Cac/Gac	11/15	0.535102378809471	1	FACETS	0.977	0.886	1	0.977	0.886	1	CLONAL	1	TRUE	0	0.535102378809471	1		255	283	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39233566	39233566	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	100	271	0	ENST00000402219.2:c.2778T>G	p.Cys926Trp	p.C926W	ENST00000402219	NM_005633.3	926	tgT/tgG	17/23	1	2	FACETS	0.816	0.733	0.904	0.816	0.733	0.904	CLONAL	1	TRUE	1	0.535102378809471	2		271	458	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22161984	22161984	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	123	356	0	ENST00000215832.6:c.271C>T	p.Arg91Ter	p.R91*	ENST00000215832	NM_002745.4	91	Cga/Tga	2/9	1	2	FACETS	0.934	0.85	1	0.934	0.85	1	CLONAL	1	TRUE	1	0.535102378809471	2		356	492	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97863997	97863997	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	109	382	0	ENST00000289081.3:c.1669C>T	p.Gln557Ter	p.Q557*	ENST00000289081	NM_000136.2	557	Caa/Taa	15/15	1	2	FACETS	0.886	0.8	0.975	0.886	0.8	0.975	CLONAL	1	TRUE	1	0.535102378809471	2		382	460	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	135	320	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.81753522479668	2		321	312	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265479	152265479	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766779326	NA	P-0037942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	231	512	2	ENST00000206249.3:c.932C>T	p.Thr311Met	p.T311M	ENST00000206249	NM_000125.3	311	aCg/aTg	4/8	0.81753522479668	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.81753522479668	1		514	311	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111959605	111959605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758499440	NA	P-0037942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	218	454	0	ENST00000375549.3:c.184G>A	p.Ala62Thr	p.A62T	ENST00000375549	NM_003002.3	62	Gca/Aca	3/4	1	2	FACETS	0.942	0.883	1	0.942	0.883	1	CLONAL	1	TRUE	1	0.81753522479668	2		454	566	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945085	31945085	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	237	537	1	ENST00000340398.3:c.16C>T	p.Gln6Ter	p.Q6*	ENST00000340398	NM_001013699.2	6	Cag/Tag	1/1	1	2	FACETS	0.907	0.852	0.963	0.907	0.852	0.963	CLONAL	1	TRUE	1	0.81753522479668	2		538	639	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522585	106522585	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	137	382	0	ENST00000359195.3:c.2562T>G	p.Ile854Met	p.I854M	ENST00000359195	NM_002649.2	854	atT/atG	7/11	0.647466704850839	4	FACETS	0.939	0.856	1	0.313	0.285	0.342	CLONAL	1	TRUE	1	0.81753522479668	4		382	649	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418475	49418479	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTC	CTCTC	-	novel	NA	P-0037947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	285	580	0	ENST00000301067.7:c.15934_15938del	p.Glu5312LeufsTer31	p.E5312Lfs*31	ENST00000301067	NM_003482.3	5312	GAGAGc/c	50/54	1	2	FACETS	0.951	0.899	1	0.951	0.899	1	CLONAL	1	TRUE	1	0.791628424338634	2		580	757	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42861514	42861514	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs745667670	NA	P-0037947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	306	552	0	ENST00000398585.3:c.356A>G	p.Lys119Arg	p.K119R	ENST00000398585	NM_001135099.1	119	aAg/aGg	4/14	1	2	FACETS	0.962	0.91	1	0.962	0.91	1	CLONAL	1	TRUE	1	0.791628424338634	2		552	804	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0037950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	134	557	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	1	2	FACETS	0.961	0.876	1	0.961	0.876	1	CLONAL	1	TRUE	1	0.427579248279246	2		557	652	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0037950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	173	532	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.427579248279246	2		533	803	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793287	242793287	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	189	746	1	ENST00000334409.5:c.790C>A	p.Arg264Ser	p.R264S	ENST00000334409	NM_005018.2	264	Cgc/Agc	5/5	0.427579248279246	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.427579248279246	1		747	626	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056330	26056330	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	110	517	0	ENST00000343677.2:c.327G>C	p.Lys109Asn	p.K109N	ENST00000343677	NM_005319.3	109	aaG/aaC	1/1	0.427579248279246	3	FACETS	1	0.951	1	0.545	0.491	0.602	CLONAL	1	TRUE	1	0.427579248279246	3		517	573	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554893	187554893	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0037950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	252	429	0	ENST00000441802.2:c.4268C>G	p.Ser1423Ter	p.S1423*	ENST00000441802	NM_005245.3	1423	tCa/tGa	7/27	0.427579248279246	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.427579248279246	2		429	549	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435173	18435173	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	79	366	0	ENST00000266497.5:c.158A>T	p.His53Leu	p.H53L	ENST00000266497		53	cAc/cTc	1/31	0.240907588526505	1	FACETS	0.792	0.701	0.888	0.792	0.701	0.888	INDETERMINATE	1	TRUE	0	0.427579248279246	1		366	367	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760803	59760803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	116	497	0	ENST00000259008.2:c.3604G>A	p.Glu1202Lys	p.E1202K	ENST00000259008	NM_032043.2	1202	Gaa/Aaa	20/20	1	2	FACETS	0.955	0.864	1	0.955	0.864	1	CLONAL	1	TRUE	1	0.427579248279246	2		497	568	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732948	30732948	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	90	314	0	ENST00000295754.5:c.1561T>C	p.Trp521Arg	p.W521R	ENST00000295754	NM_003242.5	521	Tgg/Cgg	7/7	0.427579248279246	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.427579248279246	1		314	302	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902808	1902809	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0037950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	131	583	0	ENST00000382891.5:c.430dup	p.Cys144LeufsTer3	p.C144Lfs*3	ENST00000382891	NM_133335.3	143	att/aTtt	2/22	0.427579248279246	1	FACETS	0.859	0.783	0.938	0.859	0.783	0.938	CLONAL	1	TRUE	0	0.427579248279246	1		583	561	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604632	55604632	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	261	564	0	ENST00000288135.5:c.2840A>T	p.Gln947Leu	p.Q947L	ENST00000288135	NM_000222.2	947	cAg/cTg	21/21	0.427579248279246	2	FACETS	0.985	0.93	1	0.985	0.93	1	CLONAL	2	TRUE	0	0.427579248279246	2		564	620	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177403	56177403	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	78	340	0	ENST00000399503.3:c.2376G>T	p.Lys792Asn	p.K792N	ENST00000399503	NM_005921.1	792	aaG/aaT	14/20	1	2	FACETS	0.903	0.798	1	0.903	0.798	1	CLONAL	1	TRUE	1	0.427579248279246	2		340	404	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123234427	123234428	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0037950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	84	355	0	ENST00000218089.9:c.3789dup	p.Gly1264TrpfsTer12	p.G1264Wfs*12	ENST00000218089	NM_001042749.1	1263	ctt/cTtt	35/35	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.427579248279246	2		355	390	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	61	320	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.451318584601937	2		321	263	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0037958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	107	222	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.451318584601937	2		222	450	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791730	42791730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	32	653	1	ENST00000575354.2:c.616G>A	p.Ala206Thr	p.A206T	ENST00000575354	NM_015125.3	206	Gcc/Acc	5/20	0.451318584601937	1	FACETS	0.183	0.148	0.223	0.183	0.148	0.223	SUBCLONAL	1	TRUE	0	0.451318584601937	1		654	600	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	77	320	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.998	0.879	1	0.998	0.879	1	CLONAL	1	TRUE	1	0.34	2		321	454	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374244	138374244	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	92	378	0	ENST00000289153.2:c.3200A>T	p.Asp1067Val	p.D1067V	ENST00000289153	NM_006219.2	1067	gAc/gTc	22/22	1	2	FACETS	0.997	0.888	1	0.997	0.888	1	CLONAL	1	TRUE	1	0.34	2		378	543	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711973	89711973	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	46	333	0	ENST00000371953.3:c.591G>C	p.Lys197Asn	p.K197N	ENST00000371953	NM_000314.4	197	aaG/aaC	6/9	0.296219956320266	1	FACETS	0.483	0.407	0.567	0.483	0.407	0.567	SUBCLONAL	1	TRUE	0	0.34	1		333	465	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0038021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	270	546	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.525403150159412	3	FACETS	0.855	0.806	0.906	0.855	0.806	0.906	CLONAL	2	TRUE	1	0.5232242486429	3		546	761	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0038021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	85	445	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.779	0.692	0.871	0.779	0.692	0.871	SUBCLONAL	1	TRUE	1	0.5232242486429	2		445	417	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249029	55249029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs483352806	NA	P-0038021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	285	531	0	ENST00000275493.2:c.2327G>A	p.Arg776His	p.R776H	ENST00000275493	NM_005228.3	776	cGc/cAc	20/28	0.525403150159412	3	FACETS	0.916	0.866	0.967	0.916	0.866	0.967	CLONAL	2	TRUE	1	0.5232242486429	3		531	750	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711971	89711971	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1554900629	NA	P-0038021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	74	306	0	ENST00000371953.3:c.589A>T	p.Lys197Ter	p.K197*	ENST00000371953	NM_000314.4	197	Aag/Tag	6/9	0.5232242486429	1	FACETS	0.746	0.66	0.836	0.746	0.66	0.836	SUBCLONAL	1	TRUE	0	0.5232242486429	1		306	280	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514692	103514692	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	115	335	0	ENST00000355739.4:c.1193A>G	p.Asp398Gly	p.D398G	ENST00000355739	NM_000123.3	398	gAc/gGc	8/15	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.5232242486429	2		335	431	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0038022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	108	554	0	ENST00000397752.3:c.3028+1G>A		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.325831229683171	1	FACETS	0.858	0.771	0.949	0.858	0.771	0.949	CLONAL	1	TRUE	0	0.325831229683171	1		554	647	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622515	28622515	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	63	314	0	ENST00000241453.7:c.1102T>C	p.Cys368Arg	p.C368R	ENST00000241453	NM_004119.2	368	Tgt/Cgt	9/24	1	2	FACETS	0.904	0.784	1	0.904	0.784	1	CLONAL	1	TRUE	1	0.325831229683171	2		314	428	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56911020	56911020	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	93	439	0	ENST00000519728.1:c.1166C>T	p.Ala389Val	p.A389V	ENST00000519728	NM_002350.3	389	gCt/gTt	11/13	1	2	FACETS	0.922	0.821	1	0.922	0.821	1	CLONAL	1	TRUE	1	0.325831229683171	2		439	619	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426267	49426268	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0038398-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	405	871	1	ENST00000301067.7:c.12220_12221del	p.Gln4074ThrfsTer32	p.Q4074Tfs*32	ENST00000301067	NM_003482.3	4074	CAa/a	39/54	0.174614572673269	3	FACETS	0.891	0.849	0.934	0.594	0.566	0.623	INDETERMINATE	2	TRUE	0	0.485602262022941	3		872	1163	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427018	49427043	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGGCCCTGGGGGCCCAAAGCTCCA	GAGGGCCCTGGGGGCCCAAAGCTCCA	-	novel	NA	P-0038398-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	160	699	0	ENST00000301067.7:c.11445_11470del	p.Gly3816GlnfsTer187	p.G3816Qfs*187	ENST00000301067	NM_003482.3	3815	ccTGGAGCTTTGGGCCCCCAGGGCCCTCac/ccac	39/54	0.174614572673269	3	FACETS	0.927	0.851	1	0.309	0.283	0.336	INDETERMINATE	1	TRUE	0	0.485602262022941	3		699	883	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569895	95569895	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs148696745	NA	P-0038398-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	120	461	0	ENST00000393063.1:c.3838A>T	p.Ser1280Cys	p.S1280C	ENST00000393063	NM_030621.3	1280	Agc/Tgc	22/28	0.485602262022941	3	FACETS	0.986	0.893	1	0.493	0.446	0.542	CLONAL	1	TRUE	1	0.485602262022941	3		461	623	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647314	23647314	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0038398-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	183	613	0	ENST00000261584.4:c.553A>T	p.Lys185Ter	p.K185*	ENST00000261584	NM_024675.3	185	Aaa/Taa	4/13	0.485602262022941	2	FACETS	0.925	0.855	0.997	0.462	0.427	0.499	CLONAL	1	TRUE	0	0.485602262022941	2		613	815	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0038398-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	432	649	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	0.485602262022941	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.485602262022941	2		649	822	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856347	45856347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038398-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	244	730	1	ENST00000391945.4:c.1825G>A	p.Asp609Asn	p.D609N	ENST00000391945	NM_000400.3	609	Gac/Aac	19/23	0.110711045343855	5	FACETS	0.758	0.707	0.81			1	INDETERMINATE	2	TRUE	NA	0.485602262022941	5		731	1146	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439782	220439782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148567617	NA	P-0038398-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	185	775	0	ENST00000243786.2:c.635C>T	p.Thr212Met	p.T212M	ENST00000243786	NM_002191.3	212	aCg/aTg	2/2	0.485602262022941	3	FACETS	0.924	0.852	0.998	0.308	0.284	0.333	CLONAL	1	TRUE	0	0.485602262022941	3		775	1025	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379354	225379354	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038398-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	366	618	0	ENST00000264414.4:c.514G>C	p.Glu172Gln	p.E172Q	ENST00000264414	NM_003590.4	172	Gag/Cag	4/16	NA	2	FACETS	0.996	0.951	1			1	INDETERMINATE	2	TRUE	NA	0.485602262022941	2		618	757	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89176407	89176407	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038398-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	79	312	0	ENST00000336596.2:c.137C>T	p.Ser46Phe	p.S46F	ENST00000336596	NM_005233.5	46	tCt/tTt	2/17	0.158399010376655	3	FACETS	0.911	0.804	1	0.455	0.402	0.512	INDETERMINATE	1	TRUE	1	0.485602262022941	3		312	444	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589623	67589634	+	inframe_deletion	In_Frame_Del	DEL	ATATGATAGATT	ATATGATAGATT	-	novel	NA	P-0038398-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	33	317	0	ENST00000274335.5:c.1392_1403del	p.Asp464_Tyr467del	p.D464_Y467del	ENST00000274335		462	gaATATGATAGATTa/gaa	10/15	0.485602262022941	2	FACETS	0.321	0.261	0.389	0.161	0.13	0.195	SUBCLONAL	1	TRUE	0	0.485602262022941	2		317	423	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971115	21971133	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTCGGGTGAGAGTGGCG	GGGTCGGGTGAGAGTGGCG	-	rs730881674	NA	P-0038398-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	122	530	0	ENST00000304494.5:c.225_243del	p.Ala76CysfsTer64	p.A76Cfs*64	ENST00000304494	NM_000077.4	75	ccCGCCACTCTCACCCGACCC/cc	2/3	0.485602262022941	1	FACETS	0.702	0.637	0.77	0.702	0.637	0.77	SUBCLONAL	1	TRUE	0	0.485602262022941	1		530	542	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248121	98248121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780705	NA	P-0038398-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	354	515	1	ENST00000331920.6:c.430C>T	p.Arg144Cys	p.R144C	ENST00000331920	NM_000264.3	144	Cgc/Tgc	3/24	0.485602262022941	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.485602262022941	4		516	1056	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623686	43623686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532862288	NA	P-0038961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	120	406	1	ENST00000355710.3:c.3314C>T	p.Ala1105Val	p.A1105V	ENST00000355710	NM_020975.4	1105	gCg/gTg	20/20	0.364873795000378	3	FACETS	0.933	0.842	1	0.466	0.421	0.514	CLONAL	1	TRUE	1	0.364873795000378	3		407	834	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39311705	39311705	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	79	676	0	ENST00000373001.3:c.954C>G	p.Ile318Met	p.I318M	ENST00000373001	NM_022157.3	318	atC/atG	6/7	0.345621151740652	2	FACETS	0.409	0.359	0.464	0.205	0.179	0.232	SUBCLONAL	1	TRUE	0	0.364873795000378	2		676	1058	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432854	432854	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	96	429	0	ENST00000399788.2:c.2062C>A	p.Leu688Ile	p.L688I	ENST00000399788	NM_001042603.1	688	Ctc/Atc	15/28	1	2	FACETS	0.772	0.688	0.861	0.772	0.688	0.861	SUBCLONAL	1	TRUE	1	0.364873795000378	2		429	682	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579365	7579388	+	inframe_deletion	In_Frame_Del	DEL	CGTAGCTGCCCTGGTAGGTTTTCT	CGTAGCTGCCCTGGTAGGTTTTCT	-	novel	NA	P-0038961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	148	745	0	ENST00000269305.4:c.299_322del	p.Gln100_Gly108delinsArg	p.Q100_G108delinsR	ENST00000269305	NM_001126112.2	100	cAGAAAACCTACCAGGGCAGCTACGgt/cgt	4/11	0.316803248088106	1	FACETS	0.734	0.671	0.802	0.734	0.671	0.802	SUBCLONAL	1	TRUE	0	0.364873795000378	1		745	903	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808958	1808958	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	182	557	0	ENST00000260795.2:c.2393del	p.Pro798HisfsTer22	p.P798Hfs*22	ENST00000260795		797	gCc/gc	17/17	0.161834583662052	3	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.364873795000378	3		557	936	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054233	30054233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555994816	NA	P-0038973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	285	511	1	ENST00000338641.4:c.655G>A	p.Val219Met	p.V219M	ENST00000338641	NM_000268.3	219	Gtg/Atg	7/16	0.610122174129926	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.610122174129926	1		512	641	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0039032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	118	422	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.136544855585251	4	FACETS	0.926	0.84	1	1	0.976	1	CLONAL	4	TRUE	1	0.158842695429516	4		422	465	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217315	11217335	+	inframe_deletion	In_Frame_Del	DEL	CGTGCAGTTTCTCATACCAGG	CGTGCAGTTTCTCATACCAGG	-	novel	NA	P-0039032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	67	592	0	ENST00000361445.4:c.4343_4363del	p.Thr1448_Glu1455delinsLys	p.T1448_E1455delinsK	ENST00000361445	NM_004958.3	1448	aCCTGGTATGAGAAACTGCACGag/aag	30/58	0.158842695429516	0	FACETS	1	0.959	1			1	CLONAL	1	TRUE	0	0.158842695429516	0		592	558	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435979	49435979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	143	701	0	ENST00000301067.7:c.6002G>A	p.Arg2001Gln	p.R2001Q	ENST00000301067	NM_003482.3	2001	cGg/cAg	28/54	1	2	FACETS	1	0.915	1	1	0.991	1	CLONAL	2	TRUE	1	0.158842695429516	2		701	897	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549263	21549263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780614508	NA	P-0039032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	91	761	2	ENST00000382592.4:c.3013G>A	p.Val1005Ile	p.V1005I	ENST00000382592	NM_014572.2	1005	Gta/Ata	8/8	1	2	FACETS	0.757	0.672	0.848	1	0.979	1	SUBCLONAL	2	TRUE	1	0.158842695429516	2		763	757	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046611	30046611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556530827	NA	P-0039032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	84	437	0	ENST00000331968.5:c.2572C>T	p.Arg858Cys	p.R858C	ENST00000331968	NM_002742.2	858	Cgc/Tgc	18/18	1	2	FACETS	0.976	0.864	1	1	0.984	1	CLONAL	2	TRUE	1	0.158842695429516	2		437	542	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457304	67457304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223765	NA	P-0039032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	47	546	1	ENST00000327367.4:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000327367	NM_005902.3	93	cGa/cAa	2/9	1	2	FACETS	0.87	0.733	1	0.87	0.733	1	CLONAL	1	TRUE	1	0.158842695429516	2		547	680	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473635	67473635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906853	NA	P-0039032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	129	561	0	ENST00000327367.4:c.715G>A	p.Glu239Lys	p.E239K	ENST00000327367	NM_005902.3	239	Gag/Aag	6/9	0.124980737730721	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.158842695429516	2		561	731	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394805	45394805	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	32	204	0	ENST00000262160.6:c.544C>T	p.Arg182Ter	p.R182*	ENST00000262160	NM_005901.5	182	Cga/Tga	5/11	0.158842695429516	0	FACETS	0.906	0.743	1			1	CLONAL	2	TRUE	0	0.158842695429516	0		204	187	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0039032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	31	167	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	1	2	FACETS	0.952	0.776	1	1	0.958	1	CLONAL	2	TRUE	1	0.158842695429516	2		167	205	SUCCESS
APC	324	MSKCC	GRCh37	5	112174119	112174119	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1554084512	NA	P-0039032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	45	217	0	ENST00000257430.4:c.2828C>A	p.Ser943Ter	p.S943*	ENST00000257430	NM_000038.5	943	tCa/tAa	16/16	1	2	FACETS	1	0.886	1	1	0.973	1	CLONAL	2	TRUE	1	0.158842695429516	2		217	268	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0039032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	55	245	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	1	0.951	1	1	0.98	1	CLONAL	2	TRUE	1	0.158842695429516	2		245	279	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150382	157150382	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	81	415	0	ENST00000346085.5:c.1564G>C	p.Val522Leu	p.V522L	ENST00000346085	NM_020732.3	522	Gtg/Ctg	2/20	1	2	FACETS	1	0.917	1	1	0.985	1	CLONAL	2	TRUE	1	0.158842695429516	2		415	487	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002734	37002734	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	112	534	0	ENST00000358127.4:c.515C>T	p.Thr172Met	p.T172M	ENST00000358127	NM_001280556.1	172	aCg/aTg	5/10	0.158842695429516	3	FACETS	0.988	0.889	1	0.659	0.593	0.729	CLONAL	2	TRUE	0	0.158842695429516	3		534	770	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0039078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	140	426	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.388934759992825	2		426	685	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651195	206651195	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	168	712	1	ENST00000367120.3:c.805C>A	p.Leu269Met	p.L269M	ENST00000367120	NM_014002.3	269	Ctg/Atg	8/22	1	2	FACETS	0.873	0.801	0.947	0.873	0.801	0.947	CLONAL	1	TRUE	1	0.388934759992825	2		713	990	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100427	8100427	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	156	778	0	ENST00000346208.3:c.401C>A	p.Pro134His	p.P134H	ENST00000346208		134	cCc/cAc	3/6	1	2	FACETS	0.852	0.779	0.927	0.852	0.779	0.927	CLONAL	1	TRUE	1	0.388934759992825	2		778	942	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220505	1220505	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs886039554	NA	P-0039078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	426	778	1	ENST00000326873.7:c.597+1G>T		p.X199_splice	ENST00000326873	NM_000455.4	199			0.388934759992825	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.388934759992825	2		779	1031	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015690	27015690	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	169	537	1	ENST00000335756.4:c.277G>T	p.Ala93Ser	p.A93S	ENST00000335756	NM_001809.3	93	Gcc/Tcc	3/5	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.388934759992825	2		538	766	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47601037	47601037	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	195	570	1	ENST00000263735.4:c.275A>T	p.Asp92Val	p.D92V	ENST00000263735	NM_002354.2	92	gAt/gTt	3/9	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.388934759992825	2		571	901	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242695	98242695	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773704443	NA	P-0039078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	123	432	2	ENST00000331920.6:c.922G>A	p.Ala308Thr	p.A308T	ENST00000331920	NM_000264.3	308	Gcc/Acc	6/24	1	2	FACETS	0.99	0.897	1	0.99	0.897	1	CLONAL	1	TRUE	1	0.388934759992825	2		434	639	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0039110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	49	416	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.88	0.744	1	0.88	0.744	1	CLONAL	1	TRUE	1	0.17	2		416	655	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0039110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	64	749	0	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.17	2		749	670	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0039113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	84	431	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.941	0.833	1	0.941	0.833	1	CLONAL	1	TRUE	1	0.34	2		432	525	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0039113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	39	442	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.772	0.643	0.915	0.772	0.643	0.915	CLONAL	1	TRUE	1	0.34	2		442	297	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0039113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	97	479	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.34	2		483	563	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0039113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	48	403	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.726	0.615	0.847	0.726	0.615	0.847	SUBCLONAL	1	TRUE	1	0.34	2		403	389	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438316	110438317	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	rs532810290	NA	P-0039113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	17	166	0	ENST00000375856.3:c.82_84dup	p.Asn28dup	p.N28dup	ENST00000375856	NM_003749.2	28	-/AAC	1/2	1	2	FACETS	0.521	0.39	0.675	0.521	0.39	0.675	SUBCLONAL	1	TRUE	1	0.34	2		166	192	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038896	12038896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	77	390	0	ENST00000396373.4:c.1189G>A	p.Ala397Thr	p.A397T	ENST00000396373	NM_001987.4	397	Gcc/Acc	7/8	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.34	2		390	347	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116263	209116263	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	28	243	1	ENST00000345146.2:c.13del	p.Ile5SerfsTer7	p.I5Sfs*7	ENST00000345146	NM_005896.2	5	Atc/tc	3/10	1	2	FACETS	0.726	0.583	0.886	0.726	0.583	0.886	SUBCLONAL	1	TRUE	1	0.34	2		244	227	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0039113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	86	442	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.34	2		447	410	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905055	50905055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	113	635	4	ENST00000440232.2:c.342del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	113	Ggg/gg	4/27	0.3	3	FACETS	0.84	0.76	0.923	0.84	0.76	0.923	CLONAL	2	TRUE	1	0.34	3		639	463	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499363	89499363	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1317589623	NA	P-0039113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	48	397	0	ENST00000336596.2:c.2538del	p.Met847TrpfsTer10	p.M847Wfs*10	ENST00000336596	NM_005233.5	845	Ccc/cc	15/17	1	2	FACETS	0.731	0.62	0.854	0.731	0.62	0.854	SUBCLONAL	1	TRUE	1	0.34	2		397	386	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295774	212295774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754127388	NA	P-0039113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	71	606	0	ENST00000342788.4:c.2539C>T	p.Arg847Cys	p.R847C	ENST00000342788	NM_005235.2	847	Cgt/Tgt	21/28	1	2	FACETS	0.881	0.771	0.999	0.881	0.771	0.999	CLONAL	1	TRUE	1	0.34	2		606	474	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098422	11098422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764188556	NA	P-0039113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	70	483	1	ENST00000358026.2:c.940G>A	p.Ala314Thr	p.A314T	ENST00000358026	NM_001128849.1	314	Gcg/Acg	6/36	0.3	1	FACETS	0.963	0.845	1	0.963	0.845	1	CLONAL	1	TRUE	0	0.34	1		484	355	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005513	42005517	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAA	GAAAA	-	novel	NA	P-0039113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	104	606	0	ENST00000219905.7:c.3255_3259del	p.Arg1085SerfsTer5	p.R1085Sfs*5	ENST00000219905	NM_001164273.1	1083	ttGAAAAga/ttga	9/24	1	2	FACETS	0.9	0.806	0.998	0.9	0.806	0.998	CLONAL	1	TRUE	1	0.34	2		606	680	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592336	29592336	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs876658492	NA	P-0039113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	74	505	1	ENST00000356175.3:c.4756del	p.Tyr1586IlefsTer17	p.Y1586Ifs*17	ENST00000356175	NM_000267.3	1584	aTt/at	35/57	1	2	FACETS	0.983	0.864	1	0.983	0.864	1	CLONAL	1	TRUE	1	0.34	2		506	443	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856448	111856448	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1445323886	NA	P-0039113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	35	205	0	ENST00000341259.2:c.499G>A	p.Gly167Arg	p.G167R	ENST00000341259	NM_005475.2	167	Gga/Aga	2/8	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.34	2		205	193	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948747	71948748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760925109	NA	P-0039113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	63	735	3	ENST00000298229.2:c.3466dup	p.Arg1156ProfsTer59	p.R1156Pfs*59	ENST00000298229	NM_001567.3	1153	-/C	26/28	1	2	FACETS	0.777	0.673	0.889	0.777	0.673	0.889	SUBCLONAL	1	TRUE	1	0.34	2		738	477	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226352	2226352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758688224	NA	P-0039113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	114	898	0	ENST00000398665.3:c.3832G>A	p.Ala1278Thr	p.A1278T	ENST00000398665	NM_032482.2	1278	Gcc/Acc	27/28	0.3	1	FACETS	0.852	0.769	0.94	0.852	0.769	0.94	CLONAL	1	TRUE	0	0.34	1		898	653	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089556	27089556	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753334968	NA	P-0039113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	75	741	0	ENST00000324856.7:c.2512G>A	p.Gly838Arg	p.G838R	ENST00000324856	NM_006015.4	838	Gga/Aga	8/20	1	2	FACETS	0.796	0.699	0.901	0.796	0.699	0.901	CLONAL	1	TRUE	1	0.34	2		741	554	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622023	43622024	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GA	GA	AC	novel	NA	P-0039113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	45	332	0	ENST00000355710.3:c.3040_3041delinsAC	p.Asp1014Thr	p.D1014T	ENST00000355710	NM_020975.4	1014	GAc/ACc	19/20	1	2	FACETS	0.91	0.769	1	0.91	0.769	1	CLONAL	1	TRUE	1	0.34	2		332	291	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944177	71944178	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs1226924888	NA	P-0039113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	80	723	0	ENST00000298229.2:c.2012_2013del	p.Tyr671CysfsTer19	p.Y671Cfs*19	ENST00000298229	NM_001567.3	670	acATat/acat	17/28	1	2	FACETS	0.934	0.824	1	0.934	0.824	1	CLONAL	1	TRUE	1	0.34	2		723	504	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383279	4383279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	33	601	0	ENST00000261254.3:c.73C>T	p.Arg25Cys	p.R25C	ENST00000261254	NM_001759.3	25	Cgc/Tgc	1/5	1	2	FACETS	0.479	0.39	0.58	0.479	0.39	0.58	SUBCLONAL	1	TRUE	1	0.34	2		601	405	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492642	56492642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	80	529	0	ENST00000267101.3:c.2792C>T	p.Ala931Val	p.A931V	ENST00000267101	NM_001982.3	931	gCa/gTa	23/28	1	2	FACETS	0.968	0.855	1	0.968	0.855	1	CLONAL	1	TRUE	1	0.34	2		529	486	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514959	103514959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560626350	NA	P-0039113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	36	395	0	ENST00000355739.4:c.1460C>T	p.Pro487Leu	p.P487L	ENST00000355739	NM_000123.3	487	cCg/cTg	8/15	1	2	FACETS	0.784	0.648	0.935	0.784	0.648	0.935	CLONAL	1	TRUE	1	0.34	2		395	270	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95592979	95592980	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	62	394	0	ENST00000393063.1:c.840dup	p.Ile281TyrfsTer3	p.I281Yfs*3	ENST00000393063	NM_030621.3	280	-/T	8/28	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.34	2		394	355	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88671962	88671962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	41	289	0	ENST00000360948.2:c.1208G>A	p.Ser403Asn	p.S403N	ENST00000360948	NM_001012338.2	403	aGc/aAc	10/19	1	2	FACETS	0.984	0.826	1	0.984	0.826	1	CLONAL	1	TRUE	1	0.34	2		289	245	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15978969	15978971	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0039113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	63	479	0	ENST00000268712.3:c.3547_3549del	p.Val1183del	p.V1183del	ENST00000268712	NM_006311.3	1183	GTG/-	27/46	1	2	FACETS	0.797	0.691	0.912	0.797	0.691	0.912	CLONAL	1	TRUE	1	0.34	2		479	465	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552270	29552270	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1421531300	NA	P-0039113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	49	458	0	ENST00000356175.3:c.2001+2T>C		p.X667_splice	ENST00000356175	NM_000267.3	667			1	2	FACETS	0.858	0.73	0.997	0.858	0.73	0.997	CLONAL	1	TRUE	1	0.34	2		458	336	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653256	29653257	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0039113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	24	284	0	ENST00000356175.3:c.5192_5193del	p.Lys1731SerfsTer4	p.K1731Sfs*4	ENST00000356175	NM_000267.3	1731	AAa/a	36/57	1	2	FACETS	0.598	0.471	0.744	0.598	0.471	0.744	SUBCLONAL	1	TRUE	1	0.34	2		284	236	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52621423	52621423	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	88	521	0	ENST00000394830.3:c.2994del	p.Tyr998Ter	p.Y998*	ENST00000394830	NM_018313.4	998	taC/ta	20/30	0.3	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.34	1		521	371	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169953085	169953086	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs767213844	NA	P-0039113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	78	521	0	ENST00000295797.4:c.169_170del	p.Met57ValfsTer4	p.M57Vfs*4	ENST00000295797	NM_002740.5	57	ATg/g	2/18	1	2	FACETS	0.948	0.836	1	0.948	0.836	1	CLONAL	1	TRUE	1	0.34	2		521	484	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981761	70981761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1268843071	NA	P-0039113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	87	987	4	ENST00000276594.2:c.335C>T	p.Pro112Leu	p.P112L	ENST00000276594	NM_024504.3	112	cCg/cTg	2/8	1	2	FACETS	0.791	0.701	0.887	0.791	0.701	0.887	SUBCLONAL	1	TRUE	1	0.34	2		991	647	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740624	145740625	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TC	TC	-	rs776743331	NA	P-0039113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	89	848	0	ENST00000428558.2:c.1392_1393del	p.Glu464AspfsTer4	p.E464Dfs*4	ENST00000428558	NM_004260.3	464	gaGAcg/gacg	8/22	1	2	FACETS	0.977	0.868	1	0.977	0.868	1	CLONAL	1	TRUE	1	0.34	2		848	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	160	431	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.541482610895961	1	FACETS	0.991	0.918	1	0.991	0.918	1	CLONAL	1	TRUE	0	0.541482610895961	1		432	435	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	105	442	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.541482610895961	2		442	364	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	150	479	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.944	0.867	1	0.944	0.867	1	CLONAL	1	TRUE	1	0.541482610895961	2		483	587	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	115	403	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.822	0.743	0.903	0.822	0.743	0.903	CLONAL	1	TRUE	1	0.541482610895961	2		403	517	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438316	110438317	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	rs532810290	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	20	166	0	ENST00000375856.3:c.82_84dup	p.Asn28dup	p.N28dup	ENST00000375856	NM_003749.2	28	-/AAC	1/2	1	2	FACETS	0.48	0.37	0.606	0.48	0.37	0.606	SUBCLONAL	1	TRUE	1	0.541482610895961	2		166	154	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038896	12038896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	117	390	0	ENST00000396373.4:c.1189G>A	p.Ala397Thr	p.A397T	ENST00000396373	NM_001987.4	397	Gcc/Acc	7/8	0.166419469062725	3	FACETS	1	0.965	1	0.566	0.513	0.621	INDETERMINATE	1	TRUE	1	0.541482610895961	3		390	485	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116263	209116263	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	62	243	1	ENST00000345146.2:c.13del	p.Ile5SerfsTer7	p.I5Sfs*7	ENST00000345146	NM_005896.2	5	Atc/tc	3/10	1	2	FACETS	0.736	0.641	0.839	0.736	0.641	0.839	SUBCLONAL	1	TRUE	1	0.541482610895961	2		244	311	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	103	442	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.902	0.812	0.995	0.902	0.812	0.995	CLONAL	1	TRUE	1	0.541482610895961	2		447	422	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905055	50905055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	250	635	4	ENST00000440232.2:c.342del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	113	Ggg/gg	4/27	0.541482610895961	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.541482610895961	3		639	558	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499363	89499363	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1317589623	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	114	397	0	ENST00000336596.2:c.2538del	p.Met847TrpfsTer10	p.M847Wfs*10	ENST00000336596	NM_005233.5	845	Ccc/cc	15/17	1	2	FACETS	0.998	0.905	1	0.998	0.905	1	CLONAL	1	TRUE	1	0.541482610895961	2		397	422	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295774	212295774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754127388	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	142	606	0	ENST00000342788.4:c.2539C>T	p.Arg847Cys	p.R847C	ENST00000342788	NM_005235.2	847	Cgt/Tgt	21/28	1	2	FACETS	0.917	0.839	0.997	0.917	0.839	0.997	CLONAL	1	TRUE	1	0.541482610895961	2		606	572	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098422	11098422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764188556	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	85	483	1	ENST00000358026.2:c.940G>A	p.Ala314Thr	p.A314T	ENST00000358026	NM_001128849.1	314	Gcg/Acg	6/36	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.541482610895961	2		484	281	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005513	42005517	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAA	GAAAA	-	novel	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	184	606	0	ENST00000219905.7:c.3255_3259del	p.Arg1085SerfsTer5	p.R1085Sfs*5	ENST00000219905	NM_001164273.1	1083	ttGAAAAga/ttga	9/24	1	2	FACETS	0.961	0.89	1	0.961	0.89	1	CLONAL	1	TRUE	1	0.541482610895961	2		606	707	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592336	29592336	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs876658492	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	151	505	1	ENST00000356175.3:c.4756del	p.Tyr1586IlefsTer17	p.Y1586Ifs*17	ENST00000356175	NM_000267.3	1584	aTt/at	35/57	1	2	FACETS	0.989	0.909	1	0.989	0.909	1	CLONAL	1	TRUE	1	0.541482610895961	2		506	564	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856448	111856448	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1445323886	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	71	205	0	ENST00000341259.2:c.499G>A	p.Gly167Arg	p.G167R	ENST00000341259	NM_005475.2	167	Gga/Aga	2/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.541482610895961	2		205	220	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948747	71948748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760925109	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	151	735	3	ENST00000298229.2:c.3466dup	p.Arg1156ProfsTer59	p.R1156Pfs*59	ENST00000298229	NM_001567.3	1153	-/C	26/28	1	2	FACETS	0.947	0.87	1	0.947	0.87	1	CLONAL	1	TRUE	1	0.541482610895961	2		738	589	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226352	2226352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758688224	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	193	898	0	ENST00000398665.3:c.3832G>A	p.Ala1278Thr	p.A1278T	ENST00000398665	NM_032482.2	1278	Gcc/Acc	27/28	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.541482610895961	2		898	627	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089556	27089556	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753334968	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	148	741	0	ENST00000324856.7:c.2512G>A	p.Gly838Arg	p.G838R	ENST00000324856	NM_006015.4	838	Gga/Aga	8/20	1	2	FACETS	0.923	0.847	1	0.923	0.847	1	CLONAL	1	TRUE	1	0.541482610895961	2		741	592	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944177	71944178	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs1226924888	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	118	723	0	ENST00000298229.2:c.2012_2013del	p.Tyr671CysfsTer19	p.Y671Cfs*19	ENST00000298229	NM_001567.3	670	acATat/acat	17/28	1	2	FACETS	0.77	0.697	0.847	0.77	0.697	0.847	SUBCLONAL	1	TRUE	1	0.541482610895961	2		723	566	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383279	4383279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	93	601	0	ENST00000261254.3:c.73C>T	p.Arg25Cys	p.R25C	ENST00000261254	NM_001759.3	25	Cgc/Tgc	1/5	1	2	FACETS	0.883	0.791	0.98	0.883	0.791	0.98	CLONAL	1	TRUE	1	0.541482610895961	2		601	389	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492642	56492642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	141	529	0	ENST00000267101.3:c.2792C>T	p.Ala931Val	p.A931V	ENST00000267101	NM_001982.3	931	gCa/gTa	23/28	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.541482610895961	2		529	498	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514959	103514959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560626350	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	96	395	0	ENST00000355739.4:c.1460C>T	p.Pro487Leu	p.P487L	ENST00000355739	NM_000123.3	487	cCg/cTg	8/15	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.541482610895961	2		395	328	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95592979	95592980	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	131	394	0	ENST00000393063.1:c.840dup	p.Ile281TyrfsTer3	p.I281Yfs*3	ENST00000393063	NM_030621.3	280	-/T	8/28	1	2	FACETS	0.898	0.819	0.98	0.898	0.819	0.98	CLONAL	1	TRUE	1	0.541482610895961	2		394	539	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88671962	88671962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	75	289	0	ENST00000360948.2:c.1208G>A	p.Ser403Asn	p.S403N	ENST00000360948	NM_001012338.2	403	aGc/aAc	10/19	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.541482610895961	2		289	270	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15978969	15978971	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	131	479	0	ENST00000268712.3:c.3547_3549del	p.Val1183del	p.V1183del	ENST00000268712	NM_006311.3	1183	GTG/-	27/46	1	2	FACETS	0.966	0.882	1	0.966	0.882	1	CLONAL	1	TRUE	1	0.541482610895961	2		479	501	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552270	29552270	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1421531300	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	97	458	0	ENST00000356175.3:c.2001+2T>C		p.X667_splice	ENST00000356175	NM_000267.3	667			1	2	FACETS	0.824	0.739	0.913	0.824	0.739	0.913	CLONAL	1	TRUE	1	0.541482610895961	2		458	435	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653256	29653257	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	83	284	0	ENST00000356175.3:c.5192_5193del	p.Lys1731SerfsTer4	p.K1731Sfs*4	ENST00000356175	NM_000267.3	1731	AAa/a	36/57	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.541482610895961	2		284	295	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52621423	52621423	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	151	521	0	ENST00000394830.3:c.2994del	p.Tyr998Ter	p.Y998*	ENST00000394830	NM_018313.4	998	taC/ta	20/30	0.541482610895961	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.541482610895961	1		521	406	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169953085	169953086	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs767213844	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	139	521	0	ENST00000295797.4:c.169_170del	p.Met57ValfsTer4	p.M57Vfs*4	ENST00000295797	NM_002740.5	57	ATg/g	2/18	1	2	FACETS	0.87	0.795	0.948	0.87	0.795	0.948	CLONAL	1	TRUE	1	0.541482610895961	2		521	590	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981761	70981761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1268843071	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	187	987	4	ENST00000276594.2:c.335C>T	p.Pro112Leu	p.P112L	ENST00000276594	NM_024504.3	112	cCg/cTg	2/8	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.541482610895961	2		991	659	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740624	145740625	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TC	TC	-	rs776743331	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	161	848	0	ENST00000428558.2:c.1392_1393del	p.Glu464AspfsTer4	p.E464Dfs*4	ENST00000428558	NM_004260.3	464	gaGAcg/gacg	8/22	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.541482610895961	2		848	584	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210935	133210935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	121	629	0	ENST00000320574.5:c.5841G>T	p.Glu1947Asp	p.E1947D	ENST00000320574	NM_006231.2	1947	gaG/gaT	43/49	1	2	FACETS	0.899	0.817	0.985	0.899	0.817	0.985	CLONAL	1	TRUE	1	0.541482610895961	2		629	497	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	98	418	3	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.838	0.752	0.928	0.838	0.752	0.928	CLONAL	1	TRUE	1	0.541482610895961	2		421	432	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	116	441	2	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.541482610895961	2		443	403	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	112	589	5	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.541482610895961	2		594	389	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	202	607	11	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.973	0.904	1	0.973	0.904	1	CLONAL	1	TRUE	1	0.541482610895961	2		618	767	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622024	43622024	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	74	378	0	ENST00000355710.3:c.3041A>C	p.Asp1014Ala	p.D1014A	ENST00000355710	NM_020975.4	1014	gAc/gCc	19/20	1	2	FACETS	0.882	0.779	0.99	0.882	0.779	0.99	CLONAL	1	TRUE	1	0.541482610895961	2		378	310	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096298	2096298	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	219	836	0	ENST00000219066.1:c.209G>T	p.Gly70Val	p.G70V	ENST00000219066	NM_002528.5	70	gGc/gTc	2/6	0.541482610895961	3	FACETS	1	0.98	1	0.568	0.529	0.608	CLONAL	1	TRUE	1	0.541482610895961	3		836	905	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732524	74732524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	32	198	0	ENST00000359995.5:c.385C>T	p.Arg129Ter	p.R129*	ENST00000359995	NM_001195427.1	129	Cga/Tga	2/3	1	2	FACETS	0.946	0.782	1	0.946	0.782	1	CLONAL	1	TRUE	1	0.541482610895961	2		198	125	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62305396	62305396	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202157063	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	153	706	2	ENST00000360203.5:c.869C>T	p.Ala290Val	p.A290V	ENST00000360203	NM_001283009.1	290	gCg/gTg	10/35	1	2	FACETS	0.94	0.864	1	0.94	0.864	1	CLONAL	1	TRUE	1	0.541482610895961	2		708	601	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73108207	73108207	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	31	53	0	ENST00000356692.5:c.307C>T	p.Arg103Ter	p.R103*	ENST00000356692		103	Cga/Tga	4/9	0.541482610895961	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.541482610895961	1		53	68	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31483720	31483721	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	74	235	0	ENST00000344624.3:c.2011_2012delinsAT	p.Asp671Ile	p.D671I	ENST00000344624		671	GAc/ATc	13/33	1	2	FACETS	0.987	0.874	1	0.987	0.874	1	CLONAL	1	TRUE	1	0.541482610895961	2		235	277	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564754	139564755	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs878890965	NA	P-0039113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	161	828	1	ENST00000308874.7:c.549dup	p.Arg184GlnfsTer100	p.R184Qfs*100	ENST00000308874		181	-/C	7/10	1	2	FACETS	0.938	0.864	1	0.938	0.864	1	CLONAL	1	TRUE	1	0.541482610895961	2		829	634	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	53	320	1				ENST00000310581	NM_198253.2	-/1132			0.370477865287394	1	FACETS	0.884	0.763	1	0.884	0.763	1	CLONAL	1	TRUE	0	0.428402704666659	1		321	220	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957157	81957157	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202210217	NA	P-0039116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	85	543	0	ENST00000359376.3:c.2375G>A	p.Arg792His	p.R792H	ENST00000359376	NM_002661.3	792	cGt/cAt	22/33	1	2	FACETS	0.872	0.774	0.976	0.872	0.774	0.976	CLONAL	1	TRUE	1	0.428402704666659	2		543	455	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528504	29528505	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0039116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	81	303	0	ENST00000356175.3:c.1260+2dup		p.X420_splice	ENST00000356175	NM_000267.3	420			1	2	FACETS	0.829	0.733	0.931	0.829	0.733	0.931	CLONAL	1	TRUE	1	0.428402704666659	2		303	456	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625302	69625302	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782573423	NA	P-0039116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	96	802	2	ENST00000334134.2:c.491G>A	p.Arg164His	p.R164H	ENST00000334134	NM_005247.2	164	cGc/cAc	3/3	0.370477865287394	1	FACETS	0.652	0.583	0.726	0.652	0.583	0.726	SUBCLONAL	1	TRUE	0	0.428402704666659	1		804	540	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0039237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	47	426	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.663	0.558	0.778	0.663	0.558	0.778	SUBCLONAL	1	TRUE	1	0.24	2		426	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577115	7577115	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	44	519	0	ENST00000269305.4:c.823T>G	p.Cys275Gly	p.C275G	ENST00000269305	NM_001126112.2	275	Tgt/Ggt	8/11	1	2	FACETS	0.348	0.29	0.412	0.348	0.29	0.412	SUBCLONAL	1	TRUE	1	0.24	2		519	1055	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101353	27101354	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCTT	novel	NA	P-0039237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	62	556	0	ENST00000324856.7:c.4638_4641dup	p.His1548PhefsTer25	p.H1548Ffs*25	ENST00000324856	NM_006015.4	1545	-/CCTT	18/20	1	2	FACETS	0.548	0.472	0.632	0.548	0.472	0.632	SUBCLONAL	1	TRUE	1	0.24	2		556	942	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117194	7117194	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	76	589	1	ENST00000302850.5:c.4022G>T	p.Gly1341Val	p.G1341V	ENST00000302850	NM_000208.2	1341	gGg/gTg	22/22	1	2	FACETS	0.66	0.578	0.75	0.66	0.578	0.75	SUBCLONAL	1	TRUE	1	0.24	2		590	959	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382202	152382202	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	40	358	0	ENST00000206249.3:c.1312A>T	p.Met438Leu	p.M438L	ENST00000206249	NM_000125.3	438	Atg/Ttg	6/8	1	2	FACETS	0.509	0.422	0.606	0.509	0.422	0.606	SUBCLONAL	1	TRUE	1	0.24	2		358	655	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141568617	141568617	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	106	488	0	ENST00000220592.5:c.845G>T	p.Cys282Phe	p.C282F	ENST00000220592	NM_012154.3	282	tGc/tTc	7/19	1	2	FACETS	0.986	0.883	1	0.986	0.883	1	CLONAL	1	TRUE	1	0.24	2		488	896	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562577	176562577	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039361-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	75	411	0	ENST00000439151.2:c.473G>C	p.Cys158Ser	p.C158S	ENST00000439151	NM_022455.4	158	tGt/tCt	2/23	0.495909495304838	3	FACETS	0.694	0.609	0.785	0.347	0.304	0.393	SUBCLONAL	1	TRUE	1	0.508865055856824	3		411	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0039396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	981	711	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.752172178661826	4	FACETS	0.971	0.956	0.985	0.971	0.956	0.985	CLONAL	4	TRUE	0	0.771743823143072	4		711	1160	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22412950	22412950	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	58	137	0	ENST00000344548.3:c.197G>C	p.Arg66Thr	p.R66T	ENST00000344548	NM_001039802.1	66	aGa/aCa	5/7	0.771743823143072	5	FACETS	1	0.968	1	0.476	0.414	0.542	CLONAL	1	TRUE	2	0.771743823143072	5		137	227	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602918	10602918	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	491	750	0	ENST00000171111.5:c.660C>G	p.Phe220Leu	p.F220L	ENST00000171111	NM_203500.1	220	ttC/ttG	3/6	0.739980679191711	2	FACETS	0.927	0.9	0.954	0.927	0.9	0.954	CLONAL	2	TRUE	0	0.771743823143072	2		750	686	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663013	227663013	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	620	602	0	ENST00000305123.5:c.442G>C	p.Asp148His	p.D148H	ENST00000305123	NM_005544.2	148	Gac/Cac	1/2	0.669777155883645	4	FACETS	0.876	0.849	0.904	0.876	0.849	0.904	CLONAL	3	TRUE	1	0.771743823143072	4		602	1083	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	231	320	1				ENST00000310581	NM_198253.2	-/1132			0.739615102423855	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.746104788901742	2		321	309	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576486	67576487	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	313	258	0	ENST00000274335.5:c.770dup	p.Asn257LysfsTer10	p.N257Kfs*10	ENST00000274335		255	-/A	5/15	NA	2	FACETS	0.894	0.859	0.929			1	INDETERMINATE	2	TRUE	NA	0.746104788901742	2		258	469	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678170	58678170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1461	406	640	0	ENST00000305921.3:c.395C>T	p.Ser132Leu	p.S132L	ENST00000305921	NM_003620.3	132	tCg/tTg	1/6	0.644227293508961	4	FACETS	1	0.986	1	0.37	0.351	0.39	CLONAL	1	TRUE	1	0.644227293508961	4		640	1867	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36931978	36931978	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	300	651	0	ENST00000361632.4:c.2491G>T	p.Glu831Ter	p.E831*	ENST00000361632		831	Gag/Tag	16/16	1	2	FACETS	0.995	0.939	1	0.995	0.939	1	CLONAL	1	TRUE	1	0.644227293508961	2		651	936	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65349064	65349064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1212685019	NA	P-0039434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	247	561	0	ENST00000342505.4:c.101C>T	p.Pro34Leu	p.P34L	ENST00000342505	NM_002227.2	34	cCa/cTa	3/25	1	2	FACETS	0.988	0.927	1	0.988	0.927	1	CLONAL	1	TRUE	1	0.644227293508961	2		561	776	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850759	63850759	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	196	494	0	ENST00000279873.7:c.1537G>C	p.Asp513His	p.D513H	ENST00000279873	NM_032199.2	513	Gac/Cac	10/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.644227293508961	2		494	600	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125523680	125523680	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	396	351	0	ENST00000428830.2:c.1273A>T	p.Ile425Phe	p.I425F	ENST00000428830	NM_001114121.2	425	Att/Ttt	12/14	0.644227293508961	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.644227293508961	3		351	523	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910640	32910640	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	153	421	0	ENST00000380152.3:c.2148G>T	p.Gln716His	p.Q716H	ENST00000380152		716	caG/caT	11/27	0.644227293508961	2	FACETS	0.979	0.903	1	0.49	0.451	0.529	CLONAL	1	TRUE	0	0.644227293508961	2		421	485	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941669	48941669	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0039434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	188	223	0	ENST00000267163.4:c.979A>T	p.Lys327Ter	p.K327*	ENST00000267163	NM_000321.2	327	Aaa/Taa	10/27	0.644227293508961	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.644227293508961	2		223	274	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845589	68845589	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1444822940	NA	P-0039434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	211	491	0	ENST00000261769.5:c.835A>G	p.Thr279Ala	p.T279A	ENST00000261769	NM_004360.3	279	Acc/Gcc	7/16	1	2	FACETS	0.963	0.899	1	0.963	0.899	1	CLONAL	1	TRUE	1	0.644227293508961	2		491	680	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584402	39584402	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	125	378	0	ENST00000262039.4:c.1067A>T	p.Lys356Met	p.K356M	ENST00000262039	NM_002647.2	356	aAg/aTg	10/25	1	2	FACETS	0.79	0.719	0.864	0.79	0.719	0.864	SUBCLONAL	1	TRUE	1	0.644227293508961	2		378	491	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224564	36224564	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	445	1044	0	ENST00000222270.7:c.7026G>C	p.Glu2342Asp	p.E2342D	ENST00000222270	NM_014727.1	2342	gaG/gaC	29/37	0.644227293508961	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.644227293508961	1		1044	898	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583431	46583431	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	210	455	0	ENST00000263734.3:c.359G>T	p.Gly120Val	p.G120V	ENST00000263734	NM_001430.4	120	gGa/gTa	3/16	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.644227293508961	2		455	596	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952063	178952063	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	141	347	0	ENST00000263967.3:c.3118A>T	p.Met1040Leu	p.M1040L	ENST00000263967	NM_006218.2	1040	Atg/Ttg	21/21	1	2	FACETS	0.884	0.811	0.96	0.884	0.811	0.96	CLONAL	1	TRUE	1	0.644227293508961	2		347	495	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542757	187542757	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	180	391	0	ENST00000441802.2:c.4983C>A	p.Asp1661Glu	p.D1661E	ENST00000441802	NM_005245.3	1661	gaC/gaA	10/27	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.644227293508961	2		391	548	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932403	39932403	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	323	874	0	ENST00000378444.4:c.2196C>A	p.His732Gln	p.H732Q	ENST00000378444	NM_001123385.1	732	caC/caA	4/15	NA	2	FACETS	0.89	0.841	0.94			1	INDETERMINATE	1	TRUE	NA	0.644227293508961	2		874	1127	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412662	63412662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	211	647	0	ENST00000330258.3:c.505C>A	p.Leu169Ile	p.L169I	ENST00000330258	NM_152424.3	169	Cta/Ata	2/2	NA	2	FACETS	0.85	0.791	0.91			1	INDETERMINATE	1	TRUE	NA	0.644227293508961	2		647	771	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357738	70357738	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1556339260	NA	P-0039434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	298	847	0	ENST00000374080.3:c.5989G>T	p.Gly1997Cys	p.G1997C	ENST00000374080		1997	Ggc/Tgc	41/45	NA	2	FACETS	0.828	0.78	0.878			1	INDETERMINATE	1	TRUE	NA	0.644227293508961	2		847	1117	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347846	347846	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	41	857	0	ENST00000262320.3:c.1660G>A	p.Ala554Thr	p.A554T	ENST00000262320	NM_003502.3	554	Gcc/Acc	6/11	0.163139829106729	1	FACETS	0.757	0.629	0.899	0.757	0.629	0.899	SUBCLONAL	1	FALSE	0	0.163139829106729	1		857	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578195	7578202	+	frameshift_variant	Frame_Shift_Del	DEL	CACCACCA	CACCACCA	-	novel	NA	P-0039449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	42	612	0	ENST00000269305.4:c.647_654del	p.Val216AlafsTer3	p.V216Afs*3	ENST00000269305	NM_001126112.2	216	gTGGTGGTG/g	6/11	1	2	FACETS	0.919	0.767	1	0.919	0.767	1	CLONAL	1	FALSE	1	0.163139829106729	2		612	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0039450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	507	547	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.929010462923888	1	FACETS	0.987	0.967	1	0.987	0.967	1	CLONAL	1	TRUE	0	0.929010462923888	1		547	592	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951137	48951153	+	frameshift_variant	Frame_Shift_Del	DEL	TGTGGGACAGGGTTGTG	TGTGGGACAGGGTTGTG	AAA	novel	NA	P-0039450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	52	378	1	ENST00000267163.4:c.1299_1315delinsAAA	p.Val434AsnfsTer24	p.V434Nfs*24	ENST00000267163	NM_000321.2	433	gcTGTGGGACAGGGTTGTGtc/gcAAAtc	13/27	0.929010462923888	1	FACETS	0.779	0.703	0.849	0.779	0.703	0.849	SUBCLONAL	1	TRUE	0	0.929010462923888	1		379	77	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940277	31940277	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	742	768	7	ENST00000375333.2:c.419G>T	p.Arg140Leu	p.R140L	ENST00000375333	NM_032454.1	140	cGg/cTg	2/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.929010462923888	2		775	1584	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524695	137524695	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs374675376	NA	P-0039450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	252	476	4	ENST00000367739.4:c.674G>T	p.Gly225Val	p.G225V	ENST00000367739	NM_000416.2	225	gGt/gTt	5/7	1	2	FACETS	0.876	0.826	0.927	0.876	0.826	0.927	CLONAL	1	TRUE	1	0.929010462923888	2		480	619	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	111	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.302380866806039	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.29	1		452	599	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0039592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	46	235	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.675	0.569	0.792	0.675	0.569	0.792	SUBCLONAL	1	TRUE	1	0.29	2		235	470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577543	7577543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1019340046	NA	P-0039592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	64	625	1	ENST00000269305.4:c.738G>A	p.Met246Ile	p.M246I	ENST00000269305	NM_001126112.2	246	atG/atA	7/11	0.302380866806039	1	FACETS	0.41	0.354	0.471	0.41	0.354	0.471	SUBCLONAL	1	TRUE	0	0.29	1		626	920	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044550	47044550	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	138	458	0	ENST00000377604.3:c.2047G>T	p.Glu683Ter	p.E683*	ENST00000377604	NM_001204468.1	683	Gag/Tag	18/24	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.29	1		458	567	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873657	35873678	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTCCGAGCCGCGCGGCACCT	GGCTCCGAGCCGCGCGGCACCT	-	novel	NA	P-0039592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	98	345	0	ENST00000216797.5:c.173_194del	p.Glu58AlafsTer25	p.E58Afs*25	ENST00000216797	NM_020529.2	58	gAGGTGCCGCGCGGCTCGGAGCCc/gc	1/6	1	2	FACETS	0.939	0.838	1	0.939	0.838	1	CLONAL	1	TRUE	1	0.29	2		345	720	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60795967	60795967	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	100	513	0	ENST00000333681.4:c.611C>A	p.Pro204His	p.P204H	ENST00000333681		204	cCc/cAc	3/3	0.302380866806039	1	FACETS	0.728	0.65	0.811	0.728	0.65	0.811	SUBCLONAL	1	TRUE	0	0.29	1		513	810	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248541	212248541	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0039592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	102	543	0	ENST00000342788.4:c.3726C>G	p.Tyr1242Ter	p.Y1242*	ENST00000342788	NM_005235.2	1242	taC/taG	28/28	1	2	FACETS	0.716	0.639	0.798	0.716	0.639	0.798	SUBCLONAL	1	TRUE	1	0.29	2		543	982	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250049	53250049	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	139	340	0	ENST00000375401.3:c.200C>G	p.Pro67Arg	p.P67R	ENST00000375401	NM_004187.3	67	cCc/cGc	2/26	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.29	1		340	568	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143993	11143993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568509370	NA	P-0039631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	265	755	1	ENST00000358026.2:c.3574C>T	p.Arg1192Cys	p.R1192C	ENST00000358026	NM_001128849.1	1192	Cgc/Tgc	26/36	0.742234746359922	3	FACETS	0.967	0.918	1	0.967	0.918	1	CLONAL	2	TRUE	1	0.741164785859136	3		756	507	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514780	44514780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769567889	NA	P-0039631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	221	637	0	ENST00000291552.4:c.467G>A	p.Arg156His	p.R156H	ENST00000291552	NM_006758.2	156	cGt/cAt	6/8	0.49920301109907	4	FACETS	0.946	0.888	1	0.946	0.888	1	CLONAL	2	TRUE	2	0.741164785859136	4		637	549	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514780	44514780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769567889	NA	P-0039631-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	216	637	0	ENST00000291552.4:c.467G>A	p.Arg156His	p.R156H	ENST00000291552	NM_006758.2	156	cGt/cAt	6/8	1	2	FACETS	0.967	0.909	1	0.967	0.909	1	CLONAL	1	TRUE	1	0.886121260742901	2		637	504	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039631-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	56	661	0	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	0.379834967699564	1	FACETS	0.15	0.129	0.174	0.15	0.129	0.174	INDETERMINATE	1	TRUE	0	0.886121260742901	1		661	468	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138548	11138548	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039631-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	301	966	0	ENST00000358026.2:c.3304T>C	p.Phe1102Leu	p.F1102L	ENST00000358026	NM_001128849.1	1102	Ttc/Ctc	24/36	0.130134654251243	3	FACETS	0.915	0.873	0.956	0.61	0.582	0.637	INDETERMINATE	2	TRUE	0	0.886121260742901	3		966	536	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914722	39914722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	100	294	0	ENST00000378444.4:c.4640G>A	p.Arg1547Gln	p.R1547Q	ENST00000378444	NM_001123385.1	1547	cGa/cAa	12/15	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.342224306059239	1		294	344	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608960	100608960	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	80	252	0	ENST00000308731.7:c.1648G>T	p.Glu550Ter	p.E550*	ENST00000308731	NM_000061.2	550	Gaa/Taa	17/19	1	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.342224306059239	1		252	284	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189895	11189895	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	27	472	0	ENST00000361445.4:c.5614G>C	p.Asp1872His	p.D1872H	ENST00000361445	NM_004958.3	1872	Gat/Cat	40/58	0.326076776750518	1	FACETS	0.243	0.192	0.301	0.243	0.192	0.301	SUBCLONAL	1	TRUE	0	0.342224306059239	1		472	539	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059215	27059215	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	52	554	0	ENST00000324856.7:c.1852A>G	p.Met618Val	p.M618V	ENST00000324856	NM_006015.4	618	Atg/Gtg	4/20	0.326076776750518	1	FACETS	0.394	0.334	0.459	0.394	0.334	0.459	SUBCLONAL	1	TRUE	0	0.342224306059239	1		554	640	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962520	100962520	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	50	527	0	ENST00000325455.5:c.1877A>T	p.Lys626Met	p.K626M	ENST00000325455	NM_001202474.3	626	aAg/aTg	3/8	1	2	FACETS	0.514	0.435	0.6	0.514	0.435	0.6	SUBCLONAL	1	TRUE	1	0.342224306059239	2		527	569	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285612	46285612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	79	365	0	ENST00000334344.6:c.4972G>A	p.Gly1658Arg	p.G1658R	ENST00000334344	NM_152641.2	1658	Gga/Aga	17/21	1	2	FACETS	0.997	0.88	1	0.997	0.88	1	CLONAL	1	TRUE	1	0.342224306059239	2		365	463	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108770	2108770	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	69	761	1	ENST00000219476.3:c.871C>A	p.Leu291Met	p.L291M	ENST00000219476	NM_000548.3	291	Ctg/Atg	10/42	1	2	FACETS	0.512	0.445	0.585	0.512	0.445	0.585	SUBCLONAL	1	TRUE	1	0.342224306059239	2		762	787	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226166	2226166	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	96	936	0	ENST00000326181.6:c.1863C>A	p.Tyr621Ter	p.Y621*	ENST00000326181	NM_032271.2	621	taC/taA	19/21	1	2	FACETS	0.673	0.599	0.752	0.673	0.599	0.752	SUBCLONAL	1	TRUE	1	0.342224306059239	2		936	834	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984534	72984534	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	169	936	1	ENST00000268489.5:c.3050A>T	p.His1017Leu	p.H1017L	ENST00000268489	NM_006885.3	1017	cAc/cTc	3/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.342224306059239	2		937	888	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0039650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	224	869	0	ENST00000269305.4:c.376-1del		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.216523981991497	2	FACETS	1	0.991	1	0.722	0.673	0.772	CLONAL	1	TRUE	0	0.342224306059239	2		869	907	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16022782	16022782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	96	387	0	ENST00000268712.3:c.1870G>A	p.Glu624Lys	p.E624K	ENST00000268712	NM_006311.3	624	Gag/Aag	17/46	0.216523981991497	2	FACETS	1	0.98	1	0.719	0.646	0.797	CLONAL	1	TRUE	0	0.342224306059239	2		387	390	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207598	2207599	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0039650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	192	803	2	ENST00000398665.3:c.882_883delinsTT	p.Glu295Ter	p.E295*	ENST00000398665	NM_032482.2	294	gtGGag/gtTTag	11/28	0.342224306059239	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.342224306059239	1		805	746	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602322	10602322	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs779729664	NA	P-0039650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	241	1018	0	ENST00000171111.5:c.1256G>C	p.Gly419Ala	p.G419A	ENST00000171111	NM_203500.1	419	gGg/gCg	3/6	0.342224306059239	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.342224306059239	1		1018	866	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107188	11107188	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	159	710	1	ENST00000358026.2:c.1780G>T	p.Gly594Ter	p.G594*	ENST00000358026	NM_001128849.1	594	Gga/Tga	11/36	0.342224306059239	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.342224306059239	1		711	702	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799342	42799342	+	stop_lost	Nonstop_Mutation	SNP	G	G	T	novel	NA	P-0039650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	73	386	0	ENST00000575354.2:c.4826G>T	p.Ter1609LeuextTer63	p.*1609Lext*63	ENST00000575354	NM_015125.3	1609	tGa/tTa	20/20	0.342224306059239	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.342224306059239	1		386	245	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022283	31022283	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	84	393	0	ENST00000375687.4:c.1768A>G	p.Thr590Ala	p.T590A	ENST00000375687	NM_015338.5	590	Act/Gct	13/13	1	2	FACETS	0.897	0.794	1	0.897	0.794	1	CLONAL	1	TRUE	1	0.342224306059239	2		393	547	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933708	49933708	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	77	991	0	ENST00000296474.3:c.2569T>C	p.Phe857Leu	p.F857L	ENST00000296474	NM_002447.2	857	Ttt/Ctt	10/20	1	2	FACETS	0.524	0.459	0.594	0.524	0.459	0.594	SUBCLONAL	1	TRUE	1	0.342224306059239	2		991	859	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205023	128205023	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	69	857	0	ENST00000341105.2:c.418G>C	p.Val140Leu	p.V140L	ENST00000341105	NM_032638.4	140	Gtg/Ctg	3/6	1	2	FACETS	0.56	0.487	0.639	0.56	0.487	0.639	SUBCLONAL	1	TRUE	1	0.342224306059239	2		857	720	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185028	32185028	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs140082058	NA	P-0039650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	159	764	1	ENST00000375023.3:c.1640G>T	p.Arg547Leu	p.R547L	ENST00000375023	NM_004557.3	547	cGa/cTa	10/30	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.342224306059239	2		765	780	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982102	93982102	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	85	439	0	ENST00000369303.4:c.1363C>G	p.Leu455Val	p.L455V	ENST00000369303	NM_004440.3	455	Ctg/Gtg	6/17	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.342224306059239	2		439	467	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453081	140453081	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	70	342	0	ENST00000288602.6:c.1854G>T	p.Leu618Phe	p.L618F	ENST00000288602	NM_004333.4	618	ttG/ttT	15/18	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.342224306059239	2		342	363	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	76	369	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.318116734211674	4	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	FALSE	2	0.318116734211674	4		369	278	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073742	8073743	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1212152375	NA	P-0039703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	46	383	0	ENST00000377482.5:c.916dup	p.Thr306AsnfsTer6	p.T306Nfs*6	ENST00000377482	NM_018948.3	306	act/aAct	4/4	0.318116734211674	1	FACETS	0.961	0.816	1	0.961	0.816	1	CLONAL	1	FALSE	0	0.318116734211674	1		383	253	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0039788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	182	354	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	1	2	FACETS	0.915	0.853	0.978	0.915	0.853	0.978	CLONAL	1	TRUE	1	0.855518162106339	2		354	465	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0039788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	459	560	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.855518162106339	2	FACETS	0.861	0.836	0.886	0.861	0.836	0.886	CLONAL	2	TRUE	0	0.855518162106339	2		561	623	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599338	55599338	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	243	348	0	ENST00000288135.5:c.2464A>T	p.Asn822Tyr	p.N822Y	ENST00000288135	NM_000222.2	822	Aat/Tat	17/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.855518162106339	2		348	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0039792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	265	749	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.509956392708501	1	FACETS	0.964	0.908	1	0.964	0.908	1	CLONAL	1	TRUE	0	0.55899446218149	1		749	709	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653829	89653829	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554893808	NA	P-0039792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	127	290	0	ENST00000371953.3:c.127G>T	p.Glu43Ter	p.E43*	ENST00000371953	NM_000314.4	43	Gaa/Taa	2/9	0.55899446218149	1	FACETS	0.938	0.86	1	0.938	0.86	1	CLONAL	1	TRUE	0	0.55899446218149	1		290	349	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508245	38508245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	88	455	1	ENST00000254066.5:c.553G>A	p.Gly185Arg	p.G185R	ENST00000254066	NM_000964.3	185	Ggg/Agg	5/9	0.282359315244047	4	FACETS	0.49	0.433	0.552			1	INDETERMINATE	1	TRUE	NA	0.55899446218149	4		456	1001	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564936	226564936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369900729	NA	P-0039792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	86	412	0	ENST00000366794.5:c.1814C>T	p.Pro605Leu	p.P605L	ENST00000366794	NM_001618.3	605	cCg/cTg	13/23	1	2	FACETS	0.385	0.34	0.433	0.385	0.34	0.433	SUBCLONAL	1	TRUE	1	0.55899446218149	2		412	799	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249752	133249752	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs776770625	NA	P-0039792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	136	324	0	ENST00000320574.5:c.1471G>A	p.Glu491Lys	p.E491K	ENST00000320574	NM_006231.2	491	Gag/Aag	14/49	1	2	FACETS	0.918	0.839	1	0.918	0.839	1	CLONAL	1	TRUE	1	0.55899446218149	2		324	530	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678539	88678539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	148	355	0	ENST00000360948.2:c.997C>A	p.Leu333Met	p.L333M	ENST00000360948	NM_001012338.2	333	Ctg/Atg	9/19	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.55899446218149	2		355	521	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946328	55946328	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	79	179	0	ENST00000263923.4:c.3851G>T	p.Gly1284Val	p.G1284V	ENST00000263923	NM_002253.2	1284	gGa/gTa	30/30	0.55899446218149	1	FACETS	0.993	0.891	1	0.993	0.891	1	CLONAL	1	TRUE	0	0.55899446218149	1		179	205	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245344	153245344	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	156	368	0	ENST00000281708.4:c.1847del	p.Thr616AsnfsTer12	p.T616Nfs*12	ENST00000281708	NM_033632.3	616	aCa/aa	11/12	0.55899446218149	1	FACETS	0.986	0.913	1	0.986	0.913	1	CLONAL	1	TRUE	0	0.55899446218149	1		368	408	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205363	38205373	+	frameshift_variant	Frame_Shift_Del	DEL	AGTGGGGCTAA	AGTGGGGCTAA	-	novel	NA	P-0039792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	328	563	0	ENST00000317025.8:c.317_327del	p.Phe106Ter	p.F106*	ENST00000317025	NM_023034.1	106	tTTAGCCCCACT/t	2/24	0.419117095643044	3	FACETS	1	0.971	1			1	CLONAL	1	TRUE	NA	0.55899446218149	3		563	1437	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412005	63412005	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	132	310	0	ENST00000330258.3:c.1162G>T	p.Val388Leu	p.V388L	ENST00000330258	NM_152424.3	388	Gtg/Ttg	2/2	1	1	FACETS	0.751	0.687	0.818	0.751	0.687	0.818	SUBCLONAL	1	TRUE	0	0.55899446218149	1		310	453	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0039796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	787	673	0				ENST00000310581	NM_198253.2	-/1132			0.842330951234876	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.842330951234876	3		673	1286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579317	7579317	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	378	665	0	ENST00000269305.4:c.370T>C	p.Cys124Arg	p.C124R	ENST00000269305	NM_001126112.2	124	Tgc/Cgc	4/11	0.827367341938256	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.842330951234876	1		665	488	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292400	15292400	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	487	799	0	ENST00000263388.2:c.2779G>C	p.Asp927His	p.D927H	ENST00000263388	NM_000435.2	927	Gac/Cac	17/33	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.842330951234876	2		799	1140	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918986	50918986	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	403	757	1	ENST00000440232.2:c.2723G>C	p.Arg908Thr	p.R908T	ENST00000440232	NM_002691.3	908	aGg/aCg	22/27	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.842330951234876	2		758	932	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119666194	119666194	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	59	137	0	ENST00000316626.5:c.287G>T	p.Arg96Leu	p.R96L	ENST00000316626		96	cGa/cTa	3/12	NA	2	FACETS	0.67	0.585	0.76			1	INDETERMINATE	1	TRUE	NA	0.842330951234876	2		137	209	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141570596	141570596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	149	567	0	ENST00000220592.5:c.532G>A	p.Gly178Ser	p.G178S	ENST00000220592	NM_012154.3	178	Ggc/Agc	5/19	0.842330951234876	3	FACETS	0.433	0.395	0.474	0.217	0.197	0.237	SUBCLONAL	1	TRUE	1	0.842330951234876	3		567	1161	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437801	52437802	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	149	680	0	ENST00000460680.1:c.1359dup	p.Glu454ArgfsTer15	p.E454Rfs*15	ENST00000460680	NM_004656.3	453	-/A	13/17	0.37376476164009	1	FACETS	0.775	0.708	0.844	0.775	0.708	0.844	SUBCLONAL	1	TRUE	0	0.386541076320444	1		680	803	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191524	10191524	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	149	559	0	ENST00000256474.2:c.517G>T	p.Glu173Ter	p.E173*	ENST00000256474	NM_000551.3	173	Gag/Tag	3/3	0.37376476164009	1	FACETS	0.941	0.862	1	0.941	0.862	1	CLONAL	1	TRUE	0	0.386541076320444	1		559	661	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597492	52597511	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	TGAGGAACAATTGGTTTTCT	TGAGGAACAATTGGTTTTCT	-	novel	NA	P-0039992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	80	398	0	ENST00000394830.3:c.3801-2_3818del		p.X1267_splice	ENST00000394830	NM_018313.4	1267		25/30	0.37376476164009	1	FACETS	0.693	0.612	0.779	0.693	0.612	0.779	SUBCLONAL	1	TRUE	0	0.386541076320444	1		398	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0040025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	204	532	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.351264955783199	2		533	1049	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391214	89391214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs530556931	NA	P-0040025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	167	391	0	ENST00000336596.2:c.1280C>T	p.Ala427Val	p.A427V	ENST00000336596	NM_005233.5	427	gCg/gTg	5/17	0.221978898523659	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.351264955783199	4		391	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572991	7572991	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	104	490	0	ENST00000269305.4:c.1118del	p.Lys373ArgfsTer49	p.K373Rfs*49	ENST00000269305	NM_001126112.2	373	aAg/ag	11/11	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.351264955783199	2		490	572	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100093	157100120	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCGGCGGCGGCAGCAGCAGGAGGCG	GCGGCGGCGGCGGCAGCAGCAGGAGGCG	-	rs1554247989	NA	P-0040025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	22	32	0	ENST00000346085.5:c.1044_1071del	p.Ala349MetfsTer11	p.A349Mfs*11	ENST00000346085	NM_020732.3	344	GCGGCGGCGGCGGCAGCAGCAGGAGGCGgc/gc	1/20	0.351264955783199	3	FACETS	0.969	0.773	1	0.969	0.773	1	CLONAL	2	TRUE	1	0.351264955783199	3		32	76	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201508	67201508	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	177	832	2	ENST00000312629.5:c.952del	p.Asp318MetfsTer14	p.D318Mfs*14	ENST00000312629	NM_003952.2	317	Ggg/gg	11/15	0.351264955783199	3	FACETS	0.892	0.82	0.968	0.446	0.41	0.484	CLONAL	1	TRUE	1	0.351264955783199	3		834	1328	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859694	57859694	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	120	471	0	ENST00000228682.2:c.748G>C	p.Glu250Gln	p.E250Q	ENST00000228682	NM_005269.2	250	Gag/Cag	7/12	0.351264955783199	3	FACETS	1	0.969	1	0.586	0.53	0.645	CLONAL	1	TRUE	1	0.351264955783199	3		471	685	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293210	91293210	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	46	404	0	ENST00000355112.3:c.712A>G	p.Ile238Val	p.I238V	ENST00000355112	NM_000057.2	238	Atc/Gtc	3/22	1	2	FACETS	0.464	0.391	0.546	0.464	0.391	0.546	SUBCLONAL	1	TRUE	1	0.351264955783199	2		404	564	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732442	74732442	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	76	384	0	ENST00000359995.5:c.467del	p.Arg156HisfsTer76	p.R156Hfs*76	ENST00000359995	NM_001195427.1	156	cGa/ca	2/3	0.351264955783199	3	FACETS	0.763	0.669	0.864	0.381	0.334	0.432	SUBCLONAL	1	TRUE	1	0.351264955783199	3		384	667	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726601	41726601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775741490	NA	P-0040025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	223	818	0	ENST00000301178.4:c.146G>A	p.Gly49Glu	p.G49E	ENST00000301178	NM_021913.4	49	gGa/gAa	2/20	0.351264955783199	3	FACETS	1	0.989	1	0.661	0.615	0.709	CLONAL	1	TRUE	1	0.351264955783199	3		818	1129	SUCCESS
APC	324	MSKCC	GRCh37	5	112170705	112170705	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	330	486	1	ENST00000257430.4:c.1801G>T	p.Glu601Ter	p.E601*	ENST00000257430	NM_000038.5	601	Gag/Tag	15/16	0.351264955783199	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	0	0.351264955783199	3		487	703	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401737	401737	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	194	712	1	ENST00000380956.4:c.1059C>A	p.Asp353Glu	p.D353E	ENST00000380956	NM_001195286.1	353	gaC/gaA	7/9	0.351264955783199	3	FACETS	1	0.988	1	0.674	0.624	0.727	CLONAL	1	TRUE	1	0.351264955783199	3		713	963	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92244558	92244558	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	40	378	0	ENST00000265734.4:c.877A>C	p.Ser293Arg	p.S293R	ENST00000265734	NM_001259.6	293	Agt/Cgt	8/8	0.351264955783199	3	FACETS	0.499	0.414	0.593	0.166	0.138	0.198	SUBCLONAL	1	TRUE	0	0.351264955783199	3		378	537	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0040037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	72	207	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.31555562610393	3	FACETS	0.814	0.712	0.924	0.407	0.356	0.462	CLONAL	1	TRUE	1	0.377627619463723	3		207	557	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	107	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.31555562610393	3	FACETS	1	0.983	1	0.734	0.662	0.809	CLONAL	1	TRUE	1	0.377627619463723	3		452	459	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170453	11170453	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555795884	NA	P-0040037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	267	763	1	ENST00000358026.2:c.4756C>T	p.Gln1586Ter	p.Q1586*	ENST00000358026	NM_001128849.1	1586	Cag/Tag	34/36	0.0736720287501242	4	FACETS	0.928	0.87	0.987	0.928	0.87	0.987	INDETERMINATE	2	TRUE	2	0.377627619463723	4		764	1050	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15827362	15827362	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1461565397	NA	P-0040037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	162	534	2	ENST00000307771.7:c.478G>A	p.Val160Met	p.V160M	ENST00000307771	NM_005089.3	160	Gtg/Atg	7/11	0.105602665677129	5	FACETS	0.946	0.871	1	0.631	0.58	0.684	INDETERMINATE	2	TRUE	2	0.377627619463723	5		536	710	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187847	11187847	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	86	556	0	ENST00000361445.4:c.6050T>C	p.Ile2017Thr	p.I2017T	ENST00000361445	NM_004958.3	2017	aTc/aCc	44/58	1	2	FACETS	0.947	0.841	1	0.947	0.841	1	CLONAL	1	TRUE	1	0.377627619463723	2		556	481	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104527	193104527	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	47	382	0	ENST00000367435.3:c.314C>A	p.Ser105Ter	p.S105*	ENST00000367435	NM_024529.4	105	tCg/tAg	4/17	0.312108719857929	4	FACETS	0.728	0.615	0.853	0.243	0.205	0.285	SUBCLONAL	1	TRUE	1	0.377627619463723	4		382	471	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976702	2976702	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755090332	NA	P-0040037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	83	560	4	ENST00000396946.4:c.1310G>A	p.Arg437His	p.R437H	ENST00000396946	NM_032415.4	437	cGc/cAc	9/25	0.144592473234837	5	FACETS	0.956	0.844	1	0.319	0.281	0.359	INDETERMINATE	1	TRUE	2	0.377627619463723	5		564	720	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729709	41729709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768547360	NA	P-0040037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	183	548	2	ENST00000242208.4:c.820G>A	p.Gly274Arg	p.G274R	ENST00000242208	NM_002192.2	274	Gga/Aga	3/3	0.144592473234837	5	FACETS	1	0.95	1	0.689	0.638	0.743	INDETERMINATE	2	TRUE	2	0.377627619463723	5		550	734	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0040042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	32	422	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.234446084348381	0	FACETS	0.826	0.675	0.994			1	CLONAL	1	FALSE	0	0.263068842189429	0		422	217	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154815	2154815	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	122	772	0	ENST00000434045.2:c.406C>A	p.Leu136Met	p.L136M	ENST00000434045	NM_001127598.1	136	Ctg/Atg	4/5	1	2	FACETS	0.837	0.755	0.924	0.837	0.755	0.924	CLONAL	1	FALSE	1	0.263068842189429	2		772	1108	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243983	53243983	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	68	606	0	ENST00000375401.3:c.1010A>G	p.Asp337Gly	p.D337G	ENST00000375401	NM_004187.3	337	gAc/gGc	8/26	0.263068842189429	1	FACETS	0.459	0.398	0.525	0.459	0.398	0.525	SUBCLONAL	1	FALSE	0	0.263068842189429	1		606	979	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259009	16259009	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	59	478	0	ENST00000375759.3:c.6274A>G	p.Ser2092Gly	p.S2092G	ENST00000375759	NM_015001.2	2092	Agt/Ggt	11/15	1	2	FACETS	0.635	0.546	0.733	0.635	0.546	0.733	SUBCLONAL	1	FALSE	1	0.263068842189429	2		478	706	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92244457	92244468	+	inframe_deletion	In_Frame_Del	DEL	GGCTGTATTCAG	GGCTGTATTCAG	-	novel	NA	P-0040042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	55	226	0	ENST00000265734.4:c.967_978del	p.Leu323_Ala326del	p.L323_A326del	ENST00000265734	NM_001259.6	323	CTGAATACAGCC/-	8/8	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	FALSE	1	0.263068842189429	2		226	358	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537247	80537247	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	65	426	0	ENST00000286548.4:c.151G>C	p.Gly51Arg	p.G51R	ENST00000286548	NM_002072.3	51	Ggc/Cgc	2/7	0.263068842189429	1	FACETS	0.833	0.724	0.952	0.833	0.724	0.952	CLONAL	1	FALSE	0	0.263068842189429	1		426	515	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242484	+	inframe_deletion	In_Frame_Del	DEL	AATTAAGAGAAGCAACAT	AATTAAGAGAAGCAACAT	-	rs121913422	NA	P-0040079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	23	377	0	ENST00000275493.2:c.2237_2254del	p.Glu746_Ser752delinsAla	p.E746_S752delinsA	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATct/gct	19/28	1	2	FACETS	0.352	0.274	0.444	0.352	0.274	0.444	SUBCLONAL	1	TRUE	1	0.274793020011359	2		377	475	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109315685	109315685	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	72	411	0	ENST00000436639.2:c.1100G>C	p.Ser367Thr	p.S367T	ENST00000436639	NM_014454.2	367	aGt/aCt	6/10	1	2	FACETS	0.729	0.636	0.829	0.729	0.636	0.829	SUBCLONAL	1	TRUE	1	0.274793020011359	2		411	719	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	121	673	0				ENST00000310581	NM_198253.2	-/1132			0.198252526963314	4	FACETS	1	0.984	1	0.722	0.655	0.792	INDETERMINATE	1	TRUE	2	0.441941325497886	4		673	547	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	109	430	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.218408009396031	3	FACETS	1	0.97	1	0.399	0.36	0.44	INDETERMINATE	1	TRUE	0	0.441941325497886	3		431	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	362	638	1	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	0.379527422376237	3	FACETS	1	0.993	1	0.812	0.774	0.85	CLONAL	2	TRUE	0	0.441941325497886	3		639	821	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286761	212286761	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	72	261	0	ENST00000342788.4:c.2935C>T	p.Arg979Ter	p.R979*	ENST00000342788	NM_005235.2	979	Cga/Tga	24/28	0.300637574857944	4	FACETS	0.904	0.791	1	0.452	0.395	0.513	CLONAL	1	TRUE	2	0.441941325497886	4		261	520	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	258	461	0	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	0.321798733591991	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.441941325497886	3		461	678	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642495	117642495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs9489124	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	298	535	0	ENST00000368508.3:c.5704G>A	p.Glu1902Lys	p.E1902K	ENST00000368508	NM_002944.2	1902	Gaa/Aaa	35/43	0.436229327937653	2	FACETS	0.962	0.912	1	0.962	0.912	1	CLONAL	2	TRUE	0	0.441941325497886	2		535	701	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857500	9857500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	81	391	0	ENST00000330684.3:c.3901G>A	p.Glu1301Lys	p.E1301K	ENST00000330684	NM_001134407.1	1301	Gag/Aag	13/13	1	2	FACETS	0.877	0.777	0.983	0.877	0.777	0.983	CLONAL	1	TRUE	1	0.441941325497886	2		391	418	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056291	180056291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199942873	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	178	745	2	ENST00000261937.6:c.953G>A	p.Arg318Gln	p.R318Q	ENST00000261937	NM_182925.4	318	cGa/cAa	7/30	0.427808941001223	2	FACETS	1	0.975	1	0.563	0.52	0.607	CLONAL	1	TRUE	0	0.441941325497886	2		747	716	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523329	9523329	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867092977	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	89	397	1	ENST00000353224.5:c.1908G>A	p.Met636Ile	p.M636I	ENST00000353224	NM_177990.2	636	atG/atA	9/10	0.353712695148351	3	FACETS	0.839	0.745	0.939	0.42	0.372	0.47	CLONAL	1	TRUE	1	0.441941325497886	3		398	586	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956529	93956529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	119	216	0	ENST00000369303.4:c.2707C>T	p.Pro903Ser	p.P903S	ENST00000369303	NM_004440.3	903	Ccc/Tcc	15/17	0.436229327937653	2	FACETS	0.763	0.696	0.831	0.763	0.696	0.831	SUBCLONAL	2	TRUE	0	0.441941325497886	2		216	353	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956676	93956676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465960814	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	127	258	0	ENST00000369303.4:c.2560C>T	p.Arg854Cys	p.R854C	ENST00000369303	NM_004440.3	854	Cgt/Tgt	15/17	0.436229327937653	2	FACETS	1	0.984	1	0.681	0.622	0.742	CLONAL	1	TRUE	0	0.441941325497886	2		258	422	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597849	43597849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564490056	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	316	716	1	ENST00000355710.3:c.397C>T	p.Arg133Cys	p.R133C	ENST00000355710	NM_020975.4	133	Cgt/Tgt	3/20	0.353712695148351	3	FACETS	0.911	0.862	0.962	0.911	0.862	0.962	CLONAL	2	TRUE	1	0.441941325497886	3		717	958	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031885	26031885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	33	192	0	ENST00000244661.2:c.404G>A	p.Arg135Lys	p.R135K	ENST00000244661	NM_003537.3	135	aGa/aAa	1/1	0.191163733257045	3	FACETS	0.61	0.498	0.735	0.203	0.166	0.245	INDETERMINATE	1	TRUE	0	0.441941325497886	3		192	299	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627284	12627284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	275	414	0	ENST00000251849.4:c.1432G>A	p.Glu478Lys	p.E478K	ENST00000251849	NM_002880.3	478	Gaa/Aaa	14/17	0.441941325497886	4	FACETS	0.974	0.923	1	0.974	0.923	1	CLONAL	3	TRUE	1	0.441941325497886	4		414	614	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683963	117683963	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761293495	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	172	386	0	ENST00000368508.3:c.3184G>A	p.Glu1062Lys	p.E1062K	ENST00000368508	NM_002944.2	1062	Gaa/Aaa	21/43	0.436229327937653	2	FACETS	1	0.989	1	0.722	0.669	0.777	CLONAL	1	TRUE	0	0.441941325497886	2		386	539	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214713	36214714	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	83	481	0	ENST00000222270.7:c.3145dup	p.Ala1049GlyfsTer39	p.A1049Gfs*39	ENST00000222270	NM_014727.1	1047	cgg/cGgg	8/37	0.185098461075923	3	FACETS	0.805	0.711	0.904	0.402	0.355	0.452	INDETERMINATE	1	TRUE	1	0.441941325497886	3		481	570	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246459	10246459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	373	670	0	ENST00000340748.4:c.4678C>T	p.Pro1560Ser	p.P1560S	ENST00000340748		1560	Cct/Tct	38/40	0.321798733591991	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.441941325497886	3		670	1011	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686388	30686388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	51	272	0	ENST00000295754.5:c.244G>A	p.Glu82Lys	p.E82K	ENST00000295754	NM_003242.5	82	Gaa/Aaa	2/7	0.441941325497886	4	FACETS	0.676	0.575	0.787	0.225	0.191	0.263	SUBCLONAL	1	TRUE	1	0.441941325497886	4		272	492	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969117	93969117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	156	265	0	ENST00000369303.4:c.1879G>A	p.Glu627Lys	p.E627K	ENST00000369303	NM_004440.3	627	Gag/Aag	10/17	0.436229327937653	2	FACETS	0.929	0.862	0.997	0.929	0.862	0.997	CLONAL	2	TRUE	0	0.441941325497886	2		265	380	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992790	72992790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	279	519	0	ENST00000268489.5:c.1255C>T	p.Pro419Ser	p.P419S	ENST00000268489	NM_006885.3	419	Ccc/Tcc	2/10	0.409394351686511	2	FACETS	0.946	0.895	0.998	0.946	0.895	0.998	CLONAL	2	TRUE	0	0.441941325497886	2		519	667	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245954	16245954	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	47	264	0	ENST00000375759.3:c.1577C>T	p.Ser526Leu	p.S526L	ENST00000375759	NM_015001.2	526	tCg/tTg	8/15	0.218408009396031	3	FACETS	0.523	0.441	0.613	0.174	0.147	0.205	INDETERMINATE	1	TRUE	0	0.441941325497886	3		264	497	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426993	49426993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	99	539	0	ENST00000301067.7:c.11495C>T	p.Ser3832Phe	p.S3832F	ENST00000301067	NM_003482.3	3832	tCc/tTc	39/54	0.218408009396031	3	FACETS	0.918	0.821	1	0.306	0.273	0.34	INDETERMINATE	1	TRUE	0	0.441941325497886	3		539	596	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434796	49434796	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	112	720	0	ENST00000301067.7:c.6757G>A	p.Asp2253Asn	p.D2253N	ENST00000301067	NM_003482.3	2253	Gat/Aat	31/54	0.218408009396031	3	FACETS	0.665	0.597	0.737	0.222	0.199	0.246	INDETERMINATE	1	TRUE	0	0.441941325497886	3		720	931	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858346	9858346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs933333894	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	108	346	0	ENST00000330684.3:c.3055G>A	p.Asp1019Asn	p.D1019N	ENST00000330684	NM_001134407.1	1019	Gat/Aat	13/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.441941325497886	2		346	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577037	7577037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	177	620	0	ENST00000269305.4:c.901C>T	p.Pro301Ser	p.P301S	ENST00000269305	NM_001126112.2	301	Cca/Tca	8/11	0.379527422376237	3	FACETS	1	0.969	1	0.366	0.337	0.396	CLONAL	1	TRUE	0	0.441941325497886	3		620	891	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677251	29677251	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	123	288	0	ENST00000356175.3:c.7309A>T	p.Arg2437Ter	p.R2437*	ENST00000356175	NM_000267.3	2437	Aga/Tga	49/57	0.409394351686511	2	FACETS	0.831	0.761	0.902	0.831	0.761	0.902	CLONAL	2	TRUE	0	0.441941325497886	2		288	335	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172197	99172197	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	87	460	0	ENST00000074304.5:c.1763C>T	p.Pro588Leu	p.P588L	ENST00000074304	NM_001134224.1	588	cCc/cTc	17/26	0.300637574857944	4	FACETS	0.736	0.651	0.827	0.368	0.325	0.414	SUBCLONAL	1	TRUE	2	0.441941325497886	4		460	771	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281572	198281572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1014653152	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	197	366	0	ENST00000335508.6:c.559G>A	p.Ala187Thr	p.A187T	ENST00000335508	NM_012433.2	187	Gca/Aca	6/25	0.300637574857944	4	FACETS	0.784	0.727	0.843	0.784	0.727	0.843	SUBCLONAL	2	TRUE	2	0.441941325497886	4		366	820	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225360643	225360643	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	112	264	0	ENST00000264414.4:c.1748C>G	p.Thr583Ser	p.T583S	ENST00000264414	NM_003590.4	583	aCt/aGt	13/16	0.300637574857944	4	FACETS	1	0.984	1	0.747	0.676	0.822	CLONAL	1	TRUE	2	0.441941325497886	4		264	489	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730767	40730767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	196	421	0	ENST00000373198.4:c.3768G>A	p.Met1256Ile	p.M1256I	ENST00000373198	NM_133170.3	1256	atG/atA	27/32	NA	2	FACETS	0.763	0.711	0.817			1	INDETERMINATE	2	TRUE	NA	0.441941325497886	2		421	581	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306678	41306678	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	148	581	0	ENST00000373198.4:c.981T>A	p.Tyr327Ter	p.Y327*	ENST00000373198	NM_133170.3	327	taT/taA	7/32	NA	2	FACETS	0.812	0.742	0.885			1	INDETERMINATE	1	TRUE	NA	0.441941325497886	2		581	825	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845348	42845348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	160	676	0	ENST00000398585.3:c.914C>T	p.Pro305Leu	p.P305L	ENST00000398585	NM_001135099.1	305	cCc/cTc	9/14	0.297011216731957	3	FACETS	1	0.969	1	0.557	0.512	0.605	CLONAL	1	TRUE	1	0.441941325497886	3		676	793	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47061296	47061296	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	67	321	0	ENST00000409792.3:c.7385C>T	p.Thr2462Ile	p.T2462I	ENST00000409792	NM_014159.6	2462	aCc/aTc	19/21	0.441941325497886	4	FACETS	0.741	0.644	0.846	0.247	0.214	0.282	SUBCLONAL	1	TRUE	1	0.441941325497886	4		321	590	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670216	134670216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	94	348	1	ENST00000398015.3:c.127G>A	p.Glu43Lys	p.E43K	ENST00000398015	NM_004441.4	43	Gaa/Aaa	3/16	0.321798733591991	3	FACETS	1	0.924	1	0.521	0.466	0.581	CLONAL	1	TRUE	1	0.441941325497886	3		349	498	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956233	55956233	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	194	334	0	ENST00000263923.4:c.3082G>A	p.Asp1028Asn	p.D1028N	ENST00000263923	NM_002253.2	1028	Gac/Aac	23/30	0.436229327937653	2	FACETS	0.965	0.903	1	0.965	0.903	1	CLONAL	2	TRUE	0	0.441941325497886	2		334	455	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383851	84383851	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	207	417	0	ENST00000321945.7:c.1001A>T	p.Glu334Val	p.E334V	ENST00000321945	NM_139076.2	334	gAa/gTa	9/9	0.436229327937653	2	FACETS	0.915	0.857	0.973	0.915	0.857	0.973	CLONAL	2	TRUE	0	0.441941325497886	2		417	512	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176516628	176516629	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	268	584	1	ENST00000292408.4:c.25_26delinsAA	p.Gly9Lys	p.G9K	ENST00000292408	NM_213647.1	9	GGg/AAg	2/18	0.427808941001223	2	FACETS	0.926	0.874	0.978	0.926	0.874	0.978	CLONAL	2	TRUE	0	0.441941325497886	2		585	655	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680650	30680650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	127	434	0	ENST00000376406.3:c.1069G>A	p.Gly357Ser	p.G357S	ENST00000376406	NM_014641.2	357	Ggt/Agt	5/15	0.191163733257045	3	FACETS	1	0.982	1	0.441	0.401	0.483	INDETERMINATE	1	TRUE	0	0.441941325497886	3		434	530	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545759	106545759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	110	419	0	ENST00000359195.3:c.3236G>A	p.Gly1079Glu	p.G1079E	ENST00000359195	NM_002649.2	1079	gGa/gAa	11/11	1	2	FACETS	0.857	0.772	0.946	0.857	0.772	0.946	CLONAL	1	TRUE	1	0.441941325497886	2		419	581	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851876	128851876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	133	601	3	ENST00000249373.3:c.1948G>A	p.Glu650Lys	p.E650K	ENST00000249373	NM_005631.4	650	Gaa/Aaa	12/12	0.222643337594953	6	FACETS	0.97	0.879	1			1	INDETERMINATE	1	TRUE	NA	0.441941325497886	6		604	1169	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884890	151884890	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762784550	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	69	316	0	ENST00000262189.6:c.4703C>T	p.Ser1568Phe	p.S1568F	ENST00000262189	NM_170606.2	1568	tCc/tTc	32/59	1	2	FACETS	0.803	0.703	0.91	0.803	0.703	0.91	CLONAL	1	TRUE	1	0.441941325497886	2		316	389	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29195997	29195997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	194	574	0	ENST00000240100.2:c.601C>T	p.Pro201Ser	p.P201S	ENST00000240100	NM_001394.6	201	Ccc/Tcc	3/4	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.441941325497886	2		574	814	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863073	56863073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs969084724	NA	P-0040114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	108	450	0	ENST00000519728.1:c.340C>T	p.Pro114Ser	p.P114S	ENST00000519728	NM_002350.3	114	Ccc/Tcc	5/13	1	2	FACETS	0.783	0.704	0.867	0.783	0.704	0.867	SUBCLONAL	1	TRUE	1	0.441941325497886	2		450	624	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	164	320	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.749	0.692	0.807	0.749	0.692	0.807	SUBCLONAL	1	TRUE	1	0.823555641919658	2		321	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0040120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2588	279	499	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.823555641919658	NA		501	2867	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720679	89720679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123329	NA	P-0040120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	21	39	0	ENST00000371953.3:c.830C>T	p.Thr277Ile	p.T277I	ENST00000371953	NM_000314.4	277	aCa/aTa	8/9	0.754655565115727	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.823555641919658	1		39	26	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209390	98209390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571030658	NA	P-0040120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	295	584	1	ENST00000331920.6:c.4148C>T	p.Pro1383Leu	p.P1383L	ENST00000331920	NM_000264.3	1383	cCg/cTg	23/24	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.823555641919658	2		585	705	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489220	2489220	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	266	637	1	ENST00000355716.4:c.125G>T	p.Cys42Phe	p.C42F	ENST00000355716	NM_003820.2	42	tGc/tTc	2/8	1	2	FACETS	0.873	0.822	0.924	0.873	0.822	0.924	CLONAL	1	TRUE	1	0.823555641919658	2		638	740	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0040145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	4440	575	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.225111833768212	65	FACETS	1	0.994	1			1	CLONAL	66	TRUE	NA	0.225111833768212	65		575	4836	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047527	49047527	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587778850	NA	P-0040145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	18	215	0	ENST00000267163.4:c.2520+1G>T		p.X840_splice	ENST00000267163	NM_000321.2	840			0.182009314030066	2	FACETS	0.769	0.581	0.99	0.384	0.29	0.495	CLONAL	1	TRUE	0	0.225111833768212	2		215	208	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0040145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	107	534	0	ENST00000269305.4:c.920-2A>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			1	2	FACETS	0.909	0.818	1	1	0.987	1	CLONAL	2	TRUE	1	0.225111833768212	2		534	523	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845502	72845502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	24	490	0	ENST00000268489.5:c.3838G>A	p.Asp1280Asn	p.D1280N	ENST00000268489	NM_006885.3	1280	Gac/Aac	7/10	1	2	FACETS	0.491	0.384	0.615	0.491	0.384	0.615	SUBCLONAL	1	TRUE	1	0.225111833768212	2		490	434	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543544	9543544	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	19	373	0	ENST00000353224.5:c.1610A>G	p.His537Arg	p.H537R	ENST00000353224	NM_177990.2	537	cAc/cGc	6/10	1	2	FACETS	0.47	0.356	0.605	0.47	0.356	0.605	SUBCLONAL	1	TRUE	1	0.225111833768212	2		373	359	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005029	150005029	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0040145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	16	360	0	ENST00000253339.5:c.1196C>G	p.Ser399Ter	p.S399*	ENST00000253339		399	tCa/tGa	3/7	1	2	FACETS	0.508	0.375	0.666	0.508	0.375	0.666	SUBCLONAL	1	TRUE	1	0.225111833768212	2		360	280	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034440	47034440	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	71	541	0	ENST00000377604.3:c.525del	p.Phe175LeufsTer91	p.F175Lfs*91	ENST00000377604	NM_001204468.1	175	ttC/tt	6/24	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.225111833768212	2		541	629	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487283	56487283	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	186	397	0	ENST00000267101.3:c.1429C>T	p.Pro477Ser	p.P477S	ENST00000267101	NM_001982.3	477	Cct/Tct	12/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.629743642351639	2		397	537	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485783	8485783	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	20	293	0	ENST00000356435.5:c.3034A>T	p.Arg1012Trp	p.R1012W	ENST00000356435		1012	Agg/Tgg	17/35	1	2	FACETS	0.177	0.135	0.227	0.177	0.135	0.227	SUBCLONAL	1	TRUE	1	0.629743642351639	2		293	358	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133710894	133710896	+	missense_variant	Missense_Mutation	TNP	TCC	TCC	AAG	novel	NA	P-0040153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	46	359	1	ENST00000318560.5:c.61_63delinsAAG	p.Ser21Lys	p.S21K	ENST00000318560	NM_005157.4	21	TCC/AAG	1/11	1	2	FACETS	0.312	0.263	0.367	0.312	0.263	0.367	SUBCLONAL	1	TRUE	1	0.629743642351639	2		360	468	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	87	304	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.658	0.587	0.733	0.658	0.587	0.733	SUBCLONAL	1	TRUE	1	0.730449030783513	2		304	362	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	141	479	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.617	0.564	0.672	0.617	0.564	0.672	SUBCLONAL	1	TRUE	1	0.730449030783513	2		483	626	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	216	442	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.730449030783513	2		447	427	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948747	71948748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760925109	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	110	735	3	ENST00000298229.2:c.3466dup	p.Arg1156ProfsTer59	p.R1156Pfs*59	ENST00000298229	NM_001567.3	1153	-/C	26/28	1	2	FACETS	0.518	0.467	0.573	0.518	0.467	0.573	SUBCLONAL	1	TRUE	1	0.730449030783513	2		738	581	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	172	445	5	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.730449030783513	2		450	441	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	180	333	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.730449030783513	2		333	363	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31381362	31381362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113400552	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	131	426	1	ENST00000328111.2:c.1087C>T	p.Arg363Cys	p.R363C	ENST00000328111	NM_006892.3	363	Cgt/Tgt	10/23	1	2	FACETS	0.691	0.63	0.754	0.691	0.63	0.754	SUBCLONAL	1	TRUE	1	0.730449030783513	2		427	519	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	120	328	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.579	0.525	0.637	0.579	0.525	0.637	SUBCLONAL	1	TRUE	1	0.730449030783513	2		328	567	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	27	329	0	ENST00000375687.4:c.1933_1934dup	p.Gly646ValfsTer58	p.G646Vfs*58	ENST00000375687	NM_015338.5	642	-/GG	13/13	1	2	FACETS	0.338	0.27	0.414	0.338	0.27	0.414	SUBCLONAL	1	TRUE	1	0.730449030783513	2		329	219	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	62	581	0	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.301	0.26	0.346	0.301	0.26	0.346	SUBCLONAL	1	TRUE	1	0.730449030783513	2		581	564	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	156	797	3	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.815	0.751	0.881	0.815	0.751	0.881	CLONAL	1	TRUE	1	0.730449030783513	2		800	524	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	112	477	1	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.739	0.67	0.811	0.739	0.67	0.811	SUBCLONAL	1	TRUE	1	0.730449030783513	2		478	415	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781157	135781157	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	161	613	0	ENST00000298552.3:c.1808del	p.Pro603ArgfsTer26	p.P603Rfs*26	ENST00000298552	NM_001162426.1	603	cCg/cg	15/23	1	2	FACETS	0.704	0.648	0.762	0.704	0.648	0.762	SUBCLONAL	1	TRUE	1	0.730449030783513	2		613	626	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	111	409	1	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	1	2	FACETS	0.591	0.534	0.652	0.591	0.534	0.652	SUBCLONAL	1	TRUE	1	0.730449030783513	2		410	514	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	115	431	4	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.716	0.649	0.785	0.716	0.649	0.785	SUBCLONAL	1	TRUE	1	0.730449030783513	2		435	440	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647028	23647028	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1555461597	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	129	630	0	ENST00000261584.4:c.839del	p.Asn280ThrfsTer8	p.N280Tfs*8	ENST00000261584	NM_024675.3	280	aAc/ac	4/13	1	2	FACETS	0.564	0.513	0.618	0.564	0.513	0.618	SUBCLONAL	1	TRUE	1	0.730449030783513	2		630	626	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	141	519	1	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.745	0.683	0.81	0.745	0.683	0.81	SUBCLONAL	1	TRUE	1	0.730449030783513	2		520	518	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672462	30672462	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148215318	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	130	568	0	ENST00000376406.3:c.4498G>A	p.Ala1500Thr	p.A1500T	ENST00000376406	NM_014641.2	1500	Gcc/Acc	10/15	1	2	FACETS	0.678	0.618	0.74	0.678	0.618	0.74	SUBCLONAL	1	TRUE	1	0.730449030783513	2		568	525	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98003011	98003011	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	53	252	1	ENST00000289081.3:c.265del	p.Ile89PhefsTer2	p.I89Ffs*2	ENST00000289081	NM_000136.2	89	Att/tt	4/15	1	2	FACETS	0.61	0.525	0.7	0.61	0.525	0.7	SUBCLONAL	1	TRUE	1	0.730449030783513	2		253	238	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517769	176517769	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs142240686	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	151	663	1	ENST00000292408.4:c.379G>T	p.Asp127Tyr	p.D127Y	ENST00000292408	NM_213647.1	127	Gat/Tat	4/18	1	2	FACETS	0.654	0.6	0.71	0.654	0.6	0.71	SUBCLONAL	1	TRUE	1	0.730449030783513	2		664	632	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894928	101894928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	81	323	0	ENST00000374994.4:c.481G>A	p.Glu161Lys	p.E161K	ENST00000374994	NM_004612.2	161	Gaa/Aaa	3/9	1	2	FACETS	0.647	0.574	0.723	0.647	0.574	0.723	SUBCLONAL	1	TRUE	1	0.730449030783513	2		323	343	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741255	145741255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376045624	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	178	728	0	ENST00000428558.2:c.1151G>A	p.Arg384Gln	p.R384Q	ENST00000428558	NM_004260.3	384	cGg/cAg	6/22	0.556458470694177	3	FACETS	0.747	0.688	0.807	0.373	0.344	0.404	SUBCLONAL	1	TRUE	1	0.730449030783513	3		728	891	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446388	29446388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769322016	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	149	699	0	ENST00000389048.3:c.3179G>A	p.Arg1060His	p.R1060H	ENST00000389048	NM_004304.4	1060	cGc/cAc	20/29	1	2	FACETS	0.659	0.604	0.716	0.659	0.604	0.716	SUBCLONAL	1	TRUE	1	0.730449030783513	2		699	619	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631883	90631883	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	151	621	0	ENST00000330062.3:c.470T>C	p.Ile157Thr	p.I157T	ENST00000330062	NM_002168.2	157	aTc/aCc	4/11	1	2	FACETS	0.652	0.598	0.708	0.652	0.598	0.708	SUBCLONAL	1	TRUE	1	0.730449030783513	2		621	634	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395001	395001	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1300046652	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	95	396	1	ENST00000380956.4:c.402del	p.Gly135GlufsTer14	p.G135Efs*14	ENST00000380956	NM_001195286.1	133	Aaa/aa	3/9	1	2	FACETS	0.609	0.545	0.676	0.609	0.545	0.676	SUBCLONAL	1	TRUE	1	0.730449030783513	2		397	427	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	138	627	1	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.569	0.519	0.621	0.569	0.519	0.621	SUBCLONAL	1	TRUE	1	0.730449030783513	2		628	664	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245357	153245357	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	97	460	0	ENST00000281708.4:c.1834C>T	p.Gln612Ter	p.Q612*	ENST00000281708	NM_033632.3	612	Cag/Tag	11/12	1	2	FACETS	0.618	0.554	0.685	0.618	0.554	0.685	SUBCLONAL	1	TRUE	1	0.730449030783513	2		460	430	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794356	242794356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144217487	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	150	685	3	ENST00000334409.5:c.586G>A	p.Ala196Thr	p.A196T	ENST00000334409	NM_005018.2	196	Gca/Aca	3/5	1	2	FACETS	0.666	0.611	0.723	0.666	0.611	0.723	SUBCLONAL	1	TRUE	1	0.730449030783513	2		688	617	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40460280	40460280	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	135	543	0	ENST00000345506.4:c.1991G>A	p.Ser664Asn	p.S664N	ENST00000345506	NM_003152.3	664	aGc/aAc	17/20	1	2	FACETS	0.701	0.641	0.764	0.701	0.641	0.764	SUBCLONAL	1	TRUE	1	0.730449030783513	2		543	527	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73991987	73991987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770116040	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	157	631	0	ENST00000318443.5:c.7C>T	p.Arg3Cys	p.R3C	ENST00000318443	NM_001024736.1	3	Cgt/Tgt	2/10	1	2	FACETS	0.68	0.625	0.737	0.68	0.625	0.737	SUBCLONAL	1	TRUE	1	0.730449030783513	2		631	632	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41021708	41021708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	76	338	0	ENST00000267868.3:c.650C>T	p.Ala217Val	p.A217V	ENST00000267868	NM_002875.4	217	gCa/gTa	8/10	1	2	FACETS	0.685	0.606	0.767	0.685	0.606	0.767	SUBCLONAL	1	TRUE	1	0.730449030783513	2		338	304	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390962	139390962	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560981171	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	218	877	0	ENST00000277541.6:c.7229C>T	p.Pro2410Leu	p.P2410L	ENST00000277541	NM_017617.3	2410	cCg/cTg	34/34	1	2	FACETS	0.771	0.719	0.824	0.771	0.719	0.824	SUBCLONAL	1	TRUE	1	0.730449030783513	2		877	774	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249927	110249927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	128	579	0	ENST00000374672.4:c.748G>A	p.Val250Ile	p.V250I	ENST00000374672	NM_004235.4	250	Gtc/Atc	3/5	1	2	FACETS	0.678	0.617	0.741	0.678	0.617	0.741	SUBCLONAL	1	TRUE	1	0.730449030783513	2		579	517	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217223	66217223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	130	393	0	ENST00000273854.3:c.2392C>T	p.His798Tyr	p.H798Y	ENST00000273854	NM_004439.5	798	Cat/Tat	14/18	1	2	FACETS	0.832	0.761	0.905	0.832	0.761	0.905	CLONAL	1	TRUE	1	0.730449030783513	2		393	428	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517886	187517886	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs373689624	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	124	422	0	ENST00000441802.2:c.12808C>T	p.Arg4270Ter	p.R4270*	ENST00000441802	NM_005245.3	4270	Cga/Tga	25/27	1	2	FACETS	0.793	0.723	0.866	0.793	0.723	0.866	SUBCLONAL	1	TRUE	1	0.730449030783513	2		422	428	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799130	42799131	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	143	763	0	ENST00000575354.2:c.4620dup	p.Thr1541HisfsTer18	p.T1541Hfs*18	ENST00000575354	NM_015125.3	1538	-/C	20/20	1	2	FACETS	0.599	0.547	0.652	0.599	0.547	0.652	SUBCLONAL	1	TRUE	1	0.730449030783513	2		763	654	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100097	27100098	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	54	654	1	ENST00000324856.7:c.3896dup	p.Asn1299LysfsTer24	p.N1299Kfs*24	ENST00000324856	NM_006015.4	1298	gga/ggAa	16/20	1	2	FACETS	0.223	0.19	0.259	0.223	0.19	0.259	SUBCLONAL	1	TRUE	1	0.730449030783513	2		655	664	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45800107	45800107	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	162	581	0	ENST00000450313.1:c.113A>C	p.Lys38Thr	p.K38T	ENST00000450313	NM_012222.2	38	aAg/aCg	2/16	1	2	FACETS	0.695	0.64	0.752	0.695	0.64	0.752	SUBCLONAL	1	TRUE	1	0.730449030783513	2		581	638	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458968	120458968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	194	689	0	ENST00000256646.2:c.6377C>T	p.Ala2126Val	p.A2126V	ENST00000256646	NM_024408.3	2126	gCc/gTc	34/34	1	2	FACETS	0.839	0.78	0.899	0.839	0.78	0.899	CLONAL	1	TRUE	1	0.730449030783513	2		689	633	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830871	156830871	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	137	524	0	ENST00000524377.1:c.145C>T	p.Arg49Ter	p.R49*	ENST00000524377	NM_002529.3	49	Cga/Tga	1/17	0.540221064700739	4	FACETS	0.85	0.774	0.929	0.283	0.258	0.31	CLONAL	1	TRUE	1	0.730449030783513	4		524	764	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852218	63852218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs916811022	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	128	535	0	ENST00000279873.7:c.2996G>A	p.Arg999Gln	p.R999Q	ENST00000279873	NM_032199.2	999	cGg/cAg	10/10	1	2	FACETS	0.7	0.637	0.764	0.7	0.637	0.764	SUBCLONAL	1	TRUE	1	0.730449030783513	2		535	501	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100561	102100561	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	122	462	1	ENST00000282441.5:c.1405G>T	p.Glu469Ter	p.E469*	ENST00000282441	NM_001130145.2	469	Gag/Tag	9/9	1	2	FACETS	0.763	0.694	0.833	0.763	0.694	0.833	SUBCLONAL	1	TRUE	1	0.730449030783513	2		463	438	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930708	32930708	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555286293	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	128	449	0	ENST00000380152.3:c.7579G>A	p.Val2527Ile	p.V2527I	ENST00000380152		2527	Gta/Ata	15/27	1	2	FACETS	0.769	0.701	0.838	0.769	0.701	0.838	SUBCLONAL	1	TRUE	1	0.730449030783513	2		449	456	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066889	30066889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1303923680	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	92	537	0	ENST00000331968.5:c.2242G>A	p.Ala748Thr	p.A748T	ENST00000331968	NM_002742.2	748	Gct/Act	16/18	1	2	FACETS	0.514	0.458	0.573	0.514	0.458	0.573	SUBCLONAL	1	TRUE	1	0.730449030783513	2		537	490	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420260	88420260	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	124	522	1	ENST00000360948.2:c.2426G>T	p.Arg809Met	p.R809M	ENST00000360948	NM_001012338.2	809	aGg/aTg	19/19	1	2	FACETS	0.679	0.618	0.743	0.679	0.618	0.743	SUBCLONAL	1	TRUE	1	0.730449030783513	2		523	500	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821945	72821946	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	51	329	0	ENST00000268489.5:c.10229dup	p.Asp3411ArgfsTer20	p.D3411Rfs*20	ENST00000268489	NM_006885.3	3410	cca/ccCa	10/10	1	2	FACETS	0.473	0.405	0.548	0.473	0.405	0.548	SUBCLONAL	1	TRUE	1	0.730449030783513	2		329	295	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993551	72993551	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	161	626	0	ENST00000268489.5:c.494C>A	p.Pro165His	p.P165H	ENST00000268489	NM_006885.3	165	cCt/cAt	2/10	1	2	FACETS	0.787	0.726	0.85	0.787	0.726	0.85	SUBCLONAL	1	TRUE	1	0.730449030783513	2		626	560	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350617	89350617	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	162	663	0	ENST00000301030.4:c.2333A>C	p.Lys778Thr	p.K778T	ENST00000301030	NM_001256183.1	778	aAg/aCg	9/13	1	2	FACETS	0.561	0.515	0.608	0.561	0.515	0.608	SUBCLONAL	1	TRUE	1	0.730449030783513	2		663	791	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40457661	40457661	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	129	612	0	ENST00000345506.4:c.1414G>T	p.Gly472Cys	p.G472C	ENST00000345506	NM_003152.3	472	Ggc/Tgc	13/20	1	2	FACETS	0.591	0.537	0.647	0.591	0.537	0.647	SUBCLONAL	1	TRUE	1	0.730449030783513	2		612	598	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55339517	55339517	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	144	480	0	ENST00000284073.2:c.279del	p.Val95LeufsTer20	p.V95Lfs*20	ENST00000284073	NM_138962.2	92	gaC/ga	5/14	1	2	FACETS	0.682	0.625	0.742	0.682	0.625	0.742	SUBCLONAL	1	TRUE	1	0.730449030783513	2		480	578	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2193765	2193765	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	147	511	0	ENST00000398665.3:c.571C>A	p.Pro191Thr	p.P191T	ENST00000398665	NM_032482.2	191	Ccg/Acg	6/28	1	2	FACETS	0.663	0.608	0.721	0.663	0.608	0.721	SUBCLONAL	1	TRUE	1	0.730449030783513	2		511	607	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221684	36221684	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	184	778	0	ENST00000222270.7:c.5353C>T	p.Pro1785Ser	p.P1785S	ENST00000222270	NM_014727.1	1785	Cca/Tca	26/37	1	2	FACETS	0.677	0.627	0.729	0.677	0.627	0.729	SUBCLONAL	1	TRUE	1	0.730449030783513	2		778	744	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920494	50920494	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	134	592	0	ENST00000440232.2:c.3186G>T	p.Gln1062His	p.Q1062H	ENST00000440232	NM_002691.3	1062	caG/caT	26/27	1	2	FACETS	0.743	0.679	0.809	0.743	0.679	0.809	SUBCLONAL	1	TRUE	1	0.730449030783513	2		592	494	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249912	39249912	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	145	530	0	ENST00000402219.2:c.1657A>G	p.Met553Val	p.M553V	ENST00000402219	NM_005633.3	553	Atg/Gtg	10/23	1	2	FACETS	0.664	0.608	0.722	0.664	0.608	0.722	SUBCLONAL	1	TRUE	1	0.730449030783513	2		530	598	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248605	212248605	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	106	455	0	ENST00000342788.4:c.3662A>G	p.Tyr1221Cys	p.Y1221C	ENST00000342788	NM_005235.2	1221	tAc/tGc	28/28	1	2	FACETS	0.596	0.537	0.658	0.596	0.537	0.658	SUBCLONAL	1	TRUE	1	0.730449030783513	2		455	487	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661677	227661677	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	25	613	0	ENST00000305123.5:c.1778A>T	p.Glu593Val	p.E593V	ENST00000305123	NM_005544.2	593	gAg/gTg	1/2	1	2	FACETS	0.14	0.109	0.175	0.14	0.109	0.175	SUBCLONAL	1	TRUE	1	0.730449030783513	2		613	490	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557751	187557752	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	81	307	0	ENST00000441802.2:c.3959_3960del	p.Tyr1320Ter	p.Y1320*	ENST00000441802	NM_005245.3	1320	tAT/t	5/27	1	2	FACETS	0.7	0.622	0.781	0.7	0.622	0.781	SUBCLONAL	1	TRUE	1	0.730449030783513	2		307	317	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31466379	31466379	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	134	559	0	ENST00000344624.3:c.2376del	p.Lys792AsnfsTer7	p.K792Nfs*7	ENST00000344624		792	aaA/aa	16/33	1	2	FACETS	0.651	0.593	0.71	0.651	0.593	0.71	SUBCLONAL	1	TRUE	1	0.730449030783513	2		559	564	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168825	56168825	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	86	354	0	ENST00000399503.3:c.1679G>T	p.Trp560Leu	p.W560L	ENST00000399503	NM_005921.1	560	tGg/tTg	9/20	1	2	FACETS	0.599	0.533	0.669	0.599	0.533	0.669	SUBCLONAL	1	TRUE	1	0.730449030783513	2		354	393	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449811	149449811	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	179	669	0	ENST00000286301.3:c.1253del	p.Leu418CysfsTer12	p.L418Cfs*12	ENST00000286301	NM_005211.3	418	tTg/tg	9/22	1	2	FACETS	0.695	0.643	0.749	0.695	0.643	0.749	SUBCLONAL	1	TRUE	1	0.730449030783513	2		669	705	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510227	149510227	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	102	498	0	ENST00000261799.4:c.1244-2A>G		p.X415_splice	ENST00000261799	NM_002609.3	415			1	2	FACETS	0.557	0.5	0.617	0.557	0.5	0.617	SUBCLONAL	1	TRUE	1	0.730449030783513	2		498	501	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518701	176518701	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	145	597	0	ENST00000292408.4:c.619T>C	p.Trp207Arg	p.W207R	ENST00000292408	NM_213647.1	207	Tgg/Cgg	6/18	1	2	FACETS	0.673	0.616	0.732	0.673	0.616	0.732	SUBCLONAL	1	TRUE	1	0.730449030783513	2		597	590	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031750	69031750	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	100	452	0	ENST00000288368.4:c.3504+1G>A		p.X1168_splice	ENST00000288368	NM_024870.2	1168			0.556458470694177	3	FACETS	0.586	0.524	0.652	0.293	0.262	0.326	SUBCLONAL	1	TRUE	1	0.730449030783513	3		452	638	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460555	8460555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	84	347	0	ENST00000356435.5:c.3731G>A	p.Ser1244Asn	p.S1244N	ENST00000356435		1244	aGc/aAc	22/35	1	2	FACETS	0.53	0.47	0.593	0.53	0.47	0.593	SUBCLONAL	1	TRUE	1	0.730449030783513	2		347	434	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230732	53230732	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	29	293	0	ENST00000375401.3:c.2061G>T	p.Lys687Asn	p.K687N	ENST00000375401	NM_004187.3	687	aaG/aaT	14/26	1	1	FACETS	0.169	0.136	0.207	0.169	0.136	0.207	SUBCLONAL	1	TRUE	0	0.730449030783513	1		293	298	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs879253911	NA	P-0040269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	95	857	0	ENST00000269305.4:c.538G>T	p.Glu180Ter	p.E180*	ENST00000269305	NM_001126112.2	180	Gag/Tag	5/11	1	2	FACETS	0.733	0.65	0.821	0.733	0.65	0.821	SUBCLONAL	1	TRUE	1	0.22	2		857	1179	SUCCESS
AR	367	MSKCC	GRCh37	X	66766261	66766261	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	41	404	0	ENST00000374690.3:c.1273G>T	p.Gly425Trp	p.G425W	ENST00000374690	NM_000044.3	425	Ggg/Tgg	1/8	1	2	FACETS	0.599	0.498	0.712	0.599	0.498	0.712	SUBCLONAL	1	TRUE	1	0.22	2		404	622	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225300	2225300	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0040269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	87	942	0	ENST00000326181.6:c.1387-2A>T		p.X463_splice	ENST00000326181	NM_032271.2	463			1	2	FACETS	0.663	0.585	0.747	0.663	0.585	0.747	SUBCLONAL	1	TRUE	1	0.22	2		942	1193	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867035	45867035	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	67	596	0	ENST00000391945.4:c.1084G>T	p.Ala362Ser	p.A362S	ENST00000391945	NM_000400.3	362	Gcc/Tcc	11/23	1	2	FACETS	0.601	0.521	0.689	0.601	0.521	0.689	SUBCLONAL	1	TRUE	1	0.22	2		596	1013	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627264	86627265	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	36	347	0	ENST00000274376.6:c.642dup	p.Ser215ValfsTer8	p.S215Vfs*8	ENST00000274376	NM_002890.2	213	-/G	2/25	1	2	FACETS	0.662	0.544	0.795	0.662	0.544	0.795	SUBCLONAL	1	TRUE	1	0.22	2		347	494	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411155	63411155	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0040269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	55	791	0	ENST00000330258.3:c.2012C>G	p.Ser671Ter	p.S671*	ENST00000330258	NM_152424.3	671	tCa/tGa	2/2	1	2	FACETS	0.504	0.43	0.586	0.504	0.43	0.586	SUBCLONAL	1	TRUE	1	0.22	2		791	992	SUCCESS
AR	367	MSKCC	GRCh37	X	66863181	66863181	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	47	592	0	ENST00000374690.3:c.1700C>G	p.Ala567Gly	p.A567G	ENST00000374690	NM_000044.3	567	gCt/gGt	2/8	1	2	FACETS	0.487	0.41	0.573	0.487	0.41	0.573	SUBCLONAL	1	TRUE	1	0.22	2		592	877	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	57	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.717	0.617	0.825	0.717	0.617	0.825	SUBCLONAL	1	TRUE	1	0.404438476493101	2		452	393	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0040310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	65	399	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.977	0.853	1	0.977	0.853	1	CLONAL	1	TRUE	1	0.404438476493101	2		399	329	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0040310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	73	281	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.978	0.861	1	0.978	0.861	1	CLONAL	1	TRUE	1	0.404438476493101	2		282	369	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919691	96919691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200327514	NA	P-0040310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	86	471	0	ENST00000258439.3:c.572C>T	p.Thr191Met	p.T191M	ENST00000258439	NM_001193304.2	191	aCg/aTg	4/4	1	2	FACETS	0.798	0.708	0.894	0.798	0.708	0.894	SUBCLONAL	1	TRUE	1	0.404438476493101	2		471	533	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916526	39916526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265777184	NA	P-0040310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	147	553	1	ENST00000378444.4:c.4477C>T	p.Arg1493Trp	p.R1493W	ENST00000378444	NM_001123385.1	1493	Cgg/Tgg	11/15	1	2	FACETS	0.977	0.893	1	0.977	0.893	1	CLONAL	1	TRUE	1	0.404438476493101	2		554	744	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0040310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	181	626	0	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.404438476493101	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.404438476493101	1		626	685	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727880	41727880	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756018335	NA	P-0040310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	145	615	2	ENST00000301178.4:c.505G>A	p.Val169Met	p.V169M	ENST00000301178	NM_021913.4	169	Gtg/Atg	4/20	1	2	FACETS	0.899	0.82	0.98	0.899	0.82	0.98	CLONAL	1	TRUE	1	0.404438476493101	2		617	798	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374890	45374890	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	98	419	0	ENST00000262160.6:c.953A>T	p.Asn318Ile	p.N318I	ENST00000262160	NM_005901.5	318	aAt/aTt	8/11	0.404438476493101	1	FACETS	0.852	0.764	0.944	0.852	0.764	0.944	CLONAL	1	TRUE	0	0.404438476493101	1		419	454	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0040346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	99	506	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.188091662458671	3	FACETS	0.969	0.867	1	0.969	0.867	1	CLONAL	2	TRUE	1	0.192733857781018	3		506	581	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575022	64575022	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0040346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	22	240	0	ENST00000312049.6:c.783+2T>A		p.X261_splice	ENST00000312049	NM_130799.2	261			1	2	FACETS	0.885	0.687	1	0.885	0.687	1	CLONAL	1	TRUE	1	0.192733857781018	2		240	258	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842410	68842411	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	105	399	0	ENST00000261769.5:c.472dup	p.Ile158AsnfsTer10	p.I158Nfs*10	ENST00000261769	NM_004360.3	157	-/A	4/16	0.192733857781018	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.192733857781018	2		399	474	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70442657	70442657	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	10	312	0	ENST00000373644.4:c.4979G>T	p.Gly1660Val	p.G1660V	ENST00000373644	NM_030625.2	1660	gGg/gTg	10/12	0.184028392426946	3	FACETS	0.885	0.643	1	0.885	0.643	1	INDETERMINATE	3	TRUE	0	0.372328887307599	3		312	24	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140165	50140165	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	49	630	0	ENST00000246792.3:c.260A>T	p.Gln87Leu	p.Q87L	ENST00000246792	NM_006270.3	87	cAg/cTg	3/6	0.372328887307599	3	FACETS	1	0.931	1	1	0.931	1	CLONAL	3	TRUE	0	0.372328887307599	3		630	96	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967231	25967231	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	19	299	0	ENST00000435504.4:c.1975G>T	p.Asp659Tyr	p.D659Y	ENST00000435504		659	Gac/Tac	13/13	0.372328887307599	4	FACETS	0.834	0.658	1	0.834	0.658	1	CLONAL	3	TRUE	1	0.372328887307599	4		299	56	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516923	187516923	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	16	313	1	ENST00000441802.2:c.13058C>T	p.Ser4353Phe	p.S4353F	ENST00000441802	NM_005245.3	4353	tCc/tTc	26/27	0.342340510859276	3	FACETS	1	0.783	1	1	0.783	1	CLONAL	2	TRUE	1	0.372328887307599	3		314	50	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543699	29543700	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0040358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	11	383	0	ENST00000389048.3:c.1463_1464insTC	p.Trp489ProfsTer19	p.W489Pfs*19	ENST00000389048	NM_004304.4	488	ggc/ggTCc	7/29	0.372328887307599	4	FACETS	0.819	0.571	1	0.273	0.19	0.374	CLONAL	1	TRUE	1	0.372328887307599	4		383	99	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0040382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	527	692	1	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.5152175346263	2	FACETS	0.864	0.833	0.895	0.864	0.833	0.895	CLONAL	2	TRUE	0	0.603772364871084	2		693	1010	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941654	48941654	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs776534331	NA	P-0040382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	198	190	0	ENST00000267163.4:c.964G>T	p.Glu322Ter	p.E322*	ENST00000267163	NM_000321.2	322	Gaa/Taa	10/27	0.553253224967949	2	FACETS	0.802	0.753	0.851	0.802	0.753	0.851	CLONAL	2	TRUE	0	0.603772364871084	2		190	409	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076827	72076827	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	558	381	0	ENST00000357731.5:c.670G>T	p.Ala224Ser	p.A224S	ENST00000357731	NM_173808.2	224	Gct/Tct	5/7	0.472289528236394	4	FACETS	0.882	0.856	0.908	0.882	0.856	0.908	CLONAL	4	TRUE	0	0.603772364871084	4		381	840	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633514	69633514	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	104	299	0	ENST00000334134.2:c.188G>T	p.Arg63Leu	p.R63L	ENST00000334134	NM_005247.2	63	cGc/cTc	1/3	0.517437477351312	3	FACETS	0.946	0.852	1	0.473	0.426	0.523	CLONAL	1	TRUE	1	0.603772364871084	3		299	474	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670033	29670033	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	41	336	0	ENST00000356175.3:c.7006G>C	p.Glu2336Gln	p.E2336Q	ENST00000356175	NM_000267.3	2336	Gag/Cag	47/57	0.603772364871084	3	FACETS	0.263	0.218	0.313	0.132	0.109	0.157	SUBCLONAL	1	TRUE	1	0.603772364871084	3		336	672	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858880	78858880	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	465	749	1	ENST00000306801.3:c.1915A>T	p.Thr639Ser	p.T639S	ENST00000306801	NM_020761.2	639	Acc/Tcc	17/34	0.603772364871084	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.603772364871084	1		750	923	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089163	37089163	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	160	402	0	ENST00000231790.2:c.1885G>C	p.Glu629Gln	p.E629Q	ENST00000231790	NM_000249.3	629	Gaa/Caa	16/19	1	2	FACETS	0.869	0.8	0.94	0.869	0.8	0.94	CLONAL	1	TRUE	1	0.603772364871084	2		402	610	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281357	142281357	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0040382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	403	587	0	ENST00000350721.4:c.887C>G	p.Ser296Ter	p.S296*	ENST00000350721	NM_001184.3	296	tCa/tGa	4/47	0.502190056993469	4	FACETS	0.846	0.805	0.888	0.846	0.805	0.888	CLONAL	2	TRUE	2	0.603772364871084	4		587	1265	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955906	55955906	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	379	531	0	ENST00000263923.4:c.3256A>T	p.Ser1086Cys	p.S1086C	ENST00000263923	NM_002253.2	1086	Agt/Tgt	24/30	0.55426612261639	2	FACETS	0.926	0.888	0.963	0.926	0.888	0.963	CLONAL	2	TRUE	0	0.603772364871084	2		531	678	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522612	176522613	+	missense_variant	Missense_Mutation	DNP	CC	CC	TG	novel	NA	P-0040382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	442	768	0	ENST00000292408.4:c.1709_1710delinsTG	p.Pro570Leu	p.P570L	ENST00000292408	NM_213647.1	570	cCC/cTG	13/18	0.539824746898022	2	FACETS	0.815	0.782	0.848	0.815	0.782	0.848	CLONAL	2	TRUE	0	0.603772364871084	2		768	898	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680791	30680791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1366797290	NA	P-0040382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	200	574	0	ENST00000376406.3:c.928C>T	p.Pro310Ser	p.P310S	ENST00000376406	NM_014641.2	310	Cct/Tct	5/15	0.534132944287043	4	FACETS	1	0.962	1	0.265	0.245	0.286	CLONAL	1	TRUE	0	0.603772364871084	4		574	1002	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508148	106508148	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	113	328	1	ENST00000359195.3:c.142C>A	p.Gln48Lys	p.Q48K	ENST00000359195	NM_002649.2	48	Cag/Aag	2/11	1	2	FACETS	0.972	0.883	1	0.972	0.883	1	CLONAL	1	TRUE	1	0.603772364871084	2		329	385	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435715	116435715	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	120	417	0	ENST00000397752.3:c.3807del	p.Phe1269LeufsTer8	p.F1269Lfs*8	ENST00000397752	NM_000245.2	1269	Ttt/tt	20/21	1	2	FACETS	0.816	0.741	0.894	0.816	0.741	0.894	CLONAL	1	TRUE	1	0.603772364871084	2		417	487	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852084	128852084	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1327533871	NA	P-0040382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	284	826	0	ENST00000249373.3:c.2156G>A	p.Trp719Ter	p.W719*	ENST00000249373	NM_005631.4	719	tGg/tAg	12/12	1	2	FACETS	0.982	0.925	1	0.982	0.925	1	CLONAL	1	TRUE	1	0.603772364871084	2		826	958	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859911	117859911	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	178	242	0	ENST00000297338.2:c.1724G>T	p.Gly575Val	p.G575V	ENST00000297338	NM_006265.2	575	gGa/gTa	14/14	0.202801818563268	3	FACETS	0.888	0.828	0.949	0.592	0.552	0.633	INDETERMINATE	2	TRUE	0	0.603772364871084	3		242	432	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522612	176522612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	442	768	0	ENST00000292408.4:c.1709C>T	p.Pro570Leu	p.P570L	ENST00000292408	NM_213647.1	570	cCc/cTc	13/18	0.539824746898022	2	FACETS	0.815	0.782	0.848	0.815	0.782	0.848	CLONAL	2	TRUE	0	0.603772364871084	2		768	898	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0040448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	246	454	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.847556580021881	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.847556580021881	1		454	321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0040448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	803	781	0	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	0.847556580021881	2	FACETS	0.997	0.98	1	0.997	0.98	1	CLONAL	2	TRUE	0	0.847556580021881	2		781	950	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420104	41420104	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	435	278	1	ENST00000373198.4:c.217T>A	p.Ser73Thr	p.S73T	ENST00000373198	NM_133170.3	73	Tct/Act	3/32	0.376412955222733	5	FACETS	1	0.977	1	0.805	0.782	0.828	INDETERMINATE	4	TRUE	0	0.847556580021881	5		279	579	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80063814	80063814	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	201	486	1	ENST00000265081.6:c.1959A>C	p.Gln653His	p.Q653H	ENST00000265081	NM_002439.4	653	caA/caC	14/24	1	2	FACETS	0.978	0.916	1	0.978	0.916	1	CLONAL	1	TRUE	1	0.847556580021881	2		487	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0040489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	133	431	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.3	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.32	1		432	536	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0040489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	79	421	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.112107738371738	3	FACETS	1	0.943	1	0.558	0.492	0.629	INDETERMINATE	1	TRUE	1	0.32	3		421	513	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969848	81969848	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568724894	NA	P-0040489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	108	542	1	ENST00000359376.3:c.2917G>A	p.Asp973Asn	p.D973N	ENST00000359376	NM_002661.3	973	Gac/Aac	27/33	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.32	2		543	606	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411576	63411576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	127	757	1	ENST00000330258.3:c.1591C>T	p.Arg531Ter	p.R531*	ENST00000330258	NM_152424.3	531	Cga/Tga	2/2	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.32	2		758	736	SUCCESS
APC	324	MSKCC	GRCh37	5	112175642	112175642	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	48	263	0	ENST00000257430.4:c.4351G>T	p.Glu1451Ter	p.E1451*	ENST00000257430	NM_000038.5	1451	Gaa/Taa	16/16	0.112107738371738	3	FACETS	0.969	0.822	1	0.485	0.411	0.565	INDETERMINATE	1	TRUE	1	0.32	3		263	359	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670255	134670255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1426484610	NA	P-0040489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	70	469	0	ENST00000398015.3:c.166C>T	p.Arg56Cys	p.R56C	ENST00000398015	NM_004441.4	56	Cgc/Tgc	3/16	1	2	FACETS	0.85	0.742	0.965	0.85	0.742	0.965	CLONAL	1	TRUE	1	0.32	2		469	515	SUCCESS
APC	324	MSKCC	GRCh37	5	112116598	112116598	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs137854577	NA	P-0040489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	46	288	0	ENST00000257430.4:c.643C>T	p.Gln215Ter	p.Q215*	ENST00000257430	NM_000038.5	215	Cag/Tag	6/16	0.112107738371738	3	FACETS	0.828	0.698	0.97	0.414	0.349	0.485	INDETERMINATE	1	TRUE	1	0.32	3		288	403	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911561	114911561	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	91	440	0	ENST00000543371.1:c.1079A>C	p.Tyr360Ser	p.Y360S	ENST00000543371	NM_001198531.1	360	tAt/tCt	10/14	NA	2	FACETS	1	0.926	1			1	INDETERMINATE	1	TRUE	NA	0.32	2		440	541	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274222	10274222	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	53	403	0	ENST00000330684.3:c.47T>C	p.Leu16Pro	p.L16P	ENST00000330684	NM_001134407.1	16	cTg/cCg	2/13	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.32	2		403	331	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120123	70120124	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0040489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	41	169	0	ENST00000245479.2:c.1126dup	p.Gln376ProfsTer202	p.Q376Pfs*202	ENST00000245479	NM_000346.3	375	-/C	3/3	0.3	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.32	1		169	158	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604674	48604674	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	61	340	0	ENST00000342988.3:c.1496G>A	p.Cys499Tyr	p.C499Y	ENST00000342988	NM_005359.5	499	tGc/tAc	12/12	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.32	2		340	337	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128849216	128849216	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755295928	NA	P-0040489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	98	494	0	ENST00000249373.3:c.1444C>T	p.Arg482Cys	p.R482C	ENST00000249373	NM_005631.4	482	Cgc/Tgc	8/12	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.32	2		494	555	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137323752	137323752	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	121	748	0	ENST00000481739.1:c.1045G>T	p.Val349Leu	p.V349L	ENST00000481739	NM_002957.4	349	Gtg/Ttg	8/10	0.3	3	FACETS	1	0.935	1	0.523	0.472	0.576	CLONAL	1	TRUE	1	0.32	3		748	839	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42057249	42057254	+	inframe_deletion	In_Frame_Del	DEL	TGGCTC	TGGCTC	-	novel	NA	P-0040493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	83	447	0	ENST00000219905.7:c.7911_7916del	p.Ala2638_Leu2639del	p.A2638_L2639del	ENST00000219905	NM_001164273.1	2637	gTGGCTCta/gta	23/24	1	2	FACETS	0.886	0.783	0.995	0.886	0.783	0.995	CLONAL	1	TRUE	1	0.349029729474678	2		447	537	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	61	320	1				ENST00000310581	NM_198253.2	-/1132			0.214305312024735	0	FACETS	0.457	0.397	0.522			1	INDETERMINATE	1	TRUE	0	0.454571084425706	0		321	320	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166506	118166506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753542382	NA	P-0040506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	67	323	1	ENST00000369448.3:c.1016G>A	p.Arg339His	p.R339H	ENST00000369448	NM_017709.3	339	cGt/cAt	2/2	1	2	FACETS	0.83	0.726	0.942	0.83	0.726	0.942	CLONAL	1	TRUE	1	0.454571084425706	2		324	355	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926249	112926249	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs397509344	NA	P-0040506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	84	344	0	ENST00000351677.2:c.1382C>G	p.Ala461Gly	p.A461G	ENST00000351677	NM_002834.3	461	gCt/gGt	12/16	1	2	FACETS	0.872	0.774	0.975	0.872	0.774	0.975	CLONAL	1	TRUE	1	0.454571084425706	2		344	424	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676175	29676175	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	52	264	0	ENST00000356175.3:c.7164del	p.Val2389SerfsTer8	p.V2389Sfs*8	ENST00000356175	NM_000267.3	2388	acA/ac	48/57	0.445661601574013	1	FACETS	0.713	0.613	0.82	0.713	0.613	0.82	SUBCLONAL	1	TRUE	0	0.454571084425706	1		264	248	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321670	30321670	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	46	420	0	ENST00000322652.5:c.1525C>T	p.Gln509Ter	p.Q509*	ENST00000322652	NM_015355.2	509	Caa/Taa	13/16	0.445661601574013	1	FACETS	0.377	0.318	0.442	0.377	0.318	0.442	SUBCLONAL	1	TRUE	0	0.454571084425706	1		420	415	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981576	70981576	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	155	812	0	ENST00000276594.2:c.520C>T	p.Pro174Ser	p.P174S	ENST00000276594	NM_024504.3	174	Ccc/Tcc	2/8	1	2	FACETS	0.914	0.838	0.993	0.914	0.838	0.993	CLONAL	1	TRUE	1	0.454571084425706	2		812	746	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068939	30068939	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	177	618	0	ENST00000331968.5:c.1990G>T	p.Gly664Ter	p.G664*	ENST00000331968	NM_002742.2	664	Gga/Tga	14/18	1	2	FACETS	0.883	0.814	0.954	0.883	0.814	0.954	CLONAL	1	TRUE	1	0.486107927044692	2		618	825	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207064	1207065	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1131690917	NA	P-0040510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	210	879	0	ENST00000326873.7:c.157dup	p.Asp53GlyfsTer110	p.D53Gfs*110	ENST00000326873	NM_000455.4	51	atg/atGg	1/10	0.486107927044692	1	FACETS	0.906	0.844	0.969	0.906	0.844	0.969	CLONAL	1	TRUE	0	0.486107927044692	1		879	722	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0040510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	155	509	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.486107927044692	2		509	601	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194884	29194885	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0040510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	192	793	0	ENST00000240100.2:c.843_844delinsTT	p.Gln281_Ala282delinsHisSer	p.Q281_A282delinsHS	ENST00000240100	NM_001394.6	281	caGGcg/caTTcg	4/4	0.465971972959734	3	FACETS	0.946	0.874	1	0.473	0.437	0.51	CLONAL	1	TRUE	1	0.486107927044692	3		793	1038	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207717	29207717	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1268692884	NA	P-0040510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	200	691	0	ENST00000240100.2:c.79G>A	p.Gly27Ser	p.G27S	ENST00000240100	NM_001394.6	27	Ggc/Agc	1/4	0.465971972959734	3	FACETS	1	0.962	1	0.529	0.49	0.569	CLONAL	1	TRUE	1	0.486107927044692	3		691	967	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750438	133750438	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	171	541	0	ENST00000318560.5:c.1269G>T	p.Trp423Cys	p.W423C	ENST00000318560	NM_005157.4	423	tgG/tgT	7/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.486107927044692	2		541	684	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248998	55248999	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCAGCG	rs727504263	NA	P-0040513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	166	447	0	ENST00000275493.2:c.2300_2308dup	p.Ala767_Val769dup	p.A767_V769dup	ENST00000275493	NM_005228.3	767	atg/aTGGCCAGCGtg	20/28	0.3	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	TRUE	0	0.18	3		447	609	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95584087	95584088	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAATCTAAGAAAATTATACA	novel	NA	P-0040513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	21	256	0	ENST00000393063.1:c.1377-16_1380dup	p.Ile461CysfsTer7	p.I461Cfs*7	ENST00000393063	NM_030621.3	460	-/TGTATAATTTTCTTAGATTG	10/28	1	2	FACETS	0.738	0.569	0.936	0.738	0.569	0.936	CLONAL	1	TRUE	1	0.18	2		256	316	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474823	138474823	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0040513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	17	285	0	ENST00000289153.2:c.172-2A>G		p.X58_splice	ENST00000289153	NM_006219.2	58			1	2	FACETS	0.609	0.454	0.794	0.609	0.454	0.794	SUBCLONAL	1	TRUE	1	0.18	2		285	310	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969888	161969888	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	36	487	0	ENST00000366898.1:c.1081G>A	p.Gly361Arg	p.G361R	ENST00000366898	NM_004562.2	361	Ggg/Agg	9/12	1	2	FACETS	0.808	0.664	0.97	0.808	0.664	0.97	CLONAL	1	TRUE	1	0.18	2		487	495	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632350	215632350	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	41	394	0	ENST00000260947.4:c.1424A>T	p.Lys475Met	p.K475M	ENST00000260947	NM_000465.2	475	aAg/aTg	6/11	1	2	FACETS	0.157	0.13	0.187	0.157	0.13	0.187	SUBCLONAL	1	TRUE	1	0.879493553694064	2		394	593	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0040530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	12	509	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	0.088	0.061	0.122	0.088	0.061	0.122	SUBCLONAL	1	TRUE	1	0.62	2		509	439	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986588	36986601	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGCTGGCGGCGT	GGGGCTGGCGGCGT	-	novel	NA	P-0040530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	36	601	0	ENST00000354822.5:c.1088_1101del	p.His363ArgfsTer71	p.H363Rfs*71	ENST00000354822	NM_001079668.2	363	cACGCCGCCAGCCCC/c	3/3	1	2	FACETS	0.236	0.193	0.283	0.236	0.193	0.283	SUBCLONAL	1	TRUE	1	0.62	2		601	493	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0040538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	240	445	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.591852854346473	3	FACETS	0.934	0.883	0.986	0.934	0.883	0.986	CLONAL	2	TRUE	1	0.700576423792046	3		445	495	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439821	51439821	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	202	554	1	ENST00000262662.1:c.386A>G	p.Asn129Ser	p.N129S	ENST00000262662		129	aAt/aGt	4/4	0.344016767555884	4	FACETS	0.799	0.745	0.854	0.799	0.745	0.854	INDETERMINATE	2	TRUE	2	0.700576423792046	4		555	614	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576889	7576890	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	411	808	0	ENST00000269305.4:c.956_957insT	p.Lys319AsnfsTer18	p.K319Nfs*18	ENST00000269305	NM_001126112.2	319	aag/aaTg	9/11	0.699941593282996	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.700576423792046	2		808	572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0040555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	40	532	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.207474107502395	3	FACETS	0.198	0.164	0.236	0.099	0.082	0.118	INDETERMINATE	1	TRUE	1	0.62	3		533	854	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0040555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	8	358	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.295249614891018	5	FACETS	0.192	0.123	0.282	0.064	0.041	0.094	INDETERMINATE	1	TRUE	2	0.62	5		358	259	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954180	32954180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45580035	NA	P-0040555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	24	494	0	ENST00000380152.3:c.9154C>T	p.Arg3052Trp	p.R3052W	ENST00000380152		3052	Cgg/Tgg	24/27	0.244109659826697	5	FACETS	0.385	0.301	0.482	0.128	0.1	0.161	INDETERMINATE	1	TRUE	2	0.62	5		494	388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0040596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	166	756	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.985	0.907	1	0.985	0.907	1	CLONAL	1	TRUE	1	0.445267021519188	2		756	757	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0040596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	81	299	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	1	2	FACETS	0.916	0.812	1	0.916	0.812	1	CLONAL	1	TRUE	1	0.445267021519188	2		299	397	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247328	153247328	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	178	245	1	ENST00000281708.4:c.1474C>T	p.Gln492Ter	p.Q492*	ENST00000281708	NM_033632.3	492	Cag/Tag	10/12	0.445267021519188	2	FACETS	0.847	0.788	0.907	0.847	0.788	0.907	CLONAL	2	TRUE	0	0.445267021519188	2		246	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0040596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	143	709	0	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	0.969	0.886	1	0.969	0.886	1	CLONAL	1	TRUE	1	0.445267021519188	2		709	663	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652464	48652464	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	293	513	1	ENST00000376670.3:c.1135C>A	p.Leu379Ile	p.L379I	ENST00000376670	NM_002049.3	379	Ctc/Atc	6/6	0.397323159603009	2	FACETS	0.899	0.859	0.938			1	CLONAL	3	TRUE	NA	0.445267021519188	2		514	488	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532535	63532535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	87	910	0	ENST00000307078.5:c.2044G>A	p.Asp682Asn	p.D682N	ENST00000307078	NM_004655.3	682	Gac/Aac	8/11	1	2	FACETS	0.411	0.363	0.463	0.411	0.363	0.463	SUBCLONAL	1	TRUE	1	0.445267021519188	2		910	951	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749499	41749499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	138	641	0	ENST00000226382.2:c.296G>A	p.Arg99Gln	p.R99Q	ENST00000226382	NM_003924.3	99	cGg/cAg	2/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.445267021519188	2		641	539	SUCCESS
APC	324	MSKCC	GRCh37	5	112175419	112175419	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	55	369	0	ENST00000257430.4:c.4128del	p.Tyr1376Ter	p.Y1376*	ENST00000257430	NM_000038.5	1376	taT/ta	16/16	1	2	FACETS	0.733	0.63	0.844	0.733	0.63	0.844	SUBCLONAL	1	TRUE	1	0.445267021519188	2		369	337	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035103	30035103	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	65	453	0	ENST00000338641.4:c.265G>T	p.Glu89Ter	p.E89*	ENST00000338641	NM_000268.3	89	Gaa/Taa	3/16	0.376956272294613	1	FACETS	0.775	0.678	0.88	0.775	0.678	0.88	SUBCLONAL	1	TRUE	0	0.427901897354459	1		453	308	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0040688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	1525	566	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.735248776525862	6	FACETS	1	0.996	1	1	0.996	1	CLONAL	5	TRUE	1	0.735248776525862	6		566	1984	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0040688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	187	673	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.986	0.918	1	0.986	0.918	1	CLONAL	1	TRUE	1	0.735248776525862	2		673	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0040688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	303	797	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.732482006239525	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.735248776525862	1		797	504	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012653	36012653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	131	220	0	ENST00000358208.4:c.97C>T	p.Pro33Ser	p.P33S	ENST00000358208		33	Ccc/Tcc	2/12	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.735248776525862	2		220	327	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645472	67645472	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs777993880	NA	P-0040688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	130	345	0	ENST00000264010.4:c.737T>C	p.Val246Ala	p.V246A	ENST00000264010	NM_006565.3	246	gTt/gCt	3/12	0.725759101424913	1	FACETS	0.936	0.87	1	0.936	0.87	1	CLONAL	1	TRUE	0	0.735248776525862	1		345	239	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729153	66729153	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519856	NA	P-0040744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	65	576	0	ENST00000307102.5:c.361T>A	p.Cys121Ser	p.C121S	ENST00000307102	NM_002755.3	121	Tgc/Agc	3/11	1	2	FACETS	0.745	0.645	0.854	0.745	0.645	0.854	SUBCLONAL	1	TRUE	1	0.22	2		576	793	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852239	63852239	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	77	520	0	ENST00000279873.7:c.3017T>A	p.Ile1006Asn	p.I1006N	ENST00000279873	NM_032199.2	1006	aTt/aAt	10/10	1	2	FACETS	0.962	0.844	1	0.962	0.844	1	CLONAL	1	TRUE	1	0.22	2		520	728	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438566	49438566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	58	665	0	ENST00000301067.7:c.4924G>A	p.Asp1642Asn	p.D1642N	ENST00000301067	NM_003482.3	1642	Gat/Aat	19/54	1	2	FACETS	0.597	0.512	0.691	0.597	0.512	0.691	SUBCLONAL	1	TRUE	1	0.22	2		665	883	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336063	73336063	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	25	165	0	ENST00000377767.4:c.2340A>C	p.Arg780Ser	p.R780S	ENST00000377767	NM_014953.3	780	agA/agC	17/21	1	2	FACETS	0.92	0.728	1	0.92	0.728	1	CLONAL	1	TRUE	1	0.22	2		165	247	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729149	66729149	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	60	570	0	ENST00000307102.5:c.357T>G	p.His119Gln	p.H119Q	ENST00000307102	NM_002755.3	119	caT/caG	3/11	1	2	FACETS	0.699	0.601	0.806	0.699	0.601	0.806	SUBCLONAL	1	TRUE	1	0.22	2		570	780	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105590	11105591	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0040744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	74	665	1	ENST00000358026.2:c.1506_1507delinsTT	p.Lys502_Ala503delinsAsnSer	p.K502_A503delinsNS	ENST00000358026	NM_001128849.1	502	aaGGca/aaTTca	9/36	1	2	FACETS	0.754	0.659	0.857	0.754	0.659	0.857	SUBCLONAL	1	TRUE	1	0.22	2		666	892	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	302	673	0				ENST00000310581	NM_198253.2	-/1132			0.402287714439514	5	FACETS	1	0.96	1	1	0.96	1	CLONAL	3	TRUE	2	0.402287714439514	5		673	789	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	299	688	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.250523086044149	5	FACETS	1	0.97	1	0.698	0.657	0.739	CLONAL	2	TRUE	2	0.402287714439514	5		688	1139	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432773	78432773	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	37	293	0	ENST00000370768.2:c.303G>C	p.Met101Ile	p.M101I	ENST00000370768	NM_003902.3	101	atG/atC	5/20	0.402287714439514	5	FACETS	0.855	0.706	1	0.214	0.176	0.255	CLONAL	1	TRUE	1	0.402287714439514	5		293	345	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471040	25471040	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761452501	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	299	678	2	ENST00000264709.3:c.721G>A	p.Glu241Lys	p.E241K	ENST00000264709	NM_175629.2	241	Gag/Aag	7/23	0.343536582500227	4	FACETS	0.968	0.912	1	0.645	0.608	0.683	CLONAL	2	TRUE	1	0.402287714439514	4		680	1077	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	230	576	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.250523086044149	5	FACETS	0.993	0.927	1	0.662	0.618	0.708	CLONAL	2	TRUE	2	0.402287714439514	5		576	923	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	71	434	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.402287714439514	6	FACETS	0.771	0.672	0.879	0.193	0.168	0.22	SUBCLONAL	1	TRUE	2	0.402287714439514	6		434	826	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602493	10602493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	136	627	0	ENST00000171111.5:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000171111	NM_203500.1	362	cGg/cAg	3/6	0.343536582500227	4	FACETS	0.985	0.894	1	0.328	0.298	0.36	CLONAL	1	TRUE	1	0.402287714439514	4		627	963	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182575	99182575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1231375445	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	87	515	0	ENST00000074304.5:c.2378G>A	p.Arg793Gln	p.R793Q	ENST00000074304	NM_001134224.1	793	cGa/cAa	22/26	0.343536582500227	4	FACETS	0.791	0.7	0.888	0.264	0.233	0.297	SUBCLONAL	1	TRUE	1	0.402287714439514	4		515	767	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333863	70333863	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs750883311	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	21	326	1	ENST00000373644.4:c.1768C>T	p.Arg590Ter	p.R590*	ENST00000373644	NM_030625.2	590	Cga/Tga	2/12	1	2	FACETS	0.295	0.227	0.375	0.295	0.227	0.375	SUBCLONAL	1	TRUE	1	0.402287714439514	2		327	354	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354044	15354044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	274	369	0	ENST00000263377.2:c.2836C>T	p.Pro946Ser	p.P946S	ENST00000263377	NM_058243.2	946	Cct/Tct	14/20	0.343536582500227	4	FACETS	0.986	0.932	1	0.986	0.932	1	CLONAL	3	TRUE	1	0.402287714439514	4		369	646	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131498	202131498	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	31	356	0	ENST00000358485.4:c.466C>G	p.Gln156Glu	p.Q156E	ENST00000358485	NM_001080125.1	156	Caa/Gaa	2/9	0.343536582500227	4	FACETS	0.399	0.322	0.486	0.133	0.107	0.162	SUBCLONAL	1	TRUE	1	0.402287714439514	4		356	542	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780068	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	391	652	0	ENST00000269305.4:c.472C>T	p.Arg158Cys	p.R158C	ENST00000269305	NM_001126112.2	158	Cgc/Tgc	5/11	0.250523086044149	5	FACETS	1	0.991	1	0.788	0.749	0.829	CLONAL	2	TRUE	2	0.402287714439514	5		652	1318	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250250	133250250	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs483352909	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	110	584	0	ENST00000320574.5:c.1270C>G	p.Leu424Val	p.L424V	ENST00000320574	NM_006231.2	424	Ctc/Gtc	13/49	0.402287714439514	3	FACETS	0.779	0.7	0.864	0.39	0.35	0.432	SUBCLONAL	1	TRUE	1	0.402287714439514	3		584	843	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052693	42052693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	112	409	2	ENST00000219905.7:c.7364C>T	p.Ser2455Phe	p.S2455F	ENST00000219905	NM_001164273.1	2455	tCt/tTt	20/24	0.402287714439514	3	FACETS	1	0.968	1	0.392	0.354	0.433	CLONAL	1	TRUE	0	0.402287714439514	3		411	568	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068429	16068429	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765365064	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	18	80	0	ENST00000268712.3:c.482C>T	p.Ser161Leu	p.S161L	ENST00000268712	NM_006311.3	161	tCg/tTg	5/46	0.250523086044149	5	FACETS	1	0.831	1	0.374	0.284	0.477	CLONAL	1	TRUE	2	0.402287714439514	5		80	128	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101280	27101280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	147	611	0	ENST00000324856.7:c.4562C>T	p.Pro1521Leu	p.P1521L	ENST00000324856	NM_006015.4	1521	cCc/cTc	18/20	0.402287714439514	5	FACETS	1	0.918	1	0.252	0.229	0.276	CLONAL	1	TRUE	1	0.402287714439514	5		611	1163	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609925	81609925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772490052	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	121	294	0	ENST00000298171.2:c.1523C>T	p.Ser508Leu	p.S508L	ENST00000298171	NM_000369.2	508	tCg/tTg	10/10	0.392849402315433	3	FACETS	0.858	0.782	0.938	0.858	0.782	0.938	CLONAL	2	TRUE	1	0.402287714439514	3		294	421	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858615	9858615	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767268773	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	191	400	0	ENST00000330684.3:c.2786C>T	p.Ser929Phe	p.S929F	ENST00000330684	NM_001134407.1	929	tCc/tTc	13/13	0.402287714439514	3	FACETS	1	0.933	1	1	0.933	1	CLONAL	2	TRUE	1	0.402287714439514	3		400	569	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510233	120510233	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	73	325	0	ENST00000256646.2:c.1276C>T	p.Pro426Ser	p.P426S	ENST00000256646	NM_024408.3	426	Cct/Tct	8/34	0.402287714439514	5	FACETS	0.983	0.86	1	0.246	0.215	0.279	CLONAL	1	TRUE	1	0.402287714439514	5		325	592	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366981	15366981	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	39	415	0	ENST00000263377.2:c.1645G>C	p.Glu549Gln	p.E549Q	ENST00000263377	NM_058243.2	549	Gaa/Caa	9/20	0.343536582500227	4	FACETS	0.398	0.329	0.476	0.133	0.109	0.159	SUBCLONAL	1	TRUE	1	0.402287714439514	4		415	683	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375016	45375016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226662382	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	68	305	0	ENST00000262160.6:c.827C>T	p.Ser276Leu	p.S276L	ENST00000262160	NM_005901.5	276	tCg/tTg	8/11	0.402287714439514	4	FACETS	0.977	0.852	1	0.326	0.284	0.371	CLONAL	1	TRUE	1	0.402287714439514	4		305	485	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607246	189607246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1374623968	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	293	525	0	ENST00000264731.3:c.1625C>T	p.Pro542Leu	p.P542L	ENST00000264731	NM_003722.4	542	cCg/cTg	12/14	0.402287714439514	6	FACETS	1	0.956	1	0.51	0.479	0.542	CLONAL	2	TRUE	2	0.402287714439514	6		525	1288	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208335	5208335	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148478353	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	146	680	0	ENST00000357368.4:c.5555C>T	p.Ser1852Leu	p.S1852L	ENST00000357368	NM_002850.3	1852	tCg/tTg	36/38	0.402287714439514	3	FACETS	0.96	0.876	1	0.48	0.438	0.524	CLONAL	1	TRUE	1	0.402287714439514	3		680	908	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934283	68934283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773476490	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	75	370	0	ENST00000288368.4:c.349C>T	p.Arg117Cys	p.R117C	ENST00000288368	NM_024870.2	117	Cgt/Tgt	4/40	0.250523086044149	5	FACETS	1	0.933	1	0.365	0.32	0.413	CLONAL	1	TRUE	2	0.402287714439514	5		370	546	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223176	36223176	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1246	215	891	0	ENST00000222270.7:c.5726C>T	p.Pro1909Leu	p.P1909L	ENST00000222270	NM_014727.1	1909	cCc/cTc	28/37	0.343536582500227	4	FACETS	1	0.947	1	0.342	0.317	0.368	CLONAL	1	TRUE	1	0.402287714439514	4		891	1461	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765640	41765640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	282	675	0	ENST00000301178.4:c.2516G>A	p.Gly839Glu	p.G839E	ENST00000301178	NM_021913.4	839	gGa/gAa	20/20	0.402287714439514	6	FACETS	0.952	0.893	1	0.381	0.357	0.405	CLONAL	2	TRUE	1	0.402287714439514	6		675	1329	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2492117	2492117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs944782838	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	168	581	1	ENST00000355716.4:c.515C>T	p.Pro172Leu	p.P172L	ENST00000355716	NM_003820.2	172	cCc/cTc	5/8	0.402287714439514	5	FACETS	1	0.954	1	0.265	0.242	0.288	CLONAL	1	TRUE	1	0.402287714439514	5		582	1265	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564560	55564560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	139	516	0	ENST00000288135.5:c.448G>A	p.Gly150Arg	p.G150R	ENST00000288135	NM_000222.2	150	Ggg/Agg	3/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.402287714439514	2		516	555	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010560	48010560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	108	420	1	ENST00000234420.5:c.188C>T	p.Ser63Phe	p.S63F	ENST00000234420	NM_000179.2	63	tCc/tTc	1/10	0.343536582500227	4	FACETS	1	0.905	1	0.336	0.301	0.373	CLONAL	1	TRUE	1	0.402287714439514	4		421	747	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526594	31526594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	228	480	0	ENST00000344624.3:c.446C>T	p.Pro149Leu	p.P149L	ENST00000344624		149	cCc/cTc	2/33	0.402287714439514	5	FACETS	1	0.937	1	0.669	0.624	0.716	CLONAL	2	TRUE	2	0.402287714439514	5		480	905	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759654	133759655	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	139	734	1	ENST00000318560.5:c.1977_1978delinsTT	p.Pro660Ser	p.P660S	ENST00000318560	NM_005157.4	659	tcCCca/tcTTca	11/11	0.402287714439514	4	FACETS	0.859	0.78	0.942	0.286	0.26	0.314	CLONAL	1	TRUE	1	0.402287714439514	4		735	1128	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793263	242793263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754424677	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	496	743	1	ENST00000334409.5:c.814C>T	p.Arg272Trp	p.R272W	ENST00000334409	NM_005018.2	272	Cgg/Tgg	5/5	0.343536582500227	4	FACETS	0.907	0.869	0.945	0.907	0.869	0.945	CLONAL	3	TRUE	1	0.402287714439514	4		744	1271	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864663	68864663	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773560075	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	71	246	0	ENST00000288368.4:c.34G>A	p.Glu12Lys	p.E12K	ENST00000288368	NM_024870.2	12	Gag/Aag	1/40	0.250523086044149	5	FACETS	1	0.955	1	0.401	0.35	0.454	CLONAL	1	TRUE	2	0.402287714439514	5		246	471	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873694	151873695	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	95	445	1	ENST00000262189.6:c.8843_8844delinsTT	p.Ser2948Phe	p.S2948F	ENST00000262189	NM_170606.2	2948	tCC/tTT	38/59	0.392849402315433	3	FACETS	0.9	0.803	1	0.45	0.401	0.502	CLONAL	1	TRUE	1	0.402287714439514	3		446	630	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445178	49445178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771291128	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	177	751	0	ENST00000301067.7:c.2288C>T	p.Pro763Leu	p.P763L	ENST00000301067	NM_003482.3	763	cCg/cTg	10/54	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.402287714439514	2		751	832	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417916	138417916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	51	319	0	ENST00000289153.2:c.1603C>T	p.Leu535Phe	p.L535F	ENST00000289153	NM_006219.2	535	Ctt/Ttt	11/22	0.402287714439514	6	FACETS	0.648	0.55	0.757	0.162	0.137	0.19	SUBCLONAL	1	TRUE	2	0.402287714439514	6		319	706	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210796	36210796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	182	759	0	ENST00000222270.7:c.547G>A	p.Glu183Lys	p.E183K	ENST00000222270	NM_014727.1	183	Gag/Aag	3/37	0.343536582500227	4	FACETS	0.975	0.898	1	0.325	0.299	0.352	CLONAL	1	TRUE	1	0.402287714439514	4		759	1301	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888769	76888769	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs782269520	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	36	220	0	ENST00000373344.5:c.5060G>C	p.Arg1687Thr	p.R1687T	ENST00000373344	NM_000489.3	1687	aGa/aCa	19/35	0.402287714439514	3	FACETS	0.544	0.448	0.652			1	SUBCLONAL	1	TRUE	NA	0.402287714439514	3		220	395	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258616	16258616	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745908478	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	107	452	0	ENST00000375759.3:c.5881G>A	p.Asp1961Asn	p.D1961N	ENST00000375759	NM_015001.2	1961	Gat/Aat	11/15	0.402287714439514	5	FACETS	0.986	0.884	1	0.247	0.221	0.274	CLONAL	1	TRUE	1	0.402287714439514	5		452	865	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748729	43748729	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	164	744	0	ENST00000382044.4:c.2077C>T	p.Pro693Ser	p.P693S	ENST00000382044	NM_001141980.1	693	Ccg/Tcg	12/28	0.402287714439514	3	FACETS	1	0.959	1	0.358	0.328	0.388	CLONAL	1	TRUE	0	0.402287714439514	3		744	913	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117755	70117755	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	157	676	0	ENST00000245479.2:c.223G>C	p.Glu75Gln	p.E75Q	ENST00000245479	NM_000346.3	75	Gag/Cag	1/3	0.402287714439514	3	FACETS	0.924	0.845	1	0.308	0.281	0.336	CLONAL	1	TRUE	0	0.402287714439514	3		676	1015	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434090	49434090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779629382	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	140	593	1	ENST00000301067.7:c.7463C>T	p.Ser2488Leu	p.S2488L	ENST00000301067	NM_003482.3	2488	tCg/tTg	31/54	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.402287714439514	2		594	654	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601304	28601304	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	75	332	0	ENST00000241453.7:c.2128T>A	p.Phe710Ile	p.F710I	ENST00000241453	NM_004119.2	710	Ttt/Att	17/24	0.402287714439514	3	FACETS	0.947	0.832	1	0.473	0.416	0.535	CLONAL	1	TRUE	1	0.402287714439514	3		332	473	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912816	100912816	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs776604342	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	148	304	0	ENST00000325455.5:c.2506C>T	p.Arg836Ter	p.R836*	ENST00000325455	NM_001202474.3	836	Cga/Tga	7/8	0.402287714439514	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	1	0.402287714439514	3		304	430	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471676	120471676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1557808434	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	91	406	0	ENST00000256646.2:c.3815C>T	p.Pro1272Leu	p.P1272L	ENST00000256646	NM_024408.3	1272	cCc/cTc	23/34	0.402287714439514	5	FACETS	0.866	0.768	0.97	0.216	0.192	0.243	CLONAL	1	TRUE	1	0.402287714439514	5		406	838	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484315	50484315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	105	497	0	ENST00000394963.4:c.1075C>T	p.Gln359Ter	p.Q359*	ENST00000394963	NM_003076.4	359	Cag/Tag	9/13	1	2	FACETS	0.86	0.772	0.953	0.86	0.772	0.953	CLONAL	1	TRUE	1	0.402287714439514	2		497	607	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134459	41134459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756553520	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	75	427	0	ENST00000379561.5:c.1169C>T	p.Ser390Leu	p.S390L	ENST00000379561	NM_002015.3	390	tCg/tTg	2/3	0.402287714439514	3	FACETS	0.734	0.644	0.832	0.367	0.322	0.416	SUBCLONAL	1	TRUE	1	0.402287714439514	3		427	610	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805653	43805653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765133601	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	130	510	0	ENST00000372470.3:c.709G>A	p.Glu237Lys	p.E237K	ENST00000372470	NM_005373.2	237	Gag/Aag	5/12	0.402287714439514	5	FACETS	1	0.973	1	0.3	0.271	0.329	CLONAL	1	TRUE	1	0.402287714439514	5		510	865	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291006	11291006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	68	301	0	ENST00000361445.4:c.2755G>A	p.Glu919Lys	p.E919K	ENST00000361445	NM_004958.3	919	Gaa/Aaa	18/58	0.402287714439514	5	FACETS	0.844	0.734	0.963	0.211	0.183	0.241	CLONAL	1	TRUE	1	0.402287714439514	5		301	642	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11292555	11292555	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	73	340	0	ENST00000361445.4:c.2452G>C	p.Asp818His	p.D818H	ENST00000361445	NM_004958.3	818	Gat/Cat	16/58	0.402287714439514	5	FACETS	0.884	0.773	1	0.221	0.193	0.251	CLONAL	1	TRUE	1	0.402287714439514	5		340	658	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255278	16255278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	190	390	1	ENST00000375759.3:c.2543C>T	p.Pro848Leu	p.P848L	ENST00000375759	NM_015001.2	848	cCt/cTt	11/15	0.402287714439514	5	FACETS	0.955	0.885	1	0.477	0.442	0.514	CLONAL	2	TRUE	1	0.402287714439514	5		391	793	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258578	16258578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	117	470	0	ENST00000375759.3:c.5843C>T	p.Pro1948Leu	p.P1948L	ENST00000375759	NM_015001.2	1948	cCt/cTt	11/15	0.402287714439514	5	FACETS	0.989	0.891	1	0.247	0.222	0.274	CLONAL	1	TRUE	1	0.402287714439514	5		470	943	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598974	28598974	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	188	646	0	ENST00000253063.3:c.534C>G	p.Ile178Met	p.I178M	ENST00000253063	NM_031459.4	178	atC/atG	4/10	0.402287714439514	5	FACETS	1	0.975	1	0.284	0.262	0.308	CLONAL	1	TRUE	1	0.402287714439514	5		646	1318	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36814381	36814382	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	569	617	1	ENST00000373129.3:c.658_659delinsAA	p.Gly220Lys	p.G220K	ENST00000373129	NM_032017.1	220	GGg/AAg	8/12	0.402287714439514	5	FACETS	0.962	0.927	0.996	0.962	0.927	0.996	CLONAL	4	TRUE	1	0.402287714439514	5		618	1179	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521558	46521558	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	98	454	0	ENST00000262741.5:c.850C>G	p.Gln284Glu	p.Q284E	ENST00000262741	NM_003629.3	284	Caa/Gaa	7/10	0.402287714439514	5	FACETS	0.949	0.846	1	0.237	0.211	0.265	CLONAL	1	TRUE	1	0.402287714439514	5		454	823	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466463	120466463	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	135	598	0	ENST00000256646.2:c.4656G>C	p.Leu1552Phe	p.L1552F	ENST00000256646	NM_024408.3	1552	ttG/ttC	26/34	0.402287714439514	5	FACETS	0.936	0.849	1	0.234	0.212	0.257	CLONAL	1	TRUE	1	0.402287714439514	5		598	1150	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834541	156834542	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1452	155	696	1	ENST00000524377.1:c.309_310delinsTT	p.Arg104Cys	p.R104C	ENST00000524377	NM_002529.3	103	ctCCgt/ctTTgt	3/17	0.402287714439514	6	FACETS	0.865	0.789	0.946	0.288	0.263	0.316	CLONAL	1	TRUE	3	0.402287714439514	6		697	1607	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729762	162729762	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746630159	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	84	479	0	ENST00000367921.3:c.848C>T	p.Thr283Ile	p.T283I	ENST00000367921	NM_006182.2	283	aCc/aTc	8/18	0.402287714439514	6	FACETS	0.684	0.603	0.773	0.228	0.201	0.258	SUBCLONAL	1	TRUE	3	0.402287714439514	6		479	1101	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740252	162740252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	87	362	0	ENST00000367921.3:c.1454C>T	p.Ser485Phe	p.S485F	ENST00000367921	NM_006182.2	485	tCc/tTc	12/18	0.402287714439514	6	FACETS	0.893	0.789	1	0.298	0.263	0.335	CLONAL	1	TRUE	3	0.402287714439514	6		362	874	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944377	206944377	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	92	415	0	ENST00000423557.1:c.253G>C	p.Glu85Gln	p.E85Q	ENST00000423557	NM_000572.2	85	Gag/Cag	3/5	0.402287714439514	6	FACETS	0.893	0.792	1	0.298	0.264	0.334	CLONAL	1	TRUE	3	0.402287714439514	6		415	924	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243675680	243675680	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	103	219	0	ENST00000263826.5:c.1300T>C	p.Tyr434His	p.Y434H	ENST00000263826	NM_005465.4	434	Tat/Cat	12/13	0.402287714439514	6	FACETS	0.873	0.789	0.96	0.873	0.789	0.96	CLONAL	3	TRUE	3	0.402287714439514	6		219	353	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245912935	245912935	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	58	242	0	ENST00000388985.4:c.1217G>C	p.Arg406Thr	p.R406T	ENST00000388985		406	aGa/aCa	12/12	0.402287714439514	6	FACETS	0.842	0.723	0.972	0.281	0.241	0.324	CLONAL	1	TRUE	3	0.402287714439514	6		242	618	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690810	89690810	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	28	223	0	ENST00000371953.3:c.217G>C	p.Glu73Gln	p.E73Q	ENST00000371953	NM_000314.4	73	Gaa/Caa	4/9	1	2	FACETS	0.795	0.642	0.967	0.795	0.642	0.967	CLONAL	1	TRUE	1	0.402287714439514	2		223	175	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104269061	104269061	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	79	414	1	ENST00000369902.3:c.317+1G>A		p.X106_splice	ENST00000369902	NM_016169.3	106			1	2	FACETS	0.903	0.798	1	0.903	0.798	1	CLONAL	1	TRUE	1	0.402287714439514	2		415	435	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724630	112724630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057517872	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	93	428	1	ENST00000369452.4:c.514C>T	p.Arg172Trp	p.R172W	ENST00000369452	NM_007373.3	172	Cgg/Tgg	2/9	1	2	FACETS	0.982	0.877	1	0.982	0.877	1	CLONAL	1	TRUE	1	0.402287714439514	2		429	471	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199936	108199937	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	48	183	0	ENST00000278616.4:c.7278_7279delinsTT	p.Leu2427Phe	p.L2427F	ENST00000278616	NM_000051.3	2426	ctCCtt/ctTTtt	49/63	0.402287714439514	3	FACETS	1	0.961	1	0.709	0.607	0.819	CLONAL	1	TRUE	1	0.402287714439514	3		183	202	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342854	118342855	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	77	241	0	ENST00000534358.1:c.980_981delinsTT	p.Pro327Leu	p.P327L	ENST00000534358	NM_005933.3	327	cCC/cTT	3/36	0.402287714439514	3	FACETS	1	0.977	1	0.737	0.653	0.825	CLONAL	1	TRUE	1	0.402287714439514	3		241	312	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425349	49425350	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	149	731	4	ENST00000301067.7:c.13138_13139delinsTT	p.Pro4380Leu	p.P4380L	ENST00000301067	NM_003482.3	4380	CCa/TTa	39/54	1	2	FACETS	0.895	0.818	0.975	0.895	0.818	0.975	CLONAL	1	TRUE	1	0.402287714439514	2		735	828	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425626	49425627	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	127	618	0	ENST00000301067.7:c.12861_12862delinsTT	p.Arg4288Trp	p.R4288W	ENST00000301067	NM_003482.3	4287	ccCCgg/ccTTgg	39/54	1	2	FACETS	0.931	0.845	1	0.931	0.845	1	CLONAL	1	TRUE	1	0.402287714439514	2		618	678	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443587	49443587	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	136	584	0	ENST00000301067.7:c.3784G>A	p.Asp1262Asn	p.D1262N	ENST00000301067	NM_003482.3	1262	Gac/Aac	11/54	1	2	FACETS	0.963	0.877	1	0.963	0.877	1	CLONAL	1	TRUE	1	0.402287714439514	2		584	702	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444310	49444310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	170	733	0	ENST00000301067.7:c.3061C>T	p.Pro1021Ser	p.P1021S	ENST00000301067	NM_003482.3	1021	Cct/Tct	11/54	1	2	FACETS	0.945	0.87	1	0.945	0.87	1	CLONAL	1	TRUE	1	0.402287714439514	2		733	894	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484304	50484304	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	102	492	0	ENST00000394963.4:c.1064C>G	p.Ser355Ter	p.S355*	ENST00000394963	NM_003076.4	355	tCa/tGa	9/13	1	2	FACETS	0.807	0.723	0.897	0.807	0.723	0.897	CLONAL	1	TRUE	1	0.402287714439514	2		492	628	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858473	57858473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	110	504	0	ENST00000228682.2:c.211C>T	p.Pro71Ser	p.P71S	ENST00000228682	NM_005269.2	71	Ccc/Tcc	4/12	1	2	FACETS	0.94	0.847	1	0.94	0.847	1	CLONAL	1	TRUE	1	0.402287714439514	2		504	582	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133242031	133242031	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	111	547	1	ENST00000320574.5:c.2325G>C	p.Trp775Cys	p.W775C	ENST00000320574	NM_006231.2	775	tgG/tgC	21/49	0.402287714439514	3	FACETS	0.839	0.754	0.929	0.42	0.377	0.465	CLONAL	1	TRUE	1	0.402287714439514	3		548	790	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953742	48953743	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	62	213	0	ENST00000267163.4:c.1345_1346delinsAA	p.Gly449Lys	p.G449K	ENST00000267163	NM_000321.2	449	GGa/AAa	14/27	0.402287714439514	3	FACETS	1	0.97	1	0.72	0.629	0.817	CLONAL	1	TRUE	1	0.402287714439514	3		213	257	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030367	49030367	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs761397680	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	46	248	0	ENST00000267163.4:c.1842G>T	p.Lys614Asn	p.K614N	ENST00000267163	NM_000321.2	614	aaG/aaT	19/27	0.402287714439514	3	FACETS	0.822	0.695	0.961	0.411	0.347	0.481	CLONAL	1	TRUE	1	0.402287714439514	3		248	334	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281195	49281195	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1258128809	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	156	612	0	ENST00000282018.3:c.242C>T	p.Ala81Val	p.A81V	ENST00000282018	NM_020377.2	81	gCc/gTc	1/1	0.402287714439514	3	FACETS	1	0.922	1	0.504	0.461	0.548	CLONAL	1	TRUE	1	0.402287714439514	3		612	925	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527742	103527742	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	67	250	0	ENST00000355739.4:c.3050G>A	p.Arg1017Lys	p.R1017K	ENST00000355739	NM_000123.3	1017	aGa/aAa	15/15	0.402287714439514	3	FACETS	1	0.915	1	0.531	0.463	0.603	CLONAL	1	TRUE	1	0.402287714439514	3		250	377	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988281	41988281	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	74	400	0	ENST00000219905.7:c.1073C>G	p.Ala358Gly	p.A358G	ENST00000219905	NM_001164273.1	358	gCc/gGc	3/24	0.402287714439514	3	FACETS	0.779	0.683	0.883	0.26	0.227	0.295	SUBCLONAL	1	TRUE	0	0.402287714439514	3		400	567	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712700	43712700	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1282655302	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	450	680	0	ENST00000382044.4:c.4484G>A	p.Arg1495His	p.R1495H	ENST00000382044	NM_001141980.1	1495	cGt/cAt	21/28	0.402287714439514	3	FACETS	0.989	0.949	1	0.989	0.949	1	CLONAL	3	TRUE	0	0.402287714439514	3		680	906	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748912	43748912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	494	719	0	ENST00000382044.4:c.1894G>A	p.Ala632Thr	p.A632T	ENST00000382044	NM_001141980.1	632	Gca/Aca	12/28	0.402287714439514	3	FACETS	0.984	0.947	1	0.984	0.947	1	CLONAL	3	TRUE	0	0.402287714439514	3		719	999	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749302	43749302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1379752908	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	113	525	0	ENST00000382044.4:c.1504C>T	p.Pro502Ser	p.P502S	ENST00000382044	NM_001141980.1	502	Cca/Tca	12/28	0.402287714439514	3	FACETS	1	0.946	1	0.358	0.323	0.396	CLONAL	1	TRUE	0	0.402287714439514	3		525	628	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304168	91304168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	243	458	0	ENST00000355112.3:c.1565G>A	p.Gly522Glu	p.G522E	ENST00000355112	NM_000057.2	522	gGa/gAa	7/22	0.402287714439514	3	FACETS	0.899	0.848	0.95	0.899	0.848	0.95	CLONAL	3	TRUE	0	0.402287714439514	3		458	538	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640505	3640505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	175	790	1	ENST00000294008.3:c.3134C>T	p.Pro1045Leu	p.P1045L	ENST00000294008	NM_032444.2	1045	cCc/cTc	12/15	0.402287714439514	3	FACETS	0.979	0.901	1	0.49	0.45	0.531	CLONAL	1	TRUE	1	0.402287714439514	3		791	1067	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864530	56864530	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	102	410	0	ENST00000308159.5:c.1018C>T	p.Arg340Ter	p.R340*	ENST00000308159	NM_014669.4	340	Cga/Tga	10/22	0.402287714439514	3	FACETS	0.896	0.802	0.995	0.448	0.401	0.498	CLONAL	1	TRUE	1	0.402287714439514	3		410	680	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830832	72830832	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	115	597	0	ENST00000268489.5:c.5749G>C	p.Glu1917Gln	p.E1917Q	ENST00000268489	NM_006885.3	1917	Gag/Cag	9/10	0.402287714439514	3	FACETS	0.91	0.82	1	0.455	0.41	0.503	CLONAL	1	TRUE	1	0.402287714439514	3		597	755	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40461480	40461481	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	132	751	1	ENST00000345506.4:c.2200_2201delinsTT	p.Pro734Phe	p.P734F	ENST00000345506	NM_003152.3	734	CCc/TTc	19/20	0.402287714439514	3	FACETS	0.775	0.702	0.852	0.258	0.234	0.284	SUBCLONAL	1	TRUE	0	0.402287714439514	3		752	1017	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39600645	39600645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	29	210	0	ENST00000262039.4:c.1460C>T	p.Ser487Leu	p.S487L	ENST00000262039	NM_002647.2	487	tCa/tTa	13/25	0.402287714439514	4	FACETS	0.907	0.732	1	0.302	0.244	0.368	CLONAL	1	TRUE	1	0.402287714439514	4		210	223	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56338916	56338916	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	10	12	0	ENST00000348428.3:c.41C>T	p.Ser14Leu	p.S14L	ENST00000348428	NM_006785.3	14	tCg/tTg	1/17	0.402287714439514	4	FACETS	1	0.822	1	0.438	0.304	0.598	CLONAL	1	TRUE	1	0.402287714439514	4		12	53	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56377266	56377266	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	41	209	0	ENST00000348428.3:c.887G>T	p.Arg296Leu	p.R296L	ENST00000348428	NM_006785.3	296	cGa/cTa	6/17	0.402287714439514	4	FACETS	0.874	0.731	1	0.291	0.243	0.344	CLONAL	1	TRUE	1	0.402287714439514	4		209	327	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226268	2226268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs927525441	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	203	865	0	ENST00000398665.3:c.3748G>A	p.Asp1250Asn	p.D1250N	ENST00000398665	NM_032482.2	1250	Gac/Aac	27/28	0.402287714439514	3	FACETS	1	0.973	1	0.553	0.512	0.595	CLONAL	1	TRUE	1	0.402287714439514	3		865	1097	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3094671	3094671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	43	202	0	ENST00000078429.4:c.22G>A	p.Ala8Thr	p.A8T	ENST00000078429	NM_002067.2	8	Gcg/Acg	1/7	0.402287714439514	3	FACETS	0.755	0.634	0.888	0.378	0.317	0.444	SUBCLONAL	1	TRUE	1	0.402287714439514	3		202	340	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5207972	5207972	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	157	763	0	ENST00000357368.4:c.5739G>C	p.Lys1913Asn	p.K1913N	ENST00000357368	NM_002850.3	1913	aaG/aaC	37/38	0.402287714439514	3	FACETS	0.91	0.833	0.991	0.455	0.416	0.496	CLONAL	1	TRUE	1	0.402287714439514	3		763	1030	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215550	5215550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	163	578	1	ENST00000357368.4:c.4153C>T	p.Leu1385Phe	p.L1385F	ENST00000357368	NM_002850.3	1385	Ctc/Ttc	27/38	0.402287714439514	3	FACETS	1	0.943	1	0.518	0.475	0.563	CLONAL	1	TRUE	1	0.402287714439514	3		579	940	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097093	11097093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	191	762	0	ENST00000358026.2:c.584C>T	p.Pro195Leu	p.P195L	ENST00000358026	NM_001128849.1	195	cCc/cTc	4/36	0.343536582500227	4	FACETS	1	0.98	1	0.391	0.36	0.422	CLONAL	1	TRUE	1	0.402287714439514	4		762	1136	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272402	15272403	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	170	822	2	ENST00000263388.2:c.6036_6037delinsTT	p.Gln2013Ter	p.Q2013*	ENST00000263388	NM_000435.2	2012	gcCCag/gcTTag	33/33	0.343536582500227	4	FACETS	0.861	0.789	0.936	0.287	0.263	0.312	CLONAL	1	TRUE	1	0.402287714439514	4		824	1377	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387414	17387415	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	305	724	1	ENST00000359435.4:c.680_681delinsTT	p.Ser227Phe	p.S227F	ENST00000359435	NM_001033549.1	227	tCC/tTT	7/9	0.343536582500227	4	FACETS	0.916	0.863	0.97	0.61	0.575	0.647	CLONAL	2	TRUE	1	0.402287714439514	4		725	1161	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224550	36224550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1269	187	885	1	ENST00000222270.7:c.7012G>A	p.Asp2338Asn	p.D2338N	ENST00000222270	NM_014727.1	2338	Gat/Aat	29/37	0.343536582500227	4	FACETS	0.895	0.825	0.969	0.298	0.275	0.324	CLONAL	1	TRUE	1	0.402287714439514	4		886	1456	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967289	25967290	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	64	369	1	ENST00000435504.4:c.1916_1917delinsAA	p.Arg639Lys	p.R639K	ENST00000435504		639	aGG/aAA	13/13	0.343536582500227	4	FACETS	0.721	0.624	0.826	0.24	0.208	0.276	SUBCLONAL	1	TRUE	1	0.402287714439514	4		370	619	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445426	29445426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	450	651	0	ENST00000389048.3:c.3407C>T	p.Ser1136Phe	p.S1136F	ENST00000389048	NM_004304.4	1136	tCc/tTc	21/29	0.343536582500227	4	FACETS	0.94	0.899	0.98	0.94	0.899	0.98	CLONAL	3	TRUE	1	0.402287714439514	4		651	1113	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754908	29754908	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	105	403	0	ENST00000389048.3:c.1027G>A	p.Glu343Lys	p.E343K	ENST00000389048	NM_004304.4	343	Gag/Aag	4/29	0.343536582500227	4	FACETS	1	0.939	1	0.356	0.319	0.395	CLONAL	1	TRUE	1	0.402287714439514	4		403	686	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872649	136872649	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	74	375	0	ENST00000241393.3:c.849G>A	p.Trp283Ter	p.W283*	ENST00000241393	NM_003467.2	283	tgG/tgA	2/2	0.343536582500227	4	FACETS	0.818	0.716	0.927	0.273	0.238	0.309	CLONAL	1	TRUE	1	0.402287714439514	4		375	631	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795069	242795070	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	162	773	2	ENST00000334409.5:c.139_140delinsAA	p.Gly47Lys	p.G47K	ENST00000334409	NM_005018.2	47	GGg/AAg	2/5	0.343536582500227	4	FACETS	0.897	0.821	0.977	0.299	0.273	0.326	CLONAL	1	TRUE	1	0.402287714439514	4		775	1259	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012762	36012762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	45	157	0	ENST00000358208.4:c.206C>T	p.Ser69Phe	p.S69F	ENST00000358208		69	tCc/tTc	2/12	0.402287714439514	4	FACETS	1	0.897	1	0.361	0.305	0.422	CLONAL	1	TRUE	1	0.402287714439514	4		157	290	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980857	40980857	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	59	516	0	ENST00000373198.4:c.1629C>G	p.Phe543Leu	p.F543L	ENST00000373198	NM_133170.3	543	ttC/ttG	10/32	0.402287714439514	3	FACETS	0.484	0.416	0.559	0.242	0.208	0.28	SUBCLONAL	1	TRUE	1	0.402287714439514	3		516	728	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62322220	62322220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1333134074	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	203	821	0	ENST00000360203.5:c.2476C>T	p.Pro826Ser	p.P826S	ENST00000360203	NM_001283009.1	826	Cct/Tct	27/35	0.392849402315433	3	FACETS	1	0.93	1	0.503	0.465	0.542	CLONAL	1	TRUE	1	0.402287714439514	3		821	1206	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42843884	42843884	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	222	387	0	ENST00000398585.3:c.1035G>A	p.Trp345Ter	p.W345*	ENST00000398585	NM_001135099.1	345	tgG/tgA	10/14	0.402287714439514	5	FACETS	1	0.986	1	0.803	0.75	0.857	CLONAL	2	TRUE	2	0.402287714439514	5		387	735	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050686	30050686	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	129	317	0	ENST00000338641.4:c.488T>A	p.Leu163Ter	p.L163*	ENST00000338641	NM_000268.3	163	tTg/tAg	5/16	0.166556213411996	5	FACETS	0.972	0.886	1	0.648	0.59	0.708	INDETERMINATE	2	TRUE	2	0.402287714439514	5		317	529	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573524	41573524	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	59	656	0	ENST00000263253.7:c.5809G>C	p.Glu1937Gln	p.E1937Q	ENST00000263253	NM_001429.3	1937	Gag/Cag	31/31	0.166556213411996	5	FACETS	0.458	0.393	0.53	0.153	0.131	0.177	INDETERMINATE	1	TRUE	2	0.402287714439514	5		656	1026	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182651	38182651	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	86	320	0	ENST00000396334.3:c.804C>G	p.Ile268Met	p.I268M	ENST00000396334	NM_002468.4	268	atC/atG	5/5	0.402287714439514	5	FACETS	1	0.954	1	0.383	0.339	0.43	CLONAL	1	TRUE	2	0.402287714439514	5		320	596	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620622	52620622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	179	319	1	ENST00000394830.3:c.3131C>T	p.Ser1044Phe	p.S1044F	ENST00000394830	NM_018313.4	1044	tCt/tTt	21/30	0.402287714439514	5	FACETS	0.973	0.9	1	0.649	0.6	0.7	CLONAL	2	TRUE	2	0.402287714439514	5		320	733	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52675981	52675981	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	107	464	0	ENST00000394830.3:c.1076C>G	p.Ala359Gly	p.A359G	ENST00000394830	NM_018313.4	359	gCt/gGt	11/30	0.402287714439514	5	FACETS	0.996	0.893	1	0.332	0.297	0.369	CLONAL	1	TRUE	2	0.402287714439514	5		464	856	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461605	138461605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	151	360	0	ENST00000289153.2:c.416C>T	p.Ser139Phe	p.S139F	ENST00000289153	NM_006219.2	139	tCc/tTc	3/22	0.402287714439514	6	FACETS	1	0.965	1	0.548	0.503	0.595	CLONAL	2	TRUE	2	0.402287714439514	6		360	618	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226925	142226925	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	83	360	0	ENST00000350721.4:c.4879C>G	p.Gln1627Glu	p.Q1627E	ENST00000350721	NM_001184.3	1627	Cag/Gag	28/47	0.402287714439514	6	FACETS	0.958	0.845	1	0.24	0.211	0.27	CLONAL	1	TRUE	2	0.402287714439514	6		360	777	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191013	185191013	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1399	140	703	1	ENST00000265026.3:c.1894C>G	p.His632Asp	p.H632D	ENST00000265026	NM_004721.4	632	Cat/Gat	11/14	0.402287714439514	6	FACETS	0.816	0.74	0.896	0.204	0.185	0.224	CLONAL	1	TRUE	2	0.402287714439514	6		704	1539	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505307	186505307	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	72	285	0	ENST00000323963.5:c.933G>C	p.Glu311Asp	p.E311D	ENST00000323963		311	gaG/gaC	9/11	0.402287714439514	6	FACETS	1	0.878	1	0.251	0.219	0.286	CLONAL	1	TRUE	2	0.402287714439514	6		285	643	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803142	1803142	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	186	775	0	ENST00000260795.2:c.494C>T	p.Ala165Val	p.A165V	ENST00000260795		165	gCc/gTc	4/17	1	2	FACETS	0.965	0.891	1	0.965	0.891	1	CLONAL	1	TRUE	1	0.402287714439514	2		775	958	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007320	143007320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	59	280	0	ENST00000262992.4:c.2464G>A	p.Glu822Lys	p.E822K	ENST00000262992	NM_001101669.1	822	Gaa/Aaa	22/24	1	2	FACETS	0.978	0.848	1	0.978	0.848	1	CLONAL	1	TRUE	1	0.402287714439514	2		280	300	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143033819	143033819	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs375132273	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	58	313	0	ENST00000262992.4:c.2152G>C	p.Glu718Gln	p.E718Q	ENST00000262992	NM_001101669.1	718	Gag/Cag	20/24	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.402287714439514	2		313	284	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532919	187532920	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	51	262	0	ENST00000441802.2:c.9473_9474delinsAA	p.Arg3158Gln	p.R3158Q	ENST00000441802	NM_005245.3	3158	cGG/cAA	14/27	1	2	FACETS	0.994	0.853	1	0.994	0.853	1	CLONAL	1	TRUE	1	0.402287714439514	2		262	255	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155677	56155678	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	88	304	0	ENST00000399503.3:c.769_770delinsTT	p.Pro257Leu	p.P257L	ENST00000399503	NM_005921.1	257	CCa/TTa	3/20	0.194589345893113	5	FACETS	0.766	0.681	0.855			1	INDETERMINATE	2	TRUE	NA	0.402287714439514	5		304	458	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178622	56178622	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	53	192	0	ENST00000399503.3:c.3595C>A	p.Gln1199Lys	p.Q1199K	ENST00000399503	NM_005921.1	1199	Cag/Aag	14/20	0.194589345893113	5	FACETS	1	0.949	1			1	INDETERMINATE	1	TRUE	NA	0.402287714439514	5		192	337	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048749	180048749	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	167	769	0	ENST00000261937.6:c.1813C>T	p.Pro605Ser	p.P605S	ENST00000261937	NM_182925.4	605	Ccg/Tcg	13/30	0.402287714439514	3	FACETS	0.962	0.883	1	0.481	0.441	0.522	CLONAL	1	TRUE	1	0.402287714439514	3		769	1037	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056518	26056519	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	157	207	0	ENST00000343677.2:c.138_139delinsAA	p.Ala47Thr	p.A47T	ENST00000343677	NM_005319.3	46	aaGGct/aaAAct	1/1	0.402287714439514	5	FACETS	0.933	0.863	1	0.933	0.863	1	CLONAL	3	TRUE	2	0.402287714439514	5		207	447	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673587	30673587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	143	617	1	ENST00000376406.3:c.3373C>T	p.Pro1125Ser	p.P1125S	ENST00000376406	NM_014641.2	1125	Cct/Tct	10/15	0.402287714439514	5	FACETS	0.88	0.8	0.964	0.293	0.266	0.322	CLONAL	1	TRUE	2	0.402287714439514	5		618	1296	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163540	32163540	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	144	553	0	ENST00000375023.3:c.5686C>G	p.His1896Asp	p.H1896D	ENST00000375023	NM_004557.3	1896	Cat/Gat	30/30	0.402287714439514	5	FACETS	0.979	0.891	1	0.326	0.297	0.358	CLONAL	1	TRUE	2	0.402287714439514	5		553	1172	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188644	32188644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773175586	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	132	582	0	ENST00000375023.3:c.811C>T	p.Pro271Ser	p.P271S	ENST00000375023	NM_004557.3	271	Cca/Tca	5/30	0.402287714439514	5	FACETS	0.902	0.817	0.992	0.301	0.272	0.331	CLONAL	1	TRUE	2	0.402287714439514	5		582	1166	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798128	32798128	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	151	698	0	ENST00000374899.4:c.1551G>C	p.Gln517His	p.Q517H	ENST00000374899	NM_018833.2	517	caG/caC	9/12	0.402287714439514	5	FACETS	0.919	0.838	1	0.306	0.279	0.335	CLONAL	1	TRUE	2	0.402287714439514	5		698	1310	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199885	138199885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	101	436	0	ENST00000237289.4:c.1303C>T	p.Leu435Phe	p.L435F	ENST00000237289	NM_001270507.1	435	Ctc/Ttc	7/9	0.402287714439514	3	FACETS	1	0.955	1	0.558	0.501	0.62	CLONAL	1	TRUE	1	0.402287714439514	3		436	540	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004706	150004706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	83	416	0	ENST00000253339.5:c.1519G>A	p.Glu507Lys	p.E507K	ENST00000253339		507	Gag/Aag	3/7	0.402287714439514	3	FACETS	0.765	0.675	0.861	0.382	0.337	0.431	SUBCLONAL	1	TRUE	1	0.402287714439514	3		416	648	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959196	2959196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	309	705	0	ENST00000396946.4:c.2320G>A	p.Asp774Asn	p.D774N	ENST00000396946	NM_032415.4	774	Gac/Aac	18/25	0.402287714439514	5	FACETS	0.953	0.897	1	0.635	0.598	0.673	CLONAL	2	TRUE	2	0.402287714439514	5		705	1293	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987307	2987307	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	355	510	0	ENST00000396946.4:c.122A>G	p.Lys41Arg	p.K41R	ENST00000396946	NM_032415.4	41	aAg/aGg	3/25	0.402287714439514	5	FACETS	0.939	0.891	0.987	0.939	0.891	0.987	CLONAL	3	TRUE	2	0.402287714439514	5		510	1005	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935616	13935616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	174	374	0	ENST00000405192.2:c.1240G>A	p.Asp414Asn	p.D414N	ENST00000405192	NM_001163147.1	414	Gac/Aac	12/12	0.402287714439514	5	FACETS	0.996	0.92	1	0.664	0.613	0.717	CLONAL	2	TRUE	2	0.402287714439514	5		374	696	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467996	50467996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	111	530	0	ENST00000331340.3:c.1231C>T	p.Leu411Phe	p.L411F	ENST00000331340	NM_006060.4	411	Ctc/Ttc	8/8	0.402287714439514	5	FACETS	1	0.902	1	0.335	0.3	0.371	CLONAL	1	TRUE	2	0.402287714439514	5		530	881	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435761	116435761	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	123	488	0	ENST00000397752.3:c.3851A>T	p.Tyr1284Phe	p.Y1284F	ENST00000397752	NM_000245.2	1284	tAt/tTt	20/21	0.392849402315433	3	FACETS	1	0.947	1	0.533	0.483	0.586	CLONAL	1	TRUE	1	0.402287714439514	3		488	689	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151850009	151850009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1221667616	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	114	303	0	ENST00000262189.6:c.12307G>A	p.Asp4103Asn	p.D4103N	ENST00000262189	NM_170606.2	4103	Gac/Aac	49/59	0.392849402315433	3	FACETS	0.868	0.789	0.951	0.868	0.789	0.951	CLONAL	2	TRUE	1	0.402287714439514	3		303	392	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29197692	29197693	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	289	618	1	ENST00000240100.2:c.501_502delinsTT	p.Pro168Ser	p.P168S	ENST00000240100	NM_001394.6	167	atCCca/atTTca	2/4	0.402287714439514	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.402287714439514	2		619	711	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68993031	68993031	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	65	253	0	ENST00000288368.4:c.1836A>T	p.Lys612Asn	p.K612N	ENST00000288368	NM_024870.2	612	aaA/aaT	17/40	0.250523086044149	5	FACETS	1	0.957	1	0.417	0.363	0.476	CLONAL	1	TRUE	2	0.402287714439514	5		253	414	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117874099	117874099	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	29	324	0	ENST00000297338.2:c.355C>G	p.Gln119Glu	p.Q119E	ENST00000297338	NM_006265.2	119	Cag/Gag	4/14	0.250523086044149	5	FACETS	0.612	0.491	0.749	0.204	0.163	0.25	SUBCLONAL	1	TRUE	2	0.402287714439514	5		324	378	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145736837	145736837	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	151	620	0	ENST00000428558.2:c.3604G>C	p.Glu1202Gln	p.E1202Q	ENST00000428558	NM_004260.3	1202	Gag/Cag	22/22	0.250523086044149	5	FACETS	1	0.978	1	0.407	0.371	0.444	CLONAL	1	TRUE	2	0.402287714439514	5		620	987	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341911	8341911	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	59	371	0	ENST00000356435.5:c.4729A>C	p.Lys1577Gln	p.K1577Q	ENST00000356435		1577	Aaa/Caa	29/35	0.402287714439514	3	FACETS	0.742	0.639	0.853	0.371	0.319	0.427	SUBCLONAL	1	TRUE	1	0.402287714439514	3		371	475	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966682	36966683	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	95	419	0	ENST00000358127.4:c.643_644delinsTT	p.Pro215Leu	p.P215L	ENST00000358127	NM_001280556.1	215	CCg/TTg	6/10	0.402287714439514	3	FACETS	0.881	0.785	0.983	0.44	0.392	0.492	CLONAL	1	TRUE	1	0.402287714439514	3		419	644	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37006491	37006491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	79	261	0	ENST00000358127.4:c.454C>T	p.Pro152Ser	p.P152S	ENST00000358127	NM_001280556.1	152	Cca/Tca	4/10	0.402287714439514	3	FACETS	1	0.942	1	0.554	0.489	0.622	CLONAL	1	TRUE	1	0.402287714439514	3		261	426	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409393	80409393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	72	421	0	ENST00000286548.4:c.721G>A	p.Glu241Lys	p.E241K	ENST00000286548	NM_002072.3	241	Gag/Aag	5/7	0.402287714439514	4	FACETS	0.928	0.812	1	0.309	0.27	0.351	CLONAL	1	TRUE	1	0.402287714439514	4		421	541	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413959	139413960	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTGCA	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	170	725	0	ENST00000277541.6:c.796_800dup	p.Lys267AsnfsTer12	p.K267Nfs*12	ENST00000277541	NM_017617.3	267	aag/aaTGCAAg	5/34	0.402287714439514	4	FACETS	0.988	0.906	1	0.329	0.302	0.358	CLONAL	1	TRUE	1	0.402287714439514	4		725	1200	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430407	47430407	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	115	263	0	ENST00000377045.4:c.1682C>T	p.Pro561Leu	p.P561L	ENST00000377045	NM_001654.4	561	cCc/cTc	15/16	0.402287714439514	3	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.402287714439514	3		263	522	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240701	53240701	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	143	300	0	ENST00000375401.3:c.1379G>T	p.Arg460Leu	p.R460L	ENST00000375401	NM_004187.3	460	cGg/cTg	10/26	0.402287714439514	3	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.402287714439514	3		300	635	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907831	76907832	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	21	59	0	ENST00000373344.5:c.4329_4330delinsAA	p.Glu1444Lys	p.E1444K	ENST00000373344	NM_000489.3	1443	gaGGaa/gaAAaa	15/35	0.402287714439514	3	FACETS	1	0.878	1			1	CLONAL	1	TRUE	NA	0.402287714439514	3		59	105	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123026612	123026612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	202	154	0	ENST00000355640.3:c.1088C>T	p.Thr363Ile	p.T363I	ENST00000355640		363	aCt/aTt	5/7	0.402287714439514	3	FACETS	0.928	0.88	0.975			1	CLONAL	4	TRUE	NA	0.402287714439514	3		154	325	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0040829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	157	304	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.433690095765155	3	FACETS	0.892	0.823	0.962	0.892	0.823	0.962	CLONAL	2	FALSE	1	0.432746675540764	3		304	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934874	NA	P-0040829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	422	850	0	ENST00000269305.4:c.451C>A	p.Pro151Thr	p.P151T	ENST00000269305	NM_001126112.2	151	Ccc/Acc	5/11	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	2	FALSE	NA	0.432746675540764	2		850	940	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361214	66361214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375878596	NA	P-0040829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	21	352	0	ENST00000273854.3:c.958G>A	p.Gly320Ser	p.G320S	ENST00000273854	NM_004439.5	320	Ggc/Agc	4/18	0.432746675540764	1	FACETS	0.245	0.188	0.31	0.245	0.188	0.31	SUBCLONAL	1	FALSE	0	0.432746675540764	1		352	311	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857127	9857127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs976259560	NA	P-0040829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	134	375	0	ENST00000330684.3:c.4274C>T	p.Ser1425Leu	p.S1425L	ENST00000330684	NM_001134407.1	1425	tCg/tTg	13/13	0.433690095765155	3	FACETS	0.893	0.818	0.969	0.893	0.818	0.969	CLONAL	2	FALSE	1	0.432746675540764	3		375	422	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231380	98231380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372555269	NA	P-0040829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	279	668	0	ENST00000331920.6:c.1903G>A	p.Asp635Asn	p.D635N	ENST00000331920	NM_000264.3	635	Gac/Aac	14/24	0.407630463295981	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	FALSE	1	0.432746675540764	3		668	780	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991700	72991700	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs62639304	NA	P-0040829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	10	207	0	ENST00000268489.5:c.2345C>T	p.Ala782Val	p.A782V	ENST00000268489	NM_006885.3	782	gCg/gTg	2/10	0.26531261041843	3	FACETS	0.312	0.211	0.439	0.156	0.105	0.22	SUBCLONAL	1	FALSE	1	0.432746675540764	3		207	180	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631917	90631918	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs747216375	NA	P-0040829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	145	727	3	ENST00000330062.3:c.435dup	p.Thr146AspfsTer126	p.T146Dfs*126	ENST00000330062	NM_002168.2	145	-/G	4/11	0.418645907167107	2	FACETS	0.796	0.726	0.869	0.398	0.363	0.435	SUBCLONAL	1	FALSE	0	0.432746675540764	2		730	842	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133695	2133695	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0040829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	68	607	0	ENST00000219476.3:c.3884-1G>T		p.X1295_splice	ENST00000219476	NM_000548.3	1295			0.433690095765155	3	FACETS	0.598	0.52	0.683	0.299	0.26	0.342	SUBCLONAL	1	FALSE	1	0.432746675540764	3		607	639	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869481	102869481	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	94	538	0	ENST00000307046.8:c.160T>C	p.Cys54Arg	p.C54R	ENST00000307046	NM_001111285.1	54	Tgc/Cgc	2/4	0.317082252728454	3	FACETS	1	0.931	1	0.352	0.314	0.392	CLONAL	1	FALSE	0	0.432746675540764	3		538	500	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115111981	115111981	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	125	737	0	ENST00000257566.3:c.1759C>A	p.Leu587Met	p.L587M	ENST00000257566	NM_016569.3	587	Ctg/Atg	7/8	0.317082252728454	3	FACETS	0.922	0.835	1	0.307	0.278	0.338	CLONAL	1	FALSE	0	0.432746675540764	3		737	762	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492880	56492881	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TAGC	novel	NA	P-0040829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	146	375	0	ENST00000407977.2:c.55_58dup	p.Thr20SerfsTer21	p.T20Sfs*21	ENST00000407977		20	acc/aGCTAcc	2/10	0.418645907167107	2	FACETS	0.85	0.784	0.917	0.85	0.784	0.917	CLONAL	2	FALSE	0	0.432746675540764	2		375	397	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982523	10982523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	12	86	0	ENST00000327064.4:c.145C>T	p.Arg49Trp	p.R49W	ENST00000327064	NM_199141.1	49	Cgg/Tgg	1/16	0.301979736036018	2	FACETS	0.319	0.224	0.434	0.159	0.112	0.217	SUBCLONAL	1	FALSE	0	0.432746675540764	2		86	174	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57474016	57474016	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	40	317	0	ENST00000371085.3:c.233A>G	p.Gln78Arg	p.Q78R	ENST00000371085	NM_000516.4	78	cAg/cGg	3/13	0.433690095765155	3	FACETS	0.377	0.312	0.449	0.188	0.156	0.225	SUBCLONAL	1	FALSE	1	0.432746675540764	3		317	597	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851735	134851735	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867526874	NA	P-0040829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	74	569	0	ENST00000398015.3:c.1141C>T	p.Pro381Ser	p.P381S	ENST00000398015	NM_004441.4	381	Ccc/Tcc	5/16	0.301979736036018	2	FACETS	0.649	0.569	0.735	0.324	0.284	0.368	SUBCLONAL	1	FALSE	0	0.432746675540764	2		569	527	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781504	NA	P-0040833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	84	725	0	ENST00000269305.4:c.314G>T	p.Gly105Val	p.G105V	ENST00000269305	NM_001126112.2	105	gGc/gTc	4/11	0.796057940117471	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.796057940117471	1		725	121	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742680	39742680	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	66	402	0	ENST00000361337.2:c.1523G>T	p.Arg508Leu	p.R508L	ENST00000361337	NM_003286.2	508	cGt/cTt	15/21	0.245728542713268	3	FACETS	1	0.977	1	0.743	0.662	0.826	INDETERMINATE	1	TRUE	1	0.796057940117471	3		402	156	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73351578	73351578	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs757502879	NA	P-0040833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	30	207	0	ENST00000377767.4:c.634G>T	p.Ala212Ser	p.A212S	ENST00000377767	NM_014953.3	212	Gct/Tct	4/21	0.245728542713268	3	FACETS	0.893	0.734	1	0.446	0.367	0.533	INDETERMINATE	1	TRUE	1	0.796057940117471	3		207	118	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438188	56438188	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	109	744	0	ENST00000407977.2:c.805del	p.Ala269ProfsTer150	p.A269Pfs*150	ENST00000407977		269	Gcc/cc	7/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.796057940117471	2		744	259	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097643	11097643	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	82	848	0	ENST00000358026.2:c.823C>A	p.Gln275Lys	p.Q275K	ENST00000358026	NM_001128849.1	275	Cag/Aag	5/36	1	2	FACETS	0.928	0.833	1	0.928	0.833	1	CLONAL	1	TRUE	1	0.796057940117471	2		848	222	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0040888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	297	575	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.283368883085872	7	FACETS	0.915	0.863	0.969	0.915	0.863	0.969	CLONAL	4	FALSE	3	0.283368883085872	7		575	978	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0040888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	102	720	2	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.283368883085872	1	FACETS	0.99	0.887	1	0.99	0.887	1	CLONAL	1	FALSE	0	0.283368883085872	1		722	624	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459130	120459130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	276	532	0	ENST00000256646.2:c.6215C>T	p.Pro2072Leu	p.P2072L	ENST00000256646	NM_024408.3	2072	cCa/cTa	34/34	0.283368883085872	3	FACETS	0.964	0.909	1	0.964	0.909	1	CLONAL	3	FALSE	0	0.283368883085872	3		532	769	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927432	245927432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	71	424	0	ENST00000388985.4:c.1096C>T	p.His366Tyr	p.H366Y	ENST00000388985		366	Cat/Tat	11/12	0.283368883085872	7	FACETS	0.917	0.798	1	0.153	0.133	0.175	CLONAL	1	FALSE	1	0.283368883085872	7		424	934	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732896	74732896	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	64	247	0	ENST00000359995.5:c.347G>C	p.Gly116Ala	p.G116A	ENST00000359995	NM_001195427.1	116	gGa/gCa	1/3	0.283368883085872	7	FACETS	1	0.951	1	0.244	0.211	0.28	CLONAL	1	FALSE	2	0.283368883085872	7		247	633	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016208	31016209	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0040888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	137	308	0	ENST00000375687.4:c.455dup	p.Tyr152Ter	p.Y152*	ENST00000375687	NM_015338.5	152	tac/tAac	6/13	0.283368883085872	3	FACETS	1	0.981	1	0.833	0.764	0.904	CLONAL	2	FALSE	0	0.283368883085872	3		308	442	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670840	134670840	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	56	371	0	ENST00000398015.3:c.751G>C	p.Gly251Arg	p.G251R	ENST00000398015	NM_004441.4	251	Ggg/Cgg	3/16	0.283368883085872	3	FACETS	0.906	0.777	1	0.453	0.388	0.524	CLONAL	1	FALSE	1	0.283368883085872	3		371	498	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351431	70351431	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	90	481	0	ENST00000374080.3:c.4080del	p.Leu1361TrpfsTer6	p.L1361Wfs*6	ENST00000374080		1360	tCc/tc	29/45	0.264996494915252	3	FACETS	0.981	0.871	1	0.491	0.435	0.55	CLONAL	1	FALSE	1	0.283368883085872	3		481	739	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219677	36219677	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	153	935	0	ENST00000222270.7:c.4574G>A	p.Gly1525Glu	p.G1525E	ENST00000222270	NM_014727.1	1525	gGa/gAa	20/37	1	2	FACETS	0.528	0.484	0.575	0.528	0.484	0.575	SUBCLONAL	1	TRUE	1	0.733247323477399	2		935	790	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608640	189608640	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	107	708	1	ENST00000264731.3:c.1715C>A	p.Thr572Asn	p.T572N	ENST00000264731	NM_003722.4	572	aCc/aAc	13/14	0.325036799181171	3	FACETS	0.405	0.363	0.451	0.135	0.121	0.151	INDETERMINATE	1	TRUE	0	0.733247323477399	3		709	984	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	177	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.522942769953859	2		452	665	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101271	27101298	+	frameshift_variant	Frame_Shift_Del	DEL	CCCAGGGCCCCGCCTATCATGGCGTGAA	CCCAGGGCCCCGCCTATCATGGCGTGAA	-	novel	NA	P-0040934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	123	744	0	ENST00000324856.7:c.4555_4582del	p.Gln1519GlufsTer37	p.Q1519Efs*37	ENST00000324856	NM_006015.4	1518	cCCCAGGGCCCCGCCTATCATGGCGTGAAc/cc	18/20	1	2	FACETS	0.519	0.469	0.572	0.519	0.469	0.572	SUBCLONAL	1	TRUE	1	0.522942769953859	2		744	906	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851456	63851456	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	233	531	1	ENST00000279873.7:c.2234C>A	p.Ala745Glu	p.A745E	ENST00000279873	NM_032199.2	745	gCg/gAg	10/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.522942769953859	2		532	789	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646238	3646238	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	367	952	0	ENST00000294008.3:c.1840G>T	p.Asp614Tyr	p.D614Y	ENST00000294008	NM_032444.2	614	Gac/Tac	8/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.522942769953859	2		952	1306	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038357	180038357	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	296	737	0	ENST00000261937.6:c.3660C>A	p.Ser1220Arg	p.S1220R	ENST00000261937	NM_182925.4	1220	agC/agA	27/30	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.522942769953859	2		737	1059	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	277	673	0				ENST00000310581	NM_198253.2	-/1132			0.673138309715673	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.727282875880438	4		673	624	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	376	1096	1	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.727282875880438	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.727282875880438	3		1097	699	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780071	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	207	765	0	ENST00000269305.4:c.580C>T	p.Leu194Phe	p.L194F	ENST00000269305	NM_001126112.2	194	Ctt/Ttt	6/11	0.727282875880438	3	FACETS	0.968	0.9	1	0.484	0.45	0.519	CLONAL	1	TRUE	1	0.727282875880438	3		765	802	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413099	139413099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	445	809	0	ENST00000277541.6:c.1043C>T	p.Ala348Val	p.A348V	ENST00000277541	NM_017617.3	348	gCc/gTc	6/34	0.268671126338122	5	FACETS	0.859	0.823	0.895	0.859	0.823	0.895	INDETERMINATE	3	TRUE	2	0.727282875880438	5		809	993	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3795278	3795278	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	266	471	0	ENST00000262367.5:c.3914G>A	p.Gly1305Asp	p.G1305D	ENST00000262367	NM_004380.2	1305	gGt/gAt	22/31	0.510973733961809	4	FACETS	0.979	0.925	1	0.979	0.925	1	CLONAL	2	TRUE	2	0.727282875880438	4		471	645	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703539	47703539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1203462814	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	180	606	0	ENST00000233146.2:c.2039G>A	p.Arg680Gln	p.R680Q	ENST00000233146	NM_000251.2	680	cGa/cAa	13/16	0.608698937868477	5	FACETS	1	0.979	1	0.392	0.361	0.423	CLONAL	1	TRUE	2	0.727282875880438	5		606	881	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654718	67654718	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	264	432	0	ENST00000264010.4:c.1205C>T	p.Ser402Leu	p.S402L	ENST00000264010	NM_006565.3	402	tCa/tTa	6/12	0.510973733961809	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.727282875880438	4		432	607	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100947	41100947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372070542	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	314	697	1	ENST00000373198.4:c.1409G>A	p.Arg470Gln	p.R470Q	ENST00000373198	NM_133170.3	470	cGa/cAa	8/32	0.510973733961809	4	FACETS	0.972	0.922	1	0.972	0.922	1	CLONAL	2	TRUE	2	0.727282875880438	4		698	767	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459317	120459318	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	194	410	0	ENST00000256646.2:c.6028-1_6028delinsAA		p.X2010_splice	ENST00000256646	NM_024408.3	2010		34/34	0.616692195957732	4	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	2	0.727282875880438	4		410	455	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424741	49424742	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	196	775	1	ENST00000301067.7:c.13605_13606delinsTT	p.Arg4536Ter	p.R4536*	ENST00000301067	NM_003482.3	4535	tcCCga/tcTTga	40/54	NA	2	FACETS	0.923	0.86	0.987			1	INDETERMINATE	1	TRUE	NA	0.727282875880438	2		776	584	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249242	133249242	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854844	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	188	732	0	ENST00000320574.5:c.1657C>T	p.Arg553Cys	p.R553C	ENST00000320574	NM_006231.2	553	Cgc/Tgc	15/49	0.727282875880438	3	FACETS	0.828	0.766	0.893	0.414	0.383	0.447	CLONAL	1	TRUE	1	0.727282875880438	3		732	851	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748497	43748497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	250	810	1	ENST00000382044.4:c.2309C>T	p.Ser770Phe	p.S770F	ENST00000382044	NM_001141980.1	770	tCt/tTt	12/28	NA	2	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.727282875880438	2		811	671	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944310	81944310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760763002	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	138	708	0	ENST00000359376.3:c.1919C>T	p.Pro640Leu	p.P640L	ENST00000359376	NM_002661.3	640	cCc/cTc	18/33	0.510973733961809	4	FACETS	0.847	0.771	0.926	0.423	0.385	0.463	CLONAL	1	TRUE	2	0.727282875880438	4		708	774	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667645	29667646	+	missense_variant	Missense_Mutation	DNP	CC	CC	GT	novel	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	170	443	0	ENST00000356175.3:c.6981_6982delinsGT	p.Arg2328Cys	p.R2328C	ENST00000356175	NM_000267.3	2327	ctCCgt/ctGTgt	46/57	0.693748686087459	3	FACETS	1	0.972	1	0.551	0.51	0.594	CLONAL	1	TRUE	1	0.727282875880438	3		443	578	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006616	62006616	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	389	710	0	ENST00000392795.3:c.663G>T	p.Trp221Cys	p.W221C	ENST00000392795	NM_001039933.1	221	tgG/tgT	6/6	0.693748686087459	3	FACETS	0.852	0.814	0.89	0.852	0.814	0.89	CLONAL	2	TRUE	1	0.727282875880438	3		710	856	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120053	70120053	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	17	17	0	ENST00000245479.2:c.1055C>T	p.Ala352Val	p.A352V	ENST00000245479	NM_000346.3	352	gCc/gTc	3/3	0.673138309715673	4	FACETS	1	0.887	1	1	0.887	1	CLONAL	2	TRUE	2	0.727282875880438	4		17	34	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265058	5265058	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	229	876	0	ENST00000357368.4:c.529C>T	p.Pro177Ser	p.P177S	ENST00000357368	NM_002850.3	177	Cct/Tct	5/38	0.32365289068147	4	FACETS	1	0.983	1	0.58	0.541	0.621	INDETERMINATE	1	TRUE	2	0.727282875880438	4		876	937	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366182	15366182	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1417719873	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	168	785	0	ENST00000263377.2:c.1973C>T	p.Thr658Ile	p.T658I	ENST00000263377	NM_058243.2	658	aCc/aTc	10/20	0.32365289068147	4	FACETS	0.866	0.796	0.94	0.433	0.398	0.47	INDETERMINATE	1	TRUE	2	0.727282875880438	4		785	921	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211919	36211919	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	623	1112	0	ENST00000222270.7:c.1670T>G	p.Val557Gly	p.V557G	ENST00000222270	NM_014727.1	557	gTg/gGg	3/37	0.673138309715673	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.727282875880438	4		1112	1397	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47730013	47730013	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	313	526	0	ENST00000449228.1:c.378-2A>G		p.X126_splice	ENST00000449228	NM_001127240.2	126			0.673138309715673	4	FACETS	0.998	0.947	1	0.998	0.947	1	CLONAL	2	TRUE	2	0.727282875880438	4		526	745	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082913	16082913	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	330	317	0	ENST00000281043.3:c.727C>T	p.Gln243Ter	p.Q243*	ENST00000281043	NM_005378.4	243	Cag/Tag	2/3	0.608698937868477	5	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	2	0.727282875880438	5		317	566	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478779	57478779	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	255	553	0	ENST00000371085.3:c.365C>T	p.Pro122Leu	p.P122L	ENST00000371085	NM_000516.4	122	cCc/cTc	5/13	0.510973733961809	4	FACETS	0.985	0.929	1	0.985	0.929	1	CLONAL	2	TRUE	2	0.727282875880438	4		553	615	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531826	41531826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	258	556	0	ENST00000263253.7:c.1538C>T	p.Pro513Leu	p.P513L	ENST00000263253	NM_001429.3	513	cCt/cTt	7/31	0.727282875880438	4	FACETS	1	0.991	1	0.668	0.627	0.711	CLONAL	1	TRUE	2	0.727282875880438	4		556	917	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521093	187521094	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	254	487	1	ENST00000441802.2:c.12061_12062delinsTT	p.Pro4021Phe	p.P4021F	ENST00000441802	NM_005245.3	4021	CCt/TTt	22/27	0.673138309715673	4	FACETS	0.914	0.861	0.968	0.914	0.861	0.968	CLONAL	2	TRUE	2	0.727282875880438	4		488	660	SUCCESS
APC	324	MSKCC	GRCh37	5	112175502	112175502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	133	426	0	ENST00000257430.4:c.4211C>T	p.Ser1404Phe	p.S1404F	ENST00000257430	NM_000038.5	1404	tCc/tTc	16/16	0.673138309715673	4	FACETS	1	0.973	1	0.582	0.531	0.635	CLONAL	1	TRUE	2	0.727282875880438	4		426	543	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931276	131931276	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	230	368	0	ENST00000265335.6:c.1981G>T	p.Gly661Ter	p.G661*	ENST00000265335		661	Gga/Tga	13/25	0.673138309715673	4	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	2	0.727282875880438	4		368	542	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138433	37138433	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1218840909	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	148	479	2	ENST00000373509.5:c.82G>A	p.Gly28Ser	p.G28S	ENST00000373509	NM_002648.3	28	Ggc/Agc	1/6	0.727282875880438	3	FACETS	1	0.958	1	0.533	0.489	0.577	CLONAL	1	TRUE	1	0.727282875880438	3		481	521	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553350	106553350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs926688107	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	141	548	0	ENST00000369096.4:c.1315C>T	p.Leu439Phe	p.L439F	ENST00000369096	NM_001198.3	439	Ctc/Ttc	5/7	0.377640549892468	3	FACETS	1	0.982	1	0.628	0.577	0.68	INDETERMINATE	1	TRUE	1	0.727282875880438	3		548	421	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023241	150023241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	138	500	0	ENST00000253339.5:c.22G>A	p.Glu8Lys	p.E8K	ENST00000253339		8	Gaa/Aaa	1/7	0.377640549892468	3	FACETS	1	0.983	1	0.639	0.587	0.692	INDETERMINATE	1	TRUE	1	0.727282875880438	3		500	405	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418325	139418325	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	355	1044	0	ENST00000277541.6:c.247del	p.Ala83GlnfsTer17	p.A83Qfs*17	ENST00000277541	NM_017617.3	83	Gca/ca	3/34	0.268671126338122	5	FACETS	1	0.96	1	0.675	0.641	0.71	INDETERMINATE	2	TRUE	2	0.727282875880438	5		1044	1008	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923789	39923789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1192993784	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	324	937	0	ENST00000378444.4:c.3302C>T	p.Pro1101Leu	p.P1101L	ENST00000378444	NM_001123385.1	1101	cCt/cTt	7/15	0.268671126338122	5	FACETS	0.939	0.889	0.99	0.626	0.592	0.66	INDETERMINATE	2	TRUE	2	0.727282875880438	5		937	992	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339307	70339307	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1039763693	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	112	612	0	ENST00000374080.3:c.184G>T	p.Val62Phe	p.V62F	ENST00000374080		62	Gtc/Ttc	2/45	0.344539129081727	3	FACETS	0.67	0.604	0.74	0.223	0.201	0.247	INDETERMINATE	1	TRUE	0	0.727282875880438	3		612	627	SUCCESS
BTK	695	MSKCC	GRCh37	X	100629559	100629559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	120	628	0	ENST00000308731.7:c.205C>T	p.Pro69Ser	p.P69S	ENST00000308731	NM_000061.2	69	Cct/Tct	3/19	0.344539129081727	3	FACETS	0.688	0.622	0.757	0.229	0.207	0.253	INDETERMINATE	1	TRUE	0	0.727282875880438	3		628	654	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459317	120459317	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	194	410	0	ENST00000256646.2:c.6028G>A	p.Glu2010Lys	p.E2010K	ENST00000256646	NM_024408.3	2010	Gaa/Aaa	34/34	0.616692195957732	4	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	2	0.727282875880438	4		410	455	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3795277	3795277	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0040940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	259	477	0	ENST00000262367.5:c.3914+1del		p.X1305_splice	ENST00000262367	NM_004380.2	1305			0.510973733961809	4	FACETS	0.954	0.9	1	0.954	0.9	1	CLONAL	2	TRUE	2	0.727282875880438	4		477	645	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	32	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		452	267	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0040954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	48	426	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		426	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579494	7579494	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1555526721	NA	P-0040954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	50	878	0	ENST00000269305.4:c.193A>T	p.Arg65Ter	p.R65*	ENST00000269305	NM_001126112.2	65	Aga/Tga	4/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		878	328	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145430	58145430	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894340	NA	P-0040954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	29	530	0	ENST00000257904.6:c.71G>T	p.Arg24Leu	p.R24L	ENST00000257904	NM_000075.3	24	cGt/cTt	2/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		530	340	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202753	108202753	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs781215442	NA	P-0040954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	26	367	0	ENST00000278616.4:c.7777C>T	p.Gln2593Ter	p.Q2593*	ENST00000278616	NM_000051.3	2593	Cag/Tag	52/63	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		367	207	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	223	320	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.996	0.935	1	0.996	0.935	1	CLONAL	1	TRUE	1	0.79	2		321	567	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931683	39931684	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0040962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	395	679	0	ENST00000378444.4:c.2915dup	p.Tyr972Ter	p.Y972*	ENST00000378444	NM_001123385.1	972	tac/taAc	4/15	1	2	FACETS	0.976	0.93	1	0.976	0.93	1	CLONAL	1	TRUE	1	0.79	2		679	1025	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056330	26056330	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	46	517	0	ENST00000343677.2:c.327G>C	p.Lys109Asn	p.K109N	ENST00000343677	NM_005319.3	109	aaG/aaC	1/1	0.260411870698785	3	FACETS	0.686	0.577	0.807	0.343	0.288	0.404	SUBCLONAL	1	TRUE	1	0.260411870698785	3		517	582	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0040964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	136	664	1	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.260411870698785	2		665	728	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0040964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	109	480	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.260411870698785	2		480	659	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566738	212566738	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	38	357	0	ENST00000342788.4:c.1443C>G	p.Ile481Met	p.I481M	ENST00000342788	NM_005235.2	481	atC/atG	12/28	0.188028185541518	3	FACETS	0.595	0.491	0.712	0.298	0.245	0.356	SUBCLONAL	1	TRUE	1	0.260411870698785	3		357	554	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808863	3808863	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866498372	NA	P-0040964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	47	498	3	ENST00000262367.5:c.3361G>A	p.Gly1121Arg	p.G1121R	ENST00000262367	NM_004380.2	1121	Gga/Aga	17/31	0.170579557525704	3	FACETS	0.703	0.593	0.825	0.352	0.296	0.413	SUBCLONAL	1	TRUE	1	0.260411870698785	3		501	580	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471754	120471754	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	41	537	0	ENST00000256646.2:c.3737G>C	p.Gly1246Ala	p.G1246A	ENST00000256646	NM_024408.3	1246	gGa/gCa	23/34	0.170579557525704	3	FACETS	0.569	0.473	0.677	0.285	0.236	0.339	SUBCLONAL	1	TRUE	1	0.260411870698785	3		537	625	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838306	156838306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs552776147	NA	P-0040964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	50	802	1	ENST00000524377.1:c.584C>T	p.Thr195Met	p.T195M	ENST00000524377	NM_002529.3	195	aCg/aTg	6/17	0.170579557525704	3	FACETS	0.744	0.631	0.869	0.372	0.315	0.435	SUBCLONAL	1	TRUE	1	0.260411870698785	3		803	583	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631192	69631192	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs946999197	NA	P-0040964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	43	470	1	ENST00000334134.2:c.221-1G>T		p.X74_splice	ENST00000334134	NM_005247.2	74			0.170579557525704	3	FACETS	0.76	0.636	0.898	0.38	0.318	0.449	SUBCLONAL	1	TRUE	1	0.260411870698785	3		471	491	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650668	18650668	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1162221589	NA	P-0040964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	29	393	0	ENST00000266497.5:c.2879C>T	p.Thr960Ile	p.T960I	ENST00000266497		960	aCa/aTa	20/31	0.113745436271191	4	FACETS	0.573	0.459	0.703	0.286	0.229	0.352	INDETERMINATE	1	TRUE	2	0.260411870698785	4		393	490	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041745	29041745	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0040964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	31	357	0	ENST00000282397.4:c.74C>G	p.Ser25Ter	p.S25*	ENST00000282397	NM_002019.4	25	tCa/tGa	2/30	0.190726208829525	2	FACETS	0.468	0.377	0.57	0.234	0.188	0.285	SUBCLONAL	1	TRUE	0	0.260411870698785	2		357	509	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653169	29653169	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	41	432	0	ENST00000356175.3:c.5104C>A	p.Gln1702Lys	p.Q1702K	ENST00000356175	NM_000267.3	1702	Caa/Aaa	36/57	1	2	FACETS	0.686	0.571	0.813	0.686	0.571	0.813	SUBCLONAL	1	TRUE	1	0.260411870698785	2		432	459	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629005	14629005	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	92	640	0	ENST00000254322.2:c.157G>T	p.Asp53Tyr	p.D53Y	ENST00000254322	NM_006145.1	53	Gac/Tac	1/3	0.256583911839475	2	FACETS	1	0.896	1	0.504	0.448	0.564	CLONAL	1	TRUE	0	0.260411870698785	2		640	701	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52709296	52709296	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	121	561	0	ENST00000322088.6:c.250G>C	p.Glu84Gln	p.E84Q	ENST00000322088	NM_014225.5	84	Gag/Cag	3/15	0.188028185541518	3	FACETS	0.762	0.69	0.839	0.762	0.69	0.839	SUBCLONAL	2	TRUE	1	0.260411870698785	3		561	689	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051644	128051644	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	97	597	0	ENST00000285398.2:c.14A>T	p.Asp5Val	p.D5V	ENST00000285398	NM_000122.1	5	gAc/gTc	1/15	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.260411870698785	2		597	564	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41554473	41554473	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	49	551	0	ENST00000263253.7:c.3559C>G	p.Arg1187Gly	p.R1187G	ENST00000263253	NM_001429.3	1187	Cgt/Ggt	19/31	0.190726208829525	2	FACETS	0.612	0.518	0.716	0.306	0.259	0.358	SUBCLONAL	1	TRUE	0	0.260411870698785	2		551	615	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271112	26271445	+	coding_sequence_variant,3_prime_UTR_variant	Frame_Shift_Del	DEL	TGATTAGTTAATCACAGCTATTTTCGGGTGAAAGTAGGCGGCTCTTAAAAGAGCCTTTTTAAGTTGGATAGAATTACTGCCCGGAAACCTCTACGCTCTCTCCCCACGAATGCGGCGAGCGAGCTGAATGTCCTTGGGCATGATAGTCACTCGCTTAGCATGGATGGCACACAGGTTGGTATCCTCAAAGAGCCCCACCAAGTAGGCCTCGCAGGCCTCCTGCAGGGCCATCACCGCGGAACTCTGAAAGCGCAGATCTGTCTTGAAGTCCTGAGCGATTTCTCGCACCAGGCGTTGGAAAGGCAACTTGCGGATCAGCAGCTCAGTCGACTTC	TGATTAGTTAATCACAGCTATTTTCGGGTGAAAGTAGGCGGCTCTTAAAAGAGCCTTTTTAAGTTGGATAGAATTACTGCCCGGAAACCTCTACGCTCTCTCCCCACGAATGCGGCGAGCGAGCTGAATGTCCTTGGGCATGATAGTCACTCGCTTAGCATGGATGGCACACAGGTTGGTATCCTCAAAGAGCCCCACCAAGTAGGCCTCGCAGGCCTCCTGCAGGGCCATCACCGCGGAACTCTGAAAGCGCAGATCTGTCTTGAAGTCCTGAGCGATTTCTCGCACCAGGCGTTGGAAAGGCAACTTGCGGATCAGCAGCTCAGTCGACTTC	-	novel	NA	P-0040964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	45	178	0				ENST00000305910	NM_003534.2	56		1/1	0.260411870698785	3	FACETS	1	0.906	1	1	0.906	1	CLONAL	2	TRUE	1	0.260411870698785	3		178	180	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37141857	37141857	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771419466	NA	P-0040964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	40	530	0	ENST00000373509.5:c.932C>T	p.Pro311Leu	p.P311L	ENST00000373509	NM_002648.3	311	cCc/cTc	6/6	0.260411870698785	3	FACETS	0.565	0.468	0.672	0.282	0.234	0.336	SUBCLONAL	1	TRUE	1	0.260411870698785	3		530	615	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012354	152012354	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	91	449	0	ENST00000262189.6:c.459C>A	p.Phe153Leu	p.F153L	ENST00000262189	NM_170606.2	153	ttC/ttA	4/59	0.135240317059936	3	FACETS	1	0.975	1	0.454	0.404	0.507	INDETERMINATE	1	TRUE	0	0.260411870698785	3		449	580	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	139	320	1				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.993	0.912	1			1	INDETERMINATE	1	TRUE	NA	0.674924600684708	2		321	415	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0040979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	119	440	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	0.674924600684708	1	FACETS	0.878	0.808	0.95	0.878	0.808	0.95	CLONAL	1	TRUE	0	0.674924600684708	1		440	266	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210075	55210075	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17818	1818	439	0	ENST00000275493.2:c.185T>G	p.Leu62Arg	p.L62R	ENST00000275493	NM_005228.3	62	cTt/cGt	2/28	0.674924600684708	53	FACETS	0.999	0.973	1			1	CLONAL	5	TRUE	NA	0.674924600684708	53		439	19636	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249015	55249016	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCCCACGTG	novel	NA	P-0040979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18345	486	529	0	ENST00000275493.2:c.2314_2322dup	p.Pro772_Val774dup	p.P772_V774dup	ENST00000275493	NM_005228.3	772	-/CCCCACGTG	20/28	0.674924600684708	53	FACETS	1	0.995	1			1	CLONAL	1	TRUE	NA	0.674924600684708	53		529	18831	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835909	151835909	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	78	381	0	ENST00000262189.6:c.14615C>A	p.Ser4872Tyr	p.S4872Y	ENST00000262189	NM_170606.2	4872	tCc/tAc	58/59	0.674924600684708	3	FACETS	0.539	0.474	0.608	0.269	0.237	0.304	SUBCLONAL	1	TRUE	1	0.674924600684708	3		381	574	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0041023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	935	422	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.597364140250927	7	FACETS	0.935	0.918	0.952			1	CLONAL	7	TRUE	NA	0.597364140250927	7		422	1192	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155174	108155174	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	151	364	0	ENST00000278616.4:c.3970del	p.Ser1324ValfsTer25	p.S1324Vfs*25	ENST00000278616	NM_000051.3	1323	Aaa/aa	26/63	0.597364140250927	2	FACETS	0.936	0.876	0.996	0.936	0.876	0.996	CLONAL	2	TRUE	0	0.597364140250927	2		364	270	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155178	108155178	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1456873569	NA	P-0041023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	156	347	0	ENST00000278616.4:c.3971G>T	p.Ser1324Ile	p.S1324I	ENST00000278616	NM_000051.3	1324	aGt/aTt	26/63	0.597364140250927	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	0	0.597364140250927	2		347	260	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041860	42041860	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	110	382	0	ENST00000219905.7:c.6055G>T	p.Glu2019Ter	p.E2019*	ENST00000219905	NM_001164273.1	2019	Gaa/Taa	17/24	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.597364140250927	2		382	356	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274171	10274171	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	521	452	0	ENST00000330684.3:c.98C>A	p.Ala33Glu	p.A33E	ENST00000330684	NM_001134407.1	33	gCg/gAg	2/13	0.52876509931735	4	FACETS	0.974	0.939	1			1	CLONAL	3	TRUE	NA	0.597364140250927	4		452	954	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556068	29556068	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	175	215	0	ENST00000356175.3:c.2435T>C	p.Ile812Thr	p.I812T	ENST00000356175	NM_000267.3	812	aTt/aCt	21/57	0.540384141101585	5	FACETS	0.855	0.796	0.915	0.855	0.796	0.915	CLONAL	3	TRUE	2	0.597364140250927	5		215	433	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955065	17955065	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	264	720	0	ENST00000458235.1:c.162C>G	p.Cys54Trp	p.C54W	ENST00000458235	NM_000215.3	54	tgC/tgG	2/24	0.597364140250927	3	FACETS	0.957	0.896	1	0.478	0.448	0.51	CLONAL	1	TRUE	1	0.597364140250927	3		720	1200	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794793	242794793	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	301	444	0	ENST00000334409.5:c.416G>C	p.Arg139Pro	p.R139P	ENST00000334409	NM_005018.2	139	cGg/cCg	2/5	0.597364140250927	3	FACETS	0.977	0.927	1	0.977	0.927	1	CLONAL	2	TRUE	1	0.597364140250927	3		444	670	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017790	31017790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564841799	NA	P-0041023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	611	722	0	ENST00000375687.4:c.652C>T	p.Arg218Cys	p.R218C	ENST00000375687	NM_015338.5	218	Cgt/Tgt	8/13	0.54224322041126	5	FACETS	0.92	0.887	0.954	0.69	0.665	0.715	CLONAL	3	TRUE	1	0.597364140250927	5		722	1405	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748143	41748143	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	252	316	0	ENST00000226382.2:c.626G>T	p.Gly209Val	p.G209V	ENST00000226382	NM_003924.3	209	gGg/gTg	3/3	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	2	TRUE	NA	0.597364140250927	2		316	394	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056599	26056599	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	90	203	0	ENST00000343677.2:c.58G>T	p.Val20Leu	p.V20L	ENST00000343677	NM_005319.3	20	Gta/Tta	1/1	0.597364140250927	3	FACETS	1	0.899	1	0.503	0.449	0.56	CLONAL	1	TRUE	1	0.597364140250927	3		203	389	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739584	145739584	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	506	713	0	ENST00000428558.2:c.1867C>A	p.Arg623Ser	p.R623S	ENST00000428558	NM_004260.3	623	Cgc/Agc	11/22	0.41869112037961	4	FACETS	0.936	0.897	0.977	0.936	0.897	0.977	CLONAL	2	TRUE	2	0.597364140250927	4		713	1445	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93607730	93607730	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	83	209	0	ENST00000375746.1:c.432G>T	p.Glu144Asp	p.E144D	ENST00000375746	NM_001174167.1	144	gaG/gaT	3/14	0.597364140250927	4	FACETS	0.944	0.837	1	0.315	0.279	0.353	CLONAL	1	TRUE	1	0.597364140250927	4		209	470	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039905	47039905	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	479	694	0	ENST00000377604.3:c.1248G>T	p.Gln416His	p.Q416H	ENST00000377604	NM_001204468.1	416	caG/caT	12/24	NA	2	FACETS	0.973	0.939	1			1	INDETERMINATE	2	TRUE	NA	0.597364140250927	2		694	824	SUCCESS
AR	367	MSKCC	GRCh37	X	66863189	66863189	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	325	465	0	ENST00000374690.3:c.1708T>C	p.Cys570Arg	p.C570R	ENST00000374690	NM_000044.3	570	Tgt/Cgt	2/8	0.184150620241054	5	FACETS	0.974	0.927	1			1	INDETERMINATE	3	TRUE	NA	0.597364140250927	5		465	706	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849187	76849187	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	473	260	1	ENST00000373344.5:c.6089C>A	p.Ala2030Glu	p.A2030E	ENST00000373344	NM_000489.3	2030	gCa/gAa	26/35	0.597364140250927	8	FACETS	1	0.992	1			1	CLONAL	6	TRUE	NA	0.597364140250927	8		261	691	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964125	28964125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377395740	NA	P-0041037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	58	438	1	ENST00000282397.4:c.1777C>T	p.Arg593Trp	p.R593W	ENST00000282397	NM_002019.4	593	Cgg/Tgg	13/30	1	2	FACETS	0.783	0.675	0.9	0.783	0.675	0.9	SUBCLONAL	1	TRUE	1	0.351063471782366	2		439	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579316	7579317	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	135	683	0	ENST00000269305.4:c.370dup	p.Cys124LeufsTer25	p.C124Lfs*25	ENST00000269305	NM_001126112.2	124	tgc/tTgc	4/11	0.351063471782366	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.351063471782366	1		683	622	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604776	48604776	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs377767382	NA	P-0041037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	76	416	0	ENST00000342988.3:c.1598T>C	p.Leu533Pro	p.L533P	ENST00000342988	NM_005359.5	533	cTc/cCc	12/12	0.351063471782366	1	FACETS	0.838	0.738	0.944	0.838	0.738	0.944	CLONAL	1	TRUE	0	0.351063471782366	1		416	426	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416536	49416536	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	150	588	0	ENST00000301067.7:c.16175G>A	p.Arg5392His	p.R5392H	ENST00000301067	NM_003482.3	5392	cGc/cAc	51/54	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.351063471782366	2		588	778	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375037	45375037	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0041037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	36	365	0	ENST00000262160.6:c.806C>G	p.Ser269Ter	p.S269*	ENST00000262160	NM_005901.5	269	tCa/tGa	8/11	0.351063471782366	1	FACETS	0.631	0.521	0.752	0.631	0.521	0.752	SUBCLONAL	1	TRUE	0	0.351063471782366	1		365	268	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0041053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	462	499	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.182724971566235	4	FACETS	1	0.971	1			1	CLONAL	4	TRUE	NA	0.249434906641906	4		501	1136	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241679	55241681	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	rs397517086	NA	P-0041053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	223	643	0	ENST00000275493.2:c.2127_2129del	p.Glu709_Thr710delinsAsp	p.E709_T710delinsD	ENST00000275493	NM_005228.3	709	gaAACt/gat	18/28	0.199283215146047	4	FACETS	0.861	0.803	0.921	0.861	0.803	0.921	CLONAL	3	TRUE	1	0.249434906641906	4		643	865	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894898	101894898	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	32	240	0	ENST00000374994.4:c.451C>A	p.Arg151Ser	p.R151S	ENST00000374994	NM_004612.2	151	Cgc/Agc	3/9	1	2	FACETS	0.894	0.728	1	0.894	0.728	1	CLONAL	1	TRUE	1	0.249434906641906	2		240	287	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0041057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	28	264	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.938	0.75	1	0.938	0.75	1	CLONAL	1	TRUE	1	0.15	2		264	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0041057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	67	732	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	1	2	FACETS	0.969	0.84	1	0.969	0.84	1	CLONAL	1	TRUE	1	0.15	2		732	922	SUCCESS
EED	8726	MSKCC	GRCh37	11	85956278	85956278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	18	202	0	ENST00000263360.6:c.7G>A	p.Glu3Lys	p.E3K	ENST00000263360	NM_003797.3	3	Gag/Aag	1/12	1	2	FACETS	0.721	0.542	0.932	0.721	0.542	0.932	CLONAL	1	TRUE	1	0.15	2		202	333	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50830261	50830261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	56	385	0	ENST00000398568.2:c.2704C>T	p.Gln902Ter	p.Q902*	ENST00000398568	NM_001042412.1	902	Caa/Taa	18/18	0.127057699962142	4	FACETS	1	0.961	1	0.692	0.593	0.802	CLONAL	1	TRUE	2	0.15	4		385	620	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974676	21974676	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0041057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	44	405	0	ENST00000304494.5:c.150+1G>A		p.X50_splice	ENST00000304494	NM_000077.4	50			0.123250029748002	0	FACETS	0.866	0.725	1			1	CLONAL	1	TRUE	0	0.15	0		405	576	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427912	49427912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	68	600	0	ENST00000301067.7:c.10678G>A	p.Asp3560Asn	p.D3560N	ENST00000301067	NM_003482.3	3560	Gat/Aat	38/54	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.15	2		600	863	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445944	49445944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	76	1012	1	ENST00000301067.7:c.1522G>A	p.Glu508Lys	p.E508K	ENST00000301067	NM_003482.3	508	Gaa/Aaa	10/54	1	2	FACETS	0.835	0.73	0.95	0.835	0.73	0.95	CLONAL	1	TRUE	1	0.15	2		1013	1213	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719535	61719535	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	29	434	0	ENST00000401558.2:c.1648C>G	p.Gln550Glu	p.Q550E	ENST00000401558	NM_003400.3	550	Caa/Gaa	15/25	1	2	FACETS	0.667	0.534	0.819	0.667	0.534	0.819	SUBCLONAL	1	TRUE	1	0.15	2		434	580	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045649	26045649	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	16	200	0	ENST00000540144.1:c.11C>G	p.Thr4Arg	p.T4R	ENST00000540144	NM_003531.2	4	aCg/aGg	1/1	0.155460138982106	3	FACETS	0.783	0.578	1			1	CLONAL	1	TRUE	NA	0.15	3		200	293	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0041066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	116	506	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.308013203465197	2		506	717	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665110	29665110	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658541	NA	P-0041066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	116	416	0	ENST00000356175.3:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000356175	NM_000267.3	2237	Cga/Tga	44/57	1	2	FACETS	0.9	0.811	0.994	0.9	0.811	0.994	CLONAL	1	TRUE	1	0.308013203465197	2		416	837	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027732	152027732	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	136	653	1	ENST00000262189.6:c.343G>T	p.Glu115Ter	p.E115*	ENST00000262189	NM_170606.2	115	Gaa/Taa	3/59	0.141600992379513	3	FACETS	1	0.918	1	0.337	0.306	0.37	INDETERMINATE	1	TRUE	0	0.308013203465197	3		654	1007	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0041066-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	145	506	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.396886859909194	2		506	723	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665110	29665110	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658541	NA	P-0041066-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	103	416	0	ENST00000356175.3:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000356175	NM_000267.3	2237	Cga/Tga	44/57	1	2	FACETS	0.678	0.606	0.753	0.678	0.606	0.753	SUBCLONAL	1	TRUE	1	0.396886859909194	2		416	766	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027732	152027732	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041066-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	164	653	1	ENST00000262189.6:c.343G>T	p.Glu115Ter	p.E115*	ENST00000262189	NM_170606.2	115	Gaa/Taa	3/59	0.275619969984787	3	FACETS	0.939	0.861	1	0.313	0.287	0.34	CLONAL	1	TRUE	0	0.396886859909194	3		654	1055	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487891	56487891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759562930	NA	P-0041074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	111	596	1	ENST00000267101.3:c.1622G>A	p.Arg541Gln	p.R541Q	ENST00000267101	NM_001982.3	541	cGa/cAa	14/28	1	2	FACETS	0.666	0.601	0.734	0.666	0.601	0.734	SUBCLONAL	1	TRUE	1	0.640868635883772	2		597	520	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62323153	62323155	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs1568715177	NA	P-0041074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	74	628	0	ENST00000360203.5:c.2619_2621del	p.Gly874del	p.G874del	ENST00000360203	NM_001283009.1	872	cGAGga/cga	28/35	0.517837023853077	3	FACETS	0.507	0.444	0.575	0.254	0.222	0.288	SUBCLONAL	1	TRUE	1	0.640868635883772	3		628	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577541	7577541	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201762	NA	P-0041128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	381	495	0	ENST00000269305.4:c.740A>T	p.Asn247Ile	p.N247I	ENST00000269305	NM_001126112.2	247	aAc/aTc	7/11	0.30646377440473	2	FACETS	1	0.992	1	1	0.996	1	CLONAL	3	TRUE	0	0.30646377440473	2		495	722	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067899	30067899	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315498	NA	P-0041128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	129	538	0	ENST00000338641.4:c.1084C>T	p.Gln362Ter	p.Q362*	ENST00000338641	NM_000268.3	362	Cag/Tag	11/16	0.30646377440473	2	FACETS	1	0.973	1	0.592	0.537	0.649	CLONAL	1	TRUE	0	0.30646377440473	2		538	711	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888722	76888725	+	frameshift_variant	Frame_Shift_Del	DEL	TTTC	TTTC	-	novel	NA	P-0041128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	95	458	0	ENST00000373344.5:c.5104_5107del	p.Glu1702TyrfsTer22	p.E1702Yfs*22	ENST00000373344	NM_000489.3	1702	GAAAta/ta	19/35	0.30646377440473	3	FACETS	1	0.976	1	0.676	0.603	0.752	CLONAL	1	TRUE	1	0.30646377440473	3		458	529	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582821	95582821	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs993582806	NA	P-0041128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	36	231	1	ENST00000393063.1:c.1721A>G	p.Glu574Gly	p.E574G	ENST00000393063	NM_030621.3	574	gAa/gGa	11/28	0.223179396597154	5	FACETS	0.895	0.737	1	0.298	0.245	0.358	CLONAL	1	TRUE	2	0.30646377440473	5		232	383	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117790	70117790	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	135	592	0	ENST00000245479.2:c.258G>C	p.Trp86Cys	p.W86C	ENST00000245479	NM_000346.3	86	tgG/tgC	1/3	0.30646377440473	8	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.30646377440473	8		592	1166	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0041152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	28	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.75	0.598	0.925	0.75	0.598	0.925	CLONAL	1	TRUE	1	0.13	2		452	574	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100998	41100998	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772057709	NA	P-0041152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	54	762	0	ENST00000373198.4:c.1358G>A	p.Arg453His	p.R453H	ENST00000373198	NM_133170.3	453	cGc/cAc	8/32	1	2	FACETS	0.981	0.836	1	0.981	0.836	1	CLONAL	1	TRUE	1	0.13	2		762	847	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577557	7577557	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519982	NA	P-0041152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	52	748	2	ENST00000269305.4:c.724T>C	p.Cys242Arg	p.C242R	ENST00000269305	NM_001126112.2	242	Tgc/Cgc	7/11	1	2	FACETS	0.973	0.826	1	0.973	0.826	1	CLONAL	1	TRUE	1	0.13	2		750	822	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0041206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	75	346	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.2	2		346	576	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038828	47038828	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	233	443	0	ENST00000377604.3:c.835C>T	p.Gln279Ter	p.Q279*	ENST00000377604	NM_001204468.1	279	Cag/Tag	9/24	0.265012852340506	2	FACETS	1	0.972	1			1	CLONAL	4	TRUE	NA	0.2	2		443	552	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443910	18443910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	17	353	1	ENST00000266497.5:c.883G>A	p.Asp295Asn	p.D295N	ENST00000266497		295	Gat/Aat	3/31	1	2	FACETS	0.57	0.425	0.743	0.57	0.425	0.743	SUBCLONAL	1	TRUE	1	0.2	2		354	298	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164750	47164751	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	119	364	0	ENST00000409792.3:c.1375dup	p.Ser459PhefsTer2	p.S459Ffs*2	ENST00000409792	NM_014159.6	459	tct/tTct	3/21	0.257742050572344	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.2	2		364	490	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356124	70356153	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGAGCAGGGTCTACAGGTTTCCACCAAACA	GGAGCAGGGTCTACAGGTTTCCACCAAACA	-	novel	NA	P-0041206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	149	400	0	ENST00000374080.3:c.5026-6_5049del		p.X1676_splice	ENST00000374080		1676		37/45	1	1	FACETS	0.947	0.872	1	1	0.993	1	CLONAL	3	TRUE	0	0.2	1		400	472	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928340	69928340	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	43	426	0	ENST00000352241.4:c.160A>G	p.Thr54Ala	p.T54A	ENST00000352241	NM_198159.2	54	Aca/Gca	2/10	1	2	FACETS	0.619	0.517	0.732	0.619	0.517	0.732	SUBCLONAL	1	TRUE	1	0.22	2		426	632	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189389	56189389	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	47	544	0	ENST00000399503.3:c.4421C>G	p.Pro1474Arg	p.P1474R	ENST00000399503	NM_005921.1	1474	cCt/cGt	20/20	1	2	FACETS	0.553	0.466	0.651	0.553	0.466	0.651	SUBCLONAL	1	TRUE	1	0.22	2		544	772	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739335	46739335	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748191191	NA	P-0041218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	38	542	0	ENST00000371975.4:c.1526G>A	p.Arg509Gln	p.R509Q	ENST00000371975	NM_003579.3	509	cGa/cAa	14/18	0.240966450913962	3	FACETS	0.541	0.446	0.648	0.271	0.223	0.324	SUBCLONAL	1	FALSE	1	0.240966450913962	3		542	653	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173696	108173697	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0041218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	68	472	0	ENST00000278616.4:c.5436_5437insG	p.Phe1813ValfsTer10	p.F1813Vfs*10	ENST00000278616	NM_000051.3	1812	-/G	36/63	0.240966450913962	3	FACETS	0.758	0.662	0.861	0.758	0.662	0.861	SUBCLONAL	2	FALSE	1	0.240966450913962	3		472	417	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444165	49444165	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	49	853	0	ENST00000301067.7:c.3206A>T	p.Glu1069Val	p.E1069V	ENST00000301067	NM_003482.3	1069	gAg/gTg	11/54	0.240966450913962	4	FACETS	0.544	0.459	0.638	0.181	0.153	0.213	SUBCLONAL	1	FALSE	1	0.240966450913962	4		853	928	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26978166	26978166	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	91	639	1	ENST00000381527.3:c.1343C>T	p.Ser448Leu	p.S448L	ENST00000381527	NM_001260.1	448	tCa/tTa	13/13	0.240966450913962	4	FACETS	1	0.97	1	0.427	0.379	0.479	CLONAL	1	FALSE	1	0.240966450913962	4		640	731	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	364672	364672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	180	699	1	ENST00000262320.3:c.890G>A	p.Trp297Ter	p.W297*	ENST00000262320	NM_003502.3	297	tGg/tAg	3/11	0.184652427563972	3	FACETS	1	0.979	1			1	CLONAL	2	FALSE	NA	0.240966450913962	3		700	720	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795346	39795346	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	240	576	0	ENST00000288319.7:c.374T>G	p.Val125Gly	p.V125G	ENST00000288319	NM_182918.3	125	gTt/gGt	3/10	0.240966450913962	6	FACETS	0.907	0.849	0.966			1	CLONAL	4	FALSE	NA	0.240966450913962	6		576	814	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293776	1293776	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	51	812	0	ENST00000310581.5:c.1225C>G	p.Leu409Val	p.L409V	ENST00000310581	NM_198253.2	409	Ctc/Gtc	2/16	0.240966450913962	4	FACETS	0.562	0.476	0.657	0.281	0.238	0.329	SUBCLONAL	1	FALSE	2	0.240966450913962	4		812	935	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163782	152163782	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	40	557	0	ENST00000206249.3:c.503C>G	p.Thr168Ser	p.T168S	ENST00000206249	NM_000125.3	168	aCc/aGc	2/8	0.240966450913962	3	FACETS	0.603	0.5	0.718			1	SUBCLONAL	1	FALSE	NA	0.240966450913962	3		557	617	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876974	151876974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750213944	NA	P-0041218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	49	484	0	ENST00000262189.6:c.7387C>T	p.Arg2463Cys	p.R2463C	ENST00000262189	NM_170606.2	2463	Cgt/Tgt	37/59	0.240966450913962	4	FACETS	1	0.857	1	0.506	0.428	0.591	CLONAL	1	FALSE	2	0.240966450913962	4		484	499	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006002	22006002	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	153	769	0	ENST00000276925.6:c.401C>A	p.Thr134Lys	p.T134K	ENST00000276925	NM_004936.3	134	aCa/aAa	2/2	0.240966450913962	6	FACETS	0.843	0.77	0.92			1	CLONAL	2	FALSE	NA	0.240966450913962	6		769	1116	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390791	139390791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375025242	NA	P-0041218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	87	752	2	ENST00000277541.6:c.7400C>T	p.Ser2467Leu	p.S2467L	ENST00000277541	NM_017617.3	2467	tCg/tTg	34/34	0.240966450913962	4	FACETS	0.933	0.825	1	0.467	0.412	0.525	CLONAL	1	FALSE	2	0.240966450913962	4		754	960	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0041247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	206	641	0	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	0.317903103709751	2	FACETS	0.898	0.838	0.959	0.898	0.838	0.959	CLONAL	2	TRUE	0	0.370661207061611	2		641	619	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0041247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	177	369	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.370661207061611	4	FACETS	0.841	0.781	0.902	0.841	0.781	0.902	CLONAL	3	TRUE	1	0.370661207061611	4		369	519	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027249	49027249	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0041247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	33	336	0	ENST00000267163.4:c.1814+2T>C		p.X605_splice	ENST00000267163	NM_000321.2	605			0.317903103709751	2	FACETS	0.989	0.814	1	0.495	0.407	0.591	CLONAL	1	TRUE	0	0.370661207061611	2		336	180	SUCCESS
APC	324	MSKCC	GRCh37	5	112179531	112179531	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774747249	NA	P-0041247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	44	367	0	ENST00000257430.4:c.8240C>T	p.Pro2747Leu	p.P2747L	ENST00000257430	NM_000038.5	2747	cCt/cTt	16/16	0.370661207061611	3	FACETS	0.793	0.667	0.931	0.396	0.333	0.466	CLONAL	1	TRUE	1	0.370661207061611	3		367	355	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	87	320	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.983	0.881	1	0.983	0.881	1	CLONAL	1	TRUE	1	0.63	2		321	281	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0041248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	110	304	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.63	2		304	347	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701185	43701185	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	191	493	0	ENST00000382044.4:c.5510A>T	p.His1837Leu	p.H1837L	ENST00000382044	NM_001141980.1	1837	cAt/cTt	26/28	1	2	FACETS	0.947	0.88	1	0.947	0.88	1	CLONAL	1	TRUE	1	0.63	2		493	640	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629841	187629841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	46	627	0	ENST00000441802.2:c.1141C>T	p.Pro381Ser	p.P381S	ENST00000441802	NM_005245.3	381	Cct/Tct	2/27	1	2	FACETS	0.227	0.19	0.267	0.227	0.19	0.267	SUBCLONAL	1	TRUE	1	0.63	2		627	644	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	150	320	1				ENST00000310581	NM_198253.2	-/1132			0.256390836633222	1	FACETS	0.817	0.752	0.883	0.817	0.752	0.883	INDETERMINATE	1	TRUE	0	0.546974948647352	1		321	488	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0041248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	171	506	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.893	0.824	0.965	0.893	0.824	0.965	CLONAL	1	TRUE	1	0.546974948647352	2		506	700	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0041248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	137	304	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.211976895444133	1	FACETS	0.807	0.74	0.876	0.807	0.74	0.876	INDETERMINATE	1	TRUE	0	0.546974948647352	1		304	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0041248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	378	781	0	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	0.526377881971631	2	FACETS	0.863	0.824	0.901	0.863	0.824	0.901	CLONAL	2	TRUE	0	0.546974948647352	2		781	801	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701185	43701185	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	178	493	0	ENST00000382044.4:c.5510A>T	p.His1837Leu	p.H1837L	ENST00000382044	NM_001141980.1	1837	cAt/cTt	26/28	1	2	FACETS	0.872	0.806	0.941	0.872	0.806	0.941	CLONAL	1	TRUE	1	0.546974948647352	2		493	746	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830412	72830412	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	277	350	0	ENST00000268489.5:c.6169C>T	p.Gln2057Ter	p.Q2057*	ENST00000268489	NM_006885.3	2057	Cag/Tag	9/10	0.546974948647352	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.546974948647352	3		350	600	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010443	48010443	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	195	492	0	ENST00000234420.5:c.71C>G	p.Ser24Trp	p.S24W	ENST00000234420	NM_000179.2	24	tCg/tGg	1/10	0.211976895444133	1	FACETS	0.779	0.724	0.835	0.779	0.724	0.835	INDETERMINATE	1	TRUE	0	0.546974948647352	1		492	665	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161807885	161807885	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	139	364	0	ENST00000366898.1:c.1108G>T	p.Glu370Ter	p.E370*	ENST00000366898	NM_004562.2	370	Gaa/Taa	10/12	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.546974948647352	2		364	489	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372532	55372532	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	327	803	0	ENST00000297316.4:c.1222T>G	p.Tyr408Asp	p.Y408D	ENST00000297316	NM_022454.3	408	Tac/Gac	2/2	1	2	FACETS	0.984	0.929	1	0.984	0.929	1	CLONAL	1	TRUE	1	0.546974948647352	2		803	1215	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998393	100998394	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0041250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	34	128	1	ENST00000325455.5:c.1408_1409delinsAA	p.Pro470Asn	p.P470N	ENST00000325455	NM_001202474.3	470	CCc/AAc	1/8	0.185588441368781	3	FACETS	1	0.889	1	0.556	0.458	0.665	INDETERMINATE	1	TRUE	1	0.326163637442772	3		129	218	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578522	7578522	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs758781593	NA	P-0041250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	183	709	0	ENST00000269305.4:c.408A>T	p.Gln136His	p.Q136H	ENST00000269305	NM_001126112.2	136	caA/caT	5/11	0.288342301204111	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.326163637442772	1		709	817	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266748	18266748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs929809973	NA	P-0041250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	47	463	0	ENST00000222254.8:c.59C>T	p.Pro20Leu	p.P20L	ENST00000222254	NM_005027.3	20	cCg/cTg	2/16	1	2	FACETS	0.309	0.259	0.364	0.309	0.259	0.364	SUBCLONAL	1	TRUE	1	0.326163637442772	2		463	933	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762959	40762959	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs387906659	NA	P-0041250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	126	459	0	ENST00000392038.2:c.49G>A	p.Glu17Lys	p.E17K	ENST00000392038	NM_001626.4	17	Gaa/Aaa	3/14	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.326163637442772	2		459	547	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951962	178951962	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	35	452	0	ENST00000263967.3:c.3017T>G	p.Leu1006Arg	p.L1006R	ENST00000263967	NM_006218.2	1006	cTt/cGt	21/21	0.287637970084449	4	FACETS	0.995	0.819	1	0.498	0.409	0.596	CLONAL	1	TRUE	2	0.326163637442772	4		452	286	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565871	55565871	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767174569	NA	P-0041250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	30	464	1	ENST00000288135.5:c.695C>T	p.Thr232Met	p.T232M	ENST00000288135	NM_000222.2	232	aCg/aTg	4/21	1	2	FACETS	0.554	0.447	0.675	0.554	0.447	0.675	SUBCLONAL	1	TRUE	1	0.326163637442772	2		465	332	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997760	149997760	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	198	428	0	ENST00000253339.5:c.2707C>T	p.Gln903Ter	p.Q903*	ENST00000253339		903	Cag/Tag	5/7	0.251579439461142	3	FACETS	1	0.983	1	0.783	0.73	0.838	CLONAL	2	TRUE	0	0.326163637442772	3		428	601	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938361	76938361	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	24	550	0	ENST00000373344.5:c.2387A>G	p.Lys796Arg	p.K796R	ENST00000373344	NM_000489.3	796	aAa/aGa	9/35	0.244468208716767	0	FACETS	0.519	0.41	0.644			1	SUBCLONAL	1	TRUE	0	0.326163637442772	0		550	191	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938763	76938763	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	17	571	0	ENST00000373344.5:c.1985C>A	p.Thr662Lys	p.T662K	ENST00000373344	NM_000489.3	662	aCa/aAa	9/35	0.244468208716767	0	FACETS	0.265	0.198	0.345			1	SUBCLONAL	1	TRUE	0	0.326163637442772	0		571	265	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414967	78414967	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	74	504	0	ENST00000370768.2:c.1799C>A	p.Pro600Gln	p.P600Q	ENST00000370768	NM_003902.3	600	cCg/cAg	19/20	1	2	FACETS	0.787	0.689	0.893	0.787	0.689	0.893	SUBCLONAL	1	TRUE	1	0.288341843323473	2		504	652	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914604	32914604	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778123	NA	P-0041282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	118	688	0	ENST00000380152.3:c.6112C>T	p.His2038Tyr	p.H2038Y	ENST00000380152		2038	Cat/Tat	11/27	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.288341843323473	2		688	767	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191525	10191528	+	frameshift_variant	Frame_Shift_Del	DEL	AGAA	AGAA	-	novel	NA	P-0041282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	90	586	0	ENST00000256474.2:c.518_521del	p.Glu173ValfsTer28	p.E173Vfs*28	ENST00000256474	NM_000551.3	173	gAGAAt/gt	3/3	0.288341843323473	1	FACETS	0.904	0.803	1	0.904	0.803	1	CLONAL	1	TRUE	0	0.288341843323473	1		586	591	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534299	187534299	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	95	680	0	ENST00000441802.2:c.9427C>G	p.Leu3143Val	p.L3143V	ENST00000441802	NM_005245.3	3143	Ctg/Gtg	13/27	1	2	FACETS	0.927	0.825	1	0.927	0.825	1	CLONAL	1	TRUE	1	0.288341843323473	2		680	711	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278114	41278114	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	61	553	0	ENST00000349496.5:c.1990G>A	p.Glu664Lys	p.E664K	ENST00000349496	NM_001904.3	664	Gag/Aag	13/15	1	2	FACETS	0.818	0.706	0.94	0.818	0.706	0.94	CLONAL	1	TRUE	1	0.278189253307758	2		553	536	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0041284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	140	1073	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.278189253307758	2		1073	835	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487277	56487277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035001455	NA	P-0041284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	150	699	0	ENST00000267101.3:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000267101	NM_001982.3	475	Cgg/Tgg	12/28	0.200619234411935	2	FACETS	0.763	0.698	0.83	0.763	0.698	0.83	SUBCLONAL	2	TRUE	0	0.278189253307758	2		699	707	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928935	44928935	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	93	578	1	ENST00000377967.4:c.2035C>T	p.Gln679Ter	p.Q679*	ENST00000377967	NM_021140.2	679	Cag/Tag	17/29	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.278189253307758	2		579	595	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100115	27100115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	106	751	0	ENST00000324856.7:c.3914del	p.Pro1305HisfsTer176	p.P1305Hfs*176	ENST00000324856	NM_006015.4	1304	gCc/gc	16/20	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.278189253307758	2		751	760	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342573	118342573	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	64	373	0	ENST00000534358.1:c.699C>G	p.Ile233Met	p.I233M	ENST00000534358	NM_005933.3	233	atC/atG	3/36	1	2	FACETS	0.937	0.813	1	0.937	0.813	1	CLONAL	1	TRUE	1	0.278189253307758	2		373	491	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342821	118342821	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	48	437	0	ENST00000534358.1:c.947C>A	p.Ser316Ter	p.S316*	ENST00000534358	NM_005933.3	316	tCg/tAg	3/36	1	2	FACETS	0.731	0.618	0.855	0.731	0.618	0.855	SUBCLONAL	1	TRUE	1	0.278189253307758	2		437	472	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343925	118343925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782402408	NA	P-0041284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	63	497	0	ENST00000534358.1:c.2051C>T	p.Ser684Phe	p.S684F	ENST00000534358	NM_005933.3	684	tCt/tTt	3/36	1	2	FACETS	0.85	0.736	0.973	0.85	0.736	0.973	CLONAL	1	TRUE	1	0.278189253307758	2		497	533	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281774	49281774	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	293	831	0	ENST00000282018.3:c.821G>A	p.Trp274Ter	p.W274*	ENST00000282018	NM_020377.2	274	tGg/tAg	1/1	0.278189253307758	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.278189253307758	3		831	1045	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830776	3830776	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	81	610	0	ENST00000262367.5:c.1780G>T	p.Glu594Ter	p.E594*	ENST00000262367	NM_004380.2	594	Gaa/Taa	8/31	1	2	FACETS	0.89	0.785	1	0.89	0.785	1	CLONAL	1	TRUE	1	0.278189253307758	2		610	654	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40860003	40860003	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	84	764	1	ENST00000428826.2:c.1633G>T	p.Glu545Ter	p.E545*	ENST00000428826		545	Gag/Tag	15/21	1	2	FACETS	0.749	0.661	0.844	0.749	0.661	0.844	SUBCLONAL	1	TRUE	1	0.278189253307758	2		765	806	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092935	29092935	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	96	683	1	ENST00000328354.6:c.1049C>T	p.Pro350Leu	p.P350L	ENST00000328354	NM_007194.3	350	cCa/cTa	10/15	0.278189253307758	1	FACETS	0.966	0.862	1	0.966	0.862	1	CLONAL	1	TRUE	0	0.278189253307758	1		684	615	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278129	41278129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	66	554	0	ENST00000349496.5:c.2005G>A	p.Asp669Asn	p.D669N	ENST00000349496	NM_001904.3	669	Gat/Aat	13/15	1	2	FACETS	0.832	0.723	0.951	0.832	0.723	0.951	CLONAL	1	TRUE	1	0.278189253307758	2		554	570	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933651	49933651	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	105	980	0	ENST00000296474.3:c.2626G>C	p.Glu876Gln	p.E876Q	ENST00000296474	NM_002447.2	876	Gag/Cag	10/20	1	2	FACETS	0.822	0.736	0.915	0.822	0.736	0.915	CLONAL	1	TRUE	1	0.278189253307758	2		980	918	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0041286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	72	434	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.964	0.844	1	0.964	0.844	1	CLONAL	1	TRUE	1	0.29	2		434	515	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0041286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	46	258	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.816	0.688	0.955	0.816	0.688	0.955	CLONAL	1	TRUE	1	0.29	2		258	389	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920422	114920422	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	138	664	0	ENST00000543371.1:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000543371	NM_001198531.1	455	Cga/Tga	13/14	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.29	2		664	859	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729609	41729609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	120	627	0	ENST00000242208.4:c.920G>A	p.Arg307Gln	p.R307Q	ENST00000242208	NM_002192.2	307	cGg/cAg	3/3	0.304313586311827	5	FACETS	1	0.969	1	0.396	0.357	0.437	CLONAL	1	TRUE	2	0.29	5		627	1000	SUCCESS
APC	324	MSKCC	GRCh37	5	112175491	112175492	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0041286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	79	447	0	ENST00000257430.4:c.4201_4202dup	p.Ala1402LeufsTer14	p.A1402Lfs*14	ENST00000257430	NM_000038.5	1400	-/AT	16/16	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.29	2		447	501	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69012043	69012043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	99	610	0	ENST00000288368.4:c.2680G>A	p.Glu894Lys	p.E894K	ENST00000288368	NM_024870.2	894	Gaa/Aaa	23/40	0.286469666385886	3	FACETS	1	0.964	1	0.591	0.528	0.658	CLONAL	1	TRUE	1	0.29	3		610	661	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850696	63850696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	54	372	0	ENST00000279873.7:c.1474G>A	p.Asp492Asn	p.D492N	ENST00000279873	NM_032199.2	492	Gac/Aac	10/10	1	2	FACETS	0.774	0.663	0.896	0.774	0.663	0.896	SUBCLONAL	1	TRUE	1	0.32	2		372	436	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112940005	112940005	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	80	628	1	ENST00000351677.2:c.1657A>G	p.Thr553Ala	p.T553A	ENST00000351677	NM_002834.3	553	Acg/Gcg	14/16	0.0787564377500809	0	FACETS	0.532	0.468	0.6			1	INDETERMINATE	1	TRUE	0	0.32	0		629	639	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432155	121432155	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	59	656	0	ENST00000257555.6:c.902C>G	p.Ala301Gly	p.A301G	ENST00000257555		301	gCt/gGt	4/10	0.0787564377500809	0	FACETS	0.55	0.474	0.632			1	INDETERMINATE	1	TRUE	0	0.32	0		656	456	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988374	41988374	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	67	480	0	ENST00000219905.7:c.1166A>G	p.Tyr389Cys	p.Y389C	ENST00000219905	NM_001164273.1	389	tAt/tGt	3/24	1	2	FACETS	0.733	0.638	0.837	0.733	0.638	0.837	SUBCLONAL	1	TRUE	1	0.32	2		480	571	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396746	396746	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	68	693	0	ENST00000262320.3:c.280G>T	p.Asp94Tyr	p.D94Y	ENST00000262320	NM_003502.3	94	Gat/Tat	2/11	1	2	FACETS	0.805	0.701	0.917	0.805	0.701	0.917	CLONAL	1	TRUE	1	0.32	2		693	528	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548867	29548867	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1555613185	NA	P-0041304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	67	355	0	ENST00000356175.3:c.1642-1G>T		p.X548_splice	ENST00000356175	NM_000267.3	548			1	2	FACETS	0.773	0.672	0.881	0.773	0.672	0.881	SUBCLONAL	1	TRUE	1	0.32	2		355	542	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0041304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	68	538	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.320038677577594	3	FACETS	0.744	0.647	0.849	0.372	0.323	0.425	SUBCLONAL	1	TRUE	1	0.32	3		539	663	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480469	89480469	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	47	336	0	ENST00000336596.2:c.2306G>T	p.Arg769Leu	p.R769L	ENST00000336596	NM_005233.5	769	cGt/cTt	13/17	1	2	FACETS	0.749	0.634	0.876	0.749	0.634	0.876	SUBCLONAL	1	TRUE	1	0.32	2		336	392	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508782	106508782	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	76	550	0	ENST00000359195.3:c.776T>C	p.Met259Thr	p.M259T	ENST00000359195	NM_002649.2	259	aTg/aCg	2/11	1	2	FACETS	0.861	0.756	0.973	0.861	0.756	0.973	CLONAL	1	TRUE	1	0.32	2		550	552	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041046	47041046	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0041304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	73	376	0	ENST00000377604.3:c.1575+1G>A		p.X525_splice	ENST00000377604	NM_001204468.1	525			1	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.32	1		376	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0041316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	827	644	1	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	NA	2	FACETS	1	0.998	1			1	INDETERMINATE	2	TRUE	NA	0.845715753718684	2		645	898	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916733	48916733	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0041316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	64	287	0	ENST00000267163.4:c.265-2A>T		p.X89_splice	ENST00000267163	NM_000321.2	89			0.845715753718684	1	FACETS	0.901	0.821	0.976	0.901	0.821	0.976	CLONAL	1	TRUE	0	0.845715753718684	1		287	97	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491274	2491274	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	363	578	0	ENST00000355716.4:c.317G>T	p.Arg106Leu	p.R106L	ENST00000355716	NM_003820.2	106	cGc/cTc	4/8	NA	2	FACETS	0.783	0.743	0.823			1	INDETERMINATE	1	TRUE	NA	0.845715753718684	2		578	1097	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597871	43597871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	772	731	0	ENST00000355710.3:c.419C>T	p.Pro140Leu	p.P140L	ENST00000355710	NM_020975.4	140	cCa/cTa	3/20	0.845715753718684	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.845715753718684	3		731	1267	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425376	49425376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	683	666	0	ENST00000301067.7:c.13112del	p.Ser4371ThrfsTer13	p.S4371Tfs*13	ENST00000301067	NM_003482.3	4371	aGc/ac	39/54	0.845715753718684	3	FACETS	1	0.991	1	0.698	0.678	0.717	CLONAL	2	TRUE	0	0.845715753718684	3		666	1098	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881472	48881472	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	56	237	0	ENST00000267163.4:c.194A>C	p.Lys65Thr	p.K65T	ENST00000267163	NM_000321.2	65	aAg/aCg	2/27	0.845715753718684	1	FACETS	0.944	0.858	1	0.944	0.858	1	CLONAL	1	TRUE	0	0.845715753718684	1		237	81	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527711	103527711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	189	276	0	ENST00000355739.4:c.3019G>A	p.Ala1007Thr	p.A1007T	ENST00000355739	NM_000123.3	1007	Gct/Act	15/15	0.845715753718684	2	FACETS	0.951	0.913	0.986	0.951	0.913	0.986	CLONAL	2	TRUE	0	0.845715753718684	2		276	235	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112528	2112528	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	583	697	3	ENST00000219476.3:c.1288A>G	p.Arg430Gly	p.R430G	ENST00000219476	NM_000548.3	430	Aga/Gga	13/42	0.845715753718684	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.845715753718684	3		700	952	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858360	9858360	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	197	397	0	ENST00000330684.3:c.3041G>T	p.Trp1014Leu	p.W1014L	ENST00000330684	NM_001134407.1	1014	tGg/tTg	13/13	0.845715753718684	3	FACETS	1	0.987	1	0.625	0.584	0.668	CLONAL	1	TRUE	1	0.845715753718684	3		397	530	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857418	68857418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs550612843	NA	P-0041316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	236	473	0	ENST00000261769.5:c.2053G>A	p.Val685Met	p.V685M	ENST00000261769	NM_004360.3	685	Gtg/Atg	13/16	0.845715753718684	3	FACETS	1	0.936	1	0.5	0.468	0.533	CLONAL	1	TRUE	1	0.845715753718684	3		473	794	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724594	724594	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	171	439	0	ENST00000314574.4:c.1462G>T	p.Gly488Ter	p.G488*	ENST00000314574	NM_005433.3	488	Gga/Tga	12/12	0.707625054680535	3	FACETS	0.908	0.838	0.979			1	CLONAL	1	TRUE	NA	0.845715753718684	3		439	634	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240267	5240268	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0041316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1314	379	715	2	ENST00000357368.4:c.1646_1647delinsTT	p.Arg549Leu	p.R549L	ENST00000357368	NM_002850.3	549	cGG/cTT	12/38	0.845715753718684	4	FACETS	0.977	0.925	1	0.326	0.308	0.344	CLONAL	1	TRUE	1	0.845715753718684	4		717	1693	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288430	15288430	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	90	479	0	ENST00000263388.2:c.4309T>C	p.Phe1437Leu	p.F1437L	ENST00000263388	NM_000435.2	1437	Ttc/Ctc	24/33	0.845715753718684	4	FACETS	0.97	0.866	1	0.323	0.288	0.36	CLONAL	1	TRUE	1	0.845715753718684	4		479	405	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965229	25965229	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	179	494	0	ENST00000435504.4:c.3977G>C	p.Ser1326Thr	p.S1326T	ENST00000435504		1326	aGc/aCc	13/13	1	2	FACETS	0.945	0.88	1	0.945	0.88	1	CLONAL	1	TRUE	1	0.845715753718684	2		494	448	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535420	187535420	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	266	402	0	ENST00000441802.2:c.9154A>T	p.Ile3052Phe	p.I3052F	ENST00000441802	NM_005245.3	3052	Atc/Ttc	12/27	0.845715753718684	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.845715753718684	2		402	314	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294684	1294685	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0041316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	159	376	0	ENST00000310581.5:c.316_317delinsTT	p.Gly106Leu	p.G106L	ENST00000310581	NM_198253.2	106	GGg/TTg	2/16	0.845715753718684	6	FACETS	0.812	0.743	0.885	0.203	0.185	0.222	CLONAL	1	TRUE	2	0.845715753718684	6		376	1246	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417503	139417503	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	655	712	0	ENST00000277541.6:c.541G>T	p.Glu181Ter	p.E181*	ENST00000277541	NM_017617.3	181	Gag/Tag	4/34	0.63519121975505	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	2	0.845715753718684	4		712	1340	SUCCESS
AR	367	MSKCC	GRCh37	X	66765473	66765473	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	311	698	0	ENST00000374690.3:c.485C>G	p.Ser162Cys	p.S162C	ENST00000374690	NM_000044.3	162	tCc/tGc	1/8	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.845715753718684	2		698	694	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348487	70348487	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	161	435	1	ENST00000374080.3:c.3394G>T	p.Val1132Phe	p.V1132F	ENST00000374080		1132	Gtt/Ttt	24/45	NA	2	FACETS	0.84	0.778	0.904			1	INDETERMINATE	1	TRUE	NA	0.845715753718684	2		436	453	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356131	70356131	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	319	562	0	ENST00000374080.3:c.5026G>T	p.Gly1676Cys	p.G1676C	ENST00000374080		1676	Ggt/Tgt	37/45	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.845715753718684	2		562	671	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0041325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	82	544	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	1	2	FACETS	0.574	0.506	0.648	0.574	0.506	0.648	SUBCLONAL	1	TRUE	1	0.37	2		544	772	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	48	491	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	1	2	FACETS	0.347	0.293	0.408	0.347	0.293	0.408	SUBCLONAL	1	TRUE	1	0.37	2		491	747	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182641	38182641	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs387907272	NA	P-0041325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	27	325	0	ENST00000396334.3:c.794T>C	p.Leu265Pro	p.L265P	ENST00000396334	NM_002468.4	265	cTg/cCg	5/5	1	2	FACETS	0.387	0.308	0.478	0.387	0.308	0.478	SUBCLONAL	1	TRUE	1	0.37	2		325	377	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992223	11992223	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	27	331	0	ENST00000396373.4:c.313C>G	p.Arg105Gly	p.R105G	ENST00000396373	NM_001987.4	105	Cga/Gga	3/8	0.158635273968783	3	FACETS	0.321	0.255	0.398	0.161	0.127	0.199	INDETERMINATE	1	TRUE	1	0.37	3		331	538	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152050	11152053	+	frameshift_variant	Frame_Shift_Del	DEL	GCAA	GCAA	-	novel	NA	P-0041325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	77	541	0	ENST00000358026.2:c.4336_4339del	p.Lys1446GlufsTer48	p.K1446Efs*48	ENST00000358026	NM_001128849.1	1445	cGCAAg/cg	31/36	1	2	FACETS	0.536	0.47	0.607	0.536	0.47	0.607	SUBCLONAL	1	TRUE	1	0.37	2		541	777	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216187	36216187	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs750568281	NA	P-0041325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	108	626	0	ENST00000222270.7:c.3595G>T	p.Gly1199Cys	p.G1199C	ENST00000222270	NM_014727.1	1199	Ggc/Tgc	11/37	1	2	FACETS	0.646	0.579	0.717	0.646	0.579	0.717	SUBCLONAL	1	TRUE	1	0.37	2		626	904	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812299	212812299	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	21	273	0	ENST00000342788.4:c.277C>G	p.Gln93Glu	p.Q93E	ENST00000342788	NM_005235.2	93	Cag/Gag	3/28	1	2	FACETS	0.333	0.256	0.423	0.333	0.256	0.423	SUBCLONAL	1	TRUE	1	0.37	2		273	341	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	20	776	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.141	0.107	0.181	0.141	0.107	0.181	SUBCLONAL	1	TRUE	1	0.38	2		777	746	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188823	32188823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs8192585	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	121	688	0	ENST00000375023.3:c.731C>T	p.Ser244Leu	p.S244L	ENST00000375023	NM_004557.3	244	tCg/tTg	4/30	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.38	2		688	567	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	130	359	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.38	2		359	617	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103513972	103513972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61749896	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	65	279	0	ENST00000355739.4:c.788G>A	p.Arg263Gln	p.R263Q	ENST00000355739	NM_000123.3	263	cGa/cAa	7/15	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.38	2		279	342	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522598	157522598	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554236040	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	157	520	0	ENST00000346085.5:c.4870C>T	p.Arg1624Ter	p.R1624*	ENST00000346085	NM_020732.3	1624	Cga/Tga	18/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.38	2		520	753	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788617	3788617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519884	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	88	359	0	ENST00000262367.5:c.4337G>A	p.Arg1446His	p.R1446H	ENST00000262367	NM_004380.2	1446	cGc/cAc	26/31	1	2	FACETS	0.957	0.851	1	0.957	0.851	1	CLONAL	1	TRUE	1	0.38	2		359	484	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	88	314	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.955	0.849	1	0.955	0.849	1	CLONAL	1	TRUE	1	0.38	2		314	485	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518099	8518099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764400127	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	59	368	1	ENST00000356435.5:c.1292C>T	p.Ser431Leu	p.S431L	ENST00000356435		431	tCg/tTg	10/35	1	2	FACETS	0.944	0.817	1	0.944	0.817	1	CLONAL	1	TRUE	1	0.38	2		369	329	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256942	16256942	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	101	464	0	ENST00000375759.3:c.4207C>T	p.Arg1403Ter	p.R1403*	ENST00000375759	NM_015001.2	1403	Cga/Tga	11/15	1	2	FACETS	0.886	0.794	0.984	0.886	0.794	0.984	CLONAL	1	TRUE	1	0.38	2		464	600	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720870	89720870	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1554825652	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	87	207	0	ENST00000371953.3:c.1021T>G	p.Phe341Val	p.F341V	ENST00000371953	NM_000314.4	341	Ttt/Gtt	8/9	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.38	2		207	427	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	135	478	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.38	2		478	537	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916248	9916248	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397518472	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	55	329	2	ENST00000330684.3:c.2041C>T	p.Arg681Ter	p.R681*	ENST00000330684	NM_001134407.1	681	Cga/Tga	10/13	1	2	FACETS	0.691	0.592	0.798	0.691	0.592	0.798	SUBCLONAL	1	TRUE	1	0.38	2		331	419	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857197	9857197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866121846	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	72	454	0	ENST00000330684.3:c.4204C>T	p.Arg1402Trp	p.R1402W	ENST00000330684	NM_001134407.1	1402	Cgg/Tgg	13/13	1	2	FACETS	0.806	0.706	0.913	0.806	0.706	0.913	CLONAL	1	TRUE	1	0.38	2		454	470	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800978	243800978	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	64	297	0	ENST00000263826.5:c.496C>T	p.Arg166Ter	p.R166*	ENST00000263826	NM_005465.4	166	Cga/Tga	5/13	1	2	FACETS	0.723	0.627	0.826	0.723	0.627	0.826	SUBCLONAL	1	TRUE	1	0.38	2		297	466	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606679	29606679	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs865931787	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	80	501	0	ENST00000389048.3:c.1201C>T	p.Arg401Ter	p.R401*	ENST00000389048	NM_004304.4	401	Cga/Tga	5/29	1	2	FACETS	0.773	0.681	0.87	0.773	0.681	0.87	SUBCLONAL	1	TRUE	1	0.38	2		501	545	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509723	106509723	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	87	438	0	ENST00000359195.3:c.1717G>T	p.Glu573Ter	p.E573*	ENST00000359195	NM_002649.2	573	Gaa/Taa	2/11	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.38	2		438	456	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102874103	102874103	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	36	154	0	ENST00000307046.8:c.57C>A	p.Phe19Leu	p.F19L	ENST00000307046	NM_001111285.1	19	ttC/ttA	1/4	1	2	FACETS	0.583	0.48	0.697	0.583	0.48	0.697	SUBCLONAL	1	TRUE	1	0.38	2		154	325	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311662	30311662	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	80	277	0	ENST00000262643.3:c.516C>A	p.Phe172Leu	p.F172L	ENST00000262643	NM_001238.2	172	ttC/ttA	7/12	1	2	FACETS	0.883	0.78	0.993	0.883	0.78	0.993	CLONAL	1	TRUE	1	0.38	2		277	477	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539951	187539951	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs777631605	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	52	375	0	ENST00000441802.2:c.7789C>T	p.Arg2597Ter	p.R2597*	ENST00000441802	NM_005245.3	2597	Cga/Tga	10/27	1	2	FACETS	0.715	0.61	0.828	0.715	0.61	0.828	SUBCLONAL	1	TRUE	1	0.38	2		375	383	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342967	225342967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	68	337	0	ENST00000264414.4:c.2125C>T	p.Arg709Trp	p.R709W	ENST00000264414	NM_003590.4	709	Cgg/Tgg	15/16	1	2	FACETS	0.741	0.646	0.843	0.741	0.646	0.843	SUBCLONAL	1	TRUE	1	0.38	2		337	483	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120219	94120219	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs2278106	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	31	179	0	ENST00000369303.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000369303	NM_004440.3	278	Ccc/Tcc	3/17	1	2	FACETS	0.709	0.577	0.857	0.709	0.577	0.857	SUBCLONAL	1	TRUE	1	0.38	2		179	230	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10257072	10257072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	120	588	1	ENST00000340748.4:c.2801G>A	p.Arg934Gln	p.R934Q	ENST00000340748		934	cGa/cAa	27/40	1	2	FACETS	0.981	0.888	1	0.981	0.888	1	CLONAL	1	TRUE	1	0.38	2		589	644	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430668	80430668	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	65	307	0	ENST00000286548.4:c.340C>T	p.Arg114Ter	p.R114*	ENST00000286548	NM_002072.3	114	Cga/Tga	3/7	1	2	FACETS	0.822	0.716	0.937	0.822	0.716	0.937	CLONAL	1	TRUE	1	0.38	2		307	416	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281484	142281484	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	107	413	0	ENST00000350721.4:c.760G>T	p.Glu254Ter	p.E254*	ENST00000350721	NM_001184.3	254	Gaa/Taa	4/47	1	2	FACETS	0.964	0.867	1	0.964	0.867	1	CLONAL	1	TRUE	1	0.38	2		413	584	SUCCESS
APC	324	MSKCC	GRCh37	5	112177901	112177901	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs752654519	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	62	221	0	ENST00000257430.4:c.6610C>T	p.Arg2204Ter	p.R2204*	ENST00000257430	NM_000038.5	2204	Cga/Tga	16/16	1	2	FACETS	0.93	0.808	1	0.93	0.808	1	CLONAL	1	TRUE	1	0.38	2		221	351	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	49	236	1	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.899	0.766	1	0.899	0.766	1	CLONAL	1	TRUE	1	0.38	2		237	287	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068387	26068387	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	64	221	0	ENST00000435504.4:c.103C>A	p.Leu35Ile	p.L35I	ENST00000435504		35	Ctt/Att	2/13	1	2	FACETS	0.723	0.627	0.826	0.723	0.627	0.826	SUBCLONAL	1	TRUE	1	0.38	2		221	466	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103510743	103510743	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	20	229	0	ENST00000355739.4:c.647G>T	p.Arg216Ile	p.R216I	ENST00000355739	NM_000123.3	216	aGa/aTa	6/15	1	2	FACETS	0.301	0.229	0.384	0.301	0.229	0.384	SUBCLONAL	1	TRUE	1	0.38	2		229	350	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609467	81609467	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	75	367	1	ENST00000298171.2:c.1065C>A	p.Phe355Leu	p.F355L	ENST00000298171	NM_000369.2	355	ttC/ttA	10/10	1	2	FACETS	0.975	0.858	1	0.975	0.858	1	CLONAL	1	TRUE	1	0.38	2		368	405	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485115	57485115	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754097818	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	54	352	1	ENST00000371085.3:c.949C>T	p.Arg317Cys	p.R317C	ENST00000371085	NM_000516.4	317	Cgc/Tgc	11/13	1	2	FACETS	0.785	0.673	0.906	0.785	0.673	0.906	CLONAL	1	TRUE	1	0.38	2		353	362	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582439	119582439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775606264	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	43	179	0	ENST00000316626.5:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000316626		321	cGa/cAa	10/12	1	2	FACETS	0.939	0.792	1	0.939	0.792	1	CLONAL	1	TRUE	1	0.38	2		179	241	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674233	86674233	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1463885690	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	43	229	0	ENST00000274376.6:c.2365C>T	p.Arg789Ter	p.R789*	ENST00000274376	NM_002890.2	789	Cga/Tga	18/25	1	2	FACETS	0.77	0.647	0.904	0.77	0.647	0.904	CLONAL	1	TRUE	1	0.38	2		229	294	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522568	106522568	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs754441790	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	68	236	0	ENST00000359195.3:c.2545C>T	p.Arg849Ter	p.R849*	ENST00000359195	NM_002649.2	849	Cga/Tga	7/11	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.38	2		236	328	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412094	63412094	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374751715	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	145	774	0	ENST00000330258.3:c.1073G>A	p.Arg358Gln	p.R358Q	ENST00000330258	NM_152424.3	358	cGa/cAa	2/2	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.38	2		774	756	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	80	326	0	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	1	2	FACETS	0.863	0.762	0.97	0.863	0.762	0.97	CLONAL	1	TRUE	1	0.38	2		326	488	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274121	10274121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	112	577	0	ENST00000330684.3:c.148G>A	p.Glu50Lys	p.E50K	ENST00000330684	NM_001134407.1	50	Gaa/Aaa	2/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.38	2		577	534	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649005	86649005	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	62	171	0	ENST00000274376.6:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000274376	NM_002890.2	429	Gaa/Taa	9/25	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.38	2		171	305	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99203950	99203950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755469992	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	41	226	0	ENST00000074304.5:c.2813G>A	p.Arg938Gln	p.R938Q	ENST00000074304	NM_001134224.1	938	cGa/cAa	26/26	1	2	FACETS	0.66	0.552	0.779	0.66	0.552	0.779	SUBCLONAL	1	TRUE	1	0.38	2		226	327	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	126	614	0	ENST00000267101.3:c.273G>T	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atT	3/28	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.38	2		614	642	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152033	11152033	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1384070535	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	117	493	0	ENST00000358026.2:c.4317G>T	p.Lys1439Asn	p.K1439N	ENST00000358026	NM_001128849.1	1439	aaG/aaT	31/36	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.38	2		493	546	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670234	134670234	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764139128	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	22	435	1	ENST00000398015.3:c.145G>A	p.Asp49Asn	p.D49N	ENST00000398015	NM_004441.4	49	Gat/Aat	3/16	1	2	FACETS	0.283	0.219	0.358	0.283	0.219	0.358	SUBCLONAL	1	TRUE	1	0.38	2		436	409	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832265	72832265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267604632	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	63	430	0	ENST00000268489.5:c.4316G>A	p.Arg1439Gln	p.R1439Q	ENST00000268489	NM_006885.3	1439	cGa/cAa	9/10	1	2	FACETS	0.795	0.69	0.908	0.795	0.69	0.908	CLONAL	1	TRUE	1	0.38	2		430	417	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937393	76937393	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	52	202	0	ENST00000373344.5:c.3355G>T	p.Glu1119Ter	p.E1119*	ENST00000373344	NM_000489.3	1119	Gaa/Taa	9/35	1	2	FACETS	0.872	0.746	1	0.872	0.746	1	CLONAL	1	TRUE	1	0.38	2		202	314	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541679	187541679	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs185406112	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	56	271	0	ENST00000441802.2:c.6061C>T	p.Arg2021Cys	p.R2021C	ENST00000441802	NM_005245.3	2021	Cgc/Tgc	10/27	1	2	FACETS	0.957	0.825	1	0.957	0.825	1	CLONAL	1	TRUE	1	0.38	2		271	308	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390072	89390072	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765502894	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	35	208	0	ENST00000336596.2:c.821G>A	p.Arg274Gln	p.R274Q	ENST00000336596	NM_005233.5	274	cGa/cAa	4/17	1	2	FACETS	0.764	0.63	0.913	0.764	0.63	0.913	CLONAL	1	TRUE	1	0.38	2		208	241	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101909998	101909998	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	39	156	0	ENST00000374994.4:c.1318G>T	p.Glu440Ter	p.E440*	ENST00000374994	NM_004612.2	440	Gaa/Taa	8/9	1	2	FACETS	0.873	0.73	1	0.873	0.73	1	CLONAL	1	TRUE	1	0.38	2		156	235	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800930	243800930	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	47	213	0	ENST00000263826.5:c.544G>T	p.Glu182Ter	p.E182*	ENST00000263826	NM_005465.4	182	Gaa/Taa	5/13	1	2	FACETS	0.723	0.613	0.844	0.723	0.613	0.844	SUBCLONAL	1	TRUE	1	0.38	2		213	342	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412937	63412937	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201650985	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	143	741	1	ENST00000330258.3:c.230G>A	p.Arg77Gln	p.R77Q	ENST00000330258	NM_152424.3	77	cGg/cAg	2/2	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.38	2		742	745	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483945	88483945	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1313486936	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	110	614	0	ENST00000360948.2:c.1625G>A	p.Arg542Gln	p.R542Q	ENST00000360948	NM_001012338.2	542	cGa/cAa	14/19	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.38	2		614	523	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324496	31324496	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs2308559	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	20	342	2	ENST00000412585.2:c.312C>A	p.Asn104Lys	p.N104K	ENST00000412585	NM_005514.6	104	aaC/aaA	2/8	1	2	FACETS	0.263	0.201	0.337	0.263	0.201	0.337	SUBCLONAL	1	TRUE	1	0.38	2		344	400	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139865	55139865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	69	379	0	ENST00000257290.5:c.1526C>T	p.Ala509Val	p.A509V	ENST00000257290	NM_006206.4	509	gCt/gTt	10/23	1	2	FACETS	0.982	0.86	1	0.982	0.86	1	CLONAL	1	TRUE	1	0.38	2		379	370	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622241	117622241	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs148104006	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	23	282	0	ENST00000368508.3:c.6629G>T	p.Arg2210Ile	p.R2210I	ENST00000368508	NM_002944.2	2210	aGa/aTa	42/43	1	2	FACETS	0.325	0.253	0.409	0.325	0.253	0.409	SUBCLONAL	1	TRUE	1	0.38	2		282	372	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906766	32906766	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41293475	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	100	505	0	ENST00000380152.3:c.1151C>T	p.Ser384Phe	p.S384F	ENST00000380152		384	tCc/tTc	10/27	1	2	FACETS	0.932	0.834	1	0.932	0.834	1	CLONAL	1	TRUE	1	0.38	2		505	565	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80021291	80021291	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs539295465	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	68	266	1	ENST00000265081.6:c.1360C>T	p.Arg454Ter	p.R454*	ENST00000265081	NM_002439.4	454	Cga/Tga	9/24	1	2	FACETS	0.766	0.668	0.872	0.766	0.668	0.872	SUBCLONAL	1	TRUE	1	0.38	2		267	467	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588810	69588810	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	121	755	0	ENST00000168712.1:c.426G>T	p.Lys142Asn	p.K142N	ENST00000168712	NM_002007.2	142	aaG/aaT	2/3	1	2	FACETS	0.997	0.902	1	0.997	0.902	1	CLONAL	1	TRUE	1	0.38	2		755	639	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131421	202131421	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	72	363	0	ENST00000358485.4:c.389G>T	p.Arg130Ile	p.R130I	ENST00000358485	NM_001080125.1	130	aGa/aTa	2/9	1	2	FACETS	0.767	0.672	0.869	0.767	0.672	0.869	SUBCLONAL	1	TRUE	1	0.38	2		363	494	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663425	227663425	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	48	329	0	ENST00000305123.5:c.30C>A	p.Phe10Leu	p.F10L	ENST00000305123	NM_005544.2	10	ttC/ttA	1/2	1	2	FACETS	0.763	0.648	0.889	0.763	0.648	0.889	SUBCLONAL	1	TRUE	1	0.38	2		329	331	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46276031	46276031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146235035	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	109	487	0	ENST00000371998.3:c.3467G>A	p.Arg1156Gln	p.R1156Q	ENST00000371998		1156	cGa/cAa	18/23	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.38	2		487	529	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945021	151945021	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs756918375	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	11	60	0	ENST00000262189.6:c.2498G>T	p.Arg833Ile	p.R833I	ENST00000262189	NM_170606.2	833	aGa/aTa	14/59	1	2	FACETS	0.327	0.226	0.452	0.327	0.226	0.452	SUBCLONAL	1	TRUE	1	0.38	2		60	177	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371771	116371771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	71	329	0	ENST00000397752.3:c.1250G>A	p.Arg417Gln	p.R417Q	ENST00000397752	NM_000245.2	417	cGa/cAa	3/21	1	2	FACETS	0.886	0.776	1	0.886	0.776	1	CLONAL	1	TRUE	1	0.38	2		329	422	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864117	57864117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749783306	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	86	506	0	ENST00000228682.2:c.1594C>T	p.Arg532Cys	p.R532C	ENST00000228682	NM_005269.2	532	Cgc/Tgc	12/12	1	2	FACETS	0.984	0.874	1	0.984	0.874	1	CLONAL	1	TRUE	1	0.38	2		506	460	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230538	46230538	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	43	287	0	ENST00000334344.6:c.787G>T	p.Glu263Ter	p.E263*	ENST00000334344	NM_152641.2	263	Gaa/Taa	8/21	1	2	FACETS	0.623	0.523	0.734	0.623	0.523	0.734	SUBCLONAL	1	TRUE	1	0.38	2		287	363	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060728	38060728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	151	784	0	ENST00000250448.2:c.1261G>A	p.Glu421Lys	p.E421K	ENST00000250448	NM_004496.3	421	Gaa/Aaa	2/2	1	2	FACETS	0.981	0.898	1	0.981	0.898	1	CLONAL	1	TRUE	1	0.38	2		784	810	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512334	38512334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	100	582	0	ENST00000254066.5:c.1245G>T	p.Glu415Asp	p.E415D	ENST00000254066	NM_000964.3	415	gaG/gaT	9/9	1	2	FACETS	0.867	0.776	0.964	0.867	0.776	0.964	CLONAL	1	TRUE	1	0.38	2		582	607	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105688	27105688	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	66	346	0	ENST00000324856.7:c.5299G>T	p.Glu1767Ter	p.E1767*	ENST00000324856	NM_006015.4	1767	Gaa/Taa	20/20	0.3	0	FACETS	0.828	0.727	0.935			1	CLONAL	1	TRUE	0	0.38	0		346	260	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394020	31394020	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	78	238	0	ENST00000328111.2:c.2307G>T	p.Lys769Asn	p.K769N	ENST00000328111	NM_006892.3	769	aaG/aaT	22/23	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.38	2		238	354	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98003008	98003008	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	63	159	0	ENST00000289081.3:c.268C>A	p.Leu90Ile	p.L90I	ENST00000289081	NM_000136.2	90	Cta/Ata	4/15	1	2	FACETS	0.887	0.771	1	0.887	0.771	1	CLONAL	1	TRUE	1	0.38	2		159	374	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136246	202136246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	68	301	0	ENST00000358485.4:c.490C>T	p.Leu164Phe	p.L164F	ENST00000358485	NM_001080125.1	164	Ctc/Ttc	3/9	1	2	FACETS	0.856	0.748	0.972	0.856	0.748	0.972	CLONAL	1	TRUE	1	0.38	2		301	418	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518429	8518429	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs995119754	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	38	169	0	ENST00000356435.5:c.962C>T	p.Ala321Val	p.A321V	ENST00000356435		321	gCc/gTc	10/35	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.38	2		169	179	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933047	39933047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	125	652	1	ENST00000378444.4:c.1552G>A	p.Glu518Lys	p.E518K	ENST00000378444	NM_001123385.1	518	Gaa/Aaa	4/15	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.38	2		653	651	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522657	67522657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	36	251	0	ENST00000274335.5:c.154G>T	p.Glu52Ter	p.E52*	ENST00000274335		52	Gaa/Taa	1/15	1	2	FACETS	0.662	0.547	0.791	0.662	0.547	0.791	SUBCLONAL	1	TRUE	1	0.38	2		251	286	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692815	89692815	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	68	164	0	ENST00000371953.3:c.299T>G	p.Leu100Arg	p.L100R	ENST00000371953	NM_000314.4	100	cTt/cGt	5/9	1	2	FACETS	0.788	0.696	0.885	1	0.978	1	SUBCLONAL	2	TRUE	1	0.38	2		164	227	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654607	67654607	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	106	363	0	ENST00000264010.4:c.1094A>C	p.Lys365Thr	p.K365T	ENST00000264010	NM_006565.3	365	aAa/aCa	6/12	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.38	2		363	535	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141557714	141557714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	99	620	0	ENST00000220592.5:c.1601G>A	p.Arg534His	p.R534H	ENST00000220592	NM_012154.3	534	cGc/cAc	13/19	1	2	FACETS	0.913	0.817	1	0.913	0.817	1	CLONAL	1	TRUE	1	0.38	2		620	571	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056108	26056108	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	111	353	0	ENST00000343677.2:c.549G>T	p.Lys183Asn	p.K183N	ENST00000343677	NM_005319.3	183	aaG/aaT	1/1	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.38	2		353	496	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39772513	39772513	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	67	427	1	ENST00000288319.7:c.728G>T	p.Arg243Ile	p.R243I	ENST00000288319	NM_182918.3	243	aGa/aTa	6/10	1	2	FACETS	0.763	0.665	0.869	0.763	0.665	0.869	SUBCLONAL	1	TRUE	1	0.38	2		428	462	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562133	176562133	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	88	406	0	ENST00000439151.2:c.29G>T	p.Arg10Ile	p.R10I	ENST00000439151	NM_022455.4	10	aGa/aTa	2/23	1	2	FACETS	0.988	0.879	1	0.988	0.879	1	CLONAL	1	TRUE	1	0.38	2		406	469	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29106017	29106017	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs749963436	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	59	178	0	ENST00000328354.6:c.823G>T	p.Glu275Ter	p.E275*	ENST00000328354	NM_007194.3	275	Gaa/Taa	7/15	1	2	FACETS	0.897	0.776	1	0.897	0.776	1	CLONAL	1	TRUE	1	0.38	2		178	346	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917635	94917635	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	94	326	0	ENST00000536441.1:c.886G>T	p.Glu296Ter	p.E296*	ENST00000536441	NM_144665.3	296	Gaa/Taa	6/10	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.38	2		326	480	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910767	32910767	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	67	268	0	ENST00000380152.3:c.2275C>A	p.Leu759Ile	p.L759I	ENST00000380152		759	Ctt/Att	11/27	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.38	2		268	329	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912136	127912136	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	61	208	0	ENST00000373547.4:c.734A>C	p.Lys245Thr	p.K245T	ENST00000373547	NM_002721.4	245	aAa/aCa	7/7	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.38	2		208	218	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346314	73346314	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	46	183	0	ENST00000377767.4:c.1486G>T	p.Glu496Ter	p.E496*	ENST00000377767	NM_014953.3	496	Gaa/Taa	10/21	1	2	FACETS	0.935	0.793	1	0.935	0.793	1	CLONAL	1	TRUE	1	0.38	2		183	259	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40468866	40468866	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	80	348	0	ENST00000264657.5:c.2198C>A	p.Ser733Ter	p.S733*	ENST00000264657	NM_139276.2	733	tCa/tAa	23/24	1	2	FACETS	0.87	0.768	0.978	0.87	0.768	0.978	CLONAL	1	TRUE	1	0.38	2		348	484	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608279	28608279	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	82	362	1	ENST00000241453.7:c.1777G>T	p.Asp593Tyr	p.D593Y	ENST00000241453	NM_004119.2	593	Gat/Tat	14/24	1	2	FACETS	0.97	0.859	1	0.97	0.859	1	CLONAL	1	TRUE	1	0.38	2		363	445	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906894	32906894	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	58	316	0	ENST00000380152.3:c.1279G>T	p.Asp427Tyr	p.D427Y	ENST00000380152		427	Gac/Tac	10/27	1	2	FACETS	0.846	0.73	0.97	0.846	0.73	0.97	CLONAL	1	TRUE	1	0.38	2		316	361	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53253955	53253955	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	100	577	0	ENST00000375401.3:c.117G>T	p.Glu39Asp	p.E39D	ENST00000375401	NM_004187.3	39	gaG/gaT	1/26	1	2	FACETS	0.957	0.857	1	0.957	0.857	1	CLONAL	1	TRUE	1	0.38	2		577	550	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107275	193107275	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	31	204	0	ENST00000367435.3:c.484G>T	p.Glu162Ter	p.E162*	ENST00000367435	NM_024529.4	162	Gaa/Taa	6/17	1	2	FACETS	0.683	0.555	0.825	0.683	0.555	0.825	SUBCLONAL	1	TRUE	1	0.38	2		204	239	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798781	135798781	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1214441043	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	36	225	0	ENST00000298552.3:c.462C>A	p.Phe154Leu	p.F154L	ENST00000298552	NM_001162426.1	154	ttC/ttA	6/23	1	2	FACETS	0.613	0.506	0.733	0.613	0.506	0.733	SUBCLONAL	1	TRUE	1	0.38	2		225	309	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738308	190738308	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	77	190	0	ENST00000441310.2:c.2560C>A	p.Leu854Ile	p.L854I	ENST00000441310	NM_000534.4	854	Ctt/Att	12/13	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.38	2		190	372	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307699	11307699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1226783220	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	71	402	0	ENST00000361445.4:c.1208G>A	p.Arg403Gln	p.R403Q	ENST00000361445	NM_004958.3	403	cGa/cAa	8/58	1	2	FACETS	0.8	0.7	0.907	0.8	0.7	0.907	CLONAL	1	TRUE	1	0.38	2		402	467	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305334	39305334	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	100	425	0	ENST00000373001.3:c.1091A>C	p.His364Pro	p.H364P	ENST00000373001	NM_022157.3	364	cAt/cCt	7/7	1	2	FACETS	0.869	0.777	0.965	0.869	0.777	0.965	CLONAL	1	TRUE	1	0.38	2		425	606	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241878	72241878	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	44	228	0	ENST00000357731.5:c.512C>A	p.Ser171Tyr	p.S171Y	ENST00000357731	NM_173808.2	171	tCt/tAt	3/7	1	2	FACETS	0.671	0.565	0.788	0.671	0.565	0.788	SUBCLONAL	1	TRUE	1	0.38	2		228	345	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166202	118166202	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	53	324	0	ENST00000369448.3:c.712G>T	p.Glu238Ter	p.E238*	ENST00000369448	NM_017709.3	238	Gaa/Taa	2/2	1	2	FACETS	0.79	0.677	0.913	0.79	0.677	0.913	CLONAL	1	TRUE	1	0.38	2		324	353	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163313606	163313606	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	37	112	0	ENST00000271452.3:c.753A>C	p.Leu251Phe	p.L251F	ENST00000271452	NM_145697.2	251	ttA/ttC	10/14	1	2	FACETS	0.755	0.626	0.897	0.755	0.626	0.897	SUBCLONAL	1	TRUE	1	0.38	2		112	258	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332221	70332221	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1224328336	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	61	306	0	ENST00000373644.4:c.126G>T	p.Lys42Asn	p.K42N	ENST00000373644	NM_030625.2	42	aaG/aaT	2/12	1	2	FACETS	0.912	0.791	1	0.912	0.791	1	CLONAL	1	TRUE	1	0.38	2		306	352	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70441196	70441196	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	81	289	0	ENST00000373644.4:c.4865G>T	p.Arg1622Leu	p.R1622L	ENST00000373644	NM_030625.2	1622	cGa/cTa	9/12	1	2	FACETS	0.851	0.752	0.957	0.851	0.752	0.957	CLONAL	1	TRUE	1	0.38	2		289	501	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692920	89692920	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs370795352	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	97	345	0	ENST00000371953.3:c.404T>C	p.Ile135Thr	p.I135T	ENST00000371953	NM_000314.4	135	aTa/aCa	5/9	1	2	FACETS	0.984	0.88	1	0.984	0.88	1	CLONAL	1	TRUE	1	0.38	2		345	519	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77043862	77043862	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	118	608	1	ENST00000356341.3:c.1464G>T	p.Glu488Asp	p.E488D	ENST00000356341	NM_002576.4	488	gaG/gaT	14/15	1	2	FACETS	0.885	0.799	0.975	0.885	0.799	0.975	CLONAL	1	TRUE	1	0.38	2		609	702	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94153324	94153324	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	74	145	0	ENST00000323929.3:c.2094G>T	p.Met698Ile	p.M698I	ENST00000323929	NM_005591.3	698	atG/atT	20/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.38	2		145	344	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94170355	94170355	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	58	145	0	ENST00000323929.3:c.1914G>T	p.Lys638Asn	p.K638N	ENST00000323929	NM_005591.3	638	aaG/aaT	17/20	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.38	2		145	291	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155196	108155196	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	40	263	0	ENST00000278616.4:c.3989A>C	p.Lys1330Thr	p.K1330T	ENST00000278616	NM_000051.3	1330	aAa/aCa	26/63	1	2	FACETS	0.78	0.652	0.92	0.78	0.652	0.92	CLONAL	1	TRUE	1	0.38	2		263	270	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343505	118343505	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	63	310	0	ENST00000534358.1:c.1631A>C	p.Lys544Thr	p.K544T	ENST00000534358	NM_005933.3	544	aAa/aCa	3/36	1	2	FACETS	0.88	0.764	1	0.88	0.764	1	CLONAL	1	TRUE	1	0.38	2		310	377	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374794	118374794	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	53	271	0	ENST00000534358.1:c.8187T>G	p.Ser2729Arg	p.S2729R	ENST00000534358	NM_005933.3	2729	agT/agG	27/36	1	2	FACETS	0.909	0.78	1	0.909	0.78	1	CLONAL	1	TRUE	1	0.38	2		271	307	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394656	394656	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	71	444	0	ENST00000399788.2:c.5039A>C	p.Lys1680Thr	p.K1680T	ENST00000399788	NM_001042603.1	1680	aAa/aCa	28/28	0.3	2	FACETS	0.83	0.727	0.941			1	CLONAL	1	TRUE	NA	0.38	2		444	450	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426198	49426198	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	105	663	0	ENST00000301067.7:c.12290T>C	p.Leu4097Pro	p.L4097P	ENST00000301067	NM_003482.3	4097	cTt/cCt	39/54	1	2	FACETS	0.937	0.841	1	0.937	0.841	1	CLONAL	1	TRUE	1	0.38	2		663	590	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445656	49445656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	156	918	1	ENST00000301067.7:c.1810G>A	p.Glu604Lys	p.E604K	ENST00000301067	NM_003482.3	604	Gaa/Aaa	10/54	1	2	FACETS	0.9	0.824	0.98	0.9	0.824	0.98	CLONAL	1	TRUE	1	0.38	2		919	912	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484082	50484082	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	132	529	0	ENST00000394963.4:c.932C>G	p.Thr311Ser	p.T311S	ENST00000394963	NM_003076.4	311	aCt/aGt	8/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.38	2		529	609	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869449	102869449	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	79	416	0	ENST00000307046.8:c.192C>A	p.Phe64Leu	p.F64L	ENST00000307046	NM_001111285.1	64	ttC/ttA	2/4	1	2	FACETS	0.879	0.776	0.989	0.879	0.776	0.989	CLONAL	1	TRUE	1	0.38	2		416	473	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212568	133212568	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	104	415	0	ENST00000320574.5:c.5721C>A	p.Phe1907Leu	p.F1907L	ENST00000320574	NM_006231.2	1907	ttC/ttA	42/49	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.38	2		415	522	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218812	133218812	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	104	578	1	ENST00000320574.5:c.5124C>A	p.Phe1708Leu	p.F1708L	ENST00000320574	NM_006231.2	1708	ttC/ttA	38/49	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.38	2		579	545	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237712	133237712	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	107	449	0	ENST00000320574.5:c.2903T>C	p.Leu968Pro	p.L968P	ENST00000320574	NM_006231.2	968	cTc/cCc	25/49	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.38	2		449	525	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28903808	28903808	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	91	518	0	ENST00000282397.4:c.2651A>G	p.His884Arg	p.H884R	ENST00000282397	NM_002019.4	884	cAc/cGc	19/30	1	2	FACETS	0.926	0.825	1	0.926	0.825	1	CLONAL	1	TRUE	1	0.38	2		518	517	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907370	32907370	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs431825285	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	57	248	1	ENST00000380152.3:c.1755G>T	p.Lys585Asn	p.K585N	ENST00000380152		585	aaG/aaT	10/27	1	2	FACETS	0.92	0.794	1	0.92	0.794	1	CLONAL	1	TRUE	1	0.38	2		249	326	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910870	32910870	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	31	236	0	ENST00000380152.3:c.2378A>C	p.Lys793Thr	p.K793T	ENST00000380152		793	aAa/aCa	11/27	1	2	FACETS	0.442	0.358	0.538	0.442	0.358	0.538	SUBCLONAL	1	TRUE	1	0.38	2		236	369	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911058	32911058	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	69	233	0	ENST00000380152.3:c.2566A>C	p.Asn856His	p.N856H	ENST00000380152		856	Aat/Cat	11/27	1	2	FACETS	0.974	0.853	1	0.974	0.853	1	CLONAL	1	TRUE	1	0.38	2		233	373	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912349	32912349	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	57	176	0	ENST00000380152.3:c.3857A>T	p.Lys1286Ile	p.K1286I	ENST00000380152		1286	aAa/aTa	11/27	1	2	FACETS	0.88	0.759	1	0.88	0.759	1	CLONAL	1	TRUE	1	0.38	2		176	341	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912521	32912521	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	89	242	0	ENST00000380152.3:c.4029A>T	p.Lys1343Asn	p.K1343N	ENST00000380152		1343	aaA/aaT	11/27	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.38	2		242	390	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914082	32914082	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	51	283	0	ENST00000380152.3:c.5590G>T	p.Asp1864Tyr	p.D1864Y	ENST00000380152		1864	Gac/Tac	11/27	1	2	FACETS	0.763	0.651	0.884	0.763	0.651	0.884	SUBCLONAL	1	TRUE	1	0.38	2		283	352	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916828	48916828	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	64	226	0	ENST00000267163.4:c.358C>A	p.Leu120Ile	p.L120I	ENST00000267163	NM_000321.2	120	Cta/Ata	3/27	1	2	FACETS	0.979	0.853	1	0.979	0.853	1	CLONAL	1	TRUE	1	0.38	2		226	344	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514971	103514971	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs774961421	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	50	301	0	ENST00000355739.4:c.1472A>C	p.Glu491Ala	p.E491A	ENST00000355739	NM_000123.3	491	gAg/gCg	8/15	1	2	FACETS	0.886	0.757	1	0.886	0.757	1	CLONAL	1	TRUE	1	0.38	2		301	297	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544673	65544673	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	95	549	0	ENST00000358664.4:c.253A>G	p.Ile85Val	p.I85V	ENST00000358664	NM_002382.4	85	Att/Gtt	4/5	1	2	FACETS	0.766	0.682	0.854	0.766	0.682	0.854	SUBCLONAL	1	TRUE	1	0.38	2		549	653	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609343	81609343	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	38	248	0	ENST00000298171.2:c.941C>A	p.Ser314Tyr	p.S314Y	ENST00000298171	NM_000369.2	314	tCt/tAt	10/10	1	2	FACETS	0.667	0.553	0.792	0.667	0.553	0.792	SUBCLONAL	1	TRUE	1	0.38	2		248	300	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590878	95590878	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	48	169	0	ENST00000393063.1:c.1031T>G	p.Phe344Cys	p.F344C	ENST00000393063	NM_030621.3	344	tTt/tGt	9/28	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.38	2		169	251	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748846	43748846	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	128	620	0	ENST00000382044.4:c.1960G>T	p.Glu654Ter	p.E654*	ENST00000382044	NM_001141980.1	654	Gaa/Taa	12/28	1	2	FACETS	0.953	0.865	1	0.953	0.865	1	CLONAL	1	TRUE	1	0.38	2		620	707	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66735671	66735671	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	73	249	0	ENST00000307102.5:c.492A>C	p.Gln164His	p.Q164H	ENST00000307102	NM_002755.3	164	caA/caC	4/11	1	2	FACETS	0.949	0.834	1	0.949	0.834	1	CLONAL	1	TRUE	1	0.38	2		249	405	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984844	9984844	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	90	390	2	ENST00000330684.3:c.1121del	p.Lys374ArgfsTer10	p.K374Rfs*10	ENST00000330684	NM_001134407.1	374	aAg/ag	4/13	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.38	2		392	431	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041966	14041966	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	60	299	0	ENST00000311895.7:c.2513T>G	p.Leu838Arg	p.L838R	ENST00000311895	NM_005236.2	838	cTt/cGt	11/11	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.38	2		299	294	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853187	68853187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373605261	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	71	398	5	ENST00000261769.5:c.1570C>T	p.Arg524Trp	p.R524W	ENST00000261769	NM_004360.3	524	Cgg/Tgg	11/16	1	2	FACETS	0.825	0.722	0.935	0.825	0.722	0.935	CLONAL	1	TRUE	1	0.38	2		403	453	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831351	72831351	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753503557	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	68	316	0	ENST00000268489.5:c.5230A>G	p.Thr1744Ala	p.T1744A	ENST00000268489	NM_006885.3	1744	Acg/Gcg	9/10	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.38	2		316	321	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990636	7990636	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	111	566	0	ENST00000319144.4:c.125G>T	p.Gly42Val	p.G42V	ENST00000319144	NM_001139.2	42	gGg/gTg	1/15	1	2	FACETS	0.921	0.83	1	0.921	0.83	1	CLONAL	1	TRUE	1	0.38	2		566	634	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958217	11958217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	24	196	0	ENST00000353533.5:c.127G>A	p.Ala43Thr	p.A43T	ENST00000353533	NM_003010.3	43	Gca/Aca	2/11	1	2	FACETS	0.406	0.318	0.507	0.406	0.318	0.507	SUBCLONAL	1	TRUE	1	0.38	2		196	311	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508455	29508455	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	69	176	0	ENST00000356175.3:c.602T>G	p.Phe201Cys	p.F201C	ENST00000356175	NM_000267.3	201	tTt/tGt	6/57	1	2	FACETS	0.884	0.773	1	0.884	0.773	1	CLONAL	1	TRUE	1	0.38	2		176	411	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550489	29550489	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	52	131	0	ENST00000356175.3:c.1749G>T	p.Lys583Asn	p.K583N	ENST00000356175	NM_000267.3	583	aaG/aaT	16/57	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.38	2		131	227	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264368	30264368	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1224696424	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	22	289	0	ENST00000322652.5:c.103A>G	p.Thr35Ala	p.T35A	ENST00000322652	NM_015355.2	35	Acg/Gcg	1/16	1	2	FACETS	0.351	0.272	0.443	0.351	0.272	0.443	SUBCLONAL	1	TRUE	1	0.38	2		289	330	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573424	48573424	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	24	103	0	ENST00000342988.3:c.8A>C	p.Asn3Thr	p.N3T	ENST00000342988	NM_005359.5	3	aAt/aCt	2/12	1	2	FACETS	0.871	0.691	1	0.871	0.691	1	CLONAL	1	TRUE	1	0.38	2		103	145	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56377230	56377230	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	16	146	0	ENST00000348428.3:c.851A>G	p.His284Arg	p.H284R	ENST00000348428	NM_006785.3	284	cAc/cGc	6/17	1	2	FACETS	0.314	0.232	0.412	0.314	0.232	0.412	SUBCLONAL	1	TRUE	1	0.38	2		146	268	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134218	11134218	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	124	602	0	ENST00000358026.2:c.2884A>G	p.Ile962Val	p.I962V	ENST00000358026	NM_001128849.1	962	Att/Gtt	20/36	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.38	2		602	548	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912049	50912049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200864923	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	120	748	1	ENST00000440232.2:c.1783G>A	p.Asp595Asn	p.D595N	ENST00000440232	NM_002691.3	595	Gac/Aac	15/27	1	2	FACETS	0.902	0.816	0.993	0.902	0.816	0.993	CLONAL	1	TRUE	1	0.38	2		749	700	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965130	25965130	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	84	444	1	ENST00000435504.4:c.4076C>A	p.Ser1359Ter	p.S1359*	ENST00000435504		1359	tCa/tAa	13/13	1	2	FACETS	0.965	0.856	1	0.965	0.856	1	CLONAL	1	TRUE	1	0.38	2		445	458	SUCCESS
ALK	238	MSKCC	GRCh37	2	29430052	29430052	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	81	511	0	ENST00000389048.3:c.3923C>A	p.Ser1308Tyr	p.S1308Y	ENST00000389048	NM_004304.4	1308	tCt/tAt	26/29	1	2	FACETS	0.901	0.797	1	0.901	0.797	1	CLONAL	1	TRUE	1	0.38	2		511	473	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583923	46583923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	77	398	0	ENST00000263734.3:c.430C>T	p.Arg144Cys	p.R144C	ENST00000263734	NM_001430.4	144	Cgt/Tgt	4/16	1	2	FACETS	0.956	0.843	1	0.956	0.843	1	CLONAL	1	TRUE	1	0.38	2		398	424	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630608	158630608	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	52	191	0	ENST00000263640.3:c.635A>T	p.Glu212Val	p.E212V	ENST00000263640	NM_001105.4	212	gAg/gTg	6/11	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.38	2		191	273	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113291	209113291	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	72	283	0	ENST00000345146.2:c.216A>C	p.Lys72Asn	p.K72N	ENST00000345146	NM_005896.2	72	aaA/aaC	4/10	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.38	2		283	361	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285282	212285282	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	51	304	0	ENST00000342788.4:c.3019C>A	p.Leu1007Ile	p.L1007I	ENST00000342788	NM_005235.2	1007	Ctc/Atc	25/28	1	2	FACETS	0.836	0.715	0.968	0.836	0.715	0.968	CLONAL	1	TRUE	1	0.38	2		304	321	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215609799	215609799	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	39	185	0	ENST00000260947.4:c.1895A>C	p.Lys632Thr	p.K632T	ENST00000260947	NM_000465.2	632	aAa/aCa	9/11	1	2	FACETS	0.607	0.505	0.721	0.607	0.505	0.721	SUBCLONAL	1	TRUE	1	0.38	2		185	338	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024873	31024873	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	91	472	0	ENST00000375687.4:c.4358G>A	p.Ser1453Asn	p.S1453N	ENST00000375687	NM_015338.5	1453	aGc/aAc	13/13	1	2	FACETS	0.872	0.777	0.974	0.872	0.777	0.974	CLONAL	1	TRUE	1	0.38	2		472	549	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40709559	40709559	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	85	375	0	ENST00000373198.4:c.4343T>G	p.Phe1448Cys	p.F1448C	ENST00000373198	NM_133170.3	1448	tTt/tGt	32/32	1	2	FACETS	0.954	0.847	1	0.954	0.847	1	CLONAL	1	TRUE	1	0.38	2		375	469	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101183	41101183	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	82	566	0	ENST00000373198.4:c.1173G>T	p.Gln391His	p.Q391H	ENST00000373198	NM_133170.3	391	caG/caT	8/32	0.3	0	FACETS	0.51	0.45	0.573			1	SUBCLONAL	1	TRUE	0	0.38	0		566	525	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46271045	46271045	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	86	416	0	ENST00000371998.3:c.3169C>G	p.Leu1057Val	p.L1057V	ENST00000371998		1057	Ctg/Gtg	17/23	1	2	FACETS	0.819	0.726	0.917	0.819	0.726	0.917	CLONAL	1	TRUE	1	0.38	2		416	553	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775513	39775513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	94	599	0	ENST00000288319.7:c.507C>A	p.Cys169Ter	p.C169*	ENST00000288319	NM_182918.3	169	tgC/tgA	4/10	1	2	FACETS	0.849	0.757	0.946	0.849	0.757	0.946	CLONAL	1	TRUE	1	0.38	2		599	583	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458392	12458392	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	104	550	0	ENST00000287820.6:c.1009C>A	p.Leu337Ile	p.L337I	ENST00000287820	NM_015869.4	337	Ctt/Att	6/7	1	2	FACETS	0.877	0.787	0.973	0.877	0.787	0.973	CLONAL	1	TRUE	1	0.38	2		550	624	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164312	47164312	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1382756465	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	57	181	0	ENST00000409792.3:c.1814A>C	p.Lys605Thr	p.K605T	ENST00000409792	NM_014159.6	605	aAa/aCa	3/21	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.38	2		181	286	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52676006	52676006	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	80	366	1	ENST00000394830.3:c.1051T>C	p.Tyr351His	p.Y351H	ENST00000394830	NM_018313.4	351	Tat/Cat	11/30	1	2	FACETS	0.835	0.737	0.94	0.835	0.737	0.94	CLONAL	1	TRUE	1	0.38	2		367	504	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977865	134977865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	56	291	0	ENST00000398015.3:c.2858G>A	p.Arg953Lys	p.R953K	ENST00000398015	NM_004441.4	953	aGa/aAa	16/16	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.38	2		291	292	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138376582	138376582	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs763059581	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	71	355	0	ENST00000289153.2:c.2892C>A	p.Phe964Leu	p.F964L	ENST00000289153	NM_006219.2	964	ttC/ttA	20/22	1	2	FACETS	0.818	0.716	0.927	0.818	0.716	0.927	CLONAL	1	TRUE	1	0.38	2		355	457	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138423326	138423326	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs769614863	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	54	272	0	ENST00000289153.2:c.1540A>C	p.Lys514Gln	p.K514Q	ENST00000289153	NM_006219.2	514	Aag/Cag	10/22	1	2	FACETS	0.789	0.677	0.911	0.789	0.677	0.911	CLONAL	1	TRUE	1	0.38	2		272	360	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433370	138433370	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	69	262	0	ENST00000289153.2:c.1242G>T	p.Lys414Asn	p.K414N	ENST00000289153	NM_006219.2	414	aaG/aaT	7/22	1	2	FACETS	0.8	0.699	0.908	0.8	0.699	0.908	CLONAL	1	TRUE	1	0.38	2		262	454	SUCCESS
ATR	545	MSKCC	GRCh37	3	142224124	142224124	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	19	222	0	ENST00000350721.4:c.5053G>T	p.Glu1685Ter	p.E1685*	ENST00000350721	NM_001184.3	1685	Gaa/Taa	29/47	1	2	FACETS	0.348	0.264	0.447	0.348	0.264	0.447	SUBCLONAL	1	TRUE	1	0.38	2		222	287	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272144	142272144	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	131	286	0	ENST00000350721.4:c.2730A>C	p.Glu910Asp	p.E910D	ENST00000350721	NM_001184.3	910	gaA/gaC	13/47	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.38	2		286	530	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951989	178951989	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	57	267	0	ENST00000263967.3:c.3044C>A	p.Ser1015Tyr	p.S1015Y	ENST00000263967	NM_006218.2	1015	tCt/tAt	21/21	1	2	FACETS	0.938	0.809	1	0.938	0.809	1	CLONAL	1	TRUE	1	0.38	2		267	320	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444685	187444685	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	32	276	0	ENST00000232014.4:c.1542G>T	p.Glu514Asp	p.E514D	ENST00000232014	NM_001130845.1	514	gaG/gaT	7/10	1	2	FACETS	0.55	0.448	0.666	0.55	0.448	0.666	SUBCLONAL	1	TRUE	1	0.38	2		276	306	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955581	55955581	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	67	301	0	ENST00000263923.4:c.3364G>T	p.Gly1122Ter	p.G1122*	ENST00000263923	NM_002253.2	1122	Gga/Tga	25/30	1	2	FACETS	0.871	0.76	0.99	0.871	0.76	0.99	CLONAL	1	TRUE	1	0.38	2		301	405	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467823	66467823	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	41	218	0	ENST00000273854.3:c.446A>G	p.Glu149Gly	p.E149G	ENST00000273854	NM_004439.5	149	gAa/gGa	3/18	1	2	FACETS	0.888	0.745	1	0.888	0.745	1	CLONAL	1	TRUE	1	0.38	2		218	243	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157710	106157710	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs767929296	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	39	185	0	ENST00000380013.4:c.2611A>T	p.Asn871Tyr	p.N871Y	ENST00000380013	NM_001127208.2	871	Aat/Tat	3/11	1	2	FACETS	0.828	0.691	0.978	0.828	0.691	0.978	CLONAL	1	TRUE	1	0.38	2		185	248	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007409	143007409	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	39	150	0	ENST00000262992.4:c.2375A>C	p.Tyr792Ser	p.Y792S	ENST00000262992	NM_001101669.1	792	tAt/tCt	22/24	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.38	2		150	194	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094808	143094808	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	49	208	0	ENST00000262992.4:c.1336T>G	p.Ser446Ala	p.S446A	ENST00000262992	NM_001101669.1	446	Tct/Gct	14/24	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.38	2		208	239	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271223	153271223	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	46	146	0	ENST00000281708.4:c.555G>T	p.Lys185Asn	p.K185N	ENST00000281708	NM_033632.3	185	aaG/aaT	3/12	1	2	FACETS	0.804	0.681	0.939	0.804	0.681	0.939	CLONAL	1	TRUE	1	0.38	2		146	301	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521160	187521160	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	79	509	0	ENST00000441802.2:c.11995A>C	p.Ile3999Leu	p.I3999L	ENST00000441802	NM_005245.3	3999	Atc/Ctc	22/27	1	2	FACETS	0.872	0.769	0.981	0.872	0.769	0.981	CLONAL	1	TRUE	1	0.38	2		509	477	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31437392	31437392	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	90	412	0	ENST00000344624.3:c.2896G>T	p.Glu966Ter	p.E966*	ENST00000344624		966	Gaa/Taa	21/33	1	2	FACETS	0.821	0.73	0.918	0.821	0.73	0.918	CLONAL	1	TRUE	1	0.38	2		412	577	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468109	31468109	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	110	500	0	ENST00000344624.3:c.2303C>A	p.Thr768Asn	p.T768N	ENST00000344624		768	aCt/aAt	15/33	1	2	FACETS	0.978	0.881	1	0.978	0.881	1	CLONAL	1	TRUE	1	0.38	2		500	592	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80088568	80088568	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	55	183	0	ENST00000265081.6:c.2560G>T	p.Glu854Ter	p.E854*	ENST00000265081	NM_002439.4	854	Gaa/Taa	19/24	1	2	FACETS	0.91	0.783	1	0.91	0.783	1	CLONAL	1	TRUE	1	0.38	2		183	318	SUCCESS
APC	324	MSKCC	GRCh37	5	112175493	112175493	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	40	268	0	ENST00000257430.4:c.4202T>A	p.Ile1401Asn	p.I1401N	ENST00000257430	NM_000038.5	1401	aTt/aAt	16/16	1	2	FACETS	0.816	0.682	0.963	0.816	0.682	0.963	CLONAL	1	TRUE	1	0.38	2		268	258	SUCCESS
APC	324	MSKCC	GRCh37	5	112178325	112178325	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	67	284	0	ENST00000257430.4:c.7034T>G	p.Leu2345Arg	p.L2345R	ENST00000257430	NM_000038.5	2345	cTt/cGt	16/16	1	2	FACETS	0.938	0.819	1	0.938	0.819	1	CLONAL	1	TRUE	1	0.38	2		284	376	SUCCESS
APC	324	MSKCC	GRCh37	5	112178781	112178781	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	28	344	0	ENST00000257430.4:c.7490C>A	p.Ser2497Ter	p.S2497*	ENST00000257430	NM_000038.5	2497	tCg/tAg	16/16	1	2	FACETS	0.441	0.353	0.542	0.441	0.353	0.542	SUBCLONAL	1	TRUE	1	0.38	2		344	334	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131972841	131972841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	66	235	0	ENST00000265335.6:c.3424G>A	p.Glu1142Lys	p.E1142K	ENST00000265335		1142	Gaa/Aaa	22/25	1	2	FACETS	0.929	0.81	1	0.929	0.81	1	CLONAL	1	TRUE	1	0.38	2		235	374	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636787	176636787	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	62	322	0	ENST00000439151.2:c.1387G>T	p.Asp463Tyr	p.D463Y	ENST00000439151	NM_022455.4	463	Gat/Tat	5/23	1	2	FACETS	0.768	0.665	0.878	0.768	0.665	0.878	SUBCLONAL	1	TRUE	1	0.38	2		322	425	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637822	176637822	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	105	384	0	ENST00000439151.2:c.2422G>T	p.Glu808Ter	p.E808*	ENST00000439151	NM_022455.4	808	Gag/Tag	5/23	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.38	2		384	538	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673751	176673751	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	78	284	0	ENST00000439151.2:c.4451A>C	p.Lys1484Thr	p.K1484T	ENST00000439151	NM_022455.4	1484	aAa/aCa	10/23	1	2	FACETS	0.84	0.74	0.946	0.84	0.74	0.946	CLONAL	1	TRUE	1	0.38	2		284	489	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166901	32166901	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	133	837	0	ENST00000375023.3:c.4337C>A	p.Pro1446His	p.P1446H	ENST00000375023	NM_004557.3	1446	cCc/cAc	24/30	1	2	FACETS	0.83	0.754	0.911	0.83	0.754	0.911	CLONAL	1	TRUE	1	0.38	2		837	843	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288252	33288252	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	87	466	0	ENST00000374542.5:c.1156A>C	p.Ser386Arg	p.S386R	ENST00000374542	NM_001141970.1	386	Agt/Cgt	4/8	1	2	FACETS	0.859	0.763	0.962	0.859	0.763	0.962	CLONAL	1	TRUE	1	0.38	2		466	533	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903815	41903815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	113	581	0	ENST00000372991.4:c.742G>A	p.Glu248Lys	p.E248K	ENST00000372991	NM_001760.3	248	Gaa/Aaa	5/5	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.38	2		581	537	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41904434	41904434	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	100	549	0	ENST00000372991.4:c.575-1G>T		p.X192_splice	ENST00000372991	NM_001760.3	192			1	2	FACETS	0.92	0.824	1	0.92	0.824	1	CLONAL	1	TRUE	1	0.38	2		549	572	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109319915	109319915	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	62	396	0	ENST00000436639.2:c.773T>G	p.Leu258Trp	p.L258W	ENST00000436639	NM_014454.2	258	tTg/tGg	5/10	1	2	FACETS	0.659	0.57	0.756	0.659	0.57	0.756	SUBCLONAL	1	TRUE	1	0.38	2		396	495	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638382	117638382	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	39	307	0	ENST00000368508.3:c.6059A>C	p.Glu2020Ala	p.E2020A	ENST00000368508	NM_002944.2	2020	gAa/gCa	38/43	1	2	FACETS	0.664	0.553	0.788	0.664	0.553	0.788	SUBCLONAL	1	TRUE	1	0.38	2		307	309	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117645579	117645579	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	62	304	0	ENST00000368508.3:c.5558-1G>T		p.X1853_splice	ENST00000368508	NM_002944.2	1853			1	2	FACETS	0.796	0.69	0.91	0.796	0.69	0.91	CLONAL	1	TRUE	1	0.38	2		304	410	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519179	137519179	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	13	143	0	ENST00000367739.4:c.1459G>A	p.Glu487Lys	p.E487K	ENST00000367739	NM_000416.2	487	Gaa/Aaa	7/7	1	2	FACETS	0.346	0.247	0.466	0.346	0.247	0.466	SUBCLONAL	1	TRUE	1	0.38	2		143	198	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157256675	157256675	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	84	254	0	ENST00000346085.5:c.2002A>G	p.Asn668Asp	p.N668D	ENST00000346085	NM_020732.3	668	Aac/Gac	5/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.38	2		254	369	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971145	13971145	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	24	246	0	ENST00000405192.2:c.784G>A	p.Asp262Asn	p.D262N	ENST00000405192	NM_001163147.1	262	Gat/Aat	8/12	1	2	FACETS	0.547	0.43	0.68	0.547	0.43	0.68	SUBCLONAL	1	TRUE	1	0.38	2		246	231	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14027743	14027743	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	60	233	0	ENST00000405192.2:c.101T>G	p.Phe34Cys	p.F34C	ENST00000405192	NM_001163147.1	34	tTc/tGc	3/12	1	2	FACETS	0.88	0.762	1	0.88	0.762	1	CLONAL	1	TRUE	1	0.38	2		233	359	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388074	81388074	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	69	262	0	ENST00000222390.5:c.301T>C	p.Phe101Leu	p.F101L	ENST00000222390	NM_000601.4	101	Ttc/Ctc	3/18	1	2	FACETS	0.822	0.718	0.933	0.822	0.718	0.933	CLONAL	1	TRUE	1	0.38	2		262	442	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340162	116340162	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	49	227	0	ENST00000397752.3:c.1024C>A	p.Leu342Ile	p.L342I	ENST00000397752	NM_000245.2	342	Ctt/Att	2/21	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.38	2		227	255	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403126	116403126	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	56	281	1	ENST00000397752.3:c.2387C>A	p.Ser796Ter	p.S796*	ENST00000397752	NM_000245.2	796	tCa/tAa	11/21	1	2	FACETS	0.864	0.744	0.994	0.864	0.744	0.994	CLONAL	1	TRUE	1	0.38	2		282	341	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403241	116403241	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs45450897	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	95	322	0	ENST00000397752.3:c.2502T>G	p.Ile834Met	p.I834M	ENST00000397752	NM_000245.2	834	atT/atG	11/21	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.38	2		322	460	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852036	128852036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761586263	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	95	732	0	ENST00000249373.3:c.2108G>A	p.Arg703Gln	p.R703Q	ENST00000249373	NM_005631.4	703	cGa/cAa	12/12	1	2	FACETS	0.839	0.748	0.935	0.839	0.748	0.935	CLONAL	1	TRUE	1	0.38	2		732	596	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511154	148511154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1563201455	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	93	393	0	ENST00000320356.2:c.1748G>A	p.Arg583Gln	p.R583Q	ENST00000320356	NM_004456.4	583	cGa/cAa	15/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.38	2		393	441	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148513855	148513855	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	92	317	0	ENST00000320356.2:c.1426G>A	p.Val476Ile	p.V476I	ENST00000320356	NM_004456.4	476	Gtc/Atc	12/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.38	2		317	379	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859470	151859470	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	72	381	0	ENST00000262189.6:c.11192A>G	p.Gln3731Arg	p.Q3731R	ENST00000262189	NM_170606.2	3731	cAa/cGa	43/59	1	2	FACETS	0.936	0.821	1	0.936	0.821	1	CLONAL	1	TRUE	1	0.38	2		381	405	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874200	151874200	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	58	250	0	ENST00000262189.6:c.8338C>A	p.Pro2780Thr	p.P2780T	ENST00000262189	NM_170606.2	2780	Cca/Aca	38/59	1	2	FACETS	0.83	0.716	0.952	0.83	0.716	0.952	CLONAL	1	TRUE	1	0.38	2		250	368	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027816	152027816	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	78	329	1	ENST00000262189.6:c.259G>T	p.Glu87Ter	p.E87*	ENST00000262189	NM_170606.2	87	Gaa/Taa	3/59	1	2	FACETS	0.896	0.791	1	0.896	0.791	1	CLONAL	1	TRUE	1	0.38	2		330	458	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031705	69031705	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	87	332	0	ENST00000288368.4:c.3460A>C	p.Lys1154Gln	p.K1154Q	ENST00000288368	NM_024870.2	1154	Aaa/Caa	28/40	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.38	2		332	447	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033254	69033254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1450803336	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	82	359	0	ENST00000288368.4:c.3694C>T	p.Leu1232Phe	p.L1232F	ENST00000288368	NM_024870.2	1232	Ctt/Ttt	30/40	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.38	2		359	423	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859828	117859828	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	48	165	0	ENST00000297338.2:c.1807C>A	p.Leu603Ile	p.L603I	ENST00000297338	NM_006265.2	603	Ctt/Att	14/14	1	2	FACETS	0.851	0.723	0.989	0.851	0.723	0.989	CLONAL	1	TRUE	1	0.38	2		165	297	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862877	117862877	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	30	244	0	ENST00000297338.2:c.1600G>T	p.Glu534Ter	p.E534*	ENST00000297338	NM_006265.2	534	Gaa/Taa	12/14	1	2	FACETS	0.384	0.309	0.469	0.384	0.309	0.469	SUBCLONAL	1	TRUE	1	0.38	2		244	411	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069064	5069064	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	59	189	0	ENST00000381652.3:c.1369A>C	p.Asn457His	p.N457H	ENST00000381652	NM_004972.3	457	Aat/Cat	11/25	1	2	FACETS	0.933	0.807	1	0.933	0.807	1	CLONAL	1	TRUE	1	0.38	2		189	333	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080273	5080273	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	31	145	0	ENST00000381652.3:c.2176A>C	p.Asn726His	p.N726H	ENST00000381652	NM_004972.3	726	Aat/Cat	17/25	1	2	FACETS	0.745	0.607	0.899	0.745	0.607	0.899	SUBCLONAL	1	TRUE	1	0.38	2		145	219	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460421	8460421	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	49	245	1	ENST00000356435.5:c.3865C>A	p.Leu1289Ile	p.L1289I	ENST00000356435		1289	Ctt/Att	22/35	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.38	2		246	246	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485907	8485907	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	21	313	0	ENST00000356435.5:c.2910G>T	p.Gln970His	p.Q970H	ENST00000356435		970	caG/caT	17/35	1	2	FACETS	0.37	0.285	0.469	0.37	0.285	0.469	SUBCLONAL	1	TRUE	1	0.38	2		313	299	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633425	8633425	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	55	302	0	ENST00000356435.5:c.244C>A	p.Leu82Ile	p.L82I	ENST00000356435		82	Ctc/Atc	3/35	1	2	FACETS	0.962	0.828	1	0.962	0.828	1	CLONAL	1	TRUE	1	0.38	2		302	301	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317274	87317274	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs890209390	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	83	319	0	ENST00000277120.3:c.299A>G	p.Asp100Gly	p.D100G	ENST00000277120		100	gAt/gGt	4/19	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.38	2		319	406	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87356828	87356828	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	50	202	0	ENST00000277120.3:c.1181A>G	p.Asp394Gly	p.D394G	ENST00000277120		394	gAt/gGt	10/19	1	2	FACETS	0.7	0.596	0.814	0.7	0.596	0.814	SUBCLONAL	1	TRUE	1	0.38	2		202	376	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93626877	93626877	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1211510060	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	67	347	1	ENST00000375746.1:c.724G>A	p.Glu242Lys	p.E242K	ENST00000375746	NM_001174167.1	242	Gag/Aag	5/14	1	2	FACETS	0.852	0.743	0.968	0.852	0.743	0.968	CLONAL	1	TRUE	1	0.38	2		348	414	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753939	133753939	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	83	440	1	ENST00000318560.5:c.1408G>T	p.Glu470Ter	p.E470*	ENST00000318560	NM_005157.4	470	Gaa/Taa	8/11	1	2	FACETS	0.995	0.882	1	0.995	0.882	1	CLONAL	1	TRUE	1	0.38	2		441	439	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781078	135781078	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	109	526	1	ENST00000298552.3:c.1887G>T	p.Lys629Asn	p.K629N	ENST00000298552	NM_001162426.1	629	aaG/aaT	15/23	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.38	2		527	566	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300116	137300116	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	114	706	0	ENST00000481739.1:c.401T>G	p.Ile134Ser	p.I134S	ENST00000481739	NM_002957.4	134	aTc/aGc	3/10	1	2	FACETS	0.772	0.695	0.854	0.772	0.695	0.854	SUBCLONAL	1	TRUE	1	0.38	2		706	777	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411707	63411707	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	101	719	0	ENST00000330258.3:c.1460T>C	p.Leu487Pro	p.L487P	ENST00000330258	NM_152424.3	487	cTg/cCg	2/2	1	2	FACETS	0.829	0.742	0.922	0.829	0.742	0.922	CLONAL	1	TRUE	1	0.38	2		719	641	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361782	70361782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	136	671	0	ENST00000374080.3:c.6458C>T	p.Ala2153Val	p.A2153V	ENST00000374080		2153	gCt/gTt	44/45	1	2	FACETS	0.906	0.824	0.992	0.906	0.824	0.992	CLONAL	1	TRUE	1	0.38	2		671	790	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615596	100615596	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	59	480	0	ENST00000308731.7:c.736G>T	p.Glu246Ter	p.E246*	ENST00000308731	NM_000061.2	246	Gaa/Taa	8/19	1	2	FACETS	0.711	0.613	0.816	0.711	0.613	0.816	SUBCLONAL	1	TRUE	1	0.38	2		480	437	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123040904	123040904	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	85	439	0	ENST00000355640.3:c.1367G>T	p.Arg456Ile	p.R456I	ENST00000355640		456	aGa/aTa	7/7	1	2	FACETS	0.865	0.767	0.97	0.865	0.767	0.97	CLONAL	1	TRUE	1	0.38	2		439	517	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224433	123224433	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	78	365	0	ENST00000218089.9:c.3286A>C	p.Ser1096Arg	p.S1096R	ENST00000218089	NM_001042749.1	1096	Agt/Cgt	31/35	1	2	FACETS	0.923	0.814	1	0.923	0.814	1	CLONAL	1	TRUE	1	0.38	2		365	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201059	NA	P-0041371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	132	526	0	ENST00000269305.4:c.856G>T	p.Glu286Ter	p.E286*	ENST00000269305	NM_001126112.2	286	Gaa/Taa	8/11	0.623014755454511	1	FACETS	0.966	0.892	1	0.966	0.892	1	CLONAL	1	TRUE	0	0.623014755454511	1		526	302	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948160	178948160	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	63	215	0	ENST00000263967.3:c.2932G>C	p.Glu978Gln	p.E978Q	ENST00000263967	NM_006218.2	978	Gag/Cag	20/21	0.623014755454511	7	FACETS	1	0.964	1			1	CLONAL	1	TRUE	NA	0.623014755454511	7		215	387	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240695	55240695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764359156	NA	P-0041371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	166	848	1	ENST00000275493.2:c.1939G>A	p.Ala647Thr	p.A647T	ENST00000275493	NM_005228.3	647	Gcc/Acc	17/28	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.623014755454511	2		849	529	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845334	76845334	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	80	340	0	ENST00000373344.5:c.6187G>C	p.Glu2063Gln	p.E2063Q	ENST00000373344	NM_000489.3	2063	Gaa/Caa	27/35	1	2	FACETS	0.702	0.622	0.786	0.702	0.622	0.786	SUBCLONAL	1	TRUE	1	0.623014755454511	2		340	366	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407859	139407859	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756642176	NA	P-0041371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	76	605	0	ENST00000277541.6:c.2338C>T	p.Arg780Trp	p.R780W	ENST00000277541	NM_017617.3	780	Cgg/Tgg	14/34	0.623014755454511	1	FACETS	0.587	0.521	0.657	0.587	0.521	0.657	SUBCLONAL	1	TRUE	0	0.623014755454511	1		605	286	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374132	118374132	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	101	400	0	ENST00000534358.1:c.7525G>C	p.Glu2509Gln	p.E2509Q	ENST00000534358	NM_005933.3	2509	Gaa/Caa	27/36	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.623014755454511	2		400	320	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375590	118375590	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	73	312	1	ENST00000534358.1:c.8983G>T	p.Asp2995Tyr	p.D2995Y	ENST00000534358	NM_005933.3	2995	Gat/Tat	27/36	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.623014755454511	2		313	218	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024607	14024607	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	91	333	0	ENST00000311895.7:c.833G>T	p.Gly278Val	p.G278V	ENST00000311895	NM_005236.2	278	gGa/gTa	5/11	0.623014755454511	3	FACETS	0.564	0.501	0.632	0.282	0.25	0.316	SUBCLONAL	1	TRUE	1	0.623014755454511	3		333	679	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0041374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	608	552	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.676565976760538	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.676565976760538	2		552	880	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916851	48916851	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1131690902	NA	P-0041374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	171	279	0	ENST00000267163.4:c.380+1G>A		p.X127_splice	ENST00000267163	NM_000321.2	127			0.676565976760538	2	FACETS	0.983	0.931	1	0.983	0.931	1	CLONAL	2	TRUE	0	0.676565976760538	2		279	257	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442441	49442441	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0041374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	222	558	0	ENST00000301067.7:c.4131+1G>T		p.X1377_splice	ENST00000301067	NM_003482.3	1377			0.676565976760538	3	FACETS	0.917	0.854	0.982	0.458	0.427	0.491	CLONAL	1	TRUE	1	0.676565976760538	3		558	958	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445089	49445089	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1360040004	NA	P-0041374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	583	670	0	ENST00000301067.7:c.2377G>T	p.Glu793Ter	p.E793*	ENST00000301067	NM_003482.3	793	Gag/Tag	10/54	0.676565976760538	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.676565976760538	3		670	1144	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56873443	56873443	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	198	405	0	ENST00000308159.5:c.2147G>T	p.Arg716Leu	p.R716L	ENST00000308159	NM_014669.4	716	cGc/cTc	20/22	0.676565976760538	3	FACETS	0.913	0.847	0.982	0.456	0.423	0.491	CLONAL	1	TRUE	1	0.676565976760538	3		405	858	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965838	18965838	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	266	482	0	ENST00000262803.5:c.1416C>A	p.Asn472Lys	p.N472K	ENST00000262803	NM_002911.3	472	aaC/aaA	10/24	0.676565976760538	3	FACETS	1	0.976	1	0.538	0.505	0.572	CLONAL	1	TRUE	1	0.676565976760538	3		482	978	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762505	41762505	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	159	361	0	ENST00000301178.4:c.2185A>G	p.Lys729Glu	p.K729E	ENST00000301178	NM_021913.4	729	Aag/Gag	18/20	0.676565976760538	3	FACETS	1	0.939	1	0.511	0.471	0.554	CLONAL	1	TRUE	1	0.676565976760538	3		361	615	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539723	187539724	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	331	379	0	ENST00000441802.2:c.8016dup	p.Val2673CysfsTer2	p.V2673Cfs*2	ENST00000441802	NM_005245.3	2672	-/T	10/27	0.676565976760538	2	FACETS	0.982	0.945	1	0.982	0.945	1	CLONAL	2	TRUE	0	0.676565976760538	2		379	498	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953117	38953117	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	67	202	0	ENST00000357387.3:c.2867C>T	p.Ala956Val	p.A956V	ENST00000357387	NM_152756.3	956	gCa/gTa	29/38	0.676565976760538	5	FACETS	0.726	0.631	0.828	0.242	0.21	0.276	SUBCLONAL	1	TRUE	2	0.676565976760538	5		202	550	SUCCESS
APC	324	MSKCC	GRCh37	5	112177335	112177335	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	231	264	0	ENST00000257430.4:c.6044A>T	p.Glu2015Val	p.E2015V	ENST00000257430	NM_000038.5	2015	gAa/gTa	16/16	0.676565976760538	2	FACETS	0.869	0.825	0.912	0.869	0.825	0.912	CLONAL	2	TRUE	0	0.676565976760538	2		264	393	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874227	151874227	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	280	332	0	ENST00000262189.6:c.8311A>T	p.Ser2771Cys	p.S2771C	ENST00000262189	NM_170606.2	2771	Agc/Tgc	38/59	0.668315861521064	4	FACETS	0.976	0.922	1	0.976	0.922	1	CLONAL	2	TRUE	2	0.676565976760538	4		332	711	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508746	29508746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	174	437	0	ENST00000356175.3:c.673G>A	p.Glu225Lys	p.E225K	ENST00000356175	NM_000267.3	225	Gaa/Aaa	7/57	0.350218203884505	4	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.707301893656962	4		437	615	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575553	64575553	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	214	535	0	ENST00000312049.6:c.464C>G	p.Ser155Cys	p.S155C	ENST00000312049	NM_130799.2	155	tCc/tGc	3/10	NA	2	FACETS	1	0.962	1			1	INDETERMINATE	1	TRUE	NA	0.707301893656962	2		535	582	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968928	32968928	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	533	306	0	ENST00000380152.3:c.9359T>G	p.Ile3120Ser	p.I3120S	ENST00000380152		3120	aTt/aGt	25/27	0.707301893656962	8	FACETS	0.984	0.95	1			1	CLONAL	5	TRUE	NA	0.707301893656962	8		306	956	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004792	16004792	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	193	566	0	ENST00000268712.3:c.2462C>A	p.Ser821Tyr	p.S821Y	ENST00000268712	NM_006311.3	821	tCt/tAt	20/46	0.707301893656962	3	FACETS	0.873	0.809	0.94	0.437	0.404	0.47	CLONAL	1	TRUE	1	0.707301893656962	3		566	846	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067371	37067371	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	148	421	0	ENST00000231790.2:c.1282G>T	p.Asp428Tyr	p.D428Y	ENST00000231790	NM_000249.3	428	Gat/Tat	12/19	0.707301893656962	3	FACETS	0.947	0.869	1	0.474	0.434	0.515	CLONAL	1	TRUE	1	0.707301893656962	3		421	598	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0041417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	159	304	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.742276340747306	2		304	399	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440295	52440295	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs776240891	NA	P-0041417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	260	482	0	ENST00000460680.1:c.757C>T	p.Gln253Ter	p.Q253*	ENST00000460680	NM_004656.3	253	Cag/Tag	9/17	0.737136595379047	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.742276340747306	1		482	421	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407979	139407979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200816814	NA	P-0041462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	313	576	0	ENST00000277541.6:c.2218G>A	p.Asp740Asn	p.D740N	ENST00000277541	NM_017617.3	740	Gac/Aac	14/34	0.222208208796671	3	FACETS	0.98	0.93	1	0.654	0.62	0.688	INDETERMINATE	2	TRUE	0	0.513016279818908	3		576	782	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037891	49037891	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	101	325	0	ENST00000267163.4:c.2131del	p.Ile711TyrfsTer4	p.I711Yfs*4	ENST00000267163	NM_000321.2	711	Ata/ta	21/27	0.513016279818908	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.513016279818908	1		325	280	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330572	65330572	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	127	441	1	ENST00000342505.4:c.1074G>C	p.Lys358Asn	p.K358N	ENST00000342505	NM_002227.2	358	aaG/aaC	8/25	0.436094421796549	4	FACETS	0.85	0.77	0.935	0.283	0.256	0.312	CLONAL	1	TRUE	1	0.513016279818908	4		442	881	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812138	43812138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139770726	NA	P-0041513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	134	737	1	ENST00000372470.3:c.1003G>A	p.Glu335Lys	p.E335K	ENST00000372470	NM_005373.2	335	Gaa/Aaa	7/12	1	2	FACETS	0.903	0.826	0.984	0.903	0.826	0.984	CLONAL	1	TRUE	1	0.586350004152132	2		738	506	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542584	141542592	+	inframe_deletion	In_Frame_Del	DEL	GCTGGGATG	GCTGGGATG	-	novel	NA	P-0041513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	195	1037	2	ENST00000220592.5:c.2394_2402del	p.Ile799_Ala801del	p.I799_A801del	ENST00000220592	NM_012154.3	798	tcCATCCCAGCg/tcg	18/19	1	2	FACETS	0.893	0.829	0.959	0.893	0.829	0.959	CLONAL	1	TRUE	1	0.586350004152132	2		1039	745	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0041521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	118	426	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.321954891812737	2		426	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0041521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	139	772	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.321954891812737	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.321954891812737	1		772	665	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0041521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	44	373	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	0.321954891812737	1	FACETS	0.644	0.542	0.757	0.644	0.542	0.757	SUBCLONAL	1	TRUE	0	0.321954891812737	1		373	356	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451474	187451474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145456310	NA	P-0041521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	112	411	1	ENST00000232014.4:c.8C>T	p.Ser3Leu	p.S3L	ENST00000232014	NM_001130845.1	3	tCg/tTg	3/10	0.188681214147798	3	FACETS	0.805	0.727	0.886	0.805	0.727	0.886	INDETERMINATE	2	TRUE	1	0.321954891812737	3		412	502	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502828	186502828	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	107	544	0	ENST00000323963.5:c.286G>C	p.Glu96Gln	p.E96Q	ENST00000323963		96	Gag/Cag	4/11	0.188681214147798	3	FACETS	1	0.982	1	0.719	0.647	0.794	INDETERMINATE	1	TRUE	1	0.321954891812737	3		544	537	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868516	117868516	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	21	284	0	ENST00000297338.2:c.826G>C	p.Asp276His	p.D276H	ENST00000297338	NM_006265.2	276	Gat/Cat	8/14	0.315023190171384	4	FACETS	0.48	0.369	0.61	0.24	0.184	0.305	SUBCLONAL	1	TRUE	2	0.321954891812737	4		284	359	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445575	49445575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	126	934	1	ENST00000301067.7:c.1891G>A	p.Glu631Lys	p.E631K	ENST00000301067	NM_003482.3	631	Gag/Aag	10/54	1	2	FACETS	0.92	0.833	1	0.92	0.833	1	CLONAL	1	TRUE	1	0.321954891812737	2		935	851	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40854926	40854926	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	156	631	0	ENST00000428826.2:c.2152C>T	p.Gln718Ter	p.Q718*	ENST00000428826		718	Caa/Taa	20/21	0.188681214147798	3	FACETS	0.899	0.826	0.974	0.899	0.826	0.974	INDETERMINATE	2	TRUE	1	0.321954891812737	3		631	626	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741835	17741875	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCGCCCCCTGGCGCCGCAGCCGCCTTCTATGCGCCGGGC	CCGCGCCCCCTGGCGCCGCAGCCGCCTTCTATGCGCCGGGC	-	novel	NA	P-0041521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	58	213	0	ENST00000250003.3:c.510_550del	p.Pro171AlafsTer93	p.P171Afs*93	ENST00000250003	NM_002478.4	169	gCCGCGCCCCCTGGCGCCGCAGCCGCCTTCTATGCGCCGGGC/g	1/3	1	2	FACETS	0.78	0.678	0.888	1	0.973	1	SUBCLONAL	2	TRUE	1	0.321954891812737	2		213	231	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111965548	111965551	+	frameshift_variant	Frame_Shift_Del	DEL	ACTG	ACTG	-	rs587776648	NA	P-0041521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	45	229	0	ENST00000375549.3:c.337_340del	p.Asp113MetfsTer21	p.D113Mfs*21	ENST00000375549	NM_003002.3	112	ACTGac/ac	4/4	1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	1	0.321954891812737	2		229	276	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109925	115109925	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs757838938	NA	P-0041521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	104	673	0	ENST00000257566.3:c.1953C>G	p.Asp651Glu	p.D651E	ENST00000257566	NM_016569.3	651	gaC/gaG	8/8	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.321954891812737	2		673	632	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135409	30135409	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	57	383	1	ENST00000331968.5:c.409G>T	p.Ala137Ser	p.A137S	ENST00000331968	NM_002742.2	137	Gcc/Tcc	3/18	0.177766022122376	3	FACETS	1	0.884	1			1	INDETERMINATE	1	TRUE	NA	0.321954891812737	3		384	399	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989222	41989222	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0041521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	60	427	0	ENST00000219905.7:c.2013+1G>T		p.X671_splice	ENST00000219905	NM_001164273.1	671			0.321954891812737	1	FACETS	0.838	0.726	0.96	0.838	0.726	0.96	CLONAL	1	TRUE	0	0.321954891812737	1		427	373	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40854949	40854949	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	164	627	1	ENST00000428826.2:c.2129G>T	p.Gly710Val	p.G710V	ENST00000428826		710	gGg/gTg	20/21	0.188681214147798	3	FACETS	0.903	0.832	0.976	0.903	0.832	0.976	INDETERMINATE	2	TRUE	1	0.321954891812737	3		628	655	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031565	11031565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	112	790	1	ENST00000327064.4:c.1480G>A	p.Glu494Lys	p.E494K	ENST00000327064	NM_199141.1	494	Gaa/Aaa	13/16	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.321954891812737	2		791	679	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668664	52668664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1343496358	NA	P-0041521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	99	563	0	ENST00000394830.3:c.1255G>A	p.Asp419Asn	p.D419N	ENST00000394830	NM_018313.4	419	Gat/Aat	12/30	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.321954891812737	2		563	588	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398910	398910	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	73	537	0	ENST00000380956.4:c.720G>T	p.Arg240Ser	p.R240S	ENST00000380956	NM_001195286.1	240	agG/agT	6/9	NA	2	FACETS	0.841	0.737	0.953			1	INDETERMINATE	1	TRUE	NA	0.321954891812737	2		537	539	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964367	93964367	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	66	419	0	ENST00000369303.4:c.2530G>A	p.Asp844Asn	p.D844N	ENST00000369303	NM_004440.3	844	Gat/Aat	14/17	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.321954891812737	2		419	399	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392159	81392159	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1241118241	NA	P-0041521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	20	302	0	ENST00000222390.5:c.118C>A	p.His40Asn	p.H40N	ENST00000222390	NM_000601.4	40	Cat/Aat	2/18	0.321954891812737	3	FACETS	0.374	0.285	0.478	0.187	0.142	0.239	SUBCLONAL	1	TRUE	1	0.321954891812737	3		302	386	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968088	68968088	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	92	520	0	ENST00000288368.4:c.1117G>T	p.Asp373Tyr	p.D373Y	ENST00000288368	NM_024870.2	373	Gat/Tat	10/40	0.321954891812737	3	FACETS	0.955	0.849	1	0.477	0.424	0.534	CLONAL	1	TRUE	1	0.321954891812737	3		520	695	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141549505	141549505	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	70	490	2	ENST00000220592.5:c.2083G>C	p.Glu695Gln	p.E695Q	ENST00000220592	NM_012154.3	695	Gaa/Caa	16/19	0.315023190171384	4	FACETS	0.874	0.761	0.995	0.437	0.38	0.498	CLONAL	1	TRUE	2	0.321954891812737	4		492	658	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410837	63410837	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	93	714	0	ENST00000330258.3:c.2330C>A	p.Thr777Asn	p.T777N	ENST00000330258	NM_152424.3	777	aCc/aAc	2/2	1	2	FACETS	0.942	0.839	1	0.942	0.839	1	CLONAL	1	TRUE	1	0.321954891812737	2		714	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	190	571	0	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	0.344738971546948	2	FACETS	0.83	0.772	0.888	0.83	0.772	0.888	CLONAL	2	TRUE	0	0.40754935206278	2		571	562	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940012	76940012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs122445105	NA	P-0041554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	88	558	1	ENST00000373344.5:c.736C>T	p.Arg246Cys	p.R246C	ENST00000373344	NM_000489.3	246	Cgc/Tgc	9/35	0.40754935206278	1	FACETS	0.759	0.676	0.847	0.759	0.676	0.847	SUBCLONAL	1	TRUE	0	0.40754935206278	1		559	453	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026204	48026204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750440	NA	P-0041554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	50	390	0	ENST00000234420.5:c.1082G>A	p.Arg361His	p.R361H	ENST00000234420	NM_000179.2	361	cGc/cAc	4/10	0.329719556788793	2	FACETS	0.717	0.611	0.833	0.359	0.305	0.417	SUBCLONAL	1	TRUE	0	0.40754935206278	2		390	342	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922363	178922363	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	52	344	0	ENST00000263967.3:c.1132T>C	p.Cys378Arg	p.C378R	ENST00000263967	NM_006218.2	378	Tgt/Cgt	6/21	0.223398477486896	5	FACETS	0.947	0.808	1	0.316	0.269	0.367	INDETERMINATE	1	TRUE	2	0.40754935206278	5		344	434	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391880	139391880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	110	655	0	ENST00000277541.6:c.6311G>A	p.Arg2104His	p.R2104H	ENST00000277541	NM_017617.3	2104	cGc/cAc	34/34	0.360802912458803	3	FACETS	0.865	0.778	0.958	0.433	0.389	0.479	CLONAL	1	TRUE	1	0.40754935206278	3		655	751	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62316910	62316926	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGTTCCCCAGCAGGG	CTGGTTCCCCAGCAGGG	-	novel	NA	P-0041554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	75	516	0	ENST00000360203.5:c.1230_1246del	p.Ser411GlyfsTer6	p.S411Gfs*6	ENST00000360203	NM_001283009.1	409	cCTGGTTCCCCAGCAGGG/c	15/35	0.360802912458803	3	FACETS	0.801	0.703	0.907	0.401	0.351	0.454	CLONAL	1	TRUE	1	0.40754935206278	3		516	553	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905121	50905121	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	93	529	0	ENST00000440232.2:c.403T>C	p.Phe135Leu	p.F135L	ENST00000440232	NM_002691.3	135	Ttc/Ctc	4/27	0.360802912458803	3	FACETS	0.876	0.78	0.978	0.438	0.39	0.489	CLONAL	1	TRUE	1	0.40754935206278	3		529	627	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61760926	61760926	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	45	461	0	ENST00000401558.2:c.107A>G	p.Tyr36Cys	p.Y36C	ENST00000401558	NM_003400.3	36	tAc/tGc	2/25	0.329719556788793	2	FACETS	0.615	0.518	0.721	0.308	0.259	0.361	SUBCLONAL	1	TRUE	0	0.40754935206278	2		461	359	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537157	80537157	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	65	457	0	ENST00000286548.4:c.241C>G	p.Gln81Glu	p.Q81E	ENST00000286548	NM_002072.3	81	Cag/Gag	2/7	0.401941624747559	2	FACETS	0.818	0.712	0.931	0.409	0.356	0.466	CLONAL	1	TRUE	0	0.40754935206278	2		457	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577569	7577569	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519981	NA	P-0041582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	226	522	0	ENST00000269305.4:c.712T>G	p.Cys238Gly	p.C238G	ENST00000269305	NM_001126112.2	238	Tgt/Ggt	7/11	0.223319791852416	3	FACETS	1	0.987	1	0.812	0.76	0.866	CLONAL	2	FALSE	0	0.3	3		522	711	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253826	153253826	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	117	268	0	ENST00000281708.4:c.907C>T	p.Gln303Ter	p.Q303*	ENST00000281708	NM_033632.3	303	Caa/Taa	6/12	0.273408366181006	2	FACETS	0.863	0.783	0.946	0.863	0.783	0.946	CLONAL	2	FALSE	0	0.3	2		268	452	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77069942	77069942	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0041582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	43	359	0	ENST00000356341.3:c.597+1G>T		p.X199_splice	ENST00000356341	NM_002576.4	199			0.260881335185718	3	FACETS	0.591	0.494	0.699	0.295	0.247	0.35	SUBCLONAL	1	FALSE	1	0.3	3		359	558	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81971384	81971384	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	132	396	0	ENST00000359376.3:c.3074A>T	p.His1025Leu	p.H1025L	ENST00000359376	NM_002661.3	1025	cAc/cTc	28/33	0.113886998200438	4	FACETS	0.991	0.904	1	0.991	0.904	1	INDETERMINATE	2	FALSE	2	0.3	4		396	577	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39751860	39751860	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	31	379	0	ENST00000361337.2:c.2221G>C	p.Glu741Gln	p.E741Q	ENST00000361337	NM_003286.2	741	Gag/Cag	21/21	0.113886998200438	4	FACETS	0.462	0.373	0.564	0.231	0.186	0.282	INDETERMINATE	1	FALSE	2	0.3	4		379	581	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508819	31508819	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	42	556	0	ENST00000344624.3:c.1496C>G	p.Ser499Cys	p.S499C	ENST00000344624		499	tCt/tGt	7/33	0.3	3	FACETS	0.4	0.332	0.475	0.2	0.166	0.238	SUBCLONAL	1	FALSE	1	0.3	3		556	806	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355209	81355209	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	36	166	0	ENST00000222390.5:c.1165C>T	p.Gln389Ter	p.Q389*	ENST00000222390	NM_000601.4	389	Caa/Taa	9/18	0.140695874856632	3	FACETS	1	0.852	1	0.517	0.427	0.616	INDETERMINATE	1	FALSE	1	0.3	3		166	267	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395003	139395003	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0041582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	86	401	0	ENST00000277541.6:c.5934+1G>A		p.X1978_splice	ENST00000277541	NM_017617.3	1978			0.3	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	0	0.3	1		401	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0041587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	709	618	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.594495387864297	2	FACETS	1	0.993	1	1	0.998	1	CLONAL	3	TRUE	0	0.594495387864297	2		618	785	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0041587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	118	236	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.594495387864297	2		236	290	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287287	46287291	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGA	GAGGA	-	novel	NA	P-0041587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	40	455	1	ENST00000334344.6:c.5237_5241del	p.Arg1746IlefsTer12	p.R1746Ifs*12	ENST00000334344	NM_152641.2	1744	ctGAGGAga/ctga	19/21	1	2	FACETS	0.237	0.196	0.282	0.237	0.196	0.282	SUBCLONAL	1	TRUE	1	0.594495387864297	2		456	568	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937606	76937606	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0041587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	188	146	0	ENST00000373344.5:c.3142A>T	p.Lys1048Ter	p.K1048*	ENST00000373344	NM_000489.3	1048	Aaa/Taa	9/35	1	1	FACETS	0.97	0.933	1	1	0.995	1	CLONAL	2	TRUE	0	0.594495387864297	1		146	229	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858517	9858517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765370528	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	95	417	0	ENST00000330684.3:c.2884G>A	p.Glu962Lys	p.E962K	ENST00000330684	NM_001134407.1	962	Gaa/Aaa	13/13	1	2	FACETS	0.673	0.601	0.748	0.673	0.601	0.748	SUBCLONAL	1	TRUE	1	0.593478784978778	2		417	476	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793483	18793483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603405	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	39	268	0	ENST00000266497.5:c.4180G>A	p.Glu1394Lys	p.E1394K	ENST00000266497		1394	Gaa/Aaa	30/31	0.463865351229979	1	FACETS	0.571	0.48	0.668	0.571	0.48	0.668	SUBCLONAL	1	TRUE	0	0.593478784978778	1		268	162	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781193	135781193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768985094	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	202	492	0	ENST00000298552.3:c.1772C>T	p.Pro591Leu	p.P591L	ENST00000298552	NM_001162426.1	591	cCg/cTg	15/23	0.498143166730169	1	FACETS	0.777	0.725	0.831	0.777	0.725	0.831	SUBCLONAL	1	TRUE	0	0.593478784978778	1		492	616	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857556	9857556	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1480366023	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	102	349	0	ENST00000330684.3:c.3845A>G	p.Asn1282Ser	p.N1282S	ENST00000330684	NM_001134407.1	1282	aAc/aGc	13/13	1	2	FACETS	0.816	0.735	0.902	0.816	0.735	0.902	CLONAL	1	TRUE	1	0.593478784978778	2		349	421	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795073	242795073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1429395114	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	319	728	0	ENST00000334409.5:c.136G>A	p.Glu46Lys	p.E46K	ENST00000334409	NM_005018.2	46	Gaa/Aaa	2/5	0.32212740173999	3	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.593478784978778	3		728	1351	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578214	28578214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778369	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	119	426	2	ENST00000241453.7:c.2957C>T	p.Pro986Leu	p.P986L	ENST00000241453	NM_004119.2	986	cCg/cTg	24/24	1	2	FACETS	0.682	0.617	0.75	0.682	0.617	0.75	SUBCLONAL	1	TRUE	1	0.593478784978778	2		428	588	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	436	675	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	0.593478784978778	3	FACETS	0.767	0.732	0.803	0.767	0.732	0.803	SUBCLONAL	2	TRUE	1	0.593478784978778	3		675	1242	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117650583	117650583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	48	432	0	ENST00000368508.3:c.5275C>T	p.Pro1759Ser	p.P1759S	ENST00000368508	NM_002944.2	1759	Ccc/Tcc	32/43	0.3702784493507	1	FACETS	0.542	0.463	0.626	0.542	0.463	0.626	SUBCLONAL	1	TRUE	0	0.593478784978778	1		432	210	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679798	88679798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774739739	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	190	471	1	ENST00000360948.2:c.665G>A	p.Arg222Gln	p.R222Q	ENST00000360948	NM_001012338.2	222	cGa/cAa	7/19	1	2	FACETS	0.76	0.703	0.818	0.76	0.703	0.818	SUBCLONAL	1	TRUE	1	0.593478784978778	2		472	843	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27203119	27203119	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	107	374	1	ENST00000380036.4:c.2209+2T>C		p.X737_splice	ENST00000380036	NM_000459.3	737			0.498143166730169	1	FACETS	0.808	0.734	0.884	0.808	0.734	0.884	CLONAL	1	TRUE	0	0.593478784978778	1		375	314	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626694	28626694	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	151	339	0	ENST00000241453.7:c.602C>T	p.Ser201Leu	p.S201L	ENST00000241453	NM_004119.2	201	tCa/tTa	5/24	1	2	FACETS	0.85	0.78	0.922	0.85	0.78	0.922	CLONAL	1	TRUE	1	0.593478784978778	2		339	599	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922009	39922009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	200	506	0	ENST00000378444.4:c.4163C>T	p.Ala1388Val	p.A1388V	ENST00000378444	NM_001123385.1	1388	gCc/gTc	9/15	0.238032403736613	1	FACETS	0.605	0.562	0.65	0.605	0.562	0.65	INDETERMINATE	1	TRUE	0	0.593478784978778	1		506	783	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813599	50813599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	93	421	0	ENST00000398568.2:c.1153C>T	p.Leu385Phe	p.L385F	ENST00000398568	NM_001042412.1	385	Ctt/Ttt	8/18	1	2	FACETS	0.634	0.566	0.707	0.634	0.566	0.707	SUBCLONAL	1	TRUE	1	0.593478784978778	2		421	494	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900639	32900639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41293469	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	63	317	0	ENST00000380152.3:c.520C>T	p.Arg174Cys	p.R174C	ENST00000380152		174	Cgt/Tgt	7/27	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.593478784978778	2		317	211	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263415	123263415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757125418	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	157	383	0	ENST00000358487.5:c.1328C>T	p.Pro443Leu	p.P443L	ENST00000358487	NM_000141.4	443	cCg/cTg	10/18	0.3702784493507	1	FACETS	0.77	0.711	0.831	0.77	0.711	0.831	SUBCLONAL	1	TRUE	0	0.593478784978778	1		383	483	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860908	151860908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	51	231	0	ENST00000262189.6:c.9754C>T	p.Arg3252Cys	p.R3252C	ENST00000262189	NM_170606.2	3252	Cgt/Tgt	43/59	0.526982462491452	3	FACETS	0.847	0.726	0.978	0.424	0.363	0.489	CLONAL	1	TRUE	1	0.593478784978778	3		231	263	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678334	88678334	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	167	492	0	ENST00000360948.2:c.1202C>T	p.Pro401Leu	p.P401L	ENST00000360948	NM_001012338.2	401	cCa/cTa	9/19	1	2	FACETS	0.773	0.712	0.837	0.773	0.712	0.837	SUBCLONAL	1	TRUE	1	0.593478784978778	2		492	728	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221162	5221162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	296	594	1	ENST00000357368.4:c.3304C>T	p.Arg1102Cys	p.R1102C	ENST00000357368	NM_002850.3	1102	Cgc/Tgc	20/38	0.112916994651603	4	FACETS	0.751	0.708	0.796	0.751	0.708	0.796	INDETERMINATE	2	TRUE	2	0.593478784978778	4		595	1058	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958126	2958126	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs763435728	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	569	645	2	ENST00000396946.4:c.2606G>A	p.Arg869Gln	p.R869Q	ENST00000396946	NM_032415.4	869	cGg/cAg	19/25	0.526982462491452	3	FACETS	0.906	0.872	0.941	0.906	0.872	0.941	CLONAL	2	TRUE	1	0.593478784978778	3		647	1372	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982408	201982408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	301	672	1	ENST00000359651.3:c.787G>A	p.Gly263Ser	p.G263S	ENST00000359651		263	Ggc/Agc	6/8	1	2	FACETS	0.771	0.725	0.818	0.771	0.725	0.818	SUBCLONAL	1	TRUE	1	0.593478784978778	2		673	1316	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858062	152858062	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	219	489	0	ENST00000406277.2:c.553C>T	p.Gln185Ter	p.Q185*	ENST00000406277	NM_152274.4	185	Cag/Tag	6/7	0.238032403736613	1	FACETS	0.697	0.65	0.744	0.697	0.65	0.744	INDETERMINATE	1	TRUE	0	0.593478784978778	1		489	745	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243668595	243668595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	51	313	1	ENST00000263826.5:c.1396C>T	p.Pro466Ser	p.P466S	ENST00000263826	NM_005465.4	466	Ccg/Tcg	13/13	1	2	FACETS	0.433	0.369	0.503	0.433	0.369	0.503	SUBCLONAL	1	TRUE	1	0.593478784978778	2		314	397	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246498709	246498709	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	100	460	0	ENST00000388985.4:c.296C>T	p.Pro99Leu	p.P99L	ENST00000388985		99	cCa/cTa	3/12	1	2	FACETS	0.722	0.648	0.799	0.722	0.648	0.799	SUBCLONAL	1	TRUE	1	0.593478784978778	2		460	467	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100331	8100332	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1318	268	655	0	ENST00000346208.3:c.305_306delinsTT	p.Ala102Val	p.A102V	ENST00000346208		102	gCC/gTT	3/6	0.3702784493507	1	FACETS	0.4	0.374	0.428	0.4	0.374	0.428	SUBCLONAL	1	TRUE	0	0.593478784978778	1		655	1586	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724352	112724352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	154	498	0	ENST00000369452.4:c.236C>T	p.Pro79Leu	p.P79L	ENST00000369452	NM_007373.3	79	cCt/cTt	2/9	0.3702784493507	1	FACETS	0.737	0.68	0.797	0.737	0.68	0.797	SUBCLONAL	1	TRUE	0	0.593478784978778	1		498	495	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	430261	430261	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	51	238	0	ENST00000399788.2:c.2441G>A	p.Ser814Asn	p.S814N	ENST00000399788	NM_001042603.1	814	aGt/aAt	18/28	NA	2	FACETS	0.747	0.642	0.86			1	INDETERMINATE	1	TRUE	NA	0.593478784978778	2		238	230	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446909	18446909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	14	272	0	ENST00000266497.5:c.994C>T	p.His332Tyr	p.H332Y	ENST00000266497		332	Cat/Tat	4/31	0.463865351229979	1	FACETS	0.316	0.231	0.417	0.316	0.231	0.417	SUBCLONAL	1	TRUE	0	0.593478784978778	1		272	105	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492563	50492563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	244	579	0	ENST00000394963.4:c.1459G>A	p.Ala487Thr	p.A487T	ENST00000394963	NM_003076.4	487	Gct/Act	12/13	1	2	FACETS	0.795	0.743	0.849	0.795	0.743	0.849	SUBCLONAL	1	TRUE	1	0.593478784978778	2		579	1034	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557727	21557727	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	261	585	0	ENST00000382592.4:c.2118C>A	p.Asn706Lys	p.N706K	ENST00000382592	NM_014572.2	706	aaC/aaA	5/8	1	2	FACETS	0.962	0.903	1	0.962	0.903	1	CLONAL	1	TRUE	1	0.593478784978778	2		585	914	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562727	21562727	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	202	522	1	ENST00000382592.4:c.1192C>T	p.Pro398Ser	p.P398S	ENST00000382592	NM_014572.2	398	Cct/Tct	4/8	1	2	FACETS	0.744	0.69	0.8	0.744	0.69	0.8	SUBCLONAL	1	TRUE	1	0.593478784978778	2		523	915	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906780	32906781	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	47	540	0	ENST00000380152.3:c.1165_1166delinsTT	p.Pro389Leu	p.P389L	ENST00000380152		389	CCg/TTg	10/27	1	2	FACETS	0.425	0.359	0.496	0.425	0.359	0.496	SUBCLONAL	1	TRUE	1	0.593478784978778	2		540	373	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30102104	30102104	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	96	425	0	ENST00000331968.5:c.1363C>T	p.Gln455Ter	p.Q455*	ENST00000331968	NM_002742.2	455	Cag/Tag	9/18	1	2	FACETS	0.943	0.849	1	0.943	0.849	1	CLONAL	1	TRUE	1	0.593478784978778	2		425	343	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476351	88476351	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	227	536	1	ENST00000360948.2:c.1781A>G	p.Asn594Ser	p.N594S	ENST00000360948	NM_001012338.2	594	aAc/aGc	15/19	1	2	FACETS	0.814	0.759	0.871	0.814	0.759	0.871	CLONAL	1	TRUE	1	0.593478784978778	2		537	940	SUCCESS
BLM	641	MSKCC	GRCh37	15	91298061	91298061	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs748581308	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	53	257	0	ENST00000355112.3:c.980C>G	p.Thr327Ser	p.T327S	ENST00000355112	NM_000057.2	327	aCc/aGc	5/22	1	2	FACETS	0.925	0.801	1	0.925	0.801	1	CLONAL	1	TRUE	1	0.593478784978778	2		257	193	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096334	2096334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139165943	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	344	657	1	ENST00000219066.1:c.173C>T	p.Pro58Leu	p.P58L	ENST00000219066	NM_002528.5	58	cCg/cTg	2/6	1	2	FACETS	0.784	0.74	0.828	0.784	0.74	0.828	SUBCLONAL	1	TRUE	1	0.593478784978778	2		658	1479	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032494	12032494	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	41	261	0	ENST00000353533.5:c.930G>A	p.Trp310Ter	p.W310*	ENST00000353533	NM_003010.3	310	tgG/tgA	9/11	0.525904169168585	1	FACETS	0.6	0.507	0.699	0.6	0.507	0.699	SUBCLONAL	1	TRUE	0	0.593478784978778	1		261	162	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661898	29661899	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	32	378	1	ENST00000356175.3:c.5792_5793delinsAA	p.Trp1931Ter	p.W1931*	ENST00000356175	NM_000267.3	1931	tGG/tAA	39/57	1	2	FACETS	0.43	0.35	0.518	0.43	0.35	0.518	SUBCLONAL	1	TRUE	1	0.593478784978778	2		379	251	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224393	36224393	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	325	753	0	ENST00000222270.7:c.6943G>A	p.Gly2315Arg	p.G2315R	ENST00000222270	NM_014727.1	2315	Ggg/Agg	28/37	0.112916994651603	4	FACETS	1	0.993	1	0.671	0.633	0.71	INDETERMINATE	1	TRUE	2	0.593478784978778	4		753	1300	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754509	41754509	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	264	646	0	ENST00000301178.4:c.1628G>A	p.Gly543Glu	p.G543E	ENST00000301178	NM_021913.4	543	gGa/gAa	13/20	0.112916994651603	4	FACETS	1	0.991	1	0.665	0.623	0.708	INDETERMINATE	1	TRUE	2	0.593478784978778	4		646	1066	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791051	42791051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	160	394	1	ENST00000575354.2:c.196G>A	p.Val66Met	p.V66M	ENST00000575354	NM_015125.3	66	Gtg/Atg	2/20	0.112916994651603	4	FACETS	1	0.986	1	0.663	0.61	0.718	INDETERMINATE	1	TRUE	2	0.593478784978778	4		395	648	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794760	42794760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756285021	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	246	525	2	ENST00000575354.2:c.1840C>T	p.Pro614Ser	p.P614S	ENST00000575354	NM_015125.3	614	Ccc/Tcc	10/20	0.112916994651603	4	FACETS	1	0.99	1	0.649	0.607	0.693	INDETERMINATE	1	TRUE	2	0.593478784978778	4		527	1017	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022302	26022302	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	132	479	0	ENST00000435504.4:c.355G>A	p.Asp119Asn	p.D119N	ENST00000435504		119	Gat/Aat	5/13	0.583432896979503	3	FACETS	0.638	0.579	0.701	0.319	0.289	0.351	SUBCLONAL	1	TRUE	1	0.593478784978778	3		479	904	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719658	190719658	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	13	170	0	ENST00000441310.2:c.1660G>T	p.Asp554Tyr	p.D554Y	ENST00000441310	NM_000534.4	554	Gat/Tat	9/13	1	2	FACETS	0.695	0.508	0.912	0.695	0.508	0.912	SUBCLONAL	1	TRUE	1	0.593478784978778	2		170	63	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735635	204735635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	96	282	1	ENST00000302823.3:c.436G>A	p.Gly146Arg	p.G146R	ENST00000302823	NM_005214.4	146	Gga/Aga	2/4	1	2	FACETS	0.737	0.66	0.818	0.737	0.66	0.818	SUBCLONAL	1	TRUE	1	0.593478784978778	2		283	439	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537927	212537927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	88	388	0	ENST00000342788.4:c.1678G>A	p.Glu560Lys	p.E560K	ENST00000342788	NM_005235.2	560	Gag/Aag	14/28	1	2	FACETS	0.564	0.501	0.631	0.564	0.501	0.631	SUBCLONAL	1	TRUE	1	0.593478784978778	2		388	526	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371718	225371718	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	39	377	2	ENST00000264414.4:c.886C>T	p.Leu296Phe	p.L296F	ENST00000264414	NM_003590.4	296	Ctt/Ttt	7/16	1	2	FACETS	0.555	0.463	0.655	0.555	0.463	0.655	SUBCLONAL	1	TRUE	1	0.593478784978778	2		379	237	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39746834	39746835	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	90	373	0	ENST00000361337.2:c.1848_1849delinsTT	p.Leu617Phe	p.L617F	ENST00000361337	NM_003286.2	616	atCCtt/atTTtt	18/21	1	2	FACETS	0.717	0.64	0.799	0.717	0.64	0.799	SUBCLONAL	1	TRUE	1	0.593478784978778	2		373	423	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264119	46264119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1250026993	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	76	261	0	ENST00000371998.3:c.1166C>T	p.Pro389Leu	p.P389L	ENST00000371998		389	cCa/cTa	11/23	1	2	FACETS	0.758	0.67	0.851	0.758	0.67	0.851	SUBCLONAL	1	TRUE	1	0.593478784978778	2		261	338	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295204	1295205	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	119	297	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.621	0.561	0.683	0.621	0.561	0.683	SUBCLONAL	1	TRUE	1	0.593478784978778	2		297	646	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514405	149514405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17853027	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	167	448	0	ENST00000261799.4:c.539C>T	p.Ser180Phe	p.S180F	ENST00000261799	NM_002609.3	180	tCt/tTt	4/23	1	2	FACETS	0.786	0.724	0.85	0.786	0.724	0.85	SUBCLONAL	1	TRUE	1	0.593478784978778	2		448	716	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637387	176637387	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	76	397	0	ENST00000439151.2:c.1987C>T	p.Leu663Phe	p.L663F	ENST00000439151	NM_022455.4	663	Ctt/Ttt	5/23	1	2	FACETS	0.8	0.708	0.898	0.8	0.708	0.898	SUBCLONAL	1	TRUE	1	0.593478784978778	2		397	320	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665451	176665451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	167	320	0	ENST00000439151.2:c.4135C>T	p.Pro1379Ser	p.P1379S	ENST00000439151	NM_022455.4	1379	Ccg/Tcg	7/23	1	2	FACETS	0.842	0.777	0.911	0.842	0.777	0.911	CLONAL	1	TRUE	1	0.593478784978778	2		320	668	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041152	180041152	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	344	684	0	ENST00000261937.6:c.3247C>T	p.Pro1083Ser	p.P1083S	ENST00000261937	NM_182925.4	1083	Cct/Tct	24/30	1	2	FACETS	0.892	0.843	0.941	0.892	0.843	0.941	CLONAL	1	TRUE	1	0.593478784978778	2		684	1300	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043431	180043431	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	304	611	0	ENST00000261937.6:c.3155A>G	p.Lys1052Arg	p.K1052R	ENST00000261937	NM_182925.4	1052	aAg/aGg	23/30	1	2	FACETS	0.871	0.821	0.923	0.871	0.821	0.923	CLONAL	1	TRUE	1	0.593478784978778	2		611	1176	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335056	81335056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	33	241	0	ENST00000222390.5:c.1771G>A	p.Asp591Asn	p.D591N	ENST00000222390	NM_000601.4	591	Gat/Aat	16/18	0.526982462491452	3	FACETS	0.71	0.583	0.851	0.355	0.291	0.426	SUBCLONAL	1	TRUE	1	0.593478784978778	3		241	203	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412000	116412000	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	97	571	0	ENST00000397752.3:c.2985G>A	p.Met995Ile	p.M995I	ENST00000397752	NM_000245.2	995	atG/atA	14/21	0.526982462491452	3	FACETS	0.775	0.693	0.862	0.387	0.346	0.431	SUBCLONAL	1	TRUE	1	0.593478784978778	3		571	547	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151868380	151868380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	119	423	0	ENST00000262189.6:c.9422G>A	p.Gly3141Glu	p.G3141E	ENST00000262189	NM_170606.2	3141	gGa/gAa	40/59	0.526982462491452	3	FACETS	0.811	0.734	0.893	0.406	0.367	0.447	CLONAL	1	TRUE	1	0.593478784978778	3		423	641	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945084	151945084	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	35	527	0	ENST00000262189.6:c.2435T>G	p.Met812Arg	p.M812R	ENST00000262189	NM_170606.2	812	aTg/aGg	14/59	0.526982462491452	3	FACETS	0.342	0.28	0.412	0.171	0.14	0.206	SUBCLONAL	1	TRUE	1	0.593478784978778	3		527	447	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974732	21974732	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	143	288	0	ENST00000304494.5:c.95T>G	p.Leu32Arg	p.L32R	ENST00000304494	NM_000077.4	32	cTg/cGg	1/3	0.498143166730169	1	FACETS	0.827	0.761	0.894	0.827	0.761	0.894	CLONAL	1	TRUE	0	0.593478784978778	1		288	410	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128268667	128268667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756247676	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	320	539	0	ENST00000265960.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000265960	NM_001006617.1	330	Gag/Aag	8/12	0.498143166730169	1	FACETS	0.823	0.78	0.868	0.823	0.78	0.868	CLONAL	1	TRUE	0	0.593478784978778	1		539	921	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778817	76778817	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	52	400	0	ENST00000373344.5:c.6762T>A	p.His2254Gln	p.H2254Q	ENST00000373344	NM_000489.3	2254	caT/caA	31/35	0.238032403736613	1	FACETS	0.493	0.423	0.568	0.493	0.423	0.568	INDETERMINATE	1	TRUE	0	0.593478784978778	1		400	250	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191755	123191755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	40	333	0	ENST00000218089.9:c.1344G>A	p.Met448Ile	p.M448I	ENST00000218089	NM_001042749.1	448	atG/atA	15/35	0.238032403736613	1	FACETS	0.409	0.342	0.481	0.409	0.342	0.481	INDETERMINATE	1	TRUE	0	0.593478784978778	1		333	232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0041593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	554	587	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.915591550222012	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.915591550222012	2		587	580	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622125	43622125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774347808	NA	P-0041593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	397	470	2	ENST00000355710.3:c.3142C>T	p.Leu1048Phe	p.L1048F	ENST00000355710	NM_020975.4	1048	Ctc/Ttc	19/20	0.915591550222012	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.915591550222012	2		472	426	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224518	108224518	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1333079704	NA	P-0041593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	133	243	0	ENST00000278616.4:c.8697C>G	p.Ile2899Met	p.I2899M	ENST00000278616	NM_000051.3	2899	atC/atG	60/63	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.915591550222012	2		243	275	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916811	48916811	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	490	348	0	ENST00000267163.4:c.341C>A	p.Ser114Ter	p.S114*	ENST00000267163	NM_000321.2	114	tCg/tAg	3/27	0.915591550222012	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.915591550222012	3		348	506	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89839741	89839741	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	769	680	0	ENST00000389301.3:c.1952G>A	p.Gly651Glu	p.G651E	ENST00000389301	NM_000135.2	651	gGa/gAa	22/43	0.915591550222012	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.915591550222012	3		680	797	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457240	25457240	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	269	526	0	ENST00000264709.3:c.2647T>A	p.Leu883Met	p.L883M	ENST00000264709	NM_175629.2	883	Ttg/Atg	23/23	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.915591550222012	2		526	574	SUCCESS
APC	324	MSKCC	GRCh37	5	112164589	112164589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	110	213	0	ENST00000257430.4:c.1663G>A	p.Ala555Thr	p.A555T	ENST00000257430	NM_000038.5	555	Gca/Aca	14/16	0.915591550222012	3	FACETS	1	0.953	1	0.358	0.325	0.392	CLONAL	1	TRUE	0	0.915591550222012	3		213	326	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139440236	139440236	+	start_lost	Translation_Start_Site	SNP	C	C	A	novel	NA	P-0041593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	38	49	0	ENST00000277541.6:c.3G>T	p.Met1?	p.M1?	ENST00000277541	NM_017617.3	1	atG/atT	1/34	0.748144409037115	4	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	2	0.915591550222012	4		49	71	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0041601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	76	422	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.226784061884817	2	FACETS	1	0.968	1	0.654	0.576	0.736	CLONAL	1	TRUE	0	0.282863919388186	2		422	411	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495212	212495212	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs758422014	NA	P-0041601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	56	392	1	ENST00000342788.4:c.2054C>A	p.Ala685Asp	p.A685D	ENST00000342788	NM_005235.2	685	gCc/gAc	17/28	1	2	FACETS	0.764	0.655	0.883	0.764	0.655	0.883	SUBCLONAL	1	TRUE	1	0.282863919388186	2		393	518	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722220	176722220	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	50	503	0	ENST00000439151.2:c.7851G>T	p.Leu2617Phe	p.L2617F	ENST00000439151	NM_022455.4	2617	ttG/ttT	23/23	1	2	FACETS	0.794	0.675	0.925	0.794	0.675	0.925	CLONAL	1	TRUE	1	0.282863919388186	2		503	445	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0041615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	100	426	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.277419490631469	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.357369612618551	1		426	410	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0041615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	70	235	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.188677864231873	3	FACETS	1	0.93	1	0.547	0.479	0.62	INDETERMINATE	1	TRUE	1	0.357369612618551	3		235	422	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519378	176519378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148292303	NA	P-0041615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	159	673	1	ENST00000292408.4:c.784G>A	p.Val262Met	p.V262M	ENST00000292408	NM_213647.1	262	Gtg/Atg	7/18	0.104069841931393	4	FACETS	1	0.937	1			1	INDETERMINATE	2	TRUE	NA	0.357369612618551	4		674	592	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865761	57865761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	57	704	0	ENST00000228682.2:c.3238C>A	p.Pro1080Thr	p.P1080T	ENST00000228682	NM_005269.2	1080	Ccc/Acc	12/12	0.108567131262207	3	FACETS	0.455	0.389	0.527	0.227	0.194	0.264	INDETERMINATE	1	TRUE	1	0.357369612618551	3		704	827	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058653	72058653	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0041615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	42	279	0	ENST00000357731.5:c.789-2A>T		p.X263_splice	ENST00000357731	NM_173808.2	263			1	2	FACETS	0.768	0.644	0.904	0.768	0.644	0.904	CLONAL	1	TRUE	1	0.357369612618551	2		279	306	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458146	120458146	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	71	647	1	ENST00000256646.2:c.7199G>T	p.Arg2400Leu	p.R2400L	ENST00000256646	NM_024408.3	2400	cGa/cTa	34/34	1	2	FACETS	0.625	0.545	0.711	0.625	0.545	0.711	SUBCLONAL	1	TRUE	1	0.357369612618551	2		648	636	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495064	56495064	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1170241416	NA	P-0041615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	115	674	1	ENST00000267101.3:c.3421A>T	p.Thr1141Ser	p.T1141S	ENST00000267101	NM_001982.3	1141	Act/Tct	27/28	0.108567131262207	3	FACETS	1	0.965	1	0.576	0.519	0.635	INDETERMINATE	1	TRUE	1	0.357369612618551	3		675	659	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285815	39285815	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	104	450	0	ENST00000402219.2:c.344A>T	p.Lys115Met	p.K115M	ENST00000402219	NM_005633.3	115	aAg/aTg	3/23	0.148520970822413	4	FACETS	0.787	0.708	0.87	0.787	0.708	0.87	INDETERMINATE	2	TRUE	2	0.357369612618551	4		450	502	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039418	47039418	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	177	634	1	ENST00000377604.3:c.1041C>A	p.Phe347Leu	p.F347L	ENST00000377604	NM_001204468.1	347	ttC/ttA	10/24	0.31125826101343	2	FACETS	0.928	0.861	0.996	0.928	0.861	0.996	CLONAL	2	TRUE	0	0.357369612618551	2		635	534	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0041617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1325	151	506	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.901197701393759	9	FACETS	0.943	0.859	1	0.135	0.122	0.148	CLONAL	1	TRUE	2	0.901197701393759	9		506	1476	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398262	25398262	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913538	NA	P-0041617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	213	116	0	ENST00000311936.3:c.57G>C	p.Leu19Phe	p.L19F	ENST00000311936	NM_004985.3	19	ttG/ttC	2/5	0.901197701393759	5	FACETS	1	0.979	1	0.378	0.351	0.406	CLONAL	1	TRUE	2	0.901197701393759	5		116	980	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587782197	NA	P-0041617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	589	312	0	ENST00000269305.4:c.434T>A	p.Leu145Gln	p.L145Q	ENST00000269305	NM_001126112.2	145	cTg/cAg	5/11	0.885833523673316	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.901197701393759	2		312	643	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476272	88476272	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	107	180	0	ENST00000360948.2:c.1860G>A	p.Met620Ile	p.M620I	ENST00000360948	NM_001012338.2	620	atG/atA	15/19	NA	2	FACETS	0.515	0.464	0.568			1	INDETERMINATE	1	TRUE	NA	0.901197701393759	2		180	461	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104359302	104359302	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776578	NA	P-0041617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	298	153	0	ENST00000369902.3:c.1022+1G>A		p.X341_splice	ENST00000369902	NM_016169.3	341			NA	2	FACETS	0.97	0.945	0.993			1	INDETERMINATE	2	TRUE	NA	0.901197701393759	2		153	341	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25462077	25462077	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752626029	NA	P-0041617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	256	174	0	ENST00000264709.3:c.2330C>T	p.Pro777Leu	p.P777L	ENST00000264709	NM_175629.2	777	cCt/cTt	20/23	0.896846619199695	4	FACETS	0.899	0.848	0.949	0.899	0.848	0.949	CLONAL	2	TRUE	2	0.901197701393759	4		174	601	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216463	2216463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1401443478	NA	P-0041617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	164	280	0	ENST00000398665.3:c.2107C>T	p.His703Tyr	p.H703Y	ENST00000398665	NM_032482.2	703	Cac/Tac	20/28	0.604957790694864	4	FACETS	0.98	0.902	1	0.49	0.451	0.531	CLONAL	1	TRUE	2	0.901197701393759	4		280	706	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223529	36223529	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	185	325	0	ENST00000222270.7:c.6079G>C	p.Glu2027Gln	p.E2027Q	ENST00000222270	NM_014727.1	2027	Gag/Cag	28/37	0.800294205484434	4	FACETS	0.951	0.879	1	0.475	0.439	0.513	CLONAL	1	TRUE	2	0.901197701393759	4		325	821	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46608744	46608744	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	146	235	0	ENST00000263734.3:c.2055G>C	p.Lys685Asn	p.K685N	ENST00000263734	NM_001430.4	685	aaG/aaC	13/16	0.896846619199695	4	FACETS	0.793	0.724	0.864	0.396	0.362	0.432	SUBCLONAL	1	TRUE	2	0.901197701393759	4		235	777	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47596691	47596691	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	132	134	0	ENST00000263735.4:c.47C>A	p.Ala16Glu	p.A16E	ENST00000263735	NM_002354.2	16	gCg/gAg	1/9	0.896846619199695	4	FACETS	1	0.971	1	0.572	0.522	0.623	CLONAL	1	TRUE	2	0.901197701393759	4		134	487	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128036845	128036845	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	375	196	0	ENST00000285398.2:c.1634A>G	p.Gln545Arg	p.Q545R	ENST00000285398	NM_000122.1	545	cAg/cGg	10/15	0.896846619199695	4	FACETS	0.88	0.839	0.922	0.88	0.839	0.922	CLONAL	2	TRUE	2	0.901197701393759	4		196	899	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872839	136872839	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	191	136	0	ENST00000241393.3:c.659G>A	p.Cys220Tyr	p.C220Y	ENST00000241393	NM_003467.2	220	tGc/tAc	2/2	0.896846619199695	4	FACETS	0.916	0.857	0.975	0.916	0.857	0.975	CLONAL	2	TRUE	2	0.901197701393759	4		136	440	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342966	225342966	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1159640544	NA	P-0041617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	394	177	0	ENST00000264414.4:c.2126G>A	p.Arg709Gln	p.R709Q	ENST00000264414	NM_003590.4	709	cGg/cAg	15/16	0.262752796175858	3	FACETS	0.94	0.919	0.959			1	INDETERMINATE	3	TRUE	NA	0.901197701393759	3		177	450	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417859	138417859	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	134	141	0	ENST00000289153.2:c.1660G>C	p.Glu554Gln	p.E554Q	ENST00000289153	NM_006219.2	554	Gaa/Caa	11/22	0.901197701393759	7	FACETS	0.747	0.677	0.821			1	SUBCLONAL	1	TRUE	NA	0.901197701393759	7		141	1295	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461465	138461465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	122	155	0	ENST00000289153.2:c.556G>A	p.Glu186Lys	p.E186K	ENST00000289153	NM_006219.2	186	Gaa/Aaa	3/22	0.901197701393759	7	FACETS	0.705	0.635	0.779			1	SUBCLONAL	1	TRUE	NA	0.901197701393759	7		155	1250	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629109	86629109	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	11	91	0	ENST00000274376.6:c.854G>C	p.Arg285Pro	p.R285P	ENST00000274376	NM_002890.2	285	cGa/cCa	4/25	0.102371801886693	1	FACETS	0.064	0.043	0.088	0.064	0.043	0.088	INDETERMINATE	1	TRUE	0	0.901197701393759	1		91	211	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675668	86675668	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0041617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	53	79	0	ENST00000274376.6:c.2603+1G>C		p.X868_splice	ENST00000274376	NM_002890.2	868			NA	2	FACETS	0.817	0.713	0.924			1	INDETERMINATE	1	TRUE	NA	0.901197701393759	2		79	144	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729255	41729255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	149	95	0	ENST00000242208.4:c.1274G>T	p.Cys425Phe	p.C425F	ENST00000242208	NM_002192.2	425	tGc/tTc	3/3	0.800294205484434	4	FACETS	0.933	0.865	1	0.933	0.865	1	CLONAL	2	TRUE	2	0.901197701393759	4		95	337	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0041623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	451	575	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.300330569888792	4	FACETS	1	0.963	1	0.752	0.722	0.781	INDETERMINATE	3	TRUE	0	0.536842069558054	4		575	859	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251730	212251730	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	64	353	0	ENST00000342788.4:c.3329C>G	p.Thr1110Ser	p.T1110S	ENST00000342788	NM_005235.2	1110	aCc/aGc	27/28	1	2	FACETS	0.557	0.484	0.636	0.557	0.484	0.636	SUBCLONAL	1	TRUE	1	0.536842069558054	2		353	428	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0041637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	188	207	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.340853285489511	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.340853285489511	2		207	507	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0041637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	287	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.340853285489511	5	FACETS	0.918	0.869	0.968			1	CLONAL	4	TRUE	NA	0.340853285489511	5		452	693	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440372	52440372	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	39	410	0	ENST00000460680.1:c.680G>C	p.Arg227Pro	p.R227P	ENST00000460680	NM_004656.3	227	cGc/cCc	9/17	0.340853285489511	2	FACETS	0.309	0.255	0.37	0.155	0.127	0.185	SUBCLONAL	1	TRUE	0	0.340853285489511	2		410	740	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579569	7579569	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	186	674	0	ENST00000269305.4:c.118A>G	p.Met40Val	p.M40V	ENST00000269305	NM_001126112.2	40	Atg/Gtg	4/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.340853285489511	2		674	879	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420492	49420492	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775506569	NA	P-0041637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	200	665	0	ENST00000301067.7:c.15257G>A	p.Arg5086Gln	p.R5086Q	ENST00000301067	NM_003482.3	5086	cGa/cAa	48/54	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.340853285489511	2		665	851	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347102	89347102	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	87	580	1	ENST00000301030.4:c.5848T>A	p.Trp1950Arg	p.W1950R	ENST00000301030	NM_001256183.1	1950	Tgg/Agg	9/13	0.340853285489511	1	FACETS	0.629	0.557	0.706	0.629	0.557	0.706	SUBCLONAL	1	TRUE	0	0.340853285489511	1		581	673	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349307	89349307	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	153	947	0	ENST00000301030.4:c.3643G>A	p.Glu1215Lys	p.E1215K	ENST00000301030	NM_001256183.1	1215	Gaa/Aaa	9/13	0.340853285489511	1	FACETS	0.595	0.543	0.65	0.595	0.543	0.65	SUBCLONAL	1	TRUE	0	0.340853285489511	1		947	1252	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971010	55971010	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1282839301	NA	P-0041637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	83	520	0	ENST00000263923.4:c.1787G>A	p.Gly596Glu	p.G596E	ENST00000263923	NM_002253.2	596	gGa/gAa	13/30	0.340853285489511	1	FACETS	0.677	0.598	0.761	0.677	0.598	0.761	SUBCLONAL	1	TRUE	0	0.340853285489511	1		520	597	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197848	66197848	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0041637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	30	234	0	ENST00000273854.3:c.2853-2A>G		p.X951_splice	ENST00000273854	NM_004439.5	951			0.340853285489511	1	FACETS	0.709	0.575	0.858	0.709	0.575	0.858	SUBCLONAL	1	TRUE	0	0.340853285489511	1		234	206	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293668	1293668	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1833	588	771	0	ENST00000310581.5:c.1333C>A	p.Pro445Thr	p.P445T	ENST00000310581	NM_198253.2	445	Ccc/Acc	2/16	0.340853285489511	8	FACETS	0.961	0.92	1	0.576	0.552	0.602	CLONAL	3	TRUE	3	0.340853285489511	8		771	2421	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512102	148512102	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	48	402	0	ENST00000320356.2:c.1576C>G	p.Gln526Glu	p.Q526E	ENST00000320356	NM_004456.4	526	Caa/Gaa	14/20	1	2	FACETS	0.437	0.368	0.512	0.437	0.368	0.512	SUBCLONAL	1	TRUE	1	0.340853285489511	2		402	645	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930892	39930892	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	52	399	0	ENST00000378444.4:c.3049G>A	p.Glu1017Lys	p.E1017K	ENST00000378444	NM_001123385.1	1017	Gag/Aag	5/15	0.340853285489511	1	FACETS	0.578	0.493	0.671	0.578	0.493	0.671	SUBCLONAL	1	TRUE	0	0.340853285489511	1		399	438	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044916	47044916	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	265	820	1	ENST00000377604.3:c.2242G>T	p.Glu748Ter	p.E748*	ENST00000377604	NM_001204468.1	748	Gag/Tag	20/24	0.340853285489511	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.340853285489511	1		821	973	SUCCESS
APC	324	MSKCC	GRCh37	5	112175171	112175171	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085373	NA	P-0041640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	61	193	0	ENST00000257430.4:c.3880C>T	p.Gln1294Ter	p.Q1294*	ENST00000257430	NM_000038.5	1294	Cag/Tag	16/16	1	2	FACETS	0.94	0.827	1	0.94	0.827	1	CLONAL	1	TRUE	1	0.728861785961516	2		193	178	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520008	NA	P-0041640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	261	783	0	ENST00000269305.4:c.613T>G	p.Tyr205Asp	p.Y205D	ENST00000269305	NM_001126112.2	205	Tat/Gat	6/11	0.728861785961516	1	FACETS	0.987	0.939	1	0.987	0.939	1	CLONAL	1	TRUE	0	0.728861785961516	1		783	461	SUCCESS
APC	324	MSKCC	GRCh37	5	112175015	112175015	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1460397656	NA	P-0041640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	81	179	0	ENST00000257430.4:c.3724C>T	p.Gln1242Ter	p.Q1242*	ENST00000257430	NM_000038.5	1242	Cag/Tag	16/16	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.728861785961516	2		179	216	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914339	32914341	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0041640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	113	428	0	ENST00000380152.3:c.5848_5850del	p.Val1950del	p.V1950del	ENST00000380152		1949	gaTGTt/gat	11/27	0.728861785961516	4	FACETS	0.924	0.834	1	0.308	0.278	0.34	CLONAL	1	TRUE	1	0.728861785961516	4		428	580	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670703	67670703	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0041640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	236	569	0	ENST00000264010.4:c.1948A>T	p.Lys650Ter	p.K650*	ENST00000264010	NM_006565.3	650	Aag/Tag	11/12	1	2	FACETS	0.98	0.92	1	0.98	0.92	1	CLONAL	1	TRUE	1	0.728861785961516	2		569	661	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096193	71096194	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	108	361	0	ENST00000318789.4:c.563dup	p.Met188IlefsTer107	p.M188Ifs*107	ENST00000318789	NM_032682.5	188	atg/atTg	10/21	1	2	FACETS	0.869	0.789	0.952	0.869	0.789	0.952	CLONAL	1	TRUE	1	0.728861785961516	2		361	341	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442820	99442820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148662051	NA	P-0041673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	151	533	0	ENST00000268035.6:c.1217G>A	p.Arg406His	p.R406H	ENST00000268035	NM_000875.3	406	cGc/cAc	5/21	0.238748705727648	3	FACETS	1	0.973	1	0.57	0.523	0.618	INDETERMINATE	1	TRUE	1	0.610307519758707	3		533	567	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435201	18435202	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1565550462	NA	P-0041673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	84	306	0	ENST00000266497.5:c.192dup	p.Val65CysfsTer16	p.V65Cfs*16	ENST00000266497		62	-/T	1/31	0.610307519758707	3	FACETS	0.891	0.792	0.997	0.446	0.396	0.499	CLONAL	1	TRUE	1	0.610307519758707	3		306	403	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225343053	225343053	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	117	458	0	ENST00000264414.4:c.2039A>G	p.Lys680Arg	p.K680R	ENST00000264414	NM_003590.4	680	aAa/aGa	15/16	0.573876276648729	4	FACETS	0.888	0.802	0.979	0.444	0.401	0.49	CLONAL	1	TRUE	2	0.610307519758707	4		458	695	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839898	27839898	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	163	665	2	ENST00000328488.2:c.196C>A	p.Leu66Ile	p.L66I	ENST00000328488	NM_003533.2	66	Cta/Ata	1/1	0.535464961829956	5	FACETS	1	0.918	1	0.334	0.306	0.363	CLONAL	1	TRUE	2	0.610307519758707	5		667	1022	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0041718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	254	454	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	0.842	0.792	0.893	0.842	0.792	0.893	CLONAL	1	TRUE	1	0.841426164520656	2		454	717	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023438	27023438	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	82	434	0	ENST00000324856.7:c.544G>T	p.Ala182Ser	p.A182S	ENST00000324856	NM_006015.4	182	Gca/Tca	1/20	1	2	FACETS	0.968	0.855	1	0.968	0.855	1	CLONAL	1	TRUE	1	0.310260140054016	2		434	546	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058799	42058799	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	52	365	0	ENST00000219905.7:c.8519A>G	p.Asp2840Gly	p.D2840G	ENST00000219905	NM_001164273.1	2840	gAc/gGc	24/24	0.310260140054016	1	FACETS	0.896	0.767	1	0.896	0.767	1	CLONAL	1	TRUE	0	0.310260140054016	1		365	316	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993878	72993878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	89	579	0	ENST00000268489.5:c.167C>T	p.Pro56Leu	p.P56L	ENST00000268489	NM_006885.3	56	cCc/cTc	2/10	1	2	FACETS	0.924	0.82	1	0.924	0.82	1	CLONAL	1	TRUE	1	0.310260140054016	2		579	621	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934366	81934367	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0041730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	96	622	2	ENST00000359376.3:c.1343_1344delinsTT	p.Arg448Leu	p.R448L	ENST00000359376	NM_002661.3	448	cGG/cTT	14/33	1	2	FACETS	0.887	0.79	0.989	0.887	0.79	0.989	CLONAL	1	TRUE	1	0.310260140054016	2		624	698	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220400	1220400	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1359582062	NA	P-0041730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	123	739	1	ENST00000326873.7:c.493G>T	p.Glu165Ter	p.E165*	ENST00000326873	NM_000455.4	165	Gag/Tag	4/10	0.310260140054016	1	FACETS	0.86	0.778	0.946	0.86	0.778	0.946	CLONAL	1	TRUE	0	0.310260140054016	1		740	779	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469627	25469627	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	148	673	1	ENST00000264709.3:c.1141G>T	p.Gly381Trp	p.G381W	ENST00000264709	NM_175629.2	381	Ggg/Tgg	10/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.310260140054016	2		674	879	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0041730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	28	401	0	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	1	2	FACETS	0.654	0.524	0.801	0.654	0.524	0.801	SUBCLONAL	1	TRUE	1	0.310260140054016	2		401	276	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928908	49928908	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	138	834	3	ENST00000296474.3:c.3458C>A	p.Pro1153His	p.P1153H	ENST00000296474	NM_002447.2	1153	cCt/cAt	16/20	1	2	FACETS	0.887	0.806	0.972	0.887	0.806	0.972	CLONAL	1	TRUE	1	0.310260140054016	2		837	1003	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521331	8521331	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	59	466	0	ENST00000356435.5:c.907G>A	p.Val303Ile	p.V303I	ENST00000356435		303	Gtt/Att	9/35	1	2	FACETS	0.893	0.77	1	0.893	0.77	1	CLONAL	1	TRUE	1	0.310260140054016	2		466	426	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227712	53227712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556839436	NA	P-0041730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	122	338	1	ENST00000375401.3:c.2476G>A	p.Val826Met	p.V826M	ENST00000375401	NM_004187.3	826	Gtg/Atg	17/26	1	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.310260140054016	1		339	490	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0041832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	20	426	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	0.593	0.452	0.759	0.593	0.452	0.759	SUBCLONAL	1	TRUE	1	0.14	2		426	482	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315383	30315383	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	29	752	0	ENST00000322652.5:c.1068G>T	p.Gln356His	p.Q356H	ENST00000322652	NM_015355.2	356	caG/caT	10/16	1	2	FACETS	0.732	0.586	0.899	0.732	0.586	0.899	SUBCLONAL	1	TRUE	1	0.14	2		752	566	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0041835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	101	575	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.856	0.764	0.953	0.856	0.764	0.953	CLONAL	1	TRUE	1	0.288620740059509	2		575	818	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0041856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	15	506	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.305951943036386	6	FACETS	0.136	0.099	0.182	0.034	0.024	0.046	INDETERMINATE	1	TRUE	2	0.727118501964366	6		506	743	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0041856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	897	732	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.727118501964366	3	FACETS	0.997	0.978	1			1	CLONAL	3	TRUE	NA	0.727118501964366	3		732	1125	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459468	50459468	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	45	279	0	ENST00000331340.3:c.757C>A	p.Leu253Met	p.L253M	ENST00000331340	NM_006060.4	253	Ctg/Atg	7/8	0.223005958689467	5	FACETS	0.616	0.518	0.724	0.205	0.172	0.242	INDETERMINATE	1	TRUE	2	0.727118501964366	5		279	420	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150232	108150232	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs189445371	NA	P-0041856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	22	429	0	ENST00000278616.4:c.3299C>G	p.Thr1100Arg	p.T1100R	ENST00000278616	NM_000051.3	1100	aCg/aGg	23/63	0.727118501964366	1	FACETS	0.116	0.089	0.146	0.116	0.089	0.146	SUBCLONAL	1	TRUE	0	0.727118501964366	1		429	333	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431487	49431488	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0041856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	53	838	0	ENST00000301067.7:c.9651_9652del	p.Ser3217ArgfsTer15	p.S3217Rfs*15	ENST00000301067	NM_003482.3	3217	agTGgg/aggg	34/54	0.197282828023985	4	FACETS	0.331	0.282	0.386	0.166	0.141	0.193	INDETERMINATE	1	TRUE	2	0.727118501964366	4		838	760	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050845	49050846	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	165	285	0	ENST00000267163.4:c.2531dup	p.Phe845ValfsTer10	p.F845Vfs*10	ENST00000267163	NM_000321.2	843	-/A	25/27	0.727118501964366	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.727118501964366	1		285	279	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675458	40675458	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	177	845	1	ENST00000249776.8:c.239C>A	p.Thr80Asn	p.T80N	ENST00000249776	NM_033286.3	80	aCc/aAc	2/9	0.490963322516952	3	FACETS	0.734	0.677	0.794	0.367	0.338	0.397	SUBCLONAL	1	TRUE	1	0.727118501964366	3		846	904	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627796	14627802	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTGAA	AGCTGAA	-	novel	NA	P-0041856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	38	734	2	ENST00000254322.2:c.268_274del	p.Phe90ThrfsTer53	p.F90Tfs*53	ENST00000254322	NM_006145.1	90	TTCAGCTac/ac	2/3	1	2	FACETS	0.145	0.119	0.174	0.145	0.119	0.174	SUBCLONAL	1	TRUE	1	0.727118501964366	2		736	720	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405199	139405213	+	frameshift_variant	Frame_Shift_Del	DEL	TGCGCCGTGCCGGCA	TGCGCCGTGCCGGCA	C	novel	NA	P-0041856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	784	955	0	ENST00000277541.6:c.2632_2646delinsG	p.Cys878ValfsTer61	p.C878Vfs*61	ENST00000277541	NM_017617.3	878	TGCCGGCACGGCGCA/G	17/34	0.711568169800222	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.727118501964366	3		955	969	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	1063	426	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.363521321417171	15	FACETS	1	0.991	1			1	CLONAL	13	TRUE	NA	0.363521321417171	15		426	1482	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220428	123220428	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	96	553	0	ENST00000218089.9:c.3085C>T	p.Gln1029Ter	p.Q1029*	ENST00000218089	NM_001042749.1	1029	Cag/Tag	30/35	0.33839725990143	2	FACETS	0.967	0.864	1	0.484	0.432	0.538	CLONAL	1	TRUE	0	0.363521321417171	2		553	546	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882319	89882319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	68	682	0	ENST00000389301.3:c.155G>A	p.Arg52Gln	p.R52Q	ENST00000389301	NM_000135.2	52	cGa/cAa	2/43	0.153785285898488	4	FACETS	0.587	0.509	0.671	0.294	0.254	0.336	INDETERMINATE	1	TRUE	2	0.363521321417171	4		682	869	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380277	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913238	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2047	208	637	1	ENST00000311936.3:c.181C>G	p.Gln61Glu	p.Q61E	ENST00000311936	NM_004985.3	61	Caa/Gaa	3/5	0.363521321417171	15	FACETS	0.853	0.788	0.922			1	CLONAL	2	TRUE	NA	0.363521321417171	15		638	2255	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227019	2227019	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	128	603	0	ENST00000398665.3:c.4499C>G	p.Ser1500Cys	p.S1500C	ENST00000398665	NM_032482.2	1500	tCt/tGt	27/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.363521321417171	2		603	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863224499	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	509	916	1	ENST00000269305.4:c.672+1G>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.326839012376167	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.363521321417171	3		917	1041	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813626	50813626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149427272	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	249	806	1	ENST00000398568.2:c.1180C>T	p.Arg394Cys	p.R394C	ENST00000398568	NM_001042412.1	394	Cgt/Tgt	8/18	0.153785285898488	4	FACETS	0.941	0.881	1	0.941	0.881	1	INDETERMINATE	2	TRUE	2	0.363521321417171	4		807	992	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266490	55266490	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	89	763	0	ENST00000275493.2:c.2782G>C	p.Glu928Gln	p.E928Q	ENST00000275493	NM_005228.3	928	Gag/Cag	23/28	0.257949997340346	3	FACETS	0.707	0.626	0.794	0.354	0.313	0.397	SUBCLONAL	1	TRUE	1	0.363521321417171	3		763	818	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169940469	169940469	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1082973	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	49	560	0	ENST00000295797.4:c.12G>C	p.Gln4His	p.Q4H	ENST00000295797	NM_002740.5	4	caG/caC	1/18	0.257949997340346	3	FACETS	0.583	0.494	0.682	0.292	0.247	0.341	SUBCLONAL	1	TRUE	1	0.363521321417171	3		560	546	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390623	139390623	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554826328	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	98	1157	1	ENST00000277541.6:c.7568C>T	p.Ser2523Leu	p.S2523L	ENST00000277541	NM_017617.3	2523	tCg/tTg	34/34	0.33839725990143	2	FACETS	0.523	0.466	0.585	0.262	0.233	0.293	SUBCLONAL	1	TRUE	0	0.363521321417171	2		1158	1030	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8105995	8105995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	156	631	0	ENST00000346208.3:c.815C>T	p.Pro272Leu	p.P272L	ENST00000346208		272	cCa/cTa	4/6	0.186378129361413	3	FACETS	0.797	0.733	0.864	0.797	0.733	0.864	INDETERMINATE	2	TRUE	1	0.363521321417171	3		631	636	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446232	29446232	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	196	759	1	ENST00000389048.3:c.3335C>A	p.Pro1112Gln	p.P1112Q	ENST00000389048	NM_004304.4	1112	cCg/cAg	20/29	0.360510931550783	3	FACETS	0.933	0.867	1	0.933	0.867	1	CLONAL	2	TRUE	1	0.363521321417171	3		760	683	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430001	78430001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	37	313	0	ENST00000370768.2:c.878G>A	p.Arg293Lys	p.R293K	ENST00000370768	NM_003902.3	293	aGa/aAa	11/20	1	2	FACETS	0.57	0.471	0.681	0.57	0.471	0.681	SUBCLONAL	1	TRUE	1	0.363521321417171	2		313	357	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727042	243727042	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	80	461	0	ENST00000263826.5:c.928C>G	p.Pro310Ala	p.P310A	ENST00000263826	NM_005465.4	310	Cca/Gca	9/13	0.306439957001222	4	FACETS	0.999	0.88	1	0.333	0.293	0.376	CLONAL	1	TRUE	1	0.363521321417171	4		461	601	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076704	102076704	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	213	646	0	ENST00000282441.5:c.883A>T	p.Met295Leu	p.M295L	ENST00000282441	NM_001130145.2	295	Atg/Ttg	5/9	0.227570001206643	5	FACETS	1	0.96	1	0.697	0.648	0.747	CLONAL	2	TRUE	2	0.363521321417171	5		646	866	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380809	118380809	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	35	463	0	ENST00000534358.1:c.11047C>G	p.Gln3683Glu	p.Q3683E	ENST00000534358	NM_005933.3	3683	Cag/Gag	30/36	0.227570001206643	5	FACETS	0.564	0.461	0.679	0.188	0.153	0.227	SUBCLONAL	1	TRUE	2	0.363521321417171	5		463	528	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498227	498227	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	49	393	0	ENST00000399788.2:c.31del	p.Ala11ArgfsTer55	p.A11Rfs*55	ENST00000399788	NM_001042603.1	11	Gcg/cg	1/28	0.363521321417171	3	FACETS	0.732	0.621	0.854			1	SUBCLONAL	1	TRUE	NA	0.363521321417171	3		393	435	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650628	18650628	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	59	560	1	ENST00000266497.5:c.2839G>T	p.Gly947Cys	p.G947C	ENST00000266497		947	Ggc/Tgc	20/31	1	2	FACETS	0.816	0.704	0.936	0.816	0.704	0.936	CLONAL	1	TRUE	1	0.363521321417171	2		561	398	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748729	43748729	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	108	1048	0	ENST00000382044.4:c.2077C>A	p.Pro693Thr	p.P693T	ENST00000382044	NM_001141980.1	693	Ccg/Acg	12/28	0.360510931550783	3	FACETS	0.666	0.596	0.74	0.333	0.298	0.37	SUBCLONAL	1	TRUE	1	0.363521321417171	3		1048	1054	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74000683	74000683	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	244	783	1	ENST00000318443.5:c.1373A>T	p.Gln458Leu	p.Q458L	ENST00000318443	NM_001024736.1	458	cAg/cTg	7/10	0.360510931550783	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.363521321417171	3		784	783	SUCCESS
BLM	641	MSKCC	GRCh37	15	91298083	91298084	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	58	474	0	ENST00000355112.3:c.1002_1003delinsAT	p.Leu335Phe	p.L335F	ENST00000355112	NM_000057.2	334	gtTCtt/gtATtt	5/22	0.360510931550783	3	FACETS	0.834	0.718	0.96	0.417	0.359	0.48	CLONAL	1	TRUE	1	0.363521321417171	3		474	452	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99491803	99491803	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	70	493	1	ENST00000268035.6:c.3588G>T	p.Trp1196Cys	p.W1196C	ENST00000268035	NM_000875.3	1196	tgG/tgT	20/21	0.360510931550783	3	FACETS	1	0.884	1	0.506	0.442	0.574	CLONAL	1	TRUE	1	0.363521321417171	3		494	450	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658581	3658581	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1295	208	1034	0	ENST00000294008.3:c.385C>A	p.Gln129Lys	p.Q129K	ENST00000294008	NM_032444.2	129	Caa/Aaa	2/15	0.363521321417171	5	FACETS	1	0.981	1	0.294	0.272	0.317	CLONAL	1	TRUE	1	0.363521321417171	5		1034	1503	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868347	56868347	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	90	414	0	ENST00000308159.5:c.1730G>T	p.Ser577Ile	p.S577I	ENST00000308159	NM_014669.4	577	aGc/aTc	15/22	0.153785285898488	4	FACETS	1	0.979	1	0.737	0.657	0.822	INDETERMINATE	1	TRUE	2	0.363521321417171	4		414	458	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40872357	40872357	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	147	946	0	ENST00000428826.2:c.598G>T	p.Gly200Ter	p.G200*	ENST00000428826		200	Gga/Tga	7/21	0.363521321417171	4	FACETS	0.897	0.817	0.981	0.299	0.272	0.327	CLONAL	1	TRUE	1	0.363521321417171	4		946	1230	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217051	2217051	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	150	930	1	ENST00000398665.3:c.2506G>T	p.Gly836Trp	p.G836W	ENST00000398665	NM_032482.2	836	Ggg/Tgg	21/28	1	2	FACETS	0.972	0.889	1	0.972	0.889	1	CLONAL	1	TRUE	1	0.363521321417171	2		931	849	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296482	15296482	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	170	1160	0	ENST00000263388.2:c.1960T>C	p.Cys654Arg	p.C654R	ENST00000263388	NM_000435.2	654	Tgt/Cgt	13/33	1	2	FACETS	0.923	0.848	1	0.923	0.848	1	CLONAL	1	TRUE	1	0.363521321417171	2		1160	1013	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353853	15353853	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	110	715	0	ENST00000263377.2:c.3027A>T	p.Gln1009His	p.Q1009H	ENST00000263377	NM_058243.2	1009	caA/caT	14/20	1	2	FACETS	0.938	0.844	1	0.938	0.844	1	CLONAL	1	TRUE	1	0.363521321417171	2		715	645	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376786	31376786	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	185	789	0	ENST00000328111.2:c.781G>T	p.Val261Phe	p.V261F	ENST00000328111	NM_006892.3	261	Gtc/Ttc	7/23	0.247575040668362	3	FACETS	1	0.989	1	0.709	0.655	0.765	CLONAL	1	TRUE	1	0.363521321417171	3		789	848	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919164	178919164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223886939	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	38	255	0	ENST00000263967.3:c.649C>T	p.Pro217Ser	p.P217S	ENST00000263967	NM_006218.2	217	Cca/Tca	4/21	0.257949997340346	3	FACETS	0.782	0.649	0.93	0.391	0.324	0.465	CLONAL	1	TRUE	1	0.363521321417171	3		255	316	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604286	189604286	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	47	603	0	ENST00000264731.3:c.1453C>G	p.Gln485Glu	p.Q485E	ENST00000264731	NM_003722.4	485	Cag/Gag	11/14	0.257949997340346	3	FACETS	0.402	0.338	0.473	0.201	0.169	0.237	SUBCLONAL	1	TRUE	1	0.363521321417171	3		603	760	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041191	112041191	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	211	722	0	ENST00000368678.4:c.64C>A	p.Leu22Met	p.L22M	ENST00000368678		22	Ctg/Atg	3/13	0.363521321417171	2	FACETS	0.908	0.848	0.97	0.908	0.848	0.97	CLONAL	2	TRUE	0	0.363521321417171	2		722	639	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975442	13975442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	59	474	0	ENST00000405192.2:c.445C>T	p.His149Tyr	p.H149Y	ENST00000405192	NM_001163147.1	149	Cat/Tat	7/12	0.257949997340346	3	FACETS	0.78	0.672	0.897	0.39	0.336	0.449	SUBCLONAL	1	TRUE	1	0.363521321417171	3		474	492	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266546	55266546	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	78	665	0	ENST00000275493.2:c.2838C>G	p.Ile946Met	p.I946M	ENST00000275493	NM_005228.3	946	atC/atG	23/28	0.257949997340346	3	FACETS	0.721	0.634	0.816	0.361	0.317	0.408	SUBCLONAL	1	TRUE	1	0.363521321417171	3		665	703	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69032510	69032510	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs995332079	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	145	709	0	ENST00000288368.4:c.3584G>A	p.Arg1195Gln	p.R1195Q	ENST00000288368	NM_024870.2	1195	cGa/cAa	29/40	0.363521321417171	3	FACETS	1	0.98	1	0.62	0.566	0.676	CLONAL	1	TRUE	1	0.363521321417171	3		709	760	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970889	70970889	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	198	646	1	ENST00000276594.2:c.1372C>A	p.His458Asn	p.H458N	ENST00000276594	NM_024504.3	458	Cac/Aac	6/8	0.363521321417171	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.363521321417171	3		647	632	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341821	8341821	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	192	752	0	ENST00000356435.5:c.4819G>T	p.Asp1607Tyr	p.D1607Y	ENST00000356435		1607	Gat/Tat	29/35	0.33839725990143	2	FACETS	0.819	0.761	0.878	0.819	0.761	0.878	CLONAL	2	TRUE	0	0.363521321417171	2		752	645	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401783	139401783	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754056142	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	120	1048	0	ENST00000277541.6:c.3617A>G	p.Lys1206Arg	p.K1206R	ENST00000277541	NM_017617.3	1206	aAg/aGg	22/34	0.33839725990143	2	FACETS	0.826	0.746	0.911	0.413	0.373	0.456	CLONAL	1	TRUE	0	0.363521321417171	2		1048	799	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045953	47045953	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	146	1020	0	ENST00000377604.3:c.2748G>C	p.Glu916Asp	p.E916D	ENST00000377604	NM_001204468.1	916	gaG/gaC	24/24	0.33839725990143	2	FACETS	0.917	0.837	1	0.458	0.418	0.501	CLONAL	1	TRUE	0	0.363521321417171	2		1020	876	SUCCESS
AR	367	MSKCC	GRCh37	X	66931322	66931322	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	338	661	0	ENST00000374690.3:c.1964A>G	p.Glu655Gly	p.E655G	ENST00000374690	NM_000044.3	655	gAg/gGg	4/8	0.128505178350208	3	FACETS	1	0.961	1			1	INDETERMINATE	3	TRUE	NA	0.363521321417171	3		661	726	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608322	100608322	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	190	739	0	ENST00000308731.7:c.1768A>C	p.Ile590Leu	p.I590L	ENST00000308731	NM_000061.2	590	Att/Ctt	18/19	0.33839725990143	2	FACETS	0.89	0.828	0.954	0.89	0.828	0.954	CLONAL	2	TRUE	0	0.363521321417171	2		739	587	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220419	123220419	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	86	523	0	ENST00000218089.9:c.3076A>C	p.Met1026Leu	p.M1026L	ENST00000218089	NM_001042749.1	1026	Atg/Ctg	30/35	0.33839725990143	2	FACETS	0.924	0.82	1	0.462	0.41	0.518	CLONAL	1	TRUE	0	0.363521321417171	2		523	512	SUCCESS
BLM	641	MSKCC	GRCh37	15	91298084	91298084	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	58	472	0	ENST00000355112.3:c.1003C>T	p.Leu335Phe	p.L335F	ENST00000355112	NM_000057.2	335	Ctt/Ttt	5/22	0.360510931550783	3	FACETS	0.834	0.718	0.96	0.417	0.359	0.48	CLONAL	1	TRUE	1	0.363521321417171	3		472	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0041880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	47	885	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	0.467	0.392	0.549	0.467	0.392	0.549	SUBCLONAL	1	TRUE	1	0.23	2		885	876	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0041880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	20	506	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.284206694876695	3	FACETS	0.241	0.183	0.31	0.121	0.091	0.155	SUBCLONAL	1	TRUE	1	0.23	3		506	803	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321351	1321351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763354527	NA	P-0041880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	50	896	2	ENST00000400841.2:c.404C>T	p.Thr135Met	p.T135M	ENST00000400841		135	aCg/aTg	4/6	1	2	FACETS	0.507	0.428	0.593	0.507	0.428	0.593	SUBCLONAL	1	TRUE	1	0.23	2		898	858	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0041883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	64	426	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.18	2		426	688	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165756	108165756	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886039592	NA	P-0041883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	44	480	0	ENST00000278616.4:c.4879C>T	p.Gln1627Ter	p.Q1627*	ENST00000278616	NM_000051.3	1627	Cag/Tag	32/63	1	2	FACETS	0.786	0.658	0.928	0.786	0.658	0.928	CLONAL	1	TRUE	1	0.18	2		480	622	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106405	108106405	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	21	214	0	ENST00000278616.4:c.340A>T	p.Arg114Trp	p.R114W	ENST00000278616	NM_000051.3	114	Agg/Tgg	5/63	1	2	FACETS	0.877	0.677	1	0.877	0.677	1	CLONAL	1	TRUE	1	0.18	2		214	266	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164106	108164106	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0041883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	43	339	0	ENST00000278616.4:c.4678A>T	p.Lys1560Ter	p.K1560*	ENST00000278616	NM_000051.3	1560	Aag/Tag	31/63	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.18	2		339	465	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420721	49420721	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	63	857	0	ENST00000301067.7:c.15028G>T	p.Ala5010Ser	p.A5010S	ENST00000301067	NM_003482.3	5010	Gca/Tca	48/54	1	2	FACETS	0.906	0.782	1	0.906	0.782	1	CLONAL	1	TRUE	1	0.18	2		857	773	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290986	15290986	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	45	1124	0	ENST00000263388.2:c.3224G>T	p.Gly1075Val	p.G1075V	ENST00000263388	NM_000435.2	1075	gGc/gTc	20/33	1	2	FACETS	0.576	0.482	0.68	0.576	0.482	0.68	SUBCLONAL	1	TRUE	1	0.18	2		1124	868	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302295	15302295	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	56	1001	0	ENST00000263388.2:c.976G>T	p.Gly326Trp	p.G326W	ENST00000263388	NM_000435.2	326	Ggg/Tgg	6/33	1	2	FACETS	0.649	0.554	0.753	0.649	0.554	0.753	SUBCLONAL	1	TRUE	1	0.18	2		1001	959	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214705	36214705	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	35	824	1	ENST00000222270.7:c.3131G>T	p.Gly1044Val	p.G1044V	ENST00000222270	NM_014727.1	1044	gGc/gTc	8/37	1	2	FACETS	0.568	0.464	0.685	0.568	0.464	0.685	SUBCLONAL	1	TRUE	1	0.18	2		825	685	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267370	198267370	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	63	595	0	ENST00000335508.6:c.1987A>G	p.Thr663Ala	p.T663A	ENST00000335508	NM_012433.2	663	Act/Gct	14/25	1	2	FACETS	0.921	0.795	1	0.921	0.795	1	CLONAL	1	TRUE	1	0.18	2		595	760	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790033	40790033	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	62	796	0	ENST00000373198.4:c.2698A>T	p.Met900Leu	p.M900L	ENST00000373198	NM_133170.3	900	Atg/Ttg	18/32	1	2	FACETS	0.952	0.821	1	0.952	0.821	1	CLONAL	1	TRUE	1	0.18	2		796	724	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101188	41101188	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	76	761	0	ENST00000373198.4:c.1168C>G	p.Pro390Ala	p.P390A	ENST00000373198	NM_133170.3	390	Cca/Gca	8/32	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.18	2		761	737	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142947	47142947	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0041883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	56	564	0	ENST00000409792.3:c.5015+1G>T		p.X1672_splice	ENST00000409792	NM_014159.6	1672			1	2	FACETS	0.985	0.843	1	0.985	0.843	1	CLONAL	1	TRUE	1	0.18	2		564	632	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	256470	256470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3211483	NA	P-0041883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	56	817	0	ENST00000264932.6:c.1930G>A	p.Val644Met	p.V644M	ENST00000264932	NM_004168.2	644	Gtg/Atg	15/15	1	2	FACETS	0.731	0.625	0.848	0.731	0.625	0.848	SUBCLONAL	1	TRUE	1	0.18	2		817	851	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457681	149457681	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	50	840	0	ENST00000286301.3:c.723C>A	p.Asn241Lys	p.N241K	ENST00000286301	NM_005211.3	241	aaC/aaA	5/22	0.249271494616654	0	FACETS	0.598	0.506	0.699			1	SUBCLONAL	1	TRUE	0	0.18	0		840	762	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851893	128851893	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1199268301	NA	P-0041883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	51	961	0	ENST00000249373.3:c.1965G>C	p.Trp655Cys	p.W655C	ENST00000249373	NM_005631.4	655	tgG/tgC	12/12	1	2	FACETS	0.734	0.622	0.857	0.734	0.622	0.857	SUBCLONAL	1	TRUE	1	0.18	2		961	772	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032526	47032526	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0041883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	48	398	0	ENST00000377604.3:c.433-1G>C		p.X145_splice	ENST00000377604	NM_001204468.1	145			1	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.18	1		398	372	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0041893-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	159	420	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.472011316209754	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.472011316209754	1		420	513	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0041893-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	337	668	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.472011316209754	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.472011316209754	1		668	928	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088646	27088646	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041893-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	209	631	0	ENST00000324856.7:c.2255A>G	p.Tyr752Cys	p.Y752C	ENST00000324856	NM_006015.4	752	tAt/tGt	7/20	0.245490351062994	1	FACETS	0.695	0.646	0.747	0.695	0.646	0.747	INDETERMINATE	1	TRUE	0	0.472011316209754	1		631	973	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249019	55249020	+	protein_altering_variant	In_Frame_Ins	INS	-	-	CTAACCCCT	novel	NA	P-0041893-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	338	598	0	ENST00000275493.2:c.2317_2318insCTAACCCCT	p.His773delinsProAsnProTyr	p.H773delinsPNPY	ENST00000275493	NM_005228.3	773	cac/cCTAACCCCTac	20/28	0.218762462926029	3	FACETS	0.772	0.731	0.815	0.772	0.731	0.815	INDETERMINATE	2	TRUE	1	0.472011316209754	3		598	1146	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0041909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	74	422	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.287101929874862	2		422	479	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259206	36259206	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	119	526	0	ENST00000300305.3:c.285del	p.Asn96ThrfsTer26	p.N96Tfs*26	ENST00000300305		95	ccC/cc	3/8	1	2	FACETS	0.849	0.771	0.931	1	0.988	1	CLONAL	2	TRUE	1	0.287101929874862	2		526	488	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206818	36206818	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	41	610	3	ENST00000300305.3:c.694C>T	p.Arg232Trp	p.R232W	ENST00000300305		232	Cgg/Tgg	6/8	1	2	FACETS	0.579	0.482	0.687	0.579	0.482	0.687	SUBCLONAL	1	TRUE	1	0.287101929874862	2		613	493	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937704	36937704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	86	861	0	ENST00000361632.4:c.1034G>A	p.Arg345Lys	p.R345K	ENST00000361632		345	aGg/aAg	8/16	1	2	FACETS	0.946	0.838	1	0.946	0.838	1	CLONAL	1	TRUE	1	0.287101929874862	2		861	633	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959112	2959112	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	126	836	0	ENST00000396946.4:c.2404C>A	p.His802Asn	p.H802N	ENST00000396946	NM_032415.4	802	Cac/Aac	18/25	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.287101929874862	2		836	709	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0041941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	198	405	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.424601713031164	2		405	777	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197800	123197800	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	101	187	0	ENST00000218089.9:c.1924G>A	p.Glu642Lys	p.E642K	ENST00000218089	NM_001042749.1	642	Gaa/Aaa	20/35	0.424601713031164	3	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.424601713031164	3		187	415	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0041965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	126	673	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.746853934921245	2		673	315	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17355094	17355094	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs398122805	NA	P-0041965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	145	255	0	ENST00000375499.3:c.423+1G>A		p.X141_splice	ENST00000375499	NM_003000.2	141			1	2	FACETS	0.855	0.787	0.926	0.855	0.787	0.926	CLONAL	1	TRUE	1	0.746853934921245	2		255	454	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830093	72830093	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	149	818	0	ENST00000268489.5:c.6488A>C	p.Tyr2163Ser	p.Y2163S	ENST00000268489	NM_006885.3	2163	tAt/tCt	9/10	1	2	FACETS	0.592	0.542	0.644	0.592	0.542	0.644	SUBCLONAL	1	TRUE	1	0.746853934921245	2		818	674	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954901	2954901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1394063331	NA	P-0041965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	316	791	0	ENST00000396946.4:c.2809G>A	p.Ala937Thr	p.A937T	ENST00000396946	NM_032415.4	937	Gcc/Acc	21/25	0.746853934921245	4	FACETS	1	0.977	1	0.357	0.336	0.378	CLONAL	1	TRUE	1	0.746853934921245	4		791	1382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0041969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	834	641	0	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	0.871036490569601	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.871036490569601	1		641	983	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0041969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	24	1096	1	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.871036490569601	1	FACETS	0.037	0.028	0.047	0.037	0.028	0.047	SUBCLONAL	1	TRUE	0	0.871036490569601	1		1097	840	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413162	139413162	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1634	1349	1005	1	ENST00000277541.6:c.980G>A	p.Trp327Ter	p.W327*	ENST00000277541	NM_017617.3	327	tGg/tAg	6/34	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.871036490569601	2		1006	2983	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471047	8471047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201751722	NA	P-0041969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	74	274	3	ENST00000356435.5:c.3452G>A	p.Arg1151His	p.R1151H	ENST00000356435		1151	cGc/cAc	20/35	0.112752673536802	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.871036490569601	0		277	186	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554840	106554840	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	404	439	0	ENST00000369096.4:c.1957C>T	p.His653Tyr	p.H653Y	ENST00000369096	NM_001198.3	653	Cat/Tat	7/7	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.871036490569601	2		439	834	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794502	242794502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	676	765	0	ENST00000334409.5:c.440G>A	p.Arg147Lys	p.R147K	ENST00000334409	NM_005018.2	147	aGa/aAa	3/5	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.871036490569601	2		765	1528	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953195	81953195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs187454354	NA	P-0041969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	444	363	0	ENST00000359376.3:c.2161G>A	p.Glu721Lys	p.E721K	ENST00000359376	NM_002661.3	721	Gag/Aag	20/33	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.871036490569601	2		363	976	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39762920	39762920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	96	327	0	ENST00000288319.7:c.916C>T	p.Pro306Ser	p.P306S	ENST00000288319	NM_182918.3	306	Cca/Tca	9/10	1	2	FACETS	0.922	0.837	1	0.922	0.837	1	CLONAL	1	TRUE	1	0.871036490569601	2		327	239	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204760	94204761	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	37	303	0	ENST00000323929.3:c.824_825delinsTT	p.Ser275Phe	p.S275F	ENST00000323929	NM_005591.3	275	tCC/tTT	8/20	1	2	FACETS	0.833	0.707	0.965	0.833	0.707	0.965	CLONAL	1	TRUE	1	0.871036490569601	2		303	102	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376036	8376036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	127	276	0	ENST00000356435.5:c.4561G>A	p.Asp1521Asn	p.D1521N	ENST00000356435		1521	Gat/Aat	28/35	0.112752673536802	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.871036490569601	0		276	293	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046482	69046482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	247	514	0	ENST00000288368.4:c.3955C>T	p.His1319Tyr	p.H1319Y	ENST00000288368	NM_024870.2	1319	Cac/Tac	32/40	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.871036490569601	2		514	559	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163446	32163446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2057	2099	703	0	ENST00000375023.3:c.5780C>T	p.Pro1927Leu	p.P1927L	ENST00000375023	NM_004557.3	1927	cCt/cTt	30/30	1	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	1	0.871036490569601	2		703	4156	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965749	93965749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	62	208	0	ENST00000369303.4:c.2179G>A	p.Asp727Asn	p.D727N	ENST00000369303	NM_004440.3	727	Gat/Aat	13/17	1	2	FACETS	0.913	0.808	1	0.913	0.808	1	CLONAL	1	TRUE	1	0.871036490569601	2		208	156	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282428	115282429	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	100	456	0	ENST00000438362.2:c.221_222delinsAA	p.Gly74Glu	p.G74E	ENST00000438362	NM_001242891.1	74	gGG/gAA	3/20	1	2	FACETS	0.778	0.705	0.854	0.778	0.705	0.854	SUBCLONAL	1	TRUE	1	0.871036490569601	2		456	295	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432683	29432683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	498	581	0	ENST00000389048.3:c.3805G>A	p.Gly1269Arg	p.G1269R	ENST00000389048	NM_004304.4	1269	Gga/Aga	25/29	1	2	FACETS	0.921	0.883	0.96	0.921	0.883	0.96	CLONAL	1	TRUE	1	0.871036490569601	2		581	1241	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388039	31388039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	211	325	0	ENST00000328111.2:c.1840G>A	p.Gly614Arg	p.G614R	ENST00000328111	NM_006892.3	614	Gga/Aga	17/23	1	2	FACETS	0.881	0.825	0.938	0.881	0.825	0.938	CLONAL	1	TRUE	1	0.871036490569601	2		325	550	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62322173	62322174	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	800	758	2	ENST00000360203.5:c.2429_2430delinsAA	p.Gly810Glu	p.G810E	ENST00000360203	NM_001283009.1	810	gGG/gAA	27/35	1	2	FACETS	0.928	0.898	0.959	0.928	0.898	0.959	CLONAL	1	TRUE	1	0.871036490569601	2		760	1979	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175767	24175767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	508	509	0	ENST00000263121.7:c.995C>T	p.Pro332Leu	p.P332L	ENST00000263121	NM_003073.3	332	cCt/cTt	8/9	1	2	FACETS	0.972	0.933	1	0.972	0.933	1	CLONAL	1	TRUE	1	0.871036490569601	2		509	1200	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442032	52442033	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGCTGCTGCAGTT	novel	NA	P-0041969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	787	538	0	ENST00000460680.1:c.304_316dup	p.Val106GlufsTer24	p.V106Efs*24	ENST00000460680	NM_004656.3	106	gtg/gAACTGCAGCAGCGtg	5/17	0.871036490569601	1	FACETS	0.912	0.891	0.933	0.912	0.891	0.933	CLONAL	1	TRUE	0	0.871036490569601	1		538	1118	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391129	89391129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	413	587	0	ENST00000336596.2:c.1195C>T	p.Leu399Phe	p.L399F	ENST00000336596	NM_005233.5	399	Ctt/Ttt	5/17	0.871036490569601	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.871036490569601	1		587	504	SUCCESS
ATR	545	MSKCC	GRCh37	3	142232356	142232356	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	19	297	0	ENST00000350721.4:c.4628A>C	p.Glu1543Ala	p.E1543A	ENST00000350721	NM_001184.3	1543	gAa/gCa	26/47	0.627752807478992	1	FACETS	0.17	0.13	0.216	0.17	0.13	0.216	SUBCLONAL	1	TRUE	0	0.871036490569601	1		297	145	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212768	27212768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	887	757	0	ENST00000380036.4:c.2750G>A	p.Ser917Asn	p.S917N	ENST00000380036	NM_000459.3	917	aGc/aAc	17/23	0.112752673536802	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.871036490569601	0		757	1973	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215904	98215904	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0041969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	666	601	0	ENST00000331920.6:c.3307-2A>C		p.X1103_splice	ENST00000331920	NM_000264.3	1103			0.871036490569601	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.871036490569601	1		601	773	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0041981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	279	513	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.207400609238627	5	FACETS	0.856	0.81	0.902	0.856	0.81	0.902	INDETERMINATE	3	FALSE	2	0.666831657146857	5		513	652	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0041981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	80	232	0	ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	4/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.666831657146857	2		232	169	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0041981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	405	210	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.207400609238627	5	FACETS	0.946	0.906	0.987	0.946	0.906	0.987	INDETERMINATE	3	FALSE	2	0.666831657146857	5		210	856	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907685	76907689	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTG	TTCTG	-	novel	NA	P-0041981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	142	398	0	ENST00000373344.5:c.4472_4476del	p.Thr1491AsnfsTer6	p.T1491Nfs*6	ENST00000373344	NM_000489.3	1491	aCAGAA/a	15/35	0.568147376202737	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	0	0.666831657146857	1		398	204	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0042006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	148	673	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.941	0.863	1	0.941	0.863	1	CLONAL	1	TRUE	1	0.552977213729209	2		673	569	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562657	29562660	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs1064794276	NA	P-0042006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	97	447	0	ENST00000356175.3:c.3739_3742del	p.Phe1247IlefsTer18	p.F1247Ifs*18	ENST00000356175	NM_000267.3	1246	cTGTTt/ct	28/57	1	2	FACETS	0.822	0.737	0.911	0.822	0.737	0.911	CLONAL	1	TRUE	1	0.552977213729209	2		447	427	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161324	55161324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514550	NA	P-0042006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	146	508	0	ENST00000257290.5:c.3155C>T	p.Thr1052Met	p.T1052M	ENST00000257290	NM_006206.4	1052	aCg/aTg	23/23	1	2	FACETS	0.869	0.796	0.944	0.869	0.796	0.944	CLONAL	1	TRUE	1	0.552977213729209	2		508	608	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs149840192	NA	P-0042006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	288	914	0	ENST00000275493.2:c.866C>A	p.Ala289Asp	p.A289D	ENST00000275493	NM_005228.3	289	gCc/gAc	7/28	0.552977213729209	3	FACETS	0.988	0.927	1	0.494	0.463	0.525	CLONAL	1	TRUE	1	0.552977213729209	3		914	1346	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586056	29586056	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1135402857	NA	P-0042006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	43	368	0	ENST00000356175.3:c.4276C>T	p.Gln1426Ter	p.Q1426*	ENST00000356175	NM_000267.3	1426	Cag/Tag	32/57	1	2	FACETS	0.978	0.833	1	0.978	0.833	1	CLONAL	1	TRUE	1	0.552977213729209	2		368	159	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720865	89720866	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0042006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	76	357	0	ENST00000371953.3:c.1016_1017del	p.Pro339GlnfsTer3	p.P339Qfs*3	ENST00000371953	NM_000314.4	339	cCA/c	8/9	0.552977213729209	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.552977213729209	1		357	147	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456465	89456465	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	119	474	0	ENST00000336596.2:c.1641T>G	p.Ile547Met	p.I547M	ENST00000336596	NM_005233.5	547	atT/atG	8/17	0.521388398293912	3	FACETS	1	0.956	1	0.545	0.494	0.598	CLONAL	1	TRUE	1	0.552977213729209	3		474	504	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294253	1294253	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	218	746	0	ENST00000310581.5:c.748C>T	p.Pro250Ser	p.P250S	ENST00000310581	NM_198253.2	250	Ccc/Tcc	2/16	1	2	FACETS	0.969	0.903	1	0.969	0.903	1	CLONAL	1	TRUE	1	0.552977213729209	2		746	814	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413025	63413025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777329368	NA	P-0042006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	241	975	0	ENST00000330258.3:c.142G>A	p.Gly48Ser	p.G48S	ENST00000330258	NM_152424.3	48	Ggc/Agc	2/2	1	2	FACETS	0.845	0.79	0.903	0.845	0.79	0.903	CLONAL	1	TRUE	1	0.552977213729209	2		975	1031	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0042007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	154	756	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.220596398641522	2	FACETS	0.979	0.898	1	0.979	0.898	1	CLONAL	2	TRUE	0	0.220596398641522	2		756	713	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0042007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	41	437	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.218450620659365	2	FACETS	0.929	0.783	1	0.929	0.783	1	CLONAL	2	TRUE	0	0.220596398641522	2		437	200	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	66	476	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	0.220596398641522	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	2	TRUE	0	0.220596398641522	2		476	282	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0042007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	91	353	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.220596398641522	3	FACETS	1	0.952	1			1	CLONAL	2	TRUE	NA	0.220596398641522	3		353	410	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0042007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	135	544	1	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.849	0.773	0.929	1	0.989	1	CLONAL	2	TRUE	1	0.220596398641522	2		545	721	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998673	100998674	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0042007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	229	805	0	ENST00000325455.5:c.1128_1129del	p.Tyr377Ter	p.Y377*	ENST00000325455	NM_001202474.3	376	ctCTat/ctat	1/8	0.113644086711353	5	FACETS	1	0.976	1	0.82	0.766	0.876	INDETERMINATE	3	TRUE	1	0.220596398641522	5		805	842	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371712	55371713	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0042007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	50	605	0	ENST00000297316.4:c.403dup	p.Tyr135LeufsTer27	p.Y135Lfs*27	ENST00000297316	NM_022454.3	134	-/T	2/2	0.113644086711353	5	FACETS	0.899	0.762	1	0.225	0.19	0.263	INDETERMINATE	1	TRUE	1	0.220596398641522	5		605	671	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181807	56181807	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	39	369	0	ENST00000399503.3:c.4031C>A	p.Ser1344Ter	p.S1344*	ENST00000399503	NM_005921.1	1344	tCa/tAa	17/20	0.166640903694288	2	FACETS	0.871	0.729	1	0.871	0.729	1	CLONAL	2	TRUE	0	0.220596398641522	2		369	203	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092859	27092860	+	splice_donor_variant,intron_variant	Splice_Site	DEL	TA	TA	-	novel	NA	P-0042007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	60	565	1	ENST00000324856.7:c.2878+2_2878+3del		p.X960_splice	ENST00000324856	NM_006015.4	960			1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.220596398641522	2		566	526	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118361923	118361923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	23	289	0	ENST00000534358.1:c.4709C>T	p.Pro1570Leu	p.P1570L	ENST00000534358	NM_005933.3	1570	cCt/cTt	14/36	0.113644086711353	5	FACETS	1	0.911	1	0.34	0.266	0.424	INDETERMINATE	1	TRUE	1	0.220596398641522	5		289	204	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359636	40359636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773533491	NA	P-0042007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	52	615	0	ENST00000293328.3:c.2017C>T	p.Arg673Trp	p.R673W	ENST00000293328	NM_012448.3	673	Cgg/Tgg	16/19	0.220596398641522	2	FACETS	0.698	0.594	0.814	0.349	0.297	0.407	SUBCLONAL	1	TRUE	0	0.220596398641522	2		615	675	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589545	67589568	+	inframe_deletion	In_Frame_Del	DEL	TGTCAAAGAAGATAATATTGAAGC	TGTCAAAGAAGATAATATTGAAGC	-	novel	NA	P-0042007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	19	223	0	ENST00000274335.5:c.1311_1334del	p.Lys438_Val445del	p.K438_V445del	ENST00000274335		436	gtTGTCAAAGAAGATAATATTGAAGCt/gtt	10/15	0.166640903694288	2	FACETS	0.844	0.651	1	0.844	0.651	1	CLONAL	2	TRUE	0	0.220596398641522	2		223	102	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359983	87359983	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	16	366	0	ENST00000277120.3:c.1291C>T	p.Leu431Phe	p.L431F	ENST00000277120		431	Ctc/Ttc	11/19	0.166640903694288	2	FACETS	0.48	0.354	0.631	0.24	0.177	0.316	SUBCLONAL	1	TRUE	0	0.220596398641522	2		366	302	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0042009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	142	399	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.784	0.72	0.851	1	0.989	1	SUBCLONAL	2	FALSE	1	0.364983202994076	2		399	496	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649927	88649927	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1564714834	NA	P-0042009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	191	633	0	ENST00000372037.3:c.176T>A	p.Leu59Ter	p.L59*	ENST00000372037	NM_004329.2	59	tTa/tAa	4/13	1	2	FACETS	0.762	0.707	0.818	1	0.991	1	SUBCLONAL	2	FALSE	1	0.364983202994076	2		633	687	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56873486	56873486	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	47	564	0	ENST00000308159.5:c.2190A>T	p.Arg730Ser	p.R730S	ENST00000308159	NM_014669.4	730	agA/agT	20/22	0.225215428577734	3	FACETS	0.374	0.314	0.44	0.187	0.157	0.22	SUBCLONAL	1	FALSE	1	0.364983202994076	3		564	815	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0042009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	358	773	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.315544425750934	0	FACETS	0.838	0.8	0.876			1	CLONAL	2	FALSE	0	0.364983202994076	0		773	743	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0042009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	19876	832	7	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.364983202994076	48	FACETS	1	0.999	1			1	CLONAL	50	FALSE	NA	0.364983202994076	48		839	20389	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37622735	37622735	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	69	874	0	ENST00000249071.6:c.557A>C	p.Lys186Thr	p.K186T	ENST00000249071	NM_002872.4	186	aAg/aCg	6/7	0.353214149091534	1	FACETS	0.336	0.292	0.384	0.336	0.292	0.384	SUBCLONAL	1	FALSE	0	0.364983202994076	1		874	920	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467990	66467990	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0042009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	30	337	0	ENST00000273854.3:c.279T>G	p.Tyr93Ter	p.Y93*	ENST00000273854	NM_004439.5	93	taT/taG	3/18	0.364983202994076	1	FACETS	0.421	0.34	0.513	0.421	0.34	0.513	SUBCLONAL	1	FALSE	0	0.364983202994076	1		337	319	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915029	131915029	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	25	428	0	ENST00000265335.6:c.386T>C	p.Leu129Pro	p.L129P	ENST00000265335		129	cTg/cCg	4/25	1	2	FACETS	0.299	0.235	0.373	0.299	0.235	0.373	SUBCLONAL	1	FALSE	1	0.364983202994076	2		428	458	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665248	176665248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760426933	NA	P-0042009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	92	390	0	ENST00000439151.2:c.3932G>A	p.Arg1311His	p.R1311H	ENST00000439151	NM_022455.4	1311	cGc/cAc	7/23	NA	2	FACETS	0.955	0.851	1			1	INDETERMINATE	1	FALSE	NA	0.364983202994076	2		390	528	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522605	106522605	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	72	497	0	ENST00000359195.3:c.2582A>C	p.Asp861Ala	p.D861A	ENST00000359195	NM_002649.2	861	gAt/gCt	7/11	0.324454867290374	3	FACETS	0.723	0.632	0.822	0.362	0.316	0.411	SUBCLONAL	1	FALSE	1	0.364983202994076	3		497	645	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	112	320	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.903	0.818	0.991	0.903	0.818	0.991	CLONAL	1	TRUE	1	0.590690110557336	2		321	420	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559194	29559194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	140	410	0	ENST00000356175.3:c.3301C>T	p.Gln1101Ter	p.Q1101*	ENST00000356175	NM_000267.3	1101	Cag/Tag	25/57	1	2	FACETS	0.924	0.847	1	0.924	0.847	1	CLONAL	1	TRUE	1	0.590690110557336	2		410	513	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664446	29664447	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCTGTTTGGCATTA	novel	NA	P-0042010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	136	565	0	ENST00000356175.3:c.6428_6441dup	p.Lys2148CysfsTer36	p.K2148Cfs*36	ENST00000356175	NM_000267.3	2142	ttg/ttGCTGTTTGGCATTAg	42/57	1	2	FACETS	0.669	0.61	0.732	0.669	0.61	0.732	SUBCLONAL	1	TRUE	1	0.590690110557336	2		565	688	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878422	151878422	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	237	845	0	ENST00000262189.6:c.6523A>T	p.Ser2175Cys	p.S2175C	ENST00000262189	NM_170606.2	2175	Agt/Tgt	36/59	0.139152042866528	4	FACETS	1	0.974	1	1	0.996	1	CLONAL	5	FALSE	2	0.225928748545485	4		845	489	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	104	320	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.402437986557611	2		321	452	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936983	48936983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690863	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	134	418	0	ENST00000267163.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000267163	NM_000321.2	251	Cga/Tga	8/27	0.402437986557611	2	FACETS	0.886	0.814	0.959	0.886	0.814	0.959	CLONAL	2	FALSE	0	0.402437986557611	2		418	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	184	842	3	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.402437986557611	2		845	772	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88672017	88672017	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1131691185	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	52	530	0	ENST00000372037.3:c.551C>G	p.Ser184Ter	p.S184*	ENST00000372037	NM_004329.2	184	tCa/tGa	8/13	1	2	FACETS	0.907	0.778	1	0.907	0.778	1	CLONAL	1	FALSE	1	0.402437986557611	2		530	285	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058361	42058362	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	69	409	1	ENST00000219905.7:c.8081_8082delinsTT	p.Ser2694Phe	p.S2694F	ENST00000219905	NM_001164273.1	2694	tCC/tTT	24/24	1	2	FACETS	0.997	0.874	1	0.997	0.874	1	CLONAL	1	FALSE	1	0.402437986557611	2		410	344	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321280	1321280	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763471203	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	73	467	0	ENST00000400841.2:c.475G>A	p.Glu159Lys	p.E159K	ENST00000400841		159	Gag/Aag	4/6	1	1	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	FALSE	0	0.402437986557611	1		467	287	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917832	29917832	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	176	863	1	ENST00000389048.3:c.836C>T	p.Pro279Leu	p.P279L	ENST00000389048	NM_004304.4	279	cCa/cTa	3/29	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.402437986557611	2		864	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	216	631	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.402437986557611	2		631	749	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076775	72076775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	118	547	1	ENST00000357731.5:c.722G>A	p.Gly241Asp	p.G241D	ENST00000357731	NM_173808.2	241	gGc/gAc	5/7	0.16754779477658	2	FACETS	1	0.951	1	0.539	0.488	0.592	INDETERMINATE	1	FALSE	0	0.402437986557611	2		548	544	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223966	36223967	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	182	820	0	ENST00000222270.7:c.6516_6517delinsTT	p.Arg2173Trp	p.R2173W	ENST00000222270	NM_014727.1	2172	gtCCgg/gtTTgg	28/37	0.150003142228095	3	FACETS	1	0.983	1	0.614	0.567	0.663	INDETERMINATE	1	FALSE	1	0.402437986557611	3		820	885	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539051	187539051	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1169115609	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	68	589	1	ENST00000441802.2:c.8689C>T	p.Gln2897Ter	p.Q2897*	ENST00000441802	NM_005245.3	2897	Cag/Tag	10/27	1	2	FACETS	0.921	0.806	1	0.921	0.806	1	CLONAL	1	FALSE	1	0.402437986557611	2		590	367	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692787	89692787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554898062	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	23	360	0	ENST00000371953.3:c.271G>A	p.Glu91Lys	p.E91K	ENST00000371953	NM_000314.4	91	Gaa/Aaa	5/9	1	2	FACETS	0.461	0.36	0.577	0.461	0.36	0.577	SUBCLONAL	1	FALSE	1	0.402437986557611	2		360	248	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984897	55984897	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	100	534	1	ENST00000263923.4:c.232G>A	p.Glu78Lys	p.E78K	ENST00000263923	NM_002253.2	78	Gag/Aag	3/30	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	1	0.402437986557611	2		535	450	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873233	71873233	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	56	446	0	ENST00000357731.5:c.961G>A	p.Gly321Arg	p.G321R	ENST00000357731	NM_173808.2	321	Gga/Aga	7/7	0.16754779477658	2	FACETS	0.878	0.757	1	0.439	0.378	0.504	INDETERMINATE	1	FALSE	0	0.402437986557611	2		446	317	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946940	71946940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	265	896	0	ENST00000298229.2:c.2789G>A	p.Arg930Lys	p.R930K	ENST00000298229	NM_001567.3	930	aGg/aAg	25/28	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	1	0.402437986557611	2		896	958	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225449666	225449667	+	missense_variant	Missense_Mutation	DNP	AG	AG	TA	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	113	369	1	ENST00000264414.4:c.60_61delinsTA	p.Phe21Ile	p.F21I	ENST00000264414	NM_003590.4	20	gcCTtt/gcTAtt	1/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.402437986557611	2		370	499	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334776	81334776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1267493094	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	129	496	0	ENST00000222390.5:c.1940G>A	p.Arg647Gln	p.R647Q	ENST00000222390	NM_000601.4	647	cGa/cAa	17/18	0.245984777495224	3	FACETS	0.941	0.861	1	0.628	0.574	0.683	CLONAL	2	FALSE	0	0.402437986557611	3		496	409	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595857	52595857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	184	692	0	ENST00000394830.3:c.4058C>T	p.Ser1353Phe	p.S1353F	ENST00000394830	NM_018313.4	1353	tCt/tTt	26/30	0.402437986557611	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	0	0.402437986557611	1		692	599	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233459	69233459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	77	491	0	ENST00000462284.1:c.1324G>A	p.Glu442Lys	p.E442K	ENST00000462284	NM_002392.5	442	Gaa/Aaa	11/11	0.150003142228095	3	FACETS	1	0.918	1	0.526	0.463	0.592	INDETERMINATE	1	FALSE	1	0.402437986557611	3		491	437	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325845	30325846	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	32	389	0	ENST00000322652.5:c.2043_2044delinsTT	p.Arg682Cys	p.R682C	ENST00000322652	NM_015355.2	681	ctCCgt/ctTTgt	16/16	0.402437986557611	1	FACETS	0.642	0.525	0.77	0.642	0.525	0.77	SUBCLONAL	1	FALSE	0	0.402437986557611	1		389	198	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174892	11174892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	120	620	0	ENST00000361445.4:c.7142G>A	p.Arg2381Lys	p.R2381K	ENST00000361445	NM_004958.3	2381	aGa/aAa	52/58	0.362967009799034	5	FACETS	1	0.96	1	0.281	0.253	0.31	CLONAL	1	FALSE	1	0.402437986557611	5		620	852	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260753	16260753	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	121	625	0	ENST00000375759.3:c.8018A>G	p.Lys2673Arg	p.K2673R	ENST00000375759	NM_015001.2	2673	aAg/aGg	11/15	0.362967009799034	5	FACETS	1	0.973	1	0.303	0.273	0.334	CLONAL	1	FALSE	1	0.402437986557611	5		625	796	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282384	115282384	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	104	545	0	ENST00000438362.2:c.266C>T	p.Ser89Leu	p.S89L	ENST00000438362	NM_001242891.1	89	tCa/tTa	3/20	0.16754779477658	2	FACETS	1	0.977	1	0.644	0.581	0.71	INDETERMINATE	1	FALSE	0	0.402437986557611	2		545	401	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282400	115282400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	70	532	0	ENST00000438362.2:c.250G>A	p.Gly84Arg	p.G84R	ENST00000438362	NM_001242891.1	84	Gga/Aga	3/20	0.16754779477658	2	FACETS	0.883	0.774	1	0.441	0.387	0.5	INDETERMINATE	1	FALSE	0	0.402437986557611	2		532	394	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466418	120466419	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	111	708	0	ENST00000256646.2:c.4700_4701delinsAA	p.Arg1567Gln	p.R1567Q	ENST00000256646	NM_024408.3	1567	cGG/cAA	26/34	0.16754779477658	2	FACETS	1	0.957	1	0.554	0.5	0.61	INDETERMINATE	1	FALSE	0	0.402437986557611	2		708	498	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107218	193107218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	61	298	0	ENST00000367435.3:c.427G>A	p.Glu143Lys	p.E143K	ENST00000367435	NM_024529.4	143	Gaa/Aaa	6/17	0.16754779477658	2	FACETS	0.892	0.774	1	0.446	0.387	0.509	INDETERMINATE	1	FALSE	0	0.402437986557611	2		298	340	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852317	63852317	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	102	733	1	ENST00000279873.7:c.3095C>T	p.Ser1032Phe	p.S1032F	ENST00000279873	NM_032199.2	1032	tCt/tTt	10/10	1	2	FACETS	0.91	0.816	1	0.91	0.816	1	CLONAL	1	FALSE	1	0.402437986557611	2		734	557	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451564	70451565	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	110	634	0	ENST00000373644.4:c.6404_6405delinsAA	p.Trp2135Ter	p.W2135*	ENST00000373644	NM_030625.2	2135	tGG/tAA	12/12	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	FALSE	1	0.402437986557611	2		634	534	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119772	108119772	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1025339570	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	36	260	0	ENST00000278616.4:c.1178G>A	p.Trp393Ter	p.W393*	ENST00000278616	NM_000051.3	393	tGg/tAg	9/63	1	2	FACETS	0.895	0.743	1	0.895	0.743	1	CLONAL	1	FALSE	1	0.402437986557611	2		260	200	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344651	118344651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	98	445	0	ENST00000534358.1:c.2777C>T	p.Ser926Phe	p.S926F	ENST00000534358	NM_005933.3	926	tCt/tTt	3/36	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.402437986557611	2		445	418	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431148	49431148	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	242	739	0	ENST00000301067.7:c.9991C>T	p.Pro3331Ser	p.P3331S	ENST00000301067	NM_003482.3	3331	Ccc/Tcc	34/54	0.402437986557611	5	FACETS	0.932	0.87	0.995			1	CLONAL	2	FALSE	NA	0.402437986557611	5		739	1035	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445194	49445195	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	175	844	3	ENST00000301067.7:c.2271_2272delinsAA	p.Glu758Lys	p.E758K	ENST00000301067	NM_003482.3	757	gaGGag/gaAAag	10/54	0.402437986557611	5	FACETS	0.775	0.714	0.838			1	SUBCLONAL	2	FALSE	NA	0.402437986557611	5		847	900	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120638	115120638	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	183	871	0	ENST00000257566.3:c.368T>C	p.Met123Thr	p.M123T	ENST00000257566	NM_016569.3	123	aTg/aCg	1/8	0.150003142228095	3	FACETS	1	0.989	1	0.724	0.67	0.781	INDETERMINATE	1	FALSE	1	0.402437986557611	3		871	754	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435256	110435257	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	202	354	4	ENST00000375856.3:c.3144_3145delinsAA	p.Ala1049Thr	p.A1049T	ENST00000375856	NM_003749.2	1048	tcGGcc/tcAAcc	1/2	0.402437986557611	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	FALSE	0	0.402437986557611	2		358	403	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68934952	68934952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	45	382	0	ENST00000487270.1:c.1021G>A	p.Gly341Ser	p.G341S	ENST00000487270	NM_133509.3	341	Ggc/Agc	10/11	1	2	FACETS	0.63	0.531	0.739	0.63	0.531	0.739	SUBCLONAL	1	FALSE	1	0.402437986557611	2		382	355	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614584	38614584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749378713	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	30	580	1	ENST00000299084.4:c.350G>A	p.Arg117Gln	p.R117Q	ENST00000299084	NM_152594.2	117	cGa/cAa	3/7	1	2	FACETS	0.529	0.427	0.643	0.529	0.427	0.643	SUBCLONAL	1	FALSE	1	0.402437986557611	2		581	282	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034909	42034909	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267604189	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	136	613	0	ENST00000219905.7:c.4751C>T	p.Ser1584Phe	p.S1584F	ENST00000219905	NM_001164273.1	1584	tCt/tTt	15/24	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.402437986557611	2		613	521	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778006	3778006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	262	1019	0	ENST00000262367.5:c.7042C>T	p.Pro2348Ser	p.P2348S	ENST00000262367	NM_004380.2	2348	Cct/Tct	31/31	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.402437986557611	2		1019	973	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820764	3820765	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	229	931	2	ENST00000262367.5:c.2686_2687delinsAA	p.Gly896Lys	p.G896K	ENST00000262367	NM_004380.2	896	GGg/AAg	14/31	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.402437986557611	2		933	1024	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860653	3860653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	170	752	1	ENST00000262367.5:c.926C>T	p.Thr309Ile	p.T309I	ENST00000262367	NM_004380.2	309	aCc/aTc	3/31	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.402437986557611	2		753	745	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50830304	50830304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	93	512	0	ENST00000398568.2:c.2747C>T	p.Ser916Phe	p.S916F	ENST00000398568	NM_001042412.1	916	tCt/tTt	18/18	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.402437986557611	2		512	410	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671769	67671770	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	125	686	0	ENST00000264010.4:c.2178_2179delinsTT	p.Arg727Trp	p.R727W	ENST00000264010	NM_006565.3	726	gaCCgg/gaTTgg	12/12	1	2	FACETS	0.999	0.906	1	0.999	0.906	1	CLONAL	1	FALSE	1	0.402437986557611	2		686	622	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829499	72829499	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	111	694	0	ENST00000268489.5:c.7082A>C	p.Asp2361Ala	p.D2361A	ENST00000268489	NM_006885.3	2361	gAc/gCc	9/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	1	0.402437986557611	2		694	506	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81902828	81902829	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	90	515	2	ENST00000359376.3:c.489_490delinsTT	p.Arg164Ter	p.R164*	ENST00000359376	NM_002661.3	163	ctCCga/ctTTga	6/33	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	FALSE	1	0.402437986557611	2		517	439	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953132	81953132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778773333	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	63	424	1	ENST00000359376.3:c.2098C>T	p.Arg700Trp	p.R700W	ENST00000359376	NM_002661.3	700	Cgg/Tgg	20/33	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	FALSE	1	0.402437986557611	2		425	295	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216155	7216156	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	130	432	0	ENST00000380728.2:c.903_904delinsAA	p.Gly302Ser	p.G302S	ENST00000380728		301	tcGGgc/tcAAgc	11/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.402437986557611	2		432	579	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552179	29552179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	47	352	0	ENST00000356175.3:c.1912G>A	p.Gly638Arg	p.G638R	ENST00000356175	NM_000267.3	638	Gga/Aga	17/57	0.402437986557611	1	FACETS	0.872	0.744	1	0.872	0.744	1	CLONAL	1	FALSE	0	0.402437986557611	1		352	214	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40872313	40872313	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	156	723	0	ENST00000428826.2:c.642G>C	p.Lys214Asn	p.K214N	ENST00000428826		214	aaG/aaC	7/21	0.402437986557611	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	0	0.402437986557611	1		723	585	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277027	18277027	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	197	655	0	ENST00000222254.8:c.1474G>A	p.Glu492Lys	p.E492K	ENST00000222254	NM_005027.3	492	Gaa/Aaa	12/16	0.150003142228095	3	FACETS	1	0.989	1	0.698	0.647	0.751	INDETERMINATE	1	FALSE	1	0.402437986557611	3		655	842	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211304	36211304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752770016	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	291	994	0	ENST00000222270.7:c.1055C>T	p.Pro352Leu	p.P352L	ENST00000222270	NM_014727.1	352	cCt/cTt	3/37	0.150003142228095	3	FACETS	1	0.993	1	0.723	0.68	0.768	INDETERMINATE	1	FALSE	1	0.402437986557611	3		994	1201	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919753	50919753	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	39	791	0	ENST00000440232.2:c.2921T>C	p.Leu974Pro	p.L974P	ENST00000440232	NM_002691.3	974	cTg/cCg	23/27	0.150003142228095	3	FACETS	0.31	0.256	0.371	0.155	0.128	0.186	INDETERMINATE	1	FALSE	1	0.402437986557611	3		791	750	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416653	29416653	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778085426	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	67	529	0	ENST00000389048.3:c.4300G>A	p.Glu1434Lys	p.E1434K	ENST00000389048	NM_004304.4	1434	Gag/Aag	29/29	1	2	FACETS	0.96	0.839	1	0.96	0.839	1	CLONAL	1	FALSE	1	0.402437986557611	2		529	347	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172133	99172133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	128	726	0	ENST00000074304.5:c.1699G>A	p.Gly567Ser	p.G567S	ENST00000074304	NM_001134224.1	567	Ggc/Agc	17/26	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.402437986557611	2		726	527	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793216	242793217	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	216	840	0	ENST00000334409.5:c.860_861delinsTT	p.Pro287Leu	p.P287L	ENST00000334409	NM_005018.2	287	cCC/cTT	5/5	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.402437986557611	2		840	784	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023508	31023509	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	102	607	0	ENST00000375687.4:c.2993_2994delinsTT	p.Ser998Phe	p.S998F	ENST00000375687	NM_015338.5	998	tCC/tTT	13/13	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	1	0.402437986557611	2		607	477	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375249	31375249	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	139	740	0	ENST00000328111.2:c.646G>A	p.Glu216Lys	p.E216K	ENST00000328111	NM_006892.3	216	Gag/Aag	6/23	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.402437986557611	2		740	586	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098772	47098772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	145	802	2	ENST00000409792.3:c.6502C>T	p.Pro2168Ser	p.P2168S	ENST00000409792	NM_014159.6	2168	Cca/Tca	15/21	0.402437986557611	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	0	0.402437986557611	1		804	509	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73110205	73110205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	64	399	0	ENST00000356692.5:c.413C>T	p.Ser138Phe	p.S138F	ENST00000356692		138	tCt/tTt	5/9	0.402437986557611	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	FALSE	0	0.402437986557611	1		399	221	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182679142	182679142	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	49	424	0	ENST00000292782.4:c.392G>T	p.Cys131Phe	p.C131F	ENST00000292782	NM_020640.2	131	tGt/tTt	4/7	0.150003142228095	3	FACETS	0.858	0.73	0.998	0.429	0.365	0.499	INDETERMINATE	1	FALSE	1	0.402437986557611	3		424	341	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807165	1807166	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	210	838	2	ENST00000260795.2:c.1496_1497delinsTT	p.Ala499Val	p.A499V	ENST00000260795		499	gCC/gTT	10/17	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.402437986557611	2		840	788	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628173	187628174	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	73	741	2	ENST00000441802.2:c.2808_2809delinsTT	p.Arg937Ter	p.R937*	ENST00000441802	NM_005245.3	936	gtCCga/gtTTga	2/27	1	2	FACETS	0.724	0.635	0.82	0.724	0.635	0.82	SUBCLONAL	1	FALSE	1	0.402437986557611	2		743	501	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876400	35876401	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	98	713	0	ENST00000303115.3:c.1192_1193delinsTT	p.Pro398Phe	p.P398F	ENST00000303115	NM_002185.3	398	CCt/TTt	8/8	1	2	FACETS	0.919	0.823	1	0.919	0.823	1	CLONAL	1	FALSE	1	0.402437986557611	2		713	530	SUCCESS
APC	324	MSKCC	GRCh37	5	112102970	112102970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	83	489	0	ENST00000257430.4:c.305C>T	p.Ser102Phe	p.S102F	ENST00000257430	NM_000038.5	102	tCt/tTt	4/16	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	FALSE	1	0.402437986557611	2		489	377	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056163	26056163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	228	555	1	ENST00000343677.2:c.494C>T	p.Thr165Ile	p.T165I	ENST00000343677	NM_005319.3	165	aCt/aTt	1/1	0.402437986557611	5	FACETS	1	0.988	1			1	CLONAL	2	FALSE	NA	0.402437986557611	5		556	739	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673434	30673435	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	125	622	1	ENST00000376406.3:c.3525_3526delinsTT	p.Gln1176Ter	p.Q1176*	ENST00000376406	NM_014641.2	1175	gaCCag/gaTTag	10/15	1	2	FACETS	0.992	0.901	1	0.992	0.901	1	CLONAL	1	FALSE	1	0.402437986557611	2		623	626	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984005	2984006	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	250	827	0	ENST00000396946.4:c.524_525delinsTT	p.Thr175Ile	p.T175I	ENST00000396946	NM_032415.4	175	aCC/aTT	5/25	1	2	FACETS	0.773	0.725	0.821	1	0.993	1	SUBCLONAL	2	FALSE	1	0.402437986557611	2		827	804	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737878	145737879	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	214	900	1	ENST00000428558.2:c.2951_2952delinsTT	p.Ser984Phe	p.S984F	ENST00000428558	NM_004260.3	984	tCC/tTT	18/22	0.143982955296467	0	FACETS	0.701	0.652	0.751			1	INDETERMINATE	1	FALSE	0	0.402437986557611	0		901	907	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566534	139566534	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	229	812	1	ENST00000308874.7:c.793G>A	p.Gly265Arg	p.G265R	ENST00000308874		265	Ggg/Agg	9/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.402437986557611	2		813	837	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245146	53245146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	130	351	2	ENST00000375401.3:c.794C>T	p.Pro265Leu	p.P265L	ENST00000375401	NM_004187.3	265	cCt/cTt	7/26	1	1	FACETS	0.938	0.868	1	1	0.991	1	CLONAL	2	FALSE	0	0.402437986557611	1		353	275	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0042053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	204	465	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	1	2	FACETS	0.929	0.864	0.995	0.929	0.864	0.995	CLONAL	1	TRUE	1	0.610950557925094	2		465	719	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933593	39933594	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0042053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	281	700	1	ENST00000378444.4:c.1005dup	p.Ser336LeufsTer45	p.S336Lfs*45	ENST00000378444	NM_001123385.1	335	-/C	4/15	1	2	FACETS	0.967	0.91	1	0.967	0.91	1	CLONAL	1	TRUE	1	0.610950557925094	2		701	951	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	150	320	1				ENST00000310581	NM_198253.2	-/1132			0.221994439555003	3	FACETS	0.959	0.882	1	1	0.988	1	CLONAL	3	TRUE	1	0.221994439555003	3		321	522	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0042078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	155	304	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.882	0.812	0.953	1	0.993	1	CLONAL	3	TRUE	1	0.221994439555003	2		304	528	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097653	27097654	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0042078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	273	750	0	ENST00000324856.7:c.3245_3246dup	p.Gly1083TrpfsTer11	p.G1083Wfs*11	ENST00000324856	NM_006015.4	1081	aat/aaTGt	12/20	1	2	FACETS	0.956	0.899	1	1	0.996	1	CLONAL	3	TRUE	1	0.221994439555003	2		750	858	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120546229	120546230	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0042078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	221	749	0	ENST00000229340.5:c.94_95del	p.Thr32PhefsTer79	p.T32Ffs*79	ENST00000229340	NM_006861.6	32	ACt/t	2/6	1	2	FACETS	0.874	0.816	0.934	1	0.995	1	CLONAL	3	TRUE	1	0.221994439555003	2		749	759	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759828	133759837	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCGCCTCC	CTCCGCCTCC	-	novel	NA	P-0042078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	226	764	0	ENST00000318560.5:c.2151_2160del	p.Ser718AlafsTer55	p.S718Afs*55	ENST00000318560	NM_005157.4	717	tgCTCCGCCTCC/tg	11/11	1	2	FACETS	0.854	0.797	0.912	1	0.995	1	CLONAL	3	TRUE	1	0.221994439555003	2		764	795	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	169	358	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.672058540440142	2		358	433	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118793	115118794	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	339	780	0	ENST00000257566.3:c.547dup	p.Arg183LysfsTer44	p.R183Kfs*44	ENST00000257566	NM_016569.3	183	agg/aAgg	2/8	1	2	FACETS	0.949	0.899	1	0.949	0.899	1	CLONAL	1	TRUE	1	0.672058540440142	2		780	1063	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	197	499	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	0.672058540440142	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.672058540440142	1		499	361	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	214	637	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.672058540440142	2		637	635	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098380	11098380	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	163	897	2	ENST00000358026.2:c.898C>T	p.Gln300Ter	p.Q300*	ENST00000358026	NM_001128849.1	300	Cag/Tag	6/36	0.420241508083419	1	FACETS	0.331	0.304	0.36	0.331	0.304	0.36	SUBCLONAL	1	TRUE	0	0.672058540440142	1		899	972	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732318	74732318	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	221	621	0	ENST00000359995.5:c.591G>C	p.Lys197Asn	p.K197N	ENST00000359995	NM_001195427.1	197	aaG/aaC	2/3	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.672058540440142	2		621	649	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259331	36259331	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	158	732	0	ENST00000300305.3:c.160G>A	p.Glu54Lys	p.E54K	ENST00000300305		54	Gag/Aag	3/8	1	2	FACETS	0.509	0.466	0.554	0.509	0.466	0.554	SUBCLONAL	1	TRUE	1	0.672058540440142	2		732	924	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164447	47164447	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	101	508	0	ENST00000409792.3:c.1679C>G	p.Ser560Ter	p.S560*	ENST00000409792	NM_014159.6	560	tCa/tGa	3/21	1	2	FACETS	0.465	0.416	0.517	0.465	0.416	0.517	SUBCLONAL	1	TRUE	1	0.672058540440142	2		508	646	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518306	187518306	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	95	431	0	ENST00000441802.2:c.12388G>C	p.Glu4130Gln	p.E4130Q	ENST00000441802	NM_005245.3	4130	Gag/Cag	25/27	1	2	FACETS	0.584	0.522	0.65	0.584	0.522	0.65	SUBCLONAL	1	TRUE	1	0.672058540440142	2		431	484	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201936	102201936	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	63	430	0	ENST00000263464.3:c.1288G>T	p.Glu430Ter	p.E430*	ENST00000263464	NM_001165.4	430	Gag/Tag	6/9	NA	2	FACETS	0.346	0.299	0.397			1	INDETERMINATE	1	TRUE	NA	0.672058540440142	2		430	542	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739115	40739115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	273	790	0	ENST00000373198.4:c.3169G>A	p.Glu1057Lys	p.E1057K	ENST00000373198	NM_133170.3	1057	Gag/Aag	24/32	1	2	FACETS	0.949	0.893	1	0.949	0.893	1	CLONAL	1	TRUE	1	0.672058540440142	2		790	856	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864883	57864883	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	62	1066	0	ENST00000228682.2:c.2360C>G	p.Ser787Cys	p.S787C	ENST00000228682	NM_005269.2	787	tCt/tGt	12/12	1	2	FACETS	0.156	0.133	0.18	0.156	0.133	0.18	SUBCLONAL	1	TRUE	1	0.672058540440142	2		1066	1186	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609711	117609711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	233	662	0	ENST00000368508.3:c.6988G>A	p.Glu2330Lys	p.E2330K	ENST00000368508	NM_002944.2	2330	Gaa/Aaa	43/43	0.672058540440142	1	FACETS	0.977	0.923	1	0.977	0.923	1	CLONAL	1	TRUE	0	0.672058540440142	1		662	471	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790830	89790830	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	141	910	0	ENST00000336032.3:c.217C>G	p.Arg73Gly	p.R73G	ENST00000336032	NM_006813.2	73	Cgc/Ggc	1/2	0.672058540440142	1	FACETS	0.398	0.363	0.435	0.398	0.363	0.435	SUBCLONAL	1	TRUE	0	0.672058540440142	1		910	700	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436194	110436194	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs918898281	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	119	784	1	ENST00000375856.3:c.2207C>T	p.Ser736Phe	p.S736F	ENST00000375856	NM_003749.2	736	tCc/tTc	1/2	1	2	FACETS	0.4	0.36	0.441	0.4	0.36	0.441	SUBCLONAL	1	TRUE	1	0.672058540440142	2		785	886	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844247	68844247	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	G	rs1555515469	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	274	647	0	ENST00000261769.5:c.832+3A>G		p.X278_splice	ENST00000261769	NM_004360.3	278			0.672058540440142	1	FACETS	0.972	0.922	1	0.972	0.922	1	CLONAL	1	TRUE	0	0.672058540440142	1		647	557	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652140	3652140	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759447034	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	402	1101	1	ENST00000294008.3:c.929G>A	p.Arg310Gln	p.R310Q	ENST00000294008	NM_032444.2	310	cGa/cAa	4/15	1	2	FACETS	0.953	0.907	1	0.953	0.907	1	CLONAL	1	TRUE	1	0.672058540440142	2		1102	1255	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243940	41243940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55930959	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	321	1002	2	ENST00000357654.3:c.3608G>A	p.Arg1203Gln	p.R1203Q	ENST00000357654	NM_007294.3	1203	cGa/cAa	10/23	0.672058540440142	1	FACETS	0.901	0.857	0.945	0.901	0.857	0.945	CLONAL	1	TRUE	0	0.672058540440142	1		1004	704	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554371	141554371	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	174	1106	0	ENST00000220592.5:c.1780C>G	p.Leu594Val	p.L594V	ENST00000220592	NM_012154.3	594	Ctg/Gtg	14/19	1	2	FACETS	0.382	0.351	0.416	0.382	0.351	0.416	SUBCLONAL	1	TRUE	1	0.672058540440142	2		1106	1354	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097649	11097649	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767947665	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	210	1060	0	ENST00000358026.2:c.829C>T	p.Pro277Ser	p.P277S	ENST00000358026	NM_001128849.1	277	Cct/Tct	5/36	0.420241508083419	1	FACETS	0.34	0.315	0.366	0.34	0.315	0.366	SUBCLONAL	1	TRUE	0	0.672058540440142	1		1060	1221	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012211	16012211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1391053845	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	51	607	1	ENST00000268712.3:c.2071C>T	p.Arg691Cys	p.R691C	ENST00000268712	NM_006311.3	691	Cgt/Tgt	19/46	0.672058540440142	1	FACETS	0.186	0.158	0.217	0.186	0.158	0.217	SUBCLONAL	1	TRUE	0	0.672058540440142	1		608	542	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258091	16258091	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	133	739	0	ENST00000375759.3:c.5356G>A	p.Asp1786Asn	p.D1786N	ENST00000375759	NM_015001.2	1786	Gat/Aat	11/15	0.672058540440142	1	FACETS	0.478	0.436	0.522	0.478	0.436	0.522	SUBCLONAL	1	TRUE	0	0.672058540440142	1		739	550	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995592	68995592	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	380	780	0	ENST00000288368.4:c.1996C>G	p.Leu666Val	p.L666V	ENST00000288368	NM_024870.2	666	Cta/Gta	18/40	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.672058540440142	2		780	1036	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165380	47165380	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	256	510	0	ENST00000409792.3:c.746C>A	p.Ser249Tyr	p.S249Y	ENST00000409792	NM_014159.6	249	tCt/tAt	3/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.672058540440142	2		510	716	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911577	39911577	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	144	893	0	ENST00000378444.4:c.5053C>A	p.Pro1685Thr	p.P1685T	ENST00000378444	NM_001123385.1	1685	Cca/Aca	15/15	NA	2	FACETS	0.394	0.358	0.431			1	INDETERMINATE	1	TRUE	NA	0.672058540440142	2		893	1089	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056387	26056387	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	206	613	0	ENST00000343677.2:c.270G>T	p.Lys90Asn	p.K90N	ENST00000343677	NM_005319.3	90	aaG/aaT	1/1	1	2	FACETS	0.989	0.923	1	0.989	0.923	1	CLONAL	1	TRUE	1	0.672058540440142	2		613	620	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174441	11174441	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	168	982	0	ENST00000361445.4:c.7234G>C	p.Asp2412His	p.D2412H	ENST00000361445	NM_004958.3	2412	Gac/Cac	53/58	0.672058540440142	1	FACETS	0.399	0.366	0.432	0.399	0.366	0.432	SUBCLONAL	1	TRUE	0	0.672058540440142	1		982	833	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258622	16258622	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	57	822	0	ENST00000375759.3:c.5887G>T	p.Glu1963Ter	p.E1963*	ENST00000375759	NM_015001.2	1963	Gag/Tag	11/15	0.672058540440142	1	FACETS	0.17	0.145	0.197	0.17	0.145	0.197	SUBCLONAL	1	TRUE	0	0.672058540440142	1		822	662	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260854	16260854	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	133	894	0	ENST00000375759.3:c.8119C>G	p.Leu2707Val	p.L2707V	ENST00000375759	NM_015001.2	2707	Ctc/Gtc	11/15	0.672058540440142	1	FACETS	0.43	0.392	0.47	0.43	0.392	0.47	SUBCLONAL	1	TRUE	0	0.672058540440142	1		894	611	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36934763	36934763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	358	908	0	ENST00000361632.4:c.1570G>A	p.Glu524Lys	p.E524K	ENST00000361632		524	Gaa/Aaa	11/16	0.672058540440142	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.672058540440142	1		908	687	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939224	36939224	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	345	1057	0	ENST00000361632.4:c.486-1G>A		p.X162_splice	ENST00000361632		162			0.672058540440142	1	FACETS	0.989	0.945	1	0.989	0.945	1	CLONAL	1	TRUE	0	0.672058540440142	1		1057	689	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941272	36941272	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	136	951	0	ENST00000361632.4:c.67C>G	p.Leu23Val	p.L23V	ENST00000361632		23	Ctg/Gtg	3/16	0.672058540440142	1	FACETS	0.386	0.351	0.422	0.386	0.351	0.422	SUBCLONAL	1	TRUE	0	0.672058540440142	1		951	696	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309816	65309816	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	49	874	0	ENST00000342505.4:c.2334C>G	p.Ser778Arg	p.S778R	ENST00000342505	NM_002227.2	778	agC/agG	17/25	0.672058540440142	1	FACETS	0.143	0.121	0.168	0.143	0.121	0.168	SUBCLONAL	1	TRUE	0	0.672058540440142	1		874	676	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416867	416867	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	302	697	0	ENST00000399788.2:c.3683C>G	p.Ser1228Ter	p.S1228*	ENST00000399788	NM_001042603.1	1228	tCa/tGa	23/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.672058540440142	2		697	889	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480069	50480069	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	161	960	0	ENST00000394963.4:c.303G>C	p.Lys101Asn	p.K101N	ENST00000394963	NM_003076.4	101	aaG/aaC	2/13	1	2	FACETS	0.437	0.4	0.476	0.437	0.4	0.476	SUBCLONAL	1	TRUE	1	0.672058540440142	2		960	1096	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416746	121416746	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	193	1203	0	ENST00000257555.6:c.175G>C	p.Glu59Gln	p.E59Q	ENST00000257555		59	Gag/Cag	1/10	1	2	FACETS	0.449	0.414	0.485	0.449	0.414	0.485	SUBCLONAL	1	TRUE	1	0.672058540440142	2		1203	1279	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209048	133209048	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	121	867	0	ENST00000320574.5:c.6183G>C	p.Gln2061His	p.Q2061H	ENST00000320574	NM_006231.2	2061	caG/caC	45/49	1	2	FACETS	0.385	0.347	0.425	0.385	0.347	0.425	SUBCLONAL	1	TRUE	1	0.672058540440142	2		867	936	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437046	110437046	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	47	149	0	ENST00000375856.3:c.1355G>T	p.Ser452Ile	p.S452I	ENST00000375856	NM_003749.2	452	aGc/aTc	1/2	1	2	FACETS	0.669	0.571	0.774	0.669	0.571	0.774	SUBCLONAL	1	TRUE	1	0.672058540440142	2		149	209	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437088	110437088	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1021390879	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	19	205	0	ENST00000375856.3:c.1313C>G	p.Ser438Trp	p.S438W	ENST00000375856	NM_003749.2	438	tCg/tGg	1/2	1	2	FACETS	0.218	0.166	0.28	0.218	0.166	0.28	SUBCLONAL	1	TRUE	1	0.672058540440142	2		205	259	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42026771	42026771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	215	516	0	ENST00000219905.7:c.3895G>A	p.Asp1299Asn	p.D1299N	ENST00000219905	NM_001164273.1	1299	Gat/Aat	12/24	1	2	FACETS	0.934	0.872	0.997	0.934	0.872	0.997	CLONAL	1	TRUE	1	0.672058540440142	2		516	685	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640653	3640653	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	407	1145	0	ENST00000294008.3:c.2986G>C	p.Glu996Gln	p.E996Q	ENST00000294008	NM_032444.2	996	Gag/Cag	12/15	1	2	FACETS	0.971	0.924	1	0.971	0.924	1	CLONAL	1	TRUE	1	0.672058540440142	2		1145	1248	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828782	72828782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	40	861	0	ENST00000268489.5:c.7799C>T	p.Ser2600Leu	p.S2600L	ENST00000268489	NM_006885.3	2600	tCa/tTa	9/10	0.672058540440142	1	FACETS	0.119	0.098	0.142	0.119	0.098	0.142	SUBCLONAL	1	TRUE	0	0.672058540440142	1		861	663	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040717	16040717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	48	356	0	ENST00000268712.3:c.1417G>A	p.Asp473Asn	p.D473N	ENST00000268712	NM_006311.3	473	Gat/Aat	14/46	0.672058540440142	1	FACETS	0.291	0.247	0.339	0.291	0.247	0.339	SUBCLONAL	1	TRUE	0	0.672058540440142	1		356	326	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245012	41245012	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	378	1004	0	ENST00000357654.3:c.2536G>C	p.Glu846Gln	p.E846Q	ENST00000357654	NM_007294.3	846	Gaa/Caa	10/23	0.672058540440142	1	FACETS	0.985	0.943	1	0.985	0.943	1	CLONAL	1	TRUE	0	0.672058540440142	1		1004	758	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117556	70117556	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1452893426	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	58	875	0	ENST00000245479.2:c.24G>A	p.Met8Ile	p.M8I	ENST00000245479	NM_000346.3	8	atG/atA	1/3	1	2	FACETS	0.165	0.141	0.191	0.165	0.141	0.191	SUBCLONAL	1	TRUE	1	0.672058540440142	2		875	1047	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134206	11134206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	141	756	0	ENST00000358026.2:c.2872G>A	p.Glu958Lys	p.E958K	ENST00000358026	NM_001128849.1	958	Gag/Aag	20/36	1	2	FACETS	0.453	0.412	0.496	0.453	0.412	0.496	SUBCLONAL	1	TRUE	1	0.672058540440142	2		756	927	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965470	25965470	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	327	987	0	ENST00000435504.4:c.3736G>A	p.Glu1246Lys	p.E1246K	ENST00000435504		1246	Gag/Aag	13/13	1	2	FACETS	0.908	0.859	0.958	0.908	0.859	0.958	CLONAL	1	TRUE	1	0.672058540440142	2		987	1072	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972605	25972605	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	47	622	0	ENST00000435504.4:c.1820G>C	p.Arg607Thr	p.R607T	ENST00000435504		607	aGa/aCa	12/13	1	2	FACETS	0.2	0.168	0.235	0.2	0.168	0.235	SUBCLONAL	1	TRUE	1	0.672058540440142	2		622	701	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027037	48027037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143517321	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	217	600	0	ENST00000234420.5:c.1915G>A	p.Glu639Lys	p.E639K	ENST00000234420	NM_000179.2	639	Gag/Aag	4/10	1	2	FACETS	0.891	0.831	0.952	0.891	0.831	0.952	CLONAL	1	TRUE	1	0.672058540440142	2		600	725	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027709	48027709	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	172	466	0	ENST00000234420.5:c.2587G>C	p.Glu863Gln	p.E863Q	ENST00000234420	NM_000179.2	863	Gaa/Caa	4/10	1	2	FACETS	0.981	0.909	1	0.981	0.909	1	CLONAL	1	TRUE	1	0.672058540440142	2		466	522	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661582	227661582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	365	1020	4	ENST00000305123.5:c.1873G>A	p.Gly625Ser	p.G625S	ENST00000305123	NM_005544.2	625	Ggc/Agc	1/2	1	2	FACETS	0.99	0.94	1	0.99	0.94	1	CLONAL	1	TRUE	1	0.672058540440142	2		1024	1097	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739128	40739128	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	231	736	0	ENST00000373198.4:c.3157-1G>A		p.X1053_splice	ENST00000373198	NM_133170.3	1053			1	2	FACETS	0.915	0.857	0.976	0.915	0.857	0.976	CLONAL	1	TRUE	1	0.672058540440142	2		736	751	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277936	41277936	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	96	618	0	ENST00000349496.5:c.1900G>T	p.Glu634Ter	p.E634*	ENST00000349496	NM_001904.3	634	Gag/Tag	12/15	1	2	FACETS	0.405	0.361	0.452	0.405	0.361	0.452	SUBCLONAL	1	TRUE	1	0.672058540440142	2		618	705	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165737	47165737	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs550723354	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	264	755	0	ENST00000409792.3:c.389C>A	p.Ser130Tyr	p.S130Y	ENST00000409792	NM_014159.6	130	tCt/tAt	3/21	1	2	FACETS	0.916	0.861	0.972	0.916	0.861	0.972	CLONAL	1	TRUE	1	0.672058540440142	2		755	858	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696218	52696218	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	59	968	0	ENST00000394830.3:c.459G>C	p.Gln153His	p.Q153H	ENST00000394830	NM_018313.4	153	caG/caC	5/30	0.672058540440142	1	FACETS	0.169	0.145	0.195	0.169	0.145	0.195	SUBCLONAL	1	TRUE	0	0.672058540440142	1		968	691	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426042	138426042	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	102	558	0	ENST00000289153.2:c.1489G>A	p.Glu497Lys	p.E497K	ENST00000289153	NM_006219.2	497	Gag/Aag	9/22	0.672058540440142	3	FACETS	0.388	0.346	0.433	0.194	0.173	0.217	SUBCLONAL	1	TRUE	1	0.672058540440142	3		558	1044	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930715	131930715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658686	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	52	564	1	ENST00000265335.6:c.1948G>A	p.Glu650Lys	p.E650K	ENST00000265335		650	Gaa/Aaa	12/25	1	2	FACETS	0.197	0.167	0.23	0.197	0.167	0.23	SUBCLONAL	1	TRUE	1	0.672058540440142	2		565	785	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709096	117709096	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759714879	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	286	785	1	ENST00000368508.3:c.1861G>A	p.Glu621Lys	p.E621K	ENST00000368508	NM_002944.2	621	Gaa/Aaa	13/43	0.672058540440142	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.672058540440142	1		786	546	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55231447	55231447	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	135	858	0	ENST00000275493.2:c.1653G>T	p.Glu551Asp	p.E551D	ENST00000275493	NM_005228.3	551	gaG/gaT	14/28	1	2	FACETS	0.38	0.344	0.417	0.38	0.344	0.417	SUBCLONAL	1	TRUE	1	0.672058540440142	2		858	1058	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859595	151859595	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	242	726	0	ENST00000262189.6:c.11067C>G	p.Phe3689Leu	p.F3689L	ENST00000262189	NM_170606.2	3689	ttC/ttG	43/59	1	2	FACETS	0.855	0.801	0.911	0.855	0.801	0.911	CLONAL	1	TRUE	1	0.672058540440142	2		726	842	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8339013	8339013	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	43	673	0	ENST00000356435.5:c.5288C>G	p.Ser1763Cys	p.S1763C	ENST00000356435		1763	tCt/tGt	32/35	1	2	FACETS	0.16	0.133	0.19	0.16	0.133	0.19	SUBCLONAL	1	TRUE	1	0.672058540440142	2		673	801	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197402	27197402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	169	863	0	ENST00000380036.4:c.1714G>A	p.Asp572Asn	p.D572N	ENST00000380036	NM_000459.3	572	Gat/Aat	12/23	1	2	FACETS	0.495	0.454	0.537	0.495	0.454	0.537	SUBCLONAL	1	TRUE	1	0.672058540440142	2		863	1017	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211582	46211585	+	stop_gained	Nonsense_Mutation	ONP	TATC	TATC	AATG	novel	NA	P-0042083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	197	467	1	ENST00000334344.6:c.548_551delinsAATG	p.Leu183_Ser184delinsGlnTer	p.L183_S184delinsQ*	ENST00000334344	NM_152641.2	183	cTATCa/cAATGa	5/21	1	2	FACETS	0.997	0.929	1	0.997	0.929	1	CLONAL	1	TRUE	1	0.672058540440142	2		468	588	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259439	55259439	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs397517126	NA	P-0042088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	329	614	0	ENST00000275493.2:c.2497T>G	p.Leu833Val	p.L833V	ENST00000275493	NM_005228.3	833	Ttg/Gtg	21/28	0.274886516128754	5	FACETS	1	0.95	1	1	0.995	1	CLONAL	6	TRUE	1	0.14	5		614	945	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259446	55259446	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs397517128	NA	P-0042088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	344	664	0	ENST00000275493.2:c.2504A>T	p.His835Leu	p.H835L	ENST00000275493	NM_005228.3	835	cAc/cTc	21/28	0.274886516128754	5	FACETS	1	0.954	1	1	0.995	1	CLONAL	6	TRUE	1	0.14	5		664	985	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821802	59821802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	37	486	1	ENST00000259008.2:c.2248G>A	p.Gly750Arg	p.G750R	ENST00000259008	NM_032043.2	750	Gga/Aga	15/20	1	2	FACETS	0.887	0.73	1	0.887	0.73	1	CLONAL	1	TRUE	1	0.14	2		487	596	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166351	7166352	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0042088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	64	932	1	ENST00000302850.5:c.1674_1675delinsTT	p.Val559Leu	p.V559L	ENST00000302850	NM_000208.2	558	gtGGta/gtTTta	8/22	1	2	FACETS	0.999	0.863	1	0.999	0.863	1	CLONAL	1	TRUE	1	0.14	2		933	915	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561280	9561280	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1197179795	NA	P-0042088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	37	604	0	ENST00000353224.5:c.502C>A	p.Gln168Lys	p.Q168K	ENST00000353224	NM_177990.2	168	Caa/Aaa	4/10	1	2	FACETS	0.882	0.726	1	0.882	0.726	1	CLONAL	1	TRUE	1	0.14	2		604	599	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0042110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	138	673	0				ENST00000310581	NM_198253.2	-/1132			0.267709762151578	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.893290093603992	0		673	288	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0042110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	312	1073	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.893290093603992	2		1073	630	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982356	25982356	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	79	230	0	ENST00000435504.4:c.934C>T	p.Arg312Ter	p.R312*	ENST00000435504		312	Cga/Tga	9/13	0.178861445748401	1	FACETS	0.526	0.473	0.58	0.526	0.473	0.58	INDETERMINATE	1	TRUE	0	0.893290093603992	1		230	186	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913253	39913253	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	143	329	0	ENST00000378444.4:c.4862del	p.Pro1621GlnfsTer53	p.P1621Qfs*53	ENST00000378444	NM_001123385.1	1621	cCa/ca	14/15	1	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.893290093603992	1		329	175	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978935	25978935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	138	445	0	ENST00000435504.4:c.988G>A	p.Glu330Lys	p.E330K	ENST00000435504		330	Gaa/Aaa	10/13	0.178861445748401	1	FACETS	0.588	0.544	0.631	0.588	0.544	0.631	INDETERMINATE	1	TRUE	0	0.893290093603992	1		445	291	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778008	27778008	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	181	567	0	ENST00000369163.2:c.157C>T	p.Arg53Cys	p.R53C	ENST00000369163	NM_003536.2	53	Cgc/Tgc	1/1	0.729783742470308	4	FACETS	0.976	0.913	1			1	CLONAL	2	TRUE	NA	0.893290093603992	4		567	393	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572350	41572350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	198	809	0	ENST00000263253.7:c.4879C>T	p.Arg1627Trp	p.R1627W	ENST00000263253	NM_001429.3	1627	Cgg/Tgg	30/31	0.170784282134441	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.893290093603992	0		809	496	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410571	63410571	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	179	387	0	ENST00000330258.3:c.2596G>T	p.Val866Leu	p.V866L	ENST00000330258	NM_152424.3	866	Gtg/Ttg	2/2	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.893290093603992	1		387	204	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939825	71939825	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	576	953	1	ENST00000298229.2:c.452C>T	p.Ser151Phe	p.S151F	ENST00000298229	NM_001567.3	151	tCt/tTt	4/28	0.79700874141527	4	FACETS	0.939	0.911	0.966	0.939	0.911	0.966	CLONAL	3	TRUE	1	0.893290093603992	4		954	867	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636664	176636664	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	106	375	0	ENST00000439151.2:c.1264G>A	p.Glu422Lys	p.E422K	ENST00000439151	NM_022455.4	422	Gaa/Aaa	5/23	0.170784282134441	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.893290093603992	0		375	226	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32814981	32814981	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	188	637	1	ENST00000354258.4:c.2084A>G	p.Glu695Gly	p.E695G	ENST00000354258	NM_000593.5	695	gAg/gGg	10/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.893290093603992	2		638	377	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942853	44942853	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	117	268	0	ENST00000377967.4:c.3433G>C	p.Gly1145Arg	p.G1145R	ENST00000377967	NM_021140.2	1145	Ggt/Cgt	23/29	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.893290093603992	1		268	127	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	104	369	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.7295198651076	3	FACETS	1	0.945	1	0.533	0.482	0.587	CLONAL	1	TRUE	1	0.7295198651076	3		369	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579716	7579716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526933	NA	P-0042112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	215	647	1	ENST00000269305.4:c.80C>T	p.Pro27Leu	p.P27L	ENST00000269305	NM_001126112.2	27	cCt/cTt	3/11	0.668519648017879	2	FACETS	0.942	0.898	0.984	0.942	0.898	0.984	CLONAL	2	TRUE	0	0.7295198651076	2		648	313	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434944	110434946	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0042112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	200	910	0	ENST00000375856.3:c.3455_3457del	p.Phe1152del	p.F1152del	ENST00000375856	NM_003749.2	1152	tTCTcc/tcc	1/2	0.644795073498859	4	FACETS	0.998	0.925	1	0.499	0.462	0.537	CLONAL	1	TRUE	2	0.7295198651076	4		910	950	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469073	25469073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200845575	NA	P-0042112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	250	731	2	ENST00000264709.3:c.1385C>T	p.Ala462Val	p.A462V	ENST00000264709	NM_175629.2	462	gCg/gTg	11/23	0.7295198651076	3	FACETS	0.997	0.946	1	0.997	0.946	1	CLONAL	2	TRUE	1	0.7295198651076	3		733	469	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8733794	8733794	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs949202374	NA	P-0042112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	244	596	0	ENST00000356435.5:c.50G>T	p.Arg17Leu	p.R17L	ENST00000356435		17	cGc/cTc	1/35	0.623148060814736	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.7295198651076	3		596	446	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982415	201982416	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0042112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	226	802	0	ENST00000359651.3:c.796_797del	p.Ser266GlnfsTer34	p.S266Qfs*34	ENST00000359651		265	aAG/a	6/8	0.662316029376354	3	FACETS	1	0.965	1	0.525	0.49	0.561	CLONAL	1	TRUE	1	0.7295198651076	3		802	805	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405344	70405344	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	22	588	0	ENST00000373644.4:c.2858T>G	p.Leu953Arg	p.L953R	ENST00000373644	NM_030625.2	953	cTt/cGt	4/12	0.22162468561634	6	FACETS	0.354	0.274	0.448	0.118	0.091	0.15	INDETERMINATE	1	TRUE	3	0.7295198651076	6		588	419	SUCCESS
APC	324	MSKCC	GRCh37	5	112175438	112175448	+	frameshift_variant	Frame_Shift_Del	DEL	ATGTTTAGCAG	ATGTTTAGCAG	-	novel	NA	P-0042112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	94	302	0	ENST00000257430.4:c.4151_4161del	p.Phe1384TyrfsTer7	p.F1384Yfs*7	ENST00000257430	NM_000038.5	1383	ATGTTTAGCAGa/a	16/16	0.668519648017879	2	FACETS	0.934	0.868	0.996	0.934	0.868	0.996	CLONAL	2	TRUE	0	0.7295198651076	2		302	138	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942783	68942783	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	26	593	1	ENST00000288368.4:c.595G>T	p.Glu199Ter	p.E199*	ENST00000288368	NM_024870.2	199	Gaa/Taa	6/40	0.164226839685759	3	FACETS	0.238	0.188	0.296	0.079	0.062	0.099	INDETERMINATE	1	TRUE	0	0.7295198651076	3		594	408	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0042113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	393	499	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.616438768571188	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	FALSE	0	0.623919987350583	2		501	615	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0042113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	301	421	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.623919987350583	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	FALSE	0	0.623919987350583	3		421	389	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752965	128752965	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	375	510	0	ENST00000377970.2:c.1126G>C	p.Val376Leu	p.V376L	ENST00000377970	NM_002467.4	376	Gtc/Ctc	3/3	0.623919987350583	4	FACETS	0.993	0.953	1	0.993	0.953	1	CLONAL	3	FALSE	1	0.623919987350583	4		510	655	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0042113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	125	415	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	0.411141851023467	3	FACETS	0.792	0.726	0.859	0.792	0.726	0.859	SUBCLONAL	2	FALSE	1	0.623919987350583	3		415	332	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692896	89692896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123322	NA	P-0042113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	176	463	0	ENST00000371953.3:c.380G>A	p.Gly127Glu	p.G127E	ENST00000371953	NM_000314.4	127	gGa/gAa	5/9	0.561085102254227	4	FACETS	0.983	0.914	1	0.983	0.914	1	CLONAL	2	FALSE	2	0.623919987350583	4		463	466	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424679	47424679	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775921012	NA	P-0042113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	218	812	0	ENST00000377045.4:c.487G>A	p.Gly163Arg	p.G163R	ENST00000377045	NM_001654.4	163	Gga/Aga	6/16	0.623919987350583	3	FACETS	1	0.986	1	0.61	0.569	0.652	CLONAL	1	FALSE	1	0.623919987350583	3		812	752	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738222	133738222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	328	595	1	ENST00000318560.5:c.622G>A	p.Gly208Arg	p.G208R	ENST00000318560	NM_005157.4	208	Ggg/Agg	4/11	0.623919987350583	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	FALSE	0	0.623919987350583	2		596	495	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797387	45797387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772113192	NA	P-0042113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	60	756	1	ENST00000450313.1:c.1132G>A	p.Glu378Lys	p.E378K	ENST00000450313	NM_012222.2	378	Gaa/Aaa	12/16	0.623919987350583	9	FACETS	0.595	0.511	0.687			1	SUBCLONAL	1	FALSE	NA	0.623919987350583	9		757	1029	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465354	120465354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	292	552	1	ENST00000256646.2:c.4907C>T	p.Ser1636Leu	p.S1636L	ENST00000256646	NM_024408.3	1636	tCa/tTa	27/34	0.561085102254227	4	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	FALSE	2	0.623919987350583	4		553	760	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653834	89653835	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0042113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	184	376	0	ENST00000371953.3:c.132_133insT	p.Val45CysfsTer7	p.V45Cfs*7	ENST00000371953	NM_000314.4	44	-/T	2/9	0.561085102254227	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	FALSE	2	0.623919987350583	4		376	403	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996832	100996833	+	missense_variant	Missense_Mutation	DNP	CT	CT	AA	novel	NA	P-0042113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	200	672	2	ENST00000325455.5:c.1694_1695delinsTT	p.Lys565Ile	p.K565I	ENST00000325455	NM_001202474.3	565	aAG/aTT	2/8	0.623919987350583	3	FACETS	0.941	0.882	1	0.941	0.882	1	CLONAL	2	FALSE	1	0.623919987350583	3		674	447	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120651	115120651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	397	988	1	ENST00000257566.3:c.355C>T	p.Arg119Trp	p.R119W	ENST00000257566	NM_016569.3	119	Cgg/Tgg	1/8	0.623919987350583	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	FALSE	2	0.623919987350583	4		989	980	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541709	120541709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	319	747	2	ENST00000229340.5:c.148G>A	p.Val50Met	p.V50M	ENST00000229340	NM_006861.6	50	Gtg/Atg	3/6	0.623919987350583	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	FALSE	2	0.623919987350583	4		749	805	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169569	27169577	+	inframe_deletion	In_Frame_Del	DEL	GGCCAGGTA	GGCCAGGTA	-	novel	NA	P-0042113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	103	755	0	ENST00000380036.4:c.570_578del	p.Ala191_Tyr193del	p.A191_Y193del	ENST00000380036	NM_000459.3	190	tcGGCCAGGTAt/tct	4/23	0.623919987350583	2	FACETS	0.752	0.677	0.831	0.376	0.338	0.416	SUBCLONAL	1	FALSE	0	0.623919987350583	2		755	439	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106562	27106562	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	GG	novel	NA	P-0042113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	253	882	0	ENST00000324856.7:c.6173delinsGG	p.Glu2058GlyfsTer41	p.E2058Gfs*41	ENST00000324856	NM_006015.4	2058	gAa/gGGa	20/20	0.316148630479905	6	FACETS	1	0.979	1	0.729	0.684	0.776	INDETERMINATE	2	FALSE	3	0.623919987350583	6		882	833	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0042115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	315	426	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.0972164971255099	12	FACETS	0.994	0.946	1	1	0.993	1	CLONAL	15	TRUE	0	0.0972164971255099	12		426	646	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260214	16260214	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	41	602	2	ENST00000375759.3:c.7484del	p.Pro2495LeufsTer4	p.P2495Lfs*4	ENST00000375759	NM_015001.2	2493	agC/ag	11/15	0.0959272149549237	2	FACETS	0.943	0.786	1	0.943	0.786	1	CLONAL	2	TRUE	0	0.0972164971255099	2		604	447	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143999	11143999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1171822727	NA	P-0042115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	46	714	0	ENST00000358026.2:c.3580G>A	p.Gly1194Arg	p.G1194R	ENST00000358026	NM_001128849.1	1194	Ggg/Agg	26/36	1	2	FACETS	0.817	0.687	0.961	1	0.964	1	CLONAL	2	TRUE	1	0.0972164971255099	2		714	579	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073874	8073875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0042115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	40	314	0	ENST00000377482.5:c.784dup	p.Ile262AsnfsTer14	p.I262Nfs*14	ENST00000377482	NM_018948.3	262	ata/aAta	4/4	0.0959272149549237	2	FACETS	0.98	0.815	1	0.98	0.815	1	CLONAL	2	TRUE	0	0.0972164971255099	2		314	420	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711995	89711995	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	61	120	0	ENST00000371953.3:c.613A>T	p.Met205Leu	p.M205L	ENST00000371953	NM_000314.4	205	Atg/Ttg	6/9	0.0959272149549237	2	FACETS	1	0.94	1	1	0.976	1	CLONAL	3	TRUE	0	0.0972164971255099	2		120	363	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946469	71946469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778999359	NA	P-0042115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	65	900	1	ENST00000298229.2:c.2633G>A	p.Arg878His	p.R878H	ENST00000298229	NM_001567.3	878	cGc/cAc	23/28	0.011820921689383	4	FACETS	0.835	0.722	0.957	0.835	0.722	0.957	INDETERMINATE	2	TRUE	2	0.0972164971255099	4		901	879	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373872	118373872	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	22	165	0	ENST00000534358.1:c.7265G>C	p.Gly2422Ala	p.G2422A	ENST00000534358	NM_005933.3	2422	gGa/gCa	27/36	0.0972164971255099	3	FACETS	1	0.901	1			1	CLONAL	1	TRUE	NA	0.0972164971255099	3		165	355	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425062	49425070	+	inframe_deletion	In_Frame_Del	DEL	TGCTGAGTT	TGCTGAGTT	-	novel	NA	P-0042115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	62	1031	0	ENST00000301067.7:c.13418_13426del	p.Gln4473_Thr4476delinsPro	p.Q4473_T4476delinsP	ENST00000301067	NM_003482.3	4473	cAACTCAGCAct/cct	39/54	0.0972164971255099	3	FACETS	1	0.965	1	0.473	0.407	0.545	CLONAL	1	TRUE	0	0.0972164971255099	3		1031	942	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003294	42003294	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	48	414	0	ENST00000219905.7:c.2831G>T	p.Gly944Val	p.G944V	ENST00000219905	NM_001164273.1	944	gGc/gTc	8/24	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.0972164971255099	2		414	667	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937713	17937713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752088869	NA	P-0042115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	35	637	0	ENST00000458235.1:c.3214G>A	p.Glu1072Lys	p.E1072K	ENST00000458235	NM_000215.3	1072	Gag/Aag	24/24	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.0972164971255099	2		637	562	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799602	72799602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	98	559	0	ENST00000325599.8:c.1567G>A	p.Gly523Arg	p.G523R	ENST00000325599	NM_018130.2	523	Gga/Aga	11/11	0.0959272149549237	2	FACETS	1	0.958	1	1	0.984	1	CLONAL	3	TRUE	0	0.0972164971255099	2		559	587	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185044	32185044	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1380780475	NA	P-0042115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	32	738	0	ENST00000375023.3:c.1625-1G>A		p.X542_splice	ENST00000375023	NM_004557.3	542			1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.0972164971255099	2		738	583	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038804	47038804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	58	496	0	ENST00000377604.3:c.814del	p.Leu272CysfsTer36	p.L272Cfs*36	ENST00000377604	NM_001204468.1	271	Ccc/cc	9/24	1	1	FACETS	0.978	0.843	1	1	0.983	1	CLONAL	3	TRUE	0	0.0972164971255099	1		496	387	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313481	30313481	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	38	826	0	ENST00000262643.3:c.1081C>G	p.Gln361Glu	p.Q361E	ENST00000262643	NM_001238.2	361	Cag/Gag	11/12	0.400928952268482	1	FACETS	0.497	0.412	0.591	0.497	0.412	0.591	SUBCLONAL	1	FALSE	0	0.400928952268482	1		826	305	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519874	NA	P-0042121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	166	404	0	ENST00000356142.4:c.85C>A	p.Pro29Thr	p.P29T	ENST00000356142	NM_018890.3	29	Cct/Act	2/7	0.238374070745092	2	FACETS	1	0.974	1	1	0.974	1	INDETERMINATE	2	FALSE	0	0.400928952268482	2		404	379	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468114	50468114	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	10	631	0	ENST00000331340.3:c.1349G>A	p.Arg450His	p.R450H	ENST00000331340	NM_006060.4	450	cGc/cAc	8/8	0.238374070745092	2	FACETS	0.351	0.238	0.492	0.176	0.119	0.246	INDETERMINATE	1	FALSE	0	0.400928952268482	2		631	142	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129833	55129833	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0042121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	17	463	0	ENST00000257290.5:c.368-1G>T		p.X123_splice	ENST00000257290	NM_006206.4	123			1	2	FACETS	0.523	0.393	0.677	0.523	0.393	0.677	SUBCLONAL	1	FALSE	1	0.400928952268482	2		463	162	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57567440	57567440	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	199	798	0	ENST00000316660.6:c.31C>T	p.Gln11Ter	p.Q11*	ENST00000316660	NM_021127.2	11	Caa/Taa	1/2	0.303136651216468	3	FACETS	0.865	0.804	0.927	0.577	0.536	0.618	CLONAL	2	FALSE	0	0.400928952268482	3		798	689	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472652	88472652	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1007258350	NA	P-0042121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	61	470	0	ENST00000360948.2:c.1903G>T	p.Asp635Tyr	p.D635Y	ENST00000360948	NM_001012338.2	635	Gat/Tat	16/19	0.238374070745092	2	FACETS	0.85	0.748	0.956	0.85	0.748	0.956	INDETERMINATE	2	FALSE	0	0.400928952268482	2		470	179	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578395	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGTGGG	novel	NA	P-0042121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	62	833	0	ENST00000269305.4:c.530_535dup	p.Pro177_His178dup	p.P177_H178dup	ENST00000269305	NM_001126112.2	177	cat/cCCCACCat	5/11	0.261881889246933	3	FACETS	0.844	0.739	0.954	0.563	0.493	0.636	CLONAL	2	FALSE	0	0.400928952268482	3		833	220	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765793	41765793	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	92	585	1	ENST00000301178.4:c.2669A>G	p.Gln890Arg	p.Q890R	ENST00000301178	NM_021913.4	890	cAg/cGg	20/20	0.400928952268482	5	FACETS	0.854	0.768	0.942	0.854	0.768	0.942	CLONAL	3	FALSE	2	0.400928952268482	5		586	287	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385144	41385144	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	46	902	0	ENST00000373198.4:c.817G>T	p.Gly273Cys	p.G273C	ENST00000373198	NM_133170.3	273	Ggt/Tgt	6/32	0.238374070745092	2	FACETS	0.964	0.819	1	0.482	0.409	0.561	INDETERMINATE	1	FALSE	0	0.400928952268482	2		902	238	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191010	185191010	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	48	938	0	ENST00000265026.3:c.1891C>T	p.Leu631Phe	p.L631F	ENST00000265026	NM_004721.4	631	Ctt/Ttt	11/14	0.400928952268482	6	FACETS	1	0.906	1	0.274	0.232	0.321	CLONAL	1	FALSE	2	0.400928952268482	6		938	393	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156610	55156610	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	78	687	0	ENST00000257290.5:c.3011A>T	p.Glu1004Val	p.E1004V	ENST00000257290	NM_006206.4	1004	gAg/gTg	22/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.400928952268482	2		687	260	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155570	56155570	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	55	456	0	ENST00000399503.3:c.662A>G	p.Asp221Gly	p.D221G	ENST00000399503	NM_005921.1	221	gAt/gGt	3/20	0.400928952268482	5	FACETS	1	0.956	1	0.832	0.725	0.945	CLONAL	2	FALSE	2	0.400928952268482	5		456	176	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55270231	55270231	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	81	881	0	ENST00000275493.2:c.3184G>C	p.Glu1062Gln	p.E1062Q	ENST00000275493	NM_005228.3	1062	Gaa/Caa	27/28	0.238374070745092	2	FACETS	0.914	0.82	1	0.914	0.82	1	INDETERMINATE	2	FALSE	0	0.400928952268482	2		881	221	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968109	68968109	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	21	579	0	ENST00000288368.4:c.1138G>T	p.Glu380Ter	p.E380*	ENST00000288368	NM_024870.2	380	Gaa/Taa	10/40	0.400928952268482	5	FACETS	0.987	0.765	1	0.329	0.255	0.414	CLONAL	1	FALSE	2	0.400928952268482	5		579	170	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915880	127915880	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	44	596	0	ENST00000373547.4:c.601G>C	p.Asp201His	p.D201H	ENST00000373547	NM_002721.4	201	Gat/Cat	6/7	0.400928952268482	2	FACETS	1	0.952	1	0.661	0.563	0.765	CLONAL	1	FALSE	0	0.400928952268482	2		596	166	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776281	76776281	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	16	368	0	ENST00000373344.5:c.7185G>C	p.Leu2395Phe	p.L2395F	ENST00000373344	NM_000489.3	2395	ttG/ttC	34/35	0.300094198658351	2	FACETS	0.682	0.51	0.883			1	SUBCLONAL	1	FALSE	NA	0.400928952268482	2		368	117	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0042133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	147	646	7	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.794	0.725	0.868	1	0.988	1	SUBCLONAL	2	TRUE	1	0.19	2		653	974	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436684	8436684	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1294993838	NA	P-0042133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	30	383	0	ENST00000356435.5:c.3994G>T	p.Ala1332Ser	p.A1332S	ENST00000356435		1332	Gct/Tct	24/35	1	2	FACETS	0.872	0.703	1	0.872	0.703	1	CLONAL	1	TRUE	1	0.19	2		383	362	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026840	71026840	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	35	306	0	ENST00000318789.4:c.1382A>G	p.Asn461Ser	p.N461S	ENST00000318789	NM_032682.5	461	aAc/aGc	16/21	1	2	FACETS	0.967	0.794	1	0.967	0.794	1	CLONAL	1	TRUE	1	0.19	2		306	381	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465471	99465471	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	60	599	0	ENST00000268035.6:c.2296A>C	p.Thr766Pro	p.T766P	ENST00000268035	NM_000875.3	766	Acc/Ccc	11/21	0.15940842150345	1	FACETS	0.831	0.715	0.957	0.831	0.715	0.957	CLONAL	1	TRUE	0	0.19	1		599	688	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030374	49030374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	26	373	0	ENST00000267163.4:c.1849G>A	p.Gly617Ser	p.G617S	ENST00000267163	NM_000321.2	617	Ggt/Agt	19/27	1	2	FACETS	0.58	0.458	0.72	0.58	0.458	0.72	SUBCLONAL	1	TRUE	1	0.19	2		373	472	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994839	73994839	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	20	243	0	ENST00000318443.5:c.323G>T	p.Arg108Met	p.R108M	ENST00000318443	NM_001024736.1	108	aGg/aTg	3/10	0.15940842150345	1	FACETS	0.818	0.627	1	0.818	0.627	1	CLONAL	1	TRUE	0	0.19	1		243	233	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943727	9943727	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	66	852	0	ENST00000330684.3:c.1214A>G	p.His405Arg	p.H405R	ENST00000330684	NM_001134407.1	405	cAt/cGt	5/13	1	2	FACETS	0.89	0.771	1	0.89	0.771	1	CLONAL	1	TRUE	1	0.19	2		852	781	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674311	86674324	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGACTCTATTTT	AAAGACTCTATTTT	-	novel	NA	P-0042133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	37	333	0	ENST00000274376.6:c.2448_2461del	p.Ser817AsnfsTer8	p.S817Nfs*8	ENST00000274376	NM_002890.2	815	AAAGACTCTATTTTa/a	18/25	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.19	2		333	362	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	183	320	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.921	0.856	0.987	0.921	0.856	0.987	CLONAL	1	TRUE	1	0.727944567550663	2		321	546	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439743	51439743	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	216	381	0	ENST00000262662.1:c.308G>T	p.Gly103Val	p.G103V	ENST00000262662		103	gGg/gTg	4/4	0.727944567550663	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.727944567550663	1		381	352	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0042154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	88	426	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA	2	FACETS	1	0.957	1			1	INDETERMINATE	1	TRUE	NA	0.235114325317689	2		426	643	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031979	10031979	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	199	867	0	ENST00000330684.3:c.844G>T	p.Asp282Tyr	p.D282Y	ENST00000330684	NM_001134407.1	282	Gat/Tat	3/13	0.201167145473746	1	FACETS	0.945	0.878	1	1	0.993	1	CLONAL	2	TRUE	0	0.235114325317689	1		867	790	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223304	2223304	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	225	852	3	ENST00000398665.3:c.3415G>T	p.Glu1139Ter	p.E1139*	ENST00000398665	NM_032482.2	1139	Gag/Tag	25/28	0.15503094844514	3	FACETS	1	0.936	1	0.67	0.624	0.718	CLONAL	2	TRUE	0	0.235114325317689	3		855	1064	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097631	8097631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	16	241	0	ENST00000346208.3:c.13G>T	p.Ala5Ser	p.A5S	ENST00000346208		5	Gcg/Tcg	2/6	1	2	FACETS	0.597	0.442	0.782	0.597	0.442	0.782	SUBCLONAL	1	TRUE	1	0.235114325317689	2		241	228	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763221	59763221	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	41	750	0	ENST00000259008.2:c.2881A>T	p.Ser961Cys	p.S961C	ENST00000259008	NM_032043.2	961	Agc/Tgc	19/20	0.139673335279487	4	FACETS	0.577	0.479	0.687	0.289	0.239	0.344	INDETERMINATE	1	TRUE	2	0.235114325317689	4		750	746	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052875	180052875	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	114	816	0	ENST00000261937.6:c.1415G>T	p.Arg472Leu	p.R472L	ENST00000261937	NM_182925.4	472	cGt/cTt	10/30	0.235114325317689	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.235114325317689	1		816	817	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460502	8460502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	58	793	0	ENST00000356435.5:c.3784G>A	p.Asp1262Asn	p.D1262N	ENST00000356435		1262	Gat/Aat	22/35	1	2	FACETS	0.669	0.573	0.773	0.669	0.573	0.773	SUBCLONAL	1	TRUE	1	0.235114325317689	2		793	738	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390965	139390965	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	162	1001	0	ENST00000277541.6:c.7226A>G	p.Gln2409Arg	p.Q2409R	ENST00000277541	NM_017617.3	2409	cAg/cGg	34/34	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.235114325317689	2		1001	1094	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410306	63410306	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	113	910	1	ENST00000330258.3:c.2861G>T	p.Gly954Val	p.G954V	ENST00000330258	NM_152424.3	954	gGg/gTg	2/2	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.235114325317689	2		911	829	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341907	8341907	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	AT	novel	NA	P-0042154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	54	558	0	ENST00000356435.5:c.4733delinsAT	p.Thr1578AsnfsTer30	p.T1578Nfs*30	ENST00000356435		1578	aCt/aATt	29/35	1				0.697	0.946				CLONAL	1	TRUE	1	0.235114325317689	2		558	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0042222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	420	983	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	0.340379818108612	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.352299956068432	2		983	1140	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376302	118376302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1052748793	NA	P-0042222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	99	614	0	ENST00000534358.1:c.9695G>A	p.Arg3232Gln	p.R3232Q	ENST00000534358	NM_005933.3	3232	cGa/cAa	27/36	0.220508307517907	4	FACETS	0.79	0.704	0.882			1	SUBCLONAL	1	TRUE	NA	0.352299956068432	4		614	962	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118666	11118666	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	187	843	0	ENST00000358026.2:c.2090A>C	p.Asp697Ala	p.D697A	ENST00000358026	NM_001128849.1	697	gAc/gCc	14/36	0.344949527174529	3	FACETS	0.963	0.887	1	0.321	0.295	0.348	CLONAL	1	TRUE	0	0.352299956068432	3		843	1297	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984350	201984350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762671088	NA	P-0042253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	58	484	1	ENST00000359651.3:c.1015C>T	p.Arg339Trp	p.R339W	ENST00000359651		339	Cgg/Tgg	8/8	1	2	FACETS	0.319	0.274	0.368	0.319	0.274	0.368	SUBCLONAL	1	FALSE	1	0.802430564927016	2		485	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0042277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	368	556	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	1	2	FACETS	0.977	0.931	1	0.977	0.931	1	CLONAL	1	TRUE	1	0.88843258589601	2		556	848	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0042277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	138	222	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.941	0.87	1	0.941	0.87	1	CLONAL	1	TRUE	1	0.88843258589601	2		222	330	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814313	76814313	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	129	257	0	ENST00000373344.5:c.6331C>T	p.Arg2111Ter	p.R2111*	ENST00000373344	NM_000489.3	2111	Cga/Tga	29/35	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.88843258589601	2		257	281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0042277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	514	696	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	1	2	FACETS	0.986	0.948	1	0.986	0.948	1	CLONAL	1	TRUE	1	0.88843258589601	2		696	1173	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577238	64577238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1114167507	NA	P-0042277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	74	804	2	ENST00000312049.6:c.344G>A	p.Arg115His	p.R115H	ENST00000312049	NM_130799.2	115	cGt/cAt	2/10	1	2	FACETS	0.15	0.131	0.171	0.15	0.131	0.171	SUBCLONAL	1	TRUE	1	0.88843258589601	2		806	1110	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038530	47038530	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	101	664	0	ENST00000377604.3:c.692A>T	p.Glu231Val	p.E231V	ENST00000377604	NM_001204468.1	231	gAg/gTg	8/24	1	2	FACETS	0.245	0.218	0.273	0.245	0.218	0.273	SUBCLONAL	1	TRUE	1	0.88843258589601	2		664	929	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344617	70344617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	277	484	0	ENST00000374080.3:c.1978C>T	p.Pro660Ser	p.P660S	ENST00000374080		660	Cca/Tca	14/45	1	2	FACETS	0.842	0.794	0.889	0.842	0.794	0.889	CLONAL	1	TRUE	1	0.88843258589601	2		484	741	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608275	100608275	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	483	676	0	ENST00000308731.7:c.1815G>C	p.Glu605Asp	p.E605D	ENST00000308731	NM_000061.2	605	gaG/gaC	18/19	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.88843258589601	2		676	1048	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655488	67655488	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	202	406	0	ENST00000264010.4:c.1351G>C	p.Asp451His	p.D451H	ENST00000264010	NM_006565.3	451	Gat/Cat	7/12	0.661376090923386	1	FACETS	0.983	0.924	1	0.983	0.924	1	CLONAL	1	TRUE	0	0.661376090923386	1		406	416	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50811826	50811826	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs886040872	NA	P-0042279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	223	374	0	ENST00000398568.2:c.1103C>A	p.Ser368Ter	p.S368*	ENST00000398568	NM_001042412.1	368	tCa/tAa	7/18	0.661376090923386	1	FACETS	0.99	0.934	1	0.99	0.934	1	CLONAL	1	TRUE	0	0.661376090923386	1		374	456	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194766	30194766	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370180862	NA	P-0042279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	245	523	1	ENST00000331968.5:c.379G>A	p.Asp127Asn	p.D127N	ENST00000331968	NM_002742.2	127	Gat/Aat	2/18	1	2	FACETS	0.905	0.848	0.963	0.905	0.848	0.963	CLONAL	1	TRUE	1	0.661376090923386	2		524	819	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0042308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	156	506	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.863895962004302	4	FACETS	1	0.944	1	0.344	0.316	0.374	CLONAL	1	TRUE	1	0.91528677352043	4		506	632	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0042308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	210	346	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.855491622589433	4	FACETS	0.844	0.8	0.887	0.844	0.8	0.887	CLONAL	3	TRUE	1	0.91528677352043	4		346	347	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89839769	89839769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	232	794	1	ENST00000389301.3:c.1924G>A	p.Glu642Lys	p.E642K	ENST00000389301	NM_000135.2	642	Gaa/Aaa	22/43	0.913428283314007	3	FACETS	0.993	0.93	1	0.331	0.31	0.353	CLONAL	1	TRUE	0	0.91528677352043	3		795	744	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376262	225376262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	85	269	0	ENST00000264414.4:c.692C>T	p.Ser231Leu	p.S231L	ENST00000264414	NM_003590.4	231	tCa/tTa	6/16	0.89981445656238	3	FACETS	1	0.929	1	0.348	0.312	0.386	CLONAL	1	TRUE	0	0.91528677352043	3		269	259	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1952853	1952853	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	182	637	0	ENST00000382891.5:c.1936G>A	p.Glu646Lys	p.E646K	ENST00000382891	NM_133335.3	646	Gaa/Aaa	10/22	0.656394032303187	4	FACETS	1	0.944	1	0.512	0.473	0.552	CLONAL	1	TRUE	2	0.91528677352043	4		637	744	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0042311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	150	442	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.625241802541349	2		442	467	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0042311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	172	673	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.625241802541349	2		673	460	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0042311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	323	764	3	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.508208252207733	3	FACETS	1	0.993	1	0.651	0.616	0.688	CLONAL	1	TRUE	1	0.625241802541349	3		767	1041	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211079	55211079	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519888	NA	P-0042311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	57	551	0	ENST00000275493.2:c.322A>G	p.Arg108Gly	p.R108G	ENST00000275493	NM_005228.3	108	Aga/Gga	3/28	0.508208252207733	3	FACETS	0.312	0.267	0.362	0.156	0.133	0.181	SUBCLONAL	1	TRUE	1	0.625241802541349	3		551	767	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27183554	27183554	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	181	484	0	ENST00000380036.4:c.1128del	p.Leu377TyrfsTer7	p.L377Yfs*7	ENST00000380036	NM_000459.3	376	ccG/cc	8/23	1	2	FACETS	0.976	0.906	1	0.976	0.906	1	CLONAL	1	TRUE	1	0.625241802541349	2		484	593	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	266	590	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.984	0.927	1	0.984	0.927	1	CLONAL	1	TRUE	1	0.720057552893348	2		590	751	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	327	707	2	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	1	2	FACETS	0.987	0.936	1	0.987	0.936	1	CLONAL	1	TRUE	1	0.720057552893348	2		709	920	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	147	387	1	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.934	0.861	1	0.934	0.861	1	CLONAL	1	TRUE	1	0.720057552893348	2		388	437	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	177	478	18	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	0.652629109991651	1	FACETS	0.942	0.884	0.999	0.942	0.884	0.999	CLONAL	1	TRUE	0	0.720057552893348	1		496	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578245	7578245	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780072	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	250	696	1	ENST00000269305.4:c.604C>T	p.Arg202Cys	p.R202C	ENST00000269305	NM_001126112.2	202	Cgt/Tgt	6/11	1	2	FACETS	0.92	0.864	0.977	0.92	0.864	0.977	CLONAL	1	TRUE	1	0.720057552893348	2		697	755	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890149	76890150	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	210	498	2	ENST00000373344.5:c.4744dup	p.Thr1582AsnfsTer19	p.T1582Nfs*19	ENST00000373344	NM_000489.3	1582	aca/aAca	17/35	NA	2	FACETS	0.921	0.86	0.984			1	INDETERMINATE	1	TRUE	NA	0.720057552893348	2		500	633	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	105	257	0	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			0.720057552893348	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.720057552893348	1		257	175	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654553	29654553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876657714	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	107	316	0	ENST00000356175.3:c.5242C>T	p.Arg1748Ter	p.R1748*	ENST00000356175	NM_000267.3	1748	Cga/Tga	37/57	0.672988812629284	1	FACETS	0.813	0.745	0.882	0.813	0.745	0.882	CLONAL	1	TRUE	0	0.720057552893348	1		316	234	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798822	42798822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	123	859	2	ENST00000575354.2:c.4394G>A	p.Arg1465His	p.R1465H	ENST00000575354	NM_015125.3	1465	cGc/cAc	19/20	1	2	FACETS	0.425	0.384	0.468	0.425	0.384	0.468	SUBCLONAL	1	TRUE	1	0.720057552893348	2		861	804	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441147	149441147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	255	711	0	ENST00000286301.3:c.1765G>A	p.Gly589Arg	p.G589R	ENST00000286301	NM_005211.3	589	Gga/Aga	13/22	1	2	FACETS	0.998	0.939	1	0.998	0.939	1	CLONAL	1	TRUE	1	0.720057552893348	2		711	710	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814728	139814728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1345839275	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	224	706	0	ENST00000247668.2:c.721C>T	p.Arg241Trp	p.R241W	ENST00000247668	NM_021138.3	241	Cgg/Tgg	8/11	1	2	FACETS	0.91	0.851	0.969	0.91	0.851	0.969	CLONAL	1	TRUE	1	0.720057552893348	2		706	684	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790072	40790072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753667	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	245	688	2	ENST00000373198.4:c.2659G>A	p.Ala887Thr	p.A887T	ENST00000373198	NM_133170.3	887	Gcc/Acc	18/32	1	2	FACETS	0.937	0.88	0.996	0.937	0.88	0.996	CLONAL	1	TRUE	1	0.720057552893348	2		690	726	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866516	56866516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376329765	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	309	779	1	ENST00000519728.1:c.763G>A	p.Ala255Thr	p.A255T	ENST00000519728	NM_002350.3	255	Gct/Act	8/13	1	2	FACETS	0.92	0.869	0.971	0.92	0.869	0.971	CLONAL	1	TRUE	1	0.720057552893348	2		780	933	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538979	23538979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771028824	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	248	691	0	ENST00000380871.4:c.460C>T	p.Arg154Trp	p.R154W	ENST00000380871	NM_006167.3	154	Cgg/Tgg	2/2	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.720057552893348	2		691	664	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672300	30672300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140008669	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	249	694	0	ENST00000376406.3:c.4660C>T	p.Arg1554Trp	p.R1554W	ENST00000376406	NM_014641.2	1554	Cgg/Tgg	10/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.720057552893348	2		694	677	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391832	139391832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766836819	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	265	806	2	ENST00000277541.6:c.6359G>A	p.Arg2120His	p.R2120H	ENST00000277541	NM_017617.3	2120	cGc/cAc	34/34	1	2	FACETS	0.983	0.926	1	0.983	0.926	1	CLONAL	1	TRUE	1	0.720057552893348	2		808	749	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436599	49436599	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886041405	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	297	825	2	ENST00000301067.7:c.5707C>T	p.Arg1903Ter	p.R1903*	ENST00000301067	NM_003482.3	1903	Cga/Tga	26/54	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.720057552893348	2		827	780	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745593	162745593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769532262	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	185	565	0	ENST00000367921.3:c.2008G>A	p.Glu670Lys	p.E670K	ENST00000367921	NM_006182.2	670	Gag/Aag	15/18	1	2	FACETS	0.864	0.802	0.927	0.864	0.802	0.927	CLONAL	1	TRUE	1	0.720057552893348	2		565	595	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815644	139815644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763841128	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	203	545	0	ENST00000247668.2:c.1115G>A	p.Arg372His	p.R372H	ENST00000247668	NM_021138.3	372	cGc/cAc	9/11	1	2	FACETS	0.93	0.868	0.994	0.93	0.868	0.994	CLONAL	1	TRUE	1	0.720057552893348	2		545	606	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537237	80537237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	184	595	0	ENST00000286548.4:c.161C>T	p.Thr54Met	p.T54M	ENST00000286548	NM_002072.3	54	aCg/aTg	2/7	1	2	FACETS	0.936	0.87	1	0.936	0.87	1	CLONAL	1	TRUE	1	0.720057552893348	2		595	546	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99204042	99204042	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529481819	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	176	348	0	ENST00000074304.5:c.2905G>A	p.Glu969Lys	p.E969K	ENST00000074304	NM_001134224.1	969	Gaa/Aaa	26/26	1	2	FACETS	0.994	0.923	1	0.994	0.923	1	CLONAL	1	TRUE	1	0.720057552893348	2		348	492	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953237	81953237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs963117904	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	152	374	0	ENST00000359376.3:c.2203G>A	p.Val735Met	p.V735M	ENST00000359376	NM_002661.3	735	Gtg/Atg	20/33	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.720057552893348	2		374	402	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281360	49281360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201503697	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	360	847	1	ENST00000282018.3:c.407G>A	p.Arg136His	p.R136H	ENST00000282018	NM_020377.2	136	cGt/cAt	1/1	0.720057552893348	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.720057552893348	1		848	601	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701263	43701263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1157211964	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	211	514	0	ENST00000382044.4:c.5432C>T	p.Ala1811Val	p.A1811V	ENST00000382044	NM_001141980.1	1811	gCg/gTg	26/28	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.720057552893348	2		514	567	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164466	36164466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	148	399	0	ENST00000300305.3:c.1409C>T	p.Ala470Val	p.A470V	ENST00000300305		470	gCg/gTg	8/8	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.720057552893348	2		399	390	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244682	46244682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766416912	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	203	608	0	ENST00000334344.6:c.2776G>A	p.Val926Ile	p.V926I	ENST00000334344	NM_152641.2	926	Gta/Ata	15/21	1	2	FACETS	0.961	0.897	1	0.961	0.897	1	CLONAL	1	TRUE	1	0.720057552893348	2		608	587	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885299	111885299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200936167	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	207	634	0	ENST00000341259.2:c.1187C>T	p.Thr396Met	p.T396M	ENST00000341259	NM_005475.2	396	aCg/aTg	6/8	1	2	FACETS	0.91	0.849	0.972	0.91	0.849	0.972	CLONAL	1	TRUE	1	0.720057552893348	2		634	632	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348059	89348059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1402377065	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	324	995	2	ENST00000301030.4:c.4891C>T	p.Arg1631Trp	p.R1631W	ENST00000301030	NM_001256183.1	1631	Cgg/Tgg	9/13	1	2	FACETS	0.931	0.881	0.981	0.931	0.881	0.981	CLONAL	1	TRUE	1	0.720057552893348	2		997	967	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515149	148515149	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	174	458	0	ENST00000320356.2:c.1060C>T	p.Arg354Cys	p.R354C	ENST00000320356	NM_004456.4	354	Cgt/Tgt	10/20	NA	2	FACETS	0.866	0.802	0.932			1	INDETERMINATE	1	TRUE	NA	0.720057552893348	2		458	558	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464920	120464920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1233590749	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	181	507	1	ENST00000256646.2:c.5152C>T	p.Arg1718Cys	p.R1718C	ENST00000256646	NM_024408.3	1718	Cgc/Tgc	28/34	1	2	FACETS	0.941	0.875	1	0.941	0.875	1	CLONAL	1	TRUE	1	0.720057552893348	2		508	534	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466975	18466975	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	138	436	0	ENST00000266497.5:c.1114G>T	p.Ala372Ser	p.A372S	ENST00000266497		372	Gct/Tct	5/31	1	2	FACETS	0.816	0.748	0.886	0.816	0.748	0.886	CLONAL	1	TRUE	1	0.720057552893348	2		436	470	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95577677	95577677	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	21	386	0	ENST00000393063.1:c.2233C>G	p.Arg745Gly	p.R745G	ENST00000393063	NM_030621.3	745	Cga/Gga	15/28	0.720057552893348	1	FACETS	0.119	0.091	0.151	0.119	0.091	0.151	SUBCLONAL	1	TRUE	0	0.720057552893348	1		386	315	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988943	41988943	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	190	544	0	ENST00000219905.7:c.1735G>A	p.Gly579Arg	p.G579R	ENST00000219905	NM_001164273.1	579	Gga/Aga	3/24	1	2	FACETS	0.947	0.882	1	0.947	0.882	1	CLONAL	1	TRUE	1	0.720057552893348	2		544	557	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434635	99434635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148823172	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	239	638	0	ENST00000268035.6:c.722C>T	p.Ala241Val	p.A241V	ENST00000268035	NM_000875.3	241	gCg/gTg	3/21	1	2	FACETS	0.958	0.899	1	0.958	0.899	1	CLONAL	1	TRUE	1	0.720057552893348	2		638	693	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993852	72993852	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	201	604	0	ENST00000268489.5:c.193A>G	p.Thr65Ala	p.T65A	ENST00000268489	NM_006885.3	65	Acc/Gcc	2/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.720057552893348	2		604	503	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485817	57485817	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1569032625	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	208	490	1	ENST00000371085.3:c.1118G>A	p.Arg373His	p.R373H	ENST00000371085	NM_000516.4	373	cGc/cAc	13/13	1	2	FACETS	0.984	0.92	1	0.984	0.92	1	CLONAL	1	TRUE	1	0.720057552893348	2		491	587	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281600	142281600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368507270	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	200	484	0	ENST00000350721.4:c.644G>A	p.Arg215His	p.R215H	ENST00000350721	NM_001184.3	215	cGt/cAt	4/47	1	2	FACETS	0.959	0.895	1	0.959	0.895	1	CLONAL	1	TRUE	1	0.720057552893348	2		484	579	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137320989	137320989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	331	845	0	ENST00000481739.1:c.946C>T	p.Arg316Cys	p.R316C	ENST00000481739	NM_002957.4	316	Cgc/Tgc	7/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.720057552893348	2		845	878	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0042326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	122	426	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.453276086760991	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.453276086760991	2		426	239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0042326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	270	547	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.453276086760991	2	FACETS	0.947	0.895	0.999	0.947	0.895	0.999	CLONAL	2	TRUE	0	0.453276086760991	2		547	629	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138528	2138528	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	203	700	1	ENST00000219476.3:c.5341C>T	p.Pro1781Ser	p.P1781S	ENST00000219476	NM_000548.3	1781	Cca/Tca	42/42	0.453276086760991	2	FACETS	1	0.979	1	0.566	0.526	0.608	CLONAL	1	TRUE	0	0.453276086760991	2		701	791	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924255	11924255	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	24	46	1	ENST00000353533.5:c.52A>T	p.Ser18Cys	p.S18C	ENST00000353533	NM_003010.3	18	Agc/Tgc	1/11	0.160652565160555	6	FACETS	0.926	0.74	1	0.617	0.493	0.755	INDETERMINATE	2	TRUE	3	0.453276086760991	6		47	109	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604733	48604736	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	novel	NA	P-0042326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	197	365	0	ENST00000342988.3:c.1558_1561del	p.Glu520HisfsTer16	p.E520Hfs*16	ENST00000342988	NM_005359.5	519	AAAGaa/aa	12/12	0.453276086760991	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.453276086760991	2		365	423	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732611	190732611	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	108	348	0	ENST00000441310.2:c.2429A>T	p.Asp810Val	p.D810V	ENST00000441310	NM_000534.4	810	gAt/gTt	11/13	0.306918882291929	4	FACETS	0.931	0.843	1	0.931	0.843	1	CLONAL	2	TRUE	2	0.453276086760991	4		348	372	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520135	9520135	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	96	349	1	ENST00000353224.5:c.2134del	p.Leu712SerfsTer2	p.L712Sfs*2	ENST00000353224	NM_177990.2	712	Ctc/tc	10/10	0.452940565435858	3	FACETS	0.959	0.857	1	0.479	0.428	0.534	CLONAL	1	TRUE	1	0.453276086760991	3		350	542	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023163	31023163	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	198	540	0	ENST00000375687.4:c.2648A>G	p.Glu883Gly	p.E883G	ENST00000375687	NM_015338.5	883	gAa/gGa	13/13	0.452940565435858	3	FACETS	0.987	0.921	1	0.987	0.921	1	CLONAL	2	TRUE	1	0.453276086760991	3		540	543	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005378	150005378	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	246	519	0	ENST00000253339.5:c.847T>C	p.Tyr283His	p.Y283H	ENST00000253339		283	Tac/Cac	3/7	0.160652565160555	6	FACETS	1	0.987	1	0.794	0.744	0.845	INDETERMINATE	2	TRUE	3	0.453276086760991	6		519	869	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0042327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	72	207	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.18389525591341	4	FACETS	0.871	0.767	0.981	0.871	0.767	0.981	INDETERMINATE	2	TRUE	2	0.344087243219818	4		207	323	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665024	138665024	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	84	109	0	ENST00000330315.3:c.541G>T	p.Ala181Ser	p.A181S	ENST00000330315	NM_023067.3	181	Gcc/Tcc	1/1	0.18389525591341	4	FACETS	1	0.926	1	1	0.926	1	INDETERMINATE	2	TRUE	2	0.344087243219818	4		109	313	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100435	102100435	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	92	312	0	ENST00000282441.5:c.1279G>A	p.Asp427Asn	p.D427N	ENST00000282441	NM_001130145.2	427	Gat/Aat	9/9	0.18389525591341	4	FACETS	1	0.98	1	0.746	0.665	0.831	INDETERMINATE	1	TRUE	2	0.344087243219818	4		312	482	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935294	36935294	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	253	692	0	ENST00000361632.4:c.1433G>T	p.Arg478Met	p.R478M	ENST00000361632		478	aGg/aTg	10/16	0.306358852221083	2	FACETS	0.939	0.882	0.997	0.939	0.882	0.997	CLONAL	2	TRUE	0	0.344087243219818	2		692	783	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983123	201983123	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	300	579	0	ENST00000359651.3:c.972G>T	p.Met324Ile	p.M324I	ENST00000359651		324	atG/atT	7/8	0.119010098906733	6	FACETS	1	0.976	1	1	0.976	1	INDETERMINATE	3	TRUE	3	0.344087243219818	6		579	926	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100535	102100535	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	146	421	0	ENST00000282441.5:c.1379G>T	p.Gly460Val	p.G460V	ENST00000282441	NM_001130145.2	460	gGa/gTa	9/9	0.18389525591341	4	FACETS	0.769	0.702	0.838	0.769	0.702	0.838	INDETERMINATE	2	TRUE	2	0.344087243219818	4		421	742	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475158	475158	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0042327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	73	513	0	ENST00000399788.2:c.479C>G	p.Ser160Ter	p.S160*	ENST00000399788	NM_001042603.1	160	tCa/tGa	4/28	0.119010098906733	6	FACETS	1	0.969	1	0.453	0.397	0.514	INDETERMINATE	1	TRUE	3	0.344087243219818	6		513	527	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244406	46244406	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	157	395	0	ENST00000334344.6:c.2500C>G	p.Gln834Glu	p.Q834E	ENST00000334344	NM_152641.2	834	Caa/Gaa	15/21	0.119010098906733	6	FACETS	0.941	0.867	1	0.941	0.867	1	INDETERMINATE	3	TRUE	3	0.344087243219818	6		395	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577093	7577113	+	inframe_deletion	In_Frame_Del	DEL	CGGTCTCTCCCAGGACAGGCA	CGGTCTCTCCCAGGACAGGCA	-	novel	NA	P-0042327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	442	600	0	ENST00000269305.4:c.825_845del	p.Cys275_Arg282delinsTrp	p.C275_R282delinsW	ENST00000269305	NM_001126112.2	275	tgTGCCTGTCCTGGGAGAGACCGg/tgg	8/11	0.344087243219818	4	FACETS	1	0.988	1	0.812	0.777	0.848	CLONAL	3	TRUE	0	0.344087243219818	4		600	1063	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602620	10602621	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0042327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	197	668	0	ENST00000171111.5:c.957_958insG	p.Arg320AlafsTer30	p.R320Afs*30	ENST00000171111	NM_203500.1	319	-/G	3/6	0.344087243219818	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.344087243219818	1		668	705	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726594	41726594	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	241	607	0	ENST00000301178.4:c.139G>T	p.Ala47Ser	p.A47S	ENST00000301178	NM_021913.4	47	Gcc/Tcc	2/20	0.18389525591341	4	FACETS	1	0.976	1	1	0.976	1	INDETERMINATE	2	TRUE	2	0.344087243219818	4		607	865	SUCCESS
APC	324	MSKCC	GRCh37	5	112137040	112137040	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755437577	NA	P-0042327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	115	338	0	ENST00000257430.4:c.794G>A	p.Gly265Glu	p.G265E	ENST00000257430	NM_000038.5	265	gGa/gAa	8/16	0.344087243219818	2	FACETS	0.823	0.748	0.902	0.823	0.748	0.902	CLONAL	2	TRUE	0	0.344087243219818	2		338	406	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163407	32163407	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs45458498	NA	P-0042327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	297	637	0	ENST00000375023.3:c.5819G>T	p.Arg1940Leu	p.R1940L	ENST00000375023	NM_004557.3	1940	cGc/cTc	30/30	0.322402884296617	4	FACETS	0.922	0.867	0.979	0.922	0.867	0.979	CLONAL	2	TRUE	2	0.344087243219818	4		637	1258	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0042329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	51	235	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.241509104239223	4	FACETS	1	0.956	1	0.676	0.576	0.784	CLONAL	1	TRUE	2	0.241509104239223	4		235	388	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398282	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0042329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	42	487	0	ENST00000311936.3:c.37_38delinsTT	p.Gly13Phe	p.G13F	ENST00000311936	NM_004985.3	13	GGc/TTc	2/5	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.241509104239223	2		487	334	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535353	187535353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747181352	NA	P-0042329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	18	537	0	ENST00000441802.2:c.9221C>T	p.Pro3074Leu	p.P3074L	ENST00000441802	NM_005245.3	3074	cCa/cTa	12/27	0.241509104239223	3	FACETS	0.514	0.387	0.665	0.257	0.193	0.333	SUBCLONAL	1	TRUE	1	0.241509104239223	3		537	325	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039686	47039686	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	112	973	0	ENST00000377604.3:c.1138G>T	p.Glu380Ter	p.E380*	ENST00000377604	NM_001204468.1	380	Gag/Tag	11/24	0.241509104239223	3	FACETS	0.851	0.767	0.939	0.851	0.767	0.939	CLONAL	2	TRUE	1	0.241509104239223	3		973	611	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480641	50480641	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	17	441	0	ENST00000394963.4:c.511G>T	p.Ala171Ser	p.A171S	ENST00000394963	NM_003076.4	171	Gcc/Tcc	4/13	0.241509104239223	5	FACETS	0.576	0.429	0.751	0.288	0.214	0.376	SUBCLONAL	1	TRUE	3	0.241509104239223	5		441	333	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992900	72992900	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	56	791	0	ENST00000268489.5:c.1145G>T	p.Gly382Val	p.G382V	ENST00000268489	NM_006885.3	382	gGc/gTc	2/10	0.241509104239223	3	FACETS	0.935	0.801	1	0.467	0.4	0.541	CLONAL	1	TRUE	1	0.241509104239223	3		791	556	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663898	29663901	+	frameshift_variant	Frame_Shift_Del	DEL	CTCT	CTCT	-	novel	NA	P-0042329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	28	486	0	ENST00000356175.3:c.6332_6335del	p.Ser2111CysfsTer17	p.S2111Cfs*17	ENST00000356175	NM_000267.3	2110	caCTCT/ca	41/57	1	2	FACETS	0.676	0.541	0.83	0.676	0.541	0.83	SUBCLONAL	1	TRUE	1	0.241509104239223	2		486	343	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719886	52719886	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	52	840	0	ENST00000322088.6:c.1098G>T	p.Leu366Phe	p.L366F	ENST00000322088	NM_014225.5	366	ttG/ttT	9/15	0.241509104239223	3	FACETS	0.81	0.689	0.943	0.405	0.344	0.472	CLONAL	1	TRUE	1	0.241509104239223	3		840	596	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913523	39913523	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	48	696	0	ENST00000378444.4:c.4805G>T	p.Gly1602Val	p.G1602V	ENST00000378444	NM_001123385.1	1602	gGc/gTc	13/15	0.241509104239223	3	FACETS	0.823	0.696	0.964	0.412	0.348	0.482	CLONAL	1	TRUE	1	0.241509104239223	3		696	541	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913476	NA	P-0042334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	58	409	0	ENST00000358487.5:c.1647T>G	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaG	12/18	1	2	FACETS	0.682	0.59	0.781	0.682	0.59	0.781	SUBCLONAL	1	FALSE	1	0.563122674936347	2		409	302	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436306	110436306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	11	171	0	ENST00000375856.3:c.2095G>A	p.Ala699Thr	p.A699T	ENST00000375856	NM_003749.2	699	Gcc/Acc	1/2	0.242352284557189	1	FACETS	0.144	0.099	0.199	0.144	0.099	0.199	INDETERMINATE	1	FALSE	0	0.563122674936347	1		171	195	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591888	48591888	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519739	NA	P-0042334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	75	386	1	ENST00000342988.3:c.1051G>C	p.Asp351His	p.D351H	ENST00000342988	NM_005359.5	351	Gat/Cat	9/12	0.388899766490953	1	FACETS	0.608	0.537	0.682	0.608	0.537	0.682	SUBCLONAL	1	FALSE	0	0.563122674936347	1		387	315	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484858	57485003	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTTTGTGGAGTGACCGCCCACCCCCTGCGCTTGCCCAGGAGGCCCTGGTCTGCACTGTTTATAGAGAAGAACCCCGTGCAAGCATTCCAGACCCCTGGCCGAAAGCGCGCTTCTCCCAAGCATTCACACGGCCTCCCTTCTTGT	AGGTTTGTGGAGTGACCGCCCACCCCCTGCGCTTGCCCAGGAGGCCCTGGTCTGCACTGTTTATAGAGAAGAACCCCGTGCAAGCATTCCAGACCCCTGGCCGAAAGCGCGCTTCTCCCAAGCATTCACACGGCCTCCCTTCTTGT	-	novel	NA	P-0042334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	56	384	0	ENST00000371085.3:c.839+1_840-1del		p.X280_splice	ENST00000371085	NM_000516.4	280		10/13	0.124417955979585	0	FACETS	0.203	0.174	0.235			1	INDETERMINATE	1	FALSE	0	0.563122674936347	0		384	428	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485136	57485387	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTGTGTATGGCTTCCACTCTTGCTGGCTGTTCATTGCGGTGGTTCTTTTTCAAACGGTCAGGCTGAAAACCCCCATCCCCCTCCCACCACCAAACCATAAAGGATCTATAAGAGAAGCAAGAAAAACGCACTCCCACTAATTCTCATATGGAAAAATCAGGGTTTTGAAGACTTCAGGAGCTACAGAGATGCTAGCACCCCAGCTCTGCTTGAATTTTAAATTACATTAATATGTATTCCCTTTTTATATA	GGTGTGTATGGCTTCCACTCTTGCTGGCTGTTCATTGCGGTGGTTCTTTTTCAAACGGTCAGGCTGAAAACCCCCATCCCCCTCCCACCACCAAACCATAAAGGATCTATAAGAGAAGCAAGAAAAACGCACTCCCACTAATTCTCATATGGAAAAATCAGGGTTTTGAAGACTTCAGGAGCTACAGAGATGCTAGCACCCCAGCTCTGCTTGAATTTTAAATTACATTAATATGTATTCCCTTTTTATATA	-	novel	NA	P-0042334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	32	257	0	ENST00000371085.3:c.970+1_971-1del		p.X324_splice	ENST00000371085	NM_000516.4	324		11/13	0.124417955979585	0	FACETS	0.172	0.14	0.208			1	INDETERMINATE	1	FALSE	0	0.563122674936347	0		257	289	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485456	57485736	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTGAGTCGAGCCTGTCTTTAGTTTCCTCTCTTGTTCCTCCTCTTTTTCTCATGGATGTAAATTTACTTAATTCCAAATTCAGGGGTTCAGCTACCCAGTTCCATGGTTTTAGTTCACGCACATCCAGTGTGGATTTGAGCTCTTTGCGCCCCTCTTTTTGCTTTTGTTTTCATATGACATCAGAGGCTGGCTGACAGCCGTCCCTGGTAGGTGTCCCCATCAGGGATAGGGTGGTTCCTGGCGAGGGTGTCACTGACAAGTCCCCTTGTTTGTGCCCGCA	GGTGAGTCGAGCCTGTCTTTAGTTTCCTCTCTTGTTCCTCCTCTTTTTCTCATGGATGTAAATTTACTTAATTCCAAATTCAGGGGTTCAGCTACCCAGTTCCATGGTTTTAGTTCACGCACATCCAGTGTGGATTTGAGCTCTTTGCGCCCCTCTTTTTGCTTTTGTTTTCATATGACATCAGAGGCTGGCTGACAGCCGTCCCTGGTAGGTGTCCCCATCAGGGATAGGGTGGTTCCTGGCGAGGGTGTCACTGACAAGTCCCCTTGTTTGTGCCCGCA	-	novel	NA	P-0042334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	52	316	1	ENST00000371085.3:c.1038+1_1039-1del		p.X346_splice	ENST00000371085	NM_000516.4	346		12/13	0.124417955979585	0	FACETS	0.222	0.19	0.258			1	INDETERMINATE	1	FALSE	0	0.563122674936347	0		317	363	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443583	49443583	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0042334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	104	508	0	ENST00000301067.7:c.3788C>G	p.Ser1263Ter	p.S1263*	ENST00000301067	NM_003482.3	1263	tCa/tGa	11/54	1	2	FACETS	0.801	0.721	0.885	0.801	0.721	0.885	CLONAL	1	FALSE	1	0.563122674936347	2		508	461	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362593	118362594	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0042334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	102	342	0	ENST00000534358.1:c.4955_4956del	p.Thr1652SerfsTer41	p.T1652Sfs*41	ENST00000534358	NM_005933.3	1652	ACa/a	15/36	0.511342887998923	1	FACETS	0.735	0.664	0.809	0.735	0.664	0.809	SUBCLONAL	1	FALSE	0	0.563122674936347	1		342	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578477	7578523	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTGTGGAATCAACCCACAGCTGCACAGGGCAGGTCTTGGCCAGTT	GGGTGTGGAATCAACCCACAGCTGCACAGGGCAGGTCTTGGCCAGTT	-	novel	NA	P-0042334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	124	570	0	ENST00000269305.4:c.407_453del	p.Gln136ProfsTer29	p.Q136Pfs*29	ENST00000269305	NM_001126112.2	136	cAACTGGCCAAGACCTGCCCTGTGCAGCTGTGGGTTGATTCCACACCC/c	5/11	0.563122674936347	1	FACETS	0.889	0.813	0.966	0.889	0.813	0.966	CLONAL	1	FALSE	0	0.563122674936347	1		570	356	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125869	47125869	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	31	132	0	ENST00000409792.3:c.5401del	p.Ile1801Ter	p.I1801*	ENST00000409792	NM_014159.6	1801	Ata/ta	12/21	0.511342887998923	1	FACETS	0.799	0.663	0.944	0.799	0.663	0.944	CLONAL	1	FALSE	0	0.563122674936347	1		132	99	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961447	1961447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771867435	NA	P-0042334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	41	379	2	ENST00000382891.5:c.3235G>A	p.Ala1079Thr	p.A1079T	ENST00000382891	NM_133335.3	1079	Gcc/Acc	17/22	1	2	FACETS	0.361	0.301	0.428	0.361	0.301	0.428	SUBCLONAL	1	FALSE	1	0.563122674936347	2		381	403	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751258	128751258	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	49	312	0	ENST00000377970.2:c.795C>G	p.Ser265Arg	p.S265R	ENST00000377970	NM_002467.4	265	agC/agG	2/3	0.550348274988519	4	FACETS	0.611	0.518	0.713	0.204	0.172	0.238	SUBCLONAL	1	FALSE	1	0.563122674936347	4		312	445	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797253	135797253	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	52	240	0	ENST00000298552.3:c.616C>T	p.His206Tyr	p.H206Y	ENST00000298552	NM_001162426.1	206	Cat/Tat	7/23	0.563122674936347	1	FACETS	0.814	0.707	0.927	0.814	0.707	0.927	CLONAL	1	FALSE	0	0.563122674936347	1		240	163	SUCCESS
APC	324	MSKCC	GRCh37	5	112175994	112175994	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	22	188	0	ENST00000257430.4:c.4703A>G	p.Asp1568Gly	p.D1568G	ENST00000257430	NM_000038.5	1568	gAt/gGt	16/16	1	2	FACETS	0.18	0.139	0.228	0.18	0.139	0.228	SUBCLONAL	1	TRUE	1	0.64	2		188	381	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129671	2129671	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs137854208	NA	P-0042354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	252	469	0	ENST00000219476.3:c.3397+1G>A		p.X1133_splice	ENST00000219476	NM_000548.3	1133			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.64	2		469	730	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134513	2134513	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs45517334	NA	P-0042354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	274	559	0	ENST00000219476.3:c.4290G>A	p.Trp1430Ter	p.W1430*	ENST00000219476	NM_000548.3	1430	tgG/tgA	34/42	1	2	FACETS	0.998	0.94	1	0.998	0.94	1	CLONAL	1	TRUE	1	0.64	2		559	858	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196080	138196080	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	160	340	0	ENST00000237289.4:c.394G>T	p.Glu132Ter	p.E132*	ENST00000237289	NM_001270507.1	132	Gaa/Taa	3/9	0.3	16	FACETS	0.978	0.894	1			1	INDETERMINATE	2	TRUE	NA	0.8	16		340	1350	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	105	236	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.917	0.836	0.999	1	0.992	1	CLONAL	5	TRUE	1	0.175524218469342	2		236	261	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868346	45868346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776313922	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	96	688	0	ENST00000391945.4:c.431C>T	p.Ala144Val	p.A144V	ENST00000391945	NM_000400.3	144	gCg/gTg	6/23	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.175524218469342	2		688	959	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412252	139412252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057523819	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	224	778	0	ENST00000277541.6:c.1393G>A	p.Ala465Thr	p.A465T	ENST00000277541	NM_017617.3	465	Gcc/Acc	8/34	0.175524218469342	1	FACETS	0.912	0.851	0.975	1	0.995	1	CLONAL	3	TRUE	0	0.175524218469342	1		778	851	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431394	121431394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193922598	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	58	593	0	ENST00000257555.6:c.598C>T	p.Arg200Trp	p.R200W	ENST00000257555		200	Cgg/Tgg	3/10	1	2	FACETS	0.885	0.759	1	0.885	0.759	1	CLONAL	1	TRUE	1	0.175524218469342	2		593	747	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439924	56439924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780231969	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	72	567	1	ENST00000407977.2:c.668G>A	p.Arg223His	p.R223H	ENST00000407977		223	cGc/cAc	6/10	1	2	FACETS	0.951	0.829	1	0.951	0.829	1	CLONAL	1	TRUE	1	0.175524218469342	2		568	863	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662389	227662389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773817315	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	65	657	2	ENST00000305123.5:c.1066G>A	p.Ala356Thr	p.A356T	ENST00000305123	NM_005544.2	356	Gcc/Acc	1/2	1	2	FACETS	0.953	0.825	1	0.953	0.825	1	CLONAL	1	TRUE	1	0.175524218469342	2		659	777	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829753	76829756	+	frameshift_variant	Frame_Shift_Del	DEL	CTTC	CTTC	-	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	158	297	0	ENST00000373344.5:c.6285_6288del	p.Lys2096SerfsTer12	p.K2096Sfs*12	ENST00000373344	NM_000489.3	2095	agGAAG/ag	28/35	0.15365103094897	2	FACETS	1	0.974	1			1	CLONAL	9	TRUE	NA	0.175524218469342	2		297	195	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722761	49722761	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs62262682	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	10	15	0	ENST00000449682.2:c.1478G>T	p.Arg493Leu	p.R493L	ENST00000449682	NM_020998.3	493	cGt/cTt	13/18	1	2	FACETS	1	0.799	1	1	0.9	1	CLONAL	2	TRUE	1	0.175524218469342	2		15	47	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989562	212989562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755026855	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	112	369	1	ENST00000342788.4:c.149G>A	p.Arg50His	p.R50H	ENST00000342788	NM_005235.2	50	cGc/cAc	2/28	1	2	FACETS	1	0.969	1	1	0.99	1	CLONAL	2	TRUE	1	0.175524218469342	2		370	541	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992354	72992354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770703902	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	145	740	2	ENST00000268489.5:c.1691C>T	p.Ala564Val	p.A564V	ENST00000268489	NM_006885.3	564	gCg/gTg	2/10	1	2	FACETS	0.804	0.732	0.879	1	0.988	1	CLONAL	2	TRUE	1	0.175524218469342	2		742	1028	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293799	1293799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs539667998	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	56	778	1	ENST00000310581.5:c.1202C>T	p.Ala401Val	p.A401V	ENST00000310581	NM_198253.2	401	gCg/gTg	2/16	1	2	FACETS	0.777	0.664	0.901	0.777	0.664	0.901	CLONAL	1	TRUE	1	0.175524218469342	2		779	821	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953835	131953835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	51	326	0	ENST00000265335.6:c.3238G>A	p.Gly1080Ser	p.G1080S	ENST00000265335		1080	Ggt/Agt	21/25	1	2	FACETS	0.922	0.788	1	1	0.973	1	CLONAL	2	TRUE	1	0.175524218469342	2		326	315	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434583	110434583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	137	574	1	ENST00000375856.3:c.3818C>T	p.Pro1273Leu	p.P1273L	ENST00000375856	NM_003749.2	1273	cCg/cTg	1/2	1	2	FACETS	1	0.975	1	1	0.992	1	CLONAL	2	TRUE	1	0.175524218469342	2		575	658	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965476	15965476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	75	425	0	ENST00000268712.3:c.5330G>A	p.Gly1777Glu	p.G1777E	ENST00000268712	NM_006311.3	1777	gGa/gAa	36/46	1	2	FACETS	0.835	0.733	0.943	1	0.979	1	CLONAL	2	TRUE	1	0.175524218469342	2		425	512	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938141	36938141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759587248	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	45	662	0	ENST00000361632.4:c.820C>T	p.Arg274Cys	p.R274C	ENST00000361632		274	Cgt/Tgt	6/16	1	2	FACETS	0.639	0.536	0.755	0.639	0.536	0.755	SUBCLONAL	1	TRUE	1	0.175524218469342	2		662	802	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032374	11032374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs909244932	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	104	710	3	ENST00000327064.4:c.1768G>A	p.Ala590Thr	p.A590T	ENST00000327064	NM_199141.1	590	Gcc/Acc	16/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.175524218469342	2		713	841	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55597546	55597546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	46	407	0	ENST00000288135.5:c.2194G>A	p.Val732Ile	p.V732I	ENST00000288135	NM_000222.2	732	Gtc/Atc	15/21	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.175524218469342	2		407	501	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112760206	112760206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	24	462	0	ENST00000369452.4:c.875G>A	p.Arg292Lys	p.R292K	ENST00000369452	NM_007373.3	292	aGa/aAa	4/9	1	2	FACETS	0.665	0.521	0.832	0.665	0.521	0.832	SUBCLONAL	1	TRUE	1	0.175524218469342	2		462	411	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862985	117862985	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	34	394	0	ENST00000297338.2:c.1492G>A	p.Glu498Lys	p.E498K	ENST00000297338	NM_006265.2	498	Gaa/Aaa	12/14	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.175524218469342	2		394	300	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023048	27023048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	37	87	0	ENST00000324856.7:c.154G>A	p.Ala52Thr	p.A52T	ENST00000324856	NM_006015.4	52	Gca/Aca	1/20	1	2	FACETS	0.925	0.768	1	1	0.964	1	CLONAL	2	TRUE	1	0.175524218469342	2		87	228	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579592	7579592	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	530	510	0	ENST00000269305.4:c.97-2A>C		p.X33_splice	ENST00000269305	NM_001126112.2	33			NA	2	FACETS	0.985	0.966	1			1	INDETERMINATE	10	TRUE	NA	0.175524218469342	2		510	613	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16174646	16174646	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	74	300	0	ENST00000375759.3:c.83+1G>A		p.X28_splice	ENST00000375759	NM_015001.2	28			1	2	FACETS	0.927	0.814	1	1	0.981	1	CLONAL	2	TRUE	1	0.175524218469342	2		300	455	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255962	16255962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	108	514	0	ENST00000375759.3:c.3227C>T	p.Ser1076Phe	p.S1076F	ENST00000375759	NM_015001.2	1076	tCt/tTt	11/15	1	2	FACETS	0.954	0.858	1	1	0.987	1	CLONAL	2	TRUE	1	0.175524218469342	2		514	645	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944292	206944292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	137	510	0	ENST00000423557.1:c.338G>A	p.Gly113Glu	p.G113E	ENST00000423557	NM_000572.2	113	gGg/gAg	3/5	1	2	FACETS	1	0.947	1	1	0.991	1	CLONAL	2	TRUE	1	0.175524218469342	2		510	739	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931690	28931690	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	69	355	0	ENST00000282397.4:c.2248+1G>A		p.X750_splice	ENST00000282397	NM_002019.4	750			1	2	FACETS	0.921	0.805	1	1	0.98	1	CLONAL	2	TRUE	1	0.175524218469342	2		355	427	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133044	30133044	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	100	459	1	ENST00000331968.5:c.557A>G	p.Lys186Arg	p.K186R	ENST00000331968	NM_002742.2	186	aAg/aGg	4/18	1	2	FACETS	1	0.942	1	1	0.988	1	CLONAL	2	TRUE	1	0.175524218469342	2		460	530	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961120	41961120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	42	283	0	ENST00000219905.7:c.28G>A	p.Ala10Thr	p.A10T	ENST00000219905	NM_001164273.1	10	Gct/Act	2/24	1	2	FACETS	0.777	0.652	0.915	1	0.959	1	CLONAL	2	TRUE	1	0.175524218469342	2		283	308	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774689	73774689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	10	48	0	ENST00000254810.4:c.398G>A	p.Gly133Glu	p.G133E	ENST00000254810	NM_005324.3	133	gGa/gAa	4/4	1	2	FACETS	0.95	0.657	1	1	0.881	1	CLONAL	2	TRUE	1	0.175524218469342	2		48	60	SUCCESS
AXL	558	MSKCC	GRCh37	19	41736913	41736913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779718472	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	155	716	0	ENST00000301178.4:c.628G>A	p.Ala210Thr	p.A210T	ENST00000301178	NM_021913.4	210	Gcc/Acc	5/20	1	2	FACETS	0.97	0.888	1	1	0.991	1	CLONAL	2	TRUE	1	0.175524218469342	2		716	910	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731472	47731472	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	22	61	0	ENST00000449228.1:c.320G>A	p.Gly107Glu	p.G107E	ENST00000449228	NM_001127240.2	107	gGg/gAg	2/4	1	2	FACETS	0.755	0.59	0.944	1	0.923	1	CLONAL	2	TRUE	1	0.175524218469342	2		61	166	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47604193	47604193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	60	366	0	ENST00000263735.4:c.532C>T	p.Pro178Ser	p.P178S	ENST00000263735	NM_002354.2	178	Cca/Tca	5/9	1	2	FACETS	0.971	0.841	1	1	0.978	1	CLONAL	2	TRUE	1	0.175524218469342	2		366	352	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419876	41419876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	134	559	1	ENST00000373198.4:c.445G>A	p.Ala149Thr	p.A149T	ENST00000373198	NM_133170.3	149	Gca/Aca	3/32	1	2	FACETS	0.99	0.9	1	1	0.99	1	CLONAL	2	TRUE	1	0.175524218469342	2		560	771	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665421	182665421	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	26	188	0	ENST00000292782.4:c.521-1G>A		p.X174_splice	ENST00000292782	NM_020640.2	174			1	2	FACETS	0.805	0.643	0.988	1	0.94	1	CLONAL	2	TRUE	1	0.175524218469342	2		188	184	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531166	187531166	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	44	307	1	ENST00000441802.2:c.9857C>T	p.Ala3286Val	p.A3286V	ENST00000441802	NM_005245.3	3286	gCc/gTc	15/27	1	2	FACETS	0.798	0.673	0.936	1	0.963	1	CLONAL	2	TRUE	1	0.175524218469342	2		308	314	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911583	131911583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	36	346	0	ENST00000265335.6:c.328G>A	p.Glu110Lys	p.E110K	ENST00000265335		110	Gaa/Aaa	3/25	1	2	FACETS	0.774	0.64	0.923	1	0.953	1	CLONAL	2	TRUE	1	0.175524218469342	2		346	265	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536181	106536181	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	120	467	0	ENST00000369096.4:c.148A>G	p.Thr50Ala	p.T50A	ENST00000369096	NM_001198.3	50	Aca/Gca	2/7	1	2	FACETS	1	0.963	1	1	0.99	1	CLONAL	2	TRUE	1	0.175524218469342	2		467	606	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553506	106553506	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	78	411	0	ENST00000369096.4:c.1471G>A	p.Ala491Thr	p.A491T	ENST00000369096	NM_001198.3	491	Gcg/Acg	5/7	1	2	FACETS	0.945	0.834	1	1	0.983	1	CLONAL	2	TRUE	1	0.175524218469342	2		411	470	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043632	6043632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	18	297	0	ENST00000265849.7:c.221G>A	p.Gly74Glu	p.G74E	ENST00000265849	NM_000535.5	74	gGg/gAg	3/15	0.175524218469342	0	FACETS	0.89	0.682	1			1	CLONAL	2	TRUE	0	0.175524218469342	0		297	95	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467736	50467736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	34	657	2	ENST00000331340.3:c.971C>T	p.Ala324Val	p.A324V	ENST00000331340	NM_006060.4	324	gCc/gTc	8/8	1	2	FACETS	0.586	0.477	0.709	0.586	0.477	0.709	SUBCLONAL	1	TRUE	1	0.175524218469342	2		659	661	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328323	137328323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	140	619	1	ENST00000481739.1:c.1252C>T	p.Leu418Phe	p.L418F	ENST00000481739	NM_002957.4	418	Ctc/Ttc	10/10	0.175524218469342	1	FACETS	0.904	0.824	0.988	1	0.99	1	CLONAL	2	TRUE	0	0.175524218469342	1		620	805	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650795	48650795	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	183	399	0	ENST00000376670.3:c.664C>T	p.His222Tyr	p.H222Y	ENST00000376670	NM_002049.3	222	Cac/Tac	4/6	0.15365103094897	2	FACETS	1	0.967	1			1	CLONAL	4	TRUE	NA	0.175524218469342	2		399	490	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134555	41134555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	83	457	0	ENST00000379561.5:c.1073C>T	p.Thr358Ile	p.T358I	ENST00000379561	NM_002015.3	358	aCt/aTt	2/3	1	2	FACETS	0.785	0.694	0.883	1	0.979	1	SUBCLONAL	2	TRUE	1	0.175524218469342	2		457	602	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996802	73996802	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	33	407	0	ENST00000318443.5:c.1358T>C	p.Val453Ala	p.V453A	ENST00000318443	NM_001024736.1	453	gTc/gCc	6/10	1	2	FACETS	0.809	0.658	0.979	0.809	0.658	0.979	CLONAL	1	TRUE	1	0.175524218469342	2		407	465	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934942	9934942	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	53	329	0	ENST00000330684.3:c.1348A>G	p.Met450Val	p.M450V	ENST00000330684	NM_001134407.1	450	Atg/Gtg	6/13	1	2	FACETS	0.921	0.789	1	1	0.974	1	CLONAL	2	TRUE	1	0.175524218469342	2		329	328	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40478183	40478183	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	78	597	0	ENST00000264657.5:c.1316T>C	p.Ile439Thr	p.I439T	ENST00000264657	NM_139276.2	439	aTc/aCc	15/24	1	2	FACETS	0.968	0.849	1	0.968	0.849	1	CLONAL	1	TRUE	1	0.175524218469342	2		597	918	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440886	56440886	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	120	676	0	ENST00000407977.2:c.450+1G>A		p.X150_splice	ENST00000407977		150			1	2	FACETS	0.777	0.701	0.857	1	0.985	1	SUBCLONAL	2	TRUE	1	0.175524218469342	2		676	880	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006633	62006633	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	65	563	0	ENST00000392795.3:c.646A>G	p.Thr216Ala	p.T216A	ENST00000392795	NM_001039933.1	216	Aca/Gca	6/6	1	2	FACETS	0.899	0.778	1	0.899	0.778	1	CLONAL	1	TRUE	1	0.175524218469342	2		563	824	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210487	5210487	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	40	552	0	ENST00000357368.4:c.5480A>T	p.Asp1827Val	p.D1827V	ENST00000357368	NM_002850.3	1827	gAt/gTt	35/38	1	2	FACETS	0.668	0.554	0.796	0.668	0.554	0.796	SUBCLONAL	1	TRUE	1	0.175524218469342	2		552	682	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976961	18976961	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs757371840	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	34	633	0	ENST00000262803.5:c.3346T>C	p.Ser1116Pro	p.S1116P	ENST00000262803	NM_002911.3	1116	Tcc/Ccc	23/24	1	2	FACETS	0.595	0.485	0.72	0.595	0.485	0.72	SUBCLONAL	1	TRUE	1	0.175524218469342	2		633	651	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72842137	72842137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	27	308	0	ENST00000325599.8:c.1111G>A	p.Glu371Lys	p.E371K	ENST00000325599	NM_018130.2	371	Gaa/Aaa	10/11	1	2	FACETS	0.785	0.624	0.969	0.785	0.624	0.969	CLONAL	1	TRUE	1	0.175524218469342	2		308	392	SUCCESS
ATR	545	MSKCC	GRCh37	3	142218550	142218550	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	74	376	0	ENST00000350721.4:c.5299A>G	p.Thr1767Ala	p.T1767A	ENST00000350721	NM_001184.3	1767	Aca/Gca	31/47	1	2	FACETS	1	0.896	1	1	0.983	1	CLONAL	2	TRUE	1	0.175524218469342	2		376	413	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575634	55575634	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	40	456	0	ENST00000288135.5:c.1160G>A	p.Gly387Glu	p.G387E	ENST00000288135	NM_000222.2	387	gGa/gAa	7/21	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.175524218469342	2		456	409	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055951	180055951	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	66	714	0	ENST00000261937.6:c.1034C>T	p.Ala345Val	p.A345V	ENST00000261937	NM_182925.4	345	gCc/gTc	8/30	1	2	FACETS	0.944	0.818	1	0.944	0.818	1	CLONAL	1	TRUE	1	0.175524218469342	2		714	797	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680362	30680362	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	88	583	0	ENST00000376406.3:c.1357A>C	p.Ser453Arg	p.S453R	ENST00000376406	NM_014641.2	453	Agt/Cgt	5/15	1	2	FACETS	0.764	0.677	0.857	1	0.979	1	SUBCLONAL	2	TRUE	1	0.175524218469342	2		583	656	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89791127	89791127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1439522660	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	30	156	0	ENST00000336032.3:c.514C>T	p.Pro172Ser	p.P172S	ENST00000336032	NM_006813.2	172	Ccc/Tcc	1/2	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.175524218469342	2		156	288	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553542	106553542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	49	387	0	ENST00000369096.4:c.1507G>A	p.Ala503Thr	p.A503T	ENST00000369096	NM_001198.3	503	Gcc/Acc	5/7	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.175524218469342	2		387	512	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627284	12627284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	111	414	0	ENST00000251849.4:c.1432G>A	p.Glu478Lys	p.E478K	ENST00000251849	NM_002880.3	478	Gaa/Aaa	14/17	0.231467958832799	2	FACETS	1	0.974	1	0.613	0.555	0.674	INDETERMINATE	1	TRUE	0	0.421792418458753	2		414	429	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625164	69625164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115452181	NA	P-0042402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	41	851	0	ENST00000334134.2:c.629G>A	p.Arg210Gln	p.R210Q	ENST00000334134	NM_005247.2	210	cGg/cAg	3/3	0.231467958832799	2	FACETS	0.328	0.272	0.39	0.164	0.136	0.195	INDETERMINATE	1	TRUE	0	0.421792418458753	2		851	593	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600369	10600369	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	289	850	0	ENST00000171111.5:c.1486G>T	p.Glu496Ter	p.E496*	ENST00000171111	NM_203500.1	496	Gag/Tag	4/6	0.314559991325622	2	FACETS	0.883	0.834	0.932	0.883	0.834	0.932	CLONAL	2	TRUE	0	0.421792418458753	2		850	776	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917023	50917023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145473716	NA	P-0042402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	47	692	0	ENST00000440232.2:c.2275G>A	p.Val759Ile	p.V759I	ENST00000440232	NM_002691.3	759	Gtc/Atc	19/27	0.423077324575121	1	FACETS	0.323	0.272	0.379	0.323	0.272	0.379	SUBCLONAL	1	TRUE	0	0.421792418458753	1		692	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578525	7578525	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519976	NA	P-0042402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	274	936	0	ENST00000269305.4:c.405C>G	p.Cys135Trp	p.C135W	ENST00000269305	NM_001126112.2	135	tgC/tgG	5/11	0.408752034842527	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.421792418458753	1		936	871	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449727	8449727	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs772305581	NA	P-0042402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	174	607	0	ENST00000356435.5:c.3986C>T	p.Pro1329Leu	p.P1329L	ENST00000356435		1329	cCg/cTg	23/35	0.314559991325622	2	FACETS	1	0.99	1	0.737	0.682	0.792	CLONAL	1	TRUE	0	0.421792418458753	2		607	560	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076745	72076745	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	98	560	0	ENST00000357731.5:c.752C>A	p.Pro251Gln	p.P251Q	ENST00000357731	NM_173808.2	251	cCg/cAg	5/7	1	2	FACETS	0.751	0.671	0.836	0.751	0.671	0.836	SUBCLONAL	1	TRUE	1	0.421792418458753	2		560	619	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612754	228612754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	284	698	0	ENST00000366696.1:c.273G>A	p.Met91Ile	p.M91I	ENST00000366696	NM_003493.2	91	atG/atA	1/1	0.421792418458753	2	FACETS	0.967	0.915	1	0.967	0.915	1	CLONAL	2	TRUE	0	0.421792418458753	2		698	696	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682371	52682371	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	80	300	0	ENST00000394830.3:c.802C>T	p.Gln268Ter	p.Q268*	ENST00000394830	NM_018313.4	268	Caa/Taa	8/30	0.231467958832799	2	FACETS	1	0.959	1	0.589	0.523	0.658	INDETERMINATE	1	TRUE	0	0.421792418458753	2		300	322	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519036	66519036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	49	431	0	ENST00000358598.2:c.317C>T	p.Thr106Met	p.T106M	ENST00000358598	NM_212471.2	106	aCg/aTg	3/11	0.172891930414698	3	FACETS	0.529	0.448	0.618	0.176	0.149	0.206	INDETERMINATE	1	TRUE	0	0.421792418458753	3		431	532	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699514	117699514	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	33	361	0	ENST00000369458.3:c.127G>T	p.Ala43Ser	p.A43S	ENST00000369458	NM_024626.3	43	Gcc/Tcc	3/6	0.423077324575121	1	FACETS	0.466	0.381	0.561	0.466	0.381	0.561	SUBCLONAL	1	TRUE	0	0.421792418458753	1		361	265	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748370	162748370	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	123	342	0	ENST00000367921.3:c.2284G>T	p.Gly762Cys	p.G762C	ENST00000367921	NM_006182.2	762	Ggc/Tgc	17/18	0.28671556455996	5	FACETS	1	0.945	1	0.701	0.638	0.766	CLONAL	2	TRUE	2	0.421792418458753	5		342	453	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175916375	175916375	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	98	331	0	ENST00000367669.3:c.2134G>T	p.Glu712Ter	p.E712*	ENST00000367669	NM_022457.5	712	Gag/Tag	19/20	0.28671556455996	5	FACETS	0.834	0.748	0.924	0.556	0.498	0.616	CLONAL	2	TRUE	2	0.421792418458753	5		331	455	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607728	46607728	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	152	771	0	ENST00000263734.3:c.1917G>C	p.Trp639Cys	p.W639C	ENST00000263734	NM_001430.4	639	tgG/tgC	12/16	1	2	FACETS	0.919	0.842	1	0.919	0.842	1	CLONAL	1	TRUE	1	0.421792418458753	2		771	784	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356293	66356293	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	51	516	0	ENST00000273854.3:c.1204G>T	p.Ala402Ser	p.A402S	ENST00000273854	NM_004439.5	402	Gca/Tca	5/18	1	2	FACETS	0.499	0.424	0.58	0.499	0.424	0.58	SUBCLONAL	1	TRUE	1	0.421792418458753	2		516	485	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361213	66361213	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	76	349	0	ENST00000273854.3:c.959G>T	p.Gly320Val	p.G320V	ENST00000273854	NM_004439.5	320	gGc/gTc	4/18	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.421792418458753	2		349	354	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112025243	112025244	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0042402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	178	590	1	ENST00000368678.4:c.505_506delinsAA	p.Pro169Lys	p.P169K	ENST00000368678		169	CCa/AAa	6/13	0.345089166644355	2	FACETS	1	0.99	1	0.743	0.689	0.798	CLONAL	1	TRUE	0	0.421792418458753	2		591	568	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92300822	92300822	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	68	436	1	ENST00000265734.4:c.565G>T	p.Glu189Ter	p.E189*	ENST00000265734	NM_001259.6	189	Gaa/Taa	5/8	0.187728499540232	4	FACETS	0.765	0.666	0.873	0.383	0.333	0.437	INDETERMINATE	1	TRUE	2	0.421792418458753	4		437	599	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945075	151945075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	31	430	0	ENST00000262189.6:c.2444C>T	p.Thr815Ile	p.T815I	ENST00000262189	NM_170606.2	815	aCt/aTt	14/59	0.187728499540232	4	FACETS	0.468	0.378	0.569	0.234	0.189	0.285	INDETERMINATE	1	TRUE	2	0.421792418458753	4		430	447	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485295	8485295	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	130	482	0	ENST00000356435.5:c.3085G>T	p.Val1029Leu	p.V1029L	ENST00000356435		1029	Gta/Tta	18/35	0.314559991325622	2	FACETS	1	0.981	1	0.635	0.58	0.693	CLONAL	1	TRUE	0	0.421792418458753	2		482	485	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499700	8499700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	148	532	0	ENST00000356435.5:c.2269G>A	p.Gly757Ser	p.G757S	ENST00000356435		757	Ggt/Agt	14/35	0.314559991325622	2	FACETS	0.758	0.698	0.82	0.758	0.698	0.82	SUBCLONAL	2	TRUE	0	0.421792418458753	2		532	463	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0042417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	302	346	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.386288261299363	7	FACETS	0.967	0.919	1	0.805	0.765	0.846	CLONAL	5	TRUE	1	0.386288261299363	7		346	636	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971124	21971125	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0042417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	85	418	0	ENST00000304494.5:c.233_234del	p.Leu78HisfsTer41	p.L78Hfs*41	ENST00000304494	NM_000077.4	78	cTC/c	2/3	0.386288261299363	1	FACETS	0.973	0.866	1	0.973	0.866	1	CLONAL	1	TRUE	0	0.386288261299363	1		418	365	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032098	26032098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773862626	NA	P-0042417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	99	386	0	ENST00000244661.2:c.191G>A	p.Arg64Gln	p.R64Q	ENST00000244661	NM_003537.3	64	cGg/cAg	1/1	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.386288261299363	2		386	432	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711873	89711873	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs587781784	NA	P-0042417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	90	270	0	ENST00000371953.3:c.493-2A>G		p.X165_splice	ENST00000371953	NM_000314.4	165			0.386288261299363	1	FACETS	0.767	0.692	0.844	1	0.983	1	SUBCLONAL	2	TRUE	0	0.386288261299363	1		270	245	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830734	156830734	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	13	73	0	ENST00000524377.1:c.8G>C	p.Arg3Pro	p.R3P	ENST00000524377	NM_002529.3	3	cGa/cCa	1/17	0.373863895292495	3	FACETS	1	0.737	1	0.339	0.246	0.448	CLONAL	1	TRUE	0	0.386288261299363	3		73	79	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236197	108236197	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555152033	NA	P-0042417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	124	462	0	ENST00000278616.4:c.9133C>T	p.Leu3045Phe	p.L3045F	ENST00000278616	NM_000051.3	3045	Ctc/Ttc	63/63	0.386288261299363	3	FACETS	1	0.973	1	0.6	0.544	0.659	CLONAL	1	TRUE	1	0.386288261299363	3		462	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578543	7578546	+	frameshift_variant	Frame_Shift_Del	DEL	GGCA	GGCA	-	novel	NA	P-0042417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	250	730	0	ENST00000269305.4:c.384_387del	p.Ala129SerfsTer40	p.A129Sfs*40	ENST00000269305	NM_001126112.2	128	ccTGCC/cc	5/11	0.386288261299363	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.386288261299363	1		730	781	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271364	18271364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	95	554	0	ENST00000222254.8:c.406G>A	p.Glu136Lys	p.E136K	ENST00000222254	NM_005027.3	136	Gaa/Aaa	3/16	0.207169578519586	3	FACETS	0.917	0.817	1	0.458	0.408	0.512	INDETERMINATE	1	TRUE	1	0.386288261299363	3		554	640	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940056	76940056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1353833841	NA	P-0042417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	70	479	0	ENST00000373344.5:c.692G>A	p.Cys231Tyr	p.C231Y	ENST00000373344	NM_000489.3	231	tGt/tAt	9/35	0.207169578519586	3	FACETS	0.994	0.87	1	0.497	0.435	0.564	INDETERMINATE	1	TRUE	1	0.386288261299363	3		479	435	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0042440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	72	236	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.995	0.88	1	0.995	0.88	1	CLONAL	1	TRUE	1	0.576841927257223	2		236	251	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309845	104309845	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060501109	NA	P-0042440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	96	310	0	ENST00000369902.3:c.436C>T	p.Arg146Ter	p.R146*	ENST00000369902	NM_016169.3	146	Cga/Tga	3/12	0.576841927257223	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.576841927257223	1		310	221	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	55	369	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.3	1	FACETS	0.947	0.811	1	0.947	0.811	1	CLONAL	1	TRUE	0	0.19	1		369	553	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0042477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	15	83	0				ENST00000310581	NM_198253.2	-/1132			0.0795055567105516	0	FACETS	0.711	0.521	0.936			1	INDETERMINATE	1	TRUE	0	0.19	0		83	180	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500304	99500304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45512296	NA	P-0042477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	40	436	1	ENST00000268035.6:c.3737G>A	p.Arg1246His	p.R1246H	ENST00000268035	NM_000875.3	1246	cGc/cAc	21/21	1	2	FACETS	0.693	0.574	0.825	0.693	0.574	0.825	SUBCLONAL	1	TRUE	1	0.19	2		437	608	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137186	64137186	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	35	322	0	ENST00000334205.4:c.1618G>T	p.Asp540Tyr	p.D540Y	ENST00000334205	NM_003942.2	540	Gac/Tac	14/17	1	2	FACETS	0.657	0.537	0.791	0.657	0.537	0.791	SUBCLONAL	1	TRUE	1	0.19	2		322	561	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181346	185181346	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	33	257	0	ENST00000265026.3:c.1287G>C	p.Trp429Cys	p.W429C	ENST00000265026	NM_004721.4	429	tgG/tgC	8/14	1	2	FACETS	0.954	0.778	1	0.954	0.778	1	CLONAL	1	TRUE	1	0.19	2		257	364	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524636	106524636	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	19	201	0	ENST00000359195.3:c.2797G>T	p.Ala933Ser	p.A933S	ENST00000359195	NM_002649.2	933	Gca/Tca	9/11	1	2	FACETS	0.571	0.433	0.735	0.571	0.433	0.735	SUBCLONAL	1	TRUE	1	0.19	2		201	350	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039395	47039395	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	62	503	0	ENST00000377604.3:c.1018C>T	p.Gln340Ter	p.Q340*	ENST00000377604	NM_001204468.1	340	Caa/Taa	10/24	1	2	FACETS	0.938	0.809	1	0.938	0.809	1	CLONAL	1	TRUE	1	0.19	2		503	696	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411870	63411870	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	62	709	0	ENST00000330258.3:c.1297C>A	p.His433Asn	p.H433N	ENST00000330258	NM_152424.3	433	Cac/Aac	2/2	1	2	FACETS	0.724	0.623	0.833	0.724	0.623	0.833	SUBCLONAL	1	TRUE	1	0.19	2		709	902	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220295	55220295	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	1471	911	0	ENST00000275493.2:c.685A>T	p.Ser229Cys	p.S229C	ENST00000275493	NM_005228.3	229	Agt/Tgt	6/28	0.229270559274523	19	FACETS	0.988	0.969	1	0.988	0.969	1	CLONAL	17	TRUE	2	0.229270559274523	19		911	2253	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245440	46245440	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	83	484	0	ENST00000334344.6:c.3536del	p.Asn1179IlefsTer9	p.N1179Ifs*9	ENST00000334344	NM_152641.2	1178	ccA/cc	15/21	0.229270559274523	5	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	3	0.229270559274523	5		484	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0042495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	198	812	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.323006331682252	2		812	852	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0042495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	239	445	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.323006331682252	3	FACETS	0.884	0.836	0.933	1	0.989	1	CLONAL	4	TRUE	0	0.323006331682252	3		445	486	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs371769427	NA	P-0042495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	66	331	0	ENST00000291552.4:c.101C>A	p.Ser34Tyr	p.S34Y	ENST00000291552	NM_006758.2	34	tCt/tAt	2/8	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.323006331682252	2		331	340	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952052	178952052	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	39	397	0	ENST00000263967.3:c.3107T>C	p.Leu1036Ser	p.L1036S	ENST00000263967	NM_006218.2	1036	tTg/tCg	21/21	1	2	FACETS	0.986	0.823	1	0.986	0.823	1	CLONAL	1	TRUE	1	0.323006331682252	2		397	245	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100070	27100070	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0042495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	364	764	1	ENST00000324856.7:c.3867-1G>A		p.X1289_splice	ENST00000324856	NM_006015.4	1289			0.323006331682252	3	FACETS	0.939	0.898	0.979	1	0.994	1	CLONAL	4	TRUE	0	0.323006331682252	3		765	697	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562430	21562430	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	120	477	0	ENST00000382592.4:c.1489G>A	p.Ala497Thr	p.A497T	ENST00000382592	NM_014572.2	497	Gca/Aca	4/8	1	2	FACETS	0.76	0.69	0.833	1	0.986	1	SUBCLONAL	2	TRUE	1	0.323006331682252	2		477	489	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663428	67663440	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGACAGTGGTAA	CTGACAGTGGTAA	-	novel	NA	P-0042495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	40	321	0	ENST00000264010.4:c.1829_1837+4del		p.X610_splice	ENST00000264010	NM_006565.3	610		10/12	1	2	FACETS	0.971	0.813	1	0.971	0.813	1	CLONAL	1	TRUE	1	0.323006331682252	2		321	255	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508274	106508274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778022267	NA	P-0042495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	52	461	0	ENST00000359195.3:c.268C>T	p.Arg90Trp	p.R90W	ENST00000359195	NM_002649.2	90	Cgg/Tgg	2/11	1	2	FACETS	0.805	0.687	0.933	0.805	0.687	0.933	CLONAL	1	TRUE	1	0.323006331682252	2		461	400	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560464	95560464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	32	614	0	ENST00000393063.1:c.5125G>A	p.Asp1709Asn	p.D1709N	ENST00000393063	NM_030621.3	1709	Gat/Aat	25/28	1	2	FACETS	0.492	0.398	0.598	0.492	0.398	0.598	SUBCLONAL	1	FALSE	1	0.232098805567738	2		614	561	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	114	320	1				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.941	1			1	INDETERMINATE	1	TRUE	NA	0.616681425763097	2		321	354	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717715	89717716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587782341	NA	P-0042515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	169	499	0	ENST00000371953.3:c.741dup	p.Pro248ThrfsTer5	p.P248Tfs*5	ENST00000371953	NM_000314.4	247	tta/ttAa	7/9	0.616681425763097	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.616681425763097	1		499	373	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166422	118166422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	103	393	0	ENST00000369448.3:c.932G>A	p.Arg311His	p.R311H	ENST00000369448	NM_017709.3	311	cGc/cAc	2/2	1	2	FACETS	0.764	0.688	0.844	0.764	0.688	0.844	SUBCLONAL	1	TRUE	1	0.616681425763097	2		393	437	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447456	187447456	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	240	767	0	ENST00000232014.4:c.737C>G	p.Thr246Ser	p.T246S	ENST00000232014	NM_001130845.1	246	aCt/aGt	5/10	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.616681425763097	2		767	775	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959093	2959093	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	319	900	0	ENST00000396946.4:c.2423A>G	p.Tyr808Cys	p.Y808C	ENST00000396946	NM_032415.4	808	tAc/tGc	18/25	0.616681425763097	3	FACETS	0.989	0.933	1	0.495	0.466	0.524	CLONAL	1	TRUE	1	0.616681425763097	3		900	1368	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808844	1808844	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	107	1043	0	ENST00000260795.2:c.2276A>C	p.Glu759Ala	p.E759A	ENST00000260795		759	gAg/gCg	17/17	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.616681425763097	NA		1043	1242	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0042526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	42	426	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.329861933602709	1	FACETS	0.967	0.815	1	0.967	0.815	1	CLONAL	1	TRUE	0	0.329861933602709	1		426	220	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577135	7577135	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	93	665	0	ENST00000269305.4:c.803A>T	p.Asn268Ile	p.N268I	ENST00000269305	NM_001126112.2	268	aAc/aTc	8/11	0.329861933602709	1	FACETS	0.717	0.638	0.801	0.717	0.638	0.801	SUBCLONAL	1	TRUE	0	0.329861933602709	1		665	657	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492784	56492784	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	64	550	0	ENST00000407977.2:c.155C>T	p.Pro52Leu	p.P52L	ENST00000407977		52	cCc/cTc	2/10	1	2	FACETS	0.973	0.846	1	0.973	0.846	1	CLONAL	1	TRUE	1	0.329861933602709	2		550	399	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346338	73346338	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	18	314	0	ENST00000377767.4:c.1462G>T	p.Asp488Tyr	p.D488Y	ENST00000377767	NM_014953.3	488	Gat/Tat	10/21	0.329861933602709	1	FACETS	0.86	0.657	1	0.86	0.657	1	CLONAL	1	TRUE	0	0.329861933602709	1		314	106	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867412	35867412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1419637074	NA	P-0042526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	16	321	1	ENST00000303115.3:c.226G>A	p.Ala76Thr	p.A76T	ENST00000303115	NM_002185.3	76	Gcc/Acc	3/8	0.239099276832256	1	FACETS	0.536	0.399	0.698	0.536	0.399	0.698	SUBCLONAL	1	TRUE	0	0.329861933602709	1		322	151	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543330	65543330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	89	602	0	ENST00000358664.4:c.347C>T	p.Pro116Leu	p.P116L	ENST00000358664	NM_002382.4	116	cCc/cTc	5/5	0.239099276832256	1	FACETS	0.657	0.582	0.736	0.657	0.582	0.736	SUBCLONAL	1	TRUE	0	0.329861933602709	1		602	686	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44919321	44919321	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	45	458	0	ENST00000377967.4:c.1249C>G	p.Pro417Ala	p.P417A	ENST00000377967	NM_021140.2	417	Cct/Gct	13/29	1	2	FACETS	0.724	0.61	0.849	0.724	0.61	0.849	SUBCLONAL	1	TRUE	1	0.329861933602709	2		458	377	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782334	9782334	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	110	739	0	ENST00000377346.4:c.2267T>A	p.Met756Lys	p.M756K	ENST00000377346	NM_005026.3	756	aTg/aAg	18/24	1	2	FACETS	0.763	0.685	0.846	0.763	0.685	0.846	SUBCLONAL	1	TRUE	1	0.329861933602709	2		739	874	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317082	11317082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	82	617	1	ENST00000361445.4:c.412G>A	p.Asp138Asn	p.D138N	ENST00000361445	NM_004958.3	138	Gac/Aac	4/58	1	2	FACETS	0.681	0.6	0.768	0.681	0.6	0.768	SUBCLONAL	1	TRUE	1	0.329861933602709	2		618	730	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426785	121426785	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	122	644	0	ENST00000257555.6:c.476G>T	p.Arg159Leu	p.R159L	ENST00000257555		159	cGg/cTg	2/10	0.329861933602709	1	FACETS	0.959	0.869	1	0.959	0.869	1	CLONAL	1	TRUE	0	0.329861933602709	1		644	644	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246830	41246830	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886040313	NA	P-0042526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	38	324	0	ENST00000357654.3:c.718C>T	p.Gln240Ter	p.Q240*	ENST00000357654	NM_007294.3	240	Caa/Taa	10/23	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.329861933602709	2		324	184	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56801411	56801411	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	28	471	0	ENST00000337432.4:c.915G>A	p.Trp305Ter	p.W305*	ENST00000337432	NM_058216.2	305	tgG/tgA	7/9	1	2	FACETS	0.933	0.752	1	0.933	0.752	1	CLONAL	1	TRUE	1	0.329861933602709	2		471	182	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120019	70120019	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	10	65	0	ENST00000245479.2:c.1021G>T	p.Ala341Ser	p.A341S	ENST00000245479	NM_000346.3	341	Gcg/Tcg	3/3	1	2	FACETS	0.612	0.418	0.851	0.612	0.418	0.851	SUBCLONAL	1	TRUE	1	0.329861933602709	2		65	99	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2220170	2220170	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	124	795	0	ENST00000398665.3:c.2755G>T	p.Gly919Cys	p.G919C	ENST00000398665	NM_032482.2	919	Ggt/Tgt	23/28	0.317632969166517	1	FACETS	0.785	0.71	0.864	0.785	0.71	0.864	SUBCLONAL	1	TRUE	0	0.329861933602709	1		795	800	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538332	9538332	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	22	456	0	ENST00000353224.5:c.1666C>A	p.Leu556Ile	p.L556I	ENST00000353224	NM_177990.2	556	Ctc/Atc	7/10	1	2	FACETS	0.505	0.392	0.636	0.505	0.392	0.636	SUBCLONAL	1	TRUE	1	0.329861933602709	2		456	264	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419849	41419849	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	54	444	0	ENST00000373198.4:c.472C>A	p.Pro158Thr	p.P158T	ENST00000373198	NM_133170.3	158	Cca/Aca	3/32	1	2	FACETS	0.692	0.592	0.802	0.692	0.592	0.802	SUBCLONAL	1	TRUE	1	0.329861933602709	2		444	473	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045999	26045999	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1277418855	NA	P-0042526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	60	369	0	ENST00000540144.1:c.361A>T	p.Met121Leu	p.M121L	ENST00000540144	NM_003531.2	121	Atg/Ttg	1/1	1	2	FACETS	0.983	0.851	1	0.983	0.851	1	CLONAL	1	TRUE	1	0.329861933602709	2		369	370	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29195803	29195803	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	53	708	0	ENST00000240100.2:c.795C>A	p.Tyr265Ter	p.Y265*	ENST00000240100	NM_001394.6	265	taC/taA	3/4	0.239099276832256	1	FACETS	0.48	0.409	0.558	0.48	0.409	0.558	SUBCLONAL	1	TRUE	0	0.329861933602709	1		708	559	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356822	70356822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751294090	NA	P-0042526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	136	752	0	ENST00000374080.3:c.5494C>T	p.Leu1832Phe	p.L1832F	ENST00000374080		1832	Ctt/Ttt	38/45	1	2	FACETS	0.906	0.823	0.993	0.906	0.823	0.993	CLONAL	1	TRUE	1	0.329861933602709	2		752	910	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211877	123211877	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	22	435	0	ENST00000218089.9:c.2744G>T	p.Cys915Phe	p.C915F	ENST00000218089	NM_001042749.1	915	tGt/tTt	27/35	1	2	FACETS	0.981	0.769	1	0.981	0.769	1	CLONAL	1	TRUE	1	0.329861933602709	2		435	136	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0042533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	75	743	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	1	2	FACETS	0.355	0.31	0.404	0.355	0.31	0.404	SUBCLONAL	1	TRUE	1	0.46	2		743	918	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141528	11141528	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	44	722	0	ENST00000358026.2:c.3505G>T	p.Asp1169Tyr	p.D1169Y	ENST00000358026	NM_001128849.1	1169	Gac/Tac	25/36	1	2	FACETS	0.252	0.21	0.298	0.252	0.21	0.298	SUBCLONAL	1	TRUE	1	0.46	2		722	759	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0042585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	189	566	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.286679001732545	3	FACETS	0.963	0.893	1	0.963	0.893	1	CLONAL	2	TRUE	1	0.343960679324617	3		566	669	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0042585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	136	673	0				ENST00000310581	NM_198253.2	-/1132			0.298996093877845	2	FACETS	0.93	0.854	1	0.93	0.854	1	CLONAL	2	TRUE	0	0.343960679324617	2		673	425	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483877	88483877	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	75	664	1	ENST00000360948.2:c.1693G>A	p.Asp565Asn	p.D565N	ENST00000360948	NM_001012338.2	565	Gac/Aac	14/19	1	2	FACETS	0.815	0.716	0.922	0.815	0.716	0.922	CLONAL	1	TRUE	1	0.343960679324617	2		665	535	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146487	185146487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	45	471	0	ENST00000265026.3:c.118C>T	p.Pro40Ser	p.P40S	ENST00000265026	NM_004721.4	40	Ccc/Tcc	2/14	1	2	FACETS	0.713	0.601	0.836	0.713	0.601	0.836	SUBCLONAL	1	TRUE	1	0.343960679324617	2		471	367	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299856	15299856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1188038977	NA	P-0042585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	167	851	1	ENST00000263388.2:c.1322G>A	p.Arg441Gln	p.R441Q	ENST00000263388	NM_000435.2	441	cGa/cAa	8/33	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.343960679324617	2		852	746	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609846	117609846	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1442895655	NA	P-0042585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	85	575	1	ENST00000368508.3:c.6853G>A	p.Glu2285Lys	p.E2285K	ENST00000368508	NM_002944.2	2285	Gaa/Aaa	43/43	1	2	FACETS	0.985	0.873	1	0.985	0.873	1	CLONAL	1	TRUE	1	0.343960679324617	2		576	502	SUCCESS
APC	324	MSKCC	GRCh37	5	112177484	112177484	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	89	328	0	ENST00000257430.4:c.6193C>T	p.Pro2065Ser	p.P2065S	ENST00000257430	NM_000038.5	2065	Ccc/Tcc	16/16	0.335869740017378	2	FACETS	0.868	0.779	0.961	0.868	0.779	0.961	CLONAL	2	TRUE	0	0.343960679324617	2		328	298	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37059090	37059090	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs63750144	NA	P-0042585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	56	414	0	ENST00000231790.2:c.884G>A	p.Ser295Asn	p.S295N	ENST00000231790	NM_000249.3	295	aGt/aAt	10/19	1	2	FACETS	0.841	0.723	0.969	0.841	0.723	0.969	CLONAL	1	TRUE	1	0.343960679324617	2		414	387	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69230522	69230522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	37	340	1	ENST00000462284.1:c.911C>T	p.Ser304Phe	p.S304F	ENST00000462284	NM_002392.5	304	tCc/tTc	10/11	1	2	FACETS	0.631	0.521	0.753	0.631	0.521	0.753	SUBCLONAL	1	TRUE	1	0.343960679324617	2		341	341	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793398	242793398	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	88	886	0	ENST00000334409.5:c.679G>A	p.Asp227Asn	p.D227N	ENST00000334409	NM_005018.2	227	Gat/Aat	5/5	1	2	FACETS	0.827	0.733	0.926	0.827	0.733	0.926	CLONAL	1	TRUE	1	0.343960679324617	2		886	619	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719947	18719947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437834329	NA	P-0042585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	67	443	0	ENST00000266497.5:c.3844C>T	p.His1282Tyr	p.H1282Y	ENST00000266497		1282	Cat/Tat	27/31	1	2	FACETS	0.891	0.777	1	0.891	0.777	1	CLONAL	1	TRUE	1	0.343960679324617	2		443	437	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690570	88690570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	54	433	1	ENST00000360948.2:c.460G>A	p.Glu154Lys	p.E154K	ENST00000360948	NM_001012338.2	154	Gaa/Aaa	5/19	1	2	FACETS	0.671	0.574	0.777	0.671	0.574	0.777	SUBCLONAL	1	TRUE	1	0.343960679324617	2		434	468	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117753470	117753470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1248358199	NA	P-0042585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	55	530	0	ENST00000369458.3:c.8C>T	p.Ser3Phe	p.S3F	ENST00000369458	NM_024626.3	3	tCc/tTc	1/6	0.286679001732545	3	FACETS	0.786	0.673	0.909	0.393	0.336	0.455	CLONAL	1	TRUE	1	0.343960679324617	3		530	477	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466287	120466287	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	126	450	0	ENST00000256646.2:c.4832C>T	p.Pro1611Leu	p.P1611L	ENST00000256646	NM_024408.3	1611	cCt/cTt	26/34	0.286679001732545	3	FACETS	0.88	0.801	0.961	0.88	0.801	0.961	CLONAL	2	TRUE	1	0.343960679324617	3		450	488	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63661930	63661930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749069080	NA	P-0042585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	54	333	0	ENST00000279873.7:c.34C>T	p.Pro12Ser	p.P12S	ENST00000279873	NM_032199.2	12	Ccg/Tcg	2/10	1	2	FACETS	0.86	0.738	0.993	0.86	0.738	0.993	CLONAL	1	TRUE	1	0.343960679324617	2		333	365	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	364561	364561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	71	832	0	ENST00000262320.3:c.1001C>T	p.Ser334Phe	p.S334F	ENST00000262320	NM_003502.3	334	tCc/tTc	3/11	1	2	FACETS	0.616	0.537	0.701	0.616	0.537	0.701	SUBCLONAL	1	TRUE	1	0.343960679324617	2		832	670	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110784	2110786	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	rs137854367	NA	P-0042585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	84	804	0	ENST00000219476.3:c.1093_1095del	p.Ile365del	p.I365del	ENST00000219476	NM_000548.3	363	aaCATc/aac	11/42	1	2	FACETS	0.787	0.695	0.884	0.787	0.695	0.884	SUBCLONAL	1	TRUE	1	0.343960679324617	2		804	621	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220126	36220126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	183	788	0	ENST00000222270.7:c.4846G>A	p.Ala1616Thr	p.A1616T	ENST00000222270	NM_014727.1	1616	Gcg/Acg	22/37	0.296380621408514	2	FACETS	0.85	0.788	0.913	0.85	0.788	0.913	CLONAL	2	TRUE	0	0.343960679324617	2		788	626	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220138	36220138	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	182	770	0	ENST00000222270.7:c.4858G>T	p.Glu1620Ter	p.E1620*	ENST00000222270	NM_014727.1	1620	Gag/Tag	22/37	0.296380621408514	2	FACETS	0.858	0.795	0.922	0.858	0.795	0.922	CLONAL	2	TRUE	0	0.343960679324617	2		770	617	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224168	36224168	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1442182686	NA	P-0042585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	180	713	0	ENST00000222270.7:c.6718C>T	p.Leu2240Phe	p.L2240F	ENST00000222270	NM_014727.1	2240	Ctc/Ttc	28/37	0.296380621408514	2	FACETS	0.839	0.777	0.902	0.839	0.777	0.902	CLONAL	2	TRUE	0	0.343960679324617	2		713	624	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750491	41750491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	59	567	1	ENST00000226382.2:c.137C>T	p.Pro46Leu	p.P46L	ENST00000226382	NM_003924.3	46	cCg/cTg	1/3	1	2	FACETS	0.776	0.669	0.892	0.776	0.669	0.892	SUBCLONAL	1	TRUE	1	0.343960679324617	2		568	442	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515168	106515168	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	65	446	0	ENST00000359195.3:c.2311C>G	p.Leu771Val	p.L771V	ENST00000359195	NM_002649.2	771	Ctt/Gtt	5/11	0.286679001732545	3	FACETS	0.936	0.814	1	0.468	0.407	0.535	CLONAL	1	TRUE	1	0.343960679324617	3		446	473	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021667	69021667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	53	471	0	ENST00000288368.4:c.2955G>A	p.Met985Ile	p.M985I	ENST00000288368	NM_024870.2	985	atG/atA	25/40	1	2	FACETS	0.778	0.666	0.901	0.778	0.666	0.901	CLONAL	1	TRUE	1	0.343960679324617	2		471	396	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050648	69050648	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0042585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	51	351	0	ENST00000288368.4:c.3985-2A>G		p.X1329_splice	ENST00000288368	NM_024870.2	1329			1	2	FACETS	0.963	0.823	1	0.963	0.823	1	CLONAL	1	TRUE	1	0.343960679324617	2		351	308	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465629	8465629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	53	482	0	ENST00000356435.5:c.3551G>A	p.Arg1184Lys	p.R1184K	ENST00000356435		1184	aGa/aAa	21/35	0.343960679324617	1	FACETS	0.868	0.745	1	0.868	0.745	1	CLONAL	1	TRUE	0	0.343960679324617	1		482	294	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034413	123034414	+	missense_variant	Missense_Mutation	DNP	GA	GA	AC	novel	NA	P-0042585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	52	464	1	ENST00000355640.3:c.1170_1171delinsAC	p.Lys391Gln	p.K391Q	ENST00000355640		390	aaGAaa/aaACaa	6/7	1	2	FACETS	0.737	0.629	0.855	0.737	0.629	0.855	SUBCLONAL	1	TRUE	1	0.343960679324617	2		465	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782177	NA	P-0042593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	366	690	1	ENST00000269305.4:c.644G>T	p.Ser215Ile	p.S215I	ENST00000269305	NM_001126112.2	215	aGt/aTt	6/11	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	2	TRUE	NA	0.461019678485195	2		691	770	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024877	31024888	+	inframe_deletion	In_Frame_Del	DEL	TAATTATTCCTC	TAATTATTCCTC	-	novel	NA	P-0042593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	127	567	0	ENST00000375687.4:c.4364_4375del	p.Asn1455_Ser1458del	p.N1455_S1458del	ENST00000375687	NM_015338.5	1454	ttTAATTATTCCTCt/ttt	13/13	0.2754043680917	4	FACETS	0.914	0.827	1	0.457	0.413	0.503	INDETERMINATE	1	TRUE	2	0.461019678485195	4		567	881	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0042599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	70	426	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.969	0.848	1	0.969	0.848	1	CLONAL	1	TRUE	1	0.312002302329456	2		426	463	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222987	1222987	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	107	403	0	ENST00000326873.7:c.924G>T	p.Trp308Cys	p.W308C	ENST00000326873	NM_000455.4	308	tgG/tgT	8/10	0.292481746432001	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.312002302329456	1		403	574	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600323	10600323	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0042599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	96	532	0	ENST00000171111.5:c.1531+1G>T		p.X511_splice	ENST00000171111	NM_203500.1	511			0.292481746432001	1	FACETS	0.906	0.809	1	0.906	0.809	1	CLONAL	1	TRUE	0	0.312002302329456	1		532	573	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517766	187517766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258298769	NA	P-0042599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	62	236	1	ENST00000441802.2:c.12928C>T	p.Pro4310Ser	p.P4310S	ENST00000441802	NM_005245.3	4310	Ccc/Tcc	25/27	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.312002302329456	2		237	317	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827946	40827946	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	33	707	0	ENST00000373198.4:c.2482A>G	p.Thr828Ala	p.T828A	ENST00000373198	NM_133170.3	828	Acc/Gcc	17/32	0.313117184464316	3	FACETS	0.415	0.337	0.502	0.207	0.168	0.251	SUBCLONAL	1	TRUE	1	0.399326645954158	3		707	478	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0042657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	79	426	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.3	2		426	520	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472554	88472554	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	121	653	0	ENST00000360948.2:c.2001G>T	p.Met667Ile	p.M667I	ENST00000360948	NM_001012338.2	667	atG/atT	16/19	0.299441518745554	1	FACETS	0.991	0.896	1	0.991	0.896	1	CLONAL	1	TRUE	0	0.3	1		653	692	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220640	1220640	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690940	NA	P-0042657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	218	738	0	ENST00000326873.7:c.658C>T	p.Gln220Ter	p.Q220*	ENST00000326873	NM_000455.4	220	Cag/Tag	5/10	NA	2	FACETS	0.755	0.703	0.81			1	INDETERMINATE	2	TRUE	NA	0.3	2		738	962	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11269480	11269480	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	47	592	0	ENST00000361445.4:c.3690G>T	p.Leu1230Phe	p.L1230F	ENST00000361445	NM_004958.3	1230	ttG/ttT	25/58	0.104773833917777	0	FACETS	0.362	0.305	0.425			1	INDETERMINATE	1	TRUE	0	0.3	0		592	606	SUCCESS
ATM	472	MSKCC	GRCh37	11	108138042	108138042	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	136	293	0	ENST00000278616.4:c.2611G>T	p.Glu871Ter	p.E871*	ENST00000278616	NM_000051.3	871	Gaa/Taa	17/63	0.143005655880369	3	FACETS	0.885	0.808	0.966	0.59	0.538	0.644	INDETERMINATE	2	TRUE	0	0.3	3		293	589	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154395	2154395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	72	981	0	ENST00000434045.2:c.533C>T	p.Ser178Phe	p.S178F	ENST00000434045	NM_001127598.1	178	tCc/tTc	5/5	0.139448104499945	0	FACETS	0.357	0.311	0.407			1	INDETERMINATE	1	TRUE	0	0.3	0		981	941	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413581	32413581	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	92	487	0	ENST00000332351.3:c.1369C>A	p.Gln457Lys	p.Q457K	ENST00000332351	NM_024426.4	457	Cag/Aag	9/10	0.143005655880369	3	FACETS	1	0.969	1	0.418	0.372	0.466	INDETERMINATE	1	TRUE	0	0.3	3		487	563	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236234	108236234	+	stop_lost	Nonstop_Mutation	SNP	G	G	T	novel	NA	P-0042657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	59	548	0	ENST00000278616.4:c.9170G>T	p.Ter3057LeuextTer29	p.*3057Lext*29	ENST00000278616	NM_000051.3	3057	tGa/tTa	63/63	0.143005655880369	3	FACETS	0.643	0.552	0.741	0.214	0.184	0.247	INDETERMINATE	1	TRUE	0	0.3	3		548	704	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687337	37687337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778522020	NA	P-0042657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	56	605	0	ENST00000447079.4:c.4241C>T	p.Pro1414Leu	p.P1414L	ENST00000447079	NM_015083.1	1414	cCg/cTg	14/14	0.143005655880369	3	FACETS	0.542	0.463	0.629	0.181	0.154	0.21	INDETERMINATE	1	TRUE	0	0.3	3		605	792	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954223	17954223	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	137	804	2	ENST00000458235.1:c.386T>C	p.Leu129Pro	p.L129P	ENST00000458235	NM_000215.3	129	cTt/cCt	4/24	1	2	FACETS	0.993	0.902	1	0.993	0.902	1	CLONAL	1	TRUE	1	0.3	2		806	920	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505581	25505581	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0042657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	82	841	0	ENST00000264709.3:c.178-1G>C		p.X60_splice	ENST00000264709	NM_175629.2	60			1	2	FACETS	0.56	0.492	0.632	0.56	0.492	0.632	SUBCLONAL	1	TRUE	1	0.3	2		841	977	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142949975	142949975	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	97	585	0	ENST00000262992.4:c.2735A>T	p.Tyr912Phe	p.Y912F	ENST00000262992	NM_001101669.1	912	tAc/tTc	24/24	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.3	2		585	612	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045913	143045913	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	80	405	0	ENST00000262992.4:c.1721A>T	p.Glu574Val	p.E574V	ENST00000262992	NM_001101669.1	574	gAg/gTg	17/24	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.3	2		405	456	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635120	87635120	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0042657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	39	332	0	ENST00000277120.3:c.2173-1G>T		p.X725_splice	ENST00000277120		725			1	2	FACETS	0.628	0.521	0.747	0.628	0.521	0.747	SUBCLONAL	1	TRUE	1	0.3	2		332	414	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	202	320	1				ENST00000310581	NM_198253.2	-/1132			0.372815978008989	3	FACETS	0.941	0.882	1	0.941	0.882	1	CLONAL	2	TRUE	1	0.560658291638918	3		321	490	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0042679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	24	351	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.163	0.127	0.205	0.163	0.127	0.205	SUBCLONAL	1	TRUE	1	0.560658291638918	2		351	525	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656914	45656914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	242	766	0	ENST00000407780.3:c.242G>A	p.Arg81Gln	p.R81Q	ENST00000407780	NM_001283052.1	81	cGg/cAg	3/7	1	2	FACETS	0.914	0.855	0.976	0.914	0.855	0.976	CLONAL	1	TRUE	1	0.560658291638918	2		766	944	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439918	56439918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367688879	NA	P-0042679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	195	675	0	ENST00000407977.2:c.674G>A	p.Arg225His	p.R225H	ENST00000407977		225	cGc/cAc	6/10	1	2	FACETS	0.909	0.844	0.977	0.909	0.844	0.977	CLONAL	1	TRUE	1	0.560658291638918	2		675	765	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0042679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	216	684	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.560658291638918	2		684	707	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101194	41101194	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200107921	NA	P-0042679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	168	600	1	ENST00000373198.4:c.1162C>A	p.His388Asn	p.H388N	ENST00000373198	NM_133170.3	388	Cat/Aat	8/32	1	2	FACETS	0.971	0.897	1	0.971	0.897	1	CLONAL	1	TRUE	1	0.560658291638918	2		601	617	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204511986	204511986	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	101	349	0	ENST00000367182.3:c.586G>T	p.Ala196Ser	p.A196S	ENST00000367182	NM_001278516.1	196	Gct/Tct	8/11	0.332724206372387	1	FACETS	0.604	0.543	0.668	0.604	0.543	0.668	INDETERMINATE	1	TRUE	0	0.560658291638918	1		349	429	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724439	112724439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	154	505	0	ENST00000369452.4:c.323C>T	p.Ser108Phe	p.S108F	ENST00000369452	NM_007373.3	108	tCc/tTc	2/9	1	2	FACETS	0.807	0.74	0.876	0.807	0.74	0.876	CLONAL	1	TRUE	1	0.560658291638918	2		505	681	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022708	12022708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	152	503	0	ENST00000396373.4:c.814C>T	p.Pro272Ser	p.P272S	ENST00000396373	NM_001987.4	272	Ccc/Tcc	5/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.560658291638918	2		503	494	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041569	42041569	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs370986027	NA	P-0042679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	180	488	0	ENST00000219905.7:c.5764A>G	p.Ile1922Val	p.I1922V	ENST00000219905	NM_001164273.1	1922	Ata/Gta	17/24	1	2	FACETS	0.95	0.879	1	0.95	0.879	1	CLONAL	1	TRUE	1	0.560658291638918	2		488	676	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347661	89347661	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	164	746	0	ENST00000301030.4:c.5289G>C	p.Arg1763Ser	p.R1763S	ENST00000301030	NM_001256183.1	1763	agG/agC	9/13	1	2	FACETS	0.817	0.752	0.885	0.817	0.752	0.885	CLONAL	1	TRUE	1	0.560658291638918	2		746	716	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696617	47696617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	172	385	0	ENST00000347630.2:c.331G>A	p.Gly111Arg	p.G111R	ENST00000347630	NM_001007230.1	111	Gga/Aga	5/11	1	2	FACETS	0.96	0.887	1	0.96	0.887	1	CLONAL	1	TRUE	1	0.560658291638918	2		385	639	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376793	31376793	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs776562712	NA	P-0042679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	156	504	0	ENST00000328111.2:c.788G>A	p.Trp263Ter	p.W263*	ENST00000328111	NM_006892.3	263	tGg/tAg	7/23	1	2	FACETS	0.903	0.831	0.979	0.903	0.831	0.979	CLONAL	1	TRUE	1	0.560658291638918	2		504	616	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170015162	170015162	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368665283	NA	P-0042679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	440	553	3	ENST00000295797.4:c.1568G>A	p.Arg523Gln	p.R523Q	ENST00000295797	NM_002740.5	523	cGa/cAa	16/18	0.506411505695787	3	FACETS	0.945	0.911	0.978	0.945	0.911	0.978	CLONAL	3	TRUE	0	0.560658291638918	3		556	709	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522454	187522475	+	frameshift_variant	Frame_Shift_Del	DEL	TACATGACAACCGCATGCGTGG	TACATGACAACCGCATGCGTGG	-	novel	NA	P-0042679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	102	541	0	ENST00000441802.2:c.11588_11609del	p.Ser3863LeufsTer49	p.S3863Lfs*49	ENST00000441802	NM_005245.3	3863	tCCACGCATGCGGTTGTCATGTAt/tt	21/27	1	2	FACETS	0.611	0.547	0.678	0.611	0.547	0.678	SUBCLONAL	1	TRUE	1	0.560658291638918	2		541	596	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554910	187554911	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0042679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	155	404	0	ENST00000441802.2:c.4250_4251del	p.Leu1417ArgfsTer34	p.L1417Rfs*34	ENST00000441802	NM_005245.3	1417	cTT/c	7/27	1	2	FACETS	0.975	0.897	1	0.975	0.897	1	CLONAL	1	TRUE	1	0.560658291638918	2		404	567	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0042804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	22	431	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.392506664210213	1	FACETS	0.138	0.106	0.175	0.138	0.106	0.175	SUBCLONAL	1	TRUE	0	0.392506664210213	1		432	655	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0042804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	13	506	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.414	0.296	0.556	0.414	0.296	0.556	SUBCLONAL	1	TRUE	1	0.392506664210213	2		506	160	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0042804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	65	369	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.209548136034674	3	FACETS	1	0.97	1	0.468	0.41	0.531	INDETERMINATE	1	TRUE	0	0.392506664210213	3		369	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579327	7579327	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	133	616	0	ENST00000269305.4:c.360G>T	p.Lys120Asn	p.K120N	ENST00000269305	NM_001126112.2	120	aaG/aaT	4/11	0.392506664210213	1	FACETS	0.813	0.74	0.889	0.813	0.74	0.889	CLONAL	1	TRUE	0	0.392506664210213	1		616	670	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030378	49030378	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0042804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	22	248	0	ENST00000267163.4:c.1853C>G	p.Ser618Ter	p.S618*	ENST00000267163	NM_000321.2	618	tCa/tGa	19/27	0.392506664210213	1	FACETS	0.683	0.535	0.849	0.683	0.535	0.849	SUBCLONAL	1	TRUE	0	0.392506664210213	1		248	132	SUCCESS
AR	367	MSKCC	GRCh37	X	66943643	66943643	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1131691681	NA	P-0042804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	97	528	0	ENST00000374690.3:c.2723T>A	p.Leu908His	p.L908H	ENST00000374690	NM_000044.3	908	cTt/cAt	8/8	0.311025839486892	3	FACETS	0.999	0.892	1	0.499	0.446	0.556	CLONAL	1	TRUE	1	0.392506664210213	3		528	592	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0042809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	263	551	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.367612393812097	2	FACETS	0.914	0.86	0.969	0.914	0.86	0.969	CLONAL	2	TRUE	0	0.367612393812097	2		551	783	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874937	151874937	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	90	382	0	ENST00000262189.6:c.7601del	p.Pro2534GlnfsTer28	p.P2534Qfs*28	ENST00000262189	NM_170606.2	2534	cCa/ca	38/59	NA	2	FACETS	1	0.892	1			1	INDETERMINATE	1	TRUE	NA	0.367612393812097	2		382	489	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0042812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	59	442	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.212357229827925	3	FACETS	0.895	0.774	1	0.895	0.774	1	CLONAL	2	TRUE	1	0.214807288412451	3		442	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203436	NA	P-0042812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	352	943	0	ENST00000269305.4:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269305	NM_001126112.2	163	Tac/Cac	5/11	0.178249631884321	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	4	TRUE	0	0.214807288412451	4		943	943	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0042881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	214	328	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.670143550940306	4	FACETS	0.876	0.812	0.941	0.219	0.203	0.236	CLONAL	1	TRUE	0	0.670143550940306	4		328	1218	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665110	29665110	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658541	NA	P-0042881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	371	416	0	ENST00000356175.3:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000356175	NM_000267.3	2237	Cga/Tga	44/57	0.645003086642418	2	FACETS	0.9	0.865	0.935	0.9	0.865	0.935	CLONAL	2	TRUE	0	0.670143550940306	2		416	615	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807373	36807373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780619377	NA	P-0042881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	199	715	1	ENST00000373129.3:c.1291C>T	p.Arg431Cys	p.R431C	ENST00000373129	NM_032017.1	431	Cgc/Tgc	12/12	0.663911550784271	3	FACETS	0.792	0.734	0.853	0.264	0.244	0.285	SUBCLONAL	1	TRUE	0	0.670143550940306	3		716	1001	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0042881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	355	463	1	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.643805515217949	2	FACETS	0.913	0.877	0.949	0.913	0.877	0.949	CLONAL	2	TRUE	0	0.670143550940306	2		464	580	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864849	57864849	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	543	785	0	ENST00000228682.2:c.2326A>G	p.Thr776Ala	p.T776A	ENST00000228682	NM_005269.2	776	Acc/Gcc	12/12	0.645003086642418	2	FACETS	0.986	0.956	1	0.986	0.956	1	CLONAL	2	TRUE	0	0.670143550940306	2		785	822	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885568	111885568	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	275	774	0	ENST00000341259.2:c.1345G>A	p.Glu449Lys	p.E449K	ENST00000341259	NM_005475.2	449	Gag/Aag	7/8	0.645003086642418	2	FACETS	0.914	0.86	0.969	0.457	0.43	0.485	CLONAL	1	TRUE	0	0.670143550940306	2		774	898	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033844	49033844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853294	NA	P-0042881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	153	334	0	ENST00000267163.4:c.1981C>T	p.Arg661Trp	p.R661W	ENST00000267163	NM_000321.2	661	Cgg/Tgg	20/27	0.66849580448801	1	FACETS	0.896	0.832	0.959	0.896	0.832	0.959	CLONAL	1	TRUE	0	0.670143550940306	1		334	339	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560500	65560500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs387906651	NA	P-0042881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	329	413	0	ENST00000358664.4:c.97C>T	p.Arg33Ter	p.R33*	ENST00000358664	NM_002382.4	33	Cga/Tga	3/5	0.562403320086309	3	FACETS	1	0.994	1	0.829	0.795	0.862	CLONAL	2	TRUE	0	0.670143550940306	3		413	527	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862106	68862106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622198	NA	P-0042881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	195	486	1	ENST00000261769.5:c.2194C>T	p.Arg732Trp	p.R732W	ENST00000261769	NM_004360.3	732	Cgg/Tgg	14/16	0.645003086642418	2	FACETS	0.93	0.865	0.996	0.465	0.432	0.498	CLONAL	1	TRUE	0	0.670143550940306	2		487	626	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912664	NA	P-0042881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	493	724	3	ENST00000269305.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000269305	NM_001126112.2	337	cGc/cAc	10/11	0.645003086642418	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.670143550940306	2		727	734	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619328	1619328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769758535	NA	P-0042881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	290	772	0	ENST00000344749.5:c.1313G>A	p.Arg438Gln	p.R438Q	ENST00000344749	NM_001136139.2	438	cGg/cAg	15/19	0.645003086642418	2	FACETS	1	0.967	1	0.517	0.488	0.547	CLONAL	1	TRUE	0	0.670143550940306	2		772	837	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11027109	11027109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173812039	NA	P-0042881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	644	897	0	ENST00000327064.4:c.874G>A	p.Val292Ile	p.V292I	ENST00000327064	NM_199141.1	292	Gtc/Atc	7/16	0.645003086642418	2	FACETS	0.957	0.93	0.984	0.957	0.93	0.984	CLONAL	2	TRUE	0	0.670143550940306	2		897	1004	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141492	11141492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	561	716	0	ENST00000358026.2:c.3469C>T	p.Arg1157Trp	p.R1157W	ENST00000358026	NM_001128849.1	1157	Cgg/Tgg	25/36	0.645003086642418	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.670143550940306	2		716	834	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560898	9560898	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767455314	NA	P-0042881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	310	423	0	ENST00000353224.5:c.884C>T	p.Pro295Leu	p.P295L	ENST00000353224	NM_177990.2	295	cCg/cTg	4/10	0.645003086642418	2	FACETS	0.997	0.958	1	0.997	0.958	1	CLONAL	2	TRUE	0	0.670143550940306	2		423	464	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933803	49933803	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759370688	NA	P-0042881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	259	726	0	ENST00000296474.3:c.2474G>A	p.Arg825His	p.R825H	ENST00000296474	NM_002447.2	825	cGc/cAc	10/20	0.643805515217949	2	FACETS	0.94	0.884	0.998	0.47	0.442	0.499	CLONAL	1	TRUE	0	0.670143550940306	2		726	822	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518038	176518038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111435837	NA	P-0042881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	259	782	0	ENST00000292408.4:c.536C>T	p.Thr179Met	p.T179M	ENST00000292408	NM_213647.1	179	aCg/aTg	5/18	0.670143550940306	3	FACETS	0.916	0.858	0.977	0.458	0.429	0.489	CLONAL	1	TRUE	1	0.670143550940306	3		782	1126	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390606	139390606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1052013977	NA	P-0042881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	724	970	0	ENST00000277541.6:c.7585G>A	p.Val2529Ile	p.V2529I	ENST00000277541	NM_017617.3	2529	Gtc/Atc	34/34	0.645003086642418	2	FACETS	0.982	0.956	1	0.982	0.956	1	CLONAL	2	TRUE	0	0.670143550940306	2		970	1100	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424713	47424713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1387037979	NA	P-0042881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	509	744	2	ENST00000377045.4:c.521G>A	p.Arg174His	p.R174H	ENST00000377045	NM_001654.4	174	cGc/cAc	6/16	NA	2	FACETS	0.984	0.953	1			1	INDETERMINATE	2	TRUE	NA	0.670143550940306	2		746	772	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0042909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	36	431	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	NA	2	FACETS	0.662	0.543	0.796			1	INDETERMINATE	1	TRUE	NA	0.178099976678527	2		432	611	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0042909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	98	776	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	NA	2	FACETS	1	0.9	1			1	INDETERMINATE	2	TRUE	NA	0.178099976678527	2		777	547	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239124	98239124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745669155	NA	P-0042909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	11	338	0	ENST00000331920.6:c.1519G>A	p.Ala507Thr	p.A507T	ENST00000331920	NM_000264.3	507	Gct/Act	11/24	0.178099976678527	5	FACETS	0.9	0.623	1	0.3	0.207	0.414	CLONAL	1	TRUE	2	0.178099976678527	5		338	174	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046023	180046023	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1396816704	NA	P-0042909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	23	64	1	ENST00000261937.6:c.2848G>A	p.Ala950Thr	p.A950T	ENST00000261937	NM_182925.4	950	Gcg/Acg	20/30	1	2	FACETS	1	0.809	1	1	0.948	1	CLONAL	2	TRUE	1	0.178099976678527	2		65	126	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484164	120484164	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs782704056	NA	P-0042909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	23	410	0	ENST00000256646.2:c.2966A>G	p.Asn989Ser	p.N989S	ENST00000256646	NM_024408.3	989	aAt/aGt	18/34	0.178099976678527	5	FACETS	1	0.834	1	0.361	0.282	0.453	CLONAL	1	TRUE	2	0.178099976678527	5		410	302	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0042996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	42	422	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.21	2		422	372	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117365	115117365	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	40	385	0	ENST00000257566.3:c.809C>A	p.Thr270Lys	p.T270K	ENST00000257566	NM_016569.3	270	aCa/aAa	4/8	1	2	FACETS	0.634	0.526	0.755	0.634	0.526	0.755	SUBCLONAL	1	TRUE	1	0.21	2		385	601	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250256	133250256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745356467	NA	P-0042996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	58	611	1	ENST00000320574.5:c.1264C>T	p.His422Tyr	p.H422Y	ENST00000320574	NM_006231.2	422	Cat/Tat	13/49	1	2	FACETS	0.539	0.462	0.625	0.539	0.462	0.625	SUBCLONAL	1	TRUE	1	0.21	2		612	1024	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110043	115110043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	98	657	1	ENST00000257566.3:c.1835C>T	p.Ala612Val	p.A612V	ENST00000257566	NM_016569.3	612	gCg/gTg	8/8	1	2	FACETS	0.807	0.718	0.903	0.807	0.718	0.903	CLONAL	1	TRUE	1	0.21	2		658	1156	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554598	29554598	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	19	309	0	ENST00000356175.3:c.2383C>G	p.Pro795Ala	p.P795A	ENST00000356175	NM_000267.3	795	Cca/Gca	20/57	0.132468933178156	3	FACETS	0.6	0.455	0.771	0.3	0.227	0.386	SUBCLONAL	1	TRUE	1	0.21	3		309	333	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430928	181430928	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1233857840	NA	P-0042996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	76	675	1	ENST00000325404.1:c.780C>A	p.His260Gln	p.H260Q	ENST00000325404	NM_003106.3	260	caC/caA	1/1	0.159496182815647	1	FACETS	0.612	0.535	0.695	0.612	0.535	0.695	SUBCLONAL	1	TRUE	0	0.21	1		676	1059	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393412	139393412	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs780257585	NA	P-0042996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	147	752	1	ENST00000277541.6:c.6119A>G	p.Asn2040Ser	p.N2040S	ENST00000277541	NM_017617.3	2040	aAt/aGt	33/34	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.21	2		753	1235	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045190	47045190	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0042996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	71	579	0	ENST00000377604.3:c.2430+1G>C		p.X810_splice	ENST00000377604	NM_001204468.1	810			0.159496182815647	1	FACETS	0.661	0.575	0.753	0.661	0.575	0.753	SUBCLONAL	1	TRUE	0	0.21	1		579	916	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0043034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	134	222	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.695036387686361	2		222	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578260	7578260	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786204041	NA	P-0043034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	537	1069	0	ENST00000269305.4:c.589G>T	p.Val197Leu	p.V197L	ENST00000269305	NM_001126112.2	197	Gtg/Ttg	6/11	0.695036387686361	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.695036387686361	2		1069	738	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0043046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	69	369	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.761	0.671	0.855	0.761	0.671	0.855	SUBCLONAL	1	TRUE	1	0.714239263170905	2		369	254	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	80	320	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.965	0.859	1	0.965	0.859	1	CLONAL	1	TRUE	1	0.58	2		321	286	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0043062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	113	304	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.58	2		304	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0043062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	19	649	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	1	2	FACETS	0.109	0.082	0.141	0.109	0.082	0.141	SUBCLONAL	1	TRUE	1	0.58	2		649	602	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0043062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	39	551	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.287	0.238	0.343	0.287	0.238	0.343	SUBCLONAL	1	TRUE	1	0.58	2		551	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0043064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	629	688	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.938192535561238	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.938192535561238	1		688	699	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130105	143130105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	215	177	0	ENST00000262992.4:c.911G>A	p.Cys304Tyr	p.C304Y	ENST00000262992	NM_001101669.1	304	tGt/tAt	11/24	1	2	FACETS	0.881	0.827	0.936	0.881	0.827	0.936	CLONAL	1	TRUE	1	0.938192535561238	2		177	520	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102874144	102874145	+	missense_variant	Missense_Mutation	DNP	TG	TG	AT	novel	NA	P-0043064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	118	122	0	ENST00000307046.8:c.15_16delinsAT	p.Ser5_Ser6delinsArgCys	p.S5_S6delinsRC	ENST00000307046	NM_001111285.1	5	agCAgt/agATgt	1/4	1	2	FACETS	0.719	0.656	0.783	0.719	0.656	0.783	SUBCLONAL	1	TRUE	1	0.938192535561238	2		122	350	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568569	41568569	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	299	210	0	ENST00000263253.7:c.4519G>C	p.Asp1507His	p.D1507H	ENST00000263253	NM_001429.3	1507	Gat/Cat	28/31	0.938192535561238	1	FACETS	0.972	0.946	0.997	0.972	0.946	0.997	CLONAL	1	TRUE	0	0.938192535561238	1		210	348	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169940528	169940528	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	757	706	0	ENST00000295797.4:c.71A>G	p.His24Arg	p.H24R	ENST00000295797	NM_002740.5	24	cAc/cGc	1/18	1	2	FACETS	0.988	0.956	1	0.988	0.956	1	CLONAL	1	TRUE	1	0.938192535561238	2		706	1634	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280053	66280053	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	197	222	0	ENST00000273854.3:c.1636G>A	p.Ala546Thr	p.A546T	ENST00000273854	NM_004439.5	546	Gca/Aca	7/18	1	2	FACETS	0.944	0.884	1	0.944	0.884	1	CLONAL	1	TRUE	1	0.938192535561238	2		222	445	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509862	187509862	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs775695644	NA	P-0043064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	325	367	1	ENST00000441802.2:c.13651G>T	p.Ala4551Ser	p.A4551S	ENST00000441802	NM_005245.3	4551	Gcc/Tcc	27/27	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.938192535561238	2		368	677	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200097	138200097	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	961	504	0	ENST00000237289.4:c.1515C>A	p.His505Gln	p.H505Q	ENST00000237289	NM_001270507.1	505	caC/caA	7/9	0.938192535561238	3	FACETS	0.997	0.973	1	0.997	0.973	1	CLONAL	2	TRUE	1	0.938192535561238	3		504	1510	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394339	162394339	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	275	269	0	ENST00000366898.1:c.729C>A	p.Asp243Glu	p.D243E	ENST00000366898	NM_004562.2	243	gaC/gaA	6/12	0.938192535561238	3	FACETS	1	0.945	1	0.502	0.472	0.532	CLONAL	1	TRUE	1	0.938192535561238	3		269	858	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386602	81386602	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	210	170	0	ENST00000222390.5:c.385A>G	p.Ile129Val	p.I129V	ENST00000222390	NM_000601.4	129	Atc/Gtc	4/18	1	2	FACETS	0.959	0.901	1	0.959	0.901	1	CLONAL	1	TRUE	1	0.938192535561238	2		170	467	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250200	110250200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	701	766	0	ENST00000374672.4:c.475G>T	p.Asp159Tyr	p.D159Y	ENST00000374672	NM_004235.4	159	Gac/Tac	3/5	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.938192535561238	2		766	1494	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879855	44879857	+	stop_gained,frameshift_variant,splice_region_variant	Nonsense_Mutation	DEL	GGC	GGC	AA	novel	NA	P-0043064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	173	66	1	ENST00000377967.4:c.444_446delinsAA	p.Trp148Ter	p.W148*	ENST00000377967	NM_021140.2	148	tgGGCa/tgAAa	6/29	1	1	FACETS	0.823	0.783	0.861	0.823	0.783	0.861	CLONAL	1	TRUE	0	0.938192535561238	1		67	238	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456764	32456764	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0043066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	43	581	0	ENST00000332351.3:c.128T>A	p.Leu43Ter	p.L43*	ENST00000332351	NM_024426.4	43	tTa/tAa	1/10	0.247859668977619	3	FACETS	0.317	0.265	0.376	0.159	0.132	0.188	INDETERMINATE	1	TRUE	1	0.5218302245578	3		581	655	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457998	69457998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866931401	NA	P-0043066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	152	393	1	ENST00000227507.2:c.398G>A	p.Arg133Gln	p.R133Q	ENST00000227507	NM_053056.2	133	cGg/cAg	2/5	0.265266679100422	4	FACETS	0.869	0.8	0.94	0.869	0.8	0.94	INDETERMINATE	2	TRUE	2	0.5218302245578	4		394	510	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953270	81953270	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0043066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	82	297	0	ENST00000359376.3:c.2235+1G>T		p.X745_splice	ENST00000359376	NM_002661.3	745			NA	2	FACETS	0.875	0.778	0.979			1	INDETERMINATE	1	TRUE	NA	0.5218302245578	2		297	359	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573986	7573986	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	392	830	0	ENST00000269305.4:c.1041del	p.Leu348TrpfsTer22	p.L348Wfs*22	ENST00000269305	NM_001126112.2	347	gcC/gc	10/11	0.5218302245578	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.5218302245578	2		830	699	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220717	1220717	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587782018	NA	P-0043066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	266	659	0	ENST00000326873.7:c.734+1G>T		p.X245_splice	ENST00000326873	NM_000455.4	245			0.5218302245578	1	FACETS	0.775	0.737	0.813	1	0.995	1	SUBCLONAL	2	TRUE	0	0.5218302245578	1		659	486	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602911	10602911	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	40	922	1	ENST00000171111.5:c.667C>A	p.Leu223Met	p.L223M	ENST00000171111	NM_203500.1	223	Ctg/Atg	3/6	0.5218302245578	1	FACETS	0.147	0.122	0.176	0.147	0.122	0.176	SUBCLONAL	1	TRUE	0	0.5218302245578	1		923	769	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610630	10610630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	279	714	0	ENST00000171111.5:c.80C>T	p.Ala27Val	p.A27V	ENST00000171111	NM_203500.1	27	gCa/gTa	2/6	0.5218302245578	1	FACETS	0.751	0.714	0.788	1	0.995	1	SUBCLONAL	2	TRUE	0	0.5218302245578	1		714	526	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225362513	225362513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	192	449	0	ENST00000264414.4:c.1664G>A	p.Gly555Asp	p.G555D	ENST00000264414	NM_003590.4	555	gGt/gAt	12/16	0.146647049462783	3	FACETS	0.867	0.808	0.927	0.578	0.539	0.618	INDETERMINATE	2	TRUE	0	0.5218302245578	3		449	535	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827960	40827960	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	305	530	0	ENST00000373198.4:c.2468C>A	p.Ala823Asp	p.A823D	ENST00000373198	NM_133170.3	823	gCc/gAc	17/32	0.5218302245578	3	FACETS	0.993	0.942	1	0.993	0.942	1	CLONAL	2	TRUE	1	0.5218302245578	3		530	742	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939821	49939821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	247	826	1	ENST00000296474.3:c.1222C>T	p.Pro408Ser	p.P408S	ENST00000296474	NM_002447.2	408	Ccc/Tcc	1/20	0.5218302245578	3	FACETS	1	0.984	1	0.582	0.544	0.621	CLONAL	1	TRUE	1	0.5218302245578	3		827	1026	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939833	49939833	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	262	849	0	ENST00000296474.3:c.1210C>G	p.Pro404Ala	p.P404A	ENST00000296474	NM_002447.2	404	Ccc/Gcc	1/20	0.5218302245578	3	FACETS	1	0.986	1	0.59	0.553	0.628	CLONAL	1	TRUE	1	0.5218302245578	3		849	1073	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755583	57755583	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs372211010	NA	P-0043066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	53	634	0	ENST00000274289.3:c.204G>T	p.Glu68Asp	p.E68D	ENST00000274289	NM_006622.3	68	gaG/gaT	1/14	0.258706565772074	5	FACETS	0.541	0.461	0.63	0.18	0.153	0.21	INDETERMINATE	1	TRUE	2	0.5218302245578	5		634	669	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956607	93956607	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	101	389	0	ENST00000369303.4:c.2629C>A	p.Arg877Ser	p.R877S	ENST00000369303	NM_004440.3	877	Cgt/Agt	15/17	1	2	FACETS	0.797	0.715	0.882	0.797	0.715	0.882	SUBCLONAL	1	TRUE	1	0.5218302245578	2		389	486	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704571	117704571	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	119	438	0	ENST00000368508.3:c.2405A>T	p.Tyr802Phe	p.Y802F	ENST00000368508	NM_002944.2	802	tAc/tTc	16/43	1	2	FACETS	0.972	0.883	1	0.972	0.883	1	CLONAL	1	TRUE	1	0.5218302245578	2		438	469	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392072	81392072	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	112	316	0	ENST00000222390.5:c.205C>A	p.Gln69Lys	p.Q69K	ENST00000222390	NM_000601.4	69	Caa/Aaa	2/18	0.5218302245578	3	FACETS	1	0.973	1	0.607	0.549	0.667	CLONAL	1	TRUE	1	0.5218302245578	3		316	446	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913351	NA	P-0043066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	322	445	0	ENST00000288602.6:c.1397G>C	p.Gly466Ala	p.G466A	ENST00000288602	NM_004333.4	466	gGa/gCa	11/18	0.5218302245578	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.5218302245578	3		445	674	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902253	151902253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	97	373	0	ENST00000262189.6:c.3899G>A	p.Arg1300Lys	p.R1300K	ENST00000262189	NM_170606.2	1300	aGa/aAa	25/59	0.5218302245578	3	FACETS	0.821	0.734	0.913	0.41	0.367	0.457	CLONAL	1	TRUE	1	0.5218302245578	3		373	571	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133867	38133867	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	1239	912	0	ENST00000317025.8:c.4019A>G	p.Asp1340Gly	p.D1340G	ENST00000317025	NM_023034.1	1340	gAc/gGc	23/24	0.5218302245578	6	FACETS	0.978	0.958	0.999			1	CLONAL	5	TRUE	NA	0.5218302245578	6		912	1984	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993102	90993103	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0043066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	249	289	1	ENST00000265433.3:c.339_340delinsTT	p.Leu113_Val114delinsPhePhe	p.L113_V114delinsFF	ENST00000265433	NM_002485.4	113	ttGGtt/ttTTtt	4/16	0.5218302245578	4	FACETS	0.926	0.884	0.968	0.926	0.884	0.968	CLONAL	4	TRUE	0	0.5218302245578	4		290	392	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347870	128347870	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	211	700	0	ENST00000265960.3:c.635G>T	p.Trp212Leu	p.W212L	ENST00000265960	NM_001006617.1	212	tGg/tTg	5/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.5218302245578	2		700	708	SUCCESS
AR	367	MSKCC	GRCh37	X	66941720	66941720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	121	626	1	ENST00000374690.3:c.2364G>A	p.Met788Ile	p.M788I	ENST00000374690	NM_000044.3	788	atG/atA	6/8	0.218781070078738	2	FACETS	0.781	0.707	0.858	0.39	0.353	0.429	INDETERMINATE	1	TRUE	0	0.5218302245578	2		627	594	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0043089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	71	411	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.871	0.76	0.992	0.871	0.76	0.992	CLONAL	1	TRUE	1	0.218746293645777	2		411	745	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627860	14627860	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0043089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	82	681	0	ENST00000254322.2:c.212-2A>G		p.X71_splice	ENST00000254322	NM_006145.1	71			0.218746293645777	1	FACETS	0.905	0.797	1	0.905	0.797	1	CLONAL	1	TRUE	0	0.218746293645777	1		681	738	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449522	31449522	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	35	181	1	ENST00000344624.3:c.2687C>G	p.Ala896Gly	p.A896G	ENST00000344624		896	gCc/gGc	19/33	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.218746293645777	2		182	305	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913343	NA	P-0043105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	324	734	0	ENST00000269305.4:c.817C>A	p.Arg273Ser	p.R273S	ENST00000269305	NM_001126112.2	273	Cgt/Agt	8/11	0.616604762717669	1	FACETS	0.945	0.898	0.993	0.945	0.898	0.993	CLONAL	1	TRUE	0	0.616604762717669	1		734	769	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807890	1807890	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913105	NA	P-0043105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	647	885	0	ENST00000260795.2:c.1949A>T	p.Lys650Met	p.K650M	ENST00000260795		650	aAg/aTg	13/17	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.616604762717669	2		885	1005	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449806	29449806	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	377	983	1	ENST00000389048.3:c.3049G>A	p.Asp1017Asn	p.D1017N	ENST00000389048	NM_004304.4	1017	Gat/Aat	18/29	0.372265931041613	1	FACETS	0.824	0.784	0.865	0.824	0.784	0.865	CLONAL	1	TRUE	0	0.616604762717669	1		984	1026	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420327	88420327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548727485	NA	P-0043105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	188	562	0	ENST00000360948.2:c.2359C>T	p.Arg787Cys	p.R787C	ENST00000360948	NM_001012338.2	787	Cgt/Tgt	19/19	1	2	FACETS	0.957	0.889	1	0.957	0.889	1	CLONAL	1	TRUE	1	0.616604762717669	2		562	637	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948437	71948437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766000787	NA	P-0043105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	366	1114	0	ENST00000298229.2:c.3149C>T	p.Pro1050Leu	p.P1050L	ENST00000298229	NM_001567.3	1050	cCt/cTt	26/28	0.49143036771691	3	FACETS	1	0.959	1	0.508	0.48	0.536	CLONAL	1	TRUE	1	0.616604762717669	3		1114	1530	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536902	120536902	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	310	850	0	ENST00000229340.5:c.284C>G	p.Ser95Cys	p.S95C	ENST00000229340	NM_006861.6	95	tCc/tGc	4/6	0.406236328742673	1	FACETS	0.809	0.765	0.853	0.809	0.765	0.853	CLONAL	1	TRUE	0	0.616604762717669	1		850	860	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41962003	41962003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	122	513	0	ENST00000219905.7:c.911C>T	p.Pro304Leu	p.P304L	ENST00000219905	NM_001164273.1	304	cCa/cTa	2/24	1	2	FACETS	0.513	0.463	0.565	0.513	0.463	0.565	SUBCLONAL	1	TRUE	1	0.616604762717669	2		513	772	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346771	89346771	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	96	629	0	ENST00000301030.4:c.6179C>G	p.Ser2060Cys	p.S2060C	ENST00000301030	NM_001256183.1	2060	tCc/tGc	9/13	1	2	FACETS	0.552	0.493	0.615	0.552	0.493	0.615	SUBCLONAL	1	TRUE	1	0.616604762717669	2		629	564	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683594	29683594	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	148	281	0	ENST00000356175.3:c.7669G>C	p.Glu2557Gln	p.E2557Q	ENST00000356175	NM_000267.3	2557	Gaa/Caa	51/57	0.616604762717669	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.616604762717669	1		281	315	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627439	37627439	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1462735881	NA	P-0043105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	317	698	0	ENST00000447079.4:c.1354A>C	p.Lys452Gln	p.K452Q	ENST00000447079	NM_015083.1	452	Aaa/Caa	2/14	0.616604762717669	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.616604762717669	1		698	710	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354086	15354086	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	250	652	0	ENST00000263377.2:c.2794C>G	p.Leu932Val	p.L932V	ENST00000263377	NM_058243.2	932	Ctg/Gtg	14/20	0.306434835477393	3	FACETS	1	0.978	1	0.365	0.341	0.389	INDETERMINATE	1	TRUE	0	0.616604762717669	3		652	970	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024062	31024062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	114	584	0	ENST00000375687.4:c.3547G>A	p.Glu1183Lys	p.E1183K	ENST00000375687	NM_015338.5	1183	Gaa/Aaa	13/13	0.406236328742673	1	FACETS	0.388	0.349	0.428	0.388	0.349	0.428	SUBCLONAL	1	TRUE	0	0.616604762717669	1		584	660	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37622819	37622819	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0043105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	172	898	0	ENST00000249071.6:c.473C>G	p.Ser158Ter	p.S158*	ENST00000249071	NM_002872.4	158	tCa/tGa	6/7	1	2	FACETS	0.474	0.435	0.515	0.474	0.435	0.515	SUBCLONAL	1	TRUE	1	0.616604762717669	2		898	1176	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143033836	143033836	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0043105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	145	348	0	ENST00000262992.4:c.2136-1G>C		p.X712_splice	ENST00000262992	NM_001101669.1	712			0.616604762717669	1	FACETS	0.998	0.925	1	0.998	0.925	1	CLONAL	1	TRUE	0	0.616604762717669	1		348	326	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514398	149514398	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	124	633	0	ENST00000261799.4:c.546C>G	p.Ile182Met	p.I182M	ENST00000261799	NM_002609.3	182	atC/atG	4/23	0.616604762717669	1	FACETS	0.389	0.352	0.427	0.389	0.352	0.427	SUBCLONAL	1	TRUE	0	0.616604762717669	1		633	716	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967931	93967931	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	268	518	0	ENST00000369303.4:c.1996A>T	p.Thr666Ser	p.T666S	ENST00000369303	NM_004440.3	666	Acc/Tcc	11/17	0.616604762717669	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.616604762717669	1		518	576	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100175	157100175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1226373127	NA	P-0043105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	54	71	0	ENST00000346085.5:c.1112C>T	p.Pro371Leu	p.P371L	ENST00000346085	NM_020732.3	371	cCc/cTc	1/20	0.616604762717669	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.616604762717669	1		71	101	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952970	2952970	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	138	887	0	ENST00000396946.4:c.2970G>C	p.Gln990His	p.Q990H	ENST00000396946	NM_032415.4	990	caG/caC	22/25	0.289844436877787	1	FACETS	0.311	0.282	0.341	0.311	0.282	0.341	INDETERMINATE	1	TRUE	0	0.616604762717669	1		887	997	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418408	139418409	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0043105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	289	896	2	ENST00000277541.6:c.163_164delinsTT	p.Pro55Leu	p.P55L	ENST00000277541	NM_017617.3	55	CCg/TTg	3/34	1	2	FACETS	0.866	0.815	0.919	0.866	0.815	0.919	CLONAL	1	TRUE	1	0.616604762717669	2		898	1082	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0043151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	89	426	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.115805375654877	3	FACETS	1	0.919	1	0.521	0.463	0.583	INDETERMINATE	1	FALSE	1	0.363872529423074	3		426	555	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1040408	1040408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370272002	NA	P-0043151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	51	616	0	ENST00000358495.3:c.164G>A	p.Arg55His	p.R55H	ENST00000358495	NM_134424.2	55	cGc/cAc	3/12	NA	2	FACETS	0.409	0.346	0.477			1	INDETERMINATE	1	FALSE	NA	0.363872529423074	2		616	686	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597401	10597401	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	165	893	0	ENST00000171111.5:c.1802G>T	p.Arg601Leu	p.R601L	ENST00000171111	NM_203500.1	601	cGg/cTg	6/6	0.363872529423074	1	FACETS	0.939	0.864	1	0.939	0.864	1	CLONAL	1	FALSE	0	0.363872529423074	1		893	790	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504371	8504371	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	136	540	0	ENST00000356435.5:c.1712G>T	p.Arg571Met	p.R571M	ENST00000356435		571	aGg/aTg	12/35	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.363872529423074	2		540	653	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030817	69030817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	96	409	0	ENST00000288368.4:c.3359C>T	p.Ser1120Phe	p.S1120F	ENST00000288368	NM_024870.2	1120	tCc/tTc	27/40	1	2	FACETS	0.927	0.828	1	0.927	0.828	1	CLONAL	1	FALSE	1	0.363872529423074	2		409	569	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532780	187532780	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1200316021	NA	P-0043151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	103	561	0	ENST00000441802.2:c.9613G>T	p.Gly3205Cys	p.G3205C	ENST00000441802	NM_005245.3	3205	Ggc/Tgc	14/27	1	2	FACETS	0.746	0.667	0.829	0.746	0.667	0.829	SUBCLONAL	1	FALSE	1	0.363872529423074	2		561	759	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459655	149459655	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	158	715	0	ENST00000286301.3:c.552del	p.Lys185ArgfsTer2	p.K185Rfs*2	ENST00000286301	NM_005211.3	184	agG/ag	4/22	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.363872529423074	2		715	801	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371843	55371843	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	32	177	0	ENST00000297316.4:c.533G>T	p.Gly178Val	p.G178V	ENST00000297316	NM_022454.3	178	gGc/gTc	2/2	1	2	FACETS	0.684	0.558	0.825	0.684	0.558	0.825	SUBCLONAL	1	FALSE	1	0.363872529423074	2		177	257	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	434	779	2	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	0.586354139946348	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.586354139946348	2		781	712	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	385	749	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.586354139946348	2	FACETS	0.992	0.953	1	0.992	0.953	1	CLONAL	2	TRUE	0	0.586354139946348	2		749	662	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551410	150551410	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769198905	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2340	250	970	0	ENST00000369026.2:c.597G>T	p.Met199Ile	p.M199I	ENST00000369026	NM_021960.4	199	atG/atT	1/3	0.586354139946348	9	FACETS	1	0.935	1			1	CLONAL	1	TRUE	NA	0.586354139946348	9		970	2590	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175942	176175942	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	40	162	0	ENST00000367669.3:c.173C>A	p.Ser58Ter	p.S58*	ENST00000367669	NM_022457.5	58	tCg/tAg	1/20	0.586354139946348	5	FACETS	1	0.883	1	0.267	0.223	0.315	CLONAL	1	TRUE	1	0.586354139946348	5		162	240	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450735	70450735	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs774165175	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	131	558	0	ENST00000373644.4:c.5575C>G	p.Pro1859Ala	p.P1859A	ENST00000373644	NM_030625.2	1859	Cca/Gca	12/12	0.541690895497167	3	FACETS	0.882	0.802	0.966	0.441	0.401	0.483	CLONAL	1	TRUE	1	0.586354139946348	3		558	655	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456371	32456371	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	205	831	0	ENST00000332351.3:c.521C>G	p.Ala174Gly	p.A174G	ENST00000332351	NM_024426.4	174	gCc/gGc	1/10	1	2	FACETS	0.978	0.911	1	0.978	0.911	1	CLONAL	1	TRUE	1	0.586354139946348	2		831	715	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138148	64138148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	197	820	0	ENST00000334205.4:c.2071C>T	p.Leu691Phe	p.L691F	ENST00000334205	NM_003942.2	691	Ctc/Ttc	16/17	0.221336763723811	6	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.586354139946348	6		820	990	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445092	49445092	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs201778313	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	163	747	0	ENST00000301067.7:c.2374G>C	p.Ala792Pro	p.A792P	ENST00000301067	NM_003482.3	792	Gct/Cct	10/54	0.586354139946348	3	FACETS	0.89	0.818	0.965	0.445	0.409	0.483	CLONAL	1	TRUE	1	0.586354139946348	3		747	808	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514403	103514403	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	42	234	0	ENST00000355739.4:c.904G>T	p.Glu302Ter	p.E302*	ENST00000355739	NM_000123.3	302	Gaa/Taa	8/15	0.586354139946348	3	FACETS	0.556	0.466	0.656	0.278	0.233	0.328	SUBCLONAL	1	TRUE	1	0.586354139946348	3		234	333	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678427	88678427	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	214	918	0	ENST00000360948.2:c.1109A>T	p.His370Leu	p.H370L	ENST00000360948	NM_001012338.2	370	cAc/cTc	9/19	1	2	FACETS	0.88	0.82	0.943	0.88	0.82	0.943	CLONAL	1	TRUE	1	0.586354139946348	2		918	829	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478227	99478227	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	91	431	0	ENST00000268035.6:c.3131G>C	p.Arg1044Thr	p.R1044T	ENST00000268035	NM_000875.3	1044	aGg/aCg	16/21	1	2	FACETS	0.85	0.761	0.944	0.85	0.761	0.944	CLONAL	1	TRUE	1	0.586354139946348	2		431	365	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778858	3778858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	345	775	1	ENST00000262367.5:c.6190C>T	p.Pro2064Ser	p.P2064S	ENST00000262367	NM_004380.2	2064	Ccc/Tcc	31/31	0.586354139946348	3	FACETS	0.889	0.845	0.933	0.889	0.845	0.933	CLONAL	2	TRUE	1	0.586354139946348	3		776	856	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116212	67116212	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	154	625	0	ENST00000412916.2:c.495+1G>T		p.X165_splice	ENST00000412916		165			0.586354139946348	3	FACETS	0.864	0.792	0.94	0.432	0.396	0.47	CLONAL	1	TRUE	1	0.586354139946348	3		625	786	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993287	72993287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	255	949	0	ENST00000268489.5:c.758G>A	p.Ser253Asn	p.S253N	ENST00000268489	NM_006885.3	253	aGc/aAc	2/10	0.586354139946348	3	FACETS	1	0.94	1	0.502	0.47	0.536	CLONAL	1	TRUE	1	0.586354139946348	3		949	1120	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41258490	41258490	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	380	494	0	ENST00000357654.3:c.195G>C	p.Lys65Asn	p.K65N	ENST00000357654	NM_007294.3	65	aaG/aaC	4/23	0.586354139946348	6	FACETS	0.86	0.818	0.902	0.645	0.613	0.677	CLONAL	3	TRUE	2	0.586354139946348	6		494	1092	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78704506	78704506	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	202	433	0	ENST00000306801.3:c.654G>T	p.Glu218Asp	p.E218D	ENST00000306801	NM_020761.2	218	gaG/gaT	5/34	0.586354139946348	7	FACETS	0.851	0.789	0.916	0.426	0.394	0.458	CLONAL	2	TRUE	3	0.586354139946348	7		433	998	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214173	36214173	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	637	784	0	ENST00000222270.7:c.2999G>T	p.Cys1000Phe	p.C1000F	ENST00000222270	NM_014727.1	1000	tGt/tTt	6/37	0.586354139946348	5	FACETS	0.994	0.959	1	0.994	0.959	1	CLONAL	3	TRUE	2	0.586354139946348	5		784	1370	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214678	36214678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	314	709	0	ENST00000222270.7:c.3104C>T	p.Ser1035Phe	p.S1035F	ENST00000222270	NM_014727.1	1035	tCt/tTt	8/37	0.586354139946348	5	FACETS	0.881	0.832	0.932	0.588	0.554	0.622	CLONAL	2	TRUE	2	0.586354139946348	5		709	1142	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212289026	212289026	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	106	422	0	ENST00000342788.4:c.2720G>A	p.Gly907Glu	p.G907E	ENST00000342788	NM_005235.2	907	gGa/gAa	23/28	0.582895936930135	4	FACETS	0.985	0.886	1	0.493	0.443	0.546	CLONAL	1	TRUE	2	0.586354139946348	4		422	582	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439904	220439904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	457	928	0	ENST00000243786.2:c.757C>A	p.Pro253Thr	p.P253T	ENST00000243786	NM_002191.3	253	Ccg/Acg	2/2	0.582895936930135	4	FACETS	0.968	0.925	1	0.968	0.925	1	CLONAL	2	TRUE	2	0.586354139946348	4		928	1277	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445035	89445035	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	93	549	0	ENST00000336596.2:c.1355G>T	p.Ser452Ile	p.S452I	ENST00000336596	NM_005233.5	452	aGc/aTc	6/17	0.586354139946348	5	FACETS	0.531	0.471	0.596			1	SUBCLONAL	1	TRUE	NA	0.586354139946348	5		549	1123	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456522	89456522	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	86	305	0	ENST00000336596.2:c.1697+1G>T		p.X566_splice	ENST00000336596	NM_005233.5	566			0.586354139946348	5	FACETS	0.696	0.615	0.783			1	SUBCLONAL	1	TRUE	NA	0.586354139946348	5		305	792	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968183	134968183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	755	483	1	ENST00000398015.3:c.2696C>T	p.Ser899Phe	p.S899F	ENST00000398015	NM_004441.4	899	tCc/tTc	15/16	0.586354139946348	7	FACETS	0.96	0.936	0.983			1	CLONAL	6	TRUE	NA	0.586354139946348	7		484	1103	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664981	138664981	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	88	349	0	ENST00000330315.3:c.584T>A	p.Leu195Gln	p.L195Q	ENST00000330315	NM_023067.3	195	cTg/cAg	1/1	0.586354139946348	6	FACETS	0.93	0.824	1			1	CLONAL	1	TRUE	NA	0.586354139946348	6		349	701	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582193	189582193	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	125	462	0	ENST00000264731.3:c.752G>T	p.Arg251Leu	p.R251L	ENST00000264731	NM_003722.4	251	cGt/cTt	5/14	0.586354139946348	5	FACETS	0.892	0.807	0.982	0.297	0.269	0.328	CLONAL	1	TRUE	2	0.586354139946348	5		462	898	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808870	1808870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560280646	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	250	870	1	ENST00000260795.2:c.2302G>A	p.Glu768Lys	p.E768K	ENST00000260795		768	Gag/Aag	17/17	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.586354139946348	2		871	820	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31485003	31485003	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	89	331	0	ENST00000344624.3:c.1981G>T	p.Asp661Tyr	p.D661Y	ENST00000344624		661	Gac/Tac	12/33	0.582895936930135	4	FACETS	0.838	0.744	0.937	0.419	0.372	0.469	CLONAL	1	TRUE	2	0.586354139946348	4		331	575	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680482	30680482	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	159	611	0	ENST00000376406.3:c.1237G>T	p.Ala413Ser	p.A413S	ENST00000376406	NM_014641.2	413	Gcg/Tcg	5/15	0.566859799035424	2	FACETS	1	0.969	1	0.547	0.505	0.59	CLONAL	1	TRUE	0	0.586354139946348	2		611	496	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202200	138202200	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3734553	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	151	549	0	ENST00000237289.4:c.2117G>A	p.Arg706Gln	p.R706Q	ENST00000237289	NM_001270507.1	706	cGa/cAa	9/9	0.566859799035424	2	FACETS	0.949	0.872	1	0.474	0.436	0.514	CLONAL	1	TRUE	0	0.586354139946348	2		549	543	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026850	6026850	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	468	532	0	ENST00000265849.7:c.1546A>C	p.Ser516Arg	p.S516R	ENST00000265849	NM_000535.5	516	Agc/Cgc	11/15	0.586354139946348	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	1	0.586354139946348	4		532	801	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512086	148512086	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	126	522	0	ENST00000320356.2:c.1592C>T	p.Pro531Leu	p.P531L	ENST00000320356	NM_004456.4	531	cCa/cTa	14/20	1	2	FACETS	0.909	0.828	0.992	0.909	0.828	0.992	CLONAL	1	TRUE	1	0.586354139946348	2		522	473	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336316	80336316	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	219	342	1	ENST00000286548.4:c.1003G>T	p.Glu335Ter	p.E335*	ENST00000286548	NM_002072.3	335	Gag/Tag	7/7	0.586354139946348	2	FACETS	0.909	0.859	0.958	0.909	0.859	0.958	CLONAL	2	TRUE	0	0.586354139946348	2		343	411	SUCCESS
AR	367	MSKCC	GRCh37	X	66766111	66766111	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	382	387	0	ENST00000374690.3:c.1124del	p.Pro375ArgfsTer104	p.P375Rfs*104	ENST00000374690	NM_000044.3	375	Ccg/cg	1/8	0.586354139946348	2	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.586354139946348	2		387	563	SUCCESS
AR	367	MSKCC	GRCh37	X	66766228	66766228	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	172	332	0	ENST00000374690.3:c.1240C>A	p.Leu414Met	p.L414M	ENST00000374690	NM_000044.3	414	Ctg/Atg	1/8	0.586354139946348	2	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.586354139946348	2		332	451	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0043176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	143	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.432949933656911	3	FACETS	1	0.987	1	0.719	0.658	0.781	CLONAL	1	TRUE	1	0.432949933656911	3		452	559	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0043176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	51	560	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.457	0.388	0.532	0.457	0.388	0.532	SUBCLONAL	1	TRUE	1	0.432949933656911	2		561	516	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998684	100998684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	97	870	0	ENST00000325455.5:c.1118C>T	p.Ala373Val	p.A373V	ENST00000325455	NM_001202474.3	373	gCg/gTg	1/8	1	2	FACETS	0.629	0.561	0.702	0.629	0.561	0.702	SUBCLONAL	1	TRUE	1	0.432949933656911	2		870	712	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094798	143094798	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	31	309	0	ENST00000262992.4:c.1346T>C	p.Met449Thr	p.M449T	ENST00000262992	NM_001101669.1	449	aTg/aCg	14/24	1	2	FACETS	0.45	0.365	0.547	0.45	0.365	0.547	SUBCLONAL	1	TRUE	1	0.432949933656911	2		309	318	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0043187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	143	426	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.318229652783714	5	FACETS	1	0.978	1	0.797	0.73	0.866	CLONAL	2	TRUE	2	0.321064368489792	5		426	552	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175445	108175445	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	140	276	0	ENST00000278616.4:c.5540A>G	p.His1847Arg	p.H1847R	ENST00000278616	NM_000051.3	1847	cAt/cGt	37/63	0.280801465483186	3	FACETS	0.885	0.816	0.957	0.885	0.816	0.957	CLONAL	3	TRUE	0	0.321064368489792	3		276	381	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120811	115120811	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	148	600	0	ENST00000257566.3:c.195G>C	p.Met65Ile	p.M65I	ENST00000257566	NM_016569.3	65	atG/atC	1/8	0.204650148770849	2	FACETS	0.866	0.796	0.939	0.866	0.796	0.939	CLONAL	2	TRUE	0	0.321064368489792	2		600	532	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436071	110436071	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	155	806	0	ENST00000375856.3:c.2330C>G	p.Thr777Arg	p.T777R	ENST00000375856	NM_003749.2	777	aCg/aGg	1/2	1	2	FACETS	0.883	0.807	0.962	0.883	0.807	0.962	CLONAL	1	TRUE	1	0.321064368489792	2		806	1094	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961656	41961657	+	stop_gained	Nonsense_Mutation	DNP	AG	AG	TT	novel	NA	P-0043187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	112	435	0	ENST00000219905.7:c.564_565delinsTT	p.Gln188_Glu189delinsHisTer	p.Q188_E189delinsH*	ENST00000219905	NM_001164273.1	188	caAGaa/caTTaa	2/24	0.233472411079584	2	FACETS	0.831	0.753	0.912	0.831	0.753	0.912	CLONAL	2	TRUE	0	0.321064368489792	2		435	420	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645244	67645244	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	77	635	0	ENST00000264010.4:c.509G>T	p.Gly170Val	p.G170V	ENST00000264010	NM_006565.3	170	gGg/gTg	3/12	1	2	FACETS	0.61	0.535	0.691	0.61	0.535	0.691	SUBCLONAL	1	TRUE	1	0.321064368489792	2		635	786	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991853	72991853	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	87	627	0	ENST00000268489.5:c.2192G>C	p.Cys731Ser	p.C731S	ENST00000268489	NM_006885.3	731	tGt/tCt	2/10	1	2	FACETS	0.622	0.55	0.7	0.622	0.55	0.7	SUBCLONAL	1	TRUE	1	0.321064368489792	2		627	871	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371799	45371799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	172	341	0	ENST00000262160.6:c.1192G>T	p.Val398Phe	p.V398F	ENST00000262160	NM_005901.5	398	Gtt/Ttt	10/11	0.280801465483186	3	FACETS	0.897	0.833	0.962	0.897	0.833	0.962	CLONAL	3	TRUE	0	0.321064368489792	3		341	462	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258541	19258541	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	241	855	0	ENST00000162023.5:c.359G>T	p.Gly120Val	p.G120V	ENST00000162023		120	gGg/gTg	8/13	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.321064368489792	2		855	1004	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306604	41306604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	187	656	0	ENST00000373198.4:c.1055C>T	p.Pro352Leu	p.P352L	ENST00000373198	NM_133170.3	352	cCc/cTc	7/32	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.321064368489792	2		656	894	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032755	30032755	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	53	343	0	ENST00000338641.4:c.131del	p.Lys44ArgfsTer79	p.K44Rfs*79	ENST00000338641	NM_000268.3	44	Aag/ag	2/16	1	2	FACETS	0.782	0.669	0.906	0.782	0.669	0.906	CLONAL	1	TRUE	1	0.321064368489792	2		343	422	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180367	38180367	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0043187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	339	827	0	ENST00000396334.3:c.215T>A	p.Leu72Ter	p.L72*	ENST00000396334	NM_002468.4	72	tTg/tAg	1/5	0.318229652783714	5	FACETS	0.926	0.877	0.977	0.926	0.877	0.977	CLONAL	3	TRUE	2	0.321064368489792	5		827	1126	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436398	52436399	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0043187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	138	679	3	ENST00000460680.1:c.2095_2096delinsTT	p.Arg699Leu	p.R699L	ENST00000460680	NM_004656.3	699	CGg/TTg	17/17	0.318229652783714	5	FACETS	1	0.985	1	0.472	0.429	0.517	CLONAL	1	TRUE	2	0.321064368489792	5		682	900	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851688	134851688	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	178	502	0	ENST00000398015.3:c.1094C>A	p.Ala365Glu	p.A365E	ENST00000398015	NM_004441.4	365	gCa/gAa	5/16	0.318229652783714	5	FACETS	0.848	0.785	0.913	0.848	0.785	0.913	CLONAL	3	TRUE	2	0.321064368489792	5		502	646	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217129	66217129	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	120	405	0	ENST00000273854.3:c.2486C>A	p.Pro829His	p.P829H	ENST00000273854	NM_004439.5	829	cCc/cAc	14/18	0.257704694446761	3	FACETS	0.811	0.735	0.89	0.811	0.735	0.89	CLONAL	2	TRUE	1	0.321064368489792	3		405	535	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114239	143114239	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0043187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	28	237	0	ENST00000262992.4:c.1181+1G>T		p.X394_splice	ENST00000262992	NM_001101669.1	394			0.257704694446761	3	FACETS	0.698	0.559	0.855	0.349	0.279	0.428	SUBCLONAL	1	TRUE	1	0.321064368489792	3		237	290	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226022	226022	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	45	109	0	ENST00000264932.6:c.481A>T	p.Ser161Cys	p.S161C	ENST00000264932	NM_004168.2	161	Agc/Tgc	5/15	0.321064368489792	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	2	TRUE	0	0.321064368489792	2		109	139	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522688	176522688	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	84	876	0	ENST00000292408.4:c.1785G>T	p.Gln595His	p.Q595H	ENST00000292408	NM_213647.1	595	caG/caT	13/18	0.321064368489792	4	FACETS	0.697	0.614	0.786	0.232	0.204	0.262	SUBCLONAL	1	TRUE	1	0.321064368489792	4		876	992	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066653	94066653	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	132	454	0	ENST00000369303.4:c.1106G>T	p.Cys369Phe	p.C369F	ENST00000369303	NM_004440.3	369	tGt/tTt	5/17	0.267287468310179	2	FACETS	1	0.985	1	0.71	0.647	0.776	CLONAL	1	TRUE	0	0.321064368489792	2		454	579	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510782	157510782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1321954955	NA	P-0043187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	69	488	0	ENST00000346085.5:c.3557C>T	p.Ser1186Leu	p.S1186L	ENST00000346085	NM_020732.3	1186	tCg/tTg	14/20	0.267287468310179	2	FACETS	0.808	0.705	0.919	0.404	0.352	0.46	CLONAL	1	TRUE	0	0.321064368489792	2		488	532	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979385	2979385	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	316	435	0	ENST00000396946.4:c.862C>T	p.Gln288Ter	p.Q288*	ENST00000396946	NM_032415.4	288	Cag/Tag	6/25	0.321064368489792	6	FACETS	1	0.976	1	0.839	0.796	0.882	CLONAL	4	TRUE	1	0.321064368489792	6		435	771	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386550	81386550	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	98	435	1	ENST00000222390.5:c.437G>T	p.Gly146Val	p.G146V	ENST00000222390	NM_000601.4	146	gGc/gTc	4/18	0.321064368489792	6	FACETS	1	0.979	1	0.361	0.322	0.403	CLONAL	1	TRUE	2	0.321064368489792	6		436	694	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485951	8485952	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0043187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	95	410	0	ENST00000356435.5:c.2865_2866delinsAT	p.Leu956Phe	p.L956F	ENST00000356435		955	acCCtt/acATtt	17/35	0.318229652783714	5	FACETS	1	0.979	1	0.476	0.424	0.531	CLONAL	1	TRUE	2	0.321064368489792	5		410	614	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937185	76937185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	125	241	0	ENST00000373344.5:c.3563C>T	p.Ser1188Phe	p.S1188F	ENST00000373344	NM_000489.3	1188	tCc/tTc	9/35	0.145064627754351	2	FACETS	1	0.965	1			1	INDETERMINATE	2	TRUE	NA	0.321064368489792	2		241	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0043234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	117	720	2	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.3	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.25	1		722	613	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0043234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	27	320	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.215952801479592	2	FACETS	0.766	0.618	0.93	0.766	0.618	0.93	CLONAL	2	TRUE	0	0.25	2		320	141	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0043234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	17	338	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.25	2		338	110	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495360	149495360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs114435947	NA	P-0043234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	164	805	0	ENST00000261799.4:c.3287C>T	p.Ala1096Val	p.A1096V	ENST00000261799	NM_002609.3	1096	gCg/gTg	23/23	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.25	2		805	925	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024169	112024169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465963577	NA	P-0043234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	18	478	0	ENST00000368678.4:c.616C>T	p.Arg206Cys	p.R206C	ENST00000368678		206	Cgc/Tgc	7/13	0.209611863416933	2	FACETS	1	0.874	1	0.626	0.477	0.797	CLONAL	1	TRUE	0	0.25	2		478	115	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799642	3799652	+	frameshift_variant	Frame_Shift_Del	DEL	GGTATCATTTT	GGTATCATTTT	-	novel	NA	P-0043234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	14	357	0	ENST00000262367.5:c.3812_3822del	p.Lys1271IlefsTer8	p.K1271Ifs*8	ENST00000262367	NM_004380.2	1271	aAAAATGATACC/a	21/31	0.215952801479592	2	FACETS	1	0.743	1	0.509	0.372	0.672	CLONAL	1	TRUE	0	0.25	2		357	110	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575168	48575168	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0043234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	23	302	0	ENST00000342988.3:c.362T>A	p.Leu121Ter	p.L121*	ENST00000342988	NM_005359.5	121	tTa/tAa	3/12	0.215952801479592	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	2	TRUE	0	0.25	2		302	80	SUCCESS
APC	324	MSKCC	GRCh37	5	112175771	112175775	+	frameshift_variant	Frame_Shift_Ins	INS	GAAAG	GAAAG	AAAAGT	novel	NA	P-0043234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	26	331	0	ENST00000257430.4:c.4480_4484delinsAAAAGT	p.Glu1494LysfsTer20	p.E1494Kfs*20	ENST00000257430	NM_000038.5	1494	GAAAGt/AAAAGTt	16/16	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.25	2		331	143	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0043236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	121	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.476360034056965	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.479528592682928	1		452	333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782177	NA	P-0043236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	424	780	0	ENST00000269305.4:c.644G>A	p.Ser215Asn	p.S215N	ENST00000269305	NM_001126112.2	215	aGt/aAt	6/11	0.479528592682928	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.479528592682928	1		780	955	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0043236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	219	538	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.0628475375728619	4	FACETS	0.79	0.736	0.846	0.79	0.736	0.846	INDETERMINATE	2	TRUE	2	0.479528592682928	4		539	855	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562171	21562171	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753951508	NA	P-0043236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	592	1044	0	ENST00000382592.4:c.1748A>G	p.Asn583Ser	p.N583S	ENST00000382592	NM_014572.2	583	aAc/aGc	4/8	1	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	1	0.479528592682928	2		1044	1737	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454661	99454661	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	275	601	0	ENST00000268035.6:c.1580A>G	p.Tyr527Cys	p.Y527C	ENST00000268035	NM_000875.3	527	tAc/tGc	7/21	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.479528592682928	2		601	943	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0043243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	129	346	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.308046466340678	3	FACETS	0.767	0.697	0.84	0.767	0.697	0.84	SUBCLONAL	2	TRUE	1	0.308046466340678	3		346	630	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0043243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	38	235	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.54	0.446	0.645	0.54	0.446	0.645	SUBCLONAL	1	TRUE	1	0.308046466340678	2		235	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0043243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	183	683	0	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.308046466340678	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.308046466340678	1		683	953	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952076	178952076	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	44	366	0	ENST00000263967.3:c.3131A>T	p.Asn1044Ile	p.N1044I	ENST00000263967	NM_006218.2	1044	aAt/aTt	21/21	1	2	FACETS	0.543	0.455	0.641	0.543	0.455	0.641	SUBCLONAL	1	TRUE	1	0.308046466340678	2		366	526	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0043273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	174	384	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.5	2		384	632	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0043344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	357	426	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.614417415011147	2	FACETS	0.986	0.948	1	0.986	0.948	1	CLONAL	2	TRUE	0	0.644125927085799	2		426	562	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221989	1221989	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1085307466	NA	P-0043344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	293	716	0	ENST00000326873.7:c.904C>T	p.Gln302Ter	p.Q302*	ENST00000326873	NM_000455.4	302	Cag/Tag	7/10	0.644125927085799	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.644125927085799	1		716	596	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2185872	2185872	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	380	743	1	ENST00000398665.3:c.146del	p.Pro49ArgfsTer12	p.P49Rfs*12	ENST00000398665	NM_032482.2	48	atC/at	3/28	0.644125927085799	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.644125927085799	1		744	774	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602438	10602438	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	318	723	0	ENST00000171111.5:c.1140G>T	p.Arg380Ser	p.R380S	ENST00000171111	NM_203500.1	380	agG/agT	3/6	0.644125927085799	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.644125927085799	1		723	647	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	256	320	1				ENST00000310581	NM_198253.2	-/1132			0.595009668160019	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.595009668160019	1		321	431	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	301	396	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.109821213566898	4	FACETS	0.938	0.887	0.99	0.938	0.887	0.99	INDETERMINATE	2	TRUE	2	0.595009668160019	4		396	860	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189048	32189048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	340	703	0	ENST00000375023.3:c.506G>A	p.Gly169Glu	p.G169E	ENST00000375023	NM_004557.3	169	gGg/gAg	4/30	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.595009668160019	2		703	964	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650881	93650881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200438123	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	339	565	0	ENST00000375746.1:c.1807G>A	p.Asp603Asn	p.D603N	ENST00000375746	NM_001174167.1	603	Gat/Aat	13/14	0.109821213566898	4	FACETS	0.907	0.86	0.955	0.907	0.86	0.955	INDETERMINATE	2	TRUE	2	0.595009668160019	4		565	1002	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845844	72845844	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760400785	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	317	681	0	ENST00000268489.5:c.3623C>T	p.Ser1208Leu	p.S1208L	ENST00000268489	NM_006885.3	1208	tCg/tTg	6/10	1	2	FACETS	0.993	0.938	1	0.993	0.938	1	CLONAL	1	TRUE	1	0.595009668160019	2		681	1073	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926270	112926270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918457	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	294	580	0	ENST00000351677.2:c.1403C>T	p.Thr468Met	p.T468M	ENST00000351677	NM_002834.3	468	aCg/aTg	12/16	0.109821213566898	4	FACETS	0.783	0.737	0.829	0.783	0.737	0.829	INDETERMINATE	2	TRUE	2	0.595009668160019	4		580	1007	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	256	366	0	ENST00000304494.5:c.151-1G>A		p.X51_splice	ENST00000304494	NM_000077.4	51			0.109821213566898	4	FACETS	0.856	0.804	0.909	0.856	0.804	0.909	INDETERMINATE	2	TRUE	2	0.595009668160019	4		366	802	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120795639	120795639	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	297	461	0	ENST00000257552.2:c.514C>T	p.His172Tyr	p.H172Y	ENST00000257552	NM_002442.3	172	Cat/Tat	8/15	0.109821213566898	4	FACETS	0.893	0.843	0.943	0.893	0.843	0.943	INDETERMINATE	2	TRUE	2	0.595009668160019	4		461	892	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546122	29546122	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs894292181	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	305	434	0	ENST00000356175.3:c.1627C>T	p.Gln543Ter	p.Q543*	ENST00000356175	NM_000267.3	543	Cag/Tag	14/57	0.214122655677304	3	FACETS	0.868	0.823	0.914	0.868	0.823	0.914	INDETERMINATE	2	TRUE	1	0.595009668160019	3		434	766	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577540	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	rs1555525498	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	349	664	1	ENST00000269305.4:c.741_742delinsTT	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	247	aaCCgg/aaTTgg	7/11	0.595009668160019	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.595009668160019	1		665	717	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553486	106553486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	276	474	0	ENST00000369096.4:c.1451C>T	p.Pro484Leu	p.P484L	ENST00000369096	NM_001198.3	484	cCc/cTc	5/7	0.368636154403517	3	FACETS	0.819	0.773	0.866	0.819	0.773	0.866	CLONAL	2	TRUE	1	0.595009668160019	3		474	735	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18747431	18747431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	205	311	0	ENST00000266497.5:c.3892G>A	p.Asp1298Asn	p.D1298N	ENST00000266497		1298	Gat/Aat	28/31	0.595009668160019	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.595009668160019	1		311	407	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259355	11259355	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	303	675	0	ENST00000361445.4:c.4213C>T	p.Gln1405Ter	p.Q1405*	ENST00000361445	NM_004958.3	1405	Cag/Tag	28/58	0.368636154403517	3	FACETS	1	0.985	1	0.562	0.529	0.596	CLONAL	1	TRUE	1	0.595009668160019	3		675	1175	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532630	46532630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs903957905	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	326	455	0	ENST00000262741.5:c.448C>T	p.Pro150Ser	p.P150S	ENST00000262741	NM_003629.3	150	Ccc/Tcc	4/10	0.368636154403517	3	FACETS	0.814	0.772	0.857	0.814	0.772	0.857	CLONAL	2	TRUE	1	0.595009668160019	3		455	873	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604668	43604668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371731991	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	332	567	1	ENST00000355710.3:c.1253G>A	p.Arg418Gln	p.R418Q	ENST00000355710	NM_020975.4	418	cGa/cAa	6/20	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.595009668160019	2		568	971	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711887	89711888	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	277	424	5	ENST00000371953.3:c.505_506delinsTT	p.Pro169Phe	p.P169F	ENST00000371953	NM_000314.4	169	CCc/TTc	6/9	0.595009668160019	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.595009668160019	1		429	588	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435135	18435135	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	261	449	0	ENST00000266497.5:c.120T>G	p.Phe40Leu	p.F40L	ENST00000266497		40	ttT/ttG	1/31	0.595009668160019	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.595009668160019	1		449	544	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647187	2647187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	361	621	3	ENST00000342085.4:c.1465C>T	p.Pro489Ser	p.P489S	ENST00000342085	NM_002613.4	489	Cct/Tct	13/14	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.595009668160019	2		624	1006	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664900	29664900	+	splice_donor_variant	Splice_Site	SNP	T	T	G	rs1555534928	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	178	395	0	ENST00000356175.3:c.6641+2T>G		p.X2214_splice	ENST00000356175	NM_000267.3	2214			0.214122655677304	3	FACETS	1	0.975	1	0.562	0.519	0.606	INDETERMINATE	1	TRUE	1	0.595009668160019	3		395	691	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40376887	40376887	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	226	532	0	ENST00000293328.3:c.286-1G>A		p.X96_splice	ENST00000293328	NM_012448.3	96			0.214122655677304	3	FACETS	1	0.982	1	0.57	0.532	0.61	INDETERMINATE	1	TRUE	1	0.595009668160019	3		532	864	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625663	1625664	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	216	771	2	ENST00000344749.5:c.410_411delinsTT	p.Pro137Leu	p.P137L	ENST00000344749	NM_001136139.2	137	cCC/cTT	7/19	1	2	FACETS	0.742	0.69	0.796	0.742	0.69	0.796	SUBCLONAL	1	TRUE	1	0.595009668160019	2		773	978	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627728	14627729	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	329	659	1	ENST00000254322.2:c.341_342delinsTT	p.Thr114Ile	p.T114I	ENST00000254322	NM_006145.1	114	aCC/aTT	2/3	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.595009668160019	2		660	1018	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355234	15355234	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465481670	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	269	565	0	ENST00000263377.2:c.2389C>T	p.Pro797Ser	p.P797S	ENST00000263377	NM_058243.2	797	Ccc/Tcc	13/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.595009668160019	2		565	897	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314625	30314625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	276	620	0	ENST00000262643.3:c.1174G>A	p.Gly392Arg	p.G392R	ENST00000262643	NM_001238.2	392	Ggg/Agg	12/12	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.595009668160019	2		620	919	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445253	29445253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	393	656	0	ENST00000389048.3:c.3472G>A	p.Glu1158Lys	p.E1158K	ENST00000389048	NM_004304.4	1158	Gaa/Aaa	22/29	0.109821213566898	4	FACETS	0.975	0.929	1	0.975	0.929	1	INDETERMINATE	2	TRUE	2	0.595009668160019	4		656	1080	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285854	39285854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	362	544	1	ENST00000402219.2:c.305C>T	p.Pro102Leu	p.P102L	ENST00000402219	NM_005633.3	102	cCt/cTt	3/23	0.109821213566898	4	FACETS	0.939	0.892	0.987	0.939	0.892	0.987	INDETERMINATE	2	TRUE	2	0.595009668160019	4		545	1033	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607420	46607420	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs137853036	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	387	774	0	ENST00000263734.3:c.1609G>T	p.Gly537Trp	p.G537W	ENST00000263734	NM_001430.4	537	Ggg/Tgg	12/16	0.109821213566898	4	FACETS	0.798	0.758	0.839	0.798	0.758	0.839	INDETERMINATE	2	TRUE	2	0.595009668160019	4		774	1300	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137410	202137410	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	271	429	0	ENST00000358485.4:c.638A>G	p.Glu213Gly	p.E213G	ENST00000358485	NM_001080125.1	213	gAa/gGa	4/9	0.109821213566898	4	FACETS	0.892	0.84	0.946	0.892	0.84	0.946	INDETERMINATE	2	TRUE	2	0.595009668160019	4		429	814	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808562	1808562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377402598	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	414	791	0	ENST00000260795.2:c.2175G>A	p.Met725Ile	p.M725I	ENST00000260795		725	atG/atA	16/17	0.206992427256068	3	FACETS	0.754	0.718	0.79	0.754	0.718	0.79	INDETERMINATE	2	TRUE	1	0.595009668160019	3		791	1198	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224566	224566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553997357	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	402	585	0	ENST00000264932.6:c.242C>T	p.Ser81Phe	p.S81F	ENST00000264932	NM_004168.2	81	tCt/tTt	3/15	0.595009668160019	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.595009668160019	1		585	752	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026694	6026694	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1171	65	804	0	ENST00000265849.7:c.1702C>A	p.Pro568Thr	p.P568T	ENST00000265849	NM_000535.5	568	Cca/Aca	11/15	0.17296443329212	2	FACETS	0.177	0.152	0.204	0.088	0.076	0.102	INDETERMINATE	1	TRUE	0	0.595009668160019	2		804	1236	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509426	106509426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	173	651	1	ENST00000359195.3:c.1420C>T	p.Leu474Phe	p.L474F	ENST00000359195	NM_002649.2	474	Ctc/Ttc	2/11	0.17296443329212	2	FACETS	0.623	0.573	0.674	0.311	0.286	0.337	INDETERMINATE	1	TRUE	0	0.595009668160019	2		652	934	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848000	151848000	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	166	302	0	ENST00000262189.6:c.12759A>T	p.Lys4253Asn	p.K4253N	ENST00000262189	NM_170606.2	4253	aaA/aaT	51/59	0.17296443329212	2	FACETS	1	0.981	1	0.59	0.546	0.634	INDETERMINATE	1	TRUE	0	0.595009668160019	2		302	473	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485258	8485258	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs724159856	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	292	551	0	ENST00000356435.5:c.3122C>T	p.Pro1041Leu	p.P1041L	ENST00000356435		1041	cCa/cTa	18/35	0.109821213566898	4	FACETS	0.81	0.764	0.858	0.81	0.764	0.858	INDETERMINATE	2	TRUE	2	0.595009668160019	4		551	966	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518239	8518239	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	222	409	1	ENST00000356435.5:c.1152T>A	p.Ser384Arg	p.S384R	ENST00000356435		384	agT/agA	10/35	0.109821213566898	4	FACETS	0.884	0.827	0.943	0.884	0.827	0.943	INDETERMINATE	2	TRUE	2	0.595009668160019	4		410	673	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158045	27158045	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	421	720	0	ENST00000380036.4:c.269G>A	p.Arg90Lys	p.R90K	ENST00000380036	NM_000459.3	90	aGa/aAa	2/23	0.109821213566898	4	FACETS	0.916	0.873	0.959	0.916	0.873	0.959	INDETERMINATE	2	TRUE	2	0.595009668160019	4		720	1232	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133748259	133748259	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760861323	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	367	588	0	ENST00000318560.5:c.920G>A	p.Arg307Gln	p.R307Q	ENST00000318560	NM_005157.4	307	cGg/cAg	6/11	0.109821213566898	4	FACETS	0.936	0.89	0.983	0.936	0.89	0.983	INDETERMINATE	2	TRUE	2	0.595009668160019	4		588	1051	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755465	133755465	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	344	609	0	ENST00000318560.5:c.1434G>A	p.Trp478Ter	p.W478*	ENST00000318560	NM_005157.4	478	tgG/tgA	9/11	0.109821213566898	4	FACETS	0.835	0.791	0.88	0.835	0.791	0.88	INDETERMINATE	2	TRUE	2	0.595009668160019	4		609	1104	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356165	70356165	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	677	371	0	ENST00000374080.3:c.5060C>T	p.Pro1687Leu	p.P1687L	ENST00000374080		1687	cCc/cTc	37/45	0.595009668160019	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.595009668160019	2		371	932	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858114	152858114	+	synonymous_variant	Silent	SNP	G	G	A	rs376060545	NA	P-0043349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	465	378	0	ENST00000406277.2:c.501C>T	p.Thr167=	p.T167=	ENST00000406277	NM_152274.4	167	acC/acT	6/7	0.595009668160019	2	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.595009668160019	2		378	698	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0043356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	281	506	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.298199410591045	8	FACETS	1	0.984	1	0.285	0.267	0.304	CLONAL	2	TRUE	0	0.32	8		506	1511	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874280	155874280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869025196	NA	P-0043356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	137	549	2	ENST00000368323.3:c.251C>T	p.Ala84Val	p.A84V	ENST00000368323	NM_006912.5	84	gCc/gTc	5/6	1	2	FACETS	0.985	0.896	1	0.985	0.896	1	CLONAL	1	TRUE	1	0.32	2		551	869	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846363	156846363	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs763758904	NA	P-0043356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	125	639	0	ENST00000524377.1:c.1804C>T	p.Arg602Ter	p.R602*	ENST00000524377	NM_002529.3	602	Cga/Tga	14/17	1	2	FACETS	0.853	0.771	0.939	0.853	0.771	0.939	CLONAL	1	TRUE	1	0.32	2		639	916	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447294	187447294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1630	103	658	1	ENST00000232014.4:c.899G>A	p.Ser300Asn	p.S300N	ENST00000232014	NM_001130845.1	300	aGc/aAc	5/10	0.298199410591045	8	FACETS	0.728	0.649	0.813	0.091	0.081	0.102	SUBCLONAL	1	TRUE	0	0.32	8		659	1733	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673149	30673149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs927536226	NA	P-0043356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	105	541	0	ENST00000376406.3:c.3811G>A	p.Gly1271Arg	p.G1271R	ENST00000376406	NM_014641.2	1271	Gga/Aga	10/15	0.294832180598165	2	FACETS	0.752	0.673	0.836	0.376	0.336	0.418	SUBCLONAL	1	TRUE	0	0.32	2		541	873	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401424	401424	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	38	224	0	ENST00000380956.4:c.746A>G	p.Asp249Gly	p.D249G	ENST00000380956	NM_001195286.1	249	gAc/gGc	7/9	1	2	FACETS	0.957	0.797	1	0.957	0.797	1	CLONAL	1	TRUE	1	0.330953906227924	2		224	240	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114208	115114208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	61	658	0	ENST00000257566.3:c.1009G>A	p.Asp337Asn	p.D337N	ENST00000257566	NM_016569.3	337	Gat/Aat	6/8	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.25	NA		658	943	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579329	7579329	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs121912658	NA	P-0043373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	189	621	0	ENST00000269305.4:c.358A>T	p.Lys120Ter	p.K120*	ENST00000269305	NM_001126112.2	120	Aag/Tag	4/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.25	NA		621	938	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604580	43604580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs895556824	NA	P-0043373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	94	759	0	ENST00000355710.3:c.1165C>T	p.Leu389Phe	p.L389F	ENST00000355710	NM_020975.4	389	Ctc/Ttc	6/20	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.25	NA		759	966	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218233	133218233	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	144	631	0	ENST00000320574.5:c.5378G>T	p.Arg1793Met	p.R1793M	ENST00000320574	NM_006231.2	1793	aGg/aTg	39/49	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.25	NA		631	921	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437102	110437102	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1009278565	NA	P-0043373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	21	135	0	ENST00000375856.3:c.1299G>T	p.Met433Ile	p.M433I	ENST00000375856	NM_003749.2	433	atG/atT	1/2	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.25	NA		135	273	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061538	38061538	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	954	337	0	ENST00000250448.2:c.451A>G	p.Ser151Gly	p.S151G	ENST00000250448	NM_004496.3	151	Agc/Ggc	2/2	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.25	NA		337	1418	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003380	42003380	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	51	432	0	ENST00000219905.7:c.2917G>T	p.Ala973Ser	p.A973S	ENST00000219905	NM_001164273.1	973	Gca/Tca	8/24	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.25	NA		432	599	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553558	29553558	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	35	260	0	ENST00000356175.3:c.2107G>T	p.Val703Phe	p.V703F	ENST00000356175	NM_000267.3	703	Gtt/Ttt	18/57	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.25	NA		260	417	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735386	204735386	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	42	331	0	ENST00000302823.3:c.187C>A	p.Pro63Thr	p.P63T	ENST00000302823	NM_005214.4	63	Cca/Aca	2/4	1	2	FACETS	0.769	0.642	0.909	0.769	0.642	0.909	CLONAL	1	TRUE	1	0.25	2		331	437	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62325763	62325763	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	79	647	2	ENST00000360203.5:c.3031G>T	p.Ala1011Ser	p.A1011S	ENST00000360203	NM_001283009.1	1011	Gct/Tct	31/35	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.25	NA		649	1039	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520260	176520260	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	100	748	0	ENST00000292408.4:c.1179G>T	p.Gln393His	p.Q393H	ENST00000292408	NM_213647.1	393	caG/caT	9/18	1	2	FACETS	0.861	0.768	0.961	0.861	0.768	0.961	CLONAL	1	TRUE	1	0.25	2		748	929	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675813	30675813	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	161	756	0	ENST00000376406.3:c.2543G>T	p.Gly848Val	p.G848V	ENST00000376406	NM_014641.2	848	gGa/gTa	8/15	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.25	NA		756	979	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410391	63410391	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	72	406	0	ENST00000330258.3:c.2776G>C	p.Glu926Gln	p.E926Q	ENST00000330258	NM_152424.3	926	Gaa/Caa	2/2	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.25	NA		406	542	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050645	30050645	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0043401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	89	309	0	ENST00000338641.4:c.448-1G>A		p.X150_splice	ENST00000338641	NM_000268.3	150			0.3	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	0	0.3	1		309	383	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557497	21557497	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	123	549	0	ENST00000382592.4:c.2348A>T	p.His783Leu	p.H783L	ENST00000382592	NM_014572.2	783	cAc/cTc	5/8	0.3	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	0	0.3	1		549	649	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	59	320	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.95	0.836	1	0.95	0.836	1	CLONAL	1	TRUE	1	0.766680118071206	2		321	162	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0043402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	29	222	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.7	0.575	0.837	0.7	0.575	0.837	SUBCLONAL	1	TRUE	1	0.766680118071206	2		222	108	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0043402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	8	432	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.053	0.034	0.079	0.053	0.034	0.079	SUBCLONAL	1	TRUE	1	0.766680118071206	2		432	392	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791757	42791757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568504941	NA	P-0043402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	24	528	1	ENST00000575354.2:c.643C>T	p.Arg215Trp	p.R215W	ENST00000575354	NM_015125.3	215	Cgg/Tgg	5/20	0.766680118071206	1	FACETS	0.153	0.12	0.19	0.153	0.12	0.19	SUBCLONAL	1	TRUE	0	0.766680118071206	1		529	253	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791836	42791836	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	102	552	0	ENST00000575354.2:c.722T>G	p.Leu241Arg	p.L241R	ENST00000575354	NM_015125.3	241	cTg/cGg	5/20	0.766680118071206	1	FACETS	0.713	0.651	0.776	0.713	0.651	0.776	SUBCLONAL	1	TRUE	0	0.766680118071206	1		552	230	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593667	55593669	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	rs1060502543	NA	P-0043409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	245	78	0	ENST00000288135.5:c.1735_1737del	p.Asp579del	p.D579del	ENST00000288135	NM_000222.2	578	tATGat/tat	11/21	1	2	FACETS	0.901	0.848	0.955	0.901	0.848	0.955	CLONAL	1	TRUE	1	0.884139756347983	2		78	615	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0043411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	283	566	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.974	1	1	0.996	1	CLONAL	2	TRUE	1	0.325477293281802	2		566	823	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0043411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	198	673	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	1	0.325477293281802	2		673	487	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539951	187539951	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs777631605	NA	P-0043411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	185	375	0	ENST00000441802.2:c.7789C>T	p.Arg2597Ter	p.R2597*	ENST00000441802	NM_005245.3	2597	Cga/Tga	10/27	1	2	FACETS	1	0.969	1	1	0.994	1	CLONAL	2	TRUE	1	0.325477293281802	2		375	529	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424958105	NA	P-0043411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	195	373	0	ENST00000334344.6:c.940C>T	p.Arg314Cys	p.R314C	ENST00000334344	NM_152641.2	314	Cgt/Tgt	8/21	1	2	FACETS	1	0.976	1	1	0.994	1	CLONAL	2	TRUE	1	0.325477293281802	2		373	545	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990351	81990351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	235	499	0	ENST00000359376.3:c.3622G>A	p.Glu1208Lys	p.E1208K	ENST00000359376	NM_002661.3	1208	Gaa/Aaa	32/33	1	2	FACETS	1	0.963	1	1	0.995	1	CLONAL	2	TRUE	1	0.325477293281802	2		499	696	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268137	153268137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752114536	NA	P-0043411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	218	339	1	ENST00000281708.4:c.671G>A	p.Arg224Gln	p.R224Q	ENST00000281708	NM_033632.3	224	cGa/cAa	4/12	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	1	0.325477293281802	2		340	543	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485926	8485926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770180884	NA	P-0043411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	168	403	0	ENST00000356435.5:c.2891C>T	p.Pro964Leu	p.P964L	ENST00000356435		964	cCc/cTc	17/35	1	2	FACETS	1	0.964	1	1	0.993	1	CLONAL	2	TRUE	1	0.325477293281802	2		403	485	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858202	9858202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	212	461	1	ENST00000330684.3:c.3199C>T	p.Arg1067Trp	p.R1067W	ENST00000330684	NM_001134407.1	1067	Cgg/Tgg	13/13	1	2	FACETS	1	0.983	1	1	0.995	1	CLONAL	2	TRUE	1	0.325477293281802	2		462	569	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477164	67477164	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1480492577	NA	P-0043411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	272	544	0	ENST00000327367.4:c.971A>G	p.Tyr324Cys	p.Y324C	ENST00000327367	NM_005902.3	324	tAt/tGt	7/9	1	2	FACETS	1	0.982	1	1	0.996	1	CLONAL	2	TRUE	1	0.325477293281802	2		544	762	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650845	37650845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	353	676	0	ENST00000447079.4:c.2317C>T	p.Arg773Cys	p.R773C	ENST00000447079	NM_015083.1	773	Cgt/Tgt	5/14	1	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	2	TRUE	1	0.325477293281802	2		676	950	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662307	67662307	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	232	422	0	ENST00000264010.4:c.1553C>T	p.Thr518Ile	p.T518I	ENST00000264010	NM_006565.3	518	aCc/aTc	9/12	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.325477293281802	2		422	625	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969189	93969189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868510824	NA	P-0043411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	143	293	1	ENST00000369303.4:c.1807C>T	p.Pro603Ser	p.P603S	ENST00000369303	NM_004440.3	603	Cca/Tca	10/17	1	2	FACETS	1	0.942	1	1	0.992	1	CLONAL	2	TRUE	1	0.325477293281802	2		294	427	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717757	89717758	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1554825249	NA	P-0043411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	61	338	1	ENST00000371953.3:c.783_784del	p.Asn262GlnfsTer35	p.N262Qfs*35	ENST00000371953	NM_000314.4	261	cAG/c	7/9	0.325477293281802	1	FACETS	0.797	0.69	0.912	0.797	0.69	0.912	CLONAL	1	TRUE	0	0.325477293281802	1		339	394	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798510	32798510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746574637	NA	P-0043411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	358	729	1	ENST00000374899.4:c.1346G>A	p.Arg449Gln	p.R449Q	ENST00000374899	NM_018833.2	449	cGa/cAa	8/12	0.325477293281802	5	FACETS	1	0.986	1	0.742	0.702	0.784	CLONAL	2	TRUE	2	0.325477293281802	5		730	1470	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223707	36223707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1468457510	NA	P-0043411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	430	926	1	ENST00000222270.7:c.6257C>T	p.Ser2086Leu	p.S2086L	ENST00000222270	NM_014727.1	2086	tCg/tTg	28/37	1	2	FACETS	1	0.991	1	1	0.997	1	CLONAL	2	TRUE	1	0.325477293281802	2		927	1161	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394695	394695	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	305	593	0	ENST00000399788.2:c.5000C>T	p.Pro1667Leu	p.P1667L	ENST00000399788	NM_001042603.1	1667	cCa/cTa	28/28	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.325477293281802	2		593	792	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427372	49427372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	387	666	0	ENST00000301067.7:c.11116C>T	p.Leu3706Phe	p.L3706F	ENST00000301067	NM_003482.3	3706	Ctt/Ttt	39/54	1	2	FACETS	1	0.99	1	1	0.997	1	CLONAL	2	TRUE	1	0.325477293281802	2		666	1045	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112884133	112884133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	359	546	0	ENST00000351677.2:c.68G>A	p.Arg23Lys	p.R23K	ENST00000351677	NM_002834.3	23	aGa/aAa	2/16	1	2	FACETS	0.909	0.866	0.952	1	0.997	1	CLONAL	3	TRUE	1	0.325477293281802	2		546	809	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55693385	55693385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749045445	NA	P-0043411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	375	737	0	ENST00000284073.2:c.592G>A	p.Gly198Ser	p.G198S	ENST00000284073	NM_138962.2	198	Ggc/Agc	9/14	1	2	FACETS	1	0.99	1	1	0.997	1	CLONAL	2	TRUE	1	0.325477293281802	2		737	1001	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56338945	56338945	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1027827994	NA	P-0043411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	23	13	0	ENST00000348428.3:c.70C>T	p.Pro24Ser	p.P24S	ENST00000348428	NM_006785.3	24	Cct/Tct	1/17	1	2	FACETS	1	0.859	1	1	0.967	1	CLONAL	4	TRUE	1	0.325477293281802	2		13	35	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295130	15295130	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	414	777	0	ENST00000263388.2:c.2542C>T	p.Gln848Ter	p.Q848*	ENST00000263388	NM_000435.2	848	Cag/Tag	16/33	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	1	0.325477293281802	2		777	1097	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216389	36216389	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	455	818	0	ENST00000222270.7:c.3652T>C	p.Cys1218Arg	p.C1218R	ENST00000222270	NM_014727.1	1218	Tgt/Cgt	12/37	1	2	FACETS	1	0.994	1	1	0.997	1	CLONAL	2	TRUE	1	0.325477293281802	2		818	1156	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268730	46268731	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0043411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	261	568	0	ENST00000371998.3:c.3015_3016delinsTT	p.Gln1006Ter	p.Q1006*	ENST00000371998		1005	aaCCaa/aaTTaa	16/23	0.325477293281802	4	FACETS	0.964	0.903	1	0.642	0.602	0.684	CLONAL	2	TRUE	1	0.325477293281802	4		568	1103	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090479	71090479	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	158	309	0	ENST00000318789.4:c.869G>A	p.Ser290Asn	p.S290N	ENST00000318789	NM_032682.5	290	aGt/aAt	11/21	1	2	FACETS	1	0.964	1	1	0.993	1	CLONAL	2	TRUE	1	0.325477293281802	2		309	453	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149243902	149243902	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	279	450	0	ENST00000360632.3:c.916C>T	p.His306Tyr	p.H306Y	ENST00000360632	NM_015472.4	306	Cat/Tat	6/7	1	2	FACETS	1	0.987	1	1	0.996	1	CLONAL	2	TRUE	1	0.325477293281802	2		450	747	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612089	189612089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	284	660	1	ENST00000264731.3:c.1841C>T	p.Ser614Phe	p.S614F	ENST00000264731	NM_003722.4	614	tCt/tTt	14/14	1	2	FACETS	1	0.985	1	1	0.996	1	CLONAL	2	TRUE	1	0.325477293281802	2		661	781	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293689	1293689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	376	785	1	ENST00000310581.5:c.1312C>T	p.Pro438Ser	p.P438S	ENST00000310581	NM_198253.2	438	Ccc/Tcc	2/16	1	2	FACETS	1	0.988	1	1	0.997	1	CLONAL	2	TRUE	1	0.325477293281802	2		786	1038	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751945	57751945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	263	476	0	ENST00000274289.3:c.1292G>A	p.Gly431Glu	p.G431E	ENST00000274289	NM_006622.3	431	gGa/gAa	10/14	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.325477293281802	2		476	685	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962352	2962352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	337	708	1	ENST00000396946.4:c.2185G>A	p.Asp729Asn	p.D729N	ENST00000396946	NM_032415.4	729	Gac/Aac	17/25	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.325477293281802	2		709	919	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468169	50468170	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0043411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	249	526	1	ENST00000331340.3:c.1404_1405delinsAA	p.Val469Met	p.V469M	ENST00000331340	NM_006060.4	468	cgGGtg/cgAAtg	8/8	1	2	FACETS	1	0.953	1	1	0.995	1	CLONAL	2	TRUE	1	0.325477293281802	2		527	752	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080566	5080566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	133	302	0	ENST00000381652.3:c.2317C>T	p.Pro773Ser	p.P773S	ENST00000381652	NM_004972.3	773	Cct/Tct	18/25	1	2	FACETS	1	0.959	1	1	0.991	1	CLONAL	2	TRUE	1	0.325477293281802	2		302	381	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845323	76845323	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	20	161	0	ENST00000373344.5:c.6198T>G	p.Asp2066Glu	p.D2066E	ENST00000373344	NM_000489.3	2066	gaT/gaG	27/35	1	1	FACETS	0.98	0.762	1	0.98	0.762	1	CLONAL	1	TRUE	0	0.325477293281802	1		161	105	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231326	46231329	+	frameshift_variant	Frame_Shift_Del	DEL	TTTT	TTTT	ATC	novel	NA	P-0043411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	141	321	0	ENST00000334344.6:c.1166_1169delinsATC	p.Val389AspfsTer27	p.V389Dfs*27	ENST00000334344	NM_152641.2	389	gTTTTa/gATCa	10/21	1	2	FACETS	1	0.976	1	1	0.992	1	CLONAL	2	TRUE	1	0.325477293281802	2		321	377	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0043508-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	85	251	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.353692888264625	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.353692888264625	3		251	236	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747084	40747084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762809890	NA	P-0043508-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	221	391	1	ENST00000373198.4:c.2998G>A	p.Ala1000Thr	p.A1000T	ENST00000373198	NM_133170.3	1000	Gcc/Acc	22/32	0.353692888264625	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.353692888264625	3		392	666	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221320	1221320	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587776656	NA	P-0043508-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	187	461	0	ENST00000326873.7:c.843del	p.Leu282SerfsTer5	p.L282Sfs*5	ENST00000326873	NM_000455.4	281	ccG/cc	6/10	0.334998394134325	2	FACETS	0.871	0.809	0.935	0.871	0.809	0.935	CLONAL	2	TRUE	0	0.353692888264625	2		461	607	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610490	10610490	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043508-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	204	419	0	ENST00000171111.5:c.220C>T	p.Gln74Ter	p.Q74*	ENST00000171111	NM_203500.1	74	Cag/Tag	2/6	0.334998394134325	2	FACETS	0.953	0.89	1	0.953	0.89	1	CLONAL	2	TRUE	0	0.353692888264625	2		419	605	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692819	89692819	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043508-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	19	232	0	ENST00000371953.3:c.303C>G	p.Ile101Met	p.I101M	ENST00000371953	NM_000314.4	101	atC/atG	5/9	0.353692888264625	3	FACETS	0.795	0.608	1	0.398	0.304	0.506	CLONAL	1	TRUE	1	0.353692888264625	3		232	159	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091749	29091749	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1435731482	NA	P-0043508-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	17	215	0	ENST00000328354.6:c.1208G>T	p.Gly403Val	p.G403V	ENST00000328354	NM_007194.3	403	gGg/gTg	11/15	0.180013108926472	2	FACETS	0.311	0.232	0.406	0.156	0.116	0.203	INDETERMINATE	1	TRUE	0	0.353692888264625	2		215	309	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925348	114925348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043508-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	93	421	0	ENST00000543371.1:c.1426G>T	p.Glu476Ter	p.E476*	ENST00000543371	NM_001198531.1	476	Gaa/Taa	14/14	0.353692888264625	3	FACETS	0.896	0.797	1	0.448	0.398	0.501	CLONAL	1	TRUE	1	0.353692888264625	3		421	691	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008249	29008249	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043508-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	39	246	0	ENST00000282397.4:c.622G>T	p.Glu208Ter	p.E208*	ENST00000282397	NM_002019.4	208	Gaa/Taa	5/30	1	2	FACETS	0.723	0.602	0.857	0.723	0.602	0.857	SUBCLONAL	1	TRUE	1	0.353692888264625	2		246	305	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636892	158636893	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0043508-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	139	340	0	ENST00000263640.3:c.287_288delinsTT	p.Gly96Val	p.G96V	ENST00000263640	NM_001105.4	96	gGG/gTT	4/11	0.324956657397711	3	FACETS	0.883	0.808	0.96	0.883	0.808	0.96	CLONAL	2	TRUE	1	0.353692888264625	3		340	524	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134885791	134885791	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043508-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	240	388	0	ENST00000398015.3:c.1702G>T	p.Ala568Ser	p.A568S	ENST00000398015	NM_004441.4	568	Gct/Tct	9/16	0.318512366932792	4	FACETS	0.891	0.837	0.947	0.891	0.837	0.947	CLONAL	3	TRUE	1	0.353692888264625	4		388	687	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577595	7577598	+	frameshift_variant	Frame_Shift_Del	DEL	CAGT	CAGT	-	novel	NA	P-0043559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	257	594	0	ENST00000269305.4:c.683_686del	p.Asp228ValfsTer18	p.D228Vfs*18	ENST00000269305	NM_001126112.2	228	gACTGt/gt	7/11	0.389728105827262	3	FACETS	0.987	0.929	1	0.658	0.619	0.698	CLONAL	2	TRUE	0	0.433864923012716	3		594	730	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288885	33288885	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	328	487	0	ENST00000374542.5:c.667del	p.Leu223CysfsTer6	p.L223Cfs*6	ENST00000374542	NM_001141970.1	223	Ctg/tg	3/8	0.328138970779344	3	FACETS	0.865	0.823	0.907	0.865	0.823	0.907	CLONAL	3	TRUE	0	0.433864923012716	3		487	709	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436047	51436047	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	55	359	0	ENST00000262662.1:c.7G>T	p.Glu3Ter	p.E3*	ENST00000262662		3	Gag/Tag	3/4	1	2	FACETS	0.701	0.601	0.81	0.701	0.601	0.81	SUBCLONAL	1	TRUE	1	0.34708555132843	2		359	452	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99472841	99472841	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	80	539	0	ENST00000268035.6:c.2837T>G	p.Leu946Trp	p.L946W	ENST00000268035	NM_000875.3	946	tTg/tGg	14/21	1	2	FACETS	0.615	0.54	0.694	0.615	0.54	0.694	SUBCLONAL	1	TRUE	1	0.34708555132843	2		539	750	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411902	116411902	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0043562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	219	733	0	ENST00000397752.3:c.2888-1G>C		p.X963_splice	ENST00000397752	NM_000245.2	963			0.285399666143723	2	FACETS	1	0.992	1	0.748	0.698	0.801	CLONAL	1	TRUE	0	0.34708555132843	2		733	843	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	522	320	1				ENST00000310581	NM_198253.2	-/1132			0.753668105297238	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.753668105297238	1		321	748	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423413	116423413	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913247	NA	P-0043589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	273	310	0	ENST00000397752.3:c.3688T>C	p.Tyr1230His	p.Y1230H	ENST00000397752	NM_000245.2	1230	Tat/Cat	19/21	0.753668105297238	2	FACETS	0.997	0.94	1	0.498	0.47	0.527	CLONAL	1	TRUE	0	0.753668105297238	2		310	727	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054241	30054241	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0043589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	409	559	0	ENST00000338641.4:c.663C>G	p.Tyr221Ter	p.Y221*	ENST00000338641	NM_000268.3	221	taC/taG	7/16	0.753668105297238	1	FACETS	0.979	0.942	1	0.979	0.942	1	CLONAL	1	TRUE	0	0.753668105297238	1		559	691	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38504616	38504616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1258	295	861	0	ENST00000254066.5:c.227C>T	p.Pro76Leu	p.P76L	ENST00000254066	NM_000964.3	76	cCc/cTc	3/9	0.371920707514077	2	FACETS	0.504	0.473	0.536	0.252	0.236	0.268	INDETERMINATE	1	TRUE	0	0.753668105297238	2		861	1553	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0043590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	297	346	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.281066163234511	5	FACETS	0.96	0.905	1			1	CLONAL	3	TRUE	NA	0.281066163234511	5		346	1043	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519985	NA	P-0043590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	203	883	0	ENST00000269305.4:c.857A>G	p.Glu286Gly	p.E286G	ENST00000269305	NM_001126112.2	286	gAa/gGa	8/11	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.281066163234511	2		883	1348	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86667995	86667995	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	27	324	0	ENST00000274376.6:c.1759A>C	p.Asn587His	p.N587H	ENST00000274376	NM_002890.2	587	Aat/Cat	13/25	0.188186704390376	4	FACETS	0.339	0.269	0.419	0.17	0.134	0.21	INDETERMINATE	1	TRUE	2	0.525779870949989	4		324	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0043656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	258	513	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.409511496413445	1	FACETS	0.904	0.847	0.962	0.904	0.847	0.962	CLONAL	1	FALSE	0	0.445084476175433	1		513	997	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242480	55242503	+	inframe_deletion	In_Frame_Del	DEL	AACATCTCCGAAAGCCAACAAGGA	AACATCTCCGAAAGCCAACAAGGA	-	novel	NA	P-0043656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	820	375	0	ENST00000275493.2:c.2252_2275del	p.Thr751_Glu758del	p.T751_E758del	ENST00000275493	NM_005228.3	750	gcAACATCTCCGAAAGCCAACAAGGAa/gca	19/28	0.445084476175433	16	FACETS	1	0.99	1			1	CLONAL	10	FALSE	NA	0.445084476175433	16		375	1463	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040940	47040941	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs1556779417	NA	P-0043656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	233	923	0	ENST00000377604.3:c.1473_1474del	p.Ser492AspfsTer25	p.S492Dfs*25	ENST00000377604	NM_001204468.1	490	tcTGtg/tctg	14/24	0.409511496413445	1	FACETS	0.843	0.786	0.901	0.843	0.786	0.901	CLONAL	1	FALSE	0	0.445084476175433	1		923	966	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421849	49421849	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	125	783	1	ENST00000301067.7:c.14458C>T	p.Pro4820Ser	p.P4820S	ENST00000301067	NM_003482.3	4820	Cca/Tca	46/54	1	2	FACETS	0.458	0.413	0.506	0.458	0.413	0.506	SUBCLONAL	1	FALSE	1	0.445084476175433	2		784	1226	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951082	48951082	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	134	197	0	ENST00000267163.4:c.1244T>G	p.Ile415Arg	p.I415R	ENST00000267163	NM_000321.2	415	aTa/aGa	13/27	0.409511496413445	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	0	0.445084476175433	1		197	422	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058658	42058658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	68	218	0	ENST00000219905.7:c.8378G>A	p.Arg2793Lys	p.R2793K	ENST00000219905	NM_001164273.1	2793	aGg/aAg	24/24	0.409511496413445	1	FACETS	0.738	0.647	0.835	0.738	0.647	0.835	SUBCLONAL	1	FALSE	0	0.445084476175433	1		218	322	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	159	320	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.579992289324083	2		321	527	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0043669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	232	285	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	0.579992289324083	3	FACETS	0.908	0.854	0.963	0.908	0.854	0.963	CLONAL	2	TRUE	1	0.579992289324083	3		285	568	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633380	8633380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768353460	NA	P-0043669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	145	414	1	ENST00000356435.5:c.289G>A	p.Glu97Lys	p.E97K	ENST00000356435		97	Gaa/Aaa	3/35	0.452209519634138	1	FACETS	0.719	0.66	0.779	0.719	0.66	0.779	SUBCLONAL	1	TRUE	0	0.579992289324083	1		415	494	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735422	204735422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	135	416	1	ENST00000302823.3:c.223C>T	p.Arg75Trp	p.R75W	ENST00000302823	NM_005214.4	75	Cgg/Tgg	2/4	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.579992289324083	2		417	432	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120377	94120377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	104	280	0	ENST00000369303.4:c.674C>T	p.Ser225Phe	p.S225F	ENST00000369303	NM_004440.3	225	tCc/tTc	3/17	0.24840968601851	3	FACETS	1	0.977	1	0.637	0.576	0.701	INDETERMINATE	1	TRUE	1	0.579992289324083	3		280	363	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143027	30143027	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	284	915	0	ENST00000389048.3:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000389048	NM_004304.4	167	Cag/Tag	1/29	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.579992289324083	2		915	949	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298174	123298174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	118	435	0	ENST00000358487.5:c.680G>A	p.Gly227Glu	p.G227E	ENST00000358487	NM_000141.4	227	gGa/gAa	6/18	1	2	FACETS	0.807	0.732	0.886	0.807	0.732	0.886	CLONAL	1	TRUE	1	0.579992289324083	2		435	504	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420081	152420081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	131	458	0	ENST00000206249.3:c.1768G>A	p.Gly590Ser	p.G590S	ENST00000206249	NM_000125.3	590	Ggt/Agt	8/8	0.579992289324083	1	FACETS	0.941	0.865	1	0.941	0.865	1	CLONAL	1	TRUE	0	0.579992289324083	1		458	341	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485990	40485990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	183	707	0	ENST00000264657.5:c.875C>T	p.Ser292Phe	p.S292F	ENST00000264657	NM_139276.2	292	tCc/tTc	9/24	1	2	FACETS	0.731	0.675	0.789	0.731	0.675	0.789	SUBCLONAL	1	TRUE	1	0.579992289324083	2		707	863	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111855986	111855986	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	222	633	1	ENST00000341259.2:c.37T>A	p.Ser13Thr	p.S13T	ENST00000341259	NM_005475.2	13	Tcc/Acc	2/8	0.579992289324083	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.579992289324083	1		634	542	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29422358	29422358	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658658	NA	P-0043669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	261	757	0	ENST00000356175.3:c.31C>T	p.Gln11Ter	p.Q11*	ENST00000356175	NM_000267.3	11	Cag/Tag	1/57	0.579992289324083	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.579992289324083	1		757	602	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245497	41245497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	232	842	1	ENST00000357654.3:c.2051C>T	p.Pro684Leu	p.P684L	ENST00000357654	NM_007294.3	684	cCa/cTa	10/23	1	2	FACETS	0.755	0.704	0.808	0.755	0.704	0.808	SUBCLONAL	1	TRUE	1	0.579992289324083	2		843	1059	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492697	56492697	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	158	435	0	ENST00000407977.2:c.242A>G	p.Lys81Arg	p.K81R	ENST00000407977		81	aAa/aGa	2/10	1	2	FACETS	0.969	0.893	1	0.969	0.893	1	CLONAL	1	TRUE	1	0.579992289324083	2		435	562	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905600	50905600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	287	973	0	ENST00000440232.2:c.728C>T	p.Pro243Leu	p.P243L	ENST00000440232	NM_002691.3	243	cCc/cTc	6/27	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.579992289324083	2		973	975	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906424	50906424	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	260	983	0	ENST00000440232.2:c.1085C>T	p.Pro362Leu	p.P362L	ENST00000440232	NM_002691.3	362	cCc/cTc	9/27	1	2	FACETS	0.877	0.822	0.934	0.877	0.822	0.934	CLONAL	1	TRUE	1	0.579992289324083	2		983	1022	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149724	202149724	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	184	542	0	ENST00000358485.4:c.1165G>T	p.Glu389Ter	p.E389*	ENST00000358485	NM_001080125.1	389	Gag/Tag	8/9	1	2	FACETS	0.953	0.883	1	0.953	0.883	1	CLONAL	1	TRUE	1	0.579992289324083	2		542	666	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546760	9546760	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	112	346	0	ENST00000353224.5:c.1262A>C	p.Asp421Ala	p.D421A	ENST00000353224	NM_177990.2	421	gAc/gCc	5/10	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.579992289324083	2		346	377	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755501	39755501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	148	512	0	ENST00000288319.7:c.1264C>T	p.His422Tyr	p.H422Y	ENST00000288319	NM_182918.3	422	Cac/Tac	10/10	1	2	FACETS	0.921	0.846	0.999	0.921	0.846	0.999	CLONAL	1	TRUE	1	0.579992289324083	2		512	554	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050697	30050697	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	123	313	1	ENST00000338641.4:c.499G>T	p.Glu167Ter	p.E167*	ENST00000338641	NM_000268.3	167	Gaa/Taa	5/16	1	2	FACETS	0.83	0.754	0.909	0.83	0.754	0.909	CLONAL	1	TRUE	1	0.579992289324083	2		314	511	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077474	30077491	+	inframe_deletion	In_Frame_Del	DEL	GAACTCAAGACAGAAATC	GAACTCAAGACAGAAATC	-	novel	NA	P-0043669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	89	326	0	ENST00000338641.4:c.1623_1640del	p.Leu542_Glu547del	p.L542_E547del	ENST00000338641	NM_000268.3	541	GAACTCAAGACAGAAATC/-	15/16	1	2	FACETS	0.702	0.626	0.783	0.702	0.626	0.783	SUBCLONAL	1	TRUE	1	0.579992289324083	2		326	437	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920511	134920511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	209	534	0	ENST00000398015.3:c.2326C>T	p.Pro776Ser	p.P776S	ENST00000398015	NM_004441.4	776	Ccc/Tcc	12/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.579992289324083	2		534	644	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293688	1293688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	299	999	0	ENST00000310581.5:c.1313C>T	p.Pro438Leu	p.P438L	ENST00000310581	NM_198253.2	438	cCc/cTc	2/16	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.579992289324083	2		999	1030	SUCCESS
APC	324	MSKCC	GRCh37	5	112175246	112175246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	86	227	0	ENST00000257430.4:c.3955C>T	p.Pro1319Ser	p.P1319S	ENST00000257430	NM_000038.5	1319	Cct/Tct	16/16	1	2	FACETS	0.947	0.847	1	0.947	0.847	1	CLONAL	1	TRUE	1	0.579992289324083	2		227	313	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962271	2962271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867239716	NA	P-0043669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	250	464	0	ENST00000396946.4:c.2266G>A	p.Glu756Lys	p.E756K	ENST00000396946	NM_032415.4	756	Gaa/Aaa	17/25	1	2	FACETS	0.952	0.892	1	0.952	0.892	1	CLONAL	1	TRUE	1	0.579992289324083	2		464	906	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68993035	68993035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	63	297	0	ENST00000288368.4:c.1840C>T	p.Pro614Ser	p.P614S	ENST00000288368	NM_024870.2	614	Cca/Tca	17/40	1	2	FACETS	0.614	0.534	0.7	0.614	0.534	0.7	SUBCLONAL	1	TRUE	1	0.579992289324083	2		297	354	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033173	69033173	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	167	386	0	ENST00000288368.4:c.3613G>A	p.Glu1205Lys	p.E1205K	ENST00000288368	NM_024870.2	1205	Gaa/Aaa	30/40	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.579992289324083	2		386	562	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517895	8517895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	107	306	0	ENST00000356435.5:c.1496G>A	p.Gly499Glu	p.G499E	ENST00000356435		499	gGa/gAa	10/35	0.452209519634138	1	FACETS	0.806	0.732	0.883	0.806	0.732	0.883	CLONAL	1	TRUE	0	0.579992289324083	1		306	325	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169568	27169568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778829843	NA	P-0043669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	103	675	0	ENST00000380036.4:c.569C>T	p.Ser190Leu	p.S190L	ENST00000380036	NM_000459.3	190	tCg/tTg	4/23	0.452209519634138	1	FACETS	0.346	0.309	0.385	0.346	0.309	0.385	SUBCLONAL	1	TRUE	0	0.579992289324083	1		675	729	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212785	27212785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	123	803	0	ENST00000380036.4:c.2767G>A	p.Asp923Asn	p.D923N	ENST00000380036	NM_000459.3	923	Gac/Aac	17/23	0.452209519634138	1	FACETS	0.358	0.323	0.394	0.358	0.323	0.394	SUBCLONAL	1	TRUE	0	0.579992289324083	1		803	842	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36846881	36846881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs865878221	NA	P-0043669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	180	561	0	ENST00000358127.4:c.1058C>T	p.Ser353Leu	p.S353L	ENST00000358127	NM_001280556.1	353	tCg/tTg	9/10	0.452209519634138	1	FACETS	0.801	0.744	0.86	0.801	0.744	0.86	CLONAL	1	TRUE	0	0.579992289324083	1		561	550	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223505	53223505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	163	318	0	ENST00000375401.3:c.3854C>T	p.Ala1285Val	p.A1285V	ENST00000375401	NM_004187.3	1285	gCc/gTc	23/26	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.579992289324083	1		318	283	SUCCESS
AR	367	MSKCC	GRCh37	X	66765374	66765374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760296797	NA	P-0043669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	233	428	0	ENST00000374690.3:c.386G>A	p.Arg129Lys	p.R129K	ENST00000374690	NM_000044.3	129	aGa/aAa	1/8	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.579992289324083	1		428	434	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	216	320	1				ENST00000310581	NM_198253.2	-/1132			0.220876868401997	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.738607963017023	0		321	570	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0043672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	930	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.738607963017023	11	FACETS	0.966	0.95	0.982			1	CLONAL	10	TRUE	NA	0.738607963017023	11		452	1127	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944555	40944555	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	209	558	0	ENST00000373198.4:c.1947del	p.Val650Ter	p.V650*	ENST00000373198	NM_133170.3	649	ccC/cc	12/32	0.738607963017023	3	FACETS	1	0.966	1	0.53	0.494	0.568	CLONAL	1	TRUE	1	0.738607963017023	3		558	731	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509761	106509761	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	123	536	0	ENST00000359195.3:c.1757del	p.Pro586GlnfsTer11	p.P586Qfs*11	ENST00000359195	NM_002649.2	585	caC/ca	2/11	0.738607963017023	3	FACETS	0.804	0.73	0.882	0.402	0.365	0.441	CLONAL	1	TRUE	1	0.738607963017023	3		536	567	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0043692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	181	673	0				ENST00000310581	NM_198253.2	-/1132			0.0676403990601042	4	FACETS	0.931	0.861	1	1	0.988	1	INDETERMINATE	3	TRUE	2	0.201953317578583	4		673	771	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545585	106545585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376453517	NA	P-0043692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	51	296	0	ENST00000359195.3:c.3062G>A	p.Arg1021His	p.R1021H	ENST00000359195	NM_002649.2	1021	cGt/cAt	11/11	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.201953317578583	2		296	495	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0043692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	124	450	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.194530767955774	2	FACETS	0.912	0.827	1	0.912	0.827	1	CLONAL	2	TRUE	0	0.201953317578583	2		450	673	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103515	77103515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	42	266	0	ENST00000356341.3:c.51G>A	p.Met17Ile	p.M17I	ENST00000356341	NM_002576.4	17	atG/atA	2/15	1	2	FACETS	0.881	0.736	1	0.881	0.736	1	CLONAL	1	TRUE	1	0.201953317578583	2		266	472	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989078	41989078	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	75	437	0	ENST00000219905.7:c.1870A>C	p.Lys624Gln	p.K624Q	ENST00000219905	NM_001164273.1	624	Aag/Cag	3/24	0.201953317578583	1	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	0	0.201953317578583	1		437	650	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923728	72923728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	104	594	0	ENST00000268489.5:c.3350G>A	p.Ser1117Asn	p.S1117N	ENST00000268489	NM_006885.3	1117	aGc/aAc	4/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.201953317578583	2		594	799	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572973	7572973	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	69	410	0	ENST00000269305.4:c.1136del	p.Arg379ProfsTer43	p.R379Pfs*43	ENST00000269305	NM_001126112.2	379	cGc/cc	11/11	0.182904658458551	1	FACETS	0.913	0.795	1	0.913	0.795	1	CLONAL	1	TRUE	0	0.201953317578583	1		410	673	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374920	45374920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	59	391	0	ENST00000262160.6:c.923C>T	p.Ser308Leu	p.S308L	ENST00000262160	NM_005901.5	308	tCa/tTa	8/11	0.182904658458551	1	FACETS	0.88	0.757	1	0.88	0.757	1	CLONAL	1	TRUE	0	0.201953317578583	1		391	597	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92355047	92355047	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	31	246	0	ENST00000265734.4:c.430C>T	p.Arg144Cys	p.R144C	ENST00000265734	NM_001259.6	144	Cgc/Tgc	4/8	1	2	FACETS	0.906	0.734	1	0.906	0.734	1	CLONAL	1	TRUE	1	0.201953317578583	2		246	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0043696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	135	779	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.21	2		779	1039	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874261	155874261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352822	NA	P-0043696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	49	450	0	ENST00000368323.3:c.270G>A	p.Met90Ile	p.M90I	ENST00000368323	NM_006912.5	90	atG/atA	5/6	1	2	FACETS	0.639	0.54	0.749	0.639	0.54	0.749	SUBCLONAL	1	TRUE	1	0.21	2		450	730	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247530	71247530	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0043696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	41	279	0	ENST00000318789.4:c.3G>A	p.Met1?	p.M1?	ENST00000318789	NM_032682.5	1	atG/atA	6/21	1	2	FACETS	0.877	0.731	1	0.877	0.731	1	CLONAL	1	TRUE	1	0.21	2		279	445	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97876938	97876938	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	48	418	0	ENST00000289081.3:c.1127G>C	p.Arg376Thr	p.R376T	ENST00000289081	NM_000136.2	376	aGa/aCa	12/15	1	2	FACETS	0.737	0.622	0.864	0.737	0.622	0.864	SUBCLONAL	1	TRUE	1	0.21	2		418	620	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105869	27105878	+	frameshift_variant	Frame_Shift_Del	DEL	GCTCAGATAA	GCTCAGATAA	-	novel	NA	P-0043696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	68	468	0	ENST00000324856.7:c.5483_5492del	p.Ser1828LeufsTer52	p.S1828Lfs*52	ENST00000324856	NM_006015.4	1827	tGCTCAGATAAg/tg	20/20	1	2	FACETS	0.986	0.857	1	0.986	0.857	1	CLONAL	1	TRUE	1	0.21	2		468	657	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880262	155880262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1165493340	NA	P-0043696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	35	346	0	ENST00000368323.3:c.142G>A	p.Glu48Lys	p.E48K	ENST00000368323	NM_006912.5	48	Gaa/Aaa	3/6	1	2	FACETS	0.702	0.575	0.845	0.702	0.575	0.845	SUBCLONAL	1	TRUE	1	0.21	2		346	475	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195400	102195400	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	36	272	1	ENST00000263464.3:c.160G>T	p.Gly54Cys	p.G54C	ENST00000263464	NM_001165.4	54	Ggt/Tgt	2/9	1	2	FACETS	0.708	0.582	0.85	0.708	0.582	0.85	SUBCLONAL	1	TRUE	1	0.21	2		273	484	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212542	133212542	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	160	451	0	ENST00000320574.5:c.5747G>T	p.Trp1916Leu	p.W1916L	ENST00000320574	NM_006231.2	1916	tGg/tTg	42/49	NA	2	FACETS	1	0.978	1			1	INDETERMINATE	2	TRUE	NA	0.21	2		451	650	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95583034	95583034	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0043696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	16	162	0	ENST00000393063.1:c.1510-2A>T		p.X504_splice	ENST00000393063	NM_030621.3	504			1	2	FACETS	0.798	0.592	1	0.798	0.592	1	CLONAL	1	TRUE	1	0.21	2		162	191	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50811766	50811766	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	21	279	0	ENST00000398568.2:c.1043G>C	p.Arg348Thr	p.R348T	ENST00000398568	NM_001042412.1	348	aGa/aCa	7/18	1	2	FACETS	0.592	0.455	0.751	0.592	0.455	0.751	SUBCLONAL	1	TRUE	1	0.21	2		279	338	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251533	10251533	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	136	629	0	ENST00000340748.4:c.3399G>T	p.Glu1133Asp	p.E1133D	ENST00000340748		1133	gaG/gaT	31/40	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.21	2		629	920	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105546	11105546	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	116	553	0	ENST00000358026.2:c.1462G>T	p.Glu488Ter	p.E488*	ENST00000358026	NM_001128849.1	488	Gaa/Taa	9/36	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.21	2		553	837	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31379511	31379512	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0043696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	43	367	1	ENST00000328111.2:c.918_919delinsAA	p.Glu307Lys	p.E307K	ENST00000328111	NM_006892.3	306	ctGGag/ctAAag	8/23	1	2	FACETS	0.824	0.689	0.973	0.824	0.689	0.973	CLONAL	1	TRUE	1	0.21	2		368	497	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72881617	72881617	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	53	329	0	ENST00000325599.8:c.502G>T	p.Val168Phe	p.V168F	ENST00000325599	NM_018130.2	168	Gtt/Ttt	5/11	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.21	2		329	453	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502442	186502442	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	23	250	0	ENST00000323963.5:c.165G>T	p.Lys55Asn	p.K55N	ENST00000323963		55	aaG/aaT	3/11	0.3	1	FACETS	0.693	0.541	0.868	0.693	0.541	0.868	SUBCLONAL	1	TRUE	0	0.21	1		250	283	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974678	21974678	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	rs587778189	NA	P-0043696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	40	445	0	ENST00000304494.5:c.149A>T	p.Gln50Leu	p.Q50L	ENST00000304494	NM_000077.4	50	cAg/cTg	1/3	0.3	1	FACETS	0.615	0.511	0.732	0.615	0.511	0.732	SUBCLONAL	1	TRUE	0	0.21	1		445	554	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931732	39931732	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	198	581	0	ENST00000378444.4:c.2867A>T	p.Lys956Ile	p.K956I	ENST00000378444	NM_001123385.1	956	aAa/aTa	4/15	0.110160422296155	3	FACETS	0.956	0.884	1			1	INDETERMINATE	2	TRUE	NA	0.21	3		581	1090	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357787	70357788	+	missense_variant	Missense_Mutation	DNP	CT	CT	TC	novel	NA	P-0043696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	197	657	0	ENST00000374080.3:c.6038_6039delinsTC	p.Thr2013Ile	p.T2013I	ENST00000374080		2013	aCT/aTC	41/45	0.16335454993943	2	FACETS	0.91	0.842	0.98	0.91	0.842	0.98	CLONAL	2	TRUE	0	0.21	2		657	1031	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288887	212288887	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	19	193	0	ENST00000342788.4:c.2859G>T	p.Met953Ile	p.M953I	ENST00000342788	NM_005235.2	953	atG/atT	23/28	1	2	FACETS	0.745	0.566	0.954	0.745	0.566	0.954	CLONAL	1	TRUE	1	0.21	2		193	243	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692819	89692819	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	143	232	0	ENST00000371953.3:c.303C>G	p.Ile101Met	p.I101M	ENST00000371953	NM_000314.4	101	atC/atG	5/9	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.785941042295303	2		232	341	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665213	138665213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1247	349	793	0	ENST00000330315.3:c.352G>A	p.Glu118Lys	p.E118K	ENST00000330315	NM_023067.3	118	Gag/Aag	1/1	0.785941042295303	4	FACETS	0.994	0.939	1	0.331	0.313	0.35	CLONAL	1	TRUE	1	0.785941042295303	4		793	1596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0043711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	478	883	1	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	1	2	FACETS	0.959	0.918	1	0.959	0.918	1	CLONAL	1	TRUE	1	0.785941042295303	2		884	1268	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039133	49039133	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs587776786	NA	P-0043711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	89	155	0	ENST00000267163.4:c.2212-1G>A		p.X738_splice	ENST00000267163	NM_000321.2	738			0.785941042295303	1	FACETS	0.917	0.842	0.989	0.917	0.842	0.989	CLONAL	1	TRUE	0	0.785941042295303	1		155	150	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333632	70333632	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	220	454	0	ENST00000373644.4:c.1537C>T	p.Gln513Ter	p.Q513*	ENST00000373644	NM_030625.2	513	Cag/Tag	2/12	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.785941042295303	2		454	553	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560455	65560455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	225	358	0	ENST00000358664.4:c.142G>A	p.Asp48Asn	p.D48N	ENST00000358664	NM_002382.4	48	Gac/Aac	3/5	0.785941042295303	1	FACETS	0.979	0.932	1	0.979	0.932	1	CLONAL	1	TRUE	0	0.785941042295303	1		358	355	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55334132	55334132	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	257	468	0	ENST00000284073.2:c.29C>A	p.Ser10Ter	p.S10*	ENST00000284073	NM_138962.2	10	tCg/tAg	1/14	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.785941042295303	2		468	594	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050300	13050300	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	254	503	0	ENST00000316448.5:c.252C>G	p.Phe84Leu	p.F84L	ENST00000316448	NM_004343.3	84	ttC/ttG	3/9	1	2	FACETS	0.912	0.858	0.967	0.912	0.858	0.967	CLONAL	1	TRUE	1	0.785941042295303	2		503	709	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547841	41547841	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	345	366	0	ENST00000263253.7:c.2822C>A	p.Ser941Tyr	p.S941Y	ENST00000263253	NM_001429.3	941	tCc/tAc	15/31	0.771199494128976	2	FACETS	0.952	0.921	0.982	0.952	0.921	0.982	CLONAL	2	TRUE	0	0.785941042295303	2		366	461	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553365	41553365	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	344	442	0	ENST00000263253.7:c.3454G>A	p.Glu1152Lys	p.E1152K	ENST00000263253	NM_001429.3	1152	Gaa/Aaa	18/31	0.771199494128976	2	FACETS	0.91	0.878	0.941	0.91	0.878	0.941	CLONAL	2	TRUE	0	0.785941042295303	2		442	481	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250784	26250784	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	174	385	0	ENST00000446824.2:c.50C>G	p.Pro17Arg	p.P17R	ENST00000446824	NM_021018.2	17	cCg/cGg	1/1	0.771199494128976	2	FACETS	1	0.966	1	0.53	0.493	0.566	CLONAL	1	TRUE	0	0.785941042295303	2		385	418	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	148	320	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.836582606361342	2		321	350	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0043716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	192	864	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	0.9	0.84	0.961	0.9	0.84	0.961	CLONAL	1	TRUE	1	0.836582606361342	2		864	510	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521624	89521624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	161	287	0	ENST00000336596.2:c.2701C>T	p.Leu901Phe	p.L901F	ENST00000336596	NM_005233.5	901	Ctt/Ttt	16/17	1	2	FACETS	0.943	0.875	1	0.943	0.875	1	CLONAL	1	TRUE	1	0.836582606361342	2		287	408	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791818	42791818	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	287	674	1	ENST00000575354.2:c.704G>A	p.Gly235Asp	p.G235D	ENST00000575354	NM_015125.3	235	gGc/gAc	5/20	0.836582606361342	1	FACETS	0.99	0.952	1	0.99	0.952	1	CLONAL	1	TRUE	0	0.836582606361342	1		675	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578440	7578440	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs879254249	NA	P-0043798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	412	737	0	ENST00000269305.4:c.490A>G	p.Lys164Glu	p.K164E	ENST00000269305	NM_001126112.2	164	Aag/Gag	5/11	0.704776859318553	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.704776859318553	1		737	709	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951099	48951100	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0043798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	88	291	0	ENST00000267163.4:c.1265_1266dup	p.Gly423Ter	p.G423*	ENST00000267163	NM_000321.2	421	gat/gATat	13/27	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.704776859318553	2		291	225	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951076	48951286	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAGTATACTGAAAAGAGTGAAGGATATAGGATACATCTTTAAAGAGAAATTTGCTAAAGCTGTGGGACAGGGTTGTGTCGAAATTGGATCACAGGTAACTTGAATTCATTGTAATTCGTGGTACTATAGAGTAATAATATTAAAAGCAGCATCTTTCCAGTTCGTATAAATACTCTAACAGTATTTGTCTAGTAGTATAAAATACTGTCA	AAAGTATACTGAAAAGAGTGAAGGATATAGGATACATCTTTAAAGAGAAATTTGCTAAAGCTGTGGGACAGGGTTGTGTCGAAATTGGATCACAGGTAACTTGAATTCATTGTAATTCGTGGTACTATAGAGTAATAATATTAAAAGCAGCATCTTTCCAGTTCGTATAAATACTCTAACAGTATTTGTCTAGTAGTATAAAATACTGTCA	-	novel	NA	P-0043798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	11	236	0	ENST00000267163.4:c.1238_1332+116del		p.X413_splice	ENST00000267163	NM_000321.2	413		13/27	1	2	FACETS	0.17	0.117	0.235	0.17	0.117	0.235	SUBCLONAL	1	TRUE	1	0.704776859318553	2		236	184	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0043802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	81	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.278188250055699	2		452	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782620	NA	P-0043802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	224	715	0	ENST00000269305.4:c.427G>A	p.Val143Met	p.V143M	ENST00000269305	NM_001126112.2	143	Gtg/Atg	5/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.278188250055699	2		715	1150	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608291	100608291	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	59	331	0	ENST00000308731.7:c.1799G>C	p.Arg600Thr	p.R600T	ENST00000308731	NM_000061.2	600	aGa/aCa	18/19	0.27710666002945	2	FACETS	0.766	0.659	0.882			1	SUBCLONAL	1	TRUE	NA	0.278188250055699	2		331	554	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097803	27097803	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	39	384	0	ENST00000324856.7:c.3392A>T	p.Gln1131Leu	p.Q1131L	ENST00000324856	NM_006015.4	1131	cAg/cTg	12/20	0.278188250055699	1	FACETS	0.4	0.33	0.477	0.4	0.33	0.477	SUBCLONAL	1	TRUE	0	0.278188250055699	1		384	604	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873354	151873354	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	81	311	0	ENST00000262189.6:c.9184G>T	p.Glu3062Ter	p.E3062*	ENST00000262189	NM_170606.2	3062	Gaa/Taa	38/59	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.278188250055699	2		311	475	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970998	21970999	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCCT	novel	NA	P-0043802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	108	443	0	ENST00000304494.5:c.356_359dup	p.Leu121GlyfsTer22	p.L121Gfs*22	ENST00000304494	NM_000077.4	120	gag/gaAGGAg	2/3	0.278188250055699	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.278188250055699	1		443	645	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346431	152346431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	28	274	1	ENST00000359321.1:c.139C>T	p.His47Tyr	p.H47Y	ENST00000359321	NM_005431.1	47	Cat/Tat	3/3	0.234775454357034	6	FACETS	0.666	0.531	0.821			1	SUBCLONAL	1	TRUE	NA	0.234775454357034	6		275	526	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0043815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	66	369	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.234775454357034	2		369	393	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0043815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	45	235	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.151481985248551	3	FACETS	1	0.925	1	0.587	0.494	0.688	CLONAL	1	TRUE	1	0.234775454357034	3		235	365	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433873	78433873	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	38	260	0	ENST00000370768.2:c.226A>G	p.Lys76Glu	p.K76E	ENST00000370768	NM_003902.3	76	Aag/Gag	3/20	0.234775454357034	3	FACETS	1	0.897	1	0.558	0.463	0.664	CLONAL	1	TRUE	1	0.234775454357034	3		260	324	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838314	156838314	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	137	576	0	ENST00000524377.1:c.592G>T	p.Val198Phe	p.V198F	ENST00000524377	NM_002529.3	198	Gtc/Ttc	6/17	0.21928427946554	4	FACETS	0.845	0.768	0.925	0.845	0.768	0.925	CLONAL	2	TRUE	2	0.234775454357034	4		576	853	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164127	108164127	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	17	182	0	ENST00000278616.4:c.4699G>C	p.Asp1567His	p.D1567H	ENST00000278616	NM_000051.3	1567	Gac/Cac	31/63	0.23047766757128	2	FACETS	0.647	0.483	0.839	0.323	0.241	0.42	SUBCLONAL	1	TRUE	0	0.234775454357034	2		182	224	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434762	110434762	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	83	503	0	ENST00000375856.3:c.3639G>T	p.Leu1213Phe	p.L1213F	ENST00000375856	NM_003749.2	1213	ttG/ttT	1/2	0.234775454357034	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.234775454357034	1		503	542	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs483352695	NA	P-0043815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	83	433	0	ENST00000269305.4:c.736A>T	p.Met246Leu	p.M246L	ENST00000269305	NM_001126112.2	246	Atg/Ttg	7/11	0.234775454357034	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.234775454357034	1		433	581	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488718	212488718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267599191	NA	P-0043815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	54	418	1	ENST00000342788.4:c.2131C>T	p.Arg711Cys	p.R711C	ENST00000342788	NM_005235.2	711	Cgt/Tgt	18/28	1	2	FACETS	0.811	0.693	0.941	0.811	0.693	0.941	CLONAL	1	TRUE	1	0.234775454357034	2		419	567	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523315	9523315	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	47	365	0	ENST00000353224.5:c.1922C>A	p.Pro641His	p.P641H	ENST00000353224	NM_177990.2	641	cCc/cAc	9/10	1	2	FACETS	0.72	0.607	0.845	0.72	0.607	0.845	SUBCLONAL	1	TRUE	1	0.234775454357034	2		365	556	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521723	89521723	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	54	326	0	ENST00000336596.2:c.2800G>T	p.Gly934Cys	p.G934C	ENST00000336596	NM_005233.5	934	Ggt/Tgt	16/17	0.151481985248551	3	FACETS	1	0.885	1	0.52	0.445	0.603	CLONAL	1	TRUE	1	0.234775454357034	3		326	494	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156981	106156981	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	30	334	0	ENST00000380013.4:c.1882G>C	p.Glu628Gln	p.E628Q	ENST00000380013	NM_001127208.2	628	Gag/Cag	3/11	1	2	FACETS	0.558	0.449	0.682	0.558	0.449	0.682	SUBCLONAL	1	TRUE	1	0.234775454357034	2		334	458	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164787	106164787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	78	390	1	ENST00000380013.4:c.3655C>T	p.His1219Tyr	p.H1219Y	ENST00000380013	NM_001127208.2	1219	Cac/Tac	6/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.234775454357034	2		391	527	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159054	143159054	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	15	258	0	ENST00000262992.4:c.799G>C	p.Glu267Gln	p.E267Q	ENST00000262992	NM_001101669.1	267	Gaa/Caa	10/24	1	2	FACETS	0.526	0.385	0.695	0.526	0.385	0.695	SUBCLONAL	1	TRUE	1	0.234775454357034	2		258	243	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159059	143159059	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	18	263	0	ENST00000262992.4:c.794C>A	p.Pro265His	p.P265H	ENST00000262992	NM_001101669.1	265	cCt/cAt	10/24	1	2	FACETS	0.613	0.462	0.791	0.613	0.462	0.791	SUBCLONAL	1	TRUE	1	0.234775454357034	2		263	250	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143191851	143191851	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	63	365	0	ENST00000262992.4:c.580G>C	p.Ala194Pro	p.A194P	ENST00000262992	NM_001101669.1	194	Gcc/Ccc	8/24	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.234775454357034	2		365	509	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181471	32181471	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	90	430	0	ENST00000375023.3:c.2314G>T	p.Val772Leu	p.V772L	ENST00000375023	NM_004557.3	772	Gtg/Ttg	14/30	0.151481985248551	3	FACETS	1	0.977	1	0.709	0.63	0.793	CLONAL	1	TRUE	1	0.234775454357034	3		430	604	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508499	106508499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752602335	NA	P-0043815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	20	246	0	ENST00000359195.3:c.493G>A	p.Val165Ile	p.V165I	ENST00000359195	NM_002649.2	165	Gtc/Atc	2/11	0.234775454357034	3	FACETS	0.635	0.485	0.809	0.317	0.242	0.405	SUBCLONAL	1	TRUE	1	0.234775454357034	3		246	300	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346014	152346014	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	41	380	0	ENST00000359321.1:c.556G>C	p.Asp186His	p.D186H	ENST00000359321	NM_005431.1	186	Gac/Cac	3/3	0.234775454357034	6	FACETS	0.684	0.568	0.814			1	SUBCLONAL	1	TRUE	NA	0.234775454357034	6		380	750	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971185	21971185	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	34	351	0	ENST00000304494.5:c.173G>A	p.Arg58Gln	p.R58Q	ENST00000304494	NM_000077.4	58	cGa/cAa	2/3	1	2	FACETS	0.726	0.593	0.875	0.726	0.593	0.875	SUBCLONAL	1	TRUE	1	0.234775454357034	2		351	399	SUCCESS
AXL	558	MSKCC	GRCh37	19	41736935	41736935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776682499	NA	P-0043829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	248	591	2	ENST00000301178.4:c.650G>A	p.Arg217His	p.R217H	ENST00000301178	NM_021913.4	217	cGc/cAc	5/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.384962156799301	2		593	1059	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412156	63412156	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	262	768	2	ENST00000330258.3:c.1011G>T	p.Met337Ile	p.M337I	ENST00000330258	NM_152424.3	337	atG/atT	2/2	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.384962156799301	2		770	1286	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159103	24159103	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	167	424	0	ENST00000263121.7:c.775G>C	p.Asp259His	p.D259H	ENST00000263121	NM_003073.3	259	Gac/Cac	6/9	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.384962156799301	2		424	765	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041647	42041647	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	176	449	1	ENST00000219905.7:c.5842C>T	p.Gln1948Ter	p.Q1948*	ENST00000219905	NM_001164273.1	1948	Cag/Tag	17/24	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.384962156799301	2		450	779	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472583	88472583	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	68	474	0	ENST00000360948.2:c.1972C>A	p.His658Asn	p.H658N	ENST00000360948	NM_001012338.2	658	Cac/Aac	16/19	1	2	FACETS	0.483	0.419	0.551	0.483	0.419	0.551	SUBCLONAL	1	TRUE	1	0.384962156799301	2		474	732	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600528	10600528	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	195	419	0	ENST00000171111.5:c.1327T>A	p.Tyr443Asn	p.Y443N	ENST00000171111	NM_203500.1	443	Tat/Aat	4/6	0.384962156799301	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.384962156799301	1		419	658	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286776	33286776	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	182	480	0	ENST00000374542.5:c.2161A>C	p.Lys721Gln	p.K721Q	ENST00000374542	NM_001141970.1	721	Aag/Cag	7/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.384962156799301	2		480	818	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288391	15288391	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201082692	NA	P-0043841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	362	753	0	ENST00000263388.2:c.4348G>A	p.Ala1450Thr	p.A1450T	ENST00000263388	NM_000435.2	1450	Gcc/Acc	24/33	0.624654006030385	3	FACETS	1	0.985	1	0.551	0.522	0.581	CLONAL	1	TRUE	1	0.624654006030385	3		753	1380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578505	7578505	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	953	1045	0	ENST00000269305.4:c.425del	p.Pro142LeufsTer28	p.P142Lfs*28	ENST00000269305	NM_001126112.2	142	cCt/ct	5/11	0.624654006030385	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.624654006030385	2		1045	1444	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262097	16262097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1481024603	NA	P-0043841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	148	357	0	ENST00000375759.3:c.9362G>A	p.Arg3121Gln	p.R3121Q	ENST00000375759	NM_015001.2	3121	cGg/cAg	11/15	0.504578858337659	4	FACETS	0.987	0.902	1	0.494	0.451	0.538	CLONAL	1	TRUE	2	0.624654006030385	4		357	780	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267340	198267340	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1332470056	NA	P-0043841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	430	497	0	ENST00000335508.6:c.2017A>G	p.Ile673Val	p.I673V	ENST00000335508	NM_012433.2	673	Att/Gtt	14/25	0.624654006030385	3	FACETS	0.987	0.946	1	0.987	0.946	1	CLONAL	2	TRUE	1	0.624654006030385	3		497	915	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347612	89347612	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs75362060	NA	P-0043841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	652	809	0	ENST00000301030.4:c.5338G>T	p.Ala1780Ser	p.A1780S	ENST00000301030	NM_001256183.1	1780	Gcc/Tcc	9/13	0.624654006030385	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.624654006030385	2		809	1025	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120467979	120467979	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	130	776	0	ENST00000256646.2:c.4460T>G	p.Val1487Gly	p.V1487G	ENST00000256646	NM_024408.3	1487	gTc/gGc	25/34	0.0861909065337509	3	FACETS	0.453	0.41	0.499			1	INDETERMINATE	1	TRUE	NA	0.624654006030385	3		776	1206	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444053	49444053	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	561	717	0	ENST00000301067.7:c.3318del	p.Ser1107AlafsTer12	p.S1107Afs*12	ENST00000301067	NM_003482.3	1106	ccC/cc	11/54	0.566201078276316	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.624654006030385	4		717	1394	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975453	26975453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	333	500	0	ENST00000381527.3:c.1079C>T	p.Thr360Met	p.T360M	ENST00000381527	NM_001260.1	360	aCg/aTg	11/13	0.624654006030385	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.624654006030385	2		500	519	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941669	48941678	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAATAAAG	AAAAATAAAG	-	novel	NA	P-0043841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	149	258	1	ENST00000267163.4:c.980_989del	p.Lys327IlefsTer2	p.K327Ifs*2	ENST00000267163	NM_000321.2	327	AAAAATAAAGat/at	10/27	0.624654006030385	2	FACETS	0.883	0.826	0.941	0.883	0.826	0.941	CLONAL	2	TRUE	0	0.624654006030385	2		259	270	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992196	72992196	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs111320371	NA	P-0043841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	732	927	0	ENST00000268489.5:c.1849G>T	p.Val617Phe	p.V617F	ENST00000268489	NM_006885.3	617	Gtt/Ttt	2/10	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.624654006030385	2		927	1116	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805477	46805477	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	776	972	0	ENST00000290295.7:c.479A>C	p.His160Pro	p.H160P	ENST00000290295	NM_006361.5	160	cAt/cCt	1/2	0.566201078276316	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.624654006030385	4		972	1983	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554027	63554027	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	528	629	0	ENST00000307078.5:c.712G>T	p.Asp238Tyr	p.D238Y	ENST00000307078	NM_004655.3	238	Gac/Tac	2/11	0.566201078276316	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.624654006030385	4		629	1269	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121018	29121018	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs137853009	NA	P-0043841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	251	708	1	ENST00000328354.6:c.539G>T	p.Arg180Leu	p.R180L	ENST00000328354	NM_007194.3	180	cGc/cTc	4/15	0.624654006030385	3	FACETS	1	0.962	1	0.52	0.486	0.554	CLONAL	1	TRUE	1	0.624654006030385	3		709	1015	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266513	41266513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763882677	NA	P-0043841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	420	445	0	ENST00000349496.5:c.310G>A	p.Asp104Asn	p.D104N	ENST00000349496	NM_001904.3	104	Gat/Aat	4/15	0.624654006030385	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.624654006030385	2		445	620	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851762	134851762	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1479	535	680	0	ENST00000398015.3:c.1168C>A	p.Arg390Ser	p.R390S	ENST00000398015	NM_004441.4	390	Cgc/Agc	5/16	0.624654006030385	6	FACETS	0.957	0.915	0.999	0.478	0.457	0.5	CLONAL	2	TRUE	2	0.624654006030385	6		680	2014	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286281	66286282	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GA	GA	AG	novel	NA	P-0043841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	226	319	0	ENST00000273854.3:c.1404_1405delinsCT	p.Pro469Ser	p.P469S	ENST00000273854	NM_004439.5	468	gcTCca/gcCTca	6/18	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.624654006030385	2		319	328	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995553	68995553	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	223	710	0	ENST00000288368.4:c.1957G>T	p.Asp653Tyr	p.D653Y	ENST00000288368	NM_024870.2	653	Gat/Tat	18/40	0.566201078276316	4	FACETS	0.872	0.81	0.936	0.436	0.405	0.468	CLONAL	1	TRUE	2	0.624654006030385	4		710	1331	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141583015	141583015	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	682	793	0	ENST00000220592.5:c.232A>C	p.Met78Leu	p.M78L	ENST00000220592	NM_012154.3	78	Atg/Ctg	3/19	0.566201078276316	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	2	0.624654006030385	4		793	1664	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0043852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	275	673	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.898187251148478	2		673	565	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0043852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	421	563	0	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	1	2	FACETS	0.958	0.916	1	0.958	0.916	1	CLONAL	1	TRUE	1	0.898187251148478	2		563	979	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913255	NA	P-0043852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	430	601	0	ENST00000369535.4:c.183A>T	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caT	3/7	1	2	FACETS	0.94	0.899	0.981	0.94	0.899	0.981	CLONAL	1	TRUE	1	0.898187251148478	2		601	1019	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47087991	47087991	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	403	425	0	ENST00000409792.3:c.7084C>T	p.Gln2362Ter	p.Q2362*	ENST00000409792	NM_014159.6	2362	Cag/Tag	16/21	1	2	FACETS	0.948	0.905	0.99	0.948	0.905	0.99	CLONAL	1	TRUE	1	0.898187251148478	2		425	947	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486253	8486253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1256737547	NA	P-0043852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	279	411	0	ENST00000356435.5:c.2564G>A	p.Gly855Asp	p.G855D	ENST00000356435		855	gGc/gAc	17/35	0.855767559225222	2	FACETS	0.91	0.86	0.96	0.455	0.43	0.48	CLONAL	1	TRUE	0	0.898187251148478	2		411	683	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528471	157528471	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	437	631	0	ENST00000346085.5:c.6196C>T	p.Pro2066Ser	p.P2066S	ENST00000346085	NM_020732.3	2066	Ccc/Tcc	20/20	0.898187251148478	1	FACETS	0.916	0.889	0.942	0.916	0.889	0.942	CLONAL	1	TRUE	0	0.898187251148478	1		631	585	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623798	28623798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	269	629	0	ENST00000241453.7:c.856G>A	p.Glu286Lys	p.E286K	ENST00000241453	NM_004119.2	286	Gaa/Aaa	7/24	0.306484411586122	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.898187251148478	0		629	600	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231473	5231473	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	493	722	0	ENST00000357368.4:c.2003C>T	p.Pro668Leu	p.P668L	ENST00000357368	NM_002850.3	668	cCc/cTc	14/38	1	2	FACETS	0.918	0.88	0.956	0.918	0.88	0.956	CLONAL	1	TRUE	1	0.898187251148478	2		722	1196	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553184	106553185	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0043852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	462	600	4	ENST00000369096.4:c.1149_1150delinsAA	p.Glu384Lys	p.E384K	ENST00000369096	NM_001198.3	383	acGGaa/acAAaa	5/7	0.898187251148478	1	FACETS	0.92	0.894	0.945	0.92	0.894	0.945	CLONAL	1	TRUE	0	0.898187251148478	1		604	616	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970983	21970990	+	frameshift_variant	Frame_Shift_Del	DEL	ATCGCGAT	ATCGCGAT	-	novel	NA	P-0043852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	652	515	0	ENST00000304494.5:c.368_375del	p.His123ArgfsTer16	p.H123Rfs*16	ENST00000304494	NM_000077.4	123	cATCGCGAT/c	2/3	0.855767559225222	2	FACETS	0.921	0.903	0.939	0.921	0.903	0.939	CLONAL	2	TRUE	0	0.898187251148478	2		515	788	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0043856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	1282	426	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.581569129478779	8	FACETS	0.949	0.934	0.963			1	CLONAL	8	TRUE	NA	0.581569129478779	8		426	1594	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0043856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	456	590	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.255969663033617	3	FACETS	1	0.989	1	0.719	0.69	0.747	INDETERMINATE	2	TRUE	0	0.581569129478779	3		590	939	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105513	27105513	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0043856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	104	357	0	ENST00000324856.7:c.5125-1G>C		p.X1709_splice	ENST00000324856	NM_006015.4	1709			0.391011213036323	3	FACETS	0.717	0.643	0.795	0.358	0.321	0.398	SUBCLONAL	1	TRUE	1	0.581569129478779	3		357	644	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112745443	112745443	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	312	500	0	ENST00000369452.4:c.761C>T	p.Pro254Leu	p.P254L	ENST00000369452	NM_007373.3	254	cCa/cTa	3/9	0.505307698777714	3	FACETS	0.758	0.717	0.799	0.758	0.717	0.799	SUBCLONAL	2	TRUE	1	0.581569129478779	3		500	914	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944127	81944127	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1369745419	NA	P-0043856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	326	470	0	ENST00000359376.3:c.1736G>T	p.Arg579Leu	p.R579L	ENST00000359376	NM_002661.3	579	cGg/cTg	18/33	0.219919680294413	5	FACETS	1	0.977	1	0.706	0.668	0.745	INDETERMINATE	2	TRUE	2	0.581569129478779	5		470	991	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896557	78896557	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	369	598	0	ENST00000306801.3:c.2554G>T	p.Asp852Tyr	p.D852Y	ENST00000306801	NM_020761.2	852	Gac/Tac	22/34	0.219919680294413	5	FACETS	0.778	0.736	0.821	0.519	0.491	0.547	INDETERMINATE	2	TRUE	2	0.581569129478779	5		598	1527	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770615	40770615	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	211	406	0	ENST00000373198.4:c.2767T>C	p.Trp923Arg	p.W923R	ENST00000373198	NM_133170.3	923	Tgg/Cgg	19/32	NA	2	FACETS	0.904	0.841	0.968			1	INDETERMINATE	1	TRUE	NA	0.581569129478779	2		406	803	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038233	30038233	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	320	389	0	ENST00000338641.4:c.406G>T	p.Glu136Ter	p.E136*	ENST00000338641	NM_000268.3	136	Gag/Tag	4/16	0.471916184476973	2	FACETS	0.789	0.751	0.828	0.789	0.751	0.828	SUBCLONAL	2	TRUE	0	0.581569129478779	2		389	697	SUCCESS
ATR	545	MSKCC	GRCh37	3	142255004	142255005	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	60	201	0	ENST00000350721.4:c.3764dup	p.Leu1255PhefsTer3	p.L1255Ffs*3	ENST00000350721	NM_001184.3	1255	tta/ttTa	20/47	0.391011213036323	3	FACETS	0.637	0.551	0.731	0.319	0.275	0.366	SUBCLONAL	1	TRUE	1	0.581569129478779	3		201	418	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549787	187549787	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	250	378	0	ENST00000441802.2:c.4454A>C	p.Glu1485Ala	p.E1485A	ENST00000441802	NM_005245.3	1485	gAg/gCg	8/27	0.391011213036323	3	FACETS	1	0.992	1	0.686	0.643	0.729	CLONAL	1	TRUE	1	0.581569129478779	3		378	809	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518243	8518243	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	72	312	0	ENST00000356435.5:c.1148T>G	p.Leu383Arg	p.L383R	ENST00000356435		383	cTa/cGa	10/35	0.581569129478779	5	FACETS	0.421	0.367	0.481	0.14	0.122	0.161	SUBCLONAL	1	TRUE	2	0.581569129478779	5		312	1100	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955499	48955499	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	392	340	0	ENST00000267163.4:c.1615G>T	p.Glu539Ter	p.E539*	ENST00000267163	NM_000321.2	539	Gaa/Taa	17/27	0.582068792116484	4	FACETS	0.909	0.877	0.94	0.909	0.877	0.94	CLONAL	4	TRUE	0	0.582068792116484	4		340	586	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528623	89528623	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1237297238	NA	P-0043867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	133	234	0	ENST00000336596.2:c.2923C>T	p.Gln975Ter	p.Q975*	ENST00000336596	NM_005233.5	975	Caa/Taa	17/17	0.582068792116484	4	FACETS	0.951	0.874	1			1	CLONAL	2	TRUE	NA	0.582068792116484	4		234	380	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276641	115276641	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	108	485	0	ENST00000438362.2:c.818A>G	p.Asp273Gly	p.D273G	ENST00000438362	NM_001242891.1	273	gAt/gGt	8/20	0.527877313401801	4	FACETS	0.829	0.745	0.919	0.276	0.248	0.307	CLONAL	1	TRUE	1	0.582068792116484	4		485	708	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40447710	40447710	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	88	618	0	ENST00000345506.4:c.449A>G	p.Glu150Gly	p.E150G	ENST00000345506	NM_003152.3	150	gAg/gGg	6/20	0.582068792116484	3	FACETS	0.557	0.493	0.625	0.186	0.164	0.209	SUBCLONAL	1	TRUE	0	0.582068792116484	3		618	701	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462697	29462697	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0043867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	183	644	0	ENST00000389048.3:c.2205-1G>C		p.X735_splice	ENST00000389048	NM_004304.4	735			0.582068792116484	3	FACETS	1	0.987	1	0.652	0.604	0.7	CLONAL	1	TRUE	1	0.582068792116484	3		644	623	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467670	66467670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	86	303	0	ENST00000273854.3:c.599G>A	p.Arg200Lys	p.R200K	ENST00000273854	NM_004439.5	200	aGa/aAa	3/18	1	2	FACETS	0.988	0.884	1	0.988	0.884	1	CLONAL	1	TRUE	1	0.582068792116484	2		303	299	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521433	187521433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	91	462	0	ENST00000441802.2:c.11722G>A	p.Asp3908Asn	p.D3908N	ENST00000441802	NM_005245.3	3908	Gat/Aat	22/27	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.582068792116484	2		462	299	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0043872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	24	426	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.777	0.616	0.957	0.777	0.616	0.957	CLONAL	1	TRUE	1	0.435314970266624	2		426	142	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422708	49422708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	109	636	0	ENST00000301067.7:c.14285G>A	p.Gly4762Asp	p.G4762D	ENST00000301067	NM_003482.3	4762	gGc/gAc	45/54	0.194785558259465	5	FACETS	0.807	0.728	0.89	0.538	0.485	0.593	INDETERMINATE	2	TRUE	2	0.435314970266624	5		636	513	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	110	565	0	ENST00000326873.7:c.667G>T	p.Glu223Ter	p.E223*	ENST00000326873	NM_000455.4	223	Gag/Tag	5/10	0.435314970266624	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.435314970266624	1		565	378	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597401	10597401	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	159	808	0	ENST00000171111.5:c.1802G>C	p.Arg601Pro	p.R601P	ENST00000171111	NM_203500.1	601	cGg/cCg	6/6	0.435314970266624	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.435314970266624	1		808	448	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095970	11095970	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0043872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	125	809	0	ENST00000358026.2:c.244A>T	p.Lys82Ter	p.K82*	ENST00000358026	NM_001128849.1	82	Aag/Tag	3/36	0.435314970266624	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.435314970266624	1		809	434	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873020	136873020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147198552	NA	P-0043872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	30	331	1	ENST00000241393.3:c.478G>A	p.Val160Ile	p.V160I	ENST00000241393	NM_003467.2	160	Gtc/Atc	2/2	1	2	FACETS	0.378	0.304	0.461	0.378	0.304	0.461	SUBCLONAL	1	TRUE	1	0.435314970266624	2		332	365	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80169106	80169106	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	29	325	0	ENST00000265081.6:c.3302G>T	p.Arg1101Ile	p.R1101I	ENST00000265081	NM_002439.4	1101	aGa/aTa	23/24	0.435314970266624	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.435314970266624	1		325	87	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939672	76939672	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	48	628	0	ENST00000373344.5:c.1076T>C	p.Leu359Pro	p.L359P	ENST00000373344	NM_000489.3	359	cTg/cCg	9/35	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.435314970266624	2		628	209	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020354	123020354	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	36	375	0	ENST00000355640.3:c.842A>T	p.Lys281Met	p.K281M	ENST00000355640		281	aAg/aTg	2/7	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.435314970266624	2		375	160	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195710	123195710	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	46	575	0	ENST00000218089.9:c.1626del	p.Thr543GlnfsTer33	p.T543Qfs*33	ENST00000218089	NM_001042749.1	542	Ggg/gg	17/35	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.435314970266624	2		575	187	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	92	320	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.709116136668008	2		321	217	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888165	112888165	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507510	NA	P-0043908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	13	485	1	ENST00000351677.2:c.181G>T	p.Asp61Tyr	p.D61Y	ENST00000351677	NM_002834.3	61	Gat/Tat	3/16	1	2	FACETS	0.063	0.045	0.087	0.063	0.045	0.087	SUBCLONAL	1	TRUE	1	0.709116136668008	2		486	578	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888211	112888211	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121918465	NA	P-0043908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	83	450	0	ENST00000351677.2:c.227A>T	p.Glu76Val	p.E76V	ENST00000351677	NM_002834.3	76	gAg/gTg	3/16	1	2	FACETS	0.453	0.4	0.509	0.453	0.4	0.509	SUBCLONAL	1	TRUE	1	0.709116136668008	2		450	517	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559149	29559149	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	124	261	0	ENST00000356175.3:c.3256C>T	p.Gln1086Ter	p.Q1086*	ENST00000356175	NM_000267.3	1086	Cag/Tag	25/57	1	2	FACETS	0.861	0.786	0.939	0.861	0.786	0.939	CLONAL	1	TRUE	1	0.709116136668008	2		261	406	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0043908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	152	333	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	0.979	0.904	1	0.979	0.904	1	CLONAL	1	TRUE	1	0.709116136668008	2		333	438	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229291	55229291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4465	563	522	0	ENST00000275493.2:c.1598G>A	p.Arg533Lys	p.R533K	ENST00000275493	NM_005228.3	533	aGg/aAg	13/28	0.709116136668008	20	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.709116136668008	20		522	5028	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659675	NA	P-0043946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	33	439	0	ENST00000269305.4:c.764T>C	p.Ile255Thr	p.I255T	ENST00000269305	NM_001126112.2	255	aTc/aCc	7/11	1	2	FACETS	0.73	0.593	0.885	0.73	0.593	0.885	SUBCLONAL	1	TRUE	1	0.15	2		439	603	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482607	56482607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs993665271	NA	P-0043946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	58	485	0	ENST00000267101.3:c.1064C>T	p.Thr355Ile	p.T355I	ENST00000267101	NM_001982.3	355	aCc/aTc	9/28	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.15	2		485	672	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40498603	40498603	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	28	325	0	ENST00000264657.5:c.257T>G	p.Ile86Ser	p.I86S	ENST00000264657	NM_139276.2	86	aTc/aGc	3/24	1	2	FACETS	0.85	0.679	1	0.85	0.679	1	CLONAL	1	TRUE	1	0.15	2		325	439	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905538	50905538	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	33	579	0	ENST00000440232.2:c.667del	p.Ala223ProfsTer53	p.A223Pfs*53	ENST00000440232	NM_002691.3	222	ccG/cc	6/27	1	2	FACETS	0.709	0.576	0.859	0.709	0.576	0.859	SUBCLONAL	1	TRUE	1	0.15	2		579	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0044005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	334	646	7	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.306997239706764	2	FACETS	0.818	0.782	0.853	0.818	0.782	0.853	INDETERMINATE	2	TRUE	0	0.686567799571807	2		653	595	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170136	32170136	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771019003	NA	P-0044005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	112	571	0	ENST00000375023.3:c.3472C>T	p.Arg1158Ter	p.R1158*	ENST00000375023	NM_004557.3	1158	Cga/Tga	21/30	1	2	FACETS	0.548	0.494	0.605	0.548	0.494	0.605	SUBCLONAL	1	TRUE	1	0.686567799571807	2		571	595	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0044005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	112	253	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.650615948164231	1	FACETS	0.802	0.735	0.871	0.802	0.735	0.871	CLONAL	1	TRUE	0	0.686567799571807	1		253	267	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597396	10597396	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	303	480	0	ENST00000171111.5:c.1807G>T	p.Gly603Trp	p.G603W	ENST00000171111	NM_203500.1	603	Ggg/Tgg	6/6	0.550564355700917	2	FACETS	0.753	0.717	0.789	0.753	0.717	0.789	SUBCLONAL	2	TRUE	0	0.686567799571807	2		480	586	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164005	106164005	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	25	223	0	ENST00000380013.4:c.3515G>T	p.Gly1172Val	p.G1172V	ENST00000380013	NM_001127208.2	1172	gGt/gTt	5/11	0.306997239706764	2	FACETS	0.328	0.26	0.406	0.164	0.13	0.203	INDETERMINATE	1	TRUE	0	0.686567799571807	2		223	222	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600572	43600572	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	249	412	0	ENST00000355710.3:c.798C>G	p.Asp266Glu	p.D266E	ENST00000355710	NM_020975.4	266	gaC/gaG	4/20	0.550564355700917	2	FACETS	0.777	0.736	0.817	0.777	0.736	0.817	SUBCLONAL	2	TRUE	0	0.686567799571807	2		412	467	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279540	123279540	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	264	435	0	ENST00000358487.5:c.892G>C	p.Gly298Arg	p.G298R	ENST00000358487	NM_000141.4	298	Ggc/Cgc	7/18	NA	2	FACETS	0.772	0.733	0.811			1	INDETERMINATE	2	TRUE	NA	0.686567799571807	2		435	498	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136072	64136072	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	186	417	0	ENST00000334205.4:c.1333A>T	p.Arg445Trp	p.R445W	ENST00000334205	NM_003942.2	445	Agg/Tgg	11/17	0.329726297286036	3	FACETS	1	0.986	1	0.622	0.578	0.667	INDETERMINATE	1	TRUE	1	0.686567799571807	3		417	585	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821783	72821783	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	35	289	0	ENST00000268489.5:c.10392G>T	p.Lys3464Asn	p.K3464N	ENST00000268489	NM_006885.3	3464	aaG/aaT	10/10	0.531928066432575	3	FACETS	0.29	0.237	0.349	0.097	0.079	0.117	SUBCLONAL	1	TRUE	0	0.686567799571807	3		289	473	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732352	74732352	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs145534754	NA	P-0044005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	206	259	0	ENST00000359995.5:c.557G>T	p.Arg186Leu	p.R186L	ENST00000359995	NM_001195427.1	186	cGg/cTg	2/3	0.686567799571807	3	FACETS	1	0.992	1	0.493	0.461	0.526	CLONAL	1	TRUE	0	0.686567799571807	3		259	545	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213619	36213619	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	297	554	0	ENST00000222270.7:c.2721G>T	p.Glu907Asp	p.E907D	ENST00000222270	NM_014727.1	907	gaG/gaT	5/37	0.116612976968864	4	FACETS	0.959	0.907	1	0.639	0.605	0.674	INDETERMINATE	2	TRUE	1	0.686567799571807	4		554	761	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25459857	25459857	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	178	396	0	ENST00000264709.3:c.2426T>C	p.Val809Ala	p.V809A	ENST00000264709	NM_175629.2	809	gTg/gCg	21/23	0.616860378584208	3	FACETS	1	0.948	1	0.515	0.476	0.555	CLONAL	1	TRUE	1	0.686567799571807	3		396	676	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426799	212426799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	34	260	0	ENST00000342788.4:c.2316G>T	p.Met772Ile	p.M772I	ENST00000342788	NM_005235.2	772	atG/atT	20/28	0.392238697466262	6	FACETS	0.482	0.393	0.582	0.12	0.098	0.146	INDETERMINATE	1	TRUE	2	0.686567799571807	6		260	488	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84393430	84393430	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	25	166	0	ENST00000321945.7:c.227C>G	p.Ser76Cys	p.S76C	ENST00000321945	NM_139076.2	76	tCt/tGt	4/9	0.306997239706764	2	FACETS	0.398	0.316	0.491	0.199	0.158	0.246	INDETERMINATE	1	TRUE	0	0.686567799571807	2		166	183	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196553	106196553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	94	265	0	ENST00000380013.4:c.4886C>T	p.Pro1629Leu	p.P1629L	ENST00000380013	NM_001127208.2	1629	cCa/cTa	11/11	0.306997239706764	2	FACETS	1	0.955	1	0.548	0.495	0.601	INDETERMINATE	1	TRUE	0	0.686567799571807	2		265	250	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397530	116397530	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	426	289	0	ENST00000397752.3:c.1902C>G	p.Phe634Leu	p.F634L	ENST00000397752	NM_000245.2	634	ttC/ttG	7/21	0.686567799571807	5	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	2	0.686567799571807	5		289	773	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850288	128850290	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0044005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	62	484	0	ENST00000249373.3:c.1552_1554del	p.Glu518del	p.E518del	ENST00000249373	NM_005631.4	517	gtGGAg/gtg	9/12	0.686567799571807	5	FACETS	0.338	0.29	0.389	0.113	0.096	0.13	SUBCLONAL	1	TRUE	2	0.686567799571807	5		484	1086	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873836	151873836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	155	311	0	ENST00000262189.6:c.8702C>T	p.Pro2901Leu	p.P2901L	ENST00000262189	NM_170606.2	2901	cCt/cTt	38/59	0.616860378584208	3	FACETS	0.751	0.695	0.807	0.751	0.695	0.807	SUBCLONAL	2	TRUE	1	0.686567799571807	3		311	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0044028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	379	655	1	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.356464793371077	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.356464793371077	2		656	892	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023909	27023923	+	inframe_deletion	In_Frame_Del	DEL	GCTGCGGCGGCGGCA	GCTGCGGCGGCGGCA	-	rs751352361	NA	P-0044028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	10	73	0	ENST00000324856.7:c.1029_1043del	p.Ala345_Ala349del	p.A345_A349del	ENST00000324856	NM_006015.4	339	GCTGCGGCGGCGGCA/-	1/20	0.356464793371077	4	FACETS	0.692	0.472	0.964			1	SUBCLONAL	1	TRUE	NA	0.356464793371077	4		73	110	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11204706	11204706	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	57	330	0	ENST00000361445.4:c.4871A>C	p.Gln1624Pro	p.Q1624P	ENST00000361445	NM_004958.3	1624	cAg/cCg	34/58	0.269677936860917	4	FACETS	0.747	0.64	0.863	0.373	0.32	0.432	SUBCLONAL	1	TRUE	2	0.356464793371077	4		330	581	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248324	59248324	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	61	182	0	ENST00000371222.2:c.419C>G	p.Ala140Gly	p.A140G	ENST00000371222	NM_002228.3	140	gCa/gGa	1/1	0.310094457308509	4	FACETS	0.947	0.827	1	0.947	0.827	1	CLONAL	2	TRUE	2	0.356464793371077	4		182	245	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129685	11129685	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0044028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	328	553	0	ENST00000358026.2:c.2491A>T	p.Lys831Ter	p.K831*	ENST00000358026	NM_001128849.1	831	Aag/Tag	17/36	0.33271228704012	3	FACETS	0.915	0.869	0.961	0.915	0.869	0.961	CLONAL	3	TRUE	0	0.356464793371077	3		553	790	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732688	204732688	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs138279736	NA	P-0044028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	136	310	0	ENST00000302823.3:c.23G>T	p.Arg8Leu	p.R8L	ENST00000302823	NM_005214.4	8	cGg/cTg	1/4	0.269677936860917	4	FACETS	0.948	0.866	1	0.948	0.866	1	CLONAL	2	TRUE	2	0.356464793371077	4		310	546	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37628905	37628905	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	336	819	0	ENST00000249071.6:c.161G>T	p.Gly54Val	p.G54V	ENST00000249071	NM_002872.4	54	gGg/gTg	3/7	0.356464793371077	3	FACETS	0.95	0.899	1	0.95	0.899	1	CLONAL	2	TRUE	1	0.356464793371077	3		819	1169	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928509	69928509	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	274	597	2	ENST00000352241.4:c.329C>A	p.Thr110Lys	p.T110K	ENST00000352241	NM_198159.2	110	aCg/aAg	2/10	0.269677936860917	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.356464793371077	4		599	973	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332753	153332753	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	64	439	0	ENST00000281708.4:c.203G>T	p.Gly68Val	p.G68V	ENST00000281708	NM_033632.3	68	gGc/gTc	2/12	1	2	FACETS	0.762	0.662	0.871	0.762	0.662	0.871	SUBCLONAL	1	TRUE	1	0.356464793371077	2		439	471	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636760	176636760	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	133	434	0	ENST00000439151.2:c.1360G>T	p.Asp454Tyr	p.D454Y	ENST00000439151	NM_022455.4	454	Gat/Tat	5/23	0.315940979092207	3	FACETS	1	0.983	1	0.447	0.406	0.489	CLONAL	1	TRUE	0	0.356464793371077	3		434	656	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189020	38189020	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1297087312	NA	P-0044028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	214	565	0	ENST00000317025.8:c.994G>T	p.Gly332Cys	p.G332C	ENST00000317025	NM_023034.1	332	Ggt/Tgt	5/24	0.310094457308509	4	FACETS	0.918	0.854	0.984	0.918	0.854	0.984	CLONAL	2	TRUE	2	0.356464793371077	4		565	887	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0044045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	38	304	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.958	0.795	1	0.958	0.795	1	CLONAL	1	TRUE	1	0.26	2		304	305	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6029571	6029571	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs200513014	NA	P-0044045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	30	375	0	ENST00000265849.7:c.1004A>G	p.Asn335Ser	p.N335S	ENST00000265849	NM_000535.5	335	aAt/aGt	10/15	1	2	FACETS	0.543	0.437	0.663	0.543	0.437	0.663	SUBCLONAL	1	TRUE	1	0.26	2		375	425	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059154	47059154	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	54	444	0	ENST00000409792.3:c.7507del	p.Glu2503LysfsTer10	p.E2503Kfs*10	ENST00000409792	NM_014159.6	2503	Gaa/aa	20/21	1	2	FACETS	0.808	0.691	0.937	0.808	0.691	0.937	CLONAL	1	TRUE	1	0.26	2		444	514	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162054	47162055	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0044045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	55	298	0	ENST00000409792.3:c.4070_4071dup	p.Leu1358PhefsTer16	p.L1358Ffs*16	ENST00000409792	NM_014159.6	1357	-/TT	3/21	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.26	2		298	370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691022	NA	P-0044057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	503	475	1	ENST00000269305.4:c.1024del	p.Arg342GlufsTer3	p.R342Efs*3	ENST00000269305	NM_001126112.2	342	Cga/ga	10/11	0.767755159125758	2	FACETS	0.98	0.955	1	0.98	0.955	1	CLONAL	2	TRUE	0	0.792152918013957	2		476	648	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602620	10602620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	927	519	1	ENST00000171111.5:c.958C>T	p.Arg320Trp	p.R320W	ENST00000171111	NM_203500.1	320	Cgg/Tgg	3/6	0.792152918013957	5	FACETS	1	0.984	1	1	0.984	1	CLONAL	4	TRUE	1	0.792152918013957	5		520	1273	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699288	18699288	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867629250	NA	P-0044057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	382	263	0	ENST00000266497.5:c.3389G>A	p.Gly1130Glu	p.G1130E	ENST00000266497		1130	gGa/gAa	24/31	0.792152918013957	5	FACETS	1	0.961	1	1	0.961	1	CLONAL	3	TRUE	2	0.792152918013957	5		263	702	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971058	21971058	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	285	270	0	ENST00000304494.5:c.300del	p.Ala102ArgfsTer44	p.A102Rfs*44	ENST00000304494	NM_000077.4	100	gcC/gc	2/3	0.792152918013957	2	FACETS	0.927	0.893	0.96	0.927	0.893	0.96	CLONAL	2	TRUE	0	0.792152918013957	2		270	388	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965643	93965643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762713500	NA	P-0044057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	286	360	0	ENST00000369303.4:c.2285G>A	p.Arg762His	p.R762H	ENST00000369303	NM_004440.3	762	cGc/cAc	13/17	0.79045974304507	2	FACETS	0.96	0.926	0.993	0.96	0.926	0.993	CLONAL	2	TRUE	0	0.792152918013957	2		360	376	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684080	29684080	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587781502	NA	P-0044057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	357	401	0	ENST00000356175.3:c.7778A>G	p.Lys2593Arg	p.K2593R	ENST00000356175	NM_000267.3	2593	aAg/aGg	52/57	0.727149042653293	4	FACETS	0.941	0.896	0.987	0.941	0.896	0.987	CLONAL	2	TRUE	2	0.792152918013957	4		401	858	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814980	43814980	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	383	376	0	ENST00000372470.3:c.1515C>A	p.Ser505Arg	p.S505R	ENST00000372470	NM_005373.2	505	agC/agA	10/12	0.792152918013957	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.792152918013957	2		376	478	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59871025	59871025	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	264	300	0	ENST00000259008.2:c.1406G>C	p.Ser469Thr	p.S469T	ENST00000259008	NM_032043.2	469	aGt/aCt	10/20	0.792152918013957	6	FACETS	0.855	0.802	0.91	0.428	0.401	0.455	CLONAL	2	TRUE	2	0.792152918013957	6		300	1007	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945618	54945618	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	254	250	0	ENST00000312783.6:c.952C>G	p.Leu318Val	p.L318V	ENST00000312783	NM_198436.1	318	Ctt/Gtt	9/10	0.651470039516564	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	2	0.792152918013957	4		250	477	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202781	128202781	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	411	553	0	ENST00000341105.2:c.939C>A	p.His313Gln	p.H313Q	ENST00000341105	NM_032638.4	313	caC/caA	4/6	0.148817542455883	6	FACETS	1	0.993	1			1	INDETERMINATE	3	TRUE	NA	0.792152918013957	6		553	775	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127463	55127463	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	391	417	0	ENST00000257290.5:c.251T>C	p.Val84Ala	p.V84A	ENST00000257290	NM_006206.4	84	gTc/gCc	3/23	0.651470039516564	4	FACETS	0.873	0.832	0.915	0.873	0.832	0.915	CLONAL	2	TRUE	2	0.792152918013957	4		417	1013	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549314	187549314	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	350	340	0	ENST00000441802.2:c.4804G>T	p.Glu1602Ter	p.E1602*	ENST00000441802	NM_005245.3	1602	Gag/Tag	9/27	0.79045974304507	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.792152918013957	2		340	426	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64290020	64290020	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	167	396	0	ENST00000370651.3:c.463A>G	p.Lys155Glu	p.K155E	ENST00000370651	NM_003463.4	155	Aaa/Gaa	6/6	0.778506153417285	3	FACETS	0.999	0.923	1	0.5	0.461	0.539	CLONAL	1	TRUE	1	0.792152918013957	3		396	589	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100207	157100207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	19	41	0	ENST00000346085.5:c.1144C>T	p.Pro382Ser	p.P382S	ENST00000346085	NM_020732.3	382	Ccc/Tcc	1/20	0.691140336109817	3	FACETS	0.72	0.557	0.904	0.36	0.278	0.452	CLONAL	1	TRUE	1	0.792152918013957	3		41	93	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836861	151836861	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	264	401	0	ENST00000262189.6:c.14359G>T	p.Ala4787Ser	p.A4787S	ENST00000262189	NM_170606.2	4787	Gct/Tct	56/59	0.36223953620902	5	FACETS	1	0.961	1	0.683	0.643	0.723	INDETERMINATE	2	TRUE	2	0.792152918013957	5		401	712	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981903	70981903	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs747860295	NA	P-0044057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	457	526	0	ENST00000276594.2:c.193G>T	p.Ala65Ser	p.A65S	ENST00000276594	NM_024504.3	65	Gcc/Tcc	2/8	0.778506153417285	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.792152918013957	3		526	803	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140165	50140165	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	212	630	0	ENST00000246792.3:c.260A>T	p.Gln87Leu	p.Q87L	ENST00000246792	NM_006270.3	87	cAg/cTg	3/6	0.299282466502384	2	FACETS	0.97	0.906	1	0.97	0.906	1	CLONAL	2	TRUE	0	0.317526243590447	2		630	688	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0044077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	232	664	1	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	0.299282466502384	2	FACETS	0.931	0.871	0.992	0.931	0.871	0.992	CLONAL	2	TRUE	0	0.317526243590447	2		665	785	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359084	81359084	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747693036	NA	P-0044077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	157	374	0	ENST00000222390.5:c.877A>G	p.Met293Val	p.M293V	ENST00000222390	NM_000601.4	293	Atg/Gtg	8/18	0.306978776634997	4	FACETS	0.965	0.892	1	0.965	0.892	1	CLONAL	3	TRUE	1	0.317526243590447	4		374	450	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456671	32456671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	65	258	0	ENST00000332351.3:c.221G>A	p.Arg74Gln	p.R74Q	ENST00000332351	NM_024426.4	74	cGg/cAg	1/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.317526243590447	2		258	344	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715350	117715350	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1466068877	NA	P-0044077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	47	325	0	ENST00000368508.3:c.1139G>T	p.Arg380Ile	p.R380I	ENST00000368508	NM_002944.2	380	aGa/aTa	10/43	0.299282466502384	2	FACETS	1	0.925	1	0.574	0.488	0.667	CLONAL	1	TRUE	0	0.317526243590447	2		325	258	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176176008	176176008	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	118	352	0	ENST00000367669.3:c.107C>A	p.Ser36Ter	p.S36*	ENST00000367669	NM_022457.5	36	tCg/tAg	1/20	0.247698307004141	5	FACETS	0.974	0.882	1	0.65	0.588	0.714	CLONAL	2	TRUE	2	0.317526243590447	5		352	563	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047173	77047173	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	286	589	0	ENST00000356341.3:c.1371G>C	p.Met457Ile	p.M457I	ENST00000356341	NM_002576.4	457	atG/atC	13/15	0.298493966038945	3	FACETS	0.868	0.819	0.917	0.868	0.819	0.917	CLONAL	3	TRUE	0	0.317526243590447	3		589	802	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118706	115118706	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	91	548	0	ENST00000257566.3:c.635A>C	p.Asn212Thr	p.N212T	ENST00000257566	NM_016569.3	212	aAc/aCc	2/8	0.282515727843114	3	FACETS	0.957	0.85	1	0.479	0.425	0.536	CLONAL	1	TRUE	1	0.317526243590447	3		548	694	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423642	88423642	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	72	423	0	ENST00000360948.2:c.2193G>T	p.Met731Ile	p.M731I	ENST00000360948	NM_001012338.2	731	atG/atT	18/19	1	2	FACETS	0.984	0.862	1	0.984	0.862	1	CLONAL	1	TRUE	1	0.317526243590447	2		423	461	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500646	99500646	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779623011	NA	P-0044077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	81	485	0	ENST00000268035.6:c.4079C>T	p.Pro1360Leu	p.P1360L	ENST00000268035	NM_000875.3	1360	cCg/cTg	21/21	1	2	FACETS	0.911	0.804	1	0.911	0.804	1	CLONAL	1	TRUE	1	0.317526243590447	2		485	560	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026227	36026227	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	277	797	0	ENST00000358208.4:c.829G>T	p.Gly277Cys	p.G277C	ENST00000358208		277	Ggc/Tgc	7/12	0.286138001908423	3	FACETS	0.986	0.927	1	0.986	0.927	1	CLONAL	2	TRUE	1	0.317526243590447	3		797	1025	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871240	35871240	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs749131336	NA	P-0044077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	107	403	1	ENST00000303115.3:c.462C>A	p.His154Gln	p.H154Q	ENST00000303115	NM_002185.3	154	caC/caA	4/8	0.317526243590447	5	FACETS	0.782	0.703	0.866	0.521	0.468	0.578	SUBCLONAL	2	TRUE	2	0.317526243590447	5		404	636	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176666785	176666785	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	81	432	0	ENST00000439151.2:c.4221A>T	p.Lys1407Asn	p.K1407N	ENST00000439151	NM_022455.4	1407	aaA/aaT	8/23	0.299282466502384	2	FACETS	1	0.978	1	0.739	0.657	0.827	CLONAL	1	TRUE	0	0.317526243590447	2		432	345	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974330	93974330	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	79	421	1	ENST00000369303.4:c.1724G>T	p.Gly575Val	p.G575V	ENST00000369303	NM_004440.3	575	gGc/gTc	8/17	0.299282466502384	2	FACETS	0.832	0.739	0.929	0.832	0.739	0.929	CLONAL	2	TRUE	0	0.317526243590447	2		422	299	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020560	69020560	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	209	405	0	ENST00000288368.4:c.2932G>T	p.Glu978Ter	p.E978*	ENST00000288368	NM_024870.2	978	Gag/Tag	24/40	0.317526243590447	5	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	2	0.317526243590447	5		405	610	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342863	87342863	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	164	445	0	ENST00000277120.3:c.1148G>T	p.Gly383Val	p.G383V	ENST00000277120		383	gGa/gTa	9/19	0.309157617162576	4	FACETS	0.854	0.79	0.921	0.854	0.79	0.921	CLONAL	3	TRUE	1	0.317526243590447	4		445	531	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250364	110250364	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	124	701	0	ENST00000374672.4:c.311A>G	p.Asp104Gly	p.D104G	ENST00000374672	NM_004235.4	104	gAc/gGc	3/5	0.309157617162576	4	FACETS	1	0.908	1	0.335	0.303	0.37	CLONAL	1	TRUE	1	0.317526243590447	4		701	1023	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028841	47028841	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	216	767	0	ENST00000377604.3:c.146del	p.Gly49AlafsTer85	p.G49Afs*85	ENST00000377604	NM_001204468.1	49	Ggc/gc	3/24	0.299282466502384	2	FACETS	0.885	0.825	0.946	0.885	0.825	0.946	CLONAL	2	TRUE	0	0.317526243590447	2		767	769	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0044081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	233	430	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.643250971826531	4	FACETS	0.939	0.881	0.997	0.626	0.587	0.665	CLONAL	2	TRUE	1	0.643250971826531	4		431	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0044081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	484	590	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.63378557962013	2	FACETS	0.985	0.952	1	0.985	0.952	1	CLONAL	2	TRUE	0	0.643250971826531	2		590	764	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622630	158622630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	173	514	1	ENST00000263640.3:c.869C>T	p.Ser290Leu	p.S290L	ENST00000263640	NM_001105.4	290	tCg/tTg	8/11	0.643250971826531	3	FACETS	1	0.923	1	0.5	0.461	0.54	CLONAL	1	TRUE	1	0.643250971826531	3		515	711	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989385	7989385	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200663524	NA	P-0044081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	504	815	1	ENST00000319144.4:c.301G>A	p.Ala101Thr	p.A101T	ENST00000319144	NM_001139.2	101	Gcc/Acc	2/15	0.63378557962013	2	FACETS	0.984	0.952	1	0.984	0.952	1	CLONAL	2	TRUE	0	0.643250971826531	2		816	796	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451028	70451040	+	frameshift_variant	Frame_Shift_Del	DEL	AATGGAAGAAGAT	AATGGAAGAAGAT	-	novel	NA	P-0044081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	158	534	0	ENST00000373644.4:c.5868_5880del	p.Met1957SerfsTer59	p.M1957Sfs*59	ENST00000373644	NM_030625.2	1956	ccAATGGAAGAAGAT/cc	12/12	1	2	FACETS	0.885	0.816	0.957	0.885	0.816	0.957	CLONAL	1	TRUE	1	0.643250971826531	2		534	555	SUCCESS
APC	324	MSKCC	GRCh37	5	112151280	112151281	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0044081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	200	340	0	ENST00000257430.4:c.926dup	p.Thr310AsnfsTer17	p.T310Nfs*17	ENST00000257430	NM_000038.5	308	ctg/ctGg	9/16	0.63378557962013	2	FACETS	0.904	0.854	0.953	0.904	0.854	0.953	CLONAL	2	TRUE	0	0.643250971826531	2		340	344	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87366999	87366999	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	126	450	0	ENST00000277120.3:c.1395A>C	p.Lys465Asn	p.K465N	ENST00000277120		465	aaA/aaC	12/19	0.643250971826531	3	FACETS	0.87	0.791	0.954	0.435	0.395	0.477	CLONAL	1	TRUE	1	0.643250971826531	3		450	595	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107140	27107140	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	304	560	1	ENST00000324856.7:c.6753del	p.Phe2251LeufsTer16	p.F2251Lfs*16	ENST00000324856	NM_006015.4	2251	Ttt/tt	20/20	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		561	950	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870252	44870252	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	15	215	0	ENST00000377967.4:c.431A>G	p.Asn144Ser	p.N144S	ENST00000377967	NM_021140.2	144	aAt/aGt	5/29	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		215	250	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0044100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	79	207	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	0.287609066064263	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	2	TRUE	0	0.287609066064263	2		207	262	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386505	81386505	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1305340910	NA	P-0044100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	24	371	0	ENST00000222390.5:c.482G>T	p.Ser161Ile	p.S161I	ENST00000222390	NM_000601.4	161	aGc/aTc	4/18	0.275513824795786	2	FACETS	0.506	0.396	0.632	0.253	0.198	0.316	SUBCLONAL	1	TRUE	0	0.287609066064263	2		371	330	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202797	128202797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	229	930	0	ENST00000341105.2:c.923G>A	p.Arg308Gln	p.R308Q	ENST00000341105	NM_032638.4	308	cGg/cAg	4/6	0.287609066064263	3	FACETS	1	0.989	1	0.669	0.622	0.718	CLONAL	1	TRUE	1	0.287609066064263	3		930	1361	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456629	32456629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	63	355	2	ENST00000332351.3:c.263G>A	p.Gly88Asp	p.G88D	ENST00000332351	NM_024426.4	88	gGc/gAc	1/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.287609066064263	2		357	334	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416395	49416395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	88	582	1	ENST00000301067.7:c.16316G>A	p.Arg5439Gln	p.R5439Q	ENST00000301067	NM_003482.3	5439	cGg/cAg	51/54	1	2	FACETS	0.929	0.823	1	0.929	0.823	1	CLONAL	1	TRUE	1	0.287609066064263	2		583	659	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133236016	133236016	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	76	805	0	ENST00000320574.5:c.3140G>A	p.Gly1047Glu	p.G1047E	ENST00000320574	NM_006231.2	1047	gGg/gAg	26/49	1	2	FACETS	0.699	0.612	0.792	0.699	0.612	0.792	SUBCLONAL	1	TRUE	1	0.287609066064263	2		805	756	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371778	45371778	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	52	443	0	ENST00000262160.6:c.1213G>C	p.Val405Leu	p.V405L	ENST00000262160	NM_005901.5	405	Gtc/Ctc	10/11	0.255068027808084	4	FACETS	0.869	0.74	1			1	CLONAL	1	TRUE	NA	0.287609066064263	4		443	536	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928973	49928973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	181	905	0	ENST00000296474.3:c.3393G>C	p.Glu1131Asp	p.E1131D	ENST00000296474	NM_002447.2	1131	gaG/gaC	16/20	0.275513824795786	2	FACETS	1	0.985	1	0.643	0.593	0.695	CLONAL	1	TRUE	0	0.287609066064263	2		905	979	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046592	30046592	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	109	672	0	ENST00000331968.5:c.2591G>C	p.Ser864Thr	p.S864T	ENST00000331968	NM_002742.2	864	aGt/aCt	18/18	0.287609066064263				0.919	1				CLONAL	1	TRUE	1	0.287609066064263	3		672	844	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248002	59248003	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	197	768	0	ENST00000371222.2:c.740dup	p.Met247IlefsTer63	p.M247Ifs*63	ENST00000371222	NM_002228.3	247	atg/atTg	1/1	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.639053892908764	2		768	518	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805698	89805698	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs761988162	NA	P-0044126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	29	592	0	ENST00000389301.3:c.4011-1G>A		p.X1337_splice	ENST00000389301	NM_000135.2	1337			0.598135795982925	3	FACETS	0.329	0.264	0.403	0.165	0.132	0.202	SUBCLONAL	1	TRUE	1	0.639053892908764	3		592	364	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266607	198266607	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	47	313	0	ENST00000335508.6:c.2229G>T	p.Leu743Phe	p.L743F	ENST00000335508	NM_012433.2	743	ttG/ttT	16/25	0.639053892908764	3	FACETS	0.929	0.793	1	0.464	0.396	0.537	CLONAL	1	TRUE	1	0.639053892908764	3		313	209	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0044127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	160	552	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.369589092957292	1	FACETS	0.923	0.847	1	0.923	0.847	1	CLONAL	1	TRUE	0	0.369589092957292	1		552	765	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148875	119148875	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs397517076	NA	P-0044127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	32	259	0	ENST00000264033.4:c.1096-1G>T		p.X366_splice	ENST00000264033	NM_005188.3	366			1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	1	0.369589092957292	2		259	167	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602565	10602565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	178	875	1	ENST00000171111.5:c.1013C>T	p.Ser338Leu	p.S338L	ENST00000171111	NM_203500.1	338	tCg/tTg	3/6	0.369589092957292	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.369589092957292	1		876	761	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144147	11144147	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064795161	NA	P-0044127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	175	829	1	ENST00000358026.2:c.3728G>A	p.Arg1243Gln	p.R1243Q	ENST00000358026	NM_001128849.1	1243	cGg/cAg	26/36	0.369589092957292	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.369589092957292	1		830	761	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212113	36212113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757405245	NA	P-0044127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	146	706	2	ENST00000222270.7:c.1864C>T	p.Pro622Ser	p.P622S	ENST00000222270	NM_014727.1	622	Ccc/Tcc	3/37	0.369589092957292	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.369589092957292	1		708	640	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385218	4385218	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	163	462	0	ENST00000261254.3:c.243G>T	p.Met81Ile	p.M81I	ENST00000261254	NM_001759.3	81	atG/atT	2/5	0.369589092957292	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.369589092957292	1		462	608	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450873	70450873	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	143	532	0	ENST00000373644.4:c.5713G>T	p.Gly1905Cys	p.G1905C	ENST00000373644	NM_030625.2	1905	Ggc/Tgc	12/12	0.120355275889616	3	FACETS	1	0.982	1	0.644	0.588	0.702	INDETERMINATE	1	TRUE	1	0.369589092957292	3		532	712	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245403	46245403	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	82	451	0	ENST00000334344.6:c.3497G>T	p.Gly1166Val	p.G1166V	ENST00000334344	NM_152641.2	1166	gGg/gTg	15/21	1	2	FACETS	0.837	0.74	0.941	0.837	0.74	0.941	CLONAL	1	TRUE	1	0.369589092957292	2		451	530	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245776	46245776	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	67	433	0	ENST00000334344.6:c.3872del	p.Gly1291GlufsTer4	p.G1291Efs*4	ENST00000334344	NM_152641.2	1290	gtG/gt	15/21	1	2	FACETS	0.775	0.675	0.882	0.775	0.675	0.882	SUBCLONAL	1	TRUE	1	0.369589092957292	2		433	468	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476298	88476298	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs373273419	NA	P-0044127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	104	635	2	ENST00000360948.2:c.1834C>A	p.Pro612Thr	p.P612T	ENST00000360948	NM_001012338.2	612	Ccc/Acc	15/19	0.369589092957292	1	FACETS	0.577	0.516	0.642	0.577	0.516	0.642	SUBCLONAL	1	TRUE	0	0.369589092957292	1		637	795	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857244	9857244	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1277391984	NA	P-0044127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	95	588	0	ENST00000330684.3:c.4157C>A	p.Pro1386His	p.P1386H	ENST00000330684	NM_001134407.1	1386	cCt/cAt	13/13	0.369589092957292	1	FACETS	0.637	0.567	0.711	0.637	0.567	0.711	SUBCLONAL	1	TRUE	0	0.369589092957292	1		588	658	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923784	72923784	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	194	651	0	ENST00000268489.5:c.3294G>T	p.Lys1098Asn	p.K1098N	ENST00000268489	NM_006885.3	1098	aaG/aaT	4/10	0.258806978599606	3	FACETS	1	0.99	1	0.712	0.659	0.766	CLONAL	1	TRUE	1	0.369589092957292	3		651	874	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483930	212483930	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1241007104	NA	P-0044127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	48	492	0	ENST00000342788.4:c.2273G>C	p.Gly758Ala	p.G758A	ENST00000342788	NM_005235.2	758	gGt/gCt	19/28	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.369589092957292	2		492	246	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561384	9561384	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	104	544	0	ENST00000353224.5:c.398G>A	p.Ser133Asn	p.S133N	ENST00000353224	NM_177990.2	133	aGc/aAc	4/10	1	2	FACETS	0.886	0.795	0.983	0.886	0.795	0.983	CLONAL	1	TRUE	1	0.369589092957292	2		544	635	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119545703	119545703	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs1309366195	NA	P-0044127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	79	288	0	ENST00000316626.5:c.1235-1G>C		p.X412_splice	ENST00000316626		412			1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.369589092957292	2		288	416	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430605	181430605	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs981843968	NA	P-0044127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	180	625	0	ENST00000325404.1:c.457G>T	p.Val153Leu	p.V153L	ENST00000325404	NM_003106.3	153	Gtg/Ttg	1/1	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.369589092957292	2		625	800	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972006	55972006	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	79	387	0	ENST00000263923.4:c.1638C>A	p.His546Gln	p.H546Q	ENST00000263923	NM_002253.2	546	caC/caA	12/30	1	2	FACETS	0.816	0.719	0.919	0.816	0.719	0.919	CLONAL	1	TRUE	1	0.369589092957292	2		387	524	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541451	187541451	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	115	447	0	ENST00000441802.2:c.6289G>T	p.Gly2097Cys	p.G2097C	ENST00000441802	NM_005245.3	2097	Ggc/Tgc	10/27	1	2	FACETS	0.972	0.878	1	0.972	0.878	1	CLONAL	1	TRUE	1	0.369589092957292	2		447	640	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940183	31940183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	164	997	1	ENST00000375333.2:c.325C>T	p.Arg109Trp	p.R109W	ENST00000375333	NM_032454.1	109	Cgg/Tgg	2/8	1	2	FACETS	0.95	0.872	1	0.95	0.872	1	CLONAL	1	TRUE	1	0.369589092957292	2		998	934	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730078	41730078	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	102	511	0	ENST00000242208.4:c.451G>T	p.Glu151Ter	p.E151*	ENST00000242208	NM_002192.2	151	Gag/Tag	3/3	1	2	FACETS	0.73	0.653	0.812	0.73	0.653	0.812	SUBCLONAL	1	TRUE	1	0.369589092957292	2		511	756	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81340800	81340800	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	32	196	0	ENST00000222390.5:c.1441G>C	p.Asp481His	p.D481H	ENST00000222390	NM_000601.4	481	Gac/Cac	12/18	1	2	FACETS	0.821	0.671	0.987	0.821	0.671	0.987	CLONAL	1	TRUE	1	0.369589092957292	2		196	211	SUCCESS
ATM	472	MSKCC	GRCh37	11	108183190	108183191	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	95	259	0	ENST00000278616.4:c.5977dup	p.Ser1993LysfsTer2	p.S1993Kfs*2	ENST00000278616	NM_000051.3	1991	gaa/gAaa	40/63	0.926877799219453	1	FACETS	0.873	0.818	0.923	0.873	0.818	0.923	CLONAL	1	TRUE	0	0.926877799219453	1		259	126	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0044246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	210	430	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.511229685241794	5	FACETS	1	0.986	1	0.804	0.751	0.857	CLONAL	2	TRUE	2	0.511229685241794	5		431	602	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207092	1207092	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs778376925	NA	P-0044246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	359	758	0	ENST00000326873.7:c.180C>A	p.Tyr60Ter	p.Y60*	ENST00000326873	NM_000455.4	60	taC/taA	1/10	0.381721469948915	2	FACETS	0.758	0.721	0.796	0.758	0.721	0.796	SUBCLONAL	2	TRUE	0	0.511229685241794	2		758	926	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984451	201984451	+	frameshift_variant,stop_lost	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	179	407	0	ENST00000359651.3:c.1116del	p.Ter372TrpfsTer75	p.*372Wfs*75	ENST00000359651		372	tgA/tg	8/8	0.246540170410002	4	FACETS	1	0.989	1	0.713	0.659	0.769	INDETERMINATE	1	TRUE	2	0.511229685241794	4		407	742	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205781	108205781	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs879254209	NA	P-0044246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	123	283	0	ENST00000278616.4:c.8096C>G	p.Pro2699Arg	p.P2699R	ENST00000278616	NM_000051.3	2699	cCa/cGa	55/63	0.381721469948915	2	FACETS	0.797	0.732	0.863	0.797	0.732	0.863	SUBCLONAL	2	TRUE	0	0.511229685241794	2		283	302	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247243	153247243	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	230	270	0	ENST00000281708.4:c.1559A>G	p.Asp520Gly	p.D520G	ENST00000281708	NM_033632.3	520	gAt/gGt	10/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.762965502765851	2		270	553	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610154	10610154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	461	640	0	ENST00000171111.5:c.556G>A	p.Gly186Ser	p.G186S	ENST00000171111	NM_203500.1	186	Ggc/Agc	2/6	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.762965502765851	2		640	1117	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31423030	31423030	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	147	394	0	ENST00000344624.3:c.3283C>T	p.Arg1095Ter	p.R1095*	ENST00000344624		1095	Cga/Tga	26/33	1	2	FACETS	0.811	0.746	0.878	0.811	0.746	0.878	CLONAL	1	TRUE	1	0.762965502765851	2		394	475	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245912888	245912888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767335863	NA	P-0044248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	135	265	0	ENST00000388985.4:c.1264G>A	p.Asp422Asn	p.D422N	ENST00000388985		422	Gac/Aac	12/12	1	2	FACETS	0.919	0.845	0.996	0.919	0.845	0.996	CLONAL	1	TRUE	1	0.762965502765851	2		265	385	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104359267	104359267	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	299	500	0	ENST00000369902.3:c.988C>T	p.Gln330Ter	p.Q330*	ENST00000369902	NM_016169.3	330	Cag/Tag	8/12	0.762965502765851	1	FACETS	0.96	0.917	1	0.96	0.917	1	CLONAL	1	TRUE	0	0.762965502765851	1		500	505	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200098	67200098	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	48	505	0	ENST00000312629.5:c.485G>C	p.Arg162Pro	p.R162P	ENST00000312629	NM_003952.2	162	cGa/cCa	6/15	1	2	FACETS	0.144	0.121	0.169	0.144	0.121	0.169	SUBCLONAL	1	TRUE	1	0.762965502765851	2		505	875	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976101	18976101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755841787	NA	P-0044248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	342	559	0	ENST00000262803.5:c.2861G>A	p.Arg954Gln	p.R954Q	ENST00000262803	NM_002911.3	954	cGg/cAg	21/24	1	2	FACETS	0.982	0.932	1	0.982	0.932	1	CLONAL	1	TRUE	1	0.762965502765851	2		559	913	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238584	142238584	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	47	238	0	ENST00000350721.4:c.4309G>T	p.Gly1437Cys	p.G1437C	ENST00000350721	NM_001184.3	1437	Ggc/Tgc	24/47	0.762348075494702	3	FACETS	0.349	0.294	0.409	0.174	0.147	0.205	SUBCLONAL	1	TRUE	1	0.762965502765851	3		238	488	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251558	251558	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	55	473	1	ENST00000264932.6:c.1769G>T	p.Gly590Val	p.G590V	ENST00000264932	NM_004168.2	590	gGc/gTc	13/15	1	2	FACETS	0.189	0.161	0.22	0.189	0.161	0.22	SUBCLONAL	1	TRUE	1	0.762965502765851	2		474	762	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672813	86672813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763915835	NA	P-0044248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	139	251	0	ENST00000274376.6:c.2300C>T	p.Ser767Leu	p.S767L	ENST00000274376	NM_002890.2	767	tCg/tTg	17/25	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.762965502765851	2		251	348	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324935	31324935	+	start_lost	Translation_Start_Site	SNP	T	T	A	novel	NA	P-0044248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	164	549	0	ENST00000412585.2:c.1A>T	p.Met1?	p.M1?	ENST00000412585	NM_005514.6	1	Atg/Ttg	1/8	1	2	FACETS	0.469	0.43	0.509	0.469	0.43	0.509	SUBCLONAL	1	TRUE	1	0.762965502765851	2		549	917	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163233	32163233	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	506	820	1	ENST00000375023.3:c.5993G>T	p.Gly1998Val	p.G1998V	ENST00000375023	NM_004557.3	1998	gGa/gTa	30/30	1	2	FACETS	0.981	0.94	1	0.981	0.94	1	CLONAL	1	TRUE	1	0.762965502765851	2		821	1352	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	28	320	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.819	1	1	0.819	1	CLONAL	1	TRUE	1	0.18	2		321	304	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0044261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	14	278	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	1	2	FACETS	0.309	0.222	0.415	0.309	0.222	0.415	SUBCLONAL	1	TRUE	1	0.18	2		278	504	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0044261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	52	533	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.852	0.724	0.993	0.852	0.724	0.993	CLONAL	1	TRUE	1	0.18	2		533	678	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602533	10602533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1048289	NA	P-0044261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	45	604	1	ENST00000171111.5:c.1045G>A	p.Asp349Asn	p.D349N	ENST00000171111	NM_203500.1	349	Gac/Aac	3/6	1	2	FACETS	0.688	0.576	0.811	0.688	0.576	0.811	SUBCLONAL	1	TRUE	1	0.18	2		605	727	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0044287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	57	369	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.215939308890576	3	FACETS	1	0.938	1	0.587	0.504	0.678	CLONAL	1	FALSE	1	0.215939308890576	3		369	498	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0044287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	95	627	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.103336980222977	0	FACETS	0.939	0.836	1			1	INDETERMINATE	1	FALSE	0	0.215939308890576	0		627	735	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391205	139391205	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	97	788	2	ENST00000277541.6:c.6986G>T	p.Ser2329Ile	p.S2329I	ENST00000277541	NM_017617.3	2329	aGt/aTt	34/34	1	2	FACETS	0.864	0.768	0.966	0.864	0.768	0.966	CLONAL	1	FALSE	1	0.215939308890576	2		790	1040	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346832	70346832	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	74	444	0	ENST00000374080.3:c.2699T>C	p.Leu900Pro	p.L900P	ENST00000374080		900	cTg/cCg	20/45	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	FALSE	1	0.215939308890576	2		444	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1064795203	NA	P-0044332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	354	476	0	ENST00000269305.4:c.532C>G	p.His178Asp	p.H178D	ENST00000269305	NM_001126112.2	178	Cac/Gac	5/11	0.263177572289585	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.336275169700535	3		476	759	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593482	215593482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782246	NA	P-0044332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	60	249	0	ENST00000260947.4:c.2252G>A	p.Arg751Gln	p.R751Q	ENST00000260947	NM_000465.2	751	cGg/cAg	11/11	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.336275169700535	2		249	343	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266522	41266522	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	81	327	0	ENST00000349496.5:c.319A>G	p.Met107Val	p.M107V	ENST00000349496	NM_001904.3	107	Atg/Gtg	4/15	0.336275169700535	6	FACETS	1	0.923	1			1	CLONAL	1	TRUE	NA	0.336275169700535	6		327	757	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244267	98244267	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	70	467	0	ENST00000331920.6:c.710A>T	p.Glu237Val	p.E237V	ENST00000331920	NM_000264.3	237	gAa/gTa	5/24	0.322800794806648	3	FACETS	0.756	0.659	0.861	0.378	0.329	0.431	SUBCLONAL	1	TRUE	1	0.336275169700535	3		467	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0044347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	215	782	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.277452953723898	2	FACETS	0.879	0.82	0.941	0.879	0.82	0.941	CLONAL	2	TRUE	0	0.30828616646175	2		782	793	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974751	21974751	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	103	224	0	ENST00000304494.5:c.76G>T	p.Glu26Ter	p.E26*	ENST00000304494	NM_000077.4	26	Gag/Tag	1/3	0.277452953723898	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.30828616646175	2		224	300	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172506	108172506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	51	299	0	ENST00000278616.4:c.5309C>T	p.Ser1770Leu	p.S1770L	ENST00000278616	NM_000051.3	1770	tCa/tTa	35/63	0.30828616646175	4	FACETS	1	0.959	1	0.345	0.294	0.399	CLONAL	1	TRUE	0	0.30828616646175	4		299	314	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974739	21974739	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	114	248	1	ENST00000304494.5:c.88G>T	p.Ala30Ser	p.A30S	ENST00000304494	NM_000077.4	30	Gcg/Tcg	1/3	0.277452953723898	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.30828616646175	2		249	344	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164046	108164046	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	17	148	0	ENST00000278616.4:c.4618G>A	p.Asp1540Asn	p.D1540N	ENST00000278616	NM_000051.3	1540	Gac/Aac	31/63	0.30828616646175	4	FACETS	0.78	0.584	1	0.195	0.146	0.253	CLONAL	1	TRUE	0	0.30828616646175	4		148	185	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739485	145739485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772074149	NA	P-0044347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	117	770	1	ENST00000428558.2:c.1885C>T	p.Arg629Trp	p.R629W	ENST00000428558	NM_004260.3	629	Cgg/Tgg	12/22	0.30828616646175	5	FACETS	1	0.914	1	0.254	0.228	0.282	CLONAL	1	TRUE	1	0.30828616646175	5		771	1091	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243030	105243030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1566818890	NA	P-0044347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	238	791	3	ENST00000349310.3:c.253G>A	p.Glu85Lys	p.E85K	ENST00000349310	NM_001014432.1	85	Gaa/Aaa	5/15	0.30828616646175	3	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	1	0.30828616646175	3		794	891	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434170	121434170	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	155	768	0	ENST00000257555.6:c.1061C>A	p.Thr354Lys	p.T354K	ENST00000257555		354	aCg/aAg	5/10	0.30828616646175	3	FACETS	1	0.986	1	0.687	0.629	0.747	CLONAL	1	TRUE	1	0.30828616646175	3		768	845	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432665	29432665	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs543620241	NA	P-0044347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	61	671	0	ENST00000389048.3:c.3823C>T	p.Arg1275Ter	p.R1275*	ENST00000389048	NM_004304.4	1275	Cga/Tga	25/29	0.30828616646175	6	FACETS	0.678	0.583	0.782	0.17	0.145	0.196	SUBCLONAL	1	TRUE	2	0.30828616646175	6		671	943	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075445	8075554	+	splice_acceptor_variant,splice_donor_variant,intron_variant	Splice_Site	DEL	CTGAAAGGAGAGGAAGCTACTTTGGTCATAAGCGAAGAGCAATCACAGCCTCTCCCATTTTAGTGTCACATATTTATCCAGATTACAGCAGCATTACATCCTCTACTTAC	CTGAAAGGAGAGGAAGCTACTTTGGTCATAAGCGAAGAGCAATCACAGCCTCTCCCATTTTAGTGTCACATATTTATCCAGATTACAGCAGCATTACATCCTCTACTTAC	-	novel	NA	P-0044347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	44	336	0	ENST00000377482.5:c.125+1_126-1del		p.X42_splice	ENST00000377482	NM_018948.3	42			0.30828616646175	5	FACETS	1	0.847	1			1	CLONAL	1	TRUE	NA	0.30828616646175	5		336	414	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447284	49447284	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	178	616	0	ENST00000301067.7:c.814G>T	p.Glu272Ter	p.E272*	ENST00000301067	NM_003482.3	272	Gaa/Taa	6/54	0.251583315946576	4	FACETS	0.855	0.789	0.925	0.855	0.789	0.925	CLONAL	2	TRUE	2	0.30828616646175	4		616	883	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438085	110438085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1194924964	NA	P-0044347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	108	439	1	ENST00000375856.3:c.316G>A	p.Asp106Asn	p.D106N	ENST00000375856	NM_003749.2	106	Gac/Aac	1/2	0.30828616646175	6	FACETS	1	0.911	1	0.17	0.152	0.189	CLONAL	1	TRUE	0	0.30828616646175	6		440	1111	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246510	105246510	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	102	705	0	ENST00000349310.3:c.90G>C	p.Lys30Asn	p.K30N	ENST00000349310	NM_001014432.1	30	aaG/aaC	4/15	0.30828616646175	3	FACETS	1	0.896	1	0.501	0.448	0.558	CLONAL	1	TRUE	1	0.30828616646175	3		705	762	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779840	3779840	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	112	823	1	ENST00000262367.5:c.5208G>C	p.Lys1736Asn	p.K1736N	ENST00000262367	NM_004380.2	1736	aaG/aaC	31/31	0.30828616646175	3	FACETS	0.971	0.872	1	0.485	0.436	0.538	CLONAL	1	TRUE	1	0.30828616646175	3		824	864	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350102	89350102	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	191	786	0	ENST00000301030.4:c.2848G>T	p.Asp950Tyr	p.D950Y	ENST00000301030	NM_001256183.1	950	Gac/Tac	9/13	0.30828616646175	3	FACETS	0.82	0.759	0.883	0.82	0.759	0.883	CLONAL	2	TRUE	1	0.30828616646175	3		786	872	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89806432	89806432	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs878853665	NA	P-0044347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	168	584	0	ENST00000389301.3:c.3904T>C	p.Trp1302Arg	p.W1302R	ENST00000389301	NM_000135.2	1302	Tgg/Cgg	39/43	0.30828616646175	3	FACETS	0.86	0.793	0.931	0.86	0.793	0.931	CLONAL	2	TRUE	1	0.30828616646175	3		584	731	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217641	7217641	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	62	523	0	ENST00000380728.2:c.286G>C	p.Glu96Gln	p.E96Q	ENST00000380728		96	Gag/Cag	4/11	0.277452953723898	2	FACETS	0.762	0.659	0.874	0.381	0.329	0.437	SUBCLONAL	1	TRUE	0	0.30828616646175	2		523	528	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52676062	52676062	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1258762163	NA	P-0044347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	48	274	3	ENST00000394830.3:c.996-1G>T		p.X332_splice	ENST00000394830	NM_018313.4	332			0.293998214686613	3	FACETS	1	0.96	1	0.713	0.608	0.827	CLONAL	1	TRUE	1	0.30828616646175	3		277	252	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461621	138461621	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs1450143044	NA	P-0044347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	103	359	0	ENST00000289153.2:c.400C>G	p.Leu134Val	p.L134V	ENST00000289153	NM_006219.2	134	Ctg/Gtg	3/22	0.30828616646175	3	FACETS	0.969	0.874	1	0.969	0.874	1	CLONAL	2	TRUE	1	0.30828616646175	3		359	398	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141079	55141080	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0044347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	146	387	1	ENST00000257290.5:c.1725_1726delinsTT	p.Asp576Tyr	p.D576Y	ENST00000257290	NM_006206.4	575	gtGGac/gtTTac	12/23	0.30828616646175	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.30828616646175	3		388	481	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540863	187540863	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	104	343	0	ENST00000441802.2:c.6877T>C	p.Ser2293Pro	p.S2293P	ENST00000441802	NM_005245.3	2293	Tct/Cct	10/27	0.292588682734759	4	FACETS	0.929	0.836	1	0.929	0.836	1	CLONAL	2	TRUE	2	0.30828616646175	4		343	475	SUCCESS
APC	324	MSKCC	GRCh37	5	112178100	112178100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878853466	NA	P-0044347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	54	397	0	ENST00000257430.4:c.6809C>T	p.Ser2270Phe	p.S2270F	ENST00000257430	NM_000038.5	2270	tCt/tTt	16/16	0.277452953723898	2	FACETS	0.876	0.75	1	0.438	0.375	0.506	CLONAL	1	TRUE	0	0.30828616646175	2		397	400	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015871	112015871	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	67	446	0	ENST00000368678.4:c.1070G>C	p.Arg357Thr	p.R357T	ENST00000368678		357	aGa/aCa	10/13	0.251583315946576	4	FACETS	1	0.887	1	0.51	0.444	0.582	CLONAL	1	TRUE	2	0.30828616646175	4		446	557	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786887	135786887	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	76	442	0	ENST00000298552.3:c.982C>G	p.Gln328Glu	p.Q328E	ENST00000298552	NM_001162426.1	328	Cag/Gag	10/23	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.30828616646175	2		442	474	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0044380-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	1363	346	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.349852936707819	25	FACETS	0.989	0.973	1			1	CLONAL	22	TRUE	NA	0.349852936707819	25		346	1799	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574000	7574000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044380-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	158	558	0	ENST00000269305.4:c.1027G>T	p.Glu343Ter	p.E343*	ENST00000269305	NM_001126112.2	343	Gag/Tag	10/11	0.349852936707819	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.349852936707819	1		558	730	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033633	48033633	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs764507968	NA	P-0044380-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	99	293	0	ENST00000234420.5:c.3844A>G	p.Thr1282Ala	p.T1282A	ENST00000234420	NM_000179.2	1282	Act/Gct	9/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.349852936707819	2		293	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0044402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	254	532	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.815239352066324	1	FACETS	0.971	0.929	1	0.971	0.929	1	CLONAL	1	TRUE	0	0.815239352066324	1		532	380	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321357	1321357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	128	428	1	ENST00000400841.2:c.398C>T	p.Ala133Val	p.A133V	ENST00000400841		133	gCa/gTa	4/6	0.149503700362056	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.815239352066324	0		429	362	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0044411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	154	575	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.223035877136394	4	FACETS	1	0.987	1	0.738	0.676	0.804	CLONAL	1	FALSE	2	0.296435758687777	4		575	912	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0044411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	248	623	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.209252956373686	3	FACETS	1	0.983	1	0.759	0.711	0.808	CLONAL	2	FALSE	0	0.296435758687777	3		623	844	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333045	70333045	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	166	687	0	ENST00000373644.4:c.950T>A	p.Leu317His	p.L317H	ENST00000373644	NM_030625.2	317	cTt/cAt	2/12	0.295387738102933	3	FACETS	0.954	0.879	1	0.954	0.879	1	CLONAL	2	FALSE	1	0.296435758687777	3		687	674	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348691	89348691	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs142828350	NA	P-0044411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	157	753	0	ENST00000301030.4:c.4259T>C	p.Ile1420Thr	p.I1420T	ENST00000301030	NM_001256183.1	1420	aTt/aCt	9/13	0.288584077699025	4	FACETS	0.92	0.845	0.999	0.92	0.845	0.999	CLONAL	2	FALSE	2	0.296435758687777	4		753	746	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637566	52637601	+	inframe_deletion	In_Frame_Del	DEL	TCTTCCTCTATTTCTTTTGGCAATTTTTCCTTTCTC	TCTTCCTCTATTTCTTTTGGCAATTTTTCCTTTCTC	-	novel	NA	P-0044411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	12	323	0	ENST00000394830.3:c.2715_2750del	p.Glu905_Glu916del	p.E905_E916del	ENST00000394830	NM_018313.4	905	gaGAGAAAGGAAAAATTGCCAAAAGAAATAGAGGAAGAt/gat	18/30	1	2	FACETS	0.587	0.414	0.796	0.587	0.414	0.796	SUBCLONAL	1	FALSE	1	0.296435758687777	2		323	138	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500792	149500792	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1480906257	NA	P-0044411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	216	580	0	ENST00000261799.4:c.2438G>A	p.Gly813Asp	p.G813D	ENST00000261799	NM_002609.3	813	gGc/gAc	17/23	0.288584077699025	4	FACETS	0.995	0.926	1	0.995	0.926	1	CLONAL	2	FALSE	2	0.296435758687777	4		580	949	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440295	52440295	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs776240891	NA	P-0044444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	372	482	0	ENST00000460680.1:c.757C>T	p.Gln253Ter	p.Q253*	ENST00000460680	NM_004656.3	253	Cag/Tag	9/17	0.458154303236011	2	FACETS	0.97	0.925	1	0.97	0.925	1	CLONAL	2	TRUE	0	0.46173494044602	2		482	831	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654596	29654597	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	39	309	0	ENST00000356175.3:c.5287dup	p.Tyr1763LeufsTer6	p.Y1763Lfs*6	ENST00000356175	NM_000267.3	1762	tat/taTt	37/57	1	2	FACETS	0.571	0.474	0.68	0.571	0.474	0.68	SUBCLONAL	1	FALSE	1	0.316824633699685	2		309	431	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0044481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	109	454	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	0.819	0.741	0.899	0.819	0.741	0.899	CLONAL	1	TRUE	1	0.684593596790564	2		454	389	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532809	187532809	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	166	500	0	ENST00000441802.2:c.9584A>G	p.Tyr3195Cys	p.Y3195C	ENST00000441802	NM_005245.3	3195	tAc/tGc	14/27	1	2	FACETS	0.765	0.705	0.826	0.765	0.705	0.826	SUBCLONAL	1	TRUE	1	0.684593596790564	2		500	634	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547234	106547234	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	38	290	0	ENST00000369096.4:c.471C>G	p.Asn157Lys	p.N157K	ENST00000369096	NM_001198.3	157	aaC/aaG	4/7	NA	2	FACETS	0.298	0.247	0.356			1	INDETERMINATE	1	TRUE	NA	0.684593596790564	2		290	372	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0044508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	72	646	7	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.180711192665407	1	FACETS	0.139	0.121	0.159	0.139	0.121	0.159	INDETERMINATE	1	TRUE	0	0.69622853269813	1		653	967	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750600586	NA	P-0044508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	808	838	0	ENST00000269305.4:c.413C>T	p.Ala138Val	p.A138V	ENST00000269305	NM_001126112.2	138	gCc/gTc	5/11	0.180711192665407	1	FACETS	1	0.997	1	1	0.997	1	INDETERMINATE	1	TRUE	0	0.69622853269813	1		838	1238	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	92	207	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.277774831927239	2	FACETS	0.981	0.872	1	0.49	0.436	0.549	CLONAL	1	TRUE	0	0.27873546954723	2		207	673	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781509	9781509	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	126	531	0	ENST00000377346.4:c.1819G>A	p.Glu607Lys	p.E607K	ENST00000377346	NM_005026.3	607	Gag/Aag	15/24	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.27873546954723	2		531	703	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003747	45003747	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs1057519877	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	46	481	0	ENST00000558401.1:c.3G>A	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	atG/atA	1/4	0.239954058533732	2	FACETS	0.471	0.395	0.554	0.235	0.197	0.277	SUBCLONAL	1	TRUE	0	0.27873546954723	2		481	701	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578458	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	207	926	4	ENST00000269305.4:c.472_473delinsTT	p.Arg158Phe	p.R158F	ENST00000269305	NM_001126112.2	158	CGc/TTc	5/11	0.26194547814156	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.27873546954723	1		930	983	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139822	55139822	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868384918	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	37	559	0	ENST00000257290.5:c.1483G>A	p.Glu495Lys	p.E495K	ENST00000257290	NM_006206.4	495	Gag/Aag	10/23	1	2	FACETS	0.369	0.303	0.444	0.369	0.303	0.444	SUBCLONAL	1	TRUE	1	0.27873546954723	2		559	719	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946060	13946060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	45	290	0	ENST00000405192.2:c.1036G>A	p.Glu346Lys	p.E346K	ENST00000405192	NM_001163147.1	346	Gaa/Aaa	10/12	0.205190590571613	3	FACETS	1	0.847	1	0.503	0.423	0.59	CLONAL	1	TRUE	1	0.27873546954723	3		290	366	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372495	118372495	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	82	594	0	ENST00000534358.1:c.6428C>G	p.Ser2143Ter	p.S2143*	ENST00000534358	NM_005933.3	2143	tCa/tGa	26/36	0.27873546954723	2	FACETS	0.769	0.678	0.867	0.385	0.339	0.434	SUBCLONAL	1	TRUE	0	0.27873546954723	2		594	765	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602848	10602848	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	200	1051	1	ENST00000171111.5:c.730G>A	p.Glu244Lys	p.E244K	ENST00000171111	NM_203500.1	244	Gag/Aag	3/6	0.27873546954723	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.27873546954723	1		1052	1232	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549706	226549706	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	68	485	0	ENST00000366794.5:c.2927C>T	p.Ser976Leu	p.S976L	ENST00000366794	NM_001618.3	976	tCa/tTa	22/23	0.205190590571613	3	FACETS	0.782	0.68	0.893	0.391	0.34	0.447	SUBCLONAL	1	TRUE	1	0.27873546954723	3		485	711	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151833982	151833982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	45	492	0	ENST00000262189.6:c.14671G>A	p.Glu4891Lys	p.E4891K	ENST00000262189	NM_170606.2	4891	Gaa/Aaa	59/59	0.27873546954723	3	FACETS	0.521	0.437	0.615	0.261	0.218	0.308	SUBCLONAL	1	TRUE	1	0.27873546954723	3		492	706	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400855	72400855	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	50	343	0	ENST00000357731.5:c.316C>A	p.Gln106Lys	p.Q106K	ENST00000357731	NM_173808.2	106	Cag/Aag	2/7	1	2	FACETS	0.804	0.683	0.937	0.804	0.683	0.937	CLONAL	1	TRUE	1	0.27873546954723	2		343	446	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600468	43600468	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	91	632	0	ENST00000355710.3:c.694G>C	p.Glu232Gln	p.E232Q	ENST00000355710	NM_020975.4	232	Gag/Cag	4/20	0.27873546954723	3	FACETS	0.846	0.75	0.949	0.423	0.375	0.475	CLONAL	1	TRUE	1	0.27873546954723	3		632	879	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118353178	118353178	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1376886285	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	36	304	0	ENST00000534358.1:c.4054A>G	p.Ser1352Gly	p.S1352G	ENST00000534358	NM_005933.3	1352	Agt/Ggt	8/36	0.27873546954723	2	FACETS	0.615	0.506	0.737	0.308	0.253	0.369	SUBCLONAL	1	TRUE	0	0.27873546954723	2		304	420	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441782	49441782	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1214991700	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	43	600	0	ENST00000301067.7:c.4202C>G	p.Ser1401Cys	p.S1401C	ENST00000301067	NM_003482.3	1401	tCt/tGt	14/54	1	2	FACETS	0.385	0.321	0.457	0.385	0.321	0.457	SUBCLONAL	1	TRUE	1	0.27873546954723	2		600	801	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572122	95572122	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	29	316	0	ENST00000393063.1:c.2988-2A>C		p.X996_splice	ENST00000393063	NM_030621.3	996			1	2	FACETS	0.47	0.376	0.576	0.47	0.376	0.576	SUBCLONAL	1	TRUE	1	0.27873546954723	2		316	443	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675055	40675055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	213	800	0	ENST00000249776.8:c.19C>T	p.Pro7Ser	p.P7S	ENST00000249776	NM_033286.3	7	Ccg/Tcg	1/9	0.239954058533732	2	FACETS	0.756	0.702	0.811	0.756	0.702	0.811	SUBCLONAL	2	TRUE	0	0.27873546954723	2		800	1011	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129182	2129182	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	164	864	1	ENST00000219476.3:c.3116C>T	p.Thr1039Met	p.T1039M	ENST00000219476	NM_000548.3	1039	aCg/aTg	27/42	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.27873546954723	2		865	1083	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640763	3640763	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs999262527	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	58	668	0	ENST00000294008.3:c.2876C>T	p.Ser959Phe	p.S959F	ENST00000294008	NM_032444.2	959	tCc/tTc	12/15	1	2	FACETS	0.469	0.401	0.542	0.469	0.401	0.542	SUBCLONAL	1	TRUE	1	0.27873546954723	2		668	888	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656561	3656561	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs768845750	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	143	845	0	ENST00000294008.3:c.674G>C	p.Arg225Thr	p.R225T	ENST00000294008	NM_032444.2	225	aGa/aCa	3/15	1	2	FACETS	0.945	0.86	1	0.945	0.86	1	CLONAL	1	TRUE	1	0.27873546954723	2		845	1086	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934531	9934531	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	107	426	1	ENST00000330684.3:c.1624G>T	p.Gly542Cys	p.G542C	ENST00000330684	NM_001134407.1	542	Ggc/Tgc	7/13	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.27873546954723	2		427	700	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827575	72827575	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	117	700	0	ENST00000268489.5:c.9006G>T	p.Lys3002Asn	p.K3002N	ENST00000268489	NM_006885.3	3002	aaG/aaT	9/10	1	2	FACETS	0.93	0.838	1	0.93	0.838	1	CLONAL	1	TRUE	1	0.27873546954723	2		700	903	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348335	89348335	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1232258259	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	156	990	0	ENST00000301030.4:c.4615G>A	p.Glu1539Lys	p.E1539K	ENST00000301030	NM_001256183.1	1539	Gag/Aag	9/13	1	2	FACETS	0.957	0.874	1	0.957	0.874	1	CLONAL	1	TRUE	1	0.27873546954723	2		990	1170	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246785	41246785	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	38	479	0	ENST00000357654.3:c.763G>C	p.Glu255Gln	p.E255Q	ENST00000357654	NM_007294.3	255	Gag/Cag	10/23	1	2	FACETS	0.38	0.313	0.455	0.38	0.313	0.455	SUBCLONAL	1	TRUE	1	0.27873546954723	2		479	718	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436128	56436128	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1170091784	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	55	729	0	ENST00000407977.2:c.1009C>G	p.Arg337Gly	p.R337G	ENST00000407977		337	Cga/Gga	9/10	1	2	FACETS	0.433	0.369	0.504	0.433	0.369	0.504	SUBCLONAL	1	TRUE	1	0.27873546954723	2		729	911	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724516	724516	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	58	268	0	ENST00000314574.4:c.1540G>C	p.Asp514His	p.D514H	ENST00000314574	NM_005433.3	514	Gat/Cat	12/12	0.187526474203098	3	FACETS	1	0.93	1			1	CLONAL	1	TRUE	NA	0.27873546954723	3		268	419	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60795989	60795989	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	68	491	0	ENST00000333681.4:c.589G>T	p.Ala197Ser	p.A197S	ENST00000333681		197	Gcc/Tcc	3/3	1	2	FACETS	0.801	0.697	0.914	0.801	0.697	0.914	CLONAL	1	TRUE	1	0.27873546954723	2		491	609	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198272784	198272784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	55	493	0	ENST00000335508.6:c.1177G>A	p.Asp393Asn	p.D393N	ENST00000335508	NM_012433.2	393	Gat/Aat	9/25	0.205190590571613	3	FACETS	0.517	0.441	0.601	0.258	0.22	0.301	SUBCLONAL	1	TRUE	1	0.27873546954723	3		493	870	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131273	202131273	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	90	447	0	ENST00000358485.4:c.241C>T	p.Leu81Phe	p.L81F	ENST00000358485	NM_001080125.1	81	Ctc/Ttc	2/9	0.205190590571613	3	FACETS	1	0.956	1	0.578	0.513	0.647	CLONAL	1	TRUE	1	0.27873546954723	3		447	637	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662214	227662214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	129	868	0	ENST00000305123.5:c.1241C>T	p.Ala414Val	p.A414V	ENST00000305123	NM_005544.2	414	gCt/gTt	1/2	0.205190590571613	3	FACETS	0.878	0.794	0.967	0.439	0.397	0.484	CLONAL	1	TRUE	1	0.27873546954723	3		868	1201	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230899	66230899	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	53	329	0	ENST00000273854.3:c.2072G>T	p.Ser691Ile	p.S691I	ENST00000273854	NM_004439.5	691	aGt/aTt	12/18	1	2	FACETS	0.889	0.759	1	0.889	0.759	1	CLONAL	1	TRUE	1	0.27873546954723	2		329	428	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509762	106509762	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	80	570	0	ENST00000359195.3:c.1756C>A	p.Pro586Thr	p.P586T	ENST00000359195	NM_002649.2	586	Cca/Aca	2/11	0.27873546954723	3	FACETS	0.806	0.709	0.911	0.403	0.354	0.456	CLONAL	1	TRUE	1	0.27873546954723	3		570	811	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934305	68934305	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	100	482	0	ENST00000288368.4:c.371G>T	p.Ser124Ile	p.S124I	ENST00000288368	NM_024870.2	124	aGt/aTt	4/40	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.27873546954723	2		482	673	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211500	98211500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	94	605	0	ENST00000331920.6:c.3655G>A	p.Asp1219Asn	p.D1219N	ENST00000331920	NM_000264.3	1219	Gat/Aat	22/24	1	2	FACETS	0.913	0.812	1	0.913	0.812	1	CLONAL	1	TRUE	1	0.27873546954723	2		605	739	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798873	135798873	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	34	240	0	ENST00000298552.3:c.370A>T	p.Thr124Ser	p.T124S	ENST00000298552	NM_001162426.1	124	Act/Tct	6/23	1	2	FACETS	0.765	0.627	0.919	0.765	0.627	0.919	CLONAL	1	TRUE	1	0.27873546954723	2		240	319	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404364	139404364	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	133	903	0	ENST00000277541.6:c.2790C>G	p.Phe930Leu	p.F930L	ENST00000277541	NM_017617.3	930	ttC/ttG	18/34	1	2	FACETS	0.858	0.778	0.943	0.858	0.778	0.943	CLONAL	1	TRUE	1	0.27873546954723	2		903	1112	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504057	123504057	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	60	304	0	ENST00000371139.4:c.233G>T	p.Arg78Leu	p.R78L	ENST00000371139	NM_001114937.2	78	cGg/cTg	3/4	NA	2	FACETS	1	0.923	1			1	INDETERMINATE	1	TRUE	NA	0.27873546954723	2		304	392	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562657	29562660	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs1064794276	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	220	447	0	ENST00000356175.3:c.3739_3742del	p.Phe1247IlefsTer18	p.F1247Ifs*18	ENST00000356175	NM_000267.3	1246	cTGTTt/ct	28/57	1	2	FACETS	0.989	0.927	1	0.989	0.927	1	CLONAL	1	TRUE	1	0.755612962450127	2		447	589	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	351	707	2	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.755612962450127	2		709	840	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	276	281	0	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	0.755612962450127	3	FACETS	0.892	0.847	0.938	0.892	0.847	0.938	CLONAL	2	TRUE	1	0.755612962450127	3		281	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	249	499	2	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.755612962450127	2		501	658	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974695	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691187	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	20	297	0	ENST00000304494.5:c.132del	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	taC/ta	1/3	0.755612962450127	1	FACETS	0.198	0.152	0.251	0.198	0.152	0.251	SUBCLONAL	1	TRUE	0	0.755612962450127	1		297	166	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046958	128046958	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs772883177	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	193	453	0	ENST00000285398.2:c.777A>T	p.Glu259Asp	p.E259D	ENST00000285398	NM_000122.1	259	gaA/gaT	6/15	1	2	FACETS	0.779	0.724	0.835	0.779	0.724	0.835	SUBCLONAL	1	TRUE	1	0.755612962450127	2		453	656	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219102	133219102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532781183	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	201	475	0	ENST00000320574.5:c.4942G>A	p.Glu1648Lys	p.E1648K	ENST00000320574	NM_006231.2	1648	Gag/Aag	37/49	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.755612962450127	2		475	512	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924771	49924771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs541003810	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	229	594	2	ENST00000296474.3:c.4172G>A	p.Arg1391Gln	p.R1391Q	ENST00000296474	NM_002447.2	1391	cGg/cAg	20/20	1	2	FACETS	0.857	0.803	0.913	0.857	0.803	0.913	CLONAL	1	TRUE	1	0.755612962450127	2		596	707	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037475	12037475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs724159946	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	152	324	0	ENST00000396373.4:c.1106G>A	p.Arg369Gln	p.R369Q	ENST00000396373	NM_001987.4	369	cGg/cAg	6/8	1	2	FACETS	0.906	0.836	0.978	0.906	0.836	0.978	CLONAL	1	TRUE	1	0.755612962450127	2		324	444	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843278	128843278	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41303402	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	239	574	2	ENST00000249373.3:c.385G>A	p.Val129Ile	p.V129I	ENST00000249373	NM_005631.4	129	Gta/Ata	2/12	1	2	FACETS	0.861	0.807	0.916	0.861	0.807	0.916	CLONAL	1	TRUE	1	0.755612962450127	2		576	735	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159112	24159112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1341827515	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	190	304	2	ENST00000263121.7:c.784G>A	p.Val262Ile	p.V262I	ENST00000263121	NM_003073.3	262	Gtc/Atc	6/9	0.755612962450127	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.755612962450127	1		306	309	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905596	50905596	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910905700	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	274	635	1	ENST00000440232.2:c.724G>A	p.Ala242Thr	p.A242T	ENST00000440232	NM_002691.3	242	Gcg/Acg	6/27	1	2	FACETS	0.998	0.942	1	0.998	0.942	1	CLONAL	1	TRUE	1	0.755612962450127	2		636	727	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324302	62324302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781430438	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	454	570	2	ENST00000360203.5:c.2797G>A	p.Ala933Thr	p.A933T	ENST00000360203	NM_001283009.1	933	Gcc/Acc	29/35	0.716425886881364	3	FACETS	0.99	0.953	1	0.99	0.953	1	CLONAL	2	TRUE	1	0.755612962450127	3		572	836	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500768	8500768	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757479150	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	20	287	0	ENST00000356435.5:c.2114G>A	p.Arg705Gln	p.R705Q	ENST00000356435		705	cGa/cAa	13/35	0.705164901775413	1	FACETS	0.116	0.088	0.148	0.116	0.088	0.148	SUBCLONAL	1	TRUE	0	0.755612962450127	1		287	285	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596033	43596033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs192489011	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	189	511	1	ENST00000355710.3:c.200G>A	p.Arg67His	p.R67H	ENST00000355710	NM_020975.4	67	cGc/cAc	2/20	0.755612962450127	1	FACETS	0.848	0.797	0.899	0.848	0.797	0.899	CLONAL	1	TRUE	0	0.755612962450127	1		512	367	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300216	15300216	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	35	556	2	ENST00000263388.2:c.1060G>A	p.Ala354Thr	p.A354T	ENST00000263388	NM_000435.2	354	Gcc/Acc	7/33	1	2	FACETS	0.138	0.112	0.167	0.138	0.112	0.167	SUBCLONAL	1	TRUE	1	0.755612962450127	2		558	672	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958189	2958189	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1211022340	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	101	508	1	ENST00000396946.4:c.2543G>A	p.Arg848His	p.R848H	ENST00000396946	NM_032415.4	848	cGc/cAc	19/25	1	2	FACETS	0.515	0.462	0.571	0.515	0.462	0.571	SUBCLONAL	1	TRUE	1	0.755612962450127	2		509	519	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446977	187446977	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	242	563	0	ENST00000232014.4:c.1216C>T	p.Arg406Ter	p.R406*	ENST00000232014	NM_001130845.1	406	Cga/Tga	5/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.755612962450127	2		563	610	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224214	36224214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774855256	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	230	532	0	ENST00000222270.7:c.6764C>T	p.Pro2255Leu	p.P2255L	ENST00000222270	NM_014727.1	2255	cCg/cTg	28/37	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.755612962450127	2		532	603	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015326	176015326	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	150	243	0	ENST00000367669.3:c.1412C>T	p.Ser471Leu	p.S471L	ENST00000367669	NM_022457.5	471	tCg/tTg	12/20	1	2	FACETS	0.943	0.871	1	0.943	0.871	1	CLONAL	1	TRUE	1	0.755612962450127	2		243	421	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345797	152345797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149186933	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	195	309	0	ENST00000359321.1:c.773G>A	p.Arg258His	p.R258H	ENST00000359321	NM_005431.1	258	cGt/cAt	3/3	1	2	FACETS	0.927	0.864	0.991	0.927	0.864	0.991	CLONAL	1	TRUE	1	0.755612962450127	2		309	557	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536697	120536697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768711168	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	281	528	1	ENST00000229340.5:c.395C>T	p.Thr132Met	p.T132M	ENST00000229340	NM_006861.6	132	aCg/aTg	5/6	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.755612962450127	2		529	694	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110794	2110794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757844109	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	208	506	0	ENST00000219476.3:c.1099C>T	p.Arg367Trp	p.R367W	ENST00000219476	NM_000548.3	367	Cgg/Tgg	11/42	1	2	FACETS	0.898	0.839	0.959	0.898	0.839	0.959	CLONAL	1	TRUE	1	0.755612962450127	2		506	613	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351310	89351310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766646838	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	277	644	0	ENST00000301030.4:c.1640G>A	p.Arg547Gln	p.R547Q	ENST00000301030	NM_001256183.1	547	cGg/cAg	9/13	0.755612962450127	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.755612962450127	1		644	430	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664546	29664547	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	224	394	0	ENST00000356175.3:c.6527_6528del	p.Phe2176CysfsTer44	p.F2176Cfs*44	ENST00000356175	NM_000267.3	2175	acTTtt/actt	42/57	1	2	FACETS	0.938	0.879	0.998	0.938	0.879	0.998	CLONAL	1	TRUE	1	0.755612962450127	2		394	632	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873624	37873624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755483857	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	267	588	0	ENST00000269571.5:c.1789G>A	p.Val597Met	p.V597M	ENST00000269571		597	Gtg/Atg	15/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.755612962450127	2		588	661	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246289	41246289	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	39	421	0	ENST00000357654.3:c.1259A>T	p.Asp420Val	p.D420V	ENST00000357654	NM_007294.3	420	gAt/gTt	10/23	1	2	FACETS	0.162	0.133	0.193	0.162	0.133	0.193	SUBCLONAL	1	TRUE	1	0.755612962450127	2		421	639	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584488	39584488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs375465653	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	167	259	0	ENST00000262039.4:c.1153C>T	p.Arg385Ter	p.R385*	ENST00000262039	NM_002647.2	385	Cga/Tga	10/25	1	2	FACETS	0.91	0.843	0.978	0.91	0.843	0.978	CLONAL	1	TRUE	1	0.755612962450127	2		259	486	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661717	227661717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144912682	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	172	451	0	ENST00000305123.5:c.1738C>T	p.Arg580Cys	p.R580C	ENST00000305123	NM_005544.2	580	Cgc/Tgc	1/2	1	2	FACETS	0.87	0.807	0.936	0.87	0.807	0.936	CLONAL	1	TRUE	1	0.755612962450127	2		451	523	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021646	31021646	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1299423705	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	197	408	0	ENST00000375687.4:c.1645C>T	p.Arg549Cys	p.R549C	ENST00000375687	NM_015338.5	549	Cgt/Tgt	12/13	0.716425886881364	3	FACETS	0.975	0.905	1	0.487	0.452	0.523	CLONAL	1	TRUE	1	0.755612962450127	3		408	737	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155031	55155031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1560491736	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	211	385	1	ENST00000257290.5:c.2740C>T	p.Arg914Trp	p.R914W	ENST00000257290	NM_006206.4	914	Cgg/Tgg	20/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.755612962450127	2		386	524	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111995809	111995809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	150	362	1	ENST00000368678.4:c.1289C>T	p.Thr430Met	p.T430M	ENST00000368678		430	aCg/aTg	12/13	1	2	FACETS	0.871	0.803	0.941	0.871	0.803	0.941	CLONAL	1	TRUE	1	0.755612962450127	2		363	456	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405215	139405215	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371050668	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	513	580	0	ENST00000277541.6:c.2630C>T	p.Pro877Leu	p.P877L	ENST00000277541	NM_017617.3	877	cCg/cTg	17/34	0.716425886881364	3	FACETS	0.961	0.926	0.996	0.961	0.926	0.996	CLONAL	2	TRUE	1	0.755612962450127	3		580	973	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921480	39921480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	296	285	0	ENST00000378444.4:c.4340G>A	p.Arg1447His	p.R1447H	ENST00000378444	NM_001123385.1	1447	cGc/cAc	10/15	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.755612962450127	1		285	383	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410022	63410022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs780779666	NA	P-0044553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	159	226	0	ENST00000330258.3:c.3145C>T	p.Arg1049Ter	p.R1049*	ENST00000330258	NM_152424.3	1049	Cga/Tga	2/2	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.755612962450127	1		226	231	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220371	1220371	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	189	353	0	ENST00000326873.7:c.465-1G>C		p.X155_splice	ENST00000326873	NM_000455.4	155			0.322641677265796	2	FACETS	0.957	0.889	1	0.957	0.889	1	CLONAL	2	TRUE	0	0.322641677265796	2		353	612	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247328	153247328	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	126	245	1	ENST00000281708.4:c.1474C>T	p.Gln492Ter	p.Q492*	ENST00000281708	NM_033632.3	492	Cag/Tag	10/12	0.284324347710919	4	FACETS	0.905	0.822	0.991	0.905	0.822	0.991	CLONAL	2	TRUE	2	0.322641677265796	4		246	571	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201059	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	442	526	0	ENST00000269305.4:c.856G>T	p.Glu286Ter	p.E286*	ENST00000269305	NM_001126112.2	286	Gaa/Taa	8/11	0.322641677265796	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	0	0.322641677265796	3		526	1029	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962271	2962271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867239716	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	105	464	0	ENST00000396946.4:c.2266G>A	p.Glu756Lys	p.E756K	ENST00000396946	NM_032415.4	756	Gaa/Aaa	17/25	0.284324347710919	4	FACETS	0.906	0.811	1	0.453	0.405	0.504	CLONAL	1	TRUE	2	0.322641677265796	4		464	950	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22417970	22417970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	68	64	1	ENST00000344548.3:c.536C>T	p.Pro179Leu	p.P179L	ENST00000344548	NM_001039802.1	179	cCt/cTt	7/7	0.322641677265796	3	FACETS	1	0.904	1	1	0.904	1	CLONAL	3	TRUE	0	0.322641677265796	3		65	161	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716170	243716170	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	283	423	0	ENST00000263826.5:c.1024G>T	p.Gly342Trp	p.G342W	ENST00000263826	NM_005465.4	342	Ggg/Tgg	10/13	0.322641677265796	5	FACETS	0.983	0.926	1	0.983	0.926	1	CLONAL	3	TRUE	2	0.322641677265796	5		423	883	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154256	2154256	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	259	529	1	ENST00000434045.2:c.672del	p.His224GlnfsTer32	p.H224Qfs*32	ENST00000434045	NM_001127598.1	224	caC/ca	5/5	0.303894318828993	3	FACETS	0.981	0.92	1	0.981	0.92	1	CLONAL	2	TRUE	1	0.322641677265796	3		530	950	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414266	32414266	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	91	284	0	ENST00000332351.3:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000332351	NM_024426.4	429	Gaa/Taa	8/10	0.303894318828993	3	FACETS	1	0.906	1	0.511	0.454	0.572	CLONAL	1	TRUE	1	0.322641677265796	3		284	641	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998999	100998999	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	139	367	0	ENST00000325455.5:c.803T>G	p.Val268Gly	p.V268G	ENST00000325455	NM_001202474.3	268	gTc/gGc	1/8	0.303894318828993	3	FACETS	0.778	0.71	0.849	0.778	0.71	0.849	SUBCLONAL	2	TRUE	1	0.322641677265796	3		367	643	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859402	57859402	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	182	361	0	ENST00000228682.2:c.547C>A	p.Leu183Met	p.L183M	ENST00000228682	NM_005269.2	183	Ctg/Atg	6/12	0.322641677265796	5	FACETS	0.908	0.838	0.981	0.605	0.558	0.654	CLONAL	2	TRUE	2	0.322641677265796	5		361	922	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861264	57861264	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	248	374	0	ENST00000228682.2:c.1061G>T	p.Arg354Leu	p.R354L	ENST00000228682	NM_005269.2	354	cGg/cTg	9/12	0.322641677265796	5	FACETS	1	0.972	1	0.713	0.667	0.761	CLONAL	2	TRUE	2	0.322641677265796	5		374	1066	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865101	57865101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	132	542	0	ENST00000228682.2:c.2578C>T	p.Leu860Phe	p.L860F	ENST00000228682	NM_005269.2	860	Ctc/Ttc	12/12	0.322641677265796	5	FACETS	0.906	0.82	0.997	0.302	0.273	0.333	CLONAL	1	TRUE	2	0.322641677265796	5		542	1340	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254238	133254238	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	285	378	0	ENST00000320574.5:c.646G>C	p.Asp216His	p.D216H	ENST00000320574	NM_006231.2	216	Gac/Cac	7/49	0.322641677265796	3	FACETS	0.938	0.887	0.99	0.938	0.887	0.99	CLONAL	3	TRUE	0	0.322641677265796	3		378	729	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436027	110436027	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	269	493	1	ENST00000375856.3:c.2374G>T	p.Gly792Trp	p.G792W	ENST00000375856	NM_003749.2	792	Ggg/Tgg	1/2	0.322641677265796	2	FACETS	0.972	0.914	1	0.972	0.914	1	CLONAL	2	TRUE	0	0.322641677265796	2		494	858	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046662	30046662	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	149	320	0	ENST00000331968.5:c.2521G>T	p.Asp841Tyr	p.D841Y	ENST00000331968	NM_002742.2	841	Gac/Tac	18/18	0.303894318828993	3	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	1	0.322641677265796	3		320	522	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582047	95582062	+	frameshift_variant	Frame_Shift_Del	DEL	CACCATCGTCAGGCCT	CACCATCGTCAGGCCT	-	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	97	209	0	ENST00000393063.1:c.1849_1864del	p.Arg617ValfsTer28	p.R617Vfs*28	ENST00000393063	NM_030621.3	617	AGGCCTGACGATGGTGgt/gt	12/28	0.303894318828993	3	FACETS	0.831	0.746	0.921	0.831	0.746	0.921	CLONAL	2	TRUE	1	0.322641677265796	3		209	420	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003405	42003405	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	197	350	0	ENST00000219905.7:c.2942A>T	p.Gln981Leu	p.Q981L	ENST00000219905	NM_001164273.1	981	cAg/cTg	8/24	0.303894318828993	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.322641677265796	3		350	686	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274102	10274102	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769971551	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	232	486	0	ENST00000330684.3:c.167G>T	p.Gly56Val	p.G56V	ENST00000330684	NM_001134407.1	56	gGc/gTc	2/13	0.322641677265796	2	FACETS	0.988	0.925	1	0.988	0.925	1	CLONAL	2	TRUE	0	0.322641677265796	2		486	728	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868073	56868073	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	124	316	0	ENST00000308159.5:c.1571G>T	p.Arg524Leu	p.R524L	ENST00000308159	NM_014669.4	524	cGg/cTg	14/22	0.303894318828993	3	FACETS	1	0.977	1	0.631	0.572	0.694	CLONAL	1	TRUE	1	0.322641677265796	3		316	707	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992078	72992078	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	261	391	0	ENST00000268489.5:c.1967G>T	p.Gly656Val	p.G656V	ENST00000268489	NM_006885.3	656	gGc/gTc	2/10	0.303894318828993	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.322641677265796	3		391	802	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347299	89347299	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526636	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	101	480	0	ENST00000301030.4:c.5651C>T	p.Ser1884Leu	p.S1884L	ENST00000301030	NM_001256183.1	1884	tCa/tTa	9/13	0.303894318828993	3	FACETS	0.822	0.734	0.917	0.411	0.367	0.459	CLONAL	1	TRUE	1	0.322641677265796	3		480	884	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89833592	89833592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	128	288	0	ENST00000389301.3:c.2558G>T	p.Arg853Leu	p.R853L	ENST00000389301	NM_000135.2	853	cGa/cTa	27/43	0.303894318828993	3	FACETS	0.858	0.781	0.938	0.858	0.781	0.938	CLONAL	2	TRUE	1	0.322641677265796	3		288	537	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560177	29560177	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	128	225	0	ENST00000356175.3:c.3654A>T	p.Gln1218His	p.Q1218H	ENST00000356175	NM_000267.3	1218	caA/caT	27/57	0.322641677265796	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	2	0.322641677265796	4		225	484	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120092	70120092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1201663893	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	25	33	0	ENST00000245479.2:c.1094C>T	p.Ala365Val	p.A365V	ENST00000245479	NM_000346.3	365	gCg/gTg	3/3	0.322641677265796	4	FACETS	1	0.822	1	1	0.942	1	CLONAL	3	TRUE	2	0.322641677265796	4		33	68	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602595	10602595	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	279	490	0	ENST00000171111.5:c.983T>C	p.Ile328Thr	p.I328T	ENST00000171111	NM_203500.1	328	aTc/aCc	3/6	0.322641677265796	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.322641677265796	2		490	818	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105504	11105504	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	182	323	0	ENST00000358026.2:c.1420G>T	p.Glu474Ter	p.E474*	ENST00000358026	NM_001128849.1	474	Gaa/Taa	9/36	0.322641677265796	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.322641677265796	2		323	521	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36217231	36217231	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1392289007	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	364	482	0	ENST00000222270.7:c.3980G>C	p.Arg1327Thr	p.R1327T	ENST00000222270	NM_014727.1	1327	aGg/aCg	14/37	0.322641677265796	3	FACETS	0.989	0.942	1	0.989	0.942	1	CLONAL	3	TRUE	0	0.322641677265796	3		482	883	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082410	16082410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	122	481	0	ENST00000281043.3:c.224C>T	p.Pro75Leu	p.P75L	ENST00000281043	NM_005378.4	75	cCg/cTg	2/3	0.274044303736562	5	FACETS	1	0.902	1	0.25	0.225	0.276	CLONAL	1	TRUE	1	0.322641677265796	5		481	1122	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190656573	190656573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377084219	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	196	153	1	ENST00000441310.2:c.38C>T	p.Ser13Leu	p.S13L	ENST00000441310	NM_000534.4	13	tCa/tTa	2/13	0.322641677265796	8	FACETS	0.949	0.89	1			1	CLONAL	6	TRUE	NA	0.322641677265796	8		154	420	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718963	190718963	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	77	118	0	ENST00000441310.2:c.967-2A>G		p.X323_splice	ENST00000441310	NM_000534.4	323			0.322641677265796	8	FACETS	1	0.962	1			1	CLONAL	2	TRUE	NA	0.322641677265796	8		118	383	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439743	220439743	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	407	521	0	ENST00000243786.2:c.596G>C	p.Arg199Pro	p.R199P	ENST00000243786	NM_002191.3	199	cGc/cCc	2/2	0.322641677265796	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	TRUE	1	0.322641677265796	4		521	1084	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660840	227660840	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	102	406	2	ENST00000305123.5:c.2615C>A	p.Pro872His	p.P872H	ENST00000305123	NM_005544.2	872	cCt/cAt	1/2	0.322641677265796	4	FACETS	1	0.942	1	0.36	0.322	0.401	CLONAL	1	TRUE	1	0.322641677265796	4		408	774	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520249	9520249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs575889963	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	128	309	0	ENST00000353224.5:c.2020C>T	p.Arg674Trp	p.R674W	ENST00000353224	NM_177990.2	674	Cgg/Tgg	10/10	0.284324347710919	4	FACETS	0.834	0.758	0.914	0.834	0.758	0.914	CLONAL	2	TRUE	2	0.322641677265796	4		309	629	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546901	9546901	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	182	345	1	ENST00000353224.5:c.1121C>A	p.Pro374Gln	p.P374Q	ENST00000353224	NM_177990.2	374	cCg/cAg	5/10	0.284324347710919	4	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	2	0.322641677265796	4		346	741	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727142	40727142	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	197	403	0	ENST00000373198.4:c.3822C>A	p.Asn1274Lys	p.N1274K	ENST00000373198	NM_133170.3	1274	aaC/aaA	28/32	0.284324347710919	4	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	2	0.322641677265796	4		403	807	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159032	24159032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	105	459	0	ENST00000263121.7:c.704C>T	p.Pro235Leu	p.P235L	ENST00000263121	NM_003073.3	235	cCa/cTa	6/9	1	2	FACETS	0.82	0.734	0.911	0.82	0.734	0.911	CLONAL	1	TRUE	1	0.322641677265796	2		459	794	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89176389	89176391	+	frameshift_variant	Frame_Shift_Ins	INS	GGG	GGG	CGGA	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	91	183	1	ENST00000336596.2:c.119_121delinsCGGA	p.Gly40AlafsTer21	p.G40Afs*21	ENST00000336596	NM_005233.5	40	gGGGag/gCGGAag	2/17	0.322641677265796	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	0	0.322641677265796	2		184	264	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445067	89445067	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	192	309	1	ENST00000336596.2:c.1387C>A	p.Pro463Thr	p.P463T	ENST00000336596	NM_005233.5	463	Cct/Act	6/17	0.322641677265796	3	FACETS	1	0.986	1	0.821	0.765	0.879	CLONAL	2	TRUE	0	0.322641677265796	3		310	561	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664784	138664784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	142	186	1	ENST00000330315.3:c.781G>A	p.Val261Met	p.V261M	ENST00000330315	NM_023067.3	261	Gtg/Atg	1/1	0.322641677265796	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	TRUE	0	0.322641677265796	3		187	315	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602933	55602933	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	140	288	0	ENST00000288135.5:c.2643G>T	p.Lys881Asn	p.K881N	ENST00000288135	NM_000222.2	881	aaG/aaT	19/21	0.284324347710919	4	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	2	0.322641677265796	4		288	564	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231750	66231750	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	50	240	0	ENST00000273854.3:c.1950C>G	p.Tyr650Ter	p.Y650*	ENST00000273854	NM_004439.5	650	taC/taG	11/18	0.284324347710919	4	FACETS	0.995	0.846	1	0.498	0.423	0.579	CLONAL	1	TRUE	2	0.322641677265796	4		240	412	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383965	84383965	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	88	322	0	ENST00000321945.7:c.887C>G	p.Ser296Ter	p.S296*	ENST00000321945	NM_139076.2	296	tCa/tGa	9/9	0.284324347710919	4	FACETS	1	0.924	1	0.527	0.467	0.592	CLONAL	1	TRUE	2	0.322641677265796	4		322	684	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539055	187539055	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	87	337	0	ENST00000441802.2:c.8685G>T	p.Lys2895Asn	p.K2895N	ENST00000441802	NM_005245.3	2895	aaG/aaT	10/27	0.284324347710919	4	FACETS	0.928	0.821	1	0.464	0.41	0.521	CLONAL	1	TRUE	2	0.322641677265796	4		337	769	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515117	149515117	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	98	390	0	ENST00000261799.4:c.364+1G>T		p.X122_splice	ENST00000261799	NM_002609.3	122			0.322641677265796	1	FACETS	0.849	0.759	0.945	0.849	0.759	0.945	CLONAL	1	TRUE	0	0.322641677265796	1		390	600	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523672	176523672	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	263	532	0	ENST00000292408.4:c.2083G>T	p.Val695Leu	p.V695L	ENST00000292408	NM_213647.1	695	Gtg/Ttg	16/18	0.322641677265796	2	FACETS	0.95	0.893	1	0.95	0.893	1	CLONAL	2	TRUE	0	0.322641677265796	2		532	858	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393205	393205	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1000698747	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	179	317	0	ENST00000380956.4:c.53G>T	p.Ser18Ile	p.S18I	ENST00000380956	NM_001195286.1	18	aGc/aTc	2/9	0.322641677265796	4	FACETS	0.897	0.828	0.969	0.897	0.828	0.969	CLONAL	2	TRUE	2	0.322641677265796	4		317	818	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187474	32187474	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	222	489	0	ENST00000375023.3:c.1405G>T	p.Gly469Cys	p.G469C	ENST00000375023	NM_004557.3	469	Ggc/Tgc	8/30	0.322641677265796	4	FACETS	0.887	0.826	0.951	0.887	0.826	0.951	CLONAL	2	TRUE	2	0.322641677265796	4		489	1026	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816548	32816548	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	291	557	0	ENST00000354258.4:c.1627G>T	p.Asp543Tyr	p.D543Y	ENST00000354258	NM_000593.5	543	Gac/Tac	7/11	0.322641677265796	4	FACETS	0.984	0.925	1	0.984	0.925	1	CLONAL	2	TRUE	2	0.322641677265796	4		557	1212	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522175	157522175	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	192	448	0	ENST00000346085.5:c.4447G>C	p.Gly1483Arg	p.G1483R	ENST00000346085	NM_020732.3	1483	Ggc/Cgc	18/20	0.322641677265796	2	FACETS	0.904	0.84	0.97	0.904	0.84	0.97	CLONAL	2	TRUE	0	0.322641677265796	2		448	658	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974723	21974723	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs746834149	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	188	275	0	ENST00000304494.5:c.104G>T	p.Gly35Val	p.G35V	ENST00000304494	NM_000077.4	35	gGg/gTg	1/3	0.316690285281614	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.322641677265796	2		275	501	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27168493	27168493	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	137	258	0	ENST00000380036.4:c.365C>A	p.Ala122Asp	p.A122D	ENST00000380036	NM_000459.3	122	gCt/gAt	3/23	0.316690285281614	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	0	0.322641677265796	2		258	415	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911584	101911584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	101	254	0	ENST00000374994.4:c.1509G>A	p.Met503Ile	p.M503I	ENST00000374994	NM_004612.2	503	atG/atA	9/9	0.322641677265796	4	FACETS	0.774	0.694	0.858	0.774	0.694	0.858	SUBCLONAL	2	TRUE	2	0.322641677265796	4		254	535	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250378	110250378	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	126	579	0	ENST00000374672.4:c.297C>G	p.Phe99Leu	p.F99L	ENST00000374672	NM_004235.4	99	ttC/ttG	3/5	0.322641677265796	4	FACETS	0.949	0.858	1	0.475	0.429	0.523	CLONAL	1	TRUE	2	0.322641677265796	4		579	1088	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139810999	139810999	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	251	469	0	ENST00000247668.2:c.610G>C	p.Asp204His	p.D204H	ENST00000247668	NM_021138.3	204	Gac/Cac	7/11	0.322641677265796	4	FACETS	0.976	0.913	1	0.976	0.913	1	CLONAL	2	TRUE	2	0.322641677265796	4		469	1054	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650296	48650296	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781920985	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	243	260	0	ENST00000376670.3:c.266G>A	p.Gly89Glu	p.G89E	ENST00000376670	NM_002049.3	89	gGg/gAg	3/6	0.309223436790409	2	FACETS	0.983	0.928	1			1	CLONAL	3	TRUE	NA	0.322641677265796	2		260	511	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412698	63412698	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	210	206	0	ENST00000330258.3:c.469G>T	p.Glu157Ter	p.E157*	ENST00000330258	NM_152424.3	157	Gag/Tag	2/2	0.309223436790409	2	FACETS	1	0.969	1			1	CLONAL	3	TRUE	NA	0.322641677265796	2		206	416	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210214	123210214	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	97	173	0	ENST00000218089.9:c.2566G>C	p.Glu856Gln	p.E856Q	ENST00000218089	NM_001042749.1	856	Gaa/Caa	26/35	0.309223436790409	2	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.322641677265796	2		173	401	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244250	41244250	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	AA	novel	NA	P-0044557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	192	389	1	ENST00000357654.3:c.3298delinsTT	p.Gly1100LeufsTer3	p.G1100Lfs*3	ENST00000357654	NM_007294.3	1100	Gga/TTga	10/23	0.322641677265796	4	FACETS	0.909	0.841	0.979	0.909	0.841	0.979	CLONAL	2	TRUE	2	0.322641677265796	4		390	866	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0044573-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	78	426	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.923	0.816	1	0.923	0.816	1	CLONAL	1	TRUE	1	0.437776201967032	2		426	386	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0044573-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	27	544	1	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	NA	2	FACETS	0.233	0.185	0.289			1	INDETERMINATE	1	TRUE	NA	0.437776201967032	2		545	529	SUCCESS
ATM	472	MSKCC	GRCh37	11	108138042	108138042	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044573-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	57	293	0	ENST00000278616.4:c.2611G>T	p.Glu871Ter	p.E871*	ENST00000278616	NM_000051.3	871	Gaa/Taa	17/63	0.437776201967032	1	FACETS	0.807	0.7	0.922	0.807	0.7	0.922	CLONAL	1	TRUE	0	0.437776201967032	1		293	252	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207021	1207021	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913324	NA	P-0044573-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	156	634	0	ENST00000326873.7:c.109C>T	p.Gln37Ter	p.Q37*	ENST00000326873	NM_000455.4	37	Cag/Tag	1/10	0.437776201967032	1	FACETS	0.992	0.914	1	0.992	0.914	1	CLONAL	1	TRUE	0	0.437776201967032	1		634	561	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858574	57858574	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1566558833	NA	P-0044573-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	149	605	0	ENST00000228682.2:c.312C>G	p.Ser104Arg	p.S104R	ENST00000228682	NM_005269.2	104	agC/agG	4/12	1	2	FACETS	0.994	0.91	1	0.994	0.91	1	CLONAL	1	TRUE	1	0.437776201967032	2		605	685	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644821	67644821	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044573-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	78	428	0	ENST00000264010.4:c.86G>T	p.Arg29Leu	p.R29L	ENST00000264010	NM_006565.3	29	cGg/cTg	3/12	1	2	FACETS	0.768	0.677	0.865	0.768	0.677	0.865	SUBCLONAL	1	TRUE	1	0.437776201967032	2		428	464	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990625	7990625	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044573-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	141	448	0	ENST00000319144.4:c.136G>A	p.Ala46Thr	p.A46T	ENST00000319144	NM_001139.2	46	Gca/Aca	1/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.437776201967032	2		448	584	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38955718	38955718	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs750704208	NA	P-0044573-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	123	287	0	ENST00000357387.3:c.2588A>G	p.Tyr863Cys	p.Y863C	ENST00000357387	NM_152756.3	863	tAt/tGt	26/38	0.437776201967032	3	FACETS	0.941	0.86	1	0.941	0.86	1	CLONAL	2	TRUE	1	0.437776201967032	3		287	364	SUCCESS
APC	324	MSKCC	GRCh37	5	112162822	112162822	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044573-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	67	317	0	ENST00000257430.4:c.1426G>T	p.Ala476Ser	p.A476S	ENST00000257430	NM_000038.5	476	Gca/Tca	12/16	1	2	FACETS	0.987	0.865	1	0.987	0.865	1	CLONAL	1	TRUE	1	0.437776201967032	2		317	310	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376034	8376034	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044573-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	57	260	0	ENST00000356435.5:c.4563T>A	p.Asp1521Glu	p.D1521E	ENST00000356435		1521	gaT/gaA	28/35	0.437776201967032	1	FACETS	0.834	0.723	0.951	0.834	0.723	0.951	CLONAL	1	TRUE	0	0.437776201967032	1		260	244	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37006481	37006481	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044573-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	48	244	0	ENST00000358127.4:c.464G>T	p.Ser155Ile	p.S155I	ENST00000358127	NM_001280556.1	155	aGt/aTt	4/10	0.17784469456023	1	FACETS	0.634	0.54	0.737	0.634	0.54	0.737	INDETERMINATE	1	TRUE	0	0.437776201967032	1		244	270	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204830	128204830	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1460001422	NA	P-0044575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	432	587	1	ENST00000341105.2:c.611G>A	p.Arg204Gln	p.R204Q	ENST00000341105	NM_032638.4	204	cGa/cAa	3/6	0.54639112625904	4	FACETS	0.949	0.906	0.992	0.949	0.906	0.992	CLONAL	2	TRUE	2	0.665944392906749	4		588	1139	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281657	49281657	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	235	529	0	ENST00000282018.3:c.704A>T	p.Glu235Val	p.E235V	ENST00000282018	NM_020377.2	235	gAa/gTa	1/1	0.665944392906749	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.665944392906749	1		529	421	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128305365	128305365	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	297	468	0	ENST00000265960.3:c.931C>T	p.Arg311Ter	p.R311*	ENST00000265960	NM_001006617.1	311	Cga/Tga	7/12	0.54639112625904	4	FACETS	0.944	0.893	0.996	0.944	0.893	0.996	CLONAL	2	TRUE	2	0.665944392906749	4		468	787	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874644	151874644	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	185	556	0	ENST00000262189.6:c.7894C>T	p.Gln2632Ter	p.Q2632*	ENST00000262189	NM_170606.2	2632	Caa/Taa	38/59	0.319705810223052	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.319705810223052	1		556	820	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0044656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	336	625	3	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.713773176758318	3	FACETS	0.964	0.938	0.987	0.964	0.938	0.987	CLONAL	3	FALSE	0	0.828001851129017	3		628	397	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656934	47656936	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs1295803849	NA	P-0044656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	123	320	1	ENST00000233146.2:c.1134_1136del	p.Glu378del	p.E378del	ENST00000233146	NM_000251.2	377	cAAGaa/caa	7/16	0.63513136394257	4	FACETS	0.857	0.786	0.929	0.857	0.786	0.929	CLONAL	2	FALSE	2	0.828001851129017	4		321	317	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541504	187541504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1272319296	NA	P-0044656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	19	415	0	ENST00000441802.2:c.6236C>T	p.Pro2079Leu	p.P2079L	ENST00000441802	NM_005245.3	2079	cCg/cTg	10/27	0.813248514822703	4	FACETS	0.239	0.181	0.308	0.12	0.09	0.154	SUBCLONAL	1	FALSE	2	0.828001851129017	4		415	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579361	7579361	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1064796722	NA	P-0044661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	428	663	0	ENST00000269305.4:c.326T>G	p.Phe109Cys	p.F109C	ENST00000269305	NM_001126112.2	109	tTc/tGc	4/11	0.459337032570843	2	FACETS	0.863	0.826	0.9	0.863	0.826	0.9	CLONAL	2	TRUE	0	0.517614422897938	2		663	958	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499520	89499520	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	168	283	0	ENST00000336596.2:c.2690G>T	p.Arg897Met	p.R897M	ENST00000336596	NM_005233.5	897	aGg/aTg	15/17	0.365785687963267	4	FACETS	0.964	0.893	1	0.964	0.893	1	CLONAL	2	TRUE	2	0.517614422897938	4		283	511	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38981989	38981989	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	63	356	0	ENST00000357387.3:c.733C>T	p.Arg245Ter	p.R245*	ENST00000357387	NM_152756.3	245	Cga/Tga	8/38	0.449286776271447	3	FACETS	0.651	0.564	0.744	0.325	0.282	0.372	SUBCLONAL	1	TRUE	1	0.517614422897938	3		356	471	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	461475	461475	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs998253161	NA	P-0044661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	221	338	0	ENST00000399788.2:c.1045C>G	p.Arg349Gly	p.R349G	ENST00000399788	NM_001042603.1	349	Cga/Gga	9/28	0.442355015884187	5	FACETS	1	0.975	1	0.723	0.676	0.772	CLONAL	2	TRUE	2	0.517614422897938	5		338	699	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300386	11300386	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	302	400	1	ENST00000361445.4:c.1760G>T	p.Arg587Leu	p.R587L	ENST00000361445	NM_004958.3	587	cGa/cTa	11/58	0.365785687963267	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.517614422897938	4		401	808	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88651963	88651963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	69	316	0	ENST00000372037.3:c.310G>A	p.Glu104Lys	p.E104K	ENST00000372037	NM_004329.2	104	Gaa/Aaa	5/13	0.350771214013647	3	FACETS	0.788	0.689	0.894	0.394	0.344	0.447	SUBCLONAL	1	TRUE	1	0.517614422897938	3		316	426	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94201044	94201044	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	119	241	1	ENST00000323929.3:c.1033G>T	p.Glu345Ter	p.E345*	ENST00000323929	NM_005591.3	345	Gaa/Taa	10/20	0.463088069863414	3	FACETS	0.866	0.792	0.943	0.866	0.792	0.943	CLONAL	2	TRUE	1	0.517614422897938	3		242	334	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434708	49434708	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	67	748	0	ENST00000301067.7:c.6845G>C	p.Arg2282Pro	p.R2282P	ENST00000301067	NM_003482.3	2282	cGg/cCg	31/54	0.237877790772671	2	FACETS	0.24	0.207	0.275	0.12	0.103	0.138	INDETERMINATE	1	TRUE	0	0.517614422897938	2		748	1079	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521512	8521513	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0044661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	233	486	0	ENST00000356435.5:c.725_726delinsAA	p.Pro242Gln	p.P242Q	ENST00000356435		242	cCC/cAA	9/35	0.350771214013647	3	FACETS	0.807	0.756	0.859	0.807	0.756	0.859	CLONAL	2	TRUE	1	0.517614422897938	3		486	702	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937324	76937324	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	65	354	0	ENST00000373344.5:c.3424T>G	p.Ser1142Ala	p.S1142A	ENST00000373344	NM_000489.3	1142	Tca/Gca	9/35	0.517736299770647	4	FACETS	0.687	0.596	0.785			1	SUBCLONAL	1	TRUE	NA	0.517614422897938	4		354	555	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	35	320	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.856	0.703	1	0.856	0.703	1	CLONAL	1	TRUE	1	0.222773480466358	2		321	367	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	85	797	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.222773480466358	2		797	546	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017790	31017790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564841799	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	80	722	0	ENST00000375687.4:c.652C>T	p.Arg218Cys	p.R218C	ENST00000375687	NM_015338.5	218	Cgt/Tgt	8/13	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.222773480466358	2		722	638	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37058999	37058999	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs63751194	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	42	328	0	ENST00000231790.2:c.793C>T	p.Arg265Cys	p.R265C	ENST00000231790	NM_000249.3	265	Cgt/Tgt	10/19	1	2	FACETS	0.947	0.792	1	0.947	0.792	1	CLONAL	1	TRUE	1	0.222773480466358	2		328	398	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713350	40713350	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	85	681	0	ENST00000373198.4:c.4165A>T	p.Arg1389Trp	p.R1389W	ENST00000373198	NM_133170.3	1389	Agg/Tgg	30/32	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.222773480466358	2		681	658	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733217	40733217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	67	480	0	ENST00000373198.4:c.3589G>A	p.Glu1197Lys	p.E1197K	ENST00000373198	NM_133170.3	1197	Gaa/Aaa	26/32	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.222773480466358	2		480	584	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423632	88423632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1478926904	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	92	372	0	ENST00000360948.2:c.2203C>T	p.Arg735Cys	p.R735C	ENST00000360948	NM_001012338.2	735	Cgc/Tgc	18/19	0.222773480466358	3	FACETS	1	0.917	1	1	0.917	1	CLONAL	2	TRUE	1	0.222773480466358	3		372	445	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36846865	36846865	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	61	452	0	ENST00000358127.4:c.1074G>A	p.Trp358Ter	p.W358*	ENST00000358127	NM_001280556.1	358	tgG/tgA	9/10	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.222773480466358	2		452	501	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555057	106555057	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs940196192	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	65	502	1	ENST00000369096.4:c.2174G>A	p.Arg725Gln	p.R725Q	ENST00000369096	NM_001198.3	725	cGa/cAa	7/7	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.222773480466358	2		503	571	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440904	56440904	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1458799446	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	87	632	0	ENST00000407977.2:c.433C>T	p.Arg145Ter	p.R145*	ENST00000407977		145	Cga/Tga	4/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.222773480466358	2		632	626	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716344	18716344	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778895247	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	33	311	0	ENST00000266497.5:c.3691G>A	p.Glu1231Lys	p.E1231K	ENST00000266497		1231	Gaa/Aaa	26/31	1	2	FACETS	0.772	0.629	0.932	0.772	0.629	0.932	CLONAL	1	TRUE	1	0.222773480466358	2		311	384	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279423	1279423	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	74	801	1	ENST00000310581.5:c.2113G>A	p.Glu705Lys	p.E705K	ENST00000310581	NM_198253.2	705	Gag/Aag	5/16	1	2	FACETS	0.968	0.848	1	0.968	0.848	1	CLONAL	1	TRUE	1	0.222773480466358	2		802	686	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321372	1321372	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1319865856	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	85	464	1	ENST00000400841.2:c.383C>T	p.Ser128Leu	p.S128L	ENST00000400841		128	tCg/tTg	4/6	NA	2	FACETS	0.762	0.675	0.853			1	INDETERMINATE	2	TRUE	NA	0.222773480466358	2		465	501	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805719	43805719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528834914	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	84	691	0	ENST00000372470.3:c.775G>A	p.Glu259Lys	p.E259K	ENST00000372470	NM_005373.2	259	Gaa/Aaa	5/12	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.222773480466358	2		691	625	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961538	54961538	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1338142196	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	47	462	0	ENST00000312783.6:c.94C>T	p.Pro32Ser	p.P32S	ENST00000312783	NM_198436.1	32	Cct/Tct	4/10	1	2	FACETS	0.756	0.638	0.887	0.756	0.638	0.887	SUBCLONAL	1	TRUE	1	0.222773480466358	2		462	558	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15365052	15365052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	81	612	1	ENST00000263377.2:c.2069C>T	p.Ala690Val	p.A690V	ENST00000263377	NM_058243.2	690	gCc/gTc	11/20	0.222773480466358	3	FACETS	1	0.927	1	0.537	0.473	0.607	CLONAL	1	TRUE	1	0.222773480466358	3		613	752	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561124	9561124	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	30	394	0	ENST00000353224.5:c.658C>T	p.Gln220Ter	p.Q220*	ENST00000353224	NM_177990.2	220	Cag/Tag	4/10	1	2	FACETS	0.836	0.675	1	0.836	0.675	1	CLONAL	1	TRUE	1	0.222773480466358	2		394	322	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412982	49412982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	110	607	0	ENST00000418115.1:c.41G>A	p.Gly14Glu	p.G14E	ENST00000418115	NM_001664.2	14	gGa/gAa	2/5	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.222773480466358	2		607	739	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202731	128202731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	82	703	1	ENST00000341105.2:c.989G>A	p.Arg330Gln	p.R330Q	ENST00000341105	NM_032638.4	330	cGa/cAa	4/6	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.222773480466358	2		704	672	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562641	29562641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854562	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	46	370	0	ENST00000356175.3:c.3721C>T	p.Arg1241Ter	p.R1241*	ENST00000356175	NM_000267.3	1241	Cga/Tga	28/57	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.222773480466358	2		370	401	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351737	89351737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1385566000	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	92	789	0	ENST00000301030.4:c.1213C>T	p.Arg405Cys	p.R405C	ENST00000301030	NM_001256183.1	405	Cgt/Tgt	9/13	1	2	FACETS	0.825	0.731	0.926	0.825	0.731	0.926	CLONAL	1	TRUE	1	0.222773480466358	2		789	1001	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578253	28578253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144397269	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	79	466	0	ENST00000241453.7:c.2918G>A	p.Arg973Gln	p.R973Q	ENST00000241453	NM_004119.2	973	cGa/cAa	24/24	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.222773480466358	2		466	679	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88428957	88428957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	33	258	0	ENST00000360948.2:c.2143C>T	p.Pro715Ser	p.P715S	ENST00000360948	NM_001012338.2	715	Cca/Tca	17/19	0.222773480466358	3	FACETS	1	0.869	1	0.54	0.441	0.651	CLONAL	1	TRUE	1	0.222773480466358	3		258	305	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794699	42794699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	170	827	0	ENST00000575354.2:c.1779G>A	p.Met593Ile	p.M593I	ENST00000575354	NM_015125.3	593	atG/atA	10/20	0.222773480466358	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.222773480466358	3		827	769	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900273	101900273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863223812	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	36	319	0	ENST00000374994.4:c.707C>T	p.Ser236Phe	p.S236F	ENST00000374994	NM_004612.2	236	tCt/tTt	4/9	1	2	FACETS	0.738	0.607	0.885	0.738	0.607	0.885	SUBCLONAL	1	TRUE	1	0.222773480466358	2		319	438	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129903	69129903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752113779	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	38	361	0	ENST00000288368.4:c.4657G>A	p.Gly1553Arg	p.G1553R	ENST00000288368	NM_024870.2	1553	Gga/Aga	38/40	1	2	FACETS	0.93	0.77	1	0.93	0.77	1	CLONAL	1	TRUE	1	0.222773480466358	2		361	367	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144565	55144565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	49	376	0	ENST00000257290.5:c.2039G>A	p.Gly680Glu	p.G680E	ENST00000257290	NM_006206.4	680	gGa/gAa	15/23	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.222773480466358	2		376	377	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522605	176522605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	89	846	1	ENST00000292408.4:c.1702C>T	p.Pro568Ser	p.P568S	ENST00000292408	NM_213647.1	568	Cca/Tca	13/18	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.222773480466358	2		847	651	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100912	41100912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866253502	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	54	468	0	ENST00000373198.4:c.1444G>A	p.Glu482Lys	p.E482K	ENST00000373198	NM_133170.3	482	Gaa/Aaa	8/32	1	2	FACETS	0.979	0.837	1	0.979	0.837	1	CLONAL	1	TRUE	1	0.222773480466358	2		468	495	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907743	76907743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	68	192	0	ENST00000373344.5:c.4418C>T	p.Pro1473Leu	p.P1473L	ENST00000373344	NM_000489.3	1473	cCt/cTt	15/35	NA	2	FACETS	1	0.899	1			1	INDETERMINATE	2	TRUE	NA	0.222773480466358	2		192	297	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472453	88472453	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	119	543	0	ENST00000360948.2:c.2102C>T	p.Ser701Phe	p.S701F	ENST00000360948	NM_001012338.2	701	tCc/tTc	16/19	0.222773480466358	3	FACETS	0.954	0.864	1	0.954	0.864	1	CLONAL	2	TRUE	1	0.222773480466358	3		543	622	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650169	93650169	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	43	417	0	ENST00000375746.1:c.1720C>T	p.Arg574Ter	p.R574*	ENST00000375746	NM_001174167.1	574	Cga/Tga	12/14	1	2	FACETS	0.926	0.776	1	0.926	0.776	1	CLONAL	1	TRUE	1	0.222773480466358	2		417	417	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457275	25457275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1419990763	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	83	550	0	ENST00000264709.3:c.2612C>T	p.Pro871Leu	p.P871L	ENST00000264709	NM_175629.2	871	cCa/cTa	23/23	0.222773480466358	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.222773480466358	1		550	504	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652390	206652390	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	101	692	0	ENST00000367120.3:c.1097C>T	p.Ser366Leu	p.S366L	ENST00000367120	NM_014002.3	366	tCa/tTa	10/22	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.222773480466358	2		692	709	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058471	69058471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	37	369	0	ENST00000288368.4:c.4115G>A	p.Gly1372Glu	p.G1372E	ENST00000288368	NM_024870.2	1372	gGa/gAa	34/40	1	2	FACETS	0.814	0.672	0.973	0.814	0.672	0.973	CLONAL	1	TRUE	1	0.222773480466358	2		369	408	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710637	40710637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1161104430	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	74	492	1	ENST00000373198.4:c.4214G>A	p.Gly1405Glu	p.G1405E	ENST00000373198	NM_133170.3	1405	gGa/gAa	31/32	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.222773480466358	2		493	492	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199974	128199974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781161922	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	91	668	0	ENST00000341105.2:c.1331C>T	p.Pro444Leu	p.P444L	ENST00000341105	NM_032638.4	444	cCg/cTg	6/6	1	2	FACETS	0.751	0.668	0.838	1	0.98	1	SUBCLONAL	2	TRUE	1	0.222773480466358	2		668	544	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343319	118343319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	42	320	0	ENST00000534358.1:c.1445C>T	p.Pro482Leu	p.P482L	ENST00000534358	NM_005933.3	482	cCc/cTc	3/36	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.222773480466358	2		320	303	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972864	55972864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866807777	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	46	314	0	ENST00000263923.4:c.1526G>A	p.Gly509Glu	p.G509E	ENST00000263923	NM_002253.2	509	gGa/gAa	11/30	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.222773480466358	2		314	385	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163297332	163297332	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1292835761	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	52	370	0	ENST00000271452.3:c.178C>T	p.Arg60Ter	p.R60*	ENST00000271452	NM_145697.2	60	Cga/Tga	3/14	1	2	FACETS	0.995	0.849	1	0.995	0.849	1	CLONAL	1	TRUE	1	0.222773480466358	2		370	469	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717750	89717750	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	40	331	1	ENST00000371953.3:c.775C>T	p.His259Tyr	p.H259Y	ENST00000371953	NM_000314.4	259	Cac/Tac	7/9	1	2	FACETS	0.914	0.76	1	0.914	0.76	1	CLONAL	1	TRUE	1	0.222773480466358	2		332	393	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183063	32183063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	85	867	0	ENST00000375023.3:c.1961G>A	p.Gly654Glu	p.G654E	ENST00000375023	NM_004557.3	654	gGa/gAa	12/30	1	2	FACETS	0.915	0.808	1	0.915	0.808	1	CLONAL	1	TRUE	1	0.222773480466358	2		867	834	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56871593	56871593	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1299064324	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	67	462	0	ENST00000308159.5:c.1973C>T	p.Ser658Phe	p.S658F	ENST00000308159	NM_014669.4	658	tCc/tTc	18/22	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.222773480466358	2		462	534	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240386	98240386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	66	418	0	ENST00000331920.6:c.1298C>T	p.Ser433Phe	p.S433F	ENST00000331920	NM_000264.3	433	tCc/tTc	9/24	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.222773480466358	2		418	555	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925402	114925402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766781345	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	79	669	0	ENST00000543371.1:c.1480C>T	p.Pro494Ser	p.P494S	ENST00000543371	NM_001198531.1	494	Ccc/Tcc	14/14	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.222773480466358	2		669	627	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530202	212530202	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs750966942	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	33	240	0	ENST00000342788.4:c.1717G>A	p.Gly573Ser	p.G573S	ENST00000342788	NM_005235.2	573	Ggt/Agt	15/28	0.222773480466358	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.222773480466358	1		240	215	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582180	189582180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553856553	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	60	362	0	ENST00000264731.3:c.739C>T	p.His247Tyr	p.H247Y	ENST00000264731	NM_003722.4	247	Cat/Tat	5/14	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.222773480466358	2		362	483	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215552	5215552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs114166264	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	100	784	2	ENST00000357368.4:c.4151G>A	p.Arg1384Gln	p.R1384Q	ENST00000357368	NM_002850.3	1384	cGg/cAg	27/38	0.222773480466358	3	FACETS	1	0.964	1	0.593	0.529	0.661	CLONAL	1	TRUE	1	0.222773480466358	3		786	842	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163892	47163892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	30	373	0	ENST00000409792.3:c.2234C>T	p.Pro745Leu	p.P745L	ENST00000409792	NM_014159.6	745	cCa/cTa	3/21	1	2	FACETS	0.718	0.579	0.876	0.718	0.579	0.876	SUBCLONAL	1	TRUE	1	0.222773480466358	2		373	375	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211599	98211599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	53	592	0	ENST00000331920.6:c.3556C>T	p.Pro1186Ser	p.P1186S	ENST00000331920	NM_000264.3	1186	Cca/Tca	22/24	1	2	FACETS	0.933	0.796	1	0.933	0.796	1	CLONAL	1	TRUE	1	0.222773480466358	2		592	510	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36934801	36934801	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	87	562	1	ENST00000361632.4:c.1532C>T	p.Thr511Ile	p.T511I	ENST00000361632		511	aCc/aTc	11/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.222773480466358	2		563	657	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166043	118166043	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	61	403	0	ENST00000369448.3:c.553C>T	p.Gln185Ter	p.Q185*	ENST00000369448	NM_017709.3	185	Caa/Taa	2/2	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.222773480466358	2		403	432	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683457	88683457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	10	20	0	ENST00000372037.3:c.1580C>T	p.Ser527Phe	p.S527F	ENST00000372037	NM_004329.2	527	tCc/tTc	13/13	1	2	FACETS	0.855	0.605	1	1	0.906	1	CLONAL	3	TRUE	1	0.222773480466358	2		20	35	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14300963	14300963	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	56	471	0	ENST00000256196.4:c.535C>T	p.Gln179Ter	p.Q179*	ENST00000256196		179	Caa/Taa	6/6	1	2	FACETS	0.893	0.765	1	0.893	0.765	1	CLONAL	1	TRUE	1	0.222773480466358	2		471	563	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375794	118375794	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	54	435	0	ENST00000534358.1:c.9187T>C	p.Ser3063Pro	p.S3063P	ENST00000534358	NM_005933.3	3063	Tcc/Ccc	27/36	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.222773480466358	2		435	435	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376453	118376454	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	51	384	0	ENST00000534358.1:c.9846_9847delinsTT	p.Arg3283Ter	p.R3283*	ENST00000534358	NM_005933.3	3282	caCCga/caTTga	27/36	1	2	FACETS	0.976	0.831	1	0.976	0.831	1	CLONAL	1	TRUE	1	0.222773480466358	2		384	469	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864681	57864682	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	54	782	1	ENST00000228682.2:c.2158_2159delinsTT	p.Pro720Phe	p.P720F	ENST00000228682	NM_005269.2	720	CCc/TTc	12/12	1	2	FACETS	0.718	0.612	0.834	0.718	0.612	0.834	SUBCLONAL	1	TRUE	1	0.222773480466358	2		783	675	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865815	57865815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	46	522	1	ENST00000228682.2:c.3292G>A	p.Glu1098Lys	p.E1098K	ENST00000228682	NM_005269.2	1098	Gaa/Aaa	12/12	1	2	FACETS	0.846	0.713	0.993	0.846	0.713	0.993	CLONAL	1	TRUE	1	0.222773480466358	2		523	488	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134993	41134993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	25	197	0	ENST00000379561.5:c.635C>T	p.Ser212Leu	p.S212L	ENST00000379561	NM_002015.3	212	tCa/tTa	2/3	1	2	FACETS	0.927	0.734	1	0.927	0.734	1	CLONAL	1	TRUE	1	0.222773480466358	2		197	242	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878138	48878139	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AT	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	15	123	0	ENST00000267163.4:c.90_91delinsAT	p.Glu31Ter	p.E31*	ENST00000267163	NM_000321.2	30	gaGGag/gaATag	1/27	1	2	FACETS	0.904	0.665	1	0.904	0.665	1	CLONAL	1	TRUE	1	0.222773480466358	2		123	149	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574714	95574714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	44	343	0	ENST00000393063.1:c.2383C>T	p.Pro795Ser	p.P795S	ENST00000393063	NM_030621.3	795	Cct/Tct	16/28	1	2	FACETS	0.985	0.828	1	0.985	0.828	1	CLONAL	1	TRUE	1	0.222773480466358	2		343	401	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961590	41961591	+	missense_variant	Missense_Mutation	DNP	TC	TC	AG	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	37	445	0	ENST00000219905.7:c.498_499delinsAG	p.His167Asp	p.H167D	ENST00000219905	NM_001164273.1	166	ggTCat/ggAGat	2/24	0.222773480466358	1	FACETS	0.671	0.553	0.803	0.671	0.553	0.803	SUBCLONAL	1	TRUE	0	0.222773480466358	1		445	440	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50811799	50811799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	32	369	0	ENST00000398568.2:c.1076C>T	p.Ser359Phe	p.S359F	ENST00000398568	NM_001042412.1	359	tCt/tTt	7/18	1	2	FACETS	0.626	0.507	0.76	0.626	0.507	0.76	SUBCLONAL	1	TRUE	1	0.222773480466358	2		369	459	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993938	72993938	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167713053	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	73	711	0	ENST00000268489.5:c.107C>T	p.Pro36Leu	p.P36L	ENST00000268489	NM_006885.3	36	cCc/cTc	2/10	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.222773480466358	2		711	590	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349730	89349730	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	104	787	0	ENST00000301030.4:c.3220A>T	p.Lys1074Ter	p.K1074*	ENST00000301030	NM_001256183.1	1074	Aaa/Taa	9/13	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.222773480466358	2		787	917	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004957	16004957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	94	636	0	ENST00000268712.3:c.2297C>T	p.Ser766Phe	p.S766F	ENST00000268712	NM_006311.3	766	tCc/tTc	20/46	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.222773480466358	2		636	758	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552248	29552248	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	55	388	0	ENST00000356175.3:c.1981G>T	p.Gly661Ter	p.G661*	ENST00000356175	NM_000267.3	661	Gga/Tga	17/57	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.222773480466358	2		388	477	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556107	29556107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	16	166	0	ENST00000356175.3:c.2474C>T	p.Ser825Phe	p.S825F	ENST00000356175	NM_000267.3	825	tCc/tTc	21/57	1	2	FACETS	0.85	0.631	1	0.85	0.631	1	CLONAL	1	TRUE	1	0.222773480466358	2		166	169	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661910	29661910	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	60	396	0	ENST00000356175.3:c.5804T>C	p.Leu1935Pro	p.L1935P	ENST00000356175	NM_000267.3	1935	cTa/cCa	39/57	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.222773480466358	2		396	513	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611807	1611807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	163	740	0	ENST00000344749.5:c.1855G>A	p.Glu619Lys	p.E619K	ENST00000344749	NM_001136139.2	619	Gaa/Aaa	19/19	0.222773480466358	3	FACETS	0.937	0.86	1	0.937	0.86	1	CLONAL	2	TRUE	1	0.222773480466358	3		740	868	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292421	15292421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	86	729	0	ENST00000263388.2:c.2758C>T	p.His920Tyr	p.H920Y	ENST00000263388	NM_000435.2	920	Cac/Tac	17/33	0.222773480466358	3	FACETS	1	0.924	1	0.53	0.468	0.597	CLONAL	1	TRUE	1	0.222773480466358	3		729	809	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353923	15353923	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	63	456	0	ENST00000263377.2:c.2957C>T	p.Pro986Leu	p.P986L	ENST00000263377	NM_058243.2	986	cCc/cTc	14/20	0.222773480466358	3	FACETS	1	0.897	1	0.522	0.451	0.599	CLONAL	1	TRUE	1	0.222773480466358	3		456	602	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976399	18976399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749634234	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	231	797	0	ENST00000262803.5:c.3049C>T	p.Arg1017Cys	p.R1017C	ENST00000262803	NM_002911.3	1017	Cgt/Tgt	22/24	0.222773480466358	3	FACETS	0.852	0.795	0.91	1	0.989	1	CLONAL	3	TRUE	1	0.222773480466358	3		797	902	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758285	41758285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	84	579	0	ENST00000301178.4:c.1741G>A	p.Asp581Asn	p.D581N	ENST00000301178	NM_021913.4	581	Gat/Aat	15/20	0.222773480466358	3	FACETS	1	0.964	1	0.617	0.545	0.694	CLONAL	1	TRUE	1	0.222773480466358	3		579	679	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009144	27009144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	19	140	0	ENST00000335756.4:c.80C>T	p.Ser27Phe	p.S27F	ENST00000335756	NM_001809.3	27	tCc/tTc	1/5	0.222773480466358	1	FACETS	1	0.768	1	1	0.768	1	CLONAL	1	TRUE	0	0.222773480466358	1		140	151	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605083	46605084	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	107	833	2	ENST00000263734.3:c.1300_1301delinsTT	p.Pro434Leu	p.P434L	ENST00000263734	NM_001430.4	434	CCg/TTg	10/16	0.222773480466358	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.222773480466358	1		835	614	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99154358	99154358	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	87	514	0	ENST00000074304.5:c.500C>T	p.Thr167Ile	p.T167I	ENST00000074304	NM_001134224.1	167	aCc/aTc	8/26	0.222773480466358	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.222773480466358	1		514	524	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881336	111881336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749642894	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	65	329	0	ENST00000393256.3:c.14C>T	p.Pro5Leu	p.P5L	ENST00000393256	NM_006538.4	5	cCt/cTt	2/4	0.222773480466358	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.222773480466358	1		329	428	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031649	36031649	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780921646	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	71	800	0	ENST00000358208.4:c.1478C>T	p.Ser493Phe	p.S493F	ENST00000358208		493	tCc/tTc	12/12	1	2	FACETS	0.903	0.787	1	0.903	0.787	1	CLONAL	1	TRUE	1	0.222773480466358	2		800	706	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39713174	39713174	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	25	208	0	ENST00000361337.2:c.580A>C	p.Lys194Gln	p.K194Q	ENST00000361337	NM_003286.2	194	Aag/Cag	8/21	1	2	FACETS	0.717	0.566	0.891	0.717	0.566	0.891	SUBCLONAL	1	TRUE	1	0.222773480466358	2		208	313	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306682	41306682	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	60	593	0	ENST00000373198.4:c.977A>T	p.Glu326Val	p.E326V	ENST00000373198	NM_133170.3	326	gAa/gTa	7/32	1	2	FACETS	0.935	0.806	1	0.935	0.806	1	CLONAL	1	TRUE	1	0.222773480466358	2		593	576	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264724	46264724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	50	359	0	ENST00000371998.3:c.1594G>A	p.Gly532Ser	p.G532S	ENST00000371998		532	Ggt/Agt	12/23	1	2	FACETS	0.995	0.846	1	0.995	0.846	1	CLONAL	1	TRUE	1	0.222773480466358	2		359	451	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22123497	22123497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	53	338	0	ENST00000215832.6:c.1079C>T	p.Ser360Phe	p.S360F	ENST00000215832	NM_002745.4	360	tCt/tTt	8/9	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.222773480466358	2		338	436	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527398	41527398	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	67	489	0	ENST00000263253.7:c.1289T>C	p.Leu430Ser	p.L430S	ENST00000263253	NM_001429.3	430	tTg/tCg	6/31	1	2	FACETS	0.999	0.869	1	0.999	0.869	1	CLONAL	1	TRUE	1	0.222773480466358	2		489	602	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458644	12458644	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	55	378	0	ENST00000287820.6:c.1261C>T	p.Leu421Phe	p.L421F	ENST00000287820	NM_015869.4	421	Ctc/Ttc	6/7	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.222773480466358	2		378	397	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070414	37070414	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs63751705	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	29	266	0	ENST00000231790.2:c.1549G>C	p.Gly517Arg	p.G517R	ENST00000231790	NM_000249.3	517	Gga/Cga	13/19	1	2	FACETS	0.799	0.642	0.976	0.799	0.642	0.976	CLONAL	1	TRUE	1	0.222773480466358	2		266	326	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391193	89391193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	41	415	0	ENST00000336596.2:c.1259C>T	p.Ser420Phe	p.S420F	ENST00000336596	NM_005233.5	420	tCc/tTc	5/17	1	2	FACETS	0.876	0.731	1	0.876	0.731	1	CLONAL	1	TRUE	1	0.222773480466358	2		415	420	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189349352	189349353	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	28	278	0	ENST00000264731.3:c.48_49delinsAT	p.Asp16_Pro17delinsGluSer	p.D16_P17delinsES	ENST00000264731	NM_003722.4	16	gaCCct/gaATct	1/14	1	2	FACETS	0.665	0.531	0.817	0.665	0.531	0.817	SUBCLONAL	1	TRUE	1	0.222773480466358	2		278	378	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807524	1807524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	184	807	0	ENST00000260795.2:c.1693G>A	p.Glu565Lys	p.E565K	ENST00000260795		565	Gag/Aag	12/17	1	2	FACETS	1	0.958	1	1	0.993	1	CLONAL	2	TRUE	1	0.222773480466358	2		807	784	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136873	55136873	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	56	442	0	ENST00000257290.5:c.1195G>A	p.Glu399Lys	p.E399K	ENST00000257290	NM_006206.4	399	Gaa/Aaa	8/23	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.222773480466358	2		442	433	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352410	143352410	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	57	489	0	ENST00000262992.4:c.3G>A	p.Met1?	p.M1?	ENST00000262992	NM_001101669.1	1	atG/atA	2/24	1	2	FACETS	0.942	0.809	1	0.942	0.809	1	CLONAL	1	TRUE	1	0.222773480466358	2		489	543	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517791	176517791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1370781803	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	77	621	0	ENST00000292408.4:c.401G>A	p.Arg134Lys	p.R134K	ENST00000292408	NM_213647.1	134	aGg/aAg	4/18	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.222773480466358	2		621	612	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524640	176524640	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	70	783	0	ENST00000292408.4:c.2372C>T	p.Ser791Phe	p.S791F	ENST00000292408	NM_213647.1	791	tCc/tTc	18/18	1	2	FACETS	0.841	0.733	0.959	0.841	0.733	0.959	CLONAL	1	TRUE	1	0.222773480466358	2		783	747	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047658	180047658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753669084	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	87	731	0	ENST00000261937.6:c.2357C>T	p.Ala786Val	p.A786V	ENST00000261937	NM_182925.4	786	gCt/gTt	16/30	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.222773480466358	2		731	704	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169264	32169264	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	62	561	1	ENST00000375023.3:c.3769C>T	p.Gln1257Ter	p.Q1257*	ENST00000375023	NM_004557.3	1257	Cag/Tag	22/30	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.222773480466358	2		562	500	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987377	2987377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	73	507	0	ENST00000396946.4:c.52G>A	p.Glu18Lys	p.E18K	ENST00000396946	NM_032415.4	18	Gaa/Aaa	3/25	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.222773480466358	2		507	627	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435999	116435999	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	75	625	0	ENST00000397752.3:c.3994G>A	p.Glu1332Lys	p.E1332K	ENST00000397752	NM_000245.2	1332	Gaa/Aaa	21/21	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.222773480466358	2		625	653	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372373	55372373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	99	680	0	ENST00000297316.4:c.1063C>T	p.Leu355Phe	p.L355F	ENST00000297316	NM_022454.3	355	Ctc/Ttc	2/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.222773480466358	2		680	690	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879439	56879439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	86	600	0	ENST00000519728.1:c.956C>T	p.Thr319Ile	p.T319I	ENST00000519728	NM_002350.3	319	aCc/aTc	9/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.222773480466358	2		600	662	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046326	69046326	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	50	344	0	ENST00000288368.4:c.3799T>A	p.Phe1267Ile	p.F1267I	ENST00000288368	NM_024870.2	1267	Ttc/Atc	32/40	1	2	FACETS	0.984	0.836	1	0.984	0.836	1	CLONAL	1	TRUE	1	0.222773480466358	2		344	456	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482286	87482286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	56	524	0	ENST00000277120.3:c.1573C>T	p.Pro525Ser	p.P525S	ENST00000277120		525	Cct/Tct	14/19	1	2	FACETS	0.891	0.764	1	0.891	0.764	1	CLONAL	1	TRUE	1	0.222773480466358	2		524	564	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402735	139402736	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	81	860	1	ENST00000277541.6:c.3273_3274delinsTT	p.Leu1092Phe	p.L1092F	ENST00000277541	NM_017617.3	1091	ggCCtt/ggTTtt	20/34	1	2	FACETS	0.929	0.817	1	0.929	0.817	1	CLONAL	1	TRUE	1	0.222773480466358	2		861	783	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923022	39923022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	90	302	0	ENST00000378444.4:c.3686C>T	p.Pro1229Leu	p.P1229L	ENST00000378444	NM_001123385.1	1229	cCt/cTt	8/15	NA	2	FACETS	1	0.948	1			1	INDETERMINATE	2	TRUE	NA	0.222773480466358	2		302	367	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222412	53222413	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0044662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	98	442	0	ENST00000375401.3:c.4419_4420delinsTT	p.Arg1474Ter	p.R1474*	ENST00000375401	NM_004187.3	1473	gcCCga/gcTTga	26/26	NA	2	FACETS	1	0.953	1			1	INDETERMINATE	2	TRUE	NA	0.222773480466358	2		442	398	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0044699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	74	506	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.278780542382929	2		506	459	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0044699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	71	673	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.278780542382929	2		673	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780068	NA	P-0044699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	20	652	0	ENST00000269305.4:c.472C>T	p.Arg158Cys	p.R158C	ENST00000269305	NM_001126112.2	158	Cgc/Tgc	5/11	0.214169168197378	2	FACETS	0.182	0.138	0.234	0.091	0.069	0.117	SUBCLONAL	1	TRUE	0	0.278780542382929	2		652	788	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0044699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	75	375	0	ENST00000311936.3:c.180_181delinsAA	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggAAaa	3/5	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.278780542382929	2		375	482	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163373	47163373	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	79	233	0	ENST00000409792.3:c.2753C>A	p.Ser918Ter	p.S918*	ENST00000409792	NM_014159.6	918	tCa/tAa	3/21	0.278780542382929	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.278780542382929	2		233	238	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439953	49439953	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs749332791	NA	P-0044699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	95	506	0	ENST00000301067.7:c.4588A>G	p.Met1530Val	p.M1530V	ENST00000301067	NM_003482.3	1530	Atg/Gtg	17/54	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.278780542382929	2		506	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579854	7579854	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0044699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	93	540	0	ENST00000269305.4:c.59C>G	p.Ser20Ter	p.S20*	ENST00000269305	NM_001126112.2	20	tCa/tGa	2/11	0.214169168197378	2	FACETS	1	0.961	1	0.585	0.521	0.653	CLONAL	1	TRUE	0	0.278780542382929	2		540	570	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054625	13054625	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	60	348	0	ENST00000316448.5:c.1152C>G	p.Asp384Glu	p.D384E	ENST00000316448	NM_004343.3	384	gaC/gaG	9/9	1	2	FACETS	0.828	0.714	0.951	0.828	0.714	0.951	CLONAL	1	TRUE	1	0.278780542382929	2		348	520	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503784	186503785	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0044699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	56	367	0	ENST00000323963.5:c.463_464del	p.Ile155CysfsTer10	p.I155Cfs*10	ENST00000323963		154	cAT/c	5/11	1	2	FACETS	0.768	0.658	0.888	0.768	0.658	0.888	SUBCLONAL	1	TRUE	1	0.278780542382929	2		367	523	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80169084	80169084	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	52	352	0	ENST00000265081.6:c.3280G>T	p.Glu1094Ter	p.E1094*	ENST00000265081	NM_002439.4	1094	Gaa/Taa	23/24	1	2	FACETS	0.992	0.848	1	0.992	0.848	1	CLONAL	1	TRUE	1	0.278780542382929	2		352	376	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874977	151874977	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	25	154	0	ENST00000262189.6:c.7561G>C	p.Asp2521His	p.D2521H	ENST00000262189	NM_170606.2	2521	Gat/Cat	38/59	0.100784074142539	4	FACETS	0.721	0.569	0.896	0.361	0.284	0.448	INDETERMINATE	1	TRUE	2	0.278780542382929	4		154	318	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923086	39923087	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	47	269	0	ENST00000378444.4:c.3621dup	p.Gln1208ThrfsTer8	p.Q1208Tfs*8	ENST00000378444	NM_001123385.1	1207	-/A	8/15	1	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.13	1		269	470	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438647	49438647	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	53	568	0	ENST00000301067.7:c.4843C>T	p.Arg1615Ter	p.R1615*	ENST00000301067	NM_003482.3	1615	Cga/Tga	19/54	1	2	FACETS	0.886	0.753	1	0.886	0.753	1	CLONAL	1	TRUE	1	0.13	2		568	920	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427927	49427927	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	56	611	0	ENST00000301067.7:c.10663G>T	p.Glu3555Ter	p.E3555*	ENST00000301067	NM_003482.3	3555	Gag/Tag	38/54	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.13	2		611	841	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755554	39755554	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	83	402	0	ENST00000288319.7:c.1211del	p.Pro404ArgfsTer25	p.P404Rfs*25	ENST00000288319	NM_182918.3	404	cCg/cg	10/10	1	2	FACETS	0.95	0.84	1	0.95	0.84	1	CLONAL	1	TRUE	1	0.309196681930519	2		402	565	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409154	139409154	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	68	641	0	ENST00000277541.6:c.2015G>A	p.Gly672Glu	p.G672E	ENST00000277541	NM_017617.3	672	gGg/gAg	13/34	1	2	FACETS	0.502	0.435	0.574	0.502	0.435	0.574	SUBCLONAL	1	TRUE	1	0.309196681930519	2		641	877	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041518	14041518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149364215	NA	P-0044759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	34	309	0	ENST00000311895.7:c.2065C>T	p.Arg689Cys	p.R689C	ENST00000311895	NM_005236.2	689	Cgt/Tgt	11/11	1	2	FACETS	0.457	0.373	0.552	0.457	0.373	0.552	SUBCLONAL	1	TRUE	1	0.309196681930519	2		309	481	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489535	56489535	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	139	429	0	ENST00000267101.3:c.2000G>T	p.Arg667Leu	p.R667L	ENST00000267101	NM_001982.3	667	cGt/cTt	17/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.309196681930519	2		429	783	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89811409	89811409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138013482	NA	P-0044759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	90	691	0	ENST00000389301.3:c.3584G>A	p.Arg1195Gln	p.R1195Q	ENST00000389301	NM_000135.2	1195	cGg/cAg	36/43	1	2	FACETS	0.597	0.528	0.671	0.597	0.528	0.671	SUBCLONAL	1	TRUE	1	0.309196681930519	2		691	975	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412233	139412233	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	78	633	1	ENST00000277541.6:c.1412T>A	p.Ile471Asn	p.I471N	ENST00000277541	NM_017617.3	471	aTt/aAt	8/34	1	2	FACETS	0.562	0.493	0.637	0.562	0.493	0.637	SUBCLONAL	1	TRUE	1	0.309196681930519	2		634	897	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245494	16245494	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	28	280	0	ENST00000375759.3:c.1469G>T	p.Cys490Phe	p.C490F	ENST00000375759	NM_015001.2	490	tGt/tTt	7/15	1	2	FACETS	0.464	0.371	0.571	0.464	0.371	0.571	SUBCLONAL	1	TRUE	1	0.309196681930519	2		280	390	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245539	16245539	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1471081719	NA	P-0044759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	25	230	0	ENST00000375759.3:c.1514G>T	p.Arg505Leu	p.R505L	ENST00000375759	NM_015001.2	505	cGc/cTc	7/15	1	2	FACETS	0.496	0.391	0.617	0.496	0.391	0.617	SUBCLONAL	1	TRUE	1	0.309196681930519	2		230	326	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456630	32456630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	54	168	1	ENST00000332351.3:c.262G>A	p.Gly88Ser	p.G88S	ENST00000332351	NM_024426.4	88	Ggc/Agc	1/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.309196681930519	2		169	238	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444387	49444387	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	69	643	0	ENST00000301067.7:c.2984C>T	p.Pro995Leu	p.P995L	ENST00000301067	NM_003482.3	995	cCt/cTt	11/54	1	2	FACETS	0.508	0.442	0.581	0.508	0.442	0.581	SUBCLONAL	1	TRUE	1	0.309196681930519	2		643	878	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123868754	123868754	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	70	489	0	ENST00000330479.4:c.9A>T	p.Arg3Ser	p.R3S	ENST00000330479	NM_020382.3	3	agA/agT	1/9	1	2	FACETS	0.556	0.483	0.634	0.556	0.483	0.634	SUBCLONAL	1	TRUE	1	0.309196681930519	2		489	815	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396651	30396651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	21	64	0	ENST00000331968.5:c.68C>T	p.Ala23Val	p.A23V	ENST00000331968	NM_002742.2	23	gCg/gTg	1/18	0.246010969577568	3	FACETS	1	0.841	1	1	0.841	1	CLONAL	2	TRUE	1	0.309196681930519	3		64	73	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610567	81610567	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	30	265	0	ENST00000298171.2:c.2165A>G	p.Gln722Arg	p.Q722R	ENST00000298171	NM_000369.2	722	cAa/cGa	10/10	0.246010969577568	3	FACETS	0.462	0.371	0.565	0.231	0.185	0.283	SUBCLONAL	1	TRUE	1	0.309196681930519	3		265	485	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812223	212812223	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	26	218	0	ENST00000342788.4:c.353C>A	p.Ala118Glu	p.A118E	ENST00000342788	NM_005235.2	118	gCa/gAa	3/28	1	2	FACETS	0.478	0.378	0.592	0.478	0.378	0.592	SUBCLONAL	1	TRUE	1	0.309196681930519	2		218	352	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081548	143081548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775054204	NA	P-0044759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	79	351	0	ENST00000262992.4:c.1526C>T	p.Ser509Phe	p.S509F	ENST00000262992	NM_001101669.1	509	tCc/tTc	15/24	1	2	FACETS	0.945	0.832	1	0.945	0.832	1	CLONAL	1	TRUE	1	0.309196681930519	2		351	541	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675260	176675260	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	44	259	0	ENST00000439151.2:c.4576C>A	p.Pro1526Thr	p.P1526T	ENST00000439151	NM_022455.4	1526	Cct/Act	11/23	1	2	FACETS	0.647	0.543	0.762	0.647	0.543	0.762	SUBCLONAL	1	TRUE	1	0.309196681930519	2		259	440	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969088	93969088	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	61	204	0	ENST00000369303.4:c.1908G>T	p.Glu636Asp	p.E636D	ENST00000369303	NM_004440.3	636	gaG/gaT	10/17	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.309196681930519	2		204	347	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409801	139409801	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	70	699	0	ENST00000277541.6:c.1955C>A	p.Ser652Ter	p.S652*	ENST00000277541	NM_017617.3	652	tCg/tAg	12/34	1	2	FACETS	0.474	0.412	0.542	0.474	0.412	0.542	SUBCLONAL	1	TRUE	1	0.309196681930519	2		699	955	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413962	139413962	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	85	728	0	ENST00000277541.6:c.798C>G	p.Cys266Trp	p.C266W	ENST00000277541	NM_017617.3	266	tgC/tgG	5/34	1	2	FACETS	0.573	0.505	0.646	0.573	0.505	0.646	SUBCLONAL	1	TRUE	1	0.309196681930519	2		728	959	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	132	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.515192379577757	6	FACETS	1	0.984	1	0.459	0.418	0.502	INDETERMINATE	1	FALSE	3	0.873427096597276	6		452	603	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0044763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	102	325	0	ENST00000349496.5:c.101G>A	p.Gly34Glu	p.G34E	ENST00000349496	NM_001904.3	34	gGa/gAa	3/15	0.873427096597276	4	FACETS	0.921	0.828	1	0.23	0.207	0.255	CLONAL	1	FALSE	0	0.873427096597276	4		325	475	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481403	140481403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913357	NA	P-0044763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	333	408	0	ENST00000288602.6:c.1405G>A	p.Gly469Arg	p.G469R	ENST00000288602	NM_004333.4	469	Gga/Aga	11/18	0.546918447814518	6	FACETS	0.942	0.903	0.98	0.942	0.903	0.98	CLONAL	4	FALSE	2	0.873427096597276	6		408	556	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945033	31945033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	515	755	0	ENST00000340398.3:c.68C>T	p.Thr23Met	p.T23M	ENST00000340398	NM_001013699.2	23	aCg/aTg	1/1	0.515192379577757	6	FACETS	1	0.971	1	1	0.971	1	INDETERMINATE	3	FALSE	3	0.873427096597276	6		755	1068	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375035	104375049	+	inframe_deletion	In_Frame_Del	DEL	GACAGCCTGGAAAGT	GACAGCCTGGAAAGT	-	novel	NA	P-0044763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	88	463	0	ENST00000369902.3:c.1039_1053del	p.Leu347_Ser351del	p.L347_S351del	ENST00000369902	NM_016169.3	345	GACAGCCTGGAAAGT/-	9/12	0.873427096597276	2	FACETS	0.522	0.465	0.582	0.261	0.232	0.291	SUBCLONAL	1	FALSE	0	0.873427096597276	2		463	386	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	131	320	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.722220366948858	2		321	308	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	40	445	0	ENST00000425967.3:c.1731C>G	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaG	13/19	1	2	FACETS	0.227	0.188	0.27	0.227	0.188	0.27	SUBCLONAL	1	TRUE	1	0.722220366948858	2		445	489	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29422330	29422330	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0044766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	242	601	0	ENST00000356175.3:c.3G>A	p.Met1?	p.M1?	ENST00000356175	NM_000267.3	1	atG/atA	1/57	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.722220366948858	2		601	606	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665815	29665815	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	67	176	0	ENST00000356175.3:c.6850del	p.Asn2285IlefsTer13	p.N2285Ifs*13	ENST00000356175	NM_000267.3	2284	Ctt/tt	45/57	1	2	FACETS	0.982	0.87	1	0.982	0.87	1	CLONAL	1	TRUE	1	0.722220366948858	2		176	189	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858137	152858137	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	383	946	0	ENST00000406277.2:c.478C>T	p.Gln160Ter	p.Q160*	ENST00000406277	NM_152274.4	160	Cag/Tag	6/7	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.722220366948858	2		946	920	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794353	242794353	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1282191832	NA	P-0044814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	70	986	1	ENST00000334409.5:c.589C>T	p.Arg197Ter	p.R197*	ENST00000334409	NM_005018.2	197	Cga/Tga	3/5	1	2	FACETS	0.576	0.501	0.658	0.576	0.501	0.658	SUBCLONAL	1	TRUE	1	0.273793958294643	2		987	887	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032175	26032175	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	44	465	0	ENST00000244661.2:c.114G>C	p.Lys38Asn	p.K38N	ENST00000244661	NM_003537.3	38	aaG/aaC	1/1	1	2	FACETS	0.561	0.47	0.662	0.561	0.47	0.662	SUBCLONAL	1	TRUE	1	0.273793958294643	2		465	573	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	52	584	0	ENST00000397752.3:c.3028G>C	p.Asp1010His	p.D1010H	ENST00000397752	NM_000245.2	1010	Gat/Cat	14/21	1	2	FACETS	0.459	0.389	0.535	0.459	0.389	0.535	SUBCLONAL	1	TRUE	1	0.273793958294643	2		584	828	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874014	151874014	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	38	412	0	ENST00000262189.6:c.8524A>T	p.Asn2842Tyr	p.N2842Y	ENST00000262189	NM_170606.2	2842	Aat/Tat	38/59	1	2	FACETS	0.511	0.422	0.611	0.511	0.422	0.611	SUBCLONAL	1	TRUE	1	0.273793958294643	2		412	543	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184041	123184041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1375196362	NA	P-0044814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	31	270	0	ENST00000218089.9:c.899C>T	p.Ala300Val	p.A300V	ENST00000218089	NM_001042749.1	300	gCg/gTg	11/35	1	2	FACETS	0.614	0.497	0.746	0.614	0.497	0.746	SUBCLONAL	1	TRUE	1	0.273793958294643	2		270	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0044849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	237	646	7	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.24959568005259	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.24959568005259	2		653	902	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584540	187584540	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	68	487	0	ENST00000441802.2:c.3493G>C	p.Asp1165His	p.D1165H	ENST00000441802	NM_005245.3	1165	Gat/Cat	3/27	0.225665984692003	4	FACETS	1	0.952	1			1	CLONAL	1	TRUE	NA	0.24959568005259	4		487	566	SUCCESS
RET	5979	MSKCC	GRCh37	10	43598018	43598018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753707182	NA	P-0044849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	233	983	2	ENST00000355710.3:c.566G>A	p.Arg189His	p.R189H	ENST00000355710	NM_020975.4	189	cGc/cAc	3/20	1	2	FACETS	0.912	0.85	0.975	1	0.994	1	CLONAL	2	TRUE	1	0.24959568005259	2		985	1024	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276256	15276256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759704420	NA	P-0044849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	248	999	2	ENST00000263388.2:c.5738C>T	p.Ala1913Val	p.A1913V	ENST00000263388	NM_000435.2	1913	gCg/gTg	31/33	0.225665984692003	4	FACETS	1	0.979	1			1	CLONAL	2	TRUE	NA	0.24959568005259	4		1001	1122	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716326	52716326	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	308	851	0	ENST00000322088.6:c.770G>C	p.Trp257Ser	p.W257S	ENST00000322088	NM_014225.5	257	tGg/tCg	6/15	0.225665984692003	4	FACETS	0.915	0.862	0.968			1	CLONAL	3	TRUE	NA	0.24959568005259	4		851	1124	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137046	64137046	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	122	791	2	ENST00000334205.4:c.1557C>A	p.Phe519Leu	p.F519L	ENST00000334205	NM_003942.2	519	ttC/ttA	13/17	0.24959568005259	2	FACETS	1	0.953	1	0.546	0.493	0.602	CLONAL	1	TRUE	0	0.24959568005259	2		793	895	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953536	32953536	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs431825371	NA	P-0044849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	79	584	0	ENST00000380152.3:c.8837T>A	p.Leu2946Ter	p.L2946*	ENST00000380152		2946	tTg/tAg	22/27	0.24959568005259	3	FACETS	1	0.947	1	0.57	0.501	0.643	CLONAL	1	TRUE	1	0.24959568005259	3		584	625	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947622	48947622	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0044849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	34	312	0	ENST00000267163.4:c.1209T>A	p.Tyr403Ter	p.Y403*	ENST00000267163	NM_000321.2	403	taT/taA	12/27	0.221602099844829	4	FACETS	1	0.827	1	0.505	0.413	0.608	CLONAL	1	TRUE	2	0.24959568005259	4		312	337	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125455	47125455	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	66	432	0	ENST00000409792.3:c.5815G>C	p.Asp1939His	p.D1939H	ENST00000409792	NM_014159.6	1939	Gat/Cat	12/21	0.24959568005259	3	FACETS	0.969	0.841	1	0.484	0.42	0.554	CLONAL	1	TRUE	1	0.24959568005259	3		432	614	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448609	89448609	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	66	615	0	ENST00000336596.2:c.1573G>C	p.Glu525Gln	p.E525Q	ENST00000336596	NM_005233.5	525	Gag/Cag	7/17	0.24959568005259	4	FACETS	0.699	0.605	0.802	0.35	0.302	0.401	SUBCLONAL	1	TRUE	2	0.24959568005259	4		615	945	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584645	187584645	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	60	536	1	ENST00000441802.2:c.3388G>T	p.Glu1130Ter	p.E1130*	ENST00000441802	NM_005245.3	1130	Gag/Tag	3/27	0.225665984692003	4	FACETS	0.847	0.729	0.977			1	CLONAL	1	TRUE	NA	0.24959568005259	4		537	709	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589598	67589599	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCAGTT	novel	NA	P-0044849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	78	282	0	ENST00000274335.5:c.1365_1370dup	p.Phe456_Gln457dup	p.F456_Q457dup	ENST00000274335		456	act/acTCAGTTt	10/15	0.221602099844829	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	2	0.24959568005259	4		282	315	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188861	32188861	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0044849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	98	1030	0	ENST00000375023.3:c.693T>A	p.Cys231Ter	p.C231*	ENST00000375023	NM_004557.3	231	tgT/tgA	4/30	0.24959568005259	4	FACETS	0.834	0.742	0.932	0.417	0.371	0.466	CLONAL	1	TRUE	2	0.24959568005259	4		1030	1177	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981578	70981578	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1457	124	1077	0	ENST00000276594.2:c.518C>A	p.Ser173Ter	p.S173*	ENST00000276594	NM_024504.3	173	tCa/tAa	2/8	0.24959568005259	6	FACETS	0.942	0.849	1	0.314	0.283	0.347	CLONAL	1	TRUE	3	0.24959568005259	6		1077	1581	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0044886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	48	304	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.186463908114157	3	FACETS	1	0.956	1	0.692	0.587	0.807	CLONAL	1	TRUE	1	0.217916124422483	3		304	353	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092809	27092809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	33	431	0	ENST00000324856.7:c.2830C>T	p.Gln944Ter	p.Q944*	ENST00000324856	NM_006015.4	944	Cag/Tag	9/20	1	2	FACETS	0.597	0.486	0.724	0.597	0.486	0.724	SUBCLONAL	1	TRUE	1	0.217916124422483	2		431	507	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058705	47058706	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	51	349	0	ENST00000409792.3:c.7572dup	p.Lys2525Ter	p.K2525*	ENST00000409792	NM_014159.6	2524	-/T	21/21	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.217916124422483	2		349	387	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244401	46244401	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	31	375	0	ENST00000334344.6:c.2495C>T	p.Ser832Leu	p.S832L	ENST00000334344	NM_152641.2	832	tCa/tTa	15/21	1	2	FACETS	0.589	0.476	0.718	0.589	0.476	0.718	SUBCLONAL	1	TRUE	1	0.217916124422483	2		375	483	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762067	43762067	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	27	412	0	ENST00000382044.4:c.1378C>T	p.Gln460Ter	p.Q460*	ENST00000382044	NM_001141980.1	460	Cag/Tag	11/28	1	2	FACETS	0.596	0.473	0.736	0.596	0.473	0.736	SUBCLONAL	1	TRUE	1	0.217916124422483	2		412	416	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157256700	157256700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	13	207	0	ENST00000346085.5:c.2027C>T	p.Ser676Leu	p.S676L	ENST00000346085	NM_020732.3	676	tCa/tTa	5/20	0.217916124422483	1	FACETS	0.434	0.309	0.586	0.434	0.309	0.586	SUBCLONAL	1	TRUE	0	0.217916124422483	1		207	245	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779805	3779812	+	frameshift_variant	Frame_Shift_Del	DEL	CCCAGCCC	CCCAGCCC	-	novel	NA	P-0044886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	83	652	0	ENST00000262367.5:c.5236_5243del	p.Gly1746ProfsTer3	p.G1746Pfs*3	ENST00000262367	NM_004380.2	1746	GGGCTGGGc/c	31/31	0.164431251379397	2	FACETS	1	0.969	1	0.647	0.571	0.727	CLONAL	1	TRUE	0	0.217916124422483	2		652	589	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990330	81990330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761018891	NA	P-0044886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	28	355	0	ENST00000359376.3:c.3601C>T	p.Arg1201Cys	p.R1201C	ENST00000359376	NM_002661.3	1201	Cgc/Tgc	32/33	0.164431251379397	2	FACETS	0.616	0.492	0.758	0.308	0.246	0.379	SUBCLONAL	1	TRUE	0	0.217916124422483	2		355	417	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320921	30320921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	23	401	0	ENST00000322652.5:c.1331C>T	p.Ala444Val	p.A444V	ENST00000322652	NM_015355.2	444	gCa/gTa	12/16	1	2	FACETS	0.506	0.394	0.637	0.506	0.394	0.637	SUBCLONAL	1	TRUE	1	0.217916124422483	2		401	417	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503923	149503923	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	44	429	0	ENST00000261799.4:c.1913C>A	p.Ser638Tyr	p.S638Y	ENST00000261799	NM_002609.3	638	tCc/tAc	14/23	1	2	FACETS	0.959	0.806	1	0.959	0.806	1	CLONAL	1	TRUE	1	0.217916124422483	2		429	421	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0044902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	284	310	0	ENST00000311936.3:c.34_35delinsTT	p.Gly12Phe	p.G12F	ENST00000311936	NM_004985.3	12	GGt/TTt	2/5	0.292227776125249	6	FACETS	0.918	0.866	0.971			1	CLONAL	4	TRUE	NA	0.292227776125249	6		310	839	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044925	47044925	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	248	906	0	ENST00000377604.3:c.2251G>T	p.Glu751Ter	p.E751*	ENST00000377604	NM_001204468.1	751	Gag/Tag	20/24	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.292227776125249	2		906	1222	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998664	100998664	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	226	771	0	ENST00000325455.5:c.1138T>A	p.Phe380Ile	p.F380I	ENST00000325455	NM_001202474.3	380	Ttc/Atc	1/8	0.138265522081183	4	FACETS	0.876	0.815	0.939	0.876	0.815	0.939	INDETERMINATE	2	TRUE	2	0.292227776125249	4		771	1141	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180942	108180942	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	61	223	0	ENST00000278616.4:c.5818G>T	p.Glu1940Ter	p.E1940*	ENST00000278616	NM_000051.3	1940	Gaa/Taa	39/63	0.138265522081183	4	FACETS	1	0.956	1	0.632	0.546	0.724	INDETERMINATE	1	TRUE	2	0.292227776125249	4		223	427	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406333	406333	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	86	492	0	ENST00000399788.2:c.4108G>C	p.Glu1370Gln	p.E1370Q	ENST00000399788	NM_001042603.1	1370	Gaa/Caa	25/28	NA	2	FACETS	0.731	0.646	0.822			1	INDETERMINATE	1	TRUE	NA	0.292227776125249	2		492	805	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762184	43762184	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	99	634	1	ENST00000382044.4:c.1261G>T	p.Glu421Ter	p.E421*	ENST00000382044	NM_001141980.1	421	Gag/Tag	11/28	1	2	FACETS	0.651	0.58	0.728	0.651	0.58	0.728	SUBCLONAL	1	TRUE	1	0.292227776125249	2		635	1040	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785784	50785784	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	132	437	0	ENST00000398568.2:c.774A>T	p.Lys258Asn	p.K258N	ENST00000398568	NM_001042412.1	258	aaA/aaT	4/18	0.138265522081183	4	FACETS	1	0.985	1	0.734	0.667	0.805	INDETERMINATE	1	TRUE	2	0.292227776125249	4		437	795	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825473	50825473	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	89	264	0	ENST00000398568.2:c.2104G>T	p.Ala702Ser	p.A702S	ENST00000398568	NM_001042412.1	702	Gca/Tca	14/18	0.138265522081183	4	FACETS	0.917	0.818	1	0.917	0.818	1	INDETERMINATE	2	TRUE	2	0.292227776125249	4		264	429	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821140	72821140	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs780518082	NA	P-0044902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	203	623	1	ENST00000268489.5:c.11035G>T	p.Val3679Leu	p.V3679L	ENST00000268489	NM_006885.3	3679	Gtg/Ttg	10/10	0.138265522081183	4	FACETS	0.83	0.769	0.893	0.83	0.769	0.893	INDETERMINATE	2	TRUE	2	0.292227776125249	4		624	1082	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946143	55946143	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	73	302	0	ENST00000263923.4:c.4036G>T	p.Asp1346Tyr	p.D1346Y	ENST00000263923	NM_002253.2	1346	Gac/Tac	30/30	1	2	FACETS	0.966	0.847	1	0.966	0.847	1	CLONAL	1	TRUE	1	0.292227776125249	2		302	517	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956984	2956984	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	221	536	0	ENST00000396946.4:c.2643C>A	p.Ser881Arg	p.S881R	ENST00000396946	NM_032415.4	881	agC/agA	20/25	0.138265522081183	4	FACETS	0.976	0.909	1	0.976	0.909	1	INDETERMINATE	2	TRUE	2	0.292227776125249	4		536	1001	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967086	18967086	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	182	775	0	ENST00000262803.5:c.1801A>G	p.Thr601Ala	p.T601A	ENST00000262803	NM_002911.3	601	Acc/Gcc	13/24	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.582544318908786	2		775	615	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0044917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	16	434	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.097	0.071	0.129	0.097	0.071	0.129	SUBCLONAL	1	TRUE	1	0.781253065641342	2		434	421	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	243	320	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.74	2		321	547	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0044931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	170	313	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.99	0.919	1	0.99	0.919	1	CLONAL	1	TRUE	1	0.74	2		313	464	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0044931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	277	542	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.74	2		542	747	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216546	108216546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529296539	NA	P-0044931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	166	314	0	ENST00000278616.4:c.8495G>A	p.Arg2832His	p.R2832H	ENST00000278616	NM_000051.3	2832	cGt/cAt	58/63	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.74	2		314	405	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17380492	17380492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199848267	NA	P-0044931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	279	791	0	ENST00000375499.3:c.23C>T	p.Ser8Phe	p.S8F	ENST00000375499	NM_003000.2	8	tCc/tTc	1/8	1	2	FACETS	0.801	0.754	0.85	0.801	0.754	0.85	CLONAL	1	TRUE	1	0.74	2		791	941	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148692	20148693	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0044931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	186	416	0	ENST00000379607.5:c.370_371delinsTT	p.Gly124Leu	p.G124L	ENST00000379607	NM_001412.3	124	GGa/TTa	6/7	1	2	FACETS	0.958	0.891	1	0.958	0.891	1	CLONAL	1	TRUE	1	0.74	2		416	525	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196241	106196241	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	48	247	0	ENST00000380013.4:c.4576del	p.Gln1526SerfsTer45	p.Q1526Sfs*45	ENST00000380013	NM_001127208.2	1525	tCc/tc	11/11	1	2	FACETS	0.386	0.328	0.45	0.386	0.328	0.45	SUBCLONAL	1	TRUE	1	0.74	2		247	336	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610179	81610179	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	261	420	0	ENST00000298171.2:c.1777G>T	p.Ala593Ser	p.A593S	ENST00000298171	NM_000369.2	593	Gcc/Tcc	10/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.74	2		420	588	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528119	29528120	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	261	455	0	ENST00000356175.3:c.1127_1128insA	p.Met376IlefsTer3	p.M376Ifs*3	ENST00000356175	NM_000267.3	376	atg/atAg	10/57	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.74	2		455	646	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0044956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	113	207	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	NA	2	FACETS	0.888	0.801	0.979			1	INDETERMINATE	1	FALSE	NA	0.415986255537455	2		207	612	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0044956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	181	532	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.38974187716586	3	FACETS	1	0.973	1	0.559	0.515	0.604	CLONAL	1	FALSE	1	0.415986255537455	3		533	941	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643299	38643299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1404721092	NA	P-0044956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	49	483	0	ENST00000299084.4:c.769C>T	p.Arg257Cys	p.R257C	ENST00000299084	NM_152594.2	257	Cgc/Tgc	7/7	0.340150322799863	4	FACETS	0.525	0.443	0.614	0.262	0.221	0.307	SUBCLONAL	1	FALSE	2	0.415986255537455	4		483	636	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165728	118165728	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	67	466	0	ENST00000369448.3:c.238T>G	p.Leu80Val	p.L80V	ENST00000369448	NM_017709.3	80	Ttg/Gtg	2/2	NA	2	FACETS	0.627	0.545	0.714			1	INDETERMINATE	1	FALSE	NA	0.415986255537455	2		466	514	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372419	118372419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555045700	NA	P-0044956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	72	575	0	ENST00000534358.1:c.6352G>A	p.Glu2118Lys	p.E2118K	ENST00000534358	NM_005933.3	2118	Gaa/Aaa	26/36	0.308442664447299	5	FACETS	0.719	0.627	0.818			1	SUBCLONAL	1	FALSE	NA	0.415986255537455	5		575	782	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607771	46607771	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375135104	NA	P-0044956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	94	953	1	ENST00000263734.3:c.1960G>A	p.Val654Ile	p.V654I	ENST00000263734	NM_001430.4	654	Gtc/Atc	12/16	0.344148200074616	5	FACETS	0.692	0.614	0.776	0.231	0.204	0.259	SUBCLONAL	1	FALSE	2	0.415986255537455	5		954	1060	SUCCESS
APC	324	MSKCC	GRCh37	5	112175429	112175430	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCCACTCATGTTTAGCAG	novel	NA	P-0044956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	29	303	0	ENST00000257430.4:c.4139_4157dup	p.Arg1386SerfsTer6	p.R1386Sfs*6	ENST00000257430	NM_000038.5	1380	acc/aCCCCACTCATGTTTAGCAGcc	16/16	0.419910950979517	3	FACETS	0.538	0.433	0.658	0.269	0.216	0.329	SUBCLONAL	1	FALSE	1	0.415986255537455	3		303	313	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492934	56492953	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	CTCATGCTACCAGCTGCAGC	CTCATGCTACCAGCTGCAGC	GCT	novel	NA	P-0044956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	18	230	1	ENST00000407977.2:c.-15_5delinsAGC		p.*5*	ENST00000407977		?-2/783		2/10	0.419910950979517	3	FACETS	0.311	0.234	0.403	0.156	0.117	0.202	SUBCLONAL	1	FALSE	1	0.415986255537455	3		231	336	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	272	452	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.28749675531159	3	FACETS	1	0.98	1	1	0.995	1	CLONAL	3	TRUE	1	0.28749675531159	3		452	669	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347494	89347494	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	119	549	0	ENST00000301030.4:c.5456C>G	p.Ser1819Cys	p.S1819C	ENST00000301030	NM_001256183.1	1819	tCc/tGc	9/13	0.28749675531159	1	FACETS	0.938	0.847	1	0.938	0.847	1	CLONAL	1	TRUE	0	0.28749675531159	1		549	756	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41022160	41022160	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	88	477	0	ENST00000267868.3:c.884C>A	p.Ala295Glu	p.A295E	ENST00000267868	NM_002875.4	295	gCa/gAa	9/10	1	2	FACETS	0.788	0.697	0.885	0.788	0.697	0.885	SUBCLONAL	1	TRUE	1	0.28749675531159	2		477	777	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122748	7122748	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	148	640	0	ENST00000302850.5:c.3406A>G	p.Met1136Val	p.M1136V	ENST00000302850	NM_000208.2	1136	Atg/Gtg	19/22	0.28749675531159	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.28749675531159	1		640	847	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488717	212488717	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	98	409	0	ENST00000342788.4:c.2132G>T	p.Arg711Leu	p.R711L	ENST00000342788	NM_005235.2	711	cGt/cTt	18/28	1	2	FACETS	0.894	0.797	0.996	0.894	0.797	0.996	CLONAL	1	TRUE	1	0.28749675531159	2		409	763	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755513	39755513	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1203601203	NA	P-0044969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	74	453	0	ENST00000288319.7:c.1252A>G	p.Met418Val	p.M418V	ENST00000288319	NM_182918.3	418	Atg/Gtg	10/10	1	2	FACETS	0.69	0.603	0.784	0.69	0.603	0.784	SUBCLONAL	1	TRUE	1	0.28749675531159	2		453	746	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540110	187540110	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	60	315	0	ENST00000441802.2:c.7630G>C	p.Glu2544Gln	p.E2544Q	ENST00000441802	NM_005245.3	2544	Gag/Cag	10/27	1	2	FACETS	0.756	0.652	0.87	0.756	0.652	0.87	SUBCLONAL	1	TRUE	1	0.28749675531159	2		315	552	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814559	43814559	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1304504402	NA	P-0045011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	95	537	0	ENST00000372470.3:c.1354C>T	p.Arg452Cys	p.R452C	ENST00000372470	NM_005373.2	452	Cgc/Tgc	9/12	0.750305396216508	1	FACETS	0.31	0.276	0.345	0.31	0.276	0.345	SUBCLONAL	1	TRUE	0	0.750305396216508	1		537	511	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784406	9784406	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	385	603	0	ENST00000377346.4:c.2791C>A	p.Pro931Thr	p.P931T	ENST00000377346	NM_005026.3	931	Cca/Aca	22/24	0.249764235314165	2	FACETS	1	0.994	1	0.619	0.591	0.647	INDETERMINATE	1	TRUE	0	0.750305396216508	2		603	829	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045134-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	120	320	1				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		321	558	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0045134-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	13	207	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		207	43	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806092	1806092	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913484	NA	P-0045134-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	66	789	0	ENST00000260795.2:c.1111A>T	p.Ser371Cys	p.S371C	ENST00000260795		371	Agt/Tgt	8/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		789	200	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057727	27057727	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045134-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	10	715	0	ENST00000324856.7:c.1435C>T	p.Gln479Ter	p.Q479*	ENST00000324856	NM_006015.4	479	Cag/Tag	3/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		715	49	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793253	33793253	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs137852728	NA	P-0045134-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	94	164	0	ENST00000498907.2:c.68del	p.Pro23ArgfsTer137	p.P23Rfs*137	ENST00000498907	NM_004364.3	23	cCg/cg	1/1	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		164	386	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0046036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	77	673	0				ENST00000310581	NM_198253.2	-/1132			0.219106694624074	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.793572664802436	0		673	189	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537981	212537981	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs535202189	NA	P-0046036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	69	328	0	ENST00000342788.4:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000342788	NM_005235.2	542	Gaa/Aaa	14/28	0.336866816046697	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.793572664802436	0		328	256	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955863	55955863	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868047715	NA	P-0046036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	88	334	0	ENST00000263923.4:c.3299C>T	p.Ser1100Phe	p.S1100F	ENST00000263923	NM_002253.2	1100	tCc/tTc	24/30	0.260110054067712	1	FACETS	0.555	0.5	0.612	0.555	0.5	0.612	INDETERMINATE	1	FALSE	0	0.793572664802436	1		334	241	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370789	55370789	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	61	357	0	ENST00000297316.4:c.91C>A	p.Pro31Thr	p.P31T	ENST00000297316	NM_022454.3	31	Ccc/Acc	1/2	0.402765753063635	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.793572664802436	0		357	216	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152864448	152864448	+	synonymous_variant	Silent	SNP	G	G	A	novel	NA	P-0046036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	53	34	1	ENST00000406277.2:c.78C>T	p.Phe26=	p.F26=	ENST00000406277	NM_152274.4	26	ttC/ttT	3/7	NA		FACETS		NA	1				INDETERMINATE	NA	FALSE	NA	0.793572664802436	NA		35	81	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256529	+	missense_variant	Missense_Mutation	DNP	TT	TT	CA	rs1057519695	NA	P-0046036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	184	540	1	ENST00000369535.4:c.182_183delinsTG	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAA/cTG	3/7	1	2	FACETS	0.843	0.784	0.904	0.843	0.784	0.904	CLONAL	1	FALSE	1	0.793572664802436	2		541	550	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690317	117690317	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	161	401	0	ENST00000369458.3:c.812C>A	p.Ala271Glu	p.A271E	ENST00000369458	NM_024626.3	271	gCa/gAa	5/6	1	2	FACETS	0.912	0.845	0.981	0.912	0.845	0.981	CLONAL	1	FALSE	1	0.793572664802436	2		401	445	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578374	212578374	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0046036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	74	231	0	ENST00000342788.4:c.884-1G>A		p.X295_splice	ENST00000342788	NM_005235.2	295			0.336866816046697	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.793572664802436	0		231	163	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46271126	46271126	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	104	348	0	ENST00000371998.3:c.3250C>T	p.Gln1084Ter	p.Q1084*	ENST00000371998		1084	Cag/Tag	17/23	0.260110054067712	1	FACETS	0.485	0.439	0.532	0.485	0.439	0.532	INDETERMINATE	1	FALSE	0	0.793572664802436	1		348	326	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877820	151877823	+	frameshift_variant	Frame_Shift_Del	DEL	TTGG	TTGG	-	novel	NA	P-0046036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	100	285	0	ENST00000262189.6:c.7122_7125del	p.Ala2376IlefsTer5	p.A2376Ifs*5	ENST00000262189	NM_170606.2	2374	gcCCAA/gc	36/59	1	2	FACETS	0.937	0.85	1	0.937	0.85	1	CLONAL	1	FALSE	1	0.793572664802436	2		285	269	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	133	320	1				ENST00000310581	NM_198253.2	-/1132			0.185195529345479	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	FALSE	2	0.291068332872273	4		321	479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0046089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	67	431	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.291068332872273	1	FACETS	0.428	0.37	0.49	0.428	0.37	0.49	SUBCLONAL	1	FALSE	0	0.291068332872273	1		432	920	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057520000	NA	P-0046089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	484	690	0	ENST00000269305.4:c.452C>G	p.Pro151Arg	p.P151R	ENST00000269305	NM_001126112.2	151	cCc/cGc	5/11	0.291068332872273	1	FACETS	1	0.971	1	1	0.997	1	CLONAL	2	FALSE	0	0.291068332872273	1		690	1395	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255461	16255461	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	171	267	0	ENST00000375759.3:c.2726A>G	p.Lys909Arg	p.K909R	ENST00000375759	NM_015001.2	909	aAa/aGa	11/15	1	2	FACETS	0.793	0.731	0.857	1	0.99	1	SUBCLONAL	2	FALSE	1	0.291068332872273	2		267	741	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418481	49418482	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0046089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	218	435	0	ENST00000301067.7:c.15931dup	p.Val5311GlyfsTer34	p.V5311Gfs*34	ENST00000301067	NM_003482.3	5311	gtg/gGtg	50/54	0.251677564714959	0	FACETS	0.627	0.584	0.671			1	SUBCLONAL	2	FALSE	0	0.291068332872273	0		435	847	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425755	49425755	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	179	423	2	ENST00000301067.7:c.12733G>A	p.Glu4245Lys	p.E4245K	ENST00000301067	NM_003482.3	4245	Gag/Aag	39/54	0.251677564714959	0	FACETS	0.823	0.758	0.89			1	CLONAL	1	FALSE	0	0.291068332872273	0		425	1060	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438297	49438298	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AT	novel	NA	P-0046089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	121	360	0	ENST00000301067.7:c.4971_4972delinsAT	p.Glu1658Ter	p.E1658*	ENST00000301067	NM_003482.3	1657	gtGGag/gtATag	20/54	0.251677564714959	0	FACETS	0.801	0.724	0.882			1	CLONAL	1	FALSE	0	0.291068332872273	0		360	736	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954204	48954204	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	69	218	0	ENST00000267163.4:c.1405del	p.Ser469ProfsTer9	p.S469Pfs*9	ENST00000267163	NM_000321.2	469	Tcc/cc	15/27	0.144380138532479	0	FACETS	0.789	0.69	0.895			1	INDETERMINATE	1	FALSE	0	0.291068332872273	0		218	426	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039413	49039413	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	225	348	0	ENST00000267163.4:c.2399del	p.Pro800LeufsTer10	p.P800Lfs*10	ENST00000267163	NM_000321.2	800	Cct/ct	23/27	0.144380138532479	0	FACETS	1	0.986	1			1	INDETERMINATE	1	FALSE	0	0.291068332872273	0		348	903	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504494	103504495	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	82	154	0	ENST00000355739.4:c.117dup	p.Lys40Ter	p.K40*	ENST00000355739	NM_000123.3	39	ctt/cTtt	2/15	NA	2	FACETS	1	0.974	1			1	INDETERMINATE	1	FALSE	NA	0.291068332872273	2		154	409	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060618	38060619	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	324	450	0	ENST00000250448.2:c.1370dup	p.Ala458GlyfsTer100	p.A458Gfs*100	ENST00000250448	NM_004496.3	457	ccg/ccCg	2/2	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	FALSE	1	0.291068332872273	2		450	1527	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842060	3842061	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0046089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	147	169	0	ENST00000262367.5:c.1251_1252del	p.His418LeufsTer8	p.H418Lfs*8	ENST00000262367	NM_004380.2	417	tcTCat/tcat	5/31	1	2	FACETS	0.785	0.719	0.854	1	0.989	1	SUBCLONAL	2	FALSE	1	0.291068332872273	2		169	643	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0046722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	408	337	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	0.968	0.942	0.993	1	0.997	1	CLONAL	2	TRUE	1	0.832931351383127	2		337	506	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0046722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	155	648	1	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.832931351383127	3	FACETS	0.959	0.898	1	0.959	0.898	1	CLONAL	2	TRUE	1	0.832931351383127	3		649	275	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985468	2985468	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	292	335	0	ENST00000396946.4:c.343T>A	p.Phe115Ile	p.F115I	ENST00000396946	NM_032415.4	115	Ttc/Atc	4/25	1	2	FACETS	0.955	0.904	1	0.955	0.904	1	CLONAL	1	TRUE	1	0.832931351383127	2		335	734	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453148	140453148	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507483	NA	P-0046722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	105	216	0	ENST00000288602.6:c.1787G>A	p.Gly596Asp	p.G596D	ENST00000288602	NM_004333.4	596	gGt/gAt	15/18	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.832931351383127	2		216	236	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803172	1803172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775241791	NA	P-0046722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	638	814	4	ENST00000260795.2:c.524G>A	p.Arg175His	p.R175H	ENST00000260795		175	cGc/cAc	4/17	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.832931351383127	2		818	1474	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420017	49420018	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	rs1555185610	NA	P-0046722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	367	418	1	ENST00000301067.7:c.15731_15732del	p.Lys5244SerfsTer13	p.K5244Sfs*13	ENST00000301067	NM_003482.3	5244	aAA/a	48/54	0.832931351383127	3	FACETS	0.948	0.898	0.998	0.474	0.449	0.499	CLONAL	1	TRUE	1	0.832931351383127	3		419	1317	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057934	27057934	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	486	487	1	ENST00000324856.7:c.1642C>T	p.Gln548Ter	p.Q548*	ENST00000324856	NM_006015.4	548	Cag/Tag	3/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.832931351383127	2		488	1139	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100093	157100117	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCGGCGGCGGCAGCAGCAGGAG	GCGGCGGCGGCGGCAGCAGCAGGAG	-	novel	NA	P-0046722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	25	8	0	ENST00000346085.5:c.1044_1068del	p.Ala350MetfsTer11	p.A350Mfs*11	ENST00000346085	NM_020732.3	344	GCGGCGGCGGCGGCAGCAGCAGGAGgc/gc	1/20	1	2	FACETS	0.8	0.652	0.959	0.8	0.652	0.959	CLONAL	1	TRUE	1	0.832931351383127	2		8	75	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551670	150551670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	270	306	1	ENST00000369026.2:c.337G>A	p.Ala113Thr	p.A113T	ENST00000369026	NM_021960.4	113	Gcc/Acc	1/3	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.832931351383127	2		307	595	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426178	49426178	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	915	638	2	ENST00000301067.7:c.12310C>T	p.Gln4104Ter	p.Q4104*	ENST00000301067	NM_003482.3	4104	Caa/Taa	39/54	0.832931351383127	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.832931351383127	3		640	1543	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819704	81819705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	450	497	0	ENST00000359376.3:c.110_111insA	p.Glu39ArgfsTer21	p.E39Rfs*21	ENST00000359376	NM_002661.3	37	acc/acAc	2/33	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.832931351383127	2		497	990	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872674	37872674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150203173	NA	P-0046722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	599	819	3	ENST00000269571.5:c.1634G>A	p.Arg545Gln	p.R545Q	ENST00000269571		545	cGa/cAa	13/27	1	2	FACETS	0.984	0.947	1	0.984	0.947	1	CLONAL	1	TRUE	1	0.832931351383127	2		822	1462	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223301	2223301	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	521	687	0	ENST00000398665.3:c.3412C>A	p.Leu1138Met	p.L1138M	ENST00000398665	NM_032482.2	1138	Ctg/Atg	25/28	0.832931351383127	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.832931351383127	1		687	720	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031986	26031986	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	466	323	0	ENST00000244661.2:c.303G>C	p.Leu101Phe	p.L101F	ENST00000244661	NM_003537.3	101	ttG/ttC	1/1	0.832931351383127	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.832931351383127	2		323	543	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911175	29911176	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCGGCGGACATGGCG	novel	NA	P-0046722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	147	561	0	ENST00000376809.5:c.477_491dup	p.Ala160_Ala164dup	p.A160_A164dup	ENST00000376809	NM_002116.7	160	-/GCGGCGGACATGGCG	3/8	0.832931351383127	2	FACETS	0.406	0.371	0.443	0.203	0.185	0.222	SUBCLONAL	1	TRUE	0	0.832931351383127	2		561	869	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324478	31324478	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	690	300	0	ENST00000412585.2:c.330C>G	p.Asn110Lys	p.N110K	ENST00000412585	NM_005514.6	110	aaC/aaG	2/8	0.832931351383127	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.832931351383127	2		300	762	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324891	31324942	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	CGCCGAGAGCAGCAGGAGGACGGTTCGGGGCGCCATGACCAGCATCTCGGCG	CGCCGAGAGCAGCAGGAGGACGGTTCGGGGCGCCATGACCAGCATCTCGGCG	-	novel	NA	P-0046722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	65	498	0	ENST00000412585.2:c.-7_45del		p.*3*	ENST00000412585	NM_005514.6	?-15/362		1/8	0.832931351383127	2	FACETS	0.835	0.738	0.935	0.417	0.369	0.468	CLONAL	1	TRUE	0	0.832931351383127	2		498	187	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341779	8341779	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	130	422	0	ENST00000356435.5:c.4861C>T	p.Pro1621Ser	p.P1621S	ENST00000356435		1621	Cca/Tca	29/35	1	2	FACETS	0.749	0.685	0.814	0.749	0.685	0.814	SUBCLONAL	1	TRUE	1	0.832931351383127	2		422	417	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910785	29910787	+	missense_variant	Missense_Mutation	TNP	TAC	TAC	CAG	novel	NA	P-0046722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	248	465	0	ENST00000376809.5:c.325_327delinsCAG	p.Tyr109Gln	p.Y109Q	ENST00000376809	NM_002116.7	109	TAC/CAG	2/8	0.832931351383127	2	FACETS	0.88	0.827	0.933	0.44	0.413	0.467	CLONAL	1	TRUE	0	0.832931351383127	2		465	677	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551541	150551541	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs755770114	NA	P-0049880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	134	819	0	ENST00000369026.2:c.466A>G	p.Thr156Ala	p.T156A	ENST00000369026	NM_021960.4	156	Acg/Gcg	1/3	1	2	FACETS	0.865	0.783	0.951	0.865	0.783	0.951	CLONAL	1	FALSE	1	0.24229196151338	2		819	1279	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0054419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	171	499	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.294935442212172	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.419217715150457	1		501	554	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752801	42752801	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	180	866	0	ENST00000222329.4:c.1463G>T	p.Trp488Leu	p.W488L	ENST00000222329	NM_006494.2	488	tGg/tTg	4/4	0.407542486296269	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.419217715150457	1		866	622	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53244019	53244020	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	127	581	0	ENST00000375401.3:c.973dup	p.Tyr325LeufsTer11	p.Y325Lfs*11	ENST00000375401	NM_004187.3	325	tat/tTat	8/26	0.33800029056523	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.419217715150457	1		581	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0054419-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	170	499	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.707938971250778	1	FACETS	0.932	0.872	0.991	0.932	0.872	0.991	CLONAL	1	TRUE	0	0.707938971250778	1		501	333	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752801	42752801	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054419-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	181	866	0	ENST00000222329.4:c.1463G>T	p.Trp488Leu	p.W488L	ENST00000222329	NM_006494.2	488	tGg/tTg	4/4	0.707938971250778	1	FACETS	0.983	0.924	1	0.983	0.924	1	CLONAL	1	TRUE	0	0.707938971250778	1		866	336	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53244019	53244020	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054419-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	157	581	0	ENST00000375401.3:c.973dup	p.Tyr325LeufsTer11	p.Y325Lfs*11	ENST00000375401	NM_004187.3	325	tat/tTat	8/26	0.444932049207451	1	FACETS	0.634	0.586	0.683	0.634	0.586	0.683	SUBCLONAL	1	TRUE	0	0.707938971250778	1		581	452	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0054442-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	322	575	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.209540855490271	5	FACETS	1	0.99	1	0.81	0.765	0.856	INDETERMINATE	2	TRUE	2	0.369309708426576	5		575	1115	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0054442-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	31	506	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.361	0.291	0.44	0.361	0.291	0.44	SUBCLONAL	1	TRUE	1	0.369309708426576	2		506	465	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054442-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	21	369	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.228647188052882	2	FACETS	0.289	0.222	0.367	0.144	0.111	0.184	SUBCLONAL	1	TRUE	0	0.369309708426576	2		369	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579536	7579536	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567556930	NA	P-0054442-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	234	519	1	ENST00000269305.4:c.151G>T	p.Glu51Ter	p.E51*	ENST00000269305	NM_001126112.2	51	Gaa/Taa	4/11	0.193153470605212	2	FACETS	1	0.989	1	0.655	0.611	0.7	INDETERMINATE	1	TRUE	0	0.369309708426576	2		520	968	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250922	153250922	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054442-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	13	280	0	ENST00000281708.4:c.1138G>C	p.Asp380His	p.D380H	ENST00000281708	NM_033632.3	380	Gat/Cat	8/12	0.369309708426576	1	FACETS	0.293	0.209	0.395	0.293	0.209	0.395	SUBCLONAL	1	TRUE	0	0.369309708426576	1		280	196	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190588	11190588	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054442-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	63	342	0	ENST00000361445.4:c.5611G>C	p.Glu1871Gln	p.E1871Q	ENST00000361445	NM_004958.3	1871	Gag/Cag	39/58	0.369309708426576	5	FACETS	0.67	0.579	0.77	0.223	0.192	0.257	SUBCLONAL	1	TRUE	2	0.369309708426576	5		342	791	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717715	89717717	+	inframe_deletion	In_Frame_Del	DEL	TAC	TAC	-	novel	NA	P-0054442-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	105	443	0	ENST00000371953.3:c.740_742del	p.Leu247_Pro248delinsSer	p.L247_P248delinsS	ENST00000371953	NM_000314.4	247	tTACct/tct	7/9	0.354756347955876	1	FACETS	0.989	0.89	1	0.989	0.89	1	CLONAL	1	TRUE	0	0.369309708426576	1		443	469	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981635	101981636	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCCTTCGCA	novel	NA	P-0054442-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	12	107	0	ENST00000282441.5:c.60_68dup	p.Ser21_Pro23dup	p.S21_P23dup	ENST00000282441	NM_001130145.2	21	ccg/ccGCCTTCGCAg	1/9	0.175596250204668	3	FACETS	0.383	0.269	0.523	0.192	0.134	0.262	INDETERMINATE	1	TRUE	1	0.369309708426576	3		107	201	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951042	48951056	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TACCTCCTAAAGAAC	TACCTCCTAAAGAAC	-	novel	NA	P-0054442-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	50	209	0	ENST00000267163.4:c.1216-11_1219del		p.X406_splice	ENST00000267163	NM_000321.2	406		13/27	0.26989254737449	2	FACETS	0.796	0.688	0.911	0.796	0.688	0.911	CLONAL	2	TRUE	0	0.369309708426576	2		209	170	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374383	31374383	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054442-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	186	501	1	ENST00000328111.2:c.382C>T	p.Gln128Ter	p.Q128*	ENST00000328111	NM_006892.3	128	Cag/Tag	5/23	0.244495391677455	3	FACETS	1	0.972	1	0.555	0.512	0.6	CLONAL	1	TRUE	1	0.369309708426576	3		502	1075	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540714	187540714	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs546878527	NA	P-0054442-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	45	323	0	ENST00000441802.2:c.7026C>G	p.Ile2342Met	p.I2342M	ENST00000441802	NM_005245.3	2342	atC/atG	10/27	0.369309708426576	1	FACETS	0.546	0.46	0.64	0.546	0.46	0.64	SUBCLONAL	1	TRUE	0	0.369309708426576	1		323	364	SUCCESS
APC	324	MSKCC	GRCh37	5	112177069	112177069	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1244090932	NA	P-0054442-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	41	376	0	ENST00000257430.4:c.5778A>G	p.Ile1926Met	p.I1926M	ENST00000257430	NM_000038.5	1926	atA/atG	16/16	1	2	FACETS	0.562	0.469	0.665	0.562	0.469	0.665	SUBCLONAL	1	TRUE	1	0.369309708426576	2		376	395	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715503	117715503	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054442-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	24	244	0	ENST00000368508.3:c.986C>G	p.Ser329Cys	p.S329C	ENST00000368508	NM_002944.2	329	tCt/tGt	10/43	1	2	FACETS	0.436	0.342	0.544	0.436	0.342	0.544	SUBCLONAL	1	TRUE	1	0.369309708426576	2		244	298	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412059	63412059	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054442-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	191	673	0	ENST00000330258.3:c.1108G>T	p.Glu370Ter	p.E370*	ENST00000330258	NM_152424.3	370	Gag/Tag	2/2	0.369309708426576	1	FACETS	0.983	0.91	1	0.983	0.91	1	CLONAL	1	TRUE	0	0.369309708426576	1		673	858	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0054501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	115	673	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.728	0.656	0.804	0.728	0.656	0.804	SUBCLONAL	1	TRUE	1	0.402538844340302	2		673	785	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562738	29562739	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555615472	NA	P-0054501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	62	529	0	ENST00000356175.3:c.3822_3823del	p.Phe1275ProfsTer8	p.F1275Pfs*8	ENST00000356175	NM_000267.3	1273	aCT/a	28/57	1	2	FACETS	0.711	0.616	0.814	0.711	0.616	0.814	SUBCLONAL	1	TRUE	1	0.402538844340302	2		529	433	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777159	9777159	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749687214	NA	P-0054501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	123	961	0	ENST00000377346.4:c.923C>T	p.Ala308Val	p.A308V	ENST00000377346	NM_005026.3	308	gCg/gTg	7/24	1	2	FACETS	0.681	0.615	0.751	0.681	0.615	0.751	SUBCLONAL	1	TRUE	1	0.402538844340302	2		961	897	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717697	89717697	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	110	476	0	ENST00000371953.3:c.722T>G	p.Phe241Cys	p.F241C	ENST00000371953	NM_000314.4	241	tTt/tGt	7/9	0.402538844340302	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.402538844340302	1		476	425	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0054568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	92	422	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.924	0.824	1	0.924	0.824	1	CLONAL	1	TRUE	1	0.384313013842445	2		422	518	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0054568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	81	442	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.985	0.872	1	0.985	0.872	1	CLONAL	1	TRUE	1	0.384313013842445	2		442	428	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024001	27024002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0054568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	28	121	0	ENST00000324856.7:c.1113dup	p.Gln372AlafsTer28	p.Q372Afs*28	ENST00000324856	NM_006015.4	369	-/G	1/20	1	2	FACETS	0.916	0.741	1	0.916	0.741	1	CLONAL	1	TRUE	1	0.384313013842445	2		121	159	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395788	45395788	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	54	416	0	ENST00000262160.6:c.346C>T	p.Gln116Ter	p.Q116*	ENST00000262160	NM_005901.5	116	Cag/Tag	4/11	1	2	FACETS	0.774	0.664	0.894	0.774	0.664	0.894	SUBCLONAL	1	TRUE	1	0.384313013842445	2		416	363	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368252	45368252	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	96	497	0	ENST00000262160.6:c.1350C>A	p.Asp450Glu	p.D450E	ENST00000262160	NM_005901.5	450	gaC/gaA	11/11	1	2	FACETS	0.889	0.794	0.99	0.889	0.794	0.99	CLONAL	1	TRUE	1	0.384313013842445	2		497	562	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14015970	14015970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768270013	NA	P-0054568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	88	327	0	ENST00000311895.7:c.290G>A	p.Arg97His	p.R97H	ENST00000311895	NM_005236.2	97	cGc/cAc	2/11	1	2	FACETS	0.956	0.85	1	0.956	0.85	1	CLONAL	1	TRUE	1	0.384313013842445	2		327	479	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114196	115114197	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0054568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	52	811	0	ENST00000257566.3:c.1020dup	p.Ser341GlnfsTer2	p.S341Qfs*2	ENST00000257566	NM_016569.3	340	-/C	6/8	1	2	FACETS	0.306	0.26	0.358	0.306	0.26	0.358	SUBCLONAL	1	TRUE	1	0.384313013842445	2		811	884	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457638	67457638	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	364	936	0	ENST00000327367.4:c.449del	p.Phe150SerfsTer36	p.F150Sfs*36	ENST00000327367	NM_005902.3	150	Ttc/tc	3/9	0.384313013842445	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.384313013842445	2		936	902	SUCCESS
APC	324	MSKCC	GRCh37	5	112173964	112173965	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0054568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	100	373	0	ENST00000257430.4:c.2673_2674delinsTT	p.Met891_Glu892delinsIleTer	p.M891_E892delinsI*	ENST00000257430	NM_000038.5	891	atGGaa/atTTaa	16/16	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.384313013842445	2		373	459	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413165	63413165	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1400771893	NA	P-0054568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	144	430	0	ENST00000330258.3:c.2T>C	p.Met1?	p.M1?	ENST00000330258	NM_152424.3	1	aTg/aCg	2/2	1	1	FACETS	0.816	0.753	0.88	1	0.99	1	CLONAL	2	TRUE	0	0.384313013842445	1		430	371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0054867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	274	513	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.72922947136647	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.727115876601347	2		513	361	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346977	73346977	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	366	437	0	ENST00000377767.4:c.1240G>C	p.Gly414Arg	p.G414R	ENST00000377767	NM_014953.3	414	Gga/Cga	9/21	0.72922947136647	4	FACETS	1	0.991	1			1	CLONAL	4	TRUE	NA	0.727115876601347	4		437	421	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424405	49424405	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555187117	NA	P-0054867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	97	593	0	ENST00000301067.7:c.13818C>G	p.Tyr4606Ter	p.Y4606*	ENST00000301067	NM_003482.3	4606	taC/taG	41/54	0.224928752154619	5	FACETS	0.752	0.676	0.831			1	INDETERMINATE	2	TRUE	NA	0.727115876601347	5		593	371	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444308	50444308	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	51	688	0	ENST00000331340.3:c.238G>A	p.Glu80Lys	p.E80K	ENST00000331340	NM_006060.4	80	Gag/Aag	4/8	0.340278134253568	2	FACETS	0.546	0.468	0.63	0.273	0.234	0.315	INDETERMINATE	1	TRUE	0	0.727115876601347	2		688	257	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142576	119142576	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	239	477	0	ENST00000264033.4:c.575A>G	p.Lys192Arg	p.K192R	ENST00000264033	NM_005188.3	192	aAa/aGa	3/16	0.728269135663622	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.727115876601347	3		477	278	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448380	49448380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	116	653	0	ENST00000301067.7:c.331C>T	p.Pro111Ser	p.P111S	ENST00000301067	NM_003482.3	111	Ccc/Tcc	3/54	0.224928752154619	5	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.727115876601347	5		653	448	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528188	103528188	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0054867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	188	507	0	ENST00000355739.4:c.3496A>T	p.Arg1166Ter	p.R1166*	ENST00000355739	NM_000123.3	1166	Aga/Tga	15/15	NA	2	FACETS	0.947	0.9	0.992			1	INDETERMINATE	2	TRUE	NA	0.727115876601347	2		507	273	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060755	38060756	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	AT	novel	NA	P-0054867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	116	776	0	ENST00000250448.2:c.1233_1234delinsAT	p.Gln412Ter	p.Q412*	ENST00000250448	NM_004496.3	411	caGCag/caATag	2/2	0.72922947136647	3	FACETS	0.956	0.867	1	0.478	0.433	0.525	CLONAL	1	TRUE	1	0.727115876601347	3		776	455	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440000	56440000	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	125	615	0	ENST00000407977.2:c.592G>C	p.Asp198His	p.D198H	ENST00000407977		198	Gat/Cat	6/10	0.72922947136647	3	FACETS	1	0.976	1	0.598	0.546	0.651	CLONAL	1	TRUE	1	0.727115876601347	3		615	392	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469956	25469956	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	114	608	0	ENST00000264709.3:c.1086G>C	p.Gln362His	p.Q362H	ENST00000264709	NM_175629.2	362	caG/caC	9/23	0.72922947136647	3	FACETS	1	0.946	1	0.53	0.481	0.581	CLONAL	1	TRUE	1	0.727115876601347	3		608	403	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295795	212295795	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	134	569	0	ENST00000342788.4:c.2518G>C	p.Val840Leu	p.V840L	ENST00000342788	NM_005235.2	840	Gtt/Ctt	21/28	0.72922947136647	2	FACETS	0.991	0.936	1	0.991	0.936	1	CLONAL	2	TRUE	0	0.727115876601347	2		569	186	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447145	187447145	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	221	742	0	ENST00000232014.4:c.1048A>G	p.Ser350Gly	p.S350G	ENST00000232014	NM_001130845.1	350	Agt/Ggt	5/10	0.440932113663359	4	FACETS	0.961	0.903	1	0.961	0.903	1	CLONAL	2	TRUE	2	0.727115876601347	4		742	546	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047211	180047211	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	228	637	0	ENST00000261937.6:c.2504C>A	p.Ala835Asp	p.A835D	ENST00000261937	NM_182925.4	835	gCc/gAc	17/30	0.72922947136647	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	1	0.727115876601347	3		637	425	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048671	180048671	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	135	757	0	ENST00000261937.6:c.1891del	p.Ala631ArgfsTer8	p.A631Rfs*8	ENST00000261937	NM_182925.4	631	Gcg/cg	13/30	0.72922947136647	3	FACETS	1	0.943	1	0.52	0.475	0.566	CLONAL	1	TRUE	1	0.727115876601347	3		757	487	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968283	2968283	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	254	634	0	ENST00000396946.4:c.1703C>G	p.Pro568Arg	p.P568R	ENST00000396946	NM_032415.4	568	cCg/cGg	13/25	0.727115876601347	6	FACETS	1	0.987	1	0.584	0.549	0.62	CLONAL	2	TRUE	2	0.727115876601347	6		634	734	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434716	128434716	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	185	480	0	ENST00000265960.3:c.138G>T	p.Met46Ile	p.M46I	ENST00000265960	NM_001006617.1	46	atG/atT	2/12	0.648227319292628	5	FACETS	1	0.979	1	0.747	0.696	0.798	CLONAL	2	TRUE	2	0.727115876601347	5		480	475	SUCCESS
SCG5	6447	MSKCC	GRCh37	15	32935928	32935928	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	285	551	0	ENST00000300175.4:c.135T>A	p.His45Gln	p.H45Q	ENST00000300175	NM_001144757.1	45	caT/caA	2/6	0.72922947136647	3	FACETS	0.995	0.962	1	0.995	0.962	1	CLONAL	3	TRUE	0	0.727115876601347	3		551	358	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0055088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	103	516	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.262059050834254	5	FACETS	0.886	0.794	0.983	0.591	0.529	0.655	CLONAL	2	TRUE	2	0.262059050834254	5		516	618	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451087	70451087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	197	755	0	ENST00000373644.4:c.5927C>T	p.Ser1976Phe	p.S1976F	ENST00000373644	NM_030625.2	1976	tCt/tTt	12/12	0.262059050834254	3	FACETS	0.932	0.864	1			1	CLONAL	2	TRUE	NA	0.262059050834254	3		755	912	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577544	7577544	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587780074	NA	P-0055088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	178	736	0	ENST00000269305.4:c.737T>G	p.Met246Arg	p.M246R	ENST00000269305	NM_001126112.2	246	aTg/aGg	7/11	NA	2	FACETS	0.855	0.79	0.924			1	INDETERMINATE	2	TRUE	NA	0.262059050834254	2		736	794	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89815158	89815158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	121	832	2	ENST00000389301.3:c.3257C>T	p.Pro1086Leu	p.P1086L	ENST00000389301	NM_000135.2	1086	cCt/cTt	33/43	0.243399452595874	4	FACETS	1	0.951	1	0.544	0.49	0.601	CLONAL	1	TRUE	2	0.262059050834254	4		834	1071	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973806	15973806	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	48	586	0	ENST00000268712.3:c.4186C>T	p.Gln1396Ter	p.Q1396*	ENST00000268712	NM_006311.3	1396	Caa/Taa	31/46	0.262059050834254	3	FACETS	0.638	0.539	0.749	0.319	0.269	0.375	SUBCLONAL	1	TRUE	1	0.262059050834254	3		586	649	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678773	52678773	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	80	403	0	ENST00000394830.3:c.846G>A	p.Met282Ile	p.M282I	ENST00000394830	NM_018313.4	282	atG/atA	9/30	0.240515328393749	2	FACETS	0.795	0.704	0.891	0.795	0.704	0.891	SUBCLONAL	2	TRUE	0	0.262059050834254	2		403	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0055825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	84	646	7	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.984	0.867	1	0.984	0.867	1	CLONAL	1	TRUE	1	0.17	2		653	1004	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0055825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	43	304	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.0800916258846775	3	FACETS	1	0.897	1	0.55	0.46	0.65	INDETERMINATE	1	TRUE	1	0.17	3		304	499	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799334	88799334	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1288166921	NA	P-0055825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	44	615	0	ENST00000360948.2:c.51G>T	p.Leu17Phe	p.L17F	ENST00000360948	NM_001012338.2	17	ttG/ttT	2/19	1	2	FACETS	0.762	0.638	0.901	0.762	0.638	0.901	CLONAL	1	TRUE	1	0.17	2		615	679	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440943	56440943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786205215	NA	P-0055825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	71	890	6	ENST00000407977.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000407977		132	Cga/Tga	4/10	1	2	FACETS	0.956	0.832	1	0.956	0.832	1	CLONAL	1	TRUE	1	0.17	2		896	874	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591889	48591889	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1060500741	NA	P-0055825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	50	610	0	ENST00000342988.3:c.1052A>T	p.Asp351Val	p.D351V	ENST00000342988	NM_005359.5	351	gAt/gTt	9/12	1	2	FACETS	0.836	0.708	0.977	0.836	0.708	0.977	CLONAL	1	TRUE	1	0.17	2		610	704	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735467	40735467	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776642212	NA	P-0055825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	68	934	4	ENST00000373198.4:c.3406C>T	p.Arg1136Cys	p.R1136C	ENST00000373198	NM_133170.3	1136	Cgt/Tgt	25/32	0.289824447700648	0	FACETS	0.729	0.632	0.834			1	SUBCLONAL	1	TRUE	0	0.17	0		938	911	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0055825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	20	498	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.402	0.306	0.516	0.402	0.306	0.516	SUBCLONAL	1	TRUE	1	0.17	2		498	585	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356239	66356239	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370503988	NA	P-0055825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	47	734	1	ENST00000273854.3:c.1258G>A	p.Gly420Ser	p.G420S	ENST00000273854	NM_004439.5	420	Ggc/Agc	5/18	0.167622496054225	0	FACETS	0.676	0.569	0.794			1	SUBCLONAL	1	TRUE	0	0.17	0		735	679	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265431	152265431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776270356	NA	P-0057777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	53	584	1	ENST00000206249.3:c.884C>T	p.Pro295Leu	p.P295L	ENST00000206249	NM_000125.3	295	cCg/cTg	4/8	NA	2	FACETS	0.772	0.667	0.885			1	INDETERMINATE	1	TRUE	NA	0.62976192055185	2		585	218	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	110	320	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.928	1	1	0.991	1	CLONAL	3	FALSE	1	0.220476785971624	2		321	325	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032179	26032179	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	397	594	0	ENST00000244661.2:c.110A>T	p.Lys37Ile	p.K37I	ENST00000244661	NM_003537.3	37	aAa/aTa	1/1	1	2	FACETS	1	0.99	1	1	0.997	1	CLONAL	3	FALSE	1	0.220476785971624	2		594	1053	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0061447-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	250	432	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.376625401528118	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.417832274662109	2		432	562	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443591	29443591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747643140	NA	P-0061447-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	144	483	0	ENST00000389048.3:c.3626G>A	p.Arg1209Gln	p.R1209Q	ENST00000389048	NM_004304.4	1209	cGa/cAa	23/29	0.405152000372763	3	FACETS	1	0.982	1	0.638	0.583	0.695	CLONAL	1	TRUE	1	0.417832274662109	3		483	653	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117594	70117594	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061447-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	142	550	2	ENST00000245479.2:c.66del	p.Ser23AlafsTer38	p.S23Afs*38	ENST00000245479	NM_000346.3	21	gCc/gc	1/3	0.417832274662109	2	FACETS	1	0.963	1	0.549	0.502	0.598	CLONAL	1	TRUE	0	0.417832274662109	2		552	619	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650595	18650595	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061447-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	87	406	0	ENST00000266497.5:c.2806A>G	p.Ile936Val	p.I936V	ENST00000266497		936	Att/Gtt	20/31	0.405152000372763	3	FACETS	1	0.924	1	0.526	0.467	0.588	CLONAL	1	TRUE	1	0.417832274662109	3		406	479	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112280	115112280	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061447-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	101	527	0	ENST00000257566.3:c.1460A>C	p.Asp487Ala	p.D487A	ENST00000257566	NM_016569.3	487	gAc/gCc	7/8	0.405152000372763	3	FACETS	1	0.901	1	0.503	0.45	0.559	CLONAL	1	TRUE	1	0.417832274662109	3		527	581	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610066	81610066	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061447-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	92	608	0	ENST00000298171.2:c.1664T>G	p.Leu555Arg	p.L555R	ENST00000298171	NM_000369.2	555	cTt/cGt	10/10	0.231159757567471	3	FACETS	0.782	0.695	0.874	0.261	0.231	0.292	INDETERMINATE	1	TRUE	0	0.417832274662109	3		608	681	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082797	16082797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1229803179	NA	P-0061447-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	221	392	0	ENST00000281043.3:c.611C>T	p.Pro204Leu	p.P204L	ENST00000281043	NM_005378.4	204	cCc/cTc	2/3	0.339051712325364	4	FACETS	1	0.954	1			1	CLONAL	3	TRUE	NA	0.417832274662109	4		392	492	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295729	1295729	+	upstream_gene_variant	5'Flank	SNP	C	C	G	novel	NA	P-0061447-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	69	644	0				ENST00000310581	NM_198253.2	-/1132			0.373012914074968	4	FACETS	0.529	0.46	0.605	0.265	0.23	0.303	SUBCLONAL	1	TRUE	2	0.417832274662109	4		644	885	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124492003	124492003	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061447-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	89	302	0	ENST00000357628.3:c.872A>T	p.Asp291Val	p.D291V	ENST00000357628	NM_015450.2	291	gAt/gTt	11/19	0.405152000372763	3	FACETS	0.894	0.803	0.989	0.894	0.803	0.989	CLONAL	2	TRUE	1	0.417832274662109	3		302	288	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696719	47696719	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	419	435	0	ENST00000347630.2:c.229G>C	p.Asp77His	p.D77H	ENST00000347630	NM_001007230.1	77	Gat/Cat	5/11	0.606350957934375	2	FACETS	0.999	0.962	1	0.999	0.962	1	CLONAL	2	TRUE	0	0.606350957934375	2		435	692	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102132	27102132	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	220	531	0	ENST00000324856.7:c.5058G>A	p.Trp1686Ter	p.W1686*	ENST00000324856	NM_006015.4	1686	tgG/tgA	19/20	1	2	FACETS	0.921	0.859	0.984	0.921	0.859	0.984	CLONAL	1	TRUE	1	0.606350957934375	2		531	788	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101381	27101381	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	144	362	0	ENST00000324856.7:c.4663del	p.Tyr1555MetfsTer10	p.Y1555Mfs*10	ENST00000324856	NM_006015.4	1555	Tat/at	18/20	1	2	FACETS	0.901	0.827	0.978	0.901	0.827	0.978	CLONAL	1	TRUE	1	0.606350957934375	2		362	527	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562511	21562511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	201	344	0	ENST00000382592.4:c.1408G>A	p.Ala470Thr	p.A470T	ENST00000382592	NM_014572.2	470	Gcc/Acc	4/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.606350957934375	2		344	525	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880988	37880989	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGA	novel	NA	P-0062079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	1117	600	0	ENST00000269571.5:c.2320_2322dup	p.Met774dup	p.M774dup	ENST00000269571		774	gtg/gTGAtg	20/27	0.537028876243	4	FACETS	0.951	0.932	0.969			1	CLONAL	4	TRUE	NA	0.606350957934375	4		600	1556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0062163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	355	552	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.70426076155227	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.703045364728537	2		552	465	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350785	15350785	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs199727585	NA	P-0062163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	109	426	0	ENST00000263377.2:c.3218T>C	p.Met1073Thr	p.M1073T	ENST00000263377	NM_058243.2	1073	aTg/aCg	15/20	0.70426076155227	5	FACETS	0.929	0.835	1	0.232	0.208	0.257	CLONAL	1	TRUE	1	0.703045364728537	5		426	686	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187558055	187558055	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	142	429	0	ENST00000441802.2:c.3656A>G	p.Asp1219Gly	p.D1219G	ENST00000441802	NM_005245.3	1219	gAc/gGc	5/27	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.703045364728537	2		429	401	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0062327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	65	207	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.511401194373462	3	FACETS	0.998	0.886	1	0.998	0.886	1	CLONAL	2	TRUE	1	0.511401194373462	3		207	160	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	55	594	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.448	0.384	0.518	0.448	0.384	0.518	SUBCLONAL	1	TRUE	1	0.511401194373462	2		594	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0062327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	131	529	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.471270102791334	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.511401194373462	1		529	336	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420075	420075	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	114	504	0	ENST00000399788.2:c.3192G>C	p.Lys1064Asn	p.K1064N	ENST00000399788	NM_001042603.1	1064	aaG/aaC	21/28	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.511401194373462	2		504	436	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066772	30066772	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	75	425	0	ENST00000331968.5:c.2359G>A	p.Glu787Lys	p.E787K	ENST00000331968	NM_002742.2	787	Gaa/Aaa	16/18	1	2	FACETS	0.974	0.862	1	0.974	0.862	1	CLONAL	1	TRUE	1	0.511401194373462	2		425	301	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991400	72991400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201144589	NA	P-0062327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	246	491	0	ENST00000268489.5:c.2645C>T	p.Ser882Leu	p.S882L	ENST00000268489	NM_006885.3	882	tCg/tTg	2/10	0.511401194373462	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.511401194373462	3		491	527	SUCCESS
APC	324	MSKCC	GRCh37	5	112179502	112179502	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1366190280	NA	P-0062327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	108	507	0	ENST00000257430.4:c.8211G>C	p.Glu2737Asp	p.E2737D	ENST00000257430	NM_000038.5	2737	gaG/gaC	16/16	0.511401194373462	3	FACETS	0.954	0.859	1	0.477	0.429	0.527	CLONAL	1	TRUE	1	0.511401194373462	3		507	556	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46512227	46512227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	71	433	0	ENST00000262741.5:c.1012G>A	p.Asp338Asn	p.D338N	ENST00000262741	NM_003629.3	338	Gat/Aat	8/10	1	2	FACETS	0.765	0.672	0.864	0.765	0.672	0.864	SUBCLONAL	1	TRUE	1	0.511401194373462	2		433	363	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194128	94194128	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	39	266	0	ENST00000323929.3:c.1300A>G	p.Lys434Glu	p.K434E	ENST00000323929	NM_005591.3	434	Aaa/Gaa	12/20	0.163321401192409	5	FACETS	1	0.841	1	0.336	0.28	0.398	INDETERMINATE	1	TRUE	2	0.511401194373462	5		266	267	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024486	16024486	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	129	557	0	ENST00000268712.3:c.1732C>T	p.Gln578Ter	p.Q578*	ENST00000268712	NM_006311.3	578	Cag/Tag	16/46	0.153363436468703	0	FACETS	0.647	0.593	0.703			1	INDETERMINATE	1	TRUE	0	0.511401194373462	0		557	381	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486063	29486064	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs771115661	NA	P-0062327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	46	261	0	ENST00000356175.3:c.246_247del	p.Gln83ValfsTer23	p.Q83Vfs*23	ENST00000356175	NM_000267.3	80	taTCtc/tatc	3/57	0.511401194373462	1	FACETS	0.792	0.678	0.914	0.792	0.678	0.914	CLONAL	1	TRUE	0	0.511401194373462	1		261	169	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804170	46804170	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	123	506	0	ENST00000290295.7:c.837G>C	p.Lys279Asn	p.K279N	ENST00000290295	NM_006361.5	279	aaG/aaC	2/2	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.511401194373462	2		506	392	SUCCESS
ALB	213	MSKCC	GRCh37	4	74283364	74283364	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	58	340	0	ENST00000295897.4:c.1406G>C	p.Arg469Thr	p.R469T	ENST00000295897	NM_000477.5	469	aGa/aCa	11/15	1	2	FACETS	0.744	0.643	0.851	0.744	0.643	0.851	SUBCLONAL	1	TRUE	1	0.511401194373462	2		340	305	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53253993	53253993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	87	500	0	ENST00000375401.3:c.79C>T	p.Pro27Ser	p.P27S	ENST00000375401	NM_004187.3	27	Cct/Tct	1/26	0.415036316379119	3	FACETS	0.956	0.85	1	0.478	0.425	0.534	CLONAL	1	TRUE	1	0.511401194373462	3		500	447	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0062409-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	100	732	2	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.13501931104381	0	FACETS	0.556	0.496	0.619			1	INDETERMINATE	1	TRUE	0	0.308915121988385	0		734	805	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0062409-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	116	369	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.308915121988385	3	FACETS	1	0.917	1	1	0.917	1	CLONAL	2	TRUE	1	0.308915121988385	3		369	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0062409-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	135	696	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.308915121988385	1	FACETS	0.893	0.811	0.978	0.893	0.811	0.978	CLONAL	1	TRUE	0	0.308915121988385	1		696	828	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935634	13935634	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062409-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	125	602	0	ENST00000405192.2:c.1222C>T	p.Arg408Cys	p.R408C	ENST00000405192	NM_001163147.1	408	Cgt/Tgt	12/12	1	2	FACETS	0.967	0.875	1	0.967	0.875	1	CLONAL	1	TRUE	1	0.308915121988385	2		602	837	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958789	55958789	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062409-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	37	454	0	ENST00000263923.4:c.3064C>T	p.Arg1022Ter	p.R1022*	ENST00000263923	NM_002253.2	1022	Cga/Tga	22/30	0.194559837339738	1	FACETS	0.381	0.313	0.456	0.381	0.313	0.456	SUBCLONAL	1	TRUE	0	0.308915121988385	1		454	532	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428067	49428067	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772010347	NA	P-0062409-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	78	653	0	ENST00000301067.7:c.10523G>A	p.Arg3508Gln	p.R3508Q	ENST00000301067	NM_003482.3	3508	cGg/cAg	38/54	1	2	FACETS	0.614	0.538	0.695	0.614	0.538	0.695	SUBCLONAL	1	TRUE	1	0.308915121988385	2		653	823	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633319	8633319	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs778130827	NA	P-0062534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	33	560	0	ENST00000356435.5:c.350G>A	p.Arg117Gln	p.R117Q	ENST00000356435		117	cGg/cAg	3/35	1	2	FACETS	0.889	0.722	1	0.889	0.722	1	CLONAL	1	TRUE	1	0.12	2		560	619	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061218	38061232	+	inframe_deletion	In_Frame_Del	DEL	GCCGTTCTCGAACAT	GCCGTTCTCGAACAT	-	novel	NA	P-0062534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	26	817	0	ENST00000250448.2:c.757_771del	p.Met253_Gly257del	p.M253_G257del	ENST00000250448	NM_004496.3	253	ATGTTCGAGAACGGC/-	2/2	1	2	FACETS	0.722	0.57	0.898	0.722	0.57	0.898	SUBCLONAL	1	TRUE	1	0.12	2		817	600	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124511047	124511047	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	21	374	1	ENST00000357628.3:c.173C>A	p.Thr58Asn	p.T58N	ENST00000357628	NM_015450.2	58	aCt/aAt	7/19	1	2	FACETS	1	0.82	1	1	0.82	1	CLONAL	1	TRUE	1	0.12	2		375	325	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0062742-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	84	749	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	0.847	0.748	0.953	0.847	0.748	0.953	CLONAL	1	TRUE	1	0.286082417638581	2		749	693	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0062742-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	89	910	1	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	1	2	FACETS	0.859	0.762	0.964	0.859	0.762	0.964	CLONAL	1	TRUE	1	0.286082417638581	2		911	724	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986589	36986689	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCTGGCGGCGTGGTGCGCCAGGTCCGGAGACTGGCCTGCGCTGCCTGGCTGGTGGCCCGGGTGTGCGCCAAGGCCGGCGCCACCGCTGCCCACGGAGAT	GGGCTGGCGGCGTGGTGCGCCAGGTCCGGAGACTGGCCTGCGCTGCCTGGCTGGTGGCCCGGGTGTGCGCCAAGGCCGGCGCCACCGCTGCCCACGGAGAT	-	novel	NA	P-0062742-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	64	713	0	ENST00000354822.5:c.1000_1100del	p.Ile334ArgfsTer71	p.I334Rfs*71	ENST00000354822	NM_001079668.2	334	ATCTCCGTGGGCAGCGGTGGCGCCGGCCTTGGCGCACACCCGGGCCACCAGCCAGGCAGCGCAGGCCAGTCTCCGGACCTGGCGCACCACGCCGCCAGCCCc/c	3/3	0.220139798568255	2	FACETS	0.994	0.863	1	0.497	0.431	0.568	CLONAL	1	TRUE	0	0.286082417638581	2		713	450	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821353	32821353	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1053746422	NA	P-0062742-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	71	805	0	ENST00000354258.4:c.241G>T	p.Ala81Ser	p.A81S	ENST00000354258	NM_000593.5	81	Gca/Tca	1/11	0.286082417638581	3	FACETS	0.972	0.849	1	0.486	0.424	0.552	CLONAL	1	TRUE	1	0.286082417638581	3		805	584	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864895	117864895	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062742-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	156	595	0	ENST00000297338.2:c.1214G>T	p.Arg405Met	p.R405M	ENST00000297338	NM_006265.2	405	aGg/aTg	10/14	0.196179970569316	3	FACETS	1	0.976	1	0.767	0.706	0.829	CLONAL	2	TRUE	0	0.286082417638581	3		595	542	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215857	98215858	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0062760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	36	467	0	ENST00000331920.6:c.3351dup	p.Ala1118CysfsTer27	p.A1118Cfs*27	ENST00000331920	NM_000264.3	1117	-/T	20/24	1	2	FACETS	0.589	0.483	0.709	0.589	0.483	0.709	SUBCLONAL	1	TRUE	1	0.17	2		467	719	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034489	47034489	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	20	232	0	ENST00000377604.3:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000377604	NM_001204468.1	192	Cag/Tag	6/24	1	1	FACETS	0.683	0.523	0.872	0.683	0.523	0.872	SUBCLONAL	1	TRUE	0	0.17	1		232	315	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33430314	33430314	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	40	641	0	ENST00000345365.6:c.697G>C	p.Glu233Gln	p.E233Q	ENST00000345365	NM_002878.3	233	Gag/Cag	8/10	1	2	FACETS	0.654	0.542	0.779	0.654	0.542	0.779	SUBCLONAL	1	TRUE	1	0.17	2		641	720	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880991	37880991	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	39	661	0	ENST00000269571.5:c.2320A>G	p.Met774Val	p.M774V	ENST00000269571		774	Atg/Gtg	20/27	1	2	FACETS	0.609	0.503	0.728	0.609	0.503	0.728	SUBCLONAL	1	TRUE	1	0.17	2		661	753	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	43	320	1				ENST00000310581	NM_198253.2	-/1132			0.597548619153878	5	FACETS	0.992	0.851	1			1	CLONAL	2	TRUE	NA	0.748330829464573	5		321	123	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0062843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	123	210	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.748330829464573	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.748330829464573	1		210	158	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	60	198	0	ENST00000267101.3:c.310G>C	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ctg	3/28	0.3288972754257	1	FACETS	0.512	0.448	0.579	0.512	0.448	0.579	INDETERMINATE	1	TRUE	0	0.748330829464573	1		198	196	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572256	41572256	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	123	159	0	ENST00000263253.7:c.4785C>G	p.Phe1595Leu	p.F1595L	ENST00000263253	NM_001429.3	1595	ttC/ttG	30/31	0.725768573694042	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.748330829464573	1		159	155	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186757	108186757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs864622251	NA	P-0062843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	30	128	1	ENST00000278616.4:c.6115G>A	p.Glu2039Lys	p.E2039K	ENST00000278616	NM_000051.3	2039	Gaa/Aaa	42/63	0.238958768664778	2	FACETS	0.674	0.553	0.804	0.337	0.276	0.402	INDETERMINATE	1	TRUE	0	0.748330829464573	2		129	119	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042523	42042523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	37	111	0	ENST00000219905.7:c.6718G>A	p.Glu2240Lys	p.E2240K	ENST00000219905	NM_001164273.1	2240	Gaa/Aaa	17/24	0.232912563563934	2	FACETS	1	0.938	1	0.596	0.511	0.682	INDETERMINATE	1	TRUE	0	0.748330829464573	2		111	83	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220410	123220410	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	26	45	0	ENST00000218089.9:c.3067G>T	p.Glu1023Ter	p.E1023*	ENST00000218089	NM_001042749.1	1023	Gaa/Taa	30/35	0.387493228990237	2	FACETS	0.965	0.841	1			1	INDETERMINATE	2	TRUE	NA	0.748330829464573	2		45	36	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042397	42042397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764969290	NA	P-0062843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	66	160	0	ENST00000219905.7:c.6592G>A	p.Asp2198Asn	p.D2198N	ENST00000219905	NM_001164273.1	2198	Gac/Aac	17/24	0.232912563563934	2	FACETS	1	0.978	1	0.711	0.64	0.782	INDETERMINATE	1	TRUE	0	0.748330829464573	2		160	124	SUCCESS
ATR	545	MSKCC	GRCh37	3	142285073	142285073	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	13	99	0	ENST00000350721.4:c.182C>G	p.Ser61Cys	p.S61C	ENST00000350721	NM_001184.3	61	tCt/tGt	3/47	0.238958768664778	2	FACETS	0.62	0.455	0.809	0.31	0.227	0.405	INDETERMINATE	1	TRUE	0	0.748330829464573	2		99	56	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418679	49418679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	68	209	0	ENST00000301067.7:c.15835G>A	p.Asp5279Asn	p.D5279N	ENST00000301067	NM_003482.3	5279	Gac/Aac	49/54	0.3288972754257	1	FACETS	0.544	0.481	0.61	0.544	0.481	0.61	INDETERMINATE	1	TRUE	0	0.748330829464573	1		209	209	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955578	48955578	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	90	71	0	ENST00000267163.4:c.1694C>A	p.Ser565Ter	p.S565*	ENST00000267163	NM_000321.2	565	tCa/tAa	17/27	0.748330829464573	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	3	TRUE	0	0.748330829464573	3		71	109	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042661	42042661	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	71	138	0	ENST00000219905.7:c.6856G>C	p.Glu2286Gln	p.E2286Q	ENST00000219905	NM_001164273.1	2286	Gag/Cag	17/24	0.232912563563934	2	FACETS	1	0.98	1	0.724	0.655	0.793	INDETERMINATE	1	TRUE	0	0.748330829464573	2		138	131	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490346	29490346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	64	136	0	ENST00000356175.3:c.431C>T	p.Ser144Phe	p.S144F	ENST00000356175	NM_000267.3	144	tCt/tTt	4/57	0.324468083094549	1	FACETS	0.817	0.731	0.904	0.817	0.731	0.904	INDETERMINATE	1	TRUE	0	0.748330829464573	1		136	131	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839778	27839778	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	102	370	0	ENST00000328488.2:c.316G>C	p.Glu106Gln	p.E106Q	ENST00000328488	NM_003533.2	106	Gag/Cag	1/1	0.205577602470392	3	FACETS	1	0.979	1	0.648	0.588	0.71	INDETERMINATE	1	TRUE	1	0.748330829464573	3		370	289	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839934	27839934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779848426	NA	P-0062843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	27	372	0	ENST00000328488.2:c.160C>T	p.Arg54Cys	p.R54C	ENST00000328488	NM_003533.2	54	Cgc/Tgc	1/1	0.205577602470392	3	FACETS	0.233	0.185	0.288	0.117	0.092	0.144	INDETERMINATE	1	TRUE	1	0.748330829464573	3		372	425	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949036	151949036	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062843-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	11	83	0	ENST00000262189.6:c.1609G>C	p.Glu537Gln	p.E537Q	ENST00000262189	NM_170606.2	537	Gag/Cag	11/59	0.447217892298053	1	FACETS	0.15	0.104	0.206	0.15	0.104	0.206	INDETERMINATE	1	TRUE	0	0.748330829464573	1		83	123	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0000825-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	42	218	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.182673859994702	2	FACETS	1	0.888	1	1	0.975	1	CLONAL	4	TRUE	0	0.241956095780473	2		218	85	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165657	118165657	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs565811357	NA	P-0000825-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	11	305	0	ENST00000369448.3:c.167G>T	p.Arg56Leu	p.R56L	ENST00000369448	NM_017709.3	56	cGc/cTc	2/2	0.241956095780473	4	FACETS	1	0.708	1	0.339	0.236	0.465	CLONAL	1	TRUE	1	0.241956095780473	4		305	111	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682974	241682974	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs755886213	NA	P-0000825-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	14	268	0	ENST00000366560.3:c.49G>C	p.Ala17Pro	p.A17P	ENST00000366560	NM_000143.3	17	Gct/Cct	1/10	NA	2	FACETS	0.661	0.479	0.88			1	INDETERMINATE	1	TRUE	NA	0.241956095780473	2		268	175	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668681	52668681	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0000825-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	37	387	0	ENST00000394830.3:c.1238C>G	p.Ser413Ter	p.S413*	ENST00000394830	NM_018313.4	413	tCa/tGa	12/30	0.241956095780473	1	FACETS	0.89	0.746	1	1	0.964	1	CLONAL	2	TRUE	0	0.241956095780473	1		387	151	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799628	72799628	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000825-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	24	339	0	ENST00000325599.8:c.1541C>G	p.Ala514Gly	p.A514G	ENST00000325599	NM_018130.2	514	gCc/gGc	11/11	0.241956095780473	3	FACETS	1	0.923	1			1	CLONAL	1	TRUE	NA	0.241956095780473	3		339	156	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100324	8100324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs904307886	NA	P-0000825-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	21	503	0	ENST00000346208.3:c.298G>A	p.Gly100Ser	p.G100S	ENST00000346208		100	Ggc/Agc	3/6	0.241956095780473	6	FACETS	0.876	0.681	1	0.438	0.34	0.55	CLONAL	2	TRUE	2	0.241956095780473	6		503	147	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420529	49420529	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000825-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	26	262	0	ENST00000301067.7:c.15220G>T	p.Gly5074Cys	p.G5074C	ENST00000301067	NM_003482.3	5074	Ggc/Tgc	48/54	0.241956095780473	3	FACETS	1	0.822	1	1	0.822	1	CLONAL	2	TRUE	1	0.241956095780473	3		262	118	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109968	115109968	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000825-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	12	118	0	ENST00000257566.3:c.1910G>T	p.Arg637Leu	p.R637L	ENST00000257566	NM_016569.3	637	cGg/cTg	8/8	0.241956095780473	3	FACETS	0.869	0.624	1	0.869	0.624	1	CLONAL	2	TRUE	1	0.241956095780473	3		118	64	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911271	32911271	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786201837	NA	P-0000825-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	11	230	0	ENST00000380152.3:c.2779A>G	p.Met927Val	p.M927V	ENST00000380152		927	Atg/Gtg	11/27	0.241956095780473	1	FACETS	0.484	0.335	0.669	0.484	0.335	0.669	SUBCLONAL	1	TRUE	0	0.241956095780473	1		230	165	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526445	66526445	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000825-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	31	196	0	ENST00000358598.2:c.1001C>T	p.Pro334Leu	p.P334L	ENST00000358598	NM_212471.2	334	cCt/cTt	11/11	0.241956095780473	3	FACETS	1	0.937	1	0.704	0.574	0.849	CLONAL	1	TRUE	1	0.241956095780473	3		196	204	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221215	1221215	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs137853083	NA	P-0000825-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	34	575	0	ENST00000326873.7:c.738C>G	p.Tyr246Ter	p.Y246*	ENST00000326873	NM_000455.4	246	taC/taG	6/10	0.241956095780473	1	FACETS	1	0.921	1	1	0.97	1	CLONAL	2	TRUE	0	0.241956095780473	1		575	105	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610466	10610466	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000825-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	23	302	0	ENST00000171111.5:c.244C>T	p.Gln82Ter	p.Q82*	ENST00000171111	NM_203500.1	82	Cag/Tag	2/6	0.241956095780473	1	FACETS	0.844	0.672	1	1	0.94	1	CLONAL	2	TRUE	0	0.241956095780473	1		302	99	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755657	39755657	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000825-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	29	420	0	ENST00000288319.7:c.1108C>G	p.Arg370Gly	p.R370G	ENST00000288319	NM_182918.3	370	Cgt/Ggt	10/10	0.241956095780473	3	FACETS	1	0.866	1	1	0.866	1	CLONAL	2	TRUE	1	0.241956095780473	3		420	125	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11205075	11205075	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000825-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	32	450	0	ENST00000361445.4:c.4714del	p.Asp1572MetfsTer4	p.D1572Mfs*4	ENST00000361445	NM_004958.3	1572	Gat/at	33/58	1	2	FACETS	1	0.897	1	1	0.966	1	CLONAL	2	TRUE	1	0.241956095780473	2		450	118	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129327	152129328	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000825-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	12	382	0	ENST00000206249.3:c.281dup	p.Leu100ThrfsTer57	p.L100Tfs*57	ENST00000206249	NM_000125.3	94	ctg/cTtg	1/8	0.182673859994702	2	FACETS	1	0.753	1	0.533	0.379	0.718	CLONAL	1	TRUE	0	0.241956095780473	2		382	93	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627729	187627729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758545401	NA	P-0000840-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	10	346	0	ENST00000441802.2:c.3253G>A	p.Gly1085Ser	p.G1085S	ENST00000441802	NM_005245.3	1085	Ggt/Agt	2/27	0.08357683056419	1	FACETS	0.434	0.296	0.605	0.434	0.296	0.605	INDETERMINATE	1	TRUE	0	0.338711032410258	1		346	113	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638347	117638347	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519788	NA	P-0000840-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	12	378	0	ENST00000368508.3:c.6094G>A	p.Gly2032Arg	p.G2032R	ENST00000368508	NM_002944.2	2032	Gga/Aga	38/43	0.338711032410258	1	FACETS	0.764	0.546	1	0.764	0.546	1	CLONAL	1	TRUE	0	0.338711032410258	1		378	77	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001425-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	41	82	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.335560810845841	2		82	189	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0001425-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	109	665	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.335560810845841	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.335560810845841	1		665	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579845	7579845	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001425-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	128	820	0	ENST00000269305.4:c.68G>A	p.Trp23Ter	p.W23*	ENST00000269305	NM_001126112.2	23	tGg/tAg	2/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.335560810845841	2		820	704	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931740	39931740	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001425-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	135	889	1	ENST00000378444.4:c.2859A>T	p.Lys953Asn	p.K953N	ENST00000378444	NM_001123385.1	953	aaA/aaT	4/15	1	2	FACETS	0.923	0.838	1	0.923	0.838	1	CLONAL	1	TRUE	1	0.335560810845841	2		890	872	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667633	29667633	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001425-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	117	700	1	ENST00000356175.3:c.6971del	p.Leu2324Ter	p.L2324*	ENST00000356175	NM_000267.3	2323	acT/ac	46/57	0.335560810845841	1	FACETS	0.964	0.872	1	0.964	0.872	1	CLONAL	1	TRUE	0	0.335560810845841	1		701	602	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872219	45872219	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001425-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	129	908	0	ENST00000391945.4:c.215A>G	p.Tyr72Cys	p.Y72C	ENST00000391945	NM_000400.3	72	tAc/tGc	4/23	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.335560810845841	2		908	767	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713469	30713470	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0001425-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	96	691	0	ENST00000295754.5:c.795_796del	p.Asn266HisfsTer6	p.N266Hfs*6	ENST00000295754	NM_003242.5	265	cAG/c	4/7	0.3288726716508	3	FACETS	0.956	0.852	1	0.478	0.426	0.533	CLONAL	1	TRUE	1	0.335560810845841	3		691	699	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0002281-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	136	689	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.309468429767038	2		689	850	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097304	178097304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763097686	NA	P-0002281-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	85	451	1	ENST00000397062.3:c.410C>T	p.Ser137Leu	p.S137L	ENST00000397062	NM_006164.4	137	tCg/tTg	4/5	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.309468429767038	2		452	529	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247846	59247847	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002281-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	188	954	0	ENST00000371222.2:c.896dup	p.Asn299LysfsTer11	p.N299Kfs*11	ENST00000371222	NM_002228.3	299	aac/aaAc	1/1	0.309468429767038	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.309468429767038	1		954	987	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063316	67063338	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCGTCGTGCCCGACCAGAGAA	GCGCGTCGTGCCCGACCAGAGAA	-	novel	NA	P-0002281-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	28	153	0	ENST00000412916.2:c.8_30del	p.Arg3GlnfsTer9	p.R3Qfs*9	ENST00000412916		2	ccGCGCGTCGTGCCCGACCAGAGAAgc/ccgc	1/6	0.309468429767038	1	FACETS	0.879	0.709	1	0.879	0.709	1	CLONAL	1	TRUE	0	0.309468429767038	1		153	174	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857532	68857532	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	C	novel	NA	P-0002281-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	113	598	0	ENST00000261769.5:c.2164+3A>C		p.X722_splice	ENST00000261769	NM_004360.3	722			0.309468429767038	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.309468429767038	1		598	582	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949766	151949766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002281-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	99	536	0	ENST00000262189.6:c.1334C>T	p.Ser445Phe	p.S445F	ENST00000262189	NM_170606.2	445	tCt/tTt	10/59	1	2	FACETS	0.85	0.758	0.947	0.85	0.758	0.947	CLONAL	1	TRUE	1	0.309468429767038	2		536	753	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003233-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	102	615	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		615	373	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0003233-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	152	653	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		653	579	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203436	NA	P-0003233-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	172	920	0	ENST00000269305.4:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269305	NM_001126112.2	163	Tac/Cac	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		920	494	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271460	26271460	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003233-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	150	626	1	ENST00000305910.3:c.153G>C	p.Glu51Asp	p.E51D	ENST00000305910	NM_003534.2	51	gaG/gaC	1/1	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		627	631	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41489079	41489079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373061594	NA	P-0003233-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	230	636	0	ENST00000263253.7:c.71C>T	p.Ser24Leu	p.S24L	ENST00000263253	NM_001429.3	24	tCg/tTg	1/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		636	636	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849304	76849304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003233-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	107	647	0	ENST00000373344.5:c.5972C>T	p.Ser1991Phe	p.S1991F	ENST00000373344	NM_000489.3	1991	tCt/tTt	26/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		647	292	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916747	48916747	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690915	NA	P-0003233-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	99	601	0	ENST00000267163.4:c.277C>T	p.Gln93Ter	p.Q93*	ENST00000267163	NM_000321.2	93	Caa/Taa	3/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		601	271	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812594	43812594	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003233-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	131	702	0	ENST00000372470.3:c.1297C>T	p.Gln433Ter	p.Q433*	ENST00000372470	NM_005373.2	433	Cag/Tag	8/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		702	584	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65300313	65300313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003233-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	102	459	0	ENST00000342505.4:c.3397G>A	p.Glu1133Lys	p.E1133K	ENST00000342505	NM_002227.2	1133	Gaa/Aaa	25/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		459	436	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940138	71940138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003233-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	153	785	1	ENST00000298229.2:c.523C>T	p.Pro175Ser	p.P175S	ENST00000298229	NM_001567.3	175	Ccc/Tcc	5/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		786	620	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426712	121426712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003233-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	184	772	1	ENST00000257555.6:c.403G>A	p.Asp135Asn	p.D135N	ENST00000257555		135	Gat/Aat	2/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		773	448	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40477080	40477080	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003233-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	100	506	0	ENST00000264657.5:c.1366-1G>A		p.X456_splice	ENST00000264657	NM_139276.2	456			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		506	261	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125401	7125401	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003233-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	167	911	1	ENST00000302850.5:c.3151G>A	p.Glu1051Lys	p.E1051K	ENST00000302850	NM_000208.2	1051	Gag/Aag	17/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		912	681	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170513	11170513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003233-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	154	909	1	ENST00000358026.2:c.4816G>T	p.Glu1606Ter	p.E1606*	ENST00000358026	NM_001128849.1	1606	Gag/Tag	34/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		910	569	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170519	11170519	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1235280916	NA	P-0003233-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	155	898	0	ENST00000358026.2:c.4822G>A	p.Glu1608Lys	p.E1608K	ENST00000358026	NM_001128849.1	1608	Gag/Aag	34/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		898	566	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170531	11170531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003233-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	154	883	1	ENST00000358026.2:c.4834G>A	p.Glu1612Lys	p.E1612K	ENST00000358026	NM_001128849.1	1612	Gag/Aag	34/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		884	544	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216232	36216232	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003233-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	159	841	3	ENST00000222270.7:c.3640G>A	p.Glu1214Lys	p.E1214K	ENST00000222270	NM_014727.1	1214	Gag/Aag	11/37	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		844	565	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40761077	40761077	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764512283	NA	P-0003233-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	151	701	0	ENST00000392038.2:c.275C>T	p.Ser92Phe	p.S92F	ENST00000392038	NM_001626.4	92	tCt/tTt	4/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		701	579	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754511	41754511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1311838879	NA	P-0003233-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	109	764	0	ENST00000301178.4:c.1630G>A	p.Glu544Lys	p.E544K	ENST00000301178	NM_021913.4	544	Gag/Aag	13/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		764	505	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275140	41275140	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003233-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	103	446	0	ENST00000349496.5:c.1306A>T	p.Met436Leu	p.M436L	ENST00000349496	NM_001904.3	436	Atg/Ttg	9/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		446	368	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032111	26032111	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003233-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	124	530	0	ENST00000244661.2:c.178G>C	p.Glu60Gln	p.E60Q	ENST00000244661	NM_003537.3	60	Gag/Cag	1/1	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		530	521	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418946	116418946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003233-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	80	525	1	ENST00000397752.3:c.3457C>T	p.Pro1153Ser	p.P1153S	ENST00000397752	NM_000245.2	1153	Ccg/Tcg	17/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		526	403	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960160	151960160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003233-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	135	645	0	ENST00000262189.6:c.1240C>T	p.His414Tyr	p.H414Y	ENST00000262189	NM_170606.2	414	Cat/Tat	9/59	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		645	484	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5081765	5081765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003233-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	89	472	0	ENST00000381652.3:c.2475G>A	p.Met825Ile	p.M825I	ENST00000381652	NM_004972.3	825	atG/atA	19/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		472	393	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932114	39932114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003233-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	326	852	0	ENST00000378444.4:c.2485G>A	p.Glu829Lys	p.E829K	ENST00000378444	NM_001123385.1	829	Gag/Aag	4/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		852	770	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579463	7579463	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	115	201	0	ENST00000269305.4:c.224del	p.Pro75LeufsTer48	p.P75Lfs*48	ENST00000269305	NM_001126112.2	75	cCt/ct	4/11	0.579215787768355	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.579215787768355	1		201	241	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0003553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	104	78	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	NA	2	FACETS	1	0.952	1			1	INDETERMINATE	2	TRUE	NA	0.579215787768355	2		78	173	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780908	9780908	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	51	342	0	ENST00000377346.4:c.1630G>C	p.Glu544Gln	p.E544Q	ENST00000377346	NM_005026.3	544	Gag/Cag	13/24	0.508765922187874	3	FACETS	0.462	0.392	0.537	0.231	0.196	0.269	SUBCLONAL	1	TRUE	1	0.579215787768355	3		342	492	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932943	49932943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	88	588	0	ENST00000296474.3:c.3001C>T	p.Gln1001Ter	p.Q1001*	ENST00000296474	NM_002447.2	1001	Cag/Tag	13/20	0.426788366002168	3	FACETS	0.445	0.394	0.501			1	SUBCLONAL	1	TRUE	NA	0.579215787768355	3		588	880	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213784	66213784	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	125	322	0	ENST00000273854.3:c.2646G>T	p.Met882Ile	p.M882I	ENST00000273854	NM_004439.5	882	atG/atT	15/18	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.579215787768355	2		322	417	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213891	66213891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	122	367	0	ENST00000273854.3:c.2539C>A	p.Pro847Thr	p.P847T	ENST00000273854	NM_004439.5	847	Cca/Aca	15/18	1	2	FACETS	0.885	0.805	0.968	0.885	0.805	0.968	CLONAL	1	TRUE	1	0.579215787768355	2		367	476	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081639	143081639	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	110	283	0	ENST00000262992.4:c.1435G>T	p.Gly479Ter	p.G479*	ENST00000262992	NM_001101669.1	479	Gga/Tga	15/24	1	2	FACETS	0.954	0.865	1	0.954	0.865	1	CLONAL	1	TRUE	1	0.579215787768355	2		283	398	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332772	153332772	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	158	313	0	ENST00000281708.4:c.184G>C	p.Val62Leu	p.V62L	ENST00000281708	NM_033632.3	62	Gta/Cta	2/12	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.579215787768355	2		313	533	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670658	86670658	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	46	157	0	ENST00000274376.6:c.1936G>A	p.Asp646Asn	p.D646N	ENST00000274376	NM_002890.2	646	Gat/Aat	15/25	0.555573278931744	2	FACETS	0.495	0.418	0.578	0.247	0.209	0.289	SUBCLONAL	1	TRUE	0	0.579215787768355	2		157	321	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271350	26271350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs532386575	NA	P-0003553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	526	839	1	ENST00000305910.3:c.263C>T	p.Ser88Phe	p.S88F	ENST00000305910	NM_003534.2	88	tCc/tTc	1/1	0.52645825376425	3	FACETS	0.925	0.895	0.954	0.925	0.895	0.954	CLONAL	3	TRUE	0	0.579215787768355	3		840	844	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683796	162683796	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	36	206	0	ENST00000366898.1:c.173A>T	p.Asn58Ile	p.N58I	ENST00000366898	NM_004562.2	58	aAt/aTt	3/12	0.331336506506218	3	FACETS	0.512	0.422	0.612	0.256	0.211	0.306	INDETERMINATE	1	TRUE	1	0.579215787768355	3		206	313	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128848638	128848638	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	521	420	0	ENST00000249373.3:c.1303G>T	p.Gly435Trp	p.G435W	ENST00000249373	NM_005631.4	435	Ggg/Tgg	7/12	0.565678084332518	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	4	TRUE	0	0.579215787768355	4		420	702	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5029857	5029857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	152	299	1	ENST00000381652.3:c.301G>A	p.Val101Ile	p.V101I	ENST00000381652	NM_004972.3	101	Gtc/Atc	4/25	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	1	TRUE	NA	0.579215787768355	2		300	470	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8733783	8733783	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	115	343	0	ENST00000356435.5:c.61G>C	p.Glu21Gln	p.E21Q	ENST00000356435		21	Gag/Cag	1/35	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.579215787768355	NA		343	486	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760285	133760285	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	114	283	0	ENST00000318560.5:c.2608G>T	p.Ala870Ser	p.A870S	ENST00000318560	NM_005157.4	870	Gcc/Tcc	11/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.579215787768355	2		283	330	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760703	133760703	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	104	374	0	ENST00000318560.5:c.3026G>T	p.Arg1009Leu	p.R1009L	ENST00000318560	NM_005157.4	1009	cGa/cTa	11/11	1	2	FACETS	0.82	0.739	0.905	0.82	0.739	0.905	CLONAL	1	TRUE	1	0.579215787768355	2		374	438	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246071	46246071	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	245	253	0	ENST00000334344.6:c.4165G>T	p.Glu1389Ter	p.E1389*	ENST00000334344	NM_152641.2	1389	Gag/Tag	15/21	NA	2	FACETS	0.998	0.948	1			1	INDETERMINATE	2	TRUE	NA	0.579215787768355	2		253	424	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912735	32912735	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507327	NA	P-0003553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	115	641	0	ENST00000380152.3:c.4243G>A	p.Glu1415Lys	p.E1415K	ENST00000380152		1415	Gag/Aag	11/27	0.564108482569504	2	FACETS	0.5	0.45	0.553	0.25	0.225	0.277	SUBCLONAL	1	TRUE	0	0.579215787768355	2		641	794	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913155	32913155	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	105	696	1	ENST00000380152.3:c.4663G>T	p.Glu1555Ter	p.E1555*	ENST00000380152		1555	Gaa/Taa	11/27	0.564108482569504	2	FACETS	0.453	0.405	0.503	0.226	0.202	0.252	SUBCLONAL	1	TRUE	0	0.579215787768355	2		697	801	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	T	rs1023835002	NA	P-0003553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	64	286	0	ENST00000558401.1:c.1A>T	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Ttg	1/4	0.579215787768355	1	FACETS	0.633	0.555	0.716	0.633	0.555	0.716	SUBCLONAL	1	TRUE	0	0.579215787768355	1		286	248	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348241	348241	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	61	165	0	ENST00000262320.3:c.1265G>T	p.Gly422Val	p.G422V	ENST00000262320	NM_003502.3	422	gGt/gTt	6/11	0.508765922187874	3	FACETS	0.933	0.812	1	0.467	0.406	0.532	CLONAL	1	TRUE	1	0.579215787768355	3		165	291	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827904	72827904	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	88	697	0	ENST00000268489.5:c.8677G>C	p.Gly2893Arg	p.G2893R	ENST00000268489	NM_006885.3	2893	Ggt/Cgt	9/10	1	2	FACETS	0.367	0.325	0.413	0.367	0.325	0.413	SUBCLONAL	1	TRUE	1	0.579215787768355	2		697	827	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024467	16024467	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	142	335	0	ENST00000268712.3:c.1751G>T	p.Arg584Leu	p.R584L	ENST00000268712	NM_006311.3	584	cGg/cTg	16/46	0.579215787768355	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.579215787768355	1		335	311	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948834	17948834	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	410	454	0	ENST00000458235.1:c.1608C>A	p.Tyr536Ter	p.Y536*	ENST00000458235	NM_000215.3	536	taC/taA	12/24	0.579215787768355	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.579215787768355	2		454	613	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795860	42795860	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0003553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	59	437	0	ENST00000575354.2:c.2849C>G	p.Ser950Ter	p.S950*	ENST00000575354	NM_015125.3	950	tCa/tGa	11/20	0.488960855783264	4	FACETS	0.345	0.296	0.399			1	SUBCLONAL	1	TRUE	NA	0.579215787768355	4		437	933	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710649	40710649	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	38	204	0	ENST00000373198.4:c.4202G>T	p.Gly1401Val	p.G1401V	ENST00000373198	NM_133170.3	1401	gGa/gTa	31/32	0.504953287933454	4	FACETS	0.507	0.419	0.604	0.169	0.139	0.202	SUBCLONAL	1	TRUE	1	0.579215787768355	4		204	409	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513268	41513268	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	212	343	0	ENST00000263253.7:c.172G>C	p.Gly58Arg	p.G58R	ENST00000263253	NM_001429.3	58	Ggt/Cgt	2/31	0.301516933904759	4	FACETS	0.872	0.814	0.931	0.581	0.542	0.621	INDETERMINATE	2	TRUE	1	0.579215787768355	4		343	663	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268452	142268453	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0003553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	57	187	0	ENST00000350721.4:c.3039_3040del	p.Ile1014SerfsTer12	p.I1014Sfs*12	ENST00000350721	NM_001184.3	1013	ctCAtt/cttt	15/47	0.426788366002168	3	FACETS	0.533	0.458	0.615			1	SUBCLONAL	1	TRUE	NA	0.579215787768355	3		187	476	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103665	47103666	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs36092203	NA	P-0003553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	65	258	0	ENST00000409792.3:c.6280dup	p.Arg2094LysfsTer4	p.R2094Kfs*4	ENST00000409792	NM_014159.6	2094	agg/aAgg	14/21	0.409080118021669	4	FACETS	0.639	0.554	0.73	0.16	0.138	0.183	SUBCLONAL	1	TRUE	0	0.579215787768355	4		258	555	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217039	2217039	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	272	355	0	ENST00000398665.3:c.2497del	p.Leu833CysfsTer18	p.L833Cfs*18	ENST00000398665	NM_032482.2	832	Ccc/cc	21/28	0.579215787768355	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.579215787768355	2		355	409	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030373	49030374	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	T	novel	NA	P-0003553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	180	234	2	ENST00000267163.4:c.1848_1849delinsT	p.Lys616AsnfsTer7	p.K616Nfs*7	ENST00000267163	NM_000321.2	616	aaAGgt/aaTgt	19/27	0.543289155175516	2	FACETS	0.925	0.869	0.98	0.925	0.869	0.98	CLONAL	2	TRUE	0	0.579215787768355	2		236	336	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682533	37682533	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	260	326	0	ENST00000447079.4:c.3724C>T	p.Arg1242Ter	p.R1242*	ENST00000447079	NM_015083.1	1242	Cga/Tga	13/14	0.3	7	FACETS	0.929	0.879	0.979			1	CLONAL	6	TRUE	NA	0.29	7		326	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0004327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	60	413	0	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	0.3	3	FACETS	1	0.968	1			1	CLONAL	1	TRUE	NA	0.29	3		413	328	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039164	49039164	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913297	NA	P-0004327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	38	265	1	ENST00000267163.4:c.2242G>T	p.Glu748Ter	p.E748*	ENST00000267163	NM_000321.2	748	Gag/Tag	22/27	0.252847786689803	3	FACETS	1	0.932	1	0.625	0.52	0.74	CLONAL	1	TRUE	1	0.29	3		266	240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578245	7578245	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780072	NA	P-0004327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	8	446	2	ENST00000269305.4:c.604C>T	p.Arg202Cys	p.R202C	ENST00000269305	NM_001126112.2	202	Cgt/Tgt	6/11	0.3	3	FACETS	0.163	0.104	0.24			1	SUBCLONAL	1	TRUE	NA	0.29	3		448	388	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175996772	175996772	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	25	395	0	ENST00000367669.3:c.1665G>C	p.Lys555Asn	p.K555N	ENST00000367669	NM_022457.5	555	aaG/aaC	15/20	NA	2	FACETS	0.556	0.439	0.691			1	INDETERMINATE	1	TRUE	NA	0.29	2		395	310	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439785	220439785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1037869771	NA	P-0004327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	53	476	0	ENST00000243786.2:c.638C>T	p.Pro213Leu	p.P213L	ENST00000243786	NM_002191.3	213	cCc/cTc	2/2	0.3	1	FACETS	0.919	0.788	1	0.919	0.788	1	CLONAL	1	TRUE	0	0.29	1		476	340	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981455	55981455	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	36	437	0	ENST00000263923.4:c.482T>A	p.Leu161His	p.L161H	ENST00000263923	NM_002253.2	161	cTt/cAt	4/30	1	2	FACETS	0.83	0.685	0.992	0.83	0.685	0.992	CLONAL	1	TRUE	1	0.29	2		437	299	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532825	187532825	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	31	462	0	ENST00000441802.2:c.9568G>T	p.Glu3190Ter	p.E3190*	ENST00000441802	NM_005245.3	3190	Gaa/Taa	14/27	0.3	1	FACETS	0.771	0.627	0.932	0.771	0.627	0.932	CLONAL	1	TRUE	0	0.29	1		462	237	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519477	176519477	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	35	420	0	ENST00000292408.4:c.883G>T	p.Gly295Ter	p.G295*	ENST00000292408	NM_213647.1	295	Gga/Tga	7/18	1	2	FACETS	0.667	0.547	0.8	0.667	0.547	0.8	SUBCLONAL	1	TRUE	1	0.29	2		420	362	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056366	26056366	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	80	266	0	ENST00000343677.2:c.291A>T	p.Lys97Asn	p.K97N	ENST00000343677	NM_005319.3	97	aaA/aaT	1/1	0.3	11	FACETS	1	0.885	1			1	CLONAL	2	TRUE	NA	0.29	11		266	633	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2969703	2969703	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	27	328	0	ENST00000396946.4:c.1576G>T	p.Gly526Trp	p.G526W	ENST00000396946	NM_032415.4	526	Ggg/Tgg	12/25	1	2	FACETS	0.497	0.395	0.613	0.497	0.395	0.613	SUBCLONAL	1	TRUE	1	0.29	2		328	375	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729784	41729784	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	65	453	0	ENST00000242208.4:c.745G>T	p.Glu249Ter	p.E249*	ENST00000242208	NM_002192.2	249	Gag/Tag	3/3	1	2	FACETS	0.987	0.858	1	0.987	0.858	1	CLONAL	1	TRUE	1	0.29	2		453	454	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741773	145741773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756213173	NA	P-0004327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	32	366	0	ENST00000428558.2:c.730G>A	p.Glu244Lys	p.E244K	ENST00000428558	NM_004260.3	244	Gaa/Aaa	5/22	1	2	FACETS	0.625	0.508	0.757	0.625	0.508	0.757	SUBCLONAL	1	TRUE	1	0.29	2		366	353	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612158	43612158	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	14	282	0	ENST00000355710.3:c.2263G>C	p.Val755Leu	p.V755L	ENST00000355710	NM_020975.4	755	Gtg/Ctg	12/20	NA	2	FACETS	0.422	0.305	0.563			1	INDETERMINATE	1	TRUE	NA	0.29	2		282	229	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864358	57864358	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	27	545	0	ENST00000228682.2:c.1835T>C	p.Ile612Thr	p.I612T	ENST00000228682	NM_005269.2	612	aTa/aCa	12/12	0.3	3	FACETS	0.463	0.368	0.573	0.232	0.184	0.287	SUBCLONAL	1	TRUE	1	0.29	3		545	460	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109670	115109670	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	18	360	0	ENST00000257566.3:c.2208C>A	p.Asp736Glu	p.D736E	ENST00000257566	NM_016569.3	736	gaC/gaA	8/8	1	2	FACETS	0.376	0.283	0.487	0.376	0.283	0.487	SUBCLONAL	1	TRUE	1	0.29	2		360	330	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435625	110435625	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	33	58	0	ENST00000375856.3:c.2776G>T	p.Glu926Ter	p.E926*	ENST00000375856	NM_003749.2	926	Gag/Tag	1/2	0.252847786689803	3	FACETS	0.931	0.771	1	0.931	0.771	1	CLONAL	2	TRUE	1	0.29	3		58	140	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877462	40877462	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	17	245	0	ENST00000373198.4:c.2234G>T	p.Gly745Val	p.G745V	ENST00000373198	NM_133170.3	745	gGt/gTt	15/32	0.3	1	FACETS	0.583	0.437	0.754	0.583	0.437	0.754	SUBCLONAL	1	TRUE	0	0.29	1		245	172	SUCCESS
AR	367	MSKCC	GRCh37	X	66766207	66766207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	16	117	0	ENST00000374690.3:c.1219C>T	p.Arg407Cys	p.R407C	ENST00000374690	NM_000044.3	407	Cgc/Tgc	1/8	0.3	0	FACETS	0.658	0.492	0.853			1	SUBCLONAL	1	TRUE	NA	0.29	0		117	119	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272831	142272831	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004327-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	27	324	0	ENST00000350721.4:c.2368del	p.Cys790ValfsTer13	p.C790Vfs*13	ENST00000350721	NM_001184.3	790	Tgt/gt	11/47	1	2	FACETS	0.692	0.552	0.851	0.692	0.552	0.851	SUBCLONAL	1	TRUE	1	0.29	2		324	269	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336074	73336074	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	70	370	0	ENST00000377767.4:c.2329T>C	p.Ser777Pro	p.S777P	ENST00000377767	NM_014953.3	777	Tca/Cca	17/21	1	2	FACETS	0.868	0.758	0.986	0.868	0.758	0.986	CLONAL	1	TRUE	1	0.326541450515242	2		370	494	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482926	140482927	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs777474487	NA	P-0005786-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	97	499	2	ENST00000288602.6:c.1208dup	p.Ala404CysfsTer9	p.A404Cfs*9	ENST00000288602	NM_004333.4	403	cct/ccCt	10/18	1	2	FACETS	0.777	0.692	0.867	0.777	0.692	0.867	SUBCLONAL	1	TRUE	1	0.326541450515242	2		501	765	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005909-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	33	459	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.403	0.327	0.49	0.403	0.327	0.49	SUBCLONAL	1	TRUE	1	0.18	2		459	910	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0005909-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	32	584	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	1	2	FACETS	0.297	0.239	0.362	0.297	0.239	0.362	SUBCLONAL	1	TRUE	1	0.18	2		584	1198	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0006291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	208	724	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.851157492964737	3	FACETS	0.931	0.88	0.982	0.931	0.88	0.982	CLONAL	2	TRUE	1	0.851157492964737	3		724	374	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0006291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	74	548	1				ENST00000310581	NM_198253.2	-/1132			0.851157492964737	3	FACETS	0.832	0.735	0.934	0.416	0.367	0.467	CLONAL	1	TRUE	1	0.851157492964737	3		549	298	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929545	44929546	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	290	299	0	ENST00000377967.4:c.2646dup	p.Pro883ThrfsTer23	p.P883Tfs*23	ENST00000377967	NM_021140.2	882	ata/atAa	17/29	0.851157492964737	2	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.851157492964737	2		299	322	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615035	43615035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142318626	NA	P-0006291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	119	901	0	ENST00000355710.3:c.2449C>T	p.Arg817Cys	p.R817C	ENST00000355710	NM_020975.4	817	Cgc/Tgc	14/20	0.791776702425416	4	FACETS	0.948	0.859	1	0.474	0.429	0.521	CLONAL	1	TRUE	2	0.851157492964737	4		901	546	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175838	24175839	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	238	751	0	ENST00000263121.7:c.1067dup	p.Thr357AspfsTer4	p.T357Dfs*4	ENST00000263121	NM_003073.3	356	ctg/cTtg	8/9	0.690808425872592	4	FACETS	0.924	0.871	0.979	0.924	0.871	0.979	CLONAL	2	TRUE	2	0.851157492964737	4		751	560	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588172	69588172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550329316	NA	P-0006291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	163	1065	1	ENST00000168712.1:c.526G>A	p.Gly176Ser	p.G176S	ENST00000168712	NM_002007.2	176	Ggc/Agc	3/3	0.851157492964737	3	FACETS	0.927	0.855	1	0.464	0.427	0.501	CLONAL	1	TRUE	1	0.851157492964737	3		1066	589	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983059	201983060	+	stop_gained	Nonsense_Mutation	DNP	TC	TC	AA	novel	NA	P-0006291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	426	1049	2	ENST00000359651.3:c.908_909delinsAA	p.Phe303Ter	p.F303*	ENST00000359651		303	tTC/tAA	7/8	0.690808425872592	4	FACETS	0.958	0.917	1	0.958	0.917	1	CLONAL	2	TRUE	2	0.851157492964737	4		1051	967	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0006582-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	105	505	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	0.192901268956868	5	FACETS	0.976	0.877	1	0.65	0.584	0.72	CLONAL	2	TRUE	2	0.264068746282742	5		505	569	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152041	11152041	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006582-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	203	366	1	ENST00000358026.2:c.4325C>A	p.Ser1442Ter	p.S1442*	ENST00000358026	NM_001128849.1	1442	tCa/tAa	31/36	0.256055323681718	4	FACETS	0.922	0.862	0.983	0.922	0.862	0.983	CLONAL	4	TRUE	0	0.264068746282742	4		367	527	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480403	89480403	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006582-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	48	306	0	ENST00000336596.2:c.2240T>A	p.Leu747His	p.L747H	ENST00000336596	NM_005233.5	747	cTc/cAc	13/17	0.264068746282742	3	FACETS	1	0.878	1	0.521	0.441	0.608	CLONAL	1	TRUE	1	0.264068746282742	3		306	395	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671846	30671846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006582-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	171	750	0	ENST00000376406.3:c.5114C>T	p.Thr1705Ile	p.T1705I	ENST00000376406	NM_014641.2	1705	aCc/aTc	10/15	0.192901268956868	5	FACETS	1	0.948	1	0.693	0.638	0.75	CLONAL	2	TRUE	2	0.264068746282742	5		750	870	SUCCESS
AR	367	MSKCC	GRCh37	X	66941674	66941674	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0006582-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	93	434	0	ENST00000374690.3:c.2319-1G>A		p.X773_splice	ENST00000374690	NM_000044.3	773			0.207154719555211	3	FACETS	0.917	0.819	1	0.611	0.546	0.679	CLONAL	2	TRUE	0	0.264068746282742	3		434	435	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112116	115112116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780879062	NA	P-0006582-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	71	586	0	ENST00000257566.3:c.1624C>T	p.Leu542Phe	p.L542F	ENST00000257566	NM_016569.3	542	Ctc/Ttc	7/8	0.264068746282742	3	FACETS	0.988	0.863	1	0.494	0.431	0.562	CLONAL	1	TRUE	1	0.264068746282742	3		586	616	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221983	1222003	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	ATCCGGCAGATCCGGCAGCAC	ATCCGGCAGATCCGGCAGCAC	GGAT	novel	NA	P-0006582-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	204	569	2	ENST00000326873.7:c.898_918delinsGGAT	p.Ile300GlyfsTer2	p.I300Gfs*2	ENST00000326873	NM_000455.4	300	ATCCGGCAGATCCGGCAGCAC/GGAT	7/10	0.256055323681718	4	FACETS	1	0.964	1	0.789	0.736	0.843	CLONAL	3	TRUE	0	0.264068746282742	4		571	619	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287494	33287494	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	139	298	0	ENST00000374542.5:c.1603G>T	p.Glu535Ter	p.E535*	ENST00000374542	NM_001141970.1	535	Gaa/Taa	6/8	0.532437278296666	3	FACETS	1	0.985	1	0.798	0.746	0.849	CLONAL	2	TRUE	0	0.656322712294008	3		298	235	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575069	64575069	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	181	379	0	ENST00000312049.6:c.738del	p.Ile247LeufsTer34	p.I247Lfs*34	ENST00000312049	NM_130799.2	246	tcC/tc	4/10	0.597104974652487	2	FACETS	0.913	0.862	0.964	0.913	0.862	0.964	CLONAL	2	TRUE	0	0.656322712294008	2		379	302	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0008836-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	117	414	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.72536283746643	2		414	274	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0009993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	411	610	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		610	863	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0009993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	65	663	1	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		664	751	SUCCESS
APC	324	MSKCC	GRCh37	5	112162803	112162803	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1064794163	NA	P-0009993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	149	388	0	ENST00000257430.4:c.1409-2A>G		p.X470_splice	ENST00000257430	NM_000038.5	470			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		388	375	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015040	37015040	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756345939	NA	P-0009993-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	117	494	0	ENST00000358127.4:c.364C>T	p.Arg122Trp	p.R122W	ENST00000358127	NM_001280556.1	122	Cgg/Tgg	3/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		494	499	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023217	27023227	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCTAGGCCC	GCCCTAGGCCC	-	novel	NA	P-0010183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	93	229	0	ENST00000324856.7:c.328_338del	p.Arg110GlufsTer3	p.R110Efs*3	ENST00000324856	NM_006015.4	108	gGCCCTAGGCCC/g	1/20	NA	2	FACETS	0.484	0.433	0.538			1	INDETERMINATE	1	TRUE	NA	0.955564978534858	2		229	402	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243905	46243905	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	497	491	0	ENST00000334344.6:c.1999A>C	p.Met667Leu	p.M667L	ENST00000334344	NM_152641.2	667	Atg/Ctg	15/21	0.465079973306389	1	FACETS	0.638	0.615	0.66	0.638	0.615	0.66	INDETERMINATE	1	TRUE	0	0.955564978534858	1		491	852	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341502	89341502	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1466808569	NA	P-0010183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	313	495	0	ENST00000301030.4:c.7568G>A	p.Arg2523Gln	p.R2523Q	ENST00000301030	NM_001256183.1	2523	cGg/cAg	10/13	1	2	FACETS	0.519	0.489	0.55	0.519	0.489	0.55	SUBCLONAL	1	TRUE	1	0.955564978534858	2		495	1262	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593600	55593650	+	inframe_deletion	In_Frame_Del	DEL	CAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGAC	CAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGAC	-	novel	NA	P-0010183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	403	543	0	ENST00000288135.5:c.1667_1717del	p.Gln556_Asp572del	p.Q556_D572del	ENST00000288135	NM_000222.2	556	CAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGAC/-	11/21	1	2	FACETS	0.684	0.651	0.718	0.684	0.651	0.718	SUBCLONAL	1	TRUE	1	0.955564978534858	2		543	1233	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0010593-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	76	460	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.223847232687206	4	FACETS	0.964	0.849	1	0.964	0.849	1	CLONAL	2	FALSE	2	0.223847232687206	4		460	431	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0010593-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	8	640	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.223847232687206	4	FACETS	0.415	0.266	0.607	0.207	0.133	0.304	SUBCLONAL	1	FALSE	2	0.223847232687206	4		640	211	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0010593-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	56	863	0	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	FALSE	1	0.223847232687206	2		863	471	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063702	67063702	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010593-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	56	290	0	ENST00000412916.2:c.151G>A	p.Gly51Ser	p.G51S	ENST00000412916		51	Ggc/Agc	2/6	0.223847232687206	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	0	0.223847232687206	1		290	328	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348106	89348106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010593-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	29	1004	0	ENST00000301030.4:c.4844C>T	p.Ser1615Phe	p.S1615F	ENST00000301030	NM_001256183.1	1615	tCc/tTc	9/13	0.223847232687206	0	FACETS	0.675	0.543	0.824			1	SUBCLONAL	1	FALSE	0	0.223847232687206	0		1004	298	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853213	68853213	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010593-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	42	568	0	ENST00000261769.5:c.1596G>A	p.Trp532Ter	p.W532*	ENST00000261769	NM_004360.3	532	tgG/tgA	11/16	0.223847232687206	1	FACETS	0.913	0.764	1	0.913	0.764	1	CLONAL	1	FALSE	0	0.223847232687206	1		568	365	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93953163	93953163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010593-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	21	453	0	ENST00000369303.4:c.2978G>A	p.Gly993Glu	p.G993E	ENST00000369303	NM_004440.3	993	gGa/gAa	17/17	0.159586736644891	4	FACETS	1	0.906	1	0.688	0.533	0.864	CLONAL	1	FALSE	2	0.223847232687206	4		453	167	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239994	53239994	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010593-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	40	816	0	ENST00000375401.3:c.1447G>T	p.Glu483Ter	p.E483*	ENST00000375401	NM_004187.3	483	Gaa/Taa	11/26	0.223847232687206	0	FACETS	0.802	0.668	0.95			1	CLONAL	1	FALSE	0	0.223847232687206	0		816	346	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106662	27106662	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010928-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	256	686	0	ENST00000324856.7:c.6273G>A	p.Trp2091Ter	p.W2091*	ENST00000324856	NM_006015.4	2091	tgG/tgA	20/20	1	2	FACETS	0.963	0.903	1	0.963	0.903	1	CLONAL	1	TRUE	1	0.548123303924433	2		686	970	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122714	108122714	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010928-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	429	532	0	ENST00000278616.4:c.1760del	p.Gly587ValfsTer3	p.G587Vfs*3	ENST00000278616	NM_000051.3	586	gaG/ga	11/63	0.502369949382815	3	FACETS	0.863	0.83	0.896	0.863	0.83	0.896	CLONAL	3	TRUE	0	0.548123303924433	3		532	770	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129798	108129798	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555076748	NA	P-0010928-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	58	485	0	ENST00000278616.4:c.2462G>C	p.Ser821Thr	p.S821T	ENST00000278616	NM_000051.3	821	aGt/aCt	16/63	0.502369949382815	3	FACETS	0.397	0.341	0.459	0.132	0.113	0.153	SUBCLONAL	1	TRUE	0	0.548123303924433	3		485	679	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43739603	43739603	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010928-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	149	516	0	ENST00000382044.4:c.2797C>G	p.His933Asp	p.H933D	ENST00000382044	NM_001141980.1	933	Cac/Gac	13/28	0.548123303924433	3	FACETS	0.998	0.914	1	0.499	0.457	0.543	CLONAL	1	TRUE	1	0.548123303924433	3		516	694	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408894	41408894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1420220673	NA	P-0010928-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	52	451	2	ENST00000373198.4:c.532G>A	p.Ala178Thr	p.A178T	ENST00000373198	NM_133170.3	178	Gcc/Acc	4/32	0.20522525119508	4	FACETS	0.487	0.414	0.567	0.244	0.207	0.284	INDETERMINATE	1	TRUE	2	0.548123303924433	4		453	603	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136826	69136826	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1236733726	NA	P-0010928-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	72	432	0	ENST00000288368.4:c.4740G>T	p.Leu1580Phe	p.L1580F	ENST00000288368	NM_024870.2	1580	ttG/ttT	39/40	0.247986271957227	2	FACETS	0.516	0.452	0.585	0.258	0.226	0.293	INDETERMINATE	1	TRUE	0	0.548123303924433	2		432	509	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159752	20159752	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010928-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	276	604	0	ENST00000379607.5:c.7A>G	p.Lys3Glu	p.K3E	ENST00000379607	NM_001412.3	3	Aag/Gag	1/7	0.196713681789203	2	FACETS	1	0.992	1	0.661	0.623	0.699	INDETERMINATE	1	TRUE	0	0.548123303924433	2		604	762	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577075	7577076	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCTCTTCC	novel	NA	P-0013636-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	354	574	0	ENST00000269305.4:c.855_862dup	p.Asn288ArgfsTer60	p.N288Rfs*60	ENST00000269305	NM_001126112.2	288	aat/aGGAAGAGAat	8/11	0.55331592530075	2	FACETS	0.841	0.802	0.88	0.841	0.802	0.88	CLONAL	2	FALSE	0	0.55331592530075	2		574	761	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434074	49434074	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013636-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	107	427	1	ENST00000301067.7:c.7479del	p.Phe2494SerfsTer49	p.F2494Sfs*49	ENST00000301067	NM_003482.3	2493	ggG/gg	31/54	0.55331592530075	2	FACETS	0.607	0.545	0.672	0.304	0.272	0.336	SUBCLONAL	1	FALSE	0	0.55331592530075	2		428	637	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50784100	50784100	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013636-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	138	464	0	ENST00000398568.2:c.491G>C	p.Gly164Ala	p.G164A	ENST00000398568	NM_001042412.1	164	gGa/gCa	3/18	0.397951090844127	3	FACETS	0.92	0.839	1	0.46	0.419	0.503	CLONAL	1	FALSE	1	0.55331592530075	3		464	692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0014096-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	632	509	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.710637598652761	3	FACETS	0.987	0.964	1	0.987	0.964	1	CLONAL	3	TRUE	0	0.710637598652761	3		509	814	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856658	111856658	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014096-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	197	286	0	ENST00000341259.2:c.709C>A	p.Leu237Met	p.L237M	ENST00000341259	NM_005475.2	237	Ctg/Atg	2/8	0.702581386276885	2	FACETS	0.966	0.919	1	0.966	0.919	1	CLONAL	2	TRUE	0	0.710637598652761	2		286	287	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242279	98242279	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1060502279	NA	P-0014096-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	356	429	0	ENST00000331920.6:c.1039G>T	p.Val347Phe	p.V347F	ENST00000331920	NM_000264.3	347	Gtc/Ttc	7/24	0.697526278715882	4	FACETS	0.902	0.857	0.947	0.902	0.857	0.947	CLONAL	2	TRUE	2	0.710637598652761	4		429	950	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410498	139410520	+	frameshift_variant	Frame_Shift_Del	DEL	GTGCTGGCACACTCGTCCACATC	GTGCTGGCACACTCGTCCACATC	-	novel	NA	P-0014096-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	358	630	0	ENST00000277541.6:c.1582_1604del	p.Asp528ProfsTer34	p.D528Pfs*34	ENST00000277541	NM_017617.3	528	GATGTGGACGAGTGTGCCAGCACc/c	10/34	0.702796433607136	2	FACETS	0.788	0.755	0.821	0.788	0.755	0.821	SUBCLONAL	2	TRUE	0	0.710637598652761	2		630	639	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951122	48951128	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	GAAATTT	GAAATTT	TGTATAGGATACATCTTTAAA	novel	NA	P-0014096-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	175	311	0	ENST00000267163.4:c.1284_1290delinsTGTATAGGATACATCTTTAAA	p.Glu428AspfsTer3	p.E428Dfs*3	ENST00000267163	NM_000321.2	428	gaGAAATTT/gaTGTATAGGATACATCTTTAAA	13/27	0.702581386276885	2	FACETS	0.929	0.88	0.977	0.929	0.88	0.977	CLONAL	2	TRUE	0	0.710637598652761	2		311	265	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044602	47044602	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014096-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	702	644	0	ENST00000377604.3:c.2099A>C	p.Lys700Thr	p.K700T	ENST00000377604	NM_001204468.1	700	aAg/aCg	18/24	0.710637598652761	6	FACETS	0.87	0.84	0.901			1	CLONAL	3	TRUE	NA	0.710637598652761	6		644	1832	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983945	15983945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014096-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	307	402	0	ENST00000268712.3:c.3274C>G	p.Arg1092Gly	p.R1092G	ENST00000268712	NM_006311.3	1092	Cgg/Ggg	24/46	0.710637598652761	3	FACETS	0.963	0.917	1	0.642	0.611	0.673	CLONAL	2	TRUE	0	0.710637598652761	3		402	608	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256205	16256205	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0014117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	105	604	0	ENST00000375759.3:c.3475del	p.Ile1159LeufsTer28	p.I1159Lfs*28	ENST00000375759	NM_015001.2	1157	gAa/ga	11/15	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	1	0.158562649413476	2		604	1213	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242484	55242507	+	inframe_deletion	In_Frame_Del	DEL	TCTCCGAAAGCCAACAAGGAAATC	TCTCCGAAAGCCAACAAGGAAATC	-	rs121913463	NA	P-0014117-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	82	455	0	ENST00000275493.2:c.2254_2277del	p.Ser752_Ile759del	p.S752_I759del	ENST00000275493	NM_005228.3	752	TCTCCGAAAGCCAACAAGGAAATC/-	19/28	0.158562649413476	3	FACETS	1	0.928	1	0.539	0.474	0.609	CLONAL	1	FALSE	1	0.158562649413476	3		455	1036	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0014129-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	271	702	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.751673339514199	1	FACETS	0.981	0.938	1	0.981	0.938	1	CLONAL	1	TRUE	0	0.787816405091022	1		702	425	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563077	21563077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014129-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	314	851	0	ENST00000382592.4:c.842C>T	p.Pro281Leu	p.P281L	ENST00000382592	NM_014572.2	281	cCg/cTg	4/8	0.787816405091022	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.787816405091022	1		851	439	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723122	49723122	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014129-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	222	641	0	ENST00000449682.2:c.1294T>G	p.Phe432Val	p.F432V	ENST00000449682	NM_020998.3	432	Ttc/Gtc	11/18	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.787816405091022	2		641	558	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591116	67591151	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TTATCCAGCTGAGAAAGACGAGAGACCAATACTTGA	TTATCCAGCTGAGAAAGACGAGAGACCAATACTTGA	-	novel	NA	P-0014129-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	96	293	0	ENST00000274335.5:c.1710_1745del	p.Ile571_Met582del	p.I571_M582del	ENST00000274335		570	cTTATCCAGCTGAGAAAGACGAGAGACCAATACTTGAtg/ctg	12/15	0.787816405091022	1	FACETS	0.89	0.819	0.959	0.89	0.819	0.959	CLONAL	1	TRUE	0	0.787816405091022	1		293	166	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962548	100962548	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0014129-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	104	681	0	ENST00000325455.5:c.1849A>T	p.Lys617Ter	p.K617*	ENST00000325455	NM_001202474.3	617	Aaa/Taa	3/8	1	2	FACETS	0.42	0.377	0.466	0.42	0.377	0.466	SUBCLONAL	1	TRUE	1	0.787816405091022	2		681	628	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307271	118307271	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014129-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	10	92	0	ENST00000534358.1:c.44C>A	p.Thr15Asn	p.T15N	ENST00000534358	NM_005933.3	15	aCc/aAc	1/36	1	2	FACETS	0.27	0.184	0.375	0.27	0.184	0.375	SUBCLONAL	1	TRUE	1	0.787816405091022	2		92	94	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119634997	119634997	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014129-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	35	198	0	ENST00000316626.5:c.502A>C	p.Ser168Arg	p.S168R	ENST00000316626		168	Agt/Cgt	5/12	1	2	FACETS	0.369	0.304	0.44	0.369	0.304	0.44	SUBCLONAL	1	TRUE	1	0.787816405091022	2		198	241	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523740	176523742	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GCT	GCT	-	novel	NA	P-0014129-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	230	588	0	ENST00000292408.4:c.2152_2153+1del		p.ELdel	ENST00000292408	NM_213647.1	717	gaGCTg/gag	16/18	0.787816405091022	1	FACETS	0.978	0.931	1	0.978	0.931	1	CLONAL	1	TRUE	0	0.787816405091022	1		588	362	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0014833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	751	696	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.286944337212218	11	FACETS	0.968	0.941	0.994	0.968	0.941	0.994	CLONAL	10	TRUE	1	0.286944337212218	11		696	1239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0014833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	130	858	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.286944337212218	2		858	693	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	65	1048	1	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	1	2	FACETS	0.585	0.506	0.67	0.585	0.506	0.67	SUBCLONAL	1	TRUE	1	0.286944337212218	2		1049	775	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28929495	NA	P-0014833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	702	578	1	ENST00000275493.2:c.2155G>T	p.Gly719Cys	p.G719C	ENST00000275493	NM_005228.3	719	Ggc/Tgc	18/28	0.286944337212218	11	FACETS	0.968	0.941	0.995	0.968	0.941	0.995	CLONAL	10	TRUE	1	0.286944337212218	11		579	1158	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431322	49431322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	33	307	0	ENST00000301067.7:c.9817G>A	p.Ala3273Thr	p.A3273T	ENST00000301067	NM_003482.3	3273	Gcc/Acc	34/54	0.286944337212218	3	FACETS	0.936	0.765	1	0.468	0.382	0.564	CLONAL	1	TRUE	1	0.286944337212218	3		307	281	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136841	2136841	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	251	703	0	ENST00000219476.3:c.4958C>A	p.Ser1653Tyr	p.S1653Y	ENST00000219476	NM_000548.3	1653	tCc/tAc	38/42	0.286944337212218	6	FACETS	0.999	0.936	1	0.599	0.561	0.638	CLONAL	3	TRUE	1	0.286944337212218	6		703	919	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945112	44945112	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	11	313	1	ENST00000377967.4:c.3436C>T	p.His1146Tyr	p.H1146Y	ENST00000377967	NM_021140.2	1146	Cat/Tat	24/29	0.185039874599138	3	FACETS	0.432	0.298	0.598			1	SUBCLONAL	1	TRUE	NA	0.286944337212218	3		314	203	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354291	70354291	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	90	923	0	ENST00000374080.3:c.4702G>T	p.Gly1568Cys	p.G1568C	ENST00000374080		1568	Ggc/Tgc	34/45	1	2	FACETS	0.786	0.697	0.882	0.786	0.697	0.882	SUBCLONAL	1	TRUE	1	0.286944337212218	2		923	798	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0015825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	276	519	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.365253008153933	1	FACETS	0.713	0.673	0.753	0.713	0.673	0.753	INDETERMINATE	1	TRUE	0	0.68889230316917	1		519	737	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601342	28601342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	147	475	0	ENST00000241453.7:c.2090G>A	p.Gly697Asp	p.G697D	ENST00000241453	NM_004119.2	697	gGt/gAt	17/24	0.301271268563138	3	FACETS	0.508	0.463	0.556	0.254	0.231	0.278	INDETERMINATE	1	TRUE	1	0.68889230316917	3		475	1129	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602739	10602739	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	1030	672	0	ENST00000171111.5:c.839del	p.Phe280SerfsTer37	p.F280Sfs*37	ENST00000171111	NM_203500.1	280	tTc/tc	3/6	0.630625302057379	2	FACETS	0.917	0.896	0.938	0.917	0.896	0.938	CLONAL	2	TRUE	0	0.68889230316917	2		672	1630	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213947	36213947	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1244332454	NA	P-0015825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	584	797	2	ENST00000222270.7:c.2773G>T	p.Gly925Ter	p.G925*	ENST00000222270	NM_014727.1	925	Gga/Tga	6/37	0.630625302057379	2	FACETS	1	0.988	1	0.535	0.513	0.556	CLONAL	1	TRUE	0	0.68889230316917	2		799	1586	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889122	76889122	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	404	291	0	ENST00000373344.5:c.4888A>G	p.Thr1630Ala	p.T1630A	ENST00000373344	NM_000489.3	1630	Act/Gct	18/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.68889230316917	1		291	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0016141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	88	422	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.220906976222135	2		422	682	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057835	27057835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	240	512	0	ENST00000324856.7:c.1543C>T	p.Gln515Ter	p.Q515*	ENST00000324856	NM_006015.4	515	Cag/Tag	3/20	1	2	FACETS	1	0.982	1	1	0.995	1	CLONAL	2	TRUE	1	0.220906976222135	2		512	953	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467843	50467843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	38	252	1	ENST00000331340.3:c.1078C>T	p.Arg360Cys	p.R360C	ENST00000331340	NM_006060.4	360	Cgc/Tgc	8/8	1	2	FACETS	0.882	0.73	1	0.882	0.73	1	CLONAL	1	TRUE	1	0.220906976222135	2		253	390	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847363	68847368	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGTG	CCAGTG	AA	novel	NA	P-0016141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	80	328	1	ENST00000261769.5:c.1285_1290delinsAA	p.Pro429LysfsTer7	p.P429Kfs*7	ENST00000261769	NM_004360.3	429	CCAGTG/AA	9/16	0.220906976222135	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.220906976222135	1		329	537	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880188	37880188	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	71	272	0	ENST00000269571.5:c.2232G>T	p.Glu744Asp	p.E744D	ENST00000269571		744	gaG/gaT	19/27	0.220906976222135	13	FACETS	1	0.965	1			1	CLONAL	1	TRUE	NA	0.220906976222135	13		272	1064	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748145	43748145	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	57	366	0	ENST00000382044.4:c.2661G>C	p.Gln887His	p.Q887H	ENST00000382044	NM_001141980.1	887	caG/caC	12/28	1	2	FACETS	0.727	0.623	0.841	0.727	0.623	0.841	SUBCLONAL	1	TRUE	1	0.220906976222135	2		366	710	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748354	43748354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	59	546	0	ENST00000382044.4:c.2452G>A	p.Glu818Lys	p.E818K	ENST00000382044	NM_001141980.1	818	Gaa/Aaa	12/28	1	2	FACETS	0.606	0.52	0.701	0.606	0.52	0.701	SUBCLONAL	1	TRUE	1	0.220906976222135	2		546	881	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748504	43748504	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	80	502	0	ENST00000382044.4:c.2302G>C	p.Glu768Gln	p.E768Q	ENST00000382044	NM_001141980.1	768	Gag/Cag	12/28	1	2	FACETS	0.888	0.78	1	0.888	0.78	1	CLONAL	1	TRUE	1	0.220906976222135	2		502	816	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748582	43748582	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	81	574	0	ENST00000382044.4:c.2224G>C	p.Glu742Gln	p.E742Q	ENST00000382044	NM_001141980.1	742	Gaa/Caa	12/28	1	2	FACETS	0.772	0.679	0.873	0.772	0.679	0.873	SUBCLONAL	1	TRUE	1	0.220906976222135	2		574	950	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109311984	109311984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	25	318	1	ENST00000436639.2:c.1288G>A	p.Val430Met	p.V430M	ENST00000436639	NM_014454.2	430	Gtg/Atg	8/10	0.162552749011076	1	FACETS	0.408	0.321	0.509	0.408	0.321	0.509	SUBCLONAL	1	TRUE	0	0.220906976222135	1		319	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520006	NA	P-0016531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	129	641	0	ENST00000269305.4:c.821T>G	p.Val274Gly	p.V274G	ENST00000269305	NM_001126112.2	274	gTt/gGt	8/11	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.265411534588102	2		641	957	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855019	76855019	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	98	230	0	ENST00000373344.5:c.5817del	p.Asp1940IlefsTer15	p.D1940Ifs*15	ENST00000373344	NM_000489.3	1939	aaA/aa	25/35	1	1	FACETS	0.995	0.897	1	1	0.988	1	CLONAL	2	TRUE	0	0.265411534588102	1		230	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	128	606	0	ENST00000269305.4:c.814del	p.Val272CysfsTer73	p.V272Cfs*73	ENST00000269305	NM_001126112.2	272	Gtg/tg	8/11	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.265411534588102	2		606	933	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245963	16245963	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	164	360	0	ENST00000375759.3:c.1586C>G	p.Ser529Ter	p.S529*	ENST00000375759	NM_015001.2	529	tCa/tGa	8/15	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.597805035062461	2		360	546	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059264	27059264	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	144	393	0	ENST00000324856.7:c.1901C>G	p.Ser634Ter	p.S634*	ENST00000324856	NM_006015.4	634	tCa/tGa	4/20	1	2	FACETS	0.831	0.761	0.903	0.831	0.761	0.903	CLONAL	1	TRUE	1	0.597805035062461	2		393	580	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608306	43608306	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	271	751	1	ENST00000355710.3:c.1654A>T	p.Thr552Ser	p.T552S	ENST00000355710	NM_020975.4	552	Acc/Tcc	9/20	0.450069770330877	3	FACETS	1	0.948	1			1	CLONAL	1	TRUE	NA	0.597805035062461	3		752	1163	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77048425	77048425	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	344	495	1	ENST00000356341.3:c.1160A>T	p.His387Leu	p.H387L	ENST00000356341	NM_002576.4	387	cAc/cTc	12/15	0.597805035062461	3	FACETS	0.956	0.91	1	0.956	0.91	1	CLONAL	2	TRUE	1	0.597805035062461	3		496	782	SUCCESS
ATM	472	MSKCC	GRCh37	11	108128305	108128305	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	263	357	2	ENST00000278616.4:c.2348G>T	p.Cys783Phe	p.C783F	ENST00000278616	NM_000051.3	783	tGt/tTt	15/63	0.597805035062461	3	FACETS	0.994	0.94	1	0.994	0.94	1	CLONAL	2	TRUE	1	0.597805035062461	3		359	575	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343622	118343622	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	188	386	0	ENST00000534358.1:c.1748C>G	p.Pro583Arg	p.P583R	ENST00000534358	NM_005933.3	583	cCt/cGt	3/36	NA	2	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.597805035062461	2		386	561	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222581	69222581	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs576062594	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	128	341	0	ENST00000462284.1:c.554G>A	p.Arg185Gln	p.R185Q	ENST00000462284	NM_002392.5	185	cGa/cAa	8/11	0.597805035062461	3	FACETS	0.984	0.896	1	0.492	0.448	0.539	CLONAL	1	TRUE	1	0.597805035062461	3		341	565	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114164	115114165	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	403	547	0	ENST00000257566.3:c.1052dup	p.Ala352GlyfsTer23	p.A352Gfs*23	ENST00000257566	NM_016569.3	351	cag/caAg	6/8	0.597805035062461	2	FACETS	0.956	0.919	0.993	0.956	0.919	0.993	CLONAL	2	TRUE	0	0.597805035062461	2		547	705	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118888	115118888	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	243	337	1	ENST00000257566.3:c.453A>T	p.Leu151Phe	p.L151F	ENST00000257566	NM_016569.3	151	ttA/ttT	2/8	0.597805035062461	2	FACETS	0.909	0.862	0.956	0.909	0.862	0.956	CLONAL	2	TRUE	0	0.597805035062461	2		338	447	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029110	14029110	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747564755	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	79	180	0	ENST00000311895.7:c.1321G>C	p.Glu441Gln	p.E441Q	ENST00000311895	NM_005236.2	441	Gag/Cag	8/11	0.597805035062461	3	FACETS	0.954	0.845	1	0.477	0.422	0.535	CLONAL	1	TRUE	1	0.597805035062461	3		180	360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579460	7579461	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	374	581	0	ENST00000269305.4:c.226dup	p.Ala76GlyfsTer73	p.A76Gfs*73	ENST00000269305	NM_001126112.2	76	gca/gGca	4/11	0.597805035062461	2	FACETS	0.927	0.889	0.965	0.927	0.889	0.965	CLONAL	2	TRUE	0	0.597805035062461	2		581	675	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548939	29548939	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	63	302	0	ENST00000356175.3:c.1713G>T	p.Trp571Cys	p.W571C	ENST00000356175	NM_000267.3	571	tgG/tgT	15/57	0.254969349660323	5	FACETS	0.77	0.667	0.882			1	INDETERMINATE	1	TRUE	NA	0.597805035062461	5		302	519	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33446558	33446558	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	310	486	0	ENST00000345365.6:c.75C>G	p.Ile25Met	p.I25M	ENST00000345365	NM_002878.3	25	atC/atG	1/10	0.254969349660323	5	FACETS	1	0.979	1			1	INDETERMINATE	2	TRUE	NA	0.597805035062461	5		486	918	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853919	59853919	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	204	265	0	ENST00000259008.2:c.1940G>T	p.Trp647Leu	p.W647L	ENST00000259008	NM_032043.2	647	tGg/tTg	14/20	0.597805035062461	4	FACETS	0.972	0.908	1	0.972	0.908	1	CLONAL	2	TRUE	2	0.597805035062461	4		265	561	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39618809	39618809	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	99	153	0	ENST00000262039.4:c.2033A>T	p.Lys678Ile	p.K678I	ENST00000262039	NM_002647.2	678	aAa/aTa	18/25	0.597805035062461	2	FACETS	0.82	0.75	0.89	0.82	0.75	0.89	CLONAL	2	TRUE	0	0.597805035062461	2		153	202	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117152	7117152	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	442	581	0	ENST00000302850.5:c.4064A>T	p.Tyr1355Phe	p.Y1355F	ENST00000302850	NM_000208.2	1355	tAc/tTc	22/22	0.597805035062461	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.597805035062461	2		581	707	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291782	15291782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs940948912	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	663	645	0	ENST00000263388.2:c.2984C>T	p.Pro995Leu	p.P995L	ENST00000263388	NM_000435.2	995	cCg/cTg	18/33	0.450069770330877	3	FACETS	1	0.986	1			1	CLONAL	3	TRUE	NA	0.597805035062461	3		645	944	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223707	36223707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1468457510	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	251	722	2	ENST00000222270.7:c.6257C>T	p.Ser2086Leu	p.S2086L	ENST00000222270	NM_014727.1	2086	tCg/tTg	28/37	0.521515022990037	4	FACETS	1	0.965	1	0.525	0.49	0.561	CLONAL	1	TRUE	2	0.597805035062461	4		724	1279	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873491	45873491	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	253	340	0	ENST00000391945.4:c.6-1G>T		p.X2_splice	ENST00000391945	NM_000400.3	2			0.521515022990037	4	FACETS	0.925	0.87	0.981	0.925	0.87	0.981	CLONAL	2	TRUE	2	0.597805035062461	4		340	731	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902125	50902125	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs778275831	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	256	365	0	ENST00000440232.2:c.17G>C	p.Arg6Pro	p.R6P	ENST00000440232	NM_002691.3	6	cGg/cCg	2/27	0.521515022990037	4	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	2	0.597805035062461	4		365	683	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61708370	61708370	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	80	247	0	ENST00000401558.2:c.3019G>C	p.Asp1007His	p.D1007H	ENST00000401558	NM_003400.3	1007	Gat/Cat	24/25	0.597805035062461	3	FACETS	0.832	0.736	0.934	0.416	0.368	0.467	CLONAL	1	TRUE	1	0.597805035062461	3		247	418	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30090752	30090752	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	215	521	0	ENST00000338641.4:c.1749G>C	p.Gln583His	p.Q583H	ENST00000338641	NM_000268.3	583	caG/caC	16/16	0.597805035062461	2	FACETS	0.985	0.919	1	0.493	0.459	0.527	CLONAL	1	TRUE	0	0.597805035062461	2		521	730	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021828	71021828	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	59	169	0	ENST00000318789.4:c.1531-1G>C		p.X511_splice	ENST00000318789	NM_032682.5	511			1	2	FACETS	0.949	0.829	1	0.949	0.829	1	CLONAL	1	TRUE	1	0.597805035062461	2		169	208	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448551	89448551	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	284	422	0	ENST00000336596.2:c.1515C>A	p.Tyr505Ter	p.Y505*	ENST00000336596	NM_005233.5	505	taC/taA	7/17	1	2	FACETS	0.968	0.923	1	1	0.996	1	CLONAL	2	TRUE	1	0.597805035062461	2		422	491	SUCCESS
ATR	545	MSKCC	GRCh37	3	142241639	142241639	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	162	411	0	ENST00000350721.4:c.4197G>T	p.Glu1399Asp	p.E1399D	ENST00000350721	NM_001184.3	1399	gaG/gaT	23/47	1	2	FACETS	0.953	0.879	1	0.953	0.879	1	CLONAL	1	TRUE	1	0.597805035062461	2		411	569	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505015	186505015	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	120	317	0	ENST00000323963.5:c.871G>C	p.Glu291Gln	p.E291Q	ENST00000323963		291	Gag/Cag	8/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.597805035062461	2		317	377	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564654	55564654	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	316	423	2	ENST00000288135.5:c.542G>T	p.Arg181Leu	p.R181L	ENST00000288135	NM_000222.2	181	cGg/cTg	3/21	0.597805035062461	2	FACETS	0.949	0.907	0.991	0.949	0.907	0.991	CLONAL	2	TRUE	0	0.597805035062461	2		425	557	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391396	84391396	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	242	599	0	ENST00000321945.7:c.436A>T	p.Thr146Ser	p.T146S	ENST00000321945	NM_139076.2	146	Act/Tct	5/9	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.597805035062461	2		599	771	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067001	143067001	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	86	321	1	ENST00000262992.4:c.1712A>T	p.His571Leu	p.H571L	ENST00000262992	NM_001101669.1	571	cAc/cTc	16/24	1	2	FACETS	0.73	0.65	0.815	0.73	0.65	0.815	SUBCLONAL	1	TRUE	1	0.597805035062461	2		322	394	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247384	153247384	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	83	131	0	ENST00000281708.4:c.1419-1G>C		p.X473_splice	ENST00000281708	NM_033632.3	473			1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.597805035062461	2		131	242	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120423	94120423	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	104	274	0	ENST00000369303.4:c.628G>C	p.Glu210Gln	p.E210Q	ENST00000369303	NM_004440.3	210	Gag/Cag	3/17	0.597805035062461	2	FACETS	1	0.915	1	0.506	0.457	0.556	CLONAL	1	TRUE	0	0.597805035062461	2		274	344	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710566	117710566	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	178	166	0	ENST00000368508.3:c.1706G>T	p.Gly569Val	p.G569V	ENST00000368508	NM_002944.2	569	gGc/gTc	12/43	0.597805035062461	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.597805035062461	2		166	278	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971292	13971292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772105404	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	116	379	0	ENST00000405192.2:c.637C>T	p.Arg213Cys	p.R213C	ENST00000405192	NM_001163147.1	213	Cgc/Tgc	8/12	0.466540222202893	4	FACETS	0.864	0.779	0.953	0.288	0.259	0.318	CLONAL	1	TRUE	1	0.597805035062461	4		379	718	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397789	116397789	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	148	522	0	ENST00000397752.3:c.2063G>C	p.Arg688Thr	p.R688T	ENST00000397752	NM_000245.2	688	aGa/aCa	8/21	0.466540222202893	4	FACETS	0.914	0.834	0.996	0.305	0.278	0.332	CLONAL	1	TRUE	1	0.597805035062461	4		522	866	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860359	151860359	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	190	393	0	ENST00000262189.6:c.10303G>T	p.Gly3435Cys	p.G3435C	ENST00000262189	NM_170606.2	3435	Ggt/Tgt	43/59	0.466540222202893	4	FACETS	1	0.983	1	0.404	0.374	0.436	CLONAL	1	TRUE	1	0.597805035062461	4		393	837	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874275	151874275	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	344	413	0	ENST00000262189.6:c.8263G>C	p.Asp2755His	p.D2755H	ENST00000262189	NM_170606.2	2755	Gat/Cat	38/59	0.466540222202893	4	FACETS	0.871	0.831	0.911	0.871	0.831	0.911	CLONAL	3	TRUE	1	0.597805035062461	4		413	704	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38135901	38135901	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	117	390	0	ENST00000317025.8:c.3790G>C	p.Asp1264His	p.D1264H	ENST00000317025	NM_023034.1	1264	Gat/Cat	22/24	0.597805035062461	2	FACETS	0.826	0.749	0.906	0.413	0.374	0.453	CLONAL	1	TRUE	0	0.597805035062461	2		390	474	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136857	69136857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	251	245	0	ENST00000288368.4:c.4771C>T	p.Pro1591Ser	p.P1591S	ENST00000288368	NM_024870.2	1591	Cca/Tca	39/40	0.597805035062461	6	FACETS	0.91	0.857	0.965	0.683	0.642	0.724	CLONAL	3	TRUE	2	0.597805035062461	6		245	675	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402515	139402515	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs758304923	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	239	668	0	ENST00000277541.6:c.3402G>T	p.Gln1134His	p.Q1134H	ENST00000277541	NM_017617.3	1134	caG/caT	21/34	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.597805035062461	2		668	776	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040650	47040650	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	202	274	0	ENST00000377604.3:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000377604	NM_001204468.1	429	Gag/Tag	13/24	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.597805035062461	1		274	325	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76764050	76764050	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	245	348	0	ENST00000373344.5:c.7258C>G	p.Gln2420Glu	p.Q2420E	ENST00000373344	NM_000489.3	2420	Cag/Gag	35/35	0.277369941341593	3	FACETS	0.798	0.75	0.847			1	INDETERMINATE	2	TRUE	NA	0.597805035062461	3		348	667	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937038	76937038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1557136793	NA	P-0017158-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	187	263	0	ENST00000373344.5:c.3710C>T	p.Ser1237Leu	p.S1237L	ENST00000373344	NM_000489.3	1237	tCa/tTa	9/35	0.277369941341593	3	FACETS	0.852	0.795	0.91			1	INDETERMINATE	2	TRUE	NA	0.597805035062461	3		263	477	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0018196-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	173	404	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.266288299677023	2	FACETS	0.765	0.705	0.828	0.765	0.705	0.828	SUBCLONAL	2	TRUE	0	0.273603486093364	2		404	826	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0018196-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	218	352	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.170225467750352	2	FACETS	0.791	0.736	0.849	0.791	0.736	0.849	SUBCLONAL	2	TRUE	0	0.273603486093364	2		353	1007	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732960	30732960	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018196-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	44	231	0	ENST00000295754.5:c.1573C>A	p.Pro525Thr	p.P525T	ENST00000295754	NM_003242.5	525	Cca/Aca	7/7	0.207250775434707	2	FACETS	0.816	0.686	0.96	0.408	0.343	0.48	CLONAL	1	TRUE	0	0.273603486093364	2		231	394	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056406	26056406	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018196-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	26	210	0	ENST00000343677.2:c.251T>C	p.Leu84Pro	p.L84P	ENST00000343677	NM_005319.3	84	cTc/cCc	1/1	1	2	FACETS	0.51	0.403	0.631	0.51	0.403	0.631	SUBCLONAL	1	TRUE	1	0.273603486093364	2		210	373	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483931	212483931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018196-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	47	403	0	ENST00000342788.4:c.2272G>A	p.Gly758Ser	p.G758S	ENST00000342788	NM_005235.2	758	Ggt/Agt	19/28	1	2	FACETS	0.579	0.488	0.68	0.579	0.488	0.68	SUBCLONAL	1	TRUE	1	0.273603486093364	2		403	593	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664738	138664738	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018196-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	53	256	2	ENST00000330315.3:c.827G>A	p.Gly276Asp	p.G276D	ENST00000330315	NM_023067.3	276	gGc/gAc	1/1	0.230365038116791	3	FACETS	0.854	0.728	0.991	0.285	0.242	0.331	CLONAL	1	TRUE	0	0.273603486093364	3		258	516	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0018288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	155	259	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.65496169076615	1	FACETS	0.989	0.921	1	0.989	0.921	1	CLONAL	1	TRUE	0	0.65496169076615	1		259	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578376	7578379	+	frameshift_variant	Frame_Shift_Del	DEL	CTAT	CTAT	-	novel	NA	P-0018288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	186	397	0	ENST00000269305.4:c.551_554del	p.Asp184AlafsTer62	p.D184Afs*62	ENST00000269305	NM_001126112.2	184	gATAGc/gc	5/11	0.65496169076615	1	FACETS	0.939	0.879	0.999	0.939	0.879	0.999	CLONAL	1	TRUE	0	0.65496169076615	1		397	407	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833957	44833957	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	272	351	0	ENST00000377967.4:c.381G>A	p.Trp127Ter	p.W127*	ENST00000377967	NM_021140.2	127	tgG/tgA	4/29	1	2	FACETS	0.997	0.939	1	0.997	0.939	1	CLONAL	1	TRUE	1	0.65496169076615	2		351	833	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094386	27094386	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	219	295	1	ENST00000324856.7:c.3094G>T	p.Glu1032Ter	p.E1032*	ENST00000324856	NM_006015.4	1032	Gag/Tag	11/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.65496169076615	2		296	609	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754574	42754574	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768322408	NA	P-0018288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	318	527	0	ENST00000222329.4:c.166G>A	p.Val56Ile	p.V56I	ENST00000222329	NM_006494.2	56	Gtc/Atc	2/4	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.65496169076615	2		527	918	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149506162	149506162	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	149	280	0	ENST00000261799.4:c.1595T>C	p.Val532Ala	p.V532A	ENST00000261799	NM_002609.3	532	gTg/gCg	11/23	1	2	FACETS	0.841	0.773	0.912	0.841	0.773	0.912	CLONAL	1	TRUE	1	0.65496169076615	2		280	541	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68982089	68982089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376775544	NA	P-0018288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	226	446	1	ENST00000288368.4:c.1463G>A	p.Arg488His	p.R488H	ENST00000288368	NM_024870.2	488	cGt/cAt	13/40	0.65496169076615	3	FACETS	0.797	0.742	0.855	0.399	0.371	0.428	SUBCLONAL	1	TRUE	1	0.65496169076615	3		447	1149	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65349159	65349159	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0018288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	185	303	0	ENST00000342505.4:c.7-1G>C		p.X3_splice	ENST00000342505	NM_002227.2	3			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.65496169076615	2		303	541	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0018546-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1365	81	753	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.214867673450047	7	FACETS	0.801	0.703	0.908	0.2	0.175	0.227	CLONAL	1	TRUE	3	0.214867673450047	7		753	1446	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	364607	364607	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018546-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	64	694	0	ENST00000262320.3:c.955A>C	p.Asn319His	p.N319H	ENST00000262320	NM_003502.3	319	Aac/Cac	3/11	1	2	FACETS	0.482	0.415	0.554	0.482	0.415	0.554	SUBCLONAL	1	TRUE	1	0.214867673450047	2		694	1237	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0018681-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	77	545	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.2537201979791	2		545	580	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0018681-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	239	714	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.2537201979791	8	FACETS	1	0.987	1	0.494	0.46	0.53	CLONAL	2	TRUE	3	0.2537201979791	8		714	1342	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0018681-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	207	502	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.2537201979791	8	FACETS	0.892	0.83	0.957	0.714	0.664	0.766	CLONAL	4	TRUE	3	0.2537201979791	8		502	805	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0018681-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	32	319	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.245652095570802	3	FACETS	0.656	0.533	0.797	0.328	0.266	0.399	SUBCLONAL	1	TRUE	1	0.2537201979791	3		319	433	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958195	2958195	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018681-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1504	114	618	0	ENST00000396946.4:c.2537T>G	p.Leu846Arg	p.L846R	ENST00000396946	NM_032415.4	846	cTg/cGg	19/25	0.2537201979791	10	FACETS	1	0.955	1	0.16	0.143	0.178	CLONAL	1	TRUE	3	0.2537201979791	10		618	1618	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611083	100611083	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018681-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	113	701	0	ENST00000308731.7:c.1523C>A	p.Ala508Asp	p.A508D	ENST00000308731	NM_000061.2	508	gCc/gAc	15/19	0.245652095570802	3	FACETS	1	0.932	1	0.524	0.471	0.58	CLONAL	1	TRUE	1	0.2537201979791	3		701	958	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256190	16256190	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018681-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	87	557	1	ENST00000375759.3:c.3455C>T	p.Ser1152Leu	p.S1152L	ENST00000375759	NM_015001.2	1152	tCa/tTa	11/15	0.232299368342757	4	FACETS	0.994	0.879	1	0.331	0.293	0.373	CLONAL	1	TRUE	1	0.2537201979791	4		558	865	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0019459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	171	785	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	1	2	FACETS	0.695	0.639	0.752	0.695	0.639	0.752	SUBCLONAL	1	TRUE	1	0.582636589114462	2		785	845	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0019459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	149	406	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.899	0.825	0.975	0.899	0.825	0.975	CLONAL	1	TRUE	1	0.582636589114462	2		406	569	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241722	55241722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1051753269	NA	P-0019459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	198	637	2	ENST00000275493.2:c.2170G>A	p.Gly724Ser	p.G724S	ENST00000275493	NM_005228.3	724	Ggc/Agc	18/28	1	2	FACETS	0.802	0.744	0.863	0.802	0.744	0.863	CLONAL	1	TRUE	1	0.582636589114462	2		639	847	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366883	40366883	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	284	814	0	ENST00000397332.2:c.314C>A	p.Ser105Tyr	p.S105Y	ENST00000397332	NM_001033082.2	105	tCc/tAc	2/3	1	2	FACETS	0.87	0.817	0.923	0.87	0.817	0.923	CLONAL	1	TRUE	1	0.582636589114462	2		814	1121	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357753	70357753	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	294	539	0	ENST00000374080.3:c.6004C>T	p.Gln2002Ter	p.Q2002*	ENST00000374080		2002	Cag/Tag	41/45	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.582636589114462	1		539	531	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0019595-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	25	395	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.460786944788561	2		396	95	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0019595-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	52	120	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	NA	2	FACETS	0.885	0.793	0.974			1	INDETERMINATE	3	TRUE	NA	0.460786944788561	2		120	85	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42790991	42790992	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCAG	novel	NA	P-0019595-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	16	99	0	ENST00000575354.2:c.143_146dup	p.Asp50AlafsTer2	p.D50Afs*2	ENST00000575354	NM_015125.3	46	ccc/cCCAGcc	2/20	0.460786944788561	0	FACETS	0.913	0.71	1			1	CLONAL	1	TRUE	0	0.460786944788561	0		99	41	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820859	36820859	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	169	580	1	ENST00000373129.3:c.518A>T	p.Glu173Val	p.E173V	ENST00000373129	NM_032017.1	173	gAg/gTg	6/12	0.258367656769442	2	FACETS	1	0.987	1	0.679	0.626	0.733	CLONAL	1	TRUE	0	0.372133563495027	2		581	669	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880464	155880465	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0019687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	189	654	1	ENST00000368323.3:c.88_89delinsTT	p.Gly30Phe	p.G30F	ENST00000368323	NM_006912.5	30	GGt/TTt	2/6	0.300282397627673	2	FACETS	0.781	0.725	0.839	0.781	0.725	0.839	SUBCLONAL	2	TRUE	0	0.372133563495027	2		655	650	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097629	8097630	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0019687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	44	225	0	ENST00000346208.3:c.13dup	p.Ala5GlyfsTer48	p.A5Gfs*48	ENST00000346208		4	acg/acGg	2/6	0.302546368480973	4	FACETS	0.917	0.771	1			1	CLONAL	1	TRUE	NA	0.372133563495027	4		225	354	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865192	57865192	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	335	984	0	ENST00000228682.2:c.2669C>A	p.Thr890Lys	p.T890K	ENST00000228682	NM_005269.2	890	aCa/aAa	12/12	0.316818297398562	2	FACETS	0.781	0.738	0.824	0.781	0.738	0.824	SUBCLONAL	2	TRUE	0	0.372133563495027	2		984	1153	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120848	115120848	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	106	407	1	ENST00000257566.3:c.158C>A	p.Ala53Glu	p.A53E	ENST00000257566	NM_016569.3	53	gCg/gAg	1/8	0.316818297398562	2	FACETS	1	0.984	1	0.746	0.674	0.82	CLONAL	1	TRUE	0	0.372133563495027	2		408	382	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220533	133220533	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	211	689	0	ENST00000320574.5:c.4180G>C	p.Val1394Leu	p.V1394L	ENST00000320574	NM_006231.2	1394	Gtc/Ctc	33/49	0.316818297398562	2	FACETS	0.797	0.743	0.853	0.797	0.743	0.853	SUBCLONAL	2	TRUE	0	0.372133563495027	2		689	711	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347843	73347844	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0019687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	93	355	0	ENST00000377767.4:c.1217_1218delinsTT	p.Pro406Leu	p.P406L	ENST00000377767	NM_014953.3	406	cCC/cTT	8/21	0.300282397627673	2	FACETS	1	0.981	1	0.731	0.656	0.809	CLONAL	1	TRUE	0	0.372133563495027	2		355	342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577035	7577038	+	frameshift_variant	Frame_Shift_Del	DEL	TGGG	TGGG	CC	novel	NA	P-0019687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	134	775	2	ENST00000269305.4:c.900_903delinsGG	p.Pro301GlyfsTer4	p.P301Gfs*4	ENST00000269305	NM_001126112.2	300	ccCCCA/ccGG	8/11	0.307027073377585	1	FACETS	0.846	0.77	0.925	0.846	0.77	0.925	CLONAL	1	TRUE	0	0.372133563495027	1		777	693	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657375	29657375	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs878853904	NA	P-0019687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	213	871	2	ENST00000356175.3:c.5608C>T	p.Gln1870Ter	p.Q1870*	ENST00000356175	NM_000267.3	1870	Cag/Tag	38/57	0.130644809025804	5	FACETS	0.959	0.892	1	0.48	0.446	0.515	INDETERMINATE	2	TRUE	1	0.372133563495027	5		873	930	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600449	10600449	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs973016645	NA	P-0019687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	377	999	1	ENST00000171111.5:c.1406A>G	p.Asn469Ser	p.N469S	ENST00000171111	NM_203500.1	469	aAt/aGt	4/6	0.316818297398562	2	FACETS	0.867	0.823	0.911	0.867	0.823	0.911	CLONAL	2	TRUE	0	0.372133563495027	2		1000	1169	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976833	55976834	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0019687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	109	753	4	ENST00000263923.4:c.1078_1079delinsAA	p.Pro360Lys	p.P360K	ENST00000263923	NM_002253.2	360	CCa/AAa	8/30	1	2	FACETS	0.708	0.636	0.785	0.708	0.636	0.785	SUBCLONAL	1	TRUE	1	0.372133563495027	2		757	827	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264670	1264670	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1435	382	1142	0	ENST00000310581.5:c.2692G>T	p.Val898Leu	p.V898L	ENST00000310581	NM_198253.2	898	Gtg/Ttg	11/16	0.372133563495027	5	FACETS	0.88	0.833	0.929	0.587	0.555	0.619	CLONAL	2	TRUE	2	0.372133563495027	5		1142	1817	SUCCESS
APC	324	MSKCC	GRCh37	5	112174781	112174781	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	168	469	0	ENST00000257430.4:c.3490A>T	p.Ile1164Leu	p.I1164L	ENST00000257430	NM_000038.5	1164	Ata/Tta	16/16	0.300282397627673	2	FACETS	0.867	0.802	0.933	0.867	0.802	0.933	CLONAL	2	TRUE	0	0.372133563495027	2		469	521	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637367	176637367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs910345852	NA	P-0019687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	217	710	0	ENST00000439151.2:c.1967C>T	p.Ser656Leu	p.S656L	ENST00000439151	NM_022455.4	656	tCa/tTa	5/23	0.300282397627673	2	FACETS	0.793	0.74	0.848	0.793	0.74	0.848	SUBCLONAL	2	TRUE	0	0.372133563495027	2		710	735	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288513	33288513	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	121	388	0	ENST00000374542.5:c.1039G>T	p.Gly347Cys	p.G347C	ENST00000374542	NM_001141970.1	347	Ggc/Tgc	3/8	0.26954107545417	2	FACETS	1	0.985	1	0.727	0.662	0.796	CLONAL	1	TRUE	0	0.372133563495027	2		388	447	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492909	8492909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	315	643	0	ENST00000356435.5:c.2420G>T	p.Gly807Val	p.G807V	ENST00000356435		807	gGa/gTa	16/35	0.372133563495027	3	FACETS	1	0.987	1	0.755	0.715	0.796	CLONAL	2	TRUE	0	0.372133563495027	3		643	886	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528615	8528615	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	225	553	0	ENST00000356435.5:c.517G>T	p.Gly173Cys	p.G173C	ENST00000356435		173	Ggt/Tgt	4/35	0.372133563495027	3	FACETS	1	0.983	1	0.759	0.711	0.808	CLONAL	2	TRUE	0	0.372133563495027	3		553	630	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974690	21974690	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1554656241	NA	P-0019687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	339	531	0	ENST00000304494.5:c.137G>C	p.Arg46Pro	p.R46P	ENST00000304494	NM_000077.4	46	cGg/cCg	1/3	0.372133563495027	3	FACETS	0.988	0.941	1	0.988	0.941	1	CLONAL	3	TRUE	0	0.372133563495027	3		531	729	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0019687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	43	414	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.577	0.484	0.679	0.577	0.484	0.679	SUBCLONAL	1	TRUE	1	0.439553979905003	2		414	339	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147551	47147551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	62	285	0	ENST00000409792.3:c.4775G>A	p.Arg1592Gln	p.R1592Q	ENST00000409792	NM_014159.6	1592	cGa/cAa	6/21	1	2	FACETS	0.675	0.585	0.772	0.675	0.585	0.772	SUBCLONAL	1	TRUE	1	0.439553979905003	2		285	418	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226294	2226294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	150	766	1	ENST00000326181.6:c.1907C>T	p.Thr636Met	p.T636M	ENST00000326181	NM_032271.2	636	aCg/aTg	20/21	1	2	FACETS	0.715	0.653	0.781	0.715	0.653	0.781	SUBCLONAL	1	TRUE	1	0.439553979905003	2		767	954	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602584	10602584	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1208201314	NA	P-0019687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	270	614	0	ENST00000171111.5:c.994G>T	p.Gly332Cys	p.G332C	ENST00000171111	NM_203500.1	332	Ggc/Tgc	3/6	0.327084835448077	2	FACETS	1	0.992	1	0.674	0.633	0.715	CLONAL	1	TRUE	0	0.439553979905003	2		614	912	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222987	1222987	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	120	494	1	ENST00000326873.7:c.924G>T	p.Trp308Cys	p.W308C	ENST00000326873	NM_000455.4	308	tgG/tgT	8/10	0.331168752639805	1	FACETS	0.692	0.626	0.76	0.692	0.626	0.76	SUBCLONAL	1	TRUE	0	0.439553979905003	1		495	616	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729968	41729968	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	109	499	0	ENST00000242208.4:c.561C>A	p.Asp187Glu	p.D187E	ENST00000242208	NM_002192.2	187	gaC/gaA	3/3	0.224917894319425	0	FACETS	0.4	0.359	0.443			1	INDETERMINATE	1	TRUE	0	0.439553979905003	0		499	695	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900635	32900635	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs81002849	NA	P-0019687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	44	258	0	ENST00000380152.3:c.517-1G>T		p.X173_splice	ENST00000380152		173			0.414680845786639	0	FACETS	0.519	0.44	0.605			1	SUBCLONAL	1	TRUE	0	0.439553979905003	0		258	216	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624897	9624897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	37	402	0	ENST00000353224.5:c.80C>T	p.Pro27Leu	p.P27L	ENST00000353224	NM_177990.2	27	cCa/cTa	3/10	0.411264448792906	1	FACETS	0.354	0.292	0.423	0.354	0.292	0.423	SUBCLONAL	1	TRUE	0	0.439553979905003	1		402	371	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260210	16260210	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	82	443	0	ENST00000375759.3:c.7475A>T	p.Gln2492Leu	p.Q2492L	ENST00000375759	NM_015001.2	2492	cAg/cTg	11/15	0.297446480971377	1	FACETS	0.599	0.53	0.673	0.599	0.53	0.673	SUBCLONAL	1	TRUE	0	0.439553979905003	1		443	486	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004233	29004233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778277302	NA	P-0019687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	68	281	0	ENST00000282397.4:c.1060C>T	p.Arg354Trp	p.R354W	ENST00000282397	NM_002019.4	354	Cgg/Tgg	8/30	0.331168752639805	1	FACETS	0.63	0.551	0.715	0.63	0.551	0.715	SUBCLONAL	1	TRUE	0	0.439553979905003	1		281	383	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107930	30107930	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	101	348	0	ENST00000331968.5:c.877G>T	p.Gly293Trp	p.G293W	ENST00000331968	NM_002742.2	293	Ggg/Tgg	5/18	1	2	FACETS	0.887	0.796	0.983	0.887	0.796	0.983	CLONAL	1	TRUE	1	0.439553979905003	2		348	518	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133048	30133048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	61	286	0	ENST00000331968.5:c.553C>T	p.His185Tyr	p.H185Y	ENST00000331968	NM_002742.2	185	Cat/Tat	4/18	1	2	FACETS	0.648	0.561	0.743	0.648	0.561	0.743	SUBCLONAL	1	TRUE	1	0.439553979905003	2		286	428	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872484	35872484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771984394	NA	P-0019687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	117	466	0	ENST00000216797.5:c.419G>A	p.Arg140Gln	p.R140Q	ENST00000216797	NM_020529.2	140	cGa/cAa	3/6	1	2	FACETS	0.626	0.564	0.692	0.626	0.564	0.692	SUBCLONAL	1	TRUE	1	0.439553979905003	2		466	850	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684353	29684353	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	46	353	0	ENST00000356175.3:c.7873G>T	p.Ala2625Ser	p.A2625S	ENST00000356175	NM_000267.3	2625	Gcc/Tcc	53/57	1	2	FACETS	0.6	0.507	0.702	0.6	0.507	0.702	SUBCLONAL	1	TRUE	1	0.439553979905003	2		353	349	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40457721	40457721	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0019687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	91	411	0	ENST00000345506.4:c.1473+1G>T		p.X491_splice	ENST00000345506	NM_003152.3	491			1	2	FACETS	0.592	0.525	0.662	0.592	0.525	0.662	SUBCLONAL	1	TRUE	1	0.439553979905003	2		411	700	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40871178	40871178	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	94	396	0	ENST00000428826.2:c.712A>C	p.Ser238Arg	p.S238R	ENST00000428826		238	Agt/Cgt	8/21	1	2	FACETS	0.737	0.657	0.822	0.737	0.657	0.822	SUBCLONAL	1	TRUE	1	0.439553979905003	2		396	580	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897376	78897376	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	245	706	0	ENST00000306801.3:c.2711G>T	p.Gly904Val	p.G904V	ENST00000306801	NM_020761.2	904	gGc/gTc	23/34	0.439752697679794	3	FACETS	1	0.991	1	0.682	0.638	0.728	CLONAL	1	TRUE	1	0.439553979905003	3		706	997	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573474	48573474	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1568202971	NA	P-0019687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	31	192	0	ENST00000342988.3:c.58G>T	p.Val20Leu	p.V20L	ENST00000342988	NM_005359.5	20	Gtg/Ttg	2/12	0.331168752639805	1	FACETS	0.701	0.574	0.84	0.701	0.574	0.84	SUBCLONAL	1	TRUE	0	0.439553979905003	1		192	157	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113759	11113759	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	302	599	0	ENST00000358026.2:c.1867G>T	p.Glu623Ter	p.E623*	ENST00000358026	NM_001128849.1	623	Gag/Tag	12/36	0.327084835448077	2	FACETS	0.776	0.734	0.82	0.776	0.734	0.82	SUBCLONAL	2	TRUE	0	0.439553979905003	2		599	885	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905539	50905539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	161	782	0	ENST00000440232.2:c.667G>T	p.Ala223Ser	p.A223S	ENST00000440232	NM_002691.3	223	Gcc/Tcc	6/27	1	2	FACETS	0.83	0.761	0.901	0.83	0.761	0.901	CLONAL	1	TRUE	1	0.439553979905003	2		782	883	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872801	136872801	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1419294193	NA	P-0019687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	81	317	0	ENST00000241393.3:c.697C>A	p.Gln233Lys	p.Q233K	ENST00000241393	NM_003467.2	233	Cag/Aag	2/2	1	2	FACETS	0.642	0.566	0.723	0.642	0.566	0.723	SUBCLONAL	1	TRUE	1	0.439553979905003	2		317	574	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728630	190728630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770849733	NA	P-0019687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	67	303	0	ENST00000441310.2:c.2018C>T	p.Ser673Phe	p.S673F	ENST00000441310	NM_000534.4	673	tCt/tTt	10/13	1	2	FACETS	0.847	0.74	0.961	0.847	0.74	0.961	CLONAL	1	TRUE	1	0.439553979905003	2		303	360	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059226	47059226	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	50	250	0	ENST00000409792.3:c.7435T>A	p.Ser2479Thr	p.S2479T	ENST00000409792	NM_014159.6	2479	Tcc/Acc	20/21	1	2	FACETS	0.594	0.505	0.691	0.594	0.505	0.691	SUBCLONAL	1	TRUE	1	0.439553979905003	2		250	383	SUCCESS
ATR	545	MSKCC	GRCh37	3	142234270	142234270	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	54	272	0	ENST00000350721.4:c.4470G>T	p.Trp1490Cys	p.W1490C	ENST00000350721	NM_001184.3	1490	tgG/tgT	25/47	1	2	FACETS	0.662	0.568	0.765	0.662	0.568	0.765	SUBCLONAL	1	TRUE	1	0.439553979905003	2		272	371	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584686	187584686	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	94	404	0	ENST00000441802.2:c.3347T>C	p.Val1116Ala	p.V1116A	ENST00000441802	NM_005245.3	1116	gTc/gCc	3/27	1	2	FACETS	0.845	0.755	0.941	0.845	0.755	0.941	CLONAL	1	TRUE	1	0.439553979905003	2		404	506	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189003	32189003	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	151	645	0	ENST00000375023.3:c.551C>G	p.Pro184Arg	p.P184R	ENST00000375023	NM_004557.3	184	cCg/cGg	4/30	1	2	FACETS	0.771	0.705	0.84	0.771	0.705	0.84	SUBCLONAL	1	TRUE	1	0.439553979905003	2		645	891	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273447	38273447	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	153	754	0	ENST00000425967.3:c.1888G>T	p.Asp630Tyr	p.D630Y	ENST00000425967	NM_001174067.1	630	Gac/Tac	14/19	NA	2	FACETS	0.861	0.788	0.936			1	INDETERMINATE	1	TRUE	NA	0.439553979905003	2		754	809	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636752	8636752	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	62	282	0	ENST00000356435.5:c.157C>A	p.Pro53Thr	p.P53T	ENST00000356435		53	Cct/Act	2/35	0.387207682354502	1	FACETS	0.657	0.571	0.749	0.657	0.571	0.749	SUBCLONAL	1	TRUE	0	0.439553979905003	1		282	335	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137326013	137326014	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0019687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	132	873	1	ENST00000481739.1:c.1201_1202delinsTT	p.Glu401Leu	p.E401L	ENST00000481739	NM_002957.4	401	GAg/TTg	9/10	0.439752697679794	3	FACETS	0.622	0.564	0.685	0.311	0.282	0.343	SUBCLONAL	1	TRUE	1	0.439553979905003	3		874	1177	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941979	44941979	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	55	222	0	ENST00000377967.4:c.3229G>C	p.Gly1077Arg	p.G1077R	ENST00000377967	NM_021140.2	1077	Gga/Cga	22/29	0.266970746492833	1	FACETS	0.618	0.532	0.711	0.618	0.532	0.711	SUBCLONAL	1	TRUE	0	0.439553979905003	1		222	316	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223000	53223000	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	60	731	1	ENST00000375401.3:c.4072A>G	p.Thr1358Ala	p.T1358A	ENST00000375401	NM_004187.3	1358	Acc/Gcc	24/26	0.266970746492833	1	FACETS	0.268	0.23	0.31	0.268	0.23	0.31	SUBCLONAL	1	TRUE	0	0.439553979905003	1		732	794	SUCCESS
AR	367	MSKCC	GRCh37	X	66943605	66943605	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	107	472	0	ENST00000374690.3:c.2685G>T	p.Met895Ile	p.M895I	ENST00000374690	NM_000044.3	895	atG/atT	8/8	0.266970746492833	1	FACETS	0.714	0.643	0.789	0.714	0.643	0.789	SUBCLONAL	1	TRUE	0	0.439553979905003	1		472	532	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0020051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	59	405	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		405	431	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138384011	138384011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759151757	NA	P-0020051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	107	725	2	ENST00000289153.2:c.2539C>T	p.Arg847Cys	p.R847C	ENST00000289153	NM_006219.2	847	Cgc/Tgc	18/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		727	613	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206777	36206777	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	59	791	0	ENST00000300305.3:c.735del	p.Thr246ArgfsTer8	p.T246Rfs*8	ENST00000300305		245	ccC/cc	6/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		791	645	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771340	68771341	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0020051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	41	372	0	ENST00000261769.5:c.25_26del	p.Ser9GlyfsTer24	p.S9Gfs*24	ENST00000261769	NM_004360.3	8	CTc/c	1/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		372	269	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913355	NA	P-0020343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	49	586	0	ENST00000288602.6:c.1406G>T	p.Gly469Val	p.G469V	ENST00000288602	NM_004333.4	469	gGa/gTa	11/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		586	174	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981775	201981776	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	212	982	0	ENST00000359651.3:c.487dup	p.Ser163LysfsTer33	p.S163Kfs*33	ENST00000359651		162	-/A	4/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		982	562	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948712	71948712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374001069	NA	P-0020343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	106	856	0	ENST00000298229.2:c.3424C>T	p.Arg1142Cys	p.R1142C	ENST00000298229	NM_001567.3	1142	Cgc/Tgc	26/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		856	264	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579360	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTTC	novel	NA	P-0020343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	79	850	0	ENST00000269305.4:c.327_328insGAAA	p.Arg110GlufsTer40	p.R110Efs*40	ENST00000269305	NM_001126112.2	109	-/GAAA	4/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		850	196	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0020971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	249	810	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.519281694967604	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.519281694967604	1		810	650	SUCCESS
APC	324	MSKCC	GRCh37	5	112128170	112128170	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	210	719	0	ENST00000257430.4:c.673G>T	p.Glu225Ter	p.E225*	ENST00000257430	NM_000038.5	225	Gaa/Taa	7/16	0.469632945894989	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.519281694967604	1		719	553	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927984	178927984	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	190	472	0	ENST00000263967.3:c.1262C>G	p.Pro421Arg	p.P421R	ENST00000263967	NM_006218.2	421	cCa/cGa	8/21	0.47416263283205	2	FACETS	0.901	0.845	0.958	0.901	0.845	0.958	CLONAL	2	TRUE	0	0.519281694967604	2		472	406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0021007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	66	721	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.715	0.619	0.819	0.715	0.619	0.819	SUBCLONAL	1	TRUE	1	0.224451272812436	2		723	823	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0021007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	35	548	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.533	0.436	0.643	0.533	0.436	0.643	SUBCLONAL	1	TRUE	1	0.224451272812436	2		548	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0021445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	125	742	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.323720647145937	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.351141122071455	2		742	329	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233286	69233288	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	rs1434404181	NA	P-0021445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	17	332	0	ENST00000462284.1:c.1156_1158del	p.Asp386del	p.D386del	ENST00000462284	NM_002392.5	384	aATGat/aat	11/11	0.351141122071455	2	FACETS	0.968	0.734	1	0.484	0.367	0.619	CLONAL	1	TRUE	0	0.351141122071455	2		332	100	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871751	35871751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	28	547	0	ENST00000216797.5:c.755C>T	p.Ser252Phe	p.S252F	ENST00000216797	NM_020529.2	252	tCt/tTt	5/6	0.351141122071455	2	FACETS	0.464	0.371	0.569	0.232	0.185	0.285	SUBCLONAL	1	TRUE	0	0.351141122071455	2		547	344	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633144	3633144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771178344	NA	P-0021445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	37	776	2	ENST00000294008.3:c.5107G>A	p.Val1703Met	p.V1703M	ENST00000294008	NM_032444.2	1703	Gtg/Atg	14/15	0.204363511754973	5	FACETS	0.773	0.638	0.925	0.258	0.212	0.309	INDETERMINATE	1	TRUE	2	0.351141122071455	5		778	416	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863267	56863267	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	27	609	0	ENST00000519728.1:c.411G>C	p.Lys137Asn	p.K137N	ENST00000519728	NM_002350.3	137	aaG/aaC	6/13	0.285351614686406	3	FACETS	0.563	0.449	0.694	0.282	0.224	0.347	SUBCLONAL	1	TRUE	1	0.351141122071455	3		609	321	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357070	70357070	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773713291	NA	P-0021445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	97	798	0	ENST00000374080.3:c.5585G>A	p.Arg1862His	p.R1862H	ENST00000374080		1862	cGc/cAc	39/45	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.351141122071455	2		798	432	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	43	640	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		640	295	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612352	1612352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748738693	NA	P-0021722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	155	929	1	ENST00000344749.5:c.1667G>A	p.Arg556Gln	p.R556Q	ENST00000344749	NM_001136139.2	556	cGg/cAg	18/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		930	559	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	175	82	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.838011371668511	2		82	354	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0021786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	82	395	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.914	0.822	1	0.914	0.822	1	CLONAL	1	TRUE	1	0.838011371668511	2		396	214	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791758	42791758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1380826096	NA	P-0021786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	294	827	0	ENST00000575354.2:c.644G>A	p.Arg215Gln	p.R215Q	ENST00000575354	NM_015125.3	215	cGg/cAg	5/20	0.838011371668511	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.838011371668511	1		827	377	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61710206	61710206	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	152	552	0	ENST00000401558.2:c.2698C>G	p.Leu900Val	p.L900V	ENST00000401558	NM_003400.3	900	Ctc/Gtc	22/25	1	2	FACETS	0.93	0.861	1	0.93	0.861	1	CLONAL	1	TRUE	1	0.838011371668511	2		552	390	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522551	176522551	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	311	804	0	ENST00000292408.4:c.1648G>C	p.Val550Leu	p.V550L	ENST00000292408	NM_213647.1	550	Gtg/Ctg	13/18	0.815646577490023	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.815646577490023	2		804	363	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522393	176522393	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	442	817	0	ENST00000292408.4:c.1582G>T	p.Gly528Cys	p.G528C	ENST00000292408	NM_213647.1	528	Ggc/Tgc	12/18	0.815646577490023	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.815646577490023	2		817	526	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0021834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	43	672	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.775	0.65	0.914	0.775	0.65	0.914	CLONAL	1	TRUE	1	0.279338734047298	2		672	397	SUCCESS
APC	324	MSKCC	GRCh37	5	112175147	112175147	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	61	251	3	ENST00000257430.4:c.3856G>T	p.Glu1286Ter	p.E1286*	ENST00000257430	NM_000038.5	1286	Gaa/Taa	16/16	0.279338734047298	3	FACETS	1	0.937	1	1	0.937	1	CLONAL	3	TRUE	0	0.279338734047298	3		254	152	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633565	69633565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	29	386	1	ENST00000334134.2:c.137G>A	p.Arg46His	p.R46H	ENST00000334134	NM_005247.2	46	cGc/cAc	1/3	0.262232478322928	3	FACETS	1	0.895	1	0.586	0.473	0.711	CLONAL	1	TRUE	1	0.279338734047298	3		387	202	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562774	95562774	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	42	479	0	ENST00000393063.1:c.4483del	p.Ser1495HisfsTer65	p.S1495Hfs*65	ENST00000393063	NM_030621.3	1495	Tca/ca	24/28	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.279338734047298	2		479	274	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933190	49933190	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	29	714	0	ENST00000296474.3:c.2920A>C	p.Thr974Pro	p.T974P	ENST00000296474	NM_002447.2	974	Act/Cct	12/20	0.129978971419773	5	FACETS	0.677	0.543	0.83	0.226	0.181	0.277	INDETERMINATE	1	TRUE	2	0.279338734047298	5		714	435	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851736	134851736	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	45	624	0	ENST00000398015.3:c.1142C>G	p.Pro381Arg	p.P381R	ENST00000398015	NM_004441.4	381	cCc/cGc	5/16	0.129978971419773	5	FACETS	1	0.906	1	0.37	0.311	0.435	INDETERMINATE	1	TRUE	2	0.279338734047298	5		624	412	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169977788	169977788	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	33	572	0	ENST00000295797.4:c.255G>C	p.Glu85Asp	p.E85D	ENST00000295797	NM_002740.5	85	gaG/gaC	3/18	0.129978971419773	5	FACETS	0.901	0.735	1	0.3	0.245	0.363	INDETERMINATE	1	TRUE	2	0.279338734047298	5		572	372	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	56	460	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.737	0.63	0.855	0.737	0.63	0.855	SUBCLONAL	1	TRUE	1	0.196998757495489	2		460	771	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0021835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	122	929	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.196998757495489	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.196998757495489	1		929	1006	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0021835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	55	631	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	1	2	FACETS	0.767	0.655	0.89	0.767	0.655	0.89	SUBCLONAL	1	TRUE	1	0.196998757495489	2		631	728	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443857	49443857	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	118	898	0	ENST00000301067.7:c.3514T>C	p.Cys1172Arg	p.C1172R	ENST00000301067	NM_003482.3	1172	Tgc/Cgc	11/54	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.196998757495489	2		898	1091	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143001	30143001	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	116	938	0	ENST00000389048.3:c.525T>G	p.Ser175Arg	p.S175R	ENST00000389048	NM_004304.4	175	agT/agG	1/29	1	2	FACETS	0.98	0.881	1	0.98	0.881	1	CLONAL	1	TRUE	1	0.196998757495489	2		938	1202	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0021837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	160	476	1	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.938	0.868	1	0.938	0.868	1	CLONAL	1	TRUE	1	0.755087843073346	2		477	452	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342150	70342150	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	337	792	0	ENST00000374080.3:c.1202C>G	p.Pro401Arg	p.P401R	ENST00000374080		401	cCg/cGg	8/45	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.755087843073346	2		792	793	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242477	+	protein_altering_variant	In_Frame_Del	DEL	ATTAAGAGAA	ATTAAGAGAA	C	novel	NA	P-0021837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	234	732	0	ENST00000275493.2:c.2238_2247delinsC	p.Glu746_Glu749delinsAsp	p.E746_E749delinsD	ENST00000275493	NM_005228.3	746	gaATTAAGAGAA/gaC	19/28	1	2	FACETS	0.894	0.838	0.951	0.894	0.838	0.951	CLONAL	1	TRUE	1	0.755087843073346	2		732	693	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0021840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	421	915	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.873529635804732	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.873529635804732	1		915	541	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929087	32929087	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	295	784	0	ENST00000380152.3:c.7097del	p.Leu2366ArgfsTer10	p.L2366Rfs*10	ENST00000380152		2366	cTg/cg	14/27	0.873529635804732	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.873529635804732	1		784	360	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725291	49725291	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs745364054	NA	P-0021840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	246	484	0	ENST00000449682.2:c.134del	p.Gly45AlafsTer33	p.G45Afs*33	ENST00000449682	NM_020998.3	45	gGc/gc	2/18	1	2	FACETS	0.94	0.886	0.995	0.94	0.886	0.995	CLONAL	1	TRUE	1	0.873529635804732	2		484	599	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918920	76918921	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	391	1105	1	ENST00000373344.5:c.4070dup	p.Thr1358AspfsTer4	p.T1358Dfs*4	ENST00000373344	NM_000489.3	1357	aag/aaAg	12/35	1	2	FACETS	0.871	0.83	0.912	0.871	0.83	0.912	CLONAL	1	TRUE	1	0.873529635804732	2		1106	1028	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0022811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	192	352	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.38200503343219	1	FACETS	0.95	0.88	1	0.95	0.88	1	CLONAL	1	TRUE	0	0.38200503343219	1		353	856	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0022811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	132	753	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.282521721215485	4	FACETS	1	0.945	1	0.697	0.637	0.758	CLONAL	2	TRUE	1	0.38200503343219	4		753	457	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482843	67482843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	154	730	0	ENST00000327367.4:c.1247C>T	p.Ser416Phe	p.S416F	ENST00000327367	NM_005902.3	416	tCc/tTc	9/9	1	2	FACETS	0.953	0.873	1	0.953	0.873	1	CLONAL	1	TRUE	1	0.38200503343219	2		730	846	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416428	49416428	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	145	762	0	ENST00000301067.7:c.16283G>C	p.Gly5428Ala	p.G5428A	ENST00000301067	NM_003482.3	5428	gGc/gCc	51/54	0.282521721215485	4	FACETS	1	0.953	1	0.357	0.325	0.39	CLONAL	1	TRUE	1	0.38200503343219	4		762	980	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575047	48575056	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTTCTAGG	TTTTTCTAGG	-	novel	NA	P-0022811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	44	441	0	ENST00000342988.3:c.250-8_251del		p.X84_splice	ENST00000342988	NM_005359.5	84		3/12	0.367460385675069	1	FACETS	0.867	0.735	1	0.867	0.735	1	CLONAL	1	TRUE	0	0.38200503343219	1		441	215	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191524	10191524	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	121	702	0	ENST00000256474.2:c.517G>C	p.Glu173Gln	p.E173Q	ENST00000256474	NM_000551.3	173	Gag/Cag	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		702	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578463	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371524413	NA	P-0022878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	477	1208	0	ENST00000269305.4:c.467G>C	p.Arg156Pro	p.R156P	ENST00000269305	NM_001126112.2	156	cGc/cCc	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1208	923	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317687	163317687	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	87	456	0	ENST00000271452.3:c.1083G>C	p.Lys361Asn	p.K361N	ENST00000271452	NM_145697.2	361	aaG/aaC	12/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		456	632	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910883	114910883	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0022878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	37	536	0	ENST00000543371.1:c.1001+1G>C		p.X334_splice	ENST00000543371	NM_001198531.1	334			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		536	432	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0023439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	232	502	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.356509448405267	5	FACETS	0.932	0.868	0.997	0.621	0.579	0.665	CLONAL	2	TRUE	2	0.356509448405267	5		502	1072	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0023439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	411	905	2	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.321476491931517	2	FACETS	0.93	0.885	0.975	0.93	0.885	0.975	CLONAL	2	TRUE	0	0.356509448405267	2		907	1240	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662487	227662487	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	146	450	0	ENST00000305123.5:c.968C>T	p.Ser323Phe	p.S323F	ENST00000305123	NM_005544.2	323	tCc/tTc	1/2	0.349354777934977	3	FACETS	1	0.963	1	0.551	0.503	0.602	CLONAL	1	TRUE	1	0.356509448405267	3		450	875	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286263	66286263	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	90	429	0	ENST00000273854.3:c.1423G>T	p.Val475Leu	p.V475L	ENST00000273854	NM_004439.5	475	Gtg/Ttg	6/18	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.356509448405267	2		429	498	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	134	82	0				ENST00000310581	NM_198253.2	-/1132			0.500912852022393	3	FACETS	0.982	0.917	1	0.982	0.917	1	CLONAL	3	TRUE	0	0.500912852022393	3		82	227	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0023785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	119	358	1	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.404350160881462	4	FACETS	0.851	0.774	0.931			1	CLONAL	2	TRUE	NA	0.500912852022393	4		359	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0023785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	243	419	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	0.485723070568827	3	FACETS	0.93	0.882	0.977	0.93	0.882	0.977	CLONAL	3	TRUE	0	0.500912852022393	3		419	435	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258697	115258697	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	26	258	0	ENST00000369535.4:c.85G>T	p.Val29Leu	p.V29L	ENST00000369535	NM_002524.4	29	Gta/Tta	2/7	0.500912852022393	1	FACETS	0.512	0.41	0.626	0.512	0.41	0.626	SUBCLONAL	1	TRUE	0	0.500912852022393	1		258	152	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054911	176054911	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0023785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	46	253	0	ENST00000367669.3:c.1141+1G>T		p.X381_splice	ENST00000367669	NM_022457.5	381			1	2	FACETS	0.928	0.791	1	0.928	0.791	1	CLONAL	1	TRUE	1	0.500912852022393	2		253	198	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204785	94204785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	104	338	0	ENST00000323929.3:c.800G>A	p.Gly267Glu	p.G267E	ENST00000323929	NM_005591.3	267	gGa/gAa	8/20	0.254709506473045	3	FACETS	0.787	0.712	0.864	0.787	0.712	0.864	INDETERMINATE	2	TRUE	1	0.500912852022393	3		338	330	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865423	57865423	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	119	462	0	ENST00000228682.2:c.2900C>A	p.Pro967His	p.P967H	ENST00000228682	NM_005269.2	967	cCt/cAt	12/12	0.254709506473045	3	FACETS	1	0.974	1	0.605	0.549	0.664	INDETERMINATE	1	TRUE	1	0.500912852022393	3		462	491	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670459	88670459	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0023785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	93	235	0	ENST00000360948.2:c.1229-2A>T		p.X410_splice	ENST00000360948	NM_001012338.2	410			0.463038989025857	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	2	TRUE	0	0.500912852022393	2		235	185	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527492	29527492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	83	324	0	ENST00000356175.3:c.942del	p.Arg314SerfsTer3	p.R314Sfs*3	ENST00000356175	NM_000267.3	314	aGg/ag	9/57	0.338622559319682	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.500912852022393	1		324	230	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007181	62007182	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0023785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	82	476	1	ENST00000392795.3:c.500_501delinsTT	p.Thr167Ile	p.T167I	ENST00000392795	NM_001039933.1	167	aCG/aTT	4/6	1	2	FACETS	0.859	0.763	0.961	0.859	0.763	0.961	CLONAL	1	TRUE	1	0.500912852022393	2		477	381	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62311206	62311206	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs773153863	NA	P-0023785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	97	226	0	ENST00000360203.5:c.1042A>G	p.Ile348Val	p.I348V	ENST00000360203	NM_001283009.1	348	Atc/Gtc	13/35	0.404350160881462	4	FACETS	0.989	0.893	1			1	CLONAL	2	TRUE	NA	0.500912852022393	4		226	294	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42851119	42851119	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	33	304	0	ENST00000398585.3:c.774C>G	p.Ile258Met	p.I258M	ENST00000398585	NM_001135099.1	258	atC/atG	7/14	0.254709506473045	3	FACETS	0.426	0.347	0.515	0.213	0.173	0.258	INDETERMINATE	1	TRUE	1	0.500912852022393	3		304	387	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655221	45655221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1467027997	NA	P-0023785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	44	357	0	ENST00000407780.3:c.631G>A	p.Val211Met	p.V211M	ENST00000407780	NM_001283052.1	211	Gtg/Atg	4/7	0.254709506473045	3	FACETS	0.621	0.522	0.729	0.31	0.261	0.365	INDETERMINATE	1	TRUE	1	0.500912852022393	3		357	354	SUCCESS
ATR	545	MSKCC	GRCh37	3	142297537	142297537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373534503	NA	P-0023785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	80	343	0	ENST00000350721.4:c.10C>T	p.His4Tyr	p.H4Y	ENST00000350721	NM_001184.3	4	Cat/Tat	1/47	0.274464595115929	5	FACETS	0.795	0.705	0.89	0.53	0.47	0.593	INDETERMINATE	2	TRUE	2	0.500912852022393	5		343	352	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459782	149459782	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	356	391	0	ENST00000286301.3:c.425G>T	p.Arg142Leu	p.R142L	ENST00000286301	NM_005211.3	142	cGt/cTt	4/22	0.49644425644031	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	4	TRUE	0	0.500912852022393	4		391	526	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058511	69058511	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	127	399	0	ENST00000288368.4:c.4155T>G	p.Ser1385Arg	p.S1385R	ENST00000288368	NM_024870.2	1385	agT/agG	34/40	0.485723070568827	3	FACETS	0.85	0.778	0.924	0.567	0.519	0.616	CLONAL	2	TRUE	0	0.500912852022393	3		399	373	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340433	8340433	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	198	272	0	ENST00000356435.5:c.5163G>T	p.Leu1721Phe	p.L1721F	ENST00000356435		1721	ttG/ttT	31/35	0.484833244483297	3	FACETS	0.952	0.899	1	0.952	0.899	1	CLONAL	3	TRUE	0	0.500912852022393	3		272	346	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971079	21971079	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	217	263	0	ENST00000304494.5:c.279del	p.Leu94TrpfsTer52	p.L94Wfs*52	ENST00000304494	NM_000077.4	93	acG/ac	2/3	0.484833244483297	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	0	0.500912852022393	3		263	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882019	NA	P-0023788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	65	443	1	ENST00000269305.4:c.455del	p.Pro152ArgfsTer18	p.P152Rfs*18	ENST00000269305	NM_001126112.2	152	cCg/cg	5/11	0.196760329442111	1	FACETS	0.96	0.832	1	0.96	0.832	1	CLONAL	1	TRUE	0	0.206573151184573	1		444	588	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552618	18552618	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	53	289	0	ENST00000266497.5:c.2029T>G	p.Leu677Val	p.L677V	ENST00000266497		677	Tta/Gta	14/31	0.206573151184573	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.206573151184573	1		289	389	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554393	63554393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	36	407	1	ENST00000307078.5:c.346G>A	p.Gly116Arg	p.G116R	ENST00000307078	NM_004655.3	116	Gga/Aga	2/11	1	2	FACETS	0.678	0.557	0.814	0.678	0.557	0.814	SUBCLONAL	1	TRUE	1	0.206573151184573	2		408	514	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541526	187541526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	28	330	0	ENST00000441802.2:c.6214G>A	p.Glu2072Lys	p.E2072K	ENST00000441802	NM_005245.3	2072	Gaa/Aaa	10/27	1	2	FACETS	0.679	0.543	0.835	0.679	0.543	0.835	SUBCLONAL	1	TRUE	1	0.206573151184573	2		330	399	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199966	138199966	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	21	255	0	ENST00000237289.4:c.1384C>A	p.Pro462Thr	p.P462T	ENST00000237289	NM_001270507.1	462	Ccg/Acg	7/9	0.192454684625731	2	FACETS	0.607	0.467	0.77	0.303	0.233	0.385	SUBCLONAL	1	TRUE	0	0.206573151184573	2		255	335	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81340795	81340795	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0023788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	61	216	0	ENST00000222390.5:c.1444+2T>C		p.X482_splice	ENST00000222390	NM_000601.4	482			0.192454684625731	2	FACETS	0.871	0.756	0.995	0.871	0.756	0.995	CLONAL	2	TRUE	0	0.206573151184573	2		216	339	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577330	64577333	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	rs587776841	NA	P-0023837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	151	387	0	ENST00000312049.6:c.249_252del	p.Ile85SerfsTer33	p.I85Sfs*33	ENST00000312049	NM_130799.2	83	ctGTCT/ct	2/10	0.617758826646819	1	FACETS	0.965	0.896	1	0.965	0.896	1	CLONAL	1	TRUE	0	0.617758826646819	1		387	350	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845940	156845940	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	173	453	0	ENST00000524377.1:c.1570G>T	p.Val524Phe	p.V524F	ENST00000524377	NM_002529.3	524	Gtc/Ttc	13/17	0.617758826646819	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.617758826646819	1		453	379	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286806	33286806	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1443274655	NA	P-0023837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	101	337	1	ENST00000374542.5:c.2131del	p.His711IlefsTer55	p.H711Ifs*55	ENST00000374542	NM_001141970.1	711	Cat/at	7/8	0.617758826646819	1	FACETS	0.919	0.836	1	0.919	0.836	1	CLONAL	1	TRUE	0	0.617758826646819	1		338	246	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0023920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	219	651	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.632315960961566	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.652937155566321	2		651	327	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003747	45003747	+	start_lost	Translation_Start_Site	SNP	G	G	T	novel	NA	P-0023920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	156	524	0	ENST00000558401.1:c.3G>T	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	atG/atT	1/4	0.275992549086433	2	FACETS	1	0.951	1	0.519	0.48	0.56	INDETERMINATE	1	TRUE	0	0.652937155566321	2		524	460	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193172974	193172974	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	89	364	0	ENST00000367435.3:c.1022C>G	p.Pro341Arg	p.P341R	ENST00000367435	NM_024529.4	341	cCa/cGa	11/17	0.652937155566321	4	FACETS	0.98	0.872	1	0.49	0.436	0.547	CLONAL	1	TRUE	2	0.652937155566321	4		364	460	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74000685	74000685	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	30	697	0	ENST00000318443.5:c.1375C>G	p.Pro459Ala	p.P459A	ENST00000318443	NM_001024736.1	459	Cct/Gct	7/10	0.275992549086433	2	FACETS	0.315	0.254	0.383	0.157	0.127	0.192	INDETERMINATE	1	TRUE	0	0.652937155566321	2		697	292	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212485	36212485	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	49	928	0	ENST00000222270.7:c.2236A>G	p.Thr746Ala	p.T746A	ENST00000222270	NM_014727.1	746	Acc/Gcc	3/37	0.511856136118688	4	FACETS	0.653	0.554	0.76	0.326	0.277	0.38	SUBCLONAL	1	TRUE	2	0.652937155566321	4		928	380	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386617	81386617	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	75	340	0	ENST00000222390.5:c.370T>A	p.Tyr124Asn	p.Y124N	ENST00000222390	NM_000601.4	124	Tac/Aac	4/18	0.554654887376758	6	FACETS	0.99	0.869	1	0.248	0.217	0.28	CLONAL	1	TRUE	2	0.652937155566321	6		340	535	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	273	460	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		460	741	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0024285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	193	338	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		338	569	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0024285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	280	454	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		454	787	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867192	68867192	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0024285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	228	385	1	ENST00000261769.5:c.2440-1G>T		p.X814_splice	ENST00000261769	NM_004360.3	814			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		386	408	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212455	36212455	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	341	549	2	ENST00000222270.7:c.2206C>T	p.Gln736Ter	p.Q736*	ENST00000222270	NM_014727.1	736	Cag/Tag	3/37	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		551	1031	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99204042	99204042	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529481819	NA	P-0024285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	168	251	0	ENST00000074304.5:c.2905G>A	p.Glu969Lys	p.E969K	ENST00000074304	NM_001134224.1	969	Gaa/Aaa	26/26	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		251	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0024900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	125	490	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.25	2		490	793	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575194	48575194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555685186	NA	P-0024900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	56	287	0	ENST00000342988.3:c.388C>T	p.Pro130Ser	p.P130S	ENST00000342988	NM_005359.5	130	Cca/Tca	3/12	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.25	2		287	428	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1040463	1040463	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	123	517	1	ENST00000358495.3:c.109C>A	p.Gln37Lys	p.Q37K	ENST00000358495	NM_134424.2	37	Cag/Aag	3/12	0.198995333732064	3	FACETS	1	0.968	1	0.585	0.528	0.645	CLONAL	1	TRUE	1	0.25	3		518	946	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66525014	66525014	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	125	225	0	ENST00000358598.2:c.773C>T	p.Ser258Phe	p.S258F	ENST00000358598	NM_212471.2	258	tCt/tTt	9/11	0.258172379020184	3	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	1	0.25	3		225	541	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61722610	61722610	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	51	244	0	ENST00000401558.2:c.1027C>G	p.Leu343Val	p.L343V	ENST00000401558	NM_003400.3	343	Ctc/Gtc	11/25	1	2	FACETS	0.962	0.82	1	0.962	0.82	1	CLONAL	1	TRUE	1	0.25	2		244	424	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412039	116412046	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGAAGGTA	AGAAGGTA	TG	novel	NA	P-0024900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	595	560	2	ENST00000397752.3:c.3024_3028+3delinsTG		p.X1008_splice	ENST00000397752	NM_000245.2	1008		14/21	0.3	6	FACETS	1	0.988	1			1	CLONAL	5	TRUE	NA	0.25	6		562	1350	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11151982	11151982	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0024900-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	43	321	0	ENST00000358026.2:c.4267-1G>T		p.X1423_splice	ENST00000358026	NM_001128849.1	1423			1	2	FACETS	0.8	0.67	0.944	0.8	0.67	0.944	CLONAL	1	TRUE	1	0.25	2		321	430	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0026302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	105	352	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.167728997056776	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	FALSE	0	0.215497260828166	2		353	443	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115437	115115437	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	25	218	0	ENST00000257566.3:c.889A>C	p.Asn297His	p.N297H	ENST00000257566	NM_016569.3	297	Aac/Cac	5/8	0.134046598796886	4	FACETS	1	0.801	1	0.507	0.4	0.629	CLONAL	1	FALSE	2	0.215497260828166	4		218	278	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835779	68835780	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	61	249	0	ENST00000261769.5:c.371dup	p.Pro127AlafsTer41	p.P127Afs*41	ENST00000261769	NM_004360.3	124	cgc/cGgc	3/16	0.167728997056776	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	2	FALSE	0	0.215497260828166	2		249	263	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15379844	15379844	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	51	107	0	ENST00000263377.2:c.295A>C	p.Lys99Gln	p.K99Q	ENST00000263377	NM_058243.2	99	Aag/Cag	3/20	0.215497260828166	6	FACETS	0.99	0.851	1	0.99	0.851	1	CLONAL	3	FALSE	3	0.215497260828166	6		107	228	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0026308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	766	430	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.3	11	FACETS	0.966	0.941	0.99			1	CLONAL	13	TRUE	NA	0.2	11		430	1159	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs863224451	NA	P-0026308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	47	410	0	ENST00000269305.4:c.824G>C	p.Cys275Ser	p.C275S	ENST00000269305	NM_001126112.2	275	tGt/tCt	8/11	1	2	FACETS	0.892	0.752	1	0.892	0.752	1	CLONAL	1	TRUE	1	0.2	2		410	527	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044879	47044879	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	93	308	0	ENST00000377604.3:c.2205del	p.Ser736ValfsTer66	p.S736Vfs*66	ENST00000377604	NM_001204468.1	735	gaG/ga	20/24	1	1	FACETS	0.892	0.797	0.993	1	0.985	1	CLONAL	2	TRUE	0	0.2	1		308	469	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027727-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	106	82	0				ENST00000310581	NM_198253.2	-/1132			0.121616618020813	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.692234664551172	0		82	366	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0027727-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	345	724	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.689541698885858	2	FACETS	0.887	0.851	0.922	0.887	0.851	0.922	CLONAL	2	TRUE	0	0.692234664551172	2		724	562	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781324	3781326	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs587783502	NA	P-0027727-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	266	1001	0	ENST00000262367.5:c.5039_5041del	p.Ser1680del	p.S1680del	ENST00000262367	NM_004380.2	1680	tCCTtg/ttg	30/31	1	2	FACETS	0.766	0.719	0.815	0.766	0.719	0.815	SUBCLONAL	1	TRUE	1	0.692234664551172	2		1001	1003	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436440	110436440	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027727-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	326	984	0	ENST00000375856.3:c.1961del	p.Met654SerfsTer3	p.M654Sfs*3	ENST00000375856	NM_003749.2	654	aTg/ag	1/2	1	2	FACETS	0.869	0.822	0.917	0.869	0.822	0.917	CLONAL	1	TRUE	1	0.692234664551172	2		984	1084	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437840	52437840	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1559587104	NA	P-0027727-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	359	882	3	ENST00000460680.1:c.1321C>T	p.Gln441Ter	p.Q441*	ENST00000460680	NM_004656.3	441	Cag/Tag	13/17	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.692234664551172	2		885	1015	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443864	52443864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027727-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	302	784	0	ENST00000460680.1:c.31G>A	p.Asp11Asn	p.D11N	ENST00000460680	NM_004656.3	11	Gac/Aac	1/17	1	2	FACETS	0.929	0.877	0.982	0.929	0.877	0.982	CLONAL	1	TRUE	1	0.692234664551172	2		784	939	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938404	44938404	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027727-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	212	279	0	ENST00000377967.4:c.2952C>G	p.Phe984Leu	p.F984L	ENST00000377967	NM_021140.2	984	ttC/ttG	20/29	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.692234664551172	1		279	337	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670652	67670652	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027727-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	151	432	0	ENST00000264010.4:c.1897G>T	p.Glu633Ter	p.E633*	ENST00000264010	NM_006565.3	633	Gaa/Taa	11/12	1	2	FACETS	0.889	0.818	0.961	0.889	0.818	0.961	CLONAL	1	TRUE	1	0.692234664551172	2		432	491	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243556	46243556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	211	228	1	ENST00000334344.6:c.1909G>A	p.Ala637Thr	p.A637T	ENST00000334344	NM_152641.2	637	Gca/Aca	14/21	0.738567109864656	4	FACETS	0.895	0.838	0.953	0.895	0.838	0.953	CLONAL	2	TRUE	2	0.738567109864656	4		229	555	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440094	49440094	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1218	296	653	0	ENST00000301067.7:c.4532A>G	p.His1511Arg	p.H1511R	ENST00000301067	NM_003482.3	1511	cAt/cGt	16/54	0.738567109864656	4	FACETS	0.92	0.864	0.978	0.46	0.432	0.489	CLONAL	1	TRUE	2	0.738567109864656	4		653	1514	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987179	36987179	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	805	637	0	ENST00000354822.5:c.510G>T	p.Met170Ile	p.M170I	ENST00000354822	NM_001079668.2	170	atG/atT	3/3	0.332665146419656	6	FACETS	1	0.996	1			1	INDETERMINATE	4	TRUE	NA	0.738567109864656	6		637	1232	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304000	91304000	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	792	571	0	ENST00000355112.3:c.1397G>T	p.Gly466Val	p.G466V	ENST00000355112	NM_000057.2	466	gGg/gTg	7/22	0.738567109864656	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.738567109864656	3		571	947	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579329	7579329	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912658	NA	P-0028087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	589	565	0	ENST00000269305.4:c.358A>G	p.Lys120Glu	p.K120E	ENST00000269305	NM_001126112.2	120	Aag/Gag	4/11	0.738567109864656	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.738567109864656	2		565	752	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113822	11113822	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	623	614	0	ENST00000358026.2:c.1930G>T	p.Glu644Ter	p.E644*	ENST00000358026	NM_001128849.1	644	Gag/Tag	12/36	0.738567109864656	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.738567109864656	2		614	785	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645990	215645990	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1323808192	NA	P-0028087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	355	409	0	ENST00000260947.4:c.608G>C	p.Gly203Ala	p.G203A	ENST00000260947	NM_000465.2	203	gGa/gCa	4/11	0.445360130304021	3	FACETS	1	0.992	1	0.753	0.723	0.782	CLONAL	2	TRUE	0	0.738567109864656	3		409	583	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599358	55599358	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	355	471	0	ENST00000288135.5:c.2484C>A	p.Asn828Lys	p.N828K	ENST00000288135	NM_000222.2	828	aaC/aaA	17/21	0.738567109864656	2	FACETS	0.999	0.966	1	0.999	0.966	1	CLONAL	2	TRUE	0	0.738567109864656	2		471	481	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973991	55973991	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs766459956	NA	P-0028087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	464	560	0	ENST00000263923.4:c.1325C>A	p.Thr442Lys	p.T442K	ENST00000263923	NM_002253.2	442	aCg/aAg	10/30	0.738567109864656	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.738567109864656	2		560	612	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875645	35875645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	203	451	1	ENST00000303115.3:c.832G>T	p.Asp278Tyr	p.D278Y	ENST00000303115	NM_002185.3	278	Gat/Tat	7/8	0.594530993505393	4	FACETS	1	0.974	1	0.367	0.34	0.395	CLONAL	1	TRUE	1	0.738567109864656	4		452	868	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165219	32165219	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	542	534	0	ENST00000375023.3:c.4909C>A	p.Pro1637Thr	p.P1637T	ENST00000375023	NM_004557.3	1637	Ccc/Acc	27/30	0.738567109864656	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.738567109864656	2		534	700	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161970003	161970003	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	278	620	0	ENST00000366898.1:c.966G>T	p.Glu322Asp	p.E322D	ENST00000366898	NM_004562.2	322	gaG/gaT	9/12	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.738567109864656	2		620	738	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513227	106513227	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	128	316	0	ENST00000359195.3:c.2131C>A	p.Gln711Lys	p.Q711K	ENST00000359195	NM_002649.2	711	Cag/Aag	4/11	1	2	FACETS	0.81	0.74	0.882	0.81	0.74	0.882	CLONAL	1	TRUE	1	0.738567109864656	2		316	428	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982779	90982779	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0028087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	213	307	0	ENST00000265433.3:c.709A>T	p.Lys237Ter	p.K237*	ENST00000265433	NM_002485.4	237	Aaa/Taa	7/16	0.738567109864656	6	FACETS	0.843	0.785	0.904	0.422	0.392	0.452	CLONAL	2	TRUE	2	0.738567109864656	6		307	847	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500882	8500882	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	429	457	0	ENST00000356435.5:c.2000C>A	p.Ser667Ter	p.S667*	ENST00000356435		667	tCg/tAg	13/35	NA	2	FACETS	0.98	0.949	1			1	INDETERMINATE	2	TRUE	NA	0.738567109864656	2		457	593	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0028730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	35	460	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		460	227	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0028730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	13	286	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		286	311	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371712	55371713	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	50	392	0	ENST00000297316.4:c.403dup	p.Tyr135LeufsTer27	p.Y135Lfs*27	ENST00000297316	NM_022454.3	134	-/T	2/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		392	287	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755719	39755719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	26	427	0	ENST00000288319.7:c.1046G>A	p.Arg349Gln	p.R349Q	ENST00000288319	NM_182918.3	349	cGg/cAg	10/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		427	432	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711882	89711883	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0028730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	38	409	0	ENST00000371953.3:c.500_501del	p.Thr167AsnfsTer12	p.T167Nfs*12	ENST00000371953	NM_000314.4	167	aCT/a	6/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		409	302	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3824634	3824634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1206236240	NA	P-0028730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	46	506	0	ENST00000262367.5:c.2219G>A	p.Gly740Glu	p.G740E	ENST00000262367	NM_004380.2	740	gGa/gAa	12/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		506	458	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857351	9857351	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	38	401	0	ENST00000330684.3:c.4050C>A	p.Asp1350Glu	p.D1350E	ENST00000330684	NM_001134407.1	1350	gaC/gaA	13/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		401	427	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374413	31374413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756280552	NA	P-0028730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	24	486	0	ENST00000328111.2:c.412G>A	p.Val138Met	p.V138M	ENST00000328111	NM_006892.3	138	Gtg/Atg	5/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		486	397	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578207	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0029236-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	554	625	0	ENST00000269305.4:c.642_643del	p.His214GlnfsTer7	p.H214Qfs*7	ENST00000269305	NM_001126112.2	214	caTAgt/cagt	6/11	NA	2	FACETS	0.977	0.964	0.989			1	INDETERMINATE	2	TRUE	NA	0.965809142992678	2		625	587	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	34	82	0				ENST00000310581	NM_198253.2	-/1132			0.102676268573572	3	FACETS	1	0.945	1	0.681	0.569	0.799	INDETERMINATE	1	TRUE	1	0.574117054983841	3		82	112	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0029371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	167	375	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.574117054983841	2	FACETS	0.954	0.895	1	0.954	0.895	1	CLONAL	2	TRUE	0	0.574117054983841	2		375	305	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591247	67591247	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0029371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	79	236	0	ENST00000274335.5:c.1746-1G>C		p.X582_splice	ENST00000274335		582			0.102676268573572	3	FACETS	1	0.925	1	0.529	0.469	0.592	INDETERMINATE	1	TRUE	1	0.574117054983841	3		236	335	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711875	89711875	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587782603	NA	P-0029371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	100	272	0	ENST00000371953.3:c.493G>A	p.Gly165Arg	p.G165R	ENST00000371953	NM_000314.4	165	Gga/Aga	6/9	0.574117054983841	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.574117054983841	1		272	208	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828875	26828875	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	65	121	0	ENST00000381527.3:c.97G>A	p.Gly33Ser	p.G33S	ENST00000381527	NM_001260.1	33	Ggt/Agt	1/13	0.574117054983841	1	FACETS	0.99	0.879	1	0.99	0.879	1	CLONAL	1	TRUE	0	0.574117054983841	1		121	163	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0029455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	100	507	0	ENST00000288602.6:c.1397G>T	p.Gly466Val	p.G466V	ENST00000288602	NM_004333.4	466	gGa/gTa	11/18	0.287401269226441	4	FACETS	1	0.962	1	0.39	0.348	0.435	CLONAL	1	TRUE	1	0.28	4		507	781	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs760043106	NA	P-0029455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	128	689	0	ENST00000269305.4:c.584T>A	p.Ile195Asn	p.I195N	ENST00000269305	NM_001126112.2	195	aTc/aAc	6/11	0.298190444955723	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.28	1		689	723	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033889	49033889	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	81	559	0	ENST00000267163.4:c.2027del	p.Leu676Ter	p.L676*	ENST00000267163	NM_000321.2	676	Tta/ta	20/27	0.298190444955723	1	FACETS	0.829	0.731	0.934	0.829	0.731	0.934	CLONAL	1	TRUE	0	0.28	1		559	600	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420203	88420203	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	99	668	0	ENST00000360948.2:c.2483G>C	p.Gly828Ala	p.G828A	ENST00000360948	NM_001012338.2	828	gGg/gCg	19/19	1	2	FACETS	0.985	0.88	1	0.985	0.88	1	CLONAL	1	TRUE	1	0.28	2		668	718	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774732	73774732	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	40	160	0	ENST00000254810.4:c.355A>T	p.Thr119Ser	p.T119S	ENST00000254810	NM_005324.3	119	Acc/Tcc	4/4	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.28	2		160	227	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096138	178096138	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	35	512	0	ENST00000397062.3:c.1193A>T	p.His398Leu	p.H398L	ENST00000397062	NM_006164.4	398	cAt/cTt	5/5	1	2	FACETS	0.414	0.338	0.499	0.414	0.338	0.499	SUBCLONAL	1	TRUE	1	0.28	2		512	604	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273255	198273255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	70	622	2	ENST00000335508.6:c.955G>T	p.Gly319Cys	p.G319C	ENST00000335508	NM_012433.2	319	Ggt/Tgt	8/25	1	2	FACETS	0.633	0.551	0.722	0.633	0.551	0.722	SUBCLONAL	1	TRUE	1	0.28	2		624	790	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660923	227660923	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	76	792	0	ENST00000305123.5:c.2532G>C	p.Lys844Asn	p.K844N	ENST00000305123	NM_005544.2	844	aaG/aaC	1/2	1	2	FACETS	0.603	0.527	0.684	0.603	0.527	0.684	SUBCLONAL	1	TRUE	1	0.28	2		792	901	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662388	227662388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	78	617	0	ENST00000305123.5:c.1067C>T	p.Ala356Val	p.A356V	ENST00000305123	NM_005544.2	356	gCc/gTc	1/2	1	2	FACETS	0.731	0.642	0.827	0.731	0.642	0.827	SUBCLONAL	1	TRUE	1	0.28	2		617	762	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871316	35871316	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0029455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	69	440	0	ENST00000303115.3:c.537+1G>T		p.X179_splice	ENST00000303115	NM_002185.3	179			0.298190444955723	4	FACETS	0.876	0.762	1	0.292	0.254	0.334	CLONAL	1	TRUE	1	0.28	4		440	720	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164726	32164726	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	111	705	0	ENST00000375023.3:c.5176G>T	p.Asp1726Tyr	p.D1726Y	ENST00000375023	NM_004557.3	1726	Gac/Tac	28/30	1	2	FACETS	0.918	0.824	1	0.918	0.824	1	CLONAL	1	TRUE	1	0.28	2		705	864	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168689	32168689	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	145	788	0	ENST00000375023.3:c.4234C>A	p.Leu1412Ile	p.L1412I	ENST00000375023	NM_004557.3	1412	Ctt/Att	23/30	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.28	2		788	984	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370780	55370780	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	275	425	1	ENST00000297316.4:c.82G>T	p.Gly28Cys	p.G28C	ENST00000297316	NM_022454.3	28	Ggc/Tgc	1/2	0.221453396441959	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	3	TRUE	0	0.28	3		426	739	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70355087	70355087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	152	845	0	ENST00000374080.3:c.5009C>T	p.Ser1670Phe	p.S1670F	ENST00000374080		1670	tCc/tTc	36/45	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.28	2		845	1067	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907844	76907844	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0029455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	15	123	0	ENST00000373344.5:c.4318-1G>T		p.X1440_splice	ENST00000373344	NM_000489.3	1440			1	2	FACETS	0.94	0.695	1	0.94	0.695	1	CLONAL	1	TRUE	1	0.28	2		123	114	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156731	20156731	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	156	326	0	ENST00000379607.5:c.26G>T	p.Gly9Val	p.G9V	ENST00000379607	NM_001412.3	9	gGt/gTt	2/7	0.33358287906362	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.33358287906362	1		326	644	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426812	121426812	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377110124	NA	P-0029779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	113	317	1	ENST00000257555.6:c.503G>A	p.Arg168His	p.R168H	ENST00000257555		168	cGc/cAc	2/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.33358287906362	2		318	619	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101242	27101242	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0029779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	168	398	0	ENST00000324856.7:c.4524T>A	p.Tyr1508Ter	p.Y1508*	ENST00000324856	NM_006015.4	1508	taT/taA	18/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.33358287906362	2		398	788	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902581	1902581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029779-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	285	473	0	ENST00000382891.5:c.200G>A	p.Gly67Asp	p.G67D	ENST00000382891	NM_133335.3	67	gGc/gAc	2/22	0.33358287906362	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.33358287906362	3		473	928	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513280	106513280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752876335	NA	P-0030007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	80	229	0	ENST00000359195.3:c.2184G>A	p.Met728Ile	p.M728I	ENST00000359195	NM_002649.2	728	atG/atA	4/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.36	2		229	313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0030551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	323	777	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.645220156713211	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.645220156713211	1		777	633	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955538	48955538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913303	NA	P-0030551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	18	411	0	ENST00000267163.4:c.1654C>T	p.Arg552Ter	p.R552*	ENST00000267163	NM_000321.2	552	Cga/Tga	17/27	0.645220156713211	1	FACETS	0.106	0.079	0.137	0.106	0.079	0.137	SUBCLONAL	1	TRUE	0	0.645220156713211	1		411	358	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0031415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	158	617	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	0.787	0.728	0.848	0.787	0.728	0.848	SUBCLONAL	1	TRUE	1	0.874593066248507	2		617	459	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47087991	47087991	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	238	500	0	ENST00000409792.3:c.7084C>T	p.Gln2362Ter	p.Q2362*	ENST00000409792	NM_014159.6	2362	Cag/Tag	16/21	1	2	FACETS	0.845	0.811	0.878	1	0.996	1	CLONAL	2	TRUE	1	0.874593066248507	2		500	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579542	7579545	+	frameshift_variant	Frame_Shift_Del	DEL	CGTC	CGTC	-	novel	NA	P-0031632-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	129	873	0	ENST00000269305.4:c.142_145del	p.Asp48IlefsTer74	p.D48Ifs*74	ENST00000269305	NM_001126112.2	48	GACGat/at	4/11	0.519976713107845	1	FACETS	0.794	0.738	0.85	1	0.99	1	SUBCLONAL	2	TRUE	0	0.508772931610808	1		873	238	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0032016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	53	414	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.176377742918134	3	FACETS	0.97	0.832	1	0.647	0.554	0.747	CLONAL	2	TRUE	0	0.176377742918134	3		414	337	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729536	41729536	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	79	667	0	ENST00000242208.4:c.993G>T	p.Lys331Asn	p.K331N	ENST00000242208	NM_002192.2	331	aaG/aaT	3/3	0.176377742918134	3	FACETS	1	0.973	1	0.7	0.616	0.791	CLONAL	1	TRUE	1	0.176377742918134	3		667	696	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607569	43607570	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0032016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	166	927	3	ENST00000355710.3:c.1545_1546delinsAA	p.Cys515_Pro516delinsTer	p.C515_P516delins*	ENST00000355710	NM_020975.4	515	tgCCcc/tgAAcc	8/20	1	2	FACETS	1	0.955	1	1	0.992	1	CLONAL	2	TRUE	1	0.176377742918134	2		930	890	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588156	69588156	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	49	782	0	ENST00000168712.1:c.542T>C	p.Leu181Pro	p.L181P	ENST00000168712	NM_002007.2	181	cTg/cCg	3/3	0.149887917980482	2	FACETS	0.644	0.544	0.755	0.322	0.272	0.378	SUBCLONAL	1	TRUE	0	0.176377742918134	2		782	863	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625156	69625156	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	54	842	0	ENST00000334134.2:c.637C>A	p.Gln213Lys	p.Q213K	ENST00000334134	NM_005247.2	213	Cag/Aag	3/3	0.149887917980482	2	FACETS	0.602	0.512	0.701	0.301	0.256	0.351	SUBCLONAL	1	TRUE	0	0.176377742918134	2		842	1017	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121641	108121673	+	inframe_deletion	In_Frame_Del	DEL	CTGGAATAAAATTTGGTGTATTACCTTTCGTGG	CTGGAATAAAATTTGGTGTATTACCTTTCGTGG	-	novel	NA	P-0032016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	40	508	0	ENST00000278616.4:c.1449_1481del	p.Trp484_Gly494del	p.W484_G494del	ENST00000278616	NM_000051.3	483	ctCTGGAATAAAATTTGGTGTATTACCTTTCGTGGt/ctt	10/63	0.149887917980482	2	FACETS	1	0.932	1	0.625	0.52	0.741	CLONAL	1	TRUE	0	0.176377742918134	2		508	363	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371784	118371784	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	70	399	0	ENST00000534358.1:c.6241G>T	p.Val2081Phe	p.V2081F	ENST00000534358	NM_005933.3	2081	Gtc/Ttc	25/36	0.149887917980482	2	FACETS	0.859	0.751	0.975	0.859	0.751	0.975	CLONAL	2	TRUE	0	0.176377742918134	2		399	462	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394791	394791	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	98	467	0	ENST00000399788.2:c.4904G>A	p.Trp1635Ter	p.W1635*	ENST00000399788	NM_001042603.1	1635	tGg/tAg	28/28	0.176377742918134	3	FACETS	0.944	0.847	1	0.944	0.847	1	CLONAL	3	TRUE	0	0.176377742918134	3		467	427	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444039	49444039	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	56	761	0	ENST00000301067.7:c.3332C>G	p.Ala1111Gly	p.A1111G	ENST00000301067	NM_003482.3	1111	gCc/gGc	11/54	0.171428978987572	3	FACETS	0.845	0.722	0.98	0.422	0.361	0.49	CLONAL	1	TRUE	1	0.176377742918134	3		761	818	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001309	29001309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	53	365	0	ENST00000282397.4:c.1423C>T	p.His475Tyr	p.H475Y	ENST00000282397	NM_002019.4	475	Cat/Tat	10/30	0.149887917980482	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	2	TRUE	0	0.176377742918134	2		365	271	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322632	30322633	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0032016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	49	497	0	ENST00000322652.5:c.1645_1646delinsTT	p.Gly549Leu	p.G549L	ENST00000322652	NM_015355.2	549	GGg/TTg	14/16	0.149887917980482	2	FACETS	0.847	0.721	0.984	0.847	0.721	0.984	CLONAL	2	TRUE	0	0.176377742918134	2		497	328	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313457	30313457	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	89	656	0	ENST00000262643.3:c.1057G>C	p.Ala353Pro	p.A353P	ENST00000262643	NM_001238.2	353	Gct/Cct	11/12	0.176377742918134	3	FACETS	0.776	0.688	0.87	0.776	0.688	0.87	SUBCLONAL	2	TRUE	1	0.176377742918134	3		656	708	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416347	29416347	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752701859	NA	P-0032016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	191	880	0	ENST00000389048.3:c.4606G>A	p.Glu1536Lys	p.E1536K	ENST00000389048	NM_004304.4	1536	Gag/Aag	29/29	1	2	FACETS	1	0.954	1	1	0.993	1	CLONAL	2	TRUE	1	0.176377742918134	2		880	1037	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661796	227661796	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	50	893	0	ENST00000305123.5:c.1659G>T	p.Glu553Asp	p.E553D	ENST00000305123	NM_005544.2	553	gaG/gaT	1/2	NA	2	FACETS	0.702	0.594	0.821			1	INDETERMINATE	1	TRUE	NA	0.176377742918134	2		893	808	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721114	39721114	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	25	398	0	ENST00000361337.2:c.617G>T	p.Trp206Leu	p.W206L	ENST00000361337	NM_003286.2	206	tGg/tTg	9/21	1	2	FACETS	0.75	0.591	0.933	0.75	0.591	0.933	CLONAL	1	TRUE	1	0.176377742918134	2		398	378	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101136	41101136	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	60	769	0	ENST00000373198.4:c.1220G>T	p.Trp407Leu	p.W407L	ENST00000373198	NM_133170.3	407	tGg/tTg	8/32	1	2	FACETS	0.908	0.781	1	0.908	0.781	1	CLONAL	1	TRUE	1	0.176377742918134	2		769	749	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201827	152201827	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	60	421	0	ENST00000206249.3:c.681C>G	p.Cys227Trp	p.C227W	ENST00000206249	NM_000125.3	227	tgC/tgG	3/8	0.176377742918134	3	FACETS	0.932	0.806	1	0.622	0.537	0.712	CLONAL	2	TRUE	0	0.176377742918134	3		421	397	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622188	162622188	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	73	394	0	ENST00000366898.1:c.509G>T	p.Arg170Met	p.R170M	ENST00000366898	NM_004562.2	170	aGg/aTg	4/12	0.176377742918134	3	FACETS	0.934	0.819	1	0.623	0.546	0.705	CLONAL	2	TRUE	0	0.176377742918134	3		394	482	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273078	55273078	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs865825533	NA	P-0032016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	127	634	0	ENST00000275493.2:c.3401G>T	p.Gly1134Val	p.G1134V	ENST00000275493	NM_005228.3	1134	gGc/gTc	28/28	0.176377742918134	3	FACETS	0.976	0.884	1	0.976	0.884	1	CLONAL	2	TRUE	1	0.176377742918134	3		634	803	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334819	81334819	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	32	429	0	ENST00000222390.5:c.1897C>A	p.His633Asn	p.H633N	ENST00000222390	NM_000601.4	633	Cat/Aat	17/18	0.176377742918134	3	FACETS	1	0.926	1	0.654	0.532	0.79	CLONAL	1	TRUE	1	0.176377742918134	3		429	302	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992980	68992980	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs1181417548	NA	P-0032016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	20	335	0	ENST00000288368.4:c.1786-1G>C		p.X596_splice	ENST00000288368	NM_024870.2	596			1	2	FACETS	0.982	0.753	1	0.982	0.753	1	CLONAL	1	TRUE	1	0.176377742918134	2		335	231	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1315015	1315015	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0032016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	61	556	0	ENST00000400841.2:c.647-1G>A		p.X216_splice	ENST00000400841		216			1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.176377742918134	2		556	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0032098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	461	754	6	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.77382200073377	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.776198580395998	1		760	711	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094782	143094783	+	splice_donor_variant,intron_variant	Splice_Site	DNP	TA	TA	AC	novel	NA	P-0032098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	110	364	2	ENST00000262992.4:c.1359+2_1359+3delinsGT		p.X453_splice	ENST00000262992	NM_001101669.1	453			0.776198580395998	1	FACETS	0.923	0.855	0.989	0.923	0.855	0.989	CLONAL	1	TRUE	0	0.776198580395998	1		366	188	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0032247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	365	635	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.356625887308184	2	FACETS	1	0.996	1	0.734	0.704	0.764	INDETERMINATE	1	TRUE	0	0.781941569849753	2		635	636	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0032261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	343	430	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.398792871650768	4	FACETS	1	0.977	1			1	CLONAL	3	FALSE	NA	0.398792871650768	4		430	769	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0032261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	243	473	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.392000218893139	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	FALSE	0	0.398792871650768	2		473	607	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829665	72829665	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	152	647	1	ENST00000268489.5:c.6916G>A	p.Glu2306Lys	p.E2306K	ENST00000268489	NM_006885.3	2306	Gag/Aag	9/10	0.339156312338221	4	FACETS	0.979	0.894	1	0.326	0.298	0.357	CLONAL	1	FALSE	1	0.398792871650768	4		648	1089	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757393	40757393	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0032261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	111	432	0	ENST00000373198.4:c.2904+1G>C		p.X968_splice	ENST00000373198	NM_133170.3	968			NA	2	FACETS	0.923	0.832	1			1	INDETERMINATE	1	FALSE	NA	0.398792871650768	2		432	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0032386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	22	425	0	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	1	2	FACETS	0.333	0.257	0.423	0.333	0.257	0.423	SUBCLONAL	1	TRUE	1	0.14	2		425	943	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578502	7578502	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032788-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	151	941	1	ENST00000269305.4:c.428T>C	p.Val143Ala	p.V143A	ENST00000269305	NM_001126112.2	143	gTg/gCg	5/11	0.230330397042755	1	FACETS	0.921	0.84	1	0.921	0.84	1	CLONAL	1	TRUE	0	0.230330397042755	1		942	1259	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0033071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	21900	580	0	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.882676838631705	43	FACETS	0.993	0.991	0.995			1	CLONAL	42	TRUE	NA	0.882676838631705	43		580	22725	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876658468	NA	P-0033071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	320	505	0	ENST00000269305.4:c.577C>G	p.His193Asp	p.H193D	ENST00000269305	NM_001126112.2	193	Cat/Gat	6/11	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.882676838631705	2		505	624	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447396	12447396	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553647989	NA	P-0033071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	244	530	0	ENST00000287820.6:c.635G>A	p.Arg212Gln	p.R212Q	ENST00000287820	NM_015869.4	212	cGg/cAg	5/7	1	2	FACETS	0.923	0.869	0.977	0.923	0.869	0.977	CLONAL	1	TRUE	1	0.882676838631705	2		530	599	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0033071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	135	395	1				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.882676838631705	2		396	283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579328	7579329	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0033071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	34	483	0	ENST00000269305.4:c.358_359del	p.Lys120ValfsTer28	p.K120Vfs*28	ENST00000269305	NM_001126112.2	120	AAg/g	4/11	1	2	FACETS	0.139	0.113	0.169	0.139	0.113	0.169	SUBCLONAL	1	TRUE	1	0.882676838631705	2		483	553	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0033556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	190	615	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.873576104482129	1	FACETS	0.48	0.448	0.514	0.48	0.448	0.514	SUBCLONAL	1	TRUE	0	0.873576104482129	1		615	510	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398283	25398284	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCAGCT	novel	NA	P-0033556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	336	408	0	ENST00000311936.3:c.30_35dup	p.Ala11_Gly12dup	p.A11_G12dup	ENST00000311936	NM_004985.3	11	ggt/ggAGCTGGt	2/5	1	2	FACETS	0.865	0.821	0.91	0.865	0.821	0.91	CLONAL	1	TRUE	1	0.873576104482129	2		408	889	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0033712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	111	414	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.268205523667371	2		414	567	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251169	115251169	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	67	489	0	ENST00000369535.4:c.557G>T	p.Cys186Phe	p.C186F	ENST00000369535	NM_002524.4	186	tGt/tTt	5/7	1	2	FACETS	0.706	0.613	0.807	0.706	0.613	0.807	SUBCLONAL	1	TRUE	1	0.268205523667371	2		489	708	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458814	120458814	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	51	543	0	ENST00000256646.2:c.6531G>T	p.Gln2177His	p.Q2177H	ENST00000256646	NM_024408.3	2177	caG/caT	34/34	1	2	FACETS	0.526	0.446	0.614	0.526	0.446	0.614	SUBCLONAL	1	TRUE	1	0.268205523667371	2		543	723	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456314	32456314	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	54	479	0	ENST00000332351.3:c.578C>A	p.Ala193Asp	p.A193D	ENST00000332351	NM_024426.4	193	gCc/gAc	1/10	1	2	FACETS	0.746	0.637	0.865	0.746	0.637	0.865	SUBCLONAL	1	TRUE	1	0.268205523667371	2		479	540	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988640	41988640	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0033712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	50	449	0	ENST00000219905.7:c.1432A>T	p.Arg478Ter	p.R478*	ENST00000219905	NM_001164273.1	478	Aga/Tga	3/24	0.268205523667371	1	FACETS	0.666	0.565	0.776	0.666	0.565	0.776	SUBCLONAL	1	TRUE	0	0.268205523667371	1		449	485	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498431	89498431	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	42	349	0	ENST00000336596.2:c.2403C>A	p.Phe801Leu	p.F801L	ENST00000336596	NM_005233.5	801	ttC/ttA	14/17	1	2	FACETS	0.607	0.506	0.719	0.607	0.506	0.719	SUBCLONAL	1	TRUE	1	0.268205523667371	2		349	516	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851624	134851624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	53	430	0	ENST00000398015.3:c.1030C>T	p.Pro344Ser	p.P344S	ENST00000398015	NM_004441.4	344	Cct/Tct	5/16	1	2	FACETS	0.775	0.661	0.899	0.775	0.661	0.899	SUBCLONAL	1	TRUE	1	0.268205523667371	2		430	510	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144078	55144078	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	76	382	0	ENST00000257290.5:c.1907G>A	p.Ser636Asn	p.S636N	ENST00000257290	NM_006206.4	636	aGt/aAt	14/23	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.268205523667371	2		382	553	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539386	187539386	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	47	428	0	ENST00000441802.2:c.8354A>T	p.Asp2785Val	p.D2785V	ENST00000441802	NM_005245.3	2785	gAt/gTt	10/27	1	2	FACETS	0.635	0.535	0.745	0.635	0.535	0.745	SUBCLONAL	1	TRUE	1	0.268205523667371	2		428	552	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518687	103518687	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs570252494	NA	P-0033714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	154	326	0	ENST00000355739.4:c.2275C>T	p.Arg759Trp	p.R759W	ENST00000355739	NM_000123.3	759	Cgg/Tgg	10/15	0.174088962978532	5	FACETS	1	0.98	1	0.769	0.715	0.824	INDETERMINATE	2	TRUE	2	0.928012300692257	5		326	344	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701892	43701892	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	89	299	0	ENST00000382044.4:c.5353C>G	p.Leu1785Val	p.L1785V	ENST00000382044	NM_001141980.1	1785	Ctt/Gtt	25/28	0.741648611627264	4	FACETS	1	0.929	1	0.35	0.313	0.389	CLONAL	1	TRUE	1	0.928012300692257	4		299	352	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858648	9858648	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	219	575	0	ENST00000330684.3:c.2753C>A	p.Pro918His	p.P918H	ENST00000330684	NM_001134407.1	918	cCc/cAc	13/13	0.434559526027311	4	FACETS	0.855	0.798	0.913	0.855	0.798	0.913	CLONAL	2	TRUE	2	0.556026429277086	4		575	717	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18439803	18439803	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	124	349	0	ENST00000266497.5:c.701T>A	p.Leu234Gln	p.L234Q	ENST00000266497		234	cTa/cAa	2/31	0.484324911296226	5	FACETS	1	0.983	1	0.466	0.423	0.511	CLONAL	1	TRUE	2	0.556026429277086	5		349	585	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74001998	74001998	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	135	583	0	ENST00000318443.5:c.1514A>G	p.Asp505Gly	p.D505G	ENST00000318443	NM_001024736.1	505	gAc/gGc	8/10	1	2	FACETS	0.823	0.751	0.898	0.823	0.751	0.898	CLONAL	1	TRUE	1	0.556026429277086	2		583	590	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483904	88483904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371770675	NA	P-0033949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	137	635	1	ENST00000360948.2:c.1666G>A	p.Glu556Lys	p.E556K	ENST00000360948	NM_001012338.2	556	Gag/Aag	14/19	1	2	FACETS	0.827	0.755	0.902	0.827	0.755	0.902	CLONAL	1	TRUE	1	0.556026429277086	2		636	596	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099414	4099414	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0033949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	257	553	0	ENST00000262948.5:c.706-2A>G		p.X236_splice	ENST00000262948	NM_030662.3	236			0.431303173709989	3	FACETS	0.837	0.788	0.887	0.837	0.788	0.887	CLONAL	2	TRUE	1	0.556026429277086	3		553	706	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50143243	50143243	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	36	352	0	ENST00000246792.3:c.113G>A	p.Gly38Asp	p.G38D	ENST00000246792	NM_006270.3	38	gGc/gAc	1/6	0.264598333526578	1	FACETS	0.204	0.167	0.245	0.204	0.167	0.245	INDETERMINATE	1	TRUE	0	0.556026429277086	1		352	458	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543628	29543628	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	198	515	0	ENST00000389048.3:c.1535A>T	p.Gln512Leu	p.Q512L	ENST00000389048	NM_004304.4	512	cAg/cTg	7/29	0.431303173709989	3	FACETS	1	0.991	1	0.744	0.693	0.796	CLONAL	1	TRUE	1	0.556026429277086	3		515	612	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547900	41547900	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	41	450	0	ENST00000263253.7:c.2881G>C	p.Glu961Gln	p.E961Q	ENST00000263253	NM_001429.3	961	Gaa/Caa	15/31	0.45832948065669	3	FACETS	0.308	0.256	0.367	0.154	0.128	0.184	SUBCLONAL	1	TRUE	1	0.556026429277086	3		450	611	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89176398	89176398	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	71	309	0	ENST00000336596.2:c.128G>T	p.Gly43Val	p.G43V	ENST00000336596	NM_005233.5	43	gGc/gTc	2/17	0.431303173709989	3	FACETS	0.875	0.768	0.989	0.438	0.384	0.495	CLONAL	1	TRUE	1	0.556026429277086	3		309	373	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462335	89462335	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	102	489	0	ENST00000336596.2:c.1807G>C	p.Glu603Gln	p.E603Q	ENST00000336596	NM_005233.5	603	Gaa/Caa	10/17	0.431303173709989	3	FACETS	0.867	0.778	0.961	0.433	0.389	0.481	CLONAL	1	TRUE	1	0.556026429277086	3		489	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882019	NA	P-0034102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	260	443	1	ENST00000269305.4:c.455del	p.Pro152ArgfsTer18	p.P152Rfs*18	ENST00000269305	NM_001126112.2	152	cCg/cg	5/11	0.447834011976023	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.475710891750407	1		444	778	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696405	47696405	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	141	554	0	ENST00000347630.2:c.418G>T	p.Asp140Tyr	p.D140Y	ENST00000347630	NM_001007230.1	140	Gat/Tat	6/11	1	2	FACETS	0.834	0.761	0.91	0.834	0.761	0.91	CLONAL	1	TRUE	1	0.475710891750407	2		554	711	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937718	44937718	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	111	596	0	ENST00000377967.4:c.2906T>G	p.Val969Gly	p.V969G	ENST00000377967	NM_021140.2	969	gTa/gGa	19/29	0.478159437071496	0	FACETS	0.577	0.522	0.634			1	SUBCLONAL	1	TRUE	0	0.475710891750407	0		596	424	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602619	10602619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	126	586	1	ENST00000171111.5:c.959G>A	p.Arg320Gln	p.R320Q	ENST00000171111	NM_203500.1	320	cGg/cAg	3/6	0.350941897996013	1	FACETS	0.905	0.822	0.993	0.905	0.822	0.993	CLONAL	1	TRUE	0	0.350941897996013	1		587	654	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0034133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	104	505	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.350941897996013	2		505	590	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983049	201983049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	129	606	1	ENST00000359651.3:c.898G>A	p.Glu300Lys	p.E300K	ENST00000359651		300	Gaa/Aaa	7/8	1	2	FACETS	0.886	0.803	0.973	0.886	0.803	0.973	CLONAL	1	TRUE	1	0.350941897996013	2		607	830	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444363	49444363	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	127	486	1	ENST00000301067.7:c.3008C>A	p.Pro1003Gln	p.P1003Q	ENST00000301067	NM_003482.3	1003	cCa/cAa	11/54	1	2	FACETS	0.981	0.889	1	0.981	0.889	1	CLONAL	1	TRUE	1	0.350941897996013	2		487	738	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281956	49281956	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	135	596	0	ENST00000282018.3:c.1003C>T	p.Pro335Ser	p.P335S	ENST00000282018	NM_020377.2	335	Cct/Tct	1/1	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.350941897996013	2		596	764	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040998	47040998	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	137	304	0	ENST00000377604.3:c.1528C>T	p.Gln510Ter	p.Q510*	ENST00000377604	NM_001204468.1	510	Caa/Taa	14/24	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.350941897996013	1		304	431	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0034330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	90	414	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.106733324643556	3	FACETS	1	0.951	1	0.375	0.333	0.42	INDETERMINATE	1	FALSE	0	0.317049366289467	3		414	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0034330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	88	778	2	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.317049366289467	1	FACETS	0.655	0.58	0.735	0.655	0.58	0.735	SUBCLONAL	1	FALSE	0	0.317049366289467	1		780	713	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974782	21974782	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs138677674	NA	P-0034330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	30	173	0	ENST00000304494.5:c.45G>A	p.Trp15Ter	p.W15*	ENST00000304494	NM_000077.4	15	tgG/tgA	1/3	0.304657121761149	0	FACETS	0.845	0.69	1			1	CLONAL	1	FALSE	0	0.317049366289467	0		173	153	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551696	150551696	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1351372864	NA	P-0034330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	25	325	0	ENST00000369026.2:c.311G>T	p.Arg104Leu	p.R104L	ENST00000369026	NM_021960.4	104	cGc/cTc	1/3	0.317049366289467	6	FACETS	0.691	0.544	0.86			1	SUBCLONAL	1	FALSE	NA	0.317049366289467	6		325	373	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149434821	149434821	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	72	748	1	ENST00000286301.3:c.2633C>A	p.Pro878His	p.P878H	ENST00000286301	NM_005211.3	878	cCt/cAt	20/22	1	2	FACETS	0.577	0.503	0.657	0.577	0.503	0.657	SUBCLONAL	1	FALSE	1	0.317049366289467	2		749	787	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121684	108121684	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	61	546	0	ENST00000278616.4:c.1492G>T	p.Glu498Ter	p.E498*	ENST00000278616	NM_000051.3	498	Gag/Tag	10/63	1	2	FACETS	0.589	0.508	0.678	0.589	0.508	0.678	SUBCLONAL	1	FALSE	1	0.317049366289467	2		546	653	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344479	118344479	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	43	273	0	ENST00000534358.1:c.2605G>T	p.Glu869Ter	p.E869*	ENST00000534358	NM_005933.3	869	Gag/Tag	3/36	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	FALSE	1	0.317049366289467	2		273	268	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923423	9923423	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	43	700	0	ENST00000330684.3:c.1864C>A	p.Pro622Thr	p.P622T	ENST00000330684	NM_001134407.1	622	Cct/Act	9/13	0.317049366289467	1	FACETS	0.615	0.516	0.725	0.615	0.516	0.725	SUBCLONAL	1	FALSE	0	0.317049366289467	1		700	371	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610361	10610361	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	68	853	0	ENST00000171111.5:c.349G>A	p.Glu117Lys	p.E117K	ENST00000171111	NM_203500.1	117	Gag/Aag	2/6	0.317049366289467	1	FACETS	0.511	0.444	0.583	0.511	0.444	0.583	SUBCLONAL	1	FALSE	0	0.317049366289467	1		853	707	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443655	29443655	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	56	687	0	ENST00000389048.3:c.3562C>A	p.Gln1188Lys	p.Q1188K	ENST00000389048	NM_004304.4	1188	Caa/Aaa	23/29	0.283568145469702	1	FACETS	0.515	0.441	0.596	0.515	0.441	0.596	SUBCLONAL	1	FALSE	0	0.317049366289467	1		687	577	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419938	41419938	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	20	542	0	ENST00000373198.4:c.383G>T	p.Gly128Val	p.G128V	ENST00000373198	NM_133170.3	128	gGt/gTt	3/32	0.317049366289467	0	FACETS	0.246	0.188	0.315			1	SUBCLONAL	1	FALSE	0	0.317049366289467	0		542	350	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213804	66213804	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	28	457	0	ENST00000273854.3:c.2626G>T	p.Glu876Ter	p.E876*	ENST00000273854	NM_004439.5	876	Gag/Tag	15/18	0.283568145469702	1	FACETS	0.318	0.254	0.392	0.318	0.254	0.392	SUBCLONAL	1	FALSE	0	0.317049366289467	1		457	467	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517765	187517765	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	26	242	0	ENST00000441802.2:c.12929C>G	p.Pro4310Arg	p.P4310R	ENST00000441802	NM_005245.3	4310	cCc/cGc	25/27	0.283568145469702	1	FACETS	0.648	0.516	0.797	0.648	0.516	0.797	SUBCLONAL	1	FALSE	0	0.317049366289467	1		242	213	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524890	187524890	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	72	794	2	ENST00000441802.2:c.10790del	p.Gly3597AlafsTer3	p.G3597Afs*3	ENST00000441802	NM_005245.3	3597	gGc/gc	19/27	0.283568145469702	1	FACETS	0.658	0.575	0.747	0.658	0.575	0.747	SUBCLONAL	1	FALSE	0	0.317049366289467	1		796	581	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526321	31526321	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	85	1023	0	ENST00000344624.3:c.719G>C	p.Arg240Pro	p.R240P	ENST00000344624		240	cGa/cCa	2/33	0.317049366289467	1	FACETS	0.643	0.568	0.723	0.643	0.568	0.723	SUBCLONAL	1	FALSE	0	0.317049366289467	1		1023	702	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520524	176520524	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	78	900	0	ENST00000292408.4:c.1369G>T	p.Asp457Tyr	p.D457Y	ENST00000292408	NM_213647.1	457	Gac/Tac	10/18	1	2	FACETS	0.815	0.716	0.92	0.815	0.716	0.92	CLONAL	1	FALSE	1	0.317049366289467	2		900	604	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168743	32168743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	47	701	0	ENST00000375023.3:c.4180C>T	p.Pro1394Ser	p.P1394S	ENST00000375023	NM_004557.3	1394	Cct/Tct	23/30	1	2	FACETS	0.603	0.508	0.706	0.603	0.508	0.706	SUBCLONAL	1	FALSE	1	0.317049366289467	2		701	492	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345752	152345752	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	23	274	0	ENST00000359321.1:c.818G>T	p.Gly273Val	p.G273V	ENST00000359321	NM_005431.1	273	gGa/gTa	3/3	1	2	FACETS	0.576	0.45	0.72	0.576	0.45	0.72	SUBCLONAL	1	FALSE	1	0.317049366289467	2		274	252	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0035032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	67	488	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.196152289285577	3	FACETS	0.816	0.725	0.91	0.816	0.725	0.91	INDETERMINATE	2	TRUE	1	0.617238024704567	3		488	174	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100442	8100442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	41	926	0	ENST00000346208.3:c.416C>T	p.Ser139Phe	p.S139F	ENST00000346208		139	tCc/tTc	3/6	1	2	FACETS	0.942	0.801	1	0.942	0.801	1	CLONAL	1	TRUE	1	0.617238024704567	2		926	141	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	507	487	0	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	0.886329618488617	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.899360094960136	2		487	563	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522569	106522569	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746783339	NA	P-0035701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	275	360	0	ENST00000359195.3:c.2546G>A	p.Arg849Gln	p.R849Q	ENST00000359195	NM_002649.2	849	cGa/cAa	7/11	0.899360094960136	3	FACETS	0.951	0.907	0.995	0.951	0.907	0.995	CLONAL	2	TRUE	1	0.899360094960136	3		360	466	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786766	3786766	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587783496	NA	P-0035701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	464	486	0	ENST00000262367.5:c.4445A>G	p.Tyr1482Cys	p.Y1482C	ENST00000262367	NM_004380.2	1482	tAc/tGc	27/31	0.772055887569604	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.899360094960136	4		486	954	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280147	66280147	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	82	276	1	ENST00000273854.3:c.1542C>A	p.Ser514Arg	p.S514R	ENST00000273854	NM_004439.5	514	agC/agA	7/18	0.899360094960136	3	FACETS	0.694	0.616	0.776			1	SUBCLONAL	1	TRUE	NA	0.899360094960136	3		277	381	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748052	72748052	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	213	422	0	ENST00000357731.5:c.126G>C	p.Trp42Cys	p.W42C	ENST00000357731	NM_173808.2	42	tgG/tgC	1/7	0.899360094960136	3	FACETS	1	0.974	1	0.54	0.504	0.576	CLONAL	1	TRUE	1	0.899360094960136	3		422	636	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432574	78432574	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	144	418	0	ENST00000370768.2:c.409G>T	p.Ala137Ser	p.A137S	ENST00000370768	NM_003902.3	137	Gct/Tct	6/20	0.899360094960136	3	FACETS	0.914	0.839	0.991	0.457	0.419	0.496	CLONAL	1	TRUE	1	0.899360094960136	3		418	508	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841488	156841488	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	470	546	0	ENST00000524377.1:c.791C>A	p.Thr264Lys	p.T264K	ENST00000524377	NM_002529.3	264	aCg/aAg	7/17	0.772055887569604	4	FACETS	0.997	0.957	1	0.997	0.957	1	CLONAL	2	TRUE	2	0.899360094960136	4		546	996	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144734	119144734	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	263	269	0	ENST00000264033.4:c.747G>T	p.Gln249His	p.Q249H	ENST00000264033	NM_005188.3	249	caG/caT	4/16	0.899360094960136	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.899360094960136	3		269	420	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205275	46205275	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	394	373	0	ENST00000334344.6:c.359C>A	p.Pro120Gln	p.P120Q	ENST00000334344	NM_152641.2	120	cCa/cAa	4/21	0.530225928978586	4	FACETS	0.906	0.874	0.939	0.906	0.874	0.939	INDETERMINATE	3	TRUE	1	0.899360094960136	4		373	612	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033843	49033843	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	319	341	0	ENST00000267163.4:c.1981del	p.Arg661GlyfsTer2	p.R661Gfs*2	ENST00000267163	NM_000321.2	660	ctC/ct	20/27	0.886329618488617	2	FACETS	0.966	0.942	0.989	0.966	0.942	0.989	CLONAL	2	TRUE	0	0.899360094960136	2		341	367	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046554	30046554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	578	496	0	ENST00000331968.5:c.2629G>A	p.Gly877Arg	p.G877R	ENST00000331968	NM_002742.2	877	Ggg/Agg	18/18	0.884763890002436	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.899360094960136	2		496	640	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786138	3786138	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	595	667	0	ENST00000262367.5:c.4627G>C	p.Asp1543His	p.D1543H	ENST00000262367	NM_004380.2	1543	Gat/Cat	28/31	0.772055887569604	4	FACETS	0.939	0.905	0.974	0.939	0.905	0.974	CLONAL	2	TRUE	2	0.899360094960136	4		667	1338	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647649	23647649	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	234	255	0	ENST00000261584.4:c.218A>G	p.Lys73Arg	p.K73R	ENST00000261584	NM_024675.3	73	aAa/aGa	4/13	0.772055887569604	4	FACETS	0.961	0.907	1	0.961	0.907	1	CLONAL	2	TRUE	2	0.899360094960136	4		255	514	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828302	72828302	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	422	448	0	ENST00000268489.5:c.8279T>A	p.Met2760Lys	p.M2760K	ENST00000268489	NM_006885.3	2760	aTg/aAg	9/10	0.886329618488617	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.899360094960136	2		448	469	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228801	36228801	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	797	617	2	ENST00000222270.7:c.7700G>T	p.Arg2567Leu	p.R2567L	ENST00000222270	NM_014727.1	2567	cGt/cTt	35/37	0.822491769698078	5	FACETS	0.954	0.927	0.982	0.954	0.927	0.982	CLONAL	3	TRUE	2	0.899360094960136	5		619	1454	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462330	89462330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751984150	NA	P-0035701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	40	351	1	ENST00000336596.2:c.1802C>T	p.Thr601Ile	p.T601I	ENST00000336596	NM_005233.5	601	aCa/aTa	10/17	NA	2	FACETS	0.297	0.247	0.351			1	INDETERMINATE	1	TRUE	NA	0.899360094960136	2		352	300	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480348	89480348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	32	214	0	ENST00000336596.2:c.2185G>A	p.Gly729Arg	p.G729R	ENST00000336596	NM_005233.5	729	Ggg/Agg	13/17	NA	2	FACETS	0.315	0.257	0.379			1	INDETERMINATE	1	TRUE	NA	0.899360094960136	2		214	226	SUCCESS
ATR	545	MSKCC	GRCh37	3	142185274	142185274	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	164	397	0	ENST00000350721.4:c.6789A>T	p.Gln2263His	p.Q2263H	ENST00000350721	NM_001184.3	2263	caA/caT	40/47	0.899360094960136	3	FACETS	0.99	0.915	1	0.495	0.457	0.534	CLONAL	1	TRUE	1	0.899360094960136	3		397	534	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149498314	149498314	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	387	414	0	ENST00000261799.4:c.2900A>G	p.Lys967Arg	p.K967R	ENST00000261799	NM_002609.3	967	aAa/aGa	21/23	0.890862859872137	2	FACETS	0.987	0.966	1	0.987	0.966	1	CLONAL	2	TRUE	0	0.899360094960136	2		414	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	732	723	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		723	866	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123889566	123889566	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	170	202	2	ENST00000330479.4:c.793G>T	p.Asp265Tyr	p.D265Y	ENST00000330479	NM_020382.3	265	Gac/Tac	7/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		204	272	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932944	39932944	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	602	597	0	ENST00000378444.4:c.1655C>T	p.Ala552Val	p.A552V	ENST00000378444	NM_001123385.1	552	gCt/gTt	4/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		597	1233	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148875	119148875	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs397517076	NA	P-0035890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	196	224	0	ENST00000264033.4:c.1096-1G>T		p.X366_splice	ENST00000264033	NM_005188.3	366			0.3	4	FACETS	0.888	0.831	0.947	1	0.985	1	CLONAL	4	TRUE	1	0.3	4		224	478	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172434	108172434	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs879254135	NA	P-0035890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	142	455	2	ENST00000278616.4:c.5237G>T	p.Gly1746Val	p.G1746V	ENST00000278616	NM_000051.3	1746	gGa/gTa	35/63	NA	2	FACETS	0.891	0.817	0.969			1	INDETERMINATE	2	TRUE	NA	0.3	2		457	531	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127420	17127420	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	127	546	0	ENST00000285071.4:c.434A>T	p.Asp145Val	p.D145V	ENST00000285071	NM_144997.5	145	gAt/gTt	6/14	0.299699967821341	3	FACETS	0.917	0.829	1	0.458	0.414	0.505	CLONAL	1	TRUE	1	0.3	3		546	1062	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0036134-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	173	697	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.986	0.911	1	0.986	0.911	1	CLONAL	1	TRUE	1	0.513760083262499	2		697	683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0036134-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	174	818	0	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	0.513760083262499	1	FACETS	0.924	0.856	0.993	0.924	0.856	0.993	CLONAL	1	TRUE	0	0.513760083262499	1		818	545	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0036134-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	178	545	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.513760083262499	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.513760083262499	1		545	376	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020768	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs926053251	NA	P-0036134-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	131	506	0	ENST00000358127.4:c.77T>G	p.Val26Gly	p.V26G	ENST00000358127	NM_001280556.1	26	gTt/gGt	2/10	0.513760083262499	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.513760083262499	1		506	362	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945988	17945988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747131454	NA	P-0036134-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	165	707	0	ENST00000458235.1:c.1951C>T	p.Arg651Trp	p.R651W	ENST00000458235	NM_000215.3	651	Cgg/Tgg	15/24	1	2	FACETS	0.927	0.854	1	0.927	0.854	1	CLONAL	1	TRUE	1	0.513760083262499	2		707	693	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439778	220439778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036134-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	186	869	3	ENST00000243786.2:c.631G>A	p.Ala211Thr	p.A211T	ENST00000243786	NM_002191.3	211	Gcc/Acc	2/2	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.513760083262499	2		872	720	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880882	134880882	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs936404830	NA	P-0036501-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	100	371	0	ENST00000398015.3:c.1445C>T	p.Ser482Phe	p.S482F	ENST00000398015	NM_004441.4	482	tCc/tTc	7/16	0.117971234311905	0	FACETS	0.369	0.333	0.407			1	INDETERMINATE	1	TRUE	0	0.608915257254568	0		371	348	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948780	55948780	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763426023	NA	P-0036501-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	103	404	3	ENST00000263923.4:c.3685C>T	p.Arg1229Ter	p.R1229*	ENST00000263923	NM_002253.2	1229	Cga/Tga	28/30	1	2	FACETS	0.964	0.871	1	0.964	0.871	1	CLONAL	1	TRUE	1	0.608915257254568	2		407	351	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911194	29911201	+	frameshift_variant	Frame_Shift_Del	DEL	CAGATCAC	CAGATCAC	-	novel	NA	P-0036501-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	947	393	0	ENST00000376809.5:c.495_502del	p.Ile166AlafsTer8	p.I166Afs*8	ENST00000376809	NM_002116.7	165	CAGATCACc/c	3/8	0.608915257254568	5	FACETS	1	0.996	1	1	0.996	1	CLONAL	5	TRUE	0	0.608915257254568	5		393	1136	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0036964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	23	544	1	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	1	2	FACETS	0.454	0.352	0.572	0.454	0.352	0.572	SUBCLONAL	1	TRUE	1	0.15	2		545	676	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89846329	89846329	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	35	547	0	ENST00000389301.3:c.1663A>T	p.Ile555Phe	p.I555F	ENST00000389301	NM_000135.2	555	Atc/Ttc	18/43	1	2	FACETS	0.776	0.635	0.936	0.776	0.635	0.936	CLONAL	1	TRUE	1	0.15	2		547	601	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600446	10600446	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	21	638	0	ENST00000171111.5:c.1409G>C	p.Arg470Pro	p.R470P	ENST00000171111	NM_203500.1	470	cGt/cCt	4/6	1	2	FACETS	0.461	0.354	0.588	0.461	0.354	0.588	SUBCLONAL	1	TRUE	1	0.15	2		638	607	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0036979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	59	699	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.0940355544964025	3	FACETS	1	0.929	1	0.566	0.487	0.653	INDETERMINATE	1	TRUE	1	0.17	3		699	665	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912414	32912414	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs80358638	NA	P-0036979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	22	134	0	ENST00000380152.3:c.3922G>T	p.Glu1308Ter	p.E1308*	ENST00000380152		1308	Gaa/Taa	11/27	0.279027089991462	3	FACETS	0.751	0.581	0.948	0.375	0.29	0.474	CLONAL	1	TRUE	1	0.17	3		134	374	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998919	11998919	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	28	135	0	ENST00000353533.5:c.421G>T	p.Glu141Ter	p.E141*	ENST00000353533	NM_003010.3	141	Gaa/Taa	4/11	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.17	2		135	279	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390970	139390970	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	52	1063	1	ENST00000277541.6:c.7221C>A	p.Ser2407Arg	p.S2407R	ENST00000277541	NM_017617.3	2407	agC/agA	34/34	1	2	FACETS	0.734	0.623	0.857	0.734	0.623	0.857	SUBCLONAL	1	TRUE	1	0.17	2		1064	833	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849242	76849242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	28	301	0	ENST00000373344.5:c.6034G>A	p.Glu2012Lys	p.E2012K	ENST00000373344	NM_000489.3	2012	Gag/Aag	26/35	1	2	FACETS	0.598	0.477	0.737	0.598	0.477	0.737	SUBCLONAL	1	TRUE	1	0.17	2		301	551	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266602	198266602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	42	310	0	ENST00000335508.6:c.2234C>T	p.Ala745Val	p.A745V	ENST00000335508	NM_012433.2	745	gCt/gTt	16/25	1	2	FACETS	0.67	0.56	0.79	0.67	0.56	0.79	SUBCLONAL	1	TRUE	1	0.338174645287662	2		310	371	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	166	477	5	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	0.338174645287662	2	FACETS	0.974	0.902	1	0.974	0.902	1	CLONAL	2	TRUE	0	0.338174645287662	2		482	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	131	490	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.338174645287662	1	FACETS	0.951	0.865	1	0.951	0.865	1	CLONAL	1	TRUE	0	0.338174645287662	1		490	677	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294665	1294665	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	77	543	1	ENST00000310581.5:c.336del	p.Glu113ArgfsTer15	p.E113Rfs*15	ENST00000310581	NM_198253.2	112	ccC/cc	2/16	1	2	FACETS	0.771	0.677	0.871	0.771	0.677	0.871	SUBCLONAL	1	TRUE	1	0.338174645287662	2		544	591	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	147	412	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.811	0.745	0.88	1	0.989	1	CLONAL	2	TRUE	1	0.338174645287662	2		412	536	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101370	27101370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748819428	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	103	524	4	ENST00000324856.7:c.4652G>A	p.Arg1551His	p.R1551H	ENST00000324856	NM_006015.4	1551	cGc/cAc	18/20	0.338174645287662	2	FACETS	0.908	0.813	1	0.454	0.406	0.504	CLONAL	1	TRUE	0	0.338174645287662	2		528	671	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625281	69625281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35983315	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	96	636	1	ENST00000334134.2:c.512G>A	p.Arg171His	p.R171H	ENST00000334134	NM_005247.2	171	cGc/cAc	3/3	1	2	FACETS	0.832	0.742	0.929	0.832	0.742	0.929	CLONAL	1	TRUE	1	0.338174645287662	2		637	682	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508904	106508904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	51	367	0	ENST00000359195.3:c.898G>A	p.Gly300Arg	p.G300R	ENST00000359195	NM_002649.2	300	Gga/Aga	2/11	0.315859354500002	3	FACETS	0.7	0.595	0.815	0.35	0.297	0.408	SUBCLONAL	1	TRUE	1	0.338174645287662	3		367	504	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553478	29553478	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781807	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	106	539	3	ENST00000356175.3:c.2033del	p.Pro678ArgfsTer10	p.P678Rfs*10	ENST00000356175	NM_000267.3	676	aCc/ac	18/57	1	2	FACETS	0.874	0.784	0.97	0.874	0.784	0.97	CLONAL	1	TRUE	1	0.338174645287662	2		542	717	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	147	589	2	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.338174645287662	2		591	813	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620470	52620470	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	95	430	0	ENST00000394830.3:c.3283C>T	p.Arg1095Ter	p.R1095*	ENST00000394830	NM_018313.4	1095	Cga/Tga	21/30	0.338174645287662	1	FACETS	0.809	0.722	0.902	0.809	0.722	0.902	CLONAL	1	TRUE	0	0.338174645287662	1		430	577	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489582	56489582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56387488	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	87	347	0	ENST00000267101.3:c.2047C>T	p.Arg683Trp	p.R683W	ENST00000267101	NM_001982.3	683	Cgg/Tgg	17/28	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.338174645287662	2		347	467	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347484	91347484	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	88	455	1	ENST00000355112.3:c.3651del	p.Lys1217AsnfsTer62	p.K1217Nfs*62	ENST00000355112	NM_000057.2	1216	Aaa/aa	19/22	1	2	FACETS	0.955	0.848	1	0.955	0.848	1	CLONAL	1	TRUE	1	0.338174645287662	2		456	545	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630605	187630605	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	105	630	0	ENST00000441802.2:c.377del	p.Asn126IlefsTer20	p.N126Ifs*20	ENST00000441802	NM_005245.3	126	aAt/at	2/27	0.315859354500002	3	FACETS	0.774	0.692	0.861	0.387	0.346	0.431	SUBCLONAL	1	TRUE	1	0.338174645287662	3		630	938	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988309	36988309	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776709	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	56	455	1	ENST00000354822.5:c.344del	p.Gly115AlafsTer10	p.G115Afs*10	ENST00000354822	NM_001079668.2	115	gGc/gc	2/3	1	2	FACETS	0.561	0.481	0.65	0.561	0.481	0.65	SUBCLONAL	1	TRUE	1	0.338174645287662	2		456	590	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	131	524	1	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	0.973	0.884	1	0.973	0.884	1	CLONAL	1	TRUE	1	0.338174645287662	2		525	796	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119023	70119024	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	88	499	0	ENST00000245479.2:c.600dup	p.Asn201GlnfsTer51	p.N201Qfs*51	ENST00000245479	NM_000346.3	199	tcc/tCcc	2/3	1	2	FACETS	0.91	0.808	1	0.91	0.808	1	CLONAL	1	TRUE	1	0.338174645287662	2		499	572	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156935	106156936	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs763386429	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	30	313	0	ENST00000380013.4:c.1842dup	p.Leu615AlafsTer23	p.L615Afs*23	ENST00000380013	NM_001127208.2	612	-/G	3/11	0.315859354500002	3	FACETS	0.462	0.372	0.565	0.231	0.186	0.283	SUBCLONAL	1	TRUE	1	0.338174645287662	3		313	449	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946340	2946340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1171346123	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	305	748	0	ENST00000396946.4:c.3397C>T	p.Arg1133Cys	p.R1133C	ENST00000396946	NM_032415.4	1133	Cgc/Tgc	25/25	0.315859354500002	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.338174645287662	3		748	988	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929412	44929415	+	frameshift_variant	Frame_Shift_Del	DEL	ACAA	ACAA	-	rs786205676	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	96	256	0	ENST00000377967.4:c.2515_2518del	p.Asn839ValfsTer27	p.N839Vfs*27	ENST00000377967	NM_021140.2	838	ACAAac/ac	17/29	1	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.338174645287662	1		256	386	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250135	110250136	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	56	590	0	ENST00000374672.4:c.539dup	p.Pro181SerfsTer76	p.P181Sfs*76	ENST00000374672	NM_004235.4	180	cct/ccCt	3/5	1	2	FACETS	0.533	0.456	0.617	0.533	0.456	0.617	SUBCLONAL	1	TRUE	1	0.338174645287662	2		590	621	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727122	243727122	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	78	454	1	ENST00000263826.5:c.848G>A	p.Gly283Asp	p.G283D	ENST00000263826	NM_005465.4	283	gGc/gAc	9/13	0.300510602603202	1	FACETS	0.737	0.649	0.831	0.737	0.649	0.831	SUBCLONAL	1	TRUE	0	0.338174645287662	1		455	520	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948279	71948280	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	162	859	2	ENST00000298229.2:c.2996dup	p.Glu1000GlyfsTer43	p.E1000Gfs*43	ENST00000298229	NM_001567.3	997	-/C	26/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.338174645287662	2		861	906	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385259	4385259	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	89	412	0	ENST00000261254.3:c.284A>C	p.Lys95Thr	p.K95T	ENST00000261254	NM_001759.3	95	aAg/aCg	2/5	NA	2	FACETS	0.962	0.855	1			1	INDETERMINATE	1	TRUE	NA	0.338174645287662	2		412	547	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421066	49421066	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	69	410	0	ENST00000301067.7:c.14683A>G	p.Thr4895Ala	p.T4895A	ENST00000301067	NM_003482.3	4895	Acc/Gcc	48/54	1	2	FACETS	0.777	0.678	0.884	0.777	0.678	0.884	SUBCLONAL	1	TRUE	1	0.338174645287662	2		410	525	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060983	38060983	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	45	359	0	ENST00000250448.2:c.1006G>A	p.Asp336Asn	p.D336N	ENST00000250448	NM_004496.3	336	Gac/Aac	2/2	1	2	FACETS	0.754	0.636	0.884	0.754	0.636	0.884	SUBCLONAL	1	TRUE	1	0.338174645287662	2		359	353	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66781607	66781610	+	frameshift_variant	Frame_Shift_Del	DEL	AATA	AATA	-	novel	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	97	419	0	ENST00000307102.5:c.1018_1021del	p.Lys340AlafsTer2	p.K340Afs*2	ENST00000307102	NM_002755.3	339	AATAaa/aa	9/11	1	2	FACETS	0.999	0.893	1	0.999	0.893	1	CLONAL	1	TRUE	1	0.338174645287662	2		419	574	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81891931	81891931	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1280791888	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	89	456	0	ENST00000359376.3:c.401T>C	p.Met134Thr	p.M134T	ENST00000359376	NM_002661.3	134	aTg/aCg	4/33	0.338174645287662	1	FACETS	0.738	0.655	0.826	0.738	0.655	0.826	SUBCLONAL	1	TRUE	0	0.338174645287662	1		456	593	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676226	29676226	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1567623508	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	82	305	0	ENST00000356175.3:c.7215T>A	p.Cys2405Ter	p.C2405*	ENST00000356175	NM_000267.3	2405	tgT/tgA	48/57	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.338174645287662	2		305	373	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78933974	78933974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375708825	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	120	617	0	ENST00000306801.3:c.3574G>A	p.Val1192Ile	p.V1192I	ENST00000306801	NM_020761.2	1192	Gtc/Atc	30/34	1	2	FACETS	0.949	0.857	1	0.949	0.857	1	CLONAL	1	TRUE	1	0.338174645287662	2		617	748	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208046	5208046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142977438	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	102	494	0	ENST00000357368.4:c.5665G>A	p.Val1889Ile	p.V1889I	ENST00000357368	NM_002850.3	1889	Gtc/Atc	37/38	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.338174645287662	2		494	554	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229608	5229608	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	38	109	0	ENST00000357368.4:c.2243G>A	p.Arg748Gln	p.R748Q	ENST00000357368	NM_002850.3	748	cGg/cAg	15/38	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.338174645287662	2		109	159	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212003	36212003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs189407972	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	174	842	0	ENST00000222270.7:c.1754G>A	p.Arg585His	p.R585H	ENST00000222270	NM_014727.1	585	cGt/cAt	3/37	1	2	FACETS	0.99	0.911	1	0.99	0.911	1	CLONAL	1	TRUE	1	0.338174645287662	2		842	1039	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223256	36223257	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	140	851	0	ENST00000222270.7:c.5810dup	p.Gln1938SerfsTer34	p.Q1938Sfs*34	ENST00000222270	NM_014727.1	1936	tcc/tCcc	28/37	1	2	FACETS	0.8	0.727	0.876	0.8	0.727	0.876	SUBCLONAL	1	TRUE	1	0.338174645287662	2		851	1035	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089047	37089047	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs1553662753	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	92	345	0	ENST00000231790.2:c.1769T>G	p.Leu590Ter	p.L590*	ENST00000231790	NM_000249.3	590	tTa/tGa	16/19	0.338174645287662	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.338174645287662	1		345	374	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266658	41266658	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1333019206	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	97	457	0	ENST00000349496.5:c.455C>T	p.Ala152Val	p.A152V	ENST00000349496	NM_001904.3	152	gCa/gTa	4/15	0.338174645287662	1	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	0	0.338174645287662	1		457	475	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805717	32805718	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	61	563	0	ENST00000374899.4:c.293dup	p.Trp99LeufsTer68	p.W99Lfs*68	ENST00000374899	NM_018833.2	98	cct/ccCt	2/12	0.338174645287662	1	FACETS	0.581	0.502	0.667	0.581	0.502	0.667	SUBCLONAL	1	TRUE	0	0.338174645287662	1		563	516	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288774	33288774	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	72	433	0	ENST00000374542.5:c.778C>A	p.Arg260Ser	p.R260S	ENST00000374542	NM_001141970.1	260	Cgt/Agt	3/8	0.338174645287662	1	FACETS	0.827	0.725	0.935	0.827	0.725	0.935	CLONAL	1	TRUE	0	0.338174645287662	1		433	428	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021749	69021749	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	38	406	0	ENST00000288368.4:c.3037T>C	p.Tyr1013His	p.Y1013H	ENST00000288368	NM_024870.2	1013	Tat/Cat	25/40	0.25515132950967	3	FACETS	0.41	0.338	0.491	0.205	0.169	0.246	SUBCLONAL	1	TRUE	1	0.338174645287662	3		406	641	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738258	133738258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753573200	NA	P-0036993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	89	422	0	ENST00000318560.5:c.658C>T	p.Arg220Cys	p.R220C	ENST00000318560	NM_005157.4	220	Cgc/Tgc	4/11	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.338174645287662	2		422	514	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521560	46521560	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1349710966	NA	P-0037071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	321	790	0	ENST00000262741.5:c.848A>G	p.Asn283Ser	p.N283S	ENST00000262741	NM_003629.3	283	aAt/aGt	7/10	0.654508451788083	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.654508451788083	1		790	660	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18496281	18496281	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	99	241	0	ENST00000266497.5:c.1416G>C	p.Glu472Asp	p.E472D	ENST00000266497		472	gaG/gaC	9/31	1	2	FACETS	0.836	0.753	0.922	0.836	0.753	0.922	CLONAL	1	TRUE	1	0.654508451788083	2		241	362	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032818	30032818	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	197	465	2	ENST00000338641.4:c.193C>T	p.Gln65Ter	p.Q65*	ENST00000338641	NM_000268.3	65	Cag/Tag	2/16	0.654508451788083	1	FACETS	0.983	0.923	1	0.983	0.923	1	CLONAL	1	TRUE	0	0.654508451788083	1		467	412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577029	7577042	+	frameshift_variant	Frame_Shift_Del	DEL	GCTCCCTGGGGGCA	GCTCCCTGGGGGCA	-	rs1555525054	NA	P-0037082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	219	572	0	ENST00000269305.4:c.896_909del	p.Leu299HisfsTer2	p.L299Hfs*2	ENST00000269305	NM_001126112.2	299	cTGCCCCCAGGGAGC/c	8/11	0.376539283847519	3	FACETS	0.942	0.886	0.999	0.942	0.886	0.999	CLONAL	3	TRUE	0	0.376539283847519	3		572	489	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0037129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	110	621	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.19	2		622	954	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911534	101911534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111426349	NA	P-0037129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	58	364	1	ENST00000374994.4:c.1459C>T	p.Arg487Trp	p.R487W	ENST00000374994	NM_004612.2	487	Cgg/Tgg	9/9	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.19	2		365	610	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0037129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	83	702	1	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.114034916525097	3	FACETS	0.955	0.841	1	0.477	0.42	0.539	CLONAL	1	TRUE	1	0.19	3		703	1002	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900171	101900171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564161322	NA	P-0037129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	28	343	0	ENST00000374994.4:c.605C>T	p.Ala202Val	p.A202V	ENST00000374994	NM_004612.2	202	gCg/gTg	4/9	1	2	FACETS	0.639	0.51	0.787	0.639	0.51	0.787	SUBCLONAL	1	TRUE	1	0.19	2		343	461	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218086	108218086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781814	NA	P-0037129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	58	448	1	ENST00000278616.4:c.8665G>A	p.Asp2889Asn	p.D2889N	ENST00000278616	NM_000051.3	2889	Gat/Aat	59/63	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.19	2		449	607	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438749	49438749	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0037129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	75	596	1	ENST00000301067.7:c.4742-1G>A		p.X1581_splice	ENST00000301067	NM_003482.3	1581			0.180306135470259	4	FACETS	1	0.914	1	0.528	0.462	0.6	CLONAL	1	TRUE	2	0.19	4		597	889	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714414	40714414	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	47	530	1	ENST00000373198.4:c.3983A>G	p.Asp1328Gly	p.D1328G	ENST00000373198	NM_133170.3	1328	gAc/gGc	29/32	0.309517820361774	0	FACETS	0.75	0.633	0.88			1	SUBCLONAL	1	TRUE	0	0.19	0		531	534	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0037156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	163	401	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.703752728478451	6	FACETS	1	0.967	1			1	CLONAL	4	FALSE	NA	0.703752728478451	6		401	268	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458372	120458372	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	20	435	0	ENST00000256646.2:c.6973C>T	p.Gln2325Ter	p.Q2325*	ENST00000256646	NM_024408.3	2325	Cag/Tag	34/34	1	2	FACETS	0.8	0.611	1	0.8	0.611	1	CLONAL	1	TRUE	1	0.14	2		435	357	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443772	49443826	+	frameshift_variant	Frame_Shift_Del	DEL	ATGAGAGTGGGTGGTGTGGGGGCCACCGGTGCACGTGGCTCTTCCTGTTCTTCAC	ATGAGAGTGGGTGGTGTGGGGGCCACCGGTGCACGTGGCTCTTCCTGTTCTTCAC	-	novel	NA	P-0037165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	35	719	0	ENST00000301067.7:c.3545_3599del	p.Cys1182SerfsTer12	p.C1182Sfs*12	ENST00000301067	NM_003482.3	1182	tGTGAAGAACAGGAAGAGCCACGTGCACCGGTGGCCCCCACACCACCCACTCTCATc/tc	11/54	1	2	FACETS	0.885	0.724	1	0.885	0.724	1	CLONAL	1	TRUE	1	0.14	2		719	565	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0037219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	18	615	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.499	0.374	0.647	0.499	0.374	0.647	SUBCLONAL	1	TRUE	1	0.15	2		615	481	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574005	7574005	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	52	825	0	ENST00000269305.4:c.1022T>A	p.Phe341Tyr	p.F341Y	ENST00000269305	NM_001126112.2	341	tTc/tAc	10/11	1	2	FACETS	0.689	0.584	0.804	0.689	0.584	0.804	SUBCLONAL	1	TRUE	1	0.15	2		825	1007	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436312	110436312	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	21	285	0	ENST00000375856.3:c.2089G>T	p.Ala697Ser	p.A697S	ENST00000375856	NM_003749.2	697	Gcc/Tcc	1/2	1	2	FACETS	0.826	0.636	1	0.826	0.636	1	CLONAL	1	TRUE	1	0.15	2		285	339	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450268	50450268	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	43	543	0	ENST00000331340.3:c.452G>T	p.Gly151Val	p.G151V	ENST00000331340	NM_006060.4	151	gGg/gTg	5/8	1	2	FACETS	0.885	0.739	1	0.885	0.739	1	CLONAL	1	TRUE	1	0.15	2		543	648	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045882	47045882	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556782783	NA	P-0037219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	17	327	2	ENST00000377604.3:c.2677C>T	p.Arg893Trp	p.R893W	ENST00000377604	NM_001204468.1	893	Cgg/Tgg	24/24	1	1	FACETS	0.645	0.481	0.841	0.645	0.481	0.841	SUBCLONAL	1	TRUE	0	0.15	1		329	325	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0037226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	235	214	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.588371593300682	2		214	773	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618616	37618616	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	122	670	0	ENST00000447079.4:c.292G>T	p.Glu98Ter	p.E98*	ENST00000447079	NM_015083.1	98	Gaa/Taa	1/14	NA	2	FACETS	0.557	0.504	0.614			1	INDETERMINATE	1	TRUE	NA	0.588371593300682	2		670	744	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0037226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	252	767	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.588371593300682	1	FACETS	0.983	0.927	1	0.983	0.927	1	CLONAL	1	TRUE	0	0.588371593300682	1		767	615	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233279	69233279	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	131	373	0	ENST00000462284.1:c.1144G>A	p.Glu382Lys	p.E382K	ENST00000462284	NM_002392.5	382	Gag/Aag	11/11	1	2	FACETS	0.992	0.907	1	0.992	0.907	1	CLONAL	1	TRUE	1	0.588371593300682	2		373	449	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544705	65544705	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	305	839	0	ENST00000358664.4:c.221del	p.Met74SerfsTer96	p.M74Sfs*96	ENST00000358664	NM_002382.4	74	aTg/ag	4/5	0.588371593300682	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.588371593300682	1		839	711	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470539	25470539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	298	801	0	ENST00000264709.3:c.935C>T	p.Ser312Phe	p.S312F	ENST00000264709	NM_175629.2	312	tCt/tTt	8/23	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.588371593300682	2		801	986	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513238	44513238	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	161	410	0	ENST00000291552.4:c.697G>T	p.Asp233Tyr	p.D233Y	ENST00000291552	NM_006758.2	233	Gat/Tat	8/8	0.588371593300682	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.588371593300682	1		410	377	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401453	401453	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1407719860	NA	P-0037226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	212	314	0	ENST00000380956.4:c.775C>T	p.Arg259Trp	p.R259W	ENST00000380956	NM_001195286.1	259	Cgg/Tgg	7/9	0.506133046066048	3	FACETS	0.849	0.804	0.894	0.849	0.804	0.894	CLONAL	3	TRUE	0	0.588371593300682	3		314	366	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0037232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	65	466	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.261975777122369	2		466	416	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	80	82	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.261975777122369	2		82	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0037232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	125	667	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	NA	3	FACETS	1	0.953	1			1	INDETERMINATE	1	TRUE	NA	0.261975777122369	3		667	990	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416302	29416302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	87	742	0	ENST00000389048.3:c.4651C>T	p.Pro1551Ser	p.P1551S	ENST00000389048	NM_004304.4	1551	Ccg/Tcg	29/29	1	2	FACETS	0.733	0.648	0.825	0.733	0.648	0.825	SUBCLONAL	1	TRUE	1	0.261975777122369	2		742	906	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762959	40762959	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs387906659	NA	P-0037232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	61	561	0	ENST00000392038.2:c.49G>A	p.Glu17Lys	p.E17K	ENST00000392038	NM_001626.4	17	Gaa/Aaa	3/14	1	2	FACETS	0.633	0.545	0.729	0.633	0.545	0.729	SUBCLONAL	1	TRUE	1	0.261975777122369	2		561	736	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161221	56161221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781300314	NA	P-0037232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	53	577	0	ENST00000399503.3:c.1090C>T	p.Arg364Trp	p.R364W	ENST00000399503	NM_005921.1	364	Cgg/Tgg	5/20	1	2	FACETS	0.717	0.612	0.833	0.717	0.612	0.833	SUBCLONAL	1	TRUE	1	0.261975777122369	2		577	564	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174420	11174420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587777900	NA	P-0037232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	77	806	0	ENST00000361445.4:c.7255G>A	p.Glu2419Lys	p.E2419K	ENST00000361445	NM_004958.3	2419	Gaa/Aaa	53/58	1	2	FACETS	0.576	0.504	0.654	0.576	0.504	0.654	SUBCLONAL	1	TRUE	1	0.261975777122369	2		806	1020	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266570	115266570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	65	698	0	ENST00000438362.2:c.1945C>T	p.Arg649Cys	p.R649C	ENST00000438362	NM_001242891.1	649	Cgc/Tgc	16/20	1	2	FACETS	0.556	0.48	0.638	0.556	0.48	0.638	SUBCLONAL	1	TRUE	1	0.261975777122369	2		698	893	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864663	68864663	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773560075	NA	P-0037232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	39	316	0	ENST00000288368.4:c.34G>A	p.Glu12Lys	p.E12K	ENST00000288368	NM_024870.2	12	Gag/Aag	1/40	1	2	FACETS	0.761	0.632	0.905	0.761	0.632	0.905	CLONAL	1	TRUE	1	0.261975777122369	2		316	391	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911987	94911987	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	33	504	0	ENST00000536441.1:c.943G>C	p.Glu315Gln	p.E315Q	ENST00000536441	NM_144665.3	315	Gag/Cag	7/10	1	2	FACETS	0.508	0.413	0.615	0.508	0.413	0.615	SUBCLONAL	1	TRUE	1	0.261975777122369	2		504	496	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647212	23647212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	84	909	1	ENST00000261584.4:c.655G>A	p.Asp219Asn	p.D219N	ENST00000261584	NM_024675.3	219	Gac/Aac	4/13	1	2	FACETS	0.734	0.647	0.827	0.734	0.647	0.827	SUBCLONAL	1	TRUE	1	0.261975777122369	2		910	874	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577502	7577502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	122	699	0	ENST00000269305.4:c.779C>T	p.Ser260Phe	p.S260F	ENST00000269305	NM_001126112.2	260	tCc/tTc	7/11	NA	3	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.261975777122369	3		699	867	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55674294	55674294	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	65	431	0	ENST00000284073.2:c.520G>C	p.Glu174Gln	p.E174Q	ENST00000284073	NM_138962.2	174	Gaa/Caa	8/14	1	2	FACETS	0.732	0.634	0.838	0.732	0.634	0.838	SUBCLONAL	1	TRUE	1	0.261975777122369	2		431	678	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3094754	3094754	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	29	358	1	ENST00000078429.4:c.105C>A	p.Asp35Glu	p.D35E	ENST00000078429	NM_002067.2	35	gaC/gaA	1/7	1	2	FACETS	0.443	0.355	0.544	0.443	0.355	0.544	SUBCLONAL	1	TRUE	1	0.261975777122369	2		359	500	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027773	48027773	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs561217424	NA	P-0037232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	28	432	0	ENST00000234420.5:c.2651C>G	p.Ser884Cys	p.S884C	ENST00000234420	NM_000179.2	884	tCt/tGt	4/10	1	2	FACETS	0.42	0.335	0.518	0.42	0.335	0.518	SUBCLONAL	1	TRUE	1	0.261975777122369	2		432	509	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225752	26225752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368380591	NA	P-0037232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	64	446	0	ENST00000360408.1:c.370G>A	p.Asp124Asn	p.D124N	ENST00000360408	NM_003532.2	124	Gac/Aac	1/1	1	2	FACETS	0.751	0.649	0.86	0.751	0.649	0.86	SUBCLONAL	1	TRUE	1	0.261975777122369	2		446	651	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534960	5534960	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	34	465	0	ENST00000397747.3:c.271C>G	p.Gln91Glu	p.Q91E	ENST00000397747	NM_025239.3	91	Caa/Gaa	3/7	0.261975777122369	1	FACETS	0.436	0.356	0.527	0.436	0.356	0.527	SUBCLONAL	1	TRUE	0	0.261975777122369	1		465	517	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	148	459	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.553691642478289	3	FACETS	0.888	0.812	0.967	0.444	0.406	0.484	CLONAL	1	TRUE	1	0.568562606484462	3		459	753	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012444	29012444	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	140	417	0	ENST00000282397.4:c.427C>A	p.Pro143Thr	p.P143T	ENST00000282397	NM_002019.4	143	Ccc/Acc	4/30	0.399240741600621	3	FACETS	0.97	0.886	1	0.485	0.443	0.529	CLONAL	1	TRUE	1	0.568562606484462	3		417	652	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81962185	81962185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	92	591	0	ENST00000359376.3:c.2537G>A	p.Gly846Glu	p.G846E	ENST00000359376	NM_002661.3	846	gGg/gAg	24/33	0.150370475564577	3	FACETS	0.624	0.555	0.698	0.208	0.185	0.233	INDETERMINATE	1	TRUE	0	0.568562606484462	3		591	666	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120452	70120452	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	384	655	0	ENST00000245479.2:c.1454G>T	p.Gly485Val	p.G485V	ENST00000245479	NM_000346.3	485	gGg/gTg	3/3	0.427709049242809	5	FACETS	0.969	0.92	1	0.646	0.613	0.68	CLONAL	2	TRUE	2	0.568562606484462	5		655	1291	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602256	10602256	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	479	451	0	ENST00000171111.5:c.1322A>G	p.Glu441Gly	p.E441G	ENST00000171111	NM_203500.1	441	gAg/gGg	3/6	0.568562606484462	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	0	0.568562606484462	3		451	711	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770575	40770575	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	74	465	0	ENST00000373198.4:c.2807G>T	p.Arg936Leu	p.R936L	ENST00000373198	NM_133170.3	936	cGa/cTa	19/32	0.167741238376606	2	FACETS	0.514	0.451	0.582	0.257	0.225	0.291	INDETERMINATE	1	TRUE	0	0.568562606484462	2		465	506	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428267	72428267	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	321	444	0	ENST00000477973.2:c.625G>C	p.Asp209His	p.D209H	ENST00000477973	NM_012234.5	209	Gat/Cat	3/4	0.483106961544127	2	FACETS	0.877	0.835	0.918	0.877	0.835	0.918	CLONAL	2	TRUE	0	0.568562606484462	2		444	644	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729775	41729775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	147	358	0	ENST00000242208.4:c.754G>A	p.Ala252Thr	p.A252T	ENST00000242208	NM_002192.2	252	Gcc/Acc	3/3	0.408500063536302	5	FACETS	0.925	0.85	1	0.617	0.566	0.669	CLONAL	2	TRUE	2	0.568562606484462	5		358	518	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739644	41739644	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	280	557	0	ENST00000242208.4:c.329G>T	p.Arg110Met	p.R110M	ENST00000242208	NM_002192.2	110	aGg/aTg	2/3	0.408500063536302	5	FACETS	0.885	0.832	0.939	0.59	0.555	0.626	CLONAL	2	TRUE	2	0.568562606484462	5		557	1031	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211081	55211081	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	393	448	0	ENST00000275493.2:c.324A>T	p.Arg108Ser	p.R108S	ENST00000275493	NM_005228.3	108	agA/agT	3/28	0.408500063536302	5	FACETS	0.961	0.919	1	0.961	0.919	1	CLONAL	3	TRUE	2	0.568562606484462	5		448	888	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349410	89349410	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs758010258	NA	P-0037238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	56	834	0	ENST00000301030.4:c.3540G>T	p.Glu1180Asp	p.E1180D	ENST00000301030	NM_001256183.1	1180	gaG/gaT	9/13	1	2	FACETS	0.471	0.402	0.548	0.471	0.402	0.548	SUBCLONAL	1	TRUE	1	0.212212579608891	2		834	1120	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55693366	55693366	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	99	619	0	ENST00000284073.2:c.573G>T	p.Met191Ile	p.M191I	ENST00000284073	NM_138962.2	191	atG/atT	9/14	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.212212579608891	2		619	905	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0037239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	39	406	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.922	0.763	1	0.922	0.763	1	CLONAL	1	TRUE	1	0.16	2		406	529	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713513	30713513	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	27	574	0	ENST00000295754.5:c.840del	p.Tyr281MetfsTer19	p.Y281Mfs*19	ENST00000295754	NM_003242.5	280	Ccc/cc	4/7	1	2	FACETS	0.785	0.624	0.969	0.785	0.624	0.969	CLONAL	1	TRUE	1	0.16	2		574	430	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174395	11174395	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1085307113	NA	P-0037254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	74	501	0	ENST00000361445.4:c.7280T>A	p.Leu2427Gln	p.L2427Q	ENST00000361445	NM_004958.3	2427	cTg/cAg	53/58	1	2	FACETS	0.991	0.868	1	0.991	0.868	1	CLONAL	1	TRUE	1	0.24	2		501	622	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033730	48033730	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	30	352	0	ENST00000234420.5:c.3941A>G	p.Gln1314Arg	p.Q1314R	ENST00000234420	NM_000179.2	1314	cAa/cGa	9/10	1	2	FACETS	0.958	0.775	1	0.958	0.775	1	CLONAL	1	TRUE	1	0.24	2		352	261	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61761026	61761026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	33	314	0	ENST00000401558.2:c.7G>A	p.Ala3Thr	p.A3T	ENST00000401558	NM_003400.3	3	Gca/Aca	2/25	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.24	2		314	259	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188215	10188215	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0037254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	72	544	1	ENST00000256474.2:c.358A>T	p.Arg120Ter	p.R120*	ENST00000256474	NM_000551.3	120	Aga/Tga	2/3	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.24	2		545	579	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47108609	47108609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0037254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	37	379	0	ENST00000409792.3:c.6061-1G>A		p.X2021_splice	ENST00000409792	NM_014159.6	2021			1	2	FACETS	0.946	0.782	1	0.946	0.782	1	CLONAL	1	TRUE	1	0.24	2		379	326	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922695	44922695	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	268	370	0	ENST00000377967.4:c.1556G>C	p.Arg519Pro	p.R519P	ENST00000377967	NM_021140.2	519	cGa/cCa	16/29	0.545495182005043	3	FACETS	1	0.967	1			1	CLONAL	2	TRUE	NA	0.627150059944407	3		370	547	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0037265-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	354	462	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.818207619142461	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.818207619142461	2		462	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579349	7579349	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1567555667	NA	P-0037265-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	466	602	0	ENST00000269305.4:c.338T>G	p.Phe113Cys	p.F113C	ENST00000269305	NM_001126112.2	113	tTc/tGc	4/11	0.818207619142461	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.818207619142461	2		602	526	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817892	3817892	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	158	479	0	ENST00000262367.5:c.3079C>T	p.Gln1027Ter	p.Q1027*	ENST00000262367	NM_004380.2	1027	Caa/Taa	16/31	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.559330241749264	2		479	565	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922139	39922143	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCA	AGGCA	T	novel	NA	P-0037267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	195	348	0	ENST00000378444.4:c.4029_4033delinsA	p.Ala1344ProfsTer24	p.A1344Pfs*24	ENST00000378444	NM_001123385.1	1343	gcTGCCTcc/gcAcc	9/15	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.559330241749264	1		348	371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0037269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	273	218	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.613180268983396	1	FACETS	0.98	0.927	1	0.98	0.927	1	CLONAL	1	TRUE	0	0.613180268983396	1		218	630	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520017	NA	P-0037269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	239	549	1	ENST00000326873.7:c.647C>T	p.Ser216Phe	p.S216F	ENST00000326873	NM_000455.4	216	tCc/tTc	5/10	0.613180268983396	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.613180268983396	1		550	506	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858941	57858941	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754019701	NA	P-0037269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	274	671	1	ENST00000228682.2:c.437C>T	p.Ser146Leu	p.S146L	ENST00000228682	NM_005269.2	146	tCg/tTg	5/12	0.613180268983396	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.613180268983396	1		672	586	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598357	28598357	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	252	665	0	ENST00000253063.3:c.329C>G	p.Ser110Cys	p.S110C	ENST00000253063	NM_031459.4	110	tCc/tGc	3/10	0.165853094525374	2	FACETS	0.956	0.896	1	0.478	0.448	0.509	INDETERMINATE	1	TRUE	0	0.613180268983396	2		665	860	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118379906	118379906	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	119	271	0	ENST00000534358.1:c.10891G>C	p.Glu3631Gln	p.E3631Q	ENST00000534358	NM_005933.3	3631	Gaa/Caa	29/36	1	2	FACETS	0.988	0.9	1	0.988	0.9	1	CLONAL	1	TRUE	1	0.613180268983396	2		271	393	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205217	46205217	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	141	453	0	ENST00000334344.6:c.301G>T	p.Glu101Ter	p.E101*	ENST00000334344	NM_152641.2	101	Gag/Tag	4/21	0.613180268983396	1	FACETS	0.906	0.837	0.977	0.906	0.837	0.977	CLONAL	1	TRUE	0	0.613180268983396	1		453	352	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891654	28891654	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	195	595	0	ENST00000282397.4:c.3367G>C	p.Glu1123Gln	p.E1123Q	ENST00000282397	NM_002019.4	1123	Gag/Cag	25/30	0.613180268983396	1	FACETS	0.898	0.839	0.958	0.898	0.839	0.958	CLONAL	1	TRUE	0	0.613180268983396	1		595	491	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133841	41133841	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	143	388	0	ENST00000379561.5:c.1787A>T	p.Glu596Val	p.E596V	ENST00000379561	NM_002015.3	596	gAg/gTg	2/3	0.613180268983396	1	FACETS	0.983	0.91	1	0.983	0.91	1	CLONAL	1	TRUE	0	0.613180268983396	1		388	329	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039446	49039446	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1371240619	NA	P-0037269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	185	489	0	ENST00000267163.4:c.2431A>G	p.Ser811Gly	p.S811G	ENST00000267163	NM_000321.2	811	Agt/Ggt	23/27	0.613180268983396	1	FACETS	0.932	0.87	0.995	0.932	0.87	0.995	CLONAL	1	TRUE	0	0.613180268983396	1		489	449	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643386	38643386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	181	543	0	ENST00000299084.4:c.856G>A	p.Asp286Asn	p.D286N	ENST00000299084	NM_152594.2	286	Gac/Aac	7/7	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.613180268983396	2		543	578	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830454	72830454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1386537099	NA	P-0037269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	190	445	0	ENST00000268489.5:c.6127C>T	p.Pro2043Ser	p.P2043S	ENST00000268489	NM_006885.3	2043	Ccc/Tcc	9/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.613180268983396	2		445	569	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347000	89347000	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	161	455	0	ENST00000301030.4:c.5950C>G	p.Pro1984Ala	p.P1984A	ENST00000301030	NM_001256183.1	1984	Cca/Gca	9/13	1	2	FACETS	0.934	0.862	1	0.934	0.862	1	CLONAL	1	TRUE	1	0.613180268983396	2		455	562	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508475	29508476	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0037269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	118	417	0	ENST00000356175.3:c.624_625del	p.Gln209ValfsTer6	p.Q209Vfs*6	ENST00000356175	NM_000267.3	208	GCg/g	6/57	0.613180268983396	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.613180268983396	1		417	259	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604749	48604749	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs377767375	NA	P-0037269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	169	416	0	ENST00000342988.3:c.1571G>T	p.Trp524Leu	p.W524L	ENST00000342988	NM_005359.5	524	tGg/tTg	12/12	0.613180268983396	1	FACETS	0.993	0.925	1	0.993	0.925	1	CLONAL	1	TRUE	0	0.613180268983396	1		416	385	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403199	213403199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	166	393	0	ENST00000342788.4:c.56C>T	p.Thr19Ile	p.T19I	ENST00000342788	NM_005235.2	19	aCc/aTc	1/28	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.613180268983396	2		393	515	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064391	30064391	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	171	456	0	ENST00000338641.4:c.955C>T	p.Gln319Ter	p.Q319*	ENST00000338641	NM_000268.3	319	Cag/Tag	10/16	0.613180268983396	1	FACETS	0.997	0.93	1	0.997	0.93	1	CLONAL	1	TRUE	0	0.613180268983396	1		456	388	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072491	5072491	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0037269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	89	284	0	ENST00000381652.3:c.1642-1G>C		p.X548_splice	ENST00000381652	NM_004972.3	548			0.613180268983396	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.613180268983396	1		284	173	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636775	8636775	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	181	441	0	ENST00000356435.5:c.134G>T	p.Cys45Phe	p.C45F	ENST00000356435		45	tGc/tTc	2/35	0.613180268983396	1	FACETS	0.89	0.829	0.952	0.89	0.829	0.952	CLONAL	1	TRUE	0	0.613180268983396	1		441	460	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0037276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	351	700	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.868775753128066	2		701	754	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414399	6414399	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	86	150	0	ENST00000356142.4:c.33C>A	p.Asp11Glu	p.D11E	ENST00000356142	NM_018890.3	11	gaC/gaA	1/7	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.868775753128066	2		150	192	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199469669	NA	P-0037276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	286	234	0	ENST00000374080.3:c.130G>T	p.Gly44Cys	p.G44C	ENST00000374080		44	Ggt/Tgt	2/45	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.868775753128066	2		234	638	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295192	1295193	+	upstream_gene_variant	5'Flank	INS	-	-	GCGGAAAGGAAGGGGAGGGGCT	novel	NA	P-0037276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	30	108	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.384	0.312	0.463	0.384	0.312	0.463	SUBCLONAL	1	TRUE	1	0.868775753128066	2		108	180	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042106	42042110	+	frameshift_variant	Frame_Shift_Del	DEL	TTAAG	TTAAG	-	novel	NA	P-0037276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	189	566	0	ENST00000219905.7:c.6302_6306del	p.Leu2101Ter	p.L2101*	ENST00000219905	NM_001164273.1	2101	TTAAGt/t	17/24	1	2	FACETS	0.928	0.866	0.99	0.928	0.866	0.99	CLONAL	1	TRUE	1	0.868775753128066	2		566	469	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162298	47162299	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTGTCAGGTTG	novel	NA	P-0037276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	151	482	0	ENST00000409792.3:c.3817_3827dup	p.Ser1277AsnfsTer59	p.S1277Nfs*59	ENST00000409792	NM_014159.6	1276	agt/agCAACCTGACAGt	3/21	1	2	FACETS	0.73	0.673	0.789	0.73	0.673	0.789	SUBCLONAL	1	TRUE	1	0.868775753128066	2		482	476	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164559	47164559	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	164	436	0	ENST00000409792.3:c.1567G>T	p.Glu523Ter	p.E523*	ENST00000409792	NM_014159.6	523	Gaa/Taa	3/21	1	2	FACETS	0.978	0.91	1	0.978	0.91	1	CLONAL	1	TRUE	1	0.868775753128066	2		436	386	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180630	32180630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	254	547	0	ENST00000375023.3:c.2497C>T	p.Pro833Ser	p.P833S	ENST00000375023	NM_004557.3	833	Ccc/Tcc	16/30	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.868775753128066	2		547	500	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913517	NA	P-0037285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	60	451	0	ENST00000288135.5:c.1676T>A	p.Val559Asp	p.V559D	ENST00000288135	NM_000222.2	559	gTt/gAt	11/21	1	2	FACETS	0.917	0.802	1	0.917	0.802	1	CLONAL	1	TRUE	1	0.648156286232996	2		451	202	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457270	25457271	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0037285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	65	541	0	ENST00000264709.3:c.2615_2616dup	p.His873SerfsTer9	p.H873Sfs*9	ENST00000264709	NM_175629.2	872	-/TC	23/23	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.648156286232996	2		541	188	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0037315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	53	414	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.14	2		414	726	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044907	47044907	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	75	542	1	ENST00000377604.3:c.2237del	p.Gly746AlafsTer56	p.G746Afs*56	ENST00000377604	NM_001204468.1	745	Ggg/gg	20/24	1	2	FACETS	0.973	0.85	1	0.973	0.85	1	CLONAL	1	TRUE	1	0.14	2		543	1101	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138197263	138197263	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	34	300	0	ENST00000237289.4:c.765T>A	p.His255Gln	p.H255Q	ENST00000237289	NM_001270507.1	255	caT/caA	5/9	NA	2	FACETS	0.938	0.765	1			1	INDETERMINATE	1	TRUE	NA	0.14	2		300	518	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089478	27089478	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	49	625	0	ENST00000324856.7:c.2434C>T	p.Gln812Ter	p.Q812*	ENST00000324856	NM_006015.4	812	Cag/Tag	8/20	1	2	FACETS	0.851	0.718	0.997	0.851	0.718	0.997	CLONAL	1	TRUE	1	0.14	2		625	823	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155055	108155055	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	39	482	0	ENST00000278616.4:c.3848T>G	p.Leu1283Arg	p.L1283R	ENST00000278616	NM_000051.3	1283	cTa/cGa	26/63	1	2	FACETS	0.812	0.671	0.97	0.812	0.671	0.97	CLONAL	1	TRUE	1	0.14	2		482	686	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247459	71247459	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	47	623	0	ENST00000318789.4:c.74A>T	p.His25Leu	p.H25L	ENST00000318789	NM_032682.5	25	cAc/cTc	6/21	1	2	FACETS	0.784	0.66	0.923	0.784	0.66	0.923	CLONAL	1	TRUE	1	0.14	2		623	856	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982700	90982700	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	43	377	0	ENST00000265433.3:c.788T>G	p.Phe263Cys	p.F263C	ENST00000265433	NM_002485.4	263	tTt/tGt	7/16	1	2	FACETS	0.988	0.825	1	0.988	0.825	1	CLONAL	1	TRUE	1	0.14	2		377	622	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0037326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	77	714	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.246123832617985	2		714	559	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0037326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	29	367	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	1	2	FACETS	0.656	0.527	0.803	0.656	0.527	0.803	SUBCLONAL	1	TRUE	1	0.246123832617985	2		367	359	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0037355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	27	214	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.190965426613306	3	FACETS	1	0.866	1	1	0.866	1	CLONAL	2	TRUE	1	0.19	3		214	142	SUCCESS
APC	324	MSKCC	GRCh37	5	112175536	112175536	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	30	401	0	ENST00000257430.4:c.4245del	p.Ser1415ArgfsTer4	p.S1415Rfs*4	ENST00000257430	NM_000038.5	1415	agT/ag	16/16	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.19	2		401	285	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058499	72058499	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0037355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	37	452	1	ENST00000357731.5:c.940+1G>A		p.X314_splice	ENST00000357731	NM_173808.2	314			1	2	FACETS	0.871	0.718	1	0.871	0.718	1	CLONAL	1	TRUE	1	0.19	2		453	447	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989060	41989060	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	22	590	0	ENST00000219905.7:c.1852C>T	p.Arg618Ter	p.R618*	ENST00000219905	NM_001164273.1	618	Cga/Tga	3/24	0.3	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.19	1		590	147	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710659	114710659	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	34	352	0	ENST00000543371.1:c.144del	p.Val49SerfsTer59	p.V49Sfs*59	ENST00000543371	NM_001198531.1	48	ctA/ct	1/14	0.190965426613306	3	FACETS	1	0.905	1	0.587	0.48	0.706	CLONAL	1	TRUE	1	0.19	3		352	334	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161690	56161690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	10	547	0	ENST00000399503.3:c.1187G>A	p.Arg396His	p.R396H	ENST00000399503	NM_005921.1	396	cGt/cAt	6/20	1	2	FACETS	0.666	0.452	0.934	0.666	0.452	0.934	SUBCLONAL	1	TRUE	1	0.19	2		547	158	SUCCESS
APC	324	MSKCC	GRCh37	5	112173637	112173637	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	14	429	0	ENST00000257430.4:c.2347del	p.Ala783HisfsTer37	p.A783Hfs*37	ENST00000257430	NM_000038.5	782	aaG/aa	16/16	1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	1	0.19	2		429	116	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946418	71946418	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	201	615	0	ENST00000298229.2:c.2582A>T	p.Glu861Val	p.E861V	ENST00000298229	NM_001567.3	861	gAg/gTg	23/28	0.493421310518782	3	FACETS	0.978	0.906	1	0.489	0.453	0.526	CLONAL	1	TRUE	1	0.504992006978427	3		615	1020	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427645	49427645	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs984314815	NA	P-0037378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	348	537	1	ENST00000301067.7:c.10843G>T	p.Ala3615Ser	p.A3615S	ENST00000301067	NM_003482.3	3615	Gct/Tct	39/54	0.504992006978427	2	FACETS	0.993	0.948	1	0.993	0.948	1	CLONAL	2	TRUE	0	0.504992006978427	2		538	694	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577514	7577522	+	inframe_deletion	In_Frame_Del	DEL	GTGATGATG	GTGATGATG	-	novel	NA	P-0037378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	336	543	0	ENST00000269305.4:c.759_767del	p.Ile254_Thr256del	p.I254_T256del	ENST00000269305	NM_001126112.2	253	acCATCATCACa/aca	7/11	0.504992006978427	2	FACETS	0.891	0.848	0.934	0.891	0.848	0.934	CLONAL	2	TRUE	0	0.504992006978427	2		543	747	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654737	29654737	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs771529172	NA	P-0037378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	199	225	0	ENST00000356175.3:c.5426G>T	p.Arg1809Leu	p.R1809L	ENST00000356175	NM_000267.3	1809	cGc/cTc	37/57	0.493421310518782	3	FACETS	0.88	0.821	0.94	0.88	0.821	0.94	CLONAL	2	TRUE	1	0.504992006978427	3		225	561	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31020700	31020700	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	131	181	0	ENST00000375687.4:c.997A>C	p.Met333Leu	p.M333L	ENST00000375687	NM_015338.5	333	Atg/Ctg	11/13	0.493421310518782	3	FACETS	0.973	0.895	1	0.973	0.895	1	CLONAL	2	TRUE	1	0.504992006978427	3		181	334	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944512	40944512	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	106	410	0	ENST00000373198.4:c.1990T>C	p.Phe664Leu	p.F664L	ENST00000373198	NM_133170.3	664	Ttt/Ctt	12/32	NA	2	FACETS	0.679	0.61	0.752			1	INDETERMINATE	1	TRUE	NA	0.504992006978427	2		410	618	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876407	35876407	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	340	486	0	ENST00000303115.3:c.1199T>A	p.Val400Glu	p.V400E	ENST00000303115	NM_002185.3	400	gTg/gAg	8/8	0.442309420061552	4	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	2	0.504992006978427	4		486	1009	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341893	8341893	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	119	453	0	ENST00000356435.5:c.4747G>T	p.Gly1583Cys	p.G1583C	ENST00000356435		1583	Ggc/Tgc	29/35	0.504992006978427	3	FACETS	0.666	0.601	0.736	0.222	0.2	0.246	SUBCLONAL	1	TRUE	0	0.504992006978427	3		453	886	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914768	39914768	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0037378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	206	171	0	ENST00000378444.4:c.4596-2A>T		p.X1532_splice	ENST00000378444	NM_001123385.1	1532			0.438727444151657	2	FACETS	0.895	0.852	0.936			1	CLONAL	3	TRUE	NA	0.504992006978427	2		171	304	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0037379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	406	430	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.277170641106676	6	FACETS	1	0.988	1	1	0.988	1	CLONAL	5	TRUE	1	0.277170641106676	6		430	842	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828144	72828186	+	frameshift_variant	Frame_Shift_Del	DEL	AGTCTTCAATCCCTTCCACCTTAATGGAGGAAGGGCTTAGAAG	AGTCTTCAATCCCTTCCACCTTAATGGAGGAAGGGCTTAGAAG	-	novel	NA	P-0037379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	54	540	0	ENST00000268489.5:c.8395_8437del	p.Leu2800LysfsTer10	p.L2800Kfs*10	ENST00000268489	NM_006885.3	2799	CTTCTAAGCCCTTCCTCCATTAAGGTGGAAGGGATTGAAGACTtt/tt	9/10	1	2	FACETS	0.509	0.433	0.592	0.509	0.433	0.592	SUBCLONAL	1	TRUE	1	0.277170641106676	2		540	766	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484288	50484288	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	53	666	0	ENST00000394963.4:c.1048C>T	p.Gln350Ter	p.Q350*	ENST00000394963	NM_003076.4	350	Caa/Taa	9/13	1	2	FACETS	0.723	0.616	0.84	0.723	0.616	0.84	SUBCLONAL	1	TRUE	1	0.242847154489759	2		666	604	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245067	53245067	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	17	408	0	ENST00000375401.3:c.873C>G	p.Phe291Leu	p.F291L	ENST00000375401	NM_004187.3	291	ttC/ttG	7/26	1	1	FACETS	0.409	0.305	0.532	0.409	0.305	0.532	SUBCLONAL	1	TRUE	0	0.242847154489759	1		408	301	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0037405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	82	319	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	1	2	FACETS	0.938	0.843	1	0.938	0.843	1	CLONAL	1	TRUE	1	0.787195877871768	2		319	222	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	231	523	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.787195877871768	2		523	575	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0037405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	79	335	0	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.787195877871768	2		335	196	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100702	67100702	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0037405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	202	508	0	ENST00000412916.2:c.399+1G>T		p.X133_splice	ENST00000412916		133			0.778919764785604	1	FACETS	0.955	0.905	1	0.955	0.905	1	CLONAL	1	TRUE	0	0.787195877871768	1		508	326	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398035	4398035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	218	574	0	ENST00000261254.3:c.599C>T	p.Ser200Leu	p.S200L	ENST00000261254	NM_001759.3	200	tCg/tTg	4/5	1	2	FACETS	0.926	0.867	0.986	0.926	0.867	0.986	CLONAL	1	TRUE	1	0.787195877871768	2		574	598	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862104	68862104	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	176	387	0	ENST00000261769.5:c.2193del	p.Arg732GlyfsTer38	p.R732Gfs*38	ENST00000261769	NM_004360.3	731	cTt/ct	14/16	0.778919764785604	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.787195877871768	1		387	267	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0037441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	95	460	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.281759487096227	5	FACETS	1	0.935	1	0.702	0.631	0.777	CLONAL	2	TRUE	2	0.416003589423809	5		460	352	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0037441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	269	748	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.231485198817549	5	FACETS	0.981	0.931	1	0.785	0.745	0.825	INDETERMINATE	4	TRUE	0	0.416003589423809	5		749	535	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913399	NA	P-0037441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	94	320	0	ENST00000349496.5:c.100G>C	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Cga	3/15	0.341369709976327	5	FACETS	1	0.913	1	0.68	0.61	0.753	CLONAL	2	TRUE	2	0.416003589423809	5		320	360	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851568	134851568	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	89	484	0	ENST00000398015.3:c.974G>A	p.Gly325Asp	p.G325D	ENST00000398015	NM_004441.4	325	gGt/gAt	5/16	0.281759487096227	5	FACETS	0.942	0.841	1	0.628	0.561	0.698	CLONAL	2	TRUE	2	0.416003589423809	5		484	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0037456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	81	621	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.533	0.468	0.602	0.533	0.468	0.602	SUBCLONAL	1	TRUE	1	0.37	2		622	822	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	31	82	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.574	0.465	0.696	0.574	0.465	0.696	SUBCLONAL	1	TRUE	1	0.37	2		82	292	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0037456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	73	509	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.609	0.532	0.691	0.609	0.532	0.691	SUBCLONAL	1	TRUE	1	0.37	2		509	648	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792755	33792757	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs746430067	NA	P-0037456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	10	63	1	ENST00000498907.2:c.564_566del	p.Pro189del	p.P189del	ENST00000498907	NM_004364.3	188	ccGCCc/ccc	1/1	1	2	FACETS	0.693	0.476	0.958	0.693	0.476	0.958	SUBCLONAL	1	TRUE	1	0.37	2		64	78	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412618	139412618	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	51	574	0	ENST00000277541.6:c.1226G>C	p.Cys409Ser	p.C409S	ENST00000277541	NM_017617.3	409	tGc/tCc	7/34	1	2	FACETS	0.506	0.43	0.589	0.506	0.43	0.589	SUBCLONAL	1	TRUE	1	0.37	2		574	545	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	45	82	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.21	2		82	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0037465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	71	929	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.3	3	FACETS	0.847	0.738	0.966			1	CLONAL	1	TRUE	NA	0.21	3		929	882	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477837	140477851	+	inframe_deletion	In_Frame_Del	DEL	TAGGTGCTGTCACAT	TAGGTGCTGTCACAT	-	novel	NA	P-0037465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	96	503	0	ENST00000288602.6:c.1457_1471del	p.Asn486_Pro490del	p.N486_P490del	ENST00000288602	NM_004333.4	486	aATGTGACAGCACCTAca/aca	12/18	0.197876019800582	3	FACETS	1	0.923	1	0.523	0.465	0.586	CLONAL	1	TRUE	1	0.21	3		503	965	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0037476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	614	673	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.549949001194956	3	FACETS	0.99	0.961	1	0.99	0.961	1	CLONAL	3	TRUE	0	0.549949001194956	3		673	959	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068078	94068078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765322526	NA	P-0037476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	155	362	0	ENST00000369303.4:c.884G>A	p.Arg295His	p.R295H	ENST00000369303	NM_004440.3	295	cGt/cAt	4/17	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.549949001194956	2		362	412	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429960	78429960	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	185	514	0	ENST00000370768.2:c.919G>C	p.Val307Leu	p.V307L	ENST00000370768	NM_003902.3	307	Gtt/Ctt	11/20	0.549949001194956	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.549949001194956	1		514	468	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409116	139409148	+	frameshift_variant	Frame_Shift_Del	DEL	TGCCCGCACACTCATCGATGTTGATGTTACACA	TGCCCGCACACTCATCGATGTTGATGTTACACA	GGCATGCC	novel	NA	P-0037476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	268	801	2	ENST00000277541.6:c.2021_2053delinsGGCATGCC	p.Met674ArgfsTer90	p.M674Rfs*90	ENST00000277541	NM_017617.3	674	aTGTGTAACATCAACATCGATGAGTGTGCGGGCAac/aGGCATGCCac	13/34	0.506313684537519	2	FACETS	1	0.993	1	0.709	0.669	0.75	CLONAL	1	TRUE	0	0.549949001194956	2		803	687	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641389	18641389	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1229278001	NA	P-0037477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	23	244	0	ENST00000266497.5:c.2393del	p.Asn798MetfsTer16	p.N798Mfs*16	ENST00000266497		796	ctA/ct	17/31	0.23540268870404	2	FACETS	0.534	0.416	0.669	0.267	0.208	0.335	SUBCLONAL	1	TRUE	0	0.288285559173323	2		244	299	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670106	29670106	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs878853912	NA	P-0037477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	50	533	0	ENST00000356175.3:c.7079A>G	p.Asn2360Ser	p.N2360S	ENST00000356175	NM_000267.3	2360	aAt/aGt	47/57	0.288285559173323	3	FACETS	0.474	0.4	0.554	0.237	0.2	0.277	SUBCLONAL	1	TRUE	1	0.288285559173323	3		533	838	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434730	49434731	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0037477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	186	665	0	ENST00000301067.7:c.6822_6823del	p.Pro2276ThrfsTer22	p.P2276Tfs*22	ENST00000301067	NM_003482.3	2274	tcGCcc/tccc	31/54	0.166954034226714	4	FACETS	0.78	0.72	0.843	0.78	0.72	0.843	INDETERMINATE	2	TRUE	2	0.288285559173323	4		665	1065	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021360	42021360	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0037507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	192	253	0	ENST00000219905.7:c.3658-2A>T		p.X1220_splice	ENST00000219905	NM_001164273.1	1220			0.699783164868405	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.699783164868405	1		253	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0037507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	498	466	0	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	0.649560761390221	2	FACETS	0.917	0.887	0.946	0.917	0.887	0.946	CLONAL	2	TRUE	0	0.699783164868405	2		466	776	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604773	48604773	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs377767380	NA	P-0037507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	140	294	0	ENST00000342988.3:c.1597del	p.Leu533SerfsTer4	p.L533Sfs*4	ENST00000342988	NM_005359.5	532	gCc/gc	12/12	0.693932771661553	1	FACETS	0.949	0.883	1	0.949	0.883	1	CLONAL	1	TRUE	0	0.699783164868405	1		294	274	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228043	36228043	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	713	475	0	ENST00000222270.7:c.7429G>T	p.Glu2477Ter	p.E2477*	ENST00000222270	NM_014727.1	2477	Gag/Tag	33/37	0.575055157072515	4	FACETS	0.945	0.917	0.972	0.945	0.917	0.972	CLONAL	3	TRUE	1	0.699783164868405	4		475	1222	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251577	212251577	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1559116228	NA	P-0037507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	81	303	0	ENST00000342788.4:c.3481+1G>T		p.X1161_splice	ENST00000342788	NM_005235.2	1161			0.356072746536896	3	FACETS	0.478	0.421	0.539	0.239	0.21	0.27	INDETERMINATE	1	TRUE	1	0.699783164868405	3		303	654	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815316	32815316	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	147	546	0	ENST00000354258.4:c.2057C>G	p.Ser686Cys	p.S686C	ENST00000354258	NM_000593.5	686	tCt/tGt	9/11	0.309517581711037	2	FACETS	0.434	0.396	0.474	0.217	0.198	0.237	INDETERMINATE	1	TRUE	0	0.699783164868405	2		546	968	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0037513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	166	640	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		640	416	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225884	2225884	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	240	512	0	ENST00000326181.6:c.1676G>T	p.Gly559Val	p.G559V	ENST00000326181	NM_032271.2	559	gGt/gTt	18/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		512	645	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	65	82	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.378726898712172	2		82	272	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111959631	111959631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	89	332	0	ENST00000375549.3:c.210G>T	p.Arg70Ser	p.R70S	ENST00000375549	NM_003002.3	70	agG/agT	3/4	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.378726898712172	2		332	445	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244401	46244401	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	165	379	0	ENST00000334344.6:c.2495C>A	p.Ser832Ter	p.S832*	ENST00000334344	NM_152641.2	832	tCa/tAa	15/21	0.227317350918415	2	FACETS	0.828	0.766	0.892	0.828	0.766	0.892	CLONAL	2	TRUE	0	0.378726898712172	2		379	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0037517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	236	481	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.355309306517874	2	FACETS	0.854	0.8	0.909	0.854	0.8	0.909	CLONAL	2	TRUE	0	0.378726898712172	2		481	730	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397710	49397710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	116	464	0	ENST00000418115.1:c.514G>A	p.Glu172Lys	p.E172K	ENST00000418115	NM_001664.2	172	Gaa/Aaa	5/5	0.268024057010076	3	FACETS	1	0.939	1	0.527	0.476	0.582	CLONAL	1	TRUE	1	0.378726898712172	3		464	691	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138402553	138402553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	114	369	0	ENST00000289153.2:c.2392G>A	p.Asp798Asn	p.D798N	ENST00000289153	NM_006219.2	798	Gat/Aat	16/22	0.304451272976603	3	FACETS	1	0.98	1	0.67	0.606	0.738	CLONAL	1	TRUE	1	0.378726898712172	3		369	534	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950111	44950111	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0037517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	127	166	0	ENST00000377967.4:c.3878+2T>C		p.X1293_splice	ENST00000377967	NM_021140.2	1293			0.378726898712172	2	FACETS	1	0.936	1			1	CLONAL	2	TRUE	NA	0.378726898712172	2		166	328	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	50	82	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.908	0.789	1	0.908	0.789	1	CLONAL	1	TRUE	1	0.798368916451784	2		82	138	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0037551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	285	562	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.755785268477575	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.798368916451784	2		562	354	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781386	135781386	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203549	NA	P-0037551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	110	586	0	ENST00000298552.3:c.1579C>T	p.Gln527Ter	p.Q527*	ENST00000298552	NM_001162426.1	527	Cag/Tag	15/23	0.798368916451784	1	FACETS	0.756	0.696	0.816	0.756	0.696	0.816	SUBCLONAL	1	TRUE	0	0.798368916451784	1		586	219	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591120	67591131	+	inframe_deletion	In_Frame_Del	DEL	CCAGCTGAGAAA	CCAGCTGAGAAA	-	novel	NA	P-0037551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	71	340	0	ENST00000274335.5:c.1713_1724del	p.Ile571_Lys575delinsMet	p.I571_K575delinsM	ENST00000274335		571	atCCAGCTGAGAAAg/atg	12/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.798368916451784	2		340	119	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0037577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	181	617	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.318333298008217	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.46782041405659	1		617	579	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427224	49427224	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	39	819	0	ENST00000301067.7:c.11264A>G	p.Gln3755Arg	p.Q3755R	ENST00000301067	NM_003482.3	3755	cAg/cGg	39/54	1	2	FACETS	0.247	0.204	0.296	0.247	0.204	0.296	SUBCLONAL	1	TRUE	1	0.46782041405659	2		819	674	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865169	57865169	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	63	844	0	ENST00000228682.2:c.2646C>A	p.Asp882Glu	p.D882E	ENST00000228682	NM_005269.2	882	gaC/gaA	12/12	1	2	FACETS	0.376	0.324	0.432	0.376	0.324	0.432	SUBCLONAL	1	TRUE	1	0.46782041405659	2		844	717	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251703	212251703	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	70	392	0	ENST00000342788.4:c.3356T>C	p.Val1119Ala	p.V1119A	ENST00000342788	NM_005235.2	1119	gTc/gCc	27/28	0.275000280332798	1	FACETS	0.646	0.567	0.73	0.646	0.567	0.73	INDETERMINATE	1	TRUE	0	0.46782041405659	1		392	355	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35860974	35860974	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	33	330	0	ENST00000303115.3:c.103C>G	p.Leu35Val	p.L35V	ENST00000303115	NM_002185.3	35	Ctg/Gtg	2/8	0.256419255642854	5	FACETS	0.401	0.325	0.486	0.08	0.065	0.098	INDETERMINATE	1	TRUE	0	0.46782041405659	5		330	599	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0037578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	431	490	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.954	0.921	0.988	1	0.997	1	CLONAL	2	TRUE	1	0.659277505328357	2		490	685	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0037578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	99	395	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.998	0.902	1	0.998	0.902	1	CLONAL	1	TRUE	1	0.659277505328357	2		396	301	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814303	76814306	+	frameshift_variant	Frame_Shift_Del	DEL	ATAA	ATAA	-	novel	NA	P-0037578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	117	131	0	ENST00000373344.5:c.6338_6341del	p.Phe2113SerfsTer9	p.F2113Sfs*9	ENST00000373344	NM_000489.3	2113	tTTATc/tc	29/35	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.659277505328357	1		131	195	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255142	16255145	+	frameshift_variant	Frame_Shift_Del	DEL	GAGA	GAGA	-	novel	NA	P-0037578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	132	262	0	ENST00000375759.3:c.2415_2418del	p.Glu805AspfsTer3	p.E805Dfs*3	ENST00000375759	NM_015001.2	803	GAGAga/ga	11/15	1	2	FACETS	0.991	0.909	1	0.991	0.909	1	CLONAL	1	TRUE	1	0.659277505328357	2		262	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579463	7579463	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037618-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	172	201	0	ENST00000269305.4:c.224del	p.Pro75LeufsTer48	p.P75Lfs*48	ENST00000269305	NM_001126112.2	75	cCt/ct	4/11	0.469469587194159	1	FACETS	0.982	0.909	1	0.982	0.909	1	CLONAL	1	TRUE	0	0.469469587194159	1		201	571	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752411	57752412	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0037618-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	90	215	0	ENST00000274289.3:c.1161_1162del	p.Arg387SerfsTer3	p.R387Sfs*3	ENST00000274289	NM_006622.3	387	agAGtg/agtg	9/14	1	2	FACETS	0.854	0.761	0.952	0.854	0.761	0.952	CLONAL	1	TRUE	1	0.469469587194159	2		215	449	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971228	13971228	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037618-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	57	381	0	ENST00000405192.2:c.701C>A	p.Pro234Gln	p.P234Q	ENST00000405192	NM_001163147.1	234	cCa/cAa	8/12	1	2	FACETS	0.371	0.317	0.429	0.371	0.317	0.429	SUBCLONAL	1	TRUE	1	0.469469587194159	2		381	655	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0037665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	81	485	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.508748764332085	1	FACETS	0.355	0.312	0.4	0.355	0.312	0.4	SUBCLONAL	1	TRUE	0	0.508748764332085	1		485	669	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0037665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	384	555	0	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	0.48156238651649	2	FACETS	1	0.995	1	0.69	0.656	0.724	CLONAL	1	TRUE	0	0.508748764332085	2		555	1094	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051652	30051652	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555993336	NA	P-0037665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	158	254	0	ENST00000338641.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000338641	NM_000268.3	196	Cga/Tga	6/16	0.508748764332085	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.508748764332085	1		254	461	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557596	21557596	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	104	531	0	ENST00000382592.4:c.2249G>T	p.Gly750Val	p.G750V	ENST00000382592	NM_014572.2	750	gGt/gTt	5/8	0.508748764332085	1	FACETS	0.403	0.361	0.448	0.403	0.361	0.448	SUBCLONAL	1	TRUE	0	0.508748764332085	1		531	756	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441328	52441328	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	191	398	0	ENST00000460680.1:c.442G>T	p.Glu148Ter	p.E148*	ENST00000460680	NM_004656.3	148	Gag/Tag	7/17	0.508748764332085	1	FACETS	0.927	0.862	0.994	0.927	0.862	0.994	CLONAL	1	TRUE	0	0.508748764332085	1		398	604	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913381	NA	P-0037687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	114	278	0	ENST00000304494.5:c.322G>T	p.Asp108Tyr	p.D108Y	ENST00000304494	NM_000077.4	108	Gat/Tat	2/3	0.574441973528439	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.574441973528439	1		278	202	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101750	71101751	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0037687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	80	363	0	ENST00000318789.4:c.447dup	p.Gln150ThrfsTer20	p.Q150Tfs*20	ENST00000318789	NM_032682.5	149	-/A	9/21	0.574441973528439	1	FACETS	0.735	0.655	0.819	0.735	0.655	0.819	SUBCLONAL	1	TRUE	0	0.574441973528439	1		363	270	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439622	51439622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	151	412	1	ENST00000262662.1:c.187C>T	p.Pro63Ser	p.P63S	ENST00000262662		63	Ccc/Tcc	4/4	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.574441973528439	2		413	476	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373139	118373139	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	251	450	0	ENST00000534358.1:c.6532A>G	p.Ile2178Val	p.I2178V	ENST00000534358	NM_005933.3	2178	Ata/Gta	27/36	0.574441973528439	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.574441973528439	2		450	416	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	461436	461436	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	180	552	0	ENST00000399788.2:c.1084A>G	p.Thr362Ala	p.T362A	ENST00000399788	NM_001042603.1	362	Aca/Gca	9/28	0.414672692878552	3	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.574441973528439	3		552	726	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786752	3786752	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	160	685	0	ENST00000262367.5:c.4459C>G	p.His1487Asp	p.H1487D	ENST00000262367	NM_004380.2	1487	Cac/Gac	27/31	1	2	FACETS	0.924	0.851	0.999	0.924	0.851	0.999	CLONAL	1	TRUE	1	0.574441973528439	2		685	603	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118629	11118629	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	203	590	0	ENST00000358026.2:c.2053G>T	p.Glu685Ter	p.E685*	ENST00000358026	NM_001128849.1	685	Gag/Tag	14/36	0.53723856022329	2	FACETS	0.918	0.865	0.97	0.918	0.865	0.97	CLONAL	2	TRUE	0	0.574441973528439	2		590	385	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942529	17942529	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs761651756	NA	P-0037687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	222	598	0	ENST00000458235.1:c.2759G>T	p.Arg920Leu	p.R920L	ENST00000458235	NM_000215.3	920	cGc/cTc	20/24	0.53723856022329	2	FACETS	0.947	0.896	0.998	0.947	0.896	0.998	CLONAL	2	TRUE	0	0.574441973528439	2		598	408	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662577	227662577	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	63	601	0	ENST00000305123.5:c.878C>G	p.Pro293Arg	p.P293R	ENST00000305123	NM_005544.2	293	cCg/cGg	1/2	0.435758323620122	1	FACETS	0.453	0.394	0.517	0.453	0.394	0.517	SUBCLONAL	1	TRUE	0	0.574441973528439	1		601	345	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141017	55141017	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs878854823	NA	P-0037687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	49	463	0	ENST00000257290.5:c.1663T>C	p.Tyr555His	p.Y555H	ENST00000257290	NM_006206.4	555	Tat/Cat	12/23	0.435758323620122	1	FACETS	0.394	0.335	0.457	0.394	0.335	0.457	SUBCLONAL	1	TRUE	0	0.574441973528439	1		463	309	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861005	35861005	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	107	481	0	ENST00000303115.3:c.134A>T	p.Gln45Leu	p.Q45L	ENST00000303115	NM_002185.3	45	cAg/cTg	2/8	0.516252691494868	3	FACETS	0.924	0.832	1	0.462	0.416	0.51	CLONAL	1	TRUE	1	0.574441973528439	3		481	519	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0037729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	44	689	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.447	0.374	0.529	0.447	0.374	0.529	SUBCLONAL	1	TRUE	1	0.254546063182177	2		689	773	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138729528	NA	P-0037729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	129	698	0	ENST00000269305.4:c.523C>G	p.Arg175Gly	p.R175G	ENST00000269305	NM_001126112.2	175	Cgc/Ggc	5/11	0.254546063182177	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.254546063182177	1		698	682	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667521	29667521	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0037729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	36	429	0	ENST00000356175.3:c.6859-2A>C		p.X2287_splice	ENST00000356175	NM_000267.3	2287			0.254546063182177	1	FACETS	0.628	0.517	0.753	0.628	0.517	0.753	SUBCLONAL	1	TRUE	0	0.254546063182177	1		429	393	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865263	40865263	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	65	552	0	ENST00000428826.2:c.1168A>T	p.Arg390Trp	p.R390W	ENST00000428826		390	Agg/Tgg	11/21	1	2	FACETS	0.765	0.662	0.875	0.765	0.662	0.875	SUBCLONAL	1	TRUE	1	0.254546063182177	2		552	668	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466795	57466795	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	20	140	0	ENST00000371085.3:c.14G>A	p.Gly5Glu	p.G5E	ENST00000371085	NM_000516.4	5	gGg/gAg	1/13	0.108721088388564	4	FACETS	1	0.792	1	0.516	0.396	0.654	INDETERMINATE	1	TRUE	2	0.254546063182177	4		140	191	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205175	128205175	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0037729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	64	668	0	ENST00000341105.2:c.266T>A	p.Leu89Ter	p.L89*	ENST00000341105	NM_032638.4	89	tTg/tAg	3/6	1	2	FACETS	0.63	0.545	0.723	0.63	0.545	0.723	SUBCLONAL	1	TRUE	1	0.254546063182177	2		668	798	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542166	187542166	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	81	383	0	ENST00000441802.2:c.5574del	p.Phe1858LeufsTer8	p.F1858Lfs*8	ENST00000441802	NM_005245.3	1858	ttT/tt	10/27	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.254546063182177	2		383	523	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439405	149439405	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	164	566	0	ENST00000286301.3:c.1990G>C	p.Glu664Gln	p.E664Q	ENST00000286301	NM_005211.3	664	Gag/Cag	15/22	0.147278648413044	3	FACETS	0.932	0.857	1			1	INDETERMINATE	2	TRUE	NA	0.254546063182177	3		566	779	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852183	128852183	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	255	845	0	ENST00000249373.3:c.2255C>A	p.Ala752Glu	p.A752E	ENST00000249373	NM_005631.4	752	gCa/gAa	12/12	0.234733603998634	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.254546063182177	2		845	939	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227777	53227777	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	135	703	0	ENST00000375401.3:c.2411G>C	p.Arg804Pro	p.R804P	ENST00000375401	NM_004187.3	804	cGg/cCg	17/26	0.108721088388564	4	FACETS	0.775	0.704	0.849	0.775	0.704	0.849	INDETERMINATE	2	TRUE	2	0.254546063182177	4		703	859	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0037770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	550	428	0	ENST00000311936.3:c.34_35delinsTT	p.Gly12Phe	p.G12F	ENST00000311936	NM_004985.3	12	GGt/TTt	2/5	0.883908084647687	4	FACETS	0.929	0.901	0.956	0.929	0.901	0.956	CLONAL	3	TRUE	1	0.902368717818278	4		428	832	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599868	10599868	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	339	756	1	ENST00000171111.5:c.1708G>A	p.Gly570Arg	p.G570R	ENST00000171111	NM_203500.1	570	Gga/Aga	5/6	0.902368717818278	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.902368717818278	1		757	410	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524191	18524191	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	174	639	0	ENST00000266497.5:c.1703C>A	p.Ala568Glu	p.A568E	ENST00000266497		568	gCa/gAa	11/31	0.883908084647687	4	FACETS	0.8	0.737	0.866	0.267	0.245	0.289	SUBCLONAL	1	TRUE	1	0.902368717818278	4		639	917	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7128930	7128930	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	120	572	0	ENST00000302850.5:c.2878G>T	p.Gly960Cys	p.G960C	ENST00000302850	NM_000208.2	960	Ggc/Tgc	15/22	0.902368717818278	1	FACETS	0.942	0.891	0.988	0.942	0.891	0.988	CLONAL	1	TRUE	0	0.902368717818278	1		572	155	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138549	11138549	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	341	755	0	ENST00000358026.2:c.3305T>C	p.Phe1102Ser	p.F1102S	ENST00000358026	NM_001128849.1	1102	tTc/tCc	24/36	0.902368717818278	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.902368717818278	1		755	408	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624788	9624788	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	197	436	0	ENST00000353224.5:c.189G>C	p.Gln63His	p.Q63H	ENST00000353224	NM_177990.2	63	caG/caC	3/10	1	2	FACETS	0.977	0.915	1	0.977	0.915	1	CLONAL	1	TRUE	1	0.902368717818278	2		436	447	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670361	30670361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	286	584	0	ENST00000376406.3:c.6071C>T	p.Thr2024Ile	p.T2024I	ENST00000376406	NM_014641.2	2024	aCa/aTa	14/15	0.182502464685405	4	FACETS	0.841	0.795	0.887	0.841	0.795	0.887	INDETERMINATE	2	TRUE	2	0.902368717818278	4		584	717	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549514	5549514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544152379	NA	P-0037770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	359	780	0	ENST00000397747.3:c.541C>T	p.Arg181Cys	p.R181C	ENST00000397747	NM_025239.3	181	Cgc/Tgc	4/7	1	2	FACETS	0.928	0.884	0.973	0.928	0.884	0.973	CLONAL	1	TRUE	1	0.902368717818278	2		780	857	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221293	1221298	+	stop_gained	Nonsense_Mutation	ONP	CGCCAT	CGCCAT	GGCAAC	novel	NA	P-0037770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	327	698	0	ENST00000326873.7:c.816_821delinsGGCAAC	p.Tyr272_Ile274delinsTer	p.Y272_I274delins*	ENST00000326873	NM_000455.4	272	taCGCCATc/taGGCAACc	6/10	0.902368717818278	1	FACETS	0.977	0.948	1	0.977	0.948	1	CLONAL	1	TRUE	0	0.902368717818278	1		698	407	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0037775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	289	649	1	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.557266669610385	3	FACETS	1	0.959	1	0.514	0.482	0.546	CLONAL	1	TRUE	1	0.557266669610385	3		650	1291	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	253	296	0	ENST00000304494.5:c.250G>C	p.Asp84His	p.D84H	ENST00000304494	NM_000077.4	84	Gac/Cac	2/3	0.505514246002134	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.533893663955658	2		296	434	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993117	90993117	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587780096	NA	P-0037789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	34	271	0	ENST00000265433.3:c.325G>T	p.Glu109Ter	p.E109*	ENST00000265433	NM_002485.4	109	Gag/Tag	4/16	0.428004887509336	4	FACETS	0.7	0.574	0.84	0.233	0.191	0.28	SUBCLONAL	1	TRUE	1	0.533893663955658	4		271	279	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849860	156849860	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	486	687	0	ENST00000524377.1:c.2116A>G	p.Thr706Ala	p.T706A	ENST00000524377	NM_002529.3	706	Acc/Gcc	16/17	0.289435245891285	4	FACETS	0.985	0.943	1	0.985	0.943	1	INDETERMINATE	2	TRUE	2	0.533893663955658	4		687	1417	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588121	69588123	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0037789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	207	681	0	ENST00000168712.1:c.575_577del	p.Arg192_Val193delinsLeu	p.R192_V193delinsL	ENST00000168712	NM_002007.2	192	cGAGtg/ctg	3/3	NA	2	FACETS	0.935	0.87	1			1	INDETERMINATE	1	TRUE	NA	0.533893663955658	2		681	829	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426750	121426750	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	262	809	0	ENST00000257555.6:c.441C>G	p.His147Gln	p.H147Q	ENST00000257555		147	caC/caG	2/10	0.155052380604728	3	FACETS	0.978	0.915	1	0.326	0.305	0.348	INDETERMINATE	1	TRUE	0	0.533893663955658	3		809	1272	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592681	28592681	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	380	633	0	ENST00000241453.7:c.2464G>T	p.Gly822Trp	p.G822W	ENST00000241453	NM_004119.2	822	Ggg/Tgg	20/24	0.533893663955658	2	FACETS	0.99	0.948	1	0.99	0.948	1	CLONAL	2	TRUE	0	0.533893663955658	2		633	719	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003290	143003290	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0037789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	134	583	0	ENST00000262992.4:c.2536A>T	p.Lys846Ter	p.K846*	ENST00000262992	NM_001101669.1	846	Aaa/Taa	23/24	1	2	FACETS	0.931	0.85	1	0.931	0.85	1	CLONAL	1	TRUE	1	0.533893663955658	2		583	539	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554979	187554979	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0037789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	71	279	0	ENST00000441802.2:c.4184-2A>T		p.X1395_splice	ENST00000441802	NM_005245.3	1395			0.533893663955658	1	FACETS	0.907	0.805	1	0.907	0.805	1	CLONAL	1	TRUE	0	0.533893663955658	1		279	215	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863295	56863295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	150	634	1	ENST00000519728.1:c.439G>A	p.Gly147Arg	p.G147R	ENST00000519728	NM_002350.3	147	Gga/Aga	6/13	0.428004887509336	4	FACETS	0.902	0.823	0.984	0.301	0.274	0.328	CLONAL	1	TRUE	1	0.533893663955658	4		635	956	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562676	21562676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1165374192	NA	P-0037804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	131	281	1	ENST00000382592.4:c.1243C>T	p.Arg415Trp	p.R415W	ENST00000382592	NM_014572.2	415	Cgg/Tgg	4/8	1	2	FACETS	0.928	0.851	1	0.928	0.851	1	CLONAL	1	TRUE	1	0.72	2		282	392	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620114	21620114	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	247	609	1	ENST00000382592.4:c.52C>T	p.Arg18Ter	p.R18*	ENST00000382592	NM_014572.2	18	Cga/Tga	2/8	1	2	FACETS	0.92	0.863	0.977	0.92	0.863	0.977	CLONAL	1	TRUE	1	0.72	2		610	746	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	23	82	0				ENST00000310581	NM_198253.2	-/1132			0.531259851933698	3	FACETS	0.8	0.631	0.99	0.4	0.315	0.495	CLONAL	1	TRUE	1	0.531259851933698	3		82	137	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0037805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	150	672	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	0.487857690054131	4	FACETS	0.928	0.855	1	0.928	0.855	1	CLONAL	2	TRUE	2	0.531259851933698	4		672	466	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522123	157522123	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554235726	NA	P-0037805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	119	664	0	ENST00000346085.5:c.4395G>A	p.Trp1465Ter	p.W1465*	ENST00000346085	NM_020732.3	1465	tgG/tgA	18/20	0.531259851933698	3	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	1	0.531259851933698	3		664	278	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665213	138665213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	222	734	1	ENST00000330315.3:c.352G>A	p.Glu118Lys	p.E118K	ENST00000330315	NM_023067.3	118	Gag/Aag	1/1	0.460959021397252	6	FACETS	1	0.991	1	0.372	0.345	0.4	CLONAL	1	TRUE	2	0.460959021397252	6		735	1244	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	310	617	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.443456332294536	2	FACETS	0.899	0.853	0.946	0.899	0.853	0.946	CLONAL	2	TRUE	0	0.460959021397252	2		617	748	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955381	48955381	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs1258442224	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	145	213	0	ENST00000267163.4:c.1499-2A>T		p.X500_splice	ENST00000267163	NM_000321.2	500			0.443456332294536	2	FACETS	0.989	0.918	1	0.989	0.918	1	CLONAL	2	TRUE	0	0.460959021397252	2		213	318	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248766	212248766	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs549128376	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	113	287	0	ENST00000342788.4:c.3501G>T	p.Glu1167Asp	p.E1167D	ENST00000342788	NM_005235.2	1167	gaG/gaT	28/28	0.248146023064021	3	FACETS	0.762	0.691	0.835	0.762	0.691	0.835	INDETERMINATE	2	TRUE	1	0.460959021397252	3		287	396	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464457	25464457	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	313	520	0	ENST00000264709.3:c.2056del	p.Asp686ThrfsTer19	p.D686Tfs*19	ENST00000264709	NM_175629.2	686	Gac/ac	17/23	0.461398411420663	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.460959021397252	3		520	729	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600336	10600336	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs751088754	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	291	676	1	ENST00000171111.5:c.1519C>T	p.Arg507Ter	p.R507*	ENST00000171111	NM_203500.1	507	Cga/Tga	4/6	0.445586092368292	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.460959021397252	2		677	601	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602334	10602334	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	200	777	0	ENST00000171111.5:c.1244G>T	p.Arg415Leu	p.R415L	ENST00000171111	NM_203500.1	415	cGc/cTc	3/6	0.445586092368292	2	FACETS	1	0.977	1	0.559	0.519	0.6	CLONAL	1	TRUE	0	0.460959021397252	2		777	776	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625191	69625191	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	127	786	0	ENST00000334134.2:c.602C>A	p.Pro201His	p.P201H	ENST00000334134	NM_005247.2	201	cCc/cAc	3/3	0.461398411420663	3	FACETS	0.869	0.788	0.955	0.435	0.394	0.478	CLONAL	1	TRUE	1	0.460959021397252	3		786	780	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076967	41076967	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	85	471	1	ENST00000373198.4:c.1453C>T	p.Pro485Ser	p.P485S	ENST00000373198	NM_133170.3	485	Cca/Tca	9/32	0.199371554518997	3	FACETS	0.834	0.739	0.936	0.278	0.246	0.312	INDETERMINATE	1	TRUE	0	0.460959021397252	3		472	544	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058539	72058539	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	110	494	0	ENST00000357731.5:c.901A>T	p.Asn301Tyr	p.N301Y	ENST00000357731	NM_173808.2	301	Aac/Tac	6/7	0.443456332294536	2	FACETS	0.82	0.739	0.906	0.41	0.369	0.453	CLONAL	1	TRUE	0	0.460959021397252	2		494	582	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551357	150551357	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2380	212	918	0	ENST00000369026.2:c.650G>T	p.Gly217Val	p.G217V	ENST00000369026	NM_021960.4	217	gGg/gTg	1/3	0.460959021397252	12	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.460959021397252	12		918	2592	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193205424	193205424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	99	445	0	ENST00000367435.3:c.1355G>T	p.Trp452Leu	p.W452L	ENST00000367435	NM_024529.4	452	tGg/tTg	15/17	0.377727021180392	3	FACETS	0.796	0.711	0.886	0.398	0.355	0.443	SUBCLONAL	1	TRUE	1	0.460959021397252	3		445	664	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612793	228612793	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	129	682	0	ENST00000366696.1:c.234C>A	p.Asp78Glu	p.D78E	ENST00000366696	NM_003493.2	78	gaC/gaA	1/1	0.461398411420663	3	FACETS	0.834	0.756	0.916	0.417	0.378	0.458	CLONAL	1	TRUE	1	0.460959021397252	3		682	826	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100744	8100744	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	251	797	2	ENST00000346208.3:c.718C>A	p.Leu240Met	p.L240M	ENST00000346208		240	Ctg/Atg	3/6	0.445586092368292	2	FACETS	0.914	0.862	0.966	0.914	0.862	0.966	CLONAL	2	TRUE	0	0.460959021397252	2		799	596	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279539	123279539	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	148	645	0	ENST00000358487.5:c.893G>C	p.Gly298Ala	p.G298A	ENST00000358487	NM_000141.4	298	gGc/gCc	7/18	0.445586092368292	2	FACETS	0.927	0.848	1	0.463	0.424	0.504	CLONAL	1	TRUE	0	0.460959021397252	2		645	693	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102094422	102094422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	151	487	0	ENST00000282441.5:c.1102C>T	p.Pro368Ser	p.P368S	ENST00000282441	NM_001130145.2	368	Ccc/Tcc	7/9	0.461398411420663	3	FACETS	0.983	0.899	1	0.492	0.449	0.536	CLONAL	1	TRUE	1	0.460959021397252	3		487	820	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352667	118352667	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	248	583	1	ENST00000534358.1:c.3872C>G	p.Ser1291Cys	p.S1291C	ENST00000534358	NM_005933.3	1291	tCc/tGc	7/36	0.461398411420663	3	FACETS	0.907	0.852	0.963	0.907	0.852	0.963	CLONAL	2	TRUE	1	0.460959021397252	3		584	730	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50483716	50483716	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	244	579	1	ENST00000394963.4:c.821G>T	p.Arg274Leu	p.R274L	ENST00000394963	NM_003076.4	274	cGg/cTg	7/13	0.435283166112694	4	FACETS	0.831	0.777	0.886	0.831	0.777	0.886	CLONAL	2	TRUE	2	0.460959021397252	4		580	931	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864148	57864148	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs766159479	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	222	611	0	ENST00000228682.2:c.1625G>T	p.Arg542Leu	p.R542L	ENST00000228682	NM_005269.2	542	cGc/cTc	12/12	0.435283166112694	4	FACETS	0.938	0.876	1	0.938	0.876	1	CLONAL	2	TRUE	2	0.460959021397252	4		611	750	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245071	133245071	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	265	790	0	ENST00000320574.5:c.2044G>T	p.Glu682Ter	p.E682*	ENST00000320574	NM_006231.2	682	Gaa/Taa	19/49	0.335232176088606	4	FACETS	0.859	0.806	0.913	0.859	0.806	0.913	CLONAL	2	TRUE	2	0.460959021397252	4		790	978	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68301868	68301868	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	250	502	0	ENST00000487270.1:c.270G>C	p.Leu90Phe	p.L90F	ENST00000487270	NM_133509.3	90	ttG/ttC	4/11	0.336327587697406	4	FACETS	0.846	0.792	0.901	0.846	0.792	0.901	CLONAL	2	TRUE	2	0.460959021397252	4		502	937	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562639	95562639	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	186	386	2	ENST00000393063.1:c.4618G>T	p.Gly1540Ter	p.G1540*	ENST00000393063	NM_030621.3	1540	Gga/Tga	24/28	0.336327587697406	4	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	2	0.460959021397252	4		388	582	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226386	2226386	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	240	819	1	ENST00000326181.6:c.1998+1G>T		p.X666_splice	ENST00000326181	NM_032271.2	666			0.199371554518997	3	FACETS	0.9	0.844	0.957	0.6	0.563	0.638	INDETERMINATE	2	TRUE	0	0.460959021397252	3		820	712	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214636	36214636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376006013	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	149	814	0	ENST00000222270.7:c.3062G>A	p.Arg1021Gln	p.R1021Q	ENST00000222270	NM_014727.1	1021	cGg/cAg	8/37	0.445586092368292	2	FACETS	0.902	0.825	0.981	0.451	0.412	0.491	CLONAL	1	TRUE	0	0.460959021397252	2		814	717	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726690	41726690	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	180	844	0	ENST00000301178.4:c.235G>C	p.Ala79Pro	p.A79P	ENST00000301178	NM_021913.4	79	Gcg/Ccg	2/20	0.445586092368292	2	FACETS	1	0.943	1	0.512	0.473	0.552	CLONAL	1	TRUE	0	0.460959021397252	2		844	763	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917037	50917037	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	297	745	1	ENST00000440232.2:c.2289C>A	p.Phe763Leu	p.F763L	ENST00000440232	NM_002691.3	763	ttC/ttA	19/27	0.445586092368292	2	FACETS	0.976	0.926	1	0.976	0.926	1	CLONAL	2	TRUE	0	0.460959021397252	2		746	660	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27014998	27014998	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	232	394	0	ENST00000335756.4:c.101-1G>T		p.X34_splice	ENST00000335756	NM_001809.3	34			0.461398411420663	3	FACETS	0.992	0.932	1	0.992	0.932	1	CLONAL	2	TRUE	1	0.460959021397252	3		394	624	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462669	29462669	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	154	779	0	ENST00000389048.3:c.2232del	p.Gly746AlafsTer6	p.G746Afs*6	ENST00000389048	NM_004304.4	744	ggG/gg	13/29	0.461398411420663	3	FACETS	0.836	0.764	0.911	0.418	0.382	0.456	CLONAL	1	TRUE	1	0.460959021397252	3		779	984	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051194	128051194	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	164	613	0	ENST00000285398.2:c.129del	p.Lys44SerfsTer24	p.K44Sfs*24	ENST00000285398	NM_000122.1	43	ggG/gg	2/15	0.336327587697406	4	FACETS	1	0.981	1	0.609	0.56	0.661	CLONAL	1	TRUE	2	0.460959021397252	4		613	853	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374404	31374404	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	173	693	0	ENST00000328111.2:c.403G>T	p.Glu135Ter	p.E135*	ENST00000328111	NM_006892.3	135	Gag/Tag	5/23	0.377727021180392	3	FACETS	1	0.978	1	0.582	0.536	0.629	CLONAL	1	TRUE	1	0.460959021397252	3		693	794	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306539	41306539	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	92	550	1	ENST00000373198.4:c.1120G>T	p.Gly374Trp	p.G374W	ENST00000373198	NM_133170.3	374	Ggg/Tgg	7/32	0.199371554518997	3	FACETS	0.759	0.675	0.849	0.253	0.225	0.283	INDETERMINATE	1	TRUE	0	0.460959021397252	3		551	647	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499412	89499413	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	187	433	2	ENST00000336596.2:c.2582_2583delinsTT	p.Trp861Phe	p.W861F	ENST00000336596	NM_005233.5	861	tGG/tTT	15/17	0.344995225848275	5	FACETS	0.937	0.868	1	0.625	0.579	0.673	CLONAL	2	TRUE	2	0.460959021397252	5		435	732	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670789	134670789	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs368276671	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	94	580	0	ENST00000398015.3:c.700G>C	p.Val234Leu	p.V234L	ENST00000398015	NM_004441.4	234	Gtg/Ctg	3/16	0.344995225848275	5	FACETS	0.853	0.758	0.954	0.284	0.252	0.318	CLONAL	1	TRUE	2	0.460959021397252	5		580	809	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247256	153247256	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	134	377	0	ENST00000281708.4:c.1546A>T	p.Ser516Cys	p.S516C	ENST00000281708	NM_033632.3	516	Agt/Tgt	10/12	0.377727021180392	3	FACETS	1	0.979	1	0.624	0.569	0.681	CLONAL	1	TRUE	1	0.460959021397252	3		377	573	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628239	187628239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	281	692	0	ENST00000441802.2:c.2743G>A	p.Val915Ile	p.V915I	ENST00000441802	NM_005245.3	915	Gta/Ata	2/27	0.377727021180392	3	FACETS	0.893	0.842	0.945	0.893	0.842	0.945	CLONAL	2	TRUE	1	0.460959021397252	3		692	840	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968275	2968275	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	173	800	1	ENST00000396946.4:c.1711G>T	p.Asp571Tyr	p.D571Y	ENST00000396946	NM_032415.4	571	Gac/Tac	13/25	0.451452023118101	2	FACETS	0.945	0.871	1	0.473	0.435	0.511	CLONAL	1	TRUE	0	0.460959021397252	2		801	794	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978860	13978860	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	137	409	0	ENST00000405192.2:c.247G>T	p.Gly83Cys	p.G83C	ENST00000405192	NM_001163147.1	83	Ggc/Tgc	6/12	0.451452023118101	2	FACETS	1	0.976	1	0.593	0.543	0.645	CLONAL	1	TRUE	0	0.460959021397252	2		409	501	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667458	241667458	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	34	315	0	ENST00000366560.3:c.992C>A	p.Thr331Asn	p.T331N	ENST00000366560	NM_000143.3	331	aCt/aAt	7/10	0.432121481279238	3	FACETS	0.383	0.313	0.463	0.192	0.156	0.232	SUBCLONAL	1	FALSE	1	0.432121481279238	3		315	499	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132536	11132536	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	124	800	1	ENST00000358026.2:c.2752C>T	p.Leu918Phe	p.L918F	ENST00000358026	NM_001128849.1	918	Ctt/Ttt	19/36	0.432121481279238	0	FACETS	0.558	0.506	0.612			1	SUBCLONAL	1	FALSE	0	0.432121481279238	0		801	584	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0037863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	45	697	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.592	0.497	0.697	0.592	0.497	0.697	SUBCLONAL	1	TRUE	1	0.27	2		697	563	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0037863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	69	214	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	1	0.921	1			1	INDETERMINATE	1	TRUE	NA	0.27	2		214	475	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984924	101984924	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	31	379	0	ENST00000282441.5:c.371G>C	p.Arg124Pro	p.R124P	ENST00000282441	NM_001130145.2	124	cGa/cCa	2/9	1	2	FACETS	0.662	0.536	0.804	0.662	0.536	0.804	SUBCLONAL	1	TRUE	1	0.27	2		379	347	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779332	3779332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	87	775	1	ENST00000262367.5:c.5716C>T	p.Pro1906Ser	p.P1906S	ENST00000262367	NM_004380.2	1906	Cct/Tct	31/31	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.27	2		776	615	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088772	27088772	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	93	636	0	ENST00000324856.7:c.2381G>T	p.Gly794Val	p.G794V	ENST00000324856	NM_006015.4	794	gGg/gTg	7/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.27	2		636	635	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512284	120512284	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	54	556	0	ENST00000256646.2:c.958G>C	p.Gly320Arg	p.G320R	ENST00000256646	NM_024408.3	320	Gga/Cga	6/34	1	2	FACETS	0.791	0.676	0.916	0.791	0.676	0.916	CLONAL	1	TRUE	1	0.27	2		556	506	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163297340	163297340	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	56	421	0	ENST00000271452.3:c.186A>T	p.Glu62Asp	p.E62D	ENST00000271452	NM_145697.2	62	gaA/gaT	3/14	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.27	2		421	393	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771551	112771552	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0037863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	72	448	0	ENST00000369452.4:c.1727dup	p.Pro577SerfsTer9	p.P577Sfs*9	ENST00000369452	NM_007373.3	575	cag/caGg	9/9	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.27	2		448	524	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986956	36986956	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0037863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	169	678	0	ENST00000354822.5:c.733A>T	p.Lys245Ter	p.K245*	ENST00000354822	NM_001079668.2	245	Aaa/Taa	3/3	0.272684453101466	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.27	2		678	554	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218440	36218440	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	71	753	0	ENST00000222270.7:c.4219G>T	p.Gly1407Trp	p.G1407W	ENST00000222270	NM_014727.1	1407	Ggg/Tgg	16/37	1	2	FACETS	0.887	0.775	1	0.887	0.775	1	CLONAL	1	TRUE	1	0.27	2		753	593	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790124	40790124	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	49	690	0	ENST00000373198.4:c.2607C>A	p.Tyr869Ter	p.Y869*	ENST00000373198	NM_133170.3	869	taC/taA	18/32	0.112233761378358	0	FACETS	0.432	0.365	0.505			1	INDETERMINATE	1	TRUE	0	0.27	0		690	614	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128849225	128849225	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	84	469	0	ENST00000249373.3:c.1453C>G	p.Arg485Gly	p.R485G	ENST00000249373	NM_005631.4	485	Cgg/Ggg	8/12	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.27	2		469	507	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132871	152132871	+	start_lost	Translation_Start_Site	SNP	T	T	A	novel	NA	P-0037863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	34	511	0	ENST00000262189.6:c.1A>T	p.Met1?	p.M1?	ENST00000262189	NM_170606.2	1	Atg/Ttg	1/59	1	2	FACETS	0.529	0.432	0.639	0.529	0.432	0.639	SUBCLONAL	1	TRUE	1	0.27	2		511	476	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380282	25380282	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	62	334	0	ENST00000311936.3:c.176C>G	p.Ala59Gly	p.A59G	ENST00000311936	NM_004985.3	59	gCa/gGa	3/5	0.21099785999969	3	FACETS	0.839	0.728	0.959	0.839	0.728	0.959	CLONAL	2	TRUE	1	0.21099785999969	3		334	387	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528582	89528582	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	49	198	0	ENST00000336596.2:c.2882C>A	p.Pro961Gln	p.P961Q	ENST00000336596	NM_005233.5	961	cCa/cAa	17/17	0.21099785999969	3	FACETS	0.785	0.668	0.912	0.785	0.668	0.912	CLONAL	2	TRUE	1	0.21099785999969	3		198	327	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953011	2953011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1172378918	NA	P-0037879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	43	647	1	ENST00000396946.4:c.2929G>A	p.Val977Met	p.V977M	ENST00000396946	NM_032415.4	977	Gtg/Atg	22/25	0.0605067165283457	4	FACETS	1	0.874	1	0.526	0.44	0.621	INDETERMINATE	1	TRUE	2	0.21099785999969	4		648	469	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005607	42005607	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	43	321	0	ENST00000219905.7:c.3343G>T	p.Gly1115Ter	p.G1115*	ENST00000219905	NM_001164273.1	1115	Gga/Tga	9/24	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.21099785999969	2		321	309	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548866	29548866	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0037879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	53	443	0	ENST00000356175.3:c.1642-2A>T		p.X548_splice	ENST00000356175	NM_000267.3	548			1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.21099785999969	2		443	421	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	443	82	0				ENST00000310581	NM_198253.2	-/1132			0.49818622106017	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	1	0.561660636009119	4		82	783	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0037922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	195	374	0	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	1	2	FACETS	0.842	0.78	0.905	0.842	0.78	0.905	CLONAL	1	TRUE	1	0.561660636009119	2		374	825	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118379879	118379879	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139119128	NA	P-0037922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	98	270	0	ENST00000534358.1:c.10864G>T	p.Val3622Leu	p.V3622L	ENST00000534358	NM_005933.3	3622	Gtg/Ttg	29/36	1	2	FACETS	0.881	0.792	0.975	0.881	0.792	0.975	CLONAL	1	TRUE	1	0.561660636009119	2		270	396	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61720069	61720070	+	missense_variant	Missense_Mutation	DNP	CT	CT	TC	novel	NA	P-0037922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	90	317	0	ENST00000401558.2:c.1364_1365delinsGA	p.Lys455Arg	p.K455R	ENST00000401558	NM_003400.3	455	aAG/aGA	13/25	1	2	FACETS	0.774	0.691	0.862	0.774	0.691	0.862	SUBCLONAL	1	TRUE	1	0.561660636009119	2		317	414	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932348	39932348	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	309	1078	0	ENST00000378444.4:c.2251G>T	p.Glu751Ter	p.E751*	ENST00000378444	NM_001123385.1	751	Gag/Tag	4/15	1	2	FACETS	0.98	0.924	1	0.98	0.924	1	CLONAL	1	TRUE	1	0.561660636009119	2		1078	1123	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0037924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	13	214	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.193056040746241	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		214	187	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0038019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	96	430	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.2	2		430	710	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578179	7578179	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	56	740	0	ENST00000269305.4:c.670G>T	p.Glu224Ter	p.E224*	ENST00000269305	NM_001126112.2	224	Gag/Tag	6/11	1	2	FACETS	0.822	0.704	0.952	0.822	0.704	0.952	CLONAL	1	TRUE	1	0.2	2		740	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0038164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	819	778	2	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	NA	2	FACETS	1	0.998	1			1	INDETERMINATE	2	TRUE	NA	0.738430801863717	2		780	926	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945139	32945139	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	142	365	0	ENST00000380152.3:c.8534G>C	p.Arg2845Thr	p.R2845T	ENST00000380152		2845	aGa/aCa	20/27	0.734929598756886	4	FACETS	0.862	0.794	0.931	0.862	0.794	0.931	CLONAL	2	TRUE	2	0.738430801863717	4		365	388	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528087	103528087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	258	381	0	ENST00000355739.4:c.3395C>T	p.Ser1132Leu	p.S1132L	ENST00000355739	NM_000123.3	1132	tCa/tTa	15/15	0.734929598756886	4	FACETS	0.992	0.937	1	0.992	0.937	1	CLONAL	2	TRUE	2	0.738430801863717	4		381	612	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644791	67644791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	256	545	0	ENST00000264010.4:c.56G>A	p.Gly19Glu	p.G19E	ENST00000264010	NM_006565.3	19	gGa/gAa	3/12	0.396009805458814	5	FACETS	1	0.985	1	0.755	0.712	0.799	INDETERMINATE	2	TRUE	2	0.738430801863717	5		545	645	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216995	7216995	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	502	489	0	ENST00000380728.2:c.526G>C	p.Glu176Gln	p.E176Q	ENST00000380728		176	Gag/Cag	7/11	NA	2	FACETS	1	0.997	1			1	INDETERMINATE	2	TRUE	NA	0.738430801863717	2		489	577	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015661	27015661	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	333	503	0	ENST00000335756.4:c.248A>G	p.Asp83Gly	p.D83G	ENST00000335756	NM_001809.3	83	gAc/gGc	3/5	0.601737946076898	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.738430801863717	4		503	746	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39251176	39251176	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	192	477	0	ENST00000402219.2:c.1177A>C	p.Lys393Gln	p.K393Q	ENST00000402219	NM_005633.3	393	Aaa/Caa	9/23	0.601737946076898	4	FACETS	0.846	0.789	0.905	0.846	0.789	0.905	CLONAL	2	TRUE	2	0.738430801863717	4		477	534	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215617226	215617226	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777937955	NA	P-0038164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	127	352	0	ENST00000260947.4:c.1622C>T	p.Ser541Leu	p.S541L	ENST00000260947	NM_000465.2	541	tCg/tTg	7/11	0.45266031332963	4	FACETS	0.961	0.884	1	0.961	0.884	1	CLONAL	2	TRUE	2	0.738430801863717	4		352	311	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022557	31022557	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	808	495	0	ENST00000375687.4:c.2042C>T	p.Pro681Leu	p.P681L	ENST00000375687	NM_015338.5	681	cCg/cTg	13/13	0.738430801863717	6	FACETS	1	0.995	1	1	0.995	1	CLONAL	5	TRUE	1	0.738430801863717	6		495	1027	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138195999	138195999	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	150	180	0	ENST00000237289.4:c.313A>T	p.Met105Leu	p.M105L	ENST00000237289	NM_001270507.1	105	Atg/Ttg	3/9	0.730099236527367	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.738430801863717	2		180	190	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950724	79950725	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCGCAGCGC	rs1554066076	NA	P-0038164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	20	242	4	ENST00000265081.6:c.181_189dup	p.Ala61_Pro63dup	p.A61_P63dup	ENST00000265081	NM_002439.4	61	gcc/gCCGCAGCGCcc	1/24	0.696261953970152	2	FACETS	0.334	0.257	0.423	0.167	0.128	0.212	SUBCLONAL	1	TRUE	0	0.738430801863717	2		246	162	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748832	43748832	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	485	644	0	ENST00000382044.4:c.1974C>G	p.His658Gln	p.H658Q	ENST00000382044	NM_001141980.1	658	caC/caG	12/28	0.775558343204709	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.775558343204709	1		644	718	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578376	7578377	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TATCTGAGCAGCGCTCATGGTGGGGGCAGCGCCTCACA	novel	NA	P-0038768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	169	500	0	ENST00000269305.4:c.516_553dup	p.Ser185MetfsTer2	p.S185Mfs*2	ENST00000269305	NM_001126112.2	185	agc/aTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAgc	5/11	0.759757198891749	1	FACETS	0.395	0.364	0.427	0.395	0.364	0.427	SUBCLONAL	1	TRUE	0	0.775558343204709	1		500	676	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059127	47059127	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0038768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	255	338	0	ENST00000409792.3:c.7533+1G>C		p.X2511_splice	ENST00000409792	NM_014159.6	2511			0.775558343204709	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.775558343204709	1		338	390	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288157	33288157	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	255	319	0	ENST00000374542.5:c.1251G>T	p.Glu417Asp	p.E417D	ENST00000374542	NM_001141970.1	417	gaG/gaT	4/8	0.775558343204709	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.775558343204709	1		319	399	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577363	64577377	+	frameshift_variant	Frame_Shift_Del	DEL	GCCAGGCGGGTCGGG	GCCAGGCGGGTCGGG	T	novel	NA	P-0038768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	303	617	0	ENST00000312049.6:c.205_219delinsA	p.Pro69ArgfsTer43	p.P69Rfs*43	ENST00000312049	NM_130799.2	69	CCCGACCCGCCTGGC/A	2/10	0.775558343204709	1	FACETS	0.899	0.859	0.939	0.899	0.859	0.939	CLONAL	1	TRUE	0	0.775558343204709	1		617	532	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	114	82	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.946	0.858	1	0.946	0.858	1	CLONAL	1	TRUE	1	0.535448729886945	2		82	450	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0038820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	151	345	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	0.995	0.914	1	0.995	0.914	1	CLONAL	1	TRUE	1	0.535448729886945	2		345	567	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684361	29684362	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0038820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	168	415	0	ENST00000356175.3:c.7884_7885del	p.Phe2629SerfsTer9	p.F2629Sfs*9	ENST00000356175	NM_000267.3	2627	gtTGtg/gttg	53/57	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.535448729886945	2		415	573	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0038972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	102	414	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.21228161675077	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.21228161675077	1		414	712	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289922	15289922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1358	92	860	0	ENST00000263388.2:c.3632C>T	p.Ser1211Leu	p.S1211L	ENST00000263388	NM_000435.2	1211	tCa/tTa	22/33	1	2	FACETS	0.598	0.529	0.672	0.598	0.529	0.672	SUBCLONAL	1	TRUE	1	0.21228161675077	2		860	1450	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572549	64572549	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1201	75	738	0	ENST00000312049.6:c.1307G>T	p.Trp436Leu	p.W436L	ENST00000312049	NM_130799.2	436	tGg/tTg	9/10	0.21228161675077	1	FACETS	0.495	0.432	0.563	0.495	0.432	0.563	SUBCLONAL	1	TRUE	0	0.21228161675077	1		738	1276	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044970	47044970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	164	877	0	ENST00000377604.3:c.2296C>T	p.Arg766Cys	p.R766C	ENST00000377604	NM_001204468.1	766	Cgc/Tgc	20/24	0.21228161675077	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.21228161675077	1		877	1309	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933061	39933062	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0038972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	73	849	1	ENST00000378444.4:c.1537_1538delinsCT	p.Gly513Leu	p.G513L	ENST00000378444	NM_001123385.1	513	GGg/CTg	4/15	NA	2	FACETS	0.541	0.471	0.617			1	INDETERMINATE	1	TRUE	NA	0.21228161675077	2		850	1272	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243215	123243215	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	119	907	0	ENST00000358487.5:c.2298T>G	p.Asn766Lys	p.N766K	ENST00000358487	NM_000141.4	766	aaT/aaG	17/18	0.21228161675077	1	FACETS	0.925	0.833	1	0.925	0.833	1	CLONAL	1	TRUE	0	0.21228161675077	1		907	1083	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007750	45007796	+	frameshift_variant	Frame_Shift_Del	DEL	TTGAAAAAGTGGAGCATTCAGACTTGTCTTTCAGCAAGGACTGGTCT	TTGAAAAAGTGGAGCATTCAGACTTGTCTTTCAGCAAGGACTGGTCT	-	novel	NA	P-0038972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	39	480	0	ENST00000558401.1:c.199_245del	p.Glu67LeufsTer7	p.E67Lfs*7	ENST00000558401	NM_004048.2	66	aTTGAAAAAGTGGAGCATTCAGACTTGTCTTTCAGCAAGGACTGGTCT/a	2/4	0.21228161675077	1	FACETS	0.443	0.366	0.53	0.443	0.366	0.53	SUBCLONAL	1	TRUE	0	0.21228161675077	1		480	741	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858238	9858238	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs370107080	NA	P-0038972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	121	486	0	ENST00000330684.3:c.3163G>C	p.Glu1055Gln	p.E1055Q	ENST00000330684	NM_001134407.1	1055	Gag/Cag	13/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.21228161675077	2		486	777	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014077	14014077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1431	79	685	0	ENST00000311895.7:c.55G>A	p.Glu19Lys	p.E19K	ENST00000311895	NM_005236.2	19	Gag/Aag	1/11	1	2	FACETS	0.493	0.431	0.56	0.493	0.431	0.56	SUBCLONAL	1	TRUE	1	0.21228161675077	2		685	1510	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971339	15971339	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	135	713	0	ENST00000268712.3:c.4610G>T	p.Gly1537Val	p.G1537V	ENST00000268712	NM_006311.3	1537	gGg/gTg	32/46	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.21228161675077	2		713	1172	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873571	37873571	+	splice_acceptor_variant	Splice_Site	DEL	A	A	-	novel	NA	P-0038972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	71	660	0	ENST00000269571.5:c.1738-2del		p.X580_splice	ENST00000269571		580			1	2	FACETS	0.614	0.534	0.701	0.614	0.534	0.701	SUBCLONAL	1	TRUE	1	0.21228161675077	2		660	1089	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376078	225376078	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	50	489	0	ENST00000264414.4:c.876G>C	p.Lys292Asn	p.K292N	ENST00000264414	NM_003590.4	292	aaG/aaC	6/16	1	2	FACETS	0.803	0.68	0.937	0.803	0.68	0.937	CLONAL	1	TRUE	1	0.21228161675077	2		489	587	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636706	176636706	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	83	526	1	ENST00000439151.2:c.1306G>T	p.Gly436Trp	p.G436W	ENST00000439151	NM_022455.4	436	Ggg/Tgg	5/23	0.21228161675077	3	FACETS	0.839	0.738	0.947	0.419	0.369	0.474	CLONAL	1	TRUE	1	0.21228161675077	3		527	1031	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729877	41729877	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	88	592	0	ENST00000242208.4:c.652T>A	p.Trp218Arg	p.W218R	ENST00000242208	NM_002192.2	218	Tgg/Agg	3/3	1	2	FACETS	0.888	0.785	0.998	0.888	0.785	0.998	CLONAL	1	TRUE	1	0.21228161675077	2		592	934	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415099	116415099	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	187	660	0	ENST00000397752.3:c.3193G>T	p.Ala1065Ser	p.A1065S	ENST00000397752	NM_000245.2	1065	Gca/Tca	15/21	1	2	FACETS	0.779	0.718	0.842	1	0.99	1	SUBCLONAL	2	TRUE	1	0.21228161675077	2		660	1131	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923600	39923600	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	60	716	0	ENST00000378444.4:c.3491G>T	p.Arg1164Leu	p.R1164L	ENST00000378444	NM_001123385.1	1164	cGa/cTa	7/15	NA	2	FACETS	0.502	0.431	0.581			1	INDETERMINATE	1	TRUE	NA	0.21228161675077	2		716	1125	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039040-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	89	214	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.355341476342107	3	FACETS	0.793	0.708	0.882	0.793	0.708	0.882	SUBCLONAL	2	FALSE	1	0.355341476342107	3		214	372	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912806	100912806	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768389545	NA	P-0039040-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	44	467	0	ENST00000325455.5:c.2516C>A	p.Thr839Asn	p.T839N	ENST00000325455	NM_001202474.3	839	aCc/aAc	7/8	1	2	FACETS	0.744	0.626	0.873	0.744	0.626	0.873	SUBCLONAL	1	FALSE	1	0.355341476342107	2		467	333	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827841	170827841	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0039040-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	10	227	0	ENST00000296930.5:c.583-2A>T		p.X195_splice	ENST00000296930	NM_002520.6	195			1	2	FACETS	0.447	0.304	0.624	0.447	0.304	0.624	SUBCLONAL	1	FALSE	1	0.355341476342107	2		227	126	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0039079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1305	303	714	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.182579624509154	9	FACETS	1	0.984	1			1	CLONAL	3	TRUE	NA	0.182579624509154	9		714	1608	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0039079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	195	502	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.182579624509154	9	FACETS	0.91	0.842	0.98			1	CLONAL	4	TRUE	NA	0.182579624509154	9		502	962	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764146326	NA	P-0039079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	213	924	2	ENST00000269305.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000269305	NM_001126112.2	281	Gac/Aac	8/11	1	2	FACETS	0.939	0.871	1	1	0.993	1	CLONAL	2	TRUE	1	0.182579624509154	2		926	1242	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	277	606	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	1	2	FACETS	0.979	0.926	1	0.979	0.926	1	CLONAL	1	TRUE	1	0.867830816902042	2		606	652	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480345	89480345	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs774448099	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	118	255	0	ENST00000336596.2:c.2182C>T	p.Arg728Ter	p.R728*	ENST00000336596	NM_005233.5	728	Cga/Tga	13/17	0.867830816902042	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.867830816902042	1		255	140	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637049	93637049	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	185	450	0	ENST00000375746.1:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000375746	NM_001174167.1	367	Cga/Tga	9/14	1	2	FACETS	0.907	0.846	0.969	0.907	0.846	0.969	CLONAL	1	TRUE	1	0.867830816902042	2		450	470	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584747	187584747	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1358297166	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	111	354	0	ENST00000441802.2:c.3286C>T	p.Arg1096Ter	p.R1096*	ENST00000441802	NM_005245.3	1096	Cga/Tga	3/27	1	2	FACETS	0.91	0.832	0.991	0.91	0.832	0.991	CLONAL	1	TRUE	1	0.867830816902042	2		354	281	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9928072	9928072	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780349	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	143	289	0	ENST00000330684.3:c.1667C>T	p.Ser556Phe	p.S556F	ENST00000330684	NM_001134407.1	556	tCt/tTt	8/13	1	2	FACETS	0.975	0.902	1	0.975	0.902	1	CLONAL	1	TRUE	1	0.867830816902042	2		289	338	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395478	116395478	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45602940	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	170	433	0	ENST00000397752.3:c.1771C>T	p.Arg591Trp	p.R591W	ENST00000397752	NM_000245.2	591	Cgg/Tgg	6/21	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.867830816902042	2		433	389	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222510	39222510	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167317994	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	211	477	0	ENST00000402219.2:c.3100C>T	p.Pro1034Ser	p.P1034S	ENST00000402219	NM_005633.3	1034	Ccc/Tcc	20/23	1	2	FACETS	0.961	0.901	1	0.961	0.901	1	CLONAL	1	TRUE	1	0.867830816902042	2		477	506	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412663	139412663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	327	770	1	ENST00000277541.6:c.1181G>A	p.Gly394Asp	p.G394D	ENST00000277541	NM_017617.3	394	gGc/gAc	7/34	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.867830816902042	2		771	741	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663707	117663707	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1489503636	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	88	234	0	ENST00000368508.3:c.4525G>A	p.Glu1509Lys	p.E1509K	ENST00000368508	NM_002944.2	1509	Gaa/Aaa	28/43	1	2	FACETS	0.975	0.883	1	0.975	0.883	1	CLONAL	1	TRUE	1	0.867830816902042	2		234	208	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579312	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	229	498	1	ENST00000269305.4:c.375_375+1delinsAA		p.X125_splice	ENST00000269305	NM_001126112.2	125		4/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.867830816902042	2		499	493	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407472	139407472	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	155	552	0	ENST00000277541.6:c.2467+1G>A		p.X823_splice	ENST00000277541	NM_017617.3	823			1	2	FACETS	0.825	0.763	0.889	0.825	0.763	0.889	CLONAL	1	TRUE	1	0.867830816902042	2		552	433	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220143	133220143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	250	591	0	ENST00000320574.5:c.4294C>T	p.Pro1432Ser	p.P1432S	ENST00000320574	NM_006231.2	1432	Ccg/Tcg	34/49	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.867830816902042	2		591	571	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302774	15302774	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	212	712	0	ENST00000263388.2:c.676C>T	p.Pro226Ser	p.P226S	ENST00000263388	NM_000435.2	226	Cct/Tct	4/33	1	2	FACETS	0.951	0.892	1	0.951	0.892	1	CLONAL	1	TRUE	1	0.867830816902042	2		712	514	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781303	135781303	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs118203554	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	222	576	0	ENST00000298552.3:c.1662del	p.Ile555Ter	p.I555*	ENST00000298552	NM_001162426.1	554	ccC/cc	15/23	1	2	FACETS	0.964	0.905	1	0.964	0.905	1	CLONAL	1	TRUE	1	0.867830816902042	2		576	531	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332569	65332570	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	116	292	1	ENST00000342505.4:c.969_970delinsTT	p.Gln324Ter	p.Q324*	ENST00000342505	NM_002227.2	323	atCCag/atTTag	7/25	0.847618783624256	3	FACETS	0.919	0.835	1	0.46	0.417	0.504	CLONAL	1	TRUE	1	0.867830816902042	3		293	417	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468412	120468413	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	194	558	5	ENST00000256646.2:c.4026_4027delinsTT	p.Gln1343Ter	p.Q1343*	ENST00000256646	NM_024408.3	1342	tgCCag/tgTTag	25/34	1	2	FACETS	0.891	0.832	0.951	0.891	0.832	0.951	CLONAL	1	TRUE	1	0.867830816902042	2		563	502	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717739	89717739	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1564566998	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	177	380	0	ENST00000371953.3:c.764T>A	p.Val255Glu	p.V255E	ENST00000371953	NM_000314.4	255	gTa/gAa	7/9	0.867830816902042	1	FACETS	0.995	0.951	1	0.995	0.951	1	CLONAL	1	TRUE	0	0.867830816902042	1		380	232	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186638	108186638	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs139770721	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	147	292	0	ENST00000278616.4:c.6095G>A	p.Arg2032Lys	p.R2032K	ENST00000278616	NM_000051.3	2032	aGa/aAa	41/63	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.867830816902042	2		292	321	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	443569	443569	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	153	321	1	ENST00000399788.2:c.1328G>A	p.Trp443Ter	p.W443*	ENST00000399788	NM_001042603.1	443	tGg/tAg	11/28	NA	2	FACETS	0.971	0.901	1			1	INDETERMINATE	1	TRUE	NA	0.867830816902042	2		322	363	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246036	46246036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	123	310	1	ENST00000334344.6:c.4130C>T	p.Pro1377Leu	p.P1377L	ENST00000334344	NM_152641.2	1377	cCa/cTa	15/21	1	2	FACETS	0.864	0.792	0.938	0.864	0.792	0.938	CLONAL	1	TRUE	1	0.867830816902042	2		311	328	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954220	48954221	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	113	227	1	ENST00000267163.4:c.1421_1421+1delinsAA		p.X474_splice	ENST00000267163	NM_000321.2	474		15/27	0.867830816902042	1	FACETS	0.964	0.907	1	0.964	0.907	1	CLONAL	1	TRUE	0	0.867830816902042	1		228	153	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724540	43724540	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	311	832	2	ENST00000382044.4:c.3527C>T	p.Thr1176Ile	p.T1176I	ENST00000382044	NM_001141980.1	1176	aCc/aTc	17/28	1	2	FACETS	0.917	0.869	0.965	0.917	0.869	0.965	CLONAL	1	TRUE	1	0.867830816902042	2		834	782	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678551	88678551	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	37	411	0	ENST00000360948.2:c.985C>T	p.Pro329Ser	p.P329S	ENST00000360948	NM_001012338.2	329	Ccc/Tcc	9/19	1	2	FACETS	0.266	0.22	0.318	0.266	0.22	0.318	SUBCLONAL	1	TRUE	1	0.867830816902042	2		411	320	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292998	91292998	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	221	499	0	ENST00000355112.3:c.500A>C	p.Lys167Thr	p.K167T	ENST00000355112	NM_000057.2	167	aAa/aCa	3/22	1	2	FACETS	0.989	0.93	1	0.989	0.93	1	CLONAL	1	TRUE	1	0.867830816902042	2		499	515	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658596	3658596	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	310	766	1	ENST00000294008.3:c.370A>T	p.Arg124Trp	p.R124W	ENST00000294008	NM_032444.2	124	Agg/Tgg	2/15	1	2	FACETS	0.915	0.867	0.963	0.915	0.867	0.963	CLONAL	1	TRUE	1	0.867830816902042	2		767	781	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14022058	14022058	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	220	394	0	ENST00000311895.7:c.758C>T	p.Ser253Phe	p.S253F	ENST00000311895	NM_005236.2	253	tCt/tTt	4/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.867830816902042	2		394	461	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346539	89346540	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	184	592	1	ENST00000301030.4:c.6410_6411delinsTT	p.Ser2137Phe	p.S2137F	ENST00000301030	NM_001256183.1	2137	tCC/tTT	9/13	1	2	FACETS	0.957	0.894	1	0.957	0.894	1	CLONAL	1	TRUE	1	0.867830816902042	2		593	443	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883224	37883224	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	264	692	1	ENST00000269571.5:c.3127G>A	p.Val1043Ile	p.V1043I	ENST00000269571		1043	Gtc/Atc	25/27	1	2	FACETS	0.978	0.924	1	0.978	0.924	1	CLONAL	1	TRUE	1	0.867830816902042	2		693	622	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884056	37884057	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	180	766	1	ENST00000269571.5:c.3527_3528delinsAA	p.Gly1176Glu	p.G1176E	ENST00000269571		1176	gGG/gAA	27/27	1	2	FACETS	0.617	0.571	0.665	0.617	0.571	0.665	SUBCLONAL	1	TRUE	1	0.867830816902042	2		767	672	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7163211	7163211	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	169	436	0	ENST00000302850.5:c.1862-1G>A		p.X621_splice	ENST00000302850	NM_000208.2	621			1	2	FACETS	0.986	0.918	1	0.986	0.918	1	CLONAL	1	TRUE	1	0.867830816902042	2		436	395	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758822	41758823	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	276	741	1	ENST00000301178.4:c.1876_1877delinsAA	p.Gly626Lys	p.G626K	ENST00000301178	NM_021913.4	626	GGa/AAa	16/20	1	2	FACETS	0.948	0.896	1	0.948	0.896	1	CLONAL	1	TRUE	1	0.867830816902042	2		742	671	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61725893	61725893	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1300617385	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	124	418	1	ENST00000401558.2:c.674C>T	p.Thr225Ile	p.T225I	ENST00000401558	NM_003400.3	225	aCc/aTc	9/25	1	2	FACETS	0.608	0.553	0.665	0.608	0.553	0.665	SUBCLONAL	1	TRUE	1	0.867830816902042	2		419	470	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543895	212543896	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	174	350	0	ENST00000342788.4:c.1503_1504delinsAA	p.Met501_Val502delinsIleMet	p.M501_V502delinsIM	ENST00000342788	NM_005235.2	501	atGGtg/atAAtg	13/28	1	2	FACETS	0.964	0.898	1	0.964	0.898	1	CLONAL	1	TRUE	1	0.867830816902042	2		350	416	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546793	9546793	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	85	307	0	ENST00000353224.5:c.1229C>A	p.Thr410Asn	p.T410N	ENST00000353224	NM_177990.2	410	aCc/aAc	5/10	1	2	FACETS	0.751	0.673	0.831	0.751	0.673	0.831	SUBCLONAL	1	TRUE	1	0.867830816902042	2		307	261	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021400	31021401	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	154	546	0	ENST00000375687.4:c.1399_1400delinsTT	p.Pro467Leu	p.P467L	ENST00000375687	NM_015338.5	467	CCa/TTa	12/13	1	2	FACETS	0.874	0.809	0.941	0.874	0.809	0.941	CLONAL	1	TRUE	1	0.867830816902042	2		546	406	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730888	40730889	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	270	651	0	ENST00000373198.4:c.3646_3647delinsAA	p.Gly1216Lys	p.G1216K	ENST00000373198	NM_133170.3	1216	GGg/AAg	27/32	1	2	FACETS	0.986	0.932	1	0.986	0.932	1	CLONAL	1	TRUE	1	0.867830816902042	2		651	631	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076964	41076964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	186	456	0	ENST00000373198.4:c.1456G>A	p.Gly486Arg	p.G486R	ENST00000373198	NM_133170.3	486	Gga/Aga	9/32	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.867830816902042	2		456	416	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139876	55139876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	100	360	0	ENST00000257290.5:c.1537G>A	p.Glu513Lys	p.E513K	ENST00000257290	NM_006206.4	513	Gag/Aag	10/23	1	2	FACETS	0.67	0.604	0.738	0.67	0.604	0.738	SUBCLONAL	1	TRUE	1	0.867830816902042	2		360	344	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526651	31526651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1883	237	640	0	ENST00000344624.3:c.389C>T	p.Pro130Leu	p.P130L	ENST00000344624		130	cCc/cTc	2/33	0.867830816902042	9	FACETS	1	0.956	1	0.13	0.12	0.14	CLONAL	1	TRUE	1	0.867830816902042	9		640	2120	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043389	180043389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs961025049	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	293	661	0	ENST00000261937.6:c.3197C>T	p.Pro1066Leu	p.P1066L	ENST00000261937	NM_182925.4	1066	cCc/cTc	23/30	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.867830816902042	2		661	622	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180050963	180050963	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	275	872	1	ENST00000261937.6:c.1520G>A	p.Trp507Ter	p.W507*	ENST00000261937	NM_182925.4	507	tGg/tAg	11/30	1	2	FACETS	0.879	0.83	0.929	0.879	0.83	0.929	CLONAL	1	TRUE	1	0.867830816902042	2		873	721	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488399	20488399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	188	493	3	ENST00000346618.3:c.1055C>T	p.Pro352Leu	p.P352L	ENST00000346618	NM_001949.4	352	cCa/cTa	6/7	1	2	FACETS	0.938	0.876	1	0.938	0.876	1	CLONAL	1	TRUE	1	0.867830816902042	2		496	462	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30668379	30668380	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	241	528	2	ENST00000376406.3:c.6132_6133delinsAA	p.Asp2045Asn	p.D2045N	ENST00000376406	NM_014641.2	2044	caGGac/caAAac	15/15	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.867830816902042	2		530	553	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168976	32168976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1301281297	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	315	818	1	ENST00000375023.3:c.4057G>A	p.Gly1353Arg	p.G1353R	ENST00000375023	NM_004557.3	1353	Gga/Aga	22/30	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.867830816902042	2		819	692	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935653	13935653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	194	428	1	ENST00000405192.2:c.1203G>A	p.Met401Ile	p.M401I	ENST00000405192	NM_001163147.1	401	atG/atA	12/12	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.867830816902042	2		429	431	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68984729	68984729	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	108	243	0	ENST00000288368.4:c.1494-1G>A		p.X498_splice	ENST00000288368	NM_024870.2	498			1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.867830816902042	2		243	245	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980487	70980487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	267	682	0	ENST00000276594.2:c.890G>A	p.Gly297Glu	p.G297E	ENST00000276594	NM_024504.3	297	gGa/gAa	4/8	1	2	FACETS	0.945	0.893	0.998	0.945	0.893	0.998	CLONAL	1	TRUE	1	0.867830816902042	2		682	651	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518125	8518126	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	198	419	1	ENST00000356435.5:c.1265_1266delinsAA	p.Arg422Lys	p.R422K	ENST00000356435		422	aGG/aAA	10/35	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.867830816902042	2		420	428	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44919321	44919321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	113	212	0	ENST00000377967.4:c.1249C>T	p.Pro417Ser	p.P417S	ENST00000377967	NM_021140.2	417	Cct/Tct	13/29	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.867830816902042	1		212	127	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0039171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	414	482	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.570986986046271	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.570986986046271	1		482	1000	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781306	9781306	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs754072203	NA	P-0039171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	316	649	0	ENST00000377346.4:c.1811C>T	p.Thr604Met	p.T604M	ENST00000377346	NM_005026.3	604	aCg/aTg	14/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.570986986046271	2		649	1069	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803824	43803824	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs145714475	NA	P-0039171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	295	681	0	ENST00000372470.3:c.134T>C	p.Phe45Ser	p.F45S	ENST00000372470	NM_005373.2	45	tTt/tCt	2/12	1	2	FACETS	0.933	0.879	0.989	0.933	0.879	0.989	CLONAL	1	TRUE	1	0.570986986046271	2		681	1107	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111048	193111048	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	60	216	0	ENST00000367435.3:c.581G>C	p.Arg194Thr	p.R194T	ENST00000367435	NM_024529.4	194	aGa/aCa	7/17	1	2	FACETS	0.725	0.629	0.826	0.725	0.629	0.826	SUBCLONAL	1	TRUE	1	0.570986986046271	2		216	290	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953727	48953755	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAGCGATACAAACTTGGAGTTCGCTTGTA	TAGCGATACAAACTTGGAGTTCGCTTGTA	-	novel	NA	P-0039171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	33	168	0	ENST00000267163.4:c.1333-2_1359del		p.X445_splice	ENST00000267163	NM_000321.2	445		14/27	0.559716084566547	2	FACETS	0.608	0.5	0.728	0.304	0.25	0.364	SUBCLONAL	1	TRUE	0	0.570986986046271	2		168	190	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17129491	17129491	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	310	583	0	ENST00000285071.4:c.395A>C	p.Glu132Ala	p.E132A	ENST00000285071	NM_144997.5	132	gAg/gCg	5/14	0.570986986046271	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.570986986046271	1		583	733	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144595	55144595	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	198	356	0	ENST00000257290.5:c.2069G>C	p.Arg690Thr	p.R690T	ENST00000257290	NM_006206.4	690	aGg/aCg	15/23	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.570986986046271	2		356	649	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981475	70981475	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	411	891	0	ENST00000276594.2:c.621C>A	p.Tyr207Ter	p.Y207*	ENST00000276594	NM_024504.3	207	taC/taA	2/8	1	2	FACETS	0.995	0.946	1	0.995	0.946	1	CLONAL	1	TRUE	1	0.570986986046271	2		891	1447	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44919378	44919378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	191	335	0	ENST00000377967.4:c.1306G>A	p.Gly436Ser	p.G436S	ENST00000377967	NM_021140.2	436	Ggt/Agt	13/29	1	2	FACETS	0.963	0.893	1	0.963	0.893	1	CLONAL	1	TRUE	1	0.570986986046271	2		335	695	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039350-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	236	82	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		82	612	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0039359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	351	502	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.339781893043364	5	FACETS	1	0.991	1	0.788	0.747	0.828	CLONAL	2	TRUE	2	0.526434173928824	5		502	1010	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1064795203	NA	P-0039359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	225	706	0	ENST00000269305.4:c.532C>G	p.His178Asp	p.H178D	ENST00000269305	NM_001126112.2	178	Cac/Gac	5/11	0.526434173928824	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.526434173928824	1		706	611	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647438	3647438	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1377493011	NA	P-0039359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1181	149	814	0	ENST00000294008.3:c.1625T>C	p.Met542Thr	p.M542T	ENST00000294008	NM_032444.2	542	aTg/aCg	7/15	0.526434173928824	3	FACETS	0.538	0.49	0.588	0.269	0.245	0.294	SUBCLONAL	1	TRUE	1	0.526434173928824	3		814	1330	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224483	39224484	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	163	659	0	ENST00000402219.2:c.2874dup	p.Ser959Ter	p.S959*	ENST00000402219	NM_005633.3	958	-/T	18/23	0.287770870065016	3	FACETS	0.873	0.801	0.948	0.291	0.267	0.316	INDETERMINATE	1	TRUE	0	0.526434173928824	3		659	896	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285189	198285189	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	84	525	0	ENST00000335508.6:c.378G>A	p.Met126Ile	p.M126I	ENST00000335508	NM_012433.2	126	atG/atA	4/25	0.371543861052771	1	FACETS	0.376	0.332	0.423	0.376	0.332	0.423	SUBCLONAL	1	TRUE	0	0.526434173928824	1		525	626	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	124	82	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.68	0.616	0.746	0.68	0.616	0.746	SUBCLONAL	1	TRUE	1	0.586719009314646	2		82	622	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0039371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	160	390	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.586719009314646	2		390	479	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589573	67589587	+	inframe_deletion	In_Frame_Del	DEL	GGGAAAAAATTACAT	GGGAAAAAATTACAT	-	novel	NA	P-0039371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	99	257	0	ENST00000274335.5:c.1337_1351del	p.Gly446_His450del	p.G446_H450del	ENST00000274335		446	GGGAAAAAATTACAT/-	10/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.586719009314646	2		257	305	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	254	82	0				ENST00000310581	NM_198253.2	-/1132			0.336780166133605	5	FACETS	1	0.978	1	0.725	0.68	0.772	CLONAL	2	TRUE	2	0.438205634069095	5		82	883	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0039386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	634	825	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.306005449085539	6	FACETS	0.939	0.905	0.972	0.939	0.905	0.972	CLONAL	4	TRUE	2	0.438205634069095	6		825	1446	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0039386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	172	338	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.323983608759105	4	FACETS	0.798	0.737	0.862	0.798	0.737	0.862	SUBCLONAL	2	TRUE	2	0.438205634069095	4		338	707	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0039386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	319	660	0	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	0.306005449085539	6	FACETS	1	0.963	1	0.514	0.484	0.544	CLONAL	2	TRUE	2	0.438205634069095	6		660	1329	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106593	27106593	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	334	714	0	ENST00000324856.7:c.6207del	p.Gln2070SerfsTer65	p.Q2070Sfs*65	ENST00000324856	NM_006015.4	2068	tcG/tc	20/20	0.438205634069095	3	FACETS	0.884	0.837	0.932	0.884	0.837	0.932	CLONAL	2	TRUE	1	0.438205634069095	3		714	1051	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578223	7578223	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	639	684	0	ENST00000269305.4:c.626G>C	p.Arg209Thr	p.R209T	ENST00000269305	NM_001126112.2	209	aGa/aCa	6/11	0.306005449085539	6	FACETS	0.925	0.892	0.958	0.925	0.892	0.958	CLONAL	4	TRUE	2	0.438205634069095	6		684	1479	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120611957	120611957	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	27	65	0	ENST00000256646.2:c.64C>A	p.Pro22Thr	p.P22T	ENST00000256646	NM_024408.3	22	Ccc/Acc	1/34	0.438205634069095	2	FACETS	1	0.899	1	0.587	0.477	0.706	CLONAL	1	TRUE	0	0.438205634069095	2		65	105	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366466	118366466	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0039386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	276	516	0	ENST00000534358.1:c.5415T>A	p.Tyr1805Ter	p.Y1805*	ENST00000534358	NM_005933.3	1805	taT/taA	19/36	0.428661316297197	4	FACETS	0.981	0.923	1	0.981	0.923	1	CLONAL	2	TRUE	2	0.438205634069095	4		516	923	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	656	790	0	ENST00000269305.4:c.880G>C	p.Glu294Gln	p.E294Q	ENST00000269305	NM_001126112.2	294	Gag/Cag	8/11	0.306005449085539	6	FACETS	0.905	0.873	0.937	0.905	0.873	0.937	CLONAL	4	TRUE	2	0.438205634069095	6		790	1552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577599	7577599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	432	543	1	ENST00000269305.4:c.682G>A	p.Asp228Asn	p.D228N	ENST00000269305	NM_001126112.2	228	Gac/Aac	7/11	0.306005449085539	6	FACETS	1	0.991	1	0.846	0.809	0.884	CLONAL	3	TRUE	2	0.438205634069095	6		544	1093	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8111088	8111089	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAAGTG	novel	NA	P-0039386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1364	115	727	0	ENST00000585124.1:c.113_118dup	p.Ala38_Leu39dup	p.A38_L39dup	ENST00000585124	NM_004217.3	38	gtc/gCACTTGtc	3/9	0.306005449085539	6	FACETS	0.666	0.597	0.739	0.166	0.149	0.185	SUBCLONAL	1	TRUE	2	0.438205634069095	6		727	1479	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873460	45873460	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	325	640	4	ENST00000391945.4:c.36C>A	p.Phe12Leu	p.F12L	ENST00000391945	NM_000400.3	12	ttC/ttA	2/23	0.438205634069095	3	FACETS	0.913	0.864	0.963	0.913	0.864	0.963	CLONAL	2	TRUE	1	0.438205634069095	3		644	990	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170872	99170872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	348	709	2	ENST00000074304.5:c.1501G>A	p.Asp501Asn	p.D501N	ENST00000074304	NM_001134224.1	501	Gac/Aac	16/26	NA	2	FACETS	0.956	0.909	1			1	INDETERMINATE	2	TRUE	NA	0.438205634069095	2		711	831	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946315	55946315	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	93	260	1	ENST00000263923.4:c.3864C>A	p.Ser1288Arg	p.S1288R	ENST00000263923	NM_002253.2	1288	agC/agA	30/30	0.438205634069095	3	FACETS	1	0.975	1	0.66	0.591	0.733	CLONAL	1	TRUE	1	0.438205634069095	3		261	392	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168942	32168942	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2111	166	770	1	ENST00000375023.3:c.4091C>G	p.Ala1364Gly	p.A1364G	ENST00000375023	NM_004557.3	1364	gCc/gGc	22/30	0.438205634069095	8	FACETS	0.77	0.704	0.84	0.128	0.117	0.14	SUBCLONAL	1	TRUE	2	0.438205634069095	8		771	2277	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933111	39933111	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	506	375	0	ENST00000378444.4:c.1488C>G	p.Ile496Met	p.I496M	ENST00000378444	NM_001123385.1	496	atC/atG	4/15	0.438205634069095	2	FACETS	1	0.975	1			1	CLONAL	3	TRUE	NA	0.438205634069095	2		375	764	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972617	76972617	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	314	256	0	ENST00000373344.5:c.124C>G	p.Gln42Glu	p.Q42E	ENST00000373344	NM_000489.3	42	Caa/Gaa	2/35	0.438205634069095	2	FACETS	0.87	0.832	0.908			1	CLONAL	3	TRUE	NA	0.438205634069095	2		256	549	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	35	214	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.14	2		214	397	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226561	2226561	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	60	798	1	ENST00000326181.6:c.1999G>T	p.Val667Phe	p.V667F	ENST00000326181	NM_032271.2	667	Gtt/Ttt	21/21	1	2	FACETS	0.863	0.741	0.997	0.863	0.741	0.997	CLONAL	1	TRUE	1	0.14	2		799	993	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0039436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	249	754	6	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.90350524255219	4	FACETS	0.936	0.875	0.999	0.312	0.291	0.333	CLONAL	1	TRUE	1	0.903626170164278	4		760	1121	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578515	7578515	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1212996409	NA	P-0039436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	1131	789	0	ENST00000269305.4:c.415A>T	p.Lys139Ter	p.K139*	ENST00000269305	NM_001126112.2	139	Aag/Tag	5/11	0.90350524255219	4	FACETS	0.998	0.979	1	0.998	0.979	1	CLONAL	3	TRUE	1	0.903626170164278	4		789	1591	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445173	49445173	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs560581125	NA	P-0039436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	78	414	26	ENST00000301067.7:c.2293G>C	p.Ala765Pro	p.A765P	ENST00000301067	NM_003482.3	765	Gct/Cct	10/54	0.903626170164278	3	FACETS	1	0.977	1	0.452	0.406	0.498	CLONAL	1	TRUE	0	0.903626170164278	3		440	185	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670544	134670544	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	664	706	0	ENST00000398015.3:c.455G>T	p.Gly152Val	p.G152V	ENST00000398015	NM_004441.4	152	gGg/gTg	3/16	0.87518040112271	3	FACETS	0.991	0.962	1	0.991	0.962	1	CLONAL	2	TRUE	1	0.903626170164278	3		706	1077	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245521	153245521	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	183	381	0	ENST00000281708.4:c.1670G>T	p.Gly557Val	p.G557V	ENST00000281708	NM_033632.3	557	gGa/gTa	11/12	0.87518040112271	3	FACETS	1	0.975	1	0.553	0.514	0.593	CLONAL	1	TRUE	1	0.903626170164278	3		381	532	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610496	10610496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	951	670	1	ENST00000171111.5:c.214C>T	p.Leu72Phe	p.L72F	ENST00000171111	NM_203500.1	72	Ctc/Ttc	2/6	0.903626170164278	3	FACETS	1	0.998	1	1	0.998	1	CLONAL	3	TRUE	0	0.903626170164278	3		671	992	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920740	100920740	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	588	422	0	ENST00000325455.5:c.2408A>T	p.Gln803Leu	p.Q803L	ENST00000325455	NM_001202474.3	803	cAg/cTg	6/8	0.903626170164278	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.903626170164278	3		422	617	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993350	72993350	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	573	709	0	ENST00000268489.5:c.695G>T	p.Arg232Leu	p.R232L	ENST00000268489	NM_006885.3	232	cGc/cTc	2/10	0.771076210798163	4	FACETS	0.923	0.888	0.957			1	CLONAL	2	TRUE	NA	0.903626170164278	4		709	1308	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989627	15989627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	422	332	0	ENST00000268712.3:c.3146C>T	p.Pro1049Leu	p.P1049L	ENST00000268712	NM_006311.3	1049	cCa/cTa	23/46	0.90350524255219	4	FACETS	0.972	0.94	1	0.972	0.94	1	CLONAL	3	TRUE	1	0.903626170164278	4		332	610	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17120390	17120390	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	59	439	0	ENST00000285071.4:c.1169T>C	p.Val390Ala	p.V390A	ENST00000285071	NM_144997.5	390	gTa/gCa	10/14	0.90350524255219	4	FACETS	0.276	0.236	0.319	0.092	0.078	0.107	SUBCLONAL	1	TRUE	1	0.903626170164278	4		439	901	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222991	1222993	+	frameshift_variant	Frame_Shift_Del	DEL	CGG	CGG	TT	novel	NA	P-0039436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	529	572	1	ENST00000326873.7:c.928_930delinsTT	p.Arg310LeufsTer26	p.R310Lfs*26	ENST00000326873	NM_000455.4	310	CGG/TT	8/10	0.903626170164278	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.903626170164278	2		573	551	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210945	36210945	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	344	786	1	ENST00000222270.7:c.696G>T	p.Arg232Ser	p.R232S	ENST00000222270	NM_014727.1	232	agG/agT	3/37	0.771076210798163	4	FACETS	0.973	0.919	1			1	CLONAL	1	TRUE	NA	0.903626170164278	4		787	1490	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99154409	99154409	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	290	585	0	ENST00000074304.5:c.551C>A	p.Thr184Asn	p.T184N	ENST00000074304	NM_001134224.1	184	aCc/aAc	8/26	0.903626170164278	3	FACETS	1	0.973	1	0.525	0.495	0.556	CLONAL	1	TRUE	1	0.903626170164278	3		585	887	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127556	55127556	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	285	273	0	ENST00000257290.5:c.344G>T	p.Arg115Met	p.R115M	ENST00000257290	NM_006206.4	115	aGg/aTg	3/23	0.87518040112271	3	FACETS	0.952	0.909	0.995	0.952	0.909	0.995	CLONAL	2	TRUE	1	0.903626170164278	3		273	481	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153603	55153603	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	378	413	0	ENST00000257290.5:c.2569C>A	p.Leu857Met	p.L857M	ENST00000257290	NM_006206.4	857	Ctg/Atg	19/23	0.87518040112271	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.903626170164278	3		413	605	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981479	55981479	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	188	393	0	ENST00000263923.4:c.458C>G	p.Ser153Cys	p.S153C	ENST00000263923	NM_002253.2	153	tCc/tGc	4/30	0.87518040112271	3	FACETS	0.935	0.868	1	0.468	0.434	0.502	CLONAL	1	TRUE	1	0.903626170164278	3		393	646	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467692	66467692	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	291	311	0	ENST00000273854.3:c.577A>G	p.Met193Val	p.M193V	ENST00000273854	NM_004439.5	193	Atg/Gtg	3/18	0.87518040112271	3	FACETS	0.954	0.911	0.996	0.954	0.911	0.996	CLONAL	2	TRUE	1	0.903626170164278	3		311	490	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371837	116371853	+	frameshift_variant	Frame_Shift_Del	DEL	TAACATCTATATCCACC	TAACATCTATATCCACC	-	novel	NA	P-0039436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	184	431	0	ENST00000397752.3:c.1317_1333del	p.Leu439PhefsTer3	p.L439Ffs*3	ENST00000397752	NM_000245.2	439	tTAACATCTATATCCACC/t	3/21	0.87518040112271	3	FACETS	0.901	0.835	0.969	0.451	0.417	0.485	CLONAL	1	TRUE	1	0.903626170164278	3		431	656	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69039612	69039612	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0039436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	466	337	0	ENST00000288368.4:c.3725-1G>T		p.X1242_splice	ENST00000288368	NM_024870.2	1242			0.903626170164278	4	FACETS	1	0.996	1	1	0.996	1	CLONAL	4	TRUE	0	0.903626170164278	4		337	481	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741686	145741686	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1367	329	663	0	ENST00000428558.2:c.817G>C	p.Ala273Pro	p.A273P	ENST00000428558	NM_004260.3	273	Gca/Cca	5/22	0.903626170164278	5	FACETS	1	0.952	1			1	CLONAL	1	TRUE	NA	0.903626170164278	5		663	1696	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741693	145741693	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1361	328	690	0	ENST00000428558.2:c.810G>T	p.Glu270Asp	p.E270D	ENST00000428558	NM_004260.3	270	gaG/gaT	5/22	0.903626170164278	5	FACETS	1	0.952	1			1	CLONAL	1	TRUE	NA	0.903626170164278	5		690	1689	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70967581	70967596	+	frameshift_variant	Frame_Shift_Del	DEL	CGCATGTGTTTGTTTA	CGCATGTGTTTGTTTA	-	novel	NA	P-0039436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	89	535	0	ENST00000276594.2:c.1427_1442del	p.Leu476GlnfsTer85	p.L476Qfs*85	ENST00000276594	NM_024504.3	476	cTAAACAAACACATGCGa/ca	7/8	0.903626170164278	4	FACETS	0.381	0.337	0.429	0.095	0.084	0.108	SUBCLONAL	1	TRUE	0	0.903626170164278	4		535	983	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0039483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	85	476	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.237464158820861	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.237464158820861	1		476	585	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522458	157522458	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	62	681	0	ENST00000346085.5:c.4730C>G	p.Ser1577Cys	p.S1577C	ENST00000346085	NM_020732.3	1577	tCt/tGt	18/20	0.0642967023175582	4	FACETS	0.677	0.583	0.779	0.338	0.291	0.39	INDETERMINATE	1	TRUE	2	0.237464158820861	4		681	955	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0039544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1195	48	651	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	1	2	FACETS	0.515	0.433	0.606	0.515	0.433	0.606	SUBCLONAL	1	TRUE	1	0.15	2		651	1243	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374366	31374366	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757657111	NA	P-0039604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	287	641	0	ENST00000328111.2:c.365G>A	p.Arg122His	p.R122H	ENST00000328111	NM_006892.3	122	cGt/cAt	5/23	NA	2	FACETS	0.682	0.641	0.724			1	INDETERMINATE	1	TRUE	NA	0.771304554981569	2		641	1091	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0039604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	137	263	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.764864035035744	1	FACETS	0.913	0.852	0.973	0.913	0.852	0.973	CLONAL	1	TRUE	0	0.771304554981569	1		263	239	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575168	48575168	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0039604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	146	264	0	ENST00000342988.3:c.362T>G	p.Leu121Ter	p.L121*	ENST00000342988	NM_005359.5	121	tTa/tGa	3/12	0.771304554981569	1	FACETS	0.927	0.867	0.985	0.927	0.867	0.985	CLONAL	1	TRUE	0	0.771304554981569	1		264	251	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467978	50467978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	239	544	0	ENST00000331340.3:c.1213G>A	p.Glu405Lys	p.E405K	ENST00000331340	NM_006060.4	405	Gag/Aag	8/8	0.678207826343113	3	FACETS	0.878	0.82	0.938	0.439	0.41	0.469	CLONAL	1	TRUE	1	0.771304554981569	3		544	978	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222222	53222222	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782534108	NA	P-0039604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	181	959	0	ENST00000375401.3:c.4610C>T	p.Ser1537Leu	p.S1537L	ENST00000375401	NM_004187.3	1537	tCg/tTg	26/26	NA	2	FACETS	0.425	0.391	0.46			1	INDETERMINATE	1	TRUE	NA	0.771304554981569	2		959	1104	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0039729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	524	929	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.902935901048326	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.902935901048326	1		929	600	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0039729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	460	479	2	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.902935901048326	2		481	978	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984911	55984911	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	342	343	2	ENST00000263923.4:c.218G>T	p.Arg73Met	p.R73M	ENST00000263923	NM_002253.2	73	aGg/aTg	3/30	0.902935901048326	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.902935901048326	1		345	390	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266618	115266618	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	303	485	1	ENST00000438362.2:c.1897G>T	p.Gly633Cys	p.G633C	ENST00000438362	NM_001242891.1	633	Ggc/Tgc	16/20	0.483258758600831	1	FACETS	0.682	0.651	0.713	0.682	0.651	0.713	INDETERMINATE	1	TRUE	0	0.902935901048326	1		486	540	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944283	206944283	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	359	366	3	ENST00000423557.1:c.347T>C	p.Leu116Pro	p.L116P	ENST00000423557	NM_000572.2	116	cTg/cCg	3/5	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.902935901048326	2		369	775	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111886048	111886048	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	393	487	4	ENST00000341259.2:c.1670T>A	p.Met557Lys	p.M557K	ENST00000341259	NM_005475.2	557	aTg/aAg	8/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.902935901048326	2		491	854	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514682	103514682	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	246	286	0	ENST00000355739.4:c.1183C>G	p.Leu395Val	p.L395V	ENST00000355739	NM_000123.3	395	Ctt/Gtt	8/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.902935901048326	2		286	529	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89851263	89851263	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	365	408	1	ENST00000389301.3:c.1469A>T	p.Gln490Leu	p.Q490L	ENST00000389301	NM_000135.2	490	cAg/cTg	15/43	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.902935901048326	2		409	758	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985691	60985691	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	54	61	0	ENST00000333681.4:c.209C>G	p.Ser70Trp	p.S70W	ENST00000333681		70	tCg/tGg	2/3	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.902935901048326	2		61	101	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530084	212530084	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	159	218	3	ENST00000342788.4:c.1835G>T	p.Arg612Leu	p.R612L	ENST00000342788	NM_005235.2	612	cGg/cTg	15/28	1	2	FACETS	0.855	0.792	0.918	0.855	0.792	0.918	CLONAL	1	TRUE	1	0.902935901048326	2		221	412	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967236	134967236	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	402	543	3	ENST00000398015.3:c.2575G>T	p.Asp859Tyr	p.D859Y	ENST00000398015	NM_004441.4	859	Gac/Tac	14/16	1	2	FACETS	0.94	0.898	0.983	0.94	0.898	0.983	CLONAL	1	TRUE	1	0.902935901048326	2		546	947	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201844	66201844	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0039729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	186	306	0	ENST00000273854.3:c.2659-1G>C		p.X887_splice	ENST00000273854	NM_004439.5	887			0.902935901048326	1	FACETS	0.966	0.926	1	0.966	0.926	1	CLONAL	1	TRUE	0	0.902935901048326	1		306	234	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235444	235444	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs528628545	NA	P-0039729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	568	658	6	ENST00000264932.6:c.1250A>G	p.Tyr417Cys	p.Y417C	ENST00000264932	NM_004168.2	417	tAc/tGc	9/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.902935901048326	2		664	1206	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2966423	2966423	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	447	568	4	ENST00000396946.4:c.1757C>T	p.Thr586Ile	p.T586I	ENST00000396946	NM_032415.4	586	aCa/aTa	14/25	1	2	FACETS	0.949	0.909	0.99	0.949	0.909	0.99	CLONAL	1	TRUE	1	0.902935901048326	2		572	1043	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741403	145741403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766344677	NA	P-0039729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1272	350	857	2	ENST00000428558.2:c.1100G>A	p.Arg367Gln	p.R367Q	ENST00000428558	NM_004260.3	367	cGg/cAg	5/22	1	2	FACETS	0.478	0.451	0.505	0.478	0.451	0.505	SUBCLONAL	1	TRUE	1	0.902935901048326	2		859	1622	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391886	139391893	+	frameshift_variant	Frame_Shift_Del	DEL	TGTGCGAT	TGTGCGAT	-	novel	NA	P-0039729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	687	801	13	ENST00000277541.6:c.6298_6305del	p.Ile2100GlyfsTer165	p.I2100Gfs*165	ENST00000277541	NM_017617.3	2100	ATCGCACAg/g	34/34	1	2	FACETS	0.952	0.92	0.985	0.952	0.92	0.985	CLONAL	1	TRUE	1	0.902935901048326	2		814	1598	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321390	1321390	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	255	382	5	ENST00000400841.2:c.365C>A	p.Pro122Gln	p.P122Q	ENST00000400841		122	cCg/cAg	4/6	1	1	FACETS	0.474	0.446	0.502	0.474	0.446	0.502	SUBCLONAL	1	TRUE	0	0.902935901048326	1		387	654	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	65	459	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.164373085858178	2	FACETS	1	0.942	1	0.571	0.498	0.648	INDETERMINATE	1	TRUE	0	0.354816123337442	2		459	321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0039781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	91	617	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.348277648251581	1	FACETS	0.498	0.442	0.559	0.498	0.442	0.559	SUBCLONAL	1	TRUE	0	0.354816123337442	1		617	847	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044892	47044892	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	124	1013	1	ENST00000377604.3:c.2218G>T	p.Glu740Ter	p.E740*	ENST00000377604	NM_001204468.1	740	Gag/Tag	20/24	0.348277648251581	1	FACETS	0.585	0.528	0.645	0.585	0.528	0.645	SUBCLONAL	1	TRUE	0	0.354816123337442	1		1014	983	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177458	56177458	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs189290632	NA	P-0039781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	32	344	0	ENST00000399503.3:c.2431A>G	p.Met811Val	p.M811V	ENST00000399503	NM_005921.1	811	Atg/Gtg	14/20	1	2	FACETS	0.702	0.572	0.847	0.702	0.572	0.847	SUBCLONAL	1	TRUE	1	0.354816123337442	2		344	257	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306568	163306568	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	36	427	0	ENST00000271452.3:c.365G>C	p.Ser122Thr	p.S122T	ENST00000271452	NM_145697.2	122	aGt/aCt	6/14	1	2	FACETS	0.882	0.731	1	0.882	0.731	1	CLONAL	1	TRUE	1	0.354816123337442	2		427	230	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426991	49426991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1002386392	NA	P-0039781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	134	666	0	ENST00000301067.7:c.11497C>T	p.Arg3833Trp	p.R3833W	ENST00000301067	NM_003482.3	3833	Cgg/Tgg	39/54	0.164373085858178	2	FACETS	1	0.973	1	0.586	0.534	0.641	INDETERMINATE	1	TRUE	0	0.354816123337442	2		666	644	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602936	55602936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	28	384	0	ENST00000288135.5:c.2646G>A	p.Met882Ile	p.M882I	ENST00000288135	NM_000222.2	882	atG/atA	19/21	1	2	FACETS	0.327	0.26	0.403	0.327	0.26	0.403	SUBCLONAL	1	TRUE	1	0.354816123337442	2		384	483	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0039812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	87	460	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.239664025552292	2		460	708	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0039812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	84	321	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.239664025552292	2		321	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0039812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	171	638	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.239664025552292	1	FACETS	0.968	0.889	1	0.968	0.889	1	CLONAL	1	TRUE	0	0.239664025552292	1		638	1297	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187191	11187191	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	129	593	9	ENST00000361445.4:c.6227G>T	p.Arg2076Leu	p.R2076L	ENST00000361445	NM_004958.3	2076	cGa/cTa	45/58	0.193417980516536	3	FACETS	1	0.955	1	0.546	0.494	0.602	CLONAL	1	TRUE	1	0.239664025552292	3		602	1103	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604762	48604763	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	rs876660150	NA	P-0039812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	82	491	0	ENST00000342988.3:c.1585_1586dup	p.Leu529PhefsTer9	p.L529Ffs*9	ENST00000342988	NM_005359.5	528	-/TT	12/12	0.239664025552292	1	FACETS	0.841	0.741	0.948	0.841	0.741	0.948	CLONAL	1	TRUE	0	0.239664025552292	1		491	716	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134849	41134849	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1319703616	NA	P-0039812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	69	466	1	ENST00000379561.5:c.779A>G	p.Asn260Ser	p.N260S	ENST00000379561	NM_002015.3	260	aAc/aGc	2/3	1	2	FACETS	0.836	0.727	0.953	0.836	0.727	0.953	CLONAL	1	TRUE	1	0.239664025552292	2		467	689	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348200	348200	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1344	159	1027	1	ENST00000262320.3:c.1306C>T	p.His436Tyr	p.H436Y	ENST00000262320	NM_003502.3	436	Cac/Tac	6/11	1	2	FACETS	0.883	0.806	0.963	0.883	0.806	0.963	CLONAL	1	TRUE	1	0.239664025552292	2		1028	1503	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779764	3779765	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGAC	novel	NA	P-0039812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1181	116	990	1	ENST00000262367.5:c.5280_5283dup	p.Lys1762ValfsTer205	p.K1762Vfs*205	ENST00000262367	NM_004380.2	1761	-/GTCA	31/31	1	2	FACETS	0.746	0.67	0.827	0.746	0.67	0.827	SUBCLONAL	1	TRUE	1	0.239664025552292	2		991	1297	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602304	10602304	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	153	938	4	ENST00000171111.5:c.1274T>C	p.Ile425Thr	p.I425T	ENST00000171111	NM_203500.1	425	aTc/aCc	3/6	NA	2	FACETS	0.983	0.897	1			1	INDETERMINATE	1	TRUE	NA	0.239664025552292	2		942	1299	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806221	1806221	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	149	902	0	ENST00000260795.2:c.1240A>T	p.Ile414Phe	p.I414F	ENST00000260795		414	Atc/Ttc	8/17	1	2	FACETS	0.939	0.856	1	0.939	0.856	1	CLONAL	1	TRUE	1	0.239664025552292	2		902	1324	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	92	459	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.188857895146045	3	FACETS	0.933	0.836	1	0.933	0.836	1	INDETERMINATE	2	TRUE	1	0.317324490950317	3		459	360	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263850	133263850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	28	183	0	ENST00000320574.5:c.52G>A	p.Glu18Lys	p.E18K	ENST00000320574	NM_006231.2	18	Gag/Aag	1/49	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.317324490950317	NA		183	206	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345240	73345240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	54	286	0	ENST00000377767.4:c.1649C>T	p.Ser550Phe	p.S550F	ENST00000377767	NM_014953.3	550	tCc/tTc	12/21	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.317324490950317	2		286	306	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937175	39937175	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	88	552	0	ENST00000378444.4:c.8C>G	p.Ser3Ter	p.S3*	ENST00000378444	NM_001123385.1	3	tCa/tGa	2/15	1	2	FACETS	0.902	0.8	1	0.902	0.8	1	CLONAL	1	TRUE	1	0.317324490950317	2		552	615	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981761	101981761	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	138	399	0	ENST00000282441.5:c.182C>G	p.Ser61Trp	p.S61W	ENST00000282441	NM_001130145.2	61	tCg/tGg	1/9	0.188857895146045	3	FACETS	0.901	0.824	0.982	0.901	0.824	0.982	INDETERMINATE	2	TRUE	1	0.317324490950317	3		399	559	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056210	26056210	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	128	324	0	ENST00000343677.2:c.447G>C	p.Lys149Asn	p.K149N	ENST00000343677	NM_005319.3	149	aaG/aaC	1/1	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.317324490950317	2		324	569	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5225783	5225783	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1159864455	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	103	625	1	ENST00000357368.4:c.2449G>A	p.Asp817Asn	p.D817N	ENST00000357368	NM_002850.3	817	Gat/Aat	17/38	0.317324490950317	3	FACETS	0.804	0.718	0.895	0.402	0.359	0.448	CLONAL	1	TRUE	1	0.317324490950317	3		626	936	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183005	32183005	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	96	396	0	ENST00000375023.3:c.2019G>C	p.Gln673His	p.Q673H	ENST00000375023	NM_004557.3	673	caG/caC	12/30	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.317324490950317	2		396	417	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292580	15292580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867505691	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	105	661	2	ENST00000263388.2:c.2599G>A	p.Gly867Ser	p.G867S	ENST00000263388	NM_000435.2	867	Ggc/Agc	17/33	0.317324490950317	3	FACETS	0.855	0.765	0.95	0.427	0.382	0.475	CLONAL	1	TRUE	1	0.317324490950317	3		663	897	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913409	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	52	237	0	ENST00000349496.5:c.134C>G	p.Ser45Cys	p.S45C	ENST00000349496	NM_001904.3	45	tCt/tGt	3/15	1	2	FACETS	0.815	0.696	0.945	0.815	0.696	0.945	CLONAL	1	TRUE	1	0.317324490950317	2		237	402	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762430	41762430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781426924	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	39	523	0	ENST00000301178.4:c.2110C>T	p.Arg704Cys	p.R704C	ENST00000301178	NM_021913.4	704	Cgc/Tgc	18/20	0.188857895146045	3	FACETS	0.389	0.321	0.464	0.194	0.16	0.232	INDETERMINATE	1	TRUE	1	0.317324490950317	3		523	733	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946463	2946463	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs777458922	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	64	466	0	ENST00000396946.4:c.3274C>T	p.Arg1092Ter	p.R1092*	ENST00000396946	NM_032415.4	1092	Cga/Tga	25/25	1	2	FACETS	0.83	0.72	0.949	0.83	0.72	0.949	CLONAL	1	TRUE	1	0.317324490950317	2		466	486	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034491	47034491	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	70	529	0	ENST00000377604.3:c.576G>T	p.Gln192His	p.Q192H	ENST00000377604	NM_001204468.1	192	caG/caT	6/24	1	2	FACETS	0.726	0.633	0.826	0.726	0.633	0.826	SUBCLONAL	1	TRUE	1	0.317324490950317	2		529	608	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163315571	163315571	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	37	233	0	ENST00000271452.3:c.911C>G	p.Ser304Ter	p.S304*	ENST00000271452	NM_145697.2	304	tCa/tGa	11/14	0.308703657111848	3	FACETS	0.776	0.642	0.927	0.259	0.214	0.309	CLONAL	1	TRUE	0	0.317324490950317	3		233	348	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099508	157099508	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	72	218	0	ENST00000346085.5:c.445C>A	p.Gln149Lys	p.Q149K	ENST00000346085	NM_020732.3	149	Cag/Aag	1/20	0.253861053063542	2	FACETS	0.856	0.757	0.96	0.856	0.757	0.96	CLONAL	2	TRUE	0	0.317324490950317	2		218	265	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414268	32414268	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	100	336	0	ENST00000332351.3:c.1283G>C	p.Cys428Ser	p.C428S	ENST00000332351	NM_024426.4	428	tGt/tCt	8/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.317324490950317	2		336	539	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245268	133245268	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	94	577	0	ENST00000320574.5:c.1979G>C	p.Gly660Ala	p.G660A	ENST00000320574	NM_006231.2	660	gGa/gCa	18/49	1	2	FACETS	0.869	0.773	0.97	0.869	0.773	0.97	CLONAL	1	TRUE	1	0.317324490950317	2		577	682	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258672	16258672	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	65	424	0	ENST00000375759.3:c.5937G>C	p.Glu1979Asp	p.E1979D	ENST00000375759	NM_015001.2	1979	gaG/gaC	11/15	0.25342416366421	1	FACETS	0.735	0.639	0.839	0.735	0.639	0.839	SUBCLONAL	1	TRUE	0	0.317324490950317	1		424	469	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885815	23885815	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	67	445	0	ENST00000374561.5:c.103G>C	p.Glu35Gln	p.E35Q	ENST00000374561	NM_002167.4	35	Gag/Cag	1/3	0.25342416366421	1	FACETS	0.727	0.633	0.828	0.727	0.633	0.828	SUBCLONAL	1	TRUE	0	0.317324490950317	1		445	489	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458246	120458246	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	96	532	0	ENST00000256646.2:c.7099C>G	p.Gln2367Glu	p.Q2367E	ENST00000256646	NM_024408.3	2367	Cag/Gag	34/34	0.25342416366421	1	FACETS	0.936	0.836	1	0.936	0.836	1	CLONAL	1	TRUE	0	0.317324490950317	1		532	544	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458732	120458732	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	82	422	0	ENST00000256646.2:c.6613C>G	p.His2205Asp	p.H2205D	ENST00000256646	NM_024408.3	2205	Cat/Gat	34/34	0.25342416366421	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.317324490950317	1		422	404	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459131	120459131	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	88	505	0	ENST00000256646.2:c.6214C>G	p.Pro2072Ala	p.P2072A	ENST00000256646	NM_024408.3	2072	Cca/Gca	34/34	0.25342416366421	1	FACETS	0.799	0.709	0.895	0.799	0.709	0.895	SUBCLONAL	1	TRUE	0	0.317324490950317	1		505	584	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944390	206944390	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	46	307	0	ENST00000423557.1:c.240C>G	p.Cys80Trp	p.C80W	ENST00000423557	NM_000572.2	80	tgC/tgG	3/5	0.308703657111848	3	FACETS	0.631	0.531	0.742	0.21	0.177	0.248	SUBCLONAL	1	TRUE	0	0.317324490950317	3		307	532	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724749	112724749	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1050720476	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	75	290	0	ENST00000369452.4:c.633C>G	p.Ile211Met	p.I211M	ENST00000369452	NM_007373.3	211	atC/atG	2/9	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.317324490950317	2		290	443	SUCCESS
ATM	472	MSKCC	GRCh37	11	108159769	108159769	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	40	248	0	ENST00000278616.4:c.4175A>T	p.Tyr1392Phe	p.Y1392F	ENST00000278616	NM_000051.3	1392	tAt/tTt	28/63	0.188857895146045	3	FACETS	0.872	0.727	1	0.436	0.363	0.516	INDETERMINATE	1	TRUE	1	0.317324490950317	3		248	335	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69229743	69229743	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	31	210	0	ENST00000462284.1:c.819A>T	p.Glu273Asp	p.E273D	ENST00000462284	NM_002392.5	273	gaA/gaT	9/11	1	2	FACETS	0.656	0.532	0.795	0.656	0.532	0.795	SUBCLONAL	1	TRUE	1	0.317324490950317	2		210	298	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063327	67063327	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	27	211	0	ENST00000412916.2:c.17C>T	p.Pro6Leu	p.P6L	ENST00000412916		6	cCc/cTc	1/6	1	2	FACETS	0.579	0.461	0.712	0.579	0.461	0.712	SUBCLONAL	1	TRUE	1	0.317324490950317	2		211	294	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17117021	17117021	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	113	480	0	ENST00000285071.4:c.1688C>G	p.Ser563Ter	p.S563*	ENST00000285071	NM_144997.5	563	tCa/tGa	14/14	0.317324490950317	1	FACETS	0.981	0.885	1	0.981	0.885	1	CLONAL	1	TRUE	0	0.317324490950317	1		480	611	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665721	29665721	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	35	174	0	ENST00000356175.3:c.6757-1G>T		p.X2253_splice	ENST00000356175	NM_000267.3	2253			0.188857895146045	3	FACETS	1	0.931	1	0.636	0.526	0.757	INDETERMINATE	1	TRUE	1	0.317324490950317	3		174	201	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618478	37618478	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	57	412	0	ENST00000447079.4:c.154G>C	p.Asp52His	p.D52H	ENST00000447079	NM_015083.1	52	Gac/Cac	1/14	0.188857895146045	3	FACETS	0.58	0.496	0.671	0.29	0.248	0.336	INDETERMINATE	1	TRUE	1	0.317324490950317	3		412	718	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271648	15271648	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	131	760	0	ENST00000263388.2:c.6791C>G	p.Ser2264Ter	p.S2264*	ENST00000263388	NM_000435.2	2264	tCa/tGa	33/33	0.317324490950317	3	FACETS	0.946	0.857	1	0.473	0.428	0.52	CLONAL	1	TRUE	1	0.317324490950317	3		760	1011	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272291	15272291	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	95	516	0	ENST00000263388.2:c.6148C>G	p.Leu2050Val	p.L2050V	ENST00000263388	NM_000435.2	2050	Ctc/Gtc	33/33	0.317324490950317	3	FACETS	0.927	0.826	1	0.464	0.413	0.518	CLONAL	1	TRUE	1	0.317324490950317	3		516	748	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462623	29462623	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	55	587	0	ENST00000389048.3:c.2278C>A	p.Leu760Met	p.L760M	ENST00000389048	NM_004304.4	760	Ctg/Atg	13/29	1	2	FACETS	0.453	0.386	0.526	0.453	0.386	0.526	SUBCLONAL	1	TRUE	1	0.317324490950317	2		587	766	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736158	204736159	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	33	256	0	ENST00000302823.3:c.519dup	p.Leu174ValfsTer5	p.L174Vfs*5	ENST00000302823	NM_005214.4	172	tcg/tcGg	3/4	1	2	FACETS	0.501	0.408	0.606	0.501	0.408	0.606	SUBCLONAL	1	TRUE	1	0.317324490950317	2		256	415	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546612	9546612	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	70	365	0	ENST00000353224.5:c.1410C>A	p.His470Gln	p.H470Q	ENST00000353224	NM_177990.2	470	caC/caA	5/10	1	2	FACETS	0.802	0.7	0.912	0.802	0.7	0.912	CLONAL	1	TRUE	1	0.317324490950317	2		365	550	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164031	47164031	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	18	219	0	ENST00000409792.3:c.2095G>C	p.Asp699His	p.D699H	ENST00000409792	NM_014159.6	699	Gat/Cat	3/21	1	2	FACETS	0.373	0.281	0.483	0.373	0.281	0.483	SUBCLONAL	1	TRUE	1	0.317324490950317	2		219	304	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169991111	169991111	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	72	259	0	ENST00000295797.4:c.629C>G	p.Ser210Cys	p.S210C	ENST00000295797	NM_002740.5	210	tCt/tGt	7/18	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.317324490950317	2		259	412	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152036	55152036	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	56	384	1	ENST00000257290.5:c.2468A>G	p.Asn823Ser	p.N823S	ENST00000257290	NM_006206.4	823	aAc/aGc	18/23	1	2	FACETS	0.757	0.65	0.874	0.757	0.65	0.874	SUBCLONAL	1	TRUE	1	0.317324490950317	2		385	466	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249534	153249534	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	62	312	0	ENST00000281708.4:c.1244G>C	p.Arg415Thr	p.R415T	ENST00000281708	NM_033632.3	415	aGa/aCa	9/12	1	2	FACETS	0.898	0.778	1	0.898	0.778	1	CLONAL	1	TRUE	1	0.317324490950317	2		312	435	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026415	6026415	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs778531080	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	48	237	0	ENST00000265849.7:c.1981G>T	p.Glu661Ter	p.E661*	ENST00000265849	NM_000535.5	661	Gaa/Taa	11/15	0.317324490950317	3	FACETS	0.94	0.797	1	0.47	0.398	0.548	CLONAL	1	TRUE	1	0.317324490950317	3		237	373	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92247433	92247433	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	85	239	0	ENST00000265734.4:c.787G>C	p.Glu263Gln	p.E263Q	ENST00000265734	NM_001259.6	263	Gag/Cag	7/8	0.317324490950317	3	FACETS	0.757	0.673	0.846	0.757	0.673	0.846	SUBCLONAL	2	TRUE	1	0.317324490950317	3		239	410	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346058	152346058	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	149	423	0	ENST00000359321.1:c.512C>G	p.Ser171Cys	p.S171C	ENST00000359321	NM_005431.1	171	tCt/tGt	3/3	0.317324490950317	3	FACETS	0.93	0.854	1	0.93	0.854	1	CLONAL	2	TRUE	1	0.317324490950317	3		423	585	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285513	38285513	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	76	479	0	ENST00000425967.3:c.640A>T	p.Thr214Ser	p.T214S	ENST00000425967	NM_001174067.1	214	Acc/Tcc	6/19	0.188857895146045	3	FACETS	0.867	0.761	0.982	0.434	0.38	0.491	INDETERMINATE	1	TRUE	1	0.317324490950317	3		479	640	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139565442	139565442	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	108	560	0	ENST00000308874.7:c.612G>C	p.Gln204His	p.Q204H	ENST00000308874		204	caG/caC	8/10	1	2	FACETS	0.961	0.864	1	0.961	0.864	1	CLONAL	1	TRUE	1	0.317324490950317	2		560	708	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1331512	1331512	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	96	378	0	ENST00000400841.2:c.16C>G	p.Leu6Val	p.L6V	ENST00000400841		6	Ctg/Gtg	1/6	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.317324490950317	2		378	602	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916546	39916546	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	58	503	0	ENST00000378444.4:c.4457A>G	p.Lys1486Arg	p.K1486R	ENST00000378444	NM_001123385.1	1486	aAg/aGg	11/15	1	2	FACETS	0.563	0.483	0.651	0.563	0.483	0.651	SUBCLONAL	1	TRUE	1	0.317324490950317	2		503	649	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361799	70361799	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	108	540	1	ENST00000374080.3:c.6475C>T	p.Gln2159Ter	p.Q2159*	ENST00000374080		2159	Caa/Taa	44/45	1	2	FACETS	0.994	0.893	1	0.994	0.893	1	CLONAL	1	TRUE	1	0.317324490950317	2		541	685	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615638	100615638	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	76	419	0	ENST00000308731.7:c.694G>T	p.Asp232Tyr	p.D232Y	ENST00000308731	NM_000061.2	232	Gat/Tat	8/19	0.12288681362727	3	FACETS	0.916	0.804	1	0.305	0.268	0.346	INDETERMINATE	1	TRUE	0	0.317324490950317	3		419	606	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0039904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	75	414	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.878	0.771	0.992	0.878	0.771	0.992	CLONAL	1	TRUE	1	0.32869129281111	2		414	520	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105642	11105642	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	47	426	0	ENST00000358026.2:c.1558G>T	p.Glu520Ter	p.E520*	ENST00000358026	NM_001128849.1	520	Gag/Tag	9/36	0.32869129281111	1	FACETS	0.321	0.27	0.378	0.321	0.27	0.378	SUBCLONAL	1	TRUE	0	0.32869129281111	1		426	744	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610035	43610035	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	191	532	0	ENST00000355710.3:c.1987T>C	p.Phe663Leu	p.F663L	ENST00000355710	NM_020975.4	663	Ttt/Ctt	11/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.32869129281111	2		532	1070	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671594	67671594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	72	204	0	ENST00000264010.4:c.2003C>T	p.Thr668Ile	p.T668I	ENST00000264010	NM_006565.3	668	aCa/aTa	12/12	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.32869129281111	2		204	417	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244808	41244808	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs80357419	NA	P-0039904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	134	400	0	ENST00000357654.3:c.2740G>T	p.Glu914Ter	p.E914*	ENST00000357654	NM_007294.3	914	Gag/Tag	10/23	1	2	FACETS	0.962	0.874	1	0.962	0.874	1	CLONAL	1	TRUE	1	0.32869129281111	2		400	848	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770057	56770057	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	106	420	0	ENST00000337432.4:c.53C>A	p.Pro18Gln	p.P18Q	ENST00000337432	NM_058216.2	18	cCg/cAg	1/9	1	2	FACETS	0.942	0.845	1	0.942	0.845	1	CLONAL	1	TRUE	1	0.32869129281111	2		420	685	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220691	1220691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	157	593	0	ENST00000326873.7:c.709G>A	p.Asp237Asn	p.D237N	ENST00000326873	NM_000455.4	237	Gac/Aac	5/10	0.32869129281111	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.32869129281111	1		593	790	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610109	10610109	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	159	492	0	ENST00000171111.5:c.601C>T	p.Gln201Ter	p.Q201*	ENST00000171111	NM_203500.1	201	Cag/Tag	2/6	0.32869129281111	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.32869129281111	1		492	762	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0039937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	8	640	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.174	0.111	0.256	0.174	0.111	0.256	SUBCLONAL	1	TRUE	1	0.24	2		640	383	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330610	65330611	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TTTTTTCCGCTTCAGTTTAT	novel	NA	P-0039937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	55	405	0	ENST00000342505.4:c.1016_1035dup	p.Leu346IlefsTer3	p.L346Ifs*3	ENST00000342505	NM_002227.2	345	-/ATAAACTGAAGCGGAAAAAA	8/25	1	2	FACETS	0.811	0.694	0.94	0.811	0.694	0.94	CLONAL	1	TRUE	1	0.24	2		405	565	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32921033	32921033	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs28897743	NA	P-0039937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	49	388	0	ENST00000380152.3:c.7007G>A	p.Arg2336His	p.R2336H	ENST00000380152		2336	cGc/cAc	13/27	1	2	FACETS	0.986	0.837	1	0.986	0.837	1	CLONAL	1	TRUE	1	0.24	2		388	414	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853251	68853251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780115	NA	P-0039937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	83	629	0	ENST00000261769.5:c.1634G>A	p.Arg545Gln	p.R545Q	ENST00000261769	NM_004360.3	545	cGg/cAg	11/16	0.231248852624773	2	FACETS	1	0.937	1	0.546	0.482	0.615	CLONAL	1	TRUE	0	0.24	2		629	633	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0039937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	201	651	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.20822621777117	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.24	2		651	797	SUCCESS
APC	324	MSKCC	GRCh37	5	112174004	112174004	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	41	262	0	ENST00000257430.4:c.2713A>C	p.Ser905Arg	p.S905R	ENST00000257430	NM_000038.5	905	Agt/Cgt	16/16	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.24	2		262	326	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509111	106509111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	68	809	0	ENST00000359195.3:c.1105G>A	p.Asp369Asn	p.D369N	ENST00000359195	NM_002649.2	369	Gat/Aat	2/11	0.340467068095354	3	FACETS	0.511	0.443	0.584	0.17	0.147	0.195	SUBCLONAL	1	TRUE	0	0.378143632086949	3		809	837	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923133	39923133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	122	822	0	ENST00000378444.4:c.3575C>T	p.Thr1192Ile	p.T1192I	ENST00000378444	NM_001123385.1	1192	aCc/aTc	8/15	NA	2	FACETS	0.949	0.859	1			1	INDETERMINATE	1	TRUE	NA	0.378143632086949	2		822	680	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606899	43606909	+	frameshift_variant	Frame_Shift_Del	DEL	CAGTGGAGGGG	CAGTGGAGGGG	-	novel	NA	P-0039941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	293	1049	0	ENST00000355710.3:c.1508_1518del	p.Thr503IlefsTer23	p.T503Ifs*23	ENST00000355710	NM_020975.4	503	aCAGTGGAGGGG/a	7/20	0.378143632086949	3	FACETS	0.884	0.833	0.937	0.884	0.833	0.937	CLONAL	2	TRUE	1	0.378143632086949	3		1049	1042	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578303	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TAAGAGCAATCAG	TAAGAGCAATCAG	-	novel	NA	P-0039941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	258	746	0	ENST00000269305.4:c.560-14_560-2del		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.37533892363131	2	FACETS	0.996	0.938	1	0.996	0.938	1	CLONAL	2	TRUE	0	0.378143632086949	2		746	685	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78519485	78519485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	121	597	0	ENST00000306801.3:c.56C>T	p.Ala19Val	p.A19V	ENST00000306801	NM_020761.2	19	gCt/gTt	1/34	0.378143632086949	3	FACETS	0.924	0.834	1	0.462	0.417	0.509	CLONAL	1	TRUE	1	0.378143632086949	3		597	824	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105585	11105586	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0039941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	200	844	0	ENST00000358026.2:c.1503dup	p.Lys502GlnfsTer32	p.K502Qfs*32	ENST00000358026	NM_001128849.1	501	acc/aCcc	9/36	0.298819644892751	2	FACETS	1	0.99	1	0.702	0.653	0.754	CLONAL	1	TRUE	0	0.378143632086949	2		844	753	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332847	152332847	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	49	562	0	ENST00000206249.3:c.1153G>T	p.Glu385Ter	p.E385*	ENST00000206249	NM_000125.3	385	Gag/Tag	5/8	1	2	FACETS	0.415	0.351	0.486	0.415	0.351	0.486	SUBCLONAL	1	TRUE	1	0.378143632086949	2		562	624	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0039979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	20	466	0	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	1	2	FACETS	0.261	0.199	0.334	0.261	0.199	0.334	SUBCLONAL	1	TRUE	1	0.424602179290314	2		466	361	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874263	155874263	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1557960039	NA	P-0039979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	55	577	0	ENST00000368323.3:c.268A>G	p.Met90Val	p.M90V	ENST00000368323	NM_006912.5	90	Atg/Gtg	5/6	1	2	FACETS	0.852	0.734	0.98	0.852	0.734	0.98	CLONAL	1	TRUE	1	0.424602179290314	2		577	304	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952085	+	missense_variant	Missense_Mutation	DNP	CA	CA	AT	novel	NA	P-0039979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	11	365	0	ENST00000263967.3:c.3139_3140delinsAT	p.His1047Ile	p.H1047I	ENST00000263967	NM_006218.2	1047	CAt/ATt	21/21	1	2	FACETS	0.179	0.123	0.249	0.179	0.123	0.249	SUBCLONAL	1	TRUE	1	0.424602179290314	2		365	289	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560133	29560133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199474732	NA	P-0039979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	66	345	0	ENST00000356175.3:c.3610C>T	p.Arg1204Trp	p.R1204W	ENST00000356175	NM_000267.3	1204	Cgg/Tgg	27/57	0.423389806401654	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.424602179290314	1		345	217	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592314	29592314	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	86	482	0	ENST00000356175.3:c.4729del	p.Thr1577LeufsTer26	p.T1577Lfs*26	ENST00000356175	NM_000267.3	1577	Act/ct	35/57	0.423389806401654	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.424602179290314	1		482	243	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775173	73775173	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	89	595	0	ENST00000254810.4:c.83A>T	p.Lys28Ile	p.K28I	ENST00000254810	NM_005324.3	28	aAa/aTa	2/4	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.424602179290314	2		595	348	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404224	139404224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759897410	NA	P-0039979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	115	694	0	ENST00000277541.6:c.2930G>A	p.Gly977Glu	p.G977E	ENST00000277541	NM_017617.3	977	gGg/gAg	18/34	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.424602179290314	2		694	444	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0039979-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	59	466	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		466	248	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0040059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	891	430	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.360811780307847	8	FACETS	1	0.984	1	1	0.984	1	CLONAL	7	FALSE	1	0.360811780307847	8		430	1451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0040059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	24	702	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.360811780307847	1	FACETS	0.213	0.166	0.267	0.213	0.166	0.267	SUBCLONAL	1	FALSE	0	0.360811780307847	1		702	513	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115573	108115573	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0040059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	65	326	0	ENST00000278616.4:c.721A>T	p.Lys241Ter	p.K241*	ENST00000278616	NM_000051.3	241	Aag/Tag	7/63	1	2	FACETS	0.866	0.754	0.987	0.866	0.754	0.987	CLONAL	1	FALSE	1	0.360811780307847	2		326	416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0040060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	74	754	6	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.962	0.84	1	0.962	0.84	1	CLONAL	1	TRUE	1	0.18	2		760	855	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0040060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	103	696	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.137765728913148	3	FACETS	1	0.98	1	0.724	0.648	0.806	CLONAL	1	TRUE	1	0.18	3		696	861	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573136	64573136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767595183	NA	P-0040060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	34	443	0	ENST00000312049.6:c.1156G>A	p.Gly386Ser	p.G386S	ENST00000312049	NM_130799.2	386	Ggc/Agc	8/10	0.27678988120767	3	FACETS	0.61	0.497	0.738	0.305	0.248	0.369	SUBCLONAL	1	TRUE	1	0.18	3		443	675	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40379630	40379630	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	56	666	0	ENST00000293328.3:c.202C>G	p.Leu68Val	p.L68V	ENST00000293328	NM_012448.3	68	Ctg/Gtg	3/19	0.137765728913148	3	FACETS	0.698	0.596	0.811	0.349	0.298	0.406	SUBCLONAL	1	TRUE	1	0.18	3		666	971	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591921	48591921	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	53	416	0	ENST00000342988.3:c.1087del	p.Cys363ValfsTer21	p.C363Vfs*21	ENST00000342988	NM_005359.5	362	Ttt/tt	9/12	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.18	2		416	569	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199957	128199957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370164300	NA	P-0040063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	157	568	0	ENST00000341105.2:c.1348G>A	p.Gly450Arg	p.G450R	ENST00000341105	NM_032638.4	450	Gga/Aga	6/6	0.28975080670569	1	FACETS	0.86	0.787	0.937	0.86	0.787	0.937	CLONAL	1	TRUE	0	0.309238089167011	1		568	998	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211651	46211651	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	17	215	0	ENST00000334344.6:c.617A>T	p.Asn206Ile	p.N206I	ENST00000334344	NM_152641.2	206	aAt/aTt	5/21	0.244262985272664	3	FACETS	0.73	0.547	0.944	0.365	0.273	0.472	CLONAL	1	TRUE	1	0.309238089167011	3		215	174	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0040133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	121	414	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.238131206456224	2	FACETS	0.787	0.714	0.864	0.787	0.714	0.864	SUBCLONAL	2	TRUE	0	0.277070193901685	2		414	555	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602334	10602334	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	230	777	0	ENST00000171111.5:c.1244G>T	p.Arg415Leu	p.R415L	ENST00000171111	NM_203500.1	415	cGc/cTc	3/6	0.238131206456224	2	FACETS	0.769	0.716	0.823	0.769	0.716	0.823	SUBCLONAL	2	TRUE	0	0.277070193901685	2		777	1080	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207021	1207021	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913324	NA	P-0040133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	220	743	1	ENST00000326873.7:c.109C>T	p.Gln37Ter	p.Q37*	ENST00000326873	NM_000455.4	37	Cag/Tag	1/10	0.238131206456224	2	FACETS	1	0.991	1	0.748	0.695	0.802	CLONAL	1	TRUE	0	0.277070193901685	2		744	1062	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615093	43615093	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	260	728	0	ENST00000355710.3:c.2507G>T	p.Ser836Ile	p.S836I	ENST00000355710	NM_020975.4	836	aGc/aTc	14/20	0.27709071410352	3	FACETS	0.993	0.93	1	0.993	0.93	1	CLONAL	2	TRUE	1	0.277070193901685	3		728	1076	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202473	67202487	+	inframe_deletion	In_Frame_Del	DEL	TCCCCTTTTGAGGGG	TCCCCTTTTGAGGGG	-	novel	NA	P-0040133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	88	750	0	ENST00000312629.5:c.1283_1297del	p.Ser428_Gly432del	p.S428_G432del	ENST00000312629	NM_003952.2	428	TCCCCTTTTGAGGGG/-	15/15	0.226285648482795	3	FACETS	0.678	0.599	0.763	0.339	0.299	0.382	SUBCLONAL	1	TRUE	1	0.277070193901685	3		750	1066	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687172	37687172	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	252	607	0	ENST00000447079.4:c.4076G>T	p.Gly1359Val	p.G1359V	ENST00000447079	NM_015083.1	1359	gGt/gTt	14/14	0.229099429193757	4	FACETS	0.865	0.811	0.921	0.865	0.811	0.921	CLONAL	3	TRUE	1	0.277070193901685	4		607	895	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371574	225371575	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0040133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	35	376	0	ENST00000264414.4:c.1028_1029dup	p.Gly344ArgfsTer6	p.G344Rfs*6	ENST00000264414	NM_003590.4	343	-/AG		0.226285648482795	3	FACETS	0.625	0.512	0.752	0.313	0.256	0.376	SUBCLONAL	1	TRUE	1	0.277070193901685	3		376	460	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866542	56866542	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	123	682	0	ENST00000519728.1:c.789G>T	p.Met263Ile	p.M263I	ENST00000519728	NM_002350.3	263	atG/atT	8/13	0.226285648482795	3	FACETS	0.874	0.788	0.964	0.437	0.394	0.482	CLONAL	1	TRUE	1	0.277070193901685	3		682	1157	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939459	68939459	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	26	362	0	ENST00000288368.4:c.444C>A	p.Asn148Lys	p.N148K	ENST00000288368	NM_024870.2	148	aaC/aaA	5/40	0.142163247415632	4	FACETS	0.483	0.382	0.6	0.242	0.191	0.3	INDETERMINATE	1	TRUE	2	0.277070193901685	4		362	496	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169566	27169566	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	199	646	0	ENST00000380036.4:c.567C>A	p.Tyr189Ter	p.Y189*	ENST00000380036	NM_000459.3	189	taC/taA	4/23	0.239438907735292	2	FACETS	0.833	0.773	0.896	0.833	0.773	0.896	CLONAL	2	TRUE	0	0.277070193901685	2		646	862	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0040135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	227	367	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.439246247222402	4	FACETS	1	0.982	1	0.75	0.703	0.798	CLONAL	2	TRUE	1	0.462133949032712	4		367	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs864622237	NA	P-0040135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	163	605	0	ENST00000269305.4:c.700T>C	p.Tyr234His	p.Y234H	ENST00000269305	NM_001126112.2	234	Tac/Cac	7/11	0.462133949032712	1	FACETS	0.904	0.834	0.977	0.904	0.834	0.977	CLONAL	1	TRUE	0	0.462133949032712	1		605	600	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249022	55249022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567477136	NA	P-0040163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	110	543	0	ENST00000275493.2:c.2320G>A	p.Val774Met	p.V774M	ENST00000275493	NM_005228.3	774	Gtg/Atg	20/28	0.253365910303136	3	FACETS	0.86	0.78	0.944			1	CLONAL	3	TRUE	NA	0.253365910303136	3		543	379	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0040163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	110	628	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.253365910303136	3	FACETS	0.903	0.82	0.99			1	CLONAL	3	TRUE	NA	0.253365910303136	3		628	361	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263850	133263850	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	18	270	0	ENST00000320574.5:c.52G>C	p.Glu18Gln	p.E18Q	ENST00000320574	NM_006231.2	18	Gag/Cag	1/49	0.181442116031824	3	FACETS	0.785	0.593	1	0.392	0.296	0.505	CLONAL	1	TRUE	1	0.253365910303136	3		270	204	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563094	21563094	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	43	801	0	ENST00000382592.4:c.825C>G	p.Phe275Leu	p.F275L	ENST00000382592	NM_014572.2	275	ttC/ttG	4/8	0.19207542384478	2	FACETS	0.832	0.697	0.981	0.416	0.348	0.491	CLONAL	1	TRUE	0	0.253365910303136	2		801	408	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063657	67063657	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	44	349	0	ENST00000412916.2:c.106C>G	p.Pro36Ala	p.P36A	ENST00000412916		36	Ccc/Gcc	2/6	0.19833366478689	4	FACETS	0.777	0.656	0.91	0.777	0.656	0.91	CLONAL	2	TRUE	2	0.253365910303136	4		349	280	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	71	82	0				ENST00000310581	NM_198253.2	-/1132			0.496082996992385	1	FACETS	0.974	0.866	1	0.974	0.866	1	CLONAL	1	TRUE	0	0.530315212094717	1		82	202	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199469669	NA	P-0040185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	224	234	0	ENST00000374080.3:c.130G>T	p.Gly44Cys	p.G44C	ENST00000374080		44	Ggt/Tgt	2/45	0.51189580044219	2	FACETS	0.903	0.864	0.94			1	CLONAL	3	TRUE	NA	0.530315212094717	2		234	312	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412982	49412982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	328	507	0	ENST00000418115.1:c.41G>A	p.Gly14Glu	p.G14E	ENST00000418115	NM_001664.2	14	gGa/gAa	2/5	0.207473259808909	5	FACETS	0.906	0.86	0.952	0.906	0.86	0.952	INDETERMINATE	3	TRUE	2	0.530315212094717	5		507	817	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618622	37618622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	63	453	0	ENST00000447079.4:c.298C>T	p.Arg100Cys	p.R100C	ENST00000447079	NM_015083.1	100	Cgt/Tgt	1/14	1	2	FACETS	0.443	0.384	0.508	0.443	0.384	0.508	SUBCLONAL	1	TRUE	1	0.530315212094717	2		453	536	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281106	49281106	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	232	559	0	ENST00000282018.3:c.153G>A	p.Trp51Ter	p.W51*	ENST00000282018	NM_020377.2	51	tgG/tgA	1/1	0.207473259808909	5	FACETS	1	0.988	1	0.817	0.766	0.868	INDETERMINATE	2	TRUE	2	0.530315212094717	5		559	641	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244137	46244137	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	62	373	0	ENST00000334344.6:c.2231T>G	p.Val744Gly	p.V744G	ENST00000334344	NM_152641.2	744	gTt/gGt	15/21	0.300950247271168	3	FACETS	1	0.934	1	0.556	0.485	0.632	INDETERMINATE	1	TRUE	1	0.530315212094717	3		373	266	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919281	48919281	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs587778870	NA	P-0040185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	92	153	0	ENST00000267163.4:c.446C>G	p.Ser149Ter	p.S149*	ENST00000267163	NM_000321.2	149	tCa/tGa	4/27	0.207473259808909	5	FACETS	1	0.962	1	0.761	0.685	0.838	INDETERMINATE	2	TRUE	2	0.530315212094717	5		153	273	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983113	201983127	+	inframe_deletion	In_Frame_Del	DEL	ACAGCAACATGACCT	ACAGCAACATGACCT	-	novel	NA	P-0040185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	246	545	0	ENST00000359651.3:c.964_978del	p.Ser322_Tyr326del	p.S322_Y326del	ENST00000359651		321	aACAGCAACATGACCTac/aac	7/8	0.251218789075001	5	FACETS	0.941	0.881	1	0.627	0.587	0.668	INDETERMINATE	2	TRUE	2	0.530315212094717	5		545	885	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984406	201984407	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCAAGCGG	novel	NA	P-0040185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	404	521	0	ENST00000359651.3:c.1072_1079dup	p.Trp361GlnfsTer89	p.W361Qfs*89	ENST00000359651		357	-/TCAAGCGG	8/8	0.251218789075001	5	FACETS	0.889	0.848	0.93	0.889	0.848	0.93	INDETERMINATE	3	TRUE	2	0.530315212094717	5		521	1026	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435120	49435136	+	frameshift_variant	Frame_Shift_Del	DEL	GCTTCAGGAACCCGTCC	GCTTCAGGAACCCGTCC	-	novel	NA	P-0040185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	150	495	0	ENST00000301067.7:c.6417_6433del	p.Asp2140AlafsTer9	p.D2140Afs*9	ENST00000301067	NM_003482.3	2139	gcGGACGGGTTCCTGAAGCcg/gccg	31/54	0.300950247271168	3	FACETS	0.897	0.829	0.966	0.897	0.829	0.966	INDETERMINATE	2	TRUE	1	0.530315212094717	3		495	399	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939033	48939033	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1160807049	NA	P-0040185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	108	167	0	ENST00000267163.4:c.865A>T	p.Lys289Ter	p.K289*	ENST00000267163	NM_000321.2	289	Aaa/Taa	9/27	0.207473259808909	5	FACETS	1	0.972	1	0.786	0.715	0.86	INDETERMINATE	2	TRUE	2	0.530315212094717	5		167	310	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250833	99250860	+	frameshift_variant	Frame_Shift_Del	DEL	TGAAGCGCCTGGAGAACTGCACGGTGAT	TGAAGCGCCTGGAGAACTGCACGGTGAT	ATCAC	novel	NA	P-0040185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	132	428	1	ENST00000268035.6:c.137_164delinsATCAC	p.Leu46HisfsTer91	p.L46Hfs*91	ENST00000268035	NM_000875.3	46	cTGAAGCGCCTGGAGAACTGCACGGTGATc/cATCACc	2/21	0.251218789075001	5	FACETS	1	0.915	1	0.667	0.61	0.725	INDETERMINATE	2	TRUE	2	0.530315212094717	5		429	447	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81973562	81973562	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762731399	NA	P-0040185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	107	441	1	ENST00000359376.3:c.3379C>A	p.Pro1127Thr	p.P1127T	ENST00000359376	NM_002661.3	1127	Cca/Aca	30/33	0.311917036392139	3	FACETS	0.915	0.823	1	0.305	0.274	0.337	INDETERMINATE	1	TRUE	0	0.530315212094717	3		442	558	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129695	11129695	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	170	442	0	ENST00000358026.2:c.2501A>G	p.Tyr834Cys	p.Y834C	ENST00000358026	NM_001128849.1	834	tAc/tGc	17/36	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.530315212094717	2		442	489	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872207	45872207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	201	547	0	ENST00000391945.4:c.227C>T	p.Thr76Ile	p.T76I	ENST00000391945	NM_000400.3	76	aCt/aTt	4/23	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.530315212094717	2		547	560	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609664	46609664	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	168	563	0	ENST00000263734.3:c.2388G>C	p.Lys796Asn	p.K796N	ENST00000263734	NM_001430.4	796	aaG/aaC	15/16	0.162364735077784	2	FACETS	0.999	0.922	1	0.5	0.461	0.54	INDETERMINATE	1	TRUE	0	0.530315212094717	2		563	634	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46271023	46271023	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	188	381	0	ENST00000371998.3:c.3147C>G	p.Asp1049Glu	p.D1049E	ENST00000371998		1049	gaC/gaG	17/23	0.300950247271168	3	FACETS	1	0.99	1	0.734	0.682	0.788	INDETERMINATE	1	TRUE	1	0.530315212094717	3		381	611	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426844	6426845	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0040185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	26	345	0	ENST00000356142.4:c.37_38delinsTT	p.Ala13Phe	p.A13F	ENST00000356142	NM_018890.3	13	GCt/TTt	2/7	0.300950247271168	3	FACETS	0.243	0.192	0.302	0.122	0.096	0.151	INDETERMINATE	1	TRUE	1	0.530315212094717	3		345	510	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	360	459	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.923	0.877	0.969	1	0.996	1	CLONAL	2	TRUE	1	0.391682169393474	2		459	996	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100006	157100008	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	rs587779748	NA	P-0040197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	23	207	0	ENST00000346085.5:c.954_956del	p.Gly319del	p.G319del	ENST00000346085	NM_020732.3	315	GGA/-	1/20	1	2	FACETS	0.918	0.725	1	0.918	0.725	1	CLONAL	1	TRUE	1	0.391682169393474	2		207	128	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0040197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	261	461	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	0.834	0.784	0.885	1	0.994	1	CLONAL	2	TRUE	1	0.391682169393474	2		461	799	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860556	45860556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	444	1816	0	ENST00000391945.4:c.1451C>T	p.Thr484Met	p.T484M	ENST00000391945	NM_000400.3	484	aCg/aTg	15/23	1	2	FACETS	0.924	0.882	0.966	1	0.997	1	CLONAL	2	TRUE	1	0.391682169393474	2		1816	1227	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023903	27023904	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	54	231	0	ENST00000324856.7:c.1015dup	p.Ala339GlyfsTer61	p.A339Gfs*61	ENST00000324856	NM_006015.4	337	tgg/tGgg	1/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.391682169393474	2		231	191	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564540	86564560	+	inframe_deletion	In_Frame_Del	DEL	CTGCTGCTGGCGTAGCTGGTG	CTGCTGCTGGCGTAGCTGGTG	-	rs745572583	NA	P-0040197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	228	1425	0	ENST00000274376.6:c.285_305del	p.Ala100_Ala106del	p.A100_A106del	ENST00000274376	NM_002890.2	91	aCTGCTGCTGGCGTAGCTGGTGct/act	1/25	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.391682169393474	2		1425	903	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528097	29528097	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	228	783	3	ENST00000356175.3:c.1105C>T	p.Gln369Ter	p.Q369*	ENST00000356175	NM_000267.3	369	Cag/Tag	10/57	1	2	FACETS	0.931	0.874	0.99	1	0.994	1	CLONAL	2	TRUE	1	0.391682169393474	2		786	625	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426253	49426253	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	401	1857	0	ENST00000301067.7:c.12235C>T	p.Gln4079Ter	p.Q4079*	ENST00000301067	NM_003482.3	4079	Caa/Taa	39/54	1	2	FACETS	0.897	0.855	0.941	1	0.996	1	CLONAL	2	TRUE	1	0.391682169393474	2		1857	1141	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057642	27057642	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0040197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	297	1203	0	ENST00000324856.7:c.1351-1G>A		p.X451_splice	ENST00000324856	NM_006015.4	451			1	2	FACETS	0.924	0.873	0.975	1	0.995	1	CLONAL	2	TRUE	1	0.391682169393474	2		1203	821	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193202279	193202279	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	286	949	1	ENST00000367435.3:c.1311A>T	p.Gln437His	p.Q437H	ENST00000367435	NM_024529.4	437	caA/caT	14/17	1	2	FACETS	0.909	0.858	0.961	1	0.995	1	CLONAL	2	TRUE	1	0.391682169393474	2		950	803	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983026	201983026	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	505	1826	0	ENST00000359651.3:c.875T>G	p.Leu292Arg	p.L292R	ENST00000359651		292	cTc/cGc	7/8	1	2	FACETS	0.974	0.933	1	1	0.997	1	CLONAL	2	TRUE	1	0.391682169393474	2		1826	1324	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199851	108199854	+	frameshift_variant	Frame_Shift_Del	DEL	ACCA	ACCA	-	novel	NA	P-0040197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	166	682	0	ENST00000278616.4:c.7194_7197del	p.Tyr2398Ter	p.Y2398*	ENST00000278616	NM_000051.3	2398	tACCAa/ta	49/63	0.391682169393474	1	FACETS	0.791	0.734	0.848	1	0.991	1	SUBCLONAL	2	TRUE	0	0.391682169393474	1		682	431	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375398	118375398	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	266	885	0	ENST00000534358.1:c.8791C>T	p.Pro2931Ser	p.P2931S	ENST00000534358	NM_005933.3	2931	Cca/Tca	27/36	0.391682169393474	1	FACETS	0.916	0.867	0.966	1	0.995	1	CLONAL	2	TRUE	0	0.391682169393474	1		885	596	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988545	36988545	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	481	1713	0	ENST00000354822.5:c.108G>C	p.Lys36Asn	p.K36N	ENST00000354822	NM_001079668.2	36	aaG/aaC	2/3	1	2	FACETS	0.965	0.924	1	1	0.997	1	CLONAL	2	TRUE	1	0.391682169393474	2		1713	1272	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592354	29592354	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	192	873	0	ENST00000356175.3:c.4769G>T	p.Arg1590Leu	p.R1590L	ENST00000356175	NM_000267.3	1590	cGg/cTg	35/57	1	2	FACETS	0.753	0.7	0.808	1	0.991	1	SUBCLONAL	2	TRUE	1	0.391682169393474	2		873	651	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41228540	41228540	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	390	1270	0	ENST00000357654.3:c.4449T>G	p.Ser1483Arg	p.S1483R	ENST00000357654	NM_007294.3	1483	agT/agG	13/23	1	2	FACETS	0.922	0.878	0.967	1	0.996	1	CLONAL	2	TRUE	1	0.391682169393474	2		1270	1080	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780595	56780595	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	339	1181	0	ENST00000337432.4:c.610A>G	p.Ile204Val	p.I204V	ENST00000337432	NM_058216.2	204	Att/Gtt	4/9	1	2	FACETS	0.919	0.872	0.967	1	0.996	1	CLONAL	2	TRUE	1	0.391682169393474	2		1181	942	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023978	31023978	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs776864243	NA	P-0040197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	390	1427	0	ENST00000375687.4:c.3463C>A	p.Leu1155Ile	p.L1155I	ENST00000375687	NM_015338.5	1155	Ctt/Att	13/13	1	2	FACETS	0.958	0.913	1	1	0.997	1	CLONAL	2	TRUE	1	0.391682169393474	2		1427	1039	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469812	157469831	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCAGGGCCCGGTATGGGT	GCCCAGGGCCCGGTATGGGT	-	novel	NA	P-0040197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	399	1541	0	ENST00000346085.5:c.2606_2625del	p.Gly869AspfsTer66	p.G869Dfs*66	ENST00000346085	NM_020732.3	869	gGCCCAGGGCCCGGTATGGGT/g	9/20	1	2	FACETS	0.868	0.827	0.911	1	0.996	1	CLONAL	2	TRUE	1	0.391682169393474	2		1541	1173	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476815	140476815	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	359	1176	0	ENST00000288602.6:c.1591T>C	p.Trp531Arg	p.W531R	ENST00000288602	NM_004333.4	531	Tgg/Cgg	13/18	1	2	FACETS	1	0.968	1	1	0.996	1	CLONAL	2	TRUE	1	0.391682169393474	2		1176	896	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845946	151845946	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0040197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	354	1438	0	ENST00000262189.6:c.13066A>T	p.Lys4356Ter	p.K4356*	ENST00000262189	NM_170606.2	4356	Aaa/Taa	52/59	1	2	FACETS	0.971	0.923	1	1	0.996	1	CLONAL	2	TRUE	1	0.391682169393474	2		1438	931	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209523	98209524	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCGG	novel	NA	P-0040197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	313	1477	0	ENST00000331920.6:c.4011_4014dup	p.Trp1339ProfsTer66	p.W1339Pfs*66	ENST00000331920	NM_000264.3	1338	-/CCGC	23/24	1	2	FACETS	0.829	0.784	0.875	1	0.995	1	CLONAL	2	TRUE	1	0.391682169393474	2		1477	964	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949995	44949995	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	293	860	0	ENST00000377967.4:c.3764G>C	p.Arg1255Pro	p.R1255P	ENST00000377967	NM_021140.2	1255	cGg/cCg	26/29	0.391682169393474	0	FACETS	0.65	0.622	0.677			1	SUBCLONAL	3	TRUE	0	0.391682169393474	0		860	467	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0040258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	105	414	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.15396350319279	3	FACETS	1	0.963	1	0.582	0.521	0.645	INDETERMINATE	1	FALSE	1	0.3	3		414	692	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604706	48604706	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	33	492	0	ENST00000342988.3:c.1528G>T	p.Gly510Ter	p.G510*	ENST00000342988	NM_005359.5	510	Gga/Tga	12/12	1	2	FACETS	0.334	0.271	0.405	0.334	0.271	0.405	SUBCLONAL	1	FALSE	1	0.3	2		492	659	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143264	108143264	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	39	270	0	ENST00000278616.4:c.3083T>C	p.Leu1028Pro	p.L1028P	ENST00000278616	NM_000051.3	1028	cTa/cCa	21/63	0.3	3	FACETS	0.653	0.541	0.777	0.326	0.27	0.389	SUBCLONAL	1	FALSE	1	0.3	3		270	458	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195433	102195433	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0040258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	71	387	0	ENST00000263464.3:c.193A>T	p.Lys65Ter	p.K65*	ENST00000263464	NM_001165.4	65	Aaa/Taa	2/9	0.3	3	FACETS	0.848	0.74	0.964	0.424	0.37	0.482	CLONAL	1	FALSE	1	0.3	3		387	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0040288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	137	776	0	ENST00000269305.4:c.376-2del		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.156816130223667	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	2	TRUE	0	0.156816130223667	2		776	865	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439124	52439124	+	splice_donor_variant	Splice_Site	DEL	A	A	-	novel	NA	P-0040288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	132	682	0	ENST00000460680.1:c.1116+2del		p.X372_splice	ENST00000460680	NM_004656.3	372			0.156816130223667	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.156816130223667	2		682	756	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623229	52623229	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141067977	NA	P-0040288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	47	408	0	ENST00000394830.3:c.2822C>T	p.Ser941Leu	p.S941L	ENST00000394830	NM_018313.4	941	tCa/tTa	19/30	0.156816130223667	2	FACETS	1	0.959	1	0.727	0.615	0.851	CLONAL	1	TRUE	0	0.156816130223667	2		408	412	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413178	139413178	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1317299348	NA	P-0040288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	143	894	0	ENST00000277541.6:c.964G>C	p.Val322Leu	p.V322L	ENST00000277541	NM_017617.3	322	Gtg/Ctg	6/34	0.156816130223667	2	FACETS	0.907	0.826	0.993	0.907	0.826	0.993	CLONAL	2	TRUE	0	0.156816130223667	2		894	1005	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0040295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	69	502	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.26	2		502	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576870	7576870	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs876659384	NA	P-0040295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	38	607	1	ENST00000269305.4:c.976G>T	p.Glu326Ter	p.E326*	ENST00000269305	NM_001126112.2	326	Gaa/Taa	9/11	1	2	FACETS	0.426	0.351	0.51	0.426	0.351	0.51	SUBCLONAL	1	TRUE	1	0.26	2		608	686	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363483	40363483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	83	586	0	ENST00000397332.2:c.746C>T	p.Pro249Leu	p.P249L	ENST00000397332	NM_001033082.2	249	cCt/cTt	3/3	1	2	FACETS	0.917	0.809	1	0.917	0.809	1	CLONAL	1	TRUE	1	0.26	2		586	696	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	129	82	0				ENST00000310581	NM_198253.2	-/1132			0.229567432396169	1	FACETS	0.556	0.513	0.6	0.556	0.513	0.6	INDETERMINATE	1	TRUE	0	0.891933861048224	1		82	288	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0040313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	240	460	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.904	0.851	0.958	0.904	0.851	0.958	CLONAL	1	TRUE	1	0.891933861048224	2		460	595	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0040313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	236	724	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.848	0.797	0.9	0.848	0.797	0.9	CLONAL	1	TRUE	1	0.891933861048224	2		724	624	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566507	41566507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	232	361	0	ENST00000263253.7:c.4384C>T	p.Arg1462Ter	p.R1462*	ENST00000263253	NM_001429.3	1462	Cga/Tga	27/31	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.891933861048224	2		361	482	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287262	33287262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	327	550	0	ENST00000374542.5:c.1835C>T	p.Ser612Phe	p.S612F	ENST00000374542	NM_001141970.1	612	tCc/tTc	6/8	1	2	FACETS	0.98	0.932	1	0.98	0.932	1	CLONAL	1	TRUE	1	0.891933861048224	2		550	748	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224296	55224296	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	284	468	0	ENST00000275493.2:c.1077C>G	p.Phe359Leu	p.F359L	ENST00000275493	NM_005228.3	359	ttC/ttG	9/28	1	2	FACETS	0.99	0.938	1	0.99	0.938	1	CLONAL	1	TRUE	1	0.891933861048224	2		468	643	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568504	41568504	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	245	347	0	ENST00000263253.7:c.4454A>T	p.Asp1485Val	p.D1485V	ENST00000263253	NM_001429.3	1485	gAt/gTt	28/31	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.891933861048224	2		347	541	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287202	33287202	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	325	562	0	ENST00000374542.5:c.1895C>G	p.Ser632Cys	p.S632C	ENST00000374542	NM_001141970.1	632	tCt/tGt	6/8	1	2	FACETS	0.992	0.943	1	0.992	0.943	1	CLONAL	1	TRUE	1	0.891933861048224	2		562	735	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287268	33287268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1489463159	NA	P-0040313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	335	547	0	ENST00000374542.5:c.1829C>T	p.Ser610Phe	p.S610F	ENST00000374542	NM_001141970.1	610	tCt/tTt	6/8	1	2	FACETS	0.991	0.943	1	0.991	0.943	1	CLONAL	1	TRUE	1	0.891933861048224	2		547	758	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984353	201984353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751139092	NA	P-0040313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	425	605	0	ENST00000359651.3:c.1018G>A	p.Glu340Lys	p.E340K	ENST00000359651		340	Gag/Aag	8/8	0.852809508162968	3	FACETS	1	0.971	1	0.513	0.488	0.538	CLONAL	1	TRUE	1	0.891933861048224	3		605	1344	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256620	133256620	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	237	438	0	ENST00000320574.5:c.343G>C	p.Glu115Gln	p.E115Q	ENST00000320574	NM_006231.2	115	Gaa/Caa	5/49	1	2	FACETS	0.934	0.879	0.989	0.934	0.879	0.989	CLONAL	1	TRUE	1	0.891933861048224	2		438	569	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772252	68772252	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	445	838	0	ENST00000261769.5:c.101C>G	p.Ala34Gly	p.A34G	ENST00000261769	NM_004360.3	34	gCc/gGc	2/16	1	2	FACETS	0.979	0.938	1	0.979	0.938	1	CLONAL	1	TRUE	1	0.891933861048224	2		838	1019	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983318	15983318	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	255	395	0	ENST00000268712.3:c.3461C>A	p.Ser1154Ter	p.S1154*	ENST00000268712	NM_006311.3	1154	tCa/tAa	26/46	0.891933861048224	1	FACETS	0.99	0.956	1	0.99	0.956	1	CLONAL	1	TRUE	0	0.891933861048224	1		395	320	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374906	149374906	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1427667024	NA	P-0040313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	372	501	1	ENST00000360632.3:c.188G>T	p.Arg63Leu	p.R63L	ENST00000360632	NM_015472.4	63	cGc/cTc	2/7	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.891933861048224	2		502	821	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950185	38950185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772137802	NA	P-0040313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	293	440	0	ENST00000357387.3:c.3765G>A	p.Met1255Ile	p.M1255I	ENST00000357387	NM_152756.3	1255	atG/atA	31/38	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.891933861048224	2		440	643	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287967	33287967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	292	428	0	ENST00000374542.5:c.1286C>T	p.Ser429Phe	p.S429F	ENST00000374542	NM_001141970.1	429	tCt/tTt	5/8	1	2	FACETS	0.977	0.926	1	0.977	0.926	1	CLONAL	1	TRUE	1	0.891933861048224	2		428	670	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878180	151878180	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	315	537	0	ENST00000262189.6:c.6765A>C	p.Gln2255His	p.Q2255H	ENST00000262189	NM_170606.2	2255	caA/caC	36/59	1	2	FACETS	0.943	0.895	0.991	0.943	0.895	0.991	CLONAL	1	TRUE	1	0.891933861048224	2		537	749	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285474	38285474	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	401	646	0	ENST00000425967.3:c.679G>C	p.Glu227Gln	p.E227Q	ENST00000425967	NM_001174067.1	227	Gaa/Caa	6/19	1	2	FACETS	0.963	0.92	1	0.963	0.92	1	CLONAL	1	TRUE	1	0.891933861048224	2		646	934	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97897696	97897696	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	543	400	0	ENST00000289081.3:c.775G>C	p.Glu259Gln	p.E259Q	ENST00000289081	NM_000136.2	259	Gaa/Caa	8/15	0.891933861048224	2	FACETS	0.99	0.972	1	0.99	0.972	1	CLONAL	2	TRUE	0	0.891933861048224	2		400	615	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44733180	44733294	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGTTCGTGAGATTTCATGAAGATGGCGCCAGGACGAAGGCCCTACTGGGCAAGGTAAGGCAGCTGCGAGTCGGAGCGCGGACACCGTCTCCCTGGCCGGCGCCGCGCTCGCCCC	GGGTTCGTGAGATTTCATGAAGATGGCGCCAGGACGAAGGCCCTACTGGGCAAGGTAAGGCAGCTGCGAGTCGGAGCGCGGACACCGTCTCCCTGGCCGGCGCCGCGCTCGCCCC	-	novel	NA	P-0040313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	137	398	0	ENST00000377967.4:c.175_225+64del		p.X59_splice	ENST00000377967	NM_021140.2	59		2/29	0.891933861048224	1	FACETS	0.818	0.769	0.866	0.818	0.769	0.866	CLONAL	1	TRUE	0	0.891933861048224	1		398	208	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	109	459	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.764	0.69	0.841	1	0.984	1	SUBCLONAL	2	TRUE	1	0.318392762993108	2		459	448	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039297	47039297	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	217	740	0	ENST00000377604.3:c.920T>G	p.Leu307Arg	p.L307R	ENST00000377604	NM_001204468.1	307	cTg/cGg	10/24	1	2	FACETS	0.896	0.835	0.957	1	0.993	1	CLONAL	2	TRUE	1	0.318392762993108	2		740	761	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038879	12038879	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	126	365	0	ENST00000396373.4:c.1172A>C	p.Tyr391Ser	p.Y391S	ENST00000396373	NM_001987.4	391	tAt/tCt	7/8	1	2	FACETS	0.858	0.783	0.937	1	0.989	1	CLONAL	2	TRUE	1	0.318392762993108	2		365	461	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713853	30713853	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	200	746	0	ENST00000295754.5:c.1178G>T	p.Cys393Phe	p.C393F	ENST00000295754	NM_003242.5	393	tGc/tTc	4/7	1	2	FACETS	0.792	0.736	0.851	1	0.992	1	SUBCLONAL	2	TRUE	1	0.318392762993108	2		746	793	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058719	180058719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770143594	NA	P-0040332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	196	764	1	ENST00000261937.6:c.118G>A	p.Val40Ile	p.V40I	ENST00000261937	NM_182925.4	40	Gtc/Atc	2/30	0.193387752447181	0	FACETS	1	0.962	1			1	CLONAL	1	TRUE	0	0.318392762993108	0		765	794	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412530	63412530	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	160	628	0	ENST00000330258.3:c.637C>T	p.Gln213Ter	p.Q213*	ENST00000330258	NM_152424.3	213	Cag/Tag	2/2	1	2	FACETS	0.798	0.734	0.863	1	0.99	1	SUBCLONAL	2	TRUE	1	0.318392762993108	2		628	630	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713858	30713859	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	191	757	0	ENST00000295754.5:c.1184dup	p.Cys396ValfsTer2	p.C396Vfs*2	ENST00000295754	NM_003242.5	395	ctg/cTtg	4/7	1	2	FACETS	0.759	0.703	0.817	1	0.991	1	SUBCLONAL	2	TRUE	1	0.318392762993108	2		757	790	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350045	70350045	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201044355	NA	P-0040332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	175	502	0	ENST00000374080.3:c.4028G>A	p.Arg1343His	p.R1343H	ENST00000374080		1343	cGc/cAc	28/45	1	2	FACETS	0.894	0.827	0.962	1	0.992	1	CLONAL	2	TRUE	1	0.318392762993108	2		502	615	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0040360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	183	696	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.25804762657813	5	FACETS	1	0.985	1	0.829	0.767	0.892	CLONAL	2	FALSE	2	0.312540971957722	5		696	692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0040360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	112	432	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	NA	2	FACETS	0.762	0.69	0.839			1	INDETERMINATE	2	FALSE	NA	0.312540971957722	2		432	470	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692835	89692835	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs57374291	NA	P-0040360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	25	130	1	ENST00000371953.3:c.319G>T	p.Asp107Tyr	p.D107Y	ENST00000371953	NM_000314.4	107	Gat/Tat	5/9	0.256161885798003	1	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	FALSE	0	0.312540971957722	1		131	122	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0040366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	10	684	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	0.197	0.133	0.279	0.197	0.133	0.279	SUBCLONAL	1	FALSE	1	0.235597844242073	2		684	430	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853288	68853288	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	55	366	0	ENST00000261769.5:c.1671G>C	p.Lys557Asn	p.K557N	ENST00000261769	NM_004360.3	557	aaG/aaC	11/16	1	2	FACETS	0.936	0.801	1	0.936	0.801	1	CLONAL	1	FALSE	1	0.235597844242073	2		366	499	SUCCESS
APC	324	MSKCC	GRCh37	5	112176739	112176739	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	17	128	0	ENST00000257430.4:c.5448G>C	p.Leu1816Phe	p.L1816F	ENST00000257430	NM_000038.5	1816	ttG/ttC	16/16	1	2	FACETS	0.891	0.679	1	1	0.924	1	CLONAL	2	FALSE	1	0.235597844242073	2		128	81	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610498	10610498	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	111	413	1	ENST00000171111.5:c.212G>T	p.Arg71Leu	p.R71L	ENST00000171111	NM_203500.1	71	cGg/cTg	2/6	0.235597844242073	1	FACETS	0.764	0.689	0.843	1	0.984	1	SUBCLONAL	2	FALSE	0	0.235597844242073	1		414	544	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925096	81925096	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867804190	NA	P-0040366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	33	278	0	ENST00000359376.3:c.887C>T	p.Ser296Leu	p.S296L	ENST00000359376	NM_002661.3	296	tCa/tTa	11/33	1	2	FACETS	0.715	0.582	0.864	0.715	0.582	0.864	SUBCLONAL	1	FALSE	1	0.235597844242073	2		278	392	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106069	27106069	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	27	347	0	ENST00000324856.7:c.5680C>T	p.Gln1894Ter	p.Q1894*	ENST00000324856	NM_006015.4	1894	Cag/Tag	20/20	1	2	FACETS	0.52	0.413	0.642	0.52	0.413	0.642	SUBCLONAL	1	FALSE	1	0.235597844242073	2		347	441	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484436	57484436	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	41	286	0	ENST00000371085.3:c.617G>A	p.Gly206Glu	p.G206E	ENST00000371085	NM_000516.4	206	gGa/gAa	8/13	0.235597844242073	3	FACETS	0.838	0.699	0.994	0.419	0.349	0.497	CLONAL	1	FALSE	1	0.235597844242073	3		286	464	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104700	69104700	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149428879	NA	P-0040366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	76	362	0	ENST00000288368.4:c.4544C>T	p.Ser1515Leu	p.S1515L	ENST00000288368	NM_024870.2	1515	tCg/tTg	37/40	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	FALSE	1	0.235597844242073	2		362	590	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436052	56436052	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	84	315	0	ENST00000407977.2:c.1085C>A	p.Ser362Tyr	p.S362Y	ENST00000407977		362	tCc/tAc	9/10	1	2	FACETS	0.812	0.721	0.909	1	0.981	1	CLONAL	2	FALSE	1	0.235597844242073	2		315	439	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027529	48027529	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	37	185	0	ENST00000234420.5:c.2407G>C	p.Asp803His	p.D803H	ENST00000234420	NM_000179.2	803	Gac/Cac	4/10	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	FALSE	1	0.235597844242073	2		185	241	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340144	116340144	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	37	158	0	ENST00000397752.3:c.1006A>G	p.Ser336Gly	p.S336G	ENST00000397752	NM_000245.2	336	Agc/Ggc	2/21	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	FALSE	1	0.235597844242073	2		158	243	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549382	5549382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	101	360	0	ENST00000397747.3:c.409G>A	p.Asp137Asn	p.D137N	ENST00000397747	NM_025239.3	137	Gat/Aat	4/7	0.235597844242073	3	FACETS	0.878	0.787	0.973	0.878	0.787	0.973	CLONAL	2	FALSE	1	0.235597844242073	3		360	546	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376083	8376083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1337096946	NA	P-0040366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	17	148	0	ENST00000356435.5:c.4514C>T	p.Ser1505Leu	p.S1505L	ENST00000356435		1505	tCa/tTa	28/35	0.235597844242073	3	FACETS	0.881	0.661	1	0.441	0.33	0.571	CLONAL	1	FALSE	1	0.235597844242073	3		148	183	SUCCESS
AR	367	MSKCC	GRCh37	X	66931333	66931333	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0040366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	20	161	0	ENST00000374690.3:c.1975A>T	p.Lys659Ter	p.K659*	ENST00000374690	NM_000044.3	659	Aag/Tag	4/8	0.19929854326012	2	FACETS	0.606	0.464	0.773			1	SUBCLONAL	1	FALSE	NA	0.235597844242073	2		161	280	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0040370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	44	460	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	1	2	FACETS	0.613	0.515	0.719	0.613	0.515	0.719	SUBCLONAL	1	FALSE	1	0.421223844621551	2		460	341	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88677046	88677047	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	89	239	0	ENST00000372037.3:c.832dup	p.Tyr278LeufsTer9	p.Y278Lfs*9	ENST00000372037	NM_004329.2	277	-/T	9/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.421223844621551	2		239	355	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173746	108173746	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	32	153	0	ENST00000278616.4:c.5486C>T	p.Pro1829Leu	p.P1829L	ENST00000278616	NM_000051.3	1829	cCa/cTa	36/63	1	2	FACETS	0.932	0.766	1	0.932	0.766	1	CLONAL	1	FALSE	1	0.421223844621551	2		153	163	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040679	47040679	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0040370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	140	523	0	ENST00000377604.3:c.1314C>G	p.Tyr438Ter	p.Y438*	ENST00000377604	NM_001204468.1	438	taC/taG	13/24	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.421223844621551	2		523	629	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0040463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	346	509	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.51417312125372	2	FACETS	0.952	0.908	0.995	0.952	0.908	0.995	CLONAL	2	TRUE	0	0.51417312125372	2		509	707	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357061	70357061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763700798	NA	P-0040463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	216	879	0	ENST00000374080.3:c.5576G>A	p.Arg1859His	p.R1859H	ENST00000374080		1859	cGt/cAt	39/45	1	2	FACETS	0.879	0.817	0.942	0.879	0.817	0.942	CLONAL	1	TRUE	1	0.51417312125372	2		879	956	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120805885	120805885	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	201	801	0	ENST00000257552.2:c.193T>C	p.Phe65Leu	p.F65L	ENST00000257552	NM_002442.3	65	Ttc/Ctc	4/15	1	2	FACETS	0.779	0.722	0.839	0.779	0.722	0.839	SUBCLONAL	1	TRUE	1	0.51417312125372	2		801	1003	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240330	41240330	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	98	383	0	ENST00000379561.5:c.20del	p.Val7GlyfsTer65	p.V7Gfs*65	ENST00000379561	NM_002015.3	7	gTg/gg	1/3	0.51417312125372	1	FACETS	0.835	0.753	0.921	0.835	0.753	0.921	CLONAL	1	TRUE	0	0.51417312125372	1		383	339	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152238	11152238	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0040463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	132	519	0	ENST00000358026.2:c.4520+2T>G		p.X1507_splice	ENST00000358026	NM_001128849.1	1507			1	2	FACETS	0.937	0.855	1	0.937	0.855	1	CLONAL	1	TRUE	1	0.51417312125372	2		519	548	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175212	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	30	222	0	ENST00000257430.4:c.3921A>G	p.Ile1307Met	p.I1307M	ENST00000257430	NM_000038.5	1307	atA/atG	16/16	0.51417312125372	1	FACETS	0.466	0.379	0.563	0.466	0.379	0.563	SUBCLONAL	1	TRUE	0	0.51417312125372	1		222	186	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609837	117609837	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1167721609	NA	P-0040463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	111	556	0	ENST00000368508.3:c.6862T>C	p.Ser2288Pro	p.S2288P	ENST00000368508	NM_002944.2	2288	Tct/Cct	43/43	NA	2	FACETS	0.517	0.464	0.573			1	INDETERMINATE	1	TRUE	NA	0.51417312125372	2		556	835	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0040472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	126	214	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.275493117776153	4	FACETS	0.966	0.879	1	0.966	0.879	1	CLONAL	2	TRUE	2	0.324969614841537	4		214	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0040472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	244	754	6	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	NA	2	FACETS	0.959	0.899	1			1	INDETERMINATE	2	TRUE	NA	0.324969614841537	2		760	783	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057850	27057850	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	230	777	1	ENST00000324856.7:c.1558C>T	p.Gln520Ter	p.Q520*	ENST00000324856	NM_006015.4	520	Cag/Tag	3/20	0.309761620823717	2	FACETS	0.98	0.918	1	0.98	0.918	1	CLONAL	2	TRUE	0	0.324969614841537	2		778	722	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435129	110435129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533420684	NA	P-0040472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	228	589	1	ENST00000375856.3:c.3272C>T	p.Pro1091Leu	p.P1091L	ENST00000375856	NM_003749.2	1091	cCg/cTg	1/2	0.324969614841537	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.324969614841537	2		590	615	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28605607	28605607	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0040472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	134	500	2	ENST00000253063.3:c.1212-1G>T		p.X404_splice	ENST00000253063	NM_031459.4	404			0.309761620823717	2	FACETS	0.891	0.815	0.969	0.891	0.815	0.969	CLONAL	2	TRUE	0	0.324969614841537	2		502	463	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998679	100998679	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1028866384	NA	P-0040472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	146	819	0	ENST00000325455.5:c.1123C>T	p.Pro375Ser	p.P375S	ENST00000325455	NM_001202474.3	375	Cct/Tct	1/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.324969614841537	2		819	764	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098501	108098501	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0040472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	47	258	0	ENST00000278616.4:c.73-2A>T		p.X25_splice	ENST00000278616	NM_000051.3	25			1	2	FACETS	0.974	0.827	1	0.974	0.827	1	CLONAL	1	TRUE	1	0.324969614841537	2		258	297	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50816326	50816326	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	65	400	0	ENST00000398568.2:c.1766A>G	p.Lys589Arg	p.K589R	ENST00000398568	NM_001042412.1	589	aAa/aGa	10/18	0.276989199423412	3	FACETS	0.775	0.672	0.887	0.388	0.336	0.444	SUBCLONAL	1	TRUE	1	0.324969614841537	3		400	600	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827246	72827246	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	99	607	0	ENST00000268489.5:c.9335C>A	p.Pro3112His	p.P3112H	ENST00000268489	NM_006885.3	3112	cCt/cAt	9/10	0.276989199423412	3	FACETS	1	0.897	1	0.502	0.448	0.56	CLONAL	1	TRUE	1	0.324969614841537	3		607	705	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554461	63554483	+	frameshift_variant	Frame_Shift_Del	DEL	TAAGCACCGTCTTGATCGCCCAA	TAAGCACCGTCTTGATCGCCCAA	-	novel	NA	P-0040472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	142	637	2	ENST00000307078.5:c.256_278del	p.Leu86ProfsTer47	p.L86Pfs*47	ENST00000307078	NM_004655.3	86	TTGGGCGATCAAGACGGTGCTTAc/c	2/11	0.172879371205621	4	FACETS	1	0.987	1	0.743	0.678	0.812	INDETERMINATE	1	TRUE	2	0.324969614841537	4		639	779	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643840	52643840	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	64	512	1	ENST00000394830.3:c.2056A>G	p.Arg686Gly	p.R686G	ENST00000394830	NM_018313.4	686	Agg/Ggg	17/30	0.324969614841537	2	FACETS	0.853	0.74	0.974	0.426	0.37	0.487	CLONAL	1	TRUE	0	0.324969614841537	2		513	462	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955876	55955876	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	107	449	0	ENST00000263923.4:c.3286T>A	p.Trp1096Arg	p.W1096R	ENST00000263923	NM_002253.2	1096	Tgg/Agg	24/30	0.217504418252198	4	FACETS	0.825	0.743	0.911	0.825	0.743	0.911	CLONAL	2	TRUE	2	0.324969614841537	4		449	529	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250681	26250681	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	136	616	0	ENST00000446824.2:c.153A>C	p.Glu51Asp	p.E51D	ENST00000446824	NM_021018.2	51	gaA/gaC	1/1	0.217504418252198	4	FACETS	0.78	0.71	0.853	0.78	0.71	0.853	SUBCLONAL	2	TRUE	2	0.324969614841537	4		616	711	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207713	29207713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	92	318	0	ENST00000240100.2:c.83C>T	p.Ala28Val	p.A28V	ENST00000240100	NM_001394.6	28	gCg/gTg	1/4	0.309761620823717	2	FACETS	1	0.98	1	0.722	0.646	0.802	CLONAL	1	TRUE	0	0.324969614841537	2		318	392	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69032465	69032465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	240	728	1	ENST00000288368.4:c.3539C>T	p.Ala1180Val	p.A1180V	ENST00000288368	NM_024870.2	1180	gCt/gTt	29/40	0.276989199423412	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.324969614841537	3		729	824	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389246	8389246	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	122	511	0	ENST00000356435.5:c.4372G>T	p.Glu1458Ter	p.E1458*	ENST00000356435		1458	Gaa/Taa	26/35	0.309761620823717	2	FACETS	0.834	0.759	0.912	0.834	0.759	0.912	CLONAL	2	TRUE	0	0.324969614841537	2		511	450	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933577	39933577	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	160	660	0	ENST00000378444.4:c.1022C>G	p.Pro341Arg	p.P341R	ENST00000378444	NM_001123385.1	341	cCc/cGc	4/15	0.196948622090921	3	FACETS	0.752	0.691	0.816			1	SUBCLONAL	2	TRUE	NA	0.324969614841537	3		660	761	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239900	53239900	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	77	677	0	ENST00000375401.3:c.1541A>G	p.His514Arg	p.H514R	ENST00000375401	NM_004187.3	514	cAt/cGt	11/26	1	2	FACETS	0.618	0.542	0.7	0.618	0.542	0.7	SUBCLONAL	1	TRUE	1	0.324969614841537	2		677	767	SUCCESS
AR	367	MSKCC	GRCh37	X	66766361	66766361	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	39	77	0	ENST00000374690.3:c.1373G>C	p.Gly458Ala	p.G458A	ENST00000374690	NM_000044.3	458	gGc/gCc	1/8	1	2	FACETS	1	0.915	1	1	0.973	1	CLONAL	2	TRUE	1	0.324969614841537	2		77	108	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651513	52651513	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	66	260	0	ENST00000394830.3:c.1583A>T	p.Asn528Ile	p.N528I	ENST00000394830	NM_018313.4	528	aAt/aTt	15/30	0.248960795314513	1	FACETS	0.825	0.724	0.931	1	0.978	1	CLONAL	2	TRUE	0	0.266737319193083	1		260	260	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188252	10188252	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1559428134	NA	P-0040516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	112	407	0	ENST00000256474.2:c.397del	p.Thr133LeufsTer26	p.T133Lfs*26	ENST00000256474	NM_000551.3	132	cAa/ca	2/3	0.238960066346402	4	FACETS	1	0.918	1	1	0.918	1	CLONAL	3	TRUE	1	0.266737319193083	4		407	351	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144877	47144877	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	48	280	0	ENST00000409792.3:c.4876T>G	p.Phe1626Val	p.F1626V	ENST00000409792	NM_014159.6	1626	Ttc/Gtc	7/21	0.248960795314513	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.266737319193083	1		280	243	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149238747	149238747	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	186	459	1	ENST00000360632.3:c.1048A>T	p.Ile350Phe	p.I350F	ENST00000360632	NM_015472.4	350	Atc/Ttc	7/7	0.238960066346402	4	FACETS	1	0.985	1	0.824	0.763	0.886	CLONAL	2	TRUE	1	0.266737319193083	4		460	715	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0040543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	106	395	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.828	0.75	0.908	0.828	0.75	0.908	CLONAL	1	TRUE	1	0.75754312451903	2		396	338	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808895	3808895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	256	495	0	ENST00000262367.5:c.3329C>T	p.Pro1110Leu	p.P1110L	ENST00000262367	NM_004380.2	1110	cCt/cTt	17/31	1	2	FACETS	0.984	0.926	1	0.984	0.926	1	CLONAL	1	TRUE	1	0.75754312451903	2		495	687	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653807	89653807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554893782	NA	P-0040543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	87	315	0	ENST00000371953.3:c.105G>A	p.Met35Ile	p.M35I	ENST00000371953	NM_000314.4	35	atG/atA	2/9	0.75754312451903	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.75754312451903	1		315	138	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910653	32910653	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	40	308	0	ENST00000380152.3:c.2161C>A	p.Pro721Thr	p.P721T	ENST00000380152		721	Cca/Aca	11/27	1	2	FACETS	0.265	0.22	0.315	0.265	0.22	0.315	SUBCLONAL	1	TRUE	1	0.75754312451903	2		308	398	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66728949	66729101	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAACTTGTTTGTAACAACTTAACCTGTTTCTCCTCCCTCTACCTTAAAGAGCTTAAACATTTAACAAGACTATATCTTTCATCCCTTCCTCCCTCTTTCTTTCATAAAACCTCTCTTTCTTCCACCTTTCTCCAGCTAATTCATCTGGAGATC	AAACTTGTTTGTAACAACTTAACCTGTTTCTCCTCCCTCTACCTTAAAGAGCTTAAACATTTAACAAGACTATATCTTTCATCCCTTCCTCCCTCTTTCTTTCATAAAACCTCTCTTTCTTCCACCTTTCTCCAGCTAATTCATCTGGAGATC	-	novel	NA	P-0040566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	14	125	0	ENST00000307102.5:c.292-131_313del		p.X98_splice	ENST00000307102	NM_002755.3	98		3/11	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		125	130	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0040571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	61	621	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.521	0.449	0.6	0.521	0.449	0.6	SUBCLONAL	1	FALSE	1	0.327068010359194	2		622	716	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743520	46743520	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141523334	NA	P-0040571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	48	572	0	ENST00000371975.4:c.1901G>A	p.Arg634His	p.R634H	ENST00000371975	NM_003579.3	634	cGt/cAt	17/18	1	2	FACETS	0.435	0.367	0.51	0.435	0.367	0.51	SUBCLONAL	1	FALSE	1	0.327068010359194	2		572	675	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356406	66356406	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	36	422	0	ENST00000273854.3:c.1091C>A	p.Ala364Asp	p.A364D	ENST00000273854	NM_004439.5	364	gCc/gAc	5/18	1	2	FACETS	0.471	0.387	0.566	0.471	0.387	0.566	SUBCLONAL	1	FALSE	1	0.327068010359194	2		422	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0040576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	236	651	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.564476869106567	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.564476869106567	1		651	558	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576091	29576091	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1131691087	NA	P-0040576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	214	562	0	ENST00000356175.3:c.4064C>G	p.Ser1355Ter	p.S1355*	ENST00000356175	NM_000267.3	1355	tCa/tGa	30/57	1	2	FACETS	0.99	0.923	1	0.99	0.923	1	CLONAL	1	TRUE	1	0.564476869106567	2		562	766	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663681	29663681	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	152	405	0	ENST00000356175.3:c.6113A>G	p.Asp2038Gly	p.D2038G	ENST00000356175	NM_000267.3	2038	gAc/gGc	41/57	1	2	FACETS	0.986	0.907	1	0.986	0.907	1	CLONAL	1	TRUE	1	0.564476869106567	2		405	546	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752657	128752657	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	90	280	0	ENST00000377970.2:c.818A>G	p.Asp273Gly	p.D273G	ENST00000377970	NM_002467.4	273	gAt/gGt	3/3	1	2	FACETS	0.908	0.813	1	0.908	0.813	1	CLONAL	1	TRUE	1	0.564476869106567	2		280	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0040634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	271	595	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	0.571546408237484	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.593135749072204	1		595	623	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199958	138199958	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	164	499	1	ENST00000237289.4:c.1376C>T	p.Ser459Leu	p.S459L	ENST00000237289	NM_001270507.1	459	tCg/tTg	7/9	0.162120184510311	2	FACETS	1	0.947	1	0.516	0.476	0.556	INDETERMINATE	1	TRUE	0	0.593135749072204	2		500	536	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0040634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	97	523	0	ENST00000311936.3:c.180_181delinsAA	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggAAaa	3/5	0.321396409672403	1	FACETS	0.62	0.557	0.686	0.62	0.557	0.686	INDETERMINATE	1	TRUE	0	0.593135749072204	1		523	371	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437578	56437578	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs746762909	NA	P-0040634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	190	629	0	ENST00000407977.2:c.884A>G	p.His295Arg	p.H295R	ENST00000407977		295	cAt/cGt	8/10	0.571546408237484	1	FACETS	0.867	0.808	0.927	0.867	0.808	0.927	CLONAL	1	TRUE	0	0.593135749072204	1		629	520	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794899	242794899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	194	796	1	ENST00000334409.5:c.310C>T	p.Arg104Cys	p.R104C	ENST00000334409	NM_005018.2	104	Cgt/Tgt	2/5	1	2	FACETS	0.929	0.863	0.998	0.929	0.863	0.998	CLONAL	1	TRUE	1	0.593135749072204	2		797	704	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323262	31323262	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs77665001	NA	P-0040634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	75	448	1	ENST00000412585.2:c.727C>T	p.Arg243Trp	p.R243W	ENST00000412585	NM_005514.6	243	Cgg/Tgg	4/8	1	2	FACETS	0.531	0.467	0.6	0.531	0.467	0.6	SUBCLONAL	1	TRUE	1	0.593135749072204	2		449	476	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749947	162749947	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	56	458	0	ENST00000367921.3:c.2479C>A	p.Leu827Met	p.L827M	ENST00000367921	NM_006182.2	827	Ctg/Atg	18/18	0.303245244695397	0	FACETS	0.192	0.164	0.221			1	INDETERMINATE	1	TRUE	0	0.593135749072204	0		458	401	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493506	56493506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	70	475	0	ENST00000267101.3:c.2914C>T	p.Pro972Ser	p.P972S	ENST00000267101	NM_001982.3	972	Cca/Tca	24/28	1	2	FACETS	0.428	0.374	0.487	0.428	0.374	0.487	SUBCLONAL	1	TRUE	1	0.593135749072204	2		475	551	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41022147	41022149	+	inframe_deletion	In_Frame_Del	DEL	ATC	ATC	-	novel	NA	P-0040634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	70	590	0	ENST00000267868.3:c.874_876del	p.Ile292del	p.I292del	ENST00000267868	NM_002875.4	291	ATC/-	9/10	0.289980054902311	1	FACETS	0.349	0.305	0.396	0.349	0.305	0.396	INDETERMINATE	1	TRUE	0	0.593135749072204	1		590	476	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229449	36229449	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	80	474	0	ENST00000222270.7:c.8139C>A	p.Phe2713Leu	p.F2713L	ENST00000222270	NM_014727.1	2713	ttC/ttA	37/37	0.321396409672403	1	FACETS	0.383	0.338	0.432	0.383	0.338	0.432	INDETERMINATE	1	TRUE	0	0.593135749072204	1		474	495	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159118	143159118	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	27	419	0	ENST00000262992.4:c.735C>G	p.Asp245Glu	p.D245E	ENST00000262992	NM_001101669.1	245	gaC/gaG	10/24	0.593135749072204	1	FACETS	0.889	0.734	1	0.889	0.734	1	CLONAL	1	TRUE	0	0.593135749072204	1		419	72	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572667	141572667	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs757740707	NA	P-0040634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	340	650	0	ENST00000220592.5:c.403G>C	p.Val135Leu	p.V135L	ENST00000220592	NM_012154.3	135	Gtg/Ctg	4/19	0.592780018080525	2	FACETS	0.92	0.88	0.96	0.92	0.88	0.96	CLONAL	2	TRUE	0	0.593135749072204	2		650	623	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44894180	44894180	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	46	460	0	ENST00000377967.4:c.569T>G	p.Phe190Cys	p.F190C	ENST00000377967	NM_021140.2	190	tTt/tGt	7/29	0.42992226073516	1	FACETS	0.763	0.656	0.875	0.763	0.656	0.875	SUBCLONAL	1	TRUE	0	0.593135749072204	1		460	143	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0040649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	70	428	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.276689177541753	1	FACETS	0.711	0.62	0.81	0.711	0.62	0.81	SUBCLONAL	1	TRUE	0	0.276689177541753	1		428	613	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457295	67457295	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	81	507	0	ENST00000327367.4:c.269G>T	p.Arg90Leu	p.R90L	ENST00000327367	NM_005902.3	90	cGc/cTc	2/9	0.276689177541753	1	FACETS	0.757	0.667	0.854	0.757	0.667	0.854	SUBCLONAL	1	TRUE	0	0.276689177541753	1		507	666	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577151	7577151	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs72661119	NA	P-0040649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	59	400	0	ENST00000269305.4:c.787A>G	p.Asn263Asp	p.N263D	ENST00000269305	NM_001126112.2	263	Aat/Gat	8/11	0.276689177541753	1	FACETS	0.652	0.561	0.751	0.652	0.561	0.751	SUBCLONAL	1	TRUE	0	0.276689177541753	1		400	564	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395639	45395640	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0040649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	42	217	0	ENST00000262160.6:c.494dup	p.Tyr165Ter	p.Y165*	ENST00000262160	NM_005901.5	165	tac/taAc	4/11	0.276689177541753	1	FACETS	0.81	0.679	0.954	0.81	0.679	0.954	CLONAL	1	TRUE	0	0.276689177541753	1		217	323	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117581	4117581	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	51	456	0	ENST00000262948.5:c.139G>C	p.Asp47His	p.D47H	ENST00000262948	NM_030662.3	47	Gac/Cac	2/11	1	2	FACETS	0.57	0.483	0.665	0.57	0.483	0.665	SUBCLONAL	1	TRUE	1	0.276689177541753	2		456	647	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026843	48026843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	65	306	0	ENST00000234420.5:c.1721C>T	p.Ser574Leu	p.S574L	ENST00000234420	NM_000179.2	574	tCa/tTa	4/10	1	2	FACETS	0.995	0.865	1	0.995	0.865	1	CLONAL	1	TRUE	1	0.276689177541753	2		306	472	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532715	187532716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	65	382	0	ENST00000441802.2:c.9677dup	p.Asn3226LysfsTer6	p.N3226Kfs*6	ENST00000441802	NM_005245.3	3226	aac/aaAc	14/27	1	2	FACETS	0.829	0.719	0.948	0.829	0.719	0.948	CLONAL	1	TRUE	1	0.276689177541753	2		382	567	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591121	67591121	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1390357148	NA	P-0040649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	42	241	0	ENST00000274335.5:c.1714C>T	p.Gln572Ter	p.Q572*	ENST00000274335		572	Cag/Tag	12/15	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.276689177541753	2		241	298	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412010	116412010	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	86	554	3	ENST00000397752.3:c.2995G>T	p.Glu999Ter	p.E999*	ENST00000397752	NM_000245.2	999	Gaa/Taa	14/21	0.276689177541753	3	FACETS	0.951	0.841	1	0.476	0.42	0.535	CLONAL	1	TRUE	1	0.276689177541753	3		557	744	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041355	47041355	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	101	488	0	ENST00000377604.3:c.1701del	p.Asp568ThrfsTer136	p.D568Tfs*136	ENST00000377604	NM_001204468.1	567	Ccc/cc	16/24	0.233248590799281	1	FACETS	0.849	0.759	0.945	0.849	0.759	0.945	CLONAL	1	TRUE	0	0.276689177541753	1		488	741	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412044	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	INS	GG	GG	AATA	novel	NA	P-0040649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	140	537	0	ENST00000397752.3:c.3028_3028+1delinsAATA		p.X1010_splice	ENST00000397752	NM_000245.2	1010		14/21	0.276689177541753	3	FACETS	0.794	0.725	0.868	0.794	0.725	0.868	SUBCLONAL	2	TRUE	1	0.276689177541753	3		537	725	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0040730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	189	502	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	0.905	0.845	0.967	0.905	0.845	0.967	CLONAL	1	TRUE	1	0.84863623787791	2		502	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0040730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	435	638	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.84863623787791	1	FACETS	0.963	0.933	0.992	0.963	0.933	0.992	CLONAL	1	TRUE	0	0.84863623787791	1		638	613	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724437	112724450	+	frameshift_variant	Frame_Shift_Del	DEL	ATCCAAGAGATCTA	ATCCAAGAGATCTA	-	novel	NA	P-0040730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	277	522	0	ENST00000369452.4:c.321_334del	p.Leu107PhefsTer22	p.L107Ffs*22	ENST00000369452	NM_007373.3	107	ttATCCAAGAGATCTAta/ttta	2/9	0.4061216566254	1	FACETS	0.683	0.649	0.718	0.683	0.649	0.718	INDETERMINATE	1	TRUE	0	0.84863623787791	1		522	550	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458335	12458335	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs72551362	NA	P-0040730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	348	550	1	ENST00000287820.6:c.952G>A	p.Val318Met	p.V318M	ENST00000287820	NM_015869.4	318	Gtg/Atg	6/7	0.806878793348913	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.84863623787791	1		551	463	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467421	66467421	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	111	205	0	ENST00000273854.3:c.848T>G	p.Leu283Arg	p.L283R	ENST00000273854	NM_004439.5	283	cTg/cGg	3/18	0.426448143316797	1	FACETS	0.646	0.594	0.699	0.646	0.594	0.699	INDETERMINATE	1	TRUE	0	0.84863623787791	1		205	233	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910375	29910401	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GGCCCTGGCCCTGACCCAGACCTGGGC	GGCCCTGGCCCTGACCCAGACCTGGGC	-	novel	NA	P-0040730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	310	673	0	ENST00000376809.5:c.47_73del	p.Ala16_Ala24del	p.A16_A24del	ENST00000376809	NM_002116.7	15	ggGGCCCTGGCCCTGACCCAGACCTGGGCg/ggg	1/8	1	2	FACETS	0.784	0.741	0.828	0.784	0.741	0.828	SUBCLONAL	1	TRUE	1	0.84863623787791	2		673	932	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866647	117866647	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	103	410	0	ENST00000297338.2:c.998A>T	p.Asp333Val	p.D333V	ENST00000297338	NM_006265.2	333	gAt/gTt	9/14	0.84863623787791	4	FACETS	0.503	0.449	0.56	0.168	0.149	0.187	SUBCLONAL	1	TRUE	1	0.84863623787791	4		410	892	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650063	93650110	+	inframe_deletion	In_Frame_Del	DEL	GTACGCTCCGGAATGCATCAACTACTACAAGTTCTCCAGCAAAAGCGA	GTACGCTCCGGAATGCATCAACTACTACAAGTTCTCCAGCAAAAGCGA	-	novel	NA	P-0040730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	102	427	0	ENST00000375746.1:c.1614_1661del	p.Trp538_Asp554delinsCys	p.W538_D554delinsC	ENST00000375746	NM_001174167.1	538	tgGTACGCTCCGGAATGCATCAACTACTACAAGTTCTCCAGCAAAAGCGAt/tgt	12/14	0.4061216566254	1	FACETS	0.275	0.247	0.305	0.275	0.247	0.305	INDETERMINATE	1	TRUE	0	0.84863623787791	1		427	503	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336065	73336065	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040732-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	71	271	0	ENST00000377767.4:c.2338A>G	p.Arg780Gly	p.R780G	ENST00000377767	NM_014953.3	780	Aga/Gga	17/21	0.255989532321232	2	FACETS	1	0.975	1	0.702	0.625	0.781	INDETERMINATE	1	TRUE	0	0.521536478721665	2		271	194	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033492	48033492	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs972387746	NA	P-0040732-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	112	570	0	ENST00000234420.5:c.3796C>T	p.His1266Tyr	p.H1266Y	ENST00000234420	NM_000179.2	1266	Cat/Tat	8/10	0.263121856020961	3	FACETS	1	0.975	1	0.413	0.374	0.454	INDETERMINATE	1	TRUE	0	0.521536478721665	3		570	437	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130069	143130069	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040732-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	76	464	0	ENST00000262992.4:c.947C>A	p.Thr316Lys	p.T316K	ENST00000262992	NM_001101669.1	316	aCa/aAa	11/24	1	2	FACETS	0.971	0.861	1	0.971	0.861	1	CLONAL	1	TRUE	1	0.521536478721665	2		464	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577098	7577098	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	256	814	0	ENST00000269305.4:c.840A>T	p.Arg280Ser	p.R280S	ENST00000269305	NM_001126112.2	280	agA/agT	8/11	0.334119048586962	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.352252275199235	2		814	713	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271405	26271405	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	187	622	0	ENST00000305910.3:c.208C>A	p.Arg70Ser	p.R70S	ENST00000305910	NM_003534.2	70	Cgc/Agc	1/1	0.352252275199235	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.352252275199235	2		622	452	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	199	82	0				ENST00000310581	NM_198253.2	-/1132			0.498163442203129	6	FACETS	0.906	0.85	0.964	0.906	0.85	0.964	INDETERMINATE	3	TRUE	3	0.90175815416095	6		82	455	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839802	27839802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	166	676	0	ENST00000328488.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000328488	NM_003533.2	98	Gag/Aag	1/1	0.90175815416095	4	FACETS	0.966	0.889	1	0.322	0.296	0.349	CLONAL	1	TRUE	1	0.90175815416095	4		676	725	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1427441061	NA	P-0040806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	372	519	0	ENST00000269305.4:c.560-2A>G		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.90175815416095	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.90175815416095	2		519	389	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184760	32184760	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	262	717	0	ENST00000375023.3:c.1823C>A	p.Pro608Gln	p.P608Q	ENST00000375023	NM_004557.3	608	cCa/cAa	11/30	0.819172319265912	4	FACETS	0.958	0.906	1	0.638	0.604	0.673	CLONAL	2	TRUE	1	0.90175815416095	4		717	577	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43817889	43817889	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	180	494	0	ENST00000372470.3:c.1568G>A	p.Arg523Lys	p.R523K	ENST00000372470	NM_005373.2	523	aGa/aAa	11/12	0.529862340297923	4	FACETS	0.755	0.702	0.809	0.503	0.468	0.539	INDETERMINATE	2	TRUE	1	0.90175815416095	4		494	503	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120467995	120467995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	174	710	2	ENST00000256646.2:c.4444G>A	p.Glu1482Lys	p.E1482K	ENST00000256646	NM_024408.3	1482	Gag/Aag	25/34	0.529862340297923	4	FACETS	1	0.984	1	0.413	0.382	0.445	INDETERMINATE	1	TRUE	1	0.90175815416095	4		712	592	SUCCESS
EED	8726	MSKCC	GRCh37	11	85956380	85956380	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	109	302	0	ENST00000263360.6:c.109G>C	p.Glu37Gln	p.E37Q	ENST00000263360	NM_003797.3	37	Gag/Cag	1/12	0.90175815416095	3	FACETS	1	0.984	1	0.464	0.424	0.504	CLONAL	1	TRUE	0	0.90175815416095	3		302	252	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94963999	94963999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318902387	NA	P-0040806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	253	288	0	ENST00000536441.1:c.26C>T	p.Ser9Leu	p.S9L	ENST00000536441	NM_144665.3	9	tCg/tTg	1/10	0.90175815416095	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.90175815416095	3		288	262	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427041	49427041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1330907821	NA	P-0040806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	120	677	0	ENST00000301067.7:c.11447G>A	p.Gly3816Glu	p.G3816E	ENST00000301067	NM_003482.3	3816	gGa/gAa	39/54	0.821959690298637	4	FACETS	1	0.972	1	0.391	0.355	0.427	CLONAL	1	TRUE	1	0.90175815416095	4		677	432	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641437	47641437	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs781569442	NA	P-0040806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	170	518	0	ENST00000233146.2:c.822C>G	p.Ile274Met	p.I274M	ENST00000233146	NM_000251.2	274	atC/atG	5/16	0.90175815416095	3	FACETS	0.912	0.843	0.983	0.456	0.421	0.492	CLONAL	1	TRUE	1	0.90175815416095	3		518	600	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719670	190719670	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	54	222	1	ENST00000441310.2:c.1672G>T	p.Gly558Ter	p.G558*	ENST00000441310	NM_000534.4	558	Gga/Tga	9/13	1	2	FACETS	0.951	0.836	1	0.951	0.836	1	CLONAL	1	TRUE	1	0.90175815416095	2		223	126	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598154	52598154	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	238	594	0	ENST00000394830.3:c.3712G>C	p.Glu1238Gln	p.E1238Q	ENST00000394830	NM_018313.4	1238	Gag/Cag	24/30	0.90175815416095	3	FACETS	1	0.993	1	0.476	0.449	0.504	CLONAL	1	TRUE	0	0.90175815416095	3		594	536	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81340808	81340808	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	249	321	0	ENST00000222390.5:c.1433T>C	p.Val478Ala	p.V478A	ENST00000222390	NM_000601.4	478	gTc/gCc	12/18	0.90175815416095	6	FACETS	0.981	0.928	1	0.589	0.556	0.621	CLONAL	3	TRUE	1	0.90175815416095	6		321	526	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127951985	127951985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	171	639	0	ENST00000373547.4:c.13G>C	p.Asp5His	p.D5H	ENST00000373547	NM_002721.4	5	Gac/Cac	1/7	0.649714905802748	3	FACETS	1	0.975	1	0.556	0.515	0.597	CLONAL	1	TRUE	1	0.90175815416095	3		639	495	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044907	47044907	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	121	542	1	ENST00000377604.3:c.2237del	p.Gly746AlafsTer56	p.G746Afs*56	ENST00000377604	NM_001204468.1	745	Ggg/gg	20/24	1	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.18	1		543	872	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0040818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	30	460	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	1	2	FACETS	0.427	0.343	0.524	0.427	0.343	0.524	SUBCLONAL	1	TRUE	1	0.18	2		460	780	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485953	8485953	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs763256154	NA	P-0040818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	56	467	0	ENST00000356435.5:c.2864C>A	p.Thr955Asn	p.T955N	ENST00000356435		955	aCc/aAc	17/35	1	2	FACETS	0.815	0.697	0.945	0.815	0.697	0.945	CLONAL	1	TRUE	1	0.18	2		467	763	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434849	128434849	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	54	558	0	ENST00000265960.3:c.5C>T	p.Ala2Val	p.A2V	ENST00000265960	NM_001006617.1	2	gCc/gTc	2/12	1	2	FACETS	0.69	0.588	0.803	0.69	0.588	0.803	SUBCLONAL	1	TRUE	1	0.18	2		558	869	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200023	123200023	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0040830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	18	212	0	ENST00000218089.9:c.2097-2A>C		p.X699_splice	ENST00000218089	NM_001042749.1	699			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		212	95	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0040860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	267	214	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.233234384324639	2	FACETS	0.817	0.776	0.858	0.817	0.776	0.858	INDETERMINATE	2	FALSE	0	0.645697910414241	2		214	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0040862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	303	595	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	0.745185249102392	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.745185249102392	2		595	376	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169929	32169929	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	250	721	1	ENST00000375023.3:c.3679G>T	p.Gly1227Trp	p.G1227W	ENST00000375023	NM_004557.3	1227	Ggg/Tgg	21/30	0.745185249102392	3	FACETS	0.995	0.944	1	0.995	0.944	1	CLONAL	2	TRUE	1	0.745185249102392	3		722	463	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21629857	21629857	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs751366408	NA	P-0040862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	37	407	0	ENST00000421138.2:c.937A>G	p.Lys313Glu	p.K313E	ENST00000421138		313	Aaa/Gaa	9/16	0.745185249102392	3	FACETS	0.947	0.794	1	0.473	0.397	0.555	CLONAL	1	TRUE	1	0.745185249102392	3		407	144	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033968	49033968	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	102	329	0	ENST00000267163.4:c.2106del	p.Ile703LeufsTer2	p.I703Lfs*2	ENST00000267163	NM_000321.2	702	cAa/ca	20/27	0.724055004747208	2	FACETS	0.938	0.875	0.996	0.938	0.875	0.996	CLONAL	2	TRUE	0	0.745185249102392	2		329	146	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761384	59761384	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	108	428	0	ENST00000259008.2:c.3023T>C	p.Leu1008Ser	p.L1008S	ENST00000259008	NM_032043.2	1008	tTg/tCg	20/20	0.724683996838747	3	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	1	0.745185249102392	3		428	197	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713484	40713484	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	175	595	1	ENST00000373198.4:c.4031C>A	p.Pro1344Gln	p.P1344Q	ENST00000373198	NM_133170.3	1344	cCa/cAa	30/32	0.745185249102392	3	FACETS	0.895	0.838	0.953	0.895	0.838	0.953	CLONAL	2	TRUE	1	0.745185249102392	3		596	360	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629535	187629561	+	inframe_deletion	In_Frame_Del	DEL	TGACAGTAGTACCAATGGGCACGTTCT	TGACAGTAGTACCAATGGGCACGTTCT	-	novel	NA	P-0040862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	122	553	0	ENST00000441802.2:c.1421_1447del	p.Glu474_Met483delinsVal	p.E474_M483delinsV	ENST00000441802	NM_005245.3	474	gAGAACGTGCCCATTGGTACTACTGTCAtg/gtg	2/27	0.724055004747208	2	FACETS	0.783	0.729	0.837	0.783	0.729	0.837	SUBCLONAL	2	TRUE	0	0.745185249102392	2		553	209	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419980	152419980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs79626648	NA	P-0040862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	219	576	0	ENST00000206249.3:c.1667G>A	p.Gly556Glu	p.G556E	ENST00000206249	NM_000125.3	556	gGa/gAa	8/8	0.523153511876393	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.745185249102392	4		576	431	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	56	82	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.22	2		82	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0040866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	62	721	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.55	0.474	0.634	0.55	0.474	0.634	SUBCLONAL	1	TRUE	1	0.22	2		723	1024	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628571	90628571	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	82	817	0	ENST00000330062.3:c.1016G>T	p.Gly339Val	p.G339V	ENST00000330062	NM_002168.2	339	gGg/gTg	8/11	1	2	FACETS	0.625	0.549	0.707	0.625	0.549	0.707	SUBCLONAL	1	TRUE	1	0.22	2		817	1192	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412033	116412044	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TTTTCCAGAAGG	TTTTCCAGAAGG	-	novel	NA	P-0040866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	41	630	0	ENST00000397752.3:c.3019_3028+2del		p.X1007_splice	ENST00000397752	NM_000245.2	1007		14/21	1	2	FACETS	0.731	0.608	0.867	0.731	0.608	0.867	SUBCLONAL	1	TRUE	1	0.22	2		630	510	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0040875-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	211	778	1	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.43215276314792	1	FACETS	0.915	0.852	0.981	0.915	0.852	0.981	CLONAL	1	TRUE	0	0.438061880947267	1		779	822	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349262	70349262	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040875-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	228	461	0	ENST00000374080.3:c.3674A>T	p.Lys1225Met	p.K1225M	ENST00000374080		1225	aAg/aTg	26/45	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.438061880947267	1		461	588	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074381	8074381	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040875-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	97	347	0	ENST00000377482.5:c.278C>G	p.Pro93Arg	p.P93R	ENST00000377482	NM_018948.3	93	cCc/cGc	4/4	1	2	FACETS	0.858	0.768	0.954	0.858	0.768	0.954	CLONAL	1	TRUE	1	0.438061880947267	2		347	516	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254662	16254662	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040875-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	84	485	0	ENST00000375759.3:c.1927C>G	p.Pro643Ala	p.P643A	ENST00000375759	NM_015001.2	643	Cct/Gct	11/15	1	2	FACETS	0.45	0.396	0.507	0.45	0.396	0.507	SUBCLONAL	1	TRUE	1	0.438061880947267	2		485	853	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922208	100922208	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1205217316	NA	P-0040875-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	109	273	0	ENST00000325455.5:c.2304C>A	p.Tyr768Ter	p.Y768*	ENST00000325455	NM_001202474.3	768	taC/taA	5/8	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.438061880947267	2		273	469	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164071	108164071	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1448017467	NA	P-0040875-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	41	66	0	ENST00000278616.4:c.4643A>G	p.Asp1548Gly	p.D1548G	ENST00000278616	NM_000051.3	1548	gAt/gGt	31/63	1	2	FACETS	0.832	0.699	0.977	0.832	0.699	0.977	CLONAL	1	TRUE	1	0.438061880947267	2		66	225	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420654	49420655	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0040875-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	85	675	0	ENST00000301067.7:c.15094_15095delinsCT	p.Cys5032Leu	p.C5032L	ENST00000301067	NM_003482.3	5032	TGc/CTc	48/54	1	2	FACETS	0.484	0.427	0.545	0.484	0.427	0.545	SUBCLONAL	1	TRUE	1	0.438061880947267	2		675	802	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465443	99465443	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040875-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	164	523	0	ENST00000268035.6:c.2268C>A	p.Asn756Lys	p.N756K	ENST00000268035	NM_000875.3	756	aaC/aaA	11/21	0.235723821731975	1	FACETS	0.928	0.856	1	0.928	0.856	1	INDETERMINATE	1	TRUE	0	0.438061880947267	1		523	630	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786708	3786708	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040875-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	99	647	0	ENST00000262367.5:c.4503G>C	p.Glu1501Asp	p.E1501D	ENST00000262367	NM_004380.2	1501	gaG/gaC	27/31	0.235723821731975	1	FACETS	0.447	0.398	0.498	0.447	0.398	0.498	INDETERMINATE	1	TRUE	0	0.438061880947267	1		647	790	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645012	67645012	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040875-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	198	549	0	ENST00000264010.4:c.277A>T	p.Thr93Ser	p.T93S	ENST00000264010	NM_006565.3	93	Acc/Tcc	3/12	0.235723821731975	1	FACETS	0.923	0.857	0.991	0.923	0.857	0.991	INDETERMINATE	1	TRUE	0	0.438061880947267	1		549	765	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175854	24175854	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040875-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	371	653	0	ENST00000263121.7:c.1082T>C	p.Met361Thr	p.M361T	ENST00000263121	NM_003073.3	361	aTg/aCg	8/9	0.438061880947267	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.438061880947267	3		653	1024	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593477	55593477	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040875-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	26	253	0	ENST00000288135.5:c.1634A>G	p.Tyr545Cys	p.Y545C	ENST00000288135	NM_000222.2	545	tAc/tGc	10/21	0.307053830158827	1	FACETS	0.259	0.205	0.321	0.259	0.205	0.321	SUBCLONAL	1	TRUE	0	0.438061880947267	1		253	358	SUCCESS
APC	324	MSKCC	GRCh37	5	112155028	112155028	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040875-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	126	391	0	ENST00000257430.4:c.1299G>T	p.Gln433His	p.Q433H	ENST00000257430	NM_000038.5	433	caG/caT	10/16	0.43215276314792	1	FACETS	0.893	0.813	0.976	0.893	0.813	0.976	CLONAL	1	TRUE	0	0.438061880947267	1		391	503	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694562	176694562	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0040875-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	98	243	0	ENST00000439151.2:c.5147-1G>A		p.X1716_splice	ENST00000439151	NM_022455.4	1716			0.334840866618531	1	FACETS	0.996	0.897	1	0.996	0.897	1	CLONAL	1	TRUE	0	0.438061880947267	1		243	351	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873545	151873545	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040875-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	141	497	0	ENST00000262189.6:c.8993C>A	p.Ser2998Ter	p.S2998*	ENST00000262189	NM_170606.2	2998	tCa/tAa	38/59	0.43215276314792	1	FACETS	0.879	0.804	0.956	0.879	0.804	0.956	CLONAL	1	TRUE	0	0.438061880947267	1		497	572	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56860277	56860278	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AT	novel	NA	P-0040875-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	181	332	0	ENST00000519728.1:c.279_280delinsAT	p.Glu94Ter	p.E94*	ENST00000519728	NM_002350.3	93	ctGGag/ctATag	4/13	0.437252975202162	2	FACETS	0.931	0.868	0.994	0.931	0.868	0.994	CLONAL	2	TRUE	0	0.438061880947267	2		332	444	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223022	53223022	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040875-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	184	377	0	ENST00000375401.3:c.4050A>C	p.Leu1350Phe	p.L1350F	ENST00000375401	NM_004187.3	1350	ttA/ttC	24/26	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.438061880947267	1		377	448	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0040887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	27	214	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.819	0.651	1	0.819	0.651	1	CLONAL	1	TRUE	1	0.14	2		214	471	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0040887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	42	331	0	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.14	2		331	528	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11554273	NA	P-0040887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	38	330	0	ENST00000371085.3:c.601C>A	p.Arg201Ser	p.R201S	ENST00000371085	NM_000516.4	201	Cgt/Agt	8/13	1	2	FACETS	0.923	0.762	1	0.923	0.762	1	CLONAL	1	TRUE	1	0.14	2		330	588	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0040932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	175	488	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.497025121532805	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.497025121532805	1		488	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0040932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	497	785	2	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.497025121532805	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.497025121532805	2		787	932	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332868	152332868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745723014	NA	P-0040932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	151	527	1	ENST00000206249.3:c.1174G>A	p.Val392Ile	p.V392I	ENST00000206249	NM_000125.3	392	Gtc/Atc	5/8	0.497025121532805	1	FACETS	0.921	0.848	0.996	0.921	0.848	0.996	CLONAL	1	TRUE	0	0.497025121532805	1		528	496	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139818342	139818342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs972932325	NA	P-0040932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	156	806	0	ENST00000247668.2:c.1177C>T	p.Arg393Cys	p.R393C	ENST00000247668	NM_021138.3	393	Cgt/Tgt	10/11	0.497025121532805	1	FACETS	0.48	0.439	0.523	0.48	0.439	0.523	SUBCLONAL	1	TRUE	0	0.497025121532805	1		806	983	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663346	227663346	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1024227751	NA	P-0040932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	142	604	0	ENST00000305123.5:c.109G>C	p.Glu37Gln	p.E37Q	ENST00000305123	NM_005544.2	37	Gag/Cag	1/2	1	2	FACETS	0.989	0.905	1	0.989	0.905	1	CLONAL	1	TRUE	1	0.497025121532805	2		604	578	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511760	46511760	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	260	500	0	ENST00000262741.5:c.1017G>C	p.Glu339Asp	p.E339D	ENST00000262741	NM_003629.3	339	gaG/gaC	9/10	0.497025121532805	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.497025121532805	1		500	561	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425051	49425051	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	526	960	0	ENST00000301067.7:c.13437del	p.Ser4480ProfsTer39	p.S4480Pfs*39	ENST00000301067	NM_003482.3	4479	ggG/gg	39/54	0.491727687015346	2	FACETS	0.982	0.945	1	0.982	0.945	1	CLONAL	2	TRUE	0	0.497025121532805	2		960	1078	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221256	36221256	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	262	944	0	ENST00000222270.7:c.5090C>G	p.Pro1697Arg	p.P1697R	ENST00000222270	NM_014727.1	1697	cCc/cGc	24/37	0.309106573279874	2	FACETS	0.911	0.853	0.971	0.456	0.426	0.486	CLONAL	1	TRUE	0	0.497025121532805	2		944	1157	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0040935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	235	367	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.46357411169236	5	FACETS	1	0.982	1			1	CLONAL	4	TRUE	NA	0.495141725438817	5		367	387	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255141	16255142	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0040935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	83	635	2	ENST00000375759.3:c.2417_2418dup	p.Arg807AspfsTer3	p.R807Dfs*3	ENST00000375759	NM_015001.2	802	-/GA	11/15	0.458286782736342	4	FACETS	1	0.931	1	0.536	0.474	0.601	CLONAL	1	TRUE	2	0.495141725438817	4		637	468	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807991	3807991	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	108	628	0	ENST00000262367.5:c.3428A>G	p.Asp1143Gly	p.D1143G	ENST00000262367	NM_004380.2	1143	gAc/gGc	18/31	0.495141725438817	3	FACETS	1	0.948	1	0.54	0.487	0.596	CLONAL	1	TRUE	1	0.495141725438817	3		628	504	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682204	37682204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	205	763	0	ENST00000447079.4:c.3395C>T	p.Pro1132Leu	p.P1132L	ENST00000447079	NM_015083.1	1132	cCt/cTt	13/14	0.447922515115946	4	FACETS	1	0.988	1	0.666	0.618	0.716	CLONAL	1	TRUE	2	0.495141725438817	4		763	929	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610176	81610176	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	65	531	1	ENST00000298171.2:c.1774G>T	p.Val592Phe	p.V592F	ENST00000298171	NM_000369.2	592	Gtt/Ttt	10/10	0.495141725438817	6	FACETS	0.968	0.84	1	0.242	0.21	0.277	CLONAL	1	TRUE	2	0.495141725438817	6		532	540	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878113	151878113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764593264	NA	P-0040935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	122	614	0	ENST00000262189.6:c.6832C>T	p.Pro2278Ser	p.P2278S	ENST00000262189	NM_170606.2	2278	Ccc/Tcc	36/59	0.492569559965661	3	FACETS	0.757	0.69	0.826	0.505	0.46	0.551	SUBCLONAL	2	TRUE	0	0.495141725438817	3		614	406	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428415	47428415	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1183909266	NA	P-0040935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	350	810	1	ENST00000377045.4:c.1283G>T	p.Arg428Leu	p.R428L	ENST00000377045	NM_001654.4	428	cGa/cTa	12/16	0.472489964409008	4	FACETS	1	0.992	1			1	CLONAL	3	TRUE	NA	0.495141725438817	4		811	612	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	220	395	1				ENST00000310581	NM_198253.2	-/1132			0.91458587525827	3	FACETS	0.962	0.898	1	0.481	0.449	0.514	CLONAL	1	TRUE	1	0.91458587525827	3		396	729	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775767	9775767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1315288471	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	600	826	1	ENST00000377346.4:c.310C>T	p.Arg104Cys	p.R104C	ENST00000377346	NM_005026.3	104	Cgt/Tgt	4/24	NA	2	FACETS	1	0.997	1			1	INDETERMINATE	1	TRUE	NA	0.91458587525827	2		827	1032	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056253	27056255	+	frameshift_variant	Frame_Shift_Del	DEL	TAC	TAC	CA	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	327	680	0	ENST00000324856.7:c.1249_1251delinsCA	p.Tyr417HisfsTer16	p.Y417Hfs*16	ENST00000324856	NM_006015.4	417	TAC/CA	2/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.91458587525827	2		680	639	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088691	27088691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	401	829	0	ENST00000324856.7:c.2300C>T	p.Pro767Leu	p.P767L	ENST00000324856	NM_006015.4	767	cCc/cTc	7/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.91458587525827	2		829	870	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088783	27088783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	330	634	0	ENST00000324856.7:c.2392C>T	p.Pro798Ser	p.P798S	ENST00000324856	NM_006015.4	798	Ccc/Tcc	7/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.91458587525827	2		634	684	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982365	201982366	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	412	860	2	ENST00000359651.3:c.744_745delinsTT	p.Arg249Trp	p.R249W	ENST00000359651		248	ggCCgg/ggTTgg	6/8	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.91458587525827	2		862	899	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650117	206650117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	383	785	0	ENST00000367120.3:c.637C>T	p.His213Tyr	p.H213Y	ENST00000367120	NM_014002.3	213	Cat/Tat	7/22	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.91458587525827	2		785	823	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549725	226549725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1191796720	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	356	618	0	ENST00000366794.5:c.2908C>T	p.Pro970Ser	p.P970S	ENST00000366794	NM_001618.3	970	Cct/Tct	22/23	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.91458587525827	2		618	739	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612087	43612087	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	280	656	0	ENST00000355710.3:c.2192G>A	p.Gly731Glu	p.G731E	ENST00000355710	NM_020975.4	731	gGa/gAa	12/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.91458587525827	2		656	601	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518550	69518550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	315	619	0	ENST00000294312.3:c.95C>T	p.Pro32Leu	p.P32L	ENST00000294312	NM_005117.2	32	cCc/cTc	1/3	0.590582505774443	1	FACETS	0.795	0.764	0.826	0.795	0.764	0.826	SUBCLONAL	1	TRUE	0	0.91458587525827	1		619	470	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625236	69625236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	171	825	0	ENST00000334134.2:c.557G>A	p.Arg186Lys	p.R186K	ENST00000334134	NM_005247.2	186	aGg/aAg	3/3	0.590582505774443	1	FACETS	0.365	0.338	0.393	0.365	0.338	0.393	SUBCLONAL	1	TRUE	0	0.91458587525827	1		825	556	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912831	100912831	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	109	401	0	ENST00000325455.5:c.2491C>T	p.Pro831Ser	p.P831S	ENST00000325455	NM_001202474.3	831	Cct/Tct	7/8	0.590582505774443	1	FACETS	0.322	0.291	0.354	0.322	0.291	0.354	SUBCLONAL	1	TRUE	0	0.91458587525827	1		401	402	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999386	100999386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1450269762	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	379	947	0	ENST00000325455.5:c.416C>T	p.Ser139Phe	p.S139F	ENST00000325455	NM_001202474.3	139	tCt/tTt	1/8	0.590582505774443	1	FACETS	0.698	0.671	0.726	0.698	0.671	0.726	SUBCLONAL	1	TRUE	0	0.91458587525827	1		947	644	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307348	118307348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1224934712	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	10	23	0	ENST00000534358.1:c.121C>T	p.Pro41Ser	p.P41S	ENST00000534358	NM_005933.3	41	Ccc/Tcc	1/36	0.590582505774443	1	FACETS	0.424	0.304	0.555	0.424	0.304	0.555	SUBCLONAL	1	TRUE	0	0.91458587525827	1		23	28	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344269	118344269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	288	558	0	ENST00000534358.1:c.2395C>T	p.Pro799Ser	p.P799S	ENST00000534358	NM_005933.3	799	Cct/Tct	3/36	0.590582505774443	1	FACETS	0.743	0.711	0.775	0.743	0.711	0.775	SUBCLONAL	1	TRUE	0	0.91458587525827	1		558	460	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856398	111856398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769643863	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	167	243	0	ENST00000341259.2:c.449C>T	p.Ser150Leu	p.S150L	ENST00000341259	NM_005475.2	150	tCg/tTg	2/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.91458587525827	2		243	325	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114201	115114201	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	354	759	0	ENST00000257566.3:c.1016C>A	p.Ser339Tyr	p.S339Y	ENST00000257566	NM_016569.3	339	tCc/tAc	6/8	1	2	FACETS	0.96	0.915	1	0.96	0.915	1	CLONAL	1	TRUE	1	0.91458587525827	2		759	806	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432029	121432029	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	360	955	0	ENST00000257555.6:c.776T>G	p.Val259Gly	p.V259G	ENST00000257555		259	gTc/gGc	4/10	1	2	FACETS	0.943	0.898	0.988	0.943	0.898	0.988	CLONAL	1	TRUE	1	0.91458587525827	2		955	835	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123880939	123880939	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1328563147	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	231	490	0	ENST00000330479.4:c.557C>T	p.Pro186Leu	p.P186L	ENST00000330479	NM_020382.3	186	cCt/cTt	5/9	1	2	FACETS	0.875	0.823	0.929	0.875	0.823	0.929	CLONAL	1	TRUE	1	0.91458587525827	2		490	577	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557874	21557874	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	292	676	0	ENST00000382592.4:c.1971G>C	p.Arg657Ser	p.R657S	ENST00000382592	NM_014572.2	657	agG/agC	5/8	1	2	FACETS	0.871	0.824	0.918	0.871	0.824	0.918	CLONAL	1	TRUE	1	0.91458587525827	2		676	733	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562913	21562913	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	353	821	0	ENST00000382592.4:c.1006C>T	p.Gln336Ter	p.Q336*	ENST00000382592	NM_014572.2	336	Cag/Tag	4/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.91458587525827	2		821	746	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588650	28588650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	241	515	1	ENST00000241453.7:c.2798G>A	p.Arg933Gln	p.R933Q	ENST00000241453	NM_004119.2	933	cGg/cAg	23/24	1	2	FACETS	0.861	0.81	0.913	0.861	0.81	0.913	CLONAL	1	TRUE	1	0.91458587525827	2		516	612	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608527	28608527	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	315	601	0	ENST00000241453.7:c.1615C>T	p.Gln539Ter	p.Q539*	ENST00000241453	NM_004119.2	539	Caa/Taa	13/24	1	2	FACETS	0.976	0.927	1	0.976	0.927	1	CLONAL	1	TRUE	1	0.91458587525827	2		601	706	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001422	29001422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752383804	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	227	397	1	ENST00000282397.4:c.1310C>T	p.Ser437Leu	p.S437L	ENST00000282397	NM_002019.4	437	tCg/tTg	10/30	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.91458587525827	2		398	475	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32905080	32905080	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1359997059	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	185	326	0	ENST00000380152.3:c.706C>T	p.His236Tyr	p.H236Y	ENST00000380152		236	Cat/Tat	9/27	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.91458587525827	2		326	374	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915102	32915102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	313	583	0	ENST00000380152.3:c.6610C>T	p.Pro2204Ser	p.P2204S	ENST00000380152		2204	Cct/Tct	11/27	1	2	FACETS	0.971	0.922	1	0.971	0.922	1	CLONAL	1	TRUE	1	0.91458587525827	2		583	705	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134184	41134184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	221	457	0	ENST00000379561.5:c.1444C>T	p.Pro482Ser	p.P482S	ENST00000379561	NM_002015.3	482	Cct/Tct	2/3	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.91458587525827	2		457	435	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986517	36986517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	353	650	1	ENST00000354822.5:c.1172C>T	p.Ser391Phe	p.S391F	ENST00000354822	NM_001079668.2	391	tCc/tTc	3/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.91458587525827	2		651	737	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591683	38591683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	316	591	0	ENST00000299084.4:c.142C>T	p.Pro48Ser	p.P48S	ENST00000299084	NM_152594.2	48	Cct/Tct	2/7	1	2	FACETS	0.948	0.9	0.996	0.948	0.9	0.996	CLONAL	1	TRUE	1	0.91458587525827	2		591	729	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	507	688	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.91458587525827	2		688	1006	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	480	1107	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.91458587525827	2		1107	1047	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472644	88472644	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	169	435	0	ENST00000360948.2:c.1911G>A	p.Met637Ile	p.M637I	ENST00000360948	NM_001012338.2	637	atG/atA	16/19	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.91458587525827	2		435	365	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633219	3633219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	443	982	1	ENST00000294008.3:c.5032C>T	p.Pro1678Ser	p.P1678S	ENST00000294008	NM_032444.2	1678	Cca/Tca	14/15	1	2	FACETS	0.995	0.953	1	0.995	0.953	1	CLONAL	1	TRUE	1	0.91458587525827	2		983	974	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640275	3640275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	519	1004	1	ENST00000294008.3:c.3364C>T	p.Pro1122Ser	p.P1122S	ENST00000294008	NM_032444.2	1122	Ccg/Tcg	12/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.91458587525827	2		1005	1098	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857047	9857047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568622613	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	171	334	0	ENST00000330684.3:c.4354C>T	p.Arg1452Cys	p.R1452C	ENST00000330684	NM_001134407.1	1452	Cgc/Tgc	13/13	1	2	FACETS	0.976	0.911	1	0.976	0.911	1	CLONAL	1	TRUE	1	0.91458587525827	2		334	383	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857956	9857956	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	309	696	1	ENST00000330684.3:c.3445G>A	p.Asp1149Asn	p.D1149N	ENST00000330684	NM_001134407.1	1149	Gac/Aac	13/13	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.91458587525827	2		697	646	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858484	9858484	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	274	653	1	ENST00000330684.3:c.2917G>A	p.Asp973Asn	p.D973N	ENST00000330684	NM_001134407.1	973	Gat/Aat	13/13	1	2	FACETS	0.97	0.918	1	0.97	0.918	1	CLONAL	1	TRUE	1	0.91458587525827	2		654	618	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858730	9858730	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	208	413	0	ENST00000330684.3:c.2671C>A	p.Gln891Lys	p.Q891K	ENST00000330684	NM_001134407.1	891	Cag/Aag	13/13	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.91458587525827	2		413	444	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916121	9916121	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	207	522	0	ENST00000330684.3:c.2168G>A	p.Gly723Glu	p.G723E	ENST00000330684	NM_001134407.1	723	gGg/gAg	10/13	1	2	FACETS	0.967	0.908	1	0.967	0.908	1	CLONAL	1	TRUE	1	0.91458587525827	2		522	468	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943662	9943662	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560839364	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	328	746	0	ENST00000330684.3:c.1279G>A	p.Glu427Lys	p.E427K	ENST00000330684	NM_001134407.1	427	Gag/Aag	5/13	1	2	FACETS	0.989	0.941	1	0.989	0.941	1	CLONAL	1	TRUE	1	0.91458587525827	2		746	725	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943704	9943704	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866275641	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	314	748	0	ENST00000330684.3:c.1237G>A	p.Glu413Lys	p.E413K	ENST00000330684	NM_001134407.1	413	Gag/Aag	5/13	1	2	FACETS	0.984	0.935	1	0.984	0.935	1	CLONAL	1	TRUE	1	0.91458587525827	2		748	698	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032006	10032006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	354	765	0	ENST00000330684.3:c.817C>T	p.Pro273Ser	p.P273S	ENST00000330684	NM_001134407.1	273	Cca/Tca	3/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.91458587525827	2		765	729	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274177	10274177	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	196	609	0	ENST00000330684.3:c.92C>T	p.Pro31Leu	p.P31L	ENST00000330684	NM_001134407.1	31	cCc/cTc	2/13	1	2	FACETS	0.963	0.902	1	0.963	0.902	1	CLONAL	1	TRUE	1	0.91458587525827	2		609	445	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634329	23634329	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	365	650	0	ENST00000261584.4:c.2957A>C	p.Asp986Ala	p.D986A	ENST00000261584	NM_024675.3	986	gAt/gCt	9/13	1	2	FACETS	0.929	0.885	0.973	0.929	0.885	0.973	CLONAL	1	TRUE	1	0.91458587525827	2		650	859	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845591	72845591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	397	830	0	ENST00000268489.5:c.3749C>T	p.Pro1250Leu	p.P1250L	ENST00000268489	NM_006885.3	1250	cCc/cTc	7/10	1	2	FACETS	0.997	0.953	1	0.997	0.953	1	CLONAL	1	TRUE	1	0.91458587525827	2		830	871	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993158	72993158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1332687082	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	487	861	2	ENST00000268489.5:c.887C>T	p.Ser296Leu	p.S296L	ENST00000268489	NM_006885.3	296	tCg/tTg	2/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.91458587525827	2		863	1061	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578289	7578290	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	259	735	1	ENST00000269305.4:c.560-1_560delinsAA		p.X187_splice	ENST00000269305	NM_001126112.2	187		6/11	0.91458587525827	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.91458587525827	1		736	297	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976105	7976105	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	370	757	0	ENST00000319144.4:c.2090A>G	p.Asn697Ser	p.N697S	ENST00000319144	NM_001139.2	697	aAc/aGc	15/15	0.91458587525827	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.91458587525827	1		757	419	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560043	29560043	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs868450405	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	195	368	0	ENST00000356175.3:c.3520C>T	p.Gln1174Ter	p.Q1174*	ENST00000356175	NM_000267.3	1174	Cag/Tag	27/57	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.91458587525827	2		368	393	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654691	29654691	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	230	425	0	ENST00000356175.3:c.5380C>T	p.Gln1794Ter	p.Q1794*	ENST00000356175	NM_000267.3	1794	Cag/Tag	37/57	1	2	FACETS	0.975	0.918	1	0.975	0.918	1	CLONAL	1	TRUE	1	0.91458587525827	2		425	516	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684350	29684350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	294	607	0	ENST00000356175.3:c.7870G>A	p.Glu2624Lys	p.E2624K	ENST00000356175	NM_000267.3	2624	Gag/Aag	53/57	1	2	FACETS	0.936	0.887	0.985	0.936	0.887	0.985	CLONAL	1	TRUE	1	0.91458587525827	2		607	687	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37863275	37863275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	338	775	0	ENST00000269571.5:c.106C>T	p.Pro36Ser	p.P36S	ENST00000269571		36	Cct/Tct	2/27	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.91458587525827	2		775	712	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40854926	40854926	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	341	626	0	ENST00000428826.2:c.2152C>T	p.Gln718Ter	p.Q718*	ENST00000428826		718	Caa/Taa	20/21	1	2	FACETS	0.984	0.937	1	0.984	0.937	1	CLONAL	1	TRUE	1	0.91458587525827	2		626	758	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858062	40858062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	386	763	0	ENST00000428826.2:c.1802C>T	p.Ser601Phe	p.S601F	ENST00000428826		601	tCc/tTc	16/21	1	2	FACETS	0.993	0.949	1	0.993	0.949	1	CLONAL	1	TRUE	1	0.91458587525827	2		763	850	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435092	56435092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	351	868	1	ENST00000407977.2:c.2045C>T	p.Pro682Leu	p.P682L	ENST00000407977		682	cCc/cTc	9/10	1	2	FACETS	0.999	0.953	1	0.999	0.953	1	CLONAL	1	TRUE	1	0.91458587525827	2		869	768	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78854287	78854287	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	272	530	1	ENST00000306801.3:c.1582C>T	p.Pro528Ser	p.P528S	ENST00000306801	NM_020761.2	528	Cca/Tca	14/34	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.91458587525827	2		531	566	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591862	48591862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	126	536	0	ENST00000342988.3:c.1025C>T	p.Pro342Leu	p.P342L	ENST00000342988	NM_005359.5	342	cCt/cTt	9/12	0.72820404767776	1	FACETS	0.374	0.341	0.407	0.374	0.341	0.407	SUBCLONAL	1	TRUE	0	0.91458587525827	1		536	400	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611833	1611833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770019485	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	329	762	1	ENST00000344749.5:c.1829C>T	p.Pro610Leu	p.P610L	ENST00000344749	NM_001136139.2	610	cCc/cTc	19/19	1	2	FACETS	0.988	0.94	1	0.988	0.94	1	CLONAL	1	TRUE	1	0.91458587525827	2		763	728	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267901	7267901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	165	377	0	ENST00000302850.5:c.107C>T	p.Pro36Leu	p.P36L	ENST00000302850	NM_000208.2	36	cCc/cTc	2/22	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.91458587525827	2		377	356	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271945	15271945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	334	899	2	ENST00000263388.2:c.6494C>T	p.Pro2165Leu	p.P2165L	ENST00000263388	NM_000435.2	2165	cCt/cTt	33/33	1	2	FACETS	0.967	0.921	1	0.967	0.921	1	CLONAL	1	TRUE	1	0.91458587525827	2		901	755	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353948	15353948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	181	346	0	ENST00000263377.2:c.2932C>T	p.Pro978Ser	p.P978S	ENST00000263377	NM_058243.2	978	Cca/Tca	14/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.91458587525827	2		346	331	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955183	17955183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1457535594	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	413	883	1	ENST00000458235.1:c.44C>T	p.Ser15Leu	p.S15L	ENST00000458235	NM_000215.3	15	tCa/tTa	2/24	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.91458587525827	2		884	896	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214660	36214660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	353	796	1	ENST00000222270.7:c.3086C>T	p.Pro1029Leu	p.P1029L	ENST00000222270	NM_014727.1	1029	cCc/cTc	8/37	1	2	FACETS	0.99	0.943	1	0.99	0.943	1	CLONAL	1	TRUE	1	0.91458587525827	2		797	780	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216515	36216515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372953726	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	436	923	0	ENST00000222270.7:c.3778C>T	p.Arg1260Cys	p.R1260C	ENST00000222270	NM_014727.1	1260	Cgt/Tgt	12/37	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.91458587525827	2		923	937	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228800	36228800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393734909	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	380	845	1	ENST00000222270.7:c.7699C>T	p.Arg2567Cys	p.R2567C	ENST00000222270	NM_014727.1	2567	Cgt/Tgt	35/37	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.91458587525827	2		846	827	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752973	42752973	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	374	887	0	ENST00000222329.4:c.1291del	p.Ser431ArgfsTer8	p.S431Rfs*8	ENST00000222329	NM_006494.2	431	Tcg/cg	4/4	1	2	FACETS	0.963	0.919	1	0.963	0.919	1	CLONAL	1	TRUE	1	0.91458587525827	2		887	849	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752973	42752975	+	frameshift_variant	Frame_Shift_Del	DEL	AGA	AGA	GG	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	381	891	2	ENST00000222329.4:c.1289_1291delinsCC	p.Ile430ThrfsTer9	p.I430Tfs*9	ENST00000222329	NM_006494.2	430	aTCTcg/aCCcg	4/4	1	2	FACETS	0.97	0.926	1	0.97	0.926	1	CLONAL	1	TRUE	1	0.91458587525827	2		893	859	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966694	25966694	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	307	687	0	ENST00000435504.4:c.2512C>T	p.Pro838Ser	p.P838S	ENST00000435504		838	Cct/Tct	13/13	1	2	FACETS	0.963	0.914	1	0.963	0.914	1	CLONAL	1	TRUE	1	0.91458587525827	2		687	697	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015052	27015052	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs776697460	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	276	558	0	ENST00000335756.4:c.154C>T	p.Arg52Ter	p.R52*	ENST00000335756	NM_001809.3	52	Cga/Tga	2/5	1	2	FACETS	0.983	0.931	1	0.983	0.931	1	CLONAL	1	TRUE	1	0.91458587525827	2		558	614	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169254	99169254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	257	499	0	ENST00000074304.5:c.1184C>T	p.Ser395Leu	p.S395L	ENST00000074304	NM_001134224.1	395	tCa/tTa	15/26	1	2	FACETS	0.964	0.911	1	0.964	0.911	1	CLONAL	1	TRUE	1	0.91458587525827	2		499	583	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128029031	128029031	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	211	398	0	ENST00000285398.2:c.1828-2A>G		p.X610_splice	ENST00000285398	NM_000122.1	610			1	2	FACETS	0.949	0.891	1	0.949	0.891	1	CLONAL	1	TRUE	1	0.91458587525827	2		398	486	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044362	128044362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	351	696	0	ENST00000285398.2:c.1259C>T	p.Ser420Phe	p.S420F	ENST00000285398	NM_000122.1	420	tCc/tTc	8/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.91458587525827	2		696	742	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537981	212537981	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs535202189	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	210	405	0	ENST00000342788.4:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000342788	NM_005235.2	542	Gaa/Aaa	14/28	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.91458587525827	2		405	457	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793311	242793311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1021665035	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	371	906	0	ENST00000334409.5:c.766G>A	p.Gly256Arg	p.G256R	ENST00000334409	NM_005018.2	256	Gga/Aga	5/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.91458587525827	2		906	784	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523329	9523329	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867092977	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	251	555	0	ENST00000353224.5:c.1908G>A	p.Met636Ile	p.M636I	ENST00000353224	NM_177990.2	636	atG/atA	9/10	1	2	FACETS	0.95	0.896	1	0.95	0.896	1	CLONAL	1	TRUE	1	0.91458587525827	2		555	578	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525080	9525080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	275	585	0	ENST00000353224.5:c.1805C>T	p.Ser602Leu	p.S602L	ENST00000353224	NM_177990.2	602	tCa/tTa	8/10	1	2	FACETS	0.953	0.902	1	0.953	0.902	1	CLONAL	1	TRUE	1	0.91458587525827	2		585	631	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546734	9546734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	180	482	0	ENST00000353224.5:c.1288G>A	p.Glu430Lys	p.E430K	ENST00000353224	NM_177990.2	430	Gaa/Aaa	5/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.91458587525827	2		482	366	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546962	9546963	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	152	479	3	ENST00000353224.5:c.1059_1060delinsTT	p.Pro354Ser	p.P354S	ENST00000353224	NM_177990.2	353	ggCCct/ggTTct	5/10	1	2	FACETS	0.829	0.767	0.892	0.829	0.767	0.892	CLONAL	1	TRUE	1	0.91458587525827	2		482	401	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561184	9561184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	249	561	0	ENST00000353224.5:c.598C>T	p.His200Tyr	p.H200Y	ENST00000353224	NM_177990.2	200	Cac/Tac	4/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.91458587525827	2		561	532	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561520	9561520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	280	639	0	ENST00000353224.5:c.262G>A	p.Asp88Asn	p.D88N	ENST00000353224	NM_177990.2	88	Gat/Aat	4/10	1	2	FACETS	0.925	0.875	0.975	0.925	0.875	0.975	CLONAL	1	TRUE	1	0.91458587525827	2		639	662	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40709551	40709551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568484928	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	262	457	0	ENST00000373198.4:c.4351G>A	p.Glu1451Lys	p.E1451K	ENST00000373198	NM_133170.3	1451	Gag/Aag	32/32	1	2	FACETS	0.988	0.934	1	0.988	0.934	1	CLONAL	1	TRUE	1	0.91458587525827	2		457	580	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713382	40713382	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770379585	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	370	787	1	ENST00000373198.4:c.4133G>A	p.Arg1378Gln	p.R1378Q	ENST00000373198	NM_133170.3	1378	cGa/cAa	30/32	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.91458587525827	2		788	778	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713470	40713470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318044562	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	332	754	2	ENST00000373198.4:c.4045C>T	p.Arg1349Cys	p.R1349C	ENST00000373198	NM_133170.3	1349	Cgt/Tgt	30/32	1	2	FACETS	0.989	0.941	1	0.989	0.941	1	CLONAL	1	TRUE	1	0.91458587525827	2		756	734	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739013	40739013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	326	708	0	ENST00000373198.4:c.3271C>T	p.Leu1091Phe	p.L1091F	ENST00000373198	NM_133170.3	1091	Ctc/Ttc	24/32	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.91458587525827	2		708	671	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101158	41101158	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	305	746	0	ENST00000373198.4:c.1198G>A	p.Ala400Thr	p.A400T	ENST00000373198	NM_133170.3	400	Gcc/Acc	8/32	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.91458587525827	2		746	640	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385263	41385263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	279	628	0	ENST00000373198.4:c.698G>A	p.Arg233Lys	p.R233K	ENST00000373198	NM_133170.3	233	aGg/aAg	6/32	1	2	FACETS	0.942	0.891	0.992	0.942	0.891	0.992	CLONAL	1	TRUE	1	0.91458587525827	2		628	648	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46252678	46252678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762389152	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	202	362	0	ENST00000371998.3:c.107G>A	p.Arg36Gln	p.R36Q	ENST00000371998		36	cGg/cAg	4/23	1	2	FACETS	0.956	0.897	1	0.956	0.897	1	CLONAL	1	TRUE	1	0.91458587525827	2		362	462	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39762962	39762962	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	221	481	0	ENST00000288319.7:c.874C>T	p.Pro292Ser	p.P292S	ENST00000288319	NM_182918.3	292	Cct/Tct	9/10	1	2	FACETS	0.908	0.853	0.964	0.908	0.853	0.964	CLONAL	1	TRUE	1	0.91458587525827	2		481	532	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42843792	42843792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1242962903	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	325	588	0	ENST00000398585.3:c.1127C>T	p.Ser376Phe	p.S376F	ENST00000398585	NM_001135099.1	376	tCc/tTc	10/14	1	2	FACETS	0.991	0.943	1	0.991	0.943	1	CLONAL	1	TRUE	1	0.91458587525827	2		588	717	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845417	42845417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	267	624	0	ENST00000398585.3:c.845G>A	p.Gly282Glu	p.G282E	ENST00000398585	NM_001135099.1	282	gGg/gAg	9/14	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.91458587525827	2		624	560	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691762	30691762	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs1215812419	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	183	437	0	ENST00000295754.5:c.264G>A	p.Trp88Ter	p.W88*	ENST00000295754	NM_003242.5	88	tgG/tgA	3/7	1	2	FACETS	0.889	0.83	0.95	0.889	0.83	0.95	CLONAL	1	TRUE	1	0.91458587525827	2		437	450	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729980	30729981	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	264	527	1	ENST00000295754.5:c.1501_1502delinsTT	p.Pro501Phe	p.P501F	ENST00000295754	NM_003242.5	501	CCc/TTc	6/7	1	2	FACETS	0.954	0.902	1	0.954	0.902	1	CLONAL	1	TRUE	1	0.91458587525827	2		528	605	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067143	37067143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1162924533	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	104	281	0	ENST00000231790.2:c.1054C>T	p.Leu352Phe	p.L352F	ENST00000231790	NM_000249.3	352	Ctt/Ttt	12/19	1	2	FACETS	0.812	0.738	0.888	0.812	0.738	0.888	CLONAL	1	TRUE	1	0.91458587525827	2		281	280	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155462	47155462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	271	451	0	ENST00000409792.3:c.4619C>T	p.Ser1540Phe	p.S1540F	ENST00000409792	NM_014159.6	1540	tCc/tTc	5/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.91458587525827	2		451	575	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162099	47162099	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	209	444	0	ENST00000409792.3:c.4027C>T	p.Gln1343Ter	p.Q1343*	ENST00000409792	NM_014159.6	1343	Caa/Taa	3/21	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.91458587525827	2		444	452	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722761	49722761	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs62262682	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	18	40	2	ENST00000449682.2:c.1478G>T	p.Arg493Leu	p.R493L	ENST00000449682	NM_020998.3	493	cGt/cTt	13/18	1	2	FACETS	0.635	0.493	0.79	0.635	0.493	0.79	SUBCLONAL	1	TRUE	1	0.91458587525827	2		42	62	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71064722	71064722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866245092	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	237	507	0	ENST00000318789.4:c.952G>A	p.Glu318Lys	p.E318K	ENST00000318789	NM_032682.5	318	Gaa/Aaa	12/21	1	2	FACETS	0.859	0.808	0.912	0.859	0.808	0.912	CLONAL	1	TRUE	1	0.91458587525827	2		507	603	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204771	128204771	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	459	940	0	ENST00000341105.2:c.670G>A	p.Glu224Lys	p.E224K	ENST00000341105	NM_032638.4	224	Gaa/Aaa	3/6	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.91458587525827	2		940	994	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185169106	185169106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775670152	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	352	571	1	ENST00000265026.3:c.1201C>T	p.Arg401Trp	p.R401W	ENST00000265026	NM_004721.4	401	Cgg/Tgg	7/14	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.91458587525827	2		572	750	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447162	187447163	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	261	738	1	ENST00000232014.4:c.1030_1031delinsTT	p.Pro344Phe	p.P344F	ENST00000232014	NM_001130845.1	344	CCc/TTc	5/10	1	2	FACETS	0.863	0.814	0.913	0.863	0.814	0.913	CLONAL	1	TRUE	1	0.91458587525827	2		739	661	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608604	189608604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	306	643	1	ENST00000264731.3:c.1679C>T	p.Ser560Leu	p.S560L	ENST00000264731	NM_003722.4	560	tCa/tTa	13/14	1	2	FACETS	0.983	0.933	1	0.983	0.933	1	CLONAL	1	TRUE	1	0.91458587525827	2		644	681	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808942	1808942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376043260	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	338	750	0	ENST00000260795.2:c.2374G>A	p.Asp792Asn	p.D792N	ENST00000260795		792	Gac/Aac	17/17	1	2	FACETS	0.951	0.905	0.998	0.951	0.905	0.998	CLONAL	1	TRUE	1	0.91458587525827	2		750	777	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594198	55594198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766264502	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	221	468	1	ENST00000288135.5:c.1901G>A	p.Arg634Gln	p.R634Q	ENST00000288135	NM_000222.2	634	cGg/cAg	13/21	0.91458587525827	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.91458587525827	1		469	248	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964962	55964962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	196	321	0	ENST00000263923.4:c.2275G>A	p.Glu759Lys	p.E759K	ENST00000263923	NM_002253.2	759	Gaa/Aaa	16/30	0.91458587525827	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.91458587525827	1		321	225	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157539	106157539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs192553789	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	198	402	0	ENST00000380013.4:c.2440C>T	p.Arg814Cys	p.R814C	ENST00000380013	NM_001127208.2	814	Cgt/Tgt	3/11	0.91458587525827	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.91458587525827	1		402	221	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530432	187530432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	177	399	0	ENST00000441802.2:c.10111C>T	p.His3371Tyr	p.H3371Y	ENST00000441802	NM_005245.3	3371	Cac/Tac	16/27	0.91458587525827	1	FACETS	0.996	0.958	1	0.996	0.958	1	CLONAL	1	TRUE	0	0.91458587525827	1		399	211	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861085	35861085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	185	424	0	ENST00000303115.3:c.214G>A	p.Glu72Lys	p.E72K	ENST00000303115	NM_002185.3	72	Gaa/Aaa	2/8	0.91458587525827	3	FACETS	1	0.956	1	0.52	0.483	0.558	CLONAL	1	TRUE	1	0.91458587525827	3		424	567	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876121	35876121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	242	516	0	ENST00000303115.3:c.913G>A	p.Asp305Asn	p.D305N	ENST00000303115	NM_002185.3	305	Gac/Aac	8/8	0.91458587525827	3	FACETS	0.942	0.882	1	0.471	0.441	0.502	CLONAL	1	TRUE	1	0.91458587525827	3		516	819	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876352	35876352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	247	642	1	ENST00000303115.3:c.1144C>T	p.Leu382Phe	p.L382F	ENST00000303115	NM_002185.3	382	Ctc/Ttc	8/8	0.91458587525827	3	FACETS	0.924	0.866	0.983	0.462	0.433	0.492	CLONAL	1	TRUE	1	0.91458587525827	3		643	852	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950588	38950588	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	252	555	0	ENST00000357387.3:c.3362C>T	p.Ser1121Leu	p.S1121L	ENST00000357387	NM_152756.3	1121	tCa/tTa	31/38	0.91458587525827	3	FACETS	0.937	0.879	0.997	0.469	0.439	0.499	CLONAL	1	TRUE	1	0.91458587525827	3		555	857	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950622	38950622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748585755	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	248	517	0	ENST00000357387.3:c.3328C>T	p.Arg1110Cys	p.R1110C	ENST00000357387	NM_152756.3	1110	Cgt/Tgt	31/38	0.91458587525827	3	FACETS	0.951	0.892	1	0.476	0.446	0.506	CLONAL	1	TRUE	1	0.91458587525827	3		517	831	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515442	149515442	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	310	612	0	ENST00000261799.4:c.41-1G>A		p.X14_splice	ENST00000261799	NM_002609.3	14			1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.91458587525827	2		612	611	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524565	176524565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	389	987	1	ENST00000292408.4:c.2297C>T	p.Pro766Leu	p.P766L	ENST00000292408	NM_213647.1	766	cCc/cTc	18/18	1	2	FACETS	0.948	0.905	0.992	0.948	0.905	0.992	CLONAL	1	TRUE	1	0.91458587525827	2		988	897	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524585	176524585	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	392	966	0	ENST00000292408.4:c.2317A>C	p.Ser773Arg	p.S773R	ENST00000292408	NM_213647.1	773	Agc/Cgc	18/18	1	2	FACETS	0.962	0.919	1	0.962	0.919	1	CLONAL	1	TRUE	1	0.91458587525827	2		966	891	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057557	180057557	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	321	675	0	ENST00000261937.6:c.398G>A	p.Arg133Lys	p.R133K	ENST00000261937	NM_182925.4	133	aGa/aAa	3/30	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.91458587525827	2		675	663	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401626	401627	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	280	701	1	ENST00000380956.4:c.948_949delinsTT	p.Leu317Phe	p.L317F	ENST00000380956	NM_001195286.1	316	gtCCtc/gtTTtc	7/9	0.313555092656337	3	FACETS	1	0.988	1	0.391	0.369	0.413	INDETERMINATE	1	TRUE	0	0.91458587525827	3		702	761	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158419	26158419	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	327	822	0	ENST00000289316.2:c.22G>A	p.Ala8Thr	p.A8T	ENST00000289316	NM_138720.2	8	Gct/Act	1/2	0.313555092656337	3	FACETS	0.836	0.79	0.884	0.279	0.263	0.295	INDETERMINATE	1	TRUE	0	0.91458587525827	3		822	1246	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163452	32163452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	279	856	0	ENST00000375023.3:c.5774C>T	p.Pro1925Leu	p.P1925L	ENST00000375023	NM_004557.3	1925	cCc/cTc	30/30	0.313555092656337	3	FACETS	0.886	0.834	0.941	0.295	0.278	0.314	INDETERMINATE	1	TRUE	0	0.91458587525827	3		856	1003	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166207	32166207	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761193848	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	267	741	0	ENST00000375023.3:c.4747C>T	p.Arg1583Cys	p.R1583C	ENST00000375023	NM_004557.3	1583	Cgt/Tgt	26/30	0.313555092656337	3	FACETS	0.831	0.78	0.884	0.277	0.26	0.295	INDETERMINATE	1	TRUE	0	0.91458587525827	3		741	1024	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170241	32170241	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	316	824	2	ENST00000375023.3:c.3367C>T	p.Pro1123Ser	p.P1123S	ENST00000375023	NM_004557.3	1123	Cct/Tct	21/30	0.313555092656337	3	FACETS	1	0.958	1	0.338	0.32	0.358	INDETERMINATE	1	TRUE	0	0.91458587525827	3		826	992	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974346	93974346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762911058	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	233	470	0	ENST00000369303.4:c.1708G>A	p.Val570Met	p.V570M	ENST00000369303	NM_004440.3	570	Gtg/Atg	8/17	0.91458587525827	1	FACETS	0.984	0.951	1	0.984	0.951	1	CLONAL	1	TRUE	0	0.91458587525827	1		470	281	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106543568	106543568	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	192	361	0	ENST00000369096.4:c.370G>A	p.Asp124Asn	p.D124N	ENST00000369096	NM_001198.3	124	Gac/Aac	3/7	0.91458587525827	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.91458587525827	1		361	222	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609831	117609831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	329	666	0	ENST00000368508.3:c.6868G>A	p.Gly2290Ser	p.G2290S	ENST00000368508	NM_002944.2	2290	Ggt/Agt	43/43	0.91458587525827	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.91458587525827	1		666	385	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686860	117686860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	236	476	0	ENST00000368508.3:c.2857G>A	p.Glu953Lys	p.E953K	ENST00000368508	NM_002944.2	953	Gag/Aag	19/43	0.91458587525827	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.91458587525827	1		476	276	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163748	152163748	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs104893956	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	242	567	1	ENST00000206249.3:c.469C>T	p.Arg157Ter	p.R157*	ENST00000206249	NM_000125.3	157	Cga/Tga	2/8	0.91458587525827	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.91458587525827	1		568	285	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979427	2979427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	304	644	0	ENST00000396946.4:c.820G>A	p.Glu274Lys	p.E274K	ENST00000396946	NM_032415.4	274	Gaa/Aaa	6/25	0.91458587525827	3	FACETS	0.927	0.874	0.981	0.464	0.437	0.491	CLONAL	1	TRUE	1	0.91458587525827	3		644	1045	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508944	106508944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	228	599	0	ENST00000359195.3:c.938C>T	p.Pro313Leu	p.P313L	ENST00000359195	NM_002649.2	313	cCg/cTg	2/11	1	2	FACETS	0.946	0.89	1	0.946	0.89	1	CLONAL	1	TRUE	1	0.91458587525827	2		599	527	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508955	106508955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759136884	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	223	609	0	ENST00000359195.3:c.949G>A	p.Glu317Lys	p.E317K	ENST00000359195	NM_002649.2	317	Gag/Aag	2/11	1	2	FACETS	0.905	0.85	0.96	0.905	0.85	0.96	CLONAL	1	TRUE	1	0.91458587525827	2		609	539	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509039	106509039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	311	706	0	ENST00000359195.3:c.1033G>A	p.Asp345Asn	p.D345N	ENST00000359195	NM_002649.2	345	Gac/Aac	2/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.91458587525827	2		706	663	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509064	106509064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868263278	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	316	709	0	ENST00000359195.3:c.1058C>T	p.Ser353Phe	p.S353F	ENST00000359195	NM_002649.2	353	tCc/tTc	2/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.91458587525827	2		709	687	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403179	116403179	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	295	540	0	ENST00000397752.3:c.2440C>T	p.Pro814Ser	p.P814S	ENST00000397752	NM_000245.2	814	Ccc/Tcc	11/21	1	2	FACETS	0.972	0.922	1	0.972	0.922	1	CLONAL	1	TRUE	1	0.91458587525827	2		540	664	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403302	116403302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	314	635	1	ENST00000397752.3:c.2563G>A	p.Glu855Lys	p.E855K	ENST00000397752	NM_000245.2	855	Gaa/Aaa	11/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.91458587525827	2		636	678	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423357	116423357	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	206	334	0	ENST00000397752.3:c.3633-1G>A		p.X1211_splice	ENST00000397752	NM_000245.2	1211			1	2	FACETS	0.988	0.928	1	0.988	0.928	1	CLONAL	1	TRUE	1	0.91458587525827	2		334	456	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140507827	140507827	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	328	553	0	ENST00000288602.6:c.644C>T	p.Ser215Phe	p.S215F	ENST00000288602	NM_004333.4	215	tCc/tTc	5/18	1	2	FACETS	0.963	0.916	1	0.963	0.916	1	CLONAL	1	TRUE	1	0.91458587525827	2		553	745	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849961	151849961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	231	531	0	ENST00000262189.6:c.12355C>T	p.Pro4119Ser	p.P4119S	ENST00000262189	NM_170606.2	4119	Cca/Tca	49/59	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.91458587525827	2		531	487	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372151	55372151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	124	544	0	ENST00000297316.4:c.841C>T	p.Pro281Ser	p.P281S	ENST00000297316	NM_022454.3	281	Ccc/Tcc	2/2	0.710275232153693	1	FACETS	0.373	0.34	0.406	0.373	0.34	0.406	SUBCLONAL	1	TRUE	0	0.91458587525827	1		544	395	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912075	56912075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	334	680	1	ENST00000519728.1:c.1303G>A	p.Glu435Lys	p.E435K	ENST00000519728	NM_002350.3	435	Gaa/Aaa	12/13	0.710275232153693	1	FACETS	0.682	0.653	0.711	0.682	0.653	0.711	SUBCLONAL	1	TRUE	0	0.91458587525827	1		681	581	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995497	68995497	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	169	559	0	ENST00000288368.4:c.1901A>T	p.Lys634Ile	p.K634I	ENST00000288368	NM_024870.2	634	aAa/aTa	18/40	0.710275232153693	1	FACETS	0.336	0.31	0.363	0.336	0.31	0.363	SUBCLONAL	1	TRUE	0	0.91458587525827	1		559	597	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69143606	69143606	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs754901389	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	177	342	1	ENST00000288368.4:c.4814A>T	p.Glu1605Val	p.E1605V	ENST00000288368	NM_024870.2	1605	gAa/gTa	40/40	0.710275232153693	1	FACETS	0.68	0.64	0.719	0.68	0.64	0.719	SUBCLONAL	1	TRUE	0	0.91458587525827	1		343	309	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868516	117868516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	99	311	0	ENST00000297338.2:c.826G>A	p.Asp276Asn	p.D276N	ENST00000297338	NM_006265.2	276	Gat/Aat	8/14	0.710275232153693	1	FACETS	0.363	0.327	0.4	0.363	0.327	0.4	SUBCLONAL	1	TRUE	0	0.91458587525827	1		311	324	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141545610	141545610	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	485	862	0	ENST00000220592.5:c.2228C>T	p.Pro743Leu	p.P743L	ENST00000220592	NM_012154.3	743	cCc/cTc	17/19	0.710275232153693	1	FACETS	0.714	0.689	0.739	0.714	0.689	0.739	SUBCLONAL	1	TRUE	0	0.91458587525827	1		862	806	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090902	5090902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	95	228	0	ENST00000381652.3:c.3050C>T	p.Pro1017Leu	p.P1017L	ENST00000381652	NM_004972.3	1017	cCc/cTc	22/25	0.91458587525827	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.91458587525827	1		228	112	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465636	8465636	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	223	480	0	ENST00000356435.5:c.3544del	p.Tyr1182MetfsTer7	p.Y1182Mfs*7	ENST00000356435		1182	Tat/at	21/35	0.91458587525827	1	FACETS	0.973	0.939	1	0.973	0.939	1	CLONAL	1	TRUE	0	0.91458587525827	1		480	272	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486344	8486344	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	109	343	0	ENST00000356435.5:c.2473G>A	p.Gly825Arg	p.G825R	ENST00000356435		825	Ggg/Agg	17/35	0.91458587525827	1	FACETS	0.965	0.915	1	0.965	0.915	1	CLONAL	1	TRUE	0	0.91458587525827	1		343	134	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974679	21974679	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs864622636	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	279	566	0	ENST00000304494.5:c.148C>T	p.Gln50Ter	p.Q50*	ENST00000304494	NM_000077.4	50	Cag/Tag	1/3	0.91458587525827	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.91458587525827	1		566	325	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317421	1317421	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs377299533	NA	P-0040959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	180	587	0	ENST00000400841.2:c.644G>A	p.Arg215Gln	p.R215Q	ENST00000400841		215	cGg/cAg	5/6	0.91458587525827	0	FACETS		NA	1			1	NA	1	TRUE	NA	0.91458587525827	0		587	369	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0040961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	76	214	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.182873353761348	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.17	3		214	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0040961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	40	748	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	0.783	0.649	0.932	0.783	0.649	0.932	CLONAL	1	TRUE	1	0.17	2		749	601	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974697	21974701	+	frameshift_variant	Frame_Shift_Del	DEL	AACTA	AACTA	-	novel	NA	P-0040961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	32	463	0	ENST00000304494.5:c.126_130del	p.Asn42LysfsTer76	p.N42Kfs*76	ENST00000304494	NM_000077.4	42	aaTAGTTac/aaac	1/3	0.0881411405580621	0	FACETS	0.777	0.631	0.942			1	INDETERMINATE	1	TRUE	0	0.17	0		463	402	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343121	118343121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	45	363	1	ENST00000534358.1:c.1247C>T	p.Ala416Val	p.A416V	ENST00000534358	NM_005933.3	416	gCt/gTt	3/36	0.3	3	FACETS	1	0.957	1			1	CLONAL	1	TRUE	NA	0.17	3		364	395	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219215	133219215	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	52	731	0	ENST00000320574.5:c.4829del	p.Pro1610LeufsTer23	p.P1610Lfs*23	ENST00000320574	NM_006231.2	1610	cCt/ct	37/49	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.17	2		731	580	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943686	9943686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	43	661	2	ENST00000330684.3:c.1255G>A	p.Val419Met	p.V419M	ENST00000330684	NM_001134407.1	419	Gtg/Atg	5/13	0.3	0	FACETS	0.84	0.703	0.992			1	CLONAL	1	TRUE	0	0.17	0		663	500	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719734	190719744	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTTTTTGTT	CTCTTTTTGTT	-	novel	NA	P-0040961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	14	309	0	ENST00000441310.2:c.1737_1747del	p.Leu580ArgfsTer12	p.L580Rfs*12	ENST00000441310	NM_000534.4	579	gCTCTTTTTGTT/g	9/13	1	2	FACETS	0.947	0.687	1	0.947	0.687	1	CLONAL	1	TRUE	1	0.17	2		309	174	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624544	21624561	+	frameshift_variant	Frame_Shift_Del	DEL	ATCTCTGCAGTACTCTGT	ATCTCTGCAGTACTCTGT	C	novel	NA	P-0040961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	33	529	0	ENST00000421138.2:c.1468_1485delinsG	p.Thr490AlafsTer13	p.T490Afs*13	ENST00000421138		490	ACAGAGTACTGCAGAGAT/G	14/16	0.182873353761348	3	FACETS	1	0.912	1	0.607	0.495	0.733	CLONAL	1	TRUE	1	0.17	3		529	347	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	50	82	0				ENST00000310581	NM_198253.2	-/1132			0.327858604337858	1	FACETS	0.58	0.501	0.663	0.58	0.501	0.663	INDETERMINATE	1	TRUE	0	0.681298513799745	1		82	167	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772950	135772951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs118203724	NA	P-0040976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	132	381	1	ENST00000298552.3:c.2672dup	p.Asn891LysfsTer13	p.N891Kfs*13	ENST00000298552	NM_001162426.1	891	aac/aaAc	21/23	0.168362996558391	4	FACETS	1	0.95	1	1	0.95	1	INDETERMINATE	2	TRUE	2	0.681298513799745	4		382	313	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236676	236676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138277996	NA	P-0040976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	8	534	1	ENST00000264932.6:c.1394G>A	p.Arg465Gln	p.R465Q	ENST00000264932	NM_004168.2	465	cGg/cAg	10/15	0.327858604337858	1	FACETS	0.055	0.035	0.08	0.055	0.035	0.08	INDETERMINATE	1	TRUE	0	0.681298513799745	1		535	284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0040990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	667	490	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.806016273634898	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.806016273634898	1		490	886	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615532	43615532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145170911	NA	P-0040990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	283	493	5	ENST00000355710.3:c.2611G>A	p.Val871Ile	p.V871I	ENST00000355710	NM_020975.4	871	Gtt/Att	15/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.806016273634898	2		498	696	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422874	12422874	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	109	556	0	ENST00000287820.6:c.364C>A	p.Leu122Ile	p.L122I	ENST00000287820	NM_015869.4	122	Ctc/Atc	3/7	1	2	FACETS	0.388	0.348	0.43	0.388	0.348	0.43	SUBCLONAL	1	TRUE	1	0.806016273634898	2		556	697	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157454308	157454309	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs1314750809	NA	P-0040990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	242	445	1	ENST00000346085.5:c.2519dup	p.Tyr840Ter	p.Y840*	ENST00000346085	NM_020732.3	840	tac/tAac	8/20	0.806016273634898	1	FACETS	0.87	0.827	0.913	0.87	0.827	0.913	CLONAL	1	TRUE	0	0.806016273634898	1		446	412	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528852	157528852	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	358	598	0	ENST00000346085.5:c.6577G>A	p.Asp2193Asn	p.D2193N	ENST00000346085	NM_020732.3	2193	Gac/Aac	20/20	0.806016273634898	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.806016273634898	1		598	522	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0040991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	154	214	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.363906002567206	3	FACETS	1	0.985	1	0.657	0.604	0.711	CLONAL	1	TRUE	1	0.521404202514461	3		214	567	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	159	82	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.521404202514461	2		82	523	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222983	1222983	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs398123406	NA	P-0040991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	154	569	0	ENST00000326873.7:c.921-1G>T		p.X307_splice	ENST00000326873	NM_000455.4	307			0.383111566533262	1	FACETS	0.655	0.601	0.711	0.655	0.601	0.711	SUBCLONAL	1	TRUE	0	0.521404202514461	1		569	667	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098422	11098422	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	221	544	0	ENST00000358026.2:c.940G>T	p.Ala314Ser	p.A314S	ENST00000358026	NM_001128849.1	314	Gcg/Tcg	6/36	0.383111566533262	1	FACETS	0.95	0.888	1	0.95	0.888	1	CLONAL	1	TRUE	0	0.521404202514461	1		544	660	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404560	8404561	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	159	244	0	ENST00000356435.5:c.4186dup	p.Arg1396ProfsTer14	p.R1396Pfs*14	ENST00000356435		1396	cgg/cCgg	25/35	0.494232443903184	2	FACETS	0.881	0.821	0.942	0.881	0.821	0.942	CLONAL	2	TRUE	0	0.521404202514461	2		244	346	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195562	102195562	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	166	501	0	ENST00000263464.3:c.322A>T	p.Thr108Ser	p.T108S	ENST00000263464	NM_001165.4	108	Acc/Tcc	2/9	0.477066106355204	3	FACETS	0.893	0.82	0.969	0.446	0.41	0.485	CLONAL	1	TRUE	1	0.521404202514461	3		501	899	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439695	51439695	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	187	402	0	ENST00000262662.1:c.260A>T	p.Gln87Leu	p.Q87L	ENST00000262662		87	cAg/cTg	4/4	0.521404202514461	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.521404202514461	1		402	480	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332103	70332103	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	35	181	0	ENST00000373644.4:c.8G>T	p.Arg3Leu	p.R3L	ENST00000373644	NM_030625.2	3	cGa/cTa	2/12	1	2	FACETS	0.661	0.547	0.787	0.661	0.547	0.787	SUBCLONAL	1	TRUE	1	0.521404202514461	2		181	203	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112760302	112760302	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	49	297	0	ENST00000369452.4:c.971A>T	p.Glu324Val	p.E324V	ENST00000369452	NM_007373.3	324	gAg/gTg	4/9	1	2	FACETS	0.669	0.57	0.776	0.669	0.57	0.776	SUBCLONAL	1	TRUE	1	0.521404202514461	2		297	281	SUCCESS
EED	8726	MSKCC	GRCh37	11	85956344	85956344	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1459981515	NA	P-0040991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	100	318	0	ENST00000263360.6:c.73A>G	p.Ser25Gly	p.S25G	ENST00000263360	NM_003797.3	25	Agt/Ggt	1/12	0.477066106355204	3	FACETS	0.871	0.781	0.967	0.436	0.39	0.484	CLONAL	1	TRUE	1	0.521404202514461	3		318	555	SUCCESS
ATM	472	MSKCC	GRCh37	11	108159822	108159822	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0040991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	46	124	0	ENST00000278616.4:c.4228A>T	p.Lys1410Ter	p.K1410*	ENST00000278616	NM_000051.3	1410	Aaa/Taa	28/63	0.477066106355204	3	FACETS	0.897	0.776	1	0.897	0.776	1	CLONAL	2	TRUE	1	0.521404202514461	3		124	124	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206674	108206674	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	71	320	0	ENST00000278616.4:c.8254A>T	p.Ile2752Phe	p.I2752F	ENST00000278616	NM_000051.3	2752	Atc/Ttc	56/63	0.477066106355204	3	FACETS	0.66	0.577	0.75	0.33	0.288	0.375	SUBCLONAL	1	TRUE	1	0.521404202514461	3		320	520	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483885	88483885	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	110	738	0	ENST00000360948.2:c.1685C>A	p.Pro562Gln	p.P562Q	ENST00000360948	NM_001012338.2	562	cCg/cAg	14/19	0.383111566533262	1	FACETS	0.334	0.299	0.37	0.334	0.299	0.37	SUBCLONAL	1	TRUE	0	0.521404202514461	1		738	935	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40447652	40447652	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs762072134	NA	P-0040991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	159	566	0	ENST00000345506.4:c.391G>T	p.Gly131Trp	p.G131W	ENST00000345506	NM_003152.3	131	Ggg/Tgg	6/20	1	2	FACETS	0.811	0.745	0.88	0.811	0.745	0.88	CLONAL	1	TRUE	1	0.521404202514461	2		566	752	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221215	1221215	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	109	750	0	ENST00000326873.7:c.738C>A	p.Tyr246Ter	p.Y246*	ENST00000326873	NM_000455.4	246	taC/taA	6/10	0.383111566533262	1	FACETS	0.352	0.315	0.39	0.352	0.315	0.39	SUBCLONAL	1	TRUE	0	0.521404202514461	1		750	879	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2199918	2199918	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	234	733	0	ENST00000398665.3:c.687G>T	p.Arg229Ser	p.R229S	ENST00000398665	NM_032482.2	229	agG/agT	8/28	0.383111566533262	1	FACETS	0.696	0.65	0.744	0.696	0.65	0.744	SUBCLONAL	1	TRUE	0	0.521404202514461	1		733	953	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143991	11143991	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	118	580	0	ENST00000358026.2:c.3572A>T	p.His1191Leu	p.H1191L	ENST00000358026	NM_001128849.1	1191	cAc/cTc	26/36	0.383111566533262	1	FACETS	0.407	0.366	0.449	0.407	0.366	0.449	SUBCLONAL	1	TRUE	0	0.521404202514461	1		580	823	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367901	15367902	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	215	930	0	ENST00000263377.2:c.1424dup	p.Pro476SerfsTer17	p.P476Sfs*17	ENST00000263377	NM_058243.2	475	cct/ccCt	8/20	0.383111566533262	1	FACETS	0.6	0.558	0.644	0.6	0.558	0.644	SUBCLONAL	1	TRUE	0	0.521404202514461	1		930	1016	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52728969	52728969	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0040991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	172	500	2	ENST00000322088.6:c.1662-1G>A		p.X554_splice	ENST00000322088	NM_014225.5	554			1	2	FACETS	0.894	0.825	0.966	0.894	0.825	0.966	CLONAL	1	TRUE	1	0.521404202514461	2		502	738	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480313	89480313	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	75	240	0	ENST00000336596.2:c.2150A>T	p.Gln717Leu	p.Q717L	ENST00000336596	NM_005233.5	717	cAg/cTg	13/17	1	2	FACETS	0.851	0.752	0.957	0.851	0.752	0.957	CLONAL	1	TRUE	1	0.521404202514461	2		240	338	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523153	176523153	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	118	747	1	ENST00000292408.4:c.1917C>A	p.His639Gln	p.H639Q	ENST00000292408	NM_213647.1	639	caC/caA	14/18	0.383111566533262	1	FACETS	0.396	0.357	0.437	0.396	0.357	0.437	SUBCLONAL	1	TRUE	0	0.521404202514461	1		748	845	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405885	157405885	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	38	430	0	ENST00000346085.5:c.2127A>C	p.Gln709His	p.Q709H	ENST00000346085	NM_020732.3	709	caA/caC	6/20	0.383111566533262	1	FACETS	0.158	0.13	0.19	0.158	0.13	0.19	SUBCLONAL	1	TRUE	0	0.521404202514461	1		430	680	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508207	106508207	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	71	289	0	ENST00000359195.3:c.202del	p.Glu68SerfsTer3	p.E68Sfs*3	ENST00000359195	NM_002649.2	67	gtG/gt	2/11	1	2	FACETS	0.642	0.563	0.727	0.642	0.563	0.727	SUBCLONAL	1	TRUE	1	0.521404202514461	2		289	424	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852036	128852036	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	350	716	0	ENST00000249373.3:c.2108G>T	p.Arg703Leu	p.R703L	ENST00000249373	NM_005631.4	703	cGa/cTa	12/12	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.521404202514461	2		716	1075	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980586	70980586	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	672	649	0	ENST00000276594.2:c.791C>G	p.Pro264Arg	p.P264R	ENST00000276594	NM_024504.3	264	cCa/cGa	4/8	0.521404202514461	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	1	0.521404202514461	3		649	1411	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0041056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	85	395	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.988	0.89	1	1	0.991	1	CLONAL	7	FALSE	1	0.112779101001729	2		396	218	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0041056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	187	623	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	1	2	FACETS	0.995	0.929	1	1	0.995	1	CLONAL	7	FALSE	1	0.112779101001729	2		623	476	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445140	49445140	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	135	835	0	ENST00000301067.7:c.2326G>T	p.Glu776Ter	p.E776*	ENST00000301067	NM_003482.3	776	Gag/Tag	10/54	0.184317461614792	3	FACETS	0.976	0.898	1	1	0.993	1	CLONAL	7	FALSE	1	0.112779101001729	3		835	370	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354424	40354424	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139131471	NA	P-0041056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	136	1010	0	ENST00000293328.3:c.2171C>T	p.Thr724Met	p.T724M	ENST00000293328	NM_012448.3	724	aCg/aTg	18/19	1	2	FACETS	1	0.959	1	1	0.994	1	CLONAL	7	FALSE	1	0.112779101001729	2		1010	325	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0041065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	18	466	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		466	401	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	116	723	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	NA	2	FACETS	1	0.926	1			1	INDETERMINATE	2	TRUE	NA	0.21	2		723	538	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0041174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	74	367	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.283928074900627	3	FACETS	0.811	0.712	0.917	0.811	0.712	0.917	CLONAL	2	TRUE	1	0.21	3		367	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	298	723	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.240380380749363	2	FACETS	0.968	0.918	1	0.968	0.918	1	INDETERMINATE	2	TRUE	0	0.440948539304195	2		723	698	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0041180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	59	423	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.307737828211776	1	FACETS	0.621	0.537	0.711	0.621	0.537	0.711	SUBCLONAL	1	TRUE	0	0.440948539304195	1		423	336	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057936	27057937	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1415146710	NA	P-0041180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	130	611	0	ENST00000324856.7:c.1650dup	p.Tyr551LeufsTer72	p.Y551Lfs*72	ENST00000324856	NM_006015.4	548	-/C	3/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.440948539304195	2		611	531	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0041180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	19	209	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	0.307737828211776	1	FACETS	0.343	0.261	0.438	0.343	0.261	0.438	SUBCLONAL	1	TRUE	0	0.440948539304195	1		209	196	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998283	100998283	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	18	217	0	ENST00000325455.5:c.1519G>A	p.Ala507Thr	p.A507T	ENST00000325455	NM_001202474.3	507	Gcg/Acg	1/8	0.240380380749363	2	FACETS	0.507	0.384	0.65	0.254	0.192	0.325	INDETERMINATE	1	TRUE	0	0.440948539304195	2		217	161	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692887	89692887	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	26	314	0	ENST00000371953.3:c.371G>T	p.Cys124Phe	p.C124F	ENST00000371953	NM_000314.4	124	tGt/tTt	5/9	0.240380380749363	2	FACETS	0.34	0.269	0.421	0.17	0.134	0.211	INDETERMINATE	1	TRUE	0	0.440948539304195	2		314	347	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123892117	123892117	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	18	90	0	ENST00000330479.4:c.926T>G	p.Leu309Arg	p.L309R	ENST00000330479	NM_020382.3	309	cTg/cGg	8/9	1	2	FACETS	0.938	0.721	1	0.938	0.721	1	CLONAL	1	TRUE	1	0.440948539304195	2		90	87	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897035	28897035	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	104	502	0	ENST00000282397.4:c.2845C>A	p.Leu949Met	p.L949M	ENST00000282397	NM_002019.4	949	Ctg/Atg	21/30	0.390125795693982	3	FACETS	0.956	0.858	1	0.478	0.429	0.53	CLONAL	1	TRUE	1	0.440948539304195	3		502	602	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437712	110437712	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	44	812	0	ENST00000375856.3:c.689A>G	p.Lys230Arg	p.K230R	ENST00000375856	NM_003749.2	230	aAg/aGg	1/2	0.390125795693982	3	FACETS	0.281	0.235	0.333	0.141	0.117	0.167	SUBCLONAL	1	TRUE	1	0.440948539304195	3		812	866	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805044	89805044	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	44	803	0	ENST00000389301.3:c.4333G>T	p.Asp1445Tyr	p.D1445Y	ENST00000389301	NM_000135.2	1445	Gac/Tac	43/43	1	2	FACETS	0.251	0.21	0.298	0.251	0.21	0.298	SUBCLONAL	1	TRUE	1	0.440948539304195	2		803	794	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227927	55227927	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	38	405	0	ENST00000275493.2:c.1394G>T	p.Gly465Val	p.G465V	ENST00000275493	NM_005228.3	465	gGa/gTa	12/28	0.234614592528376	4	FACETS	0.503	0.415	0.601	0.251	0.207	0.301	INDETERMINATE	1	TRUE	2	0.440948539304195	4		405	494	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162834	38162834	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	38	705	0	ENST00000317025.8:c.2372del	p.Gly791AspfsTer26	p.G791Dfs*26	ENST00000317025	NM_023034.1	791	gGa/ga	13/24	0.37616317354913	3	FACETS	0.282	0.232	0.338	0.141	0.116	0.169	SUBCLONAL	1	TRUE	1	0.440948539304195	3		705	747	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221313	1221314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs121913321	NA	P-0041182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	472	709	3	ENST00000326873.7:c.842dup	p.Leu282AlafsTer3	p.L282Afs*3	ENST00000326873	NM_000455.4	279	ggc/ggCc	6/10	NA	2	FACETS	0.921	0.893	0.949			1	INDETERMINATE	2	TRUE	NA	0.763570275623944	2		712	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913343	NA	P-0041182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	240	744	1	ENST00000269305.4:c.817C>A	p.Arg273Ser	p.R273S	ENST00000269305	NM_001126112.2	273	Cgt/Agt	8/11	0.737274689317056	1	FACETS	0.986	0.939	1	0.986	0.939	1	CLONAL	1	TRUE	0	0.763570275623944	1		745	394	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187966	32187966	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	479	721	1	ENST00000375023.3:c.1255C>A	p.Leu419Met	p.L419M	ENST00000375023	NM_004557.3	419	Ctg/Atg	7/30	0.761154910926936	3	FACETS	0.966	0.93	1	0.966	0.93	1	CLONAL	2	TRUE	1	0.763570275623944	3		722	897	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809525	36809525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	312	830	0	ENST00000373129.3:c.940G>A	p.Asp314Asn	p.D314N	ENST00000373129	NM_032017.1	314	Gac/Aac	10/12	0.763570275623944	3	FACETS	0.99	0.934	1	0.495	0.467	0.524	CLONAL	1	TRUE	1	0.763570275623944	3		830	1141	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949317	71949317	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	512	880	0	ENST00000298229.2:c.3697G>A	p.Glu1233Lys	p.E1233K	ENST00000298229	NM_001567.3	1233	Gag/Aag	28/28	0.763570275623944	3	FACETS	0.938	0.903	0.972	0.938	0.903	0.972	CLONAL	2	TRUE	1	0.763570275623944	3		880	988	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039133	49039133	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0041182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	89	156	1	ENST00000267163.4:c.2212-1G>T		p.X738_splice	ENST00000267163	NM_000321.2	738			0.763570275623944	2	FACETS	0.897	0.832	0.958	0.897	0.832	0.958	CLONAL	2	TRUE	0	0.763570275623944	2		157	130	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602822	10602823	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0041182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	643	903	2	ENST00000171111.5:c.755_756delinsTT	p.Trp252Phe	p.W252F	ENST00000171111	NM_203500.1	252	tGG/tTT	3/6	0.75919487637676	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.763570275623944	2		905	840	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902528	1902528	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	553	699	2	ENST00000382891.5:c.147C>G	p.Ser49Arg	p.S49R	ENST00000382891	NM_133335.3	49	agC/agG	2/22	0.763570275623944	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.763570275623944	2		701	686	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139799	55139799	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	365	626	2	ENST00000257290.5:c.1460G>T	p.Arg487Leu	p.R487L	ENST00000257290	NM_006206.4	487	cGt/cTt	10/23	0.601190134391328	4	FACETS	0.909	0.866	0.954	0.909	0.866	0.954	CLONAL	2	TRUE	2	0.763570275623944	4		628	927	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629775	187629775	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0041182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	406	724	0	ENST00000441802.2:c.1207A>T	p.Lys403Ter	p.K403*	ENST00000441802	NM_005245.3	403	Aaa/Taa	2/27	0.763570275623944	2	FACETS	0.977	0.948	1	0.977	0.948	1	CLONAL	2	TRUE	0	0.763570275623944	2		724	544	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31493334	31493335	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	198	295	0	ENST00000344624.3:c.1821dup	p.Ala608CysfsTer12	p.A608Cfs*12	ENST00000344624		607	-/T	10/33	0.763570275623944	8	FACETS	1	0.956	1	0.347	0.322	0.374	CLONAL	2	TRUE	2	0.763570275623944	8		295	819	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961079	79961079	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	260	494	2	ENST00000265081.6:c.476G>T	p.Arg159Ile	p.R159I	ENST00000265081	NM_002439.4	159	aGa/aTa	3/24	0.763570275623944	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.763570275623944	2		496	338	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944320	131944320	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	122	266	0	ENST00000265335.6:c.2732A>T	p.Gln911Leu	p.Q911L	ENST00000265335		911	cAg/cTg	17/25	0.763570275623944	2	FACETS	0.929	0.874	0.981	0.929	0.874	0.981	CLONAL	2	TRUE	0	0.763570275623944	2		266	172	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459696	149459696	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	483	800	2	ENST00000286301.3:c.511C>G	p.Gln171Glu	p.Q171E	ENST00000286301	NM_005211.3	171	Cag/Gag	4/22	0.763570275623944	2	FACETS	0.982	0.955	1	0.982	0.955	1	CLONAL	2	TRUE	0	0.763570275623944	2		802	644	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022115	5022116	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0041182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	106	495	0	ENST00000381652.3:c.129_130del	p.Tyr44ProfsTer7	p.Y44Pfs*7	ENST00000381652	NM_004972.3	43	cTT/c	3/25	0.763570275623944	1	FACETS	0.928	0.858	0.997	0.928	0.858	0.997	CLONAL	1	TRUE	0	0.763570275623944	1		495	185	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1331504	1331504	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	160	455	0	ENST00000400841.2:c.24G>C	p.Trp8Cys	p.W8C	ENST00000400841		8	tgG/tgC	1/6	1	1	FACETS	0.611	0.566	0.657	0.611	0.566	0.657	SUBCLONAL	1	TRUE	0	0.763570275623944	1		455	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0041210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	139	721	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.997	0.91	1	0.997	0.91	1	CLONAL	1	TRUE	1	0.4	2		723	697	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0041210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	116	404	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.253782120391108	4	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.4	4		404	620	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578400	7578400	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs751477326	NA	P-0041210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	24	758	0	ENST00000269305.4:c.530C>G	p.Pro177Arg	p.P177R	ENST00000269305	NM_001126112.2	177	cCc/cGc	5/11	1	2	FACETS	0.176	0.137	0.221	0.176	0.137	0.221	SUBCLONAL	1	TRUE	1	0.4	2		758	681	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0041219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	457	502	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.68698284781001	5	FACETS	0.969	0.937	1	0.969	0.937	1	CLONAL	4	TRUE	1	0.68698284781001	5		502	697	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851083	63851083	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	219	656	0	ENST00000279873.7:c.1861G>C	p.Asp621His	p.D621H	ENST00000279873	NM_032199.2	621	Gat/Cat	10/10	0.648515817406664	4	FACETS	1	0.986	1	0.405	0.377	0.434	CLONAL	1	TRUE	1	0.68698284781001	4		656	885	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285880	46285880	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0041219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	276	456	0	ENST00000334344.6:c.5147+1G>A		p.X1716_splice	ENST00000334344	NM_152641.2	1716			0.68698284781001	4	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.68698284781001	4		456	624	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482607	56482607	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	52	716	0	ENST00000267101.3:c.1064C>G	p.Thr355Ser	p.T355S	ENST00000267101	NM_001982.3	355	aCc/aGc	9/28	0.68698284781001	3	FACETS	0.23	0.195	0.269			1	SUBCLONAL	1	TRUE	NA	0.68698284781001	3		716	884	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954022	32954023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs397507419	NA	P-0041219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	207	490	6	ENST00000380152.3:c.9097dup	p.Thr3033AsnfsTer11	p.T3033Nfs*11	ENST00000380152		3030	aca/acAa	23/27	0.68698284781001	2	FACETS	0.994	0.947	1	0.994	0.947	1	CLONAL	2	TRUE	0	0.68698284781001	2		496	303	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178129266	178129267	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	CT	novel	NA	P-0041219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	128	348	0	ENST00000397062.3:c.38_39delinsAG	p.Ser13Ter	p.S13*	ENST00000397062	NM_006164.4	13	tCC/tAG	1/5	0.58180117730394	4	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.68698284781001	4		348	533	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178129267	178129267	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	128	344	0	ENST00000397062.3:c.38C>A	p.Ser13Tyr	p.S13Y	ENST00000397062	NM_006164.4	13	tCc/tAc	1/5	0.58180117730394	4	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.68698284781001	4		344	533	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664727	138664727	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	81	167	0	ENST00000330315.3:c.838C>T	p.Pro280Ser	p.P280S	ENST00000330315	NM_023067.3	280	Ccg/Tcg	1/1	0.68698284781001	5	FACETS	1	0.92	1	0.35	0.309	0.393	CLONAL	1	TRUE	2	0.68698284781001	5		167	456	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021065	26021079	+	inframe_deletion	In_Frame_Del	DEL	GCGCGTCACTATCAT	GCGCGTCACTATCAT	-	novel	NA	P-0041219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	97	536	0	ENST00000357647.3:c.350_364del	p.Arg117_Met121del	p.R117_M121del	ENST00000357647	NM_003529.2	116	aaGCGCGTCACTATCATg/aag	1/1	0.68698284781001	3	FACETS	0.734	0.656	0.816	0.367	0.328	0.408	SUBCLONAL	1	TRUE	1	0.68698284781001	3		536	517	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423612	88423612	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	149	510	0	ENST00000360948.2:c.2223C>A	p.Ser741Arg	p.S741R	ENST00000360948	NM_001012338.2	741	agC/agA	18/19	0.849659157692011	4	FACETS	0.846	0.774	0.921	0.282	0.258	0.307	CLONAL	1	TRUE	1	0.87483151288101	4		510	755	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578448	7578448	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1064795691	NA	P-0041245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	916	700	0	ENST00000269305.4:c.482C>A	p.Ala161Asp	p.A161D	ENST00000269305	NM_001126112.2	161	gCc/gAc	5/11	0.857382130764893	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.87483151288101	3		700	987	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453145	140453145	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913366	NA	P-0041245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	332	345	0	ENST00000288602.6:c.1790T>G	p.Leu597Arg	p.L597R	ENST00000288602	NM_004333.4	597	cTa/cGa	15/18	0.84823566408415	4	FACETS	0.992	0.945	1	0.992	0.945	1	CLONAL	2	TRUE	2	0.87483151288101	4		345	717	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797729	45797729	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs776362892	NA	P-0041245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	263	662	0	ENST00000450313.1:c.963del	p.Ser322AlafsTer86	p.S322Afs*86	ENST00000450313	NM_012222.2	321	ggG/gg	11/16	0.87483151288101	3	FACETS	0.96	0.902	1	0.48	0.451	0.51	CLONAL	1	TRUE	1	0.87483151288101	3		662	900	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450874	70450874	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	181	500	0	ENST00000373644.4:c.5714G>T	p.Gly1905Val	p.G1905V	ENST00000373644	NM_030625.2	1905	gGc/gTc	12/12	0.87483151288101	3	FACETS	0.956	0.886	1	0.478	0.443	0.514	CLONAL	1	TRUE	1	0.87483151288101	3		500	622	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861808	57861808	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs768582577	NA	P-0041245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	255	588	0	ENST00000228682.2:c.1109C>A	p.Thr370Asn	p.T370N	ENST00000228682	NM_005269.2	370	aCc/aAc	10/12	0.87483151288101	4	FACETS	1	0.971	1	0.354	0.331	0.378	CLONAL	1	TRUE	1	0.87483151288101	4		588	1029	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041751	29041751	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	119	268	0	ENST00000282397.4:c.68C>G	p.Ser23Cys	p.S23C	ENST00000282397	NM_002019.4	23	tCt/tGt	2/30	1	2	FACETS	0.965	0.886	1	0.965	0.886	1	CLONAL	1	TRUE	1	0.87483151288101	2		268	282	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220375	1220377	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0041245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	421	602	0	ENST00000326873.7:c.470_472del	p.Phe157del	p.F157del	ENST00000326873	NM_000455.4	156	taCTTc/tac	4/10	0.87483151288101	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.87483151288101	2		602	474	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47607036	47607036	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	460	549	0	ENST00000263735.4:c.786G>T	p.Gln262His	p.Q262H	ENST00000263735	NM_002354.2	262	caG/caT	7/9	0.87483151288101	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	2	0.87483151288101	4		549	985	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385101	41385101	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0041245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	708	608	0	ENST00000373198.4:c.859+1G>C		p.X287_splice	ENST00000373198	NM_133170.3	287			0.777587925573362	5	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	2	0.87483151288101	5		608	1231	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142949952	142949952	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	187	494	0	ENST00000262992.4:c.2758G>T	p.Gly920Ter	p.G920*	ENST00000262992	NM_001101669.1	920	Gga/Tga	24/24	1	2	FACETS	0.948	0.885	1	0.948	0.885	1	CLONAL	1	TRUE	1	0.87483151288101	2		494	451	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032197	26032197	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	132	344	0	ENST00000244661.2:c.92C>A	p.Pro31Gln	p.P31Q	ENST00000244661	NM_003537.3	31	cCg/cAg	1/1	0.87483151288101	3	FACETS	1	0.934	1	0.512	0.468	0.556	CLONAL	1	TRUE	1	0.87483151288101	3		344	424	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553599	106553599	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	146	383	1	ENST00000369096.4:c.1564G>T	p.Ala522Ser	p.A522S	ENST00000369096	NM_001198.3	522	Gcc/Tcc	5/7	1	2	FACETS	0.988	0.915	1	0.988	0.915	1	CLONAL	1	TRUE	1	0.87483151288101	2		384	338	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843381	128843381	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	505	602	0	ENST00000249373.3:c.488G>T	p.Trp163Leu	p.W163L	ENST00000249373	NM_005631.4	163	tGg/tTg	2/12	0.84823566408415	4	FACETS	0.978	0.939	1	0.978	0.939	1	CLONAL	2	TRUE	2	0.87483151288101	4		602	1107	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70971050	70971050	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	462	566	1	ENST00000276594.2:c.1211G>C	p.Arg404Thr	p.R404T	ENST00000276594	NM_024504.3	404	aGa/aCa	6/8	0.87483151288101	4	FACETS	0.949	0.91	0.989	0.475	0.455	0.495	CLONAL	2	TRUE	0	0.87483151288101	4		567	1043	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521514	8521514	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	364	532	0	ENST00000356435.5:c.724C>A	p.Pro242Thr	p.P242T	ENST00000356435		242	Ccc/Acc	9/35	0.868564655793426	2	FACETS	0.991	0.967	1	0.991	0.967	1	CLONAL	2	TRUE	0	0.87483151288101	2		532	420	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549106	87549106	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	339	444	0	ENST00000277120.3:c.1663G>T	p.Val555Phe	p.V555F	ENST00000277120		555	Gtt/Ttt	15/19	0.87483151288101	2	FACETS	0.976	0.951	0.999	0.976	0.951	0.999	CLONAL	2	TRUE	0	0.87483151288101	2		444	397	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220502	1220502	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	rs121913317	NA	P-0041251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	240	704	0	ENST00000326873.7:c.595G>T	p.Glu199Ter	p.E199*	ENST00000326873	NM_000455.4	199	Gag/Tag	4/10	0.268029987693851	4	FACETS	0.911	0.857	0.966	0.911	0.857	0.966	CLONAL	4	TRUE	0	0.268029987693851	4		704	623	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602290	10602290	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	333	755	0	ENST00000171111.5:c.1288G>T	p.Gly430Cys	p.G430C	ENST00000171111	NM_203500.1	430	Ggc/Tgc	3/6	0.268029987693851	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	4	TRUE	0	0.268029987693851	4		755	745	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0041251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	67	290	0	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	0.261576729885283	4	FACETS	0.888	0.776	1			1	CLONAL	2	TRUE	NA	0.268029987693851	4		290	357	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577071	7577072	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0041251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	159	780	0	ENST00000269305.4:c.866_867del	p.Leu289ProfsTer16	p.L289Pfs*16	ENST00000269305	NM_001126112.2	289	cTC/c	8/11	0.268029987693851	2	FACETS	0.881	0.81	0.955	0.881	0.81	0.955	CLONAL	2	TRUE	0	0.268029987693851	2		780	673	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832774	3832774	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	130	596	0	ENST00000262367.5:c.1484A>C	p.Gln495Pro	p.Q495P	ENST00000262367	NM_004380.2	495	cAg/cCg	6/31	0.256437078703177	3	FACETS	0.991	0.903	1	0.991	0.903	1	CLONAL	2	TRUE	1	0.268029987693851	3		596	555	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797816	42797816	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	160	744	1	ENST00000575354.2:c.3870del	p.Thr1291LeufsTer11	p.T1291Lfs*11	ENST00000575354	NM_015125.3	1290	Ccc/cc	16/20	0.268029987693851	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.268029987693851	2		745	503	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583373	46583373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs181240421	NA	P-0041251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	146	588	0	ENST00000263734.3:c.301G>A	p.Val101Met	p.V101M	ENST00000263734	NM_001430.4	101	Gtg/Atg	3/16	0.261576729885283	4	FACETS	1	0.95	1			1	CLONAL	2	TRUE	NA	0.268029987693851	4		588	656	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536104	106536104	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	35	338	0	ENST00000369096.4:c.71T>G	p.Val24Gly	p.V24G	ENST00000369096	NM_001198.3	24	gTg/gGg	2/7	0.256437078703177	3	FACETS	0.818	0.672	0.982	0.409	0.336	0.491	CLONAL	1	TRUE	1	0.268029987693851	3		338	362	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486095	8486095	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	92	603	0	ENST00000356435.5:c.2722G>C	p.Val908Leu	p.V908L	ENST00000356435		908	Gtg/Ctg	17/35	0.221741148187598	4	FACETS	0.805	0.717	0.898	0.805	0.717	0.898	CLONAL	2	TRUE	2	0.268029987693851	4		603	541	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359948	87359948	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	98	457	0	ENST00000277120.3:c.1256C>A	p.Ser419Tyr	p.S419Y	ENST00000277120		419	tCc/tAc	11/19	0.221741148187598	4	FACETS	0.892	0.798	0.99	0.892	0.798	0.99	CLONAL	2	TRUE	2	0.268029987693851	4		457	520	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0041256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	175	466	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.38765484913281	5	FACETS	0.989	0.925	1	0.989	0.925	1	CLONAL	4	TRUE	1	0.38765484913281	5		466	361	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0041256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	50	366	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.357245166639692	4	FACETS	0.967	0.824	1	0.484	0.412	0.562	CLONAL	1	TRUE	2	0.38765484913281	4		366	370	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537933	212537933	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	125	485	1	ENST00000342788.4:c.1672C>A	p.Gln558Lys	p.Q558K	ENST00000342788	NM_005235.2	558	Cag/Aag	14/28	0.38765484913281	3	FACETS	0.965	0.881	1	0.965	0.881	1	CLONAL	2	TRUE	1	0.38765484913281	3		486	399	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138938	64138938	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	63	417	0	ENST00000334205.4:c.2305C>A	p.Leu769Met	p.L769M	ENST00000334205	NM_003942.2	769	Ctg/Atg	17/17	0.38765484913281	4	FACETS	0.913	0.791	1	0.304	0.263	0.349	CLONAL	1	TRUE	1	0.38765484913281	4		417	494	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373137	118373137	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	39	341	1	ENST00000534358.1:c.6530A>T	p.Glu2177Val	p.E2177V	ENST00000534358	NM_005933.3	2177	gAa/gTa	27/36	0.38765484913281	4	FACETS	0.763	0.634	0.906	0.254	0.211	0.302	CLONAL	1	TRUE	1	0.38765484913281	4		342	366	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209106858	209106858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	55	449	0	ENST00000345146.2:c.710C>T	p.Ser237Phe	p.S237F	ENST00000345146	NM_005896.2	237	tCc/tTc	7/10	0.38765484913281	3	FACETS	0.901	0.774	1	0.45	0.387	0.52	CLONAL	1	TRUE	1	0.38765484913281	3		449	376	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514480	41514480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1030044339	NA	P-0041256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	205	513	0	ENST00000373198.4:c.181G>A	p.Glu61Lys	p.E61K	ENST00000373198	NM_133170.3	61	Gag/Aag	2/32	0.38765484913281	5	FACETS	0.908	0.847	0.97	0.908	0.847	0.97	CLONAL	3	TRUE	2	0.38765484913281	5		513	614	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584483	189584483	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	89	336	0	ENST00000264731.3:c.779C>A	p.Pro260His	p.P260H	ENST00000264731	NM_003722.4	260	cCt/cAt	6/14	0.315495007835237	4	FACETS	1	0.908	1	1	0.908	1	CLONAL	2	TRUE	2	0.38765484913281	4		336	314	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540214	187540214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1420663657	NA	P-0041256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	195	467	1	ENST00000441802.2:c.7526C>T	p.Thr2509Ile	p.T2509I	ENST00000441802	NM_005245.3	2509	aCc/aTc	10/27	0.369418019127697	3	FACETS	0.984	0.923	1	0.984	0.923	1	CLONAL	3	TRUE	0	0.38765484913281	3		468	407	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517993	176517993	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	158	597	0	ENST00000292408.4:c.491C>G	p.Ala164Gly	p.A164G	ENST00000292408	NM_213647.1	164	gCg/gGg	5/18	0.38765484913281	3	FACETS	0.829	0.763	0.897	0.829	0.763	0.897	CLONAL	2	TRUE	1	0.38765484913281	3		597	587	SUCCESS
APC	324	MSKCC	GRCh37	5	112164669	112164669	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	25	220	0	ENST00000257430.4:c.1743G>T	p.Lys581Asn	p.K581N	ENST00000257430	NM_000038.5	581	aaG/aaT	14/16	0.38765484913281	3	FACETS	0.802	0.636	0.989	0.401	0.318	0.495	CLONAL	1	TRUE	1	0.38765484913281	3		220	192	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0041269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	617	352	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.875486391216342	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.875486391216342	1		353	785	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666654	206666654	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782009287	NA	P-0041269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	505	610	2	ENST00000367120.3:c.1988C>T	p.Ala663Val	p.A663V	ENST00000367120	NM_014002.3	663	gCc/gTc	20/22	1	2	FACETS	0.994	0.954	1	0.994	0.954	1	CLONAL	1	TRUE	1	0.875486391216342	2		612	1161	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872775	136872782	+	frameshift_variant	Frame_Shift_Del	DEL	TGTGGTCT	TGTGGTCT	-	novel	NA	P-0041269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	300	478	0	ENST00000241393.3:c.716_723del	p.Lys239SerfsTer34	p.K239Sfs*34	ENST00000241393	NM_003467.2	239	aAGACCACA/a	2/2	1	2	FACETS	0.925	0.876	0.974	0.925	0.876	0.974	CLONAL	1	TRUE	1	0.875486391216342	2		478	741	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430209	181430209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	350	251	0	ENST00000325404.1:c.61G>A	p.Gly21Ser	p.G21S	ENST00000325404	NM_003106.3	21	Ggc/Agc	1/1	0.863363392211117	2	FACETS	1	0.992	1	0.592	0.566	0.619	CLONAL	1	TRUE	0	0.875486391216342	2		251	675	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020703	26020718	+	coding_sequence_variant,5_prime_UTR_variant	Frame_Shift_Del	DEL	TGCTGTTTTTCCGTCA	TGCTGTTTTTCCGTCA	-	novel	NA	P-0041269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	98	240	0				ENST00000357647	NM_003529.2	?-1/136		1/1	0.492108173931743	4	FACETS	1	0.979	1	0.671	0.605	0.738	INDETERMINATE	1	TRUE	2	0.875486391216342	4		240	313	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485821	8485821	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	182	338	0	ENST00000356435.5:c.2996G>C	p.Ser999Thr	p.S999T	ENST00000356435		999	aGc/aCc	17/35	0.875486391216342	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.875486391216342	1		338	220	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519990	NA	P-0041330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	500	712	0	ENST00000269305.4:c.796G>C	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Cga	8/11	0.5372288475154	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.5372288475154	1		712	989	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530091	212530091	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	165	345	0	ENST00000342788.4:c.1828C>T	p.Pro610Ser	p.P610S	ENST00000342788	NM_005235.2	610	Cca/Tca	15/28	0.5372288475154	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.5372288475154	1		345	406	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119475	193119475	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0041387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	44	375	0	ENST00000367435.3:c.870T>A	p.Tyr290Ter	p.Y290*	ENST00000367435	NM_024529.4	290	taT/taA	9/17	0.14611031515016	2	FACETS	0.482	0.405	0.565	0.241	0.202	0.283	INDETERMINATE	1	TRUE	0	0.556944206660635	2		375	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579502	7579503	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CATCTGGACCTGGGTCTTCAGTGAAC	novel	NA	P-0041387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	119	879	0	ENST00000269305.4:c.159_184dup	p.Glu62GlyfsTer70	p.E62Gfs*70	ENST00000269305	NM_001126112.2	62	gaa/gGTTCACTGAAGACCCAGGTCCAGATGaa	4/11	0.55272279282083	2	FACETS	0.803	0.728	0.882	0.402	0.364	0.441	CLONAL	1	TRUE	0	0.556944206660635	2		879	532	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909971	50910565	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTATGACCTTGTCTCTGCTTTCCTGGCCTGACCACAGGTCCACGGTGGCCTTCAGGCTGCTCCCTCCTCCTCCCTCTGGCCCTGTGGACTCCCTGGCCCCCAACCCTACCTCCATCCCCACCCAGACCCTGACGACTTGGAGGGCCCTCCTGCCCGCCTCACCTCCCAGGCCCTCCCCAGGCTACCTCACCCTGACCCCCACTTCCTTCTCCTGCTCCACCTCCCACCCCCAACCCCTGGTCCCTGACCCCATCCGTGCCCATCCCCAGAATGGGAACGACCAGACCCGCCGCCGCCTGGCTGTGTACTGCCTGAAGGATGCCTACCTGCCACTGCGGCTGCTGGAGCGGCTCATGGTGCTGGTGAACGCCGTGGAGATGGCGAGGGTCACTGGCGTGCCCCTCAGCTACCTGCTCAGTCGTGGCCAGCAGGTCAAGGTCGTATCCCAGCTGTTGCGGCAGGTCAGTAGCCGAGACTTGTCCTCGCCACCCCCCACCAGGCACGTCTGTGGCCCCCTCCAGGCAATGGCATCCTGGATGCACTTTTTCTCCCCACTCCCAATCCGCACGGCCCCACCTATACCCACTCCATTTCC	CTATGACCTTGTCTCTGCTTTCCTGGCCTGACCACAGGTCCACGGTGGCCTTCAGGCTGCTCCCTCCTCCTCCCTCTGGCCCTGTGGACTCCCTGGCCCCCAACCCTACCTCCATCCCCACCCAGACCCTGACGACTTGGAGGGCCCTCCTGCCCGCCTCACCTCCCAGGCCCTCCCCAGGCTACCTCACCCTGACCCCCACTTCCTTCTCCTGCTCCACCTCCCACCCCCAACCCCTGGTCCCTGACCCCATCCGTGCCCATCCCCAGAATGGGAACGACCAGACCCGCCGCCGCCTGGCTGTGTACTGCCTGAAGGATGCCTACCTGCCACTGCGGCTGCTGGAGCGGCTCATGGTGCTGGTGAACGCCGTGGAGATGGCGAGGGTCACTGGCGTGCCCCTCAGCTACCTGCTCAGTCGTGGCCAGCAGGTCAAGGTCGTATCCCAGCTGTTGCGGCAGGTCAGTAGCCGAGACTTGTCCTCGCCACCCCCCACCAGGCACGTCTGTGGCCCCCTCCAGGCAATGGCATCCTGGATGCACTTTTTCTCCCCACTCCCAATCCGCACGGCCCCACCTATACCCACTCCATTTCC	-	novel	NA	P-0041387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	123	156	0	ENST00000440232.2:c.1494+198_1687-18del		p.X498_splice	ENST00000440232	NM_002691.3	498		13/27	0.506403124357994	2	FACETS	1	0.991	1	1	0.993	1	CLONAL	3	TRUE	0	0.556944206660635	2		156	132	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971124	55971124	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	96	542	0	ENST00000263923.4:c.1673A>C	p.Asp558Ala	p.D558A	ENST00000263923	NM_002253.2	558	gAc/gCc	13/30	0.193860815560425	2	FACETS	0.759	0.68	0.843	0.38	0.34	0.422	INDETERMINATE	1	TRUE	0	0.556944206660635	2		542	454	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003208	42003208	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0041411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	361	594	0	ENST00000219905.7:c.2745T>G	p.Tyr915Ter	p.Y915*	ENST00000219905	NM_001164273.1	915	taT/taG	8/24	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.842699231053247	2		594	838	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0041416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	201	502	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.34766653527943	5	FACETS	0.965	0.9	1	0.724	0.675	0.773	CLONAL	3	TRUE	1	0.371661404956278	5		502	582	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257892	198257892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	84	428	0	ENST00000335508.6:c.3560C>T	p.Thr1187Met	p.T1187M	ENST00000335508	NM_012433.2	1187	aCg/aTg	24/25	0.371661404956278	4	FACETS	0.99	0.876	1			1	CLONAL	1	TRUE	NA	0.371661404956278	4		428	626	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937198	36937198	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	133	778	0	ENST00000361632.4:c.1121C>A	p.Ser374Tyr	p.S374Y	ENST00000361632		374	tCt/tAt	9/16	0.337197177875449	3	FACETS	1	0.947	1	0.354	0.321	0.388	CLONAL	1	TRUE	0	0.371661404956278	3		778	800	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463390	463390	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs774502944	NA	P-0041416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	61	295	0	ENST00000399788.2:c.881A>G	p.Tyr294Cys	p.Y294C	ENST00000399788	NM_001042603.1	294	tAt/tGt	8/28	0.354510517639086	2	FACETS	0.925	0.802	1	0.462	0.401	0.529	CLONAL	1	TRUE	0	0.371661404956278	2		295	355	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574006	7574007	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0041416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	217	793	0	ENST00000269305.4:c.1020dup	p.Phe341ValfsTer6	p.F341Vfs*6	ENST00000269305	NM_001126112.2	340	-/G	10/11	0.319424539233268	2	FACETS	0.809	0.755	0.864	0.809	0.755	0.864	CLONAL	2	TRUE	0	0.371661404956278	2		793	722	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207162	1207162	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs137853076	NA	P-0041459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	68	753	0	ENST00000326873.7:c.250A>T	p.Lys84Ter	p.K84*	ENST00000326873	NM_000455.4	84	Aag/Tag	1/10	0.158971120727598	2	FACETS	0.915	0.797	1	0.457	0.398	0.521	INDETERMINATE	1	FALSE	0	0.283785399114343	2		753	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0041459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	82	490	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.283785399114343	2		490	480	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481417	140481417	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913348	NA	P-0041459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	59	354	0	ENST00000288602.6:c.1391G>T	p.Gly464Val	p.G464V	ENST00000288602	NM_004333.4	464	gGa/gTa	11/18	0.154625692146727	2	FACETS	1	0.969	1	0.732	0.635	0.836	INDETERMINATE	1	FALSE	0	0.283785399114343	2		354	284	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248536	8248536	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	60	439	0	ENST00000335790.3:c.351G>T	p.Gln117His	p.Q117H	ENST00000335790	NM_002315.2	117	caG/caT	3/4	1	2	FACETS	0.986	0.852	1	0.986	0.852	1	CLONAL	1	FALSE	1	0.283785399114343	2		439	429	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933355	100933355	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	34	418	0	ENST00000325455.5:c.2035C>G	p.Gln679Glu	p.Q679E	ENST00000325455	NM_001202474.3	679	Caa/Gaa	4/8	1	2	FACETS	0.786	0.644	0.944	0.786	0.644	0.944	CLONAL	1	FALSE	1	0.283785399114343	2		418	305	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531142	187531142	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	58	257	0	ENST00000441802.2:c.9881A>T	p.Asp3294Val	p.D3294V	ENST00000441802	NM_005245.3	3294	gAt/gTt	15/27	0.159118401345652	2	FACETS	0.751	0.651	0.858	0.751	0.651	0.858	INDETERMINATE	2	FALSE	0	0.283785399114343	2		257	272	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040053	180040053	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	55	639	0	ENST00000261937.6:c.3389A>T	p.Asp1130Val	p.D1130V	ENST00000261937	NM_182925.4	1130	gAc/gTc	25/30	0.252849693525255	3	FACETS	0.754	0.645	0.874			1	SUBCLONAL	1	FALSE	NA	0.283785399114343	3		639	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	436	1057	6	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.579266764200747	2	FACETS	0.954	0.917	0.99	0.954	0.917	0.99	CLONAL	2	TRUE	0	0.579266764200747	2		1063	789	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937461	178937461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776503460	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	194	232	0	ENST00000263967.3:c.1849C>T	p.Arg617Trp	p.R617W	ENST00000263967	NM_006218.2	617	Cgg/Tgg	12/21	0.579266764200747	8	FACETS	0.804	0.743	0.868	0.322	0.297	0.347	CLONAL	2	TRUE	3	0.579266764200747	8		232	1140	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600005	10600005	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	396	745	0	ENST00000171111.5:c.1571del	p.Gly524AlafsTer8	p.G524Afs*8	ENST00000171111	NM_203500.1	524	gGc/gc	5/6	0.579266764200747	2	FACETS	0.916	0.879	0.954	0.916	0.879	0.954	CLONAL	2	TRUE	0	0.579266764200747	2		745	746	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436088	49436088	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	305	606	0	ENST00000301067.7:c.5893G>T	p.Glu1965Ter	p.E1965*	ENST00000301067	NM_003482.3	1965	Gaa/Taa	28/54	NA	2	FACETS	0.95	0.907	0.994			1	INDETERMINATE	2	TRUE	NA	0.579266764200747	2		606	554	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956704	93956704	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	171	333	1	ENST00000369303.4:c.2533-1G>T		p.X845_splice	ENST00000369303	NM_004440.3	845			0.492386343305307	4	FACETS	0.925	0.858	0.994	0.925	0.858	0.994	CLONAL	2	TRUE	2	0.579266764200747	4		334	504	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335015	65335015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	279	546	0	ENST00000342505.4:c.626C>T	p.Pro209Leu	p.P209L	ENST00000342505	NM_002227.2	209	cCa/cTa	6/25	0.579266764200747	3	FACETS	0.941	0.89	0.992	0.941	0.89	0.992	CLONAL	2	TRUE	1	0.579266764200747	3		546	660	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649539	206649539	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	178	756	0	ENST00000367120.3:c.374A>T	p.His125Leu	p.H125L	ENST00000367120	NM_014002.3	125	cAc/cTc	6/22	0.579266764200747	4	FACETS	1	0.958	1	0.353	0.325	0.382	CLONAL	1	TRUE	1	0.579266764200747	4		756	917	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625453	69625453	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	362	703	0	ENST00000334134.2:c.340G>T	p.Glu114Ter	p.E114*	ENST00000334134	NM_005247.2	114	Gag/Tag	3/3	0.579266764200747	3	FACETS	0.954	0.909	0.999	0.954	0.909	0.999	CLONAL	2	TRUE	1	0.579266764200747	3		703	845	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446897	18446897	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	375	275	0	ENST00000266497.5:c.982C>A	p.Leu328Ile	p.L328I	ENST00000266497		328	Ctc/Atc	4/31	0.579266764200747	5	FACETS	1	0.993	1	0.872	0.835	0.908	CLONAL	3	TRUE	1	0.579266764200747	5		275	694	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420788	49420788	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	352	792	1	ENST00000301067.7:c.14961G>T	p.Trp4987Cys	p.W4987C	ENST00000301067	NM_003482.3	4987	tgG/tgT	48/54	NA	2	FACETS	0.919	0.879	0.959			1	INDETERMINATE	2	TRUE	NA	0.579266764200747	2		793	661	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589802	28589802	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	293	508	0	ENST00000241453.7:c.2578C>A	p.Leu860Met	p.L860M	ENST00000241453	NM_004119.2	860	Ctg/Atg	21/24	0.579266764200747	3	FACETS	0.883	0.835	0.931	0.883	0.835	0.931	CLONAL	2	TRUE	1	0.579266764200747	3		508	739	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437173	110437173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	21	428	0	ENST00000375856.3:c.1228G>A	p.Gly410Ser	p.G410S	ENST00000375856	NM_003749.2	410	Ggc/Agc	1/2	0.579266764200747	3	FACETS	1	0.894	1	1	0.894	1	CLONAL	2	TRUE	1	0.579266764200747	3		428	41	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40682130	40682130	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	288	477	0	ENST00000249776.8:c.685G>T	p.Ala229Ser	p.A229S	ENST00000249776	NM_033286.3	229	Gct/Tct	6/9	0.566434598845528	2	FACETS	0.897	0.854	0.941	0.897	0.854	0.941	CLONAL	2	TRUE	0	0.579266764200747	2		477	554	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762141	43762141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1471395709	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	476	600	0	ENST00000382044.4:c.1304C>T	p.Pro435Leu	p.P435L	ENST00000382044	NM_001141980.1	435	cCa/cTa	11/28	0.566434598845528	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.579266764200747	2		600	817	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778672	3778672	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs200780672	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	387	838	0	ENST00000262367.5:c.6376G>T	p.Gly2126Cys	p.G2126C	ENST00000262367	NM_004380.2	2126	Ggc/Tgc	31/31	0.553522501997424	4	FACETS	0.908	0.863	0.953	0.908	0.863	0.953	CLONAL	2	TRUE	2	0.579266764200747	4		838	1162	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783985	50783985	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	307	569	0	ENST00000398568.2:c.376G>T	p.Asp126Tyr	p.D126Y	ENST00000398568	NM_001042412.1	126	Gac/Tac	3/18	0.534637948999553	3	FACETS	0.879	0.832	0.925	0.879	0.832	0.925	CLONAL	2	TRUE	1	0.579266764200747	3		569	778	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347699	89347699	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	317	782	0	ENST00000301030.4:c.5251G>T	p.Ala1751Ser	p.A1751S	ENST00000301030	NM_001256183.1	1751	Gct/Tct	9/13	0.534637948999553	3	FACETS	0.886	0.84	0.932	0.886	0.84	0.932	CLONAL	2	TRUE	1	0.579266764200747	3		782	797	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441469	40441469	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	364	604	0	ENST00000345506.4:c.40G>C	p.Ala14Pro	p.A14P	ENST00000345506	NM_003152.3	14	Gcg/Ccg	3/20	0.553522501997424	4	FACETS	0.967	0.919	1	0.967	0.919	1	CLONAL	2	TRUE	2	0.579266764200747	4		604	1026	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453351	40453351	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	531	756	0	ENST00000345506.4:c.1048G>T	p.Ala350Ser	p.A350S	ENST00000345506	NM_003152.3	350	Gcc/Tcc	10/20	0.553522501997424	4	FACETS	0.979	0.939	1	0.979	0.939	1	CLONAL	2	TRUE	2	0.579266764200747	4		756	1479	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245390	41245390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80356875	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	427	512	0	ENST00000357654.3:c.2158G>A	p.Glu720Lys	p.E720K	ENST00000357654	NM_007294.3	720	Gaa/Aaa	10/23	0.553522501997424	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.579266764200747	4		512	1086	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117643	70117644	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	361	819	0	ENST00000245479.2:c.111_112delinsAT	p.Gly38Cys	p.G38C	ENST00000245479	NM_000346.3	37	tcGGgc/tcATgc	1/3	0.553522501997424	4	FACETS	0.956	0.908	1	0.956	0.908	1	CLONAL	2	TRUE	2	0.579266764200747	4		819	1030	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47602386	47602386	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	291	330	0	ENST00000263735.4:c.439G>T	p.Glu147Ter	p.E147*	ENST00000263735	NM_002354.2	147	Gaa/Taa	4/9	0.579266764200747	3	FACETS	0.929	0.889	0.968	0.929	0.889	0.968	CLONAL	3	TRUE	0	0.579266764200747	3		330	465	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190670445	190670445	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	325	411	0	ENST00000441310.2:c.383A>T	p.His128Leu	p.H128L	ENST00000441310	NM_000534.4	128	cAc/cTc	4/13	0.563088782980502	3	FACETS	0.963	0.925	1	0.963	0.925	1	CLONAL	3	TRUE	0	0.579266764200747	3		411	501	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378276	225378276	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	318	355	0	ENST00000264414.4:c.619G>T	p.Ala207Ser	p.A207S	ENST00000264414	NM_003590.4	207	Gct/Tct	5/16	0.563088782980502	3	FACETS	0.983	0.945	1	0.983	0.945	1	CLONAL	3	TRUE	0	0.579266764200747	3		355	480	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659793	227659793	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	413	511	0	ENST00000305123.5:c.3662G>T	p.Arg1221Leu	p.R1221L	ENST00000305123	NM_005544.2	1221	cGc/cTc	1/2	0.563088782980502	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	0	0.579266764200747	3		511	601	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546649	9546649	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	459	718	0	ENST00000353224.5:c.1373G>T	p.Gly458Val	p.G458V	ENST00000353224	NM_177990.2	458	gGc/gTc	5/10	0.485884306335508	4	FACETS	1	0.975	1			1	CLONAL	3	TRUE	NA	0.579266764200747	4		718	821	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385246	41385246	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	168	602	0	ENST00000373198.4:c.715G>T	p.Val239Phe	p.V239F	ENST00000373198	NM_133170.3	239	Gtc/Ttc	6/32	0.534637948999553	3	FACETS	0.94	0.865	1	0.47	0.432	0.509	CLONAL	1	TRUE	1	0.579266764200747	3		602	796	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292808	62292808	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	302	689	0	ENST00000360203.5:c.260C>T	p.Ser87Leu	p.S87L	ENST00000360203	NM_001283009.1	87	tCa/tTa	3/35	0.579266764200747	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	1	0.579266764200747	3		689	672	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574116	41574116	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	380	732	0	ENST00000263253.7:c.6401A>T	p.Asn2134Ile	p.N2134I	ENST00000263253	NM_001429.3	2134	aAt/aTt	31/31	0.565395086260775	3	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.579266764200747	3		732	803	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170016897	170016897	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	262	365	0	ENST00000295797.4:c.1702del	p.Asp568MetfsTer4	p.D568Mfs*4	ENST00000295797	NM_002740.5	568	Gat/at	17/18	0.579266764200747	6	FACETS	0.905	0.848	0.963			1	CLONAL	2	TRUE	NA	0.579266764200747	6		365	1079	SUCCESS
APC	324	MSKCC	GRCh37	5	112116555	112116555	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	326	458	0	ENST00000257430.4:c.600G>T	p.Met200Ile	p.M200I	ENST00000257430	NM_000038.5	200	atG/atT	6/16	0.563088782980502	3	FACETS	0.964	0.926	1	0.964	0.926	1	CLONAL	3	TRUE	0	0.579266764200747	3		458	502	SUCCESS
APC	324	MSKCC	GRCh37	5	112176998	112176998	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	440	634	0	ENST00000257430.4:c.5707A>T	p.Asn1903Tyr	p.N1903Y	ENST00000257430	NM_000038.5	1903	Aac/Tac	16/16	0.563088782980502	3	FACETS	0.975	0.942	1	0.975	0.942	1	CLONAL	3	TRUE	0	0.579266764200747	3		634	670	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520671	176520671	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1166961756	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	438	597	0	ENST00000292408.4:c.1414C>A	p.Pro472Thr	p.P472T	ENST00000292408	NM_213647.1	472	Ccc/Acc	11/18	0.532507278008479	5	FACETS	1	0.955	1			1	CLONAL	2	TRUE	NA	0.579266764200747	5		597	1410	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045811	26045812	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	256	915	0	ENST00000540144.1:c.173_174delinsAA	p.Ser58Ter	p.S58*	ENST00000540144	NM_003531.2	58	tCC/tAA	1/1	0.579266764200747	4	FACETS	0.754	0.707	0.802	0.754	0.707	0.802	SUBCLONAL	2	TRUE	2	0.579266764200747	4		915	926	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324581	31324581	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs151341152	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	254	618	0	ENST00000412585.2:c.227T>G	p.Ile76Arg	p.I76R	ENST00000412585	NM_005514.6	76	aTa/aGa	2/8	0.579266764200747	4	FACETS	1	0.989	1	0.63	0.589	0.671	CLONAL	1	TRUE	2	0.579266764200747	4		618	1100	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431620	6431620	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	83	265	0	ENST00000356142.4:c.173C>A	p.Thr58Lys	p.T58K	ENST00000356142	NM_018890.3	58	aCa/aAa	3/7	0.574804532406383	5	FACETS	0.897	0.793	1	0.224	0.198	0.253	CLONAL	1	TRUE	1	0.579266764200747	5		265	597	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467783	50467783	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	341	671	0	ENST00000331340.3:c.1018G>T	p.Val340Leu	p.V340L	ENST00000331340	NM_006060.4	340	Gtg/Ttg	8/8	0.579266764200747	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	1	0.579266764200747	3		671	754	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141582913	141582913	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0041477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	182	588	0	ENST00000220592.5:c.334A>T	p.Lys112Ter	p.K112*	ENST00000220592	NM_012154.3	112	Aag/Tag	3/19	0.553522501997424	4	FACETS	0.921	0.848	0.996	0.46	0.424	0.498	CLONAL	1	TRUE	2	0.579266764200747	4		588	1078	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	409	1057	6	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.612658619223865	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.613501090717209	2		1063	654	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937461	178937461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776503460	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	91	232	0	ENST00000263967.3:c.1849C>T	p.Arg617Trp	p.R617W	ENST00000263967	NM_006218.2	617	Cgg/Tgg	12/21	0.613501090717209	9	FACETS	1	0.977	1	0.237	0.21	0.266	CLONAL	1	TRUE	3	0.613501090717209	9		232	656	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600005	10600005	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	366	745	0	ENST00000171111.5:c.1571del	p.Gly524AlafsTer8	p.G524Afs*8	ENST00000171111	NM_203500.1	524	gGc/gc	5/6	0.612658619223865	2	FACETS	0.989	0.95	1	0.989	0.95	1	CLONAL	2	TRUE	0	0.613501090717209	2		745	603	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436088	49436088	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	251	606	0	ENST00000301067.7:c.5893G>T	p.Glu1965Ter	p.E1965*	ENST00000301067	NM_003482.3	1965	Gaa/Taa	28/54	NA	2	FACETS	0.991	0.944	1			1	INDETERMINATE	2	TRUE	NA	0.613501090717209	2		606	413	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956704	93956704	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	143	333	1	ENST00000369303.4:c.2533-1G>T		p.X845_splice	ENST00000369303	NM_004440.3	845			0.459731111054721	4	FACETS	0.99	0.913	1	0.99	0.913	1	CLONAL	2	TRUE	2	0.613501090717209	4		334	380	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335015	65335015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	233	546	0	ENST00000342505.4:c.626C>T	p.Pro209Leu	p.P209L	ENST00000342505	NM_002227.2	209	cCa/cTa	6/25	0.528972300483197	3	FACETS	0.86	0.809	0.912	0.86	0.809	0.912	CLONAL	2	TRUE	1	0.613501090717209	3		546	577	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649539	206649539	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	319	756	0	ENST00000367120.3:c.374A>T	p.His125Leu	p.H125L	ENST00000367120	NM_014002.3	125	cAc/cTc	6/22	0.345761110434843	5	FACETS	1	0.971	1	0.693	0.656	0.732	INDETERMINATE	2	TRUE	2	0.613501090717209	5		756	960	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625453	69625453	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	274	703	0	ENST00000334134.2:c.340G>T	p.Glu114Ter	p.E114*	ENST00000334134	NM_005247.2	114	Gag/Tag	3/3	0.355765949072768	5	FACETS	1	0.99	1	0.81	0.765	0.856	INDETERMINATE	2	TRUE	2	0.613501090717209	5		703	706	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446897	18446897	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	226	275	0	ENST00000266497.5:c.982C>A	p.Leu328Ile	p.L328I	ENST00000266497		328	Ctc/Atc	4/31	0.613501090717209	5	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	TRUE	2	0.613501090717209	5		275	453	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420788	49420788	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	376	792	1	ENST00000301067.7:c.14961G>T	p.Trp4987Cys	p.W4987C	ENST00000301067	NM_003482.3	4987	tgG/tgT	48/54	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	2	TRUE	NA	0.613501090717209	2		793	608	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589802	28589802	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	330	508	0	ENST00000241453.7:c.2578C>A	p.Leu860Met	p.L860M	ENST00000241453	NM_004119.2	860	Ctg/Atg	21/24	0.345761110434843	5	FACETS	0.894	0.85	0.939	0.894	0.85	0.939	INDETERMINATE	3	TRUE	2	0.613501090717209	5		508	770	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437173	110437173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	139	428	0	ENST00000375856.3:c.1228G>A	p.Gly410Ser	p.G410S	ENST00000375856	NM_003749.2	410	Ggc/Agc	1/2	0.345761110434843	5	FACETS	1	0.98	1	0.799	0.737	0.863	INDETERMINATE	2	TRUE	2	0.613501090717209	5		428	363	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40682130	40682130	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	250	477	0	ENST00000249776.8:c.685G>T	p.Ala229Ser	p.A229S	ENST00000249776	NM_033286.3	229	Gct/Tct	6/9	0.613027007805008	2	FACETS	0.952	0.906	0.998	0.952	0.906	0.998	CLONAL	2	TRUE	0	0.613501090717209	2		477	428	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762141	43762141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1471395709	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	373	600	0	ENST00000382044.4:c.1304C>T	p.Pro435Leu	p.P435L	ENST00000382044	NM_001141980.1	435	cCa/cTa	11/28	0.613027007805008	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.613501090717209	2		600	593	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778672	3778672	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs200780672	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	281	838	0	ENST00000262367.5:c.6376G>T	p.Gly2126Cys	p.G2126C	ENST00000262367	NM_004380.2	2126	Ggc/Tgc	31/31	0.459731111054721	4	FACETS	0.847	0.798	0.896	0.847	0.798	0.896	CLONAL	2	TRUE	2	0.613501090717209	4		838	873	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783985	50783985	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	295	569	0	ENST00000398568.2:c.376G>T	p.Asp126Tyr	p.D126Y	ENST00000398568	NM_001042412.1	126	Gac/Tac	3/18	0.275430599294313	3	FACETS	1	0.984	1	0.721	0.686	0.756	INDETERMINATE	2	TRUE	0	0.613501090717209	3		569	581	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347699	89347699	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	365	782	0	ENST00000301030.4:c.5251G>T	p.Ala1751Ser	p.A1751S	ENST00000301030	NM_001256183.1	1751	Gct/Tct	9/13	0.275430599294313	3	FACETS	1	0.989	1	0.734	0.702	0.766	INDETERMINATE	2	TRUE	0	0.613501090717209	3		782	706	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441469	40441469	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	264	604	0	ENST00000345506.4:c.40G>C	p.Ala14Pro	p.A14P	ENST00000345506	NM_003152.3	14	Gcg/Ccg	3/20	0.570760326367277	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.613501090717209	4		604	646	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453351	40453351	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	340	756	0	ENST00000345506.4:c.1048G>T	p.Ala350Ser	p.A350S	ENST00000345506	NM_003152.3	350	Gcc/Tcc	10/20	0.570760326367277	4	FACETS	0.931	0.884	0.98	0.931	0.884	0.98	CLONAL	2	TRUE	2	0.613501090717209	4		756	960	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245390	41245390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80356875	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	245	512	0	ENST00000357654.3:c.2158G>A	p.Glu720Lys	p.E720K	ENST00000357654	NM_007294.3	720	Gaa/Aaa	10/23	0.570760326367277	4	FACETS	0.93	0.874	0.987	0.93	0.874	0.987	CLONAL	2	TRUE	2	0.613501090717209	4		512	693	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117643	70117644	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	272	819	0	ENST00000245479.2:c.111_112delinsAT	p.Gly38Cys	p.G38C	ENST00000245479	NM_000346.3	37	tcGGgc/tcATgc	1/3	0.570760326367277	4	FACETS	0.868	0.817	0.92	0.868	0.817	0.92	CLONAL	2	TRUE	2	0.613501090717209	4		819	824	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47602386	47602386	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	248	330	0	ENST00000263735.4:c.439G>T	p.Glu147Ter	p.E147*	ENST00000263735	NM_002354.2	147	Gaa/Taa	4/9	0.613501090717209	4	FACETS	0.945	0.897	0.994	0.945	0.897	0.994	CLONAL	3	TRUE	1	0.613501090717209	4		330	460	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190670445	190670445	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	344	411	0	ENST00000441310.2:c.383A>T	p.His128Leu	p.H128L	ENST00000441310	NM_000534.4	128	cAc/cTc	4/13	0.613501090717209	3	FACETS	0.997	0.961	1	0.997	0.961	1	CLONAL	3	TRUE	0	0.613501090717209	3		411	490	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378276	225378276	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	253	355	0	ENST00000264414.4:c.619G>T	p.Ala207Ser	p.A207S	ENST00000264414	NM_003590.4	207	Gct/Tct	5/16	0.613501090717209	3	FACETS	0.966	0.924	1	0.966	0.924	1	CLONAL	3	TRUE	0	0.613501090717209	3		355	372	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659793	227659793	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	366	511	0	ENST00000305123.5:c.3662G>T	p.Arg1221Leu	p.R1221L	ENST00000305123	NM_005544.2	1221	cGc/cTc	1/2	0.613501090717209	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	TRUE	0	0.613501090717209	3		511	516	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546649	9546649	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	490	718	0	ENST00000353224.5:c.1373G>T	p.Gly458Val	p.G458V	ENST00000353224	NM_177990.2	458	gGc/gTc	5/10	0.570989530875738	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	1	0.613501090717209	4		718	846	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385246	41385246	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	133	602	0	ENST00000373198.4:c.715G>T	p.Val239Phe	p.V239F	ENST00000373198	NM_133170.3	239	Gtc/Ttc	6/32	0.25128686349293	2	FACETS	0.818	0.747	0.892	0.409	0.373	0.446	INDETERMINATE	1	TRUE	0	0.613501090717209	2		602	530	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292808	62292808	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	385	689	0	ENST00000360203.5:c.260C>T	p.Ser87Leu	p.S87L	ENST00000360203	NM_001283009.1	87	tCa/tTa	3/35	0.613501090717209	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.613501090717209	3		689	742	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574116	41574116	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	407	732	0	ENST00000263253.7:c.6401A>T	p.Asn2134Ile	p.N2134I	ENST00000263253	NM_001429.3	2134	aAt/aTt	31/31	0.469847713301746	5	FACETS	0.952	0.911	0.994			1	CLONAL	3	TRUE	NA	0.613501090717209	5		732	892	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170016897	170016897	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	189	365	0	ENST00000295797.4:c.1702del	p.Asp568MetfsTer4	p.D568Mfs*4	ENST00000295797	NM_002740.5	568	Gat/at	17/18	0.613501090717209	9	FACETS	1	0.983	1	0.401	0.371	0.433	CLONAL	2	TRUE	3	0.613501090717209	9		365	805	SUCCESS
APC	324	MSKCC	GRCh37	5	112116555	112116555	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	317	458	0	ENST00000257430.4:c.600G>T	p.Met200Ile	p.M200I	ENST00000257430	NM_000038.5	200	atG/atT	6/16	0.585111276667572	3	FACETS	0.936	0.899	0.972	0.936	0.899	0.972	CLONAL	3	TRUE	0	0.613501090717209	3		458	481	SUCCESS
APC	324	MSKCC	GRCh37	5	112176998	112176998	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	430	634	0	ENST00000257430.4:c.5707A>T	p.Asn1903Tyr	p.N1903Y	ENST00000257430	NM_000038.5	1903	Aac/Tac	16/16	0.585111276667572	3	FACETS	0.915	0.884	0.947	0.915	0.884	0.947	CLONAL	3	TRUE	0	0.613501090717209	3		634	667	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520671	176520671	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1166961756	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	234	597	0	ENST00000292408.4:c.1414C>A	p.Pro472Thr	p.P472T	ENST00000292408	NM_213647.1	472	Ccc/Acc	11/18	0.533441465255286	5	FACETS	0.919	0.86	0.98	0.613	0.573	0.653	CLONAL	2	TRUE	2	0.613501090717209	5		597	797	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045811	26045812	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	331	915	0	ENST00000540144.1:c.173_174delinsAA	p.Ser58Ter	p.S58*	ENST00000540144	NM_003531.2	58	tCC/tAA	1/1	0.459731111054721	4	FACETS	0.916	0.868	0.965	0.916	0.868	0.965	CLONAL	2	TRUE	2	0.613501090717209	4		915	950	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324581	31324581	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs151341152	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	199	618	0	ENST00000412585.2:c.227T>G	p.Ile76Arg	p.I76R	ENST00000412585	NM_005514.6	76	aTa/aGa	2/8	0.459731111054721	4	FACETS	1	0.99	1	0.697	0.647	0.748	CLONAL	1	TRUE	2	0.613501090717209	4		618	751	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431620	6431620	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	88	265	0	ENST00000356142.4:c.173C>A	p.Thr58Lys	p.T58K	ENST00000356142	NM_018890.3	58	aCa/aAa	3/7	0.613501090717209	5	FACETS	1	0.965	1	0.303	0.269	0.338	CLONAL	1	TRUE	1	0.613501090717209	5		265	455	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467783	50467783	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	237	671	0	ENST00000331340.3:c.1018G>T	p.Val340Leu	p.V340L	ENST00000331340	NM_006060.4	340	Gtg/Ttg	8/8	0.400110650500718	3	FACETS	0.875	0.823	0.927	0.875	0.823	0.927	CLONAL	2	TRUE	1	0.613501090717209	3		671	577	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141582913	141582913	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	157	588	0	ENST00000220592.5:c.334A>T	p.Lys112Ter	p.K112*	ENST00000220592	NM_012154.3	112	Aag/Tag	3/19	0.355765949072768	5	FACETS	1	0.982	1	0.417	0.383	0.454	INDETERMINATE	1	TRUE	2	0.613501090717209	5		588	785	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317499	163317559	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTTCTAAATCCTAATTGGTTATGTTGACTTTAAATACTTCTTATAAAATACAGAGCCTGA	ATTTCTAAATCCTAATTGGTTATGTTGACTTTAAATACTTCTTATAAAATACAGAGCCTGA	-	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	41	178	0	ENST00000271452.3:c.949-53_956del		p.X317_splice	ENST00000271452	NM_145697.2	317		12/14	0.345761110434843	5	FACETS	1	0.881	1	0.354	0.296	0.416	INDETERMINATE	1	TRUE	2	0.613501090717209	5		178	242	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47598965	47598965	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	345	701	0	ENST00000430070.2:c.635C>A	p.Ser212Ter	p.S212*	ENST00000430070	NM_018095.4	212	tCg/tAg	2/4	0.355765949072768	5	FACETS	0.889	0.846	0.932	0.889	0.846	0.932	INDETERMINATE	3	TRUE	2	0.613501090717209	5		701	810	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50733604	50733604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	183	450	0	ENST00000307179.4:c.163G>A	p.Asp55Asn	p.D55N	ENST00000307179		55	Gat/Aat	3/20	0.613027007805008	2	FACETS	0.904	0.851	0.957	0.904	0.851	0.957	CLONAL	2	TRUE	0	0.613501090717209	2		450	330	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679864	33679864	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	292	640	0	ENST00000308377.4:c.2217G>T	p.Lys739Asn	p.K739N	ENST00000308377	NM_152270.3	739	aaG/aaT	5/5	0.570760326367277	4	FACETS	0.955	0.903	1	0.955	0.903	1	CLONAL	2	TRUE	2	0.613501090717209	4		640	804	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690442	33690442	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	330	683	1	ENST00000308377.4:c.385A>G	p.Ser129Gly	p.S129G	ENST00000308377	NM_152270.3	129	Agt/Ggt	2/5	0.570760326367277	4	FACETS	0.939	0.89	0.989	0.939	0.89	0.989	CLONAL	2	TRUE	2	0.613501090717209	4		684	924	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61323266	61323266	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	43	43	0	ENST00000283752.5:c.798G>C	p.Leu266Phe	p.L266F	ENST00000283752	NM_006919.2	266	ttG/ttC	8/8	0.598143685258756	2	FACETS	0.865	0.79	0.93	1	0.973	1	CLONAL	3	TRUE	0	0.613501090717209	2		43	54	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010593	48010593	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	113	683	0	ENST00000234420.5:c.221G>C	p.Gly74Ala	p.G74A	ENST00000234420	NM_000179.2	74	gGa/gCa	1/10	0.613501090717209	4	FACETS	0.764	0.687	0.845	0.255	0.229	0.282	SUBCLONAL	1	TRUE	1	0.613501090717209	4		683	778	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21345981	21345981	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	305	809	1	ENST00000215739.8:c.856G>T	p.Gly286Trp	p.G286W	ENST00000215739	NM_006767.3	286	Ggg/Tgg	9/21	0.400110650500718	3	FACETS	0.937	0.89	0.985	0.937	0.89	0.985	CLONAL	2	TRUE	1	0.613501090717209	3		810	693	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796232	57796232	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041477-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	309	531	0	ENST00000309042.7:c.1208A>T	p.Asn403Ile	p.N403I	ENST00000309042	NM_005612.4	403	aAt/aTt	4/4	0.612658619223865	2	FACETS	0.965	0.923	1	0.965	0.923	1	CLONAL	2	TRUE	0	0.613501090717209	2		531	522	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610363	10610363	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	292	649	0	ENST00000171111.5:c.347G>C	p.Arg116Pro	p.R116P	ENST00000171111	NM_203500.1	116	cGg/cCg	2/6	0.615429069423558	1	FACETS	0.944	0.894	0.993	0.944	0.894	0.993	CLONAL	1	TRUE	0	0.63	1		649	673	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207064	1207065	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1131690917	NA	P-0041484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	258	692	0	ENST00000326873.7:c.157dup	p.Asp53GlyfsTer110	p.D53Gfs*110	ENST00000326873	NM_000455.4	51	atg/atGg	1/10	0.615429069423558	1	FACETS	0.912	0.861	0.964	0.912	0.861	0.964	CLONAL	1	TRUE	0	0.63	1		692	615	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205071	123205071	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	151	230	0	ENST00000218089.9:c.2431G>T	p.Glu811Ter	p.E811*	ENST00000218089	NM_001042749.1	811	Gag/Tag	25/35	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.63	1		230	253	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259227	89259227	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	150	438	0	ENST00000336596.2:c.371A>T	p.Tyr124Phe	p.Y124F	ENST00000336596	NM_005233.5	124	tAc/tTc	3/17	1	2	FACETS	0.932	0.857	1	0.932	0.857	1	CLONAL	1	TRUE	1	0.63	2		438	511	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097619	8097619	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0041484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	76	241	0	ENST00000346208.3:c.1A>G	p.Met1?	p.M1?	ENST00000346208		1	Atg/Gtg	2/6	1	2	FACETS	0.847	0.751	0.947	0.847	0.751	0.947	CLONAL	1	TRUE	1	0.63	2		241	285	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0041522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	162	714	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.3	3	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	1	0.23	3		714	778	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0041522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	226	430	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.3	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.23	3		430	922	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0041522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	53	409	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	0.813	0.693	0.944	0.813	0.693	0.944	CLONAL	1	TRUE	1	0.23	2		409	567	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019943	123019943	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	117	606	0	ENST00000355640.3:c.431G>C	p.Gly144Ala	p.G144A	ENST00000355640		144	gGg/gCg	2/7	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.23	2		606	819	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591895	48591895	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs377767346	NA	P-0041524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	127	504	0	ENST00000342988.3:c.1058A>G	p.Tyr353Cys	p.Y353C	ENST00000342988	NM_005359.5	353	tAc/tGc	9/12	0.328814150744553	2	FACETS	0.826	0.754	0.901	0.826	0.754	0.901	CLONAL	2	TRUE	0	0.346918593510226	2		504	443	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134564	41134564	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	65	460	0	ENST00000379561.5:c.1064T>C	p.Met355Thr	p.M355T	ENST00000379561	NM_002015.3	355	aTg/aCg	2/3	0.346918593510226	3	FACETS	0.883	0.767	1	0.441	0.383	0.504	CLONAL	1	TRUE	1	0.346918593510226	3		460	498	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411883	116411905	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCTTTCTCTCTGTTTTAAGATC	TTCTTTCTCTCTGTTTTAAGATC	-	novel	NA	P-0041524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	361	1005	0	ENST00000397752.3:c.2888-19_2891del		p.X963_splice	ENST00000397752	NM_000245.2	963		14/21	0.346918593510226	3	FACETS	0.97	0.925	1	0.97	0.925	1	CLONAL	3	TRUE	0	0.346918593510226	3		1005	839	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0041527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	27	615	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.22	0.174	0.273	0.22	0.174	0.273	SUBCLONAL	1	TRUE	1	0.456577083351545	2		615	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578451	7578458	+	frameshift_variant	Frame_Shift_Del	DEL	ATGGCGCG	ATGGCGCG	-	novel	NA	P-0041535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	191	901	0	ENST00000269305.4:c.472_479del	p.Arg158GlyfsTer20	p.R158Gfs*20	ENST00000269305	NM_001126112.2	158	CGCGCCATg/g	5/11	0.45050086458711	1	FACETS	0.965	0.896	1	0.965	0.896	1	CLONAL	1	TRUE	0	0.45050086458711	1		901	681	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907100	101907100	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	77	391	0	ENST00000374994.4:c.1060C>A	p.Leu354Met	p.L354M	ENST00000374994	NM_004612.2	354	Ctg/Atg	6/9	1	2	FACETS	0.81	0.714	0.912	0.81	0.714	0.912	CLONAL	1	TRUE	1	0.45050086458711	2		391	422	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390759	139390760	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0041535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	154	1119	0	ENST00000277541.6:c.7431dup	p.Ala2478ArgfsTer29	p.A2478Rfs*29	ENST00000277541	NM_017617.3	2477	-/C	34/34	1	2	FACETS	0.858	0.786	0.933	0.858	0.786	0.933	CLONAL	1	TRUE	1	0.45050086458711	2		1119	797	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	187	82	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.938	0.869	1	0.938	0.869	1	CLONAL	1	TRUE	1	0.54697770535719	2		82	729	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806089	1806089	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913479	NA	P-0041577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	785	796	0	ENST00000260795.2:c.1108G>T	p.Gly370Cys	p.G370C	ENST00000260795		370	Ggc/Tgc	8/17	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.54697770535719	2		796	1329	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793881	NA	P-0041577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	372	644	1	ENST00000269305.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGg/gAg	8/11	0.54697770535719	1	FACETS	0.999	0.951	1	0.999	0.951	1	CLONAL	1	TRUE	0	0.54697770535719	1		645	989	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349973	70349973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1421325265	NA	P-0041577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	289	664	4	ENST00000374080.3:c.3956G>A	p.Arg1319His	p.R1319H	ENST00000374080		1319	cGc/cAc	28/45	1	2	FACETS	0.934	0.879	0.991	0.934	0.879	0.991	CLONAL	1	TRUE	1	0.54697770535719	2		668	1131	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870210	44870210	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	42	397	0	ENST00000377967.4:c.389C>A	p.Ala130Asp	p.A130D	ENST00000377967	NM_021140.2	130	gCt/gAt	5/29	1	2	FACETS	0.434	0.363	0.512	0.434	0.363	0.512	SUBCLONAL	1	TRUE	1	0.54697770535719	2		397	354	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717738	89717739	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TAGA	novel	NA	P-0041577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	82	360	0	ENST00000371953.3:c.764_767dup	p.Glu256AspfsTer43	p.E256Dfs*43	ENST00000371953	NM_000314.4	255	gta/gTAGAta	7/9	0.54697770535719	1	FACETS	0.784	0.699	0.871	0.784	0.699	0.871	SUBCLONAL	1	TRUE	0	0.54697770535719	1		360	278	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422940	12422940	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	156	516	1	ENST00000287820.6:c.430G>C	p.Asp144His	p.D144H	ENST00000287820	NM_015869.4	144	Gat/Cat	3/7	0.519155138044982	1	FACETS	0.814	0.751	0.879	0.814	0.751	0.879	CLONAL	1	TRUE	0	0.54697770535719	1		517	509	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054591	5054591	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1443023071	NA	P-0041577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	16	239	0	ENST00000381652.3:c.643C>T	p.Arg215Ter	p.R215*	ENST00000381652	NM_004972.3	215	Cga/Tga	7/25	0.54697770535719	1	FACETS	0.24	0.178	0.314	0.24	0.178	0.314	SUBCLONAL	1	TRUE	0	0.54697770535719	1		239	177	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041577-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	181	82	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.343889145324245	2		82	860	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806089	1806089	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913479	NA	P-0041577-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	627	796	0	ENST00000260795.2:c.1108G>T	p.Gly370Cys	p.G370C	ENST00000260795		370	Ggc/Tgc	8/17	1	2	FACETS	1	0.996	1	1	0.998	1	CLONAL	2	TRUE	1	0.343889145324245	2		796	1494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793881	NA	P-0041577-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	262	644	1	ENST00000269305.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGg/gAg	8/11	0.343889145324245	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.343889145324245	1		645	1118	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349973	70349973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1421325265	NA	P-0041577-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	205	664	4	ENST00000374080.3:c.3956G>A	p.Arg1319His	p.R1319H	ENST00000374080		1319	cGc/cAc	28/45	1	2	FACETS	0.995	0.922	1	0.995	0.922	1	CLONAL	1	TRUE	1	0.343889145324245	2		668	1198	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870210	44870210	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041577-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	23	397	0	ENST00000377967.4:c.389C>A	p.Ala130Asp	p.A130D	ENST00000377967	NM_021140.2	130	gCt/gAt	5/29	1	2	FACETS	0.341	0.265	0.429	0.341	0.265	0.429	SUBCLONAL	1	TRUE	1	0.343889145324245	2		397	392	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717738	89717739	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TAGA	novel	NA	P-0041577-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	53	360	0	ENST00000371953.3:c.764_767dup	p.Glu256AspfsTer43	p.E256Dfs*43	ENST00000371953	NM_000314.4	255	gta/gTAGAta	7/9	0.343889145324245	1	FACETS	0.993	0.855	1	0.993	0.855	1	CLONAL	1	TRUE	0	0.343889145324245	1		360	257	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422940	12422940	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041577-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	73	516	1	ENST00000287820.6:c.430G>C	p.Asp144His	p.D144H	ENST00000287820	NM_015869.4	144	Gat/Cat	3/7	0.343889145324245	1	FACETS	0.875	0.769	0.987	0.875	0.769	0.987	CLONAL	1	TRUE	0	0.343889145324245	1		517	402	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440899	52440899	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	172	537	0	ENST00000460680.1:c.605G>A	p.Trp202Ter	p.W202*	ENST00000460680	NM_004656.3	202	tGg/tAg	8/17	0.385200972308246	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.385200972308246	1		537	637	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1932488	1932488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	154	657	0	ENST00000382891.5:c.1546G>A	p.Glu516Lys	p.E516K	ENST00000382891	NM_133335.3	516	Gaa/Aaa	6/22	1	2	FACETS	0.979	0.896	1	0.979	0.896	1	CLONAL	1	TRUE	1	0.385200972308246	2		657	817	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0041624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	476	621	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.480783967649377	3	FACETS	1	0.996	1	0.829	0.8	0.859	CLONAL	2	TRUE	0	0.60681607918808	3		622	822	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921566	178921566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793349	NA	P-0041624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	102	283	0	ENST00000263967.3:c.1048G>A	p.Asp350Asn	p.D350N	ENST00000263967	NM_006218.2	350	Gac/Aac	5/21	0.60681607918808	4	FACETS	1	0.981	1	0.702	0.632	0.774	CLONAL	1	TRUE	2	0.60681607918808	4		283	385	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004667	150004676	+	frameshift_variant	Frame_Shift_Del	DEL	TCCAAGAAGG	TCCAAGAAGG	-	novel	NA	P-0041624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	206	580	0	ENST00000253339.5:c.1549_1558del	p.Pro517TyrfsTer21	p.P517Yfs*21	ENST00000253339		517	CCTTCTTGGAta/ta	3/7	0.400557934028509	5	FACETS	0.769	0.715	0.825	0.513	0.476	0.55	SUBCLONAL	2	TRUE	2	0.60681607918808	5		580	843	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796882	42796883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761345552	NA	P-0041625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	314	959	6	ENST00000575354.2:c.3347dup	p.Ser1117LysfsTer34	p.S1117Kfs*34	ENST00000575354	NM_015125.3	1114	gcc/gCcc	14/20	1	2	FACETS	0.873	0.828	0.919	0.873	0.828	0.919	CLONAL	1	TRUE	1	0.89	2		965	808	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293850	1293850	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1167344136	NA	P-0041625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	264	1082	2	ENST00000310581.5:c.1151A>G	p.Gln384Arg	p.Q384R	ENST00000310581	NM_198253.2	384	cAg/cGg	2/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.89	2		1084	593	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157404	106157404	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs751233117	NA	P-0041630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	200	406	0	ENST00000380013.4:c.2305C>T	p.Gln769Ter	p.Q769*	ENST00000380013	NM_001127208.2	769	Cag/Tag	3/11	0.512525322011893	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.51483600850699	2		406	338	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0041630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	114	612	0	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	0.249399727223536	0	FACETS	0.547	0.496	0.599			1	INDETERMINATE	1	TRUE	0	0.51483600850699	0		612	393	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65300283	65300283	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	89	355	0	ENST00000342505.4:c.3427C>T	p.Gln1143Ter	p.Q1143*	ENST00000342505	NM_002227.2	1143	Cag/Tag	25/25	1	2	FACETS	0.858	0.765	0.955	0.858	0.765	0.955	CLONAL	1	TRUE	1	0.51483600850699	2		355	403	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873782	151873782	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0041630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	92	442	0	ENST00000262189.6:c.8756C>G	p.Ser2919Ter	p.S2919*	ENST00000262189	NM_170606.2	2919	tCa/tGa	38/59	NA	2	FACETS	0.943	0.844	1			1	INDETERMINATE	1	TRUE	NA	0.51483600850699	2		442	379	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874644	151874644	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	101	555	0	ENST00000262189.6:c.7894C>T	p.Gln2632Ter	p.Q2632*	ENST00000262189	NM_170606.2	2632	Caa/Taa	38/59	NA	2	FACETS	0.923	0.831	1			1	INDETERMINATE	1	TRUE	NA	0.51483600850699	2		555	425	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324917	31324917	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs776780353	NA	P-0041630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	177	1492	0	ENST00000412585.2:c.19C>T	p.Arg7Ter	p.R7*	ENST00000412585	NM_005514.6	7	Cga/Tga	1/8	0.51483600850699	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.51483600850699	1		1492	419	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	139	333	0	ENST00000397062.3:c.92G>T	p.Gly31Val	p.G31V	ENST00000397062	NM_006164.4	31	gGa/gTa	2/5	NA	2	FACETS	1	0.957	1			1	INDETERMINATE	1	TRUE	NA	0.51483600850699	2		333	505	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912276	29912276	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0041630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	227	826	0	ENST00000376809.5:c.896-1G>A		p.X299_splice	ENST00000376809	NM_002116.7	299			0.51483600850699	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.51483600850699	1		826	577	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207590	2207590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	145	794	1	ENST00000398665.3:c.874C>T	p.Arg292Cys	p.R292C	ENST00000398665	NM_032482.2	292	Cgc/Tgc	11/28	0.453147252628904	1	FACETS	0.925	0.851	1	0.925	0.851	1	CLONAL	1	TRUE	0	0.51483600850699	1		795	452	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228002	36228002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	129	810	0	ENST00000222270.7:c.7388G>A	p.Arg2463Lys	p.R2463K	ENST00000222270	NM_014727.1	2463	aGa/aAa	33/37	1	2	FACETS	0.926	0.844	1	0.926	0.844	1	CLONAL	1	TRUE	1	0.51483600850699	2		810	541	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198269898	198269898	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	117	336	0	ENST00000335508.6:c.1441G>C	p.Asp481His	p.D481H	ENST00000335508	NM_012433.2	481	Gat/Cat	11/25	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.51483600850699	2		336	406	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	119	688	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	1	2	FACETS	0.824	0.742	0.912	0.824	0.742	0.912	CLONAL	1	TRUE	1	0.24	2		688	1203	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528768	8528768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	24	322	0	ENST00000356435.5:c.364C>T	p.Pro122Ser	p.P122S	ENST00000356435		122	Ccc/Tcc	4/35	0.200333286721931	1	FACETS	0.432	0.338	0.541	0.432	0.338	0.541	SUBCLONAL	1	TRUE	0	0.24	1		322	407	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486101	8486101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	53	500	0	ENST00000356435.5:c.2716G>A	p.Glu906Lys	p.E906K	ENST00000356435		906	Gag/Aag	17/35	0.200333286721931	1	FACETS	0.636	0.542	0.74	0.636	0.542	0.74	SUBCLONAL	1	TRUE	0	0.24	1		500	611	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716098	243716098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	92	484	0	ENST00000263826.5:c.1096C>T	p.Pro366Ser	p.P366S	ENST00000263826	NM_005465.4	366	Cct/Tct	10/13	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.24	2		484	712	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295674	212295674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1362156940	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	41	332	0	ENST00000342788.4:c.2639G>A	p.Gly880Glu	p.G880E	ENST00000342788	NM_005235.2	880	gGa/gAa	21/28	1	2	FACETS	0.709	0.59	0.841	0.709	0.59	0.841	SUBCLONAL	1	TRUE	1	0.24	2		332	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578476	7578476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767328513	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	20	805	1	ENST00000269305.4:c.454C>T	p.Pro152Ser	p.P152S	ENST00000269305	NM_001126112.2	152	Ccg/Tcg	5/11	0.200333286721931	1	FACETS	0.17	0.129	0.218	0.17	0.129	0.218	SUBCLONAL	1	TRUE	0	0.24	1		806	863	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315429	30315429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758186567	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	68	588	0	ENST00000322652.5:c.1114C>T	p.Pro372Ser	p.P372S	ENST00000322652	NM_015355.2	372	Cct/Tct	10/16	1	2	FACETS	0.727	0.632	0.831	0.727	0.632	0.831	SUBCLONAL	1	TRUE	1	0.24	2		588	779	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076812	72076812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	47	416	0	ENST00000357731.5:c.685G>A	p.Glu229Lys	p.E229K	ENST00000357731	NM_173808.2	229	Gaa/Aaa	5/7	1	2	FACETS	0.777	0.656	0.911	0.777	0.656	0.911	CLONAL	1	TRUE	1	0.24	2		416	504	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259967	16259967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	94	620	0	ENST00000375759.3:c.7232C>T	p.Ser2411Leu	p.S2411L	ENST00000375759	NM_015001.2	2411	tCg/tTg	11/15	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.24	2		620	756	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944967	31944967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	71	582	0	ENST00000340398.3:c.134C>T	p.Thr45Ile	p.T45I	ENST00000340398	NM_001013699.2	45	aCc/aTc	1/1	1	2	FACETS	0.901	0.786	1	0.901	0.786	1	CLONAL	1	TRUE	1	0.24	2		582	657	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932047	36932047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146617729	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	79	640	0	ENST00000361632.4:c.2422G>A	p.Glu808Lys	p.E808K	ENST00000361632		808	Gag/Aag	16/16	1	2	FACETS	0.882	0.776	0.998	0.882	0.776	0.998	CLONAL	1	TRUE	1	0.24	2		640	746	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388076	81388076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	61	425	0	ENST00000222390.5:c.299C>T	p.Pro100Leu	p.P100L	ENST00000222390	NM_000601.4	100	cCc/cTc	3/18	1	2	FACETS	0.837	0.722	0.963	0.837	0.722	0.963	CLONAL	1	TRUE	1	0.24	2		425	607	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346575	81346575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	37	330	0	ENST00000222390.5:c.1378C>T	p.Pro460Ser	p.P460S	ENST00000222390	NM_000601.4	460	Cct/Tct	11/18	1	2	FACETS	0.743	0.613	0.888	0.743	0.613	0.888	SUBCLONAL	1	TRUE	1	0.24	2		330	415	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029408	14029408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368830992	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	52	371	0	ENST00000311895.7:c.1619C>T	p.Ser540Leu	p.S540L	ENST00000311895	NM_005236.2	540	tCg/tTg	8/11	1	2	FACETS	0.881	0.75	1	0.881	0.75	1	CLONAL	1	TRUE	1	0.24	2		371	492	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587251	212587251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868149408	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	34	372	0	ENST00000342788.4:c.750G>A	p.Met250Ile	p.M250I	ENST00000342788	NM_005235.2	250	atG/atA	7/28	1	2	FACETS	0.574	0.468	0.693	0.574	0.468	0.693	SUBCLONAL	1	TRUE	1	0.24	2		372	494	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817882	3817882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757051244	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	83	471	0	ENST00000262367.5:c.3089C>T	p.Ser1030Phe	p.S1030F	ENST00000262367	NM_004380.2	1030	tCc/tTc	16/31	1	2	FACETS	0.982	0.867	1	0.982	0.867	1	CLONAL	1	TRUE	1	0.24	2		471	704	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561705	55561705	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	39	278	0	ENST00000288135.5:c.95G>A	p.Gly32Glu	p.G32E	ENST00000288135	NM_000222.2	32	gGg/gAg	2/21	0.200333286721931	1	FACETS	0.792	0.658	0.941	0.792	0.658	0.941	CLONAL	1	TRUE	0	0.24	1		278	361	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982021	93982021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867625037	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	22	280	0	ENST00000369303.4:c.1444G>A	p.Glu482Lys	p.E482K	ENST00000369303	NM_004440.3	482	Gag/Aag	6/17	1	2	FACETS	0.512	0.396	0.647	0.512	0.396	0.647	SUBCLONAL	1	TRUE	1	0.24	2		280	358	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857935	9857935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	83	620	0	ENST00000330684.3:c.3466G>A	p.Glu1156Lys	p.E1156K	ENST00000330684	NM_001134407.1	1156	Gaa/Aaa	13/13	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.24	2		620	628	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356430	66356430	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs943944162	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	23	300	0	ENST00000273854.3:c.1067G>A	p.Arg356Lys	p.R356K	ENST00000273854	NM_004439.5	356	aGa/aAa	5/18	0.200333286721931	1	FACETS	0.513	0.4	0.643	0.513	0.4	0.643	SUBCLONAL	1	TRUE	0	0.24	1		300	329	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052602	42052602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	58	434	0	ENST00000219905.7:c.7273C>T	p.Arg2425Cys	p.R2425C	ENST00000219905	NM_001164273.1	2425	Cgc/Tgc	20/24	1	2	FACETS	0.914	0.786	1	0.914	0.786	1	CLONAL	1	TRUE	1	0.24	2		434	529	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486824	56486824	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1023742896	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	87	517	0	ENST00000267101.3:c.1238C>T	p.Ser413Phe	p.S413F	ENST00000267101	NM_001982.3	413	tCc/tTc	11/28	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.24	2		517	724	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460582	149460582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	85	597	0	ENST00000286301.3:c.55G>A	p.Gly19Arg	p.G19R	ENST00000286301	NM_005211.3	19	Gga/Aga	3/22	0.116440304425289	0	FACETS	0.807	0.714	0.907			1	INDETERMINATE	1	TRUE	0	0.24	0		597	667	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942172	81942172	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	75	471	0	ENST00000359376.3:c.1709C>T	p.Pro570Leu	p.P570L	ENST00000359376	NM_002661.3	570	cCc/cTc	17/33	1	2	FACETS	0.933	0.817	1	0.933	0.817	1	CLONAL	1	TRUE	1	0.24	2		471	670	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642515	117642515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	68	562	1	ENST00000368508.3:c.5684G>A	p.Gly1895Glu	p.G1895E	ENST00000368508	NM_002944.2	1895	gGg/gAg	35/43	1	2	FACETS	0.675	0.586	0.771	0.675	0.586	0.771	SUBCLONAL	1	TRUE	1	0.24	2		563	840	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164691	36164691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868527382	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	92	803	1	ENST00000300305.3:c.1184C>T	p.Pro395Leu	p.P395L	ENST00000300305		395	cCg/cTg	8/8	1	2	FACETS	0.938	0.833	1	0.938	0.833	1	CLONAL	1	TRUE	1	0.24	2		804	817	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012419	29012419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867762505	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	71	580	0	ENST00000282397.4:c.452G>A	p.Gly151Glu	p.G151E	ENST00000282397	NM_002019.4	151	gGa/gAa	4/30	0.200333286721931	1	FACETS	0.731	0.638	0.833	0.731	0.638	0.833	SUBCLONAL	1	TRUE	0	0.24	1		580	712	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418373	139418373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	109	837	0	ENST00000277541.6:c.199C>T	p.Pro67Ser	p.P67S	ENST00000277541	NM_017617.3	67	Ccc/Tcc	3/34	0.200333286721931	1	FACETS	0.963	0.864	1	0.963	0.864	1	CLONAL	1	TRUE	0	0.24	1		837	830	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141112	55141112	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	50	413	0	ENST00000257290.5:c.1758G>A	p.Trp586Ter	p.W586*	ENST00000257290	NM_006206.4	586	tgG/tgA	12/23	0.200333286721931	1	FACETS	0.748	0.635	0.872	0.748	0.635	0.872	SUBCLONAL	1	TRUE	0	0.24	1		413	490	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332469	70332469	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866518744	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	69	573	0	ENST00000373644.4:c.374C>T	p.Ser125Phe	p.S125F	ENST00000373644	NM_030625.2	125	tCc/tTc	2/12	1	2	FACETS	0.729	0.634	0.832	0.729	0.634	0.832	SUBCLONAL	1	TRUE	1	0.24	2		573	789	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917081	50917081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs541483366	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	82	824	0	ENST00000440232.2:c.2333C>T	p.Ala778Val	p.A778V	ENST00000440232	NM_002691.3	778	gCc/gTc	19/27	1	2	FACETS	0.744	0.655	0.841	0.744	0.655	0.841	SUBCLONAL	1	TRUE	1	0.24	2		824	918	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578264	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	69	631	2	ENST00000269305.4:c.585_586delinsTT	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	195	atCCga/atTTga	6/11	0.200333286721931	1	FACETS	0.754	0.656	0.86	0.754	0.656	0.86	SUBCLONAL	1	TRUE	0	0.24	1		633	671	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664486	138664486	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	50	502	0	ENST00000330315.3:c.1079A>C	p.Tyr360Ser	p.Y360S	ENST00000330315	NM_023067.3	360	tAc/tCc	1/1	1	2	FACETS	0.731	0.62	0.853	0.731	0.62	0.853	SUBCLONAL	1	TRUE	1	0.24	2		502	570	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177990	56177990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326307145	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	40	431	0	ENST00000399503.3:c.2963C>T	p.Ser988Phe	p.S988F	ENST00000399503	NM_005921.1	988	tCt/tTt	14/20	1	2	FACETS	0.633	0.525	0.752	0.633	0.525	0.752	SUBCLONAL	1	TRUE	1	0.24	2		431	527	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250440	26250440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	54	449	0	ENST00000446824.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000446824	NM_021018.2	132	Cgc/Tgc	1/1	1	2	FACETS	0.832	0.711	0.964	0.832	0.711	0.964	CLONAL	1	TRUE	1	0.24	2		449	541	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359392	118359392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	54	346	0	ENST00000534358.1:c.4396C>T	p.Pro1466Ser	p.P1466S	ENST00000534358	NM_005933.3	1466	Cct/Tct	11/36	1	2	FACETS	0.776	0.662	0.9	0.776	0.662	0.9	SUBCLONAL	1	TRUE	1	0.24	2		346	580	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371984	55371984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	64	532	0	ENST00000297316.4:c.674C>T	p.Ser225Phe	p.S225F	ENST00000297316	NM_022454.3	225	tCc/tTc	2/2	1	2	FACETS	0.984	0.853	1	0.984	0.853	1	CLONAL	1	TRUE	1	0.24	2		532	542	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014293	70014293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	90	606	0	ENST00000394351.3:c.1154C>T	p.Pro385Leu	p.P385L	ENST00000394351	NM_000248.3	385	cCc/cTc	9/9	0.200333286721931	1	FACETS	0.943	0.837	1	0.943	0.837	1	CLONAL	1	TRUE	0	0.24	1		606	700	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964400	93964400	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1051471746	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	43	461	0	ENST00000369303.4:c.2497G>A	p.Gly833Arg	p.G833R	ENST00000369303	NM_004440.3	833	Gga/Aga	14/17	1	2	FACETS	0.559	0.467	0.662	0.559	0.467	0.662	SUBCLONAL	1	TRUE	1	0.24	2		461	641	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566814	212566814	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	43	268	0	ENST00000342788.4:c.1367G>A	p.Gly456Glu	p.G456E	ENST00000342788	NM_005235.2	456	gGa/gAa	12/28	1	2	FACETS	0.907	0.761	1	0.907	0.761	1	CLONAL	1	TRUE	1	0.24	2		268	395	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166227	7166227	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745372291	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	103	635	1	ENST00000302850.5:c.1799C>T	p.Ser600Leu	p.S600L	ENST00000302850	NM_000208.2	600	tCg/tTg	8/22	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.24	2		636	829	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940544	49940544	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	99	833	1	ENST00000296474.3:c.499C>T	p.His167Tyr	p.H167Y	ENST00000296474	NM_002447.2	167	Cac/Tac	1/20	0.200333286721931	1	FACETS	0.922	0.823	1	0.922	0.823	1	CLONAL	1	TRUE	0	0.24	1		834	787	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648329	206648329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55721947	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	85	579	2	ENST00000367120.3:c.350G>A	p.Arg117His	p.R117H	ENST00000367120	NM_014002.3	117	cGc/cAc	5/22	1	2	FACETS	0.914	0.807	1	0.914	0.807	1	CLONAL	1	TRUE	1	0.24	2		581	775	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639149	3639149	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	69	809	2	ENST00000294008.3:c.4490C>T	p.Ser1497Phe	p.S1497F	ENST00000294008	NM_032444.2	1497	tCc/tTc	12/15	1	2	FACETS	0.7	0.609	0.8	0.7	0.609	0.8	SUBCLONAL	1	TRUE	1	0.24	2		811	821	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032077	10032077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	76	614	0	ENST00000330684.3:c.746C>T	p.Thr249Ile	p.T249I	ENST00000330684	NM_001134407.1	249	aCc/aTc	3/13	1	2	FACETS	0.991	0.87	1	0.991	0.87	1	CLONAL	1	TRUE	1	0.24	2		614	639	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243944	5243944	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	69	567	0	ENST00000357368.4:c.1538C>T	p.Ser513Leu	p.S513L	ENST00000357368	NM_002850.3	513	tCg/tTg	11/38	1	2	FACETS	0.877	0.763	0.999	0.877	0.763	0.999	CLONAL	1	TRUE	1	0.24	2		567	656	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434960	49434960	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	78	549	3	ENST00000301067.7:c.6593C>T	p.Pro2198Leu	p.P2198L	ENST00000301067	NM_003482.3	2198	cCc/cTc	31/54	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.24	2		552	597	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978697	70978697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760525174	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	84	648	0	ENST00000276594.2:c.956G>A	p.Gly319Glu	p.G319E	ENST00000276594	NM_024504.3	319	gGa/gAa	5/8	1	2	FACETS	0.876	0.773	0.987	0.876	0.773	0.987	CLONAL	1	TRUE	1	0.24	2		648	799	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710528	117710528	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	16	186	0	ENST00000368508.3:c.1744C>T	p.Leu582Phe	p.L582F	ENST00000368508	NM_002944.2	582	Ctt/Ttt	12/43	1	2	FACETS	0.663	0.492	0.867	0.663	0.492	0.867	SUBCLONAL	1	TRUE	1	0.24	2		186	201	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112893802	112893802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	53	412	1	ENST00000351677.2:c.691C>T	p.Arg231Ter	p.R231*	ENST00000351677	NM_002834.3	231	Cga/Tga	6/16	1	2	FACETS	0.763	0.65	0.886	0.763	0.65	0.886	SUBCLONAL	1	TRUE	1	0.24	2		413	579	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228564	36228564	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	95	691	0	ENST00000222270.7:c.7578C>A	p.Phe2526Leu	p.F2526L	ENST00000222270	NM_014727.1	2526	ttC/ttA	34/37	1	2	FACETS	0.82	0.729	0.918	0.82	0.729	0.918	CLONAL	1	TRUE	1	0.24	2		691	965	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023865	31023865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	60	565	0	ENST00000375687.4:c.3350C>T	p.Pro1117Leu	p.P1117L	ENST00000375687	NM_015338.5	1117	cCc/cTc	13/13	1	2	FACETS	0.776	0.668	0.894	0.776	0.668	0.894	SUBCLONAL	1	TRUE	1	0.24	2		565	644	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349221	11349221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	11	125	0	ENST00000332029.2:c.115C>T	p.Pro39Ser	p.P39S	ENST00000332029	NM_003745.1	39	Ccg/Tcg	2/2	1	2	FACETS	0.632	0.438	0.871	0.632	0.438	0.871	SUBCLONAL	1	TRUE	1	0.24	2		125	145	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196610	106196610	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	62	409	1	ENST00000380013.4:c.4943C>T	p.Ser1648Phe	p.S1648F	ENST00000380013	NM_001127208.2	1648	tCc/tTc	11/11	1	2	FACETS	0.895	0.774	1	0.895	0.774	1	CLONAL	1	TRUE	1	0.24	2		410	577	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224505	224505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	32	238	0	ENST00000264932.6:c.181G>A	p.Glu61Lys	p.E61K	ENST00000264932	NM_004168.2	61	Gaa/Aaa	3/15	0.3	1	FACETS	0.759	0.618	0.918	0.759	0.618	0.918	CLONAL	1	TRUE	0	0.24	1		238	309	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961580	41961580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	66	455	0	ENST00000219905.7:c.488C>T	p.Pro163Leu	p.P163L	ENST00000219905	NM_001164273.1	163	cCt/cTt	2/24	1	2	FACETS	0.788	0.683	0.902	0.788	0.683	0.902	CLONAL	1	TRUE	1	0.24	2		455	698	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468082	120468083	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	62	634	0	ENST00000256646.2:c.4356_4357delinsAA	p.Gly1453Ser	p.G1453S	ENST00000256646	NM_024408.3	1452	ggGGgt/ggAAgt	25/34	1	2	FACETS	0.69	0.595	0.793	0.69	0.595	0.793	SUBCLONAL	1	TRUE	1	0.24	2		634	749	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745441	162745441	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	26	273	0	ENST00000367921.3:c.1857-1G>A		p.X619_splice	ENST00000367921	NM_006182.2	619			1	2	FACETS	0.607	0.481	0.752	0.607	0.481	0.752	SUBCLONAL	1	TRUE	1	0.24	2		273	357	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651591	206651591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	103	757	0	ENST00000367120.3:c.901G>A	p.Glu301Lys	p.E301K	ENST00000367120	NM_014002.3	301	Gag/Aag	9/22	1	2	FACETS	0.939	0.839	1	0.939	0.839	1	CLONAL	1	TRUE	1	0.24	2		757	914	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021911	246021912	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	87	628	1	ENST00000388985.4:c.962_963delinsTT	p.Pro321Leu	p.P321L	ENST00000388985		321	cCC/cTT	10/12	1	2	FACETS	0.913	0.808	1	0.913	0.808	1	CLONAL	1	TRUE	1	0.24	2		629	794	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235901	108235901	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	63	371	0	ENST00000278616.4:c.8943C>A	p.His2981Gln	p.H2981Q	ENST00000278616	NM_000051.3	2981	caC/caA	62/63	1	2	FACETS	0.933	0.807	1	0.933	0.807	1	CLONAL	1	TRUE	1	0.24	2		371	563	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424193	49424194	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	64	342	1	ENST00000301067.7:c.13868_13869delinsTT	p.Pro4623Leu	p.P4623L	ENST00000301067	NM_003482.3	4623	cCC/cTT	42/54	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.24	2		343	452	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425254	49425254	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	79	758	0	ENST00000301067.7:c.13234C>T	p.Gln4412Ter	p.Q4412*	ENST00000301067	NM_003482.3	4412	Caa/Taa	39/54	1	2	FACETS	0.741	0.65	0.838	0.741	0.65	0.838	SUBCLONAL	1	TRUE	1	0.24	2		758	889	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431466	49431466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	80	721	1	ENST00000301067.7:c.9673G>A	p.Gly3225Arg	p.G3225R	ENST00000301067	NM_003482.3	3225	Gga/Aga	34/54	1	2	FACETS	0.83	0.73	0.938	0.83	0.73	0.938	CLONAL	1	TRUE	1	0.24	2		722	803	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439876	49439877	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	96	702	1	ENST00000301067.7:c.4664_4665delinsTT	p.Ser1555Phe	p.S1555F	ENST00000301067	NM_003482.3	1555	tCC/tTT	17/54	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.24	2		703	757	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486853	56486853	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	67	397	0	ENST00000267101.3:c.1267C>T	p.Leu423Phe	p.L423F	ENST00000267101	NM_001982.3	423	Ctc/Ttc	11/28	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.24	2		397	545	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863245	57863245	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	56	551	0	ENST00000228682.2:c.1340C>T	p.Ser447Phe	p.S447F	ENST00000228682	NM_005269.2	447	tCc/tTc	11/12	1	2	FACETS	0.884	0.758	1	0.884	0.758	1	CLONAL	1	TRUE	1	0.24	2		551	528	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865629	57865629	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763752118	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	131	895	1	ENST00000228682.2:c.3106C>A	p.Pro1036Thr	p.P1036T	ENST00000228682	NM_005269.2	1036	Ccc/Acc	12/12	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.24	2		896	1055	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975691	26975691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs529227329	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	65	456	0	ENST00000381527.3:c.1199C>T	p.Pro400Leu	p.P400L	ENST00000381527	NM_001260.1	400	cCg/cTg	12/13	0.200333286721931	1	FACETS	0.829	0.719	0.948	0.829	0.719	0.948	CLONAL	1	TRUE	0	0.24	1		456	575	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554332	81554332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1414102266	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	36	418	0	ENST00000298171.2:c.352G>A	p.Asp118Asn	p.D118N	ENST00000298171	NM_000369.2	118	Gac/Aac	4/10	1	2	FACETS	0.567	0.465	0.681	0.567	0.465	0.681	SUBCLONAL	1	TRUE	1	0.24	2		418	529	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566196	95566197	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	80	575	1	ENST00000393063.1:c.4126_4127delinsTT	p.Pro1376Phe	p.P1376F	ENST00000393063	NM_030621.3	1376	CCc/TTc	23/28	1	2	FACETS	0.784	0.689	0.887	0.784	0.689	0.887	SUBCLONAL	1	TRUE	1	0.24	2		576	850	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40990959	40990959	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	56	332	0	ENST00000267868.3:c.3G>A	p.Met1?	p.M1?	ENST00000267868	NM_002875.4	1	atG/atA	2/10	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.24	2		332	463	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058976	42058976	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	61	342	0	ENST00000219905.7:c.8696C>T	p.Pro2899Leu	p.P2899L	ENST00000219905	NM_001164273.1	2899	cCc/cTc	24/24	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.24	2		342	452	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339570	339570	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	98	741	2	ENST00000262320.3:c.2332C>T	p.Gln778Ter	p.Q778*	ENST00000262320	NM_003502.3	778	Cag/Tag	10/11	1	2	FACETS	0.952	0.848	1	0.952	0.848	1	CLONAL	1	TRUE	1	0.24	2		743	858	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343679	343680	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	97	889	0	ENST00000262320.3:c.1994_1995delinsTT	p.Ser665Phe	p.S665F	ENST00000262320	NM_003502.3	665	tCC/tTT	8/11	1	2	FACETS	0.827	0.736	0.925	0.827	0.736	0.925	CLONAL	1	TRUE	1	0.24	2		889	977	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096246	2096246	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	114	804	1	ENST00000219066.1:c.261G>A	p.Trp87Ter	p.W87*	ENST00000219066	NM_002528.5	87	tgG/tgA	2/6	1	2	FACETS	0.983	0.884	1	0.983	0.884	1	CLONAL	1	TRUE	1	0.24	2		805	966	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2218144	2218144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	88	792	1	ENST00000326181.6:c.206C>T	p.Ser69Phe	p.S69F	ENST00000326181	NM_032271.2	69	tCc/tTc	4/21	1	2	FACETS	0.826	0.73	0.928	0.826	0.73	0.928	CLONAL	1	TRUE	1	0.24	2		793	888	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658746	3658746	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	103	773	1	ENST00000294008.3:c.220A>G	p.Arg74Gly	p.R74G	ENST00000294008	NM_032444.2	74	Agg/Ggg	2/15	1	2	FACETS	0.944	0.844	1	0.944	0.844	1	CLONAL	1	TRUE	1	0.24	2		774	909	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857699	9857699	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	64	406	0	ENST00000330684.3:c.3702C>A	p.Phe1234Leu	p.F1234L	ENST00000330684	NM_001134407.1	1234	ttC/ttA	13/13	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.24	2		406	478	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923644	72923644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	59	555	0	ENST00000268489.5:c.3434C>T	p.Pro1145Leu	p.P1145L	ENST00000268489	NM_006885.3	1145	cCc/cTc	4/10	1	2	FACETS	0.797	0.685	0.919	0.797	0.685	0.919	CLONAL	1	TRUE	1	0.24	2		555	617	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993096	72993096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	105	834	0	ENST00000268489.5:c.949C>T	p.Leu317Phe	p.L317F	ENST00000268489	NM_006885.3	317	Ctt/Ttt	2/10	1	2	FACETS	0.87	0.778	0.968	0.87	0.778	0.968	CLONAL	1	TRUE	1	0.24	2		834	1006	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89345485	89345485	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	57	469	1	ENST00000301030.4:c.7465C>T	p.Pro2489Ser	p.P2489S	ENST00000301030	NM_001256183.1	2489	Ccc/Tcc	9/13	1	2	FACETS	0.886	0.761	1	0.886	0.761	1	CLONAL	1	TRUE	1	0.24	2		470	536	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627545	37627546	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	68	558	0	ENST00000447079.4:c.1460_1461delinsTT	p.Ser487Phe	p.S487F	ENST00000447079	NM_015083.1	487	tCC/tTT	2/14	1	2	FACETS	0.763	0.663	0.871	0.763	0.663	0.871	SUBCLONAL	1	TRUE	1	0.24	2		558	743	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872850	37872850	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	79	605	0	ENST00000269571.5:c.1729T>G	p.Phe577Val	p.F577V	ENST00000269571		577	Ttt/Gtt	14/27	1	2	FACETS	0.918	0.807	1	0.918	0.807	1	CLONAL	1	TRUE	1	0.24	2		605	717	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243811	41243811	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	78	503	1	ENST00000357654.3:c.3737C>T	p.Thr1246Ile	p.T1246I	ENST00000357654	NM_007294.3	1246	aCc/aTc	10/23	1	2	FACETS	0.945	0.83	1	0.945	0.83	1	CLONAL	1	TRUE	1	0.24	2		504	688	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244594	41244594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	87	619	0	ENST00000357654.3:c.2954C>T	p.Pro985Leu	p.P985L	ENST00000357654	NM_007294.3	985	cCc/cTc	10/23	1	2	FACETS	0.831	0.735	0.935	0.831	0.735	0.935	CLONAL	1	TRUE	1	0.24	2		619	872	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41249297	41249297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55688530	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	75	419	1	ENST00000357654.3:c.557C>T	p.Ser186Phe	p.S186F	ENST00000357654	NM_007294.3	186	tCt/tTt	8/23	1	2	FACETS	0.809	0.708	0.917	0.809	0.708	0.917	CLONAL	1	TRUE	1	0.24	2		420	773	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805641	46805642	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	92	879	1	ENST00000290295.7:c.314_315delinsTT	p.Thr105Ile	p.T105I	ENST00000290295	NM_006361.5	105	aCC/aTT	1/2	1	2	FACETS	0.874	0.776	0.98	0.874	0.776	0.98	CLONAL	1	TRUE	1	0.24	2		880	877	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223347	2223347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	97	774	1	ENST00000398665.3:c.3458C>T	p.Ser1153Phe	p.S1153F	ENST00000398665	NM_032482.2	1153	tCc/tTc	25/28	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.24	2		775	800	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222989	5222990	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	64	714	3	ENST00000357368.4:c.2813_2814delinsTT	p.Ala938Val	p.A938V	ENST00000357368	NM_002850.3	938	gCC/gTT	18/38	1	2	FACETS	0.826	0.715	0.946	0.826	0.715	0.946	CLONAL	1	TRUE	1	0.24	2		717	646	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262476	10262476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	96	629	2	ENST00000340748.4:c.2019G>A	p.Met673Ile	p.M673I	ENST00000340748		673	atG/atA	22/40	1	2	FACETS	0.964	0.858	1	0.964	0.858	1	CLONAL	1	TRUE	1	0.24	2		631	830	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291065	10291065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138841970	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	79	639	0	ENST00000340748.4:c.406C>T	p.Arg136Cys	p.R136C	ENST00000340748		136	Cgc/Tgc	4/40	1	2	FACETS	0.851	0.747	0.962	0.851	0.747	0.962	CLONAL	1	TRUE	1	0.24	2		639	774	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051571	13051571	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	54	470	0	ENST00000316448.5:c.830C>T	p.Pro277Leu	p.P277L	ENST00000316448	NM_004343.3	277	cCc/cTc	7/9	1	2	FACETS	0.809	0.691	0.939	0.809	0.691	0.939	CLONAL	1	TRUE	1	0.24	2		470	556	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271475	15271475	+	stop_lost	Nonstop_Mutation	SNP	A	A	C	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	123	1002	0	ENST00000263388.2:c.6964T>G	p.Ter2322GlyextTer106	p.*2322Gext*106	ENST00000263388	NM_000435.2	2322	Tga/Gga	33/33	1	2	FACETS	0.852	0.768	0.941	0.852	0.768	0.941	CLONAL	1	TRUE	1	0.24	2		1002	1203	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366208	15366209	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	87	727	1	ENST00000263377.2:c.1946_1947delinsTT	p.Pro649Leu	p.P649L	ENST00000263377	NM_058243.2	649	cCC/cTT	10/20	1	2	FACETS	0.866	0.766	0.974	0.866	0.766	0.974	CLONAL	1	TRUE	1	0.24	2		728	837	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945910	17945910	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	111	819	0	ENST00000458235.1:c.2029G>C	p.Ala677Pro	p.A677P	ENST00000458235	NM_000215.3	677	Gct/Cct	15/24	1	2	FACETS	0.91	0.817	1	0.91	0.817	1	CLONAL	1	TRUE	1	0.24	2		819	1016	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213587	36213588	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	108	916	0	ENST00000222270.7:c.2689_2690delinsTT	p.Pro897Phe	p.P897F	ENST00000222270	NM_014727.1	897	CCt/TTt	5/37	1	2	FACETS	0.913	0.818	1	0.913	0.818	1	CLONAL	1	TRUE	1	0.24	2		916	986	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40739807	40739807	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	84	761	0	ENST00000392038.2:c.1418T>G	p.Phe473Cys	p.F473C	ENST00000392038	NM_001626.4	473	tTc/tGc	14/14	1	2	FACETS	0.703	0.619	0.793	0.703	0.619	0.793	SUBCLONAL	1	TRUE	1	0.24	2		761	996	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796904	42796904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	121	847	0	ENST00000575354.2:c.3362C>T	p.Thr1121Ile	p.T1121I	ENST00000575354	NM_015125.3	1121	aCt/aTt	14/20	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.24	2		847	994	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906412	50906412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854518	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	94	738	0	ENST00000440232.2:c.1073G>A	p.Arg358Gln	p.R358Q	ENST00000440232	NM_002691.3	358	cGg/cAg	9/27	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.24	2		738	780	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50916778	50916779	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	80	545	1	ENST00000440232.2:c.2250_2250+1delinsAA		p.X750_splice	ENST00000440232	NM_002691.3	750		18/27	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.24	2		546	601	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973170	25973170	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	38	360	0	ENST00000435504.4:c.1255C>T	p.Leu419Phe	p.L419F	ENST00000435504		419	Ctt/Ttt	12/13	1	2	FACETS	0.641	0.529	0.766	0.641	0.529	0.766	SUBCLONAL	1	TRUE	1	0.24	2		360	494	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149816	202149816	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	79	497	1	ENST00000358485.4:c.1257T>A	p.Cys419Ter	p.C419*	ENST00000358485	NM_001080125.1	419	tgT/tgA	8/9	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.24	2		498	612	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561433	9561433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	67	531	0	ENST00000353224.5:c.349C>T	p.Pro117Ser	p.P117S	ENST00000353224	NM_177990.2	117	Cca/Tca	4/10	1	2	FACETS	0.697	0.605	0.798	0.697	0.605	0.798	SUBCLONAL	1	TRUE	1	0.24	2		531	801	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024345	31024345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	58	638	1	ENST00000375687.4:c.3830C>T	p.Pro1277Leu	p.P1277L	ENST00000375687	NM_015338.5	1277	cCa/cTa	13/13	1	2	FACETS	0.735	0.63	0.848	0.735	0.63	0.848	SUBCLONAL	1	TRUE	1	0.24	2		639	658	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012782	36012783	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	43	188	1	ENST00000358208.4:c.226_227delinsTT	p.Pro76Leu	p.P76L	ENST00000358208		76	CCg/TTg	2/12	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.24	2		189	303	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547937	41547938	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	73	459	1	ENST00000263253.7:c.2918_2919delinsTT	p.Ser973Phe	p.S973F	ENST00000263253	NM_001429.3	973	tCC/tTT	15/31	1	2	FACETS	0.822	0.718	0.934	0.822	0.718	0.934	CLONAL	1	TRUE	1	0.24	2		460	740	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084141	47084141	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	77	527	0	ENST00000409792.3:c.7148C>G	p.Pro2383Arg	p.P2383R	ENST00000409792	NM_014159.6	2383	cCt/cGt	17/21	0.200333286721931	1	FACETS	0.909	0.799	1	0.909	0.799	1	CLONAL	1	TRUE	0	0.24	1		527	621	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651447	52651447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	80	498	1	ENST00000394830.3:c.1649C>T	p.Pro550Leu	p.P550L	ENST00000394830	NM_018313.4	550	cCa/cTa	15/30	0.200333286721931	1	FACETS	0.928	0.818	1	0.928	0.818	1	CLONAL	1	TRUE	0	0.24	1		499	632	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670709	134670709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	75	513	0	ENST00000398015.3:c.620C>T	p.Pro207Leu	p.P207L	ENST00000398015	NM_004441.4	207	cCa/cTa	3/16	0.200333286721931	1	FACETS	0.914	0.801	1	0.914	0.801	1	CLONAL	1	TRUE	0	0.24	1		513	602	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664826	138664826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	30	166	0	ENST00000330315.3:c.739G>A	p.Gly247Arg	p.G247R	ENST00000330315	NM_023067.3	247	Ggg/Agg	1/1	1	2	FACETS	0.973	0.787	1	0.973	0.787	1	CLONAL	1	TRUE	1	0.24	2		166	257	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902413	1902413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	77	581	0	ENST00000382891.5:c.32C>T	p.Ser11Phe	p.S11F	ENST00000382891	NM_133335.3	11	tCt/tTt	2/22	0.200333286721931	1	FACETS	0.785	0.689	0.889	0.785	0.689	0.889	SUBCLONAL	1	TRUE	0	0.24	1		581	719	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598137	55598138	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	50	479	0	ENST00000288135.5:c.2334_2335delinsAA	p.Gly779Ser	p.G779S	ENST00000288135	NM_000222.2	778	aaGGgc/aaAAgc	16/21	0.200333286721931	1	FACETS	0.611	0.518	0.714	0.611	0.518	0.714	SUBCLONAL	1	TRUE	0	0.24	1		479	600	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143181656	143181656	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	62	437	0	ENST00000262992.4:c.677T>A	p.Phe226Tyr	p.F226Y	ENST00000262992	NM_001101669.1	226	tTt/tAt	9/24	1	2	FACETS	0.711	0.613	0.817	0.711	0.613	0.817	SUBCLONAL	1	TRUE	1	0.24	2		437	727	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945724	38945724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	38	265	0	ENST00000357387.3:c.4502C>T	p.Ser1501Phe	p.S1501F	ENST00000357387	NM_152756.3	1501	tCt/tTt	34/38	1	2	FACETS	0.82	0.679	0.978	0.82	0.679	0.978	CLONAL	1	TRUE	1	0.24	2		265	386	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177933	56177934	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	68	450	0	ENST00000399503.3:c.2906_2907delinsTT	p.Ser969Phe	p.S969F	ENST00000399503	NM_005921.1	969	tCC/tTT	14/20	1	2	FACETS	0.837	0.728	0.955	0.837	0.728	0.955	CLONAL	1	TRUE	1	0.24	2		450	677	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79966068	79966068	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	82	477	0	ENST00000265081.6:c.732A>C	p.Lys244Asn	p.K244N	ENST00000265081	NM_002439.4	244	aaA/aaC	4/24	1	2	FACETS	0.915	0.806	1	0.915	0.806	1	CLONAL	1	TRUE	1	0.24	2		477	747	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439312	149439312	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	77	610	0	ENST00000286301.3:c.2083G>A	p.Gly695Arg	p.G695R	ENST00000286301	NM_005211.3	695	Gga/Aga	15/22	0.116440304425289	0	FACETS	0.616	0.54	0.698			1	INDETERMINATE	1	TRUE	0	0.24	0		610	792	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058708	180058709	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	117	837	0	ENST00000261937.6:c.128_129delinsTT	p.Thr43Ile	p.T43I	ENST00000261937	NM_182925.4	43	aCC/aTT	2/30	0.200333286721931	1	FACETS	0.921	0.829	1	0.921	0.829	1	CLONAL	1	TRUE	0	0.24	1		837	932	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679741	30679742	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	59	641	0	ENST00000376406.3:c.1977_1978delinsTT	p.Gln660Ter	p.Q660*	ENST00000376406	NM_014641.2	659	acCCag/acTTag	5/15	1	2	FACETS	0.7	0.602	0.808	0.7	0.602	0.808	SUBCLONAL	1	TRUE	1	0.24	2		641	702	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652131	36652131	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	75	728	0	ENST00000244741.5:c.253G>A	p.Gly85Ser	p.G85S	ENST00000244741	NM_000389.4	85	Ggc/Agc	2/3	1	2	FACETS	0.862	0.755	0.978	0.862	0.755	0.978	CLONAL	1	TRUE	1	0.24	2		728	725	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066711	94066711	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	55	434	0	ENST00000369303.4:c.1048G>T	p.Glu350Ter	p.E350*	ENST00000369303	NM_004440.3	350	Gaa/Taa	5/17	1	2	FACETS	0.86	0.736	0.995	0.86	0.736	0.995	CLONAL	1	TRUE	1	0.24	2		434	533	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120690	94120691	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	35	384	1	ENST00000369303.4:c.360_361delinsAA	p.Glu121Lys	p.E121K	ENST00000369303	NM_004440.3	120	aaGGaa/aaAAaa	3/17	1	2	FACETS	0.613	0.502	0.738	0.613	0.502	0.738	SUBCLONAL	1	TRUE	1	0.24	2		385	476	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469895	157469896	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	59	620	2	ENST00000346085.5:c.2689_2690delinsAA	p.Gly897Lys	p.G897K	ENST00000346085	NM_020732.3	897	GGa/AAa	9/20	1	2	FACETS	0.675	0.58	0.78	0.675	0.58	0.78	SUBCLONAL	1	TRUE	1	0.24	2		622	728	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979523	2979523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	61	468	1	ENST00000396946.4:c.724G>A	p.Glu242Lys	p.E242K	ENST00000396946	NM_032415.4	242	Gaa/Aaa	6/25	1	2	FACETS	0.843	0.727	0.969	0.843	0.727	0.969	CLONAL	1	TRUE	1	0.24	2		469	603	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346569	81346569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	38	321	0	ENST00000222390.5:c.1384G>A	p.Asp462Asn	p.D462N	ENST00000222390	NM_000601.4	462	Gat/Aat	11/18	1	2	FACETS	0.798	0.66	0.951	0.798	0.66	0.951	CLONAL	1	TRUE	1	0.24	2		321	397	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350121	81350121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	35	357	0	ENST00000222390.5:c.1211C>T	p.Ser404Phe	p.S404F	ENST00000222390	NM_000601.4	404	tCc/tTc	10/18	1	2	FACETS	0.497	0.406	0.599	0.497	0.406	0.599	SUBCLONAL	1	TRUE	1	0.24	2		357	587	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508630	106508631	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	51	470	1	ENST00000359195.3:c.624_625delinsAA	p.Glu209Lys	p.E209K	ENST00000359195	NM_002649.2	208	ccGGag/ccAAag	2/11	1	2	FACETS	0.708	0.601	0.826	0.708	0.601	0.826	SUBCLONAL	1	TRUE	1	0.24	2		471	600	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509490	106509490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	62	572	0	ENST00000359195.3:c.1484G>A	p.Gly495Glu	p.G495E	ENST00000359195	NM_002649.2	495	gGa/gAa	2/11	1	2	FACETS	0.755	0.652	0.868	0.755	0.652	0.868	SUBCLONAL	1	TRUE	1	0.24	2		572	684	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509556	106509557	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	56	600	1	ENST00000359195.3:c.1550_1551delinsTT	p.Ser517Phe	p.S517F	ENST00000359195	NM_002649.2	517	tCC/tTT	2/11	1	2	FACETS	0.721	0.617	0.835	0.721	0.617	0.835	SUBCLONAL	1	TRUE	1	0.24	2		601	647	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411582	116411583	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	58	378	1	ENST00000397752.3:c.2761_2762delinsAA	p.Gly921Lys	p.G921K	ENST00000397752	NM_000245.2	921	GGa/AAa	13/21	1	2	FACETS	0.919	0.79	1	0.919	0.79	1	CLONAL	1	TRUE	1	0.24	2		379	526	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852134	128852134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	87	811	1	ENST00000249373.3:c.2206C>T	p.Pro736Ser	p.P736S	ENST00000249373	NM_005631.4	736	Cca/Tca	12/12	1	2	FACETS	0.785	0.693	0.883	0.785	0.693	0.883	SUBCLONAL	1	TRUE	1	0.24	2		812	924	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494248	140494248	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	126	883	0	ENST00000288602.6:c.1000C>T	p.Pro334Ser	p.P334S	ENST00000288602	NM_004333.4	334	Ccg/Tcg	8/18	1	2	FACETS	0.848	0.766	0.935	0.848	0.766	0.935	CLONAL	1	TRUE	1	0.24	2		883	1238	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151168669	151168669	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375061279	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	92	435	0	ENST00000262187.5:c.298C>T	p.His100Tyr	p.H100Y	ENST00000262187	NM_005614.3	100	Cat/Tat	5/8	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.24	2		435	729	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194670	29194670	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772256235	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	92	804	0	ENST00000240100.2:c.1058G>A	p.Arg353Gln	p.R353Q	ENST00000240100	NM_001394.6	353	cGg/cAg	4/4	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.24	2		804	759	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372351	55372351	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	91	685	1	ENST00000297316.4:c.1041C>A	p.Asp347Glu	p.D347E	ENST00000297316	NM_022454.3	347	gaC/gaA	2/2	1	2	FACETS	0.898	0.797	1	0.898	0.797	1	CLONAL	1	TRUE	1	0.24	2		686	844	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319833	8319833	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs753209923	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	33	254	0	ENST00000356435.5:c.5668G>A	p.Glu1890Lys	p.E1890K	ENST00000356435		1890	Gag/Aag	34/35	0.200333286721931	1	FACETS	0.658	0.536	0.794	0.658	0.536	0.794	SUBCLONAL	1	TRUE	0	0.24	1		254	368	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465545	8465545	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	59	505	0	ENST00000356435.5:c.3635G>A	p.Gly1212Asp	p.G1212D	ENST00000356435		1212	gGt/gAt	21/35	0.200333286721931	1	FACETS	0.635	0.546	0.733	0.635	0.546	0.733	SUBCLONAL	1	TRUE	0	0.24	1		505	681	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517850	8517850	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	31	229	0	ENST00000356435.5:c.1541G>A	p.Gly514Glu	p.G514E	ENST00000356435		514	gGa/gAa	10/35	0.200333286721931	1	FACETS	0.651	0.527	0.791	0.651	0.527	0.791	SUBCLONAL	1	TRUE	0	0.24	1		229	349	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221908	98221926	+	frameshift_variant	Frame_Shift_Del	DEL	TCGGCTTTGTCGTGGACCC	TCGGCTTTGTCGTGGACCC	-	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	32	521	0	ENST00000331920.6:c.2843_2861del	p.Trp948SerfsTer8	p.W948Sfs*8	ENST00000331920	NM_000264.3	948	tGGGTCCACGACAAAGCCGAc/tc	17/24	0.200333286721931	1	FACETS	0.432	0.35	0.525	0.432	0.35	0.525	SUBCLONAL	1	TRUE	0	0.24	1		521	543	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900230	101900230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1328696339	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	49	357	0	ENST00000374994.4:c.664G>A	p.Gly222Arg	p.G222R	ENST00000374994	NM_004612.2	222	Gga/Aga	4/9	0.200333286721931	1	FACETS	0.651	0.551	0.761	0.651	0.551	0.761	SUBCLONAL	1	TRUE	0	0.24	1		357	552	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820258	139820258	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	91	663	0	ENST00000247668.2:c.1411C>T	p.Leu471Phe	p.L471F	ENST00000247668	NM_021138.3	471	Ctc/Ttc	11/11	0.200333286721931	1	FACETS	0.952	0.845	1	0.952	0.845	1	CLONAL	1	TRUE	0	0.24	1		663	701	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428427	47428427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	65	299	0	ENST00000377045.4:c.1295C>T	p.Ser432Phe	p.S432F	ENST00000377045	NM_001654.4	432	tCt/tTt	12/16	1	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.24	1		299	321	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964398	70964398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1289330671	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	47	413	0	ENST00000276594.2:c.1630G>A	p.Asp544Asn	p.D544N	ENST00000276594	NM_024504.3	544	Gat/Aat	8/8	1	2	FACETS	0.765	0.645	0.897	0.765	0.645	0.897	SUBCLONAL	1	TRUE	1	0.24	2		413	512	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851156	63851156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	61	573	1	ENST00000279873.7:c.1937del	p.Pro646GlnfsTer17	p.P646Qfs*17	ENST00000279873	NM_032199.2	645	aCc/ac	10/10	1	2	FACETS	0.713	0.614	0.821	0.713	0.614	0.821	SUBCLONAL	1	TRUE	1	0.24	2		574	713	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0041733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	191	858	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.40285633326149	2	FACETS	0.958	0.894	1	0.958	0.894	1	CLONAL	2	TRUE	0	0.40285633326149	2		858	495	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518279	187518279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779582047	NA	P-0041733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	67	372	0	ENST00000441802.2:c.12415G>A	p.Gly4139Arg	p.G4139R	ENST00000441802	NM_005245.3	4139	Ggg/Agg	25/27	0.356178524615246	3	FACETS	1	0.964	1	0.431	0.377	0.488	CLONAL	1	TRUE	0	0.40285633326149	3		372	309	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876188	35876188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536561203	NA	P-0041735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	264	558	0	ENST00000303115.3:c.980C>T	p.Thr327Met	p.T327M	ENST00000303115	NM_002185.3	327	aCg/aTg	8/8	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.85	2		558	621	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20152120	20152120	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	193	382	0	ENST00000379607.5:c.210G>C	p.Trp70Cys	p.W70C	ENST00000379607	NM_001412.3	70	tgG/tgC	4/7	1	2	FACETS	0.779	0.725	0.834	0.779	0.725	0.834	SUBCLONAL	1	TRUE	1	0.85	2		382	583	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105631	27105631	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	95	554	0	ENST00000324856.7:c.5244del	p.Arg1749GlyfsTer21	p.R1749Gfs*21	ENST00000324856	NM_006015.4	1748	Ggg/gg	20/20	1	2	FACETS	0.339	0.302	0.379	0.339	0.302	0.379	SUBCLONAL	1	TRUE	1	0.85	2		554	659	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0041830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	17	545	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.487301321846756	1	FACETS	0.312	0.234	0.404	0.312	0.234	0.404	SUBCLONAL	1	TRUE	0	0.487301321846756	1		545	169	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0041830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	166	290	0	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	0.415073150558665	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.487301321846756	4		290	454	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672534	30672534	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs774404458	NA	P-0041830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	316	725	0	ENST00000376406.3:c.4426G>T	p.Gly1476Ter	p.G1476*	ENST00000376406	NM_014641.2	1476	Gga/Tga	10/15	0.406873876334243	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.487301321846756	3		725	764	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0041830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	316	674	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.474167741927451	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.487301321846756	2		674	629	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355047	73355047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	205	443	0	ENST00000377767.4:c.323G>A	p.Arg108His	p.R108H	ENST00000377767	NM_014953.3	108	cGc/cAc	2/21	0.487301321846756	2	FACETS	0.983	0.924	1	0.983	0.924	1	CLONAL	2	TRUE	0	0.487301321846756	2		443	428	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771570	112771570	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	71	489	0	ENST00000369452.4:c.1743G>T	p.Met581Ile	p.M581I	ENST00000369452	NM_007373.3	581	atG/atT	9/9	0.170419824756747	3	FACETS	0.855	0.749	0.968	0.285	0.249	0.323	INDETERMINATE	1	TRUE	0	0.487301321846756	3		489	424	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447022	49447023	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0041830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	170	458	1	ENST00000301067.7:c.921_922delinsTT	p.Met307_Glu308delinsIleTer	p.M307_E308delinsI*	ENST00000301067	NM_003482.3	307	atGGag/atTTag	7/54	0.362085624249103	4	FACETS	0.907	0.839	0.977	0.907	0.839	0.977	CLONAL	2	TRUE	2	0.487301321846756	4		459	572	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245527	133245527	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0041830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	140	406	0	ENST00000320574.5:c.1795-2A>T		p.X599_splice	ENST00000320574	NM_006231.2	599			0.362085624249103	4	FACETS	0.778	0.712	0.847	0.778	0.712	0.847	SUBCLONAL	2	TRUE	2	0.487301321846756	4		406	549	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628291	90628291	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	366	825	0	ENST00000330062.3:c.1120G>T	p.Ala374Ser	p.A374S	ENST00000330062	NM_002168.2	374	Gcc/Tcc	9/11	0.477841682219662	2	FACETS	0.953	0.91	0.997	0.953	0.91	0.997	CLONAL	2	TRUE	0	0.487301321846756	2		825	788	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519919	66519919	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	178	454	0	ENST00000358598.2:c.402G>C	p.Lys134Asn	p.K134N	ENST00000358598	NM_212471.2	134	aaG/aaC	4/11	0.362085624249103	4	FACETS	0.852	0.788	0.917	0.852	0.788	0.917	CLONAL	2	TRUE	2	0.487301321846756	4		454	638	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210647	2210647	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	274	673	0	ENST00000398665.3:c.1144G>T	p.Gly382Ter	p.G382*	ENST00000398665	NM_032482.2	382	Gga/Tga	14/28	0.487301321846756	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.487301321846756	2		673	549	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086125	16086125	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	211	618	0	ENST00000281043.3:c.1301A>T	p.Gln434Leu	p.Q434L	ENST00000281043	NM_005378.4	434	cAg/cTg	3/3	0.415073150558665	4	FACETS	0.809	0.753	0.867	0.809	0.753	0.867	CLONAL	2	TRUE	2	0.487301321846756	4		618	796	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634681	158634681	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	98	374	0	ENST00000263640.3:c.505G>T	p.Gly169Trp	p.G169W	ENST00000263640	NM_001105.4	169	Ggg/Tgg	5/11	0.415073150558665	4	FACETS	1	0.972	1	0.627	0.562	0.696	CLONAL	1	TRUE	2	0.487301321846756	4		374	477	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215674193	215674193	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876659387	NA	P-0041830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	202	723	1	ENST00000260947.4:c.101G>T	p.Trp34Leu	p.W34L	ENST00000260947	NM_000465.2	34	tGg/tTg	1/11	0.415073150558665	4	FACETS	1	0.991	1	0.746	0.693	0.801	CLONAL	1	TRUE	2	0.487301321846756	4		724	826	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561387	9561387	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs760277504	NA	P-0041830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	246	547	0	ENST00000353224.5:c.395C>A	p.Ser132Tyr	p.S132Y	ENST00000353224	NM_177990.2	132	tCc/tAc	4/10	0.362085624249103	4	FACETS	0.946	0.887	1	0.946	0.887	1	CLONAL	2	TRUE	2	0.487301321846756	4		547	794	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201805	66201805	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	160	487	1	ENST00000273854.3:c.2697C>A	p.Ser899Arg	p.S899R	ENST00000273854	NM_004439.5	899	agC/agA	16/18	0.487301321846756	8	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.487301321846756	8		488	1117	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293902	1293902	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	439	816	0	ENST00000310581.5:c.1099G>T	p.Gly367Cys	p.G367C	ENST00000310581	NM_198253.2	367	Ggt/Tgt	2/16	0.211172525228547	6	FACETS	1	0.955	1	1	0.955	1	INDETERMINATE	3	TRUE	3	0.487301321846756	6		816	1186	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974695	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	19	360	0	ENST00000304494.5:c.132C>A	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	taC/taA	1/3	0.487301321846756	1	FACETS	0.289	0.22	0.37	0.289	0.22	0.37	SUBCLONAL	1	TRUE	0	0.487301321846756	1		360	204	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0041833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	98	214	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.356646517615093	3	FACETS	1	0.971	1	0.778	0.709	0.848	CLONAL	2	FALSE	0	0.4614028238076	3		214	224	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215674193	215674193	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876659387	NA	P-0041833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1532	370	723	1	ENST00000260947.4:c.101G>T	p.Trp34Leu	p.W34L	ENST00000260947	NM_000465.2	34	tGg/tTg	1/11	0.45512872769296	3	FACETS	1	0.97	1	0.519	0.49	0.548	CLONAL	1	FALSE	1	0.4614028238076	3		724	1902	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419049	419049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	19	400	0	ENST00000399788.2:c.3298G>A	p.Glu1100Lys	p.E1100K	ENST00000399788	NM_001042603.1	1100	Gaa/Aaa	22/28	0.356646517615093	3	FACETS	0.437	0.332	0.559	0.146	0.11	0.187	SUBCLONAL	1	FALSE	0	0.4614028238076	3		400	232	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58701021	58701021	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	10	675	0	ENST00000305921.3:c.612G>T	p.Lys204Asn	p.K204N	ENST00000305921	NM_003620.3	204	aaG/aaT	2/6	0.259596275760644	5	FACETS	0.369	0.249	0.518	0.123	0.083	0.173	INDETERMINATE	1	FALSE	2	0.4614028238076	5		675	199	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285801	87285801	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	400	749	0	ENST00000277120.3:c.138C>A	p.Ser46Arg	p.S46R	ENST00000277120		46	agC/agA	2/19	0.3256727573661	4	FACETS	1	0.977	1	0.773	0.739	0.806	CLONAL	3	FALSE	0	0.4614028238076	4		749	820	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648274	206648274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs917655681	NA	P-0041833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	62	764	0	ENST00000367120.3:c.295G>A	p.Glu99Lys	p.E99K	ENST00000367120	NM_014002.3	99	Gag/Aag	5/22	0.323507379223846	6	FACETS	1	0.971	1	0.371	0.322	0.424	CLONAL	1	FALSE	2	0.4614028238076	6		764	348	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201561	133201561	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	262	776	0	ENST00000320574.5:c.6677G>T	p.Gly2226Val	p.G2226V	ENST00000320574	NM_006231.2	2226	gGg/gTg	48/49	0.313477287337078	4	FACETS	1	0.99	1	0.657	0.614	0.7	CLONAL	1	FALSE	2	0.4614028238076	4		776	1264	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012477	29012477	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	18	366	0	ENST00000282397.4:c.394G>T	p.Gly132Cys	p.G132C	ENST00000282397	NM_002019.4	132	Ggt/Tgt	4/30	0.294243667751021	2	FACETS	1	0.902	1	0.673	0.524	0.834	CLONAL	1	FALSE	0	0.4614028238076	2		366	58	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244061	5244061	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	423	779	1	ENST00000357368.4:c.1421A>G	p.Asn474Ser	p.N474S	ENST00000357368	NM_002850.3	474	aAc/aGc	11/38	0.4614028238076	4	FACETS	0.895	0.852	0.939	0.597	0.568	0.626	CLONAL	2	FALSE	1	0.4614028238076	4		780	1497	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965718	25965718	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	36	745	0	ENST00000435504.4:c.3488A>T	p.Tyr1163Phe	p.Y1163F	ENST00000435504		1163	tAt/tTt	13/13	0.259596275760644	5	FACETS	1	0.946	1	0.466	0.387	0.552	INDETERMINATE	1	FALSE	2	0.4614028238076	5		745	189	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390950	89390950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	28	534	0	ENST00000336596.2:c.1016C>T	p.Thr339Ile	p.T339I	ENST00000336596	NM_005233.5	339	aCc/aTc	5/17	0.4614028238076	4	FACETS	1	0.924	1	0.438	0.355	0.529	CLONAL	1	FALSE	1	0.4614028238076	4		534	135	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31435904	31435904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	16	483	0	ENST00000344624.3:c.3010G>T	p.Val1004Phe	p.V1004F	ENST00000344624		1004	Gtt/Ttt	22/33	NA	2	FACETS	0.867	0.654	1			1	INDETERMINATE	1	FALSE	NA	0.4614028238076	2		483	80	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184774	32184774	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	101	686	0	ENST00000375023.3:c.1809C>A	p.Ser603Arg	p.S603R	ENST00000375023	NM_004557.3	603	agC/agA	11/30	0.307577540858146	1	FACETS	0.81	0.741	0.878	1	0.987	1	CLONAL	2	FALSE	0	0.4614028238076	1		686	208	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120890	94120890	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0041833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	14	406	0	ENST00000369303.4:c.163-2A>T		p.X55_splice	ENST00000369303	NM_004440.3	55			0.226691285382776	3	FACETS	1	0.894	1	0.498	0.372	0.638	INDETERMINATE	1	FALSE	0	0.4614028238076	3		406	50	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001443	150001443	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	15	581	0	ENST00000253339.5:c.2161C>G	p.Leu721Val	p.L721V	ENST00000253339		721	Cta/Gta	4/7	0.218183553483064	3	FACETS	0.817	0.62	1	0.817	0.62	1	INDETERMINATE	2	FALSE	1	0.4614028238076	3		581	49	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509204	106509204	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	195	714	0	ENST00000359195.3:c.1198A>G	p.Ser400Gly	p.S400G	ENST00000359195	NM_002649.2	400	Agc/Ggc	2/11	0.323507379223846	6	FACETS	0.872	0.812	0.935	0.654	0.609	0.701	CLONAL	3	FALSE	2	0.4614028238076	6		714	621	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981921	70981921	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs770422998	NA	P-0041833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	515	796	0	ENST00000276594.2:c.175G>T	p.Ala59Ser	p.A59S	ENST00000276594	NM_024504.3	59	Gca/Tca	2/8	0.45512872769296	3	FACETS	0.821	0.785	0.857	0.821	0.785	0.857	CLONAL	2	FALSE	1	0.4614028238076	3		796	1673	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862887	117862887	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	19	407	0	ENST00000297338.2:c.1590G>C	p.Glu530Asp	p.E530D	ENST00000297338	NM_006265.2	530	gaG/gaC	12/14	0.45512872769296	3	FACETS	0.845	0.649	1	0.422	0.324	0.534	CLONAL	1	FALSE	1	0.4614028238076	3		407	120	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231174	98231174	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	78	719	0	ENST00000331920.6:c.2109G>T	p.Glu703Asp	p.E703D	ENST00000331920	NM_000264.3	703	gaG/gaT	14/24	0.3256727573661	4	FACETS	1	0.976	1	0.362	0.321	0.406	CLONAL	1	FALSE	0	0.4614028238076	4		719	341	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858115	152858115	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1840	381	902	0	ENST00000406277.2:c.500C>G	p.Thr167Ser	p.T167S	ENST00000406277	NM_152274.4	167	aCc/aGc	6/7	0.259596275760644	5	FACETS	1	0.992	1	0.419	0.396	0.443	INDETERMINATE	1	FALSE	2	0.4614028238076	5		902	2221	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069291	30069291	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	CA	novel	NA	P-0041833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	118	702	0	ENST00000338641.4:c.1156delinsCA	p.Glu386GlnfsTer21	p.E386Qfs*21	ENST00000338641	NM_000268.3	386	Gaa/CAaa	12/16	0.226691285382776	3	FACETS	1	0.983	1	0.468	0.425	0.513	INDETERMINATE	1	FALSE	0	0.4614028238076	3		702	448	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	62	82	0				ENST00000310581	NM_198253.2	-/1132			0.211485541319899	3	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	1	0.265469024582081	3		82	243	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0041852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	268	509	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.265469024582081	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.265469024582081	3		509	660	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367233	50367233	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0041852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	30	319	0	ENST00000331340.3:c.41-1G>T		p.X14_splice	ENST00000331340	NM_006060.4	14			0.130155051305712	4	FACETS	1	0.817	1	0.337	0.272	0.41	INDETERMINATE	1	TRUE	1	0.265469024582081	4		319	283	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249002	55249003	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGTGGA	rs397517109	NA	P-0041864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	91	617	0	ENST00000275493.2:c.2303_2311dup	p.Ser768_Asp770dup	p.S768_D770dup	ENST00000275493	NM_005228.3	768	gcc/gcCAGCGTGGAc	20/28	0.296834465422764	3	FACETS	0.863	0.767	0.967	0.432	0.383	0.484	CLONAL	1	TRUE	1	0.349207017751013	3		617	709	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468167	50468167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	44	660	2	ENST00000331340.3:c.1402C>T	p.Arg468Trp	p.R468W	ENST00000331340	NM_006060.4	468	Cgg/Tgg	8/8	0.296834465422764	3	FACETS	0.408	0.341	0.483	0.204	0.17	0.242	SUBCLONAL	1	TRUE	1	0.349207017751013	3		662	725	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0041872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	91	283	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.50171578715863	1	FACETS	0.96	0.864	1	0.96	0.864	1	CLONAL	1	TRUE	0	0.50171578715863	1		283	283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577584	7577584	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	376	663	1	ENST00000269305.4:c.697del	p.His233ThrfsTer14	p.H233Tfs*14	ENST00000269305	NM_001126112.2	233	Cac/ac	7/11	0.50171578715863	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.50171578715863	1		664	822	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11172917	11172917	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	198	660	0	ENST00000361445.4:c.7358A>T	p.Gln2453Leu	p.Q2453L	ENST00000361445	NM_004958.3	2453	cAg/cTg	54/58	0.50171578715863	1	FACETS	0.961	0.896	1	0.961	0.896	1	CLONAL	1	TRUE	0	0.50171578715863	1		660	615	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120478097	120478097	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	77	506	0	ENST00000256646.2:c.3653G>C	p.Arg1218Pro	p.R1218P	ENST00000256646	NM_024408.3	1218	cGg/cCg	22/34	0.311709857088795	1	FACETS	0.411	0.361	0.464	0.411	0.361	0.464	SUBCLONAL	1	TRUE	0	0.50171578715863	1		506	560	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499737	18499737	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	182	472	0	ENST00000266497.5:c.1592C>A	p.Ala531Glu	p.A531E	ENST00000266497		531	gCa/gAa	10/31	0.499755624488354	2	FACETS	0.836	0.78	0.892	0.836	0.78	0.892	CLONAL	2	TRUE	0	0.50171578715863	2		472	434	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556138	29556139	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0041872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	12	119	0	ENST00000356175.3:c.2505_2506delinsTT	p.Gln835_Glu836delinsHisTer	p.Q835_E836delinsH*	ENST00000356175	NM_000267.3	835	caGGaa/caTTaa	21/57	0.50171578715863	1	FACETS	0.491	0.351	0.656	0.491	0.351	0.656	SUBCLONAL	1	TRUE	0	0.50171578715863	1		119	73	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58700975	58700975	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	713	704	0	ENST00000305921.3:c.566A>C	p.His189Pro	p.H189P	ENST00000305921	NM_003620.3	189	cAc/cCc	2/6	0.497060270880831	4	FACETS	1	0.994	1	0.82	0.795	0.845	CLONAL	3	TRUE	0	0.50171578715863	4		704	1301	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661995	227661995	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	252	742	0	ENST00000305123.5:c.1460G>T	p.Arg487Leu	p.R487L	ENST00000305123	NM_005544.2	487	cGg/cTg	1/2	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.50171578715863	2		742	851	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204759	128204759	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs375298899	NA	P-0041872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	464	1021	0	ENST00000341105.2:c.682C>A	p.Pro228Thr	p.P228T	ENST00000341105	NM_032638.4	228	Ccc/Acc	3/6	NA	2	FACETS	0.887	0.85	0.923			1	INDETERMINATE	2	TRUE	NA	0.50171578715863	2		1021	1043	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538915	23538915	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	211	666	1	ENST00000380871.4:c.524G>A	p.Arg175Lys	p.R175K	ENST00000380871	NM_006167.3	175	aGa/aAa	2/2	0.50171578715863	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.50171578715863	1		667	617	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869637	117869637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	175	541	0	ENST00000297338.2:c.557C>T	p.Thr186Ile	p.T186I	ENST00000297338	NM_006265.2	186	aCt/aTt	6/14	0.482837426938938	5	FACETS	1	0.942	1	0.257	0.236	0.28	CLONAL	1	TRUE	1	0.50171578715863	5		541	1187	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0041942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	101	509	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.30121425565464	1	FACETS	0.815	0.73	0.905	0.815	0.73	0.905	CLONAL	1	TRUE	0	0.35	1		509	584	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0041942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	28	267	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.284460499233852	1	FACETS	0.402	0.322	0.494	0.402	0.322	0.494	SUBCLONAL	1	TRUE	0	0.35	1		267	328	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435101	56435101	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	129	568	0	ENST00000407977.2:c.2036del	p.Gln679ArgfsTer21	p.Q679Rfs*21	ENST00000407977		679	cAg/cg	9/10	1	2	FACETS	0.985	0.894	1	0.985	0.894	1	CLONAL	1	TRUE	1	0.35	2		568	748	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220489	1220489	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786202134	NA	P-0041942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	36	666	0	ENST00000326873.7:c.582C>G	p.Asp194Glu	p.D194E	ENST00000326873	NM_000455.4	194	gaC/gaG	4/10	0.30121425565464	1	FACETS	0.284	0.232	0.342	0.284	0.232	0.342	SUBCLONAL	1	TRUE	0	0.35	1		666	598	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	38	82	0				ENST00000310581	NM_198253.2	-/1132			0.161779085509034	2	FACETS	0.697	0.584	0.819	0.348	0.292	0.41	INDETERMINATE	1	TRUE	0	0.641467115268264	2		82	170	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0041963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	394	879	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.641467115268264	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.641467115268264	1		879	719	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039501	49039501	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0041963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	125	301	0	ENST00000267163.4:c.2486C>G	p.Ser829Ter	p.S829*	ENST00000267163	NM_000321.2	829	tCa/tGa	23/27	0.641467115268264	1	FACETS	0.945	0.871	1	0.945	0.871	1	CLONAL	1	TRUE	0	0.641467115268264	1		301	280	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546098	29546098	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1567843917	NA	P-0041963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	231	401	0	ENST00000356175.3:c.1603C>T	p.Gln535Ter	p.Q535*	ENST00000356175	NM_000267.3	535	Cag/Tag	14/57	0.641467115268264	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.641467115268264	1		401	459	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653782	89653782	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs886041877	NA	P-0041963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	68	179	0	ENST00000371953.3:c.80A>C	p.Tyr27Ser	p.Y27S	ENST00000371953	NM_000314.4	27	tAt/tCt	2/9	0.641467115268264	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.641467115268264	1		179	124	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0041976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	631	367	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.47486927917172	12	FACETS	0.967	0.941	0.993			1	CLONAL	10	TRUE	NA	0.47486927917172	12		367	927	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0041976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	342	721	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.475651252145235	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.47486927917172	2		723	712	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864884	117864884	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	93	437	0	ENST00000297338.2:c.1225G>T	p.Glu409Ter	p.E409*	ENST00000297338	NM_006265.2	409	Gag/Tag	10/14	0.47486927917172	6	FACETS	1	0.92	1			1	CLONAL	1	TRUE	NA	0.47486927917172	6		437	732	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023241	150023241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	79	412	0	ENST00000253339.5:c.22G>A	p.Glu8Lys	p.E8K	ENST00000253339		8	Gaa/Aaa	1/7	0.475651252145235	4	FACETS	0.91	0.802	1			1	CLONAL	1	TRUE	NA	0.47486927917172	4		412	539	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555202	226555202	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	101	477	0	ENST00000366794.5:c.2385G>C	p.Glu795Asp	p.E795D	ENST00000366794	NM_001618.3	795	gaG/gaC	17/23	0.475651252145235	4	FACETS	1	0.92	1	0.344	0.308	0.382	CLONAL	1	TRUE	1	0.47486927917172	4		477	608	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28963991	28963991	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	161	338	0	ENST00000282397.4:c.1911A>T	p.Arg637Ser	p.R637S	ENST00000282397	NM_002019.4	637	agA/agT	13/30	0.475651252145235	3	FACETS	0.935	0.876	0.995	0.935	0.876	0.995	CLONAL	3	TRUE	0	0.47486927917172	3		338	299	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716361	52716361	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	150	659	0	ENST00000322088.6:c.805G>A	p.Glu269Lys	p.E269K	ENST00000322088	NM_014225.5	269	Gag/Aag	6/15	0.454385466386821	3	FACETS	0.873	0.798	0.952			1	CLONAL	1	TRUE	NA	0.47486927917172	3		659	895	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748585	43748585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752153816	NA	P-0041976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	456	426	2	ENST00000523873.1:c.539G>A	p.Gly180Asp	p.G180D	ENST00000523873		180	gGc/gAc	6/8	0.47486927917172	5	FACETS	1	0.991	1	1	0.991	1	CLONAL	4	TRUE	1	0.47486927917172	5		428	762	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257321	16257322	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	111	518	0	ENST00000375759.3:c.4592dup	p.Leu1531PhefsTer7	p.L1531Ffs*7	ENST00000375759	NM_015001.2	1529	cgt/cgTt	11/15	1	2	FACETS	0.758	0.684	0.835	0.758	0.684	0.835	SUBCLONAL	1	TRUE	1	0.58	2		518	505	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261772	16261772	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	147	520	0	ENST00000375759.3:c.9037G>C	p.Val3013Leu	p.V3013L	ENST00000375759	NM_015001.2	3013	Gtc/Ctc	11/15	1	2	FACETS	0.973	0.894	1	0.973	0.894	1	CLONAL	1	TRUE	1	0.58	2		520	521	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1232964733	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	20	53	0	ENST00000324856.7:c.1015del	p.Ala339LeufsTer24	p.A339Lfs*24	ENST00000324856	NM_006015.4	337	tGg/tg	1/20	1	2	FACETS	1	0.821	1	1	0.821	1	CLONAL	1	TRUE	1	0.58	2		53	66	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935356	36935356	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	50	685	0	ENST00000361632.4:c.1371G>T	p.Gln457His	p.Q457H	ENST00000361632		457	caG/caT	10/16	1	2	FACETS	0.293	0.248	0.343	0.293	0.248	0.343	SUBCLONAL	1	TRUE	1	0.58	2		685	588	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941011	36941011	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	173	652	0	ENST00000361632.4:c.328C>T	p.Gln110Ter	p.Q110*	ENST00000361632		110	Cag/Tag	3/16	1	2	FACETS	0.951	0.88	1	0.951	0.88	1	CLONAL	1	TRUE	1	0.58	2		652	627	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681327	88681327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780107	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	78	390	1	ENST00000372037.3:c.1217G>A	p.Arg406His	p.R406H	ENST00000372037	NM_004329.2	406	cGc/cAc	11/13	1	2	FACETS	0.868	0.77	0.971	0.868	0.77	0.971	CLONAL	1	TRUE	1	0.58	2		391	310	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692874	89692874	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786204930	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	76	252	0	ENST00000371953.3:c.358G>A	p.Ala120Thr	p.A120T	ENST00000371953	NM_000314.4	120	Gca/Aca	5/9	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.58	2		252	236	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	216	371	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.924	0.873	0.975	1	0.995	1	CLONAL	2	TRUE	1	0.58	2		376	403	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239421	123239421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764959117	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	34	420	0	ENST00000358487.5:c.2416G>A	p.Glu806Lys	p.E806K	ENST00000358487	NM_000141.4	806	Gaa/Aaa	18/18	1	2	FACETS	0.309	0.252	0.372	0.309	0.252	0.372	SUBCLONAL	1	TRUE	1	0.58	2		420	380	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195499	102195499	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	102	381	0	ENST00000263464.3:c.263del	p.Lys88SerfsTer12	p.K88Sfs*12	ENST00000263464	NM_001165.4	87	Aaa/aa	2/9	0.3	1	FACETS	0.785	0.711	0.862	0.785	0.711	0.862	INDETERMINATE	1	TRUE	0	0.58	1		381	318	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098418	108098418	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs746235533	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	50	260	0	ENST00000278616.4:c.67C>T	p.Arg23Ter	p.R23*	ENST00000278616	NM_000051.3	23	Cga/Tga	2/63	1	2	FACETS	0.701	0.6	0.809	0.701	0.6	0.809	SUBCLONAL	1	TRUE	1	0.58	2		260	246	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170378	119170378	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	87	369	0	ENST00000264033.4:c.2608T>G	p.Ser870Ala	p.S870A	ENST00000264033	NM_005188.3	870	Tcc/Gcc	16/16	1	2	FACETS	0.833	0.744	0.928	0.833	0.744	0.928	CLONAL	1	TRUE	1	0.58	2		369	360	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112353	115112353	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	53	139	0	ENST00000257566.3:c.1387G>T	p.Ala463Ser	p.A463S	ENST00000257566	NM_016569.3	463	Gcg/Tcg	7/8	1	2	FACETS	0.967	0.838	1	0.967	0.838	1	CLONAL	1	TRUE	1	0.58	2		139	189	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007896	45007897	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	76	256	0	ENST00000558401.1:c.346+1dup		p.W115fs	ENST00000558401	NM_004048.2	115	tgg/tGgg	2/4	1	2	FACETS	0.816	0.722	0.916	0.816	0.722	0.916	CLONAL	1	TRUE	1	0.58	2		256	321	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222251	2222251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771233423	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	223	792	1	ENST00000326181.6:c.535G>A	p.Glu179Lys	p.E179K	ENST00000326181	NM_032271.2	179	Gag/Aag	8/21	1	2	FACETS	0.991	0.925	1	0.991	0.925	1	CLONAL	1	TRUE	1	0.58	2		793	776	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89828358	89828358	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs755546887	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	103	387	0	ENST00000389301.3:c.2851C>T	p.Arg951Trp	p.R951W	ENST00000389301	NM_000135.2	951	Cgg/Tgg	29/43	1	2	FACETS	0.892	0.805	0.984	0.892	0.805	0.984	CLONAL	1	TRUE	1	0.58	2		387	398	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858352	89858352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762736991	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	143	502	0	ENST00000389301.3:c.1208C>T	p.Ala403Val	p.A403V	ENST00000389301	NM_000135.2	403	gCg/gTg	13/43	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.58	2		502	475	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	140	550	2	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.58	2		552	460	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486050	29486050	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1438566555	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	50	238	0	ENST00000356175.3:c.233del	p.Asn78IlefsTer7	p.N78Ifs*7	ENST00000356175	NM_000267.3	76	gAa/ga	3/57	1	2	FACETS	0.813	0.699	0.936	0.813	0.699	0.936	CLONAL	1	TRUE	1	0.58	2		238	212	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552152	29552152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199474738	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	54	255	0	ENST00000356175.3:c.1885G>A	p.Gly629Arg	p.G629R	ENST00000356175	NM_000267.3	629	Ggg/Agg	17/57	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.58	2		255	185	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663652	29663652	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	65	269	0	ENST00000356175.3:c.6085-1G>T		p.X2029_splice	ENST00000356175	NM_000267.3	2029			1	2	FACETS	0.776	0.678	0.879	0.776	0.678	0.879	SUBCLONAL	1	TRUE	1	0.58	2		269	289	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264357	30264357	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	31	129	0	ENST00000322652.5:c.92T>C	p.Val31Ala	p.V31A	ENST00000322652	NM_015355.2	31	gTg/gCg	1/16	1	2	FACETS	0.81	0.666	0.966	0.81	0.666	0.966	CLONAL	1	TRUE	1	0.58	2		129	132	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881082	37881082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	175	760	0	ENST00000269571.5:c.2411G>A	p.Gly804Asp	p.G804D	ENST00000269571		804	gGc/gAc	20/27	1	2	FACETS	0.876	0.809	0.945	0.876	0.809	0.945	CLONAL	1	TRUE	1	0.58	2		760	689	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883774	37883774	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	203	759	2	ENST00000269571.5:c.3391del	p.Leu1131Ter	p.L1131*	ENST00000269571		1129	gCc/gc	26/27	1	2	FACETS	0.947	0.881	1	0.947	0.881	1	CLONAL	1	TRUE	1	0.58	2		761	739	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40500498	40500498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	136	501	0	ENST00000264657.5:c.37C>T	p.Arg13Trp	p.R13W	ENST00000264657	NM_139276.2	13	Cgg/Tgg	2/24	1	2	FACETS	0.925	0.846	1	0.925	0.846	1	CLONAL	1	TRUE	1	0.58	2		501	507	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	147	964	8	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.932	0.855	1	0.932	0.855	1	CLONAL	1	TRUE	1	0.58	2		972	544	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740836	58740836	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs747668756	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	133	469	1	ENST00000305921.3:c.1741C>T	p.Arg581Ter	p.R581*	ENST00000305921	NM_003620.3	581	Cga/Tga	6/6	1	2	FACETS	0.91	0.831	0.992	0.91	0.831	0.992	CLONAL	1	TRUE	1	0.58	2		470	504	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78865613	78865613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752600548	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	154	441	1	ENST00000306801.3:c.2077G>A	p.Ala693Thr	p.A693T	ENST00000306801	NM_020761.2	693	Gcc/Acc	18/34	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.58	2		442	456	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611735	1611735	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375296938	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	186	665	0	ENST00000344749.5:c.1927G>A	p.Glu643Lys	p.E643K	ENST00000344749	NM_001136139.2	643	Gaa/Aaa	19/19	1	2	FACETS	0.94	0.872	1	0.94	0.872	1	CLONAL	1	TRUE	1	0.58	2		665	682	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030355	11030355	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	112	477	0	ENST00000327064.4:c.1105A>G	p.Arg369Gly	p.R369G	ENST00000327064	NM_199141.1	369	Agg/Ggg	9/16	1	2	FACETS	0.937	0.85	1	0.937	0.85	1	CLONAL	1	TRUE	1	0.58	2		477	412	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285135	15285135	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184438857	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	198	733	0	ENST00000263388.2:c.4480G>A	p.Gly1494Ser	p.G1494S	ENST00000263388	NM_000435.2	1494	Ggc/Agc	25/33	1	2	FACETS	0.962	0.894	1	0.962	0.894	1	CLONAL	1	TRUE	1	0.58	2		733	710	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965520	18965520	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	153	607	0	ENST00000262803.5:c.1265+2T>C		p.X422_splice	ENST00000262803	NM_002911.3	422			1	2	FACETS	0.762	0.699	0.828	0.762	0.699	0.828	SUBCLONAL	1	TRUE	1	0.58	2		607	692	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214714	36214714	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774265693	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	94	559	0	ENST00000222270.7:c.3140G>A	p.Arg1047Gln	p.R1047Q	ENST00000222270	NM_014727.1	1047	cGg/cAg	8/37	1	2	FACETS	0.851	0.763	0.943	0.851	0.763	0.943	CLONAL	1	TRUE	1	0.58	2		559	381	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214866	36214866	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568372429	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	232	783	0	ENST00000222270.7:c.3296del	p.Gly1099AlafsTer83	p.G1099Afs*83	ENST00000222270	NM_014727.1	1098	Ggg/gg	8/37	1	2	FACETS	0.96	0.898	1	0.96	0.898	1	CLONAL	1	TRUE	1	0.58	2		783	833	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753602	42753602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779162156	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	166	807	0	ENST00000222329.4:c.662C>T	p.Pro221Leu	p.P221L	ENST00000222329	NM_006494.2	221	cCg/cTg	4/4	1	2	FACETS	0.922	0.85	0.996	0.922	0.85	0.996	CLONAL	1	TRUE	1	0.58	2		807	621	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796883	42796883	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	196	845	0	ENST00000575354.2:c.3347del	p.Pro1116GlnfsTer45	p.P1116Qfs*45	ENST00000575354	NM_015125.3	1114	gCc/gc	14/20	1	2	FACETS	0.918	0.853	0.986	0.918	0.853	0.986	CLONAL	1	TRUE	1	0.58	2		845	736	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25536786	25536786	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1174462913	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	176	554	0	ENST00000264709.3:c.68G>A	p.Arg23Gln	p.R23Q	ENST00000264709	NM_175629.2	23	cGa/cAa	2/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.58	2		554	567	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022316	26022316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	129	519	0	ENST00000435504.4:c.341G>A	p.Ser114Asn	p.S114N	ENST00000435504		114	aGc/aAc	5/13	1	2	FACETS	0.854	0.778	0.933	0.854	0.778	0.933	CLONAL	1	TRUE	1	0.58	2		519	521	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47596650	47596651	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	60	178	0	ENST00000263735.4:c.11dup	p.Gln5AlafsTer26	p.Q5Afs*26	ENST00000263735	NM_002354.2	2	-/C	1/9	1	2	FACETS	0.915	0.799	1	0.915	0.799	1	CLONAL	1	TRUE	1	0.58	2		178	226	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656889	47656889	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	35	91	0	ENST00000233146.2:c.1085T>C	p.Leu362Ser	p.L362S	ENST00000233146	NM_000251.2	362	tTa/tCa	7/16	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.58	2		91	112	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131411	202131411	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs777784105	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	133	442	0	ENST00000358485.4:c.379C>T	p.Arg127Ter	p.R127*	ENST00000358485	NM_001080125.1	127	Cga/Tga	2/9	1	2	FACETS	0.997	0.912	1	0.997	0.912	1	CLONAL	1	TRUE	1	0.58	2		442	460	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570063	212570063	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746784831	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	96	325	0	ENST00000342788.4:c.1178G>A	p.Arg393Gln	p.R393Q	ENST00000342788	NM_005235.2	393	cGg/cAg	10/28	1	2	FACETS	0.83	0.744	0.919	0.83	0.744	0.919	CLONAL	1	TRUE	1	0.58	2		325	399	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	109	299	6	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	0.979	0.905	1	1	0.99	1	CLONAL	2	TRUE	1	0.58	2		305	192	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735460	40735460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	177	582	0	ENST00000373198.4:c.3413T>G	p.Leu1138Arg	p.L1138R	ENST00000373198	NM_133170.3	1138	cTc/cGc	25/32	1	2	FACETS	0.983	0.91	1	0.983	0.91	1	CLONAL	1	TRUE	1	0.58	2		582	621	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651187	45651187	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs749300015	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	154	494	0	ENST00000407780.3:c.838C>T	p.Arg280Ter	p.R280*	ENST00000407780	NM_001283052.1	280	Cga/Tga	5/7	1	2	FACETS	0.94	0.865	1	0.94	0.865	1	CLONAL	1	TRUE	1	0.58	2		494	565	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	74	287	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.773	0.682	0.87	0.773	0.682	0.87	SUBCLONAL	1	TRUE	1	0.58	2		287	330	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438494	52438494	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756443059	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	152	504	0	ENST00000460680.1:c.1225G>A	p.Val409Met	p.V409M	ENST00000460680	NM_004656.3	409	Gtg/Atg	12/17	1	2	FACETS	0.98	0.901	1	0.98	0.901	1	CLONAL	1	TRUE	1	0.58	2		504	535	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662971	52662971	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755190183	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	116	324	0	ENST00000394830.3:c.1382G>A	p.Arg461His	p.R461H	ENST00000394830	NM_018313.4	461	cGc/cAc	13/30	1	2	FACETS	0.98	0.891	1	0.98	0.891	1	CLONAL	1	TRUE	1	0.58	2		324	408	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247442	71247442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750746668	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	159	542	0	ENST00000318789.4:c.91G>A	p.Gly31Ser	p.G31S	ENST00000318789	NM_032682.5	31	Ggt/Agt	6/21	1	2	FACETS	0.934	0.86	1	0.934	0.86	1	CLONAL	1	TRUE	1	0.58	2		542	587	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468397	89468398	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1467832547	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	49	237	1	ENST00000336596.2:c.1938dup	p.Glu647ArgfsTer7	p.E647Rfs*7	ENST00000336596	NM_005233.5	644	tca/tcAa	11/17	1	2	FACETS	0.808	0.693	0.932	0.808	0.693	0.932	CLONAL	1	TRUE	1	0.58	2		238	209	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468402	89468405	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	40	246	0	ENST00000336596.2:c.1937_1940del	p.Lys646ArgfsTer9	p.K646Rfs*9	ENST00000336596	NM_005233.5	646	AAAGag/ag	11/17	1	2	FACETS	0.663	0.557	0.779	0.663	0.557	0.779	SUBCLONAL	1	TRUE	1	0.58	2		246	208	SUCCESS
ATR	545	MSKCC	GRCh37	3	142172034	142172034	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	100	384	0	ENST00000350721.4:c.7697G>A	p.Ser2566Asn	p.S2566N	ENST00000350721	NM_001184.3	2566	aGt/aAt	46/47	1	2	FACETS	0.823	0.74	0.91	0.823	0.74	0.91	CLONAL	1	TRUE	1	0.58	2		384	419	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	41	496	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.321	0.268	0.381	0.321	0.268	0.381	SUBCLONAL	1	TRUE	1	0.58	2		496	440	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446890	187446890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753955082	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	206	721	0	ENST00000232014.4:c.1303G>A	p.Gly435Arg	p.G435R	ENST00000232014	NM_001130845.1	435	Ggg/Agg	5/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.58	2		721	664	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197772	66197772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	72	312	0	ENST00000273854.3:c.2927C>T	p.Ala976Val	p.A976V	ENST00000273854	NM_004439.5	976	gCa/gTa	17/18	1	2	FACETS	0.709	0.624	0.8	0.709	0.624	0.8	SUBCLONAL	1	TRUE	1	0.58	2		312	350	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007332	143007332	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	73	254	2	ENST00000262992.4:c.2452del	p.Arg818GlufsTer4	p.R818Efs*4	ENST00000262992	NM_001101669.1	818	Aga/ga	22/24	1	2	FACETS	0.842	0.743	0.946	0.842	0.743	0.946	CLONAL	1	TRUE	1	0.58	2		256	299	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268144	153268144	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs920052554	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	121	302	1	ENST00000281708.4:c.664C>T	p.Arg222Ter	p.R222*	ENST00000281708	NM_033632.3	222	Cga/Tga	4/12	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.58	2		303	408	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254597	1254597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1418488828	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	138	598	0	ENST00000310581.5:c.3181G>A	p.Ala1061Thr	p.A1061T	ENST00000310581	NM_198253.2	1061	Gcc/Acc	15/16	1	2	FACETS	0.942	0.863	1	0.942	0.863	1	CLONAL	1	TRUE	1	0.58	2		598	505	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	77	262	3	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.922	0.818	1	0.922	0.818	1	CLONAL	1	TRUE	1	0.58	2		265	288	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	191	430	9	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.58	2		439	564	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86648999	86648999	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs975191415	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	62	243	1	ENST00000274376.6:c.1279C>T	p.Arg427Ter	p.R427*	ENST00000274376	NM_002890.2	427	Cga/Tga	9/25	1	2	FACETS	0.798	0.696	0.906	0.798	0.696	0.906	CLONAL	1	TRUE	1	0.58	2		244	268	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675571	86675571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1561325048	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	51	183	0	ENST00000274376.6:c.2513del	p.Asn838MetfsTer4	p.N838Mfs*4	ENST00000274376	NM_002890.2	836	gAa/ga	19/25	1	2	FACETS	0.771	0.663	0.888	0.771	0.663	0.888	SUBCLONAL	1	TRUE	1	0.58	2		183	228	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	91	596	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.926	0.83	1	0.926	0.83	1	CLONAL	1	TRUE	1	0.58	2		596	339	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	72	314	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.88	0.777	0.989	0.88	0.777	0.989	CLONAL	1	TRUE	1	0.58	2		314	282	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930612	131930612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	72	287	0	ENST00000265335.6:c.1849del	p.Arg617GlufsTer26	p.R617Efs*26	ENST00000265335		615	ctA/ct	12/25	1	2	FACETS	0.865	0.764	0.972	0.865	0.764	0.972	CLONAL	1	TRUE	1	0.58	2		287	287	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057785	180057786	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	92	444	0	ENST00000261937.6:c.169dup	p.Leu57ProfsTer80	p.L57Pfs*80	ENST00000261937	NM_182925.4	57	ctc/cCtc	3/30	1	2	FACETS	0.779	0.697	0.866	0.779	0.697	0.866	SUBCLONAL	1	TRUE	1	0.58	2		444	407	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163855	32163855	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	131	458	1	ENST00000375023.3:c.5371del	p.Ala1791GlnfsTer11	p.A1791Qfs*11	ENST00000375023	NM_004557.3	1791	Gca/ca	30/30	1	2	FACETS	0.898	0.82	0.979	0.898	0.82	0.979	CLONAL	1	TRUE	1	0.58	2		459	503	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	383	783	0	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	0.925	0.886	0.963	1	0.997	1	CLONAL	2	TRUE	1	0.58	2		783	714	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521922	157521922	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	47	527	0	ENST00000346085.5:c.4195del	p.Gln1399SerfsTer49	p.Q1399Sfs*49	ENST00000346085	NM_020732.3	1398	agC/ag	18/20	1	2	FACETS	0.343	0.29	0.403	0.343	0.29	0.403	SUBCLONAL	1	TRUE	1	0.58	2		527	472	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521932	157521932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	50	545	0	ENST00000346085.5:c.4204G>A	p.Glu1402Lys	p.E1402K	ENST00000346085	NM_020732.3	1402	Gag/Aag	18/20	1	2	FACETS	0.351	0.298	0.41	0.351	0.298	0.41	SUBCLONAL	1	TRUE	1	0.58	2		545	491	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	162	698	3	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.898	0.827	0.971	0.898	0.827	0.971	CLONAL	1	TRUE	1	0.58	2		701	622	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987341	2987341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145474800	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	173	528	1	ENST00000396946.4:c.88C>T	p.Arg30Trp	p.R30W	ENST00000396946	NM_032415.4	30	Cgg/Tgg	3/25	1	2	FACETS	0.967	0.894	1	0.967	0.894	1	CLONAL	1	TRUE	1	0.58	2		529	617	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511073	148511073	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	32	268	0	ENST00000320356.2:c.1829G>C	p.Ser610Thr	p.S610T	ENST00000320356	NM_004456.4	610	aGt/aCt	15/20	1	2	FACETS	0.32	0.26	0.387	0.32	0.26	0.387	SUBCLONAL	1	TRUE	1	0.58	2		268	345	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845550	151845550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753793539	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	142	535	1	ENST00000262189.6:c.13462G>A	p.Ala4488Thr	p.A4488T	ENST00000262189	NM_170606.2	4488	Gcc/Acc	52/59	1	2	FACETS	0.788	0.721	0.859	0.788	0.721	0.859	SUBCLONAL	1	TRUE	1	0.58	2		536	621	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	101	356	0	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	0.944	0.851	1	0.944	0.851	1	CLONAL	1	TRUE	1	0.58	2		356	369	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006029	22006029	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	115	512	0	ENST00000276925.6:c.374A>G	p.His125Arg	p.H125R	ENST00000276925	NM_004936.3	125	cAc/cGc	2/2	1	2	FACETS	0.778	0.704	0.855	0.778	0.704	0.855	SUBCLONAL	1	TRUE	1	0.58	2		512	510	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772921	135772921	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	174	424	0	ENST00000298552.3:c.2702G>T	p.Arg901Met	p.R901M	ENST00000298552	NM_001162426.1	901	aGg/aTg	21/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.58	2		424	546	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413115	139413115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	233	805	2	ENST00000277541.6:c.1027G>A	p.Ala343Thr	p.A343T	ENST00000277541	NM_017617.3	343	Gcc/Acc	6/34	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.58	2		807	793	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923087	39923087	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	152	572	0	ENST00000378444.4:c.3621del	p.Lys1207AsnfsTer31	p.K1207Nfs*31	ENST00000378444	NM_001123385.1	1207	aaA/aa	8/15	1	2	FACETS	0.803	0.736	0.872	0.803	0.736	0.872	CLONAL	1	TRUE	1	0.58	2		572	653	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411411	63411411	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	152	645	1	ENST00000330258.3:c.1756C>T	p.Arg586Ter	p.R586*	ENST00000330258	NM_152424.3	586	Cga/Tga	2/2	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.58	2		646	511	SUCCESS
AR	367	MSKCC	GRCh37	X	66765242	66765243	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCA	rs753526329	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	75	440	0	ENST00000374690.3:c.271_273dup	p.Gln91dup	p.Q91dup	ENST00000374690	NM_000044.3	91	agg/agGCAg	1/8	1	2	FACETS	0.777	0.686	0.873	0.777	0.686	0.873	SUBCLONAL	1	TRUE	1	0.58	2		440	333	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70353057	70353057	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	35	410	0	ENST00000374080.3:c.4612A>G	p.Asn1538Asp	p.N1538D	ENST00000374080		1538	Aac/Gac	33/45	1	2	FACETS	0.28	0.229	0.337	0.28	0.229	0.337	SUBCLONAL	1	TRUE	1	0.58	2		410	431	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814283	76814283	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	70	273	0	ENST00000373344.5:c.6361T>C	p.Ser2121Pro	p.S2121P	ENST00000373344	NM_000489.3	2121	Tct/Cct	29/35	1	2	FACETS	0.832	0.733	0.938	0.832	0.733	0.938	CLONAL	1	TRUE	1	0.58	2		273	290	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938229	76938230	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	97	508	3	ENST00000373344.5:c.2518dup	p.Arg840LysfsTer9	p.R840Kfs*9	ENST00000373344	NM_000489.3	840	aga/aAga	9/35	1	2	FACETS	0.665	0.595	0.739	0.665	0.595	0.739	SUBCLONAL	1	TRUE	1	0.58	2		511	503	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0042027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	111	395	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.756	0.684	0.831	0.756	0.684	0.831	SUBCLONAL	1	TRUE	1	0.687704068718881	2		396	427	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711889	89711892	+	frameshift_variant	Frame_Shift_Del	DEL	CAGT	CAGT	-	novel	NA	P-0042027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	122	368	0	ENST00000371953.3:c.510_513del	p.Ser170ArgfsTer12	p.S170Rfs*12	ENST00000371953	NM_000314.4	169	ccCAGT/cc	6/9	0.687704068718881	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.687704068718881	1		368	226	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556884	29556885	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGAACAAACCATAGCTATAATGA	novel	NA	P-0042027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	51	252	0	ENST00000356175.3:c.2888_2910dup	p.Leu971LysfsTer3	p.L971Kfs*3	ENST00000356175	NM_000267.3	961	gta/gtAGAACAAACCATAGCTATAATGAa	22/57	0.687704068718881	1	FACETS	0.695	0.605	0.789	0.695	0.605	0.789	SUBCLONAL	1	TRUE	0	0.687704068718881	1		252	140	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799155	42799155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276734164	NA	P-0042027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	239	750	1	ENST00000575354.2:c.4639C>T	p.Pro1547Ser	p.P1547S	ENST00000575354	NM_015125.3	1547	Cct/Tct	20/20	1	2	FACETS	0.912	0.855	0.971	0.912	0.855	0.971	CLONAL	1	TRUE	1	0.687704068718881	2		751	762	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752965	128752965	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	162	602	0	ENST00000377970.2:c.1126G>C	p.Val376Leu	p.V376L	ENST00000377970	NM_002467.4	376	Gtc/Ctc	3/3	1	2	FACETS	0.84	0.771	0.912	1	0.993	1	CLONAL	3	FALSE	1	0.156967246287043	2		602	819	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198263228	198263228	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	27	436	0	ENST00000335508.6:c.3091G>T	p.Val1031Leu	p.V1031L	ENST00000335508	NM_012433.2	1031	Gta/Tta	21/25	1	2	FACETS	0.758	0.602	0.936	0.758	0.602	0.936	CLONAL	1	FALSE	1	0.156967246287043	2		436	454	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	40	82	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.14	2		82	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577518	7577518	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519995	NA	P-0042085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	47	848	1	ENST00000269305.4:c.763A>T	p.Ile255Phe	p.I255F	ENST00000269305	NM_001126112.2	255	Atc/Ttc	7/11	1	2	FACETS	0.711	0.598	0.837	0.711	0.598	0.837	SUBCLONAL	1	TRUE	1	0.14	2		849	944	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879810	37879810	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	52	745	0	ENST00000269571.5:c.2105C>G	p.Pro702Arg	p.P702R	ENST00000269571		702	cCt/cGt	18/27	1	2	FACETS	0.965	0.82	1	0.965	0.82	1	CLONAL	1	TRUE	1	0.14	2		745	770	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430599	181430599	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	39	817	0	ENST00000325404.1:c.451G>C	p.Ala151Pro	p.A151P	ENST00000325404	NM_003106.3	151	Gcg/Ccg	1/1	1	2	FACETS	0.813	0.672	0.971	0.813	0.672	0.971	CLONAL	1	TRUE	1	0.14	2		817	685	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0042165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	122	466	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.754	0.684	0.829	0.754	0.684	0.829	SUBCLONAL	1	TRUE	1	0.525040499967112	2		466	616	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	124	82	0				ENST00000310581	NM_198253.2	-/1132			0.386489426950823	1	FACETS	0.698	0.635	0.764	0.698	0.635	0.764	SUBCLONAL	1	TRUE	0	0.525040499967112	1		82	499	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245834	46245834	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	96	481	0	ENST00000334344.6:c.3930del	p.Ile1312PhefsTer10	p.I1312Ffs*10	ENST00000334344	NM_152641.2	1310	Ggg/gg	15/21	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.525040499967112	2		481	363	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239933	41239934	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	67	68	0	ENST00000379561.5:c.416_417delinsTT	p.Pro139Leu	p.P139L	ENST00000379561	NM_002015.3	139	cCC/cTT	1/3	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.525040499967112	2		68	175	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39593499	39593499	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	74	353	1	ENST00000262039.4:c.1264A>T	p.Ser422Cys	p.S422C	ENST00000262039	NM_002647.2	422	Agt/Tgt	11/25	0.386489426950823	1	FACETS	0.859	0.763	0.959	0.859	0.763	0.959	CLONAL	1	TRUE	0	0.525040499967112	1		354	242	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395673	45395673	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	115	488	0	ENST00000262160.6:c.461A>T	p.Asn154Ile	p.N154I	ENST00000262160	NM_005901.5	154	aAt/aTt	4/11	0.386489426950823	1	FACETS	0.802	0.728	0.878	0.802	0.728	0.878	CLONAL	1	TRUE	0	0.525040499967112	1		488	403	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951140	17951140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	320	681	0	ENST00000458235.1:c.1153G>A	p.Ala385Thr	p.A385T	ENST00000458235	NM_000215.3	385	Gcc/Acc	9/24	0.133520181760439	3	FACETS	1	0.992	1	0.65	0.614	0.688	INDETERMINATE	1	TRUE	1	0.525040499967112	3		681	1183	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956629	93956629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	49	497	1	ENST00000369303.4:c.2607G>A	p.Met869Ile	p.M869I	ENST00000369303	NM_004440.3	869	atG/atA	15/17	0.520170706044334	1	FACETS	0.404	0.343	0.47	0.404	0.343	0.47	SUBCLONAL	1	TRUE	0	0.525040499967112	1		498	341	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224274	55224274	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	88	561	0	ENST00000275493.2:c.1055A>C	p.Asn352Thr	p.N352T	ENST00000275493	NM_005228.3	352	aAt/aCt	9/28	0.133520181760439	3	FACETS	0.564	0.5	0.634	0.282	0.25	0.317	INDETERMINATE	1	TRUE	1	0.525040499967112	3		561	750	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	66	82	0				ENST00000310581	NM_198253.2	-/1132			0.397558042486625	3	FACETS	1	0.959	1	0.622	0.544	0.705	CLONAL	1	TRUE	1	0.397558042486625	3		82	320	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73350187	73350187	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	66	376	2	ENST00000377767.4:c.698C>T	p.Pro233Leu	p.P233L	ENST00000377767	NM_014953.3	233	cCc/cTc	5/21	0.397558042486625	3	FACETS	1	0.878	1	0.504	0.439	0.573	CLONAL	1	TRUE	1	0.397558042486625	3		378	395	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979282	93979282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	158	524	0	ENST00000369303.4:c.1546C>T	p.Arg516Trp	p.R516W	ENST00000369303	NM_004440.3	516	Cgg/Tgg	7/17	0.397558042486625	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.397558042486625	2		524	384	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485864	57485864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	297	554	0	ENST00000371085.3:c.1165C>T	p.Arg389Cys	p.R389C	ENST00000371085	NM_000516.4	389	Cgt/Tgt	13/13	0.397558042486625	5	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	2	0.397558042486625	5		554	727	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943744	71943744	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1619	289	1017	1	ENST00000298229.2:c.1787C>T	p.Ser596Phe	p.S596F	ENST00000298229	NM_001567.3	596	tCt/tTt	15/28	0.397558042486625	10	FACETS	0.987	0.925	1			1	CLONAL	2	TRUE	NA	0.397558042486625	10		1018	1908	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231320	5231321	+	inframe_insertion,splice_region_variant	In_Frame_Ins	INS	-	-	CATCCTCGT	novel	NA	P-0042178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	78	697	0	ENST00000357368.4:c.2147_2155dup	p.Asp716_Asp718dup	p.D716_D718dup	ENST00000357368	NM_002850.3	716	gtg/gACGAGGATGtg		0.135922572741092	5	FACETS	0.762	0.673	0.857	0.381	0.336	0.429	INDETERMINATE	2	TRUE	1	0.397558042486625	5		697	411	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727065	40727065	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	79	603	2	ENST00000373198.4:c.3899C>A	p.Ala1300Asp	p.A1300D	ENST00000373198	NM_133170.3	1300	gCc/gAc	28/32	NA	2	FACETS	0.729	0.642	0.822			1	INDETERMINATE	1	TRUE	NA	0.397558042486625	2		605	545	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528705	157528705	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	96	762	0	ENST00000346085.5:c.6430C>G	p.Leu2144Val	p.L2144V	ENST00000346085	NM_020732.3	2144	Cta/Gta	20/20	0.397558042486625	2	FACETS	1	0.931	1	0.526	0.471	0.584	CLONAL	1	TRUE	0	0.397558042486625	2		762	459	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554401	141554401	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	234	910	0	ENST00000220592.5:c.1750C>T	p.Pro584Ser	p.P584S	ENST00000220592	NM_012154.3	584	Ccg/Tcg	14/19	0.397558042486625	5	FACETS	1	0.933	1	0.666	0.622	0.712	CLONAL	2	TRUE	2	0.397558042486625	5		910	940	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0042213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	127	443	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.911	0.835	0.989	0.911	0.835	0.989	CLONAL	1	TRUE	1	0.770456103248089	2		443	362	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023756	27023756	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	343	476	0	ENST00000324856.7:c.862C>T	p.Gln288Ter	p.Q288*	ENST00000324856	NM_006015.4	288	Cag/Tag	1/20	0.752266015872122	1	FACETS	0.89	0.852	0.928	0.89	0.852	0.928	CLONAL	1	TRUE	0	0.770456103248089	1		476	615	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226534	1226534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558040549	NA	P-0042213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	500	876	0	ENST00000326873.7:c.1190C>T	p.Ala397Val	p.A397V	ENST00000326873	NM_000455.4	397	gCg/gTg	9/10	1	2	FACETS	0.969	0.928	1	0.969	0.928	1	CLONAL	1	TRUE	1	0.770456103248089	2		876	1340	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702606	52702606	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	198	405	0	ENST00000394830.3:c.292del	p.Gln98AsnfsTer4	p.Q98Nfs*4	ENST00000394830	NM_018313.4	98	Caa/aa	4/30	0.752266015872122	1	FACETS	0.819	0.77	0.867	0.819	0.77	0.867	CLONAL	1	TRUE	0	0.770456103248089	1		405	386	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	114	82	0				ENST00000310581	NM_198253.2	-/1132			0.603006018313156	1	FACETS	0.831	0.758	0.905	0.831	0.758	0.905	CLONAL	1	TRUE	0	0.603006018313156	1		82	318	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0042228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	6312	367	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.603006018313156	42	FACETS	0.991	0.987	0.995			1	CLONAL	41	TRUE	NA	0.603006018313156	42		367	6729	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805991	32805991	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	245	925	0	ENST00000374899.4:c.20G>C	p.Arg7Thr	p.R7T	ENST00000374899	NM_018833.2	7	aGa/aCa	2/12	1	2	FACETS	0.936	0.877	0.997	0.936	0.877	0.997	CLONAL	1	TRUE	1	0.612715017805732	2		925	854	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522740	67522741	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0042282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	28	308	0	ENST00000274335.5:c.244dup	p.Ile82AsnfsTer24	p.I82Nfs*24	ENST00000274335		79	-/A	1/15	1	2	FACETS	0.376	0.301	0.462	0.376	0.301	0.462	SUBCLONAL	1	TRUE	1	0.421503892339182	2		308	353	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519010	103519010	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	197	428	0	ENST00000355739.4:c.2348A>G	p.Tyr783Cys	p.Y783C	ENST00000355739	NM_000123.3	783	tAc/tGc	11/15	1	2	FACETS	0.999	0.935	1	1	0.994	1	CLONAL	2	TRUE	1	0.421503892339182	2		428	468	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054341	42054343	+	inframe_deletion	In_Frame_Del	DEL	GTG	GTG	-	novel	NA	P-0042282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	29	317	0	ENST00000219905.7:c.7527_7529del	p.Val2510del	p.V2510del	ENST00000219905	NM_001164273.1	2509	GTG/-	22/24	0.421503892339182	0	FACETS	0.463	0.375	0.56			1	SUBCLONAL	1	TRUE	0	0.421503892339182	0		317	172	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921756	111921756	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	116	443	0	ENST00000393256.3:c.546del	p.Ile183SerfsTer59	p.I183Sfs*59	ENST00000393256	NM_006538.4	182	gTt/gt	4/4	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.421503892339182	2		443	533	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573999	41574011	+	frameshift_variant	Frame_Shift_Del	DEL	CTAATCCACAACC	CTAATCCACAACC	-	novel	NA	P-0042282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	95	622	0	ENST00000263253.7:c.6285_6297del	p.Asn2096SerfsTer34	p.N2096Sfs*34	ENST00000263253	NM_001429.3	2095	tCTAATCCACAACCc/tc	31/31	1	2	FACETS	0.874	0.78	0.972	0.874	0.78	0.972	CLONAL	1	TRUE	1	0.421503892339182	2		622	516	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576798	67576799	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0042282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	14	364	0	ENST00000274335.5:c.883_884dup	p.Thr296GlnfsTer23	p.T296Qfs*23	ENST00000274335		294	atc/aTCtc	6/15	1	2	FACETS	0.274	0.198	0.367	0.274	0.198	0.367	SUBCLONAL	1	TRUE	1	0.421503892339182	2		364	242	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219252	94219252	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0042313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	55	269	0	ENST00000323929.3:c.154-2A>T		p.X52_splice	ENST00000323929	NM_005591.3	52			0.326236299115742	3	FACETS	0.986	0.859	1	0.986	0.859	1	CLONAL	2	TRUE	1	0.359423235273915	3		269	183	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426769	121426769	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	183	735	1	ENST00000257555.6:c.460A>G	p.Met154Val	p.M154V	ENST00000257555		154	Atg/Gtg	2/10	0.333077941067195	2	FACETS	0.903	0.839	0.969	0.903	0.839	0.969	CLONAL	2	TRUE	0	0.359423235273915	2		736	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0042313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	162	633	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.326196972630507	2	FACETS	0.857	0.791	0.924	0.857	0.791	0.924	CLONAL	2	TRUE	0	0.359423235273915	2		633	526	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654535	29654535	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	80	260	0	ENST00000356175.3:c.5224C>T	p.Gln1742Ter	p.Q1742*	ENST00000356175	NM_000267.3	1742	Caa/Taa	37/57	0.326196972630507	2	FACETS	0.897	0.802	0.997	0.897	0.802	0.997	CLONAL	2	TRUE	0	0.359423235273915	2		260	248	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437359	220437360	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0042313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	74	701	0	ENST00000243786.2:c.266_267dup	p.Asp90GlnfsTer38	p.D90Qfs*38	ENST00000243786	NM_002191.3	88	gcc/gcCAc	1/2	1	2	FACETS	0.837	0.735	0.947	0.837	0.735	0.947	CLONAL	1	TRUE	1	0.359423235273915	2		701	492	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685209	86685209	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0042313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	46	190	0	ENST00000274376.6:c.2926-1G>C		p.X976_splice	ENST00000274376	NM_002890.2	976			0.323065801970785	2	FACETS	1	0.958	1	0.692	0.591	0.8	CLONAL	1	TRUE	0	0.359423235273915	2		190	185	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225588	26225588	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	139	415	0	ENST00000360408.1:c.206A>T	p.Gln69Leu	p.Q69L	ENST00000360408	NM_003532.2	69	cAg/cTg	1/1	0.359423235273915	6	FACETS	1	0.976	1	0.79	0.722	0.86	CLONAL	2	TRUE	3	0.359423235273915	6		415	561	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100080	157100094	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGCGGCCGC	GGCGGCGGCGGCCGC	-	rs775733700	NA	P-0042313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	34	34	0	ENST00000346085.5:c.1029_1043del	p.Ala346_Ala350del	p.A346_A350del	ENST00000346085	NM_020732.3	339	gtGGCGGCGGCGGCCGCg/gtg	1/20	0.18217050857956	3	FACETS	1	0.919	1			1	INDETERMINATE	3	TRUE	NA	0.359423235273915	3		34	67	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162475160	162475160	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	44	424	0	ENST00000366898.1:c.581del	p.Gly194ValfsTer31	p.G194Vfs*31	ENST00000366898	NM_004562.2	194	gGt/gt	5/12	NA	2	FACETS	0.805	0.679	0.944			1	INDETERMINATE	1	TRUE	NA	0.359423235273915	2		424	304	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513160	106513160	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	49	227	0	ENST00000359195.3:c.2064C>A	p.Asn688Lys	p.N688K	ENST00000359195	NM_002649.2	688	aaC/aaA	4/11	0.208494901337049	5	FACETS	0.853	0.729	0.987	0.569	0.486	0.658	INDETERMINATE	2	TRUE	2	0.359423235273915	5		227	246	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	130	214	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.250727034868151	3	FACETS	0.943	0.858	1	0.943	0.858	1	CLONAL	2	TRUE	1	0.250727034868151	3		214	619	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974245	2974245	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	227	628	0	ENST00000396946.4:c.1360C>A	p.Pro454Thr	p.P454T	ENST00000396946	NM_032415.4	454	Cca/Aca	10/25	0.250727034868151	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.250727034868151	3		628	990	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0042407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	548	742	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	2	TRUE	NA	0.646506414610805	2		742	842	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052945	180052945	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760476680	NA	P-0042407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	856	1066	2	ENST00000261937.6:c.1345G>A	p.Gly449Arg	p.G449R	ENST00000261937	NM_182925.4	449	Ggg/Agg	10/30	0.615049773587535	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	1	0.646506414610805	4		1068	1427	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425124	49425124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372839823	NA	P-0042407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	154	991	1	ENST00000301067.7:c.13364G>A	p.Arg4455His	p.R4455H	ENST00000301067	NM_003482.3	4455	cGc/cAc	39/54	0.646506414610805	3	FACETS	0.659	0.603	0.719	0.33	0.301	0.36	SUBCLONAL	1	TRUE	1	0.646506414610805	3		992	956	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421589	32421589	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	232	507	0	ENST00000332351.3:c.1003C>G	p.His335Asp	p.H335D	ENST00000332351	NM_024426.4	335	Cac/Gac	6/10	0.597340882434922	2	FACETS	0.906	0.848	0.966	0.453	0.424	0.483	CLONAL	1	TRUE	0	0.646506414610805	2		507	792	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959024	28959024	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	55	347	0	ENST00000282397.4:c.2114C>G	p.Pro705Arg	p.P705R	ENST00000282397	NM_002019.4	705	cCt/cGt	14/30	0.344564131293226	4	FACETS	0.665	0.571	0.769	0.333	0.285	0.385	INDETERMINATE	1	TRUE	2	0.646506414610805	4		347	421	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437194	52437194	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	150	839	0	ENST00000460680.1:c.1850G>C	p.Arg617Thr	p.R617T	ENST00000460680	NM_004656.3	617	aGg/aCg	14/17	0.34713947882346	3	FACETS	0.67	0.612	0.73	0.335	0.306	0.365	INDETERMINATE	1	TRUE	1	0.646506414610805	3		839	917	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500492	149500492	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1184721015	NA	P-0042407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	109	819	0	ENST00000261799.4:c.2545C>G	p.Arg849Gly	p.R849G	ENST00000261799	NM_002609.3	849	Cga/Gga	18/23	0.310155902178284	3	FACETS	0.571	0.512	0.633	0.285	0.256	0.317	INDETERMINATE	1	TRUE	1	0.646506414610805	3		819	782	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004244	150004244	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	98	341	0	ENST00000253339.5:c.1981A>G	p.Lys661Glu	p.K661E	ENST00000253339		661	Aaa/Gaa	3/7	0.597340882434922	2	FACETS	0.876	0.807	0.945	0.876	0.807	0.945	CLONAL	2	TRUE	0	0.646506414610805	2		341	173	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0042414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	365	395	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	0.355769990196104	3	FACETS	0.924	0.881	0.967			1	CLONAL	3	TRUE	NA	0.387054845208978	3		395	812	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080560	5080560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	40	121	0	ENST00000381652.3:c.2311C>T	p.Gln771Ter	p.Q771*	ENST00000381652	NM_004972.3	771	Cag/Tag	18/25	0.387054845208978	5	FACETS	1	0.841	1	0.336	0.28	0.398	CLONAL	1	TRUE	2	0.387054845208978	5		121	324	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481601	40481601	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	82	323	0	ENST00000264657.5:c.1204G>C	p.Gly402Arg	p.G402R	ENST00000264657	NM_139276.2	402	Ggc/Cgc	13/24	0.387054845208978	4	FACETS	0.702	0.618	0.793			1	SUBCLONAL	1	TRUE	NA	0.387054845208978	4		323	837	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282709	1282709	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	84	336	0	ENST00000310581.5:c.1604G>C	p.Arg535Pro	p.R535P	ENST00000310581	NM_198253.2	535	cGt/cCt	3/16	0.387054845208978	4	FACETS	0.812	0.717	0.915			1	CLONAL	1	TRUE	NA	0.387054845208978	4		336	741	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015643	112015643	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	187	260	0	ENST00000368678.4:c.1199T>C	p.Ile400Thr	p.I400T	ENST00000368678		400	aTa/aCa	11/13	0.387054845208978	5	FACETS	1	0.967	1	0.537	0.497	0.578	CLONAL	2	TRUE	1	0.387054845208978	5		260	711	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	116	658	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.268697214226489	1	FACETS	0.852	0.767	0.942	0.852	0.767	0.942	CLONAL	1	FALSE	0	0.268697214226489	1		658	877	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	128	358	1	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.268697214226489	2		359	796	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954652	17954652	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	156	795	0	ENST00000458235.1:c.242G>T	p.Trp81Leu	p.W81L	ENST00000458235	NM_000215.3	81	tGg/tTg	3/24	1	2	FACETS	0.936	0.855	1	0.936	0.855	1	CLONAL	1	FALSE	1	0.268697214226489	2		795	1241	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	32	344	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	0.491	0.398	0.597	0.491	0.398	0.597	SUBCLONAL	1	FALSE	1	0.268697214226489	2		344	485	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001930	29001930	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	78	489	0	ENST00000282397.4:c.1235C>A	p.Ser412Ter	p.S412*	ENST00000282397	NM_002019.4	412	tCa/tAa	9/30	0.12208277987562	0	FACETS	0.653	0.574	0.738			1	INDETERMINATE	1	FALSE	0	0.268697214226489	0		489	650	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202423	123202423	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	38	485	0	ENST00000218089.9:c.2275C>A	p.Leu759Met	p.L759M	ENST00000218089	NM_001042749.1	759	Ctg/Atg	24/35	1	2	FACETS	0.47	0.387	0.562	0.47	0.387	0.562	SUBCLONAL	1	FALSE	1	0.268697214226489	2		485	602	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156657	106156657	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	91	503	0	ENST00000380013.4:c.1559del	p.Gly520ValfsTer13	p.G520Vfs*13	ENST00000380013	NM_001127208.2	520	Ggt/gt	3/11	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	FALSE	1	0.268697214226489	2		503	639	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023501	31023501	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	73	622	0	ENST00000375687.4:c.2986G>T	p.Gly996Cys	p.G996C	ENST00000375687	NM_015338.5	996	Ggt/Tgt	13/13	1	2	FACETS	0.591	0.516	0.673	0.591	0.516	0.673	SUBCLONAL	1	FALSE	1	0.268697214226489	2		622	919	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181423	38181423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	252	525	0	ENST00000396334.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000396334	NM_002468.4	146	Gct/Act	2/5	0.268697214226489	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	FALSE	1	0.268697214226489	3		525	996	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834189	156834189	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs774266965	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1231	93	786	0	ENST00000524377.1:c.256G>T	p.Asp86Tyr	p.D86Y	ENST00000524377	NM_002529.3	86	Gat/Tat	2/17	0.268697214226489	3	FACETS	0.593	0.525	0.666	0.297	0.262	0.333	SUBCLONAL	1	FALSE	1	0.268697214226489	3		786	1324	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759849	63759849	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	96	390	0	ENST00000279873.7:c.503-1G>T		p.X168_splice	ENST00000279873	NM_032199.2	168			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.268697214226489	2		390	583	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410617	32410617	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	101	547	1	ENST00000332351.3:c.1541A>T	p.Gln514Leu	p.Q514L	ENST00000332351	NM_024426.4	514	cAg/cTg	10/10	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	FALSE	1	0.268697214226489	2		548	712	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120819	115120819	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	64	471	0	ENST00000257566.3:c.187C>A	p.Pro63Thr	p.P63T	ENST00000257566	NM_016569.3	63	Ccg/Acg	1/8	1	2	FACETS	0.719	0.622	0.824	0.719	0.622	0.824	SUBCLONAL	1	FALSE	1	0.268697214226489	2		471	663	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663652	29663653	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	81	415	2	ENST00000356175.3:c.6085-1_6085delinsTT		p.X2029_splice	ENST00000356175	NM_000267.3	2029		41/57	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	FALSE	1	0.268697214226489	2		417	583	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216748	2216748	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	123	727	1	ENST00000398665.3:c.2392A>C	p.Ser798Arg	p.S798R	ENST00000398665	NM_032482.2	798	Agt/Cgt	20/28	1	2	FACETS	0.906	0.818	0.999	0.906	0.818	0.999	CLONAL	1	FALSE	1	0.268697214226489	2		728	1011	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274109	18274109	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	113	799	0	ENST00000222254.8:c.1327G>T	p.Gly443Cys	p.G443C	ENST00000222254	NM_005027.3	443	Ggc/Tgc	11/16	1	2	FACETS	0.817	0.733	0.905	0.817	0.733	0.905	CLONAL	1	FALSE	1	0.268697214226489	2		799	1030	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920459	134920459	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	167	680	0	ENST00000398015.3:c.2274C>A	p.Cys758Ter	p.C758*	ENST00000398015	NM_004441.4	758	tgC/tgA	12/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.268697214226489	2		680	985	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188343	142188343	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	74	527	0	ENST00000350721.4:c.6388A>T	p.Thr2130Ser	p.T2130S	ENST00000350721	NM_001184.3	2130	Aca/Tca	38/47	1	2	FACETS	0.637	0.556	0.724	0.637	0.556	0.724	SUBCLONAL	1	FALSE	1	0.268697214226489	2		527	865	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946139	55946139	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	77	425	0	ENST00000263923.4:c.4040C>A	p.Ser1347Ter	p.S1347*	ENST00000263923	NM_002253.2	1347	tCg/tAg	30/30	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	1	0.268697214226489	2		425	491	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295432	1295432	+	upstream_gene_variant	5'Flank	DEL	G	G	-	novel	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	22	26	0				ENST00000310581	NM_198253.2	-/1132			0.260560900104938	5	FACETS	1	0.842	1	0.798	0.638	0.971	CLONAL	3	FALSE	1	0.268697214226489	5		26	72	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111629	56111629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1348132934	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	39	209	1	ENST00000399503.3:c.229C>T	p.Pro77Ser	p.P77S	ENST00000399503	NM_005921.1	77	Ccg/Tcg	1/20	1	2	FACETS	0.882	0.734	1	0.882	0.734	1	CLONAL	1	FALSE	1	0.268697214226489	2		210	329	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250534	26250534	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	157	698	0	ENST00000446824.2:c.300C>A	p.Tyr100Ter	p.Y100*	ENST00000446824	NM_021018.2	100	taC/taA	1/1	0.188138752643057	0	FACETS	0.806	0.737	0.878			1	CLONAL	1	FALSE	0	0.268697214226489	0		698	1060	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552983	106552983	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	102	774	0	ENST00000369096.4:c.948C>A	p.Tyr316Ter	p.Y316*	ENST00000369096	NM_001198.3	316	taC/taA	5/7	0.12208277987562	0	FACETS	0.575	0.513	0.641			1	INDETERMINATE	1	FALSE	0	0.268697214226489	0		774	966	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521885	157521885	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1049209609	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	64	556	0	ENST00000346085.5:c.4157G>T	p.Arg1386Leu	p.R1386L	ENST00000346085	NM_020732.3	1386	cGc/cTc	18/20	0.12208277987562	0	FACETS	0.469	0.405	0.538			1	INDETERMINATE	1	FALSE	0	0.268697214226489	0		556	743	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987272	2987272	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	169	649	0	ENST00000396946.4:c.157G>T	p.Asp53Tyr	p.D53Y	ENST00000396946	NM_032415.4	53	Gat/Tat	3/25	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.268697214226489	2		649	954	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334803	81334803	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	52	476	0	ENST00000222390.5:c.1913G>T	p.Gly638Val	p.G638V	ENST00000222390	NM_000601.4	638	gGa/gTa	17/18	1	2	FACETS	0.582	0.495	0.678	0.582	0.495	0.678	SUBCLONAL	1	FALSE	1	0.268697214226489	2		476	665	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509432	106509432	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs567756361	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	132	643	0	ENST00000359195.3:c.1426C>A	p.Arg476Ser	p.R476S	ENST00000359195	NM_002649.2	476	Cgc/Agc	2/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.268697214226489	2		643	907	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104574	69104574	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	211	689	0	ENST00000288368.4:c.4418T>A	p.Met1473Lys	p.M1473K	ENST00000288368	NM_024870.2	1473	aTg/aAg	37/40	0.268697214226489	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	0	0.268697214226489	1		689	1031	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993643	90993643	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	84	370	0	ENST00000265433.3:c.280G>T	p.Gly94Trp	p.G94W	ENST00000265433	NM_002485.4	94	Ggg/Tgg	3/16	1	2	FACETS	0.977	0.863	1	0.977	0.863	1	CLONAL	1	FALSE	1	0.268697214226489	2		370	640	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486061	8486061	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs73426355	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	57	644	0	ENST00000356435.5:c.2756C>A	p.Thr919Asn	p.T919N	ENST00000356435		919	aCt/aAt	17/35	1	2	FACETS	0.516	0.442	0.598	0.516	0.442	0.598	SUBCLONAL	1	FALSE	1	0.268697214226489	2		644	822	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242695	98242695	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	112	492	1	ENST00000331920.6:c.922G>T	p.Ala308Ser	p.A308S	ENST00000331920	NM_000264.3	308	Gcc/Tcc	6/24	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.268697214226489	2		493	651	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239969	53239969	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	93	836	0	ENST00000375401.3:c.1472A>G	p.Asn491Ser	p.N491S	ENST00000375401	NM_004187.3	491	aAt/aGt	11/26	1	2	FACETS	0.674	0.598	0.756	0.674	0.598	0.756	SUBCLONAL	1	FALSE	1	0.268697214226489	2		836	1027	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829762	76829762	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	95	661	0	ENST00000373344.5:c.6279G>T	p.Gln2093His	p.Q2093H	ENST00000373344	NM_000489.3	2093	caG/caT	28/35	1	2	FACETS	0.782	0.695	0.875	0.782	0.695	0.875	SUBCLONAL	1	FALSE	1	0.268697214226489	2		661	904	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891416	76891416	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	64	442	0	ENST00000373344.5:c.4689T>A	p.His1563Gln	p.H1563Q	ENST00000373344	NM_000489.3	1563	caT/caA	16/35	1	2	FACETS	0.782	0.677	0.896	0.782	0.677	0.896	SUBCLONAL	1	FALSE	1	0.268697214226489	2		442	609	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164886	123164886	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	47	379	0	ENST00000218089.9:c.199C>A	p.Pro67Thr	p.P67T	ENST00000218089	NM_001042749.1	67	Cca/Aca	5/35	1	2	FACETS	0.631	0.532	0.741	0.631	0.532	0.741	SUBCLONAL	1	FALSE	1	0.268697214226489	2		379	554	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0042477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	44	628	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	1	2	FACETS	0.613	0.513	0.723	0.613	0.513	0.723	SUBCLONAL	1	TRUE	1	0.27	2		628	532	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0042477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	58	449	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	1	2	FACETS	0.644	0.553	0.744	0.644	0.553	0.744	SUBCLONAL	1	TRUE	1	0.27	2		449	667	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341247	341247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	83	539	0	ENST00000262320.3:c.2237G>A	p.Cys746Tyr	p.C746Y	ENST00000262320	NM_003502.3	746	tGc/tAc	9/11	1	2	FACETS	0.914	0.806	1	0.914	0.806	1	CLONAL	1	TRUE	1	0.27	2		539	673	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935391	36935391	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	94	547	0	ENST00000361632.4:c.1336T>C	p.Trp446Arg	p.W446R	ENST00000361632		446	Tgg/Cgg	10/16	1	2	FACETS	0.978	0.87	1	0.978	0.87	1	CLONAL	1	TRUE	1	0.27	2		547	712	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345916	70345916	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	54	391	0	ENST00000374080.3:c.2453A>G	p.Asn818Ser	p.N818S	ENST00000374080		818	aAc/aGc	18/45	0.3	2	FACETS	0.644	0.55	0.748			1	SUBCLONAL	1	TRUE	NA	0.27	2		391	621	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	292	82	0				ENST00000310581	NM_198253.2	-/1132			0.865717567893753	3	FACETS	0.984	0.94	1	0.984	0.94	1	CLONAL	2	TRUE	1	0.865717567893753	3		82	491	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0042480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	231	640	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.994	0.935	1	0.994	0.935	1	CLONAL	1	TRUE	1	0.865717567893753	2		640	537	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593597	55593611	+	inframe_deletion	In_Frame_Del	DEL	GTACAGTGGAAGGTT	GTACAGTGGAAGGTT	-	novel	NA	P-0042490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	96	432	0	ENST00000288135.5:c.1665_1679del	p.Gln556_Val560del	p.Q556_V560del	ENST00000288135	NM_000222.2	555	GTACAGTGGAAGGTT/-	11/21	0.364367042184182	1	FACETS	0.511	0.464	0.559	0.511	0.464	0.559	INDETERMINATE	1	TRUE	0	0.901303324412175	1		432	229	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590736	189590736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558374141	NA	P-0042490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	263	597	1	ENST00000264731.3:c.1301C>T	p.Thr434Met	p.T434M	ENST00000264731	NM_003722.4	434	aCg/aTg	10/14	1	2	FACETS	0.954	0.901	1	0.954	0.901	1	CLONAL	1	TRUE	1	0.901303324412175	2		598	612	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49929233	49929233	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	383	838	0	ENST00000296474.3:c.3310C>G	p.Gln1104Glu	p.Q1104E	ENST00000296474	NM_002447.2	1104	Cag/Gag	15/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.901303324412175	2		838	849	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178941910	178941910	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	157	453	0	ENST00000263967.3:c.2229T>G	p.Asp743Glu	p.D743E	ENST00000263967	NM_006218.2	743	gaT/gaG	15/21	1	2	FACETS	0.944	0.877	1	0.944	0.877	1	CLONAL	1	TRUE	1	0.901303324412175	2		453	369	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	72	955	0	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	1	2	FACETS	0.945	0.824	1	0.945	0.824	1	CLONAL	1	TRUE	1	0.16	2		955	952	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591924	48591924	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs377767348	NA	P-0042497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	30	483	0	ENST00000342988.3:c.1087T>C	p.Cys363Arg	p.C363R	ENST00000342988	NM_005359.5	363	Tgt/Cgt	9/12	1	2	FACETS	0.744	0.598	0.91	0.744	0.598	0.91	CLONAL	1	TRUE	1	0.16	2		483	504	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738360	133738360	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	66	655	0	ENST00000318560.5:c.760G>A	p.Gly254Arg	p.G254R	ENST00000318560	NM_005157.4	254	Ggg/Agg	4/11	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.16	2		655	812	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0042497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	77	576	0	ENST00000269305.4:c.97-1G>A		p.X33_splice	ENST00000269305	NM_001126112.2	33			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.16	2		576	673	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926910	112926910	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	25	674	1	ENST00000351677.2:c.1530G>T	p.Gln510His	p.Q510H	ENST00000351677	NM_002834.3	510	caG/caT	13/16	1	2	FACETS	0.504	0.396	0.629	0.504	0.396	0.629	SUBCLONAL	1	TRUE	1	0.16	2		675	620	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377157	118377157	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	71	472	1	ENST00000534358.1:c.10550G>A	p.Gly3517Asp	p.G3517D	ENST00000534358	NM_005933.3	3517	gGt/gAt	27/36	1	2	FACETS	0.759	0.662	0.862	1	0.974	1	SUBCLONAL	2	TRUE	1	0.16	2		473	585	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211207	36211207	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1349	101	1240	0	ENST00000222270.7:c.958T>C	p.Ser320Pro	p.S320P	ENST00000222270	NM_014727.1	320	Tcc/Ccc	3/37	1	2	FACETS	0.871	0.775	0.973	0.871	0.775	0.973	CLONAL	1	TRUE	1	0.16	2		1240	1450	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169988294	169988294	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	39	440	0	ENST00000295797.4:c.536A>G	p.His179Arg	p.H179R	ENST00000295797	NM_002740.5	179	cAt/cGt	6/18	1	2	FACETS	0.804	0.666	0.96	0.804	0.666	0.96	CLONAL	1	TRUE	1	0.16	2		440	606	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138584	55138584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	45	572	0	ENST00000257290.5:c.1261G>A	p.Val421Ile	p.V421I	ENST00000257290	NM_006206.4	421	Gtc/Atc	9/23	1	2	FACETS	0.767	0.643	0.905	0.767	0.643	0.905	CLONAL	1	TRUE	1	0.16	2		572	733	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	104	652	0	ENST00000397752.3:c.3028G>C	p.Asp1010His	p.D1010H	ENST00000397752	NM_000245.2	1010	Gat/Cat	14/21	1	2	FACETS	0.427	0.382	0.474	0.427	0.382	0.474	SUBCLONAL	1	TRUE	1	0.7	2		652	696	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312737	91312737	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1319281718	NA	P-0042506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	64	432	0	ENST00000355112.3:c.2476G>T	p.Val826Leu	p.V826L	ENST00000355112	NM_000057.2	826	Gtg/Ttg	12/22	1	2	FACETS	0.368	0.319	0.421	0.368	0.319	0.421	SUBCLONAL	1	TRUE	1	0.7	2		432	497	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801028	1801028	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	98	1076	0	ENST00000260795.2:c.157A>C	p.Ser53Arg	p.S53R	ENST00000260795		53	Agc/Cgc	2/17	1	2	FACETS	0.34	0.303	0.38	0.34	0.303	0.38	SUBCLONAL	1	TRUE	1	0.7	2		1076	823	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0042514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	79	404	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.379196081596426	3	FACETS	1	0.962	1	0.607	0.537	0.682	CLONAL	1	TRUE	1	0.379196081596426	3		404	408	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624272	89624273	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs876661009	NA	P-0042514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	31	375	0	ENST00000371953.3:c.47dup	p.Tyr16Ter	p.Y16*	ENST00000371953	NM_000314.4	16	tat/tAat	1/9	0.379196081596426	1	FACETS	0.351	0.283	0.426	0.351	0.283	0.426	SUBCLONAL	1	TRUE	0	0.379196081596426	1		375	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578393	7578393	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876660821	NA	P-0042514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	47	687	0	ENST00000269305.4:c.537T>G	p.His179Gln	p.H179Q	ENST00000269305	NM_001126112.2	179	caT/caG	5/11	0.379196081596426	1	FACETS	0.325	0.273	0.381	0.325	0.273	0.381	SUBCLONAL	1	TRUE	0	0.379196081596426	1		687	619	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857680	9857680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303700994	NA	P-0042514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	55	402	1	ENST00000330684.3:c.3721C>T	p.Arg1241Trp	p.R1241W	ENST00000330684	NM_001134407.1	1241	Cgg/Tgg	13/13	1	2	FACETS	0.729	0.625	0.841	0.729	0.625	0.841	SUBCLONAL	1	TRUE	1	0.379196081596426	2		403	398	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362230	40362230	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	63	462	0	ENST00000293328.3:c.1865C>T	p.Ser622Leu	p.S622L	ENST00000293328	NM_012448.3	622	tCa/tTa	15/19	1	2	FACETS	0.646	0.56	0.74	0.646	0.56	0.74	SUBCLONAL	1	TRUE	1	0.379196081596426	2		462	514	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085828	16085828	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	32	524	0	ENST00000281043.3:c.1004C>T	p.Pro335Leu	p.P335L	ENST00000281043	NM_005378.4	335	cCc/cTc	3/3	1	2	FACETS	0.328	0.266	0.399	0.328	0.266	0.399	SUBCLONAL	1	TRUE	1	0.379196081596426	2		524	514	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249522	153249522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	56	382	0	ENST00000281708.4:c.1256G>A	p.Gly419Glu	p.G419E	ENST00000281708	NM_033632.3	419	gGa/gAa	9/12	1	2	FACETS	0.695	0.597	0.802	0.695	0.597	0.802	SUBCLONAL	1	TRUE	1	0.379196081596426	2		382	425	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241673	55241673	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	329	654	0	ENST00000275493.2:c.2121G>T	p.Leu707Phe	p.L707F	ENST00000275493	NM_005228.3	707	ttG/ttT	18/28	0.379196081596426	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.379196081596426	3		654	947	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360624	70360629	+	inframe_deletion	In_Frame_Del	DEL	CAGCAG	CAGCAG	-	rs754533796	NA	P-0042557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	40	429	0	ENST00000374080.3:c.6195_6200del	p.Gln2075_Gln2076del	p.Q2075_Q2076del	ENST00000374080		2062	CAGCAG/-	42/45	1	2	FACETS	0.255	0.212	0.303	0.255	0.212	0.303	SUBCLONAL	1	TRUE	1	0.831759016045324	2		429	377	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798189	32798189	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	175	678	0	ENST00000374899.4:c.1490A>T	p.Glu497Val	p.E497V	ENST00000374899	NM_018833.2	497	gAg/gTg	9/12	0.831759016045324	3	FACETS	0.515	0.474	0.559	0.258	0.237	0.28	SUBCLONAL	1	TRUE	1	0.831759016045324	3		678	1156	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61717848	61717853	+	inframe_deletion	In_Frame_Del	DEL	CTTGTA	CTTGTA	-	novel	NA	P-0042557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	273	559	0	ENST00000401558.2:c.1946_1951del	p.Val649_Gln650del	p.V649_Q650del	ENST00000401558	NM_003400.3	649	gTACAAGaa/gaa	17/25	0.202593621083317	5	FACETS	0.822	0.774	0.872			1	INDETERMINATE	2	TRUE	NA	0.831759016045324	5		559	897	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248409	59248409	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	212	468	0	ENST00000371222.2:c.334G>T	p.Glu112Ter	p.E112*	ENST00000371222	NM_002228.3	112	Gag/Tag	1/1	1	2	FACETS	0.941	0.881	1	0.941	0.881	1	CLONAL	1	TRUE	1	0.831759016045324	2		468	542	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423500	88423500	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0042557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	128	537	0	ENST00000360948.2:c.2334+1G>T		p.X778_splice	ENST00000360948	NM_001012338.2	778			0.787778694318767	1	FACETS	0.473	0.433	0.514	0.473	0.433	0.514	SUBCLONAL	1	TRUE	0	0.831759016045324	1		537	380	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641551	23641551	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs730881865	NA	P-0042557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	286	590	2	ENST00000261584.4:c.1924del	p.Met642CysfsTer18	p.M642Cfs*18	ENST00000261584	NM_024675.3	642	Atg/tg	5/13	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.831759016045324	2		592	685	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765646	41765647	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0042557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	315	744	0	ENST00000301178.4:c.2528dup	p.Thr844AsnfsTer6	p.T844Nfs*6	ENST00000301178	NM_021913.4	841	gac/gaCc	20/20	1	2	FACETS	0.98	0.93	1	0.98	0.93	1	CLONAL	1	TRUE	1	0.831759016045324	2		744	773	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029207	26029207	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0042557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	76	311	0	ENST00000435504.4:c.144-1G>A		p.X48_splice	ENST00000435504		48			0.479895540595617	3	FACETS	0.549	0.483	0.62	0.275	0.241	0.31	INDETERMINATE	1	TRUE	1	0.831759016045324	3		311	471	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461412	138461412	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	176	312	0	ENST00000289153.2:c.609del	p.Phe203LeufsTer16	p.F203Lfs*16	ENST00000289153	NM_006219.2	203	ttT/tt	3/22	0.831759016045324	3	FACETS	0.992	0.919	1	0.496	0.459	0.534	CLONAL	1	TRUE	1	0.831759016045324	3		312	604	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664467	138664467	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	109	506	0	ENST00000330315.3:c.1098G>C	p.Lys366Asn	p.K366N	ENST00000330315	NM_023067.3	366	aaG/aaC	1/1	0.831759016045324	3	FACETS	0.503	0.452	0.557	0.251	0.225	0.279	SUBCLONAL	1	TRUE	1	0.831759016045324	3		506	738	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971375	13971375	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0042557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	150	345	0	ENST00000405192.2:c.555-1G>C		p.X185_splice	ENST00000405192	NM_001163147.1	185			1	2	FACETS	0.748	0.689	0.809	0.748	0.689	0.809	SUBCLONAL	1	TRUE	1	0.831759016045324	2		345	482	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879634	151879634	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	119	271	1	ENST00000262189.6:c.5311C>G	p.Gln1771Glu	p.Q1771E	ENST00000262189	NM_170606.2	1771	Cag/Gag	36/59	0.787778694318767	1	FACETS	0.944	0.884	1	0.944	0.884	1	CLONAL	1	TRUE	0	0.831759016045324	1		272	177	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44920659	44920659	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	141	394	0	ENST00000377967.4:c.1420T>A	p.Leu474Ile	p.L474I	ENST00000377967	NM_021140.2	474	Tta/Ata	14/29	0.831759016045324	1	FACETS	0.556	0.513	0.6	0.556	0.513	0.6	SUBCLONAL	1	TRUE	0	0.831759016045324	1		394	356	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861551	152861551	+	synonymous_variant	Silent	SNP	A	A	C	novel	NA	P-0042557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	296	852	0	ENST00000406277.2:c.201T>G	p.Pro67=	p.P67=	ENST00000406277	NM_152274.4	67	ccT/ccG	4/7	1		FACETS		0.901	1				CLONAL	1	TRUE	1	0.831759016045324	2		852	748	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602659	55602679	+	coding_sequence_variant,intron_variant	Frame_Shift_Del	DEL	TACAGGCTCGACTACCTGTGA	TACAGGCTCGACTACCTGTGA	AATAGGCTTCTATTAC	novel	NA	P-0042557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	136	308	1	ENST00000288135.5:c.2485-5_2500delinsAATAGGCTTCTATTAC		p.*829fs*	ENST00000288135	NM_000222.2	?-834/976		18/21	1	2	FACETS	0.839	0.771	0.908	0.839	0.771	0.908	CLONAL	1	TRUE	1	0.831759016045324	2		309	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577025	7577025	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0042594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	619	689	0	ENST00000269305.4:c.913A>T	p.Lys305Ter	p.K305*	ENST00000269305	NM_001126112.2	305	Aag/Tag	8/11	0.743926284965063	2	FACETS	0.972	0.947	0.996	0.972	0.947	0.996	CLONAL	2	TRUE	0	0.754844527759862	2		689	844	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945090	31945090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	1488	648	0	ENST00000340398.3:c.11C>T	p.Thr4Ile	p.T4I	ENST00000340398	NM_001013699.2	4	aCc/aTc	1/1	0.658993900895967	6	FACETS	0.991	0.975	1			1	CLONAL	5	TRUE	NA	0.754844527759862	6		648	1997	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551808	150551808	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1245371992	NA	P-0042594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	16	24	0	ENST00000369026.2:c.199T>G	p.Ser67Ala	p.S67A	ENST00000369026	NM_021960.4	67	Tcc/Gcc	1/3	0.269776494908082	5	FACETS	1	0.896	1	0.471	0.358	0.598	INDETERMINATE	1	TRUE	2	0.754844527759862	5		24	64	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8105971	8105975	+	frameshift_variant	Frame_Shift_Del	DEL	TGAAC	TGAAC	-	novel	NA	P-0042594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	159	400	0	ENST00000346208.3:c.793_797del	p.Asn265TrpfsTer36	p.N265Wfs*36	ENST00000346208		264	gTGAAC/g	4/6	0.754844527759862	4	FACETS	0.791	0.724	0.86	0.264	0.241	0.287	SUBCLONAL	1	TRUE	1	0.754844527759862	4		400	935	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114756	108114756	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	254	397	0	ENST00000278616.4:c.573T>G	p.Ile191Met	p.I191M	ENST00000278616	NM_000051.3	191	atT/atG	6/63	0.235712865767666	3	FACETS	0.925	0.877	0.974	0.617	0.584	0.649	INDETERMINATE	2	TRUE	0	0.754844527759862	3		397	501	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114769	108114769	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0042594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	271	452	0	ENST00000278616.4:c.586A>T	p.Lys196Ter	p.K196*	ENST00000278616	NM_000051.3	196	Aaa/Taa	6/63	0.235712865767666	3	FACETS	0.916	0.869	0.962	0.611	0.579	0.642	INDETERMINATE	2	TRUE	0	0.754844527759862	3		452	540	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120911	115120911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1029030166	NA	P-0042594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	33	280	0	ENST00000257566.3:c.95C>T	p.Ala32Val	p.A32V	ENST00000257566	NM_016569.3	32	gCg/gTg	1/8	1	2	FACETS	0.212	0.172	0.257	0.212	0.172	0.257	SUBCLONAL	1	TRUE	1	0.754844527759862	2		280	412	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38632010	38632010	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	302	527	1	ENST00000299084.4:c.496G>T	p.Glu166Ter	p.E166*	ENST00000299084	NM_152594.2	166	Gag/Tag	5/7	0.754844527759862	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.754844527759862	1		528	414	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597429	10597430	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0042594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	471	761	1	ENST00000171111.5:c.1773_1774delinsTT	p.Trp591_Ser592delinsCysCys	p.W591_S592delinsCC	ENST00000171111	NM_203500.1	591	tgGAgc/tgTTgc	6/6	0.754844527759862	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.754844527759862	1		762	718	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976591	55976591	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	131	454	0	ENST00000263923.4:c.1234G>T	p.Val412Leu	p.V412L	ENST00000263923	NM_002253.2	412	Gtg/Ttg	9/30	0.396149253478077	1	FACETS	0.446	0.407	0.486	0.446	0.407	0.486	INDETERMINATE	1	TRUE	0	0.754844527759862	1		454	485	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969072	93969072	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	104	217	0	ENST00000369303.4:c.1924G>T	p.Gly642Ter	p.G642*	ENST00000369303	NM_004440.3	642	Gga/Tga	10/17	0.754844527759862	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.754844527759862	1		217	165	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042594-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	143	82	0				ENST00000310581	NM_198253.2	-/1132			0.118756218179859	3	FACETS	0.993	0.913	1	0.993	0.913	1	INDETERMINATE	2	TRUE	1	0.381010259272653	3		82	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0042594-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	219	721	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.381010259272653	2		723	865	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030486	49030486	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0042594-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	63	338	0	ENST00000267163.4:c.1960+1G>A		p.X654_splice	ENST00000267163	NM_000321.2	654			1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.381010259272653	2		338	321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577599	7577599	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042594-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	87	556	0	ENST00000269305.4:c.682G>C	p.Asp228His	p.D228H	ENST00000269305	NM_001126112.2	228	Gac/Cac	7/11	1	2	FACETS	0.591	0.522	0.664	0.591	0.522	0.664	SUBCLONAL	1	TRUE	1	0.381010259272653	2		556	773	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542332	187542332	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0042594-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	24	354	0	ENST00000441802.2:c.5408C>G	p.Ser1803Ter	p.S1803*	ENST00000441802	NM_005245.3	1803	tCa/tGa	10/27	1	2	FACETS	0.313	0.245	0.391	0.313	0.245	0.391	SUBCLONAL	1	TRUE	1	0.381010259272653	2		354	403	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0042594-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	90	463	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	0.326793925646099	1	FACETS	0.608	0.54	0.681	0.608	0.54	0.681	SUBCLONAL	1	TRUE	0	0.381010259272653	1		463	629	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134239	11134239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042594-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	152	736	0	ENST00000358026.2:c.2905C>T	p.His969Tyr	p.H969Y	ENST00000358026	NM_001128849.1	969	Cac/Tac	20/36	0.326793925646099	1	FACETS	0.694	0.634	0.756	0.694	0.634	0.756	SUBCLONAL	1	TRUE	0	0.381010259272653	1		736	931	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542624	141542624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759574901	NA	P-0042594-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	84	779	2	ENST00000220592.5:c.2362C>T	p.His788Tyr	p.H788Y	ENST00000220592	NM_012154.3	788	Cac/Tac	18/19	1	2	FACETS	0.432	0.38	0.487	0.432	0.38	0.487	SUBCLONAL	1	TRUE	1	0.381010259272653	2		781	1021	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844175	68844175	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042594-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	115	678	0	ENST00000261769.5:c.763C>T	p.Gln255Ter	p.Q255*	ENST00000261769	NM_004360.3	255	Cag/Tag	6/16	0.326793925646099	1	FACETS	0.536	0.482	0.594	0.536	0.482	0.594	SUBCLONAL	1	TRUE	0	0.381010259272653	1		678	911	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152056	11152056	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854225	NA	P-0042594-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	147	691	0	ENST00000358026.2:c.4340G>A	p.Arg1447Gln	p.R1447Q	ENST00000358026	NM_001128849.1	1447	cGa/cAa	31/36	0.326793925646099	1	FACETS	0.715	0.652	0.78	0.715	0.652	0.78	SUBCLONAL	1	TRUE	0	0.381010259272653	1		691	874	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0042594-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	23	634	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	1	2	FACETS	0.117	0.09	0.148	0.117	0.09	0.148	SUBCLONAL	1	TRUE	1	0.381010259272653	2		634	1032	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163372	32163372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042594-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	74	841	1	ENST00000375023.3:c.5854G>A	p.Asp1952Asn	p.D1952N	ENST00000375023	NM_004557.3	1952	Gat/Aat	30/30	1	2	FACETS	0.333	0.29	0.38	0.333	0.29	0.38	SUBCLONAL	1	TRUE	1	0.381010259272653	2		842	1166	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953788	48953788	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0042594-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	59	181	0	ENST00000267163.4:c.1389+2T>G		p.X463_splice	ENST00000267163	NM_000321.2	463			1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.381010259272653	2		181	298	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088733	27088734	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACACA	novel	NA	P-0042594-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	155	700	0	ENST00000324856.7:c.2343_2347dup	p.Thr783AsnfsTer52	p.T783Nfs*52	ENST00000324856	NM_006015.4	781	ata/atACACAa	7/20	1	2	FACETS	0.8	0.732	0.872	0.8	0.732	0.872	SUBCLONAL	1	TRUE	1	0.381010259272653	2		700	1017	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025638	1025638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042594-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	52	592	1	ENST00000358495.3:c.737C>T	p.Ser246Leu	p.S246L	ENST00000358495	NM_134424.2	246	tCa/tTa	9/12	1	2	FACETS	0.34	0.289	0.397	0.34	0.289	0.397	SUBCLONAL	1	TRUE	1	0.381010259272653	2		593	802	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427018	49427018	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042594-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	132	682	0	ENST00000301067.7:c.11470C>G	p.His3824Asp	p.H3824D	ENST00000301067	NM_003482.3	3824	Cac/Gac	39/54	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.381010259272653	2		682	675	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443575	49443575	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042594-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	68	719	0	ENST00000301067.7:c.3796G>C	p.Glu1266Gln	p.E1266Q	ENST00000301067	NM_003482.3	1266	Gag/Cag	11/54	1	2	FACETS	0.402	0.349	0.46	0.402	0.349	0.46	SUBCLONAL	1	TRUE	1	0.381010259272653	2		719	888	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654616	67654616	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042594-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	36	467	0	ENST00000264010.4:c.1103G>T	p.Arg368Leu	p.R368L	ENST00000264010	NM_006565.3	368	cGt/cTt	6/12	0.326793925646099	1	FACETS	0.237	0.194	0.286	0.237	0.194	0.286	SUBCLONAL	1	TRUE	0	0.381010259272653	1		467	645	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109319801	109319801	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042594-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	57	507	0	ENST00000436639.2:c.887C>T	p.Ser296Phe	p.S296F	ENST00000436639	NM_014454.2	296	tCt/tTt	5/10	1	2	FACETS	0.457	0.392	0.529	0.457	0.392	0.529	SUBCLONAL	1	TRUE	1	0.381010259272653	2		507	654	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026633	6026633	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042594-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1249	120	1039	0	ENST00000265849.7:c.1763C>G	p.Ser588Cys	p.S588C	ENST00000265849	NM_000535.5	588	tCt/tGt	11/15	1	2	FACETS	0.46	0.414	0.509	0.46	0.414	0.509	SUBCLONAL	1	TRUE	1	0.381010259272653	2		1039	1369	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604655	48604655	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121912578	NA	P-0042596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	24	294	0	ENST00000342988.3:c.1477G>C	p.Asp493His	p.D493H	ENST00000342988	NM_005359.5	493	Gat/Cat	12/12	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		294	307	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866493	42866493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	79	722	0	ENST00000398585.3:c.139G>T	p.Ala47Ser	p.A47S	ENST00000398585	NM_001135099.1	47	Gct/Tct	3/14	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		722	848	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0042605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	113	621	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.407330406448315	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.478894122427607	1		622	335	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0042605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	228	502	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.478894122427607	5	FACETS	0.891	0.841	0.941	0.891	0.841	0.941	CLONAL	4	TRUE	1	0.478894122427607	5		502	459	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039709	47039709	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1556778444	NA	P-0042605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	117	916	0	ENST00000377604.3:c.1160+1G>T		p.X387_splice	ENST00000377604	NM_001204468.1	387			1	2	FACETS	0.971	0.88	1	0.971	0.88	1	CLONAL	1	TRUE	1	0.478894122427607	2		916	503	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110025	115110025	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	74	899	0	ENST00000257566.3:c.1853C>T	p.Ala618Val	p.A618V	ENST00000257566	NM_016569.3	618	gCa/gTa	8/8	1	2	FACETS	0.544	0.477	0.617	0.544	0.477	0.617	SUBCLONAL	1	TRUE	1	0.478894122427607	2		899	568	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170011204	170011204	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	77	569	0	ENST00000295797.4:c.1325T>G	p.Leu442Arg	p.L442R	ENST00000295797	NM_002740.5	442	cTc/cGc	14/18	1	2	FACETS	0.927	0.82	1	0.927	0.82	1	CLONAL	1	TRUE	1	0.478894122427607	2		569	347	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411883	116411905	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCTTTCTCTCTGTTTTAAGATC	TTCTTTCTCTCTGTTTTAAGATC	-	novel	NA	P-0042607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	163	1005	0	ENST00000397752.3:c.2888-19_2891del		p.X963_splice	ENST00000397752	NM_000245.2	963		14/21	1	2	FACETS	0.789	0.723	0.858	0.789	0.723	0.858	SUBCLONAL	1	TRUE	1	0.38	2		1005	1088	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439658	51439658	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	47	428	0	ENST00000262662.1:c.223C>T	p.His75Tyr	p.H75Y	ENST00000262662		75	Cat/Tat	4/4	1	2	FACETS	0.491	0.414	0.575	0.491	0.414	0.575	SUBCLONAL	1	TRUE	1	0.38	2		428	504	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94201040	94201040	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	26	394	0	ENST00000323929.3:c.1037A>G	p.Asn346Ser	p.N346S	ENST00000323929	NM_005591.3	346	aAt/aGt	10/20	1	2	FACETS	0.44	0.349	0.544	0.44	0.349	0.544	SUBCLONAL	1	TRUE	1	0.38	2		394	311	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026215	48026215	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	21	376	0	ENST00000234420.5:c.1093T>A	p.Trp365Arg	p.W365R	ENST00000234420	NM_000179.2	365	Tgg/Agg	4/10	1	2	FACETS	0.288	0.221	0.366	0.288	0.221	0.366	SUBCLONAL	1	TRUE	1	0.38	2		376	384	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0042613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	41	699	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	1	2	FACETS	0.979	0.814	1	0.979	0.814	1	CLONAL	1	TRUE	1	0.12	2		699	698	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0042613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	23	754	6	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.522	0.405	0.658	0.522	0.405	0.658	SUBCLONAL	1	TRUE	1	0.12	2		760	735	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100301	157100301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	17	352	2	ENST00000346085.5:c.1238C>T	p.Ser413Leu	p.S413L	ENST00000346085	NM_020732.3	413	tCg/tTg	1/20	1	2	FACETS	0.951	0.709	1	0.951	0.709	1	CLONAL	1	TRUE	1	0.12	2		354	298	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0042616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	450	712	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.458297722623701	3	FACETS	0.879	0.844	0.915			1	CLONAL	3	TRUE	NA	0.458297722623701	3		712	915	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0042616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	305	302	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.33116459199956	5	FACETS	0.911	0.872	0.949	0.911	0.872	0.949	CLONAL	5	TRUE	0	0.458297722623701	5		302	493	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086010	16086010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	427	671	1	ENST00000281043.3:c.1186G>A	p.Asp396Asn	p.D396N	ENST00000281043	NM_005378.4	396	Gac/Aac	3/3	0.458297722623701	6	FACETS	1	0.984	1	0.796	0.76	0.832	CLONAL	3	TRUE	2	0.458297722623701	6		672	1122	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821903	72821903	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs749869759	NA	P-0042616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	51	315	0	ENST00000268489.5:c.10272G>C	p.Gln3424His	p.Q3424H	ENST00000268489	NM_006885.3	3424	caG/caC	10/10	0.458297722623701	3	FACETS	0.648	0.552	0.753	0.324	0.276	0.377	SUBCLONAL	1	TRUE	1	0.458297722623701	3		315	422	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021728	71021728	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	50	402	0	ENST00000318789.4:c.1630C>G	p.Arg544Gly	p.R544G	ENST00000318789	NM_032682.5	544	Cga/Gga	18/21	0.346569511218975	3	FACETS	0.666	0.566	0.774	0.222	0.188	0.258	SUBCLONAL	1	TRUE	0	0.458297722623701	3		402	403	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522606	176522606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	435	1038	3	ENST00000292408.4:c.1703C>T	p.Pro568Leu	p.P568L	ENST00000292408	NM_213647.1	568	cCa/cTa	13/18	0.346569511218975	3	FACETS	1	0.991	1	0.751	0.718	0.784	CLONAL	2	TRUE	0	0.458297722623701	3		1041	1036	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0042626-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	94	754	6	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.387	0.344	0.434	0.387	0.344	0.434	SUBCLONAL	1	TRUE	1	0.608883370911769	2		760	797	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0042626-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	31	525	0	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	1	2	FACETS	0.133	0.107	0.163	0.133	0.107	0.163	SUBCLONAL	1	TRUE	1	0.608883370911769	2		525	766	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0042626-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	125	667	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	0.553	0.5	0.608	0.553	0.5	0.608	SUBCLONAL	1	TRUE	1	0.608883370911769	2		667	743	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503838	149503838	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs864309711	NA	P-0042626-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	40	535	0	ENST00000261799.4:c.1998C>A	p.Asn666Lys	p.N666K	ENST00000261799	NM_002609.3	666	aaC/aaA	14/23	1	2	FACETS	0.173	0.143	0.207	0.173	0.143	0.207	SUBCLONAL	1	TRUE	1	0.608883370911769	2		535	758	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735547	40735547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756810336	NA	P-0042626-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	50	414	0	ENST00000373198.4:c.3326G>A	p.Arg1109Gln	p.R1109Q	ENST00000373198	NM_133170.3	1109	cGg/cAg	25/32	1	2	FACETS	0.238	0.202	0.279	0.238	0.202	0.279	SUBCLONAL	1	TRUE	1	0.608883370911769	2		414	689	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223826	36223826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042626-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	119	795	0	ENST00000222270.7:c.6376G>A	p.Asp2126Asn	p.D2126N	ENST00000222270	NM_014727.1	2126	Gat/Aat	28/37	1	2	FACETS	0.355	0.32	0.393	0.355	0.32	0.393	SUBCLONAL	1	TRUE	1	0.608883370911769	2		795	1100	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557981	187557981	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042626-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	23	308	0	ENST00000441802.2:c.3730C>T	p.Gln1244Ter	p.Q1244*	ENST00000441802	NM_005245.3	1244	Cag/Tag	5/27	1	2	FACETS	0.181	0.141	0.228	0.181	0.141	0.228	SUBCLONAL	1	TRUE	1	0.608883370911769	2		308	417	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584660	187584661	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0042626-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	41	398	0	ENST00000441802.2:c.3372_3373del	p.Glu1124AspfsTer6	p.E1124Dfs*6	ENST00000441802	NM_005245.3	1124	gaGAtc/gatc	3/27	1	2	FACETS	0.237	0.197	0.282	0.237	0.197	0.282	SUBCLONAL	1	TRUE	1	0.608883370911769	2		398	568	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294970	1294971	+	missense_variant	Missense_Mutation	DNP	CG	CG	TT	novel	NA	P-0042626-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	48	68	1	ENST00000310581.5:c.134_135delinsAA	p.Ala45Glu	p.A45E	ENST00000310581	NM_198253.2	45	gCG/gAA	1/16	0.458900021173039	5	FACETS	1	0.917	1	0.723	0.626	0.825	CLONAL	2	TRUE	2	0.608883370911769	5		69	139	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729420	41729420	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0042626-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	55	506	0	ENST00000242208.4:c.1109C>G	p.Ser370Ter	p.S370*	ENST00000242208	NM_002192.2	370	tCa/tGa	3/3	1	2	FACETS	0.236	0.201	0.274	0.236	0.201	0.274	SUBCLONAL	1	TRUE	1	0.608883370911769	2		506	765	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847400	68847400	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0042627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	92	553	0	ENST00000261769.5:c.1320+2T>C		p.X440_splice	ENST00000261769	NM_004360.3	440			1	2	FACETS	0.815	0.726	0.91	1	0.982	1	CLONAL	2	TRUE	1	0.19	2		553	594	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667596	29667596	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0042627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	84	618	0	ENST00000356175.3:c.6932C>G	p.Ser2311Ter	p.S2311*	ENST00000356175	NM_000267.3	2311	tCa/tGa	46/57	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.19	2		618	727	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095995	11095995	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	148	951	0	ENST00000358026.2:c.269A>G	p.Tyr90Cys	p.Y90C	ENST00000358026	NM_001128849.1	90	tAc/tGc	3/36	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.19	2		951	1135	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968131	68968131	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	86	624	1	ENST00000288368.4:c.1160A>T	p.Lys387Ile	p.K387I	ENST00000288368	NM_024870.2	387	aAa/aTa	10/40	0.260831510102188	3	FACETS	1	0.978	1	0.742	0.657	0.833	CLONAL	1	TRUE	1	0.19	3		625	668	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221666	36221666	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1568379151	NA	P-0042651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	117	978	0	ENST00000222270.7:c.5335C>T	p.Arg1779Ter	p.R1779*	ENST00000222270	NM_014727.1	1779	Cga/Tga	26/37	0.157839416982795	5	FACETS	0.675	0.607	0.748			1	INDETERMINATE	1	TRUE	NA	0.471585162800792	5		978	1255	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600505	10600505	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	331	781	0	ENST00000171111.5:c.1350G>A	p.Trp450Ter	p.W450*	ENST00000171111	NM_203500.1	450	tgG/tgA	4/6	0.471585162800792	2	FACETS	0.952	0.906	0.999	0.952	0.906	0.999	CLONAL	2	TRUE	0	0.471585162800792	2		781	737	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744952	39744952	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	128	496	0	ENST00000361337.2:c.1742T>C	p.Met581Thr	p.M581T	ENST00000361337	NM_003286.2	581	aTg/aCg	17/21	0.458857458201696	3	FACETS	1	0.909	1	0.501	0.454	0.549	CLONAL	1	TRUE	1	0.471585162800792	3		496	670	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946129	13946129	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	127	596	0	ENST00000405192.2:c.967G>C	p.Asp323His	p.D323H	ENST00000405192	NM_001163147.1	323	Gat/Cat	10/12	0.288435059206225	3	FACETS	0.972	0.882	1	0.486	0.441	0.533	CLONAL	1	TRUE	1	0.471585162800792	3		596	685	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729640	41729640	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	142	646	0	ENST00000242208.4:c.889G>C	p.Ala297Pro	p.A297P	ENST00000242208	NM_002192.2	297	Gcc/Ccc	3/3	0.288435059206225	3	FACETS	1	0.93	1	0.51	0.466	0.557	CLONAL	1	TRUE	1	0.471585162800792	3		646	729	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436641	8436641	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	36	554	0	ENST00000356435.5:c.4037T>A	p.Ile1346Asn	p.I1346N	ENST00000356435		1346	aTt/aAt	24/35	0.436723138487041	3	FACETS	0.343	0.281	0.412	0.114	0.093	0.138	SUBCLONAL	1	TRUE	0	0.471585162800792	3		554	550	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0042652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	239	395	1				ENST00000310581	NM_198253.2	-/1132			0.520090321548046	3	FACETS	0.836	0.791	0.88	1	0.991	1	CLONAL	3	TRUE	1	0.520090321548046	3		396	462	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851754	134851754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56396912	NA	P-0042652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	167	630	0	ENST00000398015.3:c.1160C>T	p.Thr387Met	p.T387M	ENST00000398015	NM_004441.4	387	aCg/aTg	5/16	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.520090321548046	2		630	633	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	CT	rs121913227	NA	P-0042652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	309	443	1	ENST00000288602.6:c.1798_1799delinsAG	p.Val600Arg	p.V600R	ENST00000288602	NM_004333.4	600	GTg/AGg	15/18	0.520090321548046	6	FACETS	0.945	0.904	0.985	0.945	0.904	0.985	CLONAL	5	TRUE	1	0.520090321548046	6		444	513	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247617	123247617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	83	459	0	ENST00000358487.5:c.1874G>A	p.Arg625Gln	p.R625Q	ENST00000358487	NM_000141.4	625	cGa/cAa	14/18	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.520090321548046	2		459	312	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610228	81610228	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139352934	NA	P-0042652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	229	490	1	ENST00000298171.2:c.1826G>A	p.Arg609Gln	p.R609Q	ENST00000298171	NM_000369.2	609	cGa/cAa	10/10	0.108706352962888	4	FACETS	0.858	0.808	0.909			1	INDETERMINATE	3	TRUE	NA	0.520090321548046	4		491	520	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610028	81610028	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	169	416	0	ENST00000298171.2:c.1626G>A	p.Met542Ile	p.M542I	ENST00000298171	NM_000369.2	542	atG/atA	10/10	0.108706352962888	4	FACETS	1	0.978	1			1	INDETERMINATE	2	TRUE	NA	0.520090321548046	4		416	438	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873670	35873670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	144	395	1	ENST00000303115.3:c.626C>T	p.Pro209Leu	p.P209L	ENST00000303115	NM_002185.3	209	cCt/cTt	5/8	0.520090321548046	3	FACETS	0.983	0.909	1	0.983	0.909	1	CLONAL	2	TRUE	1	0.520090321548046	3		396	355	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257084	16257084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	107	676	0	ENST00000375759.3:c.4349G>A	p.Arg1450Lys	p.R1450K	ENST00000375759	NM_015001.2	1450	aGa/aAa	11/15	0.520090321548046	3	FACETS	1	0.939	1	0.529	0.477	0.584	CLONAL	1	TRUE	1	0.520090321548046	3		676	490	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609027	43609027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483605155	NA	P-0042652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	130	720	0	ENST00000355710.3:c.1783G>A	p.Glu595Lys	p.E595K	ENST00000355710	NM_020975.4	595	Gag/Aag	10/20	1	2	FACETS	0.947	0.863	1	0.947	0.863	1	CLONAL	1	TRUE	1	0.520090321548046	2		720	528	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926561	59926561	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	76	590	0	ENST00000259008.2:c.436A>G	p.Ile146Val	p.I146V	ENST00000259008	NM_032043.2	146	Ata/Gta	5/20	0.503357282304163	3	FACETS	1	0.938	1	0.548	0.484	0.615	CLONAL	1	TRUE	1	0.520090321548046	3		590	336	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182102	99182103	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0042652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	163	467	1	ENST00000074304.5:c.2168-1_2168delinsAA		p.X723_splice	ENST00000074304	NM_001134224.1	723		21/26	0.520090321548046	3	FACETS	0.942	0.875	1	0.942	0.875	1	CLONAL	2	TRUE	1	0.520090321548046	3		468	419	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213908	66213908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	37	415	0	ENST00000273854.3:c.2522C>T	p.Pro841Leu	p.P841L	ENST00000273854	NM_004439.5	841	cCa/cTa	15/18	1	2	FACETS	0.753	0.628	0.89	0.753	0.628	0.89	SUBCLONAL	1	TRUE	1	0.520090321548046	2		415	189	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909688	76909688	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	43	378	0	ENST00000373344.5:c.4217C>T	p.Ser1406Phe	p.S1406F	ENST00000373344	NM_000489.3	1406	tCt/tTt	14/35	0.498935314174552	1	FACETS	0.716	0.608	0.831	0.716	0.608	0.831	SUBCLONAL	1	TRUE	0	0.520090321548046	1		378	171	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217344	123217344	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	76	606	0	ENST00000218089.9:c.2998C>T	p.Leu1000Phe	p.L1000F	ENST00000218089	NM_001042749.1	1000	Ctt/Ttt	29/35	0.498935314174552	1	FACETS	0.693	0.613	0.777	0.693	0.613	0.777	SUBCLONAL	1	TRUE	0	0.520090321548046	1		606	312	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936103	49936103	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs141097970	NA	P-0042652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	191	759	1	ENST00000296474.3:c.1567C>T	p.Gln523Ter	p.Q523*	ENST00000296474	NM_002447.2	523	Caa/Taa	4/20	1	2	FACETS	0.966	0.896	1	0.966	0.896	1	CLONAL	1	TRUE	1	0.520090321548046	2		760	760	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612175	189612175	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1560311554	NA	P-0042659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	135	623	5	ENST00000264731.3:c.1927C>T	p.Arg643Ter	p.R643*	ENST00000264731	NM_003722.4	643	Cga/Tga	14/14	1	2	FACETS	0.939	0.856	1	0.939	0.856	1	CLONAL	1	TRUE	1	0.47000234512607	2		628	612	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085677	16085677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779959007	NA	P-0042664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	203	643	0	ENST00000281043.3:c.853C>T	p.Arg285Trp	p.R285W	ENST00000281043	NM_005378.4	285	Cgg/Tgg	3/3	1	2	FACETS	0.923	0.858	0.989	0.923	0.858	0.989	CLONAL	1	TRUE	1	0.584439032129479	2		643	753	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21627818	21627818	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	156	603	0	ENST00000421138.2:c.1312C>T	p.Gln438Ter	p.Q438*	ENST00000421138		438	Cag/Tag	12/16	1	2	FACETS	0.932	0.858	1	0.932	0.858	1	CLONAL	1	TRUE	1	0.584439032129479	2		603	573	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635695	47635695	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs267607924	NA	P-0042664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	59	361	0	ENST00000233146.2:c.366+1G>A		p.X122_splice	ENST00000233146	NM_000251.2	122			1	2	FACETS	0.905	0.789	1	0.905	0.789	1	CLONAL	1	TRUE	1	0.584439032129479	2		361	223	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174386	11174386	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	108	487	0	ENST00000361445.4:c.7289G>T	p.Arg2430Met	p.R2430M	ENST00000361445	NM_004958.3	2430	aGg/aTg	53/58	0.321104651845985	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.321104651845985	1		487	552	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161740	47161741	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0042697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	54	271	0	ENST00000409792.3:c.4385_4386del	p.Glu1462ValfsTer12	p.E1462Vfs*12	ENST00000409792	NM_014159.6	1462	gAA/g	3/21	0.321104651845985	1	FACETS	0.994	0.856	1	0.994	0.856	1	CLONAL	1	TRUE	0	0.321104651845985	1		271	284	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439929	52439929	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0042697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	81	378	0	ENST00000460680.1:c.784-1G>T		p.X262_splice	ENST00000460680	NM_004656.3	262			0.321104651845985	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.321104651845985	1		378	372	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058423	47058659	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	TTTTGTGGCCTTCAGTTGACATCTGCAGGGTTGAATTCCCCAGGGTGATGTATCATCAGTAGCACAGTGCTGACAGGGGTGGGACAGAAAGGCCCACAGGATTTCCTCTCCCTAGAGTCTGTCTTACCTGACCACCCATCCTCCCACCCTGGCCCAACAGTCACTCTAATTCAGTGTCCTCTTTGGGTTTGTAAACAGCCCCAAACTTCTGCATGTACTTCTTAATGTACTCCTTGG	TTTTGTGGCCTTCAGTTGACATCTGCAGGGTTGAATTCCCCAGGGTGATGTATCATCAGTAGCACAGTGCTGACAGGGGTGGGACAGAAAGGCCCACAGGATTTCCTCTCCCTAGAGTCTGTCTTACCTGACCACCCATCCTCCCACCCTGGCCCAACAGTCACTCTAATTCAGTGTCCTCTTTGGGTTTGTAAACAGCCCCAAACTTCTGCATGTACTTCTTAATGTACTCCTTGG	-	novel	NA	P-0042755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	25	102	0	ENST00000409792.3:c.7619_*160del		p.*2540*	ENST00000409792	NM_014159.6	2540		21/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		102	71	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	41	214	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.1177167964714	4	FACETS	0.939	0.791	1	0.939	0.791	1	INDETERMINATE	2	TRUE	2	0.275667604024649	4		214	202	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0042782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	91	507	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.275667604024649	3	FACETS	1	0.959	1	1	0.984	1	CLONAL	4	TRUE	0	0.275667604024649	3		507	173	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0042782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	30	461	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.275667604024649	2		461	171	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	92	759	2	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.275667604024649	2		761	471	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671655	67671655	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1400980130	NA	P-0042782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	20	507	2	ENST00000264010.4:c.2070del	p.Glu691SerfsTer30	p.E691Sfs*30	ENST00000264010	NM_006565.3	688	gtA/gt	12/12	1	2	FACETS	0.569	0.436	0.724	0.569	0.436	0.724	SUBCLONAL	1	TRUE	1	0.275667604024649	2		509	255	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524464	187524464	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs74511500	NA	P-0042782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	14	584	1	ENST00000441802.2:c.11216C>T	p.Ala3739Val	p.A3739V	ENST00000441802	NM_005245.3	3739	gCg/gTg	19/27	1	2	FACETS	0.516	0.373	0.687	0.516	0.373	0.687	SUBCLONAL	1	TRUE	1	0.275667604024649	2		585	197	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422384	47422384	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	38	508	0	ENST00000377045.4:c.23del	p.Pro8LeufsTer26	p.P8Lfs*26	ENST00000377045	NM_001654.4	6	ggC/gg	2/16	0.275667604024649	1	FACETS	0.874	0.726	1	0.874	0.726	1	CLONAL	1	TRUE	0	0.275667604024649	1		508	272	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	50	572	3	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.275667604024649	2		575	246	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656840	45656840	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	69	616	1	ENST00000407780.3:c.316del	p.Gln106ArgfsTer11	p.Q106Rfs*11	ENST00000407780	NM_001283052.1	106	Cag/ag	3/7	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.275667604024649	2		617	382	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290896	15290896	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	19	779	1	ENST00000263388.2:c.3314del	p.Gly1105AlafsTer167	p.G1105Afs*167	ENST00000263388	NM_000435.2	1105	gGc/gc	20/33	1	2	FACETS	0.452	0.343	0.58	0.452	0.343	0.58	SUBCLONAL	1	TRUE	1	0.275667604024649	2		780	305	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912133	50912133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768773535	NA	P-0042782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	36	740	3	ENST00000440232.2:c.1867C>T	p.Arg623Trp	p.R623W	ENST00000440232	NM_002691.3	623	Cgg/Tgg	15/27	1	2	FACETS	0.923	0.762	1	0.923	0.762	1	CLONAL	1	TRUE	1	0.275667604024649	2		743	283	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273878	10273878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	63	681	0	ENST00000330684.3:c.391G>A	p.Ala131Thr	p.A131T	ENST00000330684	NM_001134407.1	131	Gca/Aca	2/13	1	2	FACETS	0.914	0.8	1	1	0.979	1	CLONAL	2	TRUE	1	0.275667604024649	2		681	250	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993776	72993776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200056605	NA	P-0042782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	50	570	0	ENST00000268489.5:c.269G>A	p.Ser90Asn	p.S90N	ENST00000268489	NM_006885.3	90	aGc/aAc	2/10	1	2	FACETS	0.765	0.656	0.883	1	0.967	1	SUBCLONAL	2	TRUE	1	0.275667604024649	2		570	237	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681326	88681326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781332	NA	P-0042782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	24	383	0	ENST00000372037.3:c.1216C>T	p.Arg406Cys	p.R406C	ENST00000372037	NM_004329.2	406	Cgc/Tgc	11/13	0.275667604024649	3	FACETS	0.847	0.675	1	0.564	0.45	0.692	CLONAL	2	TRUE	0	0.275667604024649	3		383	117	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467170	25467170	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	39	565	0	ENST00000264709.3:c.1705C>T	p.Pro569Ser	p.P569S	ENST00000264709	NM_175629.2	569	Ccg/Tcg	15/23	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.275667604024649	2		565	218	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101701	27101733	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAAAGACATTGGTAAGGAGATCTTCCTCATTCG	GAAAGACATTGGTAAGGAGATCTTCCTCATTCG	-	novel	NA	P-0042782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	60	716	0	ENST00000324856.7:c.4984_4993+23del		p.X1662_splice	ENST00000324856	NM_006015.4	1662		18/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.275667604024649	2		716	335	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161332126	161332126	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	11	133	0	ENST00000367975.2:c.413A>G	p.Asp138Gly	p.D138G	ENST00000367975	NM_003001.3	138	gAc/gGc	6/6	0.275667604024649	3	FACETS	0.873	0.62	1	0.873	0.62	1	CLONAL	2	TRUE	1	0.275667604024649	3		133	52	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351031	89351031	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	70	755	0	ENST00000301030.4:c.1919del	p.Asn640ThrfsTer13	p.N640Tfs*13	ENST00000301030	NM_001256183.1	640	aAc/ac	9/13	1	2	FACETS	0.827	0.727	0.933	1	0.978	1	CLONAL	2	TRUE	1	0.275667604024649	2		755	307	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882974	89882974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326963514	NA	P-0042782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	11	280	2	ENST00000389301.3:c.50G>A	p.Gly17Asp	p.G17D	ENST00000389301	NM_000135.2	17	gGc/gAc	1/43	1	2	FACETS	0.387	0.267	0.536	0.387	0.267	0.536	SUBCLONAL	1	TRUE	1	0.275667604024649	2		282	206	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637928	39637928	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	47	573	0	ENST00000262039.4:c.2345A>G	p.Glu782Gly	p.E782G	ENST00000262039	NM_002647.2	782	gAa/gGa	22/25	1	2	FACETS	0.771	0.658	0.894	1	0.965	1	SUBCLONAL	2	TRUE	1	0.275667604024649	2		573	221	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602767	10602767	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	22	779	0	ENST00000171111.5:c.811del	p.Val271CysfsTer6	p.V271Cfs*6	ENST00000171111	NM_203500.1	271	Gtg/tg	3/6	1	2	FACETS	0.387	0.299	0.49	0.387	0.299	0.49	SUBCLONAL	1	TRUE	1	0.275667604024649	2		779	412	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229048	36229048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866415691	NA	P-0042782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	83	779	1	ENST00000222270.7:c.7828C>T	p.Arg2610Cys	p.R2610C	ENST00000222270	NM_014727.1	2610	Cgc/Tgc	36/37	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.275667604024649	2		780	402	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912404	50912405	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0042782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	13	729	0	ENST00000440232.2:c.1923dup	p.Thr642HisfsTer97	p.T642Hfs*97	ENST00000440232	NM_002691.3	640	acc/aCcc	16/27	1	2	FACETS	0.367	0.261	0.496	0.367	0.261	0.496	SUBCLONAL	1	TRUE	1	0.275667604024649	2		729	257	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572441	41572441	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	45	862	0	ENST00000263253.7:c.4970A>C	p.Glu1657Ala	p.E1657A	ENST00000263253	NM_001429.3	1657	gAg/gCg	30/31	1	2	FACETS	0.816	0.687	0.958	0.816	0.687	0.958	CLONAL	1	TRUE	1	0.275667604024649	2		862	400	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1962803	1962803	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	13	523	0	ENST00000382891.5:c.3297G>T	p.Glu1099Asp	p.E1099D	ENST00000382891	NM_133335.3	1099	gaG/gaT	18/22	1	2	FACETS	0.366	0.26	0.494	0.366	0.26	0.494	SUBCLONAL	1	TRUE	1	0.275667604024649	2		523	258	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280373	1280373	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	13	716	0	ENST00000310581.5:c.1850T>C	p.Leu617Pro	p.L617P	ENST00000310581	NM_198253.2	617	cTg/cCg	4/16	0.275667604024649	0	FACETS	0.265	0.188	0.358			1	SUBCLONAL	1	TRUE	0	0.275667604024649	0		716	258	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497269	149497269	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1428098106	NA	P-0042782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	19	771	0	ENST00000261799.4:c.3049G>T	p.Gly1017Cys	p.G1017C	ENST00000261799	NM_002609.3	1017	Ggt/Tgt	22/23	1	2	FACETS	0.461	0.35	0.592	0.461	0.35	0.592	SUBCLONAL	1	TRUE	1	0.275667604024649	2		771	299	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90990542	90990542	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	30	400	1	ENST00000265433.3:c.490G>A	p.Ala164Thr	p.A164T	ENST00000265433	NM_002485.4	164	Gca/Aca	5/16	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.275667604024649	2		401	183	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015169	37015169	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	13	569	0	ENST00000358127.4:c.235A>G	p.Lys79Glu	p.K79E	ENST00000358127	NM_001280556.1	79	Aag/Gag	3/10	1	2	FACETS	0.524	0.374	0.705	0.524	0.374	0.705	SUBCLONAL	1	TRUE	1	0.275667604024649	2		569	180	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763897	76763897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	12	639	0	ENST00000373344.5:c.7411C>T	p.Pro2471Ser	p.P2471S	ENST00000373344	NM_000489.3	2471	Cca/Tca	35/35	0.275667604024649	1	FACETS	0.387	0.272	0.528	0.387	0.272	0.528	SUBCLONAL	1	TRUE	0	0.275667604024649	1		639	194	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593613	55593613	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913521	NA	P-0042799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	11	404	0	ENST00000288135.5:c.1679T>G	p.Val560Gly	p.V560G	ENST00000288135	NM_000222.2	560	gTt/gGt	11/21	1	2	FACETS	0.131	0.09	0.183	0.131	0.09	0.183	SUBCLONAL	1	TRUE	1	0.321056286536516	2		404	523	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971733	18971733	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	174	1053	0	ENST00000262803.5:c.2399G>T	p.Arg800Leu	p.R800L	ENST00000262803	NM_002911.3	800	cGc/cTc	17/24	1	2	FACETS	0.92	0.846	0.998	0.92	0.846	0.998	CLONAL	1	TRUE	1	0.321056286536516	2		1053	1178	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926248	112926249	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0042799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	84	672	3	ENST00000351677.2:c.1381_1382delinsAA	p.Ala461Asn	p.A461N	ENST00000351677	NM_002834.3	461	GCt/AAt	12/16	1	2	FACETS	0.664	0.586	0.748	0.664	0.586	0.748	SUBCLONAL	1	TRUE	1	0.321056286536516	2		675	788	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602728	10602728	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	235	1116	0	ENST00000171111.5:c.850C>G	p.Gln284Glu	p.Q284E	ENST00000171111	NM_203500.1	284	Cag/Gag	3/6	0.321056286536516	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.321056286536516	1		1116	1155	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053523	37053523	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	135	599	0	ENST00000231790.2:c.610G>T	p.Val204Phe	p.V204F	ENST00000231790	NM_000249.3	204	Gtt/Ttt	8/19	0.306914141774526	4	FACETS	0.87	0.788	0.956			1	CLONAL	1	TRUE	NA	0.321056286536516	4		599	1277	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443814	52443856	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCCTCCTCA	CATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCCTCCTCA	-	novel	NA	P-0042799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	55	987	0	ENST00000460680.1:c.37+2_37+44del		p.X13_splice	ENST00000460680	NM_004656.3	13			0.321056286536516	1	FACETS	0.307	0.261	0.357	0.307	0.261	0.357	SUBCLONAL	1	TRUE	0	0.321056286536516	1		987	937	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0042822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	295	459	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.592985533331769	3	FACETS	0.926	0.887	0.963	0.926	0.887	0.963	CLONAL	3	TRUE	0	0.604055586872279	3		459	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0042822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	277	509	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.604055586872279	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.604055586872279	1		509	498	SUCCESS
APC	324	MSKCC	GRCh37	5	112175162	112175162	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561588104	NA	P-0042822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	106	175	1	ENST00000257430.4:c.3871C>T	p.Gln1291Ter	p.Q1291*	ENST00000257430	NM_000038.5	1291	Cag/Tag	16/16	0.55874279373769	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.604055586872279	2		176	170	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318764	163318764	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	33	329	0	ENST00000271452.3:c.1154G>C	p.Gly385Ala	p.G385A	ENST00000271452	NM_145697.2	385	gGt/gCt	13/14	0.240552261266097	5	FACETS	0.452	0.367	0.547	0.151	0.122	0.183	INDETERMINATE	1	TRUE	2	0.604055586872279	5		329	461	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982145	201982146	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCAAGC	novel	NA	P-0042822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	346	787	0	ENST00000359651.3:c.670_676dup	p.Leu226ArgfsTer11	p.L226Rfs*11	ENST00000359651		223	-/GGCAAGC	5/8	0.240552261266097	5	FACETS	0.944	0.894	0.995	0.629	0.596	0.663	INDETERMINATE	2	TRUE	2	0.604055586872279	5		787	1157	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123829	46123829	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	49	271	0	ENST00000334344.6:c.95C>A	p.Ser32Ter	p.S32*	ENST00000334344	NM_152641.2	32	tCg/tAg	2/21	0.592985533331769	3	FACETS	0.675	0.575	0.784	0.225	0.191	0.262	SUBCLONAL	1	TRUE	0	0.604055586872279	3		271	313	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243977	46243977	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	143	393	0	ENST00000334344.6:c.2071C>G	p.His691Asp	p.H691D	ENST00000334344	NM_152641.2	691	Cat/Gat	15/21	0.592985533331769	3	FACETS	1	0.941	1	0.345	0.315	0.375	CLONAL	1	TRUE	0	0.604055586872279	3		393	596	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573598	48573598	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	118	259	0	ENST00000342988.3:c.182T>A	p.Ile61Lys	p.I61K	ENST00000342988	NM_005359.5	61	aTa/aAa	2/12	0.604055586872279	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.604055586872279	1		259	213	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	95	82	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.861	0.769	0.959	0.861	0.769	0.959	CLONAL	1	TRUE	1	0.397587918643073	2		82	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0042856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	464	352	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.344792225583659	2	FACETS	0.971	0.929	1	0.971	0.929	1	CLONAL	2	TRUE	0	0.397587918643073	2		353	1202	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426121	47426121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519786	NA	P-0042856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	222	1171	0	ENST00000377045.4:c.641C>T	p.Ser214Phe	p.S214F	ENST00000377045	NM_001654.4	214	tCc/tTc	7/16	0.397587918643073	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.397587918643073	1		1171	847	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514821	103514821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112825485	NA	P-0042856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	76	491	0	ENST00000355739.4:c.1322C>T	p.Pro441Leu	p.P441L	ENST00000355739	NM_000123.3	441	cCg/cTg	8/15	0.350579069514516	1	FACETS	0.709	0.624	0.799	0.709	0.624	0.799	SUBCLONAL	1	TRUE	0	0.397587918643073	1		491	432	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938202	36938202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	165	1043	0	ENST00000361632.4:c.759G>A	p.Trp253Ter	p.W253*	ENST00000361632		253	tgG/tgA	6/16	1	2	FACETS	0.905	0.831	0.982	0.905	0.831	0.982	CLONAL	1	TRUE	1	0.397587918643073	2		1043	917	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971156	21971156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	204	627	0	ENST00000304494.5:c.202G>A	p.Ala68Thr	p.A68T	ENST00000304494	NM_000077.4	68	Gcg/Acg	2/3	1	2	FACETS	0.985	0.917	1	0.985	0.917	1	CLONAL	1	TRUE	1	0.596052238251105	2		627	695	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579378	7579378	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0042866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	587	1112	0	ENST00000269305.4:c.309C>G	p.Tyr103Ter	p.Y103*	ENST00000269305	NM_001126112.2	103	taC/taG	4/11	0.596052238251105	2	FACETS	0.962	0.931	0.993	0.962	0.931	0.993	CLONAL	2	TRUE	0	0.596052238251105	2		1112	1024	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857584	9857584	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs762745084	NA	P-0042866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	113	610	0	ENST00000330684.3:c.3817C>T	p.Gln1273Ter	p.Q1273*	ENST00000330684	NM_001134407.1	1273	Cag/Tag	13/13	1	2	FACETS	0.901	0.817	0.988	0.901	0.817	0.988	CLONAL	1	TRUE	1	0.596052238251105	2		610	421	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0042876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	50	459	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.16	2		459	471	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0042876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	9	204	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.615	0.407	0.879	0.615	0.407	0.879	SUBCLONAL	1	TRUE	1	0.16	2		204	183	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322755	39322755	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0042876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	23	355	0	ENST00000373001.3:c.238-1G>T		p.X80_splice	ENST00000373001	NM_022157.3	80			1	2	FACETS	0.843	0.657	1	0.843	0.657	1	CLONAL	1	TRUE	1	0.16	2		355	341	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986739	36986740	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0042876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	12	99	0	ENST00000354822.5:c.949dup	p.Gln317ProfsTer122	p.Q317Pfs*122	ENST00000354822	NM_001079668.2	317	cag/cCag	3/3	1	2	FACETS	1	0.775	1	1	0.775	1	CLONAL	1	TRUE	1	0.16	2		99	134	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986853	36986854	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0042876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	21	278	0	ENST00000354822.5:c.835_836del	p.Gln279GlyfsTer159	p.Q279Gfs*159	ENST00000354822	NM_001079668.2	279	CAg/g	3/3	1	2	FACETS	0.733	0.564	0.931	0.733	0.564	0.931	CLONAL	1	TRUE	1	0.16	2		278	358	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587780070	NA	P-0042908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	76	530	0	ENST00000269305.4:c.535C>A	p.His179Asn	p.H179N	ENST00000269305	NM_001126112.2	179	Cat/Aat	5/11	1	2	FACETS	0.964	0.846	1	0.964	0.846	1	CLONAL	1	TRUE	1	0.24	2		530	657	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480480	120480480	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	41	230	0	ENST00000256646.2:c.3337G>C	p.Gly1113Arg	p.G1113R	ENST00000256646	NM_024408.3	1113	Ggt/Cgt	20/34	1	2	FACETS	0.973	0.813	1	0.973	0.813	1	CLONAL	1	TRUE	1	0.24	2		230	351	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490375	29490375	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	65	323	1	ENST00000356175.3:c.462del	p.Phe154LeufsTer11	p.F154Lfs*11	ENST00000356175	NM_000267.3	154	Ttt/tt	4/57	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.24	2		324	515	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412702	139412702	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	116	680	0	ENST00000277541.6:c.1142G>A	p.Cys381Tyr	p.C381Y	ENST00000277541	NM_017617.3	381	tGt/tAt	7/34	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.24	2		680	885	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0042910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	204	395	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.877197975075847	2		396	370	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0042910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	99	395	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.877197975075847	2		396	221	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791718	42791718	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1344635105	NA	P-0042910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	33	553	1	ENST00000575354.2:c.604C>T	p.Arg202Trp	p.R202W	ENST00000575354	NM_015125.3	202	Cgg/Tgg	5/20	0.877197975075847	1	FACETS	0.13	0.106	0.157	0.13	0.106	0.157	SUBCLONAL	1	TRUE	0	0.877197975075847	1		554	325	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101427	27101430	+	frameshift_variant	Frame_Shift_Del	DEL	CTAA	CTAA	-	novel	NA	P-0042910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	210	550	0	ENST00000324856.7:c.4712_4715del	p.Asn1571ThrfsTer40	p.N1571Tfs*40	ENST00000324856	NM_006015.4	1570	tCTAAc/tc	18/20	0.877197975075847	1	FACETS	0.988	0.948	1	0.988	0.948	1	CLONAL	1	TRUE	0	0.877197975075847	1		550	272	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430843	78430848	+	frameshift_variant	Frame_Shift_Del	DEL	TCCATC	TCCATC	GGATT	novel	NA	P-0042910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	223	526	2	ENST00000370768.2:c.541_546delinsAATCC	p.Asp181AsnfsTer11	p.D181Nfs*11	ENST00000370768	NM_003902.3	181	GATGGA/AATCC	8/20	0.877197975075847	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.877197975075847	1		528	279	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796599	42796599	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	229	717	0	ENST00000575354.2:c.3156del	p.Phe1052LeufsTer41	p.F1052Lfs*41	ENST00000575354	NM_015125.3	1052	ttC/tt	13/20	0.877197975075847	1	FACETS	0.98	0.942	1	0.98	0.942	1	CLONAL	1	TRUE	0	0.877197975075847	1		717	299	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0042968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	166	466	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.312599843257825	4	FACETS	0.933	0.86	1	0.933	0.86	1	CLONAL	2	TRUE	2	0.326206025096999	4		466	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0042968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	235	461	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.326206025096999	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.326206025096999	2		461	701	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0042968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	32	548	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.788	0.643	0.95	0.788	0.643	0.95	CLONAL	1	TRUE	1	0.326206025096999	2		549	249	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436084	49436084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	84	474	0	ENST00000301067.7:c.5897C>T	p.Pro1966Leu	p.P1966L	ENST00000301067	NM_003482.3	1966	cCc/cTc	28/54	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.326206025096999	2		474	477	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212077	36212077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs911830364	NA	P-0042968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	120	775	0	ENST00000222270.7:c.1828C>T	p.Arg610Cys	p.R610C	ENST00000222270	NM_014727.1	610	Cgc/Tgc	3/37	0.326206025096999	3	FACETS	0.937	0.846	1	0.469	0.423	0.517	CLONAL	1	TRUE	1	0.326206025096999	3		775	913	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574737	41574737	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	222	819	2	ENST00000263253.7:c.7022C>T	p.Ser2341Phe	p.S2341F	ENST00000263253	NM_001429.3	2341	tCc/tTc	31/31	0.326206025096999	4	FACETS	0.871	0.811	0.934			1	CLONAL	2	TRUE	NA	0.326206025096999	4		821	1036	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18958566	18958566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	121	655	0	ENST00000262803.5:c.385C>T	p.His129Tyr	p.H129Y	ENST00000262803	NM_002911.3	129	Cac/Tac	3/24	0.326206025096999	3	FACETS	0.959	0.865	1	0.479	0.432	0.529	CLONAL	1	TRUE	1	0.326206025096999	3		655	900	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574695	41574695	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764378639	NA	P-0042968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	266	796	0	ENST00000263253.7:c.6980C>T	p.Pro2327Leu	p.P2327L	ENST00000263253	NM_001429.3	2327	cCt/cTt	31/31	0.326206025096999	4	FACETS	1	0.945	1			1	CLONAL	2	TRUE	NA	0.326206025096999	4		796	1072	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121912651	NA	P-0042976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	111	598	0	ENST00000269305.4:c.742C>G	p.Arg248Gly	p.R248G	ENST00000269305	NM_001126112.2	248	Cgg/Ggg	7/11	0.364045016613175	1	FACETS	0.822	0.74	0.907	0.822	0.74	0.907	CLONAL	1	TRUE	0	0.364045016613175	1		598	607	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974809	21974809	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	21	91	0	ENST00000304494.5:c.18del	p.Ser7AlafsTer19	p.S7Afs*19	ENST00000304494	NM_000077.4	6	ggG/gg	1/3	0.294227765494305	1	FACETS	0.993	0.78	1	0.993	0.78	1	CLONAL	1	TRUE	0	0.364045016613175	1		91	95	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163307858	163307858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	78	423	0	ENST00000271452.3:c.484G>A	p.Ala162Thr	p.A162T	ENST00000271452	NM_145697.2	162	Gca/Aca	7/14	1	2	FACETS	0.854	0.752	0.962	0.854	0.752	0.962	CLONAL	1	TRUE	1	0.364045016613175	2		423	502	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588797	69588797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	47	592	2	ENST00000168712.1:c.439G>A	p.Gly147Ser	p.G147S	ENST00000168712	NM_002007.2	147	Ggc/Agc	2/3	0.364052013492776	0	FACETS	0.449	0.38	0.524			1	SUBCLONAL	1	TRUE	0	0.364045016613175	0		594	366	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905178	50905178	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	33	744	0	ENST00000440232.2:c.460C>T	p.Pro154Ser	p.P154S	ENST00000440232	NM_002691.3	154	Cct/Tct	4/27	0.329569621281897	0	FACETS	0.204	0.166	0.248			1	SUBCLONAL	1	TRUE	0	0.364045016613175	0		744	564	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193507	99193507	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1471383993	NA	P-0042976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	82	588	0	ENST00000074304.5:c.2702G>T	p.Arg901Leu	p.R901L	ENST00000074304	NM_001134224.1	901	cGt/cTt	25/26	0.294227765494305	1	FACETS	0.725	0.641	0.815	0.725	0.641	0.815	SUBCLONAL	1	TRUE	0	0.364045016613175	1		588	508	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873533	151873533	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	79	553	0	ENST00000262189.6:c.9005A>T	p.His3002Leu	p.H3002L	ENST00000262189	NM_170606.2	3002	cAc/cTc	38/59	1	2	FACETS	0.741	0.652	0.836	0.741	0.652	0.836	SUBCLONAL	1	TRUE	1	0.364045016613175	2		553	586	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0042994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	213	651	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.276999307498514	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.283326922441125	2		651	733	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144146	11144146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	244	814	2	ENST00000358026.2:c.3727C>T	p.Arg1243Trp	p.R1243W	ENST00000358026	NM_001128849.1	1243	Cgg/Tgg	26/36	0.283326922441125	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.283326922441125	2		816	693	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70967582	70967582	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	149	721	1	ENST00000276594.2:c.1441C>T	p.Arg481Ter	p.R481*	ENST00000276594	NM_024504.3	481	Cga/Tga	7/8	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.283326922441125	2		722	721	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143109	30143109	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	37	831	0	ENST00000389048.3:c.417G>C	p.Lys139Asn	p.K139N	ENST00000389048	NM_004304.4	139	aaG/aaC	1/29	1	2	FACETS	0.424	0.349	0.509	0.424	0.349	0.509	SUBCLONAL	1	TRUE	1	0.283326922441125	2		831	616	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0043000-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	89	406	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.390841914722446	1	FACETS	0.748	0.665	0.835	0.748	0.665	0.835	SUBCLONAL	1	FALSE	0	0.390841914722446	1		406	490	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106477	108106477	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043000-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	42	205	0	ENST00000278616.4:c.412G>T	p.Gly138Ter	p.G138*	ENST00000278616	NM_000051.3	138	Gga/Tga	5/63	1	2	FACETS	0.827	0.695	0.971	0.827	0.695	0.971	CLONAL	1	FALSE	1	0.390841914722446	2		205	260	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696254	52696254	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043000-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	68	515	0	ENST00000394830.3:c.423G>A	p.Trp141Ter	p.W141*	ENST00000394830	NM_018313.4	141	tgG/tgA	5/30	0.390841914722446	1	FACETS	0.628	0.548	0.714	0.628	0.548	0.714	SUBCLONAL	1	FALSE	0	0.390841914722446	1		515	446	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	106	82	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.93	1			1	INDETERMINATE	1	TRUE	NA	0.562441548281431	2		82	365	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610521	81610521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568577739	NA	P-0043002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	127	474	3	ENST00000298171.2:c.2119C>T	p.Arg707Trp	p.R707W	ENST00000298171	NM_000369.2	707	Cgg/Tgg	10/10	1	2	FACETS	0.92	0.838	1	0.92	0.838	1	CLONAL	1	TRUE	1	0.562441548281431	2		477	491	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383249	42383249	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137953079	NA	P-0043002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	175	750	0	ENST00000221972.3:c.269C>T	p.Thr90Met	p.T90M	ENST00000221972	NM_021601.3	90	aCg/aTg	2/5	0.541108808943727	3	FACETS	1	0.93	1	0.505	0.465	0.545	CLONAL	1	TRUE	1	0.562441548281431	3		750	790	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249803	133249806	+	missense_variant	Missense_Mutation	ONP	CGTA	CGTA	TGTT	novel	NA	P-0043002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	159	624	2	ENST00000320574.5:c.1417_1420delinsAACA	p.Tyr473_Val474delinsAsnIle	p.Y473_V474delinsNI	ENST00000320574	NM_006231.2	473	TACGtc/AACAtc	14/49	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.562441548281431	2		626	541	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248120	110248120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	119	461	1	ENST00000374672.4:c.1352C>T	p.Thr451Met	p.T451M	ENST00000374672	NM_004235.4	451	aCg/aTg	5/5	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.292625963004672	2		462	698	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0043018-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	305	754	6	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.448963453223882	2	FACETS	0.993	0.943	1	0.993	0.943	1	CLONAL	2	TRUE	0	0.448963453223882	2		760	684	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248980	55248981	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	TCCAGGAAGCAT	novel	NA	P-0043018-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	267	387	0	ENST00000275493.2:c.2288_2289insATTCCAGGAAGC		p.X763_splice	ENST00000275493	NM_005228.3	763			0.398164138717837	5	FACETS	1	0.988	1	0.794	0.746	0.842	CLONAL	2	TRUE	2	0.448963453223882	5		387	836	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926888	112926888	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507546	NA	P-0043067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	247	709	0	ENST00000351677.2:c.1508G>T	p.Gly503Val	p.G503V	ENST00000351677	NM_002834.3	503	gGg/gTg	13/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.590078887995255	2		709	783	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207089	1207090	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0043067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	460	1044	1	ENST00000326873.7:c.177_178del	p.Tyr60ArgfsTer102	p.Y60Rfs*102	ENST00000326873	NM_000455.4	59	tcTTac/tcac	1/10	0.590078887995255	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.590078887995255	1		1045	974	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602874	10602874	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	253	1120	0	ENST00000171111.5:c.704A>G	p.Asp235Gly	p.D235G	ENST00000171111	NM_203500.1	235	gAc/gGc	3/6	0.590078887995255	1	FACETS	0.659	0.618	0.702	0.659	0.618	0.702	SUBCLONAL	1	TRUE	0	0.590078887995255	1		1120	917	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054827	5054828	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0043067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	96	438	0	ENST00000381652.3:c.881dup	p.Gly295TrpfsTer10	p.G295Wfs*10	ENST00000381652	NM_004972.3	293	-/G	7/25	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.590078887995255	2		438	265	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519886	NA	P-0043123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	17	154	0	ENST00000349496.5:c.97T>C	p.Ser33Pro	p.S33P	ENST00000349496	NM_001904.3	33	Tct/Cct	3/15	0.372370386916398	2	FACETS	0.223	0.166	0.291	0.112	0.083	0.146	SUBCLONAL	1	TRUE	0	0.377359103405342	2		154	404	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148544338	148544338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	94	176	0	ENST00000320356.2:c.53G>A	p.Arg18His	p.R18H	ENST00000320356	NM_004456.4	18	cGt/cAt	2/20	0.334521678520861	3	FACETS	0.88	0.783	0.983	0.44	0.391	0.492	CLONAL	1	TRUE	1	0.377359103405342	3		176	673	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456334	99456334	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1471109147	NA	P-0043123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	84	156	0	ENST00000268035.6:c.1651A>C	p.Met551Leu	p.M551L	ENST00000268035	NM_000875.3	551	Atg/Ctg	8/21	0.372370386916398	2	FACETS	0.817	0.723	0.917	0.408	0.361	0.459	CLONAL	1	TRUE	0	0.377359103405342	2		156	545	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163607	47163607	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	97	135	0	ENST00000409792.3:c.2519A>T	p.Asn840Ile	p.N840I	ENST00000409792	NM_014159.6	840	aAt/aTt	3/21	0.372370386916398	2	FACETS	0.935	0.846	1	0.935	0.846	1	CLONAL	2	TRUE	0	0.377359103405342	2		135	275	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972900	32972911	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	ATATCTAAGCAT	ATATCTAAGCAT	CG	novel	NA	P-0043123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	36	87	0	ENST00000380152.3:c.10250_*4delinsCG		p.*3417*	ENST00000380152		3417		27/27	0.372370386916398	2	FACETS	0.694	0.573	0.828	0.347	0.286	0.414	SUBCLONAL	1	TRUE	0	0.377359103405342	2		87	275	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237689	133237689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500820	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	224	630	1	ENST00000320574.5:c.2926C>T	p.Arg976Cys	p.R976C	ENST00000320574	NM_006231.2	976	Cgc/Tgc	25/49	0.294316348979075	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.316252507557297	1		631	921	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246279	46246279	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	42	335	0	ENST00000334344.6:c.4373C>G	p.Ser1458Ter	p.S1458*	ENST00000334344	NM_152641.2	1458	tCa/tGa	15/21	0.297857318388382	3	FACETS	0.603	0.503	0.714	0.302	0.251	0.357	SUBCLONAL	1	TRUE	1	0.316252507557297	3		335	510	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233073	69233073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	42	271	0	ENST00000462284.1:c.938C>T	p.Ser313Leu	p.S313L	ENST00000462284	NM_002392.5	313	tCa/tTa	11/11	0.297857318388382	3	FACETS	0.801	0.67	0.946	0.401	0.335	0.473	CLONAL	1	TRUE	1	0.316252507557297	3		271	384	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179506	56179506	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	30	223	1	ENST00000399503.3:c.3819G>T	p.Gln1273His	p.Q1273H	ENST00000399503	NM_005921.1	1273	caG/caT	15/20	0.316252507557297	1	FACETS	0.726	0.589	0.88	0.726	0.589	0.88	SUBCLONAL	1	TRUE	0	0.316252507557297	1		224	220	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554352	106554352	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	65	371	0	ENST00000369096.4:c.1880G>A	p.Gly627Glu	p.G627E	ENST00000369096	NM_001198.3	627	gGa/gAa	6/7	1	2	FACETS	0.717	0.622	0.82	0.717	0.622	0.82	SUBCLONAL	1	TRUE	1	0.316252507557297	2		371	573	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650802	93650802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	72	308	0	ENST00000375746.1:c.1728G>A	p.Met576Ile	p.M576I	ENST00000375746	NM_001174167.1	576	atG/atA	13/14	0.316252507557297	2	FACETS	1	0.936	1	0.553	0.485	0.625	CLONAL	1	TRUE	0	0.316252507557297	2		308	412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	185	560	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.128919619014345	3	FACETS	1	0.988	1	0.688	0.635	0.743	INDETERMINATE	1	TRUE	1	0.316252507557297	3		560	985	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518706	204518706	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	28	269	0	ENST00000367182.3:c.1369C>G	p.Leu457Val	p.L457V	ENST00000367182	NM_001278516.1	457	Ctt/Gtt	11/11	1	2	FACETS	0.341	0.272	0.421	0.341	0.272	0.421	SUBCLONAL	1	TRUE	1	0.316252507557297	2		269	519	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41197783	41197783	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs273902776	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	106	599	0	ENST00000357654.3:c.5504G>A	p.Arg1835Gln	p.R1835Q	ENST00000357654	NM_007294.3	1835	cGa/cAa	23/23	0.128919619014345	3	FACETS	0.738	0.66	0.821	0.369	0.33	0.411	INDETERMINATE	1	TRUE	1	0.316252507557297	3		599	1052	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251857	212251857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	49	253	0	ENST00000342788.4:c.3202G>A	p.Asp1068Asn	p.D1068N	ENST00000342788	NM_005235.2	1068	Gat/Aat	27/28	0.308982888225809	4	FACETS	0.904	0.767	1	0.301	0.255	0.352	CLONAL	1	TRUE	1	0.316252507557297	4		253	451	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528930	157528930	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1371496107	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	76	509	0	ENST00000346085.5:c.6655G>T	p.Glu2219Ter	p.E2219*	ENST00000346085	NM_020732.3	2219	Gag/Tag	20/20	1	2	FACETS	0.747	0.656	0.846	0.747	0.656	0.846	SUBCLONAL	1	TRUE	1	0.316252507557297	2		509	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579374	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	194	766	1	ENST00000269305.4:c.313_314delinsTT	p.Gly105Phe	p.G105F	ENST00000269305	NM_001126112.2	105	GGc/TTc	4/11	0.128919619014345	3	FACETS	1	0.982	1	0.599	0.553	0.646	INDETERMINATE	1	TRUE	1	0.316252507557297	3		767	1187	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210843	2210843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	55	385	0	ENST00000398665.3:c.1340C>T	p.Ser447Phe	p.S447F	ENST00000398665	NM_032482.2	447	tCc/tTc	14/28	0.316252507557297	1	FACETS	0.691	0.592	0.798	0.691	0.592	0.798	SUBCLONAL	1	TRUE	0	0.316252507557297	1		385	424	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772605	135772605	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	64	468	0	ENST00000298552.3:c.2941G>C	p.Glu981Gln	p.E981Q	ENST00000298552	NM_001162426.1	981	Gaa/Caa	22/23	0.316252507557297	2	FACETS	0.622	0.538	0.713	0.311	0.269	0.357	SUBCLONAL	1	TRUE	0	0.316252507557297	2		468	651	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483899	88483899	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	93	693	0	ENST00000360948.2:c.1671C>G	p.Cys557Trp	p.C557W	ENST00000360948	NM_001012338.2	557	tgC/tgG	14/19	0.245365296331004	2	FACETS	0.698	0.62	0.781	0.349	0.31	0.391	SUBCLONAL	1	TRUE	0	0.316252507557297	2		693	843	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719424	190719424	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	25	288	0	ENST00000441310.2:c.1426G>C	p.Asp476His	p.D476H	ENST00000441310	NM_000534.4	476	Gat/Cat	9/13	0.146161398996943	4	FACETS	0.619	0.488	0.77			1	INDETERMINATE	1	TRUE	NA	0.316252507557297	4		288	336	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405688	139405688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377353441	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	426	829	0	ENST00000277541.6:c.2503C>T	p.Pro835Ser	p.P835S	ENST00000277541	NM_017617.3	835	Ccc/Tcc	16/34	0.316252507557297	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.316252507557297	2		829	1182	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2493180	2493180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	102	702	0	ENST00000355716.4:c.620C>T	p.Ser207Leu	p.S207L	ENST00000355716	NM_003820.2	207	tCa/tTa	6/8	0.297857318388382	3	FACETS	0.809	0.723	0.902	0.405	0.361	0.451	CLONAL	1	TRUE	1	0.316252507557297	3		702	923	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300435	11300435	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	181	557	0	ENST00000361445.4:c.1711A>G	p.Thr571Ala	p.T571A	ENST00000361445	NM_004958.3	571	Acg/Gcg	11/58	0.297857318388382	3	FACETS	0.927	0.858	0.999	0.927	0.858	0.999	CLONAL	2	TRUE	1	0.316252507557297	3		557	715	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237688	16237688	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	75	612	0	ENST00000375759.3:c.1135G>T	p.Gly379Cys	p.G379C	ENST00000375759	NM_015001.2	379	Ggt/Tgt	5/15	0.297857318388382	3	FACETS	0.72	0.63	0.817	0.36	0.315	0.409	SUBCLONAL	1	TRUE	1	0.316252507557297	3		612	763	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242772	16242772	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	51	424	0	ENST00000375759.3:c.1393G>T	p.Val465Leu	p.V465L	ENST00000375759	NM_015001.2	465	Gtg/Ttg	6/15	0.297857318388382	3	FACETS	0.632	0.537	0.737	0.316	0.268	0.369	SUBCLONAL	1	TRUE	1	0.316252507557297	3		424	591	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120478170	120478170	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	60	411	0	ENST00000256646.2:c.3580C>G	p.Gln1194Glu	p.Q1194E	ENST00000256646	NM_024408.3	1194	Cag/Gag	22/34	NA	2	FACETS	0.572	0.492	0.659			1	INDETERMINATE	1	TRUE	NA	0.316252507557297	2		411	663	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120478217	120478217	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	46	348	0	ENST00000256646.2:c.3533G>C	p.Gly1178Ala	p.G1178A	ENST00000256646	NM_024408.3	1178	gGc/gCc	22/34	NA	2	FACETS	0.538	0.452	0.632			1	INDETERMINATE	1	TRUE	NA	0.316252507557297	2		348	541	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731084	162731084	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	398	480	0	ENST00000367921.3:c.939G>A	p.Trp313Ter	p.W313*	ENST00000367921	NM_006182.2	313	tgG/tgA	9/18	0.316252507557297	7	FACETS	0.988	0.94	1	0.79	0.752	0.828	CLONAL	4	TRUE	2	0.316252507557297	7		480	1141	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615649	43615649	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	62	390	1	ENST00000355710.3:c.2728C>A	p.Gln910Lys	p.Q910K	ENST00000355710	NM_020975.4	910	Cag/Aag	15/20	0.128919619014345	3	FACETS	0.872	0.754	0.999	0.436	0.377	0.5	INDETERMINATE	1	TRUE	1	0.316252507557297	3		391	521	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851548	63851548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	149	561	0	ENST00000279873.7:c.2326G>A	p.Glu776Lys	p.E776K	ENST00000279873	NM_032199.2	776	Gag/Aag	10/10	0.128919619014345	3	FACETS	1	0.984	1	0.665	0.608	0.725	INDETERMINATE	1	TRUE	1	0.316252507557297	3		561	820	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248592	8248592	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	222	688	0	ENST00000335790.3:c.295G>T	p.Glu99Ter	p.E99*	ENST00000335790	NM_002315.2	99	Gag/Tag	3/4	0.316252507557297	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.316252507557297	1		688	846	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143494	108143494	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	44	415	0	ENST00000278616.4:c.3199G>C	p.Asp1067His	p.D1067H	ENST00000278616	NM_000051.3	1067	Gac/Cac	22/63	1	2	FACETS	0.628	0.527	0.74	0.628	0.527	0.74	SUBCLONAL	1	TRUE	1	0.316252507557297	2		415	443	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142578	119142578	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	36	358	0	ENST00000264033.4:c.577G>T	p.Ala193Ser	p.A193S	ENST00000264033	NM_005188.3	193	Gct/Tct	3/16	1	2	FACETS	0.622	0.512	0.745	0.622	0.512	0.745	SUBCLONAL	1	TRUE	1	0.316252507557297	2		358	366	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420634	49420634	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	200	605	0	ENST00000301067.7:c.15115G>T	p.Gly5039Cys	p.G5039C	ENST00000301067	NM_003482.3	5039	Ggt/Tgt	48/54	0.297857318388382	3	FACETS	0.891	0.827	0.957	0.891	0.827	0.957	CLONAL	2	TRUE	1	0.316252507557297	3		605	822	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425663	49425663	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	99	642	1	ENST00000301067.7:c.12825G>T	p.Gln4275His	p.Q4275H	ENST00000301067	NM_003482.3	4275	caG/caT	39/54	0.297857318388382	3	FACETS	0.806	0.718	0.899	0.403	0.359	0.45	CLONAL	1	TRUE	1	0.316252507557297	3		643	900	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446082	49446082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1262	148	887	0	ENST00000301067.7:c.1384C>T	p.Pro462Ser	p.P462S	ENST00000301067	NM_003482.3	462	Cct/Tct	10/54	0.297857318388382	3	FACETS	0.769	0.7	0.842	0.384	0.35	0.421	SUBCLONAL	1	TRUE	1	0.316252507557297	3		887	1410	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562400	21562400	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	290	531	1	ENST00000382592.4:c.1519G>T	p.Gly507Ter	p.G507*	ENST00000382592	NM_014572.2	507	Gga/Tga	4/8	0.133525567716042	5	FACETS	0.965	0.91	1			1	INDETERMINATE	3	TRUE	NA	0.316252507557297	5		532	934	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906746	32906746	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	94	625	0	ENST00000380152.3:c.1131G>T	p.Glu377Asp	p.E377D	ENST00000380152		377	gaG/gaT	10/27	1	2	FACETS	0.812	0.723	0.908	0.812	0.723	0.908	CLONAL	1	TRUE	1	0.316252507557297	2		625	732	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434572	99434572	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	77	458	0	ENST00000268035.6:c.659G>T	p.Gly220Val	p.G220V	ENST00000268035	NM_000875.3	220	gGg/gTg	3/21	0.245365296331004	2	FACETS	0.825	0.725	0.933	0.413	0.362	0.467	CLONAL	1	TRUE	0	0.316252507557297	2		458	590	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440040	99440040	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	77	402	0	ENST00000268035.6:c.1008G>C	p.Lys336Asn	p.K336N	ENST00000268035	NM_000875.3	336	aaG/aaC	4/21	0.245365296331004	2	FACETS	0.863	0.759	0.975	0.432	0.379	0.488	CLONAL	1	TRUE	0	0.316252507557297	2		402	564	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785607	50785607	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	130	616	2	ENST00000398568.2:c.597G>T	p.Leu199Phe	p.L199F	ENST00000398568	NM_001042412.1	199	ttG/ttT	4/18	1	2	FACETS	0.976	0.886	1	0.976	0.886	1	CLONAL	1	TRUE	1	0.316252507557297	2		618	842	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556260	29556260	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	79	401	0	ENST00000356175.3:c.2627C>G	p.Ser876Cys	p.S876C	ENST00000356175	NM_000267.3	876	tCt/tGt	21/57	0.128919619014345	3	FACETS	0.835	0.734	0.943	0.417	0.367	0.472	INDETERMINATE	1	TRUE	1	0.316252507557297	3		401	693	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37882819	37882819	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	82	549	0	ENST00000269571.5:c.2877G>A	p.Trp959Ter	p.W959*	ENST00000269571		959	tgG/tgA	24/27	0.128919619014345	3	FACETS	0.707	0.623	0.799	0.354	0.311	0.4	INDETERMINATE	1	TRUE	1	0.316252507557297	3		549	849	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519004	66519004	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	68	456	0	ENST00000358598.2:c.285G>T	p.Arg95Ser	p.R95S	ENST00000358598	NM_212471.2	95	agG/agT	3/11	0.128919619014345	3	FACETS	0.628	0.545	0.718	0.314	0.272	0.359	INDETERMINATE	1	TRUE	1	0.316252507557297	3		456	793	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732438	74732515	+	inframe_deletion	In_Frame_Del	DEL	AGATCGAGAACGAGTGCGGGACCGAGACTTCGAGCGGCTGTAGCGAGATCGGCTGCGAGACCTGGAACGACTCCGACT	AGATCGAGAACGAGTGCGGGACCGAGACTTCGAGCGGCTGTAGCGAGATCGGCTGCGAGACCTGGAACGACTCCGACT	-	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	28	350	0	ENST00000359995.5:c.394_471del	p.Ser132_Ser157del	p.S132_S157del	ENST00000359995	NM_001195427.1	132	AGTCGGAGTCGTTCCAGGTCTCGCAGCCGATCTCGCTACAGCCGCTCGAAGTCTCGGTCCCGCACTCGTTCTCGATCT/-	2/3	0.128919619014345	3	FACETS	0.426	0.34	0.525	0.213	0.17	0.263	INDETERMINATE	1	TRUE	1	0.316252507557297	3		350	481	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681800	78681800	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	156	655	0	ENST00000306801.3:c.507+1G>T		p.X169_splice	ENST00000306801	NM_020761.2	169			0.128919619014345	3	FACETS	1	0.971	1	0.568	0.519	0.619	INDETERMINATE	1	TRUE	1	0.316252507557297	3		655	1006	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78865623	78865623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	62	449	0	ENST00000306801.3:c.2087C>T	p.Ser696Phe	p.S696F	ENST00000306801	NM_020761.2	696	tCt/tTt	18/34	0.128919619014345	3	FACETS	0.623	0.537	0.716	0.311	0.268	0.358	INDETERMINATE	1	TRUE	1	0.316252507557297	3		449	729	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5239041	5239041	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	261	759	0	ENST00000357368.4:c.1738G>T	p.Val580Leu	p.V580L	ENST00000357368	NM_002850.3	580	Gtg/Ttg	13/38	0.316252507557297	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.316252507557297	1		759	1017	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599915	10599915	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	244	672	1	ENST00000171111.5:c.1661G>T	p.Arg554Leu	p.R554L	ENST00000171111	NM_203500.1	554	cGa/cTa	5/6	0.316252507557297	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.316252507557297	1		673	939	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308438	30308438	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	133	430	0	ENST00000262643.3:c.452G>T	p.Trp151Leu	p.W151L	ENST00000262643	NM_001238.2	151	tGg/tTg	6/12	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.316252507557297	2		430	689	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637379	47637379	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	94	651	0	ENST00000233146.2:c.513G>C	p.Arg171Ser	p.R171S	ENST00000233146	NM_000251.2	171	agG/agC	3/16	0.316252507557297	3	FACETS	0.686	0.609	0.769	0.343	0.304	0.385	SUBCLONAL	1	TRUE	1	0.316252507557297	3		651	1003	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026125	48026125	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	186	352	0	ENST00000234420.5:c.1003A>T	p.Asn335Tyr	p.N335Y	ENST00000234420	NM_000179.2	335	Aat/Tat	4/10	0.316252507557297	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.316252507557297	3		352	596	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61706035	61706035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	66	504	0	ENST00000401558.2:c.3136G>A	p.Asp1046Asn	p.D1046N	ENST00000401558	NM_003400.3	1046	Gat/Aat	25/25	0.316252507557297	3	FACETS	0.549	0.475	0.629	0.274	0.237	0.315	SUBCLONAL	1	TRUE	1	0.316252507557297	3		504	881	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248683	212248683	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	78	412	0	ENST00000342788.4:c.3584C>G	p.Pro1195Arg	p.P1195R	ENST00000342788	NM_005235.2	1195	cCa/cGa	28/28	0.308982888225809	4	FACETS	0.981	0.862	1	0.327	0.287	0.37	CLONAL	1	TRUE	1	0.316252507557297	4		412	662	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812318	212812318	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	82	284	0	ENST00000342788.4:c.258C>A	p.Tyr86Ter	p.Y86*	ENST00000342788	NM_005235.2	86	taC/taA	3/28	0.308982888225809	4	FACETS	0.783	0.693	0.878	0.522	0.462	0.585	SUBCLONAL	2	TRUE	1	0.316252507557297	4		284	436	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645645	215645645	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	187	476	1	ENST00000260947.4:c.953A>T	p.Asn318Ile	p.N318I	ENST00000260947	NM_000465.2	318	aAt/aTt	4/11	0.308982888225809	4	FACETS	1	0.932	1	0.671	0.621	0.723	CLONAL	2	TRUE	1	0.316252507557297	4		477	773	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440070	220440070	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	94	816	0	ENST00000243786.2:c.923C>A	p.Pro308His	p.P308H	ENST00000243786	NM_002191.3	308	cCt/cAt	2/2	0.308982888225809	4	FACETS	0.619	0.549	0.694	0.206	0.183	0.232	SUBCLONAL	1	TRUE	1	0.316252507557297	4		816	1264	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371613	225371613	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	60	443	0	ENST00000264414.4:c.991G>T	p.Glu331Ter	p.E331*	ENST00000264414	NM_003590.4	331	Gaa/Taa	7/16	0.308982888225809	4	FACETS	0.913	0.787	1	0.304	0.262	0.35	CLONAL	1	TRUE	1	0.316252507557297	4		443	547	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561172	9561172	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs774601283	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	57	389	0	ENST00000353224.5:c.610G>T	p.Asp204Tyr	p.D204Y	ENST00000353224	NM_177990.2	204	Gac/Tac	4/10	0.316252507557297	6	FACETS	0.714	0.611	0.827			1	SUBCLONAL	1	TRUE	NA	0.316252507557297	6		389	824	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770597	40770597	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	200	416	0	ENST00000373198.4:c.2785G>C	p.Asp929His	p.D929H	ENST00000373198	NM_133170.3	929	Gat/Cat	19/32	0.316252507557297	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.316252507557297	3		416	704	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545123	41545123	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	153	605	0	ENST00000263253.7:c.2323A>C	p.Met775Leu	p.M775L	ENST00000263253	NM_001429.3	775	Atg/Ctg	13/31	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.316252507557297	2		605	784	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102872	71102873	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	55	334	0	ENST00000318789.4:c.334dup	p.Met112AsnfsTer37	p.M112Nfs*37	ENST00000318789	NM_032682.5	112	atg/aAtg	8/21	0.245365296331004	2	FACETS	0.734	0.629	0.849	0.367	0.314	0.425	SUBCLONAL	1	TRUE	0	0.316252507557297	2		334	474	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72891482	72891482	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	89	449	0	ENST00000325599.8:c.280C>G	p.Leu94Val	p.L94V	ENST00000325599	NM_018130.2	94	Ctt/Gtt	3/11	0.245365296331004	2	FACETS	0.885	0.785	0.991	0.442	0.392	0.496	CLONAL	1	TRUE	0	0.316252507557297	2		449	636	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177876	142177876	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	94	397	0	ENST00000350721.4:c.7427G>T	p.Arg2476Leu	p.R2476L	ENST00000350721	NM_001184.3	2476	cGt/cTt	44/47	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.316252507557297	2		397	474	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269112	142269112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	56	327	0	ENST00000350721.4:c.2838G>A	p.Met946Ile	p.M946I	ENST00000350721	NM_001184.3	946	atG/atA	14/47	1	2	FACETS	0.64	0.549	0.741	0.64	0.549	0.741	SUBCLONAL	1	TRUE	1	0.316252507557297	2		327	553	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170015149	170015149	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	72	582	0	ENST00000295797.4:c.1555C>A	p.His519Asn	p.H519N	ENST00000295797	NM_002740.5	519	Cac/Aac	16/18	0.277288372295232	5	FACETS	0.736	0.642	0.839	0.245	0.214	0.28	SUBCLONAL	1	TRUE	2	0.316252507557297	5		582	912	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747970	41747970	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1446644422	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	27	149	0	ENST00000226382.2:c.799G>T	p.Gly267Trp	p.G267W	ENST00000226382	NM_003924.3	267	Ggg/Tgg	3/3	1	2	FACETS	0.959	0.77	1	0.959	0.77	1	CLONAL	1	TRUE	1	0.316252507557297	2		149	178	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55987283	55987283	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	59	387	1	ENST00000263923.4:c.142A>T	p.Thr48Ser	p.T48S	ENST00000263923	NM_002253.2	48	Act/Tct	2/30	1	2	FACETS	0.729	0.628	0.839	0.729	0.628	0.839	SUBCLONAL	1	TRUE	1	0.316252507557297	2		388	512	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55987326	55987326	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs149870540	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	64	366	0	ENST00000263923.4:c.99G>T	p.Arg33Ser	p.R33S	ENST00000263923	NM_002253.2	33	agG/agT	2/30	1	2	FACETS	0.748	0.648	0.856	0.748	0.648	0.856	SUBCLONAL	1	TRUE	1	0.316252507557297	2		366	541	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627903	187627903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	93	649	0	ENST00000441802.2:c.3079G>A	p.Glu1027Lys	p.E1027K	ENST00000441802	NM_005245.3	1027	Gag/Aag	2/27	1	2	FACETS	0.76	0.675	0.85	0.76	0.675	0.85	SUBCLONAL	1	TRUE	1	0.316252507557297	2		649	774	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293898	1293898	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	114	890	0	ENST00000310581.5:c.1103C>G	p.Ser368Cys	p.S368C	ENST00000310581	NM_198253.2	368	tCc/tGc	2/16	1	2	FACETS	0.695	0.624	0.77	0.695	0.624	0.77	SUBCLONAL	1	TRUE	1	0.316252507557297	2		890	1038	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31431779	31431779	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	39	305	0	ENST00000344624.3:c.3049G>C	p.Glu1017Gln	p.E1017Q	ENST00000344624		1017	Gaa/Caa	23/33	0.316252507557297	3	FACETS	0.563	0.466	0.672	0.282	0.233	0.336	SUBCLONAL	1	TRUE	1	0.316252507557297	3		305	507	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435808	149435808	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	115	604	0	ENST00000286301.3:c.2416G>C	p.Asp806His	p.D806H	ENST00000286301	NM_005211.3	806	Gac/Cac	18/22	0.316252507557297	1	FACETS	0.864	0.779	0.953	0.864	0.779	0.953	CLONAL	1	TRUE	0	0.316252507557297	1		604	709	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441160	149441160	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	83	638	0	ENST00000286301.3:c.1754-2A>C		p.X585_splice	ENST00000286301	NM_005211.3	585			0.316252507557297	1	FACETS	0.715	0.631	0.804	0.715	0.631	0.804	SUBCLONAL	1	TRUE	0	0.316252507557297	1		638	618	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638624	176638624	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	117	660	0	ENST00000439151.2:c.3224G>T	p.Gly1075Val	p.G1075V	ENST00000439151	NM_022455.4	1075	gGa/gTa	5/23	0.316252507557297	1	FACETS	0.75	0.676	0.828	0.75	0.676	0.828	SUBCLONAL	1	TRUE	0	0.316252507557297	1		660	831	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665268	176665268	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	45	298	0	ENST00000439151.2:c.3952C>G	p.Leu1318Val	p.L1318V	ENST00000439151	NM_022455.4	1318	Cta/Gta	7/23	0.316252507557297	1	FACETS	0.569	0.479	0.669	0.569	0.479	0.669	SUBCLONAL	1	TRUE	0	0.316252507557297	1		298	421	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163761	152163761	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	70	415	0	ENST00000206249.3:c.482G>T	p.Gly161Val	p.G161V	ENST00000206249	NM_000125.3	161	gGc/gTc	2/8	1	2	FACETS	0.786	0.686	0.894	0.786	0.686	0.894	SUBCLONAL	1	TRUE	1	0.316252507557297	2		415	563	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739939	41739939	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1488241309	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	36	429	0	ENST00000242208.4:c.34G>T	p.Ala12Ser	p.A12S	ENST00000242208	NM_002192.2	12	Gca/Tca	2/3	0.128919619014345	3	FACETS	0.411	0.337	0.495	0.206	0.168	0.248	INDETERMINATE	1	TRUE	1	0.316252507557297	3		429	641	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513346	106513346	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	88	289	0	ENST00000359195.3:c.2250A>T	p.Lys750Asn	p.K750N	ENST00000359195	NM_002649.2	750	aaA/aaT	4/11	0.128919619014345	3	FACETS	1	0.967	1	0.617	0.548	0.691	INDETERMINATE	1	TRUE	1	0.316252507557297	3		289	522	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976654	90976654	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	82	369	0	ENST00000265433.3:c.978G>T	p.Gln326His	p.Q326H	ENST00000265433	NM_002485.4	326	caG/caT	8/16	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.316252507557297	2		369	504	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759992	133759992	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	99	884	0	ENST00000318560.5:c.2315C>T	p.Ser772Phe	p.S772F	ENST00000318560	NM_005157.4	772	tCt/tTt	11/11	0.316252507557297	2	FACETS	0.561	0.499	0.627	0.281	0.249	0.314	SUBCLONAL	1	TRUE	0	0.316252507557297	2		884	1116	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227980	123227980	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs182467825	NA	P-0043131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	85	196	0	ENST00000218089.9:c.3691A>G	p.Met1231Val	p.M1231V	ENST00000218089	NM_001042749.1	1231	Atg/Gtg	33/35	0.146161398996943	2	FACETS	1	0.968	1			1	INDETERMINATE	2	TRUE	NA	0.316252507557297	2		196	225	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0043153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	72	358	1	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.757	0.662	0.86	0.757	0.662	0.86	SUBCLONAL	1	TRUE	1	0.328500923634053	2		359	579	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579582	7579583	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	118	759	0	ENST00000269305.4:c.104dup	p.Leu35PhefsTer8	p.L35Ffs*8	ENST00000269305	NM_001126112.2	35	ttg/ttTg	4/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.328500923634053	2		759	612	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807919	3807919	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587783481	NA	P-0043153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	114	557	0	ENST00000262367.5:c.3500A>G	p.Tyr1167Cys	p.Y1167C	ENST00000262367	NM_004380.2	1167	tAt/tGt	18/31	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.328500923634053	2		557	630	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602438	10602438	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	193	944	0	ENST00000171111.5:c.1140G>C	p.Arg380Ser	p.R380S	ENST00000171111	NM_203500.1	380	agG/agC	3/6	0.328500923634053	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.328500923634053	1		944	775	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115267842	115267842	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	116	470	0	ENST00000438362.2:c.1891G>T	p.Val631Leu	p.V631L	ENST00000438362	NM_001242891.1	631	Gtg/Ttg	15/20	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.328500923634053	2		470	706	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895650	28895650	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	91	601	0	ENST00000282397.4:c.3124G>T	p.Gly1042Cys	p.G1042C	ENST00000282397	NM_002019.4	1042	Ggc/Tgc	23/30	1	2	FACETS	0.775	0.688	0.868	0.775	0.688	0.868	SUBCLONAL	1	TRUE	1	0.328500923634053	2		601	715	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523023	25523023	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	94	885	0	ENST00000264709.3:c.162G>T	p.Lys54Asn	p.K54N	ENST00000264709	NM_175629.2	54	aaG/aaT	3/23	1	2	FACETS	0.623	0.554	0.698	0.623	0.554	0.698	SUBCLONAL	1	TRUE	1	0.328500923634053	2		885	918	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0043197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1331	78	772	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	0.469	0.41	0.532	0.469	0.41	0.532	SUBCLONAL	1	FALSE	1	0.236212207248921	2		772	1409	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0043200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	148	505	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.396093602952418	2		505	714	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450405	50450405	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	112	416	0	ENST00000331340.3:c.589G>T	p.Val197Phe	p.V197F	ENST00000331340	NM_006060.4	197	Gtt/Ttt	5/8	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.396093602952418	2		416	529	SUCCESS
BTK	695	MSKCC	GRCh37	X	100612503	100612503	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	128	501	0	ENST00000308731.7:c.1171G>T	p.Gly391Ter	p.G391*	ENST00000308731	NM_000061.2	391	Gga/Tga	13/19	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.396093602952418	2		501	635	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858114	9858114	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs773991023	NA	P-0043200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	176	696	0	ENST00000330684.3:c.3287A>T	p.Lys1096Met	p.K1096M	ENST00000330684	NM_001134407.1	1096	aAg/aTg	13/13	1	2	FACETS	0.973	0.897	1	0.973	0.897	1	CLONAL	1	TRUE	1	0.396093602952418	2		696	913	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518304	187518304	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	88	345	0	ENST00000441802.2:c.12390G>T	p.Glu4130Asp	p.E4130D	ENST00000441802	NM_005245.3	4130	gaG/gaT	25/27	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.396093602952418	2		345	411	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799210	45799210	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	130	439	0	ENST00000450313.1:c.223G>T	p.Val75Leu	p.V75L	ENST00000450313	NM_012222.2	75	Gtg/Ttg	3/16	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.326048856392757	2		439	792	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953384	17953384	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	164	698	0	ENST00000458235.1:c.602T>A	p.Leu201Gln	p.L201Q	ENST00000458235	NM_000215.3	201	cTg/cAg	6/24	0.326048856392757	2	FACETS	1	0.952	1	0.527	0.483	0.572	CLONAL	1	TRUE	0	0.326048856392757	2		698	955	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657003	45657003	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0043224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	205	521	0	ENST00000407780.3:c.153C>G	p.Tyr51Ter	p.Y51*	ENST00000407780	NM_001283052.1	51	taC/taG	3/7	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.326048856392757	2		521	915	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0043250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	617	214	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.370422857377769	18	FACETS	0.975	0.948	1			1	CLONAL	15	FALSE	NA	0.370422857377769	18		214	903	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520253	176520253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375466821	NA	P-0043250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1415	129	737	0	ENST00000292408.4:c.1172G>A	p.Arg391Gln	p.R391Q	ENST00000292408	NM_213647.1	391	cGa/cAa	9/18	0.370422857377769	11	FACETS	1	0.972	1			1	CLONAL	1	FALSE	NA	0.370422857377769	11		737	1544	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602337	10602337	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	396	846	0	ENST00000171111.5:c.1241A>T	p.Asn414Ile	p.N414I	ENST00000171111	NM_203500.1	414	aAc/aTc	3/6	0.370422857377769	3	FACETS	0.94	0.898	0.982	0.94	0.898	0.982	CLONAL	3	FALSE	0	0.370422857377769	3		846	899	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899067	40899067	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	191	662	0	ENST00000373198.4:c.2203C>A	p.Pro735Thr	p.P735T	ENST00000373198	NM_133170.3	735	Ccg/Acg	14/32	NA	2	FACETS	0.768	0.713	0.825			1	INDETERMINATE	2	FALSE	NA	0.370422857377769	2		662	671	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667495	241667495	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	116	298	0	ENST00000366560.3:c.955G>T	p.Asp319Tyr	p.D319Y	ENST00000366560	NM_000143.3	319	Gac/Tac	7/10	0.370422857377769	5	FACETS	0.905	0.824	0.988	0.905	0.824	0.988	CLONAL	3	FALSE	2	0.370422857377769	5		298	359	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554335	81554335	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	73	379	0	ENST00000298171.2:c.355C>A	p.Pro119Thr	p.P119T	ENST00000298171	NM_000369.2	119	Cct/Act	4/10	0.370422857377769	4	FACETS	0.781	0.687	0.879	0.781	0.687	0.879	SUBCLONAL	2	FALSE	2	0.370422857377769	4		379	346	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576259	88576259	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	222	481	0	ENST00000360948.2:c.1414A>T	p.Ser472Cys	p.S472C	ENST00000360948	NM_001012338.2	472	Agt/Tgt	13/19	0.178322759931066	3	FACETS	0.925	0.87	0.981			1	INDETERMINATE	3	FALSE	NA	0.370422857377769	3		481	512	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857196	9857196	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	132	531	0	ENST00000330684.3:c.4205G>T	p.Arg1402Leu	p.R1402L	ENST00000330684	NM_001134407.1	1402	cGg/cTg	13/13	0.226838054699437	5	FACETS	1	0.953	1	0.711	0.649	0.775	CLONAL	2	FALSE	2	0.370422857377769	5		531	520	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371673	89371673	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	126	759	0	ENST00000301030.4:c.167G>C	p.Ser56Thr	p.S56T	ENST00000301030	NM_001256183.1	56	aGc/aCc	4/13	0.240736533798355	5	FACETS	1	0.965	1	0.38	0.343	0.418	CLONAL	1	FALSE	2	0.370422857377769	5		759	929	SUCCESS
AR	367	MSKCC	GRCh37	X	66765473	66765473	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	226	788	0	ENST00000374690.3:c.485C>A	p.Ser162Tyr	p.S162Y	ENST00000374690	NM_000044.3	162	tCc/tAc	1/8	0.354380931452821	1	FACETS	0.84	0.788	0.892	1	0.994	1	CLONAL	2	FALSE	0	0.370422857377769	1		788	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577560	7577560	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520002	NA	P-0043251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	109	603	0	ENST00000269305.4:c.721T>C	p.Ser241Pro	p.S241P	ENST00000269305	NM_001126112.2	241	Tcc/Ccc	7/11	0.312136253681803	1	FACETS	0.869	0.782	0.962	0.869	0.782	0.962	CLONAL	1	TRUE	0	0.312136253681803	1		603	678	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163315582	163315582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	46	304	2	ENST00000271452.3:c.922G>A	p.Glu308Lys	p.E308K	ENST00000271452	NM_145697.2	308	Gaa/Aaa	11/14	1	2	FACETS	0.797	0.673	0.932	0.797	0.673	0.932	CLONAL	1	TRUE	1	0.312136253681803	2		306	370	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470580	25470580	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	106	767	0	ENST00000264709.3:c.894del	p.Lys299AsnfsTer17	p.K299Nfs*17	ENST00000264709	NM_175629.2	298	ggG/gg	8/23	1	2	FACETS	0.907	0.813	1	0.907	0.813	1	CLONAL	1	TRUE	1	0.312136253681803	2		767	749	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561780	55561780	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	73	382	0	ENST00000288135.5:c.170T>C	p.Leu57Ser	p.L57S	ENST00000288135	NM_000222.2	57	tTa/tCa	2/21	1	2	FACETS	0.921	0.807	1	0.921	0.807	1	CLONAL	1	TRUE	1	0.312136253681803	2		382	508	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156221	119156221	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	94	513	0	ENST00000264033.4:c.1886A>T	p.Glu629Val	p.E629V	ENST00000264033	NM_005188.3	629	gAg/gTg	11/16	1	2	FACETS	0.983	0.876	1	0.983	0.876	1	CLONAL	1	TRUE	1	0.312136253681803	2		513	613	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626932	14626932	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	92	681	0	ENST00000254322.2:c.843A>G	p.Ile281Met	p.I281M	ENST00000254322	NM_006145.1	281	atA/atG	3/3	1	2	FACETS	0.782	0.694	0.875	0.782	0.694	0.875	SUBCLONAL	1	TRUE	1	0.312136253681803	2		681	754	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306526	41306526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	177	495	0	ENST00000373198.4:c.1133C>T	p.Thr378Ile	p.T378I	ENST00000373198	NM_133170.3	378	aCc/aTc	7/32	0.312136253681803	3	FACETS	1	0.976	1	0.747	0.692	0.804	CLONAL	2	TRUE	0	0.312136253681803	3		495	585	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755522	57755522	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	45	404	0	ENST00000274289.3:c.265G>C	p.Gly89Arg	p.G89R	ENST00000274289	NM_006622.3	89	Gga/Cga	1/14	1	2	FACETS	0.66	0.555	0.775	0.66	0.555	0.775	SUBCLONAL	1	TRUE	1	0.312136253681803	2		404	437	SUCCESS
APC	324	MSKCC	GRCh37	5	112175334	112175335	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	71	230	0	ENST00000257430.4:c.4043_4044insA	p.His1349AlafsTer5	p.H1349Afs*5	ENST00000257430	NM_000038.5	1348	agg/agAg	16/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.312136253681803	2		230	310	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917759	94917759	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0043277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	218	350	0	ENST00000536441.1:c.763-1G>C		p.X255_splice	ENST00000536441	NM_144665.3	255			0.417004396224316	3	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	1	0.454887686935866	3		350	586	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43699623	43699623	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	238	610	0	ENST00000382044.4:c.5892C>G	p.Phe1964Leu	p.F1964L	ENST00000382044	NM_001141980.1	1964	ttC/ttG	28/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.454887686935866	2		610	982	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821182	72821182	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	250	648	0	ENST00000268489.5:c.10993G>A	p.Asp3665Asn	p.D3665N	ENST00000268489	NM_006885.3	3665	Gac/Aac	10/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.454887686935866	2		648	1054	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880998	37880998	+	protein_altering_variant	In_Frame_Ins	INS	G	G	TTGT	novel	NA	P-0043277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	253	717	0	ENST00000269571.5:c.2327delinsTTGT	p.Gly776delinsValVal	p.G776delinsVV	ENST00000269571		776	gGt/gTTGTt	20/27	1	2	FACETS	0.918	0.858	0.98	0.918	0.858	0.98	CLONAL	1	TRUE	1	0.454887686935866	2		717	1212	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220450	1220452	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	novel	NA	P-0043277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	244	779	0	ENST00000326873.7:c.543_545del	p.Asn181_Leu182delinsLys	p.N181_L182delinsK	ENST00000326873	NM_000455.4	181	aaCCTg/aag	4/10	0.454887686935866	1	FACETS	0.87	0.813	0.927	0.87	0.813	0.927	CLONAL	1	TRUE	0	0.454887686935866	1		779	953	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250915	10250915	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	235	702	0	ENST00000340748.4:c.3565G>A	p.Glu1189Lys	p.E1189K	ENST00000340748		1189	Gag/Aag	32/40	0.454887686935866	1	FACETS	0.979	0.916	1	0.979	0.916	1	CLONAL	1	TRUE	0	0.454887686935866	1		702	815	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152041	11152041	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	215	366	1	ENST00000358026.2:c.4325C>A	p.Ser1442Ter	p.S1442*	ENST00000358026	NM_001128849.1	1442	tCa/tAa	31/36	0.454887686935866	1	FACETS	0.975	0.909	1	0.975	0.909	1	CLONAL	1	TRUE	0	0.454887686935866	1		367	749	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029132	26029132	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	179	417	0	ENST00000435504.4:c.218A>C	p.Lys73Thr	p.K73T	ENST00000435504		73	aAg/aCg	4/13	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.454887686935866	2		417	777	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52675997	52675997	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	245	619	0	ENST00000394830.3:c.1060G>C	p.Glu354Gln	p.E354Q	ENST00000394830	NM_018313.4	354	Gaa/Caa	11/30	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.454887686935866	2		619	1037	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52676053	52676053	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	131	329	0	ENST00000394830.3:c.1004G>C	p.Arg335Thr	p.R335T	ENST00000394830	NM_018313.4	335	aGa/aCa	11/30	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.454887686935866	2		329	524	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866654	117866654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	139	540	0	ENST00000297338.2:c.991G>A	p.Glu331Lys	p.E331K	ENST00000297338	NM_006265.2	331	Gag/Aag	9/14	1	2	FACETS	0.816	0.744	0.892	0.816	0.744	0.892	CLONAL	1	TRUE	1	0.454887686935866	2		540	749	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080532	5080532	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0043277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	83	289	0	ENST00000381652.3:c.2284-1G>A		p.X762_splice	ENST00000381652	NM_004972.3	762			0.454887686935866	1	FACETS	0.972	0.868	1	0.972	0.868	1	CLONAL	1	TRUE	0	0.454887686935866	1		289	290	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325449	1325449	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	261	698	0	ENST00000400841.2:c.226C>T	p.Leu76Phe	p.L76F	ENST00000400841		76	Ctc/Ttc	3/6	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.454887686935866	2		698	1076	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222205	53222205	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	233	722	0	ENST00000375401.3:c.4627C>G	p.Leu1543Val	p.L1543V	ENST00000375401	NM_004187.3	1543	Ctg/Gtg	26/26	1	2	FACETS	0.943	0.879	1	0.943	0.879	1	CLONAL	1	TRUE	1	0.454887686935866	2		722	1086	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0043283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	141	689	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.454	0.413	0.497	0.454	0.413	0.497	SUBCLONAL	1	TRUE	1	0.638655413948674	2		689	973	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0043283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	161	724	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.896	0.826	0.967	0.896	0.826	0.967	CLONAL	1	TRUE	1	0.638655413948674	2		724	563	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	10	341	0	ENST00000288602.6:c.1742A>T	p.Asn581Ile	p.N581I	ENST00000288602	NM_004333.4	581	aAt/aTt	15/18	0.598797195145491	3	FACETS	0.15	0.101	0.212	0.075	0.05	0.106	SUBCLONAL	1	TRUE	1	0.638655413948674	3		341	275	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs530941076	NA	P-0043283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	217	825	2	ENST00000269305.4:c.658T>C	p.Tyr220His	p.Y220H	ENST00000269305	NM_001126112.2	220	Tat/Cat	6/11	0.19254664750467	2	FACETS	0.721	0.67	0.772	0.36	0.335	0.386	INDETERMINATE	1	TRUE	0	0.638655413948674	2		827	943	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890138	76890138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	144	335	0	ENST00000373344.5:c.4756C>T	p.Pro1586Ser	p.P1586S	ENST00000373344	NM_000489.3	1586	Cca/Tca	17/35	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.638655413948674	1		335	231	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121074	3121074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	281	837	0	ENST00000078429.4:c.977C>T	p.Ser326Leu	p.S326L	ENST00000078429	NM_002067.2	326	tCa/tTa	7/7	1	2	FACETS	0.965	0.909	1	0.965	0.909	1	CLONAL	1	TRUE	1	0.638655413948674	2		837	912	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139894	55139894	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	159	465	0	ENST00000257290.5:c.1555C>T	p.Pro519Ser	p.P519S	ENST00000257290	NM_006206.4	519	Ccc/Tcc	10/23	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.638655413948674	2		465	495	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609973	43609975	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0043283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	317	906	0	ENST00000355710.3:c.1927_1929del	p.Leu643del	p.L643del	ENST00000355710	NM_020975.4	642	gTCCtc/gtc	11/20	1	2	FACETS	0.988	0.934	1	0.988	0.934	1	CLONAL	1	TRUE	1	0.638655413948674	2		906	1005	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421654	49421654	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	234	777	1	ENST00000301067.7:c.14575C>T	p.Gln4859Ter	p.Q4859*	ENST00000301067	NM_003482.3	4859	Cag/Tag	47/54	1	2	FACETS	0.964	0.903	1	0.964	0.903	1	CLONAL	1	TRUE	1	0.638655413948674	2		778	760	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428074	49428074	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	244	762	0	ENST00000301067.7:c.10516del	p.Asp3506ThrfsTer20	p.D3506Tfs*20	ENST00000301067	NM_003482.3	3506	Gac/ac	38/54	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.638655413948674	2		762	728	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961786	41961786	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	142	573	0	ENST00000219905.7:c.694G>C	p.Glu232Gln	p.E232Q	ENST00000219905	NM_001164273.1	232	Gaa/Caa	2/24	1	2	FACETS	0.975	0.896	1	0.975	0.896	1	CLONAL	1	TRUE	1	0.638655413948674	2		573	456	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3824575	3824576	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CACTGAGC	novel	NA	P-0043283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	59	503	0	ENST00000262367.5:c.2270_2277dup	p.Pro760AlafsTer19	p.P760Afs*19	ENST00000262367	NM_004380.2	759	-/GCTCAGTG	12/31	1	2	FACETS	0.341	0.293	0.393	0.341	0.293	0.393	SUBCLONAL	1	TRUE	1	0.638655413948674	2		503	542	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7141690	7141690	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	40	686	0	ENST00000302850.5:c.2680G>T	p.Glu894Ter	p.E894*	ENST00000302850	NM_000208.2	894	Gag/Tag	13/22	1	2	FACETS	0.175	0.145	0.209	0.175	0.145	0.209	SUBCLONAL	1	TRUE	1	0.638655413948674	2		686	716	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097182	178097182	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	41	572	0	ENST00000397062.3:c.532G>C	p.Asp178His	p.D178H	ENST00000397062	NM_006164.4	178	Gac/Cac	4/5	1	2	FACETS	0.219	0.182	0.261	0.219	0.182	0.261	SUBCLONAL	1	TRUE	1	0.638655413948674	2		572	586	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652121	36652134	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCCGGCGAGGCC	GCCCCGGCGAGGCC	-	novel	NA	P-0043283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	81	802	0	ENST00000244741.5:c.244_257del	p.Pro82GlyfsTer2	p.P82Gfs*2	ENST00000244741	NM_000389.4	81	ggGCCCCGGCGAGGCCgg/gggg	2/3	1	2	FACETS	0.305	0.268	0.344	0.305	0.268	0.344	SUBCLONAL	1	TRUE	1	0.638655413948674	2		802	833	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845677	151845678	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CTAG	novel	NA	P-0043283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	435	741	0	ENST00000262189.6:c.13334_13335insCTAG	p.Ala4446Ter	p.A4446*	ENST00000262189	NM_170606.2	4445	ggt/ggCTAGt	52/59	0.598797195145491	3	FACETS	0.895	0.857	0.934	0.895	0.857	0.934	CLONAL	2	TRUE	1	0.638655413948674	3		741	1004	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341894	8341894	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0043283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	87	636	0	ENST00000356435.5:c.4746T>A	p.Tyr1582Ter	p.Y1582*	ENST00000356435		1582	taT/taA	29/35	1	2	FACETS	0.604	0.537	0.675	0.604	0.537	0.675	SUBCLONAL	1	TRUE	1	0.638655413948674	2		636	451	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242327	98242327	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	195	653	0	ENST00000331920.6:c.991T>C	p.Ser331Pro	p.S331P	ENST00000331920	NM_000264.3	331	Tcc/Ccc	7/24	1	2	FACETS	0.962	0.895	1	0.962	0.895	1	CLONAL	1	TRUE	1	0.638655413948674	2		653	635	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929371	44929371	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0043283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	117	406	0	ENST00000377967.4:c.2471C>G	p.Ser824Ter	p.S824*	ENST00000377967	NM_021140.2	824	tCa/tGa	17/29	1	1	FACETS	0.512	0.464	0.562	0.512	0.464	0.562	SUBCLONAL	1	TRUE	0	0.638655413948674	1		406	487	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890131	76890131	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	150	343	1	ENST00000373344.5:c.4763C>T	p.Ser1588Leu	p.S1588L	ENST00000373344	NM_000489.3	1588	tCa/tTa	17/35	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.638655413948674	1		344	239	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195080	123195081	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0043283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	59	208	0	ENST00000218089.9:c.1424_1425del	p.Glu475AlafsTer8	p.E475Afs*8	ENST00000218089	NM_001042749.1	475	GAg/g	16/35	1	1	FACETS	0.662	0.579	0.748	0.662	0.579	0.748	SUBCLONAL	1	TRUE	0	0.638655413948674	1		208	190	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295190	1295196	+	upstream_gene_variant	5'Flank	DEL	GCCGCGG	GCCGCGG	ACGGGA	novel	NA	P-0043283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	106	356	0				ENST00000310581	NM_198253.2	-/1132			0.186797327823973	3	FACETS	0.831	0.748	0.919	0.416	0.374	0.46	INDETERMINATE	1	TRUE	1	0.638655413948674	3		356	527	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	274	82	0				ENST00000310581	NM_198253.2	-/1132			0.565509252389377	5	FACETS	1	0.99	1	0.806	0.76	0.852	CLONAL	2	TRUE	2	0.584610064441665	5		82	728	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292745	91292745	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	210	687	0	ENST00000355112.3:c.247C>T	p.Gln83Ter	p.Q83*	ENST00000355112	NM_000057.2	83	Cag/Tag	3/22	0.584610064441665	2	FACETS	1	0.958	1	0.518	0.483	0.554	CLONAL	1	TRUE	0	0.584610064441665	2		687	693	SUCCESS
EED	8726	MSKCC	GRCh37	11	85956278	85956278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	95	301	0	ENST00000263360.6:c.7G>A	p.Glu3Lys	p.E3K	ENST00000263360	NM_003797.3	3	Gag/Aag	1/12	0.584610064441665	3	FACETS	1	0.959	1	0.568	0.509	0.628	CLONAL	1	TRUE	1	0.584610064441665	3		301	370	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129655	11129655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	674	771	0	ENST00000358026.2:c.2461G>A	p.Glu821Lys	p.E821K	ENST00000358026	NM_001128849.1	821	Gag/Aag	17/36	0.584610064441665	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.584610064441665	3		771	920	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180417	94180417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565212475	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	219	619	0	ENST00000323929.3:c.1751C>T	p.Ser584Leu	p.S584L	ENST00000323929	NM_005591.3	584	tCa/tTa	15/20	0.584610064441665	3	FACETS	1	0.977	1	0.556	0.518	0.595	CLONAL	1	TRUE	1	0.584610064441665	3		619	871	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778251	27778251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761484168	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	278	481	1	ENST00000369163.2:c.400G>A	p.Glu134Lys	p.E134K	ENST00000369163	NM_003536.2	134	Gag/Aag	1/1	0.584610064441665	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.584610064441665	2		482	439	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856356	45856356	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	358	830	0	ENST00000391945.4:c.1816G>C	p.Glu606Gln	p.E606Q	ENST00000391945	NM_000400.3	606	Gag/Cag	19/23	0.584610064441665	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.584610064441665	3		830	790	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97887418	97887418	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs776529713	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	209	666	1	ENST00000289081.3:c.946C>T	p.Gln316Ter	p.Q316*	ENST00000289081	NM_000136.2	316	Cag/Tag	10/15	0.578074625566503	3	FACETS	1	0.966	1	0.532	0.494	0.57	CLONAL	1	TRUE	1	0.584610064441665	3		667	869	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792752	33792752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555742114	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	29	96	0	ENST00000498907.2:c.569C>T	p.Ser190Leu	p.S190L	ENST00000498907	NM_004364.3	190	tCg/tTg	1/1	0.584610064441665	3	FACETS	1	0.911	1	0.599	0.491	0.715	CLONAL	1	TRUE	1	0.584610064441665	3		96	107	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099403	157099426	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAGCAA	CAGCAGCAGCAGCAGCAGCAGCAA	-	rs770869529	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	24	254	0	ENST00000346085.5:c.369_392del	p.Gln124_Gln131del	p.Q124_Q131del	ENST00000346085	NM_020732.3	114	CAGCAGCAGCAGCAGCAGCAGCAA/-	1/20	1	2	FACETS	0.408	0.322	0.507	0.408	0.322	0.507	SUBCLONAL	1	TRUE	1	0.584610064441665	2		254	201	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307593	118307593	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	191	675	0	ENST00000534358.1:c.366C>G	p.Ile122Met	p.I122M	ENST00000534358	NM_005933.3	122	atC/atG	1/36	0.584610064441665	3	FACETS	1	0.982	1	0.587	0.545	0.631	CLONAL	1	TRUE	1	0.584610064441665	3		675	719	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69788803	69788803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	108	447	0	ENST00000352241.4:c.55G>A	p.Glu19Lys	p.E19K	ENST00000352241	NM_198159.2	19	Gaa/Aaa	1/10	1	2	FACETS	0.834	0.753	0.918	0.834	0.753	0.918	CLONAL	1	TRUE	1	0.584610064441665	2		447	443	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735548	40735548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1301	215	512	0	ENST00000373198.4:c.3325C>T	p.Arg1109Trp	p.R1109W	ENST00000373198	NM_133170.3	1109	Cgg/Tgg	25/32	0.584610064441665	9	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.584610064441665	9		512	1516	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944498	71944498	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	370	677	0	ENST00000298229.2:c.2054T>C	p.Val685Ala	p.V685A	ENST00000298229	NM_001567.3	685	gTg/gCg	18/28	0.584610064441665	4	FACETS	0.983	0.935	1			1	CLONAL	2	TRUE	NA	0.584610064441665	4		677	1020	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11313949	11313949	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	648	750	0	ENST00000361445.4:c.787G>C	p.Gly263Arg	p.G263R	ENST00000361445	NM_004958.3	263	Gga/Cga	6/58	0.377124941978947	3	FACETS	0.994	0.967	1			1	CLONAL	3	TRUE	NA	0.584610064441665	3		750	961	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344790	65344790	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	85	452	0	ENST00000342505.4:c.247G>C	p.Glu83Gln	p.E83Q	ENST00000342505	NM_002227.2	83	Gag/Cag	4/25	0.570923091762509	3	FACETS	0.675	0.597	0.757	0.337	0.298	0.379	SUBCLONAL	1	TRUE	1	0.584610064441665	3		452	557	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414900	78414900	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	306	479	0	ENST00000370768.2:c.1866A>C	p.Gln622His	p.Q622H	ENST00000370768	NM_003902.3	622	caA/caC	19/20	0.570923091762509	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.584610064441665	3		479	642	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683422	88683422	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	64	250	0	ENST00000372037.3:c.1545G>C	p.Leu515Phe	p.L515F	ENST00000372037	NM_004329.2	515	ttG/ttC	13/13	0.584610064441665	2	FACETS	0.956	0.839	1	0.478	0.419	0.54	CLONAL	1	TRUE	0	0.584610064441665	2		250	229	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943315	71943315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	380	792	1	ENST00000298229.2:c.1647G>A	p.Met549Ile	p.M549I	ENST00000298229	NM_001567.3	549	atG/atA	14/28	0.584610064441665	4	FACETS	0.991	0.943	1			1	CLONAL	2	TRUE	NA	0.584610064441665	4		793	1039	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	493235	493235	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	225	514	0	ENST00000399788.2:c.328G>C	p.Val110Leu	p.V110L	ENST00000399788	NM_001042603.1	110	Gta/Cta	3/28	0.584610064441665	4	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.584610064441665	4		514	955	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624576	21624576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	253	466	0	ENST00000421138.2:c.1453G>A	p.Glu485Lys	p.E485K	ENST00000421138		485	Gaa/Aaa	14/16	0.246086927755403	5	FACETS	1	0.987	1	0.778	0.732	0.825	INDETERMINATE	2	TRUE	2	0.584610064441665	5		466	696	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488253	56488253	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	347	672	0	ENST00000267101.3:c.1772A>C	p.His591Pro	p.H591P	ENST00000267101	NM_001982.3	591	cAt/cCt	15/28	0.550342011774434	3	FACETS	0.965	0.919	1	0.965	0.919	1	CLONAL	2	TRUE	1	0.584610064441665	3		672	795	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69202996	69202996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	325	496	0	ENST00000462284.1:c.23G>A	p.Cys8Tyr	p.C8Y	ENST00000462284	NM_002392.5	8	tGc/tAc	2/11	0.584610064441665	4	FACETS	1	0.953	1			1	CLONAL	2	TRUE	NA	0.584610064441665	4		496	876	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947524	48947553	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTTTTATCCCCTCTAGGACTGTTATGAAC	ATTTTTATCCCCTCTAGGACTGTTATGAAC	-	novel	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	64	369	0	ENST00000267163.4:c.1128-16_1141del		p.X376_splice	ENST00000267163	NM_000321.2	376		12/27	0.584610064441665	1	FACETS	0.659	0.578	0.745	0.659	0.578	0.745	SUBCLONAL	1	TRUE	0	0.584610064441665	1		369	235	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437108	110437109	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATGGA	novel	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	110	148	1	ENST00000375856.3:c.1288_1292dup	p.Met431IlefsTer115	p.M431Ifs*115	ENST00000375856	NM_003749.2	431	atg/atTCCATg	1/2	0.550838601035097	3	FACETS	1	0.973	1			1	CLONAL	2	TRUE	NA	0.584610064441665	3		149	214	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569907	95569907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	213	413	0	ENST00000393063.1:c.3826G>A	p.Asp1276Asn	p.D1276N	ENST00000393063	NM_030621.3	1276	Gat/Aat	22/28	0.570923091762509	3	FACETS	0.932	0.875	0.99	0.932	0.875	0.99	CLONAL	2	TRUE	1	0.584610064441665	3		413	505	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029026	14029026	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	152	262	0	ENST00000311895.7:c.1237G>C	p.Asp413His	p.D413H	ENST00000311895	NM_005236.2	413	Gat/Cat	8/11	0.50165178474891	4	FACETS	0.904	0.834	0.975			1	CLONAL	2	TRUE	NA	0.584610064441665	4		262	456	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618767	37618767	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	357	649	0	ENST00000447079.4:c.443C>G	p.Ser148Trp	p.S148W	ENST00000447079	NM_015083.1	148	tCg/tGg	1/14	0.584610064441665	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.584610064441665	3		649	724	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554066	63554066	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	501	676	1	ENST00000307078.5:c.673C>G	p.Leu225Val	p.L225V	ENST00000307078	NM_004655.3	225	Ctc/Gtc	2/11	0.584610064441665	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	TRUE	1	0.584610064441665	4		677	897	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792336	33792336	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	376	822	0	ENST00000498907.2:c.985G>T	p.Glu329Ter	p.E329*	ENST00000498907	NM_004364.3	329	Gaa/Taa	1/1	0.584610064441665	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.584610064441665	3		822	788	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50138910	50138910	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	406	977	0	ENST00000246792.3:c.580C>G	p.Gln194Glu	p.Q194E	ENST00000246792	NM_006270.3	194	Cag/Gag	6/6	0.246086927755403	5	FACETS	1	0.979	1	0.699	0.665	0.733	INDETERMINATE	2	TRUE	2	0.584610064441665	5		977	1243	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57470677	57470677	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	68	323	0	ENST00000371085.3:c.150A>C	p.Glu50Asp	p.E50D	ENST00000371085	NM_000516.4	50	gaA/gaC	2/13	NA	2	FACETS	0.517	0.451	0.588			1	INDETERMINATE	1	TRUE	NA	0.584610064441665	2		323	450	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29099544	29099544	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555917019	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	237	406	0	ENST00000328354.6:c.857T>C	p.Ile286Thr	p.I286T	ENST00000328354	NM_007194.3	286	aTc/aCc	8/15	0.584610064441665	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.584610064441665	2		406	404	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119545660	119545660	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	130	449	0	ENST00000316626.5:c.1277C>G	p.Ser426Cys	p.S426C	ENST00000316626		426	tCt/tGt	12/12	0.584610064441665	3	FACETS	0.96	0.873	1	0.48	0.436	0.525	CLONAL	1	TRUE	1	0.584610064441665	3		449	599	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963997	2963997	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1562484010	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	111	588	0	ENST00000396946.4:c.1810G>A	p.Asp604Asn	p.D604N	ENST00000396946	NM_032415.4	604	Gac/Aac	15/25	0.584610064441665	2	FACETS	0.764	0.69	0.842	0.382	0.345	0.421	SUBCLONAL	1	TRUE	0	0.584610064441665	2		588	497	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551355	141551355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1386824799	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	187	891	1	ENST00000220592.5:c.1942G>A	p.Glu648Lys	p.E648K	ENST00000220592	NM_012154.3	648	Gag/Aag	15/19	0.372169140501828	4	FACETS	0.869	0.801	0.939	0.434	0.4	0.47	CLONAL	1	TRUE	2	0.584610064441665	4		892	1167	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915940	127915940	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	139	569	0	ENST00000373547.4:c.541C>G	p.Arg181Gly	p.R181G	ENST00000373547	NM_002721.4	181	Cgg/Ggg	6/7	0.584610064441665	3	FACETS	0.858	0.783	0.937	0.429	0.391	0.469	CLONAL	1	TRUE	1	0.584610064441665	3		569	716	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759700	133759700	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	129	679	0	ENST00000318560.5:c.2023G>C	p.Glu675Gln	p.E675Q	ENST00000318560	NM_005157.4	675	Gag/Cag	11/11	0.584610064441665	3	FACETS	0.973	0.886	1	0.487	0.443	0.533	CLONAL	1	TRUE	1	0.584610064441665	3		679	586	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781278	135781278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	331	626	0	ENST00000298552.3:c.1687G>A	p.Asp563Asn	p.D563N	ENST00000298552	NM_001162426.1	563	Gat/Aat	15/23	0.584610064441665	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.584610064441665	3		626	680	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912188	114912188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043314-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	41	522	0	ENST00000543371.1:c.1258C>T	p.Arg420Trp	p.R420W	ENST00000543371	NM_001198531.1	420	Cgg/Tgg	11/14	0.747868808024208	1	FACETS	0.107	0.089	0.128	0.107	0.089	0.128	SUBCLONAL	1	TRUE	0	0.747868808024208	1		522	640	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303676	30303676	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043314-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	54	529	0	ENST00000262643.3:c.104T>C	p.Val35Ala	p.V35A	ENST00000262643	NM_001238.2	35	gTg/gCg	3/12	1	2	FACETS	0.145	0.123	0.169	0.145	0.123	0.169	SUBCLONAL	1	TRUE	1	0.747868808024208	2		529	999	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538993	187538993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043314-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	44	489	0	ENST00000441802.2:c.8747C>T	p.Pro2916Leu	p.P2916L	ENST00000441802	NM_005245.3	2916	cCa/cTa	10/27	1	2	FACETS	0.142	0.118	0.168	0.142	0.118	0.168	SUBCLONAL	1	TRUE	1	0.747868808024208	2		489	828	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43772110	43772110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756804341	NA	P-0043335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	229	662	0	ENST00000382044.4:c.605C>T	p.Ser202Leu	p.S202L	ENST00000382044	NM_001141980.1	202	tCa/tTa	6/28	0.250351799993739	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.375428614649537	1		662	935	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946381	71946463	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCAACAGTTCCTGACCTTCCTATCCCACCGTGGCGAGGAGACAGGCAATATCAGAGGCTCCATGAAGGTGCGGGTGCCCAC	GCCCAACAGTTCCTGACCTTCCTATCCCACCGTGGCGAGGAGACAGGCAATATCAGAGGCTCCATGAAGGTGCGGGTGCCCAC	-	novel	NA	P-0043335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	120	795	0	ENST00000298229.2:c.2546_2628del	p.Ala849GlyfsTer7	p.A849Gfs*7	ENST00000298229	NM_001567.3	849	GCCCAACAGTTCCTGACCTTCCTATCCCACCGTGGCGAGGAGACAGGCAATATCAGAGGCTCCATGAAGGTGCGGGTGCCCACg/g	23/28	0.375428614649537	1	FACETS	0.764	0.691	0.84	0.764	0.691	0.84	SUBCLONAL	1	TRUE	0	0.375428614649537	1		795	680	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658344	18658344	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs764493941	NA	P-0043335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	114	437	0	ENST00000266497.5:c.3149T>C	p.Ile1050Thr	p.I1050T	ENST00000266497		1050	aTt/aCt	22/31	1	2	FACETS	0.901	0.812	0.995	0.901	0.812	0.995	CLONAL	1	TRUE	1	0.375428614649537	2		437	674	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821063	72821063	+	stop_lost	Nonstop_Mutation	SNP	T	T	A	novel	NA	P-0043335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	224	581	0	ENST00000268489.5:c.11112A>T	p.Ter3704TyrextTer10	p.*3704Yext*10	ENST00000268489	NM_006885.3	3704	taA/taT	10/10	0.191071332669404	3	FACETS	0.77	0.718	0.824	0.77	0.718	0.824	INDETERMINATE	2	TRUE	1	0.375428614649537	3		581	920	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578320	7578464	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGGGACCCTGGGCAACCAGCCCTGTCGTCTCTCCAGCCCCAGCTGCTCACCATCGCTATCTGAGCAGCGCTCATGGTGGGGGCAGCGCCTCACAACCTCCGTCATGTGCTGTGACTGCTTGTAGATGGCCATGGCGCGGACGCG	TGGGGACCCTGGGCAACCAGCCCTGTCGTCTCTCCAGCCCCAGCTGCTCACCATCGCTATCTGAGCAGCGCTCATGGTGGGGGCAGCGCCTCACAACCTCCGTCATGTGCTGTGACTGCTTGTAGATGGCCATGGCGCGGACGCG	-	novel	NA	P-0043335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	189	567	0	ENST00000269305.4:c.466_560-31del		p.X156_splice	ENST00000269305	NM_001126112.2	156		5/11	0.375428614649537	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.375428614649537	1		567	551	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905095	50905095	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	81	668	0	ENST00000440232.2:c.377G>T	p.Arg126Leu	p.R126L	ENST00000440232	NM_002691.3	126	cGc/cTc	4/27	1	2	FACETS	0.6	0.528	0.677	0.6	0.528	0.677	SUBCLONAL	1	TRUE	1	0.375428614649537	2		668	719	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543672	29543672	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	135	631	0	ENST00000389048.3:c.1491C>A	p.His497Gln	p.H497Q	ENST00000389048	NM_004304.4	497	caC/caA	7/29	1	2	FACETS	0.89	0.809	0.975	0.89	0.809	0.975	CLONAL	1	TRUE	1	0.375428614649537	2		631	808	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248766	212248766	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	58	282	0	ENST00000342788.4:c.3501G>C	p.Glu1167Asp	p.E1167D	ENST00000342788	NM_005235.2	1167	gaG/gaC	28/28	0.375428614649537	1	FACETS	0.857	0.742	0.98	0.857	0.742	0.98	CLONAL	1	TRUE	0	0.375428614649537	1		282	293	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946421	2946421	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	136	710	0	ENST00000396946.4:c.3316A>C	p.Lys1106Gln	p.K1106Q	ENST00000396946	NM_032415.4	1106	Aag/Cag	25/25	0.375428614649537	1	FACETS	0.928	0.847	1	0.928	0.847	1	CLONAL	1	TRUE	0	0.375428614649537	1		710	634	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633371	8633371	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	104	544	0	ENST00000356435.5:c.298G>C	p.Ala100Pro	p.A100P	ENST00000356435		100	Gcc/Ccc	3/35	0.375428614649537	3	FACETS	0.823	0.736	0.914	0.411	0.368	0.457	CLONAL	1	TRUE	1	0.375428614649537	3		544	800	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639988	93639988	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	157	412	0	ENST00000375746.1:c.1317C>A	p.Cys439Ter	p.C439*	ENST00000375746	NM_001174167.1	439	tgC/tgA	10/14	0.330137668928486	2	FACETS	0.911	0.842	0.982	0.911	0.842	0.982	CLONAL	2	TRUE	0	0.375428614649537	2		412	459	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410088	139410088	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	212	742	0	ENST00000277541.6:c.1750G>T	p.Val584Phe	p.V584F	ENST00000277541	NM_017617.3	584	Gtc/Ttc	11/34	0.330137668928486	2	FACETS	0.829	0.774	0.886	0.829	0.774	0.886	CLONAL	2	TRUE	0	0.375428614649537	2		742	681	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593584	55593598	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	ACCCATGTATGAAGT	ACCCATGTATGAAGT	-	rs587776804	NA	P-0043343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	153	413	0	ENST00000288135.5:c.1652_1666del	p.Pro551_Val555del	p.P551_V555del	ENST00000288135	NM_000222.2	550	aaACCCATGTATGAAGTa/aaa	11/21	1	2	FACETS	0.794	0.732	0.858	0.794	0.732	0.858	SUBCLONAL	1	TRUE	1	0.79440776683242	2		413	485	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0043353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	318	696	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.236442158973855	5	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	TRUE	2	0.294285710303108	5		696	1004	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912655	NA	P-0043353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	164	584	0	ENST00000269305.4:c.725G>C	p.Cys242Ser	p.C242S	ENST00000269305	NM_001126112.2	242	tGc/tCc	7/11	1	2	FACETS	0.79	0.728	0.856	1	0.99	1	SUBCLONAL	2	TRUE	1	0.294285710303108	2		584	705	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247920	59247920	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	146	724	0	ENST00000371222.2:c.823G>T	p.Glu275Ter	p.E275*	ENST00000371222	NM_002228.3	275	Gag/Tag	1/1	0.294285710303108	3	FACETS	1	0.961	1	0.548	0.5	0.6	CLONAL	1	TRUE	1	0.294285710303108	3		724	1038	SUCCESS
FH	2271	MSKCC	GRCh37	1	241661202	241661202	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1391195810	NA	P-0043353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	51	562	0	ENST00000366560.3:c.1459A>G	p.Ile487Val	p.I487V	ENST00000366560	NM_000143.3	487	Atc/Gtc	10/10	0.294285710303108	3	FACETS	0.489	0.414	0.572	0.245	0.207	0.286	SUBCLONAL	1	TRUE	1	0.294285710303108	3		562	813	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112565	115112565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1214834962	NA	P-0043353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	95	652	0	ENST00000257566.3:c.1175C>T	p.Ala392Val	p.A392V	ENST00000257566	NM_016569.3	392	gCg/gTg	7/8	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.294285710303108	2		652	631	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42842662	42842663	+	missense_variant	Missense_Mutation	DNP	TC	TC	CA	novel	NA	P-0043353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	44	558	2	ENST00000398585.3:c.1194_1195delinsTG	p.Lys399Glu	p.K399E	ENST00000398585	NM_001135099.1	398	gtGAaa/gtTGaa	11/14	0.294285710303108	3	FACETS	0.476	0.398	0.563	0.238	0.199	0.282	SUBCLONAL	1	TRUE	1	0.294285710303108	3		560	720	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584469	52584469	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	95	502	0	ENST00000394830.3:c.4544del	p.Asn1515ThrfsTer32	p.N1515Tfs*32	ENST00000394830	NM_018313.4	1515	aAc/ac	29/30	0.218374767775969	2	FACETS	1	0.959	1	0.576	0.514	0.642	CLONAL	1	TRUE	0	0.294285710303108	2		502	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0043367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	287	651	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.436103183712875	2	FACETS	0.92	0.871	0.971	0.92	0.871	0.971	CLONAL	2	TRUE	0	0.436103183712875	2		651	715	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0043367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	142	264	0				ENST00000310581	NM_198253.2	-/1132			0.130742124552471	6	FACETS	0.854	0.784	0.926	0.854	0.784	0.926	INDETERMINATE	3	TRUE	3	0.436103183712875	6		264	476	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670527	134670527	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	161	688	0	ENST00000398015.3:c.438C>A	p.Phe146Leu	p.F146L	ENST00000398015	NM_004441.4	146	ttC/ttA	3/16	0.329632124042203	3	FACETS	1	0.983	1	0.628	0.577	0.681	CLONAL	1	TRUE	1	0.436103183712875	3		688	716	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0043374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	147	302	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.926	0.851	1	0.926	0.851	1	CLONAL	1	TRUE	1	0.629997300678552	2		302	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0043374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	431	915	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	NA	2	FACETS	0.936	0.901	0.97			1	INDETERMINATE	2	TRUE	NA	0.629997300678552	2		915	731	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085729	16085729	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	192	489	0	ENST00000281043.3:c.905G>T	p.Arg302Leu	p.R302L	ENST00000281043	NM_005378.4	302	cGt/cTt	3/3	1	2	FACETS	0.871	0.808	0.935	0.871	0.808	0.935	CLONAL	1	TRUE	1	0.629997300678552	2		489	700	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725019	162725019	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	336	352	0	ENST00000367921.3:c.491T>C	p.Val164Ala	p.V164A	ENST00000367921	NM_006182.2	164	gTc/gCc	6/18	0.629997300678552	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.629997300678552	3		352	674	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427974	49427974	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	195	550	0	ENST00000301067.7:c.10616G>T	p.Arg3539Leu	p.R3539L	ENST00000301067	NM_003482.3	3539	cGg/cTg	38/54	1	2	FACETS	0.878	0.816	0.942	0.878	0.816	0.942	CLONAL	1	TRUE	1	0.629997300678552	2		550	705	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120864	115120864	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	172	448	0	ENST00000257566.3:c.142C>A	p.Pro48Thr	p.P48T	ENST00000257566	NM_016569.3	48	Ccc/Acc	1/8	1	2	FACETS	0.925	0.856	0.997	0.925	0.856	0.997	CLONAL	1	TRUE	1	0.629997300678552	2		448	590	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690606	88690606	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	153	339	0	ENST00000360948.2:c.424C>G	p.Leu142Val	p.L142V	ENST00000360948	NM_001012338.2	142	Ctc/Gtc	5/19	1	2	FACETS	0.968	0.891	1	0.968	0.891	1	CLONAL	1	TRUE	1	0.629997300678552	2		339	502	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218444	1218444	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	270	497	0	ENST00000326873.7:c.319del	p.His107ThrfsTer22	p.H107Tfs*22	ENST00000326873	NM_000455.4	107	Cac/ac	2/10	0.629997300678552	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.629997300678552	1		497	520	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602629	10602635	+	frameshift_variant	Frame_Shift_Del	DEL	TCACCTG	TCACCTG	-	novel	NA	P-0043374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	399	548	0	ENST00000171111.5:c.943_949del	p.Gln315CysfsTer11	p.Q315Cfs*11	ENST00000171111	NM_203500.1	315	CAGGTGAtg/tg	3/6	0.629997300678552	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.629997300678552	1		548	706	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917752	29917752	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	242	553	0	ENST00000389048.3:c.916G>T	p.Gly306Trp	p.G306W	ENST00000389048	NM_004304.4	306	Ggg/Tgg	3/29	NA	2	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.629997300678552	2		553	718	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31393146	31393146	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	111	269	0	ENST00000328111.2:c.2234C>T	p.Pro745Leu	p.P745L	ENST00000328111	NM_006892.3	745	cCc/cTc	21/23	1	2	FACETS	0.874	0.792	0.96	0.874	0.792	0.96	CLONAL	1	TRUE	1	0.629997300678552	2		269	403	SUCCESS
APC	324	MSKCC	GRCh37	5	112170726	112170726	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	169	390	1	ENST00000257430.4:c.1822G>A	p.Ala608Thr	p.A608T	ENST00000257430	NM_000038.5	608	Gct/Act	15/16	1	2	FACETS	0.897	0.829	0.968	0.897	0.829	0.968	CLONAL	1	TRUE	1	0.629997300678552	2		391	598	SUCCESS
APC	324	MSKCC	GRCh37	5	112170808	112170808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881239	NA	P-0043374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	182	425	0	ENST00000257430.4:c.1904G>A	p.Gly635Glu	p.G635E	ENST00000257430	NM_000038.5	635	gGa/gAa	15/16	1	2	FACETS	0.882	0.817	0.949	0.882	0.817	0.949	CLONAL	1	TRUE	1	0.629997300678552	2		425	655	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513541	149513541	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	199	498	1	ENST00000261799.4:c.662T>A	p.Val221Glu	p.V221E	ENST00000261799	NM_002609.3	221	gTg/gAg	5/23	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.629997300678552	2		499	601	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165215	32165215	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	467	595	0	ENST00000375023.3:c.4913T>A	p.Leu1638Gln	p.L1638Q	ENST00000375023	NM_004557.3	1638	cTg/cAg	27/30	0.536485409754528	3	FACETS	0.912	0.874	0.95	0.912	0.874	0.95	CLONAL	2	TRUE	1	0.629997300678552	3		595	1069	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0043375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	133	430	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.112852174532705	4	FACETS	1	0.982	1	0.673	0.61	0.739	INDETERMINATE	1	TRUE	2	0.239433894001255	4		430	1023	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0043375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	150	757	0	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	0.239433894001255	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.239433894001255	1		757	862	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000406	42000406	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	36	202	0	ENST00000219905.7:c.2425G>A	p.Gly809Ser	p.G809S	ENST00000219905	NM_001164273.1	809	Ggt/Agt	7/24	0.22951721326842	1	FACETS	0.793	0.653	0.948	0.793	0.653	0.948	CLONAL	1	TRUE	0	0.239433894001255	1		202	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1427441061	NA	P-0043379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	1311	519	0	ENST00000269305.4:c.560-2A>G		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.786067027873274	6	FACETS	1	0.996	1			1	CLONAL	6	TRUE	NA	0.786067027873274	6		519	1416	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911614	114911614	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	232	445	0	ENST00000543371.1:c.1132G>A	p.Ala378Thr	p.A378T	ENST00000543371	NM_001198531.1	378	Gcg/Acg	10/14	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.786067027873274	2		445	529	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99136537	99136537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746072331	NA	P-0043379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	251	583	1	ENST00000074304.5:c.26G>A	p.Arg9His	p.R9H	ENST00000074304	NM_001134224.1	9	cGc/cAc	3/26	0.609948198838163	4	FACETS	1	0.97	1	0.532	0.497	0.567	CLONAL	1	TRUE	2	0.786067027873274	4		584	1073	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165681	108165681	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	84	242	1	ENST00000278616.4:c.4804G>T	p.Val1602Phe	p.V1602F	ENST00000278616	NM_000051.3	1602	Gtt/Ttt	32/63	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.786067027873274	2		243	206	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107086	27107094	+	inframe_deletion	In_Frame_Del	DEL	CGGGCTGCC	CGGGCTGCC	-	novel	NA	P-0043379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	211	395	0	ENST00000324856.7:c.6699_6707del	p.Ala2235_Ala2237del	p.A2235_A2237del	ENST00000324856	NM_006015.4	2233	CGGGCTGCC/-	20/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.786067027873274	2		395	517	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106215	2106218	+	frameshift_variant	Frame_Shift_Del	DEL	CGTC	CGTC	-	novel	NA	P-0043379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	317	670	0	ENST00000219476.3:c.620_623del	p.Val207GlyfsTer8	p.V207Gfs*8	ENST00000219476	NM_000548.3	206	tgCGTC/tg	7/42	0.786067027873274	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.786067027873274	1		670	474	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777990	3777990	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	35	858	0	ENST00000262367.5:c.7058G>C	p.Arg2353Pro	p.R2353P	ENST00000262367	NM_004380.2	2353	cGg/cCg	31/31	0.786067027873274	1	FACETS	0.086	0.07	0.105	0.086	0.07	0.105	SUBCLONAL	1	TRUE	0	0.786067027873274	1		858	625	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248626	10248626	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	200	560	0	ENST00000340748.4:c.4127A>T	p.Glu1376Val	p.E1376V	ENST00000340748		1376	gAg/gTg	35/40	0.181202604915416	3	FACETS	0.987	0.918	1	0.329	0.306	0.353	INDETERMINATE	1	TRUE	0	0.786067027873274	3		560	718	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0043492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	61	379	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	0.26578400309257	2	FACETS	0.801	0.7	0.907	0.801	0.7	0.907	CLONAL	2	TRUE	0	0.338592529376608	2		379	225	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121913370	NA	P-0043492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	68	244	0	ENST00000288602.6:c.1742A>G	p.Asn581Ser	p.N581S	ENST00000288602	NM_004333.4	581	aAt/aGt	15/18	0.338592529376608	3	FACETS	0.987	0.87	1	0.987	0.87	1	CLONAL	2	TRUE	1	0.338592529376608	3		244	238	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386318	31386318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747146892	NA	P-0043492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	229	658	0	ENST00000328111.2:c.1543G>A	p.Glu515Lys	p.E515K	ENST00000328111	NM_006892.3	515	Gag/Aag	15/23	0.215196368333291	3	FACETS	0.999	0.933	1	0.999	0.933	1	CLONAL	2	TRUE	1	0.338592529376608	3		658	792	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0043499-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	60	414	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.194341492635895	3	FACETS	1	0.926	1	0.554	0.479	0.635	CLONAL	1	TRUE	1	0.322144199966135	3		414	390	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207162	1207162	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs137853076	NA	P-0043499-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	251	753	0	ENST00000326873.7:c.250A>T	p.Lys84Ter	p.K84*	ENST00000326873	NM_000455.4	84	Aag/Tag	1/10	0.322144199966135	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.322144199966135	1		753	1243	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0043499-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	94	684	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.322144199966135	1	FACETS	0.643	0.572	0.719	0.643	0.572	0.719	SUBCLONAL	1	TRUE	0	0.322144199966135	1		684	761	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334734	81334734	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043499-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	27	463	0	ENST00000222390.5:c.1982C>A	p.Ala661Asp	p.A661D	ENST00000222390	NM_000601.4	661	gCt/gAt	17/18	1	2	FACETS	0.514	0.409	0.634	0.514	0.409	0.634	SUBCLONAL	1	TRUE	1	0.322144199966135	2		463	326	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610112	10610113	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0043499-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	155	591	0	ENST00000171111.5:c.597dup	p.His200AlafsTer150	p.H200Afs*150	ENST00000171111	NM_203500.1	199	-/G	2/6	0.322144199966135	1	FACETS	0.741	0.677	0.808	0.741	0.677	0.808	SUBCLONAL	1	TRUE	0	0.322144199966135	1		591	1090	SUCCESS
APC	324	MSKCC	GRCh37	5	112175657	112175660	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	novel	NA	P-0043499-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	78	340	0	ENST00000257430.4:c.4366_4369del	p.Lys1456HisfsTer16	p.K1456Hfs*16	ENST00000257430	NM_000038.5	1456	AAAGca/ca	16/16	0.322144199966135	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	0	0.322144199966135	1		340	396	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908204	28908204	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0043499-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	87	450	0	ENST00000282397.4:c.2551A>T	p.Lys851Ter	p.K851*	ENST00000282397	NM_002019.4	851	Aaa/Taa	18/30	1	2	FACETS	0.81	0.717	0.909	0.81	0.717	0.909	CLONAL	1	TRUE	1	0.322144199966135	2		450	667	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610669	81610669	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043499-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	48	377	0	ENST00000298171.2:c.2267C>A	p.Ser756Ter	p.S756*	ENST00000298171	NM_000369.2	756	tCa/tAa	10/10	1	2	FACETS	0.69	0.584	0.806	0.69	0.584	0.806	SUBCLONAL	1	TRUE	1	0.322144199966135	2		377	432	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0043502-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	80	414	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.305626583287492	2	FACETS	0.826	0.735	0.921	0.826	0.735	0.921	CLONAL	2	TRUE	0	0.329584327469167	2		414	294	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039371	47039371	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043502-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	63	648	0	ENST00000377604.3:c.994C>T	p.Arg332Cys	p.R332C	ENST00000377604	NM_001204468.1	332	Cgc/Tgc	10/24	0.27204296191783	3	FACETS	0.701	0.606	0.805	0.351	0.303	0.403	SUBCLONAL	1	TRUE	1	0.329584327469167	3		648	635	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220371	1220372	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0043502-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	119	409	0	ENST00000326873.7:c.465-1_465delinsTT		p.X155_splice	ENST00000326873	NM_000455.4	155		4/10	0.3156564707405	2	FACETS	0.864	0.786	0.945	0.864	0.786	0.945	CLONAL	2	TRUE	0	0.329584327469167	2		409	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0043502-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	160	501	1	ENST00000269305.4:c.560-2A>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.305626583287492	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.329584327469167	2		502	450	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805306	89805306	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs201658945	NA	P-0043502-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	141	491	0	ENST00000389301.3:c.4244T>G	p.Phe1415Cys	p.F1415C	ENST00000389301	NM_000135.2	1415	tTc/tGc	42/43	0.305626583287492	2	FACETS	0.891	0.818	0.967	0.891	0.818	0.967	CLONAL	2	TRUE	0	0.329584327469167	2		491	480	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652396	48652396	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs202091014	NA	P-0043502-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	95	696	0	ENST00000376670.3:c.1067G>T	p.Gly356Val	p.G356V	ENST00000376670	NM_002049.3	356	gGc/gTc	6/6	0.27204296191783	3	FACETS	0.924	0.822	1	0.462	0.411	0.516	CLONAL	1	TRUE	1	0.329584327469167	3		696	727	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357208	70357208	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043502-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	138	504	0	ENST00000374080.3:c.5723G>T	p.Gly1908Val	p.G1908V	ENST00000374080		1908	gGa/gTa	39/45	0.27204296191783	3	FACETS	0.774	0.707	0.845	0.774	0.707	0.845	SUBCLONAL	2	TRUE	1	0.329584327469167	3		504	630	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220447	123220447	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043502-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	86	415	0	ENST00000218089.9:c.3104A>C	p.Glu1035Ala	p.E1035A	ENST00000218089	NM_001042749.1	1035	gAg/gCg	30/35	0.27204296191783	3	FACETS	1	0.964	1	0.608	0.539	0.681	CLONAL	1	TRUE	1	0.329584327469167	3		415	500	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0043503-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	257	406	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.316325997573214	3	FACETS	0.848	0.801	0.895	0.848	0.801	0.895	CLONAL	3	TRUE	0	0.419063010356392	3		406	583	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0043503-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	176	321	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.419063010356392	3	FACETS	0.853	0.796	0.91	0.853	0.796	0.91	CLONAL	3	TRUE	0	0.419063010356392	3		321	397	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0043503-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	251	777	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.304977197963664	3	FACETS	1	0.981	1	0.732	0.689	0.775	CLONAL	2	TRUE	0	0.419063010356392	3		777	660	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144180	11144180	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043503-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	233	687	0	ENST00000358026.2:c.3761A>C	p.Glu1254Ala	p.E1254A	ENST00000358026	NM_001128849.1	1254	gAg/gCg	26/36	0.357601195455673	4	FACETS	0.847	0.79	0.904	0.847	0.79	0.904	CLONAL	2	TRUE	2	0.419063010356392	4		687	932	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033955	49033955	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043503-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	112	312	0	ENST00000267163.4:c.2092A>G	p.Arg698Gly	p.R698G	ENST00000267163	NM_000321.2	698	Agg/Ggg	20/27	0.355498474261109	2	FACETS	0.817	0.744	0.893	0.817	0.744	0.893	CLONAL	2	TRUE	0	0.419063010356392	2		312	327	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174417	11174417	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043503-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	348	690	0	ENST00000361445.4:c.7258G>C	p.Ala2420Pro	p.A2420P	ENST00000361445	NM_004958.3	2420	Gcc/Ccc	53/58	0.358136882532659	4	FACETS	0.91	0.866	0.955	0.91	0.866	0.955	CLONAL	3	TRUE	1	0.419063010356392	4		690	863	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396471	30396471	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043503-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	166	456	1	ENST00000331968.5:c.248C>A	p.Ser83Tyr	p.S83Y	ENST00000331968	NM_002742.2	83	tCc/tAc	1/18	0.419063010356392	7	FACETS	0.973	0.894	1			1	CLONAL	2	TRUE	NA	0.419063010356392	7		457	834	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873209	136873209	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1333957805	NA	P-0043503-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	36	331	0	ENST00000241393.3:c.289G>A	p.Asp97Asn	p.D97N	ENST00000241393	NM_003467.2	97	Gat/Aat	2/2	0.419063010356392	3	FACETS	0.537	0.442	0.643	0.268	0.221	0.322	SUBCLONAL	1	TRUE	1	0.419063010356392	3		331	387	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0043504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	42	631	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	1	2	FACETS	0.64	0.535	0.756	0.64	0.535	0.756	SUBCLONAL	1	TRUE	1	0.325537329179764	2		631	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0043504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	120	580	0	ENST00000269305.4:c.672+1G>C		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.261010374842595	1	FACETS	0.834	0.754	0.919	0.834	0.754	0.919	CLONAL	1	TRUE	0	0.325537329179764	1		580	740	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645945	215645945	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	70	421	0	ENST00000260947.4:c.653G>C	p.Trp218Ser	p.W218S	ENST00000260947	NM_000465.2	218	tGg/tCg	4/11	1	2	FACETS	0.71	0.619	0.808	0.71	0.619	0.808	SUBCLONAL	1	TRUE	1	0.325537329179764	2		421	606	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412506	63412506	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	82	538	0	ENST00000330258.3:c.661T>A	p.Phe221Ile	p.F221I	ENST00000330258	NM_152424.3	221	Ttc/Atc	2/2	0.325537329179764	1	FACETS	0.671	0.592	0.755	0.671	0.592	0.755	SUBCLONAL	1	TRUE	0	0.325537329179764	1		538	629	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0043646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	39	214	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.578	0.477	0.691	0.578	0.477	0.691	SUBCLONAL	1	TRUE	1	0.18	2		214	750	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220691	1220691	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs878853247	NA	P-0043646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	125	838	0	ENST00000326873.7:c.709G>T	p.Asp237Tyr	p.D237Y	ENST00000326873	NM_000455.4	237	Gac/Tac	5/10	0.3	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.18	1		838	924	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957880	1957880	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	105	519	0	ENST00000382891.5:c.2846A>G	p.Gln949Arg	p.Q949R	ENST00000382891	NM_133335.3	949	cAg/cGg	15/22	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.18	2		519	860	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039651	47039651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	82	797	0	ENST00000377604.3:c.1103C>T	p.Pro368Leu	p.P368L	ENST00000377604	NM_001204468.1	368	cCa/cTa	11/24	1	2	FACETS	0.997	0.877	1	0.997	0.877	1	CLONAL	1	TRUE	1	0.18	2		797	914	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0043654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	85	395	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.569735299597252	2		396	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0043654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	544	352	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.567067015454075	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.569735299597252	2		353	900	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875983	76875983	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	81	96	0	ENST00000373344.5:c.5152T>C	p.Cys1718Arg	p.C1718R	ENST00000373344	NM_000489.3	1718	Tgt/Cgt	20/35	1	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.569735299597252	1		96	161	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043672-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	92	82	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.873	0.782	0.969	0.873	0.782	0.969	CLONAL	1	TRUE	1	0.563465081846511	2		82	374	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0043672-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	866	459	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.563465081846511	8	FACETS	1	0.989	1			1	CLONAL	7	TRUE	NA	0.563465081846511	8		459	1162	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944555	40944555	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043672-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	128	408	0	ENST00000373198.4:c.1947del	p.Val650Ter	p.V650*	ENST00000373198	NM_133170.3	649	ccC/cc	12/32	0.51815698820631	3	FACETS	1	0.953	1	0.536	0.488	0.586	CLONAL	1	TRUE	1	0.563465081846511	3		408	543	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509761	106509761	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043672-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	116	485	0	ENST00000359195.3:c.1757del	p.Pro586GlnfsTer11	p.P586Qfs*11	ENST00000359195	NM_002649.2	585	caC/ca	2/11	0.563465081846511	3	FACETS	0.867	0.783	0.954	0.433	0.391	0.477	CLONAL	1	TRUE	1	0.563465081846511	3		485	609	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0043695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	332	810	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.395005014399995	3	FACETS	0.884	0.843	0.926	0.884	0.843	0.926	CLONAL	3	TRUE	0	0.449472280609514	3		810	682	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400774	72400774	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	820	237	0	ENST00000357731.5:c.397C>G	p.Leu133Val	p.L133V	ENST00000357731	NM_173808.2	133	Cta/Gta	2/7	0.449472280609514	7	FACETS	0.941	0.919	0.963			1	CLONAL	7	TRUE	NA	0.449472280609514	7		237	1176	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052632	42052632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779811318	NA	P-0043699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	99	347	0	ENST00000219905.7:c.7303C>T	p.Arg2435Trp	p.R2435W	ENST00000219905	NM_001164273.1	2435	Cgg/Tgg	20/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.448757372521567	2		347	363	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711910	89711910	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs1057522285	NA	P-0043699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	65	372	0	ENST00000371953.3:c.528T>G	p.Tyr176Ter	p.Y176*	ENST00000371953	NM_000314.4	176	taT/taG	6/9	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	1	0.448757372521567	2		372	265	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057904	27057904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	103	593	0	ENST00000324856.7:c.1612C>T	p.Gln538Ter	p.Q538*	ENST00000324856	NM_006015.4	538	Cag/Tag	3/20	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		593	572	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	81	82	0				ENST00000310581	NM_198253.2	-/1132			0.251203515268978	0	FACETS	0.481	0.428	0.535			1	INDETERMINATE	1	FALSE	0	0.548015519118291	0		82	278	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0043726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	143	473	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.460399750317434	3	FACETS	1	0.949	1	0.526	0.481	0.573	CLONAL	1	FALSE	1	0.548015519118291	3		473	632	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562657	29562660	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs1064794276	NA	P-0043726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	136	404	0	ENST00000356175.3:c.3739_3742del	p.Phe1247IlefsTer18	p.F1247Ifs*18	ENST00000356175	NM_000267.3	1246	cTGTTt/ct	28/57	0.548015519118291	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	FALSE	0	0.548015519118291	1		404	358	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467924	50467924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	115	473	0	ENST00000331340.3:c.1159G>A	p.Glu387Lys	p.E387K	ENST00000331340	NM_006060.4	387	Gag/Aag	8/8	0.460399750317434	3	FACETS	0.965	0.873	1	0.483	0.436	0.531	CLONAL	1	FALSE	1	0.548015519118291	3		473	554	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591125	67591125	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	85	327	0	ENST00000274335.5:c.1718T>C	p.Leu573Pro	p.L573P	ENST00000274335		573	cTg/cCg	12/15	1	2	FACETS	0.806	0.717	0.899	0.806	0.717	0.899	CLONAL	1	FALSE	1	0.548015519118291	2		327	385	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508065	106508065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1326957848	NA	P-0043726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	55	194	2	ENST00000359195.3:c.59G>A	p.Arg20His	p.R20H	ENST00000359195	NM_002649.2	20	cGc/cAc	2/11	0.548015519118291	3	FACETS	0.904	0.779	1	0.452	0.389	0.519	CLONAL	1	FALSE	1	0.548015519118291	3		196	283	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593605	55593610	+	inframe_deletion	In_Frame_Del	DEL	GAAGGT	GAAGGT	-	novel	NA	P-0043796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	176	335	0	ENST00000288135.5:c.1671_1676del	p.Trp557_Val559delinsCys	p.W557_V559delinsC	ENST00000288135	NM_000222.2	557	tgGAAGGTt/tgt	11/21	1	2	FACETS	0.724	0.672	0.779	0.724	0.672	0.779	SUBCLONAL	1	TRUE	1	0.888245381947221	2		335	547	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0043815-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	56	414	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.253639819187677	2		414	407	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36014556	36014556	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747298865	NA	P-0043815-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	82	436	0	ENST00000358208.4:c.329G>A	p.Arg110Gln	p.R110Q	ENST00000358208		110	cGg/cAg	3/12	1	2	FACETS	0.863	0.761	0.973	0.863	0.761	0.973	CLONAL	1	TRUE	1	0.253639819187677	2		436	749	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281374	49281374	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043815-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	106	548	0	ENST00000282018.3:c.421G>C	p.Val141Leu	p.V141L	ENST00000282018	NM_020377.2	141	Gtt/Ctt	1/1	1	2	FACETS	0.917	0.821	1	0.917	0.821	1	CLONAL	1	TRUE	1	0.253639819187677	2		548	911	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303038	15303038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765570204	NA	P-0043815-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	91	588	2	ENST00000263388.2:c.412C>T	p.Pro138Ser	p.P138S	ENST00000263388	NM_000435.2	138	Ccc/Tcc	4/33	1	2	FACETS	0.931	0.826	1	0.931	0.826	1	CLONAL	1	TRUE	1	0.253639819187677	2		590	771	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703527	47703527	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1057520735	NA	P-0043815-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	46	367	0	ENST00000233146.2:c.2027C>G	p.Ser676Ter	p.S676*	ENST00000233146	NM_000251.2	676	tCa/tGa	13/16	1	2	FACETS	0.773	0.652	0.908	0.773	0.652	0.908	CLONAL	1	TRUE	1	0.253639819187677	2		367	469	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602619	10602619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1174	85	586	1	ENST00000171111.5:c.959G>A	p.Arg320Gln	p.R320Q	ENST00000171111	NM_203500.1	320	cGg/cAg	3/6	1	2	FACETS	0.9	0.793	1	0.9	0.793	1	CLONAL	1	TRUE	1	0.15	2		587	1259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764146326	NA	P-0043826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1257	109	656	0	ENST00000269305.4:c.841G>T	p.Asp281Tyr	p.D281Y	ENST00000269305	NM_001126112.2	281	Gac/Tac	8/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.15	2		656	1366	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481397	140481397	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913376	NA	P-0043826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	24	316	0	ENST00000288602.6:c.1411G>T	p.Val471Phe	p.V471F	ENST00000288602	NM_004333.4	471	Gtc/Ttc	11/18	1	2	FACETS	0.691	0.541	0.865	0.691	0.541	0.865	SUBCLONAL	1	TRUE	1	0.15	2		316	463	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132644	67132644	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	47	450	0	ENST00000412916.2:c.528del	p.Asn177IlefsTer2	p.N177Ifs*2	ENST00000412916		176	tCc/tc	6/6	1	2	FACETS	0.716	0.602	0.843	0.716	0.602	0.843	SUBCLONAL	1	TRUE	1	0.15	2		450	875	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207074	1207075	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCC	novel	NA	P-0043826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1350	76	670	0	ENST00000326873.7:c.163_164insCCCC	p.Leu55ProfsTer109	p.L55Pfs*109	ENST00000326873	NM_000455.4	54	-/CCCC	1/10	1	2	FACETS	0.711	0.621	0.808	0.711	0.621	0.808	SUBCLONAL	1	TRUE	1	0.15	2		670	1426	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876502	35876502	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	55	429	0	ENST00000303115.3:c.1294G>T	p.Ala432Ser	p.A432S	ENST00000303115	NM_002185.3	432	Gct/Tct	8/8	0.118799691083153	3	FACETS	0.807	0.688	0.938	0.403	0.344	0.469	CLONAL	1	TRUE	1	0.15	3		429	977	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148513801	148513801	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	47	431	0	ENST00000320356.2:c.1480C>G	p.Pro494Ala	p.P494A	ENST00000320356	NM_004456.4	494	Cca/Gca	12/20	1	2	FACETS	0.817	0.688	0.961	0.817	0.688	0.961	CLONAL	1	TRUE	1	0.15	2		431	767	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	259	477	5	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	0.373654068949855	3	FACETS	0.959	0.902	1	0.959	0.902	1	CLONAL	2	TRUE	1	0.442830511179192	3		482	745	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	256	430	9	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.396342708142979	3	FACETS	1	0.988	1	0.774	0.731	0.818	CLONAL	2	TRUE	0	0.442830511179192	3		439	608	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	88	322	2	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	0.373654068949855	3	FACETS	0.952	0.846	1	0.476	0.423	0.532	CLONAL	1	TRUE	1	0.442830511179192	3		324	510	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099982	157099987	+	inframe_deletion	In_Frame_Del	DEL	GGCGGC	GGCGGC	-	rs587779747	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	39	133	0	ENST00000346085.5:c.939_944del	p.Gly318_Gly319del	p.G318_G319del	ENST00000346085	NM_020732.3	307	GGCGGC/-	1/20	0.427967377651104	4	FACETS	1	0.894	1	0.365	0.305	0.431	CLONAL	1	TRUE	1	0.442830511179192	4		133	232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577587	7577587	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	261	485	0	ENST00000269305.4:c.694A>T	p.Ile232Phe	p.I232F	ENST00000269305	NM_001126112.2	232	Atc/Ttc	7/11	0.442830511179192	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.442830511179192	1		485	615	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385177	41385177	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201332786	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	132	565	3	ENST00000373198.4:c.784G>A	p.Val262Ile	p.V262I	ENST00000373198	NM_133170.3	262	Gtc/Atc	6/32	0.425968331205777	5	FACETS	0.819	0.742	0.901	0.273	0.247	0.301	CLONAL	1	TRUE	2	0.442830511179192	5		568	1211	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508499	106508499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752602335	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	127	480	0	ENST00000359195.3:c.493G>A	p.Val165Ile	p.V165I	ENST00000359195	NM_002649.2	165	Gtc/Atc	2/11	0.195277967424021	5	FACETS	1	0.959	1	0.723	0.66	0.788	INDETERMINATE	2	TRUE	2	0.442830511179192	5		480	440	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129329	152129329	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	222	501	0	ENST00000206249.3:c.287del	p.Gly96ValfsTer13	p.G96Vfs*13	ENST00000206249	NM_000125.3	94	ctG/ct	1/8	0.427967377651104	4	FACETS	0.929	0.867	0.992	0.619	0.578	0.661	CLONAL	2	TRUE	1	0.442830511179192	4		501	779	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941696	48941696	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	79	219	3	ENST00000267163.4:c.1010del	p.Leu337TrpfsTer12	p.L337Wfs*12	ENST00000267163	NM_000321.2	336	Ttt/tt	10/27	0.429173303554576	2	FACETS	0.796	0.713	0.883	0.796	0.713	0.883	SUBCLONAL	2	TRUE	0	0.442830511179192	2		222	224	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154242	2154242	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755455183	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	142	618	2	ENST00000434045.2:c.686del	p.Pro229GlnfsTer27	p.P229Qfs*27	ENST00000434045	NM_001127598.1	229	cCa/ca	5/5	NA	2	FACETS	0.902	0.824	0.984			1	INDETERMINATE	1	TRUE	NA	0.442830511179192	2		620	711	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534801	18534801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759595930	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	171	441	0	ENST00000266497.5:c.1859C>T	p.Pro620Leu	p.P620L	ENST00000266497		620	cCg/cTg	12/31	0.0873254922448533	6	FACETS	1	0.967	1	0.725	0.669	0.782	INDETERMINATE	2	TRUE	3	0.442830511179192	6		441	670	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165282	47165283	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	54	300	0	ENST00000409792.3:c.843dup	p.Glu282ArgfsTer9	p.E282Rfs*9	ENST00000409792	NM_014159.6	281	-/A	3/21	0.426965003834812	2	FACETS	0.753	0.646	0.868	0.376	0.323	0.434	SUBCLONAL	1	TRUE	0	0.442830511179192	2		300	324	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073943	8073943	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs116791613	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	97	423	0	ENST00000377482.5:c.716C>T	p.Pro239Leu	p.P239L	ENST00000377482	NM_018948.3	239	cCa/cTa	4/4	0.373654068949855	3	FACETS	0.919	0.822	1	0.46	0.411	0.512	CLONAL	1	TRUE	1	0.442830511179192	3		423	582	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350059	70350059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	94	419	0	ENST00000374080.3:c.4042C>T	p.Leu1348Phe	p.L1348F	ENST00000374080		1348	Ctc/Ttc	28/45	1	2	FACETS	0.806	0.719	0.897	0.806	0.719	0.897	CLONAL	1	TRUE	1	0.442830511179192	2		419	527	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172054	32172054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	159	589	1	ENST00000375023.3:c.2978C>T	p.Ala993Val	p.A993V	ENST00000375023	NM_004557.3	993	gCc/gTc	19/30	1	2	FACETS	0.876	0.803	0.951	0.876	0.803	0.951	CLONAL	1	TRUE	1	0.442830511179192	2		590	820	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149982903	149982903	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	30	310	0	ENST00000253339.5:c.3355G>T	p.Gly1119Cys	p.G1119C	ENST00000253339		1119	Ggc/Tgc	7/7	0.427967377651104	4	FACETS	0.465	0.375	0.569	0.155	0.125	0.19	SUBCLONAL	1	TRUE	1	0.442830511179192	4		310	420	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427506	49427506	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	267	585	3	ENST00000301067.7:c.10982del	p.Gly3661ValfsTer88	p.G3661Vfs*88	ENST00000301067	NM_003482.3	3661	gGt/gt	39/54	0.410851018770177	4	FACETS	0.913	0.857	0.97			1	CLONAL	2	TRUE	NA	0.442830511179192	4		588	953	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210869	36210869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369788045	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	385	723	1	ENST00000222270.7:c.620G>A	p.Arg207Gln	p.R207Q	ENST00000222270	NM_014727.1	207	cGg/cAg	3/37	0.426965003834812	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.442830511179192	2		724	814	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228119	36228119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201885107	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	185	694	0	ENST00000222270.7:c.7505C>T	p.Pro2502Leu	p.P2502L	ENST00000222270	NM_014727.1	2502	cCg/cTg	33/37	0.426965003834812	2	FACETS	1	0.963	1	0.534	0.493	0.575	CLONAL	1	TRUE	0	0.442830511179192	2		694	783	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969982	161969983	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs745647746	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	118	567	0	ENST00000366898.1:c.986dup	p.Val330ArgfsTer17	p.V330Rfs*17	ENST00000366898	NM_004562.2	329	ggc/ggGc	9/12	0.427967377651104	4	FACETS	0.764	0.688	0.845	0.255	0.229	0.282	SUBCLONAL	1	TRUE	1	0.442830511179192	4		567	1006	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469029	25469029	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	52	589	0	ENST00000264709.3:c.1429G>T	p.Glu477Ter	p.E477*	ENST00000264709	NM_175629.2	477	Gag/Tag	11/23	0.0873254922448533	6	FACETS	0.45	0.382	0.526	0.15	0.127	0.176	INDETERMINATE	1	TRUE	3	0.442830511179192	6		589	984	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255206	16255206	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780359509	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	82	384	0	ENST00000375759.3:c.2471G>A	p.Arg824His	p.R824H	ENST00000375759	NM_015001.2	824	cGc/cAc	11/15	0.373654068949855	3	FACETS	0.724	0.639	0.815	0.362	0.319	0.408	SUBCLONAL	1	TRUE	1	0.442830511179192	3		384	625	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106765	27106765	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	118	549	0	ENST00000324856.7:c.6376A>C	p.Ser2126Arg	p.S2126R	ENST00000324856	NM_006015.4	2126	Agc/Cgc	20/20	0.373654068949855	3	FACETS	0.811	0.731	0.895	0.405	0.365	0.448	CLONAL	1	TRUE	1	0.442830511179192	3		549	803	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432633	78432633	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	65	306	0	ENST00000370768.2:c.350G>T	p.Gly117Val	p.G117V	ENST00000370768	NM_003902.3	117	gGc/gTc	6/20	0.373654068949855	3	FACETS	0.927	0.807	1	0.463	0.403	0.528	CLONAL	1	TRUE	1	0.442830511179192	3		306	387	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724632	162724632	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	261	434	0	ENST00000367921.3:c.404G>T	p.Arg135Leu	p.R135L	ENST00000367921	NM_006182.2	135	cGt/cTt	5/18	0.139869863815175	6	FACETS	0.941	0.885	0.999	0.941	0.885	0.999	INDETERMINATE	3	TRUE	3	0.442830511179192	6		434	787	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163325175	163325175	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	96	301	0	ENST00000271452.3:c.1311T>G	p.Ile437Met	p.I437M	ENST00000271452	NM_145697.2	437	atT/atG	14/14	0.139869863815175	6	FACETS	0.935	0.838	1	0.624	0.559	0.692	INDETERMINATE	2	TRUE	3	0.442830511179192	6		301	437	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941938	71941938	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	129	607	0	ENST00000298229.2:c.1296C>A	p.Asn432Lys	p.N432K	ENST00000298229	NM_001567.3	432	aaC/aaA	11/28	0.396342708142979	3	FACETS	0.918	0.833	1	0.306	0.277	0.336	CLONAL	1	TRUE	0	0.442830511179192	3		607	775	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212860	94212860	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	74	315	1	ENST00000323929.3:c.382A>T	p.Asn128Tyr	p.N128Y	ENST00000323929	NM_005591.3	128	Aat/Tat	5/20	0.396342708142979	3	FACETS	1	0.904	1	0.344	0.302	0.388	CLONAL	1	TRUE	0	0.442830511179192	3		316	396	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420109	420109	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	111	457	0	ENST00000399788.2:c.3158G>A	p.Trp1053Ter	p.W1053*	ENST00000399788	NM_001042603.1	1053	tGg/tAg	21/28	NA	2	FACETS	0.53	0.476	0.588			1	INDETERMINATE	1	TRUE	NA	0.442830511179192	2		457	945	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	495103	495103	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	80	387	0	ENST00000399788.2:c.203T>G	p.Phe68Cys	p.F68C	ENST00000399788	NM_001042603.1	68	tTt/tGt	2/28	NA	2	FACETS	0.646	0.57	0.728			1	INDETERMINATE	1	TRUE	NA	0.442830511179192	2		387	559	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433340	49433340	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	312	589	0	ENST00000301067.7:c.8107G>T	p.Glu2703Ter	p.E2703*	ENST00000301067	NM_003482.3	2703	Gag/Tag	32/54	0.410851018770177	4	FACETS	1	0.976	1			1	CLONAL	2	TRUE	NA	0.442830511179192	4		589	962	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256168	133256168	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	153	491	0	ENST00000320574.5:c.493A>G	p.Lys165Glu	p.K165E	ENST00000320574	NM_006231.2	165	Aaa/Gaa	6/49	0.36792095683128	3	FACETS	1	0.937	1	0.514	0.47	0.56	CLONAL	1	TRUE	1	0.442830511179192	3		491	821	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434853	110434853	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	49	448	0	ENST00000375856.3:c.3548G>T	p.Arg1183Met	p.R1183M	ENST00000375856	NM_003749.2	1183	aGg/aTg	1/2	0.429173303554576	2	FACETS	0.342	0.289	0.401	0.171	0.144	0.201	SUBCLONAL	1	TRUE	0	0.442830511179192	2		448	647	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557667	95557667	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	82	413	0	ENST00000393063.1:c.5400G>T	p.Glu1800Asp	p.E1800D	ENST00000393063	NM_030621.3	1800	gaG/gaT	26/28	0.426965003834812	2	FACETS	0.61	0.538	0.687	0.305	0.269	0.344	SUBCLONAL	1	TRUE	0	0.442830511179192	2		413	607	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779278	3779278	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368145743	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	279	515	0	ENST00000262367.5:c.5770G>A	p.Val1924Met	p.V1924M	ENST00000262367	NM_004380.2	1924	Gtg/Atg	31/31	0.42742269571709	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.442830511179192	3		515	736	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831128	72831128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303949536	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	95	453	0	ENST00000268489.5:c.5453C>T	p.Thr1818Ile	p.T1818I	ENST00000268489	NM_006885.3	1818	aCc/aTc	9/10	1	2	FACETS	0.888	0.794	0.988	0.888	0.794	0.988	CLONAL	1	TRUE	1	0.442830511179192	2		453	483	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216983	2216983	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	201	691	0	ENST00000398665.3:c.2438C>A	p.Pro813His	p.P813H	ENST00000398665	NM_032482.2	813	cCc/cAc	21/28	0.442830511179192	3	FACETS	0.968	0.896	1	0.323	0.298	0.348	CLONAL	1	TRUE	0	0.442830511179192	3		691	1146	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602512	10602512	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	299	575	0	ENST00000171111.5:c.1066G>C	p.Ala356Pro	p.A356P	ENST00000171111	NM_203500.1	356	Gcg/Ccg	3/6	0.442830511179192	6	FACETS	0.904	0.849	0.96			1	CLONAL	2	TRUE	NA	0.442830511179192	6		575	1409	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11018757	11018757	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1698	209	659	0	ENST00000327064.4:c.389A>G	p.His130Arg	p.H130R	ENST00000327064	NM_199141.1	130	cAc/cGc	3/16	0.442830511179192	6	FACETS	0.933	0.863	1			1	CLONAL	1	TRUE	NA	0.442830511179192	6		659	1907	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273892	18273892	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	132	603	0	ENST00000222254.8:c.1225T>C	p.Ser409Pro	p.S409P	ENST00000222254	NM_005027.3	409	Tct/Cct	10/16	NA	2	FACETS	0.69	0.626	0.757			1	INDETERMINATE	1	TRUE	NA	0.442830511179192	2		603	864	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872750	136872750	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771851938	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	104	404	0	ENST00000241393.3:c.748G>A	p.Ala250Thr	p.A250T	ENST00000241393	NM_003467.2	250	Gcc/Acc	2/2	0.0873254922448533	6	FACETS	1	0.977	1	0.448	0.401	0.497	INDETERMINATE	1	TRUE	3	0.442830511179192	6		404	659	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743850	40743850	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	87	416	0	ENST00000373198.4:c.3145A>G	p.Thr1049Ala	p.T1049A	ENST00000373198	NM_133170.3	1049	Aca/Gca	23/32	0.425968331205777	5	FACETS	0.811	0.717	0.912	0.27	0.239	0.304	CLONAL	1	TRUE	2	0.442830511179192	5		416	806	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46252777	46252777	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	146	298	0	ENST00000371998.3:c.206G>A	p.Cys69Tyr	p.C69Y	ENST00000371998		69	tGt/tAt	4/23	0.425968331205777	5	FACETS	1	0.98	1	0.802	0.738	0.868	CLONAL	2	TRUE	2	0.442830511179192	5		298	456	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37055921	37055921	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs587779035	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	97	204	0	ENST00000231790.2:c.678-2A>G		p.X226_splice	ENST00000231790	NM_000249.3	226			0.426965003834812	2	FACETS	0.94	0.855	1	0.94	0.855	1	CLONAL	2	TRUE	0	0.442830511179192	2		204	233	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200034	128200034	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	328	671	0	ENST00000341105.2:c.1271A>T	p.Lys424Met	p.K424M	ENST00000341105	NM_032638.4	424	aAg/aTg	6/6	0.442830511179192	5	FACETS	0.868	0.819	0.919	0.579	0.546	0.613	CLONAL	2	TRUE	2	0.442830511179192	5		671	1420	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960004	134960005	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	83	394	0	ENST00000398015.3:c.2363_2364del	p.Val788GlufsTer92	p.V788Efs*92	ENST00000398015	NM_004441.4	787	ccTGtg/cctg	13/16	0.442830511179192	5	FACETS	0.733	0.646	0.827	0.244	0.215	0.276	SUBCLONAL	1	TRUE	2	0.442830511179192	5		394	851	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231313	142231313	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	54	250	0	ENST00000350721.4:c.4642-1G>A		p.X1548_splice	ENST00000350721	NM_001184.3	1548			0.442830511179192	5	FACETS	0.828	0.708	0.96	0.276	0.236	0.32	CLONAL	1	TRUE	2	0.442830511179192	5		250	490	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509778	187509778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	61	254	0	ENST00000441802.2:c.13735C>T	p.Pro4579Ser	p.P4579S	ENST00000441802	NM_005245.3	4579	Ccc/Tcc	27/27	0.442830511179192	1	FACETS	0.71	0.617	0.81	0.71	0.617	0.81	SUBCLONAL	1	TRUE	0	0.442830511179192	1		254	302	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518239	187518239	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1016376045	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	65	319	0	ENST00000441802.2:c.12455A>G	p.Asn4152Ser	p.N4152S	ENST00000441802	NM_005245.3	4152	aAc/aGc	25/27	0.442830511179192	1	FACETS	0.726	0.634	0.823	0.726	0.634	0.823	SUBCLONAL	1	TRUE	0	0.442830511179192	1		319	315	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294672	1294672	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1554043093	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	82	252	0	ENST00000310581.5:c.329del	p.Gly110AlafsTer18	p.G110Afs*18	ENST00000310581	NM_198253.2	110	gGc/gc	2/16	0.0873254922448533	6	FACETS	1	0.968	1	0.43	0.38	0.484	INDETERMINATE	1	TRUE	3	0.442830511179192	6		252	541	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38996941	38996941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	84	346	0	ENST00000357387.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000357387	NM_152756.3	146	Gca/Aca	6/38	0.0873254922448533	6	FACETS	1	0.973	1	0.45	0.398	0.505	INDETERMINATE	1	TRUE	3	0.442830511179192	6		346	530	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86676344	86676345	+	stop_gained	Nonsense_Mutation	DNP	TG	TG	AT	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	84	153	0	ENST00000274376.6:c.2622_2623delinsAT	p.Tyr874_Gly875delinsTer	p.Y874_G875delins*	ENST00000274376	NM_002890.2	874	taTGgg/taATgg	20/25	0.396342708142979	3	FACETS	1	0.957	1	0.743	0.669	0.817	CLONAL	2	TRUE	0	0.442830511179192	3		153	208	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722305	176722305	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	113	447	1	ENST00000439151.2:c.7936G>A	p.Ala2646Thr	p.A2646T	ENST00000439151	NM_022455.4	2646	Gca/Aca	23/23	0.391049401290356	3	FACETS	0.913	0.822	1	0.304	0.274	0.336	CLONAL	1	TRUE	0	0.442830511179192	3		448	683	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287568	33287568	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	87	521	0	ENST00000374542.5:c.1529C>A	p.Pro510His	p.P510H	ENST00000374542	NM_001141970.1	510	cCt/cAt	6/8	1	2	FACETS	0.538	0.476	0.604	0.538	0.476	0.604	SUBCLONAL	1	TRUE	1	0.442830511179192	2		521	731	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157519994	157520014	+	inframe_deletion	In_Frame_Del	DEL	CAGCCGCCGTATGGAGGGCAC	CAGCCGCCGTATGGAGGGCAC	-	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	139	566	0	ENST00000346085.5:c.4068_4088del	p.Pro1357_Pro1363del	p.P1357_P1363del	ENST00000346085	NM_020732.3	1355	CAGCCGCCGTATGGAGGGCAC/-	17/20	0.427967377651104	4	FACETS	0.873	0.793	0.956	0.291	0.264	0.319	CLONAL	1	TRUE	1	0.442830511179192	4		566	1038	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026923	6026925	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs764854869	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	18	64	0	ENST00000265849.7:c.1471_1473del	p.Glu491del	p.E491del	ENST00000265849	NM_000535.5	491	GAG/-	11/15	0.195277967424021	5	FACETS	1	0.804	1	0.355	0.27	0.453	INDETERMINATE	1	TRUE	2	0.442830511179192	5		64	127	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508187	106508187	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	133	297	0	ENST00000359195.3:c.181G>T	p.Val61Leu	p.V61L	ENST00000359195	NM_002649.2	61	Gtg/Ttg	2/11	0.195277967424021	5	FACETS	1	0.966	1	0.741	0.678	0.805	INDETERMINATE	2	TRUE	2	0.442830511179192	5		297	450	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371629	55371629	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	130	505	0	ENST00000297316.4:c.319A>G	p.Lys107Glu	p.K107E	ENST00000297316	NM_022454.3	107	Aag/Gag	2/2	0.349264508666859	1	FACETS	0.821	0.748	0.897	0.821	0.748	0.897	CLONAL	1	TRUE	0	0.442830511179192	1		505	557	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504340	8504340	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	89	458	0	ENST00000356435.5:c.1743C>A	p.Tyr581Ter	p.Y581*	ENST00000356435		581	taC/taA	12/35	0.139869863815175	6	FACETS	0.943	0.835	1	0.314	0.278	0.353	INDETERMINATE	1	TRUE	3	0.442830511179192	6		458	804	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040731	47040731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	149	654	0	ENST00000377604.3:c.1366G>A	p.Ala456Thr	p.A456T	ENST00000377604	NM_001204468.1	456	Gcc/Acc	13/24	0.442830511179192	1	FACETS	0.97	0.892	1	0.97	0.892	1	CLONAL	1	TRUE	0	0.442830511179192	1		654	540	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907813	76907814	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	46	197	0	ENST00000373344.5:c.4347dup	p.Glu1450ArgfsTer17	p.E1450Rfs*17	ENST00000373344	NM_000489.3	1449	-/A	15/35	1	2	FACETS	0.98	0.835	1	0.98	0.835	1	CLONAL	1	TRUE	1	0.442830511179192	2		197	212	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0043830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	53	288	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	0.42	0.358	0.487	0.42	0.358	0.487	SUBCLONAL	1	TRUE	1	0.53047665454012	2		288	476	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371708	225371708	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	91	388	0	ENST00000264414.4:c.896T>G	p.Met299Arg	p.M299R	ENST00000264414	NM_003590.4	299	aTg/aGg	7/16	1	2	FACETS	0.827	0.738	0.92	0.827	0.738	0.92	CLONAL	1	TRUE	1	0.53047665454012	2		388	415	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845344	42845372	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGGGCCAGGCCCCCGGGAGCGCGCTCT	CCAGGGCCAGGCCCCCGGGAGCGCGCTCT	-	novel	NA	P-0043830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	73	579	0	ENST00000398585.3:c.890_918del	p.Glu297AlafsTer34	p.E297Afs*34	ENST00000398585	NM_001135099.1	297	gAGAGCGCGCTCCCGGGGGCCTGGCCCTGG/g	9/14	1	2	FACETS	0.388	0.338	0.441	0.388	0.338	0.441	SUBCLONAL	1	TRUE	1	0.53047665454012	2		579	710	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041149	180041149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	64	659	0	ENST00000261937.6:c.3250G>A	p.Glu1084Lys	p.E1084K	ENST00000261937	NM_182925.4	1084	Gaa/Aaa	24/30	0.2491928424632	5	FACETS	0.616	0.532	0.709	0.154	0.133	0.178	SUBCLONAL	1	TRUE	1	0.2491928424632	5		659	1145	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771502	112771502	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	51	477	1	ENST00000369452.4:c.1675C>T	p.Gln559Ter	p.Q559*	ENST00000369452	NM_007373.3	559	Cag/Tag	9/9	0.206215654342708	3	FACETS	0.604	0.512	0.706	0.302	0.256	0.353	SUBCLONAL	1	TRUE	1	0.2491928424632	3		478	762	SUCCESS
EED	8726	MSKCC	GRCh37	11	85966264	85966264	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	33	209	0	ENST00000263360.6:c.361G>T	p.Val121Phe	p.V121F	ENST00000263360	NM_003797.3	121	Gtt/Ttt	4/12	0.142205326191428	3	FACETS	0.583	0.474	0.706	0.194	0.158	0.236	INDETERMINATE	1	TRUE	0	0.2491928424632	3		209	511	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1039254	1039254	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0043854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	87	514	0	ENST00000358495.3:c.243C>G	p.Tyr81Ter	p.Y81*	ENST00000358495	NM_134424.2	81	taC/taG	4/12	0.142205326191428	3	FACETS	0.91	0.804	1	0.303	0.268	0.341	INDETERMINATE	1	TRUE	0	0.2491928424632	3		514	863	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1039292	1039292	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	88	480	0	ENST00000358495.3:c.205C>T	p.His69Tyr	p.H69Y	ENST00000358495	NM_134424.2	69	Cat/Tat	4/12	0.142205326191428	3	FACETS	1	0.896	1	0.338	0.299	0.38	INDETERMINATE	1	TRUE	0	0.2491928424632	3		480	784	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732489	74732489	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	19	254	0	ENST00000359995.5:c.420C>G	p.Ser140Arg	p.S140R	ENST00000359995	NM_001195427.1	140	agC/agG	2/3	0.2491928424632	3	FACETS	0.486	0.368	0.625	0.243	0.184	0.313	SUBCLONAL	1	TRUE	1	0.2491928424632	3		254	353	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727894	78727894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778029024	NA	P-0043854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	54	543	0	ENST00000306801.3:c.739G>A	p.Glu247Lys	p.E247K	ENST00000306801	NM_020761.2	247	Gag/Aag	6/34	0.2491928424632	3	FACETS	0.669	0.57	0.777	0.334	0.285	0.389	SUBCLONAL	1	TRUE	1	0.2491928424632	3		543	729	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623230	52623230	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	77	293	0	ENST00000394830.3:c.2821T>G	p.Ser941Ala	p.S941A	ENST00000394830	NM_018313.4	941	Tca/Gca	19/30	0.103147839802203	4	FACETS	0.769	0.677	0.868	0.769	0.677	0.868	INDETERMINATE	2	TRUE	2	0.2491928424632	4		293	502	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683688	162683688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	59	449	0	ENST00000366898.1:c.281G>A	p.Gly94Asp	p.G94D	ENST00000366898	NM_004562.2	94	gGc/gAc	3/12	0.177651886770858	2	FACETS	0.789	0.679	0.91	0.395	0.339	0.455	CLONAL	1	TRUE	0	0.2491928424632	2		449	600	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866474	56866474	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	69	602	0	ENST00000519728.1:c.721G>T	p.Glu241Ter	p.E241*	ENST00000519728	NM_002350.3	241	Gag/Tag	8/13	0.2491928424632	2	FACETS	0.629	0.547	0.719	0.315	0.273	0.36	SUBCLONAL	1	TRUE	0	0.2491928424632	2		602	880	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045567	47045567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	55	523	0	ENST00000377604.3:c.2534C>T	p.Ser845Phe	p.S845F	ENST00000377604	NM_001204468.1	845	tCt/tTt	22/24	1	2	FACETS	0.833	0.713	0.964	0.833	0.713	0.964	CLONAL	1	TRUE	1	0.2491928424632	2		523	530	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356385	70356385	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	52	541	1	ENST00000374080.3:c.5280G>C	p.Glu1760Asp	p.E1760D	ENST00000374080		1760	gaG/gaC	37/45	1	2	FACETS	0.649	0.552	0.756	0.649	0.552	0.756	SUBCLONAL	1	TRUE	1	0.2491928424632	2		542	643	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0043869-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	206	460	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.904134531556497	3	FACETS	0.84	0.781	0.9	0.42	0.39	0.45	CLONAL	1	TRUE	1	0.904134531556497	3		460	788	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732969	30732969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893810	NA	P-0043869-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	434	338	1	ENST00000295754.5:c.1582C>T	p.Arg528Cys	p.R528C	ENST00000295754	NM_003242.5	528	Cgt/Tgt	7/7	0.899159136882441	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.904134531556497	2		339	469	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236059	108236059	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043869-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	135	454	0	ENST00000278616.4:c.8995G>C	p.Asp2999His	p.D2999H	ENST00000278616	NM_000051.3	2999	Gac/Cac	63/63	1	2	FACETS	0.834	0.768	0.902	0.834	0.768	0.902	CLONAL	1	TRUE	1	0.904134531556497	2		454	358	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236120	108236120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043869-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	269	534	0	ENST00000278616.4:c.9056G>A	p.Gly3019Glu	p.G3019E	ENST00000278616	NM_000051.3	3019	gGa/gAa	63/63	1	2	FACETS	0.977	0.924	1	0.977	0.924	1	CLONAL	1	TRUE	1	0.904134531556497	2		534	609	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250614	26250614	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043869-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	162	581	0	ENST00000446824.2:c.220G>C	p.Glu74Gln	p.E74Q	ENST00000446824	NM_021018.2	74	Gag/Cag	1/1	0.904134531556497	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.904134531556497	1		581	185	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033844	49033844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853294	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	48	333	0	ENST00000267163.4:c.1981C>T	p.Arg661Trp	p.R661W	ENST00000267163	NM_000321.2	661	Cgg/Tgg	20/27	1	2	FACETS	0.602	0.509	0.705	0.602	0.509	0.705	SUBCLONAL	1	TRUE	1	0.315723020487005	2		333	505	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028264	48028264	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200492211	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	56	357	0	ENST00000234420.5:c.3142C>T	p.Gln1048Ter	p.Q1048*	ENST00000234420	NM_000179.2	1048	Cag/Tag	4/10	1	2	FACETS	0.741	0.635	0.855	0.741	0.635	0.855	SUBCLONAL	1	TRUE	1	0.315723020487005	2		357	479	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259374	89259374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141287594	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	33	366	0	ENST00000336596.2:c.518C>T	p.Pro173Leu	p.P173L	ENST00000336596	NM_005233.5	173	cCt/cTt	3/17	1	2	FACETS	0.453	0.369	0.549	0.453	0.369	0.549	SUBCLONAL	1	TRUE	1	0.315723020487005	2		366	461	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857284	9857284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	94	475	0	ENST00000330684.3:c.4117G>A	p.Asp1373Asn	p.D1373N	ENST00000330684	NM_001134407.1	1373	Gat/Aat	13/13	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.315723020487005	2		475	554	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892205	9892205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	91	513	0	ENST00000330684.3:c.2285G>A	p.Gly762Glu	p.G762E	ENST00000330684	NM_001134407.1	762	gGa/gAa	11/13	1	2	FACETS	0.827	0.734	0.926	0.827	0.734	0.926	CLONAL	1	TRUE	1	0.315723020487005	2		513	697	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230613	46230613	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	61	374	0	ENST00000334344.6:c.862C>T	p.Gln288Ter	p.Q288*	ENST00000334344	NM_152641.2	288	Cag/Tag	8/21	1	2	FACETS	0.827	0.715	0.949	0.827	0.715	0.949	CLONAL	1	TRUE	1	0.315723020487005	2		374	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519980	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	91	538	0	ENST00000269305.4:c.528C>G	p.Cys176Trp	p.C176W	ENST00000269305	NM_001126112.2	176	tgC/tgG	5/11	1	2	FACETS	0.98	0.872	1	0.98	0.872	1	CLONAL	1	TRUE	1	0.315723020487005	2		538	588	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562773	95562773	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753527258	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	39	289	0	ENST00000393063.1:c.4484C>T	p.Ser1495Leu	p.S1495L	ENST00000393063	NM_030621.3	1495	tCa/tTa	24/28	1	2	FACETS	0.675	0.561	0.802	0.675	0.561	0.802	SUBCLONAL	1	TRUE	1	0.315723020487005	2		289	366	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	89	203	0				ENST00000310581	NM_198253.2	-/1132			0.197268629135871	3	FACETS	0.87	0.777	0.968	0.87	0.777	0.968	CLONAL	2	TRUE	1	0.315723020487005	3		203	375	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116179	209116179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555882127	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	44	325	1	ENST00000345146.2:c.97C>T	p.Pro33Ser	p.P33S	ENST00000345146	NM_005896.2	33	Ccc/Tcc	3/10	1	2	FACETS	0.732	0.615	0.86	0.732	0.615	0.86	SUBCLONAL	1	TRUE	1	0.315723020487005	2		326	381	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2957001	2957001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	75	442	0	ENST00000396946.4:c.2626G>A	p.Glu876Lys	p.E876K	ENST00000396946	NM_032415.4	876	Gaa/Aaa	20/25	1	2	FACETS	0.753	0.66	0.853	0.753	0.66	0.853	SUBCLONAL	1	TRUE	1	0.315723020487005	2		442	631	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670452	88670452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143617169	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	39	270	0	ENST00000360948.2:c.1234G>A	p.Glu412Lys	p.E412K	ENST00000360948	NM_001012338.2	412	Gaa/Aaa	11/19	1	2	FACETS	0.563	0.466	0.67	0.563	0.466	0.67	SUBCLONAL	1	TRUE	1	0.315723020487005	2		270	439	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158395	106158395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372118135	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	23	220	0	ENST00000380013.4:c.3296C>T	p.Ser1099Phe	p.S1099F	ENST00000380013	NM_001127208.2	1099	tCt/tTt	3/11	1	2	FACETS	0.499	0.389	0.625	0.499	0.389	0.625	SUBCLONAL	1	TRUE	1	0.315723020487005	2		220	292	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956965	2956965	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142828146	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	80	558	0	ENST00000396946.4:c.2662C>T	p.Arg888Cys	p.R888C	ENST00000396946	NM_032415.4	888	Cgt/Tgt	20/25	1	2	FACETS	0.72	0.633	0.813	0.72	0.633	0.813	SUBCLONAL	1	TRUE	1	0.315723020487005	2		558	704	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872041	35872041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	38	466	0	ENST00000216797.5:c.572C>T	p.Ser191Phe	p.S191F	ENST00000216797	NM_020529.2	191	tCt/tTt	4/6	1	2	FACETS	0.447	0.369	0.535	0.447	0.369	0.535	SUBCLONAL	1	TRUE	1	0.315723020487005	2		466	538	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650445	48650445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	85	638	0	ENST00000376670.3:c.415G>A	p.Glu139Lys	p.E139K	ENST00000376670	NM_002049.3	139	Gag/Aag	3/6	1	2	FACETS	0.664	0.586	0.747	0.664	0.586	0.747	SUBCLONAL	1	TRUE	1	0.315723020487005	2		638	811	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739837	41739837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	65	379	0	ENST00000242208.4:c.136G>A	p.Asp46Asn	p.D46N	ENST00000242208	NM_002192.2	46	Gat/Aat	2/3	1	2	FACETS	0.787	0.683	0.9	0.787	0.683	0.9	SUBCLONAL	1	TRUE	1	0.315723020487005	2		379	523	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257053	198257053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267599149	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	30	298	0	ENST00000335508.6:c.3889C>T	p.Arg1297Cys	p.R1297C	ENST00000335508	NM_012433.2	1297	Cgt/Tgt	25/25	1	2	FACETS	0.552	0.446	0.673	0.552	0.446	0.673	SUBCLONAL	1	TRUE	1	0.315723020487005	2		298	344	SUCCESS
BTK	695	MSKCC	GRCh37	X	100609658	100609658	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782740486	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	51	394	0	ENST00000308731.7:c.1591G>A	p.Asp531Asn	p.D531N	ENST00000308731	NM_000061.2	531	Gat/Aat	16/19	1	2	FACETS	0.492	0.417	0.574	0.492	0.417	0.574	SUBCLONAL	1	TRUE	1	0.315723020487005	2		394	657	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599339	55599339	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs993022333	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	56	384	0	ENST00000288135.5:c.2465A>C	p.Asn822Thr	p.N822T	ENST00000288135	NM_000222.2	822	aAt/aCt	17/21	1	2	FACETS	0.869	0.747	1	0.869	0.747	1	CLONAL	1	TRUE	1	0.315723020487005	2		384	408	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492909	8492909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	95	496	0	ENST00000356435.5:c.2420G>A	p.Gly807Glu	p.G807E	ENST00000356435		807	gGa/gAa	16/35	0.315723020487005	1	FACETS	0.762	0.679	0.85	0.762	0.679	0.85	SUBCLONAL	1	TRUE	0	0.315723020487005	1		496	665	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295204	1295204	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs2735943	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	36	171	1				ENST00000310581	NM_198253.2	-/1132			0.197268629135871	3	FACETS	0.825	0.68	0.986	0.413	0.34	0.493	CLONAL	1	TRUE	1	0.315723020487005	3		172	320	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128201179	128201179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	78	488	2	ENST00000265960.3:c.1556C>T	p.Ser519Phe	p.S519F	ENST00000265960	NM_001006617.1	519	tCc/tTc	12/12	0.315723020487005	1	FACETS	0.742	0.653	0.837	0.742	0.653	0.837	SUBCLONAL	1	TRUE	0	0.315723020487005	1		490	561	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419977	41419977	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	66	493	0	ENST00000373198.4:c.344C>T	p.Ser115Phe	p.S115F	ENST00000373198	NM_133170.3	115	tCc/tTc	3/32	1	2	FACETS	0.698	0.606	0.798	0.698	0.606	0.798	SUBCLONAL	1	TRUE	1	0.315723020487005	2		493	599	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934321	81934321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	123	536	1	ENST00000359376.3:c.1298C>T	p.Pro433Leu	p.P433L	ENST00000359376	NM_002661.3	433	cCc/cTc	14/33	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.315723020487005	2		537	660	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474101	29474101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373846404	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	57	499	0	ENST00000389048.3:c.2074G>A	p.Gly692Arg	p.G692R	ENST00000389048	NM_004304.4	692	Ggg/Agg	12/29	1	2	FACETS	0.702	0.603	0.811	0.702	0.603	0.811	SUBCLONAL	1	TRUE	1	0.315723020487005	2		499	514	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778894	3778894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1421133831	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	41	466	1	ENST00000262367.5:c.6154C>T	p.Arg2052Trp	p.R2052W	ENST00000262367	NM_004380.2	2052	Cgg/Tgg	31/31	1	2	FACETS	0.554	0.461	0.657	0.554	0.461	0.657	SUBCLONAL	1	TRUE	1	0.315723020487005	2		467	469	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729536	41729536	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	76	667	0	ENST00000242208.4:c.993G>T	p.Lys331Asn	p.K331N	ENST00000242208	NM_002192.2	331	aaG/aaT	3/3	1	2	FACETS	0.732	0.642	0.829	0.732	0.642	0.829	SUBCLONAL	1	TRUE	1	0.315723020487005	2		667	658	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679033	117679033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	38	367	0	ENST00000368508.3:c.3788C>T	p.Pro1263Leu	p.P1263L	ENST00000368508	NM_002944.2	1263	cCc/cTc	24/43	1	2	FACETS	0.651	0.539	0.775	0.651	0.539	0.775	SUBCLONAL	1	TRUE	1	0.315723020487005	2		367	370	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008537	71008537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	19	251	0	ENST00000318789.4:c.1895C>T	p.Pro632Leu	p.P632L	ENST00000318789	NM_032682.5	632	cCt/cTt	21/21	1	2	FACETS	0.37	0.281	0.476	0.37	0.281	0.476	SUBCLONAL	1	TRUE	1	0.315723020487005	2		251	325	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8252036	8252036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	41	488	0	ENST00000335790.3:c.41C>T	p.Ser14Phe	p.S14F	ENST00000335790	NM_002315.2	14	tCc/tTc	2/4	1	2	FACETS	0.428	0.356	0.509	0.428	0.356	0.509	SUBCLONAL	1	TRUE	1	0.315723020487005	2		488	607	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674236	117674236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	94	498	1	ENST00000368508.3:c.4238G>A	p.Gly1413Glu	p.G1413E	ENST00000368508	NM_002944.2	1413	gGa/gAa	26/43	1	2	FACETS	0.843	0.751	0.942	0.843	0.751	0.942	CLONAL	1	TRUE	1	0.315723020487005	2		499	706	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069575	69069575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	29	310	0	ENST00000288368.4:c.4250G>A	p.Gly1417Glu	p.G1417E	ENST00000288368	NM_024870.2	1417	gGa/gAa	35/40	1	2	FACETS	0.467	0.375	0.573	0.467	0.375	0.573	SUBCLONAL	1	TRUE	1	0.315723020487005	2		310	393	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239501	123239501	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	79	629	0	ENST00000358487.5:c.2336A>T	p.Tyr779Phe	p.Y779F	ENST00000358487	NM_000141.4	779	tAt/tTt	18/18	1	2	FACETS	0.674	0.593	0.762	0.674	0.593	0.762	SUBCLONAL	1	TRUE	1	0.315723020487005	2		629	742	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36846881	36846881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs865878221	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	68	459	1	ENST00000358127.4:c.1058C>T	p.Ser353Leu	p.S353L	ENST00000358127	NM_001280556.1	353	tCg/tTg	9/10	0.315723020487005	1	FACETS	0.799	0.697	0.908	0.799	0.697	0.908	CLONAL	1	TRUE	0	0.315723020487005	1		460	454	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294208	11294208	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	177	507	0	ENST00000361445.4:c.2323A>C	p.Ile775Leu	p.I775L	ENST00000361445	NM_004958.3	775	Att/Ctt	14/58	NA	2	FACETS	0.82	0.758	0.884			1	INDETERMINATE	2	TRUE	NA	0.315723020487005	2		507	684	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805016	43805016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1464244274	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	146	499	0	ENST00000372470.3:c.466G>A	p.Glu156Lys	p.E156K	ENST00000372470	NM_005373.2	156	Gag/Aag	4/12	0.124276187564649	3	FACETS	0.803	0.735	0.874	0.803	0.735	0.874	INDETERMINATE	2	TRUE	1	0.315723020487005	3		499	667	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834145	156834145	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	128	539	0	ENST00000524377.1:c.213-1G>A		p.X71_splice	ENST00000524377	NM_002529.3	71			0.124276187564649	3	FACETS	1	0.976	1	0.614	0.556	0.674	INDETERMINATE	1	TRUE	1	0.315723020487005	3		539	765	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663743	241663743	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201625211	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	102	484	1	ENST00000366560.3:c.1384C>T	p.His462Tyr	p.H462Y	ENST00000366560	NM_000143.3	462	Cat/Tat	9/10	0.262467002259864	2	FACETS	1	0.954	1	0.557	0.499	0.618	CLONAL	1	TRUE	0	0.315723020487005	2		485	580	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100301	8100301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	84	632	1	ENST00000346208.3:c.275G>A	p.Gly92Glu	p.G92E	ENST00000346208		92	gGa/gAa	3/6	1	2	FACETS	0.817	0.722	0.919	0.817	0.722	0.919	CLONAL	1	TRUE	1	0.315723020487005	2		633	651	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533512	533512	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs376688893	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	102	611	0	ENST00000451590.1:c.391C>T	p.Gln131Ter	p.Q131*	ENST00000451590	NM_001130442.1	131	Cag/Tag	4/5	1	2	FACETS	0.837	0.748	0.931	0.837	0.748	0.931	CLONAL	1	TRUE	1	0.315723020487005	2		611	772	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625131	69625131	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	73	642	0	ENST00000334134.2:c.662A>C	p.Glu221Ala	p.E221A	ENST00000334134	NM_005247.2	221	gAg/gCg	3/3	1	2	FACETS	0.735	0.643	0.834	0.735	0.643	0.834	SUBCLONAL	1	TRUE	1	0.315723020487005	2		642	629	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124716	108124716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765965513	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	61	328	0	ENST00000278616.4:c.2074C>T	p.Arg692Cys	p.R692C	ENST00000278616	NM_000051.3	692	Cgc/Tgc	13/63	1	2	FACETS	0.942	0.816	1	0.942	0.816	1	CLONAL	1	TRUE	1	0.315723020487005	2		328	410	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103365	119103365	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	42	395	0	ENST00000264033.4:c.403G>A	p.Glu135Lys	p.E135K	ENST00000264033	NM_005188.3	135	Gag/Aag	2/16	1	2	FACETS	0.668	0.559	0.79	0.668	0.559	0.79	SUBCLONAL	1	TRUE	1	0.315723020487005	2		395	398	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149278	119149278	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	78	491	0	ENST00000264033.4:c.1286T>G	p.Ile429Ser	p.I429S	ENST00000264033	NM_005188.3	429	aTc/aGc	9/16	1	2	FACETS	0.828	0.728	0.935	0.828	0.728	0.935	CLONAL	1	TRUE	1	0.315723020487005	2		491	597	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205275	46205275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	53	369	0	ENST00000334344.6:c.359C>T	p.Pro120Leu	p.P120L	ENST00000334344	NM_152641.2	120	cCa/cTa	4/21	1	2	FACETS	0.662	0.565	0.769	0.662	0.565	0.769	SUBCLONAL	1	TRUE	1	0.315723020487005	2		369	507	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230418	46230418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	56	298	0	ENST00000334344.6:c.752C>T	p.Ser251Phe	p.S251F	ENST00000334344	NM_152641.2	251	tCt/tTt	7/21	1	2	FACETS	0.693	0.594	0.801	0.693	0.594	0.801	SUBCLONAL	1	TRUE	1	0.315723020487005	2		298	512	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111855984	111855984	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1261307883	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	71	418	0	ENST00000341259.2:c.35C>T	p.Ser12Phe	p.S12F	ENST00000341259	NM_005475.2	12	tCt/tTt	2/8	1	2	FACETS	0.831	0.727	0.944	0.831	0.727	0.944	CLONAL	1	TRUE	1	0.315723020487005	2		418	541	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964135	28964135	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	46	329	0	ENST00000282397.4:c.1767G>A	p.Trp589Ter	p.W589*	ENST00000282397	NM_002019.4	589	tgG/tgA	13/30	1	2	FACETS	0.73	0.616	0.856	0.73	0.616	0.856	SUBCLONAL	1	TRUE	1	0.315723020487005	2		329	399	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95579473	95579473	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs765014294	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	38	326	0	ENST00000393063.1:c.1996A>G	p.Thr666Ala	p.T666A	ENST00000393063	NM_030621.3	666	Act/Gct	13/28	1	2	FACETS	0.627	0.519	0.747	0.627	0.519	0.747	SUBCLONAL	1	TRUE	1	0.315723020487005	2		326	384	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472624	88472624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771818173	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	29	329	0	ENST00000360948.2:c.1931C>T	p.Pro644Leu	p.P644L	ENST00000360948	NM_001012338.2	644	cCa/cTa	16/19	1	2	FACETS	0.417	0.334	0.511	0.417	0.334	0.511	SUBCLONAL	1	TRUE	1	0.315723020487005	2		329	441	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483943	88483943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	78	529	0	ENST00000360948.2:c.1627G>A	p.Glu543Lys	p.E543K	ENST00000360948	NM_001012338.2	543	Gaa/Aaa	14/19	1	2	FACETS	0.695	0.61	0.786	0.695	0.61	0.786	SUBCLONAL	1	TRUE	1	0.315723020487005	2		529	711	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500486	99500486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	67	577	0	ENST00000268035.6:c.3919C>T	p.Pro1307Ser	p.P1307S	ENST00000268035	NM_000875.3	1307	Ccc/Tcc	21/21	1	2	FACETS	0.665	0.578	0.76	0.665	0.578	0.76	SUBCLONAL	1	TRUE	1	0.315723020487005	2		577	638	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639126	3639126	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	124	626	0	ENST00000294008.3:c.4513T>G	p.Phe1505Val	p.F1505V	ENST00000294008	NM_032444.2	1505	Ttt/Gtt	12/15	1	2	FACETS	0.971	0.879	1	0.971	0.879	1	CLONAL	1	TRUE	1	0.315723020487005	2		626	809	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820752	3820752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	134	657	0	ENST00000262367.5:c.2699C>T	p.Thr900Ile	p.T900I	ENST00000262367	NM_004380.2	900	aCc/aTc	14/31	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.315723020487005	2		657	840	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900662	3900663	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	50	519	0	ENST00000262367.5:c.433_434delinsTT	p.Pro145Phe	p.P145F	ENST00000262367	NM_004380.2	145	CCc/TTc	2/31	1	2	FACETS	0.524	0.444	0.612	0.524	0.444	0.612	SUBCLONAL	1	TRUE	1	0.315723020487005	2		519	605	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858156	9858156	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	59	490	0	ENST00000330684.3:c.3245C>T	p.Thr1082Ile	p.T1082I	ENST00000330684	NM_001134407.1	1082	aCc/aTc	13/13	1	2	FACETS	0.588	0.505	0.678	0.588	0.505	0.678	SUBCLONAL	1	TRUE	1	0.315723020487005	2		490	636	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032252	10032252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	53	540	0	ENST00000330684.3:c.571G>A	p.Val191Met	p.V191M	ENST00000330684	NM_001134407.1	191	Gtg/Atg	3/13	1	2	FACETS	0.512	0.436	0.595	0.512	0.436	0.595	SUBCLONAL	1	TRUE	1	0.315723020487005	2		540	656	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847363	68847363	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	44	514	0	ENST00000261769.5:c.1285C>G	p.Pro429Ala	p.P429A	ENST00000261769	NM_004360.3	429	Cca/Gca	9/16	1	2	FACETS	0.466	0.39	0.55	0.466	0.39	0.55	SUBCLONAL	1	TRUE	1	0.315723020487005	2		514	598	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032483	12032483	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	37	266	0	ENST00000353533.5:c.919T>A	p.Tyr307Asn	p.Y307N	ENST00000353533	NM_003010.3	307	Tat/Aat	9/11	1	2	FACETS	0.746	0.617	0.89	0.746	0.617	0.89	SUBCLONAL	1	TRUE	1	0.315723020487005	2		266	314	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652939	29652939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	54	303	1	ENST00000356175.3:c.4874C>T	p.Thr1625Ile	p.T1625I	ENST00000356175	NM_000267.3	1625	aCc/aTc	36/57	1	2	FACETS	0.725	0.62	0.839	0.725	0.62	0.839	SUBCLONAL	1	TRUE	1	0.315723020487005	2		304	472	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42788873	42788873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1390494320	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	65	366	1	ENST00000575354.2:c.17G>A	p.Arg6Lys	p.R6K	ENST00000575354	NM_015125.3	6	aGg/aAg	1/20	1	2	FACETS	0.869	0.755	0.991	0.869	0.755	0.991	CLONAL	1	TRUE	1	0.315723020487005	2		367	474	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306757	41306757	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	52	375	0	ENST00000373198.4:c.902G>A	p.Gly301Glu	p.G301E	ENST00000373198	NM_133170.3	301	gGg/gAg	7/32	1	2	FACETS	0.671	0.572	0.78	0.671	0.572	0.78	SUBCLONAL	1	TRUE	1	0.315723020487005	2		375	491	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627355	37627355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs910521882	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	75	739	0	ENST00000249071.6:c.364G>A	p.Asp122Asn	p.D122N	ENST00000249071	NM_002872.4	122	Gac/Aac	5/7	1	2	FACETS	0.504	0.44	0.573	0.504	0.44	0.573	SUBCLONAL	1	TRUE	1	0.315723020487005	2		739	943	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607249	189607249	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	37	598	0	ENST00000264731.3:c.1628A>C	p.Tyr543Ser	p.Y543S	ENST00000264731	NM_003722.4	543	tAt/tCt	12/14	1	2	FACETS	0.358	0.294	0.43	0.358	0.294	0.43	SUBCLONAL	1	TRUE	1	0.315723020487005	2		598	654	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749394	41749394	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	42	334	0	ENST00000226382.2:c.401A>C	p.Lys134Thr	p.K134T	ENST00000226382	NM_003924.3	134	aAg/aCg	2/3	1	2	FACETS	0.725	0.607	0.855	0.725	0.607	0.855	SUBCLONAL	1	TRUE	1	0.315723020487005	2		334	367	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99802265	99802265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	24	152	0	ENST00000280892.6:c.628C>T	p.Pro210Ser	p.P210S	ENST00000280892	NM_001130678.1	210	Cct/Tct	7/7	1	2	FACETS	0.731	0.576	0.907	0.731	0.576	0.907	CLONAL	1	TRUE	1	0.315723020487005	2		152	208	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549440	187549440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	30	448	0	ENST00000441802.2:c.4678C>T	p.Pro1560Ser	p.P1560S	ENST00000441802	NM_005245.3	1560	Ccg/Tcg	9/27	1	2	FACETS	0.322	0.259	0.395	0.322	0.259	0.395	SUBCLONAL	1	TRUE	1	0.315723020487005	2		448	590	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629276	187629276	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	54	537	0	ENST00000441802.2:c.1706T>G	p.Phe569Cys	p.F569C	ENST00000441802	NM_005245.3	569	tTt/tGt	2/27	1	2	FACETS	0.597	0.51	0.693	0.597	0.51	0.693	SUBCLONAL	1	TRUE	1	0.315723020487005	2		537	573	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295339	1295339	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	103	312	3				ENST00000310581	NM_198253.2	-/1132			0.197268629135871	3	FACETS	0.971	0.876	1	0.971	0.876	1	CLONAL	2	TRUE	1	0.315723020487005	3		315	389	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931348	131931348	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	59	375	0	ENST00000265335.6:c.2053C>T	p.Gln685Ter	p.Q685*	ENST00000265335		685	Cag/Tag	13/25	0.197268629135871	3	FACETS	0.801	0.69	0.923	0.401	0.345	0.462	CLONAL	1	TRUE	1	0.315723020487005	3		375	540	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523717	176523717	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1196666686	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	109	591	0	ENST00000292408.4:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000292408	NM_213647.1	710	Cga/Tga	16/18	1	2	FACETS	0.993	0.893	1	0.993	0.893	1	CLONAL	1	TRUE	1	0.315723020487005	2		591	695	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524646	176524646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	89	592	0	ENST00000292408.4:c.2378C>T	p.Ser793Phe	p.S793F	ENST00000292408	NM_213647.1	793	tCc/tTc	18/18	1	2	FACETS	0.827	0.733	0.927	0.827	0.733	0.927	CLONAL	1	TRUE	1	0.315723020487005	2		592	682	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672641	30672641	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	101	527	0	ENST00000376406.3:c.4319C>T	p.Ser1440Phe	p.S1440F	ENST00000376406	NM_014641.2	1440	tCc/tTc	10/15	0.315723020487005	3	FACETS	0.925	0.826	1	0.462	0.413	0.515	CLONAL	1	TRUE	1	0.315723020487005	3		527	801	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287505	33287505	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775204775	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	81	516	0	ENST00000374542.5:c.1592C>T	p.Ser531Leu	p.S531L	ENST00000374542	NM_001141970.1	531	tCg/tTg	6/8	0.315723020487005	3	FACETS	0.728	0.641	0.822	0.364	0.32	0.411	SUBCLONAL	1	TRUE	1	0.315723020487005	3		516	816	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553450	106553450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	29	355	0	ENST00000369096.4:c.1415C>T	p.Ser472Leu	p.S472L	ENST00000369096	NM_001198.3	472	tCa/tTa	5/7	1	2	FACETS	0.431	0.346	0.529	0.431	0.346	0.529	SUBCLONAL	1	TRUE	1	0.315723020487005	2		355	426	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026966	6026966	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	38	181	0	ENST00000265849.7:c.1430C>T	p.Ser477Phe	p.S477F	ENST00000265849	NM_000535.5	477	tCc/tTc	11/15	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.315723020487005	2		181	231	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002928	69002928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	43	300	1	ENST00000288368.4:c.2228G>A	p.Arg743Lys	p.R743K	ENST00000288368	NM_024870.2	743	aGg/aAg	20/40	1	2	FACETS	0.569	0.476	0.672	0.569	0.476	0.672	SUBCLONAL	1	TRUE	1	0.315723020487005	2		301	479	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737774	145737775	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	GT	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	56	565	0	ENST00000428558.2:c.3055_3055+1delinsAC		p.X1019_splice	ENST00000428558	NM_004260.3	1019		18/22	0.216851280166213	4	FACETS	0.662	0.566	0.767	0.221	0.188	0.256	SUBCLONAL	1	TRUE	1	0.315723020487005	4		565	705	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737779	145737780	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	56	571	1	ENST00000428558.2:c.3050_3051delinsAA	p.Arg1017Lys	p.R1017K	ENST00000428558	NM_004260.3	1017	aGG/aAA	18/22	0.216851280166213	4	FACETS	0.64	0.547	0.742	0.213	0.182	0.248	SUBCLONAL	1	TRUE	1	0.315723020487005	4		572	729	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197397	27197397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771377363	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	66	470	2	ENST00000380036.4:c.1709C>T	p.Ser570Leu	p.S570L	ENST00000380036	NM_000459.3	570	tCg/tTg	12/23	0.315723020487005	1	FACETS	0.582	0.505	0.665	0.582	0.505	0.665	SUBCLONAL	1	TRUE	0	0.315723020487005	1		472	605	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913265	39913265	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	87	425	0	ENST00000378444.4:c.4850T>C	p.Leu1617Ser	p.L1617S	ENST00000378444	NM_001123385.1	1617	tTa/tCa	14/15	1	2	FACETS	0.914	0.81	1	0.914	0.81	1	CLONAL	1	TRUE	1	0.315723020487005	2		425	603	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412512	63412512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1383586883	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	56	477	0	ENST00000330258.3:c.655G>A	p.Glu219Lys	p.E219K	ENST00000330258	NM_152424.3	219	Gag/Aag	2/2	1	2	FACETS	0.615	0.526	0.711	0.615	0.526	0.711	SUBCLONAL	1	TRUE	1	0.315723020487005	2		477	577	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480495	123480495	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	60	365	0	ENST00000371139.4:c.3G>A	p.Met1?	p.M1?	ENST00000371139	NM_001114937.2	1	atG/atA	1/4	1	2	FACETS	0.85	0.734	0.976	0.85	0.734	0.976	CLONAL	1	TRUE	1	0.315723020487005	2		365	447	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672428	30672430	+	frameshift_variant	Frame_Shift_Del	DEL	GTG	GTG	TA	novel	NA	P-0043916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	177	489	1	ENST00000376406.3:c.4530_4532delinsTA	p.Thr1511AsnfsTer64	p.T1511Nfs*64	ENST00000376406	NM_014641.2	1510	ccCACa/ccTAa	10/15	0.315723020487005	3	FACETS	0.857	0.792	0.926	0.857	0.792	0.926	CLONAL	2	TRUE	1	0.315723020487005	3		490	757	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0043917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	216	395	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.831	0.778	0.884	1	0.993	1	CLONAL	2	TRUE	1	0.453711708233163	2		396	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0043917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	445	712	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.427199594942878	2	FACETS	0.887	0.848	0.926	0.887	0.848	0.926	CLONAL	2	TRUE	0	0.453711708233163	2		712	1106	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491360	18491360	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	26	122	0	ENST00000266497.5:c.1273G>A	p.Glu425Lys	p.E425K	ENST00000266497		425	Gaa/Aaa	8/31	0.295199183698976	3	FACETS	0.764	0.621	0.92	0.764	0.621	0.92	CLONAL	2	TRUE	1	0.453711708233163	3		122	92	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424958105	NA	P-0043917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	132	501	0	ENST00000334344.6:c.940C>T	p.Arg314Cys	p.R314C	ENST00000334344	NM_152641.2	314	Cgt/Tgt	8/21	0.406131347816518	2	FACETS	0.996	0.921	1	0.996	0.921	1	CLONAL	2	TRUE	0	0.453711708233163	2		501	292	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510606	38510606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	479	586	0	ENST00000254066.5:c.860C>T	p.Ser287Leu	p.S287L	ENST00000254066	NM_000964.3	287	tCg/tTg	7/9	0.427199594942878	2	FACETS	0.944	0.906	0.983	0.944	0.906	0.983	CLONAL	2	TRUE	0	0.453711708233163	2		586	1118	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50358686	50358686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	105	213	0	ENST00000331340.3:c.29C>T	p.Ser10Phe	p.S10F	ENST00000331340	NM_006060.4	10	tCc/tTc	2/8	0.308017821135713	4	FACETS	0.779	0.702	0.859	0.779	0.702	0.859	SUBCLONAL	2	TRUE	2	0.453711708233163	4		213	432	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913255	NA	P-0043917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	271	490	0	ENST00000369535.4:c.183A>C	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caC	3/7	0.364626229976945	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	2	0.453711708233163	4		490	854	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777960	3777960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1266123570	NA	P-0043917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1436	412	831	0	ENST00000262367.5:c.7088C>T	p.Pro2363Leu	p.P2363L	ENST00000262367	NM_004380.2	2363	cCg/cTg	31/31	0.155897180898115	5	FACETS	0.826	0.784	0.869	0.551	0.522	0.58	INDETERMINATE	2	TRUE	2	0.453711708233163	5		831	1848	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256051	123256051	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	135	405	0	ENST00000358487.5:c.1858C>T	p.Gln620Ter	p.Q620*	ENST00000358487	NM_000141.4	620	Caa/Taa	13/18	1	2	FACETS	0.913	0.832	0.997	0.913	0.832	0.997	CLONAL	1	TRUE	1	0.453711708233163	2		405	652	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518073	8518073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1480778931	NA	P-0043917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	182	339	0	ENST00000356435.5:c.1318G>A	p.Glu440Lys	p.E440K	ENST00000356435		440	Gaa/Aaa	10/35	0.388541352469671	3	FACETS	0.818	0.758	0.878	0.818	0.758	0.878	CLONAL	2	TRUE	1	0.453711708233163	3		339	602	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940571	71940571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760513714	NA	P-0043917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	518	591	1	ENST00000298229.2:c.722C>T	p.Ser241Leu	p.S241L	ENST00000298229	NM_001567.3	241	tCg/tTg	6/28	0.406131347816518	2	FACETS	0.93	0.894	0.968	0.93	0.894	0.968	CLONAL	2	TRUE	0	0.453711708233163	2		592	1227	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946286	55946286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751241917	NA	P-0043917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	86	259	0	ENST00000263923.4:c.3893G>A	p.Gly1298Asp	p.G1298D	ENST00000263923	NM_002253.2	1298	gGc/gAc	30/30	1	2	FACETS	0.678	0.601	0.76	0.678	0.601	0.76	SUBCLONAL	1	TRUE	1	0.453711708233163	2		259	559	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954242	17954242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201419310	NA	P-0043917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	379	608	0	ENST00000458235.1:c.367G>A	p.Asp123Asn	p.D123N	ENST00000458235	NM_000215.3	123	Gat/Aat	4/24	0.334372006172349	3	FACETS	0.844	0.802	0.887	0.844	0.802	0.887	CLONAL	2	TRUE	1	0.453711708233163	3		608	1214	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385261	41385261	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	275	404	0	ENST00000373198.4:c.700G>A	p.Asp234Asn	p.D234N	ENST00000373198	NM_133170.3	234	Gac/Aac	6/32	0.308017821135713	4	FACETS	0.82	0.77	0.871	0.82	0.77	0.871	CLONAL	2	TRUE	2	0.453711708233163	4		404	1075	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007798	45007801	+	frameshift_variant	Frame_Shift_Del	DEL	TCTA	TCTA	-	novel	NA	P-0043917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	66	312	0	ENST00000558401.1:c.248_251del	p.Tyr83SerfsTer19	p.Y83Sfs*19	ENST00000558401	NM_004048.2	82	tTCTAt/tt	2/4	0.453711708233163	1	FACETS	0.792	0.694	0.896	0.792	0.694	0.896	SUBCLONAL	1	TRUE	0	0.453711708233163	1		312	284	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806210	1806210	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	191	633	0	ENST00000260795.2:c.1229C>T	p.Thr410Ile	p.T410I	ENST00000260795		410	aCc/aTc	8/17	1	2	FACETS	0.754	0.697	0.815	0.754	0.697	0.815	SUBCLONAL	1	TRUE	1	0.453711708233163	2		633	1116	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63662122	63662122	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	121	379	0	ENST00000279873.7:c.226T>C	p.Tyr76His	p.Y76H	ENST00000279873	NM_032199.2	76	Tat/Cat	2/10	1	2	FACETS	0.767	0.694	0.844	0.767	0.694	0.844	SUBCLONAL	1	TRUE	1	0.453711708233163	2		379	695	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279617	123279617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	144	442	0	ENST00000358487.5:c.815G>A	p.Gly272Glu	p.G272E	ENST00000358487	NM_000141.4	272	gGa/gAa	7/18	1	2	FACETS	0.768	0.7	0.838	0.768	0.7	0.838	SUBCLONAL	1	TRUE	1	0.453711708233163	2		442	827	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125085	46125086	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0043917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	50	183	0	ENST00000334344.6:c.272_273del	p.Gln91LeufsTer19	p.Q91Lfs*19	ENST00000334344	NM_152641.2	91	cAG/c	3/21	0.406131347816518	2	FACETS	0.81	0.705	0.92	0.81	0.705	0.92	CLONAL	2	TRUE	0	0.453711708233163	2		183	136	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012443	29012443	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1270070382	NA	P-0043917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	173	393	0	ENST00000282397.4:c.428C>T	p.Pro143Leu	p.P143L	ENST00000282397	NM_002019.4	143	cCc/cTc	4/30	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.453711708233163	2		393	530	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992699	72992699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778782642	NA	P-0043917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	275	552	1	ENST00000268489.5:c.1346G>A	p.Gly449Glu	p.G449E	ENST00000268489	NM_006885.3	449	gGg/gAg	2/10	0.155897180898115	5	FACETS	0.816	0.765	0.868	0.544	0.51	0.579	INDETERMINATE	2	TRUE	2	0.453711708233163	5		553	1249	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530103	63530103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398258340	NA	P-0043917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	368	438	0	ENST00000307078.5:c.2332C>T	p.Arg778Trp	p.R778W	ENST00000307078	NM_004655.3	778	Cgg/Tgg	10/11	0.427199594942878	2	FACETS	0.88	0.838	0.922	0.88	0.838	0.922	CLONAL	2	TRUE	0	0.453711708233163	2		438	922	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56363681	56363681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	142	300	0	ENST00000348428.3:c.460C>T	p.Pro154Ser	p.P154S	ENST00000348428	NM_006785.3	154	Cct/Tct	3/17	0.295199183698976	3	FACETS	0.79	0.725	0.857	0.79	0.725	0.857	SUBCLONAL	2	TRUE	1	0.453711708233163	3		300	486	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226371	2226372	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0043917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	247	563	1	ENST00000398665.3:c.3851_3852delinsTT	p.Ala1284Val	p.A1284V	ENST00000398665	NM_032482.2	1284	gCC/gTT	27/28	0.334372006172349	3	FACETS	1	0.949	1	0.51	0.476	0.545	CLONAL	1	TRUE	1	0.453711708233163	3		564	1310	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032054	11032054	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	175	443	0	ENST00000327064.4:c.1619A>G	p.Asn540Ser	p.N540S	ENST00000327064	NM_199141.1	540	aAc/aGc	15/16	0.334372006172349	3	FACETS	0.845	0.777	0.916	0.423	0.388	0.458	CLONAL	1	TRUE	1	0.453711708233163	3		443	1120	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290252	15290252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	442	646	0	ENST00000263388.2:c.3383C>T	p.Ser1128Phe	p.S1128F	ENST00000263388	NM_000435.2	1128	tCc/tTc	21/33	0.334372006172349	3	FACETS	0.837	0.798	0.877	0.837	0.798	0.877	CLONAL	2	TRUE	1	0.453711708233163	3		646	1428	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967048	18967048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762952797	NA	P-0043917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	352	484	0	ENST00000262803.5:c.1763C>T	p.Ser588Leu	p.S588L	ENST00000262803	NM_002911.3	588	tCg/tTg	13/24	0.334372006172349	3	FACETS	0.839	0.795	0.883	0.839	0.795	0.883	CLONAL	2	TRUE	1	0.453711708233163	3		484	1135	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31407029	31407029	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	108	412	0	ENST00000344624.3:c.3878C>T	p.Ser1293Phe	p.S1293F	ENST00000344624		1293	tCc/tTc	31/33	1	2	FACETS	0.679	0.61	0.752	0.679	0.61	0.752	SUBCLONAL	1	TRUE	1	0.453711708233163	2		412	701	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509277	106509278	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0043917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	279	465	0	ENST00000359195.3:c.1271_1272delinsTT	p.Pro424Leu	p.P424L	ENST00000359195	NM_002649.2	424	cCC/cTT	2/11	0.308017821135713	4	FACETS	0.784	0.736	0.833	0.784	0.736	0.833	SUBCLONAL	2	TRUE	2	0.453711708233163	4		465	1140	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36823907	36823907	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1215063514	NA	P-0043956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	93	568	0	ENST00000373129.3:c.275C>T	p.Thr92Ile	p.T92I	ENST00000373129	NM_032017.1	92	aCc/aTc	5/12	1	2	FACETS	0.724	0.643	0.811	0.724	0.643	0.811	SUBCLONAL	1	TRUE	1	0.30547470794709	2		568	841	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864703	57864703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241006818	NA	P-0043956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	96	806	0	ENST00000228682.2:c.2180C>T	p.Thr727Ile	p.T727I	ENST00000228682	NM_005269.2	727	aCt/aTt	12/12	0.203838389624333	3	FACETS	0.725	0.644	0.811	0.362	0.322	0.406	SUBCLONAL	1	TRUE	1	0.30547470794709	3		806	1000	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729814	41729814	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	77	419	0	ENST00000242208.4:c.715G>A	p.Asp239Asn	p.D239N	ENST00000242208	NM_002192.2	239	Gac/Aac	3/3	0.18952151009206	3	FACETS	1	0.953	1	0.583	0.513	0.658	CLONAL	1	TRUE	1	0.30547470794709	3		419	498	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508094	106508094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1212203463	NA	P-0043956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	39	288	0	ENST00000359195.3:c.88G>A	p.Ala30Thr	p.A30T	ENST00000359195	NM_002649.2	30	Gcc/Acc	2/11	0.30547470794709	6	FACETS	0.668	0.552	0.797			1	SUBCLONAL	1	TRUE	NA	0.30547470794709	6		288	616	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339843	116339844	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0043956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	50	436	0	ENST00000397752.3:c.705_706del	p.Asp236CysfsTer4	p.D236Cfs*4	ENST00000397752	NM_000245.2	235	atTGat/atat	2/21	0.30547470794709	6	FACETS	0.532	0.449	0.623			1	SUBCLONAL	1	TRUE	NA	0.30547470794709	6		436	992	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411877	116411887	+	intron_variant	Intron	DEL	AGCTCTTTCTT	AGCTCTTTCTT	-	novel	NA	P-0043956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	778	813	0	ENST00000397752.3:c.2888-26_2888-16del		p.*963*	ENST00000397752	NM_000245.2	-/1390			0.30547470794709	6	FACETS	0.921	0.892	0.951			1	CLONAL	5	TRUE	NA	0.30547470794709	6		813	1781	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	139	672	0	ENST00000397752.3:c.3028+1del		p.D1010fs	ENST00000397752	NM_000245.2	1010	Gat/at	14/21	0.33588598746093	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.33588598746093	1		672	640	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363636	40363637	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0043962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	29	395	0	ENST00000397332.2:c.592dup	p.Glu198GlyfsTer4	p.E198Gfs*4	ENST00000397332	NM_001033082.2	198	gaa/gGaa	3/3	1	2	FACETS	0.43	0.344	0.526	0.43	0.344	0.526	SUBCLONAL	1	TRUE	1	0.33588598746093	2		395	402	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40379639	40379639	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	85	706	0	ENST00000293328.3:c.193G>A	p.Val65Met	p.V65M	ENST00000293328	NM_012448.3	65	Gtg/Atg	3/19	1	2	FACETS	0.774	0.684	0.87	0.774	0.684	0.87	SUBCLONAL	1	TRUE	1	0.33588598746093	2		706	654	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030774	48030774	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs752164796	NA	P-0043962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	38	315	0	ENST00000234420.5:c.3388G>C	p.Val1130Leu	p.V1130L	ENST00000234420	NM_000179.2	1130	Gtg/Ctg	5/10	1	2	FACETS	0.802	0.667	0.952	0.802	0.667	0.952	CLONAL	1	TRUE	1	0.33588598746093	2		315	282	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983407	90983407	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	24	202	0	ENST00000265433.3:c.696del	p.Lys233AsnfsTer6	p.K233Nfs*6	ENST00000265433	NM_002485.4	232	gcC/gc	6/16	0.33588598746093	1	FACETS	0.632	0.499	0.784	0.632	0.499	0.784	SUBCLONAL	1	TRUE	0	0.33588598746093	1		202	188	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347184	70347184	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0043962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	80	531	0	ENST00000374080.3:c.2850-2A>T		p.X950_splice	ENST00000374080		950			1	2	FACETS	0.866	0.764	0.975	0.866	0.764	0.975	CLONAL	1	TRUE	1	0.33588598746093	2		531	550	SUCCESS
AR	367	MSKCC	GRCh37	X	66766357	66766395	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	-	rs746853821	NA	P-0043963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	122	60	0	ENST00000374690.3:c.1382_1420del	p.Gly461_Gly473del	p.G461_G473del	ENST00000374690	NM_000044.3	457	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC/-	1/8	1	1	FACETS	0.862	0.806	0.916	1	0.991	1	CLONAL	2	TRUE	0	0.546942126121796	1		60	188	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508563	106508563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757016725	NA	P-0043963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	27	382	0	ENST00000359195.3:c.557C>T	p.Ala186Val	p.A186V	ENST00000359195	NM_002649.2	186	gCg/gTg	2/11	0.316314903312507	3	FACETS	0.334	0.266	0.413	0.111	0.088	0.138	INDETERMINATE	1	TRUE	0	0.546942126121796	3		382	376	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856520	111856520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	112	359	0	ENST00000341259.2:c.571C>T	p.Pro191Ser	p.P191S	ENST00000341259	NM_005475.2	191	Ccg/Tcg	2/8	0.546942126121796	3	FACETS	1	0.906	1	0.501	0.453	0.553	CLONAL	1	TRUE	1	0.546942126121796	3		359	520	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708494	43708494	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	138	677	0	ENST00000382044.4:c.4802T>C	p.Leu1601Pro	p.L1601P	ENST00000382044	NM_001141980.1	1601	cTg/cCg	22/28	0.546942126121796	3	FACETS	0.766	0.697	0.838	0.383	0.348	0.419	SUBCLONAL	1	TRUE	1	0.546942126121796	3		677	839	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672251	30672251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1051478283	NA	P-0043963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	67	708	0	ENST00000376406.3:c.4709C>T	p.Ser1570Leu	p.S1570L	ENST00000376406	NM_014641.2	1570	tCa/tTa	10/15	0.546942126121796	3	FACETS	0.313	0.271	0.358	0.156	0.135	0.179	SUBCLONAL	1	TRUE	1	0.546942126121796	3		708	998	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5029843	5029843	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	52	443	0	ENST00000381652.3:c.287A>T	p.Tyr96Phe	p.Y96F	ENST00000381652	NM_004972.3	96	tAt/tTt	4/25	0.546942126121796	1	FACETS	0.593	0.51	0.682	0.593	0.51	0.682	SUBCLONAL	1	TRUE	0	0.546942126121796	1		443	233	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0043994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	336	721	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.442720041515133	2	FACETS	0.899	0.856	0.942	0.899	0.856	0.942	CLONAL	2	TRUE	0	0.51000660594865	2		723	733	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105554	30105554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757417278	NA	P-0043994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	105	491	0	ENST00000331968.5:c.1132G>A	p.Asp378Asn	p.D378N	ENST00000331968	NM_002742.2	378	Gac/Aac	7/18	1	2	FACETS	0.768	0.691	0.85	0.768	0.691	0.85	SUBCLONAL	1	TRUE	1	0.51000660594865	2		491	536	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777975	3777975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	200	907	1	ENST00000262367.5:c.7073C>T	p.Pro2358Leu	p.P2358L	ENST00000262367	NM_004380.2	2358	cCt/cTt	31/31	1	2	FACETS	0.835	0.774	0.899	0.835	0.774	0.899	CLONAL	1	TRUE	1	0.51000660594865	2		908	939	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646667	23646667	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	96	429	0	ENST00000261584.4:c.1200del	p.Gly401AlafsTer23	p.G401Afs*23	ENST00000261584	NM_024675.3	400	gaA/ga	4/13	1	2	FACETS	0.898	0.806	0.996	0.898	0.806	0.996	CLONAL	1	TRUE	1	0.51000660594865	2		429	419	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922527	56922527	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	105	529	0	ENST00000519728.1:c.1397A>G	p.Glu466Gly	p.E466G	ENST00000519728	NM_002350.3	466	gAg/gGg	13/13	0.48204642887046	2	FACETS	0.795	0.715	0.879	0.397	0.357	0.44	SUBCLONAL	1	TRUE	0	0.51000660594865	2		529	518	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994323	21994323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	231	380	0	ENST00000579755.1:c.8G>A	p.Arg3His	p.R3H	ENST00000579755		3	cGc/cAc	1/3	0.138378207533965				0.943	1				INDETERMINATE	3	TRUE	1	0.51000660594865	5		380	532	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938522	76938523	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0043994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	130	204	1	ENST00000373344.5:c.2225_2226delinsAT	p.Ser742Asn	p.S742N	ENST00000373344	NM_000489.3	742	aGC/aAT	9/35	0.51000660594865	2	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.51000660594865	2		205	208	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971138	21971138	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs760640852	NA	P-0044013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	35	315	1	ENST00000304494.5:c.220G>T	p.Asp74Tyr	p.D74Y	ENST00000304494	NM_000077.4	74	Gac/Tac	2/3	1	2	FACETS	0.746	0.612	0.897	0.746	0.612	0.897	SUBCLONAL	1	TRUE	1	0.227666483547964	2		316	412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573010	7573010	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs587781664	NA	P-0044013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	24	253	0	ENST00000269305.4:c.1101-2A>G		p.X367_splice	ENST00000269305	NM_001126112.2	367			1	2	FACETS	0.653	0.512	0.815	0.653	0.512	0.815	SUBCLONAL	1	TRUE	1	0.227666483547964	2		253	323	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132565	11132565	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	49	586	0	ENST00000358026.2:c.2782del	p.Leu928CysfsTer22	p.L928Cfs*22	ENST00000358026	NM_001128849.1	927	ttC/tt	19/36	0.201647655644639	1	FACETS	0.647	0.547	0.756	0.647	0.547	0.756	SUBCLONAL	1	TRUE	0	0.227666483547964	1		586	590	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0044016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	137	696	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.162224346108731	3	FACETS	1	0.985	1	0.719	0.654	0.787	CLONAL	1	TRUE	1	0.26890092340162	3		696	804	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041266	47041266	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0044016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	91	672	0	ENST00000377604.3:c.1693+1G>T		p.X565_splice	ENST00000377604	NM_001204468.1	565			1	2	FACETS	0.774	0.686	0.867	0.774	0.686	0.867	SUBCLONAL	1	TRUE	1	0.26890092340162	2		672	875	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579529	7579530	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	161	702	0	ENST00000269305.4:c.157dup	p.Trp53LeufsTer4	p.W53Lfs*4	ENST00000269305	NM_001126112.2	53	tgg/tTgg	4/11	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.26890092340162	2		702	922	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120493413	120493413	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	67	389	0	ENST00000256646.2:c.2413C>A	p.Leu805Met	p.L805M	ENST00000256646	NM_024408.3	805	Ctg/Atg	15/34	0.179916658383505	4	FACETS	1	0.967	1	0.687	0.599	0.783	CLONAL	1	TRUE	2	0.26890092340162	4		389	460	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437599	110437599	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	143	708	0	ENST00000375856.3:c.802G>T	p.Gly268Cys	p.G268C	ENST00000375856	NM_003749.2	268	Ggc/Tgc	1/2	0.258925677821938	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.26890092340162	1		708	835	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984880	9984880	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	54	506	0	ENST00000330684.3:c.1085T>C	p.Val362Ala	p.V362A	ENST00000330684	NM_001134407.1	362	gTg/gCg	4/13	0.26890092340162	3	FACETS	0.72	0.614	0.836	0.36	0.307	0.418	SUBCLONAL	1	TRUE	1	0.26890092340162	3		506	633	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0044017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	131	502	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.223419723795853	3	FACETS	1	0.979	1	0.62	0.565	0.677	INDETERMINATE	1	TRUE	1	0.481322028116111	3		502	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0044017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	162	595	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	0.474841490564046	1	FACETS	0.495	0.454	0.539	0.495	0.454	0.539	SUBCLONAL	1	TRUE	0	0.481322028116111	1		595	1032	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0044017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	80	422	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.474841490564046	1	FACETS	0.274	0.24	0.31	0.274	0.24	0.31	SUBCLONAL	1	TRUE	0	0.481322028116111	1		422	921	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0044017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	20	648	1	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.474841490564046	1	FACETS	0.066	0.05	0.086	0.066	0.05	0.086	SUBCLONAL	1	TRUE	0	0.481322028116111	1		649	952	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007802	45007802	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0044017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	30	271	0	ENST00000558401.1:c.249T>G	p.Tyr83Ter	p.Y83*	ENST00000558401	NM_004048.2	83	taT/taG	2/4	0.481322028116111	1	FACETS	0.263	0.212	0.321	0.263	0.212	0.321	SUBCLONAL	1	TRUE	0	0.481322028116111	1		271	360	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	40	214	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.739	0.616	0.876	0.739	0.616	0.876	SUBCLONAL	1	TRUE	1	0.31539841433694	2		214	343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0044020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	105	352	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.31539841433694	1	FACETS	0.808	0.725	0.897	0.808	0.725	0.897	CLONAL	1	TRUE	0	0.31539841433694	1		353	694	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0044020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	67	280	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.31539841433694	2		280	410	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265479	152265479	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766779326	NA	P-0044020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	63	438	0	ENST00000206249.3:c.932C>T	p.Thr311Met	p.T311M	ENST00000206249	NM_000125.3	311	aCg/aTg	4/8	1	2	FACETS	0.71	0.614	0.813	0.71	0.614	0.813	SUBCLONAL	1	TRUE	1	0.31539841433694	2		438	563	SUCCESS
APC	324	MSKCC	GRCh37	5	112175346	112175350	+	frameshift_variant	Frame_Shift_Del	DEL	TTGAA	TTGAA	-	novel	NA	P-0044020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	73	185	0	ENST00000257430.4:c.4057_4061del	p.Glu1353PhefsTer20	p.E1353Ffs*20	ENST00000257430	NM_000038.5	1352	gTTGAA/g	16/16	0.295772488072123	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	2	TRUE	0	0.31539841433694	2		185	230	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871727	35871727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781464425	NA	P-0044020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	107	411	1	ENST00000216797.5:c.779G>A	p.Arg260His	p.R260H	ENST00000216797	NM_020529.2	260	cGc/cAc	5/6	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.31539841433694	2		412	602	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245459	153245459	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	63	406	0	ENST00000281708.4:c.1732A>C	p.Thr578Pro	p.T578P	ENST00000281708	NM_033632.3	578	Aca/Cca	11/12	1	2	FACETS	0.805	0.698	0.922	0.805	0.698	0.922	CLONAL	1	TRUE	1	0.31539841433694	2		406	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934578	NA	P-0044046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	136	539	0	ENST00000269305.4:c.524G>T	p.Arg175Leu	p.R175L	ENST00000269305	NM_001126112.2	175	cGc/cTc	5/11	0.355952649697616	3	FACETS	1	0.978	1	0.608	0.555	0.662	CLONAL	1	TRUE	1	0.532762941863323	3		539	532	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248998	55248999	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCAGCG	rs727504263	NA	P-0044046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	212	426	0	ENST00000275493.2:c.2300_2308dup	p.Ala767_Val769dup	p.A767_V769dup	ENST00000275493	NM_005228.3	767	atg/aTGGCCAGCGtg	20/28	0.485045208737685	4	FACETS	1	0.978	1	0.733	0.686	0.78	CLONAL	2	TRUE	1	0.532762941863323	4		426	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519996	NA	P-0044046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	285	627	2	ENST00000269305.4:c.395A>T	p.Lys132Met	p.K132M	ENST00000269305	NM_001126112.2	132	aAg/aTg	5/11	0.355952649697616	3	FACETS	0.958	0.906	1	0.958	0.906	1	CLONAL	2	TRUE	1	0.532762941863323	3		629	707	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005561	42005566	+	inframe_deletion	In_Frame_Del	DEL	TCAGAG	TCAGAG	-	novel	NA	P-0044046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	89	451	0	ENST00000219905.7:c.3297_3302del	p.Phe1099_Arg1101delinsLeu	p.F1099_R1101delinsL	ENST00000219905	NM_001164273.1	1099	ttTCAGAGg/ttg	9/24	1	2	FACETS	0.941	0.841	1	0.941	0.841	1	CLONAL	1	TRUE	1	0.532762941863323	2		451	355	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678048	117678048	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	56	305	0	ENST00000368508.3:c.3885del	p.Phe1295LeufsTer37	p.F1295Lfs*37	ENST00000368508	NM_002944.2	1295	ttT/tt	25/43	0.532762941863323	3	FACETS	0.797	0.687	0.916	0.399	0.343	0.458	CLONAL	1	TRUE	1	0.532762941863323	3		305	334	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239970	53239970	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	206	608	0	ENST00000375401.3:c.1471A>G	p.Asn491Asp	p.N491D	ENST00000375401	NM_004187.3	491	Aat/Gat	11/26	0.498816409015151	3	FACETS	0.862	0.806	0.92	0.862	0.806	0.92	CLONAL	2	TRUE	1	0.532762941863323	3		608	568	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	161	615	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.853	0.786	0.922	1	0.993	1	CLONAL	3	TRUE	1	0.22	2		615	572	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	117	548	1				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	0.867	0.79	0.946	1	0.991	1	CLONAL	3	TRUE	0	0.22	1		549	364	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257642	16257643	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	164	430	1	ENST00000375759.3:c.4907_4908delinsTT	p.Ser1636Phe	p.S1636F	ENST00000375759	NM_015001.2	1636	tCC/tTT	11/15	1	2	FACETS	1	0.979	1	1	0.993	1	CLONAL	2	TRUE	1	0.22	2		431	633	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259445	16259445	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	148	419	0	ENST00000375759.3:c.6710C>T	p.Pro2237Leu	p.P2237L	ENST00000375759	NM_015001.2	2237	cCa/cTa	11/15	1	2	FACETS	0.838	0.77	0.909	1	0.993	1	CLONAL	3	TRUE	1	0.22	2		419	535	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459200	120459200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	214	476	0	ENST00000256646.2:c.6145G>T	p.Val2049Leu	p.V2049L	ENST00000256646	NM_024408.3	2049	Gtg/Ttg	34/34	1	2	FACETS	0.965	0.901	1	1	0.995	1	CLONAL	3	TRUE	1	0.22	2		476	672	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120509017	120509018	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	153	370	0	ENST00000256646.2:c.1548_1549delinsTT	p.Gln517Ter	p.Q517*	ENST00000256646	NM_024408.3	516	ttCCag/ttTTag	9/34	1	2	FACETS	1	0.949	1	1	0.992	1	CLONAL	2	TRUE	1	0.22	2		370	665	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162750004	162750004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	249	363	0	ENST00000367921.3:c.2536C>T	p.His846Tyr	p.H846Y	ENST00000367921	NM_006182.2	846	Cac/Tac	18/18	1	2	FACETS	1	0.97	1	1	0.996	1	CLONAL	3	TRUE	1	0.22	2		363	718	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607598	43607599	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	173	675	0	ENST00000355710.3:c.1574_1575delinsAA	p.Arg525Gln	p.R525Q	ENST00000355710	NM_020975.4	525	cGG/cAA	8/20	1	2	FACETS	0.902	0.835	0.971	1	0.994	1	CLONAL	3	TRUE	1	0.22	2		675	581	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572211	64572212	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	58	388	1	ENST00000312049.6:c.1427_1428delinsAA	p.Arg476Gln	p.R476Q	ENST00000312049	NM_130799.2	476	cGG/cAA	10/10	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.22	2		389	496	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202575	67202575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	265	596	0	ENST00000312629.5:c.1384C>T	p.Leu462Phe	p.L462F	ENST00000312629	NM_003952.2	462	Ctc/Ttc	15/15	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.22	2		596	978	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488312	56488312	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373609369	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	54	418	1	ENST00000267101.3:c.1831C>T	p.Arg611Trp	p.R611W	ENST00000267101	NM_001982.3	611	Cgg/Tgg	15/28	0.0679568550509966	4	FACETS	0.817	0.697	0.95	0.409	0.348	0.475	INDETERMINATE	1	TRUE	2	0.22	4		419	733	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426724	121426724	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	199	558	1	ENST00000257555.6:c.415C>T	p.Leu139Phe	p.L139F	ENST00000257555		139	Ctc/Ttc	2/10	0.3	1	FACETS	1	0.982	1	1	0.994	1	CLONAL	2	TRUE	0	0.22	1		559	692	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249230	133249230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754985761	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	221	486	1	ENST00000320574.5:c.1669C>T	p.Pro557Ser	p.P557S	ENST00000320574	NM_006231.2	557	Cct/Tct	15/49	0.3	1	FACETS	0.93	0.87	0.991	1	0.995	1	CLONAL	3	TRUE	0	0.22	1		487	641	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281373	49281374	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	250	585	0	ENST00000282018.3:c.420_421delinsAA	p.Met140_Val141delinsIleIle	p.M140_V141delinsII	ENST00000282018	NM_020377.2	140	atGGtt/atAAtt	1/1	1	2	FACETS	0.855	0.801	0.91	1	0.995	1	CLONAL	3	TRUE	1	0.22	2		585	886	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961123	41961123	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	107	268	0	ENST00000219905.7:c.31A>T	p.Asn11Tyr	p.N11Y	ENST00000219905	NM_001164273.1	11	Aat/Tat	2/24	1	2	FACETS	0.945	0.857	1	1	0.991	1	CLONAL	3	TRUE	1	0.22	2		268	343	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500624	99500624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373440147	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	171	445	0	ENST00000268035.6:c.4057C>T	p.Arg1353Cys	p.R1353C	ENST00000268035	NM_000875.3	1353	Cgc/Tgc	21/21	1	2	FACETS	1	0.952	1	1	0.994	1	CLONAL	3	TRUE	1	0.22	2		445	501	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652231	3652231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	226	593	0	ENST00000294008.3:c.838G>A	p.Gly280Arg	p.G280R	ENST00000294008	NM_032444.2	280	Gga/Aga	4/15	1	2	FACETS	0.916	0.856	0.977	1	0.995	1	CLONAL	3	TRUE	1	0.22	2		593	748	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857077	9857077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	78	261	0	ENST00000330684.3:c.4324C>T	p.Pro1442Ser	p.P1442S	ENST00000330684	NM_001134407.1	1442	Ccc/Tcc	13/13	1	2	FACETS	0.847	0.753	0.946	1	0.987	1	CLONAL	3	TRUE	1	0.22	2		261	279	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857502	9857502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	109	373	0	ENST00000330684.3:c.3899G>A	p.Arg1300Lys	p.R1300K	ENST00000330684	NM_001134407.1	1300	aGg/aAg	13/13	1	2	FACETS	0.865	0.783	0.949	1	0.99	1	CLONAL	3	TRUE	1	0.22	2		373	382	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858445	9858445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	90	454	0	ENST00000330684.3:c.2956C>T	p.Leu986Phe	p.L986F	ENST00000330684	NM_001134407.1	986	Ctt/Ttt	13/13	1	2	FACETS	1	0.959	1	1	0.987	1	CLONAL	2	TRUE	1	0.22	2		454	357	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923385	9923386	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	109	484	0	ENST00000330684.3:c.1901_1902delinsAA	p.Trp634Ter	p.W634*	ENST00000330684	NM_001134407.1	634	tGG/tAA	9/13	1	2	FACETS	1	0.96	1	1	0.989	1	CLONAL	2	TRUE	1	0.22	2		484	442	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827411	72827412	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	141	515	0	ENST00000268489.5:c.9169_9170delinsAA	p.Gly3057Lys	p.G3057K	ENST00000268489	NM_006885.3	3057	GGa/AAa	9/10	1	2	FACETS	0.839	0.769	0.912	1	0.992	1	CLONAL	3	TRUE	1	0.22	2		515	509	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349450	89349450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	245	655	0	ENST00000301030.4:c.3500C>T	p.Ser1167Phe	p.S1167F	ENST00000301030	NM_001256183.1	1167	tCt/tTt	9/13	1	2	FACETS	0.866	0.811	0.923	1	0.995	1	CLONAL	3	TRUE	1	0.22	2		655	857	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577540	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	rs1555525498	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	194	680	2	ENST00000269305.4:c.741_742delinsTT	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	247	aaCCgg/aaTTgg	7/11	1	2	FACETS	1	0.982	1	1	0.994	1	CLONAL	2	TRUE	1	0.22	2		682	748	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	203	556	1	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	1	2	FACETS	0.866	0.806	0.928	1	0.995	1	CLONAL	3	TRUE	1	0.22	2		557	710	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028625	12028626	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	87	319	0	ENST00000353533.5:c.828_829delinsTT	p.Pro277Ser	p.P277S	ENST00000353533	NM_003010.3	276	gaCCca/gaTTca	8/11	1	2	FACETS	1	0.95	1	1	0.987	1	CLONAL	2	TRUE	1	0.22	2		319	356	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805881	46805882	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	108	432	1	ENST00000290295.7:c.74_75delinsAA	p.Arg25Gln	p.R25Q	ENST00000290295	NM_006361.5	25	cGG/cAA	1/2	1	2	FACETS	1	0.968	1	1	0.99	1	CLONAL	2	TRUE	1	0.22	2		433	420	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120127	70120128	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	53	124	0	ENST00000245479.2:c.1129_1130delinsTT	p.Pro377Leu	p.P377L	ENST00000245479	NM_000346.3	377	CCa/TTa	3/3	1	2	FACETS	1	0.953	1	1	0.98	1	CLONAL	2	TRUE	1	0.22	2		124	193	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39567860	39567860	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	74	163	1	ENST00000262039.4:c.616G>A	p.Glu206Lys	p.E206K	ENST00000262039	NM_002647.2	206	Gag/Aag	5/25	1	2	FACETS	0.859	0.762	0.961	1	0.986	1	CLONAL	3	TRUE	1	0.22	2		164	261	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985691	60985691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1435116050	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	28	71	0	ENST00000333681.4:c.209C>T	p.Ser70Leu	p.S70L	ENST00000333681		70	tCg/tTg	2/3	1	2	FACETS	0.922	0.748	1	1	0.954	1	CLONAL	2	TRUE	1	0.22	2		71	138	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097099	11097099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs988231473	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	185	568	0	ENST00000358026.2:c.590C>T	p.Pro197Leu	p.P197L	ENST00000358026	NM_001128849.1	197	cCc/cTc	4/36	1	2	FACETS	0.834	0.773	0.897	1	0.994	1	CLONAL	3	TRUE	1	0.22	2		568	672	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271814	15271814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	163	654	1	ENST00000263388.2:c.6625C>T	p.Pro2209Ser	p.P2209S	ENST00000263388	NM_000435.2	2209	Ccg/Tcg	33/33	1	2	FACETS	0.984	0.905	1	1	0.992	1	CLONAL	2	TRUE	1	0.22	2		655	753	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271912	15271912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	242	614	0	ENST00000263388.2:c.6527C>T	p.Pro2176Leu	p.P2176L	ENST00000263388	NM_000435.2	2176	cCc/cTc	33/33	1	2	FACETS	1	0.982	1	1	0.996	1	CLONAL	3	TRUE	1	0.22	2		614	657	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350270	15350271	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	165	548	2	ENST00000263377.2:c.3508_3509delinsTT	p.Pro1170Leu	p.P1170L	ENST00000263377	NM_058243.2	1170	CCg/TTg	17/20	1	2	FACETS	1	0.975	1	1	0.993	1	CLONAL	2	TRUE	1	0.22	2		550	658	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384714	17384714	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	161	492	0	ENST00000359435.4:c.346T>A	p.Ser116Thr	p.S116T	ENST00000359435	NM_001033549.1	116	Tcc/Acc	4/9	1	2	FACETS	1	0.972	1	1	0.993	1	CLONAL	2	TRUE	1	0.22	2		492	653	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741864	40741864	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	183	544	0	ENST00000392038.2:c.1108C>T	p.Pro370Ser	p.P370S	ENST00000392038	NM_001626.4	370	Ccg/Tcg	11/14	1	2	FACETS	0.953	0.885	1	1	0.994	1	CLONAL	3	TRUE	1	0.22	2		544	582	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797938	42797939	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	194	580	2	ENST00000575354.2:c.3990_3991delinsAA	p.Val1331Met	p.V1331M	ENST00000575354	NM_015125.3	1330	aaGGtg/aaAAtg	16/20	1	2	FACETS	1	0.979	1	1	0.994	1	CLONAL	2	TRUE	1	0.22	2		582	772	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705464	47705464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	94	287	0	ENST00000233146.2:c.2264C>T	p.Ser755Phe	p.S755F	ENST00000233146	NM_000251.2	755	tCt/tTt	14/16	1	2	FACETS	1	0.968	1	1	0.988	1	CLONAL	2	TRUE	1	0.22	2		287	357	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439878	220439878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148455844	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	385	597	0	ENST00000243786.2:c.731C>T	p.Ser244Phe	p.S244F	ENST00000243786	NM_002191.3	244	tCt/tTt	2/2	0.3	2	FACETS	0.941	0.905	0.976	1	0.997	1	CLONAL	6	TRUE	0	0.22	2		597	620	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546787	9546787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	84	339	0	ENST00000353224.5:c.1235C>T	p.Pro412Leu	p.P412L	ENST00000353224	NM_177990.2	412	cCg/cTg	5/10	1	2	FACETS	1	0.956	1	1	0.987	1	CLONAL	2	TRUE	1	0.22	2		339	334	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262821	46262821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	26	436	0	ENST00000371998.3:c.994G>A	p.Val332Ile	p.V332I	ENST00000371998		332	Gta/Ata	10/23	1	2	FACETS	0.472	0.373	0.586	0.472	0.373	0.586	SUBCLONAL	1	TRUE	1	0.22	2		436	501	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41542802	41542802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	152	364	0	ENST00000263253.7:c.2113C>T	p.Arg705Ter	p.R705*	ENST00000263253	NM_001429.3	705	Cga/Tga	11/31	1	2	FACETS	1	0.982	1	1	0.993	1	CLONAL	2	TRUE	1	0.22	2		364	558	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573154	41573155	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	189	569	0	ENST00000263253.7:c.5439_5440delinsTT	p.Arg1814Trp	p.R1814W	ENST00000263253	NM_001429.3	1813	ctCCgg/ctTTgg	31/31	1	2	FACETS	0.86	0.798	0.924	1	0.994	1	CLONAL	3	TRUE	1	0.22	2		569	666	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458433	12458434	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	170	542	0	ENST00000287820.6:c.1050_1051delinsTT	p.His351Tyr	p.H351Y	ENST00000287820	NM_015869.4	350	gtCCac/gtTTac	6/7	1	2	FACETS	1	0.981	1	1	0.993	1	CLONAL	2	TRUE	1	0.22	2		542	643	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090465	37090466	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	131	362	0	ENST00000231790.2:c.2060_2061delinsAA	p.Arg687Gln	p.R687Q	ENST00000231790	NM_000249.3	687	cGG/cAA	18/19	1	2	FACETS	1	0.957	1	1	0.991	1	CLONAL	2	TRUE	1	0.22	2		362	550	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182032	38182032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	134	431	0	ENST00000396334.3:c.656C>T	p.Ser219Phe	p.S219F	ENST00000396334	NM_002468.4	219	tCt/tTt	3/5	1	2	FACETS	0.964	0.878	1	1	0.99	1	CLONAL	2	TRUE	1	0.22	2		431	632	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014359	70014359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	188	472	1	ENST00000394351.3:c.1220G>A	p.Arg407Lys	p.R407K	ENST00000394351	NM_000248.3	407	aGg/aAg	9/9	1	2	FACETS	0.906	0.841	0.972	1	0.994	1	CLONAL	3	TRUE	1	0.22	2		473	629	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953837	55953837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	144	413	1	ENST00000263923.4:c.3599C>T	p.Ser1200Phe	p.S1200F	ENST00000263923	NM_002253.2	1200	tCc/tTc	27/30	1	2	FACETS	1	0.943	1	1	0.993	1	CLONAL	3	TRUE	1	0.22	2		414	424	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155221	106155221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778756841	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	74	270	0	ENST00000380013.4:c.122C>T	p.Pro41Leu	p.P41L	ENST00000380013	NM_001127208.2	41	cCt/cTt	3/11	1	2	FACETS	1	0.913	1	1	0.984	1	CLONAL	2	TRUE	1	0.22	2		270	323	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294661	1294662	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	139	325	1	ENST00000310581.5:c.339_340delinsAA	p.Ala114Thr	p.A114T	ENST00000310581	NM_198253.2	113	gaGGcc/gaAAcc	2/16	0.3	1	FACETS	0.89	0.818	0.965	1	0.993	1	CLONAL	3	TRUE	0	0.22	1		326	421	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522769	67522769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	27	272	0	ENST00000274335.5:c.266C>T	p.Pro89Leu	p.P89L	ENST00000274335		89	cCc/cTc	1/15	0.0813159748910131	3	FACETS	0.61	0.484	0.753	0.305	0.242	0.377	INDETERMINATE	1	TRUE	1	0.22	3		272	447	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149498370	149498371	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	186	531	2	ENST00000261799.4:c.2843_2844delinsAA	p.Arg948Gln	p.R948Q	ENST00000261799	NM_002609.3	948	cGG/cAA	21/23	0.3	0	FACETS	0.928	0.859	0.998			1	CLONAL	2	TRUE	0	0.22	0		533	711	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515295	149515295	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	29	516	0	ENST00000261799.4:c.187G>A	p.Glu63Lys	p.E63K	ENST00000261799	NM_002609.3	63	Gaa/Aaa	3/23	0.3	0	FACETS	0.363	0.291	0.446			1	SUBCLONAL	1	TRUE	0	0.22	0		516	566	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120846	94120846	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1300929218	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	25	441	0	ENST00000369303.4:c.205C>G	p.Arg69Gly	p.R69G	ENST00000369303	NM_004440.3	69	Cga/Gga	3/17	1	2	FACETS	0.466	0.366	0.581	0.466	0.366	0.581	SUBCLONAL	1	TRUE	1	0.22	2		441	488	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536287	106536287	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	167	354	0	ENST00000369096.4:c.254G>A	p.Arg85Lys	p.R85K	ENST00000369096	NM_001198.3	85	aGg/aAg	2/7	1	2	FACETS	1	0.971	1	1	0.993	1	CLONAL	2	TRUE	1	0.22	2		354	683	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956937	2956938	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	172	464	1	ENST00000396946.4:c.2689_2690delinsAA	p.Gly897Asn	p.G897N	ENST00000396946	NM_032415.4	897	GGc/AAc	20/25	1	2	FACETS	0.862	0.797	0.928	1	0.994	1	CLONAL	3	TRUE	1	0.22	2		465	605	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962324	2962324	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	185	533	0	ENST00000396946.4:c.2213G>A	p.Trp738Ter	p.W738*	ENST00000396946	NM_032415.4	738	tGg/tAg	17/25	1	2	FACETS	0.872	0.809	0.937	1	0.994	1	CLONAL	3	TRUE	1	0.22	2		533	643	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335640	81335640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	124	369	0	ENST00000222390.5:c.1720C>T	p.Pro574Ser	p.P574S	ENST00000222390	NM_000601.4	574	Cct/Tct	15/18	1	2	FACETS	1	0.967	1	1	0.991	1	CLONAL	2	TRUE	1	0.22	2		369	497	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509636	106509636	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867282260	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	136	439	0	ENST00000359195.3:c.1630C>T	p.Arg544Ter	p.R544*	ENST00000359195	NM_002649.2	544	Cga/Tga	2/11	0.00586468205796153	3	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	2	TRUE	1	0.22	3		439	564	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859870	151859870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	115	300	0	ENST00000262189.6:c.10792C>T	p.Pro3598Ser	p.P3598S	ENST00000262189	NM_170606.2	3598	Cca/Tca	43/59	1	2	FACETS	1	0.969	1	1	0.99	1	CLONAL	2	TRUE	1	0.22	2		300	450	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900145	151900145	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	82	263	0	ENST00000262189.6:c.3966G>A	p.Trp1322Ter	p.W1322*	ENST00000262189	NM_170606.2	1322	tgG/tgA	26/59	1	2	FACETS	1	0.962	1	1	0.987	1	CLONAL	2	TRUE	1	0.22	2		263	314	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285590	38285590	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	28	328	0	ENST00000425967.3:c.563C>T	p.Ser188Phe	p.S188F	ENST00000425967	NM_001174067.1	188	tCc/tTc	6/19	1	2	FACETS	0.778	0.623	0.955	0.778	0.623	0.955	CLONAL	1	TRUE	1	0.22	2		328	327	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974676	21974677	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	143	397	0	ENST00000304494.5:c.150_150+1delinsAA		p.X50_splice	ENST00000304494	NM_000077.4	50		1/3	0.3	0	FACETS	0.878	0.81	0.948			1	CLONAL	3	TRUE	0	0.22	0		397	385	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781388	135781388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554815996	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	342	522	0	ENST00000298552.3:c.1577C>T	p.Ser526Phe	p.S526F	ENST00000298552	NM_001162426.1	526	tCt/tTt	15/23	0.264816238463217	4	FACETS	1	0.985	1	1	0.995	1	CLONAL	4	TRUE	1	0.22	4		522	870	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396540	139396541	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	235	479	0	ENST00000277541.6:c.5385-1_5385delinsAA		p.X1795_splice	ENST00000277541	NM_017617.3	1795		29/34	0.264816238463217	4	FACETS	1	0.979	1	1	0.993	1	CLONAL	4	TRUE	1	0.22	4		479	597	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409983	139409983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	312	587	0	ENST00000277541.6:c.1855C>T	p.Gln619Ter	p.Q619*	ENST00000277541	NM_017617.3	619	Cag/Tag	11/34	0.264816238463217	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	1	0.22	4		587	1061	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245029	53245030	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	238	240	2	ENST00000375401.3:c.910_911delinsTT	p.Pro304Phe	p.P304F	ENST00000375401	NM_004187.3	304	CCc/TTc	7/26	0.128701184269737	2	FACETS	1	0.985	1			1	INDETERMINATE	5	TRUE	NA	0.22	2		242	396	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411137	63411137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	159	255	0	ENST00000330258.3:c.2030C>T	p.Ser677Phe	p.S677F	ENST00000330258	NM_152424.3	677	tCc/tTc	2/2	0.128701184269737	2	FACETS	1	0.978	1			1	INDETERMINATE	5	TRUE	NA	0.22	2		255	266	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020270	123020270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	214	222	0	ENST00000355640.3:c.758C>T	p.Ser253Leu	p.S253L	ENST00000355640		253	tCa/tTa	2/7	0.128701184269737	2	FACETS	1	0.984	1			1	INDETERMINATE	5	TRUE	NA	0.22	2		222	355	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	68	214	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.315343509339916	1	FACETS	0.924	0.808	1	0.924	0.808	1	CLONAL	1	TRUE	0	0.315343509339916	1		214	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0044096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	134	218	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.315343509339916	1	FACETS	0.822	0.746	0.901	0.822	0.746	0.901	CLONAL	1	TRUE	0	0.315343509339916	1		218	871	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239876	53239876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	100	642	0	ENST00000375401.3:c.1565C>T	p.Ser522Phe	p.S522F	ENST00000375401	NM_004187.3	522	tCc/tTc	11/26	0.315343509339916	1	FACETS	0.775	0.693	0.863	0.775	0.693	0.863	SUBCLONAL	1	TRUE	0	0.315343509339916	1		642	689	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67462920	67462920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202094530	NA	P-0044096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	150	600	0	ENST00000327367.4:c.636G>A	p.Met212Ile	p.M212I	ENST00000327367	NM_005902.3	212	atG/atA	5/9	0.315343509339916	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.315343509339916	1		600	758	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956144	175956144	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	73	398	0	ENST00000367669.3:c.2068G>C	p.Asp690His	p.D690H	ENST00000367669	NM_022457.5	690	Gac/Cac	18/20	0.224596830054144	3	FACETS	0.937	0.82	1	0.312	0.273	0.355	CLONAL	1	TRUE	0	0.315343509339916	3		398	572	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99439991	99439991	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	48	348	0	ENST00000268035.6:c.959A>G	p.Tyr320Cys	p.Y320C	ENST00000268035	NM_000875.3	320	tAc/tGc	4/21	0.315343509339916	1	FACETS	0.625	0.53	0.73	0.625	0.53	0.73	SUBCLONAL	1	TRUE	0	0.315343509339916	1		348	410	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100042	11100042	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	127	797	2	ENST00000358026.2:c.1168G>T	p.Gly390Trp	p.G390W	ENST00000358026	NM_001128849.1	390	Ggg/Tgg	7/36	1	2	FACETS	0.819	0.74	0.901	0.819	0.74	0.901	CLONAL	1	TRUE	1	0.315343509339916	2		799	984	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0044100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	80	315	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	0.237856872559372	2	FACETS	0.947	0.84	1	0.947	0.84	1	CLONAL	2	TRUE	0	0.237856872559372	2		315	355	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0044108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	178	395	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	0.754933888924276	4	FACETS	0.927	0.855	1	0.463	0.427	0.501	CLONAL	1	TRUE	2	0.777490839770911	4		395	878	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0044108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	2029	628	1	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.777490839770911	4	FACETS	1	0.995	1			1	CLONAL	4	TRUE	NA	0.777490839770911	4		629	2300	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913273	NA	P-0044108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	14	363	0	ENST00000263967.3:c.1624G>C	p.Glu542Gln	p.E542Q	ENST00000263967	NM_006218.2	542	Gaa/Caa	10/21	0.754933888924276	4	FACETS	0.135	0.097	0.182	0.068	0.048	0.091	SUBCLONAL	1	TRUE	2	0.777490839770911	4		363	474	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038230	30038230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	271	347	0	ENST00000338641.4:c.403C>T	p.Pro135Ser	p.P135S	ENST00000338641	NM_000268.3	135	Cct/Tct	4/16	1	2	FACETS	0.95	0.896	1	0.95	0.896	1	CLONAL	1	TRUE	1	0.777490839770911	2		347	734	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639900	3639900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs978074181	NA	P-0044108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	625	627	0	ENST00000294008.3:c.3739G>A	p.Glu1247Lys	p.E1247K	ENST00000294008	NM_032444.2	1247	Gag/Aag	12/15	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.777490839770911	2		627	1446	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038255	30038255	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	231	315	0	ENST00000338641.4:c.428C>T	p.Ser143Phe	p.S143F	ENST00000338641	NM_000268.3	143	tCt/tTt	4/16	1	2	FACETS	0.931	0.874	0.99	0.931	0.874	0.99	CLONAL	1	TRUE	1	0.777490839770911	2		315	638	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175804	176175804	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044108-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	403	429	0	ENST00000367669.3:c.311C>G	p.Ser104Cys	p.S104C	ENST00000367669	NM_022457.5	104	tCc/tGc	1/20	0.777490839770911	3	FACETS	0.953	0.906	1	0.477	0.453	0.501	CLONAL	1	TRUE	1	0.777490839770911	3		429	1510	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0044129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	152	449	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.60016165446937	2		449	498	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0044129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	122	319	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.968	0.882	1	0.968	0.882	1	CLONAL	1	TRUE	1	0.60016165446937	2		319	420	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602737	10602737	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	290	1023	0	ENST00000171111.5:c.841C>A	p.Leu281Met	p.L281M	ENST00000171111	NM_203500.1	281	Ctg/Atg	3/6	0.60016165446937	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.60016165446937	1		1023	644	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156066	106156066	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1244473694	NA	P-0044129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	78	349	0	ENST00000380013.4:c.967C>T	p.Gln323Ter	p.Q323*	ENST00000380013	NM_001127208.2	323	Caa/Taa	3/11	1	2	FACETS	0.783	0.694	0.877	0.783	0.694	0.877	SUBCLONAL	1	TRUE	1	0.60016165446937	2		349	332	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207015	1207015	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	225	775	0	ENST00000326873.7:c.103del	p.Ile35SerfsTer16	p.I35Sfs*16	ENST00000326873	NM_000455.4	35	Atc/tc	1/10	0.60016165446937	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.60016165446937	1		775	483	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590439	67590439	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	78	200	0	ENST00000274335.5:c.1501C>T	p.Gln501Ter	p.Q501*	ENST00000274335		501	Caa/Taa	11/15	1	2	FACETS	0.896	0.796	1	0.896	0.796	1	CLONAL	1	TRUE	1	0.60016165446937	2		200	290	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69787826	69788780	+	coding_sequence_variant,5_prime_UTR_variant	Frame_Shift_Del	DEL	ACTCCTGAAATGCTAGGACAAATCTCATTTGAACTCCCAGTCAACTGAGAAATTAAAAGCAGAGAGCAACGACGCTATTTTGTAACTTTGTGCCTTTTAAAATTAACCGAATCTTTCAATTGCTGCTGTAGATTAGAAGTGGCTACTTGGATAAAGGGGAAAGAGCCATTCAACTGATGAATACTATTGTAAAAGTCCAGACTTAGTTCTAGAAAAGGAACGCACAAGAACAATTTCTCCAATAACGTTTTCATTACAGAGCGAAGGAAAGTTCTTCCTCGTTGTTCCAATCCGAGGACAAGCTGATATGTCGCAGCAGCCCAGGGAAGCATGCGAGCTGATAGGAAGTCCTTTTATTTTAAGACAGGCTCGAATGCTAAAACTTTCTTGTGCCAAAACCCTTGACTATTTTATTTTTAAAATAAGCACTTGGCGTGCCCTCGCAGATGTCTGAGCTGAGAGGTCGGGGCGATGGTAGAAGAGCAGTCAGTGTCCATTCTTATTCATATTAAGTAGCCAAGTCTGTACCCTTGAAGCAAGTGGGGAGAGAGGAGGGAGAGGAGCTGCTGACATTGACAATGAATCCAAACAGGAGTTGCACTAGCGGTGTCCACCACGTTGCCTCTCCCCCGCCTGGCCTTCTGGGAGCTGTAGTTTTCGTGGGAGCGGCTCCCCAGGCGAGCTGGGAATGCCCCGCCCGGGCCGAACTACAGATCCCAGGCGGCGCTCGGCCGCCAGCCCCTCCCGCCCGGGTGCGAGTGTAAACTCCCCGCGCTGGGGCGGGCGGCCGCGAGCCGGCGAGCGGGCAGAGCTCGGCACTGCGCCGGGGCGCACGGCTCGGGGGACCCAGGCCCAGCTACCTTCCCTCCGCCCCCGGGCTCTGTTCTCACTTTCCAGCAGTGGAAGGACGGGAAGCGGGAGCCATGCAGTCCGAATCGGGGATCGTGCCGGATTT	ACTCCTGAAATGCTAGGACAAATCTCATTTGAACTCCCAGTCAACTGAGAAATTAAAAGCAGAGAGCAACGACGCTATTTTGTAACTTTGTGCCTTTTAAAATTAACCGAATCTTTCAATTGCTGCTGTAGATTAGAAGTGGCTACTTGGATAAAGGGGAAAGAGCCATTCAACTGATGAATACTATTGTAAAAGTCCAGACTTAGTTCTAGAAAAGGAACGCACAAGAACAATTTCTCCAATAACGTTTTCATTACAGAGCGAAGGAAAGTTCTTCCTCGTTGTTCCAATCCGAGGACAAGCTGATATGTCGCAGCAGCCCAGGGAAGCATGCGAGCTGATAGGAAGTCCTTTTATTTTAAGACAGGCTCGAATGCTAAAACTTTCTTGTGCCAAAACCCTTGACTATTTTATTTTTAAAATAAGCACTTGGCGTGCCCTCGCAGATGTCTGAGCTGAGAGGTCGGGGCGATGGTAGAAGAGCAGTCAGTGTCCATTCTTATTCATATTAAGTAGCCAAGTCTGTACCCTTGAAGCAAGTGGGGAGAGAGGAGGGAGAGGAGCTGCTGACATTGACAATGAATCCAAACAGGAGTTGCACTAGCGGTGTCCACCACGTTGCCTCTCCCCCGCCTGGCCTTCTGGGAGCTGTAGTTTTCGTGGGAGCGGCTCCCCAGGCGAGCTGGGAATGCCCCGCCCGGGCCGAACTACAGATCCCAGGCGGCGCTCGGCCGCCAGCCCCTCCCGCCCGGGTGCGAGTGTAAACTCCCCGCGCTGGGGCGGGCGGCCGCGAGCCGGCGAGCGGGCAGAGCTCGGCACTGCGCCGGGGCGCACGGCTCGGGGGACCCAGGCCCAGCTACCTTCCCTCCGCCCCCGGGCTCTGTTCTCACTTTCCAGCAGTGGAAGGACGGGAAGCGGGAGCCATGCAGTCCGAATCGGGGATCGTGCCGGATTT	-	novel	NA	P-0044140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	76	0	0				ENST00000352241	NM_198159.2	?-11/520		1/10	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		0	416	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0044151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	35	466	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.73	0.601	0.873	0.73	0.601	0.873	SUBCLONAL	1	TRUE	1	0.341335132933007	2		466	281	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	83	82	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.795	0.702	0.894	0.795	0.702	0.894	SUBCLONAL	1	TRUE	1	0.341335132933007	2		82	612	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	146	82	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.816445367812111	2		82	327	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0044165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12309	1153	628	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.816445367812111	25	FACETS	1	0.993	1	0.087	0.084	0.091	CLONAL	2	TRUE	0	0.816445367812111	25		628	13462	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716362	18716362	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0044165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	129	335	0	ENST00000266497.5:c.3709A>T	p.Lys1237Ter	p.K1237*	ENST00000266497		1237	Aaa/Taa	26/31	1	2	FACETS	0.905	0.831	0.981	0.905	0.831	0.981	CLONAL	1	TRUE	1	0.816445367812111	2		335	349	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522829	67522829	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	124	182	0	ENST00000274335.5:c.327del	p.Glu109AspfsTer5	p.E109Dfs*5	ENST00000274335		109	gAa/ga	1/15	1	2	FACETS	0.958	0.88	1	0.958	0.88	1	CLONAL	1	TRUE	1	0.816445367812111	2		182	317	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	98	459	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.36562248111317	4	FACETS	0.914	0.828	1			1	CLONAL	3	TRUE	NA	0.36562248111317	4		459	267	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0044170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	190	352	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.36562248111317	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.36562248111317	2		353	506	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439945	56439945	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	196	850	0	ENST00000407977.2:c.647C>A	p.Ser216Ter	p.S216*	ENST00000407977		216	tCg/tAg	6/10	0.36562248111317	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.36562248111317	2		850	466	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635217	87635217	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746097417	NA	P-0044186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	186	627	2	ENST00000277120.3:c.2269G>A	p.Val757Ile	p.V757I	ENST00000277120		757	Gtc/Atc	18/19	0.22570316444005	3	FACETS	0.876	0.809	0.946	0.584	0.539	0.631	CLONAL	2	TRUE	0	0.249122412741146	3		629	958	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425503	49425503	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555187758	NA	P-0044186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1348	157	932	0	ENST00000301067.7:c.12985C>T	p.Gln4329Ter	p.Q4329*	ENST00000301067	NM_003482.3	4329	Cag/Tag	39/54	0.202233026506209	4	FACETS	1	0.945	1	0.349	0.318	0.381	CLONAL	1	TRUE	1	0.249122412741146	4		932	1505	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178569	32178569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1252701920	NA	P-0044186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	427	707	0	ENST00000375023.3:c.2825G>A	p.Gly942Glu	p.G942E	ENST00000375023	NM_004557.3	942	gGg/gAg	18/30	0.249122412741146	5	FACETS	0.956	0.911	1	0.956	0.911	1	CLONAL	4	TRUE	1	0.249122412741146	5		707	1232	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533631	63533631	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	204	897	0	ENST00000307078.5:c.1523A>T	p.Lys508Met	p.K508M	ENST00000307078	NM_004655.3	508	aAg/aTg	6/11	0.145589042896036	4	FACETS	1	0.99	1	0.737	0.682	0.795	INDETERMINATE	1	TRUE	2	0.249122412741146	4		897	1387	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347695	118347695	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	96	340	0	ENST00000534358.1:c.3332A>G	p.Asp1111Gly	p.D1111G	ENST00000534358	NM_005933.3	1111	gAt/gGt	4/36	0.215328730881771	3	FACETS	0.797	0.712	0.886	0.797	0.712	0.886	SUBCLONAL	2	TRUE	1	0.249122412741146	3		340	544	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30047491	30047491	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	36	394	0	ENST00000331968.5:c.2510C>G	p.Pro837Arg	p.P837R	ENST00000331968	NM_002742.2	837	cCt/cGt	17/18	0.202233026506209	4	FACETS	0.549	0.45	0.66	0.183	0.15	0.22	SUBCLONAL	1	TRUE	1	0.249122412741146	4		394	658	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786138	3786138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	173	817	0	ENST00000262367.5:c.4627G>A	p.Asp1543Asn	p.D1543N	ENST00000262367	NM_004380.2	1543	Gat/Aat	28/31	0.215328730881771	3	FACETS	1	0.988	1	0.719	0.661	0.78	CLONAL	1	TRUE	1	0.249122412741146	3		817	1086	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121207	11121207	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	261	656	0	ENST00000358026.2:c.2274G>T	p.Gln758His	p.Q758H	ENST00000358026	NM_001128849.1	758	caG/caT	15/36	0.22570316444005	3	FACETS	0.858	0.806	0.912	0.858	0.806	0.912	CLONAL	3	TRUE	0	0.249122412741146	3		656	915	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61710170	61710170	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	49	325	0	ENST00000401558.2:c.2734C>T	p.Gln912Ter	p.Q912*	ENST00000401558	NM_003400.3	912	Cag/Tag	22/25	0.215328730881771	3	FACETS	0.764	0.647	0.893	0.382	0.323	0.447	SUBCLONAL	1	TRUE	1	0.249122412741146	3		325	579	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872504	136872504	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1240625960	NA	P-0044186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	29	292	0	ENST00000241393.3:c.994G>T	p.Gly332Ter	p.G332*	ENST00000241393	NM_003467.2	332	Gga/Tga	2/2	0.215328730881771	3	FACETS	0.617	0.495	0.757	0.309	0.247	0.379	SUBCLONAL	1	TRUE	1	0.249122412741146	3		292	424	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077552	30077552	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	207	476	0	ENST00000338641.4:c.1699G>T	p.Asp567Tyr	p.D567Y	ENST00000338641	NM_000268.3	567	Gac/Tac	15/16	0.208409331984287	3	FACETS	0.857	0.798	0.917	0.857	0.798	0.917	CLONAL	3	TRUE	0	0.249122412741146	3		476	727	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431070	181431070	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	424	682	0	ENST00000325404.1:c.922del	p.Ile308LeufsTer63	p.I308Lfs*63	ENST00000325404	NM_003106.3	308	Att/tt	1/1	0.249122412741146	5	FACETS	0.906	0.864	0.949	0.906	0.864	0.949	CLONAL	4	TRUE	1	0.249122412741146	5		682	1290	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417569	139417569	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	435	939	2	ENST00000277541.6:c.475G>T	p.Glu159Ter	p.E159*	ENST00000277541	NM_017617.3	159	Gag/Tag	4/34	0.22570316444005	3	FACETS	0.961	0.916	1	0.961	0.916	1	CLONAL	3	TRUE	0	0.249122412741146	3		941	1362	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578448	7578452	+	missense_variant	Missense_Mutation	ONP	GCCAT	GCCAT	CCCAG	novel	NA	P-0044186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	237	885	0	ENST00000269305.4:c.478_482delinsCTGGG	p.Met160_Ala161delinsLeuGly	p.M160_A161delinsLG	ENST00000269305	NM_001126112.2	160	ATGGCc/CTGGGc	5/11	0.204705402305031	2	FACETS	0.814	0.759	0.871	0.814	0.759	0.871	CLONAL	2	TRUE	0	0.249122412741146	2		885	1169	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64126867	64126867	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749166781	NA	P-0044207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	57	746	0	ENST00000334205.4:c.73G>A	p.Glu25Lys	p.E25K	ENST00000334205	NM_003942.2	25	Gag/Aag	2/17	1	2	FACETS	0.518	0.443	0.601	0.518	0.443	0.601	SUBCLONAL	1	TRUE	1	0.242033365429459	2		746	909	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121912666	NA	P-0044207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	159	641	0	ENST00000269305.4:c.659A>C	p.Tyr220Ser	p.Y220S	ENST00000269305	NM_001126112.2	220	tAt/tCt	6/11	0.16750924142751	2	FACETS	1	0.988	1	0.749	0.687	0.814	CLONAL	1	TRUE	0	0.242033365429459	2		641	877	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584709	48584709	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0044207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	32	311	0	ENST00000342988.3:c.788-1G>C		p.X263_splice	ENST00000342988	NM_005359.5	263			1	2	FACETS	0.643	0.522	0.78	0.643	0.522	0.78	SUBCLONAL	1	TRUE	1	0.242033365429459	2		311	411	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199918	128199918	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	57	530	0	ENST00000341105.2:c.1387T>A	p.Ser463Thr	p.S463T	ENST00000341105	NM_032638.4	463	Tcc/Acc	6/6	0.180964576649681	3	FACETS	0.976	0.838	1	0.488	0.419	0.564	CLONAL	1	TRUE	1	0.242033365429459	3		530	541	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451305	70451305	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	108	567	0	ENST00000373644.4:c.6145T>C	p.Tyr2049His	p.Y2049H	ENST00000373644	NM_030625.2	2049	Tac/Cac	12/12	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.242033365429459	2		567	886	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878158	151878158	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	66	454	0	ENST00000262189.6:c.6787G>A	p.Gly2263Ser	p.G2263S	ENST00000262189	NM_170606.2	2263	Ggc/Agc	36/59	0.162811269553609	2	FACETS	0.843	0.731	0.964	0.421	0.365	0.482	CLONAL	1	TRUE	0	0.242033365429459	2		454	647	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958459	90958459	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs201781110	NA	P-0044207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	32	279	0	ENST00000265433.3:c.1979G>C	p.Arg660Thr	p.R660T	ENST00000265433	NM_002485.4	660	aGa/aCa	13/16	0.242033365429459	3	FACETS	0.521	0.422	0.634	0.26	0.211	0.317	SUBCLONAL	1	TRUE	1	0.242033365429459	3		279	569	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	109	82	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		82	424	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0044290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	157	488	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.328702954085655	2		488	702	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0044290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	56	466	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.736	0.631	0.85	0.736	0.631	0.85	SUBCLONAL	1	TRUE	1	0.328702954085655	2		466	463	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139818310	139818310	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	90	522	0	ENST00000247668.2:c.1145A>G	p.Tyr382Cys	p.Y382C	ENST00000247668	NM_021138.3	382	tAc/tGc	10/11	1	2	FACETS	0.832	0.739	0.932	0.832	0.739	0.932	CLONAL	1	TRUE	1	0.328702954085655	2		522	658	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593605	55593610	+	inframe_deletion	In_Frame_Del	DEL	GAAGGT	GAAGGT	-	novel	NA	P-0044303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	283	335	0	ENST00000288135.5:c.1671_1676del	p.Trp557_Val559delinsCys	p.W557_V559delinsC	ENST00000288135	NM_000222.2	557	tgGAAGGTt/tgt	11/21	0.848654796214529	2	FACETS	0.958	0.928	0.987	0.958	0.928	0.987	CLONAL	2	TRUE	0	0.848654796214529	2		335	348	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144879	47144879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	223	353	0	ENST00000409792.3:c.4874G>A	p.Arg1625His	p.R1625H	ENST00000409792	NM_014159.6	1625	cGt/cAt	7/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.848654796214529	2		353	488	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0044303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	219	591	3	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	0.579706500139718	4	FACETS	0.693	0.643	0.745	0.346	0.321	0.373	SUBCLONAL	1	TRUE	2	0.848654796214529	4		594	1377	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281108	49281108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	64	548	0	ENST00000282018.3:c.155G>A	p.Gly52Glu	p.G52E	ENST00000282018	NM_020377.2	52	gGa/gAa	1/1	1	2	FACETS	0.232	0.2	0.266	0.232	0.2	0.266	SUBCLONAL	1	TRUE	1	0.848654796214529	2		548	651	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361225	66361225	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	112	305	0	ENST00000273854.3:c.947T>A	p.Ile316Asn	p.I316N	ENST00000273854	NM_004439.5	316	aTc/aAc	4/18	1	2	FACETS	0.996	0.901	1	0.996	0.901	1	CLONAL	1	TRUE	1	0.478474129340445	2		305	470	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436688	52436713	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AATCTGTAGGAGAGAAGAAGACTGAG	AATCTGTAGGAGAGAAGAAGACTGAG	CATC	novel	NA	P-0044307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	294	487	2	ENST00000460680.1:c.1984-23_1986delinsGATG		p.X662_splice	ENST00000460680	NM_004656.3	662		16/17	0.444225003748519	2	FACETS	0.829	0.785	0.874	0.829	0.785	0.874	CLONAL	2	TRUE	0	0.478474129340445	2		489	741	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	105	82	0				ENST00000310581	NM_198253.2	-/1132			0.26884396688699	5	FACETS	0.836	0.753	0.924	0.558	0.502	0.616	CLONAL	2	FALSE	2	0.41196473223982	5		82	493	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40709551	40709551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568484928	NA	P-0044322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	129	457	0	ENST00000373198.4:c.4351G>A	p.Glu1451Lys	p.E1451K	ENST00000373198	NM_133170.3	1451	Gag/Aag	32/32	0.412310341739274	4	FACETS	0.823	0.75	0.9			1	CLONAL	2	FALSE	NA	0.41196473223982	4		457	537	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169376	11169376	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	118	446	0	ENST00000361445.4:c.7499T>A	p.Ile2500Asn	p.I2500N	ENST00000361445	NM_004958.3	2500	aTt/aAt	56/58	0.161576175556278	6	FACETS	1	0.96	1	0.736	0.668	0.807	INDETERMINATE	2	FALSE	3	0.41196473223982	6		446	473	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217305	123217305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	77	247	0	ENST00000218089.9:c.2959C>T	p.Pro987Ser	p.P987S	ENST00000218089	NM_001042749.1	987	Ccg/Tcg	29/35	0.395206058914882	2	FACETS	0.896	0.815	0.977			1	CLONAL	3	FALSE	NA	0.41196473223982	2		247	139	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579485	7579485	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs869312782	NA	P-0044322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	353	815	0	ENST00000269305.4:c.202G>T	p.Glu68Ter	p.E68*	ENST00000269305	NM_001126112.2	68	Gag/Tag	4/11	0.325700357853103	3	FACETS	0.93	0.887	0.972	0.93	0.887	0.972	CLONAL	3	FALSE	0	0.41196473223982	3		815	741	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023943	27023943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	17	75	0	ENST00000324856.7:c.1049C>T	p.Ser350Leu	p.S350L	ENST00000324856	NM_006015.4	350	tCg/tTg	1/20	0.161576175556278	6	FACETS	1	0.885	1	0.448	0.338	0.575	INDETERMINATE	1	FALSE	3	0.41196473223982	6		75	112	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112602	115112602	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	384	835	0	ENST00000257566.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000257566	NM_016569.3	380	Gag/Cag	7/8	0.41196473223982	5	FACETS	0.913	0.869	0.958	0.913	0.869	0.958	CLONAL	3	FALSE	2	0.41196473223982	5		835	1101	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023262	33023262	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	240	754	0	ENST00000300177.4:c.371C>G	p.Ser124Cys	p.S124C	ENST00000300177	NM_001191322.1	124	tCt/tGt	2/2	0.412310341739274	4	FACETS	1	0.963	1	0.692	0.649	0.737	CLONAL	2	FALSE	1	0.41196473223982	4		754	792	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40855827	40855827	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	214	416	0	ENST00000428826.2:c.2029G>T	p.Asp677Tyr	p.D677Y	ENST00000428826		677	Gat/Tat	19/21	0.412310341739274	4	FACETS	1	0.973	1	0.539	0.503	0.576	CLONAL	2	FALSE	0	0.41196473223982	4		416	680	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40855839	40855839	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0044322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	178	362	1	ENST00000428826.2:c.2018-1G>T		p.X673_splice	ENST00000428826		673			0.412310341739274	4	FACETS	1	0.942	1	0.509	0.472	0.548	CLONAL	2	FALSE	0	0.41196473223982	4		363	599	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135035	11135035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	283	756	0	ENST00000358026.2:c.3002C>T	p.Ser1001Phe	p.S1001F	ENST00000358026	NM_001128849.1	1001	tCt/tTt	21/36	0.412310341739274	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	FALSE	1	0.41196473223982	3		756	756	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053201	180053201	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	90	828	0	ENST00000261937.6:c.1168A>G	p.Thr390Ala	p.T390A	ENST00000261937	NM_182925.4	390	Aca/Gca	9/30	NA	2	FACETS	0.52	0.461	0.584			1	INDETERMINATE	1	FALSE	NA	0.41196473223982	2		828	840	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0044328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	70	689	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.668	0.581	0.761	0.668	0.581	0.761	SUBCLONAL	1	TRUE	1	0.274077936446432	2		689	765	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0044328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	97	476	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.273559537678859	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.274077936446432	1		476	535	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0044328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	27	241	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	0.235338375311326	4	FACETS	0.623	0.495	0.769			1	SUBCLONAL	1	TRUE	NA	0.274077936446432	4		241	403	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231296	98231296	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	75	450	0	ENST00000331920.6:c.1987C>T	p.Gln663Ter	p.Q663*	ENST00000331920	NM_000264.3	663	Cag/Tag	14/24	1	2	FACETS	0.595	0.52	0.676	0.595	0.52	0.676	SUBCLONAL	1	TRUE	1	0.274077936446432	2		450	920	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729662	162729662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	93	435	1	ENST00000367921.3:c.748G>T	p.Val250Leu	p.V250L	ENST00000367921	NM_006182.2	250	Gtg/Ttg	8/18	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.274077936446432	2		436	657	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974783	21974783	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658556	NA	P-0044328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	26	109	0	ENST00000304494.5:c.44G>A	p.Trp15Ter	p.W15*	ENST00000304494	NM_000077.4	15	tGg/tAg	1/3	0.274077936446432	1	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	0	0.274077936446432	1		109	153	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268927	55268927	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1289194907	NA	P-0044328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	74	480	0	ENST00000275493.2:c.2993A>G	p.Tyr998Cys	p.Y998C	ENST00000275493	NM_005228.3	998	tAc/tGc	25/28	0.274077936446432	1	FACETS	0.67	0.586	0.76	0.67	0.586	0.76	SUBCLONAL	1	TRUE	0	0.274077936446432	1		480	696	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944761	31944761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	44	147	0	ENST00000340398.3:c.340G>T	p.Ala114Ser	p.A114S	ENST00000340398	NM_001013699.2	114	Gct/Tct	1/1	0.0522276738470162	3	FACETS	1	0.947	1	0.654	0.552	0.766	INDETERMINATE	1	TRUE	1	0.274077936446432	3		147	279	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209331	133209331	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	201	373	0	ENST00000320574.5:c.6055G>T	p.Ala2019Ser	p.A2019S	ENST00000320574	NM_006231.2	2019	Gct/Tct	44/49	1	2	FACETS	0.902	0.838	0.969	1	0.993	1	CLONAL	2	TRUE	1	0.274077936446432	2		373	813	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061474	38061474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	72	321	0	ENST00000250448.2:c.515C>T	p.Pro172Leu	p.P172L	ENST00000250448	NM_004496.3	172	cCc/cTc	2/2	0.177261397071783	3	FACETS	1	0.929	1	0.545	0.477	0.619	CLONAL	1	TRUE	1	0.274077936446432	3		321	548	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857969	9857969	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs746900457	NA	P-0044328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	102	395	0	ENST00000330684.3:c.3432C>A	p.Asn1144Lys	p.N1144K	ENST00000330684	NM_001134407.1	1144	aaC/aaA	13/13	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.274077936446432	2		395	674	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641440	23641440	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	78	554	0	ENST00000261584.4:c.2035C>G	p.Pro679Ala	p.P679A	ENST00000261584	NM_024675.3	679	Cca/Gca	5/13	1	2	FACETS	0.597	0.523	0.677	0.597	0.523	0.677	SUBCLONAL	1	TRUE	1	0.274077936446432	2		554	953	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752720	42752720	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	74	476	0	ENST00000222329.4:c.1544G>T	p.Gly515Val	p.G515V	ENST00000222329	NM_006494.2	515	gGg/gTg	4/4	1	2	FACETS	0.786	0.688	0.892	0.786	0.688	0.892	SUBCLONAL	1	TRUE	1	0.274077936446432	2		476	687	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791007	42791007	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	34	325	0	ENST00000575354.2:c.152C>G	p.Pro51Arg	p.P51R	ENST00000575354	NM_015125.3	51	cCc/cGc	2/20	1	2	FACETS	0.425	0.346	0.514	0.425	0.346	0.514	SUBCLONAL	1	TRUE	1	0.274077936446432	2		325	584	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902262	50902262	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	150	546	0	ENST00000440232.2:c.154G>T	p.Glu52Ter	p.E52*	ENST00000440232	NM_002691.3	52	Gag/Tag	2/27	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.274077936446432	2		546	998	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444426	50444426	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	81	290	0	ENST00000331340.3:c.356G>T	p.Cys119Phe	p.C119F	ENST00000331340	NM_006060.4	119	tGt/tTt	4/8	0.274077936446432	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.274077936446432	1		290	461	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391128	139391129	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	109	438	0	ENST00000277541.6:c.7062dup	p.Ala2355CysfsTer152	p.A2355Cfs*152	ENST00000277541	NM_017617.3	2354	-/T	34/34	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.274077936446432	2		438	693	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578493	7578493	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1206165503	NA	P-0044331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	223	549	0	ENST00000269305.4:c.437G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tGg/tAg	5/11	1	2	FACETS	0.934	0.874	0.995	0.934	0.874	0.995	CLONAL	1	TRUE	1	0.718279202666172	2		549	665	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	92	82	0				ENST00000310581	NM_198253.2	-/1132			0.184526970354917	3	FACETS	0.978	0.876	1	1	0.98	1	CLONAL	3	TRUE	1	0.183613141872496	3		82	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579314	7579314	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	42	438	1	ENST00000269305.4:c.373A>G	p.Thr125Ala	p.T125A	ENST00000269305	NM_001126112.2	125	Acg/Gcg	4/11	1	2	FACETS	0.894	0.746	1	0.894	0.746	1	CLONAL	1	TRUE	1	0.183613141872496	2		439	512	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220295	55220295	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	183	531	2	ENST00000275493.2:c.685A>T	p.Ser229Cys	p.S229C	ENST00000275493	NM_005228.3	229	Agt/Tgt	6/28	0.184526970354917	4	FACETS	0.994	0.919	1	0.994	0.919	1	CLONAL	3	TRUE	1	0.183613141872496	4		533	791	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100152	27100152	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	121	462	2	ENST00000324856.7:c.3951del	p.Met1318CysfsTer163	p.M1318Cfs*163	ENST00000324856	NM_006015.4	1316	tcG/tc	16/20	1	2	FACETS	1	0.936	1	1	0.99	1	CLONAL	2	TRUE	1	0.183613141872496	2		464	632	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946375	71946375	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	73	573	1	ENST00000298229.2:c.2539del	p.Ser847AlafsTer7	p.S847Afs*7	ENST00000298229	NM_001567.3	847	Agc/gc	23/28	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.183613141872496	2		574	744	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246452	46246453	+	stop_gained,protein_altering_variant	Nonsense_Mutation	INS	-	-	ATT	novel	NA	P-0044337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	27	203	0	ENST00000334344.6:c.4547_4548insTTA	p.Lys1516delinsAsnTer	p.K1516delinsN*	ENST00000334344	NM_152641.2	1516	aag/aATTag	15/21	1	2	FACETS	0.838	0.667	1	0.838	0.667	1	CLONAL	1	TRUE	1	0.183613141872496	2		203	351	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435496	110435496	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	40	323	2	ENST00000375856.3:c.2905A>G	p.Ser969Gly	p.S969G	ENST00000375856	NM_003749.2	969	Agc/Ggc	1/2	1	2	FACETS	0.87	0.722	1	0.87	0.722	1	CLONAL	1	TRUE	1	0.183613141872496	2		325	501	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223928	36223928	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	59	538	0	ENST00000222270.7:c.6478del	p.Thr2160ProfsTer16	p.T2160Pfs*16	ENST00000222270	NM_014727.1	2160	Acc/cc	28/37	1	2	FACETS	0.879	0.755	1	0.879	0.755	1	CLONAL	1	TRUE	1	0.183613141872496	2		538	731	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432116	121432116	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1565885932	NA	P-0044354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	52	610	0	ENST00000257555.6:c.863G>C	p.Gly288Ala	p.G288A	ENST00000257555		288	gGg/gCg	4/10	0.20757319491075	1	FACETS	0.236	0.201	0.274	0.236	0.201	0.274	INDETERMINATE	1	TRUE	0	0.670212906602929	1		610	437	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154302	2154303	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCTCCC	novel	NA	P-0044354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	54	1246	0	ENST00000434045.2:c.617_625dup	p.Arg206_Ala208dup	p.R206_A208dup	ENST00000434045	NM_001127598.1	206	aaa/aGGGAGGCCAaa	5/5	0.20757319491075	1	FACETS	0.244	0.208	0.282	0.244	0.208	0.282	INDETERMINATE	1	TRUE	0	0.670212906602929	1		1246	440	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0044396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	105	430	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.29330227803595	2		430	601	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4102447	4102447	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	88	654	0	ENST00000262948.5:c.455G>A	p.Gly152Asp	p.G152D	ENST00000262948	NM_030662.3	152	gGc/gAc	4/11	1	2	FACETS	0.897	0.795	1	0.897	0.795	1	CLONAL	1	TRUE	1	0.29330227803595	2		654	669	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644774	67644789	+	frameshift_variant	Frame_Shift_Del	DEL	CGAAACTTTTATTAAA	CGAAACTTTTATTAAA	-	novel	NA	P-0044404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	249	438	0	ENST00000264010.4:c.39_54del	p.Thr15ArgfsTer42	p.T15Rfs*42	ENST00000264010	NM_006565.3	13	tcCGAAACTTTTATTAAA/tc	3/12	0.782081308761012	1	FACETS	0.836	0.793	0.879	0.836	0.793	0.879	CLONAL	1	TRUE	0	0.782028728817199	1		438	464	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38504691	38504691	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	347	599	0	ENST00000254066.5:c.302G>T	p.Gly101Val	p.G101V	ENST00000254066	NM_000964.3	101	gGg/gTg	3/9	1	2	FACETS	0.918	0.871	0.965	0.918	0.871	0.965	CLONAL	1	TRUE	1	0.782028728817199	2		599	967	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777994	27777994	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	27	403	0	ENST00000369163.2:c.143C>A	p.Ala48Asp	p.A48D	ENST00000369163	NM_003536.2	48	gCt/gAt	1/1	1	2	FACETS	0.135	0.107	0.168	0.135	0.107	0.168	SUBCLONAL	1	TRUE	1	0.782028728817199	2		403	510	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0044405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	179	858	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.774401051411534	2		858	414	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591798	48591798	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	32	338	3	ENST00000342988.3:c.961G>T	p.Glu321Ter	p.E321*	ENST00000342988	NM_005359.5	321	Gag/Tag	9/12	0.614597457805854	4	FACETS	1	0.882	1	0.698	0.592	0.806	CLONAL	2	TRUE	1	0.774401051411534	4		341	70	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225449662	225449662	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs867746441	NA	P-0044405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	102	375	0	ENST00000264414.4:c.65C>T	p.Pro22Leu	p.P22L	ENST00000264414	NM_003590.4	22	cCg/cTg	1/16	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.774401051411534	2		375	246	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923090	48923090	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0044405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	44	213	0	ENST00000267163.4:c.540-2A>G		p.X180_splice	ENST00000267163	NM_000321.2	180			0.730114758378561	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.774401051411534	2		213	52	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281105	49281105	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	66	654	1	ENST00000282018.3:c.152G>T	p.Trp51Leu	p.W51L	ENST00000282018	NM_020377.2	51	tGg/tTg	1/1	0.730114758378561	2	FACETS	0.968	0.895	1	0.968	0.895	1	CLONAL	2	TRUE	0	0.774401051411534	2		655	88	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40468897	40468897	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	11	260	0	ENST00000264657.5:c.2167G>T	p.Asp723Tyr	p.D723Y	ENST00000264657	NM_139276.2	723	Gac/Tac	23/24	1	2	FACETS	0.201	0.139	0.278	0.201	0.139	0.278	SUBCLONAL	1	TRUE	1	0.774401051411534	2		260	141	SUCCESS
ALK	238	MSKCC	GRCh37	2	29448419	29448419	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	121	962	1	ENST00000389048.3:c.3080C>A	p.Pro1027Gln	p.P1027Q	ENST00000389048	NM_004304.4	1027	cCg/cAg	19/29	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.774401051411534	2		963	276	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564662	86564662	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	127	707	0	ENST00000274376.6:c.395del	p.Gly132AlafsTer42	p.G132Afs*42	ENST00000274376	NM_002890.2	132	Ggc/gc	1/25	0.75659645159496	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.774401051411534	1		707	183	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152853904	152853904	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	28	471	0	ENST00000406277.2:c.660T>A	p.Asn220Lys	p.N220K	ENST00000406277	NM_152274.4	220	aaT/aaA	7/7	0.204363902845575	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.774401051411534	0		471	117	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0044436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	101	430	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	FALSE	1	0.350772128060301	2		430	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577113	7577113	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0044436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	160	695	0	ENST00000269305.4:c.825T>A	p.Cys275Ter	p.C275*	ENST00000269305	NM_001126112.2	275	tgT/tgA	8/11	0.350772128060301	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	0	0.350772128060301	1		695	595	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680561	241680561	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	152	410	0	ENST00000366560.3:c.188C>G	p.Pro63Arg	p.P63R	ENST00000366560	NM_000143.3	63	cCa/cGa	2/10	0.20421757083964	3	FACETS	0.887	0.815	0.962	0.887	0.815	0.962	INDETERMINATE	2	FALSE	1	0.350772128060301	3		410	574	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864132	57864132	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	169	547	0	ENST00000228682.2:c.1609G>T	p.Val537Phe	p.V537F	ENST00000228682	NM_005269.2	537	Gtc/Ttc	12/12	1	2	FACETS	0.845	0.782	0.911	1	0.991	1	CLONAL	2	FALSE	1	0.350772128060301	2		547	570	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0044440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	153	466	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.74	2		466	363	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	90	82	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.95	0.856	1	0.95	0.856	1	CLONAL	1	TRUE	1	0.74	2		82	256	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0044440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	94	319	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.898	0.81	0.989	0.898	0.81	0.989	CLONAL	1	TRUE	1	0.74	2		319	283	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099341	157099341	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587779741	NA	P-0044440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	31	303	0	ENST00000346085.5:c.278A>T	p.His93Leu	p.H93L	ENST00000346085	NM_020732.3	93	cAc/cTc	1/20	0.103391348460343	3	FACETS	0.488	0.397	0.59	0.244	0.198	0.295	INDETERMINATE	1	TRUE	1	0.74	3		303	235	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250187	110250187	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	35	627	0	ENST00000374672.4:c.488C>T	p.Ala163Val	p.A163V	ENST00000374672	NM_004235.4	163	gCg/gTg	3/5	1	2	FACETS	0.195	0.159	0.235	0.195	0.159	0.235	SUBCLONAL	1	TRUE	1	0.74	2		627	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0044461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	276	625	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.260076132575785	4	FACETS	0.973	0.916	1	0.973	0.916	1	CLONAL	3	TRUE	1	0.260076132575785	4		625	916	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56866264	56866264	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1374778377	NA	P-0044461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	56	290	0	ENST00000308159.5:c.1309C>G	p.Leu437Val	p.L437V	ENST00000308159	NM_014669.4	437	Ctc/Gtc	12/22	0.260076132575785	1	FACETS	0.781	0.67	0.901	0.781	0.67	0.901	CLONAL	1	TRUE	0	0.260076132575785	1		290	480	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692895	89692895	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs587781255	NA	P-0044461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	102	339	0	ENST00000371953.3:c.379G>T	p.Gly127Ter	p.G127*	ENST00000371953	NM_000314.4	127	Gga/Tga	5/9	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.260076132575785	2		339	593	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38981989	38981989	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	66	336	0	ENST00000357387.3:c.733C>T	p.Arg245Ter	p.R245*	ENST00000357387	NM_152756.3	245	Cga/Tga	8/38	1	2	FACETS	0.874	0.759	0.998	0.874	0.759	0.998	CLONAL	1	TRUE	1	0.260076132575785	2		336	581	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015438	176015438	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	122	317	0	ENST00000367669.3:c.1300G>T	p.Asp434Tyr	p.D434Y	ENST00000367669	NM_022457.5	434	Gac/Tac	12/20	0.224516995757243	3	FACETS	0.978	0.888	1	0.652	0.592	0.715	CLONAL	2	TRUE	0	0.260076132575785	3		317	542	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570231	95570231	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	100	257	0	ENST00000393063.1:c.3502G>T	p.Val1168Phe	p.V1168F	ENST00000393063	NM_030621.3	1168	Gtt/Ttt	22/28	0.224516995757243	3	FACETS	0.94	0.844	1	0.627	0.563	0.694	CLONAL	2	TRUE	0	0.260076132575785	3		257	462	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169299	99169299	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1281122001	NA	P-0044461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	103	516	0	ENST00000074304.5:c.1229G>C	p.Arg410Thr	p.R410T	ENST00000074304	NM_001134224.1	410	aGa/aCa	15/26	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.260076132575785	2		516	680	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133781	55133781	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	95	460	0	ENST00000257290.5:c.994G>T	p.Val332Phe	p.V332F	ENST00000257290	NM_006206.4	332	Gtc/Ttc	7/23	0.260076132575785	1	FACETS	0.924	0.823	1	0.924	0.823	1	CLONAL	1	TRUE	0	0.260076132575785	1		460	688	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143181670	143181670	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	93	419	0	ENST00000262992.4:c.663del	p.Asp222IlefsTer6	p.D222Ifs*6	ENST00000262992	NM_001101669.1	221	aaA/aa	9/24	0.260076132575785	1	FACETS	0.876	0.779	0.98	0.876	0.779	0.98	CLONAL	1	TRUE	0	0.260076132575785	1		419	710	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532907	187532907	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0044461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	60	284	0	ENST00000441802.2:c.9486C>G	p.Tyr3162Ter	p.Y3162*	ENST00000441802	NM_005245.3	3162	taC/taG	14/27	0.260076132575785	1	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	0	0.260076132575785	1		284	382	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131893126	131893126	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	54	289	0	ENST00000265335.6:c.110C>T	p.Pro37Leu	p.P37L	ENST00000265335		37	cCc/cTc	1/25	0.260076132575785	1	FACETS	0.91	0.78	1	0.91	0.78	1	CLONAL	1	TRUE	0	0.260076132575785	1		289	397	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662696	117662696	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	87	325	0	ENST00000368508.3:c.4769C>A	p.Ser1590Ter	p.S1590*	ENST00000368508	NM_002944.2	1590	tCa/tAa	29/43	0.18326659744238	2	FACETS	1	0.977	1	0.716	0.637	0.801	CLONAL	1	TRUE	0	0.260076132575785	2		325	467	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0044488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	231	395	1				ENST00000310581	NM_198253.2	-/1132			0.560603441717329	3	FACETS	0.977	0.92	1	0.977	0.92	1	CLONAL	2	TRUE	1	0.560603441717329	3		396	540	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0044488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	181	466	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.560603441717329	3	FACETS	0.901	0.839	0.963	0.901	0.839	0.963	CLONAL	2	TRUE	1	0.560603441717329	3		466	459	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971124	21971125	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0044488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	161	451	0	ENST00000304494.5:c.233_234del	p.Leu78HisfsTer41	p.L78Hfs*41	ENST00000304494	NM_000077.4	78	cTC/c	2/3	0.560603441717329	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.560603441717329	1		451	397	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200963	108200963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	65	311	0	ENST00000278616.4:c.7330G>A	p.Glu2444Lys	p.E2444K	ENST00000278616	NM_000051.3	2444	Gag/Aag	50/63	1	2	FACETS	0.739	0.645	0.838	0.739	0.645	0.838	SUBCLONAL	1	TRUE	1	0.560603441717329	2		311	314	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	135	450	0	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	1	2	FACETS	0.887	0.81	0.967	0.887	0.81	0.967	CLONAL	1	TRUE	1	0.560603441717329	2		450	543	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119795	108119795	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772529339	NA	P-0044488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	56	232	0	ENST00000278616.4:c.1201C>T	p.Gln401Ter	p.Q401*	ENST00000278616	NM_000051.3	401	Cag/Tag	9/63	1	2	FACETS	0.799	0.692	0.914	0.799	0.692	0.914	CLONAL	1	TRUE	1	0.560603441717329	2		232	250	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119700	108119700	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	51	191	0	ENST00000278616.4:c.1106C>G	p.Ser369Cys	p.S369C	ENST00000278616	NM_000051.3	369	tCt/tGt	9/63	1	2	FACETS	0.858	0.739	0.986	0.858	0.739	0.986	CLONAL	1	TRUE	1	0.560603441717329	2		191	212	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265833	16265833	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	260	703	0	ENST00000375759.3:c.10906G>A	p.Glu3636Lys	p.E3636K	ENST00000375759	NM_015001.2	3636	Gag/Aag	15/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.560603441717329	2		703	883	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803850	43803850	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	223	699	0	ENST00000372470.3:c.160G>A	p.Glu54Lys	p.E54K	ENST00000372470	NM_005373.2	54	Gag/Aag	2/12	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.560603441717329	2		699	763	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336236	73336236	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	59	238	0	ENST00000377767.4:c.2167G>C	p.Glu723Gln	p.E723Q	ENST00000377767	NM_014953.3	723	Gag/Cag	17/21	0.547497532788647	1	FACETS	0.953	0.839	1	0.953	0.839	1	CLONAL	1	TRUE	0	0.560603441717329	1		238	159	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292973	91292973	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	112	514	0	ENST00000355112.3:c.475G>A	p.Asp159Asn	p.D159N	ENST00000355112	NM_000057.2	159	Gac/Aac	3/22	1	2	FACETS	0.824	0.745	0.907	0.824	0.745	0.907	CLONAL	1	TRUE	1	0.560603441717329	2		514	485	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402552	20402552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	146	421	1	ENST00000346618.3:c.89C>T	p.Ala30Val	p.A30V	ENST00000346618	NM_001949.4	30	gCa/gTa	1/7	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.560603441717329	2		422	477	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197802	123197803	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0044488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	90	223	0	ENST00000218089.9:c.1928_1929del	p.Glu643ValfsTer17	p.E643Vfs*17	ENST00000218089	NM_001042749.1	642	gaAGag/gaag	20/35	1	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.560603441717329	1		223	179	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857046	9857046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774039446	NA	P-0044497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	22	252	0	ENST00000330684.3:c.4355G>A	p.Arg1452His	p.R1452H	ENST00000330684	NM_001134407.1	1452	cGc/cAc	13/13	1	2	FACETS	0.702	0.543	0.887	0.702	0.543	0.887	SUBCLONAL	1	TRUE	1	0.15	2		252	418	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985785	60985785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	39	311	0	ENST00000333681.4:c.115C>T	p.Pro39Ser	p.P39S	ENST00000333681		39	Ccc/Tcc	2/3	1	2	FACETS	1	0.842	1	1	0.842	1	CLONAL	1	TRUE	1	0.15	2		311	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0044501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	350	742	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.85278096399285	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.85278096399285	2		742	392	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591125	67591125	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	49	327	0	ENST00000274335.5:c.1718T>C	p.Leu573Pro	p.L573P	ENST00000274335		573	cTg/cCg	12/15	0.824458836464195	3	FACETS	0.828	0.711	0.953	0.276	0.237	0.318	CLONAL	1	TRUE	0	0.85278096399285	3		327	198	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953229	81953229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	95	379	2	ENST00000359376.3:c.2195G>A	p.Arg732His	p.R732H	ENST00000359376	NM_002661.3	732	cGc/cAc	20/33	0.848063263384157	2	FACETS	0.891	0.836	0.942	0.891	0.836	0.942	CLONAL	2	TRUE	0	0.85278096399285	2		381	125	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857781	57857781	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0044501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	290	608	0	ENST00000228682.2:c.101-1G>A		p.X34_splice	ENST00000228682	NM_005269.2	34			0.817440446424785	3	FACETS	0.96	0.933	0.984	0.96	0.933	0.984	CLONAL	3	TRUE	0	0.85278096399285	3		608	337	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348837	11348837	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	29	126	0	ENST00000332029.2:c.499C>G	p.Arg167Gly	p.R167G	ENST00000332029	NM_003745.1	167	Cgc/Ggc	2/2	0.586991085622694	4	FACETS	0.947	0.773	1	0.474	0.386	0.57	CLONAL	1	TRUE	2	0.85278096399285	4		126	133	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0044518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	85	724	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.866	0.773	0.963	0.866	0.773	0.963	CLONAL	1	TRUE	1	0.613698562593035	2		724	320	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883158	37883158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	225	892	1	ENST00000269571.5:c.3061G>A	p.Glu1021Lys	p.E1021K	ENST00000269571		1021	Gag/Aag	25/27	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.613698562593035	2		893	679	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096135	71096135	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1553709881	NA	P-0044518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	109	403	1	ENST00000318789.4:c.622C>T	p.Gln208Ter	p.Q208*	ENST00000318789	NM_032682.5	208	Cag/Tag	10/21	0.496538766030792	1	FACETS	0.892	0.814	0.972	0.892	0.814	0.972	CLONAL	1	TRUE	0	0.613698562593035	1		404	276	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830454	72830455	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	118	432	0	ENST00000268489.5:c.6126dup	p.Pro2043SerfsTer113	p.P2043Sfs*113	ENST00000268489	NM_006885.3	2042	-/T	9/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.613698562593035	2		432	313	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918081	50918081	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	143	829	0	ENST00000440232.2:c.2398C>T	p.Pro800Ser	p.P800S	ENST00000440232	NM_002691.3	800	Cca/Tca	20/27	1	2	FACETS	0.91	0.835	0.988	0.91	0.835	0.988	CLONAL	1	TRUE	1	0.613698562593035	2		829	512	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712607	52712607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542945393	NA	P-0044518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	96	363	0	ENST00000394830.3:c.145G>A	p.Val49Met	p.V49M	ENST00000394830	NM_018313.4	49	Gtg/Atg	3/30	1	2	FACETS	0.859	0.772	0.951	0.859	0.772	0.951	CLONAL	1	TRUE	1	0.613698562593035	2		363	364	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918294	44918295	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0044518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	88	157	0	ENST00000377967.4:c.920dup	p.Tyr307Ter	p.Y307*	ENST00000377967	NM_021140.2	307	tac/tAac	11/29	1	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.613698562593035	1		157	176	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579478	7579478	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	304	551	0	ENST00000269305.4:c.209del	p.Ala70ValfsTer53	p.A70Vfs*53	ENST00000269305	NM_001126112.2	70	gCt/gt	4/11	0.80673724957431	2	FACETS	0.912	0.882	0.941	0.912	0.882	0.941	CLONAL	2	TRUE	0	0.854550272418322	2		551	390	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	95	466	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.941	0.846	1	1	0.986	1	CLONAL	2	TRUE	1	0.289244674859955	2		466	349	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	352	964	8	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.979	1	1	0.997	1	CLONAL	3	TRUE	1	0.289244674859955	2		972	775	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	81	322	2	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.289244674859955	2		324	457	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154242	2154242	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755455183	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	83	618	2	ENST00000434045.2:c.686del	p.Pro229GlnfsTer27	p.P229Qfs*27	ENST00000434045	NM_001127598.1	229	cCa/ca	5/5	1	2	FACETS	0.696	0.614	0.785	0.696	0.614	0.785	SUBCLONAL	1	TRUE	1	0.289244674859955	2		620	824	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161907	47161907	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	79	333	2	ENST00000409792.3:c.4219del	p.Arg1407GlyfsTer5	p.R1407Gfs*5	ENST00000409792	NM_014159.6	1407	Agg/gg	3/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.289244674859955	2		335	415	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244943	46244943	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	118	460	0	ENST00000334344.6:c.3037C>T	p.Gln1013Ter	p.Q1013*	ENST00000334344	NM_152641.2	1013	Caa/Taa	15/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.289244674859955	2		460	746	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248611	10248611	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	208	541	0	ENST00000340748.4:c.4142C>T	p.Ala1381Val	p.A1381V	ENST00000340748		1381	gCc/gTc	35/40	1	2	FACETS	0.924	0.86	0.99	1	0.993	1	CLONAL	2	TRUE	1	0.289244674859955	2		541	778	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	29	409	1	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.627	0.504	0.766	0.627	0.504	0.766	SUBCLONAL	1	TRUE	1	0.289244674859955	2		410	320	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048756	180048756	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	60	585	0	ENST00000261937.6:c.1806del	p.His602GlnfsTer37	p.H602Qfs*37	ENST00000261937	NM_182925.4	602	caC/ca	13/30	1	2	FACETS	0.435	0.373	0.502	0.435	0.373	0.502	SUBCLONAL	1	TRUE	1	0.289244674859955	2		585	954	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	237	607	0	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.828	0.773	0.884	1	0.993	1	CLONAL	2	TRUE	1	0.289244674859955	2		607	990	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993903	72993903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751544438	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	169	494	0	ENST00000268489.5:c.142G>A	p.Gly48Arg	p.G48R	ENST00000268489	NM_006885.3	48	Ggg/Agg	2/10	1	2	FACETS	0.843	0.777	0.911	1	0.991	1	CLONAL	2	TRUE	1	0.289244674859955	2		494	693	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256699	46256699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749607074	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	96	398	0	ENST00000371998.3:c.755G>A	p.Arg252His	p.R252H	ENST00000371998		252	cGc/cAc	8/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.289244674859955	2		398	474	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760024	133760024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	221	684	0	ENST00000318560.5:c.2352del	p.Arg785GlyfsTer3	p.R785Gfs*3	ENST00000318560	NM_005157.4	783	Ccc/cc	11/11	1	2	FACETS	0.776	0.723	0.832	1	0.992	1	SUBCLONAL	2	TRUE	1	0.289244674859955	2		684	984	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216380	7216380	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	196	565	0	ENST00000380728.2:c.868del	p.Gln290SerfsTer55	p.Q290Sfs*55	ENST00000380728		290	Cag/ag	10/11	1	2	FACETS	0.873	0.81	0.938	1	0.992	1	CLONAL	2	TRUE	1	0.289244674859955	2		565	776	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967511	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	rs1349928568	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	87	259	0	ENST00000265433.3:c.1396dup	p.Arg466LysfsTer5	p.R466Kfs*5	ENST00000265433	NM_002485.4	466	agg/aAgg	10/16	1	2	FACETS	0.989	0.886	1	1	0.986	1	CLONAL	2	TRUE	1	0.289244674859955	2		259	304	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954642	17954643	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	245	673	0	ENST00000458235.1:c.251dup	p.Ser85GlufsTer46	p.S85Efs*46	ENST00000458235	NM_000215.3	84	ccg/ccCg	3/24	1	2	FACETS	0.76	0.71	0.812	1	0.993	1	SUBCLONAL	2	TRUE	1	0.289244674859955	2		673	1114	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262460	16262465	+	inframe_deletion	In_Frame_Del	DEL	CCCCCA	CCCCCA	-	rs773711901	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	42	239	0	ENST00000375759.3:c.9735_9740del	p.Thr3246_Pro3247del	p.T3246_P3247del	ENST00000375759	NM_015001.2	3242	gCCCCCAcc/gcc	11/15	1	2	FACETS	0.791	0.662	0.934	0.791	0.662	0.934	CLONAL	1	TRUE	1	0.289244674859955	2		239	367	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518587	69518587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs114327249	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	105	491	0	ENST00000294312.3:c.58G>A	p.Val20Met	p.V20M	ENST00000294312	NM_005117.2	20	Gtg/Atg	1/3	1	2	FACETS	0.957	0.857	1	0.957	0.857	1	CLONAL	1	TRUE	1	0.289244674859955	2		491	759	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339110	65339111	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	131	339	4	ENST00000342505.4:c.425dup	p.Ile143AspfsTer9	p.I143Dfs*9	ENST00000342505	NM_002227.2	142	aag/aaAg	5/25	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.289244674859955	2		343	665	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230604	46230604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	144	383	0	ENST00000334344.6:c.853C>T	p.Arg285Trp	p.R285W	ENST00000334344	NM_152641.2	285	Cgg/Tgg	8/21	1	2	FACETS	0.959	0.88	1	1	0.991	1	CLONAL	2	TRUE	1	0.289244674859955	2		383	519	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701932	43701933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	62	147	0	ENST00000382044.4:c.5312dup	p.Leu1771PhefsTer24	p.L1771Ffs*24	ENST00000382044	NM_001141980.1	1771	ttg/ttTg	25/28	1	2	FACETS	1	0.913	1	1	0.982	1	CLONAL	2	TRUE	1	0.289244674859955	2		147	204	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682809	190682810	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587778609	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	16	245	0	ENST00000441310.2:c.492dup	p.Cys165MetfsTer2	p.C165Mfs*2	ENST00000441310	NM_000534.4	162	gca/gcAa	5/13	1	2	FACETS	0.356	0.262	0.468	0.356	0.262	0.468	SUBCLONAL	1	TRUE	1	0.289244674859955	2		245	311	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65312344	65312344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	176	454	0	ENST00000342505.4:c.1975C>T	p.Arg659Cys	p.R659C	ENST00000342505	NM_002227.2	659	Cgc/Tgc	14/25	1	2	FACETS	0.939	0.869	1	1	0.992	1	CLONAL	2	TRUE	1	0.289244674859955	2		454	648	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875919	76875919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	78	316	0	ENST00000373344.5:c.5216G>A	p.Arg1739Gln	p.R1739Q	ENST00000373344	NM_000489.3	1739	cGa/cAa	20/35	1	2	FACETS	0.974	0.866	1	1	0.984	1	CLONAL	2	TRUE	1	0.289244674859955	2		316	277	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981613	101981614	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	58	151	0	ENST00000282441.5:c.40dup	p.Gln14ProfsTer98	p.Q14Pfs*98	ENST00000282441	NM_001130145.2	12	gcc/gCcc	1/9	1	2	FACETS	0.76	0.659	0.867	1	0.971	1	SUBCLONAL	2	TRUE	1	0.289244674859955	2		151	264	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213515	36213515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746928288	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	250	754	1	ENST00000222270.7:c.2617C>T	p.Arg873Cys	p.R873C	ENST00000222270	NM_014727.1	873	Cgt/Tgt	5/37	1	2	FACETS	0.768	0.718	0.82	1	0.993	1	SUBCLONAL	2	TRUE	1	0.289244674859955	2		755	1125	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739002	145739002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769675968	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	104	541	2	ENST00000428558.2:c.2153C>T	p.Ala718Val	p.A718V	ENST00000428558	NM_004260.3	718	gCg/gTg	13/22	1	2	FACETS	0.92	0.823	1	0.92	0.823	1	CLONAL	1	TRUE	1	0.289244674859955	2		543	782	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988376	36988376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751469975	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	79	314	1	ENST00000354822.5:c.277G>A	p.Ala93Thr	p.A93T	ENST00000354822	NM_001079668.2	93	Gcc/Acc	2/3	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.289244674859955	2		315	443	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42384740	42384740	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	47	354	0	ENST00000221972.3:c.502C>T	p.Arg168Ter	p.R168*	ENST00000221972	NM_021601.3	168	Cga/Tga	4/5	1	2	FACETS	0.623	0.525	0.73	0.623	0.525	0.73	SUBCLONAL	1	TRUE	1	0.289244674859955	2		354	522	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470994	25470994	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	247	617	0	ENST00000264709.3:c.767C>A	p.Pro256His	p.P256H	ENST00000264709	NM_175629.2	256	cCc/cAc	7/23	1	2	FACETS	0.926	0.867	0.987	1	0.994	1	CLONAL	2	TRUE	1	0.289244674859955	2		617	922	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497244	149497245	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	210	579	0	ENST00000261799.4:c.3073dup	p.Leu1025ProfsTer3	p.L1025Pfs*3	ENST00000261799	NM_002609.3	1025	ctg/cCtg	22/23	1	2	FACETS	0.777	0.722	0.834	1	0.992	1	SUBCLONAL	2	TRUE	1	0.289244674859955	2		579	934	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39745033	39745033	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	138	395	1	ENST00000361337.2:c.1822+1G>A		p.X608_splice	ENST00000361337	NM_003286.2	608			1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.289244674859955	2		396	645	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255866	16255866	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	77	342	1	ENST00000375759.3:c.3131T>A	p.Ile1044Asn	p.I1044N	ENST00000375759	NM_015001.2	1044	aTt/aAt	11/15	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.289244674859955	2		343	532	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248202	59248203	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	17	79	0	ENST00000371222.2:c.540_541del	p.Leu181GlufsTer128	p.L181Efs*128	ENST00000371222	NM_002228.3	180	gcGCtg/gctg	1/1	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.289244674859955	2		79	79	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450886	70450886	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	147	450	0	ENST00000373644.4:c.5726C>A	p.Pro1909His	p.P1909H	ENST00000373644	NM_030625.2	1909	cCt/cAt	12/12	1	2	FACETS	0.887	0.814	0.963	1	0.99	1	CLONAL	2	TRUE	1	0.289244674859955	2		450	573	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741373	17741373	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	145	611	0	ENST00000250003.3:c.48del	p.Asp17ThrfsTer34	p.D17Tfs*34	ENST00000250003	NM_002478.4	15	gCc/gc	1/3	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.289244674859955	2		611	925	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939801	71939801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781357595	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	84	643	0	ENST00000298229.2:c.428C>T	p.Pro143Leu	p.P143L	ENST00000298229	NM_001567.3	143	cCg/cTg	4/28	1	2	FACETS	0.627	0.553	0.707	0.627	0.553	0.707	SUBCLONAL	1	TRUE	1	0.289244674859955	2		643	926	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236131	108236131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879253964	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	152	479	0	ENST00000278616.4:c.9067G>A	p.Gly3023Ser	p.G3023S	ENST00000278616	NM_000051.3	3023	Ggc/Agc	63/63	1	2	FACETS	0.799	0.733	0.867	1	0.989	1	SUBCLONAL	2	TRUE	1	0.289244674859955	2		479	658	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244091	46244091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	57	399	0	ENST00000334344.6:c.2185C>T	p.Pro729Ser	p.P729S	ENST00000334344	NM_152641.2	729	Cct/Tct	15/21	1	2	FACETS	0.677	0.581	0.782	0.677	0.581	0.782	SUBCLONAL	1	TRUE	1	0.289244674859955	2		399	582	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428255	49428255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	213	600	0	ENST00000301067.7:c.10445G>T	p.Arg3482Leu	p.R3482L	ENST00000301067	NM_003482.3	3482	cGg/cTg	37/54	1	2	FACETS	0.893	0.831	0.956	1	0.993	1	CLONAL	2	TRUE	1	0.289244674859955	2		600	825	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847249	68847249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556110297	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	200	446	0	ENST00000261769.5:c.1171G>A	p.Val391Ile	p.V391I	ENST00000261769	NM_004360.3	391	Gtc/Atc	9/16	1	2	FACETS	0.933	0.867	1	1	0.993	1	CLONAL	2	TRUE	1	0.289244674859955	2		446	741	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976199	7976199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	128	508	0	ENST00000319144.4:c.1996C>T	p.Arg666Cys	p.R666C	ENST00000319144	NM_001139.2	666	Cgc/Tgc	15/15	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.289244674859955	2		508	870	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40468893	40468893	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	82	297	0	ENST00000264657.5:c.2171T>C	p.Leu724Pro	p.L724P	ENST00000264657	NM_139276.2	724	cTg/cCg	23/24	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.289244674859955	2		297	479	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56363640	56363640	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	38	292	2	ENST00000348428.3:c.419C>T	p.Ala140Val	p.A140V	ENST00000348428	NM_006785.3	140	gCt/gTt	3/17	1	2	FACETS	0.782	0.648	0.93	0.782	0.648	0.93	CLONAL	1	TRUE	1	0.289244674859955	2		294	336	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1623996	1623996	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748050498	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	211	599	1	ENST00000344749.5:c.503C>T	p.Thr168Met	p.T168M	ENST00000344749	NM_001136139.2	168	aCg/aTg	8/19	1	2	FACETS	0.863	0.803	0.925	1	0.993	1	CLONAL	2	TRUE	1	0.289244674859955	2		600	845	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245817	5245817	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs774918692	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	107	652	0	ENST00000357368.4:c.958A>G	p.Ile320Val	p.I320V	ENST00000357368	NM_002850.3	320	Att/Gtt	10/38	1	2	FACETS	0.722	0.646	0.803	0.722	0.646	0.803	SUBCLONAL	1	TRUE	1	0.289244674859955	2		652	1025	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873482	45873482	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	152	474	0	ENST00000391945.4:c.14T>C	p.Val5Ala	p.V5A	ENST00000391945	NM_000400.3	5	gTg/gCg	2/23	1	2	FACETS	0.859	0.788	0.932	1	0.99	1	CLONAL	2	TRUE	1	0.289244674859955	2		474	612	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014316	70014316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	151	494	1	ENST00000394351.3:c.1177C>T	p.Leu393Phe	p.L393F	ENST00000394351	NM_000248.3	393	Ctt/Ttt	9/9	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.289244674859955	2		495	815	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955189	1955190	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	165	473	0	ENST00000382891.5:c.2281dup	p.Leu761ProfsTer21	p.L761Pfs*21	ENST00000382891	NM_133335.3	759	tgc/tgCc	12/22	1	2	FACETS	0.834	0.768	0.902	1	0.991	1	CLONAL	2	TRUE	1	0.289244674859955	2		473	684	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564606	55564607	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	192	478	0	ENST00000288135.5:c.498dup	p.Lys167GlnfsTer58	p.K167Qfs*58	ENST00000288135	NM_000222.2	165	gac/gaCc	3/21	1	2	FACETS	0.923	0.857	0.992	1	0.993	1	CLONAL	2	TRUE	1	0.289244674859955	2		478	719	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532743	187532743	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	80	451	0	ENST00000441802.2:c.9650T>C	p.Ile3217Thr	p.I3217T	ENST00000441802	NM_005245.3	3217	aTt/aCt	14/27	1	2	FACETS	0.805	0.709	0.909	0.805	0.709	0.909	CLONAL	1	TRUE	1	0.289244674859955	2		451	687	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228354	228354	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	29	275	0	ENST00000264932.6:c.676A>G	p.Met226Val	p.M226V	ENST00000264932	NM_004168.2	226	Atg/Gtg	6/15	1	2	FACETS	0.533	0.428	0.653	0.533	0.428	0.653	SUBCLONAL	1	TRUE	1	0.289244674859955	2		275	376	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294981	1294981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	32	76	0	ENST00000310581.5:c.124G>A	p.Gly42Arg	p.G42R	ENST00000310581	NM_198253.2	42	Ggg/Agg	1/16	1	2	FACETS	1	0.927	1	1	0.969	1	CLONAL	2	TRUE	1	0.289244674859955	2		76	91	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030820	69030820	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	74	326	0	ENST00000288368.4:c.3362T>C	p.Phe1121Ser	p.F1121S	ENST00000288368	NM_024870.2	1121	tTc/tCc	27/40	1	2	FACETS	0.942	0.826	1	0.942	0.826	1	CLONAL	1	TRUE	1	0.289244674859955	2		326	543	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485945	8485945	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	128	359	1	ENST00000356435.5:c.2872T>C	p.Tyr958His	p.Y958H	ENST00000356435		958	Tat/Cat	17/35	1	2	FACETS	0.892	0.813	0.974	1	0.989	1	CLONAL	2	TRUE	1	0.289244674859955	2		360	496	SUCCESS
AR	367	MSKCC	GRCh37	X	66931372	66931372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	182	560	1	ENST00000374690.3:c.2014C>T	p.Pro672Ser	p.P672S	ENST00000374690	NM_000044.3	672	Ccc/Tcc	4/8	1	2	FACETS	0.832	0.77	0.897	1	0.991	1	CLONAL	2	TRUE	1	0.289244674859955	2		561	756	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349939	70349940	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	241	636	0	ENST00000374080.3:c.3924dup	p.Asp1309ArgfsTer6	p.D1309Rfs*6	ENST00000374080		1308	caa/cAaa	28/45	1	2	FACETS	0.827	0.772	0.883	1	0.993	1	CLONAL	2	TRUE	1	0.289244674859955	2		636	1008	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262139	16262139	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	85	242	0	ENST00000375759.3:c.9404A>C	p.Gln3135Pro	p.Q3135P	ENST00000375759	NM_015001.2	3135	cAg/cCg	11/15	1	2	FACETS	0.987	0.88	1	0.987	0.88	1	CLONAL	1	TRUE	1	0.504898628854962	2		242	341	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36826926	36826926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769201571	NA	P-0044550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	148	433	0	ENST00000373129.3:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000373129	NM_032017.1	3	cGg/cAg	3/12	1	2	FACETS	0.835	0.764	0.909	0.835	0.764	0.909	CLONAL	1	TRUE	1	0.504898628854962	2		433	702	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282439	115282439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	172	366	0	ENST00000438362.2:c.211C>T	p.Arg71Cys	p.R71C	ENST00000438362	NM_001242891.1	71	Cgt/Tgt	3/20	1	2	FACETS	0.912	0.841	0.986	0.912	0.841	0.986	CLONAL	1	TRUE	1	0.504898628854962	2		366	747	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236086	108236086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782292	NA	P-0044550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	166	368	0	ENST00000278616.4:c.9022C>T	p.Arg3008Cys	p.R3008C	ENST00000278616	NM_000051.3	3008	Cgt/Tgt	63/63	0.479796120254155	1	FACETS	0.889	0.821	0.958	0.889	0.821	0.958	CLONAL	1	TRUE	0	0.504898628854962	1		368	553	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432067	121432067	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555212014	NA	P-0044550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	80	537	0	ENST00000257555.6:c.814C>T	p.Arg272Cys	p.R272C	ENST00000257555		272	Cgc/Tgc	4/10	1	2	FACETS	0.374	0.329	0.423	0.374	0.329	0.423	SUBCLONAL	1	TRUE	1	0.504898628854962	2		537	847	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435391	121435391	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193922580	NA	P-0044550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	211	520	0	ENST00000257555.6:c.1424C>T	p.Pro475Leu	p.P475L	ENST00000257555		475	cCg/cTg	7/10	1	2	FACETS	0.957	0.89	1	0.957	0.89	1	CLONAL	1	TRUE	1	0.504898628854962	2		520	873	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061125	38061196	+	inframe_deletion	In_Frame_Del	DEL	CTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCG	CTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCG	-	novel	NA	P-0044550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	198	106	0	ENST00000250448.2:c.793_864del	p.Arg265_Lys288del	p.R265_K288del	ENST00000250448	NM_004496.3	265	CGCTTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGGCGCCAAG/-	2/2	1	2	FACETS	1	0.967	1	1	0.994	1	CLONAL	2	TRUE	1	0.504898628854962	2		106	377	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991060	41991060	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0044550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	95	237	0	ENST00000219905.7:c.2014-1G>T		p.X672_splice	ENST00000219905	NM_001164273.1	672			1	2	FACETS	0.958	0.859	1	0.958	0.859	1	CLONAL	1	TRUE	1	0.504898628854962	2		237	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0044550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	134	623	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.627	0.57	0.688	0.627	0.57	0.688	SUBCLONAL	1	TRUE	1	0.504898628854962	2		624	846	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115040	3115040	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	209	527	0	ENST00000078429.4:c.575A>G	p.Tyr192Cys	p.Y192C	ENST00000078429	NM_002067.2	192	tAc/tGc	4/7	1	2	FACETS	0.925	0.86	0.993	0.925	0.86	0.993	CLONAL	1	TRUE	1	0.504898628854962	2		527	895	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229680	5229680	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	10	15	0	ENST00000357368.4:c.2171C>A	p.Pro724Gln	p.P724Q	ENST00000357368	NM_002850.3	724	cCg/cAg	15/38	1	2	FACETS	1	0.765	1	1	0.765	1	CLONAL	1	TRUE	1	0.504898628854962	2		15	36	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5239041	5239041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374725933	NA	P-0044550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	53	474	1	ENST00000357368.4:c.1738G>A	p.Val580Met	p.V580M	ENST00000357368	NM_002850.3	580	Gtg/Atg	13/38	1	2	FACETS	0.244	0.207	0.285	0.244	0.207	0.285	SUBCLONAL	1	TRUE	1	0.504898628854962	2		475	860	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117189	7117189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757085718	NA	P-0044550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	198	519	1	ENST00000302850.5:c.4027C>T	p.Arg1343Trp	p.R1343W	ENST00000302850	NM_000208.2	1343	Cgg/Tgg	22/22	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.504898628854962	2		520	773	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354247	15354247	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	154	550	0	ENST00000263377.2:c.2633C>A	p.Ala878Asp	p.A878D	ENST00000263377	NM_058243.2	878	gCt/gAt	14/20	1	2	FACETS	0.591	0.54	0.644	0.591	0.54	0.644	SUBCLONAL	1	TRUE	1	0.504898628854962	2		550	1033	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0044550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	119	879	2	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.492	0.443	0.543	0.492	0.443	0.543	SUBCLONAL	1	TRUE	1	0.504898628854962	2		881	959	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753645	42753645	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555750795	NA	P-0044550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	124	571	2	ENST00000222329.4:c.619C>T	p.Arg207Ter	p.R207*	ENST00000222329	NM_006494.2	207	Cga/Tga	4/4	1	2	FACETS	0.59	0.533	0.649	0.59	0.533	0.649	SUBCLONAL	1	TRUE	1	0.504898628854962	2		573	833	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015227	128015227	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771245959	NA	P-0044550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	156	362	1	ENST00000285398.2:c.2294G>A	p.Arg765Gln	p.R765Q	ENST00000285398	NM_000122.1	765	cGg/cAg	15/15	0.504898628854962	1	FACETS	0.887	0.817	0.958	0.887	0.817	0.958	CLONAL	1	TRUE	0	0.504898628854962	1		363	521	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805543	1805543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886043604	NA	P-0044550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	142	477	0	ENST00000260795.2:c.1055C>T	p.Ala352Val	p.A352V	ENST00000260795		352	gCg/gTg	7/17	1	2	FACETS	0.775	0.707	0.845	0.775	0.707	0.845	SUBCLONAL	1	TRUE	1	0.504898628854962	2		477	726	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31429616	31429616	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	40	345	0	ENST00000344624.3:c.3182A>C	p.Lys1061Thr	p.K1061T	ENST00000344624		1061	aAg/aCg	24/33	NA	2	FACETS	0.224	0.185	0.267			1	INDETERMINATE	1	TRUE	NA	0.504898628854962	2		345	707	SUCCESS
APC	324	MSKCC	GRCh37	5	112175675	112175676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0044550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	117	240	0	ENST00000257430.4:c.4393_4394dup	p.Ser1465ArgfsTer9	p.S1465Rfs*9	ENST00000257430	NM_000038.5	1462	aag/aAGag	16/16	0.375209997338464	1	FACETS	0.802	0.728	0.878	0.802	0.728	0.878	CLONAL	1	TRUE	0	0.504898628854962	1		240	432	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038401	180038401	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	182	532	0	ENST00000261937.6:c.3616G>C	p.Ala1206Pro	p.A1206P	ENST00000261937	NM_182925.4	1206	Gcc/Ccc	27/30	1	2	FACETS	0.784	0.723	0.847	0.784	0.723	0.847	SUBCLONAL	1	TRUE	1	0.504898628854962	2		532	920	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043465	180043465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1451816005	NA	P-0044550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	185	495	0	ENST00000261937.6:c.3121C>T	p.Arg1041Trp	p.R1041W	ENST00000261937	NM_182925.4	1041	Cgg/Tgg	23/30	1	2	FACETS	0.911	0.843	0.982	0.911	0.843	0.982	CLONAL	1	TRUE	1	0.504898628854962	2		495	804	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0044550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	151	549	3	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	0.441971087286357	3	FACETS	0.627	0.572	0.685	0.313	0.286	0.343	SUBCLONAL	1	TRUE	1	0.504898628854962	3		552	1195	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347843	128347843	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758476607	NA	P-0044550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	160	395	1	ENST00000265960.3:c.662C>T	p.Pro221Leu	p.P221L	ENST00000265960	NM_001006617.1	221	cCg/cTg	5/12	1	2	FACETS	0.856	0.787	0.929	0.856	0.787	0.929	CLONAL	1	TRUE	1	0.504898628854962	2		396	740	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300039	137300040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755912201	NA	P-0044550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	177	484	1	ENST00000481739.1:c.331dup	p.Leu111ProfsTer70	p.L111Pfs*70	ENST00000481739	NM_002957.4	108	-/C	3/10	1	2	FACETS	0.819	0.755	0.885	0.819	0.755	0.885	CLONAL	1	TRUE	1	0.504898628854962	2		485	856	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279834	46279836	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	rs767107142	NA	P-0044550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	54	320	0	ENST00000371998.3:c.3762_3764del	p.Gln1276del	p.Q1276del	ENST00000371998		1254	CAA/-	20/23	1	2	FACETS	0.403	0.344	0.467	0.403	0.344	0.467	SUBCLONAL	1	TRUE	1	0.504898628854962	2		320	531	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864647	37864647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756720659	NA	P-0044556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	83	489	0	ENST00000269571.5:c.299G>A	p.Arg100Gln	p.R100Q	ENST00000269571		100	cGg/cAg	3/27	0.398706689468806	3	FACETS	0.519	0.457	0.585	0.259	0.228	0.293	SUBCLONAL	1	TRUE	1	0.475372092384977	3		489	833	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258956	16258956	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs577325205	NA	P-0044556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	70	485	0	ENST00000375759.3:c.6221A>G	p.Lys2074Arg	p.K2074R	ENST00000375759	NM_015001.2	2074	aAa/aGa	11/15	1	2	FACETS	0.394	0.343	0.449	0.394	0.343	0.449	SUBCLONAL	1	TRUE	1	0.475372092384977	2		485	748	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56809865	56809865	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	106	417	0	ENST00000337432.4:c.986C>A	p.Ser329Ter	p.S329*	ENST00000337432	NM_058216.2	329	tCa/tAa	8/9	0.398706689468806	3	FACETS	0.996	0.896	1	0.498	0.448	0.551	CLONAL	1	TRUE	1	0.475372092384977	3		417	554	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47735789	47735789	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	95	478	0	ENST00000449228.1:c.71T>A	p.Val24Asp	p.V24D	ENST00000449228	NM_001127240.2	24	gTc/gAc	1/4	0.232774375700007	3	FACETS	0.563	0.5	0.63	0.281	0.25	0.315	INDETERMINATE	1	TRUE	1	0.475372092384977	3		478	879	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553282	41553282	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	61	409	0	ENST00000263253.7:c.3371T>A	p.Met1124Lys	p.M1124K	ENST00000263253	NM_001429.3	1124	aTg/aAg	18/31	0.232774375700007	3	FACETS	0.528	0.455	0.607	0.264	0.227	0.304	INDETERMINATE	1	TRUE	1	0.475372092384977	3		409	602	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518800	176518800	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	75	442	0	ENST00000292408.4:c.718G>T	p.Asp240Tyr	p.D240Y	ENST00000292408	NM_213647.1	240	Gat/Tat	6/18	0.200668439235557	3	FACETS	0.592	0.518	0.671	0.296	0.259	0.336	INDETERMINATE	1	TRUE	1	0.475372092384977	3		442	660	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140549966	140549966	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	37	279	0	ENST00000288602.6:c.185A>G	p.Glu62Gly	p.E62G	ENST00000288602	NM_004333.4	62	gAg/gGg	2/18	0.301367006511974	6	FACETS	0.569	0.468	0.681	0.142	0.117	0.171	SUBCLONAL	1	TRUE	2	0.475372092384977	6		279	534	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309024	137309025	+	missense_variant	Missense_Mutation	DNP	CG	CG	TT	novel	NA	P-0044556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	58	531	1	ENST00000481739.1:c.631_632delinsTT	p.Arg211Phe	p.R211F	ENST00000481739	NM_002957.4	211	CGt/TTt	5/10	0.475623844252629	3	FACETS	0.345	0.295	0.4	0.173	0.147	0.2	SUBCLONAL	1	TRUE	1	0.475372092384977	3		532	875	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0044582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	148	696	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.157609344680582	2	FACETS	0.88	0.803	0.961	0.88	0.803	0.961	CLONAL	2	TRUE	0	0.17	2		696	989	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0044582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	99	519	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.83	0.741	0.924	1	0.984	1	CLONAL	2	TRUE	1	0.17	2		519	702	SUCCESS
APC	324	MSKCC	GRCh37	5	112175604	112175604	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	85	385	0	ENST00000257430.4:c.4313del	p.Thr1438AsnfsTer35	p.T1438Nfs*35	ENST00000257430	NM_000038.5	1438	aCa/aa	16/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.17	2		385	673	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920601	96920601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746883021	NA	P-0044582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	46	472	0	ENST00000258439.3:c.379C>T	p.Arg127Cys	p.R127C	ENST00000258439	NM_001193304.2	127	Cgt/Tgt	3/4	1	2	FACETS	0.756	0.635	0.89	0.756	0.635	0.89	SUBCLONAL	1	TRUE	1	0.17	2		472	716	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285704	87285704	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	70	629	0	ENST00000277120.3:c.41G>A	p.Arg14Gln	p.R14Q	ENST00000277120		14	cGg/cAg	2/19	1	2	FACETS	0.908	0.79	1	0.908	0.79	1	CLONAL	1	TRUE	1	0.17	2		629	907	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396808	139396808	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	83	783	0	ENST00000277541.6:c.5300T>C	p.Leu1767Pro	p.L1767P	ENST00000277541	NM_017617.3	1767	cTc/cCc	28/34	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.17	2		783	975	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0044584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	452	466	0	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	0.627908626361041	2	FACETS	0.908	0.876	0.94	0.908	0.876	0.94	CLONAL	2	TRUE	0	0.674366304385623	2		466	738	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039371	47039371	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	685	648	0	ENST00000377604.3:c.994C>T	p.Arg332Cys	p.R332C	ENST00000377604	NM_001204468.1	332	Cgc/Tgc	10/24	0.207224469842512	6	FACETS	0.882	0.85	0.914	0.882	0.85	0.914	INDETERMINATE	3	TRUE	3	0.674366304385623	6		648	1804	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0044584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	853	738	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.648315068518009	2	FACETS	0.932	0.909	0.955	0.932	0.909	0.955	CLONAL	2	TRUE	0	0.674366304385623	2		738	1357	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641149	117641149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1306349293	NA	P-0044584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	410	644	0	ENST00000368508.3:c.5822C>T	p.Pro1941Leu	p.P1941L	ENST00000368508	NM_002944.2	1941	cCt/cTt	36/43	0.258611534267007	5	FACETS	0.966	0.92	1	0.644	0.613	0.676	INDETERMINATE	2	TRUE	2	0.674366304385623	5		644	1266	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577526	64577526	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	286	640	0	ENST00000312049.6:c.56del	p.Val19GlyfsTer100	p.V19Gfs*100	ENST00000312049	NM_130799.2	19	gTg/gg	2/10	0.852133936076287	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.852133936076287	1		640	363	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161243	56161243	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0044605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	191	316	0	ENST00000399503.3:c.1112C>G	p.Ser371Ter	p.S371*	ENST00000399503	NM_005921.1	371	tCa/tGa	5/20	0.582836351071548	1	FACETS	0.96	0.896	1	0.96	0.896	1	CLONAL	1	TRUE	0	0.582836351071548	1		316	484	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913527	NA	P-0044605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	149	320	0	ENST00000311936.3:c.436G>C	p.Ala146Pro	p.A146P	ENST00000311936	NM_004985.3	146	Gca/Cca	4/5	1	2	FACETS	0.88	0.808	0.955	0.88	0.808	0.955	CLONAL	1	TRUE	1	0.582836351071548	2		320	581	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098973	178098973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	224	203	0	ENST00000397062.3:c.72G>C	p.Trp24Cys	p.W24C	ENST00000397062	NM_006164.4	24	tgG/tgC	2/5	1	2	FACETS	0.789	0.743	0.835	1	0.994	1	SUBCLONAL	2	TRUE	1	0.582836351071548	2		203	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0044605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	187	467	0	ENST00000269305.4:c.560-1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.582836351071548	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.582836351071548	1		467	454	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114917829	114917829	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0044605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	58	414	0	ENST00000543371.1:c.1318+1G>A		p.X440_splice	ENST00000543371	NM_001198531.1	440			1	2	FACETS	0.29	0.249	0.335	0.29	0.249	0.335	SUBCLONAL	1	TRUE	1	0.582836351071548	2		414	686	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279675	123279675	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	43	293	0	ENST00000358487.5:c.757C>T	p.Pro253Ser	p.P253S	ENST00000358487	NM_000141.4	253	Cct/Tct	7/18	1	2	FACETS	0.363	0.304	0.429	0.363	0.304	0.429	SUBCLONAL	1	TRUE	1	0.582836351071548	2		293	406	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864774	57864774	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	208	592	0	ENST00000228682.2:c.2251C>G	p.Leu751Val	p.L751V	ENST00000228682	NM_005269.2	751	Ctg/Gtg	12/12	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.582836351071548	2		592	714	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106747	27106747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	281	513	0	ENST00000324856.7:c.6358G>A	p.Glu2120Lys	p.E2120K	ENST00000324856	NM_006015.4	2120	Gaa/Aaa	20/20	0.582836351071548	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.582836351071548	1		513	565	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595962	43595962	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1488040686	NA	P-0044605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	224	625	1	ENST00000355710.3:c.129C>A	p.Asp43Glu	p.D43E	ENST00000355710	NM_020975.4	43	gaC/gaA	2/20	1	2	FACETS	0.937	0.875	1	0.937	0.875	1	CLONAL	1	TRUE	1	0.582836351071548	2		626	820	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528113	103528113	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	34	319	0	ENST00000355739.4:c.3421G>T	p.Gly1141Ter	p.G1141*	ENST00000355739	NM_000123.3	1141	Gga/Tga	15/15	1	2	FACETS	0.205	0.167	0.249	0.205	0.167	0.249	SUBCLONAL	1	TRUE	1	0.582836351071548	2		319	568	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90634809	90634814	+	frameshift_variant	Frame_Shift_Del	DEL	AATACG	AATACG	GAGAT	novel	NA	P-0044605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	155	536	2	ENST00000330062.3:c.178_183delinsATCTC	p.Arg60IlefsTer20	p.R60Ifs*20	ENST00000330062	NM_002168.2	60	CGTATT/ATCTC	2/11	1	2	FACETS	0.788	0.723	0.855	0.788	0.723	0.855	SUBCLONAL	1	TRUE	1	0.582836351071548	2		538	675	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59820399	59820399	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	152	335	0	ENST00000259008.2:c.2354C>A	p.Pro785His	p.P785H	ENST00000259008	NM_032043.2	785	cCt/cAt	16/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.582836351071548	2		335	470	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226492	1226492	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	223	539	0	ENST00000326873.7:c.1148G>C	p.Arg383Pro	p.R383P	ENST00000326873	NM_000455.4	383	cGc/cCc	9/10	0.255092124103047	0	FACETS	0.427	0.399	0.456			1	INDETERMINATE	1	TRUE	0	0.582836351071548	0		539	747	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143467	30143467	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	91	316	0	ENST00000389048.3:c.59G>T	p.Gly20Val	p.G20V	ENST00000389048	NM_004304.4	20	gGc/gTc	1/29	1	2	FACETS	0.683	0.609	0.761	0.683	0.609	0.761	SUBCLONAL	1	TRUE	1	0.582836351071548	2		316	457	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920059	1920059	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	198	532	1	ENST00000382891.5:c.1119G>T	p.Met373Ile	p.M373I	ENST00000382891	NM_133335.3	373	atG/atT	5/22	NA	2	FACETS	0.931	0.865	0.999			1	INDETERMINATE	1	TRUE	NA	0.582836351071548	2		533	730	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508817	31508817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	63	525	1	ENST00000344624.3:c.1498G>A	p.Glu500Lys	p.E500K	ENST00000344624		500	Gaa/Aaa	7/33	0.16357525656181	3	FACETS	0.268	0.231	0.309	0.089	0.077	0.103	INDETERMINATE	1	TRUE	0	0.582836351071548	3		526	1042	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876533	35876533	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	239	423	0	ENST00000303115.3:c.1325G>T	p.Gly442Val	p.G442V	ENST00000303115	NM_002185.3	442	gGa/gTa	8/8	0.16357525656181	3	FACETS	1	0.99	1	0.435	0.407	0.464	INDETERMINATE	1	TRUE	0	0.582836351071548	3		423	811	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349220	70349220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	108	546	0	ENST00000374080.3:c.3632C>A	p.Ser1211Tyr	p.S1211Y	ENST00000374080		1211	tCc/tAc	26/45	0.405553906880703	1	FACETS	0.356	0.32	0.395	0.356	0.32	0.395	SUBCLONAL	1	TRUE	0	0.582836351071548	1		546	737	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184117	123184117	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	55	257	0	ENST00000218089.9:c.975T>G	p.Asn325Lys	p.N325K	ENST00000218089	NM_001042749.1	325	aaT/aaG	11/35	0.405553906880703	1	FACETS	0.339	0.291	0.392	0.339	0.291	0.392	SUBCLONAL	1	TRUE	0	0.582836351071548	1		257	394	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190001	123190001	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	111	370	0	ENST00000218089.9:c.1220C>G	p.Ala407Gly	p.A407G	ENST00000218089	NM_001042749.1	407	gCa/gGa	14/35	0.405553906880703	1	FACETS	0.444	0.4	0.49	0.444	0.4	0.49	SUBCLONAL	1	TRUE	0	0.582836351071548	1		370	608	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	34	214	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.793	0.648	0.956	0.793	0.648	0.956	CLONAL	1	TRUE	1	0.20865900716456	2		214	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578399	7578403	+	protein_altering_variant	In_Frame_Del	DEL	GGGGC	GGGGC	AG	novel	NA	P-0044639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	86	671	2	ENST00000269305.4:c.527_531delinsCT	p.Cys176_Pro177delinsSer	p.C176_P177delinsS	ENST00000269305	NM_001126112.2	176	tGCCCC/tCT	5/11	0.20865900716456	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.20865900716456	1		673	690	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955538	48955538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913303	NA	P-0044660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	162	411	0	ENST00000267163.4:c.1654C>T	p.Arg552Ter	p.R552*	ENST00000267163	NM_000321.2	552	Cga/Tga	17/27	0.745552009826026	2	FACETS	0.894	0.845	0.942	0.894	0.845	0.942	CLONAL	2	TRUE	0	0.745552009826026	2		411	243	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871036	12871036	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	297	447	0	ENST00000228872.4:c.263A>G	p.Tyr88Cys	p.Y88C	ENST00000228872	NM_004064.3	88	tAc/tGc	1/3	0.745552009826026	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.745552009826026	2		447	377	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585361	29585361	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1555618492	NA	P-0044660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	316	444	0	ENST00000356175.3:c.4111-1G>A		p.X1371_splice	ENST00000356175	NM_000267.3	1371			0.745552009826026	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.745552009826026	2		444	401	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247516	123247516	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519795	NA	P-0044660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	321	437	1	ENST00000358487.5:c.1975A>G	p.Lys659Glu	p.K659E	ENST00000358487	NM_000141.4	659	Aag/Gag	14/18	0.745552009826026	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.745552009826026	2		438	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691039	NA	P-0044660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	575	795	0	ENST00000269305.4:c.919+1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.745552009826026	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.745552009826026	2		795	748	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600470	10600470	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	584	731	0	ENST00000171111.5:c.1385G>T	p.Gly462Val	p.G462V	ENST00000171111	NM_203500.1	462	gGg/gTg	4/6	0.745552009826026	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.745552009826026	2		731	776	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579496	7579496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	560	827	0	ENST00000269305.4:c.191C>T	p.Pro64Leu	p.P64L	ENST00000269305	NM_001126112.2	64	cCc/cTc	4/11	0.745552009826026	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.745552009826026	2		827	742	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47643492	47643492	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	325	568	0	ENST00000233146.2:c.1000A>G	p.Lys334Glu	p.K334E	ENST00000233146	NM_000251.2	334	Aaa/Gaa	6/16	0.618623002272913	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.745552009826026	4		568	743	SUCCESS
APC	324	MSKCC	GRCh37	5	112174980	112174980	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	265	201	0	ENST00000257430.4:c.3689A>T	p.Gln1230Leu	p.Q1230L	ENST00000257430	NM_000038.5	1230	cAg/cTg	16/16	0.741958492375255	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	4	TRUE	0	0.745552009826026	4		201	294	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69032475	69032477	+	missense_variant	Missense_Mutation	TNP	GGC	GGC	AAA	novel	NA	P-0044660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	195	700	3	ENST00000288368.4:c.3549_3551delinsAAA	p.Ala1184Asn	p.A1184N	ENST00000288368	NM_024870.2	1183	agGGCc/agAAAc	29/40	0.618623002272913	4	FACETS	1	0.988	1	0.659	0.612	0.707	CLONAL	1	TRUE	2	0.745552009826026	4		703	693	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285740	87285740	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	457	655	0	ENST00000277120.3:c.77G>T	p.Trp26Leu	p.W26L	ENST00000277120		26	tGg/tTg	2/19	0.618623002272913	4	FACETS	0.981	0.939	1	0.981	0.939	1	CLONAL	2	TRUE	2	0.745552009826026	4		655	1091	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249644	110249644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764221089	NA	P-0044660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	724	1108	0	ENST00000374672.4:c.1031C>T	p.Pro344Leu	p.P344L	ENST00000374672	NM_004235.4	344	cCg/cTg	3/5	0.618623002272913	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.745552009826026	4		1108	1614	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0044700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	299	748	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.671394234803349	2	FACETS	0.912	0.876	0.946	0.912	0.876	0.946	CLONAL	2	TRUE	0	0.75921948516276	2		749	432	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059173	42059173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771172244	NA	P-0044700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	75	382	0	ENST00000219905.7:c.8893C>T	p.Pro2965Ser	p.P2965S	ENST00000219905	NM_001164273.1	2965	Ccc/Tcc	24/24	0.75921948516276	3	FACETS	0.839	0.741	0.942	0.419	0.37	0.471	CLONAL	1	TRUE	1	0.75921948516276	3		382	325	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830426	72830426	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777308945	NA	P-0044700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	68	367	0	ENST00000268489.5:c.6155C>T	p.Pro2052Leu	p.P2052L	ENST00000268489	NM_006885.3	2052	cCg/cTg	9/10	0.750570883710957	5	FACETS	0.946	0.827	1	0.237	0.206	0.269	CLONAL	1	TRUE	1	0.75921948516276	5		367	405	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39623702	39623702	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	48	239	0	ENST00000262039.4:c.2109T>G	p.Phe703Leu	p.F703L	ENST00000262039	NM_002647.2	703	ttT/ttG	20/25	0.671394234803349	2	FACETS	0.795	0.685	0.911	0.398	0.342	0.456	CLONAL	1	TRUE	0	0.75921948516276	2		239	159	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210369	36210369	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0044700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	105	535	0	ENST00000222270.7:c.364-2A>C		p.X122_splice	ENST00000222270	NM_014727.1	122			0.667082791376374	2	FACETS	0.786	0.711	0.863	0.393	0.355	0.432	SUBCLONAL	1	TRUE	0	0.75921948516276	2		535	352	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178169	142178169	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	36	229	0	ENST00000350721.4:c.7249T>G	p.Leu2417Val	p.L2417V	ENST00000350721	NM_001184.3	2417	Tta/Gta	43/47	0.599864721120144	5	FACETS	0.699	0.577	0.835	0.233	0.192	0.279	SUBCLONAL	1	TRUE	2	0.75921948516276	5		229	290	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149440428	149440428	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	97	502	0	ENST00000286301.3:c.1966G>A	p.Gly656Arg	p.G656R	ENST00000286301	NM_005211.3	656	Gga/Aga	14/22	0.75921948516276	3	FACETS	0.93	0.836	1	0.465	0.418	0.515	CLONAL	1	TRUE	1	0.75921948516276	3		502	379	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168647	32168647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	118	631	0	ENST00000375023.3:c.4276C>T	p.Pro1426Ser	p.P1426S	ENST00000375023	NM_004557.3	1426	Cct/Tct	23/30	0.607312616305692	4	FACETS	0.852	0.77	0.938	0.426	0.385	0.469	CLONAL	1	TRUE	2	0.75921948516276	4		631	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0044758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	485	665	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.676125633582982	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.731864291268292	2		665	661	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039341	49039341	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	314	578	0	ENST00000267163.4:c.2330del	p.Pro777LeufsTer33	p.P777Lfs*33	ENST00000267163	NM_000321.2	776	Ccc/cc	23/27	0.676125633582982	2	FACETS	0.865	0.829	0.9	0.865	0.829	0.9	CLONAL	2	TRUE	0	0.731864291268292	2		578	496	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937138	36937138	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1994	303	765	0	ENST00000361632.4:c.1181G>C	p.Ser394Thr	p.S394T	ENST00000361632		394	aGc/aCc	9/16	0.731864291268292	8	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.731864291268292	8		765	2297	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998568	100998568	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	476	691	0	ENST00000325455.5:c.1234G>T	p.Ala412Ser	p.A412S	ENST00000325455	NM_001202474.3	412	Gca/Tca	1/8	0.714542735726109	3	FACETS	0.988	0.951	1	0.988	0.951	1	CLONAL	2	TRUE	1	0.731864291268292	3		691	899	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121910	2121910	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs370553131	NA	P-0044758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	575	917	1	ENST00000219476.3:c.2072G>T	p.Arg691Leu	p.R691L	ENST00000219476	NM_000548.3	691	cGc/cTc	19/42	0.714542735726109	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.731864291268292	3		918	1073	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992562	72992562	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1299827763	NA	P-0044758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	263	855	0	ENST00000268489.5:c.1483T>C	p.Phe495Leu	p.F495L	ENST00000268489	NM_006885.3	495	Ttt/Ctt	2/10	1	2	FACETS	0.991	0.934	1	0.991	0.934	1	CLONAL	1	TRUE	1	0.731864291268292	2		855	725	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510584	38510584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	153	634	1	ENST00000254066.5:c.838G>A	p.Glu280Lys	p.E280K	ENST00000254066	NM_000964.3	280	Gag/Aag	7/9	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.230244773747766	2		635	1203	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829039	128829040	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs570242755	NA	P-0044773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	28	29	1	ENST00000249373.3:c.67_69dup	p.Leu23dup	p.L23dup	ENST00000249373	NM_005631.4	23	ggg/ggGCTg	1/12	1	2	FACETS	1	0.854	1	1	0.959	1	CLONAL	2	TRUE	1	0.230244773747766	2		30	115	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225060	NA	P-0044773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	24	360	0	ENST00000263967.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000263967	NM_006218.2	104	cCa/cTa	2/21	1	2	FACETS	0.568	0.445	0.71	0.568	0.445	0.71	SUBCLONAL	1	TRUE	1	0.230244773747766	2		360	367	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223975	2223975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1341	229	820	0	ENST00000326181.6:c.1189G>A	p.Gly397Ser	p.G397S	ENST00000326181	NM_032271.2	397	Ggc/Agc	13/21	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.230244773747766	2		820	1570	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022289	31022289	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs951716574	NA	P-0044773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	94	440	0	ENST00000375687.4:c.1774C>T	p.Gln592Ter	p.Q592*	ENST00000375687	NM_015338.5	592	Cag/Tag	13/13	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.230244773747766	2		440	737	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508173	106508173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1315748037	NA	P-0044773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	81	290	0	ENST00000359195.3:c.167C>T	p.Thr56Met	p.T56M	ENST00000359195	NM_002649.2	56	aCg/aTg	2/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.230244773747766	2		290	588	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205835	108205835	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	82	315	0	ENST00000278616.4:c.8150A>C	p.Lys2717Thr	p.K2717T	ENST00000278616	NM_000051.3	2717	aAg/aCg	55/63	1	2	FACETS	0.998	0.886	1	1	0.985	1	CLONAL	2	TRUE	1	0.230244773747766	2		315	357	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589518	69589518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755540122	NA	P-0044773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	79	73	0	ENST00000168712.1:c.335G>A	p.Arg112His	p.R112H	ENST00000168712	NM_002007.2	112	cGc/cAc	1/3	1	2	FACETS	0.864	0.764	0.97	1	0.981	1	CLONAL	2	TRUE	1	0.230244773747766	2		73	397	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0044785-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	434	490	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.467580559826523	1	FACETS	0.562	0.539	0.586	0.562	0.539	0.586	INDETERMINATE	1	TRUE	0	0.911430249381515	1		490	922	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599338	55599338	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044785-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	174	400	0	ENST00000288135.5:c.2464A>T	p.Asn822Tyr	p.N822Y	ENST00000288135	NM_000222.2	822	Aat/Tat	17/21	0.576072059880542	1	FACETS	0.643	0.604	0.683	0.643	0.604	0.683	SUBCLONAL	1	TRUE	0	0.911430249381515	1		400	323	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125513723	125513724	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044785-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	76	376	0	ENST00000428830.2:c.852dup	p.Glu285ArgfsTer8	p.E285Rfs*8	ENST00000428830	NM_001114121.2	284	tca/tcAa	9/14	0.177863331041814	3	FACETS	0.49	0.431	0.554	0.245	0.215	0.277	INDETERMINATE	1	TRUE	1	0.911430249381515	3		376	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0044799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	492	712	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.428394214956372	4	FACETS	0.927	0.894	0.959	0.927	0.894	0.959	CLONAL	4	TRUE	0	0.439120569093739	4		712	870	SUCCESS
RET	5979	MSKCC	GRCh37	10	43598009	43598009	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	220	735	0	ENST00000355710.3:c.557A>G	p.His186Arg	p.H186R	ENST00000355710	NM_020975.4	186	cAc/cGc	3/20	0.294434400438066	4	FACETS	0.97	0.906	1	0.97	0.906	1	CLONAL	2	TRUE	2	0.439120569093739	4		735	743	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172091	99172091	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776893699	NA	P-0044799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	89	548	2	ENST00000074304.5:c.1657C>T	p.Arg553Trp	p.R553W	ENST00000074304	NM_001134224.1	553	Cgg/Tgg	17/26	0.422752336339515	3	FACETS	0.962	0.855	1	0.481	0.427	0.538	CLONAL	1	TRUE	1	0.439120569093739	3		550	514	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058531	69058531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	117	506	0	ENST00000288368.4:c.4175C>T	p.Pro1392Leu	p.P1392L	ENST00000288368	NM_024870.2	1392	cCt/cTt	34/40	0.324250403121566	5	FACETS	0.932	0.84	1			1	CLONAL	1	TRUE	NA	0.439120569093739	5		506	948	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0044848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2233	496	714	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.687702306058658	5	FACETS	1	0.984	1	0.268	0.255	0.282	CLONAL	1	TRUE	1	0.687702306058658	5		714	2729	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0044848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	840	367	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.687702306058658	5	FACETS	1	0.996	1	0.833	0.81	0.856	CLONAL	3	TRUE	1	0.687702306058658	5		367	1489	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840607	36840607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528158465	NA	P-0044848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	175	855	0	ENST00000358127.4:c.1126G>A	p.Ala376Thr	p.A376T	ENST00000358127	NM_001280556.1	376	Gcc/Acc	10/10	0.687702306058658	1	FACETS	0.399	0.368	0.432	0.399	0.368	0.432	SUBCLONAL	1	TRUE	0	0.687702306058658	1		855	837	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435828	56435828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs995358248	NA	P-0044848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	149	838	0	ENST00000407977.2:c.1309C>T	p.Arg437Trp	p.R437W	ENST00000407977		437	Cgg/Tgg	9/10	0.646511496158326	2	FACETS	0.417	0.38	0.456	0.209	0.19	0.228	SUBCLONAL	1	TRUE	0	0.687702306058658	2		838	1039	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0044848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	821	899	0	ENST00000269305.4:c.376-1G>T		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.646511496158326	2	FACETS	0.911	0.888	0.935	0.911	0.888	0.935	CLONAL	2	TRUE	0	0.687702306058658	2		899	1310	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585383	29585383	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691072	NA	P-0044848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	268	582	0	ENST00000356175.3:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000356175	NM_000267.3	1378	Cag/Tag	31/57	0.646511496158326	2	FACETS	1	0.942	1	0.5	0.471	0.53	CLONAL	1	TRUE	0	0.687702306058658	2		582	779	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763501	41763501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200271277	NA	P-0044848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	142	690	1	ENST00000301178.4:c.2300G>A	p.Arg767His	p.R767H	ENST00000301178	NM_021913.4	767	cGc/cAc	19/20	0.646511496158326	2	FACETS	0.479	0.436	0.524	0.24	0.218	0.262	SUBCLONAL	1	TRUE	0	0.687702306058658	2		691	862	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105530	30105530	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1435	136	717	0	ENST00000331968.5:c.1156G>T	p.Asp386Tyr	p.D386Y	ENST00000331968	NM_002742.2	386	Gac/Tac	7/18	0.687702306058658	3	FACETS	0.338	0.306	0.372	0.169	0.153	0.186	SUBCLONAL	1	TRUE	1	0.687702306058658	3		717	1571	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319956	62319956	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs199796539	NA	P-0044848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	168	945	2	ENST00000360203.5:c.1798G>A	p.Glu600Lys	p.E600K	ENST00000360203	NM_001283009.1	600	Gag/Aag	21/35	0.484515227710841	1	FACETS	0.271	0.249	0.295	0.271	0.249	0.295	SUBCLONAL	1	TRUE	0	0.687702306058658	1		947	1181	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80057447	80057447	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	71	390	0	ENST00000265081.6:c.1846C>G	p.Arg616Gly	p.R616G	ENST00000265081	NM_002439.4	616	Cgt/Ggt	13/24	0.148181785936086	2	FACETS	0.342	0.298	0.389	0.171	0.149	0.195	INDETERMINATE	1	TRUE	0	0.687702306058658	2		390	604	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	114	82	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	1	0.805351246222701	2		82	279	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0044882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	121	395	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	FALSE	1	0.805351246222701	2		396	300	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433848	78433851	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CAGT	CAGT	-	novel	NA	P-0044882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	76	261	0	ENST00000370768.2:c.248_250+1del		p.X83_splice	ENST00000370768	NM_003902.3	83		3/20	0.805351246222701	1	FACETS	0.456	0.406	0.509	0.456	0.406	0.509	SUBCLONAL	1	FALSE	0	0.805351246222701	1		261	247	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791733	42791733	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	180	602	0	ENST00000575354.2:c.619T>C	p.Phe207Leu	p.F207L	ENST00000575354	NM_015125.3	207	Ttc/Ctc	5/20	0.805351246222701	1	FACETS	0.551	0.512	0.59	0.551	0.512	0.59	SUBCLONAL	1	FALSE	0	0.805351246222701	1		602	485	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165007	47165010	+	frameshift_variant	Frame_Shift_Del	DEL	TCTG	TCTG	-	rs752743762	NA	P-0044882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	80	235	0	ENST00000409792.3:c.1116_1119del	p.Asp372GlufsTer111	p.D372Efs*111	ENST00000409792	NM_014159.6	372	gaCAGA/ga	3/21	1	2	FACETS	0.498	0.441	0.559	0.498	0.441	0.559	SUBCLONAL	1	FALSE	1	0.805351246222701	2		235	399	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573776	64573776	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	44	617	0	ENST00000312049.6:c.977G>A	p.Gly326Asp	p.G326D	ENST00000312049	NM_130799.2	326	gGc/gAc	7/10	1	2	FACETS	0.127	0.106	0.151	0.127	0.106	0.151	SUBCLONAL	1	FALSE	1	0.805351246222701	2		617	861	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795603	42795604	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0044882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	108	696	0	ENST00000575354.2:c.2687dup	p.Pro897ThrfsTer34	p.P897Tfs*34	ENST00000575354	NM_015125.3	895	gcc/gCcc	10/20	0.805351246222701	1	FACETS	0.312	0.281	0.345	0.312	0.281	0.345	SUBCLONAL	1	FALSE	0	0.805351246222701	1		696	513	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258694	115258694	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	28	275	0	ENST00000369535.4:c.88G>C	p.Asp30His	p.D30H	ENST00000369535	NM_002524.4	30	Gat/Cat	2/7	1	2	FACETS	0.345	0.275	0.424	0.345	0.275	0.424	SUBCLONAL	1	TRUE	1	0.37	2		275	439	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888165	112888165	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507510	NA	P-0044885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	124	472	0	ENST00000351677.2:c.181G>A	p.Asp61Asn	p.D61N	ENST00000351677	NM_002834.3	61	Gat/Aat	3/16	0.3	4	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.37	4		472	701	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888174	112888174	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	121	482	0	ENST00000351677.2:c.190G>C	p.Asp64His	p.D64H	ENST00000351677	NM_002834.3	64	Gac/Cac	3/16	0.3	4	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.37	4		482	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577540	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	rs1555525498	NA	P-0044906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	186	680	2	ENST00000269305.4:c.741_742delinsTT	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	247	aaCCgg/aaTTgg	7/11	0.238704657273246	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.310423264068442	2		682	521	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888758	76888758	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	37	213	0	ENST00000373344.5:c.5071C>T	p.Gln1691Ter	p.Q1691*	ENST00000373344	NM_000489.3	1691	Caa/Taa	19/35	0.310423264068442	2	FACETS	0.993	0.853	1			1	CLONAL	3	TRUE	NA	0.310423264068442	2		213	80	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196896	108196896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56009889	NA	P-0044906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	48	320	0	ENST00000278616.4:c.6919C>T	p.Leu2307Phe	p.L2307F	ENST00000278616	NM_000051.3	2307	Ctt/Ttt	47/63	0.310423264068442	3	FACETS	0.812	0.694	0.939	0.812	0.694	0.939	CLONAL	2	TRUE	1	0.310423264068442	3		320	220	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137784	64137784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	142	1041	0	ENST00000334205.4:c.1885C>T	p.Arg629Cys	p.R629C	ENST00000334205	NM_003942.2	629	Cgc/Tgc	15/17	0.310423264068442	5	FACETS	1	0.981	1	0.647	0.588	0.708	CLONAL	1	TRUE	3	0.310423264068442	5		1041	1037	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622131	43622131	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	51	579	1	ENST00000355710.3:c.3148C>T	p.Arg1050Ter	p.R1050*	ENST00000355710	NM_020975.4	1050	Cga/Tga	19/20	0.310423264068442	3	FACETS	0.917	0.781	1	0.458	0.39	0.533	CLONAL	1	TRUE	1	0.310423264068442	3		580	414	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754050	42754050	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	73	644	0	ENST00000222329.4:c.302G>A	p.Arg101Gln	p.R101Q	ENST00000222329	NM_006494.2	101	cGg/cAg	3/4	0.310423264068442	2	FACETS	1	0.972	1	0.698	0.615	0.786	CLONAL	1	TRUE	0	0.310423264068442	2		644	337	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874826	151874826	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142788583	NA	P-0044906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	93	344	0	ENST00000262189.6:c.7712G>A	p.Arg2571Gln	p.R2571Q	ENST00000262189	NM_170606.2	2571	cGg/cAg	38/59	0.310423264068442	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.310423264068442	3		344	305	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11318634	11318634	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	33	404	0	ENST00000361445.4:c.179C>G	p.Ser60Cys	p.S60C	ENST00000361445	NM_004958.3	60	tCt/tGt	3/58	0.310423264068442	5	FACETS	1	0.921	1	0.415	0.34	0.5	CLONAL	1	TRUE	2	0.310423264068442	5		404	250	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021895	246021895	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs762602003	NA	P-0044906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	285	653	0	ENST00000388985.4:c.979C>T	p.Gln327Ter	p.Q327*	ENST00000388985		327	Cag/Tag	10/12	0.213266258047771	5	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	2	0.310423264068442	5		653	804	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858947	57858948	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0044906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	90	831	1	ENST00000228682.2:c.443_444delinsTT	p.Ser148Phe	p.S148F	ENST00000228682	NM_005269.2	148	tCC/tTT	5/12	0.310423264068442	3	FACETS	0.972	0.863	1	0.486	0.431	0.545	CLONAL	1	TRUE	1	0.310423264068442	3		832	689	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912913	32912913	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs780660669	NA	P-0044906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	13	418	0	ENST00000380152.3:c.4421A>G	p.Lys1474Arg	p.K1474R	ENST00000380152		1474	aAa/aGa	11/27	1	2	FACETS	0.813	0.586	1	0.813	0.586	1	CLONAL	1	TRUE	1	0.310423264068442	2		418	103	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110596	8110596	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	111	669	0	ENST00000585124.1:c.296G>T	p.Ser99Ile	p.S99I	ENST00000585124	NM_004217.3	99	aGc/aTc	5/9	0.238704657273246	2	FACETS	1	0.978	1	0.657	0.593	0.725	CLONAL	1	TRUE	0	0.310423264068442	2		669	544	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511638	66511638	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	46	411	0	ENST00000358598.2:c.98A>T	p.Asp33Val	p.D33V	ENST00000358598	NM_212471.2	33	gAt/gTt	2/11	0.238704657273246	2	FACETS	0.77	0.65	0.902	0.385	0.325	0.451	CLONAL	1	TRUE	0	0.310423264068442	2		411	385	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543667	9543668	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	novel	NA	P-0044906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	54	428	1	ENST00000353224.5:c.1486_1487delinsAA	p.Val496Lys	p.V496K	ENST00000353224	NM_177990.2	496	GTg/AAg	6/10	0.213266258047771	5	FACETS	1	0.954	1	0.432	0.37	0.5	CLONAL	1	TRUE	2	0.310423264068442	5		429	393	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407582	407582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749474191	NA	P-0044906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	22	296	0	ENST00000380956.4:c.1340C>T	p.Ser447Phe	p.S447F	ENST00000380956	NM_001195286.1	447	tCc/tTc	9/9	0.310423264068442	4	FACETS	1	0.915	1	0.698	0.548	0.868	CLONAL	1	TRUE	2	0.310423264068442	4		296	133	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671634	30671634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142662059	NA	P-0044906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	70	707	0	ENST00000376406.3:c.5326C>T	p.Pro1776Ser	p.P1776S	ENST00000376406	NM_014641.2	1776	Ccc/Tcc	10/15	0.310423264068442	4	FACETS	0.982	0.856	1	0.491	0.428	0.559	CLONAL	1	TRUE	2	0.310423264068442	4		707	602	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046371	69046371	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	70	564	0	ENST00000288368.4:c.3844C>G	p.Leu1282Val	p.L1282V	ENST00000288368	NM_024870.2	1282	Ctc/Gtc	32/40	1	2	FACETS	0.951	0.832	1	0.951	0.832	1	CLONAL	1	TRUE	1	0.310423264068442	2		564	474	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212757	27212758	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0044906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	478	970	1	ENST00000380036.4:c.2739_2740delinsTT	p.Leu914Phe	p.L914F	ENST00000380036	NM_000459.3	913	ttCCtt/ttTTtt	17/23	0.310423264068442	1	FACETS	0.978	0.941	1	1	0.998	1	CLONAL	3	TRUE	0	0.310423264068442	1		971	887	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339231	70339232	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAA	novel	NA	P-0044906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	117	279	0	ENST00000374080.3:c.109_110insAAA	p.Leu36_Thr37insLys	p.L36_T37insK	ENST00000374080		36	-/AAA	2/45	0.310423264068442	2	FACETS	1	0.928	1			1	CLONAL	3	TRUE	NA	0.310423264068442	2		279	249	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0044960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	197	367	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.378921684356534	3	FACETS	0.785	0.733	0.838	0.523	0.489	0.559	INDETERMINATE	2	TRUE	0	0.637763547951652	3		367	519	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0044960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	263	460	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.32659310536755	3	FACETS	1	0.97	1	0.529	0.495	0.563	INDETERMINATE	1	TRUE	1	0.637763547951652	3		460	1029	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934874	NA	P-0044960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	1235	518	0	ENST00000269305.4:c.451C>A	p.Pro151Thr	p.P151T	ENST00000269305	NM_001126112.2	151	Ccc/Acc	5/11	0.291365154631727	4	FACETS	0.931	0.914	0.947			1	INDETERMINATE	4	TRUE	NA	0.637763547951652	4		518	1704	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881426	48881426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	125	63	0	ENST00000267163.4:c.148G>T	p.Glu50Ter	p.E50*	ENST00000267163	NM_000321.2	50	Gaa/Taa	2/27	0.59612429324711	2	FACETS	0.912	0.849	0.974	0.912	0.849	0.974	CLONAL	2	TRUE	0	0.637763547951652	2		63	215	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136847	2136965	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGACTTCAAGCTTGGCACCATCAAGGTGAGTGAGGGGCCGTCAGTGAGGCTGGGCCCCAGGCAGGTGCCCACTGCTGTGTCCCGGGTTGGTGGCAGGTCCTCCTCCCTGAGCTTCGGT	AGGACTTCAAGCTTGGCACCATCAAGGTGAGTGAGGGGCCGTCAGTGAGGCTGGGCCCCAGGCAGGTGCCCACTGCTGTGTCCCGGGTTGGTGGCAGGTCCTCCTCCCTGAGCTTCGGT	-	novel	NA	P-0044960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	120	409	0	ENST00000219476.3:c.4964_4989+93del		p.X1655_splice	ENST00000219476	NM_000548.3	1655		38/42	0.319095831468996	2	FACETS	0.385	0.347	0.426	0.193	0.173	0.213	INDETERMINATE	1	TRUE	0	0.637763547951652	2		409	977	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139736	55139736	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	296	270	0	ENST00000257290.5:c.1398del	p.Asn467ThrfsTer22	p.N467Tfs*22	ENST00000257290	NM_006206.4	466	gCc/gc	10/23	0.330556769180683	4	FACETS	0.895	0.846	0.946			1	INDETERMINATE	2	TRUE	NA	0.637763547951652	4		270	849	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0044964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	110	414	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.621727850100844	3	FACETS	1	0.978	1	0.425	0.386	0.466	CLONAL	1	TRUE	0	0.631847837162935	3		414	359	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206646622	206646622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	205	777	0	ENST00000367120.3:c.52G>A	p.Gly18Arg	p.G18R	ENST00000367120	NM_014002.3	18	Ggg/Agg	3/22	0.631847837162935	4	FACETS	0.974	0.903	1	0.487	0.451	0.524	CLONAL	1	TRUE	2	0.631847837162935	4		777	1087	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28598996	28598996	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0044964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	119	383	0	ENST00000241453.7:c.2290+2T>C		p.X764_splice	ENST00000241453	NM_004119.2	764			0.631847837162935	2	FACETS	0.914	0.832	0.999	0.457	0.416	0.5	CLONAL	1	TRUE	0	0.631847837162935	2		383	412	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554618	29554619	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0044964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	132	280	0	ENST00000356175.3:c.2405dup	p.Gln803ProfsTer4	p.Q803Pfs*4	ENST00000356175	NM_000267.3	801	-/G	20/57	0.631847837162935	3	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.631847837162935	3		280	437	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207201	1207201	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0044964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	357	588	0	ENST00000326873.7:c.289A>T	p.Lys97Ter	p.K97*	ENST00000326873	NM_000455.4	97	Aag/Tag	1/10	0.631847837162935	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.631847837162935	2		588	553	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214631	5214631	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	218	696	0	ENST00000357368.4:c.4435G>T	p.Val1479Leu	p.V1479L	ENST00000357368	NM_002850.3	1479	Gtg/Ttg	29/38	0.631847837162935	2	FACETS	1	0.96	1	0.519	0.485	0.554	CLONAL	1	TRUE	0	0.631847837162935	2		696	665	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098933	178098933	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	83	306	0	ENST00000397062.3:c.112G>C	p.Asp38His	p.D38H	ENST00000397062	NM_006164.4	38	Gac/Cac	2/5	0.631847837162935	4	FACETS	0.823	0.728	0.924	0.411	0.364	0.462	CLONAL	1	TRUE	2	0.631847837162935	4		306	521	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656839	45656839	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	526	527	0	ENST00000407780.3:c.317A>T	p.Gln106Leu	p.Q106L	ENST00000407780	NM_001283052.1	106	cAg/cTg	3/7	0.631847837162935	5	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	2	0.631847837162935	5		527	1021	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031973	26031973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	82	298	0	ENST00000244661.2:c.316G>A	p.Glu106Lys	p.E106K	ENST00000244661	NM_003537.3	106	Gag/Aag	1/1	0.616758344245724	3	FACETS	0.874	0.775	0.978	0.437	0.387	0.489	CLONAL	1	TRUE	1	0.631847837162935	3		298	391	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	213	459	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.617806514584227	3	FACETS	0.964	0.919	1	0.964	0.919	1	CLONAL	3	TRUE	0	0.617806514584227	3		459	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0044985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	244	680	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.607721294988356	2	FACETS	0.978	0.93	1	0.978	0.93	1	CLONAL	2	TRUE	0	0.617806514584227	2		680	404	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508361	106508361	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	115	254	0	ENST00000359195.3:c.355C>A	p.Leu119Met	p.L119M	ENST00000359195	NM_002649.2	119	Ctg/Atg	2/11	0.617806514584227	4	FACETS	0.91	0.83	0.992	0.91	0.83	0.992	CLONAL	2	TRUE	2	0.617806514584227	4		254	331	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652269	3652269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752160984	NA	P-0044985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	143	556	1	ENST00000294008.3:c.800C>T	p.Ala267Val	p.A267V	ENST00000294008	NM_032444.2	267	gCg/gTg	4/15	0.617806514584227	3	FACETS	0.969	0.887	1	0.485	0.443	0.528	CLONAL	1	TRUE	1	0.617806514584227	3		557	625	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683677	162683677	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	335	521	0	ENST00000366898.1:c.292G>T	p.Glu98Ter	p.E98*	ENST00000366898	NM_004562.2	98	Gag/Tag	3/12	0.591014584550243	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	3	TRUE	0	0.617806514584227	3		521	472	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248123	59248124	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs748534142	NA	P-0044985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	15	147	0	ENST00000371222.2:c.617_619dup	p.Gln206dup	p.Q206dup	ENST00000371222	NM_002228.3	206	ccg/cAGCcg	1/1	0.617806514584227	3	FACETS	0.478	0.352	0.626	0.239	0.176	0.313	SUBCLONAL	1	TRUE	1	0.617806514584227	3		147	133	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633102	3633102	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	91	505	0	ENST00000294008.3:c.5149C>T	p.Gln1717Ter	p.Q1717*	ENST00000294008	NM_032444.2	1717	Cag/Tag	14/15	0.617806514584227	3	FACETS	0.876	0.782	0.976	0.438	0.391	0.488	CLONAL	1	TRUE	1	0.617806514584227	3		505	440	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464499	25464499	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	257	605	1	ENST00000264709.3:c.2014G>T	p.Val672Leu	p.V672L	ENST00000264709	NM_175629.2	672	Gtg/Ttg	17/23	0.617806514584227	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.617806514584227	2		606	398	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713362	40713362	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	246	639	0	ENST00000373198.4:c.4153del	p.Gln1385SerfsTer14	p.Q1385Sfs*14	ENST00000373198	NM_133170.3	1385	Cag/ag	30/32	0.554160375456869	4	FACETS	0.936	0.88	0.994	0.936	0.88	0.994	CLONAL	2	TRUE	2	0.617806514584227	4		639	688	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046716	180046716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs910059826	NA	P-0044985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	318	721	0	ENST00000261937.6:c.2596G>A	p.Gly866Ser	p.G866S	ENST00000261937	NM_182925.4	866	Ggc/Agc	18/30	0.554160375456869	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.617806514584227	4		721	797	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271474	26271474	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	144	393	0	ENST00000305910.3:c.139G>T	p.Val47Leu	p.V47L	ENST00000305910	NM_003534.2	47	Gtg/Ttg	1/1	0.44682994812869	6	FACETS	1	0.928	1	0.506	0.464	0.549	CLONAL	2	TRUE	2	0.617806514584227	6		393	515	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987279	2987279	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	202	439	1	ENST00000396946.4:c.150G>T	p.Lys50Asn	p.K50N	ENST00000396946	NM_032415.4	50	aaG/aaT	3/25	0.617806514584227	4	FACETS	0.889	0.829	0.95	0.889	0.829	0.95	CLONAL	2	TRUE	2	0.617806514584227	4		440	595	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524645	106524645	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	96	223	0	ENST00000359195.3:c.2806T>A	p.Cys936Ser	p.C936S	ENST00000359195	NM_002649.2	936	Tgt/Agt	9/11	0.617806514584227	4	FACETS	0.904	0.817	0.994	0.904	0.817	0.994	CLONAL	2	TRUE	2	0.617806514584227	4		223	278	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410525	63410525	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	50	643	0	ENST00000330258.3:c.2642G>C	p.Arg881Pro	p.R881P	ENST00000330258	NM_152424.3	881	cGa/cCa	2/2	0.124120985031473	3	FACETS	0.42	0.357	0.49	0.14	0.119	0.164	INDETERMINATE	1	TRUE	0	0.617806514584227	3		643	504	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455266	29455266	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	170	419	0	ENST00000389048.3:c.2536G>T	p.Gly846Cys	p.G846C	ENST00000389048	NM_004304.4	846	Ggc/Tgc	15/29	0.617806514584227	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.617806514584227	2		419	267	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5239032	5239036	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCC	CCTCC	TTT	novel	NA	P-0044985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	310	690	0	ENST00000357368.4:c.1743_1747delinsAAA	p.Glu582LysfsTer44	p.E582Kfs*44	ENST00000357368	NM_002850.3	581	gtGGAGGac/gtAAAac	13/38	0.617806514584227	2	FACETS	0.994	0.952	1	0.994	0.952	1	CLONAL	2	TRUE	0	0.617806514584227	2		690	505	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39690066	39690066	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	41	202	0	ENST00000361337.2:c.91C>T	p.Arg31Ter	p.R31*	ENST00000361337	NM_003286.2	31	Cga/Tga	3/21	0.22319123357131	3	FACETS	1	0.896	1	0.55	0.459	0.651	CLONAL	1	TRUE	1	0.22319123357131	3		202	371	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814940	43814940	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	158	367	0	ENST00000372470.3:c.1475T>C	p.Ile492Thr	p.I492T	ENST00000372470	NM_005373.2	492	aTc/aCc	10/12	0.22319123357131	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.22319123357131	3		367	685	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968137	55968137	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	129	402	0	ENST00000263923.4:c.2193C>G	p.Asp731Glu	p.D731E	ENST00000263923	NM_002253.2	731	gaC/gaG	15/30	0.22319123357131	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	2	TRUE	0	0.22319123357131	2		402	578	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166913	32166913	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	111	750	0	ENST00000375023.3:c.4325C>A	p.Ala1442Asp	p.A1442D	ENST00000375023	NM_004557.3	1442	gCc/gAc	24/30	1	2	FACETS	0.86	0.771	0.955	0.86	0.771	0.955	CLONAL	1	TRUE	1	0.22319123357131	2		750	1156	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0045005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	111	317	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.516706331196127	1	FACETS	0.857	0.777	0.939	0.857	0.777	0.939	CLONAL	1	TRUE	0	0.516706331196127	1		317	372	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472466	88472466	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	167	735	1	ENST00000360948.2:c.2089G>T	p.Asp697Tyr	p.D697Y	ENST00000360948	NM_001012338.2	697	Gac/Tac	16/19	1	2	FACETS	0.857	0.789	0.928	0.857	0.789	0.928	CLONAL	1	TRUE	1	0.516706331196127	2		736	754	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577041	7577041	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	309	997	0	ENST00000269305.4:c.897del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	299	ctG/ct	8/11	0.516706331196127	1	FACETS	0.974	0.921	1	0.974	0.921	1	CLONAL	1	TRUE	0	0.516706331196127	1		997	911	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375094	31375094	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	263	949	0	ENST00000328111.2:c.491C>G	p.Ser164Cys	p.S164C	ENST00000328111	NM_006892.3	164	tCt/tGt	6/23	0.380257752605229	1	FACETS	0.717	0.672	0.763	0.717	0.672	0.763	SUBCLONAL	1	TRUE	0	0.516706331196127	1		949	1053	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750581	41750581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	95	745	0	ENST00000226382.2:c.47C>T	p.Ser16Phe	p.S16F	ENST00000226382	NM_003924.3	16	tCc/tTc	1/3	1	2	FACETS	0.575	0.512	0.641	0.575	0.512	0.641	SUBCLONAL	1	TRUE	1	0.516706331196127	2		745	640	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878944	151878944	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	169	653	1	ENST00000262189.6:c.6001G>T	p.Ala2001Ser	p.A2001S	ENST00000262189	NM_170606.2	2001	Gct/Tct	36/59	1	2	FACETS	0.933	0.86	1	0.933	0.86	1	CLONAL	1	TRUE	1	0.516706331196127	2		654	701	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0045005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	196	477	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.516706331196127	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.516706331196127	1		477	540	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211383	98211383	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148350525	NA	P-0045005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	234	904	0	ENST00000331920.6:c.3772G>A	p.Ala1258Thr	p.A1258T	ENST00000331920	NM_000264.3	1258	Gcc/Acc	22/24	0.516706331196127	1	FACETS	0.921	0.863	0.981	0.921	0.863	0.981	CLONAL	1	TRUE	0	0.516706331196127	1		904	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0045016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	449	680	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.906017132374432	2	FACETS	0.985	0.967	1	0.985	0.967	1	CLONAL	2	TRUE	0	0.923079368367174	2		680	494	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803562	43803562	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	428	757	0	ENST00000372470.3:c.43C>A	p.Leu15Met	p.L15M	ENST00000372470	NM_005373.2	15	Ctg/Atg	1/12	0.923079368367174	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.923079368367174	3		757	677	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332807	70332807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	221	552	0	ENST00000373644.4:c.712G>T	p.Gly238Cys	p.G238C	ENST00000373644	NM_030625.2	238	Ggt/Tgt	2/12	0.910294597439463	2	FACETS	0.963	0.906	1	0.482	0.453	0.511	CLONAL	1	TRUE	0	0.923079368367174	2		552	497	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039215	49039215	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	402	422	0	ENST00000267163.4:c.2296del	p.Thr766GlnfsTer44	p.T766Qfs*44	ENST00000267163	NM_000321.2	765	Aaa/aa	22/27	0.907631359193734	2	FACETS	0.943	0.921	0.962	0.943	0.921	0.962	CLONAL	2	TRUE	0	0.923079368367174	2		422	462	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138609	2138609	+	stop_lost	Nonstop_Mutation	SNP	T	T	A	rs1567135442	NA	P-0045016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	387	675	0	ENST00000219476.3:c.5422T>A	p.Ter1808ArgextTer19	p.*1808Rext*19	ENST00000219476	NM_000548.3	1808	Tga/Aga	42/42	0.906017132374432	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.923079368367174	2		675	418	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656826	45656826	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	203	596	0	ENST00000407780.3:c.330G>C	p.Lys110Asn	p.K110N	ENST00000407780	NM_001283052.1	110	aaG/aaC	3/7	0.475263904530919	4	FACETS	0.959	0.89	1			1	INDETERMINATE	1	TRUE	NA	0.923079368367174	4		596	882	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31493328	31493328	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	216	336	0	ENST00000344624.3:c.1828G>T	p.Ala610Ser	p.A610S	ENST00000344624		610	Gcc/Tcc	10/33	0.874102515557723	6	FACETS	0.82	0.764	0.878	0.41	0.382	0.439	CLONAL	2	TRUE	2	0.923079368367174	6		336	812	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419049	419049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	13	400	0	ENST00000399788.2:c.3298G>A	p.Glu1100Lys	p.E1100K	ENST00000399788	NM_001042603.1	1100	Gaa/Aaa	22/28	NA	2	FACETS	0.847	0.606	1			1	INDETERMINATE	1	FALSE	NA	0.176478035037041	2		400	174	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0046454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	237	405	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.907300146963039	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	1	0.907300146963039	4		405	301	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579330	7579330	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	673	635	1	ENST00000269305.4:c.357del	p.Lys120SerfsTer3	p.K120Sfs*3	ENST00000269305	NM_001126112.2	119	gcC/gc	4/11	0.907300146963039	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.907300146963039	2		636	731	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242481	+	inframe_deletion	In_Frame_Del	DEL	AATTAAGAGAAGCAA	AATTAAGAGAAGCAA	-	rs121913425	NA	P-0046454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	216	319	0	ENST00000275493.2:c.2237_2251del	p.Glu746_Thr751delinsAla	p.E746_T751delinsA	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAAca/gca	19/28	0.556756650313214	4	FACETS	0.812	0.761	0.864	0.812	0.761	0.864	CLONAL	2	TRUE	2	0.907300146963039	4		319	559	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135035	11135035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	290	756	0	ENST00000358026.2:c.3002C>T	p.Ser1001Phe	p.S1001F	ENST00000358026	NM_001128849.1	1001	tCt/tTt	21/36	0.392369005475701	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.392369005475701	2		756	736	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441976	52441976	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	92	439	0	ENST00000460680.1:c.373G>A	p.Glu125Lys	p.E125K	ENST00000460680	NM_004656.3	125	Gag/Aag	5/17	1	2	FACETS	0.953	0.85	1	0.953	0.85	1	CLONAL	1	TRUE	1	0.392369005475701	2		439	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352697	NA	P-0046667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	26	736	0	ENST00000269305.4:c.587G>A	p.Arg196Gln	p.R196Q	ENST00000269305	NM_001126112.2	196	cGa/cAa	6/11	1	2	FACETS	0.182	0.143	0.226	0.182	0.143	0.226	SUBCLONAL	1	TRUE	1	0.392369005475701	2		736	730	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324665	31324665	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	27	411	1	ENST00000412585.2:c.143C>T	p.Ser48Leu	p.S48L	ENST00000412585	NM_005514.6	48	tCa/tTa	2/8	1	2	FACETS	0.283	0.225	0.35	0.283	0.225	0.35	SUBCLONAL	1	TRUE	1	0.392369005475701	2		412	486	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946111	13946111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	93	415	1	ENST00000405192.2:c.985C>T	p.His329Tyr	p.H329Y	ENST00000405192	NM_001163147.1	329	Cat/Tat	10/12	1	2	FACETS	0.933	0.833	1	0.933	0.833	1	CLONAL	1	TRUE	1	0.392369005475701	2		416	508	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28931588	NA	P-0047360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	89	278	0	ENST00000349496.5:c.94G>C	p.Asp32His	p.D32H	ENST00000349496	NM_001904.3	32	Gac/Cac	3/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.5270233600206	2		278	293	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0047360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	46	785	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	1	2	FACETS	0.687	0.583	0.8	0.687	0.583	0.8	SUBCLONAL	1	TRUE	1	0.5270233600206	2		785	254	SUCCESS
EED	8726	MSKCC	GRCh37	11	85956318	85956318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371991859	NA	P-0047360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	56	193	0	ENST00000263360.6:c.47C>T	p.Pro16Leu	p.P16L	ENST00000263360	NM_003797.3	16	cCt/cTt	1/12	1	2	FACETS	0.853	0.739	0.976	0.853	0.739	0.976	CLONAL	1	TRUE	1	0.5270233600206	2		193	249	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646429	23646429	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1057520653	NA	P-0047360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	132	425	0	ENST00000261584.4:c.1438A>T	p.Lys480Ter	p.K480*	ENST00000261584	NM_024675.3	480	Aaa/Taa	4/13	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.5270233600206	2		425	437	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220590	1220590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782379	NA	P-0047360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	188	674	1	ENST00000326873.7:c.608C>T	p.Pro203Leu	p.P203L	ENST00000326873	NM_000455.4	203	cCg/cTg	5/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.5270233600206	2		675	594	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786008	135786008	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	166	515	1	ENST00000298552.3:c.1213G>A	p.Asp405Asn	p.D405N	ENST00000298552	NM_001162426.1	405	Gac/Aac	12/23	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.5270233600206	2		516	594	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	33	82	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.878	0.716	1	0.878	0.716	1	CLONAL	1	TRUE	1	0.21	2		82	358	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0048409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	64	554	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	1	2	FACETS	0.742	0.641	0.851	0.742	0.641	0.851	SUBCLONAL	1	TRUE	1	0.21	2		554	822	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372148	55372148	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	101	524	0	ENST00000297316.4:c.838G>T	p.Gly280Cys	p.G280C	ENST00000297316	NM_022454.3	280	Ggt/Tgt	2/2	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.21	2		524	697	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39311714	39311714	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	43	451	0	ENST00000373001.3:c.945G>T	p.Met315Ile	p.M315I	ENST00000373001	NM_022157.3	315	atG/atT	6/7	1	2	FACETS	0.607	0.506	0.718	0.607	0.506	0.718	SUBCLONAL	1	TRUE	1	0.21	2		451	675	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948533	71948533	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	63	792	0	ENST00000298229.2:c.3245G>T	p.Gly1082Val	p.G1082V	ENST00000298229	NM_001567.3	1082	gGg/gTg	26/28	1	2	FACETS	0.606	0.522	0.697	0.606	0.522	0.697	SUBCLONAL	1	TRUE	1	0.21	2		792	990	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351890	89351890	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	83	621	0	ENST00000301030.4:c.1060G>C	p.Glu354Gln	p.E354Q	ENST00000301030	NM_001256183.1	354	Gag/Cag	9/13	1	2	FACETS	0.975	0.859	1	0.975	0.859	1	CLONAL	1	TRUE	1	0.21	2		621	811	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117680976	117680976	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	34	218	0	ENST00000368508.3:c.3644C>G	p.Ser1215Cys	p.S1215C	ENST00000368508	NM_002944.2	1215	tCt/tGt	23/43	1	2	FACETS	0.892	0.73	1	0.892	0.73	1	CLONAL	1	TRUE	1	0.21	2		218	363	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81340797	81340797	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	16	149	0	ENST00000222390.5:c.1444C>A	p.His482Asn	p.H482N	ENST00000222390	NM_000601.4	482	Cat/Aat	12/18	1	2	FACETS	0.546	0.403	0.717	0.546	0.403	0.717	SUBCLONAL	1	TRUE	1	0.21	2		149	279	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250522	110250522	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	45	520	0	ENST00000374672.4:c.153G>T	p.Met51Ile	p.M51I	ENST00000374672	NM_004235.4	51	atG/atT	3/5	1	2	FACETS	0.571	0.478	0.673	0.571	0.478	0.673	SUBCLONAL	1	TRUE	1	0.21	2		520	751	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0048693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	83	367	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.3	6	FACETS	0.991	0.875	1	0.33	0.291	0.372	INDETERMINATE	1	TRUE	3	0.54	6		367	645	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0048693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	77	461	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.235861025934347	3	FACETS	0.417	0.365	0.473	0.208	0.182	0.237	INDETERMINATE	1	TRUE	1	0.54	3		461	869	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758265	41758265	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	42	413	0	ENST00000301178.4:c.1721G>T	p.Cys574Phe	p.C574F	ENST00000301178	NM_021913.4	574	tGc/tTc	15/20	0.297912297672968	4	FACETS	0.314	0.261	0.373	0.105	0.087	0.125	INDETERMINATE	1	TRUE	1	0.54	4		413	762	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	120	82	0				ENST00000310581	NM_198253.2	-/1132			0.206377959948013	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.2	3		82	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0048700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	90	648	1	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	1	2	FACETS	0.884	0.783	0.993	0.884	0.783	0.993	CLONAL	1	TRUE	1	0.2	2		649	1018	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683677	162683677	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	72	521	0	ENST00000366898.1:c.292G>T	p.Glu98Ter	p.E98*	ENST00000366898	NM_004562.2	98	Gag/Tag	3/12	0.171344359707146	1	FACETS	0.893	0.779	1	0.893	0.779	1	CLONAL	1	TRUE	0	0.2	1		521	726	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543781	212543781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866138670	NA	P-0048700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	39	293	1	ENST00000342788.4:c.1618G>A	p.Asp540Asn	p.D540N	ENST00000342788	NM_005235.2	540	Gat/Aat	13/28	1	2	FACETS	0.722	0.598	0.861	0.722	0.598	0.861	SUBCLONAL	1	TRUE	1	0.2	2		294	540	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31521267	31521267	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	126	517	0	ENST00000344624.3:c.910G>T	p.Glu304Ter	p.E304*	ENST00000344624		304	Gaa/Taa	3/33	0.206377959948013	3	FACETS	0.817	0.74	0.899	0.817	0.74	0.899	CLONAL	2	TRUE	1	0.2	3		517	848	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563036	21563036	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	61	651	1	ENST00000382592.4:c.883G>T	p.Gly295Ter	p.G295*	ENST00000382592	NM_014572.2	295	Gga/Tga	4/8	1	2	FACETS	0.548	0.47	0.632	0.548	0.47	0.632	SUBCLONAL	1	TRUE	1	0.2	2		652	1114	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120836	115120836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	45	467	0	ENST00000257566.3:c.170C>T	p.Pro57Leu	p.P57L	ENST00000257566	NM_016569.3	57	cCg/cTg	1/8	1	2	FACETS	0.622	0.521	0.733	0.622	0.521	0.733	SUBCLONAL	1	TRUE	1	0.2	2		467	724	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599142	28599142	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	165	746	0	ENST00000253063.3:c.588G>T	p.Gln196His	p.Q196H	ENST00000253063	NM_031459.4	196	caG/caT	5/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.2	2		746	1263	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103157	119103157	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0048700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	50	355	0	ENST00000264033.4:c.196-1G>T		p.X66_splice	ENST00000264033	NM_005188.3	66			1	2	FACETS	0.722	0.611	0.843	0.722	0.611	0.843	SUBCLONAL	1	TRUE	1	0.2	2		355	693	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2218112	2218112	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	90	735	0	ENST00000326181.6:c.174G>C	p.Arg58Ser	p.R58S	ENST00000326181	NM_032271.2	58	agG/agC	4/21	1	2	FACETS	0.751	0.664	0.845	0.751	0.664	0.845	SUBCLONAL	1	TRUE	1	0.2	2		735	1198	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667522	29667522	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0048700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	51	418	0	ENST00000356175.3:c.6859-1G>T		p.X2287_splice	ENST00000356175	NM_000267.3	2287			1	2	FACETS	0.768	0.652	0.896	0.768	0.652	0.896	SUBCLONAL	1	TRUE	1	0.2	2		418	664	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39576650	39576650	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	35	317	0	ENST00000262039.4:c.940G>A	p.Asp314Asn	p.D314N	ENST00000262039	NM_002647.2	314	Gat/Aat	9/25	1	2	FACETS	0.7	0.573	0.843	0.7	0.573	0.843	SUBCLONAL	1	TRUE	1	0.2	2		317	500	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213772	66213772	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	38	326	0	ENST00000273854.3:c.2658T>G	p.Asp886Glu	p.D886E	ENST00000273854	NM_004439.5	886	gaT/gaG	15/18	1	2	FACETS	0.828	0.684	0.988	0.828	0.684	0.988	CLONAL	1	TRUE	1	0.2	2		326	459	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197002	106197002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	25	278	0	ENST00000380013.4:c.5335G>A	p.Ala1779Thr	p.A1779T	ENST00000380013	NM_001127208.2	1779	Gcc/Acc	11/11	1	2	FACETS	0.525	0.413	0.655	0.525	0.413	0.655	SUBCLONAL	1	TRUE	1	0.2	2		278	476	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541747	187541747	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0048700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	42	326	0	ENST00000441802.2:c.5993T>A	p.Leu1998Ter	p.L1998*	ENST00000441802	NM_005245.3	1998	tTa/tAa	10/27	1	2	FACETS	0.672	0.56	0.797	0.672	0.56	0.797	SUBCLONAL	1	TRUE	1	0.2	2		326	625	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294483	1294483	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	80	576	0	ENST00000310581.5:c.518C>A	p.Pro173Gln	p.P173Q	ENST00000310581	NM_198253.2	173	cCg/cAg	2/16	0.206377959948013	3	FACETS	0.922	0.81	1	0.461	0.405	0.522	CLONAL	1	TRUE	1	0.2	3		576	954	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31504732	31504732	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	54	370	0	ENST00000344624.3:c.1598G>T	p.Gly533Val	p.G533V	ENST00000344624		533	gGa/gTa	8/33	0.206377959948013	3	FACETS	0.755	0.643	0.878	0.377	0.321	0.439	SUBCLONAL	1	TRUE	1	0.2	3		370	787	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519435	176519435	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	77	687	0	ENST00000292408.4:c.841A>T	p.Ile281Phe	p.I281F	ENST00000292408	NM_213647.1	281	Atc/Ttc	7/18	0.171344359707146	1	FACETS	0.624	0.546	0.709	0.624	0.546	0.709	SUBCLONAL	1	TRUE	0	0.2	1		687	1110	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663406	29663409	+	frameshift_variant	Frame_Shift_Del	DEL	GTGG	GTGG	TCT	novel	NA	P-0048700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	50	411	1	ENST00000356175.3:c.5999_6002delinsTCT	p.Gly2000ValfsTer6	p.G2000Vfs*6	ENST00000356175	NM_000267.3	2000	gGTGGc/gTCTc	40/57	1	2	FACETS	0.672	0.569	0.786	0.672	0.569	0.786	SUBCLONAL	1	TRUE	1	0.2	2		412	744	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429757	78429757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755419864	NA	P-0048830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	25	191	0	ENST00000370768.2:c.1031G>A	p.Arg344Gln	p.R344Q	ENST00000370768	NM_003902.3	344	cGa/cAa	12/20	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.24	2		191	172	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0048830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	104	827	0	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.17453606512418	1	FACETS	0.979	0.877	1	0.979	0.877	1	CLONAL	1	TRUE	0	0.24	1		827	779	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087911	27087911	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs757025491	NA	P-0048830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	61	503	0	ENST00000324856.7:c.2198C>A	p.Ser733Ter	p.S733*	ENST00000324856	NM_006015.4	733	tCg/tAg	6/20	1	2	FACETS	0.979	0.846	1	0.979	0.846	1	CLONAL	1	TRUE	1	0.24	2		503	519	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575102	48575102	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	27	207	0	ENST00000342988.3:c.296G>A	p.Trp99Ter	p.W99*	ENST00000342988	NM_005359.5	99	tGg/tAg	3/12	0.17453606512418	1	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	0	0.24	1		207	167	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420593	49420598	+	inframe_deletion	In_Frame_Del	DEL	CAGGTT	CAGGTT	-	novel	NA	P-0048830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	71	643	0	ENST00000301067.7:c.15151_15156del	p.Asn5051_Leu5052del	p.N5051_L5052del	ENST00000301067	NM_003482.3	5051	AACCTG/-	48/54	1	2	FACETS	0.906	0.791	1	0.906	0.791	1	CLONAL	1	TRUE	1	0.24	2		643	653	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543900	41543902	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	rs1215537200	NA	P-0048830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	63	357	0	ENST00000263253.7:c.2195_2197del	p.Pro732del	p.P732del	ENST00000263253	NM_001429.3	731	CCT/-	12/31	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.24	2		357	504	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873813	151873813	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	30	344	0	ENST00000262189.6:c.8725del	p.Cys2909ValfsTer3	p.C2909Vfs*3	ENST00000262189	NM_170606.2	2909	Tgt/gt	38/59	1	2	FACETS	0.746	0.602	0.909	0.746	0.602	0.909	CLONAL	1	TRUE	1	0.24	2		344	335	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517201	NA	P-0049094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	119	460	0	ENST00000263967.3:c.1637A>C	p.Gln546Pro	p.Q546P	ENST00000263967	NM_006218.2	546	cAg/cCg	10/21	1	2	FACETS	0.958	0.871	1	0.958	0.871	1	CLONAL	1	FALSE	1	0.58344238054959	2		460	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0049094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	316	620	0	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	0.576155136757206	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	FALSE	0	0.58344238054959	1		620	609	SUCCESS
APC	324	MSKCC	GRCh37	5	112174577	112174577	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587783029	NA	P-0049094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	41	356	0	ENST00000257430.4:c.3286C>T	p.Gln1096Ter	p.Q1096*	ENST00000257430	NM_000038.5	1096	Cag/Tag	16/16	0.266789944762288	0	FACETS	0.211	0.177	0.249			1	INDETERMINATE	1	FALSE	0	0.58344238054959	0		356	277	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845479	128845479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	436	577	0	ENST00000249373.3:c.776C>T	p.Ser259Leu	p.S259L	ENST00000249373	NM_005631.4	259	tCg/tTg	4/12	0.282937537435434	3	FACETS	1	0.993	1	0.773	0.742	0.803	INDETERMINATE	2	FALSE	0	0.58344238054959	3		577	833	SUCCESS
APC	324	MSKCC	GRCh37	5	112176018	112176019	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0049094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	46	218	0	ENST00000257430.4:c.4729_4730dup	p.Cys1578AsnfsTer73	p.C1578Nfs*73	ENST00000257430	NM_000038.5	1576	gaa/gaAGa	16/16	0.266789944762288	0	FACETS	0.382	0.327	0.441			1	INDETERMINATE	1	FALSE	0	0.58344238054959	0		218	172	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0050860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	69	414	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.245428927195128	2	FACETS	1	0.971	1	0.707	0.619	0.802	CLONAL	1	TRUE	0	0.245718339203867	2		414	397	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092809	27092809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	52	591	2	ENST00000324856.7:c.2830C>T	p.Gln944Ter	p.Q944*	ENST00000324856	NM_006015.4	944	Cag/Tag	9/20	1	2	FACETS	0.741	0.631	0.863	0.741	0.631	0.863	SUBCLONAL	1	TRUE	1	0.245718339203867	2		593	571	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988512	36988512	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	87	701	0	ENST00000354822.5:c.141G>C	p.Leu47Phe	p.L47F	ENST00000354822	NM_001079668.2	47	ttG/ttC	2/3	1	2	FACETS	0.956	0.846	1	0.956	0.846	1	CLONAL	1	TRUE	1	0.245718339203867	2		701	741	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770101	56770101	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782528	NA	P-0050860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	59	593	0	ENST00000337432.4:c.97C>T	p.Gln33Ter	p.Q33*	ENST00000337432	NM_058216.2	33	Cag/Tag	1/9	0.222376636553367	3	FACETS	0.837	0.72	0.965	0.419	0.36	0.483	CLONAL	1	TRUE	1	0.245718339203867	3		593	644	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775238	73775238	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	74	552	0	ENST00000254810.4:c.18G>C	p.Gln6His	p.Q6H	ENST00000254810	NM_005324.3	6	caG/caC	2/4	0.222376636553367	3	FACETS	1	0.919	1	0.533	0.467	0.605	CLONAL	1	TRUE	1	0.245718339203867	3		552	634	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105543	11105543	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0050860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	87	618	1	ENST00000358026.2:c.1459A>T	p.Lys487Ter	p.K487*	ENST00000358026	NM_001128849.1	487	Aag/Tag	9/36	1	2	FACETS	0.996	0.882	1	0.996	0.882	1	CLONAL	1	TRUE	1	0.245718339203867	2		619	711	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682877	190682877	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	105	439	0	ENST00000441310.2:c.553G>T	p.Asp185Tyr	p.D185Y	ENST00000441310	NM_000534.4	185	Gac/Tac	5/13	0.222376636553367	3	FACETS	0.941	0.846	1	0.941	0.846	1	CLONAL	2	TRUE	1	0.245718339203867	3		439	510	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159086	143159086	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	91	381	1	ENST00000262992.4:c.767C>A	p.Ser256Ter	p.S256*	ENST00000262992	NM_001101669.1	256	tCa/tAa	10/24	0.222376636553367	3	FACETS	0.963	0.859	1	0.963	0.859	1	CLONAL	2	TRUE	1	0.245718339203867	3		382	432	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2972178	2972178	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	89	643	0	ENST00000396946.4:c.1561G>C	p.Asp521His	p.D521H	ENST00000396946	NM_032415.4	521	Gat/Cat	11/25	0.190425500613471	4	FACETS	1	0.889	1	0.502	0.444	0.564	CLONAL	1	TRUE	2	0.245718339203867	4		643	899	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636773	8636773	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	66	482	0	ENST00000356435.5:c.136C>A	p.Gln46Lys	p.Q46K	ENST00000356435		46	Caa/Aaa	2/35	1	2	FACETS	0.925	0.803	1	0.925	0.803	1	CLONAL	1	TRUE	1	0.245718339203867	2		482	581	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907106	101907106	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	33	353	0	ENST00000374994.4:c.1066G>T	p.Val356Leu	p.V356L	ENST00000374994	NM_004612.2	356	Gta/Tta	6/9	1	2	FACETS	0.795	0.648	0.959	0.795	0.648	0.959	CLONAL	1	TRUE	1	0.245718339203867	2		353	338	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0050938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	298	1057	6	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.317945923253718	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.357858941392926	2		1063	772	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930687	32930687	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs80358981	NA	P-0050938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	127	455	1	ENST00000380152.3:c.7558C>T	p.Arg2520Ter	p.R2520*	ENST00000380152		2520	Cga/Tga	15/27	0.346776965248341	2	FACETS	0.789	0.72	0.86	0.789	0.72	0.86	SUBCLONAL	2	TRUE	0	0.357858941392926	2		456	450	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249954	110249954	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	246	774	1	ENST00000374672.4:c.721G>A	p.Glu241Lys	p.E241K	ENST00000374672	NM_004235.4	241	Gag/Aag	3/5	0.346776965248341	2	FACETS	0.975	0.916	1	0.975	0.916	1	CLONAL	2	TRUE	0	0.357858941392926	2		775	705	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273994	10273994	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	248	1047	2	ENST00000330684.3:c.275G>A	p.Gly92Glu	p.G92E	ENST00000330684	NM_001134407.1	92	gGg/gAg	2/13	0.297364677275131	4	FACETS	0.845	0.789	0.902	0.845	0.789	0.902	CLONAL	2	TRUE	2	0.357858941392926	4		1049	1114	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444081	49444081	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	223	853	1	ENST00000301067.7:c.3290del	p.Pro1097GlnfsTer22	p.P1097Qfs*22	ENST00000301067	NM_003482.3	1097	cCa/ca	11/54	0.349901580854052	3	FACETS	0.864	0.806	0.924	0.864	0.806	0.924	CLONAL	2	TRUE	1	0.357858941392926	3		854	850	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366396	15366396	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	89	442	0	ENST00000263377.2:c.1759G>C	p.Glu587Gln	p.E587Q	ENST00000263377	NM_058243.2	587	Gag/Cag	10/20	0.349901580854052	3	FACETS	1	0.97	1	0.632	0.563	0.705	CLONAL	1	TRUE	1	0.357858941392926	3		442	464	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796457	42796457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs767634110	NA	P-0050938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	96	1114	2	ENST00000575354.2:c.3014C>A	p.Thr1005Asn	p.T1005N	ENST00000575354	NM_015125.3	1005	aCc/aAc	13/20	0.349901580854052	3	FACETS	0.677	0.602	0.757	0.339	0.301	0.379	SUBCLONAL	1	TRUE	1	0.357858941392926	3		1116	934	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430182	181430182	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	48	207	1	ENST00000325404.1:c.34C>T	p.Pro12Ser	p.P12S	ENST00000325404	NM_003106.3	12	Ccg/Tcg	1/1	0.357858941392926	7	FACETS	1	0.949	1	0.186	0.157	0.217	CLONAL	1	TRUE	0	0.357858941392926	7		208	391	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586430	189586430	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	341	422	2	ENST00000264731.3:c.1054A>T	p.Arg352Trp	p.R352W	ENST00000264731	NM_003722.4	352	Agg/Tgg	8/14	0.357858941392926	7	FACETS	0.926	0.881	0.971	0.661	0.629	0.694	CLONAL	5	TRUE	0	0.357858941392926	7		424	780	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683716	162683716	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1042122187	NA	P-0050938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	67	684	0	ENST00000366898.1:c.253G>T	p.Gly85Cys	p.G85C	ENST00000366898	NM_004562.2	85	Ggc/Tgc	3/12	0.218153616468671	2	FACETS	0.571	0.496	0.652	0.285	0.248	0.326	SUBCLONAL	1	TRUE	0	0.357858941392926	2		684	656	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863046	56863047	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	A	novel	NA	P-0050938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	50	518	0	ENST00000519728.1:c.313_314delinsA	p.Leu105IlefsTer2	p.L105Ifs*2	ENST00000519728	NM_002350.3	105	CTt/At	5/13	0.237662117469597	4	FACETS	0.582	0.493	0.68	0.291	0.246	0.34	SUBCLONAL	1	TRUE	2	0.357858941392926	4		518	652	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164902	106164902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs937035385	NA	P-0050960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	202	574	0	ENST00000380013.4:c.3770C>T	p.Thr1257Met	p.T1257M	ENST00000380013	NM_001127208.2	1257	aCg/aTg	6/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.884402754482481	2		574	415	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056291	180056291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199942873	NA	P-0050960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	187	1528	1	ENST00000261937.6:c.953G>A	p.Arg318Gln	p.R318Q	ENST00000261937	NM_182925.4	318	cGa/cAa	7/30	0.884402754482481	3	FACETS	0.78	0.722	0.84	0.39	0.361	0.42	SUBCLONAL	1	FALSE	1	0.884402754482481	3		1529	782	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486130	8486130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	229	460	0	ENST00000356435.5:c.2687C>T	p.Ser896Leu	p.S896L	ENST00000356435		896	tCa/tTa	17/35	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.884402754482481	2		460	440	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843243	128843243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173715127	NA	P-0050960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	282	1245	0	ENST00000249373.3:c.350G>A	p.Arg117His	p.R117H	ENST00000249373	NM_005631.4	117	cGc/cAc	2/12	0.884402754482481	3	FACETS	1	0.978	1	0.536	0.505	0.568	CLONAL	1	FALSE	1	0.884402754482481	3		1245	858	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434720	128434720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	268	549	0	ENST00000265960.3:c.134C>T	p.Ser45Leu	p.S45L	ENST00000265960	NM_001006617.1	45	tCa/tTa	2/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.884402754482481	2		549	561	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509975	187509975	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	178	383	0	ENST00000441802.2:c.13538G>C	p.Arg4513Thr	p.R4513T	ENST00000441802	NM_005245.3	4513	aGa/aCa	27/27	1	2	FACETS	0.936	0.873	1	0.936	0.873	1	CLONAL	1	FALSE	1	0.884402754482481	2		383	430	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490547	56490547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	216	415	0	ENST00000267101.3:c.2191G>A	p.Glu731Lys	p.E731K	ENST00000267101	NM_001982.3	731	Gag/Aag	19/28	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.884402754482481	2		415	473	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436527	49436527	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	285	671	0	ENST00000301067.7:c.5779C>G	p.Gln1927Glu	p.Q1927E	ENST00000301067	NM_003482.3	1927	Caa/Gaa	26/54	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.884402754482481	2		671	545	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490353	56490353	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	225	384	0	ENST00000267101.3:c.2122G>C	p.Glu708Gln	p.E708Q	ENST00000267101	NM_001982.3	708	Gag/Cag	18/28	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.884402754482481	2		384	433	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584563	48584563	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876659967	NA	P-0050960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	249	530	1	ENST00000342988.3:c.736C>A	p.Pro246Thr	p.P246T	ENST00000342988	NM_005359.5	246	Cca/Aca	6/12	0.884402754482481	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	FALSE	0	0.884402754482481	1		531	273	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386587	81386587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1032300573	NA	P-0051299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	29	352	0	ENST00000222390.5:c.400C>T	p.Arg134Cys	p.R134C	ENST00000222390	NM_000601.4	134	Cgc/Tgc	4/18	1	2	FACETS	0.323	0.26	0.395	0.323	0.26	0.395	SUBCLONAL	1	TRUE	1	0.566127639273931	2		352	317	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913517	NA	P-0052570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	176	306	0	ENST00000288135.5:c.1676T>C	p.Val559Ala	p.V559A	ENST00000288135	NM_000222.2	559	gTt/gCt	11/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.700697738473464	2		306	445	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0053948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	305	689	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.359605296550037	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.359605296550037	3		689	974	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0053948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	240	477	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.359605296550037	2	FACETS	0.846	0.798	0.894	1	0.991	1	CLONAL	3	TRUE	0	0.359605296550037	2		477	526	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	69	399	0	ENST00000263967.3:c.333G>T	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaT	2/21	0.359605296550037	7	FACETS	0.993	0.864	1	0.165	0.144	0.189	CLONAL	1	TRUE	1	0.359605296550037	7		399	734	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0053948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	310	963	3	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	0.359605296550037	2	FACETS	0.939	0.888	0.991	0.939	0.888	0.991	CLONAL	2	TRUE	0	0.359605296550037	2		966	918	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0053948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	197	558	1	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	0.359605296550037	2	FACETS	0.954	0.89	1	0.954	0.89	1	CLONAL	2	TRUE	0	0.359605296550037	2		559	574	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794601	42794601	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	140	955	0	ENST00000575354.2:c.1681G>T	p.Glu561Ter	p.E561*	ENST00000575354	NM_015125.3	561	Gag/Tag	10/20	0.359605296550037	3	FACETS	0.973	0.886	1	0.487	0.443	0.533	CLONAL	1	TRUE	1	0.359605296550037	3		955	944	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910692	29910692	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs281864736	NA	P-0053948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1416	168	1725	0	ENST00000376809.5:c.232C>T	p.Gln78Ter	p.Q78*	ENST00000376809	NM_002116.7	78	Cag/Tag	2/8	0.359605296550037	2	FACETS	0.59	0.54	0.642	0.295	0.27	0.321	SUBCLONAL	1	TRUE	0	0.359605296550037	2		1725	1584	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041768	14041768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1348674133	NA	P-0053948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	231	514	0	ENST00000311895.7:c.2315G>A	p.Arg772Gln	p.R772Q	ENST00000311895	NM_005236.2	772	cGa/cAa	11/11	0.32277697879806	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	1	0.359605296550037	3		514	734	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149238663	149238663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	242	670	0	ENST00000360632.3:c.1132G>A	p.Asp378Asn	p.D378N	ENST00000360632	NM_015472.4	378	Gac/Aac	7/7	0.359605296550037	5	FACETS	1	0.956	1			1	CLONAL	2	TRUE	NA	0.359605296550037	5		670	1007	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434544	49434544	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	327	974	0	ENST00000301067.7:c.7009C>T	p.Gln2337Ter	p.Q2337*	ENST00000301067	NM_003482.3	2337	Cag/Tag	31/54	0.359605296550037	5	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.359605296550037	5		974	1237	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512344	149512344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368602685	NA	P-0053948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	327	804	2	ENST00000261799.4:c.1096G>A	p.Ala366Thr	p.A366T	ENST00000261799	NM_002609.3	366	Gcc/Acc	7/23	0.359605296550037	2	FACETS	0.929	0.879	0.979	0.929	0.879	0.979	CLONAL	2	TRUE	0	0.359605296550037	2		806	979	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589370	28589370	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	74	426	0	ENST00000241453.7:c.2677C>G	p.Pro893Ala	p.P893A	ENST00000241453	NM_004119.2	893	Ccg/Gcg	22/24	1	2	FACETS	0.948	0.834	1	0.948	0.834	1	CLONAL	1	TRUE	1	0.359605296550037	2		426	434	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785544	50785544	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	138	678	0	ENST00000398568.2:c.534C>G	p.Asp178Glu	p.D178E	ENST00000398568	NM_001042412.1	178	gaC/gaG	4/18	0.32277697879806	3	FACETS	1	0.973	1	0.586	0.533	0.641	CLONAL	1	TRUE	1	0.359605296550037	3		678	773	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81968086	81968111	+	frameshift_variant	Frame_Shift_Del	DEL	CTGACCTGGTTGTCTACTGCAAACCA	CTGACCTGGTTGTCTACTGCAAACCA	-	novel	NA	P-0053948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	71	553	0	ENST00000359376.3:c.2792_2817del	p.Ser931TyrfsTer12	p.S931Yfs*12	ENST00000359376	NM_002661.3	931	tCTGACCTGGTTGTCTACTGCAAACCA/t	26/33	0.359605296550037	3	FACETS	0.674	0.588	0.767	0.225	0.196	0.256	SUBCLONAL	1	TRUE	0	0.359605296550037	3		553	691	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044575	12044575	+	stop_lost	Nonstop_Mutation	SNP	T	T	C	novel	NA	P-0053948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	90	440	0	ENST00000353533.5:c.1198T>C	p.Ter400ArgextTer8	p.*400Rext*8	ENST00000353533	NM_003010.3	400	Tga/Cga	11/11	0.359605296550037	2	FACETS	1	0.947	1	0.552	0.492	0.616	CLONAL	1	TRUE	0	0.359605296550037	2		440	453	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170553	7170553	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	102	492	0	ENST00000302850.5:c.1478C>A	p.Ala493Glu	p.A493E	ENST00000302850	NM_000208.2	493	gCa/gAa	6/22	0.359605296550037	3	FACETS	1	0.95	1	0.55	0.493	0.611	CLONAL	1	TRUE	1	0.359605296550037	3		492	608	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906367	50906367	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	314	1158	0	ENST00000440232.2:c.1028del	p.Arg343ProfsTer50	p.R343Pfs*50	ENST00000440232	NM_002691.3	343	cGc/cc	9/27	0.359605296550037	3	FACETS	0.997	0.942	1	0.997	0.942	1	CLONAL	2	TRUE	1	0.359605296550037	3		1158	1033	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917776	29917776	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	266	845	0	ENST00000389048.3:c.892G>T	p.Ala298Ser	p.A298S	ENST00000389048	NM_004304.4	298	Gcc/Tcc	3/29	0.32277697879806	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.359605296550037	3		845	855	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182681832	182681832	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	78	398	0	ENST00000292782.4:c.226C>G	p.Gln76Glu	p.Q76E	ENST00000292782	NM_020640.2	76	Caa/Gaa	3/7	0.359605296550037	7	FACETS	0.947	0.831	1	0.158	0.138	0.179	CLONAL	1	TRUE	1	0.359605296550037	7		398	870	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564695	86564704	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCCCCCTT	CTGCCCCCTT	-	novel	NA	P-0053948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	315	926	0	ENST00000274376.6:c.427_436del	p.Leu143TrpfsTer28	p.L143Wfs*28	ENST00000274376	NM_002890.2	143	CTGCCCCCTTtg/tg	1/25	0.359605296550037	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.359605296550037	2		926	860	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449749	149449749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774962435	NA	P-0053948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	108	716	0	ENST00000286301.3:c.1315G>A	p.Asp439Asn	p.D439N	ENST00000286301	NM_005211.3	439	Gat/Aat	9/22	0.359605296550037	2	FACETS	0.871	0.782	0.964	0.435	0.391	0.482	CLONAL	1	TRUE	0	0.359605296550037	2		716	690	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911182	29911182	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	88	528	0	ENST00000376809.5:c.481G>T	p.Asp161Tyr	p.D161Y	ENST00000376809	NM_002116.7	161	Gac/Tac	3/8	0.359605296550037	2	FACETS	1	0.936	1	0.538	0.478	0.601	CLONAL	1	TRUE	0	0.359605296550037	2		528	455	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836345	151836345	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0053948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	30	510	0	ENST00000262189.6:c.14461-1G>C		p.X4821_splice	ENST00000262189	NM_170606.2	4821			0.359605296550037	2	FACETS	0.312	0.25	0.382	0.156	0.125	0.191	SUBCLONAL	1	TRUE	0	0.359605296550037	2		510	535	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396773	139396773	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	297	840	0	ENST00000277541.6:c.5335A>T	p.Ser1779Cys	p.S1779C	ENST00000277541	NM_017617.3	1779	Agc/Tgc	28/34	0.29762314129126	4	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	2	0.359605296550037	4		840	1091	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0054850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	350	352	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.67306727383635	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.67306727383635	1		353	661	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324917	31324917	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs776780353	NA	P-0054850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	446	1492	0	ENST00000412585.2:c.19C>T	p.Arg7Ter	p.R7*	ENST00000412585	NM_005514.6	7	Cga/Tga	1/8	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.67306727383635	2		1492	936	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115881	8115885	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCC	CAGCC	-	novel	NA	P-0054850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	314	951	2	ENST00000346208.3:c.1227_1231del	p.Phe409LeufsTer96	p.F409Lfs*96	ENST00000346208		409	ttCAGCCac/ttac	6/6	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.67306727383635	2		953	855	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949134	71949134	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	774	1458	0	ENST00000298229.2:c.3601A>G	p.Met1201Val	p.M1201V	ENST00000298229	NM_001567.3	1201	Atg/Gtg	27/28	0.150720224645432	6	FACETS	0.918	0.891	0.945			1	INDETERMINATE	4	TRUE	NA	0.67306727383635	6		1458	1469	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447480	12447480	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	281	784	0	ENST00000287820.6:c.719G>C	p.Arg240Pro	p.R240P	ENST00000287820	NM_015869.4	240	cGg/cCg	5/7	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.67306727383635	2		784	766	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	59	82	0				ENST00000310581	NM_198253.2	-/1132			0.163761939831572	0	FACETS	0.567	0.488	0.653			1	INDETERMINATE	1	TRUE	0	0.28	0		82	535	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508499	106508499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752602335	NA	P-0055266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	71	480	0	ENST00000359195.3:c.493G>A	p.Val165Ile	p.V165I	ENST00000359195	NM_002649.2	165	Gtc/Atc	2/11	0.294014298402159	3	FACETS	0.696	0.606	0.793	0.348	0.303	0.397	SUBCLONAL	1	TRUE	1	0.28	3		480	831	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588085	67588085	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0055266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	24	308	0	ENST00000274335.5:c.917-2A>C		p.X306_splice	ENST00000274335		306			1	2	FACETS	0.633	0.497	0.788	0.633	0.497	0.788	SUBCLONAL	1	TRUE	1	0.28	2		308	271	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057197-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	157	82	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.837	0.775	0.9	0.837	0.775	0.9	CLONAL	1	TRUE	1	0.893553226888456	2		82	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540652	NA	P-0057197-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	289	389	0	ENST00000269305.4:c.743G>C	p.Arg248Pro	p.R248P	ENST00000269305	NM_001126112.2	248	cGg/cCg	7/11	0.842595405457661	1	FACETS	0.932	0.899	0.964	0.932	0.899	0.964	CLONAL	1	TRUE	0	0.893553226888456	1		389	384	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211079	55211079	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519888	NA	P-0057197-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	25	380	0	ENST00000275493.2:c.322A>G	p.Arg108Gly	p.R108G	ENST00000275493	NM_005228.3	108	Aga/Gga	3/28	0.583444658362316	4	FACETS	0.095	0.074	0.119			1	SUBCLONAL	1	TRUE	NA	0.893553226888456	4		380	1119	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711189	61711189	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057197-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	26	310	1	ENST00000401558.2:c.2560G>A	p.Ala854Thr	p.A854T	ENST00000401558	NM_003400.3	854	Gct/Act	21/25	0.826921674729335	1	FACETS	0.09	0.071	0.112	0.09	0.071	0.112	SUBCLONAL	1	TRUE	0	0.893553226888456	1		311	357	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0057595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	26	466	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.835	0.661	1	0.835	0.661	1	CLONAL	1	TRUE	1	0.16	2		466	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0057595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	19	352	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.261	0.197	0.338	0.261	0.197	0.338	SUBCLONAL	1	TRUE	1	0.16	2		353	909	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	115	82	0				ENST00000310581	NM_198253.2	-/1132			0.0841996025614574	6	FACETS	0.905	0.833	0.978			1	INDETERMINATE	4	TRUE	NA	0.557480148001072	6		82	241	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs483352695	NA	P-0058610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	158	494	0	ENST00000269305.4:c.736A>T	p.Met246Leu	p.M246L	ENST00000269305	NM_001126112.2	246	Atg/Ttg	7/11	0.560082549187483	1	FACETS	0.824	0.777	0.871	1	0.993	1	CLONAL	2	TRUE	0	0.557480148001072	1		494	248	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549116	21549116	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	93	676	0	ENST00000382592.4:c.3160C>T	p.Arg1054Ter	p.R1054*	ENST00000382592	NM_014572.2	1054	Cga/Tga	8/8	NA	2	FACETS	0.887	0.795	0.984			1	INDETERMINATE	1	TRUE	NA	0.557480148001072	2		676	376	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191524	10191524	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	103	702	0	ENST00000256474.2:c.517G>C	p.Glu173Gln	p.E173Q	ENST00000256474	NM_000551.3	173	Gag/Cag	3/3	0.209955167401153	5	FACETS	1	0.981	1	0.479	0.431	0.53	INDETERMINATE	1	TRUE	2	0.557480148001072	5		702	472	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396310	396310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768412292	NA	P-0058610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	39	620	0	ENST00000262320.3:c.716C>T	p.Pro239Leu	p.P239L	ENST00000262320	NM_003502.3	239	cCg/cTg	2/11	1	2	FACETS	0.443	0.368	0.525	0.443	0.368	0.525	SUBCLONAL	1	TRUE	1	0.557480148001072	2		620	316	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484164	120484164	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs782704056	NA	P-0058610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	61	595	0	ENST00000256646.2:c.2966A>G	p.Asn989Ser	p.N989S	ENST00000256646	NM_024408.3	989	aAt/aGt	18/34	0.196042086638089	6	FACETS	0.571	0.492	0.658	0.19	0.164	0.22	INDETERMINATE	1	TRUE	3	0.557480148001072	6		595	810	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114718	73114718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764238159	NA	P-0058610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	60	272	0	ENST00000356692.5:c.1099G>A	p.Glu367Lys	p.E367K	ENST00000356692		367	Gaa/Aaa	9/9	0.209955167401153	5	FACETS	1	0.944	1	0.391	0.339	0.447	INDETERMINATE	1	TRUE	2	0.557480148001072	5		272	337	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125036	46125036	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	262	425	0	ENST00000334344.6:c.223G>C	p.Glu75Gln	p.E75Q	ENST00000334344	NM_152641.2	75	Gag/Cag	3/21	0.440134560808185	5	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	2	0.557480148001072	5		425	539	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197045	123197045	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1569515797	NA	P-0058610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	67	156	0	ENST00000218089.9:c.1811G>A	p.Arg604Gln	p.R604Q	ENST00000218089	NM_001042749.1	604	cGa/cAa	19/35	0.560082549187483	2	FACETS	1	0.965	1			1	CLONAL	1	TRUE	NA	0.557480148001072	2		156	193	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743307	743307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754509357	NA	P-0058610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	55	448	0	ENST00000314574.4:c.833G>A	p.Arg278Gln	p.R278Q	ENST00000314574	NM_005433.3	278	cGa/cAa	7/12	0.189223882025092	5	FACETS	0.576	0.492	0.668	0.192	0.164	0.223	INDETERMINATE	1	TRUE	2	0.557480148001072	5		448	629	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470527	25470527	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	53	588	0	ENST00000264709.3:c.947C>G	p.Thr316Arg	p.T316R	ENST00000264709	NM_175629.2	316	aCg/aGg	8/23	0.557480148001072	5	FACETS	0.594	0.506	0.69	0.198	0.168	0.23	SUBCLONAL	1	TRUE	2	0.557480148001072	5		588	588	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022364	26022364	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0058610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	272	468	0	ENST00000435504.4:c.293C>G	p.Ser98Ter	p.S98*	ENST00000435504		98	tCa/tGa	5/13	0.557480148001072	5	FACETS	0.915	0.865	0.965	0.915	0.865	0.965	CLONAL	3	TRUE	2	0.557480148001072	5		468	653	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63898320	63898320	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	91	426	0	ENST00000398590.3:c.46G>T	p.Ala16Ser	p.A16S	ENST00000398590	NM_001177387.1	16	Gcg/Tcg	3/14	0.209955167401153	5	FACETS	1	0.98	1	0.492	0.44	0.548	INDETERMINATE	1	TRUE	2	0.557480148001072	5		426	406	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415013	116415013	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	86	585	0	ENST00000397752.3:c.3107C>G	p.Thr1036Ser	p.T1036S	ENST00000397752	NM_000245.2	1036	aCt/aGt	15/21	0.560082549187483	5	FACETS	0.77	0.681	0.865	0.257	0.227	0.289	SUBCLONAL	1	TRUE	2	0.557480148001072	5		585	736	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339693	70339694	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	17	280	0	ENST00000374080.3:c.363dup	p.Gly122TrpfsTer17	p.G122Wfs*17	ENST00000374080		121	gct/gcTt	3/45	0.421156418584582	2	FACETS	0.241	0.18	0.314			1	SUBCLONAL	1	TRUE	NA	0.557480148001072	2		280	253	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772865	135772866	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0058893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	77	523	0	ENST00000298552.3:c.2756_2757dup	p.Asp920LysfsTer12	p.D920Kfs*12	ENST00000298552	NM_001162426.1	919	-/AA	21/23	1	2	FACETS	0.798	0.7	0.904	0.798	0.7	0.904	CLONAL	1	TRUE	1	0.26	2		523	742	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80040338	80040338	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	106	96	0	ENST00000265081.6:c.1667C>A	p.Thr556Asn	p.T556N	ENST00000265081	NM_002439.4	556	aCc/aAc	12/24	1	2	FACETS	0.921	0.84	1	0.921	0.84	1	CLONAL	1	TRUE	1	0.885748104127042	2		96	260	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877805	151877805	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	50	214	0	ENST00000262189.6:c.7140A>T	p.Lys2380Asn	p.K2380N	ENST00000262189	NM_170606.2	2380	aaA/aaT	36/59	1	2	FACETS	0.211	0.179	0.247	0.211	0.179	0.247	SUBCLONAL	1	TRUE	1	0.885748104127042	2		214	534	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0059466-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	87	430	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.584	0.517	0.657	0.584	0.517	0.657	SUBCLONAL	1	TRUE	1	0.36	2		430	827	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0059466-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	97	623	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.554	0.493	0.619	0.554	0.493	0.619	SUBCLONAL	1	TRUE	1	0.36	2		624	973	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035956	47035956	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0059466-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	75	456	0	ENST00000377604.3:c.634A>T	p.Lys212Ter	p.K212*	ENST00000377604	NM_001204468.1	212	Aag/Tag	7/24	1	2	FACETS	0.48	0.42	0.545	0.48	0.42	0.545	SUBCLONAL	1	TRUE	1	0.36	2		456	868	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0059527-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	38	442	0	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	1	2	FACETS	0.918	0.757	1	0.918	0.757	1	CLONAL	1	TRUE	1	0.13	2		442	637	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0059720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	28	615	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.562470201658095	3	FACETS	0.747	0.603	0.907	0.373	0.301	0.454	CLONAL	1	TRUE	1	0.592579647663465	3		615	164	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0059720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	559	636	0	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	0.592579647663465	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	4	TRUE	0	0.592579647663465	4		636	735	SUCCESS
APC	324	MSKCC	GRCh37	5	112154972	112154972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756336949	NA	P-0059720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	212	466	0	ENST00000257430.4:c.1243G>A	p.Ala415Thr	p.A415T	ENST00000257430	NM_000038.5	415	Gct/Act	10/16	0.423959628041762	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.592579647663465	4		466	549	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027144	49027144	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	55	303	0	ENST00000267163.4:c.1711G>A	p.Asp571Asn	p.D571N	ENST00000267163	NM_000321.2	571	Gat/Aat	18/27	0.548598876186031	5	FACETS	0.841	0.721	0.971	0.28	0.24	0.324	CLONAL	1	TRUE	2	0.592579647663465	5		303	417	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027169	49027169	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059720-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	74	354	0	ENST00000267163.4:c.1736G>C	p.Arg579Pro	p.R579P	ENST00000267163	NM_000321.2	579	cGa/cCa	18/27	0.548598876186031	5	FACETS	0.959	0.842	1	0.32	0.28	0.362	CLONAL	1	TRUE	2	0.592579647663465	5		354	492	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0060469-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	185	640	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.353261600600625	3	FACETS	0.989	0.924	1	0.989	0.924	1	CLONAL	2	TRUE	1	0.567939638088589	3		640	423	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974395	18974395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1322079562	NA	P-0060469-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	341	551	0	ENST00000262803.5:c.2749C>T	p.Arg917Trp	p.R917W	ENST00000262803	NM_002911.3	917	Cgg/Tgg	19/24	0.194597973688766	2	FACETS	1	0.987	1	1	0.987	1	INDETERMINATE	2	TRUE	0	0.567939638088589	2		551	561	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032006	26032006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060469-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	232	708	0	ENST00000244661.2:c.283G>A	p.Glu95Lys	p.E95K	ENST00000244661	NM_003537.3	95	Gag/Aag	1/1	0.155352043628937	3	FACETS	0.755	0.707	0.803	0.755	0.707	0.803	INDETERMINATE	2	TRUE	1	0.567939638088589	3		708	695	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578515	7578516	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0060469-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	164	603	0	ENST00000269305.4:c.414dup	p.Lys139GlnfsTer10	p.K139Qfs*10	ENST00000269305	NM_001126112.2	138	-/C	5/11	0.575338830450813	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.567939638088589	1		603	370	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955382	48955382	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0060469-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	61	309	0	ENST00000267163.4:c.1499del		p.X500_splice	ENST00000267163	NM_000321.2	500			0.443014547701522	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.567939638088589	1		309	133	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957447	175957447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060469-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	83	509	0	ENST00000367669.3:c.1949C>T	p.Ser650Phe	p.S650F	ENST00000367669	NM_022457.5	650	tCc/tTc	17/20	0.575338830450813	3	FACETS	0.787	0.697	0.882	0.262	0.232	0.294	SUBCLONAL	1	TRUE	0	0.567939638088589	3		509	477	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174889	56174889	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060469-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	231	448	0	ENST00000399503.3:c.2049del	p.Val684Ter	p.V684*	ENST00000399503	NM_005921.1	683	gTt/gt	11/20	0.575338830450813	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.567939638088589	2		448	368	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686821	117686821	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060469-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	89	465	0	ENST00000368508.3:c.2896C>G	p.Gln966Glu	p.Q966E	ENST00000368508	NM_002944.2	966	Caa/Gaa	19/43	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.567939638088589	2		465	281	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622174	162622174	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060469-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	75	538	0	ENST00000366898.1:c.523A>T	p.Thr175Ser	p.T175S	ENST00000366898	NM_004562.2	175	Acc/Tcc	4/12	1	2	FACETS	0.619	0.544	0.698	0.619	0.544	0.698	SUBCLONAL	1	TRUE	1	0.567939638088589	2		538	427	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864897	117864897	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060469-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	41	416	0	ENST00000297338.2:c.1212G>T	p.Arg404Ser	p.R404S	ENST00000297338	NM_006265.2	404	agG/agT	10/14	0.43132247893588	4	FACETS	0.435	0.361	0.516	0.217	0.18	0.258	SUBCLONAL	1	TRUE	2	0.567939638088589	4		416	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061219-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	191	762	0	ENST00000269305.4:c.470T>G	p.Val157Gly	p.V157G	ENST00000269305	NM_001126112.2	157	gTc/gGc	5/11	0.154464658767771	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	FALSE	0	0.154464658767771	3		762	808	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87322806	87322806	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144037140	NA	P-0061219-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	49	352	2	ENST00000277120.3:c.407G>A	p.Arg136His	p.R136H	ENST00000277120		136	cGt/cAt	5/19	0.154464658767771	1	FACETS	0.834	0.709	0.97	1	0.968	1	CLONAL	2	FALSE	0	0.154464658767771	1		354	351	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937094	48937094	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0061219-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	21	224	0	ENST00000267163.4:c.861+1G>A		p.X287_splice	ENST00000267163	NM_000321.2	287			0.154464658767771	1	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	FALSE	0	0.154464658767771	1		224	205	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663568	117663568	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs779188243	NA	P-0061219-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	23	343	0	ENST00000368508.3:c.4664A>G	p.Asn1555Ser	p.N1555S	ENST00000368508	NM_002944.2	1555	aAt/aGt	28/43	0.153789454980048	1	FACETS	1	0.813	1	1	0.813	1	CLONAL	1	FALSE	0	0.154464658767771	1		343	263	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858034	152858034	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061219-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	92	373	2	ENST00000406277.2:c.581T>C	p.Leu194Pro	p.L194P	ENST00000406277	NM_152274.4	194	cTc/cCc	6/7	1	1	FACETS	0.959	0.859	1	1	0.989	1	CLONAL	3	FALSE	0	0.154464658767771	1		375	382	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465274	120465274	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs752668646	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	64	702	0	ENST00000256646.2:c.4987C>G	p.Leu1663Val	p.L1663V	ENST00000256646	NM_024408.3	1663	Ctt/Gtt	27/34	1	2	FACETS	0.887	0.767	1	0.887	0.767	1	CLONAL	1	TRUE	1	0.190530429333638	2		702	757	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682947	241682947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	55	601	0	ENST00000366560.3:c.76C>T	p.Pro26Ser	p.P26S	ENST00000366560	NM_000143.3	26	Ccc/Tcc	1/10	0.150921201014486	4	FACETS	0.798	0.681	0.927	0.399	0.34	0.464	CLONAL	1	TRUE	2	0.190530429333638	4		601	861	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610154	10610154	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	84	724	0	ENST00000171111.5:c.556G>T	p.Gly186Cys	p.G186C	ENST00000171111	NM_203500.1	186	Ggc/Tgc	2/6	0.169513920408891	2	FACETS	1	0.892	1	0.506	0.446	0.571	CLONAL	1	TRUE	0	0.190530429333638	2		724	871	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498290	29498290	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	62	663	0	ENST00000389048.3:c.1890C>G	p.Ile630Met	p.I630M	ENST00000389048	NM_004304.4	630	atC/atG	10/29	1	2	FACETS	0.835	0.72	0.961	0.835	0.72	0.961	CLONAL	1	TRUE	1	0.190530429333638	2		663	779	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182858	123182858	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	42	158	0	ENST00000218089.9:c.823C>T	p.Gln275Ter	p.Q275*	ENST00000218089	NM_001042749.1	275	Cag/Tag	10/35	1	1	FACETS	0.807	0.679	0.947	1	0.962	1	CLONAL	2	TRUE	0	0.190530429333638	1		158	247	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164342	47164342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	56	496	0	ENST00000409792.3:c.1784C>T	p.Ser595Leu	p.S595L	ENST00000409792	NM_014159.6	595	tCa/tTa	3/21	1	2	FACETS	0.835	0.714	0.967	0.835	0.714	0.967	CLONAL	1	TRUE	1	0.190530429333638	2		496	704	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164591	47164591	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	66	584	0	ENST00000409792.3:c.1535C>G	p.Ser512Ter	p.S512*	ENST00000409792	NM_014159.6	512	tCa/tGa	3/21	1	2	FACETS	0.923	0.8	1	0.923	0.8	1	CLONAL	1	TRUE	1	0.190530429333638	2		584	751	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770065	56770065	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs752608224	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	63	666	0	ENST00000337432.4:c.61C>G	p.Pro21Ala	p.P21A	ENST00000337432	NM_058216.2	21	Cca/Gca	1/9	1	2	FACETS	0.831	0.717	0.955	0.831	0.717	0.955	CLONAL	1	TRUE	1	0.190530429333638	2		666	796	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89825063	89825063	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779162871	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	74	734	0	ENST00000389301.3:c.2903C>T	p.Ser968Leu	p.S968L	ENST00000389301	NM_000135.2	968	tCg/tTg	30/43	1	2	FACETS	0.862	0.753	0.98	0.862	0.753	0.98	CLONAL	1	TRUE	1	0.190530429333638	2		734	901	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041266	47041266	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	77	420	0	ENST00000377604.3:c.1693+1G>C		p.X565_splice	ENST00000377604	NM_001204468.1	565			1	1	FACETS	0.797	0.702	0.898	1	0.978	1	SUBCLONAL	2	TRUE	0	0.190530429333638	1		420	459	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111959722	111959722	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	50	470	0	ENST00000375549.3:c.301C>G	p.Leu101Val	p.L101V	ENST00000375549	NM_003002.3	101	Ctt/Gtt	3/4	1	2	FACETS	0.918	0.778	1	0.918	0.778	1	CLONAL	1	TRUE	1	0.190530429333638	2		470	572	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641473	18641473	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	74	611	0	ENST00000266497.5:c.2472G>C	p.Leu824Phe	p.L824F	ENST00000266497		824	ttG/ttC	17/31	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.190530429333638	2		611	721	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220706	1220706	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs878853992	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	116	671	0	ENST00000326873.7:c.724G>T	p.Gly242Trp	p.G242W	ENST00000326873	NM_000455.4	242	Ggg/Tgg	5/10	0.169513920408891	2	FACETS	0.917	0.828	1	0.917	0.828	1	CLONAL	2	TRUE	0	0.190530429333638	2		671	664	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518061	103518061	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	56	549	0	ENST00000355739.4:c.1999C>T	p.Gln667Ter	p.Q667*	ENST00000355739	NM_000123.3	667	Caa/Taa	9/15	1	2	FACETS	0.774	0.662	0.898	0.774	0.662	0.898	SUBCLONAL	1	TRUE	1	0.190530429333638	2		549	759	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729465	41729465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747474916	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	66	770	0	ENST00000242208.4:c.1064C>T	p.Pro355Leu	p.P355L	ENST00000242208	NM_002192.2	355	cCg/cTg	3/3	1	2	FACETS	0.865	0.749	0.991	0.865	0.749	0.991	CLONAL	1	TRUE	1	0.190530429333638	2		770	801	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803122	32803122	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745356167	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	205	621	0	ENST00000374899.4:c.754C>T	p.Arg252Trp	p.R252W	ENST00000374899	NM_018833.2	252	Cgg/Tgg	5/12	0.167960922799616	3	FACETS	0.917	0.852	0.984	0.917	0.852	0.984	CLONAL	3	TRUE	0	0.190530429333638	3		621	857	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138627	37138627	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	62	785	0	ENST00000373509.5:c.161C>G	p.Ser54Ter	p.S54*	ENST00000373509	NM_002648.3	54	tCa/tGa	2/6	0.167960922799616	3	FACETS	0.789	0.679	0.908	0.263	0.226	0.303	CLONAL	1	TRUE	0	0.190530429333638	3		785	904	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234309	39234309	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397517159	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	40	339	0	ENST00000402219.2:c.2536G>A	p.Glu846Lys	p.E846K	ENST00000402219	NM_005633.3	846	Gaa/Aaa	16/23	1	2	FACETS	0.835	0.693	0.992	0.835	0.693	0.992	CLONAL	1	TRUE	1	0.190530429333638	2		339	503	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110251297	110251297	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	56	685	0	ENST00000374672.4:c.40G>T	p.Asp14Tyr	p.D14Y	ENST00000374672	NM_004235.4	14	Gac/Tac	2/5	0.167967552187007	3	FACETS	0.783	0.669	0.908	0.392	0.334	0.454	CLONAL	1	TRUE	1	0.190530429333638	3		685	822	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217842	7217842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	131	619	0	ENST00000380728.2:c.169G>A	p.Glu57Lys	p.E57K	ENST00000380728		57	Gaa/Aaa	3/11	1	2	FACETS	0.799	0.724	0.877	1	0.987	1	SUBCLONAL	2	TRUE	1	0.190530429333638	2		619	861	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138765	37138765	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	76	769	0	ENST00000373509.5:c.198C>G	p.Ile66Met	p.I66M	ENST00000373509	NM_002648.3	66	atC/atG	3/6	0.167960922799616	3	FACETS	0.914	0.8	1	0.305	0.266	0.346	CLONAL	1	TRUE	0	0.190530429333638	3		769	956	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920419	114920419	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs750925453	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	53	520	0	ENST00000543371.1:c.1360G>C	p.Asp454His	p.D454H	ENST00000543371	NM_001198531.1	454	Gac/Cac	13/14	1	2	FACETS	0.799	0.68	0.93	0.799	0.68	0.93	CLONAL	1	TRUE	1	0.190530429333638	2		520	696	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935620	13935620	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	51	622	0	ENST00000405192.2:c.1236G>C	p.Lys412Asn	p.K412N	ENST00000405192	NM_001163147.1	412	aaG/aaC	12/12	1	2	FACETS	0.749	0.635	0.874	0.749	0.635	0.874	SUBCLONAL	1	TRUE	1	0.190530429333638	2		622	715	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121699	108121699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	68	585	0	ENST00000278616.4:c.1507G>A	p.Glu503Lys	p.E503K	ENST00000278616	NM_000051.3	503	Gaa/Aaa	10/63	1	2	FACETS	0.849	0.737	0.97	0.849	0.737	0.97	CLONAL	1	TRUE	1	0.190530429333638	2		585	841	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938135	36938135	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201037400	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	69	677	0	ENST00000361632.4:c.826G>A	p.Glu276Lys	p.E276K	ENST00000361632		276	Gaa/Aaa	6/16	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.190530429333638	2		677	646	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152300	99152300	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1247867306	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	46	461	0	ENST00000074304.5:c.379C>T	p.Gln127Ter	p.Q127*	ENST00000074304	NM_001134224.1	127	Cag/Tag	6/26	1	2	FACETS	0.799	0.672	0.94	0.799	0.672	0.94	CLONAL	1	TRUE	1	0.190530429333638	2		461	604	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1720601	1720601	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	85	665	0	ENST00000378609.4:c.807C>G	p.Ile269Met	p.I269M	ENST00000378609	NM_002074.3	269	atC/atG	10/12	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.190530429333638	2		665	796	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332846	65332846	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	51	589	0	ENST00000342505.4:c.693G>C	p.Gln231His	p.Q231H	ENST00000342505	NM_002227.2	231	caG/caC	7/25	1	2	FACETS	0.791	0.671	0.923	0.791	0.671	0.923	CLONAL	1	TRUE	1	0.190530429333638	2		589	677	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699392	117699392	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	69	701	0	ENST00000369458.3:c.249C>G	p.Phe83Leu	p.F83L	ENST00000369458	NM_024626.3	83	ttC/ttG	3/6	1	2	FACETS	0.876	0.761	1	0.876	0.761	1	CLONAL	1	TRUE	1	0.190530429333638	2		701	827	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150933107	150933107	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	64	587	0	ENST00000271640.5:c.2569C>G	p.Leu857Val	p.L857V	ENST00000271640	NM_001145415.1	857	Ctg/Gtg	16/22	0.150921201014486	4	FACETS	0.9	0.777	1	0.45	0.388	0.517	CLONAL	1	TRUE	2	0.190530429333638	4		587	889	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226576408	226576408	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	82	624	0	ENST00000366794.5:c.666G>C	p.Lys222Asn	p.K222N	ENST00000366794	NM_001618.3	222	aaG/aaC	5/23	0.150921201014486	4	FACETS	1	0.957	1	0.597	0.526	0.674	CLONAL	1	TRUE	2	0.190530429333638	4		624	858	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097784	8097784	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	62	728	0	ENST00000346208.3:c.166C>G	p.Gln56Glu	p.Q56E	ENST00000346208		56	Caa/Gaa	2/6	0.167967552187007	3	FACETS	0.739	0.637	0.852	0.37	0.318	0.426	SUBCLONAL	1	TRUE	1	0.190530429333638	3		728	964	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77991906	77991906	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	70	595	1	ENST00000361507.4:c.117G>A	p.Met39Ile	p.M39I	ENST00000361507	NM_080491.2	39	atG/atA	2/10	1	2	FACETS	0.986	0.859	1	0.986	0.859	1	CLONAL	1	TRUE	1	0.190530429333638	2		596	745	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121744	108121744	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	66	605	0	ENST00000278616.4:c.1552G>T	p.Glu518Ter	p.E518*	ENST00000278616	NM_000051.3	518	Gag/Tag	10/63	1	2	FACETS	0.865	0.749	0.991	0.865	0.749	0.991	CLONAL	1	TRUE	1	0.190530429333638	2		605	801	SUCCESS
CBL	867	MSKCC	GRCh37	11	119168119	119168119	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	77	502	0	ENST00000264033.4:c.2179G>C	p.Asp727His	p.D727H	ENST00000264033	NM_005188.3	727	Gat/Cat	14/16	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.190530429333638	2		502	715	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025520	1025520	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	69	694	0	ENST00000358495.3:c.855G>C	p.Glu285Asp	p.E285D	ENST00000358495	NM_134424.2	285	gaG/gaC	9/12	1	2	FACETS	0.895	0.778	1	0.895	0.778	1	CLONAL	1	TRUE	1	0.190530429333638	2		694	809	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038881	12038881	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	47	525	0	ENST00000396373.4:c.1174G>T	p.Glu392Ter	p.E392*	ENST00000396373	NM_001987.4	392	Gag/Tag	7/8	1	2	FACETS	0.698	0.587	0.82	0.698	0.587	0.82	SUBCLONAL	1	TRUE	1	0.190530429333638	2		525	707	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421078	49421078	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	64	699	0	ENST00000301067.7:c.14671C>G	p.Gln4891Glu	p.Q4891E	ENST00000301067	NM_003482.3	4891	Cag/Gag	48/54	1	2	FACETS	0.914	0.79	1	0.914	0.79	1	CLONAL	1	TRUE	1	0.190530429333638	2		699	735	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50490632	50490632	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	55	515	0	ENST00000394963.4:c.1270-1G>C		p.X424_splice	ENST00000394963	NM_003076.4	424			1	2	FACETS	0.948	0.81	1	0.948	0.81	1	CLONAL	1	TRUE	1	0.190530429333638	2		515	609	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911186	32911186	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	47	552	0	ENST00000380152.3:c.2694G>C	p.Arg898Ser	p.R898S	ENST00000380152		898	agG/agC	11/27	1	2	FACETS	0.729	0.614	0.856	0.729	0.614	0.856	SUBCLONAL	1	TRUE	1	0.190530429333638	2		552	677	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912549	32912549	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	46	556	0	ENST00000380152.3:c.4057G>A	p.Glu1353Lys	p.E1353K	ENST00000380152		1353	Gaa/Aaa	11/27	1	2	FACETS	0.632	0.531	0.744	0.632	0.531	0.744	SUBCLONAL	1	TRUE	1	0.190530429333638	2		556	764	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95598854	95598854	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	43	437	0	ENST00000393063.1:c.305C>G	p.Ser102Cys	p.S102C	ENST00000393063	NM_030621.3	102	tCt/tGt	4/28	1	2	FACETS	0.797	0.667	0.943	0.797	0.667	0.943	CLONAL	1	TRUE	1	0.190530429333638	2		437	566	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50791103	50791103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	79	554	0	ENST00000307179.4:c.3175C>T	p.His1059Tyr	p.H1059Y	ENST00000307179		1059	Cac/Tac	20/20	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.190530429333638	2		554	790	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774105	66774105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	61	654	0	ENST00000307102.5:c.581C>T	p.Ser194Phe	p.S194F	ENST00000307102	NM_002755.3	194	tCc/tTc	6/11	1	2	FACETS	0.745	0.641	0.858	0.745	0.641	0.858	SUBCLONAL	1	TRUE	1	0.190530429333638	2		654	860	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636853	2636853	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1022721779	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	54	711	0	ENST00000342085.4:c.1302G>C	p.Glu434Asp	p.E434D	ENST00000342085	NM_002613.4	434	gaG/gaC	11/14	1	2	FACETS	0.649	0.553	0.755	0.649	0.553	0.755	SUBCLONAL	1	TRUE	1	0.190530429333638	2		711	873	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652280	3652280	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	68	737	0	ENST00000294008.3:c.789G>C	p.Glu263Asp	p.E263D	ENST00000294008	NM_032444.2	263	gaG/gaC	4/15	1	2	FACETS	0.876	0.761	1	0.876	0.761	1	CLONAL	1	TRUE	1	0.190530429333638	2		737	815	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777797	3777797	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	88	792	0	ENST00000262367.5:c.7251G>C	p.Arg2417Ser	p.R2417S	ENST00000262367	NM_004380.2	2417	agG/agC	31/31	1	2	FACETS	0.976	0.863	1	0.976	0.863	1	CLONAL	1	TRUE	1	0.190530429333638	2		792	946	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858378	9858378	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	72	668	0	ENST00000330684.3:c.3023C>G	p.Ser1008Cys	p.S1008C	ENST00000330684	NM_001134407.1	1008	tCt/tGt	13/13	1	2	FACETS	0.855	0.745	0.974	0.855	0.745	0.974	CLONAL	1	TRUE	1	0.190530429333638	2		668	884	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858553	9858553	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555482861	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	62	688	0	ENST00000330684.3:c.2848C>T	p.Gln950Ter	p.Q950*	ENST00000330684	NM_001134407.1	950	Cag/Tag	13/13	1	2	FACETS	0.779	0.672	0.897	0.779	0.672	0.897	SUBCLONAL	1	TRUE	1	0.190530429333638	2		688	835	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830339	72830339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	69	777	0	ENST00000268489.5:c.6242C>T	p.Pro2081Leu	p.P2081L	ENST00000268489	NM_006885.3	2081	cCa/cTa	9/10	1	2	FACETS	0.844	0.734	0.964	0.844	0.734	0.964	CLONAL	1	TRUE	1	0.190530429333638	2		777	858	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81962190	81962190	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	46	529	0	ENST00000359376.3:c.2542C>G	p.Leu848Val	p.L848V	ENST00000359376	NM_002661.3	848	Ctt/Gtt	24/33	1	2	FACETS	0.764	0.642	0.899	0.764	0.642	0.899	SUBCLONAL	1	TRUE	1	0.190530429333638	2		529	632	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217681	7217681	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	140	630	0	ENST00000380728.2:c.246G>C	p.Glu82Asp	p.E82D	ENST00000380728		82	gaG/gaC	4/11	1	2	FACETS	0.844	0.768	0.923	1	0.989	1	CLONAL	2	TRUE	1	0.190530429333638	2		630	871	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650895	37650895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	76	483	0	ENST00000447079.4:c.2367G>A	p.Met789Ile	p.M789I	ENST00000447079	NM_015083.1	789	atG/atA	5/14	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.190530429333638	2		483	724	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853823	59853823	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	48	528	0	ENST00000259008.2:c.2036T>C	p.Leu679Pro	p.L679P	ENST00000259008	NM_032043.2	679	cTt/cCt	14/20	1	2	FACETS	0.694	0.585	0.814	0.694	0.585	0.814	SUBCLONAL	1	TRUE	1	0.190530429333638	2		528	726	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919581	78919581	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	59	535	0	ENST00000306801.3:c.3140G>A	p.Cys1047Tyr	p.C1047Y	ENST00000306801	NM_020761.2	1047	tGc/tAc	26/34	1	2	FACETS	0.936	0.804	1	0.936	0.804	1	CLONAL	1	TRUE	1	0.190530429333638	2		535	662	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311753	30311753	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	39	424	0	ENST00000262643.3:c.607G>C	p.Glu203Gln	p.E203Q	ENST00000262643	NM_001238.2	203	Gag/Cag	7/12	1	2	FACETS	0.676	0.559	0.806	0.676	0.559	0.806	SUBCLONAL	1	TRUE	1	0.190530429333638	2		424	606	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752922	42752922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	83	884	0	ENST00000222329.4:c.1342G>A	p.Glu448Lys	p.E448K	ENST00000222329	NM_006494.2	448	Gag/Aag	4/4	1	2	FACETS	0.927	0.816	1	0.927	0.816	1	CLONAL	1	TRUE	1	0.190530429333638	2		884	940	SUCCESS
ALK	238	MSKCC	GRCh37	2	29541185	29541185	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	72	535	0	ENST00000389048.3:c.1632G>C	p.Lys544Asn	p.K544N	ENST00000389048	NM_004304.4	544	aaG/aaC	8/29	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.190530429333638	2		535	723	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61722610	61722610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426589139	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	47	398	0	ENST00000401558.2:c.1027C>T	p.Leu343Phe	p.L343F	ENST00000401558	NM_003400.3	343	Ctc/Ttc	11/25	1	2	FACETS	0.884	0.746	1	0.884	0.746	1	CLONAL	1	TRUE	1	0.190530429333638	2		398	558	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152252	99152252	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	45	450	0	ENST00000074304.5:c.331C>T	p.Gln111Ter	p.Q111*	ENST00000074304	NM_001134224.1	111	Cag/Tag	6/26	1	2	FACETS	0.779	0.654	0.918	0.779	0.654	0.918	CLONAL	1	TRUE	1	0.190530429333638	2		450	606	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632215	215632215	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	48	428	0	ENST00000260947.4:c.1559G>C	p.Arg520Thr	p.R520T	ENST00000260947	NM_000465.2	520	aGa/aCa	6/11	1	2	FACETS	0.886	0.748	1	0.886	0.748	1	CLONAL	1	TRUE	1	0.190530429333638	2		428	569	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572503	41572503	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	91	727	0	ENST00000263253.7:c.5032G>C	p.Glu1678Gln	p.E1678Q	ENST00000263253	NM_001429.3	1678	Gag/Cag	30/31	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.190530429333638	2		727	940	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37061819	37061819	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	66	691	0	ENST00000231790.2:c.903G>C	p.Gln301His	p.Q301H	ENST00000231790	NM_000249.3	301	caG/caC	11/19	1	2	FACETS	0.969	0.84	1	0.969	0.84	1	CLONAL	1	TRUE	1	0.190530429333638	2		691	715	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69988264	69988264	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	59	482	0	ENST00000394351.3:c.277G>C	p.Glu93Gln	p.E93Q	ENST00000394351	NM_000248.3	93	Gaa/Caa	3/9	1	2	FACETS	0.999	0.859	1	0.999	0.859	1	CLONAL	1	TRUE	1	0.190530429333638	2		482	620	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138382785	138382785	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	56	466	0	ENST00000289153.2:c.2759G>T	p.Arg920Ile	p.R920I	ENST00000289153	NM_006219.2	920	aGa/aTa	19/22	1	2	FACETS	0.895	0.766	1	0.895	0.766	1	CLONAL	1	TRUE	1	0.190530429333638	2		466	657	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186796	142186796	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	42	432	0	ENST00000350721.4:c.6667C>G	p.Leu2223Val	p.L2223V	ENST00000350721	NM_001184.3	2223	Cta/Gta	39/47	1	2	FACETS	0.821	0.685	0.972	0.821	0.685	0.972	CLONAL	1	TRUE	1	0.190530429333638	2		432	537	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032111	26032111	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs753823527	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	85	918	0	ENST00000244661.2:c.178G>T	p.Glu60Ter	p.E60*	ENST00000244661	NM_003537.3	60	Gag/Tag	1/1	0.167960922799616	3	FACETS	0.894	0.788	1	0.298	0.262	0.336	CLONAL	1	TRUE	0	0.190530429333638	3		918	1093	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045798	26045798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	66	944	0	ENST00000540144.1:c.160C>T	p.Arg54Cys	p.R54C	ENST00000540144	NM_003531.2	54	Cgc/Tgc	1/1	0.167960922799616	3	FACETS	0.662	0.573	0.76	0.221	0.191	0.254	SUBCLONAL	1	TRUE	0	0.190530429333638	3		944	1146	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165267	32165267	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367830176	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	72	787	0	ENST00000375023.3:c.4861G>A	p.Asp1621Asn	p.D1621N	ENST00000375023	NM_004557.3	1621	Gat/Aat	27/30	0.167960922799616	3	FACETS	0.878	0.765	1	0.293	0.255	0.334	CLONAL	1	TRUE	0	0.190530429333638	3		787	943	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793835	89793835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	84	553	0	ENST00000336032.3:c.904G>A	p.Gly302Arg	p.G302R	ENST00000336032	NM_006813.2	302	Gga/Aga	2/2	0.190530429333638	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.190530429333638	1		553	730	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519721	137519721	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	75	555	1	ENST00000367739.4:c.917C>A	p.Ser306Ter	p.S306*	ENST00000367739	NM_000416.2	306	tCa/tAa	7/7	0.190530429333638	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.190530429333638	1		556	678	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157454319	157454319	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	58	578	0	ENST00000346085.5:c.2529G>C	p.Gln843His	p.Q843H	ENST00000346085	NM_020732.3	843	caG/caC	8/20	0.190530429333638	1	FACETS	0.92	0.79	1	0.92	0.79	1	CLONAL	1	TRUE	0	0.190530429333638	1		578	599	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935676	13935676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	54	602	0	ENST00000405192.2:c.1180G>A	p.Asp394Asn	p.D394N	ENST00000405192	NM_001163147.1	394	Gat/Aat	12/12	1	2	FACETS	0.784	0.668	0.911	0.784	0.668	0.911	CLONAL	1	TRUE	1	0.190530429333638	2		602	723	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935701	13935701	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	62	544	0	ENST00000405192.2:c.1155G>C	p.Glu385Asp	p.E385D	ENST00000405192	NM_001163147.1	385	gaG/gaC	12/12	1	2	FACETS	0.973	0.84	1	0.973	0.84	1	CLONAL	1	TRUE	1	0.190530429333638	2		544	669	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339707	70339707	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	57	294	0	ENST00000374080.3:c.376C>G	p.Leu126Val	p.L126V	ENST00000374080		126	Ctc/Gtc	3/45	1	1	FACETS	0.765	0.659	0.878	1	0.969	1	SUBCLONAL	2	TRUE	0	0.190530429333638	1		294	354	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964909	15964913	+	missense_variant	Missense_Mutation	ONP	GAATG	GAATG	AAATA	novel	NA	P-0061305-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	63	642	0	ENST00000268712.3:c.5683_5687delinsTATTT	p.His1895_Ser1896delinsTyrPhe	p.H1895_S1896delinsYF	ENST00000268712	NM_006311.3	1895	CATTCt/TATTTt	37/46	1	2	FACETS	0.814	0.703	0.936	0.814	0.703	0.936	CLONAL	1	TRUE	1	0.190530429333638	2		642	812	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1555525429	NA	P-0061753-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	162	561	0	ENST00000269305.4:c.782+1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.386174882298478	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.386174882298478	1		561	558	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136245	2136256	+	inframe_deletion	In_Frame_Del	DEL	ACGGAGTTCCTG	ACGGAGTTCCTG	-	novel	NA	P-0061753-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	181	679	0	ENST00000219476.3:c.4718_4729del	p.Glu1573_Thr1576del	p.E1573_T1576del	ENST00000219476	NM_000548.3	1572	ACGGAGTTCCTG/-	37/42	0.386174882298478	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.386174882298478	1		679	661	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18943172	18943172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528873711	NA	P-0061753-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	180	368	0	ENST00000262803.5:c.154G>A	p.Gly52Ser	p.G52S	ENST00000262803	NM_002911.3	52	Ggc/Agc	1/24	0.386174882298478	1	FACETS	0.849	0.792	0.907	1	0.992	1	CLONAL	2	TRUE	0	0.386174882298478	1		368	443	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295754	1295754	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0061753-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	201	739	0				ENST00000310581	NM_198253.2	-/1132			0.386174882298478	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.386174882298478	1		739	716	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868505	117868513	+	inframe_deletion	In_Frame_Del	DEL	ATCAGGACT	ATCAGGACT	-	novel	NA	P-0061753-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	56	381	0	ENST00000297338.2:c.829_837del	p.Pro278_Ser280del	p.P278_S280del	ENST00000297338	NM_006265.2	277	AGTCCTGAT/-	8/14	1	2	FACETS	0.661	0.567	0.762	0.661	0.567	0.762	SUBCLONAL	1	TRUE	1	0.386174882298478	2		381	439	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0062008-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	30	485	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.645	0.517	0.79	0.645	0.517	0.79	SUBCLONAL	1	TRUE	1	0.13	2		485	716	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874263	155874263	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1557960039	NA	P-0062008-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	30	577	0	ENST00000368323.3:c.268A>G	p.Met90Val	p.M90V	ENST00000368323	NM_006912.5	90	Atg/Gtg	5/6	1	2	FACETS	0.637	0.512	0.781	0.637	0.512	0.781	SUBCLONAL	1	TRUE	1	0.13	2		577	724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514495	NA	P-0062008-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	50	602	0	ENST00000269305.4:c.542G>A	p.Arg181His	p.R181H	ENST00000269305	NM_001126112.2	181	cGc/cAc	5/11	1	2	FACETS	0.864	0.731	1	0.864	0.731	1	CLONAL	1	TRUE	1	0.13	2		602	890	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0062008-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	24	186	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.13	2		186	279	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062008-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	66	507	4	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.13	2		511	711	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106861	27106861	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062008-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	19	614	1	ENST00000324856.7:c.6472C>T	p.Arg2158Ter	p.R2158*	ENST00000324856	NM_006015.4	2158	Cga/Tga	20/20	1	2	FACETS	0.375	0.283	0.484	0.375	0.283	0.484	SUBCLONAL	1	TRUE	1	0.13	2		615	780	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130441	29130441	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062008-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	43	572	0	ENST00000328354.6:c.269del	p.Pro90LeufsTer20	p.P90Lfs*20	ENST00000328354	NM_007194.3	90	cCt/ct	2/15	1	2	FACETS	0.832	0.694	0.986	0.832	0.694	0.986	CLONAL	1	TRUE	1	0.13	2		572	795	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062008-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	50	662	1	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.899	0.76	1	0.899	0.76	1	CLONAL	1	TRUE	1	0.13	2		663	856	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655479	67655479	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs769948988	NA	P-0062008-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	22	463	0	ENST00000264010.4:c.1342C>T	p.Arg448Ter	p.R448*	ENST00000264010	NM_006565.3	448	Cga/Tga	7/12	1	2	FACETS	0.591	0.456	0.748	0.591	0.456	0.748	SUBCLONAL	1	TRUE	1	0.13	2		463	573	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343543	343543	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150504240	NA	P-0062008-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	38	586	0	ENST00000262320.3:c.2131C>T	p.Arg711Cys	p.R711C	ENST00000262320	NM_003502.3	711	Cgc/Tgc	8/11	1	2	FACETS	0.775	0.639	0.929	0.775	0.639	0.929	CLONAL	1	TRUE	1	0.13	2		586	754	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186702	11186702	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062008-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	37	485	0	ENST00000361445.4:c.6503G>T	p.Arg2168Met	p.R2168M	ENST00000361445	NM_004958.3	2168	aGg/aTg	46/58	1	2	FACETS	0.82	0.674	0.984	0.82	0.674	0.984	CLONAL	1	TRUE	1	0.13	2		485	694	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26974597	26974597	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062008-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	27	384	0	ENST00000381527.3:c.941A>C	p.Lys314Thr	p.K314T	ENST00000381527	NM_001260.1	314	aAg/aCg	10/13	1	2	FACETS	0.968	0.77	1	0.968	0.77	1	CLONAL	1	TRUE	1	0.13	2		384	429	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343542	343542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769430411	NA	P-0062008-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	42	556	1	ENST00000262320.3:c.2132G>A	p.Arg711His	p.R711H	ENST00000262320	NM_003502.3	711	cGc/cAc	8/11	1	2	FACETS	0.891	0.742	1	0.891	0.742	1	CLONAL	1	TRUE	1	0.13	2		557	725	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827478	72827478	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs571460174	NA	P-0062008-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	44	520	0	ENST00000268489.5:c.9103G>A	p.Ala3035Thr	p.A3035T	ENST00000268489	NM_006885.3	3035	Gct/Act	9/10	1	2	FACETS	0.944	0.79	1	0.944	0.79	1	CLONAL	1	TRUE	1	0.13	2		520	717	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152049	11152049	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558017726	NA	P-0062008-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	46	574	0	ENST00000358026.2:c.4333C>T	p.Arg1445Cys	p.R1445C	ENST00000358026	NM_001128849.1	1445	Cgc/Tgc	31/36	1	2	FACETS	0.919	0.772	1	0.919	0.772	1	CLONAL	1	TRUE	1	0.13	2		574	770	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067254	37067254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61751644	NA	P-0062008-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	37	459	0	ENST00000231790.2:c.1165C>T	p.Arg389Trp	p.R389W	ENST00000231790	NM_000249.3	389	Cgg/Tgg	12/19	1	2	FACETS	0.864	0.71	1	0.864	0.71	1	CLONAL	1	TRUE	1	0.13	2		459	659	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933378	39933378	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062008-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	37	325	0	ENST00000378444.4:c.1221del	p.His409MetfsTer33	p.H409Mfs*33	ENST00000378444	NM_001123385.1	407	ccC/cc	4/15	1	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.13	1		325	430	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0062112-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1315	448	430	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.412952229787184	9	FACETS	1	0.955	1	0.502	0.477	0.526	CLONAL	3	TRUE	3	0.412952229787184	9		430	1763	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916640	178916666	+	inframe_deletion	In_Frame_Del	DEL	ACTGTGGGGCATCCACTTGATGCCCCC	ACTGTGGGGCATCCACTTGATGCCCCC	-	novel	NA	P-0062112-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	174	392	0	ENST00000263967.3:c.28_54del	p.Leu10_Pro18del	p.L10_P18del	ENST00000263967	NM_006218.2	9	gaACTGTGGGGCATCCACTTGATGCCCCCa/gaa	2/21	0.41183213621889	3	FACETS	0.911	0.844	0.98	0.911	0.844	0.98	CLONAL	2	TRUE	1	0.412952229787184	3		392	558	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561268	9561268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749763005	NA	P-0062112-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	179	535	0	ENST00000353224.5:c.514G>A	p.Val172Ile	p.V172I	ENST00000353224	NM_177990.2	172	Gta/Ata	4/10	0.41183213621889	3	FACETS	1	0.97	1	0.551	0.508	0.596	CLONAL	1	TRUE	1	0.412952229787184	3		535	949	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437763	110437763	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062112-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	158	499	0	ENST00000375856.3:c.638T>A	p.Leu213Gln	p.L213Q	ENST00000375856	NM_003749.2	213	cTg/cAg	1/2	0.412952229787184	3	FACETS	1	0.944	1	0.346	0.317	0.377	CLONAL	1	TRUE	0	0.412952229787184	3		499	889	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6262238	6262238	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0062112-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	148	496	0	ENST00000252674.7:c.276+1G>T		p.X92_splice	ENST00000252674	NM_005934.3	92			0.41183213621889	3	FACETS	0.964	0.88	1	0.482	0.44	0.526	CLONAL	1	TRUE	1	0.412952229787184	3		496	897	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540074	187540074	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs921535768	NA	P-0062213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	14	610	0	ENST00000441802.2:c.7666C>T	p.Arg2556Ter	p.R2556*	ENST00000441802	NM_005245.3	2556	Cga/Tga	10/27	1	2	FACETS	0.651	0.471	0.869	0.651	0.471	0.869	SUBCLONAL	1	TRUE	1	0.2	2		610	215	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412905	49412905	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519951	NA	P-0062213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	28	573	0	ENST00000418115.1:c.118G>A	p.Glu40Lys	p.E40K	ENST00000418115	NM_001664.2	40	Gag/Aag	2/5	1	2	FACETS	0.841	0.673	1	0.841	0.673	1	CLONAL	1	TRUE	1	0.2	2		573	333	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243920	41243920	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	17	679	0	ENST00000357654.3:c.3628G>C	p.Glu1210Gln	p.E1210Q	ENST00000357654	NM_007294.3	1210	Gag/Cag	10/23	1	2	FACETS	0.607	0.453	0.79	0.607	0.453	0.79	SUBCLONAL	1	TRUE	1	0.2	2		679	280	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982105	201982105	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0062213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	48	748	0	ENST00000359651.3:c.629C>G	p.Ser210Ter	p.S210*	ENST00000359651		210	tCa/tGa	5/8	1	2	FACETS	0.984	0.839	1	1	0.974	1	CLONAL	2	TRUE	1	0.2	2		748	244	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120467977	120467977	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1131691315	NA	P-0062213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	32	699	0	ENST00000256646.2:c.4462G>C	p.Glu1488Gln	p.E1488Q	ENST00000256646	NM_024408.3	1488	Gag/Cag	25/34	1	2	FACETS	0.93	0.756	1	0.93	0.756	1	CLONAL	1	TRUE	1	0.2	2		699	344	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980413	201980413	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	35	724	0	ENST00000359651.3:c.149C>A	p.Ser50Ter	p.S50*	ENST00000359651		50	tCa/tAa	1/8	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.2	2		724	294	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778843	3778843	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	15	800	0	ENST00000262367.5:c.6205G>T	p.Asp2069Tyr	p.D2069Y	ENST00000262367	NM_004380.2	2069	Gac/Tac	31/31	1	2	FACETS	0.781	0.573	1	0.781	0.573	1	CLONAL	1	TRUE	1	0.2	2		800	192	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243008	41243008	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	22	516	0	ENST00000357654.3:c.4138G>C	p.Glu1380Gln	p.E1380Q	ENST00000357654	NM_007294.3	1380	Gaa/Caa	11/23	1	2	FACETS	0.677	0.525	0.854	0.677	0.525	0.854	SUBCLONAL	1	TRUE	1	0.2	2		516	325	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627209	12627209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	18	525	0	ENST00000251849.4:c.1507G>A	p.Glu503Lys	p.E503K	ENST00000251849	NM_002880.3	503	Gaa/Aaa	14/17	1	2	FACETS	0.747	0.563	0.963	0.747	0.563	0.963	CLONAL	1	TRUE	1	0.2	2		525	241	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412965	49412965	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	25	623	0	ENST00000418115.1:c.58T>G	p.Cys20Gly	p.C20G	ENST00000418115	NM_001664.2	20	Tgc/Ggc	2/5	1	2	FACETS	0.702	0.553	0.873	0.702	0.553	0.873	SUBCLONAL	1	TRUE	1	0.2	2		623	356	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171560	32171560	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	17	585	0	ENST00000375023.3:c.3218G>C	p.Cys1073Ser	p.C1073S	ENST00000375023	NM_004557.3	1073	tGc/tCc	20/30	0.253936097367347	4	FACETS	0.803	0.6	1	0.402	0.3	0.522	CLONAL	1	TRUE	2	0.2	4		585	254	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201874	152201874	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	30	418	0	ENST00000206249.3:c.728G>C	p.Arg243Pro	p.R243P	ENST00000206249	NM_000125.3	243	cGt/cCt	3/8	0.177545536719625	3	FACETS	1	0.851	1	0.532	0.43	0.648	CLONAL	1	TRUE	1	0.2	3		418	310	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542193	187542194	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0062213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	17	662	0	ENST00000441802.2:c.5546dup	p.His1850AlafsTer2	p.H1850Afs*2	ENST00000441802	NM_005245.3	1849	gtg/gtTg	10/27	1	2	FACETS	0.939	0.704	1	0.939	0.704	1	CLONAL	1	TRUE	1	0.2	2		662	181	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0062302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	2044	505	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	0.586376338206575	19	FACETS	0.975	0.963	0.988			1	CLONAL	16	TRUE	NA	0.586376338206575	19		505	2673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0062302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	581	712	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.586376338206575	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.586376338206575	2		712	930	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023145	27023162	+	inframe_deletion	In_Frame_Del	DEL	GCGGCGGCGGAGCCGGCA	GCGGCGGCGGAGCCGGCA	-	rs749452696	NA	P-0062302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	234	503	0	ENST00000324856.7:c.261_278del	p.Ala88_Gly93del	p.A88_G93del	ENST00000324856	NM_006015.4	84	gGCGGCGGCGGAGCCGGCAgc/ggc	1/20	0.586376338206575	3	FACETS	1	0.992	1	0.723	0.677	0.769	CLONAL	1	TRUE	1	0.586376338206575	3		503	714	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987066	36987066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1325836054	NA	P-0062302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	165	461	0	ENST00000354822.5:c.623G>A	p.Arg208Gln	p.R208Q	ENST00000354822	NM_001079668.2	208	cGa/cAa	3/3	1	2	FACETS	0.938	0.865	1	0.938	0.865	1	CLONAL	1	TRUE	1	0.586376338206575	2		461	600	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860749	3860749	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	149	436	0	ENST00000262367.5:c.830G>T	p.Gly277Val	p.G277V	ENST00000262367	NM_004380.2	277	gGa/gTa	3/31	0.207361234153026	1	FACETS	0.592	0.543	0.643	0.592	0.543	0.643	INDETERMINATE	1	TRUE	0	0.586376338206575	1		436	607	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288750	15288750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	188	434	0	ENST00000263388.2:c.3989C>T	p.Ser1330Leu	p.S1330L	ENST00000263388	NM_000435.2	1330	tCg/tTg	24/33	0.586376338206575	2	FACETS	1	0.981	1	0.577	0.536	0.618	CLONAL	1	TRUE	0	0.586376338206575	2		434	556	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538364	9538364	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	294	409	0	ENST00000353224.5:c.1634T>A	p.Ile545Lys	p.I545K	ENST00000353224	NM_177990.2	545	aTa/aAa	7/10	0.378457645622724	3	FACETS	0.907	0.859	0.955	0.907	0.859	0.955	CLONAL	2	TRUE	1	0.586376338206575	3		409	715	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146574	55146574	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	189	457	0	ENST00000257290.5:c.2248G>C	p.Glu750Gln	p.E750Q	ENST00000257290	NM_006206.4	750	Gag/Cag	16/23	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.586376338206575	2		457	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0062315-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	30	490	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.389693175119886	1	FACETS	0.377	0.304	0.459	0.377	0.304	0.459	SUBCLONAL	1	TRUE	0	0.389693175119886	1		490	329	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0062315-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	132	430	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.389693175119886	3	FACETS	0.916	0.838	0.996	0.916	0.838	0.996	CLONAL	2	TRUE	1	0.389693175119886	3		430	442	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306996	65306996	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs375979659	NA	P-0062315-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	113	560	2	ENST00000342505.4:c.2581C>A	p.Pro861Thr	p.P861T	ENST00000342505	NM_002227.2	861	Cca/Aca	19/25	0.389693175119886	3	FACETS	1	0.982	1	0.703	0.636	0.773	CLONAL	1	TRUE	1	0.389693175119886	3		562	493	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976872	55976872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs551579207	NA	P-0062315-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	25	444	0	ENST00000263923.4:c.1040G>A	p.Arg347His	p.R347H	ENST00000263923	NM_002253.2	347	cGt/cAt	8/30	0.370440255599221	3	FACETS	0.343	0.27	0.428	0.171	0.135	0.214	SUBCLONAL	1	TRUE	1	0.389693175119886	3		444	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577512	7577512	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062315-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	26	500	0	ENST00000269305.4:c.769C>G	p.Leu257Val	p.L257V	ENST00000269305	NM_001126112.2	257	Ctg/Gtg	7/11	0.389693175119886	1	FACETS	0.442	0.351	0.545	0.442	0.351	0.545	SUBCLONAL	1	TRUE	0	0.389693175119886	1		500	243	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58725266	58725266	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062315-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	28	441	0	ENST00000305921.3:c.840C>G	p.Ser280Arg	p.S280R	ENST00000305921	NM_003620.3	280	agC/agG	4/6	0.370440255599221	3	FACETS	0.379	0.302	0.467	0.19	0.151	0.234	SUBCLONAL	1	TRUE	1	0.389693175119886	3		441	453	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062358-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	23	82	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.257502581430948	2		82	145	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0062358-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	8	689	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.173960239846263	4	FACETS	0.236	0.151	0.347	0.118	0.075	0.174	SUBCLONAL	1	TRUE	2	0.257502581430948	4		689	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0062358-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	118	782	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.257502581430948	5	FACETS	0.974	0.891	1	0.974	0.891	1	CLONAL	4	TRUE	1	0.257502581430948	5		782	326	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234460	41234460	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555584070	NA	P-0062358-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	17	608	0	ENST00000357654.3:c.4318G>C	p.Glu1440Gln	p.E1440Q	ENST00000357654	NM_007294.3	1440	Gag/Cag	12/23	0.173960239846263	4	FACETS	0.667	0.498	0.867	0.333	0.249	0.434	SUBCLONAL	1	TRUE	2	0.257502581430948	4		608	249	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211705	36211705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758411036	NA	P-0062358-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	16	778	0	ENST00000222270.7:c.1456C>T	p.Arg486Trp	p.R486W	ENST00000222270	NM_014727.1	486	Cgg/Tgg	3/37	0.0957822713814527	4	FACETS	0.556	0.411	0.73	0.278	0.205	0.365	INDETERMINATE	1	TRUE	2	0.257502581430948	4		778	281	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916942	178916944	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	novel	NA	P-0062358-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	19	427	0	ENST00000263967.3:c.330_332del	p.Lys111del	p.K111del	ENST00000263967	NM_006218.2	110	gAAAag/gag	2/21	0.173960239846263	4	FACETS	1	0.909	1	0.731	0.561	0.925	CLONAL	1	TRUE	2	0.257502581430948	4		427	127	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28885793	28885793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062358-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	13	464	0	ENST00000282397.4:c.3569C>T	p.Ser1190Phe	p.S1190F	ENST00000282397	NM_002019.4	1190	tCt/tTt	27/30	0.257502581430948	1	FACETS	1	0.723	1	1	0.723	1	CLONAL	1	TRUE	0	0.257502581430948	1		464	88	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288798	15288798	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062358-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	35	537	1	ENST00000263388.2:c.3941C>A	p.Ala1314Asp	p.A1314D	ENST00000263388	NM_000435.2	1314	gCc/gAc	24/33	0.0957822713814527	4	FACETS	0.784	0.648	0.934	0.784	0.648	0.934	INDETERMINATE	2	TRUE	2	0.257502581430948	4		538	218	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268455	198268455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062358-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	15	532	0	ENST00000335508.6:c.1573G>A	p.Glu525Lys	p.E525K	ENST00000335508	NM_012433.2	525	Gaa/Aaa	12/25	1	2	FACETS	0.728	0.535	0.957	0.728	0.535	0.957	CLONAL	1	TRUE	1	0.257502581430948	2		532	160	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104708	209104708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062358-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	13	566	0	ENST00000345146.2:c.870G>A	p.Met290Ile	p.M290I	ENST00000345146	NM_005896.2	290	atG/atA	8/10	1	2	FACETS	0.399	0.284	0.539	0.399	0.284	0.539	SUBCLONAL	1	TRUE	1	0.257502581430948	2		566	253	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620469	52620469	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35102895	NA	P-0062358-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	14	537	0	ENST00000394830.3:c.3284G>A	p.Arg1095Gln	p.R1095Q	ENST00000394830	NM_018313.4	1095	cGa/cAa	21/30	0.0957822713814527	4	FACETS	0.567	0.41	0.758	0.284	0.205	0.379	INDETERMINATE	1	TRUE	2	0.257502581430948	4		537	241	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342713	70342713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062358-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	30	270	1	ENST00000374080.3:c.1474G>A	p.Asp492Asn	p.D492N	ENST00000374080		492	Gat/Aat	10/45	0.114782478406931	2	FACETS	0.94	0.771	1			1	INDETERMINATE	2	TRUE	NA	0.257502581430948	2		271	124	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0062470-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	329	721	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.753246062980127	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.753246062980127	1		723	473	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70441195	70441195	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062470-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	80	294	0	ENST00000373644.4:c.4864C>T	p.Arg1622Ter	p.R1622*	ENST00000373644	NM_030625.2	1622	Cga/Tga	9/12	0.753246062980127	1	FACETS	0.92	0.838	1	0.92	0.838	1	CLONAL	1	TRUE	0	0.753246062980127	1		294	144	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913689	32913689	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062470-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	60	379	0	ENST00000380152.3:c.5197T>G	p.Ser1733Ala	p.S1733A	ENST00000380152		1733	Tcc/Gcc	11/27	0.222713504468027	1	FACETS	0.525	0.461	0.593	0.525	0.461	0.593	INDETERMINATE	1	TRUE	0	0.753246062980127	1		379	189	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502222	186502222	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062470-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	250	415	0	ENST00000323963.5:c.31G>C	p.Glu11Gln	p.E11Q	ENST00000323963		11	Gaa/Caa	2/11	0.753246062980127	3	FACETS	0.969	0.908	1			1	CLONAL	1	TRUE	NA	0.753246062980127	3		415	943	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751032	128751032	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062470-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	617	509	0	ENST00000377970.2:c.569G>C	p.Ser190Thr	p.S190T	ENST00000377970	NM_002467.4	190	aGc/aCc	2/3	0.753246062980127	5	FACETS	0.93	0.898	0.962			1	CLONAL	3	TRUE	NA	0.753246062980127	5		509	1251	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460472	8460472	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062470-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	173	432	0	ENST00000356435.5:c.3814G>T	p.Gly1272Cys	p.G1272C	ENST00000356435		1272	Ggt/Tgt	22/35	0.753246062980127	3	FACETS	1	0.964	1	0.534	0.494	0.575	CLONAL	1	TRUE	1	0.753246062980127	3		432	592	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242486	+	inframe_deletion	In_Frame_Del	DEL	TTAAGAGAAGCAACATCT	TTAAGAGAAGCAACATCT	-	rs121913440	NA	P-0062551-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	231	437	0	ENST00000275493.2:c.2239_2256del	p.Leu747_Ser752del	p.L747_S752del	ENST00000275493	NM_005228.3	747	TTAAGAGAAGCAACATCT/-	19/28	0.695514371857925	4	FACETS	0.996	0.947	1	0.996	0.947	1	CLONAL	3	TRUE	1	0.695514371857925	4		437	377	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0062607-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	79	430	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.22193927086249	2		430	677	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0062607-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	88	628	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.22193927086249	2		628	665	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218089	108218089	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587779874	NA	P-0062607-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	65	110	0	ENST00000278616.4:c.8668C>G	p.Leu2890Val	p.L2890V	ENST00000278616	NM_000051.3	2890	Cta/Gta	59/63	0.22193927086249	6	FACETS	0.896	0.787	1			1	CLONAL	4	TRUE	NA	0.22193927086249	6		110	236	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775433	39775433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168532464	NA	P-0062607-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	40	659	3	ENST00000288319.7:c.587G>A	p.Arg196Lys	p.R196K	ENST00000288319	NM_182918.3	196	aGa/aAa	4/10	1	2	FACETS	0.569	0.472	0.678	0.569	0.472	0.678	SUBCLONAL	1	TRUE	1	0.22193927086249	2		662	633	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715684	30715684	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062607-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	70	550	0	ENST00000295754.5:c.1342T>C	p.Tyr448His	p.Y448H	ENST00000295754	NM_003242.5	448	Tac/Cac	5/7	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.22193927086249	2		550	625	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271333	26271333	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs548529624	NA	P-0062607-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	55	838	7	ENST00000305910.3:c.280C>T	p.Gln94Ter	p.Q94*	ENST00000305910	NM_003534.2	94	Cag/Tag	1/1	1	2	FACETS	0.523	0.446	0.608	0.523	0.446	0.608	SUBCLONAL	1	TRUE	1	0.22193927086249	2		845	947	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89881007	89881008	+	frameshift_variant	Frame_Shift_Ins	INS	CA	CA	ATTCTAG	novel	NA	P-0062607-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	100	307	0	ENST00000389301.3:c.203_204delinsCTAGAAT	p.Leu68ProfsTer12	p.L68Pfs*12	ENST00000389301	NM_000135.2	68	cTG/cCTAGAAT	3/43	0.22193927086249	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.22193927086249	1		307	546	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0062673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	41	459	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.815	0.682	0.962	1	0.961	1	CLONAL	2	TRUE	1	0.163889326768456	2		459	307	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101909971	101909971	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	43	438	0	ENST00000374994.4:c.1291C>A	p.Leu431Ile	p.L431I	ENST00000374994	NM_004612.2	431	Ctt/Att	8/9	0.163889326768456	2	FACETS	1	0.952	1	0.705	0.592	0.831	CLONAL	1	TRUE	0	0.163889326768456	2		438	372	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584607	48584607	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	62	509	0	ENST00000342988.3:c.781del	p.His261IlefsTer75	p.H261Ifs*75	ENST00000342988	NM_005359.5	260	taC/ta	6/12	0.163889326768456	0	FACETS	0.97	0.838	1			1	CLONAL	1	TRUE	0	0.163889326768456	0		509	652	SUCCESS
ATM	472	MSKCC	GRCh37	11	108213994	108213994	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794239	NA	P-0062673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	48	450	0	ENST00000278616.4:c.8314G>A	p.Gly2772Arg	p.G2772R	ENST00000278616	NM_000051.3	2772	Gga/Aga	57/63	1	2	FACETS	0.991	0.837	1	0.991	0.837	1	CLONAL	1	TRUE	1	0.163889326768456	2		450	591	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554427	63554427	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	113	692	0	ENST00000307078.5:c.312C>A	p.Cys104Ter	p.C104*	ENST00000307078	NM_004655.3	104	tgC/tgA	2/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.163889326768456	2		692	1023	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101909977	101909981	+	missense_variant	Missense_Mutation	ONP	CCTTC	CCTTC	ACTTT	novel	NA	P-0062673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	45	469	0	ENST00000374994.4:c.1297_1301delinsACTTT	p.Pro433_Ser434delinsThrPhe	p.P433_S434delinsTF	ENST00000374994	NM_004612.2	433	CCTTCt/ACTTTt	8/9	0.163889326768456	2	FACETS	1	0.95	1	0.675	0.568	0.792	CLONAL	1	TRUE	0	0.163889326768456	2		469	407	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504614	103504614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767355056	NA	P-0062674-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	42	356	0	ENST00000355739.4:c.235G>A	p.Asp79Asn	p.D79N	ENST00000355739	NM_000123.3	79	Gat/Aat	2/15	0.222343309109701	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.24	1		356	270	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003812	45003812	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0062674-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	25	559	0	ENST00000558401.1:c.67+1G>A		p.X23_splice	ENST00000558401	NM_004048.2	23			1	2	FACETS	0.41	0.322	0.512	0.41	0.322	0.512	SUBCLONAL	1	TRUE	1	0.24	2		559	508	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856142	151856142	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062674-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	29	475	0	ENST00000262189.6:c.11476C>T	p.Gln3826Ter	p.Q3826*	ENST00000262189	NM_170606.2	3826	Caa/Taa	44/59	0.208484214497176	2	FACETS	0.735	0.59	0.898	0.367	0.295	0.449	SUBCLONAL	1	TRUE	0	0.24	2		475	329	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262827	46262827	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062674-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	33	422	0	ENST00000371998.3:c.1000C>T	p.Arg334Ter	p.R334*	ENST00000371998		334	Cga/Tga	10/23	1	2	FACETS	0.859	0.702	1	0.859	0.702	1	CLONAL	1	TRUE	1	0.24	2		422	320	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762097	43762097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs975220740	NA	P-0062674-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	16	457	0	ENST00000382044.4:c.1348C>T	p.Pro450Ser	p.P450S	ENST00000382044	NM_001141980.1	450	Cct/Tct	11/28	1	2	FACETS	0.421	0.31	0.553	0.421	0.31	0.553	SUBCLONAL	1	TRUE	1	0.24	2		457	317	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483858	88483858	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062674-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	41	447	0	ENST00000360948.2:c.1712T>C	p.Val571Ala	p.V571A	ENST00000360948	NM_001012338.2	571	gTg/gCg	14/19	1	2	FACETS	0.996	0.832	1	0.996	0.832	1	CLONAL	1	TRUE	1	0.24	2		447	343	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33689961	33689961	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062674-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	31	490	1	ENST00000308377.4:c.866C>A	p.Pro289His	p.P289H	ENST00000308377	NM_152270.3	289	cCc/cAc	2/5	1	2	FACETS	0.76	0.615	0.923	0.76	0.615	0.923	CLONAL	1	TRUE	1	0.24	2		491	340	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727929	41727929	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062674-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	55	451	0	ENST00000301178.4:c.554G>T	p.Gly185Val	p.G185V	ENST00000301178	NM_021913.4	185	gGt/gTt	4/20	1	2	FACETS	0.988	0.846	1	0.988	0.846	1	CLONAL	1	TRUE	1	0.24	2		451	464	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902533	1902533	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062674-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	50	542	0	ENST00000382891.5:c.152C>A	p.Ala51Asp	p.A51D	ENST00000382891	NM_133335.3	51	gCc/gAc	2/22	1	2	FACETS	0.976	0.83	1	0.976	0.83	1	CLONAL	1	TRUE	1	0.24	2		542	427	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0062675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	23	615	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.302	0.236	0.377	0.302	0.236	0.377	SUBCLONAL	1	TRUE	1	0.646156447447718	2		615	236	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0062675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	149	459	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.646156447447718	3	FACETS	1	0.982	1	0.615	0.566	0.666	CLONAL	1	TRUE	1	0.646156447447718	3		459	496	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0062675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	122	380	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.886	0.808	0.968	0.886	0.808	0.968	CLONAL	1	TRUE	1	0.646156447447718	2		380	426	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094455	27094456	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0062675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	287	586	0	ENST00000324856.7:c.3164_3165del	p.Tyr1055CysfsTer49	p.Y1055Cfs*49	ENST00000324856	NM_006015.4	1055	TAt/t	11/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.646156447447718	2		586	879	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576754	67576754	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0062675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	95	319	0	ENST00000274335.5:c.837-1G>A		p.X279_splice	ENST00000274335		279			1	2	FACETS	0.664	0.594	0.737	0.664	0.594	0.737	SUBCLONAL	1	TRUE	1	0.646156447447718	2		319	443	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31472258	31472258	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	254	599	0	ENST00000344624.3:c.2153A>G	p.Glu718Gly	p.E718G	ENST00000344624		718	gAg/gGg	14/33	1	2	FACETS	0.939	0.882	0.998	0.939	0.882	0.998	CLONAL	1	TRUE	1	0.646156447447718	2		599	837	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158404	26158404	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	206	518	0	ENST00000289316.2:c.7G>T	p.Glu3Ter	p.E3*	ENST00000289316	NM_138720.2	3	Gaa/Taa	1/2	0.646156447447718	3	FACETS	0.873	0.81	0.938	0.437	0.405	0.469	CLONAL	1	TRUE	1	0.646156447447718	3		518	966	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350160	81350160	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	137	290	0	ENST00000222390.5:c.1172G>T	p.Cys391Phe	p.C391F	ENST00000222390	NM_000601.4	391	tGt/tTt	10/18	1	2	FACETS	0.964	0.884	1	0.964	0.884	1	CLONAL	1	TRUE	1	0.646156447447718	2		290	440	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0062677-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	305	443	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.926	0.875	0.979	0.926	0.875	0.979	CLONAL	1	TRUE	1	0.669141268441947	2		443	984	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0062677-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	677	634	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.622693537350139	2	FACETS	0.948	0.922	0.974	0.948	0.922	0.974	CLONAL	2	TRUE	0	0.669141268441947	2		634	1067	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994595	73994602	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GGAGCCCT	GGAGCCCT	-	novel	NA	P-0062677-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	195	544	1	ENST00000318443.5:c.83_90del		p.X28_splice	ENST00000318443	NM_001024736.1	28		3/10	0.302967871932867	1	FACETS	0.446	0.413	0.481	0.446	0.413	0.481	INDETERMINATE	1	TRUE	0	0.669141268441947	1		545	869	SUCCESS
APC	324	MSKCC	GRCh37	5	112173600	112173600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062677-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	146	512	0	ENST00000257430.4:c.2309C>T	p.Ser770Leu	p.S770L	ENST00000257430	NM_000038.5	770	tCa/tTa	16/16	0.387730152127981	1	FACETS	0.381	0.348	0.416	0.381	0.348	0.416	INDETERMINATE	1	TRUE	0	0.669141268441947	1		512	762	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0062678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	89	630	7	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.707	0.629	0.79	0.707	0.629	0.79	SUBCLONAL	1	TRUE	1	0.498697231743222	2		637	505	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831971	72831971	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	146	493	0	ENST00000268489.5:c.4610del	p.Lys1537SerfsTer3	p.K1537Sfs*3	ENST00000268489	NM_006885.3	1537	aAg/ag	9/10	1	2	FACETS	0.957	0.877	1	0.957	0.877	1	CLONAL	1	TRUE	1	0.498697231743222	2		493	612	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38148017	38148017	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	123	390	0	ENST00000317025.8:c.3094del	p.Ser1032ValfsTer20	p.S1032Vfs*20	ENST00000317025	NM_023034.1	1032	Agt/gt	17/24	1	2	FACETS	0.962	0.874	1	0.962	0.874	1	CLONAL	1	TRUE	1	0.498697231743222	2		390	513	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139026	37139027	+	frameshift_variant	Frame_Shift_Ins	INS	GC	GC	CCCCGAGCCGGTGCCGAG	novel	NA	P-0062678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	125	587	0	ENST00000373509.5:c.366_367delinsCCCCGAGCCGGTGCCGAG	p.Arg122SerfsTer92	p.R122Sfs*92	ENST00000373509	NM_002648.3	122	agGCcc/agCCCCGAGCCGGTGCCGAGcc	4/6	1	2	FACETS	0.8	0.725	0.877	0.8	0.725	0.877	SUBCLONAL	1	TRUE	1	0.498697231743222	2		587	627	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976658	90976658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	46	340	0	ENST00000265433.3:c.974C>T	p.Pro325Leu	p.P325L	ENST00000265433	NM_002485.4	325	cCt/cTt	8/16	NA	2	FACETS	0.468	0.396	0.546			1	INDETERMINATE	1	TRUE	NA	0.655661039467422	2		340	300	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881415	48881415	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0062679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	12	290	0	ENST00000267163.4:c.138-1G>A		p.X46_splice	ENST00000267163	NM_000321.2	46			0.662672578186463	2	FACETS	0.172	0.12	0.235	0.086	0.06	0.118	SUBCLONAL	1	TRUE	0	0.655661039467422	2		290	213	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578385	7578385	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1567552584	NA	P-0062679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	752	617	0	ENST00000269305.4:c.545del	p.Cys182SerfsTer65	p.C182Sfs*65	ENST00000269305	NM_001126112.2	182	tGc/tc	5/11	0.662672578186463	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.655661039467422	3		617	940	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47594619	47594619	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	146	558	0	ENST00000430070.2:c.1468G>C	p.Gly490Arg	p.G490R	ENST00000430070	NM_018095.4	490	Ggg/Cgg	4/4	0.662672578186463	3	FACETS	0.741	0.677	0.808	0.371	0.338	0.404	SUBCLONAL	1	TRUE	1	0.655661039467422	3		558	798	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625305	69625305	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	69	590	0	ENST00000334134.2:c.488C>T	p.Pro163Leu	p.P163L	ENST00000334134	NM_005247.2	163	cCc/cTc	3/3	0.662672578186463	4	FACETS	0.335	0.29	0.383	0.112	0.096	0.128	SUBCLONAL	1	TRUE	1	0.655661039467422	4		590	1041	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636269	73636269	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	76	619	0	ENST00000377687.4:c.532C>A	p.Pro178Thr	p.P178T	ENST00000377687	NM_001730.3	178	Cct/Act	2/4	0.662672578186463	3	FACETS	0.387	0.339	0.439	0.129	0.113	0.147	SUBCLONAL	1	TRUE	0	0.655661039467422	3		619	795	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300143	15300143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	68	585	0	ENST00000263388.2:c.1133C>T	p.Thr378Ile	p.T378I	ENST00000263388	NM_000435.2	378	aCc/aTc	7/33	0.662672578186463	3	FACETS	0.284	0.246	0.326	0.142	0.123	0.163	SUBCLONAL	1	TRUE	1	0.655661039467422	3		585	969	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920649	127920649	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	78	292	0	ENST00000373547.4:c.250G>C	p.Asp84His	p.D84H	ENST00000373547	NM_002721.4	84	Gac/Cac	4/7	0.662672578186463	3	FACETS	1	0.92	1	0.523	0.464	0.585	CLONAL	1	TRUE	1	0.655661039467422	3		292	302	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0062680-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	171	374	0	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.423723294840187	2		374	728	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0062680-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	280	482	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.423723294840187	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.423723294840187	1		482	761	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0062680-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	47	399	0	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	1	2	FACETS	0.251	0.211	0.296	0.251	0.211	0.296	SUBCLONAL	1	TRUE	1	0.423723294840187	2		399	883	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213417	39213417	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062680-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	110	365	0	ENST00000402219.2:c.3550C>A	p.Pro1184Thr	p.P1184T	ENST00000402219	NM_005633.3	1184	Cct/Act	23/23	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.423723294840187	2		365	516	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513282	44513287	+	inframe_deletion	In_Frame_Del	DEL	CCACCG	CCACCG	-	rs745888281	NA	P-0062681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	14	417	1	ENST00000291552.4:c.648_653del	p.Gly222_Gly223del	p.G222_G223del	ENST00000291552	NM_006758.2	216	ggCGGTGGt/ggt	8/8	1	2	FACETS	0.184	0.132	0.247	0.184	0.132	0.247	SUBCLONAL	1	TRUE	1	0.22	2		418	693	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829647	72829647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750069782	NA	P-0062681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	63	415	0	ENST00000268489.5:c.6934C>T	p.Arg2312Trp	p.R2312W	ENST00000268489	NM_006885.3	2312	Cgg/Tgg	9/10	1	2	FACETS	0.924	0.799	1	0.924	0.799	1	CLONAL	1	TRUE	1	0.22	2		415	620	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174889	56174889	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	43	357	0	ENST00000399503.3:c.2048T>G	p.Val683Gly	p.V683G	ENST00000399503	NM_005921.1	683	gTt/gGt	11/20	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.22	2		357	368	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148504783	148504783	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs886990256	NA	P-0062681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	51	275	0	ENST00000320356.2:c.2211T>A	p.Asp737Glu	p.D737E	ENST00000320356	NM_004456.4	737	gaT/gaA	20/20	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.22	2		275	453	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020388	123020388	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	32	285	0	ENST00000355640.3:c.876A>C	p.Leu292Phe	p.L292F	ENST00000355640		292	ttA/ttC	2/7	1	2	FACETS	0.906	0.737	1	0.906	0.737	1	CLONAL	1	TRUE	1	0.22	2		285	321	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0062682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	98	459	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.893	0.799	0.992	0.893	0.799	0.992	CLONAL	1	TRUE	1	0.404180072380483	2		459	543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0062682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	167	352	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.368277869189667	1	FACETS	0.957	0.882	1	0.957	0.882	1	CLONAL	1	TRUE	0	0.404180072380483	1		353	689	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0062682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	147	596	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.855	0.781	0.932	0.855	0.781	0.932	CLONAL	1	TRUE	1	0.404180072380483	2		596	851	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0062682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	272	378	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.375089530451093	2	FACETS	0.861	0.811	0.911	0.861	0.811	0.911	CLONAL	2	TRUE	0	0.404180072380483	2		378	782	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777991	3777991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771546273	NA	P-0062682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	215	592	0	ENST00000262367.5:c.7057C>T	p.Arg2353Trp	p.R2353W	ENST00000262367	NM_004380.2	2353	Cgg/Tgg	31/31	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.404180072380483	2		592	1015	SUCCESS
APC	324	MSKCC	GRCh37	5	112175761	112175761	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	162	458	0	ENST00000257430.4:c.4473del	p.Phe1491LeufsTer16	p.F1491Lfs*16	ENST00000257430	NM_000038.5	1490	caT/ca	16/16	1	2	FACETS	0.925	0.849	1	0.925	0.849	1	CLONAL	1	TRUE	1	0.404180072380483	2		458	867	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	134	82	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.98	0.901	1	0.98	0.901	1	CLONAL	1	TRUE	1	0.744804452411004	2		82	367	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113296	209113296	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs73070954	NA	P-0062705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	166	479	0	ENST00000345146.2:c.211G>A	p.Val71Ile	p.V71I	ENST00000345146	NM_005896.2	71	Gtc/Atc	4/10	1	2	FACETS	0.504	0.463	0.547	0.504	0.463	0.547	SUBCLONAL	1	TRUE	1	0.744804452411004	2		479	884	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916924	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	288	325	0	ENST00000263967.3:c.311C>G	p.Pro104Arg	p.P104R	ENST00000263967	NM_006218.2	104	cCa/cGa	2/21	0.375950357491792	3	FACETS	1	0.989	1	0.592	0.558	0.627	INDETERMINATE	1	TRUE	1	0.744804452411004	3		325	896	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578349	212578349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1484791833	NA	P-0062705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	117	360	0	ENST00000342788.4:c.908C>T	p.Ser303Phe	p.S303F	ENST00000342788	NM_005235.2	303	tCt/tTt	8/28	1	2	FACETS	0.443	0.399	0.488	0.443	0.399	0.488	SUBCLONAL	1	TRUE	1	0.744804452411004	2		360	710	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486070	29486070	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs746824139	NA	P-0062705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	168	327	0	ENST00000356175.3:c.247C>T	p.Gln83Ter	p.Q83*	ENST00000356175	NM_000267.3	83	Cag/Tag	3/57	0.489193418103238	1	FACETS	0.519	0.479	0.559	0.519	0.479	0.559	SUBCLONAL	1	TRUE	0	0.744804452411004	1		327	546	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744465	41744465	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	55	490	0	ENST00000301178.4:c.1085G>C	p.Gly362Ala	p.G362A	ENST00000301178	NM_021913.4	362	gGt/gCt	8/20	0.375950357491792	3	FACETS	0.246	0.21	0.286	0.123	0.105	0.143	INDETERMINATE	1	TRUE	1	0.744804452411004	3		490	823	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425167	47425167	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	560	505	0	ENST00000404338.3:c.3235C>T	p.Gln1079Ter	p.Q1079*	ENST00000404338	NM_004491.4	1079	Cag/Tag	1/6	0.375950357491792	3	FACETS	0.946	0.912	0.979	0.946	0.912	0.979	INDETERMINATE	2	TRUE	1	0.744804452411004	3		505	1091	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249508	153249508	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	296	367	0	ENST00000281708.4:c.1270G>C	p.Val424Leu	p.V424L	ENST00000281708	NM_033632.3	424	Gta/Cta	9/12	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.744804452411004	2		367	791	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539695	187539695	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0062705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	176	464	0	ENST00000441802.2:c.8045C>G	p.Ser2682Ter	p.S2682*	ENST00000441802	NM_005245.3	2682	tCa/tGa	10/27	1	2	FACETS	0.586	0.541	0.634	0.586	0.541	0.634	SUBCLONAL	1	TRUE	1	0.744804452411004	2		464	806	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015707	112015707	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	166	455	0	ENST00000368678.4:c.1135G>T	p.Glu379Ter	p.E379*	ENST00000368678		379	Gag/Tag	11/13	1	2	FACETS	0.554	0.509	0.6	0.554	0.509	0.6	SUBCLONAL	1	TRUE	1	0.744804452411004	2		455	805	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843260	128843260	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	272	468	0	ENST00000249373.3:c.367C>T	p.Gln123Ter	p.Q123*	ENST00000249373	NM_005631.4	123	Cag/Tag	2/12	0.738747839315255	2	FACETS	1	0.993	1	0.662	0.627	0.696	CLONAL	1	TRUE	0	0.744804452411004	2		468	552	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937761	76937761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	55	396	0	ENST00000373344.5:c.2987C>T	p.Ser996Leu	p.S996L	ENST00000373344	NM_000489.3	996	tCa/tTa	9/35	1	2	FACETS	0.195	0.166	0.226	0.195	0.166	0.226	SUBCLONAL	1	TRUE	1	0.744804452411004	2		396	759	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0062706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	54	699	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	1	2	FACETS	0.404	0.343	0.471	0.404	0.343	0.471	SUBCLONAL	1	TRUE	1	0.21	2		699	1274	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243895	53243895	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	28	302	0	ENST00000375401.3:c.1098G>A	p.Trp366Ter	p.W366*	ENST00000375401	NM_004187.3	366	tgG/tgA	8/26	1	1	FACETS	0.476	0.38	0.587	0.476	0.38	0.587	SUBCLONAL	1	TRUE	0	0.21	1		302	501	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0062709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	86	459	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.359995088904322	2		459	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0062709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	142	754	6	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.307409062946979	1	FACETS	0.922	0.842	1	0.922	0.842	1	CLONAL	1	TRUE	0	0.359995088904322	1		760	702	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0062709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	170	667	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.359995088904322	1	FACETS	0.997	0.918	1	0.997	0.918	1	CLONAL	1	TRUE	0	0.359995088904322	1		667	777	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575132	48575132	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	109	463	0	ENST00000342988.3:c.326T>C	p.Leu109Pro	p.L109P	ENST00000342988	NM_005359.5	109	cTa/cCa	3/12	0.359995088904322	1	FACETS	0.983	0.887	1	0.983	0.887	1	CLONAL	1	TRUE	0	0.359995088904322	1		463	505	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099460	27099461	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0062709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	167	554	0	ENST00000324856.7:c.3698dup	p.Tyr1233Ter	p.Y1233*	ENST00000324856	NM_006015.4	1233	tat/tAat	14/20	1	2	FACETS	0.98	0.9	1	0.98	0.9	1	CLONAL	1	TRUE	1	0.359995088904322	2		554	947	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130342	11130342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	161	506	0	ENST00000358026.2:c.2581G>A	p.Glu861Lys	p.E861K	ENST00000358026	NM_001128849.1	861	Gag/Aag	18/36	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.359995088904322	2		506	858	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27183466	27183466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	78	471	0	ENST00000380036.4:c.1040G>A	p.Arg347Lys	p.R347K	ENST00000380036	NM_000459.3	347	aGg/aAg	8/23	0.359995088904322	1	FACETS	0.48	0.421	0.543	0.48	0.421	0.543	SUBCLONAL	1	TRUE	0	0.359995088904322	1		471	740	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	104	82	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.502632403616474	2		82	372	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0062710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	397	689	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.331541629065931	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.502632403616474	3		689	937	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0062710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	206	712	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.502632403616474	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.502632403616474	1		712	612	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455608	189455608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	231	598	0	ENST00000264731.3:c.142G>A	p.Glu48Lys	p.E48K	ENST00000264731	NM_003722.4	48	Gaa/Aaa	2/14	1	2	FACETS	0.898	0.837	0.96	0.898	0.837	0.96	CLONAL	1	TRUE	1	0.502632403616474	2		598	1024	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846300	156846300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150579345	NA	P-0062710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	182	699	0	ENST00000524377.1:c.1741G>A	p.Glu581Lys	p.E581K	ENST00000524377	NM_002529.3	581	Gag/Aag	14/17	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.502632403616474	2		699	664	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984417	201984417	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	248	590	1	ENST00000359651.3:c.1082G>A	p.Trp361Ter	p.W361*	ENST00000359651		361	tGg/tAg	8/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.502632403616474	2		591	870	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456507	189456507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	208	542	0	ENST00000264731.3:c.268G>A	p.Glu90Lys	p.E90K	ENST00000264731	NM_003722.4	90	Gag/Aag	3/14	1	2	FACETS	0.851	0.79	0.914	0.851	0.79	0.914	CLONAL	1	TRUE	1	0.502632403616474	2		542	973	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549716	187549716	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	179	625	0	ENST00000441802.2:c.4525C>T	p.Pro1509Ser	p.P1509S	ENST00000441802	NM_005245.3	1509	Cct/Tct	8/27	1	2	FACETS	0.835	0.77	0.902	0.835	0.77	0.902	CLONAL	1	TRUE	1	0.502632403616474	2		625	853	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0062711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	120	466	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.263691319169735	2	FACETS	1	0.985	1	0.73	0.663	0.8	CLONAL	1	TRUE	0	0.334647586807459	2		466	491	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0062711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	163	485	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.334647586807459	5	FACETS	0.789	0.724	0.857	0.526	0.483	0.572	SUBCLONAL	2	TRUE	2	0.334647586807459	5		485	927	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0062711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	292	721	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.268328263699242	3	FACETS	0.929	0.879	0.979	0.929	0.879	0.979	CLONAL	3	TRUE	0	0.334647586807459	3		723	731	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303248	11303248	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	267	579	0	ENST00000361445.4:c.1335G>T	p.Arg445Ser	p.R445S	ENST00000361445	NM_004958.3	445	agG/agT	9/58	0.237841737971631	3	FACETS	1	0.989	1	0.804	0.757	0.852	CLONAL	2	TRUE	0	0.334647586807459	3		579	772	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230459242	230459242	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	268	622	0	ENST00000391860.1:c.1159A>G	p.Ser387Gly	p.S387G	ENST00000391860	NM_001258311.1	387	Agc/Ggc	7/7	0.19744239915894	3	FACETS	0.908	0.857	0.96	0.908	0.857	0.96	INDETERMINATE	3	TRUE	0	0.334647586807459	3		622	686	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995309	15995309	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	91	538	0	ENST00000268712.3:c.2884C>G	p.Arg962Gly	p.R962G	ENST00000268712	NM_006311.3	962	Cga/Gga	22/46	0.268328263699242	3	FACETS	0.815	0.723	0.913	0.272	0.241	0.305	CLONAL	1	TRUE	0	0.334647586807459	3		538	779	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38173549	38173549	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	239	476	0	ENST00000317025.8:c.1867A>G	p.Ile623Val	p.I623V	ENST00000317025	NM_023034.1	623	Att/Gtt	10/24	0.250893648747881	3	FACETS	1	0.989	1	0.817	0.767	0.868	CLONAL	2	TRUE	0	0.334647586807459	3		476	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578518	7578518	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934875	NA	P-0062712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	352	588	0	ENST00000269305.4:c.412G>C	p.Ala138Pro	p.A138P	ENST00000269305	NM_001126112.2	138	Gcc/Ccc	5/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.667891530303624	NA		588	627	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519920	NA	P-0062712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	72	451	0	ENST00000397062.3:c.85G>C	p.Asp29His	p.D29H	ENST00000397062	NM_006164.4	29	Gat/Cat	2/5	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.667891530303624	NA		451	355	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971153	21971153	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	155	630	0	ENST00000304494.5:c.205del	p.Glu69SerfsTer77	p.E69Sfs*77	ENST00000304494	NM_000077.4	69	Gag/ag	2/3	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.667891530303624	NA		630	446	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77069962	77069962	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1221370333	NA	P-0062712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	100	561	0	ENST00000356341.3:c.578G>A	p.Arg193His	p.R193H	ENST00000356341	NM_002576.4	193	cGc/cAc	6/15	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.667891530303624	NA		561	615	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054408	13054408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	353	612	0	ENST00000316448.5:c.1018G>A	p.Glu340Lys	p.E340K	ENST00000316448	NM_004343.3	340	Gag/Aag	8/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.667891530303624	NA		612	974	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054611	13054611	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	264	728	0	ENST00000316448.5:c.1138G>A	p.Glu380Lys	p.E380K	ENST00000316448	NM_004343.3	380	Gag/Aag	9/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.667891530303624	NA		728	862	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489052	56489052	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	56	438	0	ENST00000267101.3:c.1871C>T	p.Pro624Leu	p.P624L	ENST00000267101	NM_001982.3	624	cCa/cTa	16/28	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.667891530303624	NA		438	338	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122938	2122938	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	104	570	0	ENST00000219476.3:c.2309T>C	p.Leu770Pro	p.L770P	ENST00000219476	NM_000548.3	770	cTg/cCg	21/42	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.667891530303624	NA		570	520	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984450	72984450	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	146	591	0	ENST00000268489.5:c.3134G>C	p.Cys1045Ser	p.C1045S	ENST00000268489	NM_006885.3	1045	tGt/tCt	3/10	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.667891530303624	NA		591	564	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054372	13054372	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	280	537	0	ENST00000316448.5:c.982G>C	p.Asp328His	p.D328H	ENST00000316448	NM_004343.3	328	Gac/Cac	8/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.667891530303624	NA		537	786	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054635	13054635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	265	710	0	ENST00000316448.5:c.1162G>A	p.Asp388Asn	p.D388N	ENST00000316448	NM_004343.3	388	Gat/Aat	9/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.667891530303624	NA		710	857	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18956873	18956873	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	222	526	0	ENST00000262803.5:c.316G>C	p.Glu106Gln	p.E106Q	ENST00000262803	NM_002911.3	106	Gag/Cag	2/24	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.667891530303624	NA		526	711	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792451	33792451	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	383	561	0	ENST00000498907.2:c.870G>T	p.Glu290Asp	p.E290D	ENST00000498907	NM_004364.3	290	gaG/gaT	1/1	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.667891530303624	NA		561	1320	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062715-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	187	82	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.865	0.805	0.926	0.865	0.805	0.926	CLONAL	1	TRUE	1	0.829955197551576	2		82	521	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21348936	21348941	+	inframe_deletion	In_Frame_Del	DEL	TACATC	TACATC	-	novel	NA	P-0062715-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	332	800	0	ENST00000215739.8:c.1705_1710del	p.Tyr569_Ile570del	p.Y569_I570del	ENST00000215739	NM_006767.3	569	TACATC/-	15/21	0.829955197551576	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.829955197551576	1		800	463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0062716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	337	569	0	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.4416824976387	2	FACETS	0.782	0.744	0.82	0.782	0.744	0.82	SUBCLONAL	2	TRUE	0	0.564565645550173	2		569	763	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594221	55594221	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913512	NA	P-0062716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1314	113	499	0	ENST00000288135.5:c.1924A>G	p.Lys642Glu	p.K642E	ENST00000288135	NM_000222.2	642	Aaa/Gaa	13/21	0.564565645550173	6	FACETS	0.597	0.535	0.663			1	SUBCLONAL	1	TRUE	NA	0.564565645550173	6		499	1427	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602664	55602664	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs1057519713	NA	P-0062716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	237	438	0	ENST00000288135.5:c.2485G>C	p.Ala829Pro	p.A829P	ENST00000288135	NM_000222.2	829	Gct/Cct	18/21	0.564565645550173	6	FACETS	1	0.99	1			1	CLONAL	1	TRUE	NA	0.564565645550173	6		438	1294	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119474	193119474	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	152	533	0	ENST00000367435.3:c.869A>G	p.Tyr290Cys	p.Y290C	ENST00000367435	NM_024529.4	290	tAt/tGt	9/17	0.327951884408612	4	FACETS	0.875	0.8	0.954	0.437	0.399	0.477	INDETERMINATE	1	TRUE	2	0.564565645550173	4		533	963	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446889	18446889	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1172811749	NA	P-0062716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	77	402	0	ENST00000266497.5:c.974A>G	p.Asp325Gly	p.D325G	ENST00000266497		325	gAc/gGc	4/31	NA	2	FACETS	0.506	0.445	0.572			1	INDETERMINATE	1	TRUE	NA	0.564565645550173	2		402	539	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955404	48955405	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0062716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	289	419	1	ENST00000267163.4:c.1522dup	p.Ser508PhefsTer15	p.S508Ffs*15	ENST00000267163	NM_000321.2	507	gat/gaTt	17/27	0.520116118358615	3	FACETS	1	0.988	1	0.747	0.709	0.784	CLONAL	2	TRUE	0	0.564565645550173	3		420	586	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799649	3799657	+	inframe_deletion	In_Frame_Del	DEL	TTTTTCTTC	TTTTTCTTC	-	novel	NA	P-0062716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	101	309	0	ENST00000262367.5:c.3807_3815del	p.Lys1269_Lys1271del	p.K1269_K1271del	ENST00000262367	NM_004380.2	1269	aaGAAGAAAAAt/aat	21/31	1	2	FACETS	0.768	0.69	0.85	0.768	0.69	0.85	SUBCLONAL	1	TRUE	1	0.564565645550173	2		309	466	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631906	67631906	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	430	662	2	ENST00000272342.5:c.2092G>T	p.Gly698Cys	p.G698C	ENST00000272342	NM_019002.3	698	Ggc/Tgc	5/6	0.431195893501564	4	FACETS	1	0.986	1	0.787	0.757	0.817	CLONAL	3	TRUE	0	0.564565645550173	4		664	757	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480483	57480483	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	323	579	1	ENST00000371085.3:c.478C>G	p.Arg160Gly	p.R160G	ENST00000371085	NM_000516.4	160	Cgt/Ggt	6/13	0.36903358014198	5	FACETS	0.922	0.871	0.974	0.615	0.58	0.65	CLONAL	2	TRUE	2	0.564565645550173	5		580	1146	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933977	49933977	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	412	782	0	ENST00000296474.3:c.2435G>T	p.Ser812Ile	p.S812I	ENST00000296474	NM_002447.2	812	aGc/aTc	9/20	0.439263828048971	2	FACETS	0.845	0.809	0.881	0.845	0.809	0.881	CLONAL	2	TRUE	0	0.564565645550173	2		782	864	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593646	55593647	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGA	novel	NA	P-0062716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1531	172	601	0	ENST00000288135.5:c.1713_1715dup	p.Ile571_Asp572insGlu	p.I571_D572insE	ENST00000288135	NM_000222.2	571	ata/atAGAa	11/21	0.564565645550173	6	FACETS	0.762	0.698	0.829			1	SUBCLONAL	1	TRUE	NA	0.564565645550173	6		601	1703	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344929	70344929	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	118	695	0	ENST00000374080.3:c.2159G>A	p.Gly720Glu	p.G720E	ENST00000374080		720	gGg/gAg	15/45	0.134476891596026	4	FACETS	0.628	0.565	0.694	0.314	0.282	0.347	INDETERMINATE	1	TRUE	2	0.564565645550173	4		695	1042	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0062717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	1382	684	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.900388706840283	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.910550617048617	2		684	1513	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0062732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	488	748	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.357643153856737	3	FACETS	0.95	0.911	0.989	0.95	0.911	0.989	CLONAL	3	TRUE	0	0.357643153856737	3		749	1129	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424958105	NA	P-0062732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	109	501	0	ENST00000334344.6:c.940C>T	p.Arg314Cys	p.R314C	ENST00000334344	NM_152641.2	314	Cgt/Tgt	8/21	0.332044496951848	3	FACETS	1	0.94	1	0.531	0.478	0.588	CLONAL	1	TRUE	1	0.357643153856737	3		501	676	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088749	27088755	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCTAC	CTCCTAC	GAGAA	novel	NA	P-0062732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	268	625	1	ENST00000324856.7:c.2358_2364delinsGAGAA	p.Ser787ArgfsTer29	p.S787Rfs*29	ENST00000324856	NM_006015.4	786	ggCTCCTAC/ggGAGAA	7/20	0.33376676718392	2	FACETS	0.972	0.915	1	0.972	0.915	1	CLONAL	2	TRUE	0	0.357643153856737	2		626	771	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196136	108196136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	79	426	0	ENST00000278616.4:c.6672G>A	p.Met2224Ile	p.M2224I	ENST00000278616	NM_000051.3	2224	atG/atA	46/63	1	2	FACETS	0.926	0.817	1	0.926	0.817	1	CLONAL	1	TRUE	1	0.357643153856737	2		426	477	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287469	46287469	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	133	367	0	ENST00000334344.6:c.5328A>T	p.Leu1776Phe	p.L1776F	ENST00000334344	NM_152641.2	1776	ttA/ttT	20/21	0.332044496951848	3	FACETS	0.933	0.853	1	0.933	0.853	1	CLONAL	2	TRUE	1	0.357643153856737	3		367	470	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215417	5215417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374920205	NA	P-0062732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	144	660	0	ENST00000357368.4:c.4201G>A	p.Asp1401Asn	p.D1401N	ENST00000357368	NM_002850.3	1401	Gac/Aac	28/38	1	2	FACETS	0.975	0.89	1	0.975	0.89	1	CLONAL	1	TRUE	1	0.357643153856737	2		660	826	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182744	38182744	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	136	595	0	ENST00000396334.3:c.897G>C	p.Trp299Cys	p.W299C	ENST00000396334	NM_002468.4	299	tgG/tgC	5/5	1	2	FACETS	0.892	0.811	0.977	0.892	0.811	0.977	CLONAL	1	TRUE	1	0.357643153856737	2		595	853	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161939	47161939	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs781155076	NA	P-0062732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	92	467	0	ENST00000409792.3:c.4187A>G	p.Asn1396Ser	p.N1396S	ENST00000409792	NM_014159.6	1396	aAt/aGt	3/21	1	2	FACETS	0.967	0.862	1	0.967	0.862	1	CLONAL	1	TRUE	1	0.357643153856737	2		467	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0062733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	190	617	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.608756864203581	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.608756864203581	1		617	386	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0062733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	153	596	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.943	0.868	1	0.943	0.868	1	CLONAL	1	TRUE	1	0.608756864203581	2		596	533	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0062733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	89	519	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.608756864203581	2		519	270	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134955	41134955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	42	517	0	ENST00000379561.5:c.673C>T	p.Arg225Cys	p.R225C	ENST00000379561	NM_002015.3	225	Cgt/Tgt	2/3	0.354824245229935	3	FACETS	0.384	0.32	0.454	0.192	0.16	0.227	INDETERMINATE	1	TRUE	1	0.608756864203581	3		517	469	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120580	2120580	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs45438400	NA	P-0062733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	65	601	0	ENST00000219476.3:c.1839+1G>A		p.X613_splice	ENST00000219476	NM_000548.3	613			0.608756864203581	1	FACETS	0.365	0.317	0.416	0.365	0.317	0.416	SUBCLONAL	1	TRUE	0	0.608756864203581	1		601	407	SUCCESS
APC	324	MSKCC	GRCh37	5	112175729	112175729	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	163	671	0	ENST00000257430.4:c.4438C>T	p.Gln1480Ter	p.Q1480*	ENST00000257430	NM_000038.5	1480	Cag/Tag	16/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.608756864203581	2		671	491	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210948	36210948	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	43	788	0	ENST00000222270.7:c.699G>T	p.Arg233Ser	p.R233S	ENST00000222270	NM_014727.1	233	agG/agT	3/37	1	2	FACETS	0.223	0.186	0.264	0.223	0.186	0.264	SUBCLONAL	1	TRUE	1	0.608756864203581	2		788	634	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098636	2098669	+	frameshift_variant	Frame_Shift_Del	DEL	AAGATTCAGGCTTGAAGGAGAAGTTTAAGATTCT	AAGATTCAGGCTTGAAGGAGAAGTTTAAGATTCT	-	novel	NA	P-0062733-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	131	626	0	ENST00000219476.3:c.20_53del	p.Lys7SerfsTer28	p.K7Sfs*28	ENST00000219476	NM_000548.3	7	aAAGATTCAGGCTTGAAGGAGAAGTTTAAGATTCTg/ag	2/42	0.608756864203581	1	FACETS	0.567	0.517	0.619	0.567	0.517	0.619	SUBCLONAL	1	TRUE	0	0.608756864203581	1		626	528	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0062734-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	127	466	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		466	370	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062734-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	70	82	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		82	212	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976771	2976771	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062734-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	39	747	0	ENST00000396946.4:c.1241A>G	p.Asn414Ser	p.N414S	ENST00000396946	NM_032415.4	414	aAc/aGc	9/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		747	480	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0062736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	285	964	8	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.953	0.895	1	0.953	0.895	1	CLONAL	1	TRUE	1	0.502142085319579	2		972	1191	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0062736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	85	879	2	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.28	0.247	0.317	0.28	0.247	0.317	SUBCLONAL	1	TRUE	1	0.502142085319579	2		881	1208	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0062736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	166	311	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.502142085319579	2		311	505	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851285	156851285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778520978	NA	P-0062736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	207	725	0	ENST00000524377.1:c.2242C>T	p.Arg748Trp	p.R748W	ENST00000524377	NM_002529.3	748	Cgg/Tgg	17/17	1	2	FACETS	0.94	0.873	1	0.94	0.873	1	CLONAL	1	TRUE	1	0.502142085319579	2		725	877	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885939	111885939	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	71	851	0	ENST00000341259.2:c.1566del	p.Glu523SerfsTer25	p.E523Sfs*25	ENST00000341259	NM_005475.2	521	Ccc/cc	8/8	1	2	FACETS	0.253	0.219	0.289	0.253	0.219	0.289	SUBCLONAL	1	TRUE	1	0.502142085319579	2		851	1119	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974899	15974899	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	66	597	0	ENST00000268712.3:c.3976C>T	p.Arg1326Ter	p.R1326*	ENST00000268712	NM_006311.3	1326	Cga/Tga	30/46	1	2	FACETS	0.275	0.238	0.316	0.275	0.238	0.316	SUBCLONAL	1	TRUE	1	0.502142085319579	2		597	955	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436128	56436128	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	193	737	0	ENST00000407977.2:c.1009C>T	p.Arg337Ter	p.R337*	ENST00000407977		337	Cga/Tga	9/10	1	2	FACETS	0.718	0.663	0.774	0.718	0.663	0.774	SUBCLONAL	1	TRUE	1	0.502142085319579	2		737	1071	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115416	115115416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	95	574	0	ENST00000257566.3:c.910C>T	p.Arg304Trp	p.R304W	ENST00000257566	NM_016569.3	304	Cgg/Tgg	5/8	1	2	FACETS	0.392	0.348	0.439	0.392	0.348	0.439	SUBCLONAL	1	TRUE	1	0.502142085319579	2		574	966	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412634	63412634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753930754	NA	P-0062736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	86	321	1	ENST00000330258.3:c.533G>A	p.Arg178His	p.R178H	ENST00000330258	NM_152424.3	178	cGt/cAt	2/2	1	1	FACETS	0.64	0.569	0.714	0.64	0.569	0.714	SUBCLONAL	1	TRUE	0	0.502142085319579	1		322	401	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216643	36216643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775753450	NA	P-0062736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	88	818	2	ENST00000222270.7:c.3809G>A	p.Arg1270His	p.R1270H	ENST00000222270	NM_014727.1	1270	cGc/cAc	13/37	1	2	FACETS	0.323	0.285	0.364	0.323	0.285	0.364	SUBCLONAL	1	TRUE	1	0.502142085319579	2		820	1084	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457675	67457675	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	82	791	0	ENST00000327367.4:c.488del	p.Asn163ThrfsTer23	p.N163Tfs*23	ENST00000327367	NM_005902.3	162	gAa/ga	3/9	1	2	FACETS	0.269	0.236	0.305	0.269	0.236	0.305	SUBCLONAL	1	TRUE	1	0.502142085319579	2		791	1213	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760529	133760529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371656033	NA	P-0062736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	62	779	0	ENST00000318560.5:c.2852C>T	p.Pro951Leu	p.P951L	ENST00000318560	NM_005157.4	951	cCg/cTg	11/11	1	2	FACETS	0.238	0.205	0.275	0.238	0.205	0.275	SUBCLONAL	1	TRUE	1	0.502142085319579	2		779	1037	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261373	16261373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773726905	NA	P-0062736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	106	778	3	ENST00000375759.3:c.8638G>A	p.Val2880Met	p.V2880M	ENST00000375759	NM_015001.2	2880	Gtg/Atg	11/15	1	2	FACETS	0.366	0.326	0.407	0.366	0.326	0.407	SUBCLONAL	1	TRUE	1	0.502142085319579	2		781	1155	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952300	38952300	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs557642842	NA	P-0062736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	67	491	0	ENST00000357387.3:c.3125C>T	p.Ser1042Leu	p.S1042L	ENST00000357387	NM_152756.3	1042	tCg/tTg	30/38	1	2	FACETS	0.401	0.348	0.459	0.401	0.348	0.459	SUBCLONAL	1	TRUE	1	0.502142085319579	2		491	665	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519420	176519420	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750977138	NA	P-0062736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	85	834	0	ENST00000292408.4:c.826G>A	p.Asp276Asn	p.D276N	ENST00000292408	NM_213647.1	276	Gat/Aat	7/18	1	2	FACETS	0.349	0.308	0.394	0.349	0.308	0.394	SUBCLONAL	1	TRUE	1	0.502142085319579	2		834	970	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150936507	150936507	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	90	696	0	ENST00000271640.5:c.3706T>G	p.Phe1236Val	p.F1236V	ENST00000271640	NM_001145415.1	1236	Ttc/Gtc	21/22	1	2	FACETS	0.349	0.309	0.393	0.349	0.309	0.393	SUBCLONAL	1	TRUE	1	0.502142085319579	2		696	1026	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204884	94204884	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	42	266	0	ENST00000323929.3:c.701del	p.Leu234TrpfsTer18	p.L234Wfs*18	ENST00000323929	NM_005591.3	234	tTg/tg	8/20	1	2	FACETS	0.349	0.291	0.413	0.349	0.291	0.413	SUBCLONAL	1	TRUE	1	0.502142085319579	2		266	480	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43785234	43785234	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0062736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	215	546	0	ENST00000382044.4:c.7+1G>A		p.X3_splice	ENST00000382044	NM_001141980.1	3			1	2	FACETS	0.997	0.928	1	0.997	0.928	1	CLONAL	1	TRUE	1	0.502142085319579	2		546	859	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681042	37681042	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	64	668	1	ENST00000447079.4:c.3211A>G	p.Thr1071Ala	p.T1071A	ENST00000447079	NM_015083.1	1071	Acc/Gcc	12/14	1	2	FACETS	0.24	0.207	0.277	0.24	0.207	0.277	SUBCLONAL	1	TRUE	1	0.502142085319579	2		669	1060	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38793793	38793793	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567847598	NA	P-0062736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	64	585	1	ENST00000348513.6:c.188del	p.Pro63GlnfsTer8	p.P63Qfs*8	ENST00000348513	NM_003079.4	63	cCa/ca	5/11	1	2	FACETS	0.283	0.244	0.325	0.283	0.244	0.325	SUBCLONAL	1	TRUE	1	0.502142085319579	2		586	902	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6227065	6227065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752916418	NA	P-0062736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	102	790	1	ENST00000252674.7:c.469G>A	p.Asp157Asn	p.D157N	ENST00000252674	NM_005934.3	157	Gac/Aac	5/12	1	2	FACETS	0.347	0.309	0.387	0.347	0.309	0.387	SUBCLONAL	1	TRUE	1	0.502142085319579	2		791	1172	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672730	47672731	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs63750807	NA	P-0062736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	156	382	0	ENST00000233146.2:c.1321dup	p.Thr441AsnfsTer2	p.T441Nfs*2	ENST00000233146	NM_000251.2	440	-/A	8/16	0.502142085319579	1	FACETS	0.916	0.845	0.989	0.916	0.845	0.989	CLONAL	1	TRUE	0	0.502142085319579	1		382	508	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187134	38187134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778667478	NA	P-0062736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	95	605	1	ENST00000317025.8:c.1343G>A	p.Arg448Gln	p.R448Q	ENST00000317025	NM_023034.1	448	cGg/cAg	6/24	1	2	FACETS	0.43	0.382	0.482	0.43	0.382	0.482	SUBCLONAL	1	TRUE	1	0.502142085319579	2		606	879	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737136	145737136	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202134651	NA	P-0062736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	275	828	0	ENST00000428558.2:c.3430C>T	p.Arg1144Cys	p.R1144C	ENST00000428558	NM_004260.3	1144	Cgc/Tgc	21/22	1	2	FACETS	0.998	0.937	1	0.998	0.937	1	CLONAL	1	TRUE	1	0.502142085319579	2		828	1097	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448297	56448297	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	TG	novel	NA	P-0062736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	88	717	2	ENST00000407977.2:c.350delinsCA	p.Arg117ProfsTer8	p.R117Pfs*8	ENST00000407977		117	cGc/cCAc	3/10	1	2	FACETS	0.319	0.282	0.36	0.319	0.282	0.36	SUBCLONAL	1	TRUE	1	0.502142085319579	2		719	1098	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0062745-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	67	623	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.586	0.508	0.672	0.586	0.508	0.672	SUBCLONAL	1	TRUE	1	0.22	2		624	1039	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262550	39262550	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	74	494	0	ENST00000402219.2:c.956G>T	p.Gly319Val	p.G319V	ENST00000402219	NM_005633.3	319	gGg/gTg	7/23	1	2	FACETS	0.978	0.872	1	0.978	0.872	1	CLONAL	1	TRUE	1	0.734514314203861	2		494	206	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618612	37618612	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	4533	784	0	ENST00000447079.4:c.288del	p.Asn96LysfsTer28	p.N96Kfs*28	ENST00000447079	NM_015083.1	96	aaC/aa	1/14	0.734514314203861	15	FACETS	1	0.997	1			1	CLONAL	13	TRUE	NA	0.734514314203861	15		784	5428	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627438	37627438	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062746-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2126	313	642	0	ENST00000447079.4:c.1356del	p.Lys452AsnfsTer12	p.K452Nfs*12	ENST00000447079	NM_015083.1	451	gtA/gt	2/14	0.734514314203861	15	FACETS	1	0.946	1			1	CLONAL	2	TRUE	NA	0.734514314203861	15		642	2439	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0062761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	105	414	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.456559697128946	2		414	430	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332658	65332658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs944169508	NA	P-0062761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	193	434	0	ENST00000342505.4:c.881C>T	p.Ser294Leu	p.S294L	ENST00000342505	NM_002227.2	294	tCa/tTa	7/25	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.456559697128946	2		434	778	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518693	103518693	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	137	364	0	ENST00000355739.4:c.2281G>T	p.Ala761Ser	p.A761S	ENST00000355739	NM_000123.3	761	Gct/Tct	10/15	1	2	FACETS	0.96	0.876	1	0.96	0.876	1	CLONAL	1	TRUE	1	0.456559697128946	2		364	625	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127687	47127687	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	205	312	0	ENST00000409792.3:c.5395G>T	p.Glu1799Ter	p.E1799*	ENST00000409792	NM_014159.6	1799	Gag/Tag	11/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.456559697128946	2		312	762	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139533	47139533	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	174	422	0	ENST00000409792.3:c.5054G>T	p.Cys1685Phe	p.C1685F	ENST00000409792	NM_014159.6	1685	tGc/tTc	9/21	1	2	FACETS	0.918	0.846	0.993	0.918	0.846	0.993	CLONAL	1	TRUE	1	0.456559697128946	2		422	830	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176516649	176516649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	108	373	0	ENST00000292408.4:c.46G>A	p.Gly16Arg	p.G16R	ENST00000292408	NM_213647.1	16	Ggg/Agg	2/18	1	2	FACETS	0.725	0.651	0.802	0.725	0.651	0.802	SUBCLONAL	1	TRUE	1	0.456559697128946	2		373	653	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124465366	124465366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	96	311	0	ENST00000357628.3:c.1732G>T	p.Asp578Tyr	p.D578Y	ENST00000357628	NM_015450.2	578	Gac/Tac	18/19	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.456559697128946	2		311	417	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518063	8518064	+	missense_variant	Missense_Mutation	DNP	TC	TC	CT	novel	NA	P-0062761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	135	421	0	ENST00000356435.5:c.1327_1328delinsAG	p.Glu443Arg	p.E443R	ENST00000356435		443	GAg/AGg	10/35	1	2	FACETS	0.9	0.82	0.984	0.9	0.82	0.984	CLONAL	1	TRUE	1	0.456559697128946	2		421	657	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158732	26158732	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062762-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	48	238	0	ENST00000289316.2:c.335T>A	p.Val112Glu	p.V112E	ENST00000289316	NM_138720.2	112	gTg/gAg	1/2	1	2	FACETS	0.991	0.842	1	0.991	0.842	1	CLONAL	1	TRUE	1	0.29	2		238	334	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549515	5549515	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759212126	NA	P-0062762-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	103	575	0	ENST00000397747.3:c.542G>A	p.Arg181His	p.R181H	ENST00000397747	NM_025239.3	181	cGc/cAc	4/7	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.29	2		575	674	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015048	37015048	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062762-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	89	560	0	ENST00000358127.4:c.356T>C	p.Leu119Pro	p.L119P	ENST00000358127	NM_001280556.1	119	cTg/cCg	3/10	1	2	FACETS	0.967	0.858	1	0.967	0.858	1	CLONAL	1	TRUE	1	0.29	2		560	635	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0062765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	50	459	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.935	0.796	1	0.935	0.796	1	CLONAL	1	TRUE	1	0.277031449146826	2		459	386	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0062765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	80	500	0	ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	4/10	1	2	FACETS	0.862	0.759	0.973	0.862	0.759	0.973	CLONAL	1	TRUE	1	0.277031449146826	2		500	670	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222473	2222473	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1275009442	NA	P-0062765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	100	654	0	ENST00000326181.6:c.667G>T	p.Glu223Ter	p.E223*	ENST00000326181	NM_032271.2	223	Gag/Tag	9/21	1	2	FACETS	0.949	0.847	1	0.949	0.847	1	CLONAL	1	TRUE	1	0.277031449146826	2		654	761	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527838	103527838	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs769608352	NA	P-0062765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	93	513	0	ENST00000355739.4:c.3146A>G	p.Asp1049Gly	p.D1049G	ENST00000355739	NM_000123.3	1049	gAt/gGt	15/15	1	2	FACETS	0.929	0.826	1	0.929	0.826	1	CLONAL	1	TRUE	1	0.277031449146826	2		513	723	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038878	12038878	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062785-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	190	545	0	ENST00000396373.4:c.1171T>G	p.Tyr391Asp	p.Y391D	ENST00000396373	NM_001987.4	391	Tat/Gat	7/8	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.492309675165297	2		545	540	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0000836-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	487	474	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	0.663586650890865	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.663586650890865	2		474	732	SUCCESS
RET	5979	MSKCC	GRCh37	10	43614996	43614996	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs79658334	NA	P-0000836-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	286	584	0	ENST00000355710.3:c.2410G>T	p.Val804Leu	p.V804L	ENST00000355710	NM_020975.4	804	Gtg/Ttg	14/20	0.663586650890865	2	FACETS	0.973	0.917	1	0.486	0.458	0.515	CLONAL	1	TRUE	0	0.663586650890865	2		584	886	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841515	156841515	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001876-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	73	569	0	ENST00000524377.1:c.818G>T	p.Arg273Leu	p.R273L	ENST00000524377	NM_002529.3	273	cGg/cTg	7/17	1	2	FACETS	0.494	0.431	0.562	0.494	0.431	0.562	SUBCLONAL	1	TRUE	1	0.367362824973489	2		569	805	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038349	180038349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373742042	NA	P-0001876-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	115	498	2	ENST00000261937.6:c.3668G>A	p.Arg1223His	p.R1223H	ENST00000261937	NM_182925.4	1223	cGc/cAc	27/30	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.367362824973489	2		500	600	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134611	2134611	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001876-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	140	622	0	ENST00000219476.3:c.4388T>A	p.Ile1463Asn	p.I1463N	ENST00000219476	NM_000548.3	1463	aTc/aAc	34/42	0.286101480940454	3	FACETS	0.991	0.902	1			1	CLONAL	1	TRUE	NA	0.367362824973489	3		622	910	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499662	8499662	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001876-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	56	419	0	ENST00000356435.5:c.2307G>T	p.Met769Ile	p.M769I	ENST00000356435		769	atG/atT	14/35	1	2	FACETS	0.501	0.429	0.58	0.501	0.429	0.58	SUBCLONAL	1	TRUE	1	0.367362824973489	2		419	608	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188188	32188188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370312303	NA	P-0007066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	132	277	0	ENST00000375023.3:c.1153C>T	p.Arg385Cys	p.R385C	ENST00000375023	NM_004557.3	385	Cgc/Tgc	6/30	0.463637499105793	4	FACETS	1	0.967	1	0.378	0.343	0.414	CLONAL	1	TRUE	1	0.463637499105793	4		277	735	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578507	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGG	CAGGG	-	novel	NA	P-0007066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	407	501	0	ENST00000269305.4:c.423_427del	p.Pro142AlafsTer5	p.P142Afs*5	ENST00000269305	NM_001126112.2	141	tgCCCTGtg/tgtg	5/11	0.463637499105793	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.463637499105793	2		501	869	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356279	66356279	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	124	391	0	ENST00000273854.3:c.1218G>C	p.Glu406Asp	p.E406D	ENST00000273854	NM_004439.5	406	gaG/gaC	5/18	0.120715835716867	5	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.463637499105793	5		391	719	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971262	13971262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007066-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	123	392	0	ENST00000405192.2:c.667C>T	p.Pro223Ser	p.P223S	ENST00000405192	NM_001163147.1	223	Cca/Tca	8/12	0.443725938578645	4	FACETS	0.81	0.731	0.893	0.405	0.365	0.447	CLONAL	1	TRUE	2	0.463637499105793	4		392	959	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0007736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	511	305	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.696898982056331	6	FACETS	0.941	0.907	0.974	0.941	0.907	0.974	CLONAL	4	TRUE	2	0.696898982056331	6		305	933	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0007736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	251	191	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.699645787141905	5	FACETS		NA	1			1	NA	6	TRUE	NA	0.696898982056331	5		191	258	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938406	76938406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	548	742	0	ENST00000373344.5:c.2342G>A	p.Arg781Gln	p.R781Q	ENST00000373344	NM_000489.3	781	cGa/cAa	9/35	0.691575774191614	4	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.696898982056331	4		742	1245	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0007736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	156	263	2				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS		NA	1			1	INDETERMINATE	3	TRUE	NA	0.696898982056331	2		265	167	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381466	81381466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	837	547	1	ENST00000222390.5:c.595G>A	p.Glu199Lys	p.E199K	ENST00000222390	NM_000601.4	199	Gaa/Aaa	5/18	0.696898982056331	6	FACETS	0.987	0.96	1	0.987	0.96	1	CLONAL	4	TRUE	2	0.696898982056331	6		548	1457	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518354	8518354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	365	243	1	ENST00000356435.5:c.1037G>A	p.Gly346Glu	p.G346E	ENST00000356435		346	gGg/gAg	10/35	0.239424432865397	6	FACETS	1	0.996	1			1	INDETERMINATE	6	TRUE	NA	0.696898982056331	6		244	389	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436117	110436117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745752281	NA	P-0007736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	366	411	0	ENST00000375856.3:c.2284C>T	p.Pro762Ser	p.P762S	ENST00000375856	NM_003749.2	762	Ccc/Tcc	1/2	0.696898982056331	7	FACETS	1	0.979	1	0.787	0.749	0.825	CLONAL	3	TRUE	3	0.696898982056331	7		411	915	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973778	15973778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	375	400	1	ENST00000268712.3:c.4214C>T	p.Ser1405Phe	p.S1405F	ENST00000268712	NM_006311.3	1405	tCc/tTc	31/46	0.699645787141905	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	2	0.696898982056331	4		401	749	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251817	10251817	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200950656	NA	P-0007736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	368	522	0	ENST00000340748.4:c.3310C>T	p.Arg1104Cys	p.R1104C	ENST00000340748		1104	Cgt/Tgt	30/40	0.518251709011652	5	FACETS	0.933	0.891	0.975			1	CLONAL	3	TRUE	NA	0.696898982056331	5		522	772	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907656	76907656	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	733	1049	0	ENST00000373344.5:c.4505A>G	p.Glu1502Gly	p.E1502G	ENST00000373344	NM_000489.3	1502	gAg/gGg	15/35	0.691575774191614	4	FACETS	1	0.98	1			1	CLONAL	2	TRUE	NA	0.696898982056331	4		1049	1752	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561450	9561451	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0007736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	259	368	1	ENST00000353224.5:c.331_332delinsAA	p.Gly111Lys	p.G111K	ENST00000353224	NM_177990.2	111	GGa/AAa	4/10	0.696898982056331	6	FACETS	1	0.99	1	0.619	0.582	0.656	CLONAL	2	TRUE	2	0.696898982056331	6		369	719	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443863	49443864	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	A	novel	NA	P-0007736-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	328	390	0	ENST00000301067.7:c.3507_3508delinsT	p.Glu1171AsnfsTer41	p.E1171Nfs*41	ENST00000301067	NM_003482.3	1169	taCCcc/taTcc	11/54	0.696898982056331	12	FACETS	1	0.985	1			1	CLONAL	3	TRUE	NA	0.696898982056331	12		390	1258	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0009864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	5039	471	1	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.483170828758544	68	FACETS	0.993	0.989	0.998			1	CLONAL	67	TRUE	NA	0.483170828758544	68		472	5310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579321	7579322	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs587780067	NA	P-0009864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	138	344	0	ENST00000269305.4:c.365_366del	p.Val122AspfsTer26	p.V122Dfs*26	ENST00000269305	NM_001126112.2	122	gTG/g	4/11	0.411909407065287	3	FACETS	0.835	0.775	0.896	0.835	0.775	0.896	CLONAL	3	TRUE	0	0.483170828758544	3		344	283	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954210	48954210	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1354030520	NA	P-0009864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	80	446	0	ENST00000267163.4:c.1411C>T	p.Gln471Ter	p.Q471*	ENST00000267163	NM_000321.2	471	Caa/Taa	15/27	0.328719508940376	3	FACETS	0.988	0.887	1	0.659	0.591	0.728	CLONAL	2	TRUE	0	0.483170828758544	3		446	208	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432811	432811	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009864-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	118	502	0	ENST00000399788.2:c.2105A>G	p.His702Arg	p.H702R	ENST00000399788	NM_001042603.1	702	cAt/cGt	15/28	0.391032122226233	4	FACETS	0.794	0.721	0.87			1	SUBCLONAL	2	TRUE	NA	0.483170828758544	4		502	456	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608322	28608322	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	184	428	1	ENST00000241453.7:c.1734G>T	p.Met578Ile	p.M578I	ENST00000241453	NM_004119.2	578	atG/atT	14/24	0.449950264989022	1	FACETS	0.433	0.399	0.468	0.433	0.399	0.468	SUBCLONAL	1	TRUE	0	0.592871615758973	1		429	1009	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591104	67591115	+	inframe_deletion	In_Frame_Del	DEL	TTAAACCAGACC	TTAAACCAGACC	-	novel	NA	P-0010688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	86	277	0	ENST00000274335.5:c.1700_1711del	p.Lys567_Leu570del	p.K567_L570del	ENST00000274335		566	aTTAAACCAGACCtt/att	12/15	0.592871615758973	1	FACETS	0.374	0.331	0.419	0.374	0.331	0.419	SUBCLONAL	1	TRUE	0	0.592871615758973	1		277	546	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147574	61147574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1476158837	NA	P-0010688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	82	88	1	ENST00000295025.8:c.979G>A	p.Asp327Asn	p.D327N	ENST00000295025	NM_002908.2	327	Gat/Aat	9/11	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.592871615758973	2		89	199	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525544	187525544	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0010688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	173	533	0	ENST00000441802.2:c.10535T>A	p.Leu3512Ter	p.L3512*	ENST00000441802	NM_005245.3	3512	tTa/tAa	18/27	NA	2	FACETS	0.444	0.407	0.483			1	INDETERMINATE	1	TRUE	NA	0.592871615758973	2		533	1314	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514219	69514219	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	211	556	1	ENST00000294312.3:c.462C>A	p.Tyr154Ter	p.Y154*	ENST00000294312	NM_005117.2	154	taC/taA	3/3	0.315669061346878	1	FACETS	0.383	0.355	0.412	0.383	0.355	0.412	INDETERMINATE	1	TRUE	0	0.592871615758973	1		557	1308	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252337	133252337	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	333	503	0	ENST00000320574.5:c.1090G>A	p.Gly364Arg	p.G364R	ENST00000320574	NM_006231.2	364	Ggg/Agg	11/49	0.382523017407348	1	FACETS	0.744	0.704	0.784	0.744	0.704	0.784	SUBCLONAL	1	TRUE	0	0.592871615758973	1		503	1063	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252685	133252685	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	160	459	0	ENST00000320574.5:c.1015G>T	p.Asp339Tyr	p.D339Y	ENST00000320574	NM_006231.2	339	Gat/Tat	10/49	0.382523017407348	1	FACETS	0.374	0.342	0.407	0.374	0.342	0.407	SUBCLONAL	1	TRUE	0	0.592871615758973	1		459	1016	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895610	28895610	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	187	503	0	ENST00000282397.4:c.3164G>C	p.Arg1055Thr	p.R1055T	ENST00000282397	NM_002019.4	1055	aGa/aCa	23/30	0.449950264989022	1	FACETS	0.392	0.361	0.424	0.392	0.361	0.424	SUBCLONAL	1	TRUE	0	0.592871615758973	1		503	1132	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754689	41754689	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	234	594	1	ENST00000301178.4:c.1675G>T	p.Asp559Tyr	p.D559Y	ENST00000301178	NM_021913.4	559	Gac/Tac	14/20	0.592871615758973	1	FACETS	0.388	0.361	0.417	0.388	0.361	0.417	SUBCLONAL	1	TRUE	0	0.592871615758973	1		595	1430	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572440	41572440	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	103	402	0	ENST00000263253.7:c.4969G>C	p.Glu1657Gln	p.E1657Q	ENST00000263253	NM_001429.3	1657	Gag/Cag	30/31	0.529139264585594	3	FACETS	0.334	0.298	0.373	0.111	0.099	0.125	SUBCLONAL	1	TRUE	0	0.592871615758973	3		402	1348	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965670	93965670	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	749	785	0	ENST00000369303.4:c.2258del	p.Gly753AspfsTer31	p.G753Dfs*31	ENST00000369303	NM_004440.3	753	gGa/ga	13/17	0.592871615758973	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.592871615758973	1		785	1524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578212	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	A	novel	NA	P-0010688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	470	635	1	ENST00000269305.4:c.637_638delinsT	p.Arg213TyrfsTer34	p.R213Yfs*34	ENST00000269305	NM_001126112.2	213	CGa/Ta	6/11	0.592871615758973	1	FACETS	0.905	0.866	0.944	0.905	0.866	0.944	CLONAL	1	TRUE	0	0.592871615758973	1		636	1233	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	51	306	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		306	312	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	25	279	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		279	169	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	133	320	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		325	653	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	81	249	3	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		252	576	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	87	461	7	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		468	612	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	97	283	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		288	474	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	94	397	7	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		404	539	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	213	231	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		231	543	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911548	114911548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	107	293	0	ENST00000543371.1:c.1066G>A	p.Ala356Thr	p.A356T	ENST00000543371	NM_001198531.1	356	Gca/Aca	10/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		293	577	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	132	313	0	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		313	680	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1688546	1688546	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs775006575	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	100	112	0	ENST00000378625.1:c.779C>T	p.Pro260Leu	p.P260L	ENST00000378625	NM_001198994.1	260	cCg/cTg	6/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		112	503	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150921604	150921604	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	109	230	0	ENST00000271640.5:c.1274T>C	p.Val425Ala	p.V425A	ENST00000271640	NM_001145415.1	425	gTg/gCg	11/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		230	516	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667401	241667401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749316923	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	97	505	0	ENST00000366560.3:c.1049G>A	p.Arg350Gln	p.R350Q	ENST00000366560	NM_000143.3	350	cGg/cAg	7/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		505	567	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450582	70450582	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150708897	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	120	331	0	ENST00000373644.4:c.5422G>A	p.Val1808Met	p.V1808M	ENST00000373644	NM_030625.2	1808	Gtg/Atg	12/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		331	552	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	532724	532724	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748729430	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	80	126	0	ENST00000451590.1:c.482G>A	p.Arg161His	p.R161H	ENST00000451590	NM_001130442.1	161	cGt/cAt	5/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		126	447	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128676	64128676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	121	137	0	ENST00000334205.4:c.533C>T	p.Thr178Met	p.T178M	ENST00000334205	NM_003942.2	178	aCg/aTg	5/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		137	525	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138915	64138915	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	71	79	0	ENST00000334205.4:c.2287del	p.Arg763AlafsTer21	p.R763Afs*21	ENST00000334205	NM_003942.2	761	gCc/gc	17/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		79	317	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416952	416953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs771545848	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	109	363	6	ENST00000399788.2:c.3597dup	p.Gly1200ArgfsTer7	p.G1200Rfs*7	ENST00000399788	NM_001042603.1	1199	-/A	23/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		369	631	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432248	432249	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	64	216	0	ENST00000399788.2:c.2274dup	p.Asp759ArgfsTer4	p.D759Rfs*4	ENST00000399788	NM_001042603.1	758	-/A	16/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		216	344	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437397	121437397	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	85	207	0	ENST00000257555.6:c.1735C>T	p.Gln579Ter	p.Q579*	ENST00000257555		579	Cag/Tag	9/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		207	502	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880849	28880849	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1471081750	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	133	391	0	ENST00000282397.4:c.3781A>G	p.Thr1261Ala	p.T1261A	ENST00000282397	NM_002019.4	1261	Act/Gct	29/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		391	613	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991322	41991322	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754788327	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	93	288	0	ENST00000219905.7:c.2153G>A	p.Arg718Gln	p.R718Q	ENST00000219905	NM_001164273.1	718	cGg/cAg	5/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		288	434	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134568	2134569	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs397514939	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	122	146	0	ENST00000219476.3:c.4351dup	p.Arg1451ProfsTer73	p.R1451Pfs*73	ENST00000219476	NM_000548.3	1449	tcc/tCcc	34/42	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		146	667	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820668	3820668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768030911	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	138	253	0	ENST00000262367.5:c.2783C>T	p.Pro928Leu	p.P928L	ENST00000262367	NM_004380.2	928	cCg/cTg	14/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		253	709	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857974	9857974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61758996	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	128	321	0	ENST00000330684.3:c.3427G>A	p.Glu1143Lys	p.E1143K	ENST00000330684	NM_001134407.1	1143	Gag/Aag	13/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		321	596	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119792	17119792	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771653740	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	103	173	0	ENST00000285071.4:c.1202G>A	p.Arg401His	p.R401H	ENST00000285071	NM_144997.5	401	cGc/cAc	11/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		173	457	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573556	48573556	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	81	410	0	ENST00000342988.3:c.140T>C	p.Leu47Pro	p.L47P	ENST00000342988	NM_005359.5	47	cTg/cCg	2/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		410	398	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221228	1221228	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	111	126	0	ENST00000326873.7:c.751G>T	p.Gly251Cys	p.G251C	ENST00000326873	NM_000455.4	251	Ggt/Tgt	6/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		126	558	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223055	1223055	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371264852	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	143	124	2	ENST00000326873.7:c.992G>A	p.Arg331Gln	p.R331Q	ENST00000326873	NM_000455.4	331	cGg/cAg	8/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		126	625	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619329	1619330	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	117	129	0	ENST00000344749.5:c.1311dup	p.Arg438AlafsTer37	p.R438Afs*37	ENST00000344749	NM_001136139.2	437	-/G	15/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		129	647	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226569	2226569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777538090	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	127	128	0	ENST00000398665.3:c.4049C>T	p.Pro1350Leu	p.P1350L	ENST00000398665	NM_032482.2	1350	cCg/cTg	27/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		128	620	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223086	5223086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1251374260	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	68	127	0	ENST00000357368.4:c.2717C>T	p.Ala906Val	p.A906V	ENST00000357368	NM_002850.3	906	gCg/gTg	18/38	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		127	453	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6214015	6214015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747549429	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	77	108	2	ENST00000252674.7:c.1342G>A	p.Ala448Thr	p.A448T	ENST00000252674	NM_005934.3	448	Gcc/Acc	9/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		110	450	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10259611	10259611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303994790	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	108	168	0	ENST00000340748.4:c.2621C>T	p.Ala874Val	p.A874V	ENST00000340748		874	gCg/gTg	26/40	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		168	582	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350587	15350587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs920724739	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	82	109	0	ENST00000263377.2:c.3328G>A	p.Val1110Met	p.V1110M	ENST00000263377	NM_058243.2	1110	Gtg/Atg	16/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		109	439	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256794	19256794	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146634302	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	89	149	0	ENST00000162023.5:c.919C>T	p.Arg307Cys	p.R307C	ENST00000162023		307	Cgc/Tgc	13/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		149	388	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222954	36222954	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	110	218	0	ENST00000222270.7:c.5587del	p.Ala1863LeufsTer32	p.A1863Lfs*32	ENST00000222270	NM_014727.1	1861	tcG/tc	27/37	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		218	663	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868391	45868391	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	117	159	0	ENST00000391945.4:c.386A>T	p.Asp129Val	p.D129V	ENST00000391945	NM_000400.3	129	gAc/gTc	6/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		159	614	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905461	50905461	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	115	184	0	ENST00000440232.2:c.590-1G>T		p.X197_splice	ENST00000440232	NM_002691.3	197			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		184	543	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456453	29456453	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1558630501	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	105	345	0	ENST00000389048.3:c.2465del	p.Gly822ValfsTer9	p.G822Vfs*9	ENST00000389048	NM_004304.4	822	gGt/gt	14/29	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		345	614	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026801	48026801	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	122	470	0	ENST00000234420.5:c.1679T>C	p.Phe560Ser	p.F560S	ENST00000234420	NM_000179.2	560	tTt/tCt	4/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		470	558	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030691	48030692	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs267608092	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	103	404	1	ENST00000234420.5:c.3312dup	p.Gly1105TrpfsTer3	p.G1105Wfs*3	ENST00000234420	NM_000179.2	1102	act/acTt	5/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		405	549	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116262	209116263	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs754375602	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	58	335	0	ENST00000345146.2:c.13dup	p.Ile5AsnfsTer13	p.I5Nfs*13	ENST00000345146	NM_005896.2	5	atc/aAtc	3/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		335	431	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812245	212812245	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760575423	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	107	439	0	ENST00000342788.4:c.331T>C	p.Tyr111His	p.Y111H	ENST00000342788	NM_005235.2	111	Tat/Cat	3/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		439	447	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661663	227661664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	85	500	0	ENST00000305123.5:c.1790_1791dup	p.His598GlyfsTer39	p.H598Gfs*39	ENST00000305123	NM_005544.2	597	-/GG	1/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		500	487	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499517	89499518	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	94	447	0	ENST00000336596.2:c.2689dup	p.Arg897LysfsTer22	p.R897Kfs*22	ENST00000336596	NM_005233.5	896	gca/gcAa	15/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		447	515	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204594	128204594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148024280	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	97	222	0	ENST00000341105.2:c.847C>T	p.Arg283Cys	p.R283C	ENST00000341105	NM_032638.4	283	Cgc/Tgc	3/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		222	526	SUCCESS
ATR	545	MSKCC	GRCh37	3	142243008	142243008	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	96	387	0	ENST00000350721.4:c.3979A>G	p.Thr1327Ala	p.T1327A	ENST00000350721	NM_001184.3	1327	Aca/Gca	22/47	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		387	413	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916929	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	60	468	0	ENST00000263967.3:c.316G>A	p.Gly106Ser	p.G106S	ENST00000263967	NM_006218.2	106	Ggc/Agc	2/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		468	354	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1296422	1296422	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs116210138	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	42	89	1				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		90	188	SUCCESS
APC	324	MSKCC	GRCh37	5	112154942	112154942	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779780	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	113	472	0	ENST00000257430.4:c.1213C>T	p.Arg405Ter	p.R405*	ENST00000257430	NM_000038.5	405	Cga/Tga	10/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		472	590	SUCCESS
APC	324	MSKCC	GRCh37	5	112174378	112174379	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554084685	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	72	443	0	ENST00000257430.4:c.3090dup	p.Tyr1031IlefsTer4	p.Y1031Ifs*4	ENST00000257430	NM_000038.5	1029	-/A	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		443	362	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	90	476	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		476	537	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839751	27839751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	166	595	0	ENST00000328488.2:c.343G>A	p.Ala115Thr	p.A115T	ENST00000328488	NM_003533.2	115	Gcc/Acc	1/1	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		595	768	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910405	29910405	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	119	362	1	ENST00000376809.5:c.73+2T>C		p.X25_splice	ENST00000376809	NM_002116.7	25			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		363	613	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671235	30671235	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	168	299	0	ENST00000376406.3:c.5642T>C	p.Leu1881Pro	p.L1881P	ENST00000376406	NM_014641.2	1881	cTc/cCc	11/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		299	719	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166770	32166770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs947409717	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	99	243	0	ENST00000375023.3:c.4468C>T	p.Arg1490Trp	p.R1490W	ENST00000375023	NM_004557.3	1490	Cgg/Tgg	24/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		243	553	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188371	32188371	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	119	229	0	ENST00000375023.3:c.970C>A	p.Pro324Thr	p.P324T	ENST00000375023	NM_004557.3	324	Cct/Act	6/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		229	578	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903745	41903746	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	103	291	0	ENST00000372991.4:c.811dup	p.Arg271ProfsTer53	p.R271Pfs*53	ENST00000372991	NM_001760.3	271	cgg/cCgg	5/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		291	647	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662422	117662422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	68	503	0	ENST00000368508.3:c.4955C>T	p.Thr1652Ile	p.T1652I	ENST00000368508	NM_002944.2	1652	aCt/aTt	30/43	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		503	408	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709158	117709158	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	108	465	0	ENST00000368508.3:c.1799T>C	p.Leu600Ser	p.L600S	ENST00000368508	NM_002944.2	600	tTa/tCa	13/43	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		465	519	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150022953	150022953	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	173	335	0	ENST00000253339.5:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000253339		104	Caa/Taa	1/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		335	416	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129420	152129420	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1312779938	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	41	443	0	ENST00000206249.3:c.373G>A	p.Gly125Ser	p.G125S	ENST00000206249	NM_000125.3	125	Ggc/Agc	1/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		443	472	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163836	152163836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	177	452	0	ENST00000206249.3:c.557C>T	p.Ala186Val	p.A186V	ENST00000206249	NM_000125.3	186	gCa/gTa	2/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		452	519	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435984	116435984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	116	500	0	ENST00000397752.3:c.3979C>T	p.Arg1327Cys	p.R1327C	ENST00000397752	NM_000245.2	1327	Cgc/Tgc	21/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		500	562	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218572	98218572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748726158	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	32	294	0	ENST00000331920.6:c.3292G>A	p.Val1098Ile	p.V1098I	ENST00000331920	NM_000264.3	1098	Gtt/Att	19/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		294	570	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249872	110249872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	91	331	0	ENST00000374672.4:c.803G>A	p.Gly268Asp	p.G268D	ENST00000374672	NM_004235.4	268	gGc/gAc	3/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		331	521	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250433	110250433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	85	312	1	ENST00000374672.4:c.242C>T	p.Ala81Val	p.A81V	ENST00000374672	NM_004235.4	81	gCg/gTg	3/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		313	442	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390734	139390734	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1183279486	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	147	154	0	ENST00000277541.6:c.7457C>T	p.Ser2486Leu	p.S2486L	ENST00000277541	NM_017617.3	2486	tCg/tTg	34/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		154	698	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404264	139404264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780251851	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	116	122	0	ENST00000277541.6:c.2890G>A	p.Val964Met	p.V964M	ENST00000277541	NM_017617.3	964	Gtg/Atg	18/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		122	610	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424733	47424734	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	83	236	0	ENST00000377045.4:c.547dup	p.Gln183ProfsTer11	p.Q183Pfs*11	ENST00000377045	NM_001654.4	181	acc/aCcc	6/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		236	553	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034433	123034433	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	54	232	0	ENST00000355640.3:c.1190T>A	p.Ile397Asn	p.I397N	ENST00000355640		397	aTt/aAt	6/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		232	293	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1737940	1737940	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012491-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	81	422	0	ENST00000378609.4:c.241A>G	p.Ile81Val	p.I81V	ENST00000378609	NM_002074.3	81	Atc/Gtc	6/12	1	2	FACETS	0.839	0.739	0.946	0.839	0.739	0.946	CLONAL	1	TRUE	1	0.285546380126283	2		422	676	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2132455	2132455	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012491-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	78	488	0	ENST00000219476.3:c.3833T>G	p.Leu1278Arg	p.L1278R	ENST00000219476	NM_000548.3	1278	cTg/cGg	32/42	1	2	FACETS	0.976	0.859	1	0.976	0.859	1	CLONAL	1	TRUE	1	0.285546380126283	2		488	560	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164528	36164528	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1463272999	NA	P-0012491-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	71	527	0	ENST00000300305.3:c.1347G>C	p.Gln449His	p.Q449H	ENST00000300305		449	caG/caC	8/8	1	2	FACETS	0.833	0.727	0.947	0.833	0.727	0.947	CLONAL	1	TRUE	1	0.285546380126283	2		527	597	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2199928	2199928	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	226	499	0	ENST00000398665.3:c.697G>C	p.Ala233Pro	p.A233P	ENST00000398665	NM_032482.2	233	Gcc/Ccc	8/28	1	2	FACETS	0.969	0.902	1	0.969	0.902	1	CLONAL	1	TRUE	1	0.44	2		499	1060	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0012873-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	355	723	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.63437286131958	2	FACETS	0.977	0.938	1	0.977	0.938	1	CLONAL	2	TRUE	0	0.63437286131958	2		723	573	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636974	176636974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138405802	NA	P-0012873-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	294	570	0	ENST00000439151.2:c.1574G>A	p.Arg525Gln	p.R525Q	ENST00000439151	NM_022455.4	525	cGg/cAg	5/23	0.604652399383517	5	FACETS	0.999	0.943	1	0.666	0.629	0.705	CLONAL	2	TRUE	2	0.63437286131958	5		570	905	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197847	66197847	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0012873-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	53	264	0	ENST00000273854.3:c.2853-1G>C		p.X951_splice	ENST00000273854	NM_004439.5	951			0.604652399383517	5	FACETS	0.851	0.729	0.985	0.284	0.243	0.329	CLONAL	1	TRUE	2	0.63437286131958	5		264	383	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231736	66231736	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1467468905	NA	P-0012873-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	63	329	0	ENST00000273854.3:c.1964C>T	p.Thr655Ile	p.T655I	ENST00000273854	NM_004439.5	655	aCc/aTc	11/18	0.604652399383517	5	FACETS	0.969	0.842	1	0.323	0.28	0.369	CLONAL	1	TRUE	2	0.63437286131958	5		329	400	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589623	67589634	+	inframe_deletion	In_Frame_Del	DEL	ATATGATAGATT	ATATGATAGATT	-	novel	NA	P-0014598-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	17	241	0	ENST00000274335.5:c.1392_1403del	p.Asp464_Tyr467del	p.D464_Y467del	ENST00000274335		462	gaATATGATAGATTa/gaa	10/15	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.15	2		241	161	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830841	3830841	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014598-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	30	321	0	ENST00000262367.5:c.1715G>T	p.Gly572Val	p.G572V	ENST00000262367	NM_004380.2	572	gGa/gTa	8/31	1	2	FACETS	0.985	0.794	1	0.985	0.794	1	CLONAL	1	TRUE	1	0.15	2		321	406	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149290773	149290774	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014598-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	22	297	0	ENST00000360632.3:c.445dup	p.Ile149AsnfsTer8	p.I149Nfs*8	ENST00000360632	NM_015472.4	149	atc/aAtc	3/7	1	2	FACETS	0.934	0.724	1	0.934	0.724	1	CLONAL	1	TRUE	1	0.15	2		297	314	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426061	49426061	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014598-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	45	562	0	ENST00000301067.7:c.12427del	p.Asp4143IlefsTer6	p.D4143Ifs*6	ENST00000301067	NM_003482.3	4143	Gat/at	39/54	1	2	FACETS	0.92	0.772	1	0.92	0.772	1	CLONAL	1	TRUE	1	0.15	2		562	652	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051595	13051595	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014598-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	30	471	0	ENST00000316448.5:c.854A>G	p.Tyr285Cys	p.Y285C	ENST00000316448	NM_004343.3	285	tAc/tGc	7/9	1	2	FACETS	0.691	0.555	0.846	0.691	0.555	0.846	SUBCLONAL	1	TRUE	1	0.15	2		471	579	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620470	52620470	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	30	654	0	ENST00000394830.3:c.3283C>T	p.Arg1095Ter	p.R1095*	ENST00000394830	NM_018313.4	1095	Cga/Tga	21/30	0.261301699343241	0	FACETS	0.475	0.383	0.579			1	SUBCLONAL	1	TRUE	0	0.261301699343241	0		654	357	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519920	NA	P-0014618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	10	365	0	ENST00000397062.3:c.85G>C	p.Asp29His	p.D29H	ENST00000397062	NM_006164.4	29	Gat/Cat	2/5	0.160288500190639	3	FACETS	0.196	0.132	0.278	0.098	0.066	0.139	SUBCLONAL	1	TRUE	1	0.261301699343241	3		365	441	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183762	10183764	+	missense_variant	Missense_Mutation	TNP	CAA	CAA	TAT	novel	NA	P-0014618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	157	1005	0	ENST00000256474.2:c.231_233delinsTAT	p.Asn78Ile	p.N78I	ENST00000256474	NM_000551.3	77	tgCAAt/tgTATt	1/3	0.244775021447398	0	FACETS	0.775	0.719	0.831			1	SUBCLONAL	3	TRUE	0	0.261301699343241	0		1005	382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578466	7578466	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786202752	NA	P-0019715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	419	397	0	ENST00000269305.4:c.464C>A	p.Thr155Asn	p.T155N	ENST00000269305	NM_001126112.2	155	aCc/aAc	5/11	0.747356896923726	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.747356896923726	1		397	702	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578466	7578466	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786202752	NA	P-0019715-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	85	397	0	ENST00000269305.4:c.464C>A	p.Thr155Asn	p.T155N	ENST00000269305	NM_001126112.2	155	aCc/aAc	5/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.18	2		397	816	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578466	7578466	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786202752	NA	P-0019715-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	398	397	0	ENST00000269305.4:c.464C>A	p.Thr155Asn	p.T155N	ENST00000269305	NM_001126112.2	155	aCc/aAc	5/11	0.676972681531302	1	FACETS	0.97	0.929	1	0.97	0.929	1	CLONAL	1	TRUE	0	0.676972681531302	1		397	802	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624868	9624868	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019715-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	261	218	0	ENST00000353224.5:c.109C>A	p.Gln37Lys	p.Q37K	ENST00000353224	NM_177990.2	37	Cag/Aag	3/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.676972681531302	2		218	750	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	155	305	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.433980350372566	2		305	485	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	28	253	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.255	0.203	0.314	0.255	0.203	0.314	SUBCLONAL	1	TRUE	1	0.433980350372566	2		253	506	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	39	510	2	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.422	0.35	0.502	0.422	0.35	0.502	SUBCLONAL	1	TRUE	1	0.433980350372566	2		512	426	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	256	331	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.433980350372566	2		335	498	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	123	647	2	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.433980350372566	2		649	507	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	98	565	1	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.88	0.788	0.978	0.88	0.788	0.978	CLONAL	1	TRUE	1	0.433980350372566	2		566	513	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409146	4409146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587777621	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	172	514	0	ENST00000261254.3:c.841C>T	p.Pro281Ser	p.P281S	ENST00000261254	NM_001759.3	281	Cct/Tct	5/5	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.433980350372566	2		514	601	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669547	88669547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56394626	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	109	436	0	ENST00000360948.2:c.1351G>A	p.Val451Ile	p.V451I	ENST00000360948	NM_001012338.2	451	Gtc/Atc	12/19	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.433980350372566	2		436	438	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710595	114710597	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs754968616	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	184	526	0	ENST00000543371.1:c.85_87del	p.Glu29del	p.E29del	ENST00000543371	NM_001198531.1	27	cAGGag/cag	1/14	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.433980350372566	2		526	596	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	142	320	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.433980350372566	2		325	589	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691872	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs79375991	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	297	492	18	ENST00000295754.5:c.383del	p.Lys128SerfsTer35	p.K128Sfs*35	ENST00000295754	NM_003242.5	125	gAa/ga	3/7	1	2	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	TRUE	1	0.433980350372566	2		510	574	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	221	660	2	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.433980350372566	2		662	742	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	180	397	7	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.433980350372566	2		404	630	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1688567	1688568	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs746550458	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	31	551	0	ENST00000378625.1:c.757dup	p.Ala253GlyfsTer45	p.A253Gfs*45	ENST00000378625	NM_001198994.1	253	gcc/gGcc	6/14	1	2	FACETS	0.278	0.224	0.339	0.278	0.224	0.339	SUBCLONAL	1	TRUE	1	0.433980350372566	2		551	514	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300384	11300384	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	102	532	0	ENST00000361445.4:c.1762A>G	p.Thr588Ala	p.T588A	ENST00000361445	NM_004958.3	588	Acg/Gcg	11/58	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.433980350372566	2		532	469	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300522	11300522	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	40	665	0	ENST00000361445.4:c.1624del	p.Met542CysfsTer58	p.M542Cfs*58	ENST00000361445	NM_004958.3	542	Atg/tg	11/58	1	2	FACETS	0.309	0.256	0.368	0.309	0.256	0.368	SUBCLONAL	1	TRUE	1	0.433980350372566	2		665	597	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938263	36938263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138558210	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	129	621	0	ENST00000361632.4:c.698G>A	p.Arg233Gln	p.R233Q	ENST00000361632		233	cGg/cAg	6/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.433980350372566	2		621	513	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944310	206944310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755490123	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	61	684	0	ENST00000423557.1:c.320C>T	p.Ala107Val	p.A107V	ENST00000423557	NM_000572.2	107	gCg/gTg	3/5	1	2	FACETS	0.449	0.387	0.517	0.449	0.387	0.517	SUBCLONAL	1	TRUE	1	0.433980350372566	2		684	626	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100728	8100728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs771019738	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	111	670	6	ENST00000346208.3:c.708del	p.Ser237AlafsTer28	p.S237Afs*28	ENST00000346208		234	ttC/tt	3/6	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.433980350372566	2		676	451	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137785	64137785	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779751342	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	136	673	0	ENST00000334205.4:c.1886G>A	p.Arg629His	p.R629H	ENST00000334205	NM_003942.2	629	cGc/cAc	15/17	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.433980350372566	2		673	514	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	56	699	2	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	1	2	FACETS	0.492	0.421	0.568	0.492	0.421	0.568	SUBCLONAL	1	TRUE	1	0.433980350372566	2		701	525	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941049	71941049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373511105	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	188	799	0	ENST00000298229.2:c.925G>A	p.Val309Met	p.V309M	ENST00000298229	NM_001567.3	309	Gtg/Atg	8/28	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.433980350372566	2		799	693	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114817	108114817	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786204543	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	54	388	0	ENST00000278616.4:c.640del	p.Ser214ProfsTer16	p.S214Pfs*16	ENST00000278616	NM_000051.3	212	Ttt/tt	6/63	1	2	FACETS	0.534	0.457	0.618	0.534	0.457	0.618	SUBCLONAL	1	TRUE	1	0.433980350372566	2		388	466	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196879	108196880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs773570504	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	34	390	0	ENST00000278616.4:c.6908dup	p.Glu2304GlyfsTer69	p.E2304Gfs*69	ENST00000278616	NM_000051.3	2301	gca/gcAa	47/63	1	2	FACETS	0.338	0.276	0.409	0.338	0.276	0.409	SUBCLONAL	1	TRUE	1	0.433980350372566	2		390	463	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18439827	18439827	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	118	339	0	ENST00000266497.5:c.725A>T	p.Asn242Ile	p.N242I	ENST00000266497		242	aAt/aTt	2/31	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.433980350372566	2		339	413	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	41	459	5	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.354	0.294	0.42	0.354	0.294	0.42	SUBCLONAL	1	TRUE	1	0.433980350372566	2		464	534	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884625	111884625	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	44	621	0	ENST00000341259.2:c.801G>T	p.Glu267Asp	p.E267D	ENST00000341259	NM_005475.2	267	gaG/gaT	3/8	1	2	FACETS	0.354	0.296	0.418	0.354	0.296	0.418	SUBCLONAL	1	TRUE	1	0.433980350372566	2		621	573	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562483	21562488	+	inframe_deletion	In_Frame_Del	DEL	GGGGCG	GGGGCG	-	rs550642106	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	38	400	0	ENST00000382592.4:c.1431_1436del	p.Pro479_Ala480del	p.P479_A480del	ENST00000382592	NM_014572.2	477	ccCGCCCCg/ccg	4/8	1	2	FACETS	0.826	0.689	0.976	0.826	0.689	0.976	CLONAL	1	TRUE	1	0.433980350372566	2		400	212	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133898	41133898	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	69	596	0	ENST00000379561.5:c.1730del	p.Gly577AlafsTer5	p.G577Afs*5	ENST00000379561	NM_002015.3	577	gGc/gc	2/3	1	2	FACETS	0.619	0.54	0.704	0.619	0.54	0.704	SUBCLONAL	1	TRUE	1	0.433980350372566	2		596	514	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061168	38061168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	128	586	0	ENST00000250448.2:c.821C>T	p.Ala274Val	p.A274V	ENST00000250448	NM_004496.3	274	gCc/gTc	2/2	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.433980350372566	2		586	419	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50763941	50763941	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1161410933	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	62	411	0	ENST00000307179.4:c.798A>C	p.Lys266Asn	p.K266N	ENST00000307179		266	aaA/aaC	8/20	1	2	FACETS	0.616	0.533	0.705	0.616	0.533	0.705	SUBCLONAL	1	TRUE	1	0.433980350372566	2		411	464	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632769	23632770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	88	375	0	ENST00000261584.4:c.3026dup	p.Glu1010Ter	p.E1010*	ENST00000261584	NM_024675.3	1009	cct/ccCt	10/13	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.433980350372566	2		375	386	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646980	23646981	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	75	458	0	ENST00000261584.4:c.886dup	p.Met296AsnfsTer7	p.M296Nfs*7	ENST00000261584	NM_024675.3	296	atg/aAtg	4/13	1	2	FACETS	0.61	0.535	0.69	0.61	0.535	0.69	SUBCLONAL	1	TRUE	1	0.433980350372566	2		458	567	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828335	72828335	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774192226	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	69	654	0	ENST00000268489.5:c.8246C>T	p.Ala2749Val	p.A2749V	ENST00000268489	NM_006885.3	2749	gCg/gTg	9/10	1	2	FACETS	0.545	0.475	0.621	0.545	0.475	0.621	SUBCLONAL	1	TRUE	1	0.433980350372566	2		654	583	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33445587	33445587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56026142	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	144	540	1	ENST00000345365.6:c.196G>A	p.Val66Met	p.V66M	ENST00000345365	NM_002878.3	66	Gtg/Atg	3/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.433980350372566	2		541	505	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436028	56436028	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	171	748	0	ENST00000407977.2:c.1109del	p.Pro370HisfsTer49	p.P370Hfs*49	ENST00000407977		370	cCa/ca	9/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.433980350372566	2		748	626	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119750	70119751	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	97	417	0	ENST00000245479.2:c.754dup	p.Leu252ProfsTer44	p.L252Pfs*44	ENST00000245479	NM_000346.3	251	gac/gaCc	3/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.433980350372566	2		417	348	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217055	2217055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	60	573	0	ENST00000398665.3:c.2510C>T	p.Ala837Val	p.A837V	ENST00000398665	NM_032482.2	837	gCc/gTc	21/28	1	2	FACETS	0.637	0.55	0.731	0.637	0.55	0.731	SUBCLONAL	1	TRUE	1	0.433980350372566	2		573	434	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125379	7125379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778982272	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	144	682	0	ENST00000302850.5:c.3173C>T	p.Thr1058Met	p.T1058M	ENST00000302850	NM_000208.2	1058	aCg/aTg	17/22	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.433980350372566	2		682	566	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281310	15281310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	88	708	1	ENST00000263388.2:c.4946C>T	p.Ala1649Val	p.A1649V	ENST00000263388	NM_000435.2	1649	gCg/gTg	27/33	1	2	FACETS	0.723	0.642	0.809	0.723	0.642	0.809	SUBCLONAL	1	TRUE	1	0.433980350372566	2		709	561	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290919	15290919	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	119	632	1	ENST00000263388.2:c.3291del	p.Thr1098ProfsTer174	p.T1098Pfs*174	ENST00000263388	NM_000435.2	1097	ggG/gg	20/33	1	2	FACETS	0.999	0.905	1	0.999	0.905	1	CLONAL	1	TRUE	1	0.433980350372566	2		633	549	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953860	17953860	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746488415	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	137	647	0	ENST00000458235.1:c.542C>T	p.Pro181Leu	p.P181L	ENST00000458235	NM_000215.3	181	cCg/cTg	5/24	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.433980350372566	2		647	511	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976954	18976954	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	68	592	0	ENST00000262803.5:c.3342del	p.Leu1115CysfsTer12	p.L1115Cfs*12	ENST00000262803	NM_002911.3	1113	acG/ac	23/24	1	2	FACETS	0.606	0.528	0.69	0.606	0.528	0.69	SUBCLONAL	1	TRUE	1	0.433980350372566	2		592	517	SUCCESS
AXL	558	MSKCC	GRCh37	19	41725323	41725323	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	130	519	0	ENST00000301178.4:c.26G>A	p.Gly9Asp	p.G9D	ENST00000301178	NM_021913.4	9	gGc/gAc	1/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.433980350372566	2		519	438	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905094	50905094	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622753	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	107	585	0	ENST00000440232.2:c.376C>T	p.Arg126Cys	p.R126C	ENST00000440232	NM_002691.3	126	Cgc/Tgc	4/27	0.433980350372566	1	FACETS	0.858	0.774	0.946	0.858	0.774	0.946	CLONAL	1	TRUE	0	0.433980350372566	1		585	450	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631423	67631424	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	55	400	0	ENST00000272342.5:c.1609_1610insC	p.Ile537ThrfsTer7	p.I537Tfs*7	ENST00000272342	NM_019002.3	537	att/aCtt	5/6	1	2	FACETS	0.552	0.473	0.638	0.552	0.473	0.638	SUBCLONAL	1	TRUE	1	0.433980350372566	2		400	459	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631430	67631430	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	60	406	0	ENST00000272342.5:c.1616A>T	p.Asn539Ile	p.N539I	ENST00000272342	NM_019002.3	539	aAt/aTt	5/6	1	2	FACETS	0.596	0.514	0.684	0.596	0.514	0.684	SUBCLONAL	1	TRUE	1	0.433980350372566	2		406	464	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631523	67631523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	151	456	0	ENST00000272342.5:c.1709C>T	p.Ala570Val	p.A570V	ENST00000272342	NM_019002.3	570	gCa/gTa	5/6	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.433980350372566	2		456	533	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038192	128038193	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	27	455	0	ENST00000285398.2:c.1357dup	p.Arg453LysfsTer11	p.R453Kfs*11	ENST00000285398	NM_000122.1	453	agg/aAgg	9/15	1	2	FACETS	0.235	0.186	0.291	0.235	0.186	0.291	SUBCLONAL	1	TRUE	1	0.433980350372566	2		455	529	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661632	227661632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893642	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	62	796	0	ENST00000305123.5:c.1823C>T	p.Thr608Met	p.T608M	ENST00000305123	NM_005544.2	608	aCg/aTg	1/2	1	2	FACETS	0.629	0.545	0.721	0.629	0.545	0.721	SUBCLONAL	1	TRUE	1	0.433980350372566	2		796	454	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023474	31023474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376074119	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	72	540	0	ENST00000375687.4:c.2959G>A	p.Gly987Arg	p.G987R	ENST00000375687	NM_015338.5	987	Gga/Aga	13/13	1	2	FACETS	0.599	0.524	0.68	0.599	0.524	0.68	SUBCLONAL	1	TRUE	1	0.433980350372566	2		540	554	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31393157	31393157	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	139	489	0	ENST00000328111.2:c.2245T>C	p.Ser749Pro	p.S749P	ENST00000328111	NM_006892.3	749	Tca/Cca	21/23	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.433980350372566	2		489	471	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728813	39728813	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	122	466	0	ENST00000361337.2:c.1093G>A	p.Gly365Ser	p.G365S	ENST00000361337	NM_003286.2	365	Ggc/Agc	12/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.433980350372566	2		466	493	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860342	42860342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779659161	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	164	523	0	ENST00000398585.3:c.535G>A	p.Gly179Arg	p.G179R	ENST00000398585	NM_001135099.1	179	Ggg/Agg	5/14	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.433980350372566	2		523	519	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21336681	21336681	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587777613	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	117	620	2	ENST00000215739.8:c.27del	p.Gln10ArgfsTer15	p.Q10Rfs*15	ENST00000215739	NM_006767.3	7	acG/ac	1/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.433980350372566	2		622	481	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565563	41565563	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	66	338	0	ENST00000263253.7:c.4229G>T	p.Arg1410Met	p.R1410M	ENST00000263253	NM_001429.3	1410	aGg/aTg	26/31	1	2	FACETS	0.736	0.642	0.838	0.736	0.642	0.838	SUBCLONAL	1	TRUE	1	0.433980350372566	2		338	413	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573882	41573882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758996869	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	181	701	0	ENST00000263253.7:c.6167G>A	p.Arg2056Gln	p.R2056Q	ENST00000263253	NM_001429.3	2056	cGg/cAg	31/31	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.433980350372566	2		701	588	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73047305	73047305	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	122	349	0	ENST00000356692.5:c.112A>G	p.Thr38Ala	p.T38A	ENST00000356692		38	Aca/Gca	2/9	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.433980350372566	2		349	491	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204623	128204623	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	147	669	1	ENST00000341105.2:c.818del	p.Gly273AspfsTer53	p.G273Dfs*53	ENST00000341105	NM_032638.4	273	gGa/ga	3/6	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.433980350372566	2		670	541	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586473	189586473	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	159	537	0	ENST00000264731.3:c.1097A>G	p.Asp366Gly	p.D366G	ENST00000264731	NM_003722.4	366	gAc/gGc	8/14	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.433980350372566	2		537	593	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801038	1801038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1444898156	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	135	588	0	ENST00000260795.2:c.167C>T	p.Ala56Val	p.A56V	ENST00000260795		56	gCt/gTt	2/17	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.433980350372566	2		588	432	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902779	1902779	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs140401180	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	169	595	0	ENST00000382891.5:c.398T>C	p.Met133Thr	p.M133T	ENST00000382891	NM_133335.3	133	aTg/aCg	2/22	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.433980350372566	2		595	549	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157335	106157335	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	156	538	0	ENST00000380013.4:c.2236C>G	p.Gln746Glu	p.Q746E	ENST00000380013	NM_001127208.2	746	Caa/Gaa	3/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.433980350372566	2		538	600	SUCCESS
APC	324	MSKCC	GRCh37	5	112178357	112178357	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs751861630	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	152	548	0	ENST00000257430.4:c.7066A>C	p.Thr2356Pro	p.T2356P	ENST00000257430	NM_000038.5	2356	Act/Cct	16/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.433980350372566	2		548	542	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944382	131944382	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs748536322	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	100	259	3	ENST00000265335.6:c.2801del	p.Asn934IlefsTer6	p.N934Ifs*6	ENST00000265335		932	Aaa/aa	17/25	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.433980350372566	2		262	376	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023045	150023045	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1175780468	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	140	488	0	ENST00000253339.5:c.218C>T	p.Thr73Met	p.T73M	ENST00000253339		73	aCg/aTg	1/7	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.433980350372566	2		488	538	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962331	2962331	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	35	437	0	ENST00000396946.4:c.2206G>T	p.Ala736Ser	p.A736S	ENST00000396946	NM_032415.4	736	Gcc/Tcc	17/25	1	2	FACETS	0.414	0.339	0.497	0.414	0.339	0.497	SUBCLONAL	1	TRUE	1	0.433980350372566	2		437	390	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508425	106508425	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754761135	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	113	535	0	ENST00000359195.3:c.419G>A	p.Arg140Gln	p.R140Q	ENST00000359195	NM_002649.2	140	cGg/cAg	2/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.433980350372566	2		535	386	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339709	116339709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs530932258	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	41	568	0	ENST00000397752.3:c.571C>T	p.Arg191Trp	p.R191W	ENST00000397752	NM_000245.2	191	Cgg/Tgg	2/21	1	2	FACETS	0.345	0.287	0.41	0.345	0.287	0.41	SUBCLONAL	1	TRUE	1	0.433980350372566	2		568	548	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395569	116395569	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs375951814	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	115	342	0	ENST00000397752.3:c.1862C>T	p.Thr621Ile	p.T621I	ENST00000397752	NM_000245.2	621	aCa/aTa	6/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.433980350372566	2		342	459	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829015	128829015	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs981209235	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	18	422	0	ENST00000249373.3:c.23G>A	p.Arg8Gln	p.R8Q	ENST00000249373	NM_005631.4	8	cGg/cAg	1/12	1	2	FACETS	0.503	0.381	0.645	0.503	0.381	0.645	SUBCLONAL	1	TRUE	1	0.433980350372566	2		422	165	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843774	151843775	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	136	475	0	ENST00000262189.6:c.13940dup	p.Ser4648ValfsTer2	p.S4648Vfs*2	ENST00000262189	NM_170606.2	4647	aag/aaAg	53/59	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.433980350372566	2		475	539	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878730	151878730	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1292477105	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	168	586	0	ENST00000262189.6:c.6215A>G	p.Tyr2072Cys	p.Y2072C	ENST00000262189	NM_170606.2	2072	tAt/tGt	36/59	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.433980350372566	2		586	548	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372193	55372193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753081636	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	151	695	0	ENST00000297316.4:c.883G>A	p.Val295Met	p.V295M	ENST00000297316	NM_022454.3	295	Gtg/Atg	2/2	1	2	FACETS	0.775	0.715	0.837	1	0.989	1	SUBCLONAL	2	TRUE	1	0.433980350372566	2		695	449	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2047418	2047418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1315212101	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	101	452	0	ENST00000349721.2:c.980G>A	p.Arg327His	p.R327H	ENST00000349721	NM_003070.3	327	cGc/cAc	5/34	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.433980350372566	2		452	368	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37033998	37033999	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	112	328	0	ENST00000358127.4:c.30_31del	p.Arg11AspfsTer63	p.R11Dfs*63	ENST00000358127	NM_001280556.1	10	ccTCgg/ccgg	1/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.433980350372566	2		328	401	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759406	133759406	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1371645607	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	35	546	0	ENST00000318560.5:c.1729C>T	p.Arg577Ter	p.R577*	ENST00000318560	NM_005157.4	577	Cga/Tga	11/11	1	2	FACETS	0.357	0.292	0.43	0.357	0.292	0.43	SUBCLONAL	1	TRUE	1	0.433980350372566	2		546	452	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137325960	137325960	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	144	572	0	ENST00000481739.1:c.1148T>G	p.Leu383Arg	p.L383R	ENST00000481739	NM_002957.4	383	cTc/cGc	9/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.433980350372566	2		572	488	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399832	139399833	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CA	CA	-	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	141	730	0	ENST00000277541.6:c.4515_4516del	p.Cys1505Ter	p.C1505*	ENST00000277541	NM_017617.3	1505	tgTGac/tgac	25/34	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.433980350372566	2		730	524	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933497	39933497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	183	732	0	ENST00000378444.4:c.1102C>T	p.Pro368Ser	p.P368S	ENST00000378444	NM_001123385.1	368	Cct/Tct	4/15	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.433980350372566	2		732	597	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	60	886	2	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	2	FACETS	0.435	0.374	0.501	0.435	0.374	0.501	SUBCLONAL	1	TRUE	1	0.433980350372566	2		888	636	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411062	63411062	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	122	607	0	ENST00000330258.3:c.2105A>G	p.Glu702Gly	p.E702G	ENST00000330258	NM_152424.3	702	gAg/gGg	2/2	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.433980350372566	2		607	459	SUCCESS
AR	367	MSKCC	GRCh37	X	66937379	66937379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	29	536	0	ENST00000374690.3:c.2233C>T	p.Leu745Phe	p.L745F	ENST00000374690	NM_000044.3	745	Ctc/Ttc	5/8	1	2	FACETS	0.308	0.247	0.378	0.308	0.247	0.378	SUBCLONAL	1	TRUE	1	0.433980350372566	2		536	434	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	40	412	0	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	2	FACETS	0.778	0.651	0.916	0.778	0.651	0.916	CLONAL	1	TRUE	1	0.433980350372566	2		412	237	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910715	29910716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0019887-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	79	780	1	ENST00000376809.5:c.255_256insG	p.Gln86AlafsTer13	p.Q86Afs*13	ENST00000376809	NM_002116.7	85	-/G	2/8	1	2	FACETS	0.541	0.476	0.611	0.541	0.476	0.611	SUBCLONAL	1	TRUE	1	0.433980350372566	2		781	673	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0021572-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	191	715	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	0.963	0.904	1	1	0.994	1	CLONAL	2	TRUE	1	0.505719734841592	2		715	392	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267749	198267751	+	inframe_deletion	In_Frame_Del	DEL	ACC	ACC	-	novel	NA	P-0021572-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	90	472	0	ENST00000335508.6:c.1728_1730del	p.Val577del	p.V577del	ENST00000335508	NM_012433.2	576	gtGGTc/gtc	13/25	1	2	FACETS	0.813	0.736	0.891	1	0.985	1	CLONAL	2	TRUE	1	0.505719734841592	2		472	219	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197696	123197696	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0021572-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	103	343	0	ENST00000218089.9:c.1822-2A>C		p.X608_splice	ENST00000218089	NM_001042749.1	608			1	2	FACETS	1	0.95	1	1	0.99	1	CLONAL	2	TRUE	1	0.505719734841592	2		343	195	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0022830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	74	798	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	0.691	0.605	0.784	0.691	0.605	0.784	SUBCLONAL	1	TRUE	1	0.335624110429085	2		798	638	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325763	30325763	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777479817	NA	P-0022830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	25	624	2	ENST00000322652.5:c.1961G>A	p.Arg654Gln	p.R654Q	ENST00000322652	NM_015355.2	654	cGa/cAa	16/16	0.335624110429085	3	FACETS	0.44	0.347	0.548	0.22	0.173	0.274	SUBCLONAL	1	TRUE	1	0.335624110429085	3		626	395	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0022830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	21	593	1	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	1	2	FACETS	0.258	0.198	0.329	0.258	0.198	0.329	SUBCLONAL	1	TRUE	1	0.335624110429085	2		594	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577111	7577111	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs786202082	NA	P-0022830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	106	1035	0	ENST00000269305.4:c.827C>G	p.Ala276Gly	p.A276G	ENST00000269305	NM_001126112.2	276	gCc/gGc	8/11	0.212673415853456	1	FACETS	0.726	0.651	0.805	0.726	0.651	0.805	SUBCLONAL	1	TRUE	0	0.335624110429085	1		1035	724	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896606	78896606	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	81	900	0	ENST00000306801.3:c.2603G>T	p.Gly868Val	p.G868V	ENST00000306801	NM_020761.2	868	gGc/gTc	22/34	0.335624110429085	4	FACETS	0.843	0.742	0.951	0.421	0.371	0.476	CLONAL	1	TRUE	2	0.335624110429085	4		900	765	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180685	32180685	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	51	1065	0	ENST00000375023.3:c.2442del	p.Cys815ValfsTer30	p.C815Vfs*30	ENST00000375023	NM_004557.3	814	ccC/cc	16/30	0.335624110429085	3	FACETS	0.389	0.329	0.455	0.13	0.109	0.152	SUBCLONAL	1	TRUE	0	0.335624110429085	3		1065	913	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504354	8504354	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	62	969	0	ENST00000356435.5:c.1729C>A	p.Pro577Thr	p.P577T	ENST00000356435		577	Cca/Aca	12/35	1	2	FACETS	0.519	0.447	0.597	0.519	0.447	0.597	SUBCLONAL	1	TRUE	1	0.335624110429085	2		969	712	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024021-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	480	729	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.351850584405656	5	FACETS	1	0.989	1			1	CLONAL	3	FALSE	NA	0.428034209391729	5		729	1127	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0027256-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	31	136	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.842	0.688	1	0.842	0.688	1	CLONAL	1	TRUE	1	0.39573741640017	2		136	186	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0027256-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	117	426	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.39573741640017	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.39573741640017	1		426	440	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061194	38061555	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCTTCTGGCGGCGCAAGTAGCAGCCGTTCTCGAACATGTTGCCGGAGTCCGGGTGCAGCGTCCAGTAGGAGCCCTTGCCCGGCTTGTCCGGGGAGCGTGCCACCTTGACGAAGCAGTCATTGAAGGACAGCGAGTGGCGGATGGAGTTCTGCCAGCGCTGCTGGTTCTGCCGGTAATAGGGGAAGAGGTCCATGATCCACTGGTAGATCTCGCTCAGCGTGAGCATCTTGCTGGGCGCCTGCTGGATGGCCATGGTGATGAGCGAGATGTACGAGTAGGGCGGCTTGGCGTGCGGGTAGCTGCGCTTGAACGTCTTGGCGTCGCCGCCGCCGCCCGCGCGGCTGCGGCCCAGGTTGGACG	GCGCTTCTGGCGGCGCAAGTAGCAGCCGTTCTCGAACATGTTGCCGGAGTCCGGGTGCAGCGTCCAGTAGGAGCCCTTGCCCGGCTTGTCCGGGGAGCGTGCCACCTTGACGAAGCAGTCATTGAAGGACAGCGAGTGGCGGATGGAGTTCTGCCAGCGCTGCTGGTTCTGCCGGTAATAGGGGAAGAGGTCCATGATCCACTGGTAGATCTCGCTCAGCGTGAGCATCTTGCTGGGCGCCTGCTGGATGGCCATGGTGATGAGCGAGATGTACGAGTAGGGCGGCTTGGCGTGCGGGTAGCTGCGCTTGAACGTCTTGGCGTCGCCGCCGCCGCCCGCGCGGCTGCGGCCCAGGTTGGACG	-	novel	NA	P-0027256-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	199	445	0	ENST00000250448.2:c.434_795del	p.Pro145LeufsTer27	p.P145Lfs*27	ENST00000250448	NM_004496.3	145	cCGTCCAACCTGGGCCGCAGCCGCGCGGGCGGCGGCGGCGACGCCAAGACGTTCAAGCGCAGCTACCCGCACGCCAAGCCGCCCTACTCGTACATCTCGCTCATCACCATGGCCATCCAGCAGGCGCCCAGCAAGATGCTCACGCTGAGCGAGATCTACCAGTGGATCATGGACCTCTTCCCCTATTACCGGCAGAACCAGCAGCGCTGGCAGAACTCCATCCGCCACTCGCTGTCCTTCAATGACTGCTTCGTCAAGGTGGCACGCTCCCCGGACAAGCCGGGCAAGGGCTCCTACTGGACGCTGCACCCGGACTCCGGCAACATGTTCGAGAACGGCTGCTACTTGCGCCGCCAGAAGCGC/c	2/2	1	2	FACETS	0.89	0.83	0.951	1	0.993	1	CLONAL	2	TRUE	1	0.39573741640017	2		445	565	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780690	56780690	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs755849719	NA	P-0027256-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	63	279	0	ENST00000337432.4:c.705G>T	p.Lys235Asn	p.K235N	ENST00000337432	NM_058216.2	235	aaG/aaT	4/9	1	2	FACETS	0.934	0.813	1	0.934	0.813	1	CLONAL	1	TRUE	1	0.39573741640017	2		279	341	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128305355	128305355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1204536063	NA	P-0027256-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	73	270	0	ENST00000265960.3:c.941G>A	p.Gly314Glu	p.G314E	ENST00000265960	NM_001006617.1	314	gGa/gAa	7/12	1	2	FACETS	0.956	0.841	1	0.956	0.841	1	CLONAL	1	TRUE	1	0.39573741640017	2		270	386	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575131	48575131	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027256-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	73	279	0	ENST00000342988.3:c.325C>A	p.Leu109Ile	p.L109I	ENST00000342988	NM_005359.5	109	Cta/Ata	3/12	0.39573741640017	1	FACETS	0.769	0.676	0.867	0.769	0.676	0.867	SUBCLONAL	1	TRUE	0	0.39573741640017	1		279	385	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22143085	22143085	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027256-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	70	313	0	ENST00000215832.6:c.622T>G	p.Ser208Ala	p.S208A	ENST00000215832	NM_002745.4	208	Tcc/Gcc	5/9	1	2	FACETS	0.948	0.832	1	0.948	0.832	1	CLONAL	1	TRUE	1	0.39573741640017	2		313	373	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024133	112024133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1298055854	NA	P-0028620-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	31	458	0	ENST00000368678.4:c.652C>T	p.Arg218Trp	p.R218W	ENST00000368678		218	Cgg/Tgg	7/13	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.740898130063348	2		458	68	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0031078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	85	365	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.254278119211527	3	FACETS	1	0.96	1	0.587	0.522	0.655	INDETERMINATE	1	TRUE	1	0.469470141914936	3		365	381	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0031078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	96	162	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.469470141914936	3	FACETS	0.946	0.868	1	0.946	0.868	1	CLONAL	3	TRUE	0	0.469470141914936	3		162	178	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920422	114920422	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	71	354	0	ENST00000543371.1:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000543371	NM_001198531.1	455	Cga/Tga	13/14	0.228754556472424	3	FACETS	0.765	0.67	0.868	0.255	0.223	0.29	INDETERMINATE	1	TRUE	0	0.469470141914936	3		354	488	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107090	27107091	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	79	330	0	ENST00000324856.7:c.6702dup	p.Ala2235CysfsTer43	p.A2235Cfs*43	ENST00000324856	NM_006015.4	2234	gct/gcTt	20/20	0.266432783122241	1	FACETS	0.994	0.886	1	0.994	0.886	1	INDETERMINATE	1	TRUE	0	0.469470141914936	1		330	259	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711289	114711289	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	200	245	0	ENST00000543371.1:c.304G>T	p.Gly102Cys	p.G102C	ENST00000543371	NM_001198531.1	102	Ggc/Tgc	3/14	0.228754556472424	3	FACETS	1	0.983	1	0.762	0.714	0.811	INDETERMINATE	2	TRUE	0	0.469470141914936	3		245	460	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128849178	128849178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	59	411	1	ENST00000249373.3:c.1406G>A	p.Cys469Tyr	p.C469Y	ENST00000249373	NM_005631.4	469	tGc/tAc	8/12	0.469470141914936	3	FACETS	0.701	0.604	0.805	0.234	0.201	0.269	SUBCLONAL	1	TRUE	0	0.469470141914936	3		412	443	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0032280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	59	413	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.2	2		414	569	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0032280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	25	187	13	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.3	2	FACETS	0.44	0.346	0.549			1	SUBCLONAL	1	TRUE	NA	0.2	2		200	568	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426893	6426893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519948	NA	P-0032280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	18	480	1	ENST00000356142.4:c.86C>T	p.Pro29Leu	p.P29L	ENST00000356142	NM_018890.3	29	cCt/cTt	2/7	1	2	FACETS	0.222	0.166	0.289	0.222	0.166	0.289	SUBCLONAL	1	TRUE	1	0.2	2		481	812	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231724	66231724	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	52	532	0	ENST00000273854.3:c.1976C>A	p.Pro659His	p.P659H	ENST00000273854	NM_004439.5	659	cCc/cAc	11/18	1	2	FACETS	0.908	0.772	1	0.908	0.772	1	CLONAL	1	TRUE	1	0.2	2		532	573	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143044	47143044	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	30	314	0	ENST00000409792.3:c.4919G>A	p.Trp1640Ter	p.W1640*	ENST00000409792	NM_014159.6	1640	tGg/tAg	8/21	1	2	FACETS	0.509	0.409	0.624	0.509	0.409	0.624	SUBCLONAL	1	TRUE	1	0.2	2		314	589	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543382	65543382	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0032280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	61	475	0	ENST00000358664.4:c.296-1G>T		p.X99_splice	ENST00000358664	NM_002382.4	99			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.2	2		475	501	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619211	43619211	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	41	474	1	ENST00000355710.3:c.2894A>T	p.Lys965Met	p.K965M	ENST00000355710	NM_020975.4	965	aAg/aTg	17/20	1	2	FACETS	0.86	0.716	1	0.86	0.716	1	CLONAL	1	TRUE	1	0.2	2		475	477	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549388	21549388	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	35	494	0	ENST00000382592.4:c.2888G>T	p.Gly963Val	p.G963V	ENST00000382592	NM_014572.2	963	gGg/gTg	8/8	1	2	FACETS	0.745	0.61	0.896	0.745	0.61	0.896	SUBCLONAL	1	TRUE	1	0.2	2		494	470	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896427	28896427	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	42	329	0	ENST00000282397.4:c.3023G>T	p.Arg1008Ile	p.R1008I	ENST00000282397	NM_002019.4	1008	aGa/aTa	22/30	1	2	FACETS	0.961	0.803	1	0.961	0.803	1	CLONAL	1	TRUE	1	0.2	2		329	437	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562881	95562881	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	33	308	0	ENST00000393063.1:c.4376G>T	p.Gly1459Val	p.G1459V	ENST00000393063	NM_030621.3	1459	gGg/gTg	24/28	1	2	FACETS	0.842	0.686	1	0.842	0.686	1	CLONAL	1	TRUE	1	0.2	2		308	392	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292626	91292626	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0032280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	29	205	0	ENST00000355112.3:c.128C>G	p.Ser43Ter	p.S43*	ENST00000355112	NM_000057.2	43	tCa/tGa	3/22	1	2	FACETS	0.863	0.694	1	0.863	0.694	1	CLONAL	1	TRUE	1	0.2	2		205	336	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038152	128038152	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	46	460	0	ENST00000285398.2:c.1398G>T	p.Leu466Phe	p.L466F	ENST00000285398	NM_000122.1	466	ttG/ttT	9/15	1	2	FACETS	0.849	0.714	0.997	0.849	0.714	0.997	CLONAL	1	TRUE	1	0.2	2		460	542	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560791	9560791	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0032280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	36	329	0	ENST00000353224.5:c.990+1G>T		p.X330_splice	ENST00000353224	NM_177990.2	330			1	2	FACETS	0.942	0.776	1	0.942	0.776	1	CLONAL	1	TRUE	1	0.2	2		329	382	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526738	106526738	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0032280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	34	300	0	ENST00000359195.3:c.3030+1G>T		p.X1010_splice	ENST00000359195	NM_002649.2	1010			1	2	FACETS	0.909	0.744	1	0.909	0.744	1	CLONAL	1	TRUE	1	0.2	2		300	374	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38194987	38194987	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0032280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	50	329	0	ENST00000317025.8:c.748-2A>G		p.X250_splice	ENST00000317025	NM_023034.1	250			1	2	FACETS	0.923	0.783	1	0.923	0.783	1	CLONAL	1	TRUE	1	0.2	2		329	542	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417508	139417508	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	75	843	0	ENST00000277541.6:c.536T>G	p.Val179Gly	p.V179G	ENST00000277541	NM_017617.3	179	gTc/gGc	4/34	1	2	FACETS	0.88	0.77	1	0.88	0.77	1	CLONAL	1	TRUE	1	0.2	2		843	852	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231065	53231065	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	84	587	0	ENST00000375401.3:c.1837G>C	p.Glu613Gln	p.E613Q	ENST00000375401	NM_004187.3	613	Gag/Cag	13/26	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.2	2		587	675	SUCCESS
AR	367	MSKCC	GRCh37	X	66765372	66765372	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	49	613	0	ENST00000374690.3:c.384G>C	p.Glu128Asp	p.E128D	ENST00000374690	NM_000044.3	128	gaG/gaC	1/8	1	2	FACETS	0.904	0.766	1	0.904	0.766	1	CLONAL	1	TRUE	1	0.2	2		613	542	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242640	16242640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	66	393	0	ENST00000375759.3:c.1261G>A	p.Glu421Lys	p.E421K	ENST00000375759	NM_015001.2	421	Gaa/Aaa	6/15	1	2	FACETS	0.61	0.53	0.697	0.61	0.53	0.697	SUBCLONAL	1	TRUE	1	0.39	2		393	555	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17349200	17349200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	53	467	0	ENST00000375499.3:c.668G>A	p.Arg223Lys	p.R223K	ENST00000375499	NM_003000.2	223	aGa/aAa	7/8	1	2	FACETS	0.49	0.417	0.569	0.49	0.417	0.569	SUBCLONAL	1	TRUE	1	0.39	2		467	555	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023471	27023471	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs967763683	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	85	485	1	ENST00000324856.7:c.577G>A	p.Glu193Lys	p.E193K	ENST00000324856	NM_006015.4	193	Gag/Aag	1/20	1	2	FACETS	0.584	0.515	0.657	0.584	0.515	0.657	SUBCLONAL	1	TRUE	1	0.39	2		486	747	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598814	28598814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	113	692	0	ENST00000253063.3:c.374G>A	p.Cys125Tyr	p.C125Y	ENST00000253063	NM_031459.4	125	tGt/tAt	4/10	1	2	FACETS	0.66	0.593	0.731	0.66	0.593	0.731	SUBCLONAL	1	TRUE	1	0.39	2		692	878	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695881	117695881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	94	610	0	ENST00000369458.3:c.556G>A	p.Asp186Asn	p.D186N	ENST00000369458	NM_024626.3	186	Gac/Aac	4/6	1	2	FACETS	0.607	0.54	0.679	0.607	0.54	0.679	SUBCLONAL	1	TRUE	1	0.39	2		610	794	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551491	150551492	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCC	rs759789515	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1162	120	809	0	ENST00000369026.2:c.513_515dup	p.Glu171dup	p.E171dup	ENST00000369026	NM_021960.4	171	gac/gaGGAc	1/3	1	2	FACETS	0.48	0.432	0.531	0.48	0.432	0.531	SUBCLONAL	1	TRUE	1	0.39	2		809	1282	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663871	241663871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1131691244	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	33	418	0	ENST00000366560.3:c.1256C>T	p.Ser419Leu	p.S419L	ENST00000366560	NM_000143.3	419	tCa/tTa	9/10	1	2	FACETS	0.279	0.227	0.339	0.279	0.227	0.339	SUBCLONAL	1	TRUE	1	0.39	2		418	606	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682991	241682991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226883651	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	40	325	0	ENST00000366560.3:c.32C>T	p.Ser11Leu	p.S11L	ENST00000366560	NM_000143.3	11	tCg/tTg	1/10	1	2	FACETS	0.359	0.298	0.428	0.359	0.298	0.428	SUBCLONAL	1	TRUE	1	0.39	2		325	571	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828108	243828108	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	116	487	1	ENST00000263826.5:c.250G>A	p.Glu84Lys	p.E84K	ENST00000263826	NM_005465.4	84	Gag/Aag	3/13	1	2	FACETS	0.665	0.598	0.735	0.665	0.598	0.735	SUBCLONAL	1	TRUE	1	0.39	2		488	895	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405004	70405004	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	43	554	0	ENST00000373644.4:c.2518C>G	p.His840Asp	p.H840D	ENST00000373644	NM_030625.2	840	Cac/Gac	4/12	1	2	FACETS	0.311	0.26	0.369	0.311	0.26	0.369	SUBCLONAL	1	TRUE	1	0.39	2		554	708	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112764363	112764363	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	97	352	0	ENST00000369452.4:c.973-1G>A		p.X325_splice	ENST00000369452	NM_007373.3	325			1	2	FACETS	0.826	0.738	0.92	0.826	0.738	0.92	CLONAL	1	TRUE	1	0.39	2		352	602	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939543	71939543	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	181	860	0	ENST00000298229.2:c.397+1G>A		p.X133_splice	ENST00000298229	NM_001567.3	133			1	2	FACETS	0.883	0.814	0.955	0.883	0.814	0.955	CLONAL	1	TRUE	1	0.39	2		860	1051	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100435	102100435	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	58	374	0	ENST00000282441.5:c.1279G>A	p.Asp427Asn	p.D427N	ENST00000282441	NM_001130145.2	427	Gat/Aat	9/9	1	2	FACETS	0.548	0.471	0.632	0.548	0.471	0.632	SUBCLONAL	1	TRUE	1	0.39	2		374	543	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195629	102195629	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs147101958	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	109	409	0	ENST00000263464.3:c.389A>C	p.Asn130Thr	p.N130T	ENST00000263464	NM_001165.4	130	aAc/aCc	2/9	0.140502758503196	3	FACETS	1	0.941	1	0.533	0.479	0.589	INDETERMINATE	1	TRUE	1	0.39	3		409	627	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165783	108165783	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060501627	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	27	306	0	ENST00000278616.4:c.4906C>T	p.Gln1636Ter	p.Q1636*	ENST00000278616	NM_000051.3	1636	Cag/Tag	32/63	0.140502758503196	3	FACETS	0.324	0.257	0.401	0.162	0.128	0.201	INDETERMINATE	1	TRUE	1	0.39	3		306	510	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038954	12038954	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	38	257	0	ENST00000396373.4:c.1247T>C	p.Leu416Ser	p.L416S	ENST00000396373	NM_001987.4	416	tTg/tCg	7/8	0.140502758503196	3	FACETS	0.616	0.51	0.734	0.308	0.255	0.367	INDETERMINATE	1	TRUE	1	0.39	3		257	378	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871250	12871250	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	14	144	0	ENST00000228872.4:c.475+2T>C		p.X159_splice	ENST00000228872	NM_004064.3	159			0.140502758503196	3	FACETS	0.52	0.377	0.691	0.26	0.188	0.346	INDETERMINATE	1	TRUE	1	0.39	3		144	165	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716371	18716371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773501044	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	58	331	0	ENST00000266497.5:c.3718G>A	p.Glu1240Lys	p.E1240K	ENST00000266497		1240	Gag/Aag	26/31	0.140502758503196	3	FACETS	0.62	0.533	0.716	0.31	0.266	0.358	INDETERMINATE	1	TRUE	1	0.39	3		331	573	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624480	21624480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	57	693	0	ENST00000421138.2:c.1549G>A	p.Asp517Asn	p.D517N	ENST00000421138		517	Gat/Aat	14/16	0.140502758503196	3	FACETS	0.322	0.275	0.374	0.161	0.137	0.187	INDETERMINATE	1	TRUE	1	0.39	3		693	1085	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243472	46243472	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	53	376	0	ENST00000334344.6:c.1825C>T	p.Gln609Ter	p.Q609*	ENST00000334344	NM_152641.2	609	Cag/Tag	14/21	0.140502758503196	3	FACETS	0.547	0.466	0.636	0.273	0.233	0.318	INDETERMINATE	1	TRUE	1	0.39	3		376	594	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434880	49434880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	95	704	1	ENST00000301067.7:c.6673G>A	p.Glu2225Lys	p.E2225K	ENST00000301067	NM_003482.3	2225	Gaa/Aaa	31/54	0.140502758503196	3	FACETS	0.702	0.625	0.785	0.351	0.312	0.393	INDETERMINATE	1	TRUE	1	0.39	3		705	829	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487891	56487891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759562930	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	89	507	0	ENST00000267101.3:c.1622G>A	p.Arg541Gln	p.R541Q	ENST00000267101	NM_001982.3	541	cGa/cAa	14/28	0.140502758503196	3	FACETS	0.833	0.739	0.933	0.416	0.369	0.467	INDETERMINATE	1	TRUE	1	0.39	3		507	655	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253950	133253950	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	85	482	0	ENST00000320574.5:c.800C>T	p.Pro267Leu	p.P267L	ENST00000320574	NM_006231.2	267	cCt/cTt	8/49	0.3	1	FACETS	0.533	0.471	0.599	0.533	0.471	0.599	SUBCLONAL	1	TRUE	0	0.39	1		482	658	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923311	26923311	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	83	339	0	ENST00000381527.3:c.307G>A	p.Asp103Asn	p.D103N	ENST00000381527	NM_001260.1	103	Gac/Aac	3/13	1	2	FACETS	0.751	0.664	0.844	0.751	0.664	0.844	SUBCLONAL	1	TRUE	1	0.39	2		339	567	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26927979	26927979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	43	516	0	ENST00000381527.3:c.418C>T	p.His140Tyr	p.H140Y	ENST00000381527	NM_001260.1	140	Cac/Tac	4/13	1	2	FACETS	0.306	0.255	0.363	0.306	0.255	0.363	SUBCLONAL	1	TRUE	1	0.39	2		516	720	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134873	41134873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	83	460	0	ENST00000379561.5:c.755G>A	p.Arg252Lys	p.R252K	ENST00000379561	NM_002015.3	252	aGa/aAa	2/3	1	2	FACETS	0.65	0.574	0.731	0.65	0.574	0.731	SUBCLONAL	1	TRUE	1	0.39	2		460	655	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336095	73336095	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780575971	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	43	249	0	ENST00000377767.4:c.2308C>T	p.Pro770Ser	p.P770S	ENST00000377767	NM_014953.3	770	Cca/Tca	17/21	1	2	FACETS	0.596	0.5	0.702	0.596	0.5	0.702	SUBCLONAL	1	TRUE	1	0.39	2		249	370	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396541	30396541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746045993	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	74	403	0	ENST00000331968.5:c.178G>A	p.Glu60Lys	p.E60K	ENST00000331968	NM_002742.2	60	Gag/Aag	1/18	1	2	FACETS	0.654	0.573	0.741	0.654	0.573	0.741	SUBCLONAL	1	TRUE	1	0.39	2		403	580	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68290339	68290339	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	44	329	0	ENST00000487270.1:c.79T>C	p.Cys27Arg	p.C27R	ENST00000487270	NM_133509.3	27	Tgt/Cgt	2/11	1	2	FACETS	0.524	0.439	0.616	0.524	0.439	0.616	SUBCLONAL	1	TRUE	1	0.39	2		329	431	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023037	33023037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	78	357	0	ENST00000300177.4:c.146C>T	p.Ser49Leu	p.S49L	ENST00000300177	NM_001191322.1	49	tCg/tTg	2/2	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.39	2		357	364	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675046	40675046	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	154	556	0	ENST00000249776.8:c.10C>T	p.Pro4Ser	p.P4S	ENST00000249776	NM_033286.3	4	Ccc/Tcc	1/9	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.39	2		556	778	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40998441	40998441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	160	587	0	ENST00000267868.3:c.292G>A	p.Glu98Lys	p.E98K	ENST00000267868	NM_002875.4	98	Gag/Aag	4/10	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.39	2		587	797	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782870	66782870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	85	496	0	ENST00000307102.5:c.1099G>A	p.Glu367Lys	p.E367K	ENST00000307102	NM_002755.3	367	Gag/Aag	11/11	1	2	FACETS	0.646	0.571	0.726	0.646	0.571	0.726	SUBCLONAL	1	TRUE	1	0.39	2		496	675	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138453	2138453	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375075952	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	53	742	2	ENST00000219476.3:c.5266G>A	p.Glu1756Lys	p.E1756K	ENST00000219476	NM_000548.3	1756	Gag/Aag	42/42	1	2	FACETS	0.331	0.282	0.386	0.331	0.282	0.386	SUBCLONAL	1	TRUE	1	0.39	2		744	820	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639732	3639732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759828401	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	76	935	0	ENST00000294008.3:c.3907G>A	p.Glu1303Lys	p.E1303K	ENST00000294008	NM_032444.2	1303	Gaa/Aaa	12/15	1	2	FACETS	0.37	0.323	0.421	0.37	0.323	0.421	SUBCLONAL	1	TRUE	1	0.39	2		935	1053	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614968	23614968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	60	349	0	ENST00000261584.4:c.3373G>A	p.Asp1125Asn	p.D1125N	ENST00000261584	NM_024675.3	1125	Gat/Aat	13/13	1	2	FACETS	0.622	0.536	0.714	0.622	0.536	0.714	SUBCLONAL	1	TRUE	1	0.39	2		349	495	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128253	30128253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766518304	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	46	718	0	ENST00000263025.4:c.979C>T	p.His327Tyr	p.H327Y	ENST00000263025	NM_002746.2	327	Cac/Tac	7/9	1	2	FACETS	0.276	0.231	0.325	0.276	0.231	0.325	SUBCLONAL	1	TRUE	1	0.39	2		718	855	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	57	490	1	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	1	2	FACETS	0.507	0.434	0.585	0.507	0.434	0.585	SUBCLONAL	1	TRUE	1	0.39	2		491	577	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842729	68842729	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555515287	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	93	444	0	ENST00000261769.5:c.665G>A	p.Arg222Lys	p.R222K	ENST00000261769	NM_004360.3	222	aGa/aAa	5/16	1	2	FACETS	0.796	0.709	0.889	0.796	0.709	0.889	SUBCLONAL	1	TRUE	1	0.39	2		444	599	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351577	89351577	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	63	820	0	ENST00000301030.4:c.1373G>T	p.Arg458Leu	p.R458L	ENST00000301030	NM_001256183.1	458	cGa/cTa	9/13	1	2	FACETS	0.316	0.272	0.363	0.316	0.272	0.363	SUBCLONAL	1	TRUE	1	0.39	2		820	1024	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816263	89816264	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	77	547	0	ENST00000389301.3:c.3113_3114del	p.Leu1038ArgfsTer12	p.L1038Rfs*12	ENST00000389301	NM_000135.2	1038	cTC/c	32/43	1	2	FACETS	0.534	0.468	0.604	0.534	0.468	0.604	SUBCLONAL	1	TRUE	1	0.39	2		547	740	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998985	11998985	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	39	333	0	ENST00000353533.5:c.487C>T	p.Gln163Ter	p.Q163*	ENST00000353533	NM_003010.3	163	Cag/Tag	4/11	1	2	FACETS	0.348	0.288	0.416	0.348	0.288	0.416	SUBCLONAL	1	TRUE	1	0.39	2		333	574	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654589	29654589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	61	243	0	ENST00000356175.3:c.5278G>A	p.Asp1760Asn	p.D1760N	ENST00000356175	NM_000267.3	1760	Gac/Aac	37/57	1	2	FACETS	0.788	0.682	0.902	0.788	0.682	0.902	CLONAL	1	TRUE	1	0.39	2		243	397	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245861	41245861	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs80356898	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	56	365	0	ENST00000357654.3:c.1687C>G	p.Gln563Glu	p.Q563E	ENST00000357654	NM_007294.3	563	Cag/Gag	10/23	1	2	FACETS	0.317	0.27	0.368	0.317	0.27	0.368	SUBCLONAL	1	TRUE	1	0.39	2		365	906	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770110	56770110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773998134	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	35	497	0	ENST00000337432.4:c.106G>A	p.Glu36Lys	p.E36K	ENST00000337432	NM_058216.2	36	Gag/Aag	1/9	1	2	FACETS	0.271	0.221	0.327	0.271	0.221	0.327	SUBCLONAL	1	TRUE	1	0.39	2		497	662	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780677	56780677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502588	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	152	559	0	ENST00000337432.4:c.692C>T	p.Ser231Leu	p.S231L	ENST00000337432	NM_058216.2	231	tCa/tTa	4/9	1	2	FACETS	0.902	0.825	0.983	0.902	0.825	0.983	CLONAL	1	TRUE	1	0.39	2		559	864	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821797	59821797	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	49	472	0	ENST00000259008.2:c.2253G>C	p.Glu751Asp	p.E751D	ENST00000259008	NM_032043.2	751	gaG/gaC	15/20	1	2	FACETS	0.284	0.239	0.333	0.284	0.239	0.333	SUBCLONAL	1	TRUE	1	0.39	2		472	886	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117755	70117755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	85	601	0	ENST00000245479.2:c.223G>A	p.Glu75Lys	p.E75K	ENST00000245479	NM_000346.3	75	Gag/Aag	1/3	1	2	FACETS	0.563	0.497	0.634	0.563	0.497	0.634	SUBCLONAL	1	TRUE	1	0.39	2		601	774	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56367746	56367746	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	64	362	0	ENST00000348428.3:c.572G>T	p.Arg191Leu	p.R191L	ENST00000348428	NM_006785.3	191	cGa/cTa	4/17	1	2	FACETS	0.488	0.422	0.559	0.488	0.422	0.559	SUBCLONAL	1	TRUE	1	0.39	2		362	673	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191099	2191099	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	40	551	0	ENST00000398665.3:c.353C>G	p.Ser118Trp	p.S118W	ENST00000398665	NM_032482.2	118	tCg/tGg	5/28	1	2	FACETS	0.274	0.227	0.327	0.274	0.227	0.327	SUBCLONAL	1	TRUE	1	0.39	2		551	748	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602926	10602926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	49	824	0	ENST00000171111.5:c.652G>A	p.Glu218Lys	p.E218K	ENST00000171111	NM_203500.1	218	Gag/Aag	3/6	1	2	FACETS	0.268	0.226	0.315	0.268	0.226	0.315	SUBCLONAL	1	TRUE	1	0.39	2		824	937	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051440	13051440	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769245573	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	68	376	0	ENST00000316448.5:c.788C>T	p.Pro263Leu	p.P263L	ENST00000316448	NM_004343.3	263	cCc/cTc	6/9	1	2	FACETS	0.688	0.599	0.783	0.688	0.599	0.783	SUBCLONAL	1	TRUE	1	0.39	2		376	507	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281581	15281581	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	113	813	0	ENST00000263388.2:c.4792G>A	p.Asp1598Asn	p.D1598N	ENST00000263388	NM_000435.2	1598	Gat/Aat	26/33	1	2	FACETS	0.674	0.606	0.746	0.674	0.606	0.746	SUBCLONAL	1	TRUE	1	0.39	2		813	860	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303241	15303241	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	75	778	1	ENST00000263388.2:c.287C>T	p.Ser96Leu	p.S96L	ENST00000263388	NM_000435.2	96	tCa/tTa	3/33	1	2	FACETS	0.447	0.39	0.508	0.447	0.39	0.508	SUBCLONAL	1	TRUE	1	0.39	2		779	861	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15364986	15364986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768842514	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	40	541	0	ENST00000263377.2:c.2135C>T	p.Ser712Phe	p.S712F	ENST00000263377	NM_058243.2	712	tCt/tTt	11/20	1	2	FACETS	0.319	0.264	0.38	0.319	0.264	0.38	SUBCLONAL	1	TRUE	1	0.39	2		541	644	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366186	15366186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	57	712	0	ENST00000263377.2:c.1969G>A	p.Glu657Lys	p.E657K	ENST00000263377	NM_058243.2	657	Gag/Aag	10/20	1	2	FACETS	0.334	0.286	0.387	0.334	0.286	0.387	SUBCLONAL	1	TRUE	1	0.39	2		712	875	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17389843	17389843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	127	763	0	ENST00000359435.4:c.976G>A	p.Glu326Lys	p.E326K	ENST00000359435	NM_001033549.1	326	Gag/Aag	9/9	1	2	FACETS	0.694	0.628	0.763	0.694	0.628	0.763	SUBCLONAL	1	TRUE	1	0.39	2		763	939	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266816	18266816	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750768114	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	105	495	0	ENST00000222254.8:c.127G>A	p.Val43Met	p.V43M	ENST00000222254	NM_005027.3	43	Gtg/Atg	2/16	1	2	FACETS	0.902	0.81	0.999	0.902	0.81	0.999	CLONAL	1	TRUE	1	0.39	2		495	597	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762361	41762361	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	69	412	0	ENST00000301178.4:c.2042del	p.Asn681MetfsTer41	p.N681Mfs*41	ENST00000301178	NM_021913.4	681	Aat/at	18/20	1	2	FACETS	0.661	0.577	0.753	0.661	0.577	0.753	SUBCLONAL	1	TRUE	1	0.39	2		412	535	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	96	698	0	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	1	2	FACETS	0.648	0.577	0.723	0.648	0.577	0.723	SUBCLONAL	1	TRUE	1	0.39	2		698	760	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25498371	25498372	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	39	486	0	ENST00000264709.3:c.489_490delinsAA	p.Met163_Glu164delinsIleLys	p.M163_E164delinsIK	ENST00000264709	NM_175629.2	163	atGGag/atAAag	5/23	1	2	FACETS	0.324	0.267	0.387	0.324	0.267	0.387	SUBCLONAL	1	TRUE	1	0.39	2		486	618	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978922	25978922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1217311360	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	95	419	0	ENST00000435504.4:c.1001C>T	p.Ser334Leu	p.S334L	ENST00000435504		334	tCa/tTa	10/13	1	2	FACETS	0.7	0.623	0.781	0.7	0.623	0.781	SUBCLONAL	1	TRUE	1	0.39	2		419	696	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143441	30143441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326321652	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	64	288	0	ENST00000389048.3:c.85G>A	p.Ala29Thr	p.A29T	ENST00000389048	NM_004304.4	29	Gcg/Acg	1/29	1	2	FACETS	0.861	0.749	0.982	0.861	0.749	0.982	CLONAL	1	TRUE	1	0.39	2		288	381	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250287	39250287	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1398	84	885	0	ENST00000402219.2:c.1282A>C	p.Asn428His	p.N428H	ENST00000402219	NM_005633.3	428	Aat/Cat	10/23	1	2	FACETS	0.291	0.255	0.329	0.291	0.255	0.329	SUBCLONAL	1	TRUE	1	0.39	2		885	1482	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46588072	46588072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	102	609	0	ENST00000263734.3:c.622C>T	p.His208Tyr	p.H208Y	ENST00000263734	NM_001430.4	208	Cac/Tac	6/16	1	2	FACETS	0.683	0.611	0.76	0.683	0.611	0.76	SUBCLONAL	1	TRUE	1	0.39	2		609	766	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47612312	47612312	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622286	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	53	336	0	ENST00000263735.4:c.866C>T	p.Ser289Phe	p.S289F	ENST00000263735	NM_002354.2	289	tCc/tTc	8/9	1	2	FACETS	0.549	0.468	0.637	0.549	0.468	0.637	SUBCLONAL	1	TRUE	1	0.39	2		336	495	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270162	198270162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	39	301	0	ENST00000335508.6:c.1274G>A	p.Arg425Gln	p.R425Q	ENST00000335508	NM_012433.2	425	cGa/cAa	10/25	1	2	FACETS	0.375	0.31	0.447	0.375	0.31	0.447	SUBCLONAL	1	TRUE	1	0.39	2		301	534	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285763	198285763	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	35	412	0	ENST00000335508.6:c.290C>T	p.Ser97Leu	p.S97L	ENST00000335508	NM_012433.2	97	tCa/tTa	3/25	1	2	FACETS	0.342	0.28	0.412	0.342	0.28	0.412	SUBCLONAL	1	TRUE	1	0.39	2		412	525	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209110098	209110100	+	inframe_deletion	In_Frame_Del	DEL	GGT	GGT	-	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	63	611	0	ENST00000345146.2:c.463_465del	p.Thr155del	p.T155del	ENST00000345146	NM_005896.2	155	ACC/-	5/10	1	2	FACETS	0.375	0.323	0.431	0.375	0.323	0.431	SUBCLONAL	1	TRUE	1	0.39	2		611	862	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662365	227662365	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771146954	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	48	500	0	ENST00000305123.5:c.1090C>T	p.Arg364Trp	p.R364W	ENST00000305123	NM_005544.2	364	Cgg/Tgg	1/2	1	2	FACETS	0.396	0.334	0.464	0.396	0.334	0.464	SUBCLONAL	1	TRUE	1	0.39	2		500	622	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663346	227663346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024227751	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	81	486	0	ENST00000305123.5:c.109G>A	p.Glu37Lys	p.E37K	ENST00000305123	NM_005544.2	37	Gag/Aag	1/2	1	2	FACETS	0.681	0.6	0.767	0.681	0.6	0.767	SUBCLONAL	1	TRUE	1	0.39	2		486	610	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309736	30309736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	57	514	0	ENST00000307677.4:c.286G>A	p.Glu96Lys	p.E96K	ENST00000307677	NM_138578.1	96	Gag/Aag	2/3	0.3	1	FACETS	0.325	0.278	0.376	0.325	0.278	0.376	SUBCLONAL	1	TRUE	0	0.39	1		514	725	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54956590	54956590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	54	407	0	ENST00000312783.6:c.604G>A	p.Asp202Asn	p.D202N	ENST00000312783	NM_198436.1	202	Gat/Aat	7/10	1	2	FACETS	0.546	0.467	0.633	0.546	0.467	0.633	SUBCLONAL	1	TRUE	1	0.39	2		407	507	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24135748	24135748	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	34	377	0	ENST00000263121.7:c.235C>T	p.His79Tyr	p.H79Y	ENST00000263121	NM_003073.3	79	Cac/Tac	3/9	1	2	FACETS	0.367	0.299	0.443	0.367	0.299	0.443	SUBCLONAL	1	TRUE	1	0.39	2		377	475	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090482	37090482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	29	331	0	ENST00000231790.2:c.2077G>A	p.Glu693Lys	p.E693K	ENST00000231790	NM_000249.3	693	Gag/Aag	18/19	1	2	FACETS	0.297	0.237	0.365	0.297	0.237	0.365	SUBCLONAL	1	TRUE	1	0.39	2		331	501	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	30	270	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.325	0.261	0.397	0.325	0.261	0.397	SUBCLONAL	1	TRUE	1	0.39	2		270	474	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143043	47143043	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	67	380	0	ENST00000409792.3:c.4920G>A	p.Trp1640Ter	p.W1640*	ENST00000409792	NM_014159.6	1640	tgG/tgA	8/21	1	2	FACETS	0.565	0.491	0.645	0.565	0.491	0.645	SUBCLONAL	1	TRUE	1	0.39	2		380	608	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	57	645	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	1	2	FACETS	0.334	0.286	0.388	0.334	0.286	0.388	SUBCLONAL	1	TRUE	1	0.39	2		645	874	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442080	52442080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	68	453	0	ENST00000460680.1:c.269C>T	p.Ser90Phe	p.S90F	ENST00000460680	NM_004656.3	90	tCt/tTt	5/17	1	2	FACETS	0.553	0.481	0.631	0.553	0.481	0.631	SUBCLONAL	1	TRUE	1	0.39	2		453	631	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799680	72799680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867810225	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	69	584	0	ENST00000325599.8:c.1489G>A	p.Glu497Lys	p.E497K	ENST00000325599	NM_018130.2	497	Gaa/Aaa	11/11	1	2	FACETS	0.498	0.433	0.568	0.498	0.433	0.568	SUBCLONAL	1	TRUE	1	0.39	2		584	711	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205859	128205859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760132552	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	57	297	0	ENST00000341105.2:c.16G>A	p.Glu6Lys	p.E6K	ENST00000341105	NM_032638.4	6	Gag/Aag	2/6	1	2	FACETS	0.79	0.681	0.908	0.79	0.681	0.908	CLONAL	1	TRUE	1	0.39	2		297	370	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825410	134825410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	44	475	0	ENST00000398015.3:c.926G>A	p.Arg309Gln	p.R309Q	ENST00000398015	NM_004441.4	309	cGa/cAa	4/16	1	2	FACETS	0.346	0.289	0.409	0.346	0.289	0.409	SUBCLONAL	1	TRUE	1	0.39	2		475	652	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433333	138433333	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	98	571	0	ENST00000289153.2:c.1279A>G	p.Thr427Ala	p.T427A	ENST00000289153	NM_006219.2	427	Acc/Gcc	7/22	1	2	FACETS	0.584	0.521	0.652	0.584	0.521	0.652	SUBCLONAL	1	TRUE	1	0.39	2		571	860	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231240	142231240	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	81	617	0	ENST00000350721.4:c.4714G>A	p.Asp1572Asn	p.D1572N	ENST00000350721	NM_001184.3	1572	Gat/Aat	27/47	1	2	FACETS	0.482	0.424	0.545	0.482	0.424	0.545	SUBCLONAL	1	TRUE	1	0.39	2		617	861	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272837	142272837	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	41	329	0	ENST00000350721.4:c.2362C>G	p.His788Asp	p.H788D	ENST00000350721	NM_001184.3	788	Cat/Gat	11/47	1	2	FACETS	0.34	0.283	0.405	0.34	0.283	0.405	SUBCLONAL	1	TRUE	1	0.39	2		329	618	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161268	185161268	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	87	574	0	ENST00000265026.3:c.695T>C	p.Ile232Thr	p.I232T	ENST00000265026	NM_004721.4	232	aTc/aCc	4/14	1	2	FACETS	0.501	0.442	0.563	0.501	0.442	0.563	SUBCLONAL	1	TRUE	1	0.39	2		574	891	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902418	1902418	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	75	651	1	ENST00000382891.5:c.37C>T	p.Gln13Ter	p.Q13*	ENST00000382891	NM_133335.3	13	Cag/Tag	2/22	1	2	FACETS	0.441	0.385	0.501	0.441	0.385	0.501	SUBCLONAL	1	TRUE	1	0.39	2		652	873	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156687	55156687	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	64	344	0	ENST00000257290.5:c.3088G>C	p.Glu1030Gln	p.E1030Q	ENST00000257290	NM_006206.4	1030	Gag/Cag	22/23	1	2	FACETS	0.687	0.596	0.785	0.687	0.596	0.785	SUBCLONAL	1	TRUE	1	0.39	2		344	478	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280123	66280123	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	34	354	0	ENST00000273854.3:c.1566G>C	p.Glu522Asp	p.E522D	ENST00000273854	NM_004439.5	522	gaG/gaC	7/18	1	2	FACETS	0.288	0.234	0.348	0.288	0.234	0.348	SUBCLONAL	1	TRUE	1	0.39	2		354	606	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532729	187532729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	36	465	0	ENST00000441802.2:c.9664G>A	p.Asp3222Asn	p.D3222N	ENST00000441802	NM_005245.3	3222	Gac/Aac	14/27	1	2	FACETS	0.289	0.237	0.348	0.289	0.237	0.348	SUBCLONAL	1	TRUE	1	0.39	2		465	639	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549788	187549788	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	37	545	1	ENST00000441802.2:c.4453G>A	p.Glu1485Lys	p.E1485K	ENST00000441802	NM_005245.3	1485	Gag/Aag	8/27	1	2	FACETS	0.274	0.225	0.329	0.274	0.225	0.329	SUBCLONAL	1	TRUE	1	0.39	2		546	692	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564797	86564797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	102	707	0	ENST00000274376.6:c.529C>T	p.Pro177Ser	p.P177S	ENST00000274376	NM_002890.2	177	Cca/Tca	1/25	1	2	FACETS	0.596	0.532	0.664	0.596	0.532	0.664	SUBCLONAL	1	TRUE	1	0.39	2		707	878	SUCCESS
APC	324	MSKCC	GRCh37	5	112179740	112179740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	56	227	0	ENST00000257430.4:c.8449G>A	p.Asp2817Asn	p.D2817N	ENST00000257430	NM_000038.5	2817	Gat/Aat	16/16	1	2	FACETS	0.74	0.636	0.853	0.74	0.636	0.853	SUBCLONAL	1	TRUE	1	0.39	2		227	388	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721708	176721708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	48	444	0	ENST00000439151.2:c.7339C>T	p.Gln2447Ter	p.Q2447*	ENST00000439151	NM_022455.4	2447	Cag/Tag	23/23	1	2	FACETS	0.48	0.405	0.562	0.48	0.405	0.562	SUBCLONAL	1	TRUE	1	0.39	2		444	513	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480123	20480123	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	28	337	0	ENST00000346618.3:c.440C>T	p.Ser147Leu	p.S147L	ENST00000346618	NM_001949.4	147	tCa/tTa	2/7	1	2	FACETS	0.302	0.241	0.372	0.302	0.241	0.372	SUBCLONAL	1	TRUE	1	0.39	2		337	475	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158513	26158513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750700667	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	42	512	0	ENST00000289316.2:c.116C>T	p.Ser39Leu	p.S39L	ENST00000289316	NM_138720.2	39	tCa/tTa	1/2	1	2	FACETS	0.355	0.296	0.422	0.355	0.296	0.422	SUBCLONAL	1	TRUE	1	0.39	2		512	606	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288543	33288543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	40	433	0	ENST00000374542.5:c.1009G>A	p.Gly337Ser	p.G337S	ENST00000374542	NM_001141970.1	337	Ggc/Agc	3/8	1	2	FACETS	0.372	0.309	0.443	0.372	0.309	0.443	SUBCLONAL	1	TRUE	1	0.39	2		433	551	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652005	36652005	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	62	688	0	ENST00000244741.5:c.127C>T	p.Gln43Ter	p.Q43*	ENST00000244741	NM_000389.4	43	Cag/Tag	2/3	1	2	FACETS	0.394	0.339	0.453	0.394	0.339	0.453	SUBCLONAL	1	TRUE	1	0.39	2		688	808	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163841	152163841	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	31	462	0	ENST00000206249.3:c.562T>C	p.Cys188Arg	p.C188R	ENST00000206249	NM_000125.3	188	Tgc/Cgc	2/8	1	2	FACETS	0.266	0.214	0.325	0.266	0.214	0.325	SUBCLONAL	1	TRUE	1	0.39	2		462	597	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222592	157222601	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCGCACCT	CCCCGCACCT	-	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	76	537	0	ENST00000346085.5:c.1862_1871del	p.Pro621HisfsTer44	p.P621Hfs*44	ENST00000346085	NM_020732.3	620	cCCCCGCACCTc/cc	4/20	1	2	FACETS	0.549	0.481	0.622	0.549	0.481	0.622	SUBCLONAL	1	TRUE	1	0.39	2		537	710	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528471	157528471	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	52	596	0	ENST00000346085.5:c.6196C>T	p.Pro2066Ser	p.P2066S	ENST00000346085	NM_020732.3	2066	Ccc/Tcc	20/20	1	2	FACETS	0.414	0.352	0.482	0.414	0.352	0.482	SUBCLONAL	1	TRUE	1	0.39	2		596	644	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035200	6035200	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587782833	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	32	371	0	ENST00000265849.7:c.868T>G	p.Phe290Val	p.F290V	ENST00000265849	NM_000535.5	290	Ttc/Gtc	8/15	0.180098135831511	0	FACETS	0.174	0.14	0.212			1	INDETERMINATE	1	TRUE	0	0.39	0		371	576	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048638	6048638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	91	510	0	ENST00000265849.7:c.13G>A	p.Glu5Lys	p.E5K	ENST00000265849	NM_000535.5	5	Gag/Aag	1/15	0.180098135831511	0	FACETS	0.396	0.351	0.444			1	INDETERMINATE	1	TRUE	0	0.39	0		510	719	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339695	116339695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	159	367	0	ENST00000397752.3:c.557C>T	p.Ser186Leu	p.S186L	ENST00000397752	NM_000245.2	186	tCa/tTa	2/21	0.183449114300963	4	FACETS	0.918	0.845	0.994	0.612	0.563	0.663	INDETERMINATE	2	TRUE	1	0.39	4		367	617	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008910	152008910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	46	398	1	ENST00000262189.6:c.712G>A	p.Asp238Asn	p.D238N	ENST00000262189	NM_170606.2	238	Gat/Aat	5/59	0.183449114300963	4	FACETS	0.417	0.35	0.491	0.139	0.116	0.164	INDETERMINATE	1	TRUE	1	0.39	4		399	787	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540350	23540350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752189119	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	29	274	0	ENST00000380871.4:c.53C>T	p.Ala18Val	p.A18V	ENST00000380871	NM_006167.3	18	gCg/gTg	1/2	1	2	FACETS	0.328	0.263	0.403	0.328	0.263	0.403	SUBCLONAL	1	TRUE	1	0.39	2		274	453	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172285	38172285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	57	380	0	ENST00000317025.8:c.2122G>A	p.Glu708Lys	p.E708K	ENST00000317025	NM_023034.1	708	Gaa/Aaa	12/24	1	2	FACETS	0.53	0.454	0.612	0.53	0.454	0.612	SUBCLONAL	1	TRUE	1	0.39	2		380	552	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272080	38272080	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	49	527	0	ENST00000425967.3:c.2138A>G	p.Asp713Gly	p.D713G	ENST00000425967	NM_001174067.1	713	gAt/gGt	16/19	1	2	FACETS	0.378	0.32	0.443	0.378	0.32	0.443	SUBCLONAL	1	TRUE	1	0.39	2		527	664	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372400	55372400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	53	870	0	ENST00000297316.4:c.1090G>A	p.Glu364Lys	p.E364K	ENST00000297316	NM_022454.3	364	Gaa/Aaa	2/2	0.3	1	FACETS	0.221	0.187	0.257	0.221	0.187	0.257	SUBCLONAL	1	TRUE	0	0.39	1		870	992	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741770	145741770	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	58	703	0	ENST00000428558.2:c.733G>T	p.Val245Phe	p.V245F	ENST00000428558	NM_004260.3	245	Gtc/Ttc	5/22	1	2	FACETS	0.383	0.328	0.443	0.383	0.328	0.443	SUBCLONAL	1	TRUE	1	0.39	2		703	777	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270502	98270502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	103	453	0	ENST00000331920.6:c.142G>A	p.Asp48Asn	p.D48N	ENST00000331920	NM_000264.3	48	Gac/Aac	1/24	0.3	1	FACETS	0.798	0.716	0.884	0.798	0.716	0.884	SUBCLONAL	1	TRUE	0	0.39	1		453	533	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	56	782	1	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.3	1	FACETS	0.3	0.256	0.348	0.3	0.256	0.348	SUBCLONAL	1	TRUE	0	0.39	1		783	771	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922814	44922814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761667415	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	127	199	0	ENST00000377967.4:c.1675C>T	p.Arg559Cys	p.R559C	ENST00000377967	NM_021140.2	559	Cgt/Tgt	16/29	0.228325266314882	2	FACETS	0.922	0.846	1			1	INDETERMINATE	2	TRUE	NA	0.39	2		199	353	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224133	53224133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	131	452	0	ENST00000375401.3:c.3418C>T	p.Leu1140Phe	p.L1140F	ENST00000375401	NM_004187.3	1140	Ctc/Ttc	22/26	0.228325266314882	2	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.39	2		452	572	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224144	53224144	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	136	471	0	ENST00000375401.3:c.3407C>G	p.Ser1136Cys	p.S1136C	ENST00000375401	NM_004187.3	1136	tCt/tGt	22/26	0.228325266314882	2	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.39	2		471	594	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53254068	53254068	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	77	176	0	ENST00000375401.3:c.4G>A	p.Glu2Lys	p.E2K	ENST00000375401	NM_004187.3	2	Gag/Aag	1/26	0.228325266314882	2	FACETS	0.754	0.67	0.841			1	INDETERMINATE	2	TRUE	NA	0.39	2		176	262	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349237	70349237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	69	401	0	ENST00000374080.3:c.3649G>A	p.Asp1217Asn	p.D1217N	ENST00000374080		1217	Gat/Aat	26/45	0.228325266314882	2	FACETS	0.701	0.611	0.797			1	INDETERMINATE	1	TRUE	NA	0.39	2		401	505	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732533	74732533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	19	192	0	ENST00000359995.5:c.376C>T	p.Arg126Cys	p.R126C	ENST00000359995	NM_001195427.1	126	Cgc/Tgc	2/3	1	2	FACETS	0.554	0.422	0.706	0.554	0.422	0.706	SUBCLONAL	1	TRUE	1	0.39	2		192	176	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171751	36171794	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCCTTGTATCTGAAGAGAATCAGAAAGGTCAATTATATGTAAAG	GCCTTGTATCTGAAGAGAATCAGAAAGGTCAATTATATGTAAAG	-	novel	NA	P-0032284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	66	287	0	ENST00000300305.3:c.806-35_814del		p.X269_splice	ENST00000300305		269		7/8	1	2	FACETS	0.795	0.692	0.905	0.795	0.692	0.905	CLONAL	1	TRUE	1	0.39	2		287	426	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051642	30051642	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	193	361	1	ENST00000338641.4:c.576C>A	p.Tyr192Ter	p.Y192*	ENST00000338641	NM_000268.3	192	taC/taA	6/16	0.538878104680259	2	FACETS	0.973	0.916	1	0.973	0.916	1	CLONAL	2	TRUE	0	0.538878104680259	2		362	368	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832337	72832337	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	483	471	0	ENST00000268489.5:c.4244A>C	p.Lys1415Thr	p.K1415T	ENST00000268489	NM_006885.3	1415	aAg/aCg	9/10	0.251210324313444	6	FACETS	1	0.991	1			1	INDETERMINATE	5	TRUE	NA	0.538878104680259	6		471	705	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579409	7579410	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0032298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	358	709	0	ENST00000269305.4:c.277dup	p.Leu93ProfsTer56	p.L93Pfs*56	ENST00000269305	NM_001126112.2	93	ctg/cCtg	4/11	0.538878104680259	2	FACETS	0.934	0.893	0.976	0.934	0.893	0.976	CLONAL	2	TRUE	0	0.538878104680259	2		709	711	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782329	NA	P-0032351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	391	575	0	ENST00000269305.4:c.746G>C	p.Arg249Thr	p.R249T	ENST00000269305	NM_001126112.2	249	aGg/aCg	7/11	0.419991878094346	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.432536720027352	2		575	833	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444707	49444707	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	315	634	0	ENST00000301067.7:c.2759C>A	p.Ser920Tyr	p.S920Y	ENST00000301067	NM_003482.3	920	tCt/tAt	10/54	0.304153504415142	3	FACETS	0.876	0.828	0.925	0.876	0.828	0.925	CLONAL	2	TRUE	1	0.432536720027352	3		634	1011	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274087	10274087	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs764780280	NA	P-0032351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	198	551	0	ENST00000330684.3:c.182C>A	p.Ala61Glu	p.A61E	ENST00000330684	NM_001134407.1	61	gCg/gAg	2/13	0.210182131668473	3	FACETS	1	0.991	1	0.733	0.68	0.787	INDETERMINATE	1	TRUE	1	0.432536720027352	3		551	760	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210830	2210830	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	111	360	0	ENST00000398665.3:c.1327C>T	p.Gln443Ter	p.Q443*	ENST00000398665	NM_032482.2	443	Cag/Tag	14/28	0.432536720027352	1	FACETS	0.865	0.782	0.952	0.865	0.782	0.952	CLONAL	1	TRUE	0	0.432536720027352	1		360	465	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602646	10602646	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	258	689	0	ENST00000171111.5:c.932A>C	p.His311Pro	p.H311P	ENST00000171111	NM_203500.1	311	cAc/cCc	3/6	0.432536720027352	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.432536720027352	1		689	774	SUCCESS
MET	4233	MSKCC	GRCh37	7	116417482	116417482	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	101	372	0	ENST00000397752.3:c.3299A>G	p.Asn1100Ser	p.N1100S	ENST00000397752	NM_000245.2	1100	aAt/aGt	16/21	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.432536720027352	2		372	467	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971182	21971206	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	ACTCGGGCGCTGCCCATCATCATGA	ACTCGGGCGCTGCCCATCATCATGA	-	novel	NA	P-0032351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	179	370	0	ENST00000304494.5:c.152_176del	p.Val51GlyfsTer87	p.V51Gfs*87	ENST00000304494	NM_000077.4	51	gTCATGATGATGGGCAGCGCCCGAGTg/gg	2/3	0.419991878094346	2	FACETS	0.934	0.871	0.999	0.934	0.871	0.999	CLONAL	2	TRUE	0	0.432536720027352	2		370	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578518	7578518	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934875	NA	P-0032360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	673	758	0	ENST00000269305.4:c.412G>C	p.Ala138Pro	p.A138P	ENST00000269305	NM_001126112.2	138	Gcc/Ccc	5/11	0.555845506263169	3	FACETS	0.941	0.916	0.966	0.941	0.916	0.966	CLONAL	3	TRUE	0	0.621137084509755	3		758	1006	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709162	117709162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867987684	NA	P-0032360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	91	355	0	ENST00000368508.3:c.1795G>A	p.Glu599Lys	p.E599K	ENST00000368508	NM_002944.2	599	Gaa/Aaa	13/43	0.548560517162146	3	FACETS	0.848	0.756	0.944	0.424	0.378	0.472	CLONAL	1	TRUE	1	0.621137084509755	3		355	453	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843375	128843375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773562190	NA	P-0032360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	255	541	1	ENST00000249373.3:c.482G>A	p.Arg161Gln	p.R161Q	ENST00000249373	NM_005631.4	161	cGg/cAg	2/12	0.547245169927631	3	FACETS	0.869	0.82	0.919	0.869	0.82	0.919	CLONAL	2	TRUE	1	0.621137084509755	3		542	619	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262633	16262633	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	196	339	0	ENST00000375759.3:c.9898G>T	p.Gly3300Trp	p.G3300W	ENST00000375759	NM_015001.2	3300	Ggg/Tgg	11/15	0.361071039675178	3	FACETS	1	0.973	1	0.707	0.665	0.749	INDETERMINATE	2	TRUE	0	0.621137084509755	3		339	390	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103396	119103396	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	87	300	0	ENST00000264033.4:c.434C>G	p.Ser145Cys	p.S145C	ENST00000264033	NM_005188.3	145	tCt/tGt	2/16	0.597892331872125	4	FACETS	0.847	0.752	0.949	0.282	0.25	0.317	CLONAL	1	TRUE	1	0.621137084509755	4		300	536	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860090	57860091	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0032360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	471	633	1	ENST00000228682.2:c.830_831delinsTT	p.Arg277Ile	p.R277I	ENST00000228682	NM_005269.2	277	aGG/aTT	8/12	0.562722527922516	4	FACETS	0.929	0.894	0.964	0.929	0.894	0.964	CLONAL	3	TRUE	1	0.621137084509755	4		634	882	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934918	9934918	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	125	388	0	ENST00000330684.3:c.1372G>C	p.Gly458Arg	p.G458R	ENST00000330684	NM_001134407.1	458	Ggg/Cgg	6/13	1	2	FACETS	0.82	0.746	0.896	0.82	0.746	0.896	CLONAL	1	TRUE	1	0.621137084509755	2		388	491	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349596	15349596	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs201443971	NA	P-0032360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	189	730	0	ENST00000263377.2:c.3978G>T	p.Glu1326Asp	p.E1326D	ENST00000263377	NM_058243.2	1326	gaG/gaT	19/20	0.563852452316268	2	FACETS	0.894	0.829	0.96	0.447	0.414	0.48	CLONAL	1	TRUE	0	0.621137084509755	2		730	681	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116167	209116167	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	133	348	0	ENST00000345146.2:c.109T>A	p.Leu37Met	p.L37M	ENST00000345146	NM_005896.2	37	Ttg/Atg	3/10	0.548560517162146	3	FACETS	0.869	0.791	0.95	0.434	0.395	0.475	CLONAL	1	TRUE	1	0.621137084509755	3		348	646	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183824	10183824	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs864321643	NA	P-0032360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	405	610	0	ENST00000256474.2:c.293A>G	p.Tyr98Cys	p.Y98C	ENST00000256474	NM_000551.3	98	tAc/tGc	1/3	0.555845506263169	3	FACETS	0.885	0.852	0.916	0.885	0.852	0.916	CLONAL	3	TRUE	0	0.621137084509755	3		610	644	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620704	52620704	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	218	185	0	ENST00000394830.3:c.3049G>T	p.Glu1017Ter	p.E1017*	ENST00000394830	NM_018313.4	1017	Gaa/Taa	21/30	0.555845506263169	3	FACETS	0.926	0.882	0.969	0.926	0.882	0.969	CLONAL	3	TRUE	0	0.621137084509755	3		185	331	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598093	55598093	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	161	438	0	ENST00000288135.5:c.2290C>A	p.Leu764Ile	p.L764I	ENST00000288135	NM_000222.2	764	Cta/Ata	16/21	0.240076294191347	5	FACETS	1	0.981	1	0.41	0.376	0.445	INDETERMINATE	1	TRUE	2	0.621137084509755	5		438	815	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170814954	170814954	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0032360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	36	113	0	ENST00000296930.5:c.2T>C	p.Met1?	p.M1?	ENST00000296930	NM_002520.6	1	aTg/aCg	1/11	0.57470143070786	2	FACETS	0.92	0.772	1	0.46	0.386	0.539	CLONAL	1	TRUE	0	0.621137084509755	2		113	126	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76777819	76777822	+	frameshift_variant	Frame_Shift_Del	DEL	AGGG	AGGG	-	novel	NA	P-0032360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	158	253	0	ENST00000373344.5:c.6894_6897del	p.Pro2299SerfsTer20	p.P2299Sfs*20	ENST00000373344	NM_000489.3	2298	ccCCCT/cc	32/35	1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.621137084509755	1		253	311	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937365	76937365	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	167	266	0	ENST00000373344.5:c.3383G>T	p.Arg1128Ile	p.R1128I	ENST00000373344	NM_000489.3	1128	aGa/aTa	9/35	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.621137084509755	1		266	315	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604697	48604697	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032511-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	42	459	0	ENST00000342988.3:c.1519A>G	p.Lys507Glu	p.K507E	ENST00000342988	NM_005359.5	507	Aaa/Gaa	12/12	0.22297808859419	1	FACETS	0.656	0.548	0.777	0.656	0.548	0.777	SUBCLONAL	1	TRUE	0	0.22297808859419	1		459	510	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970979	21970979	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032511-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	137	617	0	ENST00000304494.5:c.379del	p.Ala127HisfsTer19	p.A127Hfs*19	ENST00000304494	NM_000077.4	127	Gca/ca	2/3	0.22297808859419	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.22297808859419	1		617	810	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872508	35872508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032511-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	44	459	0	ENST00000216797.5:c.395G>A	p.Gly132Glu	p.G132E	ENST00000216797	NM_020529.2	132	gGa/gAa	3/6	1	2	FACETS	0.495	0.413	0.585	0.495	0.413	0.585	SUBCLONAL	1	TRUE	1	0.22297808859419	2		459	798	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0032511-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	81	409	0	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.22297808859419	2		409	584	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420825	49420825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757011865	NA	P-0032511-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	56	524	1	ENST00000301067.7:c.14924G>A	p.Arg4975His	p.R4975H	ENST00000301067	NM_003482.3	4975	cGt/cAt	48/54	1	2	FACETS	0.696	0.595	0.806	0.696	0.595	0.806	SUBCLONAL	1	TRUE	1	0.22297808859419	2		525	722	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584528	48584528	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032511-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	42	368	0	ENST00000342988.3:c.701G>A	p.Ser234Asn	p.S234N	ENST00000342988	NM_005359.5	234	aGt/aAt	6/12	0.22297808859419	1	FACETS	0.709	0.592	0.839	0.709	0.592	0.839	SUBCLONAL	1	TRUE	0	0.22297808859419	1		368	472	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509734	106509734	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032511-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	60	432	0	ENST00000359195.3:c.1728G>T	p.Trp576Cys	p.W576C	ENST00000359195	NM_002649.2	576	tgG/tgT	2/11	0.22297808859419	3	FACETS	0.92	0.792	1	0.46	0.396	0.53	CLONAL	1	TRUE	1	0.22297808859419	3		432	650	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47597166	47597167	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0032511-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	74	315	0	ENST00000430070.2:c.722_723del	p.Glu241ValfsTer38	p.E241Vfs*38	ENST00000430070	NM_018095.4	241	gAG/g	3/4	0.22297808859419	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.22297808859419	1		315	491	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242495	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAGCAACATCTCCGAAAGCC	TTAAGAGAAGCAACATCTCCGAAAGCC	GCAACA	novel	NA	P-0032511-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	69	316	1	ENST00000275493.2:c.2239_2265delinsGCAACA	p.Leu747_Ala755delinsAlaThr	p.L747_A755delinsAT	ENST00000275493	NM_005228.3	747	TTAAGAGAAGCAACATCTCCGAAAGCC/GCAACA	19/28	0.168886463909848	3	FACETS	1	0.96	1	0.633	0.552	0.721	CLONAL	1	TRUE	1	0.22297808859419	3		317	543	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032627-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	43	306	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.219517586849707	3	FACETS	0.776	0.655	0.908	0.776	0.655	0.908	CLONAL	2	TRUE	1	0.264583435895113	3		306	237	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196879	108196880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs773570504	NA	P-0032627-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	17	390	0	ENST00000278616.4:c.6908dup	p.Glu2304GlyfsTer69	p.E2304Gfs*69	ENST00000278616	NM_000051.3	2301	gca/gcAa	47/63	1	2	FACETS	0.382	0.285	0.499	0.382	0.285	0.499	SUBCLONAL	1	TRUE	1	0.264583435895113	2		390	336	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032627-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	27	293	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.264583435895113	1	FACETS	0.611	0.487	0.751	0.611	0.487	0.751	SUBCLONAL	1	TRUE	0	0.264583435895113	1		293	290	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124712	108124712	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032627-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	20	419	0	ENST00000278616.4:c.2071del	p.Asp691IlefsTer12	p.D691Ifs*12	ENST00000278616	NM_000051.3	690	ctG/ct	13/63	1	2	FACETS	0.499	0.381	0.636	0.499	0.381	0.636	SUBCLONAL	1	TRUE	1	0.264583435895113	2		419	303	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0033243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	17	401	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	1	2	FACETS	0.93	0.695	1	0.93	0.695	1	CLONAL	1	TRUE	1	0.14	2		401	261	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17354251	17354251	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	14	329	0	ENST00000375499.3:c.533A>G	p.Glu178Gly	p.E178G	ENST00000375499	NM_003000.2	178	gAg/gGg	5/8	1	2	FACETS	1	0.728	1	1	0.728	1	CLONAL	1	TRUE	1	0.14	2		329	199	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525843	148525843	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	18	302	0	ENST00000320356.2:c.614A>T	p.Asp205Val	p.D205V	ENST00000320356	NM_004456.4	205	gAt/gTt	6/20	1	2	FACETS	1	0.801	1	1	0.801	1	CLONAL	1	TRUE	1	0.14	2		302	240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0033307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	104	601	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.195198323146829	1	FACETS	0.812	0.725	0.905	0.812	0.725	0.905	CLONAL	1	FALSE	0	0.195198323146829	1		601	1184	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555687605	NA	P-0033307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	23	398	0	ENST00000342988.3:c.1610A>G	p.Asp537Gly	p.D537G	ENST00000342988	NM_005359.5	537	gAc/gGc	12/12	0.195198323146829	1	FACETS	0.412	0.32	0.519	0.412	0.32	0.519	SUBCLONAL	1	FALSE	0	0.195198323146829	1		398	516	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0033307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	120	365	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.154224258450543	2	FACETS	1	0.979	1	0.663	0.598	0.732	CLONAL	1	FALSE	0	0.195198323146829	2		365	927	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0033313-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	582	798	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.886505977331944	8	FACETS	1	0.995	1	1	0.995	1	CLONAL	6	TRUE	2	0.886505977331944	8		798	742	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0033313-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3	328	398	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.886505977331944	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.886505977331944	3		398	331	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976787	2976787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033313-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	111	404	0	ENST00000396946.4:c.1225G>A	p.Glu409Lys	p.E409K	ENST00000396946	NM_032415.4	409	Gag/Aag	9/25	0.886505977331944	8	FACETS	0.954	0.856	1	0.136	0.122	0.151	CLONAL	1	TRUE	1	0.886505977331944	8		404	961	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0033632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	844	555	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.78766554679982	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.78766554679982	2		555	1039	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121615	2121615	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	744	668	2	ENST00000219476.3:c.1944C>A	p.Tyr648Ter	p.Y648*	ENST00000219476	NM_000548.3	648	taC/taA	18/42	0.78766554679982	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.78766554679982	2		670	904	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889070	76889073	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0033632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	119	187	0	ENST00000373344.5:c.4937_4940del	p.Lys1646MetfsTer10	p.K1646Mfs*10	ENST00000373344	NM_000489.3	1646	aAAGAt/at	18/35	1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.78766554679982	1		187	165	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0034124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	15	582	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.204	0.148	0.272	0.204	0.148	0.272	SUBCLONAL	1	TRUE	1	0.238606832927671	2		582	617	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28929495	NA	P-0034124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	106	470	0	ENST00000275493.2:c.2155G>T	p.Gly719Cys	p.G719C	ENST00000275493	NM_005228.3	719	Ggc/Tgc	18/28	0.11825460978815	3	FACETS	0.836	0.751	0.925	0.836	0.751	0.925	INDETERMINATE	2	TRUE	1	0.238606832927671	3		470	595	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0034124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	90	392	1	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.11825460978815	3	FACETS	1	0.928	1	1	0.928	1	INDETERMINATE	2	TRUE	1	0.238606832927671	3		393	402	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082215	16082215	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	40	611	0	ENST00000281043.3:c.29C>A	p.Pro10Gln	p.P10Q	ENST00000281043	NM_005378.4	10	cCg/cAg	2/3	1	2	FACETS	0.628	0.521	0.747	0.628	0.521	0.747	SUBCLONAL	1	TRUE	1	0.238606832927671	2		611	534	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941724	48941724	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	55	299	0	ENST00000267163.4:c.1034C>A	p.Thr345Asn	p.T345N	ENST00000267163	NM_000321.2	345	aCt/aAt	10/27	1	2	FACETS	0.831	0.711	0.962	0.831	0.711	0.962	CLONAL	1	TRUE	1	0.238606832927671	2		299	555	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941732	48941732	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	55	301	0	ENST00000267163.4:c.1042del	p.Ile348Ter	p.I348*	ENST00000267163	NM_000321.2	348	Ata/ta	10/27	1	2	FACETS	0.849	0.726	0.983	0.849	0.726	0.983	CLONAL	1	TRUE	1	0.238606832927671	2		301	543	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929443	81929443	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	43	477	0	ENST00000359376.3:c.1105del	p.Val369SerfsTer33	p.V369Sfs*33	ENST00000359376	NM_002661.3	368	ccG/cc	13/33	1	2	FACETS	0.756	0.632	0.892	0.756	0.632	0.892	SUBCLONAL	1	TRUE	1	0.238606832927671	2		477	477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0034129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	272	503	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.581220959398662	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.661099127151384	1		503	485	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513317	149513317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147568171	NA	P-0034129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	160	338	1	ENST00000261799.4:c.766C>T	p.Arg256Trp	p.R256W	ENST00000261799	NM_002609.3	256	Cgg/Tgg	6/23	0.661099127151384	3	FACETS	1	0.981	1	0.597	0.551	0.645	CLONAL	1	TRUE	1	0.661099127151384	3		339	539	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157455	106157455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	58	280	0	ENST00000380013.4:c.2356C>T	p.His786Tyr	p.H786Y	ENST00000380013	NM_001127208.2	786	Cat/Tat	3/11	1	2	FACETS	0.76	0.661	0.865	0.76	0.661	0.865	SUBCLONAL	1	TRUE	1	0.661099127151384	2		280	231	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115279416	115279417	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0034129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	123	428	0	ENST00000438362.2:c.600_601del	p.Gly201ArgfsTer2	p.G201Rfs*2	ENST00000438362	NM_001242891.1	200	acTGga/acga	6/20	0.238884700560243	2	FACETS	1	0.949	1	0.526	0.481	0.572	INDETERMINATE	1	TRUE	0	0.661099127151384	2		428	354	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41521963	41521963	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	150	509	0	ENST00000263253.7:c.825G>T	p.Gln275His	p.Q275H	ENST00000263253	NM_001429.3	275	caG/caT	3/31	0.132128409077605	5	FACETS	0.862	0.793	0.934	0.575	0.529	0.623	INDETERMINATE	2	TRUE	2	0.661099127151384	5		509	524	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643720	52643723	+	frameshift_variant	Frame_Shift_Del	DEL	CAAC	CAAC	-	novel	NA	P-0034129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	170	527	0	ENST00000394830.3:c.2173_2176del	p.Val725ArgfsTer5	p.V725Rfs*5	ENST00000394830	NM_018313.4	725	GTTGag/ag	17/30	0.26960614588078	5	FACETS	0.935	0.865	1	0.623	0.576	0.671	INDETERMINATE	2	TRUE	2	0.661099127151384	5		527	548	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131945028	131945029	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs767281258	NA	P-0034129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	38	228	0	ENST00000265335.6:c.2979_2980del	p.His993GlnfsTer6	p.H993Qfs*6	ENST00000265335		992	aaACac/aaac	19/25	0.26960614588078	5	FACETS	0.766	0.636	0.91	0.255	0.212	0.304	INDETERMINATE	1	TRUE	2	0.661099127151384	5		228	299	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874049	151874049	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	173	482	2	ENST00000262189.6:c.8489del	p.Asn2830IlefsTer33	p.N2830Ifs*33	ENST00000262189	NM_170606.2	2830	aAt/at	38/59	0.26960614588078	5	FACETS	0.87	0.805	0.937	0.58	0.536	0.625	INDETERMINATE	2	TRUE	2	0.661099127151384	5		484	599	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0034132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	256	597	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.460470268135679	2	FACETS	0.957	0.904	1	0.957	0.904	1	CLONAL	2	TRUE	0	0.460470268135679	2		597	581	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0034132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	2125	547	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.460470268135679	18	FACETS	1	0.99	1			1	CLONAL	17	TRUE	NA	0.460470268135679	18		547	2541	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917782	29917782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56077855	NA	P-0034132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	48	477	2	ENST00000389048.3:c.886G>A	p.Glu296Lys	p.E296K	ENST00000389048	NM_004304.4	296	Gag/Aag	3/29	0.301377005579635	2	FACETS	0.384	0.324	0.45	0.192	0.162	0.225	SUBCLONAL	1	TRUE	0	0.460470268135679	2		479	543	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733265	40733265	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	131	503	0	ENST00000373198.4:c.3541A>G	p.Asn1181Asp	p.N1181D	ENST00000373198	NM_133170.3	1181	Aat/Gat	26/32	0.207743125413749	3	FACETS	1	0.982	1	0.659	0.601	0.72	INDETERMINATE	1	TRUE	1	0.460470268135679	3		503	531	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40828011	40828011	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	88	339	0	ENST00000373198.4:c.2417A>T	p.Gln806Leu	p.Q806L	ENST00000373198	NM_133170.3	806	cAg/cTg	17/32	0.207743125413749	3	FACETS	1	0.968	1	0.615	0.549	0.685	INDETERMINATE	1	TRUE	1	0.460470268135679	3		339	382	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421391	12421391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140915035	NA	P-0034132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	55	572	0	ENST00000287820.6:c.271G>A	p.Ala91Thr	p.A91T	ENST00000287820	NM_015869.4	91	Gca/Aca	2/7	0.159786289960123	2	FACETS	0.34	0.29	0.395	0.17	0.145	0.198	INDETERMINATE	1	TRUE	0	0.460470268135679	2		572	703	SUCCESS
APC	324	MSKCC	GRCh37	5	112090646	112090646	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	62	283	0	ENST00000257430.4:c.59A>C	p.Asn20Thr	p.N20T	ENST00000257430	NM_000038.5	20	aAc/aCc	2/16	1	2	FACETS	0.783	0.68	0.893	0.783	0.68	0.893	SUBCLONAL	1	TRUE	1	0.460470268135679	2		283	344	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845065	128845065	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	79	585	0	ENST00000249373.3:c.559T>C	p.Phe187Leu	p.F187L	ENST00000249373	NM_005631.4	187	Ttc/Ctc	3/12	0.460470268135679	2	FACETS	0.611	0.538	0.689	0.305	0.269	0.345	SUBCLONAL	1	TRUE	0	0.460470268135679	2		585	562	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391168	89391168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772463834	NA	P-0034234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	78	532	0	ENST00000336596.2:c.1234G>A	p.Val412Ile	p.V412I	ENST00000336596	NM_005233.5	412	Gtt/Att	5/17	1	2	FACETS	0.738	0.648	0.836	0.738	0.648	0.836	SUBCLONAL	1	TRUE	1	0.271625525653709	2		532	778	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400190	41400190	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	89	603	0	ENST00000373198.4:c.569G>A	p.Arg190Lys	p.R190K	ENST00000373198	NM_133170.3	190	aGa/aAa	5/32	1	2	FACETS	0.944	0.837	1	0.944	0.837	1	CLONAL	1	TRUE	1	0.271625525653709	2		603	694	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0034234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	275	887	2	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	0.191048583399865	3	FACETS	0.913	0.856	0.971	0.608	0.57	0.648	CLONAL	2	TRUE	0	0.271625525653709	3		889	1260	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956771	68956771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774302685	NA	P-0034234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	90	667	1	ENST00000288368.4:c.889C>T	p.Arg297Cys	p.R297C	ENST00000288368	NM_024870.2	297	Cgt/Tgt	8/40	1	2	FACETS	0.619	0.547	0.695	0.619	0.547	0.695	SUBCLONAL	1	TRUE	1	0.271625525653709	2		668	1071	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945396	151945396	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	105	695	0	ENST00000262189.6:c.2123C>T	p.Ser708Leu	p.S708L	ENST00000262189	NM_170606.2	708	tCa/tTa	14/59	0.271625525653709	3	FACETS	1	0.945	1	0.543	0.486	0.604	CLONAL	1	TRUE	1	0.271625525653709	3		695	808	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790031	40790031	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	123	656	1	ENST00000373198.4:c.2700G>A	p.Met900Ile	p.M900I	ENST00000373198	NM_133170.3	900	atG/atA	18/32	1	2	FACETS	0.855	0.772	0.944	0.855	0.772	0.944	CLONAL	1	TRUE	1	0.271625525653709	2		657	1059	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858195	40858195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777686988	NA	P-0034234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	127	716	1	ENST00000428826.2:c.1669C>T	p.Arg557Cys	p.R557C	ENST00000428826		557	Cgt/Tgt	16/21	1	2	FACETS	0.833	0.753	0.918	0.833	0.753	0.918	CLONAL	1	TRUE	1	0.271625525653709	2		717	1122	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0034234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	88	544	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.271625525653709	2		545	634	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27098997	27098997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	70	488	0	ENST00000324856.7:c.3413C>T	p.Ser1138Leu	p.S1138L	ENST00000324856	NM_006015.4	1138	tCa/tTa	13/20	1	2	FACETS	0.77	0.671	0.878	0.77	0.671	0.878	SUBCLONAL	1	TRUE	1	0.271625525653709	2		488	669	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256530	+	missense_variant	Missense_Mutation	DNP	TG	TG	AT	novel	NA	P-0034234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	182	728	1	ENST00000369535.4:c.181_182delinsAT	p.Gln61Ile	p.Q61I	ENST00000369535	NM_002524.4	61	CAa/ATa	3/7	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.271625525653709	2		729	938	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577271	64577271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	131	757	1	ENST00000312049.6:c.311C>T	p.Ser104Phe	p.S104F	ENST00000312049	NM_130799.2	104	tCc/tTc	2/10	0.271625525653709	1	FACETS	0.992	0.9	1	0.992	0.9	1	CLONAL	1	TRUE	0	0.271625525653709	1		758	840	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245486	46245486	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	54	342	0	ENST00000334344.6:c.3580del	p.Gln1194SerfsTer10	p.Q1194Sfs*10	ENST00000334344	NM_152641.2	1194	Cag/ag	15/21	0.112766054276393	4	FACETS	1	0.933	1	0.581	0.497	0.673	INDETERMINATE	1	TRUE	2	0.271625525653709	4		342	435	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245690	46245690	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0034234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	70	357	0	ENST00000334344.6:c.3784A>T	p.Lys1262Ter	p.K1262*	ENST00000334344	NM_152641.2	1262	Aaa/Taa	15/21	0.112766054276393	4	FACETS	1	0.97	1	0.697	0.609	0.791	INDETERMINATE	1	TRUE	2	0.271625525653709	4		357	470	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431496	121431496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	113	597	0	ENST00000257555.6:c.700G>A	p.Glu234Lys	p.E234K	ENST00000257555		234	Gag/Aag	3/10	0.112766054276393	4	FACETS	1	0.912	1	0.509	0.457	0.564	INDETERMINATE	1	TRUE	2	0.271625525653709	4		597	1040	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693926	47693926	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	45	413	0	ENST00000233146.2:c.1640A>C	p.Asn547Thr	p.N547T	ENST00000233146	NM_000251.2	547	aAt/aCt	10/16	1	2	FACETS	0.923	0.778	1	0.923	0.778	1	CLONAL	1	TRUE	1	0.271625525653709	2		413	359	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225360625	225360625	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	50	459	0	ENST00000264414.4:c.1766A>C	p.Lys589Thr	p.K589T	ENST00000264414	NM_003590.4	589	aAg/aCg	13/16	1	2	FACETS	0.82	0.697	0.955	0.82	0.697	0.955	CLONAL	1	TRUE	1	0.271625525653709	2		459	449	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422937	12422937	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	79	703	0	ENST00000287820.6:c.427G>A	p.Gly143Arg	p.G143R	ENST00000287820	NM_015869.4	143	Gga/Aga	3/7	1	2	FACETS	0.683	0.599	0.773	0.683	0.599	0.773	SUBCLONAL	1	TRUE	1	0.271625525653709	2		703	852	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803607	1803607	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	112	681	0	ENST00000260795.2:c.785A>G	p.Asn262Ser	p.N262S	ENST00000260795		262	aAc/aGc	6/17	1	2	FACETS	0.824	0.74	0.913	0.824	0.74	0.913	CLONAL	1	TRUE	1	0.271625525653709	2		681	1001	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295270	1295271	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0034234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	101	497	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.965	0.862	1	0.965	0.862	1	CLONAL	1	TRUE	1	0.271625525653709	2		498	771	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949013	44949013	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	45	312	0	ENST00000377967.4:c.3574T>G	p.Ser1192Ala	p.S1192A	ENST00000377967	NM_021140.2	1192	Tct/Gct	25/29	0.221138896227508	2	FACETS	1	0.922	1			1	CLONAL	1	TRUE	NA	0.271625525653709	2		312	288	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0034329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	63	355	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.23	2		355	416	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259876	142259876	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	45	520	0	ENST00000350721.4:c.3451G>T	p.Ala1151Ser	p.A1151S	ENST00000350721	NM_001184.3	1151	Gcc/Tcc	18/47	1	2	FACETS	0.722	0.606	0.85	0.722	0.606	0.85	SUBCLONAL	1	TRUE	1	0.23	2		520	542	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223892	53223892	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	53	993	0	ENST00000375401.3:c.3467del	p.Lys1156ArgfsTer108	p.K1156Rfs*108	ENST00000375401	NM_004187.3	1156	aAg/ag	23/26	1	2	FACETS	0.48	0.408	0.56	0.48	0.408	0.56	SUBCLONAL	1	TRUE	1	0.23	2		993	960	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0034332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	279	309	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.945	0.893	0.998	0.945	0.893	0.998	CLONAL	1	TRUE	1	0.814163512222377	2		309	725	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0034332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	361	715	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.814163512222377	1	FACETS	0.914	0.879	0.949	0.914	0.879	0.949	CLONAL	1	TRUE	0	0.814163512222377	1		715	575	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398279	25398279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894365	NA	P-0034332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	289	540	0	ENST00000311936.3:c.40G>A	p.Val14Ile	p.V14I	ENST00000311936	NM_004985.3	14	Gta/Ata	2/5	1	2	FACETS	0.952	0.9	1	0.952	0.9	1	CLONAL	1	TRUE	1	0.814163512222377	2		540	746	SUCCESS
APC	324	MSKCC	GRCh37	5	112175328	112175328	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	229	250	0	ENST00000257430.4:c.4037C>A	p.Ser1346Ter	p.S1346*	ENST00000257430	NM_000038.5	1346	tCa/tAa	16/16	0.811597433187915	2	FACETS	0.963	0.927	0.997	0.963	0.927	0.997	CLONAL	2	TRUE	0	0.814163512222377	2		250	292	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0034562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	113	471	1	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.144666761087432	3	FACETS	1	0.974	1	0.63	0.566	0.697	CLONAL	1	TRUE	1	0.238213378333167	3		472	843	SUCCESS
AR	367	MSKCC	GRCh37	X	66765239	66765239	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	61	322	0	ENST00000374690.3:c.251C>A	p.Pro84His	p.P84H	ENST00000374690	NM_000044.3	84	cCc/cAc	1/8	1	2	FACETS	0.961	0.83	1	0.961	0.83	1	CLONAL	1	TRUE	1	0.238213378333167	2		322	533	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045500	47045500	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	109	543	0	ENST00000377604.3:c.2467G>T	p.Glu823Ter	p.E823*	ENST00000377604	NM_001204468.1	823	Gaa/Taa	22/24	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.238213378333167	2		543	841	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570070	212570070	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs745408040	NA	P-0034562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	100	445	2	ENST00000342788.4:c.1171G>T	p.Val391Phe	p.V391F	ENST00000342788	NM_005235.2	391	Gtc/Ttc	10/28	0.199900301064286	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.238213378333167	1		447	707	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309750	30309750	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	91	538	0	ENST00000307677.4:c.272G>C	p.Arg91Thr	p.R91T	ENST00000307677	NM_138578.1	91	aGg/aCg	2/3	1	2	FACETS	0.924	0.819	1	0.924	0.819	1	CLONAL	1	TRUE	1	0.238213378333167	2		538	827	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339196	87339196	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	73	452	0	ENST00000277120.3:c.778A>T	p.Ser260Cys	p.S260C	ENST00000277120		260	Agt/Tgt	8/19	1	2	FACETS	0.827	0.723	0.94	0.827	0.723	0.94	CLONAL	1	TRUE	1	0.238213378333167	2		452	741	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411750	63411750	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1349239165	NA	P-0034562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	131	692	0	ENST00000330258.3:c.1417G>C	p.Asp473His	p.D473H	ENST00000330258	NM_152424.3	473	Gac/Cac	2/2	1	2	FACETS	0.94	0.851	1	0.94	0.851	1	CLONAL	1	TRUE	1	0.238213378333167	2		692	1170	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593519	48593519	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	33	382	0	ENST00000342988.3:c.1270G>C	p.Asp424His	p.D424H	ENST00000342988	NM_005359.5	424	Gat/Cat	10/12	0.253964317912192	1	FACETS	0.886	0.726	1	0.886	0.726	1	CLONAL	1	TRUE	0	0.253964317912192	1		382	256	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576926	7576927	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GC	GC	AT	novel	NA	P-0034606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	98	664	0	ENST00000269305.4:c.920-1_920delinsAT		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	0.249692133354734	2	FACETS	0.859	0.771	0.953	0.859	0.771	0.953	CLONAL	2	TRUE	0	0.253964317912192	2		664	449	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187558028	187558028	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1288182768	NA	P-0034606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	39	444	0	ENST00000441802.2:c.3683T>C	p.Ile1228Thr	p.I1228T	ENST00000441802	NM_005245.3	1228	aTt/aCt	5/27	0.253964317912192	3	FACETS	0.954	0.792	1	0.477	0.396	0.567	CLONAL	1	TRUE	1	0.253964317912192	3		444	363	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	301	306	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.83689237914413	3	FACETS	0.983	0.957	1	0.983	0.957	1	CLONAL	3	TRUE	0	0.83689237914413	3		306	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0034882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	273	603	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.81632352934743	2	FACETS	0.992	0.961	1	0.992	0.961	1	CLONAL	2	TRUE	0	0.83689237914413	2		603	329	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111959594	111959594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	123	752	0	ENST00000375549.3:c.173G>A	p.Gly58Asp	p.G58D	ENST00000375549	NM_003002.3	58	gGc/gAc	3/4	0.433869111319415	1	FACETS	0.384	0.35	0.42	0.384	0.35	0.42	INDETERMINATE	1	TRUE	0	0.83689237914413	1		752	445	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915532	112915532	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs774939392	NA	P-0034882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	86	626	0	ENST00000351677.2:c.931A>G	p.Met311Val	p.M311V	ENST00000351677	NM_002834.3	311	Atg/Gtg	8/16	0.83689237914413	2	FACETS	0.524	0.467	0.585	0.262	0.233	0.293	SUBCLONAL	1	TRUE	0	0.83689237914413	2		626	392	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805762	46805762	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	295	649	0	ENST00000290295.7:c.194C>A	p.Pro65Gln	p.P65Q	ENST00000290295	NM_006361.5	65	cCa/cAa	1/2	0.83689237914413	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.83689237914413	2		649	344	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139810996	139810996	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	327	703	0	ENST00000247668.2:c.607C>T	p.Gln203Ter	p.Q203*	ENST00000247668	NM_021138.3	203	Cag/Tag	7/11	0.516579375297882	4	FACETS	0.987	0.939	1			1	CLONAL	2	TRUE	NA	0.83689237914413	4		703	727	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0035166-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	101	739	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.239112729459682	5	FACETS	1	0.953	1			1	CLONAL	4	FALSE	NA	0.239112729459682	5		741	266	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202727	108202727	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035166-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	22	334	0	ENST00000278616.4:c.7751C>T	p.Thr2584Ile	p.T2584I	ENST00000278616	NM_000051.3	2584	aCt/aTt	52/63	0.239112729459682	6	FACETS	0.978	0.76	1	0.326	0.253	0.411	CLONAL	1	FALSE	3	0.239112729459682	6		334	278	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	130	394	0	ENST00000397062.3:c.101G>A	p.Arg34Gln	p.R34Q	ENST00000397062	NM_006164.4	34	cGa/cAa	2/5	0.225063898316438	4	FACETS	0.915	0.837	0.997	0.915	0.837	0.997	INDETERMINATE	2	TRUE	2	0.467294362059494	4		394	446	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0035827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	153	607	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.37162296726472	2	FACETS	0.793	0.733	0.854	0.793	0.733	0.854	SUBCLONAL	2	TRUE	0	0.467294362059494	2		607	413	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	133	559	0	ENST00000304494.5:c.322G>C	p.Asp108His	p.D108H	ENST00000304494	NM_000077.4	108	Gat/Cat	2/3	0.467294362059494	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.467294362059494	1		559	306	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562632	29562632	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1060500346	NA	P-0035827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	113	618	0	ENST00000356175.3:c.3712G>T	p.Glu1238Ter	p.E1238*	ENST00000356175	NM_000267.3	1238	Gaa/Taa	28/57	0.298344586696006	4	FACETS	1	0.977	1	0.644	0.581	0.71	CLONAL	1	TRUE	2	0.467294362059494	4		618	551	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100598	8100598	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	114	696	0	ENST00000346208.3:c.572C>A	p.Pro191His	p.P191H	ENST00000346208		191	cCc/cAc	3/6	0.284353525585649	3	FACETS	1	0.975	1	0.618	0.559	0.679	CLONAL	1	TRUE	1	0.467294362059494	3		696	487	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402046	402046	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	190	658	0	ENST00000399788.2:c.4745A>G	p.Lys1582Arg	p.K1582R	ENST00000399788	NM_001042603.1	1582	aAg/aGg	27/28	0.112272607509162	5	FACETS	1	0.987	1			1	INDETERMINATE	2	TRUE	NA	0.467294362059494	5		658	555	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219201	133219201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1565937674	NA	P-0035827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	132	877	0	ENST00000320574.5:c.4843G>A	p.Asp1615Asn	p.D1615N	ENST00000320574	NM_006231.2	1615	Gac/Aac	37/49	0.107290734187958	5	FACETS	1	0.954	1	0.533	0.487	0.58	INDETERMINATE	2	TRUE	1	0.467294362059494	5		877	451	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205315	46205315	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0035827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	53	498	0	ENST00000334344.6:c.399C>G	p.Tyr133Ter	p.Y133*	ENST00000334344	NM_152641.2	133	taC/taG	4/21	0.214175597345721	5	FACETS	1	0.92	1	0.371	0.317	0.429	INDETERMINATE	1	TRUE	2	0.467294362059494	5		498	347	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428161	47428161	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	34	966	0	ENST00000377045.4:c.1121C>G	p.Thr374Ser	p.T374S	ENST00000377045	NM_001654.4	374	aCc/aGc	11/16	0.24558737745644	2	FACETS	0.266	0.216	0.321	0.133	0.108	0.161	INDETERMINATE	1	TRUE	0	0.467294362059494	2		966	548	SUCCESS
AR	367	MSKCC	GRCh37	X	66942824	66942824	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	20	501	0	ENST00000374690.3:c.2605C>T	p.Pro869Ser	p.P869S	ENST00000374690	NM_000044.3	869	Cct/Tct	7/8	0.24558737745644	2	FACETS	0.349	0.267	0.445	0.175	0.133	0.223	INDETERMINATE	1	TRUE	0	0.467294362059494	2		501	245	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934571	NA	P-0035893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	457	663	0	ENST00000269305.4:c.747G>C	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agC	7/11	0.728396905471274	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.728396905471274	1		663	723	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011106	12011106	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0035893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	190	434	0	ENST00000353533.5:c.514-1G>T		p.X172_splice	ENST00000353533	NM_003010.3	172			0.728396905471274	1	FACETS	0.945	0.89	1	0.945	0.89	1	CLONAL	1	TRUE	0	0.728396905471274	1		434	351	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118561	17118562	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0035893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	75	579	0	ENST00000285071.4:c.1369dup	p.Asp457GlyfsTer29	p.D457Gfs*29	ENST00000285071	NM_144997.5	457	gac/gGac	12/14	0.728396905471274	1	FACETS	0.197	0.172	0.224	0.197	0.172	0.224	SUBCLONAL	1	TRUE	0	0.728396905471274	1		579	664	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223311	2223311	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	495	718	1	ENST00000398665.3:c.3422C>A	p.Thr1141Lys	p.T1141K	ENST00000398665	NM_032482.2	1141	aCa/aAa	25/28	1	2	FACETS	0.954	0.913	0.995	0.954	0.913	0.995	CLONAL	1	TRUE	1	0.728396905471274	2		719	1425	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162626	47162626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1389881036	NA	P-0035893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	297	502	0	ENST00000409792.3:c.3500G>A	p.Gly1167Glu	p.G1167E	ENST00000409792	NM_014159.6	1167	gGg/gAg	3/21	0.728396905471274	1	FACETS	0.989	0.944	1	0.989	0.944	1	CLONAL	1	TRUE	0	0.728396905471274	1		502	524	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588164	67588164	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	138	291	0	ENST00000274335.5:c.994G>T	p.Glu332Ter	p.E332*	ENST00000274335		332	Gaa/Taa	7/15	0.349908141738395	1	FACETS	0.601	0.552	0.651	0.601	0.552	0.651	INDETERMINATE	1	TRUE	0	0.728396905471274	1		291	401	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574000	7574000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	271	562	0	ENST00000269305.4:c.1027G>T	p.Glu343Ter	p.E343*	ENST00000269305	NM_001126112.2	343	Gag/Tag	10/11	0.501492297992815	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.501492297992815	1		562	765	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099403	157099429	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAGCAACAG	CAGCAGCAGCAGCAGCAGCAGCAACAG	-	rs910569810	NA	P-0036114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	60	224	0	ENST00000346085.5:c.360_386del	p.Gln123_Gln131del	p.Q123_Q131del	ENST00000346085	NM_020732.3	114	CAGCAGCAGCAGCAGCAGCAGCAACAG/-	1/20	1	2	FACETS	0.727	0.63	0.831	0.727	0.63	0.831	SUBCLONAL	1	TRUE	1	0.501492297992815	2		224	329	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539951	187539951	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs777631605	NA	P-0036114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	169	412	0	ENST00000441802.2:c.7789C>T	p.Arg2597Ter	p.R2597*	ENST00000441802	NM_005245.3	2597	Cga/Tga	10/27	0.501492297992815	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.501492297992815	1		412	471	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881982	37881982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	202	638	0	ENST00000269571.5:c.2748G>A	p.Met916Ile	p.M916I	ENST00000269571		916	atG/atA	23/27	1	2	FACETS	0.829	0.768	0.892	0.829	0.768	0.892	CLONAL	1	TRUE	1	0.501492297992815	2		638	972	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21643155	21643155	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	147	568	0	ENST00000421138.2:c.372G>C	p.Gln124His	p.Q124H	ENST00000421138		124	caG/caC	5/16	1	2	FACETS	0.821	0.751	0.894	0.821	0.751	0.894	CLONAL	1	TRUE	1	0.501492297992815	2		568	714	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476287	88476287	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	187	579	0	ENST00000360948.2:c.1845G>C	p.Met615Ile	p.M615I	ENST00000360948	NM_001012338.2	615	atG/atC	15/19	0.498901797720312	2	FACETS	0.948	0.877	1	0.474	0.438	0.511	CLONAL	1	TRUE	0	0.501492297992815	2		579	787	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783970	50783970	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0036114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	207	540	0	ENST00000398568.2:c.361A>T	p.Lys121Ter	p.K121*	ENST00000398568	NM_001042412.1	121	Aaa/Taa	3/18	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.501492297992815	2		540	801	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677944	117677944	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	159	498	0	ENST00000368508.3:c.3989A>T	p.Asn1330Ile	p.N1330I	ENST00000368508	NM_002944.2	1330	aAt/aTt	25/43	1	2	FACETS	0.911	0.837	0.988	0.911	0.837	0.988	CLONAL	1	TRUE	1	0.501492297992815	2		498	696	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401093	139401093	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0036114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	194	654	0	ENST00000277541.6:c.3902-2A>T		p.X1301_splice	ENST00000277541	NM_017617.3	1301			1	2	FACETS	0.942	0.873	1	0.942	0.873	1	CLONAL	1	TRUE	1	0.501492297992815	2		654	821	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0036408-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	96	544	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.963	0.871	1	0.963	0.871	1	CLONAL	1	TRUE	1	0.730519728578276	2		545	273	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0036408-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	212	380	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.730519728578276	3	FACETS	1	0.947	1			1	CLONAL	2	TRUE	NA	0.730519728578276	3		380	395	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105940	27105941	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036408-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	197	584	0	ENST00000324856.7:c.5551_5552insT	p.Thr1851IlefsTer3	p.T1851Ifs*3	ENST00000324856	NM_006015.4	1851	acc/aTcc	20/20	0.37635250507162	1	FACETS	0.807	0.758	0.858	0.807	0.758	0.858	INDETERMINATE	1	TRUE	0	0.730519728578276	1		584	424	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981194	201981195	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0036408-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	151	571	0	ENST00000359651.3:c.273_274insAA	p.Phe92AsnfsTer64	p.F92Nfs*64	ENST00000359651		91	-/AA	2/8	0.710299270706682	3	FACETS	0.903	0.829	0.98	0.452	0.414	0.49	CLONAL	1	TRUE	1	0.730519728578276	3		571	625	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982141	201982151	+	frameshift_variant	Frame_Shift_Del	DEL	CTGATGGCAAG	CTGATGGCAAG	-	novel	NA	P-0036408-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	336	551	0	ENST00000359651.3:c.667_677del	p.Asp223LeufsTer8	p.D223Lfs*8	ENST00000359651		222	aCTGATGGCAAG/a	5/8	0.710299270706682	3	FACETS	0.984	0.94	1	0.984	0.94	1	CLONAL	2	TRUE	1	0.730519728578276	3		551	638	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244344	46244344	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036408-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	175	503	0	ENST00000334344.6:c.2438C>G	p.Ser813Cys	p.S813C	ENST00000334344	NM_152641.2	813	tCt/tGt	15/21	1	2	FACETS	0.984	0.914	1	0.984	0.914	1	CLONAL	1	TRUE	1	0.730519728578276	2		503	487	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246315	46246315	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0036408-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	171	519	0	ENST00000334344.6:c.4409C>G	p.Ser1470Ter	p.S1470*	ENST00000334344	NM_152641.2	1470	tCa/tGa	15/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.730519728578276	2		519	453	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942177	81942177	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036408-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	111	436	0	ENST00000359376.3:c.1714G>A	p.Asp572Asn	p.D572N	ENST00000359376	NM_002661.3	572	Gac/Aac	17/33	1	2	FACETS	0.938	0.854	1	0.938	0.854	1	CLONAL	1	TRUE	1	0.730519728578276	2		436	324	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512309	38512309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036408-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	129	446	0	ENST00000254066.5:c.1220C>T	p.Pro407Leu	p.P407L	ENST00000254066	NM_000964.3	407	cCg/cTg	9/9	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.730519728578276	2		446	287	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368134	31368134	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036408-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	155	617	0	ENST00000328111.2:c.5A>T	p.Lys2Met	p.K2M	ENST00000328111	NM_006892.3	2	aAg/aTg	2/23	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.730519728578276	2		617	396	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24158955	24158955	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0036408-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	134	437	0	ENST00000263121.7:c.629-2A>T		p.X210_splice	ENST00000263121	NM_003073.3	210			0.730519728578276	3	FACETS	1	0.958	1			1	CLONAL	1	TRUE	NA	0.730519728578276	3		437	465	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092938	29092938	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036408-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	77	288	0	ENST00000328354.6:c.1046A>T	p.Lys349Met	p.K349M	ENST00000328354	NM_007194.3	349	aAg/aTg	10/15	1	2	FACETS	0.878	0.783	0.978	0.878	0.783	0.978	CLONAL	1	TRUE	1	0.730519728578276	2		288	240	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198268	138198268	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036408-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	93	376	0	ENST00000237289.4:c.861A>T	p.Lys287Asn	p.K287N	ENST00000237289	NM_001270507.1	287	aaA/aaT	6/9	0.730519728578276	1	FACETS	0.883	0.807	0.959	0.883	0.807	0.959	CLONAL	1	TRUE	0	0.730519728578276	1		376	183	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045136	47045136	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036408-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	178	292	0	ENST00000377604.3:c.2377C>T	p.Arg793Ter	p.R793*	ENST00000377604	NM_001204468.1	793	Cga/Tga	21/24	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.730519728578276	1		292	240	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040865	42040865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	86	365	0	ENST00000219905.7:c.5243C>T	p.Pro1748Leu	p.P1748L	ENST00000219905	NM_001164273.1	1748	cCa/cTa	16/24	0.206841046471774	4	FACETS	0.859	0.764	0.96	0.859	0.764	0.96	CLONAL	2	TRUE	2	0.29530209672969	4		365	439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577136	7577138	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0036770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	91	475	1	ENST00000269305.4:c.800_802del	p.Arg267_Asn268delinsHis	p.R267_N268delinsH	ENST00000269305	NM_001126112.2	267	cGGAac/cac	8/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.29530209672969	NA		476	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578493	7578493	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1206165503	NA	P-0036784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	488	772	1	ENST00000269305.4:c.437G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tGg/tAg	5/11	0.712837218337074	1	FACETS	0.983	0.948	1	0.983	0.948	1	CLONAL	1	TRUE	0	0.712837218337074	1		773	896	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604190	189604190	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs781491083	NA	P-0036784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	51	569	0	ENST00000264731.3:c.1357A>G	p.Ile453Val	p.I453V	ENST00000264731	NM_003722.4	453	Ata/Gta	11/14	0.312084095439453	3	FACETS	0.309	0.262	0.361	0.155	0.131	0.181	INDETERMINATE	1	TRUE	1	0.712837218337074	3		569	628	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972710	76972710	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	44	432	0	ENST00000373344.5:c.31T>G	p.Leu11Val	p.L11V	ENST00000373344	NM_000489.3	11	Ttg/Gtg	2/35	0.300637627865471	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.712837218337074	0		432	302	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217330	11217330	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	198	697	0	ENST00000361445.4:c.4348T>G	p.Tyr1450Asp	p.Y1450D	ENST00000361445	NM_004958.3	1450	Tat/Gat	30/58	0.745448871815271	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.745448871815271	1		697	329	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577035	7577036	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0036915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	26	350	0	ENST00000269305.4:c.902dup	p.Gly302ArgfsTer4	p.G302Rfs*4	ENST00000269305	NM_001126112.2	301	cca/ccCa	8/11	1	2	FACETS	0.716	0.568	0.887	0.716	0.568	0.887	SUBCLONAL	1	TRUE	1	0.2153564108347	2		350	337	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293295	91293295	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	33	171	0	ENST00000355112.3:c.797G>C	p.Arg266Thr	p.R266T	ENST00000355112	NM_000057.2	266	aGa/aCa	3/22	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.2153564108347	2		171	280	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675570	86675571	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	23	219	1	ENST00000274376.6:c.2513dup	p.Asn838LysfsTer2	p.N838Kfs*2	ENST00000274376	NM_002890.2	836	gaa/gAaa	19/25	1	2	FACETS	0.694	0.541	0.87	0.694	0.541	0.87	SUBCLONAL	1	TRUE	1	0.2153564108347	2		220	308	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028883	47028883	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	17	299	0	ENST00000377604.3:c.187G>T	p.Glu63Ter	p.E63*	ENST00000377604	NM_001204468.1	63	Gag/Tag	3/24	0.2153564108347	1	FACETS	0.476	0.355	0.62	0.476	0.355	0.62	SUBCLONAL	1	TRUE	0	0.2153564108347	1		299	296	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65569015	65569036	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACTCACGTCGCTCTCCACCTC	GACTCACGTCGCTCTCCACCTC	-	novel	NA	P-0036915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	36	177	0	ENST00000358664.4:c.22_36+7del		p.X8_splice	ENST00000358664	NM_002382.4	8		1/5	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.2153564108347	2		177	253	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0036931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	197	645	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.51499778482312	2		645	725	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0036931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	139	205	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.51499778482312	2		205	475	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339680	116339680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	103	340	0	ENST00000397752.3:c.542G>A	p.Gly181Glu	p.G181E	ENST00000397752	NM_000245.2	181	gGa/gAa	2/21	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.51499778482312	2		340	378	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046683	42046683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	141	498	1	ENST00000219905.7:c.7057G>A	p.Glu2353Lys	p.E2353K	ENST00000219905	NM_001164273.1	2353	Gag/Aag	18/24	1	2	FACETS	0.957	0.876	1	0.957	0.876	1	CLONAL	1	TRUE	1	0.51499778482312	2		499	572	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528097	29528097	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	99	347	0	ENST00000356175.3:c.1105C>T	p.Gln369Ter	p.Q369*	ENST00000356175	NM_000267.3	369	Cag/Tag	10/57	0.51499778482312	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.51499778482312	1		347	272	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964961	15964961	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	157	559	0	ENST00000268712.3:c.5635C>T	p.Gln1879Ter	p.Q1879*	ENST00000268712	NM_006311.3	1879	Cag/Tag	37/46	0.51499778482312	1	FACETS	0.993	0.918	1	0.993	0.918	1	CLONAL	1	TRUE	0	0.51499778482312	1		559	456	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176684035	176684035	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	164	610	0	ENST00000439151.2:c.4849G>A	p.Glu1617Lys	p.E1617K	ENST00000439151	NM_022455.4	1617	Gaa/Aaa	13/23	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.51499778482312	2		610	616	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162014	22162014	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	148	549	0	ENST00000215832.6:c.241G>A	p.Glu81Lys	p.E81K	ENST00000215832	NM_002745.4	81	Gag/Aag	2/9	1	2	FACETS	0.958	0.879	1	0.958	0.879	1	CLONAL	1	TRUE	1	0.51499778482312	2		549	600	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484303	120484303	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	120	405	0	ENST00000256646.2:c.2827G>T	p.Gly943Trp	p.G943W	ENST00000256646	NM_024408.3	943	Ggg/Tgg	18/34	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.51499778482312	2		405	451	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533611	533611	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs751137946	NA	P-0036931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	200	578	1	ENST00000451590.1:c.292G>A	p.Glu98Lys	p.E98K	ENST00000451590	NM_001130442.1	98	Gag/Aag	4/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.51499778482312	2		579	695	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937599	32937599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	161	524	1	ENST00000380152.3:c.8260C>T	p.His2754Tyr	p.H2754Y	ENST00000380152		2754	Cat/Tat	18/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.51499778482312	2		525	541	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961377	41961377	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	154	438	0	ENST00000219905.7:c.285G>T	p.Met95Ile	p.M95I	ENST00000219905	NM_001164273.1	95	atG/atT	2/24	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.51499778482312	2		438	508	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752745	42752745	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	173	726	0	ENST00000222329.4:c.1519G>A	p.Glu507Lys	p.E507K	ENST00000222329	NM_006494.2	507	Gag/Aag	4/4	1	2	FACETS	0.85	0.784	0.919	0.85	0.784	0.919	CLONAL	1	TRUE	1	0.51499778482312	2		726	790	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051154	128051154	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	184	609	0	ENST00000285398.2:c.169G>T	p.Gly57Ter	p.G57*	ENST00000285398	NM_000122.1	57	Gga/Tga	2/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.51499778482312	2		609	665	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256665	46256665	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0036931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	88	379	0	ENST00000371998.3:c.722-1G>A		p.X241_splice	ENST00000371998		241			1	2	FACETS	0.96	0.858	1	0.96	0.858	1	CLONAL	1	TRUE	1	0.51499778482312	2		379	356	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22161969	22161969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs530183395	NA	P-0036931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	139	511	0	ENST00000215832.6:c.286G>A	p.Glu96Lys	p.E96K	ENST00000215832	NM_002745.4	96	Gag/Aag	2/9	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.51499778482312	2		511	532	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191261	185191261	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	123	429	0	ENST00000265026.3:c.2142C>A	p.Asp714Glu	p.D714E	ENST00000265026	NM_004721.4	714	gaC/gaA	11/14	1	2	FACETS	0.924	0.84	1	0.924	0.84	1	CLONAL	1	TRUE	1	0.51499778482312	2		429	517	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	36	519	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.377184338587372	2		519	161	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292712	62292712	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	14	498	0	ENST00000360203.5:c.164C>G	p.Thr55Ser	p.T55S	ENST00000360203	NM_001283009.1	55	aCc/aGc	3/35	0.16846681852551	6	FACETS	0.874	0.635	1	0.219	0.158	0.29	INDETERMINATE	1	TRUE	2	0.377184338587372	6		498	149	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170002274	170002274	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	28	141	0	ENST00000295797.4:c.1093G>T	p.Ala365Ser	p.A365S	ENST00000295797	NM_002740.5	365	Gca/Tca	12/18	0.156625648642948	6	FACETS	0.843	0.689	1	0.632	0.517	0.757	INDETERMINATE	3	TRUE	2	0.377184338587372	6		141	103	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391268	139391268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	14	909	0	ENST00000277541.6:c.6923G>A	p.Cys2308Tyr	p.C2308Y	ENST00000277541	NM_017617.3	2308	tGc/tAc	34/34	1	2	FACETS	0.534	0.388	0.708	0.534	0.388	0.708	SUBCLONAL	1	TRUE	1	0.377184338587372	2		909	139	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398286	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0037011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	596	327	0	ENST00000311936.3:c.33_34delinsCT	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	11	gcTGgt/gcCTgt	2/5	0.42786440447869	7	FACETS	0.964	0.934	0.994			1	CLONAL	6	TRUE	NA	0.42786440447869	7		327	997	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947852	178947852	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	67	319	0	ENST00000263967.3:c.2727C>A	p.Phe909Leu	p.F909L	ENST00000263967	NM_006218.2	909	ttC/ttA	19/21	0.42786440447869	3	FACETS	0.847	0.738	0.964	0.423	0.369	0.482	CLONAL	1	TRUE	1	0.42786440447869	3		319	449	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306609	163306609	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	110	368	1	ENST00000271452.3:c.406G>A	p.Glu136Lys	p.E136K	ENST00000271452	NM_145697.2	136	Gaa/Aaa	6/14	0.42786440447869	5	FACETS	1	0.959	1	0.377	0.338	0.417	CLONAL	1	TRUE	2	0.42786440447869	5		369	747	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100406	8100406	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	132	641	0	ENST00000346208.3:c.380C>A	p.Pro127Gln	p.P127Q	ENST00000346208		127	cCg/cAg	3/6	0.233811664348642	4	FACETS	0.915	0.83	1	0.457	0.415	0.503	INDETERMINATE	1	TRUE	2	0.42786440447869	4		641	963	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337693	73337693	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	74	220	0	ENST00000377767.4:c.2023G>T	p.Ala675Ser	p.A675S	ENST00000377767	NM_014953.3	675	Gca/Tca	16/21	0.233811664348642	4	FACETS	1	0.971	1	0.684	0.603	0.771	INDETERMINATE	1	TRUE	2	0.42786440447869	4		220	361	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43700216	43700216	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	92	467	0	ENST00000382044.4:c.5671G>C	p.Glu1891Gln	p.E1891Q	ENST00000382044	NM_001141980.1	1891	Gag/Cag	27/28	1	2	FACETS	0.855	0.762	0.953	0.855	0.762	0.953	CLONAL	1	TRUE	1	0.42786440447869	2		467	503	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971285	15971285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	112	430	0	ENST00000268712.3:c.4664C>T	p.Thr1555Ile	p.T1555I	ENST00000268712	NM_006311.3	1555	aCt/aTt	32/46	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.42786440447869	2		430	460	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443658	29443658	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	250	509	0	ENST00000389048.3:c.3559C>A	p.Leu1187Met	p.L1187M	ENST00000389048	NM_004304.4	1187	Ctg/Atg	23/29	0.42786440447869	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.42786440447869	3		509	630	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155243	55155243	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	72	465	0	ENST00000257290.5:c.2842G>C	p.Glu948Gln	p.E948Q	ENST00000257290	NM_006206.4	948	Gag/Cag	21/23	0.42786440447869	3	FACETS	0.795	0.696	0.901	0.397	0.348	0.451	CLONAL	1	TRUE	1	0.42786440447869	3		465	514	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217125	66217125	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	80	398	0	ENST00000273854.3:c.2490G>T	p.Glu830Asp	p.E830D	ENST00000273854	NM_004439.5	830	gaG/gaT	14/18	NA	2	FACETS	0.94	0.832	1			1	INDETERMINATE	1	TRUE	NA	0.42786440447869	2		398	398	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549444	187549444	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	112	459	1	ENST00000441802.2:c.4674C>A	p.His1558Gln	p.H1558Q	ENST00000441802	NM_005245.3	1558	caC/caA	9/27	0.419168626466124	4	FACETS	1	0.96	1	0.376	0.338	0.415	CLONAL	1	TRUE	1	0.42786440447869	4		460	663	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518776	176518776	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	103	610	0	ENST00000292408.4:c.694A>T	p.Ser232Cys	p.S232C	ENST00000292408	NM_213647.1	232	Agc/Tgc	6/18	0.132737245238938	3	FACETS	0.986	0.884	1	0.329	0.294	0.365	INDETERMINATE	1	TRUE	0	0.42786440447869	3		610	593	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120864	94120864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	67	432	0	ENST00000369303.4:c.187G>A	p.Glu63Lys	p.E63K	ENST00000369303	NM_004440.3	63	Gag/Aag	3/17	0.42786440447869	3	FACETS	0.79	0.688	0.9	0.395	0.344	0.45	SUBCLONAL	1	TRUE	1	0.42786440447869	3		432	481	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002888	69002888	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	134	286	0	ENST00000288368.4:c.2188G>C	p.Glu730Gln	p.E730Q	ENST00000288368	NM_024870.2	730	Gag/Cag	20/40	0.42786440447869	6	FACETS	1	0.939	1	0.518	0.472	0.565	CLONAL	2	TRUE	2	0.42786440447869	6		286	561	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	39	737	0				ENST00000310581	NM_198253.2	-/1132			0.112359663702574	4	FACETS	0.92	0.766	1	0.46	0.383	0.545	INDETERMINATE	1	TRUE	2	0.40516412183986	4		737	294	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	178	357	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.40516412183986	1	FACETS	0.809	0.754	0.865	1	0.992	1	CLONAL	2	TRUE	0	0.40516412183986	1		357	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	144	846	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.112359663702574	4	FACETS	1	0.973	1	0.585	0.533	0.639	INDETERMINATE	1	TRUE	2	0.40516412183986	4		846	854	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519922	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	388	1006	0	ENST00000397062.3:c.235G>A	p.Glu79Lys	p.E79K	ENST00000397062	NM_006164.4	79	Gag/Aag	2/5	0.328989738439628	3	FACETS	1	0.993	1	0.8	0.763	0.837	CLONAL	2	TRUE	0	0.40516412183986	3		1006	960	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741836	40741836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	206	632	0	ENST00000392038.2:c.1136C>T	p.Ser379Phe	p.S379F	ENST00000392038	NM_001626.4	379	tCc/tTc	11/14	0.0874477349704637	5	FACETS	1	0.948	1	0.682	0.634	0.731	INDETERMINATE	2	TRUE	2	0.40516412183986	5		632	799	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267698	198267698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	145	571	0	ENST00000335508.6:c.1781G>A	p.Arg594Gln	p.R594Q	ENST00000335508	NM_012433.2	594	cGa/cAa	13/25	0.328989738439628	3	FACETS	1	0.971	1	0.738	0.681	0.796	CLONAL	2	TRUE	0	0.40516412183986	3		571	389	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413165	139413165	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	841	999	0	ENST00000277541.6:c.977G>A	p.Gly326Asp	p.G326D	ENST00000277541	NM_017617.3	326	gGc/gAc	6/34	0.40516412183986	5	FACETS	1	0.994	1	1	0.994	1	CLONAL	4	TRUE	1	0.40516412183986	5		999	1552	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667423	241667423	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913122	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	182	581	1	ENST00000366560.3:c.1027C>T	p.Arg343Ter	p.R343*	ENST00000366560	NM_000143.3	343	Cga/Tga	7/10	0.112359663702574	4	FACETS	1	0.99	1	0.741	0.684	0.8	INDETERMINATE	1	TRUE	2	0.40516412183986	4		582	852	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248064	59248064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	1903	439	0	ENST00000371222.2:c.679G>A	p.Glu227Lys	p.E227K	ENST00000371222	NM_002228.3	227	Gag/Aag	1/1	0.40516412183986	19	FACETS	1	0.992	1			1	CLONAL	18	TRUE	NA	0.40516412183986	19		439	2309	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504347	186504347	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	98	365	0	ENST00000323963.5:c.684C>A	p.Phe228Leu	p.F228L	ENST00000323963		228	ttC/ttA	7/11	0.40516412183986	4	FACETS	1	0.98	1	0.716	0.641	0.794	CLONAL	1	TRUE	2	0.40516412183986	4		365	475	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257705	16257706	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	119	597	0	ENST00000375759.3:c.4970_4971delinsTT	p.Thr1657Ile	p.T1657I	ENST00000375759	NM_015001.2	1657	aCC/aTT	11/15	0.339118697992409	3	FACETS	0.957	0.865	1	0.479	0.432	0.528	CLONAL	1	TRUE	1	0.40516412183986	3		597	738	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050287	176050288	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	57	393	0	ENST00000367669.3:c.1277_1277+1delinsAA		p.X426_splice	ENST00000367669	NM_022457.5	426		11/20	0.112359663702574	4	FACETS	1	0.96	1	0.663	0.573	0.76	INDETERMINATE	1	TRUE	2	0.40516412183986	4		393	298	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570804	226570805	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	231	677	1	ENST00000366794.5:c.1091_1092delinsTT	p.Ser364Phe	p.S364F	ENST00000366794	NM_001618.3	364	tCC/tTT	8/23	0.112359663702574	4	FACETS	0.823	0.767	0.88	0.823	0.767	0.88	INDETERMINATE	2	TRUE	2	0.40516412183986	4		678	974	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226590027	226590027	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	252	712	0	ENST00000366794.5:c.174G>A	p.Trp58Ter	p.W58*	ENST00000366794	NM_001618.3	58	tgG/tgA	2/23	0.112359663702574	4	FACETS	0.912	0.855	0.972	0.912	0.855	0.972	INDETERMINATE	2	TRUE	2	0.40516412183986	4		712	958	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14303148	14303148	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	56	655	0	ENST00000256196.4:c.527G>A	p.Arg176Lys	p.R176K	ENST00000256196		176	aGg/aAg	5/6	0.112359663702574	4	FACETS	0.839	0.72	0.968	0.419	0.36	0.484	INDETERMINATE	1	TRUE	2	0.40516412183986	4		655	463	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022533	12022534	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	239	725	1	ENST00000396373.4:c.639_640delinsTT	p.Pro214Ser	p.P214S	ENST00000396373	NM_001987.4	213	tcCCcg/tcTTcg	5/8	0.141309657191254	6	FACETS	1	0.986	1	0.788	0.737	0.841	INDETERMINATE	2	TRUE	3	0.40516412183986	6		726	903	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495832	56495832	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	73	481	0	ENST00000267101.3:c.4022G>A	p.Arg1341Lys	p.R1341K	ENST00000267101	NM_001982.3	1341	aGa/aAa	28/28	0.339118697992409	3	FACETS	0.928	0.814	1	0.464	0.407	0.525	CLONAL	1	TRUE	1	0.40516412183986	3		481	467	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576177	88576177	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	126	745	0	ENST00000360948.2:c.1496A>G	p.Asp499Gly	p.D499G	ENST00000360948	NM_001012338.2	499	gAc/gGc	13/19	0.374910381666341	1	FACETS	0.64	0.58	0.703	0.64	0.58	0.703	SUBCLONAL	1	TRUE	0	0.40516412183986	1		745	775	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679814	88679814	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	129	572	0	ENST00000360948.2:c.649G>C	p.Val217Leu	p.V217L	ENST00000360948	NM_001012338.2	217	Gtc/Ctc	7/19	0.374910381666341	1	FACETS	0.826	0.751	0.904	0.826	0.751	0.904	CLONAL	1	TRUE	0	0.40516412183986	1		572	615	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352017	89352018	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	355	986	1	ENST00000301030.4:c.932_933delinsTT	p.Ser311Phe	p.S311F	ENST00000301030	NM_001256183.1	311	tCC/tTT	9/13	0.113205074748333	3	FACETS	0.968	0.919	1	0.646	0.612	0.68	INDETERMINATE	2	TRUE	0	0.40516412183986	3		987	1088	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578450	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	332	887	2	ENST00000269305.4:c.480_481delinsAA	p.Met160_Ala161delinsIleThr	p.M160_A161delinsIT	ENST00000269305	NM_001126112.2	160	atGGcc/atAAcc	5/11	0.112359663702574	4	FACETS	1	0.959	1	1	0.959	1	INDETERMINATE	2	TRUE	2	0.40516412183986	4		889	1133	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681049	37681050	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	188	620	0	ENST00000447079.4:c.3218_3219delinsAA	p.Gly1073Glu	p.G1073E	ENST00000447079	NM_015083.1	1073	gGG/gAA	12/14	0.112359663702574	4	FACETS	0.759	0.702	0.818	0.759	0.702	0.818	INDETERMINATE	2	TRUE	2	0.40516412183986	4		620	859	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481466	40481466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193922717	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	204	664	0	ENST00000264657.5:c.1243G>A	p.Glu415Lys	p.E415K	ENST00000264657	NM_139276.2	415	Gag/Aag	14/24	0.112359663702574	4	FACETS	0.844	0.784	0.906	0.844	0.784	0.906	INDETERMINATE	2	TRUE	2	0.40516412183986	4		664	838	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56411617	56411617	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	144	686	0	ENST00000348428.3:c.1801C>T	p.Gln601Ter	p.Q601*	ENST00000348428	NM_006785.3	601	Caa/Taa	15/17	0.40516412183986	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.40516412183986	1		686	447	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353741	15353742	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	144	866	1	ENST00000263377.2:c.3138_3139delinsTT	p.Arg1047Trp	p.R1047W	ENST00000263377	NM_058243.2	1046	ccCCgg/ccTTgg	14/20	0.168705768992729	2	FACETS	0.71	0.647	0.777	0.355	0.323	0.389	INDETERMINATE	1	TRUE	0	0.40516412183986	2		867	1001	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727836	41727836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765828639	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	277	901	1	ENST00000301178.4:c.461C>T	p.Thr154Ile	p.T154I	ENST00000301178	NM_021913.4	154	aCc/aTc	4/20	0.0874477349704637	5	FACETS	1	0.978	1	0.721	0.678	0.766	INDETERMINATE	2	TRUE	2	0.40516412183986	5		902	1016	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527497	41527498	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	108	727	1	ENST00000263253.7:c.1388_1389delinsTT	p.Ser463Phe	p.S463F	ENST00000263253	NM_001429.3	463	tCC/tTT	6/31	NA	2	FACETS	0.798	0.717	0.884			1	INDETERMINATE	1	TRUE	NA	0.40516412183986	2		728	668	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574868	41574868	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752065194	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	120	790	0	ENST00000263253.7:c.7153C>T	p.Leu2385Phe	p.L2385F	ENST00000263253	NM_001429.3	2385	Ctc/Ttc	31/31	NA	2	FACETS	0.818	0.739	0.901			1	INDETERMINATE	1	TRUE	NA	0.40516412183986	2		790	724	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278881	1278881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1323064721	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	134	792	0	ENST00000310581.5:c.2161C>T	p.Pro721Ser	p.P721S	ENST00000310581	NM_198253.2	721	Ccc/Tcc	6/16	0.112359663702574	4	FACETS	1	0.955	1	0.542	0.492	0.595	INDETERMINATE	1	TRUE	2	0.40516412183986	4		792	857	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109308764	109308764	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1442130633	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	31	434	0	ENST00000436639.2:c.1639A>G	p.Thr547Ala	p.T547A	ENST00000436639	NM_014454.2	547	Acc/Gcc	10/10	0.339118697992409	3	FACETS	0.54	0.437	0.656	0.27	0.218	0.328	SUBCLONAL	1	TRUE	1	0.40516412183986	3		434	341	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402583	139402583	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	149	862	0	ENST00000277541.6:c.3334G>T	p.Val1112Phe	p.V1112F	ENST00000277541	NM_017617.3	1112	Gtt/Ttt	21/34	0.40516412183986	5	FACETS	0.939	0.856	1	0.235	0.214	0.257	CLONAL	1	TRUE	1	0.40516412183986	5		862	1259	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933496	39933497	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	258	469	1	ENST00000378444.4:c.1102_1103delinsTT	p.Pro368Phe	p.P368F	ENST00000378444	NM_001123385.1	368	CCt/TTt	4/15	0.137254071289034	2	FACETS	0.837	0.794	0.881			1	INDETERMINATE	3	TRUE	NA	0.40516412183986	2		470	507	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030538	47030538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	230	424	0	ENST00000377604.3:c.313C>T	p.Gln105Ter	p.Q105*	ENST00000377604	NM_001204468.1	105	Cag/Tag	4/24	0.137254071289034	2	FACETS	0.89	0.843	0.938			1	INDETERMINATE	3	TRUE	NA	0.40516412183986	2		424	425	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981861	201981861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	263	888	0	ENST00000359651.3:c.572C>T	p.Pro191Leu	p.P191L	ENST00000359651		191	cCt/cTt	4/8	0.112359663702574	4	FACETS	0.879	0.824	0.935	0.879	0.824	0.935	INDETERMINATE	2	TRUE	2	0.40516412183986	4		888	1038	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	92	306	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.242643889273178	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.23	1		306	693	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221320	1221320	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587776656	NA	P-0037047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	86	824	0	ENST00000326873.7:c.843del	p.Leu282SerfsTer5	p.L282Sfs*5	ENST00000326873	NM_000455.4	281	ccG/cc	6/10	0.242643889273178	1	FACETS	0.83	0.734	0.934	0.83	0.734	0.934	CLONAL	1	TRUE	0	0.23	1		824	797	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610247	10610247	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	98	717	0	ENST00000171111.5:c.463G>T	p.Val155Phe	p.V155F	ENST00000171111	NM_203500.1	155	Gtc/Ttc	2/6	0.242643889273178	1	FACETS	0.828	0.737	0.924	0.828	0.737	0.924	CLONAL	1	TRUE	0	0.23	1		717	911	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241966	72241966	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	38	472	0	ENST00000357731.5:c.424T>C	p.Tyr142His	p.Y142H	ENST00000357731	NM_173808.2	142	Tat/Cat	3/7	1	2	FACETS	0.723	0.598	0.863	0.723	0.598	0.863	SUBCLONAL	1	TRUE	1	0.23	2		472	457	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0037064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	228	471	1	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.283248313776824	3	FACETS	1	0.982	1	0.756	0.707	0.806	CLONAL	2	TRUE	0	0.31	3		472	749	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446351	70446351	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	52	578	0	ENST00000373644.4:c.5291A>T	p.Glu1764Val	p.E1764V	ENST00000373644	NM_030625.2	1764	gAg/gTg	11/12	0.239257748811235	1	FACETS	0.507	0.431	0.59	0.507	0.431	0.59	SUBCLONAL	1	TRUE	0	0.31	1		578	559	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155884	106155884	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	37	474	0	ENST00000380013.4:c.785G>T	p.Cys262Phe	p.C262F	ENST00000380013	NM_001127208.2	262	tGt/tTt	3/11	0.283248313776824	3	FACETS	0.45	0.37	0.54	0.15	0.123	0.18	SUBCLONAL	1	TRUE	0	0.31	3		474	613	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0037074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	137	544	1				ENST00000310581	NM_198253.2	-/1132			0.297452072917561	1	FACETS	0.603	0.56	0.646	0.603	0.56	0.646	INDETERMINATE	1	TRUE	0	0.915425943672445	1		545	269	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692790	89692790	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	14	485	0	ENST00000371953.3:c.274G>C	p.Asp92His	p.D92H	ENST00000371953	NM_000314.4	92	Gac/Cac	5/9	0.915425943672445	1	FACETS	0.065	0.047	0.088	0.065	0.047	0.088	SUBCLONAL	1	TRUE	0	0.915425943672445	1		485	254	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519988	NA	P-0037074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	353	771	0	ENST00000269305.4:c.808T>C	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	Ttt/Ctt	8/11	0.915425943672445	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.915425943672445	1		771	389	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940342	49940342	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1224367583	NA	P-0037074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	366	799	0	ENST00000296474.3:c.701C>T	p.Ala234Val	p.A234V	ENST00000296474	NM_002447.2	234	gCg/gTg	1/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.915425943672445	2		799	720	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720691	89720691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	45	165	0	ENST00000371953.3:c.842C>T	p.Pro281Leu	p.P281L	ENST00000371953	NM_000314.4	281	cCa/cTa	8/9	0.915425943672445	1	FACETS	0.606	0.531	0.68	0.606	0.531	0.68	SUBCLONAL	1	TRUE	0	0.915425943672445	1		165	88	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776022	9776022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	612	726	2	ENST00000377346.4:c.486G>A	p.Trp162Ter	p.W162*	ENST00000377346	NM_005026.3	162	tgG/tgA	5/24	0.71893423411379	3	FACETS	1	0.987	1			1	CLONAL	2	TRUE	NA	0.915425943672445	3		728	946	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720873	89720888	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGGTCAGTTAAATTA	AAGGTCAGTTAAATTA	-	novel	NA	P-0037074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	34	316	0	ENST00000371953.3:c.1026_1026+15del		p.X342_splice	ENST00000371953	NM_000314.4	342		8/9	0.915425943672445	1	FACETS	0.325	0.271	0.383	0.325	0.271	0.383	SUBCLONAL	1	TRUE	0	0.915425943672445	1		316	124	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966972	25966972	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	431	846	1	ENST00000435504.4:c.2234C>A	p.Pro745His	p.P745H	ENST00000435504		745	cCc/cAc	13/13	0.847214728558021	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.915425943672445	1		847	479	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916642	178916642	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	194	455	0	ENST00000263967.3:c.29T>A	p.Leu10Gln	p.L10Q	ENST00000263967	NM_006218.2	10	cTg/cAg	2/21	0.344253260603289	4	FACETS	1	0.99	1	0.688	0.64	0.737	INDETERMINATE	1	TRUE	2	0.915425943672445	4		455	590	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081651	143081651	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	321	545	0	ENST00000262992.4:c.1423A>T	p.Thr475Ser	p.T475S	ENST00000262992	NM_001101669.1	475	Act/Tct	15/24	0.335847100175419	5	FACETS	0.997	0.945	1	0.664	0.63	0.699	INDETERMINATE	2	TRUE	2	0.915425943672445	5		545	835	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782620	NA	P-0037080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	519	527	1	ENST00000269305.4:c.427G>A	p.Val143Met	p.V143M	ENST00000269305	NM_001126112.2	143	Gtg/Atg	5/11	0.443827843543055	2	FACETS	0.929	0.894	0.963	0.929	0.894	0.963	CLONAL	2	TRUE	0	0.536879796524727	2		528	1041	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922222	100922222	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	289	261	0	ENST00000325455.5:c.2290G>T	p.Gly764Ter	p.G764*	ENST00000325455	NM_001202474.3	764	Gga/Tga	5/8	0.490204200531371	3	FACETS	0.901	0.86	0.942	0.901	0.86	0.942	CLONAL	3	TRUE	0	0.536879796524727	3		261	505	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468126	31468126	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	524	323	0	ENST00000344624.3:c.2286C>G	p.Phe762Leu	p.F762L	ENST00000344624		762	ttC/ttG	15/33	0.36541473369038	4	FACETS	1	0.992	1	0.813	0.785	0.841	CLONAL	3	TRUE	0	0.536879796524727	4		323	922	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29563039	29563039	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs863224447	NA	P-0037080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	176	249	0	ENST00000356175.3:c.3974G>T	p.Arg1325Met	p.R1325M	ENST00000356175	NM_000267.3	1325	aGg/aTg	29/57	0.443827843543055	2	FACETS	0.828	0.773	0.883	0.828	0.773	0.883	CLONAL	2	TRUE	0	0.536879796524727	2		249	396	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435827	56435827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140873038	NA	P-0037080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	42	314	0	ENST00000407977.2:c.1310G>A	p.Arg437Gln	p.R437Q	ENST00000407977		437	cGg/cAg	9/10	0.443827843543055	2	FACETS	0.364	0.304	0.43	0.182	0.152	0.215	SUBCLONAL	1	TRUE	0	0.536879796524727	2		314	430	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929500	81929500	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	280	353	0	ENST00000359376.3:c.1161G>T	p.Gln387His	p.Q387H	ENST00000359376	NM_002661.3	387	caG/caT	13/33	0.49574335458387	2	FACETS	0.877	0.831	0.922	0.877	0.831	0.922	CLONAL	2	TRUE	0	0.536879796524727	2		353	595	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437614	56437614	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0037080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	174	243	0	ENST00000407977.2:c.850-2A>C		p.X284_splice	ENST00000407977		284			0.443827843543055	2	FACETS	0.855	0.799	0.912	0.855	0.799	0.912	CLONAL	2	TRUE	0	0.536879796524727	2		243	379	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281146	15281146	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	508	553	0	ENST00000263388.2:c.5110A>T	p.Met1704Leu	p.M1704L	ENST00000263388	NM_000435.2	1704	Atg/Ttg	27/33	0.490204200531371	3	FACETS	0.905	0.874	0.936	0.905	0.874	0.936	CLONAL	3	TRUE	0	0.536879796524727	3		553	884	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528614	89528614	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	61	128	0	ENST00000336596.2:c.2914C>A	p.Leu972Ile	p.L972I	ENST00000336596	NM_005233.5	972	Cta/Ata	17/17	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.536879796524727	2		128	220	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526218	189526218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316823566	NA	P-0037080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	166	469	1	ENST00000264731.3:c.482C>T	p.Pro161Leu	p.P161L	ENST00000264731	NM_003722.4	161	cCa/cTa	4/14	1	2	FACETS	0.956	0.881	1	0.956	0.881	1	CLONAL	1	TRUE	1	0.536879796524727	2		470	647	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592162	55592162	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	78	375	0	ENST00000288135.5:c.1486G>T	p.Asp496Tyr	p.D496Y	ENST00000288135	NM_000222.2	496	Gat/Tat	9/21	0.287237414621513	1	FACETS	0.337	0.296	0.382	0.337	0.296	0.382	INDETERMINATE	1	TRUE	0	0.536879796524727	1		375	630	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356259	66356259	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs745452853	NA	P-0037080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	100	411	0	ENST00000273854.3:c.1238G>T	p.Arg413Met	p.R413M	ENST00000273854	NM_004439.5	413	aGg/aTg	5/18	0.287237414621513	1	FACETS	0.401	0.358	0.446	0.401	0.358	0.446	INDETERMINATE	1	TRUE	0	0.536879796524727	1		411	680	SUCCESS
APC	324	MSKCC	GRCh37	5	112178939	112178939	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	100	205	0	ENST00000257430.4:c.7648G>C	p.Glu2550Gln	p.E2550Q	ENST00000257430	NM_000038.5	2550	Gag/Cag	16/16	0.315262273081362	1	FACETS	0.854	0.772	0.94	0.854	0.772	0.94	INDETERMINATE	1	TRUE	0	0.536879796524727	1		205	319	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346547	81346547	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0037080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	93	162	0	ENST00000222390.5:c.1405+1G>C		p.X469_splice	ENST00000222390	NM_000601.4	469			0.201678983181105	5	FACETS	0.866	0.777	0.96	0.578	0.518	0.64	INDETERMINATE	2	TRUE	2	0.536879796524727	5		162	361	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046471	69046471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	104	446	0	ENST00000288368.4:c.3944G>A	p.Gly1315Asp	p.G1315D	ENST00000288368	NM_024870.2	1315	gGt/gAt	32/40	0.502452202421159	3	FACETS	0.58	0.518	0.645	0.29	0.259	0.323	SUBCLONAL	1	TRUE	1	0.536879796524727	3		446	848	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460532	8460532	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	146	262	0	ENST00000356435.5:c.3754T>A	p.Ser1252Thr	p.S1252T	ENST00000356435		1252	Tca/Aca	22/35	0.316074119123878	2	FACETS	0.971	0.891	1	0.486	0.445	0.528	INDETERMINATE	1	TRUE	0	0.536879796524727	2		262	560	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	309	729	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.720548386013902	2		729	789	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	643	647	2	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	0.704584401751754	2	FACETS	0.997	0.972	1	0.997	0.972	1	CLONAL	2	TRUE	0	0.720548386013902	2		649	895	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097632	8097633	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0037099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	109	245	0	ENST00000346208.3:c.16dup	p.Asp6GlyfsTer47	p.D6Gfs*47	ENST00000346208		5	gcg/gcGg	2/6	1	2	FACETS	0.892	0.81	0.977	0.892	0.81	0.977	CLONAL	1	TRUE	1	0.720548386013902	2		245	339	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827862	72827862	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	354	742	0	ENST00000268489.5:c.8719G>C	p.Asp2907His	p.D2907H	ENST00000268489	NM_006885.3	2907	Gac/Cac	9/10	0.720548386013902	1	FACETS	0.99	0.948	1	0.99	0.948	1	CLONAL	1	TRUE	0	0.720548386013902	1		742	635	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119981	70119981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451445875	NA	P-0037099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	311	308	0	ENST00000245479.2:c.983C>T	p.Pro328Leu	p.P328L	ENST00000245479	NM_000346.3	328	cCg/cTg	3/3	0.720548386013902	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.720548386013902	3		308	577	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964453	93964453	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	283	693	0	ENST00000369303.4:c.2444C>T	p.Ser815Leu	p.S815L	ENST00000369303	NM_004440.3	815	tCa/tTa	14/17	1	2	FACETS	0.966	0.912	1	0.966	0.912	1	CLONAL	1	TRUE	1	0.720548386013902	2		693	813	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	145	544	1				ENST00000310581	NM_198253.2	-/1132			0.480876970278837	0	FACETS	0.726	0.669	0.785			1	SUBCLONAL	1	FALSE	0	0.480876970278837	0		545	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	238	830	0	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	0.480876970278837	0	FACETS	0.723	0.678	0.769			1	SUBCLONAL	1	FALSE	0	0.480876970278837	0		830	711	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100664	8100664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1477514775	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	172	715	1	ENST00000346208.3:c.638C>T	p.Ser213Leu	p.S213L	ENST00000346208		213	tCg/tTg	3/6	1	2	FACETS	0.981	0.905	1	0.981	0.905	1	CLONAL	1	FALSE	1	0.480876970278837	2		716	729	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602754	10602754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	265	875	0	ENST00000171111.5:c.824C>T	p.Ser275Leu	p.S275L	ENST00000171111	NM_203500.1	275	tCg/tTg	3/6	0.480876970278837	0	FACETS	0.535	0.501	0.569			1	SUBCLONAL	1	FALSE	0	0.480876970278837	0		875	1070	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494187	140494187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1158980679	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	327	874	3	ENST00000288602.6:c.1061G>A	p.Arg354Gln	p.R354Q	ENST00000288602	NM_004333.4	354	cGa/cAa	8/18	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.480876970278837	2		877	1094	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341914	8341914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	164	667	0	ENST00000356435.5:c.4726G>A	p.Glu1576Lys	p.E1576K	ENST00000356435		1576	Gaa/Aaa	29/35	0.480876970278837	0	FACETS	0.613	0.565	0.661			1	SUBCLONAL	1	FALSE	0	0.480876970278837	0		667	578	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149241	119149241	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867564832	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	217	630	0	ENST00000264033.4:c.1249C>T	p.Pro417Ser	p.P417S	ENST00000264033	NM_005188.3	417	Cct/Tct	9/16	0.480876970278837	0	FACETS	0.812	0.761	0.864			1	CLONAL	1	FALSE	0	0.480876970278837	0		630	577	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592318	29592318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	168	577	0	ENST00000356175.3:c.4733C>T	p.Ser1578Phe	p.S1578F	ENST00000356175	NM_000267.3	1578	tCc/tTc	35/57	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.480876970278837	2		577	584	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445067	89445067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	164	470	0	ENST00000336596.2:c.1387C>T	p.Pro463Ser	p.P463S	ENST00000336596	NM_005233.5	463	Cct/Tct	6/17	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.480876970278837	2		470	606	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495496	149495496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1205902689	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	318	935	2	ENST00000261799.4:c.3151G>A	p.Glu1051Lys	p.E1051K	ENST00000261799	NM_002609.3	1051	Gaa/Aaa	23/23	0.480876970278837	0	FACETS	0.811	0.768	0.854			1	CLONAL	1	FALSE	0	0.480876970278837	0		937	847	SUCCESS
ATR	545	MSKCC	GRCh37	3	142232477	142232477	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs754602382	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	131	461	1	ENST00000350721.4:c.4507C>T	p.Arg1503Ter	p.R1503*	ENST00000350721	NM_001184.3	1503	Cga/Tga	26/47	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.480876970278837	2		462	450	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908122	41908122	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3218089	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	186	644	0	ENST00000372991.4:c.400C>T	p.Pro134Ser	p.P134S	ENST00000372991	NM_001760.3	134	Ccc/Tcc	2/5	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	1	0.480876970278837	2		644	756	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248677	10248677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1259943763	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	82	424	0	ENST00000340748.4:c.4076C>T	p.Ser1359Leu	p.S1359L	ENST00000340748		1359	tCg/tTg	35/40	0.480876970278837	0	FACETS	0.422	0.373	0.473			1	SUBCLONAL	1	FALSE	0	0.480876970278837	0		424	420	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149982885	149982885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139248642	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	124	540	0	ENST00000253339.5:c.3373C>T	p.Arg1125Cys	p.R1125C	ENST00000253339		1125	Cgc/Tgc	7/7	1	2	FACETS	0.996	0.905	1	0.996	0.905	1	CLONAL	1	FALSE	1	0.480876970278837	2		540	518	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246498692	246498692	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	221	644	0	ENST00000388985.4:c.313C>T	p.Leu105Phe	p.L105F	ENST00000388985		105	Ctt/Ttt	3/12	0.480876970278837	3	FACETS	1	0.944	1	0.509	0.473	0.546	CLONAL	1	FALSE	1	0.480876970278837	3		644	1121	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676136	29676136	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs772348111	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	87	287	0	ENST00000356175.3:c.7127-2A>G		p.X2376_splice	ENST00000356175	NM_000267.3	2376			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.480876970278837	2		287	316	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924402	131924402	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	124	376	0	ENST00000265335.6:c.1075C>T	p.Arg359Cys	p.R359C	ENST00000265335		359	Cgc/Tgc	8/25	0.480876970278837	0	FACETS	0.858	0.788	0.93			1	CLONAL	1	FALSE	0	0.480876970278837	0		376	312	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032006	10032006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	197	748	0	ENST00000330684.3:c.817C>T	p.Pro273Ser	p.P273S	ENST00000330684	NM_001134407.1	273	Cca/Tca	3/13	0.294602598801206	2	FACETS	1	0.978	1	0.566	0.525	0.607	CLONAL	1	FALSE	0	0.480876970278837	2		748	724	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647308	23647308	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	230	801	0	ENST00000261584.4:c.559C>T	p.Pro187Ser	p.P187S	ENST00000261584	NM_024675.3	187	Cct/Tct	4/13	0.294602598801206	2	FACETS	0.992	0.926	1	0.496	0.463	0.531	CLONAL	1	FALSE	0	0.480876970278837	2		801	964	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524168	187524168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	95	443	0	ENST00000441802.2:c.11371C>T	p.His3791Tyr	p.H3791Y	ENST00000441802	NM_005245.3	3791	Cac/Tac	20/27	0.480876970278837	1	FACETS	0.754	0.676	0.836	0.754	0.676	0.836	SUBCLONAL	1	FALSE	0	0.480876970278837	1		443	398	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36821031	36821031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356391159	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	218	657	0	ENST00000373129.3:c.346C>T	p.Arg116Cys	p.R116C	ENST00000373129	NM_032017.1	116	Cgc/Tgc	6/12	0.480876970278837	3	FACETS	1	0.942	1	0.508	0.471	0.545	CLONAL	1	FALSE	1	0.480876970278837	3		657	1108	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104264000	104264000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	160	539	0	ENST00000369902.3:c.91C>T	p.Pro31Ser	p.P31S	ENST00000369902	NM_016169.3	31	Ccc/Tcc	1/12	0.480876970278837	1	FACETS	0.838	0.772	0.907	0.838	0.772	0.907	CLONAL	1	FALSE	0	0.480876970278837	1		539	603	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948407	71948407	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	279	1035	0	ENST00000298229.2:c.3119C>T	p.Ser1040Leu	p.S1040L	ENST00000298229	NM_001567.3	1040	tCa/tTa	26/28	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.480876970278837	2		1035	1106	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641517	18641517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	105	394	0	ENST00000266497.5:c.2516G>A	p.Gly839Glu	p.G839E	ENST00000266497		839	gGa/gAa	17/31	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	FALSE	1	0.480876970278837	2		394	433	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432461	49432461	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	235	791	0	ENST00000301067.7:c.8678C>A	p.Thr2893Asn	p.T2893N	ENST00000301067	NM_003482.3	2893	aCt/aAt	34/54	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.480876970278837	2		791	815	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897044	28897044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41291686	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	223	575	0	ENST00000282397.4:c.2836G>A	p.Glu946Lys	p.E946K	ENST00000282397	NM_002019.4	946	Gag/Aag	21/30	0.480876970278837	0	FACETS	0.778	0.729	0.828			1	SUBCLONAL	1	FALSE	0	0.480876970278837	0		575	619	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033939	49033939	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	155	429	0	ENST00000267163.4:c.2076T>G	p.Tyr692Ter	p.Y692*	ENST00000267163	NM_000321.2	692	taT/taG	20/27	0.480876970278837	0	FACETS	0.83	0.769	0.893			1	CLONAL	1	FALSE	0	0.480876970278837	0		429	403	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609417	81609417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150821978	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	180	573	0	ENST00000298171.2:c.1015G>A	p.Glu339Lys	p.E339K	ENST00000298171	NM_000369.2	339	Gaa/Aaa	10/10	0.480876970278837	0	FACETS	0.854	0.796	0.913			1	CLONAL	1	FALSE	0	0.480876970278837	0		573	455	SUCCESS
BLM	641	MSKCC	GRCh37	15	91290705	91290705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	117	414	0	ENST00000355112.3:c.83C>T	p.Ser28Leu	p.S28L	ENST00000355112	NM_000057.2	28	tCa/tTa	2/22	0.480876970278837	1	FACETS	0.886	0.806	0.97	0.886	0.806	0.97	CLONAL	1	FALSE	0	0.480876970278837	1		414	417	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641565	23641565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878855104	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	248	808	0	ENST00000261584.4:c.1910C>T	p.Pro637Leu	p.P637L	ENST00000261584	NM_024675.3	637	cCc/cTc	5/13	0.294602598801206	2	FACETS	1	0.981	1	0.561	0.525	0.597	CLONAL	1	FALSE	0	0.480876970278837	2		808	920	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827384	72827384	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	300	921	0	ENST00000268489.5:c.9197A>G	p.Tyr3066Cys	p.Y3066C	ENST00000268489	NM_006885.3	3066	tAc/tGc	9/10	0.480876970278837	0	FACETS	0.801	0.757	0.845			1	CLONAL	1	FALSE	0	0.480876970278837	0		921	809	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435641	56435641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	506	624	0	ENST00000407977.2:c.1496G>A	p.Ser499Asn	p.S499N	ENST00000407977		499	aGc/aAc	9/10	1	2	FACETS	1	0.973	1	1	0.997	1	CLONAL	2	FALSE	1	0.480876970278837	2		624	1038	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532645	63532645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881405	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	236	758	0	ENST00000307078.5:c.1934C>T	p.Pro645Leu	p.P645L	ENST00000307078	NM_004655.3	645	cCc/cTc	8/11	0.480876970278837	4	FACETS	1	0.974	1	0.363	0.338	0.39	CLONAL	1	FALSE	1	0.480876970278837	4		758	1333	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221729	36221729	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	232	905	1	ENST00000222270.7:c.5398G>A	p.Glu1800Lys	p.E1800K	ENST00000222270	NM_014727.1	1800	Gag/Aag	26/37	0.480876970278837	0	FACETS	0.526	0.491	0.563			1	SUBCLONAL	1	FALSE	0	0.480876970278837	0		906	952	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383305	42383305	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	163	555	0	ENST00000221972.3:c.325C>T	p.Gln109Ter	p.Q109*	ENST00000221972	NM_021601.3	109	Cag/Tag	2/5	0.480876970278837	0	FACETS	0.612	0.565	0.661			1	SUBCLONAL	1	FALSE	0	0.480876970278837	0		555	575	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018217	48018218	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	239	595	1	ENST00000234420.5:c.412_413delinsTT	p.Pro138Leu	p.P138L	ENST00000234420	NM_000179.2	138	CCa/TTa	2/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.480876970278837	2		596	891	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719518	190719518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	73	274	0	ENST00000441310.2:c.1520C>T	p.Ser507Leu	p.S507L	ENST00000441310	NM_000534.4	507	tCa/tTa	9/13	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	1	0.480876970278837	2		274	287	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295810	212295810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	124	565	0	ENST00000342788.4:c.2503G>A	p.Glu835Lys	p.E835K	ENST00000342788	NM_005235.2	835	Gaa/Aaa	21/28	1	2	FACETS	0.873	0.792	0.957	0.873	0.792	0.957	CLONAL	1	FALSE	1	0.480876970278837	2		565	591	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795042	242795042	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	303	994	0	ENST00000334409.5:c.167T>C	p.Phe56Ser	p.F56S	ENST00000334409	NM_005018.2	56	tTc/tCc	2/5	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.480876970278837	2		994	1136	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164912	47164912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	125	318	0	ENST00000409792.3:c.1214C>T	p.Ser405Phe	p.S405F	ENST00000409792	NM_014159.6	405	tCt/tTt	3/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.480876970278837	2		318	381	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102861	71102861	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	153	421	0	ENST00000318789.4:c.346C>T	p.Leu116Phe	p.L116F	ENST00000318789	NM_032682.5	116	Ctc/Ttc	8/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.480876970278837	2		421	507	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391156	89391156	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	179	527	0	ENST00000336596.2:c.1222G>A	p.Glu408Lys	p.E408K	ENST00000336596	NM_005233.5	408	Gag/Aag	5/17	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.480876970278837	2		527	668	SUCCESS
ATR	545	MSKCC	GRCh37	3	142183952	142183952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	152	480	0	ENST00000350721.4:c.7028C>T	p.Ser2343Phe	p.S2343F	ENST00000350721	NM_001184.3	2343	tCc/tTc	41/47	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.480876970278837	2		480	497	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937003	178937003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	172	648	0	ENST00000263967.3:c.1684C>T	p.Pro562Ser	p.P562S	ENST00000263967	NM_006218.2	562	Ccc/Tcc	11/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.480876970278837	2		648	628	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607197	189607197	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1438616472	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	260	724	0	ENST00000264731.3:c.1576C>T	p.Pro526Ser	p.P526S	ENST00000264731	NM_003722.4	526	Cct/Tct	12/14	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.480876970278837	2		724	989	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159139	143159139	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	114	370	0	ENST00000262992.4:c.714A>T	p.Leu238Phe	p.L238F	ENST00000262992	NM_001101669.1	238	ttA/ttT	10/24	0.480876970278837	1	FACETS	0.921	0.837	1	0.921	0.837	1	CLONAL	1	FALSE	0	0.480876970278837	1		370	391	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332888	153332888	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	131	531	0	ENST00000281708.4:c.68C>T	p.Pro23Leu	p.P23L	ENST00000281708	NM_033632.3	23	cCt/cTt	2/12	0.480876970278837	1	FACETS	0.649	0.59	0.71	0.649	0.59	0.71	SUBCLONAL	1	FALSE	0	0.480876970278837	1		531	638	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38964982	38964982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	74	304	0	ENST00000357387.3:c.1312C>T	p.Leu438Phe	p.L438F	ENST00000357387	NM_152756.3	438	Ctt/Ttt	16/38	0.480876970278837	0	FACETS	0.686	0.609	0.765			1	SUBCLONAL	1	FALSE	0	0.480876970278837	0		304	233	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683640	162683640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	168	514	0	ENST00000366898.1:c.329C>T	p.Ser110Leu	p.S110L	ENST00000366898	NM_004562.2	110	tCa/tTa	3/12	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.480876970278837	2		514	650	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683785	162683785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	136	472	0	ENST00000366898.1:c.184G>A	p.Asp62Asn	p.D62N	ENST00000366898	NM_004562.2	62	Gat/Aat	3/12	1	2	FACETS	0.998	0.911	1	0.998	0.911	1	CLONAL	1	FALSE	1	0.480876970278837	2		472	567	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372124	55372124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	187	569	0	ENST00000297316.4:c.814C>T	p.Pro272Ser	p.P272S	ENST00000297316	NM_022454.3	272	Ccc/Tcc	2/2	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.480876970278837	2		569	680	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485977	8485977	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	143	526	0	ENST00000356435.5:c.2840G>A	p.Arg947Lys	p.R947K	ENST00000356435		947	aGa/aAa	17/35	0.480876970278837	0	FACETS	0.58	0.532	0.631			1	SUBCLONAL	1	FALSE	0	0.480876970278837	0		526	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578493	7578493	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1206165503	NA	P-0037143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	420	772	1	ENST00000269305.4:c.437G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tGg/tAg	5/11	0.4460390352955	2	FACETS	0.942	0.901	0.983	0.942	0.901	0.983	CLONAL	2	TRUE	0	0.468958653938421	2		773	951	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649650	206649650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782109082	NA	P-0037143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	73	596	0	ENST00000367120.3:c.485G>A	p.Arg162Gln	p.R162Q	ENST00000367120	NM_014002.3	162	cGg/cAg	6/22	0.468958653938421	1	FACETS	0.392	0.343	0.445	0.392	0.343	0.445	SUBCLONAL	1	TRUE	0	0.468958653938421	1		596	608	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118345013	118345013	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258907092	NA	P-0037143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	57	177	0	ENST00000534358.1:c.3139G>A	p.Asp1047Asn	p.D1047N	ENST00000534358	NM_005933.3	1047	Gac/Aac	3/36	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.468958653938421	2		177	210	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622109	1622110	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0037143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	180	699	0	ENST00000344749.5:c.765_766del	p.Val256GlyfsTer92	p.V256Gfs*92	ENST00000344749	NM_001136139.2	255	ccGGtg/cctg	10/19	1	2	FACETS	0.852	0.786	0.921	0.852	0.786	0.921	CLONAL	1	TRUE	1	0.468958653938421	2		699	901	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0037157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	891	471	1	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.439697795991879	7	FACETS	1	0.993	1	1	0.993	1	CLONAL	6	TRUE	1	0.439697795991879	7		472	1356	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343021	70343021	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs875989806	NA	P-0037157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	47	669	1	ENST00000374080.3:c.1562G>A	p.Arg521His	p.R521H	ENST00000374080		521	cGt/cAt	11/45	1	2	FACETS	0.278	0.234	0.328	0.278	0.234	0.328	SUBCLONAL	1	TRUE	1	0.439697795991879	2		670	768	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211045	36211045	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	169	732	0	ENST00000222270.7:c.796T>C	p.Trp266Arg	p.W266R	ENST00000222270	NM_014727.1	266	Tgg/Cgg	3/37	0.139956762044487	0	FACETS	0.556	0.512	0.602			1	INDETERMINATE	1	TRUE	0	0.439697795991879	0		732	775	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55260475	55260475	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs397517136	NA	P-0037157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	1040	485	0	ENST00000275493.2:c.2642T>C	p.Met881Thr	p.M881T	ENST00000275493	NM_005228.3	881	aTg/aCg	22/28	0.439697795991879	7	FACETS	0.999	0.977	1	0.999	0.977	1	CLONAL	6	TRUE	1	0.439697795991879	7		485	1656	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0037172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	246	555	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.602775510892194	3	FACETS	0.885	0.855	0.913	1	0.994	1	CLONAL	4	TRUE	0	0.602775510892194	3		555	300	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374141	118374141	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	17	337	0	ENST00000534358.1:c.7534G>T	p.Ala2512Ser	p.A2512S	ENST00000534358	NM_005933.3	2512	Gcc/Tcc	27/36	0.108221100879677	5	FACETS	0.895	0.69	1	0.448	0.345	0.561	INDETERMINATE	2	TRUE	1	0.602775510892194	5		337	60	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487561	38487561	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	68	530	0	ENST00000254066.5:c.91A>T	p.Met31Leu	p.M31L	ENST00000254066	NM_000964.3	31	Atg/Ttg	2/9	0.602775510892194	3	FACETS	0.829	0.737	0.924	0.553	0.491	0.616	CLONAL	2	TRUE	0	0.602775510892194	3		530	177	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853827	59853827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	18	351	0	ENST00000259008.2:c.2032G>A	p.Ala678Thr	p.A678T	ENST00000259008	NM_032043.2	678	Gca/Aca	14/20	0.602775510892194	3	FACETS	1	0.846	1	0.375	0.29	0.47	CLONAL	1	TRUE	0	0.602775510892194	3		351	69	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732967	30732967	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	57	336	0	ENST00000295754.5:c.1582del	p.Arg528ValfsTer36	p.R528Vfs*36	ENST00000295754	NM_003242.5	527	gCc/gc	7/7	0.602775510892194	3	FACETS	0.912	0.804	1	0.608	0.536	0.681	CLONAL	2	TRUE	0	0.602775510892194	3		336	135	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0037174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	28	212	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.174768361922894	3	FACETS	0.304	0.242	0.375	0.152	0.121	0.188	INDETERMINATE	1	TRUE	1	0.371785332975696	3		212	588	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720741	89720741	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs371387815	NA	P-0037174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	12	153	0	ENST00000371953.3:c.892C>T	p.Gln298Ter	p.Q298*	ENST00000371953	NM_000314.4	298	Caa/Taa	8/9	0.371785332975696	1	FACETS	0.381	0.269	0.517	0.381	0.269	0.517	SUBCLONAL	1	TRUE	0	0.371785332975696	1		153	138	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246485	10246485	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393111051	NA	P-0037174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	45	578	0	ENST00000340748.4:c.4652G>A	p.Arg1551Gln	p.R1551Q	ENST00000340748		1551	cGg/cAg	38/40	0.371785332975696	1	FACETS	0.285	0.238	0.336	0.285	0.238	0.336	SUBCLONAL	1	TRUE	0	0.371785332975696	1		578	692	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334836	81334836	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	127	363	0	ENST00000222390.5:c.1880G>T	p.Gly627Val	p.G627V	ENST00000222390	NM_000601.4	627	gGc/gTc	17/18	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.371785332975696	2		363	583	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469672	NA	P-0037231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	344	573	0	ENST00000374080.3:c.131G>A	p.Gly44Asp	p.G44D	ENST00000374080		44	gGt/gAt	2/45	0.883440689174384	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.883440689174384	1		573	430	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916774	48916775	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs587778825	NA	P-0037231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	204	455	0	ENST00000267163.4:c.305_306del	p.Cys102TyrfsTer7	p.C102Yfs*7	ENST00000267163	NM_000321.2	102	TGt/t	3/27	0.883440689174384	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.883440689174384	1		455	251	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579354	7579355	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0037231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	369	745	0	ENST00000269305.4:c.332_333del	p.Leu111ArgfsTer37	p.L111Rfs*37	ENST00000269305	NM_001126112.2	111	cTG/c	4/11	0.848364436351393	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.883440689174384	1		745	464	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426460	49426461	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0037231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	510	958	0	ENST00000301067.7:c.12027_12028del	p.Ser4010Ter	p.S4010*	ENST00000301067	NM_003482.3	4009	ttTTct/ttct	39/54	1	2	FACETS	0.976	0.937	1	0.976	0.937	1	CLONAL	1	TRUE	1	0.883440689174384	2		958	1183	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555525585	NA	P-0037252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	141	392	0	ENST00000269305.4:c.673-2A>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.573431989902985	1	FACETS	0.893	0.822	0.965	0.893	0.822	0.965	CLONAL	1	TRUE	0	0.573431989902985	1		392	393	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619225	37619317	+	inframe_deletion	In_Frame_Del	DEL	TCTGTCAGTCCCTATAGCAGGAGACGGTCGTCCAGCTACGAAAGAAGTGGCTCTTACAGCGGGCGATCGCCCAGTCCCTATGGTCGAAGGCGG	TCTGTCAGTCCCTATAGCAGGAGACGGTCGTCCAGCTACGAAAGAAGTGGCTCTTACAGCGGGCGATCGCCCAGTCCCTATGGTCGAAGGCGG	-	novel	NA	P-0037252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	134	369	0	ENST00000447079.4:c.903_995del	p.Val302_Ser332del	p.V302_S332del	ENST00000447079	NM_015083.1	301	TCTGTCAGTCCCTATAGCAGGAGACGGTCGTCCAGCTACGAAAGAAGTGGCTCTTACAGCGGGCGATCGCCCAGTCCCTATGGTCGAAGGCGG/-	1/14	0.573431989902985	1	FACETS	0.944	0.869	1	0.944	0.869	1	CLONAL	1	TRUE	0	0.573431989902985	1		369	353	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456486	29456486	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	202	542	0	ENST00000389048.3:c.2432T>A	p.Val811Glu	p.V811E	ENST00000389048	NM_004304.4	811	gTg/gAg	14/29	0.553768065636258	2	FACETS	0.939	0.873	1	0.47	0.436	0.504	CLONAL	1	TRUE	0	0.573431989902985	2		542	750	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025921	48025921	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1301670893	NA	P-0037252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	76	343	0	ENST00000234420.5:c.799C>G	p.Pro267Ala	p.P267A	ENST00000234420	NM_000179.2	267	Cca/Gca	4/10	0.247595024644604	3	FACETS	0.664	0.583	0.75	0.221	0.194	0.25	INDETERMINATE	1	TRUE	0	0.573431989902985	3		343	514	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175813	24175813	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	150	445	0	ENST00000263121.7:c.1041C>G	p.Asp347Glu	p.D347E	ENST00000263121	NM_003073.3	347	gaC/gaG	8/9	1	2	FACETS	0.928	0.852	1	0.928	0.852	1	CLONAL	1	TRUE	1	0.573431989902985	2		445	564	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935494	13935494	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0037252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	85	272	0	ENST00000405192.2:c.1362T>A	p.Tyr454Ter	p.Y454*	ENST00000405192	NM_001163147.1	454	taT/taA	12/12	1	2	FACETS	0.83	0.74	0.926	0.83	0.74	0.926	CLONAL	1	TRUE	1	0.573431989902985	2		272	357	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918566	44918566	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	154	454	0	ENST00000377967.4:c.1049G>T	p.Gly350Val	p.G350V	ENST00000377967	NM_021140.2	350	gGc/gTc	12/29	0.573431989902985	1	FACETS	0.906	0.837	0.975	0.906	0.837	0.975	CLONAL	1	TRUE	0	0.573431989902985	1		454	423	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0037265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	260	482	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.805252919639301	2	FACETS	0.94	0.908	0.97	0.94	0.908	0.97	CLONAL	2	TRUE	0	0.853371040726743	2		482	324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579349	7579349	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1567555667	NA	P-0037265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	291	512	0	ENST00000269305.4:c.338T>G	p.Phe113Cys	p.F113C	ENST00000269305	NM_001126112.2	113	tTc/tGc	4/11	0.805252919639301	2	FACETS	0.942	0.912	0.97	0.942	0.912	0.97	CLONAL	2	TRUE	0	0.853371040726743	2		512	362	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916935	178916935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	8	426	0	ENST00000263967.3:c.322C>T	p.Arg108Cys	p.R108C	ENST00000263967	NM_006218.2	108	Cgt/Tgt	2/21	0.589368070345491	4	FACETS	0.104	0.066	0.153	0.052	0.033	0.077	SUBCLONAL	1	TRUE	2	0.853371040726743	4		426	334	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678508	88678508	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs183806623	NA	P-0037275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	131	514	0	ENST00000360948.2:c.1028G>T	p.Arg343Leu	p.R343L	ENST00000360948	NM_001012338.2	343	cGg/cTg	9/19	1	2	FACETS	0.933	0.852	1	0.933	0.852	1	CLONAL	1	TRUE	1	0.565159592955741	2		514	497	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007690	45007690	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1435502075	NA	P-0037275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	34	453	0	ENST00000558401.1:c.137A>G	p.Tyr46Cys	p.Y46C	ENST00000558401	NM_004048.2	46	tAt/tGt	2/4	1	2	FACETS	0.205	0.167	0.248	0.205	0.167	0.248	SUBCLONAL	1	TRUE	1	0.565159592955741	2		453	587	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684293	29684294	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0037275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	322	514	0	ENST00000356175.3:c.7814dup	p.Val2606GlyfsTer7	p.V2606Gfs*7	ENST00000356175	NM_000267.3	2605	ctg/cTtg	53/57	0.565159592955741	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.565159592955741	2		514	558	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144647	55144647	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	157	403	0	ENST00000257290.5:c.2121C>G	p.Ile707Met	p.I707M	ENST00000257290	NM_006206.4	707	atC/atG	15/23	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.565159592955741	2		403	494	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540815	187540815	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	45	397	0	ENST00000441802.2:c.6925G>T	p.Asp2309Tyr	p.D2309Y	ENST00000441802	NM_005245.3	2309	Gat/Tat	10/27	1	2	FACETS	0.309	0.259	0.364	0.309	0.259	0.364	SUBCLONAL	1	TRUE	1	0.565159592955741	2		397	515	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588190	67588190	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0037275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	76	276	0	ENST00000274335.5:c.1019+1G>T		p.X340_splice	ENST00000274335		340			1	2	FACETS	0.825	0.73	0.926	0.825	0.73	0.926	CLONAL	1	TRUE	1	0.565159592955741	2		276	326	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040062	180040062	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376188634	NA	P-0037275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	405	773	1	ENST00000261937.6:c.3380G>A	p.Arg1127Gln	p.R1127Q	ENST00000261937	NM_182925.4	1127	cGg/cAg	25/30	0.565159592955741	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.565159592955741	3		774	902	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032545	47032555	+	frameshift_variant	Frame_Shift_Del	DEL	TCGCACGGCGT	TCGCACGGCGT	C	novel	NA	P-0037275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	169	587	0	ENST00000377604.3:c.451_461delinsC	p.Ser151ArgfsTer8	p.S151Rfs*8	ENST00000377604	NM_001204468.1	151	TCGCACGGCGTg/Cg	5/24	1	2	FACETS	0.966	0.892	1	0.966	0.892	1	CLONAL	1	TRUE	1	0.565159592955741	2		587	619	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0037279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	129	309	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.887	0.806	0.971	0.887	0.806	0.971	CLONAL	1	TRUE	1	0.44228470078428	2		309	658	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390943	89390943	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	27	442	0	ENST00000336596.2:c.1009A>T	p.Asn337Tyr	p.N337Y	ENST00000336596	NM_005233.5	337	Aac/Tac	5/17	1	2	FACETS	0.237	0.188	0.294	0.237	0.188	0.294	SUBCLONAL	1	TRUE	1	0.44228470078428	2		442	515	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0037340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	111	305	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.42289348844183	3	FACETS	0.93	0.845	1	0.93	0.845	1	CLONAL	2	TRUE	1	0.42289348844183	3		305	342	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0037340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	54	253	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.42289348844183	2		253	231	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0037340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	86	333	1	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	1	2	FACETS	0.929	0.837	1	1	0.986	1	CLONAL	2	TRUE	1	0.42289348844183	2		334	219	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546725	9546725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210292896	NA	P-0037340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	40	343	0	ENST00000353224.5:c.1297C>T	p.Arg433Trp	p.R433W	ENST00000353224	NM_177990.2	433	Cgg/Tgg	5/10	1	2	FACETS	0.892	0.749	1	0.892	0.749	1	CLONAL	1	TRUE	1	0.42289348844183	2		343	212	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742480	17742480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	21	546	0	ENST00000250003.3:c.662G>A	p.Arg221Gln	p.R221Q	ENST00000250003	NM_002478.4	221	cGg/cAg	2/3	1	2	FACETS	0.255	0.195	0.324	0.255	0.195	0.324	SUBCLONAL	1	TRUE	1	0.42289348844183	2		546	390	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119900	70119943	+	frameshift_variant	Frame_Shift_Del	DEL	ACGGCCACCCGGGGGTGCCGGCCACGCACGGCCAGGTCACCTAC	ACGGCCACCCGGGGGTGCCGGCCACGCACGGCCAGGTCACCTAC	-	novel	NA	P-0037340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	60	529	0	ENST00000245479.2:c.906_949del	p.His303GlnfsTer260	p.H303Qfs*260	ENST00000245479	NM_000346.3	301	aACGGCCACCCGGGGGTGCCGGCCACGCACGGCCAGGTCACCTAC/a	3/3	1	2	FACETS	0.709	0.613	0.813	0.709	0.613	0.813	SUBCLONAL	1	TRUE	1	0.42289348844183	2		529	400	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5206828	5206828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1326058191	NA	P-0037340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	94	662	0	ENST00000357368.4:c.5804C>T	p.Ala1935Val	p.A1935V	ENST00000357368	NM_002850.3	1935	gCg/gTg	38/38	1	2	FACETS	0.932	0.833	1	0.932	0.833	1	CLONAL	1	TRUE	1	0.42289348844183	2		662	477	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812249	212812249	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	133	384	0	ENST00000342788.4:c.327A>C	p.Lys109Asn	p.K109N	ENST00000342788	NM_005235.2	109	aaA/aaC	3/28	0.408629618780886	2	FACETS	0.947	0.873	1	0.947	0.873	1	CLONAL	2	TRUE	0	0.42289348844183	2		384	332	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225365173	225365173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180155404	NA	P-0037340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	132	375	1	ENST00000264414.4:c.1517G>A	p.Arg506Gln	p.R506Q	ENST00000264414	NM_003590.4	506	cGg/cAg	11/16	0.408629618780886	2	FACETS	0.918	0.845	0.993	0.918	0.845	0.993	CLONAL	2	TRUE	0	0.42289348844183	2		376	340	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800201	32800205	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCT	CAGCT	-	novel	NA	P-0037340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	61	404	0	ENST00000374899.4:c.1177_1181del	p.Ser393TrpfsTer88	p.S393Wfs*88	ENST00000374899	NM_018833.2	393	AGCTGt/t	7/12	0.149415490565954	4	FACETS	1	0.932	1	0.561	0.486	0.641	INDETERMINATE	1	TRUE	2	0.42289348844183	4		404	366	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450301	50450301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770551610	NA	P-0037340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	84	547	1	ENST00000331340.3:c.485G>A	p.Arg162Gln	p.R162Q	ENST00000331340	NM_006060.4	162	cGg/cAg	5/8	0.42289348844183	3	FACETS	0.946	0.838	1	0.473	0.419	0.53	CLONAL	1	TRUE	1	0.42289348844183	3		548	509	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800211	32800211	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	69	386	0	ENST00000374899.4:c.1171A>C	p.Met391Leu	p.M391L	ENST00000374899	NM_018833.2	391	Atg/Ctg	7/12	0.149415490565954	4	FACETS	1	0.965	1	0.65	0.57	0.736	INDETERMINATE	1	TRUE	2	0.42289348844183	4		386	357	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0037365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	222	575	0	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	1	2	FACETS	1	0.973	1	1	0.995	1	CLONAL	3	TRUE	1	0.23	2		575	602	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239423	105239423	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	79	567	1	ENST00000349310.3:c.964G>A	p.Glu322Lys	p.E322K	ENST00000349310	NM_001014432.1	322	Gag/Aag	12/15	0.231138581553103	2	FACETS	1	0.959	1	0.604	0.532	0.681	CLONAL	1	TRUE	0	0.23	2		568	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0037376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	384	751	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.516740019857575	2		751	705	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0037376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	601	566	0	ENST00000397752.3:c.3028+1G>C		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.516740019857575	4	FACETS	0.964	0.936	0.991	0.964	0.936	0.991	CLONAL	4	TRUE	0	0.516740019857575	4		566	915	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122859	2122859	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	339	355	0	ENST00000219476.3:c.2230C>T	p.Pro744Ser	p.P744S	ENST00000219476	NM_000548.3	744	Cca/Tca	21/42	0.507276993156452	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.516740019857575	3		355	731	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933712	36933712	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	398	472	0	ENST00000361632.4:c.1687A>C	p.Thr563Pro	p.T563P	ENST00000361632		563	Acc/Ccc	12/16	0.471257051029878	3	FACETS	0.973	0.928	1	0.973	0.928	1	CLONAL	2	TRUE	1	0.516740019857575	3		472	996	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112544	115112546	+	inframe_deletion	In_Frame_Del	DEL	GTG	GTG	-	novel	NA	P-0037376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	155	413	0	ENST00000257566.3:c.1194_1196del	p.Thr399del	p.T399del	ENST00000257566	NM_016569.3	398	acCACg/acg	7/8	0.320678141371957	4	FACETS	0.852	0.779	0.929	0.426	0.389	0.465	CLONAL	1	TRUE	2	0.516740019857575	4		413	1068	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325693	30325693	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	54	146	0	ENST00000322652.5:c.1891C>G	p.Gln631Glu	p.Q631E	ENST00000322652	NM_015355.2	631	Caa/Gaa	16/16	0.429446538992177	4	FACETS	1	0.909	1	1	0.909	1	CLONAL	2	TRUE	2	0.516740019857575	4		146	151	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205068	128205068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	403	449	0	ENST00000341105.2:c.373C>T	p.Pro125Ser	p.P125S	ENST00000341105	NM_032638.4	125	Cca/Tca	3/6	0.471257051029878	3	FACETS	0.97	0.925	1	0.97	0.925	1	CLONAL	2	TRUE	1	0.516740019857575	3		449	1012	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158767	26158767	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	160	456	0	ENST00000289316.2:c.370A>G	p.Ser124Gly	p.S124G	ENST00000289316	NM_138720.2	124	Agt/Ggt	1/2	0.516740019857575	3	FACETS	0.92	0.844	0.999	0.46	0.422	0.5	CLONAL	1	TRUE	1	0.516740019857575	3		456	847	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0037396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	91	309	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.306683746167391	3	FACETS	0.798	0.712	0.888	0.798	0.712	0.888	SUBCLONAL	2	TRUE	1	0.306683746167391	3		309	429	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218500	1218500	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1131690951	NA	P-0037396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	17	440	0	ENST00000326873.7:c.374+1A>G		p.X125_splice	ENST00000326873	NM_000455.4	125			1	2	FACETS	0.342	0.255	0.446	0.342	0.255	0.446	SUBCLONAL	1	TRUE	1	0.306683746167391	2		440	324	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610415	10610415	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	45	687	0	ENST00000171111.5:c.295G>T	p.Val99Leu	p.V99L	ENST00000171111	NM_203500.1	99	Gtg/Ttg	2/6	1	2	FACETS	0.458	0.384	0.54	0.458	0.384	0.54	SUBCLONAL	1	TRUE	1	0.306683746167391	2		687	641	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066713	5066715	+	inframe_deletion	In_Frame_Del	DEL	GTA	GTA	-	novel	NA	P-0037396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	21	362	0	ENST00000381652.3:c.1250_1252del	p.Gly417_Asn418delinsAsp	p.G417_N418delinsD	ENST00000381652	NM_004972.3	417	gGTAat/gat	10/25	1	2	FACETS	0.494	0.381	0.626	0.494	0.381	0.626	SUBCLONAL	1	TRUE	1	0.306683746167391	2		362	277	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0037419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	13	413	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.13503257588361	0	FACETS	0.339	0.241	0.46			1	SUBCLONAL	1	TRUE	0	0.18	0		414	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0037419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	24	786	3	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	1	2	FACETS	0.333	0.259	0.418	0.333	0.259	0.418	SUBCLONAL	1	TRUE	1	0.18	2		789	802	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0037444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	216	657	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.207783925569621	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.272142127894823	2		657	737	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11308150	11308150	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs757384321	NA	P-0037444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	39	404	0	ENST00000361445.4:c.842G>A	p.Arg281His	p.R281H	ENST00000361445	NM_004958.3	281	cGt/cAt	7/58	0.119934461355692	5	FACETS	0.905	0.75	1	0.302	0.25	0.359	INDETERMINATE	1	TRUE	2	0.272142127894823	5		404	446	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0037448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	498	515	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.330239903631499	3	FACETS	1	0.995	1	0.631	0.605	0.657	INDETERMINATE	1	TRUE	1	0.937418629831005	3		515	1237	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126730	5126730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1437629509	NA	P-0037448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	306	389	0	ENST00000381652.3:c.3338G>A	p.Arg1113His	p.R1113H	ENST00000381652	NM_004972.3	1113	cGc/cAc	25/25	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.937418629831005	2		389	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0037448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	541	559	0	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.330239903631499	3	FACETS	0.836	0.806	0.865	0.836	0.806	0.865	INDETERMINATE	2	TRUE	1	0.937418629831005	3		559	1014	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948682	71948682	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	580	591	0	ENST00000298229.2:c.3394G>T	p.Glu1132Ter	p.E1132*	ENST00000298229	NM_001567.3	1132	Gag/Tag	26/28	0.937418629831005	1	FACETS	0.998	0.98	1	0.998	0.98	1	CLONAL	1	TRUE	0	0.937418629831005	1		591	659	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651540	206651540	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	151	482	0	ENST00000367120.3:c.850A>C	p.Ile284Leu	p.I284L	ENST00000367120	NM_014002.3	284	Atc/Ctc	9/22	0.933657993720048	1	FACETS	0.388	0.358	0.419	0.388	0.358	0.419	SUBCLONAL	1	TRUE	0	0.937418629831005	1		482	441	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99482470	99482470	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	454	473	0	ENST00000268035.6:c.3338T>A	p.Ile1113Asn	p.I1113N	ENST00000268035	NM_000875.3	1113	aTt/aAt	18/21	0.59216957826732	1	FACETS	0.782	0.757	0.806	0.782	0.757	0.806	SUBCLONAL	1	TRUE	0	0.937418629831005	1		473	658	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144466	11144466	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	233	529	0	ENST00000358026.2:c.3798C>A	p.Ser1266Arg	p.S1266R	ENST00000358026	NM_001128849.1	1266	agC/agA	27/36	1	2	FACETS	0.417	0.388	0.447	0.417	0.388	0.447	SUBCLONAL	1	TRUE	1	0.937418629831005	2		529	1193	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086103	16086103	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	432	506	0	ENST00000281043.3:c.1279A>C	p.Thr427Pro	p.T427P	ENST00000281043	NM_005378.4	427	Act/Cct	3/3	0.937418629831005	1	FACETS	0.997	0.976	1	0.997	0.976	1	CLONAL	1	TRUE	0	0.937418629831005	1		506	491	SUCCESS
APC	324	MSKCC	GRCh37	5	112175685	112175685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	55	333	1	ENST00000257430.4:c.4394G>A	p.Ser1465Asn	p.S1465N	ENST00000257430	NM_000038.5	1465	aGt/aAt	16/16	1	2	FACETS	0.197	0.168	0.228	0.197	0.168	0.228	SUBCLONAL	1	TRUE	1	0.937418629831005	2		334	597	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371737	55371737	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	56	378	0	ENST00000297316.4:c.427A>G	p.Lys143Glu	p.K143E	ENST00000297316	NM_022454.3	143	Aag/Gag	2/2	1	2	FACETS	0.203	0.173	0.235	0.203	0.173	0.235	SUBCLONAL	1	TRUE	1	0.937418629831005	2		378	590	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0037452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	206	309	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.367218995245301	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.367218995245301	3		309	642	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981167	201981167	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	106	697	0	ENST00000359651.3:c.246G>C	p.Lys82Asn	p.K82N	ENST00000359651		82	aaG/aaC	2/8	0.367218995245301	3	FACETS	0.526	0.469	0.586	0.263	0.234	0.293	SUBCLONAL	1	TRUE	1	0.367218995245301	3		697	1300	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981170	201981170	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1206	103	704	0	ENST00000359651.3:c.249C>G	p.Asn83Lys	p.N83K	ENST00000359651		83	aaC/aaG	2/8	0.367218995245301	3	FACETS	0.507	0.452	0.566	0.254	0.226	0.283	SUBCLONAL	1	TRUE	1	0.367218995245301	3		704	1309	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206595	108206595	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	207	324	0	ENST00000278616.4:c.8175T>G	p.Asp2725Glu	p.D2725E	ENST00000278616	NM_000051.3	2725	gaT/gaG	56/63	0.367218995245301	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.367218995245301	2		324	471	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000315	42000316	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0037452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	62	412	0	ENST00000219905.7:c.2337dup	p.Val780CysfsTer3	p.V780Cfs*3	ENST00000219905	NM_001164273.1	778	-/T	7/24	1	2	FACETS	0.737	0.638	0.844	0.737	0.638	0.844	SUBCLONAL	1	TRUE	1	0.367218995245301	2		412	458	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042331	42042331	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0037452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	111	517	0	ENST00000219905.7:c.6526A>T	p.Lys2176Ter	p.K2176*	ENST00000219905	NM_001164273.1	2176	Aaa/Taa	17/24	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.367218995245301	2		517	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577553	7577553	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs730882006	NA	P-0037452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	24	586	0	ENST00000269305.4:c.728T>C	p.Met243Thr	p.M243T	ENST00000269305	NM_001126112.2	243	aTg/aCg	7/11	0.362684263258521	1	FACETS	0.129	0.101	0.163	0.129	0.101	0.163	SUBCLONAL	1	TRUE	0	0.367218995245301	1		586	825	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276245	15276245	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1159412147	NA	P-0037452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	137	530	0	ENST00000263388.2:c.5749G>A	p.Ala1917Thr	p.A1917T	ENST00000263388	NM_000435.2	1917	Gca/Aca	31/33	1	2	FACETS	0.721	0.655	0.791	0.721	0.655	0.791	SUBCLONAL	1	TRUE	1	0.367218995245301	2		530	1035	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495402	149495402	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	204	595	0	ENST00000261799.4:c.3245C>A	p.Pro1082Gln	p.P1082Q	ENST00000261799	NM_002609.3	1082	cCg/cAg	23/23	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.367218995245301	2		595	1069	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137540379	137540384	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CCTGAG	CCTGAG	-	novel	NA	P-0037452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	40	273	0	ENST00000367739.4:c.81_85+1del		p.X27_splice	ENST00000367739	NM_000416.2	27		1/7	0.367218995245301	1	FACETS	0.389	0.323	0.463	0.389	0.323	0.463	SUBCLONAL	1	TRUE	0	0.367218995245301	1		273	457	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985558	2985558	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	93	405	0	ENST00000396946.4:c.253C>T	p.Gln85Ter	p.Q85*	ENST00000396946	NM_032415.4	85	Caa/Taa	4/25	NA	2	FACETS	0.666	0.592	0.746			1	INDETERMINATE	1	TRUE	NA	0.367218995245301	2		405	760	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000319	42000319	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	65	421	1	ENST00000219905.7:c.2338G>T	p.Val780Phe	p.V780F	ENST00000219905	NM_001164273.1	780	Gtt/Ttt	7/24	1	2	FACETS	0.765	0.665	0.872	0.765	0.665	0.872	SUBCLONAL	1	TRUE	1	0.367218995245301	2		422	463	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0037452-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	143	309	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.344909331468306	3	FACETS	0.902	0.827	0.98	0.902	0.827	0.98	CLONAL	2	TRUE	1	0.344909331468306	3		309	539	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206595	108206595	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037452-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	229	324	0	ENST00000278616.4:c.8175T>G	p.Asp2725Glu	p.D2725E	ENST00000278616	NM_000051.3	2725	gaT/gaG	56/63	0.344909331468306	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	0	0.344909331468306	3		324	486	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000315	42000316	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0037452-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	64	412	0	ENST00000219905.7:c.2337dup	p.Val780CysfsTer3	p.V780Cfs*3	ENST00000219905	NM_001164273.1	778	-/T	7/24	1	2	FACETS	0.744	0.645	0.85	0.744	0.645	0.85	SUBCLONAL	1	TRUE	1	0.344909331468306	2		412	499	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042331	42042331	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0037452-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	99	517	0	ENST00000219905.7:c.6526A>T	p.Lys2176Ter	p.K2176*	ENST00000219905	NM_001164273.1	2176	Aaa/Taa	17/24	1	2	FACETS	0.913	0.816	1	0.913	0.816	1	CLONAL	1	TRUE	1	0.344909331468306	2		517	629	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276245	15276245	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1159412147	NA	P-0037452-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	40	530	0	ENST00000263388.2:c.5749G>A	p.Ala1917Thr	p.A1917T	ENST00000263388	NM_000435.2	1917	Gca/Aca	31/33	0.130812401977233	0	FACETS	0.281	0.233	0.335			1	INDETERMINATE	1	TRUE	0	0.344909331468306	0		530	540	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495402	149495402	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037452-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	123	595	0	ENST00000261799.4:c.3245C>A	p.Pro1082Gln	p.P1082Q	ENST00000261799	NM_002609.3	1082	cCg/cAg	23/23	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.344909331468306	2		595	658	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985558	2985558	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037452-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	90	405	0	ENST00000396946.4:c.253C>T	p.Gln85Ter	p.Q85*	ENST00000396946	NM_032415.4	85	Caa/Taa	4/25	0.144512467795452	3	FACETS	1	0.907	1			1	INDETERMINATE	1	TRUE	NA	0.344909331468306	3		405	598	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000319	42000319	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037452-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	75	421	1	ENST00000219905.7:c.2338G>T	p.Val780Phe	p.V780F	ENST00000219905	NM_001164273.1	780	Gtt/Ttt	7/24	1	2	FACETS	0.873	0.767	0.987	0.873	0.767	0.987	CLONAL	1	TRUE	1	0.344909331468306	2		422	498	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858210	9858210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756930722	NA	P-0037452-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	79	492	0	ENST00000330684.3:c.3191C>T	p.Thr1064Met	p.T1064M	ENST00000330684	NM_001134407.1	1064	aCg/aTg	13/13	1	2	FACETS	0.898	0.792	1	0.898	0.792	1	CLONAL	1	TRUE	1	0.344909331468306	2		492	510	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0037475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	127	309	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.278639159310808	2	FACETS	0.791	0.72	0.866	0.791	0.72	0.866	SUBCLONAL	2	TRUE	0	0.291309315728944	2		309	551	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0037475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	49	205	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.291309315728944	2		205	306	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472559	88472559	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	80	583	0	ENST00000360948.2:c.1996G>T	p.Gly666Cys	p.G666C	ENST00000360948	NM_001012338.2	666	Ggt/Tgt	16/19	1	2	FACETS	0.886	0.78	0.999	0.886	0.78	0.999	CLONAL	1	TRUE	1	0.291309315728944	2		583	620	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609373	81609373	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	149	525	1	ENST00000298171.2:c.971A>T	p.Gln324Leu	p.Q324L	ENST00000298171	NM_000369.2	324	cAg/cTg	10/10	0.278639159310808	2	FACETS	0.939	0.862	1	0.939	0.862	1	CLONAL	2	TRUE	0	0.291309315728944	2		526	545	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217645	7217645	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	85	586	1	ENST00000380728.2:c.282A>T	p.Leu94Phe	p.L94F	ENST00000380728		94	ttA/ttT	4/11	1	2	FACETS	0.923	0.817	1	0.923	0.817	1	CLONAL	1	TRUE	1	0.291309315728944	2		587	632	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549697	187549697	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	173	566	0	ENST00000441802.2:c.4544A>T	p.Tyr1515Phe	p.Y1515F	ENST00000441802	NM_005245.3	1515	tAt/tTt	8/27	0.291309315728944	3	FACETS	0.859	0.792	0.929	0.859	0.792	0.929	CLONAL	2	TRUE	1	0.291309315728944	3		566	792	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128321943	128321943	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	244	556	0	ENST00000265960.3:c.817C>A	p.Leu273Met	p.L273M	ENST00000265960	NM_001006617.1	273	Ctg/Atg	6/12	0.291309315728944	3	FACETS	0.904	0.848	0.96	0.904	0.848	0.96	CLONAL	3	TRUE	0	0.291309315728944	3		556	708	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707816	43707816	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1260186612	NA	P-0037485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	333	615	0	ENST00000382044.4:c.5065C>T	p.Arg1689Cys	p.R1689C	ENST00000382044	NM_001141980.1	1689	Cgc/Tgc	23/28	0.875200333807931	3	FACETS	0.97	0.918	1	0.485	0.459	0.512	CLONAL	1	TRUE	1	0.887258472690768	3		615	1117	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2185904	2185904	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	298	488	0	ENST00000398665.3:c.179del	p.Leu60Ter	p.L60*	ENST00000398665	NM_032482.2	59	gTt/gt	3/28	0.887258472690768	1	FACETS	0.521	0.493	0.548	0.521	0.493	0.548	SUBCLONAL	1	TRUE	0	0.887258472690768	1		488	718	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971639	18971639	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	291	498	0	ENST00000262803.5:c.2305G>A	p.Glu769Lys	p.E769K	ENST00000262803	NM_002911.3	769	Gag/Aag	17/24	NA	2	FACETS	0.998	0.947	1			1	INDETERMINATE	1	TRUE	NA	0.887258472690768	2		498	657	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195294	102195294	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	97	446	0	ENST00000263464.3:c.54C>A	p.Asn18Lys	p.N18K	ENST00000263464	NM_001165.4	18	aaC/aaA	2/9	1	2	FACETS	0.814	0.727	0.905	0.814	0.727	0.905	CLONAL	1	TRUE	1	0.420580012794476	2		446	567	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389147	31389159	+	frameshift_variant	Frame_Shift_Del	DEL	GTGATGACCGGCC	GTGATGACCGGCC	-	novel	NA	P-0037489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	147	560	14	ENST00000328111.2:c.2062_2074del	p.Asp688SerfsTer9	p.D688Sfs*9	ENST00000328111	NM_006892.3	687	gGTGATGACCGGCCg/gg	19/23	1	2	FACETS	0.847	0.774	0.924	0.847	0.774	0.924	CLONAL	1	TRUE	1	0.420580012794476	2		574	825	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584763	52584774	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTTGTCCATA	CTGTTGTCCATA	TGTTGTCC	novel	NA	P-0037489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	137	547	1	ENST00000394830.3:c.4348_4359delinsGGACAACA	p.Tyr1450GlyfsTer38	p.Y1450Gfs*38	ENST00000394830	NM_018313.4	1450	TATGGACAACAG/GGACAACA	28/30	0.420580012794476	1	FACETS	0.909	0.83	0.991	0.909	0.83	0.991	CLONAL	1	TRUE	0	0.420580012794476	1		548	566	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86648783	86649024	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TATATTGAGAACATTGTTTTTTCTAAAATAATATGAATGTTATGATCATTTATTCTATTAATGTATTTGTGTTATGTGCTTTGAAAAAAATTTGCTAATTAGATAATCCTTGGCAAGAAAGTTTACACATATTTTTAAAGATTTTGCAGTTTTATGAGACAGATTAATACTAGAAATTTTTATTTTAACAGCATTGGGGACATCATAGATCACTATCGAAAAGAACAGATTGTTGAAGGATA	TATATTGAGAACATTGTTTTTTCTAAAATAATATGAATGTTATGATCATTTATTCTATTAATGTATTTGTGTTATGTGCTTTGAAAAAAATTTGCTAATTAGATAATCCTTGGCAAGAAAGTTTACACATATTTTTAAAGATTTTGCAGTTTTATGAGACAGATTAATACTAGAAATTTTTATTTTAACAGCATTGGGGACATCATAGATCACTATCGAAAAGAACAGATTGTTGAAGGATA	-	novel	NA	P-0037489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	16	24	0	ENST00000274376.6:c.1254-190_1305del		p.X418_splice	ENST00000274376	NM_002890.2	418		9/25	0.420580012794476	1	FACETS	1	0.8	1	1	0.939	1	CLONAL	2	TRUE	0	0.420580012794476	1		24	30	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0037491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	255	601	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.729421789896722	1	FACETS	0.996	0.947	1	0.996	0.947	1	CLONAL	1	TRUE	0	0.729421789896722	1		601	446	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843243	128843243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173715127	NA	P-0037491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	252	542	0	ENST00000249373.3:c.350G>A	p.Arg117His	p.R117H	ENST00000249373	NM_005631.4	117	cGc/cAc	2/12	0.729421789896722	3	FACETS	1	0.939	1	0.501	0.469	0.534	CLONAL	1	TRUE	1	0.729421789896722	3		542	941	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625457	69625457	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	265	500	0	ENST00000334134.2:c.336C>A	p.Ser112Arg	p.S112R	ENST00000334134	NM_005247.2	112	agC/agA	3/3	0.729421789896722	3	FACETS	1	0.98	1	0.548	0.514	0.582	CLONAL	1	TRUE	1	0.729421789896722	3		500	905	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0037514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	89	751	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.29730875367694	0	FACETS	0.857	0.766	0.953			1	CLONAL	1	TRUE	0	0.358854678262126	0		751	371	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549178	226549178	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	47	331	0	ENST00000366794.5:c.3028A>G	p.Lys1010Glu	p.K1010E	ENST00000366794	NM_001618.3	1010	Aag/Gag	23/23	0.232882140262456	4	FACETS	0.775	0.655	0.908	0.388	0.327	0.454	CLONAL	1	TRUE	2	0.358854678262126	4		331	459	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61729431	61729431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	55	273	0	ENST00000401558.2:c.316G>A	p.Val106Ile	p.V106I	ENST00000401558	NM_003400.3	106	Gtt/Att	5/25	1	2	FACETS	0.788	0.676	0.909	0.788	0.676	0.909	CLONAL	1	TRUE	1	0.358854678262126	2		273	389	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279768	46279768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	137	410	0	ENST00000371998.3:c.3694G>A	p.Glu1232Lys	p.E1232K	ENST00000371998		1232	Gag/Aag	20/23	0.198535145923942	3	FACETS	1	0.927	1	0.675	0.619	0.732	INDETERMINATE	2	TRUE	0	0.358854678262126	3		410	445	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675263	176675264	+	missense_variant	Missense_Mutation	DNP	GC	GC	CT	novel	NA	P-0037514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	89	241	0	ENST00000439151.2:c.4579_4580delinsCT	p.Ala1527Leu	p.A1527L	ENST00000439151	NM_022455.4	1527	GCc/CTc	11/23	0.358854678262126	3	FACETS	0.806	0.72	0.896	0.806	0.72	0.896	CLONAL	2	TRUE	1	0.358854678262126	3		241	363	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55231514	55231514	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs760471492	NA	P-0037542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	50	479	2	ENST00000275493.2:c.1720C>T	p.Arg574Trp	p.R574W	ENST00000275493	NM_005228.3	574	Cgg/Tgg	14/28	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.207210923603003	2		481	424	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134571	41134571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760394095	NA	P-0037542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	39	527	0	ENST00000379561.5:c.1057G>A	p.Ala353Thr	p.A353T	ENST00000379561	NM_002015.3	353	Gca/Aca	2/3	1	2	FACETS	0.796	0.659	0.948	0.796	0.659	0.948	CLONAL	1	TRUE	1	0.207210923603003	2		527	473	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573830	64573830	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0037556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	184	603	0	ENST00000312049.6:c.923C>G	p.Ser308Ter	p.S308*	ENST00000312049	NM_130799.2	308	tCa/tGa	7/10	0.638098597914307	1	FACETS	0.857	0.8	0.916	0.857	0.8	0.916	CLONAL	1	TRUE	0	0.638098597914307	1		603	458	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220451	1220453	+	inframe_deletion	In_Frame_Del	DEL	CTG	CTG	-	novel	NA	P-0037556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	197	751	0	ENST00000326873.7:c.549_551del	p.Leu184del	p.L184del	ENST00000326873	NM_000455.4	182	CTG/-	4/10	0.638098597914307	1	FACETS	0.862	0.806	0.918	0.862	0.806	0.918	CLONAL	1	TRUE	0	0.638098597914307	1		751	488	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600531	10600531	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0037556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	202	526	0	ENST00000171111.5:c.1326-2A>T		p.X442_splice	ENST00000171111	NM_203500.1	442			0.638098597914307	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.638098597914307	1		526	422	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233660	233660	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	108	191	0	ENST00000264932.6:c.964C>G	p.Gln322Glu	p.Q322E	ENST00000264932	NM_004168.2	322	Caa/Gaa	8/15	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.638098597914307	2		191	282	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820905	32820905	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	275	838	0	ENST00000354258.4:c.689G>A	p.Gly230Glu	p.G230E	ENST00000354258	NM_000593.5	230	gGa/gAa	1/11	1	2	FACETS	0.948	0.892	1	0.948	0.892	1	CLONAL	1	TRUE	1	0.638098597914307	2		838	909	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140487374	140487374	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	182	642	0	ENST00000288602.6:c.1151G>C	p.Arg384Thr	p.R384T	ENST00000288602	NM_004333.4	384	aGa/aCa	9/18	1	2	FACETS	0.686	0.634	0.741	0.686	0.634	0.741	SUBCLONAL	1	TRUE	1	0.638098597914307	2		642	831	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317479	1317479	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	306	783	0	ENST00000400841.2:c.586C>A	p.Pro196Thr	p.P196T	ENST00000400841		196	Cca/Aca	5/6	1	1	FACETS	0.683	0.645	0.722	0.683	0.645	0.722	SUBCLONAL	1	TRUE	0	0.638098597914307	1		783	956	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281359	49281359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764117879	NA	P-0037570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	134	862	1	ENST00000282018.3:c.406C>T	p.Arg136Cys	p.R136C	ENST00000282018	NM_020377.2	136	Cgt/Tgt	1/1	1	2	FACETS	0.637	0.578	0.7	0.637	0.578	0.7	SUBCLONAL	1	TRUE	1	0.430841928683347	2		863	976	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245980	16245980	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	108	372	1	ENST00000375759.3:c.1603C>T	p.Arg535Ter	p.R535*	ENST00000375759	NM_015001.2	535	Cga/Tga	8/15	NA	2	FACETS	0.953	0.859	1			1	INDETERMINATE	1	TRUE	NA	0.430841928683347	2		373	526	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008931	152008931	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	113	410	0	ENST00000262189.6:c.691G>T	p.Val231Phe	p.V231F	ENST00000262189	NM_170606.2	231	Gtt/Ttt	5/59	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.430841928683347	2		410	458	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842368	68842450	+	frameshift_variant	Frame_Shift_Del	DEL	CAACTCCTCTCCTGGCCTCAGAAGACAGAAGAGAGACTGGGTTATTCCTCCCATCAGCTGCCCAGAAAATGAAAAAGGCCCAT	CAACTCCTCTCCTGGCCTCAGAAGACAGAAGAGAGACTGGGTTATTCCTCCCATCAGCTGCCCAGAAAATGAAAAAGGCCCAT	A	novel	NA	P-0037570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	91	497	1	ENST00000261769.5:c.429_511delinsA	p.Asn144PhefsTer44	p.N144Ffs*44	ENST00000261769	NM_004360.3	143	ccCAACTCCTCTCCTGGCCTCAGAAGACAGAAGAGAGACTGGGTTATTCCTCCCATCAGCTGCCCAGAAAATGAAAAAGGCCCATtt/ccAtt	4/16	0.430841928683347	1	FACETS	0.73	0.651	0.813	0.73	0.651	0.813	SUBCLONAL	1	TRUE	0	0.430841928683347	1		498	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0037601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	330	570	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.301246468459718	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	3	FALSE	0	0.301122886419633	3		570	836	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112400	115112400	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770040454	NA	P-0037601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	45	375	1	ENST00000257566.3:c.1340G>A	p.Arg447His	p.R447H	ENST00000257566	NM_016569.3	447	cGc/cAc	7/8	0.301122886419633	5	FACETS	0.701	0.588	0.826	0.175	0.147	0.207	SUBCLONAL	1	FALSE	1	0.301122886419633	5		376	619	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099403	157099426	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAGCAA	CAGCAGCAGCAGCAGCAGCAGCAA	-	rs770869529	NA	P-0037601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	79	197	0	ENST00000346085.5:c.369_392del	p.Gln124_Gln131del	p.Q124_Q131del	ENST00000346085	NM_020732.3	114	CAGCAGCAGCAGCAGCAGCAGCAA/-	1/20	0.297999592942121	4	FACETS	1	0.947	1	0.558	0.495	0.623	CLONAL	2	FALSE	0	0.301122886419633	4		197	306	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023584	27023584	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	94	204	0	ENST00000324856.7:c.690del	p.Leu231Ter	p.L231*	ENST00000324856	NM_006015.4	230	gcG/gc	1/20	0.179575642233135	4	FACETS	1	0.966	1	1	0.966	1	INDETERMINATE	2	FALSE	2	0.301122886419633	4		204	345	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106498	27106498	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	121	667	0	ENST00000324856.7:c.6109C>T	p.Gln2037Ter	p.Q2037*	ENST00000324856	NM_006015.4	2037	Cag/Tag	20/20	0.179575642233135	4	FACETS	1	0.982	1	0.691	0.624	0.761	INDETERMINATE	1	FALSE	2	0.301122886419633	4		667	757	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082152	16082219	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	AAGAAGCCCTCAGTCGCCGGCCGGGAGGCGAGCCGATGCCGAGCTGCTCCACGTCCACCATGCCGGGC	AAGAAGCCCTCAGTCGCCGGCCGGGAGGCGAGCCGATGCCGAGCTGCTCCACGTCCACCATGCCGGGC	-	novel	NA	P-0037601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	89	462	0	ENST00000281043.3:c.-34_34del		p.*12*	ENST00000281043	NM_005378.4	?-11/464		2/3	0.226686742607823	5	FACETS	1	0.968	1	0.421	0.373	0.472	CLONAL	1	FALSE	2	0.301122886419633	5		462	680	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719821	190719821	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	135	321	0	ENST00000441310.2:c.1823T>G	p.Leu608Arg	p.L608R	ENST00000441310	NM_000534.4	608	cTg/cGg	9/13	0.226686742607823	5	FACETS	0.917	0.84	0.998	0.917	0.84	0.998	CLONAL	3	FALSE	2	0.301122886419633	5		321	473	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074285	30074285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1569309694	NA	P-0037601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	265	483	0	ENST00000338641.4:c.1547G>A	p.Arg516Gln	p.R516Q	ENST00000338641	NM_000268.3	516	cGg/cAg	14/16	0.297999592942121	4	FACETS	1	0.98	1	0.816	0.769	0.863	CLONAL	3	FALSE	0	0.301122886419633	4		483	702	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555687605	NA	P-0037605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	89	398	0	ENST00000342988.3:c.1610A>G	p.Asp537Gly	p.D537G	ENST00000342988	NM_005359.5	537	gAc/gGc	12/12	0.564766464483798	1	FACETS	0.584	0.522	0.651	0.584	0.522	0.651	SUBCLONAL	1	TRUE	0	0.564766464483798	1		398	387	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0037605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	70	355	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.376841068834975	1	FACETS	0.536	0.47	0.605	0.536	0.47	0.605	SUBCLONAL	1	TRUE	0	0.564766464483798	1		355	332	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0037605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	130	309	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.943	0.861	1	0.943	0.861	1	CLONAL	1	TRUE	1	0.564766464483798	2		309	488	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0037605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	96	652	1	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.831	0.746	0.921	0.831	0.746	0.921	CLONAL	1	TRUE	1	0.564766464483798	2		653	409	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1039289	1039289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11571421	NA	P-0037605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	158	423	0	ENST00000358495.3:c.208C>T	p.Arg70Trp	p.R70W	ENST00000358495	NM_134424.2	70	Cgg/Tgg	4/12	1	2	FACETS	0.849	0.781	0.92	0.849	0.781	0.92	CLONAL	1	TRUE	1	0.564766464483798	2		423	659	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411276	63411276	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	480	385	1	ENST00000330258.3:c.1891C>T	p.Arg631Ter	p.R631*	ENST00000330258	NM_152424.3	631	Cga/Tga	2/2	0.564766464483798	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.564766464483798	2		386	691	SUCCESS
APC	324	MSKCC	GRCh37	5	112174814	112174814	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085081	NA	P-0037605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	88	313	0	ENST00000257430.4:c.3523C>T	p.Gln1175Ter	p.Q1175*	ENST00000257430	NM_000038.5	1175	Cag/Tag	16/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.564766464483798	2		313	287	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43769854	43769854	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0037605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	178	654	0	ENST00000382044.4:c.892A>T	p.Lys298Ter	p.K298*	ENST00000382044	NM_001141980.1	298	Aag/Tag	8/28	1	2	FACETS	0.861	0.796	0.929	0.861	0.796	0.929	CLONAL	1	TRUE	1	0.564766464483798	2		654	732	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755524	39755524	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	59	540	0	ENST00000288319.7:c.1241A>T	p.Asp414Val	p.D414V	ENST00000288319	NM_182918.3	414	gAc/gTc	10/10	1	2	FACETS	0.319	0.274	0.368	0.319	0.274	0.368	SUBCLONAL	1	TRUE	1	0.564766464483798	2		540	655	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0037621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	263	500	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.301319610079367	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.31	2		500	795	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420229	49420229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	177	499	1	ENST00000301067.7:c.15520C>T	p.Arg5174Trp	p.R5174W	ENST00000301067	NM_003482.3	5174	Cgg/Tgg	48/54	0.235877075683454	3	FACETS	0.771	0.711	0.834	0.771	0.711	0.834	SUBCLONAL	2	TRUE	1	0.31	3		500	855	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219897	133219897	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0037621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	98	479	0	ENST00000320574.5:c.4464C>G	p.Tyr1488Ter	p.Y1488*	ENST00000320574	NM_006231.2	1488	taC/taG	35/49	0.235877075683454	3	FACETS	1	0.901	1	0.505	0.45	0.563	CLONAL	1	TRUE	1	0.31	3		479	723	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665036	138665036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	15	31	0	ENST00000330315.3:c.529G>A	p.Gly177Ser	p.G177S	ENST00000330315	NM_023067.3	177	Ggc/Agc	1/1	0.287367400417875	3	FACETS	0.901	0.678	1	0.901	0.678	1	CLONAL	2	TRUE	1	0.31	3		31	62	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24158974	24158974	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	178	454	0	ENST00000263121.7:c.646G>C	p.Glu216Gln	p.E216Q	ENST00000263121	NM_003073.3	216	Gag/Cag	6/9	1	2	FACETS	0.92	0.849	0.994	0.92	0.849	0.994	CLONAL	1	FALSE	1	0.461146351548423	2		454	839	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519934	NA	P-0037638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	195	325	0	ENST00000263967.3:c.333G>C	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaC	2/21	0.153539125442744	2	FACETS	0.805	0.752	0.86	0.805	0.752	0.86	INDETERMINATE	2	FALSE	0	0.461146351548423	2		325	525	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871948	45871948	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	207	476	0	ENST00000391945.4:c.300G>C	p.Glu100Asp	p.E100D	ENST00000391945	NM_000400.3	100	gaG/gaC	5/23	1	2	FACETS	0.971	0.901	1	0.971	0.901	1	CLONAL	1	FALSE	1	0.461146351548423	2		476	925	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469051	25469051	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	142	565	0	ENST00000264709.3:c.1407G>C	p.Glu469Asp	p.E469D	ENST00000264709	NM_175629.2	469	gaG/gaC	11/23	1	2	FACETS	0.755	0.688	0.825	0.755	0.688	0.825	SUBCLONAL	1	FALSE	1	0.461146351548423	2		565	816	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021828	71021828	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0037638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	94	338	0	ENST00000318789.4:c.1531-1G>A		p.X511_splice	ENST00000318789	NM_032682.5	511			0.153539125442744	2	FACETS	1	0.982	1	0.733	0.662	0.807	INDETERMINATE	1	FALSE	0	0.461146351548423	2		338	278	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52663035	52663035	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	51	262	0	ENST00000394830.3:c.1318C>T	p.Gln440Ter	p.Q440*	ENST00000394830	NM_018313.4	440	Caa/Taa	13/30	0.153539125442744	2	FACETS	0.844	0.724	0.974	0.422	0.362	0.487	INDETERMINATE	1	FALSE	0	0.461146351548423	2		262	262	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943359	71943359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775327646	NA	P-0037638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	153	573	0	ENST00000298229.2:c.1691C>T	p.Ser564Leu	p.S564L	ENST00000298229	NM_001567.3	564	tCg/tTg	14/28	1	2	FACETS	0.919	0.843	0.999	0.919	0.843	0.999	CLONAL	1	FALSE	1	0.461146351548423	2		573	722	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915094	32915094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	111	349	0	ENST00000380152.3:c.6602C>T	p.Ser2201Phe	p.S2201F	ENST00000380152		2201	tCt/tTt	11/27	0.461146351548423	3	FACETS	0.976	0.879	1			1	CLONAL	1	FALSE	NA	0.461146351548423	3		349	607	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503114	125503114	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	23	387	0	ENST00000428830.2:c.481G>A	p.Glu161Lys	p.E161K	ENST00000428830	NM_001114121.2	161	Gag/Aag	6/14	1	2	FACETS	0.243	0.189	0.306	0.243	0.189	0.306	SUBCLONAL	1	FALSE	1	0.461146351548423	2		387	410	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205247	46205247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	92	475	0	ENST00000334344.6:c.331G>A	p.Asp111Asn	p.D111N	ENST00000334344	NM_152641.2	111	Gat/Aat	4/21	1	2	FACETS	0.711	0.633	0.794	0.711	0.633	0.794	SUBCLONAL	1	FALSE	1	0.461146351548423	2		475	561	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549347	21549347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	184	624	0	ENST00000382592.4:c.2929G>A	p.Asp977Asn	p.D977N	ENST00000382592	NM_014572.2	977	Gac/Aac	8/8	0.157065973990253	1	FACETS	0.855	0.792	0.921	0.855	0.792	0.921	INDETERMINATE	1	FALSE	0	0.461146351548423	1		624	718	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911919	32911919	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	147	389	0	ENST00000380152.3:c.3427G>C	p.Glu1143Gln	p.E1143Q	ENST00000380152		1143	Gaa/Caa	11/27	0.461146351548423	3	FACETS	1	0.951	1			1	CLONAL	1	FALSE	NA	0.461146351548423	3		389	741	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914191	32914191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	89	413	0	ENST00000380152.3:c.5699C>T	p.Ser1900Leu	p.S1900L	ENST00000380152		1900	tCa/tTa	11/27	0.461146351548423	3	FACETS	0.888	0.789	0.993			1	CLONAL	1	FALSE	NA	0.461146351548423	3		413	535	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514044	103514044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	113	391	0	ENST00000355739.4:c.860C>T	p.Ser287Leu	p.S287L	ENST00000355739	NM_000123.3	287	tCa/tTa	7/15	0.223533010182196	3	FACETS	1	0.97	1	0.592	0.535	0.652	INDETERMINATE	1	FALSE	1	0.461146351548423	3		391	509	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351582	89351582	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	231	576	0	ENST00000301030.4:c.1368G>C	p.Lys456Asn	p.K456N	ENST00000301030	NM_001256183.1	456	aaG/aaC	9/13	0.461146351548423	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	FALSE	0	0.461146351548423	1		576	770	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576888	7576889	+	stop_gained	Nonsense_Mutation	DNP	TC	TC	AT	novel	NA	P-0037638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	203	668	0	ENST00000269305.4:c.957_958delinsAT	p.Lys320Ter	p.K320*	ENST00000269305	NM_001126112.2	319	aaGAag/aaATag	9/11	0.461146351548423	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	0	0.461146351548423	1		668	661	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37876079	37876079	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	178	491	0	ENST00000269571.5:c.1938G>T	p.Gln646His	p.Q646H	ENST00000269571		646	caG/caT	16/27	0.267632810898755	6	FACETS	1	0.988	1			1	INDETERMINATE	1	FALSE	NA	0.461146351548423	6		491	1043	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218168	36218168	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	118	424	0	ENST00000222270.7:c.4115C>T	p.Ser1372Leu	p.S1372L	ENST00000222270	NM_014727.1	1372	tCa/tTa	15/37	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.461146351548423	2		424	465	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285912	39285912	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	102	258	0	ENST00000402219.2:c.247G>T	p.Asp83Tyr	p.D83Y	ENST00000402219	NM_005633.3	83	Gat/Tat	3/23	1	2	FACETS	0.846	0.759	0.937	0.846	0.759	0.937	CLONAL	1	FALSE	1	0.461146351548423	2		258	523	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027701	48027701	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs370412074	NA	P-0037638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	95	403	0	ENST00000234420.5:c.2579C>G	p.Ser860Cys	p.S860C	ENST00000234420	NM_000179.2	860	tCt/tGt	4/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.461146351548423	2		403	363	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36028656	36028656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	196	512	0	ENST00000358208.4:c.998C>T	p.Ser333Leu	p.S333L	ENST00000358208		333	tCa/tTa	8/12	0.157171842904528	3	FACETS	1	0.988	1	0.667	0.619	0.717	INDETERMINATE	1	FALSE	1	0.461146351548423	3		512	784	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944637	40944637	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0037638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	89	444	0	ENST00000373198.4:c.1866-1G>A		p.X622_splice	ENST00000373198	NM_133170.3	622			0.157171842904528	3	FACETS	1	0.924	1	0.523	0.466	0.584	INDETERMINATE	1	FALSE	1	0.461146351548423	3		444	454	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288504	21288504	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	99	547	0	ENST00000354336.3:c.749C>T	p.Ala250Val	p.A250V	ENST00000354336	NM_005207.3	250	gCt/gTt	2/3	1	2	FACETS	0.578	0.516	0.644	0.578	0.516	0.644	SUBCLONAL	1	FALSE	1	0.461146351548423	2		547	743	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421288	12421288	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1187225480	NA	P-0037638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	71	502	0	ENST00000287820.6:c.168C>G	p.His56Gln	p.H56Q	ENST00000287820	NM_015869.4	56	caC/caG	2/7	0.153539125442744	2	FACETS	0.341	0.297	0.39	0.171	0.148	0.195	INDETERMINATE	1	FALSE	0	0.461146351548423	2		502	902	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274916	41274916	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0037638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	68	511	0	ENST00000349496.5:c.1166C>G	p.Ser389Ter	p.S389*	ENST00000349496	NM_001904.3	389	tCa/tGa	8/15	0.153539125442744	2	FACETS	0.62	0.54	0.705	0.31	0.27	0.353	INDETERMINATE	1	FALSE	0	0.461146351548423	2		511	476	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940475	49940475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	124	694	0	ENST00000296474.3:c.568G>A	p.Glu190Lys	p.E190K	ENST00000296474	NM_002447.2	190	Gag/Aag	1/20	0.153539125442744	2	FACETS	0.669	0.605	0.736	0.334	0.302	0.368	INDETERMINATE	1	FALSE	0	0.461146351548423	2		694	804	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242909	142242909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	228	481	0	ENST00000350721.4:c.4078G>A	p.Glu1360Lys	p.E1360K	ENST00000350721	NM_001184.3	1360	Gaa/Aaa	22/47	0.153539125442744	2	FACETS	1	0.991	1	0.684	0.64	0.729	INDETERMINATE	1	FALSE	0	0.461146351548423	2		481	723	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064670	80064670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	71	312	0	ENST00000265081.6:c.2101G>A	p.Glu701Lys	p.E701K	ENST00000265081	NM_002439.4	701	Gaa/Aaa	15/24	1	2	FACETS	0.817	0.717	0.923	0.817	0.717	0.923	CLONAL	1	FALSE	1	0.461146351548423	2		312	377	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199933	138199933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	45	660	0	ENST00000237289.4:c.1351G>A	p.Glu451Lys	p.E451K	ENST00000237289	NM_001270507.1	451	Gag/Aag	7/9	0.190819662276794	0	FACETS	0.232	0.194	0.273			1	INDETERMINATE	1	FALSE	0	0.461146351548423	0		660	454	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199996	138199996	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	35	680	0	ENST00000237289.4:c.1414G>C	p.Glu472Gln	p.E472Q	ENST00000237289	NM_001270507.1	472	Gag/Cag	7/9	0.190819662276794	0	FACETS	0.164	0.134	0.198			1	INDETERMINATE	1	FALSE	0	0.461146351548423	0		680	499	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879267	151879267	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	162	601	0	ENST00000262189.6:c.5678C>G	p.Ser1893Cys	p.S1893C	ENST00000262189	NM_170606.2	1893	tCt/tGt	36/59	0.223533010182196	3	FACETS	1	0.987	1	0.689	0.635	0.746	INDETERMINATE	1	FALSE	1	0.461146351548423	3		601	627	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751232	128751232	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	34	493	0	ENST00000377970.2:c.769G>A	p.Glu257Lys	p.E257K	ENST00000377970	NM_002467.4	257	Gag/Aag	2/3	0.157065973990253	1	FACETS	0.204	0.166	0.247	0.204	0.166	0.247	INDETERMINATE	1	FALSE	0	0.461146351548423	1		493	556	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751235	128751235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1467095827	NA	P-0037638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	32	490	1	ENST00000377970.2:c.772G>A	p.Glu258Lys	p.E258K	ENST00000377970	NM_002467.4	258	Gag/Aag	2/3	0.157065973990253	1	FACETS	0.194	0.157	0.236	0.194	0.157	0.236	INDETERMINATE	1	FALSE	0	0.461146351548423	1		491	551	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24158974	24158974	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	66	454	0	ENST00000263121.7:c.646G>C	p.Glu216Gln	p.E216Q	ENST00000263121	NM_003073.3	216	Gag/Cag	6/9	1	2	FACETS	0.757	0.656	0.866	0.757	0.656	0.866	SUBCLONAL	1	TRUE	1	0.249203670899079	2		454	700	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519934	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	38	325	0	ENST00000263967.3:c.333G>C	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaC	2/21	1	2	FACETS	0.733	0.606	0.874	0.733	0.606	0.874	SUBCLONAL	1	TRUE	1	0.249203670899079	2		325	416	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871948	45871948	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	69	476	0	ENST00000391945.4:c.300G>C	p.Glu100Asp	p.E100D	ENST00000391945	NM_000400.3	100	gaG/gaC	5/23	1	2	FACETS	0.798	0.694	0.91	0.798	0.694	0.91	CLONAL	1	TRUE	1	0.249203670899079	2		476	694	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469051	25469051	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	52	565	0	ENST00000264709.3:c.1407G>C	p.Glu469Asp	p.E469D	ENST00000264709	NM_175629.2	469	gaG/gaC	11/23	1	2	FACETS	0.631	0.537	0.736	0.631	0.537	0.736	SUBCLONAL	1	TRUE	1	0.249203670899079	2		565	661	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021828	71021828	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	31	338	0	ENST00000318789.4:c.1531-1G>A		p.X511_splice	ENST00000318789	NM_032682.5	511			1	2	FACETS	0.506	0.408	0.616	0.506	0.408	0.616	SUBCLONAL	1	TRUE	1	0.249203670899079	2		338	492	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52663035	52663035	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	20	262	0	ENST00000394830.3:c.1318C>T	p.Gln440Ter	p.Q440*	ENST00000394830	NM_018313.4	440	Caa/Taa	13/30	1	2	FACETS	0.448	0.342	0.573	0.448	0.342	0.573	SUBCLONAL	1	TRUE	1	0.249203670899079	2		262	358	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943359	71943359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775327646	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	67	573	0	ENST00000298229.2:c.1691C>T	p.Ser564Leu	p.S564L	ENST00000298229	NM_001567.3	564	tCg/tTg	14/28	1	2	FACETS	0.648	0.562	0.741	0.648	0.562	0.741	SUBCLONAL	1	TRUE	1	0.249203670899079	2		573	830	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915094	32915094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	46	349	0	ENST00000380152.3:c.6602C>T	p.Ser2201Phe	p.S2201F	ENST00000380152		2201	tCt/tTt	11/27	0.170529605911251	3	FACETS	0.948	0.799	1	0.474	0.399	0.556	CLONAL	1	TRUE	1	0.249203670899079	3		349	438	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503114	125503114	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	40	387	0	ENST00000428830.2:c.481G>A	p.Glu161Lys	p.E161K	ENST00000428830	NM_001114121.2	161	Gag/Aag	6/14	1	2	FACETS	0.615	0.51	0.732	0.615	0.51	0.732	SUBCLONAL	1	TRUE	1	0.249203670899079	2		387	522	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549347	21549347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	97	624	0	ENST00000382592.4:c.2929G>A	p.Asp977Asn	p.D977N	ENST00000382592	NM_014572.2	977	Gac/Aac	8/8	0.233885349477396	1	FACETS	0.948	0.845	1	0.948	0.845	1	CLONAL	1	TRUE	0	0.249203670899079	1		624	719	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911919	32911919	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	41	389	0	ENST00000380152.3:c.3427G>C	p.Glu1143Gln	p.E1143Q	ENST00000380152		1143	Gaa/Caa	11/27	0.170529605911251	3	FACETS	0.709	0.59	0.841	0.354	0.295	0.421	SUBCLONAL	1	TRUE	1	0.249203670899079	3		389	522	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914191	32914191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	49	413	0	ENST00000380152.3:c.5699C>T	p.Ser1900Leu	p.S1900L	ENST00000380152		1900	tCa/tTa	11/27	0.170529605911251	3	FACETS	0.937	0.794	1	0.468	0.397	0.547	CLONAL	1	TRUE	1	0.249203670899079	3		413	472	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514044	103514044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	55	391	0	ENST00000355739.4:c.860C>T	p.Ser287Leu	p.S287L	ENST00000355739	NM_000123.3	287	tCa/tTa	7/15	1	2	FACETS	0.945	0.81	1	0.945	0.81	1	CLONAL	1	TRUE	1	0.249203670899079	2		391	467	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351582	89351582	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	134	576	0	ENST00000301030.4:c.1368G>C	p.Lys456Asn	p.K456N	ENST00000301030	NM_001256183.1	456	aaG/aaC	9/13	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.249203670899079	2		576	718	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576888	7576889	+	stop_gained	Nonsense_Mutation	DNP	TC	TC	AT	novel	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	79	668	0	ENST00000269305.4:c.957_958delinsAT	p.Lys320Ter	p.K320*	ENST00000269305	NM_001126112.2	319	aaGAag/aaATag	9/11	1	2	FACETS	0.784	0.688	0.887	0.784	0.688	0.887	SUBCLONAL	1	TRUE	1	0.249203670899079	2		668	809	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37876079	37876079	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	96	491	0	ENST00000269571.5:c.1938G>T	p.Gln646His	p.Q646H	ENST00000269571		646	caG/caT	16/27	0.224168001775491	5	FACETS	1	0.916	1	0.345	0.307	0.387	CLONAL	1	TRUE	2	0.249203670899079	5		491	1022	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218168	36218168	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	66	424	0	ENST00000222270.7:c.4115C>T	p.Ser1372Leu	p.S1372L	ENST00000222270	NM_014727.1	1372	tCa/tTa	15/37	1	2	FACETS	0.794	0.689	0.908	0.794	0.689	0.908	CLONAL	1	TRUE	1	0.249203670899079	2		424	667	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285912	39285912	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	25	258	0	ENST00000402219.2:c.247G>T	p.Asp83Tyr	p.D83Y	ENST00000402219	NM_005633.3	83	Gat/Tat	3/23	1	2	FACETS	0.709	0.56	0.88	0.709	0.56	0.88	SUBCLONAL	1	TRUE	1	0.249203670899079	2		258	283	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027701	48027701	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs370412074	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	44	403	0	ENST00000234420.5:c.2579C>G	p.Ser860Cys	p.S860C	ENST00000234420	NM_000179.2	860	tCt/tGt	4/10	1	2	FACETS	0.759	0.637	0.895	0.759	0.637	0.895	SUBCLONAL	1	TRUE	1	0.249203670899079	2		403	465	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36028656	36028656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	90	512	0	ENST00000358208.4:c.998C>T	p.Ser333Leu	p.S333L	ENST00000358208		333	tCa/tTa	8/12	1	2	FACETS	0.97	0.86	1	0.97	0.86	1	CLONAL	1	TRUE	1	0.249203670899079	2		512	745	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944637	40944637	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	71	444	0	ENST00000373198.4:c.1866-1G>A		p.X622_splice	ENST00000373198	NM_133170.3	622			1	2	FACETS	0.986	0.861	1	0.986	0.861	1	CLONAL	1	TRUE	1	0.249203670899079	2		444	578	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421288	12421288	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1187225480	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	80	502	0	ENST00000287820.6:c.168C>G	p.His56Gln	p.H56Q	ENST00000287820	NM_015869.4	56	caC/caG	2/7	1	2	FACETS	0.803	0.706	0.907	0.803	0.706	0.907	CLONAL	1	TRUE	1	0.249203670899079	2		502	800	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274916	41274916	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	66	511	0	ENST00000349496.5:c.1166C>G	p.Ser389Ter	p.S389*	ENST00000349496	NM_001904.3	389	tCa/tGa	8/15	1	2	FACETS	0.788	0.684	0.902	0.788	0.684	0.902	CLONAL	1	TRUE	1	0.249203670899079	2		511	672	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940475	49940475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	78	694	0	ENST00000296474.3:c.568G>A	p.Glu190Lys	p.E190K	ENST00000296474	NM_002447.2	190	Gag/Aag	1/20	1	2	FACETS	0.662	0.58	0.75	0.662	0.58	0.75	SUBCLONAL	1	TRUE	1	0.249203670899079	2		694	946	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242909	142242909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	60	481	0	ENST00000350721.4:c.4078G>A	p.Glu1360Lys	p.E1360K	ENST00000350721	NM_001184.3	1360	Gaa/Aaa	22/47	1	2	FACETS	0.689	0.593	0.794	0.689	0.593	0.794	SUBCLONAL	1	TRUE	1	0.249203670899079	2		481	699	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064670	80064670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	29	312	0	ENST00000265081.6:c.2101G>A	p.Glu701Lys	p.E701K	ENST00000265081	NM_002439.4	701	Gaa/Aaa	15/24	1	2	FACETS	1	0.833	1	1	0.833	1	CLONAL	1	TRUE	1	0.249203670899079	2		312	225	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199933	138199933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	95	660	0	ENST00000237289.4:c.1351G>A	p.Glu451Lys	p.E451K	ENST00000237289	NM_001270507.1	451	Gag/Aag	7/9	0.239062087003529	1	FACETS	0.851	0.758	0.951	0.851	0.758	0.951	CLONAL	1	TRUE	0	0.249203670899079	1		660	784	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199996	138199996	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	90	680	0	ENST00000237289.4:c.1414G>C	p.Glu472Gln	p.E472Q	ENST00000237289	NM_001270507.1	472	Gag/Cag	7/9	0.239062087003529	1	FACETS	0.784	0.694	0.879	0.784	0.694	0.879	SUBCLONAL	1	TRUE	0	0.249203670899079	1		680	807	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879267	151879267	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	76	601	0	ENST00000262189.6:c.5678C>G	p.Ser1893Cys	p.S1893C	ENST00000262189	NM_170606.2	1893	tCt/tGt	36/59	1	2	FACETS	0.78	0.683	0.884	0.78	0.683	0.884	SUBCLONAL	1	TRUE	1	0.249203670899079	2		601	782	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1685012	1685012	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	60	445	0	ENST00000378625.1:c.1613G>C	p.Gly538Ala	p.G538A	ENST00000378625	NM_001198994.1	538	gGa/gCa	13/14	1	2	FACETS	0.799	0.688	0.919	0.799	0.688	0.919	CLONAL	1	TRUE	1	0.249203670899079	2		445	603	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10789635	10789635	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	59	443	0	ENST00000361367.2:c.1887A>C	p.Gln629His	p.Q629H	ENST00000361367	NM_014633.3	629	caA/caC	15/25	1	2	FACETS	0.712	0.612	0.821	0.712	0.612	0.821	SUBCLONAL	1	TRUE	1	0.249203670899079	2		443	665	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7293865	7293865	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1023611589	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	132	911	0	ENST00000302850.5:c.38C>T	p.Pro13Leu	p.P13L	ENST00000302850	NM_000208.2	13	cCg/cTg	1/22	0.216132558022051	2	FACETS	0.892	0.808	0.982	0.446	0.404	0.491	CLONAL	1	TRUE	0	0.249203670899079	2		911	1187	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2086850	2086850	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	37	490	0	ENST00000349721.2:c.2548G>A	p.Val850Met	p.V850M	ENST00000349721	NM_003070.3	850	Gtg/Atg	18/34	1	2	FACETS	0.449	0.369	0.538	0.449	0.369	0.538	SUBCLONAL	1	TRUE	1	0.249203670899079	2		490	662	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2087030	2087030	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	97	442	0	ENST00000349721.2:c.2728G>C	p.Glu910Gln	p.E910Q	ENST00000349721	NM_003070.3	910	Gaa/Caa	18/34	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.249203670899079	2		442	696	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751232	128751235	+	missense_variant	Missense_Mutation	ONP	GAGG	GAGG	AAGA	novel	NA	P-0037638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	87	473	0	ENST00000377970.2:c.769_772delinsAAGA	p.Glu257_Glu258delinsLysLys	p.E257_E258delinsKK	ENST00000377970	NM_002467.4	257	GAGGag/AAGAag	2/3	1	2	FACETS	0.904	0.8	1	0.904	0.8	1	CLONAL	1	TRUE	1	0.249203670899079	2		473	772	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984916	9984916	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	99	612	0	ENST00000330684.3:c.1049T>G	p.Phe350Cys	p.F350C	ENST00000330684	NM_001134407.1	350	tTc/tGc	4/13	0.251576110743688	6	FACETS	1	0.956	1	0.286	0.254	0.32	CLONAL	1	TRUE	2	0.251576110743688	6		612	1034	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183724	10183724	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	147	889	0	ENST00000256474.2:c.193del	p.Ser65ArgfsTer2	p.S65Rfs*2	ENST00000256474	NM_000551.3	65	Tcg/cg	1/3	0.251576110743688	2	FACETS	0.892	0.817	0.97	0.892	0.817	0.97	CLONAL	2	TRUE	0	0.251576110743688	2		889	655	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125729	47125745	+	frameshift_variant	Frame_Shift_Del	DEL	ATTCTCACTAGAATACC	ATTCTCACTAGAATACC	-	novel	NA	P-0037641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	156	496	0	ENST00000409792.3:c.5525_5541del	p.Gly1842AspfsTer12	p.G1842Dfs*12	ENST00000409792	NM_014159.6	1842	gGGTATTCTAGTGAGAAT/g	12/21	0.251576110743688	2	FACETS	0.923	0.848	1	0.923	0.848	1	CLONAL	2	TRUE	0	0.251576110743688	2		496	672	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439309	52439312	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	ATCT	ATCT	-	novel	NA	P-0037641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	142	617	0	ENST00000460680.1:c.932-2_933del		p.X311_splice	ENST00000460680	NM_004656.3	311		11/17	0.251576110743688	2	FACETS	0.927	0.848	1	0.927	0.848	1	CLONAL	2	TRUE	0	0.251576110743688	2		617	609	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0037642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	74	305	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.887	0.778	1	0.887	0.778	1	CLONAL	1	TRUE	1	0.316648628209819	2		305	527	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560382	95560382	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	149	470	0	ENST00000393063.1:c.5207G>T	p.Arg1736Leu	p.R1736L	ENST00000393063	NM_030621.3	1736	cGg/cTg	25/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.316648628209819	2		470	778	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348505	70348505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	185	250	2	ENST00000374080.3:c.3412C>T	p.Arg1138Trp	p.R1138W	ENST00000374080		1138	Cgg/Tgg	24/45	1	1	FACETS	0.873	0.812	0.937	1	0.992	1	CLONAL	2	TRUE	0	0.316648628209819	1		252	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577535	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0037642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	153	632	1	ENST00000269305.4:c.746_747del	p.Arg249ThrfsTer14	p.R249Tfs*14	ENST00000269305	NM_001126112.2	249	aGG/a	7/11	0.316648628209819	1	FACETS	0.89	0.814	0.969	0.89	0.814	0.969	CLONAL	1	TRUE	0	0.316648628209819	1		633	914	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602595	10602595	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	200	687	0	ENST00000171111.5:c.983T>A	p.Ile328Asn	p.I328N	ENST00000171111	NM_203500.1	328	aTc/aAc	3/6	0.316648628209819	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.316648628209819	1		687	921	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156936	106156936	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	91	391	0	ENST00000380013.4:c.1837G>T	p.Gly613Trp	p.G613W	ENST00000380013	NM_001127208.2	613	Ggg/Tgg	3/11	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.316648628209819	2		391	563	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0037642-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	52	305	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.311388267685185	2		305	278	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560382	95560382	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037642-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	82	470	0	ENST00000393063.1:c.5207G>T	p.Arg1736Leu	p.R1736L	ENST00000393063	NM_030621.3	1736	cGg/cTg	25/28	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.311388267685185	2		470	419	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348505	70348505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037642-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	61	250	2	ENST00000374080.3:c.3412C>T	p.Arg1138Trp	p.R1138W	ENST00000374080		1138	Cgg/Tgg	24/45	0.195582750653715	2	FACETS	0.924	0.809	1			1	CLONAL	2	TRUE	NA	0.311388267685185	2		252	212	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577535	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0037642-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	111	632	1	ENST00000269305.4:c.746_747del	p.Arg249ThrfsTer14	p.R249Tfs*14	ENST00000269305	NM_001126112.2	249	aGG/a	7/11	0.186778511946967	1	FACETS	1	0.975	1	1	0.975	1	INDETERMINATE	1	TRUE	0	0.311388267685185	1		633	483	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602595	10602595	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037642-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	112	687	0	ENST00000171111.5:c.983T>A	p.Ile328Asn	p.I328N	ENST00000171111	NM_203500.1	328	aTc/aAc	3/6	0.311388267685185	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.311388267685185	1		687	443	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156936	106156936	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037642-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	44	391	0	ENST00000380013.4:c.1837G>T	p.Gly613Trp	p.G613W	ENST00000380013	NM_001127208.2	613	Ggg/Tgg	3/11	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.311388267685185	2		391	280	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938499	76938501	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs1297294136	NA	P-0037643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	109	735	0	ENST00000373344.5:c.2247_2249del	p.Ser750del	p.S750del	ENST00000373344	NM_000489.3	749	tcTTCa/tca	9/35	0.232220034521182	3	FACETS	1	0.982	1	0.716	0.645	0.79	CLONAL	1	TRUE	1	0.335528421178981	3		735	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0037643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	199	1194	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.289738129892994	2	FACETS	0.88	0.819	0.943	0.88	0.819	0.943	CLONAL	2	TRUE	0	0.335528421178981	2		1194	674	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469896	157469896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	41	760	0	ENST00000346085.5:c.2690G>A	p.Gly897Glu	p.G897E	ENST00000346085	NM_020732.3	897	gGa/gAa	9/20	0.232220034521182	3	FACETS	0.723	0.603	0.855	0.361	0.301	0.428	SUBCLONAL	1	TRUE	1	0.335528421178981	3		760	395	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205184	128205184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	73	462	1	ENST00000341105.2:c.257G>A	p.Arg86His	p.R86H	ENST00000341105	NM_032638.4	86	cGc/cAc	3/6	0.546698811802883	2	FACETS	0.974	0.864	1	0.487	0.432	0.545	CLONAL	1	TRUE	0	0.619287556066733	2		463	242	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851762	134851762	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753407361	NA	P-0037649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	55	501	0	ENST00000398015.3:c.1168C>T	p.Arg390Cys	p.R390C	ENST00000398015	NM_004441.4	390	Cgc/Tgc	5/16	0.546698811802883	2	FACETS	0.756	0.654	0.865	0.378	0.327	0.433	SUBCLONAL	1	TRUE	0	0.619287556066733	2		501	235	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455090	50455090	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	51	323	0	ENST00000331340.3:c.637C>T	p.Arg213Ter	p.R213*	ENST00000331340	NM_006060.4	213	Cga/Tga	6/8	0.279463751912376	5	FACETS	0.764	0.652	0.885	0.509	0.435	0.59	SUBCLONAL	2	TRUE	2	0.279463751912376	5		323	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0037650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	146	767	0	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	0.114076152857186	6	FACETS	1	0.973	1			1	INDETERMINATE	3	TRUE	NA	0.279463751912376	6		767	479	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226021	53226021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781785252	NA	P-0037650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	47	414	0	ENST00000375401.3:c.2828G>A	p.Arg943Gln	p.R943Q	ENST00000375401	NM_004187.3	943	cGa/cAa	19/26	0.227962973685097	2	FACETS	1	0.932	1			1	CLONAL	1	TRUE	NA	0.279463751912376	2		414	285	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972854	25972854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1005506744	NA	P-0037650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	67	542	0	ENST00000435504.4:c.1571C>T	p.Ser524Leu	p.S524L	ENST00000435504		524	tCg/tTg	12/13	0.217822952556576	3	FACETS	1	0.966	1	0.668	0.583	0.76	CLONAL	1	TRUE	1	0.279463751912376	3		542	409	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562533	95562533	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	49	339	0	ENST00000393063.1:c.4724G>T	p.Gly1575Val	p.G1575V	ENST00000393063	NM_030621.3	1575	gGg/gTg	24/28	0.271421309731211	4	FACETS	1	0.961	1	0.481	0.409	0.559	CLONAL	1	TRUE	1	0.279463751912376	4		339	311	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90645531	90645531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	12	50	0	ENST00000330062.3:c.92C>T	p.Ser31Leu	p.S31L	ENST00000330062	NM_002168.2	31	tCg/tTg	1/11	1	2	FACETS	1	0.823	1	1	0.823	1	CLONAL	1	TRUE	1	0.279463751912376	2		50	70	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622047	43622047	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	73	397	0	ENST00000355710.3:c.3064A>T	p.Thr1022Ser	p.T1022S	ENST00000355710	NM_020975.4	1022	Act/Tct	19/20	0.279463751912376	3	FACETS	0.889	0.783	1	0.889	0.783	1	CLONAL	2	TRUE	1	0.279463751912376	3		397	335	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120535120	120535120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	283	559	0	ENST00000229340.5:c.535C>T	p.Gln179Ter	p.Q179*	ENST00000229340	NM_006861.6	179	Cag/Tag	6/6	0.279463751912376	6	FACETS	0.933	0.883	0.983	0.933	0.883	0.983	CLONAL	5	TRUE	1	0.279463751912376	6		559	677	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600438	10600438	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	129	651	0	ENST00000171111.5:c.1417del	p.Tyr473MetfsTer27	p.Y473Mfs*27	ENST00000171111	NM_203500.1	473	Tat/at	4/6	0.158519616246448	3	FACETS	0.982	0.894	1	0.654	0.596	0.715	INDETERMINATE	2	TRUE	0	0.279463751912376	3		651	536	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103898	209103898	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	34	420	0	ENST00000345146.2:c.1051G>C	p.Glu351Gln	p.E351Q	ENST00000345146	NM_005896.2	351	Gag/Cag	9/10	0.185742237903166	4	FACETS	0.916	0.75	1	0.305	0.25	0.367	CLONAL	1	TRUE	1	0.279463751912376	4		420	340	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582204	189582204	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	29	287	0	ENST00000264731.3:c.763G>C	p.Glu255Gln	p.E255Q	ENST00000264731	NM_003722.4	255	Gag/Cag	5/14	0.217822952556576	3	FACETS	0.893	0.719	1	0.446	0.359	0.544	CLONAL	1	TRUE	1	0.279463751912376	3		287	265	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876296	35876296	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	153	549	0	ENST00000303115.3:c.1088G>T	p.Arg363Ile	p.R363I	ENST00000303115	NM_002185.3	363	aGa/aTa	8/8	0.279463751912376	9	FACETS	1	0.97	1	0.673	0.617	0.73	CLONAL	3	TRUE	4	0.279463751912376	9		549	644	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852024	128852024	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	118	754	0	ENST00000249373.3:c.2096G>T	p.Ser699Ile	p.S699I	ENST00000249373	NM_005631.4	699	aGt/aTt	12/12	0.235847295595095	4	FACETS	0.96	0.869	1	0.96	0.869	1	CLONAL	2	TRUE	2	0.279463751912376	4		754	563	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534663	140534663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	36	331	0	ENST00000288602.6:c.250G>A	p.Glu84Lys	p.E84K	ENST00000288602	NM_004333.4	84	Gaa/Aaa	3/18	0.279463751912376	5	FACETS	1	0.938	1	0.446	0.369	0.533	CLONAL	1	TRUE	2	0.279463751912376	5		331	273	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195692	123195692	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	37	220	0	ENST00000218089.9:c.1606C>A	p.His536Asn	p.H536N	ENST00000218089	NM_001042749.1	536	Cat/Aat	17/35	0.187378514648181	2	FACETS	0.988	0.831	1			1	CLONAL	2	TRUE	NA	0.279463751912376	2		220	134	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0037652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	63	471	1	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.27444625602469	6	FACETS	0.996	0.872	1	0.747	0.654	0.845	CLONAL	3	TRUE	2	0.27444625602469	6		472	238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0037652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	49	663	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.241252379887247	3	FACETS	0.949	0.813	1	0.633	0.542	0.73	CLONAL	2	TRUE	0	0.27444625602469	3		663	214	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858941	57858941	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754019701	NA	P-0037652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	27	673	0	ENST00000228682.2:c.437C>T	p.Ser146Leu	p.S146L	ENST00000228682	NM_005269.2	146	tCg/tTg	5/12	1	2	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	TRUE	1	0.27444625602469	2		673	187	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949201	71949201	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	21	840	0	ENST00000298229.2:c.3668A>T	p.Asp1223Val	p.D1223V	ENST00000298229	NM_001567.3	1223	gAc/gTc	27/28	0.25076148287953	2	FACETS	0.87	0.674	1	0.435	0.337	0.547	CLONAL	1	TRUE	0	0.27444625602469	2		840	176	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434916	110434916	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs868077540	NA	P-0037652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	15	910	0	ENST00000375856.3:c.3485C>A	p.Ser1162Tyr	p.S1162Y	ENST00000375856	NM_003749.2	1162	tCc/tAc	1/2	0.169049551992199	2	FACETS	0.572	0.42	0.755	0.286	0.21	0.378	SUBCLONAL	1	TRUE	0	0.27444625602469	2		910	191	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435563	56435563	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	11	731	0	ENST00000407977.2:c.1574G>A	p.Ser525Asn	p.S525N	ENST00000407977		525	aGt/aAt	9/10	0.241252379887247	3	FACETS	0.501	0.346	0.692	0.167	0.115	0.231	SUBCLONAL	1	TRUE	0	0.27444625602469	3		731	182	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039407	47039408	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0037652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	18	344	1	ENST00000377604.3:c.1030_1031delinsTT	p.Gly344Phe	p.G344F	ENST00000377604	NM_001204468.1	344	GGc/TTc	10/24	0.245663285688894	0	FACETS	1	0.813	1			1	CLONAL	1	TRUE	NA	0.27444625602469	0		345	89	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660507	67660507	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	119	536	0	ENST00000264010.4:c.1407C>A	p.Cys469Ter	p.C469*	ENST00000264010	NM_006565.3	469	tgC/tgA	8/12	0.144968738998271	4	FACETS	1	0.983	1	0.721	0.652	0.794	INDETERMINATE	1	TRUE	2	0.30728213794487	4		536	702	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578537	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0037654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	250	819	0	ENST00000269305.4:c.393dup	p.Lys132GlnfsTer17	p.K132Qfs*17	ENST00000269305	NM_001126112.2	131	-/C	5/11	0.289342584402282	2	FACETS	0.818	0.765	0.872	0.818	0.765	0.872	CLONAL	2	TRUE	0	0.30728213794487	2		819	995	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873180	136873180	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	52	331	0	ENST00000241393.3:c.318C>A	p.Asn106Lys	p.N106K	ENST00000241393	NM_003467.2	106	aaC/aaA	2/2	0.244523052447374	3	FACETS	0.948	0.809	1	0.474	0.404	0.55	CLONAL	1	TRUE	1	0.30728213794487	3		331	412	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560824	9560824	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	219	468	0	ENST00000353224.5:c.958C>A	p.Arg320Ser	p.R320S	ENST00000353224	NM_177990.2	320	Cgc/Agc	4/10	0.276565790344248	3	FACETS	0.993	0.932	1			1	CLONAL	3	TRUE	NA	0.30728213794487	3		468	552	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099468	157099470	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	rs1429292576	NA	P-0037654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	32	289	0	ENST00000346085.5:c.413_415del	p.Asn138del	p.N138del	ENST00000346085	NM_020732.3	135	tcCAAc/tcc	1/20	1	2	FACETS	0.653	0.531	0.79	0.653	0.531	0.79	SUBCLONAL	1	TRUE	1	0.30728213794487	2		289	319	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984060	2984060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781530962	NA	P-0037654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	127	622	0	ENST00000396946.4:c.470G>A	p.Arg157Gln	p.R157Q	ENST00000396946	NM_032415.4	157	cGg/cAg	5/25	0.106144266694365	3	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.30728213794487	3		622	660	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976727	90976727	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	50	414	0	ENST00000265433.3:c.905T>A	p.Leu302His	p.L302H	ENST00000265433	NM_002485.4	302	cTt/cAt	8/16	0.244523052447374	3	FACETS	0.623	0.528	0.727	0.311	0.264	0.364	SUBCLONAL	1	TRUE	1	0.30728213794487	3		414	603	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395042	139395042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	203	720	0	ENST00000277541.6:c.5896C>T	p.His1966Tyr	p.H1966Y	ENST00000277541	NM_017617.3	1966	Cat/Tat	31/34	0.289342584402282	2	FACETS	0.933	0.868	1	0.933	0.868	1	CLONAL	2	TRUE	0	0.30728213794487	2		720	708	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448297	56448298	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1567880599	NA	P-0037654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	141	659	0	ENST00000407977.2:c.349dup	p.Arg117ProfsTer8	p.R117Pfs*8	ENST00000407977		117	cgc/cCgc	3/10	0.245718141494308	2	FACETS	1	0.987	1	0.746	0.682	0.813	CLONAL	1	TRUE	0	0.30728213794487	2		659	615	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0037692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	25	355	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.292	0.23	0.364	0.292	0.23	0.364	SUBCLONAL	1	TRUE	1	0.423377648114145	2		355	404	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0037692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	107	309	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.423377648114145	2		309	503	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876985	151876985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	81	383	1	ENST00000262189.6:c.7376C>T	p.Pro2459Leu	p.P2459L	ENST00000262189	NM_170606.2	2459	cCa/cTa	37/59	1	2	FACETS	0.886	0.784	0.994	0.886	0.784	0.994	CLONAL	1	TRUE	1	0.423377648114145	2		384	432	SUCCESS
ATM	472	MSKCC	GRCh37	11	108213982	108213982	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	91	385	0	ENST00000278616.4:c.8302G>T	p.Glu2768Ter	p.E2768*	ENST00000278616	NM_000051.3	2768	Gaa/Taa	57/63	1	2	FACETS	0.941	0.839	1	0.941	0.839	1	CLONAL	1	TRUE	1	0.423377648114145	2		385	457	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724333	52724333	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	117	526	0	ENST00000322088.6:c.1465A>T	p.Met489Leu	p.M489L	ENST00000322088	NM_014225.5	489	Atg/Ttg	12/15	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.423377648114145	2		526	540	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281942	39281942	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	55	377	0	ENST00000402219.2:c.533A>G	p.Gln178Arg	p.Q178R	ENST00000402219	NM_005633.3	178	cAa/cGa	5/23	1	2	FACETS	0.945	0.815	1	0.945	0.815	1	CLONAL	1	TRUE	1	0.423377648114145	2		377	275	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339963	116339964	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACAAGAATAATCAGGTTCTGTTCCATAAACTCTGGATTGCATTCCTACATGGA	novel	NA	P-0037692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	31	400	0	ENST00000397752.3:c.827_879dup	p.Met294GlnfsTer3	p.M294Qfs*3	ENST00000397752	NM_000245.2	275	-/ACAAGAATAATCAGGTTCTGTTCCATAAACTCTGGATTGCATTCCTACATGGA	2/21	1	2	FACETS	0.298	0.241	0.364	0.298	0.241	0.364	SUBCLONAL	1	TRUE	1	0.423377648114145	2		400	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781504	NA	P-0037693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	121	793	0	ENST00000269305.4:c.314G>T	p.Gly105Val	p.G105V	ENST00000269305	NM_001126112.2	105	gGc/gTc	4/11	0.199569538565004	3	FACETS	1	0.982	1	0.697	0.631	0.766	CLONAL	1	TRUE	1	0.309553686514041	3		793	648	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602329	10602329	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	134	800	0	ENST00000171111.5:c.1249G>T	p.Gly417Trp	p.G417W	ENST00000171111	NM_203500.1	417	Ggg/Tgg	3/6	0.182534382837864	2	FACETS	1	0.985	1	0.713	0.65	0.779	INDETERMINATE	1	TRUE	0	0.309553686514041	2		800	607	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236109	108236109	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	105	597	0	ENST00000278616.4:c.9045G>C	p.Glu3015Asp	p.E3015D	ENST00000278616	NM_000051.3	3015	gaG/gaC	63/63	0.191718443434281	3	FACETS	1	0.963	1	0.386	0.346	0.429	CLONAL	1	TRUE	0	0.309553686514041	3		597	676	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643510	52643510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	40	587	0	ENST00000394830.3:c.2386G>A	p.Glu796Lys	p.E796K	ENST00000394830	NM_018313.4	796	Gag/Aag	17/30	0.182534382837864	2	FACETS	0.479	0.397	0.57	0.239	0.198	0.285	INDETERMINATE	1	TRUE	0	0.309553686514041	2		587	540	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741912	162741912	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	46	424	0	ENST00000367921.3:c.1603G>T	p.Gly535Cys	p.G535C	ENST00000367921	NM_006182.2	535	Ggc/Tgc	13/18	0.182534382837864	2	FACETS	0.895	0.757	1	0.448	0.378	0.523	INDETERMINATE	1	TRUE	0	0.309553686514041	2		424	332	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861141	57861141	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0037693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1541	122	432	0	ENST00000228682.2:c.938C>G	p.Ser313Ter	p.S313*	ENST00000228682	NM_005269.2	313	tCa/tGa	9/12	0.309553686514041	17	FACETS	0.787	0.708	0.871			1	SUBCLONAL	2	TRUE	NA	0.309553686514041	17		432	1663	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220070	133220070	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0037693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	33	720	0	ENST00000320574.5:c.4367C>G	p.Ser1456Ter	p.S1456*	ENST00000320574	NM_006231.2	1456	tCa/tGa	34/49	1	2	FACETS	0.334	0.271	0.406	0.334	0.271	0.406	SUBCLONAL	1	TRUE	1	0.309553686514041	2		720	638	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896939	28896939	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	46	470	0	ENST00000282397.4:c.2941G>T	p.Glu981Ter	p.E981*	ENST00000282397	NM_002019.4	981	Gag/Tag	21/30	0.182534382837864	2	FACETS	0.536	0.451	0.631	0.268	0.225	0.316	INDETERMINATE	1	TRUE	0	0.309553686514041	2		470	554	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832614	72832614	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0037693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	22	217	0	ENST00000268489.5:c.3968-1G>C		p.X1323_splice	ENST00000268489	NM_006885.3	1323			0.134798499869302	5	FACETS	0.917	0.713	1	0.306	0.237	0.384	INDETERMINATE	1	TRUE	2	0.309553686514041	5		217	227	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579485	7579486	+	stop_gained	Nonsense_Mutation	DNP	CT	CT	AA	novel	NA	P-0037693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	60	801	1	ENST00000269305.4:c.201_202delinsTT	p.Glu68Ter	p.E68*	ENST00000269305	NM_001126112.2	67	ccAGag/ccTTag	4/11	0.199569538565004	3	FACETS	0.695	0.598	0.801	0.348	0.299	0.401	SUBCLONAL	1	TRUE	1	0.309553686514041	3		802	644	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448395	56448396	+	splice_acceptor_variant	Splice_Site	DNP	CT	CT	AG	novel	NA	P-0037693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	55	704	1	ENST00000407977.2:c.253-2_253-1inv		p.X85_splice	ENST00000407977		85			0.199569538565004	3	FACETS	0.61	0.521	0.707	0.305	0.26	0.354	SUBCLONAL	1	TRUE	1	0.309553686514041	3		705	673	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223304	2223304	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	124	779	1	ENST00000398665.3:c.3415G>T	p.Glu1139Ter	p.E1139*	ENST00000398665	NM_032482.2	1139	Gag/Tag	25/28	0.182534382837864	2	FACETS	0.753	0.684	0.825	0.753	0.684	0.825	INDETERMINATE	2	TRUE	0	0.309553686514041	2		780	532	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098469	11098469	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1187772743	NA	P-0037693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	63	346	0	ENST00000358026.2:c.987G>T	p.Gln329His	p.Q329H	ENST00000358026	NM_001128849.1	329	caG/caT	6/36	0.182534382837864	2	FACETS	0.827	0.724	0.936	0.827	0.724	0.936	INDETERMINATE	2	TRUE	0	0.309553686514041	2		346	246	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218513	36218513	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	42	645	0	ENST00000222270.7:c.4292T>C	p.Leu1431Pro	p.L1431P	ENST00000222270	NM_014727.1	1431	cTc/cCc	16/37	0.309553686514041	4	FACETS	0.631	0.526	0.748	0.21	0.175	0.25	SUBCLONAL	1	TRUE	1	0.309553686514041	4		645	563	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729885	47729886	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0037693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	60	376	0	ENST00000449228.1:c.503dup	p.Asp171ArgfsTer79	p.D171Rfs*79	ENST00000449228	NM_001127240.2	168	ggc/ggGc	3/4	0.309553686514041	4	FACETS	1	0.97	1	0.498	0.431	0.569	CLONAL	1	TRUE	1	0.309553686514041	4		376	340	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498376	89498376	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	60	260	0	ENST00000336596.2:c.2348G>T	p.Gly783Val	p.G783V	ENST00000336596	NM_005233.5	783	gGa/gTa	14/17	0.159034424791748	4	FACETS	0.781	0.677	0.892	0.781	0.677	0.892	INDETERMINATE	2	TRUE	2	0.309553686514041	4		260	325	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212078	142212078	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	122	653	2	ENST00000350721.4:c.5974G>T	p.Glu1992Ter	p.E1992*	ENST00000350721	NM_001184.3	1992	Gag/Tag	35/47	0.159034424791748	4	FACETS	1	0.983	1	0.705	0.638	0.776	INDETERMINATE	1	TRUE	2	0.309553686514041	4		655	732	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131139	55131140	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0037693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	94	575	0	ENST00000257290.5:c.682_683delinsCT	p.Gly228Leu	p.G228L	ENST00000257290	NM_006206.4	228	GGg/CTg	5/23	0.134798499869302	5	FACETS	1	0.977	1	0.463	0.412	0.517	INDETERMINATE	1	TRUE	2	0.309553686514041	5		575	640	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576754	67576754	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0037693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	38	388	0	ENST00000274335.5:c.837-1G>C		p.X279_splice	ENST00000274335		279			1	2	FACETS	0.655	0.542	0.78	0.655	0.542	0.78	SUBCLONAL	1	TRUE	1	0.309553686514041	2		388	375	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845240	128845240	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	29	467	0	ENST00000249373.3:c.734C>A	p.Thr245Lys	p.T245K	ENST00000249373	NM_005631.4	245	aCg/aAg	3/12	1	2	FACETS	0.571	0.459	0.698	0.571	0.459	0.698	SUBCLONAL	1	TRUE	1	0.309553686514041	2		467	328	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852054	128852054	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369342481	NA	P-0037693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	48	755	0	ENST00000249373.3:c.2126G>A	p.Arg709Gln	p.R709Q	ENST00000249373	NM_005631.4	709	cGg/cAg	12/12	1	2	FACETS	0.575	0.486	0.674	0.575	0.486	0.674	SUBCLONAL	1	TRUE	1	0.309553686514041	2		755	539	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868465	117868465	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	102	612	0	ENST00000297338.2:c.877C>G	p.Gln293Glu	p.Q293E	ENST00000297338	NM_006265.2	293	Caa/Gaa	8/14	0.189678961409969	4	FACETS	1	0.976	1	0.661	0.592	0.734	CLONAL	1	TRUE	2	0.309553686514041	4		612	653	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8525014	8525014	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	30	417	0	ENST00000356435.5:c.590G>A	p.Ser197Asn	p.S197N	ENST00000356435		197	aGt/aAt	7/35	0.309553686514041	1	FACETS	0.509	0.411	0.62	0.509	0.411	0.62	SUBCLONAL	1	TRUE	0	0.309553686514041	1		417	322	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793286	242793286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757334336	NA	P-0037714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	64	542	0	ENST00000334409.5:c.791G>A	p.Arg264His	p.R264H	ENST00000334409	NM_005018.2	264	cGc/cAc	5/5	1	2	FACETS	0.787	0.681	0.903	0.787	0.681	0.903	CLONAL	1	TRUE	1	0.22	2		542	739	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225689	26225689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	53	489	0	ENST00000360408.1:c.307G>A	p.Gly103Arg	p.G103R	ENST00000360408	NM_003532.2	103	Ggg/Agg	1/1	0.0883647879392855	0	FACETS	0.724	0.618	0.841			1	INDETERMINATE	1	TRUE	0	0.22	0		489	519	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	17	737	0				ENST00000310581	NM_198253.2	-/1132			0.273676667644921	0	FACETS	0.29	0.217	0.376			1	SUBCLONAL	1	TRUE	0	0.406463141960461	0		737	171	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0037755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	91	609	2	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.22840907161024	3	FACETS	0.746	0.662	0.836	0.373	0.331	0.418	INDETERMINATE	1	TRUE	1	0.406463141960461	3		611	722	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118968	3118968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	46	1023	1	ENST00000078429.4:c.652C>T	p.His218Tyr	p.H218Y	ENST00000078429	NM_002067.2	218	Cac/Tac	5/7	0.121293814310002	0	FACETS	0.315	0.266	0.37			1	INDETERMINATE	1	TRUE	0	0.406463141960461	0		1024	426	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162137	47162137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	59	629	0	ENST00000409792.3:c.3989C>T	p.Ser1330Phe	p.S1330F	ENST00000409792	NM_014159.6	1330	tCc/tTc	3/21	0.406896604128579	3	FACETS	0.807	0.696	0.927	0.403	0.348	0.464	CLONAL	1	TRUE	1	0.406463141960461	3		629	433	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622418	28622418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	31	666	1	ENST00000241453.7:c.1199G>A	p.Gly400Glu	p.G400E	ENST00000241453	NM_004119.2	400	gGa/gAa	9/24	0.204739485817124	0	FACETS	0.247	0.2	0.301			1	INDETERMINATE	1	TRUE	0	0.406463141960461	0		667	366	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117632271	117632271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	39	656	1	ENST00000368508.3:c.6145C>T	p.Pro2049Ser	p.P2049S	ENST00000368508	NM_002944.2	2049	Cct/Tct	39/43	1	2	FACETS	0.653	0.543	0.773	0.653	0.543	0.773	SUBCLONAL	1	TRUE	1	0.406463141960461	2		657	294	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849483	89849483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776371246	NA	P-0037755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	106	780	0	ENST00000389301.3:c.1498C>T	p.Pro500Ser	p.P500S	ENST00000389301	NM_000135.2	500	Ccc/Tcc	16/43	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.406463141960461	2		780	518	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251701	212251701	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	56	600	1	ENST00000342788.4:c.3358C>T	p.Gln1120Ter	p.Q1120*	ENST00000342788	NM_005235.2	1120	Caa/Taa	27/28	1	2	FACETS	0.749	0.644	0.862	0.749	0.644	0.862	SUBCLONAL	1	TRUE	1	0.406463141960461	2		601	368	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321678	62321678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	88	859	0	ENST00000360203.5:c.2297C>T	p.Pro766Leu	p.P766L	ENST00000360203	NM_001283009.1	766	cCc/cTc	26/35	1	2	FACETS	0.833	0.74	0.931	0.833	0.74	0.931	CLONAL	1	TRUE	1	0.406463141960461	2		859	520	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936307	49936307	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	42	737	0	ENST00000296474.3:c.1541G>A	p.Gly514Glu	p.G514E	ENST00000296474	NM_002447.2	514	gGg/gAg	3/20	0.406896604128579	3	FACETS	0.747	0.626	0.88	0.373	0.313	0.44	SUBCLONAL	1	TRUE	1	0.406463141960461	3		737	333	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162475191	162475191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	65	642	0	ENST00000366898.1:c.550G>A	p.Asp184Asn	p.D184N	ENST00000366898	NM_004562.2	184	Gat/Aat	5/12	1	2	FACETS	0.824	0.718	0.938	0.824	0.718	0.938	CLONAL	1	TRUE	1	0.406463141960461	2		642	388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	210	597	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.963	0.896	1	0.963	0.896	1	CLONAL	1	TRUE	1	0.552084025890004	2		597	790	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	283	512	6	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.802	0.76	0.845	1	0.995	1	CLONAL	2	TRUE	1	0.552084025890004	2		518	639	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	164	389	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.552084025890004	2		389	535	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117799	108117799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202160435	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	150	445	0	ENST00000278616.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000278616	NM_000051.3	337	cGt/cAt	8/63	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.552084025890004	2		445	538	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479795	67479795	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs757106110	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	230	648	1	ENST00000327367.4:c.1102C>T	p.Arg368Ter	p.R368*	ENST00000327367	NM_005902.3	368	Cga/Tga	8/9	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.552084025890004	2		649	717	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	154	510	2	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	NA	2	FACETS	0.84	0.771	0.912			1	INDETERMINATE	1	TRUE	NA	0.552084025890004	2		512	664	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	178	532	3	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	1	2	FACETS	0.908	0.84	0.979	0.908	0.84	0.979	CLONAL	1	TRUE	1	0.552084025890004	2		535	710	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969933	81969933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752209691	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	184	647	0	ENST00000359376.3:c.3002G>A	p.Arg1001His	p.R1001H	ENST00000359376	NM_002661.3	1001	cGc/cAc	27/33	0.273321845606606	1	FACETS	0.702	0.651	0.756	0.702	0.651	0.756	INDETERMINATE	1	TRUE	0	0.552084025890004	1		647	687	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681061	117681061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749977900	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	180	602	0	ENST00000368508.3:c.3559G>A	p.Val1187Ile	p.V1187I	ENST00000368508	NM_002944.2	1187	Gtt/Att	23/43	1	2	FACETS	0.929	0.859	1	0.929	0.859	1	CLONAL	1	TRUE	1	0.552084025890004	2		602	702	SUCCESS
CBL	867	MSKCC	GRCh37	11	119146717	119146717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	160	498	1	ENST00000264033.4:c.880C>T	p.Arg294Trp	p.R294W	ENST00000264033	NM_005188.3	294	Cgg/Tgg	6/16	1	2	FACETS	0.986	0.908	1	0.986	0.908	1	CLONAL	1	TRUE	1	0.552084025890004	2		499	588	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	172	717	1	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	0.827	0.763	0.894	0.827	0.763	0.894	CLONAL	1	TRUE	1	0.552084025890004	2		718	753	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275291	41275291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750554859	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	175	513	0	ENST00000349496.5:c.1457G>A	p.Arg486His	p.R486H	ENST00000349496	NM_001904.3	486	cGc/cAc	9/15	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.552084025890004	2		513	568	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	255	331	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.933	0.874	0.994	0.933	0.874	0.994	CLONAL	1	TRUE	1	0.552084025890004	2		335	990	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527259	187527259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201982861	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	180	610	0	ENST00000441802.2:c.10315G>A	p.Val3439Ile	p.V3439I	ENST00000441802	NM_005245.3	3439	Gtc/Atc	17/27	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.552084025890004	2		610	631	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515125	148515125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1193491117	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	118	556	0	ENST00000320356.2:c.1084C>T	p.Arg362Trp	p.R362W	ENST00000320356	NM_004456.4	362	Cgg/Tgg	10/20	1	2	FACETS	0.696	0.63	0.766	0.696	0.63	0.766	SUBCLONAL	1	TRUE	1	0.552084025890004	2		556	614	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303222	11303222	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747412972	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	169	705	2	ENST00000361445.4:c.1361G>A	p.Arg454His	p.R454H	ENST00000361445	NM_004958.3	454	cGc/cAc	9/58	1	2	FACETS	0.811	0.747	0.877	0.811	0.747	0.877	CLONAL	1	TRUE	1	0.552084025890004	2		707	755	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905629	50905629	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs776204287	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	209	859	1	ENST00000440232.2:c.757C>T	p.Arg253Trp	p.R253W	ENST00000440232	NM_002691.3	253	Cgg/Tgg	6/27	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.552084025890004	2		860	687	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795003	242795003	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764200391	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	232	901	4	ENST00000334409.5:c.206G>A	p.Arg69His	p.R69H	ENST00000334409	NM_005018.2	69	cGc/cAc	2/5	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.552084025890004	2		905	815	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132028	176132028	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	159	582	0	ENST00000367669.3:c.739C>T	p.Gln247Ter	p.Q247*	ENST00000367669	NM_022457.5	247	Cag/Tag	5/20	0.552084025890004	3	FACETS	0.861	0.789	0.935	0.43	0.394	0.468	CLONAL	1	TRUE	1	0.552084025890004	3		582	854	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405623	70405623	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	167	646	1	ENST00000373644.4:c.3137A>G	p.Glu1046Gly	p.E1046G	ENST00000373644	NM_030625.2	1046	gAg/gGg	4/12	1	2	FACETS	0.888	0.819	0.96	0.888	0.819	0.96	CLONAL	1	TRUE	1	0.552084025890004	2		647	681	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245162	46245162	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	163	594	1	ENST00000334344.6:c.3260del	p.Pro1087LeufsTer69	p.P1087Lfs*69	ENST00000334344	NM_152641.2	1086	Ccc/cc	15/21	0.552084025890004	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.552084025890004	1		595	421	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73348148	73348148	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	167	475	0	ENST00000377767.4:c.1037T>C	p.Val346Ala	p.V346A	ENST00000377767	NM_014953.3	346	gTa/gCa	7/21	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.552084025890004	2		475	603	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643227	38643227	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	136	450	0	ENST00000299084.4:c.697T>A	p.Ser233Thr	p.S233T	ENST00000299084	NM_152594.2	233	Tca/Aca	7/7	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.552084025890004	2		450	485	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41001295	41001295	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148345609	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	149	555	0	ENST00000267868.3:c.416C>T	p.Thr139Met	p.T139M	ENST00000267868	NM_002875.4	139	aCg/aTg	5/10	1	2	FACETS	0.889	0.816	0.966	0.889	0.816	0.966	CLONAL	1	TRUE	1	0.552084025890004	2		555	607	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133768	2133768	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	181	792	0	ENST00000219476.3:c.3956A>C	p.Asp1319Ala	p.D1319A	ENST00000219476	NM_000548.3	1319	gAc/gCc	33/42	0.273321845606606	1	FACETS	0.697	0.645	0.751	0.697	0.645	0.751	INDETERMINATE	1	TRUE	0	0.552084025890004	1		792	681	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15280950	15280950	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	212	893	0	ENST00000263388.2:c.5146del	p.Glu1716ArgfsTer17	p.E1716Rfs*17	ENST00000263388	NM_000435.2	1716	Gag/ag	28/33	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.552084025890004	2		893	750	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657024	47657024	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	170	477	0	ENST00000233146.2:c.1220T>G	p.Leu407Arg	p.L407R	ENST00000233146	NM_000251.2	407	cTc/cGc	7/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.552084025890004	2		477	531	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225365135	225365135	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	206	506	0	ENST00000264414.4:c.1555A>G	p.Thr519Ala	p.T519A	ENST00000264414	NM_003590.4	519	Aca/Gca	11/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.552084025890004	2		506	675	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385155	41385155	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	189	798	1	ENST00000373198.4:c.806T>C	p.Ile269Thr	p.I269T	ENST00000373198	NM_133170.3	269	aTc/aCc	6/32	1	2	FACETS	0.991	0.919	1	0.991	0.919	1	CLONAL	1	TRUE	1	0.552084025890004	2		799	691	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526187	189526187	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	198	672	0	ENST00000264731.3:c.451C>T	p.Gln151Ter	p.Q151*	ENST00000264731	NM_003722.4	151	Cag/Tag	4/14	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.552084025890004	2		672	695	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539759	187539759	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	32	537	0	ENST00000441802.2:c.7981del	p.Leu2661SerfsTer62	p.L2661Sfs*62	ENST00000441802	NM_005245.3	2661	Ctc/tc	10/27	1	2	FACETS	0.191	0.154	0.232	0.191	0.154	0.232	SUBCLONAL	1	TRUE	1	0.552084025890004	2		537	608	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295394	1295394	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	140	164	1				ENST00000310581	NM_198253.2	-/1132			0.381789053696377	3	FACETS	0.877	0.819	0.934	1	0.988	1	CLONAL	3	TRUE	1	0.552084025890004	3		165	246	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922670	44922670	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	121	173	0	ENST00000377967.4:c.1531A>G	p.Arg511Gly	p.R511G	ENST00000377967	NM_021140.2	511	Aga/Gga	16/29	1	1	FACETS	0.793	0.739	0.846	1	0.99	1	SUBCLONAL	2	TRUE	0	0.552084025890004	1		173	200	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045001	47045001	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	256	441	0	ENST00000377604.3:c.2327G>T	p.Arg776Leu	p.R776L	ENST00000377604	NM_001204468.1	776	cGg/cTg	20/24	1	1	FACETS	0.756	0.719	0.793	1	0.995	1	SUBCLONAL	2	TRUE	0	0.552084025890004	1		441	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0037790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	630	1104	1	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	0.925530478204348	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.925530478204348	1		1105	705	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788651	3788651	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	388	495	1	ENST00000262367.5:c.4303G>C	p.Asp1435His	p.D1435H	ENST00000262367	NM_004380.2	1435	Gat/Cat	26/31	0.925530478204348	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.925530478204348	1		496	421	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941257	36941278	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCCCGCACTCCTCCAGACCTGG	GCCCGCACTCCTCCAGACCTGG	-	novel	NA	P-0037790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	387	933	1	ENST00000361632.4:c.65-4_82del		p.X22_splice	ENST00000361632		22		3/16	1	2	FACETS	0.837	0.798	0.877	0.837	0.798	0.877	CLONAL	1	TRUE	1	0.925530478204348	2		934	999	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161284196	161284196	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs755235380	NA	P-0037790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	359	562	1	ENST00000367975.2:c.1A>G	p.Met1?	p.M1?	ENST00000367975	NM_003001.3	1	Atg/Gtg	1/6	0.925530478204348	3	FACETS	1	0.974	1	0.521	0.494	0.548	CLONAL	1	TRUE	1	0.925530478204348	3		563	1090	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426253	49426253	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	673	1202	6	ENST00000301067.7:c.12235C>T	p.Gln4079Ter	p.Q4079*	ENST00000301067	NM_003482.3	4079	Caa/Taa	39/54	1	2	FACETS	0.964	0.931	0.998	0.964	0.931	0.998	CLONAL	1	TRUE	1	0.925530478204348	2		1208	1508	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43773204	43773204	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	327	536	0	ENST00000382044.4:c.388G>C	p.Val130Leu	p.V130L	ENST00000382044	NM_001141980.1	130	Gtg/Ctg	5/28	0.925530478204348	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.925530478204348	1		536	357	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124296	2124298	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	rs137854128	NA	P-0037790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	593	1139	0	ENST00000219476.3:c.2459_2461del	p.Ile820del	p.I820del	ENST00000219476	NM_000548.3	817	gaCATc/gac	22/42	0.925530478204348	1	FACETS	0.935	0.914	0.955	0.935	0.914	0.955	CLONAL	1	TRUE	0	0.925530478204348	1		1139	736	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526125	63526125	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	498	818	4	ENST00000307078.5:c.2501G>T	p.Arg834Leu	p.R834L	ENST00000307078	NM_004655.3	834	cGg/cTg	11/11	1	2	FACETS	0.941	0.903	0.979	0.941	0.903	0.979	CLONAL	1	TRUE	1	0.925530478204348	2		822	1144	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966565	36966565	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	511	750	1	ENST00000358127.4:c.761A>C	p.Glu254Ala	p.E254A	ENST00000358127	NM_001280556.1	254	gAg/gCg	6/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.925530478204348	2		751	1099	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156607	55156607	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	45	450	0	ENST00000257290.5:c.3008G>T	p.Trp1003Leu	p.W1003L	ENST00000257290	NM_006206.4	1003	tGg/tTg	22/23	1	2	FACETS	0.639	0.536	0.752	0.639	0.536	0.752	SUBCLONAL	1	TRUE	1	0.27	2		450	522	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031761	36031761	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0037910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	22	529	0	ENST00000358208.4:c.1590C>G	p.Tyr530Ter	p.Y530*	ENST00000358208		530	taC/taG	12/12	1	2	FACETS	0.486	0.377	0.614	0.486	0.377	0.614	SUBCLONAL	1	TRUE	1	0.27	2		529	335	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448517	49448517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763644658	NA	P-0037925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	174	672	1	ENST00000301067.7:c.194G>A	p.Arg65His	p.R65H	ENST00000301067	NM_003482.3	65	cGt/cAt	3/54	0.255722530703315	4	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	2	0.358143376775976	4		673	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	225	874	1	ENST00000269305.4:c.526del	p.Cys176AlafsTer71	p.C176Afs*71	ENST00000269305	NM_001126112.2	176	Tgc/gc	5/11	0.320629165473594	2	FACETS	0.885	0.828	0.943	0.885	0.828	0.943	CLONAL	2	TRUE	0	0.358143376775976	2		875	710	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264414	30264414	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1281747941	NA	P-0037925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	207	581	0	ENST00000322652.5:c.149G>A	p.Gly50Asp	p.G50D	ENST00000322652	NM_015355.2	50	gGc/gAc	1/16	0.255722530703315	4	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	2	0.358143376775976	4		581	770	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508263	38508283	+	inframe_deletion	In_Frame_Del	DEL	GTGCGCAAAGCGCACCAGGAA	GTGCGCAAAGCGCACCAGGAA	-	novel	NA	P-0037925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	80	647	0	ENST00000254066.5:c.571_591del	p.Val191_Glu197del	p.V191_E197del	ENST00000254066	NM_000964.3	191	GTGCGCAAAGCGCACCAGGAA/-	5/9	0.255722530703315	4	FACETS	0.839	0.738	0.948	0.42	0.369	0.474	CLONAL	1	TRUE	2	0.358143376775976	4		647	723	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945083	151945083	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	40	819	0	ENST00000262189.6:c.2436G>T	p.Met812Ile	p.M812I	ENST00000262189	NM_170606.2	812	atG/atT	14/59	0.312848237401533	5	FACETS	0.468	0.388	0.559	0.156	0.129	0.187	SUBCLONAL	1	TRUE	2	0.358143376775976	5		819	733	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332337	70332337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761821309	NA	P-0037959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	90	582	1	ENST00000373644.4:c.242G>A	p.Arg81His	p.R81H	ENST00000373644	NM_030625.2	81	cGc/cAc	2/12	0.204828200744634	3	FACETS	1	0.941	1	0.55	0.487	0.617	CLONAL	1	TRUE	1	0.204828200744634	3		583	881	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182858	123182858	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	38	222	1	ENST00000218089.9:c.823C>T	p.Gln275Ter	p.Q275*	ENST00000218089	NM_001042749.1	275	Cag/Tag	10/35	0.166543098986252	4	FACETS	0.767	0.633	0.917	0.383	0.316	0.459	CLONAL	1	TRUE	2	0.204828200744634	4		223	583	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046361	180046361	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	44	636	0	ENST00000261937.6:c.2653G>A	p.Ala885Thr	p.A885T	ENST00000261937	NM_182925.4	885	Gcc/Acc	19/30	0.194596004417813	4	FACETS	0.603	0.504	0.713	0.301	0.252	0.357	SUBCLONAL	1	TRUE	2	0.204828200744634	4		636	859	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025803	1025803	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0037959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	140	486	0	ENST00000358495.3:c.725+2T>A		p.X242_splice	ENST00000358495	NM_134424.2	242			0.194596004417813	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.204828200744634	4		486	704	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498073	29498073	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	146	671	0	ENST00000389048.3:c.1933C>A	p.Leu645Met	p.L645M	ENST00000389048	NM_004304.4	645	Ctg/Atg	11/29	0.204828200744634	3	FACETS	0.954	0.871	1	0.954	0.871	1	CLONAL	2	TRUE	1	0.204828200744634	3		671	824	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939169	76939169	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	72	678	0	ENST00000373344.5:c.1579G>C	p.Asp527His	p.D527H	ENST00000373344	NM_000489.3	527	Gac/Cac	9/35	0.166543098986252	4	FACETS	0.952	0.83	1	0.476	0.415	0.542	CLONAL	1	TRUE	2	0.204828200744634	4		678	890	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939995	76939995	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	65	733	0	ENST00000373344.5:c.753G>C	p.Lys251Asn	p.K251N	ENST00000373344	NM_000489.3	251	aaG/aaC	9/35	0.166543098986252	4	FACETS	0.742	0.642	0.852	0.371	0.321	0.426	SUBCLONAL	1	TRUE	2	0.204828200744634	4		733	1030	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0037973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	64	398	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.986	0.86	1	0.986	0.86	1	CLONAL	1	TRUE	1	0.400558238921998	2		398	324	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508490	106508490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	34	384	0	ENST00000359195.3:c.484G>A	p.Val162Ile	p.V162I	ENST00000359195	NM_002649.2	162	Gtc/Atc	2/11	0.400558238921998	4	FACETS	0.877	0.72	1	0.439	0.36	0.526	CLONAL	1	TRUE	2	0.400558238921998	4		384	271	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916923	178916923	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	86	691	0	ENST00000263967.3:c.310C>A	p.Pro104Thr	p.P104T	ENST00000263967	NM_006218.2	104	Cca/Aca	2/21	1	2	FACETS	0.902	0.801	1	0.902	0.801	1	CLONAL	1	TRUE	1	0.400558238921998	2		691	476	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205175	123205175	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0037973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	59	215	0	ENST00000218089.9:c.2533+2T>A		p.X845_splice	ENST00000218089	NM_001042749.1	845			1	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.400558238921998	1		215	165	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0038018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	150	739	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.339639310789976	2	FACETS	0.811	0.747	0.877	0.811	0.747	0.877	CLONAL	2	TRUE	0	0.388597914817531	2		739	476	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115919	8115920	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0038018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	49	416	0	ENST00000346208.3:c.1266dup	p.His423AlafsTer84	p.H423Afs*84	ENST00000346208		422	atg/atGg	6/6	1	2	FACETS	0.557	0.472	0.65	0.557	0.472	0.65	SUBCLONAL	1	TRUE	1	0.388597914817531	2		416	453	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244370	41244370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	70	629	0	ENST00000357654.3:c.3178G>A	p.Glu1060Lys	p.E1060K	ENST00000357654	NM_007294.3	1060	Gaa/Aaa	10/23	0.388597914817531	6	FACETS	0.815	0.709	0.929	0.163	0.141	0.186	CLONAL	1	TRUE	1	0.388597914817531	6		629	786	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244913	41244913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80357251	NA	P-0038018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	57	549	0	ENST00000357654.3:c.2635G>A	p.Glu879Lys	p.E879K	ENST00000357654	NM_007294.3	879	Gaa/Aaa	10/23	0.388597914817531	6	FACETS	0.858	0.735	0.991	0.172	0.147	0.199	CLONAL	1	TRUE	1	0.388597914817531	6		549	608	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428469	72428469	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	68	482	0	ENST00000477973.2:c.535G>A	p.Glu179Lys	p.E179K	ENST00000477973	NM_012234.5	179	Gag/Aag	2/4	0.339639310789976	2	FACETS	0.693	0.604	0.789	0.347	0.302	0.395	SUBCLONAL	1	TRUE	0	0.388597914817531	2		482	505	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447586	187447586	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	42	622	0	ENST00000232014.4:c.607G>A	p.Val203Ile	p.V203I	ENST00000232014	NM_001130845.1	203	Gtc/Atc	5/10	0.388597914817531	5	FACETS	0.564	0.47	0.668	0.188	0.156	0.223	SUBCLONAL	1	TRUE	2	0.388597914817531	5		622	607	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534341	187534341	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	40	475	0	ENST00000441802.2:c.9385C>A	p.Pro3129Thr	p.P3129T	ENST00000441802	NM_005245.3	3129	Cct/Act	13/27	1	2	FACETS	0.548	0.456	0.649	0.548	0.456	0.649	SUBCLONAL	1	TRUE	1	0.388597914817531	2		475	376	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0038020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	79	413	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.186590251730438	3	FACETS	0.847	0.748	0.951	0.847	0.748	0.951	CLONAL	2	TRUE	1	0.244713359615209	3		414	428	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602659	10602659	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	120	669	0	ENST00000171111.5:c.919G>T	p.Glu307Ter	p.E307*	ENST00000171111	NM_203500.1	307	Gag/Tag	3/6	0.164837462971089	2	FACETS	1	0.984	1	0.734	0.664	0.808	CLONAL	1	TRUE	0	0.244713359615209	2		669	668	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218483	1218483	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs775595174	NA	P-0038020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	82	462	1	ENST00000326873.7:c.358G>T	p.Glu120Ter	p.E120*	ENST00000326873	NM_000455.4	120	Gaa/Taa	2/10	0.164837462971089	2	FACETS	1	0.971	1	0.662	0.585	0.744	CLONAL	1	TRUE	0	0.244713359615209	2		463	506	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646201	3646201	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	98	705	0	ENST00000294008.3:c.1877G>C	p.Ser626Thr	p.S626T	ENST00000294008	NM_032444.2	626	aGc/aCc	8/15	0.014199688996599	4	FACETS	0.819	0.731	0.911	0.819	0.731	0.911	INDETERMINATE	2	TRUE	2	0.244713359615209	4		705	609	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858141	9858141	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	34	529	0	ENST00000330684.3:c.3260A>T	p.Lys1087Ile	p.K1087I	ENST00000330684	NM_001134407.1	1087	aAa/aTa	13/13	0.014199688996599	4	FACETS	0.654	0.533	0.79	0.327	0.266	0.395	INDETERMINATE	1	TRUE	2	0.244713359615209	4		529	529	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764322	39764322	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	173	544	0	ENST00000288319.7:c.790G>T	p.Gly264Cys	p.G264C	ENST00000288319	NM_182918.3	264	Ggc/Tgc	7/10	0.014199688996599	4	FACETS	0.986	0.908	1	0.986	0.908	1	INDETERMINATE	2	TRUE	2	0.244713359615209	4		544	892	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155495	47155495	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0038020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	56	216	0	ENST00000409792.3:c.4587-1G>T		p.X1529_splice	ENST00000409792	NM_014159.6	1529			0.174156550723811	2	FACETS	0.817	0.706	0.937	0.817	0.706	0.937	CLONAL	2	TRUE	0	0.244713359615209	2		216	280	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876105	35876105	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	39	350	0	ENST00000303115.3:c.897T>A	p.Asn299Lys	p.N299K	ENST00000303115	NM_002185.3	299	aaT/aaA	8/8	0.186590251730438	3	FACETS	0.964	0.801	1	0.482	0.4	0.573	CLONAL	1	TRUE	1	0.244713359615209	3		350	371	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502640	149502640	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	70	401	0	ENST00000261799.4:c.2148del	p.Tyr716Ter	p.Y716*	ENST00000261799	NM_002609.3	716	taC/ta	15/23	0.186590251730438	3	FACETS	1	0.966	1	0.665	0.581	0.755	CLONAL	1	TRUE	1	0.244713359615209	3		401	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0038048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	228	559	0	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.529208820212706	2	FACETS	0.785	0.741	0.829	0.785	0.741	0.829	SUBCLONAL	2	TRUE	0	0.63409305739431	2		559	458	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872461	35872461	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	94	518	1	ENST00000216797.5:c.442del	p.Leu148TyrfsTer16	p.L148Yfs*16	ENST00000216797	NM_020529.2	148	Cta/ta	3/6	0.308271987633848	1	FACETS	0.392	0.35	0.437	0.392	0.35	0.437	INDETERMINATE	1	TRUE	0	0.63409305739431	1		519	516	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599874	10599874	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	204	651	0	ENST00000171111.5:c.1702G>T	p.Val568Phe	p.V568F	ENST00000171111	NM_203500.1	568	Gtc/Ttc	5/6	0.585034063018876	1	FACETS	0.835	0.782	0.89	0.835	0.782	0.89	CLONAL	1	TRUE	0	0.63409305739431	1		651	526	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955585	90955585	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	60	333	0	ENST00000265433.3:c.2080C>T	p.Pro694Ser	p.P694S	ENST00000265433	NM_002485.4	694	Cct/Tct	14/16	0.189685551956794	2	FACETS	0.447	0.386	0.513	0.224	0.193	0.257	INDETERMINATE	1	TRUE	0	0.63409305739431	2		333	423	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028423	42028423	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	117	328	0	ENST00000219905.7:c.3961A>G	p.Thr1321Ala	p.T1321A	ENST00000219905	NM_001164273.1	1321	Act/Gct	13/24	1	2	FACETS	0.941	0.857	1	0.941	0.857	1	CLONAL	1	TRUE	1	0.63409305739431	2		328	392	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884226	37884226	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	46	656	0	ENST00000269571.5:c.3697C>A	p.Pro1233Thr	p.P1233T	ENST00000269571		1233	Cca/Aca	27/27	0.529208820212706	2	FACETS	0.245	0.206	0.289	0.123	0.103	0.145	SUBCLONAL	1	TRUE	0	0.63409305739431	2		656	591	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435889	56435889	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	137	494	0	ENST00000407977.2:c.1248G>T	p.Trp416Cys	p.W416C	ENST00000407977		416	tgG/tgT	9/10	0.529208820212706	2	FACETS	1	0.988	1	0.706	0.653	0.76	CLONAL	1	TRUE	0	0.63409305739431	2		494	306	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313511	30313511	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0038048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	133	480	0	ENST00000262643.3:c.1110+1G>T		p.X370_splice	ENST00000262643	NM_001238.2	370			0.585034063018876	1	FACETS	0.816	0.751	0.883	0.816	0.751	0.883	CLONAL	1	TRUE	0	0.63409305739431	1		480	351	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964971	25964971	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	139	444	1	ENST00000435504.4:c.4235G>T	p.Gly1412Val	p.G1412V	ENST00000435504		1412	gGc/gTc	13/13	0.162318041763911	2	FACETS	0.772	0.706	0.841	0.386	0.353	0.421	INDETERMINATE	1	TRUE	0	0.63409305739431	2		445	568	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111659	56111659	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	70	202	0	ENST00000399503.3:c.259T>G	p.Ser87Ala	p.S87A	ENST00000399503	NM_005921.1	87	Tcc/Gcc	1/20	0.585034063018876	1	FACETS	0.705	0.625	0.788	0.705	0.625	0.788	SUBCLONAL	1	TRUE	0	0.63409305739431	1		202	214	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168985	32168985	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	204	792	0	ENST00000375023.3:c.4048A>C	p.Lys1350Gln	p.K1350Q	ENST00000375023	NM_004557.3	1350	Aag/Cag	22/30	0.50884925885163	1	FACETS	0.843	0.789	0.899	0.843	0.789	0.899	CLONAL	1	TRUE	0	0.63409305739431	1		792	521	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271274	38271274	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	178	771	0	ENST00000425967.3:c.2434C>T	p.Pro812Ser	p.P812S	ENST00000425967	NM_001174067.1	812	Ccc/Tcc	19/19	0.353767835515254	1	FACETS	0.7	0.649	0.752	0.7	0.649	0.752	INDETERMINATE	1	TRUE	0	0.63409305739431	1		771	548	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878894	117878894	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	77	265	0	ENST00000297338.2:c.75G>T	p.Lys25Asn	p.K25N	ENST00000297338	NM_006265.2	25	aaG/aaT	2/14	0.189685551956794	2	FACETS	0.513	0.452	0.579	0.257	0.226	0.29	INDETERMINATE	1	TRUE	0	0.63409305739431	2		265	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0038068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	178	663	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.24743097161688	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	0	0.294530255363433	2		663	603	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220706	1220706	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555738475	NA	P-0038068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	111	556	0	ENST00000326873.7:c.727del	p.Val243SerfsTer44	p.V243Sfs*44	ENST00000326873	NM_000455.4	242	Ggg/gg	5/10	0.294530255363433	1	FACETS	0.908	0.825	0.994	1	0.988	1	CLONAL	2	TRUE	0	0.294530255363433	1		556	354	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467974	66467974	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	30	229	0	ENST00000273854.3:c.295T>C	p.Tyr99His	p.Y99H	ENST00000273854	NM_004439.5	99	Tac/Cac	3/18	0.294530255363433	2	FACETS	0.787	0.636	0.955	0.393	0.318	0.478	CLONAL	1	TRUE	0	0.294530255363433	2		229	259	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729600	41729600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	74	409	0	ENST00000242208.4:c.929G>A	p.Arg310Gln	p.R310Q	ENST00000242208	NM_002192.2	310	cGg/cAg	3/3	0.281657232906346	3	FACETS	1	0.975	1	0.732	0.644	0.825	CLONAL	1	TRUE	1	0.294530255363433	3		409	394	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867041	45867041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038252-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	263	622	0	ENST00000391945.4:c.1078G>A	p.Gly360Ser	p.G360S	ENST00000391945	NM_000400.3	360	Ggc/Agc	11/23	0.768472286978522	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.788171550670528	1		622	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578525	7578525	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519976	NA	P-0038252-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	358	699	0	ENST00000269305.4:c.405C>G	p.Cys135Trp	p.C135W	ENST00000269305	NM_001126112.2	135	tgC/tgG	5/11	0.675842972457008	1	FACETS	0.981	0.944	1	0.981	0.944	1	CLONAL	1	TRUE	0	0.788171550670528	1		699	561	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441436	52441436	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038252-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	347	903	2	ENST00000460680.1:c.416del	p.Lys139ArgfsTer48	p.K139Rfs*48	ENST00000460680	NM_004656.3	139	aAg/ag	6/17	0.754742612257613	1	FACETS	0.972	0.934	1	0.972	0.934	1	CLONAL	1	TRUE	0	0.788171550670528	1		905	549	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354573	91354573	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038252-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	203	530	0	ENST00000355112.3:c.4013A>G	p.Lys1338Arg	p.K1338R	ENST00000355112	NM_000057.2	1338	aAg/aGg	21/22	1	2	FACETS	0.788	0.734	0.843	0.788	0.734	0.843	SUBCLONAL	1	TRUE	1	0.788171550670528	2		530	654	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	273	331	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.104247110346259	4	FACETS	0.887	0.838	0.936	1	0.992	1	INDETERMINATE	3	FALSE	2	0.44164467188023	4		335	670	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	198	647	2	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.881	0.823	0.939	1	0.993	1	CLONAL	2	FALSE	1	0.44164467188023	2		649	509	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918921	76918921	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	82	274	0	ENST00000373344.5:c.4070del	p.Lys1357ArgfsTer18	p.K1357Rfs*18	ENST00000373344	NM_000489.3	1357	aAg/ag	12/35	0.440792915582974	2	FACETS	0.906	0.803	1			1	CLONAL	1	FALSE	NA	0.44164467188023	2		274	410	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	79	537	1	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	0.44164467188023	0	FACETS	1	0.901	1			1	CLONAL	1	FALSE	0	0.44164467188023	0		538	199	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	70	166	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.44164467188023	2		166	214	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	108	658	2	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	0.481	0.431	0.535	0.481	0.431	0.535	SUBCLONAL	1	FALSE	1	0.44164467188023	2		660	1017	SUCCESS
APC	324	MSKCC	GRCh37	5	112175651	112175651	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	120	285	0	ENST00000257430.4:c.4364del	p.Asn1455IlefsTer18	p.N1455Ifs*18	ENST00000257430	NM_000038.5	1454	Aaa/aa	16/16	0.433351006841522	0	FACETS		NA	1			1	NA	3	FALSE	0	0.44164467188023	0		285	159	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	167	646	10	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	0.44164467188023	0	FACETS	0.809	0.764	0.853			1	CLONAL	2	FALSE	0	0.44164467188023	0		656	261	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	525	565	1	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	0.44164467188023	5	FACETS	1	0.972	1	1	0.997	1	CLONAL	3	FALSE	3	0.44164467188023	5		566	1298	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793211	139793212	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748531430	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	436	662	1	ENST00000247668.2:c.26dup	p.Gly10TrpfsTer70	p.G10Wfs*70	ENST00000247668	NM_021138.3	7	acc/aCcc	2/11	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	FALSE	1	0.44164467188023	2		663	1367	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430775	78430775	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	250	436	0	ENST00000370768.2:c.614del	p.Gly205GlufsTer17	p.G205Efs*17	ENST00000370768	NM_003902.3	205	gGa/ga	8/20	0.21214033030446	4	FACETS	0.882	0.831	0.933	1	0.992	1	INDETERMINATE	3	FALSE	2	0.44164467188023	4		436	617	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103487	77103487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs996658283	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	78	275	0	ENST00000356341.3:c.79G>A	p.Gly27Ser	p.G27S	ENST00000356341	NM_002576.4	27	Ggc/Agc	2/15	0.21214033030446	4	FACETS	0.688	0.604	0.779	0.344	0.302	0.39	INDETERMINATE	1	FALSE	2	0.44164467188023	4		275	740	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620542	52620542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	346	441	2	ENST00000394830.3:c.3211C>T	p.Arg1071Cys	p.R1071C	ENST00000394830	NM_018313.4	1071	Cgc/Tgc	21/30	0.281490779188	4	FACETS	0.948	0.903	0.994	1	0.995	1	CLONAL	3	FALSE	2	0.44164467188023	4		443	794	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944961	31944961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1441610501	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	278	550	0	ENST00000340398.3:c.140C>T	p.Ala47Val	p.A47V	ENST00000340398	NM_001013699.2	47	gCg/gTg	1/1	0.36341039167245	0	FACETS	0.553	0.523	0.582			1	SUBCLONAL	2	FALSE	0	0.44164467188023	0		550	636	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100934	27100934	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	271	584	1	ENST00000324856.7:c.4220del	p.Pro1407GlnfsTer74	p.P1407Qfs*74	ENST00000324856	NM_006015.4	1406	Ccc/cc	18/20	0.21214033030446	4	FACETS	1	0.99	1	1	0.99	1	INDETERMINATE	2	FALSE	2	0.44164467188023	4		585	723	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639588	47639588	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63749897	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	222	307	0	ENST00000233146.2:c.687del	p.Ala230LeufsTer16	p.A230Lfs*16	ENST00000233146	NM_000251.2	227	agA/ag	4/16	0.269386538777777	0	FACETS		NA	1			1	NA	3	FALSE	0	0.44164467188023	0		307	264	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631917	90631918	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs747216375	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	503	770	2	ENST00000330062.3:c.435dup	p.Thr146AspfsTer126	p.T146Dfs*126	ENST00000330062	NM_002168.2	145	-/G	4/11	NA	2	FACETS	0.844	0.809	0.88			1	INDETERMINATE	2	FALSE	NA	0.44164467188023	2		772	1349	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572092	64572093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767319284	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	424	795	1	ENST00000312049.6:c.1546dup	p.Arg516ProfsTer15	p.R516Pfs*15	ENST00000312049	NM_130799.2	516	cgg/cCgg	10/10	0.21214033030446	4	FACETS	0.848	0.81	0.887	1	0.994	1	INDETERMINATE	3	FALSE	2	0.44164467188023	4		796	1088	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69203005	69203005	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	318	370	1	ENST00000462284.1:c.32A>G	p.Asn11Ser	p.N11S	ENST00000462284	NM_002392.5	11	aAc/aGc	2/11	1	2	FACETS	0.909	0.862	0.956	1	0.996	1	CLONAL	2	FALSE	1	0.44164467188023	2		371	792	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1257	109	896	2	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.361	0.323	0.402	0.361	0.323	0.402	SUBCLONAL	1	FALSE	1	0.44164467188023	2		898	1366	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2492097	2492097	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs772088410	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	423	704	1	ENST00000355716.4:c.500del	p.Pro167ArgfsTer23	p.P167Rfs*23	ENST00000355716	NM_003820.2	165	tgC/tg	5/8	0.269386538777777	0	FACETS	1	0.976	1			1	CLONAL	1	FALSE	0	0.44164467188023	0		705	1038	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71050182	71050182	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1477164140	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	242	250	0	ENST00000318789.4:c.1003G>A	p.Asp335Asn	p.D335N	ENST00000318789	NM_032682.5	335	Gat/Aat	13/21	0.281490779188	4	FACETS	0.986	0.931	1	1	0.993	1	CLONAL	3	FALSE	2	0.44164467188023	4		250	534	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497907	25497907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	241	568	0	ENST00000264709.3:c.542G>A	p.Arg181His	p.R181H	ENST00000264709	NM_175629.2	181	cGt/cAt	6/23	0.210210659098426	0	FACETS	0.554	0.522	0.586			1	INDETERMINATE	2	FALSE	0	0.44164467188023	0		568	550	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435151	110435151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	279	634	0	ENST00000375856.3:c.3250C>T	p.Pro1084Ser	p.P1084S	ENST00000375856	NM_003749.2	1084	Ccg/Tcg	1/2	1	2	FACETS	0.995	0.942	1	1	0.996	1	CLONAL	2	FALSE	1	0.44164467188023	2		634	635	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560133	29560133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199474732	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	201	285	0	ENST00000356175.3:c.3610C>T	p.Arg1204Trp	p.R1204W	ENST00000356175	NM_000267.3	1204	Cgg/Tgg	27/57	0.391764850747912	5	FACETS	0.966	0.903	1			1	CLONAL	3	FALSE	NA	0.44164467188023	5		285	522	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434086	121434086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369764257	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	459	557	0	ENST00000257555.6:c.977C>T	p.Ala326Val	p.A326V	ENST00000257555		326	gCg/gTg	5/10	1	2	FACETS	1	0.983	1	1	0.997	1	CLONAL	2	FALSE	1	0.44164467188023	2		557	996	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798138	45798138	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057517765	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	520	723	0	ENST00000450313.1:c.713A>G	p.Asn238Ser	p.N238S	ENST00000450313	NM_012222.2	238	aAc/aGc	9/16	0.21214033030446	4	FACETS	0.874	0.839	0.909	1	0.996	1	INDETERMINATE	3	FALSE	2	0.44164467188023	4		723	1295	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114901061	114901061	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	241	380	0	ENST00000543371.1:c.671T>C	p.Val224Ala	p.V224A	ENST00000543371	NM_001198531.1	224	gTa/gCa	6/14	0.104247110346259	4	FACETS	0.948	0.894	1	1	0.993	1	INDETERMINATE	3	FALSE	2	0.44164467188023	4		380	553	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066733	77066733	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	187	232	0	ENST00000356341.3:c.752A>T	p.Glu251Val	p.E251V	ENST00000356341	NM_002576.4	251	gAg/gTg	7/15	0.21214033030446	4	FACETS	0.839	0.782	0.897	1	0.987	1	INDETERMINATE	3	FALSE	2	0.44164467188023	4		232	485	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076701	102076701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530664620	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	289	475	0	ENST00000282441.5:c.880G>A	p.Val294Ile	p.V294I	ENST00000282441	NM_001130145.2	294	Gtc/Atc	5/9	0.44164467188023	6	FACETS	0.954	0.904	1			1	CLONAL	4	FALSE	NA	0.44164467188023	6		475	646	SUCCESS
ATM	472	MSKCC	GRCh37	11	108099976	108099976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755326770	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	144	227	1	ENST00000278616.4:c.257C>T	p.Thr86Ile	p.T86I	ENST00000278616	NM_000051.3	86	aCa/aTa	4/63	NA	2	FACETS	0.786	0.724	0.849			1	INDETERMINATE	2	FALSE	NA	0.44164467188023	2		228	415	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362639	118362639	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782779521	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	234	300	2	ENST00000534358.1:c.5000G>A	p.Arg1667Gln	p.R1667Q	ENST00000534358	NM_005933.3	1667	cGg/cAg	15/36	0.268330387250166	5	FACETS	1	0.986	1			1	CLONAL	3	FALSE	NA	0.44164467188023	5		302	511	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373152	118373152	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	54	332	0	ENST00000534358.1:c.6545G>A	p.Gly2182Asp	p.G2182D	ENST00000534358	NM_005933.3	2182	gGt/gAt	27/36	0.268330387250166	5	FACETS	0.808	0.691	0.936			1	CLONAL	1	FALSE	NA	0.44164467188023	5		332	503	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438191	49438191	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780507577	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	455	653	0	ENST00000301067.7:c.5078G>A	p.Arg1693Gln	p.R1693Q	ENST00000301067	NM_003482.3	1693	cGg/cAg	20/54	0.44164467188023	5	FACETS	1	0.988	1	1	0.997	1	CLONAL	3	FALSE	3	0.44164467188023	5		653	1061	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937324	32937324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs431825362	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	36	258	0	ENST00000380152.3:c.7985C>T	p.Thr2662Met	p.T2662M	ENST00000380152		2662	aCg/aTg	18/27	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	1	0.44164467188023	2		258	127	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435298	110435299	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	137	238	2	ENST00000375856.3:c.3102_3103delinsAT	p.Pro1035Ser	p.P1035S	ENST00000375856	NM_003749.2	1034	ccGCcg/ccATcg	1/2	1	2	FACETS	1	0.967	1	1	0.992	1	CLONAL	2	FALSE	1	0.44164467188023	2		240	288	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831249	72831249	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	22	395	2	ENST00000268489.5:c.5332C>A	p.Pro1778Thr	p.P1778T	ENST00000268489	NM_006885.3	1778	Cct/Act	9/10	0.14382178895635	0	FACETS	0.255	0.198	0.321			1	INDETERMINATE	1	FALSE	0	0.44164467188023	0		397	218	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354386	40354386	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	505	1014	0	ENST00000293328.3:c.2209del	p.Gln737ArgfsTer29	p.Q737Rfs*29	ENST00000293328	NM_012448.3	737	Cag/ag	18/19	0.104247110346259	4	FACETS	0.92	0.883	0.957	1	0.996	1	INDETERMINATE	3	FALSE	2	0.44164467188023	4		1014	1195	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40451823	40451823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374346157	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	203	505	1	ENST00000345506.4:c.605C>T	p.Thr202Met	p.T202M	ENST00000345506	NM_003152.3	202	aCg/aTg	7/20	0.104247110346259	4	FACETS	0.94	0.881	0.999	1	0.991	1	INDETERMINATE	3	FALSE	2	0.44164467188023	4		506	470	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384940	17384940	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	485	813	0	ENST00000359435.4:c.490C>T	p.Arg164Cys	p.R164C	ENST00000359435	NM_001033549.1	164	Cgc/Tgc	5/9	1	2	FACETS	1	0.967	1	1	0.997	1	CLONAL	2	FALSE	1	0.44164467188023	2		813	1089	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224408	36224408	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs142520534	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	405	939	0	ENST00000222270.7:c.6958G>A	p.Gly2320Arg	p.G2320R	ENST00000222270	NM_014727.1	2320	Ggg/Agg	28/37	1	2	FACETS	0.967	0.924	1	1	0.997	1	CLONAL	2	FALSE	1	0.44164467188023	2		939	948	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796577	42796578	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	375	747	0	ENST00000575354.2:c.3138dup	p.Pro1047AlafsTer104	p.P1047Afs*104	ENST00000575354	NM_015125.3	1045	ctg/ctGg	13/20	1	2	FACETS	0.937	0.893	0.982	1	0.996	1	CLONAL	2	FALSE	1	0.44164467188023	2		747	906	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636959	158636959	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	267	492	0	ENST00000263640.3:c.221A>G	p.Tyr74Cys	p.Y74C	ENST00000263640	NM_001105.4	74	tAt/tGt	4/11	0.104247110346259	4	FACETS	0.897	0.847	0.947	1	0.993	1	INDETERMINATE	3	FALSE	2	0.44164467188023	4		492	648	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610563	215610563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782279	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	88	346	0	ENST00000260947.4:c.1693C>T	p.Arg565Cys	p.R565C	ENST00000260947	NM_000465.2	565	Cgt/Tgt	8/11	0.44164467188023	0	FACETS	0.849	0.763	0.938			1	CLONAL	1	FALSE	0	0.44164467188023	0		346	262	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500551	149500551	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	401	550	0	ENST00000261799.4:c.2486C>T	p.Ala829Val	p.A829V	ENST00000261799	NM_002609.3	829	gCt/gTt	18/23	1	2	FACETS	1	0.984	1	1	0.997	1	CLONAL	2	FALSE	1	0.44164467188023	2		550	858	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908284	41908284	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	401	631	0	ENST00000372991.4:c.238del	p.Leu80TrpfsTer3	p.L80Wfs*3	ENST00000372991	NM_001760.3	80	Ctg/tg	2/5	0.253832629286909	5	FACETS	1	0.98	1	1	0.98	1	INDETERMINATE	3	FALSE	2	0.44164467188023	5		631	963	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860413	151860413	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	247	504	1	ENST00000262189.6:c.10249C>T	p.Gln3417Ter	p.Q3417*	ENST00000262189	NM_170606.2	3417	Cag/Tag	43/59	1	2	FACETS	0.958	0.903	1	1	0.995	1	CLONAL	2	FALSE	1	0.44164467188023	2		505	584	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282179	38282179	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	271	619	0	ENST00000425967.3:c.877C>G	p.Pro293Ala	p.P293A	ENST00000425967	NM_001174067.1	293	Ccc/Gcc	8/19	0.260895903929162	2	FACETS	1	0.99	1	0.624	0.586	0.663	INDETERMINATE	1	FALSE	0	0.44164467188023	2		619	983	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68999990	68999990	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	75	470	0	ENST00000288368.4:c.2059C>G	p.Leu687Val	p.L687V	ENST00000288368	NM_024870.2	687	Ctt/Gtt	19/40	0.44164467188023	0	FACETS	0.556	0.491	0.625			1	SUBCLONAL	1	FALSE	0	0.44164467188023	0		470	341	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520260	9520260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038959-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	269	571	0	ENST00000353224.5:c.2009C>T	p.Ser670Phe	p.S670F	ENST00000353224	NM_177990.2	670	tCt/tTt	10/10	1	2	FACETS	0.986	0.933	1	0.986	0.933	1	CLONAL	1	TRUE	1	0.920249666941599	2		571	593	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129303	152129303	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038959-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	196	690	0	ENST00000206249.3:c.256G>A	p.Ala86Thr	p.A86T	ENST00000206249	NM_000125.3	86	Gct/Act	1/8	0.920249666941599	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.920249666941599	1		690	229	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518783	176518784	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0038959-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	190	698	0	ENST00000292408.4:c.701_702delinsAT	p.Arg234His	p.R234H	ENST00000292408	NM_213647.1	234	cGC/cAT	6/18	0.626364155248499	1	FACETS	0.719	0.68	0.757	0.719	0.68	0.757	SUBCLONAL	1	TRUE	0	0.920249666941599	1		698	310	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88678994	88678994	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	51	146	0	ENST00000372037.3:c.934C>G	p.His312Asp	p.H312D	ENST00000372037	NM_004329.2	312	Cat/Gat	10/13	1	2	FACETS	0.819	0.711	0.931	0.819	0.711	0.931	CLONAL	1	TRUE	1	0.830700216125016	2		146	150	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544711	65544711	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	308	543	0	ENST00000358664.4:c.215del	p.Gln72ArgfsTer98	p.Q72Rfs*98	ENST00000358664	NM_002382.4	72	cAg/cg	4/5	0.830700216125016	1	FACETS	0.963	0.926	1	0.963	0.926	1	CLONAL	1	TRUE	0	0.830700216125016	1		543	450	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46602858	46602858	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	361	571	0	ENST00000263734.3:c.916C>T	p.Gln306Ter	p.Q306*	ENST00000263734	NM_001430.4	306	Cag/Tag	8/16	0.536417643065666	1	FACETS	0.715	0.683	0.746	0.715	0.683	0.746	SUBCLONAL	1	TRUE	0	0.830700216125016	1		571	711	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0039031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	283	471	1	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.23305440020831	5	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	TRUE	2	0.23305440020831	5		472	1020	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026643	6026643	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs63750947	NA	P-0039031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1405	106	1137	3	ENST00000265849.7:c.1753C>A	p.Leu585Ile	p.L585I	ENST00000265849	NM_000535.5	585	Ctt/Att	11/15	1	2	FACETS	0.602	0.537	0.671	0.602	0.537	0.671	SUBCLONAL	1	TRUE	1	0.23305440020831	2		1140	1511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576901	7576901	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	46	586	0	ENST00000269305.4:c.945del	p.Gln317SerfsTer28	p.Q317Sfs*28	ENST00000269305	NM_001126112.2	315	tcT/tc	9/11	1	2	FACETS	0.554	0.465	0.652	0.554	0.465	0.652	SUBCLONAL	1	TRUE	1	0.23305440020831	2		586	713	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104715	69104715	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	90	519	0	ENST00000288368.4:c.4559G>C	p.Arg1520Thr	p.R1520T	ENST00000288368	NM_024870.2	1520	aGg/aCg	37/40	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.23305440020831	2		519	653	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227821	53227821	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0039031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	94	364	0	ENST00000375401.3:c.2369-2A>C		p.X790_splice	ENST00000375401	NM_004187.3	790			0.23305440020831	2	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.23305440020831	2		364	576	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712526	43712526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767934572	NA	P-0039219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	107	631	1	ENST00000382044.4:c.4658C>T	p.Ser1553Leu	p.S1553L	ENST00000382044	NM_001141980.1	1553	tCg/tTg	21/28	0.526834497987711	1	FACETS	0.428	0.384	0.475	0.428	0.384	0.475	SUBCLONAL	1	FALSE	0	0.526834497987711	1		632	699	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834557	156834557	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	257	746	0	ENST00000524377.1:c.325G>T	p.Asp109Tyr	p.D109Y	ENST00000524377	NM_002529.3	109	Gat/Tat	3/17	1	2	FACETS	0.917	0.859	0.977	0.917	0.859	0.977	CLONAL	1	FALSE	1	0.526834497987711	2		746	1064	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005533	42005533	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	220	488	0	ENST00000219905.7:c.3270del	p.Gly1092GlufsTer41	p.G1092Efs*41	ENST00000219905	NM_001164273.1	1090	gTt/gt	9/24	0.526834497987711	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	0	0.526834497987711	1		488	599	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233459	69233459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2144	142	354	0	ENST00000462284.1:c.1324G>A	p.Glu442Lys	p.E442K	ENST00000462284	NM_002392.5	442	Gaa/Aaa	11/11	0.285502425914887	32	FACETS	1	0.968	1			1	CLONAL	2	TRUE	NA	0.285502425914887	32		354	2286	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754505	42754505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1174086151	NA	P-0039257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	80	709	0	ENST00000222329.4:c.235G>A	p.Asp79Asn	p.D79N	ENST00000222329	NM_006494.2	79	Gac/Aac	2/4	0.285502425914887	3	FACETS	0.74	0.65	0.836	0.37	0.325	0.418	SUBCLONAL	1	TRUE	1	0.285502425914887	3		709	866	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155259	55155259	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	65	470	0	ENST00000257290.5:c.2858T>G	p.Leu953Arg	p.L953R	ENST00000257290	NM_006206.4	953	cTg/cGg	21/23	1	2	FACETS	0.882	0.766	1	0.882	0.766	1	CLONAL	1	TRUE	1	0.285502425914887	2		470	516	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0039397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	173	413	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.177340484328395	5	FACETS	1	0.976	1	1	0.991	1	CLONAL	4	FALSE	2	0.229694331862414	5		414	454	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837936	156837936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141629165	NA	P-0039397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	78	812	1	ENST00000524377.1:c.469C>T	p.Arg157Cys	p.R157C	ENST00000524377	NM_002529.3	157	Cgc/Tgc	5/17	0.229694331862414	4	FACETS	0.868	0.761	0.984	0.289	0.253	0.328	CLONAL	1	FALSE	1	0.229694331862414	4		813	962	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239501	123239501	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	140	842	0	ENST00000358487.5:c.2336A>T	p.Tyr779Phe	p.Y779F	ENST00000358487	NM_000141.4	779	tAt/tTt	18/18	0.199375766066478	3	FACETS	0.978	0.892	1	0.978	0.892	1	CLONAL	2	FALSE	1	0.229694331862414	3		842	695	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204831	94204831	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	47	500	4	ENST00000323929.3:c.754G>T	p.Ala252Ser	p.A252S	ENST00000323929	NM_005591.3	252	Gct/Tct	8/20	0.199375766066478	3	FACETS	1	0.867	1	1	0.867	1	CLONAL	2	FALSE	1	0.229694331862414	3		504	224	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249236	133249236	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	80	699	1	ENST00000320574.5:c.1663G>T	p.Asp555Tyr	p.D555Y	ENST00000320574	NM_006231.2	555	Gat/Tat	15/49	0.229694331862414	3	FACETS	1	0.933	1	0.545	0.479	0.615	CLONAL	1	FALSE	1	0.229694331862414	3		700	713	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913438	32913438	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	57	585	0	ENST00000380152.3:c.4946A>G	p.Lys1649Arg	p.K1649R	ENST00000380152		1649	aAa/aGa	11/27	0.229694331862414	2	FACETS	0.83	0.717	0.951	0.83	0.717	0.951	CLONAL	2	FALSE	0	0.229694331862414	2		585	299	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059447	42059448	+	missense_variant	Missense_Mutation	DNP	CG	CG	TC	novel	NA	P-0039397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	118	445	2	ENST00000219905.7:c.9167_9168delinsTC	p.Ser3056Phe	p.S3056F	ENST00000219905	NM_001164273.1	3056	tCG/tTC	24/24	0.229694331862414	3	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	FALSE	1	0.229694331862414	3		447	540	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992319	72992319	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs748909927	NA	P-0039397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	191	875	1	ENST00000268489.5:c.1726G>T	p.Gly576Cys	p.G576C	ENST00000268489	NM_006885.3	576	Ggc/Tgc	2/10	0.199375766066478	3	FACETS	0.976	0.902	1	0.976	0.902	1	CLONAL	2	FALSE	1	0.229694331862414	3		876	950	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0039397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	181	695	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.229694331862414	3	FACETS	0.964	0.89	1	0.964	0.89	1	CLONAL	2	FALSE	1	0.229694331862414	3		695	911	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0039397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	103	650	2	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	0.229694331862414	3	FACETS	1	0.974	1	0.641	0.573	0.713	CLONAL	1	FALSE	1	0.229694331862414	3		652	780	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248530	212248530	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	40	648	1	ENST00000342788.4:c.3737G>T	p.Ser1246Ile	p.S1246I	ENST00000342788	NM_005235.2	1246	aGc/aTc	28/28	0.229694331862414	3	FACETS	0.574	0.476	0.684	0.287	0.238	0.342	SUBCLONAL	1	FALSE	1	0.229694331862414	3		649	676	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678777	52678777	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	91	365	0	ENST00000394830.3:c.842A>G	p.Tyr281Cys	p.Y281C	ENST00000394830	NM_018313.4	281	tAt/tGt	9/30	0.229694331862414	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	FALSE	1	0.229694331862414	3		365	354	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455600	189455600	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	77	600	0	ENST00000264731.3:c.134A>G	p.Gln45Arg	p.Q45R	ENST00000264731	NM_003722.4	45	cAg/cGg	2/14	0.229694331862414	5	FACETS	0.846	0.748	0.95	0.846	0.748	0.95	CLONAL	3	FALSE	2	0.229694331862414	5		600	355	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127397	55127397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	49	702	0	ENST00000257290.5:c.185C>T	p.Ser62Phe	p.S62F	ENST00000257290	NM_006206.4	62	tCt/tTt	3/23	0.229694331862414	2	FACETS	0.686	0.58	0.803	0.343	0.29	0.402	SUBCLONAL	1	FALSE	0	0.229694331862414	2		702	622	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144543	55144543	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	56	499	0	ENST00000257290.5:c.2017A>G	p.Ile673Val	p.I673V	ENST00000257290	NM_006206.4	673	Atc/Gtc	15/23	0.229694331862414	2	FACETS	0.989	0.848	1	0.495	0.424	0.571	CLONAL	1	FALSE	0	0.229694331862414	2		499	493	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542365	187542365	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	31	444	0	ENST00000441802.2:c.5375T>A	p.Leu1792Gln	p.L1792Q	ENST00000441802	NM_005245.3	1792	cTg/cAg	10/27	0.199375766066478	3	FACETS	0.909	0.737	1	0.455	0.368	0.552	CLONAL	1	FALSE	1	0.229694331862414	3		444	331	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955088	93955088	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	31	448	1	ENST00000369303.4:c.2810T>C	p.Met937Thr	p.M937T	ENST00000369303	NM_004440.3	937	aTg/aCg	16/17	0.229694331862414	3	FACETS	1	0.941	1	0.727	0.592	0.877	CLONAL	1	FALSE	1	0.229694331862414	3		449	207	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630137	100630137	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	179	512	1	ENST00000308731.7:c.136C>A	p.Arg46Ser	p.R46S	ENST00000308731	NM_000061.2	46	Cgt/Agt	2/19	0.229694331862414	3	FACETS	0.987	0.92	1	1	0.989	1	CLONAL	4	FALSE	0	0.229694331862414	3		513	440	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732533	74732533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	30	192	0	ENST00000359995.5:c.376C>T	p.Arg126Cys	p.R126C	ENST00000359995	NM_001195427.1	126	Cgc/Tgc	2/3	0.211574859402485	3	FACETS	1	0.858	1	0.538	0.435	0.655	CLONAL	1	TRUE	1	0.212598072955679	3		192	290	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610247	10610247	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	110	717	0	ENST00000171111.5:c.463G>T	p.Val155Phe	p.V155F	ENST00000171111	NM_203500.1	155	Gtc/Ttc	2/6	0.212598072955679	1	FACETS	0.856	0.768	0.951	0.856	0.768	0.951	CLONAL	1	TRUE	0	0.212598072955679	1		717	1080	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220370	1220370	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0039409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	94	531	0	ENST00000326873.7:c.465-2A>T		p.X155_splice	ENST00000326873	NM_000455.4	155			0.212598072955679	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.212598072955679	1		531	724	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424679	47424679	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775921012	NA	P-0039409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	123	639	0	ENST00000377045.4:c.487G>A	p.Gly163Arg	p.G163R	ENST00000377045	NM_001654.4	163	Gga/Aga	6/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.212598072955679	2		639	1005	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597395	10597395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	139	728	0	ENST00000171111.5:c.1808G>A	p.Gly603Glu	p.G603E	ENST00000171111	NM_203500.1	603	gGg/gAg	6/6	0.212598072955679	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.212598072955679	1		728	1116	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387662	17387662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	106	638	1	ENST00000359435.4:c.730G>T	p.Asp244Tyr	p.D244Y	ENST00000359435	NM_001033549.1	244	Gac/Tac	8/9	0.212598072955679	1	FACETS	0.924	0.827	1	0.924	0.827	1	CLONAL	1	TRUE	0	0.212598072955679	1		639	964	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190792	106190792	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	84	466	0	ENST00000380013.4:c.4070A>T	p.Glu1357Val	p.E1357V	ENST00000380013	NM_001127208.2	1357	gAg/gTg	9/11	1	2	FACETS	0.993	0.876	1	0.993	0.876	1	CLONAL	1	TRUE	1	0.212598072955679	2		466	796	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424293	47424293	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	76	584	0	ENST00000377045.4:c.298A>T	p.Asn100Tyr	p.N100Y	ENST00000377045	NM_001654.4	100	Aat/Tat	4/16	1	2	FACETS	0.834	0.73	0.946	0.834	0.73	0.946	CLONAL	1	TRUE	1	0.212598072955679	2		584	857	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0039465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	65	544	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.779	0.678	0.889	1	0.973	1	SUBCLONAL	2	TRUE	1	0.19	2		545	439	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	33	309	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.957	0.78	1	0.957	0.78	1	CLONAL	1	TRUE	1	0.19	2		309	363	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0039465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	12	301	0	ENST00000288602.6:c.1397G>T	p.Gly466Val	p.G466V	ENST00000288602	NM_004333.4	466	gGa/gTa	11/18	1	2	FACETS	0.347	0.243	0.476	0.347	0.243	0.476	SUBCLONAL	1	TRUE	1	0.19	2		301	364	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0039465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	56	191	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.19	2		191	509	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141502	11141502	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	56	635	0	ENST00000358026.2:c.3479G>T	p.Gly1160Val	p.G1160V	ENST00000358026	NM_001128849.1	1160	gGg/gTg	25/36	1	2	FACETS	0.888	0.76	1	0.888	0.76	1	CLONAL	1	TRUE	1	0.19	2		635	664	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127733	64127733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	51	693	0	ENST00000334205.4:c.226G>A	p.Ala76Thr	p.A76T	ENST00000334205	NM_003942.2	76	Gcc/Acc	3/17	1	2	FACETS	0.822	0.698	0.959	0.822	0.698	0.959	CLONAL	1	TRUE	1	0.19	2		693	653	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857470	9857470	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	26	409	0	ENST00000330684.3:c.3931A>G	p.Ile1311Val	p.I1311V	ENST00000330684	NM_001134407.1	1311	Ata/Gta	13/13	1	2	FACETS	0.713	0.564	0.883	0.713	0.564	0.883	SUBCLONAL	1	TRUE	1	0.19	2		409	384	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101073	4101073	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs756402608	NA	P-0039465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	19	371	0	ENST00000262948.5:c.649G>T	p.Gly217Cys	p.G217C	ENST00000262948	NM_030662.3	217	Ggc/Tgc	6/11	1	2	FACETS	0.601	0.455	0.772	0.601	0.455	0.772	SUBCLONAL	1	TRUE	1	0.19	2		371	333	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210740	5210741	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0039465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	61	664	1	ENST00000357368.4:c.5310_5311del	p.Asn1771GlnfsTer94	p.N1771Qfs*94	ENST00000357368	NM_002850.3	1770	gaGAac/gaac	34/38	1	2	FACETS	0.891	0.767	1	0.891	0.767	1	CLONAL	1	TRUE	1	0.19	2		665	721	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249139	55249139	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	48	602	0	ENST00000275493.2:c.2437T>C	p.Tyr813His	p.Y813H	ENST00000275493	NM_005228.3	813	Tac/Cac	20/28	1	2	FACETS	0.859	0.726	1	0.859	0.726	1	CLONAL	1	TRUE	1	0.19	2		602	588	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410048	63410048	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	44	548	0	ENST00000330258.3:c.3119C>A	p.Ala1040Asp	p.A1040D	ENST00000330258	NM_152424.3	1040	gCc/gAc	2/2	1	2	FACETS	0.899	0.754	1	0.899	0.754	1	CLONAL	1	TRUE	1	0.19	2		548	515	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0039484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	231	305	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.596657449359584	4	FACETS	0.955	0.896	1	0.955	0.896	1	CLONAL	2	TRUE	2	0.630194706524418	4		305	626	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578206	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs886039484	NA	P-0039484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	441	704	0	ENST00000269305.4:c.643A>C	p.Ser215Arg	p.S215R	ENST00000269305	NM_001126112.2	215	Agt/Cgt	6/11	NA	2	FACETS	0.955	0.92	0.989			1	INDETERMINATE	2	TRUE	NA	0.630194706524418	2		704	733	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857311	9857311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1245573153	NA	P-0039484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	154	568	0	ENST00000330684.3:c.4090G>A	p.Asp1364Asn	p.D1364N	ENST00000330684	NM_001134407.1	1364	Gat/Aat	13/13	0.625965829461318	1	FACETS	0.861	0.797	0.925	0.861	0.797	0.925	CLONAL	1	TRUE	0	0.630194706524418	1		568	389	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880256	155880256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	282	383	0	ENST00000368323.3:c.148C>T	p.His50Tyr	p.H50Y	ENST00000368323	NM_006912.5	50	Cat/Tat	3/6	0.596657449359584	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	2	0.630194706524418	4		383	704	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422160	81422160	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276734165	NA	P-0039484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	256	496	0	ENST00000298171.2:c.136C>T	p.Arg46Cys	p.R46C	ENST00000298171	NM_000369.2	46	Cgc/Tgc	1/10	0.595366160257789	4	FACETS	0.916	0.862	0.971			1	CLONAL	2	TRUE	NA	0.630194706524418	4		496	723	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031883	10031883	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	149	639	0	ENST00000330684.3:c.940C>G	p.Pro314Ala	p.P314A	ENST00000330684	NM_001134407.1	314	Ccc/Gcc	3/13	0.625965829461318	1	FACETS	0.82	0.758	0.883	0.82	0.758	0.883	CLONAL	1	TRUE	0	0.630194706524418	1		639	395	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448333	56448342	+	frameshift_variant	Frame_Shift_Del	DEL	CTGATGAATC	CTGATGAATC	-	novel	NA	P-0039484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	472	783	0	ENST00000407977.2:c.305_314del	p.Gly102AlafsTer53	p.G102Afs*53	ENST00000407977		102	gGATTCATCAGc/gc	3/10	0.630194706524418	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.630194706524418	2		783	736	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273491	5273491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	425	792	0	ENST00000357368.4:c.341G>A	p.Gly114Glu	p.G114E	ENST00000357368	NM_002850.3	114	gGg/gAg	4/38	0.508838523355255	4	FACETS	0.998	0.953	1	0.998	0.953	1	CLONAL	2	TRUE	2	0.630194706524418	4		792	1102	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753087	42753087	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	75	754	0	ENST00000222329.4:c.1177G>T	p.Glu393Ter	p.E393*	ENST00000222329	NM_006494.2	393	Gag/Tag	4/4	0.508838523355255	4	FACETS	0.362	0.316	0.412	0.181	0.158	0.206	SUBCLONAL	1	TRUE	2	0.630194706524418	4		754	1072	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31511162	31511162	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	265	659	0	ENST00000344624.3:c.1412C>G	p.Thr471Arg	p.T471R	ENST00000344624		471	aCg/aGg	6/33	NA	2	FACETS	0.831	0.789	0.873			1	INDETERMINATE	2	TRUE	NA	0.630194706524418	2		659	506	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566108	141566108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1458970957	NA	P-0039484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	473	564	0	ENST00000220592.5:c.1156G>A	p.Ala386Thr	p.A386T	ENST00000220592	NM_012154.3	386	Gca/Aca	10/19	0.630194706524418	6	FACETS	0.871	0.833	0.909			1	CLONAL	3	TRUE	NA	0.630194706524418	6		564	1299	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921442	39921442	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	283	598	0	ENST00000378444.4:c.4378A>G	p.Lys1460Glu	p.K1460E	ENST00000378444	NM_001123385.1	1460	Aag/Gag	10/15	0.61665999099358	2	FACETS	0.922	0.88	0.964	0.922	0.88	0.964	CLONAL	2	TRUE	0	0.630194706524418	2		598	487	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940461	76940461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	244	482	1	ENST00000373344.5:c.632G>A	p.Arg211His	p.R211H	ENST00000373344	NM_000489.3	211	cGt/cAt	8/35	0.596657449359584	4	FACETS	0.867	0.814	0.921	0.867	0.814	0.921	CLONAL	2	TRUE	2	0.630194706524418	4		483	728	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0039531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	224	443	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.477042019763876	2		443	819	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0039531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	28	953	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.217313857766754	1	FACETS	0.104	0.082	0.129	0.104	0.082	0.129	INDETERMINATE	1	TRUE	0	0.477042019763876	1		953	860	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0039531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	170	702	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	1	2	FACETS	0.893	0.823	0.967	0.893	0.823	0.967	CLONAL	1	TRUE	1	0.477042019763876	2		702	798	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17124926	17124926	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	92	650	0	ENST00000285071.4:c.796G>T	p.Gly266Cys	p.G266C	ENST00000285071	NM_144997.5	266	Ggc/Tgc	8/14	0.217313857766754	1	FACETS	0.466	0.414	0.521	0.466	0.414	0.521	INDETERMINATE	1	TRUE	0	0.477042019763876	1		650	630	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210381	36210381	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	79	732	0	ENST00000222270.7:c.374G>T	p.Gly125Val	p.G125V	ENST00000222270	NM_014727.1	125	gGt/gTt	2/37	NA	2	FACETS	0.413	0.363	0.468			1	INDETERMINATE	1	TRUE	NA	0.477042019763876	2		732	801	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971307	13971307	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	186	579	0	ENST00000405192.2:c.622C>A	p.Arg208Ser	p.R208S	ENST00000405192	NM_001163147.1	208	Cgt/Agt	8/12	1	2	FACETS	0.838	0.776	0.902	0.838	0.776	0.902	CLONAL	1	TRUE	1	0.581900006249652	2		579	763	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051643	30051647	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGA	GCAGA	-	novel	NA	P-0039616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	111	361	0	ENST00000338641.4:c.580_584del	p.Glu194ProfsTer7	p.E194Pfs*7	ENST00000338641	NM_000268.3	193	GCAGAg/g	6/16	0.581900006249652	1	FACETS	0.768	0.698	0.841	0.768	0.698	0.841	SUBCLONAL	1	TRUE	0	0.581900006249652	1		361	352	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437817	52437821	+	frameshift_variant	Frame_Shift_Del	DEL	CAAGA	CAAGA	-	novel	NA	P-0039616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	244	886	0	ENST00000460680.1:c.1340_1344del	p.Val447GlyfsTer2	p.V447Gfs*2	ENST00000460680	NM_004656.3	447	gTCTTG/g	13/17	0.572128792794375	1	FACETS	0.804	0.754	0.854	0.804	0.754	0.854	CLONAL	1	TRUE	0	0.581900006249652	1		886	740	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0039620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	78	860	0	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	1	2	FACETS	0.728	0.639	0.825	0.728	0.639	0.825	SUBCLONAL	1	TRUE	1	0.263762743317354	2		860	812	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162336	47162336	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	34	438	0	ENST00000409792.3:c.3790C>T	p.Gln1264Ter	p.Q1264*	ENST00000409792	NM_014159.6	1264	Caa/Taa	3/21	1	2	FACETS	0.6	0.49	0.723	0.6	0.49	0.723	SUBCLONAL	1	TRUE	1	0.263762743317354	2		438	430	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289947	15289947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779780504	NA	P-0039620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	103	1116	1	ENST00000263388.2:c.3607G>A	p.Glu1203Lys	p.E1203K	ENST00000263388	NM_000435.2	1203	Gag/Aag	22/33	0.263762743317354	1	FACETS	0.788	0.705	0.877	0.788	0.705	0.877	SUBCLONAL	1	TRUE	0	0.263762743317354	1		1117	860	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551347	29551347	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs372472978	NA	P-0039620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	57	696	0	ENST00000389048.3:c.1283G>A	p.Gly428Glu	p.G428E	ENST00000389048	NM_004304.4	428	gGa/gAa	6/29	0.162229165554278	3	FACETS	0.704	0.603	0.814	0.352	0.301	0.407	SUBCLONAL	1	TRUE	1	0.263762743317354	3		696	695	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414397	6414397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	35	259	0	ENST00000356142.4:c.31G>A	p.Asp11Asn	p.D11N	ENST00000356142	NM_018890.3	11	Gac/Aac	1/7	1	2	FACETS	0.797	0.655	0.956	0.797	0.655	0.956	CLONAL	1	TRUE	1	0.263762743317354	2		259	333	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600470	10600470	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	107	810	0	ENST00000171111.5:c.1385G>A	p.Gly462Glu	p.G462E	ENST00000171111	NM_203500.1	462	gGg/gAg	4/6	0.263762743317354	1	FACETS	0.829	0.743	0.92	0.829	0.743	0.92	CLONAL	1	TRUE	0	0.263762743317354	1		810	850	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456575	40456575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs988135840	NA	P-0039620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	131	897	2	ENST00000345506.4:c.1285C>T	p.Arg429Trp	p.R429W	ENST00000345506	NM_003152.3	429	Cgg/Tgg	12/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.263762743317354	2		899	908	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446025	49446025	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	62	1235	1	ENST00000301067.7:c.1441G>A	p.Glu481Lys	p.E481K	ENST00000301067	NM_003482.3	481	Gag/Aag	10/54	1	2	FACETS	0.463	0.398	0.533	0.463	0.398	0.533	SUBCLONAL	1	TRUE	1	0.263762743317354	2		1236	1016	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95584006	95584006	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	57	474	0	ENST00000393063.1:c.1462C>T	p.Gln488Ter	p.Q488*	ENST00000393063	NM_030621.3	488	Cag/Tag	10/28	1	2	FACETS	0.8	0.687	0.924	0.8	0.687	0.924	CLONAL	1	TRUE	1	0.263762743317354	2		474	540	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78865611	78865611	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	62	563	0	ENST00000306801.3:c.2075A>G	p.Tyr692Cys	p.Y692C	ENST00000306801	NM_020761.2	692	tAc/tGc	18/34	1	2	FACETS	0.633	0.546	0.728	0.633	0.546	0.728	SUBCLONAL	1	TRUE	1	0.263762743317354	2		563	743	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211602	5211602	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	60	506	0	ENST00000357368.4:c.5233A>T	p.Arg1745Trp	p.R1745W	ENST00000357368	NM_002850.3	1745	Agg/Tgg	33/38	0.263762743317354	1	FACETS	0.857	0.74	0.984	0.857	0.74	0.984	CLONAL	1	TRUE	0	0.263762743317354	1		506	461	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355413	15355413	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0039620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	69	835	0	ENST00000263377.2:c.2212-2A>T		p.X738_splice	ENST00000263377	NM_058243.2	738			1	2	FACETS	0.748	0.651	0.854	0.748	0.651	0.854	SUBCLONAL	1	TRUE	1	0.263762743317354	2		835	699	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104668	209104668	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	77	607	0	ENST00000345146.2:c.910G>C	p.Glu304Gln	p.E304Q	ENST00000345146	NM_005896.2	304	Gaa/Caa	8/10	0.162229165554278	3	FACETS	0.992	0.871	1	0.496	0.435	0.562	CLONAL	1	TRUE	1	0.263762743317354	3		607	666	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573499	41573499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	88	946	0	ENST00000263253.7:c.5784G>A	p.Met1928Ile	p.M1928I	ENST00000263253	NM_001429.3	1928	atG/atA	31/31	1	2	FACETS	0.889	0.787	0.997	0.889	0.787	0.997	CLONAL	1	TRUE	1	0.263762743317354	2		946	751	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965385	68965385	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	76	831	0	ENST00000288368.4:c.997A>G	p.Thr333Ala	p.T333A	ENST00000288368	NM_024870.2	333	Aca/Gca	9/40	1	2	FACETS	0.614	0.537	0.698	0.614	0.537	0.698	SUBCLONAL	1	TRUE	1	0.263762743317354	2		831	938	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514780	44514780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769567889	NA	P-0039631-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	90	325	0	ENST00000291552.4:c.467G>A	p.Arg156His	p.R156H	ENST00000291552	NM_006758.2	156	cGt/cAt	6/8	1	2	FACETS	0.763	0.681	0.85	0.763	0.681	0.85	SUBCLONAL	1	TRUE	1	0.573810212510396	2		325	411	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138548	11138548	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039631-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	168	569	0	ENST00000358026.2:c.3304T>C	p.Phe1102Leu	p.F1102L	ENST00000358026	NM_001128849.1	1102	Ttc/Ctc	24/36	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.573810212510396	2		569	547	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	76	737	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.222837578773921	2		737	562	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0039636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	129	675	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.222837578773921	2		675	1025	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0039636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	107	556	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.167822495675195	0	FACETS	1	0.975	1			1	CLONAL	1	FALSE	0	0.222837578773921	0		556	587	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981300	201981300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	264	1033	0	ENST00000359651.3:c.379G>A	p.Asp127Asn	p.D127N	ENST00000359651		127	Gac/Aac	2/8	0.222837578773921	1	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	FALSE	0	0.222837578773921	1		1033	903	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449602	149449602	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	200	905	1	ENST00000286301.3:c.1344G>T	p.Gln448His	p.Q448H	ENST00000286301	NM_005211.3	448	caG/caT	10/22	0.222837578773921	1	FACETS	1	0.935	1	1	0.994	1	CLONAL	2	FALSE	0	0.222837578773921	1		906	792	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531840	41531843	+	frameshift_variant	Frame_Shift_Del	DEL	GGAG	GGAG	-	novel	NA	P-0039636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	68	714	0	ENST00000263253.7:c.1553_1556del	p.Gly518ValfsTer2	p.G518Vfs*2	ENST00000263253	NM_001429.3	518	GGAGgt/gt	7/31	1	2	FACETS	0.827	0.719	0.945	0.827	0.719	0.945	CLONAL	1	FALSE	1	0.222837578773921	2		714	738	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0039738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	215	398	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.425865148083837	1	FACETS	0.874	0.815	0.935	0.874	0.815	0.935	CLONAL	1	TRUE	0	0.481375270075133	1		398	776	SUCCESS
APC	324	MSKCC	GRCh37	5	112170683	112170683	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554083132	NA	P-0039738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	80	313	0	ENST00000257430.4:c.1779G>A	p.Trp593Ter	p.W593*	ENST00000257430	NM_000038.5	593	tgG/tgA	15/16	0.469810634131449	1	FACETS	0.784	0.696	0.876	0.784	0.696	0.876	SUBCLONAL	1	TRUE	0	0.481375270075133	1		313	322	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939040	48939041	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0039738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	25	100	0	ENST00000267163.4:c.873_874del	p.Tyr292PhefsTer17	p.Y292Ffs*17	ENST00000267163	NM_000321.2	291	gTT/g	9/27	0.481375270075133	1	FACETS	0.781	0.629	0.948	0.781	0.629	0.948	CLONAL	1	TRUE	0	0.481375270075133	1		100	101	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737446	204737447	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0039738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	53	296	0	ENST00000302823.3:c.583_584delinsAA	p.Pro195Asn	p.P195N	ENST00000302823	NM_005214.4	195	CCt/AAt	4/4	1	2	FACETS	0.636	0.545	0.735	0.636	0.545	0.735	SUBCLONAL	1	TRUE	1	0.481375270075133	2		296	346	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505015	186505015	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	98	304	0	ENST00000323963.5:c.871G>T	p.Glu291Ter	p.E291*	ENST00000323963		291	Gag/Tag	8/11	0.462303928258418	3	FACETS	0.832	0.744	0.926	0.416	0.372	0.463	CLONAL	1	TRUE	1	0.481375270075133	3		304	607	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38975650	38975650	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	68	433	0	ENST00000357387.3:c.878G>T	p.Arg293Leu	p.R293L	ENST00000357387	NM_152756.3	293	cGa/cTa	10/38	0.384739868721608	3	FACETS	0.48	0.416	0.548	0.24	0.208	0.274	SUBCLONAL	1	TRUE	1	0.481375270075133	3		433	731	SUCCESS
APC	324	MSKCC	GRCh37	5	112176959	112176959	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060503265	NA	P-0039738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	79	279	1	ENST00000257430.4:c.5668T>C	p.Ser1890Pro	p.S1890P	ENST00000257430	NM_000038.5	1890	Tca/Cca	16/16	0.469810634131449	1	FACETS	0.94	0.838	1	0.94	0.838	1	CLONAL	1	TRUE	0	0.481375270075133	1		280	265	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176710800	176710800	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	36	329	0	ENST00000439151.2:c.6022G>C	p.Asp2008His	p.D2008H	ENST00000439151	NM_022455.4	2008	Gat/Cat	20/23	0.469810634131449	1	FACETS	0.268	0.22	0.322	0.268	0.22	0.322	SUBCLONAL	1	TRUE	0	0.481375270075133	1		329	423	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205112	38205112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	117	539	0	ENST00000317025.8:c.578G>A	p.Arg193Lys	p.R193K	ENST00000317025	NM_023034.1	193	aGa/aAa	2/24	0.439808841060264	4	FACETS	0.759	0.683	0.839	0.253	0.227	0.28	SUBCLONAL	1	TRUE	1	0.481375270075133	4		539	949	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0039801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	38	659	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	1	2	FACETS	0.831	0.685	0.996	0.831	0.685	0.996	CLONAL	1	TRUE	1	0.11	2		659	831	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180471	94180471	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	41	676	0	ENST00000323929.3:c.1697C>G	p.Thr566Ser	p.T566S	ENST00000323929	NM_005591.3	566	aCc/aGc	15/20	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.11	2		676	700	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38147994	38147994	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	49	790	0	ENST00000317025.8:c.3117G>C	p.Lys1039Asn	p.K1039N	ENST00000317025	NM_023034.1	1039	aaG/aaC	17/24	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.11	2		790	792	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965837	90965837	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	30	402	0	ENST00000265433.3:c.1480C>T	p.Gln494Ter	p.Q494*	ENST00000265433	NM_002485.4	494	Caa/Taa	11/16	0.139108065291616	3	FACETS	1	0.846	1	0.531	0.427	0.65	CLONAL	1	TRUE	1	0.11	3		402	542	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034417	47034417	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0039801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	38	492	1	ENST00000377604.3:c.503-1G>A		p.X168_splice	ENST00000377604	NM_001204468.1	168			1	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.11	1		493	447	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361191	70361191	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	39	599	0	ENST00000374080.3:c.6382del	p.Gln2128AsnfsTer91	p.Q2128Nfs*91	ENST00000374080		2127	Ccc/cc	43/45	1	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.11	1		599	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0039853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	648	736	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.765668529838175	2	FACETS	0.963	0.94	0.984	0.963	0.94	0.984	CLONAL	2	TRUE	0	0.796672485551784	2		736	845	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486070	29486070	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs746824139	NA	P-0039853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	363	387	0	ENST00000356175.3:c.247C>T	p.Gln83Ter	p.Q83*	ENST00000356175	NM_000267.3	83	Cag/Tag	3/57	0.793131025782773	3	FACETS	0.974	0.948	0.999	0.974	0.948	0.999	CLONAL	3	TRUE	0	0.796672485551784	3		387	436	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661946	29661946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868094590	NA	P-0039853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	605	495	1	ENST00000356175.3:c.5840G>A	p.Arg1947Gln	p.R1947Q	ENST00000356175	NM_000267.3	1947	cGa/cAa	39/57	0.793131025782773	3	FACETS	0.974	0.954	0.993	0.974	0.954	0.993	CLONAL	3	TRUE	0	0.796672485551784	3		496	727	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778894	9778894	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	321	648	0	ENST00000377346.4:c.1163C>T	p.Ala388Val	p.A388V	ENST00000377346	NM_005026.3	388	gCc/gTc	9/24	0.62345146580917	4	FACETS	1	0.984	1	0.371	0.35	0.393	CLONAL	1	TRUE	1	0.796672485551784	4		648	1301	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098423	108098423	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	39	410	0	ENST00000278616.4:c.72G>C	p.Lys24Asn	p.K24N	ENST00000278616	NM_000051.3	24	aaG/aaC	2/63	0.552715508933807	5	FACETS	0.342	0.283	0.409	0.114	0.094	0.137	SUBCLONAL	1	TRUE	2	0.796672485551784	5		410	628	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552716	18552716	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	493	613	0	ENST00000266497.5:c.2127G>T	p.Met709Ile	p.M709I	ENST00000266497		709	atG/atT	14/31	0.796672485551784	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.796672485551784	2		613	609	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3827660	3827660	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0039853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	88	385	1	ENST00000262367.5:c.2114-2A>G		p.X705_splice	ENST00000262367	NM_004380.2	705			0.250365374500255	5	FACETS	0.753	0.668	0.844	0.251	0.222	0.282	INDETERMINATE	1	TRUE	2	0.796672485551784	5		386	644	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836306	89836306	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	424	829	0	ENST00000389301.3:c.2443C>T	p.Pro815Ser	p.P815S	ENST00000389301	NM_000135.2	815	Cct/Tct	26/43	0.227542755442045	4	FACETS	0.867	0.828	0.907	0.867	0.828	0.907	INDETERMINATE	2	TRUE	2	0.796672485551784	4		829	1103	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217590	142217590	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0039853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	33	518	0	ENST00000350721.4:c.5407A>T	p.Arg1803Ter	p.R1803*	ENST00000350721	NM_001184.3	1803	Aga/Tga	32/47	0.796672485551784	2	FACETS	0.153	0.124	0.186	0.077	0.062	0.093	SUBCLONAL	1	TRUE	0	0.796672485551784	2		518	541	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230913	66230937	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAATTCACCTTGTGATAAAGATGAA	AAATTCACCTTGTGATAAAGATGAA	-	novel	NA	P-0039853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	20	391	0	ENST00000273854.3:c.2051-17_2058del		p.X684_splice	ENST00000273854	NM_004439.5	684		12/18	1	2	FACETS	0.136	0.103	0.174	0.136	0.103	0.174	SUBCLONAL	1	TRUE	1	0.796672485551784	2		391	370	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021651	69021651	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	344	446	0	ENST00000288368.4:c.2939G>T	p.Gly980Val	p.G980V	ENST00000288368	NM_024870.2	980	gGg/gTg	25/40	0.796672485551784	7	FACETS	0.852	0.804	0.9	0.243	0.229	0.258	CLONAL	2	TRUE	0	0.796672485551784	7		446	1517	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141632	202141632	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	88	469	2	ENST00000358485.4:c.920G>T	p.Arg307Leu	p.R307L	ENST00000358485	NM_001080125.1	307	cGg/cTg	7/9	0.311115214482283	3	FACETS	0.902	0.799	1	0.451	0.399	0.507	CLONAL	1	TRUE	1	0.311293085568818	3		471	724	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223048	1223048	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0039869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	182	1084	0	ENST00000326873.7:c.985A>T	p.Lys329Ter	p.K329*	ENST00000326873	NM_000455.4	329	Aag/Tag	8/10	0.311293085568818	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.311293085568818	1		1084	967	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061517	38061517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771653601	NA	P-0039869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	46	276	0	ENST00000250448.2:c.472G>A	p.Asp158Asn	p.D158N	ENST00000250448	NM_004496.3	158	Gac/Aac	2/2	0.311293085568818	4	FACETS	0.875	0.738	1	0.437	0.369	0.513	CLONAL	1	TRUE	2	0.311293085568818	4		276	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0039869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	289	885	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.294312017601264	2	FACETS	0.995	0.938	1	0.995	0.938	1	CLONAL	2	TRUE	0	0.311293085568818	2		885	933	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685271	89685271	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	102	210	2	ENST00000371953.3:c.170del	p.Leu57TrpfsTer42	p.L57Wfs*42	ENST00000371953	NM_000314.4	56	Ttt/tt	3/9	0.311115214482283	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.311293085568818	3		212	325	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032573	47032573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	257	903	2	ENST00000377604.3:c.479G>A	p.Arg160Gln	p.R160Q	ENST00000377604	NM_001204468.1	160	cGg/cAg	5/24	0.235490930770757	4	FACETS	0.88	0.823	0.939	0.88	0.823	0.939	CLONAL	2	TRUE	2	0.311293085568818	4		905	1230	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845261	151845261	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	88	519	0	ENST00000262189.6:c.13751G>A	p.Arg4584Gln	p.R4584Q	ENST00000262189	NM_170606.2	4584	cGg/cAg	52/59	0.311293085568818	3	FACETS	0.817	0.723	0.917			1	CLONAL	1	TRUE	NA	0.311293085568818	3		519	800	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951157	48951157	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	156	389	0	ENST00000267163.4:c.1321del	p.Ile441LeufsTer16	p.I441Lfs*16	ENST00000267163	NM_000321.2	440	gAa/ga	13/27	0.294312017601264	2	FACETS	0.956	0.882	1	0.956	0.882	1	CLONAL	2	TRUE	0	0.311293085568818	2		389	524	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189292	99189292	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768206909	NA	P-0039869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	113	582	0	ENST00000074304.5:c.2548C>T	p.Arg850Cys	p.R850C	ENST00000074304	NM_001134224.1	850	Cgc/Tgc	24/26	0.311115214482283	3	FACETS	1	0.942	1	0.533	0.479	0.59	CLONAL	1	TRUE	1	0.311293085568818	3		582	787	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964430	55964430	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	320	515	0	ENST00000263923.4:c.2383G>C	p.Gly795Arg	p.G795R	ENST00000263923	NM_002253.2	795	Ggg/Cgg	17/30	0.311293085568818	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	1	0.311293085568818	4		515	826	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030315	180030315	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	147	1092	2	ENST00000261937.6:c.3969G>T	p.Glu1323Asp	p.E1323D	ENST00000261937	NM_182925.4	1323	gaG/gaT	30/30	0.311115214482283	3	FACETS	0.882	0.803	0.965	0.441	0.401	0.483	CLONAL	1	TRUE	1	0.311293085568818	3		1094	1238	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6027000	6027000	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	272	779	0	ENST00000265849.7:c.1396G>T	p.Gly466Cys	p.G466C	ENST00000265849	NM_000535.5	466	Ggc/Tgc	11/15	0.311115214482283	3	FACETS	0.939	0.882	0.999	0.939	0.882	0.999	CLONAL	2	TRUE	1	0.311293085568818	3		779	1075	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578520	7578520	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	451	680	1	ENST00000269305.4:c.410T>A	p.Leu137Gln	p.L137Q	ENST00000269305	NM_001126112.2	137	cTg/cAg	5/11	0.941866661385568	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.941866661385568	1		681	478	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144819	58144819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150281463	NA	P-0039900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	98	424	0	ENST00000257904.6:c.409G>A	p.Val137Ile	p.V137I	ENST00000257904	NM_000075.3	137	Gtt/Att	4/8	1	2	FACETS	0.367	0.328	0.408	0.367	0.328	0.408	SUBCLONAL	1	TRUE	1	0.941866661385568	2		424	567	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873105	134873105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749312347	NA	P-0039900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	51	477	0	ENST00000398015.3:c.1409G>A	p.Arg470Gln	p.R470Q	ENST00000398015	NM_004441.4	470	cGg/cAg	6/16	1	2	FACETS	0.189	0.16	0.221	0.189	0.16	0.221	SUBCLONAL	1	TRUE	1	0.941866661385568	2		477	573	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325763	30325763	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777479817	NA	P-0039900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	105	624	2	ENST00000322652.5:c.1961G>A	p.Arg654Gln	p.R654Q	ENST00000322652	NM_015355.2	654	cGa/cAa	16/16	1	2	FACETS	0.761	0.691	0.832	0.761	0.691	0.832	SUBCLONAL	1	TRUE	1	0.941866661385568	2		626	293	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372112	55372112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1385441707	NA	P-0039900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	250	380	1	ENST00000297316.4:c.802G>A	p.Gly268Ser	p.G268S	ENST00000297316	NM_022454.3	268	Ggt/Agt	2/2	0.784809177996785	4	FACETS	1	0.992	1	0.458	0.43	0.487	CLONAL	1	TRUE	1	0.941866661385568	4		381	750	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252066	226252066	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	150	199	0	ENST00000366813.1:c.14A>T	p.Lys5Met	p.K5M	ENST00000366813		5	aAg/aTg	1/3	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.941866661385568	2		199	302	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221315	36221315	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	66	677	2	ENST00000222270.7:c.5149C>T	p.Arg1717Trp	p.R1717W	ENST00000222270	NM_014727.1	1717	Cgg/Tgg	24/37	1	2	FACETS	0.147	0.127	0.169	0.147	0.127	0.169	SUBCLONAL	1	TRUE	1	0.941866661385568	2		679	952	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920349	134920349	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	235	401	2	ENST00000398015.3:c.2164G>A	p.Val722Met	p.V722M	ENST00000398015	NM_004441.4	722	Gtg/Atg	12/16	1	2	FACETS	0.919	0.866	0.973	0.919	0.866	0.973	CLONAL	1	TRUE	1	0.941866661385568	2		403	543	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0039943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	30	371	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	0.484402313037221	3	FACETS	0.777	0.631	0.94	0.389	0.315	0.47	CLONAL	1	TRUE	1	0.484402313037221	3		371	198	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888165	112888165	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507510	NA	P-0039943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	14	695	0	ENST00000351677.2:c.181G>T	p.Asp61Tyr	p.D61Y	ENST00000351677	NM_002834.3	61	Gat/Tat	3/16	0.330327316882016	1	FACETS	0.275	0.2	0.366	0.275	0.2	0.366	SUBCLONAL	1	TRUE	0	0.484402313037221	1		695	159	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890149	76890150	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	26	319	0	ENST00000373344.5:c.4744dup	p.Thr1582AsnfsTer19	p.T1582Nfs*19	ENST00000373344	NM_000489.3	1582	aca/aAca	17/35	1	1	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	0	0.484402313037221	1		319	72	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586122	29586122	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	72	484	0	ENST00000356175.3:c.4345del	p.Ser1449AlafsTer13	p.S1449Afs*13	ENST00000356175	NM_000267.3	1448	Aaa/aa	32/57	0.482116388896504	2	FACETS	0.812	0.725	0.901	0.812	0.725	0.901	CLONAL	2	TRUE	0	0.484402313037221	2		484	183	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0039950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	625	675	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.505072300879826	3	FACETS	0.953	0.923	0.982	0.953	0.923	0.982	CLONAL	3	TRUE	0	0.516657529261792	3		675	1065	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657040	45657040	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	143	500	0	ENST00000407780.3:c.116G>C	p.Cys39Ser	p.C39S	ENST00000407780	NM_001283052.1	39	tGc/tCc	3/7	0.453904819860664	3	FACETS	0.895	0.817	0.977	0.448	0.408	0.489	CLONAL	1	TRUE	1	0.516657529261792	3		500	778	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439894	52439894	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	148	508	0	ENST00000460680.1:c.818C>G	p.Thr273Ser	p.T273S	ENST00000460680	NM_004656.3	273	aCc/aGc	10/17	0.499622440005913	3	FACETS	0.882	0.806	0.962	0.441	0.403	0.481	CLONAL	1	TRUE	1	0.516657529261792	3		508	817	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520008	NA	P-0039968-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	296	651	0	ENST00000269305.4:c.613T>C	p.Tyr205His	p.Y205H	ENST00000269305	NM_001126112.2	205	Tat/Cat	6/11	0.236263058642241	3	FACETS	1	0.974	1	0.704	0.663	0.745	CLONAL	2	FALSE	0	0.334706501041317	3		651	978	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244952	41244952	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41286300	NA	P-0039968-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	55	571	0	ENST00000357654.3:c.2596C>T	p.Arg866Cys	p.R866C	ENST00000357654	NM_007294.3	866	Cgc/Tgc	10/23	0.236263058642241	3	FACETS	0.533	0.455	0.618	0.178	0.151	0.206	SUBCLONAL	1	FALSE	0	0.334706501041317	3		571	720	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057743	27057756	+	frameshift_variant	Frame_Shift_Del	DEL	CCTACTCCCAGCAA	CCTACTCCCAGCAA	-	novel	NA	P-0039968-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	426	792	0	ENST00000324856.7:c.1453_1466del	p.Tyr485ThrfsTer133	p.Y485Tfs*133	ENST00000324856	NM_006015.4	484	cCCTACTCCCAGCAA/c	3/20	0.251061760408065	3	FACETS	1	0.992	1	0.786	0.749	0.823	CLONAL	2	FALSE	0	0.334706501041317	3		792	1260	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251918	8251918	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039968-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	65	752	1	ENST00000335790.3:c.159C>A	p.Cys53Ter	p.C53*	ENST00000335790	NM_002315.2	53	tgC/tgA	2/4	0.334706501041317	1	FACETS	0.354	0.306	0.407	0.354	0.306	0.407	SUBCLONAL	1	FALSE	0	0.334706501041317	1		753	913	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343064	118343064	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039968-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	24	273	0	ENST00000534358.1:c.1190G>C	p.Arg397Thr	p.R397T	ENST00000534358	NM_005933.3	397	aGa/aCa	3/36	0.250319627255427	4	FACETS	0.43	0.336	0.539			1	SUBCLONAL	1	FALSE	NA	0.334706501041317	4		273	445	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343120	118343120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039968-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	28	346	0	ENST00000534358.1:c.1246G>A	p.Ala416Thr	p.A416T	ENST00000534358	NM_005933.3	416	Gct/Act	3/36	0.250319627255427	4	FACETS	0.415	0.331	0.512			1	SUBCLONAL	1	FALSE	NA	0.334706501041317	4		346	538	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223742	36223742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751646243	NA	P-0039968-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1358	103	858	0	ENST00000222270.7:c.6292G>A	p.Ala2098Thr	p.A2098T	ENST00000222270	NM_014727.1	2098	Gct/Act	28/37	0.191707493638036	5	FACETS	0.633	0.564	0.706	0.211	0.188	0.236	INDETERMINATE	1	FALSE	2	0.334706501041317	5		858	1461	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557206	187557206	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039968-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	59	449	0	ENST00000441802.2:c.4156G>C	p.Gly1386Arg	p.G1386R	ENST00000441802	NM_005245.3	1386	Ggc/Cgc	6/27	0.334706501041317	1	FACETS	0.531	0.457	0.611	0.531	0.457	0.611	SUBCLONAL	1	FALSE	0	0.334706501041317	1		449	553	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871297	35871297	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039968-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	72	330	0	ENST00000303115.3:c.520del	p.Asp174MetfsTer8	p.D174Mfs*8	ENST00000303115	NM_002185.3	173	aaG/aa	4/8	0.269777290199456	5	FACETS	1	0.97	1	0.461	0.404	0.523	CLONAL	1	FALSE	2	0.334706501041317	5		330	467	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954221	48954221	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0039971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	119	211	0	ENST00000267163.4:c.1421+1G>A		p.X474_splice	ENST00000267163	NM_000321.2	474			0.724178985583765	1	FACETS	0.971	0.9	1	0.971	0.9	1	CLONAL	1	TRUE	0	0.724178985583765	1		211	216	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940370	49940370	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	270	706	0	ENST00000296474.3:c.673G>C	p.Ala225Pro	p.A225P	ENST00000296474	NM_002447.2	225	Gcc/Ccc	1/20	0.268283391869536	5	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.724178985583765	5		706	1215	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0039983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	128	413	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.94	1	1	0.99	1	CLONAL	2	TRUE	1	0.21	2		414	584	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278049	18278049	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs372272045	NA	P-0039983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	46	620	0	ENST00000222254.8:c.1669G>T	p.Asp557Tyr	p.D557Y	ENST00000222254	NM_005027.3	557	Gac/Tac	13/16	1	2	FACETS	0.502	0.421	0.592	0.502	0.421	0.592	SUBCLONAL	1	TRUE	1	0.21	2		620	873	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs878854073	NA	P-0039983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	43	446	0	ENST00000269305.4:c.673-1G>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			1	2	FACETS	0.696	0.582	0.824	0.696	0.582	0.824	SUBCLONAL	1	TRUE	1	0.21	2		446	588	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584533	48584533	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	34	331	0	ENST00000342988.3:c.706G>T	p.Gly236Ter	p.G236*	ENST00000342988	NM_005359.5	236	Gga/Tga	6/12	1	2	FACETS	0.771	0.63	0.929	0.771	0.63	0.929	CLONAL	1	TRUE	1	0.21	2		331	420	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974839	15974839	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	29	337	0	ENST00000268712.3:c.4036G>T	p.Glu1346Ter	p.E1346*	ENST00000268712	NM_006311.3	1346	Gaa/Taa	30/46	1	2	FACETS	0.535	0.429	0.657	0.535	0.429	0.657	SUBCLONAL	1	TRUE	1	0.21	2		337	516	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449878	29449878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	72	843	0	ENST00000389048.3:c.2977G>A	p.Asp993Asn	p.D993N	ENST00000389048	NM_004304.4	993	Gac/Aac	18/29	1	2	FACETS	0.643	0.56	0.734	0.643	0.56	0.734	SUBCLONAL	1	TRUE	1	0.21	2		843	1066	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971161	21971161	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs756750256	NA	P-0039983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	33	383	0	ENST00000304494.5:c.197A>C	p.His66Pro	p.H66P	ENST00000304494	NM_000077.4	66	cAc/cCc	2/3	0.166016581853555	1	FACETS	0.614	0.5	0.743	0.614	0.5	0.743	SUBCLONAL	1	TRUE	0	0.21	1		383	458	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611935	100611935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	30	447	0	ENST00000308731.7:c.1186G>A	p.Glu396Lys	p.E396K	ENST00000308731	NM_000061.2	396	Gaa/Aaa	14/19	1	2	FACETS	0.479	0.385	0.587	0.479	0.385	0.587	SUBCLONAL	1	TRUE	1	0.21	2		447	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0039998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	75	398	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.209818700822259	1	FACETS	0.895	0.784	1	0.895	0.784	1	CLONAL	1	TRUE	0	0.209818700822259	1		398	715	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226595555	226595555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	49	368	0	ENST00000366794.5:c.76G>A	p.Glu26Lys	p.E26K	ENST00000366794	NM_001618.3	26	Gag/Aag	1/23	0.155555604573028	3	FACETS	1	0.903	1	0.363	0.307	0.424	CLONAL	1	TRUE	0	0.209818700822259	3		368	474	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912276	29912276	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0039998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	53	739	0	ENST00000376809.5:c.896-1G>C		p.X299_splice	ENST00000376809	NM_002116.7	299			1	2	FACETS	0.666	0.567	0.776	0.666	0.567	0.776	SUBCLONAL	1	TRUE	1	0.209818700822259	2		739	758	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992229	11992229	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	19	263	0	ENST00000396373.4:c.319C>A	p.Pro107Thr	p.P107T	ENST00000396373	NM_001987.4	107	Cct/Act	3/8	NA	2	FACETS	0.492	0.373	0.633			1	INDETERMINATE	1	TRUE	NA	0.209818700822259	2		263	368	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435962	49435962	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	74	682	0	ENST00000301067.7:c.6019G>T	p.Glu2007Ter	p.E2007*	ENST00000301067	NM_003482.3	2007	Gag/Tag	28/54	1	2	FACETS	0.865	0.756	0.983	0.865	0.756	0.983	CLONAL	1	TRUE	1	0.209818700822259	2		682	815	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027753	152027753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	61	561	0	ENST00000262189.6:c.322C>T	p.Leu108Phe	p.L108F	ENST00000262189	NM_170606.2	108	Ctt/Ttt	3/59	1	2	FACETS	0.811	0.699	0.933	0.811	0.699	0.933	CLONAL	1	TRUE	1	0.209818700822259	2		561	717	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0040065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	49	304	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.299533754446886	5	FACETS	0.956	0.841	1			1	INDETERMINATE	3	TRUE	NA	0.686489083000586	5		304	101	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520000	NA	P-0040065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	190	773	1	ENST00000269305.4:c.452C>A	p.Pro151His	p.P151H	ENST00000269305	NM_001126112.2	151	cCc/cAc	5/11	0.697191994722565	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.686489083000586	1		774	261	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056209	26056211	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs779842031	NA	P-0040065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	12	377	0	ENST00000343677.2:c.446_448del	p.Lys149del	p.K149del	ENST00000343677	NM_005319.3	149	aAGAgc/agc	1/1	0.485060516564093	3	FACETS	0.322	0.227	0.437	0.161	0.113	0.219	SUBCLONAL	1	TRUE	1	0.686489083000586	3		377	146	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845366	151845366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	21	477	1	ENST00000262189.6:c.13646G>A	p.Arg4549His	p.R4549H	ENST00000262189	NM_170606.2	4549	cGc/cAc	52/59	0.299533754446886	5	FACETS	0.634	0.49	0.799			1	INDETERMINATE	1	TRUE	NA	0.686489083000586	5		478	196	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039294	47039294	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	287	380	0	ENST00000377604.3:c.917A>T	p.Asn306Ile	p.N306I	ENST00000377604	NM_001204468.1	306	aAc/aTc	10/24	0.407386245399715	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	NA	0.686489083000586	0		380	511	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066641	94066641	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs772199348	NA	P-0040065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	66	406	0	ENST00000369303.4:c.1118G>T	p.Ser373Ile	p.S373I	ENST00000369303	NM_004440.3	373	aGt/aTt	5/17	0.528236265262335	3	FACETS	0.906	0.831	0.977	0.906	0.831	0.977	CLONAL	3	TRUE	0	0.686489083000586	3		406	95	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528505	157528505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	22	516	0	ENST00000346085.5:c.6230C>T	p.Ser2077Leu	p.S2077L	ENST00000346085	NM_020732.3	2077	tCg/tTg	20/20	0.697191994722565	1	FACETS	0.36	0.283	0.446	0.36	0.283	0.446	SUBCLONAL	1	TRUE	0	0.686489083000586	1		516	117	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023211	27023212	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CG	novel	NA	P-0040065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	212	147	0	ENST00000324856.7:c.320_321dup	p.Gly108ArgfsTer7	p.G108Rfs*7	ENST00000324856	NM_006015.4	106	aac/aaCGc	1/20	0.516577350840414	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.686489083000586	1		147	388	SUCCESS
CBL	867	MSKCC	GRCh37	11	119077186	119077186	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750572996	NA	P-0040065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1253	677	505	0	ENST00000264033.4:c.59C>T	p.Ser20Leu	p.S20L	ENST00000264033	NM_005188.3	20	tCg/tTg	1/16	0.690001931854203	4	FACETS	0.862	0.83	0.894			1	CLONAL	2	TRUE	NA	0.686489083000586	4		505	1930	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425053	49425053	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs745381478	NA	P-0040065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	212	753	0	ENST00000301067.7:c.13435G>T	p.Gly4479Trp	p.G4479W	ENST00000301067	NM_003482.3	4479	Ggg/Tgg	39/54	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.686489083000586	2		753	496	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538280	9538280	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	31	389	1	ENST00000353224.5:c.1718C>A	p.Ser573Tyr	p.S573Y	ENST00000353224	NM_177990.2	573	tCc/tAc	7/10	0.379189924787502	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.686489083000586	0		390	76	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713407	40713407	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	176	679	0	ENST00000373198.4:c.4108C>G	p.Arg1370Gly	p.R1370G	ENST00000373198	NM_133170.3	1370	Cgc/Ggc	30/32	0.697191994722565	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.686489083000586	1		679	309	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256394	46256394	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	20	365	0	ENST00000371998.3:c.622C>G	p.Leu208Val	p.L208V	ENST00000371998		208	Ctg/Gtg	7/23	0.214105924491971	5	FACETS	1	0.82	1			1	INDETERMINATE	1	TRUE	NA	0.686489083000586	5		365	111	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142948	47142948	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	48	316	0	ENST00000409792.3:c.5015G>T	p.Gly1672Val	p.G1672V	ENST00000409792	NM_014159.6	1672	gGa/gTa	8/21	0.697191994722565	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.686489083000586	1		316	63	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275353	142275353	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	20	355	0	ENST00000350721.4:c.1950G>T	p.Glu650Asp	p.E650D	ENST00000350721	NM_001184.3	650	gaG/gaT	9/47	0.550090124766405	6	FACETS	0.922	0.711	1			1	CLONAL	1	TRUE	NA	0.686489083000586	6		355	150	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953926	55953926	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0040065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	29	264	1	ENST00000263923.4:c.3511-1G>T		p.X1171_splice	ENST00000263923	NM_002253.2	1171			0.690071200275104	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.686489083000586	1		265	47	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130108	143130108	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	56	400	0	ENST00000262992.4:c.908A>T	p.His303Leu	p.H303L	ENST00000262992	NM_001101669.1	303	cAc/cTc	11/24	0.561064023017623	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.686489083000586	1		400	74	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321369	1321369	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	73	467	0	ENST00000400841.2:c.386G>T	p.Trp129Leu	p.W129L	ENST00000400841		129	tGg/tTg	4/6	0.61634111910756	0	FACETS		NA	1			1	NA	1	TRUE	NA	0.686489083000586	0		467	349	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0040089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	500	205	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.469546162454555	2	FACETS	0.764	0.741	0.786	0.764	0.741	0.786	INDETERMINATE	2	TRUE	0	0.907969404799652	2		205	721	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579716	7579716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1192416464	NA	P-0040089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	718	676	0	ENST00000269305.4:c.80del	p.Pro27LeufsTer17	p.P27Lfs*17	ENST00000269305	NM_001126112.2	27	cCt/ct	3/11	0.907969404799652	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.907969404799652	1		676	793	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023169	27023212	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGGCCCGGCGCGGAGCCGGACCTGAAGAACTCGAACGGGAAC	GCGGGCCCGGCGCGGAGCCGGACCTGAAGAACTCGAACGGGAAC	-	novel	NA	P-0040089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	66	73	0	ENST00000324856.7:c.283_326del	p.Gly95Ter	p.G95*	ENST00000324856	NM_006015.4	92	gGCGGGCCCGGCGCGGAGCCGGACCTGAAGAACTCGAACGGGAAC/g	1/20	0.89393085690962	2	FACETS	0.808	0.744	0.866	0.808	0.744	0.866	CLONAL	2	TRUE	0	0.907969404799652	2		73	90	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259419	89259419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1187836345	NA	P-0040089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	66	474	0	ENST00000336596.2:c.563C>T	p.Ala188Val	p.A188V	ENST00000336596	NM_005233.5	188	gCt/gTt	3/17	0.469546162454555	2	FACETS	0.171	0.148	0.197	0.086	0.074	0.099	INDETERMINATE	1	TRUE	0	0.907969404799652	2		474	849	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525888	148525889	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAT	rs587778303	NA	P-0040089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	267	360	0	ENST00000320356.2:c.566_568dup	p.Asp189dup	p.D189dup	ENST00000320356	NM_004456.4	189	gga/gATGga	6/20	0.371835240951622	3	FACETS	0.986	0.927	1	0.493	0.463	0.524	INDETERMINATE	1	TRUE	1	0.907969404799652	3		360	867	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207077	1207077	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs121913319	NA	P-0040095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	260	1156	1	ENST00000326873.7:c.169del	p.Glu57LysfsTer7	p.E57Kfs*7	ENST00000326873	NM_000455.4	55	ctG/ct	1/10	0.197706954845181	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	0	0.197706954845181	2		1157	1297	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602746	10602746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	289	1083	0	ENST00000171111.5:c.832C>T	p.Pro278Ser	p.P278S	ENST00000171111	NM_203500.1	278	Ccg/Tcg	3/6	0.197706954845181	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.197706954845181	2		1083	1372	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95592924	95592924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755944755	NA	P-0040095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	27	327	0	ENST00000393063.1:c.896C>T	p.Ser299Leu	p.S299L	ENST00000393063	NM_030621.3	299	tCg/tTg	8/28	1	2	FACETS	0.695	0.553	0.858	0.695	0.553	0.858	SUBCLONAL	1	TRUE	1	0.197706954845181	2		327	393	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11301620	11301620	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	151	809	0	ENST00000361445.4:c.1531G>C	p.Val511Leu	p.V511L	ENST00000361445	NM_004958.3	511	Gtg/Ctg	10/58	0.197706954845181	2	FACETS	0.859	0.785	0.936	0.859	0.785	0.936	CLONAL	2	TRUE	0	0.197706954845181	2		809	889	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153252014	153252014	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	88	390	0	ENST00000281708.4:c.992A>G	p.Asp331Gly	p.D331G	ENST00000281708	NM_033632.3	331	gAt/gGt	7/12	0.197753108385555	3	FACETS	0.992	0.882	1	0.992	0.882	1	CLONAL	2	TRUE	1	0.197706954845181	3		390	493	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0040124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	359	588	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.691068422932515	3	FACETS	0.951	0.908	0.994	0.951	0.908	0.994	CLONAL	2	TRUE	1	0.691068422932515	3		588	735	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577549	64577550	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0040124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	316	466	0	ENST00000312049.6:c.32_33insG	p.Phe11LeufsTer106	p.F11Lfs*106	ENST00000312049	NM_130799.2	11	ttc/ttGc	2/10	0.691068422932515	2	FACETS	0.915	0.877	0.951	0.915	0.877	0.951	CLONAL	2	TRUE	0	0.691068422932515	2		466	500	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196875	108196875	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1565520641	NA	P-0040124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	294	382	0	ENST00000278616.4:c.6898T>G	p.Trp2300Gly	p.W2300G	ENST00000278616	NM_000051.3	2300	Tgg/Ggg	47/63	0.691068422932515	2	FACETS	0.992	0.952	1	0.992	0.952	1	CLONAL	2	TRUE	0	0.691068422932515	2		382	429	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493638	56493638	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	31	388	1	ENST00000267101.3:c.2954G>C	p.Gly985Ala	p.G985A	ENST00000267101	NM_001982.3	985	gGa/gCa	25/28	0.691068422932515	3	FACETS	0.2	0.161	0.244	0.1	0.08	0.122	SUBCLONAL	1	TRUE	1	0.691068422932515	3		389	604	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266035	41266100	+	inframe_deletion	In_Frame_Del	DEL	ACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACT	ACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACT	-	novel	NA	P-0040124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	90	270	0	ENST00000349496.5:c.32_97del	p.Asp11_Ser33delinsAla	p.D11_S33delinsA	ENST00000349496	NM_001904.3	11	gACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTct/gct	3/15	1	2	FACETS	0.84	0.754	0.93	0.84	0.754	0.93	CLONAL	1	TRUE	1	0.691068422932515	2		270	310	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0040125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	475	544	1				ENST00000310581	NM_198253.2	-/1132			0.672847594674861	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.672847594674861	2		545	651	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0040125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	137	253	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.672847594674861	2		253	316	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524698	106524698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	62	290	0	ENST00000359195.3:c.2859G>A	p.Met953Ile	p.M953I	ENST00000359195	NM_002649.2	953	atG/atA	9/11	0.672847594674861	3	FACETS	0.896	0.781	1	0.448	0.39	0.509	CLONAL	1	TRUE	1	0.672847594674861	3		290	275	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967269	134967269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749666684	NA	P-0040125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	208	633	0	ENST00000398015.3:c.2608C>T	p.Arg870Trp	p.R870W	ENST00000398015	NM_004441.4	870	Cgg/Tgg	14/16	1	2	FACETS	0.985	0.919	1	0.985	0.919	1	CLONAL	1	TRUE	1	0.672847594674861	2		633	628	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426731	47426731	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1452639448	NA	P-0040125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	299	323	0	ENST00000377045.4:c.976C>T	p.Arg326Ter	p.R326*	ENST00000377045	NM_001654.4	326	Cga/Tga	10/16	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.672847594674861	1		323	455	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105864	27105864	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	401	506	0	ENST00000324856.7:c.5476del	p.Asp1826ThrfsTer57	p.D1826Tfs*57	ENST00000324856	NM_006015.4	1825	gtG/gt	20/20	NA	2	FACETS	0.969	0.935	1			1	INDETERMINATE	2	TRUE	NA	0.672847594674861	2		506	615	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176719124	176719124	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	238	294	0	ENST00000439151.2:c.6428A>T	p.His2143Leu	p.H2143L	ENST00000439151	NM_022455.4	2143	cAc/cTc	22/23	0.663840563436578	2	FACETS	0.953	0.909	0.997	0.953	0.909	0.997	CLONAL	2	TRUE	0	0.672847594674861	2		294	371	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021064	26021064	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	137	387	1	ENST00000357647.3:c.347A>G	p.Lys116Arg	p.K116R	ENST00000357647	NM_003529.2	116	aAg/aGg	1/1	0.518333611577671	4	FACETS	0.848	0.772	0.928	0.283	0.257	0.31	CLONAL	1	TRUE	1	0.672847594674861	4		388	803	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242341	98242359	+	frameshift_variant	Frame_Shift_Del	DEL	CCACCATTCAAAACAAGGG	CCACCATTCAAAACAAGGG	-	novel	NA	P-0040125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	233	507	0	ENST00000331920.6:c.959_977del	p.Ala320AspfsTer16	p.A320Dfs*16	ENST00000331920	NM_000264.3	320	gCCCTTGTTTTGAATGGTGGa/ga	7/24	0.672847594674861	2	FACETS	0.832	0.789	0.875	0.832	0.789	0.875	CLONAL	2	TRUE	0	0.672847594674861	2		507	416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579718	7579718	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	207	745	0	ENST00000269305.4:c.78del	p.Pro27LeufsTer17	p.P27Lfs*17	ENST00000269305	NM_001126112.2	26	ctT/ct	3/11	0.547670098389992	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.547670098389992	1		745	534	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268479	46268479	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	82	419	0	ENST00000371998.3:c.2866G>T	p.Gly956Cys	p.G956C	ENST00000371998		956	Ggc/Tgc	15/23	1	2	FACETS	0.93	0.828	1	0.93	0.828	1	CLONAL	1	TRUE	1	0.547670098389992	2		419	322	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849224	76849224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	39	434	2	ENST00000373344.5:c.6052G>A	p.Gly2018Arg	p.G2018R	ENST00000373344	NM_000489.3	2018	Ggg/Agg	26/35	0.201689757488839	2	FACETS	0.526	0.438	0.622	0.263	0.219	0.311	INDETERMINATE	1	TRUE	0	0.547670098389992	2		436	271	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956162	175956162	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	70	383	0	ENST00000367669.3:c.2050A>C	p.Lys684Gln	p.K684Q	ENST00000367669	NM_022457.5	684	Aaa/Caa	18/20	1	2	FACETS	0.784	0.689	0.885	0.784	0.689	0.885	SUBCLONAL	1	TRUE	1	0.547670098389992	2		383	326	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425151	49425166	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGTTCCTGGTGCCC	CTGGTTCCTGGTGCCC	-	novel	NA	P-0040138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	44	979	0	ENST00000301067.7:c.13322_13337del	p.Gly4441AlafsTer73	p.G4441Afs*73	ENST00000301067	NM_003482.3	4441	gGGGCACCAGGAACCAGc/gc	39/54	1	2	FACETS	0.207	0.172	0.245	0.207	0.172	0.245	SUBCLONAL	1	TRUE	1	0.547670098389992	2		979	778	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112454	115112454	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	134	607	0	ENST00000257566.3:c.1286A>G	p.Asp429Gly	p.D429G	ENST00000257566	NM_016569.3	429	gAc/gGc	7/8	1	2	FACETS	0.791	0.72	0.864	0.791	0.72	0.864	SUBCLONAL	1	TRUE	1	0.547670098389992	2		607	619	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001989	29001989	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	106	511	0	ENST00000282397.4:c.1176C>G	p.Ile392Met	p.I392M	ENST00000282397	NM_002019.4	392	atC/atG	9/30	0.547670098389992	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.547670098389992	1		511	246	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039196	49039196	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	91	365	0	ENST00000267163.4:c.2275del	p.Val759SerfsTer6	p.V759Sfs*6	ENST00000267163	NM_000321.2	758	tcG/tc	22/27	0.547670098389992	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.547670098389992	1		365	216	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350623	15350623	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	262	920	1	ENST00000263377.2:c.3292G>T	p.Ala1098Ser	p.A1098S	ENST00000263377	NM_058243.2	1098	Gct/Tct	16/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.547670098389992	2		921	931	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030808	48030808	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	39	301	0	ENST00000234420.5:c.3422C>A	p.Ser1141Tyr	p.S1141Y	ENST00000234420	NM_000179.2	1141	tCt/tAt	5/10	1	2	FACETS	0.742	0.622	0.872	0.742	0.622	0.872	SUBCLONAL	1	TRUE	1	0.547670098389992	2		301	192	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564735	41564735	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	88	664	0	ENST00000263253.7:c.4036A>T	p.Ser1346Cys	p.S1346C	ENST00000263253	NM_001429.3	1346	Agt/Tgt	25/31	1	2	FACETS	0.782	0.697	0.872	0.782	0.697	0.872	SUBCLONAL	1	TRUE	1	0.547670098389992	2		664	411	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401541	401541	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	113	664	0	ENST00000380956.4:c.863A>T	p.Asp288Val	p.D288V	ENST00000380956	NM_001195286.1	288	gAc/gTc	7/9	1	2	FACETS	0.738	0.667	0.814	0.738	0.667	0.814	SUBCLONAL	1	TRUE	1	0.547670098389992	2		664	559	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771178	161771178	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	167	737	0	ENST00000366898.1:c.1351T>A	p.Cys451Ser	p.C451S	ENST00000366898	NM_004562.2	451	Tgc/Agc	12/12	1	2	FACETS	0.757	0.696	0.82	0.757	0.696	0.82	SUBCLONAL	1	TRUE	1	0.547670098389992	2		737	806	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845831	151845831	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	107	729	0	ENST00000262189.6:c.13181C>T	p.Pro4394Leu	p.P4394L	ENST00000262189	NM_170606.2	4394	cCt/cTt	52/59	1	2	FACETS	0.868	0.784	0.957	0.868	0.784	0.957	CLONAL	1	TRUE	1	0.547670098389992	2		729	450	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357729	70357729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556339256	NA	P-0040138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	52	896	4	ENST00000374080.3:c.5980C>T	p.Arg1994Trp	p.R1994W	ENST00000374080		1994	Cgg/Tgg	41/45	0.201689757488839	2	FACETS	0.254	0.215	0.296	0.127	0.107	0.148	INDETERMINATE	1	TRUE	0	0.547670098389992	2		900	748	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019562	123019562	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	61	366	0	ENST00000355640.3:c.50T>A	p.Ile17Asn	p.I17N	ENST00000355640		17	aTc/aAc	2/7	0.201689757488839	2	FACETS	0.735	0.639	0.838	0.368	0.319	0.419	INDETERMINATE	1	TRUE	0	0.547670098389992	2		366	303	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123505207	123505207	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	64	223	0	ENST00000371139.4:c.353G>T	p.Arg118Ile	p.R118I	ENST00000371139	NM_001114937.2	118	aGa/aTa	4/4	0.201689757488839	2	FACETS	1	0.974	1	0.708	0.627	0.791	INDETERMINATE	1	TRUE	0	0.547670098389992	2		223	165	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	133	737	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.907	0.83	0.987	0.907	0.83	0.987	CLONAL	1	TRUE	1	0.636056060490994	2		737	461	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786136	3786136	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	233	533	0	ENST00000262367.5:c.4629T>A	p.Asp1543Glu	p.D1543E	ENST00000262367	NM_004380.2	1543	gaT/gaA	28/31	1	2	FACETS	0.972	0.91	1	0.972	0.91	1	CLONAL	1	TRUE	1	0.636056060490994	2		533	754	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655178	45655178	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	136	386	0	ENST00000407780.3:c.674A>C	p.Asn225Thr	p.N225T	ENST00000407780	NM_001283052.1	225	aAc/aCc	4/7	1	2	FACETS	0.867	0.794	0.944	0.867	0.794	0.944	CLONAL	1	TRUE	1	0.636056060490994	2		386	493	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131196	55131196	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3307	8032	338	0	ENST00000257290.5:c.739T>C	p.Trp247Arg	p.W247R	ENST00000257290	NM_006206.4	247	Tgg/Cgg	5/23	0.636056060490994	43	FACETS	1	0.997	1			1	CLONAL	31	TRUE	NA	0.636056060490994	43		338	11339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0040204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	191	597	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.39184331307313	2	FACETS	0.825	0.772	0.878	0.825	0.772	0.878	CLONAL	2	TRUE	0	0.5386569142278	2		597	430	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	11	737	0				ENST00000310581	NM_198253.2	-/1132			0.356677330900596	0	FACETS	0.168	0.117	0.231			1	SUBCLONAL	1	TRUE	0	0.5386569142278	0		737	112	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0040204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	140	1157	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	0.235823787504088	1	FACETS	1	0.983	1	1	0.983	1	INDETERMINATE	1	TRUE	0	0.5386569142278	1		1157	309	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813307	102813307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764732420	NA	P-0040204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	33	747	1	ENST00000307046.8:c.382G>A	p.Asp128Asn	p.D128N	ENST00000307046	NM_001111285.1	128	Gac/Aac	3/4	1	2	FACETS	0.519	0.425	0.624	0.519	0.425	0.624	SUBCLONAL	1	TRUE	1	0.5386569142278	2		748	236	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434354	49434354	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	108	967	1	ENST00000301067.7:c.7199del	p.Pro2400LeufsTer26	p.P2400Lfs*26	ENST00000301067	NM_003482.3	2400	cCt/ct	31/54	0.416217975554292	5	FACETS	0.79	0.713	0.87	0.527	0.475	0.58	SUBCLONAL	2	TRUE	2	0.5386569142278	5		968	459	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218524	5218524	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1052009018	NA	P-0040204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	92	1135	0	ENST00000357368.4:c.3955C>T	p.Pro1319Ser	p.P1319S	ENST00000357368	NM_002850.3	1319	Ccc/Tcc	25/38	0.214016929145306	4	FACETS	1	0.914	1	0.257	0.229	0.287	INDETERMINATE	1	TRUE	0	0.5386569142278	4		1135	511	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818189	32818189	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777683307	NA	P-0040204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	86	933	2	ENST00000354258.4:c.1336G>A	p.Glu446Lys	p.E446K	ENST00000354258	NM_000593.5	446	Gaa/Aaa	5/11	0.5386569142278	6	FACETS	0.859	0.759	0.966	0.215	0.189	0.242	CLONAL	1	TRUE	2	0.5386569142278	6		935	772	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	181	737	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.618115084716177	2		737	509	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436089	51436094	+	inframe_deletion	In_Frame_Del	DEL	GACCTA	GACCTA	-	novel	NA	P-0040242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	177	395	0	ENST00000262662.1:c.51_56del	p.Asp17_Leu18del	p.D17_L18del	ENST00000262662		17	GACCTA/-	3/4	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.618115084716177	2		395	570	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439721	51439722	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	130	394	0	ENST00000262662.1:c.288dup	p.Asn97Ter	p.N97*	ENST00000262662		96	gtt/gTtt	4/4	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.618115084716177	2		394	409	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140729	55140730	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTCCTGGTGCTGTTGGTGATTGTGATCATCTCACTTATTGTCCTG	novel	NA	P-0040242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	129	600	0	ENST00000257290.5:c.1593_1637dup	p.Leu532_Val546dup	p.L532_V546dup	ENST00000257290	NM_006206.4	532	-/GTCCTGGTGCTGTTGGTGATTGTGATCATCTCACTTATTGTCCTG	11/23	1	2	FACETS	0.461	0.417	0.507	0.461	0.417	0.507	SUBCLONAL	1	TRUE	1	0.618115084716177	2		600	906	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0040265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	383	305	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.555011012097203	4	FACETS	0.937	0.9	0.972	0.937	0.9	0.972	CLONAL	3	TRUE	1	0.756560784508177	4		305	633	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933480	100933480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766277966	NA	P-0040265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	96	183	0	ENST00000325455.5:c.1910G>A	p.Arg637Gln	p.R637Q	ENST00000325455	NM_001202474.3	637	cGa/cAa	4/8	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.756560784508177	2		183	228	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843533	156843533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	323	896	0	ENST00000524377.1:c.959C>T	p.Ser320Phe	p.S320F	ENST00000524377	NM_002529.3	320	tCc/tTc	8/17	0.442769827395159	3	FACETS	1	0.973	1	0.524	0.494	0.553	INDETERMINATE	1	TRUE	1	0.756560784508177	3		896	1124	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444318	50444318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1427077431	NA	P-0040265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	153	333	1	ENST00000331340.3:c.248G>A	p.Arg83Gln	p.R83Q	ENST00000331340	NM_006060.4	83	cGa/cAa	4/8	0.555011012097203	4	FACETS	1	0.969	1	0.371	0.34	0.402	CLONAL	1	TRUE	1	0.756560784508177	4		334	639	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518175	8518175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1354824749	NA	P-0040265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	341	399	0	ENST00000356435.5:c.1216G>A	p.Glu406Lys	p.E406K	ENST00000356435		406	Gaa/Aaa	10/35	0.756560784508177	2	FACETS	0.982	0.949	1	0.982	0.949	1	CLONAL	2	TRUE	0	0.756560784508177	2		399	459	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0040265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	145	297	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.756560784508177	2		299	313	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135385	30135385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	183	398	0	ENST00000331968.5:c.433C>T	p.Arg145Cys	p.R145C	ENST00000331968	NM_002742.2	145	Cgt/Tgt	3/18	1	2	FACETS	0.929	0.864	0.995	0.929	0.864	0.995	CLONAL	1	TRUE	1	0.756560784508177	2		398	521	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432368	432368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1362895739	NA	P-0040265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	93	201	0	ENST00000399788.2:c.2155C>T	p.Arg719Cys	p.R719C	ENST00000399788	NM_001042603.1	719	Cgc/Tgc	16/28	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.756560784508177	2		201	227	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500816	8500816	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	329	475	0	ENST00000356435.5:c.2066C>A	p.Ala689Asp	p.A689D	ENST00000356435		689	gCc/gAc	13/35	0.756560784508177	2	FACETS	0.887	0.854	0.921	0.887	0.854	0.921	CLONAL	2	TRUE	0	0.756560784508177	2		475	490	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439623	51439623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	155	401	0	ENST00000262662.1:c.188C>T	p.Pro63Leu	p.P63L	ENST00000262662		63	cCc/cTc	4/4	1	2	FACETS	0.973	0.9	1	0.973	0.9	1	CLONAL	1	TRUE	1	0.756560784508177	2		401	421	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741919	17741919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180300708	NA	P-0040265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	92	242	1	ENST00000250003.3:c.590C>T	p.Ser197Phe	p.S197F	ENST00000250003	NM_002478.4	197	tCc/tTc	1/3	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.756560784508177	2		243	235	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857757	9857757	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	241	523	0	ENST00000330684.3:c.3644G>T	p.Arg1215Ile	p.R1215I	ENST00000330684	NM_001134407.1	1215	aGa/aTa	13/13	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.756560784508177	2		523	588	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78820297	78820297	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	702	957	0	ENST00000306801.3:c.1237C>A	p.Leu413Met	p.L413M	ENST00000306801	NM_020761.2	413	Ctg/Atg	11/34	0.723617270201326	3	FACETS	0.962	0.932	0.992	0.962	0.932	0.992	CLONAL	2	TRUE	1	0.756560784508177	3		957	1329	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436372	52436373	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	307	943	2	ENST00000460680.1:c.2121_2122delinsTT	p.Arg708Trp	p.R708W	ENST00000460680	NM_004656.3	707	ggCCgg/ggTTgg	17/17	1	2	FACETS	0.915	0.865	0.966	0.915	0.865	0.966	CLONAL	1	TRUE	1	0.756560784508177	2		945	887	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672006	30672006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	307	807	0	ENST00000376406.3:c.4954C>T	p.Pro1652Ser	p.P1652S	ENST00000376406	NM_014641.2	1652	Cca/Tca	10/15	0.737806905380674	4	FACETS	0.94	0.884	0.998	0.313	0.294	0.333	CLONAL	1	TRUE	1	0.756560784508177	4		807	1516	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185043	32185043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	249	692	0	ENST00000375023.3:c.1625G>A	p.Gly542Glu	p.G542E	ENST00000375023	NM_004557.3	542	gGa/gAa	10/30	0.737806905380674	4	FACETS	0.936	0.874	1	0.312	0.291	0.334	CLONAL	1	TRUE	1	0.756560784508177	4		692	1235	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69143596	69143596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751488995	NA	P-0040265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	130	289	0	ENST00000288368.4:c.4804C>T	p.Pro1602Ser	p.P1602S	ENST00000288368	NM_024870.2	1602	Cca/Tca	40/40	0.752382906449993	4	FACETS	0.775	0.703	0.85	0.258	0.234	0.284	SUBCLONAL	1	TRUE	1	0.756560784508177	4		289	779	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218500	1218500	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1131690951	NA	P-0040267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	81	440	0	ENST00000326873.7:c.374+1A>G		p.X125_splice	ENST00000326873	NM_000455.4	125			0.243184897947733	1	FACETS	0.974	0.859	1	0.974	0.859	1	CLONAL	1	TRUE	0	0.243184897947733	1		440	601	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279500	123279500	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	49	530	0	ENST00000358487.5:c.932T>C	p.Val311Ala	p.V311A	ENST00000358487	NM_000141.4	311	gTt/gCt	7/18	0.243184897947733	1	FACETS	0.462	0.39	0.542	0.462	0.39	0.542	SUBCLONAL	1	TRUE	0	0.243184897947733	1		530	766	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0040267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	106	289	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.848	0.763	0.937	1	0.986	1	CLONAL	2	TRUE	1	0.243184897947733	2		289	514	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888130	81888130	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	93	534	0	ENST00000359376.3:c.275A>C	p.Glu92Ala	p.E92A	ENST00000359376	NM_002661.3	92	gAa/gCa	3/33	1	2	FACETS	0.913	0.811	1	0.913	0.811	1	CLONAL	1	TRUE	1	0.243184897947733	2		534	838	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610227	10610227	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	171	870	0	ENST00000171111.5:c.483G>T	p.Met161Ile	p.M161I	ENST00000171111	NM_203500.1	161	atG/atT	2/6	0.243184897947733	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.243184897947733	1		870	1225	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223277	36223277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1391	187	1094	0	ENST00000222270.7:c.5827C>T	p.Pro1943Ser	p.P1943S	ENST00000222270	NM_014727.1	1943	Cct/Tct	28/37	1	2	FACETS	0.975	0.897	1	0.975	0.897	1	CLONAL	1	TRUE	1	0.243184897947733	2		1094	1578	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595839	52595839	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	73	492	0	ENST00000394830.3:c.4076G>A	p.Arg1359His	p.R1359H	ENST00000394830	NM_018313.4	1359	cGc/cAc	26/30	1	2	FACETS	0.714	0.623	0.812	0.714	0.623	0.812	SUBCLONAL	1	TRUE	1	0.243184897947733	2		492	841	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72864554	72864554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	16	269	0	ENST00000325599.8:c.883G>T	p.Val295Phe	p.V295F	ENST00000325599	NM_018130.2	295	Gtt/Ttt	8/11	1	2	FACETS	0.431	0.318	0.567	0.431	0.318	0.567	SUBCLONAL	1	TRUE	1	0.243184897947733	2		269	305	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0040308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	50	309	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.193125057955674	0	FACETS	0.792	0.689	0.897			1	SUBCLONAL	4	FALSE	0	0.193082395971143	0		309	132	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577069	7577069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55819519	NA	P-0040308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	8	791	0	ENST00000269305.4:c.869G>A	p.Arg290His	p.R290H	ENST00000269305	NM_001126112.2	290	cGc/cAc	8/11	1	2	FACETS	0.243	0.156	0.357	0.243	0.156	0.357	SUBCLONAL	1	FALSE	1	0.193082395971143	2		791	341	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120535068	120535068	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1012300179	NA	P-0040308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	12	469	0	ENST00000229340.5:c.587G>A	p.Arg196Gln	p.R196Q	ENST00000229340	NM_006861.6	196	cGa/cAa	6/6	0.193082395971143	6	FACETS	0.849	0.597	1	0.283	0.199	0.386	CLONAL	1	FALSE	3	0.193082395971143	6		469	203	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259469	55259469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146795390	NA	P-0040308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	10	518	0	ENST00000275493.2:c.2527G>A	p.Val843Ile	p.V843I	ENST00000275493	NM_005228.3	843	Gta/Ata	21/28	0.193125057955674	0	FACETS	0.513	0.348	0.719			1	SUBCLONAL	1	FALSE	0	0.193082395971143	0		518	163	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307414	118307416	+	inframe_deletion	In_Frame_Del	DEL	GCG	GCG	-	rs781936420	NA	P-0040308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	12	20	0	ENST00000534358.1:c.200_202del	p.Ala67del	p.A67del	ENST00000534358	NM_005933.3	63	GCG/-	1/36	1	2	FACETS	1	0.776	1	1	0.91	1	CLONAL	2	FALSE	1	0.193082395971143	2		20	57	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520087	106520087	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774448553	NA	P-0040312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	67	192	0	ENST00000359195.3:c.2515C>T	p.Arg839Cys	p.R839C	ENST00000359195	NM_002649.2	839	Cgc/Tgc	6/11	1	2	FACETS	0.656	0.576	0.739	0.656	0.576	0.739	SUBCLONAL	1	TRUE	1	0.807868030730813	2		192	253	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	38	306	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.128141973607372	3	FACETS	0.79	0.652	0.944	0.395	0.326	0.472	CLONAL	1	TRUE	1	0.2	3		306	529	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038879	12038879	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	41	217	0	ENST00000396373.4:c.1172A>C	p.Tyr391Ser	p.Y391S	ENST00000396373	NM_001987.4	391	tAt/tCt	7/8	0.128141973607372	3	FACETS	1	0.896	1	0.551	0.46	0.653	CLONAL	1	TRUE	1	0.2	3		217	409	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57474021	57474021	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	49	272	0	ENST00000371085.3:c.238G>T	p.Ala80Ser	p.A80S	ENST00000371085	NM_000516.4	80	Gca/Tca	3/13	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.2	2		272	367	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713853	30713853	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	65	517	1	ENST00000295754.5:c.1178G>T	p.Cys393Phe	p.C393F	ENST00000295754	NM_003242.5	393	tGc/tTc	4/7	1	2	FACETS	0.983	0.852	1	0.983	0.852	1	CLONAL	1	TRUE	1	0.2	2		518	661	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058719	180058719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770143594	NA	P-0040332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	53	787	0	ENST00000261937.6:c.118G>A	p.Val40Ile	p.V40I	ENST00000261937	NM_182925.4	40	Gtc/Atc	2/30	0.138155265950809	0	FACETS	0.504	0.428	0.587			1	SUBCLONAL	1	TRUE	0	0.2	0		787	842	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412530	63412530	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	44	658	0	ENST00000330258.3:c.637C>T	p.Gln213Ter	p.Q213*	ENST00000330258	NM_152424.3	213	Cag/Tag	2/2	1	2	FACETS	0.799	0.669	0.942	0.799	0.669	0.942	CLONAL	1	TRUE	1	0.2	2		658	551	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0040375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	806	289	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.786825023895307	7	FACETS	1	0.993	1			1	CLONAL	6	TRUE	NA	0.786825023895307	7		289	989	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59793361	59793361	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	51	376	0	ENST00000259008.2:c.2443C>T	p.Gln815Ter	p.Q815*	ENST00000259008	NM_032043.2	815	Cag/Tag	17/20	0.786825023895307	3	FACETS	0.348	0.296	0.406	0.174	0.148	0.203	SUBCLONAL	1	TRUE	1	0.786825023895307	3		376	519	SUCCESS
AR	367	MSKCC	GRCh37	X	66766199	66766199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035114992	NA	P-0040375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	40	324	0	ENST00000374690.3:c.1211C>T	p.Ala404Val	p.A404V	ENST00000374690	NM_000044.3	404	gCg/gTg	1/8	0.552425747141516	1	FACETS	0.25	0.209	0.295	0.25	0.209	0.295	SUBCLONAL	1	TRUE	0	0.786825023895307	1		324	247	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206581	108206581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	102	208	0	ENST00000278616.4:c.8161G>A	p.Asp2721Asn	p.D2721N	ENST00000278616	NM_000051.3	2721	Gac/Aac	56/63	0.786825023895307	1	FACETS	0.925	0.856	0.993	0.925	0.856	0.993	CLONAL	1	TRUE	0	0.786825023895307	1		208	170	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984914	9984914	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	93	390	0	ENST00000330684.3:c.1051A>G	p.Thr351Ala	p.T351A	ENST00000330684	NM_001134407.1	351	Act/Gct	4/13	0.435978747518402	1	FACETS	0.382	0.342	0.424	0.382	0.342	0.424	INDETERMINATE	1	TRUE	0	0.786825023895307	1		390	375	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622057	1622057	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	175	545	0	ENST00000344749.5:c.818G>T	p.Arg273Leu	p.R273L	ENST00000344749	NM_001136139.2	273	cGt/cTt	10/19	1	2	FACETS	0.993	0.924	1	0.993	0.924	1	CLONAL	1	TRUE	1	0.786825023895307	2		545	448	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1940259	1940259	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	50	233	0	ENST00000382891.5:c.1756G>T	p.Ala586Ser	p.A586S	ENST00000382891	NM_133335.3	586	Gca/Tca	8/22	1	2	FACETS	0.714	0.616	0.818	0.714	0.616	0.818	SUBCLONAL	1	TRUE	1	0.786825023895307	2		233	178	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974718	21974725	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCCCCC	GCGCCCCC	-	novel	NA	P-0040375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	119	287	0	ENST00000304494.5:c.102_109del	p.Gly35AlafsTer6	p.G35Afs*6	ENST00000304494	NM_000077.4	34	gcGGGGGCGCtg/gctg	1/3	0.786825023895307	1	FACETS	0.771	0.712	0.83	0.771	0.712	0.83	SUBCLONAL	1	TRUE	0	0.786825023895307	1		287	238	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044463	47044463	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	173	464	0	ENST00000377604.3:c.1960G>C	p.Asp654His	p.D654H	ENST00000377604	NM_001204468.1	654	Gac/Cac	18/24	0.552425747141516	1	FACETS	0.64	0.596	0.684	0.64	0.596	0.684	SUBCLONAL	1	TRUE	0	0.786825023895307	1		464	417	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239471	123239471	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	102	450	0	ENST00000358487.5:c.2366C>G	p.Ser789Cys	p.S789C	ENST00000358487	NM_000141.4	789	tCt/tGt	18/18	1	2	FACETS	0.487	0.437	0.54	0.487	0.437	0.54	SUBCLONAL	1	TRUE	1	0.786825023895307	2		450	532	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350578	15350578	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	101	591	0	ENST00000263377.2:c.3337G>C	p.Glu1113Gln	p.E1113Q	ENST00000263377	NM_058243.2	1113	Gag/Cag	16/20	1	2	FACETS	0.442	0.396	0.491	0.442	0.396	0.491	SUBCLONAL	1	TRUE	1	0.786825023895307	2		591	581	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945924	17945924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	217	628	1	ENST00000458235.1:c.2015C>T	p.Pro672Leu	p.P672L	ENST00000458235	NM_000215.3	672	cCt/cTt	15/24	1	2	FACETS	0.921	0.862	0.981	0.921	0.862	0.981	CLONAL	1	TRUE	1	0.786825023895307	2		629	599	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573851	41573852	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	273	592	0	ENST00000263253.7:c.6137dup	p.Ser2047ValfsTer26	p.S2047Vfs*26	ENST00000263253	NM_001429.3	2046	gtg/gTtg	31/31	0.435978747518402	1	FACETS	0.69	0.653	0.727	0.69	0.653	0.727	INDETERMINATE	1	TRUE	0	0.786825023895307	1		592	610	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440277	52440277	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1559589659	NA	P-0040375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	68	380	0	ENST00000460680.1:c.775C>G	p.Leu259Val	p.L259V	ENST00000460680	NM_004656.3	259	Ctg/Gtg	9/17	1	2	FACETS	0.511	0.448	0.579	0.511	0.448	0.579	SUBCLONAL	1	TRUE	1	0.786825023895307	2		380	338	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176548	142176548	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	129	324	0	ENST00000350721.4:c.7553A>G	p.Asn2518Ser	p.N2518S	ENST00000350721	NM_001184.3	2518	aAt/aGt	45/47	1	2	FACETS	0.988	0.908	1	0.988	0.908	1	CLONAL	1	TRUE	1	0.786825023895307	2		324	332	SUCCESS
ATR	545	MSKCC	GRCh37	3	142253968	142253968	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	139	222	0	ENST00000350721.4:c.3899G>T	p.Arg1300Leu	p.R1300L	ENST00000350721	NM_001184.3	1300	cGt/cTt	21/47	1	2	FACETS	0.87	0.8	0.942	0.87	0.8	0.942	CLONAL	1	TRUE	1	0.786825023895307	2		222	406	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251909	153251909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	118	297	0	ENST00000281708.4:c.1097G>A	p.Arg366Lys	p.R366K	ENST00000281708	NM_033632.3	366	aGg/aAg	7/12	0.157875775353569	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.786825023895307	0		297	371	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8525021	8525021	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs528492752	NA	P-0040375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	84	240	0	ENST00000356435.5:c.583G>C	p.Glu195Gln	p.E195Q	ENST00000356435		195	Gag/Cag	7/35	0.786825023895307	1	FACETS	0.841	0.767	0.914	0.841	0.767	0.914	CLONAL	1	TRUE	0	0.786825023895307	1		240	154	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040626	47040626	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	166	395	0	ENST00000377604.3:c.1264del	p.Glu422ArgfsTer63	p.E422Rfs*63	ENST00000377604	NM_001204468.1	421	Ggg/gg	13/24	0.552425747141516	1	FACETS	0.733	0.684	0.782	0.733	0.684	0.782	SUBCLONAL	1	TRUE	0	0.786825023895307	1		395	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578446	7578446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	302	601	0	ENST00000269305.4:c.484del	p.Ile162SerfsTer8	p.I162Sfs*8	ENST00000269305	NM_001126112.2	162	Atc/tc	5/11	0.339238871364373	2	FACETS	0.852	0.804	0.901	0.852	0.804	0.901	CLONAL	2	TRUE	0	0.374287858948695	2		601	947	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984094	2984094	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	217	522	0	ENST00000396946.4:c.436G>T	p.Asp146Tyr	p.D146Y	ENST00000396946	NM_032415.4	146	Gac/Tac	5/25	0.242287135438667	3	FACETS	0.771	0.717	0.826	0.771	0.717	0.826	SUBCLONAL	2	TRUE	1	0.374287858948695	3		522	893	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115849	8115850	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	103	853	0	ENST00000346208.3:c.1196dup	p.His399GlnfsTer108	p.H399Qfs*108	ENST00000346208		399	cac/cAac	6/6	1	2	FACETS	0.808	0.722	0.899	0.808	0.722	0.899	CLONAL	1	TRUE	1	0.289375739875061	2		853	881	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577503	7577504	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	105	718	0	ENST00000269305.4:c.777dup	p.Ser260LeufsTer4	p.S260Lfs*4	ENST00000269305	NM_001126112.2	259	-/C	7/11	1	2	FACETS	0.899	0.805	0.999	0.899	0.805	0.999	CLONAL	1	TRUE	1	0.289375739875061	2		718	807	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0040411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	9	205	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.083	0.054	0.12	0.083	0.054	0.12	SUBCLONAL	1	TRUE	1	0.503044772318292	2		205	432	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	129	737	0				ENST00000310581	NM_198253.2	-/1132			0.423836983911462	3	FACETS	0.934	0.869	0.998	1	0.988	1	CLONAL	3	TRUE	1	0.503044772318292	3		737	229	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806119	1806119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931614	NA	P-0040411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	19	606	0	ENST00000260795.2:c.1138G>A	p.Gly380Arg	p.G380R	ENST00000260795		380	Ggg/Agg	8/17	1	2	FACETS	0.098	0.074	0.127	0.098	0.074	0.127	SUBCLONAL	1	TRUE	1	0.503044772318292	2		606	770	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088672	27088672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	191	670	1	ENST00000324856.7:c.2281C>T	p.Gln761Ter	p.Q761*	ENST00000324856	NM_006015.4	761	Cag/Tag	7/20	1	2	FACETS	0.98	0.908	1	0.98	0.908	1	CLONAL	1	TRUE	1	0.503044772318292	2		671	775	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586503	189586503	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs143591434	NA	P-0040411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	111	366	1	ENST00000264731.3:c.1127G>A	p.Arg376His	p.R376H	ENST00000264731	NM_003722.4	376	cGc/cAc	8/14	1	2	FACETS	0.912	0.824	1	0.912	0.824	1	CLONAL	1	TRUE	1	0.503044772318292	2		367	484	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475550	12475550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479145908	NA	P-0040411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	170	556	0	ENST00000287820.6:c.1424C>T	p.Thr475Met	p.T475M	ENST00000287820	NM_015869.4	475	aCg/aTg	7/7	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.503044772318292	2		556	665	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339003	225339003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	101	425	0	ENST00000264414.4:c.2266C>T	p.Arg756Ter	p.R756*	ENST00000264414	NM_003590.4	756	Cga/Tga	16/16	1	2	FACETS	0.867	0.779	0.96	0.867	0.779	0.96	CLONAL	1	TRUE	1	0.503044772318292	2		425	463	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296404	15296404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1250956327	NA	P-0040411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	190	801	0	ENST00000263388.2:c.2038C>T	p.Arg680Cys	p.R680C	ENST00000263388	NM_000435.2	680	Cgc/Tgc	13/33	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.503044772318292	2		801	741	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0040449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	122	212	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.596	0.539	0.656	0.596	0.539	0.656	SUBCLONAL	1	TRUE	1	0.590718779269849	2		212	693	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244091	153244091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	27	430	0	ENST00000281708.4:c.2066G>A	p.Arg689Gln	p.R689Q	ENST00000281708	NM_033632.3	689	cGg/cAg	12/12	1	2	FACETS	0.158	0.125	0.196	0.158	0.125	0.196	SUBCLONAL	1	TRUE	1	0.590718779269849	2		430	577	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0040449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	98	363	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.398606662640925	1	FACETS	0.662	0.596	0.731	0.662	0.596	0.731	SUBCLONAL	1	TRUE	0	0.590718779269849	1		363	353	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962834	2962834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778151	NA	P-0040449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	88	795	2	ENST00000396946.4:c.2074G>A	p.Val692Met	p.V692M	ENST00000396946	NM_032415.4	692	Gtg/Atg	16/25	1	2	FACETS	0.392	0.346	0.44	0.392	0.346	0.44	SUBCLONAL	1	TRUE	1	0.590718779269849	2		797	761	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369241	118369241	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	65	278	0	ENST00000534358.1:c.5959del	p.Glu1987LysfsTer23	p.E1987Kfs*23	ENST00000534358	NM_005933.3	1987	Gaa/aa	22/36	1	2	FACETS	0.611	0.533	0.695	0.611	0.533	0.695	SUBCLONAL	1	TRUE	1	0.590718779269849	2		278	360	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946433	2946433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775862540	NA	P-0040449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	173	850	1	ENST00000396946.4:c.3304G>A	p.Val1102Met	p.V1102M	ENST00000396946	NM_032415.4	1102	Gtg/Atg	25/25	1	2	FACETS	0.764	0.704	0.825	0.764	0.704	0.825	SUBCLONAL	1	TRUE	1	0.590718779269849	2		851	767	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	245	737	0				ENST00000310581	NM_198253.2	-/1132			0.503408890880614	4	FACETS	0.897	0.853	0.94	0.897	0.853	0.94	CLONAL	3	FALSE	1	0.781972577838919	4		737	415	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409146	4409146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587777621	NA	P-0040482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	129	514	0	ENST00000261254.3:c.841C>T	p.Pro281Ser	p.P281S	ENST00000261254	NM_001759.3	281	Cct/Tct	5/5	0.382329825732163	5	FACETS	1	0.944	1	0.351	0.319	0.386	INDETERMINATE	1	FALSE	2	0.781972577838919	5		514	680	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459268	99459268	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	336	596	0	ENST00000268035.6:c.1904C>G	p.Ser635Cys	p.S635C	ENST00000268035	NM_000875.3	635	tCt/tGt	9/21	0.528174014961228	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	FALSE	2	0.781972577838919	4		596	761	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607180	189607180	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	369	731	0	ENST00000264731.3:c.1559G>A	p.Ser520Asn	p.S520N	ENST00000264731	NM_003722.4	520	aGc/aAc	12/14	0.781972577838919	4	FACETS	0.912	0.868	0.956	0.912	0.868	0.956	CLONAL	2	FALSE	2	0.781972577838919	4		731	922	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485917	8485917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757868633	NA	P-0040482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	74	416	1	ENST00000356435.5:c.2900C>T	p.Pro967Leu	p.P967L	ENST00000356435		967	cCg/cTg	17/35	0.781972577838919	2	FACETS	0.644	0.569	0.722	0.322	0.284	0.361	SUBCLONAL	1	FALSE	0	0.781972577838919	2		417	294	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0040485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	134	212	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.335073735573483	6	FACETS	1	0.967	1	0.74	0.678	0.804	INDETERMINATE	2	TRUE	3	0.639782464823402	6		212	430	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	136	623	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	0.639782464823402	3	FACETS	0.946	0.864	1	0.473	0.432	0.516	CLONAL	1	TRUE	1	0.639782464823402	3		623	593	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578538	7578538	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1131691037	NA	P-0040488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	272	958	0	ENST00000269305.4:c.392A>T	p.Asn131Ile	p.N131I	ENST00000269305	NM_001126112.2	131	aAc/aTc	5/11	0.697385073423591	1	FACETS	0.937	0.89	0.985	0.937	0.89	0.985	CLONAL	1	TRUE	0	0.697385073423591	1		958	542	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885832	23885832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	240	544	0	ENST00000374561.5:c.86G>A	p.Gly29Glu	p.G29E	ENST00000374561	NM_002167.4	29	gGg/gAg	1/3	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.697385073423591	2		544	586	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741360	17741360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781508900	NA	P-0040488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	135	925	0	ENST00000250003.3:c.31G>A	p.Val11Ile	p.V11I	ENST00000250003	NM_002478.4	11	Gta/Ata	1/3	0.125983037311607	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.697385073423591	0		925	660	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303178	11303178	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763879621	NA	P-0040488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	110	658	2	ENST00000361445.4:c.1405G>A	p.Ala469Thr	p.A469T	ENST00000361445	NM_004958.3	469	Gcc/Acc	9/58	0.191977167933225	5	FACETS	0.933	0.839	1			1	INDETERMINATE	1	TRUE	NA	0.697385073423591	5		660	692	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193228	11193228	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	159	639	0	ENST00000361445.4:c.5273A>C	p.Gln1758Pro	p.Q1758P	ENST00000361445	NM_004958.3	1758	cAg/cCg	38/58	0.191977167933225	5	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.697385073423591	5		639	767	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910840	114910840	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	111	603	0	ENST00000543371.1:c.959A>G	p.Lys320Arg	p.K320R	ENST00000543371	NM_001198531.1	320	aAa/aGa	9/14	1	2	FACETS	0.575	0.518	0.634	0.575	0.518	0.634	SUBCLONAL	1	TRUE	1	0.697385073423591	2		603	554	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239519	123239610	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGAGGTCCAAGTATTCCTGAAAGAAGGGAAGAGAGACGTTTTATTTCATCTTGGGTCAGGATAACAAGGTGAATACGGTTCGAGAGGCTGA	CTGAGGTCCAAGTATTCCTGAAAGAAGGGAAGAGAGACGTTTTATTTCATCTTGGGTCAGGATAACAAGGTGAATACGGTTCGAGAGGCTGA	-	novel	NA	P-0040488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	101	943	0	ENST00000358487.5:c.2302-75_2318del		p.X768_splice	ENST00000358487	NM_000141.4	768		18/18	1	2	FACETS	0.464	0.415	0.516	0.464	0.415	0.516	SUBCLONAL	1	TRUE	1	0.697385073423591	2		943	624	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230372	46230372	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	80	323	0	ENST00000334344.6:c.706T>C	p.Phe236Leu	p.F236L	ENST00000334344	NM_152641.2	236	Ttt/Ctt	7/21	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.697385073423591	2		323	226	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980914	40980914	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	268	440	0	ENST00000373198.4:c.1572G>T	p.Lys524Asn	p.K524N	ENST00000373198	NM_133170.3	524	aaG/aaT	10/32	0.670040694441453	3	FACETS	0.995	0.944	1	0.995	0.944	1	CLONAL	2	TRUE	1	0.697385073423591	3		440	521	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424421	47424422	+	stop_gained	Nonsense_Mutation	DNP	TC	TC	AA	novel	NA	P-0040488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	142	790	0	ENST00000377045.4:c.341_342delinsAA	p.Phe114Ter	p.F114*	ENST00000377045	NM_001654.4	114	tTC/tAA	5/16	0.697385073423591	4	FACETS	0.636	0.578	0.697			1	SUBCLONAL	1	TRUE	NA	0.697385073423591	4		790	1087	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0040507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	82	205	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.933	0.825	1	0.933	0.825	1	CLONAL	1	TRUE	1	0.328411941864065	2		205	535	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0040507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	182	798	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.310697806939617	4	FACETS	1	0.978	1	0.762	0.706	0.82	CLONAL	2	TRUE	1	0.328411941864065	4		798	644	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098954	178098954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553488015	NA	P-0040507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	62	270	0	ENST00000397062.3:c.91G>A	p.Gly31Arg	p.G31R	ENST00000397062	NM_006164.4	31	Gga/Aga	2/5	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.328411941864065	2		270	377	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883071	37883071	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	115	642	0	ENST00000269571.5:c.2974G>A	p.Glu992Lys	p.E992K	ENST00000269571		992	Gag/Aag	25/27	1	2	FACETS	0.892	0.804	0.986	0.892	0.804	0.986	CLONAL	1	TRUE	1	0.328411941864065	2		642	785	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607637	43607637	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs148406803	NA	P-0040507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	165	823	0	ENST00000355710.3:c.1613C>A	p.Thr538Lys	p.T538K	ENST00000355710	NM_020975.4	538	aCa/aAa	8/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.328411941864065	2		823	938	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579507	7579523	+	frameshift_variant	Frame_Shift_Del	DEL	TGGACCTGGGTCTTCAG	TGGACCTGGGTCTTCAG	-	novel	NA	P-0040507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	121	701	0	ENST00000269305.4:c.164_180del	p.Thr55ArgfsTer2	p.T55Rfs*2	ENST00000269305	NM_001126112.2	55	aCTGAAGACCCAGGTCCA/a	4/11	0.328411941864065	1	FACETS	0.848	0.767	0.934	0.848	0.767	0.934	CLONAL	1	TRUE	0	0.328411941864065	1		701	726	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438494	52438494	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756443059	NA	P-0040507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	111	472	1	ENST00000460680.1:c.1225G>A	p.Val409Met	p.V409M	ENST00000460680	NM_004656.3	409	Gtg/Atg	12/17	0.328411941864065	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	0	0.328411941864065	1		473	560	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729975	41729975	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs868188277	NA	P-0040507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	125	579	0	ENST00000242208.4:c.554G>C	p.Ser185Thr	p.S185T	ENST00000242208	NM_002192.2	185	aGc/aCc	3/3	0.310697806939617	4	FACETS	1	0.906	1	0.334	0.302	0.368	CLONAL	1	TRUE	1	0.328411941864065	4		579	1009	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27220069	27220069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs955187413	NA	P-0040507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	146	592	0	ENST00000380036.4:c.3126G>A	p.Met1042Ile	p.M1042I	ENST00000380036	NM_000459.3	1042	atG/atA	21/23	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.328411941864065	2		592	787	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114724375	114724375	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	55	305	0	ENST00000543371.1:c.442G>A	p.Ala148Thr	p.A148T	ENST00000543371	NM_001198531.1	148	Gca/Aca	4/14	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.189302264846701	2		305	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0040544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	102	557	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.189302264846701	2		557	732	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	44	267	0	ENST00000397062.3:c.101G>C	p.Arg34Pro	p.R34P	ENST00000397062	NM_006164.4	34	cGa/cCa	2/5	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.189302264846701	2		267	359	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660099	227660099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs774812399	NA	P-0040544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	86	503	0	ENST00000305123.5:c.3356T>C	p.Phe1119Ser	p.F1119S	ENST00000305123	NM_005544.2	1119	tTt/tCt	1/2	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.189302264846701	2		503	626	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565507	41565508	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0040544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	20	209	0	ENST00000263253.7:c.4176_4177del	p.Arg1392SerfsTer8	p.R1392Sfs*8	ENST00000263253	NM_001429.3	1391	agGAga/agga	26/31	0.189302264846701	2	FACETS	0.777	0.595	0.99	0.388	0.297	0.495	CLONAL	1	TRUE	0	0.189302264846701	2		209	272	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188232	10188232	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	47	481	0	ENST00000256474.2:c.375C>G	p.His125Gln	p.H125Q	ENST00000256474	NM_000551.3	125	caC/caG	2/3	0.0993559356569567	4	FACETS	0.784	0.66	0.922	0.392	0.33	0.461	INDETERMINATE	1	TRUE	2	0.189302264846701	4		481	753	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801524	1801524	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	102	666	0	ENST00000260795.2:c.430A>G	p.Thr144Ala	p.T144A	ENST00000260795		144	Aca/Gca	3/17	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.189302264846701	2		666	870	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	327	737	0				ENST00000310581	NM_198253.2	-/1132			0.287985890863623	5	FACETS	0.985	0.932	1			1	CLONAL	3	TRUE	NA	0.287985890863623	5		737	1100	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	187	795	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.287985890863623	1	FACETS	0.882	0.813	0.954	0.882	0.813	0.954	CLONAL	1	TRUE	0	0.287985890863623	1		795	1261	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545734	106545734	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	149	700	1	ENST00000359195.3:c.3211C>A	p.Gln1071Lys	p.Q1071K	ENST00000359195	NM_002649.2	1071	Cag/Aag	11/11	1	2	FACETS	0.885	0.807	0.967	0.885	0.807	0.967	CLONAL	1	TRUE	1	0.287985890863623	2		701	1169	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30061031	30061031	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	122	490	0	ENST00000338641.4:c.863C>G	p.Ser288Ter	p.S288*	ENST00000338641	NM_000268.3	288	tCa/tGa	9/16	0.287985890863623	1	FACETS	0.956	0.864	1	0.956	0.864	1	CLONAL	1	TRUE	0	0.287985890863623	1		490	759	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251620	212251620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	76	496	0	ENST00000342788.4:c.3439G>A	p.Glu1147Lys	p.E1147K	ENST00000342788	NM_005235.2	1147	Gag/Aag	27/28	1	2	FACETS	0.634	0.555	0.719	0.634	0.555	0.719	SUBCLONAL	1	TRUE	1	0.287985890863623	2		496	833	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2114289	2114289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	146	826	0	ENST00000219476.3:c.1460C>T	p.Ser487Leu	p.S487L	ENST00000219476	NM_000548.3	487	tCa/tTa	15/42	1	2	FACETS	0.83	0.755	0.908	0.83	0.755	0.908	CLONAL	1	TRUE	1	0.287985890863623	2		826	1222	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047519	49047519	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1131690908	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	67	288	0	ENST00000267163.4:c.2513C>G	p.Ser838Ter	p.S838*	ENST00000267163	NM_000321.2	838	tCa/tGa	24/27	0.287985890863623	1	FACETS	0.864	0.753	0.984	0.864	0.753	0.984	CLONAL	1	TRUE	0	0.287985890863623	1		288	461	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339110	65339111	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	216	508	7	ENST00000342505.4:c.425dup	p.Ile143AspfsTer9	p.I143Dfs*9	ENST00000342505	NM_002227.2	142	aag/aaAg	5/25	0.287985890863623	2	FACETS	0.901	0.84	0.965	0.901	0.84	0.965	CLONAL	2	TRUE	0	0.287985890863623	2		515	832	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772254	68772254	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	205	954	0	ENST00000261769.5:c.103G>T	p.Glu35Ter	p.E35*	ENST00000261769	NM_004360.3	35	Gag/Tag	2/16	0.287985890863623	1	FACETS	0.951	0.881	1	0.951	0.881	1	CLONAL	1	TRUE	0	0.287985890863623	1		954	1281	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434618	49434618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs949690934	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1347	210	1007	0	ENST00000301067.7:c.6935C>T	p.Ser2312Leu	p.S2312L	ENST00000301067	NM_003482.3	2312	tCa/tTa	31/54	1	2	FACETS	0.937	0.867	1	0.937	0.867	1	CLONAL	1	TRUE	1	0.287985890863623	2		1007	1557	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216515	108216515	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	51	339	0	ENST00000278616.4:c.8464G>C	p.Asp2822His	p.D2822H	ENST00000278616	NM_000051.3	2822	Gat/Cat	58/63	1	2	FACETS	0.601	0.511	0.701	0.601	0.511	0.701	SUBCLONAL	1	TRUE	1	0.287985890863623	2		339	589	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421877	49421877	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	188	901	0	ENST00000301067.7:c.14430G>C	p.Lys4810Asn	p.K4810N	ENST00000301067	NM_003482.3	4810	aaG/aaC	46/54	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.287985890863623	2		901	1288	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572022239	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1228	195	1003	1	ENST00000301067.7:c.7061C>T	p.Pro2354Leu	p.P2354L	ENST00000301067	NM_003482.3	2354	cCt/cTt	31/54	1	2	FACETS	0.952	0.878	1	0.952	0.878	1	CLONAL	1	TRUE	1	0.287985890863623	2		1004	1423	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856313	111856313	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	16	43	0	ENST00000341259.2:c.364G>C	p.Glu122Gln	p.E122Q	ENST00000341259	NM_005475.2	122	Gag/Cag	2/8	1	2	FACETS	0.966	0.722	1	0.966	0.722	1	CLONAL	1	TRUE	1	0.287985890863623	2		43	115	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120478	2120478	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	123	829	1	ENST00000219476.3:c.1738G>A	p.Ala580Thr	p.A580T	ENST00000219476	NM_000548.3	580	Gca/Aca	17/42	1	2	FACETS	0.678	0.612	0.749	0.678	0.612	0.749	SUBCLONAL	1	TRUE	1	0.287985890863623	2		830	1259	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244538	41244538	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786202534	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	167	730	0	ENST00000357654.3:c.3010G>C	p.Glu1004Gln	p.E1004Q	ENST00000357654	NM_007294.3	1004	Gag/Cag	10/23	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.287985890863623	2		730	1138	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519938	66519938	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	114	527	0	ENST00000358598.2:c.421C>A	p.Leu141Ile	p.L141I	ENST00000358598	NM_212471.2	141	Ctt/Att	4/11	1	2	FACETS	0.948	0.853	1	0.948	0.853	1	CLONAL	1	TRUE	1	0.287985890863623	2		527	835	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349205	15349205	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	112	527	0	ENST00000263377.2:c.4072G>C	p.Glu1358Gln	p.E1358Q	ENST00000263377	NM_058243.2	1358	Gaa/Caa	20/20	1	2	FACETS	0.882	0.792	0.977	0.882	0.792	0.977	CLONAL	1	TRUE	1	0.287985890863623	2		527	882	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143514	30143514	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	72	312	0	ENST00000389048.3:c.12C>G	p.Ile4Met	p.I4M	ENST00000389048	NM_004304.4	4	atC/atG	1/29	0.227369125459928	3	FACETS	1	0.898	1	0.515	0.451	0.585	CLONAL	1	TRUE	1	0.287985890863623	3		312	555	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288946	212288946	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	80	515	0	ENST00000342788.4:c.2800G>C	p.Glu934Gln	p.E934Q	ENST00000342788	NM_005235.2	934	Gag/Cag	23/28	1	2	FACETS	0.667	0.586	0.754	0.667	0.586	0.754	SUBCLONAL	1	TRUE	1	0.287985890863623	2		515	833	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72866391	72866391	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	88	334	0	ENST00000325599.8:c.872G>T	p.Gly291Val	p.G291V	ENST00000325599	NM_018130.2	291	gGa/gTa	7/11	1	2	FACETS	0.932	0.826	1	0.932	0.826	1	CLONAL	1	TRUE	1	0.287985890863623	2		334	656	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156150	106156150	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	68	355	0	ENST00000380013.4:c.1051G>A	p.Glu351Lys	p.E351K	ENST00000380013	NM_001127208.2	351	Gaa/Aaa	3/11	1	2	FACETS	0.736	0.64	0.839	0.736	0.64	0.839	SUBCLONAL	1	TRUE	1	0.287985890863623	2		355	642	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	218493	218493	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs878854631	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	79	153	0	ENST00000264932.6:c.23C>G	p.Ser8Trp	p.S8W	ENST00000264932	NM_004168.2	8	tCg/tGg	1/15	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.287985890863623	NA		153	436	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651987	36651988	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	193	838	0	ENST00000244741.5:c.110_111dup	p.Met38Ter	p.M38*	ENST00000244741	NM_000389.4	37	cta/cTAta	2/3	1	2	FACETS	0.969	0.894	1	0.969	0.894	1	CLONAL	1	TRUE	1	0.287985890863623	2		838	1383	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652250	36652251	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGC	novel	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	154	851	0	ENST00000244741.5:c.373_376dup	p.Gln126ArgfsTer4	p.Q126Rfs*4	ENST00000244741	NM_000389.4	124	-/GAGC	2/3	1	2	FACETS	0.862	0.787	0.941	0.862	0.787	0.941	CLONAL	1	TRUE	1	0.287985890863623	2		851	1241	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845691	151845691	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	176	659	0	ENST00000262189.6:c.13321G>C	p.Glu4441Gln	p.E4441Q	ENST00000262189	NM_170606.2	4441	Gag/Cag	52/59	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.287985890863623	2		659	1039	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117870635	117870635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	106	420	0	ENST00000297338.2:c.437G>A	p.Arg146Lys	p.R146K	ENST00000297338	NM_006265.2	146	aGa/aAa	5/14	0.287985890863623	3	FACETS	0.871	0.779	0.968	0.435	0.389	0.484	CLONAL	1	TRUE	1	0.287985890863623	3		420	967	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117870648	117870648	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	97	451	0	ENST00000297338.2:c.424G>C	p.Glu142Gln	p.E142Q	ENST00000297338	NM_006265.2	142	Gag/Cag	5/14	0.287985890863623	3	FACETS	0.794	0.707	0.888	0.397	0.353	0.444	SUBCLONAL	1	TRUE	1	0.287985890863623	3		451	970	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117874081	117874081	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	103	350	0	ENST00000297338.2:c.373G>C	p.Asp125His	p.D125H	ENST00000297338	NM_006265.2	125	Gat/Cat	4/14	0.287985890863623	3	FACETS	1	0.953	1	0.557	0.499	0.62	CLONAL	1	TRUE	1	0.287985890863623	3		350	734	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93640016	93640016	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	72	445	0	ENST00000375746.1:c.1345G>C	p.Glu449Gln	p.E449Q	ENST00000375746	NM_001174167.1	449	Gag/Cag	10/14	0.233913620843427	1	FACETS	0.707	0.618	0.804	0.707	0.618	0.804	SUBCLONAL	1	TRUE	0	0.287985890863623	1		445	605	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923064	39923064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	166	401	0	ENST00000378444.4:c.3644G>A	p.Arg1215Lys	p.R1215K	ENST00000378444	NM_001123385.1	1215	aGa/aAa	8/15	1	1	FACETS	0.769	0.709	0.831	1	0.99	1	SUBCLONAL	2	TRUE	0	0.287985890863623	1		401	642	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938390	44938390	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	85	201	0	ENST00000377967.4:c.2939-1G>C		p.X980_splice	ENST00000377967	NM_021140.2	980			1	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.287985890863623	1		201	398	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937678	76937678	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	116	205	0	ENST00000373344.5:c.3070G>C	p.Glu1024Gln	p.E1024Q	ENST00000373344	NM_000489.3	1024	Gaa/Caa	9/35	1	1	FACETS	0.787	0.714	0.863	1	0.986	1	SUBCLONAL	2	TRUE	0	0.287985890863623	1		205	438	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938716	76938716	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	216	339	0	ENST00000373344.5:c.2032G>T	p.Asp678Tyr	p.D678Y	ENST00000373344	NM_000489.3	678	Gat/Tat	9/35	1	1	FACETS	0.921	0.86	0.984	1	0.994	1	CLONAL	2	TRUE	0	0.287985890863623	1		339	697	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76949315	76949315	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	69	196	0	ENST00000373344.5:c.482G>A	p.Gly161Glu	p.G161E	ENST00000373344	NM_000489.3	161	gGa/gAa	6/35	1	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.287985890863623	1		196	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	454	675	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.110267626569347	4	FACETS	0.889	0.849	0.929	0.889	0.849	0.929	INDETERMINATE	2	TRUE	2	0.67	4		675	1273	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912750	32912750	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28897727	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	201	347	0	ENST00000380152.3:c.4258G>T	p.Asp1420Tyr	p.D1420Y	ENST00000380152		1420	Gat/Tat	11/27	1	2	FACETS	0.912	0.849	0.976	0.912	0.849	0.976	CLONAL	1	TRUE	1	0.67	2		347	658	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462371	89462371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866025221	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	394	560	0	ENST00000336596.2:c.1843G>A	p.Glu615Lys	p.E615K	ENST00000336596	NM_005233.5	615	Gaa/Aaa	10/17	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.67	2		560	1160	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47684731	47684731	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	238	351	2	ENST00000347630.2:c.718C>T	p.Arg240Ter	p.R240*	ENST00000347630	NM_001007230.1	240	Cga/Tga	9/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.67	2		353	642	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479811	67479811	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500766	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	314	590	0	ENST00000327367.4:c.1118G>A	p.Arg373His	p.R373H	ENST00000327367	NM_005902.3	373	cGc/cAc	8/9	0.3	1	FACETS	0.621	0.586	0.656	0.621	0.586	0.656	INDETERMINATE	1	TRUE	0	0.67	1		590	1004	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459239	120459239	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	283	518	0	ENST00000256646.2:c.6106C>T	p.Arg2036Ter	p.R2036*	ENST00000256646	NM_024408.3	2036	Cga/Tga	34/34	0.3	1	FACETS	0.663	0.625	0.702	0.663	0.625	0.702	INDETERMINATE	1	TRUE	0	0.67	1		518	847	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	448	643	0	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	0.110267626569347	4	FACETS	0.875	0.836	0.915	0.875	0.836	0.915	INDETERMINATE	2	TRUE	2	0.67	4		643	1276	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231707	66231707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1211795184	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	373	380	1	ENST00000273854.3:c.1993G>A	p.Glu665Lys	p.E665K	ENST00000273854	NM_004439.5	665	Gaa/Aaa	11/18	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.67	2		381	946	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777640	9777640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148703447	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	582	797	2	ENST00000377346.4:c.976G>A	p.Glu326Lys	p.E326K	ENST00000377346	NM_005026.3	326	Gag/Aag	8/24	0.292455180492658	3	FACETS	1	0.997	1			1	INDETERMINATE	1	TRUE	NA	0.67	3		799	1556	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453486	138453486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451809865	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	162	331	1	ENST00000289153.2:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000289153	NM_006219.2	321	cGa/cAa	5/22	1	2	FACETS	0.848	0.783	0.916	0.848	0.783	0.916	CLONAL	1	TRUE	1	0.67	2		332	570	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793710	89793710	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	371	353	0	ENST00000336032.3:c.779A>C	p.Lys260Thr	p.K260T	ENST00000336032	NM_006813.2	260	aAa/aCa	2/2	0.140411193283748	3	FACETS	0.772	0.735	0.81	0.772	0.735	0.81	INDETERMINATE	2	TRUE	1	0.67	3		353	957	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	626	454	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	0.228661763914847	1	FACETS	1	0.997	1	1	0.997	1	INDETERMINATE	1	TRUE	0	0.67	1		454	929	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210733	5210733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779302415	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	421	630	0	ENST00000357368.4:c.5318C>T	p.Ser1773Leu	p.S1773L	ENST00000357368	NM_002850.3	1773	tCg/tTg	34/38	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.67	2		630	1231	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945129	32945129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80359104	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	150	311	1	ENST00000380152.3:c.8524C>T	p.Arg2842Cys	p.R2842C	ENST00000380152		2842	Cgc/Tgc	20/27	1	2	FACETS	0.888	0.817	0.962	0.888	0.817	0.962	CLONAL	1	TRUE	1	0.67	2		312	504	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155627	56155627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768025328	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	268	349	0	ENST00000399503.3:c.719C>T	p.Ala240Val	p.A240V	ENST00000399503	NM_005921.1	240	gCg/gTg	3/20	0.106444737938325	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.67	0		349	740	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424958105	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	237	262	0	ENST00000334344.6:c.940C>T	p.Arg314Cys	p.R314C	ENST00000334344	NM_152641.2	314	Cgt/Tgt	8/21	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.67	2		262	668	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881438	48881438	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	109	153	0	ENST00000267163.4:c.160G>T	p.Glu54Ter	p.E54*	ENST00000267163	NM_000321.2	54	Gaa/Taa	2/27	1	2	FACETS	0.924	0.839	1	0.924	0.839	1	CLONAL	1	TRUE	1	0.67	2		153	352	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	156	365	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.864	0.796	0.934	0.864	0.796	0.934	CLONAL	1	TRUE	1	0.67	2		365	539	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631622	119631622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	194	332	0	ENST00000316626.5:c.644C>T	p.Ser215Leu	p.S215L	ENST00000316626		215	tCg/tTg	6/12	1	2	FACETS	0.919	0.855	0.985	0.919	0.855	0.985	CLONAL	1	TRUE	1	0.67	2		332	630	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029297	143029297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757219824	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	121	267	0	ENST00000262992.4:c.2323G>A	p.Glu775Lys	p.E775K	ENST00000262992	NM_001101669.1	775	Gaa/Aaa	21/24	1	2	FACETS	0.858	0.781	0.937	0.858	0.781	0.937	CLONAL	1	TRUE	1	0.67	2		267	421	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991736	25991736	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs530632623	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	85	311	1	ENST00000435504.4:c.506C>T	p.Ala169Val	p.A169V	ENST00000435504		169	gCg/gTg	7/13	1	2	FACETS	0.469	0.415	0.526	0.469	0.415	0.526	SUBCLONAL	1	TRUE	1	0.67	2		312	541	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849852	156849852	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	405	636	0	ENST00000524377.1:c.2108A>C	p.Lys703Thr	p.K703T	ENST00000524377	NM_002529.3	703	aAg/aCg	16/17	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.67	2		636	1196	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805719	43805719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528834914	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	496	567	0	ENST00000372470.3:c.775G>A	p.Glu259Lys	p.E259K	ENST00000372470	NM_005373.2	259	Gaa/Aaa	5/12	0.140411193283748	3	FACETS	1	0.996	1	0.723	0.692	0.754	INDETERMINATE	1	TRUE	1	0.67	3		567	1367	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267600319	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	44	369	1	ENST00000257430.4:c.4199C>T	p.Ser1400Leu	p.S1400L	ENST00000257430	NM_000038.5	1400	tCg/tTg	16/16	1	2	FACETS	0.216	0.18	0.255	0.216	0.18	0.255	SUBCLONAL	1	TRUE	1	0.67	2		370	609	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066627	94066627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	309	473	0	ENST00000369303.4:c.1132G>A	p.Glu378Lys	p.E378K	ENST00000369303	NM_004440.3	378	Gaa/Aaa	5/17	0.140411193283748	3	FACETS	1	0.993	1	0.686	0.649	0.724	INDETERMINATE	1	TRUE	1	0.67	3		473	897	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	247	340	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.986	0.925	1	0.986	0.925	1	CLONAL	1	TRUE	1	0.67	2		340	748	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176561	142176561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	308	452	0	ENST00000350721.4:c.7540C>T	p.Arg2514Cys	p.R2514C	ENST00000350721	NM_001184.3	2514	Cgc/Tgc	45/47	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.67	2		452	916	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951852	2951852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770667388	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	404	712	1	ENST00000396946.4:c.3098C>T	p.Ala1033Val	p.A1033V	ENST00000396946	NM_032415.4	1033	gCg/gTg	23/25	0.279719149156803	1	FACETS	0.71	0.676	0.744	0.71	0.676	0.744	INDETERMINATE	1	TRUE	0	0.67	1		713	1130	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266512	198266512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	160	347	0	ENST00000335508.6:c.2324G>A	p.Arg775Gln	p.R775Q	ENST00000335508	NM_012433.2	775	cGa/cAa	16/25	1	2	FACETS	0.915	0.845	0.987	0.915	0.845	0.987	CLONAL	1	TRUE	1	0.67	2		347	522	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041074	42041074	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	486	570	0	ENST00000219905.7:c.5452C>T	p.Arg1818Ter	p.R1818*	ENST00000219905	NM_001164273.1	1818	Cga/Tga	16/24	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.67	2		570	1218	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131412	202131412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339962485	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	290	480	1	ENST00000358485.4:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000358485	NM_001080125.1	127	cGa/cAa	2/9	1	2	FACETS	0.939	0.885	0.994	0.939	0.885	0.994	CLONAL	1	TRUE	1	0.67	2		481	922	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223251	5223251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199604489	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	436	659	1	ENST00000357368.4:c.2552G>A	p.Arg851His	p.R851H	ENST00000357368	NM_002850.3	851	cGc/cAc	18/38	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.67	2		660	1261	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698180	47698180	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63751411	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	140	274	0	ENST00000233146.2:c.1738G>T	p.Glu580Ter	p.E580*	ENST00000233146	NM_000251.2	580	Gaa/Taa	11/16	1	2	FACETS	0.871	0.798	0.945	0.871	0.798	0.945	CLONAL	1	TRUE	1	0.67	2		274	480	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	208	203	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	0.292455180492658	3	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.67	3		203	584	SUCCESS
YES1	7525	MSKCC	GRCh37	18	751726	751726	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1010928891	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	153	329	0	ENST00000314574.4:c.350G>T	p.Arg117Ile	p.R117I	ENST00000314574	NM_005433.3	117	aGa/aTa	3/12	1	2	FACETS	0.821	0.756	0.89	0.821	0.756	0.89	CLONAL	1	TRUE	1	0.67	2		329	556	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347916	73347916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139907646	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	188	264	0	ENST00000377767.4:c.1145G>A	p.Arg382Gln	p.R382Q	ENST00000377767	NM_014953.3	382	cGa/cAa	8/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.67	2		264	546	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203493	108203493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140263969	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	107	193	0	ENST00000278616.4:c.7793G>A	p.Arg2598Gln	p.R2598Q	ENST00000278616	NM_000051.3	2598	cGa/cAa	53/63	1	2	FACETS	0.948	0.86	1	0.948	0.86	1	CLONAL	1	TRUE	1	0.67	2		193	337	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951085	17951085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	613	602	0	ENST00000458235.1:c.1208G>A	p.Arg403His	p.R403H	ENST00000458235	NM_000215.3	403	cGc/cAc	9/24	0.3	3	FACETS	0.757	0.729	0.786			1	INDETERMINATE	2	TRUE	NA	0.67	3		602	1613	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162904	47162904	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs757432733	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	227	413	0	ENST00000409792.3:c.3222G>T	p.Lys1074Asn	p.K1074N	ENST00000409792	NM_014159.6	1074	aaG/aaT	3/21	1	2	FACETS	0.998	0.935	1	0.998	0.935	1	CLONAL	1	TRUE	1	0.67	2		413	679	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238542	142238542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148064542	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	166	238	0	ENST00000350721.4:c.4351C>T	p.Arg1451Trp	p.R1451W	ENST00000350721	NM_001184.3	1451	Cgg/Tgg	24/47	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.67	2		238	482	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461575	138461575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1225812682	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	202	406	1	ENST00000289153.2:c.446G>A	p.Arg149Gln	p.R149Q	ENST00000289153	NM_006219.2	149	cGa/cAa	3/22	1	2	FACETS	0.852	0.792	0.913	0.852	0.792	0.913	CLONAL	1	TRUE	1	0.67	2		407	708	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645512	67645512	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	130	215	0	ENST00000264010.4:c.777G>T	p.Lys259Asn	p.K259N	ENST00000264010	NM_006565.3	259	aaG/aaT	3/12	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.67	2		215	377	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669547	88669547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56394626	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	232	436	0	ENST00000360948.2:c.1351G>A	p.Val451Ile	p.V451I	ENST00000360948	NM_001012338.2	451	Gtc/Atc	12/19	0.3	1	FACETS	0.571	0.534	0.61	0.571	0.534	0.61	INDETERMINATE	1	TRUE	0	0.67	1		436	806	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332415	70332415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1419371452	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	739	614	0	ENST00000373644.4:c.320G>A	p.Arg107Gln	p.R107Q	ENST00000373644	NM_030625.2	107	cGa/cAa	2/12	1	2	FACETS	1	0.991	1	1	0.998	1	CLONAL	2	TRUE	1	0.67	2		614	1066	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120496243	120496243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782306821	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	284	451	0	ENST00000256646.2:c.2288C>T	p.Ser763Leu	p.S763L	ENST00000256646	NM_024408.3	763	tCg/tTg	14/34	1	2	FACETS	0.921	0.868	0.976	0.921	0.868	0.976	CLONAL	1	TRUE	1	0.67	2		451	920	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938406	76938406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	277	742	0	ENST00000373344.5:c.2342G>A	p.Arg781Gln	p.R781Q	ENST00000373344	NM_000489.3	781	cGa/cAa	9/35	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.67	1		742	444	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186757	108186757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs864622251	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	224	423	0	ENST00000278616.4:c.6115G>A	p.Glu2039Lys	p.E2039K	ENST00000278616	NM_000051.3	2039	Gaa/Aaa	42/63	1	2	FACETS	0.832	0.776	0.888	0.832	0.776	0.888	CLONAL	1	TRUE	1	0.67	2		423	804	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925397	114925397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773530340	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	362	701	0	ENST00000543371.1:c.1475C>T	p.Ser492Leu	p.S492L	ENST00000543371	NM_001198531.1	492	tCg/tTg	14/14	1	2	FACETS	0.968	0.919	1	0.968	0.919	1	CLONAL	1	TRUE	1	0.67	2		701	1116	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480542	50480542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559383300	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	362	434	0	ENST00000394963.4:c.412C>T	p.Arg138Cys	p.R138C	ENST00000394963	NM_003076.4	138	Cgt/Tgt	4/13	0.110267626569347	4	FACETS	0.888	0.844	0.933	0.888	0.844	0.933	INDETERMINATE	2	TRUE	2	0.67	4		434	1016	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518086	187518086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200185840	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	327	528	0	ENST00000441802.2:c.12608G>A	p.Arg4203His	p.R4203H	ENST00000441802	NM_005245.3	4203	cGt/cAt	25/27	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.67	2		528	961	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506670	103506670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1372959301	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	124	253	0	ENST00000355739.4:c.413G>A	p.Arg138Gln	p.R138Q	ENST00000355739	NM_000123.3	138	cGa/cAa	4/15	1	2	FACETS	0.748	0.68	0.818	0.748	0.68	0.818	SUBCLONAL	1	TRUE	1	0.67	2		253	495	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589618	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519838	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	125	228	1	ENST00000274335.5:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000274335		461	Cga/Tga	10/15	0.292455180492658	3	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.67	3		229	409	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319853	8319853	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	46	366	0	ENST00000356435.5:c.5648G>A	p.Arg1883Gln	p.R1883Q	ENST00000356435		1883	cGa/cAa	34/35	1	2	FACETS	0.245	0.206	0.289	0.245	0.206	0.289	SUBCLONAL	1	TRUE	1	0.67	2		366	560	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459558	50459558	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	130	283	0	ENST00000331340.3:c.847C>A	p.Leu283Ile	p.L283I	ENST00000331340	NM_006060.4	283	Ctt/Att	7/8	0.279719149156803	1	FACETS	0.563	0.515	0.614	0.563	0.515	0.614	INDETERMINATE	1	TRUE	0	0.67	1		283	458	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543633	148543633	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	285	414	0	ENST00000320356.2:c.175G>T	p.Glu59Ter	p.E59*	ENST00000320356	NM_004456.4	59	Gaa/Taa	3/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.67	2		414	827	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686299	30686299	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs767191783	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	225	374	0	ENST00000295754.5:c.155A>C	p.Lys52Thr	p.K52T	ENST00000295754	NM_003242.5	52	aAa/aCa	2/7	1	2	FACETS	0.978	0.915	1	0.978	0.915	1	CLONAL	1	TRUE	1	0.67	2		374	687	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408894	41408894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1420220673	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	266	468	0	ENST00000373198.4:c.532G>A	p.Ala178Thr	p.A178T	ENST00000373198	NM_133170.3	178	Gcc/Acc	4/32	0.3	1	FACETS	0.668	0.629	0.709	0.668	0.629	0.709	INDETERMINATE	1	TRUE	0	0.67	1		468	790	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683508	182683508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	133	402	0	ENST00000292782.4:c.37C>T	p.Arg13Cys	p.R13C	ENST00000292782	NM_020640.2	13	Cgt/Tgt	2/7	1	2	FACETS	0.606	0.552	0.663	0.606	0.552	0.663	SUBCLONAL	1	TRUE	1	0.67	2		402	655	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527278	137527278	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146914620	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	275	446	0	ENST00000367739.4:c.368G>A	p.Arg123Gln	p.R123Q	ENST00000367739	NM_000416.2	123	cGa/cAa	3/7	1	2	FACETS	0.936	0.881	0.992	0.936	0.881	0.992	CLONAL	1	TRUE	1	0.67	2		446	877	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242849	142242849	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	240	421	0	ENST00000350721.4:c.4138G>T	p.Asp1380Tyr	p.D1380Y	ENST00000350721	NM_001184.3	1380	Gat/Tat	22/47	1	2	FACETS	0.898	0.841	0.956	0.898	0.841	0.956	CLONAL	1	TRUE	1	0.67	2		421	798	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910556	29910556	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	364	261	0	ENST00000376809.5:c.96C>A	p.Phe32Leu	p.F32L	ENST00000376809	NM_002116.7	32	ttC/ttA	2/8	0.140411193283748	3	FACETS	0.938	0.896	0.981	0.938	0.896	0.981	INDETERMINATE	2	TRUE	1	0.67	3		261	773	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715350	117715350	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1466068877	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	210	298	0	ENST00000368508.3:c.1139G>T	p.Arg380Ile	p.R380I	ENST00000368508	NM_002944.2	380	aGa/aTa	10/43	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.67	2		298	590	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504585	103504585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747957305	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	201	326	0	ENST00000355739.4:c.206G>A	p.Arg69Gln	p.R69Q	ENST00000355739	NM_000123.3	69	cGa/cAa	2/15	1	2	FACETS	0.946	0.882	1	0.946	0.882	1	CLONAL	1	TRUE	1	0.67	2		326	634	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969087	93969087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1270476760	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	149	240	0	ENST00000369303.4:c.1909C>T	p.Arg637Cys	p.R637C	ENST00000369303	NM_004440.3	637	Cgt/Tgt	10/17	0.140411193283748	3	FACETS	1	0.985	1	0.648	0.597	0.701	INDETERMINATE	1	TRUE	1	0.67	3		240	458	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463578	25463578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770938712	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	599	588	1	ENST00000264709.3:c.2104G>A	p.Asp702Asn	p.D702N	ENST00000264709	NM_175629.2	702	Gat/Aat	18/23	0.279719149156803	1	FACETS	1	0.997	1	1	0.997	1	INDETERMINATE	1	TRUE	0	0.67	1		589	898	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661976	29661976	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	43	428	0	ENST00000356175.3:c.5870T>G	p.Leu1957Arg	p.L1957R	ENST00000356175	NM_000267.3	1957	cTg/cGg	39/57	1	2	FACETS	0.149	0.124	0.178	0.149	0.124	0.178	SUBCLONAL	1	TRUE	1	0.67	2		428	859	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636803	2636803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	422	694	0	ENST00000342085.4:c.1252G>A	p.Asp418Asn	p.D418N	ENST00000342085	NM_002613.4	418	Gat/Aat	11/14	1	2	FACETS	0.996	0.949	1	0.996	0.949	1	CLONAL	1	TRUE	1	0.67	2		694	1265	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250095	39250095	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	333	502	0	ENST00000402219.2:c.1474G>T	p.Glu492Ter	p.E492*	ENST00000402219	NM_005633.3	492	Gaa/Taa	10/23	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.67	2		502	952	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148544272	148544272	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	237	290	0	ENST00000320356.2:c.117+2T>C		p.X39_splice	ENST00000320356	NM_004456.4	39			1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.67	2		290	607	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184568	11184568	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	316	534	0	ENST00000361445.4:c.6649C>T	p.Arg2217Trp	p.R2217W	ENST00000361445	NM_004958.3	2217	Cgg/Tgg	47/58	0.106444737938325	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.67	0		534	974	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162868	38162868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201879366	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	303	597	0	ENST00000317025.8:c.2338C>T	p.Arg780Cys	p.R780C	ENST00000317025	NM_023034.1	780	Cgc/Tgc	13/24	1	2	FACETS	0.925	0.873	0.978	0.925	0.873	0.978	CLONAL	1	TRUE	1	0.67	2		597	978	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319934	8319934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764537367	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	160	305	0	ENST00000356435.5:c.5567C>T	p.Thr1856Met	p.T1856M	ENST00000356435		1856	aCg/aTg	34/35	1	2	FACETS	0.913	0.843	0.986	0.913	0.843	0.986	CLONAL	1	TRUE	1	0.67	2		305	523	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003374	42003374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372252914	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	289	498	2	ENST00000219905.7:c.2911C>T	p.Arg971Trp	p.R971W	ENST00000219905	NM_001164273.1	971	Cgg/Tgg	8/24	1	2	FACETS	0.985	0.929	1	0.985	0.929	1	CLONAL	1	TRUE	1	0.67	2		500	876	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420460	49420460	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	121	641	2	ENST00000301067.7:c.15289C>T	p.Arg5097Ter	p.R5097*	ENST00000301067	NM_003482.3	5097	Cga/Tga	48/54	1	2	FACETS	0.319	0.288	0.353	0.319	0.288	0.353	SUBCLONAL	1	TRUE	1	0.67	2		643	1131	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123575	108123575	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs747242300	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	178	290	0	ENST00000278616.4:c.1834C>A	p.Leu612Ile	p.L612I	ENST00000278616	NM_000051.3	612	Ctt/Att	12/63	1	2	FACETS	0.899	0.833	0.967	0.899	0.833	0.967	CLONAL	1	TRUE	1	0.67	2		290	591	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805785	32805785	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	685	739	0	ENST00000374899.4:c.226A>G	p.Thr76Ala	p.T76A	ENST00000374899	NM_018833.2	76	Act/Gct	2/12	0.140411193283748	3	FACETS	0.759	0.732	0.787	0.759	0.732	0.787	INDETERMINATE	2	TRUE	1	0.67	3		739	1798	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266570	115266570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	380	497	1	ENST00000438362.2:c.1945C>T	p.Arg649Cys	p.R649C	ENST00000438362	NM_001242891.1	649	Cgc/Tgc	16/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.67	2		498	1132	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22405051	22405051	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	165	209	0	ENST00000344548.3:c.80A>C	p.Lys27Thr	p.K27T	ENST00000344548	NM_001039802.1	27	aAa/aCa	3/7	0.140411193283748	3	FACETS	0.759	0.705	0.815	0.759	0.705	0.815	INDETERMINATE	2	TRUE	1	0.67	3		209	433	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836804	151836804	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	293	451	1	ENST00000262189.6:c.14416C>T	p.Arg4806Ter	p.R4806*	ENST00000262189	NM_170606.2	4806	Cga/Tga	56/59	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.67	2		452	834	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962629	38962629	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	51	342	0	ENST00000357387.3:c.1626G>T	p.Glu542Asp	p.E542D	ENST00000357387	NM_152756.3	542	gaG/gaT	18/38	0.106444737938325	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.67	0		342	462	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859879	117859879	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	166	224	0	ENST00000297338.2:c.1756C>T	p.Arg586Ter	p.R586*	ENST00000297338	NM_006265.2	586	Cga/Tga	14/14	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.67	2		224	442	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640169	3640169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769688259	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	612	807	2	ENST00000294008.3:c.3470C>T	p.Ser1157Leu	p.S1157L	ENST00000294008	NM_032444.2	1157	tCg/tTg	12/15	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.67	2		809	1603	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976694	90976694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881862	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	222	403	2	ENST00000265433.3:c.938C>T	p.Ala313Val	p.A313V	ENST00000265433	NM_002485.4	313	gCg/gTg	8/16	1	2	FACETS	0.97	0.908	1	0.97	0.908	1	CLONAL	1	TRUE	1	0.67	2		405	683	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557804	187557804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1321370436	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	279	462	0	ENST00000441802.2:c.3907G>A	p.Glu1303Lys	p.E1303K	ENST00000441802	NM_005245.3	1303	Gaa/Aaa	5/27	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.67	2		462	765	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047524	49047524	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs374157786	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	84	225	0	ENST00000267163.4:c.2518G>A	p.Gly840Arg	p.G840R	ENST00000267163	NM_000321.2	840	Ggg/Agg	24/27	1	2	FACETS	0.789	0.703	0.878	0.789	0.703	0.878	SUBCLONAL	1	TRUE	1	0.67	2		225	318	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500768	8500768	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757479150	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	214	378	0	ENST00000356435.5:c.2114G>A	p.Arg705Gln	p.R705Q	ENST00000356435		705	cGa/cAa	13/35	1	2	FACETS	0.995	0.93	1	0.995	0.93	1	CLONAL	1	TRUE	1	0.67	2		378	642	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394436	162394436	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	199	327	0	ENST00000366898.1:c.632A>C	p.Lys211Thr	p.K211T	ENST00000366898	NM_004562.2	211	aAa/aCa	6/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.67	2		327	561	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497533	125497533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	239	271	0	ENST00000428830.2:c.97G>A	p.Glu33Lys	p.E33K	ENST00000428830	NM_001114121.2	33	Gaa/Aaa	3/14	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.67	2		271	617	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227955	53227955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	388	326	0	ENST00000375401.3:c.2359C>T	p.Arg787Trp	p.R787W	ENST00000375401	NM_004187.3	787	Cgg/Tgg	16/26	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.67	1		326	579	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468319	50468319	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	238	488	0	ENST00000331340.3:c.1554G>A	p.Met518Ile	p.M518I	ENST00000331340	NM_006060.4	518	atG/atA	8/8	0.279719149156803	1	FACETS	0.576	0.539	0.614	0.576	0.539	0.614	INDETERMINATE	1	TRUE	0	0.67	1		488	820	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533773	41533773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	259	451	1	ENST00000263253.7:c.1739G>A	p.Arg580Gln	p.R580Q	ENST00000263253	NM_001429.3	580	cGa/cAa	8/31	1	2	FACETS	0.972	0.914	1	0.972	0.914	1	CLONAL	1	TRUE	1	0.67	2		452	795	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215595215	215595215	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587781948	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	154	259	1	ENST00000260947.4:c.1921C>T	p.Arg641Ter	p.R641*	ENST00000260947	NM_000465.2	641	Cga/Tga	10/11	1	2	FACETS	0.891	0.821	0.963	0.891	0.821	0.963	CLONAL	1	TRUE	1	0.67	2		260	516	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2185896	2185896	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	405	531	0	ENST00000398665.3:c.168G>T	p.Glu56Asp	p.E56D	ENST00000398665	NM_032482.2	56	gaG/gaT	3/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.67	2		531	1162	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859583	57859583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	457	515	0	ENST00000228682.2:c.637G>A	p.Gly213Arg	p.G213R	ENST00000228682	NM_005269.2	213	Ggg/Agg	7/12	0.110267626569347	4	FACETS	0.911	0.871	0.952	0.911	0.871	0.952	INDETERMINATE	2	TRUE	2	0.67	4		515	1250	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030813	69030813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778089198	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	172	314	0	ENST00000288368.4:c.3355G>A	p.Ala1119Thr	p.A1119T	ENST00000288368	NM_024870.2	1119	Gcc/Acc	27/40	0.279719149156803	1	FACETS	0.552	0.511	0.596	0.552	0.511	0.596	INDETERMINATE	1	TRUE	0	0.67	1		314	618	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055755	152055755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1403418496	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	245	377	0	ENST00000262189.6:c.167G>A	p.Arg56Gln	p.R56Q	ENST00000262189	NM_170606.2	56	cGa/cAa	2/59	1	2	FACETS	0.992	0.931	1	0.992	0.931	1	CLONAL	1	TRUE	1	0.67	2		377	737	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742933	17742933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	410	597	0	ENST00000250003.3:c.841C>T	p.Arg281Cys	p.R281C	ENST00000250003	NM_002478.4	281	Cgc/Tgc	3/3	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.67	2		597	1121	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218350	36218350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1454713201	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	398	755	0	ENST00000222270.7:c.4129G>A	p.Glu1377Lys	p.E1377K	ENST00000222270	NM_014727.1	1377	Gag/Aag	16/37	1	2	FACETS	0.928	0.883	0.975	0.928	0.883	0.975	CLONAL	1	TRUE	1	0.67	2		755	1280	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69012038	69012038	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	230	458	0	ENST00000288368.4:c.2675G>T	p.Arg892Ile	p.R892I	ENST00000288368	NM_024870.2	892	aGa/aTa	23/40	0.279719149156803	1	FACETS	0.626	0.586	0.667	0.626	0.586	0.667	INDETERMINATE	1	TRUE	0	0.67	1		458	729	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98003008	98003008	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	38	273	0	ENST00000289081.3:c.268C>A	p.Leu90Ile	p.L90I	ENST00000289081	NM_000136.2	90	Cta/Ata	4/15	1	2	FACETS	0.258	0.213	0.309	0.258	0.213	0.309	SUBCLONAL	1	TRUE	1	0.67	2		273	439	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11205036	11205036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	307	565	0	ENST00000361445.4:c.4753C>T	p.Arg1585Trp	p.R1585W	ENST00000361445	NM_004958.3	1585	Cgg/Tgg	33/58	0.106444737938325	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.67	0		565	1020	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27173241	27173241	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	320	641	0	ENST00000380036.4:c.782G>A	p.Gly261Asp	p.G261D	ENST00000380036	NM_000459.3	261	gGc/gAc	6/23	1	2	FACETS	0.974	0.921	1	0.974	0.921	1	CLONAL	1	TRUE	1	0.67	2		641	981	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950493	68950493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760821149	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	173	345	0	ENST00000288368.4:c.805G>A	p.Asp269Asn	p.D269N	ENST00000288368	NM_024870.2	269	Gat/Aat	7/40	0.279719149156803	1	FACETS	0.554	0.512	0.597	0.554	0.512	0.597	INDETERMINATE	1	TRUE	0	0.67	1		345	620	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163295896	163295896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748878165	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	326	515	2	ENST00000271452.3:c.55C>T	p.Arg19Cys	p.R19C	ENST00000271452	NM_145697.2	19	Cgc/Tgc	2/14	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.67	2		517	930	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30956904	30956904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	305	462	0	ENST00000375687.4:c.230G>A	p.Arg77Gln	p.R77Q	ENST00000375687	NM_015338.5	77	cGa/cAa	4/13	1	2	FACETS	0.973	0.919	1	0.973	0.919	1	CLONAL	1	TRUE	1	0.67	2		462	936	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242692	16242692	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	346	523	0	ENST00000375759.3:c.1313G>T	p.Arg438Ile	p.R438I	ENST00000375759	NM_015001.2	438	aGa/aTa	6/15	0.140411193283748	3	FACETS	1	0.991	1	0.598	0.567	0.631	INDETERMINATE	1	TRUE	1	0.67	3		523	1152	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277233	41277233	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	175	319	0	ENST00000349496.5:c.1702G>T	p.Glu568Ter	p.E568*	ENST00000349496	NM_001904.3	568	Gaa/Taa	11/15	1	2	FACETS	0.916	0.849	0.986	0.916	0.849	0.986	CLONAL	1	TRUE	1	0.67	2		319	570	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710875	117710875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140178288	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	255	389	1	ENST00000368508.3:c.1397G>A	p.Arg466Gln	p.R466Q	ENST00000368508	NM_002944.2	466	cGa/cAa	12/43	1	2	FACETS	0.975	0.916	1	0.975	0.916	1	CLONAL	1	TRUE	1	0.67	2		390	781	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713877	30713877	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	273	576	0	ENST00000295754.5:c.1202C>T	p.Ser401Phe	p.S401F	ENST00000295754	NM_003242.5	401	tCc/tTc	4/7	1	2	FACETS	0.876	0.824	0.93	0.876	0.824	0.93	CLONAL	1	TRUE	1	0.67	2		576	930	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608510	28608510	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	371	540	0	ENST00000241453.7:c.1632C>A	p.Phe544Leu	p.F544L	ENST00000241453	NM_004119.2	544	ttC/ttA	13/24	1	2	FACETS	0.997	0.947	1	0.997	0.947	1	CLONAL	1	TRUE	1	0.67	2		540	1111	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646423	23646423	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	372	493	0	ENST00000261584.4:c.1444C>A	p.Leu482Ile	p.L482I	ENST00000261584	NM_024675.3	482	Ctc/Atc	4/13	0.292455180492658	3	FACETS	1	0.995	1			1	INDETERMINATE	1	TRUE	NA	0.67	3		493	1030	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281838	39281838	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	232	406	0	ENST00000402219.2:c.637C>T	p.Arg213Ter	p.R213*	ENST00000402219	NM_005633.3	213	Cga/Tga	5/23	1	2	FACETS	0.92	0.861	0.98	0.92	0.861	0.98	CLONAL	1	TRUE	1	0.67	2		406	753	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956198	55956198	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	246	484	0	ENST00000263923.4:c.3117G>T	p.Lys1039Asn	p.K1039N	ENST00000263923	NM_002253.2	1039	aaG/aaT	23/30	1	2	FACETS	0.829	0.776	0.883	0.829	0.776	0.883	CLONAL	1	TRUE	1	0.67	2		484	886	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120882	94120882	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	258	336	0	ENST00000369303.4:c.169G>T	p.Glu57Ter	p.E57*	ENST00000369303	NM_004440.3	57	Gaa/Taa	3/17	0.140411193283748	3	FACETS	1	0.992	1	0.67	0.63	0.711	INDETERMINATE	1	TRUE	1	0.67	3		336	767	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944618	38944618	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	212	384	0	ENST00000357387.3:c.4843G>T	p.Glu1615Ter	p.E1615*	ENST00000357387	NM_152756.3	1615	Gaa/Taa	36/38	0.106444737938325	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.67	0		384	684	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785686	50785686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763792744	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	320	509	0	ENST00000398568.2:c.676G>A	p.Glu226Lys	p.E226K	ENST00000398568	NM_001042412.1	226	Gaa/Aaa	4/18	1	2	FACETS	0.932	0.881	0.984	0.932	0.881	0.984	CLONAL	1	TRUE	1	0.67	2		509	1025	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849193	76849193	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557082310	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	184	168	0	ENST00000373344.5:c.6083G>A	p.Arg2028Gln	p.R2028Q	ENST00000373344	NM_000489.3	2028	cGa/cAa	26/35	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.67	1		168	276	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645132	67645132	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	409	615	1	ENST00000264010.4:c.397G>T	p.Glu133Ter	p.E133*	ENST00000264010	NM_006565.3	133	Gaa/Taa	3/12	1	2	FACETS	0.955	0.909	1	0.955	0.909	1	CLONAL	1	TRUE	1	0.67	2		616	1279	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271393	26271393	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	537	490	0	ENST00000305910.3:c.220G>T	p.Glu74Ter	p.E74*	ENST00000305910	NM_003534.2	74	Gaa/Taa	1/1	0.3	5	FACETS	1	0.993	1	0.759	0.728	0.79	INDETERMINATE	2	TRUE	2	0.67	5		490	1412	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252720	10252720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377078524	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	385	616	1	ENST00000340748.4:c.3245G>A	p.Arg1082His	p.R1082H	ENST00000340748		1082	cGc/cAc	29/40	1	2	FACETS	0.983	0.935	1	0.983	0.935	1	CLONAL	1	TRUE	1	0.67	2		617	1169	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926543	59926543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	292	487	0	ENST00000259008.2:c.454G>T	p.Asp152Tyr	p.D152Y	ENST00000259008	NM_032043.2	152	Gat/Tat	5/20	1	2	FACETS	0.948	0.895	1	0.948	0.895	1	CLONAL	1	TRUE	1	0.67	2		487	919	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161690	56161690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	291	424	0	ENST00000399503.3:c.1187G>A	p.Arg396His	p.R396H	ENST00000399503	NM_005921.1	396	cGt/cAt	6/20	0.106444737938325	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.67	0		424	900	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701248	43701248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773338141	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	280	530	0	ENST00000382044.4:c.5447G>A	p.Arg1816Gln	p.R1816Q	ENST00000382044	NM_001141980.1	1816	cGa/cAa	26/28	1	2	FACETS	0.928	0.874	0.983	0.928	0.874	0.983	CLONAL	1	TRUE	1	0.67	2		530	901	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500473	149500473	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1292468244	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	352	561	0	ENST00000261799.4:c.2564C>T	p.Ser855Leu	p.S855L	ENST00000261799	NM_002609.3	855	tCg/tTg	18/23	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.67	2		561	1048	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630228	187630228	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	446	559	0	ENST00000441802.2:c.754G>T	p.Glu252Ter	p.E252*	ENST00000441802	NM_005245.3	252	Gaa/Taa	2/27	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.67	2		559	1209	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992157	11992157	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	290	457	1	ENST00000396373.4:c.247G>T	p.Asp83Tyr	p.D83Y	ENST00000396373	NM_001987.4	83	Gac/Tac	3/8	0.140411193283748	3	FACETS	1	0.991	1	0.639	0.603	0.676	INDETERMINATE	1	TRUE	1	0.67	3		458	904	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164059	106164059	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	158	300	0	ENST00000380013.4:c.3569C>A	p.Ser1190Tyr	p.S1190Y	ENST00000380013	NM_001127208.2	1190	tCt/tAt	5/11	1	2	FACETS	0.853	0.786	0.922	0.853	0.786	0.922	CLONAL	1	TRUE	1	0.67	2		300	553	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646974	23646974	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs763726703	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	428	630	0	ENST00000261584.4:c.893T>C	p.Val298Ala	p.V298A	ENST00000261584	NM_024675.3	298	gTc/gCc	4/13	0.292455180492658	3	FACETS	1	0.995	1			1	INDETERMINATE	1	TRUE	NA	0.67	3		630	1269	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560464	95560464	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	272	494	0	ENST00000393063.1:c.5125G>T	p.Asp1709Tyr	p.D1709Y	ENST00000393063	NM_030621.3	1709	Gat/Tat	25/28	NA	2	FACETS	0.931	0.876	0.987			1	INDETERMINATE	1	TRUE	NA	0.67	2		494	872	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22417976	22417976	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	63	56	0	ENST00000344548.3:c.542A>C	p.Glu181Ala	p.E181A	ENST00000344548	NM_001039802.1	181	gAa/gCa	7/7	0.140411193283748	3	FACETS	0.789	0.699	0.882	0.789	0.699	0.882	INDETERMINATE	2	TRUE	1	0.67	3		56	159	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39321394	39321394	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	312	427	0	ENST00000373001.3:c.627A>C	p.Glu209Asp	p.E209D	ENST00000373001	NM_022157.3	209	gaA/gaC	3/7	0.140411193283748	3	FACETS	1	0.994	1	0.703	0.665	0.742	INDETERMINATE	1	TRUE	1	0.67	3		427	884	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058632	72058632	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	198	304	1	ENST00000357731.5:c.808G>T	p.Gly270Ter	p.G270*	ENST00000357731	NM_173808.2	270	Gga/Tga	6/7	0.228661763914847	1	FACETS	0.637	0.593	0.682	0.637	0.593	0.682	INDETERMINATE	1	TRUE	0	0.67	1		305	617	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78425913	78425913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	243	366	0	ENST00000370768.2:c.1532G>A	p.Gly511Glu	p.G511E	ENST00000370768	NM_003902.3	511	gGa/gAa	16/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.67	2		366	672	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736515	85736515	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	199	261	0	ENST00000370580.1:c.132A>C	p.Lys44Asn	p.K44N	ENST00000370580	NM_003921.4	44	aaA/aaC	2/3	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.67	2		261	577	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163297308	163297308	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs991658524	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	240	438	0	ENST00000271452.3:c.154G>A	p.Ala52Thr	p.A52T	ENST00000271452	NM_145697.2	52	Gcc/Acc	3/14	1	2	FACETS	0.887	0.83	0.944	0.887	0.83	0.944	CLONAL	1	TRUE	1	0.67	2		438	808	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015392	176015392	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	261	366	0	ENST00000367669.3:c.1346A>C	p.Glu449Ala	p.E449A	ENST00000367669	NM_022457.5	449	gAa/gCa	12/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.67	2		366	703	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107275	193107275	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	148	293	0	ENST00000367435.3:c.484G>T	p.Glu162Ter	p.E162*	ENST00000367435	NM_024529.4	162	Gaa/Taa	6/17	1	2	FACETS	0.789	0.724	0.856	0.789	0.724	0.856	SUBCLONAL	1	TRUE	1	0.67	2		293	560	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984360	201984360	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	662	598	0	ENST00000359651.3:c.1025T>G	p.Leu342Arg	p.L342R	ENST00000359651		342	cTg/cGg	8/8	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.67	2		598	1721	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727112	243727112	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	318	417	0	ENST00000263826.5:c.858A>C	p.Lys286Asn	p.K286N	ENST00000263826	NM_005465.4	286	aaA/aaC	9/13	0.106444737938325	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.67	0		417	887	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858936	243858936	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	191	430	0	ENST00000263826.5:c.129A>C	p.Gln43His	p.Q43H	ENST00000263826	NM_005465.4	43	caA/caC	2/13	0.106444737938325	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.67	0		430	622	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597981	43597981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765654609	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	549	696	1	ENST00000355710.3:c.529C>T	p.Arg177Trp	p.R177W	ENST00000355710	NM_020975.4	177	Cgg/Tgg	3/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.67	2		697	1595	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617459	43617459	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	260	403	0	ENST00000355710.3:c.2796T>G	p.Ser932Arg	p.S932R	ENST00000355710	NM_020975.4	932	agT/agG	16/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.67	2		403	744	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404567	70404567	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	333	491	0	ENST00000373644.4:c.2081A>C	p.Asn694Thr	p.N694T	ENST00000373644	NM_030625.2	694	aAt/aCt	4/12	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.67	2		491	904	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70432777	70432777	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	236	414	0	ENST00000373644.4:c.4799G>T	p.Arg1600Ile	p.R1600I	ENST00000373644	NM_030625.2	1600	aGa/aTa	8/12	1	2	FACETS	0.951	0.891	1	0.951	0.891	1	CLONAL	1	TRUE	1	0.67	2		414	741	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771388	112771388	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	295	450	0	ENST00000369452.4:c.1561G>T	p.Glu521Ter	p.E521*	ENST00000369452	NM_007373.3	521	Gaa/Taa	9/9	1	2	FACETS	0.873	0.822	0.924	0.873	0.822	0.924	CLONAL	1	TRUE	1	0.67	2		450	1009	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258062	123258062	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	246	474	0	ENST00000358487.5:c.1619T>C	p.Met540Thr	p.M540T	ENST00000358487	NM_000141.4	540	aTg/aCg	12/18	1	2	FACETS	0.926	0.868	0.985	0.926	0.868	0.985	CLONAL	1	TRUE	1	0.67	2		474	793	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94922994	94922994	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	256	452	0	ENST00000536441.1:c.474T>G	p.Ile158Met	p.I158M	ENST00000536441	NM_144665.3	158	atT/atG	4/10	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.67	2		452	760	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912696	100912696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	229	399	0	ENST00000325455.5:c.2626C>T	p.Leu876Phe	p.L876F	ENST00000325455	NM_001202474.3	876	Ctt/Ttt	7/8	1	2	FACETS	0.952	0.891	1	0.952	0.891	1	CLONAL	1	TRUE	1	0.67	2		399	718	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998706	100998706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	501	676	1	ENST00000325455.5:c.1096G>A	p.Asp366Asn	p.D366N	ENST00000325455	NM_001202474.3	366	Gac/Aac	1/8	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.67	2		677	1333	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114799	108114799	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587781829	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	267	439	0	ENST00000278616.4:c.616A>C	p.Asn206His	p.N206H	ENST00000278616	NM_000051.3	206	Aat/Cat	6/63	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.67	2		439	759	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129776	108129776	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	187	332	0	ENST00000278616.4:c.2440G>T	p.Asp814Tyr	p.D814Y	ENST00000278616	NM_000051.3	814	Gac/Tac	16/63	1	2	FACETS	0.997	0.927	1	0.997	0.927	1	CLONAL	1	TRUE	1	0.67	2		332	560	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153558	108153558	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	105	279	0	ENST00000278616.4:c.3698C>A	p.Ser1233Tyr	p.S1233Y	ENST00000278616	NM_000051.3	1233	tCt/tAt	25/63	1	2	FACETS	0.802	0.724	0.882	0.802	0.724	0.882	CLONAL	1	TRUE	1	0.67	2		279	391	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118339523	118339523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	253	435	0	ENST00000534358.1:c.466G>A	p.Glu156Lys	p.E156K	ENST00000534358	NM_005933.3	156	Gaa/Aaa	2/36	1	2	FACETS	0.936	0.879	0.994	0.936	0.879	0.994	CLONAL	1	TRUE	1	0.67	2		435	807	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347664	118347664	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886041856	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	269	436	0	ENST00000534358.1:c.3301C>T	p.Arg1101Ter	p.R1101*	ENST00000534358	NM_005933.3	1101	Cga/Tga	4/36	1	2	FACETS	0.976	0.918	1	0.976	0.918	1	CLONAL	1	TRUE	1	0.67	2		436	823	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348904	118348904	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	104	229	0	ENST00000534358.1:c.3557A>T	p.Lys1186Met	p.K1186M	ENST00000534358	NM_005933.3	1186	aAg/aTg	5/36	1	2	FACETS	0.897	0.812	0.986	0.897	0.812	0.986	CLONAL	1	TRUE	1	0.67	2		229	346	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118382708	118382708	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	223	388	0	ENST00000534358.1:c.11114C>A	p.Ser3705Ter	p.S3705*	ENST00000534358	NM_005933.3	3705	tCa/tAa	31/36	1	2	FACETS	0.98	0.917	1	0.98	0.917	1	CLONAL	1	TRUE	1	0.67	2		388	679	SUCCESS
CBL	867	MSKCC	GRCh37	11	119145651	119145651	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	202	257	0	ENST00000264033.4:c.857A>G	p.His286Arg	p.H286R	ENST00000264033	NM_005188.3	286	cAc/cGc	5/16	1	2	FACETS	0.929	0.866	0.994	0.929	0.866	0.994	CLONAL	1	TRUE	1	0.67	2		257	649	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	493228	493228	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	280	372	0	ENST00000399788.2:c.335G>T	p.Arg112Ile	p.R112I	ENST00000399788	NM_001042603.1	112	aGa/aTa	3/28	0.140411193283748	3	FACETS	1	0.99	1	0.612	0.576	0.649	INDETERMINATE	1	TRUE	1	0.67	3		372	911	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992218	11992218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs575376112	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	226	410	0	ENST00000396373.4:c.308G>A	p.Arg103His	p.R103H	ENST00000396373	NM_001987.4	103	cGc/cAc	3/8	0.140411193283748	3	FACETS	1	0.987	1	0.606	0.566	0.647	INDETERMINATE	1	TRUE	1	0.67	3		410	743	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871770	12871770	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	283	221	1	ENST00000228872.4:c.487C>T	p.Gln163Ter	p.Q163*	ENST00000228872	NM_004064.3	163	Caa/Taa	2/3	0.140411193283748	3	FACETS	0.793	0.75	0.837	0.793	0.75	0.837	INDETERMINATE	2	TRUE	1	0.67	3		222	711	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21630853	21630853	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	276	499	0	ENST00000421138.2:c.751A>C	p.Ile251Leu	p.I251L	ENST00000421138		251	Att/Ctt	8/16	1	2	FACETS	0.926	0.871	0.981	0.926	0.871	0.981	CLONAL	1	TRUE	1	0.67	2		499	890	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644528	21644528	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	231	464	0	ENST00000421138.2:c.139A>T	p.Lys47Ter	p.K47*	ENST00000421138		47	Aag/Tag	4/16	1	2	FACETS	0.862	0.806	0.919	0.862	0.806	0.919	CLONAL	1	TRUE	1	0.67	2		464	800	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398249	25398249	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	313	421	0	ENST00000311936.3:c.70A>C	p.Ile24Leu	p.I24L	ENST00000311936	NM_004985.3	24	Att/Ctt	2/5	1	2	FACETS	0.986	0.932	1	0.986	0.932	1	CLONAL	1	TRUE	1	0.67	2		421	948	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145010	58145010	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	504	519	0	ENST00000257904.6:c.334T>G	p.Leu112Val	p.L112V	ENST00000257904	NM_000075.3	112	Ttg/Gtg	3/8	0.110267626569347	4	FACETS	0.878	0.841	0.916	0.878	0.841	0.916	INDETERMINATE	2	TRUE	2	0.67	4		519	1430	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416782	121416782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1447883891	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	1131	791	0	ENST00000257555.6:c.211G>A	p.Glu71Lys	p.E71K	ENST00000257555		71	Gag/Aag	1/10	0.228661763914847	1	FACETS	1	0.999	1	1	0.999	1	INDETERMINATE	1	TRUE	0	0.67	1		791	1545	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123888133	123888133	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	131	235	0	ENST00000330479.4:c.611A>C	p.Lys204Thr	p.K204T	ENST00000330479	NM_020382.3	204	aAa/aCa	6/9	0.228661763914847	1	FACETS	0.628	0.575	0.683	0.628	0.575	0.683	INDETERMINATE	1	TRUE	0	0.67	1		235	414	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202824	133202824	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	459	608	0	ENST00000320574.5:c.6410A>C	p.Glu2137Ala	p.E2137A	ENST00000320574	NM_006231.2	2137	gAg/gCg	46/49	0.228661763914847	1	FACETS	0.716	0.685	0.748	0.716	0.685	0.748	INDETERMINATE	1	TRUE	0	0.67	1		608	1272	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256608	133256608	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs879254235	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	283	467	1	ENST00000320574.5:c.355T>A	p.Phe119Ile	p.F119I	ENST00000320574	NM_006231.2	119	Ttt/Att	5/49	0.228661763914847	1	FACETS	0.649	0.612	0.688	0.649	0.612	0.688	INDETERMINATE	1	TRUE	0	0.67	1		468	865	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609759	28609759	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	432	543	0	ENST00000241453.7:c.1470A>C	p.Lys490Asn	p.K490N	ENST00000241453	NM_004119.2	490	aaA/aaC	12/24	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.67	2		543	1278	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28631513	28631513	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	193	350	0	ENST00000241453.7:c.455A>G	p.Tyr152Cys	p.Y152C	ENST00000241453	NM_004119.2	152	tAc/tGc	4/24	1	2	FACETS	0.881	0.819	0.945	0.881	0.819	0.945	CLONAL	1	TRUE	1	0.67	2		350	654	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28882990	28882990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	367	498	0	ENST00000282397.4:c.3710C>T	p.Ser1237Phe	p.S1237F	ENST00000282397	NM_002019.4	1237	tCc/tTc	28/30	1	2	FACETS	0.997	0.947	1	0.997	0.947	1	CLONAL	1	TRUE	1	0.67	2		498	1099	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919676	28919676	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	227	406	0	ENST00000282397.4:c.2261A>C	p.Lys754Thr	p.K754T	ENST00000282397	NM_002019.4	754	aAg/aCg	16/30	1	2	FACETS	0.978	0.915	1	0.978	0.915	1	CLONAL	1	TRUE	1	0.67	2		406	693	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001313	29001313	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	210	309	0	ENST00000282397.4:c.1419T>G	p.His473Gln	p.H473Q	ENST00000282397	NM_002019.4	473	caT/caG	10/30	1	2	FACETS	0.99	0.925	1	0.99	0.925	1	CLONAL	1	TRUE	1	0.67	2		309	633	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008297	29008297	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	197	325	0	ENST00000282397.4:c.574T>G	p.Phe192Val	p.F192V	ENST00000282397	NM_002019.4	192	Ttc/Gtc	5/30	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.67	2		325	580	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913277	32913277	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1060502499	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	91	463	0	ENST00000380152.3:c.4785G>T	p.Gln1595His	p.Q1595H	ENST00000380152		1595	caG/caT	11/27	1	2	FACETS	0.344	0.305	0.386	0.344	0.305	0.386	SUBCLONAL	1	TRUE	1	0.67	2		463	790	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913367	32913367	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	236	429	0	ENST00000380152.3:c.4875A>C	p.Glu1625Asp	p.E1625D	ENST00000380152		1625	gaA/gaC	11/27	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.67	2		429	701	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915064	32915064	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	247	441	0	ENST00000380152.3:c.6572A>C	p.Lys2191Thr	p.K2191T	ENST00000380152		2191	aAa/aCa	11/27	1	2	FACETS	0.896	0.84	0.953	0.896	0.84	0.953	CLONAL	1	TRUE	1	0.67	2		441	823	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972896	32972896	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	167	234	0	ENST00000380152.3:c.10246A>C	p.Lys3416Gln	p.K3416Q	ENST00000380152		3416	Aaa/Caa	27/27	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.67	2		234	475	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027133	49027133	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	192	309	0	ENST00000267163.4:c.1700C>A	p.Ser567Ter	p.S567*	ENST00000267163	NM_000321.2	567	tCa/tAa	18/27	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.67	2		309	570	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050898	49050898	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	285	408	0	ENST00000267163.4:c.2582G>T	p.Arg861Ile	p.R861I	ENST00000267163	NM_000321.2	861	aGa/aTa	25/27	1	2	FACETS	0.978	0.922	1	0.978	0.922	1	CLONAL	1	TRUE	1	0.67	2		408	870	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73334743	73334743	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	119	246	0	ENST00000377767.4:c.2717A>C	p.Lys906Thr	p.K906T	ENST00000377767	NM_014953.3	906	aAa/aCa	20/21	1	2	FACETS	0.884	0.805	0.966	0.884	0.805	0.966	CLONAL	1	TRUE	1	0.67	2		246	402	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068255	30068255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	227	384	0	ENST00000331968.5:c.2144C>T	p.Ala715Val	p.A715V	ENST00000331968	NM_002742.2	715	gCc/gTc	15/18	NA	2	FACETS	0.879	0.821	0.938			1	INDETERMINATE	1	TRUE	NA	0.67	2		384	771	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108018	30108018	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	374	563	0	ENST00000331968.5:c.789G>T	p.Leu263Phe	p.L263F	ENST00000331968	NM_002742.2	263	ttG/ttT	5/18	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.67	2		563	1046	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609756	81609756	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	262	448	0	ENST00000298171.2:c.1354C>A	p.Leu452Ile	p.L452I	ENST00000298171	NM_000369.2	452	Ctc/Atc	10/10	NA	2	FACETS	1	0.95	1			1	INDETERMINATE	1	TRUE	NA	0.67	2		448	774	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705404	43705404	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	81	745	0	ENST00000382044.4:c.5218C>A	p.Leu1740Ile	p.L1740I	ENST00000382044	NM_001141980.1	1740	Ctc/Atc	24/28	1	2	FACETS	0.194	0.17	0.22	0.194	0.17	0.22	SUBCLONAL	1	TRUE	1	0.67	2		745	1247	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43766907	43766907	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765177854	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	147	295	0	ENST00000382044.4:c.1144G>A	p.Val382Ile	p.V382I	ENST00000382044	NM_001141980.1	382	Gtt/Att	10/28	1	2	FACETS	0.886	0.815	0.96	0.886	0.815	0.96	CLONAL	1	TRUE	1	0.67	2		295	495	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43769884	43769884	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	63	473	1	ENST00000382044.4:c.862G>T	p.Glu288Ter	p.E288*	ENST00000382044	NM_001141980.1	288	Gaa/Taa	8/28	1	2	FACETS	0.194	0.167	0.223	0.194	0.167	0.223	SUBCLONAL	1	TRUE	1	0.67	2		474	971	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67459118	67459118	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	376	664	0	ENST00000327367.4:c.534G>T	p.Glu178Asp	p.E178D	ENST00000327367	NM_005902.3	178	gaG/gaT	4/9	0.3	1	FACETS	0.607	0.576	0.639	0.607	0.576	0.639	INDETERMINATE	1	TRUE	0	0.67	1		664	1229	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312764	91312764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	425	474	0	ENST00000355112.3:c.2503C>T	p.Pro835Ser	p.P835S	ENST00000355112	NM_000057.2	835	Ccc/Tcc	12/22	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.67	2		474	1155	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646270	3646270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780697002	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	471	759	1	ENST00000294008.3:c.1808C>T	p.Ser603Leu	p.S603L	ENST00000294008	NM_032444.2	603	tCg/tTg	8/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.67	2		760	1335	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647475	3647475	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1269	96	725	0	ENST00000294008.3:c.1588C>A	p.Leu530Met	p.L530M	ENST00000294008	NM_032444.2	530	Ctg/Atg	7/15	1	2	FACETS	0.21	0.186	0.236	0.21	0.186	0.236	SUBCLONAL	1	TRUE	1	0.67	2		725	1365	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807955	3807955	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs764153035	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	56	563	0	ENST00000262367.5:c.3464A>G	p.Asp1155Gly	p.D1155G	ENST00000262367	NM_004380.2	1155	gAc/gGc	18/31	1	2	FACETS	0.161	0.137	0.187	0.161	0.137	0.187	SUBCLONAL	1	TRUE	1	0.67	2		563	1038	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858756	9858756	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	168	335	0	ENST00000330684.3:c.2645C>A	p.Ser882Tyr	p.S882Y	ENST00000330684	NM_001134407.1	882	tCt/tAt	13/13	1	2	FACETS	0.979	0.907	1	0.979	0.907	1	CLONAL	1	TRUE	1	0.67	2		335	512	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916274	9916274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	185	333	0	ENST00000330684.3:c.2015G>A	p.Arg672Lys	p.R672K	ENST00000330684	NM_001134407.1	672	aGa/aAa	10/13	1	2	FACETS	0.964	0.896	1	0.964	0.896	1	CLONAL	1	TRUE	1	0.67	2		333	573	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029195	14029195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	153	290	0	ENST00000311895.7:c.1406C>T	p.Pro469Leu	p.P469L	ENST00000311895	NM_005236.2	469	cCt/cTt	8/11	0.292455180492658	3	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.67	3		290	507	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56832433	56832433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367699010	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	185	298	0	ENST00000308159.5:c.343G>A	p.Glu115Lys	p.E115K	ENST00000308159	NM_014669.4	115	Gaa/Aaa	4/22	1	2	FACETS	0.962	0.894	1	0.962	0.894	1	CLONAL	1	TRUE	1	0.67	2		298	574	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063349	67063349	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	406	293	1	ENST00000412916.2:c.39G>T	p.Glu13Asp	p.E13D	ENST00000412916		13	gaG/gaT	1/6	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.67	2		294	1134	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821514	72821514	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	307	466	0	ENST00000268489.5:c.10661A>C	p.Lys3554Thr	p.K3554T	ENST00000268489	NM_006885.3	3554	aAa/aCa	10/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.67	2		466	911	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81914518	81914518	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs551539187	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	262	363	0	ENST00000359376.3:c.652C>A	p.Leu218Ile	p.L218I	ENST00000359376	NM_002661.3	218	Ctc/Atc	8/33	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.67	2		363	717	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350831	89350831	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	458	691	0	ENST00000301030.4:c.2119G>T	p.Glu707Ter	p.E707*	ENST00000301030	NM_001256183.1	707	Gaa/Taa	9/13	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.67	2		691	1216	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351577	89351577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778960311	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	469	734	0	ENST00000301030.4:c.1373G>A	p.Arg458Gln	p.R458Q	ENST00000301030	NM_001256183.1	458	cGa/cAa	9/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.67	2		734	1365	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813010	89813010	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	450	624	0	ENST00000389301.3:c.3495A>C	p.Leu1165Phe	p.L1165F	ENST00000389301	NM_000135.2	1165	ttA/ttC	35/43	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.67	2		624	1214	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974936	15974936	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	198	332	0	ENST00000268712.3:c.3939A>C	p.Lys1313Asn	p.K1313N	ENST00000268712	NM_006311.3	1313	aaA/aaC	30/46	1	2	FACETS	0.896	0.833	0.96	0.896	0.833	0.96	CLONAL	1	TRUE	1	0.67	2		332	660	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483060	29483060	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	222	399	0	ENST00000356175.3:c.120G>T	p.Lys40Asn	p.K40N	ENST00000356175	NM_000267.3	40	aaG/aaT	2/57	1	2	FACETS	0.877	0.819	0.936	0.877	0.819	0.936	CLONAL	1	TRUE	1	0.67	2		399	756	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586092	29586092	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	170	345	0	ENST00000356175.3:c.4312G>T	p.Glu1438Ter	p.E1438*	ENST00000356175	NM_000267.3	1438	Gaa/Taa	32/57	1	2	FACETS	0.789	0.729	0.852	0.789	0.729	0.852	SUBCLONAL	1	TRUE	1	0.67	2		345	643	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320887	30320887	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	243	317	0	ENST00000322652.5:c.1297C>A	p.Leu433Ile	p.L433I	ENST00000322652	NM_015355.2	433	Ctc/Atc	12/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.67	2		317	656	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322765	30322765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	215	289	0	ENST00000322652.5:c.1778G>A	p.Arg593Lys	p.R593K	ENST00000322652	NM_015355.2	593	aGa/aAa	14/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.67	2		289	581	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646974	37646974	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	351	417	0	ENST00000447079.4:c.2096A>C	p.Lys699Thr	p.K699T	ENST00000447079	NM_015083.1	699	aAa/aCa	3/14	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.67	2		417	965	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37672051	37672051	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	297	421	0	ENST00000447079.4:c.2836G>T	p.Glu946Ter	p.E946*	ENST00000447079	NM_015083.1	946	Gaa/Taa	9/14	1	2	FACETS	0.991	0.935	1	0.991	0.935	1	CLONAL	1	TRUE	1	0.67	2		421	895	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780593	56780593	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	425	476	0	ENST00000337432.4:c.608A>T	p.Asn203Ile	p.N203I	ENST00000337432	NM_058216.2	203	aAt/aTt	4/9	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.67	2		476	1119	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526100	66526100	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	194	361	0	ENST00000358598.2:c.931G>T	p.Glu311Ter	p.E311*	ENST00000358598	NM_212471.2	311	Gag/Tag	10/11	1	2	FACETS	0.885	0.823	0.95	0.885	0.823	0.95	CLONAL	1	TRUE	1	0.67	2		361	654	SUCCESS
YES1	7525	MSKCC	GRCh37	18	742948	742948	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	216	368	0	ENST00000314574.4:c.1030A>G	p.Ile344Val	p.I344V	ENST00000314574	NM_005433.3	344	Att/Gtt	8/12	1	2	FACETS	0.98	0.916	1	0.98	0.916	1	CLONAL	1	TRUE	1	0.67	2		368	658	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56415021	56415021	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	242	408	0	ENST00000348428.3:c.2422A>C	p.Thr808Pro	p.T808P	ENST00000348428	NM_006785.3	808	Act/Cct	17/17	1	2	FACETS	0.925	0.867	0.984	0.925	0.867	0.984	CLONAL	1	TRUE	1	0.67	2		408	781	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122669	7122669	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913154	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	514	543	0	ENST00000302850.5:c.3485C>T	p.Ala1162Val	p.A1162V	ENST00000302850	NM_000208.2	1162	gCg/gTg	19/22	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.67	2		543	1416	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250486	10250486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168306248	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	107	593	0	ENST00000340748.4:c.3766G>A	p.Asp1256Asn	p.D1256N	ENST00000340748		1256	Gac/Aac	33/40	1	2	FACETS	0.309	0.276	0.343	0.309	0.276	0.343	SUBCLONAL	1	TRUE	1	0.67	2		593	1035	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627725	14627725	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1618	199	592	0	ENST00000254322.2:c.345T>G	p.Phe115Leu	p.F115L	ENST00000254322	NM_006145.1	115	ttT/ttG	2/3	0.3	5	FACETS	0.655	0.605	0.709			1	INDETERMINATE	1	TRUE	NA	0.67	5		592	1817	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367025	15367025	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	205	313	0	ENST00000263377.2:c.1601A>G	p.Asn534Ser	p.N534S	ENST00000263377	NM_058243.2	534	aAc/aGc	9/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.67	2		313	603	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948753	17948753	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	552	632	0	ENST00000458235.1:c.1689G>T	p.Lys563Asn	p.K563N	ENST00000458235	NM_000215.3	563	aaG/aaT	12/24	0.3	3	FACETS	1	0.996	1			1	INDETERMINATE	1	TRUE	NA	0.67	3		632	1556	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311687	30311687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	295	461	0	ENST00000262643.3:c.541G>A	p.Glu181Lys	p.E181K	ENST00000262643	NM_001238.2	181	Gaa/Aaa	7/12	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.67	2		461	832	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741015	40741015	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	438	764	0	ENST00000392038.2:c.1303G>A	p.Asp435Asn	p.D435N	ENST00000392038	NM_001626.4	435	Gac/Aac	13/14	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.67	2		764	1234	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50143213	50143213	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	490	460	0	ENST00000246792.3:c.143A>C	p.Gln48Pro	p.Q48P	ENST00000246792	NM_006270.3	48	cAg/cCg	1/6	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.67	2		460	1391	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574163	46574163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	405	592	2	ENST00000263734.3:c.178G>A	p.Ala60Thr	p.A60T	ENST00000263734	NM_001430.4	60	Gca/Aca	2/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.67	2		594	1141	SUCCESS
REL	5966	MSKCC	GRCh37	2	61128214	61128214	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	124	203	0	ENST00000295025.8:c.390C>A	p.Phe130Leu	p.F130L	ENST00000295025	NM_002908.2	130	ttC/ttA	4/11	1	2	FACETS	0.939	0.858	1	0.939	0.858	1	CLONAL	1	TRUE	1	0.67	2		203	394	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61729135	61729135	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	59	348	0	ENST00000401558.2:c.404T>C	p.Val135Ala	p.V135A	ENST00000401558	NM_003400.3	135	gTt/gCt	6/25	1	2	FACETS	0.274	0.235	0.316	0.274	0.235	0.316	SUBCLONAL	1	TRUE	1	0.67	2		348	643	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61753576	61753576	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	203	322	0	ENST00000401558.2:c.207T>G	p.Phe69Leu	p.F69L	ENST00000401558	NM_003400.3	69	ttT/ttG	3/25	1	2	FACETS	0.935	0.871	1	0.935	0.871	1	CLONAL	1	TRUE	1	0.67	2		322	648	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719517	190719517	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	152	238	0	ENST00000441310.2:c.1519T>G	p.Ser507Ala	p.S507A	ENST00000441310	NM_000534.4	507	Tca/Gca	9/13	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.67	2		238	445	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131192	202131192	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	159	292	0	ENST00000358485.4:c.160C>A	p.Leu54Ile	p.L54I	ENST00000358485	NM_001080125.1	54	Ctc/Atc	2/9	1	2	FACETS	0.951	0.878	1	0.951	0.878	1	CLONAL	1	TRUE	1	0.67	2		292	499	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131412	202131412	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	305	480	1	ENST00000358485.4:c.380G>T	p.Arg127Leu	p.R127L	ENST00000358485	NM_001080125.1	127	cGa/cTa	2/9	1	2	FACETS	0.987	0.933	1	0.987	0.933	1	CLONAL	1	TRUE	1	0.67	2		481	922	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488706	212488706	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	273	502	0	ENST00000342788.4:c.2143G>T	p.Glu715Ter	p.E715*	ENST00000342788	NM_005235.2	715	Gaa/Taa	18/28	1	2	FACETS	0.961	0.905	1	0.961	0.905	1	CLONAL	1	TRUE	1	0.67	2		502	848	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576805	212576805	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	232	356	0	ENST00000342788.4:c.1094A>C	p.Asn365Thr	p.N365T	ENST00000342788	NM_005235.2	365	aAt/aCt	9/28	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.67	2		356	672	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645327	215645327	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	261	455	0	ENST00000260947.4:c.1271G>T	p.Arg424Ile	p.R424I	ENST00000260947	NM_000465.2	424	aGa/aTa	4/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.67	2		455	749	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437235	220437235	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1849	129	774	0	ENST00000243786.2:c.139A>G	p.Thr47Ala	p.T47A	ENST00000243786	NM_002191.3	47	Acc/Gcc	1/2	1	2	FACETS	0.195	0.175	0.215	0.195	0.175	0.215	SUBCLONAL	1	TRUE	1	0.67	2		774	1978	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368470	225368470	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	199	402	0	ENST00000264414.4:c.1276G>T	p.Asp426Tyr	p.D426Y	ENST00000264414	NM_003590.4	426	Gat/Tat	9/16	1	2	FACETS	0.865	0.804	0.927	0.865	0.804	0.927	CLONAL	1	TRUE	1	0.67	2		402	687	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368505	225368505	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	168	329	0	ENST00000264414.4:c.1241A>C	p.Lys414Thr	p.K414T	ENST00000264414	NM_003590.4	414	aAa/aCa	9/16	1	2	FACETS	0.877	0.81	0.945	0.877	0.81	0.945	CLONAL	1	TRUE	1	0.67	2		329	572	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543578	9543578	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	313	488	0	ENST00000353224.5:c.1576C>A	p.Leu526Ile	p.L526I	ENST00000353224	NM_177990.2	526	Cta/Ata	6/10	1	2	FACETS	0.974	0.921	1	0.974	0.921	1	CLONAL	1	TRUE	1	0.67	2		488	959	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46277776	46277776	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	226	386	0	ENST00000371998.3:c.3574G>T	p.Glu1192Ter	p.E1192*	ENST00000371998		1192	Gaa/Taa	19/23	1	2	FACETS	0.991	0.927	1	0.991	0.927	1	CLONAL	1	TRUE	1	0.67	2		386	681	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948513	54948513	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	245	388	0	ENST00000312783.6:c.805G>T	p.Glu269Ter	p.E269*	ENST00000312783	NM_198436.1	269	Gag/Tag	8/10	1	2	FACETS	0.945	0.886	1	0.945	0.886	1	CLONAL	1	TRUE	1	0.67	2		388	774	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62298845	62298845	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770742969	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	420	659	0	ENST00000360203.5:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000360203	NM_001283009.1	213	cGg/cAg	8/35	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.67	2		659	1199	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321738	62321738	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	424	534	0	ENST00000360203.5:c.2357C>T	p.Thr786Ile	p.T786I	ENST00000360203	NM_001283009.1	786	aCc/aTc	26/35	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.67	2		534	1181	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39774538	39774538	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	127	345	0	ENST00000288319.7:c.614C>A	p.Ser205Ter	p.S205*	ENST00000288319	NM_182918.3	205	tCa/tAa	5/10	1	2	FACETS	0.699	0.636	0.765	0.699	0.636	0.765	SUBCLONAL	1	TRUE	1	0.67	2		345	542	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130543	29130543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	423	599	0	ENST00000328354.6:c.167G>T	p.Ser56Ile	p.S56I	ENST00000328354	NM_007194.3	56	aGc/aTc	2/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.67	2		599	1238	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434198	12434198	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	541	395	0	ENST00000287820.6:c.566A>C	p.Lys189Thr	p.K189T	ENST00000287820	NM_015869.4	189	aAa/aCa	4/7	0.3	4	FACETS	1	0.995	1	0.799	0.769	0.829	INDETERMINATE	2	TRUE	1	0.67	4		395	1125	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458537	12458537	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1254	458	606	0	ENST00000287820.6:c.1154G>T	p.Arg385Leu	p.R385L	ENST00000287820	NM_015869.4	385	cGa/cTa	6/7	0.3	4	FACETS	1	0.995	1	0.445	0.423	0.466	INDETERMINATE	1	TRUE	1	0.67	4		606	1712	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103727	47103727	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	291	403	0	ENST00000409792.3:c.6219G>T	p.Glu2073Asp	p.E2073D	ENST00000409792	NM_014159.6	2073	gaG/gaT	14/21	1	2	FACETS	0.996	0.94	1	0.996	0.94	1	CLONAL	1	TRUE	1	0.67	2		403	872	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721531	49721531	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778105210	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	401	538	0	ENST00000449682.2:c.2108G>A	p.Arg703His	p.R703H	ENST00000449682	NM_020998.3	703	cGc/cAc	18/18	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.67	2		538	1192	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442608	52442608	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	306	319	0	ENST00000460680.1:c.137T>G	p.Phe46Cys	p.F46C	ENST00000460680	NM_004656.3	46	tTt/tGt	4/17	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.67	2		319	820	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713627	52713627	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	409	460	0	ENST00000394830.3:c.101A>C	p.Lys34Thr	p.K34T	ENST00000394830	NM_018313.4	34	aAa/aCa	2/30	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.67	2		460	1090	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026849	71026849	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	202	264	0	ENST00000318789.4:c.1373T>G	p.Phe458Cys	p.F458C	ENST00000318789	NM_032682.5	458	tTt/tGt	16/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.67	2		264	512	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138400873	138400873	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	339	511	0	ENST00000289153.2:c.2440A>G	p.Met814Val	p.M814V	ENST00000289153	NM_006219.2	814	Atg/Gtg	17/22	1	2	FACETS	0.962	0.911	1	0.962	0.911	1	CLONAL	1	TRUE	1	0.67	2		511	1052	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242854	142242854	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	259	438	1	ENST00000350721.4:c.4133G>A	p.Gly1378Glu	p.G1378E	ENST00000350721	NM_001184.3	1378	gGa/gAa	22/47	1	2	FACETS	0.914	0.858	0.971	0.914	0.858	0.971	CLONAL	1	TRUE	1	0.67	2		439	846	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169988233	169988233	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	167	294	0	ENST00000295797.4:c.475G>A	p.Asp159Asn	p.D159N	ENST00000295797	NM_002740.5	159	Gac/Aac	6/18	1	2	FACETS	0.944	0.874	1	0.944	0.874	1	CLONAL	1	TRUE	1	0.67	2		294	528	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504976	186504977	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	350	377	0	ENST00000323963.5:c.837dup	p.Leu280SerfsTer12	p.L280Sfs*12	ENST00000323963		278	att/aTtt	8/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.67	2		377	964	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608582	189608582	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	335	427	0	ENST00000264731.3:c.1657T>G	p.Leu553Val	p.L553V	ENST00000264731	NM_003722.4	553	Tta/Gta	13/14	1	2	FACETS	0.972	0.92	1	0.972	0.92	1	CLONAL	1	TRUE	1	0.67	2		427	1029	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961019	55961019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	325	531	0	ENST00000263923.4:c.2921G>A	p.Ser974Asn	p.S974N	ENST00000263923	NM_002253.2	974	aGc/aAc	21/30	1	2	FACETS	0.988	0.935	1	0.988	0.935	1	CLONAL	1	TRUE	1	0.67	2		531	982	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196499	106196499	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs527895107	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	172	357	0	ENST00000380013.4:c.4832C>T	p.Ser1611Phe	p.S1611F	ENST00000380013	NM_001127208.2	1611	tCt/tTt	11/11	1	2	FACETS	0.875	0.809	0.942	0.875	0.809	0.942	CLONAL	1	TRUE	1	0.67	2		357	587	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143033738	143033738	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	266	351	0	ENST00000262992.4:c.2233C>A	p.Leu745Ile	p.L745I	ENST00000262992	NM_001101669.1	745	Ctt/Att	20/24	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.67	2		351	769	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251953	153251953	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs267600040	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	294	485	0	ENST00000281708.4:c.1053G>A	p.Trp351Ter	p.W351*	ENST00000281708	NM_033632.3	351	tgG/tgA	7/12	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.67	2		485	870	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525664	187525664	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	256	481	0	ENST00000441802.2:c.10415A>C	p.Asn3472Thr	p.N3472T	ENST00000441802	NM_005245.3	3472	aAc/aCc	18/27	1	2	FACETS	0.93	0.873	0.988	0.93	0.873	0.988	CLONAL	1	TRUE	1	0.67	2		481	822	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542870	187542870	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	190	333	0	ENST00000441802.2:c.4870G>T	p.Glu1624Ter	p.E1624*	ENST00000441802	NM_005245.3	1624	Gaa/Taa	10/27	1	2	FACETS	0.939	0.873	1	0.939	0.873	1	CLONAL	1	TRUE	1	0.67	2		333	604	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38946655	38946655	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	118	233	0	ENST00000357387.3:c.4315-1G>A		p.X1439_splice	ENST00000357387	NM_152756.3	1439			0.106444737938325	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.67	0		233	408	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982083	38982083	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	282	450	0	ENST00000357387.3:c.639A>C	p.Lys213Asn	p.K213N	ENST00000357387	NM_152756.3	213	aaA/aaC	8/38	0.106444737938325	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.67	0		450	839	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168782	56168782	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	83	419	2	ENST00000399503.3:c.1636A>G	p.Thr546Ala	p.T546A	ENST00000399503	NM_005921.1	546	Act/Gct	9/20	0.106444737938325	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.67	0		421	707	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754588	57754588	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	317	339	0	ENST00000274289.3:c.459A>C	p.Glu153Asp	p.E153D	ENST00000274289	NM_006622.3	153	gaA/gaC	3/14	0.292455180492658	3	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.67	3		339	867	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589211	67589211	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	222	318	0	ENST00000274335.5:c.1199C>A	p.Ser400Tyr	p.S400Y	ENST00000274335		400	tCt/tAt	9/15	0.292455180492658	3	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.67	3		318	653	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628460	86628460	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	105	159	0	ENST00000274376.6:c.828+1G>A		p.X276_splice	ENST00000274376	NM_002890.2	276			1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.67	2		159	303	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670713	86670713	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	79	191	0	ENST00000274376.6:c.1991A>C	p.Lys664Thr	p.K664T	ENST00000274376	NM_002890.2	664	aAa/aCa	15/25	1	2	FACETS	0.851	0.758	0.949	0.851	0.758	0.949	CLONAL	1	TRUE	1	0.67	2		191	277	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271270	26271270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238067230	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	306	482	0	ENST00000305910.3:c.343G>A	p.Ala115Thr	p.A115T	ENST00000305910	NM_003534.2	115	Gct/Act	1/1	0.3	5	FACETS	1	0.991	1	0.425	0.399	0.451	INDETERMINATE	1	TRUE	2	0.67	5		482	1437	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681841	30681841	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	444	572	0	ENST00000376406.3:c.256G>A	p.Ala86Thr	p.A86T	ENST00000376406	NM_014641.2	86	Gca/Aca	3/15	0.140411193283748	3	FACETS	1	0.994	1	0.649	0.619	0.68	INDETERMINATE	1	TRUE	1	0.67	3		572	1363	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324581	31324581	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs151341152	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	480	294	0	ENST00000412585.2:c.227T>C	p.Ile76Thr	p.I76T	ENST00000412585	NM_005514.6	76	aTa/aCa	2/8	0.140411193283748	3	FACETS	1	0.995	1	1	0.995	1	INDETERMINATE	2	TRUE	1	0.67	3		294	787	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324721	31324721	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	28	87	0	ENST00000412585.2:c.87G>T	p.Met29Ile	p.M29I	ENST00000412585	NM_005514.6	29	atG/atT	2/8	0.140411193283748	3	FACETS	0.461	0.37	0.564	0.231	0.185	0.282	INDETERMINATE	1	TRUE	1	0.67	3		87	242	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32802948	32802948	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	392	413	0	ENST00000374899.4:c.928T>C	p.Tyr310His	p.Y310H	ENST00000374899	NM_018833.2	310	Tac/Cac	5/12	0.140411193283748	3	FACETS	0.807	0.77	0.845	0.807	0.77	0.845	INDETERMINATE	2	TRUE	1	0.67	3		413	968	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803004	32803004	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769546391	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	475	525	1	ENST00000374899.4:c.872G>A	p.Arg291Gln	p.R291Q	ENST00000374899	NM_018833.2	291	cGa/cAa	5/12	0.140411193283748	3	FACETS	1	0.996	1	0.706	0.675	0.737	INDETERMINATE	1	TRUE	1	0.67	3		526	1341	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745216	43745216	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	443	522	0	ENST00000523873.1:c.129C>A	p.Phe43Leu	p.F43L	ENST00000523873		43	ttC/ttA	3/8	0.140411193283748	3	FACETS	1	0.996	1	0.725	0.693	0.758	INDETERMINATE	1	TRUE	1	0.67	3		522	1217	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553348	106553348	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	347	415	0	ENST00000369096.4:c.1313G>T	p.Gly438Val	p.G438V	ENST00000369096	NM_001198.3	438	gGc/gTc	5/7	0.249300608834068	4	FACETS	0.893	0.847	0.939			1	INDETERMINATE	2	TRUE	NA	0.67	4		415	969	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109319879	109319879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	395	533	0	ENST00000436639.2:c.809C>T	p.Ser270Phe	p.S270F	ENST00000436639	NM_014454.2	270	tCt/tTt	5/10	0.249300608834068	4	FACETS	0.857	0.816	0.899			1	INDETERMINATE	2	TRUE	NA	0.67	4		533	1149	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109321750	109321750	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1032022376	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	502	571	1	ENST00000436639.2:c.673G>T	p.Glu225Ter	p.E225*	ENST00000436639	NM_014454.2	225	Gaa/Taa	4/10	0.249300608834068	4	FACETS	0.868	0.831	0.905			1	INDETERMINATE	2	TRUE	NA	0.67	4		572	1442	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111995755	111995755	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	66	440	0	ENST00000368678.4:c.1343C>A	p.Ser448Tyr	p.S448Y	ENST00000368678		448	tCt/tAt	12/13	1	2	FACETS	0.234	0.202	0.268	0.234	0.202	0.268	SUBCLONAL	1	TRUE	1	0.67	2		440	843	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519179	137519179	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1562281992	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	143	228	0	ENST00000367739.4:c.1459G>T	p.Glu487Ter	p.E487*	ENST00000367739	NM_000416.2	487	Gaa/Taa	7/7	1	2	FACETS	0.97	0.892	1	0.97	0.892	1	CLONAL	1	TRUE	1	0.67	2		228	440	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200488	138200488	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs200138929	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	264	414	0	ENST00000237289.4:c.1906C>T	p.His636Tyr	p.H636Y	ENST00000237289	NM_001270507.1	636	Cat/Tat	7/9	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.67	2		414	762	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864379	162864379	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	287	437	0	ENST00000366898.1:c.134T>C	p.Phe45Ser	p.F45S	ENST00000366898	NM_004562.2	45	tTc/tCc	2/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.67	2		437	798	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946225	13946225	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	234	340	0	ENST00000405192.2:c.872-1G>T		p.X291_splice	ENST00000405192	NM_001163147.1	291			0.292455180492658	3	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.67	3		340	659	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978805	13978805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	327	498	1	ENST00000405192.2:c.302C>T	p.Ser101Phe	p.S101F	ENST00000405192	NM_001163147.1	101	tCt/tTt	6/12	0.292455180492658	3	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.67	3		499	967	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729320	41729320	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	288	444	0	ENST00000242208.4:c.1209C>A	p.Tyr403Ter	p.Y403*	ENST00000242208	NM_002192.2	403	taC/taA	3/3	0.279719149156803	1	FACETS	0.673	0.635	0.711	0.673	0.635	0.711	INDETERMINATE	1	TRUE	0	0.67	1		444	850	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545741	106545741	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	341	512	0	ENST00000359195.3:c.3218A>C	p.Glu1073Ala	p.E1073A	ENST00000359195	NM_002649.2	1073	gAa/gCa	11/11	0.110267626569347	4	FACETS	0.821	0.778	0.865	0.821	0.778	0.865	INDETERMINATE	2	TRUE	2	0.67	4		512	1035	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395451	116395452	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	56	430	0	ENST00000397752.3:c.1746dup	p.Ile583HisfsTer12	p.I583Hfs*12	ENST00000397752	NM_000245.2	582	acc/aCcc	6/21	0.110267626569347	4	FACETS	0.302	0.258	0.351	0.151	0.129	0.176	INDETERMINATE	1	TRUE	2	0.67	4		430	923	SUCCESS
MET	4233	MSKCC	GRCh37	7	116399486	116399486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	267	408	1	ENST00000397752.3:c.2306C>T	p.Ser769Leu	p.S769L	ENST00000397752	NM_000245.2	769	tCa/tTa	10/21	0.110267626569347	4	FACETS	0.814	0.765	0.863	0.814	0.765	0.863	INDETERMINATE	2	TRUE	2	0.67	4		409	818	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148526931	148526931	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	128	274	0	ENST00000320356.2:c.373G>T	p.Glu125Ter	p.E125*	ENST00000320356	NM_004456.4	125	Gaa/Taa	5/20	1	2	FACETS	0.889	0.812	0.968	0.889	0.812	0.968	CLONAL	1	TRUE	1	0.67	2		274	430	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860022	151860022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1342484276	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	181	321	0	ENST00000262189.6:c.10640C>T	p.Ser3547Phe	p.S3547F	ENST00000262189	NM_170606.2	3547	tCc/tTc	43/59	1	2	FACETS	0.932	0.864	1	0.932	0.864	1	CLONAL	1	TRUE	1	0.67	2		321	580	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945402	151945402	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	315	519	0	ENST00000262189.6:c.2117G>A	p.Ser706Asn	p.S706N	ENST00000262189	NM_170606.2	706	aGt/aAt	14/59	1	2	FACETS	0.958	0.905	1	0.958	0.905	1	CLONAL	1	TRUE	1	0.67	2		519	982	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152009026	152009026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369725088	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	179	260	0	ENST00000262189.6:c.596G>A	p.Arg199Gln	p.R199Q	ENST00000262189	NM_170606.2	199	cGa/cAa	5/59	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.67	2		260	470	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38173514	38173514	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1207267789	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	326	454	0	ENST00000317025.8:c.1902T>G	p.Ser634Arg	p.S634R	ENST00000317025	NM_023034.1	634	agT/agG	10/24	1	2	FACETS	0.986	0.933	1	0.986	0.933	1	CLONAL	1	TRUE	1	0.67	2		454	987	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187135	38187135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356401338	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	430	634	0	ENST00000317025.8:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000317025	NM_023034.1	448	Cgg/Tgg	6/24	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.67	2		634	1258	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285888	38285888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	367	542	0	ENST00000425967.3:c.523G>A	p.Asp175Asn	p.D175N	ENST00000425967	NM_001174067.1	175	Gat/Aat	5/19	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.67	2		542	1072	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370912	55370912	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	378	550	0	ENST00000297316.4:c.214A>G	p.Met72Val	p.M72V	ENST00000297316	NM_022454.3	72	Atg/Gtg	1/2	0.279719149156803	1	FACETS	0.674	0.641	0.708	0.674	0.641	0.708	INDETERMINATE	1	TRUE	0	0.67	1		550	1113	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930127	68930127	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	246	441	0	ENST00000288368.4:c.188A>C	p.Lys63Thr	p.K63T	ENST00000288368	NM_024870.2	63	aAa/aCa	2/40	0.279719149156803	1	FACETS	0.674	0.632	0.716	0.674	0.632	0.716	INDETERMINATE	1	TRUE	0	0.67	1		441	725	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005951	69005951	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	204	441	0	ENST00000288368.4:c.2362G>T	p.Val788Leu	p.V788L	ENST00000288368	NM_024870.2	788	Gta/Tta	21/40	0.279719149156803	1	FACETS	0.579	0.538	0.62	0.579	0.538	0.62	INDETERMINATE	1	TRUE	0	0.67	1		441	700	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319940	8319940	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	179	295	0	ENST00000356435.5:c.5561T>G	p.Phe1854Cys	p.F1854C	ENST00000356435		1854	tTc/tGc	34/35	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.67	2		295	501	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97933393	97933393	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	255	360	1	ENST00000289081.3:c.489G>T	p.Glu163Asp	p.E163D	ENST00000289081	NM_000136.2	163	gaG/gaT	6/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.67	2		361	745	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798781	135798781	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1214441043	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	172	283	0	ENST00000298552.3:c.462C>A	p.Phe154Leu	p.F154L	ENST00000298552	NM_001162426.1	154	ttC/ttA	6/23	1	2	FACETS	0.946	0.876	1	0.946	0.876	1	CLONAL	1	TRUE	1	0.67	2		283	543	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793249	139793249	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	517	663	0	ENST00000247668.2:c.57C>A	p.Phe19Leu	p.F19L	ENST00000247668	NM_021138.3	19	ttC/ttA	2/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.67	2		663	1468	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936023	44936027	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTC	CCCTC	-	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	351	263	0	ENST00000377967.4:c.2786_2790del	p.Pro929LeufsTer12	p.P929Lfs*12	ENST00000377967	NM_021140.2	928	taCCCTCcc/tacc	18/29	0.249300608834068	2	FACETS	0.977	0.94	1			1	INDETERMINATE	2	TRUE	NA	0.67	2		263	536	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650866	48650866	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	474	395	0	ENST00000376670.3:c.735G>T	p.Lys245Asn	p.K245N	ENST00000376670	NM_002049.3	245	aaG/aaT	4/6	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.67	1		395	684	SUCCESS
AR	367	MSKCC	GRCh37	X	66766214	66766214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	495	224	0	ENST00000374690.3:c.1226G>A	p.Gly409Glu	p.G409E	ENST00000374690	NM_000044.3	409	gGg/gAg	1/8	1	1	FACETS		NA	1	1	0.998	1	NA	2	TRUE	0	0.67	1		224	615	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763970	76763970	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	360	273	0	ENST00000373344.5:c.7338G>T	p.Met2446Ile	p.M2446I	ENST00000373344	NM_000489.3	2446	atG/atT	35/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.67	1		273	523	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630182	100630182	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	305	281	1	ENST00000308731.7:c.91C>A	p.Leu31Ile	p.L31I	ENST00000308731	NM_000061.2	31	Ctc/Atc	2/19	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.67	1		282	464	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0040655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	52	813	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.871	0.744	1	0.871	0.744	1	CLONAL	1	TRUE	1	0.318351825398111	2		813	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	108	650	1	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.280346950511269	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.318351825398111	1		651	563	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959073	28959073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761475937	NA	P-0040655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	44	323	0	ENST00000282397.4:c.2065G>A	p.Glu689Lys	p.E689K	ENST00000282397	NM_002019.4	689	Gag/Aag	14/30	NA	2	FACETS	0.804	0.676	0.943			1	INDETERMINATE	1	TRUE	NA	0.318351825398111	2		323	344	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145589	11145589	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0040655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	77	454	0	ENST00000358026.2:c.3952-1G>A		p.X1318_splice	ENST00000358026	NM_001128849.1	1318			0.318351825398111	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.318351825398111	1		454	363	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254728	46254728	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	47	201	0	ENST00000334344.6:c.4918A>G	p.Lys1640Glu	p.K1640E	ENST00000334344	NM_152641.2	1640	Aaa/Gaa	16/21	1	2	FACETS	0.974	0.827	1	0.974	0.827	1	CLONAL	1	TRUE	1	0.318351825398111	2		201	303	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112580	115112581	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0040655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	89	570	3	ENST00000257566.3:c.1159_1160delinsAA	p.Pro387Asn	p.P387N	ENST00000257566	NM_016569.3	387	CCc/AAc	7/8	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.318351825398111	2		573	511	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748889	41748889	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	34	473	0	ENST00000301178.4:c.1414G>T	p.Val472Phe	p.V472F	ENST00000301178	NM_021913.4	472	Gtc/Ttc	11/20	1	2	FACETS	0.461	0.376	0.557	0.461	0.376	0.557	SUBCLONAL	1	TRUE	1	0.318351825398111	2		473	463	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964388	70964388	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	56	266	0	ENST00000276594.2:c.1640C>A	p.Ser547Ter	p.S547*	ENST00000276594	NM_024504.3	547	tCa/tAa	8/8	0.12996314395604	3	FACETS	1	0.899	1	0.528	0.454	0.609	INDETERMINATE	1	TRUE	1	0.318351825398111	3		266	386	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039883	47039883	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	65	606	0	ENST00000377604.3:c.1226C>A	p.Ala409Glu	p.A409E	ENST00000377604	NM_001204468.1	409	gCg/gAg	12/24	1	2	FACETS	0.804	0.698	0.918	0.804	0.698	0.918	CLONAL	1	TRUE	1	0.318351825398111	2		606	508	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679975	30679975	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	89	570	0	ENST00000376406.3:c.1744G>A	p.Glu582Lys	p.E582K	ENST00000376406	NM_014641.2	582	Gag/Aag	5/15	0.351450743864895	4	FACETS	0.847	0.751	0.951	0.282	0.25	0.317	CLONAL	1	TRUE	1	0.382011634670354	4		570	760	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972509	81972509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755617580	NA	P-0040758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	175	557	1	ENST00000359376.3:c.3302C>T	p.Thr1101Met	p.T1101M	ENST00000359376	NM_002661.3	1101	aCg/aTg	29/33	0.382011634670354	3	FACETS	0.911	0.843	0.981	0.911	0.843	0.981	CLONAL	2	TRUE	1	0.382011634670354	3		558	599	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	338	864	0	ENST00000269305.4:c.481del	p.Ala161ProfsTer9	p.A161Pfs*9	ENST00000269305	NM_001126112.2	161	Gcc/cc	5/11	0.362838473107433	2	FACETS	0.99	0.94	1	0.99	0.94	1	CLONAL	2	TRUE	0	0.382011634670354	2		864	894	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600434	43600434	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	125	695	1	ENST00000355710.3:c.660C>A	p.Ser220Arg	p.S220R	ENST00000355710	NM_020975.4	220	agC/agA	4/20	0.377580081285285	3	FACETS	0.988	0.894	1	0.329	0.298	0.362	CLONAL	1	TRUE	0	0.382011634670354	3		696	789	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14303266	14303266	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	92	675	0	ENST00000256196.4:c.409del	p.Val137Ter	p.V137*	ENST00000256196		137	Gta/ta	5/6	0.351450743864895	4	FACETS	0.698	0.619	0.783	0.233	0.206	0.261	SUBCLONAL	1	TRUE	1	0.382011634670354	4		675	953	SUCCESS
APC	324	MSKCC	GRCh37	5	112175231	112175231	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	94	240	0	ENST00000257430.4:c.3940del	p.Arg1314GlyfsTer7	p.R1314Gfs*7	ENST00000257430	NM_000038.5	1314	Agg/gg	16/16	0.362838473107433	2	FACETS	0.888	0.802	0.978	0.888	0.802	0.978	CLONAL	2	TRUE	0	0.382011634670354	2		240	277	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520099	106520099	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	44	213	0	ENST00000359195.3:c.2527C>A	p.Leu843Ile	p.L843I	ENST00000359195	NM_002649.2	843	Ctt/Att	6/11	0.351450743864895	4	FACETS	0.863	0.725	1	0.288	0.241	0.338	CLONAL	1	TRUE	1	0.382011634670354	4		213	369	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0040796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	107	702	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.18	2		702	965	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004657	16004657	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs528790312	NA	P-0040796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	86	648	0	ENST00000268712.3:c.2597T>C	p.Ile866Thr	p.I866T	ENST00000268712	NM_006311.3	866	aTa/aCa	20/46	1	2	FACETS	0.986	0.87	1	0.986	0.87	1	CLONAL	1	TRUE	1	0.18	2		648	969	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142949972	142949972	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	70	555	1	ENST00000262992.4:c.2738G>T	p.Arg913Ile	p.R913I	ENST00000262992	NM_001101669.1	913	aGa/aTa	24/24	1	2	FACETS	0.976	0.85	1	0.976	0.85	1	CLONAL	1	TRUE	1	0.18	2		556	797	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576919	7576920	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	C	novel	NA	P-0040796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	73	702	0	ENST00000269305.4:c.926_927delinsG	p.Pro309ArgfsTer36	p.P309Rfs*36	ENST00000269305	NM_001126112.2	309	cCC/cG	9/11	1	2	FACETS	0.799	0.697	0.91	0.799	0.697	0.91	CLONAL	1	TRUE	1	0.18	2		702	1015	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578415	7578415	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	526	754	0	ENST00000269305.4:c.515T>A	p.Val172Asp	p.V172D	ENST00000269305	NM_001126112.2	172	gTt/gAt	5/11	0.543864184812965	2	FACETS	0.974	0.939	1	0.974	0.939	1	CLONAL	2	TRUE	0	0.556386165175347	2		754	971	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101547	27101547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	251	766	2	ENST00000324856.7:c.4829G>A	p.Gly1610Glu	p.G1610E	ENST00000324856	NM_006015.4	1610	gGg/gAg	18/20	0.554886217282387	3	FACETS	0.978	0.914	1	0.489	0.457	0.522	CLONAL	1	TRUE	1	0.556386165175347	3		768	1179	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224558	108224558	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs756899044	NA	P-0040800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	134	338	0	ENST00000278616.4:c.8737G>T	p.Asp2913Tyr	p.D2913Y	ENST00000278616	NM_000051.3	2913	Gat/Tat	60/63	1	2	FACETS	0.975	0.891	1	0.975	0.891	1	CLONAL	1	TRUE	1	0.556386165175347	2		338	494	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320884	30320885	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	129	341	0	ENST00000322652.5:c.1294_1295insA	p.Phe432TyrfsTer4	p.F432Yfs*4	ENST00000322652	NM_015355.2	432	ttt/tAtt	12/16	0.555098248096916	3	FACETS	0.923	0.839	1	0.308	0.279	0.337	CLONAL	1	TRUE	0	0.556386165175347	3		341	642	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0040810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	213	309	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.493525338363425	3	FACETS	0.863	0.807	0.92	0.863	0.807	0.92	CLONAL	2	TRUE	1	0.496148281458181	3		309	621	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419986	41419986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372989163	NA	P-0040810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	174	811	0	ENST00000373198.4:c.335G>A	p.Arg112His	p.R112H	ENST00000373198	NM_133170.3	112	cGt/cAt	3/32	0.496148281458181	3	FACETS	0.981	0.904	1	0.491	0.452	0.531	CLONAL	1	TRUE	1	0.496148281458181	3		811	892	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0040810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	158	279	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.935	0.859	1	0.935	0.859	1	CLONAL	1	TRUE	1	0.496148281458181	2		279	681	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306550	41306550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760520624	NA	P-0040810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	339	732	0	ENST00000373198.4:c.1109C>T	p.Thr370Met	p.T370M	ENST00000373198	NM_133170.3	370	aCg/aTg	7/32	0.496148281458181	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.496148281458181	3		732	820	SUCCESS
APC	324	MSKCC	GRCh37	5	112175777	112175777	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	72	359	0	ENST00000257430.4:c.4486del	p.Thr1496LeufsTer11	p.T1496Lfs*11	ENST00000257430	NM_000038.5	1496	Act/ct	16/16	0.496148281458181	1	FACETS	0.817	0.722	0.917	0.817	0.722	0.917	CLONAL	1	TRUE	0	0.496148281458181	1		359	267	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425278	49425278	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	511	863	2	ENST00000301067.7:c.13210G>T	p.Gly4404Ter	p.G4404*	ENST00000301067	NM_003482.3	4404	Gga/Tga	39/54	0.944641093862943	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.944641093862943	1		865	550	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891079	112891079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1385944040	NA	P-0040811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	384	566	1	ENST00000351677.2:c.413G>A	p.Arg138Gln	p.R138Q	ENST00000351677	NM_002834.3	138	cGa/cAa	4/16	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.944641093862943	2		567	737	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0040811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	979	1274	1	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.944641093862943	2		1275	1028	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78435615	78435615	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1213414237	NA	P-0040822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	459	516	0	ENST00000370768.2:c.205G>T	p.Asp69Tyr	p.D69Y	ENST00000370768	NM_003902.3	69	Gat/Tat	2/20	0.946798572235441	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.946798572235441	2		516	475	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947585	48947585	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0040822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	542	400	0	ENST00000267163.4:c.1172C>G	p.Ser391Ter	p.S391*	ENST00000267163	NM_000321.2	391	tCa/tGa	12/27	0.946798572235441	3	FACETS	1	0.998	1	1	0.998	1	CLONAL	3	TRUE	0	0.946798572235441	3		400	548	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961720	41961720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	484	513	0	ENST00000219905.7:c.628G>A	p.Glu210Lys	p.E210K	ENST00000219905	NM_001164273.1	210	Gaa/Aaa	2/24	0.946798572235441	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.946798572235441	2		513	497	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014075	14014075	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	891	777	0	ENST00000311895.7:c.53A>C	p.Tyr18Ser	p.Y18S	ENST00000311895	NM_005236.2	18	tAc/tCc	1/11	0.946798572235441	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.946798572235441	3		777	1375	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654737	29654737	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs771529172	NA	P-0040822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	464	383	0	ENST00000356175.3:c.5426G>C	p.Arg1809Pro	p.R1809P	ENST00000356175	NM_000267.3	1809	cGc/cCc	37/57	0.946798572235441	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.946798572235441	2		383	483	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211360	36211360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779453478	NA	P-0040822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	767	792	0	ENST00000222270.7:c.1111G>A	p.Glu371Lys	p.E371K	ENST00000222270	NM_014727.1	371	Gaa/Aaa	3/37	0.684289839181385	4	FACETS	0.979	0.948	1	0.979	0.948	1	CLONAL	2	TRUE	2	0.946798572235441	4		792	1611	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902710	50902710	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	918	836	0	ENST00000440232.2:c.285C>G	p.Ile95Met	p.I95M	ENST00000440232	NM_002691.3	95	atC/atG	3/27	0.684289839181385	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.946798572235441	4		836	1836	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141557648	141557648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	473	971	1	ENST00000220592.5:c.1667C>T	p.Thr556Met	p.T556M	ENST00000220592	NM_012154.3	556	aCg/aTg	13/19	0.946798572235441	3	FACETS	0.996	0.951	1	0.332	0.317	0.347	CLONAL	1	TRUE	0	0.946798572235441	3		972	1478	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0040848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	533	751	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.522475960332824	2	FACETS	0.859	0.833	0.884	1	0.997	1	CLONAL	3	TRUE	0	0.522475960332824	2		751	792	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	72	461	0	ENST00000397062.3:c.92G>A	p.Gly31Glu	p.G31E	ENST00000397062	NM_006164.4	31	gGa/gAa	2/5	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.522475960332824	2		461	203	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911585	134911585	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	139	585	1	ENST00000398015.3:c.2050G>T	p.Glu684Ter	p.E684*	ENST00000398015	NM_004441.4	684	Gag/Tag	11/16	0.175968507781732	0	FACETS	0.399	0.364	0.435			1	INDETERMINATE	1	TRUE	0	0.522475960332824	0		586	637	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944924	31944924	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	140	393	0	ENST00000340398.3:c.177G>C	p.Glu59Asp	p.E59D	ENST00000340398	NM_001013699.2	59	gaG/gaC	1/1	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.522475960332824	2		393	462	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753038	42753038	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	185	859	0	ENST00000222329.4:c.1226T>A	p.Leu409Gln	p.L409Q	ENST00000222329	NM_006494.2	409	cTg/cAg	4/4	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.522475960332824	2		859	656	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609944	117609944	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs779954823	NA	P-0040848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	37	399	1	ENST00000368508.3:c.6755G>T	p.Cys2252Phe	p.C2252F	ENST00000368508	NM_002944.2	2252	tGt/tTt	43/43	0.411511184726857	3	FACETS	0.794	0.66	0.941	0.397	0.33	0.471	CLONAL	1	TRUE	1	0.522475960332824	3		400	225	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	126	737	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.808	0.747	0.869	1	0.99	1	CLONAL	2	TRUE	1	0.6	2		737	260	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0040864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	101	253	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.852	0.768	0.941	0.852	0.768	0.941	CLONAL	1	TRUE	1	0.6	2		253	395	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0040864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	204	450	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.6	2		450	548	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624263	89624263	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	110	308	0	ENST00000371953.3:c.40del	p.Arg14GlyfsTer10	p.R14Gfs*10	ENST00000371953	NM_000314.4	13	Aaa/aa	1/9	1	2	FACETS	0.983	0.892	1	0.983	0.892	1	CLONAL	1	TRUE	1	0.6	2		308	373	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762202	43762202	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	326	698	0	ENST00000382044.4:c.1243C>G	p.Gln415Glu	p.Q415E	ENST00000382044	NM_001141980.1	415	Caa/Gaa	11/28	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.6	2		698	763	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0040869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	209	723	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.550469278952391	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.550469278952391	1		723	494	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120386	94120386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	84	256	1	ENST00000369303.4:c.665C>T	p.Ser222Leu	p.S222L	ENST00000369303	NM_004440.3	222	tCa/tTa	3/17	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.550469278952391	2		257	279	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370674	225370674	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	40	243	0	ENST00000264414.4:c.1205G>A	p.Gly402Glu	p.G402E	ENST00000264414	NM_003590.4	402	gGg/gAg	8/16	0.375490689586086	1	FACETS	0.408	0.341	0.482	0.408	0.341	0.482	SUBCLONAL	1	TRUE	0	0.550469278952391	1		243	258	SUCCESS
ATM	472	MSKCC	GRCh37	11	108126978	108126978	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	130	456	0	ENST00000278616.4:c.2161C>G	p.Leu721Val	p.L721V	ENST00000278616	NM_000051.3	721	Ctt/Gtt	14/63	1	2	FACETS	0.851	0.775	0.93	0.851	0.775	0.93	CLONAL	1	TRUE	1	0.550469278952391	2		456	555	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828021	3828021	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0040869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	145	417	0	ENST00000262367.5:c.2104A>T	p.Arg702Ter	p.R702*	ENST00000262367	NM_004380.2	702	Aga/Tga	10/31	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.550469278952391	2		417	524	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72891502	72891502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	136	403	0	ENST00000325599.8:c.260G>A	p.Gly87Glu	p.G87E	ENST00000325599	NM_018130.2	87	gGg/gAg	3/11	0.550469278952391	1	FACETS	0.914	0.84	0.99	0.914	0.84	0.99	CLONAL	1	TRUE	0	0.550469278952391	1		403	392	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720900	119720900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1025803517	NA	P-0040869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	125	361	0	ENST00000316626.5:c.275G>A	p.Arg92Lys	p.R92K	ENST00000316626		92	aGa/aAa	2/12	0.49674734810248	3	FACETS	1	0.957	1	0.544	0.495	0.596	CLONAL	1	TRUE	1	0.550469278952391	3		361	532	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	218	526	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.76	0.72	0.798	1	0.994	1	SUBCLONAL	2	TRUE	1	0.788465781188147	2		526	364	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591145	67591145	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	93	296	0	ENST00000274335.5:c.1738T>A	p.Tyr580Asn	p.Y580N	ENST00000274335		580	Tac/Aac	12/15	1	2	FACETS	0.749	0.673	0.828	0.749	0.673	0.828	SUBCLONAL	1	TRUE	1	0.788465781188147	2		296	315	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	174	409	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.823	0.763	0.885	0.823	0.763	0.885	CLONAL	1	TRUE	1	0.788465781188147	2		409	536	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	91	711	1	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.429	0.382	0.479	0.429	0.382	0.479	SUBCLONAL	1	TRUE	1	0.788465781188147	2		712	538	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	68	576	1	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	1	2	FACETS	0.213	0.184	0.243	0.213	0.184	0.243	SUBCLONAL	1	TRUE	1	0.788465781188147	2		577	811	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482927	140482927	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	179	461	1	ENST00000288602.6:c.1208del	p.Pro403LeufsTer8	p.P403Lfs*8	ENST00000288602	NM_004333.4	403	cCt/ct	10/18	1	2	FACETS	0.885	0.822	0.949	0.885	0.822	0.949	CLONAL	1	TRUE	1	0.788465781188147	2		462	513	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692901	89692901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786204929	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	302	353	0	ENST00000371953.3:c.385G>A	p.Gly129Arg	p.G129R	ENST00000371953	NM_000314.4	129	Gga/Aga	5/9	0.788465781188147	2	FACETS	0.992	0.96	1	0.992	0.96	1	CLONAL	2	TRUE	0	0.788465781188147	2		353	386	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926248	112926248	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs121918468	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	39	415	0	ENST00000351677.2:c.1381G>A	p.Ala461Thr	p.A461T	ENST00000351677	NM_002834.3	461	Gct/Act	12/16	1	2	FACETS	0.17	0.14	0.203	0.17	0.14	0.203	SUBCLONAL	1	TRUE	1	0.788465781188147	2		415	582	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223788	53223789	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	297	704	0	ENST00000375401.3:c.3570_3571del	p.Cys1190TrpfsTer13	p.C1190Wfs*13	ENST00000375401	NM_004187.3	1190	tgTGgg/tggg	23/26	1	2	FACETS	0.818	0.772	0.865	0.818	0.772	0.865	CLONAL	1	TRUE	1	0.788465781188147	2		704	921	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217557	142217557	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1268253442	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	68	375	0	ENST00000350721.4:c.5440del	p.Arg1814GlufsTer10	p.R1814Efs*10	ENST00000350721	NM_001184.3	1814	Aga/ga	32/47	0.253742367043107	1	FACETS	0.291	0.254	0.33	0.291	0.254	0.33	INDETERMINATE	1	TRUE	0	0.788465781188147	1		375	359	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817777	3817778	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	64	438	0	ENST00000262367.5:c.3193_3194del	p.Ser1065Ter	p.S1065*	ENST00000262367	NM_004380.2	1065	AGt/t	16/31	1	2	FACETS	0.245	0.212	0.281	0.245	0.212	0.281	SUBCLONAL	1	TRUE	1	0.788465781188147	2		438	663	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332152	70332153	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1196853334	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	74	224	4	ENST00000373644.4:c.65dup	p.Lys23GlufsTer37	p.K23Efs*37	ENST00000373644	NM_030625.2	19	-/A	2/12	1	2	FACETS	0.719	0.637	0.805	0.719	0.637	0.805	SUBCLONAL	1	TRUE	1	0.788465781188147	2		228	261	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188294	32188295	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs766348245	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	216	573	5	ENST00000375023.3:c.1046dup	p.Thr350HisfsTer4	p.T350Hfs*4	ENST00000375023	NM_004557.3	349	ggc/ggGc	6/30	1	2	FACETS	0.76	0.709	0.812	0.76	0.709	0.812	SUBCLONAL	1	TRUE	1	0.788465781188147	2		578	721	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11210198	11210198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	108	465	0	ENST00000361445.4:c.4555G>A	p.Ala1519Thr	p.A1519T	ENST00000361445	NM_004958.3	1519	Gct/Act	31/58	1	2	FACETS	0.48	0.432	0.53	0.48	0.432	0.53	SUBCLONAL	1	TRUE	1	0.788465781188147	2		465	571	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829075	128829075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1247591045	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	31	75	0	ENST00000249373.3:c.88del	p.Ala30ArgfsTer25	p.A30Rfs*25	ENST00000249373	NM_005631.4	28	cGg/cg	1/12	1	2	FACETS	0.678	0.56	0.805	0.678	0.56	0.805	SUBCLONAL	1	TRUE	1	0.788465781188147	2		75	116	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427265	49427266	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	rs398123707	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	113	565	0	ENST00000301067.7:c.11220_11222dup	p.Gln3745dup	p.Q3745dup	ENST00000301067	NM_003482.3	3745	caa/caGCAa	39/54	1	2	FACETS	0.508	0.459	0.56	0.508	0.459	0.56	SUBCLONAL	1	TRUE	1	0.788465781188147	2		565	564	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589606	67589606	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	43	235	0	ENST00000274335.5:c.1369C>T	p.Gln457Ter	p.Q457*	ENST00000274335		457	Caa/Taa	10/15	1	2	FACETS	0.768	0.656	0.887	0.768	0.656	0.887	SUBCLONAL	1	TRUE	1	0.788465781188147	2		235	142	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146945	38146945	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	159	603	0	ENST00000317025.8:c.3197del	p.Asn1066ThrfsTer16	p.N1066Tfs*16	ENST00000317025	NM_023034.1	1066	aAc/ac	18/24	1	2	FACETS	0.851	0.786	0.917	0.851	0.786	0.917	CLONAL	1	TRUE	1	0.788465781188147	2		603	474	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426771	49426772	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs944680171	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	96	309	1	ENST00000301067.7:c.11714_11716dup	p.Gln3905dup	p.Q3905dup	ENST00000301067	NM_003482.3	3905	ctg/cAGCtg	39/54	1	2	FACETS	0.773	0.697	0.852	0.773	0.697	0.852	SUBCLONAL	1	TRUE	1	0.788465781188147	2		310	315	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161786	56161786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	150	359	0	ENST00000399503.3:c.1283C>T	p.Thr428Met	p.T428M	ENST00000399503	NM_005921.1	428	aCg/aTg	6/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.788465781188147	2		359	315	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561755	55561755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759250095	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	76	339	0	ENST00000288135.5:c.145C>T	p.Arg49Cys	p.R49C	ENST00000288135	NM_000222.2	49	Cgc/Tgc	2/21	1	2	FACETS	0.471	0.415	0.531	0.471	0.415	0.531	SUBCLONAL	1	TRUE	1	0.788465781188147	2		339	409	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111146	193111147	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	52	330	2	ENST00000367435.3:c.687_688del	p.Arg229SerfsTer37	p.R229Sfs*37	ENST00000367435	NM_024529.4	227	AGa/a	7/17	0.788465781188147	4	FACETS	0.351	0.298	0.409	0.117	0.099	0.137	SUBCLONAL	1	TRUE	1	0.788465781188147	4		332	672	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212155	98212155	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	172	370	0	ENST00000331920.6:c.3517G>A	p.Val1173Met	p.V1173M	ENST00000331920	NM_000264.3	1173	Gtg/Atg	21/24	1	2	FACETS	0.919	0.853	0.986	0.919	0.853	0.986	CLONAL	1	TRUE	1	0.788465781188147	2		370	475	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438196	438196	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	106	286	0	ENST00000399788.2:c.1774-1G>A		p.X592_splice	ENST00000399788	NM_001042603.1	592			1	2	FACETS	0.815	0.739	0.893	0.815	0.739	0.893	CLONAL	1	TRUE	1	0.788465781188147	2		286	330	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440459	49440459	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	330	663	0	ENST00000301067.7:c.4351A>C	p.Ser1451Arg	p.S1451R	ENST00000301067	NM_003482.3	1451	Agc/Cgc	15/54	1	2	FACETS	0.977	0.927	1	0.977	0.927	1	CLONAL	1	TRUE	1	0.788465781188147	2		663	857	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893303	32893303	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs878853297	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	109	367	0	ENST00000380152.3:c.161del	p.Asn54ThrfsTer26	p.N54Tfs*26	ENST00000380152		53	Aaa/aa	3/27	1	2	FACETS	0.984	0.898	1	0.984	0.898	1	CLONAL	1	TRUE	1	0.788465781188147	2		367	281	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43769822	43769822	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	175	437	0	ENST00000382044.4:c.924G>T	p.Gln308His	p.Q308H	ENST00000382044	NM_001141980.1	308	caG/caT	8/28	1	2	FACETS	0.865	0.803	0.929	0.865	0.803	0.929	CLONAL	1	TRUE	1	0.788465781188147	2		437	513	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845856	72845856	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	276	511	0	ENST00000268489.5:c.3611del	p.Ser1204PhefsTer40	p.S1204Ffs*40	ENST00000268489	NM_006885.3	1204	tCt/tt	6/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.788465781188147	2		511	675	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348560	56348560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	116	275	0	ENST00000348428.3:c.368G>A	p.Ser123Asn	p.S123N	ENST00000348428	NM_006785.3	123	aGc/aAc	2/17	1	2	FACETS	0.943	0.862	1	0.943	0.862	1	CLONAL	1	TRUE	1	0.788465781188147	2		275	312	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247893	10247893	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1488470434	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	276	600	0	ENST00000340748.4:c.4309C>T	p.Arg1437Cys	p.R1437C	ENST00000340748		1437	Cgc/Tgc	36/40	1	2	FACETS	0.93	0.877	0.983	0.93	0.877	0.983	CLONAL	1	TRUE	1	0.788465781188147	2		600	753	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302842	15302842	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	164	634	0	ENST00000263388.2:c.608C>A	p.Pro203His	p.P203H	ENST00000263388	NM_000435.2	203	cCc/cAc	4/33	1	2	FACETS	0.49	0.45	0.532	0.49	0.45	0.532	SUBCLONAL	1	TRUE	1	0.788465781188147	2		634	849	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216700	36216700	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376193493	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	70	529	0	ENST00000222270.7:c.3866C>T	p.Thr1289Met	p.T1289M	ENST00000222270	NM_014727.1	1289	aCg/aTg	13/37	1	2	FACETS	0.267	0.233	0.305	0.267	0.233	0.305	SUBCLONAL	1	TRUE	1	0.788465781188147	2		529	664	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662553	227662553	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs958582927	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	167	515	1	ENST00000305123.5:c.902G>A	p.Arg301His	p.R301H	ENST00000305123	NM_005544.2	301	cGc/cAc	1/2	1	2	FACETS	0.756	0.699	0.815	0.756	0.699	0.815	SUBCLONAL	1	TRUE	1	0.788465781188147	2		516	560	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434188	12434188	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	150	396	0	ENST00000287820.6:c.556A>T	p.Ser186Cys	p.S186C	ENST00000287820	NM_015869.4	186	Agt/Tgt	4/7	1	2	FACETS	0.971	0.898	1	0.971	0.898	1	CLONAL	1	TRUE	1	0.788465781188147	2		396	392	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266654	41266654	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1267755116	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	170	444	0	ENST00000349496.5:c.451C>T	p.Arg151Cys	p.R151C	ENST00000349496	NM_001904.3	151	Cgt/Tgt	4/15	1	2	FACETS	0.847	0.785	0.911	0.847	0.785	0.911	CLONAL	1	TRUE	1	0.788465781188147	2		444	509	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505615	186505615	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	140	325	0	ENST00000323963.5:c.1023A>T	p.Gln341His	p.Q341H	ENST00000323963		341	caA/caT	10/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.788465781188147	2		325	329	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31495481	31495481	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	98	408	0	ENST00000344624.3:c.1669-2A>G		p.X557_splice	ENST00000344624		557			1	2	FACETS	0.504	0.452	0.56	0.504	0.452	0.56	SUBCLONAL	1	TRUE	1	0.788465781188147	2		408	493	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591236	67591258	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTGTTTTTCAGGTGGTTGACTC	ACTGTTTTTCAGGTGGTTGACTC	-	novel	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	65	330	0	ENST00000274335.5:c.1746-11_1757del		p.X582_splice	ENST00000274335		582		13/15	1	2	FACETS	0.597	0.523	0.676	0.597	0.523	0.676	SUBCLONAL	1	TRUE	1	0.788465781188147	2		330	276	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636701	176636701	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	45	362	1	ENST00000439151.2:c.1301C>A	p.Pro434His	p.P434H	ENST00000439151	NM_022455.4	434	cCc/cAc	5/23	1	2	FACETS	0.288	0.242	0.338	0.288	0.242	0.338	SUBCLONAL	1	TRUE	1	0.788465781188147	2		363	397	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056301	26056301	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs374398098	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	207	399	0	ENST00000343677.2:c.356A>C	p.Lys119Thr	p.K119T	ENST00000343677	NM_005319.3	119	aAg/aCg	1/1	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.788465781188147	2		399	525	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288635	33288636	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	123	399	0	ENST00000374542.5:c.916dup	p.Arg306ProfsTer38	p.R306Pfs*38	ENST00000374542	NM_001141970.1	306	cga/cCga	3/8	1	2	FACETS	0.731	0.666	0.798	0.731	0.666	0.798	SUBCLONAL	1	TRUE	1	0.788465781188147	2		399	427	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987340	2987340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554276653	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	266	530	1	ENST00000396946.4:c.89G>A	p.Arg30Gln	p.R30Q	ENST00000396946	NM_032415.4	30	cGg/cAg	3/25	1	2	FACETS	0.891	0.839	0.944	0.891	0.839	0.944	CLONAL	1	TRUE	1	0.788465781188147	2		531	757	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864679	68864679	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	52	299	0	ENST00000288368.4:c.50T>C	p.Leu17Pro	p.L17P	ENST00000288368	NM_024870.2	17	cTg/cCg	1/40	1	2	FACETS	0.304	0.259	0.353	0.304	0.259	0.353	SUBCLONAL	1	TRUE	1	0.788465781188147	2		299	434	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141557574	141557574	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	266	593	1	ENST00000220592.5:c.1741C>T	p.Gln581Ter	p.Q581*	ENST00000220592	NM_012154.3	581	Cag/Tag	13/19	1	2	FACETS	0.953	0.899	1	0.953	0.899	1	CLONAL	1	TRUE	1	0.788465781188147	2		594	708	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739671	145739671	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376364416	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	49	599	0	ENST00000428558.2:c.1780G>A	p.Ala594Thr	p.A594T	ENST00000428558	NM_004260.3	594	Gca/Aca	11/22	1	2	FACETS	0.162	0.137	0.191	0.162	0.137	0.191	SUBCLONAL	1	TRUE	1	0.788465781188147	2		599	765	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222789	53222789	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	296	639	1	ENST00000375401.3:c.4147C>T	p.Gln1383Ter	p.Q1383*	ENST00000375401	NM_004187.3	1383	Cag/Tag	25/26	1	2	FACETS	0.944	0.893	0.996	0.944	0.893	0.996	CLONAL	1	TRUE	1	0.788465781188147	2		640	795	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412256	63412256	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	164	702	1	ENST00000330258.3:c.911C>A	p.Pro304His	p.P304H	ENST00000330258	NM_152424.3	304	cCt/cAt	2/2	1	2	FACETS	0.51	0.468	0.553	0.51	0.468	0.553	SUBCLONAL	1	TRUE	1	0.788465781188147	2		703	816	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0040894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	376	409	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.201463984882554	6	FACETS	0.92	0.885	0.955			1	INDETERMINATE	6	TRUE	NA	0.403210724343148	6		409	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578204	7578204	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	83	491	1	ENST00000269305.4:c.645T>A	p.Ser215Arg	p.S215R	ENST00000269305	NM_001126112.2	215	agT/agA	6/11	0.403210724343148	3	FACETS	0.826	0.73	0.929	0.413	0.365	0.465	CLONAL	1	TRUE	1	0.403210724343148	3		492	599	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551823	150551823	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	111	231	0	ENST00000369026.2:c.184G>T	p.Gly62Cys	p.G62C	ENST00000369026	NM_021960.4	62	Ggc/Tgc	1/3	0.156871242652304	6	FACETS	1	0.975	1	0.821	0.744	0.901	INDETERMINATE	2	TRUE	3	0.403210724343148	6		231	404	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225367681	225367681	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0040894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	60	270	0	ENST00000264414.4:c.1485+1G>T		p.X495_splice	ENST00000264414	NM_003590.4	495			0.39316870051837	2	FACETS	0.779	0.683	0.88	0.779	0.683	0.88	SUBCLONAL	2	TRUE	0	0.403210724343148	2		270	191	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024533	31024533	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	79	456	0	ENST00000375687.4:c.4018C>G	p.Pro1340Ala	p.P1340A	ENST00000375687	NM_015338.5	1340	Cca/Gca	13/13	0.403210724343148	3	FACETS	0.897	0.791	1	0.448	0.395	0.505	CLONAL	1	TRUE	1	0.403210724343148	3		456	525	SUCCESS
APC	324	MSKCC	GRCh37	5	112175741	112175741	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1165759330	NA	P-0040894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	41	237	0	ENST00000257430.4:c.4450G>C	p.Asp1484His	p.D1484H	ENST00000257430	NM_000038.5	1484	Gat/Cat	16/16	0.39316870051837	2	FACETS	0.946	0.796	1	0.473	0.398	0.555	CLONAL	1	TRUE	0	0.403210724343148	2		237	215	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176684100	176684100	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	209	376	1	ENST00000439151.2:c.4914C>A	p.His1638Gln	p.H1638Q	ENST00000439151	NM_022455.4	1638	caC/caA	13/23	0.367808031204609	3	FACETS	1	0.988	1	0.813	0.762	0.864	CLONAL	2	TRUE	0	0.403210724343148	3		377	511	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966716	44966716	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	24	180	1	ENST00000377967.4:c.3940G>T	p.Gly1314Ter	p.G1314*	ENST00000377967	NM_021140.2	1314	Gga/Tga	27/29	0.257801773617058	2	FACETS	1	0.81	1			1	CLONAL	1	TRUE	NA	0.403210724343148	2		181	117	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939562	76939562	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0040894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	15	205	0	ENST00000373344.5:c.1186A>T	p.Lys396Ter	p.K396*	ENST00000373344	NM_000489.3	396	Aag/Tag	9/35	0.257801773617058	2	FACETS	0.493	0.362	0.647			1	SUBCLONAL	1	TRUE	NA	0.403210724343148	2		205	151	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0040936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	417	212	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.854259942796912	2		212	969	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0040936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	711	778	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.854259942796912	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.854259942796912	1		778	899	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259735	16259735	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	546	636	0	ENST00000375759.3:c.7003del	p.Thr2335GlnfsTer18	p.T2335Qfs*18	ENST00000375759	NM_015001.2	2334	Aaa/aa	11/15	1	2	FACETS	0.978	0.94	1	0.978	0.94	1	CLONAL	1	TRUE	1	0.854259942796912	2		636	1307	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117430	115117431	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0040936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	380	443	0	ENST00000257566.3:c.743dup	p.Tyr248Ter	p.Y248*	ENST00000257566	NM_016569.3	248	tac/taAc	4/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.854259942796912	2		443	867	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849442	68849448	+	frameshift_variant	Frame_Shift_Del	DEL	CAGTACA	CAGTACA	-	novel	NA	P-0040936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	575	774	0	ENST00000261769.5:c.1345_1351del	p.Gln449PhefsTer4	p.Q449Ffs*4	ENST00000261769	NM_004360.3	449	CAGTACAtt/tt	10/16	0.830453987857605	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.854259942796912	1		774	755	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106543608	106543608	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	213	282	0	ENST00000369096.4:c.410G>T	p.Arg137Met	p.R137M	ENST00000369096	NM_001198.3	137	aGg/aTg	3/7	NA	2	FACETS	0.95	0.891	1			1	INDETERMINATE	1	TRUE	NA	0.854259942796912	2		282	525	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0040945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	539	413	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.246830794738849	14	FACETS	1	0.983	1			1	CLONAL	11	TRUE	NA	0.246830794738849	14		414	959	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222982	1222982	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs727504172	NA	P-0040945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	209	681	0	ENST00000326873.7:c.921-2A>T		p.X307_splice	ENST00000326873	NM_000455.4	307			0.206634217577506	3	FACETS	1	0.984	1	0.791	0.736	0.847	CLONAL	2	TRUE	0	0.246830794738849	3		681	802	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512474	38512474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770732457	NA	P-0040945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	90	1059	1	ENST00000254066.5:c.1385C>T	p.Pro462Leu	p.P462L	ENST00000254066	NM_000964.3	462	cCg/cTg	9/9	0.246830794738849	4	FACETS	0.84	0.743	0.943	0.28	0.247	0.315	CLONAL	1	TRUE	1	0.246830794738849	4		1060	1083	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434189	12434189	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	37	537	0	ENST00000287820.6:c.557G>T	p.Ser186Ile	p.S186I	ENST00000287820	NM_015869.4	186	aGt/aTt	4/7	0.246830794738849	3	FACETS	0.585	0.481	0.701	0.292	0.24	0.351	SUBCLONAL	1	TRUE	1	0.246830794738849	3		537	576	SUCCESS
AR	367	MSKCC	GRCh37	X	66765861	66765861	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	111	1132	0	ENST00000374690.3:c.873A>T	p.Lys291Asn	p.K291N	ENST00000374690	NM_000044.3	291	aaA/aaT	1/8	0.175730744834572	3	FACETS	0.939	0.842	1	0.47	0.421	0.521	CLONAL	1	TRUE	1	0.246830794738849	3		1132	1076	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249002	55249003	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGTGGA	rs397517109	NA	P-0040952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	258	810	0	ENST00000275493.2:c.2303_2311dup	p.Ser768_Asp770dup	p.S768_D770dup	ENST00000275493	NM_005228.3	768	gcc/gcCAGCGTGGAc	20/28	0.349202208119183	5	FACETS	1	0.986	1	0.787	0.738	0.837	CLONAL	2	TRUE	2	0.349202208119183	5		810	954	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590961	95590961	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	25	367	1	ENST00000393063.1:c.948G>T	p.Trp316Cys	p.W316C	ENST00000393063	NM_030621.3	316	tgG/tgT	9/28	0.1328946256344	3	FACETS	0.394	0.31	0.491	0.197	0.155	0.246	INDETERMINATE	1	TRUE	1	0.349202208119183	3		368	427	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953898	55953898	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs143459233	NA	P-0040952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	77	580	0	ENST00000263923.4:c.3538A>T	p.Ile1180Leu	p.I1180L	ENST00000263923	NM_002253.2	1180	Ata/Tta	27/30	0.349202208119183	3	FACETS	0.889	0.781	1	0.444	0.39	0.502	CLONAL	1	TRUE	1	0.349202208119183	3		580	583	SUCCESS
APC	324	MSKCC	GRCh37	5	112173435	112173435	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	38	391	0	ENST00000257430.4:c.2144A>C	p.His715Pro	p.H715P	ENST00000257430	NM_000038.5	715	cAc/cCc	16/16	0.336030165460523	4	FACETS	0.604	0.499	0.722	0.302	0.249	0.361	SUBCLONAL	1	TRUE	2	0.349202208119183	4		391	486	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0040953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	111	413	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.946	0.852	1	1	0.988	1	CLONAL	2	TRUE	1	0.18	2		414	652	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032023	26032023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	34	443	0	ENST00000244661.2:c.266C>T	p.Ala89Val	p.A89V	ENST00000244661	NM_003537.3	89	gCg/gTg	1/1	1	2	FACETS	0.741	0.604	0.894	0.741	0.604	0.894	SUBCLONAL	1	TRUE	1	0.18	2		443	510	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001329	29001329	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	46	435	0	ENST00000282397.4:c.1403G>T	p.Trp468Leu	p.W468L	ENST00000282397	NM_002019.4	468	tGg/tTg	10/30	1	2	FACETS	0.947	0.797	1	0.947	0.797	1	CLONAL	1	TRUE	1	0.18	2		435	540	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527727	103527727	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	38	366	0	ENST00000355739.4:c.3035G>T	p.Ser1012Ile	p.S1012I	ENST00000355739	NM_000123.3	1012	aGc/aTc	15/15	1	2	FACETS	0.91	0.752	1	0.91	0.752	1	CLONAL	1	TRUE	1	0.18	2		366	464	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639255	3639255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138484365	NA	P-0040953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	202	875	8	ENST00000294008.3:c.4384G>A	p.Ala1462Thr	p.A1462T	ENST00000294008	NM_032444.2	1462	Gcc/Acc	12/15	1	2	FACETS	1	0.982	1	1	0.994	1	CLONAL	2	TRUE	1	0.18	2		883	956	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852243	128852243	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs149170801	NA	P-0040953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	85	817	1	ENST00000249373.3:c.2315G>T	p.Arg772Leu	p.R772L	ENST00000249373	NM_005631.4	772	cGc/cTc	12/12	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.18	2		818	843	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751205	128751205	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	160	514	0	ENST00000377970.2:c.742G>T	p.Gly248Cys	p.G248C	ENST00000377970	NM_002467.4	248	Ggc/Tgc	2/3	0.148543305000744	5	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	TRUE	2	0.18	5		514	676	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971019	21971045	+	inframe_deletion	In_Frame_Del	DEL	CAGACGGCCCCAGGCATCGCGCACGTC	CAGACGGCCCCAGGCATCGCGCACGTC	-	novel	NA	P-0040953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	36	577	0	ENST00000304494.5:c.313_339del	p.Asp105_Leu113del	p.D105_L113del	ENST00000304494	NM_000077.4	105	GACGTGCGCGATGCCTGGGGCCGTCTG/-	2/3	1	2	FACETS	0.866	0.712	1	0.866	0.712	1	CLONAL	1	TRUE	1	0.18	2		577	462	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321368	1321369	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0040953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	58	587	0	ENST00000400841.2:c.386_387delinsTT	p.Trp129Phe	p.W129F	ENST00000400841		129	tGG/tTT	4/6	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.18	2		587	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0040960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	512	677	0	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	0.420249834791421	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.45048087813706	3		677	868	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537237	80537237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	121	636	0	ENST00000286548.4:c.161C>T	p.Thr54Met	p.T54M	ENST00000286548	NM_002072.3	54	aCg/aTg	2/7	1	2	FACETS	0.995	0.903	1	0.995	0.903	1	CLONAL	1	TRUE	1	0.45048087813706	2		636	540	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215948	41215948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55770810	NA	P-0040960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	176	573	1	ENST00000357654.3:c.5095C>T	p.Arg1699Trp	p.R1699W	ENST00000357654	NM_007294.3	1699	Cgg/Tgg	17/23	0.250705924696185	2	FACETS	0.837	0.778	0.896	0.837	0.778	0.896	INDETERMINATE	2	TRUE	0	0.45048087813706	2		574	467	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288552	15288552	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	14	88	0	ENST00000263388.2:c.4187G>T	p.Arg1396Leu	p.R1396L	ENST00000263388	NM_000435.2	1396	cGc/cTc	24/33	0.194676609119545	5	FACETS	1	0.813	1	0.382	0.28	0.501	INDETERMINATE	1	TRUE	2	0.45048087813706	5		88	91	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792598	33792810	+	inframe_deletion	In_Frame_Del	DEL	GAGCGCGGGCGCGGGGTGCGGGCTGGGCACGGGCGTGGGCGGCGGCGTGGGGTGACCGGGCTGCAGGTGCATGGTGGTCTGGCCGCAGTGCGCGATCTGGAACTGCAGGTGCGGGGCGGCCAGGTGCGCGGGCGGCGGGTGCGGGTGCGGGTGCGAGGGCGGCGGCGGCGGCGGCGGCTGGTAAGGGAAGAGGCCGGCCAGCGCCAGCTGCTT	GAGCGCGGGCGCGGGGTGCGGGCTGGGCACGGGCGTGGGCGGCGGCGTGGGGTGACCGGGCTGCAGGTGCATGGTGGTCTGGCCGCAGTGCGCGATCTGGAACTGCAGGTGCGGGGCGGCCAGGTGCGCGGGCGGCGGGTGCGGGTGCGGGTGCGAGGGCGGCGGCGGCGGCGGCGGCTGGTAAGGGAAGAGGCCGGCCAGCGCCAGCTGCTT	-	novel	NA	P-0040960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	17	11	0	ENST00000498907.2:c.511_723del	p.Lys171_Leu241del	p.K171_L241del	ENST00000498907	NM_004364.3	171	AAGCAGCTGGCGCTGGCCGGCCTCTTCCCTTACCAGCCGCCGCCGCCGCCGCCGCCCTCGCACCCGCACCCGCACCCGCCGCCCGCGCACCTGGCCGCCCCGCACCTGCAGTTCCAGATCGCGCACTGCGGCCAGACCACCATGCACCTGCAGCCCGGTCACCCCACGCCGCCGCCCACGCCCGTGCCCAGCCCGCACCCCGCGCCCGCGCTC/-	1/1	0.148202935278953	3	FACETS	0.963	0.805	1	1	0.926	1	INDETERMINATE	4	TRUE	0	0.45048087813706	3		11	24	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230757	66230757	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	25	355	0	ENST00000273854.3:c.2214T>A	p.His738Gln	p.H738Q	ENST00000273854	NM_004439.5	738	caT/caA	12/18	0.45048087813706	1	FACETS	0.415	0.329	0.513	0.415	0.329	0.513	SUBCLONAL	1	TRUE	0	0.45048087813706	1		355	207	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0040988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	168	723	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.35751124497689	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.35751124497689	1		723	532	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056833	102056844	+	inframe_deletion	In_Frame_Del	DEL	GGCTAGACCCAA	GGCTAGACCCAA	-	novel	NA	P-0040988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	67	558	0	ENST00000282441.5:c.777_788del	p.Leu263_Arg266del	p.L263_R266del	ENST00000282441	NM_001130145.2	258	tGGCTAGACCCAAgg/tgg	4/9	0.35751124497689	1	FACETS	0.504	0.438	0.575	0.504	0.438	0.575	SUBCLONAL	1	TRUE	0	0.35751124497689	1		558	611	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256966	41256966	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs80357234	NA	P-0040988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	81	488	0	ENST00000357654.3:c.220C>T	p.Gln74Ter	p.Q74*	ENST00000357654	NM_007294.3	74	Caa/Taa	5/23	0.35751124497689	1	FACETS	0.852	0.754	0.956	0.852	0.754	0.956	CLONAL	1	TRUE	0	0.35751124497689	1		488	437	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938399	44938405	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTTCT	CTTTTCT	-	novel	NA	P-0040988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	79	424	0	ENST00000377967.4:c.2949_2955del	p.Phe984LeufsTer13	p.F984Lfs*13	ENST00000377967	NM_021140.2	983	CTTTTCTct/ct	20/29	1	2	FACETS	0.811	0.714	0.914	0.811	0.714	0.914	CLONAL	1	TRUE	1	0.35751124497689	2		424	545	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217312	123217312	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	133	527	0	ENST00000218089.9:c.2966G>T	p.Gly989Val	p.G989V	ENST00000218089	NM_001042749.1	989	gGg/gTg	29/35	0.35751124497689	3	FACETS	1	0.91	1	0.501	0.455	0.55	CLONAL	1	TRUE	1	0.35751124497689	3		527	875	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0041011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	136	754	1	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.204991534507113	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.204991534507113	1		755	1129	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039347	47039347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	119	724	2	ENST00000377604.3:c.970G>A	p.Ala324Thr	p.A324T	ENST00000377604	NM_001204468.1	324	Gcg/Acg	10/24	0.204991534507113	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.204991534507113	1		726	848	SUCCESS
APC	324	MSKCC	GRCh37	5	112175350	112175351	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	45	232	0	ENST00000257430.4:c.4063dup	p.Ser1355PhefsTer20	p.S1355Ffs*20	ENST00000257430	NM_000038.5	1353	-/T	16/16	0.204991534507113	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.204991534507113	1		232	295	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920447	114920449	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GCA	GCA	-	novel	NA	P-0041011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	65	423	0	ENST00000543371.1:c.1389_1391del	p.Cys463_Arg464delinsTrp	p.C463_R464delinsW	ENST00000543371	NM_001198531.1	463	tGCAgg/tgg	13/14	1	2	FACETS	0.957	0.829	1	0.957	0.829	1	CLONAL	1	TRUE	1	0.204991534507113	2		423	663	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416389	49416389	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	55	421	0	ENST00000301067.7:c.16322A>T	p.Lys5441Ile	p.K5441I	ENST00000301067	NM_003482.3	5441	aAa/aTa	51/54	1	2	FACETS	0.963	0.824	1	0.963	0.824	1	CLONAL	1	TRUE	1	0.204991534507113	2		421	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0041143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	472	398	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.724386558395806	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.724386558395806	1		398	824	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615153	43615153	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	443	1003	3	ENST00000355710.3:c.2567G>T	p.Trp856Leu	p.W856L	ENST00000355710	NM_020975.4	856	tGg/tTg	14/20	1	2	FACETS	0.935	0.892	0.978	0.935	0.892	0.978	CLONAL	1	TRUE	1	0.724386558395806	2		1006	1308	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238115	133238116	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0041143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	190	557	0	ENST00000320574.5:c.2860_2861dup	p.Tyr956GlyfsTer27	p.Y956Gfs*27	ENST00000320574	NM_006231.2	954	aag/aaAAg	24/49	1	2	FACETS	0.839	0.78	0.9	0.839	0.78	0.9	CLONAL	1	TRUE	1	0.724386558395806	2		557	625	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893662	28893662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	258	533	2	ENST00000282397.4:c.3184C>T	p.Pro1062Ser	p.P1062S	ENST00000282397	NM_002019.4	1062	Cct/Tct	24/30	0.724386558395806	1	FACETS	0.95	0.903	0.998	0.95	0.903	0.998	CLONAL	1	TRUE	0	0.724386558395806	1		535	478	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951122	48951122	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	162	412	0	ENST00000267163.4:c.1284G>C	p.Glu428Asp	p.E428D	ENST00000267163	NM_000321.2	428	gaG/gaC	13/27	0.724386558395806	1	FACETS	0.923	0.864	0.982	0.923	0.864	0.982	CLONAL	1	TRUE	0	0.724386558395806	1		412	309	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039341	49039341	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	343	716	3	ENST00000267163.4:c.2330del	p.Pro777LeufsTer33	p.P777Lfs*33	ENST00000267163	NM_000321.2	776	Ccc/cc	23/27	0.724386558395806	1	FACETS	0.963	0.922	1	0.963	0.922	1	CLONAL	1	TRUE	0	0.724386558395806	1		719	627	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110787	2110787	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	885	1016	0	ENST00000219476.3:c.1092C>G	p.Ile364Met	p.I364M	ENST00000219476	NM_000548.3	364	atC/atG	11/42	0.724386558395806	2	FACETS	0.958	0.937	0.979	0.958	0.937	0.979	CLONAL	2	TRUE	0	0.724386558395806	2		1016	1275	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024705	14024705	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	216	492	0	ENST00000311895.7:c.931G>C	p.Glu311Gln	p.E311Q	ENST00000311895	NM_005236.2	311	Gaa/Caa	5/11	NA	2	FACETS	0.929	0.868	0.991			1	INDETERMINATE	1	TRUE	NA	0.724386558395806	2		492	642	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562705	29562705	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	315	592	0	ENST00000356175.3:c.3785C>A	p.Ser1262Tyr	p.S1262Y	ENST00000356175	NM_000267.3	1262	tCt/tAt	28/57	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.724386558395806	2		592	806	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673764	37673764	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	321	759	0	ENST00000447079.4:c.2918A>T	p.Lys973Ile	p.K973I	ENST00000447079	NM_015083.1	973	aAa/aTa	10/14	1	2	FACETS	0.96	0.909	1	0.96	0.909	1	CLONAL	1	TRUE	1	0.724386558395806	2		759	923	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37856540	37856540	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1307888184	NA	P-0041143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	295	453	0	ENST00000269571.5:c.49C>T	p.Pro17Ser	p.P17S	ENST00000269571		17	Ccc/Tcc	1/27	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.724386558395806	2		453	735	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468382	89468382	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	149	289	1	ENST00000336596.2:c.1916G>T	p.Arg639Leu	p.R639L	ENST00000336596	NM_005233.5	639	cGc/cTc	11/17	0.724386558395806	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.724386558395806	1		290	218	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598050	55598050	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	236	476	1	ENST00000288135.5:c.2247A>T	p.Glu749Asp	p.E749D	ENST00000288135	NM_000222.2	749	gaA/gaT	16/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.724386558395806	2		477	606	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976838	2976838	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	411	935	1	ENST00000396946.4:c.1174C>T	p.Gln392Ter	p.Q392*	ENST00000396946	NM_032415.4	392	Cag/Tag	9/25	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.724386558395806	2		936	1110	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376287	225376287	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0041143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	42	317	0	ENST00000264414.4:c.667A>T	p.Lys223Ter	p.K223*	ENST00000264414	NM_003590.4	223	Aaa/Taa	6/16	0.721929863872071	3	FACETS	0.315	0.263	0.374	0.105	0.087	0.125	SUBCLONAL	1	TRUE	0	0.724386558395806	3		317	501	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	118	737	0				ENST00000310581	NM_198253.2	-/1132			0.174539231875813	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.850595913919452	0		737	285	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348011	348011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769972546	NA	P-0041195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	216	855	0	ENST00000262320.3:c.1495G>A	p.Val499Met	p.V499M	ENST00000262320	NM_003502.3	499	Gtg/Atg	6/11	0.146208014580601	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.850595913919452	0		855	507	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660602	67660602	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	181	608	0	ENST00000264010.4:c.1502A>C	p.Asp501Ala	p.D501A	ENST00000264010	NM_006565.3	501	gAt/gCt	8/12	0.174539231875813	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.850595913919452	0		608	456	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418336	139418336	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	288	986	0	ENST00000277541.6:c.236G>T	p.Arg79Leu	p.R79L	ENST00000277541	NM_017617.3	79	cGc/cTc	3/34	0.174539231875813	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.850595913919452	0		986	667	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	175	737	0				ENST00000310581	NM_198253.2	-/1132			0.516804104058717	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.531885558025349	1		737	417	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796970	45796970	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	230	675	0	ENST00000450313.1:c.1360C>T	p.Gln454Ter	p.Q454*	ENST00000450313	NM_012222.2	454	Caa/Taa	14/16	0.346027017199471	1	FACETS	0.899	0.842	0.958	0.899	0.842	0.958	CLONAL	1	TRUE	0	0.531885558025349	1		675	706	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076718	72076718	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	147	525	0	ENST00000357731.5:c.779G>A	p.Gly260Glu	p.G260E	ENST00000357731	NM_173808.2	260	gGa/gAa	5/7	0.346027017199471	1	FACETS	0.76	0.698	0.824	0.76	0.698	0.824	SUBCLONAL	1	TRUE	0	0.531885558025349	1		525	534	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510770	120510770	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	202	608	0	ENST00000256646.2:c.1194A>T	p.Gln398His	p.Q398H	ENST00000256646	NM_024408.3	398	caA/caT	7/34	0.346027017199471	1	FACETS	0.882	0.822	0.944	0.882	0.822	0.944	CLONAL	1	TRUE	0	0.531885558025349	1		608	632	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658603	206658603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	77	640	0	ENST00000367120.3:c.1576G>A	p.Glu526Lys	p.E526K	ENST00000367120	NM_014002.3	526	Gag/Aag	15/22	1	2	FACETS	0.43	0.377	0.486	0.43	0.377	0.486	SUBCLONAL	1	TRUE	1	0.531885558025349	2		640	674	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609027	43609027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483605155	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	56	846	1	ENST00000355710.3:c.1783G>A	p.Glu595Lys	p.E595K	ENST00000355710	NM_020975.4	595	Gag/Aag	10/20	0.465004482981202	1	FACETS	0.275	0.235	0.318	0.275	0.235	0.318	SUBCLONAL	1	TRUE	0	0.531885558025349	1		847	563	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852253	63852253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	90	675	0	ENST00000279873.7:c.3031C>T	p.Pro1011Ser	p.P1011S	ENST00000279873	NM_032199.2	1011	Ccg/Tcg	10/10	0.346027017199471	1	FACETS	0.372	0.33	0.417	0.372	0.33	0.417	SUBCLONAL	1	TRUE	0	0.531885558025349	1		675	668	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404693	70404693	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756914683	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	144	617	1	ENST00000373644.4:c.2207C>T	p.Ser736Leu	p.S736L	ENST00000373644	NM_030625.2	736	tCg/tTg	4/12	0.346027017199471	1	FACETS	0.8	0.734	0.867	0.8	0.734	0.867	SUBCLONAL	1	TRUE	0	0.531885558025349	1		618	497	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	418973	418973	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	159	652	0	ENST00000399788.2:c.3374T>C	p.Met1125Thr	p.M1125T	ENST00000399788	NM_001042603.1	1125	aTg/aCg	22/28	0.464385747283556	1	FACETS	0.739	0.68	0.799	0.739	0.68	0.799	SUBCLONAL	1	TRUE	0	0.531885558025349	1		652	594	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18473938	18473938	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	63	330	0	ENST00000266497.5:c.1180G>A	p.Glu394Lys	p.E394K	ENST00000266497		394	Gaa/Aaa	6/31	1	2	FACETS	0.697	0.606	0.794	0.697	0.606	0.794	SUBCLONAL	1	TRUE	1	0.531885558025349	2		330	340	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433729	49433730	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	178	1097	2	ENST00000301067.7:c.7823_7824delinsTT	p.Ser2608Phe	p.S2608F	ENST00000301067	NM_003482.3	2608	tCC/tTT	31/54	1	2	FACETS	0.695	0.64	0.752	0.695	0.64	0.752	SUBCLONAL	1	TRUE	1	0.531885558025349	2		1099	963	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912996	32912996	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	70	600	0	ENST00000380152.3:c.4504C>T	p.Gln1502Ter	p.Q1502*	ENST00000380152		1502	Caa/Taa	11/27	0.385796464825789	1	FACETS	0.373	0.325	0.424	0.373	0.325	0.424	SUBCLONAL	1	TRUE	0	0.531885558025349	1		600	518	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762259	43762259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	164	636	0	ENST00000382044.4:c.1186C>T	p.Pro396Ser	p.P396S	ENST00000382044	NM_001141980.1	396	Cca/Tca	11/28	0.531885558025349	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.531885558025349	1		636	446	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312746	91312746	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1408373309	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	325	478	1	ENST00000355112.3:c.2485C>T	p.Leu829Phe	p.L829F	ENST00000355112	NM_000057.2	829	Ctt/Ttt	12/22	0.468810842673721	5	FACETS	1	0.973	1			1	CLONAL	2	TRUE	NA	0.531885558025349	5		479	1051	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250916	99250916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs557275352	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	78	675	0	ENST00000268035.6:c.220C>T	p.Arg74Cys	p.R74C	ENST00000268035	NM_000875.3	74	Cgc/Tgc	2/21	0.468810842673721	5	FACETS	0.496	0.434	0.563			1	SUBCLONAL	1	TRUE	NA	0.531885558025349	5		675	1063	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274013	10274013	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758742694	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	157	996	1	ENST00000330684.3:c.256G>A	p.Val86Met	p.V86M	ENST00000330684	NM_001134407.1	86	Gtg/Atg	2/13	0.472303013312059	1	FACETS	0.555	0.509	0.603	0.555	0.509	0.603	SUBCLONAL	1	TRUE	0	0.531885558025349	1		997	781	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974932	15974932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769380838	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	104	454	0	ENST00000268712.3:c.3943C>T	p.Pro1315Ser	p.P1315S	ENST00000268712	NM_006311.3	1315	Ccc/Tcc	30/46	0.238422428002859	2	FACETS	0.753	0.677	0.834	0.377	0.338	0.417	INDETERMINATE	1	TRUE	0	0.531885558025349	2		454	519	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559101	29559101	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202023	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	92	162	0	ENST00000356175.3:c.3208C>T	p.Gln1070Ter	p.Q1070*	ENST00000356175	NM_000267.3	1070	Cag/Tag	25/57	0.531885558025349	1	FACETS	0.841	0.775	0.905	1	0.988	1	CLONAL	2	TRUE	0	0.531885558025349	1		162	151	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50143205	50143205	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	145	654	0	ENST00000246792.3:c.151C>T	p.Gln51Ter	p.Q51*	ENST00000246792	NM_006270.3	51	Cag/Tag	1/6	1	2	FACETS	0.763	0.697	0.831	0.763	0.697	0.831	SUBCLONAL	1	TRUE	1	0.531885558025349	2		654	715	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873458	136873458	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1558837039	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	64	411	0	ENST00000241393.3:c.40G>A	p.Glu14Lys	p.E14K	ENST00000241393	NM_003467.2	14	Gag/Aag	2/2	0.238422428002859	2	FACETS	0.529	0.459	0.604	0.264	0.229	0.302	INDETERMINATE	1	TRUE	0	0.531885558025349	2		411	455	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538328	9538328	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1205730758	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	79	506	0	ENST00000353224.5:c.1670C>T	p.Ser557Phe	p.S557F	ENST00000353224	NM_177990.2	557	tCc/tTc	7/10	0.264658895254953	2	FACETS	0.559	0.493	0.631	0.28	0.246	0.316	INDETERMINATE	1	TRUE	0	0.531885558025349	2		506	531	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877393	40877393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	205	721	1	ENST00000373198.4:c.2303G>A	p.Gly768Asp	p.G768D	ENST00000373198	NM_133170.3	768	gGc/gAc	15/32	0.456868778756601	0	FACETS	0.594	0.555	0.635			1	SUBCLONAL	1	TRUE	0	0.531885558025349	0		722	607	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22153344	22153344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	81	483	0	ENST00000215832.6:c.566C>T	p.Ala189Val	p.A189V	ENST00000215832	NM_002745.4	189	gCc/gTc	4/9	0.472303013312059	1	FACETS	0.419	0.369	0.471	0.419	0.369	0.471	SUBCLONAL	1	TRUE	0	0.531885558025349	1		483	534	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032747	30032747	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555986860	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	38	397	0	ENST00000338641.4:c.122G>A	p.Trp41Ter	p.W41*	ENST00000338641	NM_000268.3	41	tGg/tAg	2/16	0.472303013312059	1	FACETS	0.297	0.246	0.354	0.297	0.246	0.354	SUBCLONAL	1	TRUE	0	0.531885558025349	1		397	353	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928897	49928897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	341	1024	0	ENST00000296474.3:c.3469C>T	p.Pro1157Ser	p.P1157S	ENST00000296474	NM_002447.2	1157	Ccc/Tcc	16/20	0.21834304116858	2	FACETS	1	0.994	1	0.681	0.646	0.716	INDETERMINATE	1	TRUE	0	0.531885558025349	2		1024	942	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259325	89259325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	54	481	0	ENST00000336596.2:c.469C>T	p.Leu157Phe	p.L157F	ENST00000336596	NM_005233.5	157	Ctt/Ttt	3/17	0.21834304116858	2	FACETS	0.536	0.459	0.619	0.268	0.229	0.31	INDETERMINATE	1	TRUE	0	0.531885558025349	2		481	379	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564552	55564552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	72	625	0	ENST00000288135.5:c.440C>T	p.Ser147Phe	p.S147F	ENST00000288135	NM_000222.2	147	tCc/tTc	3/21	0.264658895254953	2	FACETS	0.415	0.362	0.471	0.207	0.181	0.236	INDETERMINATE	1	TRUE	0	0.531885558025349	2		625	653	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599321	55599321	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913507	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	92	521	0	ENST00000288135.5:c.2447A>T	p.Asp816Val	p.D816V	ENST00000288135	NM_000222.2	816	gAc/gTc	17/21	0.264658895254953	2	FACETS	0.643	0.573	0.717	0.322	0.286	0.359	INDETERMINATE	1	TRUE	0	0.531885558025349	2		521	538	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875645	35875645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201449880	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	151	381	0	ENST00000303115.3:c.832G>A	p.Asp278Asn	p.D278N	ENST00000303115	NM_002185.3	278	Gat/Aat	7/8	0.516804104058717	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.531885558025349	1		381	411	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111591	56111591	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1388884445	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	17	211	0	ENST00000399503.3:c.191A>G	p.Lys64Arg	p.K64R	ENST00000399503	NM_005921.1	64	aAa/aGa	1/20	0.3975674377836	2	FACETS	0.241	0.18	0.314	0.121	0.09	0.157	SUBCLONAL	1	TRUE	0	0.531885558025349	2		211	265	SUCCESS
APC	324	MSKCC	GRCh37	5	112116491	112116491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	108	283	0	ENST00000257430.4:c.536C>T	p.Ser179Phe	p.S179F	ENST00000257430	NM_000038.5	179	tCc/tTc	6/16	0.3975674377836	2	FACETS	0.883	0.81	0.956	0.883	0.81	0.956	CLONAL	2	TRUE	0	0.531885558025349	2		283	230	SUCCESS
APC	324	MSKCC	GRCh37	5	112177901	112177901	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs752654519	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	140	410	0	ENST00000257430.4:c.6610C>T	p.Arg2204Ter	p.R2204*	ENST00000257430	NM_000038.5	2204	Cga/Tga	16/16	0.3975674377836	2	FACETS	0.79	0.731	0.851	0.79	0.731	0.851	SUBCLONAL	2	TRUE	0	0.531885558025349	2		410	333	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169226	32169226	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	105	844	0	ENST00000375023.3:c.3807G>C	p.Glu1269Asp	p.E1269D	ENST00000375023	NM_004557.3	1269	gaG/gaC	22/30	0.140275662850389	5	FACETS	0.673	0.602	0.75	0.224	0.2	0.25	INDETERMINATE	1	TRUE	2	0.531885558025349	5		844	1054	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188836	32188836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1046104152	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	191	801	0	ENST00000375023.3:c.718C>T	p.Pro240Ser	p.P240S	ENST00000375023	NM_004557.3	240	Cct/Tct	4/30	0.140275662850389	5	FACETS	1	0.99	1	0.495	0.458	0.534	INDETERMINATE	1	TRUE	2	0.531885558025349	5		801	869	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200033	138200033	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	72	531	0	ENST00000237289.4:c.1451C>T	p.Pro484Leu	p.P484L	ENST00000237289	NM_001270507.1	484	cCc/cTc	7/9	NA	2	FACETS	0.529	0.463	0.6			1	INDETERMINATE	1	TRUE	NA	0.531885558025349	2		531	512	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265541	152265541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	32	613	0	ENST00000206249.3:c.994G>A	p.Asp332Asn	p.D332N	ENST00000206249	NM_000125.3	332	Gat/Aat	4/8	1	2	FACETS	0.202	0.163	0.246	0.202	0.163	0.246	SUBCLONAL	1	TRUE	1	0.531885558025349	2		613	595	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100173	157100174	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	67	106	0	ENST00000346085.5:c.1110_1111delinsTT	p.Pro371Ser	p.P371S	ENST00000346085	NM_020732.3	370	tcCCcc/tcTTcc	1/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.531885558025349	2		106	212	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935592	13935592	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	173	435	0	ENST00000405192.2:c.1264G>A	p.Glu422Lys	p.E422K	ENST00000405192	NM_001163147.1	422	Gag/Aag	12/12	0.140275662850389	5	FACETS	1	0.965	1	0.713	0.66	0.767	INDETERMINATE	2	TRUE	2	0.531885558025349	5		435	547	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224268	55224268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	126	571	0	ENST00000275493.2:c.1049C>T	p.Ser350Phe	p.S350F	ENST00000275493	NM_005228.3	350	tCc/tTc	9/28	1	2	FACETS	0.799	0.726	0.875	0.799	0.726	0.875	SUBCLONAL	1	TRUE	1	0.531885558025349	2		571	593	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266472	55266472	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs961150162	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	245	746	0	ENST00000275493.2:c.2764G>A	p.Glu922Lys	p.E922K	ENST00000275493	NM_005228.3	922	Gag/Aag	23/28	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.531885558025349	2		746	744	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335044	81335044	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	165	424	0	ENST00000222390.5:c.1783A>G	p.Ser595Gly	p.S595G	ENST00000222390	NM_000601.4	595	Agt/Ggt	16/18	0.229659013494967	4	FACETS	0.895	0.827	0.964	0.895	0.827	0.964	INDETERMINATE	2	TRUE	2	0.531885558025349	4		424	531	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389242	8389242	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	57	606	0	ENST00000356435.5:c.4376A>C	p.Glu1459Ala	p.E1459A	ENST00000356435		1459	gAa/gCa	26/35	0.392897679886508	0	FACETS	0.306	0.264	0.351			1	SUBCLONAL	1	TRUE	0	0.531885558025349	0		606	328	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471012	8471012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	73	436	0	ENST00000356435.5:c.3487G>A	p.Glu1163Lys	p.E1163K	ENST00000356435		1163	Gaa/Aaa	20/35	0.392897679886508	0	FACETS	0.434	0.383	0.488			1	SUBCLONAL	1	TRUE	0	0.531885558025349	0		436	296	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486263	8486263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	50	396	0	ENST00000356435.5:c.2554C>T	p.Pro852Ser	p.P852S	ENST00000356435		852	Cct/Tct	17/35	0.392897679886508	0	FACETS	0.303	0.259	0.352			1	SUBCLONAL	1	TRUE	0	0.531885558025349	0		396	290	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528774	8528774	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs758007107	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	41	364	0	ENST00000356435.5:c.358C>T	p.Gln120Ter	p.Q120*	ENST00000356435		120	Caa/Taa	4/35	0.392897679886508	0	FACETS	0.251	0.209	0.296			1	SUBCLONAL	1	TRUE	0	0.531885558025349	0		364	288	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482167	87482167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	119	665	0	ENST00000277120.3:c.1454C>T	p.Ser485Phe	p.S485F	ENST00000277120		485	tCc/tTc	14/19	0.456713837472473	1	FACETS	0.598	0.542	0.657	0.598	0.542	0.657	SUBCLONAL	1	TRUE	0	0.531885558025349	1		665	549	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	50	310	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.456713837472473	1	FACETS	0.384	0.327	0.447	0.384	0.327	0.447	SUBCLONAL	1	TRUE	0	0.531885558025349	1		310	359	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566514	139566514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	174	1006	0	ENST00000308874.7:c.773C>T	p.Ser258Phe	p.S258F	ENST00000308874		258	tCc/tTc	9/10	0.456713837472473	1	FACETS	0.535	0.493	0.58	0.535	0.493	0.58	SUBCLONAL	1	TRUE	0	0.531885558025349	1		1006	897	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0041226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	146	658	2	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	0.411322149523202	2	FACETS	0.956	0.874	1	0.478	0.437	0.52	CLONAL	1	TRUE	0	0.4500132951277	2		660	679	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0041226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	141	650	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.4500132951277	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.4500132951277	1		650	480	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383660	42383660	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	236	606	0	ENST00000221972.3:c.435C>G	p.Ile145Met	p.I145M	ENST00000221972	NM_021601.3	145	atC/atG	3/5	0.411322149523202	2	FACETS	0.903	0.849	0.957	0.903	0.849	0.957	CLONAL	2	TRUE	0	0.4500132951277	2		606	581	SUCCESS
APC	324	MSKCC	GRCh37	5	112175530	112175530	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	138	377	0	ENST00000257430.4:c.4240del	p.Val1414Ter	p.V1414*	ENST00000257430	NM_000038.5	1413	atG/at	16/16	0.323310543732033	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.323310543732033	2		377	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579321	7579322	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs587780067	NA	P-0041239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	202	344	0	ENST00000269305.4:c.365_366del	p.Val122AspfsTer26	p.V122Dfs*26	ENST00000269305	NM_001126112.2	122	gTG/g	4/11	0.323310543732033	2	FACETS	0.963	0.897	1	0.963	0.897	1	CLONAL	2	TRUE	0	0.323310543732033	2		344	649	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	35	851	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	0.557	0.456	0.671	0.557	0.456	0.671	SUBCLONAL	1	TRUE	1	0.220445615692257	2		851	570	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520327	176520327	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs762709356	NA	P-0041249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	60	658	0	ENST00000292408.4:c.1246C>T	p.Arg416Ter	p.R416*	ENST00000292408	NM_213647.1	416	Cga/Tga	9/18	1	2	FACETS	0.976	0.841	1	0.976	0.841	1	CLONAL	1	TRUE	1	0.220445615692257	2		658	558	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458435	120458436	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs771237928	NA	P-0041249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	28	605	0	ENST00000256646.2:c.6909dup	p.Ile2304HisfsTer9	p.I2304Hfs*9	ENST00000256646	NM_024408.3	2303	-/C	34/34	0.189295808668059	1	FACETS	0.466	0.372	0.574	0.466	0.372	0.574	SUBCLONAL	1	TRUE	0	0.220445615692257	1		605	485	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610099	10610099	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	41	638	0	ENST00000171111.5:c.611G>C	p.Arg204Pro	p.R204P	ENST00000171111	NM_203500.1	204	cGg/cCg	2/6	1	2	FACETS	0.53	0.44	0.63	0.53	0.44	0.63	SUBCLONAL	1	TRUE	1	0.220445615692257	2		638	702	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115384	115115384	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0041249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	64	289	0	ENST00000257566.3:c.941+1G>T		p.X314_splice	ENST00000257566	NM_016569.3	314			1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.220445615692257	2		289	522	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118709	115118710	+	missense_variant	Missense_Mutation	DNP	TT	TT	AG	novel	NA	P-0041249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	73	402	0	ENST00000257566.3:c.631_632delinsCT	p.Asn211Leu	p.N211L	ENST00000257566	NM_016569.3	211	AAc/CTc	2/8	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.220445615692257	2		402	562	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842406	68842406	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555515215	NA	P-0041249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	89	431	0	ENST00000261769.5:c.467G>A	p.Trp156Ter	p.W156*	ENST00000261769	NM_004360.3	156	tGg/tAg	4/16	0.220445615692257	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.220445615692257	1		431	536	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0041256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	259	305	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.383226518628517	3	FACETS	0.862	0.813	0.911	0.862	0.813	0.911	CLONAL	3	TRUE	0	0.383226518628517	3		305	623	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0041256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	90	353	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.277849939367958	3	FACETS	0.973	0.865	1	0.487	0.432	0.544	CLONAL	1	TRUE	1	0.383226518628517	3		353	575	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537933	212537933	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	79	503	0	ENST00000342788.4:c.1672C>A	p.Gln558Lys	p.Q558K	ENST00000342788	NM_005235.2	558	Cag/Aag	14/28	1	2	FACETS	0.639	0.562	0.722	0.639	0.562	0.722	SUBCLONAL	1	TRUE	1	0.383226518628517	2		503	645	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138938	64138938	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	51	364	0	ENST00000334205.4:c.2305C>A	p.Leu769Met	p.L769M	ENST00000334205	NM_003942.2	769	Ctg/Atg	17/17	0.335098121937979	4	FACETS	0.622	0.528	0.725	0.207	0.176	0.242	SUBCLONAL	1	TRUE	1	0.383226518628517	4		364	592	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373137	118373137	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	57	320	0	ENST00000534358.1:c.6530A>T	p.Glu2177Val	p.E2177V	ENST00000534358	NM_005933.3	2177	gAa/gTa	27/36	0.335098121937979	4	FACETS	0.727	0.624	0.84	0.242	0.208	0.28	SUBCLONAL	1	TRUE	1	0.383226518628517	4		320	566	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209106858	209106858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	86	452	0	ENST00000345146.2:c.710C>T	p.Ser237Phe	p.S237F	ENST00000345146	NM_005896.2	237	tCc/tTc	7/10	1	2	FACETS	0.739	0.655	0.83	0.739	0.655	0.83	SUBCLONAL	1	TRUE	1	0.383226518628517	2		452	607	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514480	41514480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1030044339	NA	P-0041256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	170	573	0	ENST00000373198.4:c.181G>A	p.Glu61Lys	p.E61K	ENST00000373198	NM_133170.3	61	Gag/Aag	2/32	0.30777228709402	4	FACETS	1	0.988	1	0.703	0.647	0.761	CLONAL	1	TRUE	2	0.383226518628517	4		573	873	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584483	189584483	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	120	306	0	ENST00000264731.3:c.779C>A	p.Pro260His	p.P260H	ENST00000264731	NM_003722.4	260	cCt/cAt	6/14	0.225490264971894	4	FACETS	0.798	0.723	0.876	0.798	0.723	0.876	INDETERMINATE	2	TRUE	2	0.383226518628517	4		306	543	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540214	187540214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1420663657	NA	P-0041256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	223	456	1	ENST00000441802.2:c.7526C>T	p.Thr2509Ile	p.T2509I	ENST00000441802	NM_005245.3	2509	aCc/aTc	10/27	0.281341423558759	3	FACETS	1	0.978	1	0.733	0.686	0.78	CLONAL	2	TRUE	0	0.383226518628517	3		457	631	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517993	176517993	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	226	671	0	ENST00000292408.4:c.491C>G	p.Ala164Gly	p.A164G	ENST00000292408	NM_213647.1	164	gCg/gGg	5/18	0.277849939367958	3	FACETS	0.786	0.733	0.841	0.786	0.733	0.841	SUBCLONAL	2	TRUE	1	0.383226518628517	3		671	894	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	55	737	0				ENST00000310581	NM_198253.2	-/1132			0.103988527229016	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		737	131	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0041275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	134	305	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.103988527229016	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		305	294	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0041277-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	223	413	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.223904273158624	10	FACETS	1	0.968	1	0.755	0.706	0.806	CLONAL	5	TRUE	3	0.223904273158624	10		414	714	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141986	108141986	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660628	NA	P-0041277-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	60	459	1	ENST00000278616.4:c.2930G>T	p.Cys977Phe	p.C977F	ENST00000278616	NM_000051.3	977	tGt/tTt	20/63	0.223904273158624	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.223904273158624	1		460	371	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427524	49427524	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs768831474	NA	P-0041277-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	129	920	0	ENST00000301067.7:c.10964T>G	p.Leu3655Arg	p.L3655R	ENST00000301067	NM_003482.3	3655	cTt/cGt	39/54	0.223904273158624	3	FACETS	0.901	0.818	0.988	0.901	0.818	0.988	CLONAL	2	TRUE	1	0.223904273158624	3		920	711	SUCCESS
AR	367	MSKCC	GRCh37	X	66766510	66766510	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041277-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	149	484	0	ENST00000374690.3:c.1522A>T	p.Met508Leu	p.M508L	ENST00000374690	NM_000044.3	508	Atg/Ttg	1/8	0.223904273158624	2	FACETS	1	0.969	1			1	CLONAL	3	TRUE	NA	0.223904273158624	2		484	405	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940041	76940041	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041277-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	164	359	0	ENST00000373344.5:c.707A>T	p.His236Leu	p.H236L	ENST00000373344	NM_000489.3	236	cAt/cTt	9/35	0.223904273158624	2	FACETS	0.92	0.855	0.986			1	CLONAL	4	TRUE	NA	0.223904273158624	2		359	398	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245273	46245273	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041277-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	135	639	1	ENST00000334344.6:c.3367G>T	p.Gly1123Trp	p.G1123W	ENST00000334344	NM_152641.2	1123	Ggg/Tgg	15/21	0.223904273158624	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.223904273158624	3		640	566	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362422	40362422	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041277-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	122	714	1	ENST00000293328.3:c.1774G>T	p.Gly592Trp	p.G592W	ENST00000293328	NM_012448.3	592	Ggg/Tgg	14/19	0.223904273158624	3	FACETS	0.982	0.89	1	0.982	0.89	1	CLONAL	2	TRUE	1	0.223904273158624	3		715	617	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274695	198274695	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041277-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	59	605	0	ENST00000335508.6:c.703A>G	p.Thr235Ala	p.T235A	ENST00000335508	NM_012433.2	235	Aca/Gca	7/25	0.223904273158624	3	FACETS	1	0.936	1	0.577	0.497	0.664	CLONAL	1	TRUE	1	0.223904273158624	3		605	508	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629788	187629788	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041277-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	179	859	0	ENST00000441802.2:c.1194G>T	p.Leu398Phe	p.L398F	ENST00000441802	NM_005245.3	398	ttG/ttT	2/27	0.223019135211968	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.223904273158624	3		859	760	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0041300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	100	375	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.240124533705895	5	FACETS	1	0.972	1			1	CLONAL	2	TRUE	NA	0.240124533705895	5		375	455	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211013	55211013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	161	364	0	ENST00000275493.2:c.256G>A	p.Ala86Thr	p.A86T	ENST00000275493	NM_005228.3	86	Gct/Act	3/28	0.240124533705895	5	FACETS	0.88	0.813	0.95			1	CLONAL	4	TRUE	NA	0.240124533705895	5		364	518	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420266	88420266	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	48	415	0	ENST00000360948.2:c.2420G>T	p.Trp807Leu	p.W807L	ENST00000360948	NM_001012338.2	807	tGg/tTg	19/19	1	2	FACETS	0.875	0.74	1	0.875	0.74	1	CLONAL	1	TRUE	1	0.240124533705895	2		415	457	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0041306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	191	357	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.571007652549851	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.571007652549851	1		357	459	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610247	10610247	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	625	717	0	ENST00000171111.5:c.463G>T	p.Val155Phe	p.V155F	ENST00000171111	NM_203500.1	155	Gtc/Ttc	2/6	0.558016249508359	2	FACETS	0.958	0.928	0.989	0.958	0.928	0.989	CLONAL	2	TRUE	0	0.571007652549851	2		717	1142	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1039289	1039289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11571421	NA	P-0041306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	95	423	0	ENST00000358495.3:c.208C>T	p.Arg70Trp	p.R70W	ENST00000358495	NM_134424.2	70	Cgg/Tgg	4/12	0.402250637616671	4	FACETS	0.821	0.732	0.915			1	CLONAL	1	TRUE	NA	0.571007652549851	4		423	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	610	678	0	ENST00000269305.4:c.472C>G	p.Arg158Gly	p.R158G	ENST00000269305	NM_001126112.2	158	Cgc/Ggc	5/11	0.564730356377603	2	FACETS	0.999	0.968	1	0.999	0.968	1	CLONAL	2	TRUE	0	0.571007652549851	2		678	1069	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696229	52696229	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	38	482	0	ENST00000394830.3:c.448G>C	p.Glu150Gln	p.E150Q	ENST00000394830	NM_018313.4	150	Gag/Cag	5/30	0.558016249508359	2	FACETS	0.274	0.226	0.328	0.137	0.113	0.164	SUBCLONAL	1	TRUE	0	0.571007652549851	2		482	485	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139818347	139818347	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs776376824	NA	P-0041306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	439	686	0	ENST00000247668.2:c.1182C>G	p.Ile394Met	p.I394M	ENST00000247668	NM_021138.3	394	atC/atG	10/11	0.571007652549851	3	FACETS	0.908	0.869	0.948	0.908	0.869	0.948	CLONAL	2	TRUE	1	0.571007652549851	3		686	1088	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141031	55141031	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	108	285	0	ENST00000257290.5:c.1677G>T	p.Trp559Cys	p.W559C	ENST00000257290	NM_006206.4	559	tgG/tgT	12/23	0.189881962900038	5	FACETS	0.929	0.841	1	0.619	0.561	0.68	INDETERMINATE	2	TRUE	2	0.571007652549851	5		285	378	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098370	108098370	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	38	228	0	ENST00000278616.4:c.19G>C	p.Asp7His	p.D7H	ENST00000278616	NM_000051.3	7	Gat/Cat	2/63	NA	2	FACETS	1	0.943	1			1	INDETERMINATE	1	TRUE	NA	0.571007652549851	2		228	106	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219221	133219221	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	249	598	0	ENST00000320574.5:c.4823T>A	p.Leu1608Gln	p.L1608Q	ENST00000320574	NM_006231.2	1608	cTg/cAg	37/49	0.571007652549851	3	FACETS	1	0.976	1	0.544	0.509	0.581	CLONAL	1	TRUE	1	0.571007652549851	3		598	1030	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249308	133249308	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	450	640	0	ENST00000320574.5:c.1591G>T	p.Gly531Ter	p.G531*	ENST00000320574	NM_006231.2	531	Gga/Tga	15/49	0.571007652549851	3	FACETS	0.852	0.814	0.89	0.852	0.814	0.89	CLONAL	2	TRUE	1	0.571007652549851	3		640	1189	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434970	110434970	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	181	737	0	ENST00000375856.3:c.3431G>T	p.Arg1144Leu	p.R1144L	ENST00000375856	NM_003749.2	1144	cGc/cTc	1/2	0.360899350195788	2	FACETS	0.475	0.437	0.515	0.238	0.218	0.258	SUBCLONAL	1	TRUE	0	0.571007652549851	2		737	1334	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472643	88472643	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	33	288	0	ENST00000360948.2:c.1912A>C	p.Ile638Leu	p.I638L	ENST00000360948	NM_001012338.2	638	Atc/Ctc	16/19	1	2	FACETS	0.271	0.22	0.328	0.271	0.22	0.328	SUBCLONAL	1	TRUE	1	0.571007652549851	2		288	427	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864539	56864539	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	153	336	0	ENST00000308159.5:c.1027C>A	p.His343Asn	p.H343N	ENST00000308159	NM_014669.4	343	Cac/Aac	10/22	0.483715942228288	4	FACETS	1	0.928	1	0.508	0.465	0.553	CLONAL	1	TRUE	2	0.571007652549851	4		336	829	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992174	72992174	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	461	570	0	ENST00000268489.5:c.1871G>T	p.Gly624Val	p.G624V	ENST00000268489	NM_006885.3	624	gGc/gTc	2/10	0.483715942228288	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.571007652549851	4		570	1255	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81939087	81939087	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	364	467	0	ENST00000359376.3:c.1442T>A	p.Leu481Gln	p.L481Q	ENST00000359376	NM_002661.3	481	cTg/cAg	15/33	0.483715942228288	4	FACETS	0.923	0.876	0.97	0.923	0.876	0.97	CLONAL	2	TRUE	2	0.571007652549851	4		467	1085	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207069	1207069	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1555734984	NA	P-0041306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	600	769	1	ENST00000326873.7:c.157G>T	p.Asp53Tyr	p.D53Y	ENST00000326873	NM_000455.4	53	Gac/Tac	1/10	NA	2	FACETS	0.942	0.91	0.973			1	INDETERMINATE	2	TRUE	NA	0.571007652549851	2		770	1116	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302882	15302882	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	644	801	0	ENST00000263388.2:c.568A>T	p.Thr190Ser	p.T190S	ENST00000263388	NM_000435.2	190	Aca/Tca	4/33	0.558016249508359	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.571007652549851	2		801	1115	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149940	202149940	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	377	544	0	ENST00000358485.4:c.1381G>C	p.Gly461Arg	p.G461R	ENST00000358485	NM_001080125.1	461	Ggg/Cgg	8/9	0.571007652549851	4	FACETS	0.935	0.889	0.982	0.935	0.889	0.982	CLONAL	2	TRUE	2	0.571007652549851	4		544	1109	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143238	24143238	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	510	590	0	ENST00000263121.7:c.470G>T	p.Gly157Val	p.G157V	ENST00000263121	NM_003073.3	157	gGc/gTc	4/9	0.558016249508359	2	FACETS	0.93	0.897	0.964	0.93	0.897	0.964	CLONAL	2	TRUE	0	0.571007652549851	2		590	960	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41554433	41554433	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	294	318	0	ENST00000263253.7:c.3519G>C	p.Gln1173His	p.Q1173H	ENST00000263253	NM_001429.3	1173	caG/caC	19/31	0.558016249508359	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.571007652549851	2		318	512	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443880	52443880	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs916069743	NA	P-0041306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	569	615	0	ENST00000460680.1:c.15G>T	p.Trp5Cys	p.W5C	ENST00000460680	NM_004656.3	5	tgG/tgT	1/17	0.558016249508359	2	FACETS	0.977	0.944	1	0.977	0.944	1	CLONAL	2	TRUE	0	0.571007652549851	2		615	1020	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526190	189526190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766297918	NA	P-0041306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1162	287	581	0	ENST00000264731.3:c.454C>T	p.Pro152Ser	p.P152S	ENST00000264731	NM_003722.4	152	Ccc/Tcc	4/14	0.571007652549851	4	FACETS	1	0.978	1	0.545	0.511	0.58	CLONAL	1	TRUE	2	0.571007652549851	4		581	1449	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575700	55575700	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	46	251	0	ENST00000288135.5:c.1226T>G	p.Val409Gly	p.V409G	ENST00000288135	NM_000222.2	409	gTg/gGg	7/21	0.189881962900038	5	FACETS	0.99	0.839	1	0.33	0.279	0.386	INDETERMINATE	1	TRUE	2	0.571007652549851	5		251	302	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595588	55595588	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	37	200	0	ENST00000288135.5:c.2078A>T	p.Lys693Met	p.K693M	ENST00000288135	NM_000222.2	693	aAg/aTg	14/21	0.189881962900038	5	FACETS	1	0.889	1	0.71	0.6	0.826	INDETERMINATE	2	TRUE	2	0.571007652549851	5		200	113	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930722	131930722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	37	313	0	ENST00000265335.6:c.1955C>T	p.Ser652Leu	p.S652L	ENST00000265335		652	tCa/tTa	12/25	0.564730356377603	2	FACETS	0.989	0.832	1	0.495	0.416	0.579	CLONAL	1	TRUE	0	0.571007652549851	2		313	131	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518702	176518702	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	206	477	0	ENST00000292408.4:c.620G>C	p.Trp207Ser	p.W207S	ENST00000292408	NM_213647.1	207	tGg/tCg	6/18	0.564730356377603	2	FACETS	0.919	0.855	0.985	0.46	0.427	0.493	CLONAL	1	TRUE	0	0.571007652549851	2		477	785	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30676011	30676011	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	131	481	0	ENST00000376406.3:c.2345C>G	p.Pro782Arg	p.P782R	ENST00000376406	NM_014641.2	782	cCt/cGt	8/15	0.534384628712575	4	FACETS	0.727	0.658	0.799	0.242	0.219	0.267	SUBCLONAL	1	TRUE	1	0.571007652549851	4		481	992	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729616	41729616	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	387	405	0	ENST00000242208.4:c.913C>G	p.His305Asp	p.H305D	ENST00000242208	NM_002192.2	305	Cat/Gat	3/3	0.571007652549851	3	FACETS	0.976	0.931	1	0.65	0.621	0.68	CLONAL	2	TRUE	0	0.571007652549851	3		405	893	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845496	128845496	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	549	638	0	ENST00000249373.3:c.793G>T	p.Val265Phe	p.V265F	ENST00000249373	NM_005631.4	265	Gtt/Ttt	4/12	0.571007652549851	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.571007652549851	2		638	928	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798752	135798752	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	65	209	0	ENST00000298552.3:c.491G>C	p.Trp164Ser	p.W164S	ENST00000298552	NM_001162426.1	164	tGg/tCg	6/23	0.571007652549851	3	FACETS	0.979	0.856	1	0.489	0.428	0.555	CLONAL	1	TRUE	1	0.571007652549851	3		209	299	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0041310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	45	413	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.17066061376633	2		414	387	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346819	91346819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140387675	NA	P-0041310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	56	402	0	ENST00000355112.3:c.3427G>A	p.Glu1143Lys	p.E1143K	ENST00000355112	NM_000057.2	1143	Gaa/Aaa	18/22	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.17066061376633	2		402	441	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044550	47044550	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	105	377	1	ENST00000377604.3:c.2047G>T	p.Glu683Ter	p.E683*	ENST00000377604	NM_001204468.1	683	Gag/Tag	18/24	1	1	FACETS	0.904	0.816	0.996	1	0.99	1	CLONAL	3	TRUE	0	0.17066061376633	1		378	415	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303766	65303766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	44	522	0	ENST00000342505.4:c.2989C>T	p.Arg997Trp	p.R997W	ENST00000342505	NM_002227.2	997	Cgg/Tgg	22/25	1	2	FACETS	0.824	0.69	0.973	0.824	0.69	0.973	CLONAL	1	TRUE	1	0.17066061376633	2		522	626	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892152	9892152	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	73	516	0	ENST00000330684.3:c.2338C>G	p.Leu780Val	p.L780V	ENST00000330684	NM_001134407.1	780	Ctt/Gtt	11/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.17066061376633	2		516	579	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747936	41747936	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	65	341	0	ENST00000226382.2:c.833G>T	p.Gly278Val	p.G278V	ENST00000226382	NM_003924.3	278	gGc/gTc	3/3	0.17066061376633	1	FACETS	0.831	0.723	0.948	1	0.976	1	CLONAL	2	TRUE	0	0.17066061376633	1		341	419	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142950056	142950056	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	48	290	0	ENST00000262992.4:c.2654G>T	p.Arg885Leu	p.R885L	ENST00000262992	NM_001101669.1	885	cGc/cTc	24/24	1	2	FACETS	0.97	0.825	1	1	0.973	1	CLONAL	2	TRUE	1	0.17066061376633	2		290	290	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737907	145737907	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	221	814	0	ENST00000428558.2:c.2923C>A	p.Pro975Thr	p.P975T	ENST00000428558	NM_004260.3	975	Cct/Act	18/22	0.17066061376633	3	FACETS	0.913	0.85	0.979	1	0.99	1	CLONAL	3	TRUE	1	0.17066061376633	3		814	1026	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606221	93606221	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	79	662	0	ENST00000375746.1:c.41C>T	p.Pro14Leu	p.P14L	ENST00000375746	NM_001174167.1	14	cCc/cTc	2/14	0.17066061376633	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.17066061376633	1		662	708	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578507	7578507	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519977	NA	P-0041381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	281	953	0	ENST00000269305.4:c.423C>G	p.Cys141Trp	p.C141W	ENST00000269305	NM_001126112.2	141	tgC/tgG	5/11	0.377536686812509	3	FACETS	1	0.992	1	0.791	0.754	0.827	INDETERMINATE	2	TRUE	0	0.647857666911961	3		953	484	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398220	25398220	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	105	334	0	ENST00000311936.3:c.99T>A	p.Asp33Glu	p.D33E	ENST00000311936	NM_004985.3	33	gaT/gaA	2/5	0.291779223308462	5	FACETS	0.843	0.762	0.928	0.562	0.508	0.619	INDETERMINATE	2	TRUE	2	0.647857666911961	5		334	379	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954927	2954927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	29	721	0	ENST00000396946.4:c.2783G>A	p.Gly928Glu	p.G928E	ENST00000396946	NM_032415.4	928	gGg/gAg	21/25	0.325736132381025	6	FACETS	0.397	0.318	0.487	0.099	0.079	0.122	INDETERMINATE	1	TRUE	2	0.647857666911961	6		721	518	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805114	43805114	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1399460857	NA	P-0041381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	188	655	0	ENST00000372470.3:c.564T>G	p.Ile188Met	p.I188M	ENST00000372470	NM_005373.2	188	atT/atG	4/12	0.492631752439284	3	FACETS	1	0.988	1	0.791	0.746	0.835	CLONAL	2	TRUE	0	0.647857666911961	3		655	324	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434112	49434112	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	203	725	0	ENST00000301067.7:c.7441G>T	p.Ala2481Ser	p.A2481S	ENST00000301067	NM_003482.3	2481	Gct/Tct	31/54	0.647857666911961	5	FACETS	0.903	0.847	0.96	1	0.991	1	CLONAL	3	TRUE	3	0.647857666911961	5		725	456	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440412	49440412	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	35	783	0	ENST00000301067.7:c.4398G>T	p.Lys1466Asn	p.K1466N	ENST00000301067	NM_003482.3	1466	aaG/aaT	15/54	0.647857666911961	5	FACETS	0.307	0.25	0.37	0.153	0.125	0.185	SUBCLONAL	1	TRUE	3	0.647857666911961	5		783	695	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911433	32911433	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0041381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	17	356	0	ENST00000380152.3:c.2941A>T	p.Lys981Ter	p.K981*	ENST00000380152		981	Aaa/Taa	11/27	0.647857666911961	4	FACETS	0.376	0.281	0.489	0.125	0.093	0.163	SUBCLONAL	1	TRUE	1	0.647857666911961	4		356	230	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25498368	25498368	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0041381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	33	430	0	ENST00000264709.3:c.492+1G>T		p.X164_splice	ENST00000264709	NM_175629.2	164			0.180147963477523	5	FACETS	0.652	0.533	0.786	0.217	0.177	0.262	INDETERMINATE	1	TRUE	2	0.647857666911961	5		430	308	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445093	89445093	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	34	409	0	ENST00000336596.2:c.1413G>C	p.Glu471Asp	p.E471D	ENST00000336596	NM_005233.5	471	gaG/gaC	6/17	0.325736132381025	6	FACETS	0.984	0.808	1	0.246	0.202	0.295	INDETERMINATE	1	TRUE	2	0.647857666911961	6		409	245	SUCCESS
APC	324	MSKCC	GRCh37	5	112175229	112175230	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TAGG	novel	NA	P-0041381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	52	215	0	ENST00000257430.4:c.3940_3943dup	p.Ser1315Ter	p.S1315*	ENST00000257430	NM_000038.5	1313	act/acTAGGt	16/16	0.492631752439284	3	FACETS	0.975	0.86	1	0.65	0.573	0.727	CLONAL	2	TRUE	0	0.647857666911961	3		215	109	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047173	180047173	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	25	580	1	ENST00000261937.6:c.2542G>T	p.Gly848Trp	p.G848W	ENST00000261937	NM_182925.4	848	Ggg/Tgg	17/30	0.647857666911961	2	FACETS	0.441	0.35	0.543	0.221	0.175	0.272	SUBCLONAL	1	TRUE	0	0.647857666911961	2		581	175	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860797	151860797	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	24	412	0	ENST00000262189.6:c.9865C>A	p.Pro3289Thr	p.P3289T	ENST00000262189	NM_170606.2	3289	Ccc/Acc	43/59	0.548308335876936	4	FACETS	0.408	0.32	0.51			1	SUBCLONAL	1	TRUE	NA	0.647857666911961	4		412	299	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	96	1090	0	ENST00000269305.4:c.853G>T	p.Glu285Ter	p.E285*	ENST00000269305	NM_001126112.2	285	Gag/Tag	8/11	1	2	FACETS	0.499	0.443	0.559	0.499	0.443	0.559	SUBCLONAL	1	TRUE	1	0.34	2		1090	1132	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149973	202149973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1272714323	NA	P-0041388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	79	577	1	ENST00000358485.4:c.1414C>T	p.Arg472Ter	p.R472*	ENST00000358485	NM_001080125.1	472	Cga/Tga	8/9	1	2	FACETS	0.493	0.433	0.559	0.493	0.433	0.559	SUBCLONAL	1	TRUE	1	0.34	2		578	942	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427324	427324	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	74	520	1	ENST00000399788.2:c.2845C>T	p.Leu949Phe	p.L949F	ENST00000399788	NM_001042603.1	949	Ctt/Ttt	19/28	1	2	FACETS	0.523	0.457	0.595	0.523	0.457	0.595	SUBCLONAL	1	TRUE	1	0.34	2		521	832	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181473	32181473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1372906994	NA	P-0041388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	80	578	0	ENST00000375023.3:c.2312G>A	p.Cys771Tyr	p.C771Y	ENST00000375023	NM_004557.3	771	tGt/tAt	14/30	1	2	FACETS	0.5	0.439	0.565	0.5	0.439	0.565	SUBCLONAL	1	TRUE	1	0.34	2		578	942	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403361	139403361	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	99	697	0	ENST00000277541.6:c.3132del	p.Arg1044SerfsTer135	p.R1044Sfs*135	ENST00000277541	NM_017617.3	1044	agG/ag	19/34	1	2	FACETS	0.62	0.553	0.692	0.62	0.553	0.692	SUBCLONAL	1	TRUE	1	0.34	2		697	939	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651703	48651703	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	60	556	0	ENST00000376670.3:c.869A>G	p.Gln290Arg	p.Q290R	ENST00000376670	NM_002049.3	290	cAg/cGg	5/6	1	2	FACETS	0.416	0.357	0.48	0.416	0.357	0.48	SUBCLONAL	1	TRUE	1	0.34	2		556	848	SUCCESS
AR	367	MSKCC	GRCh37	X	66766561	66766561	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	88	700	0	ENST00000374690.3:c.1573G>T	p.Gly525Cys	p.G525C	ENST00000374690	NM_000044.3	525	Ggc/Tgc	1/8	1	2	FACETS	0.481	0.424	0.541	0.481	0.424	0.541	SUBCLONAL	1	TRUE	1	0.34	2		700	1077	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458531	12458531	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	248	624	1	ENST00000287820.6:c.1148G>T	p.Ser383Ile	p.S383I	ENST00000287820	NM_015869.4	383	aGc/aTc	6/7	0.35449732060813	2	FACETS	0.99	0.931	1	0.99	0.931	1	CLONAL	2	TRUE	0	0.374059213602906	2		625	670	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169547	27169547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs991526480	NA	P-0041418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	110	654	0	ENST00000380036.4:c.548C>T	p.Pro183Leu	p.P183L	ENST00000380036	NM_000459.3	183	cCc/cTc	4/23	0.374059213602906	5	FACETS	0.822	0.737	0.913			1	CLONAL	1	TRUE	NA	0.374059213602906	5		654	1117	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913403	NA	P-0041470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	28	329	1	ENST00000349496.5:c.110C>A	p.Ser37Tyr	p.S37Y	ENST00000349496	NM_001904.3	37	tCt/tAt	3/15	0.124260236139792	3	FACETS	0.932	0.744	1	0.466	0.372	0.574	CLONAL	1	TRUE	1	0.129459902211841	3		330	494	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242483	55242506	+	inframe_deletion	In_Frame_Del	DEL	ATCTCCGAAAGCCAACAAGGAAAT	ATCTCCGAAAGCCAACAAGGAAAT	-	rs727504232	NA	P-0041470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	41	415	0	ENST00000275493.2:c.2253_2276del	p.Ser752_Ile759del	p.S752_I759del	ENST00000275493	NM_005228.3	751	acATCTCCGAAAGCCAACAAGGAAATc/acc	19/28	0.129459902211841	7	FACETS	0.932	0.776	1	0.466	0.388	0.552	CLONAL	2	TRUE	3	0.129459902211841	7		415	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	71	580	0	ENST00000269305.4:c.734del	p.Gly245AlafsTer2	p.G245Afs*2	ENST00000269305	NM_001126112.2	245	gGc/gc	7/11	NA	2	FACETS	0.931	0.813	1			1	INDETERMINATE	2	TRUE	NA	0.129459902211841	2		580	589	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971154	21971190	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCG	CGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCG	-	novel	NA	P-0041470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	50	413	0	ENST00000304494.5:c.168_204del	p.Ser56ArgfsTer78	p.S56Rfs*78	ENST00000304494	NM_000077.4	56	agCGCCCGAGTGGCGGAGCTGCTGCTGCTCCACGGCGCG/ag	2/3	0.129459902211841	3	FACETS	0.986	0.839	1	0.986	0.839	1	CLONAL	2	TRUE	1	0.129459902211841	3		413	417	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0041471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	167	274	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.695698747933564	3	FACETS	0.859	0.791	0.93	0.43	0.395	0.465	CLONAL	1	TRUE	1	0.704865748058589	3		274	746	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0041471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	295	608	1	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.704865748058589	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.704865748058589	1		609	538	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066676	5066676	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0041471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	201	407	0	ENST00000381652.3:c.1215-2A>G		p.X405_splice	ENST00000381652	NM_004972.3	405			1	2	FACETS	0.927	0.864	0.992	0.927	0.864	0.992	CLONAL	1	TRUE	1	0.704865748058589	2		407	615	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916747	48916747	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690915	NA	P-0041471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	203	348	0	ENST00000267163.4:c.277C>T	p.Gln93Ter	p.Q93*	ENST00000267163	NM_000321.2	93	Caa/Taa	3/27	0.704865748058589	1	FACETS	0.992	0.936	1	0.992	0.936	1	CLONAL	1	TRUE	0	0.704865748058589	1		348	376	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125245	47125245	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	200	433	0	ENST00000409792.3:c.6025G>C	p.Ala2009Pro	p.A2009P	ENST00000409792	NM_014159.6	2009	Gcc/Ccc	12/21	0.704865748058589	1	FACETS	0.988	0.931	1	0.988	0.931	1	CLONAL	1	TRUE	0	0.704865748058589	1		433	372	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282472	115282472	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	228	482	0	ENST00000438362.2:c.178A>T	p.Asn60Tyr	p.N60Y	ENST00000438362	NM_001242891.1	60	Aat/Tat	3/20	1	2	FACETS	0.865	0.809	0.922	0.865	0.809	0.922	CLONAL	1	TRUE	1	0.704865748058589	2		482	748	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874015	123874015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	44	62	0	ENST00000330479.4:c.46G>A	p.Ala16Thr	p.A16T	ENST00000330479	NM_020382.3	16	Gcg/Acg	2/9	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.704865748058589	2		62	98	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223234	5223234	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	243	671	0	ENST00000357368.4:c.2569G>A	p.Gly857Ser	p.G857S	ENST00000357368	NM_002850.3	857	Ggc/Agc	18/38	0.164170669111184	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.704865748058589	0		671	734	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033378	48033378	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587779283	NA	P-0041471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	233	460	0	ENST00000234420.5:c.3682G>C	p.Ala1228Pro	p.A1228P	ENST00000234420	NM_000179.2	1228	Gca/Cca	8/10	1	2	FACETS	0.962	0.902	1	0.962	0.902	1	CLONAL	1	TRUE	1	0.704865748058589	2		460	687	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332069	81332069	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	145	281	2	ENST00000222390.5:c.2015A>T	p.Asp672Val	p.D672V	ENST00000222390	NM_000601.4	672	gAt/gTt	18/18	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.704865748058589	2		283	390	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044477	5044477	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	263	511	0	ENST00000381652.3:c.425C>G	p.Ala142Gly	p.A142G	ENST00000381652	NM_004972.3	142	gCt/gGt	5/25	1	2	FACETS	0.987	0.929	1	0.987	0.929	1	CLONAL	1	TRUE	1	0.704865748058589	2		511	756	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0041583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	160	597	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.338014660278194	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.343380659814412	1		597	768	SUCCESS
AR	367	MSKCC	GRCh37	X	66765796	66765796	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	98	864	0	ENST00000374690.3:c.808G>T	p.Ala270Ser	p.A270S	ENST00000374690	NM_000044.3	270	Gcc/Tcc	1/8	0.223554368839766	0	FACETS	0.452	0.403	0.505			1	SUBCLONAL	1	TRUE	0	0.343380659814412	0		864	829	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161339	55161339	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	34	390	0	ENST00000257290.5:c.3170C>T	p.Ser1057Phe	p.S1057F	ENST00000257290	NM_006206.4	1057	tCc/tTc	23/23	0.230759722610238	1	FACETS	0.352	0.287	0.425	0.352	0.287	0.425	SUBCLONAL	1	TRUE	0	0.343380659814412	1		390	466	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223930	2223930	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	67	581	0	ENST00000326181.6:c.1144C>G	p.Pro382Ala	p.P382A	ENST00000326181	NM_032271.2	382	Cct/Gct	13/21	0.343380659814412	1	FACETS	0.518	0.45	0.592	0.518	0.45	0.592	SUBCLONAL	1	TRUE	0	0.343380659814412	1		581	624	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351692	89351692	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	158	708	1	ENST00000301030.4:c.1258G>C	p.Val420Leu	p.V420L	ENST00000301030	NM_001256183.1	420	Gtg/Ctg	9/13	NA	2	FACETS	1	0.916	1			1	INDETERMINATE	1	TRUE	NA	0.343380659814412	2		709	920	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226455	41226455	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555581955	NA	P-0041583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	197	581	0	ENST00000357654.3:c.4568C>T	p.Pro1523Leu	p.P1523L	ENST00000357654	NM_007294.3	1523	cCa/cTa	14/23	0.220985685242536	3	FACETS	0.799	0.741	0.859	0.799	0.741	0.859	SUBCLONAL	2	TRUE	1	0.343380659814412	3		581	841	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602727	10602727	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	168	787	0	ENST00000171111.5:c.851A>G	p.Gln284Arg	p.Q284R	ENST00000171111	NM_203500.1	284	cAg/cGg	3/6	0.343380659814412	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.343380659814412	1		787	765	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100069	11100069	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0041583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	147	731	0	ENST00000358026.2:c.1195A>T	p.Lys399Ter	p.K399*	ENST00000358026	NM_001128849.1	399	Aaa/Taa	7/36	0.343380659814412	1	FACETS	0.907	0.829	0.989	0.907	0.829	0.989	CLONAL	1	TRUE	0	0.343380659814412	1		731	782	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082874	16082874	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	10	107	0	ENST00000281043.3:c.688G>A	p.Gly230Arg	p.G230R	ENST00000281043	NM_005378.4	230	Ggg/Agg	2/3	0.230759722610238	1	FACETS	0.374	0.254	0.523	0.374	0.254	0.523	SUBCLONAL	1	TRUE	0	0.343380659814412	1		107	129	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937489	178937489	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	64	452	0	ENST00000263967.3:c.1877A>G	p.Asp626Gly	p.D626G	ENST00000263967	NM_006218.2	626	gAc/gGc	12/21	1	2	FACETS	0.89	0.773	1	0.89	0.773	1	CLONAL	1	TRUE	1	0.343380659814412	2		452	419	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573428	55573428	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0041583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	25	361	0	ENST00000288135.5:c.1090A>T	p.Lys364Ter	p.K364*	ENST00000288135	NM_000222.2	364	Aag/Tag	6/21	0.230759722610238	1	FACETS	0.32	0.252	0.398	0.32	0.252	0.398	SUBCLONAL	1	TRUE	0	0.343380659814412	1		361	377	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163665	32163665	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	41	506	0	ENST00000375023.3:c.5561G>A	p.Gly1854Glu	p.G1854E	ENST00000375023	NM_004557.3	1854	gGg/gAg	30/30	0.230759722610238	1	FACETS	0.411	0.342	0.488	0.411	0.342	0.488	SUBCLONAL	1	TRUE	0	0.343380659814412	1		506	481	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189077	32189077	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	62	519	0	ENST00000375023.3:c.477C>G	p.Phe159Leu	p.F159L	ENST00000375023	NM_004557.3	159	ttC/ttG	4/30	0.230759722610238	1	FACETS	0.469	0.405	0.539	0.469	0.405	0.539	SUBCLONAL	1	TRUE	0	0.343380659814412	1		519	638	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	107	737	0				ENST00000310581	NM_198253.2	-/1132			0.273612231232591	3	FACETS	0.975	0.88	1	0.975	0.88	1	CLONAL	2	TRUE	1	0.273612231232591	3		737	456	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0041590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	121	212	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.273612231232591	3	FACETS	0.934	0.848	1	0.934	0.848	1	CLONAL	2	TRUE	1	0.273612231232591	3		212	538	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225365140	225365140	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	33	340	0	ENST00000264414.4:c.1550C>A	p.Ser517Ter	p.S517*	ENST00000264414	NM_003590.4	517	tCa/tAa	11/16	1	2	FACETS	0.428	0.348	0.519	0.428	0.348	0.519	SUBCLONAL	1	TRUE	1	0.273612231232591	2		340	563	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517644	176517644	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1016993541	NA	P-0041590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	58	696	0	ENST00000292408.4:c.345G>C	p.Leu115Phe	p.L115F	ENST00000292408	NM_213647.1	115	ttG/ttC	3/18	1	2	FACETS	0.55	0.471	0.636	0.55	0.471	0.636	SUBCLONAL	1	TRUE	1	0.273612231232591	2		696	771	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948256	31948256	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs373414495	NA	P-0041590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	61	570	2	ENST00000375333.2:c.844G>T	p.Val282Phe	p.V282F	ENST00000375333	NM_032454.1	282	Gtc/Ttc	6/8	0.273612231232591	2	FACETS	0.665	0.573	0.765	0.332	0.286	0.383	SUBCLONAL	1	TRUE	0	0.273612231232591	2		572	671	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15840862	15840862	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	36	342	0	ENST00000307771.7:c.946G>A	p.Glu316Lys	p.E316K	ENST00000307771	NM_005089.3	316	Gaa/Aaa	11/11	0.273612231232591	3	FACETS	0.638	0.524	0.766	0.319	0.262	0.383	SUBCLONAL	1	TRUE	1	0.273612231232591	3		342	469	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0041594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	105	458	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.286855088993103	2		458	539	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860316	151860316	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	68	360	0	ENST00000262189.6:c.10346C>T	p.Ser3449Phe	p.S3449F	ENST00000262189	NM_170606.2	3449	tCc/tTc	43/59	0.286865995821112	3	FACETS	0.858	0.746	0.979	0.429	0.373	0.49	CLONAL	1	TRUE	1	0.286855088993103	3		360	632	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	120	737	0				ENST00000310581	NM_198253.2	-/1132			0.22597604431625	5	FACETS	0.984	0.891	1	0.656	0.594	0.722	CLONAL	2	TRUE	2	0.27082715031641	5		737	633	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0041611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	239	695	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.27082715031641	NA		695	1018	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050864	49050864	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886042935	NA	P-0041611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	47	358	0	ENST00000267163.4:c.2548C>T	p.Gln850Ter	p.Q850*	ENST00000267163	NM_000321.2	850	Cag/Tag	25/27	1	2	FACETS	0.666	0.562	0.781	0.666	0.562	0.781	SUBCLONAL	1	TRUE	1	0.27082715031641	2		358	521	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913355	NA	P-0041611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	47	380	0	ENST00000288602.6:c.1406G>T	p.Gly469Val	p.G469V	ENST00000288602	NM_004333.4	469	gGa/gTa	11/18	0.205046710576212	3	FACETS	0.862	0.728	1	0.431	0.364	0.505	CLONAL	1	TRUE	1	0.27082715031641	3		380	457	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922695	44922695	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	91	390	0	ENST00000377967.4:c.1556del	p.Arg519HisfsTer29	p.R519Hfs*29	ENST00000377967	NM_021140.2	519	cGa/ca	16/29	0.27082715031641	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.27082715031641	1		390	395	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881523	48881534	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	CATCTGTGGATG	CATCTGTGGATG	-	novel	NA	P-0041611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	26	195	0	ENST00000267163.4:c.245_256del	p.Ser82_Gly86delinsTer	p.S82_G86delins*	ENST00000267163	NM_000321.2	82	tCATCTGTGGATGga/tga	2/27	1	2	FACETS	0.787	0.626	0.97	0.787	0.626	0.97	CLONAL	1	TRUE	1	0.27082715031641	2		195	244	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093443	30093443	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	23	305	0	ENST00000331968.5:c.1820G>A	p.Arg607Lys	p.R607K	ENST00000331968	NM_002742.2	607	aGa/aAa	13/18	0.205046710576212	3	FACETS	0.658	0.514	0.825	0.329	0.257	0.413	SUBCLONAL	1	TRUE	1	0.27082715031641	3		305	293	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350458	89350458	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	147	842	0	ENST00000301030.4:c.2492T>G	p.Phe831Cys	p.F831C	ENST00000301030	NM_001256183.1	831	tTt/tGt	9/13	1	2	FACETS	0.983	0.896	1	0.983	0.896	1	CLONAL	1	TRUE	1	0.27082715031641	2		842	1104	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246179	41246179	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	65	498	0	ENST00000357654.3:c.1369G>A	p.Glu457Lys	p.E457K	ENST00000357654	NM_007294.3	457	Gaa/Aaa	10/23	0.205046710576212	3	FACETS	0.948	0.822	1	0.474	0.411	0.542	CLONAL	1	TRUE	1	0.27082715031641	3		498	575	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753155	128753155	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs148863193	NA	P-0041611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	97	337	0	ENST00000377970.2:c.1316G>T	p.Arg439Leu	p.R439L	ENST00000377970	NM_002467.4	439	cGa/cTa	3/3	0.205046710576212	3	FACETS	1	0.976	1	0.668	0.596	0.744	CLONAL	1	TRUE	1	0.27082715031641	3		337	609	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737096	145737096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	118	709	2	ENST00000428558.2:c.3470G>A	p.Ser1157Asn	p.S1157N	ENST00000428558	NM_004260.3	1157	aGc/aAc	21/22	0.205046710576212	3	FACETS	1	0.903	1	0.501	0.451	0.554	CLONAL	1	TRUE	1	0.27082715031641	3		711	987	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357111	70357111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	145	771	0	ENST00000374080.3:c.5626G>A	p.Gly1876Arg	p.G1876R	ENST00000374080		1876	Gga/Aga	39/45	0.27082715031641	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.27082715031641	1		771	924	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0041614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	503	833	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.64279742474468	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.64279742474468	1		833	973	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998799	100998799	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778208375	NA	P-0041614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	530	598	0	ENST00000325455.5:c.1003G>A	p.Ala335Thr	p.A335T	ENST00000325455	NM_001202474.3	335	Gct/Act	1/8	0.64279742474468	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.64279742474468	3		598	1024	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867302	68867302	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1337211551	NA	P-0041614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	326	516	0	ENST00000261769.5:c.2549C>G	p.Ser850Cys	p.S850C	ENST00000261769	NM_004360.3	850	tCc/tGc	16/16	0.64279742474468	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.64279742474468	1		516	573	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170737	99170737	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	177	320	0	ENST00000074304.5:c.1366C>G	p.Arg456Gly	p.R456G	ENST00000074304	NM_001134224.1	456	Cgg/Ggg	16/26	0.127003776270647	3	FACETS	0.81	0.755	0.867	0.81	0.755	0.867	INDETERMINATE	2	TRUE	1	0.64279742474468	3		320	449	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215661784	215661784	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0041614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	107	329	0	ENST00000260947.4:c.215+1G>A		p.X72_splice	ENST00000260947	NM_000465.2	72			0.127003776270647	3	FACETS	1	0.984	1	0.731	0.664	0.799	INDETERMINATE	1	TRUE	1	0.64279742474468	3		329	301	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225365200	225365200	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	73	235	0	ENST00000264414.4:c.1490C>G	p.Ser497Cys	p.S497C	ENST00000264414	NM_003590.4	497	tCt/tGt	11/16	0.127003776270647	3	FACETS	0.648	0.569	0.733	0.324	0.284	0.367	INDETERMINATE	1	TRUE	1	0.64279742474468	3		235	463	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729632	41729632	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	256	447	0	ENST00000242208.4:c.897G>T	p.Gln299His	p.Q299H	ENST00000242208	NM_002192.2	299	caG/caT	3/3	0.64279742474468	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.64279742474468	1		447	486	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434681	128434681	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559227539	NA	P-0041614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	288	572	0	ENST00000265960.3:c.173A>G	p.Asn58Ser	p.N58S	ENST00000265960	NM_001006617.1	58	aAt/aGt	2/12	0.102561110103983	5	FACETS	1	0.967	1			1	INDETERMINATE	3	TRUE	NA	0.64279742474468	5		572	574	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938438	76938438	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs782715802	NA	P-0041614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	140	468	0	ENST00000373344.5:c.2310G>C	p.Gln770His	p.Q770H	ENST00000373344	NM_000489.3	770	caG/caC	9/35	0.64279742474468	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.64279742474468	1		468	279	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611833	100611849	+	frameshift_variant	Frame_Shift_Del	DEL	TGATGGCCACGTCGTAC	TGATGGCCACGTCGTAC	-	novel	NA	P-0041614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	29	589	0	ENST00000308731.7:c.1272_1288del	p.Tyr425AspfsTer9	p.Y425Dfs*9	ENST00000308731	NM_000061.2	424	caGTACGACGTGGCCATCAag/caag	14/19	0.64279742474468	1	FACETS	0.106	0.084	0.13	0.106	0.084	0.13	SUBCLONAL	1	TRUE	0	0.64279742474468	1		589	580	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609958	117609958	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	406	415	0	ENST00000368508.3:c.6741T>A	p.Asp2247Glu	p.D2247E	ENST00000368508	NM_002944.2	2247	gaT/gaA	43/43	0.160412226146315	24	FACETS	1	0.98	1	1	0.98	1	CLONAL	23	FALSE	1	0.160412226146315	24		415	596	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220622	1220622	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690923	NA	P-0041637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	241	736	0	ENST00000326873.7:c.640C>T	p.Gln214Ter	p.Q214*	ENST00000326873	NM_000455.4	214	Cag/Tag	5/10	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	FALSE	NA	0.439046776998945	2		736	983	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453132	140453132	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913365	NA	P-0041637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	72	346	0	ENST00000288602.6:c.1803A>T	p.Lys601Asn	p.K601N	ENST00000288602	NM_004333.4	601	aaA/aaT	15/18	1	2	FACETS	0.641	0.561	0.726	0.641	0.561	0.726	SUBCLONAL	1	FALSE	1	0.439046776998945	2		346	512	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790072	40790072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753667	NA	P-0041637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	176	633	0	ENST00000373198.4:c.2659G>A	p.Ala887Thr	p.A887T	ENST00000373198	NM_133170.3	887	Gcc/Acc	18/32	NA	2	FACETS	0.985	0.909	1			1	INDETERMINATE	1	FALSE	NA	0.439046776998945	2		633	814	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261128	16261128	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772466830	NA	P-0041637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	74	483	0	ENST00000375759.3:c.8393C>T	p.Ala2798Val	p.A2798V	ENST00000375759	NM_015001.2	2798	gCa/gTa	11/15	1	2	FACETS	0.57	0.5	0.647	0.57	0.5	0.647	SUBCLONAL	1	FALSE	1	0.439046776998945	2		483	591	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50483693	50483693	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	63	419	0	ENST00000394963.4:c.798G>T	p.Glu266Asp	p.E266D	ENST00000394963	NM_003076.4	266	gaG/gaT	7/13	1	2	FACETS	0.428	0.369	0.491	0.428	0.369	0.491	SUBCLONAL	1	FALSE	1	0.439046776998945	2		419	671	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288762	33288762	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1260764171	NA	P-0041637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	37	413	0	ENST00000374542.5:c.790T>C	p.Tyr264His	p.Y264H	ENST00000374542	NM_001141970.1	264	Tac/Cac	3/8	1	2	FACETS	0.271	0.223	0.325	0.271	0.223	0.325	SUBCLONAL	1	FALSE	1	0.439046776998945	2		413	622	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938079	76938079	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	94	563	0	ENST00000373344.5:c.2669C>A	p.Ser890Ter	p.S890*	ENST00000373344	NM_000489.3	890	tCa/tAa	9/35	1	2	FACETS	0.487	0.432	0.545	0.487	0.432	0.545	SUBCLONAL	1	FALSE	1	0.439046776998945	2		563	880	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0041641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	340	926	2	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.358114468959558	2	FACETS	0.867	0.824	0.912	0.867	0.824	0.912	CLONAL	2	TRUE	0	0.437973334803278	2		928	895	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981555	70981555	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1570	248	1630	0	ENST00000276594.2:c.541G>T	p.Gly181Cys	p.G181C	ENST00000276594	NM_024504.3	181	Ggt/Tgt	2/8	0.41421760410794	3	FACETS	0.759	0.707	0.814	0.38	0.353	0.407	SUBCLONAL	1	TRUE	1	0.437973334803278	3		1630	1818	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107003	11107003	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	285	869	1	ENST00000358026.2:c.1708C>T	p.Gln570Ter	p.Q570*	ENST00000358026	NM_001128849.1	570	Cag/Tag	10/36	0.356763117105423	2	FACETS	1	0.994	1	0.739	0.696	0.782	CLONAL	1	TRUE	0	0.437973334803278	2		870	881	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435375	121435375	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1506	142	1059	0	ENST00000257555.6:c.1408C>A	p.Pro470Thr	p.P470T	ENST00000257555		470	Ccc/Acc	7/10	0.437973334803278	4	FACETS	0.566	0.513	0.621			1	SUBCLONAL	1	TRUE	NA	0.437973334803278	4		1059	1648	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420273	88420273	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	235	686	0	ENST00000360948.2:c.2413G>T	p.Gly805Trp	p.G805W	ENST00000360948	NM_001012338.2	805	Ggg/Tgg	19/19	0.393664306401497	3	FACETS	1	0.99	1	0.44	0.411	0.471	CLONAL	1	TRUE	0	0.437973334803278	3		686	990	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112497	2112497	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0041641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	349	917	0	ENST00000219476.3:c.1258-1G>T		p.X420_splice	ENST00000219476	NM_000548.3	420			0.357927875347179	2	FACETS	0.837	0.795	0.88	0.837	0.795	0.88	CLONAL	2	TRUE	0	0.437973334803278	2		917	952	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739077	40739078	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0041641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	245	933	1	ENST00000373198.4:c.3206_3207delinsTT	p.Trp1069Phe	p.W1069F	ENST00000373198	NM_133170.3	1069	tGG/tTT	24/32	0.351226999501752	4	FACETS	1	0.992	1	0.726	0.678	0.775	CLONAL	1	TRUE	2	0.437973334803278	4		934	1108	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531892	41531892	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0041641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	142	525	0	ENST00000263253.7:c.1604C>G	p.Ser535Ter	p.S535*	ENST00000263253	NM_001429.3	535	tCa/tGa	7/31	0.358114468959558	2	FACETS	0.847	0.78	0.914	0.847	0.78	0.914	CLONAL	2	TRUE	0	0.437973334803278	2		525	383	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148526880	148526880	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	77	306	0	ENST00000320356.2:c.424G>T	p.Asp142Tyr	p.D142Y	ENST00000320356	NM_004456.4	142	Gat/Tat	5/20	0.358114468959558	2	FACETS	1	0.975	1	0.692	0.616	0.772	CLONAL	1	TRUE	0	0.437973334803278	2		306	254	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942817	68942817	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	268	819	0	ENST00000288368.4:c.629A>T	p.Asn210Ile	p.N210I	ENST00000288368	NM_024870.2	210	aAc/aTc	6/40	0.41421760410794	3	FACETS	0.803	0.754	0.853	0.803	0.754	0.853	CLONAL	2	TRUE	1	0.437973334803278	3		819	929	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412147	63412147	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	370	583	0	ENST00000330258.3:c.1020G>T	p.Met340Ile	p.M340I	ENST00000330258	NM_152424.3	340	atG/atT	2/2	0.357532626440814	2	FACETS	1	0.99	1			1	CLONAL	2	TRUE	NA	0.437973334803278	2		583	753	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	274	1020	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.228162151821452	3	FACETS	1	0.988	1	0.796	0.749	0.845	CLONAL	2	FALSE	0	0.276227921443452	3		1022	945	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760663	133760663	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	235	1228	1	ENST00000318560.5:c.2986C>T	p.Gln996Ter	p.Q996*	ENST00000318560	NM_005157.4	996	Cag/Tag	11/11	0.276227921443452	2	FACETS	0.831	0.775	0.888	0.831	0.775	0.888	CLONAL	2	FALSE	0	0.276227921443452	2		1229	1024	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420213	88420213	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	80	558	1	ENST00000360948.2:c.2473C>A	p.His825Asn	p.H825N	ENST00000360948	NM_001012338.2	825	Cat/Aat	19/19	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	FALSE	1	0.276227921443452	2		559	543	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396527	139396527	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	251	882	1	ENST00000277541.6:c.5398G>T	p.Ala1800Ser	p.A1800S	ENST00000277541	NM_017617.3	1800	Gct/Tct	29/34	0.266518491577993	5	FACETS	0.913	0.856	0.973	0.913	0.856	0.973	CLONAL	3	FALSE	2	0.276227921443452	5		883	938	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946340	71946340	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	495	879	3	ENST00000298229.2:c.2504G>T	p.Gly835Val	p.G835V	ENST00000298229	NM_001567.3	835	gGg/gTg	23/28	0.276227921443452	6	FACETS	0.937	0.899	0.976	0.937	0.899	0.976	CLONAL	5	FALSE	1	0.276227921443452	6		882	1187	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867421	35867421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1354581284	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	166	318	0	ENST00000303115.3:c.235G>A	p.Glu79Lys	p.E79K	ENST00000303115	NM_002185.3	79	Gag/Aag	3/8	0.276227921443452	8	FACETS	1	0.974	1	0.743	0.688	0.799	CLONAL	4	FALSE	2	0.276227921443452	8		318	493	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254750	16254750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	250	590	1	ENST00000375759.3:c.2015G>T	p.Arg672Leu	p.R672L	ENST00000375759	NM_015001.2	672	cGa/cTa	11/15	0.276227921443452	5	FACETS	1	0.986	1	0.874	0.822	0.928	CLONAL	3	FALSE	1	0.276227921443452	5		591	732	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154886	2154886	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1268424766	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	244	865	2	ENST00000434045.2:c.335C>T	p.Ala112Val	p.A112V	ENST00000434045	NM_001127598.1	112	gCa/gTa	4/5	0.276227921443452	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	FALSE	0	0.276227921443452	2		867	880	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154896	2154896	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	222	834	0	ENST00000434045.2:c.326-1G>T		p.X109_splice	ENST00000434045	NM_001127598.1	109			0.276227921443452		FACETS		0.934	1				CLONAL	2	FALSE	0	0.276227921443452	2		834	803	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943774	71943774	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	117	817	0	ENST00000298229.2:c.1817G>T	p.Gly606Val	p.G606V	ENST00000298229	NM_001567.3	606	gGg/gTg	15/28	0.276227921443452	6	FACETS	0.992	0.891	1	0.198	0.178	0.22	CLONAL	1	FALSE	1	0.276227921443452	6		817	1326	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180415	94180415	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	214	529	0	ENST00000323929.3:c.1753G>T	p.Ala585Ser	p.A585S	ENST00000323929	NM_005591.3	585	Gca/Tca	15/20	0.276227921443452	6	FACETS	1	0.983	1	0.471	0.438	0.506	CLONAL	2	FALSE	1	0.276227921443452	6		529	1021	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909867	100909867	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	80	207	0	ENST00000325455.5:c.2782C>G	p.Leu928Val	p.L928V	ENST00000325455	NM_001202474.3	928	Ctt/Gtt	8/8	0.254243193031197	4	FACETS	0.899	0.801	1			1	CLONAL	3	FALSE	NA	0.276227921443452	4		207	274	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076701	102076701	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	91	527	0	ENST00000282441.5:c.880G>C	p.Val294Leu	p.V294L	ENST00000282441	NM_001130145.2	294	Gtc/Ctc	5/9	0.254243193031197	4	FACETS	1	0.97	1			1	CLONAL	1	FALSE	NA	0.276227921443452	4		527	657	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120791138	120791138	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs748263600	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	120	850	0	ENST00000257552.2:c.697A>G	p.Thr233Ala	p.T233A	ENST00000257552	NM_002442.3	233	Aca/Gca	10/15	0.21046460463911	4	FACETS	1	0.946	1	0.537	0.484	0.594	CLONAL	1	FALSE	2	0.276227921443452	4		850	1032	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007776	45007777	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	50	310	0	ENST00000558401.1:c.223_224delinsAA	p.Ser75Asn	p.S75N	ENST00000558401	NM_004048.2	75	TCt/AAt	2/4	1	2	FACETS	0.917	0.78	1	0.917	0.78	1	CLONAL	1	FALSE	1	0.276227921443452	2		310	395	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857160	9857160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	110	435	0	ENST00000330684.3:c.4241G>A	p.Arg1414Lys	p.R1414K	ENST00000330684	NM_001134407.1	1414	aGg/aAg	13/13	0.266518491577993	5	FACETS	1	0.908	1	0.672	0.605	0.741	CLONAL	2	FALSE	2	0.276227921443452	5		435	559	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858586	9858586	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	84	446	0	ENST00000330684.3:c.2815G>A	p.Gly939Arg	p.G939R	ENST00000330684	NM_001134407.1	939	Ggg/Agg	13/13	0.266518491577993	5	FACETS	0.789	0.698	0.886	0.526	0.465	0.591	SUBCLONAL	2	FALSE	2	0.276227921443452	5		446	545	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56792548	56792548	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs769436848	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	108	449	0	ENST00000308159.5:c.278T>G	p.Val93Gly	p.V93G	ENST00000308159	NM_014669.4	93	gTg/gGg	3/22	0.261912298325207	3	FACETS	0.795	0.715	0.878	0.795	0.715	0.878	SUBCLONAL	2	FALSE	1	0.276227921443452	3		449	560	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676329	37676329	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	199	512	0	ENST00000447079.4:c.3084G>T	p.Met1028Ile	p.M1028I	ENST00000447079	NM_015083.1	1028	atG/atT	11/14	0.276227921443452	3	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	FALSE	1	0.276227921443452	3		512	815	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226419	41226419	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	91	677	0	ENST00000357654.3:c.4604A>C	p.Glu1535Ala	p.E1535A	ENST00000357654	NM_007294.3	1535	gAg/gCg	14/23	0.276227921443452	3	FACETS	0.913	0.81	1	0.457	0.405	0.512	CLONAL	1	FALSE	1	0.276227921443452	3		677	821	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688809	47688809	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	70	320	0	ENST00000347630.2:c.491T>C	p.Val164Ala	p.V164A	ENST00000347630	NM_001007230.1	164	gTg/gCg	7/11	0.276227921443452	3	FACETS	1	0.951	1	0.592	0.517	0.673	CLONAL	1	FALSE	1	0.276227921443452	3		320	487	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256826	19256826	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs893528951	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	159	555	0	ENST00000162023.5:c.887G>T	p.Gly296Val	p.G296V	ENST00000162023		296	gGc/gTc	13/13	0.276227921443452	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	FALSE	0	0.276227921443452	2		555	511	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467408	25467409	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	67	602	0	ENST00000264709.3:c.1667_1667+1delinsTT		p.X556_splice	ENST00000264709	NM_175629.2	556		14/23	0.21046460463911	4	FACETS	1	0.899	1	0.52	0.452	0.594	CLONAL	1	FALSE	2	0.276227921443452	4		602	595	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635666	47635666	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	56	279	0	ENST00000233146.2:c.338A>T	p.Lys113Met	p.K113M	ENST00000233146	NM_000251.2	113	aAg/aTg	2/16	0.21046460463911	4	FACETS	1	0.906	1	0.537	0.46	0.62	CLONAL	1	FALSE	2	0.276227921443452	4		279	482	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016004	31016004	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	72	568	0	ENST00000375687.4:c.326A>G	p.Glu109Gly	p.E109G	ENST00000375687	NM_015338.5	109	gAg/gGg	5/13	0.276227921443452	3	FACETS	0.85	0.742	0.967	0.425	0.371	0.484	CLONAL	1	FALSE	1	0.276227921443452	3		568	698	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686408	30686408	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	60	274	0	ENST00000295754.5:c.263+1G>A		p.X88_splice	ENST00000295754	NM_003242.5	88			0.203813519634202	3	FACETS	0.892	0.776	1	0.595	0.517	0.678	CLONAL	2	FALSE	0	0.276227921443452	3		274	277	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448495	89448495	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	37	366	0	ENST00000336596.2:c.1459C>A	p.Leu487Met	p.L487M	ENST00000336596	NM_005233.5	487	Ctg/Atg	7/17	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.276227921443452	NA		366	403	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851795	134851795	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	87	791	0	ENST00000398015.3:c.1201C>A	p.Pro401Thr	p.P401T	ENST00000398015	NM_004441.4	401	Ccc/Acc	5/16	0.276227921443452	3	FACETS	0.947	0.838	1	0.474	0.419	0.532	CLONAL	1	FALSE	1	0.276227921443452	3		791	757	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322691	109322691	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	31	358	0	ENST00000436639.2:c.346A>T	p.Ile116Phe	p.I116F	ENST00000436639	NM_014454.2	116	Atc/Ttc	3/10	0.276227921443452	3	FACETS	0.531	0.429	0.647	0.266	0.214	0.324	SUBCLONAL	1	FALSE	1	0.276227921443452	3		358	481	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041202	112041202	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	154	443	0	ENST00000368678.4:c.53G>T	p.Arg18Met	p.R18M	ENST00000368678		18	aGg/aTg	3/13	0.276227921443452	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	FALSE	1	0.276227921443452	3		443	558	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129856	69129856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	73	237	0	ENST00000288368.4:c.4610C>T	p.Thr1537Ile	p.T1537I	ENST00000288368	NM_024870.2	1537	aCc/aTc	38/40	0.276227921443452	3	FACETS	0.973	0.859	1	0.973	0.859	1	CLONAL	2	FALSE	1	0.276227921443452	3		237	309	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492918	8492918	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	150	546	0	ENST00000356435.5:c.2411del	p.Thr804LysfsTer27	p.T804Kfs*27	ENST00000356435		804	aCa/aa	16/35	0.266518491577993	5	FACETS	1	0.934	1	0.683	0.625	0.743	CLONAL	2	FALSE	2	0.276227921443452	5		546	750	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211410	98211410	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	153	799	0	ENST00000331920.6:c.3745G>T	p.Gly1249Cys	p.G1249C	ENST00000331920	NM_000264.3	1249	Ggc/Tgc	22/24	0.276227921443452	2	FACETS	0.864	0.793	0.938	0.864	0.793	0.938	CLONAL	2	FALSE	0	0.276227921443452	2		799	641	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918534	44918534	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	70	193	0	ENST00000377967.4:c.1017G>T	p.Gln339His	p.Q339H	ENST00000377967	NM_021140.2	339	caG/caT	12/29	0.200115941461242	2	FACETS	1	0.934	1			1	CLONAL	2	FALSE	NA	0.276227921443452	2		193	234	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0041676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	125	306	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.537220578997338	2		306	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0041676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	104	795	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.402	0.359	0.448	0.402	0.359	0.448	SUBCLONAL	1	TRUE	1	0.537220578997338	2		795	963	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0041676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	111	387	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.924	0.836	1	0.924	0.836	1	CLONAL	1	TRUE	1	0.537220578997338	2		387	447	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0041676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	12	437	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.102	0.071	0.14	0.102	0.071	0.14	SUBCLONAL	1	TRUE	1	0.537220578997338	2		437	440	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630552	187630552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1211149994	NA	P-0041676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	203	830	0	ENST00000441802.2:c.430G>A	p.Asp144Asn	p.D144N	ENST00000441802	NM_005245.3	144	Gac/Aac	2/27	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.537220578997338	2		830	694	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0041866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	91	1020	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.705	0.626	0.791	0.705	0.626	0.791	SUBCLONAL	1	TRUE	1	0.317387631178794	2		1022	813	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466846	57466846	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	62	400	0	ENST00000371085.3:c.65C>A	p.Ala22Asp	p.A22D	ENST00000371085	NM_000516.4	22	gCc/gAc	1/13	1	2	FACETS	0.661	0.571	0.759	0.661	0.571	0.759	SUBCLONAL	1	TRUE	1	0.317387631178794	2		400	591	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673242	30673242	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	69	726	0	ENST00000376406.3:c.3718C>A	p.Pro1240Thr	p.P1240T	ENST00000376406	NM_014641.2	1240	Cct/Act	10/15	1	2	FACETS	0.772	0.673	0.879	0.772	0.673	0.879	SUBCLONAL	1	TRUE	1	0.317387631178794	2		726	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	466	675	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.753088011946342	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.753088011946342	1		675	673	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704529	117704529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	173	447	0	ENST00000368508.3:c.2447G>A	p.Gly816Glu	p.G816E	ENST00000368508	NM_002944.2	816	gGg/gAg	16/43	1	2	FACETS	0.904	0.839	0.971	0.904	0.839	0.971	CLONAL	1	TRUE	1	0.753088011946342	2		447	508	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971116	21971116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552823	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	264	353	0	ENST00000304494.5:c.242C>T	p.Pro81Leu	p.P81L	ENST00000304494	NM_000077.4	81	cCc/cTc	2/3	0.753088011946342	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.753088011946342	1		353	365	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341252	70341252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	216	775	0	ENST00000374080.3:c.811G>A	p.Glu271Lys	p.E271K	ENST00000374080		271	Gaa/Aaa	6/45	1	2	FACETS	0.819	0.765	0.875	0.819	0.765	0.875	CLONAL	1	TRUE	1	0.753088011946342	2		775	700	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413049	139413049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064795070	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	309	652	0	ENST00000277541.6:c.1093C>T	p.Arg365Cys	p.R365C	ENST00000277541	NM_017617.3	365	Cgc/Tgc	6/34	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.753088011946342	2		652	798	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361151	66361151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	164	414	0	ENST00000273854.3:c.1021G>A	p.Asp341Asn	p.D341N	ENST00000273854	NM_004439.5	341	Gat/Aat	4/18	0.753088011946342	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.753088011946342	1		414	268	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429307	47429307	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	389	956	1	ENST00000377045.4:c.1435C>T	p.Arg479Cys	p.R479C	ENST00000377045	NM_001654.4	479	Cgt/Tgt	14/16	1	2	FACETS	0.968	0.922	1	0.968	0.922	1	CLONAL	1	TRUE	1	0.753088011946342	2		957	1067	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041043	112041043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	364	670	0	ENST00000368678.4:c.212C>T	p.Ser71Phe	p.S71F	ENST00000368678		71	tCt/tTt	3/13	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.753088011946342	2		670	921	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	454	796	1	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	1	2	FACETS	0.999	0.955	1	0.999	0.955	1	CLONAL	1	TRUE	1	0.753088011946342	2		797	1207	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592623	28592623	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	321	524	0	ENST00000241453.7:c.2522A>G	p.Asn841Ser	p.N841S	ENST00000241453	NM_004119.2	841	aAc/aGc	20/24	0.609309925808674	3	FACETS	0.925	0.882	0.969	0.925	0.882	0.969	CLONAL	2	TRUE	1	0.753088011946342	3		524	634	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352234	70352234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	309	734	0	ENST00000374080.3:c.4261G>A	p.Glu1421Lys	p.E1421K	ENST00000374080		1421	Gag/Aag	31/45	1	2	FACETS	0.989	0.936	1	0.989	0.936	1	CLONAL	1	TRUE	1	0.753088011946342	2		734	830	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426355	49426355	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	437	1241	0	ENST00000301067.7:c.12133C>T	p.Gln4045Ter	p.Q4045*	ENST00000301067	NM_003482.3	4045	Cag/Tag	39/54	1	2	FACETS	0.934	0.892	0.978	0.934	0.892	0.978	CLONAL	1	TRUE	1	0.753088011946342	2		1241	1242	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538323	9538323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243986113	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	232	534	0	ENST00000353224.5:c.1675C>T	p.Leu559Phe	p.L559F	ENST00000353224	NM_177990.2	559	Ctt/Ttt	7/10	1	2	FACETS	0.969	0.909	1	0.969	0.909	1	CLONAL	1	TRUE	1	0.753088011946342	2		534	636	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446009	49446009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	609	1285	0	ENST00000301067.7:c.1457C>T	p.Ser486Phe	p.S486F	ENST00000301067	NM_003482.3	486	tCc/tTc	10/54	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.753088011946342	2		1285	1440	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545696	106545696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	232	599	0	ENST00000359195.3:c.3173G>A	p.Gly1058Glu	p.G1058E	ENST00000359195	NM_002649.2	1058	gGg/gAg	11/11	1	2	FACETS	0.97	0.911	1	0.97	0.911	1	CLONAL	1	TRUE	1	0.753088011946342	2		599	635	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588186	67588186	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	145	292	0	ENST00000274335.5:c.1016C>A	p.Ser339Ter	p.S339*	ENST00000274335		339	tCg/tAg	7/15	1	2	FACETS	0.871	0.802	0.942	0.871	0.802	0.942	CLONAL	1	TRUE	1	0.753088011946342	2		292	442	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695925	117695925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	392	787	0	ENST00000369458.3:c.512C>T	p.Pro171Leu	p.P171L	ENST00000369458	NM_024626.3	171	cCc/cTc	4/6	0.753088011946342	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.753088011946342	1		787	576	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163325161	163325161	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	318	336	0	ENST00000271452.3:c.1297T>A	p.Tyr433Asn	p.Y433N	ENST00000271452	NM_145697.2	433	Tac/Aac	14/14	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.753088011946342	2		336	725	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176145090	176145090	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	380	390	0	ENST00000367669.3:c.521A>C	p.Asn174Thr	p.N174T	ENST00000367669	NM_022457.5	174	aAc/aCc	3/20	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.753088011946342	2		390	866	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097812	8097812	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1240522310	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	424	838	0	ENST00000346208.3:c.194G>A	p.Gly65Glu	p.G65E	ENST00000346208		65	gGa/gAa	2/6	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.753088011946342	2		838	1060	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150237	108150237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147557621	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	166	382	0	ENST00000278616.4:c.3304G>A	p.Gly1102Arg	p.G1102R	ENST00000278616	NM_000051.3	1102	Gga/Aga	23/63	1	2	FACETS	0.804	0.744	0.867	0.804	0.744	0.867	CLONAL	1	TRUE	1	0.753088011946342	2		382	548	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344819	118344820	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	126	446	0	ENST00000534358.1:c.2945_2946delinsTT	p.Ser982Phe	p.S982F	ENST00000534358	NM_005933.3	982	tCC/tTT	3/36	1	2	FACETS	0.799	0.729	0.87	0.799	0.729	0.87	SUBCLONAL	1	TRUE	1	0.753088011946342	2		446	419	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992100	11992100	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	163	462	0	ENST00000396373.4:c.190G>A	p.Asp64Asn	p.D64N	ENST00000396373	NM_001987.4	64	Gat/Aat	3/8	NA	2	FACETS	0.856	0.791	0.922			1	INDETERMINATE	1	TRUE	NA	0.753088011946342	2		462	506	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864799	57864799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	360	941	0	ENST00000228682.2:c.2276C>T	p.Thr759Ile	p.T759I	ENST00000228682	NM_005269.2	759	aCc/aTc	12/12	1	2	FACETS	0.996	0.947	1	0.996	0.947	1	CLONAL	1	TRUE	1	0.753088011946342	2		941	960	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039449	49039449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264333384	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	255	494	0	ENST00000267163.4:c.2434C>T	p.Pro812Ser	p.P812S	ENST00000267163	NM_000321.2	812	Cca/Tca	23/27	0.609309925808674	3	FACETS	0.991	0.929	1	0.495	0.464	0.527	CLONAL	1	TRUE	1	0.753088011946342	3		494	941	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986529	36986529	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	399	800	0	ENST00000354822.5:c.1160A>G	p.Tyr387Cys	p.Y387C	ENST00000354822	NM_001079668.2	387	tAc/tGc	3/3	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.753088011946342	2		800	1052	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	397004	397004	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	404	992	0	ENST00000262320.3:c.22T>A	p.Phe8Ile	p.F8I	ENST00000262320	NM_003502.3	8	Ttc/Atc	2/11	1	2	FACETS	0.962	0.917	1	0.962	0.917	1	CLONAL	1	TRUE	1	0.753088011946342	2		992	1115	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641503	23641504	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	251	728	0	ENST00000261584.4:c.1971_1972delinsAA	p.Glu658Lys	p.E658K	ENST00000261584	NM_024675.3	657	gaGGaa/gaAAaa	5/13	1	2	FACETS	0.876	0.823	0.93	0.876	0.823	0.93	CLONAL	1	TRUE	1	0.753088011946342	2		728	761	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128261	30128261	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1329197803	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	413	1000	0	ENST00000263025.4:c.971C>T	p.Ala324Val	p.A324V	ENST00000263025	NM_002746.2	324	gCg/gTg	7/9	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.753088011946342	2		1000	1080	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805887	46805888	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	207	654	0	ENST00000290295.7:c.68_69delinsAA	p.Gly23Glu	p.G23E	ENST00000290295	NM_006361.5	23	gGG/gAA	1/2	1	2	FACETS	0.956	0.894	1	0.956	0.894	1	CLONAL	1	TRUE	1	0.753088011946342	2		654	575	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56432318	56432318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35445516	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	322	652	0	ENST00000407977.2:c.2338G>A	p.Glu780Lys	p.E780K	ENST00000407977		780	Gaa/Aaa	10/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.753088011946342	2		652	843	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436124	56436124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	377	925	0	ENST00000407977.2:c.1013G>A	p.Arg338Lys	p.R338K	ENST00000407977		338	aGa/aAa	9/10	1	2	FACETS	0.965	0.918	1	0.965	0.918	1	CLONAL	1	TRUE	1	0.753088011946342	2		925	1038	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78519578	78519578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	256	515	0	ENST00000306801.3:c.149G>A	p.Arg50Lys	p.R50K	ENST00000306801	NM_020761.2	50	aGg/aAg	1/34	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.753088011946342	2		515	610	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78914364	78914365	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	426	899	1	ENST00000306801.3:c.2988_2989delinsTT	p.Arg997Cys	p.R997C	ENST00000306801	NM_020761.2	996	agCCgt/agTTgt	25/34	1	2	FACETS	0.999	0.954	1	0.999	0.954	1	CLONAL	1	TRUE	1	0.753088011946342	2		900	1132	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602871	10602872	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	1078	1127	3	ENST00000171111.5:c.706_707delinsTT	p.Asp236Phe	p.D236F	ENST00000171111	NM_203500.1	236	GAc/TTc	3/6	0.753088011946342	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.753088011946342	2		1130	1367	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051379	13051380	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	414	596	0	ENST00000316448.5:c.727_728delinsTT	p.Pro243Phe	p.P243F	ENST00000316448	NM_004343.3	243	CCt/TTt	6/9	0.753088011946342	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.753088011946342	2		596	536	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149566	61149566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	163	376	0	ENST00000295025.8:c.1756C>T	p.Pro586Ser	p.P586S	ENST00000295025	NM_002908.2	586	Cca/Tca	11/11	1	2	FACETS	0.88	0.814	0.947	0.88	0.814	0.947	CLONAL	1	TRUE	1	0.753088011946342	2		376	492	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190670377	190670377	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	152	327	0	ENST00000441310.2:c.316-1G>A		p.X106_splice	ENST00000441310	NM_000534.4	106			1	2	FACETS	0.878	0.809	0.947	0.878	0.809	0.947	CLONAL	1	TRUE	1	0.753088011946342	2		327	460	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285250	212285250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	213	446	1	ENST00000342788.4:c.3051G>A	p.Met1017Ile	p.M1017I	ENST00000342788	NM_005235.2	1017	atG/atA	25/28	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.753088011946342	2		447	523	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546724	9546724	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757157617	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	234	443	0	ENST00000353224.5:c.1298G>A	p.Arg433Gln	p.R433Q	ENST00000353224	NM_177990.2	433	cGg/cAg	5/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.753088011946342	2		443	531	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395581	31395581	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	415	804	1	ENST00000328111.2:c.2434C>T	p.Pro812Ser	p.P812S	ENST00000328111	NM_006892.3	812	Cct/Tct	23/23	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.753088011946342	2		805	1019	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292811	62292811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758172246	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	263	508	0	ENST00000360203.5:c.263C>T	p.Ser88Phe	p.S88F	ENST00000360203	NM_001283009.1	88	tCc/tTc	3/35	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.753088011946342	2		508	607	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405908	49405908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	336	817	0	ENST00000418115.1:c.230C>T	p.Thr77Ile	p.T77I	ENST00000418115	NM_001664.2	77	aCc/aTc	3/5	0.753088011946342	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.753088011946342	1		817	542	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165578	185165578	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	296	339	0	ENST00000265026.3:c.853G>A	p.Val285Ile	p.V285I	ENST00000265026	NM_004721.4	285	Gtt/Att	5/14	0.753088011946342	3	FACETS	0.899	0.854	0.943	0.899	0.854	0.943	CLONAL	2	TRUE	1	0.753088011946342	3		339	602	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167735	185167735	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	559	618	0	ENST00000265026.3:c.1058A>G	p.Tyr353Cys	p.Y353C	ENST00000265026	NM_004721.4	353	tAc/tGc	6/14	0.753088011946342	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.753088011946342	3		618	1006	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31422934	31422934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	299	564	1	ENST00000344624.3:c.3379G>A	p.Ala1127Thr	p.A1127T	ENST00000344624		1127	Gca/Aca	26/33	0.753088011946342	3	FACETS	1	0.972	1	0.525	0.494	0.556	CLONAL	1	TRUE	1	0.753088011946342	3		565	1042	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876362	35876362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	269	756	0	ENST00000303115.3:c.1154C>T	p.Ser385Phe	p.S385F	ENST00000303115	NM_002185.3	385	tCc/tTc	8/8	0.753088011946342	3	FACETS	0.929	0.871	0.987	0.464	0.435	0.494	CLONAL	1	TRUE	1	0.753088011946342	3		756	1059	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751182	57751182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	163	403	0	ENST00000274289.3:c.1685C>T	p.Pro562Leu	p.P562L	ENST00000274289	NM_006622.3	562	cCt/cTt	12/14	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.753088011946342	2		403	431	SUCCESS
APC	324	MSKCC	GRCh37	5	112175080	112175080	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	77	231	0	ENST00000257430.4:c.3789T>A	p.Cys1263Ter	p.C1263*	ENST00000257430	NM_000038.5	1263	tgT/tgA	16/16	0.671893338754988	1	FACETS	0.892	0.81	0.973	0.892	0.81	0.973	CLONAL	1	TRUE	0	0.753088011946342	1		231	143	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93953220	93953220	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	206	387	0	ENST00000369303.4:c.2921A>C	p.Gln974Pro	p.Q974P	ENST00000369303	NM_004440.3	974	cAa/cCa	17/17	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.753088011946342	2		387	524	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622256	117622256	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	210	502	0	ENST00000368508.3:c.6614G>A	p.Arg2205Lys	p.R2205K	ENST00000368508	NM_002944.2	2205	aGa/aAa	42/43	1	2	FACETS	0.992	0.929	1	0.992	0.929	1	CLONAL	1	TRUE	1	0.753088011946342	2		502	562	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240685	55240686	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	52	1074	1	ENST00000275493.2:c.1929_1930delinsTT	p.Pro644Ser	p.P644S	ENST00000275493	NM_005228.3	643	atCCcg/atTTcg	17/28	0.737452514323931	1	FACETS	0.106	0.089	0.124	0.106	0.089	0.124	SUBCLONAL	1	TRUE	0	0.753088011946342	1		1075	814	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850866	128850867	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	386	971	1	ENST00000249373.3:c.1713_1714delinsAA	p.Ala572Thr	p.A572T	ENST00000249373	NM_005631.4	571	aaGGcc/aaAAcc	10/12	1	2	FACETS	0.979	0.932	1	0.979	0.932	1	CLONAL	1	TRUE	1	0.753088011946342	2		972	1047	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151927387	151927387	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	25	34	0	ENST00000262189.6:c.2789C>T	p.Ser930Leu	p.S930L	ENST00000262189	NM_170606.2	930	tCa/tTa	17/59	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.753088011946342	2		34	63	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393423	139393424	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	369	942	1	ENST00000277541.6:c.6107_6108delinsTT	p.Ala2036Val	p.A2036V	ENST00000277541	NM_017617.3	2036	gCC/gTT	33/34	1	2	FACETS	0.856	0.813	0.9	0.856	0.813	0.9	CLONAL	1	TRUE	1	0.753088011946342	2		943	1145	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044853	47044853	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	36	526	0	ENST00000377604.3:c.2179G>C	p.Gly727Arg	p.G727R	ENST00000377604	NM_001204468.1	727	Gga/Cga	20/24	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		526	636	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121511	193121511	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	28	269	0	ENST00000367435.3:c.909A>T	p.Glu303Asp	p.E303D	ENST00000367435	NM_024529.4	303	gaA/gaT	10/17	0.368705178382691	2	FACETS	0.496	0.397	0.609	0.248	0.198	0.305	SUBCLONAL	1	TRUE	0	0.368705178382691	2		269	306	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118361952	118361952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	36	274	0	ENST00000534358.1:c.4738G>A	p.Asp1580Asn	p.D1580N	ENST00000534358	NM_005933.3	1580	Gac/Aac	14/36	0.366881668185396	2	FACETS	0.477	0.393	0.572	0.239	0.196	0.286	SUBCLONAL	1	TRUE	0	0.368705178382691	2		274	409	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226345	2226346	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0041910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	251	937	3	ENST00000326181.6:c.1958_1959delinsTT	p.Arg653Leu	p.R653L	ENST00000326181	NM_032271.2	653	cGG/cTT	20/21	0.367021190752787	2	FACETS	1	0.985	1	0.584	0.546	0.623	CLONAL	1	TRUE	0	0.368705178382691	2		940	1166	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830820	72830820	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	226	786	0	ENST00000268489.5:c.5761T>G	p.Leu1921Val	p.L1921V	ENST00000268489	NM_006885.3	1921	Ttg/Gtg	9/10	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.368705178382691	2		786	987	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577143	7577144	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0041910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	266	710	0	ENST00000269305.4:c.794_795delinsCT	p.Leu265Pro	p.L265P	ENST00000269305	NM_001126112.2	265	cTG/cCT	8/11	0.306560253674334	2	FACETS	0.833	0.783	0.884	0.833	0.783	0.884	CLONAL	2	TRUE	0	0.368705178382691	2		710	866	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552216	29552216	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0041910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	233	490	0	ENST00000356175.3:c.1949T>G	p.Leu650Ter	p.L650*	ENST00000356175	NM_000267.3	650	tTa/tGa	17/57	0.318508647621516	3	FACETS	1	0.988	1	0.814	0.764	0.864	CLONAL	2	TRUE	0	0.368705178382691	3		490	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0041951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	735	597	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.788405811697603	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.788405811697603	2		597	874	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0041951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	95	317	0	ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	4/10	1	2	FACETS	0.913	0.825	1	0.913	0.825	1	CLONAL	1	TRUE	1	0.788405811697603	2		317	264	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939673	76939674	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	161	412	0	ENST00000373344.5:c.1074dup	p.Leu359ThrfsTer3	p.L359Tfs*3	ENST00000373344	NM_000489.3	358	-/A	9/35	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.788405811697603	1		412	220	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710595	114710597	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs754968616	NA	P-0041951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	261	526	0	ENST00000543371.1:c.85_87del	p.Glu29del	p.E29del	ENST00000543371	NM_001198531.1	27	cAGGag/cag	1/14	1	2	FACETS	0.922	0.868	0.977	0.922	0.868	0.977	CLONAL	1	TRUE	1	0.788405811697603	2		526	718	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094455	27094456	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0041951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	257	589	0	ENST00000324856.7:c.3164_3165del	p.Tyr1055CysfsTer49	p.Y1055Cfs*49	ENST00000324856	NM_006015.4	1055	TAt/t	11/20	1	2	FACETS	0.966	0.91	1	0.966	0.91	1	CLONAL	1	TRUE	1	0.788405811697603	2		589	675	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579369	7579369	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555526581	NA	P-0041954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	161	862	0	ENST00000269305.4:c.318C>G	p.Ser106Arg	p.S106R	ENST00000269305	NM_001126112.2	106	agC/agG	4/11	0.228335407234538	4	FACETS	0.95	0.879	1	1	0.985	1	CLONAL	4	TRUE	1	0.228335407234538	4		862	456	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501448	149501448	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	76	768	0	ENST00000261799.4:c.2339C>A	p.Pro780His	p.P780H	ENST00000261799	NM_002609.3	780	cCc/cAc	16/23	0.160771206167197	3	FACETS	0.752	0.661	0.849	0.752	0.661	0.849	SUBCLONAL	2	TRUE	1	0.228335407234538	3		768	493	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721232	176721232	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	57	439	0	ENST00000439151.2:c.6863C>G	p.Ser2288Cys	p.S2288C	ENST00000439151	NM_022455.4	2288	tCc/tGc	23/23	0.160771206167197	3	FACETS	0.924	0.799	1	0.924	0.799	1	CLONAL	2	TRUE	1	0.228335407234538	3		439	301	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64288908	64288908	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	65	588	0	ENST00000370651.3:c.304G>T	p.Val102Phe	p.V102F	ENST00000370651	NM_003463.4	102	Gtt/Ttt	4/6	0.228335407234538	6	FACETS	1	0.914	1	0.359	0.31	0.411	CLONAL	1	TRUE	3	0.228335407234538	6		588	771	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041963-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	52	737	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.832	0.715	0.957	0.832	0.715	0.957	CLONAL	1	FALSE	1	0.510403809547677	2		737	245	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0041963-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	442	736	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.510403809547677	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	FALSE	0	0.510403809547677	1		736	1031	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039501	49039501	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0041963-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	141	301	0	ENST00000267163.4:c.2486C>G	p.Ser829Ter	p.S829*	ENST00000267163	NM_000321.2	829	tCa/tGa	23/27	0.510403809547677	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	0	0.510403809547677	1		301	375	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546098	29546098	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1567843917	NA	P-0041963-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	275	401	0	ENST00000356175.3:c.1603C>T	p.Gln535Ter	p.Q535*	ENST00000356175	NM_000267.3	535	Cag/Tag	14/57	0.510403809547677	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	FALSE	0	0.510403809547677	1		401	582	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653782	89653782	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs886041877	NA	P-0041963-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	66	179	0	ENST00000371953.3:c.80A>C	p.Tyr27Ser	p.Y27S	ENST00000371953	NM_000314.4	27	tAt/tCt	2/9	0.510403809547677	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	0	0.510403809547677	1		179	176	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950439	68950445	+	frameshift_variant	Frame_Shift_Del	DEL	GTCTTAC	GTCTTAC	-	novel	NA	P-0041963-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	55	359	0	ENST00000288368.4:c.751_757del	p.Val251Ter	p.V251*	ENST00000288368	NM_024870.2	251	GTCTTACtg/tg	7/40	1	2	FACETS	0.484	0.415	0.56	0.484	0.415	0.56	SUBCLONAL	1	FALSE	1	0.510403809547677	2		359	445	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0041964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	103	212	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.857028550109741	4	FACETS	0.851	0.764	0.942	0.284	0.254	0.314	CLONAL	1	TRUE	1	0.893839921542524	4		212	513	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4123815	4123815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	315	394	0	ENST00000262948.5:c.58G>A	p.Glu20Lys	p.E20K	ENST00000262948	NM_030662.3	20	Gag/Aag	1/11	0.893839921542524	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.893839921542524	1		394	383	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315461	30315462	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0041964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	570	494	0	ENST00000322652.5:c.1150_1151del	p.Leu385ProfsTer10	p.L385Pfs*10	ENST00000322652	NM_015355.2	382	tcAGag/tcag	10/16	0.893839921542524	2	FACETS	0.984	0.966	1	0.984	0.966	1	CLONAL	2	TRUE	0	0.893839921542524	2		494	648	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934829	9934829	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	230	489	0	ENST00000330684.3:c.1461G>C	p.Lys487Asn	p.K487N	ENST00000330684	NM_001134407.1	487	aaG/aaC	6/13	1	2	FACETS	0.914	0.859	0.969	0.914	0.859	0.969	CLONAL	1	TRUE	1	0.893839921542524	2		489	563	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998891	11998891	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0041967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	32	183	0	ENST00000353533.5:c.394-1G>T		p.X132_splice	ENST00000353533	NM_003010.3	132			0.404222663421318	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.404222663421318	1		183	97	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274919	41274919	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	62	295	0	ENST00000349496.5:c.1169A>G	p.Asp390Gly	p.D390G	ENST00000349496	NM_001904.3	390	gAt/gGt	8/15	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.404222663421318	2		295	293	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0041982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	81	205	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.154988463454574	3	FACETS	1	0.966	1	0.638	0.562	0.719	CLONAL	1	TRUE	1	0.219066018542198	3		205	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0041982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	66	648	2	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.219066018542198	1	FACETS	0.788	0.683	0.901	0.788	0.683	0.901	CLONAL	1	TRUE	0	0.219066018542198	1		650	681	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863388	57863388	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	56	745	0	ENST00000228682.2:c.1483C>G	p.Leu495Val	p.L495V	ENST00000228682	NM_005269.2	495	Ctt/Gtt	11/12	1	2	FACETS	0.596	0.509	0.691	0.596	0.509	0.691	SUBCLONAL	1	TRUE	1	0.219066018542198	2		745	858	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562758	29562758	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	50	352	0	ENST00000356175.3:c.3839del	p.Leu1280TrpfsTer5	p.L1280Wfs*5	ENST00000356175	NM_000267.3	1280	Ttg/tg	28/57	0.219066018542198	1	FACETS	0.886	0.752	1	0.886	0.752	1	CLONAL	1	TRUE	0	0.219066018542198	1		352	459	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562782	29562782	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	41	325	0	ENST00000356175.3:c.3862T>G	p.Cys1288Gly	p.C1288G	ENST00000356175	NM_000267.3	1288	Tgt/Ggt	28/57	0.219066018542198	1	FACETS	0.796	0.663	0.942	0.796	0.663	0.942	CLONAL	1	TRUE	0	0.219066018542198	1		325	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0042003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	517	1194	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.812936115091359	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.82790771177452	1		1194	710	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0042003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	377	695	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.82790771177452	2		695	874	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853188	68853188	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	320	589	0	ENST00000261769.5:c.1572del	p.Ile525PhefsTer32	p.I525Ffs*32	ENST00000261769	NM_004360.3	524	cGg/cg	11/16	0.82790771177452	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.82790771177452	1		589	425	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120807	115120807	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	445	632	0	ENST00000257566.3:c.199C>T	p.Gln67Ter	p.Q67*	ENST00000257566	NM_016569.3	67	Caa/Taa	1/8	0.82790771177452	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.82790771177452	1		632	545	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061108	38061112	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCT	CGGCT	-	novel	NA	P-0042003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	185	280	0	ENST00000250448.2:c.877_881del	p.Ser293GlnfsTer8	p.S293Qfs*8	ENST00000250448	NM_004496.3	293	AGCCGc/c	2/2	0.424735294929478	1	FACETS	0.839	0.792	0.886	0.839	0.792	0.886	INDETERMINATE	1	TRUE	0	0.82790771177452	1		280	312	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7218277	7218277	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0042003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	355	512	0	ENST00000380728.2:c.94+1G>T		p.X32_splice	ENST00000380728		32			0.812936115091359	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.82790771177452	1		512	496	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46252797	46252797	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	85	343	0	ENST00000371998.3:c.226G>T	p.Val76Leu	p.V76L	ENST00000371998		76	Gta/Tta	4/23	1	2	FACETS	0.845	0.759	0.934	0.845	0.759	0.934	CLONAL	1	TRUE	1	0.82790771177452	2		343	243	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0042005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	139	474	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.454501767914331	1	FACETS	0.863	0.789	0.939	0.863	0.789	0.939	CLONAL	1	TRUE	0	0.454501767914331	1		474	548	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115952	8115953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0042005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	89	429	0	ENST00000346208.3:c.1300dup	p.His434ProfsTer73	p.H434Pfs*73	ENST00000346208		433	cac/caCc	6/6	1	2	FACETS	0.892	0.795	0.995	0.892	0.795	0.995	CLONAL	1	TRUE	1	0.454501767914331	2		429	439	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717705	89717705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064794675	NA	P-0042005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	138	482	0	ENST00000371953.3:c.730C>T	p.Pro244Ser	p.P244S	ENST00000371953	NM_000314.4	244	Cct/Tct	7/9	0.454501767914331	1	FACETS	0.869	0.795	0.946	0.869	0.795	0.946	CLONAL	1	TRUE	0	0.454501767914331	1		482	540	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	277	737	0				ENST00000310581	NM_198253.2	-/1132			0.373573830943529	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	3	TRUE	1	0.387964692325973	4		737	642	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911535	101911535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113605875	NA	P-0042022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	110	285	0	ENST00000374994.4:c.1460G>A	p.Arg487Gln	p.R487Q	ENST00000374994	NM_004612.2	487	cGg/cAg	9/9	0.387964692325973	1	FACETS	0.975	0.881	1	0.975	0.881	1	CLONAL	1	TRUE	0	0.387964692325973	1		285	469	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099431	27099431	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768377977	NA	P-0042022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	136	522	0	ENST00000324856.7:c.3668G>A	p.Arg1223His	p.R1223H	ENST00000324856	NM_006015.4	1223	cGc/cAc	14/20	1	2	FACETS	0.912	0.83	0.998	0.912	0.83	0.998	CLONAL	1	TRUE	1	0.387964692325973	2		522	769	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911624	134911624	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	114	493	0	ENST00000398015.3:c.2089A>G	p.Thr697Ala	p.T697A	ENST00000398015	NM_004441.4	697	Aca/Gca	11/16	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.387964692325973	2		493	554	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249018	55249019	+	inframe_insertion	In_Frame_Ins	INS	-	-	CACGTG	rs397517116	NA	P-0042022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	108	668	0	ENST00000275493.2:c.2317_2322dup	p.His773_Val774dup	p.H773_V774dup	ENST00000275493	NM_005228.3	773	-/CACGTG	20/28	1	2	FACETS	0.689	0.618	0.764	0.689	0.618	0.764	SUBCLONAL	1	TRUE	1	0.387964692325973	2		668	808	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0042034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	100	798	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	0.742	0.665	0.824	0.742	0.665	0.824	SUBCLONAL	1	TRUE	1	0.499031554547777	2		798	540	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31424569	31424569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773151368	NA	P-0042034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	275	921	0	ENST00000344624.3:c.3226G>A	p.Glu1076Lys	p.E1076K	ENST00000344624		1076	Gaa/Aaa	25/33	0.223592553667198	3	FACETS	1	0.99	1	0.638	0.599	0.678	INDETERMINATE	1	TRUE	1	0.499031554547777	3		921	1080	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588107	69588107	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	53	840	0	ENST00000168712.1:c.591G>T	p.Met197Ile	p.M197I	ENST00000168712	NM_002007.2	197	atG/atT	3/3	1	2	FACETS	0.378	0.322	0.439	0.378	0.322	0.439	SUBCLONAL	1	TRUE	1	0.499031554547777	2		840	562	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	77	737	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.909	1			1	INDETERMINATE	1	FALSE	NA	0.551578756097222	2		737	272	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	193	1194	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	1	2	FACETS	0.914	0.847	0.982	0.914	0.847	0.982	CLONAL	1	FALSE	1	0.551578756097222	2		1194	766	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	92	461	0	ENST00000397062.3:c.92G>A	p.Gly31Glu	p.G31E	ENST00000397062	NM_006164.4	31	gGa/gAa	2/5	1	2	FACETS	0.738	0.659	0.822	0.738	0.659	0.822	SUBCLONAL	1	FALSE	1	0.551578756097222	2		461	452	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937057	36937057	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776379864	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	201	877	0	ENST00000361632.4:c.1262C>T	p.Pro421Leu	p.P421L	ENST00000361632		421	cCg/cTg	9/16	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.551578756097222	2		877	602	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307173	65307173	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs181919006	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	179	689	0	ENST00000342505.4:c.2515C>T	p.Arg839Ter	p.R839*	ENST00000342505	NM_002227.2	839	Cga/Tga	18/25	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.551578756097222	2		689	536	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176105636	176105636	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	219	482	0	ENST00000367669.3:c.879T>G	p.Ile293Met	p.I293M	ENST00000367669	NM_022457.5	293	atT/atG	7/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.551578756097222	2		482	733	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333163	70333164	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	300	980	0	ENST00000373644.4:c.1068_1069delinsAA	p.Glu357Lys	p.E357K	ENST00000373644	NM_030625.2	356	caGGaa/caAAaa	2/12	0.293815997543569	2	FACETS	1	0.994	1	0.703	0.665	0.741	INDETERMINATE	1	FALSE	0	0.551578756097222	2		980	774	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137243	64137243	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs565756385	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	288	1074	2	ENST00000334205.4:c.1675C>T	p.Pro559Ser	p.P559S	ENST00000334205	NM_003942.2	559	Ccg/Tcg	14/17	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	FALSE	1	0.551578756097222	2		1076	762	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917602	94917602	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	128	530	0	ENST00000536441.1:c.919C>G	p.His307Asp	p.H307D	ENST00000536441	NM_144665.3	307	Cat/Gat	6/10	1	2	FACETS	0.785	0.714	0.86	0.785	0.714	0.86	SUBCLONAL	1	FALSE	1	0.551578756097222	2		530	591	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984903	101984903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1226365117	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	180	709	0	ENST00000282441.5:c.350C>T	p.Ala117Val	p.A117V	ENST00000282441	NM_001130145.2	117	gCc/gTc	2/9	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.551578756097222	2		709	507	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203554	108203554	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	185	427	0	ENST00000278616.4:c.7854A>T	p.Arg2618Ser	p.R2618S	ENST00000278616	NM_000051.3	2618	agA/agT	53/63	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.551578756097222	2		427	566	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344552	118344552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	221	635	0	ENST00000534358.1:c.2678G>A	p.Arg893Lys	p.R893K	ENST00000534358	NM_005933.3	893	aGg/aAg	3/36	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.551578756097222	2		635	594	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375498	118375499	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	88	516	0	ENST00000534358.1:c.8891_8892delinsTT	p.Thr2964Ile	p.T2964I	ENST00000534358	NM_005933.3	2964	aCC/aTT	27/36	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	FALSE	1	0.551578756097222	2		516	307	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552602	18552602	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	87	428	0	ENST00000266497.5:c.2013A>C	p.Glu671Asp	p.E671D	ENST00000266497		671	gaA/gaC	14/31	1	2	FACETS	0.766	0.682	0.854	0.766	0.682	0.854	SUBCLONAL	1	FALSE	1	0.551578756097222	2		428	412	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425638	49425638	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	116	1138	0	ENST00000301067.7:c.12850C>T	p.Gln4284Ter	p.Q4284*	ENST00000301067	NM_003482.3	4284	Cag/Tag	39/54	1	2	FACETS	0.943	0.856	1	0.943	0.856	1	CLONAL	1	FALSE	1	0.551578756097222	2		1138	446	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930592	32930592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358968	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	104	540	0	ENST00000380152.3:c.7463G>A	p.Arg2488Lys	p.R2488K	ENST00000380152		2488	aGa/aAa	15/27	0.366156887804242	1	FACETS	0.683	0.616	0.752	0.683	0.616	0.752	SUBCLONAL	1	FALSE	0	0.551578756097222	1		540	400	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609343	81609343	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	118	484	0	ENST00000298171.2:c.941C>T	p.Ser314Phe	p.S314F	ENST00000298171	NM_000369.2	314	tCt/tTt	10/10	0.152675827756949	4	FACETS	1	0.976	1	0.416	0.377	0.457	INDETERMINATE	1	FALSE	1	0.551578756097222	4		484	532	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243018	105243018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	283	1125	2	ENST00000349310.3:c.265C>T	p.His89Tyr	p.H89Y	ENST00000349310	NM_001014432.1	89	Cat/Tat	5/15	0.152675827756949	4	FACETS	1	0.954	1	0.674	0.636	0.713	INDETERMINATE	2	FALSE	1	0.551578756097222	4		1127	787	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991354	41991354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	131	583	0	ENST00000219905.7:c.2185G>A	p.Glu729Lys	p.E729K	ENST00000219905	NM_001164273.1	729	Gaa/Aaa	5/24	0.474754470301901	1	FACETS	0.63	0.574	0.688	0.63	0.574	0.688	SUBCLONAL	1	FALSE	0	0.551578756097222	1		583	546	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058954	42058955	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	42	638	0	ENST00000219905.7:c.8674_8675delinsAA	p.Gly2892Lys	p.G2892K	ENST00000219905	NM_001164273.1	2892	GGg/AAg	24/24	0.474754470301901	1	FACETS	0.339	0.284	0.4	0.339	0.284	0.4	SUBCLONAL	1	FALSE	0	0.551578756097222	1		638	325	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66777521	66777521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	61	894	1	ENST00000307102.5:c.887C>T	p.Pro296Leu	p.P296L	ENST00000307102	NM_002755.3	296	cCc/cTc	7/11	0.474754470301901	1	FACETS	0.373	0.322	0.427	0.373	0.322	0.427	SUBCLONAL	1	FALSE	0	0.551578756097222	1		895	430	SUCCESS
BLM	641	MSKCC	GRCh37	15	91337589	91337589	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	87	271	0	ENST00000355112.3:c.3210+2T>A		p.X1070_splice	ENST00000355112	NM_000057.2	1070			0.474754470301901	1	FACETS	0.744	0.666	0.826	0.744	0.666	0.826	SUBCLONAL	1	FALSE	0	0.551578756097222	1		271	307	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2114319	2114319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	167	1118	0	ENST00000219476.3:c.1490C>T	p.Pro497Leu	p.P497L	ENST00000219476	NM_000548.3	497	cCc/cTc	15/42	1	2	FACETS	0.873	0.804	0.944	0.873	0.804	0.944	CLONAL	1	FALSE	1	0.551578756097222	2		1118	694	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223347	2223347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1259344783	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	131	1017	0	ENST00000326181.6:c.959G>A	p.Gly320Glu	p.G320E	ENST00000326181	NM_032271.2	320	gGa/gAa	10/21	1	2	FACETS	0.762	0.694	0.834	0.762	0.694	0.834	SUBCLONAL	1	FALSE	1	0.551578756097222	2		1017	623	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647962	3647962	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1421346189	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	307	1283	0	ENST00000294008.3:c.1202C>T	p.Pro401Leu	p.P401L	ENST00000294008	NM_032444.2	401	cCc/cTc	6/15	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.551578756097222	2		1283	902	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832792	3832793	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	137	916	2	ENST00000262367.5:c.1465_1466delinsAA	p.Gly489Lys	p.G489K	ENST00000262367	NM_004380.2	489	GGa/AAa	6/31	1	2	FACETS	0.777	0.709	0.849	0.777	0.709	0.849	SUBCLONAL	1	FALSE	1	0.551578756097222	2		918	639	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858163	9858163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	209	844	1	ENST00000330684.3:c.3238C>T	p.His1080Tyr	p.H1080Y	ENST00000330684	NM_001134407.1	1080	Cac/Tac	13/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.551578756097222	2		845	639	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619299	23619299	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769342316	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	228	865	0	ENST00000261584.4:c.3236C>T	p.Ala1079Val	p.A1079V	ENST00000261584	NM_024675.3	1079	gCc/gTc	12/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.551578756097222	2		865	769	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646459	23646459	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs150636811	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	93	920	0	ENST00000261584.4:c.1408A>G	p.Thr470Ala	p.T470A	ENST00000261584	NM_024675.3	470	Aca/Gca	4/13	1	2	FACETS	0.386	0.343	0.433	0.386	0.343	0.433	SUBCLONAL	1	FALSE	1	0.551578756097222	2		920	873	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785515	50785515	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	241	673	1	ENST00000398568.2:c.505G>A	p.Glu169Lys	p.E169K	ENST00000398568	NM_001042412.1	169	Gaa/Aaa	4/18	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.551578756097222	2		674	721	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813650	50813650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	229	971	1	ENST00000398568.2:c.1204C>T	p.Pro402Ser	p.P402S	ENST00000398568	NM_001042412.1	402	Cct/Tct	8/18	1	2	FACETS	0.836	0.78	0.895	0.836	0.78	0.895	CLONAL	1	FALSE	1	0.551578756097222	2		972	993	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865781	56865782	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	83	538	1	ENST00000308159.5:c.1113_1114delinsTT	p.Arg372Trp	p.R372W	ENST00000308159	NM_014669.4	371	ctCCgg/ctTTgg	11/22	1	2	FACETS	0.715	0.634	0.8	0.715	0.634	0.8	SUBCLONAL	1	FALSE	1	0.551578756097222	2		539	421	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831747	72831747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	268	985	0	ENST00000268489.5:c.4834G>A	p.Glu1612Lys	p.E1612K	ENST00000268489	NM_006885.3	1612	Gag/Aag	9/10	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	FALSE	1	0.551578756097222	2		985	707	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89842210	89842210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1248172249	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	152	800	0	ENST00000389301.3:c.1840C>T	p.Pro614Ser	p.P614S	ENST00000389301	NM_000135.2	614	Ccc/Tcc	21/43	1	2	FACETS	0.749	0.686	0.814	0.749	0.686	0.814	SUBCLONAL	1	FALSE	1	0.551578756097222	2		800	736	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216980	7216980	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	137	912	1	ENST00000380728.2:c.541C>T	p.Gln181Ter	p.Q181*	ENST00000380728		181	Caa/Taa	7/11	1	2	FACETS	0.827	0.755	0.902	0.827	0.755	0.902	CLONAL	1	FALSE	1	0.551578756097222	2		913	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519980	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	150	1008	0	ENST00000269305.4:c.528C>G	p.Cys176Trp	p.C176W	ENST00000269305	NM_001126112.2	176	tgC/tgG	5/11	1	2	FACETS	0.865	0.793	0.939	0.865	0.793	0.939	CLONAL	1	FALSE	1	0.551578756097222	2		1008	629	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974970	15974970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	100	540	0	ENST00000268712.3:c.3905G>A	p.Arg1302Lys	p.R1302K	ENST00000268712	NM_006311.3	1302	aGa/aAa	30/46	1	2	FACETS	0.845	0.76	0.935	0.845	0.76	0.935	CLONAL	1	FALSE	1	0.551578756097222	2		540	429	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556877	29556877	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	61	333	0	ENST00000356175.3:c.2875C>T	p.Gln959Ter	p.Q959*	ENST00000356175	NM_000267.3	959	Caa/Taa	22/57	1	2	FACETS	0.702	0.61	0.801	0.702	0.61	0.801	SUBCLONAL	1	FALSE	1	0.551578756097222	2		333	315	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653001	29653001	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	163	678	0	ENST00000356175.3:c.4936C>G	p.Pro1646Ala	p.P1646A	ENST00000356175	NM_000267.3	1646	Cct/Gct	36/57	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	1	0.551578756097222	2		678	585	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226478	41226479	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	124	902	1	ENST00000357654.3:c.4544_4545delinsAA	p.Gly1515Glu	p.G1515E	ENST00000357654	NM_007294.3	1515	gGG/gAA	14/23	1	2	FACETS	0.657	0.596	0.722	0.657	0.596	0.722	SUBCLONAL	1	FALSE	1	0.551578756097222	2		903	684	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897397	78897397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	236	1186	0	ENST00000306801.3:c.2732C>T	p.Pro911Leu	p.P911L	ENST00000306801	NM_020761.2	911	cCc/cTc	23/34	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.551578756097222	2		1186	684	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223135	1223135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778696	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	93	1010	2	ENST00000326873.7:c.1072G>A	p.Asp358Asn	p.D358N	ENST00000326873	NM_000455.4	358	Gat/Aat	8/10	0.477969923040668	1	FACETS	0.396	0.352	0.442	0.396	0.352	0.442	SUBCLONAL	1	FALSE	0	0.551578756097222	1		1012	617	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611747	1611747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	211	1128	0	ENST00000344749.5:c.1915C>T	p.Pro639Ser	p.P639S	ENST00000344749	NM_001136139.2	639	Cca/Tca	19/19	0.477969923040668	1	FACETS	0.907	0.848	0.967	0.907	0.848	0.967	CLONAL	1	FALSE	0	0.551578756097222	1		1128	611	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611832	1611833	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	65	913	2	ENST00000344749.5:c.1829_1830delinsTT	p.Pro610Leu	p.P610L	ENST00000344749	NM_001136139.2	610	cCC/cTT	19/19	0.477969923040668	1	FACETS	0.291	0.252	0.333	0.291	0.252	0.333	SUBCLONAL	1	FALSE	0	0.551578756097222	1		915	586	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4102404	4102405	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	73	1118	2	ENST00000262948.5:c.497_498delinsTT	p.Pro166Leu	p.P166L	ENST00000262948	NM_030662.3	166	cCC/cTT	4/11	0.477969923040668	1	FACETS	0.333	0.292	0.378	0.333	0.292	0.378	SUBCLONAL	1	FALSE	0	0.551578756097222	1		1120	575	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290231	15290232	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	211	1226	0	ENST00000263388.2:c.3403_3404delinsAA	p.Gly1135Asn	p.G1135N	ENST00000263388	NM_000435.2	1135	GGt/AAt	21/33	0.477969923040668	1	FACETS	0.962	0.9	1	0.962	0.9	1	CLONAL	1	FALSE	0	0.551578756097222	1		1226	576	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943399	17943399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376945173	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	232	1164	0	ENST00000458235.1:c.2609G>A	p.Arg870Gln	p.R870Q	ENST00000458235	NM_000215.3	870	cGg/cAg	19/24	0.477969923040668	1	FACETS	0.857	0.803	0.912	0.857	0.803	0.912	CLONAL	1	FALSE	0	0.551578756097222	1		1164	711	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018169	48018169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143036974	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	197	999	0	ENST00000234420.5:c.364G>A	p.Glu122Lys	p.E122K	ENST00000234420	NM_000179.2	122	Gag/Aag	2/10	1	2	FACETS	0.85	0.789	0.914	0.85	0.789	0.914	CLONAL	1	FALSE	1	0.551578756097222	2		999	840	SUCCESS
REL	5966	MSKCC	GRCh37	2	61128146	61128146	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	97	218	0	ENST00000295025.8:c.322C>T	p.Arg108Ter	p.R108*	ENST00000295025	NM_002908.2	108	Cga/Tga	4/11	1	2	FACETS	0.709	0.635	0.788	0.709	0.635	0.788	SUBCLONAL	1	FALSE	1	0.551578756097222	2		218	496	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149832	202149832	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	223	930	1	ENST00000358485.4:c.1273C>T	p.Gln425Ter	p.Q425*	ENST00000358485	NM_001080125.1	425	Cag/Tag	8/9	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.551578756097222	2		931	639	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212252683	212252683	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766441342	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	52	353	0	ENST00000342788.4:c.3170C>T	p.Thr1057Ile	p.T1057I	ENST00000342788	NM_005235.2	1057	aCc/aTc	26/28	1	2	FACETS	0.717	0.616	0.826	0.717	0.616	0.826	SUBCLONAL	1	FALSE	1	0.551578756097222	2		353	263	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578369	212578369	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	57	394	0	ENST00000342788.4:c.888C>G	p.Asn296Lys	p.N296K	ENST00000342788	NM_005235.2	296	aaC/aaG	8/28	1	2	FACETS	0.603	0.52	0.692	0.603	0.52	0.692	SUBCLONAL	1	FALSE	1	0.551578756097222	2		394	343	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439473	220439473	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	104	900	0	ENST00000243786.2:c.326G>A	p.Gly109Asp	p.G109D	ENST00000243786	NM_002191.3	109	gGc/gAc	2/2	1	2	FACETS	0.838	0.755	0.925	0.838	0.755	0.925	CLONAL	1	FALSE	1	0.551578756097222	2		900	450	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757458	40757458	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	276	1081	1	ENST00000373198.4:c.2840G>A	p.Arg947Gln	p.R947Q	ENST00000373198	NM_133170.3	947	cGg/cAg	20/32	0.177668289055645	3	FACETS	0.816	0.77	0.864	0.816	0.77	0.864	INDETERMINATE	2	FALSE	1	0.551578756097222	3		1082	782	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050706	30050707	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	190	591	0	ENST00000338641.4:c.508_509delinsTT	p.Pro170Leu	p.P170L	ENST00000338641	NM_000268.3	170	CCa/TTa	5/16	0.118397046128985	6	FACETS	1	0.95	1	0.687	0.637	0.738	INDETERMINATE	2	FALSE	3	0.551578756097222	6		591	703	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568590	41568590	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	281	721	1	ENST00000263253.7:c.4540G>A	p.Glu1514Lys	p.E1514K	ENST00000263253	NM_001429.3	1514	Gaa/Aaa	28/31	0.118397046128985	6	FACETS	1	0.984	1	0.752	0.708	0.797	INDETERMINATE	2	FALSE	3	0.551578756097222	6		722	950	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573597	41573598	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	264	1125	1	ENST00000263253.7:c.5882_5883delinsTT	p.Pro1961Leu	p.P1961L	ENST00000263253	NM_001429.3	1961	cCC/cTT	31/31	0.118397046128985	6	FACETS	1	0.99	1	0.824	0.775	0.875	INDETERMINATE	2	FALSE	3	0.551578756097222	6		1126	814	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916834	178916834	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	257	745	0	ENST00000263967.3:c.221C>T	p.Thr74Ile	p.T74I	ENST00000263967	NM_006218.2	74	aCt/aTt	2/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.551578756097222	2		745	868	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539727	187539727	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	234	621	0	ENST00000441802.2:c.8013del	p.Phe2672LeufsTer51	p.F2672Lfs*51	ENST00000441802	NM_005245.3	2671	ttC/tt	10/27	0.499089054627784	2	FACETS	0.878	0.829	0.927	0.878	0.829	0.927	CLONAL	2	FALSE	0	0.551578756097222	2		621	483	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295088	1295088	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	36	163	0	ENST00000310581.5:c.17G>C	p.Arg6Pro	p.R6P	ENST00000310581	NM_198253.2	6	cGc/cCc	1/16	NA	2	FACETS	1	0.922	1			1	INDETERMINATE	1	FALSE	NA	0.551578756097222	2		163	112	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295408	1295408	+	upstream_gene_variant	5'Flank	SNP	A	A	G	rs952048039	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	25	197	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.925	0.745	1			1	INDETERMINATE	1	FALSE	NA	0.551578756097222	2		197	98	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751379	57751380	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	82	596	0	ENST00000274289.3:c.1611_1612delinsTT	p.Leu538Phe	p.L538F	ENST00000274289	NM_006622.3	537	ctCCtt/ctTTtt	11/14	0.551578756097222	1	FACETS	0.704	0.627	0.784	0.704	0.627	0.784	SUBCLONAL	1	FALSE	0	0.551578756097222	1		596	306	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685312	86685312	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	66	315	0	ENST00000274376.6:c.3028C>T	p.Arg1010Ter	p.R1010*	ENST00000274376	NM_002890.2	1010	Cga/Tga	24/25	0.551578756097222	1	FACETS	0.806	0.711	0.906	0.806	0.711	0.906	CLONAL	1	FALSE	0	0.551578756097222	1		315	215	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481448	20481448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1225039532	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	135	395	0	ENST00000346618.3:c.517C>T	p.Pro173Ser	p.P173S	ENST00000346618	NM_001949.4	173	Ccc/Tcc	3/7	0.217008067117104	3	FACETS	1	0.986	1	0.699	0.64	0.759	INDETERMINATE	1	FALSE	1	0.551578756097222	3		395	447	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163692	32163692	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	113	914	0	ENST00000375023.3:c.5534C>T	p.Thr1845Met	p.T1845M	ENST00000375023	NM_004557.3	1845	aCg/aTg	30/30	0.217008067117104	3	FACETS	1	0.969	1	0.583	0.528	0.641	INDETERMINATE	1	FALSE	1	0.551578756097222	3		914	448	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188937	32188938	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	172	1203	0	ENST00000375023.3:c.616_617delinsTT	p.Pro206Phe	p.P206F	ENST00000375023	NM_004557.3	206	CCc/TTc	4/30	0.217008067117104	3	FACETS	1	0.982	1	0.606	0.559	0.653	INDETERMINATE	1	FALSE	1	0.551578756097222	3		1203	657	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287622	33287622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	158	833	0	ENST00000374542.5:c.1475G>A	p.Gly492Glu	p.G492E	ENST00000374542	NM_001141970.1	492	gGa/gAa	6/8	0.217008067117104	3	FACETS	1	0.98	1	0.603	0.555	0.653	INDETERMINATE	1	FALSE	1	0.551578756097222	3		833	606	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196106	138196107	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	140	565	2	ENST00000237289.4:c.420_421delinsTT	p.Arg141Cys	p.R141C	ENST00000237289	NM_001270507.1	140	ttCCgc/ttTTgc	3/9	0.217008067117104	3	FACETS	1	0.979	1	0.608	0.556	0.661	INDETERMINATE	1	FALSE	1	0.551578756097222	3		567	533	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946173	13946173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1419836219	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	284	856	0	ENST00000405192.2:c.923G>A	p.Arg308Gln	p.R308Q	ENST00000405192	NM_001163147.1	308	cGg/cAg	10/12	0.217008067117104	3	FACETS	0.798	0.753	0.844	0.798	0.753	0.844	INDETERMINATE	2	FALSE	1	0.551578756097222	3		856	823	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403126	116403126	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	129	618	1	ENST00000397752.3:c.2387C>T	p.Ser796Leu	p.S796L	ENST00000397752	NM_000245.2	796	tCa/tTa	11/21	0.217008067117104	3	FACETS	1	0.936	1	0.517	0.47	0.566	INDETERMINATE	1	FALSE	1	0.551578756097222	3		619	577	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879297	151879297	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	170	792	0	ENST00000262189.6:c.5648C>T	p.Ser1883Leu	p.S1883L	ENST00000262189	NM_170606.2	1883	tCa/tTa	36/59	0.217008067117104	3	FACETS	1	0.99	1	0.748	0.692	0.804	INDETERMINATE	1	FALSE	1	0.551578756097222	3		792	526	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38137182	38137183	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	218	852	1	ENST00000317025.8:c.3635_3636delinsTT	p.Ala1212Val	p.A1212V	ENST00000317025	NM_023034.1	1212	gCC/gTT	21/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.551578756097222	2		853	745	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38173452	38173452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	143	611	0	ENST00000317025.8:c.1964C>T	p.Ser655Phe	p.S655F	ENST00000317025	NM_023034.1	655	tCt/tTt	10/24	1	2	FACETS	0.731	0.668	0.798	0.731	0.668	0.798	SUBCLONAL	1	FALSE	1	0.551578756097222	2		611	709	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738695	145738696	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	233	1189	1	ENST00000428558.2:c.2368_2369delinsAA	p.Gly790Lys	p.G790K	ENST00000428558	NM_004260.3	790	GGg/AAg	15/22	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	1	0.551578756097222	2		1190	614	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633439	8633439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	102	510	0	ENST00000356435.5:c.230G>A	p.Gly77Glu	p.G77E	ENST00000356435		77	gGg/gAg	3/35	0.437144865252403	0	FACETS	0.537	0.486	0.589			1	SUBCLONAL	1	FALSE	0	0.551578756097222	0		510	309	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	85	699	0	ENST00000304494.5:c.151-1G>A		p.X51_splice	ENST00000304494	NM_000077.4	51			0.437144865252403	0	FACETS	0.482	0.431	0.535			1	SUBCLONAL	1	FALSE	0	0.551578756097222	0		699	287	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27192522	27192522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770814923	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	147	881	0	ENST00000380036.4:c.1525C>T	p.Pro509Ser	p.P509S	ENST00000380036	NM_000459.3	509	Cct/Tct	11/23	1	2	FACETS	0.693	0.633	0.755	0.693	0.633	0.755	SUBCLONAL	1	FALSE	1	0.551578756097222	2		881	769	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248056	110248057	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	200	777	2	ENST00000374672.4:c.1415_1416delinsTT	p.Ala472Val	p.A472V	ENST00000374672	NM_004235.4	472	gCC/gTT	5/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.551578756097222	2		779	628	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412717	139412729	+	frameshift_variant	Frame_Shift_Del	DEL	CATGCGTCGTTGA	CATGCGTCGTTGA	GTGGCACAG	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	111	1134	4	ENST00000277541.6:c.1115_1127delinsCTGTGCCAC	p.Leu372ProfsTer258	p.L372Pfs*258	ENST00000277541	NM_017617.3	372	cTCAACGACGCATGc/cCTGTGCCACc	7/34	1	2	FACETS	0.62	0.558	0.685	0.62	0.558	0.685	SUBCLONAL	1	FALSE	1	0.551578756097222	2		1138	649	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413051	139413052	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	136	852	1	ENST00000277541.6:c.1090_1091delinsAA	p.Gly364Asn	p.G364N	ENST00000277541	NM_017617.3	364	GGc/AAc	6/34	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	FALSE	1	0.551578756097222	2		853	476	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413098	139413099	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	206	1097	1	ENST00000277541.6:c.1043_1044delinsTT	p.Ala348Val	p.A348V	ENST00000277541	NM_017617.3	348	gCC/gTT	6/34	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.551578756097222	2		1098	660	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314905	1314905	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	161	676	0	ENST00000400841.2:c.756G>A	p.Trp252Ter	p.W252*	ENST00000400841		252	tgG/tgA	6/6	0.165468304847873	3	FACETS	0.817	0.756	0.879	0.544	0.504	0.586	INDETERMINATE	2	FALSE	0	0.551578756097222	3		676	456	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15840971	15840971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	87	891	0	ENST00000307771.7:c.1055G>A	p.Arg352Gln	p.R352Q	ENST00000307771	NM_005089.3	352	cGg/cAg	11/11	0.165468304847873	3	FACETS	0.579	0.513	0.65	0.193	0.171	0.217	INDETERMINATE	1	FALSE	0	0.551578756097222	3		891	695	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934416	39934417	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	261	899	0	ENST00000378444.4:c.182_183delinsTT	p.Ala61Val	p.A61V	ENST00000378444	NM_001123385.1	61	gCC/gTT	4/15	0.165468304847873	3	FACETS	0.975	0.921	1	0.65	0.614	0.687	INDETERMINATE	2	FALSE	0	0.551578756097222	3		899	619	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341284	70341285	+	stop_gained,splice_region_variant	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	88	842	0	ENST00000374080.3:c.843_844delinsTT	p.Arg282Ter	p.R282*	ENST00000374080		281	ctCCga/ctTTga	6/45	0.165468304847873	3	FACETS	0.598	0.53	0.671	0.199	0.176	0.224	INDETERMINATE	1	FALSE	0	0.551578756097222	3		842	681	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854883	76854883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	336	624	0	ENST00000373344.5:c.5953G>A	p.Glu1985Lys	p.E1985K	ENST00000373344	NM_000489.3	1985	Gaa/Aaa	25/35	0.165468304847873	3	FACETS	0.961	0.913	1	0.64	0.609	0.673	INDETERMINATE	2	FALSE	0	0.551578756097222	3		624	809	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938202	76938202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	415	841	0	ENST00000373344.5:c.2546C>T	p.Ser849Phe	p.S849F	ENST00000373344	NM_000489.3	849	tCt/tTt	9/35	0.165468304847873	3	FACETS	0.998	0.954	1	0.665	0.636	0.695	INDETERMINATE	2	FALSE	0	0.551578756097222	3		841	962	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939235	76939235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782164721	NA	P-0042037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	163	904	0	ENST00000373344.5:c.1513G>A	p.Glu505Lys	p.E505K	ENST00000373344	NM_000489.3	505	Gaa/Aaa	9/35	0.165468304847873	3	FACETS	0.755	0.692	0.82	0.252	0.23	0.274	INDETERMINATE	1	FALSE	0	0.551578756097222	3		904	999	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042041-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	178	737	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.999	0.926	1	0.999	0.926	1	CLONAL	1	TRUE	1	0.61	2		737	584	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0042041-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	257	609	2	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.61	2		611	782	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0042041-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	178	586	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.3	3	FACETS	0.718	0.661	0.778	0.359	0.33	0.389	INDETERMINATE	1	TRUE	1	0.61	3		586	1060	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148727	20148727	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0042041-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	126	285	0	ENST00000379607.5:c.338-2A>G		p.X113_splice	ENST00000379607	NM_001412.3	113			1	2	FACETS	0.93	0.849	1	0.93	0.849	1	CLONAL	1	TRUE	1	0.61	2		285	444	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0042061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	65	544	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.27	2		545	473	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0042061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	54	305	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.939	0.804	1	0.939	0.804	1	CLONAL	1	TRUE	1	0.27	2		305	426	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791263	42791263	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	97	978	0	ENST00000575354.2:c.323C>G	p.Pro108Arg	p.P108R	ENST00000575354	NM_015125.3	108	cCc/cGc	3/20	1	2	FACETS	0.927	0.826	1	0.927	0.826	1	CLONAL	1	TRUE	1	0.27	2		978	775	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573817	64573817	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs386134260	NA	P-0042061-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	287	890	0	ENST00000312049.6:c.936C>G	p.Tyr312Ter	p.Y312*	ENST00000312049	NM_130799.2	312	taC/taG	7/10	0.765658460492573	1	FACETS	0.995	0.951	1	0.995	0.951	1	CLONAL	1	TRUE	0	0.765658460492573	1		890	465	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573817	64573817	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs386134260	NA	P-0042061-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	290	890	0	ENST00000312049.6:c.936C>G	p.Tyr312Ter	p.Y312*	ENST00000312049	NM_130799.2	312	taC/taG	7/10	0.933706419794176	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.933706419794176	1		890	329	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0042117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	23	212	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.183807352587263	6	FACETS	0.191	0.148	0.241	0.064	0.049	0.081	INDETERMINATE	1	TRUE	3	0.542320906188112	6		212	926	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0042117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	336	1163	1	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	0.528707386796343	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.542320906188112	1		1164	825	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790830	89790830	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	261	848	0	ENST00000336032.3:c.217C>G	p.Arg73Gly	p.R73G	ENST00000336032	NM_006813.2	73	Cgc/Ggc	1/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.542320906188112	2		848	906	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426526	49426526	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	353	1043	0	ENST00000301067.7:c.11962C>T	p.Gln3988Ter	p.Q3988*	ENST00000301067	NM_003482.3	3988	Cag/Tag	39/54	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.542320906188112	2		1043	1173	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499342	89499342	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	166	458	0	ENST00000336596.2:c.2512G>C	p.Asp838His	p.D838H	ENST00000336596	NM_005233.5	838	Gat/Cat	15/17	0.528707386796343	1	FACETS	0.945	0.876	1	0.945	0.876	1	CLONAL	1	TRUE	0	0.542320906188112	1		458	472	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433585	49433585	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	207	1124	0	ENST00000301067.7:c.7968G>T	p.Leu2656Phe	p.L2656F	ENST00000301067	NM_003482.3	2656	ttG/ttT	31/54	1	2	FACETS	0.744	0.69	0.8	0.744	0.69	0.8	SUBCLONAL	1	TRUE	1	0.542320906188112	2		1124	1026	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892149	9892149	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555488081	NA	P-0042117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	57	703	0	ENST00000330684.3:c.2341C>T	p.Gln781Ter	p.Q781*	ENST00000330684	NM_001134407.1	781	Cag/Tag	11/13	1	2	FACETS	0.297	0.254	0.344	0.297	0.254	0.344	SUBCLONAL	1	TRUE	1	0.542320906188112	2		703	708	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50816350	50816350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868852255	NA	P-0042117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	16	507	0	ENST00000398568.2:c.1790C>T	p.Ser597Phe	p.S597F	ENST00000398568	NM_001042412.1	597	tCt/tTt	10/18	0.542609817488957	1	FACETS	0.14	0.103	0.184	0.14	0.103	0.184	SUBCLONAL	1	TRUE	0	0.542320906188112	1		507	307	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791065	42791065	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	38	591	0	ENST00000575354.2:c.210G>C	p.Gln70His	p.Q70H	ENST00000575354	NM_015125.3	70	caG/caC	2/20	1	2	FACETS	0.25	0.206	0.3	0.25	0.206	0.3	SUBCLONAL	1	TRUE	1	0.542320906188112	2		591	560	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728587	190728587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747650016	NA	P-0042117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	135	651	0	ENST00000441310.2:c.1975G>A	p.Ala659Thr	p.A659T	ENST00000441310	NM_000534.4	659	Gca/Aca	10/13	1	2	FACETS	0.532	0.483	0.584	0.532	0.483	0.584	SUBCLONAL	1	TRUE	1	0.542320906188112	2		651	936	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225338972	225338972	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	158	448	0	ENST00000264414.4:c.2297A>G	p.Tyr766Cys	p.Y766C	ENST00000264414	NM_003590.4	766	tAt/tGt	16/16	1	2	FACETS	0.937	0.862	1	0.937	0.862	1	CLONAL	1	TRUE	1	0.542320906188112	2		448	622	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664858	138664858	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	111	216	0	ENST00000330315.3:c.707C>A	p.Pro236His	p.P236H	ENST00000330315	NM_023067.3	236	cCc/cAc	1/1	0.103147428622333	3	FACETS	0.903	0.825	0.984	0.903	0.825	0.984	INDETERMINATE	2	TRUE	1	0.542320906188112	3		216	288	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55225428	55225428	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	172	576	0	ENST00000275493.2:c.1280G>T	p.Arg427Leu	p.R427L	ENST00000275493	NM_005228.3	427	cGc/cTc	11/28	1	2	FACETS	0.906	0.836	0.979	0.906	0.836	0.979	CLONAL	1	TRUE	1	0.542320906188112	2		576	700	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913386	NA	P-0042117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	248	726	0	ENST00000304494.5:c.341C>A	p.Pro114His	p.P114H	ENST00000304494	NM_000077.4	114	cCc/cAc	2/3	0.528707386796343	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.542320906188112	1		726	591	SUCCESS
AR	367	MSKCC	GRCh37	X	66765398	66765398	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	183	912	0	ENST00000374690.3:c.410C>A	p.Ala137Asp	p.A137D	ENST00000374690	NM_000044.3	137	gCc/gAc	1/8	1	2	FACETS	0.874	0.808	0.942	0.874	0.808	0.942	CLONAL	1	TRUE	1	0.542320906188112	2		912	772	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325762	30325762	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs771704089	NA	P-0042139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	56	274	0	ENST00000322652.5:c.1960C>T	p.Arg654Ter	p.R654*	ENST00000322652	NM_015355.2	654	Cga/Tga	16/16	1	2	FACETS	0.875	0.758	1	0.875	0.758	1	CLONAL	1	TRUE	1	0.520115356901012	2		274	246	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0042139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	312	356	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.520115356901012	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.520115356901012	3		356	675	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934002	49934002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	222	650	0	ENST00000296474.3:c.2410C>T	p.His804Tyr	p.H804Y	ENST00000296474	NM_002447.2	804	Cat/Tat	9/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.520115356901012	2		650	788	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127933383	127933383	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	131	492	0	ENST00000373547.4:c.152G>A	p.Cys51Tyr	p.C51Y	ENST00000373547	NM_002721.4	51	tGt/tAt	2/7	0.427307275620979	1	FACETS	0.81	0.741	0.882	0.81	0.741	0.882	CLONAL	1	TRUE	0	0.520115356901012	1		492	460	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480121	50480121	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	144	438	0	ENST00000394963.4:c.355C>T	p.Arg119Ter	p.R119*	ENST00000394963	NM_003076.4	119	Cga/Tga	2/13	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.520115356901012	2		438	531	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716064	52716064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	244	664	0	ENST00000322088.6:c.629C>T	p.Ser210Phe	p.S210F	ENST00000322088	NM_014225.5	210	tCc/tTc	5/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.520115356901012	2		664	861	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406736	70406736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	56	389	0	ENST00000373644.4:c.4250C>T	p.Ser1417Phe	p.S1417F	ENST00000373644	NM_030625.2	1417	tCt/tTt	4/12	0.45508747855787	1	FACETS	0.467	0.402	0.538	0.467	0.402	0.538	SUBCLONAL	1	TRUE	0	0.520115356901012	1		389	341	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643453	38643453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	145	507	0	ENST00000299084.4:c.923C>T	p.Ser308Phe	p.S308F	ENST00000299084	NM_152594.2	308	tCt/tTt	7/7	0.427307275620979	1	FACETS	0.803	0.737	0.871	0.803	0.737	0.871	CLONAL	1	TRUE	0	0.520115356901012	1		507	514	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965567	15965567	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	82	207	0	ENST00000268712.3:c.5239C>G	p.Arg1747Gly	p.R1747G	ENST00000268712	NM_006311.3	1747	Cga/Gga	36/46	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.520115356901012	2		207	230	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78933911	78933911	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	243	652	0	ENST00000306801.3:c.3511A>G	p.Ser1171Gly	p.S1171G	ENST00000306801	NM_020761.2	1171	Agt/Ggt	30/34	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.520115356901012	2		652	814	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7163135	7163135	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	248	671	0	ENST00000302850.5:c.1937C>A	p.Ser646Tyr	p.S646Y	ENST00000302850	NM_000208.2	646	tCc/tAc	9/22	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.520115356901012	2		671	896	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026771	48026771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878853710	NA	P-0042139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	108	427	0	ENST00000234420.5:c.1649C>T	p.Ser550Phe	p.S550F	ENST00000234420	NM_000179.2	550	tCt/tTt	4/10	0.427307275620979	1	FACETS	0.737	0.666	0.811	0.737	0.666	0.811	SUBCLONAL	1	TRUE	0	0.520115356901012	1		427	417	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248702	212248702	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	100	426	0	ENST00000342788.4:c.3565C>T	p.His1189Tyr	p.H1189Y	ENST00000342788	NM_005235.2	1189	Cac/Tac	28/28	0.427307275620979	1	FACETS	0.777	0.701	0.858	0.777	0.701	0.858	SUBCLONAL	1	TRUE	0	0.520115356901012	1		426	366	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177954	56177954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777180860	NA	P-0042139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	146	428	0	ENST00000399503.3:c.2927C>T	p.Ser976Phe	p.S976F	ENST00000399503	NM_005921.1	976	tCc/tTc	14/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.520115356901012	2		428	514	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509372	106509372	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs553869172	NA	P-0042139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	354	588	0	ENST00000359195.3:c.1366G>A	p.Gly456Ser	p.G456S	ENST00000359195	NM_002649.2	456	Ggc/Agc	2/11	0.520115356901012	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.520115356901012	3		588	839	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874755	151874756	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0042139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	230	406	2	ENST00000262189.6:c.7782_7783delinsAT	p.Pro2595Ser	p.P2595S	ENST00000262189	NM_170606.2	2594	atTCcc/atATcc	38/59	0.37246977062011	3	FACETS	0.956	0.898	1	0.637	0.598	0.676	CLONAL	2	TRUE	0	0.520115356901012	3		408	583	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981498	70981498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	102	876	0	ENST00000276594.2:c.598G>A	p.Glu200Lys	p.E200K	ENST00000276594	NM_024504.3	200	Gag/Aag	2/8	0.427307275620979	1	FACETS	0.381	0.341	0.424	0.381	0.341	0.424	SUBCLONAL	1	TRUE	0	0.520115356901012	1		876	761	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321324	1321325	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	143	598	0	ENST00000400841.2:c.430_431delinsAA	p.Gly144Lys	p.G144K	ENST00000400841		144	GGg/AAg	4/6	1	1	FACETS	0.619	0.566	0.675	0.619	0.566	0.675	SUBCLONAL	1	TRUE	0	0.520115356901012	1		598	657	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0042197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	136	413	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.958	1	1	0.991	1	CLONAL	2	TRUE	1	0.2	2		414	627	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517973	8517973	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	36	345	0	ENST00000356435.5:c.1418A>T	p.Asp473Val	p.D473V	ENST00000356435		473	gAc/gTc	10/35	0.297895949062319	0	FACETS	0.647	0.532	0.776			1	SUBCLONAL	1	TRUE	0	0.2	0		345	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578371	7578371	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	108	638	0	ENST00000269305.4:c.559G>C	p.Gly187Arg	p.G187R	ENST00000269305	NM_001126112.2	187	Ggt/Cgt	5/11	1	2	FACETS	0.872	0.785	0.965	1	0.986	1	CLONAL	2	TRUE	1	0.2	2		638	619	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434344	121434344	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	54	693	1	ENST00000257555.6:c.1108G>T	p.Val370Phe	p.V370F	ENST00000257555		370	Gtc/Ttc	6/10	1	2	FACETS	0.854	0.729	0.992	0.854	0.729	0.992	CLONAL	1	TRUE	1	0.2	2		694	632	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514871	103514871	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	37	406	0	ENST00000355739.4:c.1372G>T	p.Val458Leu	p.V458L	ENST00000355739	NM_000123.3	458	Gta/Tta	8/15	1	2	FACETS	0.887	0.732	1	0.887	0.732	1	CLONAL	1	TRUE	1	0.2	2		406	417	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476294	88476294	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	103	634	0	ENST00000360948.2:c.1838T>C	p.Leu613Pro	p.L613P	ENST00000360948	NM_001012338.2	613	cTc/cCc	15/19	0.297895949062319	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.2	1		634	777	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550346	39550347	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0042197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	48	319	2	ENST00000262039.4:c.457_458delinsTT	p.Gly153Leu	p.G153L	ENST00000262039	NM_002647.2	153	GGa/TTa	4/25	1	2	FACETS	0.966	0.817	1	0.966	0.817	1	CLONAL	1	TRUE	1	0.2	2		321	497	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504363	186504363	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	22	218	0	ENST00000323963.5:c.700C>G	p.Arg234Gly	p.R234G	ENST00000323963		234	Cga/Gga	7/11	0.297895949062319	1	FACETS	0.479	0.371	0.606	0.479	0.371	0.606	SUBCLONAL	1	TRUE	0	0.2	1		218	413	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751587	57751587	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	37	266	0	ENST00000274289.3:c.1404G>T	p.Met468Ile	p.M468I	ENST00000274289	NM_006622.3	468	atG/atT	11/14	1	2	FACETS	1	0.833	1	1	0.833	1	CLONAL	1	TRUE	1	0.2	2		266	367	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412728	63412728	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	60	659	1	ENST00000330258.3:c.439G>T	p.Val147Leu	p.V147L	ENST00000330258	NM_152424.3	147	Gtg/Ttg	2/2	1	2	FACETS	0.842	0.724	0.97	0.842	0.724	0.97	CLONAL	1	TRUE	1	0.2	2		660	713	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184149	123184149	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	23	237	0	ENST00000218089.9:c.1007T>A	p.Met336Lys	p.M336K	ENST00000218089	NM_001042749.1	336	aTg/aAg	11/35	1	2	FACETS	0.667	0.52	0.837	0.667	0.52	0.837	SUBCLONAL	1	TRUE	1	0.2	2		237	345	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	114	737	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.943	0.855	1	0.943	0.855	1	CLONAL	1	TRUE	1	0.542088440309854	2		737	446	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0042202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	322	305	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.542088440309854	5	FACETS	0.946	0.899	0.994	0.946	0.899	0.994	CLONAL	3	TRUE	2	0.542088440309854	5		305	759	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0042202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	229	310	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.542088440309854	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.542088440309854	2		310	392	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612050	43612050	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	313	1004	0	ENST00000355710.3:c.2155T>C	p.Phe719Leu	p.F719L	ENST00000355710	NM_020975.4	719	Ttc/Ctc	12/20	0.542088440309854	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.542088440309854	1		1004	719	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912600	32912600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	261	282	0	ENST00000380152.3:c.4108G>A	p.Gly1370Ser	p.G1370S	ENST00000380152		1370	Ggc/Agc	11/27	0.455853179497068	3	FACETS	0.931	0.879	0.985	0.931	0.879	0.985	CLONAL	2	TRUE	1	0.542088440309854	3		282	657	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285675	87285675	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	258	567	0	ENST00000277120.3:c.12G>A	p.Trp4Ter	p.W4*	ENST00000277120		4	tgG/tgA	2/19	0.542088440309854	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.542088440309854	2		567	476	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0042210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	144	696	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	1	2	FACETS	0.989	0.902	1	0.989	0.902	1	CLONAL	1	TRUE	1	0.354819312715462	2		696	821	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0042210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1735	47	380	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.325034987722914	3	FACETS	0.175	0.146	0.207	0.058	0.048	0.069	SUBCLONAL	1	TRUE	0	0.354819312715462	3		380	1782	SUCCESS
CBL	867	MSKCC	GRCh37	11	119167743	119167743	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	41	502	1	ENST00000264033.4:c.2152C>T	p.Arg718Ter	p.R718*	ENST00000264033	NM_005188.3	718	Cga/Tga	13/16	1	2	FACETS	0.456	0.379	0.541	0.456	0.379	0.541	SUBCLONAL	1	TRUE	1	0.354819312715462	2		503	507	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057204	30057205	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CACA	novel	NA	P-0042210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	247	411	0	ENST00000338641.4:c.687_690dup	p.Glu231HisfsTer16	p.E231Hfs*16	ENST00000338641	NM_000268.3	229	ggc/ggCACAc	8/16	0.325034987722914	3	FACETS	0.92	0.867	0.973	0.92	0.867	0.973	CLONAL	3	TRUE	0	0.354819312715462	3		411	594	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0042214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	47	733	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	NA	2	FACETS	0.415	0.349	0.488			1	INDETERMINATE	1	TRUE	NA	0.308400845910177	2		733	735	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212381	5212381	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372226485	NA	P-0042214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	57	914	1	ENST00000357368.4:c.4736C>T	p.Pro1579Leu	p.P1579L	ENST00000357368	NM_002850.3	1579	cCg/cTg	31/38	1	2	FACETS	0.363	0.31	0.422	0.363	0.31	0.422	SUBCLONAL	1	TRUE	1	0.308400845910177	2		915	1017	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948865	17948865	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	43	678	0	ENST00000458235.1:c.1577A>G	p.Asn526Ser	p.N526S	ENST00000458235	NM_000215.3	526	aAc/aGc	12/24	1	2	FACETS	0.389	0.325	0.461	0.389	0.325	0.461	SUBCLONAL	1	TRUE	1	0.308400845910177	2		678	716	SUCCESS
ATR	545	MSKCC	GRCh37	3	142224126	142224126	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1197903798	NA	P-0042214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	49	202	0	ENST00000350721.4:c.5051A>G	p.His1684Arg	p.H1684R	ENST00000350721	NM_001184.3	1684	cAt/cGt	29/47	0.308400845910177	3	FACETS	1	0.95	1	0.646	0.55	0.749	CLONAL	1	TRUE	1	0.308400845910177	3		202	284	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032237	26032237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	48	290	0	ENST00000244661.2:c.52C>T	p.Arg18Cys	p.R18C	ENST00000244661	NM_003537.3	18	Cgc/Tgc	1/1	0.308400845910177	3	FACETS	0.968	0.821	1	0.484	0.41	0.565	CLONAL	1	TRUE	1	0.308400845910177	3		290	371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0042222-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	173	942	1	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	0.222559675832423	2	FACETS	0.861	0.792	0.932	0.861	0.792	0.932	CLONAL	2	TRUE	0	0.222559675832423	2		943	903	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376302	118376302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1052748793	NA	P-0042222-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	72	581	2	ENST00000534358.1:c.9695G>A	p.Arg3232Gln	p.R3232Q	ENST00000534358	NM_005933.3	3232	cGa/cAa	27/36	0.222559675832423	5	FACETS	1	0.939	1			1	CLONAL	1	TRUE	NA	0.222559675832423	5		583	763	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118666	11118666	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042222-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	91	858	0	ENST00000358026.2:c.2090A>C	p.Asp697Ala	p.D697A	ENST00000358026	NM_001128849.1	697	gAc/gCc	14/36	0.22204317973308	3	FACETS	0.79	0.7	0.888	0.263	0.233	0.296	SUBCLONAL	1	TRUE	0	0.222559675832423	3		858	1150	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0042222-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	91	942	1	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.16	2		943	997	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376302	118376302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1052748793	NA	P-0042222-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	21	581	2	ENST00000534358.1:c.9695G>A	p.Arg3232Gln	p.R3232Q	ENST00000534358	NM_005933.3	3232	cGa/cAa	27/36	1	2	FACETS	0.422	0.323	0.538	0.422	0.323	0.538	SUBCLONAL	1	TRUE	1	0.16	2		583	622	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118666	11118666	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042222-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	24	858	0	ENST00000358026.2:c.2090A>C	p.Asp697Ala	p.D697A	ENST00000358026	NM_001128849.1	697	gAc/gCc	14/36	1	2	FACETS	0.321	0.25	0.404	0.321	0.25	0.404	SUBCLONAL	1	TRUE	1	0.16	2		858	934	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0042278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	219	305	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.504934654281653	4	FACETS	0.838	0.788	0.89	1	0.989	1	CLONAL	3	TRUE	2	0.504934654281653	4		305	519	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69230513	69230513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	132	245	0	ENST00000462284.1:c.902C>T	p.Pro301Leu	p.P301L	ENST00000462284	NM_002392.5	301	cCt/cTt	10/11	0.43830725426629	4	FACETS	0.93	0.852	1	0.93	0.852	1	CLONAL	2	TRUE	2	0.504934654281653	4		245	423	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0042318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	103	609	2	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.864	0.773	0.96	0.864	0.773	0.96	CLONAL	1	TRUE	1	0.32	2		611	745	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557843	21558001	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACATAGACTTGTCCATCTTGGCCCTCTTTAACCTGTTGTAATTAGACTCTTTCTGGTAGAGGATCTTCCGCATCTGCTCCTGCTCAGCTTCACAGAGTCCAGCCTGTGTAGAAGGAAAAGGAAGGAGGAAGAATCACATTAGAGAAGTCCCATGATAAC	ACATAGACTTGTCCATCTTGGCCCTCTTTAACCTGTTGTAATTAGACTCTTTCTGGTAGAGGATCTTCCGCATCTGCTCCTGCTCAGCTTCACAGAGTCCAGCCTGTGTAGAAGGAAAAGGAAGGAGGAAGAATCACATTAGAGAAGTCCCATGATAAC	-	novel	NA	P-0042318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	66	714	0	ENST00000382592.4:c.1900-56_2002del		p.X634_splice	ENST00000382592	NM_014572.2	634		5/8	0.3	1	FACETS	0.499	0.432	0.571	0.499	0.432	0.571	SUBCLONAL	1	TRUE	0	0.32	1		714	695	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442613	52442613	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0042318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	72	270	0	ENST00000460680.1:c.132T>G	p.Tyr44Ter	p.Y44*	ENST00000460680	NM_004656.3	44	taT/taG	4/17	0.3	1	FACETS	0.995	0.874	1	0.995	0.874	1	CLONAL	1	TRUE	0	0.32	1		270	380	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288852	33288852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767991311	NA	P-0042318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	93	480	0	ENST00000374542.5:c.700C>T	p.Arg234Cys	p.R234C	ENST00000374542	NM_001141970.1	234	Cgc/Tgc	3/8	1	2	FACETS	0.958	0.853	1	0.958	0.853	1	CLONAL	1	TRUE	1	0.32	2		480	607	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937776	76937776	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	62	238	0	ENST00000373344.5:c.2972A>T	p.Glu991Val	p.E991V	ENST00000373344	NM_000489.3	991	gAa/gTa	9/35	1	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.32	1		238	234	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	106	737	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.89	0.808	0.973	0.89	0.808	0.973	CLONAL	1	TRUE	1	0.786391732213212	2		737	303	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0042344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	26	253	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.410132676530562	3	FACETS	0.153	0.12	0.19	0.076	0.06	0.095	INDETERMINATE	1	TRUE	1	0.786391732213212	3		253	603	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0042344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1872	13517	616	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.786391732213212	40	FACETS	0.989	0.985	0.993	0.913	0.909	0.917	CLONAL	36	TRUE	1	0.786391732213212	40		616	15389	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0042344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	222	404	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.786391732213212	1	FACETS	0.999	0.951	1	0.999	0.951	1	CLONAL	1	TRUE	0	0.786391732213212	1		404	343	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	495135	495135	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	41	347	0	ENST00000399788.2:c.171G>A	p.Trp57Ter	p.W57*	ENST00000399788	NM_001042603.1	57	tgG/tgA	2/28	NA	2	FACETS	0.252	0.21	0.299			1	INDETERMINATE	1	TRUE	NA	0.786391732213212	2		347	413	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285835	87285836	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGAGCCTAACAGTGTAGATCCTGAGAACA	novel	NA	P-0042344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	125	576	0	ENST00000277120.3:c.174_203dup	p.Asn67_Ile68insMetGluProAsnSerValAspProGluAsn	p.N67_I68insMEPNSVDPEN	ENST00000277120		58	ttg/tTGGAGCCTAACAGTGTAGATCCTGAGAACAtg	2/19	1	2	FACETS	0.485	0.439	0.532	0.485	0.439	0.532	SUBCLONAL	1	TRUE	1	0.786391732213212	2		576	656	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16174646	16174646	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	56	300	0	ENST00000375759.3:c.83+1G>A		p.X28_splice	ENST00000375759	NM_015001.2	28			1	2	FACETS	0.741	0.636	0.855	0.741	0.636	0.855	SUBCLONAL	1	TRUE	1	0.354015592374595	2		300	427	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255962	16255962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	86	514	0	ENST00000375759.3:c.3227C>T	p.Ser1076Phe	p.S1076F	ENST00000375759	NM_015001.2	1076	tCt/tTt	11/15	1	2	FACETS	0.701	0.62	0.788	0.701	0.62	0.788	SUBCLONAL	1	TRUE	1	0.354015592374595	2		514	693	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023048	27023048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	48	87	0	ENST00000324856.7:c.154G>A	p.Ala52Thr	p.A52T	ENST00000324856	NM_006015.4	52	Gca/Aca	1/20	1	2	FACETS	0.842	0.725	0.966	1	0.971	1	CLONAL	2	TRUE	1	0.354015592374595	2		87	161	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807562	36807562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	90	559	1	ENST00000373129.3:c.1102G>A	p.Glu368Lys	p.E368K	ENST00000373129	NM_032017.1	368	Gag/Aag	12/12	1	2	FACETS	0.704	0.625	0.789	0.704	0.625	0.789	SUBCLONAL	1	TRUE	1	0.354015592374595	2		560	722	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814560	43814560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	82	491	0	ENST00000372470.3:c.1355G>A	p.Arg452His	p.R452H	ENST00000372470	NM_005373.2	452	cGc/cAc	9/12	1	2	FACETS	0.82	0.724	0.922	0.82	0.724	0.922	CLONAL	1	TRUE	1	0.354015592374595	2		491	565	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512216	120512216	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	105	507	0	ENST00000256646.2:c.1026T>G	p.Cys342Trp	p.C342W	ENST00000256646	NM_024408.3	342	tgT/tgG	6/34	1	2	FACETS	0.743	0.666	0.826	0.743	0.666	0.826	SUBCLONAL	1	TRUE	1	0.354015592374595	2		507	798	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944292	206944292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	82	510	0	ENST00000423557.1:c.338G>A	p.Gly113Glu	p.G113E	ENST00000423557	NM_000572.2	113	gGg/gAg	3/5	1	2	FACETS	0.676	0.596	0.762	0.676	0.596	0.762	SUBCLONAL	1	TRUE	1	0.354015592374595	2		510	685	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115732	8115732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	63	375	0	ENST00000346208.3:c.1078G>A	p.Gly360Ser	p.G360S	ENST00000346208		360	Ggc/Agc	6/6	0.242730319699174	5	FACETS	0.786	0.679	0.903	0.157	0.135	0.181	CLONAL	1	TRUE	0	0.354015592374595	5		375	693	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325039	123325039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372430349	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	107	563	3	ENST00000358487.5:c.289G>A	p.Ala97Thr	p.A97T	ENST00000358487	NM_000141.4	97	Gcc/Acc	3/18	1	2	FACETS	0.727	0.652	0.808	0.727	0.652	0.808	SUBCLONAL	1	TRUE	1	0.354015592374595	2		566	831	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909954	100909954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	60	428	0	ENST00000325455.5:c.2695C>T	p.Arg899Trp	p.R899W	ENST00000325455	NM_001202474.3	899	Cgg/Tgg	8/8	1	2	FACETS	0.755	0.652	0.866	0.755	0.652	0.866	SUBCLONAL	1	TRUE	1	0.354015592374595	2		428	449	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427687	49427687	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	93	639	0	ENST00000301067.7:c.10801C>T	p.Gln3601Ter	p.Q3601*	ENST00000301067	NM_003482.3	3601	Caa/Taa	39/54	1	2	FACETS	0.707	0.629	0.791	0.707	0.629	0.791	SUBCLONAL	1	TRUE	1	0.354015592374595	2		639	743	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214600	133214600	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	62	407	1	ENST00000320574.5:c.5678G>A	p.Ser1893Asn	p.S1893N	ENST00000320574	NM_006231.2	1893	aGc/aAc	41/49	1	2	FACETS	0.688	0.595	0.789	0.688	0.595	0.789	SUBCLONAL	1	TRUE	1	0.354015592374595	2		408	509	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28631570	28631570	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	40	371	0	ENST00000241453.7:c.398T>C	p.Met133Thr	p.M133T	ENST00000241453	NM_004119.2	133	aTg/aCg	4/24	1	2	FACETS	0.457	0.38	0.544	0.457	0.38	0.544	SUBCLONAL	1	TRUE	1	0.354015592374595	2		371	494	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28631580	28631580	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	31	353	0	ENST00000241453.7:c.388A>C	p.Ile130Leu	p.I130L	ENST00000241453	NM_004119.2	130	Att/Ctt	4/24	1	2	FACETS	0.387	0.313	0.472	0.387	0.313	0.472	SUBCLONAL	1	TRUE	1	0.354015592374595	2		353	452	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28631595	28631595	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	28	321	0	ENST00000241453.7:c.373G>C	p.Val125Leu	p.V125L	ENST00000241453	NM_004119.2	125	Gtt/Ctt	4/24	1	2	FACETS	0.4	0.32	0.493	0.4	0.32	0.493	SUBCLONAL	1	TRUE	1	0.354015592374595	2		321	395	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931690	28931690	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	67	355	0	ENST00000282397.4:c.2248+1G>A		p.X750_splice	ENST00000282397	NM_002019.4	750			1	2	FACETS	0.804	0.7	0.915	0.804	0.7	0.915	CLONAL	1	TRUE	1	0.354015592374595	2		355	471	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434583	110434583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	163	574	1	ENST00000375856.3:c.3818C>T	p.Pro1273Leu	p.P1273L	ENST00000375856	NM_003749.2	1273	cCg/cTg	1/2	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.354015592374595	2		575	635	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133044	30133044	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	140	459	1	ENST00000331968.5:c.557A>G	p.Lys186Arg	p.K186R	ENST00000331968	NM_002742.2	186	aAg/aGg	4/18	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.354015592374595	2		460	539	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023081	33023081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750874632	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	48	486	1	ENST00000300177.4:c.190C>T	p.Arg64Trp	p.R64W	ENST00000300177	NM_001191322.1	64	Cgg/Tgg	2/2	1	2	FACETS	0.528	0.446	0.618	0.528	0.446	0.618	SUBCLONAL	1	TRUE	1	0.354015592374595	2		487	514	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961120	41961120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	78	283	0	ENST00000219905.7:c.28G>A	p.Ala10Thr	p.A10T	ENST00000219905	NM_001164273.1	10	Gct/Act	2/24	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.354015592374595	2		283	351	SUCCESS
BLM	641	MSKCC	GRCh37	15	91290701	91290701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	44	295	0	ENST00000355112.3:c.79C>T	p.Leu27Phe	p.L27F	ENST00000355112	NM_000057.2	27	Ctt/Ttt	2/22	1	2	FACETS	0.585	0.491	0.689	0.585	0.491	0.689	SUBCLONAL	1	TRUE	1	0.354015592374595	2		295	425	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138091	2138091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	234	760	0	ENST00000219476.3:c.5111C>T	p.Ser1704Phe	p.S1704F	ENST00000219476	NM_000548.3	1704	tCt/tTt	40/42	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.354015592374595	2		760	885	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778738	3778738	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	120	736	0	ENST00000262367.5:c.6310C>A	p.Arg2104Ser	p.R2104S	ENST00000262367	NM_004380.2	2104	Cgc/Agc	31/31	1	2	FACETS	0.786	0.709	0.867	0.786	0.709	0.867	SUBCLONAL	1	TRUE	1	0.354015592374595	2		736	863	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772204	68772204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	169	641	1	ENST00000261769.5:c.53C>T	p.Ser18Phe	p.S18F	ENST00000261769	NM_004360.3	18	tCc/tTc	2/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.354015592374595	2		642	767	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830196	72830196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	73	535	1	ENST00000268489.5:c.6385G>A	p.Ala2129Thr	p.A2129T	ENST00000268489	NM_006885.3	2129	Gcc/Acc	9/10	1	2	FACETS	0.686	0.6	0.779	0.686	0.6	0.779	SUBCLONAL	1	TRUE	1	0.354015592374595	2		536	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579592	7579592	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	498	510	0	ENST00000269305.4:c.97-2A>C		p.X33_splice	ENST00000269305	NM_001126112.2	33			NA	2	FACETS	1	0.996	1			1	INDETERMINATE	4	TRUE	NA	0.354015592374595	2		510	626	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965476	15965476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	61	425	0	ENST00000268712.3:c.5330G>A	p.Gly1777Glu	p.G1777E	ENST00000268712	NM_006311.3	1777	gGa/gAa	36/46	1	2	FACETS	0.581	0.501	0.668	0.581	0.501	0.668	SUBCLONAL	1	TRUE	1	0.354015592374595	2		425	593	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554693	63554693	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	80	482	0	ENST00000307078.5:c.46A>G	p.Ser16Gly	p.S16G	ENST00000307078	NM_004655.3	16	Agc/Ggc	2/11	1	2	FACETS	0.715	0.63	0.807	0.715	0.63	0.807	SUBCLONAL	1	TRUE	1	0.354015592374595	2		482	632	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774689	73774689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	14	48	0	ENST00000254810.4:c.398G>A	p.Gly133Glu	p.G133E	ENST00000254810	NM_005324.3	133	gGa/gAa	4/4	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.354015592374595	2		48	62	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144146	11144146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	132	651	1	ENST00000358026.2:c.3727C>T	p.Arg1243Trp	p.R1243W	ENST00000358026	NM_001128849.1	1243	Cgg/Tgg	26/36	1	2	FACETS	0.885	0.803	0.97	0.885	0.803	0.97	CLONAL	1	TRUE	1	0.354015592374595	2		652	843	SUCCESS
AXL	558	MSKCC	GRCh37	19	41736913	41736913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779718472	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	100	716	0	ENST00000301178.4:c.628G>A	p.Ala210Thr	p.A210T	ENST00000301178	NM_021913.4	210	Gcc/Acc	5/20	1	2	FACETS	0.652	0.581	0.727	0.652	0.581	0.727	SUBCLONAL	1	TRUE	1	0.354015592374595	2		716	867	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752919	42752919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329486990	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	63	870	0	ENST00000222329.4:c.1345G>A	p.Glu449Lys	p.E449K	ENST00000222329	NM_006494.2	449	Gaa/Aaa	4/4	1	2	FACETS	0.359	0.309	0.413	0.359	0.309	0.413	SUBCLONAL	1	TRUE	1	0.354015592374595	2		870	992	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858922	45858922	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	128	644	1	ENST00000391945.4:c.1543+1G>A		p.X515_splice	ENST00000391945	NM_000400.3	515			1	2	FACETS	0.813	0.737	0.894	0.813	0.737	0.894	CLONAL	1	TRUE	1	0.354015592374595	2		645	889	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731472	47731472	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	16	61	0	ENST00000449228.1:c.320G>A	p.Gly107Glu	p.G107E	ENST00000449228	NM_001127240.2	107	gGg/gAg	2/4	1	2	FACETS	0.747	0.558	0.968	0.747	0.558	0.968	CLONAL	1	TRUE	1	0.354015592374595	2		61	121	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716250	52716250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769334090	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	52	656	0	ENST00000322088.6:c.694G>A	p.Ala232Thr	p.A232T	ENST00000322088	NM_014225.5	232	Gcc/Acc	6/15	1	2	FACETS	0.394	0.335	0.46	0.394	0.335	0.46	SUBCLONAL	1	TRUE	1	0.354015592374595	2		656	745	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47604193	47604193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	128	366	0	ENST00000263735.4:c.532C>T	p.Pro178Ser	p.P178S	ENST00000263735	NM_002354.2	178	Cca/Tca	5/9	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.354015592374595	2		366	525	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182132	99182132	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	96	505	0	ENST00000074304.5:c.2197A>G	p.Ser733Gly	p.S733G	ENST00000074304	NM_001134224.1	733	Agc/Ggc	21/26	1	2	FACETS	0.912	0.814	1	0.912	0.814	1	CLONAL	1	TRUE	1	0.354015592374595	2		505	595	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	119	288	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.92	1	1	0.99	1	CLONAL	2	TRUE	1	0.354015592374595	2		288	334	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989562	212989562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755026855	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	79	369	1	ENST00000342788.4:c.149G>A	p.Arg50His	p.R50H	ENST00000342788	NM_005235.2	50	cGc/cAc	2/28	1	2	FACETS	0.85	0.749	0.958	0.85	0.749	0.958	CLONAL	1	TRUE	1	0.354015592374595	2		370	525	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660094	227660094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	148	617	0	ENST00000305123.5:c.3361G>A	p.Ala1121Thr	p.A1121T	ENST00000305123	NM_005544.2	1121	Gcg/Acg	1/2	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.354015592374595	2		617	645	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419876	41419876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	81	559	1	ENST00000373198.4:c.445G>A	p.Ala149Thr	p.A149T	ENST00000373198	NM_133170.3	149	Gca/Aca	3/32	1	2	FACETS	0.6	0.528	0.677	0.6	0.528	0.677	SUBCLONAL	1	TRUE	1	0.354015592374595	2		560	763	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321674	62321674	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	54	679	0	ENST00000360203.5:c.2293G>T	p.Ala765Ser	p.A765S	ENST00000360203	NM_001283009.1	765	Gca/Tca	26/35	1	2	FACETS	0.402	0.342	0.467	0.402	0.342	0.467	SUBCLONAL	1	TRUE	1	0.354015592374595	2		679	759	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665421	182665421	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	45	188	0	ENST00000292782.4:c.521-1G>A		p.X174_splice	ENST00000292782	NM_020640.2	174			1	2	FACETS	0.794	0.68	0.917	1	0.967	1	CLONAL	2	TRUE	1	0.354015592374595	2		188	160	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55597546	55597546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	77	407	0	ENST00000288135.5:c.2194G>A	p.Val732Ile	p.V732I	ENST00000288135	NM_000222.2	732	Gtc/Atc	15/21	1	2	FACETS	0.726	0.638	0.821	0.726	0.638	0.821	SUBCLONAL	1	TRUE	1	0.354015592374595	2		407	599	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99812388	99812388	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	55	393	1	ENST00000280892.6:c.281C>T	p.Ala94Val	p.A94V	ENST00000280892	NM_001130678.1	94	gCt/gTt	3/7	1	2	FACETS	0.594	0.508	0.688	0.594	0.508	0.688	SUBCLONAL	1	TRUE	1	0.354015592374595	2		394	523	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531166	187531166	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	27	307	1	ENST00000441802.2:c.9857C>T	p.Ala3286Val	p.A3286V	ENST00000441802	NM_005245.3	3286	gCc/gTc	15/27	1	2	FACETS	0.418	0.332	0.516	0.418	0.332	0.516	SUBCLONAL	1	TRUE	1	0.354015592374595	2		308	365	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630642	187630642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	71	495	0	ENST00000441802.2:c.340G>A	p.Asp114Asn	p.D114N	ENST00000441802	NM_005245.3	114	Gat/Aat	2/27	1	2	FACETS	0.662	0.578	0.753	0.662	0.578	0.753	SUBCLONAL	1	TRUE	1	0.354015592374595	2		495	606	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294123	1294123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1309920442	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	154	846	1	ENST00000310581.5:c.878G>A	p.Arg293His	p.R293H	ENST00000310581	NM_198253.2	293	cGc/cAc	2/16	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.354015592374595	2		847	839	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911583	131911583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	37	346	0	ENST00000265335.6:c.328G>A	p.Glu110Lys	p.E110K	ENST00000265335		110	Gaa/Aaa	3/25	1	2	FACETS	0.559	0.461	0.668	0.559	0.461	0.668	SUBCLONAL	1	TRUE	1	0.354015592374595	2		346	374	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953835	131953835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	44	326	0	ENST00000265335.6:c.3238G>A	p.Gly1080Ser	p.G1080S	ENST00000265335		1080	Ggt/Agt	21/25	1	2	FACETS	0.675	0.568	0.794	0.675	0.568	0.794	SUBCLONAL	1	TRUE	1	0.354015592374595	2		326	368	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513451	149513451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754451292	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	104	596	3	ENST00000261799.4:c.752G>A	p.Arg251His	p.R251H	ENST00000261799	NM_002609.3	251	cGc/cAc	5/23	1	2	FACETS	0.829	0.742	0.92	0.829	0.742	0.92	CLONAL	1	TRUE	1	0.354015592374595	2		599	709	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394999	394999	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	77	420	0	ENST00000380956.4:c.395C>T	p.Ala132Val	p.A132V	ENST00000380956	NM_001195286.1	132	gCc/gTc	3/9	1	2	FACETS	0.761	0.668	0.859	0.761	0.668	0.859	SUBCLONAL	1	TRUE	1	0.354015592374595	2		420	572	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323943	31323943	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	105	381	0	ENST00000412585.2:c.619+1G>A		p.X207_splice	ENST00000412585	NM_005514.6	207			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.354015592374595	2		381	445	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120780	94120780	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	70	494	0	ENST00000369303.4:c.271T>C	p.Ser91Pro	p.S91P	ENST00000369303	NM_004440.3	91	Tcc/Ccc	3/17	1	2	FACETS	0.599	0.522	0.683	0.599	0.522	0.683	SUBCLONAL	1	TRUE	1	0.354015592374595	2		494	660	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536181	106536181	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	76	467	0	ENST00000369096.4:c.148A>G	p.Thr50Ala	p.T50A	ENST00000369096	NM_001198.3	50	Aca/Gca	2/7	1	2	FACETS	0.744	0.653	0.842	0.744	0.653	0.842	SUBCLONAL	1	TRUE	1	0.354015592374595	2		467	577	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553506	106553506	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	155	411	0	ENST00000369096.4:c.1471G>A	p.Ala491Thr	p.A491T	ENST00000369096	NM_001198.3	491	Gcg/Acg	5/7	1	2	FACETS	0.847	0.78	0.915	1	0.991	1	CLONAL	2	TRUE	1	0.354015592374595	2		411	517	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043632	6043632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	20	297	0	ENST00000265849.7:c.221G>A	p.Gly74Glu	p.G74E	ENST00000265849	NM_000535.5	74	gGg/gAg	3/15	0.354015592374595	0	FACETS	0.629	0.488	0.79			1	SUBCLONAL	1	TRUE	0	0.354015592374595	0		297	116	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13949274	13949274	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	63	335	0	ENST00000405192.2:c.854T>C	p.Val285Ala	p.V285A	ENST00000405192	NM_001163147.1	285	gTc/gCc	9/12	1	2	FACETS	0.997	0.867	1	0.997	0.867	1	CLONAL	1	TRUE	1	0.354015592374595	2		335	357	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467736	50467736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	160	657	2	ENST00000331340.3:c.971C>T	p.Ala324Val	p.A324V	ENST00000331340	NM_006060.4	324	gCc/gTc	8/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.354015592374595	2		659	714	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518270	8518270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556357771	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	57	293	1	ENST00000356435.5:c.1121C>T	p.Ala374Val	p.A374V	ENST00000356435		374	gCg/gTg	10/35	0.354015592374595	1	FACETS	0.678	0.584	0.78	0.678	0.584	0.78	SUBCLONAL	1	TRUE	0	0.354015592374595	1		294	391	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521462	8521462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767340559	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	57	648	0	ENST00000356435.5:c.776C>T	p.Ala259Val	p.A259V	ENST00000356435		259	gCc/gTc	9/35	0.354015592374595	1	FACETS	0.323	0.276	0.374	0.323	0.276	0.374	SUBCLONAL	1	TRUE	0	0.354015592374595	1		648	821	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209363	98209363	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	34	606	0	ENST00000331920.6:c.4175A>C	p.Asn1392Thr	p.N1392T	ENST00000331920	NM_000264.3	1392	aAc/aCc	23/24	0.354015592374595	1	FACETS	0.251	0.204	0.304	0.251	0.204	0.304	SUBCLONAL	1	TRUE	0	0.354015592374595	1		606	629	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328323	137328323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	91	619	1	ENST00000481739.1:c.1252C>T	p.Leu418Phe	p.L418F	ENST00000481739	NM_002957.4	418	Ctc/Ttc	10/10	0.354015592374595	1	FACETS	0.552	0.489	0.618	0.552	0.489	0.618	SUBCLONAL	1	TRUE	0	0.354015592374595	1		620	767	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412252	139412252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057523819	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	507	778	0	ENST00000277541.6:c.1393G>A	p.Ala465Thr	p.A465T	ENST00000277541	NM_017617.3	465	Gcc/Acc	8/34	0.354015592374595	1	FACETS	0.873	0.842	0.904	1	0.998	1	CLONAL	3	TRUE	0	0.354015592374595	1		778	900	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923118	39923118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs952105723	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	53	306	0	ENST00000378444.4:c.3590G>A	p.Cys1197Tyr	p.C1197Y	ENST00000378444	NM_001123385.1	1197	tGc/tAc	8/15	1	1	FACETS	0.523	0.447	0.607	0.523	0.447	0.607	SUBCLONAL	1	TRUE	0	0.354015592374595	1		306	471	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650795	48650795	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	237	399	0	ENST00000376670.3:c.664C>T	p.His222Tyr	p.H222Y	ENST00000376670	NM_002049.3	222	Cac/Tac	4/6	1	1	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	0	0.354015592374595	1		399	465	SUCCESS
AR	367	MSKCC	GRCh37	X	66765635	66765635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	211	407	0	ENST00000374690.3:c.647G>A	p.Gly216Glu	p.G216E	ENST00000374690	NM_000044.3	216	gGg/gAg	1/8	1	1	FACETS	1	0.97	1	1	0.995	1	CLONAL	2	TRUE	0	0.354015592374595	1		407	466	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829753	76829756	+	frameshift_variant	Frame_Shift_Del	DEL	CTTC	CTTC	-	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	193	297	0	ENST00000373344.5:c.6285_6288del	p.Lys2096SerfsTer12	p.K2096Sfs*12	ENST00000373344	NM_000489.3	2095	agGAAG/ag	28/35	1	1	FACETS	1	0.986	1	1	0.995	1	CLONAL	3	TRUE	0	0.354015592374595	1		297	272	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179032	123179032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	21	263	0	ENST00000218089.9:c.481C>T	p.Leu161Phe	p.L161F	ENST00000218089	NM_001042749.1	161	Ctt/Ttt	8/35	1	1	FACETS	0.354	0.272	0.448	0.354	0.272	0.448	SUBCLONAL	1	TRUE	0	0.354015592374595	1		263	276	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398286	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0042415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	68	327	0	ENST00000311936.3:c.33_34delinsCT	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	11	gcTGgt/gcCTgt	2/5	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.27	2		327	425	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040995	47040995	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	151	707	0	ENST00000377604.3:c.1525C>T	p.Gln509Ter	p.Q509*	ENST00000377604	NM_001204468.1	509	Caa/Taa	14/24	1	2	FACETS	0.849	0.774	0.928	0.849	0.774	0.928	CLONAL	1	TRUE	1	0.27	2		707	1317	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413115	63413115	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	100	709	1	ENST00000330258.3:c.52G>T	p.Gly18Trp	p.G18W	ENST00000330258	NM_152424.3	18	Ggg/Tgg	2/2	1	2	FACETS	0.64	0.57	0.715	0.64	0.57	0.715	SUBCLONAL	1	TRUE	1	0.27	2		710	1158	SUCCESS
ATM	472	MSKCC	GRCh37	11	108099945	108099945	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0042415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	29	245	0	ENST00000278616.4:c.226A>T	p.Arg76Ter	p.R76*	ENST00000278616	NM_000051.3	76	Aga/Tga	4/63	1	2	FACETS	0.985	0.796	1	0.985	0.796	1	CLONAL	1	TRUE	1	0.27	2		245	218	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165705	108165705	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	29	329	0	ENST00000278616.4:c.4828A>G	p.Arg1610Gly	p.R1610G	ENST00000278616	NM_000051.3	1610	Aga/Gga	32/63	1	2	FACETS	0.524	0.42	0.642	0.524	0.42	0.642	SUBCLONAL	1	TRUE	1	0.27	2		329	410	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061225	38061225	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	113	547	0	ENST00000250448.2:c.764A>T	p.Glu255Val	p.E255V	ENST00000250448	NM_004496.3	255	gAg/gTg	2/2	0.3	3	FACETS	0.844	0.758	0.936	0.422	0.379	0.468	CLONAL	1	TRUE	1	0.27	3		547	1125	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828282	72828282	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	45	527	0	ENST00000268489.5:c.8299G>T	p.Gly2767Ter	p.G2767*	ENST00000268489	NM_006885.3	2767	Gga/Tga	9/10	1	2	FACETS	0.393	0.329	0.464	0.393	0.329	0.464	SUBCLONAL	1	TRUE	1	0.27	2		527	849	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142881	7142881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	164	638	0	ENST00000302850.5:c.2488C>T	p.Pro830Ser	p.P830S	ENST00000302850	NM_000208.2	830	Cct/Tct	12/22	0.228306949923601	2	FACETS	1	0.964	1	0.547	0.501	0.595	CLONAL	1	TRUE	0	0.27	2		638	1110	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044524	128044524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1433368312	NA	P-0042415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	57	533	0	ENST00000285398.2:c.1097A>T	p.Asn366Ile	p.N366I	ENST00000285398	NM_000122.1	366	aAc/aTc	8/15	1	2	FACETS	0.49	0.419	0.568	0.49	0.419	0.568	SUBCLONAL	1	TRUE	1	0.27	2		533	861	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660138	227660138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1448309277	NA	P-0042415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	83	604	0	ENST00000305123.5:c.3317C>T	p.Ser1106Leu	p.S1106L	ENST00000305123	NM_005544.2	1106	tCa/tTa	1/2	1	2	FACETS	0.587	0.517	0.663	0.587	0.517	0.663	SUBCLONAL	1	TRUE	1	0.27	2		604	1047	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628434	187628434	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	69	749	1	ENST00000441802.2:c.2548G>T	p.Asp850Tyr	p.D850Y	ENST00000441802	NM_005245.3	850	Gac/Tac	2/27	1	2	FACETS	0.469	0.407	0.537	0.469	0.407	0.537	SUBCLONAL	1	TRUE	1	0.27	2		750	1089	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513452	149513452	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	59	573	1	ENST00000261799.4:c.751del	p.Arg251AlafsTer11	p.R251Afs*11	ENST00000261799	NM_002609.3	251	Cgc/gc	5/23	1	2	FACETS	0.458	0.393	0.53	0.458	0.393	0.53	SUBCLONAL	1	TRUE	1	0.27	2		574	954	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410373	63410373	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	134	714	0	ENST00000330258.3:c.2794G>T	p.Asp932Tyr	p.D932Y	ENST00000330258	NM_152424.3	932	Gac/Tac	2/2	1	2	FACETS	0.806	0.731	0.886	0.806	0.731	0.886	CLONAL	1	TRUE	1	0.27	2		714	1231	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220694	1220701	+	frameshift_variant	Frame_Shift_Del	DEL	ATCTGGTC	ATCTGGTC	T	novel	NA	P-0042415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	239	838	0	ENST00000326873.7:c.712_719delinsT	p.Ile238TrpfsTer47	p.I238Wfs*47	ENST00000326873	NM_000455.4	238	ATCTGGTCg/Tg	5/10	0.228306949923601	2	FACETS	0.792	0.739	0.847	0.792	0.739	0.847	SUBCLONAL	2	TRUE	0	0.27	2		838	1117	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0042501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	22	279	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.313775633969249	1	FACETS	0.54	0.42	0.678	0.54	0.42	0.678	SUBCLONAL	1	TRUE	0	0.313775633969249	1		279	219	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0042501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	50	288	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.313775633969249	2		288	232	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101649	27101667	+	frameshift_variant	Frame_Shift_Del	DEL	GCTCTGTTGAAGCCACACA	GCTCTGTTGAAGCCACACA	-	novel	NA	P-0042501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	234	917	0	ENST00000324856.7:c.4933_4951del	p.Ser1645LeufsTer3	p.S1645Lfs*3	ENST00000324856	NM_006015.4	1644	gGCTCTGTTGAAGCCACACAg/gg	18/20	0.313775633969249	1	FACETS	0.755	0.706	0.805	1	0.992	1	SUBCLONAL	2	TRUE	0	0.313775633969249	1		917	833	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441219	52441219	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060503729	NA	P-0042501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	91	427	0	ENST00000460680.1:c.551A>G	p.Asp184Gly	p.D184G	ENST00000460680	NM_004656.3	184	gAt/gGt	7/17	0.313775633969249	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.313775633969249	1		427	394	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	143	737	0				ENST00000310581	NM_198253.2	-/1132			0.345004818051152	1	FACETS	0.708	0.652	0.766	0.708	0.652	0.766	INDETERMINATE	1	TRUE	0	0.653460759972611	1		737	416	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562657	29562660	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs1064794276	NA	P-0042510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	118	472	0	ENST00000356175.3:c.3739_3742del	p.Phe1247IlefsTer18	p.F1247Ifs*18	ENST00000356175	NM_000267.3	1246	cTGTTt/ct	28/57	0.620405568467186	1	FACETS	0.769	0.704	0.837	0.769	0.704	0.837	SUBCLONAL	1	TRUE	0	0.653460759972611	1		472	316	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653846	89653846	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762518389	NA	P-0042510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	59	283	0	ENST00000371953.3:c.144C>A	p.Asn48Lys	p.N48K	ENST00000371953	NM_000314.4	48	aaC/aaA	2/9	0.653460759972611	1	FACETS	0.85	0.751	0.951	0.85	0.751	0.951	CLONAL	1	TRUE	0	0.653460759972611	1		283	143	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280287	1280287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147521473	NA	P-0042510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	373	999	2	ENST00000310581.5:c.1936C>T	p.Arg646Cys	p.R646C	ENST00000310581	NM_198253.2	646	Cgc/Tgc	4/16	0.345004818051152	1	FACETS	0.668	0.635	0.703	0.668	0.635	0.703	INDETERMINATE	1	TRUE	0	0.653460759972611	1		1001	1150	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0042523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	224	601	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.220732607675296	3	FACETS	1	0.979	1	0.742	0.693	0.793	CLONAL	2	TRUE	0	0.282397161414259	3		601	813	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	111	309	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.24204473723655	4	FACETS	0.928	0.838	1	0.928	0.838	1	CLONAL	2	TRUE	2	0.282397161414259	4		309	543	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0042523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	119	191	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.256277289620575	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.282397161414259	2		191	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	285	789	0	ENST00000269305.4:c.481G>T	p.Ala161Ser	p.A161S	ENST00000269305	NM_001126112.2	161	Gcc/Tcc	5/11	0.343906096518101	3	FACETS	0.952	0.896	1	0.952	0.896	1	CLONAL	2	TRUE	1	0.343906096518101	3		789	1020	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	110	558	1	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.343906096518101	3	FACETS	1	0.941	1	0.533	0.479	0.59	CLONAL	1	TRUE	1	0.343906096518101	3		559	703	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788618	3788618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398124146	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	108	430	0	ENST00000262367.5:c.4336C>T	p.Arg1446Cys	p.R1446C	ENST00000262367	NM_004380.2	1446	Cgc/Tgc	26/31	0.343906096518101	3	FACETS	0.936	0.848	1	0.936	0.848	1	CLONAL	2	TRUE	1	0.343906096518101	3		430	393	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112265	115112265	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	19	95	0	ENST00000257566.3:c.1475A>T	p.His492Leu	p.H492L	ENST00000257566	NM_016569.3	492	cAc/cTc	7/8	1	2	FACETS	0.978	0.753	1	0.978	0.753	1	CLONAL	1	TRUE	1	0.343906096518101	2		95	113	SUCCESS
APC	324	MSKCC	GRCh37	5	112177001	112177001	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	14	423	0	ENST00000257430.4:c.5710C>T	p.Gln1904Ter	p.Q1904*	ENST00000257430	NM_000038.5	1904	Caa/Taa	16/16	0.293414729166905	2	FACETS	0.384	0.278	0.512	0.192	0.139	0.256	SUBCLONAL	1	TRUE	0	0.343906096518101	2		423	212	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247280	153247280	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	53	357	0	ENST00000281708.4:c.1522C>T	p.Gln508Ter	p.Q508*	ENST00000281708	NM_033632.3	508	Caa/Taa	10/12	0.307439025186985	3	FACETS	1	0.964	1	0.714	0.614	0.821	CLONAL	1	TRUE	1	0.343906096518101	3		357	253	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524698	106524698	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	11	248	0	ENST00000359195.3:c.2859G>C	p.Met953Ile	p.M953I	ENST00000359195	NM_002649.2	953	atG/atC	9/11	0.307439025186985	3	FACETS	0.564	0.391	0.776	0.282	0.195	0.388	SUBCLONAL	1	TRUE	1	0.343906096518101	3		248	133	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406219	70406220	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	43	549	0	ENST00000373644.4:c.3733_3734delinsAG	p.Gln1245Arg	p.Q1245R	ENST00000373644	NM_030625.2	1245	CAg/AGg	4/12	1	2	FACETS	0.851	0.716	0.999	0.851	0.716	0.999	CLONAL	1	TRUE	1	0.343906096518101	2		549	294	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112570	115112570	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	161	783	1	ENST00000257566.3:c.1170C>A	p.Cys390Ter	p.C390*	ENST00000257566	NM_016569.3	390	tgC/tgA	7/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.343906096518101	2		784	837	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636205	28636205	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	169	402	0	ENST00000241453.7:c.167T>C	p.Val56Ala	p.V56A	ENST00000241453	NM_004119.2	56	gTa/gCa	3/24	0.313861514006314	3	FACETS	0.873	0.811	0.936	0.873	0.811	0.936	CLONAL	3	TRUE	0	0.343906096518101	3		402	440	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134001	41134001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	272	491	0	ENST00000379561.5:c.1627G>A	p.Val543Ile	p.V543I	ENST00000379561	NM_002015.3	543	Gta/Ata	2/3	0.313861514006314	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	0	0.343906096518101	3		491	589	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050980	49050980	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	42	255	0	ENST00000267163.4:c.2663+1G>C		p.X888_splice	ENST00000267163	NM_000321.2	888			0.313861514006314	3	FACETS	0.967	0.823	1	0.645	0.548	0.747	CLONAL	2	TRUE	0	0.343906096518101	3		255	148	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713288	43713288	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	160	955	2	ENST00000382044.4:c.4185G>T	p.Lys1395Asn	p.K1395N	ENST00000382044	NM_001141980.1	1395	aaG/aaT	20/28	0.343906096518101	2	FACETS	1	0.937	1	0.513	0.47	0.558	CLONAL	1	TRUE	0	0.343906096518101	2		957	907	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347503	347872	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGAGCCAGGGTCGGGCTGTGTCCCCTAACCTTCATCTCCCACCTGAGGTCACGGCGTGGACTCCCCTGACCCAGGGCCCAGTCCACTCCCTCCAGCAGAGGGGCCTCCTGCCTGTTGCTGGCGGTCCTGGGTTTCCTGAGTTTTATGAGGAGGTTCTGGCCTTCTGCAGGGACACAGCCTCACCCCAAGCCCCCTCCTCACTGACAGGCGCACGCTCACCTGTGGGCGAGGCCATCACTGGCGTTGGGGGCAGCGCCAACACTCTCTGAGTAGCCTCGGGACCTTGCCCCATGGCTGTGTGGTTCCAGGCCCCAGGCGAAGCTGCTCTGGGCCCTGCGGGTGGCCTCGGCCTCCACCTGCTCCTTGGGCC	GGAGCCAGGGTCGGGCTGTGTCCCCTAACCTTCATCTCCCACCTGAGGTCACGGCGTGGACTCCCCTGACCCAGGGCCCAGTCCACTCCCTCCAGCAGAGGGGCCTCCTGCCTGTTGCTGGCGGTCCTGGGTTTCCTGAGTTTTATGAGGAGGTTCTGGCCTTCTGCAGGGACACAGCCTCACCCCAAGCCCCCTCCTCACTGACAGGCGCACGCTCACCTGTGGGCGAGGCCATCACTGGCGTTGGGGGCAGCGCCAACACTCTCTGAGTAGCCTCGGGACCTTGCCCCATGGCTGTGTGGTTCCAGGCCCCAGGCGAAGCTGCTCTGGGCCCTGCGGGTGGCCTCGGCCTCCACCTGCTCCTTGGGCC	-	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	170	58	0	ENST00000262320.3:c.1634_1784+219del		p.X545_splice	ENST00000262320	NM_003502.3	545		6/11	0.343906096518101	3	FACETS	1	0.991	1	1	0.995	1	CLONAL	6	TRUE	1	0.343906096518101	3		58	182	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129401	2129401	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	149	761	0	ENST00000219476.3:c.3256G>C	p.Gly1086Arg	p.G1086R	ENST00000219476	NM_000548.3	1086	Ggg/Cgg	28/42	0.343906096518101	3	FACETS	0.941	0.859	1	0.471	0.429	0.514	CLONAL	1	TRUE	1	0.343906096518101	3		761	1079	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81968081	81968081	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	58	490	0	ENST00000359376.3:c.2787G>C	p.Glu929Asp	p.E929D	ENST00000359376	NM_002661.3	929	gaG/gaC	26/33	0.313861514006314	3	FACETS	0.691	0.594	0.797	0.23	0.198	0.266	SUBCLONAL	1	TRUE	0	0.343906096518101	3		490	572	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097625	11097625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759641262	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	434	868	4	ENST00000358026.2:c.805C>T	p.Pro269Ser	p.P269S	ENST00000358026	NM_001128849.1	269	Ccc/Tcc	5/36	0.313861514006314	3	FACETS	0.967	0.925	1	0.967	0.925	1	CLONAL	3	TRUE	0	0.343906096518101	3		872	1020	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455261	29455261	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1353170300	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	211	569	0	ENST00000389048.3:c.2541G>T	p.Arg847Ser	p.R847S	ENST00000389048	NM_004304.4	847	agG/agT	15/29	0.307439025186985	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.343906096518101	3		569	608	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737488	204737488	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	24	381	0	ENST00000302823.3:c.625C>A	p.Pro209Thr	p.P209T	ENST00000302823	NM_005214.4	209	Cca/Aca	4/4	0.307439025186985	3	FACETS	0.798	0.629	0.99	0.399	0.314	0.495	CLONAL	1	TRUE	1	0.343906096518101	3		381	205	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645752	215645752	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	19	444	1	ENST00000260947.4:c.846G>T	p.Leu282Phe	p.L282F	ENST00000260947	NM_000465.2	282	ttG/ttT	4/11	0.307439025186985	3	FACETS	0.608	0.463	0.777	0.304	0.231	0.389	SUBCLONAL	1	TRUE	1	0.343906096518101	3		445	213	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845411	42845411	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	201	633	0	ENST00000398585.3:c.851A>T	p.Asn284Ile	p.N284I	ENST00000398585	NM_001135099.1	284	aAc/aTc	9/14	0.343906096518101	3	FACETS	1	0.991	1	0.746	0.692	0.802	CLONAL	1	TRUE	1	0.343906096518101	3		633	918	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920394	134920394	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	89	576	1	ENST00000398015.3:c.2209G>T	p.Glu737Ter	p.E737*	ENST00000398015	NM_004441.4	737	Gag/Tag	12/16	0.301212725830964	5	FACETS	1	0.949	1	0.375	0.332	0.42	CLONAL	1	TRUE	2	0.343906096518101	5		577	698	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55991426	55991426	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	148	758	0	ENST00000263923.4:c.35G>T	p.Trp12Leu	p.W12L	ENST00000263923	NM_002253.2	12	tGg/tTg	1/30	0.307439025186985	3	FACETS	1	0.952	1	0.531	0.485	0.58	CLONAL	1	TRUE	1	0.343906096518101	3		758	949	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535422	66535423	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	68	204	3	ENST00000273854.3:c.38_39delinsCT	p.Arg13Pro	p.R13P	ENST00000273854	NM_004439.5	13	cGG/cCT	1/18	0.307439025186985	3	FACETS	1	0.974	1	0.743	0.651	0.84	CLONAL	1	TRUE	1	0.343906096518101	3		207	312	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235377	235377	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748683825	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1394	118	646	0	ENST00000264932.6:c.1183G>A	p.Val395Ile	p.V395I	ENST00000264932	NM_004168.2	395	Gtc/Atc	9/15	0.343906096518101	8	FACETS	0.922	0.829	1	0.154	0.138	0.171	CLONAL	1	TRUE	2	0.343906096518101	8		646	1512	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279519	1279519	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs948721412	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1696	320	924	0	ENST00000310581.5:c.2017C>T	p.Pro673Ser	p.P673S	ENST00000310581	NM_198253.2	673	Ccc/Tcc	5/16	0.343906096518101	8	FACETS	0.938	0.882	0.996	0.313	0.294	0.332	CLONAL	2	TRUE	2	0.343906096518101	8		924	2016	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517459	176517459	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs572098218	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	213	744	0	ENST00000292408.4:c.160C>A	p.Arg54Ser	p.R54S	ENST00000292408	NM_213647.1	54	Cgt/Agt	3/18	0.293414729166905	2	FACETS	0.924	0.863	0.987	0.924	0.863	0.987	CLONAL	2	TRUE	0	0.343906096518101	2		744	670	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638642	176638642	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	129	618	0	ENST00000439151.2:c.3242G>T	p.Gly1081Val	p.G1081V	ENST00000439151	NM_022455.4	1081	gGg/gTg	5/23	0.293414729166905	2	FACETS	1	0.986	1	0.749	0.683	0.817	CLONAL	1	TRUE	0	0.343906096518101	2		618	501	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469985	157469985	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	135	550	0	ENST00000346085.5:c.2779G>C	p.Gly927Arg	p.G927R	ENST00000346085	NM_020732.3	927	Gga/Cga	9/20	0.343906096518101	3	FACETS	0.966	0.885	1	0.966	0.885	1	CLONAL	2	TRUE	1	0.343906096518101	3		550	476	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211005	55211005	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	51	428	0	ENST00000275493.2:c.248A>T	p.Gln83Leu	p.Q83L	ENST00000275493	NM_005228.3	83	cAg/cTg	3/28	0.307439025186985	3	FACETS	1	0.963	1	0.718	0.616	0.827	CLONAL	1	TRUE	1	0.343906096518101	3		428	242	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859801	151859802	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	25	300	0	ENST00000262189.6:c.10860_10861delinsTT	p.Lys3620_Ala3621delinsAsnSer	p.K3620_A3621delinsNS	ENST00000262189	NM_170606.2	3620	aaGGct/aaTTct	43/59	0.307439025186985	3	FACETS	0.827	0.656	1	0.414	0.328	0.511	CLONAL	1	TRUE	1	0.343906096518101	3		300	206	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372226	55372226	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	83	259	0	ENST00000297316.4:c.916G>T	p.Gly306Cys	p.G306C	ENST00000297316	NM_022454.3	306	Ggc/Tgc	2/2	0.191334529182018	2	FACETS	1	0.929	1	0.533	0.472	0.597	INDETERMINATE	1	TRUE	0	0.343906096518101	2		259	453	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636699	8636699	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	47	216	0	ENST00000356435.5:c.210G>C	p.Glu70Asp	p.E70D	ENST00000356435		70	gaG/gaC	2/35	0.313861514006314	3	FACETS	0.87	0.745	1	0.58	0.497	0.669	CLONAL	2	TRUE	0	0.343906096518101	3		216	184	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636842	8636842	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	69	378	0	ENST00000356435.5:c.67C>A	p.Pro23Thr	p.P23T	ENST00000356435		23	Cct/Act	2/35	0.313861514006314	3	FACETS	1	0.969	1	0.454	0.398	0.514	CLONAL	1	TRUE	0	0.343906096518101	3		378	345	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156716	20156716	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	35	436	0	ENST00000379607.5:c.41G>T	p.Arg14Met	p.R14M	ENST00000379607	NM_001412.3	14	aGg/aTg	2/7	0.343906096518101	3	FACETS	0.645	0.529	0.774	0.322	0.264	0.387	SUBCLONAL	1	TRUE	1	0.343906096518101	3		436	370	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911550	39911550	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	66	591	0	ENST00000378444.4:c.5080G>T	p.Glu1694Ter	p.E1694*	ENST00000378444	NM_001123385.1	1694	Gag/Tag	15/15	0.343906096518101	3	FACETS	0.926	0.805	1	0.463	0.402	0.528	CLONAL	1	TRUE	1	0.343906096518101	3		591	486	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930894	39930894	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	21	354	0	ENST00000378444.4:c.3047G>C	p.Cys1016Ser	p.C1016S	ENST00000378444	NM_001123385.1	1016	tGt/tCt	5/15	0.343906096518101	3	FACETS	0.557	0.43	0.705	0.278	0.215	0.353	SUBCLONAL	1	TRUE	1	0.343906096518101	3		354	257	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932081	39932081	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	244	782	0	ENST00000378444.4:c.2518C>G	p.Pro840Ala	p.P840A	ENST00000378444	NM_001123385.1	840	Ccc/Gcc	4/15	0.343906096518101	3	FACETS	0.841	0.786	0.897	0.841	0.786	0.897	CLONAL	2	TRUE	1	0.343906096518101	3		782	989	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409864	63409864	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	52	500	0	ENST00000330258.3:c.3303C>G	p.His1101Gln	p.H1101Q	ENST00000330258	NM_152424.3	1101	caC/caG	2/2	0.343906096518101	3	FACETS	0.706	0.601	0.821	0.353	0.3	0.411	SUBCLONAL	1	TRUE	1	0.343906096518101	3		500	502	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411475	63411475	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	112	874	0	ENST00000330258.3:c.1692C>G	p.Ile564Met	p.I564M	ENST00000330258	NM_152424.3	564	atC/atG	2/2	0.343906096518101	3	FACETS	0.882	0.793	0.977	0.441	0.396	0.489	CLONAL	1	TRUE	1	0.343906096518101	3		874	865	SUCCESS
AR	367	MSKCC	GRCh37	X	66765598	66765598	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	95	881	1	ENST00000374690.3:c.610G>T	p.Glu204Ter	p.E204*	ENST00000374690	NM_000044.3	204	Gaa/Taa	1/8	0.343906096518101	3	FACETS	0.676	0.601	0.756	0.338	0.3	0.378	SUBCLONAL	1	TRUE	1	0.343906096518101	3		882	958	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341515	70341515	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	89	698	0	ENST00000374080.3:c.950C>G	p.Ser317Cys	p.S317C	ENST00000374080		317	tCt/tGt	7/45	0.343906096518101	3	FACETS	0.726	0.642	0.815	0.363	0.321	0.408	SUBCLONAL	1	TRUE	1	0.343906096518101	3		698	836	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354666	70354666	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	147	624	0	ENST00000374080.3:c.4831C>A	p.Arg1611Ser	p.R1611S	ENST00000374080		1611	Cgt/Agt	35/45	0.343906096518101	3	FACETS	1	0.983	1	0.657	0.6	0.716	CLONAL	1	TRUE	1	0.343906096518101	3		624	763	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	62	737	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.898	0.779	1	0.898	0.779	1	CLONAL	1	TRUE	1	0.383734427008903	2		737	360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0042543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	255	768	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	NA	2	FACETS	0.945	0.89	1			1	INDETERMINATE	2	TRUE	NA	0.383734427008903	2		768	703	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692896	89692896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123322	NA	P-0042543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	90	518	0	ENST00000371953.3:c.380G>A	p.Gly127Glu	p.G127E	ENST00000371953	NM_000314.4	127	gGa/gAa	5/9	0.383734427008903	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.383734427008903	1		518	354	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954222	48954222	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0042543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	35	171	0	ENST00000267163.4:c.1421+2T>C		p.X474_splice	ENST00000267163	NM_000321.2	474			0.383734427008903	1	FACETS	0.939	0.781	1	0.939	0.781	1	CLONAL	1	TRUE	0	0.383734427008903	1		171	157	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954189	48954189	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	37	153	0	ENST00000267163.4:c.1390G>A	p.Glu464Lys	p.E464K	ENST00000267163	NM_000321.2	464	Gaa/Aaa	15/27	0.383734427008903	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.383734427008903	1		153	133	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146478	185146478	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	155	511	0	ENST00000265026.3:c.109C>A	p.His37Asn	p.H37N	ENST00000265026	NM_004721.4	37	Cac/Aac	2/14	0.172674994786516	4	FACETS	0.982	0.904	1	0.982	0.904	1	INDETERMINATE	2	TRUE	2	0.383734427008903	4		511	569	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003238	143003238	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	138	536	0	ENST00000262992.4:c.2588A>G	p.Asp863Gly	p.D863G	ENST00000262992	NM_001101669.1	863	gAt/gGt	23/24	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.383734427008903	2		536	566	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591245	67591286	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGGTGGTTGACTCAAAAAGGTGTTCGGCAAAAGAAGTTGAA	CAGGTGGTTGACTCAAAAAGGTGTTCGGCAAAAGAAGTTGAA	-	novel	NA	P-0042543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	27	452	0	ENST00000274335.5:c.1746-2_1785del		p.X582_splice	ENST00000274335		582		13/15	1	2	FACETS	0.404	0.322	0.499	0.404	0.322	0.499	SUBCLONAL	1	TRUE	1	0.383734427008903	2		452	348	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913517	NA	P-0042544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	203	413	0	ENST00000288135.5:c.1676T>A	p.Val559Asp	p.V559D	ENST00000288135	NM_000222.2	559	gTt/gAt	11/21	0.41689374149472	1	FACETS	0.634	0.596	0.673	0.634	0.596	0.673	INDETERMINATE	1	TRUE	0	0.861360493678658	1		413	423	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533553	533553	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	271	858	0	ENST00000451590.1:c.350A>C	p.Lys117Thr	p.K117T	ENST00000451590	NM_001130442.1	117	aAg/aCg	4/5	0.21768138332444	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.230191873184458	3		858	1233	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0042587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	85	471	1	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.986	0.871	1	0.986	0.871	1	CLONAL	1	FALSE	1	0.210417238707905	2		472	819	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0042587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	92	675	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.152217677749595	2	FACETS	1	0.957	1	0.58	0.515	0.649	CLONAL	1	FALSE	0	0.210417238707905	2		675	754	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0042587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	21	395	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	0.193912266148631	1	FACETS	0.521	0.401	0.661	0.521	0.401	0.661	SUBCLONAL	1	FALSE	0	0.210417238707905	1		395	343	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604655	48604655	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121912578	NA	P-0042596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	43	243	0	ENST00000342988.3:c.1477G>C	p.Asp493His	p.D493H	ENST00000342988	NM_005359.5	493	Gat/Cat	12/12	0.298373411028324	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.2	1		243	325	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866493	42866493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	139	716	0	ENST00000398585.3:c.139G>T	p.Ala47Ser	p.A47S	ENST00000398585	NM_001135099.1	47	Gct/Tct	3/14	1	2	FACETS	0.807	0.735	0.883	1	0.988	1	CLONAL	2	TRUE	1	0.2	2		716	861	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39704878	39704878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	17	131	0	ENST00000361337.2:c.223G>A	p.Glu75Lys	p.E75K	ENST00000361337	NM_003286.2	75	Gaa/Aaa	4/21	0.298373411028324	1	FACETS	0.916	0.688	1	0.916	0.688	1	CLONAL	1	TRUE	0	0.2	1		131	167	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643526	52643526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	28	378	0	ENST00000394830.3:c.2370G>A	p.Met790Ile	p.M790I	ENST00000394830	NM_018313.4	790	atG/atA	17/30	1	2	FACETS	0.629	0.502	0.774	0.629	0.502	0.774	SUBCLONAL	1	TRUE	1	0.2	2		378	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577544	7577544	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587780074	NA	P-0042611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	388	626	0	ENST00000269305.4:c.737T>C	p.Met246Thr	p.M246T	ENST00000269305	NM_001126112.2	246	aTg/aCg	7/11	0.845251987048113	1	FACETS	0.952	0.919	0.983	0.952	0.919	0.983	CLONAL	1	TRUE	0	0.845251987048113	1		626	557	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779166	135779166	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397514789	NA	P-0042611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	167	409	0	ENST00000298552.3:c.2080C>T	p.Gln694Ter	p.Q694*	ENST00000298552	NM_001162426.1	694	Cag/Tag	17/23	0.845251987048113	1	FACETS	0.514	0.477	0.552	0.514	0.477	0.552	SUBCLONAL	1	TRUE	0	0.845251987048113	1		409	444	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279672	123279672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	201	352	0	ENST00000358487.5:c.760C>T	p.His254Tyr	p.H254Y	ENST00000358487	NM_000141.4	254	Cac/Tac	7/18	0.845251987048113	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.845251987048113	1		352	266	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717325	89717705	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCTGCCACTAGAAGTCTAATTTTGGGACTTACTATTCATGAAATAGGAATTGACTTTTATATAAGTAATAGGACCTTATTTTGAAGGTTCAAACTGGAGAAAATCTTACATTGTTTATATTTTTATTTCATTTATTTCAGTTGATTTGCTTGAGATCAAGATTGCAGATACAGAATCCATATTTCGTGTATATTGCTGATATTAATCATTAAAATCGTTTTTGACAGTTTGACAGTTAAAGGCATTTCCTGTGAAATAATACTGGTATGTATTTAACCATGCAGATCCTCAGTTTGTGGTCTGCCAGCTAAAGGTGAAGATATATTCCTCCAATTCAGGACCCACACGACGGGAAGACAAGTTCATGTACTTTGAGTTCC	CTCTGCCACTAGAAGTCTAATTTTGGGACTTACTATTCATGAAATAGGAATTGACTTTTATATAAGTAATAGGACCTTATTTTGAAGGTTCAAACTGGAGAAAATCTTACATTGTTTATATTTTTATTTCATTTATTTCAGTTGATTTGCTTGAGATCAAGATTGCAGATACAGAATCCATATTTCGTGTATATTGCTGATATTAATCATTAAAATCGTTTTTGACAGTTTGACAGTTAAAGGCATTTCCTGTGAAATAATACTGGTATGTATTTAACCATGCAGATCCTCAGTTTGTGGTCTGCCAGCTAAAGGTGAAGATATATTCCTCCAATTCAGGACCCACACGACGGGAAGACAAGTTCATGTACTTTGAGTTCC	-	novel	NA	P-0042611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2	30	17	0	ENST00000371953.3:c.635-282_733del		p.X212_splice	ENST00000371953	NM_000314.4	212		7/9	0.845251987048113	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.845251987048113	1		17	32	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420640	49420640	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	263	614	0	ENST00000301067.7:c.15109G>T	p.Glu5037Ter	p.E5037*	ENST00000301067	NM_003482.3	5037	Gag/Tag	48/54	0.841283294334915	1	FACETS	0.664	0.629	0.699	0.664	0.629	0.699	SUBCLONAL	1	TRUE	0	0.845251987048113	1		614	541	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426852	49426853	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555188561	NA	P-0042611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	104	439	0	ENST00000301067.7:c.11635_11636del	p.Leu3880AspfsTer131	p.L3880Dfs*131	ENST00000301067	NM_003482.3	3879	AGt/t	39/54	0.841283294334915	1	FACETS	0.363	0.328	0.401	0.363	0.328	0.401	SUBCLONAL	1	TRUE	0	0.845251987048113	1		439	391	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0042626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	239	191	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.409075601316683	1	FACETS	0.976	0.923	1	1	0.995	1	CLONAL	2	TRUE	0	0.409075601316683	1		191	476	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43771707	43771707	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	35	556	0	ENST00000382044.4:c.676C>A	p.Gln226Lys	p.Q226K	ENST00000382044	NM_001141980.1	226	Cag/Aag	7/28	0.409075601316683	1	FACETS	0.282	0.23	0.34	0.282	0.23	0.34	SUBCLONAL	1	TRUE	0	0.409075601316683	1		556	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0042626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	125	739	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.409075601316683	2		741	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0042626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	106	689	0	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.409075601316683	2		689	493	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223826	36223826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	131	1101	1	ENST00000222270.7:c.6376G>A	p.Asp2126Asn	p.D2126N	ENST00000222270	NM_014727.1	2126	Gat/Aat	28/37	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.409075601316683	2		1102	576	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735547	40735547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756810336	NA	P-0042626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	59	577	0	ENST00000373198.4:c.3326G>A	p.Arg1109Gln	p.R1109Q	ENST00000373198	NM_133170.3	1109	cGg/cAg	25/32	1	2	FACETS	0.751	0.649	0.862	0.751	0.649	0.862	SUBCLONAL	1	TRUE	1	0.409075601316683	2		577	384	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557981	187557981	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	51	394	0	ENST00000441802.2:c.3730C>T	p.Gln1244Ter	p.Q1244*	ENST00000441802	NM_005245.3	1244	Cag/Tag	5/27	1	2	FACETS	0.721	0.615	0.835	0.721	0.615	0.835	SUBCLONAL	1	TRUE	1	0.409075601316683	2		394	346	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584660	187584661	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0042626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	123	501	0	ENST00000441802.2:c.3372_3373del	p.Glu1124AspfsTer6	p.E1124Dfs*6	ENST00000441802	NM_005245.3	1124	gaGAtc/gatc	3/27	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.409075601316683	2		501	473	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294970	1294971	+	missense_variant	Missense_Mutation	DNP	CG	CG	TT	novel	NA	P-0042626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	53	94	1	ENST00000310581.5:c.134_135delinsAA	p.Ala45Glu	p.A45E	ENST00000310581	NM_198253.2	45	gCG/gAA	1/16	0.409075601316683	4	FACETS	0.961	0.856	1	1	0.968	1	CLONAL	4	TRUE	1	0.409075601316683	4		95	95	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729420	41729420	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0042626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	125	703	0	ENST00000242208.4:c.1109C>G	p.Ser370Ter	p.S370*	ENST00000242208	NM_002192.2	370	tCa/tGa	3/3	0.130768688251504	4	FACETS	1	0.981	1	0.439	0.398	0.482	INDETERMINATE	1	TRUE	1	0.409075601316683	4		703	654	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0042649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	107	688	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.192719049591585	2	FACETS	1	0.927	1	0.52	0.467	0.577	CLONAL	1	TRUE	0	0.287153798254705	2		688	716	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279540	123279540	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779566502	NA	P-0042649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	103	801	1	ENST00000358487.5:c.892G>A	p.Gly298Ser	p.G298S	ENST00000358487	NM_000141.4	298	Ggc/Agc	7/18	1	2	FACETS	0.892	0.798	0.992	0.892	0.798	0.992	CLONAL	1	TRUE	1	0.287153798254705	2		802	804	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0042655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	307	556	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.432478658648673	3	FACETS	1	0.979	1	0.709	0.672	0.746	CLONAL	2	TRUE	0	0.466114714211235	3		556	764	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0042655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	383	707	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	0.432478658648673	3	FACETS	0.955	0.916	0.995	0.955	0.916	0.995	CLONAL	3	TRUE	0	0.466114714211235	3		707	707	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404587	8404587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	22	315	0	ENST00000356435.5:c.4160C>T	p.Ala1387Val	p.A1387V	ENST00000356435		1387	gCg/gTg	25/35	0.21066683706021	4	FACETS	0.378	0.293	0.478	0.095	0.073	0.12	INDETERMINATE	1	TRUE	0	0.466114714211235	4		315	366	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636766	8636766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776233840	NA	P-0042655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	180	506	0	ENST00000356435.5:c.143C>T	p.Thr48Met	p.T48M	ENST00000356435		48	aCg/aTg	2/35	0.21066683706021	4	FACETS	0.971	0.901	1	0.486	0.45	0.522	INDETERMINATE	2	TRUE	0	0.466114714211235	4		506	583	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0042669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	98	413	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.338007723562267	2		414	503	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207092	1207092	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs778376925	NA	P-0042669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	147	719	0	ENST00000326873.7:c.180C>A	p.Tyr60Ter	p.Y60*	ENST00000326873	NM_000455.4	60	taC/taA	1/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.338007723562267	2		719	658	SUCCESS
AR	367	MSKCC	GRCh37	X	66766312	66766312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1410383824	NA	P-0042669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	56	307	0	ENST00000374690.3:c.1324G>A	p.Glu442Lys	p.E442K	ENST00000374690	NM_000044.3	442	Gaa/Aaa	1/8	1	2	FACETS	0.893	0.768	1	0.893	0.768	1	CLONAL	1	TRUE	1	0.338007723562267	2		307	371	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300479	11300479	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	140	608	0	ENST00000361445.4:c.1667G>C	p.Gly556Ala	p.G556A	ENST00000361445	NM_004958.3	556	gGc/gCc	11/58	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.338007723562267	2		608	702	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425741	49425741	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	96	685	0	ENST00000301067.7:c.12747G>T	p.Gln4249His	p.Q4249H	ENST00000301067	NM_003482.3	4249	caG/caT	39/54	1	2	FACETS	0.922	0.823	1	0.922	0.823	1	CLONAL	1	TRUE	1	0.338007723562267	2		685	616	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285943	39285943	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	61	295	0	ENST00000402219.2:c.216A>T	p.Glu72Asp	p.E72D	ENST00000402219	NM_005633.3	72	gaA/gaT	3/23	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.338007723562267	2		295	335	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225449704	225449704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1034800855	NA	P-0042669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	25	363	0	ENST00000264414.4:c.23C>T	p.Thr8Met	p.T8M	ENST00000264414	NM_003590.4	8	aCg/aTg	1/16	1	2	FACETS	0.347	0.273	0.433	0.347	0.273	0.433	SUBCLONAL	1	TRUE	1	0.338007723562267	2		363	426	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387049	31387049	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0042669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	97	538	0	ENST00000328111.2:c.1675-1G>T		p.X559_splice	ENST00000328111	NM_006892.3	559			1	2	FACETS	0.908	0.811	1	0.908	0.811	1	CLONAL	1	TRUE	1	0.338007723562267	2		538	632	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0042706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	89	603	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.218611954184138	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.218611954184138	1		603	584	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0042706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	59	457	2	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	0.939	0.808	1	0.939	0.808	1	CLONAL	1	TRUE	1	0.218611954184138	2		459	575	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396269	139396269	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	183	728	0	ENST00000277541.6:c.5569G>T	p.Ala1857Ser	p.A1857S	ENST00000277541	NM_017617.3	1857	Gcc/Tcc	30/34	0.179610751267477	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.218611954184138	2		728	761	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255440	16255440	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	74	513	0	ENST00000375759.3:c.2705A>C	p.Lys902Thr	p.K902T	ENST00000375759	NM_015001.2	902	aAg/aCg	11/15	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.218611954184138	2		513	610	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255452	16255452	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	65	519	0	ENST00000375759.3:c.2717A>G	p.Asp906Gly	p.D906G	ENST00000375759	NM_015001.2	906	gAc/gGc	11/15	1	2	FACETS	0.972	0.842	1	0.972	0.842	1	CLONAL	1	TRUE	1	0.218611954184138	2		519	612	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647127	23647127	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	100	814	0	ENST00000261584.4:c.740C>T	p.Thr247Ile	p.T247I	ENST00000261584	NM_024675.3	247	aCa/aTa	4/13	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.218611954184138	2		814	876	SUCCESS
AXL	558	MSKCC	GRCh37	19	41736871	41736871	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0042706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	69	657	0	ENST00000301178.4:c.587-1G>T		p.X196_splice	ENST00000301178	NM_021913.4	196			1	2	FACETS	0.901	0.784	1	0.901	0.784	1	CLONAL	1	TRUE	1	0.218611954184138	2		657	701	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082274	16082274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	84	832	0	ENST00000281043.3:c.88C>T	p.Pro30Ser	p.P30S	ENST00000281043	NM_005378.4	30	Ccg/Tcg	2/3	1	2	FACETS	0.811	0.714	0.914	0.811	0.714	0.914	CLONAL	1	TRUE	1	0.218611954184138	2		832	948	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180277	38180277	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	38	562	1	ENST00000396334.3:c.125T>A	p.Val42Glu	p.V42E	ENST00000396334	NM_002468.4	42	gTg/gAg	1/5	1	2	FACETS	0.697	0.575	0.832	0.697	0.575	0.832	SUBCLONAL	1	TRUE	1	0.218611954184138	2		563	499	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508262	106508262	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	39	381	0	ENST00000359195.3:c.256G>T	p.Asp86Tyr	p.D86Y	ENST00000359195	NM_002649.2	86	Gac/Tac	2/11	1	2	FACETS	0.97	0.805	1	0.97	0.805	1	CLONAL	1	TRUE	1	0.218611954184138	2		381	368	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243966	53243966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	85	774	0	ENST00000375401.3:c.1027G>A	p.Asp343Asn	p.D343N	ENST00000375401	NM_004187.3	343	Gat/Aat	8/26	0.192489800266598	0	FACETS	0.778	0.687	0.876			1	SUBCLONAL	1	TRUE	0	0.218611954184138	0		774	781	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245931	46245931	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	26	409	0	ENST00000334344.6:c.4025A>T	p.Glu1342Val	p.E1342V	ENST00000334344	NM_152641.2	1342	gAa/gTa	15/21	1	2	FACETS	0.653	0.517	0.809	0.653	0.517	0.809	SUBCLONAL	1	TRUE	1	0.218611954184138	2		409	364	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245907	46245929	+	frameshift_variant	Frame_Shift_Del	DEL	GAGCATCTGGGAAACAGAACTCA	GAGCATCTGGGAAACAGAACTCA	-	novel	NA	P-0042706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	25	374	0	ENST00000334344.6:c.4003_4025del	p.Ala1335ThrfsTer10	p.A1335Tfs*10	ENST00000334344	NM_152641.2	1334	gGAGCATCTGGGAAACAGAACTCA/g	15/21	1	2	FACETS	0.58	0.457	0.723	0.58	0.457	0.723	SUBCLONAL	1	TRUE	1	0.218611954184138	2		374	394	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0042706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	55	413	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.312443845035262	2		414	336	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243467	46243467	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	15	488	0	ENST00000334344.6:c.1820C>T	p.Pro607Leu	p.P607L	ENST00000334344	NM_152641.2	607	cCc/cTc	14/21	1	2	FACETS	0.41	0.3	0.543	0.41	0.3	0.543	SUBCLONAL	1	TRUE	1	0.312443845035262	2		488	234	SUCCESS
AR	367	MSKCC	GRCh37	X	66941712	66941712	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	43	819	0	ENST00000374690.3:c.2356G>T	p.Val786Phe	p.V786F	ENST00000374690	NM_000044.3	786	Gtc/Ttc	6/8	1	2	FACETS	0.541	0.452	0.639	0.541	0.452	0.639	SUBCLONAL	1	TRUE	1	0.312443845035262	2		819	509	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998781	100998781	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	68	966	0	ENST00000325455.5:c.1021C>G	p.Pro341Ala	p.P341A	ENST00000325455	NM_001202474.3	341	Ccg/Gcg	1/8	1	2	FACETS	0.58	0.503	0.662	0.58	0.503	0.662	SUBCLONAL	1	TRUE	1	0.312443845035262	2		966	751	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032371	42032371	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0042706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	104	661	0	ENST00000219905.7:c.4555A>T	p.Lys1519Ter	p.K1519*	ENST00000219905	NM_001164273.1	1519	Aag/Tag	14/24	0.193912103279436	2	FACETS	1	0.98	1	0.701	0.631	0.774	CLONAL	1	TRUE	0	0.312443845035262	2		661	475	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748609	43748609	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	83	948	0	ENST00000382044.4:c.2197C>T	p.Pro733Ser	p.P733S	ENST00000382044	NM_001141980.1	733	Cct/Tct	12/28	0.193912103279436	2	FACETS	1	0.898	1	0.508	0.449	0.571	CLONAL	1	TRUE	0	0.312443845035262	2		948	523	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250527	110250527	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	51	740	0	ENST00000374672.4:c.148del	p.His50ThrfsTer2	p.H50Tfs*2	ENST00000374672	NM_004235.4	50	Cac/ac	3/5	1	2	FACETS	0.594	0.504	0.692	0.594	0.504	0.692	SUBCLONAL	1	TRUE	1	0.312443845035262	2		740	550	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410043	63410043	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	50	876	0	ENST00000330258.3:c.3124C>T	p.Gln1042Ter	p.Q1042*	ENST00000330258	NM_152424.3	1042	Cag/Tag	2/2	1	2	FACETS	0.507	0.43	0.593	0.507	0.43	0.593	SUBCLONAL	1	TRUE	1	0.312443845035262	2		876	631	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849291	76849292	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0042706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	22	531	0	ENST00000373344.5:c.5984_5985delinsAT	p.Ser1995Asn	p.S1995N	ENST00000373344	NM_000489.3	1995	aGC/aAT	26/35	1	2	FACETS	0.512	0.397	0.645	0.512	0.397	0.645	SUBCLONAL	1	TRUE	1	0.312443845035262	2		531	275	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243524	46243524	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	12	382	0	ENST00000334344.6:c.1877C>G	p.Ser626Cys	p.S626C	ENST00000334344	NM_152641.2	626	tCt/tGt	14/21	1	2	FACETS	0.392	0.275	0.535	0.392	0.275	0.535	SUBCLONAL	1	TRUE	1	0.312443845035262	2		382	196	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246299	46246299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	14	462	0	ENST00000334344.6:c.4393C>T	p.Pro1465Ser	p.P1465S	ENST00000334344	NM_152641.2	1465	Cca/Tca	15/21	1	2	FACETS	0.378	0.273	0.505	0.378	0.273	0.505	SUBCLONAL	1	TRUE	1	0.312443845035262	2		462	237	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246315	46246318	+	stop_gained	Nonsense_Mutation	ONP	CACC	CACC	GACT	novel	NA	P-0042706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	12	452	0	ENST00000334344.6:c.4409_4412delinsGACT	p.Ser1470_Pro1471delinsTer	p.S1470_P1471delins*	ENST00000334344	NM_152641.2	1470	tCACCa/tGACTa	15/21	1	2	FACETS	0.335	0.235	0.459	0.335	0.235	0.459	SUBCLONAL	1	TRUE	1	0.312443845035262	2		452	229	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256831	16256831	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	133	679	0	ENST00000375759.3:c.4096C>T	p.Arg1366Ter	p.R1366*	ENST00000375759	NM_015001.2	1366	Cga/Tga	11/15	0.602262922953626	3	FACETS	0.889	0.81	0.971	0.296	0.27	0.324	CLONAL	1	TRUE	0	0.685989992246612	3		679	586	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983123	201983123	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	331	710	0	ENST00000359651.3:c.972G>A	p.Met324Ile	p.M324I	ENST00000359651		324	atG/atA	7/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.685989992246612	2		710	907	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88672125	88672125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	181	712	0	ENST00000372037.3:c.659C>T	p.Ser220Phe	p.S220F	ENST00000372037	NM_004329.2	220	tCt/tTt	8/13	0.685989992246612	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.685989992246612	1		712	305	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859646	57859646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	138	618	1	ENST00000228682.2:c.700G>A	p.Glu234Lys	p.E234K	ENST00000228682	NM_005269.2	234	Gaa/Aaa	7/12	0.212647656861674	2	FACETS	0.636	0.58	0.694	0.318	0.29	0.347	INDETERMINATE	1	TRUE	0	0.685989992246612	2		619	633	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646911	23646911	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	124	662	0	ENST00000261584.4:c.956C>G	p.Ser319Cys	p.S319C	ENST00000261584	NM_024675.3	319	tCt/tGt	4/13	1	2	FACETS	0.798	0.727	0.872	0.798	0.727	0.872	SUBCLONAL	1	TRUE	1	0.685989992246612	2		662	453	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822480	72822480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs963874989	NA	P-0042713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	150	839	2	ENST00000268489.5:c.9695G>A	p.Arg3232His	p.R3232H	ENST00000268489	NM_006885.3	3232	cGc/cAc	10/10	1	2	FACETS	0.575	0.526	0.627	0.575	0.526	0.627	SUBCLONAL	1	TRUE	1	0.685989992246612	2		841	760	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107025	11107025	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	105	578	0	ENST00000358026.2:c.1730C>T	p.Ala577Val	p.A577V	ENST00000358026	NM_001128849.1	577	gCc/gTc	10/36	0.331465501132513	1	FACETS	0.42	0.378	0.464	0.42	0.378	0.464	INDETERMINATE	1	TRUE	0	0.685989992246612	1		578	479	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131505	202131505	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	139	402	0	ENST00000358485.4:c.473C>A	p.Ser158Tyr	p.S158Y	ENST00000358485	NM_001080125.1	158	tCt/tAt	2/9	0.331465501132513	1	FACETS	0.804	0.743	0.866	0.804	0.743	0.866	INDETERMINATE	1	TRUE	0	0.685989992246612	1		402	331	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545799	41545799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	114	698	0	ENST00000263253.7:c.2414C>T	p.Ser805Phe	p.S805F	ENST00000263253	NM_001429.3	805	tCt/tTt	14/31	0.456842796716899	1	FACETS	0.431	0.389	0.474	0.431	0.389	0.474	SUBCLONAL	1	TRUE	0	0.685989992246612	1		698	507	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805533	1805533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532318669	NA	P-0042713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	310	730	0	ENST00000260795.2:c.1045C>T	p.His349Tyr	p.H349Y	ENST00000260795		349	Cat/Tat	7/17	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.685989992246612	2		730	829	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806183	1806183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	386	804	1	ENST00000260795.2:c.1202C>T	p.Pro401Leu	p.P401L	ENST00000260795		401	cCc/cTc	8/17	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.685989992246612	2		805	980	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808955	1808955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768644781	NA	P-0042713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	330	661	0	ENST00000260795.2:c.2387C>T	p.Pro796Leu	p.P796L	ENST00000260795		796	cCg/cTg	17/17	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.685989992246612	2		661	785	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196849	106196849	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	77	388	0	ENST00000380013.4:c.5182G>A	p.Glu1728Lys	p.E1728K	ENST00000380013	NM_001127208.2	1728	Gag/Aag	11/11	1	2	FACETS	0.932	0.83	1	0.932	0.83	1	CLONAL	1	TRUE	1	0.685989992246612	2		388	241	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519213	187519213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	235	638	0	ENST00000441802.2:c.12170C>T	p.Ser4057Phe	p.S4057F	ENST00000441802	NM_005245.3	4057	tCc/tTc	23/27	0.685989992246612	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.685989992246612	1		638	421	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531165	187531165	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	76	354	0	ENST00000441802.2:c.9858del	p.Val3287TyrfsTer17	p.V3287Yfs*17	ENST00000441802	NM_005245.3	3286	gcC/gc	15/27	0.685989992246612	1	FACETS	0.904	0.815	0.994	0.904	0.815	0.994	CLONAL	1	TRUE	0	0.685989992246612	1		354	161	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729784	41729784	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	126	411	0	ENST00000242208.4:c.745G>C	p.Glu249Gln	p.E249Q	ENST00000242208	NM_002192.2	249	Gag/Cag	3/3	0.331465501132513	1	FACETS	0.658	0.602	0.715	0.658	0.602	0.715	INDETERMINATE	1	TRUE	0	0.685989992246612	1		411	367	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0042736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	141	458	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.798710139879528	5	FACETS	1	0.983	1	0.819	0.758	0.88	CLONAL	2	TRUE	2	0.798710139879528	5		458	316	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471047	8471047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201751722	NA	P-0042736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	38	307	0	ENST00000356435.5:c.3452G>A	p.Arg1151His	p.R1151H	ENST00000356435		1151	cGc/cAc	20/35	0.541196915129188	1	FACETS	0.506	0.429	0.587	0.506	0.429	0.587	SUBCLONAL	1	TRUE	0	0.798710139879528	1		307	113	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591885	48591885	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	75	472	0	ENST00000342988.3:c.1048G>T	p.Val350Phe	p.V350F	ENST00000342988	NM_005359.5	350	Gtt/Ttt	9/12	0.77509239900561	1	FACETS	0.881	0.803	0.958	0.881	0.803	0.958	CLONAL	1	TRUE	0	0.798710139879528	1		472	128	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984389	201984389	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	111	579	0	ENST00000359651.3:c.1054T>G	p.Tyr352Asp	p.Y352D	ENST00000359651		352	Tac/Gac	8/8	0.798710139879528	4	FACETS	0.929	0.839	1	0.465	0.419	0.513	CLONAL	1	TRUE	2	0.798710139879528	4		579	538	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423444	116423444	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	73	280	0	ENST00000397752.3:c.3719A>G	p.Lys1240Arg	p.K1240R	ENST00000397752	NM_000245.2	1240	aAa/aGa	19/21	0.77263837322512	3	FACETS	0.984	0.871	1	0.492	0.435	0.551	CLONAL	1	TRUE	1	0.798710139879528	3		280	260	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0042761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	235	480	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.416337508006684	1	FACETS	0.68	0.642	0.718	0.68	0.642	0.718	INDETERMINATE	1	TRUE	0	0.827207972572605	1		480	490	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523008	25523009	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	rs769876640	NA	P-0042761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	348	726	0	ENST00000264709.3:c.176dup	p.Val60GlyfsTer5	p.V60Gfs*5	ENST00000264709	NM_175629.2	59	ccg/ccCg	3/23	1	2	FACETS	0.922	0.876	0.968	0.922	0.876	0.968	CLONAL	1	TRUE	1	0.827207972572605	2		726	913	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044605	47044605	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0042761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	248	757	0	ENST00000377604.3:c.2100+2T>C		p.X700_splice	ENST00000377604	NM_001204468.1	700			1	2	FACETS	0.645	0.604	0.688	0.645	0.604	0.688	SUBCLONAL	1	TRUE	1	0.827207972572605	2		757	929	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76919014	76919014	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0042789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	51	216	0	ENST00000373344.5:c.3977C>G	p.Ser1326Ter	p.S1326*	ENST00000373344	NM_000489.3	1326	tCa/tGa	12/35	1	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.728561405873939	1		216	73	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715881	117715881	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	68	408	0	ENST00000368508.3:c.877C>A	p.Leu293Ile	p.L293I	ENST00000368508	NM_002944.2	293	Ctc/Atc	9/43	0.728561405873939	4	FACETS	1	0.952	1	0.39	0.342	0.44	CLONAL	1	TRUE	1	0.728561405873939	4		408	276	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972993	68972993	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	24	476	0	ENST00000288368.4:c.1318G>C	p.Glu440Gln	p.E440Q	ENST00000288368	NM_024870.2	440	Gaa/Caa	11/40	1	2	FACETS	0.315	0.248	0.392	0.315	0.248	0.392	SUBCLONAL	1	TRUE	1	0.728561405873939	2		476	209	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	433	1103	0	ENST00000269305.4:c.166del	p.Glu56LysfsTer67	p.E56Kfs*67	ENST00000269305	NM_001126112.2	56	Gaa/aa	4/11	0.277267302405385	2	FACETS	1	0.975	1	1	0.996	1	CLONAL	3	TRUE	0	0.277267302405385	2		1103	1014	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831834	72831834	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	213	1079	0	ENST00000268489.5:c.4747G>C	p.Gly1583Arg	p.G1583R	ENST00000268489	NM_006885.3	1583	Ggt/Cgt	9/10	1	2	FACETS	0.755	0.702	0.811	1	0.991	1	SUBCLONAL	2	TRUE	1	0.277267302405385	2		1079	1017	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0042801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	380	212	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.586757160728305	4	FACETS	0.895	0.852	0.939	0.895	0.852	0.939	CLONAL	2	TRUE	2	0.713120325740363	4		212	1020	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243045	105243045	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	1077	1206	0	ENST00000349310.3:c.238T>C	p.Trp80Arg	p.W80R	ENST00000349310	NM_001014432.1	80	Tgg/Cgg	5/15	0.179326149422864	6	FACETS	0.948	0.934	0.962			1	INDETERMINATE	6	TRUE	NA	0.713120325740363	6		1206	1288	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs786203436	NA	P-0042801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	601	1139	0	ENST00000269305.4:c.487T>A	p.Tyr163Asn	p.Y163N	ENST00000269305	NM_001126112.2	163	Tac/Aac	5/11	0.713120325740363	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.713120325740363	2		1139	787	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519896	NA	P-0042801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	178	446	3	ENST00000281708.4:c.1514G>A	p.Arg505His	p.R505H	ENST00000281708	NM_033632.3	505	cGc/cAc	10/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.713120325740363	2		449	431	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	84	737	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.99	0.879	1	0.99	0.879	1	CLONAL	1	TRUE	1	0.401984828728378	2		737	422	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0042808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	129	685	0	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	1	2	FACETS	0.803	0.728	0.882	0.803	0.728	0.882	CLONAL	1	TRUE	1	0.401984828728378	2		685	799	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653780	89653782	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGA	AGA	-	novel	NA	P-0042808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	45	159	0	ENST00000371953.3:c.80-2_80del		p.X27_splice	ENST00000371953	NM_000314.4	27		2/9	0.401984828728378	2	FACETS	0.823	0.708	0.944	0.823	0.708	0.944	CLONAL	2	TRUE	0	0.401984828728378	2		159	136	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	465659	465660	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0042808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	120	645	0	ENST00000399788.2:c.716_717del	p.Leu239ProfsTer19	p.L239Pfs*19	ENST00000399788	NM_001042603.1	239	cTT/c	6/28	0.401984828728378	1	FACETS	0.875	0.794	0.961	0.875	0.794	0.961	CLONAL	1	TRUE	0	0.401984828728378	1		645	545	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	56	737	0				ENST00000310581	NM_198253.2	-/1132			0.228744780810793	1	FACETS	0.861	0.741	0.992	0.861	0.741	0.992	CLONAL	1	FALSE	0	0.298892703356102	1		737	370	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867546	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs11466445	NA	P-0042816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	12	28	0	ENST00000374994.4:c.70_78del	p.Ala24_Ala26del	p.A24_A26del	ENST00000374994	NM_004612.2	17	ctGGCGGCGGCg/ctg	1/9	0.261609900956542	1	FACETS	0.697	0.495	0.939	0.697	0.495	0.939	SUBCLONAL	1	FALSE	0	0.298892703356102	1		28	98	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267562	7267564	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0042816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	57	783	0	ENST00000302850.5:c.444_446del	p.Lys148del	p.K148del	ENST00000302850	NM_000208.2	148	aaGAAc/aac	2/22	1	2	FACETS	0.573	0.491	0.662	0.573	0.491	0.662	SUBCLONAL	1	FALSE	1	0.298892703356102	2		783	666	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400190	41400190	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	107	603	0	ENST00000373198.4:c.569G>A	p.Arg190Lys	p.R190K	ENST00000373198	NM_133170.3	190	aGa/aAa	5/32	0.269358339953676	4	FACETS	1	0.984	1	0.745	0.673	0.819	INDETERMINATE	1	TRUE	2	0.581042884179795	4		603	391	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	90	544	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.581042884179795	2		545	218	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424958105	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	44	262	0	ENST00000334344.6:c.940C>T	p.Arg314Cys	p.R314C	ENST00000334344	NM_152641.2	314	Cgt/Tgt	8/21	0.269358339953676	4	FACETS	0.946	0.8	1	0.473	0.4	0.553	INDETERMINATE	1	TRUE	2	0.581042884179795	4		262	253	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	125	796	1	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	0.581042884179795	3	FACETS	1	0.931	1	0.514	0.467	0.563	CLONAL	1	TRUE	1	0.581042884179795	3		797	540	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	243	252	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	0.581042884179795	6	FACETS	0.923	0.873	0.973	0.923	0.873	0.973	CLONAL	4	TRUE	2	0.581042884179795	6		252	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	585	759	1	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.581042884179795	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	0	0.581042884179795	3		760	850	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419926	41419926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	88	920	0	ENST00000373198.4:c.395G>A	p.Gly132Glu	p.G132E	ENST00000373198	NM_133170.3	132	gGg/gAg	3/32	0.269358339953676	4	FACETS	0.941	0.836	1	0.47	0.418	0.526	INDETERMINATE	1	TRUE	2	0.581042884179795	4		920	509	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508805	106508805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762805000	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	200	769	0	ENST00000359195.3:c.799G>A	p.Glu267Lys	p.E267K	ENST00000359195	NM_002649.2	267	Gaa/Aaa	2/11	0.478040250714354	4	FACETS	0.967	0.902	1	0.967	0.902	1	CLONAL	2	TRUE	2	0.581042884179795	4		769	563	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984848	9984848	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	81	607	1	ENST00000330684.3:c.1117G>A	p.Glu373Lys	p.E373K	ENST00000330684	NM_001134407.1	373	Gaa/Aaa	4/13	1	2	FACETS	0.88	0.782	0.982	0.88	0.782	0.982	CLONAL	1	TRUE	1	0.581042884179795	2		608	317	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973851	131973851	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747603489	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	23	448	0	ENST00000265335.6:c.3554G>A	p.Arg1185Gln	p.R1185Q	ENST00000265335		1185	cGa/cAa	23/25	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.581042884179795	NA		448	268	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133234477	133234477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376921543	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	143	612	0	ENST00000320574.5:c.3355C>T	p.Leu1119Phe	p.L1119F	ENST00000320574	NM_006231.2	1119	Ctt/Ttt	27/49	0.269358339953676	4	FACETS	0.956	0.881	1	0.956	0.881	1	INDETERMINATE	2	TRUE	2	0.581042884179795	4		612	407	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760592	133760592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2229067	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	319	1367	0	ENST00000318560.5:c.2915C>T	p.Ser972Leu	p.S972L	ENST00000318560	NM_005157.4	972	tCg/tTg	11/11	0.568364997783188	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.581042884179795	2		1367	487	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332915	153332915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200698994	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	98	498	0	ENST00000281708.4:c.41G>A	p.Arg14Gln	p.R14Q	ENST00000281708	NM_033632.3	14	cGa/cAa	2/12	0.323702971858073	1	FACETS	0.981	0.891	1	0.981	0.891	1	INDETERMINATE	1	TRUE	0	0.581042884179795	1		498	244	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576048	29576048	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854559	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	280	447	0	ENST00000356175.3:c.4021C>T	p.Gln1341Ter	p.Q1341*	ENST00000356175	NM_000267.3	1341	Cag/Tag	30/57	0.581042884179795	3	FACETS	0.911	0.871	0.951	0.911	0.871	0.951	CLONAL	3	TRUE	0	0.581042884179795	3		447	455	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770626	40770626	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	72	488	0	ENST00000373198.4:c.2756A>G	p.Gln919Arg	p.Q919R	ENST00000373198	NM_133170.3	919	cAg/cGg	19/32	0.269358339953676	4	FACETS	1	0.955	1	0.592	0.521	0.667	INDETERMINATE	1	TRUE	2	0.581042884179795	4		488	331	SUCCESS
ALK	238	MSKCC	GRCh37	2	29430064	29430064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1013688370	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	62	850	0	ENST00000389048.3:c.3911G>A	p.Gly1304Glu	p.G1304E	ENST00000389048	NM_004304.4	1304	gGa/gAa	26/29	0.319129793087143	5	FACETS	0.698	0.603	0.801	0.14	0.12	0.161	INDETERMINATE	1	TRUE	0	0.581042884179795	5		850	572	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295704	212295704	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745376683	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	132	368	0	ENST00000342788.4:c.2609G>A	p.Gly870Glu	p.G870E	ENST00000342788	NM_005235.2	870	gGa/gAa	21/28	0.208640688811462	3	FACETS	0.928	0.855	1	0.619	0.57	0.668	INDETERMINATE	2	TRUE	0	0.581042884179795	3		368	316	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005419	29005419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55687105	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	47	288	0	ENST00000282397.4:c.842G>A	p.Arg281Gln	p.R281Q	ENST00000282397	NM_002019.4	281	cGa/cAa	7/30	0.208640688811462	3	FACETS	0.768	0.663	0.877	0.512	0.442	0.585	INDETERMINATE	2	TRUE	0	0.581042884179795	3		288	136	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036014	180036014	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761503019	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	95	972	0	ENST00000261937.6:c.3847G>A	p.Glu1283Lys	p.E1283K	ENST00000261937	NM_182925.4	1283	Gag/Aag	29/30	0.137420888419558	0	FACETS	0.423	0.38	0.467			1	INDETERMINATE	1	TRUE	0	0.581042884179795	0		972	324	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971152	55971152	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	61	559	0	ENST00000263923.4:c.1646-1G>A		p.X549_splice	ENST00000263923	NM_002253.2	549			0.323702971858073	1	FACETS	0.512	0.445	0.583	0.512	0.445	0.583	INDETERMINATE	1	TRUE	0	0.581042884179795	1		559	291	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054037	42054037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1246555872	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	21	156	0	ENST00000219905.7:c.7499C>T	p.Ser2500Leu	p.S2500L	ENST00000219905	NM_001164273.1	2500	tCg/tTg	21/24	0.581042884179795	3	FACETS	0.696	0.542	0.871	0.348	0.271	0.436	SUBCLONAL	1	TRUE	1	0.581042884179795	3		156	134	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878052	151878052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	204	532	1	ENST00000262189.6:c.6893C>T	p.Pro2298Leu	p.P2298L	ENST00000262189	NM_170606.2	2298	cCc/cTc	36/59	0.581042884179795	6	FACETS	1	0.983	1	0.845	0.794	0.897	CLONAL	3	TRUE	2	0.581042884179795	6		533	449	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793263	242793263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754424677	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	57	1223	1	ENST00000334409.5:c.814C>T	p.Arg272Trp	p.R272W	ENST00000334409	NM_005018.2	272	Cgg/Tgg	5/5	0.208640688811462	3	FACETS	0.656	0.565	0.755	0.219	0.188	0.252	INDETERMINATE	1	TRUE	0	0.581042884179795	3		1224	386	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248449	212248449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1256468343	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	120	450	1	ENST00000342788.4:c.3818G>A	p.Arg1273Gln	p.R1273Q	ENST00000342788	NM_005235.2	1273	cGg/cAg	28/28	0.208640688811462	3	FACETS	1	0.954	1	0.7	0.645	0.755	INDETERMINATE	2	TRUE	0	0.581042884179795	3		451	254	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948820	71948820	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	66	1317	0	ENST00000298229.2:c.3532C>T	p.Gln1178Ter	p.Q1178*	ENST00000298229	NM_001567.3	1178	Cag/Tag	26/28	1	2	FACETS	0.496	0.432	0.565	0.496	0.432	0.565	SUBCLONAL	1	TRUE	1	0.581042884179795	2		1317	458	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999714	100999714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	119	1203	1	ENST00000325455.5:c.88C>T	p.Arg30Cys	p.R30C	ENST00000325455	NM_001202474.3	30	Cgc/Tgc	1/8	1	2	FACETS	0.925	0.84	1	0.925	0.84	1	CLONAL	1	TRUE	1	0.581042884179795	2		1204	443	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923309	9923309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	97	697	0	ENST00000330684.3:c.1978G>A	p.Asp660Asn	p.D660N	ENST00000330684	NM_001134407.1	660	Gac/Aac	9/13	1	2	FACETS	0.93	0.837	1	0.93	0.837	1	CLONAL	1	TRUE	1	0.581042884179795	2		697	359	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828333	50828333	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	65	467	0	ENST00000398568.2:c.2671C>T	p.Arg891Trp	p.R891W	ENST00000398568	NM_001042412.1	891	Cgg/Tgg	17/18	1	2	FACETS	0.871	0.763	0.984	0.871	0.763	0.984	CLONAL	1	TRUE	1	0.581042884179795	2		467	257	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641147	93641147	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	184	531	0	ENST00000375746.1:c.1493G>A	p.Arg498Lys	p.R498K	ENST00000375746	NM_001174167.1	498	aGa/aAa	11/14	0.568364997783188	2	FACETS	0.905	0.85	0.959	0.905	0.85	0.959	CLONAL	2	TRUE	0	0.581042884179795	2		531	350	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372155	55372155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1219111000	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	105	794	0	ENST00000297316.4:c.845C>T	p.Ser282Leu	p.S282L	ENST00000297316	NM_022454.3	282	tCg/tTg	2/2	0.308370357088292	3	FACETS	1	0.98	1	0.676	0.612	0.742	INDETERMINATE	1	TRUE	1	0.581042884179795	3		794	345	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073913	8073913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	121	567	1	ENST00000377482.5:c.746C>T	p.Ser249Phe	p.S249F	ENST00000377482	NM_018948.3	249	tCt/tTt	4/4	0.308370357088292	3	FACETS	0.832	0.762	0.904	0.832	0.762	0.904	INDETERMINATE	2	TRUE	1	0.581042884179795	3		568	323	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189822	11189822	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	116	869	0	ENST00000361445.4:c.5687G>T	p.Arg1896Leu	p.R1896L	ENST00000361445	NM_004958.3	1896	cGa/cTa	40/58	0.308370357088292	3	FACETS	1	0.963	1	0.561	0.509	0.616	INDETERMINATE	1	TRUE	1	0.581042884179795	3		869	459	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305325	65305325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	119	592	0	ENST00000342505.4:c.2803G>A	p.Glu935Lys	p.E935K	ENST00000342505	NM_002227.2	935	Gag/Aag	20/25	0.308370357088292	3	FACETS	0.847	0.776	0.92	0.847	0.776	0.92	INDETERMINATE	2	TRUE	1	0.581042884179795	3		592	312	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262261	115262261	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	132	567	0	ENST00000438362.2:c.2293T>C	p.Phe765Leu	p.F765L	ENST00000438362	NM_001242891.1	765	Ttc/Ctc	18/20	0.308370357088292	3	FACETS	1	0.97	1	0.57	0.52	0.622	INDETERMINATE	1	TRUE	1	0.581042884179795	3		567	514	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667402	241667402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755436052	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	167	628	0	ENST00000366560.3:c.1048C>T	p.Arg350Trp	p.R350W	ENST00000366560	NM_000143.3	350	Cgg/Tgg	7/10	0.581042884179795	3	FACETS	0.794	0.736	0.853	0.794	0.736	0.853	SUBCLONAL	2	TRUE	1	0.581042884179795	3		628	467	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154248	2154248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773624887	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	97	1087	0	ENST00000434045.2:c.680C>T	p.Ala227Val	p.A227V	ENST00000434045	NM_001127598.1	227	gCc/gTc	5/5	1	2	FACETS	0.933	0.839	1	0.933	0.839	1	CLONAL	1	TRUE	1	0.581042884179795	2		1087	358	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77043813	77043813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	126	800	0	ENST00000356341.3:c.1513G>A	p.Asp505Asn	p.D505N	ENST00000356341	NM_002576.4	505	Gat/Aat	14/15	1	2	FACETS	0.951	0.867	1	0.951	0.867	1	CLONAL	1	TRUE	1	0.581042884179795	2		800	456	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996738	100996738	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	62	392	0	ENST00000325455.5:c.1789G>A	p.Gly597Arg	p.G597R	ENST00000325455	NM_001202474.3	597	Ggg/Agg	2/8	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.581042884179795	2		392	209	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369137	118369137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	90	527	0	ENST00000534358.1:c.5855C>T	p.Ser1952Phe	p.S1952F	ENST00000534358	NM_005933.3	1952	tCc/tTc	22/36	1	2	FACETS	0.917	0.821	1	0.917	0.821	1	CLONAL	1	TRUE	1	0.581042884179795	2		527	338	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18649006	18649006	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	74	174	0	ENST00000266497.5:c.2681A>T	p.Tyr894Phe	p.Y894F	ENST00000266497		894	tAt/tTt	19/31	0.44958502875109	6	FACETS	1	0.912	1	1	0.912	1	CLONAL	3	TRUE	3	0.581042884179795	6		174	180	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611420	28611420	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	13	204	0	ENST00000241453.7:c.1211C>T	p.Ser404Phe	p.S404F	ENST00000241453	NM_004119.2	404	tCc/tTc	10/24	0.208640688811462	3	FACETS	0.511	0.368	0.682	0.17	0.122	0.228	INDETERMINATE	1	TRUE	0	0.581042884179795	3		204	113	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913125	32913125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1566230846	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	108	333	0	ENST00000380152.3:c.4633C>T	p.Leu1545Phe	p.L1545F	ENST00000380152		1545	Ctt/Ttt	11/27	0.208640688811462	3	FACETS	0.991	0.908	1	0.661	0.605	0.717	INDETERMINATE	2	TRUE	0	0.581042884179795	3		333	242	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000379	42000379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	13	216	0	ENST00000219905.7:c.2398C>T	p.His800Tyr	p.H800Y	ENST00000219905	NM_001164273.1	800	Cat/Tat	7/24	0.581042884179795	3	FACETS	0.441	0.316	0.59	0.22	0.158	0.295	SUBCLONAL	1	TRUE	1	0.581042884179795	3		216	131	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858589	9858589	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	68	464	0	ENST00000330684.3:c.2812A>C	p.Lys938Gln	p.K938Q	ENST00000330684	NM_001134407.1	938	Aag/Cag	13/13	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.581042884179795	2		464	224	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81891924	81891924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	118	734	0	ENST00000359376.3:c.394G>A	p.Glu132Lys	p.E132K	ENST00000359376	NM_002661.3	132	Gaa/Aaa	4/33	1	2	FACETS	0.857	0.778	0.94	0.857	0.778	0.94	CLONAL	1	TRUE	1	0.581042884179795	2		734	474	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082970	16082970	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	65	738	3	ENST00000281043.3:c.784G>A	p.Asp262Asn	p.D262N	ENST00000281043	NM_005378.4	262	Gat/Aat	2/3	0.319129793087143	5	FACETS	0.831	0.721	0.949	0.166	0.144	0.19	INDETERMINATE	1	TRUE	0	0.581042884179795	5		741	504	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213171	39213171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	125	1150	1	ENST00000402219.2:c.3796C>T	p.Pro1266Ser	p.P1266S	ENST00000402219	NM_005633.3	1266	Cct/Tct	23/23	0.319129793087143	5	FACETS	0.723	0.653	0.797	0.145	0.13	0.16	INDETERMINATE	1	TRUE	0	0.581042884179795	5		1151	1114	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39233570	39233570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	24	160	0	ENST00000402219.2:c.2774C>T	p.Pro925Leu	p.P925L	ENST00000402219	NM_005633.3	925	cCa/cTa	17/23	0.319129793087143	5	FACETS	0.743	0.586	0.923	0.149	0.117	0.185	INDETERMINATE	1	TRUE	0	0.581042884179795	5		160	208	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172187	99172187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1175795483	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	66	835	0	ENST00000074304.5:c.1753C>T	p.Pro585Ser	p.P585S	ENST00000074304	NM_001134224.1	585	Cca/Tca	17/26	0.208640688811462	3	FACETS	0.852	0.744	0.967	0.284	0.248	0.323	INDETERMINATE	1	TRUE	0	0.581042884179795	3		835	344	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561531	9561532	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	113	668	0	ENST00000353224.5:c.250_251delinsAA	p.Gly84Asn	p.G84N	ENST00000353224	NM_177990.2	84	GGc/AAc	4/10	0.269358339953676	4	FACETS	1	0.977	1	0.634	0.573	0.697	INDETERMINATE	1	TRUE	2	0.581042884179795	4		668	485	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256688	46256688	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	85	257	0	ENST00000371998.3:c.744T>G	p.Cys248Trp	p.C248W	ENST00000371998		248	tgT/tgG	8/23	0.269358339953676	4	FACETS	1	0.977	1	0.699	0.623	0.778	INDETERMINATE	1	TRUE	2	0.581042884179795	4		257	331	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46271111	46271111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	113	551	0	ENST00000371998.3:c.3235C>T	p.Pro1079Ser	p.P1079S	ENST00000371998		1079	Cct/Tct	17/23	0.269358339953676	4	FACETS	0.759	0.689	0.832	0.759	0.689	0.832	INDETERMINATE	2	TRUE	2	0.581042884179795	4		551	405	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64289204	64289204	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	63	215	0	ENST00000370651.3:c.372G>A	p.Met124Ile	p.M124I	ENST00000370651	NM_003463.4	124	atG/atA	5/6	0.558644453462147	2	FACETS	0.828	0.739	0.917	0.828	0.739	0.917	CLONAL	2	TRUE	0	0.581042884179795	2		215	131	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663661	117663661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs986408985	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	36	147	0	ENST00000368508.3:c.4571C>T	p.Ser1524Leu	p.S1524L	ENST00000368508	NM_002944.2	1524	tCa/tTa	28/43	0.558644453462147	2	FACETS	0.999	0.87	1	0.999	0.87	1	CLONAL	2	TRUE	0	0.581042884179795	2		147	62	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704647	117704647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	102	314	0	ENST00000368508.3:c.2329G>A	p.Gly777Arg	p.G777R	ENST00000368508	NM_002944.2	777	Gga/Aga	16/43	0.558644453462147	2	FACETS	0.924	0.85	0.997	0.924	0.85	0.997	CLONAL	2	TRUE	0	0.581042884179795	2		314	190	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511062	148511062	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	220	362	0	ENST00000320356.2:c.1840G>A	p.Gly614Ser	p.G614S	ENST00000320356	NM_004456.4	614	Ggc/Agc	15/20	0.581042884179795	6	FACETS	0.884	0.833	0.935	0.884	0.833	0.935	CLONAL	4	TRUE	2	0.581042884179795	6		362	463	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650843	93650843	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748067972	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	219	666	1	ENST00000375746.1:c.1769G>A	p.Arg590Gln	p.R590Q	ENST00000375746	NM_001174167.1	590	cGg/cAg	13/14	0.568364997783188	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.581042884179795	2		667	334	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258734	16258734	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	125	710	0	ENST00000375759.3:c.5999G>A	p.Gly2000Glu	p.G2000E	ENST00000375759	NM_015001.2	2000	gGa/gAa	11/15	0.308370357088292	3	FACETS	0.782	0.716	0.85	0.782	0.716	0.85	INDETERMINATE	2	TRUE	1	0.581042884179795	3		710	355	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971000	21971000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	411	1060	1	ENST00000304494.5:c.358G>T	p.Glu120Ter	p.E120*	ENST00000304494	NM_000077.4	120	Gag/Tag	2/3	0.854936875333221	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.854936875333221	1		1061	513	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926885	112926885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507544	NA	P-0042853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	273	866	0	ENST00000351677.2:c.1505C>T	p.Ser502Leu	p.S502L	ENST00000351677	NM_002834.3	502	tCa/tTa	13/16	0.854936875333221	1	FACETS	0.978	0.94	1	0.978	0.94	1	CLONAL	1	TRUE	0	0.854936875333221	1		866	374	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943773	71943773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	437	1154	1	ENST00000298229.2:c.1816G>A	p.Gly606Arg	p.G606R	ENST00000298229	NM_001567.3	606	Ggg/Agg	15/28	0.854936875333221	1	FACETS	0.956	0.927	0.985	0.956	0.927	0.985	CLONAL	1	TRUE	0	0.854936875333221	1		1155	612	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977162	85977162	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	52	257	0	ENST00000263360.6:c.764G>T	p.Gly255Val	p.G255V	ENST00000263360	NM_003797.3	255	gGt/gTt	8/12	0.854936875333221	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.854936875333221	1		257	63	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708552	43708552	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	204	1065	0	ENST00000382044.4:c.4744C>T	p.Gln1582Ter	p.Q1582*	ENST00000382044	NM_001141980.1	1582	Caa/Taa	22/28	0.854936875333221	1	FACETS	0.723	0.682	0.764	0.723	0.682	0.764	SUBCLONAL	1	TRUE	0	0.854936875333221	1		1065	378	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388024	31388024	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	203	586	0	ENST00000328111.2:c.1825G>T	p.Glu609Ter	p.E609*	ENST00000328111	NM_006892.3	609	Gag/Tag	17/23	1	2	FACETS	0.967	0.906	1	0.967	0.906	1	CLONAL	1	TRUE	1	0.854936875333221	2		586	491	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0042863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	99	413	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.226827425406336	3	FACETS	0.878	0.792	0.968	1	0.967	1	CLONAL	4	TRUE	0	0.177396578291419	3		414	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0042863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	128	961	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.164269961174246	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	0	0.177396578291419	2		961	680	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156140	119156140	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	45	774	0	ENST00000264033.4:c.1808del	p.Pro603GlnfsTer12	p.P603Qfs*12	ENST00000264033	NM_005188.3	602	gCc/gc	11/16	1	2	FACETS	0.945	0.794	1	0.945	0.794	1	CLONAL	1	TRUE	1	0.177396578291419	2		774	537	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636487	21636487	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	97	530	0	ENST00000421138.2:c.523G>T	p.Ala175Ser	p.A175S	ENST00000421138		175	Gct/Tct	7/16	0.226827425406336	3	FACETS	1	0.938	1	1	0.938	1	CLONAL	3	TRUE	0	0.177396578291419	3		530	374	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120836	115120836	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	44	659	0	ENST00000257566.3:c.170C>A	p.Pro57Gln	p.P57Q	ENST00000257566	NM_016569.3	57	cCg/cAg	1/8	0.155830914567449	2	FACETS	1	0.918	1	0.577	0.484	0.679	CLONAL	1	TRUE	0	0.177396578291419	2		659	430	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726716	88726716	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	23	552	0	ENST00000360948.2:c.328A>G	p.Ile110Val	p.I110V	ENST00000360948	NM_001012338.2	110	Atc/Gtc	4/19	0.177396578291419	1	FACETS	0.785	0.613	0.984	0.785	0.613	0.984	CLONAL	1	TRUE	0	0.177396578291419	1		552	301	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782171	56782171	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	23	451	0	ENST00000308159.5:c.12G>C	p.Glu4Asp	p.E4D	ENST00000308159	NM_014669.4	4	gaG/gaC	2/22	0.164269961174246	2	FACETS	0.986	0.771	1	0.493	0.385	0.617	CLONAL	1	TRUE	0	0.177396578291419	2		451	263	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78829286	78829286	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	71	634	0	ENST00000306801.3:c.1337G>T	p.Arg446Leu	p.R446L	ENST00000306801	NM_020761.2	446	cGg/cTg	12/34	0.226827425406336	3	FACETS	0.782	0.683	0.889	0.522	0.455	0.593	SUBCLONAL	2	TRUE	0	0.177396578291419	3		634	557	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312990	30312990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	45	619	1	ENST00000262643.3:c.793G>A	p.Val265Met	p.V265M	ENST00000262643	NM_001238.2	265	Gtg/Atg	9/12	0.155830914567449	2	FACETS	1	0.954	1	0.699	0.589	0.819	CLONAL	1	TRUE	0	0.177396578291419	2		620	363	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967305	134967305	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	86	747	0	ENST00000398015.3:c.2644A>C	p.Ile882Leu	p.I882L	ENST00000398015	NM_004441.4	882	Atc/Ctc	14/16	0.164269961174246	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	2	TRUE	0	0.177396578291419	2		747	463	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31504735	31504735	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	34	537	0	ENST00000344624.3:c.1595A>T	p.Asp532Val	p.D532V	ENST00000344624		532	gAt/gTt	8/33	0.226827425406336	3	FACETS	1	0.824	1	0.504	0.412	0.608	CLONAL	1	TRUE	1	0.177396578291419	3		537	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577103	7577103	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	97	709	0	ENST00000269305.4:c.835G>T	p.Gly279Trp	p.G279W	ENST00000269305	NM_001126112.2	279	Ggg/Tgg	8/11	1	2	FACETS	0.658	0.586	0.735	0.658	0.586	0.735	SUBCLONAL	1	TRUE	1	0.35	2		709	842	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115252318	115252318	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	87	285	0	ENST00000369535.4:c.322G>T	p.Asp108Tyr	p.D108Y	ENST00000369535	NM_002524.4	108	Gat/Tat	4/7	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.35	2		285	466	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846309	156846309	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	130	688	0	ENST00000524377.1:c.1750C>A	p.Pro584Thr	p.P584T	ENST00000524377	NM_002529.3	584	Ccc/Acc	14/17	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.35	2		688	742	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398286	+	missense_variant	Missense_Mutation	DNP	CA	CA	AC	novel	NA	P-0042874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	77	382	0	ENST00000311936.3:c.33_34delinsGT	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	11	gcTGgt/gcGTgt	2/5	1	2	FACETS	0.84	0.739	0.948	0.84	0.739	0.948	CLONAL	1	TRUE	1	0.35	2		382	524	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69230530	69230531	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0042874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	33	270	0	ENST00000462284.1:c.918+2dup		p.X306_splice	ENST00000462284	NM_002392.5	306			1	2	FACETS	0.547	0.446	0.66	0.547	0.446	0.66	SUBCLONAL	1	TRUE	1	0.35	2		270	345	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675052	40675052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1418251053	NA	P-0042874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	135	606	0	ENST00000249776.8:c.16G>A	p.Ala6Thr	p.A6T	ENST00000249776	NM_033286.3	6	Gcc/Acc	1/9	1	2	FACETS	0.929	0.845	1	0.929	0.845	1	CLONAL	1	TRUE	1	0.35	2		606	830	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73992010	73992010	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	186	772	1	ENST00000318443.5:c.30G>T	p.Met10Ile	p.M10I	ENST00000318443	NM_001024736.1	10	atG/atT	2/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.35	2		773	904	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384795	17384795	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	179	692	0	ENST00000359435.4:c.427G>T	p.Glu143Ter	p.E143*	ENST00000359435	NM_001033549.1	143	Gag/Tag	4/9	0.300206392088222	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.35	1		692	754	SUCCESS
ALK	238	MSKCC	GRCh37	2	29450526	29450526	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	114	591	0	ENST00000389048.3:c.2828C>A	p.Ala943Asp	p.A943D	ENST00000389048	NM_004304.4	943	gCc/gAc	17/29	1	2	FACETS	0.965	0.87	1	0.965	0.87	1	CLONAL	1	TRUE	1	0.35	2		591	675	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750370	39750370	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	71	305	0	ENST00000361337.2:c.1985G>T	p.Arg662Leu	p.R662L	ENST00000361337	NM_003286.2	662	cGg/cTg	19/21	1	2	FACETS	0.928	0.813	1	0.928	0.813	1	CLONAL	1	TRUE	1	0.35	2		305	437	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256711	46256711	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	110	416	0	ENST00000371998.3:c.767G>C	p.Gly256Ala	p.G256A	ENST00000371998		256	gGa/gCa	8/23	1	2	FACETS	0.91	0.818	1	0.91	0.818	1	CLONAL	1	TRUE	1	0.35	2		416	691	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604307	189604307	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	43	379	0	ENST00000264731.3:c.1474C>G	p.Pro492Ala	p.P492A	ENST00000264731	NM_003722.4	492	Cct/Gct	11/14	1	2	FACETS	0.484	0.404	0.572	0.484	0.404	0.572	SUBCLONAL	1	TRUE	1	0.35	2		379	508	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509931	187509931	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	68	293	0	ENST00000441802.2:c.13582G>T	p.Glu4528Ter	p.E4528*	ENST00000441802	NM_005245.3	4528	Gag/Tag	27/27	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.35	2		293	340	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131895012	131895012	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	79	287	0	ENST00000265335.6:c.166G>T	p.Asp56Tyr	p.D56Y	ENST00000265335		56	Gat/Tat	2/25	0.201444290796455	2	FACETS	1	0.947	1	0.563	0.498	0.632	INDETERMINATE	1	TRUE	0	0.35	2		287	401	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93953221	93953221	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	67	351	0	ENST00000369303.4:c.2920C>G	p.Gln974Glu	p.Q974E	ENST00000369303	NM_004440.3	974	Caa/Gaa	17/17	1	2	FACETS	0.822	0.716	0.935	0.822	0.716	0.935	CLONAL	1	TRUE	1	0.35	2		351	466	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931878	68931878	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	212	541	0	ENST00000288368.4:c.308A>T	p.Gln103Leu	p.Q103L	ENST00000288368	NM_024870.2	103	cAa/cTa	3/40	0.248277355480403	3	FACETS	1	0.989	1	0.683	0.634	0.734	CLONAL	1	TRUE	1	0.35	3		541	1042	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0042875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	208	289	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.829643300373	5	FACETS	0.841	0.784	0.899	0.42	0.392	0.45	CLONAL	2	TRUE	1	0.877680282799374	5		289	653	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0042875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	818	545	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.488816680507288	3	FACETS	1	0.996	1			1	INDETERMINATE	3	TRUE	NA	0.877680282799374	3		545	877	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212182	98212182	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371346118	NA	P-0042875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	176	289	1	ENST00000331920.6:c.3490G>A	p.Val1164Ile	p.V1164I	ENST00000331920	NM_000264.3	1164	Gtt/Att	21/24	0.877680282799374	3	FACETS	0.922	0.853	0.993	0.461	0.426	0.497	CLONAL	1	TRUE	1	0.877680282799374	3		290	626	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513220	44513220	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	319	218	1	ENST00000291552.4:c.715C>T	p.Arg239Ter	p.R239*	ENST00000291552	NM_006758.2	239	Cga/Tga	8/8	0.488816680507288	3	FACETS	1	0.978	1			1	INDETERMINATE	2	TRUE	NA	0.877680282799374	3		219	508	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202346	138202346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780709741	NA	P-0042875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	553	519	0	ENST00000237289.4:c.2263G>A	p.Glu755Lys	p.E755K	ENST00000237289	NM_001270507.1	755	Gaa/Aaa	9/9	0.877680282799374	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.877680282799374	3		519	892	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405141	139405141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1448345366	NA	P-0042875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	391	761	1	ENST00000277541.6:c.2704C>T	p.Arg902Cys	p.R902C	ENST00000277541	NM_017617.3	902	Cgc/Tgc	17/34	0.877680282799374	3	FACETS	1	0.961	1	0.506	0.481	0.532	CLONAL	1	TRUE	1	0.877680282799374	3		762	1266	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845464	151845464	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	210	474	0	ENST00000262189.6:c.13548A>C	p.Leu4516Phe	p.L4516F	ENST00000262189	NM_170606.2	4516	ttA/ttC	52/59	0.877680282799374	3	FACETS	0.905	0.843	0.969	0.302	0.281	0.323	CLONAL	1	TRUE	0	0.877680282799374	3		474	761	SUCCESS
APC	324	MSKCC	GRCh37	5	112175350	112175354	+	frameshift_variant	Frame_Shift_Del	DEL	ATTTT	ATTTT	-	novel	NA	P-0042875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	187	211	0	ENST00000257430.4:c.4059_4063del	p.Glu1353AspfsTer20	p.E1353Dfs*20	ENST00000257430	NM_000038.5	1353	gaATTTTct/gact	16/16	0.862370068952887	2	FACETS	0.964	0.929	0.995	0.964	0.929	0.995	CLONAL	2	TRUE	0	0.877680282799374	2		211	221	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609638	81609638	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200182253	NA	P-0042875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	239	486	0	ENST00000298171.2:c.1236G>A	p.Met412Ile	p.M412I	ENST00000298171	NM_000369.2	412	atG/atA	10/10	0.862370068952887	2	FACETS	0.95	0.895	1	0.475	0.447	0.504	CLONAL	1	TRUE	0	0.877680282799374	2		486	573	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398884	398884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375133421	NA	P-0042875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	482	397	1	ENST00000380956.4:c.694G>A	p.Gly232Arg	p.G232R	ENST00000380956	NM_001195286.1	232	Gga/Aga	6/9	0.877680282799374	3	FACETS	0.967	0.933	1	0.967	0.933	1	CLONAL	2	TRUE	1	0.877680282799374	3		398	817	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63662078	63662078	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	148	310	0	ENST00000279873.7:c.182G>A	p.Trp61Ter	p.W61*	ENST00000279873	NM_032199.2	61	tGg/tAg	2/10	0.775602925595214	3	FACETS	0.867	0.795	0.94			1	CLONAL	1	TRUE	NA	0.877680282799374	3		310	560	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17940934	17940934	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	371	729	0	ENST00000458235.1:c.3190C>G	p.Pro1064Ala	p.P1064A	ENST00000458235	NM_000215.3	1064	Cct/Gct	23/24	0.877680282799374	2	FACETS	1	0.983	1	0.529	0.505	0.553	CLONAL	1	TRUE	0	0.877680282799374	2		729	799	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649020	86649020	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	84	299	0	ENST00000274376.6:c.1300G>C	p.Gly434Arg	p.G434R	ENST00000274376	NM_002890.2	434	Gga/Cga	9/25	0.862370068952887	2	FACETS	0.847	0.762	0.935	0.423	0.381	0.468	CLONAL	1	TRUE	0	0.877680282799374	2		299	226	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13949263	13949263	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	275	212	0	ENST00000405192.2:c.865T>A	p.Phe289Ile	p.F289I	ENST00000405192	NM_001163147.1	289	Ttc/Atc	9/12	0.84381164838442	5	FACETS	0.933	0.896	0.969	0.933	0.896	0.969	CLONAL	4	TRUE	1	0.877680282799374	5		212	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0042878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	130	591	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.423755611352504	1	FACETS	0.723	0.658	0.791	0.723	0.658	0.791	SUBCLONAL	1	TRUE	0	0.477579599684839	1		591	573	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409089	139409089	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs79782048	NA	P-0042878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	176	804	0	ENST00000277541.6:c.2080G>A	p.Glu694Lys	p.E694K	ENST00000277541	NM_017617.3	694	Gag/Aag	13/34	0.142214887661387	1	FACETS	0.637	0.587	0.689	0.637	0.587	0.689	INDETERMINATE	1	TRUE	0	0.477579599684839	1		804	881	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248980	55248981	+	splice_region_variant,intron_variant	In_Frame_Ins	INS	-	-	TCCAGGAAGCCT	rs397517106	NA	P-0042878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	176	463	0	ENST00000275493.2:c.2284-5_2290dup		p.A763_Y764insFQEA	ENST00000275493	NM_005228.3	763			0.477579599684839	3	FACETS	0.808	0.749	0.869	0.808	0.749	0.869	CLONAL	2	TRUE	1	0.477579599684839	3		463	565	SUCCESS
AR	367	MSKCC	GRCh37	X	66863172	66863172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	157	481	0	ENST00000374690.3:c.1691G>A	p.Gly564Glu	p.G564E	ENST00000374690	NM_000044.3	564	gGa/gAa	2/8	0.429484772780197	5	FACETS	1	0.982	1	0.423	0.387	0.46	CLONAL	1	TRUE	2	0.477579599684839	5		481	890	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233171	69233171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6084	434	238	0	ENST00000462284.1:c.1036G>A	p.Glu346Lys	p.E346K	ENST00000462284	NM_002392.5	346	Gaa/Aaa	11/11	0.882825124531575	30	FACETS	1	0.953	1			1	CLONAL	2	TRUE	NA	0.882825124531575	30		238	6518	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233396	69233396	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1225427397	NA	P-0042879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7142	506	254	0	ENST00000462284.1:c.1261G>A	p.Glu421Lys	p.E421K	ENST00000462284	NM_002392.5	421	Gaa/Aaa	11/11	0.882825124531575	30	FACETS	1	0.951	1			1	CLONAL	2	TRUE	NA	0.882825124531575	30		254	7648	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233560	69233560	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6623	440	260	0	ENST00000462284.1:c.1425G>C	p.Lys475Asn	p.K475N	ENST00000462284	NM_002392.5	475	aaG/aaC	11/11	0.882825124531575	30	FACETS	0.943	0.892	0.995			1	CLONAL	2	TRUE	NA	0.882825124531575	30		260	7063	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0042912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	92	427	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.948	1	1	0.987	1	CLONAL	2	TRUE	1	0.183919576864527	2		427	453	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933283	100933283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1222662053	NA	P-0042912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	44	362	0	ENST00000325455.5:c.2107C>T	p.His703Tyr	p.H703Y	ENST00000325455	NM_001202474.3	703	Cat/Tat	4/8	0.183919576864527	4	FACETS	0.816	0.687	0.958	0.544	0.458	0.639	CLONAL	2	TRUE	1	0.183919576864527	4		362	347	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672755	86672755	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	70	224	0	ENST00000274376.6:c.2242G>C	p.Asp748His	p.D748H	ENST00000274376	NM_002890.2	748	Gac/Cac	17/25	0.183919576864527	15	FACETS	0.939	0.821	1			1	CLONAL	4	TRUE	NA	0.183919576864527	15		224	445	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0042935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	39	212	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.832	0.693	0.986	0.832	0.693	0.986	CLONAL	1	TRUE	1	0.32	2		212	293	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144113	11144113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	139	733	3	ENST00000358026.2:c.3694G>A	p.Gly1232Ser	p.G1232S	ENST00000358026	NM_001128849.1	1232	Ggc/Agc	26/36	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.32	2		736	867	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023745	27023764	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGAACTCCCCAGCCCACC	GGGGAACTCCCCAGCCCACC	-	novel	NA	P-0042935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	39	509	0	ENST00000324856.7:c.852_871del	p.Gly285HisfsTer108	p.G285Hfs*108	ENST00000324856	NM_006015.4	284	gGGGGAACTCCCCAGCCCACC/g	1/20	1	2	FACETS	0.555	0.46	0.661	0.555	0.46	0.661	SUBCLONAL	1	TRUE	1	0.32	2		509	439	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099374	27099374	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	94	601	0	ENST00000324856.7:c.3612del	p.Met1205Ter	p.M1205*	ENST00000324856	NM_006015.4	1204	tCc/tc	14/20	1	2	FACETS	0.962	0.857	1	0.962	0.857	1	CLONAL	1	TRUE	1	0.32	2		601	611	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276699	115276699	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	33	329	0	ENST00000438362.2:c.760G>C	p.Glu254Gln	p.E254Q	ENST00000438362	NM_001242891.1	254	Gag/Cag	8/20	1	2	FACETS	0.716	0.585	0.862	0.716	0.585	0.862	SUBCLONAL	1	TRUE	1	0.32	2		329	288	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645475	67645481	+	frameshift_variant	Frame_Shift_Del	DEL	GTAATAT	GTAATAT	-	novel	NA	P-0042935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	41	306	0	ENST00000264010.4:c.741_747del	p.Asn248SerfsTer13	p.N248Sfs*13	ENST00000264010	NM_006565.3	247	gGTAATATg/gg	3/12	1	2	FACETS	0.743	0.62	0.878	0.743	0.62	0.878	SUBCLONAL	1	TRUE	1	0.32	2		306	345	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584674	187584674	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	88	547	1	ENST00000441802.2:c.3359C>A	p.Ser1120Ter	p.S1120*	ENST00000441802	NM_005245.3	1120	tCa/tAa	3/27	1	2	FACETS	0.973	0.864	1	0.973	0.864	1	CLONAL	1	TRUE	1	0.32	2		548	565	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984404	201984408	+	stop_gained	Nonsense_Mutation	ONP	AACTC	AACTC	CACTG	novel	NA	P-0042935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	105	651	0	ENST00000359651.3:c.1069_1073delinsCACTG	p.Asn357_Ser358delinsHisTer	p.N357_S358delinsH*	ENST00000359651		357	AACTCa/CACTGa	8/8	1	2	FACETS	0.822	0.736	0.914	0.822	0.736	0.914	CLONAL	1	TRUE	1	0.32	2		651	798	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0042993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	485	887	2	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.850870196303819	2		889	1078	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	236	737	0				ENST00000310581	NM_198253.2	-/1132			0.315995235383938	1	FACETS	0.653	0.617	0.69	0.653	0.617	0.69	INDETERMINATE	1	TRUE	0	0.850870196303819	1		737	488	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453136	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	rs397516897	NA	P-0042993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	258	513	1	ENST00000288602.6:c.1799_1801del	p.Val600_Lys601delinsGlu	p.V600_K601delinsE	ENST00000288602	NM_004333.4	600	gTGAaa/gaa	15/18	0.850870196303819	3	FACETS	0.969	0.922	1	0.969	0.922	1	CLONAL	2	TRUE	1	0.850870196303819	3		514	446	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444401	50444401	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	462	574	1	ENST00000331340.3:c.331C>T	p.Arg111Ter	p.R111*	ENST00000331340	NM_006060.4	111	Cga/Tga	4/8	0.850870196303819	3	FACETS	0.927	0.892	0.961	0.927	0.892	0.961	CLONAL	2	TRUE	1	0.850870196303819	3		575	835	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601881	43601881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	402	803	4	ENST00000355710.3:c.925G>A	p.Glu309Lys	p.E309K	ENST00000355710	NM_020975.4	309	Gag/Aag	5/20	0.850870196303819	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.850870196303819	1		807	536	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355283	81355283	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs5745703	NA	P-0042993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	110	409	0	ENST00000222390.5:c.1091G>A	p.Trp364Ter	p.W364*	ENST00000222390	NM_000601.4	364	tGg/tAg	9/18	0.850870196303819	3	FACETS	0.836	0.756	0.919	0.418	0.378	0.46	CLONAL	1	TRUE	1	0.850870196303819	3		409	441	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729162	66729162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519732	NA	P-0042993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	456	754	3	ENST00000307102.5:c.370C>T	p.Pro124Ser	p.P124S	ENST00000307102	NM_002755.3	124	Ccg/Tcg	3/11	NA	2	FACETS	0.861	0.823	0.899			1	INDETERMINATE	1	TRUE	NA	0.850870196303819	2		757	1245	SUCCESS
APC	324	MSKCC	GRCh37	5	112090657	112090657	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs145945630	NA	P-0042993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	97	378	1	ENST00000257430.4:c.70C>T	p.Arg24Ter	p.R24*	ENST00000257430	NM_000038.5	24	Cga/Tga	2/16	0.315995235383938	1	FACETS	0.575	0.522	0.627	0.575	0.522	0.627	INDETERMINATE	1	TRUE	0	0.850870196303819	1		379	228	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740272	162740272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757051385	NA	P-0042993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	273	488	4	ENST00000367921.3:c.1474C>T	p.Pro492Ser	p.P492S	ENST00000367921	NM_006182.2	492	Cca/Tca	12/18	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.850870196303819	2		492	642	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590669	189590669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	189	535	2	ENST00000264731.3:c.1234G>A	p.Glu412Lys	p.E412K	ENST00000264731	NM_003722.4	412	Gaa/Aaa	10/14	0.731335843165989	1	FACETS	0.902	0.856	0.946	0.902	0.856	0.946	CLONAL	1	TRUE	0	0.850870196303819	1		537	283	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625228	69625228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868995912	NA	P-0042993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1239	406	913	2	ENST00000334134.2:c.565G>A	p.Glu189Lys	p.E189K	ENST00000334134	NM_005247.2	189	Gag/Aag	3/3	0.737827459482237	5	FACETS	1	0.994	1			1	CLONAL	1	TRUE	NA	0.850870196303819	5		915	1645	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983071	149983071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	122	680	3	ENST00000253339.5:c.3187G>A	p.Gly1063Arg	p.G1063R	ENST00000253339		1063	Gga/Aga	7/7	1	2	FACETS	0.962	0.884	1	0.962	0.884	1	CLONAL	1	TRUE	1	0.850870196303819	2		683	298	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197235	26197235	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	354	578	6	ENST00000356476.2:c.244G>A	p.Asp82Asn	p.D82N	ENST00000356476		82	Gat/Aat	1/1	0.351541729956141	3	FACETS	0.766	0.73	0.802	0.766	0.73	0.802	INDETERMINATE	2	TRUE	1	0.850870196303819	3		584	774	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099851	27099851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550840683	NA	P-0042993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	301	653	2	ENST00000324856.7:c.3730C>T	p.Pro1244Ser	p.P1244S	ENST00000324856	NM_006015.4	1244	Ccc/Tcc	15/20	1	2	FACETS	0.988	0.937	1	0.988	0.937	1	CLONAL	1	TRUE	1	0.850870196303819	2		655	716	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873224	71873224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756093179	NA	P-0042993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	165	579	1	ENST00000357731.5:c.970G>A	p.Gly324Arg	p.G324R	ENST00000357731	NM_173808.2	324	Ggg/Agg	7/7	1	2	FACETS	0.935	0.868	1	0.935	0.868	1	CLONAL	1	TRUE	1	0.850870196303819	2		580	415	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483213	120483213	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	275	591	0	ENST00000256646.2:c.3148A>T	p.Ser1050Cys	p.S1050C	ENST00000256646	NM_024408.3	1050	Agc/Tgc	19/34	1	2	FACETS	0.941	0.889	0.993	0.941	0.889	0.993	CLONAL	1	TRUE	1	0.850870196303819	2		591	687	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450061	32450061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751432306	NA	P-0042993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	311	733	3	ENST00000332351.3:c.751G>A	p.Gly251Ser	p.G251S	ENST00000332351	NM_024426.4	251	Ggc/Agc	2/10	0.315995235383938	1	FACETS	0.637	0.606	0.669	0.637	0.606	0.669	INDETERMINATE	1	TRUE	0	0.850870196303819	1		736	659	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623815	28623815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866905017	NA	P-0042993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	123	677	0	ENST00000241453.7:c.839G>A	p.Gly280Glu	p.G280E	ENST00000241453	NM_004119.2	280	gGa/gAa	7/24	0.183850106954515	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.850870196303819	0		677	368	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647482	23647482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1174443228	NA	P-0042993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	221	764	3	ENST00000261584.4:c.385C>T	p.Pro129Ser	p.P129S	ENST00000261584	NM_024675.3	129	Ccc/Tcc	4/13	0.315995235383938	1	FACETS	0.502	0.471	0.535	0.502	0.471	0.535	INDETERMINATE	1	TRUE	0	0.850870196303819	1		767	594	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553328	106553328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	288	623	3	ENST00000369096.4:c.1293G>A	p.Met431Ile	p.M431I	ENST00000369096	NM_001198.3	431	atG/atA	5/7	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.850870196303819	2		626	656	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724424	117724424	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1279832487	NA	P-0042993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	257	685	4	ENST00000368508.3:c.455C>T	p.Ser152Phe	p.S152F	ENST00000368508	NM_002944.2	152	tCc/tTc	6/43	1	2	FACETS	0.877	0.826	0.929	0.877	0.826	0.929	CLONAL	1	TRUE	1	0.850870196303819	2		689	689	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913286	NA	P-0043006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	23	550	0	ENST00000263967.3:c.1636C>G	p.Gln546Glu	p.Q546E	ENST00000263967	NM_006218.2	546	Cag/Gag	10/21	0.77140905945823	1	FACETS	0.109	0.085	0.138	0.109	0.085	0.138	SUBCLONAL	1	TRUE	0	0.77140905945823	1		550	335	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374245	138374245	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	33	496	0	ENST00000289153.2:c.3199G>T	p.Asp1067Tyr	p.D1067Y	ENST00000289153	NM_006219.2	1067	Gac/Tac	22/22	0.77140905945823	1	FACETS	0.116	0.094	0.141	0.116	0.094	0.141	SUBCLONAL	1	TRUE	0	0.77140905945823	1		496	453	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941293	71941293	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	32	661	0	ENST00000298229.2:c.1068G>A	p.Trp356Ter	p.W356*	ENST00000298229	NM_001567.3	356	tgG/tgA	9/28	0.77140905945823	1	FACETS	0.083	0.067	0.101	0.083	0.067	0.101	SUBCLONAL	1	TRUE	0	0.77140905945823	1		661	614	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624238	89624239	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	231	155	0	ENST00000371953.3:c.13dup	p.Ile5AsnfsTer6	p.I5Nfs*6	ENST00000371953	NM_000314.4	4	-/A	1/9	0.77140905945823	2	FACETS	0.927	0.888	0.965	0.927	0.888	0.965	CLONAL	2	TRUE	0	0.77140905945823	2		155	323	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943350	71943350	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	26	571	0	ENST00000298229.2:c.1682A>C	p.His561Pro	p.H561P	ENST00000298229	NM_001567.3	561	cAc/cCc	14/28	0.77140905945823	1	FACETS	0.095	0.074	0.118	0.095	0.074	0.118	SUBCLONAL	1	TRUE	0	0.77140905945823	1		571	438	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443613	52443613	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	306	517	0	ENST00000460680.1:c.79G>C	p.Val27Leu	p.V27L	ENST00000460680	NM_004656.3	27	Gtg/Ctg	3/17	1	2	FACETS	0.971	0.919	1	0.971	0.919	1	CLONAL	1	TRUE	1	0.77140905945823	2		517	817	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0043018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	505	739	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.67876592222032	2	FACETS	0.891	0.864	0.919	0.891	0.864	0.919	CLONAL	2	TRUE	0	0.747345415898117	2		741	758	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248980	55248981	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	TCCAGGAAGCAT	novel	NA	P-0043018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	435	711	0	ENST00000275493.2:c.2288_2289insATTCCAGGAAGC		p.X763_splice	ENST00000275493	NM_005228.3	763			0.747345415898117	5	FACETS	1	0.991	1	0.759	0.725	0.792	CLONAL	2	TRUE	2	0.747345415898117	5		711	1085	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	444	1090	0	ENST00000269305.4:c.853G>T	p.Glu285Ter	p.E285*	ENST00000269305	NM_001126112.2	285	Gag/Tag	8/11	0.397313380752194	1	FACETS	0.807	0.772	0.842	1	0.996	1	CLONAL	2	TRUE	0	0.397313380752194	1		1090	1110	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439637	140439637	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	47	243	0	ENST00000288602.6:c.2102G>C	p.Arg701Thr	p.R701T	ENST00000288602	NM_004333.4	701	aGa/aCa	17/18	1	2	FACETS	0.512	0.432	0.6	0.512	0.432	0.6	SUBCLONAL	1	TRUE	1	0.397313380752194	2		243	462	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444900	49444900	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	271	1056	0	ENST00000301067.7:c.2566G>C	p.Glu856Gln	p.E856Q	ENST00000301067	NM_003482.3	856	Gag/Cag	10/54	1	2	FACETS	0.756	0.711	0.802	1	0.993	1	SUBCLONAL	2	TRUE	1	0.397313380752194	2		1056	902	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262429	16262429	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	70	569	0	ENST00000375759.3:c.9694G>T	p.Glu3232Ter	p.E3232*	ENST00000375759	NM_015001.2	3232	Gaa/Taa	11/15	1	2	FACETS	0.877	0.768	0.993	0.877	0.768	0.993	CLONAL	1	TRUE	1	0.397313380752194	2		569	402	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097608	27097608	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0043020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	88	613	0	ENST00000324856.7:c.3199-2A>G		p.X1067_splice	ENST00000324856	NM_006015.4	1067			1	2	FACETS	0.772	0.685	0.864	0.772	0.685	0.864	SUBCLONAL	1	TRUE	1	0.397313380752194	2		613	574	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363281	40363281	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	226	918	0	ENST00000397332.2:c.948C>A	p.His316Gln	p.H316Q	ENST00000397332	NM_001033082.2	316	caC/caA	3/3	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.397313380752194	2		918	916	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115269651	115269651	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	90	370	0	ENST00000438362.2:c.1555C>G	p.Gln519Glu	p.Q519E	ENST00000438362	NM_001242891.1	519	Caa/Gaa	13/20	1	2	FACETS	0.806	0.717	0.901	0.806	0.717	0.901	CLONAL	1	TRUE	1	0.397313380752194	2		370	562	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154851	2154851	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	151	1115	0	ENST00000434045.2:c.370G>C	p.Glu124Gln	p.E124Q	ENST00000434045	NM_001127598.1	124	Gag/Cag	4/5	1	2	FACETS	0.754	0.689	0.823	0.754	0.689	0.823	SUBCLONAL	1	TRUE	1	0.397313380752194	2		1115	1008	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21643300	21643300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	77	237	0	ENST00000421138.2:c.227C>T	p.Ser76Phe	p.S76F	ENST00000421138		76	tCt/tTt	5/16	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.397313380752194	2		237	352	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690608	88690608	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	122	589	1	ENST00000360948.2:c.422C>A	p.Thr141Lys	p.T141K	ENST00000360948	NM_001012338.2	141	aCa/aAa	5/19	1	2	FACETS	0.82	0.742	0.902	0.82	0.742	0.902	CLONAL	1	TRUE	1	0.397313380752194	2		590	749	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012115	16012115	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	94	240	0	ENST00000268712.3:c.2167C>G	p.Pro723Ala	p.P723A	ENST00000268712	NM_006311.3	723	Cca/Gca	19/46	0.397313380752194	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.397313380752194	1		240	354	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170540	11170540	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	252	1076	1	ENST00000358026.2:c.4843G>T	p.Glu1615Ter	p.E1615*	ENST00000358026	NM_001128849.1	1615	Gag/Tag	34/36	0.397313380752194	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.397313380752194	1		1077	787	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086074	16086074	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	152	786	0	ENST00000281043.3:c.1250C>A	p.Ala417Asp	p.A417D	ENST00000281043	NM_005378.4	417	gCc/gAc	3/3	0.181740526313993	2	FACETS	0.789	0.721	0.86	0.394	0.36	0.43	INDETERMINATE	1	TRUE	0	0.397313380752194	2		786	970	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445423	29445423	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	150	1083	0	ENST00000389048.3:c.3410G>C	p.Gly1137Ala	p.G1137A	ENST00000389048	NM_004304.4	1137	gGa/gCa	21/29	0.181740526313993	2	FACETS	0.659	0.601	0.72	0.329	0.3	0.36	INDETERMINATE	1	TRUE	0	0.397313380752194	2		1083	1146	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189277	99189277	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0043020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	167	598	0	ENST00000074304.5:c.2534-1G>A		p.X845_splice	ENST00000074304	NM_001134224.1	845			0.397313380752194	3	FACETS	1	0.985	1	0.654	0.602	0.709	CLONAL	1	TRUE	1	0.397313380752194	3		598	770	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468539	89468539	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	30	190	0	ENST00000336596.2:c.2073A>C	p.Lys691Asn	p.K691N	ENST00000336596	NM_005233.5	691	aaA/aaC	11/17	1	2	FACETS	0.53	0.428	0.645	0.53	0.428	0.645	SUBCLONAL	1	TRUE	1	0.397313380752194	2		190	285	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561781	55561781	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs755092278	NA	P-0043020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	167	495	0	ENST00000288135.5:c.171A>T	p.Leu57Phe	p.L57F	ENST00000288135	NM_000222.2	57	ttA/ttT	2/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.397313380752194	2		495	659	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955970	55955970	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0043020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	117	326	0	ENST00000263923.4:c.3193-1G>T		p.X1065_splice	ENST00000263923	NM_002253.2	1065			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.397313380752194	2		326	508	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286187	66286187	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	43	171	0	ENST00000273854.3:c.1499T>A	p.Leu500Gln	p.L500Q	ENST00000273854	NM_004439.5	500	cTa/cAa	6/18	1	2	FACETS	0.674	0.566	0.793	0.674	0.566	0.793	SUBCLONAL	1	TRUE	1	0.397313380752194	2		171	321	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064788	80064788	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	40	141	0	ENST00000265081.6:c.2219C>T	p.Pro740Leu	p.P740L	ENST00000265081	NM_002439.4	740	cCt/cTt	15/24	0.196365599499612	3	FACETS	0.704	0.586	0.833	0.352	0.293	0.417	INDETERMINATE	1	TRUE	1	0.397313380752194	3		141	343	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778161	27778161	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	111	1040	0	ENST00000369163.2:c.310C>A	p.Leu104Ile	p.L104I	ENST00000369163	NM_003536.2	104	Ctc/Atc	1/1	0.172880809775052	3	FACETS	0.69	0.619	0.765	0.345	0.309	0.383	INDETERMINATE	1	TRUE	1	0.397313380752194	3		1040	971	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946188	13946188	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	99	487	0	ENST00000405192.2:c.908G>C	p.Gly303Ala	p.G303A	ENST00000405192	NM_001163147.1	303	gGa/gCa	10/12	1	2	FACETS	0.777	0.695	0.865	0.777	0.695	0.865	SUBCLONAL	1	TRUE	1	0.397313380752194	2		487	641	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273126	55273126	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745321541	NA	P-0043020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	334	910	0	ENST00000275493.2:c.3449C>T	p.Thr1150Ile	p.T1150I	ENST00000275493	NM_005228.3	1150	aCa/aTa	28/28	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.397313380752194	2		910	1147	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381567	81381567	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	37	175	0	ENST00000222390.5:c.494C>A	p.Ser165Ter	p.S165*	ENST00000222390	NM_000601.4	165	tCg/tAg	5/18	1	2	FACETS	0.584	0.483	0.696	0.584	0.483	0.696	SUBCLONAL	1	TRUE	1	0.397313380752194	2		175	319	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460511	8460511	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1213689339	NA	P-0043020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	213	634	0	ENST00000356435.5:c.3775C>A	p.Pro1259Thr	p.P1259T	ENST00000356435		1259	Cca/Aca	22/35	0.397313380752194	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.397313380752194	1		634	656	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0043031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	404	471	1	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.244294170400088	5	FACETS	0.944	0.898	0.991	0.944	0.898	0.991	CLONAL	3	TRUE	2	0.33	5		472	1292	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0043031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	260	663	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.254760331958459	2	FACETS	1	0.992	1	0.694	0.649	0.739	CLONAL	1	TRUE	0	0.33	2		663	1136	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216711	36216711	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770209871	NA	P-0043031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1543	93	536	0	ENST00000222270.7:c.3877C>T	p.Arg1293Cys	p.R1293C	ENST00000222270	NM_014727.1	1293	Cgc/Tgc	13/37	0.304770009535141	9	FACETS	0.742	0.657	0.834			1	SUBCLONAL	1	TRUE	NA	0.33	9		536	1636	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967054	25967054	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1303307752	NA	P-0043031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	93	660	0	ENST00000435504.4:c.2152G>A	p.Asp718Asn	p.D718N	ENST00000435504		718	Gac/Aac	13/13	0.304770009535141	3	FACETS	0.597	0.53	0.67	0.199	0.176	0.224	SUBCLONAL	1	TRUE	0	0.33	3		660	1099	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593555	215593555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881424	NA	P-0043031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	48	362	0	ENST00000260947.4:c.2179G>A	p.Asp727Asn	p.D727N	ENST00000260947	NM_000465.2	727	Gat/Aat	11/11	0.304770009535141	2	FACETS	0.457	0.386	0.536	0.229	0.193	0.268	SUBCLONAL	1	TRUE	0	0.33	2		362	636	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22142668	22142668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	17	276	0	ENST00000215832.6:c.734G>A	p.Gly245Glu	p.G245E	ENST00000215832	NM_002745.4	245	gGa/gAa	6/9	0.304770009535141	5	FACETS	0.951	0.714	1	0.238	0.178	0.307	CLONAL	1	TRUE	1	0.33	5		276	162	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15840928	15840928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	34	356	0	ENST00000307771.7:c.1012G>A	p.Glu338Lys	p.E338K	ENST00000307771	NM_005089.3	338	Gaa/Aaa	11/11	0.0700316195046855	3	FACETS	0.584	0.477	0.704			1	INDETERMINATE	1	TRUE	NA	0.33	3		356	411	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732942	44733085	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCGGCGGACTGGACAGGTACGGGCCGCCGTCACTCGCCCGGTCGGCTCCGGACGGGCAGTAGCCGCTCTCCCGGGAGGACCGAGCGCGGCTTGTCTCTGGCGGCGGCGGGGCGGGCACCTCGGTTTGGCGCTCTTCGCGCCGC	CTCGGCGGACTGGACAGGTACGGGCCGCCGTCACTCGCCCGGTCGGCTCCGGACGGGCAGTAGCCGCTCTCCCGGGAGGACCGAGCGCGGCTTGTCTCTGGCGGCGGCGGGGCGGGCACCTCGGTTTGGCGCTCTTCGCGCCGC	-	novel	NA	P-0043031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	91	564	0	ENST00000377967.4:c.148_162-82del		p.X50_splice	ENST00000377967	NM_021140.2	50		1/29	0.0700316195046855	3	FACETS	0.717	0.636	0.804			1	INDETERMINATE	1	TRUE	NA	0.33	3		564	896	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0043049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	425	555	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.3	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		555	481	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866382	42866382	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	425	780	0	ENST00000398585.3:c.250T>A	p.Ser84Thr	p.S84T	ENST00000398585	NM_001135099.1	84	Tcc/Acc	3/14	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.93	2		780	890	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0043073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	337	305	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.544966939121982	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.544966939121982	3		305	784	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0043078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	376	715	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.430579716687785	2	FACETS	0.929	0.886	0.972	0.929	0.886	0.972	CLONAL	2	TRUE	0	0.457432392500434	2		715	885	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266224	198266224	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	168	372	0	ENST00000335508.6:c.2396A>G	p.Asp799Gly	p.D799G	ENST00000335508	NM_012433.2	799	gAt/gGt	17/25	0.45325757285881	4	FACETS	0.92	0.85	0.992	0.613	0.566	0.661	CLONAL	2	TRUE	1	0.457432392500434	4		372	582	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429415	47429415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs969755578	NA	P-0043078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	112	518	0	ENST00000377045.4:c.1543C>T	p.Arg515Cys	p.R515C	ENST00000377045	NM_001654.4	515	Cgt/Tgt	14/16	0.434580851220454	3	FACETS	0.901	0.811	0.995	0.45	0.405	0.498	CLONAL	1	TRUE	1	0.457432392500434	3		518	668	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579357	7579358	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGGAAAC	rs1131691004	NA	P-0043150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	428	906	0	ENST00000269305.4:c.323_329dup	p.Leu111PhefsTer40	p.L111Ffs*40	ENST00000269305	NM_001126112.2	110	cgt/cgGTTTCCGt	4/11	0.544132781161528	2	FACETS	0.792	0.758	0.826	0.792	0.758	0.826	SUBCLONAL	2	TRUE	0	0.554388915784975	2		906	975	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545662	106545662	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1262374005	NA	P-0043150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	178	571	0	ENST00000359195.3:c.3139G>A	p.Asp1047Asn	p.D1047N	ENST00000359195	NM_002649.2	1047	Gac/Aac	11/11	0.547998212827346	3	FACETS	1	0.929	1	0.503	0.464	0.544	CLONAL	1	TRUE	1	0.554388915784975	3		571	815	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149974	202149974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301592633	NA	P-0043150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	212	676	0	ENST00000358485.4:c.1415G>A	p.Arg472Gln	p.R472Q	ENST00000358485	NM_001080125.1	472	cGa/cAa	8/9	0.554388915784975	1	FACETS	0.912	0.853	0.973	0.912	0.853	0.973	CLONAL	1	TRUE	0	0.554388915784975	1		676	606	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546324	46546324	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	118	343	1	ENST00000262741.5:c.205del	p.Asp69IlefsTer7	p.D69Ifs*7	ENST00000262741	NM_003629.3	69	Gat/at	2/10	1	2	FACETS	0.904	0.82	0.991	0.904	0.82	0.991	CLONAL	1	TRUE	1	0.554388915784975	2		344	471	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619374	1619374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753007864	NA	P-0043150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	266	1032	0	ENST00000344749.5:c.1267G>A	p.Gly423Arg	p.G423R	ENST00000344749	NM_001136139.2	423	Ggg/Agg	15/19	0.554388915784975	1	FACETS	0.942	0.888	0.998	0.942	0.888	0.998	CLONAL	1	TRUE	0	0.554388915784975	1		1032	736	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465333	120465333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs891328437	NA	P-0043150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	164	566	0	ENST00000256646.2:c.4928C>T	p.Thr1643Met	p.T1643M	ENST00000256646	NM_024408.3	1643	aCg/aTg	27/34	1	2	FACETS	0.817	0.752	0.885	0.817	0.752	0.885	CLONAL	1	TRUE	1	0.554388915784975	2		566	724	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807484	36807484	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	222	924	0	ENST00000373129.3:c.1180G>C	p.Asp394His	p.D394H	ENST00000373129	NM_032017.1	394	Gac/Cac	12/12	1	2	FACETS	0.89	0.829	0.952	0.89	0.829	0.952	CLONAL	1	TRUE	1	0.554388915784975	2		924	900	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546344	46546368	+	frameshift_variant	Frame_Shift_Del	DEL	TCCTGAAGAGAAACAGAACTGTCCT	TCCTGAAGAGAAACAGAACTGTCCT	-	novel	NA	P-0043150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	124	395	0	ENST00000262741.5:c.161_185del	p.Lys54MetfsTer14	p.K54Mfs*14	ENST00000262741	NM_003629.3	54	aAGGACAGTTCTGTTTCTCTTCAGGAt/at	2/10	1	2	FACETS	0.877	0.798	0.96	0.877	0.798	0.96	CLONAL	1	TRUE	1	0.554388915784975	2		395	510	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989403	7989403	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	495	957	0	ENST00000319144.4:c.283C>G	p.Arg95Gly	p.R95G	ENST00000319144	NM_001139.2	95	Cgt/Ggt	2/15	0.544132781161528	2	FACETS	0.963	0.928	0.998	0.963	0.928	0.998	CLONAL	2	TRUE	0	0.554388915784975	2		957	927	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527512	157527512	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	149	590	0	ENST00000346085.5:c.5237A>C	p.Glu1746Ala	p.E1746A	ENST00000346085	NM_020732.3	1746	gAg/gCg	20/20	1	2	FACETS	0.928	0.852	1	0.928	0.852	1	CLONAL	1	TRUE	1	0.554388915784975	2		590	579	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370702	55370702	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	141	679	0	ENST00000297316.4:c.4A>G	p.Ser2Gly	p.S2G	ENST00000297316	NM_022454.3	2	Agc/Ggc	1/2	0.223081342139722	3	FACETS	0.787	0.718	0.861	0.262	0.239	0.287	INDETERMINATE	1	TRUE	0	0.554388915784975	3		679	825	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651685	48651685	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	251	782	0	ENST00000376670.3:c.851T>G	p.Leu284Arg	p.L284R	ENST00000376670	NM_002049.3	284	cTc/cGc	5/6	0.554388915784975	1	FACETS	0.989	0.931	1	0.989	0.931	1	CLONAL	1	TRUE	0	0.554388915784975	1		782	662	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76764063	76764063	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	172	596	0	ENST00000373344.5:c.7245G>C	p.Gln2415His	p.Q2415H	ENST00000373344	NM_000489.3	2415	caG/caC	35/35	0.554388915784975	1	FACETS	0.948	0.881	1	0.948	0.881	1	CLONAL	1	TRUE	0	0.554388915784975	1		596	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0043155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	27	715	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.697	0.555	0.861	0.697	0.555	0.861	SUBCLONAL	1	TRUE	1	0.195038416947274	2		715	397	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0043155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	75	457	2	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.17916743144946	2	FACETS	0.916	0.806	1	0.916	0.806	1	CLONAL	2	TRUE	0	0.195038416947274	2		459	420	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802635	135802635	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203343	NA	P-0043155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	16	363	0	ENST00000298552.3:c.163C>T	p.Gln55Ter	p.Q55*	ENST00000298552	NM_001162426.1	55	Cag/Tag	4/23	1	2	FACETS	0.588	0.434	0.772	0.588	0.434	0.772	SUBCLONAL	1	TRUE	1	0.195038416947274	2		363	279	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023133	33023133	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	59	593	0	ENST00000300177.4:c.242del	p.Leu81ArgfsTer3	p.L81Rfs*3	ENST00000300177	NM_001191322.1	81	cTg/cg	2/2	1	2	FACETS	0.864	0.748	0.99	1	0.975	1	CLONAL	2	TRUE	1	0.195038416947274	2		593	350	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401285	139401285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	34	976	1	ENST00000277541.6:c.3784G>A	p.Glu1262Lys	p.E1262K	ENST00000277541	NM_017617.3	1262	Gag/Aag	23/34	1	2	FACETS	0.99	0.811	1	0.99	0.811	1	CLONAL	1	TRUE	1	0.195038416947274	2		977	352	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0043187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	140	413	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.283976209237762	4	FACETS	0.896	0.819	0.976	0.896	0.819	0.976	CLONAL	2	TRUE	2	0.355469357704525	4		414	596	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979385	2979385	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	411	409	0	ENST00000396946.4:c.862C>T	p.Gln288Ter	p.Q288*	ENST00000396946	NM_032415.4	288	Cag/Tag	6/25	0.355469357704525	6	FACETS	1	0.972	1	1	0.972	1	CLONAL	4	TRUE	2	0.355469357704525	6		409	968	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937185	76937185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	141	220	0	ENST00000373344.5:c.3563C>T	p.Ser1188Phe	p.S1188F	ENST00000373344	NM_000489.3	1188	tCc/tTc	9/35	0.306632356013424	2	FACETS	0.928	0.862	0.994			1	CLONAL	3	TRUE	NA	0.355469357704525	2		220	285	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510782	157510782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1321954955	NA	P-0043187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	116	395	0	ENST00000346085.5:c.3557C>T	p.Ser1186Leu	p.S1186L	ENST00000346085	NM_020732.3	1186	tCg/tTg	14/20	0.340526274133193	2	FACETS	1	0.958	1	0.553	0.5	0.609	CLONAL	1	TRUE	0	0.355469357704525	2		395	590	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175445	108175445	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	172	266	0	ENST00000278616.4:c.5540A>G	p.His1847Arg	p.H1847R	ENST00000278616	NM_000051.3	1847	cAt/cGt	37/63	0.355469357704525	3	FACETS	0.841	0.781	0.901	0.841	0.781	0.901	CLONAL	3	TRUE	0	0.355469357704525	3		266	452	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120811	115120811	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	131	387	0	ENST00000257566.3:c.195G>C	p.Met65Ile	p.M65I	ENST00000257566	NM_016569.3	65	atG/atC	1/8	0.355469357704525	3	FACETS	0.908	0.829	0.989	0.908	0.829	0.989	CLONAL	2	TRUE	1	0.355469357704525	3		387	478	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436071	110436071	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	125	599	0	ENST00000375856.3:c.2330C>G	p.Thr777Arg	p.T777R	ENST00000375856	NM_003749.2	777	aCg/aGg	1/2	1	2	FACETS	0.921	0.834	1	0.921	0.834	1	CLONAL	1	TRUE	1	0.355469357704525	2		599	764	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961656	41961657	+	stop_gained	Nonsense_Mutation	DNP	AG	AG	TT	novel	NA	P-0043187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	154	380	0	ENST00000219905.7:c.564_565delinsTT	p.Gln188_Glu189delinsHisTer	p.Q188_E189delinsH*	ENST00000219905	NM_001164273.1	188	caAGaa/caTTaa	2/24	0.340526274133193	2	FACETS	0.875	0.807	0.946	0.875	0.807	0.946	CLONAL	2	TRUE	0	0.355469357704525	2		380	495	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645244	67645244	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	127	552	0	ENST00000264010.4:c.509G>T	p.Gly170Val	p.G170V	ENST00000264010	NM_006565.3	170	gGg/gTg	3/12	0.355469357704525	3	FACETS	0.893	0.808	0.983	0.447	0.404	0.492	CLONAL	1	TRUE	1	0.355469357704525	3		552	942	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991853	72991853	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	108	468	0	ENST00000268489.5:c.2192G>C	p.Cys731Ser	p.C731S	ENST00000268489	NM_006885.3	731	tGt/tCt	2/10	0.355469357704525	3	FACETS	0.929	0.834	1	0.465	0.417	0.515	CLONAL	1	TRUE	1	0.355469357704525	3		468	770	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371799	45371799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	215	326	0	ENST00000262160.6:c.1192G>T	p.Val398Phe	p.V398F	ENST00000262160	NM_005901.5	398	Gtt/Ttt	10/11	0.355469357704525	3	FACETS	0.939	0.881	0.996	0.939	0.881	0.996	CLONAL	3	TRUE	0	0.355469357704525	3		326	506	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258541	19258541	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	283	625	0	ENST00000162023.5:c.359G>T	p.Gly120Val	p.G120V	ENST00000162023		120	gGg/gTg	8/13	0.355469357704525	3	FACETS	0.857	0.806	0.91	0.857	0.806	0.91	CLONAL	2	TRUE	1	0.355469357704525	3		625	1094	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306604	41306604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	189	575	0	ENST00000373198.4:c.1055C>T	p.Pro352Leu	p.P352L	ENST00000373198	NM_133170.3	352	cCc/cTc	7/32	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.355469357704525	2		575	823	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032755	30032755	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	70	295	0	ENST00000338641.4:c.131del	p.Lys44ArgfsTer79	p.K44Rfs*79	ENST00000338641	NM_000268.3	44	Aag/ag	2/16	1	2	FACETS	0.918	0.804	1	0.918	0.804	1	CLONAL	1	TRUE	1	0.355469357704525	2		295	429	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180367	38180367	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0043187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	407	554	0	ENST00000396334.3:c.215T>A	p.Leu72Ter	p.L72*	ENST00000396334	NM_002468.4	72	tTg/tAg	1/5	0.355469357704525	5	FACETS	0.91	0.866	0.955	0.91	0.866	0.955	CLONAL	3	TRUE	2	0.355469357704525	5		554	1286	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436398	52436399	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0043187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	215	593	4	ENST00000460680.1:c.2095_2096delinsTT	p.Arg699Leu	p.R699L	ENST00000460680	NM_004656.3	699	CGg/TTg	17/17	0.355469357704525	5	FACETS	0.881	0.818	0.945	0.587	0.545	0.63	CLONAL	2	TRUE	2	0.355469357704525	5		597	1053	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851688	134851688	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	291	459	0	ENST00000398015.3:c.1094C>A	p.Ala365Glu	p.A365E	ENST00000398015	NM_004441.4	365	gCa/gAa	5/16	0.355469357704525	5	FACETS	1	0.965	1	1	0.965	1	CLONAL	3	TRUE	2	0.355469357704525	5		459	814	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217129	66217129	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	169	415	0	ENST00000273854.3:c.2486C>A	p.Pro829His	p.P829H	ENST00000273854	NM_004439.5	829	cCc/cAc	14/18	0.355469357704525	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.355469357704525	3		415	529	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114239	143114239	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0043187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	44	215	0	ENST00000262992.4:c.1181+1G>T		p.X394_splice	ENST00000262992	NM_001101669.1	394			0.355469357704525	3	FACETS	0.777	0.654	0.914	0.389	0.327	0.457	CLONAL	1	TRUE	1	0.355469357704525	3		215	375	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226022	226022	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	64	87	0	ENST00000264932.6:c.481A>T	p.Ser161Cys	p.S161C	ENST00000264932	NM_004168.2	161	Agc/Tgc	5/15	0.355469357704525	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	3	TRUE	0	0.355469357704525	3		87	127	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522688	176522688	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	150	594	1	ENST00000292408.4:c.1785G>T	p.Gln595His	p.Q595H	ENST00000292408	NM_213647.1	595	caG/caT	13/18	0.349683048806814	4	FACETS	0.965	0.88	1	0.322	0.293	0.352	CLONAL	1	TRUE	1	0.355469357704525	4		595	1185	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066653	94066653	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	163	415	0	ENST00000369303.4:c.1106G>T	p.Cys369Phe	p.C369F	ENST00000369303	NM_004440.3	369	tGt/tTt	5/17	0.355469357704525	1	FACETS	0.756	0.699	0.814	1	0.99	1	SUBCLONAL	2	TRUE	0	0.355469357704525	1		415	499	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386550	81386550	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	130	334	0	ENST00000222390.5:c.437G>T	p.Gly146Val	p.G146V	ENST00000222390	NM_000601.4	146	gGc/gTc	4/18	0.355469357704525	6	FACETS	0.9	0.818	0.987	0.45	0.409	0.494	CLONAL	2	TRUE	2	0.355469357704525	6		334	695	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485951	8485952	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0043187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	68	381	0	ENST00000356435.5:c.2865_2866delinsAT	p.Leu956Phe	p.L956F	ENST00000356435		955	acCCtt/acATtt	17/35	0.320092036718943	4	FACETS	0.799	0.695	0.912	0.266	0.231	0.304	CLONAL	1	TRUE	1	0.355469357704525	4		381	649	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36931990	36931990	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043187-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	81	536	0	ENST00000361632.4:c.2479G>T	p.Val827Phe	p.V827F	ENST00000361632		827	Gtc/Ttc	16/16	0.355469357704525	3	FACETS	0.591	0.52	0.668	0.296	0.26	0.334	SUBCLONAL	1	TRUE	1	0.355469357704525	3		536	908	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0043200-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	146	471	1	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.260530123948939	3	FACETS	1	0.986	1	0.719	0.656	0.785	CLONAL	1	TRUE	1	0.26807282976215	3		472	859	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	214	565	0	ENST00000206249.3:c.1607T>C	p.Leu536Pro	p.L536P	ENST00000206249	NM_000125.3	536	cTc/cCc	8/8	0.447477691247286	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.447477691247286	1		565	704	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572185	64572185	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	208	501	1	ENST00000312049.6:c.1454G>A	p.Arg485Gln	p.R485Q	ENST00000312049	NM_130799.2	485	cGg/cAg	10/10	0.362572474057022	3	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.447477691247286	3		502	962	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220410	1220410	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	283	727	0	ENST00000326873.7:c.503A>T	p.His168Leu	p.H168L	ENST00000326873	NM_000455.4	168	cAt/cTt	4/10	0.447477691247286	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.447477691247286	1		727	917	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023247	27023265	+	frameshift_variant	Frame_Shift_Del	DEL	CGGAGCCGCCCGGCGGCGG	CGGAGCCGCCCGGCGGCGG	-	novel	NA	P-0043203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	106	209	0	ENST00000324856.7:c.356_374del	p.Glu119ValfsTer107	p.E119Vfs*107	ENST00000324856	NM_006015.4	118	aCGGAGCCGCCCGGCGGCGGc/ac	1/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.447477691247286	2		209	339	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042409	42042425	+	frameshift_variant	Frame_Shift_Del	DEL	ATTAAAGAAACAAAGAC	ATTAAAGAAACAAAGAC	-	novel	NA	P-0043203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	211	620	0	ENST00000219905.7:c.6606_6622del	p.Ile2202MetfsTer16	p.I2202Mfs*16	ENST00000219905	NM_001164273.1	2202	ATTAAAGAAACAAAGACa/a	17/24	1	2	FACETS	0.966	0.898	1	0.966	0.898	1	CLONAL	1	TRUE	1	0.447477691247286	2		620	976	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011125	12011133	+	inframe_deletion	In_Frame_Del	DEL	ATGGAACTC	ATGGAACTC	-	novel	NA	P-0043203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	84	401	0	ENST00000353533.5:c.535_543del	p.Glu179_Met181del	p.E179_M181del	ENST00000353533	NM_003010.3	178	ATGGAACTC/-	5/11	0.447477691247286	1	FACETS	0.656	0.582	0.735	0.656	0.582	0.735	SUBCLONAL	1	TRUE	0	0.447477691247286	1		401	444	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057018	180057018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767670443	NA	P-0043209-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	473	531	0	ENST00000261937.6:c.601G>A	p.Ala201Thr	p.A201T	ENST00000261937	NM_182925.4	201	Gcc/Acc	5/30	0.609413536962149	5	FACETS	0.966	0.927	1	0.966	0.927	1	CLONAL	3	TRUE	2	0.633581560525399	5		531	1005	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0043239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	151	305	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		305	588	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0043242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	93	309	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.17	2		309	757	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0043242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	89	398	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	0.904	0.799	1	0.904	0.799	1	CLONAL	1	TRUE	1	0.17	2		398	1158	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463317	25463317	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	41	491	0	ENST00000264709.3:c.2176G>T	p.Gly726Cys	p.G726C	ENST00000264709	NM_175629.2	726	Ggc/Tgc	19/23	1	2	FACETS	0.663	0.551	0.789	0.663	0.551	0.789	SUBCLONAL	1	TRUE	1	0.17	2		491	727	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151830	108151830	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876659067	NA	P-0043242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	36	480	0	ENST00000278616.4:c.3511C>T	p.Gln1171Ter	p.Q1171*	ENST00000278616	NM_000051.3	1171	Cag/Tag	24/63	1	2	FACETS	0.742	0.609	0.891	0.742	0.609	0.891	SUBCLONAL	1	TRUE	1	0.17	2		480	571	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32438066	32438066	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	54	569	0	ENST00000332351.3:c.971G>A	p.Ser324Asn	p.S324N	ENST00000332351	NM_024426.4	324	aGc/aAc	5/10	1	2	FACETS	0.792	0.675	0.921	0.792	0.675	0.921	CLONAL	1	TRUE	1	0.17	2		569	802	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056816	102056817	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0043242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	52	471	0	ENST00000282441.5:c.756_757delinsTT	p.Lys252_Asn253delinsAsnTyr	p.K252_N253delinsNY	ENST00000282441	NM_001130145.2	252	aaGAac/aaTTac	4/9	1	2	FACETS	0.778	0.661	0.908	0.778	0.661	0.908	CLONAL	1	TRUE	1	0.17	2		471	786	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804278	46804278	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	144	711	0	ENST00000290295.7:c.729G>T	p.Lys243Asn	p.K243N	ENST00000290295	NM_006361.5	243	aaG/aaT	2/2	0.148485996210981	2	FACETS	0.785	0.715	0.859	0.785	0.715	0.859	SUBCLONAL	2	TRUE	0	0.17	2		711	1079	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215674166	215674166	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1060501305	NA	P-0043242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	73	596	0	ENST00000260947.4:c.128G>T	p.Arg43Leu	p.R43L	ENST00000260947	NM_000465.2	43	cGc/cTc	1/11	1	2	FACETS	0.817	0.712	0.931	0.817	0.712	0.931	CLONAL	1	TRUE	1	0.17	2		596	1051	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1255441	1255442	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0043242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	209	658	3	ENST00000310581.5:c.3117_3118delinsTT	p.Ala1040Ser	p.A1040S	ENST00000310581	NM_198253.2	1039	acGGcc/acTTcc	14/16	0.280852064344118	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.17	3		661	1135	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388081	81388081	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	41	469	0	ENST00000222390.5:c.294G>C	p.Trp98Cys	p.W98C	ENST00000222390	NM_000601.4	98	tgG/tgC	3/18	1	2	FACETS	0.769	0.64	0.914	0.769	0.64	0.914	CLONAL	1	TRUE	1	0.17	2		469	627	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522638	106522638	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	34	358	0	ENST00000359195.3:c.2615C>A	p.Thr872Asn	p.T872N	ENST00000359195	NM_002649.2	872	aCt/aAt	7/11	1	2	FACETS	0.635	0.517	0.768	0.635	0.517	0.768	SUBCLONAL	1	TRUE	1	0.17	2		358	630	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457346	5457346	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	23	271	0	ENST00000381577.3:c.320A>G	p.Gln107Arg	p.Q107R	ENST00000381577	NM_014143.3	107	cAg/cGg	3/7	1	2	FACETS	0.599	0.466	0.753	0.599	0.466	0.753	SUBCLONAL	1	TRUE	1	0.17	2		271	452	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0043245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	95	355	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.390220711916412	3	FACETS	0.918	0.826	1	0.918	0.826	1	CLONAL	2	TRUE	1	0.390220711916412	3		355	317	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0043245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	62	458	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.389952530298294	4	FACETS	1	0.963	1	0.665	0.578	0.759	CLONAL	1	TRUE	2	0.390220711916412	4		458	332	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	169	737	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.877454390454607	2		737	371	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0043247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	146	351	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.877454390454607	1	FACETS	0.994	0.946	1	0.994	0.946	1	CLONAL	1	TRUE	0	0.877454390454607	1		351	188	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628298	187628298	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs748807574	NA	P-0043247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	286	588	0	ENST00000441802.2:c.2684T>C	p.Ile895Thr	p.I895T	ENST00000441802	NM_005245.3	895	aTt/aCt	2/27	1	2	FACETS	0.986	0.934	1	0.986	0.934	1	CLONAL	1	TRUE	1	0.877454390454607	2		588	661	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755666	39755666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	15	946	1	ENST00000288319.7:c.1099C>T	p.Arg367Cys	p.R367C	ENST00000288319	NM_182918.3	367	Cgc/Tgc	10/10	1	2	FACETS	0.374	0.273	0.496	0.374	0.273	0.496	SUBCLONAL	1	TRUE	1	0.2699835788208	2		947	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0043350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	106	754	1	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.214351606362573	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.228330875830498	1		755	777	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443481	49443481	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781156556	NA	P-0043350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	59	455	0	ENST00000301067.7:c.3890G>A	p.Arg1297His	p.R1297H	ENST00000301067	NM_003482.3	1297	cGt/cAt	11/54	1	2	FACETS	0.896	0.771	1	0.896	0.771	1	CLONAL	1	TRUE	1	0.228330875830498	2		455	577	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139527	47139527	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	67	444	0	ENST00000409792.3:c.5060del	p.Gly1687ValfsTer18	p.G1687Vfs*18	ENST00000409792	NM_014159.6	1687	gGt/gt	9/21	0.214351606362573	1	FACETS	0.996	0.867	1	0.996	0.867	1	CLONAL	1	TRUE	0	0.228330875830498	1		444	522	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120701	94120701	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	73	477	2	ENST00000369303.4:c.350G>C	p.Gly117Ala	p.G117A	ENST00000369303	NM_004440.3	117	gGa/gCa	3/17	0.228330875830498	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.228330875830498	1		479	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0043400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	148	601	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.235882322030417	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	0	0.235882322030417	1		601	955	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0043400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	192	309	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.212290845281759	4	FACETS	0.919	0.852	0.987	0.919	0.852	0.987	CLONAL	3	FALSE	1	0.235882322030417	4		309	730	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115012	3115012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555702147	NA	P-0043418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	449	797	1	ENST00000078429.4:c.547C>T	p.Arg183Cys	p.R183C	ENST00000078429	NM_002067.2	183	Cgc/Tgc	4/7	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.852489199258154	2		798	1009	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211855	123211855	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	151	144	0	ENST00000218089.9:c.2722A>G	p.Arg908Gly	p.R908G	ENST00000218089	NM_001042749.1	908	Agg/Ggg	27/35	1	1	FACETS	0.816	0.766	0.865	0.816	0.766	0.865	CLONAL	1	TRUE	0	0.852489199258154	1		144	249	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0043474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	813	695	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.900284228532451	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.900284228532451	2		695	869	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587385	29587385	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0043474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	90	260	0	ENST00000356175.3:c.4368-2A>T		p.X1456_splice	ENST00000356175	NM_000267.3	1456			0.275958820037209	3	FACETS	0.784	0.714	0.854	0.784	0.714	0.854	INDETERMINATE	2	TRUE	1	0.900284228532451	3		260	185	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221711	55221711	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	519	403	0	ENST00000275493.2:c.755G>T	p.Arg252Leu	p.R252L	ENST00000275493	NM_005228.3	252	cGc/cTc	7/28	0.546281836496219	4	FACETS	0.971	0.942	0.999	0.971	0.942	0.999	CLONAL	3	TRUE	1	0.900284228532451	4		403	752	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163307822	163307822	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	54	324	0	ENST00000271452.3:c.448G>T	p.Asp150Tyr	p.D150Y	ENST00000271452	NM_145697.2	150	Gac/Tac	7/14	0.417398842075051	1	FACETS	0.511	0.449	0.575	0.511	0.449	0.575	INDETERMINATE	1	TRUE	0	0.900284228532451	1		324	129	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490547	56490547	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	375	444	1	ENST00000267101.3:c.2191G>T	p.Glu731Ter	p.E731*	ENST00000267101	NM_001982.3	731	Gag/Tag	19/28	0.900284228532451	3	FACETS	0.928	0.89	0.965			1	CLONAL	2	TRUE	NA	0.900284228532451	3		445	651	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865480	57865480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	375	695	1	ENST00000228682.2:c.2957C>T	p.Ala986Val	p.A986V	ENST00000228682	NM_005269.2	986	gCa/gTa	12/12	1	2	FACETS	0.992	0.947	1	0.992	0.947	1	CLONAL	1	TRUE	1	0.900284228532451	2		696	840	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664898	29664899	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0043474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	68	294	0	ENST00000356175.3:c.6641_6641+1delinsTT		p.X2214_splice	ENST00000356175	NM_000267.3	2214		43/57	0.275958820037209	3	FACETS	1	0.953	1	0.573	0.508	0.641	INDETERMINATE	1	TRUE	1	0.900284228532451	3		294	191	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489575	40489575	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	294	501	1	ENST00000264657.5:c.675G>T	p.Leu225Phe	p.L225F	ENST00000264657	NM_139276.2	225	ttG/ttT	8/24	0.275958820037209	3	FACETS	1	0.994	1	0.712	0.675	0.749	INDETERMINATE	1	TRUE	1	0.900284228532451	3		502	665	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804403	46804403	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	283	437	0	ENST00000290295.7:c.604T>A	p.Ser202Thr	p.S202T	ENST00000290295	NM_006361.5	202	Tcc/Acc	2/2	0.275958820037209	3	FACETS	0.77	0.731	0.809	0.77	0.731	0.809	INDETERMINATE	2	TRUE	1	0.900284228532451	3		437	592	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350002	15350002	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	418	740	0	ENST00000263377.2:c.3650C>G	p.Ala1217Gly	p.A1217G	ENST00000263377	NM_058243.2	1217	gCc/gGc	18/20	1	2	FACETS	0.995	0.952	1	0.995	0.952	1	CLONAL	1	TRUE	1	0.900284228532451	2		740	933	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743883	41743883	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	420	765	1	ENST00000301178.4:c.818C>A	p.Ala273Glu	p.A273E	ENST00000301178	NM_021913.4	273	gCg/gAg	7/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.900284228532451	2		766	929	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770630	40770630	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	56	323	0	ENST00000373198.4:c.2752G>T	p.Gly918Trp	p.G918W	ENST00000373198	NM_133170.3	918	Ggg/Tgg	19/32	0.724348267715344	1	FACETS	0.257	0.222	0.295	0.257	0.222	0.295	SUBCLONAL	1	TRUE	0	0.900284228532451	1		323	266	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306742	41306743	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	386	513	0	ENST00000373198.4:c.916dup	p.Trp306LeufsTer41	p.W306Lfs*41	ENST00000373198	NM_133170.3	306	tgg/tTgg	7/32	0.724348267715344	1	FACETS	0.91	0.882	0.938	0.91	0.882	0.938	CLONAL	1	TRUE	0	0.900284228532451	1		513	518	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147584	47147584	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	132	284	0	ENST00000409792.3:c.4742G>T	p.Gly1581Val	p.G1581V	ENST00000409792	NM_014159.6	1581	gGa/gTa	6/21	0.275958820037209	3	FACETS	1	0.988	1	0.731	0.675	0.787	INDETERMINATE	1	TRUE	1	0.900284228532451	3		284	291	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480505	89480505	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	93	203	0	ENST00000336596.2:c.2342C>G	p.Thr781Arg	p.T781R	ENST00000336596	NM_005233.5	781	aCa/aGa	13/17	0.275958820037209	3	FACETS	1	0.977	1	0.643	0.582	0.705	INDETERMINATE	1	TRUE	1	0.900284228532451	3		203	233	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178194	142178194	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	66	266	0	ENST00000350721.4:c.7224G>T	p.Gln2408His	p.Q2408H	ENST00000350721	NM_001184.3	2408	caG/caT	43/47	0.895977099002789	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.900284228532451	1		266	71	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156615	55156615	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	243	477	0	ENST00000257290.5:c.3016G>A	p.Gly1006Ser	p.G1006S	ENST00000257290	NM_006206.4	1006	Ggt/Agt	22/23	1	2	FACETS	0.934	0.88	0.988	0.934	0.88	0.988	CLONAL	1	TRUE	1	0.900284228532451	2		477	578	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467424	66467424	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	133	225	0	ENST00000273854.3:c.845G>T	p.Trp282Leu	p.W282L	ENST00000273854	NM_004439.5	282	tGg/tTg	3/18	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.900284228532451	2		225	268	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497248	149497248	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	367	626	0	ENST00000261799.4:c.3070C>A	p.Pro1024Thr	p.P1024T	ENST00000261799	NM_002609.3	1024	Ccc/Acc	22/23	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.900284228532451	2		626	768	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200440	138200440	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	538	517	0	ENST00000237289.4:c.1858A>T	p.Asn620Tyr	p.N620Y	ENST00000237289	NM_001270507.1	620	Aac/Tac	7/9	0.900284228532451	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.900284228532451	2		517	581	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859255	151859255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	84	272	0	ENST00000262189.6:c.11407G>T	p.Asp3803Tyr	p.D3803Y	ENST00000262189	NM_170606.2	3803	Gac/Tac	43/59	1	2	FACETS	0.864	0.778	0.952	0.864	0.778	0.952	CLONAL	1	TRUE	1	0.900284228532451	2		272	216	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859257	151859257	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	82	267	0	ENST00000262189.6:c.11405A>T	p.Asp3802Val	p.D3802V	ENST00000262189	NM_170606.2	3802	gAt/gTt	43/59	1	2	FACETS	0.855	0.769	0.944	0.855	0.769	0.944	CLONAL	1	TRUE	1	0.900284228532451	2		267	213	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90994978	90994978	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0043474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	225	339	0	ENST00000265433.3:c.143T>G	p.Leu48Ter	p.L48*	ENST00000265433	NM_002485.4	48	tTa/tGa	2/16	0.744556983848259	5	FACETS	1	0.972	1	0.706	0.663	0.749	CLONAL	2	TRUE	2	0.900284228532451	5		339	555	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864938	117864938	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	96	209	0	ENST00000297338.2:c.1171C>G	p.Arg391Gly	p.R391G	ENST00000297338	NM_006265.2	391	Cgc/Ggc	10/14	0.900284228532451	4	FACETS	0.925	0.829	1	0.308	0.276	0.342	CLONAL	1	TRUE	1	0.900284228532451	4		209	438	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521333	8521333	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	113	357	0	ENST00000356435.5:c.905G>T	p.Cys302Phe	p.C302F	ENST00000356435		302	tGt/tTt	9/35	0.148189686957708	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.900284228532451	0		357	295	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521511	8521511	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	200	470	0	ENST00000356435.5:c.727A>T	p.Thr243Ser	p.T243S	ENST00000356435		243	Act/Tct	9/35	0.148189686957708	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.900284228532451	0		470	479	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549110	87549110	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	400	447	0	ENST00000277120.3:c.1667del	p.Leu556ArgfsTer5	p.L556Rfs*5	ENST00000277120		556	cTg/cg	15/19	0.900284228532451	3	FACETS	0.956	0.919	0.992	0.637	0.613	0.662	CLONAL	2	TRUE	0	0.900284228532451	3		447	674	SUCCESS
AR	367	MSKCC	GRCh37	X	66765236	66765236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	124	455	0	ENST00000374690.3:c.248G>A	p.Ser83Asn	p.S83N	ENST00000374690	NM_000044.3	83	aGc/aAc	1/8	0.87683386443178	1	FACETS	0.589	0.544	0.635	0.589	0.544	0.635	SUBCLONAL	1	TRUE	0	0.900284228532451	1		455	257	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152853841	152853841	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	30	190	0	ENST00000406277.2:c.723G>T	p.Met241Ile	p.M241I	ENST00000406277	NM_152274.4	241	atG/atT	7/7	0.788121412158567	1	FACETS	0.264	0.215	0.317	0.264	0.215	0.317	SUBCLONAL	1	TRUE	0	0.900284228532451	1		190	139	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0043530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	408	960	1	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.615614584230181	2	FACETS	0.995	0.958	1	0.995	0.958	1	CLONAL	2	TRUE	0	0.615614584230181	2		961	666	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376727	31376727	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	156	379	0	ENST00000328111.2:c.722C>T	p.Ala241Val	p.A241V	ENST00000328111	NM_006892.3	241	gCc/gTc	7/23	0.496531094825179	4	FACETS	1	0.971	1	0.375	0.344	0.408	CLONAL	1	TRUE	1	0.615614584230181	4		379	727	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778167	27778167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	364	501	0	ENST00000369163.2:c.316G>A	p.Glu106Lys	p.E106K	ENST00000369163	NM_003536.2	106	Gag/Aag	1/1	0.615614584230181	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.615614584230181	2		501	587	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353890	68353890	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	286	332	0	ENST00000487270.1:c.725T>C	p.Leu242Ser	p.L242S	ENST00000487270	NM_133509.3	242	tTg/tCg	7/11	0.615614584230181	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.615614584230181	2		332	461	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606777	43606777	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	372	612	0	ENST00000355710.3:c.1389del	p.Ile464SerfsTer4	p.I464Sfs*4	ENST00000355710	NM_020975.4	462	tcG/tc	7/20	0.615614584230181	2	FACETS	0.962	0.924	1	0.962	0.924	1	CLONAL	2	TRUE	0	0.615614584230181	2		612	628	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281417	49281417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	392	532	0	ENST00000282018.3:c.464C>T	p.Ala155Val	p.A155V	ENST00000282018	NM_020377.2	155	gCc/gTc	1/1	0.615614584230181	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.615614584230181	2		532	631	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519776	29519776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	32	427	0	ENST00000389048.3:c.1795C>T	p.Pro599Ser	p.P599S	ENST00000389048	NM_004304.4	599	Cct/Tct	9/29	0.615614584230181	3	FACETS	0.219	0.177	0.266	0.109	0.088	0.133	SUBCLONAL	1	TRUE	1	0.615614584230181	3		427	622	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164478	47164478	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	240	236	0	ENST00000409792.3:c.1648A>T	p.Ser550Cys	p.S550C	ENST00000409792	NM_014159.6	550	Agt/Tgt	3/21	0.615614584230181	2	FACETS	0.972	0.925	1	0.972	0.925	1	CLONAL	2	TRUE	0	0.615614584230181	2		236	401	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511345	157511345	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0043530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	84	311	0	ENST00000346085.5:c.3862+1G>T		p.X1288_splice	ENST00000346085	NM_020732.3	1288			0.282076879046811	4	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.615614584230181	4		311	378	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274930	38274930	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	37	514	0	ENST00000425967.3:c.1650C>G	p.Asp550Glu	p.D550E	ENST00000425967	NM_001174067.1	550	gaC/gaG	13/19	0.615614584230181	2	FACETS	0.189	0.155	0.227	0.095	0.077	0.114	SUBCLONAL	1	TRUE	0	0.615614584230181	2		514	636	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970913	21970913	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	486	546	0	ENST00000304494.5:c.445del	p.Glu149LysfsTer44	p.E149Kfs*44	ENST00000304494	NM_000077.4	149	Gaa/aa	2/3	0.615614584230181	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.615614584230181	2		546	781	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0043573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	21	306	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.879	0.676	1	0.879	0.676	1	CLONAL	1	TRUE	1	0.12	2		306	398	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923601	39923601	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	51	240	0	ENST00000378444.4:c.3490C>T	p.Arg1164Ter	p.R1164*	ENST00000378444	NM_001123385.1	1164	Cga/Tga	7/15	1	1	FACETS	0.896	0.763	1	1	0.972	1	CLONAL	2	TRUE	0	0.12	1		240	446	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221236	1221236	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	58	476	0	ENST00000326873.7:c.762del	p.Phe255SerfsTer32	p.F255Sfs*32	ENST00000326873	NM_000455.4	253	taC/ta	6/10	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.12	2		476	918	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487541	38487541	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	51	437	1	ENST00000254066.5:c.71A>G	p.Tyr24Cys	p.Y24C	ENST00000254066	NM_000964.3	24	tAc/tGc	2/9	1	2	FACETS	0.858	0.726	1	0.858	0.726	1	CLONAL	1	TRUE	1	0.12	2		438	991	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652202	36652203	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0043573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	61	496	0	ENST00000244741.5:c.325dup	p.Asp109GlyfsTer20	p.D109Gfs*20	ENST00000244741	NM_000389.4	108	-/G	2/3	1	2	FACETS	0.996	0.856	1	0.996	0.856	1	CLONAL	1	TRUE	1	0.12	2		496	1021	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391494	139391494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	54	813	0	ENST00000277541.6:c.6697C>T	p.His2233Tyr	p.H2233Y	ENST00000277541	NM_017617.3	2233	Cac/Tac	34/34	0.843000189844982	2	FACETS	0.208	0.177	0.242	0.104	0.088	0.121	SUBCLONAL	1	TRUE	0	0.855677239871608	2		813	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0043593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	332	843	1	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	0.745374122714886	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.745374122714886	1		844	502	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144892	47144892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	275	366	0	ENST00000409792.3:c.4861G>A	p.Gly1621Arg	p.G1621R	ENST00000409792	NM_014159.6	1621	Gga/Aga	7/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.745374122714886	2		366	695	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78435645	78435645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	309	364	0	ENST00000370768.2:c.175G>A	p.Gly59Ser	p.G59S	ENST00000370768	NM_003902.3	59	Ggt/Agt	2/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.745374122714886	2		364	744	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111959614	111959614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	95	583	0	ENST00000375549.3:c.193C>T	p.His65Tyr	p.H65Y	ENST00000375549	NM_003002.3	65	Cac/Tac	3/4	0.459544199533916	1	FACETS	0.262	0.233	0.293	0.262	0.233	0.293	SUBCLONAL	1	TRUE	0	0.745374122714886	1		583	610	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265348	16265348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746234410	NA	P-0043612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	84	399	0	ENST00000375759.3:c.10840G>A	p.Val3614Ile	p.V3614I	ENST00000375759	NM_015001.2	3614	Gtt/Att	14/15	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.255502762088943	2		399	641	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0043612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	147	920	1	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	0.255502762088943	1	FACETS	0.771	0.706	0.839	1	0.988	1	SUBCLONAL	2	TRUE	0	0.255502762088943	1		921	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876658468	NA	P-0043612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	115	439	0	ENST00000269305.4:c.577C>A	p.His193Asn	p.H193N	ENST00000269305	NM_001126112.2	193	Cat/Aat	6/11	0.255502762088943	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.255502762088943	1		439	578	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974744	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAGCAGCGCCCGCA	CCTCCAGCAGCGCCCGCA	-	novel	NA	P-0043612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	44	271	0	ENST00000304494.5:c.83_100del	p.Val28_Glu33del	p.V28_E33del	ENST00000304494	NM_000077.4	28	gTGCGGGCGCTGCTGGAGGcg/gcg	1/3	0.255502762088943	1	FACETS	0.755	0.634	0.888	0.755	0.634	0.888	SUBCLONAL	1	TRUE	0	0.255502762088943	1		271	398	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729681	162729681	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	75	399	0	ENST00000367921.3:c.767A>G	p.Tyr256Cys	p.Y256C	ENST00000367921	NM_006182.2	256	tAt/tGt	8/18	1	2	FACETS	0.953	0.836	1	0.953	0.836	1	CLONAL	1	TRUE	1	0.255502762088943	2		399	616	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0043625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	343	309	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.68993924483336	2		309	715	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647077	23647077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	295	739	0	ENST00000261584.4:c.790C>T	p.His264Tyr	p.H264Y	ENST00000261584	NM_024675.3	264	Cac/Tac	4/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.68993924483336	2		739	825	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987179	36987193	+	inframe_deletion	In_Frame_Del	DEL	CATGCCGCTCATGTT	CATGCCGCTCATGTT	-	novel	NA	P-0043625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	223	699	0	ENST00000354822.5:c.496_510del	p.Asn166_Met170del	p.N166_M170del	ENST00000354822	NM_001079668.2	166	AACATGAGCGGCATG/-	3/3	1	2	FACETS	0.848	0.792	0.906	0.848	0.792	0.906	CLONAL	1	TRUE	1	0.68993924483336	2		699	762	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222648	69222668	+	inframe_deletion	In_Frame_Del	DEL	AATAAGGGAGATATGTTGTGA	AATAAGGGAGATATGTTGTGA	-	novel	NA	P-0043625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	260	535	2	ENST00000462284.1:c.623_643del	p.Ile208_Glu214del	p.I208_E214del	ENST00000462284	NM_002392.5	207	gtAATAAGGGAGATATGTTGTGAa/gta	8/11	1	2	FACETS	0.971	0.914	1	0.971	0.914	1	CLONAL	1	TRUE	1	0.68993924483336	2		537	776	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892221	9892221	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	236	544	1	ENST00000330684.3:c.2269G>T	p.Ala757Ser	p.A757S	ENST00000330684	NM_001134407.1	757	Gcc/Tcc	11/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.68993924483336	2		545	652	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821927	59821927	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	163	324	1	ENST00000259008.2:c.2123G>T	p.Trp708Leu	p.W708L	ENST00000259008	NM_032043.2	708	tGg/tTg	15/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.68993924483336	2		325	426	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599904	10599904	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	353	747	0	ENST00000171111.5:c.1672G>C	p.Gly558Arg	p.G558R	ENST00000171111	NM_203500.1	558	Ggg/Cgg	5/6	0.68993924483336	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.68993924483336	1		747	620	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285857	198285857	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	190	347	0	ENST00000335508.6:c.196G>T	p.Asp66Tyr	p.D66Y	ENST00000335508	NM_012433.2	66	Gat/Tat	3/25	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.68993924483336	2		347	540	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940450	13940450	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	134	234	0	ENST00000405192.2:c.1056G>T	p.Trp352Cys	p.W352C	ENST00000405192	NM_001163147.1	352	tgG/tgT	11/12	1	2	FACETS	0.871	0.798	0.947	0.871	0.798	0.947	CLONAL	1	TRUE	1	0.68993924483336	2		234	446	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729544	41729544	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	226	558	0	ENST00000242208.4:c.985A>G	p.Ser329Gly	p.S329G	ENST00000242208	NM_002192.2	329	Agt/Ggt	3/3	1	2	FACETS	0.962	0.901	1	0.962	0.901	1	CLONAL	1	TRUE	1	0.68993924483336	2		558	681	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970978	21970986	+	inframe_deletion	In_Frame_Del	DEL	GCGACATCG	GCGACATCG	-	novel	NA	P-0043625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	234	541	0	ENST00000304494.5:c.372_380del	p.Asp125_Ala127del	p.D125_A127del	ENST00000304494	NM_000077.4	124	cgCGATGTCGCa/cga	2/3	0.68993924483336	1	FACETS	0.951	0.899	1	0.951	0.899	1	CLONAL	1	TRUE	0	0.68993924483336	1		541	467	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045137	47045137	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	277	330	0	ENST00000377604.3:c.2378G>T	p.Arg793Leu	p.R793L	ENST00000377604	NM_001204468.1	793	cGa/cTa	21/24	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.68993924483336	1		330	380	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453149	140453149	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913361	NA	P-0043628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	18	388	0	ENST00000288602.6:c.1786G>C	p.Gly596Arg	p.G596R	ENST00000288602	NM_004333.4	596	Ggt/Cgt	15/18	1	2	FACETS	0.779	0.585	1	0.779	0.585	1	CLONAL	1	TRUE	1	0.12	2		388	385	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226321	133226321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750902578	NA	P-0043628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	53	1005	1	ENST00000320574.5:c.3737C>T	p.Thr1246Met	p.T1246M	ENST00000320574	NM_006231.2	1246	aCg/aTg	30/49	1	2	FACETS	0.846	0.719	0.987	0.846	0.719	0.987	CLONAL	1	TRUE	1	0.12	2		1006	1044	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793364	242793364	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1298132910	NA	P-0043628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	56	1104	1	ENST00000334409.5:c.713C>A	p.Pro238His	p.P238H	ENST00000334409	NM_005018.2	238	cCc/cAc	5/5	1	2	FACETS	0.896	0.765	1	0.896	0.765	1	CLONAL	1	TRUE	1	0.12	2		1105	1042	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342357	70342357	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0043628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	34	296	0	ENST00000374080.3:c.1249-1G>T		p.X417_splice	ENST00000374080		417			1	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.12	1		296	395	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152104	55152104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121908588	NA	P-0043673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	341	720	0	ENST00000257290.5:c.2536G>T	p.Asp846Tyr	p.D846Y	ENST00000257290	NM_006206.4	846	Gat/Tat	18/23	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.656995096473748	2		720	959	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0043731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	218	544	1				ENST00000310581	NM_198253.2	-/1132			0.173712368607652	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.920530093164275	0		545	425	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841505	156841505	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145222195	NA	P-0043731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	883	700	0	ENST00000524377.1:c.808G>A	p.Asp270Asn	p.D270N	ENST00000524377	NM_002529.3	270	Gat/Aat	7/17	0.920530093164275	3	FACETS	0.988	0.963	1	0.988	0.963	1	CLONAL	2	TRUE	1	0.920530093164275	3		700	1418	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0043731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	264	390	0	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	1	2	FACETS	0.975	0.923	1	0.975	0.923	1	CLONAL	1	TRUE	1	0.920530093164275	2		390	588	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050314	37050314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	260	288	0	ENST00000231790.2:c.463C>T	p.Leu155Phe	p.L155F	ENST00000231790	NM_000249.3	155	Ctt/Ttt	6/19	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.920530093164275	2		288	564	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0043731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	202	196	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.920530093164275	2		196	429	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285793	46285793	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0043731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	265	322	0	ENST00000334344.6:c.5062-1G>A		p.X1688_splice	ENST00000334344	NM_152641.2	1688			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.920530093164275	2		322	540	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976872	55976872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs551579207	NA	P-0043731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	366	516	0	ENST00000263923.4:c.1040G>A	p.Arg347His	p.R347H	ENST00000263923	NM_002253.2	347	cGt/cAt	8/30	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.920530093164275	2		516	750	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873648	35873648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867618621	NA	P-0043731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	145	228	0	ENST00000303115.3:c.604G>A	p.Glu202Lys	p.E202K	ENST00000303115	NM_002185.3	202	Gag/Aag	5/8	1	2	FACETS	0.927	0.858	0.996	0.927	0.858	0.996	CLONAL	1	TRUE	1	0.920530093164275	2		228	340	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538897	23538897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1200957711	NA	P-0043731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	320	429	0	ENST00000380871.4:c.542G>A	p.Arg181Gln	p.R181Q	ENST00000380871	NM_006167.3	181	cGa/cAa	2/2	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.920530093164275	2		429	677	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433477	138433477	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	240	408	0	ENST00000289153.2:c.1135C>T	p.His379Tyr	p.H379Y	ENST00000289153	NM_006219.2	379	Cat/Tat	7/22	1	2	FACETS	0.969	0.914	1	0.969	0.914	1	CLONAL	1	TRUE	1	0.920530093164275	2		408	538	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139804390	139804390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750248731	NA	P-0043731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	453	610	0	ENST00000247668.2:c.547C>T	p.Pro183Ser	p.P183S	ENST00000247668	NM_021138.3	183	Ccc/Tcc	6/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.920530093164275	2		610	953	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233249	46233249	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs865903558	NA	P-0043731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	189	252	1	ENST00000334344.6:c.1468C>T	p.Gln490Ter	p.Q490*	ENST00000334344	NM_152641.2	490	Caa/Taa	11/21	1	2	FACETS	0.904	0.845	0.964	0.904	0.845	0.964	CLONAL	1	TRUE	1	0.920530093164275	2		253	454	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675049	40675049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764271025	NA	P-0043731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	399	546	0	ENST00000249776.8:c.13G>A	p.Glu5Lys	p.E5K	ENST00000249776	NM_033286.3	5	Gaa/Aaa	1/9	1	2	FACETS	0.995	0.952	1	0.995	0.952	1	CLONAL	1	TRUE	1	0.920530093164275	2		546	871	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719947	18719947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437834329	NA	P-0043731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	232	325	0	ENST00000266497.5:c.3844C>T	p.His1282Tyr	p.H1282Y	ENST00000266497		1282	Cat/Tat	27/31	1	2	FACETS	0.998	0.941	1	0.998	0.941	1	CLONAL	1	TRUE	1	0.920530093164275	2		325	505	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18649075	18649075	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1171906437	NA	P-0043731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	182	271	0	ENST00000266497.5:c.2750G>A	p.Ser917Asn	p.S917N	ENST00000266497		917	aGc/aAc	19/31	1	2	FACETS	0.92	0.859	0.981	0.92	0.859	0.981	CLONAL	1	TRUE	1	0.920530093164275	2		271	430	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701243	43701243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769912966	NA	P-0043731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	323	481	0	ENST00000382044.4:c.5452C>T	p.Arg1818Trp	p.R1818W	ENST00000382044	NM_001141980.1	1818	Cgg/Tgg	26/28	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.920530093164275	2		481	694	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122434	17122434	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	425	606	0	ENST00000285071.4:c.961G>T	p.Glu321Ter	p.E321*	ENST00000285071	NM_144997.5	321	Gag/Tag	9/14	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.920530093164275	2		606	906	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541603	29541603	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0043731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	142	213	0	ENST00000356175.3:c.1527T>A	p.Cys509Ter	p.C509*	ENST00000356175	NM_000267.3	509	tgT/tgA	13/57	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.920530093164275	2		213	297	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554528	63554528	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769064498	NA	P-0043731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	346	511	0	ENST00000307078.5:c.211C>T	p.Pro71Ser	p.P71S	ENST00000307078	NM_004655.3	71	Ccg/Tcg	2/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.920530093164275	2		511	675	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11019795	11019796	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0043731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	291	390	0	ENST00000327064.4:c.470_471delinsTT	p.Ser157Phe	p.S157F	ENST00000327064	NM_199141.1	157	tCC/tTT	4/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.920530093164275	2		390	613	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728699	190728699	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	226	293	0	ENST00000441310.2:c.2087T>A	p.Met696Lys	p.M696K	ENST00000441310	NM_000534.4	696	aTg/aAg	10/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.920530093164275	2		293	474	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732735	204732735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	212	321	0	ENST00000302823.3:c.70C>T	p.Leu24Phe	p.L24F	ENST00000302823	NM_005214.4	24	Ctc/Ttc	1/4	1	2	FACETS	0.837	0.784	0.891	0.837	0.784	0.891	CLONAL	1	TRUE	1	0.920530093164275	2		321	550	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164366	47164366	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	204	235	0	ENST00000409792.3:c.1760C>T	p.Ser587Phe	p.S587F	ENST00000409792	NM_014159.6	587	tCt/tTt	3/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.920530093164275	2		235	410	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927925	49927925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	306	430	1	ENST00000296474.3:c.3803C>T	p.Ser1268Phe	p.S1268F	ENST00000296474	NM_002447.2	1268	tCt/tTt	18/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.920530093164275	2		431	646	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156588	55156588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758534651	NA	P-0043731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	315	541	0	ENST00000257290.5:c.2989G>A	p.Glu997Lys	p.E997K	ENST00000257290	NM_006206.4	997	Gaa/Aaa	22/23	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.920530093164275	2		541	643	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539446	187539446	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs370927377	NA	P-0043731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	209	296	0	ENST00000441802.2:c.8294G>C	p.Ser2765Thr	p.S2765T	ENST00000441802	NM_005245.3	2765	aGt/aCt	10/27	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.920530093164275	2		296	428	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981831	70981831	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	481	711	0	ENST00000276594.2:c.265C>T	p.Leu89Phe	p.L89F	ENST00000276594	NM_024504.3	89	Ctc/Ttc	2/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.920530093164275	2		711	1023	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0043733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	179	413	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.3	3	FACETS	1	0.945	1	1	0.989	1	CLONAL	4	TRUE	0	0.19	3		414	506	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0043733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	30	556	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	1	2	FACETS	0.856	0.69	1	0.856	0.69	1	CLONAL	1	TRUE	1	0.19	2		556	369	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880288	155880288	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	34	348	0	ENST00000368323.3:c.116T>A	p.Met39Lys	p.M39K	ENST00000368323	NM_006912.5	39	aTg/aAg	3/6	1	2	FACETS	0.967	0.791	1	0.967	0.791	1	CLONAL	1	TRUE	1	0.19	2		348	370	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567635	226567635	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs745820900	NA	P-0043733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	61	447	0	ENST00000366794.5:c.1531G>T	p.Val511Phe	p.V511F	ENST00000366794	NM_001618.3	511	Gtc/Ttc	10/23	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.19	2		447	532	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793370	18793370	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	118	321	0	ENST00000266497.5:c.4067C>A	p.Pro1356Gln	p.P1356Q	ENST00000266497		1356	cCa/cAa	30/31	0.3	3	FACETS	1	0.925	1	1	0.925	1	CLONAL	3	TRUE	0	0.19	3		321	444	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019455	42019455	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	28	523	0	ENST00000219905.7:c.3508G>T	p.Glu1170Ter	p.E1170*	ENST00000219905	NM_001164273.1	1170	Gaa/Taa	10/24	0.253561966680103	1	FACETS	0.523	0.417	0.644	0.523	0.417	0.644	SUBCLONAL	1	TRUE	0	0.19	1		523	510	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587782197	NA	P-0043733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	50	833	0	ENST00000269305.4:c.434T>A	p.Leu145Gln	p.L145Q	ENST00000269305	NM_001126112.2	145	cTg/cAg	5/11	1	2	FACETS	0.751	0.636	0.878	0.751	0.636	0.878	SUBCLONAL	1	TRUE	1	0.19	2		833	701	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172442	7172442	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	31	388	0	ENST00000302850.5:c.1127A>G	p.Asn376Ser	p.N376S	ENST00000302850	NM_000208.2	376	aAt/aGt	5/22	1	2	FACETS	0.716	0.578	0.871	0.716	0.578	0.871	SUBCLONAL	1	TRUE	1	0.19	2		388	456	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551252	29551252	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	46	568	0	ENST00000389048.3:c.1378G>T	p.Asp460Tyr	p.D460Y	ENST00000389048	NM_004304.4	460	Gac/Tac	6/29	1	2	FACETS	0.775	0.651	0.911	0.775	0.651	0.911	CLONAL	1	TRUE	1	0.19	2		568	625	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42840337	42840337	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	27	377	0	ENST00000398585.3:c.1411G>T	p.Val471Phe	p.V471F	ENST00000398585	NM_001135099.1	471	Gtc/Ttc	12/14	1	2	FACETS	0.655	0.52	0.809	0.655	0.52	0.809	SUBCLONAL	1	TRUE	1	0.19	2		377	434	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160566	56160566	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs925876038	NA	P-0043733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	26	200	0	ENST00000399503.3:c.840G>C	p.Gln280His	p.Q280H	ENST00000399503	NM_005921.1	280	caG/caC	4/20	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.19	2		200	242	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730091	41730091	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	26	400	0	ENST00000242208.4:c.438C>A	p.Asp146Glu	p.D146E	ENST00000242208	NM_002192.2	146	gaC/gaA	3/3	1	2	FACETS	0.585	0.462	0.726	0.585	0.462	0.726	SUBCLONAL	1	TRUE	1	0.19	2		400	468	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515231	106515231	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0043733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	34	269	0	ENST00000359195.3:c.2374A>T	p.Lys792Ter	p.K792*	ENST00000359195	NM_002649.2	792	Aaa/Taa	5/11	1	2	FACETS	0.911	0.745	1	0.911	0.745	1	CLONAL	1	TRUE	1	0.19	2		269	393	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041266	47041266	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0043733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	41	755	0	ENST00000377604.3:c.1693+1G>T		p.X565_splice	ENST00000377604	NM_001204468.1	565			1	2	FACETS	0.659	0.548	0.783	0.659	0.548	0.783	SUBCLONAL	1	TRUE	1	0.19	2		755	655	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356759	70356759	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	33	641	1	ENST00000374080.3:c.5431C>A	p.Pro1811Thr	p.P1811T	ENST00000374080		1811	Cct/Act	38/45	1	2	FACETS	0.588	0.477	0.713	0.588	0.477	0.713	SUBCLONAL	1	TRUE	1	0.19	2		642	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	379	723	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.772790186782823	2		723	885	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	256	446	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.772790186782823	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.772790186782823	1		446	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793881	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	446	623	0	ENST00000269305.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGg/gAg	8/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.772790186782823	2		623	1064	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955063	55955063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	310	472	0	ENST00000263923.4:c.3482G>A	p.Gly1161Glu	p.G1161E	ENST00000263923	NM_002253.2	1161	gGa/gAa	26/30	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.772790186782823	2		472	731	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157380	106157380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	207	371	0	ENST00000380013.4:c.2281C>T	p.Pro761Ser	p.P761S	ENST00000380013	NM_001127208.2	761	Cct/Tct	3/11	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.772790186782823	2		371	533	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295253	+	upstream_gene_variant	5'Flank	ONP	GAGG	GAGG	AAGA	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	190	302	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.772790186782823	2		302	475	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190717451	190717451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	272	347	0	ENST00000441310.2:c.770G>A	p.Arg257Lys	p.R257K	ENST00000441310	NM_000534.4	257	aGa/aAa	7/13	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.772790186782823	2		347	696	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549706	226549706	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	336	450	0	ENST00000366794.5:c.2927C>T	p.Ser976Leu	p.S976L	ENST00000366794	NM_001618.3	976	tCa/tTa	22/23	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.772790186782823	2		450	751	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968588	55968588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	427	566	0	ENST00000263923.4:c.2075G>A	p.Gly692Glu	p.G692E	ENST00000263923	NM_002253.2	692	gGg/gAg	14/30	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.772790186782823	2		566	945	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602901	55602901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	232	368	0	ENST00000288135.5:c.2611C>T	p.Pro871Ser	p.P871S	ENST00000288135	NM_000222.2	871	Cct/Tct	19/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.772790186782823	2		368	547	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873000	134873000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	280	460	0	ENST00000398015.3:c.1304C>T	p.Ser435Phe	p.S435F	ENST00000398015	NM_004441.4	435	tCc/tTc	6/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.772790186782823	2		460	669	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463556	25463556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	338	568	1	ENST00000264709.3:c.2126C>T	p.Pro709Leu	p.P709L	ENST00000264709	NM_175629.2	709	cCc/cTc	18/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.772790186782823	2		569	836	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967241	93967241	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	179	264	0	ENST00000369303.4:c.2111G>A	p.Gly704Glu	p.G704E	ENST00000369303	NM_004440.3	704	gGg/gAg	12/17	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.772790186782823	2		264	449	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250214	133250214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	362	631	0	ENST00000320574.5:c.1306C>T	p.Pro436Ser	p.P436S	ENST00000320574	NM_006231.2	436	Ccc/Tcc	13/49	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.772790186782823	2		631	921	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259039	16259039	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	356	505	0	ENST00000375759.3:c.6304C>T	p.Pro2102Ser	p.P2102S	ENST00000375759	NM_015001.2	2102	Ccc/Tcc	11/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.772790186782823	2		505	890	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933186	36933186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	361	624	0	ENST00000361632.4:c.1931G>A	p.Gly644Glu	p.G644E	ENST00000361632		644	gGa/gAa	14/16	1	2	FACETS	0.937	0.891	0.984	0.937	0.891	0.984	CLONAL	1	TRUE	1	0.772790186782823	2		624	997	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852046	63852046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756275189	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	357	577	0	ENST00000279873.7:c.2824G>A	p.Val942Ile	p.V942I	ENST00000279873	NM_032199.2	942	Gtc/Atc	10/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.772790186782823	2		577	854	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332852	70332852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	363	584	0	ENST00000373644.4:c.757C>T	p.Pro253Ser	p.P253S	ENST00000373644	NM_030625.2	253	Ccc/Tcc	2/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.772790186782823	2		584	908	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941475	71941476	+	missense_variant	Missense_Mutation	DNP	GG	GG	TA	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	397	669	0	ENST00000298229.2:c.1160_1161delinsTA	p.Arg387Leu	p.R387L	ENST00000298229	NM_001567.3	387	cGG/cTA	10/28	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.772790186782823	2		669	1009	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922203	100922203	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs757658864	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	324	423	0	ENST00000325455.5:c.2309A>T	p.His770Leu	p.H770L	ENST00000325455	NM_001202474.3	770	cAc/cTc	5/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.772790186782823	2		423	808	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933360	100933361	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	276	480	0	ENST00000325455.5:c.2029_2030delinsTT	p.Pro677Leu	p.P677L	ENST00000325455	NM_001202474.3	677	CCa/TTa	4/8	1	2	FACETS	0.954	0.9	1	0.954	0.9	1	CLONAL	1	TRUE	1	0.772790186782823	2		480	749	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363941	118363941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	260	296	0	ENST00000534358.1:c.5174C>T	p.Ser1725Phe	p.S1725F	ENST00000534358	NM_005933.3	1725	tCt/tTt	16/36	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.772790186782823	2		296	573	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563423	21563423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	420	706	0	ENST00000382592.4:c.496C>T	p.Pro166Ser	p.P166S	ENST00000382592	NM_014572.2	166	Cca/Tca	4/8	1	2	FACETS	0.964	0.92	1	0.964	0.92	1	CLONAL	1	TRUE	1	0.772790186782823	2		706	1128	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28644644	28644644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757157975	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	329	503	0	ENST00000241453.7:c.149C>T	p.Ser50Leu	p.S50L	ENST00000241453	NM_004119.2	50	tCa/tTa	2/24	1	2	FACETS	0.958	0.908	1	0.958	0.908	1	CLONAL	1	TRUE	1	0.772790186782823	2		503	889	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437397	110437397	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	103	221	0	ENST00000375856.3:c.1004A>G	p.Gln335Arg	p.Q335R	ENST00000375856	NM_003749.2	335	cAg/cGg	1/2	1	2	FACETS	0.868	0.787	0.952	0.868	0.787	0.952	CLONAL	1	TRUE	1	0.772790186782823	2		221	307	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570173	95570174	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	206	350	0	ENST00000393063.1:c.3559_3560delinsAA	p.Gly1187Asn	p.G1187N	ENST00000393063	NM_030621.3	1187	GGc/AAc	22/28	1	2	FACETS	0.997	0.932	1	0.997	0.932	1	CLONAL	1	TRUE	1	0.772790186782823	2		350	535	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628089	90628090	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	391	698	1	ENST00000330062.3:c.1229_1230delinsTT	p.Ala410Val	p.A410V	ENST00000330062	NM_002168.2	410	gCC/gTT	10/11	1	2	FACETS	0.989	0.943	1	0.989	0.943	1	CLONAL	1	TRUE	1	0.772790186782823	2		699	1023	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99491835	99491835	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	346	471	1	ENST00000268035.6:c.3620C>T	p.Thr1207Ile	p.T1207I	ENST00000268035	NM_000875.3	1207	aCa/aTa	20/21	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.772790186782823	2		472	790	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347977	347977	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	442	692	0	ENST00000262320.3:c.1529C>T	p.Ala510Val	p.A510V	ENST00000262320	NM_003502.3	510	gCc/gTc	6/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.772790186782823	2		692	1029	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396446	396446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	413	664	1	ENST00000262320.3:c.580G>A	p.Glu194Lys	p.E194K	ENST00000262320	NM_003502.3	194	Gag/Aag	2/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.772790186782823	2		665	1036	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783893	50783893	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	105	594	0	ENST00000398568.2:c.284A>C	p.Lys95Thr	p.K95T	ENST00000398568	NM_001042412.1	95	aAg/aCg	3/18	1	2	FACETS	0.26	0.232	0.29	0.26	0.232	0.29	SUBCLONAL	1	TRUE	1	0.772790186782823	2		594	1044	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81922838	81922838	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	297	439	0	ENST00000359376.3:c.827C>T	p.Thr276Ile	p.T276I	ENST00000359376	NM_002661.3	276	aCc/aTc	10/33	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.772790186782823	2		439	742	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222163	2222164	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	371	676	1	ENST00000398665.3:c.2995_2996delinsTT	p.Pro999Phe	p.P999F	ENST00000398665	NM_032482.2	999	CCt/TTt	24/28	1	2	FACETS	0.994	0.946	1	0.994	0.946	1	CLONAL	1	TRUE	1	0.772790186782823	2		677	966	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214895	36214896	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	390	657	1	ENST00000222270.7:c.3321_3322delinsTT	p.Pro1108Ser	p.P1108S	ENST00000222270	NM_014727.1	1107	acCCcc/acTTcc	8/37	1	2	FACETS	0.995	0.949	1	0.995	0.949	1	CLONAL	1	TRUE	1	0.772790186782823	2		658	1014	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228112	36228112	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	424	754	0	ENST00000222270.7:c.7498G>A	p.Glu2500Lys	p.E2500K	ENST00000222270	NM_014727.1	2500	Gag/Aag	33/37	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.772790186782823	2		754	1008	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25459874	25459875	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	272	552	0	ENST00000264709.3:c.2409-1_2409delinsAA		p.X803_splice	ENST00000264709	NM_175629.2	803		21/23	1	2	FACETS	0.896	0.844	0.948	0.896	0.844	0.948	CLONAL	1	TRUE	1	0.772790186782823	2		552	786	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606628	29606628	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	307	450	0	ENST00000389048.3:c.1252G>A	p.Asp418Asn	p.D418N	ENST00000389048	NM_004304.4	418	Gac/Aac	5/29	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.772790186782823	2		450	728	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278319	39278319	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	353	540	0	ENST00000402219.2:c.830C>T	p.Pro277Leu	p.P277L	ENST00000402219	NM_005633.3	277	cCa/cTa	6/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.772790186782823	2		540	890	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661167	227661167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1466362855	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	409	678	0	ENST00000305123.5:c.2288C>T	p.Ser763Phe	p.S763F	ENST00000305123	NM_005544.2	763	tCc/tTc	1/2	1	2	FACETS	0.992	0.946	1	0.992	0.946	1	CLONAL	1	TRUE	1	0.772790186782823	2		678	1067	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012636	36012636	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	136	212	1	ENST00000358208.4:c.80C>T	p.Ala27Val	p.A27V	ENST00000358208		27	gCt/gTt	2/12	1	2	FACETS	0.959	0.883	1	0.959	0.883	1	CLONAL	1	TRUE	1	0.772790186782823	2		213	367	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014004	70014004	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	225	314	0	ENST00000394351.3:c.865G>A	p.Glu289Lys	p.E289K	ENST00000394351	NM_000248.3	289	Gaa/Aaa	9/9	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.772790186782823	2		314	517	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268382	142268382	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	252	375	0	ENST00000350721.4:c.3110T>G	p.Phe1037Cys	p.F1037C	ENST00000350721	NM_001184.3	1037	tTt/tGt	15/47	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.772790186782823	2		375	637	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169977762	169977762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	389	503	1	ENST00000295797.4:c.229C>T	p.Pro77Ser	p.P77S	ENST00000295797	NM_002740.5	77	Ccg/Tcg	3/18	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.772790186782823	2		504	991	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919114	178919114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	190	238	0	ENST00000263967.3:c.599C>T	p.Pro200Leu	p.P200L	ENST00000263967	NM_006218.2	200	cCa/cTa	4/21	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.772790186782823	2		238	431	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153627	55153627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	238	420	0	ENST00000257290.5:c.2593G>A	p.Glu865Lys	p.E865K	ENST00000257290	NM_006206.4	865	Gag/Aag	19/23	1	2	FACETS	0.854	0.801	0.909	0.854	0.801	0.909	CLONAL	1	TRUE	1	0.772790186782823	2		420	721	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524448	187524449	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	318	470	0	ENST00000441802.2:c.11231_11232delinsTT	p.Pro3744Leu	p.P3744L	ENST00000441802	NM_005245.3	3744	cCC/cTT	19/27	1	2	FACETS	0.998	0.946	1	0.998	0.946	1	CLONAL	1	TRUE	1	0.772790186782823	2		470	825	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503918	149503918	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	284	528	0	ENST00000261799.4:c.1918G>A	p.Ala640Thr	p.A640T	ENST00000261799	NM_002609.3	640	Gcc/Acc	14/23	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.772790186782823	2		528	719	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032111	26032111	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753823527	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	262	442	0	ENST00000244661.2:c.178G>A	p.Glu60Lys	p.E60K	ENST00000244661	NM_003537.3	60	Gag/Aag	1/1	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.772790186782823	2		442	666	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675454	30675454	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	414	601	0	ENST00000376406.3:c.2902G>A	p.Glu968Lys	p.E968K	ENST00000376406	NM_014641.2	968	Gag/Aag	8/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.772790186782823	2		601	989	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112025249	112025249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	315	457	0	ENST00000368678.4:c.500G>A	p.Gly167Glu	p.G167E	ENST00000368678		167	gGa/gAa	6/13	1	2	FACETS	0.968	0.917	1	0.968	0.917	1	CLONAL	1	TRUE	1	0.772790186782823	2		457	842	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129228	152129228	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	383	646	0	ENST00000206249.3:c.181G>A	p.Glu61Lys	p.E61K	ENST00000206249	NM_000125.3	61	Gag/Aag	1/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.772790186782823	2		646	989	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528256	157528257	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	322	527	0	ENST00000346085.5:c.5981_5982delinsTT	p.Thr1994Ile	p.T1994I	ENST00000346085	NM_020732.3	1994	aCC/aTT	20/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.772790186782823	2		527	829	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434475	140434475	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	249	362	0	ENST00000288602.6:c.2223G>C	p.Glu741Asp	p.E741D	ENST00000288602	NM_004333.4	741	gaG/gaC	18/18	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.772790186782823	2		362	641	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965331	68965331	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	305	395	0	ENST00000288368.4:c.944-1G>A		p.X315_splice	ENST00000288368	NM_024870.2	315			1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.772790186782823	2		395	705	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344138	70344139	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	336	335	0	ENST00000374080.3:c.1874_1875delinsTT	p.Ala625Val	p.A625V	ENST00000374080		625	gCC/gTT	13/45	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.772790186782823	1		335	412	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214896	36214896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374066966	NA	P-0043799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	390	647	0	ENST00000222270.7:c.3322C>T	p.Pro1108Ser	p.P1108S	ENST00000222270	NM_014727.1	1108	Ccc/Tcc	8/37	1	2	FACETS	0.995	0.949	1	0.995	0.949	1	CLONAL	1	TRUE	1	0.772790186782823	2		647	1014	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0043822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	370	413	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.343133301610919	6	FACETS	1	0.978	1	1	0.978	1	CLONAL	4	TRUE	2	0.343133301610919	6		414	873	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577098	7577098	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	287	634	0	ENST00000269305.4:c.840A>T	p.Arg280Ser	p.R280S	ENST00000269305	NM_001126112.2	280	agA/agT	8/11	0.0661142223920028	3	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.343133301610919	3		634	796	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106424	27106424	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	115	492	0	ENST00000324856.7:c.6035G>A	p.Gly2012Asp	p.G2012D	ENST00000324856	NM_006015.4	2012	gGc/gAc	20/20	0.333664814786548	3	FACETS	1	0.936	1	0.525	0.473	0.58	CLONAL	1	TRUE	1	0.343133301610919	3		492	748	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860150	57860151	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0043822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	230	558	0	ENST00000228682.2:c.891_892del	p.Lys299AlafsTer7	p.K299Afs*7	ENST00000228682	NM_005269.2	297	gGC/g	8/12	0.326845930829047	3	FACETS	0.916	0.856	0.979	0.916	0.856	0.979	CLONAL	2	TRUE	1	0.343133301610919	3		558	857	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375523	40375523	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	319	553	0	ENST00000293328.3:c.427C>T	p.Gln143Ter	p.Q143*	ENST00000293328	NM_012448.3	143	Cag/Tag	5/19	0.325978784063388	3	FACETS	0.945	0.898	0.994	0.945	0.898	0.994	CLONAL	3	TRUE	0	0.343133301610919	3		553	768	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688810	47688810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	194	303	1	ENST00000347630.2:c.490G>A	p.Val164Met	p.V164M	ENST00000347630	NM_001007230.1	164	Gtg/Atg	7/11	0.325978784063388	3	FACETS	0.883	0.825	0.943	0.883	0.825	0.943	CLONAL	3	TRUE	0	0.343133301610919	3		304	500	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119803	70119803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	116	519	1	ENST00000245479.2:c.805G>A	p.Asp269Asn	p.D269N	ENST00000245479	NM_000346.3	269	Gac/Aac	3/3	0.343133301610919	3	FACETS	1	0.907	1	0.503	0.453	0.556	CLONAL	1	TRUE	1	0.343133301610919	3		520	787	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	240505	240505	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	25	66	0	ENST00000264932.6:c.1465G>C	p.Gly489Arg	p.G489R	ENST00000264932	NM_004168.2	489	Ggg/Cgg	11/15	0.28623355023189	4	FACETS	0.923	0.742	1	0.923	0.742	1	CLONAL	2	TRUE	2	0.343133301610919	4		66	106	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	130	737	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.910663979731386	2		737	235	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0043831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	168	309	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.902	0.839	0.966	0.902	0.839	0.966	CLONAL	1	TRUE	1	0.910663979731386	2		309	409	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799063	42799065	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs751580245	NA	P-0043831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	67	615	0	ENST00000575354.2:c.4550_4552del	p.Lys1517del	p.K1517del	ENST00000575354	NM_015125.3	1516	cAGAag/cag	20/20	0.833345149162777	1	FACETS	0.159	0.138	0.181	0.159	0.138	0.181	SUBCLONAL	1	TRUE	0	0.910663979731386	1		615	505	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798839	42798839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778649585	NA	P-0043831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	196	624	1	ENST00000575354.2:c.4411C>T	p.Arg1471Trp	p.R1471W	ENST00000575354	NM_015125.3	1471	Cgg/Tgg	19/20	0.833345149162777	1	FACETS	0.496	0.463	0.528	0.496	0.463	0.528	SUBCLONAL	1	TRUE	0	0.910663979731386	1		625	473	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444686	78444686	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0043831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	78	358	0	ENST00000370768.2:c.3G>A	p.Met1?	p.M1?	ENST00000370768	NM_003902.3	1	atG/atA	1/20	0.910663979731386	1	FACETS	0.251	0.221	0.282	0.251	0.221	0.282	SUBCLONAL	1	TRUE	0	0.910663979731386	1		358	372	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52649463	52649463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	160	309	0	ENST00000394830.3:c.1828G>A	p.Asp610Asn	p.D610N	ENST00000394830	NM_018313.4	610	Gat/Aat	16/30	1	2	FACETS	0.524	0.482	0.568	0.524	0.482	0.568	SUBCLONAL	1	TRUE	1	0.910663979731386	2		309	670	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0043843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	512	739	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.656868122221443	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.656868122221443	1		739	766	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0043843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	244	411	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.14640381741875	4	FACETS	0.91	0.856	0.966	0.91	0.856	0.966	INDETERMINATE	2	TRUE	2	0.656868122221443	4		411	676	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023917	27023917	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	110	71	0	ENST00000324856.7:c.1024del	p.Ala342ArgfsTer21	p.A342Rfs*21	ENST00000324856	NM_006015.4	341	gcG/gc	1/20	0.285058785677292	1	FACETS	1	0.975	1	1	0.975	1	INDETERMINATE	1	TRUE	0	0.656868122221443	1		71	198	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592080	55592081	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	329	528	0	ENST00000288135.5:c.1407dup	p.Gly470TrpfsTer12	p.G470Wfs*12	ENST00000288135	NM_000222.2	468	-/T	9/21	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.656868122221443	2		528	816	SUCCESS
APC	324	MSKCC	GRCh37	5	112175606	112175607	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTCCA	novel	NA	P-0043843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	160	373	0	ENST00000257430.4:c.4317_4321dup	p.Pro1441LeufsTer34	p.P1441Lfs*34	ENST00000257430	NM_000038.5	1439	cct/cCTCCAct	16/16	0.14640381741875	4	FACETS	1	0.983	1	0.626	0.576	0.678	INDETERMINATE	1	TRUE	2	0.656868122221443	4		373	645	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035986	47035986	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0043843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	586	432	0	ENST00000377604.3:c.663+1G>A		p.X221_splice	ENST00000377604	NM_001204468.1	221			0.440073915926754	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.656868122221443	2		432	739	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343021	70343021	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs875989806	NA	P-0043859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	363	669	1	ENST00000374080.3:c.1562G>A	p.Arg521His	p.R521H	ENST00000374080		521	cGt/cAt	11/45	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.815214924705829	2		670	858	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257720	16257720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550078220	NA	P-0043859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	295	523	0	ENST00000375759.3:c.4985C>T	p.Thr1662Met	p.T1662M	ENST00000375759	NM_015001.2	1662	aCg/aTg	11/15	0.782083719484377	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.815214924705829	1		523	409	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28971096	28971096	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0043859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	202	331	0	ENST00000282397.4:c.1660+1G>T		p.X554_splice	ENST00000282397	NM_002019.4	554			0.281479293269135	1	FACETS	0.609	0.57	0.648	0.609	0.57	0.648	INDETERMINATE	1	TRUE	0	0.815214924705829	1		331	482	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	90	253	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.988	0.88	1	0.988	0.88	1	CLONAL	1	TRUE	1	0.398801453439548	2		253	457	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	169	331	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.927	0.853	1	0.927	0.853	1	CLONAL	1	TRUE	1	0.398801453439548	2		335	914	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872461	35872461	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	111	518	1	ENST00000216797.5:c.442del	p.Leu148TyrfsTer16	p.L148Yfs*16	ENST00000216797	NM_020529.2	148	Cta/ta	3/6	1	2	FACETS	0.795	0.716	0.879	0.795	0.716	0.879	SUBCLONAL	1	TRUE	1	0.398801453439548	2		519	700	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518270	8518270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556357771	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	86	293	1	ENST00000356435.5:c.1121C>T	p.Ala374Val	p.A374V	ENST00000356435		374	gCg/gTg	10/35	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.398801453439548	2		294	349	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701243	43701243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769912966	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	108	481	0	ENST00000382044.4:c.5452C>T	p.Arg1818Trp	p.R1818W	ENST00000382044	NM_001141980.1	1818	Cgg/Tgg	26/28	1	2	FACETS	0.857	0.771	0.948	0.857	0.771	0.948	CLONAL	1	TRUE	1	0.398801453439548	2		481	632	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	279	320	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.398801453439548	2	FACETS	0.981	0.927	1	0.981	0.927	1	CLONAL	2	TRUE	0	0.398801453439548	2		325	713	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	44	249	3	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.876	0.74	1	0.876	0.74	1	CLONAL	1	TRUE	1	0.398801453439548	2		252	252	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231437	46231437	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	86	307	0	ENST00000334344.6:c.1277C>T	p.Thr426Met	p.T426M	ENST00000334344	NM_152641.2	426	aCg/aTg	10/21	1	2	FACETS	0.982	0.873	1	0.982	0.873	1	CLONAL	1	TRUE	1	0.398801453439548	2		307	439	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007834	45007834	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	109	313	0	ENST00000558401.1:c.285del	p.Asp96MetfsTer7	p.D96Mfs*7	ENST00000558401	NM_004048.2	94	gAa/ga	2/4	1	2	FACETS	0.942	0.849	1	0.942	0.849	1	CLONAL	1	TRUE	1	0.398801453439548	2		313	580	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834552	156834552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540521894	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	153	683	2	ENST00000524377.1:c.320C>T	p.Ala107Val	p.A107V	ENST00000524377	NM_002529.3	107	gCg/gTg	3/17	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.398801453439548	2		685	707	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649640	206649640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782100237	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	151	601	0	ENST00000367120.3:c.475G>A	p.Gly159Ser	p.G159S	ENST00000367120	NM_014002.3	159	Ggc/Agc	6/22	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.398801453439548	2		601	711	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675571	86675571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1561325048	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	34	189	0	ENST00000274376.6:c.2513del	p.Asn838MetfsTer4	p.N838Mfs*4	ENST00000274376	NM_002890.2	836	gAa/ga	19/25	1	2	FACETS	0.47	0.384	0.566	0.47	0.384	0.566	SUBCLONAL	1	TRUE	1	0.398801453439548	2		189	363	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434545	121434545	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1343874863	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	159	682	0	ENST00000257555.6:c.1309G>A	p.Gly437Ser	p.G437S	ENST00000257555		437	Ggc/Agc	6/10	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.398801453439548	2		682	797	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197506	106197506	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	33	308	0	ENST00000380013.4:c.5844del	p.Val1949Ter	p.V1949*	ENST00000380013	NM_001127208.2	1947	Aaa/aa	11/11	1	2	FACETS	0.383	0.312	0.464	0.383	0.312	0.464	SUBCLONAL	1	TRUE	1	0.398801453439548	2		308	432	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176338	24176338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	163	642	2	ENST00000263121.7:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000263121	NM_003073.3	377	Cgt/Tgt	9/9	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.398801453439548	2		644	724	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	151	742	3	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.398801453439548	2		745	693	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693003	89693003	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs786204900	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	31	271	0	ENST00000371953.3:c.491del	p.Lys164ArgfsTer3	p.K164Rfs*3	ENST00000371953	NM_000314.4	163	Aaa/aa	5/9	1	2	FACETS	0.386	0.312	0.47	0.386	0.312	0.47	SUBCLONAL	1	TRUE	1	0.398801453439548	2		271	403	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939417	76939417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781932965	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	88	562	0	ENST00000373344.5:c.1331G>A	p.Arg444Gln	p.R444Q	ENST00000373344	NM_000489.3	444	cGa/cAa	9/35	1	2	FACETS	0.544	0.481	0.611	0.544	0.481	0.611	SUBCLONAL	1	TRUE	1	0.398801453439548	2		562	812	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099332	157099333	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCA	rs754114025	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	26	249	0	ENST00000346085.5:c.285_287dup	p.His96dup	p.H96dup	ENST00000346085	NM_020732.3	96	gcc/gcCCAc	1/20	1	2	FACETS	0.361	0.286	0.448	0.361	0.286	0.448	SUBCLONAL	1	TRUE	1	0.398801453439548	2		249	361	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007825	45007825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	108	310	0	ENST00000558401.1:c.276del	p.Thr93LeufsTer10	p.T93Lfs*10	ENST00000558401	NM_004048.2	91	aCc/ac	2/4	1	2	FACETS	0.915	0.823	1	0.915	0.823	1	CLONAL	1	TRUE	1	0.398801453439548	2		310	592	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	130	410	1	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	0.997	0.906	1	0.997	0.906	1	CLONAL	1	TRUE	1	0.398801453439548	2		411	654	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885939	111885939	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	122	509	3	ENST00000341259.2:c.1566del	p.Glu523SerfsTer25	p.E523Sfs*25	ENST00000341259	NM_005475.2	521	Ccc/cc	8/8	1	2	FACETS	0.981	0.889	1	0.981	0.889	1	CLONAL	1	TRUE	1	0.398801453439548	2		512	624	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253371	226253371	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	81	189	0	ENST00000366813.1:c.143C>T	p.Ala48Val	p.A48V	ENST00000366813		48	gCg/gTg	2/3	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.398801453439548	2		189	399	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197443	106197443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1452689450	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	68	292	1	ENST00000380013.4:c.5776C>T	p.Arg1926Cys	p.R1926C	ENST00000380013	NM_001127208.2	1926	Cgt/Tgt	11/11	1	2	FACETS	0.902	0.789	1	0.902	0.789	1	CLONAL	1	TRUE	1	0.398801453439548	2		293	378	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400212	139400212	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	121	572	0	ENST00000277541.6:c.4136del	p.Thr1379ArgfsTer66	p.T1379Rfs*66	ENST00000277541	NM_017617.3	1379	aCg/ag	25/34	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.398801453439548	2		572	582	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954273	32954273	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359752	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	104	350	0	ENST00000380152.3:c.9253del	p.Thr3085GlnfsTer19	p.T3085Qfs*19	ENST00000380152		3083	Aaa/aa	24/27	1	2	FACETS	0.947	0.85	1	0.947	0.85	1	CLONAL	1	TRUE	1	0.398801453439548	2		350	551	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023831	27023831	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1415214478	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	44	215	2	ENST00000324856.7:c.941del	p.Gly314AlafsTer49	p.G314Afs*49	ENST00000324856	NM_006015.4	313	Ggg/gg	1/20	1	2	FACETS	0.681	0.573	0.799	0.681	0.573	0.799	SUBCLONAL	1	TRUE	1	0.398801453439548	2		217	324	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214706	5214706	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457749790	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	58	566	0	ENST00000357368.4:c.4360G>A	p.Gly1454Ser	p.G1454S	ENST00000357368	NM_002850.3	1454	Ggc/Agc	29/38	1	2	FACETS	0.467	0.401	0.539	0.467	0.401	0.539	SUBCLONAL	1	TRUE	1	0.398801453439548	2		566	623	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862157	68862157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776975632	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	116	506	1	ENST00000261769.5:c.2245C>T	p.Arg749Trp	p.R749W	ENST00000261769	NM_004360.3	749	Cgg/Tgg	14/16	1	2	FACETS	0.854	0.771	0.942	0.854	0.771	0.942	CLONAL	1	TRUE	1	0.398801453439548	2		507	681	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096133	2096133	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs763525759	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	139	527	0	ENST00000219066.1:c.374del	p.Pro125GlnfsTer12	p.P125Qfs*12	ENST00000219066	NM_002528.5	125	cCa/ca	2/6	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.398801453439548	2		527	661	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116173	209116173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781398075	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	114	255	0	ENST00000345146.2:c.103G>A	p.Val35Met	p.V35M	ENST00000345146	NM_005896.2	35	Gtg/Atg	3/10	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.398801453439548	2		255	570	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	153	669	5	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.398801453439548	2		674	750	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166014	118166014	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	119	378	2	ENST00000369448.3:c.524G>A	p.Arg175His	p.R175H	ENST00000369448	NM_017709.3	175	cGt/cAt	2/2	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.398801453439548	2		380	555	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223328	36223328	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	153	714	2	ENST00000222270.7:c.5882del	p.Pro1961LeufsTer26	p.P1961Lfs*26	ENST00000222270	NM_014727.1	1960	Ccc/cc	28/37	1	2	FACETS	0.966	0.885	1	0.966	0.885	1	CLONAL	1	TRUE	1	0.398801453439548	2		716	794	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435279	49435279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs181521514	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	167	617	1	ENST00000301067.7:c.6274G>A	p.Asp2092Asn	p.D2092N	ENST00000301067	NM_003482.3	2092	Gac/Aac	31/54	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.398801453439548	2		618	716	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185545	27185545	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1564083506	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	102	585	1	ENST00000380036.4:c.1250del	p.Pro417LeufsTer10	p.P417Lfs*10	ENST00000380036	NM_000459.3	415	ctC/ct	9/23	1	2	FACETS	0.579	0.517	0.645	0.579	0.517	0.645	SUBCLONAL	1	TRUE	1	0.398801453439548	2		586	884	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896488	28896488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376257265	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	51	339	0	ENST00000282397.4:c.2962G>A	p.Gly988Ser	p.G988S	ENST00000282397	NM_002019.4	988	Ggt/Agt	22/30	1	2	FACETS	0.465	0.395	0.542	0.465	0.395	0.542	SUBCLONAL	1	TRUE	1	0.398801453439548	2		339	550	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522590	176522590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765924274	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	137	576	1	ENST00000292408.4:c.1687C>T	p.Arg563Trp	p.R563W	ENST00000292408	NM_213647.1	563	Cgg/Tgg	13/18	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.398801453439548	2		577	606	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210704	5210704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766174955	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	131	562	0	ENST00000357368.4:c.5347C>T	p.Arg1783Trp	p.R1783W	ENST00000357368	NM_002850.3	1783	Cgg/Tgg	34/38	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.398801453439548	2		562	633	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798428	42798428	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	39	650	1	ENST00000575354.2:c.4303del	p.Asp1435ThrfsTer19	p.D1435Tfs*19	ENST00000575354	NM_015125.3	1433	gaG/ga	18/20	1	2	FACETS	0.263	0.217	0.314	0.263	0.217	0.314	SUBCLONAL	1	TRUE	1	0.398801453439548	2		651	745	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243502	41243502	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357345	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	139	544	2	ENST00000357654.3:c.4046C>T	p.Thr1349Met	p.T1349M	ENST00000357654	NM_007294.3	1349	aCg/aTg	10/23	0.398801453439548	2	FACETS	0.945	0.861	1	0.472	0.43	0.516	CLONAL	1	TRUE	0	0.398801453439548	2		546	738	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741475	17741475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769475374	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	53	433	1	ENST00000250003.3:c.146G>A	p.Arg49His	p.R49H	ENST00000250003	NM_002478.4	49	cGc/cAc	1/3	1	2	FACETS	0.436	0.371	0.507	0.436	0.371	0.507	SUBCLONAL	1	TRUE	1	0.398801453439548	2		434	610	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221972	98221972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373120584	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	118	444	0	ENST00000331920.6:c.2797G>A	p.Ala933Thr	p.A933T	ENST00000331920	NM_000264.3	933	Gcg/Acg	17/24	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.398801453439548	2		444	591	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566042	141566042	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1460562478	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	115	437	0	ENST00000220592.5:c.1222G>A	p.Val408Met	p.V408M	ENST00000220592	NM_012154.3	408	Gtg/Atg	10/19	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.398801453439548	2		437	558	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31464401	31464401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	168	598	1	ENST00000344624.3:c.2516C>T	p.Thr839Met	p.T839M	ENST00000344624		839	aCg/aTg	17/33	1	2	FACETS	0.85	0.781	0.923	0.85	0.781	0.923	CLONAL	1	TRUE	1	0.398801453439548	2		599	991	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319093	62319093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205700	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	154	657	0	ENST00000360203.5:c.1451C>T	p.Pro484Leu	p.P484L	ENST00000360203	NM_001283009.1	484	cCg/cTg	17/35	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.398801453439548	2		657	700	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652947	29652947	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770124316	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	112	332	0	ENST00000356175.3:c.4882G>A	p.Gly1628Arg	p.G1628R	ENST00000356175	NM_000267.3	1628	Ggg/Agg	36/57	0.155240565685722	3	FACETS	0.957	0.862	1			1	INDETERMINATE	1	TRUE	NA	0.398801453439548	3		332	704	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789582	3789582	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145988918	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	88	359	0	ENST00000262367.5:c.4277C>T	p.Thr1426Met	p.T1426M	ENST00000262367	NM_004380.2	1426	aCg/aTg	25/31	1	2	FACETS	0.914	0.813	1	0.914	0.813	1	CLONAL	1	TRUE	1	0.398801453439548	2		359	483	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191229	185191229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	114	415	0	ENST00000265026.3:c.2110G>A	p.Ala704Thr	p.A704T	ENST00000265026	NM_004721.4	704	Gct/Act	11/14	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.398801453439548	2		415	486	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880980	134880980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771555643	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	130	469	0	ENST00000398015.3:c.1543G>A	p.Gly515Ser	p.G515S	ENST00000398015	NM_004441.4	515	Ggc/Agc	7/16	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.398801453439548	2		469	619	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120094	70120094	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	14	41	1	ENST00000245479.2:c.1100del	p.Pro367HisfsTer16	p.P367Hfs*16	ENST00000245479	NM_000346.3	366	Ccc/cc	3/3	0.398801453439548	2	FACETS	1	0.81	1	1	0.81	1	CLONAL	2	TRUE	0	0.398801453439548	2		42	33	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614974	23614974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757118000	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	35	345	0	ENST00000261584.4:c.3367G>A	p.Val1123Met	p.V1123M	ENST00000261584	NM_024675.3	1123	Gtg/Atg	13/13	1	2	FACETS	0.361	0.295	0.435	0.361	0.295	0.435	SUBCLONAL	1	TRUE	1	0.398801453439548	2		345	486	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41199717	41199717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	133	517	0	ENST00000357654.3:c.5410G>A	p.Val1804Ile	p.V1804I	ENST00000357654	NM_007294.3	1804	Gtc/Atc	22/23	0.398801453439548	2	FACETS	0.933	0.849	1	0.466	0.424	0.511	CLONAL	1	TRUE	0	0.398801453439548	2		517	715	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435309	110435309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	56	145	1	ENST00000375856.3:c.3092C>T	p.Pro1031Leu	p.P1031L	ENST00000375856	NM_003749.2	1031	cCg/cTg	1/2	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.398801453439548	2		146	239	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345989	152345989	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775565256	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	121	404	0	ENST00000359321.1:c.581C>T	p.Thr194Met	p.T194M	ENST00000359321	NM_005431.1	194	aCg/aTg	3/3	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.398801453439548	2		404	528	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246091262	246091262	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	53	420	2	ENST00000388985.4:c.673G>A	p.Ala225Thr	p.A225T	ENST00000388985		225	Gca/Aca	7/12	1	2	FACETS	0.42	0.357	0.488	0.42	0.357	0.488	SUBCLONAL	1	TRUE	1	0.398801453439548	2		422	633	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945420	71945420	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	149	541	0	ENST00000298229.2:c.2308T>C	p.Tyr770His	p.Y770H	ENST00000298229	NM_001567.3	770	Tac/Cac	20/28	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.398801453439548	2		541	696	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363829	118363830	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	131	445	0	ENST00000534358.1:c.5067dup	p.Glu1690ArgfsTer4	p.E1690Rfs*4	ENST00000534358	NM_005933.3	1688	tcc/tCcc	16/36	1	2	FACETS	0.952	0.866	1	0.952	0.866	1	CLONAL	1	TRUE	1	0.398801453439548	2		445	690	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50481152	50481152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	57	313	1	ENST00000394963.4:c.538C>T	p.Arg180Trp	p.R180W	ENST00000394963	NM_003076.4	180	Cgg/Tgg	5/13	1	2	FACETS	0.682	0.587	0.786	0.682	0.587	0.786	SUBCLONAL	1	TRUE	1	0.398801453439548	2		314	419	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107968	30107968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757900101	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	144	495	1	ENST00000331968.5:c.839G>A	p.Arg280Gln	p.R280Q	ENST00000331968	NM_002742.2	280	cGg/cAg	5/18	1	2	FACETS	0.954	0.871	1	0.954	0.871	1	CLONAL	1	TRUE	1	0.398801453439548	2		496	757	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371693	89371693	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	150	650	0	ENST00000301030.4:c.147G>T	p.Lys49Asn	p.K49N	ENST00000301030	NM_001256183.1	49	aaG/aaT	4/13	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.398801453439548	2		650	730	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882978	89882978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs943773590	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	38	146	0	ENST00000389301.3:c.46G>A	p.Gly16Arg	p.G16R	ENST00000389301	NM_000135.2	16	Ggg/Agg	1/43	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.398801453439548	NA		146	238	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110899	8110899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756175507	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	148	536	2	ENST00000585124.1:c.196G>A	p.Asp66Asn	p.D66N	ENST00000585124	NM_004217.3	66	Gac/Aac	4/9	1	2	FACETS	0.983	0.899	1	0.983	0.899	1	CLONAL	1	TRUE	1	0.398801453439548	2		538	755	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884146	37884146	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	102	589	0	ENST00000269571.5:c.3617A>G	p.Gln1206Arg	p.Q1206R	ENST00000269571		1206	cAg/cGg	27/27	0.398801453439548	2	FACETS	0.671	0.6	0.747	0.336	0.3	0.374	SUBCLONAL	1	TRUE	0	0.398801453439548	2		589	762	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492691	56492694	+	frameshift_variant	Frame_Shift_Del	DEL	ATTA	ATTA	-	novel	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	248	335	0	ENST00000407977.2:c.245_248del	p.Leu82CysfsTer75	p.L82Cfs*75	ENST00000407977		82	tTAATg/tg	2/10	0.398801453439548	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.398801453439548	2		335	549	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530041	63530041	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	269	349	0	ENST00000307078.5:c.2394G>T	p.Lys798Asn	p.K798N	ENST00000307078	NM_004655.3	798	aaG/aaT	10/11	0.398801453439548	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.398801453439548	2		349	587	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622192	1622192	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	91	578	0	ENST00000344749.5:c.683G>A	p.Trp228Ter	p.W228*	ENST00000344749	NM_001136139.2	228	tGg/tAg	10/19	1	2	FACETS	0.842	0.75	0.94	0.842	0.75	0.94	CLONAL	1	TRUE	1	0.398801453439548	2		578	542	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375321	15375321	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1475673288	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	84	550	0	ENST00000263377.2:c.1106A>G	p.His369Arg	p.H369R	ENST00000263377	NM_058243.2	369	cAc/cGc	6/20	1	2	FACETS	0.641	0.566	0.721	0.641	0.566	0.721	SUBCLONAL	1	TRUE	1	0.398801453439548	2		550	657	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445454	29445454	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	48	492	0	ENST00000389048.3:c.3379T>A	p.Phe1127Ile	p.F1127I	ENST00000389048	NM_004304.4	1127	Ttt/Att	21/29	1	2	FACETS	0.428	0.361	0.501	0.428	0.361	0.501	SUBCLONAL	1	TRUE	1	0.398801453439548	2		492	563	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47643538	47643538	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587779067	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	138	443	0	ENST00000233146.2:c.1046C>G	p.Pro349Arg	p.P349R	ENST00000233146	NM_000251.2	349	cCt/cGt	6/16	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.398801453439548	2		443	679	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61710179	61710181	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1164883486	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	98	295	0	ENST00000401558.2:c.2723_2725del	p.Glu908del	p.E908del	ENST00000401558	NM_003400.3	908	gAAGct/gct	22/25	1	2	FACETS	0.867	0.775	0.964	0.867	0.775	0.964	CLONAL	1	TRUE	1	0.398801453439548	2		295	567	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84390197	84390197	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	54	338	0	ENST00000321945.7:c.584T>C	p.Val195Ala	p.V195A	ENST00000321945	NM_139076.2	195	gTa/gCa	6/9	1	2	FACETS	0.453	0.386	0.526	0.453	0.386	0.526	SUBCLONAL	1	TRUE	1	0.398801453439548	2		338	598	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99850060	99850060	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1299361080	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	37	569	0	ENST00000280892.6:c.64A>G	p.Ser22Gly	p.S22G	ENST00000280892	NM_001130678.1	22	Agc/Ggc	1/7	1	2	FACETS	0.259	0.212	0.311	0.259	0.212	0.311	SUBCLONAL	1	TRUE	1	0.398801453439548	2		569	717	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858208	27858208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	115	463	0	ENST00000359303.2:c.363G>A	p.Met121Ile	p.M121I	ENST00000359303	NM_003535.2	121	atG/atA	1/1	1	2	FACETS	0.926	0.836	1	0.926	0.836	1	CLONAL	1	TRUE	1	0.398801453439548	2		463	623	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559308	141559309	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	148	549	0	ENST00000220592.5:c.1492dup	p.Ala498GlyfsTer176	p.A498Gfs*176	ENST00000220592	NM_012154.3	498	gcg/gGcg	12/19	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.398801453439548	2		549	725	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517865	8517865	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	74	248	0	ENST00000356435.5:c.1526T>C	p.Val509Ala	p.V509A	ENST00000356435		509	gTc/gCc	10/35	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.398801453439548	2		248	361	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044906	47044907	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	110	699	0	ENST00000377604.3:c.2237dup	p.Glu748Ter	p.E748*	ENST00000377604	NM_001204468.1	744	-/G	20/24	1	2	FACETS	0.747	0.672	0.828	0.747	0.672	0.828	SUBCLONAL	1	TRUE	1	0.398801453439548	2		699	738	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177866	56177869	+	frameshift_variant	Frame_Shift_Del	DEL	ACAA	ACAA	GAG	novel	NA	P-0043907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	96	345	1	ENST00000399503.3:c.2839_2842delinsGAG	p.Thr947GlufsTer21	p.T947Efs*21	ENST00000399503	NM_005921.1	947	ACAAca/GAGca	14/20	1	2	FACETS	0.963	0.861	1	0.963	0.861	1	CLONAL	1	TRUE	1	0.398801453439548	2		346	500	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0043925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	64	274	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.319218083559862	2		274	283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0043925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	251	833	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.319218083559862	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.319218083559862	1		833	1095	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121082	11121082	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	211	621	0	ENST00000358026.2:c.2149G>T	p.Glu717Ter	p.E717*	ENST00000358026	NM_001128849.1	717	Gaa/Taa	15/36	0.319218083559862	2	FACETS	0.966	0.902	1	0.966	0.902	1	CLONAL	2	TRUE	0	0.319218083559862	2		621	684	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890135	76890135	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	81	454	0	ENST00000373344.5:c.4759G>T	p.Gly1587Cys	p.G1587C	ENST00000373344	NM_000489.3	1587	Ggt/Tgt	17/35	1	2	FACETS	0.876	0.773	0.987	0.876	0.773	0.987	CLONAL	1	TRUE	1	0.319218083559862	2		454	579	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105841	27105841	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	45	494	0	ENST00000324856.7:c.5452C>G	p.Gln1818Glu	p.Q1818E	ENST00000324856	NM_006015.4	1818	Cag/Gag	20/20	1	2	FACETS	0.601	0.505	0.707	0.601	0.505	0.707	SUBCLONAL	1	TRUE	1	0.319218083559862	2		494	469	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39321574	39321574	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs779725644	NA	P-0043925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	27	271	0	ENST00000373001.3:c.447C>G	p.Asp149Glu	p.D149E	ENST00000373001	NM_022157.3	149	gaC/gaG	3/7	1	2	FACETS	0.571	0.456	0.703	0.571	0.456	0.703	SUBCLONAL	1	TRUE	1	0.319218083559862	2		271	296	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14303232	14303232	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	56	540	0	ENST00000256196.4:c.443A>G	p.Gln148Arg	p.Q148R	ENST00000256196		148	cAg/cGg	5/6	0.319218083559862	1	FACETS	0.527	0.452	0.61	0.527	0.452	0.61	SUBCLONAL	1	TRUE	0	0.319218083559862	1		540	559	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913075	32913075	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	87	445	0	ENST00000380152.3:c.4583G>T	p.Ser1528Ile	p.S1528I	ENST00000380152		1528	aGc/aTc	11/27	0.319218083559862	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.319218083559862	1		445	430	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435010	110435010	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	129	745	0	ENST00000375856.3:c.3391C>G	p.Arg1131Gly	p.R1131G	ENST00000375856	NM_003749.2	1131	Cgc/Ggc	1/2	1	2	FACETS	0.934	0.847	1	0.934	0.847	1	CLONAL	1	TRUE	1	0.319218083559862	2		745	865	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663667	29663667	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660651	NA	P-0043925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	26	233	0	ENST00000356175.3:c.6099G>A	p.Met2033Ile	p.M2033I	ENST00000356175	NM_000267.3	2033	atG/atA	41/57	1	2	FACETS	0.52	0.413	0.644	0.52	0.413	0.644	SUBCLONAL	1	TRUE	1	0.319218083559862	2		233	313	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149735	202149735	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	90	544	0	ENST00000358485.4:c.1176C>G	p.Ile392Met	p.I392M	ENST00000358485	NM_001080125.1	392	atC/atG	8/9	0.209882387421023	3	FACETS	1	0.945	1	0.551	0.49	0.617	CLONAL	1	TRUE	1	0.319218083559862	3		544	593	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037198	71037198	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	81	370	0	ENST00000318789.4:c.1093A>C	p.Met365Leu	p.M365L	ENST00000318789	NM_032682.5	365	Atg/Ctg	14/21	0.319218083559862	1	FACETS	0.933	0.825	1	0.933	0.825	1	CLONAL	1	TRUE	0	0.319218083559862	1		370	457	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177942	142177942	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	21	281	0	ENST00000350721.4:c.7361G>T	p.Arg2454Ile	p.R2454I	ENST00000350721	NM_001184.3	2454	aGa/aTa	44/47	0.319218083559862	1	FACETS	0.41	0.316	0.519	0.41	0.316	0.519	SUBCLONAL	1	TRUE	0	0.319218083559862	1		281	270	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875958	76875958	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	55	249	0	ENST00000373344.5:c.5177A>T	p.Asn1726Ile	p.N1726I	ENST00000373344	NM_000489.3	1726	aAt/aTt	20/35	1	2	FACETS	0.996	0.856	1	0.996	0.856	1	CLONAL	1	TRUE	1	0.319218083559862	2		249	346	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0043927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	41	305	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.811	0.678	0.958	0.811	0.678	0.958	CLONAL	1	FALSE	1	0.3	2		305	337	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771658	135771658	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	39	495	0	ENST00000298552.3:c.3459C>G	p.Ile1153Met	p.I1153M	ENST00000298552	NM_001162426.1	1153	atC/atG	23/23	NA	2	FACETS	0.381	0.314	0.455			1	INDETERMINATE	1	TRUE	NA	0.28	2		495	732	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0043944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	28	466	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	1	2	FACETS	0.226	0.18	0.279	0.226	0.18	0.279	SUBCLONAL	1	TRUE	1	0.374520636138669	2		466	661	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202815	133202815	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	38	506	0	ENST00000320574.5:c.6419A>T	p.Glu2140Val	p.E2140V	ENST00000320574	NM_006231.2	2140	gAg/gTg	46/49	1	2	FACETS	0.311	0.256	0.373	0.311	0.256	0.373	SUBCLONAL	1	TRUE	1	0.374520636138669	2		506	652	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191503	10191503	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs104893825	NA	P-0043944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	16	361	0	ENST00000256474.2:c.496G>T	p.Val166Phe	p.V166F	ENST00000256474	NM_000551.3	166	Gtc/Ttc	3/3	1	2	FACETS	0.187	0.137	0.247	0.187	0.137	0.247	SUBCLONAL	1	TRUE	1	0.374520636138669	2		361	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0043952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	604	739	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.906016167947676	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.906016167947676	2		739	649	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489514	40489514	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	620	526	3	ENST00000264657.5:c.736C>G	p.Arg246Gly	p.R246G	ENST00000264657	NM_139276.2	246	Cgg/Ggg	8/24	0.906016167947676	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.906016167947676	2		529	671	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864221	117864221	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	261	419	0	ENST00000297338.2:c.1436A>C	p.Lys479Thr	p.K479T	ENST00000297338	NM_006265.2	479	aAa/aCa	11/14	1	2	FACETS	0.928	0.876	0.98	0.928	0.876	0.98	CLONAL	1	TRUE	1	0.906016167947676	2		419	621	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0043993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	47	413	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.29972567597246	1	FACETS	0.674	0.57	0.788	0.674	0.57	0.788	SUBCLONAL	1	TRUE	0	0.3	1		414	395	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220469	1220469	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	125	646	0	ENST00000326873.7:c.563del	p.Gly188AlafsTer99	p.G188Afs*99	ENST00000326873	NM_000455.4	188	Ggc/gc	4/10	0.296575576546871	1	FACETS	0.942	0.853	1	0.942	0.853	1	CLONAL	1	TRUE	0	0.3	1		646	752	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92247520	92247520	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs902137115	NA	P-0043993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	53	265	0	ENST00000265734.4:c.700G>A	p.Val234Met	p.V234M	ENST00000265734	NM_001259.6	234	Gtg/Atg	7/8	1	2	FACETS	0.932	0.798	1	0.932	0.798	1	CLONAL	1	TRUE	1	0.3	2		265	379	SUCCESS
ATM	472	MSKCC	GRCh37	11	108127041	108127041	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0043993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	60	386	0	ENST00000278616.4:c.2224A>T	p.Lys742Ter	p.K742*	ENST00000278616	NM_000051.3	742	Aag/Tag	14/63	1	2	FACETS	0.935	0.808	1	0.935	0.808	1	CLONAL	1	TRUE	1	0.3	2		386	428	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654655	67654655	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	101	473	1	ENST00000264010.4:c.1142G>T	p.Cys381Phe	p.C381F	ENST00000264010	NM_006565.3	381	tGc/tTc	6/12	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.3	2		474	671	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610368	10610369	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0043993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	175	784	1	ENST00000171111.5:c.341_342delinsTT	p.Gly114Val	p.G114V	ENST00000171111	NM_203500.1	114	gGG/gTT	2/6	0.296575576546871	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.3	1		785	944	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187515	32187515	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1470084434	NA	P-0043993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	154	725	0	ENST00000375023.3:c.1364C>T	p.Thr455Ile	p.T455I	ENST00000375023	NM_004557.3	455	aCt/aTt	8/30	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.3	2		725	1016	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956969	2956969	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	114	707	2	ENST00000396946.4:c.2658C>A	p.Ser886Arg	p.S886R	ENST00000396946	NM_032415.4	886	agC/agA	20/25	1	2	FACETS	0.829	0.745	0.917	0.829	0.745	0.917	CLONAL	1	TRUE	1	0.3	2		709	917	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912096	56912096	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	99	513	0	ENST00000519728.1:c.1324A>G	p.Ile442Val	p.I442V	ENST00000519728	NM_002350.3	442	Att/Gtt	12/13	0.224543652548874	1	FACETS	0.972	0.87	1	0.972	0.87	1	CLONAL	1	TRUE	0	0.3	1		513	577	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038821	47038821	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	154	780	1	ENST00000377604.3:c.828C>A	p.Tyr276Ter	p.Y276*	ENST00000377604	NM_001204468.1	276	taC/taA	9/24	0.29972567597246	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.3	1		781	870	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0044006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	47	413	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.242284516149387	1	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	0	0.242284516149387	1		414	313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876658468	NA	P-0044006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	54	417	0	ENST00000269305.4:c.577C>G	p.His193Asp	p.H193D	ENST00000269305	NM_001126112.2	193	Cat/Gat	6/11	NA	2	FACETS	0.869	0.743	1			1	INDETERMINATE	1	TRUE	NA	0.242284516149387	2		417	513	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115931	8115931	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	52	331	0	ENST00000346208.3:c.1277C>G	p.Ser426Cys	p.S426C	ENST00000346208		426	tCc/tGc	6/6	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.242284516149387	2		331	398	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596043	43596043	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	68	453	0	ENST00000355710.3:c.210G>T	p.Gln70His	p.Q70H	ENST00000355710	NM_020975.4	70	caG/caT	2/20	1	2	FACETS	0.934	0.813	1	0.934	0.813	1	CLONAL	1	TRUE	1	0.242284516149387	2		453	601	SUCCESS
ATM	472	MSKCC	GRCh37	11	108137938	108137938	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	51	268	0	ENST00000278616.4:c.2507A>T	p.Glu836Val	p.E836V	ENST00000278616	NM_000051.3	836	gAa/gTa	17/63	0.17791988504766	2	FACETS	1	0.921	1	0.563	0.48	0.653	CLONAL	1	TRUE	0	0.242284516149387	2		268	374	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447392	49447392	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	83	483	0	ENST00000301067.7:c.706G>C	p.Gly236Arg	p.G236R	ENST00000301067	NM_003482.3	236	Ggg/Cgg	6/54	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.242284516149387	2		483	658	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88428923	88428923	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0044006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	45	280	0	ENST00000360948.2:c.2175+2T>A		p.X725_splice	ENST00000360948	NM_001012338.2	725			0.242284516149387	1	FACETS	0.839	0.707	0.985	0.839	0.707	0.985	CLONAL	1	TRUE	0	0.242284516149387	1		280	389	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992747	72992747	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	84	464	0	ENST00000268489.5:c.1298G>T	p.Gly433Val	p.G433V	ENST00000268489	NM_006885.3	433	gGc/gTc	2/10	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.242284516149387	2		464	656	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223301	36223301	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	38	702	0	ENST00000222270.7:c.5851C>G	p.Leu1951Val	p.L1951V	ENST00000222270	NM_014727.1	1951	Ctc/Gtc	28/37	0.242284516149387	1	FACETS	0.366	0.301	0.438	0.366	0.301	0.438	SUBCLONAL	1	TRUE	0	0.242284516149387	1		702	754	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139896	50139896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	88	573	0	ENST00000246792.3:c.433G>A	p.Asp145Asn	p.D145N	ENST00000246792	NM_006270.3	145	Gat/Aat	4/6	0.242284516149387	1	FACETS	0.912	0.808	1	0.912	0.808	1	CLONAL	1	TRUE	0	0.242284516149387	1		573	700	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683635	162683635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	46	327	2	ENST00000366898.1:c.334C>T	p.Leu112Phe	p.L112F	ENST00000366898	NM_004562.2	112	Ctc/Ttc	3/12	1	2	FACETS	0.833	0.702	0.977	0.833	0.702	0.977	CLONAL	1	TRUE	1	0.242284516149387	2		329	456	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325339	1325339	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	36	279	0	ENST00000400841.2:c.336G>T	p.Trp112Cys	p.W112C	ENST00000400841		112	tgG/tgT	3/6	1	1	FACETS	0.552	0.454	0.663	0.552	0.454	0.663	SUBCLONAL	1	TRUE	0	0.242284516149387	1		279	473	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031973	26031973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	133	294	0	ENST00000244661.2:c.316G>A	p.Glu106Lys	p.E106K	ENST00000244661	NM_003537.3	106	Gag/Aag	1/1	0.193118018355358	2	FACETS	0.779	0.71	0.851	0.779	0.71	0.851	SUBCLONAL	2	TRUE	0	0.292450604995477	2		294	584	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771827	135771827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs118203750	NA	P-0044018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	140	514	0	ENST00000298552.3:c.3290G>A	p.Arg1097His	p.R1097H	ENST00000298552	NM_001162426.1	1097	cGt/cAt	23/23	0.292450604995477	1	FACETS	0.964	0.878	1	0.964	0.878	1	CLONAL	1	TRUE	0	0.292450604995477	1		514	848	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs878854073	NA	P-0044018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	102	385	0	ENST00000269305.4:c.673-1G>A		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.292450604995477	1	FACETS	0.936	0.839	1	0.936	0.839	1	CLONAL	1	TRUE	0	0.292450604995477	1		385	636	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546574	9546574	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs991533102	NA	P-0044018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	94	379	1	ENST00000353224.5:c.1448G>A	p.Arg483Gln	p.R483Q	ENST00000353224	NM_177990.2	483	cGg/cAg	5/10	0.292450604995477	3	FACETS	1	0.921	1	0.522	0.464	0.583	CLONAL	1	TRUE	1	0.292450604995477	3		380	706	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0044021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	189	607	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.320594513623797	3	FACETS	0.874	0.809	0.94	0.874	0.809	0.94	CLONAL	2	FALSE	1	0.320594513623797	3		607	783	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602872	10602872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	174	855	0	ENST00000171111.5:c.706G>A	p.Asp236Asn	p.D236N	ENST00000171111	NM_203500.1	236	Gac/Aac	3/6	0.320594513623797	3	FACETS	1	0.987	1	0.686	0.632	0.743	CLONAL	1	FALSE	1	0.320594513623797	3		855	918	SUCCESS
APC	324	MSKCC	GRCh37	5	112136975	112136975	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs1554076129	NA	P-0044021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	30	258	0	ENST00000257430.4:c.730-1G>C		p.X244_splice	ENST00000257430	NM_000038.5	244			0.18049023306208	2	FACETS	1	0.939	1	0.704	0.576	0.843	INDETERMINATE	1	FALSE	0	0.320594513623797	2		258	133	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247174	153247174	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	14	238	0	ENST00000281708.4:c.1628G>C	p.Arg543Thr	p.R543T	ENST00000281708	NM_033632.3	543	aGa/aCa	10/12	1	2	FACETS	0.529	0.384	0.704	0.529	0.384	0.704	SUBCLONAL	1	FALSE	1	0.320594513623797	2		238	165	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075404	8075404	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	33	257	0	ENST00000377482.5:c.166C>G	p.Leu56Val	p.L56V	ENST00000377482	NM_018948.3	56	Ctg/Gtg	3/4	0.140947357740737	4	FACETS	0.918	0.759	1	0.918	0.759	1	INDETERMINATE	2	FALSE	2	0.320594513623797	4		257	148	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246099	41246099	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	11	507	0	ENST00000357654.3:c.1449A>G	p.Ile483Met	p.I483M	ENST00000357654	NM_007294.3	483	atA/atG	10/23	0.320594513623797	3	FACETS	0.514	0.356	0.709	0.257	0.178	0.355	SUBCLONAL	1	FALSE	1	0.320594513623797	3		507	155	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744488	41744488	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	125	762	0	ENST00000301178.4:c.1108G>T	p.Ala370Ser	p.A370S	ENST00000301178	NM_021913.4	370	Gcg/Tcg	8/20	0.140947357740737	4	FACETS	1	0.98	1	0.662	0.599	0.728	INDETERMINATE	1	FALSE	2	0.320594513623797	4		762	778	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139794970	139794970	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	106	520	0	ENST00000247668.2:c.364G>A	p.Glu122Lys	p.E122K	ENST00000247668	NM_021138.3	122	Gag/Aag	4/11	0.161898508146575	3	FACETS	1	0.966	1	0.591	0.531	0.655	INDETERMINATE	1	FALSE	1	0.320594513623797	3		520	649	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594221	55594221	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913512	NA	P-0044022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	795	418	0	ENST00000288135.5:c.1924A>G	p.Lys642Glu	p.K642E	ENST00000288135	NM_000222.2	642	Aaa/Gaa	13/21	0.942076522589562	4	FACETS	0.993	0.971	1			1	CLONAL	3	TRUE	NA	0.942076522589562	4		418	1100	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412045	116412045	+	splice_donor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0044032-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	228	558	0	ENST00000397752.3:c.3028+2del		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.507262474650884	4	FACETS	0.945	0.903	0.986			1	CLONAL	4	TRUE	NA	0.575821728107711	4		558	330	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504279	8504279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753412640	NA	P-0044032-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	45	413	0	ENST00000356435.5:c.1804G>A	p.Ala602Thr	p.A602T	ENST00000356435		602	Gct/Act	12/35	1	2	FACETS	0.611	0.517	0.712	0.611	0.517	0.712	SUBCLONAL	1	TRUE	1	0.575821728107711	2		413	256	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256213	123256213	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044032-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	81	428	0	ENST00000358487.5:c.1696T>A	p.Tyr566Asn	p.Y566N	ENST00000358487	NM_000141.4	566	Tat/Aat	13/18	0.450174120787659	3	FACETS	1	0.92	1	0.522	0.463	0.584	CLONAL	1	TRUE	1	0.575821728107711	3		428	347	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312716	30312716	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044032-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	66	461	0	ENST00000262643.3:c.697A>T	p.Ile233Phe	p.I233F	ENST00000262643	NM_001238.2	233	Att/Ttt	8/12	0.457025744476568	3	FACETS	0.923	0.807	1	0.461	0.403	0.523	CLONAL	1	TRUE	1	0.575821728107711	3		461	320	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156087	106156087	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044032-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	52	304	0	ENST00000380013.4:c.988G>C	p.Glu330Gln	p.E330Q	ENST00000380013	NM_001127208.2	330	Gag/Cag	3/11	0.575821728107711	3	FACETS	0.837	0.718	0.965	0.418	0.359	0.483	CLONAL	1	TRUE	1	0.575821728107711	3		304	278	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0044064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	201	457	2	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.378394633332208	4	FACETS	0.935	0.869	1	0.935	0.869	1	CLONAL	2	TRUE	2	0.419210210389523	4		459	728	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0044064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	306	583	0	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.419210210389523	2	FACETS	0.962	0.912	1	0.962	0.912	1	CLONAL	2	TRUE	0	0.419210210389523	2		583	759	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175549	108175549	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204433	NA	P-0044064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	155	407	1	ENST00000278616.4:c.5644C>T	p.Arg1882Ter	p.R1882*	ENST00000278616	NM_000051.3	1882	Cga/Tga	37/63	0.419210210389523	2	FACETS	0.976	0.905	1	0.976	0.905	1	CLONAL	2	TRUE	0	0.419210210389523	2		408	379	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570326	95570326	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	145	312	0	ENST00000393063.1:c.3407G>T	p.Gly1136Val	p.G1136V	ENST00000393063	NM_030621.3	1136	gGt/gTt	22/28	0.122832155673073	5	FACETS	0.958	0.884	1			1	INDETERMINATE	3	TRUE	NA	0.419210210389523	5		312	392	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983283	15983284	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GATAGAGC	novel	NA	P-0044064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	60	371	0	ENST00000268712.3:c.3488_3495dup	p.Thr1166AlafsTer21	p.T1166Afs*21	ENST00000268712	NM_006311.3	1165	-/GCTCTATC	26/46	0.378394633332208	4	FACETS	0.691	0.595	0.795	0.345	0.297	0.398	SUBCLONAL	1	TRUE	2	0.419210210389523	4		371	588	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539205	187539205	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	65	404	0	ENST00000441802.2:c.8535G>C	p.Met2845Ile	p.M2845I	ENST00000441802	NM_005245.3	2845	atG/atC	10/27	NA	2	FACETS	0.72	0.626	0.82			1	INDETERMINATE	1	TRUE	NA	0.419210210389523	2		404	431	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207500	29207500	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs757228799	NA	P-0044064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	121	450	0	ENST00000240100.2:c.296C>G	p.Ser99Cys	p.S99C	ENST00000240100	NM_001394.6	99	tCc/tGc	1/4	0.399183556408938	3	FACETS	1	0.941	1	0.527	0.476	0.579	CLONAL	1	TRUE	1	0.419210210389523	3		450	663	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593582	55593597	+	protein_altering_variant,splice_region_variant	In_Frame_Del	DEL	AAACCCATGTATGAAG	AAACCCATGTATGAAG	T	novel	NA	P-0044076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	174	327	0	ENST00000288135.5:c.1648_1663delinsT	p.Lys550_Val555delinsLeu	p.K550_V555delinsL	ENST00000288135	NM_000222.2	550	AAACCCATGTATGAAGta/Tta	11/21	1	2	FACETS	0.958	0.889	1	0.958	0.889	1	CLONAL	1	TRUE	1	0.724968761910133	2		327	501	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437175	110437175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs920062261	NA	P-0044076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	19	10	0	ENST00000375856.3:c.1226G>A	p.Cys409Tyr	p.C409Y	ENST00000375856	NM_003749.2	409	tGc/tAc	1/2	1	2	FACETS	0.819	0.675	0.955	1	0.943	1	CLONAL	2	TRUE	1	0.724968761910133	2		10	32	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42053980	42053980	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0044076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	183	319	0	ENST00000219905.7:c.7442T>A	p.Leu2481Ter	p.L2481*	ENST00000219905	NM_001164273.1	2481	tTg/tAg	21/24	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.724968761910133	2		319	502	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681130	37681130	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	280	476	0	ENST00000447079.4:c.3299A>T	p.Asp1100Val	p.D1100V	ENST00000447079	NM_015083.1	1100	gAt/gTt	12/14	0.368586971693583	3	FACETS	1	0.98	1	0.546	0.513	0.579	INDETERMINATE	1	TRUE	1	0.724968761910133	3		476	964	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467927	50467927	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	53	490	0	ENST00000331340.3:c.1162G>A	p.Ala388Thr	p.A388T	ENST00000331340	NM_006060.4	388	Gcg/Acg	8/8	1	2	FACETS	0.623	0.531	0.724	0.623	0.531	0.724	SUBCLONAL	1	TRUE	1	0.290654345222332	2		490	585	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264549	1264549	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199741493	NA	P-0044080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	48	557	1	ENST00000310581.5:c.2813G>A	p.Arg938Gln	p.R938Q	ENST00000310581	NM_198253.2	938	cGg/cAg	11/16	0.247739743998073	4	FACETS	0.493	0.415	0.579	0.164	0.138	0.193	SUBCLONAL	1	TRUE	1	0.290654345222332	4		558	865	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	164	737	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.59	2		737	555	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0044120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	55	305	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.704	0.607	0.807	0.704	0.607	0.807	SUBCLONAL	1	TRUE	1	0.59	2		305	265	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431493	49431493	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	520	962	0	ENST00000301067.7:c.9646G>T	p.Glu3216Ter	p.E3216*	ENST00000301067	NM_003482.3	3216	Gag/Tag	34/54	1	2	FACETS	0.912	0.874	0.949	0.912	0.874	0.949	CLONAL	1	TRUE	1	0.843274522454217	2		962	1353	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235919	133235919	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	892	719	0	ENST00000320574.5:c.3237C>G	p.Ile1079Met	p.I1079M	ENST00000320574	NM_006231.2	1079	atC/atG	26/49	0.839450638218022	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.843274522454217	2		719	1046	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56339000	56339000	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	150	133	0	ENST00000348428.3:c.125G>T	p.Ser42Ile	p.S42I	ENST00000348428	NM_006785.3	42	aGc/aTc	1/17	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.843274522454217	2		133	303	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394056	31394056	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	320	450	0	ENST00000328111.2:c.2343C>G	p.Ile781Met	p.I781M	ENST00000328111	NM_006892.3	781	atC/atG	22/23	0.366205007260883	3	FACETS	1	0.988	1	0.573	0.542	0.605	INDETERMINATE	1	TRUE	1	0.843274522454217	3		450	941	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153615	55153615	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	331	551	0	ENST00000257290.5:c.2581T>C	p.Trp861Arg	p.W861R	ENST00000257290	NM_006206.4	861	Tgg/Cgg	19/23	1	2	FACETS	0.952	0.904	1	0.952	0.904	1	CLONAL	1	TRUE	1	0.843274522454217	2		551	825	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349536	70349536	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	389	665	0	ENST00000374080.3:c.3698C>T	p.Ala1233Val	p.A1233V	ENST00000374080		1233	gCg/gTg	27/45	1	2	FACETS	0.843	0.802	0.884	0.843	0.802	0.884	CLONAL	1	TRUE	1	0.843274522454217	2		665	1095	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0044148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	244	305	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.966	0.908	1	0.966	0.908	1	CLONAL	1	TRUE	1	0.738417555011962	2		305	684	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469669	NA	P-0044148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	398	613	1	ENST00000374080.3:c.130G>A	p.Gly44Ser	p.G44S	ENST00000374080		44	Ggt/Agt	2/45	0.650635979413265	3	FACETS	1	0.985	1	0.544	0.517	0.572	CLONAL	1	TRUE	1	0.738417555011962	3		614	1357	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs121913292	NA	P-0044148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	251	514	0	ENST00000371953.3:c.389del	p.Arg130GlnfsTer4	p.R130Qfs*4	ENST00000371953	NM_000314.4	130	cGa/ca	5/9	0.738417555011962	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.738417555011962	1		514	424	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259047	89259047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	143	270	0	ENST00000336596.2:c.191C>T	p.Pro64Leu	p.P64L	ENST00000336596	NM_005233.5	64	cCc/cTc	3/17	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.738417555011962	2		270	369	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440924	52440924	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1553645729	NA	P-0044148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	281	630	0	ENST00000460680.1:c.581-1G>A		p.X194_splice	ENST00000460680	NM_004656.3	194			0.738417555011962	1	FACETS	0.94	0.895	0.984	0.94	0.895	0.984	CLONAL	1	TRUE	0	0.738417555011962	1		630	511	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444612	78444629	+	inframe_deletion	In_Frame_Del	DEL	CCTCCACCACCACCGCCG	CCTCCACCACCACCGCCG	-	novel	NA	P-0044148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	270	416	0	ENST00000370768.2:c.60_77del	p.Gly21_Gly26del	p.G21_G26del	ENST00000370768	NM_003902.3	20	ggCGGCGGTGGTGGTGGAGGa/gga	1/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.738417555011962	2		416	702	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690387	117690387	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1289431844	NA	P-0044148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	296	511	0	ENST00000369458.3:c.742C>T	p.Arg248Trp	p.R248W	ENST00000369458	NM_024626.3	248	Cgg/Tgg	5/6	0.738417555011962	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.738417555011962	1		511	492	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2193764	2193765	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0044148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	302	673	1	ENST00000398665.3:c.570_571delinsTT	p.Pro191Ser	p.P191S	ENST00000398665	NM_032482.2	190	atCCcg/atTTcg	6/28	NA	2	FACETS	0.953	0.901	1			1	INDETERMINATE	1	TRUE	NA	0.738417555011962	2		674	858	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264097	46264097	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	182	327	0	ENST00000371998.3:c.1144C>G	p.Pro382Ala	p.P382A	ENST00000371998		382	Cct/Gct	11/23	1	2	FACETS	0.928	0.863	0.995	0.928	0.863	0.995	CLONAL	1	TRUE	1	0.738417555011962	2		327	531	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910576	29910576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199474361	NA	P-0044148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	279	380	0	ENST00000376809.5:c.116C>T	p.Pro39Leu	p.P39L	ENST00000376809	NM_002116.7	39	cCc/cTc	2/8	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.738417555011962	2		380	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579366	7579366	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs770776262	NA	P-0044179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	534	936	0	ENST00000269305.4:c.321C>A	p.Tyr107Ter	p.Y107*	ENST00000269305	NM_001126112.2	107	taC/taA	4/11	0.600202388644765	2	FACETS	0.909	0.878	0.939	0.909	0.878	0.939	CLONAL	2	TRUE	0	0.630420164119204	2		936	932	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654553	29654553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876657714	NA	P-0044179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	148	322	0	ENST00000356175.3:c.5242C>T	p.Arg1748Ter	p.R1748*	ENST00000356175	NM_000267.3	1748	Cga/Tga	37/57	0.630420164119204	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.630420164119204	1		322	312	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263247	115263247	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	58	775	1	ENST00000438362.2:c.2103A>T	p.Gln701His	p.Q701H	ENST00000438362	NM_001242891.1	701	caA/caT	17/20	0.654997355437514	1	FACETS	0.285	0.245	0.328	0.285	0.245	0.328	SUBCLONAL	1	TRUE	0	0.654997355437514	1		776	418	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074270	30074270	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	143	512	0	ENST00000338641.4:c.1532A>G	p.Asp511Gly	p.D511G	ENST00000338641	NM_000268.3	511	gAt/gGt	14/16	0.654997355437514	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.654997355437514	1		512	222	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	133	737	0				ENST00000310581	NM_198253.2	-/1132			0.252668720006147	1	FACETS	0.755	0.691	0.82	0.755	0.691	0.82	INDETERMINATE	1	TRUE	0	0.588173240254834	1		737	423	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918583	44918584	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	209	227	0	ENST00000377967.4:c.1067dup	p.Met356IlefsTer8	p.M356Ifs*8	ENST00000377967	NM_021140.2	356	atg/aTtg	12/29	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.588173240254834	1		227	354	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	104	737	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.718280047025222	2		737	286	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0044250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	106	309	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.718280047025222	2		309	273	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791757	42791757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568504941	NA	P-0044250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	232	579	0	ENST00000575354.2:c.643C>T	p.Arg215Trp	p.R215W	ENST00000575354	NM_015125.3	215	Cgg/Tgg	5/20	0.718280047025222	1	FACETS	0.781	0.736	0.827	0.781	0.736	0.827	SUBCLONAL	1	TRUE	0	0.718280047025222	1		579	530	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197405	26197405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1427383033	NA	P-0044250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	155	250	0	ENST00000356476.2:c.74C>T	p.Ala25Val	p.A25V	ENST00000356476		25	gCt/gTt	1/1	0.633408891277901	3	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.718280047025222	3		250	474	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0044252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	37	390	0	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	1	2	FACETS	0.923	0.761	1	0.923	0.761	1	CLONAL	1	TRUE	1	0.2	2		390	401	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915455	112915455	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121918463	NA	P-0044252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	54	406	0	ENST00000351677.2:c.854T>C	p.Phe285Ser	p.F285S	ENST00000351677	NM_002834.3	285	tTt/tCt	8/16	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.2	2		406	427	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685608	29685609	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCA	novel	NA	P-0044252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	28	443	0	ENST00000356175.3:c.8021_8024dup	p.Gln2676ThrfsTer14	p.Q2676Tfs*14	ENST00000356175	NM_000267.3	2673	tcc/tcCCCAc	54/57	1	2	FACETS	0.641	0.511	0.788	0.641	0.511	0.788	SUBCLONAL	1	TRUE	1	0.2	2		443	437	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	87	309	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.25	2		309	658	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797519	45797519	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	85	702	0	ENST00000450313.1:c.1000C>T	p.Pro334Ser	p.P334S	ENST00000450313	NM_012222.2	334	Ccc/Tcc	12/16	1	2	FACETS	0.817	0.721	0.92	0.817	0.721	0.92	CLONAL	1	TRUE	1	0.25	2		702	832	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733608	85733608	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	90	437	0	ENST00000370580.1:c.404G>T	p.Arg135Ile	p.R135I	ENST00000370580	NM_003921.4	135	aGa/aTa	3/3	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.25	2		437	718	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154380	2154380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1191719522	NA	P-0044306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	93	771	0	ENST00000434045.2:c.548G>A	p.Arg183His	p.R183H	ENST00000434045	NM_001127598.1	183	cGc/cAc	5/5	1	2	FACETS	0.987	0.877	1	0.987	0.877	1	CLONAL	1	TRUE	1	0.25	2		771	754	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602662	10602662	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1457377196	NA	P-0044306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	181	719	0	ENST00000171111.5:c.916G>T	p.Glu306Ter	p.E306*	ENST00000171111	NM_203500.1	306	Gag/Tag	3/6	0.294956562421127	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.25	1		719	886	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342587	70342587	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0044306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	109	531	0	ENST00000374080.3:c.1349-1G>T		p.X450_splice	ENST00000374080		450			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.25	2		531	740	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123499636	123499637	+	missense_variant	Missense_Mutation	DNP	CG	CG	AT	novel	NA	P-0044306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	127	537	2	ENST00000371139.4:c.163_164delinsAT	p.Arg55Ile	p.R55I	ENST00000371139	NM_001114937.2	55	CGa/ATa	2/4	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.25	2		539	816	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861629	152861629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	40	625	0	ENST00000406277.2:c.123G>A	p.Met41Ile	p.M41I	ENST00000406277	NM_152274.4	41	atG/atA	4/7	1		FACETS		0.343	0.494				SUBCLONAL	1	TRUE	1	0.25	2		625	773	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0044317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	158	205	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.457190314514783	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.466232821916535	4		205	420	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141426	11141426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	313	694	0	ENST00000358026.2:c.3403C>T	p.Arg1135Trp	p.R1135W	ENST00000358026	NM_001128849.1	1135	Cgg/Tgg	25/36	0.466232821916535	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.466232821916535	1		694	852	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578530	7578530	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs267605077	NA	P-0044317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	525	808	0	ENST00000269305.4:c.400T>C	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	Ttt/Ctt	5/11	0.454496340971266	2	FACETS	0.89	0.855	0.926	0.89	0.855	0.926	CLONAL	2	TRUE	0	0.466232821916535	2		808	1265	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121541	2121541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334081822	NA	P-0044317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	418	716	0	ENST00000219476.3:c.1870G>A	p.Asp624Asn	p.D624N	ENST00000219476	NM_000548.3	624	Gac/Aac	18/42	0.466232821916535	3	FACETS	0.897	0.855	0.94	0.897	0.855	0.94	CLONAL	2	TRUE	1	0.466232821916535	3		716	1232	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	53	737	0				ENST00000310581	NM_198253.2	-/1132			0.200490329485021	1	FACETS	0.722	0.623	0.829	0.722	0.623	0.829	INDETERMINATE	1	TRUE	0	0.47585438821529	1		737	235	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169376	11169376	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	91	551	1	ENST00000361445.4:c.7499T>A	p.Ile2500Asn	p.I2500N	ENST00000361445	NM_004958.3	2500	aTt/aAt	56/58	0.184307880637385	0	FACETS	0.481	0.429	0.535			1	INDETERMINATE	1	TRUE	0	0.47585438821529	0		552	417	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40709551	40709551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568484928	NA	P-0044322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	44	548	1	ENST00000373198.4:c.4351G>A	p.Glu1451Lys	p.E1451K	ENST00000373198	NM_133170.3	1451	Gag/Aag	32/32	NA	2	FACETS	0.531	0.447	0.624			1	INDETERMINATE	1	TRUE	NA	0.47585438821529	2		549	348	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217305	123217305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	93	271	0	ENST00000218089.9:c.2959C>T	p.Pro987Ser	p.P987S	ENST00000218089	NM_001042749.1	987	Ccg/Tcg	29/35	1	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.47585438821529	1		271	203	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579485	7579485	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs869312782	NA	P-0044322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	150	815	3	ENST00000269305.4:c.202G>T	p.Glu68Ter	p.E68*	ENST00000269305	NM_001126112.2	68	Gag/Tag	4/11	0.47585438821529	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.47585438821529	1		818	461	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023943	27023943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	29	80	0	ENST00000324856.7:c.1049C>T	p.Ser350Leu	p.S350L	ENST00000324856	NM_006015.4	350	tCg/tTg	1/20	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.47585438821529	2		80	112	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112602	115112602	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	265	868	0	ENST00000257566.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000257566	NM_016569.3	380	Gag/Cag	7/8	0.192371338304656	4	FACETS	1	0.99	1	1	0.99	1	INDETERMINATE	2	TRUE	2	0.47585438821529	4		868	670	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023262	33023262	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	132	869	0	ENST00000300177.4:c.371C>G	p.Ser124Cys	p.S124C	ENST00000300177	NM_001191322.1	124	tCt/tGt	2/2	0.431481938824013	1	FACETS	0.888	0.812	0.967	0.888	0.812	0.967	CLONAL	1	TRUE	0	0.47585438821529	1		869	476	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40855827	40855827	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	145	544	0	ENST00000428826.2:c.2029G>T	p.Asp677Tyr	p.D677Y	ENST00000428826		677	Gat/Tat	19/21	0.475169515470327	2	FACETS	1	0.978	1	0.597	0.548	0.648	CLONAL	1	TRUE	0	0.47585438821529	2		544	510	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40855839	40855839	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0044322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	129	481	0	ENST00000428826.2:c.2018-1G>T		p.X673_splice	ENST00000428826		673			0.475169515470327	2	FACETS	1	0.977	1	0.605	0.553	0.659	CLONAL	1	TRUE	0	0.47585438821529	2		481	448	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135035	11135035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	150	752	0	ENST00000358026.2:c.3002C>T	p.Ser1001Phe	p.S1001F	ENST00000358026	NM_001128849.1	1001	tCt/tTt	21/36	0.184307880637385	0	FACETS	0.672	0.618	0.727			1	INDETERMINATE	1	TRUE	0	0.47585438821529	0		752	492	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053201	180053201	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	41	905	0	ENST00000261937.6:c.1168A>G	p.Thr390Ala	p.T390A	ENST00000261937	NM_182925.4	390	Aca/Gca	9/30	0.336978809880919	0	FACETS	0.221	0.184	0.262			1	SUBCLONAL	1	TRUE	0	0.47585438821529	0		905	409	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133483	55133483	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	284	351	0	ENST00000257290.5:c.787G>T	p.Glu263Ter	p.E263*	ENST00000257290	NM_006206.4	263	Gaa/Taa	6/23	0.547613968893196	2	FACETS	0.876	0.833	0.919	0.876	0.833	0.919	CLONAL	2	TRUE	0	0.585259847529015	2		351	554	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039399	49039399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	81	483	0	ENST00000267163.4:c.2384C>T	p.Ser795Leu	p.S795L	ENST00000267163	NM_000321.2	795	tCa/tTa	23/27	0.557460518437586	1	FACETS	0.555	0.492	0.621	0.555	0.492	0.621	SUBCLONAL	1	TRUE	0	0.585259847529015	1		483	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0044335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	231	387	1	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.529125749933838	4	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.585259847529015	4		388	965	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	587	578	1	ENST00000269305.4:c.472del	p.Arg158AlafsTer12	p.R158Afs*12	ENST00000269305	NM_001126112.2	158	Cgc/gc	5/11	0.529125749933838	4	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.585259847529015	4		579	1302	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350431	89350431	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	198	642	0	ENST00000301030.4:c.2519G>T	p.Arg840Leu	p.R840L	ENST00000301030	NM_001256183.1	840	cGg/cTg	9/13	0.557460518437586	1	FACETS	0.744	0.693	0.797	0.744	0.693	0.797	SUBCLONAL	1	TRUE	0	0.585259847529015	1		642	643	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845358	76845358	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	112	113	0	ENST00000373344.5:c.6163G>T	p.Glu2055Ter	p.E2055*	ENST00000373344	NM_000489.3	2055	Gaa/Taa	27/35	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.585259847529015	1		113	199	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49038250	49039272	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CATGAGTCATAGAACATTAGATATTCTTTGAAGTTATTTTTATTACTTTATAGGAAAAGCCAGTATAAATGCAGCCTTGCAAATCAATAATACAAATGTTCAGTATAAACACATTTTGTGTTTCCGGTTTACCTTCCCTTTAGAGAAATAGTAGTAGTAAAATATACTTGGTATGACACATTTCATATTGTTCTGTGGAAAGTGAGTTGAGGGGTATTTTTCCCATTTATTATTGGAGTTTTCAAAAGTAATACAAACCAAGTCATTTTTGTTTGTATGTTTGAAGTTATTTTCTAAATTCAATCATTTTAATTGTATATATCAGAGGCATCTGATATAACCTCTGTGTTTTTCCCTAAAATTTGAGTGAAATCTAACTATCACTAAAATATAGTGCTTTTACTAAATGTCTACTTCTTGCAATTGCGTAATGTATACTGAAACCCTTATAGATTGGGGGGGATACCGGGAGGTACAGGCCAGAGAATGTAGTCCAAATATTGGTGGATAATATTATTGGCTTTCGCTCAGCTCTGGCCCTTTGATTCCCATCATGCTTTCCATTCTACCAGTCTATCTACTCCTCTCTTCCCAGTCTATATACTCTTCTCTTCTTGGATGGCCAGCTCTTCCATCTGCTGCTGCCTGGCTATTTCTCTCAATCATTCTGTGACATTTCACTTCTAGAAGAGCAGCTATAATCCAAGCCTAAGAAGTAATTTTATTTATTTATTATTTTTTCCTTTATAATATGTGCTTCTTACCAGTCAAAAAGTATTATAAACTATTAGAAAAGAAAATCTAAAGGTAGAAATTTTAAAATTCATTTAACAAGTAAATTTTACTTTTTTTTTTTTTTTTTTTTTTTTACTGTTCTTCCTCAGACATTCAAACGTGTTTTGATCAAAGAAGAGGAGTATGATTCTATTATAGTATTCTATAACTCGGTCTTCATGCAGAGACTGAAAACAAATATTTTGCAGTATGCTTCCACCAGGGTAGGTCAAAAGTATCCTTTGATTG	CATGAGTCATAGAACATTAGATATTCTTTGAAGTTATTTTTATTACTTTATAGGAAAAGCCAGTATAAATGCAGCCTTGCAAATCAATAATACAAATGTTCAGTATAAACACATTTTGTGTTTCCGGTTTACCTTCCCTTTAGAGAAATAGTAGTAGTAAAATATACTTGGTATGACACATTTCATATTGTTCTGTGGAAAGTGAGTTGAGGGGTATTTTTCCCATTTATTATTGGAGTTTTCAAAAGTAATACAAACCAAGTCATTTTTGTTTGTATGTTTGAAGTTATTTTCTAAATTCAATCATTTTAATTGTATATATCAGAGGCATCTGATATAACCTCTGTGTTTTTCCCTAAAATTTGAGTGAAATCTAACTATCACTAAAATATAGTGCTTTTACTAAATGTCTACTTCTTGCAATTGCGTAATGTATACTGAAACCCTTATAGATTGGGGGGGATACCGGGAGGTACAGGCCAGAGAATGTAGTCCAAATATTGGTGGATAATATTATTGGCTTTCGCTCAGCTCTGGCCCTTTGATTCCCATCATGCTTTCCATTCTACCAGTCTATCTACTCCTCTCTTCCCAGTCTATATACTCTTCTCTTCTTGGATGGCCAGCTCTTCCATCTGCTGCTGCCTGGCTATTTCTCTCAATCATTCTGTGACATTTCACTTCTAGAAGAGCAGCTATAATCCAAGCCTAAGAAGTAATTTTATTTATTTATTATTTTTTCCTTTATAATATGTGCTTCTTACCAGTCAAAAAGTATTATAAACTATTAGAAAAGAAAATCTAAAGGTAGAAATTTTAAAATTCATTTAACAAGTAAATTTTACTTTTTTTTTTTTTTTTTTTTTTTTACTGTTCTTCCTCAGACATTCAAACGTGTTTTGATCAAAGAAGAGGAGTATGATTCTATTATAGTATTCTATAACTCGGTCTTCATGCAGAGACTGAAAACAAATATTTTGCAGTATGCTTCCACCAGGGTAGGTCAAAAGTATCCTTTGATTG	-	novel	NA	P-0044335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	59	4	0	ENST00000267163.4:c.2211+279_2325+25del		p.X737_splice	ENST00000267163	NM_000321.2	737		22/27	0.557460518437586	1	FACETS	0.403	0.348	0.462	0.403	0.348	0.462	SUBCLONAL	1	TRUE	0	0.585259847529015	1		4	354	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039435	49039435	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	87	347	0	ENST00000267163.4:c.2420C>T	p.Ser807Leu	p.S807L	ENST00000267163	NM_000321.2	807	tCa/tTa	23/27	0.557460518437586	1	FACETS	0.685	0.613	0.76	0.685	0.613	0.76	SUBCLONAL	1	TRUE	0	0.585259847529015	1		347	307	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207086	1207102	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTTACGGCAAGGTGA	CTCTTACGGCAAGGTGA	-	novel	NA	P-0044335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	483	563	0	ENST00000326873.7:c.174_190del	p.Ser59GlyfsTer98	p.S59Gfs*98	ENST00000326873	NM_000455.4	58	ggCTCTTACGGCAAGGTGAag/ggag	1/10	0.551184463741189	2	FACETS	0.883	0.849	0.916	0.883	0.849	0.916	CLONAL	2	TRUE	0	0.585259847529015	2		563	935	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279582	18279582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	181	479	0	ENST00000222254.8:c.1855G>A	p.Glu619Lys	p.E619K	ENST00000222254	NM_005027.3	619	Gaa/Aaa	15/16	0.551184463741189	2	FACETS	0.81	0.748	0.873	0.405	0.374	0.437	CLONAL	1	TRUE	0	0.585259847529015	2		479	764	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681650	30681650	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	165	347	0	ENST00000376406.3:c.447G>T	p.Glu149Asp	p.E149D	ENST00000376406	NM_014641.2	149	gaG/gaT	3/15	0.573809909061797	3	FACETS	0.92	0.846	0.997	0.46	0.423	0.499	CLONAL	1	TRUE	1	0.585259847529015	3		347	792	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170307	32170307	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	249	551	0	ENST00000375023.3:c.3301C>A	p.Leu1101Met	p.L1101M	ENST00000375023	NM_004557.3	1101	Ctg/Atg	21/30	0.573809909061797	3	FACETS	0.974	0.911	1	0.487	0.455	0.52	CLONAL	1	TRUE	1	0.585259847529015	3		551	1129	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971289	13971289	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	105	362	0	ENST00000405192.2:c.640C>T	p.Gln214Ter	p.Q214*	ENST00000405192	NM_001163147.1	214	Cag/Tag	8/12	0.419448524113449	5	FACETS	0.777	0.696	0.864	0.194	0.174	0.216	SUBCLONAL	1	TRUE	1	0.585259847529015	5		362	867	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090805	5090807	+	frameshift_variant	Frame_Shift_Del	DEL	GAG	GAG	AA	novel	NA	P-0044335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	47	256	0	ENST00000381652.3:c.2953_2955delinsAA	p.Glu985LysfsTer13	p.E985Kfs*13	ENST00000381652	NM_004972.3	985	GAG/AA	22/25	0.557460518437586	1	FACETS	0.617	0.529	0.712	0.617	0.529	0.712	SUBCLONAL	1	TRUE	0	0.585259847529015	1		256	184	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0044387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	282	578	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.272574282506112	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	0	0.290987139812582	2		578	969	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249017	55249018	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCA	rs1554350381	NA	P-0044387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	890	539	0	ENST00000275493.2:c.2317_2319dup	p.His773dup	p.H773dup	ENST00000275493	NM_005228.3	773	ccc/ccCCAc	20/28	0.290987139812582	11	FACETS	1	0.992	1	0.922	0.895	0.949	CLONAL	7	TRUE	3	0.290987139812582	11		539	1916	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346723	89346723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768819121	NA	P-0044387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	87	508	2	ENST00000301030.4:c.6227C>T	p.Pro2076Leu	p.P2076L	ENST00000301030	NM_001256183.1	2076	cCg/cTg	9/13	0.271797130191771	3	FACETS	0.867	0.767	0.974	0.434	0.383	0.487	CLONAL	1	TRUE	1	0.290987139812582	3		510	790	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039903	47039903	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	1110	318	0	ENST00000377604.3:c.1246C>T	p.Gln416Ter	p.Q416*	ENST00000377604	NM_001204468.1	416	Cag/Tag	12/24	0.290987139812582	8	FACETS	0.994	0.976	1			1	CLONAL	10	TRUE	NA	0.290987139812582	8		318	1438	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221946	1221946	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0044408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	426	586	0	ENST00000326873.7:c.863-2A>C		p.X288_splice	ENST00000326873	NM_000455.4	288			0.532832985377266	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.532832985377266	2		586	701	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99180014	99180014	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	282	553	1	ENST00000074304.5:c.1957G>T	p.Val653Leu	p.V653L	ENST00000074304	NM_001134224.1	653	Gta/Tta	19/26	0.532832985377266	3	FACETS	0.897	0.847	0.948	0.897	0.847	0.948	CLONAL	2	TRUE	1	0.532832985377266	3		554	747	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221946	1221946	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0044408-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	380	586	0	ENST00000326873.7:c.863-2A>C		p.X288_splice	ENST00000326873	NM_000455.4	288			0.636217538792376	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.636217538792376	2		586	564	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99180014	99180014	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044408-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	259	553	1	ENST00000074304.5:c.1957G>T	p.Val653Leu	p.V653L	ENST00000074304	NM_001134224.1	653	Gta/Tta	19/26	0.239317280893545	4	FACETS	1	0.968	1	1	0.968	1	INDETERMINATE	2	TRUE	2	0.636217538792376	4		554	642	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0044435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	29	258	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	FALSE	1	0.237924116437517	2		258	226	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992138	72992138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764598603	NA	P-0044435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	21	627	0	ENST00000268489.5:c.1907C>T	p.Ser636Leu	p.S636L	ENST00000268489	NM_006885.3	636	tCg/tTg	2/10	0.201198426432678	0	FACETS	0.769	0.596	0.967			1	CLONAL	1	FALSE	0	0.237924116437517	0		627	175	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842703	68842703	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	35	520	0	ENST00000261769.5:c.639G>A	p.Trp213Ter	p.W213*	ENST00000261769	NM_004360.3	213	tgG/tgA	5/16	0.201198426432678	0	FACETS	1	0.861	1			1	CLONAL	1	FALSE	0	0.237924116437517	0		520	214	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216899	7216899	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	31	433	1	ENST00000380728.2:c.622C>T	p.Gln208Ter	p.Q208*	ENST00000380728		208	Cag/Tag	7/11	0.237924116437517	3	FACETS	1	0.892	1			1	CLONAL	1	FALSE	NA	0.237924116437517	3		434	254	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216319	2216319	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs755460094	NA	P-0044435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	19	674	0	ENST00000398665.3:c.1963G>C	p.Glu655Gln	p.E655Q	ENST00000398665	NM_032482.2	655	Gag/Cag	20/28	0.237924116437517	1	FACETS	0.737	0.562	0.94	0.737	0.562	0.94	CLONAL	1	FALSE	0	0.237924116437517	1		674	191	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560226	29560226	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555615109	NA	P-0044435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	15	191	0	ENST00000356175.3:c.3703C>T	p.Gln1235Ter	p.Q1235*	ENST00000356175	NM_000267.3	1235	Cag/Tag	27/57	0.237924116437517	1	FACETS	0.823	0.606	1	0.823	0.606	1	CLONAL	1	FALSE	0	0.237924116437517	1		191	135	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197302	106197302	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs944233155	NA	P-0044435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	28	286	0	ENST00000380013.4:c.5635G>C	p.Glu1879Gln	p.E1879Q	ENST00000380013	NM_001127208.2	1879	Gag/Cag	11/11	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	1	0.237924116437517	2		286	177	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434667	99434667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375391097	NA	P-0044435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	24	591	1	ENST00000268035.6:c.754C>T	p.Arg252Cys	p.R252C	ENST00000268035	NM_000875.3	252	Cgc/Tgc	3/21	1	2	FACETS	0.93	0.732	1	0.93	0.732	1	CLONAL	1	FALSE	1	0.237924116437517	2		592	217	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877340	89877340	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	27	410	0	ENST00000389301.3:c.423G>C	p.Gln141His	p.Q141H	ENST00000389301	NM_000135.2	141	caG/caC	4/43	0.201198426432678	0	FACETS	0.896	0.719	1			1	CLONAL	1	FALSE	0	0.237924116437517	0		410	193	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190656630	190656630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	13	207	0	ENST00000441310.2:c.95C>T	p.Ser32Phe	p.S32F	ENST00000441310	NM_000534.4	32	tCc/tTc	2/13	0.237924116437517	3	FACETS	0.553	0.395	0.747			1	SUBCLONAL	1	FALSE	NA	0.237924116437517	3		207	221	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178342	56178343	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATACCCAGTGACGAGAC	novel	NA	P-0044435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	29	261	0	ENST00000399503.3:c.3317_3333dup	p.Val1112TyrfsTer11	p.V1112Yfs*11	ENST00000399503	NM_005921.1	1105	-/ATACCCAGTGACGAGAC	14/20	0.127583541501306	4	FACETS	1	0.922	1	0.656	0.529	0.798	INDETERMINATE	1	FALSE	2	0.237924116437517	4		261	230	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90970971	90970971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	28	251	0	ENST00000265433.3:c.1106C>T	p.Ser369Leu	p.S369L	ENST00000265433	NM_002485.4	369	tCa/tTa	9/16	0.127583541501306	4	FACETS	1	0.909	1	0.625	0.502	0.764	INDETERMINATE	1	FALSE	2	0.237924116437517	4		251	233	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0044441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	340	458	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.93336007836885	3	FACETS	0.853	0.816	0.891	0.853	0.816	0.891	CLONAL	2	TRUE	1	0.93336007836885	3		458	626	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0044441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	2448	190	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.93336007836885	19	FACETS	1	0.994	1			1	CLONAL	17	TRUE	NA	0.93336007836885	19		190	2746	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577062	7577062	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	989	667	1	ENST00000269305.4:c.876del	p.Glu294SerfsTer51	p.E294Sfs*51	ENST00000269305	NM_001126112.2	292	aaA/aa	8/11	0.93336007836885	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.93336007836885	2		668	1057	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162122	47162122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537154191	NA	P-0044441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	217	353	0	ENST00000409792.3:c.4004G>A	p.Arg1335His	p.R1335H	ENST00000409792	NM_014159.6	1335	cGt/cAt	3/21	0.93336007836885	3	FACETS	0.932	0.87	0.995	0.311	0.29	0.332	CLONAL	1	TRUE	0	0.93336007836885	3		353	732	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248060	110248060	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	277	336	0	ENST00000374672.4:c.1412T>C	p.Leu471Pro	p.L471P	ENST00000374672	NM_004235.4	471	cTc/cCc	5/5	0.93336007836885	2	FACETS	1	0.949	1	0.5	0.474	0.527	CLONAL	1	TRUE	0	0.93336007836885	2		336	593	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	78	737	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.815	0.717	0.919	0.815	0.717	0.919	CLONAL	1	TRUE	1	0.353912837175418	2		737	541	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0044475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	86	356	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.165302434714764	3	FACETS	0.753	0.67	0.839	0.753	0.67	0.839	INDETERMINATE	2	TRUE	1	0.353912837175418	3		356	380	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730859	40730859	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	163	836	0	ENST00000373198.4:c.3676C>T	p.Arg1226Ter	p.R1226*	ENST00000373198	NM_133170.3	1226	Cga/Tga	27/32	0.34947605864724	3	FACETS	0.916	0.839	0.997	0.458	0.419	0.499	CLONAL	1	TRUE	1	0.353912837175418	3		836	1183	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287478	33287478	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	61	662	0	ENST00000374542.5:c.1619C>T	p.Pro540Leu	p.P540L	ENST00000374542	NM_001141970.1	540	cCc/cTc	6/8	1	2	FACETS	0.504	0.434	0.58	0.504	0.434	0.58	SUBCLONAL	1	TRUE	1	0.353912837175418	2		662	684	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971121	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0044475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	139	535	3	ENST00000304494.5:c.237_238delinsTT	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	79	acCCga/acTTga	2/3	0.353912837175418	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.353912837175418	1		538	546	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546559	9546559	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs958970085	NA	P-0044475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	217	518	0	ENST00000353224.5:c.1463G>A	p.Arg488Gln	p.R488Q	ENST00000353224	NM_177990.2	488	cGa/cAa	5/10	0.34947605864724	3	FACETS	0.946	0.882	1	0.946	0.882	1	CLONAL	2	TRUE	1	0.353912837175418	3		518	763	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050701	69050701	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	32	235	1	ENST00000288368.4:c.4036G>A	p.Glu1346Lys	p.E1346K	ENST00000288368	NM_024870.2	1346	Gaa/Aaa	33/40	1	2	FACETS	0.644	0.524	0.777	0.644	0.524	0.777	SUBCLONAL	1	TRUE	1	0.353912837175418	2		236	281	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625453	69625453	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147952743	NA	P-0044475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	96	768	0	ENST00000334134.2:c.340G>A	p.Glu114Lys	p.E114K	ENST00000334134	NM_005247.2	114	Gag/Aag	3/3	1	2	FACETS	0.537	0.477	0.601	0.537	0.477	0.601	SUBCLONAL	1	TRUE	1	0.353912837175418	2		768	1011	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533883	63533883	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780894296	NA	P-0044475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	76	707	0	ENST00000307078.5:c.1271C>T	p.Ser424Phe	p.S424F	ENST00000307078	NM_004655.3	424	tCc/tTc	6/11	0.165302434714764	3	FACETS	0.609	0.533	0.691	0.305	0.266	0.346	INDETERMINATE	1	TRUE	1	0.353912837175418	3		707	830	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866080	37866080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	103	778	1	ENST00000269571.5:c.589C>T	p.Pro197Ser	p.P197S	ENST00000269571		197	Ccg/Tcg	5/27	1	2	FACETS	0.579	0.517	0.645	0.579	0.517	0.645	SUBCLONAL	1	TRUE	1	0.353912837175418	2		779	1006	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696411	47696411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs968974699	NA	P-0044475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	71	590	0	ENST00000347630.2:c.412C>T	p.Arg138Cys	p.R138C	ENST00000347630	NM_001007230.1	138	Cgt/Tgt	6/11	1	2	FACETS	0.57	0.497	0.649	0.57	0.497	0.649	SUBCLONAL	1	TRUE	1	0.353912837175418	2		590	704	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435082	18435082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	16	292	0	ENST00000266497.5:c.67G>A	p.Glu23Lys	p.E23K	ENST00000266497		23	Gaa/Aaa	1/31	1	2	FACETS	0.368	0.272	0.482	0.368	0.272	0.482	SUBCLONAL	1	TRUE	1	0.353912837175418	2		292	246	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375078	31375078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	400	847	0	ENST00000328111.2:c.475C>T	p.Pro159Ser	p.P159S	ENST00000328111	NM_006892.3	159	Ccg/Tcg	6/23	0.34947605864724	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.353912837175418	3		847	1301	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797707	45797707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147718169	NA	P-0044475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	196	858	0	ENST00000450313.1:c.985G>A	p.Val329Met	p.V329M	ENST00000450313	NM_012222.2	329	Gtg/Atg	11/16	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.353912837175418	2		858	1102	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405061	70405061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	37	496	0	ENST00000373644.4:c.2575C>T	p.Pro859Ser	p.P859S	ENST00000373644	NM_030625.2	859	Cct/Tct	4/12	0.353912837175418	1	FACETS	0.493	0.407	0.589	0.493	0.407	0.589	SUBCLONAL	1	TRUE	0	0.353912837175418	1		496	349	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445757	49445757	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1411	174	1321	0	ENST00000301067.7:c.1709C>T	p.Ser570Phe	p.S570F	ENST00000301067	NM_003482.3	570	tCt/tTt	10/54	1	2	FACETS	0.62	0.569	0.674	0.62	0.569	0.674	SUBCLONAL	1	TRUE	1	0.353912837175418	2		1321	1585	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640649	3640650	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0044475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	219	1006	2	ENST00000294008.3:c.2989_2990delinsTT	p.Pro997Leu	p.P997L	ENST00000294008	NM_032444.2	997	CCg/TTg	12/15	1	2	FACETS	0.948	0.88	1	0.948	0.88	1	CLONAL	1	TRUE	1	0.353912837175418	2		1008	1305	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117550	4117550	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121434497	NA	P-0044475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	69	477	0	ENST00000262948.5:c.170T>G	p.Phe57Cys	p.F57C	ENST00000262948	NM_030662.3	57	tTt/tGt	2/11	0.353912837175418	1	FACETS	0.637	0.556	0.724	0.637	0.556	0.724	SUBCLONAL	1	TRUE	0	0.353912837175418	1		477	504	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609807	117609807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451070985	NA	P-0044475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	42	565	2	ENST00000368508.3:c.6892G>A	p.Glu2298Lys	p.E2298K	ENST00000368508	NM_002944.2	2298	Gaa/Aaa	43/43	0.353912837175418	1	FACETS	0.376	0.313	0.445	0.376	0.313	0.445	SUBCLONAL	1	TRUE	0	0.353912837175418	1		567	520	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946111	13946111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	33	453	0	ENST00000405192.2:c.985C>T	p.His329Tyr	p.H329Y	ENST00000405192	NM_001163147.1	329	Cat/Tat	10/12	0.165302434714764	3	FACETS	0.366	0.297	0.444	0.183	0.148	0.222	INDETERMINATE	1	TRUE	1	0.353912837175418	3		453	600	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5064882	5064882	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0044475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	47	168	0	ENST00000381652.3:c.1057-1G>A		p.X353_splice	ENST00000381652	NM_004972.3	353			0.170860702111416	3	FACETS	0.878	0.753	1			1	INDETERMINATE	2	TRUE	NA	0.353912837175418	3		168	178	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209723	98209723	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	105	815	1	ENST00000331920.6:c.3815C>T	p.Pro1272Leu	p.P1272L	ENST00000331920	NM_000264.3	1272	cCc/cTc	23/24	0.353912837175418	1	FACETS	0.578	0.517	0.642	0.578	0.517	0.642	SUBCLONAL	1	TRUE	0	0.353912837175418	1		816	845	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915979	127915979	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	105	404	0	ENST00000373547.4:c.502C>G	p.Pro168Ala	p.P168A	ENST00000373547	NM_002721.4	168	Cct/Gct	6/7	0.353912837175418	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.353912837175418	1		404	403	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849209	76849209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	48	361	0	ENST00000373344.5:c.6067C>T	p.Leu2023Phe	p.L2023F	ENST00000373344	NM_000489.3	2023	Ctc/Ttc	26/35	0.353912837175418	1	FACETS	0.725	0.616	0.843	0.725	0.616	0.843	SUBCLONAL	1	TRUE	0	0.353912837175418	1		361	308	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	61	737	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.324069187070804	2		737	252	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0044486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	70	305	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.324069187070804	2		305	317	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796242	42796242	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	74	804	1	ENST00000575354.2:c.2891T>A	p.Ile964Asn	p.I964N	ENST00000575354	NM_015125.3	964	aTc/aAc	12/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.324069187070804	2		805	388	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177657	56177657	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0044486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	61	461	2	ENST00000399503.3:c.2630T>A	p.Leu877Ter	p.L877*	ENST00000399503	NM_005921.1	877	tTg/tAg	14/20	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.324069187070804	2		463	324	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0044493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	96	136	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.445937913810862	6	FACETS	0.781	0.694	0.874	0.195	0.173	0.219	SUBCLONAL	1	TRUE	2	0.445937913810862	6		136	1043	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17380492	17380492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199848267	NA	P-0044493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	230	907	0	ENST00000375499.3:c.23C>T	p.Ser8Phe	p.S8F	ENST00000375499	NM_003000.2	8	tCc/tTc	1/8	0.423625708111443	3	FACETS	0.906	0.842	0.972	0.453	0.421	0.486	CLONAL	1	TRUE	1	0.445937913810862	3		907	1393	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332196	70332196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759674654	NA	P-0044493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	69	372	0	ENST00000373644.4:c.101C>T	p.Ala34Val	p.A34V	ENST00000373644	NM_030625.2	34	gCc/gTc	2/12	0.312931829296597	3	FACETS	0.683	0.595	0.778	0.342	0.297	0.389	SUBCLONAL	1	TRUE	1	0.445937913810862	3		372	554	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129670	11129670	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	387	779	0	ENST00000358026.2:c.2476G>C	p.Ala826Pro	p.A826P	ENST00000358026	NM_001128849.1	826	Gcc/Ccc	17/36	0.379666405618918	2	FACETS	0.81	0.771	0.849	0.81	0.771	0.849	CLONAL	2	TRUE	0	0.445937913810862	2		779	1072	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363643	40363643	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0044493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	97	384	0	ENST00000397332.2:c.587-1G>C		p.X196_splice	ENST00000397332	NM_001033082.2	196			0.423625708111443	3	FACETS	0.879	0.785	0.979	0.44	0.392	0.49	CLONAL	1	TRUE	1	0.445937913810862	3		384	605	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633671	69633671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	16	30	0	ENST00000334134.2:c.31C>A	p.Leu11Met	p.L11M	ENST00000334134	NM_005247.2	11	Ctg/Atg	1/3	0.423625708111443	3	FACETS	0.77	0.575	0.996	0.385	0.287	0.498	CLONAL	1	TRUE	1	0.445937913810862	3		30	114	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56477657	56477657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	166	645	1	ENST00000267101.3:c.205G>A	p.Gly69Arg	p.G69R	ENST00000267101	NM_001982.3	69	Gga/Aga	2/28	0.429755274480506	4	FACETS	0.848	0.777	0.923	0.424	0.388	0.462	CLONAL	1	TRUE	2	0.445937913810862	4		646	1269	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432090	121432090	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	177	873	1	ENST00000257555.6:c.837C>A	p.His279Gln	p.H279Q	ENST00000257555		279	caC/caA	4/10	0.430233291819321	3	FACETS	0.754	0.693	0.818	0.377	0.346	0.409	SUBCLONAL	1	TRUE	1	0.445937913810862	3		874	1288	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829543	72829543	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	342	628	0	ENST00000268489.5:c.7038C>G	p.His2346Gln	p.H2346Q	ENST00000268489	NM_006885.3	2346	caC/caG	9/10	0.379666405618918	2	FACETS	0.863	0.819	0.907	0.863	0.819	0.907	CLONAL	2	TRUE	0	0.445937913810862	2		628	889	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872751	136872751	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	94	474	0	ENST00000241393.3:c.747C>G	p.Phe249Leu	p.F249L	ENST00000241393	NM_003467.2	249	ttC/ttG	2/2	0.423625708111443	3	FACETS	0.719	0.64	0.804	0.36	0.32	0.402	SUBCLONAL	1	TRUE	1	0.445937913810862	3		474	717	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419918	41419918	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	259	618	0	ENST00000373198.4:c.403G>T	p.Val135Leu	p.V135L	ENST00000373198	NM_133170.3	135	Gtg/Ttg	3/32	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.445937913810862	2		618	853	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259476	89259476	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	363	499	0	ENST00000336596.2:c.620A>C	p.Lys207Thr	p.K207T	ENST00000336596	NM_005233.5	207	aAg/aCg	3/17	0.312931829296597	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.445937913810862	3		499	953	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400286	139400286	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	398	877	0	ENST00000277541.6:c.4062C>G	p.Ser1354Arg	p.S1354R	ENST00000277541	NM_017617.3	1354	agC/agG	25/34	0.379666405618918	2	FACETS	0.777	0.74	0.815	0.777	0.74	0.815	SUBCLONAL	2	TRUE	0	0.445937913810862	2		877	1148	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0044496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	110	442	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.236640577068475	3	FACETS	0.792	0.713	0.876	0.792	0.713	0.876	SUBCLONAL	2	TRUE	1	0.236640577068475	3		442	656	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604789	48604789	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	84	366	1	ENST00000342988.3:c.1611C>A	p.Asp537Glu	p.D537E	ENST00000342988	NM_005359.5	537	gaC/gaA	12/12	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.236640577068475	2		367	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578209	7578209	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	132	758	0	ENST00000269305.4:c.640C>G	p.His214Asp	p.H214D	ENST00000269305	NM_001126112.2	214	Cat/Gat	6/11	0.236640577068475	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.236640577068475	1		758	954	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	153	737	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.919248214239466	2		737	329	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0044511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	446	721	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.919248214239466	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.919248214239466	1		721	509	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444053	49444053	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	329	644	0	ENST00000301067.7:c.3318del	p.Ser1107AlafsTer12	p.S1107Afs*12	ENST00000301067	NM_003482.3	1106	ccC/cc	11/54	1	2	FACETS	0.958	0.911	1	0.958	0.911	1	CLONAL	1	TRUE	1	0.919248214239466	2		644	747	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039361	49039362	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0044511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	399	516	0	ENST00000267163.4:c.2346_2347del	p.Pro783SerfsTer11	p.P783Sfs*11	ENST00000267163	NM_000321.2	782	atACct/atct	23/27	0.585879572854625	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.919248214239466	1		516	453	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281610	49281610	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	577	713	0	ENST00000282018.3:c.657C>G	p.Ile219Met	p.I219M	ENST00000282018	NM_020377.2	219	atC/atG	1/1	0.919248214239466	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.919248214239466	1		713	631	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226858	142226858	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	284	440	0	ENST00000350721.4:c.4946A>C	p.Lys1649Thr	p.K1649T	ENST00000350721	NM_001184.3	1649	aAa/aCa	28/47	1	2	FACETS	0.998	0.947	1	0.998	0.947	1	CLONAL	1	TRUE	1	0.919248214239466	2		440	619	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	278	309	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.553902077904589	2	FACETS	0.928	0.882	0.974	0.928	0.882	0.974	CLONAL	2	TRUE	0	0.553902077904589	2		309	541	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0044606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	384	639	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	0.553902077904589	2	FACETS	1	0.977	1	0.524	0.498	0.552	CLONAL	1	TRUE	0	0.553902077904589	2		639	1322	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857805	9857805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	221	445	0	ENST00000330684.3:c.3596C>T	p.Pro1199Leu	p.P1199L	ENST00000330684	NM_001134407.1	1199	cCg/cTg	13/13	NA	2	FACETS	1	0.961	1			1	INDETERMINATE	1	TRUE	NA	0.553902077904589	2		445	767	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170837531	170837531	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	32	59	0	ENST00000296930.5:c.847G>T	p.Ala283Ser	p.A283S	ENST00000296930	NM_002520.6	283	Gct/Tct	11/11	1	2	FACETS	0.837	0.691	0.997	0.837	0.691	0.997	CLONAL	1	TRUE	1	0.553902077904589	2		59	138	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117632251	117632251	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044647-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	117	431	0	ENST00000368508.3:c.6165C>A	p.Asp2055Glu	p.D2055E	ENST00000368508	NM_002944.2	2055	gaC/gaA	39/43	0.709032394306249	4	FACETS	1	0.962	1	0.558	0.506	0.613	CLONAL	1	TRUE	2	0.810894369859909	4		431	468	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955063	55955063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	74	472	0	ENST00000263923.4:c.3482G>A	p.Gly1161Glu	p.G1161E	ENST00000263923	NM_002253.2	1161	gGa/gAa	26/30	1	2	FACETS	0.816	0.724	0.911	0.816	0.724	0.911	CLONAL	1	TRUE	1	0.759291774320962	2		472	239	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559852	29559852	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1555614972	NA	P-0044657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	132	294	0	ENST00000356175.3:c.3449C>G	p.Ser1150Ter	p.S1150*	ENST00000356175	NM_000267.3	1150	tCa/tGa	26/57	0.737240552941011	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.759291774320962	2		294	164	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459498	50459498	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777862077	NA	P-0044657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	43	267	1	ENST00000331340.3:c.787G>A	p.Val263Met	p.V263M	ENST00000331340	NM_006060.4	263	Gtg/Atg	7/8	0.576844904224928	4	FACETS	1	0.962	1	0.733	0.626	0.844	CLONAL	1	TRUE	2	0.759291774320962	4		268	136	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132610	11132610	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	372	817	0	ENST00000358026.2:c.2826G>T	p.Trp942Cys	p.W942C	ENST00000358026	NM_001128849.1	942	tgG/tgT	19/36	0.756922051510409	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.759291774320962	3		817	442	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278395	39278395	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	46	492	0	ENST00000402219.2:c.754A>G	p.Ile252Val	p.I252V	ENST00000402219	NM_005633.3	252	Ata/Gta	6/23	0.431443262319169	6	FACETS	0.96	0.835	1	0.96	0.835	1	INDETERMINATE	3	TRUE	3	0.759291774320962	6		492	106	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873193	136873193	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	67	332	2	ENST00000241393.3:c.305G>C	p.Trp102Ser	p.W102S	ENST00000241393	NM_003467.2	102	tGg/tCg	2/2	0.184540179554296	3	FACETS	1	0.953	1	0.386	0.341	0.434	INDETERMINATE	1	TRUE	0	0.759291774320962	3		334	210	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	78	544	1				ENST00000310581	NM_198253.2	-/1132			0.392450511124339	1	FACETS	0.751	0.669	0.835	0.751	0.669	0.835	SUBCLONAL	1	TRUE	0	0.599041624678336	1		545	243	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	74	796	1	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	0.451004851588499	1	FACETS	0.3	0.263	0.341	0.3	0.263	0.341	SUBCLONAL	1	TRUE	0	0.599041624678336	1		797	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	394	759	1	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.599041624678336	2	FACETS	0.944	0.906	0.981	0.944	0.906	0.981	CLONAL	2	TRUE	0	0.599041624678336	2		760	697	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486134	8486134	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	103	414	0	ENST00000356435.5:c.2683C>T	p.Leu895Phe	p.L895F	ENST00000356435		895	Ctc/Ttc	17/35	1	2	FACETS	0.937	0.846	1	0.937	0.846	1	CLONAL	1	TRUE	1	0.599041624678336	2		414	367	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846398	128846398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879255280	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	120	506	0	ENST00000249373.3:c.1234C>T	p.Leu412Phe	p.L412F	ENST00000249373	NM_005631.4	412	Ctc/Ttc	6/12	1	2	FACETS	0.858	0.78	0.939	0.858	0.78	0.939	CLONAL	1	TRUE	1	0.599041624678336	2		506	467	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268985	142268985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs911751877	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	50	273	0	ENST00000350721.4:c.2965C>T	p.Arg989Cys	p.R989C	ENST00000350721	NM_001184.3	989	Cgt/Tgt	14/47	0.451004851588499	1	FACETS	0.418	0.357	0.484	0.418	0.357	0.484	SUBCLONAL	1	TRUE	0	0.599041624678336	1		273	280	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141026	55141026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765680542	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	70	302	0	ENST00000257290.5:c.1672C>T	p.Arg558Cys	p.R558C	ENST00000257290	NM_006206.4	558	Cgc/Tgc	12/23	0.451004851588499	1	FACETS	0.776	0.688	0.867	0.776	0.688	0.867	SUBCLONAL	1	TRUE	0	0.599041624678336	1		302	211	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032197	10032197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774932381	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	113	594	0	ENST00000330684.3:c.626C>T	p.Ser209Phe	p.S209F	ENST00000330684	NM_001134407.1	209	tCc/tTc	3/13	1	2	FACETS	0.903	0.818	0.99	0.903	0.818	0.99	CLONAL	1	TRUE	1	0.599041624678336	2		594	418	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776960	76776960	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	74	347	0	ENST00000373344.5:c.6992G>A	p.Gly2331Glu	p.G2331E	ENST00000373344	NM_000489.3	2331	gGa/gAa	33/35	0.392450511124339	1	FACETS	0.718	0.638	0.802	0.718	0.638	0.802	SUBCLONAL	1	TRUE	0	0.599041624678336	1		347	241	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099351	4099351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	125	830	0	ENST00000262948.5:c.767C>T	p.Ser256Phe	p.S256F	ENST00000262948	NM_030662.3	256	tCc/tTc	7/11	0.415854903463646	1	FACETS	0.674	0.614	0.735	0.674	0.614	0.735	SUBCLONAL	1	TRUE	0	0.599041624678336	1		830	434	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114277	143114277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs76891221	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	71	274	0	ENST00000262992.4:c.1144C>T	p.Arg382Trp	p.R382W	ENST00000262992	NM_001101669.1	382	Cgg/Tgg	13/24	0.451004851588499	1	FACETS	0.762	0.676	0.851	0.762	0.676	0.851	SUBCLONAL	1	TRUE	0	0.599041624678336	1		274	218	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524996	8524996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	83	276	0	ENST00000356435.5:c.608G>A	p.Gly203Glu	p.G203E	ENST00000356435		203	gGa/gAa	7/35	1	2	FACETS	0.909	0.81	1	0.909	0.81	1	CLONAL	1	TRUE	1	0.599041624678336	2		276	305	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943367	17943367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	33	639	0	ENST00000458235.1:c.2641G>A	p.Asp881Asn	p.D881N	ENST00000458235	NM_000215.3	881	Gat/Aat	19/24	0.415854903463646	1	FACETS	0.262	0.213	0.315	0.262	0.213	0.315	SUBCLONAL	1	TRUE	0	0.599041624678336	1		639	295	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383122	42383122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	137	565	0	ENST00000221972.3:c.142G>A	p.Glu48Lys	p.E48K	ENST00000221972	NM_021601.3	48	Gaa/Aaa	2/5	0.415854903463646	1	FACETS	0.78	0.716	0.845	0.78	0.716	0.845	SUBCLONAL	1	TRUE	0	0.599041624678336	1		565	411	SUCCESS
AR	367	MSKCC	GRCh37	X	66766198	66766198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	64	438	0	ENST00000374690.3:c.1210G>A	p.Ala404Thr	p.A404T	ENST00000374690	NM_000044.3	404	Gcg/Acg	1/8	0.392450511124339	1	FACETS	0.716	0.63	0.806	0.716	0.63	0.806	SUBCLONAL	1	TRUE	0	0.599041624678336	1		438	209	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630083	117630083	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	38	265	0	ENST00000368508.3:c.6443G>A	p.Gly2148Glu	p.G2148E	ENST00000368508	NM_002944.2	2148	gGa/gAa	41/43	0.409614464292561	1	FACETS	0.605	0.508	0.708	0.605	0.508	0.708	SUBCLONAL	1	TRUE	0	0.599041624678336	1		265	147	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778880	76778880	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	24	278	0	ENST00000373344.5:c.6700-1G>A		p.X2234_splice	ENST00000373344	NM_000489.3	2234			0.392450511124339	1	FACETS	0.286	0.226	0.355	0.286	0.226	0.355	SUBCLONAL	1	TRUE	0	0.599041624678336	1		278	196	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076967	41076967	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	47	330	0	ENST00000373198.4:c.1453C>T	p.Pro485Ser	p.P485S	ENST00000373198	NM_133170.3	485	Cca/Tca	9/32	0.172305335412192	2	FACETS	0.528	0.448	0.616	0.264	0.224	0.308	INDETERMINATE	1	TRUE	0	0.599041624678336	2		330	297	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741892	17741892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	22	189	0	ENST00000250003.3:c.563G>A	p.Arg188His	p.R188H	ENST00000250003	NM_002478.4	188	cGc/cAc	1/3	0.415854903463646	1	FACETS	0.396	0.31	0.492	0.396	0.31	0.492	SUBCLONAL	1	TRUE	0	0.599041624678336	1		189	130	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041765	14041765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	67	397	0	ENST00000311895.7:c.2312C>T	p.Ser771Phe	p.S771F	ENST00000311895	NM_005236.2	771	tCc/tTc	11/11	1	2	FACETS	0.45	0.392	0.513	0.45	0.392	0.513	SUBCLONAL	1	TRUE	1	0.599041624678336	2		397	497	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724558	112724558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	93	396	1	ENST00000369452.4:c.442C>T	p.Leu148Phe	p.L148F	ENST00000369452	NM_007373.3	148	Ctc/Ttc	2/9	0.211735809487417	3	FACETS	1	0.952	1	0.554	0.497	0.614	INDETERMINATE	1	TRUE	1	0.599041624678336	3		397	364	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195646	102195646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	67	323	0	ENST00000263464.3:c.406G>A	p.Gly136Ser	p.G136S	ENST00000263464	NM_001165.4	136	Ggc/Agc	2/9	1	2	FACETS	0.654	0.572	0.742	0.654	0.572	0.742	SUBCLONAL	1	TRUE	1	0.599041624678336	2		323	342	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124669	108124669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	84	424	0	ENST00000278616.4:c.2027C>T	p.Ser676Phe	p.S676F	ENST00000278616	NM_000051.3	676	tCc/tTc	13/63	1	2	FACETS	0.974	0.87	1	0.974	0.87	1	CLONAL	1	TRUE	1	0.599041624678336	2		424	288	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433716	49433716	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	195	859	0	ENST00000301067.7:c.7837C>T	p.Pro2613Ser	p.P2613S	ENST00000301067	NM_003482.3	2613	Ccg/Tcg	31/54	0.185382249128897	2	FACETS	1	0.985	1	0.595	0.555	0.636	INDETERMINATE	1	TRUE	0	0.599041624678336	2		859	547	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562892	21562892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	135	710	2	ENST00000382592.4:c.1027C>T	p.Pro343Ser	p.P343S	ENST00000382592	NM_014572.2	343	Ccc/Tcc	4/8	0.409614464292561	1	FACETS	0.82	0.753	0.888	0.82	0.753	0.888	CLONAL	1	TRUE	0	0.599041624678336	1		712	385	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563320	21563320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	93	857	1	ENST00000382592.4:c.599G>A	p.Gly200Asp	p.G200D	ENST00000382592	NM_014572.2	200	gGc/gAc	4/8	0.409614464292561	1	FACETS	0.436	0.389	0.486	0.436	0.389	0.486	SUBCLONAL	1	TRUE	0	0.599041624678336	1		858	499	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626687	28626688	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	56	333	0	ENST00000241453.7:c.608_609delinsAA	p.Gly203Glu	p.G203E	ENST00000241453	NM_004119.2	203	gGG/gAA	5/24	0.427344827198935	0	FACETS	0.27	0.233	0.309			1	SUBCLONAL	1	TRUE	0	0.599041624678336	0		333	278	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042343	42042343	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778316806	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	90	462	0	ENST00000219905.7:c.6538G>A	p.Gly2180Ser	p.G2180S	ENST00000219905	NM_001164273.1	2180	Ggc/Agc	17/24	0.451004851588499	1	FACETS	0.744	0.668	0.822	0.744	0.668	0.822	SUBCLONAL	1	TRUE	0	0.599041624678336	1		462	283	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9927961	9927961	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	65	307	0	ENST00000330684.3:c.1777+1G>A		p.X593_splice	ENST00000330684	NM_001134407.1	593			1	2	FACETS	0.882	0.774	0.996	0.882	0.774	0.996	CLONAL	1	TRUE	1	0.599041624678336	2		307	246	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50784027	50784027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748843520	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	132	517	0	ENST00000398568.2:c.418G>A	p.Glu140Lys	p.E140K	ENST00000398568	NM_001042412.1	140	Gaa/Aaa	3/18	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.599041624678336	2		517	408	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822058	72822058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1445731408	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	30	386	0	ENST00000268489.5:c.10117G>A	p.Glu3373Lys	p.E3373K	ENST00000268489	NM_006885.3	3373	Gag/Aag	10/10	1	2	FACETS	0.434	0.351	0.526	0.434	0.351	0.526	SUBCLONAL	1	TRUE	1	0.599041624678336	2		386	231	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59878615	59878615	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs569696977	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	57	175	0	ENST00000259008.2:c.1139G>T	p.Ser380Ile	p.S380I	ENST00000259008	NM_032043.2	380	aGt/aTt	8/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.599041624678336	2		175	162	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617660	39617660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	51	206	0	ENST00000262039.4:c.1844C>T	p.Ala615Val	p.A615V	ENST00000262039	NM_002647.2	615	gCc/gTc	17/25	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.599041624678336	2		206	159	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11027148	11027148	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	86	784	0	ENST00000327064.4:c.913G>A	p.Glu305Lys	p.E305K	ENST00000327064	NM_199141.1	305	Gag/Aag	7/16	0.415854903463646	1	FACETS	0.421	0.373	0.471	0.421	0.373	0.471	SUBCLONAL	1	TRUE	0	0.599041624678336	1		784	478	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670523	134670523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	58	628	0	ENST00000398015.3:c.434G>A	p.Ser145Asn	p.S145N	ENST00000398015	NM_004441.4	145	aGc/aAc	3/16	0.599041624678336	1	FACETS	0.449	0.388	0.514	0.449	0.388	0.514	SUBCLONAL	1	TRUE	0	0.599041624678336	1		628	302	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238572	142238572	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	39	247	1	ENST00000350721.4:c.4321C>T	p.Gln1441Ter	p.Q1441*	ENST00000350721	NM_001184.3	1441	Caa/Taa	24/47	0.451004851588499	1	FACETS	0.507	0.425	0.595	0.507	0.425	0.595	SUBCLONAL	1	TRUE	0	0.599041624678336	1		248	180	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510145	149510145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	87	604	0	ENST00000261799.4:c.1324C>T	p.Pro442Ser	p.P442S	ENST00000261799	NM_002609.3	442	Ccc/Tcc	9/23	0.599041624678336	1	FACETS	0.479	0.426	0.535	0.479	0.426	0.535	SUBCLONAL	1	TRUE	0	0.599041624678336	1		604	425	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839787	27839788	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	112	459	1	ENST00000328488.2:c.306_307delinsAA	p.Gly103Arg	p.G103R	ENST00000328488	NM_003533.2	102	gtGGgg/gtAAgg	1/1	0.239062935539063	3	FACETS	0.882	0.796	0.972	0.441	0.398	0.486	INDETERMINATE	1	TRUE	1	0.599041624678336	3		460	551	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940078	31940079	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	80	601	0	ENST00000375333.2:c.221-1_221delinsAA		p.X74_splice	ENST00000375333	NM_032454.1	74		2/8	0.239062935539063	3	FACETS	0.567	0.499	0.64	0.284	0.249	0.32	INDETERMINATE	1	TRUE	1	0.599041624678336	3		601	612	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978348	2978348	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	63	643	0	ENST00000396946.4:c.982G>A	p.Glu328Lys	p.E328K	ENST00000396946	NM_032415.4	328	Gag/Aag	7/25	0.392400588623182	0	FACETS	0.25	0.217	0.285			1	SUBCLONAL	1	TRUE	0	0.599041624678336	0		643	337	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334777	81334777	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs545249104	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	39	362	0	ENST00000222390.5:c.1939C>T	p.Arg647Ter	p.R647*	ENST00000222390	NM_000601.4	647	Cga/Tga	17/18	1	2	FACETS	0.437	0.363	0.518	0.437	0.363	0.518	SUBCLONAL	1	TRUE	1	0.599041624678336	2		362	298	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874311	151874311	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs952132535	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	30	341	0	ENST00000262189.6:c.8227C>T	p.Pro2743Ser	p.P2743S	ENST00000262189	NM_170606.2	2743	Ccc/Tcc	38/59	1	2	FACETS	0.41	0.332	0.498	0.41	0.332	0.498	SUBCLONAL	1	TRUE	1	0.599041624678336	2		341	244	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005921	69005921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1291560005	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	45	423	0	ENST00000288368.4:c.2332G>A	p.Asp778Asn	p.D778N	ENST00000288368	NM_024870.2	778	Gat/Aat	21/40	1	2	FACETS	0.477	0.402	0.558	0.477	0.402	0.558	SUBCLONAL	1	TRUE	1	0.599041624678336	2		423	315	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980547	70980547	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	144	645	0	ENST00000276594.2:c.830G>A	p.Gly277Glu	p.G277E	ENST00000276594	NM_024504.3	277	gGa/gAa	4/8	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.599041624678336	2		645	465	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542582	141542582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	122	550	0	ENST00000220592.5:c.2404C>T	p.Pro802Ser	p.P802S	ENST00000220592	NM_012154.3	802	Cca/Tca	18/19	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.599041624678336	2		550	399	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376054	8376054	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	34	241	0	ENST00000356435.5:c.4543C>T	p.Gln1515Ter	p.Q1515*	ENST00000356435		1515	Cag/Tag	28/35	1	2	FACETS	0.432	0.354	0.518	0.432	0.354	0.518	SUBCLONAL	1	TRUE	1	0.599041624678336	2		241	263	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209268	98209269	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	103	701	1	ENST00000331920.6:c.4269_4270delinsAA	p.Asp1424Asn	p.D1424N	ENST00000331920	NM_000264.3	1423	agGGat/agAAat	23/24	NA	2	FACETS	0.496	0.444	0.551			1	INDETERMINATE	1	TRUE	NA	0.599041624678336	2		702	694	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417565	139417565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	162	855	0	ENST00000277541.6:c.479C>T	p.Ala160Val	p.A160V	ENST00000277541	NM_017617.3	160	gCc/gTc	4/34	0.172305335412192	2	FACETS	0.874	0.805	0.945	0.437	0.402	0.473	INDETERMINATE	1	TRUE	0	0.599041624678336	2		855	619	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006759	47006760	+	5_prime_UTR_variant	5'UTR	DNP	CC	CC	TT	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	71	575	0	ENST00000377604.3:c.-122_-121delinsTT		p.*41*	ENST00000377604	NM_001204468.1	-/852		2/24	0.392450511124339	1	FACETS	0.399	0.35	0.452	0.399	0.35	0.452	SUBCLONAL	1	TRUE	0	0.599041624678336	1		575	416	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389327	8389329	+	missense_variant	Missense_Mutation	TNP	ATC	ATC	CTT	novel	NA	P-0044695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	80	411	0	ENST00000356435.5:c.4289_4291delinsAAG	p.Gly1430_Ser1431delinsGluAla	p.G1430_S1431delinsEA	ENST00000356435		1430	gGATct/gAAGct	26/35	1	2	FACETS	0.795	0.706	0.889	0.795	0.706	0.889	SUBCLONAL	1	TRUE	1	0.599041624678336	2		411	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0044696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	73	739	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.266412888357129	1	FACETS	0.532	0.465	0.603	0.532	0.465	0.603	SUBCLONAL	1	TRUE	0	0.388862529090651	1		739	569	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	464	669	0	ENST00000397752.3:c.3028G>C	p.Asp1010His	p.D1010H	ENST00000397752	NM_000245.2	1010	Gat/Cat	14/21	0.286782557930903	5	FACETS	0.937	0.899	0.975			1	CLONAL	4	TRUE	NA	0.388862529090651	5		669	1008	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28934873	NA	P-0044696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	18	849	0	ENST00000269305.4:c.398T>C	p.Met133Thr	p.M133T	ENST00000269305	NM_001126112.2	133	aTg/aCg	5/11	0.266412888357129	1	FACETS	0.09	0.067	0.117	0.09	0.067	0.117	SUBCLONAL	1	TRUE	0	0.388862529090651	1		849	831	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023157	31023157	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	100	595	0	ENST00000375687.4:c.2642G>A	p.Arg881Lys	p.R881K	ENST00000375687	NM_015338.5	881	aGa/aAa	13/13	1	2	FACETS	0.822	0.735	0.913	0.822	0.735	0.913	CLONAL	1	TRUE	1	0.388862529090651	2		595	626	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955544	48955544	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	13	353	0	ENST00000267163.4:c.1660G>T	p.Glu554Ter	p.E554*	ENST00000267163	NM_000321.2	554	Gaa/Taa	17/27	0.388862529090651	1	FACETS	0.239	0.17	0.323	0.239	0.17	0.323	SUBCLONAL	1	TRUE	0	0.388862529090651	1		353	225	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959378	26959378	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	69	342	0	ENST00000381527.3:c.545C>T	p.Ser182Leu	p.S182L	ENST00000381527	NM_001260.1	182	tCa/tTa	6/13	0.388862529090651	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.388862529090651	1		342	256	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380140	116380140	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0044696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	90	559	0	ENST00000397752.3:c.1527+2T>A		p.X509_splice	ENST00000397752	NM_000245.2	509			0.286782557930903	5	FACETS	0.977	0.867	1			1	CLONAL	1	TRUE	NA	0.388862529090651	5		559	750	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411303	63411303	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	158	811	1	ENST00000330258.3:c.1864G>T	p.Glu622Ter	p.E622*	ENST00000330258	NM_152424.3	622	Gag/Tag	2/2	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.388862529090651	2		812	801	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349271	70349271	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	167	726	0	ENST00000374080.3:c.3683T>A	p.Phe1228Tyr	p.F1228Y	ENST00000374080		1228	tTt/tAt	26/45	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.388862529090651	2		726	858	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316133	11316133	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	194	527	0	ENST00000361445.4:c.621G>C	p.Glu207Asp	p.E207D	ENST00000361445	NM_004958.3	207	gaG/gaC	5/58	0.634363312590974	1	FACETS	0.807	0.754	0.86	0.807	0.754	0.86	CLONAL	1	TRUE	0	0.66924567486842	1		527	478	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084134	47084134	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	217	449	0	ENST00000409792.3:c.7155del	p.Lys2385AsnfsTer26	p.K2385Nfs*26	ENST00000409792	NM_014159.6	2385	aaA/aa	17/21	0.66924567486842	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.66924567486842	1		449	429	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440360	52440360	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	170	511	0	ENST00000460680.1:c.692T>G	p.Met231Arg	p.M231R	ENST00000460680	NM_004656.3	231	aTg/aGg	9/17	0.66924567486842	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.66924567486842	1		511	302	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0044703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	154	212	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.234173931374344	5	FACETS	1	0.968	1	1	0.968	1	CLONAL	5	FALSE	0	0.234173931374344	5		212	332	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460515	149460515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777239066	NA	P-0044703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	115	651	1	ENST00000286301.3:c.122G>A	p.Arg41Gln	p.R41Q	ENST00000286301	NM_005211.3	41	cGa/cAa	3/22	0.162520692882933	3	FACETS	1	0.914	1	1	0.986	1	CLONAL	3	FALSE	1	0.234173931374344	3		652	364	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024029	27024030	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	58	72	0	ENST00000324856.7:c.1136dup	p.Pro380AlafsTer20	p.P380Afs*20	ENST00000324856	NM_006015.4	379	cag/cAag	1/20	0.234173931374344	5	FACETS	1	0.935	1	1	0.98	1	CLONAL	5	FALSE	2	0.234173931374344	5		72	124	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629152	14629152	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	118	428	0	ENST00000254322.2:c.10G>C	p.Asp4His	p.D4H	ENST00000254322	NM_006145.1	4	Gac/Cac	1/3	0.162520692882933	3	FACETS	0.927	0.843	1	1	0.983	1	CLONAL	3	FALSE	1	0.234173931374344	3		428	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0044704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	455	688	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	NA	2	FACETS	0.994	0.965	1			1	INDETERMINATE	2	FALSE	NA	0.75193087768606	2		688	609	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426803	121426803	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	193	526	0	ENST00000257555.6:c.494G>C	p.Trp165Ser	p.W165S	ENST00000257555		165	tGg/tCg	2/10	0.75193087768606	2	FACETS	1	0.984	1	0.577	0.54	0.614	CLONAL	1	FALSE	0	0.75193087768606	2		526	445	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753072	42753072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111793182	NA	P-0044704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	156	703	0	ENST00000222329.4:c.1192G>A	p.Gly398Ser	p.G398S	ENST00000222329	NM_006494.2	398	Ggt/Agt	4/4	0.751518810882032	2	FACETS	0.928	0.858	1	0.464	0.429	0.5	CLONAL	1	FALSE	0	0.75193087768606	2		703	447	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938812	178938812	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	76	159	0	ENST00000263967.3:c.2054G>C	p.Gly685Ala	p.G685A	ENST00000263967	NM_006218.2	685	gGc/gCc	14/21	0.75193087768606	4	FACETS	1	0.951	1	0.729	0.657	0.801	CLONAL	2	FALSE	1	0.75193087768606	4		159	162	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609714	117609714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	117	353	1	ENST00000368508.3:c.6985C>T	p.Pro2329Ser	p.P2329S	ENST00000368508	NM_002944.2	2329	Cct/Tct	43/43	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.75193087768606	2		354	267	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	34	737	0				ENST00000310581	NM_198253.2	-/1132			0.153949473219565	3	FACETS	0.78	0.639	0.939	0.26	0.213	0.313	INDETERMINATE	1	FALSE	0	0.3	3		737	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0044754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	146	684	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.0432620407044799	4	FACETS	0.825	0.754	0.899	0.825	0.754	0.899	INDETERMINATE	2	FALSE	2	0.3	4		684	767	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0044754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	266	435	2	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	0.3	3	FACETS	1	0.982	1	1	0.994	1	CLONAL	4	FALSE	0	0.3	3		437	478	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0044754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	54	402	0	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	0.3	1	FACETS	0.558	0.477	0.648	0.558	0.477	0.648	SUBCLONAL	1	FALSE	0	0.3	1		402	548	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451860	29451860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	144	669	0	ENST00000389048.3:c.2705G>A	p.Gly902Glu	p.G902E	ENST00000389048	NM_004304.4	902	gGa/gAa	16/29	0.169188205718533	3	FACETS	0.815	0.745	0.888	0.815	0.745	0.888	INDETERMINATE	2	FALSE	1	0.3	3		669	677	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340408	8340408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775122610	NA	P-0044754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	44	409	1	ENST00000356435.5:c.5188C>T	p.Arg1730Trp	p.R1730W	ENST00000356435		1730	Cgg/Tgg	31/35	0.3	4	FACETS	0.608	0.509	0.718	0.203	0.169	0.24	SUBCLONAL	1	FALSE	1	0.3	4		410	627	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352582	118352582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	130	436	0	ENST00000534358.1:c.3787C>T	p.Pro1263Ser	p.P1263S	ENST00000534358	NM_005933.3	1263	Cca/Tca	7/36	0.187065115608407	3	FACETS	0.845	0.769	0.924	0.845	0.769	0.924	CLONAL	2	FALSE	1	0.3	3		436	590	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908239	41908239	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	82	730	0	ENST00000372991.4:c.283C>G	p.Arg95Gly	p.R95G	ENST00000372991	NM_001760.3	95	Cga/Gga	2/5	0.187065115608407	3	FACETS	0.74	0.652	0.836	0.37	0.326	0.418	SUBCLONAL	1	FALSE	1	0.3	3		730	849	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004402	150004402	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	42	382	0	ENST00000253339.5:c.1823A>T	p.Lys608Ile	p.K608I	ENST00000253339		608	aAa/aTa	3/7	0.169188205718533	3	FACETS	0.925	0.775	1	0.463	0.387	0.546	INDETERMINATE	1	FALSE	1	0.3	3		382	348	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401174	139401174	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	82	655	0	ENST00000277541.6:c.3895C>T	p.His1299Tyr	p.H1299Y	ENST00000277541	NM_017617.3	1299	Cac/Tac	23/34	0.3	4	FACETS	0.967	0.852	1	0.322	0.284	0.364	CLONAL	1	FALSE	1	0.3	4		655	735	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403440	139403441	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	71	824	0	ENST00000277541.6:c.3052dup	p.Cys1018LeufsTer7	p.C1018Lfs*7	ENST00000277541	NM_017617.3	1018	tgc/tTgc	19/34	0.3	4	FACETS	0.667	0.581	0.761	0.222	0.193	0.254	SUBCLONAL	1	FALSE	1	0.3	4		824	922	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407917	139407918	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTGGA	novel	NA	P-0044754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	326	735	0	ENST00000277541.6:c.2275_2279dup	p.Cys762ThrfsTer12	p.C762Tfs*12	ENST00000277541	NM_017617.3	760	aac/aaTCCAAc	14/34	0.3	4	FACETS	0.989	0.937	1	0.989	0.937	1	CLONAL	3	FALSE	1	0.3	4		735	952	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0044757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	218	471	1	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.972	0.904	1	0.972	0.904	1	CLONAL	1	TRUE	1	0.446314067419536	2		472	1005	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243673	41243673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	70	643	0	ENST00000357654.3:c.3875C>T	p.Ser1292Phe	p.S1292F	ENST00000357654	NM_007294.3	1292	tCt/tTt	10/23	0.446314067419536	1	FACETS	0.338	0.294	0.386	0.338	0.294	0.386	SUBCLONAL	1	TRUE	0	0.446314067419536	1		643	720	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95583985	95583985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	98	367	0	ENST00000393063.1:c.1483G>C	p.Glu495Gln	p.E495Q	ENST00000393063	NM_030621.3	495	Gaa/Caa	10/28	1	2	FACETS	0.856	0.767	0.951	0.856	0.767	0.951	CLONAL	1	TRUE	1	0.446314067419536	2		367	513	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467808	50467808	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	172	643	0	ENST00000331340.3:c.1043del	p.Tyr348SerfsTer67	p.Y348Sfs*67	ENST00000331340	NM_006060.4	348	tAc/tc	8/8	1	2	FACETS	0.962	0.887	1	0.962	0.887	1	CLONAL	1	TRUE	1	0.446314067419536	2		643	801	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098815	178098815	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	210	491	0	ENST00000397062.3:c.230A>G	p.Asp77Gly	p.D77G	ENST00000397062	NM_006164.4	77	gAt/gGt	2/5	0.194295566999941	3	FACETS	1	0.971	1	1	0.994	1	CLONAL	4	FALSE	1	0.194295566999941	3		491	557	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021824	71021824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	21	156	0	ENST00000318789.4:c.1534G>A	p.Ala512Thr	p.A512T	ENST00000318789	NM_032682.5	512	Gca/Aca	18/21	1	2	FACETS	0.956	0.748	1	1	0.941	1	CLONAL	2	FALSE	1	0.194295566999941	2		156	113	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630071	117630071	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	20	267	1	ENST00000368508.3:c.6455G>T	p.Trp2152Leu	p.W2152L	ENST00000368508	NM_002944.2	2152	tGg/tTg	41/43	0.149754843111836	4	FACETS	0.788	0.608	0.996	0.788	0.608	0.996	CLONAL	2	FALSE	2	0.194295566999941	4		268	156	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066712	77066712	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1482673833	NA	P-0044771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	12	216	1	ENST00000356341.3:c.772+1G>A		p.X258_splice	ENST00000356341	NM_002576.4	258			1	2	FACETS	0.777	0.548	1	0.777	0.548	1	CLONAL	1	FALSE	1	0.194295566999941	2		217	159	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425674	49425675	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0044771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	21	684	0	ENST00000301067.7:c.12813_12814del	p.Gly4272ProfsTer61	p.G4272Pfs*61	ENST00000301067	NM_003482.3	4271	acAGgc/acgc	39/54	0.194295566999941	5	FACETS	1	0.886	1	0.421	0.325	0.532	CLONAL	1	FALSE	2	0.194295566999941	5		684	221	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426485	49426486	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	69	826	0	ENST00000301067.7:c.12002dup	p.Met4001IlefsTer11	p.M4001Ifs*11	ENST00000301067	NM_003482.3	4001	atg/atTg	39/54	0.194295566999941	5	FACETS	1	0.886	1	0.676	0.591	0.768	CLONAL	2	FALSE	2	0.194295566999941	5		826	452	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431061	49431061	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	24	578	2	ENST00000301067.7:c.10078C>T	p.Gln3360Ter	p.Q3360*	ENST00000301067	NM_003482.3	3360	Cag/Tag	34/54	0.194295566999941	5	FACETS	1	0.862	1	0.378	0.297	0.472	CLONAL	1	FALSE	2	0.194295566999941	5		580	281	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965621	93965621	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	23	341	0	ENST00000369303.4:c.2307T>A	p.Asn769Lys	p.N769K	ENST00000369303	NM_004440.3	769	aaT/aaA	13/17	0.149754843111836	4	FACETS	1	0.839	1	0.546	0.426	0.683	CLONAL	1	FALSE	2	0.194295566999941	4		341	259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0044785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	418	597	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.679094352037478	2	FACETS	0.98	0.947	1	0.98	0.947	1	CLONAL	2	TRUE	0	0.679094352037478	2		597	628	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599338	55599338	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	177	284	0	ENST00000288135.5:c.2464A>T	p.Asn822Tyr	p.N822Y	ENST00000288135	NM_000222.2	822	Aat/Tat	17/21	0.679094352037478	2	FACETS	0.999	0.947	1	0.999	0.947	1	CLONAL	2	TRUE	0	0.679094352037478	2		284	261	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125513723	125513724	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	62	324	0	ENST00000428830.2:c.852dup	p.Glu285ArgfsTer8	p.E285Rfs*8	ENST00000428830	NM_001114121.2	284	tca/tcAa	9/14	0.679094352037478	3	FACETS	0.776	0.676	0.884	0.388	0.338	0.442	SUBCLONAL	1	TRUE	1	0.679094352037478	3		324	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578520	7578520	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	420	680	1	ENST00000269305.4:c.410T>A	p.Leu137Gln	p.L137Q	ENST00000269305	NM_001126112.2	137	cTg/cAg	5/11	0.364176000287439	2	FACETS	0.799	0.761	0.838	0.799	0.761	0.838	SUBCLONAL	2	TRUE	0	0.393501755148225	2		681	1336	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039407	47039407	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	25	332	0	ENST00000377604.3:c.1030G>T	p.Gly344Cys	p.G344C	ENST00000377604	NM_001204468.1	344	Ggc/Tgc	10/24	1	1	FACETS	0.223	0.175	0.278	0.223	0.175	0.278	SUBCLONAL	1	TRUE	0	0.393501755148225	1		332	458	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023595	27023595	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	166	372	0	ENST00000324856.7:c.701C>G	p.Pro234Arg	p.P234R	ENST00000324856	NM_006015.4	234	cCg/cGg	1/20	0.272505985735726	2	FACETS	1	0.952	1	0.524	0.482	0.568	CLONAL	1	TRUE	0	0.393501755148225	2		372	805	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435586	110435586	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	44	342	0	ENST00000375856.3:c.2815C>A	p.Leu939Met	p.L939M	ENST00000375856	NM_003749.2	939	Ctg/Atg	1/2	0.331363269668896	2	FACETS	0.337	0.282	0.398	0.168	0.141	0.199	SUBCLONAL	1	TRUE	0	0.393501755148225	2		342	664	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557300	29557300	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555614502	NA	P-0044803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	22	211	0	ENST00000356175.3:c.3013A>G	p.Met1005Val	p.M1005V	ENST00000356175	NM_000267.3	1005	Atg/Gtg	23/57	0.173346279042517	0	FACETS	0.526	0.412	0.653			1	INDETERMINATE	1	TRUE	0	0.393501755148225	0		211	129	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119595346	119595346	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	15	165	0	ENST00000316626.5:c.823A>G	p.Thr275Ala	p.T275A	ENST00000316626		275	Act/Gct	8/12	0.385176197532178	2	FACETS	0.582	0.429	0.763	0.291	0.214	0.382	SUBCLONAL	1	TRUE	0	0.393501755148225	2		165	131	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876265	35876265	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	278	431	2	ENST00000303115.3:c.1057G>T	p.Asp353Tyr	p.D353Y	ENST00000303115	NM_002185.3	353	Gat/Tat	8/8	0.201740873688168	2	FACETS	0.897	0.846	0.948	0.897	0.846	0.948	INDETERMINATE	2	TRUE	0	0.393501755148225	2		433	788	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	199	486	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.537524033323815	1	FACETS	0.836	0.778	0.895	0.836	0.778	0.895	CLONAL	1	TRUE	0	0.537524033323815	1		486	648	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633625	69633625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782733556	NA	P-0044827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	54	59	0	ENST00000334134.2:c.77G>A	p.Arg26Gln	p.R26Q	ENST00000334134	NM_005247.2	26	cGg/cAg	1/3	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.537524033323815	2		59	161	SUCCESS
APC	324	MSKCC	GRCh37	5	112175707	112175707	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	96	284	0	ENST00000257430.4:c.4418del	p.Asn1473MetfsTer34	p.N1473Mfs*34	ENST00000257430	NM_000038.5	1472	gtA/gt	16/16	0.537524033323815	1	FACETS	0.787	0.708	0.868	0.787	0.708	0.868	SUBCLONAL	1	TRUE	0	0.537524033323815	1		284	332	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729447	41729447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	224	576	0	ENST00000242208.4:c.1082C>T	p.Thr361Met	p.T361M	ENST00000242208	NM_002192.2	361	aCg/aTg	3/3	0.252298191835071	3	FACETS	0.954	0.887	1	0.318	0.295	0.341	INDETERMINATE	1	TRUE	0	0.537524033323815	3		576	1109	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749198	43749198	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	181	555	0	ENST00000382044.4:c.1608G>C	p.Leu536Phe	p.L536F	ENST00000382044	NM_001141980.1	536	ttG/ttC	12/28	1	2	FACETS	0.806	0.744	0.87	0.806	0.744	0.87	CLONAL	1	TRUE	1	0.537524033323815	2		555	836	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185544	27185545	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0044828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	241	548	0	ENST00000380036.4:c.1250dup	p.Asp418Ter	p.D418*	ENST00000380036	NM_000459.3	415	ctc/ctCc	9/23	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.587868814439868	2		548	811	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070931	30070931	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0044845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	46	657	0	ENST00000338641.4:c.1446+1G>T		p.X482_splice	ENST00000338641	NM_000268.3	482			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		657	858	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0044908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	601	544	1				ENST00000310581	NM_198253.2	-/1132			0.736967925741364	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	1	0.736967925741364	3		545	1016	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0044908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	254	351	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.736967925741364	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.736967925741364	1		351	431	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729094	66729099	+	inframe_deletion	In_Frame_Del	DEL	TGGAGA	TGGAGA	-	novel	NA	P-0044908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	243	553	0	ENST00000307102.5:c.303_308del	p.Glu102_Ile103del	p.E102_I103del	ENST00000307102	NM_002755.3	101	cTGGAGAtc/ctc	3/11	0.736967925741364	1	FACETS	0.923	0.875	0.971	0.923	0.875	0.971	CLONAL	1	TRUE	0	0.736967925741364	1		553	451	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862896	9862896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1198247451	NA	P-0044908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	323	579	0	ENST00000330684.3:c.2407G>A	p.Glu803Lys	p.E803K	ENST00000330684	NM_001134407.1	803	Gag/Aag	12/13	1	2	FACETS	0.968	0.917	1	0.968	0.917	1	CLONAL	1	TRUE	1	0.736967925741364	2		579	906	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280068	66280068	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	161	265	0	ENST00000273854.3:c.1621C>T	p.Arg541Ter	p.R541*	ENST00000273854	NM_004439.5	541	Cga/Tga	7/18	1	2	FACETS	0.98	0.907	1	0.98	0.907	1	CLONAL	1	TRUE	1	0.736967925741364	2		265	446	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740098	162740098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781104392	NA	P-0044908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	166	320	0	ENST00000367921.3:c.1300C>T	p.Arg434Trp	p.R434W	ENST00000367921	NM_006182.2	434	Cgg/Tgg	12/18	1	2	FACETS	0.914	0.846	0.983	0.914	0.846	0.983	CLONAL	1	TRUE	1	0.736967925741364	2		320	493	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110245	3110245	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777099166	NA	P-0044908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	425	887	1	ENST00000078429.4:c.235G>A	p.Val79Ile	p.V79I	ENST00000078429	NM_002067.2	79	Gtc/Atc	2/7	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.736967925741364	2		888	1146	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355342	15355342	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	257	475	0	ENST00000263377.2:c.2281C>G	p.Pro761Ala	p.P761A	ENST00000263377	NM_058243.2	761	Ccc/Gcc	13/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.736967925741364	2		475	695	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31025104	31025104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	264	418	0	ENST00000375687.4:c.4589C>T	p.Pro1530Leu	p.P1530L	ENST00000375687	NM_015338.5	1530	cCc/cTc	13/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.736967925741364	2		418	691	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0044912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	81	601	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.869	0.763	0.983	0.869	0.763	0.983	CLONAL	1	TRUE	1	0.18	2		601	1036	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219336	1219336	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	71	609	0	ENST00000326873.7:c.388G>T	p.Glu130Ter	p.E130*	ENST00000326873	NM_000455.4	130	Gag/Tag	3/10	1	2	FACETS	0.859	0.748	0.98	0.859	0.748	0.98	CLONAL	1	TRUE	1	0.18	2		609	918	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	76	562	0	ENST00000267101.3:c.273G>A	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atA	3/28	0.156470219035769	3	FACETS	0.933	0.816	1	0.466	0.408	0.53	CLONAL	1	TRUE	1	0.18	3		562	987	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225060	NA	P-0044912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	37	355	0	ENST00000263967.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000263967	NM_006218.2	104	cCa/cTa	2/21	1	2	FACETS	0.754	0.621	0.904	0.754	0.621	0.904	CLONAL	1	TRUE	1	0.18	2		355	545	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059176	27059176	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	32	301	0	ENST00000324856.7:c.1813C>T	p.Gln605Ter	p.Q605*	ENST00000324856	NM_006015.4	605	Caa/Taa	4/20	1	2	FACETS	0.668	0.541	0.812	0.668	0.541	0.812	SUBCLONAL	1	TRUE	1	0.18	2		301	532	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400062	49400062	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	T	novel	NA	P-0044912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	44	323	0	ENST00000418115.1:c.278-3C>A		p.X93_splice	ENST00000418115	NM_001664.2	93			1	2	FACETS	0.816	0.684	0.963	0.816	0.684	0.963	CLONAL	1	TRUE	1	0.18	2		323	599	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602565	10602565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	75	663	0	ENST00000171111.5:c.1013C>T	p.Ser338Leu	p.S338L	ENST00000171111	NM_203500.1	338	tCg/tTg	3/6	1	2	FACETS	0.876	0.766	0.996	0.876	0.766	0.996	CLONAL	1	TRUE	1	0.18	2		663	951	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736307	243736307	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	67	382	0	ENST00000263826.5:c.740G>T	p.Arg247Leu	p.R247L	ENST00000263826	NM_005465.4	247	cGc/cTc	8/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.18	2		382	560	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998247	100998247	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	27	270	0	ENST00000325455.5:c.1555G>T	p.Gly519Trp	p.G519W	ENST00000325455	NM_001202474.3	519	Ggg/Tgg	1/8	1	2	FACETS	0.743	0.59	0.917	0.743	0.59	0.917	CLONAL	1	TRUE	1	0.18	2		270	404	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348912	11348912	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs765480579	NA	P-0044912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	41	436	0	ENST00000332029.2:c.424G>C	p.Glu142Gln	p.E142Q	ENST00000332029	NM_003745.1	142	Gag/Cag	2/2	0.3	3	FACETS	0.708	0.588	0.842			1	SUBCLONAL	1	TRUE	NA	0.18	3		436	701	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136864	55136864	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	31	365	0	ENST00000257290.5:c.1186G>A	p.Ala396Thr	p.A396T	ENST00000257290	NM_006206.4	396	Gct/Act	8/23	1	2	FACETS	0.677	0.546	0.825	0.677	0.546	0.825	SUBCLONAL	1	TRUE	1	0.18	2		365	509	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409173	31409173	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	47	384	0	ENST00000344624.3:c.3844C>G	p.Pro1282Ala	p.P1282A	ENST00000344624		1282	Cct/Gct	30/33	1	2	FACETS	0.879	0.741	1	0.879	0.741	1	CLONAL	1	TRUE	1	0.18	2		384	594	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0044913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	130	471	1	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.309771857104647	3	FACETS	0.881	0.804	0.961	0.881	0.804	0.961	CLONAL	2	TRUE	1	0.350315862527412	3		472	495	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652851	29652851	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	16	182	0	ENST00000356175.3:c.4786C>T	p.Gln1596Ter	p.Q1596*	ENST00000356175	NM_000267.3	1596	Caa/Taa	36/57	1	2	FACETS	0.491	0.364	0.642	0.491	0.364	0.642	SUBCLONAL	1	TRUE	1	0.350315862527412	2		182	186	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298581	11298581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	47	567	0	ENST00000361445.4:c.1880C>T	p.Ser627Phe	p.S627F	ENST00000361445	NM_004958.3	627	tCc/tTc	12/58	0.309771857104647	3	FACETS	0.595	0.502	0.698	0.297	0.251	0.349	SUBCLONAL	1	TRUE	1	0.350315862527412	3		567	530	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510626	38510626	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	76	771	0	ENST00000254066.5:c.880C>G	p.Arg294Gly	p.R294G	ENST00000254066	NM_000964.3	294	Cgg/Ggg	7/9	1	2	FACETS	0.813	0.714	0.918	0.813	0.714	0.918	CLONAL	1	TRUE	1	0.350315862527412	2		771	534	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891338	101891338	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	36	404	0	ENST00000374994.4:c.299G>T	p.Cys100Phe	p.C100F	ENST00000374994	NM_004612.2	100	tGc/tTc	2/9	0.209999605191537	1	FACETS	0.533	0.439	0.637	0.533	0.439	0.637	INDETERMINATE	1	TRUE	0	0.350315862527412	1		404	318	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904986	101904986	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0044913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	19	223	0	ENST00000374994.4:c.973+1G>C		p.X325_splice	ENST00000374994	NM_004612.2	325			0.209999605191537	1	FACETS	0.517	0.395	0.659	0.517	0.395	0.659	INDETERMINATE	1	TRUE	0	0.350315862527412	1		223	173	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0044929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	94	675	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.211548203532761	2		675	869	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939032	48939033	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	20	261	0	ENST00000267163.4:c.869dup	p.Asn290LysfsTer20	p.N290Kfs*20	ENST00000267163	NM_000321.2	288	-/A	9/27	1	2	FACETS	0.561	0.429	0.716	0.561	0.429	0.716	SUBCLONAL	1	TRUE	1	0.211548203532761	2		261	337	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190872	106190872	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	63	403	0	ENST00000380013.4:c.4150G>C	p.Asp1384His	p.D1384H	ENST00000380013	NM_001127208.2	1384	Gac/Cac	9/11	0.211548203532761	1	FACETS	0.943	0.816	1	0.943	0.816	1	CLONAL	1	TRUE	0	0.211548203532761	1		403	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579445	7579448	+	frameshift_variant	Frame_Shift_Del	DEL	GTAG	GTAG	-	novel	NA	P-0044929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	93	869	0	ENST00000269305.4:c.239_242del	p.Pro80HisfsTer42	p.P80Hfs*42	ENST00000269305	NM_001126112.2	80	cCTACa/ca	4/11	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.211548203532761	2		869	877	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098933	178098953	+	inframe_deletion	In_Frame_Del	DEL	CAAATACTTCTCGACTTACTC	CAAATACTTCTCGACTTACTC	-	novel	NA	P-0044929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	49	358	0	ENST00000397062.3:c.92_112del	p.Gly31_Phe37del	p.G31_F37del	ENST00000397062	NM_006164.4	31	gGAGTAAGTCGAGAAGTATTTGac/gac	2/5	0.0956542667885398	3	FACETS	0.981	0.831	1	0.491	0.415	0.573	INDETERMINATE	1	TRUE	1	0.211548203532761	3		358	522	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0044954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	66	413	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.253048119702553	3	FACETS	0.894	0.777	1	0.894	0.777	1	CLONAL	2	TRUE	1	0.15	3		414	529	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829039	128829040	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs570242755	NA	P-0044954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	16	8	0	ENST00000249373.3:c.67_69dup	p.Leu23dup	p.L23dup	ENST00000249373	NM_005631.4	23	ggg/ggGCTg	1/12	1	2	FACETS	1	0.758	1	1	0.942	1	CLONAL	3	TRUE	1	0.15	2		8	71	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988204	36988204	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	55	163	0	ENST00000354822.5:c.449del	p.Pro150ArgfsTer16	p.P150Rfs*16	ENST00000354822	NM_001079668.2	150	cCg/cg	2/3	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.15	2		163	669	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0044983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	226	310	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.721349727052499	2	FACETS	0.97	0.927	1	0.97	0.927	1	CLONAL	2	TRUE	0	0.721349727052499	2		310	323	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0044983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	500	356	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.721349727052499	6	FACETS	0.903	0.87	0.935	0.903	0.87	0.935	CLONAL	4	TRUE	2	0.721349727052499	6		356	938	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631134	69631134	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	245	772	0	ENST00000334134.2:c.278C>T	p.Ser93Phe	p.S93F	ENST00000334134	NM_005247.2	93	tCc/tTc	2/3	1	2	FACETS	0.819	0.768	0.872	0.819	0.768	0.872	CLONAL	1	TRUE	1	0.721349727052499	2		772	829	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923215	26923215	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs769996123	NA	P-0044983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	100	230	0	ENST00000381527.3:c.211C>T	p.Arg71Ter	p.R71*	ENST00000381527	NM_001260.1	71	Cga/Tga	3/13	0.721349727052499	3	FACETS	0.99	0.892	1	0.495	0.446	0.547	CLONAL	1	TRUE	1	0.721349727052499	3		230	381	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134688	41134688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1034299550	NA	P-0044983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	161	402	0	ENST00000379561.5:c.940C>T	p.Arg314Cys	p.R314C	ENST00000379561	NM_002015.3	314	Cgc/Tgc	2/3	0.721349727052499	3	FACETS	0.955	0.879	1	0.478	0.439	0.517	CLONAL	1	TRUE	1	0.721349727052499	3		402	636	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0044983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	160	459	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.932	0.862	1	0.932	0.862	1	CLONAL	1	TRUE	1	0.721349727052499	2		459	476	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522569	106522569	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746783339	NA	P-0044983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	130	307	0	ENST00000359195.3:c.2546G>A	p.Arg849Gln	p.R849Q	ENST00000359195	NM_002649.2	849	cGa/cAa	7/11	0.721349727052499	6	FACETS	0.911	0.826	1	0.228	0.206	0.251	CLONAL	1	TRUE	2	0.721349727052499	6		307	966	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967910	93967910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	186	513	0	ENST00000369303.4:c.2017G>A	p.Glu673Lys	p.E673K	ENST00000369303	NM_004440.3	673	Gaa/Aaa	11/17	1	2	FACETS	0.859	0.798	0.922	0.859	0.798	0.922	CLONAL	1	TRUE	1	0.721349727052499	2		513	600	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460546	149460546	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	302	722	1	ENST00000286301.3:c.91G>A	p.Val31Ile	p.V31I	ENST00000286301	NM_005211.3	31	Gtc/Atc	3/22	1	2	FACETS	0.931	0.88	0.984	0.931	0.88	0.984	CLONAL	1	TRUE	1	0.721349727052499	2		723	899	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624594	93624594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	397	591	0	ENST00000375746.1:c.685C>T	p.Pro229Ser	p.P229S	ENST00000375746	NM_001174167.1	229	Ccc/Tcc	4/14	0.721349727052499	2	FACETS	0.922	0.89	0.954	0.922	0.89	0.954	CLONAL	2	TRUE	0	0.721349727052499	2		591	597	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258550	16258550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	193	624	1	ENST00000375759.3:c.5815C>T	p.Gln1939Ter	p.Q1939*	ENST00000375759	NM_015001.2	1939	Cag/Tag	11/15	0.721349727052499	3	FACETS	0.836	0.774	0.9	0.418	0.387	0.45	CLONAL	1	TRUE	1	0.721349727052499	3		625	871	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117650555	117650555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	164	486	1	ENST00000368508.3:c.5303C>T	p.Ser1768Leu	p.S1768L	ENST00000368508	NM_002944.2	1768	tCa/tTa	32/43	1	2	FACETS	0.953	0.883	1	0.953	0.883	1	CLONAL	1	TRUE	1	0.721349727052499	2		487	477	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637067	93637067	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	419	510	0	ENST00000375746.1:c.1117G>A	p.Glu373Lys	p.E373K	ENST00000375746	NM_001174167.1	373	Gaa/Aaa	9/14	0.721349727052499	2	FACETS	0.986	0.955	1	0.986	0.955	1	CLONAL	2	TRUE	0	0.721349727052499	2		510	589	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553676	106553676	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	192	442	0	ENST00000369096.4:c.1641G>A	p.Met547Ile	p.M547I	ENST00000369096	NM_001198.3	547	atG/atA	5/7	1	2	FACETS	0.926	0.862	0.991	0.926	0.862	0.991	CLONAL	1	TRUE	1	0.721349727052499	2		442	575	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4102405	4102405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1255048230	NA	P-0044983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	279	797	1	ENST00000262948.5:c.497C>T	p.Pro166Leu	p.P166L	ENST00000262948	NM_030662.3	166	cCc/cTc	4/11	0.721349727052499	3	FACETS	0.867	0.814	0.922	0.434	0.407	0.461	CLONAL	1	TRUE	1	0.721349727052499	3		798	1214	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933223	100933223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1175582391	NA	P-0044983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	151	447	0	ENST00000325455.5:c.2167G>A	p.Glu723Lys	p.E723K	ENST00000325455	NM_001202474.3	723	Gag/Aag	4/8	1	2	FACETS	0.867	0.798	0.937	0.867	0.798	0.937	CLONAL	1	TRUE	1	0.721349727052499	2		447	483	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463259	463259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	143	401	0	ENST00000399788.2:c.1012C>T	p.Pro338Ser	p.P338S	ENST00000399788	NM_001042603.1	338	Cct/Tct	8/28	1	2	FACETS	0.779	0.715	0.846	0.779	0.715	0.846	SUBCLONAL	1	TRUE	1	0.721349727052499	2		401	509	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985864	60985865	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0044983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	137	407	0	ENST00000333681.4:c.35_36delinsAA	p.Arg12Gln	p.R12Q	ENST00000333681		12	cGG/cAA	2/3	1	2	FACETS	0.724	0.662	0.788	0.724	0.662	0.788	SUBCLONAL	1	TRUE	1	0.721349727052499	2		407	525	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218449	36218449	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs267605436	NA	P-0044983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	543	772	0	ENST00000222270.7:c.4228C>T	p.Gln1410Ter	p.Q1410*	ENST00000222270	NM_014727.1	1410	Cag/Tag	16/37	0.721349727052499	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.721349727052499	3		772	1003	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873125	136873125	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	186	407	0	ENST00000241393.3:c.373C>T	p.Leu125Phe	p.L125F	ENST00000241393	NM_003467.2	125	Ctc/Ttc	2/2	0.721349727052499	3	FACETS	1	0.952	1	0.517	0.48	0.557	CLONAL	1	TRUE	1	0.721349727052499	3		407	678	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795395	39795395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866682030	NA	P-0044983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	671	723	0	ENST00000288319.7:c.325G>A	p.Glu109Lys	p.E109K	ENST00000288319	NM_182918.3	109	Gag/Aag	3/10	0.661278117373587	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.721349727052499	3		723	1195	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972910	55972910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	331	439	0	ENST00000263923.4:c.1480G>A	p.Gly494Arg	p.G494R	ENST00000263923	NM_002253.2	494	Gga/Aga	11/30	0.721349727052499	3	FACETS	0.999	0.954	1	0.999	0.954	1	CLONAL	2	TRUE	1	0.721349727052499	3		439	625	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392114	81392114	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	290	273	0	ENST00000222390.5:c.163C>T	p.Pro55Ser	p.P55S	ENST00000222390	NM_000601.4	55	Cca/Tca	2/18	0.721349727052499	6	FACETS	0.926	0.883	0.97	0.926	0.883	0.97	CLONAL	4	TRUE	2	0.721349727052499	6		273	530	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395433	116395433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	723	429	0	ENST00000397752.3:c.1726G>A	p.Glu576Lys	p.E576K	ENST00000397752	NM_000245.2	576	Gaa/Aaa	6/21	0.721349727052499	6	FACETS	0.969	0.941	0.997	0.969	0.941	0.997	CLONAL	4	TRUE	2	0.721349727052499	6		429	1263	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	109	309	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.0161563489382326	4	FACETS	0.956	0.863	1	1	0.982	1	INDETERMINATE	3	TRUE	2	0.191561728750223	4		309	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577569	7577569	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519981	NA	P-0044986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	104	482	0	ENST00000269305.4:c.712T>C	p.Cys238Arg	p.C238R	ENST00000269305	NM_001126112.2	238	Tgt/Cgt	7/11	1	2	FACETS	1	0.963	1	1	0.989	1	CLONAL	2	TRUE	1	0.191561728750223	2		482	472	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99460087	99460087	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	20	314	0	ENST00000268035.6:c.2183A>G	p.Asn728Ser	p.N728S	ENST00000268035	NM_000875.3	728	aAc/aGc	10/21	1	2	FACETS	0.665	0.508	0.848	0.665	0.508	0.848	SUBCLONAL	1	TRUE	1	0.191561728750223	2		314	314	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412635	63412635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376626895	NA	P-0044986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	80	269	0	ENST00000330258.3:c.532C>T	p.Arg178Cys	p.R178C	ENST00000330258	NM_152424.3	178	Cgt/Tgt	2/2	0.101066450321154	2	FACETS	1	0.954	1			1	INDETERMINATE	3	TRUE	NA	0.191561728750223	2		269	247	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445190	49445216	+	inframe_deletion	In_Frame_Del	DEL	GGCTCCTCAGGCCGGGGGGACAGGTGC	GGCTCCTCAGGCCGGGGGGACAGGTGC	-	rs587778449	NA	P-0044986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	50	766	1	ENST00000301067.7:c.2250_2276del	p.Arg755_Pro763del	p.R755_P763del	ENST00000301067	NM_003482.3	750	ccGCACCTGTCCCCCCGGCCTGAGGAGCCa/cca	10/54	0.0161563489382326	4	FACETS	0.992	0.841	1	0.496	0.42	0.58	INDETERMINATE	1	TRUE	2	0.191561728750223	4		767	627	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606766	43606766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs539995816	NA	P-0044986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	35	687	1	ENST00000355710.3:c.1375G>A	p.Glu459Lys	p.E459K	ENST00000355710	NM_020975.4	459	Gag/Aag	7/20	0.0664771112303344	4	FACETS	0.696	0.569	0.839	0.348	0.284	0.42	INDETERMINATE	1	TRUE	2	0.191561728750223	4		688	626	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971124	21971162	+	inframe_deletion	In_Frame_Del	DEL	GAGAGTGGCGGGGTCGGCGCAGTTGGGCTCCGCGCCGTG	GAGAGTGGCGGGGTCGGCGCAGTTGGGCTCCGCGCCGTG	-	novel	NA	P-0044986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	32	508	0	ENST00000304494.5:c.196_234del	p.His66_Leu78del	p.H66_L78del	ENST00000304494	NM_000077.4	66	CACGGCGCGGAGCCCAACTGCGCCGACCCCGCCACTCTC/-	2/3	0.191561728750223	2	FACETS	0.815	0.661	0.988	0.407	0.33	0.494	CLONAL	1	TRUE	0	0.191561728750223	2		508	410	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0045018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	38	309	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.152149208711587	2		309	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0045018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	131	830	0	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	1	2	FACETS	0.863	0.782	0.948	1	0.988	1	CLONAL	2	TRUE	1	0.152149208711587	2		830	998	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956173	175956173	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	28	296	0	ENST00000367669.3:c.2039T>G	p.Phe680Cys	p.F680C	ENST00000367669	NM_022457.5	680	tTt/tGt	18/20	1	2	FACETS	0.979	0.783	1	0.979	0.783	1	CLONAL	1	TRUE	1	0.152149208711587	2		296	376	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987053	36987054	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0045018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	121	591	0	ENST00000354822.5:c.635_636del	p.Gln212ProfsTer226	p.Q212Pfs*226	ENST00000354822	NM_001079668.2	212	cAA/c	3/3	0.152149208711587	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.152149208711587	2		591	719	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340111	116340111	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	22	244	0	ENST00000397752.3:c.973C>G	p.Pro325Ala	p.P325A	ENST00000397752	NM_000245.2	325	Cct/Gct	2/21	1	2	FACETS	0.939	0.728	1	0.939	0.728	1	CLONAL	1	TRUE	1	0.152149208711587	2		244	308	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044411	5044411	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	36	375	0	ENST00000381652.3:c.359T>A	p.Phe120Tyr	p.F120Y	ENST00000381652	NM_004972.3	120	tTt/tAt	5/25	1	2	FACETS	0.878	0.721	1	0.878	0.721	1	CLONAL	1	TRUE	1	0.152149208711587	2		375	539	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421002	49421002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045021-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	110	247	0	ENST00000301067.7:c.14747del	p.Pro4916ArgfsTer79	p.P4916Rfs*79	ENST00000301067	NM_003482.3	4916	cCg/cg	48/54	0.49603442852561	6	FACETS	1	0.979	1	0.44	0.397	0.485	INDETERMINATE	1	TRUE	3	0.907922898135868	6		247	517	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0045134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	84	205	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.541665869746702	2		205	292	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	181	737	0				ENST00000310581	NM_198253.2	-/1132			0.278473927673878	3	FACETS	1	0.987	1	0.659	0.611	0.71	INDETERMINATE	1	TRUE	1	0.541665869746702	3		737	644	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806092	1806092	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913484	NA	P-0045134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	277	870	0	ENST00000260795.2:c.1111A>T	p.Ser371Cys	p.S371C	ENST00000260795		371	Agt/Tgt	8/17	0.541665869746702	1	FACETS	0.874	0.823	0.926	0.874	0.823	0.926	CLONAL	1	TRUE	0	0.541665869746702	1		870	853	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057727	27057727	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	279	680	1	ENST00000324856.7:c.1435C>T	p.Gln479Ter	p.Q479*	ENST00000324856	NM_006015.4	479	Cag/Tag	3/20	0.525203433188702	1	FACETS	0.755	0.71	0.801	0.755	0.71	0.801	SUBCLONAL	1	TRUE	0	0.541665869746702	1		681	995	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793253	33793253	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs137852728	NA	P-0045134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	69	136	1	ENST00000498907.2:c.68del	p.Pro23ArgfsTer137	p.P23Rfs*137	ENST00000498907	NM_004364.3	23	cCg/cg	1/1	1	2	FACETS	0.749	0.657	0.848	0.749	0.657	0.848	SUBCLONAL	1	TRUE	1	0.541665869746702	2		137	340	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022454	12022454	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753079378	NA	P-0045134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	323	838	0	ENST00000396373.4:c.560C>T	p.Thr187Met	p.T187M	ENST00000396373	NM_001987.4	187	aCg/aTg	5/8	1	2	FACETS	0.947	0.893	1	0.947	0.893	1	CLONAL	1	TRUE	1	0.541665869746702	2		838	1260	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797314	135797314	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	126	237	0	ENST00000298552.3:c.555del	p.Tyr185Ter	p.Y185*	ENST00000298552	NM_001162426.1	185	taC/ta	7/23	0.541665869746702	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.541665869746702	1		237	321	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39311703	39311703	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	134	554	0	ENST00000373001.3:c.956A>T	p.Lys319Met	p.K319M	ENST00000373001	NM_022157.3	319	aAg/aTg	6/7	0.525203433188702	1	FACETS	0.72	0.658	0.784	0.72	0.658	0.784	SUBCLONAL	1	TRUE	0	0.541665869746702	1		554	501	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828778	3828778	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0045134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	200	486	1	ENST00000262367.5:c.1864A>T	p.Lys622Ter	p.K622*	ENST00000262367	NM_004380.2	622	Aag/Tag	9/31	1	2	FACETS	0.921	0.855	0.989	0.921	0.855	0.989	CLONAL	1	TRUE	1	0.541665869746702	2		487	802	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265456	198265456	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	70	330	0	ENST00000335508.6:c.2701C>A	p.Gln901Lys	p.Q901K	ENST00000335508	NM_012433.2	901	Caa/Aaa	18/25	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.541665869746702	2		330	258	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956771	68956771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774302685	NA	P-0045187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	227	667	1	ENST00000288368.4:c.889C>T	p.Arg297Cys	p.R297C	ENST00000288368	NM_024870.2	297	Cgt/Tgt	8/40	1	2	FACETS	0.924	0.863	0.986	0.924	0.863	0.986	CLONAL	1	TRUE	1	0.626119383662118	2		668	785	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0045187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	300	544	1				ENST00000310581	NM_198253.2	-/1132			0.626119383662118	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.626119383662118	3		545	586	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005419	29005419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55687105	NA	P-0045187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	83	288	0	ENST00000282397.4:c.842G>A	p.Arg281Gln	p.R281Q	ENST00000282397	NM_002019.4	281	cGa/cAa	7/30	1	2	FACETS	0.852	0.76	0.949	0.852	0.76	0.949	CLONAL	1	TRUE	1	0.626119383662118	2		288	311	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0045187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	355	427	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.617176464074498	2	FACETS	0.973	0.934	1	0.973	0.934	1	CLONAL	2	TRUE	0	0.626119383662118	2		427	583	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0045187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	272	326	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.518905272380902	3	FACETS	0.907	0.858	0.956	0.907	0.858	0.956	CLONAL	2	TRUE	1	0.626119383662118	3		326	629	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644490	18644490	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs181773550	NA	P-0045187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	78	311	0	ENST00000266497.5:c.2668G>A	p.Asp890Asn	p.D890N	ENST00000266497		890	Gat/Aat	18/31	1	2	FACETS	0.771	0.684	0.864	0.771	0.684	0.864	SUBCLONAL	1	TRUE	1	0.626119383662118	2		311	323	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219847	133219847	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500822	NA	P-0045187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	201	706	0	ENST00000320574.5:c.4514C>T	p.Pro1505Leu	p.P1505L	ENST00000320574	NM_006231.2	1505	cCc/cTc	35/49	1	2	FACETS	0.999	0.93	1	0.999	0.93	1	CLONAL	1	TRUE	1	0.626119383662118	2		706	643	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566827	212566827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202247795	NA	P-0045187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	82	227	0	ENST00000342788.4:c.1354G>A	p.Glu452Lys	p.E452K	ENST00000342788	NM_005235.2	452	Gaa/Aaa	12/28	1	2	FACETS	0.842	0.75	0.939	0.842	0.75	0.939	CLONAL	1	TRUE	1	0.626119383662118	2		227	311	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971187	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0045187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	179	577	0	ENST00000304494.5:c.171_172delinsTT	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	57	gcCCga/gcTTga	2/3	0.626119383662118	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.626119383662118	1		577	350	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076945	41076945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767453141	NA	P-0045187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	152	462	0	ENST00000373198.4:c.1475C>T	p.Ser492Phe	p.S492F	ENST00000373198	NM_133170.3	492	tCc/tTc	9/32	1	2	FACETS	0.864	0.794	0.936	0.864	0.794	0.936	CLONAL	1	TRUE	1	0.626119383662118	2		462	562	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546734	9546734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	82	340	0	ENST00000353224.5:c.1288G>A	p.Glu430Lys	p.E430K	ENST00000353224	NM_177990.2	430	Gaa/Aaa	5/10	1	2	FACETS	0.837	0.745	0.933	0.837	0.745	0.933	CLONAL	1	TRUE	1	0.626119383662118	2		340	313	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244139	46244139	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	133	361	1	ENST00000334344.6:c.2233C>T	p.Gln745Ter	p.Q745*	ENST00000334344	NM_152641.2	745	Cag/Tag	15/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.626119383662118	2		362	387	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244595	41244595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555588649	NA	P-0045187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	158	524	0	ENST00000357654.3:c.2953C>T	p.Pro985Ser	p.P985S	ENST00000357654	NM_007294.3	985	Ccc/Tcc	10/23	1	2	FACETS	0.952	0.878	1	0.952	0.878	1	CLONAL	1	TRUE	1	0.626119383662118	2		524	530	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445611	49445611	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	425	993	0	ENST00000301067.7:c.1855C>T	p.Pro619Ser	p.P619S	ENST00000301067	NM_003482.3	619	Cca/Tca	10/54	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.626119383662118	2		993	1177	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849194	76849194	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	114	285	0	ENST00000373344.5:c.6082C>T	p.Arg2028Ter	p.R2028*	ENST00000373344	NM_000489.3	2028	Cga/Tga	26/35	1	2	FACETS	0.998	0.908	1	0.998	0.908	1	CLONAL	1	TRUE	1	0.626119383662118	2		285	365	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907819	76907819	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	62	193	0	ENST00000373344.5:c.4342G>A	p.Glu1448Lys	p.E1448K	ENST00000373344	NM_000489.3	1448	Gaa/Aaa	15/35	1	2	FACETS	0.934	0.819	1	0.934	0.819	1	CLONAL	1	TRUE	1	0.626119383662118	2		193	212	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057743	180057743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	219	799	0	ENST00000261937.6:c.212G>A	p.Gly71Glu	p.G71E	ENST00000261937	NM_182925.4	71	gGa/gAa	3/30	1	2	FACETS	0.954	0.891	1	0.954	0.891	1	CLONAL	1	TRUE	1	0.626119383662118	2		799	733	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805112	43805112	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	222	641	1	ENST00000372470.3:c.562A>C	p.Ile188Leu	p.I188L	ENST00000372470	NM_005373.2	188	Att/Ctt	4/12	0.0912418370124173	5	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.626119383662118	5		642	971	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125507394	125507394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771882988	NA	P-0045187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	187	298	0	ENST00000428830.2:c.769C>T	p.Pro257Ser	p.P257S	ENST00000428830	NM_001114121.2	257	Cca/Tca	8/14	0.617176464074498	2	FACETS	0.863	0.812	0.914	0.863	0.812	0.914	CLONAL	2	TRUE	0	0.626119383662118	2		298	346	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869432	102869432	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	147	391	0	ENST00000307046.8:c.209G>A	p.Gly70Asp	p.G70D	ENST00000307046	NM_001111285.1	70	gGc/gAc	2/4	1	2	FACETS	0.873	0.801	0.947	0.873	0.801	0.947	CLONAL	1	TRUE	1	0.626119383662118	2		391	538	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254292	133254293	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0045187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	99	328	0	ENST00000320574.5:c.591_592delinsAA	p.Gly198Ser	p.G198S	ENST00000320574	NM_006231.2	197	agGGgc/agAAgc	7/49	NA	2	FACETS	0.819	0.737	0.905			1	INDETERMINATE	1	TRUE	NA	0.626119383662118	2		328	386	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611367	28611367	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	141	450	0	ENST00000241453.7:c.1264A>T	p.Asn422Tyr	p.N422Y	ENST00000241453	NM_004119.2	422	Aat/Tat	10/24	1	2	FACETS	0.837	0.767	0.91	0.837	0.767	0.91	CLONAL	1	TRUE	1	0.626119383662118	2		450	538	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068984	30068984	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	145	444	0	ENST00000331968.5:c.1945T>C	p.Phe649Leu	p.F649L	ENST00000331968	NM_002742.2	649	Ttt/Ctt	14/18	1	2	FACETS	0.959	0.881	1	0.959	0.881	1	CLONAL	1	TRUE	1	0.626119383662118	2		444	483	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348679	89348679	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	498	692	0	ENST00000301030.4:c.4271C>T	p.Ser1424Phe	p.S1424F	ENST00000301030	NM_001256183.1	1424	tCt/tTt	9/13	0.626119383662118	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.626119383662118	2		692	779	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602514	10602514	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0045187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	260	916	0	ENST00000171111.5:c.1064T>A	p.Leu355Ter	p.L355*	ENST00000171111	NM_203500.1	355	tTg/tAg	3/6	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.626119383662118	2		916	803	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967060	25967060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763782415	NA	P-0045187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	239	681	0	ENST00000435504.4:c.2146G>A	p.Gly716Ser	p.G716S	ENST00000435504		716	Ggc/Agc	13/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.626119383662118	2		681	709	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158595031	158595031	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	163	369	0	ENST00000263640.3:c.1316C>T	p.Pro439Leu	p.P439L	ENST00000263640	NM_001105.4	439	cCa/cTa	10/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.626119383662118	2		369	471	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248422	212248422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	110	273	0	ENST00000342788.4:c.3845C>T	p.Pro1282Leu	p.P1282L	ENST00000342788	NM_005235.2	1282	cCt/cTt	28/28	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.626119383662118	2		273	322	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295381	1295382	+	upstream_gene_variant	5'Flank	DNP	CC	CC	TT	novel	NA	P-0045187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	92	316	0				ENST00000310581	NM_198253.2	-/1132			0.626119383662118	3	FACETS	0.965	0.863	1	0.482	0.431	0.536	CLONAL	1	TRUE	1	0.626119383662118	3		316	400	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129880	69129880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	118	345	0	ENST00000288368.4:c.4634C>T	p.Ala1545Val	p.A1545V	ENST00000288368	NM_024870.2	1545	gCc/gTc	38/40	1	2	FACETS	0.938	0.853	1	0.938	0.853	1	CLONAL	1	TRUE	1	0.626119383662118	2		345	402	SUCCESS
AR	367	MSKCC	GRCh37	X	66765029	66765029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	249	794	0	ENST00000374690.3:c.41C>T	p.Pro14Leu	p.P14L	ENST00000374690	NM_000044.3	14	cCg/cTg	1/8	1	2	FACETS	0.94	0.881	1	0.94	0.881	1	CLONAL	1	TRUE	1	0.626119383662118	2		794	846	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938743	76938743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	125	546	1	ENST00000373344.5:c.2005G>A	p.Glu669Lys	p.E669K	ENST00000373344	NM_000489.3	669	Gaa/Aaa	9/35	1	2	FACETS	0.791	0.719	0.865	0.791	0.719	0.865	SUBCLONAL	1	TRUE	1	0.626119383662118	2		547	505	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	46	737	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.567709253957604	2		737	151	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057520000	NA	P-0046089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	173	321	0	ENST00000269305.4:c.452C>G	p.Pro151Arg	p.P151R	ENST00000269305	NM_001126112.2	151	cCc/cGc	5/11	0.473171338948684	0	FACETS	0.751	0.702	0.799			1	SUBCLONAL	1	TRUE	0	0.567709253957604	0		321	351	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255461	16255461	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	74	195	0	ENST00000375759.3:c.2726A>G	p.Lys909Arg	p.K909R	ENST00000375759	NM_015001.2	909	aAa/aGa	11/15	1	2	FACETS	0.86	0.76	0.966	0.86	0.76	0.966	CLONAL	1	TRUE	1	0.567709253957604	2		195	303	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418481	49418482	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0046089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	121	269	0	ENST00000301067.7:c.15931dup	p.Val5311GlyfsTer34	p.V5311Gfs*34	ENST00000301067	NM_003482.3	5311	gtg/gGtg	50/54	0.567709253957604	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.567709253957604	1		269	266	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954204	48954204	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	47	192	0	ENST00000267163.4:c.1405del	p.Ser469ProfsTer9	p.S469Pfs*9	ENST00000267163	NM_000321.2	469	Tcc/cc	15/27	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.567709253957604	2		192	158	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039413	49039413	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	93	304	0	ENST00000267163.4:c.2399del	p.Pro800LeufsTer10	p.P800Lfs*10	ENST00000267163	NM_000321.2	800	Cct/ct	23/27	1	2	FACETS	0.966	0.868	1	0.966	0.868	1	CLONAL	1	TRUE	1	0.567709253957604	2		304	339	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504494	103504495	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	82	153	0	ENST00000355739.4:c.117dup	p.Lys40Ter	p.K40*	ENST00000355739	NM_000123.3	39	ctt/cTtt	2/15	0.307726130564371	4	FACETS	0.773	0.689	0.86			1	INDETERMINATE	2	TRUE	NA	0.567709253957604	4		153	293	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060618	38060619	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	203	217	0	ENST00000250448.2:c.1370dup	p.Ala458GlyfsTer100	p.A458Gfs*100	ENST00000250448	NM_004496.3	457	ccg/ccCg	2/2	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.567709253957604	2		217	613	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842060	3842061	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0046089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	74	136	0	ENST00000262367.5:c.1251_1252del	p.His418LeufsTer8	p.H418Lfs*8	ENST00000262367	NM_004380.2	417	tcTCat/tcat	5/31	1	2	FACETS	0.973	0.862	1	0.973	0.862	1	CLONAL	1	TRUE	1	0.567709253957604	2		136	268	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587781845	NA	P-0046285-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	338	848	0	ENST00000269305.4:c.511G>T	p.Glu171Ter	p.E171*	ENST00000269305	NM_001126112.2	171	Gag/Tag	5/11	0.797288273398866	3	FACETS	1	0.972	1	0.521	0.493	0.55	CLONAL	1	TRUE	1	0.797288273398866	3		848	1138	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0046285-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	135	237	0	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			0.797288273398866	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.797288273398866	2		237	169	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230492731	230492731	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046285-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	274	711	0	ENST00000391860.1:c.323G>T	p.Ser108Ile	p.S108I	ENST00000391860	NM_001258311.1	108	aGc/aTc	2/7	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.797288273398866	2		711	615	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499632	18499632	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs764573135	NA	P-0046285-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	172	542	0	ENST00000266497.5:c.1487T>C	p.Val496Ala	p.V496A	ENST00000266497		496	gTc/gCc	10/31	0.355257042639032	3	FACETS	1	0.966	1	0.358	0.331	0.386	INDETERMINATE	1	TRUE	0	0.797288273398866	3		542	562	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578277	7578284	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGGGGC	GGAGGGGC	-	novel	NA	P-0046285-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	632	897	0	ENST00000269305.4:c.565_572del	p.Ala189SerfsTer17	p.A189Sfs*17	ENST00000269305	NM_001126112.2	189	GCCCCTCCt/t	6/11	0.797288273398866	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.797288273398866	3		897	1068	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136170	11136170	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046285-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	409	588	0	ENST00000358026.2:c.3155del	p.Phe1052SerfsTer54	p.F1052Sfs*54	ENST00000358026	NM_001128849.1	1052	Ttc/tc	22/36	0.797288273398866	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.797288273398866	2		588	492	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146538	185146538	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046285-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	483	671	0	ENST00000265026.3:c.169A>C	p.Ile57Leu	p.I57L	ENST00000265026	NM_004721.4	57	Atc/Ctc	2/14	0.628904836526394	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.797288273398866	4		671	1082	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652527	48652527	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	164	340	0	ENST00000376670.3:c.1203del	p.Thr402ProfsTer30	p.T402Pfs*30	ENST00000376670	NM_002049.3	400	Ccc/cc	6/6	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.555789894081522	1		340	322	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598214	28598215	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	TT	novel	NA	P-0047237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	308	760	2	ENST00000253063.3:c.186_187delinsTT	p.Glu62_Gln63delinsAspTer	p.E62_Q63delinsD*	ENST00000253063	NM_031459.4	62	gaGCag/gaTTag	3/10	0.319931931873088	2	FACETS	1	0.994	1	0.717	0.679	0.755	INDETERMINATE	1	TRUE	0	0.555789894081522	2		762	773	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280694	115280694	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0047237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	65	297	0	ENST00000438362.2:c.338-1G>C		p.X113_splice	ENST00000438362	NM_001242891.1	113			0.536143594456039	1	FACETS	0.472	0.411	0.537	0.472	0.411	0.537	SUBCLONAL	1	TRUE	0	0.555789894081522	1		297	358	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923390	9923390	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	142	582	0	ENST00000330684.3:c.1897G>C	p.Val633Leu	p.V633L	ENST00000330684	NM_001134407.1	633	Gta/Cta	9/13	0.397301233343339	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.397301233343339	1		582	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574026	7574026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	325	684	1	ENST00000269305.4:c.1001G>T	p.Gly334Val	p.G334V	ENST00000269305	NM_001126112.2	334	gGg/gTg	10/11	0.324856383633541	2	FACETS	0.909	0.861	0.957	0.909	0.861	0.957	CLONAL	2	TRUE	0	0.397301233343339	2		685	900	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123836	46123837	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	20	337	1	ENST00000334344.6:c.109dup	p.Ile37AsnfsTer29	p.I37Nfs*29	ENST00000334344	NM_152641.2	34	-/A	2/21	1	2	FACETS	0.307	0.234	0.392	0.307	0.234	0.392	SUBCLONAL	1	TRUE	1	0.397301233343339	2		338	328	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023203	33023203	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	88	409	0	ENST00000300177.4:c.312C>A	p.His104Gln	p.H104Q	ENST00000300177	NM_001191322.1	104	caC/caA	2/2	0.259673705211748	4	FACETS	0.868	0.769	0.974			1	CLONAL	1	TRUE	NA	0.397301233343339	4		409	713	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743261	743261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	119	529	0	ENST00000314574.4:c.879G>T	p.Met293Ile	p.M293I	ENST00000314574	NM_005433.3	293	atG/atT	7/12	1	2	FACETS	0.886	0.801	0.976	0.886	0.801	0.976	CLONAL	1	TRUE	1	0.397301233343339	2		529	676	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632297	215632297	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	45	530	0	ENST00000260947.4:c.1477C>T	p.Gln493Ter	p.Q493*	ENST00000260947	NM_000465.2	493	Caa/Taa	6/11	1	2	FACETS	0.334	0.28	0.394	0.334	0.28	0.394	SUBCLONAL	1	TRUE	1	0.397301233343339	2		530	678	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114594	73114594	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	57	212	0	ENST00000356692.5:c.975A>T	p.Gln325His	p.Q325H	ENST00000356692		325	caA/caT	9/9	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.397301233343339	2		212	195	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	79	354	0	ENST00000263967.3:c.3012G>C	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atC	21/21	0.397301233343339	3	FACETS	0.975	0.86	1	0.487	0.43	0.549	CLONAL	1	TRUE	1	0.397301233343339	3		354	489	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523157	176523157	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	219	827	0	ENST00000292408.4:c.1921G>C	p.Asp641His	p.D641H	ENST00000292408	NM_213647.1	641	Gac/Cac	14/18	0.397301233343339	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.397301233343339	1		827	784	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146087	38146087	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	220	768	0	ENST00000317025.8:c.3419C>A	p.Thr1140Lys	p.T1140K	ENST00000317025	NM_023034.1	1140	aCa/aAa	19/24	1	2	FACETS	0.99	0.92	1	0.99	0.92	1	CLONAL	1	TRUE	1	0.397301233343339	2		768	1119	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971045	21971054	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGCCGCGC	CCAGCCGCGC	-	novel	NA	P-0047703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	274	700	0	ENST00000304494.5:c.304_313del	p.Ala102ThrfsTer41	p.A102Tfs*41	ENST00000304494	NM_000077.4	102	GCGCGGCTGGac/ac	2/3	0.397301233343339	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.397301233343339	1		700	820	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041009	47041009	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	160	929	1	ENST00000377604.3:c.1539G>T	p.Glu513Asp	p.E513D	ENST00000377604	NM_001204468.1	513	gaG/gaT	14/24	0.334523504674979	1	FACETS	0.598	0.548	0.651	0.598	0.548	0.651	SUBCLONAL	1	TRUE	0	0.397301233343339	1		930	1079	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152864490	152864490	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	13	42	0	ENST00000406277.2:c.38G>C	p.Arg13Pro	p.R13P	ENST00000406277	NM_152274.4	13	cGg/cCg	2/7	NA		FACETS		NA	1				INDETERMINATE	NA	TRUE	NA	0.397301233343339	NA		42	74	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	29	212	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.11310262094178	3	FACETS	0.63	0.505	0.773	0.21	0.168	0.258	INDETERMINATE	1	TRUE	0	0.215609080690962	3		212	473	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416459	49416459	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	881	522	0	ENST00000301067.7:c.16252G>C	p.Glu5418Gln	p.E5418Q	ENST00000301067	NM_003482.3	5418	Gaa/Caa	51/54	0.215609080690962	2	FACETS	1	0.984	1	1	0.998	1	CLONAL	5	TRUE	0	0.215609080690962	2		522	1610	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015365	176015370	+	inframe_deletion	In_Frame_Del	DEL	ACTGCA	ACTGCA	-	novel	NA	P-0048438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	23	215	0	ENST00000367669.3:c.1368_1373del	p.Asp456_Val458delinsGlu	p.D456_V458delinsE	ENST00000367669	NM_022457.5	456	gaTGCAGTg/gag	12/20	1	2	FACETS	0.811	0.634	1	0.811	0.634	1	CLONAL	1	TRUE	1	0.215609080690962	2		215	263	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416616	49416616	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	692	412	0	ENST00000301067.7:c.16095G>C	p.Gln5365His	p.Q5365H	ENST00000301067	NM_003482.3	5365	caG/caC	51/54	0.215609080690962	2	FACETS	0.963	0.933	0.993	1	0.998	1	CLONAL	5	TRUE	0	0.215609080690962	2		412	1333	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030374	49030374	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	123	263	0	ENST00000267163.4:c.1850del	p.Gly617ValfsTer6	p.G617Vfs*6	ENST00000267163	NM_000321.2	617	Ggt/gt	19/27	0.636473414945004	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.636473414945004	1		263	263	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847221	68847221	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555515863	NA	P-0049093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	149	367	0	ENST00000261769.5:c.1145del	p.Gly382ValfsTer11	p.G382Vfs*11	ENST00000261769	NM_004360.3	381	aaG/aa	9/16	0.636473414945004	1	FACETS	0.936	0.868	1	0.936	0.868	1	CLONAL	1	TRUE	0	0.636473414945004	1		367	341	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421818	49421818	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	296	677	0	ENST00000301067.7:c.14489del	p.Pro4830GlnfsTer28	p.P4830Qfs*28	ENST00000301067	NM_003482.3	4830	cCa/ca	46/54	1	2	FACETS	0.959	0.904	1	0.959	0.904	1	CLONAL	1	TRUE	1	0.636473414945004	2		677	970	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498295	29498295	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	217	405	0	ENST00000389048.3:c.1885T>C	p.Ser629Pro	p.S629P	ENST00000389048	NM_004304.4	629	Tcc/Ccc	10/29	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.636473414945004	2		405	615	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281885	142281885	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	173	363	0	ENST00000350721.4:c.359A>C	p.His120Pro	p.H120P	ENST00000350721	NM_001184.3	120	cAc/cCc	4/47	NA	2	FACETS	0.971	0.899	1			1	INDETERMINATE	1	TRUE	NA	0.636473414945004	2		363	560	SUCCESS
APC	324	MSKCC	GRCh37	5	112173310	112173310	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	97	180	0	ENST00000257430.4:c.2019T>G	p.Ser673Arg	p.S673R	ENST00000257430	NM_000038.5	673	agT/agG	16/16	0.636473414945004	3	FACETS	1	0.91	1			1	CLONAL	1	TRUE	NA	0.636473414945004	3		180	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0049116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	467	604	0	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	0.664261741590732	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.824704277731034	1		604	600	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518190	103518190	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs371246879	NA	P-0049116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	155	276	1	ENST00000355739.4:c.2128G>C	p.Val710Leu	p.V710L	ENST00000355739	NM_000123.3	710	Gtg/Ctg	9/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.824704277731034	2		277	345	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890098	76890099	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAA	novel	NA	P-0049116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	177	368	0	ENST00000373344.5:c.4793_4795dup	p.Leu1598_Gly1599insVal	p.L1598_G1599insV	ENST00000373344	NM_000489.3	1599	ggt/gTTGgt	17/35	0.824704277731034	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.824704277731034	1		368	246	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0049750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	95	738	0	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.22	2		738	852	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0049750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	489	711	2	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.3	5	FACETS	0.936	0.897	0.976			1	CLONAL	5	TRUE	NA	0.22	5		713	1263	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391183	89391183	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	29	379	0	ENST00000336596.2:c.1249G>A	p.Glu417Lys	p.E417K	ENST00000336596	NM_005233.5	417	Gag/Aag	5/17	1	2	FACETS	0.541	0.434	0.664	0.541	0.434	0.664	SUBCLONAL	1	TRUE	1	0.22	2		379	487	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842471	68842471	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1131690808	NA	P-0050062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	54	529	0	ENST00000261769.5:c.531+1G>A		p.X177_splice	ENST00000261769	NM_004360.3	177			1	2	FACETS	0.82	0.698	0.953	0.82	0.698	0.953	CLONAL	1	FALSE	1	0.162043751106667	2		529	813	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542012	187542012	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	39	453	0	ENST00000441802.2:c.5728G>T	p.Ala1910Ser	p.A1910S	ENST00000441802	NM_005245.3	1910	Gca/Tca	10/27	1	2	FACETS	0.634	0.524	0.758	0.634	0.524	0.758	SUBCLONAL	1	FALSE	1	0.162043751106667	2		453	759	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0050489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	210	556	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.24903408665692	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.24903408665692	2		556	823	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110022	115110023	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0050489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	71	740	1	ENST00000257566.3:c.1855_1856delinsAA	p.Ala619Asn	p.A619N	ENST00000257566	NM_016569.3	619	GCc/AAc	8/8	0.132863496016045	4	FACETS	0.703	0.612	0.802	0.352	0.306	0.401	INDETERMINATE	1	TRUE	2	0.24903408665692	4		741	1013	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847267	68847268	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAGTGACTG	novel	NA	P-0050489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	113	391	0	ENST00000261769.5:c.1191_1199dup	p.Thr399_Asp400insGluValThr	p.T399_D400insEVT	ENST00000261769	NM_004360.3	397	aaa/aAAGTGACTGaa	9/16	0.153429278407726	4	FACETS	0.785	0.707	0.868	0.785	0.707	0.868	SUBCLONAL	2	TRUE	2	0.24903408665692	4		391	722	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087889	27087910	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCGGCCACCCAGTGGCCAGT	CCTCGGCCACCCAGTGGCCAGT	GCCAGC	novel	NA	P-0050489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	229	429	1	ENST00000324856.7:c.2176_2197delinsGCCAGC	p.Pro726AlafsTer11	p.P726Afs*11	ENST00000324856	NM_006015.4	726	CCTCGGCCACCCAGTGGCCAGTcg/GCCAGCcg	6/20	0.179964862229765	3	FACETS	1	0.987	1	0.819	0.765	0.874	CLONAL	2	TRUE	0	0.24903408665692	3		430	842	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0050489-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	73	556	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	1	2	FACETS	0.981	0.858	1	0.981	0.858	1	CLONAL	1	TRUE	1	0.24	2		556	620	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847267	68847268	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAGTGACTG	novel	NA	P-0050489-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	46	391	0	ENST00000261769.5:c.1191_1199dup	p.Thr399_Asp400insGluValThr	p.T399_D400insEVT	ENST00000261769	NM_004360.3	397	aaa/aAAGTGACTGaa	9/16	1	2	FACETS	0.666	0.56	0.782	0.666	0.56	0.782	SUBCLONAL	1	TRUE	1	0.24	2		391	576	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087889	27087910	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCGGCCACCCAGTGGCCAGT	CCTCGGCCACCCAGTGGCCAGT	GCCAGC	novel	NA	P-0050489-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	89	429	1	ENST00000324856.7:c.2176_2197delinsGCCAGC	p.Pro726AlafsTer11	p.P726Afs*11	ENST00000324856	NM_006015.4	726	CCTCGGCCACCCAGTGGCCAGTcg/GCCAGCcg	6/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.24	2		430	610	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977949	134977949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56186270	NA	P-0051005-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	21	286	0	ENST00000398015.3:c.2942C>T	p.Thr981Met	p.T981M	ENST00000398015	NM_004441.4	981	aCg/aTg	16/16	0.264629915366455	2	FACETS	0.576	0.448	0.723	0.288	0.224	0.362	INDETERMINATE	1	TRUE	0	0.476268535399583	2		286	153	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89815074	89815074	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051005-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	44	267	0	ENST00000389301.3:c.3341C>G	p.Ser1114Cys	p.S1114C	ENST00000389301	NM_000135.2	1114	tCt/tGt	33/43	0.116502688680864	4	FACETS	1	0.875	1	0.521	0.439	0.609	INDETERMINATE	1	TRUE	2	0.476268535399583	4		267	262	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432435	49432435	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051005-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	67	397	0	ENST00000301067.7:c.8704C>T	p.Gln2902Ter	p.Q2902*	ENST00000301067	NM_003482.3	2902	Cag/Tag	34/54	0.218826369206705	4	FACETS	1	0.96	1	0.416	0.364	0.471	INDETERMINATE	1	TRUE	1	0.476268535399583	4		397	333	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539619	187539619	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051005-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	20	393	0	ENST00000441802.2:c.8121C>A	p.Phe2707Leu	p.F2707L	ENST00000441802	NM_005245.3	2707	ttC/ttA	10/27	0.149195668099001	2	FACETS	0.506	0.389	0.64	0.253	0.194	0.32	INDETERMINATE	1	TRUE	0	0.476268535399583	2		393	166	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456650	138456650	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs750830394	NA	P-0051005-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	43	256	0	ENST00000289153.2:c.700A>G	p.Ile234Val	p.I234V	ENST00000289153	NM_006219.2	234	Att/Gtt	4/22	0.264629915366455	2	FACETS	1	0.951	1	0.65	0.555	0.749	INDETERMINATE	1	TRUE	0	0.476268535399583	2		256	139	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432335	49432335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051005-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	50	477	0	ENST00000301067.7:c.8804C>T	p.Ser2935Leu	p.S2935L	ENST00000301067	NM_003482.3	2935	tCa/tTa	34/54	0.218826369206705	4	FACETS	0.948	0.808	1	0.316	0.269	0.367	INDETERMINATE	1	TRUE	1	0.476268535399583	4		477	327	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432354	49432354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051005-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	60	447	0	ENST00000301067.7:c.8785C>T	p.Leu2929Phe	p.L2929F	ENST00000301067	NM_003482.3	2929	Ctt/Ttt	34/54	0.218826369206705	4	FACETS	1	0.889	1	0.343	0.297	0.393	INDETERMINATE	1	TRUE	1	0.476268535399583	4		447	361	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432359	49432359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051005-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	61	441	0	ENST00000301067.7:c.8780C>T	p.Ser2927Leu	p.S2927L	ENST00000301067	NM_003482.3	2927	tCa/tTa	34/54	0.218826369206705	4	FACETS	1	0.884	1	0.341	0.295	0.39	INDETERMINATE	1	TRUE	1	0.476268535399583	4		441	370	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432703	49432704	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCTG	novel	NA	P-0051005-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	130	431	0	ENST00000301067.7:c.8431_8435dup	p.Gln2812HisfsTer41	p.Q2812Hfs*41	ENST00000301067	NM_003482.3	2812	cag/caCAGCAg	34/54	0.218826369206705	4	FACETS	0.881	0.812	0.951	0.881	0.812	0.951	INDETERMINATE	3	TRUE	1	0.476268535399583	4		431	305	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680645	88680645	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051005-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	24	254	0	ENST00000360948.2:c.612C>G	p.Ile204Met	p.I204M	ENST00000360948	NM_001012338.2	204	atC/atG	6/19	0.262848915685784	1	FACETS	0.415	0.327	0.514	0.415	0.327	0.514	INDETERMINATE	1	TRUE	0	0.476268535399583	1		254	185	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89815112	89815112	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051005-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	36	283	0	ENST00000389301.3:c.3303C>G	p.Ile1101Met	p.I1101M	ENST00000389301	NM_000135.2	1101	atC/atG	33/43	0.116502688680864	4	FACETS	0.803	0.663	0.958	0.401	0.331	0.479	INDETERMINATE	1	TRUE	2	0.476268535399583	4		283	278	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873688	35873688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051005-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	15	280	0	ENST00000303115.3:c.644G>A	p.Gly215Asp	p.G215D	ENST00000303115	NM_002185.3	215	gGc/gAc	5/8	0.476268535399583	3	FACETS	0.396	0.29	0.522	0.198	0.145	0.261	SUBCLONAL	1	TRUE	1	0.476268535399583	3		280	197	SUCCESS
AR	367	MSKCC	GRCh37	X	66766357	66766380	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGCGGCGGCGGCGGCGGC	GGCGGCGGCGGCGGCGGCGGCGGC	-	rs746853821	NA	P-0051086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	10	69	0	ENST00000374690.3:c.1397_1420del	p.Gly466_Gly473del	p.G466_G473del	ENST00000374690	NM_000044.3	457	GGCGGCGGCGGCGGCGGCGGCGGC/-	1/8	1	2	FACETS	0.836	0.571	1	0.836	0.571	1	CLONAL	1	TRUE	1	0.23687027988942	2		69	101	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671657	30671657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs574552499	NA	P-0051086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	103	589	0	ENST00000376406.3:c.5303C>T	p.Thr1768Ile	p.T1768I	ENST00000376406	NM_014641.2	1768	aCa/aTa	10/15	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.23687027988942	2		589	775	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578518	7578518	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934875	NA	P-0051258-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	85	758	0	ENST00000269305.4:c.412G>C	p.Ala138Pro	p.A138P	ENST00000269305	NM_001126112.2	138	Gcc/Ccc	5/11	1	2	FACETS	0.537	0.474	0.606	0.537	0.474	0.606	SUBCLONAL	1	TRUE	1	0.307437074199598	2		758	1029	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593371	67593373	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0051258-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	45	611	0	ENST00000274335.5:c.2119_2121del	p.Asn707del	p.N707del	ENST00000274335		706	cACAac/cac	15/15	1	2	FACETS	0.355	0.297	0.419	0.355	0.297	0.419	SUBCLONAL	1	TRUE	1	0.307437074199598	2		611	825	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0051842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	529	715	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.549404048384329	3	FACETS	0.894	0.865	0.922	0.894	0.865	0.922	CLONAL	3	FALSE	0	0.612891236063535	3		715	841	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0052087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	308	739	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.393690931434002	2	FACETS	0.888	0.84	0.936	0.888	0.84	0.936	CLONAL	2	TRUE	0	0.395662399400992	2		741	877	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593573	215593573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554708247	NA	P-0052087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	110	531	2	ENST00000260947.4:c.2161G>A	p.Ala721Thr	p.A721T	ENST00000260947	NM_000465.2	721	Gca/Aca	11/11	0.395662399400992	3	FACETS	0.788	0.708	0.874	0.394	0.354	0.437	SUBCLONAL	1	TRUE	1	0.395662399400992	3		533	845	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818322	43818322	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	57	815	0	ENST00000372470.3:c.1787C>A	p.Pro596His	p.P596H	ENST00000372470	NM_005373.2	596	cCt/cAt	12/12	1	2	FACETS	0.267	0.228	0.31	0.267	0.228	0.31	SUBCLONAL	1	TRUE	1	0.395662399400992	2		815	1078	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940348	49940348	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	206	858	0	ENST00000296474.3:c.695T>C	p.Phe232Ser	p.F232S	ENST00000296474	NM_002447.2	232	tTt/tCt	1/20	0.248435426072733	3	FACETS	0.987	0.914	1	0.493	0.457	0.532	CLONAL	1	TRUE	1	0.395662399400992	3		858	1264	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64288414	64288414	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0052087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	14	340	1	ENST00000370651.3:c.178A>T	p.Lys60Ter	p.K60*	ENST00000370651	NM_003463.4	60	Aaa/Taa	3/6	0.136301600241374	3	FACETS	0.307	0.221	0.411	0.102	0.073	0.137	INDETERMINATE	1	TRUE	0	0.395662399400992	3		341	276	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	151	737	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.665671648452111	2		737	419	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023064	27023079	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGCGAGGGCCCCGC	AAAGCGAGGGCCCCGC	-	novel	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	17	140	0	ENST00000324856.7:c.170_185del	p.Glu57AlafsTer39	p.E57Afs*39	ENST00000324856	NM_006015.4	57	gAAAGCGAGGGCCCCGCc/gc	1/20	0.471222246295719	1	FACETS	0.268	0.202	0.345	0.268	0.202	0.345	SUBCLONAL	1	TRUE	0	0.665671648452111	1		140	127	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023633	27023634	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCGGCTC	novel	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	130	455	0	ENST00000324856.7:c.741_747dup	p.Lys250ArgfsTer152	p.K250Rfs*152	ENST00000324856	NM_006015.4	247	gcc/gCCGGCTCcc	1/20	0.471222246295719	1	FACETS	0.617	0.565	0.672	0.617	0.565	0.672	SUBCLONAL	1	TRUE	0	0.665671648452111	1		455	422	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101468	27101468	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	128	577	0	ENST00000324856.7:c.4750C>T	p.Gln1584Ter	p.Q1584*	ENST00000324856	NM_006015.4	1584	Cag/Tag	18/20	0.471222246295719	1	FACETS	0.416	0.378	0.456	0.416	0.378	0.456	SUBCLONAL	1	TRUE	0	0.665671648452111	1		577	617	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	274	619	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.665671648452111	2		619	813	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63810704	63810704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	189	382	0	ENST00000279873.7:c.791C>T	p.Ser264Leu	p.S264L	ENST00000279873	NM_032199.2	264	tCa/tTa	5/10	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.665671648452111	2		382	566	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141801	108141801	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	81	416	0	ENST00000278616.4:c.2849T>C	p.Leu950Pro	p.L950P	ENST00000278616	NM_000051.3	950	cTt/cCt	19/63	0.410626070135016	1	FACETS	0.342	0.302	0.384	0.342	0.302	0.384	SUBCLONAL	1	TRUE	0	0.665671648452111	1		416	475	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343496	118343496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	71	471	0	ENST00000534358.1:c.1622G>A	p.Arg541Lys	p.R541K	ENST00000534358	NM_005933.3	541	aGa/aAa	3/36	0.410626070135016	1	FACETS	0.359	0.315	0.407	0.359	0.315	0.407	SUBCLONAL	1	TRUE	0	0.665671648452111	1		471	396	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372407	118372407	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	90	467	1	ENST00000534358.1:c.6340C>T	p.Gln2114Ter	p.Q2114*	ENST00000534358	NM_005933.3	2114	Caa/Taa	26/36	0.410626070135016	1	FACETS	0.376	0.335	0.42	0.376	0.335	0.42	SUBCLONAL	1	TRUE	0	0.665671648452111	1		468	480	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420493	49420493	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs727503979	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	95	724	0	ENST00000301067.7:c.15256C>T	p.Arg5086Ter	p.R5086*	ENST00000301067	NM_003482.3	5086	Cga/Tga	48/54	0.410626070135016	1	FACETS	0.318	0.284	0.355	0.318	0.284	0.355	SUBCLONAL	1	TRUE	0	0.665671648452111	1		724	598	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69230490	69230528	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TACAGATTCATTTGAAGAAGATCCTGAAATTTCCTTAGC	TACAGATTCATTTGAAGAAGATCCTGAAATTTCCTTAGC	-	novel	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	56	400	0	ENST00000462284.1:c.880_918del	p.Thr294_Ala306del	p.T294_A306del	ENST00000462284	NM_002392.5	293	gaTACAGATTCATTTGAAGAAGATCCTGAAATTTCCTTAGCt/gat	10/11	0.410626070135016	1	FACETS	0.276	0.237	0.319	0.276	0.237	0.319	SUBCLONAL	1	TRUE	0	0.665671648452111	1		400	406	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910542	32910542	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	150	333	0	ENST00000380152.3:c.2050C>T	p.Gln684Ter	p.Q684*	ENST00000380152		684	Cag/Tag	11/27	1	2	FACETS	0.973	0.897	1	0.973	0.897	1	CLONAL	1	TRUE	1	0.665671648452111	2		333	463	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060763	38060763	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1286708161	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	342	842	0	ENST00000250448.2:c.1226C>T	p.Ser409Leu	p.S409L	ENST00000250448	NM_004496.3	409	tCg/tTg	2/2	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.665671648452111	2		842	953	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647819	3647819	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	217	681	1	ENST00000294008.3:c.1345G>A	p.Glu449Lys	p.E449K	ENST00000294008	NM_032444.2	449	Gag/Aag	6/15	NA	2	FACETS	0.825	0.769	0.883			1	INDETERMINATE	1	TRUE	NA	0.665671648452111	2		682	790	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858097	9858097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770546037	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	194	543	2	ENST00000330684.3:c.3304G>A	p.Glu1102Lys	p.E1102K	ENST00000330684	NM_001134407.1	1102	Gag/Aag	13/13	0.294196144597151	3	FACETS	1	0.975	1	0.553	0.513	0.593	INDETERMINATE	1	TRUE	1	0.665671648452111	3		545	703	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856020	68856020	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	203	552	0	ENST00000261769.5:c.1828C>T	p.Gln610Ter	p.Q610*	ENST00000261769	NM_004360.3	610	Cag/Tag	12/16	0.665671648452111	1	FACETS	0.976	0.918	1	0.976	0.918	1	CLONAL	1	TRUE	0	0.665671648452111	1		552	417	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349481	89349481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	234	651	0	ENST00000301030.4:c.3469G>A	p.Glu1157Lys	p.E1157K	ENST00000301030	NM_001256183.1	1157	Gag/Aag	9/13	0.665671648452111	1	FACETS	0.963	0.909	1	0.963	0.909	1	CLONAL	1	TRUE	0	0.665671648452111	1		651	487	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218538	5218538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767763908	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	225	718	0	ENST00000357368.4:c.3941G>A	p.Arg1314His	p.R1314H	ENST00000357368	NM_002850.3	1314	cGc/cAc	25/38	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.665671648452111	2		718	663	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602479	10602479	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	282	837	0	ENST00000171111.5:c.1099G>T	p.Gly367Cys	p.G367C	ENST00000171111	NM_203500.1	367	Ggc/Tgc	3/6	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.665671648452111	2		837	815	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024104	31024104	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	224	688	1	ENST00000375687.4:c.3589C>A	p.Pro1197Thr	p.P1197T	ENST00000375687	NM_015338.5	1197	Cct/Act	13/13	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.665671648452111	2		689	662	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024158	31024161	+	missense_variant	Missense_Mutation	ONP	CCAG	CCAG	TTAA	novel	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	144	665	1	ENST00000375687.4:c.3643_3646delinsTTAA	p.Pro1215_Val1216delinsLeuMet	p.P1215_V1216delinsLM	ENST00000375687	NM_015338.5	1215	CCAGtg/TTAAtg	13/13	1	2	FACETS	0.745	0.682	0.81	0.745	0.682	0.81	SUBCLONAL	1	TRUE	1	0.665671648452111	2		666	581	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36024580	36024580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	219	705	0	ENST00000358208.4:c.569C>T	p.Ser190Leu	p.S190L	ENST00000358208		190	tCa/tTa	6/12	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.665671648452111	2		705	645	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641301	12641301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs551466727	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	133	378	1	ENST00000251849.4:c.997C>T	p.Arg333Cys	p.R333C	ENST00000251849	NM_002880.3	333	Cgt/Tgt	10/17	1	2	FACETS	0.972	0.891	1	0.972	0.891	1	CLONAL	1	TRUE	1	0.665671648452111	2		379	411	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162539	47162539	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	148	380	0	ENST00000409792.3:c.3587C>G	p.Ser1196Cys	p.S1196C	ENST00000409792	NM_014159.6	1196	tCt/tGt	3/21	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.665671648452111	2		380	416	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723618	49723618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	86	205	0	ENST00000449682.2:c.1024C>T	p.Arg342Trp	p.R342W	ENST00000449682	NM_020998.3	342	Cgg/Tgg	9/18	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.665671648452111	2		205	221	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129926	55129926	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	192	553	0	ENST00000257290.5:c.460G>C	p.Asp154His	p.D154H	ENST00000257290	NM_006206.4	154	Gat/Cat	4/23	1	2	FACETS	0.877	0.814	0.941	0.877	0.814	0.941	CLONAL	1	TRUE	1	0.665671648452111	2		553	658	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31521270	31521270	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	257	534	0	ENST00000344624.3:c.907C>G	p.Leu303Val	p.L303V	ENST00000344624		303	Ctg/Gtg	3/33	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.665671648452111	2		534	745	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959969	38959969	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	133	287	0	ENST00000357387.3:c.1963C>G	p.Leu655Val	p.L655V	ENST00000357387	NM_152756.3	655	Ctt/Gtt	21/38	1	2	FACETS	0.89	0.815	0.968	0.89	0.815	0.968	CLONAL	1	TRUE	1	0.665671648452111	2		287	449	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562418	176562418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	241	584	0	ENST00000439151.2:c.314C>T	p.Ser105Leu	p.S105L	ENST00000439151	NM_022455.4	105	tCa/tTa	2/23	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.665671648452111	2		584	708	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940250	31940250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1358401217	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	150	700	0	ENST00000375333.2:c.392G>A	p.Arg131Gln	p.R131Q	ENST00000375333	NM_032454.1	131	cGa/cAa	2/8	0.633677896373576	3	FACETS	0.519	0.473	0.567	0.26	0.236	0.284	SUBCLONAL	1	TRUE	1	0.665671648452111	3		700	1157	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869011	117869011	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	83	365	0	ENST00000297338.2:c.689-1G>C		p.X230_splice	ENST00000297338	NM_006265.2	230			0.665671648452111	3	FACETS	0.487	0.43	0.549	0.244	0.215	0.275	SUBCLONAL	1	TRUE	1	0.665671648452111	3		365	682	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750755	128750755	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	207	696	0	ENST00000377970.2:c.292C>T	p.Arg98Trp	p.R98W	ENST00000377970	NM_002467.4	98	Cgg/Tgg	2/3	0.665671648452111	3	FACETS	0.943	0.876	1	0.472	0.438	0.506	CLONAL	1	TRUE	1	0.665671648452111	3		696	879	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916538	39916538	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	267	327	1	ENST00000378444.4:c.4465G>A	p.Asp1489Asn	p.D1489N	ENST00000378444	NM_001123385.1	1489	Gat/Aat	11/15	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.665671648452111	1		328	399	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239915	53239915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	255	331	0	ENST00000375401.3:c.1526C>T	p.Ser509Leu	p.S509L	ENST00000375401	NM_004187.3	509	tCa/tTa	11/26	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.665671648452111	1		331	372	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0052279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	433	443	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.263559024334572	6	FACETS	0.971	0.929	1	0.971	0.929	1	CLONAL	5	TRUE	1	0.263559024334572	6		443	1033	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056769	102056769	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	83	244	0	ENST00000282441.5:c.709G>C	p.Glu237Gln	p.E237Q	ENST00000282441	NM_001130145.2	237	Gaa/Caa	4/9	0.263559024334572	4	FACETS	1	0.894	1	0.504	0.447	0.564	CLONAL	2	TRUE	0	0.263559024334572	4		244	395	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044534	47044537	+	frameshift_variant	Frame_Shift_Del	DEL	CTCC	CTCC	-	novel	NA	P-0052279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	120	607	0	ENST00000377604.3:c.2033_2036del	p.Ser678CysfsTer25	p.S678Cfs*25	ENST00000377604	NM_001204468.1	677	agCTCC/ag	18/24	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.263559024334572	2		607	793	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650869	37650870	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	G	novel	NA	P-0052279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	95	507	0	ENST00000447079.4:c.2341_2342delinsG	p.Leu781GlufsTer9	p.L781Efs*9	ENST00000447079	NM_015083.1	781	TTa/Ga	5/14	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.263559024334572	2		507	677	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	261	532	3	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	1	2	FACETS	0.955	0.899	1	0.955	0.899	1	CLONAL	1	TRUE	1	0.746598633533345	2		535	732	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806119	1806119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931614	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	309	606	0	ENST00000260795.2:c.1138G>A	p.Gly380Arg	p.G380R	ENST00000260795		380	Ggg/Agg	8/17	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.746598633533345	2		606	827	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475550	12475550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479145908	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	569	556	0	ENST00000287820.6:c.1424C>T	p.Thr475Met	p.T475M	ENST00000287820	NM_015869.4	475	aCg/aTg	7/7	0.746598633533345	3	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.746598633533345	3		556	995	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266570	115266570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	219	497	1	ENST00000438362.2:c.1945C>T	p.Arg649Cys	p.R649C	ENST00000438362	NM_001242891.1	649	Cgc/Tgc	16/20	1	2	FACETS	0.897	0.839	0.956	0.897	0.839	0.956	CLONAL	1	TRUE	1	0.746598633533345	2		498	654	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	43	586	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.162	0.135	0.192	0.162	0.135	0.192	SUBCLONAL	1	TRUE	1	0.746598633533345	2		586	711	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	199	461	7	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.766	0.712	0.821	0.766	0.712	0.821	SUBCLONAL	1	TRUE	1	0.746598633533345	2		468	696	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250883	153250883	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	207	373	1	ENST00000281708.4:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000281708	NM_033632.3	393	Cga/Tga	8/12	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.746598633533345	2		374	501	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637210	176637210	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784076	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	46	563	0	ENST00000439151.2:c.1810C>T	p.Arg604Ter	p.R604*	ENST00000439151	NM_022455.4	604	Cga/Tga	5/23	1	2	FACETS	0.161	0.135	0.19	0.161	0.135	0.19	SUBCLONAL	1	TRUE	1	0.746598633533345	2		563	765	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138729528	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	313	572	0	ENST00000269305.4:c.523C>T	p.Arg175Cys	p.R175C	ENST00000269305	NM_001126112.2	175	Cgc/Tgc	5/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.746598633533345	2		572	827	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506690	103506690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs4987063	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	37	259	0	ENST00000355739.4:c.433G>A	p.Val145Ile	p.V145I	ENST00000355739	NM_000123.3	145	Gtt/Att	4/15	1	2	FACETS	0.245	0.202	0.294	0.245	0.202	0.294	SUBCLONAL	1	TRUE	1	0.746598633533345	2		259	404	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	207	416	0	ENST00000335508.6:c.2704G>C	p.Glu902Gln	p.E902Q	ENST00000335508	NM_012433.2	902	Gaa/Caa	18/25	NA	2	FACETS	0.932	0.871	0.995			1	INDETERMINATE	1	TRUE	NA	0.746598633533345	2		416	595	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	250	451	0	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.746598633533345	2		451	668	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397743	49397743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	301	483	0	ENST00000418115.1:c.481G>A	p.Ala161Thr	p.A161T	ENST00000418115	NM_001664.2	161	Gca/Aca	5/5	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.746598633533345	2		483	768	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691872	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs79375991	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	338	492	18	ENST00000295754.5:c.383del	p.Lys128SerfsTer35	p.K128Sfs*35	ENST00000295754	NM_003242.5	125	gAa/ga	3/7	1	2	FACETS	0.866	0.832	0.899	1	0.996	1	CLONAL	2	TRUE	1	0.746598633533345	2		510	523	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134251	11134251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218643327	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	309	585	1	ENST00000358026.2:c.2917C>T	p.Arg973Trp	p.R973W	ENST00000358026	NM_001128849.1	973	Cgg/Tgg	20/36	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.746598633533345	2		586	762	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23635370	23635370	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45624036	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	261	536	0	ENST00000261584.4:c.2794G>A	p.Val932Met	p.V932M	ENST00000261584	NM_024675.3	932	Gtg/Atg	8/13	1	2	FACETS	0.921	0.867	0.977	0.921	0.867	0.977	CLONAL	1	TRUE	1	0.746598633533345	2		536	759	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209511	98209511	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	287	604	0	ENST00000331920.6:c.4027G>T	p.Gly1343Trp	p.G1343W	ENST00000331920	NM_000264.3	1343	Ggg/Tgg	23/24	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.746598633533345	2		604	747	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971110	21971110	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519881	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	150	221	0	ENST00000304494.5:c.248A>G	p.His83Arg	p.H83R	ENST00000304494	NM_000077.4	83	cAc/cGc	2/3	0.585484101972339	2	FACETS	0.834	0.783	0.883	0.834	0.783	0.883	CLONAL	2	TRUE	0	0.746598633533345	2		221	241	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498424	89498424	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1176464192	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	155	373	0	ENST00000336596.2:c.2396G>A	p.Arg799His	p.R799H	ENST00000336596	NM_005233.5	799	cGc/cAc	14/17	1	2	FACETS	0.993	0.919	1	0.993	0.919	1	CLONAL	1	TRUE	1	0.746598633533345	2		373	418	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707797	176707797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886041219	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	167	319	3	ENST00000439151.2:c.5854C>T	p.Arg1952Trp	p.R1952W	ENST00000439151	NM_022455.4	1952	Cgg/Tgg	18/23	1	2	FACETS	0.946	0.877	1	0.946	0.877	1	CLONAL	1	TRUE	1	0.746598633533345	2		322	473	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060911	38060912	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	196	384	1	ENST00000250448.2:c.1077dup	p.Ile360HisfsTer55	p.I360Hfs*55	ENST00000250448	NM_004496.3	359	-/C	2/2	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.746598633533345	2		385	501	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489534	56489534	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	280	494	1	ENST00000267101.3:c.1999C>A	p.Arg667Ser	p.R667S	ENST00000267101	NM_001982.3	667	Cgt/Agt	17/28	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.746598633533345	2		495	728	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	264	660	2	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.956	0.9	1	0.956	0.9	1	CLONAL	1	TRUE	1	0.746598633533345	2		662	740	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017737	31017737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	268	496	0	ENST00000375687.4:c.599G>A	p.Gly200Asp	p.G200D	ENST00000375687	NM_015338.5	200	gGc/gAc	8/13	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.746598633533345	2		496	659	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295176	1295176	+	upstream_gene_variant	5'Flank	SNP	G	G	C	novel	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	51	138	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.859	0.745	0.979	0.859	0.745	0.979	CLONAL	1	TRUE	1	0.746598633533345	2		138	159	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89871774	89871774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144420697	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	287	535	1	ENST00000389301.3:c.623C>T	p.Ser208Leu	p.S208L	ENST00000389301	NM_000135.2	208	tCg/tTg	7/43	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.746598633533345	2		536	751	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556657	41556657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	627	453	1	ENST00000263253.7:c.3602G>A	p.Cys1201Tyr	p.C1201Y	ENST00000263253	NM_001429.3	1201	tGt/tAt	20/31	0.746598633533345	5	FACETS	0.918	0.886	0.949			1	CLONAL	3	TRUE	NA	0.746598633533345	5		454	1293	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694712	176694712	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	27	381	1	ENST00000439151.2:c.5296C>T	p.Arg1766Ter	p.R1766*	ENST00000439151	NM_022455.4	1766	Cga/Tga	15/23	1	2	FACETS	0.136	0.108	0.169	0.136	0.108	0.169	SUBCLONAL	1	TRUE	1	0.746598633533345	2		382	532	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164596	36164596	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	156	191	1	ENST00000300305.3:c.1279C>T	p.Arg427Cys	p.R427C	ENST00000300305		427	Cgc/Tgc	8/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.746598633533345	2		192	352	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605102	46605102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540130771	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	68	602	1	ENST00000263734.3:c.1319C>T	p.Thr440Met	p.T440M	ENST00000263734	NM_001430.4	440	aCg/aTg	10/16	1	2	FACETS	0.224	0.194	0.256	0.224	0.194	0.256	SUBCLONAL	1	TRUE	1	0.746598633533345	2		603	813	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3645686	3645686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769084265	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	298	604	0	ENST00000294008.3:c.1933G>A	p.Val645Met	p.V645M	ENST00000294008	NM_032444.2	645	Gtg/Atg	9/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.746598633533345	2		604	742	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638467	176638467	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784095	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	115	669	2	ENST00000439151.2:c.3067C>T	p.Arg1023Ter	p.R1023*	ENST00000439151	NM_022455.4	1023	Cga/Tga	5/23	1	2	FACETS	0.341	0.307	0.378	0.341	0.307	0.378	SUBCLONAL	1	TRUE	1	0.746598633533345	2		671	903	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021749	69021749	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	449	481	0	ENST00000288368.4:c.3037T>C	p.Tyr1013His	p.Y1013H	ENST00000288368	NM_024870.2	1013	Tat/Cat	25/40	0.745656353367341	3	FACETS	0.987	0.949	1	0.987	0.949	1	CLONAL	2	TRUE	1	0.746598633533345	3		481	837	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295181	1295181	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1195843544	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	52	139	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.905	0.787	1	0.905	0.787	1	CLONAL	1	TRUE	1	0.746598633533345	2		139	154	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784401	9784401	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773911101	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	318	567	0	ENST00000377346.4:c.2786G>A	p.Arg929His	p.R929H	ENST00000377346	NM_005026.3	929	cGt/cAt	22/24	1	2	FACETS	0.993	0.941	1	0.993	0.941	1	CLONAL	1	TRUE	1	0.746598633533345	2		567	858	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257332	16257332	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	290	559	0	ENST00000375759.3:c.4597A>G	p.Ser1533Gly	p.S1533G	ENST00000375759	NM_015001.2	1533	Agc/Ggc	11/15	1	2	FACETS	0.963	0.909	1	0.963	0.909	1	CLONAL	1	TRUE	1	0.746598633533345	2		559	807	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981305	201981306	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	545	520	0	ENST00000359651.3:c.385dup	p.Thr129AsnfsTer6	p.T129Nfs*6	ENST00000359651		128	-/A	2/8	0.745656353367341	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.746598633533345	3		520	993	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226566862	226566862	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	252	475	0	ENST00000366794.5:c.1726G>T	p.Glu576Ter	p.E576*	ENST00000366794	NM_001618.3	576	Gag/Tag	12/23	0.745656353367341	3	FACETS	1	0.975	1	0.537	0.504	0.572	CLONAL	1	TRUE	1	0.746598633533345	3		475	863	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665859	241665859	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	204	422	0	ENST00000366560.3:c.1120C>G	p.Pro374Ala	p.P374A	ENST00000366560	NM_000143.3	374	Cct/Gct	8/10	0.745656353367341	3	FACETS	0.963	0.896	1	0.482	0.448	0.517	CLONAL	1	TRUE	1	0.746598633533345	3		422	779	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097685	8097685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	37	235	0	ENST00000346208.3:c.67C>T	p.His23Tyr	p.H23Y	ENST00000346208		23	Cac/Tac	2/6	1	2	FACETS	0.218	0.179	0.261	0.218	0.179	0.261	SUBCLONAL	1	TRUE	1	0.746598633533345	2		235	455	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534229	534229	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	300	595	0	ENST00000451590.1:c.94T>C	p.Tyr32His	p.Y32H	ENST00000451590	NM_001130442.1	32	Tac/Cac	2/5	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.746598633533345	2		595	785	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433119	49433119	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1336704788	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	302	621	0	ENST00000301067.7:c.8252T>C	p.Leu2751Ser	p.L2751S	ENST00000301067	NM_003482.3	2751	tTg/tCg	33/54	1	2	FACETS	0.988	0.935	1	0.988	0.935	1	CLONAL	1	TRUE	1	0.746598633533345	2		621	819	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656627	3656627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	269	699	1	ENST00000294008.3:c.608C>T	p.Pro203Leu	p.P203L	ENST00000294008	NM_032444.2	203	cCc/cTc	3/15	1	2	FACETS	0.824	0.775	0.875	0.824	0.775	0.875	CLONAL	1	TRUE	1	0.746598633533345	2		700	874	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805641	89805641	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	288	601	0	ENST00000389301.3:c.4067T>C	p.Val1356Ala	p.V1356A	ENST00000389301	NM_000135.2	1356	gTt/gCt	41/43	1	2	FACETS	0.918	0.867	0.971	0.918	0.867	0.971	CLONAL	1	TRUE	1	0.746598633533345	2		601	840	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578178	7578178	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs1131691028	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	106	557	0	ENST00000269305.4:c.671A>C	p.Glu224Ala	p.E224A	ENST00000269305	NM_001126112.2	224	gAg/gCg	6/11	1	2	FACETS	0.349	0.313	0.388	0.349	0.313	0.388	SUBCLONAL	1	TRUE	1	0.746598633533345	2		557	813	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736864	736864	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	289	591	0	ENST00000314574.4:c.1235T>C	p.Ile412Thr	p.I412T	ENST00000314574	NM_005433.3	412	aTa/aCa	10/12	1	2	FACETS	0.956	0.903	1	0.956	0.903	1	CLONAL	1	TRUE	1	0.746598633533345	2		591	810	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285101	15285101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	89	433	0	ENST00000263388.2:c.4514C>T	p.Pro1505Leu	p.P1505L	ENST00000263388	NM_000435.2	1505	cCg/cTg	25/33	0.746598633533345	4	FACETS	0.37	0.327	0.416	0.123	0.109	0.139	SUBCLONAL	1	TRUE	1	0.746598633533345	4		433	1126	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972621	25972621	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	193	401	0	ENST00000435504.4:c.1804C>T	p.Gln602Ter	p.Q602*	ENST00000435504		602	Cag/Tag	12/13	1	2	FACETS	0.937	0.873	1	0.937	0.873	1	CLONAL	1	TRUE	1	0.746598633533345	2		401	552	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014325	70014325	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199578956	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	226	521	0	ENST00000394351.3:c.1186G>A	p.Val396Met	p.V396M	ENST00000394351	NM_000248.3	396	Gtg/Atg	9/9	1	2	FACETS	0.856	0.801	0.913	0.856	0.801	0.913	CLONAL	1	TRUE	1	0.746598633533345	2		521	707	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295169	1295169	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	50	127	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.87	0.753	0.992	0.87	0.753	0.992	CLONAL	1	TRUE	1	0.746598633533345	2		127	154	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206896	162206896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	42	392	0	ENST00000366898.1:c.779G>A	p.Cys260Tyr	p.C260Y	ENST00000366898	NM_004562.2	260	tGc/tAc	7/12	0.746598633533345	2	FACETS	0.214	0.178	0.254	0.107	0.089	0.127	SUBCLONAL	1	TRUE	0	0.746598633533345	2		392	526	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242695	98242695	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	208	434	0	ENST00000331920.6:c.922G>C	p.Ala308Pro	p.A308P	ENST00000331920	NM_000264.3	308	Gcc/Ccc	6/24	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.746598633533345	2		434	551	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922815	44922830	+	frameshift_variant	Frame_Shift_Del	DEL	GTCCTGCCTGCCCTGG	GTCCTGCCTGCCCTGG	-	novel	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	235	211	0	ENST00000377967.4:c.1677_1692del	p.Pro560SerfsTer28	p.P560Sfs*28	ENST00000377967	NM_021140.2	559	cGTCCTGCCTGCCCTGGg/cg	16/29	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.746598633533345	1		211	339	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945135	151945135	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	26	215	0	ENST00000262189.6:c.2384A>G	p.Asp795Gly	p.D795G	ENST00000262189	NM_170606.2	795	gAc/gGc	14/59	NA	2	FACETS	0.25	0.198	0.309			1	INDETERMINATE	1	TRUE	NA	0.746598633533345	2		215	279	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054072-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	61	737	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.623	0.542	0.71	0.623	0.542	0.71	SUBCLONAL	1	TRUE	1	0.657069380025301	2		737	298	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0054072-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	115	309	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.657069380025301	2		309	345	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574959	41574959	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	novel	NA	P-0054072-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	152	566	1	ENST00000263253.7:c.7244A>G	p.Ter2415TrpextTer30	p.*2415Wext*30	ENST00000263253	NM_001429.3	2415	tAg/tGg	31/31	1	2	FACETS	0.832	0.765	0.901	0.832	0.765	0.901	CLONAL	1	TRUE	1	0.657069380025301	2		567	556	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435622	18435622	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754864262	NA	P-0054072-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	24	339	0	ENST00000266497.5:c.607C>T	p.Pro203Ser	p.P203S	ENST00000266497		203	Cca/Tca	1/31	1	2	FACETS	0.172	0.134	0.215	0.172	0.134	0.215	SUBCLONAL	1	TRUE	1	0.657069380025301	2		339	425	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	87	305	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.34	2		305	496	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	93	512	6	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.961	0.857	1	0.961	0.857	1	CLONAL	1	TRUE	1	0.34	2		518	569	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572092	64572093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767319284	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	113	795	1	ENST00000312049.6:c.1546dup	p.Arg516ProfsTer15	p.R516Pfs*15	ENST00000312049	NM_130799.2	516	cgg/cCgg	10/10	1	2	FACETS	0.785	0.706	0.869	0.785	0.706	0.869	SUBCLONAL	1	TRUE	1	0.34	2		796	847	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	137	320	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.999	0.909	1	0.999	0.909	1	CLONAL	1	TRUE	1	0.34	2		325	807	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785963	135785964	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs118203506	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	85	613	0	ENST00000298552.3:c.1257dup	p.Arg420GlnfsTer22	p.R420Qfs*22	ENST00000298552	NM_001162426.1	419	-/C	12/23	1	2	FACETS	0.668	0.59	0.752	0.668	0.59	0.752	SUBCLONAL	1	TRUE	1	0.34	2		613	748	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	46	892	7	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.331	0.278	0.391	0.331	0.278	0.391	SUBCLONAL	1	TRUE	1	0.34	2		899	817	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374293	138374293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	98	437	1	ENST00000289153.2:c.3151G>A	p.Glu1051Lys	p.E1051K	ENST00000289153	NM_006219.2	1051	Gaa/Aaa	22/22	1	2	FACETS	0.794	0.708	0.885	0.794	0.708	0.885	SUBCLONAL	1	TRUE	1	0.34	2		438	726	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223796	53223796	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	142	915	0	ENST00000375401.3:c.3563G>C	p.Cys1188Ser	p.C1188S	ENST00000375401	NM_004187.3	1188	tGt/tCt	23/26	1	2	FACETS	0.902	0.822	0.987	0.902	0.822	0.987	CLONAL	1	TRUE	1	0.34	2		915	926	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911534	101911534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111426349	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	75	259	0	ENST00000374994.4:c.1459C>T	p.Arg487Trp	p.R487W	ENST00000374994	NM_004612.2	487	Cgg/Tgg	9/9	1	2	FACETS	0.947	0.832	1	0.947	0.832	1	CLONAL	1	TRUE	1	0.34	2		259	466	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348211	348211	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1458136153	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	126	962	4	ENST00000262320.3:c.1295del	p.Pro432GlnfsTer48	p.P432Qfs*48	ENST00000262320	NM_003502.3	432	cCa/ca	6/11	1	2	FACETS	0.85	0.769	0.935	0.85	0.769	0.935	CLONAL	1	TRUE	1	0.34	2		966	872	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139625	202139626	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	85	249	0	ENST00000358485.4:c.790dup	p.Val264GlyfsTer13	p.V264Gfs*13	ENST00000358485	NM_001080125.1	262	-/G	6/9	1	2	FACETS	0.992	0.88	1	0.992	0.88	1	CLONAL	1	TRUE	1	0.34	2		249	504	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835781	68835781	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060501215	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	79	486	1	ENST00000261769.5:c.377del	p.Pro126ArgfsTer89	p.P126Rfs*89	ENST00000261769	NM_004360.3	124	cgC/cg	3/16	1	2	FACETS	0.651	0.572	0.736	0.651	0.572	0.736	SUBCLONAL	1	TRUE	1	0.34	2		487	714	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513282	44513287	+	inframe_deletion	In_Frame_Del	DEL	CCACCG	CCACCG	-	rs745888281	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	106	613	1	ENST00000291552.4:c.648_653del	p.Gly222_Gly223del	p.G222_G223del	ENST00000291552	NM_006758.2	216	ggCGGTGGt/ggt	8/8	1	2	FACETS	0.659	0.59	0.733	0.659	0.59	0.733	SUBCLONAL	1	TRUE	1	0.34	2		614	946	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761459	59761460	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs774684620	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	73	374	0	ENST00000259008.2:c.2947dup	p.Ile983AsnfsTer19	p.I983Nfs*19	ENST00000259008	NM_032043.2	983	att/aAtt	20/20	1	2	FACETS	0.861	0.754	0.974	0.861	0.754	0.974	CLONAL	1	TRUE	1	0.34	2		374	499	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	90	422	0	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.939	0.835	1	0.939	0.835	1	CLONAL	1	TRUE	1	0.34	2		422	564	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462643	29462643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187200776	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	118	798	0	ENST00000389048.3:c.2258G>A	p.Arg753Gln	p.R753Q	ENST00000389048	NM_004304.4	753	cGg/cAg	13/29	1	2	FACETS	0.798	0.719	0.881	0.798	0.719	0.881	SUBCLONAL	1	TRUE	1	0.34	2		798	870	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745962	745963	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	84	410	0	ENST00000314574.4:c.559_560del	p.Ser187Ter	p.S187*	ENST00000314574	NM_005433.3	187	AGt/t	5/12	1	2	FACETS	0.873	0.772	0.98	0.873	0.772	0.98	CLONAL	1	TRUE	1	0.34	2		410	566	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862207	68862207	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	93	411	0	ENST00000261769.5:c.2295G>T	p.Gln765His	p.Q765H	ENST00000261769	NM_004360.3	765	caG/caT	14/16	1	2	FACETS	0.996	0.888	1	0.996	0.888	1	CLONAL	1	TRUE	1	0.34	2		411	549	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233239	69233240	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	70	270	1	ENST00000462284.1:c.1111dup	p.Thr371AsnfsTer5	p.T371Nfs*5	ENST00000462284	NM_002392.5	368	-/A	11/11	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.34	2		271	380	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937603	76937603	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	90	371	0	ENST00000373344.5:c.3145del	p.Ile1049Ter	p.I1049*	ENST00000373344	NM_000489.3	1049	Ata/ta	9/35	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.34	2		371	491	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158132	27158132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773256013	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	65	367	0	ENST00000380036.4:c.356G>A	p.Arg119His	p.R119H	ENST00000380036	NM_000459.3	119	cGt/cAt	2/23	1	2	FACETS	0.983	0.856	1	0.983	0.856	1	CLONAL	1	TRUE	1	0.34	2		367	389	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970914	79970915	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587776701	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	117	432	6	ENST00000265081.6:c.1148dup	p.Asn385GlnfsTer19	p.N385Qfs*19	ENST00000265081	NM_002439.4	380	-/A	7/24	1	2	FACETS	0.824	0.743	0.91	0.824	0.743	0.91	CLONAL	1	TRUE	1	0.34	2		438	835	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226826	2226826	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1259363492	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	75	441	1	ENST00000398665.3:c.4306G>A	p.Gly1436Arg	p.G1436R	ENST00000398665	NM_032482.2	1436	Gga/Aga	27/28	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.34	2		442	400	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133981	38133981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	108	452	0	ENST00000317025.8:c.3905del	p.Asn1302MetfsTer4	p.N1302Mfs*4	ENST00000317025	NM_023034.1	1302	aAt/at	23/24	1	2	FACETS	0.785	0.704	0.871	0.785	0.704	0.871	SUBCLONAL	1	TRUE	1	0.34	2		452	809	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275482	38275482	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	114	562	0	ENST00000425967.3:c.1551G>T	p.Glu517Asp	p.E517D	ENST00000425967	NM_001174067.1	517	gaG/gaT	12/19	1	2	FACETS	0.792	0.712	0.876	0.792	0.712	0.876	SUBCLONAL	1	TRUE	1	0.34	2		562	847	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129868	69129868	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776942401	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	57	311	0	ENST00000288368.4:c.4622C>T	p.Thr1541Met	p.T1541M	ENST00000288368	NM_024870.2	1541	aCg/aTg	38/40	1	2	FACETS	0.849	0.731	0.977	0.849	0.731	0.977	CLONAL	1	TRUE	1	0.34	2		311	395	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119875	70119875	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	103	593	1	ENST00000245479.2:c.877G>T	p.Glu293Ter	p.E293*	ENST00000245479	NM_000346.3	293	Gag/Tag	3/3	1	2	FACETS	0.891	0.798	0.989	0.891	0.798	0.989	CLONAL	1	TRUE	1	0.34	2		594	680	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957865	1957865	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756624618	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	122	533	0	ENST00000382891.5:c.2831G>A	p.Arg944Gln	p.R944Q	ENST00000382891	NM_133335.3	944	cGg/cAg	15/22	1	2	FACETS	0.911	0.823	1	0.911	0.823	1	CLONAL	1	TRUE	1	0.34	2		533	788	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410988	31410988	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1295265844	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	91	470	0	ENST00000344624.3:c.3532C>T	p.Arg1178Ter	p.R1178*	ENST00000344624		1178	Cga/Tga	28/33	1	2	FACETS	0.788	0.7	0.882	0.788	0.7	0.882	SUBCLONAL	1	TRUE	1	0.34	2		470	679	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79974885	79974885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35121792	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	76	324	0	ENST00000265081.6:c.1313C>T	p.Ala438Val	p.A438V	ENST00000265081	NM_002439.4	438	gCg/gTg	8/24	1	2	FACETS	0.76	0.667	0.86	0.76	0.667	0.86	SUBCLONAL	1	TRUE	1	0.34	2		324	588	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019135	31019135	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775377413	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	90	369	0	ENST00000375687.4:c.730C>T	p.Arg244Cys	p.R244C	ENST00000375687	NM_015338.5	244	Cgc/Tgc	9/13	1	2	FACETS	0.9	0.8	1	0.9	0.8	1	CLONAL	1	TRUE	1	0.34	2		369	588	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2189781	2189781	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	128	789	0	ENST00000398665.3:c.251G>A	p.Ser84Asn	p.S84N	ENST00000398665	NM_032482.2	84	aGc/aAc	4/28	1	2	FACETS	0.876	0.793	0.962	0.876	0.793	0.962	CLONAL	1	TRUE	1	0.34	2		789	860	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265675	10265675	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	69	453	0	ENST00000340748.4:c.1502T>C	p.Leu501Pro	p.L501P	ENST00000340748		501	cTg/cCg	19/40	1	2	FACETS	0.715	0.623	0.814	0.715	0.623	0.814	SUBCLONAL	1	TRUE	1	0.34	2		453	568	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809465	36809465	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	101	750	0	ENST00000373129.3:c.1000T>C	p.Ser334Pro	p.S334P	ENST00000373129	NM_032017.1	334	Tca/Cca	10/12	1	2	FACETS	0.712	0.635	0.793	0.712	0.635	0.793	SUBCLONAL	1	TRUE	1	0.34	2		750	835	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652398	206652398	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	133	720	0	ENST00000367120.3:c.1105C>A	p.His369Asn	p.H369N	ENST00000367120	NM_014002.3	369	Cac/Aac	10/22	1	2	FACETS	0.966	0.877	1	0.966	0.877	1	CLONAL	1	TRUE	1	0.34	2		720	810	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577221	64577221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224812	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	117	661	0	ENST00000312049.6:c.361G>A	p.Val121Ile	p.V121I	ENST00000312049	NM_130799.2	121	Gtc/Atc	2/10	1	2	FACETS	0.898	0.81	0.991	0.898	0.81	0.991	CLONAL	1	TRUE	1	0.34	2		661	766	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343831	118343831	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555036242	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	86	423	0	ENST00000534358.1:c.1957C>T	p.Pro653Ser	p.P653S	ENST00000534358	NM_005933.3	653	Ccc/Tcc	3/36	1	2	FACETS	0.835	0.739	0.937	0.835	0.739	0.937	CLONAL	1	TRUE	1	0.34	2		423	606	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457340	67457340	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	120	759	1	ENST00000327367.4:c.314C>T	p.Ala105Val	p.A105V	ENST00000327367	NM_005902.3	105	gCc/gTc	2/9	1	2	FACETS	0.876	0.791	0.965	0.876	0.791	0.965	CLONAL	1	TRUE	1	0.34	2		760	806	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337318	89337318	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	99	515	0	ENST00000301030.4:c.7714-1G>T		p.X2572_splice	ENST00000301030	NM_001256183.1	2572			1	2	FACETS	0.956	0.855	1	0.956	0.855	1	CLONAL	1	TRUE	1	0.34	2		515	609	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439972	56439972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	124	654	0	ENST00000407977.2:c.620G>A	p.Gly207Asp	p.G207D	ENST00000407977		207	gGc/gAc	6/10	1	2	FACETS	0.952	0.862	1	0.952	0.862	1	CLONAL	1	TRUE	1	0.34	2		654	766	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123668	11123668	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	83	621	0	ENST00000358026.2:c.2318T>C	p.Leu773Pro	p.L773P	ENST00000358026	NM_001128849.1	773	cTg/cCg	16/36	1	2	FACETS	0.655	0.578	0.739	0.655	0.578	0.739	SUBCLONAL	1	TRUE	1	0.34	2		621	745	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353774	15353774	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	90	653	0	ENST00000263377.2:c.3106C>T	p.Pro1036Ser	p.P1036S	ENST00000263377	NM_058243.2	1036	Cct/Tct	14/20	1	2	FACETS	0.812	0.721	0.909	0.812	0.721	0.909	CLONAL	1	TRUE	1	0.34	2		653	652	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729974	47729974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	95	475	0	ENST00000449228.1:c.415G>A	p.Gly139Arg	p.G139R	ENST00000449228	NM_001127240.2	139	Gga/Aga	3/4	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.34	2		475	559	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965580	25965580	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	119	566	1	ENST00000435504.4:c.3626A>G	p.Asp1209Gly	p.D1209G	ENST00000435504		1209	gAc/gGc	13/13	1	2	FACETS	0.958	0.865	1	0.958	0.865	1	CLONAL	1	TRUE	1	0.34	2		567	731	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439784	220439784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758635243	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	127	914	0	ENST00000243786.2:c.637C>T	p.Pro213Ser	p.P213S	ENST00000243786	NM_002191.3	213	Ccc/Tcc	2/2	1	2	FACETS	0.879	0.796	0.966	0.879	0.796	0.966	CLONAL	1	TRUE	1	0.34	2		914	850	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376765	31376765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	70	626	0	ENST00000328111.2:c.760G>A	p.Ala254Thr	p.A254T	ENST00000328111	NM_006892.3	254	Gct/Act	7/23	1	2	FACETS	0.635	0.554	0.724	0.635	0.554	0.724	SUBCLONAL	1	TRUE	1	0.34	2		626	648	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569805	67569805	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	69	224	0	ENST00000274335.5:c.466A>G	p.Ser156Gly	p.S156G	ENST00000274335		156	Agc/Ggc	3/15	1	2	FACETS	0.927	0.81	1	0.927	0.81	1	CLONAL	1	TRUE	1	0.34	2		224	438	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813426	32813426	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	148	810	0	ENST00000354258.4:c.2357A>G	p.His786Arg	p.H786R	ENST00000354258	NM_000593.5	786	cAc/cGc	11/11	1	2	FACETS	0.926	0.845	1	0.926	0.845	1	CLONAL	1	TRUE	1	0.34	2		810	940	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157488269	157488269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1247824233	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	65	397	0	ENST00000346085.5:c.2975C>T	p.Thr992Met	p.T992M	ENST00000346085	NM_020732.3	992	aCg/aTg	10/20	1	2	FACETS	0.707	0.613	0.808	0.707	0.613	0.808	SUBCLONAL	1	TRUE	1	0.34	2		397	541	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528657	157528657	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554238072	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	101	601	1	ENST00000346085.5:c.6382C>T	p.Arg2128Ter	p.R2128*	ENST00000346085	NM_020732.3	2128	Cga/Tga	20/20	1	2	FACETS	0.859	0.768	0.955	0.859	0.768	0.955	CLONAL	1	TRUE	1	0.34	2		602	692	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371819	116371819	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs774952152	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	76	348	0	ENST00000397752.3:c.1298A>G	p.Gln433Arg	p.Q433R	ENST00000397752	NM_000245.2	433	cAa/cGa	3/21	1	2	FACETS	0.795	0.699	0.899	0.795	0.699	0.899	SUBCLONAL	1	TRUE	1	0.34	2		348	562	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185163	123185163	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0054100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	71	322	0	ENST00000218089.9:c.1117-2A>G		p.X373_splice	ENST00000218089	NM_001042749.1	373			1	2	FACETS	0.705	0.616	0.802	0.705	0.616	0.802	SUBCLONAL	1	TRUE	1	0.34	2		322	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0054111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	82	767	0	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	0.293063795988108	1	FACETS	0.378	0.332	0.428	0.378	0.332	0.428	SUBCLONAL	1	FALSE	0	0.3	1		767	1229	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242483	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACA	AATTAAGAGAAGCAACA	TTGCT	novel	NA	P-0054111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	43	437	3	ENST00000275493.2:c.2237_2253delinsTTGCT	p.Glu746_Thr751delinsValAla	p.E746_T751delinsVA	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACA/gTTGCT	19/28	0.109537658534734	4	FACETS	0.498	0.415	0.59	0.249	0.207	0.295	INDETERMINATE	1	FALSE	2	0.3	4		440	749	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594221	55594221	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913512	NA	P-0054241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	404	418	0	ENST00000288135.5:c.1924A>G	p.Lys642Glu	p.K642E	ENST00000288135	NM_000222.2	642	Aaa/Gaa	13/21	0.914522331049481	3	FACETS	1	0.987	1			1	CLONAL	2	TRUE	NA	0.952876128097197	3		418	598	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661098	227661101	+	missense_variant	Missense_Mutation	ONP	TGCC	TGCC	CGCG	novel	NA	P-0054241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	396	1108	0	ENST00000305123.5:c.2354_2357delinsCGCG	p.Arg785_His786delinsProArg	p.R785_H786delinsPR	ENST00000305123	NM_005544.2	785	cGGCAt/cCGCGt	1/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.952876128097197	2		1108	795	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777640	9777640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148703447	NA	P-0054482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	64	797	2	ENST00000377346.4:c.976G>A	p.Glu326Lys	p.E326K	ENST00000377346	NM_005026.3	326	Gag/Aag	8/24	1	2	FACETS	0.828	0.715	0.952	0.828	0.715	0.952	CLONAL	1	TRUE	1	0.14	2		799	1104	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0054482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	20	454	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	0.471	0.358	0.603	0.471	0.358	0.603	SUBCLONAL	1	TRUE	1	0.14	2		454	607	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0054482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	10	203	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	0.772	0.523	1	0.772	0.523	1	CLONAL	1	TRUE	1	0.14	2		203	185	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0054482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	31	724	2	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.513	0.413	0.627	0.513	0.413	0.627	SUBCLONAL	1	TRUE	1	0.14	2		726	864	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0054482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	23	405	0	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	1	2	FACETS	0.575	0.447	0.725	0.575	0.447	0.725	SUBCLONAL	1	TRUE	1	0.14	2		405	571	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	33	423	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	0.824	0.67	0.999	0.824	0.67	0.999	CLONAL	1	TRUE	1	0.14	2		423	572	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916933	178916933	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	20	375	0	ENST00000263967.3:c.320A>G	p.Asn107Ser	p.N107S	ENST00000263967	NM_006218.2	107	aAc/aGc	2/21	1	2	FACETS	0.943	0.721	1	0.943	0.721	1	CLONAL	1	TRUE	1	0.14	2		375	303	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120502047	120502047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs189684879	NA	P-0054482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	18	339	0	ENST00000256646.2:c.1994G>A	p.Arg665His	p.R665H	ENST00000256646	NM_024408.3	665	cGc/cAc	12/34	1	2	FACETS	0.745	0.56	0.964	0.745	0.56	0.964	CLONAL	1	TRUE	1	0.14	2		339	345	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720871	89720871	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	16	295	0	ENST00000371953.3:c.1022T>G	p.Phe341Cys	p.F341C	ENST00000371953	NM_000314.4	341	tTt/tGt	8/9	1	2	FACETS	1	0.742	1	1	0.742	1	CLONAL	1	TRUE	1	0.14	2		295	228	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439945	56439945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775028128	NA	P-0054482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	75	671	1	ENST00000407977.2:c.647C>T	p.Ser216Leu	p.S216L	ENST00000407977		216	tCg/tTg	6/10	1	2	FACETS	0.973	0.85	1	0.973	0.85	1	CLONAL	1	TRUE	1	0.14	2		672	1101	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874713	151874713	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	37	447	1	ENST00000262189.6:c.7825C>T	p.Arg2609Ter	p.R2609*	ENST00000262189	NM_170606.2	2609	Cga/Tga	38/59	1	2	FACETS	0.929	0.765	1	0.929	0.765	1	CLONAL	1	TRUE	1	0.14	2		448	569	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678001	117678001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs62430836	NA	P-0054482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	28	353	0	ENST00000368508.3:c.3932G>A	p.Arg1311Gln	p.R1311Q	ENST00000368508	NM_002944.2	1311	cGa/cAa	25/43	1	2	FACETS	0.988	0.789	1	0.988	0.789	1	CLONAL	1	TRUE	1	0.14	2		353	405	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35860991	35860991	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	27	297	0	ENST00000303115.3:c.120C>A	p.Phe40Leu	p.F40L	ENST00000303115	NM_002185.3	40	ttC/ttA	2/8	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.14	2		297	353	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181860	56181860	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	21	249	0	ENST00000399503.3:c.4084G>T	p.Glu1362Ter	p.E1362*	ENST00000399503	NM_005921.1	1362	Gaa/Taa	17/20	1	2	FACETS	1	0.838	1	1	0.838	1	CLONAL	1	TRUE	1	0.14	2		249	270	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217333	11217333	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	51	572	0	ENST00000361445.4:c.4345T>C	p.Trp1449Arg	p.W1449R	ENST00000361445	NM_004958.3	1449	Tgg/Cgg	30/58	1	2	FACETS	0.956	0.811	1	0.956	0.811	1	CLONAL	1	TRUE	1	0.14	2		572	762	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268841	115268841	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	26	411	1	ENST00000438362.2:c.1769T>C	p.Phe590Ser	p.F590S	ENST00000438362	NM_001242891.1	590	tTc/tCc	14/20	1	2	FACETS	0.809	0.64	1	0.809	0.64	1	CLONAL	1	TRUE	1	0.14	2		412	459	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729728	162729728	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	36	541	0	ENST00000367921.3:c.814A>C	p.Met272Leu	p.M272L	ENST00000367921	NM_006182.2	272	Atg/Ctg	8/18	1	2	FACETS	0.717	0.588	0.863	0.717	0.588	0.863	SUBCLONAL	1	TRUE	1	0.14	2		541	717	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649535	206649535	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	44	538	0	ENST00000367120.3:c.370A>C	p.Asn124His	p.N124H	ENST00000367120	NM_014002.3	124	Aac/Cac	6/22	1	2	FACETS	0.922	0.771	1	0.922	0.771	1	CLONAL	1	TRUE	1	0.14	2		538	682	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59938842	59938842	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	15	330	0	ENST00000259008.2:c.59A>C	p.Lys20Thr	p.K20T	ENST00000259008	NM_032043.2	20	aAa/aCa	2/20	1	2	FACETS	0.84	0.615	1	0.84	0.615	1	CLONAL	1	TRUE	1	0.14	2		330	255	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295728	15295728	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	80	986	0	ENST00000263388.2:c.2399A>G	p.Gln800Arg	p.Q800R	ENST00000263388	NM_000435.2	800	cAg/cGg	15/33	1	2	FACETS	0.964	0.845	1	0.964	0.845	1	CLONAL	1	TRUE	1	0.14	2		986	1186	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275118	41275120	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	novel	NA	P-0054482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	19	337	0	ENST00000349496.5:c.1284_1286del	p.Cys429del	p.C429del	ENST00000349496	NM_001904.3	428	acTTGc/acc	9/15	1	2	FACETS	0.835	0.634	1	0.835	0.634	1	CLONAL	1	TRUE	1	0.14	2		337	325	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539573	187539573	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	17	331	0	ENST00000441802.2:c.8167G>T	p.Asp2723Tyr	p.D2723Y	ENST00000441802	NM_005245.3	2723	Gat/Tat	10/27	1	2	FACETS	0.729	0.544	0.951	0.729	0.544	0.951	CLONAL	1	TRUE	1	0.14	2		331	333	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0055004-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	119	544	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.397445858082899	2		545	475	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265552	198265552	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055004-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	58	449	0	ENST00000335508.6:c.2605A>G	p.Met869Val	p.M869V	ENST00000335508	NM_012433.2	869	Atg/Gtg	18/25	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.397445858082899	2		449	271	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159153	143159153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055004-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	15	277	0	ENST00000262992.4:c.700C>T	p.Pro234Ser	p.P234S	ENST00000262992	NM_001101669.1	234	Cca/Tca	10/24	1	2	FACETS	0.472	0.347	0.621	0.472	0.347	0.621	SUBCLONAL	1	TRUE	1	0.397445858082899	2		277	160	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508867	31508867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055004-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	120	594	0	ENST00000344624.3:c.1448C>T	p.Ser483Phe	p.S483F	ENST00000344624		483	tCc/tTc	7/33	1	2	FACETS	0.998	0.904	1	0.998	0.904	1	CLONAL	1	TRUE	1	0.397445858082899	2		594	605	SUCCESS
APC	324	MSKCC	GRCh37	5	112177473	112177473	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055004-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	25	603	2	ENST00000257430.4:c.6186del	p.Lys2062AsnfsTer11	p.K2062Nfs*11	ENST00000257430	NM_000038.5	2061	gAa/ga	16/16	0.397445858082899	1	FACETS	0.23	0.181	0.287	0.23	0.181	0.287	SUBCLONAL	1	TRUE	0	0.397445858082899	1		605	438	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0056532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	148	413	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.281703756122869	3	FACETS	1	0.986	1	0.676	0.622	0.732	INDETERMINATE	1	TRUE	1	0.590451510902881	3		414	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0056532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	444	739	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.590451510902881	2		741	712	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0056532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	126	383	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.981	0.895	1	0.981	0.895	1	CLONAL	1	TRUE	1	0.590451510902881	2		383	435	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593492	48593492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	151	353	0	ENST00000342988.3:c.1243G>A	p.Asp415Asn	p.D415N	ENST00000342988	NM_005359.5	415	Gac/Aac	10/12	0.590451510902881	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.590451510902881	1		353	319	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163770	72163770	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	59	515	0	ENST00000357731.5:c.588C>A	p.Asp196Glu	p.D196E	ENST00000357731	NM_173808.2	196	gaC/gaA	4/7	1	2	FACETS	0.436	0.376	0.502	0.436	0.376	0.502	SUBCLONAL	1	TRUE	1	0.590451510902881	2		515	458	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138619	11138619	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	172	587	0	ENST00000358026.2:c.3375G>T	p.Arg1125Ser	p.R1125S	ENST00000358026	NM_001128849.1	1125	agG/agT	24/36	0.311235837405768	3	FACETS	0.992	0.914	1	0.496	0.457	0.536	INDETERMINATE	1	TRUE	1	0.590451510902881	3		587	761	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798447	42798447	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	241	773	0	ENST00000575354.2:c.4318G>T	p.Asp1440Tyr	p.D1440Y	ENST00000575354	NM_015125.3	1440	Gac/Tac	18/20	0.311235837405768	3	FACETS	1	0.982	1	0.568	0.531	0.607	INDETERMINATE	1	TRUE	1	0.590451510902881	3		773	930	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285931	39285931	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	215	402	0	ENST00000402219.2:c.228A>C	p.Lys76Asn	p.K76N	ENST00000402219	NM_005633.3	76	aaA/aaC	3/23	0.294352423161843	3	FACETS	1	0.963	1	0.688	0.647	0.729	INDETERMINATE	2	TRUE	0	0.590451510902881	3		402	457	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721070	61721070	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	138	480	1	ENST00000401558.2:c.1204G>A	p.Val402Ile	p.V402I	ENST00000401558	NM_003400.3	402	Gtt/Att	12/25	0.294352423161843	3	FACETS	0.996	0.909	1	0.332	0.303	0.362	INDETERMINATE	1	TRUE	0	0.590451510902881	3		481	608	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955116	55955116	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	100	435	0	ENST00000263923.4:c.3429G>C	p.Trp1143Cys	p.W1143C	ENST00000263923	NM_002253.2	1143	tgG/tgC	26/30	0.512619599995246	1	FACETS	0.455	0.407	0.505	0.455	0.407	0.505	SUBCLONAL	1	TRUE	0	0.590451510902881	1		435	525	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645121	86645121	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs137853214	NA	P-0056532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	77	323	0	ENST00000274376.6:c.1193G>T	p.Arg398Leu	p.R398L	ENST00000274376	NM_002890.2	398	cGa/cTa	8/25	1	2	FACETS	0.767	0.679	0.861	0.767	0.679	0.861	SUBCLONAL	1	TRUE	1	0.590451510902881	2		323	340	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175364	+	frameshift_variant	Frame_Shift_Del	DEL	GAATTTTCTTCAGGAGC	GAATTTTCTTCAGGAGC	-	novel	NA	P-0056532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	77	260	0	ENST00000257430.4:c.4060_4076del	p.Phe1354IlefsTer15	p.F1354Ifs*15	ENST00000257430	NM_000038.5	1353	GAATTTTCTTCAGGAGCg/g	16/16	1	2	FACETS	0.878	0.779	0.983	0.878	0.779	0.983	CLONAL	1	TRUE	1	0.590451510902881	2		260	297	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176516643	176516643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768529489	NA	P-0056532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	217	786	0	ENST00000292408.4:c.40G>A	p.Val14Met	p.V14M	ENST00000292408	NM_213647.1	14	Gtg/Atg	2/18	1	2	FACETS	0.922	0.86	0.986	0.922	0.86	0.986	CLONAL	1	TRUE	1	0.590451510902881	2		786	797	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663648	117663648	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	43	473	0	ENST00000368508.3:c.4584A>G	p.Ile1528Met	p.I1528M	ENST00000368508	NM_002944.2	1528	atA/atG	28/43	1	2	FACETS	0.41	0.344	0.483	0.41	0.344	0.483	SUBCLONAL	1	TRUE	1	0.590451510902881	2		473	355	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482294	87482294	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	112	544	0	ENST00000277120.3:c.1581T>G	p.Ile527Met	p.I527M	ENST00000277120		527	atT/atG	14/19	0.590451510902881	3	FACETS	0.584	0.524	0.646	0.292	0.262	0.323	SUBCLONAL	1	TRUE	1	0.590451510902881	3		544	842	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0056559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	169	253	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.917	0.848	0.988	1	0.992	1	CLONAL	2	FALSE	1	0.327331016846261	2		253	563	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	189	851	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.327331016846261	2		851	1092	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061162	38061188	+	inframe_deletion	In_Frame_Del	DEL	CCGCCGGCCCCCGGCTGCTTCTCGCAC	CCGCCGGCCCCCGGCTGCTTCTCGCAC	-	novel	NA	P-0056559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	375	297	0	ENST00000250448.2:c.801_827del	p.Lys267_Gly276delinsAsn	p.K267_G276delinsN	ENST00000250448	NM_004496.3	267	aaGTGCGAGAAGCAGCCGGGGGCCGGCGGc/aac	2/2	1	2	FACETS	0.877	0.842	0.912	1	0.997	1	CLONAL	4	FALSE	1	0.327331016846261	2		297	653	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572454	95572454	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	190	351	0	ENST00000393063.1:c.2911T>A	p.Tyr971Asn	p.Y971N	ENST00000393063	NM_030621.3	971	Tat/Aat	19/28	1	2	FACETS	1	0.94	1	1	0.993	1	CLONAL	2	FALSE	1	0.327331016846261	2		351	574	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168495	56168495	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	136	131	0	ENST00000399503.3:c.1452del	p.Glu484AspfsTer3	p.E484Dfs*3	ENST00000399503	NM_005921.1	484	gAa/ga	8/20	0.327331016846261	3	FACETS	1	0.958	1	1	0.99	1	CLONAL	3	FALSE	1	0.327331016846261	3		131	306	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177777	56177784	+	frameshift_variant	Frame_Shift_Del	DEL	CTACAAAA	CTACAAAA	-	novel	NA	P-0056559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	183	414	0	ENST00000399503.3:c.2750_2757del	p.Ala917ValfsTer10	p.A917Vfs*10	ENST00000399503	NM_005921.1	917	gCTACAAAA/g	14/20	0.327331016846261	3	FACETS	0.912	0.845	0.982	0.912	0.845	0.982	CLONAL	2	FALSE	1	0.327331016846261	3		414	713	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117874089	117874089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	145	206	0	ENST00000297338.2:c.365C>T	p.Pro122Leu	p.P122L	ENST00000297338	NM_006265.2	122	cCt/cTt	4/14	1	2	FACETS	0.955	0.878	1	1	0.991	1	CLONAL	2	FALSE	1	0.327331016846261	2		206	464	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754894	57754932	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCTCGTAACATTTTGCAAAGCCACCCTGAAAGGAAACA	ATCTCGTAACATTTTGCAAAGCCACCCTGAAAGGAAACA	-	novel	NA	P-0056559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	101	362	0	ENST00000274289.3:c.271-13_296del		p.X91_splice	ENST00000274289	NM_006622.3	91		2/14	0.327331016846261	3	FACETS	1	0.959	1	0.571	0.511	0.634	CLONAL	1	FALSE	1	0.327331016846261	3		362	629	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245861	41245861	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs80356898	NA	P-0056566-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	149	365	0	ENST00000357654.3:c.1687C>G	p.Gln563Glu	p.Q563E	ENST00000357654	NM_007294.3	563	Cag/Gag	10/23	0.688111133547389	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.687363499822626	2		365	210	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574000	7574000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056566-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	354	562	0	ENST00000269305.4:c.1027G>T	p.Glu343Ter	p.E343*	ENST00000269305	NM_001126112.2	343	Gag/Tag	10/11	0.688111133547389	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.687363499822626	2		562	457	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759686	133759686	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs61746126	NA	P-0056566-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	265	699	0	ENST00000318560.5:c.2009A>G	p.Asn670Ser	p.N670S	ENST00000318560	NM_005157.4	670	aAt/aGt	11/11	0.361235373010534	5	FACETS	1	0.99	1	0.809	0.764	0.855	INDETERMINATE	2	TRUE	2	0.687363499822626	5		699	645	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495511	56495511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056566-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	367	792	0	ENST00000267101.3:c.3701C>T	p.Ser1234Phe	p.S1234F	ENST00000267101	NM_001982.3	1234	tCt/tTt	28/28	0.361235373010534	5	FACETS	1	0.993	1	0.824	0.785	0.864	INDETERMINATE	2	TRUE	2	0.687363499822626	5		792	877	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974756	21974756	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894097	NA	P-0056566-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	413	723	0	ENST00000304494.5:c.71G>C	p.Arg24Pro	p.R24P	ENST00000304494	NM_000077.4	24	cGg/cCg	1/3	0.688111133547389	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.687363499822626	2		723	505	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665358	138665358	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056566-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1338	162	673	0	ENST00000330315.3:c.207G>C	p.Glu69Asp	p.E69D	ENST00000330315	NM_023067.3	69	gaG/gaC	1/1	0.687363499822626	8	FACETS	0.962	0.88	1			1	CLONAL	1	TRUE	NA	0.687363499822626	8		673	1500	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624877	9624877	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056566-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	318	668	0	ENST00000353224.5:c.100G>T	p.Gly34Cys	p.G34C	ENST00000353224	NM_177990.2	34	Ggc/Tgc	3/10	0.622084076275312	4	FACETS	1	0.985	1			1	CLONAL	2	TRUE	NA	0.687363499822626	4		668	718	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867774	45867774	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056566-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	187	772	1	ENST00000391945.4:c.626A>G	p.Tyr209Cys	p.Y209C	ENST00000391945	NM_000400.3	209	tAc/tGc	8/23	0.688111133547389	3	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.687363499822626	3		773	641	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740354	46740354	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs778442529	NA	P-0056566-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	194	610	0	ENST00000371975.4:c.1834C>G	p.Gln612Glu	p.Q612E	ENST00000371975	NM_003579.3	612	Caa/Gaa	16/18	0.610141116026844	4	FACETS	1	0.972	1	0.55	0.509	0.592	CLONAL	1	TRUE	2	0.687363499822626	4		610	866	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70412288	70412288	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs755298802	NA	P-0056566-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	197	373	0	ENST00000373644.4:c.4398A>G	p.Ile1466Met	p.I1466M	ENST00000373644	NM_030625.2	1466	atA/atG	6/12	0.688111133547389	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.687363499822626	2		373	277	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439882	49439882	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056566-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	340	692	0	ENST00000301067.7:c.4659T>G	p.Cys1553Trp	p.C1553W	ENST00000301067	NM_003482.3	1553	tgT/tgG	17/54	0.361235373010534	5	FACETS	1	0.992	1	0.817	0.777	0.857	INDETERMINATE	2	TRUE	2	0.687363499822626	5		692	820	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911181	32911181	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056566-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	596	418	0	ENST00000380152.3:c.2689G>C	p.Glu897Gln	p.E897Q	ENST00000380152		897	Gaa/Caa	11/27	0.687363499822626	8	FACETS	1	0.993	1			1	CLONAL	7	TRUE	NA	0.687363499822626	8		418	730	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816192	89816192	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1047919771	NA	P-0056566-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	373	653	0	ENST00000389301.3:c.3185G>A	p.Gly1062Glu	p.G1062E	ENST00000389301	NM_000135.2	1062	gGg/gAg	32/43	0.688111133547389	5	FACETS	1	0.984	1	0.717	0.682	0.752	CLONAL	2	TRUE	2	0.687363499822626	5		653	1025	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936023	44936023	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0056566-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	197	223	0	ENST00000377967.4:c.2784C>G	p.Tyr928Ter	p.Y928*	ENST00000377967	NM_021140.2	928	taC/taG	18/29	0.622084076275312	2	FACETS		NA	1			1	NA	3	TRUE	NA	0.687363499822626	2		223	221	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028821	47028841	+	frameshift_variant	Frame_Shift_Del	DEL	GTTCATATCCTCGCGAGTATG	GTTCATATCCTCGCGAGTATG	T	novel	NA	P-0056566-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	329	348	0	ENST00000377604.3:c.125_145delinsT	p.Arg42LeufsTer8	p.R42Lfs*8	ENST00000377604	NM_001204468.1	42	cGTTCATATCCTCGCGAGTATGgc/cTgc	3/24	0.622084076275312	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.687363499822626	2		348	401	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150916408	150916408	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056566-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	163	465	0	ENST00000271640.5:c.888C>G	p.Phe296Leu	p.F296L	ENST00000271640	NM_001145415.1	296	ttC/ttG	8/22	0.514827281632483	4	FACETS	1	0.986	1	0.654	0.603	0.707	CLONAL	1	TRUE	2	0.687363499822626	4		465	612	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524631	103524631	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056566-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	142	529	0	ENST00000355739.4:c.2762T>C	p.Leu921Ser	p.L921S	ENST00000355739	NM_000123.3	921	tTg/tCg	13/15	0.688111133547389	5	FACETS	0.949	0.865	1	0.237	0.216	0.26	CLONAL	1	TRUE	1	0.687363499822626	5		529	884	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060761	38060761	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056566-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	247	831	0	ENST00000250448.2:c.1228G>C	p.Glu410Gln	p.E410Q	ENST00000250448	NM_004496.3	410	Gag/Cag	2/2	0.688111133547389	2	FACETS	1	0.985	1	0.566	0.533	0.6	CLONAL	1	TRUE	0	0.687363499822626	2		831	635	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242064	105242064	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056566-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	179	669	0	ENST00000349310.3:c.360C>A	p.Phe120Leu	p.F120L	ENST00000349310	NM_001014432.1	120	ttC/ttA	6/15	0.687363499822626	6	FACETS	0.962	0.885	1	0.321	0.295	0.348	CLONAL	1	TRUE	3	0.687363499822626	6		669	1286	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667616	29667616	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1060500359	NA	P-0056566-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	248	435	0	ENST00000356175.3:c.6952G>T	p.Glu2318Ter	p.E2318*	ENST00000356175	NM_000267.3	2318	Gaa/Taa	46/57	0.688111133547389	3	FACETS	0.972	0.92	1	0.972	0.92	1	CLONAL	2	TRUE	1	0.687363499822626	3		435	499	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67624756	67624756	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056566-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	378	641	0	ENST00000272342.5:c.176G>A	p.Arg59Gln	p.R59Q	ENST00000272342	NM_019002.3	59	cGa/cAa	1/6	0.610141116026844	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	2	0.687363499822626	4		641	785	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608650	189608654	+	missense_variant	Missense_Mutation	ONP	GATTG	GATTG	CATTA	novel	NA	P-0056566-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	142	514	0	ENST00000264731.3:c.1725_1729delinsCATTA	p.Gln575_Glu577delinsHisIleLys	p.Q575_E577delinsHIK	ENST00000264731	NM_003722.4	575	caGATTGag/caCATTAag	13/14	0.688111133547389	5	FACETS	1	0.923	1	0.338	0.308	0.369	CLONAL	1	TRUE	2	0.687363499822626	5		514	828	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0056733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	305	309	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.103647642663655	5	FACETS	0.93	0.885	0.975			1	INDETERMINATE	3	TRUE	NA	0.76988209393101	5		309	612	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0056733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	137	227	3	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.76988209393101	2		230	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0056733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	392	1134	1	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.76988209393101	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.76988209393101	1		1135	617	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	19	538	2	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	1	2	FACETS	0.089	0.067	0.115	0.089	0.067	0.115	SUBCLONAL	1	TRUE	1	0.76988209393101	2		540	557	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874011	123874013	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs780061449	NA	P-0056733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	12	62	0	ENST00000330479.4:c.62_64del	p.Ala21del	p.A21del	ENST00000330479	NM_020382.3	14	gaGGCg/gag	2/9	0.76988209393101	2	FACETS	0.306	0.217	0.413	0.153	0.108	0.207	SUBCLONAL	1	TRUE	0	0.76988209393101	2		62	102	SUCCESS
APC	324	MSKCC	GRCh37	5	112175802	112175802	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	112	308	1	ENST00000257430.4:c.4512del	p.Ser1505AlafsTer2	p.S1505Afs*2	ENST00000257430	NM_000038.5	1504	tCc/tc	16/16	1	2	FACETS	0.898	0.818	0.98	0.898	0.818	0.98	CLONAL	1	TRUE	1	0.76988209393101	2		309	324	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348031	348031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765982081	NA	P-0056733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	432	1248	9	ENST00000262320.3:c.1475G>A	p.Arg492His	p.R492H	ENST00000262320	NM_003502.3	492	cGc/cAc	6/11	1	2	FACETS	0.983	0.939	1	0.983	0.939	1	CLONAL	1	TRUE	1	0.76988209393101	2		1257	1142	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	359972	359972	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0056733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	317	904	3	ENST00000262320.3:c.1116+1G>T		p.X372_splice	ENST00000262320	NM_003502.3	372			1	2	FACETS	0.984	0.932	1	0.984	0.932	1	CLONAL	1	TRUE	1	0.76988209393101	2		907	837	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0056858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	431	588	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.554281637338845	3	FACETS	0.956	0.914	0.998	0.956	0.914	0.998	CLONAL	2	TRUE	1	0.554281637338845	3		588	1039	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0056858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	444	1020	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.554281637338845	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.554281637338845	1		1022	1116	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964199	28964199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745653714	NA	P-0056858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	53	280	0	ENST00000282397.4:c.1703C>T	p.Thr568Met	p.T568M	ENST00000282397	NM_002019.4	568	aCg/aTg	13/30	0.280006367362073	1	FACETS	0.414	0.354	0.478	0.414	0.354	0.478	INDETERMINATE	1	TRUE	0	0.554281637338845	1		280	334	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	84	305	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.146750116442478	3	FACETS	0.759	0.679	0.842	0.759	0.679	0.842	INDETERMINATE	2	FALSE	1	0.504199673019562	3		305	275	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	172	331	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.146750116442478	3	FACETS	0.777	0.719	0.836	0.777	0.719	0.836	INDETERMINATE	2	FALSE	1	0.504199673019562	3		335	550	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	64	279	3	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	0.233806721379482	1	FACETS	0.662	0.578	0.75	0.662	0.578	0.75	INDETERMINATE	1	FALSE	0	0.504199673019562	1		282	287	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120173	70120173	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	114	396	1	ENST00000245479.2:c.1177del	p.Gln393SerfsTer10	p.Q393Sfs*10	ENST00000245479	NM_000346.3	392	tCc/tc	3/3	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.504199673019562	2		397	359	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165213	47165213	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	69	508	0	ENST00000409792.3:c.913del	p.Thr305GlnfsTer35	p.T305Qfs*35	ENST00000409792	NM_014159.6	305	Aca/ca	3/21	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	FALSE	1	0.504199673019562	2		508	267	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952086	178952086	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	57	254	0	ENST00000263967.3:c.3141T>A	p.His1047Gln	p.H1047Q	ENST00000263967	NM_006218.2	1047	caT/caA	21/21	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	FALSE	1	0.504199673019562	2		254	200	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339452	339452	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	164	661	0	ENST00000262320.3:c.2450del	p.Lys817ArgfsTer11	p.K817Rfs*11	ENST00000262320	NM_003502.3	817	aAg/ag	10/11	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	FALSE	NA	0.504199673019562	2		661	558	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	188	730	1	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.504199673019562	2		731	663	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971195	13971195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777866452	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	88	387	0	ENST00000405192.2:c.734C>T	p.Ala245Val	p.A245V	ENST00000405192	NM_001163147.1	245	gCg/gTg	8/12	0.233806721379482	1	FACETS	0.848	0.759	0.94	0.848	0.759	0.94	INDETERMINATE	1	FALSE	0	0.504199673019562	1		387	308	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521114	187521114	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760053140	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	136	410	0	ENST00000441802.2:c.12041C>T	p.Thr4014Met	p.T4014M	ENST00000441802	NM_005245.3	4014	aCg/aTg	22/27	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.504199673019562	2		410	421	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919545	78919545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776174012	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	130	398	0	ENST00000306801.3:c.3104C>T	p.Thr1035Met	p.T1035M	ENST00000306801	NM_020761.2	1035	aCg/aTg	26/34	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.504199673019562	2		398	431	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	70	313	0	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	0.504199673019562	1	FACETS	0.796	0.702	0.894	0.796	0.702	0.894	SUBCLONAL	1	FALSE	0	0.504199673019562	1		313	261	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	85	358	7	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	NA	2	FACETS	0.972	0.866	1			1	INDETERMINATE	1	FALSE	NA	0.504199673019562	2		365	347	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661664	227661664	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs761880048	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	157	543	8	ENST00000305123.5:c.1791del	p.His598ThrfsTer38	p.H598Tfs*38	ENST00000305123	NM_005544.2	597	ggG/gg	1/2	1	2	FACETS	0.756	0.7	0.813	1	0.99	1	SUBCLONAL	2	FALSE	1	0.504199673019562	2		551	412	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427491	427491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774366438	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	58	489	0	ENST00000399788.2:c.2678G>A	p.Arg893Gln	p.R893Q	ENST00000399788	NM_001042603.1	893	cGa/cAa	19/28	NA	2	FACETS	0.511	0.44	0.589			1	INDETERMINATE	1	FALSE	NA	0.504199673019562	2		489	450	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	110	283	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.504199673019562	2		288	362	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831357	72831358	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTG	rs34918837	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	48	386	2	ENST00000268489.5:c.5221_5223dup	p.Gln1741dup	p.Q1741dup	ENST00000268489	NM_006885.3	1741	-/CAA	9/10	1	2	FACETS	0.79	0.674	0.915	0.79	0.674	0.915	CLONAL	1	FALSE	1	0.504199673019562	2		388	241	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	95	397	7	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	1	0.504199673019562	2		404	365	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743896	41743896	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	201	812	2	ENST00000301178.4:c.836del	p.Pro279GlnfsTer18	p.P279Qfs*18	ENST00000301178	NM_021913.4	277	gaC/ga	7/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.504199673019562	2		814	708	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687472	37687472	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	109	370	0	ENST00000447079.4:c.4382del	p.Gly1461AlafsTer38	p.G1461Afs*38	ENST00000447079	NM_015083.1	1459	tGg/tg	14/14	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.504199673019562	2		370	350	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348566	89348568	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs753054998	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	29	789	2	ENST00000301030.4:c.4382_4384del	p.Lys1461del	p.K1461del	ENST00000301030	NM_001256183.1	1461	aAGAga/aga	9/13	NA	2	FACETS	0.156	0.124	0.192			1	INDETERMINATE	1	FALSE	NA	0.504199673019562	2		791	739	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435815	56435815	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755967475	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	106	479	0	ENST00000407977.2:c.1322del	p.Pro441LeufsTer61	p.P441Lfs*61	ENST00000407977		441	cCt/ct	9/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.504199673019562	2		479	353	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354393	354393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1488869543	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	178	656	1	ENST00000262320.3:c.1165G>A	p.Ala389Thr	p.A389T	ENST00000262320	NM_003502.3	389	Gcg/Acg	5/11	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	FALSE	NA	0.504199673019562	2		657	660	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992721	68992721	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs764112302	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	113	456	1	ENST00000288368.4:c.1693del	p.Ser565ArgfsTer10	p.S565Rfs*10	ENST00000288368	NM_024870.2	562	cgT/cg	16/40	0.445168827067297	1	FACETS	0.787	0.713	0.864	0.787	0.713	0.864	SUBCLONAL	1	FALSE	0	0.504199673019562	1		457	426	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	118	231	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.504199673019562	2		231	387	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268098	153268098	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	88	223	2	ENST00000281708.4:c.710G>A	p.Trp237Ter	p.W237*	ENST00000281708	NM_033632.3	237	tGg/tAg	4/12	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.504199673019562	2		225	316	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562744	21562744	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1442338961	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	86	227	0	ENST00000382592.4:c.1175C>T	p.Ala392Val	p.A392V	ENST00000382592	NM_014572.2	392	gCg/gTg	4/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.504199673019562	2		227	282	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686293	30686294	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	105	294	0	ENST00000295754.5:c.152_153del	p.Cys51Ter	p.C51*	ENST00000295754	NM_003242.5	50	cTG/c	2/7	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	FALSE	1	0.504199673019562	2		294	409	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601944	43601944	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1172318035	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	149	784	1	ENST00000355710.3:c.988C>T	p.Arg330Trp	p.R330W	ENST00000355710	NM_020975.4	330	Cgg/Tgg	5/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.504199673019562	2		785	555	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245584	41245584	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	159	601	0	ENST00000357654.3:c.1964A>G	p.Tyr655Cys	p.Y655C	ENST00000357654	NM_007294.3	655	tAc/tGc	10/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.504199673019562	2		601	560	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925402	114925402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748822481	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	165	624	1	ENST00000543371.1:c.1485del	p.Ser496ProfsTer5	p.S496Pfs*5	ENST00000543371	NM_001198531.1	494	Ccc/cc	14/14	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.504199673019562	2		625	607	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850820	63850820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746755575	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	76	382	0	ENST00000279873.7:c.1598C>T	p.Ala533Val	p.A533V	ENST00000279873	NM_032199.2	533	gCg/gTg	10/10	1	2	FACETS	0.874	0.772	0.981	0.874	0.772	0.981	CLONAL	1	FALSE	1	0.504199673019562	2		382	345	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999104	100999104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779926918	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	103	578	0	ENST00000325455.5:c.698C>T	p.Ala233Val	p.A233V	ENST00000325455	NM_001202474.3	233	gCg/gTg	1/8	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.504199673019562	2		578	352	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99180099	99180099	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs746971958	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	117	429	0	ENST00000074304.5:c.2042C>T	p.Thr681Met	p.T681M	ENST00000074304	NM_001134224.1	681	aCg/aTg	19/26	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.504199673019562	2		429	377	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448297	56448297	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	183	622	2	ENST00000407977.2:c.350del	p.Arg117ProfsTer41	p.R117Pfs*41	ENST00000407977		117	cGc/cc	3/10	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	1	0.504199673019562	2		624	704	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857769	9857769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	27	516	0	ENST00000330684.3:c.3632C>T	p.Ser1211Phe	p.S1211F	ENST00000330684	NM_001134407.1	1211	tCc/tTc	13/13	1	2	FACETS	0.378	0.302	0.466	0.378	0.302	0.466	SUBCLONAL	1	FALSE	1	0.504199673019562	2		516	283	SUCCESS
APC	324	MSKCC	GRCh37	5	112090706	112090706	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	67	167	0	ENST00000257430.4:c.119A>G	p.Glu40Gly	p.E40G	ENST00000257430	NM_000038.5	40	gAg/gGg	2/16	0.146750116442478	3	FACETS	0.828	0.732	0.927	0.828	0.732	0.927	INDETERMINATE	2	FALSE	1	0.504199673019562	3		167	201	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960210	151960210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761700904	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	18	136	1	ENST00000262189.6:c.1190C>T	p.Ser397Leu	p.S397L	ENST00000262189	NM_170606.2	397	tCg/tTg	9/59	0.146750116442478	3	FACETS	0.677	0.515	0.865	0.339	0.257	0.433	INDETERMINATE	1	FALSE	1	0.504199673019562	3		137	132	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542746	187542746	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761417017	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	115	323	1	ENST00000441802.2:c.4994C>T	p.Pro1665Leu	p.P1665L	ENST00000441802	NM_005245.3	1665	cCg/cTg	10/27	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	FALSE	NA	0.504199673019562	2		324	313	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197471	106197471	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	52	255	1	ENST00000380013.4:c.5804A>G	p.Tyr1935Cys	p.Y1935C	ENST00000380013	NM_001127208.2	1935	tAt/tGt	11/11	1	2	FACETS	0.968	0.835	1	0.968	0.835	1	CLONAL	1	FALSE	1	0.504199673019562	2		256	213	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323266	31323266	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	87	305	0	ENST00000412585.2:c.723G>A	p.Trp241Ter	p.W241*	ENST00000412585	NM_005514.6	241	tgG/tgA	4/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.504199673019562	2		305	290	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589652	67589652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1383740979	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	55	148	1	ENST00000274335.5:c.1415G>A	p.Arg472His	p.R472H	ENST00000274335		472	cGc/cAc	10/15	0.146750116442478	3	FACETS	1	0.959	1	0.65	0.564	0.742	INDETERMINATE	1	FALSE	1	0.504199673019562	3		149	210	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042170	6042170	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1562689635	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	117	555	0	ENST00000265849.7:c.451del	p.Arg151AlafsTer50	p.R151Afs*50	ENST00000265849	NM_000535.5	151	Cgc/gc	5/15	0.233806721379482	1	FACETS	0.592	0.536	0.652	0.592	0.536	0.652	INDETERMINATE	1	FALSE	0	0.504199673019562	1		555	586	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249173	10249173	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	145	701	2	ENST00000340748.4:c.4009C>T	p.Arg1337Trp	p.R1337W	ENST00000340748		1337	Cgg/Tgg	34/40	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	1	0.504199673019562	2		703	553	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447270	187447270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369445234	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	147	625	0	ENST00000232014.4:c.923C>T	p.Ser308Leu	p.S308L	ENST00000232014	NM_001130845.1	308	tCg/tTg	5/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.504199673019562	2		625	493	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798287	45798287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs537292657	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	157	645	0	ENST00000450313.1:c.649C>T	p.Arg217Cys	p.R217C	ENST00000450313	NM_012222.2	217	Cgc/Tgc	8/16	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.504199673019562	2		645	464	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249865	133249865	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	70	309	0	ENST00000320574.5:c.1360-2A>G		p.X454_splice	ENST00000320574	NM_006231.2	454			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.504199673019562	2		309	215	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225884	2225885	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	143	660	0	ENST00000326181.6:c.1677dup	p.Gly560TrpfsTer28	p.G560Wfs*28	ENST00000326181	NM_032271.2	559	ggt/ggTt	18/21	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	1	0.504199673019562	2		660	550	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640594	3640594	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	193	867	0	ENST00000294008.3:c.3045del	p.Leu1016TrpfsTer100	p.L1016Wfs*100	ENST00000294008	NM_032444.2	1015	ggG/gg	12/15	1	2	FACETS	0.989	0.917	1	0.989	0.917	1	CLONAL	1	FALSE	1	0.504199673019562	2		867	774	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14028091	14028091	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	57	296	0	ENST00000311895.7:c.1145A>G	p.Glu382Gly	p.E382G	ENST00000311895	NM_005236.2	382	gAg/gGg	7/11	1	2	FACETS	0.822	0.712	0.941	0.822	0.712	0.941	CLONAL	1	FALSE	1	0.504199673019562	2		296	275	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877447	89877447	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	146	479	0	ENST00000389301.3:c.316G>T	p.Gly106Trp	p.G106W	ENST00000389301	NM_000135.2	106	Ggg/Tgg	4/43	NA	2	FACETS	0.99	0.908	1			1	INDETERMINATE	1	FALSE	NA	0.504199673019562	2		479	585	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866707	37866707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775544453	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	110	690	2	ENST00000269571.5:c.874G>A	p.Gly292Ser	p.G292S	ENST00000269571		292	Ggc/Agc	7/27	1	2	FACETS	0.641	0.576	0.709	0.641	0.576	0.709	SUBCLONAL	1	FALSE	1	0.504199673019562	2		692	681	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117537	70117537	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	124	425	0	ENST00000245479.2:c.5A>G	p.Asn2Ser	p.N2S	ENST00000245479	NM_000346.3	2	aAt/aGt	1/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.504199673019562	2		425	387	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15273349	15273349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779138148	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	163	609	0	ENST00000263388.2:c.5840C>T	p.Ala1947Val	p.A1947V	ENST00000263388	NM_000435.2	1947	gCg/gTg	32/33	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.504199673019562	2		609	566	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296187	15296187	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	189	717	0	ENST00000263388.2:c.2177G>C	p.Gly726Ala	p.G726A	ENST00000263388	NM_000435.2	726	gGc/gCc	14/33	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.504199673019562	2		717	644	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223203	36223203	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	45	919	1	ENST00000222270.7:c.5753C>A	p.Pro1918His	p.P1918H	ENST00000222270	NM_014727.1	1918	cCt/cAt	28/37	1	2	FACETS	0.239	0.2	0.282	0.239	0.2	0.282	SUBCLONAL	1	FALSE	1	0.504199673019562	2		920	747	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796828	42796828	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1363225423	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	249	845	0	ENST00000575354.2:c.3286T>C	p.Tyr1096His	p.Y1096H	ENST00000575354	NM_015125.3	1096	Tac/Cac	14/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.504199673019562	2		845	786	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251671	212251671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	85	369	0	ENST00000342788.4:c.3388G>A	p.Ala1130Thr	p.A1130T	ENST00000342788	NM_005235.2	1130	Gct/Act	27/28	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.504199673019562	2		369	296	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378354	225378354	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	46	211	0	ENST00000264414.4:c.541G>T	p.Gly181Cys	p.G181C	ENST00000264414	NM_003590.4	181	Ggc/Tgc	5/16	1	2	FACETS	0.818	0.696	0.95	0.818	0.696	0.95	CLONAL	1	FALSE	1	0.504199673019562	2		211	223	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980742	40980742	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	62	383	0	ENST00000373198.4:c.1744A>G	p.Ile582Val	p.I582V	ENST00000373198	NM_133170.3	582	Att/Gtt	10/32	0.502245971458724	0	FACETS	0.542	0.474	0.613			1	SUBCLONAL	1	FALSE	0	0.504199673019562	0		383	225	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095824	29095824	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	128	411	0	ENST00000328354.6:c.1008+2T>C		p.X336_splice	ENST00000328354	NM_007194.3	336			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.504199673019562	2		411	393	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064435	30064435	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	113	312	0	ENST00000338641.4:c.999G>T	p.Gln333His	p.Q333H	ENST00000338641	NM_000268.3	333	caG/caT	10/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.504199673019562	2		312	394	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059163	47059163	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1468592664	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	121	433	0	ENST00000409792.3:c.7498A>G	p.Thr2500Ala	p.T2500A	ENST00000409792	NM_014159.6	2500	Acc/Gcc	20/21	1	2	FACETS	0.966	0.877	1	0.966	0.877	1	CLONAL	1	FALSE	1	0.504199673019562	2		433	497	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52649462	52649462	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	111	386	0	ENST00000394830.3:c.1829A>G	p.Asp610Gly	p.D610G	ENST00000394830	NM_018313.4	610	gAt/gGt	16/30	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	1	0.504199673019562	2		386	419	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027135	71027135	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	126	425	0	ENST00000318789.4:c.1192G>C	p.Ala398Pro	p.A398P	ENST00000318789	NM_032682.5	398	Gct/Cct	15/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.504199673019562	2		425	437	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72864535	72864535	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	90	274	0	ENST00000325599.8:c.902T>A	p.Ile301Asn	p.I301N	ENST00000325599	NM_018130.2	301	aTc/aAc	8/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	1	0.504199673019562	2		274	321	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156692	55156692	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	72	357	0	ENST00000257290.5:c.3093G>T	p.Glu1031Asp	p.E1031D	ENST00000257290	NM_006206.4	1031	gaG/gaT	22/23	1	2	FACETS	0.962	0.848	1	0.962	0.848	1	CLONAL	1	FALSE	1	0.504199673019562	2		357	297	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952436	38952436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs539956555	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	68	282	0	ENST00000357387.3:c.2989C>T	p.Arg997Cys	p.R997C	ENST00000357387	NM_152756.3	997	Cgc/Tgc	30/38	0.146750116442478	3	FACETS	1	0.967	1	0.655	0.576	0.737	INDETERMINATE	1	FALSE	1	0.504199673019562	3		282	258	SUCCESS
APC	324	MSKCC	GRCh37	5	112174074	112174074	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1445394695	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	13	254	0	ENST00000257430.4:c.2783C>T	p.Ala928Val	p.A928V	ENST00000257430	NM_000038.5	928	gCc/gTc	16/16	0.146750116442478	3	FACETS	0.284	0.203	0.384	0.142	0.101	0.192	INDETERMINATE	1	FALSE	1	0.504199673019562	3		254	227	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188940	32188940	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	149	686	0	ENST00000375023.3:c.614G>T	p.Cys205Phe	p.C205F	ENST00000375023	NM_004557.3	205	tGc/tTc	4/30	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.504199673019562	2		686	518	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873651	151873651	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs187761353	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	22	493	0	ENST00000262189.6:c.8887C>T	p.Arg2963Cys	p.R2963C	ENST00000262189	NM_170606.2	2963	Cgt/Tgt	38/59	0.146750116442478	3	FACETS	0.301	0.233	0.38	0.151	0.116	0.19	INDETERMINATE	1	FALSE	1	0.504199673019562	3		493	363	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5081853	5081853	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	11	206	0	ENST00000381652.3:c.2563C>T	p.Leu855Phe	p.L855F	ENST00000381652	NM_004972.3	855	Ctt/Ttt	19/25	1	2	FACETS	0.257	0.177	0.355	0.257	0.177	0.355	SUBCLONAL	1	FALSE	1	0.504199673019562	2		206	170	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500813	8500813	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs759552919	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	90	395	0	ENST00000356435.5:c.2069A>G	p.His690Arg	p.H690R	ENST00000356435		690	cAt/cGt	13/35	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	1	0.504199673019562	2		395	325	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970994	21970994	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113798404	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	155	419	0	ENST00000304494.5:c.364G>A	p.Gly122Ser	p.G122S	ENST00000304494	NM_000077.4	122	Ggc/Agc	2/3	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.504199673019562	2		419	420	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139818325	139818325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	45	543	0	ENST00000247668.2:c.1160G>A	p.Gly387Asp	p.G387D	ENST00000247668	NM_021138.3	387	gGc/gAc	10/11	1	2	FACETS	0.285	0.239	0.336	0.285	0.239	0.336	SUBCLONAL	1	FALSE	1	0.504199673019562	2		543	627	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776285	76776285	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	120	481	0	ENST00000373344.5:c.7181T>C	p.Val2394Ala	p.V2394A	ENST00000373344	NM_000489.3	2394	gTa/gCa	34/35	0.233806721379482	1	FACETS	0.886	0.807	0.967	0.886	0.807	0.967	INDETERMINATE	1	FALSE	0	0.504199673019562	1		481	402	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617190	100617190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	108	502	0	ENST00000308731.7:c.559C>T	p.Pro187Ser	p.P187S	ENST00000308731	NM_000061.2	187	Cct/Tct	7/19	0.233806721379482	1	FACETS	0.75	0.678	0.826	0.75	0.678	0.826	INDETERMINATE	1	FALSE	0	0.504199673019562	1		502	427	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200230	123200230	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	72	370	0	ENST00000218089.9:c.2209A>G	p.Thr737Ala	p.T737A	ENST00000218089	NM_001042749.1	737	Act/Gct	23/35	0.233806721379482	1	FACETS	0.6	0.527	0.677	0.6	0.527	0.677	INDETERMINATE	1	FALSE	0	0.504199673019562	1		370	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0057597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	248	611	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.806692870177409	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.806692870177409	1		611	324	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11181361	11181361	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs374052581	NA	P-0057597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	285	653	0	ENST00000361445.4:c.6875A>G	p.Asn2292Ser	p.N2292S	ENST00000361445	NM_004958.3	2292	aAt/aGt	49/58	0.806692870177409	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.806692870177409	1		653	359	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243053	105243053	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	67	1047	0	ENST00000349310.3:c.230G>T	p.Cys77Phe	p.C77F	ENST00000349310	NM_001014432.1	77	tGc/tTc	5/15	1	2	FACETS	0.211	0.183	0.242	0.211	0.183	0.242	SUBCLONAL	1	TRUE	1	0.806692870177409	2		1047	786	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980756	70980756	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	115	407	0	ENST00000276594.2:c.712C>G	p.Leu238Val	p.L238V	ENST00000276594	NM_024504.3	238	Ctt/Gtt	3/8	1	2	FACETS	0.926	0.846	1	0.926	0.846	1	CLONAL	1	TRUE	1	0.806692870177409	2		407	308	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057994-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	49	737	0				ENST00000310581	NM_198253.2	-/1132			0.298341190178269	3	FACETS	0.853	0.731	0.984	0.853	0.731	0.984	CLONAL	2	TRUE	1	0.31	3		737	214	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0057994-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	121	537	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	1	2	FACETS	0.847	0.77	0.927	1	0.988	1	CLONAL	2	TRUE	1	0.31	2		537	461	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044466	47044466	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057994-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	103	250	0	ENST00000377604.3:c.1963A>G	p.Met655Val	p.M655V	ENST00000377604	NM_001204468.1	655	Atg/Gtg	18/24	0.167566898616291	2	FACETS	0.931	0.85	1			1	INDETERMINATE	3	TRUE	NA	0.31	2		250	238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs17849781	NA	P-0057994-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	48	537	0	ENST00000269305.4:c.832C>G	p.Pro278Ala	p.P278A	ENST00000269305	NM_001126112.2	278	Cct/Gct	8/11	1	2	FACETS	0.672	0.568	0.785	0.672	0.568	0.785	SUBCLONAL	1	TRUE	1	0.31	2		537	461	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845934	72845934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759043061	NA	P-0057994-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	171	461	0	ENST00000268489.5:c.3533C>T	p.Ser1178Leu	p.S1178L	ENST00000268489	NM_006885.3	1178	tCg/tTg	6/10	0.298341190178269	5	FACETS	0.892	0.829	0.956			1	CLONAL	4	TRUE	NA	0.31	5		461	453	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56809902	56809902	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057994-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	15	285	0	ENST00000337432.4:c.1023C>G	p.Ile341Met	p.I341M	ENST00000337432	NM_058216.2	341	atC/atG	8/9	1	2	FACETS	0.576	0.423	0.758	0.576	0.423	0.758	SUBCLONAL	1	TRUE	1	0.31	2		285	168	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534741	18534741	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057994-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	33	476	0	ENST00000266497.5:c.1799A>G	p.Gln600Arg	p.Q600R	ENST00000266497		600	cAg/cGg	12/31	1	2	FACETS	0.58	0.473	0.701	0.58	0.473	0.701	SUBCLONAL	1	TRUE	1	0.31	2		476	367	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955403	48955409	+	frameshift_variant	Frame_Shift_Del	DEL	GATTCTG	GATTCTG	-	novel	NA	P-0057994-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	34	219	0	ENST00000267163.4:c.1521_1527del	p.Asp507GlufsTer10	p.D507Efs*10	ENST00000267163	NM_000321.2	507	GATTCTGga/ga	17/27	0.298341190178269	2	FACETS	0.864	0.72	1	0.864	0.72	1	CLONAL	2	TRUE	0	0.31	2		219	127	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873455	45873455	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057994-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	26	490	0	ENST00000391945.4:c.41A>G	p.Tyr14Cys	p.Y14C	ENST00000391945	NM_000400.3	14	tAc/tGc	2/23	0.298341190178269	5	FACETS	0.488	0.385	0.606	0.122	0.096	0.152	SUBCLONAL	1	TRUE	1	0.31	5		490	504	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61753571	61753571	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057994-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	35	263	0	ENST00000401558.2:c.212A>G	p.Gln71Arg	p.Q71R	ENST00000401558	NM_003400.3	71	cAg/cGg	3/25	0.279758674452662	1	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	0	0.31	1		263	182	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309169	137309169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1409447634	NA	P-0057994-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	38	547	0	ENST00000481739.1:c.776G>A	p.Ser259Asn	p.S259N	ENST00000481739	NM_002957.4	259	aGc/aAc	5/10	1	2	FACETS	0.663	0.549	0.789	0.663	0.549	0.789	SUBCLONAL	1	TRUE	1	0.31	2		547	370	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636617	73636617	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057994-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	157	695	0	ENST00000377687.4:c.880C>G	p.Pro294Ala	p.P294A	ENST00000377687	NM_001730.3	294	Cca/Gca	2/4	0.298341190178269	2	FACETS	0.947	0.873	1	0.947	0.873	1	CLONAL	2	TRUE	0	0.31	2		695	535	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782870	66782870	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057994-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	27	420	0	ENST00000307102.5:c.1099G>C	p.Glu367Gln	p.E367Q	ENST00000307102	NM_002755.3	367	Gag/Cag	11/11	1	2	FACETS	0.562	0.448	0.692	0.562	0.448	0.692	SUBCLONAL	1	TRUE	1	0.31	2		420	310	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197854	123197854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057994-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	18	134	0	ENST00000218089.9:c.1978G>A	p.Glu660Lys	p.E660K	ENST00000218089	NM_001042749.1	660	Gaa/Aaa	20/35	0.167566898616291	2	FACETS	1	0.846	1			1	INDETERMINATE	1	TRUE	NA	0.31	2		134	101	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577518	7577518	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519995	NA	P-0058270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	217	504	0	ENST00000269305.4:c.763A>T	p.Ile255Phe	p.I255F	ENST00000269305	NM_001126112.2	255	Atc/Ttc	7/11	0.605960870616513	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.605960870616513	1		504	435	SUCCESS
APC	324	MSKCC	GRCh37	5	112174438	112174438	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs863225340	NA	P-0058270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	52	166	0	ENST00000257430.4:c.3147G>A	p.Trp1049Ter	p.W1049*	ENST00000257430	NM_000038.5	1049	tgG/tgA	16/16	0.605960870616513	1	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	0	0.605960870616513	1		166	117	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001098	150001098	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	83	342	1	ENST00000253339.5:c.2506A>G	p.Ile836Val	p.I836V	ENST00000253339		836	Att/Gtt	4/7	1	2	FACETS	0.971	0.868	1	0.971	0.868	1	CLONAL	1	TRUE	1	0.605960870616513	2		343	282	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449830	8449830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	70	371	0	ENST00000356435.5:c.3883G>A	p.Ala1295Thr	p.A1295T	ENST00000356435		1295	Gca/Aca	23/35	0.345334694736615	1	FACETS	0.396	0.346	0.449	0.396	0.346	0.449	INDETERMINATE	1	TRUE	0	0.605960870616513	1		371	407	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058536	69058536	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753703	NA	P-0058282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	35	424	0	ENST00000288368.4:c.4180C>T	p.Arg1394Trp	p.R1394W	ENST00000288368	NM_024870.2	1394	Cgg/Tgg	34/40	0.394073922192328	3	FACETS	0.475	0.389	0.571	0.237	0.194	0.286	SUBCLONAL	1	TRUE	1	0.394073922192328	3		424	448	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663840	29663840	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	91	899	1	ENST00000356175.3:c.6272C>T	p.Ala2091Val	p.A2091V	ENST00000356175	NM_000267.3	2091	gCc/gTc	41/57	0.352254009219376	3	FACETS	1	0.926	1	0.526	0.468	0.587	CLONAL	1	TRUE	1	0.394073922192328	3		900	526	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038274	30038281	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTAGGCT	GGTAGGCT	-	novel	NA	P-0058282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	89	502	0	ENST00000338641.4:c.447_447+7del		p.X149_splice	ENST00000338641	NM_000268.3	149		4/16	0.331189551352185	2	FACETS	1	0.981	1	0.74	0.664	0.82	CLONAL	1	TRUE	0	0.394073922192328	2		502	305	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442062	52442062	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0058282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	109	974	3	ENST00000460680.1:c.287T>A	p.Leu96Ter	p.L96*	ENST00000460680	NM_004656.3	96	tTg/tAg	5/17	0.366933062833727	1	FACETS	0.957	0.865	1	0.957	0.865	1	CLONAL	1	TRUE	0	0.394073922192328	1		977	464	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0058418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	21	309	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.542	0.416	0.689	0.542	0.416	0.689	SUBCLONAL	1	TRUE	1	0.17	2		309	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579575	7579575	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	79	822	0	ENST00000269305.4:c.112C>T	p.Gln38Ter	p.Q38*	ENST00000269305	NM_001126112.2	38	Caa/Taa	4/11	1	2	FACETS	0.984	0.863	1	0.984	0.863	1	CLONAL	1	TRUE	1	0.17	2		822	945	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860940	45860940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs574002154	NA	P-0058418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	58	839	0	ENST00000391945.4:c.1255G>A	p.Glu419Lys	p.E419K	ENST00000391945	NM_000400.3	419	Gag/Aag	13/23	1	2	FACETS	0.649	0.556	0.752	0.649	0.556	0.752	SUBCLONAL	1	TRUE	1	0.17	2		839	1051	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492913	56492913	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	64	367	0	ENST00000407977.2:c.26del	p.Leu9ArgfsTer9	p.L9Rfs*9	ENST00000407977		9	cTg/cg	2/10	1	2	FACETS	0.811	0.704	0.927	1	0.974	1	CLONAL	2	TRUE	1	0.17	2		367	464	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	128	730	0	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	1	2	FACETS	0.939	0.85	1	0.939	0.85	1	CLONAL	1	TRUE	1	0.261615927217163	2		730	1042	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0058521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	297	676	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.261615927217163	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.261615927217163	2		676	1111	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961418	41961418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	60	421	0	ENST00000219905.7:c.326G>A	p.Arg109His	p.R109H	ENST00000219905	NM_001164273.1	109	cGt/cAt	2/24	1	2	FACETS	0.721	0.621	0.831	0.721	0.621	0.831	SUBCLONAL	1	TRUE	1	0.261615927217163	2		421	636	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472435	88472435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776296223	NA	P-0058521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	82	491	0	ENST00000360948.2:c.2120C>T	p.Thr707Met	p.T707M	ENST00000360948	NM_001012338.2	707	aCg/aTg	16/19	1	2	FACETS	0.851	0.75	0.959	0.851	0.75	0.959	CLONAL	1	TRUE	1	0.261615927217163	2		491	737	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867313	45867313	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	145	1048	0	ENST00000391945.4:c.880G>C	p.Glu294Gln	p.E294Q	ENST00000391945	NM_000400.3	294	Gag/Cag	10/23	1	2	FACETS	0.925	0.842	1	0.925	0.842	1	CLONAL	1	TRUE	1	0.261615927217163	2		1048	1199	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287303	38287303	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	125	988	0	ENST00000425967.3:c.354G>C	p.Glu118Asp	p.E118D	ENST00000425967	NM_001174067.1	118	gaG/gaC	4/19	0.261615927217163	1	FACETS	0.873	0.79	0.962	0.873	0.79	0.962	CLONAL	1	TRUE	0	0.261615927217163	1		988	951	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0058523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	427	501	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.51965091738405	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	1	0.697144393524237	4		501	641	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519985	NA	P-0058523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	403	729	0	ENST00000269305.4:c.857A>C	p.Glu286Ala	p.E286A	ENST00000269305	NM_001126112.2	286	gAa/gCa	8/11	0.493381456678166	3	FACETS	1	0.993	1	0.761	0.732	0.79	CLONAL	2	TRUE	0	0.697144393524237	3		729	683	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691948	30691952	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AGAAG	AGAAG	-	novel	NA	P-0058523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	100	298	0	ENST00000295754.5:c.450_454del	p.Glu151IlefsTer2	p.E151Ifs*2	ENST00000295754	NM_003242.5	150	tcAGAAGaa/tcaa	3/7	0.493381456678166	3	FACETS	1	0.947	1	0.693	0.637	0.749	CLONAL	2	TRUE	0	0.697144393524237	3		298	186	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058536	69058536	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753703	NA	P-0058564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	76	424	0	ENST00000288368.4:c.4180C>T	p.Arg1394Trp	p.R1394W	ENST00000288368	NM_024870.2	1394	Cgg/Tgg	34/40	0.13002348193314	6	FACETS	1	0.937	1			1	INDETERMINATE	2	FALSE	NA	0.584063991562994	6		424	261	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753146	128753146	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761932135	NA	P-0058564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	362	394	0	ENST00000377970.2:c.1307G>A	p.Arg436Gln	p.R436Q	ENST00000377970	NM_002467.4	436	cGg/cAg	3/3	0.584063991562994	12	FACETS	1	0.98	1			1	CLONAL	5	FALSE	NA	0.584063991562994	12		394	923	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390071	89390071	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	78	273	0	ENST00000336596.2:c.820C>G	p.Arg274Gly	p.R274G	ENST00000336596	NM_005233.5	274	Cga/Gga	4/17	0.46824480525413	3	FACETS	0.784	0.701	0.87			1	SUBCLONAL	2	FALSE	NA	0.584063991562994	3		273	220	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119634983	119634983	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	74	313	0	ENST00000316626.5:c.516C>G	p.Ile172Met	p.I172M	ENST00000316626		172	atC/atG	5/12	0.584063991562994	7	FACETS	1	0.959	1	0.306	0.268	0.346	CLONAL	1	FALSE	3	0.584063991562994	7		313	510	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177839	56177839	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778754223	NA	P-0058564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	85	460	0	ENST00000399503.3:c.2812C>A	p.Pro938Thr	p.P938T	ENST00000399503	NM_005921.1	938	Cct/Act	14/20	0.584063991562994	6	FACETS	1	0.976	1	0.472	0.419	0.528	CLONAL	1	FALSE	3	0.584063991562994	6		460	446	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	139	737	0				ENST00000310581	NM_198253.2	-/1132			0.626455357258263	3	FACETS	0.951	0.881	1	0.951	0.881	1	CLONAL	2	TRUE	1	0.635704308950382	3		737	303	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022959	27022959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377110828	NA	P-0058649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	89	334	0	ENST00000324856.7:c.65C>T	p.Ser22Leu	p.S22L	ENST00000324856	NM_006015.4	22	tCg/tTg	1/20	0.626455357258263	3	FACETS	0.835	0.744	0.931	0.417	0.372	0.466	CLONAL	1	TRUE	1	0.635704308950382	3		334	442	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023535	27023535	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	138	349	0	ENST00000324856.7:c.641C>G	p.Ser214Cys	p.S214C	ENST00000324856	NM_006015.4	214	tCc/tGc	1/20	0.626455357258263	3	FACETS	1	0.966	1	0.553	0.506	0.602	CLONAL	1	TRUE	1	0.635704308950382	3		349	517	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023943	27023943	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	104	390	0	ENST00000324856.7:c.1049C>A	p.Ser350Ter	p.S350*	ENST00000324856	NM_006015.4	350	tCg/tAg	1/20	0.626455357258263	3	FACETS	1	0.936	1	0.525	0.473	0.579	CLONAL	1	TRUE	1	0.635704308950382	3		390	411	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894230	NA	P-0058649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	392	366	0	ENST00000451590.1:c.35G>T	p.Gly12Val	p.G12V	ENST00000451590	NM_001130442.1	12	gGc/gTc	2/5	0.605291810398472	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	0	0.635704308950382	3		366	536	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178712	108178712	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs869312756	NA	P-0058649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	41	281	0	ENST00000278616.4:c.5762+1G>A		p.X1921_splice	ENST00000278616	NM_000051.3	1921			0.626455357258263	3	FACETS	0.339	0.282	0.403	0.17	0.141	0.202	SUBCLONAL	1	TRUE	1	0.635704308950382	3		281	501	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420213	49420213	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	488	465	0	ENST00000301067.7:c.15536G>T	p.Arg5179Leu	p.R5179L	ENST00000301067	NM_003482.3	5179	cGt/cTt	48/54	0.635704308950382	3	FACETS	1	0.985	1			1	CLONAL	3	TRUE	NA	0.635704308950382	3		465	660	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988237	36988237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	86	358	0	ENST00000354822.5:c.416C>T	p.Ser139Phe	p.S139F	ENST00000354822	NM_001079668.2	139	tCt/tTt	2/3	0.401443341354077	3	FACETS	0.931	0.829	1	0.465	0.414	0.519	CLONAL	1	TRUE	1	0.635704308950382	3		358	383	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789646	3789646	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140133512	NA	P-0058649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	559	357	0	ENST00000262367.5:c.4213G>A	p.Val1405Met	p.V1405M	ENST00000262367	NM_004380.2	1405	Gtg/Atg	25/31	0.615500304328927	4	FACETS	0.956	0.931	0.981	0.956	0.931	0.981	CLONAL	4	TRUE	0	0.635704308950382	4		357	752	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618745	37618745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	212	407	0	ENST00000447079.4:c.421G>A	p.Gly141Arg	p.G141R	ENST00000447079	NM_015083.1	141	Gga/Aga	1/14	0.570141000670993	4	FACETS	1	0.957	1	0.521	0.484	0.56	CLONAL	1	TRUE	2	0.635704308950382	4		407	1047	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936769	78936769	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	264	450	0	ENST00000306801.3:c.3851G>C	p.Gly1284Ala	p.G1284A	ENST00000306801	NM_020761.2	1284	gGa/gCa	33/34	0.570141000670993	4	FACETS	0.881	0.829	0.934	0.881	0.829	0.934	CLONAL	2	TRUE	2	0.635704308950382	4		450	771	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312915	30312915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1411284279	NA	P-0058649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	92	371	0	ENST00000262643.3:c.718C>T	p.Arg240Cys	p.R240C	ENST00000262643	NM_001238.2	240	Cgt/Tgt	9/12	0.635704308950382	3	FACETS	0.662	0.589	0.739	0.331	0.294	0.37	SUBCLONAL	1	TRUE	1	0.635704308950382	3		371	576	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027565	48027565	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377411318	NA	P-0058649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	227	329	0	ENST00000234420.5:c.2443C>T	p.Leu815Phe	p.L815F	ENST00000234420	NM_000179.2	815	Ctt/Ttt	4/10	0.635704308950382	5	FACETS	0.984	0.921	1	0.656	0.614	0.699	CLONAL	2	TRUE	2	0.635704308950382	5		329	709	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55603372	55603372	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs190512512	NA	P-0058649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	112	244	1	ENST00000288135.5:c.2728G>T	p.Asp910Tyr	p.D910Y	ENST00000288135	NM_000222.2	910	Gat/Tat	20/21	0.626455357258263	3	FACETS	1	0.943	1	0.529	0.479	0.581	CLONAL	1	TRUE	1	0.635704308950382	3		245	439	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099187	157099195	+	inframe_deletion	In_Frame_Del	DEL	GCGGCGGCA	GCGGCGGCA	-	rs769480864	NA	P-0058649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	94	387	0	ENST00000346085.5:c.133_141del	p.Ala45_Ala47del	p.A45_A47del	ENST00000346085	NM_020732.3	42	GCGGCGGCA/-	1/20	0.275472679028991	5	FACETS	0.964	0.86	1	0.321	0.286	0.359	INDETERMINATE	1	TRUE	2	0.635704308950382	5		387	599	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936995	48936995	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778842	NA	P-0058734-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	121	382	0	ENST00000267163.4:c.763C>T	p.Arg255Ter	p.R255*	ENST00000267163	NM_000321.2	255	Cga/Tga	8/27	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.75144961346301	2		382	320	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0059049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	235	739	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.671768122510697	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.671992630506284	2		739	325	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596053	43596053	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	203	634	0	ENST00000355710.3:c.220G>C	p.Gly74Arg	p.G74R	ENST00000355710	NM_020975.4	74	Ggc/Cgc	2/20	0.594868784957096	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.671992630506284	4		634	475	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396680	396680	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	168	637	0	ENST00000262320.3:c.346G>T	p.Asp116Tyr	p.D116Y	ENST00000262320	NM_003502.3	116	Gac/Tac	2/11	0.671768122510697	2	FACETS	0.984	0.931	1	0.984	0.931	1	CLONAL	2	TRUE	0	0.671992630506284	2		637	254	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2047250	2047301	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCGAGCACCCCGCAGAAGCTGCCGGTGCCCGCGCCCGGCGGCCGGCCCTC	GCCCGAGCACCCCGCAGAAGCTGCCGGTGCCCGCGCCCGGCGGCCGGCCCTC	-	novel	NA	P-0059049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	15	194	0	ENST00000349721.2:c.817_868del	p.Ser273ArgfsTer65	p.S273Rfs*65	ENST00000349721	NM_003070.3	271	gGCCCGAGCACCCCGCAGAAGCTGCCGGTGCCCGCGCCCGGCGGCCGGCCCTCg/gg	5/34	0.296282346559081	3	FACETS	0.719	0.535	0.93	0.24	0.178	0.31	INDETERMINATE	1	TRUE	0	0.671992630506284	3		194	83	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0059355-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	86	657	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.255902335085406	3	FACETS	0.858	0.772	0.947	0.858	0.772	0.947	CLONAL	3	TRUE	0	0.326417075601773	3		657	238	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481627	56481627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1429784531	NA	P-0059355-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	86	920	1	ENST00000267101.3:c.662C>T	p.Pro221Leu	p.P221L	ENST00000267101	NM_001982.3	221	cCc/cTc	6/28	0.184773079113068	4	FACETS	1	0.905	1	0.677	0.604	0.754	INDETERMINATE	2	TRUE	1	0.326417075601773	4		921	344	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911548	114911548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059355-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	38	293	0	ENST00000543371.1:c.1066G>A	p.Ala356Thr	p.A356T	ENST00000543371	NM_001198531.1	356	Gca/Aca	10/14	0.326417075601773	3	FACETS	0.95	0.789	1	0.475	0.394	0.564	CLONAL	1	TRUE	1	0.326417075601773	3		293	285	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31435970	31435970	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs777416100	NA	P-0059355-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	40	416	0	ENST00000344624.3:c.2944G>A	p.Val982Ile	p.V982I	ENST00000344624		982	Gtc/Atc	22/33	1	2	FACETS	0.851	0.72	0.99	1	0.966	1	CLONAL	2	TRUE	1	0.326417075601773	2		416	144	SUCCESS
APC	324	MSKCC	GRCh37	5	112175398	112175399	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0059355-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	153	701	3	ENST00000257430.4:c.4107_4108del	p.Pro1372ThrfsTer2	p.P1372Tfs*2	ENST00000257430	NM_000038.5	1369	ccCAaa/ccaa	16/16	0.317228231329542	4	FACETS	0.96	0.901	1	1	0.986	1	CLONAL	5	TRUE	0	0.326417075601773	4		704	259	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857210	9857210	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059355-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	31	902	0	ENST00000330684.3:c.4191T>G	p.Asn1397Lys	p.N1397K	ENST00000330684	NM_001134407.1	1397	aaT/aaG	13/13	0.326417075601773	3	FACETS	0.891	0.724	1	0.445	0.362	0.539	CLONAL	1	TRUE	1	0.326417075601773	3		902	248	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068386	26068386	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059355-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	36	195	0	ENST00000435504.4:c.104T>G	p.Leu35Arg	p.L35R	ENST00000435504		35	cTt/cGt	2/13	0.184773079113068	4	FACETS	0.841	0.708	0.982	0.841	0.708	0.982	INDETERMINATE	3	TRUE	1	0.326417075601773	4		195	116	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045987	26045987	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059355-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	44	952	4	ENST00000540144.1:c.349C>T	p.Arg117Cys	p.R117C	ENST00000540144	NM_003531.2	117	Cgc/Tgc	1/1	0.326417075601773	3	FACETS	0.852	0.717	1	0.426	0.358	0.501	CLONAL	1	TRUE	1	0.326417075601773	3		956	368	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360624	70360653	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAACAGCAACAGCAG	CAGCAGCAGCAGCAGCAACAGCAACAGCAG	-	novel	NA	P-0059355-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	29	1077	2	ENST00000374080.3:c.6199_6228del	p.Gln2067_Gln2076del	p.Q2067_Q2076del	ENST00000374080		2062	CAGCAGCAGCAGCAGCAACAGCAACAGCAG/-	42/45	1	2	FACETS	0.515	0.414	0.63	0.515	0.414	0.63	SUBCLONAL	1	TRUE	1	0.326417075601773	2		1079	345	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115111972	115111972	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059465-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	359	576	1	ENST00000257566.3:c.1768C>T	p.Gln590Ter	p.Q590*	ENST00000257566	NM_016569.3	590	Cag/Tag	7/8	1	2	FACETS	0.94	0.895	0.986	0.94	0.895	0.986	CLONAL	1	TRUE	1	0.858764781723285	2		577	889	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005888	69005888	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059465-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	266	362	0	ENST00000288368.4:c.2299G>A	p.Asp767Asn	p.D767N	ENST00000288368	NM_024870.2	767	Gac/Aac	21/40	0.858764781723285	4	FACETS	1	0.969	1	0.351	0.329	0.374	CLONAL	1	TRUE	1	0.858764781723285	4		362	1094	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571996	64571996	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059465-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	382	636	0	ENST00000312049.6:c.1643del	p.Gly548ValfsTer11	p.G548Vfs*11	ENST00000312049	NM_130799.2	548	gGt/gt	10/10	0.846877800516772	1	FACETS	0.973	0.941	1	0.973	0.941	1	CLONAL	1	TRUE	0	0.858764781723285	1		636	522	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984753	11984754	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0059465-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	159	212	0	ENST00000353533.5:c.301dup	p.Asp101GlyfsTer31	p.D101Gfs*31	ENST00000353533	NM_003010.3	100	gag/gaGg	3/11	0.836485069504074	1	FACETS	0.969	0.92	1	0.969	0.92	1	CLONAL	1	TRUE	0	0.858764781723285	1		212	218	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0059801-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	151	537	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	0.949	0.874	1	0.949	0.874	1	CLONAL	1	TRUE	1	0.637729075401029	2		537	499	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828140	3828140	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059801-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	24	344	0	ENST00000262367.5:c.1985A>C	p.Gln662Pro	p.Q662P	ENST00000262367	NM_004380.2	662	cAa/cCa	10/31	1	2	FACETS	0.205	0.16	0.256	0.205	0.16	0.256	SUBCLONAL	1	TRUE	1	0.637729075401029	2		344	368	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537255	80537256	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0059801-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	140	463	1	ENST00000286548.4:c.142_143delinsCT	p.Gly48Leu	p.G48L	ENST00000286548	NM_002072.3	48	GGa/CTa	2/7	1	2	FACETS	0.919	0.842	0.997	0.919	0.842	0.997	CLONAL	1	TRUE	1	0.637729075401029	2		464	478	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0060659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	82	306	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.273740093448367	4	FACETS	1	0.942	1	1	0.942	1	INDETERMINATE	2	TRUE	2	0.652828585538721	4		306	195	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0060659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	10	839	1	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	0.333026073392989	4	FACETS	0.116	0.078	0.165	0.058	0.039	0.083	INDETERMINATE	1	TRUE	2	0.652828585538721	4		840	436	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0060850-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	7	212	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.773	1	1	0.773	1	CLONAL	1	TRUE	1	0.19	2		212	54	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692790	89692790	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554898067	NA	P-0060850-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	38	176	0	ENST00000371953.3:c.274G>T	p.Asp92Tyr	p.D92Y	ENST00000371953	NM_000314.4	92	Gac/Tac	5/9	1	2	FACETS	0.877	0.737	1	1	0.973	1	CLONAL	3	TRUE	1	0.19	2		176	152	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652386	206652386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781784265	NA	P-0060850-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	121	499	0	ENST00000367120.3:c.1093G>A	p.Val365Ile	p.V365I	ENST00000367120	NM_014002.3	365	Gtc/Atc	10/22	0.268497120782953	3	FACETS	0.993	0.899	1	0.993	0.899	1	CLONAL	2	TRUE	1	0.19	3		499	702	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630626	158630626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912678	NA	P-0060850-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	40	348	0	ENST00000263640.3:c.617G>A	p.Arg206His	p.R206H	ENST00000263640	NM_001105.4	206	cGc/cAc	6/11	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.19	2		348	359	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27093058	27093058	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs886042036	NA	P-0060850-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	32	349	0	ENST00000324856.7:c.2988+1G>A		p.X996_splice	ENST00000324856	NM_006015.4	996			1	2	FACETS	0.893	0.726	1	0.893	0.726	1	CLONAL	1	TRUE	1	0.19	2		349	377	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225367767	225367767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753045999	NA	P-0060850-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	21	305	0	ENST00000264414.4:c.1400C>T	p.Thr467Met	p.T467M	ENST00000264414	NM_003590.4	467	aCg/aTg	10/16	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.19	2		305	181	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094420	27094421	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060850-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	57	443	0	ENST00000324856.7:c.3129dup	p.Val1044CysfsTer3	p.V1044Cfs*3	ENST00000324856	NM_006015.4	1043	gct/gcTt	11/20	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.19	2		443	513	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941041	71941041	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060850-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	71	585	0	ENST00000298229.2:c.918del	p.Ile307SerfsTer8	p.I307Sfs*8	ENST00000298229	NM_001567.3	306	aCc/ac	8/28	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.19	2		585	657	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662412	67662413	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCTT	novel	NA	P-0060850-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	41	456	0	ENST00000264010.4:c.1659_1663dup	p.Phe555TrpfsTer31	p.F555Wfs*31	ENST00000264010	NM_006565.3	553	gcg/gcGGCTTg	9/12	1	2	FACETS	0.832	0.692	0.987	0.832	0.692	0.987	CLONAL	1	TRUE	1	0.19	2		456	519	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492802	56492802	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060850-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	101	479	0	ENST00000407977.2:c.137C>A	p.Ala46Asp	p.A46D	ENST00000407977		46	gCt/gAt	2/10	0.224003082995341	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	TRUE	0	0.19	2		479	514	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591151	67591155	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATGTA	ATGTA	-	novel	NA	P-0060850-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	24	330	0	ENST00000274335.5:c.1745_1745+4del		p.X582_splice	ENST00000274335		582		12/15	1	2	FACETS	0.905	0.711	1	0.905	0.711	1	CLONAL	1	TRUE	1	0.19	2		330	279	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681190	86681190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs942447165	NA	P-0060850-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	17	225	0	ENST00000274376.6:c.2831T>C	p.Val944Ala	p.V944A	ENST00000274376	NM_002890.2	944	gTg/gCg	22/25	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.19	2		225	143	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662418	67662418	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060850-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	47	452	1	ENST00000264010.4:c.1664T>G	p.Phe555Cys	p.F555C	ENST00000264010	NM_006565.3	555	tTt/tGt	9/12	1	2	FACETS	0.968	0.817	1	0.968	0.817	1	CLONAL	1	TRUE	1	0.19	2		453	511	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536221	41536221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060850-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	35	302	0	ENST00000263253.7:c.1838G>A	p.Arg613Gln	p.R613Q	ENST00000263253	NM_001429.3	613	cGg/cAg	9/31	1	2	FACETS	0.959	0.787	1	0.959	0.787	1	CLONAL	1	TRUE	1	0.19	2		302	384	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411627	63411627	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061189-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	116	743	0	ENST00000330258.3:c.1540A>T	p.Ser514Cys	p.S514C	ENST00000330258	NM_152424.3	514	Agc/Tgc	2/2	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.201279626803275	2		743	946	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152857415	152858108	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGAACAGCACCAGCCACCTGGAAAGCTGTCCTATGCACAGGCCTACAGAGTTCCACCATCTACCCTCCATGATCTACCTATTAATACCTATCAATCACCCGCCACCCTGCCCATCAGCTCTCTCCCCTATCCATCCAGGTGTCTGTCAACTAGCCAGCTAGCTGTCACCTACCTAGCCATCCAGCCCTCTCCATAAAGCACCCCAGATGTTTCTGATGGGAAGCCAGGTTTAGTAACCTGTGATCACAGTCAAGTTCCCACTCAATTCAGTAAAAGCGGTTCTCCGCTGGGGCAACCCTCCTCCCGGGACACCGGCGACGTCGGTGGAGGCCAGCACTCCTGTTCGACATCCGGGACCCCTAAATGGCAACTGTGCCGAGGGGGAGAGCCTGTCCCAGGCCATCGCAACAGGGTACTTTCGAGCTTCCATGTTCCCCAGCAGCCCGTATCTTTCTTCATGGATAATTAATAGAATTTGGTGAGCACTGCAATACAGAGACTTCCAGAGGGAAAGGGGGCACGTCCAGTGTGCCAAGCAGCCACCTCACCTGCCACCACGGCTTCTCAGCCTCGACCTCGGCGGGCACCTCAACTCCGTAGACCTGCAGGGCCAGGTAGAGCACCGCCACGGCGATGTGCTGGGCCTGGAAGCGGAGGCACAGCGCCCCATGGTAGCTGTCCCGCAGCAGGGCC	CAGAACAGCACCAGCCACCTGGAAAGCTGTCCTATGCACAGGCCTACAGAGTTCCACCATCTACCCTCCATGATCTACCTATTAATACCTATCAATCACCCGCCACCCTGCCCATCAGCTCTCTCCCCTATCCATCCAGGTGTCTGTCAACTAGCCAGCTAGCTGTCACCTACCTAGCCATCCAGCCCTCTCCATAAAGCACCCCAGATGTTTCTGATGGGAAGCCAGGTTTAGTAACCTGTGATCACAGTCAAGTTCCCACTCAATTCAGTAAAAGCGGTTCTCCGCTGGGGCAACCCTCCTCCCGGGACACCGGCGACGTCGGTGGAGGCCAGCACTCCTGTTCGACATCCGGGACCCCTAAATGGCAACTGTGCCGAGGGGGAGAGCCTGTCCCAGGCCATCGCAACAGGGTACTTTCGAGCTTCCATGTTCCCCAGCAGCCCGTATCTTTCTTCATGGATAATTAATAGAATTTGGTGAGCACTGCAATACAGAGACTTCCAGAGGGAAAGGGGGCACGTCCAGTGTGCCAAGCAGCCACCTCACCTGCCACCACGGCTTCTCAGCCTCGACCTCGGCGGGCACCTCAACTCCGTAGACCTGCAGGGCCAGGTAGAGCACCGCCACGGCGATGTGCTGGGCCTGGAAGCGGAGGCACAGCGCCCCATGGTAGCTGTCCCGCAGCAGGGCC	-	novel	NA	P-0061189-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3	28	2	0	ENST00000406277.2:c.507_651+549del		p.X169_splice	ENST00000406277	NM_152274.4	169		6/7	1	2	FACETS	0.997	0.915	1	1	0.975	1	CLONAL	9	TRUE	1	0.201279626803275	2		2	31	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0061232-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	21	226	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	1	0.811	1	1	0.811	1	CLONAL	1	TRUE	1	0.587174331707397	2		226	70	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442051	52442055	+	frameshift_variant	Frame_Shift_Del	DEL	GCACG	GCACG	A	novel	NA	P-0061232-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	174	508	0	ENST00000460680.1:c.294_298delinsT	p.Val99SerfsTer2	p.V99Sfs*2	ENST00000460680	NM_004656.3	98	agCGTGCtc/agTtc	5/17	0.587174331707397	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.587174331707397	1		508	388	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0061432-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	16	205	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.233898366289905	5	FACETS	0.818	0.606	1	0.273	0.202	0.357	CLONAL	1	TRUE	2	0.265571676157484	5		205	206	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0061432-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	127	721	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.265571676157484	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.265571676157484	1		721	678	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467665	66467665	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061432-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	52	478	0	ENST00000273854.3:c.604G>A	p.Val202Ile	p.V202I	ENST00000273854	NM_004439.5	202	Gta/Ata	3/18	0.265571676157484	1	FACETS	0.726	0.618	0.843	0.726	0.618	0.843	SUBCLONAL	1	TRUE	0	0.265571676157484	1		478	468	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098952	178098975	+	inframe_deletion	In_Frame_Del	DEL	TCCAAGATCTATATCTTGCCTCCA	TCCAAGATCTATATCTTGCCTCCA	-	novel	NA	P-0061432-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	71	436	0	ENST00000397062.3:c.70_93del	p.Trp24_Gly31del	p.W24_G31del	ENST00000397062	NM_006164.4	24	TGGAGGCAAGATATAGATCTTGGA/-	2/5	0.205932583610221	2	FACETS	1	0.959	1	0.615	0.538	0.696	CLONAL	1	TRUE	0	0.265571676157484	2		436	435	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426843	49426843	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0061432-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	97	730	0	ENST00000301067.7:c.11645C>G	p.Ser3882Ter	p.S3882*	ENST00000301067	NM_003482.3	3882	tCa/tGa	39/54	0.212530110710207	1	FACETS	0.939	0.837	1	0.939	0.837	1	CLONAL	1	TRUE	0	0.265571676157484	1		730	675	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28903849	28903849	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061432-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	71	490	0	ENST00000282397.4:c.2610del	p.Ser870ArgfsTer6	p.S870Rfs*6	ENST00000282397	NM_002019.4	870	agC/ag	19/30	0.265571676157484	1	FACETS	0.954	0.835	1	0.954	0.835	1	CLONAL	1	TRUE	0	0.265571676157484	1		490	486	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631617	67631617	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061432-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	31	446	0	ENST00000272342.5:c.1803A>T	p.Glu601Asp	p.E601D	ENST00000272342	NM_019002.3	601	gaA/gaT	5/6	1	2	FACETS	0.489	0.395	0.596	0.489	0.395	0.596	SUBCLONAL	1	TRUE	1	0.265571676157484	2		446	477	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881702	111881702	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs745471258	NA	P-0061432-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	46	485	0	ENST00000393256.3:c.380A>G	p.Tyr127Cys	p.Y127C	ENST00000393256	NM_006538.4	127	tAt/tGt	2/4	1	2	FACETS	0.628	0.528	0.738	0.628	0.528	0.738	SUBCLONAL	1	TRUE	1	0.265571676157484	2		485	552	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061506-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	124	737	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.856	0.781	0.934	0.856	0.781	0.934	CLONAL	1	TRUE	1	0.689714874811413	2		737	420	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0061506-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	402	305	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.689714874811413	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.689714874811413	3		305	746	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858337	9858337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560057284	NA	P-0061520-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	19	569	0	ENST00000330684.3:c.3064C>T	p.Arg1022Cys	p.R1022C	ENST00000330684	NM_001134407.1	1022	Cgc/Tgc	13/13	1	2	FACETS	0.376	0.285	0.484	0.376	0.285	0.484	SUBCLONAL	1	TRUE	1	0.27	2		569	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579353	7579357	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGA	CCAGA	-	novel	NA	P-0061520-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	89	670	0	ENST00000269305.4:c.330_334del	p.Gly112LeufsTer35	p.G112Lfs*35	ENST00000269305	NM_001126112.2	110	cgTCTGGgc/cggc	4/11	0.196860554838278	4	FACETS	0.78	0.693	0.872	0.52	0.462	0.581	SUBCLONAL	2	TRUE	1	0.27	4		670	537	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860159	57860159	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061521-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	125	390	0	ENST00000228682.2:c.899C>A	p.Pro300Gln	p.P300Q	ENST00000228682	NM_005269.2	300	cCa/cAa	8/12	1	2	FACETS	0.925	0.845	1	0.925	0.845	1	CLONAL	1	TRUE	1	0.689674263538419	2		390	392	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0061586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	18	306	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.894	0.672	1	0.894	0.672	1	CLONAL	1	FALSE	1	0.0961016653548111	2		306	419	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0061586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	19	253	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.614	0.464	0.792	0.614	0.464	0.792	SUBCLONAL	1	FALSE	1	0.0961016653548111	2		253	644	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519985	NA	P-0061731-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	435	669	1	ENST00000269305.4:c.857A>G	p.Glu286Gly	p.E286G	ENST00000269305	NM_001126112.2	286	gAa/gGa	8/11	0.381859747020665	3	FACETS	0.869	0.833	0.904	0.869	0.833	0.904	CLONAL	3	TRUE	0	0.461016536246646	3		670	891	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458147	120458147	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1325403451	NA	P-0061731-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	421	733	0	ENST00000256646.2:c.7198C>T	p.Arg2400Ter	p.R2400*	ENST00000256646	NM_024408.3	2400	Cga/Tga	34/34	1	2	FACETS	0.827	0.79	0.865	1	0.996	1	CLONAL	2	TRUE	1	0.461016536246646	2		733	1104	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852488	63852488	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061731-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	222	574	0	ENST00000279873.7:c.3266C>G	p.Ser1089Trp	p.S1089W	ENST00000279873	NM_032199.2	1089	tCg/tGg	10/10	0.196968729557608	5	FACETS	0.886	0.826	0.949	0.591	0.55	0.633	INDETERMINATE	2	TRUE	2	0.461016536246646	5		574	919	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119767	70119767	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061731-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	151	443	0	ENST00000245479.2:c.769C>A	p.Arg257Ser	p.R257S	ENST00000245479	NM_000346.3	257	Cgc/Agc	3/3	0.461016536246646	3	FACETS	1	0.95	1	0.351	0.321	0.382	CLONAL	1	TRUE	0	0.461016536246646	3		443	766	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033398	48033398	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061731-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	45	427	0	ENST00000234420.5:c.3702A>T	p.Glu1234Asp	p.E1234D	ENST00000234420	NM_000179.2	1234	gaA/gaT	8/10	0.152628800936272	3	FACETS	0.39	0.327	0.46	0.195	0.163	0.23	INDETERMINATE	1	TRUE	1	0.461016536246646	3		427	616	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1941381	1941381	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1390587603	NA	P-0061731-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	67	347	0	ENST00000382891.5:c.1757C>T	p.Ala586Val	p.A586V	ENST00000382891	NM_133335.3	586	gCa/gTa	9/22	0.41916289141873	2	FACETS	0.528	0.459	0.602	0.264	0.229	0.301	SUBCLONAL	1	TRUE	0	0.461016536246646	2		347	551	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150913824	150913831	+	frameshift_variant	Frame_Shift_Del	DEL	CCTTAAGA	CCTTAAGA	TGAAGCT	novel	NA	P-0061731-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	136	345	1	ENST00000271640.5:c.467_474delinsTGAAGCT	p.Ala156ValfsTer30	p.A156Vfs*30	ENST00000271640	NM_001145415.1	156	gCCTTAAGA/gTGAAGCT	5/22	0.2492418241749	4	FACETS	1	0.961	1	0.55	0.501	0.603	INDETERMINATE	1	TRUE	2	0.461016536246646	4		346	783	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	275	646	10	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.44	2		656	880	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	62	588	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.385	0.332	0.443	0.385	0.332	0.443	SUBCLONAL	1	TRUE	1	0.44	2		588	732	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669547	88669547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56394626	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	112	436	0	ENST00000360948.2:c.1351G>A	p.Val451Ile	p.V451I	ENST00000360948	NM_001012338.2	451	Gtc/Atc	12/19	0.189110372409605	1	FACETS	0.867	0.785	0.953	0.867	0.785	0.953	INDETERMINATE	1	TRUE	0	0.44	1		436	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	190	586	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.44	2		586	762	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	50	351	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.521	0.443	0.607	0.521	0.443	0.607	SUBCLONAL	1	TRUE	1	0.44	2		351	436	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	73	920	1	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	1	2	FACETS	0.324	0.282	0.369	0.324	0.282	0.369	SUBCLONAL	1	TRUE	1	0.44	2		921	1024	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	389	320	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.44	2		325	1277	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	188	249	3	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.842	0.777	0.909	0.842	0.777	0.909	CLONAL	1	TRUE	1	0.44	2		252	1015	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	201	742	3	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	0.97	0.899	1	0.97	0.899	1	CLONAL	1	TRUE	1	0.44	2		745	942	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165213	47165213	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	117	508	0	ENST00000409792.3:c.913del	p.Thr305GlnfsTer35	p.T305Qfs*35	ENST00000409792	NM_014159.6	305	Aca/ca	3/21	1	2	FACETS	0.9	0.814	0.99	0.9	0.814	0.99	CLONAL	1	TRUE	1	0.44	2		508	591	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058536	69058536	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753703	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	68	424	0	ENST00000288368.4:c.4180C>T	p.Arg1394Trp	p.R1394W	ENST00000288368	NM_024870.2	1394	Cgg/Tgg	34/40	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.44	2		424	295	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114817	108114817	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786204543	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	37	388	0	ENST00000278616.4:c.640del	p.Ser214ProfsTer16	p.S214Pfs*16	ENST00000278616	NM_000051.3	212	Ttt/tt	6/63	1	2	FACETS	0.492	0.406	0.587	0.492	0.406	0.587	SUBCLONAL	1	TRUE	1	0.44	2		388	342	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	80	367	3	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	0.759	0.67	0.854	0.759	0.67	0.854	SUBCLONAL	1	TRUE	1	0.44	2		370	479	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260749	16260749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769855469	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	161	914	2	ENST00000375759.3:c.8014G>A	p.Val2672Met	p.V2672M	ENST00000375759	NM_015001.2	2672	Gtg/Atg	11/15	1	2	FACETS	0.663	0.607	0.722	0.663	0.607	0.722	SUBCLONAL	1	TRUE	1	0.44	2		916	1104	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087885	27087885	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	48	584	0	ENST00000324856.7:c.2172G>A	p.Met724Ile	p.M724I	ENST00000324856	NM_006015.4	724	atG/atA	6/20	1	2	FACETS	0.301	0.254	0.353	0.301	0.254	0.353	SUBCLONAL	1	TRUE	1	0.44	2		584	725	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	211	778	0	ENST00000324856.7:c.4555del	p.Gln1519ArgfsTer8	p.Q1519Rfs*8	ENST00000324856	NM_006015.4	1517	gCc/gc	18/20	1	2	FACETS	0.977	0.907	1	0.977	0.907	1	CLONAL	1	TRUE	1	0.44	2		778	982	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937710	36937710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369185176	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	131	773	0	ENST00000361632.4:c.1028G>A	p.Arg343Gln	p.R343Q	ENST00000361632		343	cGg/cAg	8/16	1	2	FACETS	0.605	0.548	0.664	0.605	0.548	0.664	SUBCLONAL	1	TRUE	1	0.44	2		773	985	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726529	46726529	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	168	786	0	ENST00000371975.4:c.608A>G	p.Gln203Arg	p.Q203R	ENST00000371975	NM_003579.3	203	cAg/cGg	7/18	1	2	FACETS	0.825	0.758	0.894	0.825	0.758	0.894	CLONAL	1	TRUE	1	0.44	2		786	926	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846342	156846342	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	57	768	0	ENST00000524377.1:c.1786del	p.Asp596ThrfsTer62	p.D596Tfs*62	ENST00000524377	NM_002529.3	595	Ggg/gg	14/17	1	2	FACETS	0.294	0.252	0.341	0.294	0.252	0.341	SUBCLONAL	1	TRUE	1	0.44	2		768	880	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851354	156851354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1324983370	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	81	912	1	ENST00000524377.1:c.2311C>T	p.Arg771Cys	p.R771C	ENST00000524377	NM_002529.3	771	Cgc/Tgc	17/17	1	2	FACETS	0.348	0.306	0.394	0.348	0.306	0.394	SUBCLONAL	1	TRUE	1	0.44	2		913	1057	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117070	193117070	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750706815	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	42	433	0	ENST00000367435.3:c.803G>A	p.Arg268Gln	p.R268Q	ENST00000367435	NM_024529.4	268	cGa/cAa	8/17	1	2	FACETS	0.34	0.283	0.403	0.34	0.283	0.403	SUBCLONAL	1	TRUE	1	0.44	2		433	562	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206664154	206664154	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1553390134	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	143	505	0	ENST00000367120.3:c.1696C>T	p.Leu566Phe	p.L566F	ENST00000367120	NM_014002.3	566	Ctt/Ttt	17/22	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.44	2		505	618	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230459181	230459181	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138064546	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	209	667	0	ENST00000391860.1:c.1220C>T	p.Pro407Leu	p.P407L	ENST00000391860	NM_001258311.1	407	cCg/cTg	7/7	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.44	2		667	803	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828162	243828162	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1399248274	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	75	341	0	ENST00000263826.5:c.196C>T	p.Arg66Ter	p.R66*	ENST00000263826	NM_005465.4	66	Cga/Tga	3/13	1	2	FACETS	0.982	0.867	1	0.982	0.867	1	CLONAL	1	TRUE	1	0.44	2		341	347	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925412	114925412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573425555	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	105	580	1	ENST00000543371.1:c.1490C>T	p.Pro497Leu	p.P497L	ENST00000543371	NM_001198531.1	497	cCg/cTg	14/14	1	2	FACETS	0.698	0.626	0.774	0.698	0.626	0.774	SUBCLONAL	1	TRUE	1	0.44	2		581	684	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298133	123298133	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1313917697	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	122	637	0	ENST00000358487.5:c.721A>G	p.Asn241Asp	p.N241D	ENST00000358487	NM_000141.4	241	Aat/Gat	6/18	1	2	FACETS	0.772	0.699	0.85	0.772	0.699	0.85	SUBCLONAL	1	TRUE	1	0.44	2		637	718	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894230	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	262	742	0	ENST00000451590.1:c.35G>A	p.Gly12Asp	p.G12D	ENST00000451590	NM_001130442.1	12	gGc/gAc	2/5	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.44	2		742	943	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518640	69518640	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	46	613	0	ENST00000294312.3:c.5G>A	p.Arg2Gln	p.R2Q	ENST00000294312	NM_005117.2	2	cGg/cAg	1/3	1	2	FACETS	0.281	0.236	0.332	0.281	0.236	0.332	SUBCLONAL	1	TRUE	1	0.44	2		613	743	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94908705	94908705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs547426358	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	61	419	0	ENST00000536441.1:c.1349G>A	p.Arg450His	p.R450H	ENST00000536441	NM_144665.3	450	cGc/cAc	9/10	1	2	FACETS	0.618	0.534	0.708	0.618	0.534	0.708	SUBCLONAL	1	TRUE	1	0.44	2		419	449	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998685	100998685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	150	776	0	ENST00000325455.5:c.1117G>A	p.Ala373Thr	p.A373T	ENST00000325455	NM_001202474.3	373	Gcg/Acg	1/8	1	2	FACETS	0.717	0.655	0.782	0.717	0.655	0.782	SUBCLONAL	1	TRUE	1	0.44	2		776	951	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236087	108236087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781894	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	101	591	0	ENST00000278616.4:c.9023G>A	p.Arg3008His	p.R3008H	ENST00000278616	NM_000051.3	3008	cGt/cAt	63/63	1	2	FACETS	0.663	0.593	0.738	0.663	0.593	0.738	SUBCLONAL	1	TRUE	1	0.44	2		591	692	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118367017	118367017	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	72	433	1	ENST00000534358.1:c.5603del	p.Pro1868GlnfsTer3	p.P1868Qfs*3	ENST00000534358	NM_005933.3	1867	Ccc/cc	20/36	1	2	FACETS	0.558	0.488	0.634	0.558	0.488	0.634	SUBCLONAL	1	TRUE	1	0.44	2		434	586	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434054	49434054	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369604891	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	97	865	0	ENST00000301067.7:c.7499C>T	p.Ala2500Val	p.A2500V	ENST00000301067	NM_003482.3	2500	gCg/gTg	31/54	1	2	FACETS	0.4	0.356	0.448	0.4	0.356	0.448	SUBCLONAL	1	TRUE	1	0.44	2		865	1101	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	72	923	2	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.298	0.259	0.341	0.298	0.259	0.341	SUBCLONAL	1	TRUE	1	0.44	2		925	1097	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446070	49446070	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201512665	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	161	1000	0	ENST00000301067.7:c.1396C>T	p.Arg466Cys	p.R466C	ENST00000301067	NM_003482.3	466	Cgc/Tgc	10/54	1	2	FACETS	0.608	0.557	0.663	0.608	0.557	0.663	SUBCLONAL	1	TRUE	1	0.44	2		1000	1203	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482369	56482369	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	156	541	1	ENST00000267101.3:c.917C>A	p.Pro306His	p.P306H	ENST00000267101	NM_001982.3	306	cCt/cAt	8/28	0.256264397206524	3	FACETS	1	0.971	1	0.565	0.518	0.614	INDETERMINATE	1	TRUE	1	0.44	3		542	765	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495714	56495715	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	48	615	0	ENST00000267101.3:c.3910dup	p.His1304ProfsTer12	p.H1304Pfs*12	ENST00000267101	NM_001982.3	1302	gcc/gCcc	28/28	0.256264397206524	3	FACETS	0.294	0.247	0.345	0.147	0.123	0.173	INDETERMINATE	1	TRUE	1	0.44	3		615	906	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145091	58145091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759017803	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	97	699	0	ENST00000257904.6:c.253C>T	p.Arg85Trp	p.R85W	ENST00000257904	NM_000075.3	85	Cgg/Tgg	3/8	0.256264397206524	3	FACETS	0.548	0.487	0.613	0.274	0.243	0.307	INDETERMINATE	1	TRUE	1	0.44	3		699	982	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432117	121432118	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776825	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	313	781	16	ENST00000257555.6:c.872dup	p.Gly292ArgfsTer25	p.G292Rfs*25	ENST00000257555		288	-/C	4/10	0.256264397206524	3	FACETS	0.786	0.742	0.831	0.786	0.742	0.831	INDETERMINATE	2	TRUE	1	0.44	3		797	1104	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219578	133219578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376530977	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	94	728	0	ENST00000320574.5:c.4556G>A	p.Arg1519His	p.R1519H	ENST00000320574	NM_006231.2	1519	cGc/cAc	36/49	0.256264397206524	3	FACETS	0.555	0.493	0.622	0.278	0.246	0.311	INDETERMINATE	1	TRUE	1	0.44	3		728	939	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597587	28597588	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	39	402	0	ENST00000241453.7:c.2317dup	p.Arg773LysfsTer14	p.R773Kfs*14	ENST00000241453	NM_004119.2	773	agg/aAgg	19/24	1	2	FACETS	0.382	0.316	0.455	0.382	0.316	0.455	SUBCLONAL	1	TRUE	1	0.44	2		402	464	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913837	32913837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359507	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	85	464	0	ENST00000380152.3:c.5351del	p.Asn1784ThrfsTer7	p.N1784Tfs*7	ENST00000380152		1782	cAa/ca	11/27	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.44	2		464	376	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240138	41240138	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1323268054	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	85	605	0	ENST00000379561.5:c.212T>C	p.Met71Thr	p.M71T	ENST00000379561	NM_002015.3	71	aTg/aCg	1/3	1	2	FACETS	0.538	0.475	0.605	0.538	0.475	0.605	SUBCLONAL	1	TRUE	1	0.44	2		605	718	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	150	512	7	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.44	2		519	604	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435493	110435493	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	258	818	0	ENST00000375856.3:c.2908C>T	p.Arg970Trp	p.R970W	ENST00000375856	NM_003749.2	970	Cgg/Tgg	1/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.44	2		818	1042	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437106	110437106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	141	726	0	ENST00000375856.3:c.1295C>T	p.Ser432Phe	p.S432F	ENST00000375856	NM_003749.2	432	tCc/tTc	1/2	1	2	FACETS	0.718	0.654	0.785	0.718	0.654	0.785	SUBCLONAL	1	TRUE	1	0.44	2		726	893	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582875	95582875	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	65	446	0	ENST00000393063.1:c.1667C>A	p.Pro556His	p.P556H	ENST00000393063	NM_030621.3	556	cCc/cAc	11/28	NA	2	FACETS	0.522	0.453	0.597			1	INDETERMINATE	1	TRUE	NA	0.44	2		446	566	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241276	105241276	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	199	782	0	ENST00000349310.3:c.632C>T	p.Thr211Ile	p.T211I	ENST00000349310	NM_001014432.1	211	aCa/aTa	8/15	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.44	2		782	845	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42053990	42053991	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	40	379	0	ENST00000219905.7:c.7457dup	p.Asn2486LysfsTer20	p.N2486Kfs*20	ENST00000219905	NM_001164273.1	2484	-/A	21/24	1	2	FACETS	0.433	0.36	0.514	0.433	0.36	0.514	SUBCLONAL	1	TRUE	1	0.44	2		379	420	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701242	43701242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368366606	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	139	534	0	ENST00000382044.4:c.5453G>A	p.Arg1818Gln	p.R1818Q	ENST00000382044	NM_001141980.1	1818	cGg/cAg	26/28	1	2	FACETS	0.9	0.821	0.983	0.9	0.821	0.983	CLONAL	1	TRUE	1	0.44	2		534	702	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50733660	50733661	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	32	332	0	ENST00000307179.4:c.226dup	p.Arg76LysfsTer3	p.R76Kfs*3	ENST00000307179		73	-/A	3/20	1	2	FACETS	0.309	0.251	0.376	0.309	0.251	0.376	SUBCLONAL	1	TRUE	1	0.44	2		332	470	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2097710	2097710	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	131	682	0	ENST00000219066.1:c.139G>T	p.Glu47Ter	p.E47*	ENST00000219066	NM_002528.5	47	Gaa/Taa	1/6	1	2	FACETS	0.739	0.671	0.811	0.739	0.671	0.811	SUBCLONAL	1	TRUE	1	0.44	2		682	806	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778282	3778282	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	85	932	0	ENST00000262367.5:c.6766del	p.Leu2256SerfsTer46	p.L2256Sfs*46	ENST00000262367	NM_004380.2	2256	Ctc/tc	31/31	1	2	FACETS	0.335	0.295	0.378	0.335	0.295	0.378	SUBCLONAL	1	TRUE	1	0.44	2		932	1153	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772234	68772234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	116	652	0	ENST00000261769.5:c.83G>A	p.Cys28Tyr	p.C28Y	ENST00000261769	NM_004360.3	28	tGc/tAc	2/16	1	2	FACETS	0.646	0.582	0.714	0.646	0.582	0.714	SUBCLONAL	1	TRUE	1	0.44	2		652	816	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830441	72830441	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	113	405	0	ENST00000268489.5:c.6140del	p.Pro2047LeufsTer54	p.P2047Lfs*54	ENST00000268489	NM_006885.3	2047	cCt/ct	9/10	1	2	FACETS	0.997	0.902	1	0.997	0.902	1	CLONAL	1	TRUE	1	0.44	2		405	515	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	81	777	2	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.391	0.344	0.443	0.391	0.344	0.443	SUBCLONAL	1	TRUE	1	0.44	2		779	941	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944264	81944264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1009796025	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	90	640	1	ENST00000359376.3:c.1873G>A	p.Ala625Thr	p.A625T	ENST00000359376	NM_002661.3	625	Gcc/Acc	18/33	1	2	FACETS	0.49	0.434	0.55	0.49	0.434	0.55	SUBCLONAL	1	TRUE	1	0.44	2		641	835	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89355072	89355072	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	60	705	1	ENST00000301030.4:c.608C>T	p.Thr203Met	p.T203M	ENST00000301030	NM_001256183.1	203	aCg/aTg	7/13	1	2	FACETS	0.312	0.268	0.361	0.312	0.268	0.361	SUBCLONAL	1	TRUE	1	0.44	2		706	873	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16062109	16062109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1373145988	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	93	468	0	ENST00000268712.3:c.697C>T	p.Arg233Cys	p.R233C	ENST00000268712	NM_006311.3	233	Cgc/Tgc	6/46	1	2	FACETS	0.627	0.558	0.701	0.627	0.558	0.701	SUBCLONAL	1	TRUE	1	0.44	2		468	674	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	67	939	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.273	0.236	0.313	0.273	0.236	0.313	SUBCLONAL	1	TRUE	1	0.44	2		939	1117	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435689	56435689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779655071	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	264	810	0	ENST00000407977.2:c.1448C>T	p.Thr483Met	p.T483M	ENST00000407977		483	aCg/aTg	9/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.44	2		810	976	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436128	56436128	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	131	717	0	ENST00000407977.2:c.1009C>T	p.Arg337Ter	p.R337*	ENST00000407977		337	Cga/Tga	9/10	1	2	FACETS	0.642	0.582	0.705	0.642	0.582	0.705	SUBCLONAL	1	TRUE	1	0.44	2		717	928	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	152	313	0	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	1	2	FACETS	0.718	0.656	0.783	0.718	0.656	0.783	SUBCLONAL	1	TRUE	1	0.44	2		313	962	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45423102	45423102	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749758342	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	120	544	0	ENST00000262160.6:c.26C>T	p.Pro9Leu	p.P9L	ENST00000262160	NM_005901.5	9	cCg/cTg	2/11	1	2	FACETS	0.707	0.639	0.78	0.707	0.639	0.78	SUBCLONAL	1	TRUE	1	0.44	2		544	771	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226767	2226767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	129	947	0	ENST00000398665.3:c.4247G>A	p.Arg1416His	p.R1416H	ENST00000398665	NM_032482.2	1416	cGc/cAc	27/28	1	2	FACETS	0.562	0.508	0.618	0.562	0.508	0.618	SUBCLONAL	1	TRUE	1	0.44	2		947	1044	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212370	5212370	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777981018	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	237	919	0	ENST00000357368.4:c.4747G>A	p.Gly1583Ser	p.G1583S	ENST00000357368	NM_002850.3	1583	Ggc/Agc	31/38	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.44	2		919	970	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223017	5223017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1313647555	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	99	920	0	ENST00000357368.4:c.2786G>A	p.Arg929His	p.R929H	ENST00000357368	NM_002850.3	929	cGt/cAt	18/38	1	2	FACETS	0.448	0.399	0.5	0.448	0.399	0.5	SUBCLONAL	1	TRUE	1	0.44	2		920	1005	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274290	5274290	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368676720	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	103	704	0	ENST00000357368.4:c.157G>A	p.Val53Met	p.V53M	ENST00000357368	NM_002850.3	53	Gtg/Atg	3/38	1	2	FACETS	0.59	0.527	0.656	0.59	0.527	0.656	SUBCLONAL	1	TRUE	1	0.44	2		704	794	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6213976	6213976	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs772076449	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	112	710	0	ENST00000252674.7:c.1381del	p.Gln461ArgfsTer46	p.Q461Rfs*46	ENST00000252674	NM_005934.3	461	Cag/ag	9/12	1	2	FACETS	0.605	0.543	0.67	0.605	0.543	0.67	SUBCLONAL	1	TRUE	1	0.44	2		710	842	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302276	15302276	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774985086	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	116	670	0	ENST00000263388.2:c.995G>A	p.Arg332His	p.R332H	ENST00000263388	NM_000435.2	332	cGc/cAc	6/33	1	2	FACETS	0.627	0.565	0.693	0.627	0.565	0.693	SUBCLONAL	1	TRUE	1	0.44	2		670	841	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257365	19257366	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	112	817	2	ENST00000162023.5:c.767dup	p.Glu257ArgfsTer28	p.E257Rfs*28	ENST00000162023		256	cca/ccCa	11/13	1	2	FACETS	0.54	0.485	0.598	0.54	0.485	0.598	SUBCLONAL	1	TRUE	1	0.44	2		819	943	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220916	36220918	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	rs1568378410	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	216	737	0	ENST00000222270.7:c.4970_4972del	p.Ser1657del	p.S1657del	ENST00000222270	NM_014727.1	1656	TCC/-	23/37	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.44	2		737	942	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228998	36228998	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	235	850	0	ENST00000222270.7:c.7778G>A	p.Arg2593His	p.R2593H	ENST00000222270	NM_014727.1	2593	cGc/cAc	36/37	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.44	2		850	1004	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47503884	47503884	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	45	608	0	ENST00000404338.3:c.4444del	p.Gln1482SerfsTer317	p.Q1482Sfs*317	ENST00000404338	NM_004491.4	1480	aCc/ac	6/6	1	2	FACETS	0.255	0.213	0.301	0.255	0.213	0.301	SUBCLONAL	1	TRUE	1	0.44	2		608	803	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920350	50920352	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	83	744	0	ENST00000440232.2:c.3119_3120+1del		p.KEdel	ENST00000440232	NM_002691.3	1039	aAGGag/aag	25/27	1	2	FACETS	0.414	0.364	0.467	0.414	0.364	0.467	SUBCLONAL	1	TRUE	1	0.44	2		744	912	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574157	46574157	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	58	704	2	ENST00000263734.3:c.172C>T	p.Arg58Ter	p.R58*	ENST00000263734	NM_001430.4	58	Cga/Tga	2/16	1	2	FACETS	0.276	0.236	0.32	0.276	0.236	0.32	SUBCLONAL	1	TRUE	1	0.44	2		706	955	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646000	215646000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	36	591	0	ENST00000260947.4:c.598G>A	p.Ala200Thr	p.A200T	ENST00000260947	NM_000465.2	200	Gca/Aca	4/11	1	2	FACETS	0.26	0.213	0.313	0.26	0.213	0.313	SUBCLONAL	1	TRUE	1	0.44	2		591	630	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	88	817	1	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	1	2	FACETS	0.404	0.357	0.454	0.404	0.357	0.454	SUBCLONAL	1	TRUE	1	0.44	2		818	991	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376801	31376801	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	218	693	0	ENST00000328111.2:c.796G>A	p.Asp266Asn	p.D266N	ENST00000328111	NM_006892.3	266	Gat/Aat	7/23	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.44	2		693	799	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022324	36022324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760138531	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	237	734	0	ENST00000358208.4:c.377C>T	p.Ser126Leu	p.S126L	ENST00000358208		126	tCg/tTg	4/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.44	2		734	872	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265436	46265436	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	91	528	0	ENST00000371998.3:c.2306G>A	p.Cys769Tyr	p.C769Y	ENST00000371998		769	tGc/tAc	12/23	1	2	FACETS	0.718	0.639	0.802	0.718	0.639	0.802	SUBCLONAL	1	TRUE	1	0.44	2		528	576	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070868	30070868	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771143279	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	86	523	0	ENST00000338641.4:c.1384C>T	p.Arg462Cys	p.R462C	ENST00000338641	NM_000268.3	462	Cgc/Tgc	13/16	1	2	FACETS	0.554	0.49	0.623	0.554	0.49	0.623	SUBCLONAL	1	TRUE	1	0.44	2		523	705	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573534	41573534	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	151	831	0	ENST00000263253.7:c.5819G>A	p.Arg1940His	p.R1940H	ENST00000263253	NM_001429.3	1940	cGc/cAc	31/31	1	2	FACETS	0.664	0.607	0.725	0.664	0.607	0.725	SUBCLONAL	1	TRUE	1	0.44	2		831	1033	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	109	566	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	1	2	FACETS	0.667	0.599	0.739	0.667	0.599	0.739	SUBCLONAL	1	TRUE	1	0.44	2		566	743	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070324	37070324	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63749795	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	91	524	0	ENST00000231790.2:c.1459C>T	p.Arg487Ter	p.R487*	ENST00000231790	NM_000249.3	487	Cga/Tga	13/19	1	2	FACETS	0.696	0.619	0.778	0.696	0.619	0.778	SUBCLONAL	1	TRUE	1	0.44	2		524	594	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161907	47161907	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	64	590	1	ENST00000409792.3:c.4219del	p.Arg1407GlyfsTer5	p.R1407Gfs*5	ENST00000409792	NM_014159.6	1407	Agg/gg	3/21	1	2	FACETS	0.403	0.348	0.462	0.403	0.348	0.462	SUBCLONAL	1	TRUE	1	0.44	2		591	722	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165918	47165918	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs775039657	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	104	559	0	ENST00000409792.3:c.208C>T	p.Arg70Ter	p.R70*	ENST00000409792	NM_014159.6	70	Cga/Tga	3/21	1	2	FACETS	0.703	0.63	0.781	0.703	0.63	0.781	SUBCLONAL	1	TRUE	1	0.44	2		559	672	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090563	71090565	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs751098424	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	85	550	0	ENST00000318789.4:c.783_785del	p.Ser262del	p.S262del	ENST00000318789	NM_032682.5	261	tcCTCt/tct	11/21	1	2	FACETS	0.512	0.452	0.577	0.512	0.452	0.577	SUBCLONAL	1	TRUE	1	0.44	2		550	754	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261555	142261555	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	25	364	0	ENST00000350721.4:c.3402del	p.Phe1134LeufsTer6	p.F1134Lfs*6	ENST00000350721	NM_001184.3	1134	ttT/tt	17/47	1	2	FACETS	0.291	0.229	0.362	0.291	0.229	0.362	SUBCLONAL	1	TRUE	1	0.44	2		364	391	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281647	142281647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	58	418	0	ENST00000350721.4:c.597G>A	p.Met199Ile	p.M199I	ENST00000350721	NM_001184.3	199	atG/atA	4/47	1	2	FACETS	0.573	0.493	0.66	0.573	0.493	0.66	SUBCLONAL	1	TRUE	1	0.44	2		418	460	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	10	433	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.101	0.067	0.143	0.101	0.067	0.143	SUBCLONAL	1	TRUE	1	0.44	2		434	452	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803120	1803120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1162571458	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	200	758	0	ENST00000260795.2:c.472C>T	p.Arg158Trp	p.R158W	ENST00000260795		158	Cgg/Tgg	4/17	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.44	2		758	871	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	152	891	5	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	1	2	FACETS	0.681	0.622	0.743	0.681	0.622	0.743	SUBCLONAL	1	TRUE	1	0.44	2		896	1014	SUCCESS
REST	5978	MSKCC	GRCh37	4	57798086	57798088	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	139	487	0	ENST00000309042.7:c.3065_3067del	p.Asn1022del	p.N1022del	ENST00000309042	NM_005612.4	1021	gACAac/gac	4/4	1	2	FACETS	0.981	0.896	1	0.981	0.896	1	CLONAL	1	TRUE	1	0.44	2		487	644	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164862	106164863	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1428898350	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	34	511	0	ENST00000380013.4:c.3732_3733del	p.Tyr1245LeufsTer22	p.Y1245Lfs*22	ENST00000380013	NM_001127208.2	1244	CTc/c	6/11	1	2	FACETS	0.234	0.19	0.283	0.234	0.19	0.283	SUBCLONAL	1	TRUE	1	0.44	2		511	661	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	109	758	1	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	0.596	0.535	0.661	0.596	0.535	0.661	SUBCLONAL	1	TRUE	1	0.44	2		759	831	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	39	440	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.334	0.277	0.399	0.334	0.277	0.399	SUBCLONAL	1	TRUE	1	0.44	2		440	530	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38954947	38954947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771642192	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	40	338	0	ENST00000357387.3:c.2626G>A	p.Val876Ile	p.V876I	ENST00000357387	NM_152756.3	876	Gtc/Atc	27/38	1	2	FACETS	0.697	0.582	0.822	0.697	0.582	0.822	SUBCLONAL	1	TRUE	1	0.44	2		338	261	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638492	176638492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780306768	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	106	698	0	ENST00000439151.2:c.3092G>A	p.Arg1031Gln	p.R1031Q	ENST00000439151	NM_022455.4	1031	cGa/cAa	5/23	1	2	FACETS	0.543	0.486	0.603	0.543	0.486	0.603	SUBCLONAL	1	TRUE	1	0.44	2		698	888	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395876	395876	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	74	640	0	ENST00000380956.4:c.433C>T	p.Gln145Ter	p.Q145*	ENST00000380956	NM_001195286.1	145	Cag/Tag	4/9	NA	2	FACETS	0.435	0.38	0.494			1	INDETERMINATE	1	TRUE	NA	0.44	2		640	774	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165128	32165128	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	52	773	0	ENST00000375023.3:c.5000G>T	p.Gly1667Val	p.G1667V	ENST00000375023	NM_004557.3	1667	gGg/gTg	27/30	1	2	FACETS	0.242	0.205	0.283	0.242	0.205	0.283	SUBCLONAL	1	TRUE	1	0.44	2		773	975	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287299	33287299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	127	771	0	ENST00000374542.5:c.1798G>A	p.Val600Ile	p.V600I	ENST00000374542	NM_001141970.1	600	Gtc/Atc	6/8	1	2	FACETS	0.634	0.573	0.697	0.634	0.573	0.697	SUBCLONAL	1	TRUE	1	0.44	2		771	911	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748585	43748586	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs374210528	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	210	699	0	ENST00000523873.1:c.544dup	p.His182ProfsTer22	p.H182Pfs*22	ENST00000523873		180	ggc/ggCc	6/8	1	2	FACETS	0.974	0.905	1	0.974	0.905	1	CLONAL	1	TRUE	1	0.44	2		699	980	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93973580	93973580	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	37	299	0	ENST00000369303.4:c.1796A>T	p.His599Leu	p.H599L	ENST00000369303	NM_004440.3	599	cAt/cTt	9/17	1	2	FACETS	0.837	0.697	0.99	0.837	0.697	0.99	CLONAL	1	TRUE	1	0.44	2		299	201	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004720	150004720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772839695	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	66	660	0	ENST00000253339.5:c.1505G>A	p.Arg502His	p.R502H	ENST00000253339		502	cGt/cAt	3/7	1	2	FACETS	0.352	0.304	0.403	0.352	0.304	0.403	SUBCLONAL	1	TRUE	1	0.44	2		660	853	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099403	157099408	+	inframe_deletion	In_Frame_Del	DEL	CAGCAG	CAGCAG	-	rs587779743	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	136	1018	0	ENST00000346085.5:c.357_362del	p.Gln130_Gln131del	p.Q130_Q131del	ENST00000346085	NM_020732.3	114	CAGCAG/-	1/20	1	2	FACETS	0.49	0.444	0.538	0.49	0.444	0.538	SUBCLONAL	1	TRUE	1	0.44	2		1018	1262	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522598	157522598	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554236040	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	34	497	0	ENST00000346085.5:c.4870C>T	p.Arg1624Ter	p.R1624*	ENST00000346085	NM_020732.3	1624	Cga/Tga	18/20	1	2	FACETS	0.233	0.19	0.282	0.233	0.19	0.282	SUBCLONAL	1	TRUE	1	0.44	2		497	663	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959058	2959058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147840048	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	212	723	0	ENST00000396946.4:c.2458G>A	p.Asp820Asn	p.D820N	ENST00000396946	NM_032415.4	820	Gac/Aac	18/25	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.44	2		723	892	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974227	2974227	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	102	629	0	ENST00000396946.4:c.1378C>T	p.Gln460Ter	p.Q460*	ENST00000396946	NM_032415.4	460	Cag/Tag	10/25	1	2	FACETS	0.638	0.57	0.709	0.638	0.57	0.709	SUBCLONAL	1	TRUE	1	0.44	2		629	727	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940435	13940436	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	141	389	0	ENST00000405192.2:c.1070dup	p.Asn357LysfsTer8	p.N357Kfs*8	ENST00000405192	NM_001163147.1	357	aac/aaAc	11/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.44	2		389	570	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729606	41729606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	227	822	0	ENST00000242208.4:c.923G>A	p.Arg308His	p.R308H	ENST00000242208	NM_002192.2	308	cGt/cAt	3/3	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.44	2		822	847	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55260517	55260517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	36	300	0	ENST00000275493.2:c.2684G>A	p.Ser895Asn	p.S895N	ENST00000275493	NM_005228.3	895	aGt/aAt	22/28	1	2	FACETS	0.347	0.285	0.417	0.347	0.285	0.417	SUBCLONAL	1	TRUE	1	0.44	2		300	471	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501350	140501350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906660	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	33	329	0	ENST00000288602.6:c.722C>T	p.Thr241Met	p.T241M	ENST00000288602	NM_004333.4	241	aCg/aTg	6/18	1	2	FACETS	0.437	0.357	0.528	0.437	0.357	0.528	SUBCLONAL	1	TRUE	1	0.44	2		329	343	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511064	148511064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561605379	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	77	464	0	ENST00000320356.2:c.1838G>A	p.Arg613Gln	p.R613Q	ENST00000320356	NM_004456.4	613	cGg/cAg	15/20	1	2	FACETS	0.609	0.535	0.688	0.609	0.535	0.688	SUBCLONAL	1	TRUE	1	0.44	2		464	575	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853400	151853400	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	40	523	0	ENST00000262189.6:c.11702del	p.Pro3901LeufsTer33	p.P3901Lfs*33	ENST00000262189	NM_170606.2	3901	cCt/ct	45/59	1	2	FACETS	0.261	0.216	0.311	0.261	0.216	0.311	SUBCLONAL	1	TRUE	1	0.44	2		523	697	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012225	152012226	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	127	408	0	ENST00000262189.6:c.587_588del	p.Arg196LysfsTer23	p.R196Kfs*23	ENST00000262189	NM_170606.2	196	aGA/a	4/59	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.44	2		408	452	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87475996	87475996	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	38	438	0	ENST00000277120.3:c.1438G>T	p.Gly480Cys	p.G480C	ENST00000277120		480	Ggt/Tgt	13/19	1	2	FACETS	0.347	0.286	0.415	0.347	0.286	0.415	SUBCLONAL	1	TRUE	1	0.44	2		438	498	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97869475	97869475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149917017	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	125	679	0	ENST00000289081.3:c.1406C>T	p.Thr469Met	p.T469M	ENST00000289081	NM_000136.2	469	aCg/aTg	14/15	1	2	FACETS	0.679	0.614	0.747	0.679	0.614	0.747	SUBCLONAL	1	TRUE	1	0.44	2		679	837	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900288	101900288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111854391	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	78	461	0	ENST00000374994.4:c.722C>T	p.Ser241Leu	p.S241L	ENST00000374994	NM_004612.2	241	tCg/tTg	4/9	1	2	FACETS	0.673	0.592	0.759	0.673	0.592	0.759	SUBCLONAL	1	TRUE	1	0.44	2		461	527	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797351	135797351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777484049	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	154	520	0	ENST00000298552.3:c.518C>T	p.Ala173Val	p.A173V	ENST00000298552	NM_001162426.1	173	gCg/gTg	7/23	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.44	2		520	673	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930298	39930298	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	102	582	0	ENST00000378444.4:c.3166G>T	p.Gly1056Ter	p.G1056*	ENST00000378444	NM_001123385.1	1056	Gga/Tga	6/15	0.29620644294968	1	FACETS	0.526	0.47	0.584	0.526	0.47	0.584	SUBCLONAL	1	TRUE	0	0.44	1		582	688	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933575	39933575	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs151177114	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	90	895	1	ENST00000378444.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000378444	NM_001123385.1	342	Cga/Tga	4/15	0.29620644294968	1	FACETS	0.331	0.293	0.372	0.331	0.293	0.372	SUBCLONAL	1	TRUE	0	0.44	1		896	963	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937104	39937104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	75	501	0	ENST00000378444.4:c.79G>A	p.Glu27Lys	p.E27K	ENST00000378444	NM_001123385.1	27	Gaa/Aaa	2/15	0.29620644294968	1	FACETS	0.489	0.429	0.553	0.489	0.429	0.553	SUBCLONAL	1	TRUE	0	0.44	1		501	544	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181290	123181290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	41	384	0	ENST00000218089.9:c.754C>T	p.Arg252Trp	p.R252W	ENST00000218089	NM_001042749.1	252	Cgg/Tgg	9/35	0.29620644294968	1	FACETS	0.575	0.482	0.676	0.575	0.482	0.676	SUBCLONAL	1	TRUE	0	0.44	1		384	253	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438316	110438317	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	rs532810290	NA	P-0061795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	131	678	2	ENST00000375856.3:c.82_84dup	p.Asn28dup	p.N28dup	ENST00000375856	NM_003749.2	28	-/AAC	1/2	1	2	FACETS	0.728	0.661	0.799	0.728	0.661	0.799	SUBCLONAL	1	TRUE	1	0.44	2		680	818	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061836-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	27	309	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.926	0.739	1	0.926	0.739	1	CLONAL	1	TRUE	1	0.223459983252891	2		309	261	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578529	7578529	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs780442292	NA	P-0061836-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	98	659	0	ENST00000269305.4:c.401T>G	p.Phe134Cys	p.F134C	ENST00000269305	NM_001126112.2	134	tTt/tGt	5/11	0.223459983252891	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.223459983252891	1		659	741	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573430	48573430	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061836-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	36	517	0	ENST00000342988.3:c.14C>G	p.Ser5Cys	p.S5C	ENST00000342988	NM_005359.5	5	tCt/tGt	2/12	0.223459983252891	1	FACETS	0.935	0.772	1	0.935	0.772	1	CLONAL	1	TRUE	0	0.223459983252891	1		517	306	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265474	46265474	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061836-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	50	493	1	ENST00000371998.3:c.2344G>T	p.Asp782Tyr	p.D782Y	ENST00000371998		782	Gac/Tac	12/23	1	2	FACETS	0.906	0.769	1	0.906	0.769	1	CLONAL	1	TRUE	1	0.223459983252891	2		494	494	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435703	56435703	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061836-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	93	712	0	ENST00000407977.2:c.1434del	p.Val479TrpfsTer23	p.V479Wfs*23	ENST00000407977		478	tcT/tc	9/10	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.223459983252891	2		712	819	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424826	47424826	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061836-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	54	684	1	ENST00000404338.3:c.2894A>T	p.Glu965Val	p.E965V	ENST00000404338	NM_004491.4	965	gAa/gTa	1/6	1	2	FACETS	0.59	0.503	0.686	0.59	0.503	0.686	SUBCLONAL	1	TRUE	1	0.223459983252891	2		685	819	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475482	12475482	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061836-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	79	654	0	ENST00000287820.6:c.1356C>A	p.Asn452Lys	p.N452K	ENST00000287820	NM_015869.4	452	aaC/aaA	7/7	1	2	FACETS	0.896	0.787	1	0.896	0.787	1	CLONAL	1	TRUE	1	0.223459983252891	2		654	789	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089838	5089852	+	inframe_deletion	In_Frame_Del	DEL	GTACAAGGGAGTGTG	GTACAAGGGAGTGTG	-	novel	NA	P-0061836-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	22	497	0	ENST00000381652.3:c.2736_2750del	p.Lys912_Cys917delinsAsn	p.K912_C917delinsN	ENST00000381652	NM_004972.3	912	aaGTACAAGGGAGTGTGc/aac	20/25	0.223459983252891	1	FACETS	0.425	0.328	0.537	0.425	0.328	0.537	SUBCLONAL	1	TRUE	0	0.223459983252891	1		497	412	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0061840-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	199	471	1	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.281276947584985	3	FACETS	1	0.976	1	0.562	0.521	0.605	INDETERMINATE	1	TRUE	1	0.475129033051328	3		472	922	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579508	7579508	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061840-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	452	1095	0	ENST00000269305.4:c.179del	p.Pro60GlnfsTer63	p.P60Qfs*63	ENST00000269305	NM_001126112.2	60	cCa/ca	4/11	0.435828395324122	2	FACETS	0.95	0.911	0.99	0.95	0.911	0.99	CLONAL	2	TRUE	0	0.475129033051328	2		1095	1001	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259442	55259442	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397517127	NA	P-0061840-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	177	659	0	ENST00000275493.2:c.2500G>T	p.Val834Leu	p.V834L	ENST00000275493	NM_005228.3	834	Gtg/Ttg	21/28	0.281276947584985	3	FACETS	1	0.97	1	0.55	0.507	0.595	INDETERMINATE	1	TRUE	1	0.475129033051328	3		659	838	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022839	12022840	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0061840-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	479	1245	1	ENST00000396373.4:c.945_946delinsAT	p.Met315_Asn316delinsIleTyr	p.M315_N316delinsIY	ENST00000396373	NM_001987.4	315	atGAac/atATac	5/8	0.435828395324122	2	FACETS	0.814	0.779	0.849	0.814	0.779	0.849	CLONAL	2	TRUE	0	0.475129033051328	2		1246	1239	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594025	55594025	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061840-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	157	627	0	ENST00000288135.5:c.1811T>C	p.Val604Ala	p.V604A	ENST00000288135	NM_000222.2	604	gTt/gCt	12/21	1	2	FACETS	0.893	0.82	0.97	0.893	0.82	0.97	CLONAL	1	TRUE	1	0.475129033051328	2		627	740	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247367	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062378-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	8	609	0	ENST00000281708.4:c.1435C>T	p.Arg479Ter	p.R479*	ENST00000281708	NM_033632.3	479	Cga/Tga	10/12	1	2	FACETS	0.186	0.119	0.273	0.186	0.119	0.273	SUBCLONAL	1	TRUE	1	0.29	2		609	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578206	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs886039484	NA	P-0062408-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	78	732	0	ENST00000269305.4:c.643A>G	p.Ser215Gly	p.S215G	ENST00000269305	NM_001126112.2	215	Agt/Ggt	6/11	0.314026831188425	1	FACETS	0.805	0.71	0.907	0.805	0.71	0.907	CLONAL	1	FALSE	0	0.34664931081423	1		732	462	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830471	72830471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062408-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	128	514	0	ENST00000268489.5:c.6110del	p.Pro2037GlnfsTer64	p.P2037Qfs*64	ENST00000268489	NM_006885.3	2037	cCa/ca	9/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.34664931081423	2		514	647	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477095	67477095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062408-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	102	602	0	ENST00000327367.4:c.902G>A	p.Gly301Glu	p.G301E	ENST00000327367	NM_005902.3	301	gGg/gAg	7/9	0.16610915945663	1	FACETS	0.656	0.586	0.729	0.656	0.586	0.729	INDETERMINATE	1	FALSE	0	0.34664931081423	1		602	742	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014036	14014036	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	50	399	0	ENST00000311895.7:c.14A>C	p.Gln5Pro	p.Q5P	ENST00000311895	NM_005236.2	5	cAg/cCg	1/11	0.305745592765641	3	FACETS	0.335	0.284	0.391	0.168	0.142	0.196	INDETERMINATE	1	TRUE	1	0.817625501258533	3		399	514	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17117010	17117010	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	109	598	0	ENST00000285071.4:c.1699T>G	p.Ser567Ala	p.S567A	ENST00000285071	NM_144997.5	567	Tcc/Gcc	14/14	1	2	FACETS	0.355	0.319	0.394	0.355	0.319	0.394	SUBCLONAL	1	TRUE	1	0.817625501258533	2		598	751	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0062512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	165	663	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.284761773654624	3	FACETS	1	0.984	1	0.812	0.753	0.871	CLONAL	2	TRUE	0	0.376252490255591	3		663	428	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	154	554	0	ENST00000349310.3:c.49G>C	p.Glu17Gln	p.E17Q	ENST00000349310	NM_001014432.1	17	Gag/Cag	4/15	0.365121618528764	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.376252490255591	2		554	400	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224351	36224351	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs758151170	NA	P-0062512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	46	827	0	ENST00000222270.7:c.6901G>C	p.Asp2301His	p.D2301H	ENST00000222270	NM_014727.1	2301	Gat/Cat	28/37	0.253621410287299	4	FACETS	0.509	0.428	0.599	0.255	0.214	0.3	SUBCLONAL	1	TRUE	2	0.376252490255591	4		827	661	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170011182	170011182	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	100	373	0	ENST00000295797.4:c.1303G>T	p.Asp435Tyr	p.D435Y	ENST00000295797	NM_002740.5	435	Gac/Tac	14/18	0.253621410287299	4	FACETS	0.877	0.789	0.97	0.877	0.789	0.97	CLONAL	2	TRUE	2	0.376252490255591	4		373	417	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190573	32190573	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	154	687	0	ENST00000375023.3:c.166G>C	p.Gly56Arg	p.G56R	ENST00000375023	NM_004557.3	56	Ggc/Cgc	3/30	0.209188627421907	5	FACETS	1	0.98	1	0.796	0.733	0.862	INDETERMINATE	2	TRUE	2	0.376252490255591	5		687	536	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	438	737	0				ENST00000310581	NM_198253.2	-/1132			0.571733318425338	5	FACETS	0.872	0.834	0.91	0.872	0.834	0.91	CLONAL	3	TRUE	2	0.619247245625366	5		737	1043	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0062513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	428	557	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.619247245625366	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.619247245625366	2		557	687	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0062513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	1301	656	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.619247245625366	6	FACETS	1	0.983	1			1	CLONAL	5	TRUE	NA	0.619247245625366	6		656	1878	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144880	47144880	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	47	248	0	ENST00000409792.3:c.4873C>T	p.Arg1625Cys	p.R1625C	ENST00000409792	NM_014159.6	1625	Cgt/Tgt	7/21	0.60893574371788	4	FACETS	0.79	0.67	0.921	0.395	0.335	0.461	CLONAL	1	TRUE	2	0.619247245625366	4		248	311	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170814959	170814959	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	65	191	0	ENST00000296930.5:c.7G>C	p.Asp3His	p.D3H	ENST00000296930	NM_002520.6	3	Gat/Cat	1/11	1	2	FACETS	0.853	0.749	0.964	0.853	0.749	0.964	CLONAL	1	TRUE	1	0.619247245625366	2		191	246	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120642	115120642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	218	756	0	ENST00000257566.3:c.364G>A	p.Glu122Lys	p.E122K	ENST00000257566	NM_016569.3	122	Gag/Aag	1/8	0.615814273214844	3	FACETS	0.844	0.785	0.906	0.422	0.392	0.453	CLONAL	1	TRUE	1	0.619247245625366	3		756	1092	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513314	106513314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559655430	NA	P-0062513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	162	496	0	ENST00000359195.3:c.2218G>A	p.Glu740Lys	p.E740K	ENST00000359195	NM_002649.2	740	Gag/Aag	4/11	0.486061272267469	3	FACETS	1	0.97	1	0.554	0.511	0.6	CLONAL	1	TRUE	1	0.619247245625366	3		496	618	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374702	118374702	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587783680	NA	P-0062513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	323	588	0	ENST00000534358.1:c.8095C>T	p.Arg2699Ter	p.R2699*	ENST00000534358	NM_005933.3	2699	Cga/Tga	27/36	0.615814273214844	3	FACETS	0.921	0.875	0.967	0.921	0.875	0.967	CLONAL	2	TRUE	1	0.619247245625366	3		588	742	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216437	36216437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	305	869	0	ENST00000222270.7:c.3700G>A	p.Glu1234Lys	p.E1234K	ENST00000222270	NM_014727.1	1234	Gag/Aag	12/37	0.619247245625366	3	FACETS	1	0.956	1	0.509	0.479	0.54	CLONAL	1	TRUE	1	0.619247245625366	3		869	1267	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912855	32912855	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	42	175	0	ENST00000380152.3:c.4363G>C	p.Glu1455Gln	p.E1455Q	ENST00000380152		1455	Gaa/Caa	11/27	0.619247245625366	3	FACETS	0.858	0.724	1	0.429	0.362	0.502	CLONAL	1	TRUE	1	0.619247245625366	3		175	207	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134033	41134033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	301	833	0	ENST00000379561.5:c.1595C>T	p.Ser532Phe	p.S532F	ENST00000379561	NM_002015.3	532	tCt/tTt	2/3	0.619247245625366	3	FACETS	1	0.977	1	0.536	0.504	0.568	CLONAL	1	TRUE	1	0.619247245625366	3		833	1188	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037880	49037880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	13	82	0	ENST00000267163.4:c.2120C>T	p.Ser707Phe	p.S707F	ENST00000267163	NM_000321.2	707	tCc/tTc	21/27	0.619247245625366	1	FACETS	0.725	0.54	0.927	0.725	0.54	0.927	CLONAL	1	TRUE	0	0.619247245625366	1		82	40	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562351	95562351	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	36	584	0	ENST00000393063.1:c.4906G>C	p.Asp1636His	p.D1636H	ENST00000393063	NM_030621.3	1636	Gac/Cac	24/28	0.486061272267469	3	FACETS	0.213	0.174	0.257	0.106	0.087	0.129	SUBCLONAL	1	TRUE	1	0.619247245625366	3		584	715	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964739	15964739	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	176	476	0	ENST00000268712.3:c.5857C>G	p.Gln1953Glu	p.Q1953E	ENST00000268712	NM_006311.3	1953	Caa/Gaa	37/46	0.619247245625366	2	FACETS	0.935	0.866	1	0.467	0.433	0.503	CLONAL	1	TRUE	0	0.619247245625366	2		476	608	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965107	15965107	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	282	676	0	ENST00000268712.3:c.5489C>G	p.Ser1830Cys	p.S1830C	ENST00000268712	NM_006311.3	1830	tCt/tGt	37/46	0.619247245625366	2	FACETS	1	0.98	1	0.543	0.512	0.575	CLONAL	1	TRUE	0	0.619247245625366	2		676	838	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275768	38275768	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	239	677	0	ENST00000425967.3:c.1501C>A	p.Arg501Ser	p.R501S	ENST00000425967	NM_001174067.1	501	Cgc/Agc	11/19	0.311895158695159	4	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.619247245625366	4		677	1035	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907844	76907844	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0062513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	18	215	0	ENST00000373344.5:c.4318-1G>C		p.X1440_splice	ENST00000373344	NM_000489.3	1440			0.419633984647849	4	FACETS	0.311	0.234	0.402	0.155	0.117	0.201	SUBCLONAL	1	TRUE	2	0.619247245625366	4		215	303	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70967607	70967609	+	stop_gained	Nonsense_Mutation	TNP	TTG	TTG	CTA	novel	NA	P-0062513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	19	366	0	ENST00000276594.2:c.1414_1416delinsTAG	p.Gln472Ter	p.Q472*	ENST00000276594	NM_024504.3	472	CAA/TAG	7/8	0.619247245625366	3	FACETS	0.212	0.16	0.273	0.106	0.08	0.137	SUBCLONAL	1	TRUE	1	0.619247245625366	3		366	379	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0062514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	24	480	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	1	2	FACETS	0.798	0.627	0.993	0.798	0.627	0.993	CLONAL	1	FALSE	1	0.234074702291833	2		480	257	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599341	55599341	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519761	NA	P-0062514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	34	424	0	ENST00000288135.5:c.2467T>G	p.Tyr823Asp	p.Y823D	ENST00000288135	NM_000222.2	823	Tat/Gat	17/21	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	FALSE	1	0.234074702291833	2		424	263	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	189	582	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.956	0.888	1	0.956	0.888	1	CLONAL	1	TRUE	1	0.609942975336652	2		582	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	17	597	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.076	0.056	0.099	0.076	0.056	0.099	SUBCLONAL	1	TRUE	1	0.609942975336652	2		597	737	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	161	253	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.609942975336652	2		253	518	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	196	652	1	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.889	0.826	0.954	0.889	0.826	0.954	CLONAL	1	TRUE	1	0.609942975336652	2		653	723	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	143	510	2	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.814	0.745	0.885	0.814	0.745	0.885	CLONAL	1	TRUE	1	0.609942975336652	2		512	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	73	675	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.377	0.329	0.428	0.377	0.329	0.428	SUBCLONAL	1	TRUE	1	0.609942975336652	2		675	635	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412530	63412530	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	178	658	0	ENST00000330258.3:c.637C>T	p.Gln213Ter	p.Q213*	ENST00000330258	NM_152424.3	213	Cag/Tag	2/2	1	2	FACETS	0.895	0.828	0.964	0.895	0.828	0.964	CLONAL	1	TRUE	1	0.609942975336652	2		658	652	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	155	711	1	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.95	0.875	1	0.95	0.875	1	CLONAL	1	TRUE	1	0.609942975336652	2		712	535	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	279	320	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.955	0.898	1	0.955	0.898	1	CLONAL	1	TRUE	1	0.609942975336652	2		325	958	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	297	283	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.857	0.816	0.898	1	0.996	1	CLONAL	2	TRUE	1	0.609942975336652	2		288	568	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	135	397	7	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.611	0.556	0.669	0.611	0.556	0.669	SUBCLONAL	1	TRUE	1	0.609942975336652	2		404	724	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	212	886	2	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	2	FACETS	0.71	0.66	0.762	0.71	0.66	0.762	SUBCLONAL	1	TRUE	1	0.609942975336652	2		888	979	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027093	71027093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200629338	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	319	707	0	ENST00000318789.4:c.1234G>A	p.Ala412Thr	p.A412T	ENST00000318789	NM_032682.5	412	Gcc/Acc	15/21	1	2	FACETS	0.914	0.863	0.967	0.914	0.863	0.967	CLONAL	1	TRUE	1	0.609942975336652	2		707	1144	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	67	367	3	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	0.968	0.853	1	0.968	0.853	1	CLONAL	1	TRUE	1	0.609942975336652	2		370	227	SUCCESS
EED	8726	MSKCC	GRCh37	11	85979574	85979574	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1301151502	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	83	284	0	ENST00000263360.6:c.937C>T	p.Arg313Ter	p.R313*	ENST00000263360	NM_003797.3	313	Cga/Tga	9/12	1	2	FACETS	0.752	0.668	0.84	0.752	0.668	0.84	SUBCLONAL	1	TRUE	1	0.609942975336652	2		284	362	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	145	661	1	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	0.631	0.576	0.688	0.631	0.576	0.688	SUBCLONAL	1	TRUE	1	0.609942975336652	2		662	754	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578245	7578245	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780072	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	183	694	0	ENST00000269305.4:c.604C>T	p.Arg202Cys	p.R202C	ENST00000269305	NM_001126112.2	202	Cgt/Tgt	6/11	1	2	FACETS	0.906	0.84	0.975	0.906	0.84	0.975	CLONAL	1	TRUE	1	0.609942975336652	2		694	662	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272337	15272337	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs771517374	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	92	786	2	ENST00000263388.2:c.6102del	p.Gly2035ValfsTer50	p.G2035Vfs*50	ENST00000263388	NM_000435.2	2034	ccC/cc	33/33	1	2	FACETS	0.41	0.364	0.46	0.41	0.364	0.46	SUBCLONAL	1	TRUE	1	0.609942975336652	2		788	735	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	195	711	1	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.609942975336652	2		712	584	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729175	66729175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908596	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	218	568	0	ENST00000307102.5:c.383G>A	p.Gly128Asp	p.G128D	ENST00000307102	NM_002755.3	128	gGc/gAc	3/11	1	2	FACETS	0.93	0.867	0.994	0.93	0.867	0.994	CLONAL	1	TRUE	1	0.609942975336652	2		568	769	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268793	98268793	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1554708751	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	164	582	1	ENST00000331920.6:c.290del	p.Asn97ThrfsTer20	p.N97Tfs*20	ENST00000331920	NM_000264.3	97	aAc/ac	2/24	1	2	FACETS	0.798	0.735	0.863	0.798	0.735	0.863	SUBCLONAL	1	TRUE	1	0.609942975336652	2		583	674	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845549	72845551	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs763986819	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	83	706	0	ENST00000268489.5:c.3789_3791del	p.Asn1263del	p.N1263del	ENST00000268489	NM_006885.3	1263	aaCAAg/aag	7/10	1	2	FACETS	0.319	0.28	0.36	0.319	0.28	0.36	SUBCLONAL	1	TRUE	1	0.609942975336652	2		706	854	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907421	32907421	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359306	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	124	334	1	ENST00000380152.3:c.1813del	p.Ile605TyrfsTer9	p.I605Yfs*9	ENST00000380152		602	ggA/gg	10/27	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.609942975336652	2		335	394	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411246	63411246	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	192	788	0	ENST00000330258.3:c.1921C>T	p.Arg641Ter	p.R641*	ENST00000330258	NM_152424.3	641	Cga/Tga	2/2	1	2	FACETS	0.857	0.795	0.921	0.857	0.795	0.921	CLONAL	1	TRUE	1	0.609942975336652	2		788	735	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779578	3779578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	199	770	0	ENST00000262367.5:c.5470G>A	p.Ala1824Thr	p.A1824T	ENST00000262367	NM_004380.2	1824	Gcc/Acc	31/31	1	2	FACETS	0.89	0.827	0.955	0.89	0.827	0.955	CLONAL	1	TRUE	1	0.609942975336652	2		770	733	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225955	2225955	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs756230613	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	155	705	0	ENST00000326181.6:c.1746+1G>A		p.X582_splice	ENST00000326181	NM_032271.2	582			1	2	FACETS	0.974	0.897	1	0.974	0.897	1	CLONAL	1	TRUE	1	0.609942975336652	2		705	522	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630605	187630605	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	151	511	1	ENST00000441802.2:c.377del	p.Asn126IlefsTer20	p.N126Ifs*20	ENST00000441802	NM_005245.3	126	aAt/at	2/27	1	2	FACETS	0.817	0.75	0.887	0.817	0.75	0.887	CLONAL	1	TRUE	1	0.609942975336652	2		512	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	138	604	0	ENST00000269305.4:c.376T>C	p.Tyr126His	p.Y126H	ENST00000269305	NM_001126112.2	126	Tac/Cac	5/11	1	2	FACETS	0.711	0.649	0.776	0.711	0.649	0.776	SUBCLONAL	1	TRUE	1	0.609942975336652	2		604	636	SUCCESS
APC	324	MSKCC	GRCh37	5	112177265	112177265	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1554087123	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	147	522	0	ENST00000257430.4:c.5978del	p.Pro1993LeufsTer51	p.P1993Lfs*51	ENST00000257430	NM_000038.5	1992	Ccc/cc	16/16	1	2	FACETS	0.828	0.759	0.899	0.828	0.759	0.899	CLONAL	1	TRUE	1	0.609942975336652	2		522	582	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905324	50905324	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	179	860	2	ENST00000440232.2:c.537del	p.Arg180GlyfsTer3	p.R180Gfs*3	ENST00000440232	NM_002691.3	178	Ggg/gg	5/27	1	2	FACETS	0.816	0.755	0.88	0.816	0.755	0.88	CLONAL	1	TRUE	1	0.609942975336652	2		862	719	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599234	28599234	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	85	774	0	ENST00000253063.3:c.685del	p.Gln229ArgfsTer18	p.Q229Rfs*18	ENST00000253063	NM_031459.4	227	gCc/gc	5/10	1	2	FACETS	0.328	0.289	0.37	0.328	0.289	0.37	SUBCLONAL	1	TRUE	1	0.609942975336652	2		774	850	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793332	139793332	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376801177	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	183	540	0	ENST00000247668.2:c.140C>T	p.Ala47Val	p.A47V	ENST00000247668	NM_021138.3	47	gCg/gTg	2/11	1	2	FACETS	0.965	0.895	1	0.965	0.895	1	CLONAL	1	TRUE	1	0.609942975336652	2		540	622	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400029	139400029	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs778742968	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	129	826	0	ENST00000277541.6:c.4319T>C	p.Ile1440Thr	p.I1440T	ENST00000277541	NM_017617.3	1440	aTc/aCc	25/34	1	2	FACETS	0.722	0.657	0.79	0.722	0.657	0.79	SUBCLONAL	1	TRUE	1	0.609942975336652	2		826	586	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350753	89350753	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886041791	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	73	438	0	ENST00000301030.4:c.2197C>T	p.Arg733Ter	p.R733*	ENST00000301030	NM_001256183.1	733	Cga/Tga	9/13	1	2	FACETS	0.665	0.585	0.75	0.665	0.585	0.75	SUBCLONAL	1	TRUE	1	0.609942975336652	2		438	360	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992720	68992721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs764112302	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	104	366	2	ENST00000288368.4:c.1693dup	p.Ser565PhefsTer3	p.S565Ffs*3	ENST00000288368	NM_024870.2	562	cgt/cgTt	16/40	1	2	FACETS	0.793	0.715	0.875	0.793	0.715	0.875	SUBCLONAL	1	TRUE	1	0.609942975336652	2		368	430	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157488275	157488275	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377351099	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	181	570	0	ENST00000346085.5:c.2981C>T	p.Ala994Val	p.A994V	ENST00000346085	NM_020732.3	994	gCg/gTg	10/20	1	2	FACETS	0.764	0.706	0.824	0.764	0.706	0.824	SUBCLONAL	1	TRUE	1	0.609942975336652	2		570	777	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224171	36224171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779883307	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	129	456	0	ENST00000222270.7:c.6721G>A	p.Gly2241Ser	p.G2241S	ENST00000222270	NM_014727.1	2241	Ggc/Agc	28/37	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.609942975336652	2		456	389	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211660	36211660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	149	702	0	ENST00000222270.7:c.1411C>T	p.Arg471Trp	p.R471W	ENST00000222270	NM_014727.1	471	Cgg/Tgg	3/37	1	2	FACETS	0.908	0.834	0.984	0.908	0.834	0.984	CLONAL	1	TRUE	1	0.609942975336652	2		702	538	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970916	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	112	332	0	ENST00000265081.6:c.1147_1148del	p.Lys383GlyfsTer20	p.K383Gfs*20	ENST00000265081	NM_002439.4	381	AAa/a	7/24	1	2	FACETS	0.772	0.698	0.849	0.772	0.698	0.849	SUBCLONAL	1	TRUE	1	0.609942975336652	2		332	476	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214395	5214395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772384138	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	180	621	0	ENST00000357368.4:c.4591G>A	p.Val1531Ile	p.V1531I	ENST00000357368	NM_002850.3	1531	Gtc/Atc	30/38	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.609942975336652	2		621	577	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40874920	40874920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756635466	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	114	452	0	ENST00000428826.2:c.380C>T	p.Thr127Met	p.T127M	ENST00000428826		127	aCg/aTg	6/21	1	2	FACETS	0.811	0.734	0.891	0.811	0.734	0.891	CLONAL	1	TRUE	1	0.609942975336652	2		452	461	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827763	72827763	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	57	569	0	ENST00000268489.5:c.8818A>G	p.Ser2940Gly	p.S2940G	ENST00000268489	NM_006885.3	2940	Agc/Ggc	9/10	1	2	FACETS	0.282	0.241	0.326	0.282	0.241	0.326	SUBCLONAL	1	TRUE	1	0.609942975336652	2		569	663	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755669	57755670	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1279983695	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	222	706	1	ENST00000274289.3:c.117dup	p.Glu40ArgfsTer66	p.E40Rfs*66	ENST00000274289	NM_006622.3	39	-/C	1/14	1	2	FACETS	0.948	0.885	1	0.948	0.885	1	CLONAL	1	TRUE	1	0.609942975336652	2		707	768	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027152	71027153	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	232	612	0	ENST00000318789.4:c.1174_1175del	p.Ser392GlnfsTer68	p.S392Qfs*68	ENST00000318789	NM_032682.5	392	TCc/c	15/21	1	2	FACETS	0.872	0.815	0.931	0.872	0.815	0.931	CLONAL	1	TRUE	1	0.609942975336652	2		612	872	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533860	63533860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751843834	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	170	750	0	ENST00000307078.5:c.1294G>A	p.Glu432Lys	p.E432K	ENST00000307078	NM_004655.3	432	Gag/Aag	6/11	1	2	FACETS	0.867	0.8	0.936	0.867	0.8	0.936	CLONAL	1	TRUE	1	0.609942975336652	2		750	643	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396205	139396205	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	107	692	0	ENST00000277541.6:c.5633G>T	p.Gly1878Val	p.G1878V	ENST00000277541	NM_017617.3	1878	gGg/gTg	30/34	1	2	FACETS	0.75	0.676	0.827	0.75	0.676	0.827	SUBCLONAL	1	TRUE	1	0.609942975336652	2		692	468	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046716	180046716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs910059826	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	185	861	0	ENST00000261937.6:c.2596G>A	p.Gly866Ser	p.G866S	ENST00000261937	NM_182925.4	866	Ggc/Agc	18/30	1	2	FACETS	0.904	0.838	0.972	0.904	0.838	0.972	CLONAL	1	TRUE	1	0.609942975336652	2		861	671	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155661	106155661	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	177	533	0	ENST00000380013.4:c.565del	p.Ser189ValfsTer18	p.S189Vfs*18	ENST00000380013	NM_001127208.2	188	Aaa/aa	3/11	1	2	FACETS	0.945	0.875	1	0.945	0.875	1	CLONAL	1	TRUE	1	0.609942975336652	2		533	614	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223189	5223189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151114416	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	162	712	1	ENST00000357368.4:c.2614C>T	p.Arg872Cys	p.R872C	ENST00000357368	NM_002850.3	872	Cgt/Tgt	18/38	1	2	FACETS	0.902	0.832	0.975	0.902	0.832	0.975	CLONAL	1	TRUE	1	0.609942975336652	2		713	589	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456560	32456560	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	25	482	0	ENST00000332351.3:c.332del	p.Pro111ArgfsTer47	p.P111Rfs*47	ENST00000332351	NM_024426.4	111	cCg/cg	1/10	1	2	FACETS	0.313	0.247	0.388	0.313	0.247	0.388	SUBCLONAL	1	TRUE	1	0.609942975336652	2		482	262	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2115921	2115921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	216	548	0	ENST00000349721.2:c.3556G>A	p.Ala1186Thr	p.A1186T	ENST00000349721	NM_003070.3	1186	Gcg/Acg	25/34	1	2	FACETS	0.891	0.83	0.953	0.891	0.83	0.953	CLONAL	1	TRUE	1	0.609942975336652	2		548	795	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784392	9784392	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	47	586	0	ENST00000377346.4:c.2777A>G	p.Asn926Ser	p.N926S	ENST00000377346	NM_005026.3	926	aAc/aGc	22/24	1	2	FACETS	0.275	0.231	0.323	0.275	0.231	0.323	SUBCLONAL	1	TRUE	1	0.609942975336652	2		586	561	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16247426	16247426	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	112	431	0	ENST00000375759.3:c.1697A>G	p.Gln566Arg	p.Q566R	ENST00000375759	NM_015001.2	566	cAa/cGa	9/15	1	2	FACETS	0.542	0.488	0.6	0.542	0.488	0.6	SUBCLONAL	1	TRUE	1	0.609942975336652	2		431	677	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612150	43612150	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs909451217	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	137	748	0	ENST00000355710.3:c.2255A>G	p.Tyr752Cys	p.Y752C	ENST00000355710	NM_020975.4	752	tAc/tGc	12/20	1	2	FACETS	0.752	0.687	0.821	0.752	0.687	0.821	SUBCLONAL	1	TRUE	1	0.609942975336652	2		748	597	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405346	70405346	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	196	563	0	ENST00000373644.4:c.2860A>G	p.Asn954Asp	p.N954D	ENST00000373644	NM_030625.2	954	Aat/Gat	4/12	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.609942975336652	2		563	643	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77936188	77936188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs2134464120	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	203	579	0	ENST00000361507.4:c.1268C>T	p.Ala423Val	p.A423V	ENST00000361507	NM_080491.2	423	gCt/gTt	5/10	1	2	FACETS	0.913	0.849	0.979	0.913	0.849	0.979	CLONAL	1	TRUE	1	0.609942975336652	2		579	729	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544080	18544080	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	70	346	0	ENST00000266497.5:c.1897G>T	p.Glu633Ter	p.E633*	ENST00000266497		633	Gag/Tag	13/31	1	2	FACETS	0.617	0.541	0.698	0.617	0.541	0.698	SUBCLONAL	1	TRUE	1	0.609942975336652	2		346	372	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562306	21562306	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	140	677	0	ENST00000382592.4:c.1613C>T	p.Ala538Val	p.A538V	ENST00000382592	NM_014572.2	538	gCa/gTa	4/8	1	2	FACETS	0.71	0.648	0.774	0.71	0.648	0.774	SUBCLONAL	1	TRUE	1	0.609942975336652	2		677	647	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563377	21563377	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1294740969	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	203	813	0	ENST00000382592.4:c.542C>T	p.Ala181Val	p.A181V	ENST00000382592	NM_014572.2	181	gCg/gTg	4/8	1	2	FACETS	0.928	0.864	0.995	0.928	0.864	0.995	CLONAL	1	TRUE	1	0.609942975336652	2		813	717	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213961	2213961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542651972	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	181	674	0	ENST00000326181.6:c.40G>A	p.Gly14Arg	p.G14R	ENST00000326181	NM_032271.2	14	Ggg/Agg	2/21	1	2	FACETS	0.936	0.867	1	0.936	0.867	1	CLONAL	1	TRUE	1	0.609942975336652	2		674	634	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234586	41234586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660331	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	27	388	0	ENST00000357654.3:c.4192G>A	p.Asp1398Asn	p.D1398N	ENST00000357654	NM_007294.3	1398	Gat/Aat	12/23	1	2	FACETS	0.185	0.147	0.229	0.185	0.147	0.229	SUBCLONAL	1	TRUE	1	0.609942975336652	2		388	478	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2208962	2208963	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	111	313	0	ENST00000398665.3:c.995dup	p.Leu334ThrfsTer25	p.L334Tfs*25	ENST00000398665	NM_032482.2	331	aac/aaCc	12/28	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.609942975336652	2		313	359	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272350	15272350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1394014476	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	225	782	0	ENST00000263388.2:c.6089C>T	p.Pro2030Leu	p.P2030L	ENST00000263388	NM_000435.2	2030	cCc/cTc	33/33	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.609942975336652	2		782	703	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40739800	40739800	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	148	658	0	ENST00000392038.2:c.1425C>G	p.Tyr475Ter	p.Y475*	ENST00000392038	NM_001626.4	475	taC/taG	14/14	1	2	FACETS	0.82	0.752	0.89	0.82	0.752	0.89	CLONAL	1	TRUE	1	0.609942975336652	2		658	592	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872202	45872202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373292179	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	204	638	2	ENST00000391945.4:c.232C>T	p.Pro78Ser	p.P78S	ENST00000391945	NM_000400.3	78	Cca/Tca	4/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.609942975336652	2		640	633	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424495	47424495	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	42	590	0	ENST00000404338.3:c.2563T>A	p.Tyr855Asn	p.Y855N	ENST00000404338	NM_004491.4	855	Tac/Aac	1/6	1	2	FACETS	0.189	0.157	0.225	0.189	0.157	0.225	SUBCLONAL	1	TRUE	1	0.609942975336652	2		590	727	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47440545	47440545	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs11548675	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	47	488	0	ENST00000404338.3:c.3706T>G	p.Ser1236Ala	p.S1236A	ENST00000404338	NM_004491.4	1236	Tcc/Gcc	2/6	1	2	FACETS	0.201	0.169	0.237	0.201	0.169	0.237	SUBCLONAL	1	TRUE	1	0.609942975336652	2		488	767	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37637667	37637667	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	148	714	0	ENST00000249071.6:c.67T>C	p.Tyr23His	p.Y23H	ENST00000249071	NM_002872.4	23	Tac/Cac	2/7	1	2	FACETS	0.666	0.609	0.725	0.666	0.609	0.725	SUBCLONAL	1	TRUE	1	0.609942975336652	2		714	729	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648377	30648377	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	163	544	0	ENST00000295754.5:c.2T>C	p.Met1?	p.M1?	ENST00000295754	NM_003242.5	1	aTg/aCg	1/7	0.590337285199307	2	FACETS	1	0.948	1	0.516	0.477	0.556	CLONAL	1	TRUE	0	0.609942975336652	2		544	518	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437755	52437755	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	169	659	0	ENST00000460680.1:c.1406G>A	p.Ser469Asn	p.S469N	ENST00000460680	NM_004656.3	469	aGc/aAc	13/17	0.590337285199307	2	FACETS	0.863	0.797	0.932	0.432	0.398	0.466	CLONAL	1	TRUE	0	0.609942975336652	2		659	642	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63976019	63976019	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	271	687	1	ENST00000398590.3:c.1529A>G	p.His510Arg	p.H510R	ENST00000398590	NM_001177387.1	510	cAt/cGt	10/14	1	2	FACETS	0.985	0.926	1	0.985	0.926	1	CLONAL	1	TRUE	1	0.609942975336652	2		688	902	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987025	69987025	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750608171	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	217	555	1	ENST00000394351.3:c.86G>A	p.Arg29Gln	p.R29Q	ENST00000394351	NM_000248.3	29	cGg/cAg	2/9	1	2	FACETS	0.876	0.817	0.938	0.876	0.817	0.938	CLONAL	1	TRUE	1	0.609942975336652	2		556	812	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242780	66242780	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	36	499	0	ENST00000273854.3:c.1792del	p.Cys598AlafsTer20	p.C598Afs*20	ENST00000273854	NM_004439.5	598	Tgc/gc	9/18	1	2	FACETS	0.173	0.141	0.208	0.173	0.141	0.208	SUBCLONAL	1	TRUE	1	0.609942975336652	2		499	683	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541877	187541877	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	152	572	0	ENST00000441802.2:c.5863T>C	p.Ser1955Pro	p.S1955P	ENST00000441802	NM_005245.3	1955	Tcc/Ccc	10/27	1	2	FACETS	0.625	0.572	0.68	0.625	0.572	0.68	SUBCLONAL	1	TRUE	1	0.609942975336652	2		572	798	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630294	187630294	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	78	650	0	ENST00000441802.2:c.688A>C	p.Lys230Gln	p.K230Q	ENST00000441802	NM_005245.3	230	Aag/Cag	2/27	1	2	FACETS	0.291	0.255	0.33	0.291	0.255	0.33	SUBCLONAL	1	TRUE	1	0.609942975336652	2		650	879	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630452	187630452	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	105	631	1	ENST00000441802.2:c.530A>G	p.Asp177Gly	p.D177G	ENST00000441802	NM_005245.3	177	gAc/gGc	2/27	1	2	FACETS	0.418	0.374	0.465	0.418	0.374	0.465	SUBCLONAL	1	TRUE	1	0.609942975336652	2		632	823	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950201	38950201	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	105	569	0	ENST00000357387.3:c.3749C>T	p.Thr1250Ile	p.T1250I	ENST00000357387	NM_152756.3	1250	aCa/aTa	31/38	1	2	FACETS	0.527	0.473	0.585	0.527	0.473	0.585	SUBCLONAL	1	TRUE	1	0.609942975336652	2		569	653	SUCCESS
APC	324	MSKCC	GRCh37	5	112177752	112177752	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	37	403	0	ENST00000257430.4:c.6461A>G	p.Gln2154Arg	p.Q2154R	ENST00000257430	NM_000038.5	2154	cAa/cGa	16/16	1	2	FACETS	0.244	0.201	0.293	0.244	0.201	0.293	SUBCLONAL	1	TRUE	1	0.609942975336652	2		403	497	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647529	117647529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	97	438	0	ENST00000368508.3:c.5415G>A	p.Met1805Ile	p.M1805I	ENST00000368508	NM_002944.2	1805	atG/atA	33/43	1	2	FACETS	0.62	0.555	0.689	0.62	0.555	0.689	SUBCLONAL	1	TRUE	1	0.609942975336652	2		438	513	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962857	2962858	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	150	530	0	ENST00000396946.4:c.2050_2051insT	p.Gly684ValfsTer25	p.G684Vfs*25	ENST00000396946	NM_032415.4	684	ggg/gTgg	16/25	1	2	FACETS	0.984	0.905	1	0.984	0.905	1	CLONAL	1	TRUE	1	0.609942975336652	2		530	500	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873584	151873584	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	43	652	0	ENST00000262189.6:c.8954A>G	p.Gln2985Arg	p.Q2985R	ENST00000262189	NM_170606.2	2985	cAg/cGg	38/59	1	2	FACETS	0.183	0.152	0.217	0.183	0.152	0.217	SUBCLONAL	1	TRUE	1	0.609942975336652	2		652	772	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995595	68995596	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	103	351	0	ENST00000288368.4:c.2001_2002del	p.Arg667SerfsTer18	p.R667Sfs*18	ENST00000288368	NM_024870.2	667	AGa/a	18/40	1	2	FACETS	0.836	0.754	0.922	0.836	0.754	0.922	CLONAL	1	TRUE	1	0.609942975336652	2		351	404	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841214	15841214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	328	881	1	ENST00000307771.7:c.1298G>A	p.Arg433His	p.R433H	ENST00000307771	NM_005089.3	433	cGc/cAc	11/11	1	2	FACETS	0.965	0.912	1	0.965	0.912	1	CLONAL	1	TRUE	1	0.609942975336652	2		882	1115	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226046	53226046	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	224	678	0	ENST00000375401.3:c.2803A>G	p.Lys935Glu	p.K935E	ENST00000375401	NM_004187.3	935	Aaa/Gaa	19/26	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.609942975336652	2		678	734	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865770	57865770	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	263	764	0	ENST00000228682.2:c.3247A>G	p.Met1083Val	p.M1083V	ENST00000228682	NM_005269.2	1083	Atg/Gtg	12/12	0.649080062636621	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.649080062636621	2		764	384	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0062517-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	66	544	1				ENST00000310581	NM_198253.2	-/1132			0.194094548466002	0	FACETS	0.981	0.863	1			1	CLONAL	2	FALSE	0	0.221820951714927	0		545	236	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0062517-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	71	387	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.777	0.681	0.879	1	0.976	1	SUBCLONAL	2	FALSE	1	0.221820951714927	2		387	412	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788626	3788626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062517-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	85	414	0	ENST00000262367.5:c.4328G>A	p.Arg1443His	p.R1443H	ENST00000262367	NM_004380.2	1443	cGt/cAt	26/31	1	2	FACETS	0.848	0.753	0.949	1	0.982	1	CLONAL	2	FALSE	1	0.221820951714927	2		414	452	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652068	36652068	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062517-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	74	710	0	ENST00000244741.5:c.190del	p.Ala64ProfsTer84	p.A64Pfs*84	ENST00000244741	NM_000389.4	64	Gcc/cc	2/3	0.13031038555541	4	FACETS	1	0.944	1	0.572	0.5	0.649	INDETERMINATE	1	FALSE	2	0.221820951714927	4		710	713	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0062518-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	148	735	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	0.299015747714925	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.299015747714925	1		735	743	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061131	38061210	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTGGCGGCGCA	GCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTGGCGGCGCA	-	novel	NA	P-0062518-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	316	680	0	ENST00000250448.2:c.779_858del	p.Leu260CysfsTer6	p.L260Cfs*6	ENST00000250448	NM_004496.3	260	tTGCGCCGCCAGAAGCGCTTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGGC/t	2/2	0.144218760258236	3	FACETS	1	0.971	1	1	0.971	1	INDETERMINATE	2	TRUE	1	0.299015747714925	3		680	1162	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061182	38061194	+	frameshift_variant	Frame_Shift_Del	DEL	CTCGCACTTGAAG	CTCGCACTTGAAG	-	novel	NA	P-0062519-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	8	824	0	ENST00000250448.2:c.795_807del	p.Phe266SerfsTer51	p.F266Sfs*51	ENST00000250448	NM_004496.3	265	cgCTTCAAGTGCGAG/cg	2/2	1	2	FACETS	0.278	0.178	0.408	0.278	0.178	0.408	SUBCLONAL	1	TRUE	1	0.21	2		824	274	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061217	38061243	+	inframe_deletion	In_Frame_Del	DEL	AGCCGTTCTCGAACATGTTGCCGGAGT	AGCCGTTCTCGAACATGTTGCCGGAGT	-	novel	NA	P-0062519-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	14	796	0	ENST00000250448.2:c.746_772del	p.Asp249_Cys258delinsGly	p.D249_C258delinsG	ENST00000250448	NM_004496.3	249	gACTCCGGCAACATGTTCGAGAACGGCTgc/ggc	2/2	1	2	FACETS	0.394	0.284	0.529	0.394	0.284	0.529	SUBCLONAL	1	TRUE	1	0.21	2		796	338	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	98	309	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.326754374679582	2	FACETS	0.817	0.735	0.903	0.817	0.735	0.903	CLONAL	2	TRUE	0	0.326754374679582	2		309	367	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	104	510	2	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	NA	2	FACETS	0.969	0.869	1			1	INDETERMINATE	1	TRUE	NA	0.326754374679582	2		512	657	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	144	526	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.326754374679582	2		526	728	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	91	442	3	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.831	0.739	0.93	0.831	0.739	0.93	CLONAL	1	TRUE	1	0.326754374679582	2		445	670	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	71	351	0	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.326754374679582	2		351	416	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509085	66509085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	30	319	1	ENST00000273854.3:c.242del	p.Asn81MetfsTer24	p.N81Mfs*24	ENST00000273854	NM_004439.5	81	aAt/at	2/18	1	2	FACETS	0.602	0.486	0.733	0.602	0.486	0.733	SUBCLONAL	1	TRUE	1	0.326754374679582	2		320	305	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021276	31021277	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886042532	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	84	639	1	ENST00000375687.4:c.1281dup	p.Gln428ThrfsTer10	p.Q428Tfs*10	ENST00000375687	NM_015338.5	425	-/A	12/13	1	2	FACETS	0.669	0.59	0.753	0.669	0.59	0.753	SUBCLONAL	1	TRUE	1	0.326754374679582	2		640	769	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772951	135772951	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs118203724	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	58	397	0	ENST00000298552.3:c.2672del	p.Asn891ThrfsTer40	p.N891Tfs*40	ENST00000298552	NM_001162426.1	891	aAc/ac	21/23	1	2	FACETS	0.625	0.537	0.721	0.625	0.537	0.721	SUBCLONAL	1	TRUE	1	0.326754374679582	2		397	568	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785963	135785964	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs118203506	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	83	613	0	ENST00000298552.3:c.1257dup	p.Arg420GlnfsTer22	p.R420Qfs*22	ENST00000298552	NM_001162426.1	419	-/C	12/23	1	2	FACETS	0.736	0.65	0.829	0.736	0.65	0.829	SUBCLONAL	1	TRUE	1	0.326754374679582	2		613	690	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653807	89653807	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	60	265	0	ENST00000371953.3:c.107del	p.Gly36AspfsTer18	p.G36Dfs*18	ENST00000371953	NM_000314.4	35	atG/at	2/9	0.326754374679582	2	FACETS	0.812	0.709	0.922	0.812	0.709	0.922	CLONAL	2	TRUE	0	0.326754374679582	2		265	226	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214630	133214630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	115	523	0	ENST00000320574.5:c.5648C>T	p.Ala1883Val	p.A1883V	ENST00000320574	NM_006231.2	1883	gCc/gTc	41/49	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.326754374679582	2		523	661	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384651	31384651	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	127	664	0	ENST00000328111.2:c.1359del	p.Leu454SerfsTer136	p.L454Sfs*136	ENST00000328111	NM_006892.3	451	gaG/ga	13/23	1	2	FACETS	0.993	0.9	1	0.993	0.9	1	CLONAL	1	TRUE	1	0.326754374679582	2		664	783	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663356	67663356	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	88	512	0	ENST00000264010.4:c.1760del	p.Asn587MetfsTer44	p.N587Mfs*44	ENST00000264010	NM_006565.3	586	gAa/ga	10/12	1	2	FACETS	0.814	0.721	0.912	0.814	0.721	0.912	CLONAL	1	TRUE	1	0.326754374679582	2		512	662	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161175	56161175	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	34	327	0	ENST00000399503.3:c.1044C>A	p.Ser348Arg	p.S348R	ENST00000399503	NM_005921.1	348	agC/agA	5/20	1	2	FACETS	0.555	0.454	0.668	0.555	0.454	0.668	SUBCLONAL	1	TRUE	1	0.326754374679582	2		327	375	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910287	50910287	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	93	616	0	ENST00000440232.2:c.1542G>T	p.Lys514Asn	p.K514N	ENST00000440232	NM_002691.3	514	aaG/aaT	13/27	1	2	FACETS	0.821	0.731	0.918	0.821	0.731	0.918	CLONAL	1	TRUE	1	0.326754374679582	2		616	693	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623187	52623187	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	101	515	0	ENST00000394830.3:c.2864del	p.Asn955ThrfsTer53	p.N955Tfs*53	ENST00000394830	NM_018313.4	955	aAc/ac	19/30	1	2	FACETS	0.854	0.763	0.95	0.854	0.763	0.95	CLONAL	1	TRUE	1	0.326754374679582	2		515	724	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317148	11317148	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	97	617	0	ENST00000361445.4:c.346C>T	p.Pro116Ser	p.P116S	ENST00000361445	NM_004958.3	116	Ccc/Tcc	4/58	1	2	FACETS	0.728	0.649	0.813	0.728	0.649	0.813	SUBCLONAL	1	TRUE	1	0.326754374679582	2		617	815	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	249	892	7	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.967	0.908	1	1	0.995	1	CLONAL	2	TRUE	1	0.326754374679582	2		899	788	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852298	63852298	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs752506951	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	147	592	0	ENST00000279873.7:c.3076A>G	p.Lys1026Glu	p.K1026E	ENST00000279873	NM_032199.2	1026	Aaa/Gaa	10/10	0.326754374679582	2	FACETS	1	0.963	1	0.55	0.502	0.6	CLONAL	1	TRUE	0	0.326754374679582	2		592	818	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644856	67644856	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	147	695	0	ENST00000264010.4:c.124del	p.Gln42ArgfsTer20	p.Q42Rfs*20	ENST00000264010	NM_006565.3	41	Ccc/cc	3/12	1	2	FACETS	0.971	0.886	1	0.971	0.886	1	CLONAL	1	TRUE	1	0.326754374679582	2		695	927	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356311	70356311	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1042718707	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	125	586	0	ENST00000374080.3:c.5206G>A	p.Ala1736Thr	p.A1736T	ENST00000374080		1736	Gcc/Acc	37/45	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.326754374679582	2		586	753	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112448	115112448	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398394014	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	138	680	0	ENST00000257566.3:c.1292C>T	p.Ala431Val	p.A431V	ENST00000257566	NM_016569.3	431	gCg/gTg	7/8	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.326754374679582	2		680	699	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626969	158626969	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	127	489	1	ENST00000263640.3:c.701T>C	p.Val234Ala	p.V234A	ENST00000263640	NM_001105.4	234	gTg/gCg	7/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.326754374679582	2		490	732	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343529	118343529	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	143	666	0	ENST00000534358.1:c.1660del	p.Gln554SerfsTer13	p.Q554Sfs*13	ENST00000534358	NM_005933.3	552	gCc/gc	3/36	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.326754374679582	2		666	872	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39658070	39658070	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	58	451	0	ENST00000361337.2:c.34-1G>A		p.X12_splice	ENST00000361337	NM_003286.2	12			1	2	FACETS	0.782	0.673	0.9	0.782	0.673	0.9	SUBCLONAL	1	TRUE	1	0.326754374679582	2		451	454	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29115460	29115460	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs886039609	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	48	234	1	ENST00000328354.6:c.606del	p.Phe202LeufsTer3	p.F202Lfs*3	ENST00000328354	NM_007194.3	202	ttT/tt	5/15	1	2	FACETS	0.862	0.731	1	0.862	0.731	1	CLONAL	1	TRUE	1	0.326754374679582	2		235	341	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752909	57752909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151304321	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	89	488	0	ENST00000274289.3:c.1019C>T	p.Pro340Leu	p.P340L	ENST00000274289	NM_006622.3	340	cCg/cTg	8/14	1	2	FACETS	0.919	0.816	1	0.919	0.816	1	CLONAL	1	TRUE	1	0.326754374679582	2		488	593	SUCCESS
MTAP	4507	MSKCC	GRCh37	9	21854745	21854745	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	111	534	1	ENST00000380172.4:c.571del	p.Ala191ArgfsTer6	p.A191Rfs*6	ENST00000380172	NM_002451.3	189	tGg/tg	6/8	1	2	FACETS	0.936	0.842	1	0.936	0.842	1	CLONAL	1	TRUE	1	0.326754374679582	2		535	726	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414268	32414268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	89	459	1	ENST00000332351.3:c.1283G>A	p.Cys428Tyr	p.C428Y	ENST00000332351	NM_024426.4	428	tGt/tAt	8/10	1	2	FACETS	0.92	0.817	1	0.92	0.817	1	CLONAL	1	TRUE	1	0.326754374679582	2		460	592	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025902	1025902	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	123	637	0	ENST00000358495.3:c.628C>T	p.Pro210Ser	p.P210S	ENST00000358495	NM_134424.2	210	Ccg/Tcg	8/12	0.326754374679582	2	FACETS	0.918	0.83	1	0.459	0.415	0.506	CLONAL	1	TRUE	0	0.326754374679582	2		637	820	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233376	69233378	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	95	482	0	ENST00000462284.1:c.1245_1247del	p.Glu415del	p.E415del	ENST00000462284	NM_002392.5	414	cAAGaa/caa	11/11	1	2	FACETS	0.886	0.79	0.989	0.886	0.79	0.989	CLONAL	1	TRUE	1	0.326754374679582	2		482	656	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712794	43712794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	121	600	0	ENST00000382044.4:c.4390C>T	p.Arg1464Cys	p.R1464C	ENST00000382044	NM_001141980.1	1464	Cgt/Tgt	21/28	1	2	FACETS	0.839	0.757	0.925	0.839	0.757	0.925	CLONAL	1	TRUE	1	0.326754374679582	2		600	883	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243782	41243782	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	75	541	0	ENST00000357654.3:c.3766A>G	p.Thr1256Ala	p.T1256A	ENST00000357654	NM_007294.3	1256	Aca/Gca	10/23	1	2	FACETS	0.734	0.644	0.832	0.734	0.644	0.832	SUBCLONAL	1	TRUE	1	0.326754374679582	2		541	625	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434913	56434913	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	117	740	0	ENST00000407977.2:c.2224del	p.Glu742ArgfsTer85	p.E742Rfs*85	ENST00000407977		742	Gag/ag	9/10	1	2	FACETS	0.836	0.753	0.923	0.836	0.753	0.923	CLONAL	1	TRUE	1	0.326754374679582	2		740	857	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78935204	78935204	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	123	612	0	ENST00000306801.3:c.3616A>G	p.Thr1206Ala	p.T1206A	ENST00000306801	NM_020761.2	1206	Acg/Gcg	31/34	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.326754374679582	2		612	674	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867756	45867756	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	145	753	0	ENST00000391945.4:c.644C>A	p.Pro215His	p.P215H	ENST00000391945	NM_000400.3	215	cCc/cAc	8/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.326754374679582	2		753	780	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044405	128044405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	81	591	0	ENST00000285398.2:c.1216G>A	p.Ala406Thr	p.A406T	ENST00000285398	NM_000122.1	406	Gcc/Acc	8/15	1	2	FACETS	0.661	0.582	0.746	0.661	0.582	0.746	SUBCLONAL	1	TRUE	1	0.326754374679582	2		591	750	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80109475	80109475	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	87	433	0	ENST00000265081.6:c.2728G>A	p.Ala910Thr	p.A910T	ENST00000265081	NM_002439.4	910	Gca/Aca	20/24	1	2	FACETS	0.88	0.78	0.987	0.88	0.78	0.987	CLONAL	1	TRUE	1	0.326754374679582	2		433	605	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707780	176707780	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	117	621	0	ENST00000439151.2:c.5840del	p.Phe1947SerfsTer22	p.F1947Sfs*22	ENST00000439151	NM_022455.4	1946	aTt/at	18/23	1	2	FACETS	0.87	0.784	0.961	0.87	0.784	0.961	CLONAL	1	TRUE	1	0.326754374679582	2		621	823	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287413	38287413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	117	616	0	ENST00000425967.3:c.244G>A	p.Asp82Asn	p.D82N	ENST00000425967	NM_001174067.1	82	Gac/Aac	4/19	0.312412213297259	3	FACETS	0.962	0.867	1	0.481	0.433	0.532	CLONAL	1	TRUE	1	0.326754374679582	3		616	866	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74859035	74859035	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	53	206	0	ENST00000284811.8:c.169A>C	p.Thr57Pro	p.T57P	ENST00000284811		57	Acc/Ccc	4/4	0.312412213297259	3	FACETS	1	0.911	1	0.544	0.466	0.629	CLONAL	1	TRUE	1	0.326754374679582	3		206	347	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866678	117866678	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	93	386	0	ENST00000297338.2:c.967A>G	p.Lys323Glu	p.K323E	ENST00000297338	NM_006265.2	323	Aag/Gag	9/14	0.312412213297259	3	FACETS	1	0.959	1	0.579	0.516	0.646	CLONAL	1	TRUE	1	0.326754374679582	3		386	572	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740546	145740546	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	142	852	0	ENST00000428558.2:c.1471C>G	p.Arg491Gly	p.R491G	ENST00000428558	NM_004260.3	491	Cgg/Ggg	8/22	0.312412213297259	3	FACETS	1	0.93	1	0.513	0.467	0.561	CLONAL	1	TRUE	1	0.326754374679582	3		852	986	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436650	8436650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868210901	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	38	361	0	ENST00000356435.5:c.4028C>T	p.Ala1343Val	p.A1343V	ENST00000356435		1343	gCa/gTa	24/35	1	2	FACETS	0.663	0.549	0.789	0.663	0.549	0.789	SUBCLONAL	1	TRUE	1	0.326754374679582	2		361	351	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412328	63412328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	119	703	0	ENST00000330258.3:c.839G>A	p.Ser280Asn	p.S280N	ENST00000330258	NM_152424.3	280	aGc/aAc	2/2	1	2	FACETS	0.895	0.808	0.987	0.895	0.808	0.987	CLONAL	1	TRUE	1	0.326754374679582	2		703	814	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347808	70347808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	88	550	0	ENST00000374080.3:c.3047G>A	p.Arg1016His	p.R1016H	ENST00000374080		1016	cGc/cAc	22/45	1	2	FACETS	0.699	0.618	0.784	0.699	0.618	0.784	SUBCLONAL	1	TRUE	1	0.326754374679582	2		550	771	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306998	65306998	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	96	526	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aAa/aa	19/25	1	2	FACETS	0.789	0.703	0.88	0.789	0.703	0.88	SUBCLONAL	1	TRUE	1	0.326754374679582	2		526	745	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0062524-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	66	555	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	0.57	0.493	0.653	0.57	0.493	0.653	SUBCLONAL	1	TRUE	1	0.263849665385258	2		555	878	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0062524-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	27	212	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.123424638615815	3	FACETS	0.994	0.795	1	0.497	0.397	0.61	INDETERMINATE	1	TRUE	1	0.263849665385258	3		212	233	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087944	27087944	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0062524-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	51	580	0	ENST00000324856.7:c.2231C>G	p.Ser744Ter	p.S744*	ENST00000324856	NM_006015.4	744	tCa/tGa	6/20	1	2	FACETS	0.477	0.404	0.557	0.477	0.404	0.557	SUBCLONAL	1	TRUE	1	0.263849665385258	2		580	811	SUCCESS
APC	324	MSKCC	GRCh37	5	112173602	112173602	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062524-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	53	526	0	ENST00000257430.4:c.2311G>T	p.Glu771Ter	p.E771*	ENST00000257430	NM_000038.5	771	Gaa/Taa	16/16	1	2	FACETS	0.673	0.573	0.782	0.673	0.573	0.782	SUBCLONAL	1	TRUE	1	0.263849665385258	2		526	597	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851708	134851708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775424447	NA	P-0062524-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	50	675	0	ENST00000398015.3:c.1114C>T	p.Arg372Cys	p.R372C	ENST00000398015	NM_004441.4	372	Cgc/Tgc	5/16	0.123424638615815	3	FACETS	0.504	0.426	0.589	0.252	0.213	0.295	INDETERMINATE	1	TRUE	1	0.263849665385258	3		675	852	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291152	10291152	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062524-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	84	916	0	ENST00000340748.4:c.319C>G	p.Leu107Val	p.L107V	ENST00000340748		107	Cta/Gta	4/40	1	2	FACETS	0.522	0.46	0.59	0.522	0.46	0.59	SUBCLONAL	1	TRUE	1	0.263849665385258	2		916	1219	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424871	47424871	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0062524-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	52	622	0	ENST00000404338.3:c.2939C>G	p.Ser980Ter	p.S980*	ENST00000404338	NM_004491.4	980	tCa/tGa	1/6	1	2	FACETS	0.44	0.374	0.514	0.44	0.374	0.514	SUBCLONAL	1	TRUE	1	0.263849665385258	2		622	895	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176662881	176662881	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062524-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	33	397	0	ENST00000439151.2:c.3856G>T	p.Glu1286Ter	p.E1286*	ENST00000439151	NM_022455.4	1286	Gaa/Taa	6/23	1	2	FACETS	0.5	0.407	0.606	0.5	0.407	0.606	SUBCLONAL	1	TRUE	1	0.263849665385258	2		397	500	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833934	44833935	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0062524-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	18	123	0	ENST00000377967.4:c.359dup	p.Tyr120Ter	p.Y120*	ENST00000377967	NM_021140.2	120	tac/tAac	4/29	1	1	FACETS	0.754	0.572	0.967	0.754	0.572	0.967	CLONAL	1	TRUE	0	0.263849665385258	1		123	157	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76777766	76777766	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0062524-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	42	269	0	ENST00000373344.5:c.6950C>G	p.Ser2317Ter	p.S2317*	ENST00000373344	NM_000489.3	2317	tCa/tGa	32/35	1	1	FACETS	0.77	0.644	0.908	0.77	0.644	0.908	CLONAL	1	TRUE	0	0.263849665385258	1		269	359	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	36	490	1	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		491	690	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469982	25469983	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGCACTGCAAAACGAGCTCAG	novel	NA	P-0062525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	45	691	0	ENST00000264709.3:c.1039_1059dup	p.Leu347_Ala353dup	p.L347_A353dup	ENST00000264709	NM_175629.2	347	-/CTGAGCTCGTTTTGCAGTGCG	9/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		691	864	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0062526-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	13	739	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.28	0.198	0.381	0.28	0.198	0.381	SUBCLONAL	1	TRUE	1	0.15	2		741	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0062527-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	27	555	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		555	862	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0062528-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	324	508	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.883591679853875	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.883591679853875	1		508	383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0062530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1378	60	736	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	1	2	FACETS	0.439	0.376	0.508	0.439	0.376	0.508	SUBCLONAL	1	TRUE	1	0.19	2		736	1438	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215361	5215361	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1237	68	761	0	ENST00000357368.4:c.4257G>C	p.Lys1419Asn	p.K1419N	ENST00000357368	NM_002850.3	1419	aaG/aaC	28/38	1	2	FACETS	0.548	0.475	0.629	0.548	0.475	0.629	SUBCLONAL	1	TRUE	1	0.19	2		761	1305	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038884	47038884	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	39	462	0	ENST00000377604.3:c.891C>A	p.Asn297Lys	p.N297K	ENST00000377604	NM_001204468.1	297	aaC/aaA	9/24	1	2	FACETS	0.53	0.437	0.633	0.53	0.437	0.633	SUBCLONAL	1	TRUE	1	0.19	2		462	775	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978935	25978935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	267	380	0	ENST00000435504.4:c.988G>A	p.Glu330Lys	p.E330K	ENST00000435504		330	Gaa/Aaa	10/13	0.797050768666573	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.797050768666573	1		380	395	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961179	41961192	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGCCAGGAAATG	GCAGCCAGGAAATG	-	novel	NA	P-0062531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	281	665	0	ENST00000219905.7:c.90_103del	p.Pro31AsnfsTer2	p.P31Nfs*2	ENST00000219905	NM_001164273.1	29	aaGCAGCCAGGAAATGgc/aagc	2/24	1	2	FACETS	0.936	0.884	0.989	0.936	0.884	0.989	CLONAL	1	TRUE	1	0.797050768666573	2		665	753	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206942042	206942042	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	145	561	0	ENST00000423557.1:c.476G>A	p.Ser159Asn	p.S159N	ENST00000423557	NM_000572.2	159	aGt/aAt	5/5	1	2	FACETS	0.864	0.79	0.942	0.864	0.79	0.942	CLONAL	1	TRUE	1	0.468524673770323	2		561	716	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890344	72890344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	57	457	0	ENST00000325599.8:c.338C>T	p.Ser113Phe	p.S113F	ENST00000325599	NM_018130.2	113	tCt/tTt	4/11	0.319915231920787	1	FACETS	0.396	0.34	0.457	0.396	0.34	0.457	SUBCLONAL	1	TRUE	0	0.468524673770323	1		457	470	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674260	86674260	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	102	517	0	ENST00000274376.6:c.2392A>T	p.Met798Leu	p.M798L	ENST00000274376	NM_002890.2	798	Atg/Ttg	18/25	1	2	FACETS	0.9	0.808	0.996	0.9	0.808	0.996	CLONAL	1	TRUE	1	0.468524673770323	2		517	484	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271393	26271393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	209	1003	0	ENST00000305910.3:c.220G>A	p.Glu74Lys	p.E74K	ENST00000305910	NM_003534.2	74	Gaa/Aaa	1/1	1	2	FACETS	0.812	0.753	0.873	0.812	0.753	0.873	CLONAL	1	TRUE	1	0.468524673770323	2		1003	1099	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0062533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	167	393	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	0.974	0.902	1	0.974	0.902	1	CLONAL	1	TRUE	1	0.713235602323376	2		393	481	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795057	45795057	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1570312788	NA	P-0062535-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	77	750	0	ENST00000450313.1:c.1571T>C	p.Met524Thr	p.M524T	ENST00000450313	NM_012222.2	524	aTg/aCg	16/16	0.325707996020179	3	FACETS	0.552	0.484	0.627	0.276	0.242	0.314	SUBCLONAL	1	TRUE	1	0.369417944746159	3		750	894	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0062535-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	427	874	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	0.369417944746159	5	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	2	0.369417944746159	5		874	1103	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47601073	47601073	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062535-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	226	639	0	ENST00000263735.4:c.311T>G	p.Leu104Arg	p.L104R	ENST00000263735	NM_002354.2	104	cTc/cGc	3/9	0.36947180051247	3	FACETS	0.977	0.913	1	0.977	0.913	1	CLONAL	2	TRUE	1	0.369417944746159	3		639	742	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643698	52643698	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062535-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	62	490	0	ENST00000394830.3:c.2198A>C	p.Asn733Thr	p.N733T	ENST00000394830	NM_018313.4	733	aAt/aCt	17/30	0.368984787371719	4	FACETS	0.641	0.553	0.737	0.321	0.276	0.369	SUBCLONAL	1	TRUE	2	0.369417944746159	4		490	717	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859750	151859750	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062535-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	147	785	0	ENST00000262189.6:c.10912del	p.Ser3638GlnfsTer9	p.S3638Qfs*9	ENST00000262189	NM_170606.2	3638	Tca/ca	43/59	0.36947180051247	3	FACETS	0.98	0.894	1	0.49	0.447	0.535	CLONAL	1	TRUE	1	0.369417944746159	3		785	962	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150931665	150931665	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062536-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	550	511	0	ENST00000271640.5:c.2342G>T	p.Cys781Phe	p.C781F	ENST00000271640	NM_001145415.1	781	tGt/tTt	15/22	0.562905202471003	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.562905202471003	2		511	950	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376106	225376106	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062536-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	40	431	0	ENST00000264414.4:c.848G>A	p.Gly283Glu	p.G283E	ENST00000264414	NM_003590.4	283	gGg/gAg	6/16	0.562905202471003	1	FACETS	0.255	0.212	0.302	0.255	0.212	0.302	SUBCLONAL	1	TRUE	0	0.562905202471003	1		431	401	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051628	30051629	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0062536-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	282	533	0	ENST00000338641.4:c.564dup	p.Thr189TyrfsTer14	p.T189Yfs*14	ENST00000338641	NM_000268.3	188	att/aTtt	6/16	0.561080532566708	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.562905202471003	1		533	694	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	19	737	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.51	0.387	0.655	0.51	0.387	0.655	SUBCLONAL	1	TRUE	1	0.25	2		737	298	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138294	2138311	+	inframe_deletion	In_Frame_Del	DEL	CGGCTCCGCCACATCAAG	CGGCTCCGCCACATCAAG	-	rs137854218	NA	P-0062537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	42	692	0	ENST00000219476.3:c.5238_5255del	p.His1746_Arg1751del	p.H1746_R1751del	ENST00000219476	NM_000548.3	1743	CGGCTCCGCCACATCAAG/-	41/42	1	2	FACETS	0.732	0.611	0.866	0.732	0.611	0.866	SUBCLONAL	1	TRUE	1	0.25	2		692	459	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913078	44913078	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	13	367	0	ENST00000377967.4:c.753G>A	p.Trp251Ter	p.W251*	ENST00000377967	NM_021140.2	251	tgG/tgA	10/29	1	2	FACETS	0.413	0.294	0.558	0.413	0.294	0.558	SUBCLONAL	1	TRUE	1	0.25	2		367	252	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55143558	55143558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs999173790	NA	P-0062537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	45	621	0	ENST00000257290.5:c.1790G>A	p.Arg597Gln	p.R597Q	ENST00000257290	NM_006206.4	597	cGg/cAg	13/23	1	2	FACETS	0.667	0.56	0.785	0.667	0.56	0.785	SUBCLONAL	1	TRUE	1	0.25	2		621	540	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612762	228612762	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	74	961	0	ENST00000366696.1:c.265del	p.Ala89ProfsTer2	p.A89Pfs*2	ENST00000366696	NM_003493.2	89	Gcc/cc	1/1	1	2	FACETS	0.75	0.656	0.852	0.75	0.656	0.852	SUBCLONAL	1	TRUE	1	0.25	2		961	789	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514837	44514837	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	48	647	0	ENST00000291552.4:c.410G>T	p.Gly137Val	p.G137V	ENST00000291552	NM_006758.2	137	gGa/gTa	6/8	1	2	FACETS	0.568	0.479	0.666	0.568	0.479	0.666	SUBCLONAL	1	TRUE	1	0.25	2		647	676	SUCCESS
ALB	213	MSKCC	GRCh37	4	74283293	74283293	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	56	473	0	ENST00000295897.4:c.1336del	p.Thr446LeufsTer3	p.T446Lfs*3	ENST00000295897	NM_000477.5	445	ccA/cc	11/15	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.25	2		473	417	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120752	94120752	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062537-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	33	558	0	ENST00000369303.4:c.299T>A	p.Val100Glu	p.V100E	ENST00000369303	NM_004440.3	100	gTa/gAa	3/17	1	2	FACETS	0.558	0.454	0.676	0.558	0.454	0.676	SUBCLONAL	1	TRUE	1	0.25	2		558	473	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183734	10183735	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0062538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	29	730	0	ENST00000256474.2:c.204dup	p.Arg69AlafsTer63	p.R69Afs*63	ENST00000256474	NM_000551.3	68	tcg/tcGg	1/3	1	2	FACETS	1	0.804	1	1	0.804	1	CLONAL	1	TRUE	1	0.13	2		730	445	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110504	8110504	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	36	660	0	ENST00000585124.1:c.388G>A	p.Ala130Thr	p.A130T	ENST00000585124	NM_004217.3	130	Gcc/Acc	5/9	1	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	TRUE	1	0.13	2		660	540	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163744	47163744	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0062538-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	27	659	0	ENST00000409792.3:c.2382C>G	p.Tyr794Ter	p.Y794*	ENST00000409792	NM_014159.6	794	taC/taG	3/21	1	2	FACETS	0.948	0.754	1	0.948	0.754	1	CLONAL	1	TRUE	1	0.13	2		659	438	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584560	48584560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	714	744	0	ENST00000342988.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000342988	NM_005359.5	245	Cag/Tag	6/12	0.710604586194925	3	FACETS	0.994	0.973	1	0.994	0.973	1	CLONAL	3	FALSE	0	0.710604586194925	3		744	913	SUCCESS
APC	324	MSKCC	GRCh37	5	112175897	112175897	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	220	673	0	ENST00000257430.4:c.4606G>T	p.Glu1536Ter	p.E1536*	ENST00000257430	NM_000038.5	1536	Gaa/Taa	16/16	0.710604586194925	2	FACETS	0.895	0.851	0.938	0.895	0.851	0.938	CLONAL	2	FALSE	0	0.710604586194925	2		673	346	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0062539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	441	800	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	0.637312913389404	3	FACETS	1	0.994	1	0.635	0.606	0.665	CLONAL	1	FALSE	1	0.710604586194925	3		800	1324	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361244	66361244	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	193	628	0	ENST00000273854.3:c.928T>C	p.Phe310Leu	p.F310L	ENST00000273854	NM_004439.5	310	Ttc/Ctc	4/18	0.710604586194925	3	FACETS	1	0.953	1	0.345	0.32	0.371	CLONAL	1	FALSE	0	0.710604586194925	3		628	711	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46240701	46240701	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	51	489	0	ENST00000334344.6:c.1561G>C	p.Glu521Gln	p.E521Q	ENST00000334344	NM_152641.2	521	Gag/Cag	12/21	0.144068653130321	3	FACETS	1	0.924	1	0.553	0.478	0.632	INDETERMINATE	1	FALSE	1	0.710604586194925	3		489	176	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636188	28636188	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1932	300	615	0	ENST00000241453.7:c.184G>C	p.Asp62His	p.D62H	ENST00000241453	NM_004119.2	62	Gac/Cac	3/24	0.710604586194925	5	FACETS	0.782	0.732	0.832	0.195	0.183	0.208	SUBCLONAL	1	FALSE	1	0.710604586194925	5		615	2232	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900412	32900412	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1483012313	NA	P-0062539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	59	429	0	ENST00000380152.3:c.509T>C	p.Phe170Ser	p.F170S	ENST00000380152		170	tTt/tCt	6/27	0.710604586194925	5	FACETS	0.647	0.557	0.745	0.162	0.139	0.187	SUBCLONAL	1	FALSE	1	0.710604586194925	5		429	530	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277009	18277009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	601	695	0	ENST00000222254.8:c.1456G>A	p.Glu486Lys	p.E486K	ENST00000222254	NM_005027.3	486	Gag/Aag	12/16	0.710604586194925	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	FALSE	1	0.710604586194925	3		695	1131	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620694	52620694	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	106	470	2	ENST00000394830.3:c.3059A>C	p.Lys1020Thr	p.K1020T	ENST00000394830	NM_018313.4	1020	aAg/aCg	21/30	0.675824287160063	3	FACETS	0.899	0.81	0.991	0.449	0.405	0.496	CLONAL	1	FALSE	1	0.710604586194925	3		472	450	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449409	31449409	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	297	548	0	ENST00000344624.3:c.2800C>T	p.His934Tyr	p.H934Y	ENST00000344624		934	Cac/Tac	19/33	0.637560821638961	6	FACETS	0.945	0.89	1	0.472	0.445	0.501	CLONAL	2	FALSE	2	0.710604586194925	6		548	1071	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861049	35861049	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	418	531	0	ENST00000303115.3:c.178G>C	p.Glu60Gln	p.E60Q	ENST00000303115	NM_002185.3	60	Gag/Cag	2/8	0.637560821638961	6	FACETS	1	0.98	1	0.526	0.501	0.552	CLONAL	2	FALSE	2	0.710604586194925	6		531	1353	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591130	67591131	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGACGAGAG	novel	NA	P-0062539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	244	519	0	ENST00000274335.5:c.1725_1733dup	p.Arg577_Asp578insGluThrArg	p.R577_D578insETR	ENST00000274335		575	aag/aAGACGAGAGag	12/15	0.710604586194925	2	FACETS	0.835	0.795	0.876	0.835	0.795	0.876	CLONAL	2	FALSE	0	0.710604586194925	2		519	411	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864596	56864596	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	92	484	0	ENST00000519728.1:c.559A>C	p.Ser187Arg	p.S187R	ENST00000519728	NM_002350.3	187	Agt/Cgt	7/13	0.710604586194925	4	FACETS	0.971	0.867	1	0.324	0.289	0.361	CLONAL	1	FALSE	1	0.710604586194925	4		484	456	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608848	100608875	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCCACTTACCAAAAGCCCAAATGTCAG	ATCCACTTACCAAAAGCCCAAATGTCAG	-	novel	NA	P-0062539-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	209	483	0	ENST00000308731.7:c.1733_1750+10del		p.X578_splice	ENST00000308731	NM_000061.2	578		17/19	0.504636198573681	4	FACETS	0.877	0.82	0.934	0.877	0.82	0.934	CLONAL	2	FALSE	2	0.710604586194925	4		483	574	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	736	737	0				ENST00000310581	NM_198253.2	-/1132			0.518026835862607	8	FACETS	0.959	0.932	0.986	0.959	0.932	0.986	CLONAL	6	TRUE	2	0.518026835862607	8		737	1261	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0062561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	108	795	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.502314119577595	3	FACETS	0.584	0.523	0.648	0.195	0.174	0.216	SUBCLONAL	1	TRUE	0	0.518026835862607	3		795	899	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	106	562	0	ENST00000267101.3:c.273G>A	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atA	3/28	0.518026835862607	3	FACETS	0.644	0.577	0.715	0.322	0.288	0.358	SUBCLONAL	1	TRUE	1	0.518026835862607	3		562	800	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259280	16259280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	132	819	0	ENST00000375759.3:c.6545C>T	p.Ala2182Val	p.A2182V	ENST00000375759	NM_015001.2	2182	gCt/gTt	11/15	0.137669836890553	3	FACETS	0.71	0.644	0.779	0.355	0.322	0.39	INDETERMINATE	1	TRUE	1	0.518026835862607	3		819	904	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69229753	69229753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	28	382	0	ENST00000462284.1:c.829G>A	p.Glu277Lys	p.E277K	ENST00000462284	NM_002392.5	277	Gaa/Aaa	9/11	0.518026835862607	3	FACETS	0.403	0.322	0.495	0.201	0.161	0.248	SUBCLONAL	1	TRUE	1	0.518026835862607	3		382	338	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050981	49050981	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs587778839	NA	P-0062561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	144	489	0	ENST00000267163.4:c.2663+2T>C		p.X888_splice	ENST00000267163	NM_000321.2	888			0.518026835862607	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.518026835862607	1		489	322	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527874	103527874	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	71	626	0	ENST00000355739.4:c.3182C>A	p.Thr1061Lys	p.T1061K	ENST00000355739	NM_000123.3	1061	aCa/aAa	15/15	0.139843066290564	5	FACETS	0.865	0.756	0.983	0.288	0.252	0.328	INDETERMINATE	1	TRUE	2	0.518026835862607	5		626	563	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438022	110438022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1186261552	NA	P-0062561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	66	472	0	ENST00000375856.3:c.379G>A	p.Glu127Lys	p.E127K	ENST00000375856	NM_003749.2	127	Gag/Aag	1/2	0.139843066290564	5	FACETS	0.729	0.633	0.834	0.243	0.211	0.278	INDETERMINATE	1	TRUE	2	0.518026835862607	5		472	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577166	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTACTCAGGAT	CTACTCAGGAT	G	novel	NA	P-0062561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	311	626	1	ENST00000269305.4:c.783-11_783-1delinsC		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.502314119577595	3	FACETS	1	0.983	1	0.717	0.681	0.753	CLONAL	2	TRUE	0	0.518026835862607	3		627	703	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16056658	16056658	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	22	286	0	ENST00000268712.3:c.784G>T	p.Glu262Ter	p.E262*	ENST00000268712	NM_006311.3	262	Gaa/Taa	7/46	0.502314119577595	3	FACETS	0.535	0.416	0.67	0.178	0.138	0.224	SUBCLONAL	1	TRUE	0	0.518026835862607	3		286	200	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772417	56772417	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	92	568	0	ENST00000337432.4:c.271C>G	p.Leu91Val	p.L91V	ENST00000337432	NM_058216.2	91	Ctt/Gtt	2/9	0.322028756723076	5	FACETS	0.908	0.807	1	0.303	0.269	0.339	CLONAL	1	TRUE	2	0.518026835862607	5		568	695	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772460	56772460	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	91	594	0	ENST00000337432.4:c.314C>A	p.Ser105Ter	p.S105*	ENST00000337432	NM_058216.2	105	tCa/tAa	2/9	0.322028756723076	5	FACETS	0.891	0.791	0.997	0.297	0.263	0.333	CLONAL	1	TRUE	2	0.518026835862607	5		594	701	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141561	11141561	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	467	704	0	ENST00000358026.2:c.3538C>A	p.Pro1180Thr	p.P1180T	ENST00000358026	NM_001128849.1	1180	Cct/Act	25/36	0.304470145884309	3	FACETS	0.871	0.838	0.903	0.871	0.838	0.903	INDETERMINATE	3	TRUE	0	0.518026835862607	3		704	869	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051617	30051617	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	71	479	0	ENST00000338641.4:c.551G>T	p.Trp184Leu	p.W184L	ENST00000338641	NM_000268.3	184	tGg/tTg	6/16	0.10925207003593	4	FACETS	0.871	0.762	0.987	0.435	0.381	0.494	INDETERMINATE	1	TRUE	2	0.518026835862607	4		479	478	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533751	41533751	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	75	480	0	ENST00000263253.7:c.1717G>T	p.Glu573Ter	p.E573*	ENST00000263253	NM_001429.3	573	Gaa/Taa	8/31	0.10925207003593	4	FACETS	0.77	0.675	0.871	0.385	0.337	0.436	INDETERMINATE	1	TRUE	2	0.518026835862607	4		480	571	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839974	27839974	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1195	126	949	0	ENST00000328488.2:c.120C>G	p.His40Gln	p.H40Q	ENST00000328488	NM_003533.2	40	caC/caG	1/1	0.322028756723076	5	FACETS	0.654	0.591	0.722	0.218	0.197	0.241	SUBCLONAL	1	TRUE	2	0.518026835862607	5		949	1321	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651960	36651960	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	363	749	0	ENST00000244741.5:c.82G>T	p.Glu28Ter	p.E28*	ENST00000244741	NM_000389.4	28	Gag/Tag	2/3	0.322028756723076	5	FACETS	1	0.991	1	0.782	0.743	0.822	CLONAL	2	TRUE	2	0.518026835862607	5		749	1061	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974792	21974792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141798398	NA	P-0062561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	127	823	0	ENST00000304494.5:c.35C>T	p.Ser12Leu	p.S12L	ENST00000304494	NM_000077.4	12	tCg/tTg	1/3	0.504860802283752	2	FACETS	0.669	0.606	0.735	0.334	0.303	0.368	SUBCLONAL	1	TRUE	0	0.518026835862607	2		823	733	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0062562-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	414	398	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.479844620952943	3	FACETS	0.848	0.815	0.881	0.848	0.815	0.881	CLONAL	3	TRUE	0	0.57242028623542	3		398	731	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062562-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	143	340	2	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	0.57242028623542	5	FACETS	1	0.979	1	0.247	0.225	0.27	CLONAL	1	TRUE	0	0.57242028623542	5		342	751	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948747	71948748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760925109	NA	P-0062562-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	118	671	8	ENST00000298229.2:c.3466dup	p.Arg1156ProfsTer59	p.R1156Pfs*59	ENST00000298229	NM_001567.3	1153	-/C	26/28	0.479786902682344	4	FACETS	0.861	0.777	0.949	0.215	0.194	0.238	CLONAL	1	TRUE	0	0.57242028623542	4		679	753	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254599	16254599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062562-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	46	388	0	ENST00000375759.3:c.1864G>A	p.Ala622Thr	p.A622T	ENST00000375759	NM_015001.2	622	Gca/Aca	11/15	0.479786902682344	4	FACETS	0.442	0.371	0.52	0.11	0.092	0.13	SUBCLONAL	1	TRUE	0	0.57242028623542	4		388	572	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614590	38614590	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062562-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	54	279	0	ENST00000299084.4:c.356C>A	p.Ala119Asp	p.A119D	ENST00000299084	NM_152594.2	119	gCt/gAt	3/7	0.481522640547507	2	FACETS	0.854	0.738	0.977	0.427	0.369	0.489	CLONAL	1	TRUE	0	0.57242028623542	2		279	221	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353971	15353972	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	novel	NA	P-0062562-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	36	205	0	ENST00000263377.2:c.2906_2908dup	p.Gln969dup	p.Q969dup	ENST00000263377	NM_058243.2	969	ctg/cAGCtg	14/20	0.514540181393667	4	FACETS	0.842	0.697	1	0.281	0.232	0.334	CLONAL	1	TRUE	1	0.57242028623542	4		205	235	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0062564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	16	205	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.206140672284072	3	FACETS	0.837	0.635	1	0.837	0.635	1	CLONAL	2	TRUE	1	0.32141985974436	3		205	69	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653805	89653805	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659443	NA	P-0062564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	41	240	0	ENST00000371953.3:c.103A>G	p.Met35Val	p.M35V	ENST00000371953	NM_000314.4	35	Atg/Gtg	2/9	0.273967656989209	4	FACETS	0.906	0.773	1	0.906	0.773	1	CLONAL	3	TRUE	1	0.32141985974436	4		240	124	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508746	106508746	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374827875	NA	P-0062564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	13	584	0	ENST00000359195.3:c.740G>A	p.Ser247Asn	p.S247N	ENST00000359195	NM_002649.2	247	aGc/aAc	2/11	0.198994921392889	4	FACETS	0.597	0.427	0.804	0.299	0.213	0.402	SUBCLONAL	1	TRUE	2	0.32141985974436	4		584	179	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991757	72991758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760959844	NA	P-0062564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	22	645	2	ENST00000268489.5:c.2287dup	p.Glu763GlyfsTer26	p.E763Gfs*26	ENST00000268489	NM_006885.3	763	gag/gGag	2/10	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.32141985974436	2		647	100	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0062564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	21	329	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.198994921392889	4	FACETS	1	0.831	1	0.543	0.421	0.682	CLONAL	1	TRUE	2	0.32141985974436	4		329	159	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640860	3640860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767916829	NA	P-0062564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	25	679	0	ENST00000294008.3:c.2779G>A	p.Ala927Thr	p.A927T	ENST00000294008	NM_032444.2	927	Gct/Act	12/15	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.32141985974436	2		679	104	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0062565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	52	398	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.161944570307223	3	FACETS	0.854	0.733	0.984	1	0.953	1	CLONAL	3	TRUE	1	0.161944570307223	3		398	271	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519985	NA	P-0062565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	190	729	0	ENST00000269305.4:c.857A>C	p.Glu286Ala	p.E286A	ENST00000269305	NM_001126112.2	286	gAa/gCa	8/11	1	2	FACETS	1	0.979	1	1	0.994	1	CLONAL	2	TRUE	1	0.161944570307223	2		729	1009	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0062565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	143	578	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	0.161944570307223	3	FACETS	0.898	0.82	0.979	1	0.984	1	CLONAL	3	TRUE	1	0.161944570307223	3		578	709	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564698	86564698	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	138	881	1	ENST00000274376.6:c.434del	p.Pro145LeufsTer29	p.P145Lfs*29	ENST00000274376	NM_002890.2	144	Ccc/cc	1/25	0.161944570307223	1	FACETS	0.788	0.716	0.864	1	0.987	1	SUBCLONAL	2	TRUE	0	0.161944570307223	1		882	994	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443618	29443618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200585833	NA	P-0062565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	64	716	0	ENST00000389048.3:c.3599C>T	p.Ala1200Val	p.A1200V	ENST00000389048	NM_004304.4	1200	gCg/gTg	23/29	1	2	FACETS	0.776	0.67	0.892	0.776	0.67	0.892	SUBCLONAL	1	TRUE	1	0.161944570307223	2		716	1018	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497937	25497937	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	91	582	0	ENST00000264709.3:c.512G>A	p.Arg171Gln	p.R171Q	ENST00000264709	NM_175629.2	171	cGg/cAg	6/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.161944570307223	2		582	760	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781211	3781211	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	122	771	1	ENST00000262367.5:c.5154G>A	p.Trp1718Ter	p.W1718*	ENST00000262367	NM_004380.2	1718	tgG/tgA	30/31	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.161944570307223	2		772	1010	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141605	202141605	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	46	573	0	ENST00000358485.4:c.893T>C	p.Ile298Thr	p.I298T	ENST00000358485	NM_001080125.1	298	aTc/aCc	7/9	1	2	FACETS	0.756	0.635	0.891	0.756	0.635	0.891	SUBCLONAL	1	TRUE	1	0.161944570307223	2		573	751	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422461	47422461	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	81	672	0	ENST00000377045.4:c.95T>A	p.Val32Glu	p.V32E	ENST00000377045	NM_001654.4	32	gTg/gAg	2/16	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.161944570307223	2		672	842	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0062637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	97	212	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.931762082784667	3	FACETS	0.985	0.888	1	0.492	0.444	0.542	CLONAL	1	TRUE	1	0.931762082784667	3		212	310	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324597	31324597	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs41545612	NA	P-0062637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	45	421	0	ENST00000412585.2:c.211C>A	p.Pro71Thr	p.P71T	ENST00000412585	NM_005514.6	71	Ccg/Acg	2/8	1	2	FACETS	0.166	0.139	0.196	0.166	0.139	0.196	SUBCLONAL	1	TRUE	1	0.931762082784667	2		421	581	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062639-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	120	737	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.949	0.861	1	0.949	0.861	1	CLONAL	1	TRUE	1	0.49707952111527	2		737	509	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0062639-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	238	515	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.49707952111527	2		515	948	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578234	7578234	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0062640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	549	521	0	ENST00000269305.4:c.615T>G	p.Tyr205Ter	p.Y205*	ENST00000269305	NM_001126112.2	205	taT/taG	6/11	0.59505570956907	3	FACETS	0.984	0.955	1	0.984	0.955	1	CLONAL	3	TRUE	0	0.595031919012111	3		521	811	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248258	59248258	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	408	531	0	ENST00000371222.2:c.485G>C	p.Ser162Thr	p.S162T	ENST00000371222	NM_002228.3	162	aGc/aCc	1/1	0.59505570956907	3	FACETS	0.999	0.955	1	0.999	0.955	1	CLONAL	2	TRUE	1	0.595031919012111	3		531	891	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47421991	47421991	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	600	456	0	ENST00000404338.3:c.59G>T	p.Gly20Val	p.G20V	ENST00000404338	NM_004491.4	20	gGa/gTa	1/6	0.56885689249324	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	TRUE	1	0.595031919012111	4		456	1072	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546578	9546578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	288	407	0	ENST00000353224.5:c.1444C>T	p.Leu482Phe	p.L482F	ENST00000353224	NM_177990.2	482	Ctc/Ttc	5/10	0.59505570956907	3	FACETS	0.98	0.929	1	0.98	0.929	1	CLONAL	2	TRUE	1	0.595031919012111	3		407	641	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182681792	182681792	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	223	313	0	ENST00000292782.4:c.266T>C	p.Phe89Ser	p.F89S	ENST00000292782	NM_020640.2	89	tTc/tCc	3/7	0.595031919012111	7	FACETS	1	0.964	1	0.421	0.392	0.451	CLONAL	2	TRUE	2	0.595031919012111	7		313	886	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15833798	15833798	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0062640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	86	280	0	ENST00000307771.7:c.558-2A>G		p.X186_splice	ENST00000307771	NM_005089.3	186			0.59505570956907	3	FACETS	1	0.911	1	0.512	0.456	0.571	CLONAL	1	TRUE	1	0.595031919012111	3		280	366	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429039	47429039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	85	472	0	ENST00000377045.4:c.1402G>A	p.Gly468Arg	p.G468R	ENST00000377045	NM_001654.4	468	Gga/Aga	13/16	0.272900044738557	3	FACETS	0.546	0.482	0.614	0.182	0.16	0.205	INDETERMINATE	1	TRUE	0	0.595031919012111	3		472	679	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650526	48650527	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0062640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	125	499	0	ENST00000376670.3:c.496_497delinsAA	p.Pro166Asn	p.P166N	ENST00000376670	NM_002049.3	166	CCt/AAt	3/6	0.272900044738557	3	FACETS	0.726	0.657	0.798	0.242	0.219	0.266	INDETERMINATE	1	TRUE	0	0.595031919012111	3		499	751	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776328	76776328	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	54	347	1	ENST00000373344.5:c.7138C>T	p.Gln2380Ter	p.Q2380*	ENST00000373344	NM_000489.3	2380	Cag/Tag	34/35	0.272900044738557	3	FACETS	0.572	0.489	0.661	0.191	0.163	0.221	INDETERMINATE	1	TRUE	0	0.595031919012111	3		348	412	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059194	47059194	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062641-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	135	404	0	ENST00000409792.3:c.7467C>A	p.Tyr2489Ter	p.Y2489*	ENST00000409792	NM_014159.6	2489	taC/taA	20/21	0.441743204067578	3	FACETS	1	0.969	1	0.571	0.52	0.624	CLONAL	1	TRUE	1	0.447277804297699	3		404	647	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399197	139399197	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062641-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	78	423	0	ENST00000277541.6:c.4946A>T	p.Lys1649Met	p.K1649M	ENST00000277541	NM_017617.3	1649	aAg/aTg	26/34	0.441743204067578	3	FACETS	0.875	0.771	0.985	0.437	0.385	0.493	CLONAL	1	TRUE	1	0.447277804297699	3		423	488	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0062643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	54	306	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.23	2		306	457	SUCCESS
APC	324	MSKCC	GRCh37	5	112174094	112174095	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs863225332	NA	P-0062643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	42	406	0	ENST00000257430.4:c.2804dup	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	tac/tAac	16/16	1	2	FACETS	0.582	0.485	0.69	0.582	0.485	0.69	SUBCLONAL	1	TRUE	1	0.23	2		406	628	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188853	32188853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs192478549	NA	P-0062643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	69	567	0	ENST00000375023.3:c.701G>A	p.Arg234Gln	p.R234Q	ENST00000375023	NM_004557.3	234	cGg/cAg	4/30	1	2	FACETS	0.735	0.639	0.84	0.735	0.639	0.84	SUBCLONAL	1	TRUE	1	0.23	2		567	816	SUCCESS
APC	324	MSKCC	GRCh37	5	112176021	112176021	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	38	420	0	ENST00000257430.4:c.4731del	p.Glu1577AspfsTer73	p.E1577Dfs*73	ENST00000257430	NM_000038.5	1577	gAa/ga	16/16	1	2	FACETS	0.504	0.416	0.604	0.504	0.416	0.604	SUBCLONAL	1	TRUE	1	0.23	2		420	655	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356238	66356238	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	40	466	0	ENST00000273854.3:c.1259G>T	p.Gly420Val	p.G420V	ENST00000273854	NM_004439.5	420	gGc/gTc	5/18	1	2	FACETS	0.469	0.388	0.559	0.469	0.388	0.559	SUBCLONAL	1	TRUE	1	0.23	2		466	742	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0062683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	262	306	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.709048837815946	5	FACETS	0.988	0.937	1	0.988	0.937	1	CLONAL	3	TRUE	2	0.725165835513864	5		306	509	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0062683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	164	371	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.627492585089032	4	FACETS	0.848	0.786	0.912	0.848	0.786	0.912	CLONAL	2	TRUE	2	0.725165835513864	4		371	460	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410720	63410720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1569191603	NA	P-0062683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	352	496	0	ENST00000330258.3:c.2447G>A	p.Arg816Gln	p.R816Q	ENST00000330258	NM_152424.3	816	cGg/cAg	2/2	0.725165835513864	6	FACETS	0.926	0.901	0.951	1	0.997	1	CLONAL	6	TRUE	2	0.725165835513864	6		496	428	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578408	+	missense_variant	Missense_Mutation	DNP	GC	GC	CA	novel	NA	P-0062683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	181	660	1	ENST00000269305.4:c.522_523delinsTG	p.Arg174_Arg175delinsSerGly	p.R174_R175delinsSG	ENST00000269305	NM_001126112.2	174	agGCgc/agTGgc	5/11	0.725165835513864	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.725165835513864	2		661	233	SUCCESS
AXL	558	MSKCC	GRCh37	19	41737094	41737094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	236	562	0	ENST00000301178.4:c.674C>T	p.Pro225Leu	p.P225L	ENST00000301178	NM_021913.4	225	cCc/cTc	6/20	0.627492585089032	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.725165835513864	4		562	543	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242484	55242507	+	inframe_deletion	In_Frame_Del	DEL	TCTCCGAAAGCCAACAAGGAAATC	TCTCCGAAAGCCAACAAGGAAATC	-	rs121913463	NA	P-0062684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	36	401	0	ENST00000275493.2:c.2254_2277del	p.Ser752_Ile759del	p.S752_I759del	ENST00000275493	NM_005228.3	752	TCTCCGAAAGCCAACAAGGAAATC/-	19/28	1	2	FACETS	0.727	0.599	0.871	0.727	0.599	0.871	SUBCLONAL	1	TRUE	1	0.280369849443811	2		401	353	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520166	9520166	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	45	472	0	ENST00000353224.5:c.2103A>T	p.Lys701Asn	p.K701N	ENST00000353224	NM_177990.2	701	aaA/aaT	10/10	1	2	FACETS	0.684	0.575	0.805	0.684	0.575	0.805	SUBCLONAL	1	TRUE	1	0.280369849443811	2		472	469	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044970	47044970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	72	597	0	ENST00000377604.3:c.2296C>T	p.Arg766Cys	p.R766C	ENST00000377604	NM_001204468.1	766	Cgc/Tgc	20/24	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.280369849443811	2		597	509	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679232	88679232	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1239415215	NA	P-0062684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	63	439	0	ENST00000360948.2:c.805A>G	p.Thr269Ala	p.T269A	ENST00000360948	NM_001012338.2	269	Acg/Gcg	8/19	0.280369849443811	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	0	0.280369849443811	1		439	365	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	76	737	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.878	0.779	0.983	0.878	0.779	0.983	CLONAL	1	TRUE	1	0.605222853088024	2		737	286	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0062686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	36	351	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.605222853088024	1	FACETS	0.339	0.28	0.404	0.339	0.28	0.404	SUBCLONAL	1	TRUE	0	0.605222853088024	1		351	245	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924822	49924822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202007332	NA	P-0062686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	156	559	0	ENST00000296474.3:c.4121G>A	p.Arg1374His	p.R1374H	ENST00000296474	NM_002447.2	1374	cGt/cAt	20/20	1	2	FACETS	0.989	0.912	1	0.989	0.912	1	CLONAL	1	TRUE	1	0.605222853088024	2		559	521	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31483681	31483681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	116	361	0	ENST00000344624.3:c.2051G>A	p.Arg684His	p.R684H	ENST00000344624		684	cGt/cAt	13/33	1	2	FACETS	0.85	0.771	0.932	0.85	0.771	0.932	CLONAL	1	TRUE	1	0.605222853088024	2		361	451	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	97	737	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.849	0.761	0.94	0.849	0.761	0.94	CLONAL	1	TRUE	1	0.549567449500089	2		737	416	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0062688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	171	446	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.982	0.907	1	0.982	0.907	1	CLONAL	1	TRUE	1	0.549567449500089	2		446	634	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034420	47034420	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	148	167	0	ENST00000377604.3:c.505C>T	p.Gln169Ter	p.Q169*	ENST00000377604	NM_001204468.1	169	Cag/Tag	6/24	1	1	FACETS	0.772	0.723	0.82	1	0.991	1	SUBCLONAL	2	TRUE	0	0.549567449500089	1		167	253	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858336	9858336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1349281989	NA	P-0062688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	180	472	0	ENST00000330684.3:c.3065G>A	p.Arg1022His	p.R1022H	ENST00000330684	NM_001134407.1	1022	cGc/cAc	13/13	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.549567449500089	2		472	623	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44894182	44894182	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	69	124	0	ENST00000377967.4:c.571C>T	p.Gln191Ter	p.Q191*	ENST00000377967	NM_021140.2	191	Cag/Tag	7/29	1	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.549567449500089	1		124	135	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975423	13975423	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0062688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	202	384	0	ENST00000405192.2:c.464C>G	p.Ser155Ter	p.S155*	ENST00000405192	NM_001163147.1	155	tCa/tGa	7/12	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.549567449500089	2		384	699	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0000118-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	380	438	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.92	2		438	786	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484595	57484595	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs797045203	NA	P-0000118-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	262	285	0	ENST00000371085.3:c.679C>A	p.Gln227Lys	p.Q227K	ENST00000371085	NM_000516.4	227	Cag/Aag	9/13	1	2	FACETS	0.98	0.927	1	0.98	0.927	1	CLONAL	1	TRUE	1	0.92	2		285	581	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473595	67473597	+	inframe_deletion	In_Frame_Del	DEL	CTA	CTA	-	novel	NA	P-0000118-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	324	430	0	ENST00000327367.4:c.677_679del	p.Tyr226del	p.Y226del	ENST00000327367	NM_005902.3	225	acCTAc/acc	6/9	1	2	FACETS	0.934	0.888	0.981	0.934	0.888	0.981	CLONAL	1	TRUE	1	0.92	2		430	754	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198285	185198285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1331568030	NA	P-0000462-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	62	289	0	ENST00000265026.3:c.2767G>A	p.Gly923Ser	p.G923S	ENST00000265026	NM_004721.4	923	Ggc/Agc	13/14	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.248947169173625	2		289	461	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717630	89717630	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554825168	NA	P-0000462-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	28	278	0	ENST00000371953.3:c.655C>T	p.Gln219Ter	p.Q219*	ENST00000371953	NM_000314.4	219	Cag/Tag	7/9	1	2	FACETS	0.648	0.518	0.796	0.648	0.518	0.796	SUBCLONAL	1	TRUE	1	0.248947169173625	2		278	347	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692819	89692820	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000462-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	18	145	0	ENST00000371953.3:c.306dup	p.Pro103ThrfsTer4	p.P103Tfs*4	ENST00000371953	NM_000314.4	101	-/A	5/9	1	2	FACETS	0.841	0.637	1	0.841	0.637	1	CLONAL	1	TRUE	1	0.248947169173625	2		145	172	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571839	64571840	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000462-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	68	751	0	ENST00000312049.6:c.1799dup	p.Ser601ValfsTer78	p.S601Vfs*78	ENST00000312049	NM_130799.2	600	ctg/ctTg	10/10	1	2	FACETS	0.477	0.413	0.547	0.477	0.413	0.547	SUBCLONAL	1	TRUE	1	0.248947169173625	2		751	1145	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268361	198268361	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000675-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	54	207	0	ENST00000335508.6:c.1667T>C	p.Ile556Thr	p.I556T	ENST00000335508	NM_012433.2	556	aTt/aCt	12/25	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.16	2		207	638	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879364	151879364	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000675-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	41	257	0	ENST00000262189.6:c.5581del	p.Arg1861GlyfsTer78	p.R1861Gfs*78	ENST00000262189	NM_170606.2	1861	Cgg/gg	36/59	1	2	FACETS	0.816	0.678	0.97	0.816	0.678	0.97	CLONAL	1	TRUE	1	0.16	2		257	628	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0000675-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	108	677	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.227825370565528	2		678	819	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795019	242795019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1319637878	NA	P-0000675-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	87	346	1	ENST00000334409.5:c.190G>A	p.Val64Met	p.V64M	ENST00000334409	NM_005018.2	64	Gtg/Atg	2/5	1	2	FACETS	0.914	0.808	1	0.914	0.808	1	CLONAL	1	TRUE	1	0.227825370565528	2		347	836	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0000675-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	42	423	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	0.713	0.595	0.844	0.713	0.595	0.844	SUBCLONAL	1	TRUE	1	0.227825370565528	2		423	517	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000675-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	33	136	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	1	2	FACETS	0.728	0.593	0.88	0.728	0.593	0.88	SUBCLONAL	1	TRUE	1	0.227825370565528	2		136	398	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875887	76875887	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002817-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	358	489	0	ENST00000373344.5:c.5248C>G	p.Pro1750Ala	p.P1750A	ENST00000373344	NM_000489.3	1750	Cca/Gca	20/35	0.20943943902391	1	FACETS	0.688	0.657	0.72	0.688	0.657	0.72	INDETERMINATE	1	TRUE	0	0.820868384493112	1		489	747	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437190	52437191	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0004047-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	330	377	0	ENST00000460680.1:c.1853_1854del	p.Pro618ArgfsTer24	p.P618Rfs*24	ENST00000460680	NM_004656.3	618	cCT/c	14/17	0.456967459559434	2	FACETS	0.815	0.774	0.857	0.815	0.774	0.857	CLONAL	2	TRUE	0	0.487914511562463	2		377	830	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0004599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	14	433	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.244042823027559	4	FACETS	1	0.792	1	1	0.792	1	CLONAL	2	TRUE	2	0.27	4		434	61	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0004599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	53	532	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.303950230651038	3	FACETS	0.928	0.817	1	1	0.959	1	CLONAL	4	TRUE	0	0.27	3		532	120	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854957	76854957	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0004599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	16	422	0	ENST00000373344.5:c.5879C>G	p.Ser1960Ter	p.S1960*	ENST00000373344	NM_000489.3	1960	tCa/tGa	25/35	0.245821626445068	0	FACETS	0.94	0.726	1			1	CLONAL	2	TRUE	NA	0.27	0		422	46	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	192	714	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.781914502105175	2		715	487	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275779	41275779	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	254	390	0	ENST00000349496.5:c.1674G>T	p.Gln558His	p.Q558H	ENST00000349496	NM_001904.3	558	caG/caT	10/15	1	2	FACETS	0.866	0.814	0.919	0.866	0.814	0.919	CLONAL	1	TRUE	1	0.781914502105175	2		390	750	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400023	49400023	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	475	538	0	ENST00000418115.1:c.314A>G	p.His105Arg	p.H105R	ENST00000418115	NM_001664.2	105	cAt/cGt	4/5	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.781914502105175	2		538	1172	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747999	41747999	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	15	49	1	ENST00000226382.2:c.770C>T	p.Ala257Val	p.A257V	ENST00000226382	NM_003924.3	257	gCg/gTg	3/3	NA	2	FACETS	0.446	0.332	0.578			1	INDETERMINATE	1	TRUE	NA	0.781914502105175	2		50	86	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189936	66189936	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	81	254	0	ENST00000273854.3:c.3010G>T	p.Asp1004Tyr	p.D1004Y	ENST00000273854	NM_004439.5	1004	Gat/Tat	18/18	NA	2	FACETS	0.946	0.849	1			1	INDETERMINATE	1	TRUE	NA	0.781914502105175	2		254	219	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099499	157099499	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	222	247	0	ENST00000346085.5:c.436G>C	p.Gly146Arg	p.G146R	ENST00000346085	NM_020732.3	146	Ggc/Cgc	1/20	1	2	FACETS	0.919	0.861	0.978	0.919	0.861	0.978	CLONAL	1	TRUE	1	0.781914502105175	2		247	618	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352454	118352454	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	26	478	0	ENST00000534358.1:c.3659C>A	p.Ser1220Tyr	p.S1220Y	ENST00000534358	NM_005933.3	1220	tCt/tAt	7/36	0.781914502105175	1	FACETS	0.089	0.07	0.111	0.089	0.07	0.111	SUBCLONAL	1	TRUE	0	0.781914502105175	1		478	454	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406338	406338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1390256045	NA	P-0004941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	186	439	0	ENST00000399788.2:c.4103G>A	p.Ser1368Asn	p.S1368N	ENST00000399788	NM_001042603.1	1368	aGt/aAt	25/28	0.663687685194793	3	FACETS	1	0.96	1	0.525	0.487	0.564	CLONAL	1	TRUE	1	0.781914502105175	3		439	630	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246429	46246429	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	338	246	0	ENST00000334344.6:c.4523G>C	p.Gly1508Ala	p.G1508A	ENST00000334344	NM_152641.2	1508	gGc/gCc	15/21	0.663687685194793	3	FACETS	0.823	0.784	0.862	0.823	0.784	0.862	CLONAL	2	TRUE	1	0.781914502105175	3		246	731	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410627	63410627	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	292	655	0	ENST00000330258.3:c.2540A>G	p.His847Arg	p.H847R	ENST00000330258	NM_152424.3	847	cAc/cGc	2/2	NA	2	FACETS	0.554	0.521	0.589			1	INDETERMINATE	1	TRUE	NA	0.781914502105175	2		655	1347	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918515	44918515	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	215	322	0	ENST00000377967.4:c.998del	p.Gln333ArgfsTer26	p.Q333Rfs*26	ENST00000377967	NM_021140.2	333	cAg/cg	12/29	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.781914502105175	2		322	541	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	67	714	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.691	0.607	0.78	0.691	0.607	0.78	SUBCLONAL	1	TRUE	1	0.72601073769567	2		715	267	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275779	41275779	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	176	390	0	ENST00000349496.5:c.1674G>T	p.Gln558His	p.Q558H	ENST00000349496	NM_001904.3	558	caG/caT	10/15	1	2	FACETS	0.761	0.704	0.82	0.761	0.704	0.82	SUBCLONAL	1	TRUE	1	0.72601073769567	2		390	637	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400023	49400023	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	212	538	0	ENST00000418115.1:c.314A>G	p.His105Arg	p.H105R	ENST00000418115	NM_001664.2	105	cAt/cGt	4/5	1	2	FACETS	0.856	0.799	0.915	0.856	0.799	0.915	CLONAL	1	TRUE	1	0.72601073769567	2		538	682	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189936	66189936	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	107	254	0	ENST00000273854.3:c.3010G>T	p.Asp1004Tyr	p.D1004Y	ENST00000273854	NM_004439.5	1004	Gat/Tat	18/18	1	2	FACETS	0.907	0.823	0.993	0.907	0.823	0.993	CLONAL	1	TRUE	1	0.72601073769567	2		254	325	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099499	157099499	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	149	247	0	ENST00000346085.5:c.436G>C	p.Gly146Arg	p.G146R	ENST00000346085	NM_020732.3	146	Ggc/Cgc	1/20	1	2	FACETS	0.91	0.839	0.983	0.91	0.839	0.983	CLONAL	1	TRUE	1	0.72601073769567	2		247	451	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406338	406338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1390256045	NA	P-0004941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	187	439	0	ENST00000399788.2:c.4103G>A	p.Ser1368Asn	p.S1368N	ENST00000399788	NM_001042603.1	1368	aGt/aAt	25/28	0.426332252624674	4	FACETS	0.919	0.848	0.991	0.306	0.282	0.331	INDETERMINATE	1	TRUE	1	0.72601073769567	4		439	968	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246429	46246429	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	233	246	0	ENST00000334344.6:c.4523G>C	p.Gly1508Ala	p.G1508A	ENST00000334344	NM_152641.2	1508	gGc/gCc	15/21	0.72601073769567	3	FACETS	0.891	0.841	0.941	0.891	0.841	0.941	CLONAL	2	TRUE	1	0.72601073769567	3		246	491	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410627	63410627	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	239	655	0	ENST00000330258.3:c.2540A>G	p.His847Arg	p.H847R	ENST00000330258	NM_152424.3	847	cAc/cGc	2/2	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.72601073769567	2		655	642	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918515	44918515	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	153	322	0	ENST00000377967.4:c.998del	p.Gln333ArgfsTer26	p.Q333Rfs*26	ENST00000377967	NM_021140.2	333	cAg/cg	12/29	1	2	FACETS	0.926	0.855	1	0.926	0.855	1	CLONAL	1	TRUE	1	0.72601073769567	2		322	455	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100988	27100988	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	86	562	1	ENST00000324856.7:c.4270C>T	p.Gln1424Ter	p.Q1424*	ENST00000324856	NM_006015.4	1424	Cag/Tag	18/20	1	2	FACETS	0.34	0.301	0.383	0.34	0.301	0.383	SUBCLONAL	1	TRUE	1	0.72601073769567	2		563	696	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38157077	38157077	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	233	539	1	ENST00000317025.8:c.2643G>A	p.Met881Ile	p.M881I	ENST00000317025	NM_023034.1	881	atG/atA	15/24	0.72601073769567	1	FACETS	0.78	0.735	0.826	0.78	0.735	0.826	SUBCLONAL	1	TRUE	0	0.72601073769567	1		540	524	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0005094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	125	466	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.19	2		466	1312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587781525	NA	P-0005094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	125	564	0	ENST00000269305.4:c.842A>T	p.Asp281Val	p.D281V	ENST00000269305	NM_001126112.2	281	gAc/gTc	8/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.19	2		564	1255	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945413	17945413	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1295	138	576	0	ENST00000458235.1:c.2317G>T	p.Val773Phe	p.V773F	ENST00000458235	NM_000215.3	773	Gtc/Ttc	17/24	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.19	2		576	1433	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0005832-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	8	161	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.173241867781702	4	FACETS	0.564	0.364	0.821	0.282	0.182	0.411	SUBCLONAL	1	TRUE	2	0.252135826439597	4		161	141	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630048	117630048	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005832-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	18	299	0	ENST00000368508.3:c.6478C>T	p.Gln2160Ter	p.Q2160*	ENST00000368508	NM_002944.2	2160	Cag/Tag	41/43	0.252135826439597	0	FACETS	0.632	0.478	0.811			1	SUBCLONAL	1	TRUE	0	0.252135826439597	0		299	169	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344788	65344788	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005832-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	40	456	0	ENST00000342505.4:c.249G>C	p.Glu83Asp	p.E83D	ENST00000342505	NM_002227.2	83	gaG/gaC	4/25	1	2	FACETS	0.713	0.593	0.847	0.713	0.593	0.847	SUBCLONAL	1	TRUE	1	0.252135826439597	2		456	445	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564794	86564794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005832-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	49	560	0	ENST00000274376.6:c.526C>T	p.Pro176Ser	p.P176S	ENST00000274376	NM_002890.2	176	Cct/Tct	1/25	0.235855371445262	4	FACETS	1	0.905	1	0.547	0.464	0.638	CLONAL	1	TRUE	2	0.252135826439597	4		560	445	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520253	176520253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375466821	NA	P-0005832-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	23	541	0	ENST00000292408.4:c.1172G>A	p.Arg391Gln	p.R391Q	ENST00000292408	NM_213647.1	391	cGa/cAa	9/18	0.24106236240661	4	FACETS	0.917	0.717	1	0.459	0.358	0.574	CLONAL	1	TRUE	2	0.252135826439597	4		541	249	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544706	65544706	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005832-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	41	512	0	ENST00000358664.4:c.220A>G	p.Met74Val	p.M74V	ENST00000358664	NM_002382.4	74	Atg/Gtg	4/5	0.173241867781702	4	FACETS	1	0.843	1	0.505	0.421	0.598	CLONAL	1	TRUE	2	0.252135826439597	4		512	403	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988919	41988919	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005832-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	38	436	0	ENST00000219905.7:c.1711G>C	p.Asp571His	p.D571H	ENST00000219905	NM_001164273.1	571	Gat/Cat	3/24	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.252135826439597	2		436	277	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857925	9857925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs534440095	NA	P-0005832-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	35	622	0	ENST00000330684.3:c.3476G>A	p.Arg1159His	p.R1159H	ENST00000330684	NM_001134407.1	1159	cGc/cAc	13/13	1	2	FACETS	0.75	0.622	0.891	1	0.951	1	SUBCLONAL	2	TRUE	1	0.252135826439597	2		622	185	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993389	72993389	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0005832-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	28	592	0	ENST00000268489.5:c.656C>G	p.Ser219Ter	p.S219*	ENST00000268489	NM_006885.3	219	tCa/tGa	2/10	0.184198125966886	1	FACETS	0.741	0.594	0.907	0.741	0.594	0.907	CLONAL	1	TRUE	0	0.252135826439597	1		592	262	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383106	42383106	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005832-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	18	374	0	ENST00000221972.3:c.126G>C	p.Leu42Phe	p.L42F	ENST00000221972	NM_021601.3	42	ttG/ttC	2/5	0.252135826439597	5	FACETS	0.596	0.448	0.771	0.199	0.149	0.257	SUBCLONAL	1	TRUE	2	0.252135826439597	5		374	330	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931616	39931616	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005832-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	29	443	0	ENST00000378444.4:c.2983C>A	p.Gln995Lys	p.Q995K	ENST00000378444	NM_001123385.1	995	Caa/Aaa	4/15	0.235855371445262	4	FACETS	0.74	0.594	0.907	0.37	0.297	0.454	CLONAL	1	TRUE	2	0.252135826439597	4		443	389	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362561	118362561	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005832-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	37	381	0	ENST00000534358.1:c.4922A>C	p.Lys1641Thr	p.K1641T	ENST00000534358	NM_005933.3	1641	aAa/aCa	15/36	0.252135826439597	4	FACETS	0.877	0.723	1	0.292	0.241	0.35	CLONAL	1	TRUE	1	0.252135826439597	4		381	419	SUCCESS
APC	324	MSKCC	GRCh37	5	112175941	112175941	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005832-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	32	398	0	ENST00000257430.4:c.4650G>C	p.Glu1550Asp	p.E1550D	ENST00000257430	NM_000038.5	1550	gaG/gaC	16/16	0.235855371445262	4	FACETS	1	0.898	1	0.58	0.472	0.7	CLONAL	1	TRUE	2	0.252135826439597	4		398	274	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638086	176638086	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005832-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	22	442	0	ENST00000439151.2:c.2686C>G	p.Gln896Glu	p.Q896E	ENST00000439151	NM_022455.4	896	Cag/Gag	5/23	0.24106236240661	4	FACETS	0.914	0.711	1	0.457	0.355	0.575	CLONAL	1	TRUE	2	0.252135826439597	4		442	239	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328377	137328377	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005832-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	26	512	0	ENST00000481739.1:c.1306C>G	p.Leu436Val	p.L436V	ENST00000481739	NM_002957.4	436	Ctc/Gtc	10/10	0.173241867781702	4	FACETS	0.929	0.738	1	0.464	0.369	0.574	CLONAL	1	TRUE	2	0.252135826439597	4		512	278	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328388	137328388	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005832-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	27	517	0	ENST00000481739.1:c.1317C>G	p.Phe439Leu	p.F439L	ENST00000481739	NM_002957.4	439	ttC/ttG	10/10	0.173241867781702	4	FACETS	0.958	0.764	1	0.479	0.382	0.589	CLONAL	1	TRUE	2	0.252135826439597	4		517	280	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438575	49438575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005832-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	24	465	0	ENST00000301067.7:c.4915G>A	p.Asp1639Asn	p.D1639N	ENST00000301067	NM_003482.3	1639	Gac/Aac	19/54	0.252135826439597	5	FACETS	0.817	0.641	1	0.272	0.213	0.34	CLONAL	1	TRUE	2	0.252135826439597	5		465	321	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51504584	51504584	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005832-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	19	393	0	ENST00000260433.2:c.1196G>C	p.Gly399Ala	p.G399A	ENST00000260433		399	gGa/gCa	9/10	1	2	FACETS	0.871	0.665	1	0.871	0.665	1	CLONAL	1	TRUE	1	0.252135826439597	2		393	173	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544993	86544993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005832-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	27	490	0	ENST00000262426.4:c.818C>T	p.Ser273Leu	p.S273L	ENST00000262426	NM_001451.2	273	tCg/tTg	1/2	0.252135826439597	0	FACETS	0.983	0.79	1			1	CLONAL	1	TRUE	0	0.252135826439597	0		490	163	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267529	198267529	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005832-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	35	392	0	ENST00000335508.6:c.1828A>G	p.Ile610Val	p.I610V	ENST00000335508	NM_012433.2	610	Atc/Gtc	14/25	0.235855371445262	4	FACETS	0.889	0.729	1	0.445	0.364	0.534	CLONAL	1	TRUE	2	0.252135826439597	4		392	391	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839887	27839887	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005832-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	80	598	0	ENST00000328488.2:c.207G>C	p.Gln69His	p.Q69H	ENST00000328488	NM_003533.2	69	caG/caC	1/1	0.252135826439597	12	FACETS	1	0.916	1			1	CLONAL	2	TRUE	NA	0.252135826439597	12		598	682	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038249	30038249	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005901-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	246	487	0	ENST00000338641.4:c.422T>G	p.Leu141Arg	p.L141R	ENST00000338641	NM_000268.3	141	cTg/cGg	4/16	0.787944556571203	1	FACETS	0.906	0.861	0.949	0.906	0.861	0.949	CLONAL	1	TRUE	0	0.786621453091495	1		487	419	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038249	30038249	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005901-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	130	487	0	ENST00000338641.4:c.422T>G	p.Leu141Arg	p.L141R	ENST00000338641	NM_000268.3	141	cTg/cGg	4/16	0.688506288511096	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.688506288511096	1		487	246	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006130-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	184	714	1				ENST00000310581	NM_198253.2	-/1132			0.762723099491405	1	FACETS	0.559	0.52	0.599	0.559	0.52	0.599	SUBCLONAL	1	TRUE	0	0.762723099491405	1		715	534	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579575	7579575	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006130-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	378	692	0	ENST00000269305.4:c.112C>T	p.Gln38Ter	p.Q38*	ENST00000269305	NM_001126112.2	38	Caa/Taa	4/11	0.762723099491405	3	FACETS	0.807	0.771	0.844	0.807	0.771	0.844	CLONAL	2	TRUE	1	0.762723099491405	3		692	848	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039169	49039169	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs587778861	NA	P-0006130-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	129	326	0	ENST00000267163.4:c.2247T>A	p.Tyr749Ter	p.Y749*	ENST00000267163	NM_000321.2	749	taT/taA	22/27	0.705476965614622	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.762723099491405	1		326	165	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260209	16260209	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006130-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	113	691	0	ENST00000375759.3:c.7474C>A	p.Gln2492Lys	p.Q2492K	ENST00000375759	NM_015001.2	2492	Cag/Aag	11/15	0.217386114131943	4	FACETS	0.492	0.441	0.545	0.246	0.22	0.273	INDETERMINATE	1	TRUE	2	0.762723099491405	4		691	1062	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056331	27056332	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0006130-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	362	585	0	ENST00000324856.7:c.1329_1330dup	p.Gly444AlafsTer176	p.G444Afs*176	ENST00000324856	NM_006015.4	443	ggc/gGCgc	2/20	0.217386114131943	4	FACETS	0.851	0.809	0.894	0.851	0.809	0.894	INDETERMINATE	2	TRUE	2	0.762723099491405	4		585	983	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579333	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CCGTGCAAGTCACAGACTTGGCT	CCGTGCAAGTCACAGACTTGGCT	A	novel	NA	P-0006130-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	313	556	0	ENST00000269305.4:c.354_375+1delinsT		p.X118_splice	ENST00000269305	NM_001126112.2	118		4/11	0.762723099491405	3	FACETS	1	0.995	1	0.742	0.704	0.781	CLONAL	1	TRUE	1	0.762723099491405	3		556	764	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006523-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	47	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.48	0.404	0.565	0.48	0.404	0.565	SUBCLONAL	1	TRUE	1	0.22	2		485	890	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440943	56440943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786205215	NA	P-0006523-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	50	553	1	ENST00000407977.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000407977		132	Cga/Tga	4/10	1	2	FACETS	0.519	0.439	0.608	0.519	0.439	0.608	SUBCLONAL	1	TRUE	1	0.22	2		554	876	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987163	36987163	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006523-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	18	304	0	ENST00000354822.5:c.526C>G	p.Leu176Val	p.L176V	ENST00000354822	NM_001079668.2	176	Ctg/Gtg	3/3	1	2	FACETS	0.477	0.359	0.617	0.477	0.359	0.617	SUBCLONAL	1	TRUE	1	0.22	2		304	343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577508	7577508	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060501201	NA	P-0006608-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	726	338	0	ENST00000269305.4:c.773A>G	p.Glu258Gly	p.E258G	ENST00000269305	NM_001126112.2	258	gAa/gGa	7/11	0.812002579009316	3	FACETS	0.947	0.931	0.963	0.947	0.931	0.963	CLONAL	3	TRUE	0	0.866530434226902	3		338	845	SUCCESS
APC	324	MSKCC	GRCh37	5	112157613	112157613	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658802	NA	P-0006608-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	459	325	0	ENST00000257430.4:c.1333C>T	p.Gln445Ter	p.Q445*	ENST00000257430	NM_000038.5	445	Cag/Tag	11/16	0.804288017101467	2	FACETS	0.928	0.904	0.95	0.928	0.904	0.95	CLONAL	2	TRUE	0	0.866530434226902	2		325	571	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117782	70117782	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006608-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	819	475	0	ENST00000245479.2:c.250T>G	p.Tyr84Asp	p.Y84D	ENST00000245479	NM_000346.3	84	Tac/Gac	1/3	0.733834711441343	4	FACETS	0.952	0.928	0.975	0.952	0.928	0.975	CLONAL	3	TRUE	1	0.866530434226902	4		475	1236	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134251	11134251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218643327	NA	P-0006608-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	240	363	0	ENST00000358026.2:c.2917C>T	p.Arg973Trp	p.R973W	ENST00000358026	NM_001128849.1	973	Cgg/Tgg	20/36	0.8193389271975	3	FACETS	0.966	0.904	1	0.483	0.452	0.515	CLONAL	1	TRUE	1	0.866530434226902	3		363	822	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119889	70119890	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0006608-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	199	338	0	ENST00000245479.2:c.892_893dup	p.Pro299CysfsTer85	p.P299Cfs*85	ENST00000245479	NM_000346.3	297	-/CT	3/3	0.733834711441343	4	FACETS	0.84	0.777	0.904	0.28	0.259	0.302	CLONAL	1	TRUE	1	0.866530434226902	4		338	1021	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879672	151879672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006608-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	123	117	0	ENST00000262189.6:c.5273G>A	p.Arg1758His	p.R1758H	ENST00000262189	NM_170606.2	1758	cGt/cAt	36/59	0.357492105848952	6	FACETS	0.898	0.826	0.971	0.898	0.826	0.971	INDETERMINATE	3	TRUE	3	0.866530434226902	6		117	288	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973928	55973928	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006608-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	214	263	0	ENST00000263923.4:c.1388A>T	p.Glu463Val	p.E463V	ENST00000263923	NM_002253.2	463	gAg/gTg	10/30	1	2	FACETS	0.95	0.891	1	0.95	0.891	1	CLONAL	1	TRUE	1	0.866530434226902	2		263	520	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610083	81610083	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006608-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	71	370	0	ENST00000298171.2:c.1681A>C	p.Ser561Arg	p.S561R	ENST00000298171	NM_000369.2	561	Agt/Cgt	10/10	0.672141908443074	4	FACETS	0.272	0.237	0.311			1	SUBCLONAL	1	TRUE	NA	0.866530434226902	4		370	1123	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560983	9560983	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006608-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1424	223	308	0	ENST00000353224.5:c.799A>T	p.Arg267Trp	p.R267W	ENST00000353224	NM_177990.2	267	Agg/Tgg	4/10	0.866530434226902	6	FACETS	0.854	0.792	0.918	0.214	0.198	0.23	CLONAL	1	TRUE	2	0.866530434226902	6		308	1647	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556435	29556452	+	inframe_deletion	In_Frame_Del	DEL	TAACAAATTGAAGAATAC	TAACAAATTGAAGAATAC	-	novel	NA	P-0006608-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	136	214	0	ENST00000356175.3:c.2802_2819del	p.Asn935_Thr940del	p.N935_T940del	ENST00000356175	NM_000267.3	934	ttTAACAAATTGAAGAATACc/ttc	21/57	0.622781350242025	5	FACETS	0.898	0.817	0.983			1	CLONAL	1	TRUE	NA	0.866530434226902	5		214	804	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577508	7577508	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060501201	NA	P-0006608-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	372	338	0	ENST00000269305.4:c.773A>G	p.Glu258Gly	p.E258G	ENST00000269305	NM_001126112.2	258	gAa/gGa	7/11	0.351849202214145	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.418565524549437	3		338	633	SUCCESS
APC	324	MSKCC	GRCh37	5	112157613	112157613	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658802	NA	P-0006608-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	103	325	0	ENST00000257430.4:c.1333C>T	p.Gln445Ter	p.Q445*	ENST00000257430	NM_000038.5	445	Cag/Tag	11/16	0.418565524549437	2	FACETS	0.95	0.865	1	0.95	0.865	1	CLONAL	2	TRUE	0	0.418565524549437	2		325	259	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117782	70117782	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006608-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	197	475	0	ENST00000245479.2:c.250T>G	p.Tyr84Asp	p.Y84D	ENST00000245479	NM_000346.3	84	Tac/Gac	1/3	0.115450588173437	5	FACETS	1	0.979	1	0.754	0.701	0.809	INDETERMINATE	2	TRUE	2	0.418565524549437	5		475	677	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134251	11134251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218643327	NA	P-0006608-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	88	363	0	ENST00000358026.2:c.2917C>T	p.Arg973Trp	p.R973W	ENST00000358026	NM_001128849.1	973	Cgg/Tgg	20/36	0.418565524549437	3	FACETS	0.923	0.819	1	0.461	0.409	0.517	CLONAL	1	TRUE	1	0.418565524549437	3		363	551	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119889	70119890	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0006608-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	158	338	0	ENST00000245479.2:c.892_893dup	p.Pro299CysfsTer85	p.P299Cfs*85	ENST00000245479	NM_000346.3	297	-/CT	3/3	0.115450588173437	5	FACETS	1	0.98	1	0.791	0.73	0.854	INDETERMINATE	2	TRUE	2	0.418565524549437	5		338	518	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879672	151879672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006608-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	42	117	0	ENST00000262189.6:c.5273G>A	p.Arg1758His	p.R1758H	ENST00000262189	NM_170606.2	1758	cGt/cAt	36/59	0.227194992854379	5	FACETS	0.878	0.743	1	0.585	0.495	0.683	INDETERMINATE	2	TRUE	2	0.418565524549437	5		117	186	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097677	27097677	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006608-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	91	507	0	ENST00000324856.7:c.3266C>A	p.Ala1089Asp	p.A1089D	ENST00000324856	NM_006015.4	1089	gCc/gAc	12/20	0.418565524549437	3	FACETS	1	0.947	1	0.551	0.491	0.615	CLONAL	1	TRUE	1	0.418565524549437	3		507	477	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593583	55593595	+	protein_altering_variant,splice_region_variant	In_Frame_Del	DEL	AACCCATGTATGA	AACCCATGTATGA	T	novel	NA	P-0006712-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	12	453	0	ENST00000288135.5:c.1649_1661delinsT	p.Lys550_Glu554delinsIle	p.K550_E554delinsI	ENST00000288135	NM_000222.2	550	aAACCCATGTATGAa/aTa	11/21	1	2	FACETS	0.576	0.404	0.79	0.576	0.404	0.79	SUBCLONAL	1	TRUE	1	0.12	2		453	347	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593583	55593595	+	protein_altering_variant,splice_region_variant	In_Frame_Del	DEL	AACCCATGTATGA	AACCCATGTATGA	T	novel	NA	P-0006712-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	71	453	0	ENST00000288135.5:c.1649_1661delinsT	p.Lys550_Glu554delinsIle	p.K550_E554delinsI	ENST00000288135	NM_000222.2	550	aAACCCATGTATGAa/aTa	11/21	1	2	FACETS	0.874	0.768	0.986	0.874	0.768	0.986	CLONAL	1	TRUE	1	0.472364923800594	2		453	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578179	7578179	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	108	518	0	ENST00000269305.4:c.670G>T	p.Glu224Ter	p.E224*	ENST00000269305	NM_001126112.2	224	Gag/Tag	6/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.15	2		518	1237	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255496	16255496	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	54	376	0	ENST00000375759.3:c.2761C>T	p.Gln921Ter	p.Q921*	ENST00000375759	NM_015001.2	921	Cag/Tag	11/15	1	2	FACETS	0.815	0.694	0.949	0.815	0.694	0.949	CLONAL	1	TRUE	1	0.15	2		376	883	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255572	16255572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	70	473	1	ENST00000375759.3:c.2837C>T	p.Ser946Leu	p.S946L	ENST00000375759	NM_015001.2	946	tCa/tTa	11/15	1	2	FACETS	0.877	0.762	1	0.877	0.762	1	CLONAL	1	TRUE	1	0.15	2		474	1064	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332864	70332864	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	99	490	0	ENST00000373644.4:c.769A>G	p.Thr257Ala	p.T257A	ENST00000373644	NM_030625.2	257	Acc/Gcc	2/12	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.15	2		490	1249	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	133	326	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.674	0.611	0.74	0.674	0.611	0.74	SUBCLONAL	1	TRUE	1	0.406666979849777	2		328	971	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	137	564	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.938	0.855	1	0.938	0.855	1	CLONAL	1	TRUE	1	0.406666979849777	2		564	718	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	66	812	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.904	0.789	1	0.904	0.789	1	CLONAL	1	TRUE	1	0.406666979849777	2		812	359	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	110	367	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.843	0.758	0.932	0.843	0.758	0.932	CLONAL	1	TRUE	1	0.406666979849777	2		367	642	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775719	9775719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557659540	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	165	341	0	ENST00000377346.4:c.262C>T	p.Arg88Cys	p.R88C	ENST00000377346	NM_005026.3	88	Cgt/Tgt	4/24	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.406666979849777	2		341	766	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775734	9775734	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	151	318	0	ENST00000377346.4:c.277C>T	p.Gln93Ter	p.Q93*	ENST00000377346	NM_005026.3	93	Cag/Tag	4/24	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.406666979849777	2		318	702	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259966	16259966	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	149	302	0	ENST00000375759.3:c.7231T>C	p.Ser2411Pro	p.S2411P	ENST00000375759	NM_015001.2	2411	Tcg/Ccg	11/15	1	2	FACETS	0.947	0.866	1	0.947	0.866	1	CLONAL	1	TRUE	1	0.406666979849777	2		302	774	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100866	27100866	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1175588677	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	162	325	0	ENST00000324856.7:c.4148G>A	p.Arg1383Gln	p.R1383Q	ENST00000324856	NM_006015.4	1383	cGg/cAg	18/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.406666979849777	2		325	729	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105664	27105664	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1441412963	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	191	357	0	ENST00000324856.7:c.5275A>G	p.Met1759Val	p.M1759V	ENST00000324856	NM_006015.4	1759	Atg/Gtg	20/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.406666979849777	2		357	882	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161310418	161310418	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	172	396	0	ENST00000367975.2:c.214C>A	p.Arg72Ser	p.R72S	ENST00000367975	NM_003001.3	72	Cgt/Agt	4/6	1	2	FACETS	0.936	0.861	1	0.936	0.861	1	CLONAL	1	TRUE	1	0.406666979849777	2		396	904	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736307	243736307	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	193	351	2	ENST00000263826.5:c.740G>A	p.Arg247His	p.R247H	ENST00000263826	NM_005465.4	247	cGc/cAc	8/13	1	2	FACETS	0.961	0.889	1	0.961	0.889	1	CLONAL	1	TRUE	1	0.406666979849777	2		353	988	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128029004	128029004	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1385827451	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	131	326	0	ENST00000285398.2:c.1853C>T	p.Pro618Leu	p.P618L	ENST00000285398	NM_000122.1	618	cCg/cTg	12/15	1	2	FACETS	0.926	0.841	1	0.926	0.841	1	CLONAL	1	TRUE	1	0.406666979849777	2		326	696	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570063	212570063	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746784831	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	113	276	0	ENST00000342788.4:c.1178G>A	p.Arg393Gln	p.R393Q	ENST00000342788	NM_005235.2	393	cGg/cAg	10/28	1	2	FACETS	0.821	0.74	0.907	0.821	0.74	0.907	CLONAL	1	TRUE	1	0.406666979849777	2		276	677	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713738	30713738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893813	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	43	193	0	ENST00000295754.5:c.1063G>A	p.Ala355Thr	p.A355T	ENST00000295754	NM_003242.5	355	Gcc/Acc	4/7	1	2	FACETS	0.457	0.382	0.539	0.457	0.382	0.539	SUBCLONAL	1	TRUE	1	0.406666979849777	2		193	463	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582209	52582209	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376146705	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	142	299	0	ENST00000394830.3:c.4619G>A	p.Arg1540His	p.R1540H	ENST00000394830	NM_018313.4	1540	cGc/cAc	30/30	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.406666979849777	2		299	655	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643864	52643864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1422119249	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	94	213	0	ENST00000394830.3:c.2032C>T	p.Arg678Cys	p.R678C	ENST00000394830	NM_018313.4	678	Cgc/Tgc	17/30	1	2	FACETS	0.833	0.743	0.928	0.833	0.743	0.928	CLONAL	1	TRUE	1	0.406666979849777	2		213	555	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670843	134670843	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	29	160	0	ENST00000398015.3:c.754C>T	p.Arg252Ter	p.R252*	ENST00000398015	NM_004441.4	252	Cga/Tga	3/16	1	2	FACETS	0.382	0.307	0.468	0.382	0.307	0.468	SUBCLONAL	1	TRUE	1	0.406666979849777	2		160	373	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602952	55602952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1237984655	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	109	280	0	ENST00000288135.5:c.2662C>T	p.Arg888Trp	p.R888W	ENST00000288135	NM_000222.2	888	Cgg/Tgg	19/21	1	2	FACETS	0.818	0.736	0.905	0.818	0.736	0.905	CLONAL	1	TRUE	1	0.406666979849777	2		280	655	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156204	106156204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150072691	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	110	257	4	ENST00000380013.4:c.1105C>T	p.Arg369Trp	p.R369W	ENST00000380013	NM_001127208.2	369	Cgg/Tgg	3/11	1	2	FACETS	0.959	0.865	1	0.959	0.865	1	CLONAL	1	TRUE	1	0.406666979849777	2		261	564	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003331	143003331	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1303434799	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	103	201	2	ENST00000262992.4:c.2495G>A	p.Arg832His	p.R832H	ENST00000262992	NM_001101669.1	832	cGc/cAc	23/24	1	2	FACETS	0.913	0.819	1	0.913	0.819	1	CLONAL	1	TRUE	1	0.406666979849777	2		203	555	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251542	251542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200397144	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	111	180	0	ENST00000264932.6:c.1753C>T	p.Arg585Trp	p.R585W	ENST00000264932	NM_004168.2	585	Cgg/Tgg	13/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.406666979849777	2		180	409	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278779	1278779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576633619	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	112	310	0	ENST00000310581.5:c.2263G>A	p.Val755Ile	p.V755I	ENST00000310581	NM_198253.2	755	Gtc/Atc	6/16	1	2	FACETS	0.832	0.749	0.919	0.832	0.749	0.919	CLONAL	1	TRUE	1	0.406666979849777	2		310	662	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279527	1279527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767382450	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	103	315	0	ENST00000310581.5:c.2009C>T	p.Ala670Val	p.A670V	ENST00000310581	NM_198253.2	670	gCg/gTg	5/16	1	2	FACETS	0.832	0.746	0.923	0.832	0.746	0.923	CLONAL	1	TRUE	1	0.406666979849777	2		315	609	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294163	1294163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199701877	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	126	288	0	ENST00000310581.5:c.838G>A	p.Glu280Lys	p.E280K	ENST00000310581	NM_198253.2	280	Gaa/Aaa	2/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.406666979849777	2		288	574	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161221	56161221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781300314	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	114	399	2	ENST00000399503.3:c.1090C>T	p.Arg364Trp	p.R364W	ENST00000399503	NM_005921.1	364	Cgg/Tgg	5/20	1	2	FACETS	0.771	0.695	0.852	0.771	0.695	0.852	SUBCLONAL	1	TRUE	1	0.406666979849777	2		401	727	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86676346	86676346	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	102	299	0	ENST00000274376.6:c.2624G>A	p.Gly875Glu	p.G875E	ENST00000274376	NM_002890.2	875	gGg/gAg	20/25	1	2	FACETS	0.871	0.781	0.966	0.871	0.781	0.966	CLONAL	1	TRUE	1	0.406666979849777	2		299	576	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	97	466	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.795	0.71	0.885	0.795	0.71	0.885	SUBCLONAL	1	TRUE	1	0.406666979849777	2		466	600	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	225	326	2	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.406666979849777	2		328	1025	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562321	176562321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	122	315	0	ENST00000439151.2:c.217C>T	p.Arg73Trp	p.R73W	ENST00000439151	NM_022455.4	73	Cgg/Tgg	2/23	1	2	FACETS	0.965	0.874	1	0.965	0.874	1	CLONAL	1	TRUE	1	0.406666979849777	2		315	622	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962930	2962930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349831751	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	143	329	0	ENST00000396946.4:c.1978C>T	p.Arg660Trp	p.R660W	ENST00000396946	NM_032415.4	660	Cgg/Tgg	16/25	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.406666979849777	2		329	688	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241722	55241722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1051753269	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	104	264	1	ENST00000275493.2:c.2170G>A	p.Gly724Ser	p.G724S	ENST00000275493	NM_005228.3	724	Ggc/Agc	18/28	1	2	FACETS	0.794	0.712	0.881	0.794	0.712	0.881	SUBCLONAL	1	TRUE	1	0.406666979849777	2		265	644	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873659	151873659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142287778	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	67	193	0	ENST00000262189.6:c.8879C>T	p.Pro2960Leu	p.P2960L	ENST00000262189	NM_170606.2	2960	cCg/cTg	38/59	1	2	FACETS	0.668	0.582	0.762	0.668	0.582	0.762	SUBCLONAL	1	TRUE	1	0.406666979849777	2		193	493	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983460	90983460	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34767364	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	76	250	0	ENST00000265433.3:c.643C>T	p.Arg215Trp	p.R215W	ENST00000265433	NM_002485.4	215	Cgg/Tgg	6/16	1	2	FACETS	0.799	0.703	0.901	0.799	0.703	0.901	CLONAL	1	TRUE	1	0.406666979849777	2		250	468	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741464	145741464	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs534507419	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	196	336	0	ENST00000428558.2:c.1039C>T	p.Arg347Cys	p.R347C	ENST00000428558	NM_004260.3	347	Cgc/Tgc	5/22	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.406666979849777	2		336	851	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006194	22006194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	99	222	0	ENST00000276925.6:c.209C>T	p.Ala70Val	p.A70V	ENST00000276925	NM_004936.3	70	gCg/gTg	2/2	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.406666979849777	2		222	459	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390743	139390743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	141	371	0	ENST00000277541.6:c.7448C>T	p.Thr2483Met	p.T2483M	ENST00000277541	NM_017617.3	2483	aCg/aTg	34/34	1	2	FACETS	0.911	0.831	0.995	0.911	0.831	0.995	CLONAL	1	TRUE	1	0.406666979849777	2		371	761	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399922	139399922	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776133530	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	160	352	0	ENST00000277541.6:c.4426G>A	p.Gly1476Ser	p.G1476S	ENST00000277541	NM_017617.3	1476	Ggc/Agc	25/34	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.406666979849777	2		352	777	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100541	8100541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1277364315	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	41	291	1	ENST00000346208.3:c.515C>T	p.Ser172Leu	p.S172L	ENST00000346208		172	tCg/tTg	3/6	1	2	FACETS	0.326	0.271	0.388	0.326	0.271	0.388	SUBCLONAL	1	TRUE	1	0.406666979849777	2		292	618	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88676945	88676945	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs759363072	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	44	109	0	ENST00000372037.3:c.730C>T	p.Arg244Ter	p.R244*	ENST00000372037	NM_004329.2	244	Cga/Tga	9/13	1	2	FACETS	0.826	0.698	0.966	0.826	0.698	0.966	CLONAL	1	TRUE	1	0.406666979849777	2		109	262	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156699	2156699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs975030738	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	161	420	0	ENST00000434045.2:c.223G>A	p.Ala75Thr	p.A75T	ENST00000434045	NM_001127598.1	75	Gcc/Acc	3/5	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.406666979849777	2		420	770	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417080	417080	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779176655	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	112	258	0	ENST00000399788.2:c.3470G>A	p.Arg1157His	p.R1157H	ENST00000399788	NM_001042603.1	1157	cGc/cAc	23/28	1	2	FACETS	0.923	0.832	1	0.923	0.832	1	CLONAL	1	TRUE	1	0.406666979849777	2		258	597	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233228	46233228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374540100	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	154	330	3	ENST00000334344.6:c.1447C>T	p.Pro483Ser	p.P483S	ENST00000334344	NM_152641.2	483	Cca/Tca	11/21	1	2	FACETS	0.833	0.762	0.907	0.833	0.762	0.907	CLONAL	1	TRUE	1	0.406666979849777	2		333	909	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432446	49432446	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	63	335	0	ENST00000301067.7:c.8693A>G	p.Gln2898Arg	p.Q2898R	ENST00000301067	NM_003482.3	2898	cAg/cGg	34/54	1	2	FACETS	0.391	0.337	0.45	0.391	0.337	0.45	SUBCLONAL	1	TRUE	1	0.406666979849777	2		335	792	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214630	133214630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	144	307	0	ENST00000320574.5:c.5648C>T	p.Ala1883Val	p.A1883V	ENST00000320574	NM_006231.2	1883	gCc/gTc	41/49	1	2	FACETS	0.909	0.83	0.992	0.909	0.83	0.992	CLONAL	1	TRUE	1	0.406666979849777	2		307	779	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346391	73346391	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	194	235	0	ENST00000377767.4:c.1409T>C	p.Leu470Pro	p.L470P	ENST00000377767	NM_014953.3	470	cTg/cCg	10/21	0.209228720617526	3	FACETS	0.905	0.842	0.971			1	INDETERMINATE	2	TRUE	NA	0.406666979849777	3		235	634	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028457	42028457	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	242	517	2	ENST00000219905.7:c.3995C>A	p.Pro1332His	p.P1332H	ENST00000219905	NM_001164273.1	1332	cCc/cAc	13/24	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.406666979849777	2		519	1055	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251057	99251057	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555434208	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	108	279	1	ENST00000268035.6:c.361G>A	p.Glu121Lys	p.E121K	ENST00000268035	NM_000875.3	121	Gag/Aag	2/21	1	2	FACETS	0.894	0.805	0.989	0.894	0.805	0.989	CLONAL	1	TRUE	1	0.406666979849777	2		280	594	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660535	67660535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	70	404	4	ENST00000264010.4:c.1435C>T	p.Arg479Cys	p.R479C	ENST00000264010	NM_006565.3	479	Cgc/Tgc	8/12	1	2	FACETS	0.359	0.312	0.41	0.359	0.312	0.41	SUBCLONAL	1	TRUE	1	0.406666979849777	2		408	960	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662405	67662405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs184167883	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	218	352	0	ENST00000264010.4:c.1651G>A	p.Val551Ile	p.V551I	ENST00000264010	NM_006565.3	551	Gtc/Atc	9/12	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.406666979849777	2		352	1011	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821344	72821344	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200992486	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	73	312	0	ENST00000268489.5:c.10831C>A	p.His3611Asn	p.H3611N	ENST00000268489	NM_006885.3	3611	Cac/Aac	10/10	1	2	FACETS	0.549	0.48	0.623	0.549	0.48	0.623	SUBCLONAL	1	TRUE	1	0.406666979849777	2		312	654	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004910	16004910	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	178	356	0	ENST00000268712.3:c.2344A>G	p.Thr782Ala	p.T782A	ENST00000268712	NM_006311.3	782	Acc/Gcc	20/46	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.406666979849777	2		356	870	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119758	70119758	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	140	322	0	ENST00000245479.2:c.760C>T	p.Arg254Ter	p.R254*	ENST00000245479	NM_000346.3	254	Cga/Tga	3/3	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.406666979849777	2		322	667	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727934	78727934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	102	267	0	ENST00000306801.3:c.779C>T	p.Ala260Val	p.A260V	ENST00000306801	NM_020761.2	260	gCt/gTt	6/34	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.406666979849777	2		267	477	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78914356	78914356	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1451626205	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	97	181	0	ENST00000306801.3:c.2980C>T	p.Arg994Ter	p.R994*	ENST00000306801	NM_020761.2	994	Cga/Tga	25/34	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.406666979849777	2		181	428	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214592	5214592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369295620	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	150	372	0	ENST00000357368.4:c.4474C>T	p.Arg1492Trp	p.R1492W	ENST00000357368	NM_002850.3	1492	Cgg/Tgg	29/38	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.406666979849777	2		372	711	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238972	5238972	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	50	290	0	ENST00000357368.4:c.1807G>T	p.Gly603Cys	p.G603C	ENST00000357368	NM_002850.3	603	Ggc/Tgc	13/38	1	2	FACETS	0.419	0.355	0.489	0.419	0.355	0.489	SUBCLONAL	1	TRUE	1	0.406666979849777	2		290	587	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274218	5274218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	140	287	2	ENST00000357368.4:c.229C>T	p.Arg77Cys	p.R77C	ENST00000357368	NM_002850.3	77	Cgc/Tgc	3/38	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.406666979849777	2		289	646	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105622	11105622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	230	343	0	ENST00000358026.2:c.1538G>A	p.Arg513Gln	p.R513Q	ENST00000358026	NM_001128849.1	513	cGg/cAg	9/36	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.406666979849777	2		343	968	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051427	13051427	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	217	508	0	ENST00000316448.5:c.775G>T	p.Gly259Ter	p.G259*	ENST00000316448	NM_004343.3	259	Gga/Tga	6/9	1	2	FACETS	0.926	0.86	0.994	0.926	0.86	0.994	CLONAL	1	TRUE	1	0.406666979849777	2		508	1153	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383867	15383867	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369254108	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	39	226	1	ENST00000263377.2:c.44C>T	p.Pro15Leu	p.P15L	ENST00000263377	NM_058243.2	15	cCa/cTa	2/20	1	2	FACETS	0.341	0.282	0.407	0.341	0.282	0.407	SUBCLONAL	1	TRUE	1	0.406666979849777	2		227	563	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484813	57484813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555891595	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	169	372	0	ENST00000371085.3:c.793C>T	p.Arg265Cys	p.R265C	ENST00000371085	NM_000516.4	265	Cgc/Tgc	10/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.406666979849777	2		372	737	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514657	44514657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	150	263	0	ENST00000291552.4:c.499G>A	p.Gly167Ser	p.G167S	ENST00000291552	NM_006758.2	167	Ggc/Agc	7/8	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.406666979849777	2		263	727	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928929	44928929	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	188	398	0	ENST00000377967.4:c.2029C>T	p.Gln677Ter	p.Q677*	ENST00000377967	NM_021140.2	677	Cag/Tag	17/29	1	2	FACETS	0.979	0.905	1	0.979	0.905	1	CLONAL	1	TRUE	1	0.406666979849777	2		398	944	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223439	53223439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1322675151	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	158	375	2	ENST00000375401.3:c.3920G>A	p.Arg1307Gln	p.R1307Q	ENST00000375401	NM_004187.3	1307	cGg/cAg	23/26	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.406666979849777	2		377	749	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231134	53231134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	188	371	0	ENST00000375401.3:c.1768G>A	p.Ala590Thr	p.A590T	ENST00000375401	NM_004187.3	590	Gca/Aca	13/26	1	2	FACETS	0.942	0.87	1	0.942	0.87	1	CLONAL	1	TRUE	1	0.406666979849777	2		371	982	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411062	63411062	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	153	370	0	ENST00000330258.3:c.2105A>C	p.Glu702Ala	p.E702A	ENST00000330258	NM_152424.3	702	gAg/gCg	2/2	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.406666979849777	2		370	746	SUCCESS
AR	367	MSKCC	GRCh37	X	66941794	66941794	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555997626	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	138	333	0	ENST00000374690.3:c.2438T>C	p.Leu813Pro	p.L813P	ENST00000374690	NM_000044.3	813	cTc/cCc	6/8	1	2	FACETS	0.856	0.779	0.936	0.856	0.779	0.936	CLONAL	1	TRUE	1	0.406666979849777	2		333	793	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939208	76939208	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	170	449	1	ENST00000373344.5:c.1540G>T	p.Asp514Tyr	p.D514Y	ENST00000373344	NM_000489.3	514	Gac/Tac	9/35	1	2	FACETS	0.851	0.783	0.923	0.851	0.783	0.923	CLONAL	1	TRUE	1	0.406666979849777	2		450	982	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979987	7979987	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746723399	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	124	236	0	ENST00000319144.4:c.1350del	p.Leu451SerfsTer16	p.L451Sfs*16	ENST00000319144	NM_001139.2	450	ggG/gg	10/15	1	2	FACETS	0.979	0.888	1	0.979	0.888	1	CLONAL	1	TRUE	1	0.406666979849777	2		236	623	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911443	32911443	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359365	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	164	346	0	ENST00000380152.3:c.2957del	p.Asn986IlefsTer5	p.N986Ifs*5	ENST00000380152		984	gAa/ga	11/27	1	2	FACETS	0.924	0.848	1	0.924	0.848	1	CLONAL	1	TRUE	1	0.406666979849777	2		346	873	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713414	40713414	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	120	301	0	ENST00000373198.4:c.4101del	p.Ser1368ProfsTer31	p.S1368Pfs*31	ENST00000373198	NM_133170.3	1367	ccC/cc	30/32	1	2	FACETS	0.932	0.844	1	0.932	0.844	1	CLONAL	1	TRUE	1	0.406666979849777	2		301	633	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	337	399	2	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.935	0.888	0.983	1	0.996	1	CLONAL	2	TRUE	1	0.406666979849777	2		401	886	SUCCESS
APC	324	MSKCC	GRCh37	5	112177864	112177864	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs775076289	NA	P-0006863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	115	269	0	ENST00000257430.4:c.6579del	p.Val2194PhefsTer5	p.V2194Ffs*5	ENST00000257430	NM_000038.5	2191	ggA/gg	16/16	1	2	FACETS	0.79	0.712	0.872	0.79	0.712	0.872	SUBCLONAL	1	TRUE	1	0.406666979849777	2		269	716	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0007490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	150	439	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.401142581398357	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.401142581398357	1		440	480	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0007490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	94	466	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.798	0.712	0.89	0.798	0.712	0.89	SUBCLONAL	1	TRUE	1	0.401142581398357	2		466	587	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001104	150001104	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	153	421	0	ENST00000253339.5:c.2500A>G	p.Ile834Val	p.I834V	ENST00000253339		834	Att/Gtt	4/7	1	2	FACETS	0.894	0.818	0.974	0.894	0.818	0.974	CLONAL	1	TRUE	1	0.401142581398357	2		421	853	SUCCESS
APC	324	MSKCC	GRCh37	5	112175751	112175752	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTTA	novel	NA	P-0007490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	111	266	0	ENST00000257430.4:c.4463_4466dup	p.Leu1489PhefsTer26	p.L1489Ffs*26	ENST00000257430	NM_000038.5	1487	act/acTTTAt	16/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.401142581398357	2		266	436	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592132	67592144	+	frameshift_variant	Frame_Shift_Del	DEL	GAGAGCAGTAAAC	GAGAGCAGTAAAC	-	novel	NA	P-0007490-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	139	299	0	ENST00000274335.5:c.1948_1960del	p.Glu650ArgfsTer8	p.E650Rfs*8	ENST00000274335		650	GAGAGCAGTAAACag/ag	14/15	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.401142581398357	2		299	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0007687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	83	477	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.711	0.626	0.802	0.711	0.626	0.802	SUBCLONAL	1	TRUE	1	0.26	2		477	898	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0007687-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	120	477	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.210306177521607	2		477	1009	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517313	157517313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752398721	NA	P-0007687-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	32	0	0	ENST00000346085.5:c.3877G>A	p.Glu1293Lys	p.E1293K	ENST00000346085	NM_020732.3	1293	Gag/Aag	16/20	0.154324370137377	2	FACETS	0.512	0.415	0.623	0.256	0.207	0.312	SUBCLONAL	1	TRUE	0	0.210306177521607	2		0	594	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0007745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	262	432	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	1	2	FACETS	0.948	0.893	1	0.948	0.893	1	CLONAL	1	TRUE	1	0.771091001618452	2		432	717	SUCCESS
APC	324	MSKCC	GRCh37	5	112175720	112175720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	264	301	0	ENST00000257430.4:c.4429C>T	p.Gln1477Ter	p.Q1477*	ENST00000257430	NM_000038.5	1477	Cag/Tag	16/16	0.771091001618452	1	FACETS	0.972	0.927	1	0.972	0.927	1	CLONAL	1	TRUE	0	0.771091001618452	1		301	433	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589623	67589634	+	inframe_deletion	In_Frame_Del	DEL	ATATGATAGATT	ATATGATAGATT	-	novel	NA	P-0007745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	115	208	0	ENST00000274335.5:c.1392_1403del	p.Asp464_Tyr467del	p.D464_Y467del	ENST00000274335		462	gaATATGATAGATTa/gaa	10/15	1	2	FACETS	0.364	0.328	0.403	0.364	0.328	0.403	SUBCLONAL	1	TRUE	1	0.771091001618452	2		208	819	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0007745-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	175	417	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	1	2	FACETS	0.534	0.491	0.578	0.534	0.491	0.578	SUBCLONAL	1	TRUE	1	0.676834317088711	2		417	969	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0007745-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	250	432	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	1	2	FACETS	0.753	0.705	0.803	0.753	0.705	0.803	SUBCLONAL	1	TRUE	1	0.676834317088711	2		432	981	SUCCESS
APC	324	MSKCC	GRCh37	5	112175720	112175720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007745-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	259	301	0	ENST00000257430.4:c.4429C>T	p.Gln1477Ter	p.Q1477*	ENST00000257430	NM_000038.5	1477	Cag/Tag	16/16	0.676834317088711	1	FACETS	0.964	0.914	1	0.964	0.914	1	CLONAL	1	TRUE	0	0.676834317088711	1		301	525	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589623	67589634	+	inframe_deletion	In_Frame_Del	DEL	ATATGATAGATT	ATATGATAGATT	-	novel	NA	P-0007745-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	81	208	0	ENST00000274335.5:c.1392_1403del	p.Asp464_Tyr467del	p.D464_Y467del	ENST00000274335		462	gaATATGATAGATTa/gaa	10/15	1	2	FACETS	0.416	0.367	0.469	0.416	0.367	0.469	SUBCLONAL	1	TRUE	1	0.676834317088711	2		208	575	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225202	53225202	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1414718926	NA	P-0007745-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	253	711	0	ENST00000375401.3:c.3016A>G	p.Ile1006Val	p.I1006V	ENST00000375401	NM_004187.3	1006	Atc/Gtc	20/26	0.431069823838378	1	FACETS	0.393	0.367	0.42	0.393	0.367	0.42	SUBCLONAL	1	TRUE	0	0.676834317088711	1		711	1257	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0008155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	369	340	1	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.277855356338889	2	FACETS	0.898	0.852	0.945	0.898	0.852	0.945	CLONAL	2	TRUE	0	0.337492756496948	2		341	1217	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0008155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	162	687	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.236102592794983	3	FACETS	0.927	0.849	1	0.464	0.424	0.505	CLONAL	1	TRUE	1	0.337492756496948	3		687	1210	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916927	178916933	+	protein_altering_variant	In_Frame_Del	DEL	TAGGCAA	TAGGCAA	G	novel	NA	P-0008155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	615	472	0	ENST00000263967.3:c.314_320delinsG	p.Val105_Asn107delinsGly	p.V105_N107delinsG	ENST00000263967	NM_006218.2	105	gTAGGCAAc/gGc	2/21	0.337492756496948	6	FACETS	0.9	0.865	0.935	0.9	0.865	0.935	CLONAL	4	TRUE	2	0.337492756496948	6		472	1696	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287494	33287494	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008707-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	448	586	0	ENST00000374542.5:c.1603G>T	p.Glu535Ter	p.E535*	ENST00000374542	NM_001141970.1	535	Gaa/Taa	6/8	0.741184924588409	2	FACETS	0.975	0.946	1	0.975	0.946	1	CLONAL	2	TRUE	0	0.745717395750884	2		586	616	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575069	64575069	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008707-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	361	583	0	ENST00000312049.6:c.738del	p.Ile247LeufsTer34	p.I247Lfs*34	ENST00000312049	NM_130799.2	246	tcC/tc	4/10	0.731222187681767	2	FACETS	0.901	0.869	0.934	0.901	0.869	0.934	CLONAL	2	TRUE	0	0.745717395750884	2		583	537	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0009029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	124	800	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.684988748735217	2		800	332	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0009029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	112	634	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.826	0.749	0.906	0.826	0.749	0.906	CLONAL	1	TRUE	1	0.684988748735217	2		634	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371524413	NA	P-0009029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	15	321	0	ENST00000269305.4:c.467G>A	p.Arg156His	p.R156H	ENST00000269305	NM_001126112.2	156	cGc/cAc	5/11	1	2	FACETS	0.073	0.053	0.098	0.073	0.053	0.098	SUBCLONAL	1	TRUE	1	0.684988748735217	2		321	596	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806564	1806564	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1391325047	NA	P-0009029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	178	653	0	ENST00000260795.2:c.1280C>G	p.Ser427Cys	p.S427C	ENST00000260795		427	tCc/tGc	9/17	1	2	FACETS	0.99	0.919	1	0.99	0.919	1	CLONAL	1	TRUE	1	0.684988748735217	2		653	525	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245720	46245720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	51	347	0	ENST00000334344.6:c.3814C>T	p.Arg1272Ter	p.R1272*	ENST00000334344	NM_152641.2	1272	Cga/Tga	15/21	1	2	FACETS	0.222	0.188	0.26	0.222	0.188	0.26	SUBCLONAL	1	TRUE	1	0.684988748735217	2		347	670	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651921	36651924	+	frameshift_variant	Frame_Shift_Del	DEL	AGCA	AGCA	-	novel	NA	P-0009029-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	146	708	0	ENST00000244741.5:c.45_48del	p.Ser15ArgfsTer15	p.S15Rfs*15	ENST00000244741	NM_000389.4	15	AGCAag/ag	2/3	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.684988748735217	2		708	418	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0009029-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	117	509	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.981	0.894	1	0.981	0.894	1	CLONAL	1	TRUE	1	0.685779922313721	2		510	348	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0009029-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	126	634	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.861	0.786	0.938	0.861	0.786	0.938	CLONAL	1	TRUE	1	0.685779922313721	2		634	427	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806564	1806564	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1391325047	NA	P-0009029-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	182	653	0	ENST00000260795.2:c.1280C>G	p.Ser427Cys	p.S427C	ENST00000260795		427	tCc/tGc	9/17	1	2	FACETS	0.923	0.857	0.991	0.923	0.857	0.991	CLONAL	1	TRUE	1	0.685779922313721	2		653	575	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651921	36651924	+	frameshift_variant	Frame_Shift_Del	DEL	AGCA	AGCA	-	novel	NA	P-0009029-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	193	708	0	ENST00000244741.5:c.45_48del	p.Ser15ArgfsTer15	p.S15Rfs*15	ENST00000244741	NM_000389.4	15	AGCAag/ag	2/3	1	2	FACETS	0.918	0.854	0.984	0.918	0.854	0.984	CLONAL	1	TRUE	1	0.685779922313721	2		708	613	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566342	141566342	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009029-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	46	424	0	ENST00000220592.5:c.1070C>G	p.Thr357Arg	p.T357R	ENST00000220592	NM_012154.3	357	aCg/aGg	9/19	1	2	FACETS	0.33	0.278	0.387	0.33	0.278	0.387	SUBCLONAL	1	TRUE	1	0.685779922313721	2		424	406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0009613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	603	724	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.915518292293659	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.927047079652236	1		724	693	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099982	157099987	+	inframe_deletion	In_Frame_Del	DEL	GGCGGC	GGCGGC	-	rs587779747	NA	P-0009613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	236	172	0	ENST00000346085.5:c.939_944del	p.Gly318_Gly319del	p.G318_G319del	ENST00000346085	NM_020732.3	307	GGCGGC/-	1/20	1	2	FACETS	0.703	0.659	0.748	0.703	0.659	0.748	SUBCLONAL	1	TRUE	1	0.927047079652236	2		172	724	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678783	52678784	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0009613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	382	538	0	ENST00000394830.3:c.835dup	p.Ile279AsnfsTer8	p.I279Nfs*8	ENST00000394830	NM_018313.4	279	ata/aAta	9/30	0.915518292293659	1	FACETS	0.839	0.811	0.865	0.839	0.811	0.865	CLONAL	1	TRUE	0	0.927047079652236	1		538	527	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41228517	41228517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	577	729	0	ENST00000357654.3:c.4472C>T	p.Pro1491Leu	p.P1491L	ENST00000357654	NM_007294.3	1491	cCa/cTa	13/23	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.927047079652236	2		729	1245	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272105	15272105	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372833545	NA	P-0009613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	281	136	0	ENST00000263388.2:c.6334G>A	p.Gly2112Ser	p.G2112S	ENST00000263388	NM_000435.2	2112	Ggt/Agt	33/33	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.927047079652236	2		136	557	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659797	227659797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201158268	NA	P-0009613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	602	530	0	ENST00000305123.5:c.3658C>T	p.Arg1220Cys	p.R1220C	ENST00000305123	NM_005544.2	1220	Cgc/Tgc	1/2	NA	2	FACETS	0.979	0.944	1			1	INDETERMINATE	1	TRUE	NA	0.927047079652236	2		530	1327	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499326	89499326	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0009613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	493	535	0	ENST00000336596.2:c.2497-1G>C		p.X833_splice	ENST00000336596	NM_005233.5	833			0.915518292293659	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.927047079652236	1		535	560	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130100	143130100	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	412	578	3	ENST00000262992.4:c.916C>A	p.Gln306Lys	p.Q306K	ENST00000262992	NM_001101669.1	306	Caa/Aaa	11/24	0.915518292293659	1	FACETS	0.948	0.923	0.971	0.948	0.923	0.971	CLONAL	1	TRUE	0	0.927047079652236	1		581	503	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557214	187557214	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	71	566	0	ENST00000441802.2:c.4148A>C	p.Glu1383Ala	p.E1383A	ENST00000441802	NM_005245.3	1383	gAg/gCg	6/27	0.915518292293659	1	FACETS	0.118	0.102	0.134	0.118	0.102	0.134	SUBCLONAL	1	TRUE	0	0.927047079652236	1		566	699	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589232	67589232	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	93	566	0	ENST00000274335.5:c.1220A>G	p.His407Arg	p.H407R	ENST00000274335		407	cAc/cGc	9/15	0.927047079652236	1	FACETS	0.312	0.28	0.346	0.312	0.28	0.346	SUBCLONAL	1	TRUE	0	0.927047079652236	1		566	345	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931468	131931468	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369560280	NA	P-0009613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	24	309	0	ENST00000265335.6:c.2173C>T	p.Arg725Trp	p.R725W	ENST00000265335		725	Cgg/Tgg	13/25	0.927047079652236	1	FACETS	0.065	0.05	0.082	0.065	0.05	0.082	SUBCLONAL	1	TRUE	0	0.927047079652236	1		309	427	SUCCESS
MET	4233	MSKCC	GRCh37	7	116409844	116409844	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	527	577	0	ENST00000397752.3:c.2729A>T	p.Glu910Val	p.E910V	ENST00000397752	NM_000245.2	910	gAg/gTg	12/21	1	2	FACETS	0.993	0.955	1	0.993	0.955	1	CLONAL	1	TRUE	1	0.927047079652236	2		577	1145	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859867	117859867	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0009613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	805	945	0	ENST00000297338.2:c.1768A>T	p.Arg590Ter	p.R590*	ENST00000297338	NM_006265.2	590	Aga/Tga	14/14	1	2	FACETS	0.955	0.925	0.985	0.955	0.925	0.985	CLONAL	1	TRUE	1	0.927047079652236	2		945	1819	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557423	21557423	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	273	688	0	ENST00000382592.4:c.2422A>G	p.Thr808Ala	p.T808A	ENST00000382592	NM_014572.2	808	Aca/Gca	5/8	0.927047079652236	1	FACETS	0.338	0.318	0.359	0.338	0.318	0.359	SUBCLONAL	1	TRUE	0	0.927047079652236	1		688	934	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611339	28611339	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	376	683	0	ENST00000241453.7:c.1292T>A	p.Phe431Tyr	p.F431Y	ENST00000241453	NM_004119.2	431	tTc/tAc	10/24	0.927047079652236	1	FACETS	0.824	0.796	0.851	0.824	0.796	0.851	CLONAL	1	TRUE	0	0.927047079652236	1		683	528	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984755	11984755	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	283	238	1	ENST00000353533.5:c.301G>T	p.Asp101Tyr	p.D101Y	ENST00000353533	NM_003010.3	101	Gac/Tac	3/11	0.915518292293659	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.927047079652236	1		239	319	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384610	31384610	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	856	717	0	ENST00000328111.2:c.1312T>C	p.Cys438Arg	p.C438R	ENST00000328111	NM_006892.3	438	Tgt/Cgt	13/23	1	2	FACETS	0.976	0.946	1	0.976	0.946	1	CLONAL	1	TRUE	1	0.927047079652236	2		717	1893	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878176	48878177	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0009613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	381	243	0	ENST00000267163.4:c.131_132del	p.Leu44ArgfsTer4	p.L44Rfs*4	ENST00000267163	NM_000321.2	43	cCT/c	1/27	0.927047079652236	1	FACETS	0.971	0.947	0.994	0.971	0.947	0.994	CLONAL	1	TRUE	0	0.927047079652236	1		243	454	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416532	29416532	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	736	583	0	ENST00000389048.3:c.4421del	p.Gly1474AspfsTer3	p.G1474Dfs*3	ENST00000389048	NM_004304.4	1474	gGa/ga	29/29	1	2	FACETS	0.905	0.875	0.936	0.905	0.875	0.936	CLONAL	1	TRUE	1	0.927047079652236	2		583	1754	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067432	37067433	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs587778906	NA	P-0009613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	544	465	0	ENST00000231790.2:c.1348dup	p.Asp450GlyfsTer29	p.D450Gfs*29	ENST00000231790	NM_000249.3	448	gag/gaGg	12/19	0.915518292293659	1	FACETS	0.91	0.888	0.931	0.91	0.888	0.931	CLONAL	1	TRUE	0	0.927047079652236	1		465	692	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426261	49426263	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs1565775366	NA	P-0009613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	739	660	0	ENST00000301067.7:c.12225_12227del	p.Leu4077del	p.L4077del	ENST00000301067	NM_003482.3	4075	ctCCTg/ctg	39/54	1	2	FACETS	0.958	0.926	0.989	0.958	0.926	0.989	CLONAL	1	TRUE	1	0.927047079652236	2		660	1665	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88679156	88679156	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	114	146	0	ENST00000372037.3:c.1100del	p.Asn367ThrfsTer32	p.N367Tfs*32	ENST00000372037	NM_004329.2	366	Aaa/aa	10/13	1	2	FACETS	0.935	0.858	1	0.935	0.858	1	CLONAL	1	TRUE	1	0.927047079652236	2		146	263	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649272	23649273	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0009613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	429	418	0	ENST00000261584.4:c.109_110del	p.Arg37CysfsTer5	p.R37Cfs*5	ENST00000261584	NM_024675.3	37	CGt/t	3/13	1	2	FACETS	0.959	0.918	1	0.959	0.918	1	CLONAL	1	TRUE	1	0.927047079652236	2		418	965	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445149	49445149	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	367	282	0	ENST00000301067.7:c.2317del	p.Gln773SerfsTer157	p.Q773Sfs*157	ENST00000301067	NM_003482.3	773	Cag/ag	10/54	1	2	FACETS	0.896	0.853	0.938	0.896	0.853	0.938	CLONAL	1	TRUE	1	0.927047079652236	2		282	884	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781792	3781793	+	missense_variant	Missense_Mutation	DNP	CA	CA	AT	novel	NA	P-0009613-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	641	507	0	ENST00000262367.5:c.4874_4875delinsAT	p.Met1625Asn	p.M1625N	ENST00000262367	NM_004380.2	1625	aTG/aAT	29/31	1	2	FACETS	0.937	0.904	0.97	0.937	0.904	0.97	CLONAL	1	TRUE	1	0.927047079652236	2		507	1476	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0010599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	136	304	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.475435255704636	3	FACETS	1	0.954	1	0.536	0.488	0.585	CLONAL	1	TRUE	1	0.475435255704636	3		304	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0010599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	423	398	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.475435255704636	3	FACETS	0.958	0.921	0.995	0.958	0.921	0.995	CLONAL	3	TRUE	0	0.475435255704636	3		398	766	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649926	88649926	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	110	293	0	ENST00000372037.3:c.175T>A	p.Leu59Ile	p.L59I	ENST00000372037	NM_004329.2	59	Tta/Ata	4/13	0.42840097151958	3	FACETS	0.942	0.848	1	0.471	0.424	0.521	CLONAL	1	TRUE	1	0.475435255704636	3		293	608	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436705	110436705	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1726	108	513	0	ENST00000375856.3:c.1696G>T	p.Asp566Tyr	p.D566Y	ENST00000375856	NM_003749.2	566	Gac/Tac	1/2	0.475435255704636	9	FACETS	0.66	0.589	0.735	0.094	0.084	0.105	SUBCLONAL	1	TRUE	2	0.475435255704636	9		513	1834	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061607	38061607	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	32	146	0	ENST00000250448.2:c.382G>T	p.Gly128Cys	p.G128C	ENST00000250448	NM_004496.3	128	Ggc/Tgc	2/2	0.445821477097899	2	FACETS	0.601	0.491	0.723	0.3	0.245	0.362	SUBCLONAL	1	TRUE	0	0.475435255704636	2		146	224	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969920	81969920	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1699	173	793	0	ENST00000359376.3:c.2989T>C	p.Tyr997His	p.Y997H	ENST00000359376	NM_002661.3	997	Tac/Cac	27/33	0.459049012319538	3	FACETS	0.481	0.441	0.524	0.16	0.147	0.175	SUBCLONAL	1	TRUE	0	0.475435255704636	3		793	1872	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523009	25523009	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs772542252	NA	P-0012084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	392	585	1	ENST00000264709.3:c.176C>T	p.Pro59Leu	p.P59L	ENST00000264709	NM_175629.2	59	cCg/cTg	3/23	0.786175661404135	4	FACETS	0.985	0.941	1	0.985	0.941	1	CLONAL	2	FALSE	2	0.803911601978163	4		586	893	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131354	202131354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	127	311	0	ENST00000358485.4:c.322C>T	p.Gln108Ter	p.Q108*	ENST00000358485	NM_001080125.1	108	Cag/Tag	2/9	0.744033120410211	2	FACETS	1	0.922	1	0.502	0.461	0.543	CLONAL	1	FALSE	0	0.803911601978163	2		311	315	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0012084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	148	354	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	0.803911601978163	7	FACETS	1	0.914	1	0.143	0.13	0.157	CLONAL	1	FALSE	0	0.803911601978163	7		354	1105	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541607	187541607	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	223	297	0	ENST00000441802.2:c.6133G>T	p.Glu2045Ter	p.E2045*	ENST00000441802	NM_005245.3	2045	Gag/Tag	10/27	0.671008644309294	3	FACETS	0.885	0.849	0.918	0.885	0.849	0.918	CLONAL	3	FALSE	0	0.803911601978163	3		297	293	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710590	117710590	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	300	332	1	ENST00000368508.3:c.1682C>A	p.Pro561Gln	p.P561Q	ENST00000368508	NM_002944.2	561	cCg/cAg	12/43	0.671008644309294	3	FACETS	0.872	0.841	0.901	0.872	0.841	0.901	CLONAL	3	FALSE	0	0.803911601978163	3		333	400	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601928	43601928	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	414	470	0	ENST00000355710.3:c.972G>T	p.Trp324Cys	p.W324C	ENST00000355710	NM_020975.4	324	tgG/tgT	5/20	0.803911601978163	3	FACETS	0.935	0.91	0.958	0.935	0.91	0.958	CLONAL	3	FALSE	0	0.803911601978163	3		470	515	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29002059	29002059	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0012084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	75	167	0	ENST00000282397.4:c.1107-1G>T		p.X369_splice	ENST00000282397	NM_002019.4	369			NA	2	FACETS	0.709	0.629	0.793			1	INDETERMINATE	1	FALSE	NA	0.803911601978163	2		167	263	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435750	110435750	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	106	78	0	ENST00000375856.3:c.2651G>T	p.Arg884Leu	p.R884L	ENST00000375856	NM_003749.2	884	cGc/cTc	1/2	0.803911601978163	3	FACETS	1	0.938	1			1	CLONAL	2	FALSE	NA	0.803911601978163	3		78	182	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900321	3900321	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750216784	NA	P-0012084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	124	533	0	ENST00000262367.5:c.775G>A	p.Ala259Thr	p.A259T	ENST00000262367	NM_004380.2	259	Gca/Aca	2/31	0.803911601978163	3	FACETS	0.643	0.582	0.706	0.321	0.291	0.353	SUBCLONAL	1	FALSE	1	0.803911601978163	3		533	673	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223154	5223154	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	283	477	0	ENST00000357368.4:c.2649C>A	p.Phe883Leu	p.F883L	ENST00000357368	NM_002850.3	883	ttC/ttA	18/38	0.786175661404135	4	FACETS	0.914	0.864	0.964	0.914	0.864	0.964	CLONAL	2	FALSE	2	0.803911601978163	4		477	695	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600378	10600378	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	374	598	0	ENST00000171111.5:c.1477G>C	p.Glu493Gln	p.E493Q	ENST00000171111	NM_203500.1	493	Gag/Cag	4/6	0.786175661404135	4	FACETS	0.969	0.924	1	0.969	0.924	1	CLONAL	2	FALSE	2	0.803911601978163	4		598	866	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600447	10600447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	349	494	0	ENST00000171111.5:c.1408C>T	p.Arg470Cys	p.R470C	ENST00000171111	NM_203500.1	470	Cgt/Tgt	4/6	0.786175661404135	4	FACETS	0.925	0.88	0.97	0.925	0.88	0.97	CLONAL	2	FALSE	2	0.803911601978163	4		494	847	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602381	10602381	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	338	560	1	ENST00000171111.5:c.1197G>A	p.Met399Ile	p.M399I	ENST00000171111	NM_203500.1	399	atG/atA	3/6	0.786175661404135	4	FACETS	0.977	0.93	1	0.977	0.93	1	CLONAL	2	FALSE	2	0.803911601978163	4		561	776	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928896	44928914	+	frameshift_variant	Frame_Shift_Del	DEL	TCCCAGCATCTCCAGGCAG	TCCCAGCATCTCCAGGCAG	-	novel	NA	P-0012084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	188	290	0	ENST00000377967.4:c.1996_2014del	p.Ser666LeufsTer19	p.S666Lfs*19	ENST00000377967	NM_021140.2	666	TCCCAGCATCTCCAGGCAGct/ct	17/29	0.590828540725616	2	FACETS	1	0.964	1			1	CLONAL	1	FALSE	NA	0.803911601978163	2		290	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577522	7577522	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567549129	NA	P-0012084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	255	436	0	ENST00000269305.4:c.759del	p.Ile254SerfsTer91	p.I254Sfs*91	ENST00000269305	NM_001126112.2	253	acC/ac	7/11	0.786175661404135	4	FACETS	0.871	0.821	0.922	0.871	0.821	0.922	CLONAL	2	FALSE	2	0.803911601978163	4		436	657	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577593	7577593	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	219	327	0	ENST00000269305.4:c.688del	p.Thr230ProfsTer17	p.T230Pfs*17	ENST00000269305	NM_001126112.2	230	Acc/cc	7/11	0.786175661404135	4	FACETS	0.885	0.831	0.941	0.885	0.831	0.941	CLONAL	2	FALSE	2	0.803911601978163	4		327	555	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0012567-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	7	324	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.429	0.266	0.647	0.429	0.266	0.647	SUBCLONAL	1	TRUE	1	0.1	2		324	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397516435	NA	P-0012567-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	19	606	0	ENST00000269305.4:c.586C>G	p.Arg196Gly	p.R196G	ENST00000269305	NM_001126112.2	196	Cga/Gga	6/11	1	2	FACETS	0.644	0.487	0.831	0.644	0.487	0.831	SUBCLONAL	1	TRUE	1	0.1	2		606	590	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231165	142231165	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012567-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	11	0	0	ENST00000350721.4:c.4789C>A	p.Gln1597Lys	p.Q1597K	ENST00000350721	NM_001184.3	1597	Cag/Aag	27/47	1	2	FACETS	0.549	0.377	0.763	0.549	0.377	0.763	SUBCLONAL	1	TRUE	1	0.1	2		0	401	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0012707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	27	312	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	0.368779848150315	4	FACETS	1	0.813	1	0.337	0.271	0.411	CLONAL	1	FALSE	1	0.496153413533289	4		312	161	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248157	110248157	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	46	477	0	ENST00000374672.4:c.1315C>T	p.Arg439Cys	p.R439C	ENST00000374672	NM_004235.4	439	Cgc/Tgc	5/5	0.439925316070606	1	FACETS	0.811	0.694	0.935	0.811	0.694	0.935	CLONAL	1	FALSE	0	0.496153413533289	1		477	172	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012707-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	51	586	0	ENST00000269305.4:c.713del	p.Cys238LeufsTer9	p.C238Lfs*9	ENST00000269305	NM_001126112.2	238	tGt/tt	7/11	0.387472294561101	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	0	0.496153413533289	1		586	136	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	481	564	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.861271627094476	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.861271627094476	1		564	618	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629325	187629325	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs550890340	NA	P-0013118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1303	85	700	0	ENST00000441802.2:c.1657G>C	p.Val553Leu	p.V553L	ENST00000441802	NM_005245.3	553	Gtc/Ctc	2/27	1	2	FACETS	0.142	0.125	0.161	0.142	0.125	0.161	SUBCLONAL	1	TRUE	1	0.861271627094476	2		700	1388	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584504	48584504	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	399	338	0	ENST00000342988.3:c.678del	p.Ser227ValfsTer14	p.S227Vfs*14	ENST00000342988	NM_005359.5	226	gCc/gc	6/12	0.861271627094476	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.861271627094476	1		338	509	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857497	68857501	+	frameshift_variant	Frame_Shift_Ins	INS	TGGGG	TGGGG	CGGGGA	novel	NA	P-0013118-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	325	512	0	ENST00000261769.5:c.2132_2136delinsCGGGGA	p.Leu711ProfsTer37	p.L711Pfs*37	ENST00000261769	NM_004360.3	711	cTGGGG/cCGGGGA	13/16	0.861271627094476	1	FACETS	0.94	0.906	0.973	0.94	0.906	0.973	CLONAL	1	TRUE	0	0.861271627094476	1		512	457	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	303	564	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.837876952110388	1	FACETS	0.966	0.929	1	0.966	0.929	1	CLONAL	1	TRUE	0	0.837876952110388	1		564	435	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584504	48584504	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	206	338	0	ENST00000342988.3:c.678del	p.Ser227ValfsTer14	p.S227Vfs*14	ENST00000342988	NM_005359.5	226	gCc/gc	6/12	0.837876952110388	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.837876952110388	1		338	273	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857497	68857497	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	221	492	0	ENST00000261769.5:c.2132T>C	p.Leu711Pro	p.L711P	ENST00000261769	NM_004360.3	711	cTg/cCg	13/16	0.837876952110388	1	FACETS	0.91	0.866	0.952	0.91	0.866	0.952	CLONAL	1	TRUE	0	0.837876952110388	1		492	337	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857501	68857502	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0013118-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	216	485	0	ENST00000261769.5:c.2137dup	p.Ile713AsnfsTer35	p.I713Nfs*35	ENST00000261769	NM_004360.3	712	-/A	13/16	0.837876952110388	1	FACETS	0.897	0.853	0.94	0.897	0.853	0.94	CLONAL	1	TRUE	0	0.837876952110388	1		485	334	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559852	29559852	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1555614972	NA	P-0013793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	169	584	0	ENST00000356175.3:c.3449C>G	p.Ser1150Ter	p.S1150*	ENST00000356175	NM_000267.3	1150	tCa/tGa	26/57	0.858551730240173	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.858551730240173	1		584	220	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46736373	46736373	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	218	639	0	ENST00000371975.4:c.1085T>G	p.Leu362Trp	p.L362W	ENST00000371975	NM_003579.3	362	tTg/tGg	10/18	0.858551730240173	3	FACETS	1	0.968	1	0.53	0.495	0.566	CLONAL	1	TRUE	1	0.858551730240173	3		639	685	SUCCESS
APC	324	MSKCC	GRCh37	5	112179093	112179093	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	109	391	0	ENST00000257430.4:c.7802G>T	p.Ser2601Ile	p.S2601I	ENST00000257430	NM_000038.5	2601	aGt/aTt	16/16	0.545818532815231	4	FACETS	1	0.95	1	0.36	0.325	0.396	CLONAL	1	TRUE	1	0.858551730240173	4		391	437	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925407	131925407	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	112	397	0	ENST00000265335.6:c.1330G>C	p.Glu444Gln	p.E444Q	ENST00000265335		444	Gag/Cag	9/25	0.545818532815231	4	FACETS	1	0.975	1	0.407	0.369	0.447	CLONAL	1	TRUE	1	0.858551730240173	4		397	397	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46736381	46736381	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs559500678	NA	P-0014569-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	60	594	0	ENST00000371975.4:c.1093C>T	p.Arg365Ter	p.R365*	ENST00000371975	NM_003579.3	365	Cga/Tga	10/18	0.397315336816765	2	FACETS	0.689	0.596	0.788	0.344	0.298	0.394	SUBCLONAL	1	TRUE	0	0.469709509388028	2		594	371	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456255	32456255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014569-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	96	522	1	ENST00000332351.3:c.637C>T	p.Arg213Cys	p.R213C	ENST00000332351	NM_024426.4	213	Cgc/Tgc	1/10	0.43571827678721	5	FACETS	0.881	0.784	0.984	0.294	0.261	0.328	CLONAL	1	TRUE	2	0.469709509388028	5		523	791	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434325	49434325	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014569-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	102	782	0	ENST00000301067.7:c.7228C>T	p.Arg2410Ter	p.R2410*	ENST00000301067	NM_003482.3	2410	Cga/Tga	31/54	0.338277815650483	4	FACETS	0.809	0.723	0.9	0.405	0.361	0.45	CLONAL	1	TRUE	2	0.469709509388028	4		782	789	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246037	41246037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56272539	NA	P-0014569-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	48	541	0	ENST00000357654.3:c.1511G>A	p.Arg504His	p.R504H	ENST00000357654	NM_007294.3	504	cGt/cAt	10/23	0.4047505107903	5	FACETS	0.797	0.675	0.931	0.266	0.225	0.311	CLONAL	1	TRUE	2	0.469709509388028	5		541	437	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423550	47423550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1029166106	NA	P-0014569-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	144	618	0	ENST00000404338.3:c.1618C>T	p.Arg540Cys	p.R540C	ENST00000404338	NM_004491.4	540	Cgt/Tgt	1/6	0.376200293139725	4	FACETS	0.935	0.859	1	0.935	0.859	1	CLONAL	2	TRUE	2	0.469709509388028	4		618	482	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594953	158594953	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs750457181	NA	P-0014569-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	55	576	0	ENST00000263640.3:c.1394C>T	p.Pro465Leu	p.P465L	ENST00000263640	NM_001105.4	465	cCg/cTg	10/11	0.397315336816765	2	FACETS	0.825	0.711	0.947	0.412	0.355	0.474	CLONAL	1	TRUE	0	0.469709509388028	2		576	284	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46276052	46276052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139321788	NA	P-0014569-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	73	637	0	ENST00000371998.3:c.3488G>A	p.Arg1163Gln	p.R1163Q	ENST00000371998		1163	cGg/cAg	18/23	0.43571827678721	5	FACETS	0.893	0.782	1	0.298	0.26	0.338	CLONAL	1	TRUE	2	0.469709509388028	5		637	593	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397767	49397767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014569-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	91	581	0	ENST00000418115.1:c.457G>A	p.Ala153Thr	p.A153T	ENST00000418115	NM_001664.2	153	Gct/Act	5/5	0.329613037086022	5	FACETS	1	0.957	1	0.384	0.342	0.43	CLONAL	1	TRUE	2	0.469709509388028	5		581	573	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72891539	72891539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755870786	NA	P-0014569-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	102	488	0	ENST00000325599.8:c.223C>T	p.Arg75Cys	p.R75C	ENST00000325599	NM_018130.2	75	Cgc/Tgc	3/11	0.263245291059694	5	FACETS	0.836	0.752	0.924	0.557	0.501	0.616	INDETERMINATE	2	TRUE	2	0.469709509388028	5		488	443	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521724	89521725	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0014569-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	71	546	0	ENST00000336596.2:c.2804_2805del	p.Val935GlyfsTer6	p.V935Gfs*6	ENST00000336596	NM_005233.5	934	gGT/g	16/17	0.263245291059694	5	FACETS	1	0.91	1	0.35	0.306	0.397	INDETERMINATE	1	TRUE	2	0.469709509388028	5		546	491	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798210	32798210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768337366	NA	P-0014569-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	95	593	0	ENST00000374899.4:c.1469C>T	p.Thr490Met	p.T490M	ENST00000374899	NM_018833.2	490	aCg/aTg	9/12	0.376200293139725	4	FACETS	0.926	0.825	1	0.463	0.412	0.517	CLONAL	1	TRUE	2	0.469709509388028	4		593	642	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042129	6042129	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014569-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	35	385	0	ENST00000265849.7:c.492del	p.Thr165HisfsTer36	p.T165Hfs*36	ENST00000265849	NM_000535.5	164	tcC/tc	5/15	0.382854203975045	3	FACETS	0.63	0.518	0.755	0.315	0.259	0.378	SUBCLONAL	1	TRUE	1	0.469709509388028	3		385	292	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864648	68864648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014569-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	62	227	0	ENST00000288368.4:c.19G>A	p.Gly7Arg	p.G7R	ENST00000288368	NM_024870.2	7	Gga/Aga	1/40	0.472716324047784	4	FACETS	0.695	0.601	0.798	0.348	0.3	0.399	SUBCLONAL	1	TRUE	2	0.469709509388028	4		227	558	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430668	80430668	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014569-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	29	284	0	ENST00000286548.4:c.340C>T	p.Arg114Ter	p.R114*	ENST00000286548	NM_002072.3	114	Cga/Tga	3/7	1	2	FACETS	0.864	0.703	1	0.864	0.703	1	CLONAL	1	TRUE	1	0.469709509388028	2		284	143	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802652	135802654	+	inframe_deletion	In_Frame_Del	DEL	TAA	TAA	-	novel	NA	P-0014569-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	69	515	0	ENST00000298552.3:c.144_146del	p.Tyr49del	p.Y49del	ENST00000298552	NM_001162426.1	48	taTTAc/tac	4/23	1	2	FACETS	0.945	0.83	1	0.945	0.83	1	CLONAL	1	TRUE	1	0.469709509388028	2		515	311	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28929495	NA	P-0014729-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	111	546	1	ENST00000275493.2:c.2155G>A	p.Gly719Ser	p.G719S	ENST00000275493	NM_005228.3	719	Ggc/Agc	18/28	0.176867383446971	4	FACETS	0.912	0.826	1	0.912	0.826	1	CLONAL	3	TRUE	1	0.247560089924542	4		547	409	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0014729-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	132	550	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.176867383446971	4	FACETS	1	0.978	1	0.82	0.748	0.895	CLONAL	2	TRUE	1	0.247560089924542	4		550	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519985	NA	P-0014729-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	135	641	0	ENST00000269305.4:c.857A>C	p.Glu286Ala	p.E286A	ENST00000269305	NM_001126112.2	286	gAa/gCa	8/11	0.247560089924542	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.247560089924542	2		641	471	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965377	25965377	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014729-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	95	709	0	ENST00000435504.4:c.3829G>T	p.Val1277Leu	p.V1277L	ENST00000435504		1277	Gtg/Ttg	13/13	0.246827662026601	2	FACETS	0.806	0.721	0.896	0.806	0.721	0.896	CLONAL	2	TRUE	0	0.247560089924542	2		709	476	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79960997	79960997	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014729-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	32	495	0	ENST00000265081.6:c.394A>G	p.Lys132Glu	p.K132E	ENST00000265081	NM_002439.4	132	Aag/Gag	3/24	1	2	FACETS	0.617	0.501	0.748	0.617	0.501	0.748	SUBCLONAL	1	TRUE	1	0.247560089924542	2		495	419	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109309785	109309785	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014729-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	87	334	0	ENST00000436639.2:c.1530G>T	p.Met510Ile	p.M510I	ENST00000436639	NM_014454.2	510	atG/atT	9/10	0.077098859330841	3	FACETS	0.853	0.758	0.953	0.853	0.758	0.953	INDETERMINATE	2	TRUE	1	0.247560089924542	3		334	463	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270610	98270610	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014729-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	14	442	0	ENST00000331920.6:c.34G>C	p.Asp12His	p.D12H	ENST00000331920	NM_000264.3	12	Gac/Cac	1/24	0.247560089924542	1	FACETS	0.563	0.408	0.749	0.563	0.408	0.749	SUBCLONAL	1	TRUE	0	0.247560089924542	1		442	176	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906448	32906448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	134	411	0	ENST00000380152.3:c.833G>A	p.Ser278Asn	p.S278N	ENST00000380152		278	aGc/aAc	10/27	1	2	FACETS	0.564	0.513	0.617	0.564	0.513	0.617	SUBCLONAL	1	TRUE	1	0.642355874317235	2		411	740	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897415	78897415	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	299	633	0	ENST00000306801.3:c.2750C>T	p.Thr917Ile	p.T917I	ENST00000306801	NM_020761.2	917	aCc/aTc	23/34	1	2	FACETS	0.951	0.897	1	0.951	0.897	1	CLONAL	1	TRUE	1	0.642355874317235	2		633	979	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0015964-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	104	703	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.59047960688555	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.59047960688555	1		703	215	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0015964-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	37	812	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.343371337462873	5	FACETS	0.838	0.714	0.967	0.838	0.714	0.967	INDETERMINATE	3	TRUE	2	0.59047960688555	5		812	94	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015964-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	7	0	0	ENST00000263967.3:c.3012G>A	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atA	21/21	0.343371337462873	5	FACETS	0.273	0.169	0.409	0.091	0.056	0.137	INDETERMINATE	1	TRUE	2	0.59047960688555	5		0	164	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168749	56168749	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015964-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	23	524	0	ENST00000399503.3:c.1603C>T	p.Gln535Ter	p.Q535*	ENST00000399503	NM_005921.1	535	Caa/Taa	9/20	0.340794822384747	1	FACETS	0.439	0.347	0.542	0.439	0.347	0.542	INDETERMINATE	1	TRUE	0	0.59047960688555	1		524	125	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288203	33288203	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015964-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	58	866	0	ENST00000374542.5:c.1205C>T	p.Ser402Phe	p.S402F	ENST00000374542	NM_001141970.1	402	tCt/tTt	4/8	0.526435357593961	3	FACETS	0.675	0.582	0.775	0.337	0.291	0.388	SUBCLONAL	1	TRUE	1	0.59047960688555	3		866	377	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114901023	114901023	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs979684293	NA	P-0015964-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	39	781	0	ENST00000543371.1:c.633C>A	p.Phe211Leu	p.F211L	ENST00000543371	NM_001198531.1	211	ttC/ttA	6/14	1	2	FACETS	0.443	0.369	0.526	0.443	0.369	0.526	SUBCLONAL	1	TRUE	1	0.59047960688555	2		781	298	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494962	56494962	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015964-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	53	697	0	ENST00000267101.3:c.3319G>C	p.Glu1107Gln	p.E1107Q	ENST00000267101	NM_001982.3	1107	Gag/Cag	27/28	0.159931083485204	3	FACETS	0.887	0.763	1	0.444	0.381	0.511	INDETERMINATE	1	TRUE	1	0.59047960688555	3		697	262	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987165	36987165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015964-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	6	0	0	ENST00000354822.5:c.524C>T	p.Ser175Leu	p.S175L	ENST00000354822	NM_001079668.2	175	tCg/tTg	3/3	1	2	FACETS	0.104	0.062	0.162	0.104	0.062	0.162	SUBCLONAL	1	TRUE	1	0.59047960688555	2		0	195	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3094724	3094724	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015964-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	29	601	0	ENST00000078429.4:c.75C>G	p.Ile25Met	p.I25M	ENST00000078429	NM_002067.2	25	atC/atG	1/7	0.59047960688555	1	FACETS	0.488	0.397	0.587	0.488	0.397	0.587	SUBCLONAL	1	TRUE	0	0.59047960688555	1		601	142	SUCCESS
ATR	545	MSKCC	GRCh37	3	142218544	142218544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015964-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	16	405	0	ENST00000350721.4:c.5305G>A	p.Glu1769Lys	p.E1769K	ENST00000350721	NM_001184.3	1769	Gaa/Aaa	31/47	1	2	FACETS	0.379	0.282	0.493	0.379	0.282	0.493	SUBCLONAL	1	TRUE	1	0.59047960688555	2		405	143	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176561	56176561	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1561198459	NA	P-0015964-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	34	605	0	ENST00000399503.3:c.2111C>G	p.Ser704Ter	p.S704*	ENST00000399503	NM_005921.1	704	tCa/tGa	12/20	0.340794822384747	1	FACETS	0.634	0.528	0.748	0.634	0.528	0.748	INDETERMINATE	1	TRUE	0	0.59047960688555	1		605	128	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679733	30679733	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015964-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	24	874	0	ENST00000376406.3:c.1986G>T	p.Gln662His	p.Q662H	ENST00000376406	NM_014641.2	662	caG/caT	5/15	0.526435357593961	3	FACETS	0.344	0.27	0.43	0.172	0.135	0.215	SUBCLONAL	1	TRUE	1	0.59047960688555	3		874	306	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965690	93965690	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015964-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	26	604	0	ENST00000369303.4:c.2238G>C	p.Met746Ile	p.M746I	ENST00000369303	NM_004440.3	746	atG/atC	13/17	1	2	FACETS	0.734	0.591	0.891	0.734	0.591	0.891	SUBCLONAL	1	TRUE	1	0.59047960688555	2		604	120	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975403	13975403	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015964-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	4	0	0	ENST00000405192.2:c.484G>T	p.Asp162Tyr	p.D162Y	ENST00000405192	NM_001163147.1	162	Gac/Tac	7/12	1	2	FACETS	0.047	0.024	0.081	0.047	0.024	0.081	SUBCLONAL	1	TRUE	1	0.59047960688555	2		0	287	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431339	49431339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015964-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	27	865	0	ENST00000301067.7:c.9800C>T	p.Ser3267Leu	p.S3267L	ENST00000301067	NM_003482.3	3267	tCa/tTa	34/54	0.159931083485204	3	FACETS	0.478	0.381	0.587	0.239	0.19	0.294	INDETERMINATE	1	TRUE	1	0.59047960688555	3		865	248	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281193	15281193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015964-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	23	817	0	ENST00000263388.2:c.5063C>T	p.Ser1688Phe	p.S1688F	ENST00000263388	NM_000435.2	1688	tCt/tTt	27/33	1	2	FACETS	0.266	0.207	0.334	0.266	0.207	0.334	SUBCLONAL	1	TRUE	1	0.59047960688555	2		817	293	SUCCESS
FH	2271	MSKCC	GRCh37	1	241677009	241677009	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1455612736	NA	P-0015964-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	16	354	0	ENST00000366560.3:c.272C>T	p.Pro91Leu	p.P91L	ENST00000366560	NM_000143.3	91	cCa/cTa	3/10	1	2	FACETS	0.677	0.511	0.867	0.677	0.511	0.867	SUBCLONAL	1	TRUE	1	0.59047960688555	2		354	80	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936125	71936125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1182922528	NA	P-0015964-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	24	654	0	ENST00000298229.2:c.97G>A	p.Glu33Lys	p.E33K	ENST00000298229	NM_001567.3	33	Gag/Aag	1/28	1	2	FACETS	0.452	0.357	0.559	0.452	0.357	0.559	SUBCLONAL	1	TRUE	1	0.59047960688555	2		654	180	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77934562	77934562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015964-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	26	815	0	ENST00000361507.4:c.1463C>T	p.Ser488Leu	p.S488L	ENST00000361507	NM_080491.2	488	tCa/tTa	6/10	1	2	FACETS	0.321	0.255	0.397	0.321	0.255	0.397	SUBCLONAL	1	TRUE	1	0.59047960688555	2		815	274	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923266	26923266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015964-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	12	589	0	ENST00000381527.3:c.262C>T	p.His88Tyr	p.H88Y	ENST00000381527	NM_001260.1	88	Cat/Tat	3/13	1	2	FACETS	0.32	0.226	0.434	0.32	0.226	0.434	SUBCLONAL	1	TRUE	1	0.59047960688555	2		589	127	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61323052	61323052	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015964-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	31	870	0	ENST00000283752.5:c.1012G>C	p.Glu338Gln	p.E338Q	ENST00000283752	NM_006919.2	338	Gag/Cag	8/8	1	2	FACETS	0.379	0.307	0.459	0.379	0.307	0.459	SUBCLONAL	1	TRUE	1	0.59047960688555	2		870	277	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016238-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	34	714	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.828	0.676	1	0.828	0.676	1	CLONAL	1	TRUE	1	0.175016622310541	2		715	469	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020754	37020754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016238-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	34	701	1	ENST00000358127.4:c.91C>T	p.Arg31Trp	p.R31W	ENST00000358127	NM_001280556.1	31	Cgg/Tgg	2/10	1	2	FACETS	0.587	0.478	0.71	0.587	0.478	0.71	SUBCLONAL	1	TRUE	1	0.175016622310541	2		702	662	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653800	89653802	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	novel	NA	P-0016238-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	28	229	0	ENST00000371953.3:c.98_100del	p.Ile33_Ala34delinsThr	p.I33_A34delinsT	ENST00000371953	NM_000314.4	33	aTTGct/act	2/9	0.175016622310541	1	FACETS	0.951	0.762	1	0.951	0.762	1	CLONAL	1	TRUE	0	0.175016622310541	1		229	307	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197757	66197757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770802873	NA	P-0016238-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	49	493	0	ENST00000273854.3:c.2942G>A	p.Arg981Gln	p.R981Q	ENST00000273854	NM_004439.5	981	cGg/cAg	17/18	1	2	FACETS	0.871	0.736	1	0.871	0.736	1	CLONAL	1	TRUE	1	0.175016622310541	2		493	643	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	113	714	1				ENST00000310581	NM_198253.2	-/1132			0.228298897419096	0	FACETS	0.853	0.786	0.919			1	CLONAL	4	TRUE	0	0.228298897419096	0		715	224	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0016649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	189	634	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.0843039502417757	3	FACETS	1	0.944	1	1	0.994	1	INDETERMINATE	4	TRUE	1	0.228298897419096	3		634	456	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0016649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	230	487	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.228298897419096	5	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	TRUE	2	0.228298897419096	5		487	827	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587780070	NA	P-0016649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	22	633	0	ENST00000269305.4:c.535C>G	p.His179Asp	p.H179D	ENST00000269305	NM_001126112.2	179	Cat/Gat	5/11	0.191875067731857	3	FACETS	0.333	0.257	0.423	0.167	0.128	0.212	SUBCLONAL	1	TRUE	1	0.228298897419096	3		633	644	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433557	49433564	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGGGTA	CCTGGGTA	-	novel	NA	P-0016649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	454	1001	0	ENST00000301067.7:c.7989_7996del	p.Thr2664ProfsTer7	p.T2664Pfs*7	ENST00000301067	NM_003482.3	2663	ggTACCCAGGac/ggac	31/54	0.228298897419096	4	FACETS	1	0.973	1	1	0.997	1	CLONAL	4	TRUE	2	0.228298897419096	4		1001	1193	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545797	41545798	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0016649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	459	681	0	ENST00000263253.7:c.2415_2416del	p.Pro806TyrfsTer31	p.P806Yfs*31	ENST00000263253	NM_001429.3	804	aaCTct/aact	14/31	0.228298897419096	4	FACETS	0.945	0.906	0.985			1	CLONAL	5	TRUE	NA	0.228298897419096	4		681	1045	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984840	55984840	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	348	535	0	ENST00000263923.4:c.289G>A	p.Asp97Asn	p.D97N	ENST00000263923	NM_002253.2	97	Gac/Aac	3/30	0.0843039502417757	3	FACETS	1	0.973	1	1	0.996	1	INDETERMINATE	4	TRUE	1	0.228298897419096	3		535	822	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879948	44879949	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	406	528	0	ENST00000377967.4:c.539dup	p.Asn180LysfsTer5	p.N180Kfs*5	ENST00000377967	NM_021140.2	179	-/A	6/29	0.228298897419096	0	FACETS	0.833	0.807	0.858			1	CLONAL	6	TRUE	0	0.228298897419096	0		528	549	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200023	123200023	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0016649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	183	218	0	ENST00000218089.9:c.2097-2A>G		p.X699_splice	ENST00000218089	NM_001042749.1	699			0.228298897419096	0	FACETS	0.881	0.844	0.916			1	CLONAL	6	TRUE	0	0.228298897419096	0		218	234	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0016917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	175	274	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.964	0.893	1	0.964	0.893	1	CLONAL	1	TRUE	1	0.609162025494172	2		274	596	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0016917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	358	424	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.333672036853264	6	FACETS	0.99	0.937	1	0.66	0.625	0.696	INDETERMINATE	2	TRUE	3	0.609162025494172	6		424	1317	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158118	47158118	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	304	397	0	ENST00000409792.3:c.4581T>G	p.Ile1527Met	p.I1527M	ENST00000409792	NM_014159.6	1527	atT/atG	4/21	1	2	FACETS	0.915	0.863	0.968	0.915	0.863	0.968	CLONAL	1	TRUE	1	0.609162025494172	2		397	1091	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0016917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	107	274	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.82	0.738	0.908	0.82	0.738	0.908	CLONAL	1	TRUE	1	0.435444095585952	2		274	599	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0016917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1182	405	424	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.401902897696286	4	FACETS	0.841	0.799	0.885	0.841	0.799	0.885	CLONAL	2	TRUE	2	0.435444095585952	4		424	1587	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158118	47158118	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	275	397	0	ENST00000409792.3:c.4581T>G	p.Ile1527Met	p.I1527M	ENST00000409792	NM_014159.6	1527	atT/atG	4/21	1	2	FACETS	0.931	0.872	0.991	0.931	0.872	0.991	CLONAL	1	TRUE	1	0.435444095585952	2		397	1357	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0016917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	173	417	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.401902897696286	4	FACETS	0.877	0.805	0.953	0.439	0.402	0.477	CLONAL	1	TRUE	2	0.435444095585952	4		417	1300	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873020	136873020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147198552	NA	P-0016917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	79	383	0	ENST00000241393.3:c.478G>A	p.Val160Ile	p.V160I	ENST00000241393	NM_003467.2	160	Gtc/Atc	2/2	0.430984602992192	3	FACETS	0.539	0.473	0.61	0.269	0.236	0.305	SUBCLONAL	1	TRUE	1	0.435444095585952	3		383	820	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0016917-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	45	349	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.193336228731099	3	FACETS	1	0.901	1	0.55	0.462	0.647	CLONAL	1	TRUE	1	0.193336228731099	3		349	464	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0016917-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	35	274	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.193336228731099	3	FACETS	1	0.899	1	0.572	0.47	0.687	CLONAL	1	TRUE	1	0.193336228731099	3		274	347	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0016917-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	74	424	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.193336228731099	5	FACETS	1	0.912	1	0.699	0.614	0.79	CLONAL	2	TRUE	2	0.193336228731099	5		424	471	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158118	47158118	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016917-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	48	397	0	ENST00000409792.3:c.4581T>G	p.Ile1527Met	p.I1527M	ENST00000409792	NM_014159.6	1527	atT/atG	4/21	0.193336228731099	3	FACETS	1	0.937	1	0.608	0.514	0.71	CLONAL	1	TRUE	1	0.193336228731099	3		397	448	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249091	55249091	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519861	NA	P-0016917-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	56	534	0	ENST00000275493.2:c.2389T>A	p.Cys797Ser	p.C797S	ENST00000275493	NM_005228.3	797	Tgc/Agc	20/28	0.193336228731099	5	FACETS	1	0.915	1	0.367	0.314	0.425	CLONAL	1	TRUE	2	0.193336228731099	5		534	679	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656629	3656629	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016917-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	77	587	0	ENST00000294008.3:c.606A>T	p.Lys202Asn	p.K202N	ENST00000294008	NM_032444.2	202	aaA/aaT	3/15	0.193336228731099	4	FACETS	1	0.949	1	0.58	0.509	0.658	CLONAL	1	TRUE	2	0.193336228731099	4		587	819	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770817	59770817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016917-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	37	328	0	ENST00000259008.2:c.2549G>A	p.Arg850Lys	p.R850K	ENST00000259008	NM_032043.2	850	aGg/aAg	18/20	0.193336228731099	4	FACETS	1	0.841	1	0.511	0.421	0.611	CLONAL	1	TRUE	2	0.193336228731099	4		328	447	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979379	93979379	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0016917-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	27	225	0	ENST00000369303.4:c.1450-1G>T		p.X484_splice	ENST00000369303	NM_004440.3	484			0.106330072384266	1	FACETS	0.997	0.797	1	0.997	0.797	1	INDETERMINATE	1	TRUE	0	0.193336228731099	1		225	253	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524714	137524714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1311661488	NA	P-0016917-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	68	373	1	ENST00000367739.4:c.655G>A	p.Gly219Arg	p.G219R	ENST00000367739	NM_000416.2	219	Gga/Aga	5/7	0.106330072384266	1	FACETS	1	0.945	1	1	0.945	1	INDETERMINATE	1	TRUE	0	0.193336228731099	1		374	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0017213-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	94	703	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.411145060498721	1	FACETS	0.948	0.85	1	0.948	0.85	1	CLONAL	1	FALSE	0	0.411145060498721	1		703	383	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0017213-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	16	349	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.272386525851468	4	FACETS	1	0.852	1	0.402	0.302	0.518	CLONAL	1	FALSE	1	0.411145060498721	4		349	91	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371734	55371734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017213-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	69	841	0	ENST00000297316.4:c.424C>T	p.Arg142Cys	p.R142C	ENST00000297316	NM_022454.3	142	Cgc/Tgc	2/2	0.146438580857696	2	FACETS	0.863	0.755	0.978	0.431	0.377	0.489	INDETERMINATE	1	FALSE	0	0.411145060498721	2		841	389	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480335	56480335	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017213-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	33	583	0	ENST00000267101.3:c.442T>C	p.Tyr148His	p.Y148H	ENST00000267101	NM_001982.3	148	Tat/Cat	4/28	1	2	FACETS	0.683	0.56	0.82	0.683	0.56	0.82	SUBCLONAL	1	FALSE	1	0.411145060498721	2		583	235	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458486	12458486	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017213-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	61	772	0	ENST00000287820.6:c.1103T>C	p.Leu368Pro	p.L368P	ENST00000287820	NM_015869.4	368	cTc/cCc	6/7	0.146438580857696	2	FACETS	0.875	0.76	0.999	0.438	0.38	0.5	INDETERMINATE	1	FALSE	0	0.411145060498721	2		772	339	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860113	151860113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017213-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	43	850	0	ENST00000262189.6:c.10549C>T	p.Pro3517Ser	p.P3517S	ENST00000262189	NM_170606.2	3517	Cct/Tct	43/59	1	2	FACETS	0.808	0.681	0.946	0.808	0.681	0.946	CLONAL	1	FALSE	1	0.411145060498721	2		850	259	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537112	80537112	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs753716491	NA	P-0017213-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	10	625	2	ENST00000286548.4:c.286A>T	p.Thr96Ser	p.T96S	ENST00000286548	NM_002072.3	96	Aca/Tca	2/7	0.399536232833124	3	FACETS	0.177	0.119	0.25	0.089	0.059	0.125	SUBCLONAL	1	FALSE	1	0.411145060498721	3		627	331	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118821	115118821	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017213-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	19	693	0	ENST00000257566.3:c.520G>C	p.Gly174Arg	p.G174R	ENST00000257566	NM_016569.3	174	Ggt/Cgt	2/8	1	2	FACETS	0.28	0.212	0.36	0.28	0.212	0.36	SUBCLONAL	1	FALSE	1	0.411145060498721	2		693	330	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184144	123184144	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	189	438	0	ENST00000218089.9:c.1002G>A	p.Trp334Ter	p.W334*	ENST00000218089	NM_001042749.1	334	tgG/tgA	11/35	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.5	2		438	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782329	NA	P-0017573-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	256	537	0	ENST00000269305.4:c.746G>C	p.Arg249Thr	p.R249T	ENST00000269305	NM_001126112.2	249	aGg/aCg	7/11	0.521970284031187	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.521970284031187	1		537	585	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0017573-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	181	324	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.381055180378569	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.521970284031187	3		324	424	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0017573-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	141	425	0	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	1	2	FACETS	0.991	0.908	1	0.991	0.908	1	CLONAL	1	TRUE	1	0.521970284031187	2		425	545	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217605	142217605	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017573-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	129	379	0	ENST00000350721.4:c.5392A>G	p.Thr1798Ala	p.T1798A	ENST00000350721	NM_001184.3	1798	Aca/Gca	32/47	0.381055180378569	3	FACETS	0.925	0.84	1	0.462	0.42	0.507	CLONAL	1	TRUE	1	0.521970284031187	3		379	674	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118944	115118944	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017573-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	83	215	0	ENST00000257566.3:c.397T>G	p.Phe133Val	p.F133V	ENST00000257566	NM_016569.3	133	Ttt/Gtt	2/8	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.521970284031187	2		215	292	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518278	187518278	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	41	280	1	ENST00000441802.2:c.12416G>T	p.Gly4139Val	p.G4139V	ENST00000441802	NM_005245.3	4139	gGg/gTg	25/27	0.313183397099503	2	FACETS	0.636	0.532	0.75	0.318	0.266	0.375	SUBCLONAL	1	TRUE	0	0.437106877195303	2		281	295	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17743008	17743008	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	58	721	1	ENST00000250003.3:c.916C>A	p.Gln306Lys	p.Q306K	ENST00000250003	NM_002478.4	306	Cag/Aag	3/3	0.373205020426154	1	FACETS	0.333	0.286	0.385	0.333	0.286	0.385	SUBCLONAL	1	TRUE	0	0.437106877195303	1		722	622	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098570	108098570	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs774185390	NA	P-0017794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	106	391	0	ENST00000278616.4:c.140C>G	p.Ser47Ter	p.S47*	ENST00000278616	NM_000051.3	47	tCa/tGa	3/63	0.373205020426154	1	FACETS	0.798	0.719	0.881	0.798	0.719	0.881	SUBCLONAL	1	TRUE	0	0.437106877195303	1		391	475	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098599	108098599	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	82	341	0	ENST00000278616.4:c.169T>G	p.Trp57Gly	p.W57G	ENST00000278616	NM_000051.3	57	Tgg/Ggg	3/63	0.373205020426154	1	FACETS	0.719	0.637	0.805	0.719	0.637	0.805	SUBCLONAL	1	TRUE	0	0.437106877195303	1		341	408	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880984	37880985	+	inframe_insertion	In_Frame_Ins	INS	-	-	TACGTGATGGCG	novel	NA	P-0017794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	215	714	0	ENST00000269571.5:c.2324_2325insGTACGTGATGGC	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/TACGTGATGGCG	20/27	0.313183397099503	2	FACETS	1	0.991	1	0.695	0.648	0.742	CLONAL	1	TRUE	0	0.437106877195303	2		714	708	SUCCESS
APC	324	MSKCC	GRCh37	5	112103087	112103087	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	42	306	0	ENST00000257430.4:c.422+1del		p.R141fs	ENST00000257430	NM_000038.5	141	aGg/ag	4/16	0.437106877195303	1	FACETS	0.507	0.426	0.597	0.507	0.426	0.597	SUBCLONAL	1	TRUE	0	0.437106877195303	1		306	296	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518278	187518278	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017794-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	90	280	1	ENST00000441802.2:c.12416G>T	p.Gly4139Val	p.G4139V	ENST00000441802	NM_005245.3	4139	gGg/gTg	25/27	0.532591456770277	3	FACETS	0.968	0.864	1	0.323	0.288	0.36	CLONAL	1	TRUE	0	0.57911294312274	3		281	414	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098570	108098570	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs774185390	NA	P-0017794-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	295	391	0	ENST00000278616.4:c.140C>G	p.Ser47Ter	p.S47*	ENST00000278616	NM_000051.3	47	tCa/tGa	3/63	0.565767365766889	2	FACETS	0.846	0.804	0.888	0.846	0.804	0.888	CLONAL	2	TRUE	0	0.57911294312274	2		391	602	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098599	108098599	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017794-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	248	341	0	ENST00000278616.4:c.169T>G	p.Trp57Gly	p.W57G	ENST00000278616	NM_000051.3	57	Tgg/Ggg	3/63	0.565767365766889	2	FACETS	0.851	0.806	0.897	0.851	0.806	0.897	CLONAL	2	TRUE	0	0.57911294312274	2		341	503	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880984	37880985	+	inframe_insertion	In_Frame_Ins	INS	-	-	TACGTGATGGCG	novel	NA	P-0017794-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	305	714	0	ENST00000269571.5:c.2324_2325insGTACGTGATGGC	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/TACGTGATGGCG	20/27	0.528442062887388	2	FACETS	0.791	0.751	0.831	0.791	0.751	0.831	SUBCLONAL	2	TRUE	0	0.57911294312274	2		714	666	SUCCESS
APC	324	MSKCC	GRCh37	5	112103087	112103087	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017794-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	122	306	0	ENST00000257430.4:c.422+1del		p.R141fs	ENST00000257430	NM_000038.5	141	aGg/ag	4/16	0.557262038976597	1	FACETS	0.891	0.816	0.968	0.891	0.816	0.968	CLONAL	1	TRUE	0	0.57911294312274	1		306	336	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425590	49425590	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017794-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	119	863	0	ENST00000301067.7:c.12898C>A	p.Pro4300Thr	p.P4300T	ENST00000301067	NM_003482.3	4300	Cca/Aca	39/54	0.532591456770277	3	FACETS	0.526	0.474	0.582	0.175	0.158	0.194	SUBCLONAL	1	TRUE	0	0.57911294312274	3		863	1007	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227986	55227986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769434273	NA	P-0017794-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	92	524	1	ENST00000275493.2:c.1453G>A	p.Gly485Ser	p.G485S	ENST00000275493	NM_005228.3	485	Ggt/Agt	12/28	0.57911294312274	3	FACETS	0.422	0.374	0.473	0.211	0.187	0.237	SUBCLONAL	1	TRUE	1	0.57911294312274	3		525	971	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	49	800	0				ENST00000310581	NM_198253.2	-/1132			0.197340472113853	3	FACETS	1	0.868	1	0.512	0.435	0.597	CLONAL	1	TRUE	1	0.27	3		800	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203436	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	107	1050	0	ENST00000269305.4:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269305	NM_001126112.2	163	Tac/Cac	5/11	0.263065677460604	2	FACETS	0.785	0.707	0.866	0.785	0.707	0.866	SUBCLONAL	2	TRUE	0	0.27	2		1050	505	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584582	189584582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	37	522	0	ENST00000264731.3:c.878C>T	p.Pro293Leu	p.P293L	ENST00000264731	NM_003722.4	293	cCc/cTc	6/14	1	2	FACETS	0.56	0.462	0.671	0.56	0.462	0.671	SUBCLONAL	1	TRUE	1	0.27	2		522	489	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188182	11188182	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	75	676	1	ENST00000361445.4:c.5912C>T	p.Ala1971Val	p.A1971V	ENST00000361445	NM_004958.3	1971	gCc/gTc	43/58	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.27	2		677	480	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458252	120458253	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	69	922	2	ENST00000256646.2:c.7092_7093delinsAA	p.Val2365Ile	p.V2365I	ENST00000256646	NM_024408.3	2364	caGGta/caAAta	34/34	1	2	FACETS	0.911	0.794	1	0.911	0.794	1	CLONAL	1	TRUE	1	0.27	2		924	561	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466441	120466441	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	83	900	0	ENST00000256646.2:c.4678C>T	p.Gln1560Ter	p.Q1560*	ENST00000256646	NM_024408.3	1560	Cag/Tag	26/34	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.27	2		900	612	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333279	70333279	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs770120735	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	84	916	1	ENST00000373644.4:c.1184T>C	p.Leu395Pro	p.L395P	ENST00000373644	NM_030625.2	395	cTa/cCa	2/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.27	2		917	497	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903742	114903742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	43	862	0	ENST00000543371.1:c.746C>T	p.Thr249Ile	p.T249I	ENST00000543371	NM_001198531.1	249	aCc/aTc	7/14	1	2	FACETS	0.512	0.428	0.606	0.512	0.428	0.606	SUBCLONAL	1	TRUE	1	0.27	2		862	622	SUCCESS
EED	8726	MSKCC	GRCh37	11	85967484	85967484	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	35	644	3	ENST00000263360.6:c.482C>T	p.Pro161Leu	p.P161L	ENST00000263360	NM_003797.3	161	cCt/cTt	5/12	1	2	FACETS	0.592	0.485	0.712	0.592	0.485	0.712	SUBCLONAL	1	TRUE	1	0.27	2		647	438	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125523648	125523648	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	67	586	0	ENST00000428830.2:c.1241T>C	p.Ile414Thr	p.I414T	ENST00000428830	NM_001114121.2	414	aTa/aCa	12/14	1	2	FACETS	0.942	0.82	1	0.942	0.82	1	CLONAL	1	TRUE	1	0.27	2		586	527	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245951	46245951	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	35	467	0	ENST00000334344.6:c.4045A>T	p.Ile1349Phe	p.I1349F	ENST00000334344	NM_152641.2	1349	Atc/Ttc	15/21	1	2	FACETS	0.566	0.464	0.681	0.566	0.464	0.681	SUBCLONAL	1	TRUE	1	0.27	2		467	458	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660604	67660604	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	93	939	0	ENST00000264010.4:c.1504T>C	p.Tyr502His	p.Y502H	ENST00000264010	NM_006565.3	502	Tac/Cac	8/12	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.27	2		939	592	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771333	68771334	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	29	597	1	ENST00000261769.5:c.15_16delinsTT	p.Arg6Cys	p.R6C	ENST00000261769	NM_004360.3	5	agCCgc/agTTgc	1/16	1	2	FACETS	0.59	0.474	0.722	0.59	0.474	0.722	SUBCLONAL	1	TRUE	1	0.27	2		598	364	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763397	59763397	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060501781	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	182	1072	0	ENST00000259008.2:c.2705T>C	p.Ile902Thr	p.I902T	ENST00000259008	NM_032043.2	902	aTa/aCa	19/20	0.263065677460604	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.27	2		1072	584	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727858	78727859	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	33	1074	3	ENST00000306801.3:c.703_704delinsTT	p.Pro235Leu	p.P235L	ENST00000306801	NM_020761.2	235	CCg/TTg	6/34	0.263065677460604	2	FACETS	0.391	0.317	0.475	0.196	0.158	0.238	SUBCLONAL	1	TRUE	0	0.27	2		1077	625	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78765303	78765303	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	69	512	0	ENST00000306801.3:c.884T>A	p.Ile295Lys	p.I295K	ENST00000306801	NM_020761.2	295	aTa/aAa	7/34	0.263065677460604	2	FACETS	0.765	0.671	0.865	0.765	0.671	0.865	SUBCLONAL	2	TRUE	0	0.27	2		512	334	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273502	5273502	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	89	1066	0	ENST00000357368.4:c.330G>C	p.Gln110His	p.Q110H	ENST00000357368	NM_002850.3	110	caG/caC	4/38	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.27	2		1066	637	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705643	47705643	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	72	549	0	ENST00000233146.2:c.2443T>A	p.Tyr815Asn	p.Y815N	ENST00000233146	NM_000251.2	815	Tat/Aat	14/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.27	2		549	417	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023127	31023127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	58	709	0	ENST00000375687.4:c.2612C>T	p.Ser871Leu	p.S871L	ENST00000375687	NM_015338.5	871	tCa/tTa	13/13	1	2	FACETS	0.78	0.67	0.899	0.78	0.67	0.899	SUBCLONAL	1	TRUE	1	0.27	2		709	551	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574564	41574564	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	83	1079	2	ENST00000263253.7:c.6849T>A	p.His2283Gln	p.H2283Q	ENST00000263253	NM_001429.3	2283	caT/caA	31/31	1	2	FACETS	0.95	0.839	1	0.95	0.839	1	CLONAL	1	TRUE	1	0.27	2		1081	647	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643461	52643461	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	69	738	0	ENST00000394830.3:c.2435C>T	p.Pro812Leu	p.P812L	ENST00000394830	NM_018313.4	812	cCc/cTc	17/30	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.27	2		738	468	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281123	142281123	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	38	561	0	ENST00000350721.4:c.1121A>T	p.Asn374Ile	p.N374I	ENST00000350721	NM_001184.3	374	aAt/aTt	4/47	1	2	FACETS	0.612	0.506	0.731	0.612	0.506	0.731	SUBCLONAL	1	TRUE	1	0.27	2		561	460	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169985790	169985790	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	72	718	0	ENST00000295797.4:c.450+2T>C		p.X150_splice	ENST00000295797	NM_002740.5	150			1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.27	2		718	509	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807564	1807565	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	29	1148	1	ENST00000260795.2:c.1733_1734delinsTT	p.Ser578Phe	p.S578F	ENST00000260795		578	tCC/tTT	12/17	0.265995693436187	1	FACETS	0.401	0.321	0.492	0.401	0.321	0.492	SUBCLONAL	1	TRUE	0	0.27	1		1149	463	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159015	143159015	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	15	518	0	ENST00000262992.4:c.836+2T>G		p.X279_splice	ENST00000262992	NM_001101669.1	279			1	2	FACETS	0.372	0.271	0.493	0.372	0.271	0.493	SUBCLONAL	1	TRUE	1	0.27	2		518	299	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279584	1279584	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	114	1078	1	ENST00000310581.5:c.1952C>T	p.Ala651Val	p.A651V	ENST00000310581	NM_198253.2	651	gCc/gTc	5/16	NA	2	FACETS	0.785	0.709	0.864			1	INDETERMINATE	2	TRUE	NA	0.27	2		1079	538	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591318	67591318	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	66	352	0	ENST00000274335.5:c.1814+2T>G		p.X605_splice	ENST00000274335		605			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.27	2		352	403	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178581	32178581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	115	1009	1	ENST00000375023.3:c.2813C>T	p.Pro938Leu	p.P938L	ENST00000375023	NM_004557.3	938	cCt/cTt	18/30	0.224007187574752	4	FACETS	0.784	0.707	0.865	0.784	0.707	0.865	SUBCLONAL	2	TRUE	2	0.27	4		1010	690	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967976	93967976	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571637670	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	25	713	0	ENST00000369303.4:c.1951C>T	p.Arg651Cys	p.R651C	ENST00000369303	NM_004440.3	651	Cgt/Tgt	11/17	0.200962999476844	2	FACETS	0.4	0.314	0.499	0.2	0.157	0.25	SUBCLONAL	1	TRUE	0	0.27	2		713	463	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674200	117674200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	48	941	0	ENST00000368508.3:c.4274G>A	p.Arg1425Lys	p.R1425K	ENST00000368508	NM_002944.2	1425	aGg/aAg	26/43	0.200962999476844	2	FACETS	0.572	0.482	0.67	0.286	0.241	0.335	SUBCLONAL	1	TRUE	0	0.27	2		941	622	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162945	38162945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs185811622	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	78	722	1	ENST00000317025.8:c.2261C>T	p.Ser754Leu	p.S754L	ENST00000317025	NM_023034.1	754	tCg/tTg	13/24	1	2	FACETS	0.958	0.843	1	0.958	0.843	1	CLONAL	1	TRUE	1	0.27	2		723	603	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341088	8341088	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	53	646	0	ENST00000356435.5:c.5126+2T>C		p.X1709_splice	ENST00000356435		1709			0.197340472113853	3	FACETS	0.895	0.764	1	0.447	0.382	0.519	CLONAL	1	TRUE	1	0.27	3		646	498	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482302	87482302	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	60	892	1	ENST00000277120.3:c.1589C>T	p.Pro530Leu	p.P530L	ENST00000277120		530	cCc/cTc	14/19	0.295562622642265	1	FACETS	0.783	0.676	0.9	0.783	0.676	0.9	SUBCLONAL	1	TRUE	0	0.27	1		893	491	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218556	98218556	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	66	565	0	ENST00000331920.6:c.3306+2T>C		p.X1102_splice	ENST00000331920	NM_000264.3	1102			0.295562622642265	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.27	1		565	347	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238322	98238323	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	56	515	3	ENST00000331920.6:c.1721_1722delinsTT	p.Ser574Phe	p.S574F	ENST00000331920	NM_000264.3	574	tCC/tTT	12/24	0.295562622642265	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.27	1		518	323	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128246829	128246829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1389464216	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	39	1001	0	ENST00000265960.3:c.1100C>T	p.Ser367Leu	p.S367L	ENST00000265960	NM_001006617.1	367	tCg/tTg	9/12	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.27	NA		1001	587	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395193	139395193	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	115	1086	2	ENST00000277541.6:c.5745C>A	p.Tyr1915Ter	p.Y1915*	ENST00000277541	NM_017617.3	1915	taC/taA	31/34	0.295562622642265	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.27	1		1088	521	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932480	39932480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	41	460	0	ENST00000378444.4:c.2119C>T	p.Pro707Ser	p.P707S	ENST00000378444	NM_001123385.1	707	Ccc/Tcc	4/15	1	1	FACETS	0.928	0.777	1	0.928	0.777	1	CLONAL	1	TRUE	0	0.27	1		460	283	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	189	800	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.937	0.868	1	0.937	0.868	1	CLONAL	1	TRUE	1	0.502264882596068	2		800	803	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203436	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	678	1050	0	ENST00000269305.4:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269305	NM_001126112.2	163	Tac/Cac	5/11	0.502264882596068	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.502264882596068	2		1050	1191	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584582	189584582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	79	522	0	ENST00000264731.3:c.878C>T	p.Pro293Leu	p.P293L	ENST00000264731	NM_003722.4	293	cCc/cTc	6/14	0.362122769136196	1	FACETS	0.398	0.35	0.449	0.398	0.35	0.449	SUBCLONAL	1	TRUE	0	0.502264882596068	1		522	592	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188182	11188182	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	219	676	1	ENST00000361445.4:c.5912C>T	p.Ala1971Val	p.A1971V	ENST00000361445	NM_004958.3	1971	gCc/gTc	43/58	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.502264882596068	2		677	680	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458252	120458253	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	244	922	2	ENST00000256646.2:c.7092_7093delinsAA	p.Val2365Ile	p.V2365I	ENST00000256646	NM_024408.3	2364	caGGta/caAAta	34/34	1	2	FACETS	0.999	0.934	1	0.999	0.934	1	CLONAL	1	TRUE	1	0.502264882596068	2		924	973	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466441	120466441	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	291	900	0	ENST00000256646.2:c.4678C>T	p.Gln1560Ter	p.Q1560*	ENST00000256646	NM_024408.3	1560	Cag/Tag	26/34	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.502264882596068	2		900	1055	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333279	70333279	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs770120735	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	271	916	1	ENST00000373644.4:c.1184T>C	p.Leu395Pro	p.L395P	ENST00000373644	NM_030625.2	395	cTa/cCa	2/12	0.392392480463327	1	FACETS	0.859	0.807	0.912	0.859	0.807	0.912	CLONAL	1	TRUE	0	0.502264882596068	1		917	941	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903742	114903742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	118	862	0	ENST00000543371.1:c.746C>T	p.Thr249Ile	p.T249I	ENST00000543371	NM_001198531.1	249	aCc/aTc	7/14	0.392392480463327	1	FACETS	0.396	0.357	0.438	0.396	0.357	0.438	SUBCLONAL	1	TRUE	0	0.502264882596068	1		862	888	SUCCESS
EED	8726	MSKCC	GRCh37	11	85967484	85967484	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	87	644	3	ENST00000263360.6:c.482C>T	p.Pro161Leu	p.P161L	ENST00000263360	NM_003797.3	161	cCt/cTt	5/12	1	2	FACETS	0.449	0.397	0.504	0.449	0.397	0.504	SUBCLONAL	1	TRUE	1	0.502264882596068	2		647	772	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125523648	125523648	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	179	586	0	ENST00000428830.2:c.1241T>C	p.Ile414Thr	p.I414T	ENST00000428830	NM_001114121.2	414	aTa/aCa	12/14	1	2	FACETS	0.929	0.858	1	0.929	0.858	1	CLONAL	1	TRUE	1	0.502264882596068	2		586	767	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245951	46245951	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	98	467	0	ENST00000334344.6:c.4045A>T	p.Ile1349Phe	p.I1349F	ENST00000334344	NM_152641.2	1349	Atc/Ttc	15/21	0.362122769136196	1	FACETS	0.512	0.457	0.569	0.512	0.457	0.569	SUBCLONAL	1	TRUE	0	0.502264882596068	1		467	571	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660604	67660604	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	300	939	0	ENST00000264010.4:c.1504T>C	p.Tyr502His	p.Y502H	ENST00000264010	NM_006565.3	502	Tac/Cac	8/12	1	2	FACETS	0.96	0.904	1	0.96	0.904	1	CLONAL	1	TRUE	1	0.502264882596068	2		939	1244	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771333	68771334	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	107	597	1	ENST00000261769.5:c.15_16delinsTT	p.Arg6Cys	p.R6C	ENST00000261769	NM_004360.3	5	agCCgc/agTTgc	1/16	1	2	FACETS	0.665	0.597	0.736	0.665	0.597	0.736	SUBCLONAL	1	TRUE	1	0.502264882596068	2		598	641	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763397	59763397	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060501781	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	565	1072	0	ENST00000259008.2:c.2705T>C	p.Ile902Thr	p.I902T	ENST00000259008	NM_032043.2	902	aTa/aCa	19/20	0.502264882596068	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.502264882596068	2		1072	1046	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727858	78727859	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	180	1074	3	ENST00000306801.3:c.703_704delinsTT	p.Pro235Leu	p.P235L	ENST00000306801	NM_020761.2	235	CCg/TTg	6/34	0.502264882596068	2	FACETS	0.562	0.517	0.609	0.281	0.258	0.305	SUBCLONAL	1	TRUE	0	0.502264882596068	2		1077	1275	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78765303	78765303	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	371	512	0	ENST00000306801.3:c.884T>A	p.Ile295Lys	p.I295K	ENST00000306801	NM_020761.2	295	aTa/aAa	7/34	0.502264882596068	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.502264882596068	2		512	696	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273502	5273502	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	343	1066	0	ENST00000357368.4:c.330G>C	p.Gln110His	p.Q110H	ENST00000357368	NM_002850.3	110	caG/caC	4/38	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.502264882596068	2		1066	1352	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705643	47705643	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	161	549	0	ENST00000233146.2:c.2443T>A	p.Tyr815Asn	p.Y815N	ENST00000233146	NM_000251.2	815	Tat/Aat	14/16	0.362122769136196	1	FACETS	0.86	0.794	0.929	0.86	0.794	0.929	CLONAL	1	TRUE	0	0.502264882596068	1		549	558	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023127	31023127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	275	709	0	ENST00000375687.4:c.2612C>T	p.Ser871Leu	p.S871L	ENST00000375687	NM_015338.5	871	tCa/tTa	13/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.502264882596068	2		709	957	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574564	41574564	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	258	1079	2	ENST00000263253.7:c.6849T>A	p.His2283Gln	p.H2283Q	ENST00000263253	NM_001429.3	2283	caT/caA	31/31	NA	2	FACETS	0.927	0.868	0.988			1	INDETERMINATE	1	TRUE	NA	0.502264882596068	2		1081	1108	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643461	52643461	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	228	738	0	ENST00000394830.3:c.2435C>T	p.Pro812Leu	p.P812L	ENST00000394830	NM_018313.4	812	cCc/cTc	17/30	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.502264882596068	2		738	771	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281123	142281123	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	84	561	0	ENST00000350721.4:c.1121A>T	p.Asn374Ile	p.N374I	ENST00000350721	NM_001184.3	374	aAt/aTt	4/47	0.362122769136196	1	FACETS	0.358	0.316	0.404	0.358	0.316	0.404	SUBCLONAL	1	TRUE	0	0.502264882596068	1		561	699	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169985790	169985790	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	281	718	0	ENST00000295797.4:c.450+2T>C		p.X150_splice	ENST00000295797	NM_002740.5	150			0.362122769136196	1	FACETS	0.935	0.881	0.991	0.935	0.881	0.991	CLONAL	1	TRUE	0	0.502264882596068	1		718	896	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807564	1807565	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	138	1148	1	ENST00000260795.2:c.1733_1734delinsTT	p.Ser578Phe	p.S578F	ENST00000260795		578	tCC/tTT	12/17	0.392392480463327	1	FACETS	0.429	0.389	0.47	0.429	0.389	0.47	SUBCLONAL	1	TRUE	0	0.502264882596068	1		1149	960	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159015	143159015	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	64	518	0	ENST00000262992.4:c.836+2T>G		p.X279_splice	ENST00000262992	NM_001101669.1	279			0.392392480463327	1	FACETS	0.436	0.378	0.498	0.436	0.378	0.498	SUBCLONAL	1	TRUE	0	0.502264882596068	1		518	438	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279584	1279584	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	440	1078	1	ENST00000310581.5:c.1952C>T	p.Ala651Val	p.A651V	ENST00000310581	NM_198253.2	651	gCc/gTc	5/16	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.502264882596068	2		1079	1245	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591318	67591318	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	162	352	0	ENST00000274335.5:c.1814+2T>G		p.X605_splice	ENST00000274335		605			0.338886946182482	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.502264882596068	1		352	480	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178581	32178581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	514	1009	1	ENST00000375023.3:c.2813C>T	p.Pro938Leu	p.P938L	ENST00000375023	NM_004557.3	938	cCt/cTt	18/30	0.263472739597233	5	FACETS	1	0.992	1	0.755	0.722	0.788	INDETERMINATE	2	TRUE	2	0.502264882596068	5		1010	1585	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967976	93967976	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571637670	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	111	713	0	ENST00000369303.4:c.1951C>T	p.Arg651Cys	p.R651C	ENST00000369303	NM_004440.3	651	Cgt/Tgt	11/17	0.502264882596068	2	FACETS	0.573	0.515	0.635	0.287	0.257	0.318	SUBCLONAL	1	TRUE	0	0.502264882596068	2		713	771	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674200	117674200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	147	941	0	ENST00000368508.3:c.4274G>A	p.Arg1425Lys	p.R1425K	ENST00000368508	NM_002944.2	1425	aGg/aAg	26/43	0.502264882596068	2	FACETS	0.578	0.527	0.632	0.289	0.263	0.316	SUBCLONAL	1	TRUE	0	0.502264882596068	2		941	1012	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341088	8341088	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	198	646	0	ENST00000356435.5:c.5126+2T>C		p.X1709_splice	ENST00000356435		1709			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.502264882596068	2		646	688	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482302	87482302	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	168	892	1	ENST00000277120.3:c.1589C>T	p.Pro530Leu	p.P530L	ENST00000277120		530	cCc/cTc	14/19	0.502264882596068	1	FACETS	0.67	0.617	0.725	0.67	0.617	0.725	SUBCLONAL	1	TRUE	0	0.502264882596068	1		893	748	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218556	98218556	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	209	565	0	ENST00000331920.6:c.3306+2T>C		p.X1102_splice	ENST00000331920	NM_000264.3	1102			0.502264882596068	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.502264882596068	1		565	514	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238322	98238323	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	157	515	3	ENST00000331920.6:c.1721_1722delinsTT	p.Ser574Phe	p.S574F	ENST00000331920	NM_000264.3	574	tCC/tTT	12/24	0.502264882596068	1	FACETS	0.988	0.912	1	0.988	0.912	1	CLONAL	1	TRUE	0	0.502264882596068	1		518	474	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128246829	128246829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1389464216	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	150	1001	0	ENST00000265960.3:c.1100C>T	p.Ser367Leu	p.S367L	ENST00000265960	NM_001006617.1	367	tCg/tTg	9/12	0.502264882596068	2	FACETS	0.531	0.484	0.58	0.265	0.242	0.29	SUBCLONAL	1	TRUE	0	0.502264882596068	2		1001	1125	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395193	139395193	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	617	1086	2	ENST00000277541.6:c.5745C>A	p.Tyr1915Ter	p.Y1915*	ENST00000277541	NM_017617.3	1915	taC/taA	31/34	0.502264882596068	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.502264882596068	2		1088	1107	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932480	39932480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	155	460	0	ENST00000378444.4:c.2119C>T	p.Pro707Ser	p.P707S	ENST00000378444	NM_001123385.1	707	Ccc/Tcc	4/15	1	1	FACETS	0.824	0.758	0.892	0.824	0.758	0.892	CLONAL	1	TRUE	0	0.502264882596068	1		460	561	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537981	212537981	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs535202189	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	108	559	0	ENST00000342788.4:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000342788	NM_005235.2	542	Gaa/Aaa	14/28	0.362122769136196	1	FACETS	0.538	0.483	0.595	0.538	0.483	0.595	SUBCLONAL	1	TRUE	0	0.502264882596068	1		559	599	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727859	78727859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778541724	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	178	1066	3	ENST00000306801.3:c.704C>T	p.Pro235Leu	p.P235L	ENST00000306801	NM_020761.2	235	cCg/cTg	6/34	0.502264882596068	2	FACETS	0.562	0.517	0.61	0.281	0.258	0.305	SUBCLONAL	1	TRUE	0	0.502264882596068	2		1069	1261	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964876	55964877	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	87	544	2	ENST00000263923.4:c.2360_2361delinsAA	p.Arg787Gln	p.R787Q	ENST00000263923	NM_002253.2	787	cGG/cAA	16/30	0.392392480463327	1	FACETS	0.404	0.358	0.454	0.404	0.358	0.454	SUBCLONAL	1	TRUE	0	0.502264882596068	1		546	642	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673376	30673376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1325	148	898	1	ENST00000376406.3:c.3584C>T	p.Ser1195Phe	p.S1195F	ENST00000376406	NM_014641.2	1195	tCt/tTt	10/15	0.263472739597233	5	FACETS	0.702	0.638	0.768	0.234	0.212	0.256	INDETERMINATE	1	TRUE	2	0.502264882596068	5		899	1473	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090524	5090524	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	84	620	0	ENST00000381652.3:c.2840G>T	p.Arg947Leu	p.R947L	ENST00000381652	NM_004972.3	947	cGg/cTg	21/25	1	2	FACETS	0.412	0.363	0.464	0.412	0.363	0.464	SUBCLONAL	1	TRUE	1	0.502264882596068	2		620	812	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0020042-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	774	509	1				ENST00000310581	NM_198253.2	-/1132			0.867752360450404	3	FACETS	1	0.993	1			1	CLONAL	3	TRUE	NA	0.877166184705473	3		510	838	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546683	9546683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020042-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	195	489	0	ENST00000353224.5:c.1339G>A	p.Glu447Lys	p.E447K	ENST00000353224	NM_177990.2	447	Gaa/Aaa	5/10	1	2	FACETS	0.971	0.909	1	0.971	0.909	1	CLONAL	1	TRUE	1	0.877166184705473	2		489	458	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793008	33793010	+	inframe_deletion	In_Frame_Del	DEL	CGC	CGC	-	rs780345232	NA	P-0020042-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	10	132	0	ENST00000498907.2:c.311_313del	p.Gly104del	p.G104del	ENST00000498907	NM_004364.3	104	gGCGac/gac	1/1	1	2	FACETS	0.125	0.085	0.176	0.125	0.085	0.176	SUBCLONAL	1	TRUE	1	0.877166184705473	2		132	182	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400190	41400190	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020042-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	230	511	0	ENST00000373198.4:c.569G>A	p.Arg190Lys	p.R190K	ENST00000373198	NM_133170.3	190	aGa/aAa	5/32	1	2	FACETS	0.96	0.904	1	0.96	0.904	1	CLONAL	1	TRUE	1	0.877166184705473	2		511	546	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463248	25463248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754613602	NA	P-0020042-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	359	748	0	ENST00000264709.3:c.2245C>T	p.Arg749Cys	p.R749C	ENST00000264709	NM_175629.2	749	Cgc/Tgc	19/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.877166184705473	2		748	800	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18762480	18762480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020042-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	104	380	0	ENST00000266497.5:c.3976C>T	p.Pro1326Ser	p.P1326S	ENST00000266497		1326	Cca/Tca	29/31	1	2	FACETS	0.758	0.687	0.831	0.758	0.687	0.831	SUBCLONAL	1	TRUE	1	0.877166184705473	2		380	313	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237724	133237724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020042-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	639	542	0	ENST00000320574.5:c.2891C>T	p.Ser964Phe	p.S964F	ENST00000320574	NM_006231.2	964	tCt/tTt	25/49	0.877166184705473	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.877166184705473	3		542	998	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134000	41134000	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020042-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	338	665	0	ENST00000379561.5:c.1628T>G	p.Val543Gly	p.V543G	ENST00000379561	NM_002015.3	543	gTa/gGa	2/3	1	2	FACETS	0.98	0.933	1	0.98	0.933	1	CLONAL	1	TRUE	1	0.877166184705473	2		665	786	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346345	73346345	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020042-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	113	370	0	ENST00000377767.4:c.1455T>A	p.Asp485Glu	p.D485E	ENST00000377767	NM_014953.3	485	gaT/gaA	10/21	1	2	FACETS	0.91	0.833	0.99	0.91	0.833	0.99	CLONAL	1	TRUE	1	0.877166184705473	2		370	283	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871818	35871818	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020042-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	375	692	2	ENST00000216797.5:c.688C>T	p.Pro230Ser	p.P230S	ENST00000216797	NM_020529.2	230	Cct/Tct	5/6	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.877166184705473	2		694	802	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643608	38643608	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0020042-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	510	544	0	ENST00000299084.4:c.1078A>T	p.Lys360Ter	p.K360*	ENST00000299084	NM_152594.2	360	Aaa/Taa	7/7	0.876150950348575	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.877166184705473	2		544	578	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032269	10032269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020042-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	288	715	0	ENST00000330684.3:c.554G>A	p.Ser185Asn	p.S185N	ENST00000330684	NM_001134407.1	185	aGc/aAc	3/13	1	2	FACETS	0.979	0.927	1	0.979	0.927	1	CLONAL	1	TRUE	1	0.877166184705473	2		715	671	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553592	29553592	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020042-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	133	276	0	ENST00000356175.3:c.2141del	p.Cys714LeufsTer34	p.C714Lfs*34	ENST00000356175	NM_000267.3	714	tGt/tt	18/57	1	2	FACETS	0.936	0.863	1	0.936	0.863	1	CLONAL	1	TRUE	1	0.877166184705473	2		276	324	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211134	2211134	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020042-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	524	1133	0	ENST00000398665.3:c.1388T>C	p.Leu463Pro	p.L463P	ENST00000398665	NM_032482.2	463	cTa/cCa	15/28	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.877166184705473	2		1133	1140	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609686	46609686	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020042-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	437	965	0	ENST00000263734.3:c.2410T>C	p.Tyr804His	p.Y804H	ENST00000263734	NM_001430.4	804	Tac/Cac	15/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.877166184705473	2		965	988	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881453	111881453	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs988452389	NA	P-0020042-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	285	626	0	ENST00000393256.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000393256	NM_006538.4	44	cCt/cTt	2/4	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.877166184705473	2		626	636	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374408	31374408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762297902	NA	P-0020042-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	406	812	1	ENST00000328111.2:c.407C>T	p.Ser136Phe	p.S136F	ENST00000328111	NM_006892.3	136	tCc/tTc	5/23	1	2	FACETS	0.942	0.899	0.985	0.942	0.899	0.985	CLONAL	1	TRUE	1	0.877166184705473	2		813	983	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750432	39750432	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0020042-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	152	373	0	ENST00000361337.2:c.2045+2T>G		p.X682_splice	ENST00000361337	NM_003286.2	682			1	2	FACETS	0.907	0.84	0.975	0.907	0.84	0.975	CLONAL	1	TRUE	1	0.877166184705473	2		373	382	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588893	52588893	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020042-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	256	582	0	ENST00000394830.3:c.4135A>T	p.Met1379Leu	p.M1379L	ENST00000394830	NM_018313.4	1379	Atg/Ttg	27/30	1	2	FACETS	0.875	0.824	0.927	0.875	0.824	0.927	CLONAL	1	TRUE	1	0.877166184705473	2		582	667	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668661	52668661	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020042-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	269	513	0	ENST00000394830.3:c.1258T>A	p.Tyr420Asn	p.Y420N	ENST00000394830	NM_018313.4	420	Tat/Aat	12/30	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.877166184705473	2		513	560	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143235881	143235882	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020042-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	125	366	1	ENST00000262992.4:c.406_407delinsTT	p.Pro136Phe	p.P136F	ENST00000262992	NM_001101669.1	136	CCc/TTc	6/24	1	2	FACETS	0.826	0.757	0.897	0.826	0.757	0.897	CLONAL	1	TRUE	1	0.877166184705473	2		367	345	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117645506	117645507	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020042-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	138	520	1	ENST00000368508.3:c.5629_5630delinsTT	p.Pro1877Leu	p.P1877L	ENST00000368508	NM_002944.2	1877	CCa/TTa	34/43	0.877166184705473	1	FACETS	0.906	0.855	0.954	0.906	0.855	0.954	CLONAL	1	TRUE	0	0.877166184705473	1		521	195	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38184326	38184326	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020042-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	234	586	0	ENST00000317025.8:c.1630A>T	p.Ile544Leu	p.I544L	ENST00000317025	NM_023034.1	544	Ata/Tta	7/24	1	2	FACETS	0.934	0.879	0.99	0.934	0.879	0.99	CLONAL	1	TRUE	1	0.877166184705473	2		586	571	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187031	38187032	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020042-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	367	799	0	ENST00000317025.8:c.1445_1446delinsTT	p.Ser482Phe	p.S482F	ENST00000317025	NM_023034.1	482	tCC/tTT	6/24	1	2	FACETS	0.944	0.9	0.99	0.944	0.9	0.99	CLONAL	1	TRUE	1	0.877166184705473	2		799	886	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0020246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	375	847	1	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.355283035132657	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.355283035132657	2		848	962	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380350	14380350	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	269	249	0	ENST00000256196.4:c.67G>T	p.Gly23Cys	p.G23C	ENST00000256196		23	Ggc/Tgc	1/6	0.337328751609042	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.355283035132657	2		249	645	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931770	39931771	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0020246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	173	448	1	ENST00000378444.4:c.2828_2829delinsAT	p.Gly943Asp	p.G943D	ENST00000378444	NM_001123385.1	943	gGA/gAT	4/15	1	1	FACETS	0.848	0.788	0.91	1	0.992	1	CLONAL	2	TRUE	0	0.355283035132657	1		449	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0020698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	205	677	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.221676069355769	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	FALSE	0	0.221676069355769	2		678	768	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131895017	131895017	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	35	572	0	ENST00000265335.6:c.171C>G	p.Phe57Leu	p.F57L	ENST00000265335		57	ttC/ttG	2/25	0.221676069355769	4	FACETS	0.943	0.774	1	0.314	0.258	0.378	CLONAL	1	FALSE	1	0.221676069355769	4		572	409	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056167	26056167	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs375244851	NA	P-0020698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	67	755	0	ENST00000343677.2:c.490G>T	p.Ala164Ser	p.A164S	ENST00000343677	NM_005319.3	164	Gcc/Tcc	1/1	0.221676069355769	9	FACETS	1	0.967	1			1	CLONAL	1	FALSE	NA	0.221676069355769	9		755	770	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606353	93606353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	53	979	0	ENST00000375746.1:c.173G>A	p.Gly58Glu	p.G58E	ENST00000375746	NM_001174167.1	58	gGg/gAg	2/14	0.221676069355769	1	FACETS	0.811	0.692	0.942	0.811	0.692	0.942	CLONAL	1	FALSE	0	0.221676069355769	1		979	524	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0021151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	37	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.747	0.614	0.897	0.747	0.614	0.897	SUBCLONAL	1	TRUE	1	0.13	2		485	762	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0021151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	39	518	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.778	0.643	0.93	0.778	0.643	0.93	CLONAL	1	TRUE	1	0.13	2		518	771	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736325	243736325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	34	707	0	ENST00000263826.5:c.722G>A	p.Arg241Gln	p.R241Q	ENST00000263826	NM_005465.4	241	cGg/cAg	8/13	0.24129215660388	3	FACETS	0.473	0.386	0.573	0.237	0.193	0.287	SUBCLONAL	1	TRUE	1	0.24129215660388	3		707	667	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0021660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	12	349	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.116	0.081	0.16	0.116	0.081	0.16	SUBCLONAL	1	TRUE	1	0.377179912295769	2		349	549	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	121	812	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.377179912295769	2		812	616	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032510	12032510	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	98	484	0	ENST00000353533.5:c.946C>T	p.Gln316Ter	p.Q316*	ENST00000353533	NM_003010.3	316	Caa/Taa	9/11	0.377179912295769	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.377179912295769	1		484	353	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434810	49434810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1228231026	NA	P-0021660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	194	1155	0	ENST00000301067.7:c.6743G>A	p.Arg2248His	p.R2248H	ENST00000301067	NM_003482.3	2248	cGc/cAc	31/54	1	2	FACETS	0.953	0.881	1	0.953	0.881	1	CLONAL	1	TRUE	1	0.377179912295769	2		1155	1079	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063669	67063669	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	117	599	1	ENST00000412916.2:c.118C>A	p.Arg40Ser	p.R40S	ENST00000412916		40	Cgc/Agc	2/6	0.377179912295769	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.377179912295769	1		600	480	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15984008	15984008	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	99	490	1	ENST00000268712.3:c.3211C>T	p.Gln1071Ter	p.Q1071*	ENST00000268712	NM_006311.3	1071	Cag/Tag	24/46	0.377179912295769	1	FACETS	0.984	0.884	1	0.984	0.884	1	CLONAL	1	TRUE	0	0.377179912295769	1		491	433	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021757	71021757	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	103	712	0	ENST00000318789.4:c.1601G>A	p.Trp534Ter	p.W534*	ENST00000318789	NM_032682.5	534	tGg/tAg	18/21	1	2	FACETS	0.895	0.803	0.993	0.895	0.803	0.993	CLONAL	1	TRUE	1	0.377179912295769	2		712	610	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900138	151900138	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	77	570	0	ENST00000262189.6:c.3973C>T	p.Gln1325Ter	p.Q1325*	ENST00000262189	NM_170606.2	1325	Cag/Tag	26/59	1	2	FACETS	0.93	0.82	1	0.93	0.82	1	CLONAL	1	TRUE	1	0.377179912295769	2		570	439	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0021691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	60	421	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.229587196078458	3	FACETS	0.87	0.749	1	0.435	0.374	0.501	CLONAL	1	TRUE	1	0.229587196078458	3		421	670	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0021691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	46	417	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.229587196078458	3	FACETS	0.824	0.694	0.968	0.412	0.347	0.484	CLONAL	1	TRUE	1	0.229587196078458	3		417	542	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569723	41569723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs952188763	NA	P-0021691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	48	591	0	ENST00000263253.7:c.4714G>A	p.Gly1572Arg	p.G1572R	ENST00000263253	NM_001429.3	1572	Ggg/Agg	29/31	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.229587196078458	2		591	384	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317703	163317703	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	58	465	0	ENST00000271452.3:c.1099A>C	p.Lys367Gln	p.K367Q	ENST00000271452	NM_145697.2	367	Aag/Cag	12/14	0.362565450761643	3	FACETS	0.857	0.738	0.986	0.429	0.369	0.493	CLONAL	1	TRUE	1	0.362565450761643	3		465	441	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370246	40370246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	345	1094	2	ENST00000293328.3:c.1092G>A	p.Met364Ile	p.M364I	ENST00000293328	NM_012448.3	364	atG/atA	9/19	0.260412617359376	4	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.362565450761643	4		1096	1168	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944566	32944566	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	190	307	0	ENST00000380152.3:c.8359C>G	p.Arg2787Gly	p.R2787G	ENST00000380152		2787	Cgc/Ggc	19/27	0.714651005412031	0	FACETS		NA	1			1	NA	1	TRUE	0	0.722666148595108	0		307	344	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944589	32944589	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs80359084	NA	P-0022156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	208	350	0	ENST00000380152.3:c.8382C>G	p.Phe2794Leu	p.F2794L	ENST00000380152		2794	ttC/ttG	19/27	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.722666148595108	NA		350	373	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936950	48936950	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0022156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	23	413	0	ENST00000267163.4:c.719-1G>A		p.X240_splice	ENST00000267163	NM_000321.2	240			0.717273609036063	1	FACETS	0.18	0.14	0.225	0.18	0.14	0.225	SUBCLONAL	1	TRUE	0	0.722666148595108	1		413	226	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058897	42058897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	26	499	0	ENST00000219905.7:c.8617G>A	p.Ala2873Thr	p.A2873T	ENST00000219905	NM_001164273.1	2873	Gca/Aca	24/24	0.587439736748702	1	FACETS	0.157	0.124	0.195	0.157	0.124	0.195	SUBCLONAL	1	TRUE	0	0.722666148595108	1		499	292	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591826	48591826	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	161	495	0	ENST00000342988.3:c.989A>T	p.Glu330Val	p.E330V	ENST00000342988	NM_005359.5	330	gAa/gTa	9/12	0.717273609036063	1	FACETS	0.995	0.933	1	0.995	0.933	1	CLONAL	1	TRUE	0	0.722666148595108	1		495	286	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268826	41268826	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	25	396	0	ENST00000349496.5:c.1064C>A	p.Pro355Gln	p.P355Q	ENST00000349496	NM_001904.3	355	cCg/cAg	7/15	1	2	FACETS	0.149	0.117	0.186	0.149	0.117	0.186	SUBCLONAL	1	TRUE	1	0.722666148595108	2		396	465	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992664	68992676	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	GTCTTTTTCTGTA	GTCTTTTTCTGTA	-	novel	NA	P-0022156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	40	636	0	ENST00000288368.4:c.1643-11_1644del		p.X548_splice	ENST00000288368	NM_024870.2	548			1	2	FACETS	0.214	0.177	0.255	0.214	0.177	0.255	SUBCLONAL	1	TRUE	1	0.722666148595108	2		636	517	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624605	93624605	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs746979231	NA	P-0022156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	118	494	0	ENST00000375746.1:c.696G>C	p.Lys232Asn	p.K232N	ENST00000375746	NM_001174167.1	232	aaG/aaC	4/14	1	2	FACETS	0.887	0.809	0.968	0.887	0.809	0.968	CLONAL	1	TRUE	1	0.722666148595108	2		494	368	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188804	32188821	+	inframe_deletion	In_Frame_Del	DEL	CTGGCAGGTGCCCCCATT	CTGGCAGGTGCCCCCATT	-	novel	NA	P-0022156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	35	932	0	ENST00000375023.3:c.733_750del	p.Asn245_Gln250del	p.N245_Q250del	ENST00000375023	NM_004557.3	245	AATGGGGGCACCTGCCAG/-	4/30	1	2	FACETS	0.199	0.163	0.24	0.199	0.163	0.24	SUBCLONAL	1	TRUE	1	0.722666148595108	2		932	486	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64286793	64286793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022156-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	14	304	0	ENST00000370651.3:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000370651	NM_003463.4	3	cGa/cAa	2/6	1	2	FACETS	0.197	0.142	0.263	0.197	0.142	0.263	SUBCLONAL	1	TRUE	1	0.704657516253766	2		304	202	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944566	32944566	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022156-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	77	307	0	ENST00000380152.3:c.8359C>G	p.Arg2787Gly	p.R2787G	ENST00000380152		2787	Cgc/Ggc	19/27	0.704657516253766	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.704657516253766	1		307	122	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944589	32944589	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs80359084	NA	P-0022156-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	95	350	0	ENST00000380152.3:c.8382C>G	p.Phe2794Leu	p.F2794L	ENST00000380152		2794	ttC/ttG	19/27	0.704657516253766	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.704657516253766	1		350	149	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591826	48591826	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022156-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	104	495	0	ENST00000342988.3:c.989A>T	p.Glu330Val	p.E330V	ENST00000342988	NM_005359.5	330	gAa/gTa	9/12	0.704657516253766	1	FACETS	0.933	0.857	1	0.933	0.857	1	CLONAL	1	TRUE	0	0.704657516253766	1		495	205	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268826	41268826	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022156-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	74	396	0	ENST00000349496.5:c.1064C>A	p.Pro355Gln	p.P355Q	ENST00000349496	NM_001904.3	355	cCg/cAg	7/15	1	2	FACETS	0.995	0.887	1	0.995	0.887	1	CLONAL	1	TRUE	1	0.704657516253766	2		396	211	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624605	93624605	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs746979231	NA	P-0022156-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	147	494	0	ENST00000375746.1:c.696G>C	p.Lys232Asn	p.K232N	ENST00000375746	NM_001174167.1	232	aaG/aaC	4/14	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.704657516253766	2		494	403	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40860910	40860910	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022156-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	31	364	0	ENST00000428826.2:c.1518G>C	p.Lys506Asn	p.K506N	ENST00000428826		506	aaG/aaC	14/21	0.704657516253766	1	FACETS	0.278	0.226	0.335	0.278	0.226	0.335	SUBCLONAL	1	TRUE	0	0.704657516253766	1		364	205	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272202	18272202	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022156-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	138	729	0	ENST00000222254.8:c.712G>T	p.Ala238Ser	p.A238S	ENST00000222254	NM_005027.3	238	Gcc/Tcc	6/16	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.704657516253766	2		729	381	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565852	55565852	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022156-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	91	383	0	ENST00000288135.5:c.676G>A	p.Gly226Arg	p.G226R	ENST00000288135	NM_000222.2	226	Ggg/Agg	4/21	0.104457819200561	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.704657516253766	0		383	296	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944562	40944562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868189942	NA	P-0022312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	63	335	1	ENST00000373198.4:c.1940C>T	p.Ser647Leu	p.S647L	ENST00000373198	NM_133170.3	647	tCg/tTg	12/32	0.301883042285735	3	FACETS	1	0.949	1	0.602	0.522	0.69	CLONAL	1	TRUE	1	0.24	3		336	488	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097712	27097713	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0022312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	68	455	0	ENST00000324856.7:c.3302_3303del	p.Tyr1101CysfsTer3	p.Y1101Cfs*3	ENST00000324856	NM_006015.4	1101	TAt/t	12/20	1	2	FACETS	0.866	0.754	0.989	0.866	0.754	0.989	CLONAL	1	TRUE	1	0.24	2		455	654	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111476	8111508	+	frameshift_variant	Frame_Shift_Del	DEL	AGACCACCACAACCACACTCTGGAGGAGGAATG	AGACCACCACAACCACACTCTGGAGGAGGAATG	TGGCATT	novel	NA	P-0022312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	66	396	2	ENST00000346208.3:c.962_994delinsTGGCATT	p.Gln321LeufsTer22	p.Q321Lfs*22	ENST00000346208		321	cAGACCACCACAACCACACTCTGGAGGAGGAATGcc/cTGGCATTcc	5/6	1	2	FACETS	0.921	0.8	1	0.921	0.8	1	CLONAL	1	TRUE	1	0.24	2		398	597	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465961	69465961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2152	155	348	0	ENST00000227507.2:c.799G>A	p.Asp267Asn	p.D267N	ENST00000227507	NM_053056.2	267	Gac/Aac	5/5	0.301883042285735	18	FACETS	0.817	0.744	0.895			1	CLONAL	2	TRUE	NA	0.24	18		348	2307	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514193	69514193	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs764070084	NA	P-0022312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1997	113	728	0	ENST00000294312.3:c.488C>G	p.Ser163Cys	p.S163C	ENST00000294312	NM_005117.2	163	tCt/tGt	3/3	0.301883042285735	18	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.24	18		728	2110	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557528	21557528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775075244	NA	P-0022312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	95	370	1	ENST00000382592.4:c.2317G>A	p.Ala773Thr	p.A773T	ENST00000382592	NM_014572.2	773	Gca/Aca	5/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.24	2		371	598	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688747	47688747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	88	292	0	ENST00000347630.2:c.553C>T	p.Arg185Trp	p.R185W	ENST00000347630	NM_001007230.1	185	Cgg/Tgg	7/11	0.301883042285735	6	FACETS	1	0.976	1	0.356	0.315	0.4	CLONAL	1	TRUE	2	0.24	6		292	763	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502882	186502882	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	94	450	0	ENST00000323963.5:c.340G>T	p.Ala114Ser	p.A114S	ENST00000323963		114	Gct/Tct	4/11	0.275015856999351	4	FACETS	0.803	0.715	0.896	0.803	0.715	0.896	CLONAL	2	TRUE	2	0.24	4		450	605	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944562	40944562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868189942	NA	P-0022312-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	83	335	1	ENST00000373198.4:c.1940C>T	p.Ser647Leu	p.S647L	ENST00000373198	NM_133170.3	647	tCg/tTg	12/32	0.33435732330965	3	FACETS	1	0.949	1	0.565	0.5	0.634	CLONAL	1	TRUE	1	0.33435732330965	3		336	513	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097712	27097713	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0022312-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	90	455	0	ENST00000324856.7:c.3302_3303del	p.Tyr1101CysfsTer3	p.Y1101Cfs*3	ENST00000324856	NM_006015.4	1101	TAt/t	12/20	1	2	FACETS	0.874	0.776	0.978	0.874	0.776	0.978	CLONAL	1	TRUE	1	0.33435732330965	2		455	616	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111476	8111508	+	frameshift_variant	Frame_Shift_Del	DEL	AGACCACCACAACCACACTCTGGAGGAGGAATG	AGACCACCACAACCACACTCTGGAGGAGGAATG	TGGCATT	novel	NA	P-0022312-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	58	396	2	ENST00000346208.3:c.962_994delinsTGGCATT	p.Gln321LeufsTer22	p.Q321Lfs*22	ENST00000346208		321	cAGACCACCACAACCACACTCTGGAGGAGGAATGcc/cTGGCATTcc	5/6	1	2	FACETS	0.665	0.571	0.766	0.665	0.571	0.766	SUBCLONAL	1	TRUE	1	0.33435732330965	2		398	522	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465961	69465961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022312-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1351	89	348	0	ENST00000227507.2:c.799G>A	p.Asp267Asn	p.D267N	ENST00000227507	NM_053056.2	267	Gac/Aac	5/5	0.33435732330965	15	FACETS	1	0.956	1			1	CLONAL	1	TRUE	NA	0.33435732330965	15		348	1440	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557528	21557528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775075244	NA	P-0022312-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	79	370	1	ENST00000382592.4:c.2317G>A	p.Ala773Thr	p.A773T	ENST00000382592	NM_014572.2	773	Gca/Aca	5/8	1	2	FACETS	0.925	0.815	1	0.925	0.815	1	CLONAL	1	TRUE	1	0.33435732330965	2		371	511	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688747	47688747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022312-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	63	292	0	ENST00000347630.2:c.553C>T	p.Arg185Trp	p.R185W	ENST00000347630	NM_001007230.1	185	Cgg/Tgg	7/11	0.33435732330965	5	FACETS	0.814	0.703	0.935	0.271	0.234	0.312	CLONAL	1	TRUE	2	0.33435732330965	5		292	695	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575149	64575149	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	300	585	0	ENST00000312049.6:c.658del	p.Trp220GlyfsTer4	p.W220Gfs*4	ENST00000312049	NM_130799.2	220	Tgg/gg	4/10	0.9045831428672	2	FACETS	0.994	0.972	1	0.994	0.972	1	CLONAL	2	TRUE	0	0.917058170037573	2		585	329	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589637	67589637	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	43	408	0	ENST00000274335.5:c.1400A>G	p.Tyr467Cys	p.Y467C	ENST00000274335		467	tAt/tGt	10/15	0.847121069760154	3	FACETS	0.814	0.692	0.945	0.407	0.346	0.473	CLONAL	1	TRUE	1	0.917058170037573	3		408	168	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271461	26271461	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	31	653	0	ENST00000305910.3:c.152A>G	p.Glu51Gly	p.E51G	ENST00000305910	NM_003534.2	51	gAg/gGg	1/1	0.902278781622754	2	FACETS	0.182	0.147	0.222	0.091	0.073	0.111	SUBCLONAL	1	TRUE	0	0.917058170037573	2		653	371	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940022	76940022	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	169	344	0	ENST00000373344.5:c.726del	p.Lys242AsnfsTer15	p.K242Nfs*15	ENST00000373344	NM_000489.3	242	aaA/aa	9/35	0.852218138666683	2	FACETS	1	0.985	1			1	CLONAL	2	TRUE	NA	0.917058170037573	2		344	181	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0025546-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	230	304	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.586751241530911	3	FACETS	0.897	0.852	0.94	0.897	0.852	0.94	CLONAL	3	TRUE	0	0.586751241530911	3		304	377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0025546-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	312	588	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.546218414447927	2	FACETS	0.969	0.925	1	0.969	0.925	1	CLONAL	2	TRUE	0	0.586751241530911	2		588	549	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732484	74732519	+	inframe_deletion	In_Frame_Del	DEL	GATCGGCTGCGAGACCTGGAACGACTCCGACTCCGG	GATCGGCTGCGAGACCTGGAACGACTCCGACTCCGG	-	rs1270919613	NA	P-0025546-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	133	577	0	ENST00000359995.5:c.390_425del	p.Ser132_Arg143del	p.S132_R143del	ENST00000359995	NM_001195427.1	130	tcCCGGAGTCGGAGTCGTTCCAGGTCTCGCAGCCGATCt/tct	2/3	0.517542443580035	4	FACETS	0.595	0.539	0.655	0.298	0.269	0.328	SUBCLONAL	1	TRUE	2	0.586751241530911	4		577	1208	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941668	48941669	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025546-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	70	147	0	ENST00000267163.4:c.983dup	p.Asn328LysfsTer2	p.N328Kfs*2	ENST00000267163	NM_000321.2	326	-/A	10/27	0.567635272433075	2	FACETS	0.846	0.761	0.931	0.846	0.761	0.931	CLONAL	2	TRUE	0	0.586751241530911	2		147	141	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444666	78444666	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025546-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	262	562	0	ENST00000370768.2:c.23del	p.Pro8LeufsTer46	p.P8Lfs*46	ENST00000370768	NM_003902.3	8	cCt/ct	1/20	0.586751241530911	3	FACETS	1	0.97	1	0.529	0.495	0.563	CLONAL	1	TRUE	1	0.586751241530911	3		562	1092	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720717	89720717	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025546-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	31	69	0	ENST00000371953.3:c.868del	p.Val290Ter	p.V290*	ENST00000371953	NM_000314.4	290	Gta/ta	8/9	0.522262208715553	2	FACETS	0.927	0.794	1	0.927	0.794	1	CLONAL	2	TRUE	0	0.586751241530911	2		69	57	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426578	49426592	+	inframe_deletion	In_Frame_Del	DEL	CTGCTGCTGTTGAAA	CTGCTGCTGTTGAAA	-	rs1195849154	NA	P-0025546-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	426	731	0	ENST00000301067.7:c.11896_11910del	p.Phe3966_Gln3970del	p.F3966_Q3970del	ENST00000301067	NM_003482.3	3966	TTTCAACAGCAGCAG/-	39/54	0.477127867863864	4	FACETS	1	0.985	1	0.712	0.681	0.745	CLONAL	2	TRUE	1	0.586751241530911	4		731	1078	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865120	57865120	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025546-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	461	582	0	ENST00000228682.2:c.2597C>A	p.Thr866Asn	p.T866N	ENST00000228682	NM_005269.2	866	aCc/aAc	12/12	0.477127867863864	4	FACETS	0.96	0.923	0.996	0.96	0.923	0.996	CLONAL	3	TRUE	1	0.586751241530911	4		582	866	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631604	119631604	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025546-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	99	348	0	ENST00000316626.5:c.662A>T	p.Tyr221Phe	p.Y221F	ENST00000316626		221	tAc/tTc	6/12	0.523779878513794	4	FACETS	1	0.949	1	0.366	0.328	0.406	CLONAL	1	TRUE	1	0.586751241530911	4		348	488	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176940	56176940	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025546-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	56	306	0	ENST00000399503.3:c.2210T>A	p.Val737Asp	p.V737D	ENST00000399503	NM_005921.1	737	gTc/gAc	13/20	0.28674661521389	2	FACETS	0.51	0.439	0.588	0.255	0.219	0.294	INDETERMINATE	1	TRUE	0	0.586751241530911	2		306	374	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465563	8465563	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025546-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	178	416	0	ENST00000356435.5:c.3617G>T	p.Gly1206Val	p.G1206V	ENST00000356435		1206	gGg/gTg	21/35	0.517542443580035	4	FACETS	1	0.99	1	0.745	0.69	0.802	CLONAL	1	TRUE	2	0.586751241530911	4		416	646	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197720	123197720	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025546-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	89	322	0	ENST00000218089.9:c.1844A>G	p.Gln615Arg	p.Q615R	ENST00000218089	NM_001042749.1	615	cAg/cGg	20/35	0.276585217105577	4	FACETS	1	0.98	1	0.738	0.661	0.819	INDETERMINATE	1	TRUE	2	0.586751241530911	4		322	326	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52722992	52722992	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1362406458	NA	P-0025546-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	94	469	0	ENST00000322088.6:c.1177G>A	p.Glu393Lys	p.E393K	ENST00000322088	NM_014225.5	393	Gag/Aag	10/15	0.517542443580035	4	FACETS	0.561	0.498	0.628	0.281	0.249	0.314	SUBCLONAL	1	TRUE	2	0.586751241530911	4		469	906	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271162	38271162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437821654	NA	P-0025546-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	59	413	0	ENST00000425967.3:c.2546G>A	p.Gly849Glu	p.G849E	ENST00000425967	NM_001174067.1	849	gGa/gAa	19/19	0.229016065915983	5	FACETS	0.623	0.536	0.718	0.208	0.178	0.24	INDETERMINATE	1	TRUE	2	0.586751241530911	5		413	607	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50785023	50785023	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025546-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	49	243	0	ENST00000307179.4:c.2360A>T	p.Tyr787Phe	p.Y787F	ENST00000307179		787	tAt/tTt	15/20	1	2	FACETS	0.831	0.713	0.957	0.831	0.713	0.957	CLONAL	1	TRUE	1	0.586751241530911	2		243	201	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38798805	38798805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025546-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	208	365	0	ENST00000348513.6:c.58C>T	p.Pro20Ser	p.P20S	ENST00000348513	NM_003079.4	20	Ccc/Tcc	4/11	0.517542443580035	4	FACETS	0.941	0.879	1	0.941	0.879	1	CLONAL	2	TRUE	2	0.586751241530911	4		365	598	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2119461	2119461	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025546-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	194	322	0	ENST00000349721.2:c.3688G>T	p.Glu1230Ter	p.E1230*	ENST00000349721	NM_003070.3	1230	Gaa/Taa	26/34	0.517542443580035	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	2	0.586751241530911	4		322	510	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	30	714	1				ENST00000310581	NM_198253.2	-/1132			0.11761592094911	4	FACETS	0.645	0.519	0.788	0.322	0.259	0.394	INDETERMINATE	1	TRUE	2	0.260671832987505	4		715	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs760043106	NA	P-0025675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	148	579	0	ENST00000269305.4:c.584T>A	p.Ile195Asn	p.I195N	ENST00000269305	NM_001126112.2	195	aTc/aAc	6/11	0.151670542849901	2	FACETS	0.796	0.729	0.867	0.796	0.729	0.867	INDETERMINATE	2	TRUE	0	0.260671832987505	2		579	713	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111959656	111959656	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	28	239	0	ENST00000375549.3:c.235C>G	p.Leu79Val	p.L79V	ENST00000375549	NM_003002.3	79	Ctg/Gtg	3/4	1	2	FACETS	0.603	0.482	0.741	0.603	0.482	0.741	SUBCLONAL	1	TRUE	1	0.260671832987505	2		239	356	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930298	39930298	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	108	586	0	ENST00000378444.4:c.3166G>A	p.Gly1056Arg	p.G1056R	ENST00000378444	NM_001123385.1	1056	Gga/Aga	6/15	0.0456920380009092	4	FACETS	0.991	0.888	1	0.496	0.444	0.551	INDETERMINATE	1	TRUE	2	0.260671832987505	4		586	1054	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0026141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	6497	421	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.423106394846714	38	FACETS	1	0.998	1			1	CLONAL	35	TRUE	NA	0.423106394846714	38		421	7492	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0026141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7175	1102	417	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.423106394846714	38	FACETS	1	0.993	1			1	CLONAL	5	TRUE	NA	0.423106394846714	38		417	8277	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112380	115112380	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374981272	NA	P-0026141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	206	360	0	ENST00000257566.3:c.1360C>T	p.Arg454Cys	p.R454C	ENST00000257566	NM_016569.3	454	Cgc/Tgc	7/8	0.408732913992389	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.423106394846714	3		360	582	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873761	35873761	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	199	382	0	ENST00000216797.5:c.90C>A	p.His30Gln	p.H30Q	ENST00000216797	NM_020529.2	30	caC/caA	1/6	0.423106394846714	5	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.423106394846714	5		382	1293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577101	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTC	CTCTC	-	novel	NA	P-0026141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	449	596	0	ENST00000269305.4:c.837_841del	p.Arg280ProfsTer24	p.R280Pfs*24	ENST00000269305	NM_001126112.2	279	ggGAGAGac/ggac	8/11	0.423106394846714	3	FACETS	1	0.994	1	0.816	0.781	0.85	CLONAL	2	TRUE	0	0.423106394846714	3		596	1051	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0026141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	2494	421	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.465193288873982	26	FACETS	0.992	0.981	1	0.992	0.981	1	CLONAL	23	TRUE	3	0.465193288873982	26		421	3094	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112380	115112380	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374981272	NA	P-0026141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	125	360	0	ENST00000257566.3:c.1360C>T	p.Arg454Cys	p.R454C	ENST00000257566	NM_016569.3	454	Cgc/Tgc	7/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.465193288873982	2		360	438	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873761	35873761	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	89	382	0	ENST00000216797.5:c.90C>A	p.His30Gln	p.H30Q	ENST00000216797	NM_020529.2	30	caC/caA	1/6	0.43262715517959	4	FACETS	0.778	0.689	0.872	0.389	0.344	0.436	SUBCLONAL	1	TRUE	2	0.465193288873982	4		382	721	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577101	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTC	CTCTC	-	novel	NA	P-0026141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	481	596	0	ENST00000269305.4:c.837_841del	p.Arg280ProfsTer24	p.R280Pfs*24	ENST00000269305	NM_001126112.2	279	ggGAGAGac/ggac	8/11	0.465193288873982	4	FACETS	1	0.991	1	0.816	0.785	0.847	CLONAL	3	TRUE	0	0.465193288873982	4		596	928	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591122	67591130	+	inframe_deletion	In_Frame_Del	DEL	AGCTGAGAA	AGCTGAGAA	-	novel	NA	P-0026141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	47	255	0	ENST00000274335.5:c.1717_1725del	p.Leu573_Lys575del	p.L573_K575del	ENST00000274335		572	cAGCTGAGAAag/cag	12/15	0.399851106169265	3	FACETS	0.618	0.522	0.723	0.309	0.261	0.362	SUBCLONAL	1	TRUE	1	0.465193288873982	3		255	403	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528133	157528133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	46	461	0	ENST00000346085.5:c.5858G>A	p.Arg1953His	p.R1953H	ENST00000346085	NM_020732.3	1953	cGt/cAt	20/20	0.465193288873982	4	FACETS	0.355	0.298	0.418	0.118	0.099	0.14	SUBCLONAL	1	TRUE	1	0.465193288873982	4		461	817	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912043	56912043	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	106	633	0	ENST00000519728.1:c.1271C>G	p.Ser424Cys	p.S424C	ENST00000519728	NM_002350.3	424	tCt/tGt	12/13	0.464908008405838	3	FACETS	0.678	0.608	0.754	0.226	0.202	0.252	SUBCLONAL	1	TRUE	0	0.465193288873982	3		633	828	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0026513-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	5	349	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.27	0.152	0.433	0.27	0.152	0.433	SUBCLONAL	1	TRUE	1	0.264917599821457	2		349	140	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0026513-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	13	330	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.397	0.283	0.537	0.397	0.283	0.537	SUBCLONAL	1	TRUE	1	0.264917599821457	2		330	247	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684357	29684363	+	frameshift_variant	Frame_Shift_Del	DEL	GTGTTGT	GTGTTGT	-	novel	NA	P-0026513-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	5	0	0	ENST00000356175.3:c.7879_7885del	p.Val2627PhefsTer29	p.V2627Ffs*29	ENST00000356175	NM_000267.3	2626	aGTGTTGTg/ag	53/57	1	2	FACETS	0.207	0.117	0.334	0.207	0.117	0.334	SUBCLONAL	1	TRUE	1	0.264917599821457	2		0	182	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948166	55948166	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026513-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	6	0	0	ENST00000263923.4:c.3805C>A	p.Leu1269Met	p.L1269M	ENST00000263923	NM_002253.2	1269	Ctg/Atg	29/30	1	2	FACETS	0.254	0.151	0.394	0.254	0.151	0.394	SUBCLONAL	1	TRUE	1	0.264917599821457	2		0	178	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	106	714	1				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		715	714	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112460	115112460	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	163	601	0	ENST00000257566.3:c.1280G>C	p.Arg427Pro	p.R427P	ENST00000257566	NM_016569.3	427	cGg/cCg	7/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		601	1177	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675070	40675070	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747846923	NA	P-0026518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	150	692	0	ENST00000249776.8:c.34G>C	p.Val12Leu	p.V12L	ENST00000249776	NM_033286.3	12	Gtt/Ctt	1/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		692	1150	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907628	111907628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	54	298	0	ENST00000393256.3:c.402G>A	p.Met134Ile	p.M134I	ENST00000393256	NM_006538.4	134	atG/atA	3/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		298	571	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468240	50468240	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	130	541	1	ENST00000331340.3:c.1475G>T	p.Cys492Phe	p.C492F	ENST00000331340	NM_006060.4	492	tGc/tTc	8/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		542	923	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772823	135772823	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0026518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	112	596	0	ENST00000298552.3:c.2800A>T	p.Lys934Ter	p.K934*	ENST00000298552	NM_001162426.1	934	Aaa/Taa	21/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		596	713	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0027586-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	136	613	2	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.459791551937094	5	FACETS	0.963	0.881	1	0.385	0.352	0.42	CLONAL	2	TRUE	0	0.459791551937094	5		615	519	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944256	206944256	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374619208	NA	P-0027586-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	148	575	0	ENST00000423557.1:c.374G>A	p.Arg125His	p.R125H	ENST00000423557	NM_000572.2	125	cGc/cAc	3/5	0.459791551937094	6	FACETS	1	0.956	1	0.532	0.488	0.577	CLONAL	2	TRUE	2	0.459791551937094	6		575	581	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0027586-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	501	482	0	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	0.459791551937094	5	FACETS	0.998	0.985	1	1	0.998	1	CLONAL	7	TRUE	0	0.459791551937094	5		482	527	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063717	+	splice_donor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0027586-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	132	547	0	ENST00000412916.2:c.165+1del		p.X55_splice	ENST00000412916		55			0.376984646576503	0	FACETS		NA	1			1	NA	3	TRUE	0	0.459791551937094	0		547	176	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842438	68842439	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027586-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	179	529	0	ENST00000261769.5:c.504dup	p.Gly169ArgfsTer5	p.G169Rfs*5	ENST00000261769	NM_004360.3	167	gaa/gAaa	4/16	0.376984646576503	0	FACETS		NA	1			1	NA	3	TRUE	0	0.459791551937094	0		529	224	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045934	47045934	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027586-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	147	752	0	ENST00000377604.3:c.2729C>A	p.Ser910Ter	p.S910*	ENST00000377604	NM_001204468.1	910	tCa/tAa	24/24	0.464469671663276	2	FACETS	0.973	0.918	1	1	0.991	1	CLONAL	3	TRUE	0	0.459791551937094	2		752	219	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10774240	10774240	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027586-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	222	444	0	ENST00000361367.2:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000361367	NM_014633.3	23	Cag/Tag	2/25	0.459791551937094	5	FACETS	0.901	0.856	0.946			1	CLONAL	5	TRUE	NA	0.459791551937094	5		444	362	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10778370	10778374	+	frameshift_variant	Frame_Shift_Del	DEL	AACCC	AACCC	-	novel	NA	P-0027586-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	83	367	0	ENST00000361367.2:c.578_582del	p.Asn193ArgfsTer18	p.N193Rfs*18	ENST00000361367	NM_014633.3	193	AACCCa/a	5/25	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.459791551937094	2		367	302	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112553	115112555	+	frameshift_variant	Frame_Shift_Del	DEL	GAG	GAG	AT	novel	NA	P-0027586-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	498	673	0	ENST00000257566.3:c.1185_1187delinsAT	p.Thr397ProfsTer235	p.T397Pfs*235	ENST00000257566	NM_016569.3	395	atCTCc/atATc	7/8	0.459791551937094	12	FACETS	1	0.99	1			1	CLONAL	9	TRUE	NA	0.459791551937094	12		673	756	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95578563	95578563	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886037684	NA	P-0028064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	212	393	1	ENST00000393063.1:c.2062C>T	p.Arg688Ter	p.R688*	ENST00000393063	NM_030621.3	688	Cga/Tga	14/28	1	2	FACETS	0.973	0.913	1	0.973	0.913	1	CLONAL	1	TRUE	1	0.87510588019693	2		394	498	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643579	38643579	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	242	477	0	ENST00000299084.4:c.1049G>A	p.Gly350Glu	p.G350E	ENST00000299084	NM_152594.2	350	gGa/gAa	7/7	1	2	FACETS	0.882	0.83	0.935	0.882	0.83	0.935	CLONAL	1	TRUE	1	0.87510588019693	2		477	627	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976821	55976821	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs368979581	NA	P-0028064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	186	434	0	ENST00000263923.4:c.1091G>T	p.Trp364Leu	p.W364L	ENST00000263923	NM_002253.2	364	tGg/tTg	8/30	NA	2	FACETS	0.947	0.884	1			1	INDETERMINATE	1	TRUE	NA	0.87510588019693	2		434	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691039	NA	P-0028898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	391	500	1	ENST00000269305.4:c.919+1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.893076725535876	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.893076725535876	1		501	471	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	192	714	1				ENST00000310581	NM_198253.2	-/1132			0.433087182752233	4	FACETS	0.952	0.887	1	0.952	0.887	1	CLONAL	2	FALSE	2	0.577549132758148	4		715	551	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050979	49050979	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	16	390	0	ENST00000267163.4:c.2663G>C	p.Ser888Thr	p.S888T	ENST00000267163	NM_000321.2	888	aGt/aCt	25/27	0.498484818397313	4	FACETS	0.633	0.472	0.823	0.211	0.157	0.275	SUBCLONAL	1	FALSE	1	0.577549132758148	4		390	138	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786117	3786117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	190	595	0	ENST00000262367.5:c.4648G>A	p.Glu1550Lys	p.E1550K	ENST00000262367	NM_004380.2	1550	Gaa/Aaa	28/31	0.433087182752233	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	FALSE	2	0.577549132758148	4		595	494	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099988	27099988	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0028898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	231	976	0	ENST00000324856.7:c.3866+1G>A		p.X1289_splice	ENST00000324856	NM_006015.4	1289			0.577549132758148	3	FACETS	0.984	0.917	1	0.492	0.458	0.527	CLONAL	1	FALSE	1	0.577549132758148	3		976	1048	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870953	12870953	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	443	812	0	ENST00000228872.4:c.180G>A	p.Trp60Ter	p.W60*	ENST00000228872	NM_004064.3	60	tgG/tgA	1/3	0.265310909007501	4	FACETS	1	0.988	1	1	0.988	1	INDETERMINATE	2	FALSE	2	0.577549132758148	4		812	1113	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860620	45860620	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	433	982	0	ENST00000391945.4:c.1387C>A	p.Pro463Thr	p.P463T	ENST00000391945	NM_000400.3	463	Ccg/Acg	15/23	0.5666712041429	5	FACETS	1	0.985	1	0.716	0.683	0.75	CLONAL	2	FALSE	2	0.577549132758148	5		982	1302	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174410	11174410	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	165	504	0	ENST00000361445.4:c.7265T>A	p.Val2422Asp	p.V2422D	ENST00000361445	NM_004958.3	2422	gTc/gAc	53/58	0.577549132758148	5	FACETS	1	0.963	1	0.362	0.332	0.393	CLONAL	1	FALSE	2	0.577549132758148	5		504	982	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22413099	22413164	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTTATAAATAGCATTAGAGGCTTGTTGATTAACAAAGGTGTATTTTAAAATACCTTTTTTTAGTGG	GTTATAAATAGCATTAGAGGCTTGTTGATTAACAAAGGTGTATTTTAAAATACCTTTTTTTAGTGG	-	novel	NA	P-0028898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	16	340	0	ENST00000344548.3:c.288+60_293del		p.X96_splice	ENST00000344548	NM_001039802.1	96		6/7	0.577549132758148	5	FACETS	0.994	0.745	1	0.331	0.248	0.428	CLONAL	1	FALSE	2	0.577549132758148	5		340	104	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576856	7576869	+	frameshift_variant	Frame_Shift_Del	DEL	AAGGGTGAAATATT	AAGGGTGAAATATT	-	novel	NA	P-0028898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	332	754	0	ENST00000269305.4:c.977_990del	p.Glu326AlafsTer6	p.E326Afs*6	ENST00000269305	NM_001126112.2	326	gAATATTTCACCCTT/g	9/11	0.516671386553303	5	FACETS	1	0.986	1	0.843	0.81	0.875	CLONAL	4	FALSE	0	0.577549132758148	5		754	509	SUCCESS
ALB	213	MSKCC	GRCh37	4	74274502	74274502	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	69	435	0	ENST00000295897.4:c.462T>A	p.Asn154Lys	p.N154K	ENST00000295897	NM_000477.5	154	aaT/aaA	4/15	0.577549132758148	3	FACETS	0.87	0.775	0.968	0.87	0.775	0.968	CLONAL	2	FALSE	1	0.577549132758148	3		435	177	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196877	106196877	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	48	620	0	ENST00000380013.4:c.5210C>A	p.Thr1737Asn	p.T1737N	ENST00000380013	NM_001127208.2	1737	aCc/aAc	11/11	0.577549132758148	3	FACETS	0.749	0.637	0.87	0.375	0.318	0.435	SUBCLONAL	1	FALSE	1	0.577549132758148	3		620	286	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008991	152008992	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACTT	novel	NA	P-0028898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	32	425	0	ENST00000262189.6:c.627_630dup	p.Val211LysfsTer10	p.V211Kfs*10	ENST00000262189	NM_170606.2	210	-/AAGT	5/59	0.175677258276442	6	FACETS	1	0.918	1			1	INDETERMINATE	2	FALSE	NA	0.577549132758148	6		425	101	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982783	90982783	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	29	287	0	ENST00000265433.3:c.705T>G	p.His235Gln	p.H235Q	ENST00000265433	NM_002485.4	235	caT/caG	7/16	0.516503545576189	5	FACETS	1	0.883	1	0.726	0.601	0.86	CLONAL	2	FALSE	2	0.577549132758148	5		287	86	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93629438	93629438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	202	516	0	ENST00000375746.1:c.872C>T	p.Ser291Leu	p.S291L	ENST00000375746	NM_001174167.1	291	tCa/tTa	7/14	0.445652896276471	5	FACETS	1	0.975	1	0.728	0.679	0.778	CLONAL	2	FALSE	2	0.577549132758148	5		516	598	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339272	116339272	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs77651398	NA	P-0028898-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	84	610	0	ENST00000397752.3:c.134A>G	p.Asn45Ser	p.N45S	ENST00000397752	NM_000245.2	45	aAc/aGc	2/21	0.560044019794119	4	FACETS	0.895	0.792	1	0.447	0.396	0.502	CLONAL	1	FALSE	2	0.577549132758148	4		610	513	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028898-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	281	714	1				ENST00000310581	NM_198253.2	-/1132			0.600290399353001	8	FACETS	1	0.984	1	0.874	0.829	0.919	CLONAL	4	TRUE	3	0.600290399353001	8		715	600	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050979	49050979	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028898-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	128	390	0	ENST00000267163.4:c.2663G>C	p.Ser888Thr	p.S888T	ENST00000267163	NM_000321.2	888	aGt/aCt	25/27	0.600290399353001	4	FACETS	1	0.98	1	0.424	0.385	0.463	CLONAL	1	TRUE	1	0.600290399353001	4		390	537	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786117	3786117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028898-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	376	595	0	ENST00000262367.5:c.4648G>A	p.Glu1550Lys	p.E1550K	ENST00000262367	NM_004380.2	1550	Gaa/Aaa	28/31	0.600290399353001	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	1	0.600290399353001	3		595	680	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099988	27099988	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0028898-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	531	976	0	ENST00000324856.7:c.3866+1G>A		p.X1289_splice	ENST00000324856	NM_006015.4	1289			0.512593394065339	5	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	2	0.600290399353001	5		976	1076	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870953	12870953	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028898-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	369	812	0	ENST00000228872.4:c.180G>A	p.Trp60Ter	p.W60*	ENST00000228872	NM_004064.3	60	tgG/tgA	1/3	0.35309158356233	6	FACETS	1	0.991	1	1	0.991	1	INDETERMINATE	3	TRUE	3	0.600290399353001	6		812	794	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860620	45860620	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028898-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	526	982	0	ENST00000391945.4:c.1387C>A	p.Pro463Thr	p.P463T	ENST00000391945	NM_000400.3	463	Ccg/Acg	15/23	0.600290399353001	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	1	0.600290399353001	4		982	849	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174410	11174410	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028898-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	136	504	0	ENST00000361445.4:c.7265T>A	p.Val2422Asp	p.V2422D	ENST00000361445	NM_004958.3	2422	gTc/gAc	53/58	0.512593394065339	5	FACETS	1	0.962	1	0.368	0.335	0.403	CLONAL	1	TRUE	2	0.600290399353001	5		504	780	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22413099	22413164	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTTATAAATAGCATTAGAGGCTTGTTGATTAACAAAGGTGTATTTTAAAATACCTTTTTTTAGTGG	GTTATAAATAGCATTAGAGGCTTGTTGATTAACAAAGGTGTATTTTAAAATACCTTTTTTTAGTGG	-	novel	NA	P-0028898-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	46	340	0	ENST00000344548.3:c.288+60_293del		p.X96_splice	ENST00000344548	NM_001039802.1	96		6/7	0.512593394065339	5	FACETS	0.558	0.47	0.656	0.186	0.156	0.219	SUBCLONAL	1	TRUE	2	0.600290399353001	5		340	522	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576856	7576869	+	frameshift_variant	Frame_Shift_Del	DEL	AAGGGTGAAATATT	AAGGGTGAAATATT	-	novel	NA	P-0028898-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	693	754	0	ENST00000269305.4:c.977_990del	p.Glu326AlafsTer6	p.E326Afs*6	ENST00000269305	NM_001126112.2	326	gAATATTTCACCCTT/g	9/11	0.600290399353001	5	FACETS	1	0.995	1	1	0.995	1	CLONAL	5	TRUE	0	0.600290399353001	5		754	835	SUCCESS
ALB	213	MSKCC	GRCh37	4	74274502	74274502	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028898-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	259	435	0	ENST00000295897.4:c.462T>A	p.Asn154Lys	p.N154K	ENST00000295897	NM_000477.5	154	aaT/aaA	4/15	0.289082653982735	4	FACETS	0.928	0.881	0.975			1	INDETERMINATE	3	TRUE	NA	0.600290399353001	4		435	496	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196877	106196877	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028898-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	108	620	0	ENST00000380013.4:c.5210C>A	p.Thr1737Asn	p.T1737N	ENST00000380013	NM_001127208.2	1737	aCc/aAc	11/11	NA	2	FACETS	1	0.955	1			1	INDETERMINATE	1	TRUE	NA	0.600290399353001	2		620	331	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008991	152008992	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACTT	novel	NA	P-0028898-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	94	425	0	ENST00000262189.6:c.627_630dup	p.Val211LysfsTer10	p.V211Kfs*10	ENST00000262189	NM_170606.2	210	-/AAGT	5/59	0.600290399353001	3	FACETS	0.928	0.83	1	0.464	0.415	0.515	CLONAL	1	TRUE	1	0.600290399353001	3		425	439	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982783	90982783	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028898-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	201	287	0	ENST00000265433.3:c.705T>G	p.His235Gln	p.H235Q	ENST00000265433	NM_002485.4	235	caT/caG	7/16	0.600290399353001	8	FACETS	1	0.979	1	0.381	0.354	0.41	CLONAL	2	TRUE	2	0.600290399353001	8		287	820	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93629438	93629438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028898-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	245	516	0	ENST00000375746.1:c.872C>T	p.Ser291Leu	p.S291L	ENST00000375746	NM_001174167.1	291	tCa/tTa	7/14	0.600290399353001	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.600290399353001	3		516	429	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814577	43814577	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1346388741	NA	P-0028898-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	142	489	0	ENST00000372470.3:c.1372C>G	p.Arg458Gly	p.R458G	ENST00000372470	NM_005373.2	458	Cgt/Ggt	9/12	0.512593394065339	5	FACETS	1	0.975	1	0.396	0.361	0.432	CLONAL	1	TRUE	2	0.600290399353001	5		489	757	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865274	40865274	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028898-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	73	355	0	ENST00000428826.2:c.1157G>C	p.Gly386Ala	p.G386A	ENST00000428826		386	gGa/gCa	11/21	0.272565417545664	3	FACETS	0.626	0.549	0.709	0.313	0.274	0.355	INDETERMINATE	1	TRUE	1	0.600290399353001	3		355	505	SUCCESS
REL	5966	MSKCC	GRCh37	2	61121605	61121605	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028898-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	84	308	0	ENST00000295025.8:c.227C>A	p.Pro76His	p.P76H	ENST00000295025	NM_002908.2	76	cCt/cAt	3/11	0.600290399353001	3	FACETS	0.883	0.784	0.988	0.442	0.392	0.494	CLONAL	1	TRUE	1	0.600290399353001	3		308	412	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486312	8486312	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769862703	NA	P-0028898-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	137	365	0	ENST00000356435.5:c.2505G>T	p.Gln835His	p.Q835H	ENST00000356435		835	caG/caT	17/35	0.35309158356233	6	FACETS	0.777	0.709	0.849	0.518	0.473	0.566	INDETERMINATE	2	TRUE	3	0.600290399353001	6		365	646	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0029064-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	38	113	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.688936695609934	3	FACETS	0.971	0.874	1	0.971	0.874	1	CLONAL	3	TRUE	0	0.705596772554234	3		113	50	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0029064-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4	37	184	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.710655512872025	2	FACETS		NA	1	1	0.975	1	NA	3	TRUE	0	0.705596772554234	2		184	41	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844241	68844241	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029064-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	27	639	0	ENST00000261769.5:c.830del	p.Pro277GlnfsTer5	p.P277Qfs*5	ENST00000261769	NM_004360.3	277	Cca/ca	6/16	0.452720587087772	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	0	0.705596772554234	1		639	45	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41489079	41489079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373061594	NA	P-0029064-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	28	506	0	ENST00000263253.7:c.71C>T	p.Ser24Leu	p.S24L	ENST00000263253	NM_001429.3	24	tCg/tTg	1/31	0.710655512872025	2	FACETS	1	0.929	1	0.62	0.518	0.725	CLONAL	1	TRUE	0	0.705596772554234	2		506	64	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465606	99465606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029064-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	22	710	1	ENST00000268035.6:c.2431G>A	p.Glu811Lys	p.E811K	ENST00000268035	NM_000875.3	811	Gag/Aag	11/21	0.710655512872025	2	FACETS	0.878	0.702	1	0.439	0.351	0.534	CLONAL	1	TRUE	0	0.705596772554234	2		711	71	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961471	54961471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029064-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	12	460	0	ENST00000312783.6:c.161C>T	p.Ser54Phe	p.S54F	ENST00000312783	NM_198436.1	54	tCc/tTc	4/10	0.705596772554234	12	FACETS	0.906	0.638	1			1	CLONAL	1	TRUE	NA	0.705596772554234	12		460	170	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427369	49427369	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1565779294	NA	P-0029064-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	10	851	1	ENST00000301067.7:c.11119C>T	p.Arg3707Ter	p.R3707*	ENST00000301067	NM_003482.3	3707	Cga/Tga	39/54	0.504465876086968	3	FACETS	0.518	0.356	0.715			1	SUBCLONAL	1	TRUE	NA	0.705596772554234	3		852	74	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058045	27058045	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029064-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	21	828	0	ENST00000324856.7:c.1753C>T	p.Gln585Ter	p.Q585*	ENST00000324856	NM_006015.4	585	Cag/Tag	3/20	0.710655512872025	2	FACETS	1	0.875	1	0.562	0.452	0.676	CLONAL	1	TRUE	0	0.705596772554234	2		828	53	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170815004	170815004	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029064-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	10	255	0	ENST00000296930.5:c.52C>G	p.Leu18Val	p.L18V	ENST00000296930	NM_002520.6	18	Ctt/Gtt	1/11	0.532385165654881	6	FACETS	0.814	0.57	1	0.407	0.285	0.548	CLONAL	2	TRUE	2	0.705596772554234	6		255	42	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185125	99185125	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029064-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	17	593	0	ENST00000074304.5:c.2527G>C	p.Glu843Gln	p.E843Q	ENST00000074304	NM_001134224.1	843	Gag/Cag	23/26	0.710655512872025	3	FACETS	0.732	0.557	0.933	0.366	0.278	0.467	CLONAL	1	TRUE	1	0.705596772554234	3		593	89	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482861	67482861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029064-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	21	689	0	ENST00000327367.4:c.1265C>T	p.Ser422Phe	p.S422F	ENST00000327367	NM_005902.3	422	tCc/tTc	9/9	0.710655512872025	2	FACETS	1	0.808	1	0.504	0.404	0.612	CLONAL	1	TRUE	0	0.705596772554234	2		689	59	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258310	16258310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542606165	NA	P-0029064-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	16	872	0	ENST00000375759.3:c.5575C>T	p.Arg1859Trp	p.R1859W	ENST00000375759	NM_015001.2	1859	Cgg/Tgg	11/15	0.710655512872025	1	FACETS	0.506	0.386	0.639	0.506	0.386	0.639	SUBCLONAL	1	TRUE	0	0.705596772554234	1		872	58	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40879737	40879737	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029064-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	20	551	0	ENST00000428826.2:c.162G>T	p.Gln54His	p.Q54H	ENST00000428826		54	caG/caT	4/21	0.710655512872025	3	FACETS	0.959	0.751	1	0.479	0.375	0.594	CLONAL	1	TRUE	1	0.705596772554234	3		551	80	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039363	47039363	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029064-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	34	884	0	ENST00000377604.3:c.986C>A	p.Ser329Tyr	p.S329Y	ENST00000377604	NM_001204468.1	329	tCc/tAc	10/24	0.710655512872025	3	FACETS	1	0.948	1	0.686	0.578	0.8	CLONAL	1	TRUE	1	0.705596772554234	3		884	95	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972664	76972667	+	missense_variant	Missense_Mutation	ONP	GATG	GATG	AATA	novel	NA	P-0029064-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	11	457	0	ENST00000373344.5:c.74_77delinsTATT	p.Ser25_Ser26delinsLeuLeu	p.S25_S26delinsLL	ENST00000373344	NM_000489.3	25	tCATCa/tTATTa	2/35	0.705596772554234	7	FACETS	1	0.769	1			1	CLONAL	1	TRUE	NA	0.705596772554234	7		457	77	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259055	153259055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029064-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	26	541	0	ENST00000281708.4:c.760G>A	p.Asp254Asn	p.D254N	ENST00000281708	NM_033632.3	254	Gat/Aat	5/12	0.710655512872025	3	FACETS	1	0.903	1	0.593	0.483	0.711	CLONAL	1	TRUE	1	0.705596772554234	3		541	84	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050770	5050770	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029064-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	20	561	0	ENST00000381652.3:c.553G>C	p.Asp185His	p.D185H	ENST00000381652	NM_004972.3	185	Gat/Cat	6/25	0.710655512872025	3	FACETS	0.902	0.706	1	0.451	0.353	0.561	CLONAL	1	TRUE	1	0.705596772554234	3		561	85	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983039	201983039	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029064-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	39	895	0	ENST00000359651.3:c.888G>C	p.Glu296Asp	p.E296D	ENST00000359651		296	gaG/gaC	7/8	0.705596772554234	7	FACETS	0.753	0.63	0.886	0.301	0.252	0.355	SUBCLONAL	2	TRUE	2	0.705596772554234	7		895	203	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243859018	243859018	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029064-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	39	430	0	ENST00000263826.5:c.47G>A	p.Gly16Glu	p.G16E	ENST00000263826	NM_005465.4	16	gGa/gAa	2/13	0.705596772554234	7	FACETS	1	0.953	1			1	CLONAL	1	TRUE	NA	0.705596772554234	7		430	211	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103510708	103510708	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029064-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	17	686	0	ENST00000355739.4:c.612C>G	p.Ile204Met	p.I204M	ENST00000355739	NM_000123.3	204	atC/atG	6/15	0.710655512872025	4	FACETS	0.893	0.678	1	0.447	0.339	0.57	CLONAL	1	TRUE	2	0.705596772554234	4		686	92	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530136	212530136	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029064-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	10	748	0	ENST00000342788.4:c.1783G>C	p.Asp595His	p.D595H	ENST00000342788	NM_005235.2	595	Gat/Cat	15/28	0.710655512872025	3	FACETS	0.372	0.254	0.518	0.186	0.127	0.259	SUBCLONAL	1	TRUE	1	0.705596772554234	3		748	103	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165737	47165737	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029064-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	17	799	0	ENST00000409792.3:c.389C>G	p.Ser130Cys	p.S130C	ENST00000409792	NM_014159.6	130	tCt/tGt	3/21	0.452720587087772	1	FACETS	0.78	0.615	0.951	0.78	0.615	0.951	CLONAL	1	TRUE	0	0.705596772554234	1		799	40	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712565	52712565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029064-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	21	586	0	ENST00000394830.3:c.187G>A	p.Glu63Lys	p.E63K	ENST00000394830	NM_018313.4	63	Gaa/Aaa	3/30	0.710655512872025	2	FACETS	0.945	0.754	1	0.472	0.377	0.575	CLONAL	1	TRUE	0	0.705596772554234	2		586	63	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79965953	79965953	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1408201880	NA	P-0029064-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	29	615	0	ENST00000265081.6:c.617C>T	p.Ser206Leu	p.S206L	ENST00000265081	NM_002439.4	206	tCa/tTa	4/24	0.710655512872025	3	FACETS	1	0.927	1	0.632	0.522	0.748	CLONAL	1	TRUE	1	0.705596772554234	3		615	88	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651981	36651981	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029064-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	26	865	0	ENST00000244741.5:c.103G>T	p.Asp35Tyr	p.D35Y	ENST00000244741	NM_000389.4	35	Gat/Tat	2/3	0.710655512872025	4	FACETS	1	0.918	1			1	CLONAL	1	TRUE	NA	0.705596772554234	4		865	98	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851911	128851911	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1180366526	NA	P-0029064-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	14	835	0	ENST00000249373.3:c.1983C>G	p.Ile661Met	p.I661M	ENST00000249373	NM_005631.4	661	atC/atG	12/12	0.710655512872025	4	FACETS	0.72	0.528	0.946	0.36	0.264	0.473	CLONAL	1	TRUE	2	0.705596772554234	4		835	94	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151167665	151167665	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029064-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	17	447	0	ENST00000262187.5:c.454G>T	p.Glu152Ter	p.E152*	ENST00000262187	NM_005614.3	152	Gaa/Taa	7/8	0.710655512872025	4	FACETS	0.775	0.587	0.993	0.388	0.293	0.497	CLONAL	1	TRUE	2	0.705596772554234	4		447	106	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400009	139400009	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029064-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	24	933	0	ENST00000277541.6:c.4339G>C	p.Glu1447Gln	p.E1447Q	ENST00000277541	NM_017617.3	1447	Gag/Cag	25/34	0.710655512872025	3	FACETS	1	0.899	1	0.598	0.483	0.721	CLONAL	1	TRUE	1	0.705596772554234	3		933	77	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47004852	47004852	+	5_prime_UTR_variant	5'UTR	DEL	G	G	-	novel	NA	P-0029064-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	11	1343	0	ENST00000377604.3:c.-156del		p.*52*	ENST00000377604	NM_001204468.1	-/852		1/24	0.710655512872025	3	FACETS	0.391	0.272	0.535	0.195	0.136	0.268	SUBCLONAL	1	TRUE	1	0.705596772554234	3		1343	108	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453135	140453136	+	missense_variant	Missense_Mutation	DNP	CA	CA	TT	rs121913377	NA	P-0029220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	61	529	2	ENST00000288602.6:c.1799_1800delinsAA	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTG/gAA	15/18	1	2	FACETS	0.961	0.831	1	0.961	0.831	1	CLONAL	1	TRUE	1	0.27	2		531	470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578197	7578197	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	879	791	0	ENST00000269305.4:c.652del	p.Val218CysfsTer29	p.V218Cfs*29	ENST00000269305	NM_001126112.2	218	Gtg/tg	6/11	0.845087166209872	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.844435665878447	2		791	1014	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261201	16261201	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	417	500	0	ENST00000375759.3:c.8466G>C	p.Gln2822His	p.Q2822H	ENST00000375759	NM_015001.2	2822	caG/caC	11/15	0.845087166209872	6	FACETS	1	0.977	1	0.521	0.496	0.546	CLONAL	2	TRUE	2	0.844435665878447	6		500	1274	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218106	36218106	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs773034213	NA	P-0029548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	224	446	0	ENST00000222270.7:c.4053G>C	p.Glu1351Asp	p.E1351D	ENST00000222270	NM_014727.1	1351	gaG/gaC	15/37	0.845087166209872	3	FACETS	0.956	0.893	1			1	CLONAL	1	TRUE	NA	0.844435665878447	3		446	789	SUCCESS
REL	5966	MSKCC	GRCh37	2	61144102	61144102	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	268	644	0	ENST00000295025.8:c.485A>G	p.Asn162Ser	p.N162S	ENST00000295025	NM_002908.2	162	aAt/aGt	5/11	0.845087166209872	3	FACETS	1	0.969	1	0.523	0.492	0.555	CLONAL	1	TRUE	1	0.844435665878447	3		644	863	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458214	12458214	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	241	507	0	ENST00000287820.6:c.831C>G	p.Ile277Met	p.I277M	ENST00000287820	NM_015869.4	277	atC/atG	6/7	0.229828969070416	3	FACETS	1	0.993	1	0.724	0.682	0.766	INDETERMINATE	1	TRUE	1	0.844435665878447	3		507	561	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274966	142274967	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0029548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	188	399	0	ENST00000350721.4:c.2093_2094del	p.Asp698GlyfsTer3	p.D698Gfs*3	ENST00000350721	NM_001184.3	698	gAT/g	10/47	0.844435665878447	7	FACETS	1	0.961	1			1	CLONAL	1	TRUE	NA	0.844435665878447	7		399	1296	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751558	57751558	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	110	309	0	ENST00000274289.3:c.1433T>G	p.Val478Gly	p.V478G	ENST00000274289	NM_006622.3	478	gTt/gGt	11/14	0.845087166209872	2	FACETS	0.749	0.68	0.82	0.374	0.34	0.41	SUBCLONAL	1	TRUE	0	0.844435665878447	2		309	348	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637393	176637419	+	inframe_deletion	In_Frame_Del	DEL	ATTCCAGATGCTTTCGATAGAACAGAG	ATTCCAGATGCTTTCGATAGAACAGAG	-	novel	NA	P-0029548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	244	532	0	ENST00000439151.2:c.1994_2020del	p.Ile665_Glu673del	p.I665_E673del	ENST00000439151	NM_022455.4	665	ATTCCAGATGCTTTCGATAGAACAGAG/-	5/23	0.845087166209872	2	FACETS	0.857	0.806	0.91	0.429	0.403	0.455	CLONAL	1	TRUE	0	0.844435665878447	2		532	674	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721214	176721214	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs539453877	NA	P-0029548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	200	390	0	ENST00000439151.2:c.6845C>G	p.Pro2282Arg	p.P2282R	ENST00000439151	NM_022455.4	2282	cCt/cGt	23/23	0.845087166209872	2	FACETS	1	0.969	1	0.526	0.493	0.56	CLONAL	1	TRUE	0	0.844435665878447	2		390	450	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543672	148543672	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	189	381	0	ENST00000320356.2:c.136C>G	p.Arg46Gly	p.R46G	ENST00000320356	NM_004456.4	46	Cgt/Ggt	3/20	0.824985837896512	5	FACETS	0.962	0.888	1	0.321	0.296	0.346	CLONAL	1	TRUE	2	0.844435665878447	5		381	1055	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271229	38271240	+	frameshift_variant	Frame_Shift_Del	DEL	AGACGGAATCCT	AGACGGAATCCT	GC	novel	NA	P-0029548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1452	228	907	2	ENST00000425967.3:c.2468_2479delinsGC	p.Glu823GlyfsTer43	p.E823Gfs*43	ENST00000425967	NM_001174067.1	823	gAGGATTCCGTCTtc/gGCtc	19/19	0.845087166209872	4	FACETS	0.593	0.55	0.637			1	SUBCLONAL	1	TRUE	NA	0.844435665878447	4		909	1680	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029958-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	429	438	1	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	0.728362588855802	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.728362588855802	3		439	744	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853286	68853286	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0029958-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	402	419	0	ENST00000261769.5:c.1669A>T	p.Lys557Ter	p.K557*	ENST00000261769	NM_004360.3	557	Aag/Tag	11/16	0.728362588855802	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.728362588855802	2		419	518	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47679246	47679246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029958-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	150	339	0	ENST00000347630.2:c.961G>A	p.Ala321Thr	p.A321T	ENST00000347630	NM_001007230.1	321	Gca/Aca	10/11	1	2	FACETS	0.911	0.84	0.984	0.911	0.84	0.984	CLONAL	1	TRUE	1	0.728362588855802	2		339	452	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0030797-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	214	424	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.486934357015632	6	FACETS	1	0.985	1	1	0.985	1	INDETERMINATE	3	TRUE	3	0.890503478464403	6		424	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0030797-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	217	635	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.890503478464403	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.890503478464403	3		635	225	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371801	55371801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746536924	NA	P-0030797-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	103	778	0	ENST00000297316.4:c.491C>T	p.Ala164Val	p.A164V	ENST00000297316	NM_022454.3	164	gCg/gTg	2/2	NA	2	FACETS	0.718	0.65	0.789			1	INDETERMINATE	1	TRUE	NA	0.890503478464403	2		778	322	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397732	139397732	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs552065719	NA	P-0030797-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	18	761	0	ENST00000277541.6:c.5069C>T	p.Ser1690Leu	p.S1690L	ENST00000277541	NM_017617.3	1690	tCg/tTg	27/34	1	2	FACETS	0.169	0.127	0.218	0.169	0.127	0.218	SUBCLONAL	1	TRUE	1	0.890503478464403	2		761	239	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694604	176694604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030797-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	82	660	0	ENST00000439151.2:c.5188C>T	p.His1730Tyr	p.H1730Y	ENST00000439151	NM_022455.4	1730	Cat/Tat	15/23	0.564003370185516	6	FACETS	0.987	0.872	1	0.247	0.218	0.278	CLONAL	1	TRUE	2	0.890503478464403	6		660	519	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158404	26158404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030797-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	493	657	0	ENST00000289316.2:c.7G>A	p.Glu3Lys	p.E3K	ENST00000289316	NM_138720.2	3	Gaa/Aaa	1/2	0.890503478464403	8	FACETS	0.915	0.875	0.955	0.549	0.525	0.573	CLONAL	3	TRUE	3	0.890503478464403	8		657	1481	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271237	26271237	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs762621647	NA	P-0030797-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	44	1008	0	ENST00000305910.3:c.376C>A	p.Gln126Lys	p.Q126K	ENST00000305910	NM_003534.2	126	Cag/Aag	1/1	0.890503478464403	8	FACETS	0.54	0.452	0.638	0.108	0.09	0.128	SUBCLONAL	1	TRUE	3	0.890503478464403	8		1008	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0032015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	213	703	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.198728758074472	6	FACETS	1	0.974	1			1	INDETERMINATE	2	TRUE	NA	0.693620572185867	6		703	676	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0032015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	107	346	0	ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	4/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.693620572185867	2		346	281	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413070	139413072	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0032015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	167	709	0	ENST00000277541.6:c.1070_1072del	p.Phe357del	p.F357del	ENST00000277541	NM_017617.3	357	tTCTac/tac	6/34	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.693620572185867	2		709	471	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298723	46298724	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0032015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	131	369	1	ENST00000334344.6:c.5371_5372del	p.Lys1791GlufsTer3	p.K1791Efs*3	ENST00000334344	NM_152641.2	1790	ttAAag/ttag	21/21	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.693620572185867	2		370	353	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161984	47161985	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0032015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	141	551	0	ENST00000409792.3:c.4141_4142del	p.Leu1381SerfsTer4	p.L1381Sfs*4	ENST00000409792	NM_014159.6	1381	TTa/a	3/21	1	2	FACETS	0.826	0.758	0.897	0.826	0.758	0.897	CLONAL	1	TRUE	1	0.693620572185867	2		551	492	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939287	76939290	+	frameshift_variant	Frame_Shift_Del	DEL	TTTA	TTTA	-	novel	NA	P-0032015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	313	485	0	ENST00000373344.5:c.1458_1461del	p.Asn486LysfsTer27	p.N486Kfs*27	ENST00000373344	NM_000489.3	486	aaTAAA/aa	9/35	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.693620572185867	1		485	449	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168726	56168727	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	200	419	0	ENST00000399503.3:c.1583dup	p.Leu528PhefsTer13	p.L528Ffs*13	ENST00000399503	NM_005921.1	527	cct/ccTt	9/20	0.593664832313592	4	FACETS	0.842	0.786	0.9	0.842	0.786	0.9	CLONAL	2	TRUE	2	0.697181663692436	4		419	578	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218357	133218357	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1335665224	NA	P-0032706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	208	661	0	ENST00000320574.5:c.5254G>T	p.Asp1752Tyr	p.D1752Y	ENST00000320574	NM_006231.2	1752	Gac/Tac	39/49	0.468899347211962	3	FACETS	0.886	0.833	0.94	0.886	0.833	0.94	CLONAL	2	TRUE	1	0.697181663692436	3		661	454	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626967	14626967	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	169	681	0	ENST00000254322.2:c.808A>G	p.Thr270Ala	p.T270A	ENST00000254322	NM_006145.1	270	Aca/Gca	3/3	1	2	FACETS	0.877	0.811	0.944	0.877	0.811	0.944	CLONAL	1	TRUE	1	0.697181663692436	2		681	553	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198283	185198284	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGCAA	novel	NA	P-0032706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	235	455	0	ENST00000265026.3:c.2767_2772dup	p.Gly923_Lys924dup	p.G923_K924dup	ENST00000265026	NM_004721.4	923	ctg/ctGGGCAAg	13/14	0.412184773003864	4	FACETS	0.935	0.878	0.992	0.935	0.878	0.992	INDETERMINATE	2	TRUE	2	0.697181663692436	4		455	612	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411931	63411950	+	frameshift_variant	Frame_Shift_Del	DEL	AGTTTCCCACAGATATTCTA	AGTTTCCCACAGATATTCTA	-	novel	NA	P-0032706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	56	806	0	ENST00000330258.3:c.1217_1236del	p.Leu406CysfsTer28	p.L406Cfs*28	ENST00000330258	NM_152424.3	406	tTAGAATATCTGTGGGAAACT/t	2/2	0.481830757197633	3	FACETS	0.335	0.286	0.388	0.167	0.143	0.194	SUBCLONAL	1	TRUE	1	0.697181663692436	3		806	647	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164722	47164741	+	frameshift_variant	Frame_Shift_Del	DEL	TGTCTTCTTATACTCTTCTT	TGTCTTCTTATACTCTTCTT	-	novel	NA	P-0032952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	266	425	0	ENST00000409792.3:c.1385_1404del	p.Glu462ValfsTer22	p.E462Vfs*22	ENST00000409792	NM_014159.6	462	gAAGAAGAGTATAAGAAGACA/g	3/21	0.793197061911238	2	FACETS	0.897	0.861	0.931	0.897	0.861	0.931	CLONAL	2	TRUE	0	0.793197061911238	2		425	374	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287182	33287182	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	429	578	0	ENST00000374542.5:c.1915del	p.Thr639GlnfsTer6	p.T639Qfs*6	ENST00000374542	NM_001141970.1	639	Aca/ca	6/8	0.793197061911238	2	FACETS	0.917	0.889	0.944	0.917	0.889	0.944	CLONAL	2	TRUE	0	0.793197061911238	2		578	590	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	84	367	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.846	0.748	0.951	0.846	0.748	0.951	CLONAL	1	TRUE	1	0.328056357274582	2		367	605	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121912666	NA	P-0033017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	98	541	0	ENST00000269305.4:c.659A>C	p.Tyr220Ser	p.Y220S	ENST00000269305	NM_001126112.2	220	tAt/tCt	6/11	0.328056357274582	1	FACETS	0.962	0.862	1	0.962	0.862	1	CLONAL	1	TRUE	0	0.328056357274582	1		541	519	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593418	48593418	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	85	362	0	ENST00000342988.3:c.1170del	p.Glu390AspfsTer25	p.E390Dfs*25	ENST00000342988	NM_005359.5	390	gAa/ga	10/12	0.328056357274582	1	FACETS	0.844	0.749	0.946	0.844	0.749	0.946	CLONAL	1	TRUE	0	0.328056357274582	1		362	513	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0033066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	326	645	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.573050124361651	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.573050124361651	1		645	698	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101118	41101118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751886972	NA	P-0033066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	159	632	1	ENST00000373198.4:c.1238C>T	p.Ala413Val	p.A413V	ENST00000373198	NM_133170.3	413	gCg/gTg	8/32	1	2	FACETS	0.794	0.73	0.861	0.794	0.73	0.861	SUBCLONAL	1	TRUE	1	0.573050124361651	2		633	699	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508424	106508424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751449393	NA	P-0033066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	85	224	0	ENST00000359195.3:c.418C>T	p.Arg140Trp	p.R140W	ENST00000359195	NM_002649.2	140	Cgg/Tgg	2/11	0.337242441423449	3	FACETS	1	0.957	1	0.575	0.513	0.64	INDETERMINATE	1	TRUE	1	0.573050124361651	3		224	332	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244233	5244233	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	115	565	1	ENST00000357368.4:c.1249G>A	p.Val417Met	p.V417M	ENST00000357368	NM_002850.3	417	Gtg/Atg	11/38	1	2	FACETS	0.735	0.665	0.809	0.735	0.665	0.809	SUBCLONAL	1	TRUE	1	0.573050124361651	2		566	546	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033074-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	135	714	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.865	0.795	0.937	0.865	0.795	0.937	CLONAL	1	TRUE	1	0.8105111091704	2		715	385	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0033074-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	306	371	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.8105111091704	3	FACETS	0.963	0.919	1	0.963	0.919	1	CLONAL	2	TRUE	1	0.8105111091704	3		371	551	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262370	16262371	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033074-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	223	524	0	ENST00000375759.3:c.9635_9636delinsTT	p.Ala3212Val	p.A3212V	ENST00000375759	NM_015001.2	3212	gCC/gTT	11/15	1	2	FACETS	0.916	0.858	0.974	0.916	0.858	0.974	CLONAL	1	TRUE	1	0.8105111091704	2		524	601	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437028	110437028	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033074-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	703	557	0	ENST00000375856.3:c.1373C>G	p.Ser458Cys	p.S458C	ENST00000375856	NM_003749.2	458	tCc/tGc	1/2	0.8105111091704	4	FACETS	0.97	0.944	0.996	0.97	0.944	0.996	CLONAL	3	TRUE	1	0.8105111091704	4		557	1079	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285080	15285080	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033074-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	222	525	0	ENST00000263388.2:c.4535T>G	p.Val1512Gly	p.V1512G	ENST00000263388	NM_000435.2	1512	gTg/gGg	25/33	1	2	FACETS	0.928	0.871	0.987	0.928	0.871	0.987	CLONAL	1	TRUE	1	0.8105111091704	2		525	590	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525142	9525142	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0033074-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	156	294	0	ENST00000353224.5:c.1744-1G>A		p.X582_splice	ENST00000353224	NM_177990.2	582			1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.8105111091704	2		294	384	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750437	41750437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033074-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	216	483	0	ENST00000226382.2:c.191C>T	p.Ser64Phe	p.S64F	ENST00000226382	NM_003924.3	64	tCc/tTc	1/3	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.8105111091704	2		483	533	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673073	30673073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033074-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	306	710	0	ENST00000376406.3:c.3887C>T	p.Ser1296Phe	p.S1296F	ENST00000376406	NM_014641.2	1296	tCc/tTc	10/15	1	2	FACETS	0.949	0.898	0.999	0.949	0.898	0.999	CLONAL	1	TRUE	1	0.8105111091704	2		710	796	SUCCESS
AR	367	MSKCC	GRCh37	X	66937404	66937404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057523747	NA	P-0033074-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	239	190	0	ENST00000374690.3:c.2258G>A	p.Arg753Gln	p.R753Q	ENST00000374690	NM_000044.3	753	cGa/cAa	5/8	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.8105111091704	1		190	301	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0033309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	65	421	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.878	0.76	1	0.878	0.76	1	CLONAL	1	TRUE	1	0.19	2		421	779	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934574	NA	P-0033309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	108	523	0	ENST00000269305.4:c.844C>G	p.Arg282Gly	p.R282G	ENST00000269305	NM_001126112.2	282	Cgg/Ggg	8/11	1	2	FACETS	0.906	0.81	1	0.906	0.81	1	CLONAL	1	TRUE	1	0.19	2		523	1255	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262249	16262249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	29	224	0	ENST00000375759.3:c.9514C>T	p.Pro3172Ser	p.P3172S	ENST00000375759	NM_015001.2	3172	Cct/Tct	11/15	1	2	FACETS	0.877	0.705	1	0.877	0.705	1	CLONAL	1	TRUE	1	0.19	2		224	348	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879806	37879806	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	73	583	0	ENST00000269571.5:c.2101A>T	p.Thr701Ser	p.T701S	ENST00000269571		701	Aca/Tca	18/27	1	2	FACETS	0.957	0.836	1	0.957	0.836	1	CLONAL	1	TRUE	1	0.19	2		583	803	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	122	367	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.51	0.463	0.558	0.51	0.463	0.558	SUBCLONAL	1	TRUE	1	0.955762013328022	2		367	501	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0033725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	118	324	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.682	0.622	0.744	0.682	0.622	0.744	SUBCLONAL	1	TRUE	1	0.955762013328022	2		324	362	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0033725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	101	300	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.656	0.593	0.722	0.656	0.593	0.722	SUBCLONAL	1	TRUE	1	0.955762013328022	2		300	322	SUCCESS
APC	324	MSKCC	GRCh37	5	112174106	112174106	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0033725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	106	376	0	ENST00000257430.4:c.2815A>T	p.Lys939Ter	p.K939*	ENST00000257430	NM_000038.5	939	Aag/Tag	16/16	1	2	FACETS	0.606	0.548	0.666	0.606	0.548	0.666	SUBCLONAL	1	TRUE	1	0.955762013328022	2		376	366	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004362	150004362	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	155	618	0	ENST00000253339.5:c.1863G>C	p.Lys621Asn	p.K621N	ENST00000253339		621	aaG/aaC	3/7	1	2	FACETS	0.564	0.519	0.611	0.564	0.519	0.611	SUBCLONAL	1	TRUE	1	0.955762013328022	2		618	575	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476265	88476265	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033921-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	60	516	0	ENST00000360948.2:c.1867G>A	p.Gly623Arg	p.G623R	ENST00000360948	NM_001012338.2	623	Gga/Aga	15/19	1	2	FACETS	0.793	0.685	0.909	0.793	0.685	0.909	CLONAL	1	TRUE	1	0.354500055925402	2		516	427	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591140	67591145	+	inframe_deletion	In_Frame_Del	DEL	ACCAAT	ACCAAT	-	rs751582616	NA	P-0033921-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	10	524	0	ENST00000274335.5:c.1735_1740del	p.Gln579_Tyr580del	p.Q579_Y580del	ENST00000274335		578	gACCAATac/gac	12/15	0.17137415801374	3	FACETS	0.134	0.09	0.19	0.067	0.045	0.095	INDETERMINATE	1	TRUE	1	0.354500055925402	3		524	495	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862939	9862939	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033921-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	27	534	0	ENST00000330684.3:c.2364G>T	p.Met788Ile	p.M788I	ENST00000330684	NM_001134407.1	788	atG/atT	12/13	0.314320470764037	3	FACETS	0.338	0.268	0.419			1	SUBCLONAL	1	TRUE	NA	0.354500055925402	3		534	530	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	220	714	1				ENST00000310581	NM_198253.2	-/1132			0.207728249810126	1	FACETS	1	0.977	1	1	0.995	1	CLONAL	3	FALSE	0	0.207728249810126	1		715	583	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0035478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	186	371	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.906	0.845	0.969	1	0.995	1	CLONAL	4	FALSE	1	0.207728249810126	2		371	494	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471052	25471052	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	362	560	0	ENST00000264709.3:c.709C>T	p.Gln237Ter	p.Q237*	ENST00000264709	NM_175629.2	237	Cag/Tag	7/23	1	2	FACETS	0.894	0.85	0.938	1	0.997	1	CLONAL	4	FALSE	1	0.207728249810126	2		560	975	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178710	32178710	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	218	447	0	ENST00000375023.3:c.2684T>A	p.Ile895Lys	p.I895K	ENST00000375023	NM_004557.3	895	aTa/aAa	18/30	0.15980685478539	1	FACETS	0.897	0.838	0.957	1	0.995	1	CLONAL	3	FALSE	0	0.207728249810126	1		447	699	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31238074	31238075	+	missense_variant	Missense_Mutation	DNP	CT	CT	AC	novel	NA	P-0035478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	12	34	0	ENST00000376228.5:c.807_808delinsGT	p.Ala270Ser	p.A270S	ENST00000376228	NM_002117.5	269	gcAGct/gcGTct	4/8	1	2	FACETS	0.781	0.558	1	1	0.877	1	CLONAL	2	FALSE	1	0.207728249810126	2		34	74	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041426	42041426	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	364	542	0	ENST00000219905.7:c.5621C>A	p.Ser1874Tyr	p.S1874Y	ENST00000219905	NM_001164273.1	1874	tCt/tAt	17/24	1	2	FACETS	1	0.99	1	1	0.997	1	CLONAL	3	FALSE	1	0.207728249810126	2		542	1006	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0035498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	1200	812	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.688861279033875	6	FACETS	1	0.996	1	1	0.996	1	CLONAL	4	TRUE	2	0.688861279033875	6		812	1911	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0035498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	575	529	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.688640398182041	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.688861279033875	2		529	805	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532615	187532615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	79	449	0	ENST00000441802.2:c.9778G>A	p.Glu3260Lys	p.E3260K	ENST00000441802	NM_005245.3	3260	Gaa/Aaa	14/27	1	2	FACETS	0.357	0.314	0.403	0.357	0.314	0.403	SUBCLONAL	1	TRUE	1	0.688861279033875	2		449	643	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561354	9561354	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	462	602	0	ENST00000353224.5:c.428C>A	p.Thr143Asn	p.T143N	ENST00000353224	NM_177990.2	143	aCc/aAc	4/10	0.46765811052149	3	FACETS	0.863	0.827	0.899	0.863	0.827	0.899	CLONAL	2	TRUE	1	0.688861279033875	3		602	1045	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051643	30051643	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	157	411	0	ENST00000338641.4:c.577G>C	p.Ala193Pro	p.A193P	ENST00000338641	NM_000268.3	193	Gca/Cca	6/16	0.162286180886	1	FACETS	0.644	0.595	0.694	0.644	0.595	0.694	INDETERMINATE	1	TRUE	0	0.688861279033875	1		411	464	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468427	89468427	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	157	302	0	ENST00000336596.2:c.1961C>A	p.Thr654Asn	p.T654N	ENST00000336596	NM_005233.5	654	aCc/aAc	11/17	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.688861279033875	2		302	377	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549857	187549857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	63	601	0	ENST00000441802.2:c.4384G>A	p.Glu1462Lys	p.E1462K	ENST00000441802	NM_005245.3	1462	Gaa/Aaa	8/27	1	2	FACETS	0.212	0.183	0.244	0.212	0.183	0.244	SUBCLONAL	1	TRUE	1	0.688861279033875	2		601	862	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0035523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	88	509	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.338507188470285	2		510	397	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0035523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	114	515	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.338507188470285	2		515	620	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0035523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	97	597	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.338507188470285	2	FACETS	1	0.976	1	0.662	0.593	0.734	CLONAL	1	TRUE	0	0.338507188470285	2		597	433	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003747	45003747	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs1057519877	NA	P-0035523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	80	386	0	ENST00000558401.1:c.3G>A	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	atG/atA	1/4	0.338507188470285	1	FACETS	0.974	0.862	1	0.974	0.862	1	CLONAL	1	TRUE	0	0.338507188470285	1		386	403	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468393	89468393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	32	192	0	ENST00000336596.2:c.1927C>T	p.Pro643Ser	p.P643S	ENST00000336596	NM_005233.5	643	Cct/Tct	11/17	0.338507188470285	1	FACETS	0.724	0.592	0.871	0.724	0.592	0.871	SUBCLONAL	1	TRUE	0	0.338507188470285	1		192	217	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692941	89692941	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs753630034	NA	P-0035523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	87	467	0	ENST00000371953.3:c.425G>C	p.Arg142Pro	p.R142P	ENST00000371953	NM_000314.4	142	cGg/cCg	5/9	0.338507188470285	1	FACETS	0.936	0.833	1	0.936	0.833	1	CLONAL	1	TRUE	0	0.338507188470285	1		467	456	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231361	46231362	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0035523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	82	411	0	ENST00000334344.6:c.1206_1207del	p.Glu402AspfsTer9	p.E402Dfs*9	ENST00000334344	NM_152641.2	401	AGa/a	10/21	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.338507188470285	2		411	459	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619300	37619300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	76	417	0	ENST00000447079.4:c.976C>T	p.Pro326Ser	p.P326S	ENST00000447079	NM_015083.1	326	Ccc/Tcc	1/14	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.338507188470285	2		417	396	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657544	37657544	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	95	503	0	ENST00000447079.4:c.2461A>C	p.Met821Leu	p.M821L	ENST00000447079	NM_015083.1	821	Atg/Ctg	6/14	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.338507188470285	2		503	512	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131319	202131319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	69	430	0	ENST00000358485.4:c.287C>T	p.Pro96Leu	p.P96L	ENST00000358485	NM_001080125.1	96	cCc/cTc	2/9	1	2	FACETS	0.908	0.793	1	0.908	0.793	1	CLONAL	1	TRUE	1	0.338507188470285	2		430	449	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164850	47164850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1184046423	NA	P-0035523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	121	353	0	ENST00000409792.3:c.1276C>T	p.His426Tyr	p.H426Y	ENST00000409792	NM_014159.6	426	Cat/Tat	3/21	0.338507188470285	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.338507188470285	2		353	339	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750431	41750431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	83	419	0	ENST00000226382.2:c.197G>A	p.Ser66Asn	p.S66N	ENST00000226382	NM_003924.3	66	aGc/aAc	1/3	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.338507188470285	2		419	428	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185242	123185245	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ACAG	ACAG	-	novel	NA	P-0035523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	76	336	0	ENST00000218089.9:c.1194_1196+1del		p.X398_splice	ENST00000218089	NM_001042749.1	398		13/35	1	2	FACETS	0.922	0.811	1	0.922	0.811	1	CLONAL	1	TRUE	1	0.338507188470285	2		336	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	158	688	1	ENST00000269305.4:c.166del	p.Glu56LysfsTer67	p.E56Kfs*67	ENST00000269305	NM_001126112.2	56	Gaa/aa	4/11	0.480223552873146	1	FACETS	0.848	0.78	0.917	0.848	0.78	0.917	CLONAL	1	TRUE	0	0.480223552873146	1		689	590	SUCCESS
APC	324	MSKCC	GRCh37	5	112128142	112128142	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0035726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	85	274	0	ENST00000257430.4:c.646-1G>A		p.X216_splice	ENST00000257430	NM_000038.5	216			0.473483378393462	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	0	0.480223552873146	1		274	265	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675658	86675659	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	73	246	0	ENST00000274376.6:c.2595dup	p.Leu866ThrfsTer19	p.L866Tfs*19	ENST00000274376	NM_002890.2	865	ata/atAa	19/25	0.473483378393462	1	FACETS	0.895	0.793	1	0.895	0.793	1	CLONAL	1	TRUE	0	0.480223552873146	1		246	258	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	129	367	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.176792200854846	4	FACETS	0.814	0.745	0.886	0.814	0.745	0.886	INDETERMINATE	2	TRUE	2	0.627329198509027	4		367	411	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395101	139395101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777423973	NA	P-0036117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	71	375	1	ENST00000277541.6:c.5837G>A	p.Arg1946His	p.R1946H	ENST00000277541	NM_017617.3	1946	cGc/cAc	31/34	0.239479552349643	1	FACETS	0.165	0.143	0.188	0.165	0.143	0.188	INDETERMINATE	1	TRUE	0	0.627329198509027	1		376	942	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456500	32456514	+	inframe_deletion	In_Frame_Del	DEL	GGTGGCGGCGGAGCC	GGTGGCGGCGGAGCC	-	novel	NA	P-0036117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	15	69	0	ENST00000332351.3:c.378_392del	p.Ala127_Pro131del	p.A127_P131del	ENST00000332351	NM_024426.4	126	ccGGCTCCGCCGCCACCc/ccc	1/10	0.305969608656269	3	FACETS	0.22	0.16	0.291	0.11	0.08	0.146	INDETERMINATE	1	TRUE	1	0.627329198509027	3		69	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579356	7579356	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	370	206	0	ENST00000269305.4:c.331del	p.Leu111TrpfsTer12	p.L111Wfs*12	ENST00000269305	NM_001126112.2	111	Ctg/tg	4/11	0.627329198509027	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.627329198509027	1		206	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578213	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs864309495	NA	P-0036484-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	73	688	2	ENST00000269305.4:c.636del	p.Arg213AspfsTer34	p.R213Dfs*34	ENST00000269305	NM_001126112.2	212	ttT/tt	6/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		690	1050	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061157	38061175	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCGCCGCCGGCCCCCGG	CCCCGCCGCCGGCCCCCGG	-	novel	NA	P-0036484-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	32	646	0	ENST00000250448.2:c.814_832del	p.Pro272AlafsTer43	p.P272Afs*43	ENST00000250448	NM_004496.3	272	CCGGGGGCCGGCGGCGGGGgc/gc	2/2	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		646	830	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579410	7579410	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567556123	NA	P-0037454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	122	634	0	ENST00000269305.4:c.277del	p.Leu93CysfsTer30	p.L93Cfs*30	ENST00000269305	NM_001126112.2	93	Ctg/tg	4/11	0.202456815844882	2	FACETS	1	0.969	1	0.584	0.529	0.643	CLONAL	1	FALSE	0	0.3	2		634	696	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653828	89653835	+	frameshift_variant	Frame_Shift_Del	DEL	TGAAGGCG	TGAAGGCG	-	novel	NA	P-0037454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	60	434	0	ENST00000371953.3:c.127_134del	p.Glu43IlefsTer6	p.E43Ifs*6	ENST00000371953	NM_000314.4	42	ctTGAAGGCGta/ctta	2/9	0.202456815844882	2	FACETS	0.847	0.732	0.973	0.424	0.366	0.487	CLONAL	1	FALSE	0	0.3	2		434	472	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853186	68853186	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs876659716	NA	P-0037454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	89	406	0	ENST00000261769.5:c.1569T>A	p.Tyr523Ter	p.Y523*	ENST00000261769	NM_004360.3	523	taT/taA	11/16	0.202456815844882	2	FACETS	1	0.973	1	0.659	0.587	0.735	CLONAL	1	FALSE	0	0.3	2		406	450	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077438	30077439	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGGAAAAG	novel	NA	P-0037454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	42	207	0	ENST00000338641.4:c.1586_1593dup	p.Ser532TrpfsTer21	p.S532Wfs*21	ENST00000338641	NM_000268.3	529	atg/aTGGAAAAGtg	15/16	0.202456815844882	2	FACETS	1	0.904	1	0.553	0.465	0.65	CLONAL	1	FALSE	0	0.3	2		207	253	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0037811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	1148	710	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.497484728901277	19	FACETS	0.988	0.97	1			1	CLONAL	16	TRUE	NA	0.497484728901277	19		710	1527	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357715	70357715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1569482448	NA	P-0037811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	89	381	0	ENST00000374080.3:c.5966G>A	p.Arg1989His	p.R1989H	ENST00000374080		1989	cGc/cAc	41/45	0.441373333523913	2	FACETS	1	0.934	1			1	CLONAL	2	TRUE	NA	0.497484728901277	2		381	174	SUCCESS
APC	324	MSKCC	GRCh37	5	112175645	112175645	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	18	322	0	ENST00000257430.4:c.4354del	p.Val1452TyrfsTer21	p.V1452Yfs*21	ENST00000257430	NM_000038.5	1452	Gta/ta	16/16	0.303988800828693	1	FACETS	0.397	0.301	0.507	0.397	0.301	0.507	SUBCLONAL	1	TRUE	0	0.497484728901277	1		322	137	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340270	116340270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749738523	NA	P-0037811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	54	231	0	ENST00000397752.3:c.1132G>A	p.Val378Ile	p.V378I	ENST00000397752	NM_000245.2	378	Gtc/Atc	2/21	0.388734617076476	5	FACETS	0.814	0.703	0.932	0.542	0.468	0.621	CLONAL	2	TRUE	2	0.497484728901277	5		231	233	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928446	69928446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	117	596	0	ENST00000352241.4:c.266G>A	p.Arg89Lys	p.R89K	ENST00000352241	NM_198159.2	89	aGa/aAa	2/10	0.497484728901277	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	2	0.497484728901277	4		596	311	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0038509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	69	509	1				ENST00000310581	NM_198253.2	-/1132			0.591544046177279	1	FACETS	0.869	0.774	0.966	0.869	0.774	0.966	CLONAL	1	FALSE	0	0.629311349949239	1		510	173	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0038509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	237	371	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.629311349949239	3	FACETS	0.956	0.902	1	0.956	0.902	1	CLONAL	2	FALSE	1	0.629311349949239	3		371	518	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80343580	80343580	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	47	350	4	ENST00000286548.4:c.739C>T	p.Arg247Ter	p.R247*	ENST00000286548	NM_002072.3	247	Cga/Tga	6/7	1	2	FACETS	0.889	0.763	1	0.889	0.763	1	CLONAL	1	FALSE	1	0.629311349949239	2		354	168	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693002	89693003	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	110	600	0	ENST00000371953.3:c.491dup	p.Val166SerfsTer14	p.V166Sfs*14	ENST00000371953	NM_000314.4	162	-/A	5/9	0.432129756296349	2	FACETS	1	0.985	1	0.716	0.657	0.777	CLONAL	1	FALSE	0	0.629311349949239	2		600	244	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0038509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	238	1043	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	1	2	FACETS	0.96	0.899	1	0.96	0.899	1	CLONAL	1	FALSE	1	0.629311349949239	2		1043	788	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28624256	28624256	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	59	669	0	ENST00000241453.7:c.718G>A	p.Glu240Lys	p.E240K	ENST00000241453	NM_004119.2	240	Gaa/Aaa	6/24	0.629311349949239	1	FACETS	0.77	0.676	0.866	0.77	0.676	0.866	SUBCLONAL	1	FALSE	0	0.629311349949239	1		669	167	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49280973	49280973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	99	613	0	ENST00000282018.3:c.20C>T	p.Ser7Phe	p.S7F	ENST00000282018	NM_020377.2	7	tCc/tTc	1/1	0.23992025020772	4	FACETS	0.777	0.701	0.855	0.777	0.701	0.855	INDETERMINATE	2	FALSE	2	0.629311349949239	4		613	330	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5557656	5557656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	97	712	0	ENST00000397747.3:c.670C>T	p.His224Tyr	p.H224Y	ENST00000397747	NM_025239.3	224	Cac/Tac	5/7	0.629311349949239	1	FACETS	0.688	0.621	0.758	0.688	0.621	0.758	SUBCLONAL	1	FALSE	0	0.629311349949239	1		712	307	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202932	27202932	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	82	608	0	ENST00000380036.4:c.2024A>G	p.Lys675Arg	p.K675R	ENST00000380036	NM_000459.3	675	aAg/aGg	13/23	0.629311349949239	1	FACETS	0.855	0.769	0.943	0.855	0.769	0.943	CLONAL	1	FALSE	0	0.629311349949239	1		608	209	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0039146-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	417	421	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.375253654257954	3	FACETS	1	0.994	1	0.789	0.76	0.818	INDETERMINATE	2	TRUE	0	0.706110345195259	3		421	675	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0039146-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	76	812	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.311222208403007	3	FACETS	0.837	0.739	0.94	0.418	0.369	0.47	INDETERMINATE	1	TRUE	1	0.706110345195259	3		812	348	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0039146-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1353	50	471	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.706110345195259	6	FACETS	0.243	0.205	0.286	0.061	0.051	0.072	SUBCLONAL	1	TRUE	2	0.706110345195259	6		471	1403	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0039146-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	159	530	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.311222208403007	3	FACETS	0.893	0.821	0.968	0.447	0.41	0.484	INDETERMINATE	1	TRUE	1	0.706110345195259	3		530	682	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241672	55241672	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039146-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	507	654	0	ENST00000275493.2:c.2120T>G	p.Leu707Trp	p.L707W	ENST00000275493	NM_005228.3	707	tTg/tGg	18/28	0.375253654257954	3	FACETS	1	0.995	1	0.782	0.756	0.808	INDETERMINATE	2	TRUE	0	0.706110345195259	3		654	828	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919239	48919239	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039146-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	229	336	0	ENST00000267163.4:c.404T>C	p.Leu135Pro	p.L135P	ENST00000267163	NM_000321.2	135	cTa/cCa	4/27	0.690861701394316	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.706110345195259	2		336	317	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164484	47164484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039146-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	236	614	0	ENST00000409792.3:c.1642C>T	p.His548Tyr	p.H548Y	ENST00000409792	NM_014159.6	548	Cat/Tat	3/21	0.311222208403007	3	FACETS	1	0.987	1	0.599	0.561	0.638	INDETERMINATE	1	TRUE	1	0.706110345195259	3		614	755	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209319	98209319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56161606	NA	P-0039146-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	100	712	0	ENST00000331920.6:c.4219G>A	p.Gly1407Ser	p.G1407S	ENST00000331920	NM_000264.3	1407	Ggc/Agc	23/24	0.3062826633238	2	FACETS	0.455	0.407	0.506	0.227	0.203	0.253	INDETERMINATE	1	TRUE	0	0.706110345195259	2		712	623	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751151	128751151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1476455361	NA	P-0039146-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1599	161	433	1	ENST00000377970.2:c.688G>A	p.Ala230Thr	p.A230T	ENST00000377970	NM_002467.4	230	Gcc/Acc	2/3	0.706110345195259	6	FACETS	0.625	0.571	0.682	0.125	0.114	0.137	SUBCLONAL	1	TRUE	1	0.706110345195259	6		434	1760	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805124	43805124	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039146-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1418	144	673	0	ENST00000372470.3:c.574A>G	p.Thr192Ala	p.T192A	ENST00000372470	NM_005373.2	192	Acc/Gcc	4/12	0.706110345195259	5	FACETS	0.538	0.488	0.59	0.179	0.162	0.197	SUBCLONAL	1	TRUE	2	0.706110345195259	5		673	1562	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0039889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	432	623	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.592981468630881	2	FACETS	0.908	0.874	0.943	0.908	0.874	0.943	CLONAL	2	TRUE	0	0.612821680494915	2		623	776	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380254	25380254	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	148	571	0	ENST00000311936.3:c.204G>T	p.Arg68Ser	p.R68S	ENST00000311936	NM_004985.3	68	agG/agT	3/5	0.327815846531025	4	FACETS	1	0.971	1	0.566	0.518	0.616	INDETERMINATE	1	TRUE	2	0.612821680494915	4		571	688	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271975	15271975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs567953412	NA	P-0039889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	256	836	0	ENST00000263388.2:c.6464G>A	p.Gly2155Glu	p.G2155E	ENST00000263388	NM_000435.2	2155	gGa/gAa	33/33	0.607703868046485	2	FACETS	1	0.955	1	0.51	0.479	0.542	CLONAL	1	TRUE	0	0.612821680494915	2		836	819	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450292	50450292	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs374333820	NA	P-0039889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	192	646	0	ENST00000331340.3:c.476A>G	p.Asn159Ser	p.N159S	ENST00000331340	NM_006060.4	159	aAc/aGc	5/8	0.327815846531025	4	FACETS	1	0.943	1	0.512	0.473	0.552	INDETERMINATE	1	TRUE	2	0.612821680494915	4		646	987	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724581	162724581	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	98	613	0	ENST00000367921.3:c.353A>G	p.Tyr118Cys	p.Y118C	ENST00000367921	NM_006182.2	118	tAc/tGc	5/18	0.603510218932656	3	FACETS	0.434	0.386	0.485	0.217	0.193	0.243	SUBCLONAL	1	TRUE	1	0.612821680494915	3		613	963	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200485	67200486	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	553	793	0	ENST00000312629.5:c.680dup	p.His227GlnfsTer8	p.H227Qfs*8	ENST00000312629	NM_003952.2	227	cac/cAac	8/15	0.497579156159635	2	FACETS	0.852	0.822	0.882	0.852	0.822	0.882	CLONAL	2	TRUE	0	0.612821680494915	2		793	1059	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572014	95572014	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0039889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	14	481	0	ENST00000393063.1:c.3093+1G>T		p.X1031_splice	ENST00000393063	NM_030621.3	1031			0.592981468630881	2	FACETS	0.184	0.133	0.246	0.092	0.066	0.123	SUBCLONAL	1	TRUE	0	0.612821680494915	2		481	248	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828633	72828633	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs748108727	NA	P-0039889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	79	828	0	ENST00000268489.5:c.7948C>A	p.Pro2650Thr	p.P2650T	ENST00000268489	NM_006885.3	2650	Ccg/Acg	9/10	0.612821680494915	3	FACETS	0.376	0.33	0.426	0.125	0.11	0.142	SUBCLONAL	1	TRUE	0	0.612821680494915	3		828	895	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234510	41234510	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660129	NA	P-0039889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	76	613	0	ENST00000357654.3:c.4268G>T	p.Ser1423Ile	p.S1423I	ENST00000357654	NM_007294.3	1423	aGc/aTc	12/23	0.598459479892788	3	FACETS	0.43	0.376	0.487	0.215	0.188	0.244	SUBCLONAL	1	TRUE	1	0.612821680494915	3		613	754	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251563	251563	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	74	731	0	ENST00000264932.6:c.1774C>A	p.His592Asn	p.H592N	ENST00000264932	NM_004168.2	592	Cat/Aat	13/15	0.612821680494915	3	FACETS	0.267	0.233	0.304	0.133	0.116	0.152	SUBCLONAL	1	TRUE	1	0.612821680494915	3		731	1182	SUCCESS
APC	324	MSKCC	GRCh37	5	112174286	112174286	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs75239284	NA	P-0039889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	33	421	2	ENST00000257430.4:c.2995C>T	p.Gln999Ter	p.Q999*	ENST00000257430	NM_000038.5	999	Caa/Taa	16/16	1	2	FACETS	0.758	0.628	0.901	0.758	0.628	0.901	CLONAL	1	TRUE	1	0.612821680494915	2		423	142	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048748	180048748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	276	871	0	ENST00000261937.6:c.1814C>T	p.Pro605Leu	p.P605L	ENST00000261937	NM_182925.4	605	cCg/cTg	13/30	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.612821680494915	2		871	864	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0040003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	266	283	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.725852424368505	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.725852424368505	3		283	485	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0040003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	209	460	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.725852424368505	2		460	559	SUCCESS
APC	324	MSKCC	GRCh37	5	112175925	112175925	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs863225356	NA	P-0040003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	88	162	0	ENST00000257430.4:c.4634C>A	p.Ser1545Ter	p.S1545*	ENST00000257430	NM_000038.5	1545	tCa/tAa	16/16	0.725852424368505	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.725852424368505	1		162	140	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31504699	31504699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1032572786	NA	P-0040003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	374	433	1	ENST00000344624.3:c.1631G>A	p.Arg544His	p.R544H	ENST00000344624		544	cGc/cAc	8/33	0.725852424368505	3	FACETS	0.946	0.905	0.987	0.946	0.905	0.987	CLONAL	2	TRUE	1	0.725852424368505	3		434	742	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0040218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	101	274	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.316522259139554	2	FACETS	0.771	0.694	0.852	0.771	0.694	0.852	SUBCLONAL	2	TRUE	0	0.316522259139554	2		274	414	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981315	68981315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866864487	NA	P-0040218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	25	283	0	ENST00000288368.4:c.1387C>T	p.Arg463Cys	p.R463C	ENST00000288368	NM_024870.2	463	Cgc/Tgc	12/40	1	2	FACETS	0.705	0.558	0.872	0.705	0.558	0.872	SUBCLONAL	1	TRUE	1	0.316522259139554	2		283	224	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481806	56481806	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	110	558	0	ENST00000267101.3:c.734C>T	p.Ala245Val	p.A245V	ENST00000267101	NM_001982.3	245	gCc/gTc	7/28	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.316522259139554	2		558	610	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888210	112888210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121918464	NA	P-0040218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	69	477	0	ENST00000351677.2:c.226G>A	p.Glu76Lys	p.E76K	ENST00000351677	NM_002834.3	76	Gag/Aag	3/16	1	2	FACETS	0.787	0.686	0.896	0.787	0.686	0.896	SUBCLONAL	1	TRUE	1	0.316522259139554	2		477	554	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473723	67473723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223740	NA	P-0040218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	107	518	0	ENST00000327367.4:c.803G>A	p.Arg268His	p.R268H	ENST00000327367	NM_005902.3	268	cGc/cAc	6/9	1	2	FACETS	0.962	0.863	1	0.962	0.863	1	CLONAL	1	TRUE	1	0.316522259139554	2		518	703	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0040218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	75	316	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	0.316522259139554	2	FACETS	1	0.926	1	0.536	0.471	0.605	CLONAL	1	TRUE	0	0.316522259139554	2		316	442	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045829	26045829	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	40	485	0	ENST00000540144.1:c.191G>A	p.Arg64Gln	p.R64Q	ENST00000540144	NM_003531.2	64	cGg/cAg	1/1	0.316522259139554	2	FACETS	0.45	0.373	0.535	0.225	0.186	0.268	SUBCLONAL	1	TRUE	0	0.316522259139554	2		485	562	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120258	70120259	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	309	659	1	ENST00000245479.2:c.1261dup	p.Ser421LysfsTer157	p.S421Kfs*157	ENST00000245479	NM_000346.3	420	-/A	3/3	0.316522259139554	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.316522259139554	2		660	914	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214065	108214074	+	frameshift_variant	Frame_Shift_Del	DEL	TTTCAGTGCC	TTTCAGTGCC	-	rs786202800	NA	P-0040218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	32	321	0	ENST00000278616.4:c.8395_8404del	p.Phe2799LysfsTer4	p.F2799Kfs*4	ENST00000278616	NM_000051.3	2795	gaTTTCAGTGCC/ga	57/63	1	2	FACETS	0.615	0.5	0.744	0.615	0.5	0.744	SUBCLONAL	1	TRUE	1	0.316522259139554	2		321	329	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955592	55955592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560674167	NA	P-0040218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	58	420	0	ENST00000263923.4:c.3353G>A	p.Arg1118Gln	p.R1118Q	ENST00000263923	NM_002253.2	1118	cGa/cAa	25/30	1	2	FACETS	0.835	0.719	0.96	0.835	0.719	0.96	CLONAL	1	TRUE	1	0.316522259139554	2		420	439	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978499	70978499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141769540	NA	P-0040218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	85	369	0	ENST00000276594.2:c.1154C>T	p.Pro385Leu	p.P385L	ENST00000276594	NM_024504.3	385	cCg/cTg	5/8	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.316522259139554	2		369	475	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087097	27087361	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGAACCCAGGAGTCAGAGGTTGCGATGAGCCGAGACGTGCCATTGCACTCCAGCCTGGGCAACGAGTGAAACACTGTCTCAAAAAAAAAAATTTTTTTTTTTAATAAAAATAGTATCATGACTAAAGAACGTGTGTGATGTATTTGCTCTTGGTTGTTTAAGGAAAATGCTAAGCAAGTAGTAGGATTATTGAAAGTAGAATCTTTCTGCCTAATATTACTAATCCATGTTCTTATATATATGTTCTAGGATCTATCTGGTTCA	TTGAACCCAGGAGTCAGAGGTTGCGATGAGCCGAGACGTGCCATTGCACTCCAGCCTGGGCAACGAGTGAAACACTGTCTCAAAAAAAAAAATTTTTTTTTTTAATAAAAATAGTATCATGACTAAAGAACGTGTGTGATGTATTTGCTCTTGGTTGTTTAAGGAAAATGCTAAGCAAGTAGTAGGATTATTGAAAGTAGAATCTTTCTGCCTAATATTACTAATCCATGTTCTTATATATATGTTCTAGGATCTATCTGGTTCA	-	novel	NA	P-0040218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	50	16	0	ENST00000324856.7:c.1921-250_1935del		p.X641_splice	ENST00000324856	NM_006015.4	641		5/20	1	2	FACETS	0.957	0.902	0.999	1	0.985	1	CLONAL	6	TRUE	1	0.316522259139554	2		16	55	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937223	36937223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768170625	NA	P-0040218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	148	622	2	ENST00000361632.4:c.1096G>A	p.Gly366Arg	p.G366R	ENST00000361632		366	Gga/Aga	9/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.316522259139554	2		624	829	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007394	45007681	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCATGTATAGAGGAATTATGAGGGAAAGATACCAAGTCACGGTTTATTCTTCAAAATGGAGGTGGCTTGTTGGGAAGGTGGAAGCTCATTTGGCCAGAGTGGAAATGGAATTGGGAGAAATCGATGACCAAATGTAAACACTTGGTGCCTGATATAGCTTGACACCAAGTTAGCCCCAAGTGAAATACCCTGGCAATATTAATGTGTCTTTTCCCGATATTCCTCAGGTACTCCAAAGATTCAGGTTTACTCACGTCATCCAGCAGAGAATGGAAAGTCAAATTTCCT	GCATGTATAGAGGAATTATGAGGGAAAGATACCAAGTCACGGTTTATTCTTCAAAATGGAGGTGGCTTGTTGGGAAGGTGGAAGCTCATTTGGCCAGAGTGGAAATGGAATTGGGAGAAATCGATGACCAAATGTAAACACTTGGTGCCTGATATAGCTTGACACCAAGTTAGCCCCAAGTGAAATACCCTGGCAATATTAATGTGTCTTTTCCCGATATTCCTCAGGTACTCCAAAGATTCAGGTTTACTCACGTCATCCAGCAGAGAATGGAAAGTCAAATTTCCT	-	novel	NA	P-0040218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	35	27	0	ENST00000558401.1:c.68-226_129del		p.X23_splice	ENST00000558401	NM_004048.2	23		2/4	1	2	FACETS	1	0.907	1	1	0.979	1	CLONAL	5	TRUE	1	0.316522259139554	2		27	44	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346992	89346993	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0040218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	79	441	0	ENST00000301030.4:c.5957_5958del	p.Arg1986IlefsTer45	p.R1986Ifs*45	ENST00000301030	NM_001256183.1	1986	aGA/a	9/13	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.316522259139554	2		441	497	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	81	714	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.873	0.779	0.971	0.873	0.779	0.971	CLONAL	1	TRUE	1	0.695103655728756	2		715	267	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690819	89690820	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0040356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	74	134	0	ENST00000371953.3:c.227_228del	p.Tyr76Ter	p.Y76*	ENST00000371953	NM_000314.4	76	TAt/t	4/9	0.695103655728756	1	FACETS	0.798	0.716	0.882	0.798	0.716	0.882	SUBCLONAL	1	TRUE	0	0.695103655728756	1		134	174	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937095	48937095	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0040356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	47	112	0	ENST00000267163.4:c.861+2T>A		p.X287_splice	ENST00000267163	NM_000321.2	287			0.679501698853552	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.695103655728756	1		112	80	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656873	45656873	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs865851162	NA	P-0040356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	129	369	2	ENST00000407780.3:c.283G>A	p.Asp95Asn	p.D95N	ENST00000407780	NM_001283052.1	95	Gac/Aac	3/7	1	2	FACETS	0.851	0.778	0.927	0.851	0.778	0.927	CLONAL	1	TRUE	1	0.695103655728756	2		371	436	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39726959	39726959	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758525665	NA	P-0040356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	63	169	0	ENST00000361337.2:c.957G>A	p.Met319Ile	p.M319I	ENST00000361337	NM_003286.2	319	atG/atA	11/21	1	2	FACETS	0.969	0.854	1	0.969	0.854	1	CLONAL	1	TRUE	1	0.695103655728756	2		169	187	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0040383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	84	371	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.316565878648326	2		371	494	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0040383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	67	423	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	0.978	0.853	1	0.978	0.853	1	CLONAL	1	TRUE	1	0.316565878648326	2		423	433	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713870	30713870	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1023568316	NA	P-0040383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	335	734	0	ENST00000295754.5:c.1195G>C	p.Gly399Arg	p.G399R	ENST00000295754	NM_003242.5	399	Ggg/Cgg	4/7	0.316565878648326	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.316565878648326	2		734	1007	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0040383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	56	235	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.316565878648326	2		235	352	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967215	134967215	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	104	648	2	ENST00000398015.3:c.2554G>T	p.Ala852Ser	p.A852S	ENST00000398015	NM_004441.4	852	Gct/Tct	14/16	1	2	FACETS	0.889	0.796	0.988	0.889	0.796	0.988	CLONAL	1	TRUE	1	0.316565878648326	2		650	739	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	71	445	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.316565878648326	2		445	388	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157822	106157822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	43	324	0	ENST00000380013.4:c.2723G>A	p.Gly908Asp	p.G908D	ENST00000380013	NM_001127208.2	908	gGt/gAt	3/11	1	2	FACETS	0.723	0.606	0.851	0.723	0.606	0.851	SUBCLONAL	1	TRUE	1	0.316565878648326	2		324	376	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876485	59876485	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753214212	NA	P-0040383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	80	464	1	ENST00000259008.2:c.1316G>A	p.Arg439Gln	p.R439Q	ENST00000259008	NM_032043.2	439	cGa/cAa	9/20	1	2	FACETS	0.999	0.882	1	0.999	0.882	1	CLONAL	1	TRUE	1	0.316565878648326	2		465	506	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55991403	55991403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	153	807	1	ENST00000263923.4:c.58G>A	p.Ala20Thr	p.A20T	ENST00000263923	NM_002253.2	20	Gcc/Acc	1/30	1	2	FACETS	0.919	0.839	1	0.919	0.839	1	CLONAL	1	TRUE	1	0.316565878648326	2		808	1052	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389318	8389318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	80	674	0	ENST00000356435.5:c.4300G>A	p.Glu1434Lys	p.E1434K	ENST00000356435		1434	Gaa/Aaa	26/35	1	2	FACETS	0.74	0.651	0.835	0.74	0.651	0.835	SUBCLONAL	1	TRUE	1	0.316565878648326	2		674	683	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844393	156844395	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs768558242	NA	P-0040383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	165	915	0	ENST00000524377.1:c.1231_1233del	p.Lys411del	p.K411del	ENST00000524377	NM_002529.3	409	gAGAag/gag	10/17	1	2	FACETS	0.906	0.831	0.986	0.906	0.831	0.986	CLONAL	1	TRUE	1	0.316565878648326	2		915	1150	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993366	72993366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140855443	NA	P-0040383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	171	829	2	ENST00000268489.5:c.679G>A	p.Val227Ile	p.V227I	ENST00000268489	NM_006885.3	227	Gtc/Atc	2/10	1	2	FACETS	0.939	0.862	1	0.939	0.862	1	CLONAL	1	TRUE	1	0.316565878648326	2		831	1151	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218864	133218864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1235110857	NA	P-0040383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	163	807	0	ENST00000320574.5:c.5072G>A	p.Arg1691His	p.R1691H	ENST00000320574	NM_006231.2	1691	cGc/cAc	38/49	1	2	FACETS	0.953	0.873	1	0.953	0.873	1	CLONAL	1	TRUE	1	0.316565878648326	2		807	1081	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120611974	120611974	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1553217924	NA	P-0040383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	12	39	0	ENST00000256646.2:c.47G>A	p.Trp16Ter	p.W16*	ENST00000256646	NM_024408.3	16	tGg/tAg	1/34	1	2	FACETS	1	0.805	1	1	0.805	1	CLONAL	1	TRUE	1	0.316565878648326	2		39	65	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215552	5215552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs114166264	NA	P-0040383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	201	792	0	ENST00000357368.4:c.4151G>A	p.Arg1384Gln	p.R1384Q	ENST00000357368	NM_002850.3	1384	cGg/cAg	27/38	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.316565878648326	2		792	1030	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202123071	202123072	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	95	502	0	ENST00000358485.4:c.117_118delinsAA	p.Glu40Lys	p.E40K	ENST00000358485	NM_001080125.1	39	tcGGag/tcAAag	1/9	1	2	FACETS	0.888	0.791	0.991	0.888	0.791	0.991	CLONAL	1	TRUE	1	0.316565878648326	2		502	676	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374244	138374244	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	120	565	0	ENST00000289153.2:c.3200A>C	p.Asp1067Ala	p.D1067A	ENST00000289153	NM_006219.2	1067	gAc/gCc	22/22	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.316565878648326	2		565	753	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202123072	202123072	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	95	498	0	ENST00000358485.4:c.118G>A	p.Glu40Lys	p.E40K	ENST00000358485	NM_001080125.1	40	Gag/Aag	1/9	1	2	FACETS	0.888	0.791	0.991	0.888	0.791	0.991	CLONAL	1	TRUE	1	0.316565878648326	2		498	676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0040521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	324	724	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.561422659509902	1	FACETS	0.999	0.949	1	0.999	0.949	1	CLONAL	1	TRUE	0	0.598770771308106	1		724	759	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94926596	94926647	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TATATTTTAAGACAGATAAACTTACTTCCTTCTCTGGAATAAAGGCACTTGG	TATATTTTAAGACAGATAAACTTACTTCCTTCTCTGGAATAAAGGCACTTGG	-	novel	NA	P-0040521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	50	319	0	ENST00000536441.1:c.118_144+25del		p.X40_splice	ENST00000536441	NM_144665.3	40		2/10	0.598770771308106	3	FACETS	0.326	0.276	0.382	0.163	0.138	0.191	SUBCLONAL	1	TRUE	1	0.598770771308106	3		319	665	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322766	31322979	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGTTAGCCCCTGTGTGCATGCTGCTTCCCAGTAATGAGGCAGGGAACACTTCTACCTGGGGCTTGAAACCCCCAGTGGGACAAGAAAACCCAGACCCCACCCCTCACCCCTTCCCTACCTGAACTCTTCCTCCTACACATCACAGCAGCGACCACAGCTCCGATGACCACAACTGCTAGGACAGCCAGGCCAGCAACAATGCCCACGATGGGGA	CGTTAGCCCCTGTGTGCATGCTGCTTCCCAGTAATGAGGCAGGGAACACTTCTACCTGGGGCTTGAAACCCCCAGTGGGACAAGAAAACCCAGACCCCACCCCTCACCCCTTCCCTACCTGAACTCTTCCTCCTACACATCACAGCAGCGACCACAGCTCCGATGACCACAACTGCTAGGACAGCCAGGCCAGCAACAATGCCCACGATGGGGA	-	novel	NA	P-0040521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	19	182	0	ENST00000412585.2:c.917_1012+118del		p.X306_splice	ENST00000412585	NM_005514.6	306		5/8	0.527367186695289	0	FACETS	0.182	0.139	0.231			1	SUBCLONAL	1	TRUE	0	0.598770771308106	0		182	140	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323107	31323124	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGGGCTTCGGCAGCCC	GAGGGGCTTCGGCAGCCC	ACAT	novel	NA	P-0040521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	86	712	130	ENST00000412585.2:c.865_882delinsATGT	p.Gly289MetfsTer40	p.G289Mfs*40	ENST00000412585	NM_005514.6	289	GGGCTGCCGAAGCCCCTC/ATGT	4/8	0.527367186695289	0	FACETS	0.181	0.16	0.204			1	SUBCLONAL	1	TRUE	0	0.598770771308106	0		842	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578274	7578302	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGAGGAGGGGCCAGACCTAAGAGCAATCA	TGAGGAGGGGCCAGACCTAAGAGCAATCA	-	novel	NA	P-0040546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	141	481	0	ENST00000269305.4:c.560-13_575del		p.X187_splice	ENST00000269305	NM_001126112.2	187		6/11	0.338362407040656	1	FACETS	0.993	0.907	1	0.993	0.907	1	CLONAL	1	TRUE	0	0.338362407040656	1		481	697	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158497	26158497	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	113	438	0	ENST00000289316.2:c.100C>T	p.Arg34Cys	p.R34C	ENST00000289316	NM_138720.2	34	Cgc/Tgc	1/2	0.197887318674993	1	FACETS	0.693	0.623	0.766	0.693	0.623	0.766	INDETERMINATE	1	TRUE	0	0.338362407040656	1		438	801	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0040691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	810	324	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.3709987580208	31	FACETS	0.987	0.974	0.999			1	CLONAL	32	TRUE	NA	0.3709987580208	31		324	882	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0040691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	57	599	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.3709987580208	1	FACETS	0.897	0.776	1	0.897	0.776	1	CLONAL	1	TRUE	0	0.3709987580208	1		599	279	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829154	72829154	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	91	588	0	ENST00000268489.5:c.7427C>G	p.Ser2476Cys	p.S2476C	ENST00000268489	NM_006885.3	2476	tCc/tGc	9/10	0.340114770557844	2	FACETS	0.933	0.831	1	0.466	0.415	0.521	CLONAL	1	TRUE	0	0.3709987580208	2		588	526	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435032	56435032	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	166	598	0	ENST00000407977.2:c.2105G>C	p.Gly702Ala	p.G702A	ENST00000407977		702	gGa/gCa	9/10	0.3709987580208	10	FACETS	0.926	0.849	1			1	CLONAL	2	TRUE	NA	0.3709987580208	10		598	1200	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180500	56180500	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	18	282	0	ENST00000399503.3:c.3829G>C	p.Val1277Leu	p.V1277L	ENST00000399503	NM_005921.1	1277	Gtc/Ctc	16/20	0.340114770557844	2	FACETS	0.882	0.673	1	0.441	0.336	0.561	CLONAL	1	TRUE	0	0.3709987580208	2		282	110	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150022976	150022976	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs373625760	NA	P-0040691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	27	470	0	ENST00000253339.5:c.287G>T	p.Arg96Leu	p.R96L	ENST00000253339		96	cGg/cTg	1/7	0.300222292965987	3	FACETS	0.693	0.554	0.851	0.346	0.277	0.426	SUBCLONAL	1	TRUE	1	0.3709987580208	3		470	249	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0040836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	88	665	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	0.31916198216957	3	FACETS	0.7	0.619	0.787	0.35	0.309	0.394	SUBCLONAL	1	TRUE	1	0.319514371110985	3		665	913	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248494	59248824	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	GGACTGGATTATCAGGCGCTCCAGCTCGGGCGACGCCAGCTTGAGCAGCCCCACGTCGGGCGAGGTGAGGAGGTCCGAGTTCTTGGCGCGGAGGTGCGGCTTCAGGCTCCCCACTGGGTCGGCCAGGTTCAGGGTCATGCTCTGTTTCAGGATCTTGGGGTTACTGTAGCCATAAGGTCCGCTCTCGGACGGGAGGAACGAGGCGTTGAGGGCATCGTCATAGAAGGTCGTTTCCATCTTTGCAGTCATAGAACAGTCCGTCACTTCACGTGAGGTTAGTTTGGGCTGCGCGCACAAGTTTCGGGGCCGCAACAGGGCTGTGGCAAGCGGG	GGACTGGATTATCAGGCGCTCCAGCTCGGGCGACGCCAGCTTGAGCAGCCCCACGTCGGGCGAGGTGAGGAGGTCCGAGTTCTTGGCGCGGAGGTGCGGCTTCAGGCTCCCCACTGGGTCGGCCAGGTTCAGGGTCATGCTCTGTTTCAGGATCTTGGGGTTACTGTAGCCATAAGGTCCGCTCTCGGACGGGAGGAACGAGGCGTTGAGGGCATCGTCATAGAAGGTCGTTTCCATCTTTGCAGTCATAGAACAGTCCGTCACTTCACGTGAGGTTAGTTTGGGCTGCGCGCACAAGTTTCGGGGCCGCAACAGGGCTGTGGCAAGCGGG	-	novel	NA	P-0040836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	55	595	0	ENST00000371222.2:c.-82_249del		p.*28*	ENST00000371222	NM_002228.3	?-83/331		1/1	1	2	FACETS	0.574	0.49	0.665	0.574	0.49	0.665	SUBCLONAL	1	TRUE	1	0.319514371110985	2		595	600	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910506	32910506	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0040836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	89	351	1	ENST00000380152.3:c.2014A>T	p.Arg672Ter	p.R672*	ENST00000380152		672	Aga/Tga	11/27	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.319514371110985	2		352	516	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835780	68835780	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	92	573	0	ENST00000261769.5:c.371del	p.Arg124ProfsTer91	p.R124Pfs*91	ENST00000261769	NM_004360.3	124	cGc/cc	3/16	0.319514371110985	1	FACETS	0.978	0.872	1	0.978	0.872	1	CLONAL	1	TRUE	0	0.319514371110985	1		573	495	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404342	139404342	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	88	816	0	ENST00000277541.6:c.2812C>G	p.Arg938Gly	p.R938G	ENST00000277541	NM_017617.3	938	Cgg/Ggg	18/34	1	2	FACETS	0.551	0.487	0.62	0.551	0.487	0.62	SUBCLONAL	1	TRUE	1	0.319514371110985	2		816	999	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248494	59248824	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	GGACTGGATTATCAGGCGCTCCAGCTCGGGCGACGCCAGCTTGAGCAGCCCCACGTCGGGCGAGGTGAGGAGGTCCGAGTTCTTGGCGCGGAGGTGCGGCTTCAGGCTCCCCACTGGGTCGGCCAGGTTCAGGGTCATGCTCTGTTTCAGGATCTTGGGGTTACTGTAGCCATAAGGTCCGCTCTCGGACGGGAGGAACGAGGCGTTGAGGGCATCGTCATAGAAGGTCGTTTCCATCTTTGCAGTCATAGAACAGTCCGTCACTTCACGTGAGGTTAGTTTGGGCTGCGCGCACAAGTTTCGGGGCCGCAACAGGGCTGTGGCAAGCGGG	GGACTGGATTATCAGGCGCTCCAGCTCGGGCGACGCCAGCTTGAGCAGCCCCACGTCGGGCGAGGTGAGGAGGTCCGAGTTCTTGGCGCGGAGGTGCGGCTTCAGGCTCCCCACTGGGTCGGCCAGGTTCAGGGTCATGCTCTGTTTCAGGATCTTGGGGTTACTGTAGCCATAAGGTCCGCTCTCGGACGGGAGGAACGAGGCGTTGAGGGCATCGTCATAGAAGGTCGTTTCCATCTTTGCAGTCATAGAACAGTCCGTCACTTCACGTGAGGTTAGTTTGGGCTGCGCGCACAAGTTTCGGGGCCGCAACAGGGCTGTGGCAAGCGGG	-	novel	NA	P-0040836-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	107	595	0	ENST00000371222.2:c.-82_249del		p.*28*	ENST00000371222	NM_002228.3	?-83/331		1/1	1	2	FACETS	0.821	0.742	0.903	0.821	0.742	0.903	CLONAL	1	TRUE	1	0.648792355264673	2		595	402	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910506	32910506	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0040836-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	76	351	1	ENST00000380152.3:c.2014A>T	p.Arg672Ter	p.R672*	ENST00000380152		672	Aga/Tga	11/27	1	2	FACETS	0.763	0.676	0.855	0.763	0.676	0.855	SUBCLONAL	1	TRUE	1	0.648792355264673	2		352	307	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835780	68835780	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040836-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	123	573	0	ENST00000261769.5:c.371del	p.Arg124ProfsTer91	p.R124Pfs*91	ENST00000261769	NM_004360.3	124	cGc/cc	3/16	0.648792355264673	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.648792355264673	1		573	250	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0040836-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	98	342	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.648792355264673	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.648792355264673	1		342	196	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865152	57865152	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040836-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	116	531	0	ENST00000228682.2:c.2629C>A	p.Pro877Thr	p.P877T	ENST00000228682	NM_005269.2	877	Ccc/Acc	12/12	1	2	FACETS	0.974	0.887	1	0.974	0.887	1	CLONAL	1	TRUE	1	0.648792355264673	2		531	367	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667792	37667792	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040836-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	83	363	0	ENST00000447079.4:c.2677A>T	p.Thr893Ser	p.T893S	ENST00000447079	NM_015083.1	893	Aca/Tca	8/14	1	2	FACETS	0.8	0.712	0.891	0.8	0.712	0.891	SUBCLONAL	1	TRUE	1	0.648792355264673	2		363	320	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057743	180057743	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040836-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	100	535	0	ENST00000261937.6:c.212G>C	p.Gly71Ala	p.G71A	ENST00000261937	NM_182925.4	71	gGa/gCa	3/30	0.0848884065361453	5	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.648792355264673	5		535	458	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992683	68992683	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	127	531	0	ENST00000288368.4:c.1648G>C	p.Glu550Gln	p.E550Q	ENST00000288368	NM_024870.2	550	Gaa/Caa	16/40	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.795485562961465	2		531	304	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577439	64577460	+	frameshift_variant	Frame_Shift_Del	DEL	AGAAAATGCTCCACGAAGCCCA	AGAAAATGCTCCACGAAGCCCA	-	novel	NA	P-0040973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	340	701	0	ENST00000312049.6:c.122_143del	p.Leu41ArgfsTer71	p.L41Rfs*71	ENST00000312049	NM_130799.2	41	cTGGGCTTCGTGGAGCATTTTCTg/cg	2/10	0.795485562961465	1	FACETS	0.96	0.923	0.998	0.96	0.923	0.998	CLONAL	1	TRUE	0	0.795485562961465	1		701	536	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545575	106545575	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	36	383	0	ENST00000359195.3:c.3052C>G	p.Leu1018Val	p.L1018V	ENST00000359195	NM_002649.2	1018	Cta/Gta	11/11	1	2	FACETS	0.229	0.188	0.274	0.229	0.188	0.274	SUBCLONAL	1	TRUE	1	0.795485562961465	2		383	396	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939408	76939408	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	10	324	0	ENST00000373344.5:c.1340A>C	p.Glu447Ala	p.E447A	ENST00000373344	NM_000489.3	447	gAa/gCa	9/35	0.775208898719681	0	FACETS		NA	1			1	NA	1	TRUE	NA	0.795485562961465	0		324	68	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0041124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	28	371	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		371	408	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	291	1247	7	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.40414899461791	2		1254	1161	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	282	339	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.40414899461791	2		342	1036	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	326	399	2	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.892	0.852	0.932	1	0.997	1	CLONAL	3	TRUE	1	0.40414899461791	2		401	603	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	230	565	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.40414899461791	2		568	905	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850705	63850705	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs201178069	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	74	423	0	ENST00000279873.7:c.1489del	p.Ile497Ter	p.I497*	ENST00000279873	NM_032199.2	495	Aaa/aa	10/10	1	2	FACETS	0.758	0.666	0.857	0.758	0.666	0.857	SUBCLONAL	1	TRUE	1	0.40414899461791	2		423	483	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	300	489	17	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	1	2	FACETS	1	0.987	1	1	0.996	1	CLONAL	2	TRUE	1	0.40414899461791	2		506	666	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	227	1159	0	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.40414899461791	2		1159	1031	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	241	1003	11	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.40414899461791	2		1014	942	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	126	456	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.40414899461791	2		457	557	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	212	969	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.40414899461791	2		969	925	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	467	1010	9	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	1	0.40414899461791	2		1019	1032	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057937	27057937	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	211	813	0	ENST00000324856.7:c.1650del	p.Tyr551ThrfsTer68	p.Y551Tfs*68	ENST00000324856	NM_006015.4	549	Ccc/cc	3/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.40414899461791	2		813	836	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781878	9781878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	230	1102	1	ENST00000377346.4:c.2015G>A	p.Cys672Tyr	p.C672Y	ENST00000377346	NM_005026.3	672	tGc/tAc	16/24	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.40414899461791	2		1103	982	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1232964733	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	26	102	0	ENST00000324856.7:c.1015del	p.Ala339LeufsTer24	p.A339Lfs*24	ENST00000324856	NM_006015.4	337	tGg/tg	1/20	1	2	FACETS	0.894	0.717	1	0.894	0.717	1	CLONAL	1	TRUE	1	0.40414899461791	2		102	144	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941090	36941090	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	208	899	0	ENST00000361632.4:c.249G>T	p.Gln83His	p.Q83H	ENST00000361632		83	caG/caT	3/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.40414899461791	2		899	920	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433329	78433329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs537242451	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	148	479	2	ENST00000370768.2:c.272C>T	p.Pro91Leu	p.P91L	ENST00000370768	NM_003902.3	91	cCg/cTg	4/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.40414899461791	2		481	613	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163315481	163315481	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	84	445	0	ENST00000271452.3:c.821A>C	p.Glu274Ala	p.E274A	ENST00000271452	NM_145697.2	274	gAg/gCg	11/14	1	2	FACETS	0.881	0.781	0.987	0.881	0.781	0.987	CLONAL	1	TRUE	1	0.40414899461791	2		445	472	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100728	8100728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs771019738	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	250	990	4	ENST00000346208.3:c.708del	p.Ser237AlafsTer28	p.S237Afs*28	ENST00000346208		234	ttC/tt	3/6	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.40414899461791	2		994	1003	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604533	43604533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs546866208	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	263	969	1	ENST00000355710.3:c.1118C>T	p.Ala373Val	p.A373V	ENST00000355710	NM_020975.4	373	gCg/gTg	6/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.40414899461791	2		970	1026	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63661491	63661491	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	111	385	0	ENST00000279873.7:c.21+2T>C		p.X7_splice	ENST00000279873	NM_032199.2	7			1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.40414899461791	2		385	499	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683144	88683144	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	128	599	0	ENST00000372037.3:c.1354G>A	p.Glu452Lys	p.E452K	ENST00000372037	NM_004329.2	452	Gaa/Aaa	12/13	1	2	FACETS	0.953	0.865	1	0.953	0.865	1	CLONAL	1	TRUE	1	0.40414899461791	2		599	665	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683253	88683253	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	152	844	0	ENST00000372037.3:c.1463A>G	p.Asn488Ser	p.N488S	ENST00000372037	NM_004329.2	488	aAc/aGc	12/13	1	2	FACETS	0.797	0.728	0.869	0.797	0.728	0.869	SUBCLONAL	1	TRUE	1	0.40414899461791	2		844	944	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114799886	114799886	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs377242639	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	209	680	0	ENST00000543371.1:c.552+1G>A		p.X184_splice	ENST00000543371	NM_001198531.1	184			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.40414899461791	2		680	861	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8284885	8284885	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	115	648	3	ENST00000335790.3:c.25G>A	p.Gly9Ser	p.G9S	ENST00000335790	NM_002315.2	9	Ggc/Agc	1/4	1	2	FACETS	0.855	0.771	0.943	0.855	0.771	0.943	CLONAL	1	TRUE	1	0.40414899461791	2		651	666	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200877	67200877	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	244	906	1	ENST00000312629.5:c.870del	p.Tyr291ThrfsTer14	p.Y291Tfs*14	ENST00000312629	NM_003952.2	289	Ccc/cc	10/15	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.40414899461791	2		907	887	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944515	71944515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878853123	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	209	902	1	ENST00000298229.2:c.2071C>T	p.Arg691Trp	p.R691W	ENST00000298229	NM_001567.3	691	Cgg/Tgg	18/28	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.40414899461791	2		903	960	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115385	115115386	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	177	637	0	ENST00000257566.3:c.940dup	p.Arg314LysfsTer13	p.R314Kfs*13	ENST00000257566	NM_016569.3	314	aga/aAga	5/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.40414899461791	2		637	791	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73334684	73334684	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	84	334	0	ENST00000377767.4:c.2776T>C	p.Ser926Pro	p.S926P	ENST00000377767	NM_014953.3	926	Tcc/Ccc	20/21	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.40414899461791	2		334	380	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355942	73355942	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	257	958	1	ENST00000377767.4:c.29del	p.Lys10ArgfsTer7	p.K10Rfs*7	ENST00000377767	NM_014953.3	10	aAg/ag	1/21	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.40414899461791	2		959	1073	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518645	103518645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	106	386	0	ENST00000355739.4:c.2233G>A	p.Ala745Thr	p.A745T	ENST00000355739	NM_000123.3	745	Gca/Aca	10/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.40414899461791	2		386	466	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609957	81609957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756016910	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	111	439	0	ENST00000298171.2:c.1555C>T	p.Arg519Cys	p.R519C	ENST00000298171	NM_000369.2	519	Cgc/Tgc	10/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.40414899461791	2		439	423	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614463	38614463	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	114	523	0	ENST00000299084.4:c.234del	p.Asp79ThrfsTer42	p.D79Tfs*42	ENST00000299084	NM_152594.2	77	Aaa/aa	3/7	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.40414899461791	2		523	527	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961400	41961400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	150	564	0	ENST00000219905.7:c.308G>A	p.Arg103His	p.R103H	ENST00000219905	NM_001164273.1	103	cGc/cAc	2/24	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.40414899461791	2		564	579	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019477	42019477	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	176	699	0	ENST00000219905.7:c.3530C>A	p.Pro1177His	p.P1177H	ENST00000219905	NM_001164273.1	1177	cCt/cAt	10/24	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.40414899461791	2		699	720	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028735	42028735	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	161	685	0	ENST00000219905.7:c.4276del	p.Met1426TrpfsTer15	p.M1426Wfs*15	ENST00000219905	NM_001164273.1	1425	Aaa/aa	13/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.40414899461791	2		685	630	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996790	73996790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775147523	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	128	467	0	ENST00000318443.5:c.1346C>T	p.Ala449Val	p.A449V	ENST00000318443	NM_001024736.1	449	gCg/gTg	6/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.40414899461791	2		467	483	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	118	339	4	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.934	0.845	1	0.934	0.845	1	CLONAL	1	TRUE	1	0.40414899461791	2		343	625	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347924	347924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756071423	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	328	1309	0	ENST00000262320.3:c.1582G>A	p.Gly528Ser	p.G528S	ENST00000262320	NM_003502.3	528	Ggc/Agc	6/11	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.40414899461791	2		1309	1211	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788617	3788617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519884	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	188	526	1	ENST00000262367.5:c.4337G>A	p.Arg1446His	p.R1446H	ENST00000262367	NM_004380.2	1446	cGc/cAc	26/31	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.40414899461791	2		527	748	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	176	628	1	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.40414899461791	2		629	722	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822585	72822586	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs764626362	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	45	689	0	ENST00000268489.5:c.9589dup	p.Gln3197ProfsTer42	p.Q3197Pfs*42	ENST00000268489	NM_006885.3	3197	cag/cCag	10/10	1	2	FACETS	0.358	0.3	0.422	0.358	0.3	0.422	SUBCLONAL	1	TRUE	1	0.40414899461791	2		689	622	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357101	89357101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	283	910	1	ENST00000301030.4:c.533G>A	p.Arg178His	p.R178H	ENST00000301030	NM_001256183.1	178	cGc/cAc	6/13	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.40414899461791	2		911	973	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877120	89877120	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	155	449	0	ENST00000389301.3:c.517del	p.Ile173TyrfsTer19	p.I173Yfs*19	ENST00000389301	NM_000135.2	173	Ata/ta	5/43	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.40414899461791	2		449	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579350	7579350	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	252	1013	1	ENST00000269305.4:c.337T>C	p.Phe113Leu	p.F113L	ENST00000269305	NM_001126112.2	113	Ttc/Ctc	4/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.40414899461791	2		1014	983	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983099	7983099	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	166	724	0	ENST00000319144.4:c.915A>C	p.Gln305His	p.Q305H	ENST00000319144	NM_001139.2	305	caA/caC	7/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.40414899461791	2		724	647	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	157	394	2	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.40414899461791	2		396	719	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428014	33428014	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	209	806	1	ENST00000345365.6:c.945del	p.Thr316ProfsTer35	p.T316Pfs*35	ENST00000345365	NM_002878.3	315	ggG/gg	10/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.40414899461791	2		807	802	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	224	772	2	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.40414899461791	2		774	932	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246532	41246532	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357569	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	171	801	2	ENST00000357654.3:c.1016del	p.Lys339ArgfsTer2	p.K339Rfs*2	ENST00000357654	NM_007294.3	339	aAg/ag	10/23	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.40414899461791	2		803	784	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581306	48581306	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	169	581	0	ENST00000342988.3:c.610T>C	p.Ser204Pro	p.S204P	ENST00000342988	NM_005359.5	204	Tct/Cct	5/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.40414899461791	2		581	715	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56401588	56401588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367866327	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	105	447	1	ENST00000348428.3:c.1450G>A	p.Ala484Thr	p.A484T	ENST00000348428	NM_006785.3	484	Gcc/Acc	12/17	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.40414899461791	2		448	516	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213955	2213955	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	267	1017	0	ENST00000398665.3:c.1767C>G	p.Asn589Lys	p.N589K	ENST00000398665	NM_032482.2	589	aaC/aaG	18/28	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.40414899461791	2		1017	1031	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222490	2222490	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs995952663	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	291	895	1	ENST00000398665.3:c.3322C>T	p.Arg1108Ter	p.R1108*	ENST00000398665	NM_032482.2	1108	Cga/Tga	24/28	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.40414899461791	2		896	1063	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211698	5211698	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	246	941	0	ENST00000357368.4:c.5137A>G	p.Asn1713Asp	p.N1713D	ENST00000357368	NM_002850.3	1713	Aac/Gac	33/38	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.40414899461791	2		941	955	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11018786	11018786	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762459878	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	364	1187	3	ENST00000327064.4:c.418C>T	p.Arg140Trp	p.R140W	ENST00000327064	NM_199141.1	140	Cgg/Tgg	3/16	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.40414899461791	2		1190	1280	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367954	15367954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	232	1055	2	ENST00000263377.2:c.1372C>T	p.Pro458Ser	p.P458S	ENST00000263377	NM_058243.2	458	Ccg/Tcg	8/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.40414899461791	2		1057	1038	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277075	18277075	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	216	682	0	ENST00000222254.8:c.1522C>A	p.Arg508Ser	p.R508S	ENST00000222254	NM_005027.3	508	Cgc/Agc	12/16	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.40414899461791	2		682	779	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256769	19256769	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	172	704	5	ENST00000162023.5:c.944del	p.Pro315GlnfsTer?	p.P315Qfs*?	ENST00000162023		315	cCa/ca	13/13	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.40414899461791	2		709	702	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221276	36221276	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	285	954	1	ENST00000222270.7:c.5110C>T	p.Arg1704Cys	p.R1704C	ENST00000222270	NM_014727.1	1704	Cgc/Tgc	24/37	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.40414899461791	2		955	1169	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727880	41727880	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756018335	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	301	1157	2	ENST00000301178.4:c.505G>A	p.Val169Met	p.V169M	ENST00000301178	NM_021913.4	169	Gtg/Atg	4/20	0.40414899461791	3	FACETS	1	0.991	1	0.638	0.599	0.677	CLONAL	1	TRUE	1	0.40414899461791	3		1159	1404	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	301	499	1	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	0.40414899461791	3	FACETS	0.876	0.832	0.921	1	0.993	1	CLONAL	3	TRUE	1	0.40414899461791	3		500	681	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795609	42795609	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	466	1067	7	ENST00000575354.2:c.2694del	p.Ala900ProfsTer24	p.A900Pfs*24	ENST00000575354	NM_015125.3	897	Ccc/cc	10/20	0.40414899461791	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.40414899461791	3		1074	1272	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796957	42796957	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	642	1141	0	ENST00000575354.2:c.3415C>T	p.Pro1139Ser	p.P1139S	ENST00000575354	NM_015125.3	1139	Cca/Tca	14/20	0.40414899461791	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	1	0.40414899461791	3		1141	1546	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905055	50905055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	198	807	1	ENST00000440232.2:c.342del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	113	Ggg/gg	4/27	0.40414899461791	3	FACETS	1	0.985	1	0.618	0.572	0.665	CLONAL	1	TRUE	1	0.40414899461791	3		808	953	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910391	50910391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201038430	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	592	1059	1	ENST00000440232.2:c.1646G>A	p.Arg549His	p.R549H	ENST00000440232	NM_002691.3	549	cGt/cAt	13/27	0.40414899461791	3	FACETS	0.834	0.803	0.866	1	0.996	1	CLONAL	3	TRUE	1	0.40414899461791	3		1060	1407	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	316	1261	7	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.40414899461791	2		1268	1269	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456453	29456453	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1558630501	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	233	877	2	ENST00000389048.3:c.2465del	p.Gly822ValfsTer9	p.G822Vfs*9	ENST00000389048	NM_004304.4	822	gGt/gt	14/29	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.40414899461791	2		879	904	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028231	48028231	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	136	430	0	ENST00000234420.5:c.3109T>A	p.Phe1037Ile	p.F1037I	ENST00000234420	NM_000179.2	1037	Ttc/Atc	4/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.40414899461791	2		430	545	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050347	128050347	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479291031	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	110	671	1	ENST00000285398.2:c.310G>A	p.Ala104Thr	p.A104T	ENST00000285398	NM_000122.1	104	Gca/Aca	3/15	1	2	FACETS	0.739	0.664	0.818	0.739	0.664	0.818	SUBCLONAL	1	TRUE	1	0.40414899461791	2		672	737	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719755	190719755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750449314	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	63	298	0	ENST00000441310.2:c.1757G>A	p.Arg586His	p.R586H	ENST00000441310	NM_000534.4	586	cGt/cAt	9/13	1	2	FACETS	0.959	0.835	1	0.959	0.835	1	CLONAL	1	TRUE	1	0.40414899461791	2		298	325	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944554	40944554	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	173	634	0	ENST00000373198.4:c.1948del	p.Val650Ter	p.V650*	ENST00000373198	NM_133170.3	650	Gtg/tg	12/32	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.40414899461791	2		634	641	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419957	41419957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369230837	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	220	767	1	ENST00000373198.4:c.364G>A	p.Val122Ile	p.V122I	ENST00000373198	NM_133170.3	122	Gtc/Atc	3/32	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.40414899461791	2		768	830	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37045935	37045935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750781	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	142	512	0	ENST00000231790.2:c.350C>T	p.Thr117Met	p.T117M	ENST00000231790	NM_000249.3	117	aCg/aTg	4/19	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.40414899461791	2		512	618	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067433	37067433	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	175	698	1	ENST00000231790.2:c.1348del	p.Asp450IlefsTer41	p.D450Ifs*41	ENST00000231790	NM_000249.3	448	gaG/ga	12/19	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.40414899461791	2		699	713	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437768	52437768	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs150029305	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	199	898	0	ENST00000460680.1:c.1393A>G	p.Ile465Val	p.I465V	ENST00000460680	NM_004656.3	465	Atc/Gtc	13/17	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.40414899461791	2		898	861	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468381	89468381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754102338	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	102	256	1	ENST00000336596.2:c.1915C>T	p.Arg639Cys	p.R639C	ENST00000336596	NM_005233.5	639	Cgc/Tgc	11/17	0.40414899461791	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.40414899461791	1		257	270	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169953087	169953087	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	158	597	0	ENST00000295797.4:c.171G>A	p.Met57Ile	p.M57I	ENST00000295797	NM_002740.5	57	atG/atA	2/18	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.40414899461791	2		597	707	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984966	55984966	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	106	466	0	ENST00000263923.4:c.163G>A	p.Gly55Arg	p.G55R	ENST00000263923	NM_002253.2	55	Gga/Aga	3/30	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.40414899461791	2		466	491	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535280	66535280	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs527913976	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	239	791	1	ENST00000273854.3:c.181G>A	p.Val61Met	p.V61M	ENST00000273854	NM_004439.5	61	Gtg/Atg	1/18	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.40414899461791	2		792	805	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	184	596	0	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.40414899461791	2		596	795	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539266	187539266	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	92	459	0	ENST00000441802.2:c.8474del	p.Gly2825GlufsTer4	p.G2825Efs*4	ENST00000441802	NM_005245.3	2825	gGa/ga	10/27	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.40414899461791	2		459	393	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751906	57751906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	180	543	1	ENST00000274289.3:c.1331C>T	p.Ala444Val	p.A444V	ENST00000274289	NM_006622.3	444	gCt/gTt	10/14	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.40414899461791	2		544	724	SUCCESS
APC	324	MSKCC	GRCh37	5	112151262	112151262	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764841552	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	143	480	0	ENST00000257430.4:c.905G>A	p.Arg302Gln	p.R302Q	ENST00000257430	NM_000038.5	302	cGa/cAa	9/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.40414899461791	2		480	541	SUCCESS
APC	324	MSKCC	GRCh37	5	112164604	112164604	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554082118	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	115	340	0	ENST00000257430.4:c.1682del	p.Lys561ArgfsTer9	p.K561Rfs*9	ENST00000257430	NM_000038.5	560	Aaa/aa	14/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.40414899461791	2		340	471	SUCCESS
APC	324	MSKCC	GRCh37	5	112175651	112175651	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	116	412	1	ENST00000257430.4:c.4364del	p.Asn1455IlefsTer18	p.N1455Ifs*18	ENST00000257430	NM_000038.5	1454	Aaa/aa	16/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.40414899461791	2		413	490	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515273	149515273	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	252	896	0	ENST00000261799.4:c.209del	p.Pro70HisfsTer18	p.P70Hfs*18	ENST00000261799	NM_002609.3	70	cCa/ca	3/23	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.40414899461791	2		896	913	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720865	176720865	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	195	641	0	ENST00000439151.2:c.6496A>G	p.Ile2166Val	p.I2166V	ENST00000439151	NM_022455.4	2166	Atc/Gtc	23/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.40414899461791	2		641	770	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058747	180058748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755445139	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	223	963	1	ENST00000261937.6:c.89dup	p.Thr31AspfsTer15	p.T31Dfs*15	ENST00000261937	NM_182925.4	30	ccg/ccCg	2/30	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.40414899461791	2		964	1010	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324006	31324006	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41543920	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	33	133	0	ENST00000412585.2:c.557G>A	p.Gly186Asp	p.G186D	ENST00000412585	NM_005514.6	186	gGc/gAc	3/8	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.40414899461791	2		133	116	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800512	32800512	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	297	1225	0	ENST00000374899.4:c.1035del	p.Phe345LeufsTer35	p.F345Lfs*35	ENST00000374899	NM_018833.2	345	ttT/tt	6/12	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.40414899461791	2		1225	1282	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149982926	149982926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777519756	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	111	484	0	ENST00000253339.5:c.3332C>T	p.Ser1111Leu	p.S1111L	ENST00000253339		1111	tCg/tTg	7/7	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.40414899461791	2		484	470	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525077	157525077	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1484341574	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	110	362	0	ENST00000346085.5:c.4972A>G	p.Ile1658Val	p.I1658V	ENST00000346085	NM_020732.3	1658	Att/Gtt	19/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.40414899461791	2		362	403	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974121	2974121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760308478	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	106	643	0	ENST00000396946.4:c.1484C>T	p.Pro495Leu	p.P495L	ENST00000396946	NM_032415.4	495	cCg/cTg	10/25	1	2	FACETS	0.808	0.726	0.896	0.808	0.726	0.896	CLONAL	1	TRUE	1	0.40414899461791	2		643	649	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6045646	6045646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	37	108	0	ENST00000265849.7:c.40G>A	p.Ala14Thr	p.A14T	ENST00000265849	NM_000535.5	14	Gcc/Acc	2/15	1	2	FACETS	0.782	0.661	0.911	1	0.96	1	CLONAL	2	TRUE	1	0.40414899461791	2		108	117	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	181	500	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.40414899461791	2		500	784	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5073768	5073768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	133	470	0	ENST00000381652.3:c.1847G>A	p.Cys616Tyr	p.C616Y	ENST00000381652	NM_004972.3	616	tGt/tAt	14/25	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.40414899461791	2		470	565	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209465	98209465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	238	945	1	ENST00000331920.6:c.4073G>A	p.Gly1358Asp	p.G1358D	ENST00000331920	NM_000264.3	1358	gGc/gAc	23/24	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.40414899461791	2		946	960	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797261	135797261	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	84	325	0	ENST00000298552.3:c.608del	p.Leu203CysfsTer7	p.L203Cfs*7	ENST00000298552	NM_001162426.1	203	tTg/tg	7/23	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.40414899461791	2		325	334	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390805	139390805	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	148	1156	0	ENST00000277541.6:c.7386del	p.Ala2463ProfsTer14	p.A2463Pfs*14	ENST00000277541	NM_017617.3	2462	ccC/cc	34/34	1	2	FACETS	0.642	0.585	0.702	0.642	0.585	0.702	SUBCLONAL	1	TRUE	1	0.40414899461791	2		1156	1140	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139811026	139811026	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	249	986	1	ENST00000247668.2:c.637C>T	p.Arg213Ter	p.R213*	ENST00000247668	NM_021138.3	213	Cga/Tga	7/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.40414899461791	2		987	1085	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820312	139820312	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	226	915	0	ENST00000247668.2:c.1465G>A	p.Ala489Thr	p.A489T	ENST00000247668	NM_021138.3	489	Gcc/Acc	11/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.40414899461791	2		915	954	SUCCESS
AR	367	MSKCC	GRCh37	X	66765142	66765142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747293337	NA	P-0041144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	147	310	0	ENST00000374690.3:c.154G>A	p.Ala52Thr	p.A52T	ENST00000374690	NM_000044.3	52	Gcc/Acc	1/8	1	1	FACETS	1	0.981	1	1	0.993	1	CLONAL	2	TRUE	0	0.40414899461791	1		310	257	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578546	7578564	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGGGAGTACTGTAGGAAG	AGGGGAGTACTGTAGGAAG	-	novel	NA	P-0041235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	201	736	0	ENST00000269305.4:c.376-10_384del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	0.402576802026679	4	FACETS	1	0.967	1	0.71	0.661	0.76	CLONAL	2	FALSE	1	0.402576802026679	4		736	658	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843697	151843697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151112171	NA	P-0041235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	49	387	0	ENST00000262189.6:c.14018G>A	p.Arg4673His	p.R4673H	ENST00000262189	NM_170606.2	4673	cGc/cAc	53/59	0.402576802026679	3	FACETS	0.845	0.719	0.983	0.423	0.359	0.492	CLONAL	1	FALSE	1	0.402576802026679	3		387	346	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778813	9778813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1179481484	NA	P-0041235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	136	645	0	ENST00000377346.4:c.1082C>T	p.Ser361Leu	p.S361L	ENST00000377346	NM_005026.3	361	tCg/tTg	9/24	0.402576802026679	6	FACETS	1	0.97	1	0.29	0.263	0.319	CLONAL	1	FALSE	2	0.402576802026679	6		645	1050	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0041296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	141	453	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.467735531448052	2		453	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0041296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	16	439	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.092	0.067	0.122	0.092	0.067	0.122	SUBCLONAL	1	TRUE	1	0.467735531448052	2		440	741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0041296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	224	755	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	1	2	FACETS	0.895	0.833	0.959	0.895	0.833	0.959	CLONAL	1	TRUE	1	0.467735531448052	2		755	1070	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139831	55139831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758137485	NA	P-0041296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	138	379	0	ENST00000257290.5:c.1492G>A	p.Ala498Thr	p.A498T	ENST00000257290	NM_006206.4	498	Gcc/Acc	10/23	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.467735531448052	2		379	574	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179139	123179139	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	30	330	0	ENST00000218089.9:c.588G>A	p.Met196Ile	p.M196I	ENST00000218089	NM_001042749.1	196	atG/atA	8/35	1	2	FACETS	0.395	0.318	0.481	0.395	0.318	0.481	SUBCLONAL	1	TRUE	1	0.467735531448052	2		330	325	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878151	48878151	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778869	NA	P-0041296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	56	129	0	ENST00000267163.4:c.103C>T	p.Gln35Ter	p.Q35*	ENST00000267163	NM_000321.2	35	Cag/Tag	1/27	0.467735531448052	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.467735531448052	1		129	168	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160488	108160488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730881369	NA	P-0041296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	107	309	0	ENST00000278616.4:c.4396C>T	p.Arg1466Ter	p.R1466*	ENST00000278616	NM_000051.3	1466	Cga/Tga	29/63	0.467735531448052	1	FACETS	0.982	0.89	1	0.982	0.89	1	CLONAL	1	TRUE	0	0.467735531448052	1		309	357	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589599	67589604	+	inframe_deletion	In_Frame_Del	DEL	TCAGTT	TCAGTT	-	novel	NA	P-0041296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	34	148	0	ENST00000274335.5:c.1365_1370del	p.Phe456_Gln457del	p.F456_Q457del	ENST00000274335		454	acTCAGTTt/act	10/15	1	2	FACETS	0.812	0.671	0.967	0.812	0.671	0.967	CLONAL	1	TRUE	1	0.467735531448052	2		148	179	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945543	54945543	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs774552788	NA	P-0041296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	174	757	0	ENST00000312783.6:c.1027C>T	p.Arg343Trp	p.R343W	ENST00000312783	NM_198436.1	343	Cgg/Tgg	9/10	1	2	FACETS	0.84	0.773	0.909	0.84	0.773	0.909	CLONAL	1	TRUE	1	0.467735531448052	2		757	886	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339565	116339565	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs779093896	NA	P-0041296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	51	206	0	ENST00000397752.3:c.427C>T	p.Arg143Ter	p.R143*	ENST00000397752	NM_000245.2	143	Cga/Tga	2/21	1	2	FACETS	0.739	0.632	0.855	0.739	0.632	0.855	SUBCLONAL	1	TRUE	1	0.467735531448052	2		206	295	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692827	89692836	+	frameshift_variant	Frame_Shift_Del	DEL	TTTGTGAAGA	TTTGTGAAGA	-	novel	NA	P-0041296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	36	135	0	ENST00000371953.3:c.312_321del	p.Cys105LeufsTer5	p.C105Lfs*5	ENST00000371953	NM_000314.4	104	tTTTGTGAAGAt/tt	5/9	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.467735531448052	2		135	130	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375375	15375375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146695616	NA	P-0041296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	183	610	0	ENST00000263377.2:c.1052C>T	p.Ser351Leu	p.S351L	ENST00000263377	NM_058243.2	351	tCg/tTg	6/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.467735531448052	2		610	740	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637700	52637700	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	88	230	0	ENST00000394830.3:c.2616T>G	p.Phe872Leu	p.F872L	ENST00000394830	NM_018313.4	872	ttT/ttG	18/30	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.467735531448052	2		230	313	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0041327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	157	515	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.898	0.826	0.972	0.898	0.826	0.972	CLONAL	1	TRUE	1	0.567877138220318	2		515	616	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222515	2222515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	193	621	0	ENST00000326181.6:c.709C>T	p.Pro237Ser	p.P237S	ENST00000326181	NM_032271.2	237	Ccc/Tcc	9/21	1	2	FACETS	0.86	0.798	0.925	0.86	0.798	0.925	CLONAL	1	TRUE	1	0.567877138220318	2		621	790	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860755	3860755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs978232300	NA	P-0041327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	98	321	0	ENST00000262367.5:c.824C>T	p.Pro275Leu	p.P275L	ENST00000262367	NM_004380.2	275	cCa/cTa	3/31	1	2	FACETS	0.76	0.682	0.843	0.76	0.682	0.843	SUBCLONAL	1	TRUE	1	0.567877138220318	2		321	454	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117541	4117541	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519808	NA	P-0041327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	115	245	0	ENST00000262948.5:c.179A>C	p.Gln60Pro	p.Q60P	ENST00000262948	NM_030662.3	60	cAg/cCg	2/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.567877138220318	2		245	350	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965997	18965997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	201	548	0	ENST00000262803.5:c.1490G>A	p.Gly497Glu	p.G497E	ENST00000262803	NM_002911.3	497	gGg/gAg	11/24	1	2	FACETS	0.919	0.854	0.986	0.919	0.854	0.986	CLONAL	1	TRUE	1	0.567877138220318	2		548	770	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0041338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	214	634	0	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.505290098073796	1	FACETS	0.912	0.851	0.974	0.912	0.851	0.974	CLONAL	1	TRUE	0	0.505290098073796	1		634	694	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966617	25966617	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	255	592	0	ENST00000435504.4:c.2589G>C	p.Lys863Asn	p.K863N	ENST00000435504		863	aaG/aaC	13/13	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.505290098073796	2		592	992	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931654	39931654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749047692	NA	P-0041338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	265	617	0	ENST00000378444.4:c.2945C>T	p.Thr982Ile	p.T982I	ENST00000378444	NM_001123385.1	982	aCc/aTc	4/15	1	2	FACETS	0.988	0.926	1	0.988	0.926	1	CLONAL	1	TRUE	1	0.505290098073796	2		617	1062	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574035	7574035	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs867389695	NA	P-0041350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	435	445	0	ENST00000269305.4:c.994-2A>G		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.751532603327399	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.751532603327399	2		445	572	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867546	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs11466445	NA	P-0041350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	19	14	0	ENST00000374994.4:c.70_78del	p.Ala24_Ala26del	p.A24_A26del	ENST00000374994	NM_004612.2	17	ctGGCGGCGGCg/ctg	1/9	0.751141517774331	3	FACETS	1	0.897	1	0.422	0.333	0.517	CLONAL	1	TRUE	0	0.751532603327399	3		14	55	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402595	20402595	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	193	290	0	ENST00000346618.3:c.132C>A	p.Phe44Leu	p.F44L	ENST00000346618	NM_001949.4	44	ttC/ttA	1/7	0.751532603327399	5	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.751532603327399	5		290	915	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184438	7184438	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	251	535	0	ENST00000302850.5:c.863A>G	p.Asp288Gly	p.D288G	ENST00000302850	NM_000208.2	288	gAc/gGc	3/22	1	2	FACETS	0.923	0.867	0.979	0.923	0.867	0.979	CLONAL	1	TRUE	1	0.751532603327399	2		535	724	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750704	39750704	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	107	217	0	ENST00000361337.2:c.2104G>T	p.Glu702Ter	p.E702*	ENST00000361337	NM_003286.2	702	Gaa/Taa	20/21	0.742763986029022	4	FACETS	0.957	0.862	1	0.319	0.287	0.353	CLONAL	1	TRUE	1	0.751532603327399	4		217	521	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620473	52620473	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	144	344	0	ENST00000394830.3:c.3280A>G	p.Ser1094Gly	p.S1094G	ENST00000394830	NM_018313.4	1094	Agt/Ggt	21/30	0.751532603327399	2	FACETS	0.873	0.803	0.945	0.436	0.401	0.473	CLONAL	1	TRUE	0	0.751532603327399	2		344	439	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562136	176562136	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	188	358	0	ENST00000439151.2:c.32A>G	p.Asn11Ser	p.N11S	ENST00000439151	NM_022455.4	11	aAt/aGt	2/23	0.751532603327399	3	FACETS	0.951	0.881	1	0.475	0.44	0.512	CLONAL	1	TRUE	1	0.751532603327399	3		358	724	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562256	176562256	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	243	480	0	ENST00000439151.2:c.152C>A	p.Ser51Ter	p.S51*	ENST00000439151	NM_022455.4	51	tCg/tAg	2/23	0.751532603327399	3	FACETS	0.963	0.901	1	0.481	0.45	0.514	CLONAL	1	TRUE	1	0.751532603327399	3		480	924	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528303	157528303	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	273	551	0	ENST00000346085.5:c.6028G>C	p.Asp2010His	p.D2010H	ENST00000346085	NM_020732.3	2010	Gat/Cat	20/20	0.751532603327399	2	FACETS	0.998	0.942	1	0.499	0.471	0.528	CLONAL	1	TRUE	0	0.751532603327399	2		551	728	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528996	157528996	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	125	245	0	ENST00000346085.5:c.6721G>C	p.Asp2241His	p.D2241H	ENST00000346085	NM_020732.3	2241	Gat/Cat	20/20	0.751532603327399	2	FACETS	0.984	0.902	1	0.492	0.451	0.534	CLONAL	1	TRUE	0	0.751532603327399	2		245	338	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879337	151879338	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0041350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	290	328	0	ENST00000262189.6:c.5607_5608del	p.Gln1870GlyfsTer18	p.Q1870Gfs*18	ENST00000262189	NM_170606.2	1869	tcTCag/tcag	36/59	0.751141517774331	3	FACETS	0.892	0.848	0.937	0.595	0.565	0.625	CLONAL	2	TRUE	0	0.751532603327399	3		328	595	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519999	NA	P-0041435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	417	738	0	ENST00000269305.4:c.716A>G	p.Asn239Ser	p.N239S	ENST00000269305	NM_001126112.2	239	aAc/aGc	7/11	0.430943575520138	2	FACETS	1	0.98	1	1	0.997	1	CLONAL	3	TRUE	0	0.430943575520138	2		738	631	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0041435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	260	404	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	0.430943575520138	6	FACETS	0.903	0.852	0.954	1	0.989	1	CLONAL	4	TRUE	3	0.430943575520138	6		404	622	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797404	42797404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748515698	NA	P-0041435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	700	996	2	ENST00000575354.2:c.3766C>T	p.Arg1256Trp	p.R1256W	ENST00000575354	NM_015125.3	1256	Cgg/Tgg	15/20	0.430943575520138	4	FACETS	0.966	0.943	0.989	1	0.997	1	CLONAL	5	TRUE	0	0.430943575520138	4		998	962	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0041456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	106	324	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.490264212495712	3	FACETS	1	0.96	1	0.56	0.506	0.616	CLONAL	1	TRUE	1	0.658931540201719	3		324	382	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115435	115115437	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	rs1319662056	NA	P-0041456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	134	350	0	ENST00000257566.3:c.889_891del	p.Asn297del	p.N297del	ENST00000257566	NM_016569.3	297	AAC/-	5/8	0.289427000148554	3	FACETS	0.897	0.818	0.979	0.448	0.409	0.49	INDETERMINATE	1	TRUE	1	0.658931540201719	3		350	603	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100340	8100341	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0041456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	169	449	0	ENST00000346208.3:c.315_316dup	p.His106ProfsTer90	p.H106Pfs*90	ENST00000346208		105	agc/agCCc	3/6	0.647676890262928	3	FACETS	1	0.948	1	0.517	0.477	0.559	CLONAL	1	TRUE	1	0.658931540201719	3		449	659	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671816	30671816	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	61	414	0	ENST00000376406.3:c.5144T>G	p.Ile1715Ser	p.I1715S	ENST00000376406	NM_014641.2	1715	aTt/aGt	10/15	1	2	FACETS	0.379	0.328	0.436	0.379	0.328	0.436	SUBCLONAL	1	TRUE	1	0.658931540201719	2		414	488	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681579	30681579	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0041456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	51	307	0	ENST00000376406.3:c.517+1G>C		p.X173_splice	ENST00000376406	NM_014641.2	173			1	2	FACETS	0.36	0.306	0.419	0.36	0.306	0.419	SUBCLONAL	1	TRUE	1	0.658931540201719	2		307	430	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0041968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	209	588	2	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.271709390118585	3	FACETS	0.875	0.816	0.935	0.875	0.816	0.935	CLONAL	3	TRUE	0	0.275334201029633	3		590	658	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377024	118377024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781919840	NA	P-0041968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	47	373	0	ENST00000534358.1:c.10417C>T	p.Arg3473Cys	p.R3473C	ENST00000534358	NM_005933.3	3473	Cgt/Tgt	27/36	0.274911888020003	4	FACETS	1	0.905	1	0.367	0.31	0.429	CLONAL	1	TRUE	1	0.275334201029633	4		373	396	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450846	70450846	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	70	460	0	ENST00000373644.4:c.5686G>C	p.Ala1896Pro	p.A1896P	ENST00000373644	NM_030625.2	1896	Gct/Cct	12/12	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.275334201029633	2		460	433	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321193	62321193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1332347156	NA	P-0041968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	248	772	1	ENST00000360203.5:c.2116G>A	p.Gly706Arg	p.G706R	ENST00000360203	NM_001283009.1	706	Gga/Aga	24/35	0.275334201029633	6	FACETS	0.933	0.873	0.995	0.7	0.655	0.746	CLONAL	3	TRUE	2	0.275334201029633	6		773	998	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547876	41547876	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	52	412	1	ENST00000263253.7:c.2857A>T	p.Asn953Tyr	p.N953Y	ENST00000263253	NM_001429.3	953	Aat/Tat	15/31	0.165762781727305	3	FACETS	1	0.87	1	0.34	0.29	0.395	CLONAL	1	TRUE	0	0.275334201029633	3		413	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs760043106	NA	P-0042169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	156	579	0	ENST00000269305.4:c.584T>A	p.Ile195Asn	p.I195N	ENST00000269305	NM_001126112.2	195	aTc/aAc	6/11	0.259513611994824	2	FACETS	0.95	0.873	1	0.95	0.873	1	CLONAL	2	TRUE	0	0.259513611994824	2		579	633	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	217	644	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.259513611994824	2	FACETS	0.864	0.808	0.922	1	0.989	1	CLONAL	3	TRUE	0	0.259513611994824	2		644	645	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939456	68939456	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0042169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	32	286	0	ENST00000288368.4:c.442-1G>T		p.X148_splice	ENST00000288368	NM_024870.2	148			1	2	FACETS	0.54	0.437	0.655	0.54	0.437	0.655	SUBCLONAL	1	TRUE	1	0.259513611994824	2		286	457	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532688	46532688	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	108	497	0	ENST00000262741.5:c.390T>G	p.Phe130Leu	p.F130L	ENST00000262741	NM_003629.3	130	ttT/ttG	4/10	1	2	FACETS	0.998	0.899	1	0.998	0.899	1	CLONAL	1	TRUE	1	0.398512835734998	2		497	543	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984776	55984776	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	146	501	0	ENST00000263923.4:c.353T>C	p.Val118Ala	p.V118A	ENST00000263923	NM_002253.2	118	gTt/gCt	3/30	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.398512835734998	2		501	660	SUCCESS
AR	367	MSKCC	GRCh37	X	66766505	66766505	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1403123525	NA	P-0042174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	181	327	0	ENST00000374690.3:c.1517G>A	p.Gly506Asp	p.G506D	ENST00000374690	NM_000044.3	506	gGc/gAc	1/8	1	1	FACETS	0.838	0.782	0.895	1	0.992	1	CLONAL	2	TRUE	0	0.398512835734998	1		327	434	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0042484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	93	564	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.74	0.663	0.821	0.74	0.663	0.821	SUBCLONAL	1	TRUE	1	0.668294152653088	2		564	376	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0042484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	209	425	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	0.668294152653088	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.668294152653088	3		425	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882025	NA	P-0042484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	292	786	0	ENST00000269305.4:c.646G>C	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ctg	6/11	0.160355732564734	1	FACETS	0.718	0.679	0.759	0.718	0.679	0.759	INDETERMINATE	1	TRUE	0	0.668294152653088	1		786	810	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578218	7578218	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060501198	NA	P-0042484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	284	783	0	ENST00000269305.4:c.631A>G	p.Thr211Ala	p.T211A	ENST00000269305	NM_001126112.2	211	Act/Gct	6/11	0.160355732564734	1	FACETS	0.73	0.689	0.772	0.73	0.689	0.772	INDETERMINATE	1	TRUE	0	0.668294152653088	1		783	775	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129330	152129330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042513-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	86	363	0	ENST00000206249.3:c.283G>A	p.Gly95Arg	p.G95R	ENST00000206249	NM_000125.3	95	Ggg/Agg	1/8	0.379515357069225	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.379515357069225	1		363	353	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112575	115112575	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042513-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	92	359	0	ENST00000257566.3:c.1165G>T	p.Ala389Ser	p.A389S	ENST00000257566	NM_016569.3	389	Gcc/Tcc	7/8	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.379515357069225	2		359	484	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938358	76938358	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042513-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	58	304	0	ENST00000373344.5:c.2390C>A	p.Ser797Ter	p.S797*	ENST00000373344	NM_000489.3	797	tCa/tAa	9/35	0.293501213280678	1	FACETS	0.575	0.495	0.661	0.575	0.495	0.661	SUBCLONAL	1	TRUE	0	0.379515357069225	1		304	431	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239669	105239669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042513-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	46	439	0	ENST00000349310.3:c.876C>A	p.Asp292Glu	p.D292E	ENST00000349310	NM_001014432.1	292	gaC/gaA	11/15	0.235671644466208	3	FACETS	0.453	0.381	0.534	0.151	0.127	0.178	SUBCLONAL	1	TRUE	0	0.379515357069225	3		439	636	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40486068	40486068	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0042513-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	95	303	0	ENST00000264657.5:c.798-1G>A		p.X266_splice	ENST00000264657	NM_139276.2	266			1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.379515357069225	2		303	486	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41558741	41558741	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042513-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	34	206	0	ENST00000263253.7:c.3686A>G	p.Glu1229Gly	p.E1229G	ENST00000263253	NM_001429.3	1229	gAa/gGa	21/31	0.379515357069225	1	FACETS	0.454	0.371	0.546	0.454	0.371	0.546	SUBCLONAL	1	TRUE	0	0.379515357069225	1		206	320	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247264	153247264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042513-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	104	355	0	ENST00000281708.4:c.1538G>A	p.Arg513Lys	p.R513K	ENST00000281708	NM_033632.3	513	aGg/aAg	10/12	1	2	FACETS	0.83	0.744	0.921	0.83	0.744	0.921	CLONAL	1	TRUE	1	0.379515357069225	2		355	660	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0042516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	297	703	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.718204044131998	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.725972546989491	1		703	492	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575035	64575035	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886039416	NA	P-0042516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	219	529	0	ENST00000312049.6:c.772C>T	p.Gln258Ter	p.Q258*	ENST00000312049	NM_130799.2	258	Cag/Tag	4/10	0.724227243376654	2	FACETS	0.979	0.917	1	0.49	0.458	0.522	CLONAL	1	TRUE	0	0.725972546989491	2		529	616	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	174	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.316026092326882	4	FACETS	1	0.979	1	0.775	0.717	0.835	CLONAL	2	TRUE	1	0.327416482670373	4		485	607	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023707	27023708	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0042764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	86	397	0	ENST00000324856.7:c.817dup	p.Ala273GlyfsTer127	p.A273Gfs*127	ENST00000324856	NM_006015.4	271	-/G	1/20	0.312226041311395	3	FACETS	0.875	0.774	0.983	0.437	0.387	0.492	CLONAL	1	TRUE	1	0.327416482670373	3		397	699	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097695	27097698	+	frameshift_variant	Frame_Shift_Del	DEL	AGTA	AGTA	-	novel	NA	P-0042764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	212	654	0	ENST00000324856.7:c.3284_3287del	p.Gln1095LeufsTer65	p.Q1095Lfs*65	ENST00000324856	NM_006015.4	1095	cAGTAt/ct	12/20	0.312226041311395	3	FACETS	0.917	0.853	0.982	0.917	0.853	0.982	CLONAL	2	TRUE	1	0.327416482670373	3		654	822	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026114	71026114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1240117000	NA	P-0042764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	164	457	1	ENST00000318789.4:c.1508G>A	p.Arg503Gln	p.R503Q	ENST00000318789	NM_032682.5	503	cGa/cAa	17/21	0.327416482670373	4	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	2	0.327416482670373	4		458	635	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042764-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	212	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.664144435370418	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	3	TRUE	1	0.664144435370418	4		485	348	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023707	27023708	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0042764-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	67	397	0	ENST00000324856.7:c.817dup	p.Ala273GlyfsTer127	p.A273Gfs*127	ENST00000324856	NM_006015.4	271	-/G	1/20	0.651509065392536	3	FACETS	0.988	0.868	1	0.494	0.434	0.558	CLONAL	1	TRUE	1	0.664144435370418	3		397	272	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097695	27097698	+	frameshift_variant	Frame_Shift_Del	DEL	AGTA	AGTA	-	novel	NA	P-0042764-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	215	654	0	ENST00000324856.7:c.3284_3287del	p.Gln1095LeufsTer65	p.Q1095Lfs*65	ENST00000324856	NM_006015.4	1095	cAGTAt/ct	12/20	0.651509065392536	3	FACETS	0.927	0.872	0.983	0.927	0.872	0.983	CLONAL	2	TRUE	1	0.664144435370418	3		654	465	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026114	71026114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1240117000	NA	P-0042764-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	185	457	1	ENST00000318789.4:c.1508G>A	p.Arg503Gln	p.R503Q	ENST00000318789	NM_032682.5	503	cGa/cAa	17/21	0.602409208254664	4	FACETS	0.898	0.836	0.962	0.898	0.836	0.962	CLONAL	2	TRUE	2	0.664144435370418	4		458	516	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0042801-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	393	812	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.329919953009691	6	FACETS	0.878	0.837	0.92	0.878	0.837	0.92	INDETERMINATE	3	TRUE	3	0.702740071788867	6		812	1021	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243045	105243045	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042801-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	1033	1172	0	ENST00000349310.3:c.238T>C	p.Trp80Arg	p.W80R	ENST00000349310	NM_001014432.1	80	Tgg/Cgg	5/15	0.645354118042423	3	FACETS	0.901	0.882	0.919			1	CLONAL	3	TRUE	NA	0.702740071788867	3		1172	1470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs786203436	NA	P-0042801-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	958	1172	1	ENST00000269305.4:c.487T>A	p.Tyr163Asn	p.Y163N	ENST00000269305	NM_001126112.2	163	Tac/Aac	5/11	0.702740071788867	2	FACETS	0.974	0.953	0.996	0.974	0.953	0.996	CLONAL	2	TRUE	0	0.702740071788867	2		1173	1399	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519896	NA	P-0042801-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	149	459	0	ENST00000281708.4:c.1514G>A	p.Arg505His	p.R505H	ENST00000281708	NM_033632.3	505	cGc/cAc	10/12	1	2	FACETS	0.918	0.846	0.992	0.918	0.846	0.992	CLONAL	1	TRUE	1	0.702740071788867	2		459	462	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0043169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	30	863	7	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.783	0.63	0.957	0.783	0.63	0.957	CLONAL	1	TRUE	1	0.16	2		870	479	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	25	331	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.795	1	1	0.795	1	CLONAL	1	TRUE	1	0.16	2		331	310	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0043169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	31	326	2	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.784	0.638	0.949	1	0.947	1	CLONAL	2	TRUE	1	0.16	2		328	247	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0043169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	13	51	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.642	0.458	0.868	0.642	0.458	0.868	SUBCLONAL	1	TRUE	1	0.16	2		51	253	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0043169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	50	801	3	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.965	0.817	1	0.965	0.817	1	CLONAL	1	TRUE	1	0.16	2		804	648	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0043169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	31	836	5	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	1	2	FACETS	0.692	0.558	0.844	0.692	0.558	0.844	SUBCLONAL	1	TRUE	1	0.16	2		841	560	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259324	36259324	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs111527738	NA	P-0043169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	12	597	0	ENST00000300305.3:c.167T>C	p.Leu56Ser	p.L56S	ENST00000300305		56	tTg/tCg	3/8	1	2	FACETS	0.346	0.242	0.476	0.346	0.242	0.476	SUBCLONAL	1	TRUE	1	0.16	2		597	433	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933593	39933594	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0043169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	24	331	1	ENST00000378444.4:c.1005dup	p.Ser336LeufsTer45	p.S336Lfs*45	ENST00000378444	NM_001123385.1	335	-/C	4/15	0.3	2	FACETS	1	0.893	1	0.62	0.488	0.771	CLONAL	1	TRUE	0	0.16	2		332	242	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631917	90631918	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs747216375	NA	P-0043169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	78	684	0	ENST00000330062.3:c.435dup	p.Thr146AspfsTer126	p.T146Dfs*126	ENST00000330062	NM_002168.2	145	-/G	4/11	0.125238942135466	0	FACETS	1	0.952	1			1	CLONAL	1	TRUE	0	0.16	0		684	700	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123616	108123616	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	14	316	0	ENST00000278616.4:c.1880del	p.Phe627SerfsTer22	p.F627Sfs*22	ENST00000278616	NM_000051.3	625	aaT/aa	12/63	1	2	FACETS	0.758	0.548	1	0.758	0.548	1	CLONAL	1	TRUE	1	0.16	2		316	231	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817720	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	17	400	0	ENST00000262367.5:c.3250dup	p.Ile1084AsnfsTer3	p.I1084Nfs*3	ENST00000262367	NM_004380.2	1084	atc/aAtc		1	2	FACETS	0.677	0.505	0.882	0.677	0.505	0.882	SUBCLONAL	1	TRUE	1	0.16	2		400	314	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982557	10982557	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	23	222	0	ENST00000327064.4:c.179T>C	p.Val60Ala	p.V60A	ENST00000327064	NM_199141.1	60	gTg/gCg	1/16	1	2	FACETS	0.981	0.766	1	0.981	0.766	1	CLONAL	1	TRUE	1	0.16	2		222	293	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94908685	94908685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764427282	NA	P-0043169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	38	524	0	ENST00000536441.1:c.1369C>T	p.Arg457Trp	p.R457W	ENST00000536441	NM_144665.3	457	Cgg/Tgg	9/10	1	2	FACETS	0.988	0.816	1	0.988	0.816	1	CLONAL	1	TRUE	1	0.16	2		524	481	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518485	69518485	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1005963395	NA	P-0043169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	27	542	1	ENST00000294312.3:c.160G>A	p.Gly54Arg	p.G54R	ENST00000294312	NM_005117.2	54	Ggg/Agg	1/3	1	2	FACETS	0.66	0.524	0.817	0.66	0.524	0.817	SUBCLONAL	1	TRUE	1	0.16	2		543	511	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088748	27088748	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769121528	NA	P-0043169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	30	638	1	ENST00000324856.7:c.2357G>A	p.Gly786Asp	p.G786D	ENST00000324856	NM_006015.4	786	gGc/gAc	7/20	1	2	FACETS	0.641	0.515	0.785	0.641	0.515	0.785	SUBCLONAL	1	TRUE	1	0.16	2		639	585	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599890	28599890	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	23	589	0	ENST00000253063.3:c.772G>A	p.Val258Met	p.V258M	ENST00000253063	NM_031459.4	258	Gtg/Atg	6/10	1	2	FACETS	0.708	0.551	0.89	0.708	0.551	0.89	SUBCLONAL	1	TRUE	1	0.16	2		589	406	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243777025	243777025	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	42	464	0	ENST00000263826.5:c.644T>C	p.Phe215Ser	p.F215S	ENST00000263826	NM_005465.4	215	tTc/tCc	7/13	1	2	FACETS	0.75	0.628	0.885	1	0.957	1	SUBCLONAL	2	TRUE	1	0.16	2		464	350	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244965	123244965	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1259590587	NA	P-0043169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	31	647	0	ENST00000358487.5:c.2139del	p.Phe713LeufsTer4	p.F713Lfs*4	ENST00000358487	NM_000141.4	713	ttT/tt	16/18	1	2	FACETS	0.751	0.606	0.915	0.751	0.606	0.915	CLONAL	1	TRUE	1	0.16	2		647	516	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435910	49435910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1352702003	NA	P-0043169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	39	860	2	ENST00000301067.7:c.6071C>T	p.Ala2024Val	p.A2024V	ENST00000301067	NM_003482.3	2024	gCc/gTc	28/54	1	2	FACETS	0.79	0.654	0.943	0.79	0.654	0.943	CLONAL	1	TRUE	1	0.16	2		862	617	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219300	133219300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556887600	NA	P-0043169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	25	612	0	ENST00000320574.5:c.4744C>T	p.Pro1582Ser	p.P1582S	ENST00000320574	NM_006231.2	1582	Ccc/Tcc	37/49	1	2	FACETS	0.758	0.597	0.944	0.758	0.597	0.944	CLONAL	1	TRUE	1	0.16	2		612	412	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557461	21557461	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	21	549	0	ENST00000382592.4:c.2384A>G	p.Asp795Gly	p.D795G	ENST00000382592	NM_014572.2	795	gAt/gGt	5/8	0.254325495792043	3	FACETS	0.756	0.581	0.96	0.378	0.29	0.48	CLONAL	1	TRUE	1	0.16	3		549	375	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3824676	3824676	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	36	553	0	ENST00000262367.5:c.2177C>T	p.Pro726Leu	p.P726L	ENST00000262367	NM_004380.2	726	cCc/cTc	12/31	1	2	FACETS	0.841	0.691	1	0.841	0.691	1	CLONAL	1	TRUE	1	0.16	2		553	535	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676240	37676240	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1436155086	NA	P-0043169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	43	564	0	ENST00000447079.4:c.2995C>T	p.His999Tyr	p.H999Y	ENST00000447079	NM_015083.1	999	Cac/Tac	11/14	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.16	2		564	434	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537140	41537140	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1405828471	NA	P-0043169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	23	557	0	ENST00000263253.7:c.1967A>G	p.Asn656Ser	p.N656S	ENST00000263253	NM_001429.3	656	aAc/aGc	10/31	1	2	FACETS	0.636	0.495	0.8	0.636	0.495	0.8	SUBCLONAL	1	TRUE	1	0.16	2		557	452	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645715	12645715	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	22	281	0	ENST00000251849.4:c.754T>G	p.Ser252Ala	p.S252A	ENST00000251849	NM_002880.3	252	Tcc/Gcc	7/17	1	2	FACETS	0.844	0.654	1	0.844	0.654	1	CLONAL	1	TRUE	1	0.16	2		281	326	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204697	128204697	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	32	785	0	ENST00000341105.2:c.744del	p.Tyr249ThrfsTer77	p.Y249Tfs*77	ENST00000341105	NM_032638.4	248	acC/ac	3/6	1	2	FACETS	0.709	0.574	0.862	0.709	0.574	0.862	SUBCLONAL	1	TRUE	1	0.16	2		785	564	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807645	1807645	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	66	895	0	ENST00000260795.2:c.1814T>C	p.Met605Thr	p.M605T	ENST00000260795		605	aTg/aCg	12/17	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.16	2		895	649	SUCCESS
APC	324	MSKCC	GRCh37	5	112174282	112174282	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0043169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	10	357	0	ENST00000257430.4:c.2991T>A	p.Tyr997Ter	p.Y997*	ENST00000257430	NM_000038.5	997	taT/taA	16/16	1	2	FACETS	0.672	0.455	0.944	0.672	0.455	0.944	SUBCLONAL	1	TRUE	1	0.16	2		357	186	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045942	26045942	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	19	491	1	ENST00000540144.1:c.304G>A	p.Val102Met	p.V102M	ENST00000540144	NM_003531.2	102	Gtg/Atg	1/1	1	2	FACETS	0.705	0.534	0.905	0.705	0.534	0.905	CLONAL	1	TRUE	1	0.16	2		492	337	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931919	39931920	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0043169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	51	419	0	ENST00000378444.4:c.2679dup	p.Leu894ValfsTer23	p.L894Vfs*23	ENST00000378444	NM_001123385.1	893	-/G	4/15	0.3	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	2	TRUE	0	0.16	2		419	312	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0043318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	245	326	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.836	0.783	0.891	0.836	0.783	0.891	CLONAL	1	TRUE	1	0.663850390156624	2		328	883	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0043318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	369	339	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.958	0.909	1	0.958	0.909	1	CLONAL	1	TRUE	1	0.663850390156624	2		342	1161	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0043318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	240	564	1	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	0.873	0.818	0.93	0.873	0.818	0.93	CLONAL	1	TRUE	1	0.663850390156624	2		565	828	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0043318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	327	687	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.972	0.919	1	0.972	0.919	1	CLONAL	1	TRUE	1	0.663850390156624	2		687	1014	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317878	8317878	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151311972	NA	P-0043318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	240	591	0	ENST00000356435.5:c.5735C>T	p.Thr1912Met	p.T1912M	ENST00000356435		1912	aCg/aTg	35/35	0.663850390156624	1	FACETS	0.927	0.875	0.98	0.927	0.875	0.98	CLONAL	1	TRUE	0	0.663850390156624	1		591	521	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429977	78429978	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1200882279	NA	P-0043318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	212	419	0	ENST00000370768.2:c.901dup	p.Ile301AsnfsTer4	p.I301Nfs*4	ENST00000370768	NM_003902.3	301	ata/aAta	11/20	1	2	FACETS	0.808	0.753	0.866	0.808	0.753	0.866	CLONAL	1	TRUE	1	0.663850390156624	2		419	790	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096916	11096916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs535299273	NA	P-0043318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	306	1124	0	ENST00000358026.2:c.407C>T	p.Ala136Val	p.A136V	ENST00000358026	NM_001128849.1	136	gCc/gTc	4/36	0.663850390156624	1	FACETS	0.85	0.806	0.894	0.85	0.806	0.894	CLONAL	1	TRUE	0	0.663850390156624	1		1124	725	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115982	8115983	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	147	490	0	ENST00000346208.3:c.1330dup	p.Ter444LeufsTer63	p.*444Lfs*63	ENST00000346208		443	ggt/ggTt	6/6	1	2	FACETS	0.913	0.84	0.989	0.913	0.84	0.989	CLONAL	1	TRUE	1	0.663850390156624	2		490	485	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456416	40456416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143067673	NA	P-0043318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	285	864	2	ENST00000345506.4:c.1226C>T	p.Thr409Met	p.T409M	ENST00000345506	NM_003152.3	409	aCg/aTg	11/20	0.306283567429483	3	FACETS	1	0.976	1	0.535	0.503	0.568	INDETERMINATE	1	TRUE	1	0.663850390156624	3		866	1068	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256950	16256950	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	164	780	3	ENST00000375759.3:c.4220del	p.Leu1407TyrfsTer2	p.L1407Yfs*2	ENST00000375759	NM_015001.2	1405	tcT/tc	11/15	1	2	FACETS	0.477	0.438	0.519	0.477	0.438	0.519	SUBCLONAL	1	TRUE	1	0.663850390156624	2		783	1035	SUCCESS
ALK	238	MSKCC	GRCh37	2	29448419	29448419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140733978	NA	P-0043318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	381	1143	0	ENST00000389048.3:c.3080C>T	p.Pro1027Leu	p.P1027L	ENST00000389048	NM_004304.4	1027	cCg/cTg	19/29	1	2	FACETS	0.961	0.913	1	0.961	0.913	1	CLONAL	1	TRUE	1	0.663850390156624	2		1143	1194	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439887	220439887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751673614	NA	P-0043318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	178	917	1	ENST00000243786.2:c.740G>A	p.Arg247His	p.R247H	ENST00000243786	NM_002191.3	247	cGc/cAc	2/2	1	2	FACETS	0.624	0.576	0.675	0.624	0.576	0.675	SUBCLONAL	1	TRUE	1	0.663850390156624	2		918	859	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128028933	128028933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759338358	NA	P-0043318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	266	693	0	ENST00000285398.2:c.1924C>T	p.Arg642Trp	p.R642W	ENST00000285398	NM_000122.1	642	Cgg/Tgg	12/15	1	2	FACETS	0.867	0.815	0.921	0.867	0.815	0.921	CLONAL	1	TRUE	1	0.663850390156624	2		693	924	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42843792	42843792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1242962903	NA	P-0043318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	158	690	0	ENST00000398585.3:c.1127C>T	p.Ser376Phe	p.S376F	ENST00000398585	NM_001135099.1	376	tCc/tTc	10/14	1	2	FACETS	0.581	0.533	0.632	0.581	0.533	0.632	SUBCLONAL	1	TRUE	1	0.663850390156624	2		690	819	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484360	120484360	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	108	496	0	ENST00000256646.2:c.2770G>T	p.Gly924Cys	p.G924C	ENST00000256646	NM_024408.3	924	Ggt/Tgt	18/34	1	2	FACETS	0.514	0.462	0.569	0.514	0.462	0.569	SUBCLONAL	1	TRUE	1	0.663850390156624	2		496	633	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243675707	243675707	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	34	239	0	ENST00000263826.5:c.1273C>A	p.Gln425Lys	p.Q425K	ENST00000263826	NM_005465.4	425	Caa/Aaa	12/13	1	2	FACETS	0.302	0.247	0.364	0.302	0.247	0.364	SUBCLONAL	1	TRUE	1	0.663850390156624	2		239	339	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942584	71942584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	186	809	1	ENST00000298229.2:c.1540G>A	p.Val514Ile	p.V514I	ENST00000298229	NM_001567.3	514	Gtc/Atc	13/28	1	2	FACETS	0.596	0.55	0.644	0.596	0.55	0.644	SUBCLONAL	1	TRUE	1	0.663850390156624	2		810	940	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220083	5220083	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	43	866	1	ENST00000357368.4:c.3632C>T	p.Ala1211Val	p.A1211V	ENST00000357368	NM_002850.3	1211	gCt/gTt	22/38	0.663850390156624	1	FACETS	0.152	0.127	0.181	0.152	0.127	0.181	SUBCLONAL	1	TRUE	0	0.663850390156624	1		867	568	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032105	11032105	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1404227792	NA	P-0043318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	292	932	1	ENST00000327064.4:c.1670C>T	p.Thr557Met	p.T557M	ENST00000327064	NM_199141.1	557	aCg/aTg	15/16	0.663850390156624	1	FACETS	0.973	0.924	1	0.973	0.924	1	CLONAL	1	TRUE	0	0.663850390156624	1		933	604	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753188	42753188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780415692	NA	P-0043318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	565	998	0	ENST00000222329.4:c.1076C>T	p.Pro359Leu	p.P359L	ENST00000222329	NM_006494.2	359	cCg/cTg	4/4	0.613360556658687	3	FACETS	0.926	0.892	0.96	0.926	0.892	0.96	CLONAL	2	TRUE	1	0.663850390156624	3		998	1224	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47724983	47724983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750787778	NA	P-0043318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	543	985	3	ENST00000449228.1:c.761C>T	p.Ala254Val	p.A254V	ENST00000449228	NM_001127240.2	254	gCg/gTg	4/4	0.613360556658687	3	FACETS	0.942	0.907	0.977	0.942	0.907	0.977	CLONAL	2	TRUE	1	0.663850390156624	3		988	1157	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971057	21971057	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894094	NA	P-0043318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	149	562	1	ENST00000304494.5:c.301G>A	p.Gly101Arg	p.G101R	ENST00000304494	NM_000077.4	101	Ggg/Agg	2/3	0.663850390156624	1	FACETS	0.714	0.659	0.77	0.714	0.659	0.77	SUBCLONAL	1	TRUE	0	0.663850390156624	1		563	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0043352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	27	439	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.428	0.339	0.531	0.428	0.339	0.531	SUBCLONAL	1	TRUE	1	0.13	2		440	971	SUCCESS
APC	324	MSKCC	GRCh37	5	112178000	112178000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768922431	NA	P-0043352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	45	462	0	ENST00000257430.4:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000257430	NM_000038.5	2237	Cga/Tga	16/16	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.13	2		462	671	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022935	31022935	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	50	558	0	ENST00000375687.4:c.2421del	p.Pro808LeufsTer10	p.P808Lfs*10	ENST00000375687	NM_015338.5	807	gTt/gt	13/13	1	2	FACETS	0.89	0.753	1	0.89	0.753	1	CLONAL	1	TRUE	1	0.13	2		558	864	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985501	2985501	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	65	507	0	ENST00000396946.4:c.310A>C	p.Lys104Gln	p.K104Q	ENST00000396946	NM_032415.4	104	Aaa/Caa	4/25	0.224690323618328	3	FACETS	0.813	0.704	0.931	0.406	0.352	0.466	CLONAL	1	TRUE	1	0.25	3		507	720	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0043514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	249	424	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.702080245026877	4	FACETS	0.836	0.793	0.88	0.836	0.793	0.88	CLONAL	3	TRUE	1	0.712691366424117	4		424	477	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221945	98221945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756465236	NA	P-0043514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	162	599	0	ENST00000331920.6:c.2824C>T	p.Arg942Trp	p.R942W	ENST00000331920	NM_000264.3	942	Cgg/Tgg	17/24	0.712691366424117	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.712691366424117	1		599	286	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	62	331	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.792	0.688	0.903	0.792	0.688	0.903	CLONAL	1	TRUE	1	0.45	2		331	348	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	153	453	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.45	2		453	558	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	69	393	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.913	0.801	1	0.913	0.801	1	CLONAL	1	TRUE	1	0.45	2		393	336	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	19	113	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.518	0.396	0.66	0.518	0.396	0.66	SUBCLONAL	1	TRUE	1	0.45	2		113	163	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101267	27101268	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	79	444	0	ENST00000324856.7:c.4555dup	p.Gln1519ProfsTer13	p.Q1519Pfs*13	ENST00000324856	NM_006015.4	1517	gcc/gCcc	18/20	1	2	FACETS	0.777	0.686	0.874	0.777	0.686	0.874	SUBCLONAL	1	TRUE	1	0.45	2		444	452	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236086	108236086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782292	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	83	330	1	ENST00000278616.4:c.9022C>T	p.Arg3008Cys	p.R3008C	ENST00000278616	NM_000051.3	3008	Cgt/Tgt	63/63	1	2	FACETS	0.895	0.794	1	0.895	0.794	1	CLONAL	1	TRUE	1	0.45	2		331	412	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	153	622	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.903	0.827	0.982	0.903	0.827	0.982	CLONAL	1	TRUE	1	0.45	2		622	753	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	56	277	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.73	0.629	0.839	0.73	0.629	0.839	SUBCLONAL	1	TRUE	1	0.45	2		277	341	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030323	180030323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745546499	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	162	506	2	ENST00000261937.6:c.3961C>T	p.Arg1321Trp	p.R1321W	ENST00000261937	NM_182925.4	1321	Cgg/Tgg	30/30	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.45	2		508	715	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739026	145739026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781121286	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	110	515	0	ENST00000428558.2:c.2129G>A	p.Arg710His	p.R710H	ENST00000428558	NM_004260.3	710	cGc/cAc	13/22	1	2	FACETS	0.811	0.73	0.896	0.811	0.73	0.896	CLONAL	1	TRUE	1	0.45	2		515	603	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660536	67660536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	85	381	0	ENST00000264010.4:c.1436G>A	p.Arg479His	p.R479H	ENST00000264010	NM_006565.3	479	cGc/cAc	8/12	1	2	FACETS	0.744	0.659	0.833	0.744	0.659	0.833	SUBCLONAL	1	TRUE	1	0.45	2		381	508	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905546	50905546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144979965	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	168	675	2	ENST00000440232.2:c.674G>A	p.Arg225His	p.R225H	ENST00000440232	NM_002691.3	225	cGt/cAt	6/27	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.45	2		677	743	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115594	108115594	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730881336	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	52	239	0	ENST00000278616.4:c.742C>T	p.Arg248Ter	p.R248*	ENST00000278616	NM_000051.3	248	Cga/Tga	7/63	1	2	FACETS	0.776	0.665	0.895	0.776	0.665	0.895	SUBCLONAL	1	TRUE	1	0.45	2		239	298	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	107	392	0	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	1	2	FACETS	0.938	0.845	1	0.938	0.845	1	CLONAL	1	TRUE	1	0.45	2		392	507	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720741	89720741	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs371387815	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	11	84	0	ENST00000371953.3:c.892C>T	p.Gln298Ter	p.Q298*	ENST00000371953	NM_000314.4	298	Caa/Taa	8/9	1	2	FACETS	0.556	0.388	0.758	0.556	0.388	0.758	SUBCLONAL	1	TRUE	1	0.45	2		84	88	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946150	13946150	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	100	404	0	ENST00000405192.2:c.946C>T	p.Gln316Ter	p.Q316*	ENST00000405192	NM_001163147.1	316	Cag/Tag	10/12	1	2	FACETS	0.825	0.739	0.915	0.825	0.739	0.915	CLONAL	1	TRUE	1	0.45	2		404	539	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557643	95557643	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	71	390	0	ENST00000393063.1:c.5424G>T	p.Met1808Ile	p.M1808I	ENST00000393063	NM_030621.3	1808	atG/atT	26/28	1	2	FACETS	0.724	0.634	0.82	0.724	0.634	0.82	SUBCLONAL	1	TRUE	1	0.45	2		390	436	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31381363	31381363	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138596278	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	116	276	0	ENST00000328111.2:c.1088G>A	p.Arg363His	p.R363H	ENST00000328111	NM_006892.3	363	cGt/cAt	10/23	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.45	2		276	470	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386436	31386436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs577581342	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	103	487	0	ENST00000328111.2:c.1661C>T	p.Thr554Met	p.T554M	ENST00000328111	NM_006892.3	554	aCg/aTg	15/23	1	2	FACETS	0.812	0.728	0.9	0.812	0.728	0.9	CLONAL	1	TRUE	1	0.45	2		487	564	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	98	328	1	ENST00000256196.4:c.68G>A	p.Gly23Asp	p.G23D	ENST00000256196		23	gGc/gAc	1/6	1	2	FACETS	0.935	0.838	1	0.935	0.838	1	CLONAL	1	TRUE	1	0.45	2		329	466	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546787	9546787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	69	290	0	ENST00000353224.5:c.1235C>T	p.Pro412Leu	p.P412L	ENST00000353224	NM_177990.2	412	cCg/cTg	5/10	1	2	FACETS	0.941	0.826	1	0.941	0.826	1	CLONAL	1	TRUE	1	0.45	2		290	326	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132982	30132982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750421913	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	121	442	2	ENST00000331968.5:c.619G>A	p.Val207Ile	p.V207I	ENST00000331968	NM_002742.2	207	Gtt/Att	4/18	1	2	FACETS	0.893	0.809	0.981	0.893	0.809	0.981	CLONAL	1	TRUE	1	0.45	2		444	602	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214891	36214891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201094135	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	169	649	1	ENST00000222270.7:c.3317G>A	p.Arg1106Gln	p.R1106Q	ENST00000222270	NM_014727.1	1106	cGg/cAg	8/37	1	2	FACETS	0.928	0.855	1	0.928	0.855	1	CLONAL	1	TRUE	1	0.45	2		650	809	SUCCESS
ATM	472	MSKCC	GRCh37	11	108168077	108168077	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	27	200	0	ENST00000278616.4:c.4973C>T	p.Ala1658Val	p.A1658V	ENST00000278616	NM_000051.3	1658	gCa/gTa	33/63	1	2	FACETS	0.625	0.501	0.764	0.625	0.501	0.764	SUBCLONAL	1	TRUE	1	0.45	2		200	192	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223707	53223707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1288544172	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	154	720	2	ENST00000375401.3:c.3652C>T	p.Arg1218Cys	p.R1218C	ENST00000375401	NM_004187.3	1218	Cgc/Tgc	23/26	1	2	FACETS	0.882	0.808	0.959	0.882	0.808	0.959	CLONAL	1	TRUE	1	0.45	2		722	776	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457615	67457615	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	127	542	1	ENST00000327367.4:c.425G>A	p.Arg142His	p.R142H	ENST00000327367	NM_005902.3	142	cGc/cAc	3/9	1	2	FACETS	0.813	0.738	0.892	0.813	0.738	0.892	CLONAL	1	TRUE	1	0.45	2		543	694	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639097	176639097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771467409	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	103	366	2	ENST00000439151.2:c.3697C>T	p.Arg1233Trp	p.R1233W	ENST00000439151	NM_022455.4	1233	Cgg/Tgg	5/23	1	2	FACETS	0.952	0.856	1	0.952	0.856	1	CLONAL	1	TRUE	1	0.45	2		368	481	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632584	3632584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372921011	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	187	624	0	ENST00000294008.3:c.5264C>T	p.Ala1755Val	p.A1755V	ENST00000294008	NM_032444.2	1755	gCg/gTg	15/15	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.45	2		624	806	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039143	49039143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs529366765	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	36	107	0	ENST00000267163.4:c.2221C>T	p.Arg741Cys	p.R741C	ENST00000267163	NM_000321.2	741	Cgt/Tgt	22/27	1	2	FACETS	0.988	0.824	1	0.988	0.824	1	CLONAL	1	TRUE	1	0.45	2		107	162	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574405	95574405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	25	146	0	ENST00000393063.1:c.2462G>A	p.Arg821His	p.R821H	ENST00000393063	NM_030621.3	821	cGc/cAc	17/28	1	2	FACETS	0.708	0.563	0.87	0.708	0.563	0.87	SUBCLONAL	1	TRUE	1	0.45	2		146	157	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518854	187518854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1263240063	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	76	339	0	ENST00000441802.2:c.12350C>T	p.Ser4117Leu	p.S4117L	ENST00000441802	NM_005245.3	4117	tCg/tTg	24/27	1	2	FACETS	0.818	0.721	0.921	0.818	0.721	0.921	CLONAL	1	TRUE	1	0.45	2		339	413	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799087	45799087	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs373766973	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	37	621	0	ENST00000450313.1:c.346C>T	p.Arg116Trp	p.R116W	ENST00000450313	NM_012222.2	116	Cgg/Tgg	3/16	1	2	FACETS	0.237	0.194	0.285	0.237	0.194	0.285	SUBCLONAL	1	TRUE	1	0.45	2		621	694	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928852	44928852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750754452	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	72	268	0	ENST00000377967.4:c.1952C>T	p.Ser651Leu	p.S651L	ENST00000377967	NM_021140.2	651	tCg/tTg	17/29	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.45	2		268	290	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250398	10250398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1010743136	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	109	446	0	ENST00000340748.4:c.3854G>A	p.Arg1285His	p.R1285H	ENST00000340748		1285	cGc/cAc	33/40	1	2	FACETS	0.987	0.89	1	0.987	0.89	1	CLONAL	1	TRUE	1	0.45	2		446	491	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884858	134884858	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774975718	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	118	385	0	ENST00000398015.3:c.1634C>T	p.Ser545Leu	p.S545L	ENST00000398015	NM_004441.4	545	tCg/tTg	8/16	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.45	2		385	516	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158521	26158521	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	100	433	0	ENST00000289316.2:c.124G>A	p.Val42Met	p.V42M	ENST00000289316	NM_138720.2	42	Gtg/Atg	1/2	1	2	FACETS	0.938	0.842	1	0.938	0.842	1	CLONAL	1	TRUE	1	0.45	2		433	474	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187719	11187719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767904339	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	107	469	0	ENST00000361445.4:c.6178C>T	p.Arg2060Trp	p.R2060W	ENST00000361445	NM_004958.3	2060	Cgg/Tgg	44/58	1	2	FACETS	0.773	0.695	0.856	0.773	0.695	0.856	SUBCLONAL	1	TRUE	1	0.45	2		469	615	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280045	18280045	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463551736	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	83	354	0	ENST00000222254.8:c.2128G>A	p.Val710Ile	p.V710I	ENST00000222254	NM_005027.3	710	Gtc/Atc	16/16	1	2	FACETS	0.838	0.743	0.939	0.838	0.743	0.939	CLONAL	1	TRUE	1	0.45	2		354	440	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644477	3644477	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs760126773	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	163	608	0	ENST00000294008.3:c.2137C>T	p.Arg713Ter	p.R713*	ENST00000294008	NM_032444.2	713	Cga/Tga	10/15	1	2	FACETS	0.888	0.816	0.963	0.888	0.816	0.963	CLONAL	1	TRUE	1	0.45	2		608	816	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37865601	37865601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745921471	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	132	675	0	ENST00000269571.5:c.470G>A	p.Arg157Gln	p.R157Q	ENST00000269571		157	cGg/cAg	4/27	1	2	FACETS	0.799	0.726	0.876	0.799	0.726	0.876	SUBCLONAL	1	TRUE	1	0.45	2		675	734	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549404	21549404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753026198	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	105	432	0	ENST00000382592.4:c.2872C>T	p.Arg958Cys	p.R958C	ENST00000382592	NM_014572.2	958	Cgc/Tgc	8/8	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.45	2		432	444	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155386	106155386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1238868376	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	49	386	0	ENST00000380013.4:c.287G>A	p.Arg96His	p.R96H	ENST00000380013	NM_001127208.2	96	cGc/cAc	3/11	1	2	FACETS	0.598	0.508	0.696	0.598	0.508	0.696	SUBCLONAL	1	TRUE	1	0.45	2		386	364	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030588	48030588	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63749843	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	64	299	0	ENST00000234420.5:c.3202C>T	p.Arg1068Ter	p.R1068*	ENST00000234420	NM_000179.2	1068	Cga/Tga	5/10	1	2	FACETS	0.786	0.684	0.895	0.786	0.684	0.895	SUBCLONAL	1	TRUE	1	0.45	2		299	362	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031345	11031345	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752773089	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	145	663	0	ENST00000327064.4:c.1345G>A	p.Asp449Asn	p.D449N	ENST00000327064	NM_199141.1	449	Gac/Aac	12/16	1	2	FACETS	0.88	0.805	0.96	0.88	0.805	0.96	CLONAL	1	TRUE	1	0.45	2		663	732	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65348959	65348959	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	36	202	0	ENST00000342505.4:c.205+1G>A		p.X69_splice	ENST00000342505	NM_002227.2	69			1	2	FACETS	0.699	0.579	0.831	0.699	0.579	0.831	SUBCLONAL	1	TRUE	1	0.45	2		202	229	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491632	120491632	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	58	221	0	ENST00000256646.2:c.2597A>G	p.Gln866Arg	p.Q866R	ENST00000256646	NM_024408.3	866	cAa/cGa	16/34	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.45	2		221	235	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851297	156851297	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	124	568	0	ENST00000524377.1:c.2254T>C	p.Cys752Arg	p.C752R	ENST00000524377	NM_002529.3	752	Tgc/Cgc	17/17	1	2	FACETS	0.903	0.82	0.991	0.903	0.82	0.991	CLONAL	1	TRUE	1	0.45	2		568	610	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448461	49448461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748173147	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	125	511	1	ENST00000301067.7:c.250C>T	p.Arg84Cys	p.R84C	ENST00000301067	NM_003482.3	84	Cgc/Tgc	3/54	1	2	FACETS	0.893	0.811	0.98	0.893	0.811	0.98	CLONAL	1	TRUE	1	0.45	2		512	622	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281578	49281578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	85	523	0	ENST00000282018.3:c.625G>A	p.Gly209Ser	p.G209S	ENST00000282018	NM_020377.2	209	Ggc/Agc	1/1	1	2	FACETS	0.691	0.612	0.775	0.691	0.612	0.775	SUBCLONAL	1	TRUE	1	0.45	2		523	547	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610284	81610284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	67	362	0	ENST00000298171.2:c.1882G>A	p.Val628Met	p.V628M	ENST00000298171	NM_000369.2	628	Gtg/Atg	10/10	1	2	FACETS	0.807	0.705	0.916	0.807	0.705	0.916	CLONAL	1	TRUE	1	0.45	2		362	369	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590579	95590579	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	36	175	0	ENST00000393063.1:c.1330G>T	p.Gly444Ter	p.G444*	ENST00000393063	NM_030621.3	444	Gga/Tga	9/28	1	2	FACETS	0.816	0.678	0.968	0.816	0.678	0.968	CLONAL	1	TRUE	1	0.45	2		175	196	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830900	72830900	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199667071	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	82	422	0	ENST00000268489.5:c.5681A>G	p.Asp1894Gly	p.D1894G	ENST00000268489	NM_006885.3	1894	gAc/gGc	9/10	1	2	FACETS	0.758	0.67	0.851	0.758	0.67	0.851	SUBCLONAL	1	TRUE	1	0.45	2		422	481	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341535	89341535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	121	466	0	ENST00000301030.4:c.7535G>A	p.Arg2512Gln	p.R2512Q	ENST00000301030	NM_001256183.1	2512	cGg/cAg	10/13	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.45	2		466	499	SUCCESS
YES1	7525	MSKCC	GRCh37	18	747962	747962	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	66	442	0	ENST00000314574.4:c.428C>T	p.Pro143Leu	p.P143L	ENST00000314574	NM_005433.3	143	cCg/cTg	4/12	1	2	FACETS	0.676	0.589	0.77	0.676	0.589	0.77	SUBCLONAL	1	TRUE	1	0.45	2		442	434	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793028	33793028	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1490895935	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	59	212	0	ENST00000498907.2:c.293C>T	p.Thr98Met	p.T98M	ENST00000498907	NM_004364.3	98	aCg/aTg	1/1	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.45	2		212	246	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098968	178098968	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	39	169	0	ENST00000397062.3:c.77A>G	p.Gln26Arg	p.Q26R	ENST00000397062	NM_006164.4	26	cAa/cGa	2/5	1	2	FACETS	0.788	0.659	0.929	0.788	0.659	0.929	CLONAL	1	TRUE	1	0.45	2		169	220	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933653	49933653	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	122	666	0	ENST00000296474.3:c.2624C>A	p.Pro875His	p.P875H	ENST00000296474	NM_002447.2	875	cCt/cAt	10/20	1	2	FACETS	0.801	0.725	0.881	0.801	0.725	0.881	CLONAL	1	TRUE	1	0.45	2		666	677	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204788	128204788	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	172	698	1	ENST00000341105.2:c.653C>T	p.Thr218Met	p.T218M	ENST00000341105	NM_032638.4	218	aCg/aTg	3/6	1	2	FACETS	0.95	0.875	1	0.95	0.875	1	CLONAL	1	TRUE	1	0.45	2		699	805	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947800	178947800	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	38	190	0	ENST00000263967.3:c.2675C>T	p.Ala892Val	p.A892V	ENST00000263967	NM_006218.2	892	gCa/gTa	19/21	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.45	2		190	165	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146787	185146787	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	84	437	0	ENST00000265026.3:c.418C>G	p.Pro140Ala	p.P140A	ENST00000265026	NM_004721.4	140	Cct/Gct	2/14	1	2	FACETS	0.819	0.726	0.917	0.819	0.726	0.917	CLONAL	1	TRUE	1	0.45	2		437	456	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356212	66356212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1385284578	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	83	442	0	ENST00000273854.3:c.1285G>A	p.Val429Met	p.V429M	ENST00000273854	NM_004439.5	429	Gtg/Atg	5/18	1	2	FACETS	0.78	0.691	0.875	0.78	0.691	0.875	SUBCLONAL	1	TRUE	1	0.45	2		442	473	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910738	29910738	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	55	565	0	ENST00000376809.5:c.278C>T	p.Ala93Val	p.A93V	ENST00000376809	NM_002116.7	93	gCc/gTc	2/8	1	2	FACETS	0.407	0.347	0.472	0.407	0.347	0.472	SUBCLONAL	1	TRUE	1	0.45	2		565	601	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007112	152007112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	96	381	0	ENST00000262189.6:c.788G>A	p.Cys263Tyr	p.C263Y	ENST00000262189	NM_170606.2	263	tGc/tAc	6/59	1	2	FACETS	0.86	0.769	0.956	0.86	0.769	0.956	CLONAL	1	TRUE	1	0.45	2		381	496	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205367	38205367	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	90	552	0	ENST00000317025.8:c.323C>A	p.Pro108His	p.P108H	ENST00000317025	NM_023034.1	108	cCc/cAc	2/24	1	2	FACETS	0.723	0.643	0.808	0.723	0.643	0.808	SUBCLONAL	1	TRUE	1	0.45	2		552	553	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907019	101907019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	28	146	0	ENST00000374994.4:c.979C>T	p.Pro327Ser	p.P327S	ENST00000374994	NM_004612.2	327	Cca/Tca	6/9	1	2	FACETS	0.929	0.754	1	0.929	0.754	1	CLONAL	1	TRUE	1	0.45	2		146	134	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	68	355	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.465	0.406	0.529	0.465	0.406	0.529	SUBCLONAL	1	TRUE	1	0.658511336522819	2		355	444	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216189	36216189	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	106	478	0	ENST00000222270.7:c.3602del	p.Pro1201ArgfsTer154	p.P1201Rfs*154	ENST00000222270	NM_014727.1	1199	ggC/gg	11/37	1	2	FACETS	0.552	0.496	0.611	0.552	0.496	0.611	SUBCLONAL	1	TRUE	1	0.658511336522819	2		478	583	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	146	339	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.799	0.733	0.867	0.799	0.733	0.867	SUBCLONAL	1	TRUE	1	0.658511336522819	2		342	555	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	160	349	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.295766470213641	3	FACETS	0.751	0.696	0.808	0.751	0.696	0.808	INDETERMINATE	2	TRUE	1	0.658511336522819	3		349	430	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	91	312	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.264814852764994	2	FACETS	0.601	0.536	0.67	0.3	0.268	0.335	INDETERMINATE	1	TRUE	0	0.658511336522819	2		313	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	174	439	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.947	0.877	1	0.947	0.877	1	CLONAL	1	TRUE	1	0.658511336522819	2		440	558	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751151	128751151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1476455361	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	169	433	1	ENST00000377970.2:c.688G>A	p.Ala230Thr	p.A230T	ENST00000377970	NM_002467.4	230	Gcc/Acc	2/3	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.658511336522819	2		434	484	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	354	565	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.957	0.919	0.993	1	0.997	1	CLONAL	2	TRUE	1	0.658511336522819	2		568	562	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	154	335	3	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.658511336522819	2		338	462	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	127	471	4	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	0.658511336522819	1	FACETS	0.941	0.869	1	0.941	0.869	1	CLONAL	1	TRUE	0	0.658511336522819	1		475	275	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	119	504	3	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.658511336522819	1	FACETS	0.929	0.855	1	0.929	0.855	1	CLONAL	1	TRUE	0	0.658511336522819	1		507	261	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508177	38508177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749735817	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	111	331	0	ENST00000254066.5:c.485G>A	p.Arg162Gln	p.R162Q	ENST00000254066	NM_000964.3	162	cGa/cAa	5/9	1	2	FACETS	0.799	0.723	0.878	0.799	0.723	0.878	SUBCLONAL	1	TRUE	1	0.658511336522819	2		331	422	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	99	192	0	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	1	2	FACETS	0.983	0.888	1	0.983	0.888	1	CLONAL	1	TRUE	1	0.658511336522819	2		192	306	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	139	394	2	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.968	0.889	1	0.968	0.889	1	CLONAL	1	TRUE	1	0.658511336522819	2		396	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	250	540	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.658511336522819	2		540	749	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495022	56495022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763808045	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	200	426	1	ENST00000267101.3:c.3379C>T	p.Arg1127Cys	p.R1127C	ENST00000267101	NM_001982.3	1127	Cgc/Tgc	27/28	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.658511336522819	2		427	595	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	111	303	2	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	1	2	FACETS	0.894	0.811	0.98	0.894	0.811	0.98	CLONAL	1	TRUE	1	0.658511336522819	2		305	377	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807573	36807573	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs774376244	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	140	364	0	ENST00000373129.3:c.1091C>T	p.Ala364Val	p.A364V	ENST00000373129	NM_032017.1	364	gCg/gTg	12/12	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.658511336522819	2		364	423	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606696	29606696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769910087	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	151	362	0	ENST00000389048.3:c.1184G>A	p.Arg395His	p.R395H	ENST00000389048	NM_004304.4	395	cGt/cAt	5/29	0.658511336522819	1	FACETS	0.941	0.874	1	0.941	0.874	1	CLONAL	1	TRUE	0	0.658511336522819	1		362	327	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	100	267	0	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	1	2	FACETS	0.748	0.673	0.827	0.748	0.673	0.827	SUBCLONAL	1	TRUE	1	0.658511336522819	2		267	406	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456932	149456932	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148357861	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	164	400	0	ENST00000286301.3:c.796G>A	p.Asp266Asn	p.D266N	ENST00000286301	NM_005211.3	266	Gat/Aat	6/22	0.445577140023185	1	FACETS	0.601	0.555	0.648	0.601	0.555	0.648	SUBCLONAL	1	TRUE	0	0.658511336522819	1		400	556	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244091	153244091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	134	363	0	ENST00000281708.4:c.2066G>A	p.Arg689Gln	p.R689Q	ENST00000281708	NM_033632.3	689	cGg/cAg	12/12	1	2	FACETS	0.85	0.777	0.925	0.85	0.777	0.925	CLONAL	1	TRUE	1	0.658511336522819	2		363	479	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420101	420101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	79	416	0	ENST00000399788.2:c.3166C>T	p.Arg1056Trp	p.R1056W	ENST00000399788	NM_001042603.1	1056	Cgg/Tgg	21/28	1	2	FACETS	0.444	0.391	0.5	0.444	0.391	0.5	SUBCLONAL	1	TRUE	1	0.658511336522819	2		416	541	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	110	459	3	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	1	2	FACETS	0.523	0.47	0.578	0.523	0.47	0.578	SUBCLONAL	1	TRUE	1	0.658511336522819	2		462	639	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199958	138199958	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	100	319	0	ENST00000237289.4:c.1376C>T	p.Ser459Leu	p.S459L	ENST00000237289	NM_001270507.1	459	tCg/tTg	7/9	1	2	FACETS	0.912	0.823	1	0.912	0.823	1	CLONAL	1	TRUE	1	0.658511336522819	2		319	333	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993848	72993848	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778500476	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	115	377	2	ENST00000268489.5:c.197C>T	p.Ala66Val	p.A66V	ENST00000268489	NM_006885.3	66	gCg/gTg	2/10	0.445577140023185	1	FACETS	0.864	0.793	0.937	0.864	0.793	0.937	CLONAL	1	TRUE	0	0.658511336522819	1		379	271	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713601	30713601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202168735	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	119	362	1	ENST00000295754.5:c.926C>T	p.Thr309Met	p.T309M	ENST00000295754	NM_003242.5	309	aCg/aTg	4/7	1	2	FACETS	0.966	0.881	1	0.966	0.881	1	CLONAL	1	TRUE	1	0.658511336522819	2		363	374	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254166	133254166	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs371882716	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	96	346	1	ENST00000320574.5:c.718G>A	p.Val240Met	p.V240M	ENST00000320574	NM_006231.2	240	Gtg/Atg	7/49	1	2	FACETS	0.778	0.698	0.86	0.778	0.698	0.86	SUBCLONAL	1	TRUE	1	0.658511336522819	2		347	375	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502666	149502666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749226501	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	177	400	1	ENST00000261799.4:c.2122C>T	p.Arg708Cys	p.R708C	ENST00000261799	NM_002609.3	708	Cgc/Tgc	15/23	0.445577140023185	1	FACETS	0.678	0.629	0.728	0.678	0.629	0.728	SUBCLONAL	1	TRUE	0	0.658511336522819	1		401	532	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661663	227661664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761880048	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	91	451	6	ENST00000305123.5:c.1791dup	p.His598AlafsTer13	p.H598Afs*13	ENST00000305123	NM_005544.2	597	-/G	1/2	1	2	FACETS	0.725	0.649	0.806	0.725	0.649	0.806	SUBCLONAL	1	TRUE	1	0.658511336522819	2		457	381	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732957	30732957	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504421	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	102	241	0	ENST00000295754.5:c.1570G>A	p.Asp524Asn	p.D524N	ENST00000295754	NM_003242.5	524	Gac/Aac	7/7	1	2	FACETS	0.993	0.899	1	0.993	0.899	1	CLONAL	1	TRUE	1	0.658511336522819	2		241	312	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527648	157527648	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	173	372	0	ENST00000346085.5:c.5373A>G	p.Ile1791Met	p.I1791M	ENST00000346085	NM_020732.3	1791	atA/atG	20/20	1	2	FACETS	0.971	0.9	1	0.971	0.9	1	CLONAL	1	TRUE	1	0.658511336522819	2		372	541	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321195	65321195	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	89	262	0	ENST00000342505.4:c.1645C>T	p.Arg549Ter	p.R549*	ENST00000342505	NM_002227.2	549	Cga/Tga	11/25	1	2	FACETS	0.802	0.718	0.89	0.802	0.718	0.89	CLONAL	1	TRUE	1	0.658511336522819	2		262	337	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536891	120536891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1337798232	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	208	511	1	ENST00000229340.5:c.295G>A	p.Val99Ile	p.V99I	ENST00000229340	NM_006861.6	99	Gtc/Atc	4/6	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.658511336522819	2		512	623	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149930	99149930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766419021	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	167	341	2	ENST00000074304.5:c.242C>T	p.Thr81Met	p.T81M	ENST00000074304	NM_001134224.1	81	aCg/aTg	5/26	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.658511336522819	2		343	499	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460390	149460390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753954924	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	178	428	0	ENST00000286301.3:c.247C>T	p.Arg83Cys	p.R83C	ENST00000286301	NM_005211.3	83	Cgc/Tgc	3/22	0.445577140023185	1	FACETS	0.707	0.657	0.758	0.707	0.657	0.758	SUBCLONAL	1	TRUE	0	0.658511336522819	1		428	513	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538941	187538941	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs113224498	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	133	299	0	ENST00000441802.2:c.8799del	p.Gly2934ValfsTer3	p.G2934Vfs*3	ENST00000441802	NM_005245.3	2933	caA/ca	10/27	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.658511336522819	2		299	385	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468398	89468398	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1467832547	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	67	174	0	ENST00000336596.2:c.1938del	p.Glu647ArgfsTer9	p.E647Rfs*9	ENST00000336596	NM_005233.5	644	tcA/tc	11/17	1	2	FACETS	0.831	0.731	0.935	0.831	0.731	0.935	CLONAL	1	TRUE	1	0.658511336522819	2		174	245	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418670	49418670	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783698	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	69	352	0	ENST00000301067.7:c.15844C>T	p.Arg5282Ter	p.R5282*	ENST00000301067	NM_003482.3	5282	Cga/Tga	49/54	1	2	FACETS	0.464	0.405	0.527	0.464	0.405	0.527	SUBCLONAL	1	TRUE	1	0.658511336522819	2		352	452	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248737	212248737	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	53	236	0	ENST00000342788.4:c.3530del	p.Asn1177MetfsTer27	p.N1177Mfs*27	ENST00000342788	NM_005235.2	1177	aAt/at	28/28	1	2	FACETS	0.735	0.634	0.842	0.735	0.634	0.842	SUBCLONAL	1	TRUE	1	0.658511336522819	2		236	219	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224279	36224279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1166713872	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	176	528	1	ENST00000222270.7:c.6829C>T	p.Arg2277Cys	p.R2277C	ENST00000222270	NM_014727.1	2277	Cgc/Tgc	28/37	1	2	FACETS	0.875	0.81	0.942	0.875	0.81	0.942	CLONAL	1	TRUE	1	0.658511336522819	2		529	611	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141557684	141557684	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1382352330	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	44	477	0	ENST00000220592.5:c.1631C>T	p.Thr544Met	p.T544M	ENST00000220592	NM_012154.3	544	aCg/aTg	13/19	1	2	FACETS	0.206	0.172	0.244	0.206	0.172	0.244	SUBCLONAL	1	TRUE	1	0.658511336522819	2		477	648	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015025	27015025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754932895	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	128	294	0	ENST00000335756.4:c.127C>T	p.Arg43Trp	p.R43W	ENST00000335756	NM_001809.3	43	Cgg/Tgg	2/5	0.658511336522819	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.658511336522819	1		294	257	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612347	1612347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200962332	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	129	585	0	ENST00000344749.5:c.1672C>T	p.Arg558Cys	p.R558C	ENST00000344749	NM_001136139.2	558	Cgc/Tgc	18/19	0.445577140023185	1	FACETS	0.432	0.393	0.473	0.432	0.393	0.473	SUBCLONAL	1	TRUE	0	0.658511336522819	1		585	608	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50784069	50784069	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	144	440	1	ENST00000398568.2:c.460G>A	p.Ala154Thr	p.A154T	ENST00000398568	NM_001042412.1	154	Gca/Aca	3/18	0.445577140023185	1	FACETS	0.743	0.685	0.802	0.743	0.685	0.802	SUBCLONAL	1	TRUE	0	0.658511336522819	1		441	395	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435968	49435968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	183	494	1	ENST00000301067.7:c.6013C>T	p.Arg2005Cys	p.R2005C	ENST00000301067	NM_003482.3	2005	Cgc/Tgc	28/54	1	2	FACETS	0.953	0.885	1	0.953	0.885	1	CLONAL	1	TRUE	1	0.658511336522819	2		495	583	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022247	31022247	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1569327372	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	38	209	0	ENST00000375687.4:c.1732C>T	p.Arg578Cys	p.R578C	ENST00000375687	NM_015338.5	578	Cgt/Tgt	13/13	1	2	FACETS	0.426	0.354	0.505	0.426	0.354	0.505	SUBCLONAL	1	TRUE	1	0.658511336522819	2		209	271	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022734	12022734	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	110	345	0	ENST00000396373.4:c.844del	p.Arg282GlyfsTer34	p.R282Gfs*34	ENST00000396373	NM_001987.4	280	aaC/aa	5/8	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.658511336522819	2		345	321	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939048	48939048	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	47	164	0	ENST00000267163.4:c.884del	p.Asn295IlefsTer6	p.N295Ifs*6	ENST00000267163	NM_000321.2	294	Aaa/aa	9/27	0.658511336522819	1	FACETS	0.863	0.751	0.977	0.863	0.751	0.977	CLONAL	1	TRUE	0	0.658511336522819	1		164	111	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143051	30143052	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1244823020	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	186	606	1	ENST00000389048.3:c.474dup	p.Gly159ArgfsTer67	p.G159Rfs*67	ENST00000389048	NM_004304.4	158	-/C	1/29	0.658511336522819	1	FACETS	0.871	0.814	0.929	0.871	0.814	0.929	CLONAL	1	TRUE	0	0.658511336522819	1		607	435	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508137	106508137	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	26	167	0	ENST00000359195.3:c.131T>C	p.Leu44Pro	p.L44P	ENST00000359195	NM_002649.2	44	cTg/cCg	2/11	0.445577140023185	1	FACETS	0.351	0.281	0.429	0.351	0.281	0.429	SUBCLONAL	1	TRUE	0	0.658511336522819	1		167	151	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435457	49435457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748389081	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	168	464	0	ENST00000301067.7:c.6215G>A	p.Arg2072His	p.R2072H	ENST00000301067	NM_003482.3	2072	cGc/cAc	30/54	1	2	FACETS	0.929	0.86	1	0.929	0.86	1	CLONAL	1	TRUE	1	0.658511336522819	2		464	549	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241912	72241912	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	106	281	0	ENST00000357731.5:c.478T>C	p.Cys160Arg	p.C160R	ENST00000357731	NM_173808.2	160	Tgt/Cgt	3/7	1	2	FACETS	0.915	0.828	1	0.915	0.828	1	CLONAL	1	TRUE	1	0.658511336522819	2		281	352	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644639	21644639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746814364	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	82	292	0	ENST00000421138.2:c.28G>A	p.Glu10Lys	p.E10K	ENST00000421138		10	Gaa/Aaa	4/16	1	2	FACETS	0.916	0.818	1	0.916	0.818	1	CLONAL	1	TRUE	1	0.658511336522819	2		292	272	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112107	115112107	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	172	585	0	ENST00000257566.3:c.1633A>G	p.Thr545Ala	p.T545A	ENST00000257566	NM_016569.3	545	Acg/Gcg	7/8	1	2	FACETS	0.921	0.853	0.992	0.921	0.853	0.992	CLONAL	1	TRUE	1	0.658511336522819	2		585	567	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28971148	28971148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	38	242	0	ENST00000282397.4:c.1609G>A	p.Ala537Thr	p.A537T	ENST00000282397	NM_002019.4	537	Gct/Act	12/30	0.658511336522819	1	FACETS	0.445	0.372	0.523	0.445	0.372	0.523	SUBCLONAL	1	TRUE	0	0.658511336522819	1		242	174	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240283	41240283	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	133	359	1	ENST00000379561.5:c.67T>C	p.Cys23Arg	p.C23R	ENST00000379561	NM_002015.3	23	Tgc/Cgc	1/3	0.658511336522819	1	FACETS	0.985	0.913	1	0.985	0.913	1	CLONAL	1	TRUE	0	0.658511336522819	1		360	275	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138534	2138534	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777166275	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	209	566	0	ENST00000219476.3:c.5347G>A	p.Glu1783Lys	p.E1783K	ENST00000219476	NM_000548.3	1783	Gag/Aag	42/42	1	2	FACETS	0.921	0.859	0.985	0.921	0.859	0.985	CLONAL	1	TRUE	1	0.658511336522819	2		566	689	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636858	2636858	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374111988	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	232	513	0	ENST00000342085.4:c.1307G>A	p.Arg436Lys	p.R436K	ENST00000342085	NM_002613.4	436	aGg/aAg	11/14	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.658511336522819	2		513	675	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805303	89805304	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	52	389	1	ENST00000389301.3:c.4246_4247del	p.Ser1416ThrfsTer8	p.S1416Tfs*8	ENST00000389301	NM_000135.2	1416	TCa/a	42/43	0.445577140023185	1	FACETS	0.295	0.252	0.342	0.295	0.252	0.342	SUBCLONAL	1	TRUE	0	0.658511336522819	1		390	359	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2189781	2189781	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	224	515	1	ENST00000398665.3:c.251G>A	p.Ser84Asn	p.S84N	ENST00000398665	NM_032482.2	84	aGc/aAc	4/28	0.445577140023185	1	FACETS	0.811	0.761	0.861	0.811	0.761	0.861	CLONAL	1	TRUE	0	0.658511336522819	1		516	563	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123650	11123650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140016398	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	97	477	0	ENST00000358026.2:c.2300C>T	p.Ser767Phe	p.S767F	ENST00000358026	NM_001128849.1	767	tCc/tTc	16/36	0.445577140023185	1	FACETS	0.418	0.374	0.464	0.418	0.374	0.464	SUBCLONAL	1	TRUE	0	0.658511336522819	1		477	473	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277999	18277999	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775277118	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	120	420	0	ENST00000222254.8:c.1619C>T	p.Thr540Met	p.T540M	ENST00000222254	NM_005027.3	540	aCg/aTg	13/16	0.445577140023185	1	FACETS	0.517	0.469	0.566	0.517	0.469	0.566	SUBCLONAL	1	TRUE	0	0.658511336522819	1		420	473	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971715	18971715	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	102	504	0	ENST00000262803.5:c.2381C>T	p.Thr794Met	p.T794M	ENST00000262803	NM_002911.3	794	aCg/aTg	17/24	0.445577140023185	1	FACETS	0.353	0.316	0.392	0.353	0.316	0.392	SUBCLONAL	1	TRUE	0	0.658511336522819	1		504	588	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795880	42795880	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	63	635	0	ENST00000575354.2:c.2869G>T	p.Ala957Ser	p.A957S	ENST00000575354	NM_015125.3	957	Gcc/Tcc	11/20	1	2	FACETS	0.268	0.231	0.308	0.268	0.231	0.308	SUBCLONAL	1	TRUE	1	0.658511336522819	2		635	715	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867276	45867276	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343419778	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	184	540	0	ENST00000391945.4:c.917C>T	p.Ala306Val	p.A306V	ENST00000391945	NM_000400.3	306	gCc/gTc	10/23	1	2	FACETS	0.964	0.895	1	0.964	0.895	1	CLONAL	1	TRUE	1	0.658511336522819	2		540	580	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637384	47637384	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs63750070	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	178	465	0	ENST00000233146.2:c.518T>C	p.Leu173Pro	p.L173P	ENST00000233146	NM_000251.2	173	cTa/cCa	3/16	0.658511336522819	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.658511336522819	1		465	361	SUCCESS
REL	5966	MSKCC	GRCh37	2	61121641	61121641	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs918803156	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	98	339	1	ENST00000295025.8:c.263A>G	p.Tyr88Cys	p.Y88C	ENST00000295025	NM_002908.2	88	tAc/tGc	3/11	1	2	FACETS	0.888	0.801	0.98	0.888	0.801	0.98	CLONAL	1	TRUE	1	0.658511336522819	2		340	335	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610539	215610539	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	132	314	0	ENST00000260947.4:c.1717A>G	p.Ile573Val	p.I573V	ENST00000260947	NM_000465.2	573	Ata/Gta	8/11	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.658511336522819	2		314	400	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39690076	39690076	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	51	194	0	ENST00000361337.2:c.101G>T	p.Arg34Leu	p.R34L	ENST00000361337	NM_003286.2	34	cGg/cTg	3/21	0.264814852764994	2	FACETS	0.462	0.395	0.536	0.231	0.197	0.268	INDETERMINATE	1	TRUE	0	0.658511336522819	2		194	335	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44520604	44520604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	37	228	0	ENST00000291552.4:c.158G>A	p.Arg53His	p.R53H	ENST00000291552	NM_006758.2	53	cGt/cAt	3/8	1	2	FACETS	0.293	0.242	0.351	0.293	0.242	0.351	SUBCLONAL	1	TRUE	1	0.658511336522819	2		228	383	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655232	45655232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776604966	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	191	410	2	ENST00000407780.3:c.620G>A	p.Arg207Gln	p.R207Q	ENST00000407780	NM_001283052.1	207	cGg/cAg	4/7	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.658511336522819	2		412	543	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655418	45655418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	228	506	2	ENST00000407780.3:c.434C>T	p.Ala145Val	p.A145V	ENST00000407780	NM_001283052.1	145	gCc/gTc	4/7	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.658511336522819	2		508	657	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430462	181430462	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	299	540	0	ENST00000325404.1:c.314A>G	p.His105Arg	p.H105R	ENST00000325404	NM_003106.3	105	cAc/cGc	1/1	0.295766470213641	3	FACETS	0.863	0.819	0.909	0.863	0.819	0.909	INDETERMINATE	2	TRUE	1	0.658511336522819	3		540	699	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961363	1961363	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	62	417	0	ENST00000382891.5:c.3151T>C	p.Phe1051Leu	p.F1051L	ENST00000382891	NM_133335.3	1051	Ttc/Ctc	17/22	1	2	FACETS	0.283	0.244	0.325	0.283	0.244	0.325	SUBCLONAL	1	TRUE	1	0.658511336522819	2		417	666	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144137	55144137	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	130	363	0	ENST00000257290.5:c.1966A>T	p.Asn656Tyr	p.N656Y	ENST00000257290	NM_006206.4	656	Aac/Tac	14/23	1	2	FACETS	0.849	0.776	0.925	0.849	0.776	0.925	CLONAL	1	TRUE	1	0.658511336522819	2		363	465	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539045	187539045	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs200538962	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	74	346	0	ENST00000441802.2:c.8695T>C	p.Ser2899Pro	p.S2899P	ENST00000441802	NM_005245.3	2899	Tcc/Ccc	10/27	1	2	FACETS	0.524	0.46	0.592	0.524	0.46	0.592	SUBCLONAL	1	TRUE	1	0.658511336522819	2		346	429	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294304	1294304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	185	564	1	ENST00000310581.5:c.697C>T	p.Pro233Ser	p.P233S	ENST00000310581	NM_198253.2	233	Ccg/Tcg	2/16	1	2	FACETS	0.975	0.906	1	0.975	0.906	1	CLONAL	1	TRUE	1	0.658511336522819	2		565	576	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977913	131977913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750133404	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	87	299	0	ENST00000265335.6:c.3796G>A	p.Val1266Ile	p.V1266I	ENST00000265335		1266	Gta/Ata	25/25	NA	2	FACETS	0.914	0.819	1			1	INDETERMINATE	1	TRUE	NA	0.658511336522819	2		299	289	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499063	149499063	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767216776	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	166	456	3	ENST00000261799.4:c.2765G>A	p.Arg922His	p.R922H	ENST00000261799	NM_002609.3	922	cGc/cAc	20/23	0.445577140023185	1	FACETS	0.632	0.584	0.681	0.632	0.584	0.681	SUBCLONAL	1	TRUE	0	0.658511336522819	1		459	535	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515306	149515306	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202213873	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	134	424	0	ENST00000261799.4:c.176C>T	p.Pro59Leu	p.P59L	ENST00000261799	NM_002609.3	59	cCg/cTg	3/23	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.658511336522819	NA		424	464	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671035	30671035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28994876	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	185	522	0	ENST00000376406.3:c.5711G>A	p.Arg1904Gln	p.R1904Q	ENST00000376406	NM_014641.2	1904	cGg/cAg	12/15	1	2	FACETS	0.977	0.908	1	0.977	0.908	1	CLONAL	1	TRUE	1	0.658511336522819	2		522	575	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92300833	92300833	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	67	291	0	ENST00000265734.4:c.554A>G	p.Tyr185Cys	p.Y185C	ENST00000265734	NM_001259.6	185	tAc/tGc	5/8	0.445577140023185	1	FACETS	0.419	0.366	0.475	0.419	0.366	0.475	SUBCLONAL	1	TRUE	0	0.658511336522819	1		291	326	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92355104	92355104	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	31	124	0	ENST00000265734.4:c.373A>G	p.Met125Val	p.M125V	ENST00000265734	NM_001259.6	125	Atg/Gtg	4/8	0.445577140023185	1	FACETS	0.376	0.307	0.452	0.376	0.307	0.452	SUBCLONAL	1	TRUE	0	0.658511336522819	1		124	168	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738710	145738710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	221	557	1	ENST00000428558.2:c.2354C>T	p.Ala785Val	p.A785V	ENST00000428558	NM_004260.3	785	gCt/gTt	15/22	1	2	FACETS	0.993	0.929	1	0.993	0.929	1	CLONAL	1	TRUE	1	0.658511336522819	2		558	676	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389380	8389380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	90	290	0	ENST00000356435.5:c.4238C>T	p.Ala1413Val	p.A1413V	ENST00000356435		1413	gCc/gTc	26/35	1	2	FACETS	0.896	0.804	0.992	0.896	0.804	0.992	CLONAL	1	TRUE	1	0.658511336522819	2		290	305	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93657847	93657847	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773478505	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	147	337	0	ENST00000375746.1:c.1873C>T	p.Arg625Trp	p.R625W	ENST00000375746	NM_001174167.1	625	Cgg/Tgg	14/14	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.658511336522819	2		337	406	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410025	139410025	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	245	651	0	ENST00000277541.6:c.1813A>G	p.Asn605Asp	p.N605D	ENST00000277541	NM_017617.3	605	Aac/Gac	11/34	1	2	FACETS	0.945	0.887	1	0.945	0.887	1	CLONAL	1	TRUE	1	0.658511336522819	2		651	787	SUCCESS
AR	367	MSKCC	GRCh37	X	66766012	66766012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753457990	NA	P-0043619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	221	374	0	ENST00000374690.3:c.1024C>T	p.Pro342Ser	p.P342S	ENST00000374690	NM_000044.3	342	Ccg/Tcg	1/8	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.658511336522819	1		374	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0043633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	216	704	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.600710791941528	1	FACETS	0.884	0.828	0.941	0.884	0.828	0.941	CLONAL	1	TRUE	0	0.600710791941528	1		704	569	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670026	29670026	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1131691114	NA	P-0043633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	146	222	0	ENST00000356175.3:c.7000-1G>T		p.X2334_splice	ENST00000356175	NM_000267.3	2334			0.545487558726077	2	FACETS	0.827	0.769	0.884	0.827	0.769	0.884	CLONAL	2	TRUE	0	0.600710791941528	2		222	294	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463186	25463186	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	176	595	0	ENST00000264709.3:c.2307C>G	p.Ile769Met	p.I769M	ENST00000264709	NM_175629.2	769	atC/atG	19/23	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.600710791941528	2		595	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0043747-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	685	724	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	NA	2	FACETS	1	0.997	1			1	INDETERMINATE	2	TRUE	NA	0.874560631668006	2		724	744	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5246054	5246054	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043747-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	173	501	0	ENST00000357368.4:c.721C>T	p.Arg241Cys	p.R241C	ENST00000357368	NM_002850.3	241	Cgc/Tgc	10/38	0.66484470579059	5	FACETS	1	0.977	1	0.384	0.354	0.415	CLONAL	1	TRUE	2	0.874560631668006	5		501	794	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231106	53231106	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043747-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	435	277	0	ENST00000375401.3:c.1796G>T	p.Arg599Leu	p.R599L	ENST00000375401	NM_004187.3	599	cGt/cTt	13/26	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.874560631668006	1		277	473	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215376	41215376	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043747-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	328	303	0	ENST00000357654.3:c.5167A>T	p.Ile1723Phe	p.I1723F	ENST00000357654	NM_007294.3	1723	Att/Ttt	18/23	0.422119989543014	6	FACETS	0.93	0.885	0.976	0.93	0.885	0.976	INDETERMINATE	3	TRUE	3	0.874560631668006	6		303	739	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456320	32456320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043747-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	164	618	0	ENST00000332351.3:c.572G>T	p.Gly191Val	p.G191V	ENST00000332351	NM_024426.4	191	gGc/gTc	1/10	0.370215692616946	6	FACETS	0.824	0.759	0.89	0.412	0.379	0.445	INDETERMINATE	2	TRUE	2	0.874560631668006	6		618	626	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661605	227661605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1205996251	NA	P-0043747-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	441	721	0	ENST00000305123.5:c.1850C>T	p.Pro617Leu	p.P617L	ENST00000305123	NM_005544.2	617	cCa/cTa	1/2	0.873289892604809	3	FACETS	0.998	0.963	1	0.666	0.641	0.689	CLONAL	2	TRUE	0	0.874560631668006	3		721	726	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204000	142204000	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043747-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	305	472	0	ENST00000350721.4:c.6203T>C	p.Ile2068Thr	p.I2068T	ENST00000350721	NM_001184.3	2068	aTa/aCa	36/47	0.870192182002633	4	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.874560631668006	4		472	1172	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274743	142274743	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0043747-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	789	395	0	ENST00000350721.4:c.2317A>T	p.Lys773Ter	p.K773*	ENST00000350721	NM_001184.3	773	Aaa/Taa	10/47	0.870192182002633	4	FACETS	0.994	0.971	1			1	CLONAL	3	TRUE	NA	0.874560631668006	4		395	1134	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322873	31322915	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCTTCCCTACCTGAACTCTTCCTCCTACACATCACAGCAGCG	CCCTTCCCTACCTGAACTCTTCCTCCTACACATCACAGCAGCG	-	novel	NA	P-0043747-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	171	544	0	ENST00000412585.2:c.981_1012+11del		p.X327_splice	ENST00000412585	NM_005514.6	327		5/8	1	2	FACETS	0.975	0.909	1	0.975	0.909	1	CLONAL	1	TRUE	1	0.874560631668006	2		544	401	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5029907	5029907	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0043747-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	557	391	0	ENST00000381652.3:c.350+1G>A		p.X117_splice	ENST00000381652	NM_004972.3	117			0.873289892604809	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.874560631668006	2		391	592	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1331479	1331479	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043747-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	210	428	0	ENST00000400841.2:c.49G>T	p.Gly17Cys	p.G17C	ENST00000400841		17	Ggc/Tgc	1/6	0.873289892604809	2	FACETS	0.868	0.813	0.925			1	CLONAL	1	TRUE	NA	0.874560631668006	2		428	553	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148681	20148681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043747-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	274	151	0	ENST00000379607.5:c.382G>A	p.Glu128Lys	p.E128K	ENST00000379607	NM_001412.3	128	Gaa/Aaa	6/7	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.874560631668006	1		151	286	SUCCESS
APC	324	MSKCC	GRCh37	5	112151216	112151216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043747-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	237	394	0	ENST00000257430.4:c.859G>T	p.Glu287Ter	p.E287*	ENST00000257430	NM_000038.5	287	Gaa/Taa	9/16	0.873289892604809	1	FACETS	0.971	0.933	1	0.971	0.933	1	CLONAL	1	TRUE	0	0.874560631668006	1		394	314	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411691	116411691	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043747-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	439	687	0	ENST00000397752.3:c.2870A>T	p.Lys957Met	p.K957M	ENST00000397752	NM_000245.2	957	aAg/aTg	13/21	0.873289892604809	3	FACETS	1	0.975	1	0.516	0.492	0.541	CLONAL	1	TRUE	1	0.874560631668006	3		687	1397	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87356833	87356833	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043747-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	30	283	0	ENST00000277120.3:c.1186A>G	p.Ile396Val	p.I396V	ENST00000277120		396	Att/Gtt	10/19	0.873289892604809	2	FACETS	0.122	0.098	0.15	0.061	0.049	0.075	SUBCLONAL	1	TRUE	0	0.874560631668006	2		283	563	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721606	49721606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138238101	NA	P-0043787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	10	157	0	ENST00000449682.2:c.2033C>T	p.Pro678Leu	p.P678L	ENST00000449682	NM_020998.3	678	cCa/cTa	18/18	1	2	FACETS	0.153	0.103	0.215	0.153	0.103	0.215	SUBCLONAL	1	TRUE	1	0.69533477556057	2		157	188	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858705	9858705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759145938	NA	P-0043787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	289	346	0	ENST00000330684.3:c.2696G>A	p.Arg899Gln	p.R899Q	ENST00000330684	NM_001134407.1	899	cGg/cAg	13/13	0.69533477556057	4	FACETS	0.881	0.832	0.93	0.587	0.554	0.62	CLONAL	2	TRUE	1	0.69533477556057	4		346	800	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197396	94197396	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555010957	NA	P-0043787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	117	369	0	ENST00000323929.3:c.1108A>G	p.Ser370Gly	p.S370G	ENST00000323929	NM_005591.3	370	Agt/Ggt	11/20	0.69533477556057	4	FACETS	1	0.929	1	0.344	0.311	0.378	CLONAL	1	TRUE	1	0.69533477556057	4		369	553	SUCCESS
ATR	545	MSKCC	GRCh37	3	142172066	142172066	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	34	315	0	ENST00000350721.4:c.7665G>C	p.Lys2555Asn	p.K2555N	ENST00000350721	NM_001184.3	2555	aaG/aaC	46/47	0.49859200752472	3	FACETS	0.34	0.277	0.409			1	SUBCLONAL	1	TRUE	NA	0.69533477556057	3		315	388	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249012	55249013	+	inframe_insertion	In_Frame_Ins	INS	-	-	AACCCCGGT	novel	NA	P-0043787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	596	570	0	ENST00000275493.2:c.2316_2317insGGTAACCCC	p.Pro772_His773insGlyAsnPro	p.P772_H773insGNP	ENST00000275493	NM_005228.3	770	-/AACCCCGGT	20/28	0.556714642041615	5	FACETS	1	0.996	1	0.825	0.794	0.856	CLONAL	2	TRUE	2	0.69533477556057	5		570	1415	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863025	56863025	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	135	340	0	ENST00000519728.1:c.292G>C	p.Glu98Gln	p.E98Q	ENST00000519728	NM_002350.3	98	Gaa/Caa	5/13	0.624502589059637	4	FACETS	1	0.936	1	0.344	0.314	0.377	CLONAL	1	TRUE	1	0.69533477556057	4		340	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121912651	NA	P-0043910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	515	563	0	ENST00000269305.4:c.742C>G	p.Arg248Gly	p.R248G	ENST00000269305	NM_001126112.2	248	Cgg/Ggg	7/11	0.779409394803913	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.779409394803913	2		563	584	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631837	90631837	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	189	578	0	ENST00000330062.3:c.516G>T	p.Arg172Ser	p.R172S	ENST00000330062	NM_002168.2	172	agG/agT	4/11	0.779409394803913	3	FACETS	0.923	0.856	0.993	0.462	0.428	0.497	CLONAL	1	TRUE	1	0.779409394803913	3		578	730	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78704418	78704418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	376	421	0	ENST00000306801.3:c.566C>T	p.Pro189Leu	p.P189L	ENST00000306801	NM_020761.2	189	cCg/cTg	5/34	0.655300072333366	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.779409394803913	4		421	835	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30954238	30954238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1378944067	NA	P-0043910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	113	334	0	ENST00000375687.4:c.109G>A	p.Val37Ile	p.V37I	ENST00000375687	NM_015338.5	37	Gtc/Atc	2/13	0.655300072333366	4	FACETS	1	0.909	1	0.503	0.454	0.554	CLONAL	1	TRUE	2	0.779409394803913	4		334	513	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120453	94120453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	140	308	0	ENST00000369303.4:c.598G>A	p.Val200Met	p.V200M	ENST00000369303	NM_004440.3	200	Gtg/Atg	3/17	0.73944514649984	3	FACETS	0.953	0.887	1	0.953	0.887	1	CLONAL	2	TRUE	1	0.779409394803913	3		308	262	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509486	106509486	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	325	553	0	ENST00000359195.3:c.1480C>G	p.Gln494Glu	p.Q494E	ENST00000359195	NM_002649.2	494	Caa/Gaa	2/11	0.655300072333366	4	FACETS	0.962	0.914	1	0.962	0.914	1	CLONAL	2	TRUE	2	0.779409394803913	4		553	771	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0043961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	191	367	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.453921599280555	4	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	2	0.739502771705356	4		367	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0043961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	331	680	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	0.711609463739098	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.739502771705356	2		680	426	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604765	48604766	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0043961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	163	319	0	ENST00000342988.3:c.1589_1590del	p.His530ProfsTer46	p.H530Pfs*46	ENST00000342988	NM_005359.5	529	ttACac/ttac	12/12	0.711609463739098	2	FACETS	0.841	0.793	0.889	0.841	0.793	0.889	CLONAL	2	TRUE	0	0.739502771705356	2		319	262	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950036	44950036	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	280	509	0	ENST00000377967.4:c.3807del	p.Met1270TrpfsTer22	p.M1270Wfs*22	ENST00000377967	NM_021140.2	1269	Ccc/cc	26/29	0.739502771705356	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.739502771705356	3		509	488	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0044082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	221	371	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.406366021409232	3	FACETS	0.927	0.866	0.988	0.927	0.866	0.988	CLONAL	2	TRUE	1	0.414989866244761	3		371	694	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492689	56492689	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	124	404	0	ENST00000407977.2:c.250C>T	p.Gln84Ter	p.Q84*	ENST00000407977		84	Cag/Tag	2/10	0.415052925450844	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.414989866244761	1		404	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578430	7578431	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0044082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	189	663	0	ENST00000269305.4:c.499_500del	p.Gln167AlafsTer13	p.Q167Afs*13	ENST00000269305	NM_001126112.2	167	CAg/g	5/11	0.415052925450844	1	FACETS	0.903	0.837	0.973	0.903	0.837	0.973	CLONAL	1	TRUE	0	0.414989866244761	1		663	799	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593477	48593477	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	119	294	0	ENST00000342988.3:c.1228C>T	p.Gln410Ter	p.Q410*	ENST00000342988	NM_005359.5	410	Cag/Tag	10/12	0.415052925450844	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.414989866244761	1		294	444	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244097	153244097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	185	398	0	ENST00000281708.4:c.2060G>A	p.Gly687Glu	p.G687E	ENST00000281708	NM_033632.3	687	gGg/gAg	12/12	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.414989866244761	2		398	805	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123246898	123246898	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	155	474	0	ENST00000358487.5:c.2027T>G	p.Phe676Cys	p.F676C	ENST00000358487	NM_000141.4	676	tTt/tGt	15/18	1	2	FACETS	0.997	0.915	1	0.997	0.915	1	CLONAL	1	TRUE	1	0.414989866244761	2		474	749	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028666	12028666	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	144	399	1	ENST00000353533.5:c.869T>G	p.Val290Gly	p.V290G	ENST00000353533	NM_003010.3	290	gTc/gGc	8/11	0.415052925450844	1	FACETS	0.939	0.86	1	0.939	0.86	1	CLONAL	1	TRUE	0	0.414989866244761	1		400	586	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216379	36216379	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0044082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	251	718	0	ENST00000222270.7:c.3643-1G>A		p.X1215_splice	ENST00000222270	NM_014727.1	1215			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.414989866244761	2		718	1077	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729549	41729549	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	294	526	0	ENST00000242208.4:c.980T>A	p.Phe327Tyr	p.F327Y	ENST00000242208	NM_002192.2	327	tTt/tAt	3/3	0.406366021409232	3	FACETS	0.889	0.838	0.941	0.889	0.838	0.941	CLONAL	2	TRUE	1	0.414989866244761	3		526	962	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115975	8115975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	41	368	0	ENST00000346208.3:c.1321G>A	p.Ala441Thr	p.A441T	ENST00000346208		441	Gcc/Acc	6/6	0.358267178219732	1	FACETS	0.373	0.316	0.433	0.373	0.316	0.433	INDETERMINATE	1	TRUE	0	0.859388658808466	1		368	146	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830138	72830138	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	116	636	0	ENST00000268489.5:c.6443C>A	p.Pro2148His	p.P2148H	ENST00000268489	NM_006885.3	2148	cCt/cAt	9/10	0.859388658808466	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.859388658808466	1		636	142	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148963	119148963	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	138	489	0	ENST00000264033.4:c.1183C>A	p.Pro395Thr	p.P395T	ENST00000264033	NM_005188.3	395	Ccc/Acc	8/16	0.859388658808466	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.859388658808466	1		489	172	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954009	32954009	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs80359159	NA	P-0044128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	82	460	0	ENST00000380152.3:c.9076C>T	p.Gln3026Ter	p.Q3026*	ENST00000380152		3026	Cag/Tag	23/27	0.591330355413711	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.859388658808466	1		460	106	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40855769	40855773	+	frameshift_variant	Frame_Shift_Del	DEL	CAGTT	CAGTT	-	novel	NA	P-0044128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	120	517	0	ENST00000428826.2:c.2083_2087del	p.Asn695LeufsTer30	p.N695Lfs*30	ENST00000428826		695	AACTGt/t	19/21	0.133756675373843	4	FACETS	0.863	0.791	0.936	0.863	0.791	0.936	INDETERMINATE	2	TRUE	2	0.859388658808466	4		517	301	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	42	714	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.388765552840112	2		715	167	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191585	10191585	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	TT	novel	NA	P-0044172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	97	559	0	ENST00000256474.2:c.578delinsTT	p.Asn193IlefsTer63	p.N193Ifs*63	ENST00000256474	NM_000551.3	193	aAt/aTTt	3/3	0.388765552840112	1	FACETS	0.998	0.896	1	0.998	0.896	1	CLONAL	1	TRUE	0	0.388765552840112	1		559	403	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	167	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.284577518834946	3	FACETS	0.808	0.745	0.873	0.808	0.745	0.873	CLONAL	2	TRUE	1	0.37623976371864	3		485	653	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0044369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	243	645	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.342450235590324	2	FACETS	0.901	0.846	0.957	0.901	0.846	0.957	CLONAL	2	TRUE	0	0.37623976371864	2		645	717	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951964	178951964	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	89	486	0	ENST00000263967.3:c.3019G>C	p.Gly1007Arg	p.G1007R	ENST00000263967	NM_006218.2	1007	Ggc/Cgc	21/21	0.357312089341763	3	FACETS	0.986	0.876	1	0.493	0.438	0.552	CLONAL	1	TRUE	1	0.37623976371864	3		486	570	SUCCESS
APC	324	MSKCC	GRCh37	5	112177660	112177660	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0044369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	55	392	0	ENST00000257430.4:c.6369T>A	p.Cys2123Ter	p.C2123*	ENST00000257430	NM_000038.5	2123	tgT/tgA	16/16	1	2	FACETS	0.75	0.643	0.865	0.75	0.643	0.865	SUBCLONAL	1	TRUE	1	0.37623976371864	2		392	390	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	120	488	4	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	0.275634037440144	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	0	0.275634037440144	1		492	611	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	106	331	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	0.275634037440144	1	FACETS	0.805	0.727	0.886	1	0.985	1	CLONAL	2	FALSE	0	0.275634037440144	1		331	412	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	56	773	6	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	0.275634037440144	1	FACETS	0.427	0.364	0.495	0.427	0.364	0.495	SUBCLONAL	1	FALSE	0	0.275634037440144	1		779	821	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300039	137300040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755912201	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	173	677	3	ENST00000481739.1:c.331dup	p.Leu111ProfsTer70	p.L111Pfs*70	ENST00000481739	NM_002957.4	108	-/C	3/10	0.275634037440144	1	FACETS	0.787	0.726	0.849	1	0.99	1	SUBCLONAL	2	FALSE	0	0.275634037440144	1		680	688	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	125	371	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.943	0.859	1	1	0.989	1	CLONAL	2	FALSE	1	0.275634037440144	2		371	481	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	258	565	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.275634037440144	1	FACETS	0.879	0.83	0.929	1	0.996	1	CLONAL	3	FALSE	0	0.275634037440144	1		568	612	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	123	326	1	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	0.234047475151385	4	FACETS	0.933	0.846	1	0.622	0.564	0.683	CLONAL	2	FALSE	1	0.275634037440144	4		327	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	401	657	0	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	0.275634037440144	2	FACETS	0.917	0.879	0.956	1	0.997	1	CLONAL	4	FALSE	0	0.275634037440144	2		657	793	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296358	15296358	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	174	724	0	ENST00000263388.2:c.2084del	p.Pro695ArgfsTer165	p.P695Rfs*165	ENST00000263388	NM_000435.2	695	cCg/cg	13/33	1	2	FACETS	0.87	0.803	0.939	1	0.991	1	CLONAL	2	FALSE	1	0.275634037440144	2		724	726	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730802	40730802	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747513450	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	350	501	3	ENST00000373198.4:c.3733G>A	p.Gly1245Arg	p.G1245R	ENST00000373198	NM_133170.3	1245	Gga/Aga	27/32	0.275634037440144	3	FACETS	1	0.989	1	1	0.996	1	CLONAL	3	FALSE	1	0.275634037440144	3		504	848	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053022	180053023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750808726	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	111	662	3	ENST00000261937.6:c.1267dup	p.Gln423ProfsTer4	p.Q423Pfs*4	ENST00000261937	NM_182925.4	423	cag/cCag	10/30	0.275634037440144	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	0	0.275634037440144	1		665	572	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	137	210	2	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	0.0986449611585969	4	FACETS	0.875	0.801	0.951	1	0.983	1	INDETERMINATE	3	FALSE	2	0.275634037440144	4		212	483	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	52	156	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.929	0.802	1	1	0.975	1	CLONAL	2	FALSE	1	0.275634037440144	2		156	203	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030479	49030479	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	62	236	0	ENST00000267163.4:c.1959del	p.Val654CysfsTer4	p.V654Cfs*4	ENST00000267163	NM_000321.2	652	Aaa/aa	19/27	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	1	0.275634037440144	2		236	366	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799098	42799098	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	214	734	2	ENST00000575354.2:c.4586del	p.Pro1529LeufsTer91	p.P1529Lfs*91	ENST00000575354	NM_015125.3	1528	Ccc/cc	20/20	1	2	FACETS	0.94	0.875	1	1	0.994	1	CLONAL	2	FALSE	1	0.275634037440144	2		736	826	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910372	29910372	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs41548119	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	136	564	0	ENST00000376809.5:c.46del	p.Ala16ProfsTer4	p.A16Pfs*4	ENST00000376809	NM_002116.7	14	tcG/tc	1/8	1	2	FACETS	0.761	0.694	0.832	1	0.987	1	SUBCLONAL	2	FALSE	1	0.275634037440144	2		564	648	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938271	36938271	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	123	650	1	ENST00000361632.4:c.690del	p.Met231CysfsTer32	p.M231Cfs*32	ENST00000361632		230	ccC/cc	6/16	0.275634037440144	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	0	0.275634037440144	1		651	665	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467855	99467856	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	74	358	0	ENST00000268035.6:c.2732_2733dup	p.Gly912LeufsTer26	p.G912Lfs*26	ENST00000268035	NM_000875.3	908	-/TC	13/21	0.275634037440144	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	0	0.275634037440144	1		358	401	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513282	44513287	+	inframe_deletion	In_Frame_Del	DEL	CCACCG	CCACCG	-	rs745888281	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	70	562	0	ENST00000291552.4:c.648_653del	p.Gly222_Gly223del	p.G222_G223del	ENST00000291552	NM_006758.2	216	ggCGGTGGt/ggt	8/8	0.275634037440144	1	FACETS	0.568	0.494	0.648	0.568	0.494	0.648	SUBCLONAL	1	FALSE	0	0.275634037440144	1		562	771	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440757	56440757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774211426	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	80	438	0	ENST00000407977.2:c.461C>T	p.Pro154Leu	p.P154L	ENST00000407977		154	cCg/cTg	5/10	0.275634037440144	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	0	0.275634037440144	1		438	437	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138915	64138915	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	78	379	0	ENST00000334205.4:c.2287del	p.Arg763AlafsTer21	p.R763Afs*21	ENST00000334205	NM_003942.2	761	gCc/gc	17/17	0.275634037440144	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	0	0.275634037440144	1		379	425	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830450	72830450	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	48	364	0	ENST00000268489.5:c.6131del	p.Pro2044LeufsTer57	p.P2044Lfs*57	ENST00000268489	NM_006885.3	2044	cCt/ct	9/10	1	2	FACETS	0.934	0.792	1	0.934	0.792	1	CLONAL	1	FALSE	1	0.275634037440144	2		364	373	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572092	64572093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767319284	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	104	545	2	ENST00000312049.6:c.1546dup	p.Arg516ProfsTer15	p.R516Pfs*15	ENST00000312049	NM_130799.2	516	cgg/cCgg	10/10	0.275634037440144	1	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	FALSE	0	0.275634037440144	1		547	642	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346220	152346220	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	150	440	4	ENST00000359321.1:c.350del	p.Leu117TrpfsTer17	p.L117Wfs*17	ENST00000359321	NM_005431.1	117	tTg/tg	3/3	1	2	FACETS	0.869	0.797	0.944	1	0.99	1	CLONAL	2	FALSE	1	0.275634037440144	2		444	626	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	173	586	11	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	0.275634037440144	1	FACETS	0.878	0.812	0.947	1	0.992	1	CLONAL	2	FALSE	0	0.275634037440144	1		597	616	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100397	157100399	+	inframe_deletion	In_Frame_Del	DEL	CGC	CGC	-	rs572236007	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	12	71	0	ENST00000346085.5:c.1348_1350del	p.Pro450del	p.P450del	ENST00000346085	NM_020732.3	445	gCGCcg/gcg	1/20	0.275634037440144	1	FACETS	0.844	0.6	1	0.844	0.6	1	CLONAL	1	FALSE	0	0.275634037440144	1		71	89	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131411	202131411	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs777784105	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	153	398	1	ENST00000358485.4:c.379C>T	p.Arg127Ter	p.R127*	ENST00000358485	NM_001080125.1	127	Cga/Tga	2/9	1	2	FACETS	0.977	0.899	1	1	0.992	1	CLONAL	2	FALSE	1	0.275634037440144	2		399	568	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973889	131973889	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs761837416	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	54	240	0	ENST00000265335.6:c.3592C>T	p.Arg1198Ter	p.R1198*	ENST00000265335		1198	Cga/Tga	23/25	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	FALSE	1	0.275634037440144	2		240	348	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561211	9561211	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	103	407	0	ENST00000353224.5:c.571G>A	p.Asp191Asn	p.D191N	ENST00000353224	NM_177990.2	191	Gat/Aat	4/10	0.275634037440144	3	FACETS	1	0.981	1	0.727	0.652	0.806	CLONAL	1	FALSE	1	0.275634037440144	3		407	585	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189323	99189323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173310435	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	34	453	0	ENST00000074304.5:c.2579G>A	p.Arg860Gln	p.R860Q	ENST00000074304	NM_001134224.1	860	cGg/cAg	24/26	1	2	FACETS	0.369	0.3	0.446	0.369	0.3	0.446	SUBCLONAL	1	FALSE	1	0.275634037440144	2		453	669	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658800	3658800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746769352	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	35	533	0	ENST00000294008.3:c.166G>A	p.Ala56Thr	p.A56T	ENST00000294008	NM_032444.2	56	Gct/Act	2/15	0.275634037440144	1	FACETS	0.33	0.269	0.398	0.33	0.269	0.398	SUBCLONAL	1	FALSE	0	0.275634037440144	1		533	664	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321665	62321665	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750251447	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	138	517	0	ENST00000360203.5:c.2284C>T	p.Arg762Trp	p.R762W	ENST00000360203	NM_001283009.1	762	Cgg/Tgg	26/35	0.275634037440144	3	FACETS	0.778	0.709	0.851	0.778	0.709	0.851	SUBCLONAL	2	FALSE	1	0.275634037440144	3		517	732	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742497	17742497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	151	599	0	ENST00000250003.3:c.679G>A	p.Glu227Lys	p.E227K	ENST00000250003	NM_002478.4	227	Gaa/Aaa	2/3	0.275634037440144	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	0	0.275634037440144	1		599	663	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591134	67591134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767013611	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	24	236	0	ENST00000274335.5:c.1727C>T	p.Thr576Met	p.T576M	ENST00000274335		576	aCg/aTg	12/15	1	2	FACETS	0.456	0.357	0.57	0.456	0.357	0.57	SUBCLONAL	1	FALSE	1	0.275634037440144	2		236	382	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836322	151836322	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064796342	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	129	428	0	ENST00000262189.6:c.14483G>A	p.Arg4828His	p.R4828H	ENST00000262189	NM_170606.2	4828	cGc/cAc	57/59	1	2	FACETS	0.833	0.758	0.911	1	0.988	1	CLONAL	2	FALSE	1	0.275634037440144	2		428	562	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430227	181430227	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	88	296	0	ENST00000325404.1:c.79G>A	p.Ala27Thr	p.A27T	ENST00000325404	NM_003106.3	27	Gcg/Acg	1/1	0.275634037440144	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	0	0.275634037440144	1		296	390	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121118	11121118	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	286	558	1	ENST00000358026.2:c.2185C>T	p.Gln729Ter	p.Q729*	ENST00000358026	NM_001128849.1	729	Cag/Tag	15/36	1	2	FACETS	1	0.981	1	1	0.996	1	CLONAL	2	FALSE	1	0.275634037440144	2		559	949	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422039	81422040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	226	370	0	ENST00000298171.2:c.17dup	p.Leu6PhefsTer56	p.L6Ffs*56	ENST00000298171	NM_000369.2	5	-/T	1/10	0.234047475151385	4	FACETS	0.888	0.833	0.943	1	0.987	1	CLONAL	4	FALSE	1	0.275634037440144	4		370	589	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262714	16262714	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1022457753	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	67	349	0	ENST00000375759.3:c.9979G>A	p.Ala3327Thr	p.A3327T	ENST00000375759	NM_015001.2	3327	Gcc/Acc	11/15	0.275634037440144	1	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	FALSE	0	0.275634037440144	1		349	411	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598207	28598207	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	212	654	0	ENST00000253063.3:c.179G>T	p.Ser60Ile	p.S60I	ENST00000253063	NM_031459.4	60	aGc/aTc	3/10	0.275634037440144	1	FACETS	0.856	0.797	0.916	1	0.993	1	CLONAL	2	FALSE	0	0.275634037440144	1		654	775	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115733	8115733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	87	334	0	ENST00000346208.3:c.1079G>A	p.Gly360Asp	p.G360D	ENST00000346208		360	gGc/gAc	6/6	0.275634037440144	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	0	0.275634037440144	1		334	428	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406039	70406039	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	140	549	0	ENST00000373644.4:c.3553A>G	p.Thr1185Ala	p.T1185A	ENST00000373644	NM_030625.2	1185	Aca/Gca	4/12	0.275634037440144	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	0	0.275634037440144	1		549	609	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573903	18573903	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	25	300	0	ENST00000266497.5:c.2221G>T	p.Ala741Ser	p.A741S	ENST00000266497		741	Gca/Tca	15/31	0.275634037440144	1	FACETS	0.331	0.26	0.412	0.331	0.26	0.412	SUBCLONAL	1	FALSE	0	0.275634037440144	1		300	473	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446840	49446840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1370093761	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	39	456	1	ENST00000301067.7:c.970C>T	p.Arg324Trp	p.R324W	ENST00000301067	NM_003482.3	324	Cgg/Tgg	8/54	1	2	FACETS	0.511	0.423	0.609	0.511	0.423	0.609	SUBCLONAL	1	FALSE	1	0.275634037440144	2		457	554	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012365	29012365	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	125	353	0	ENST00000282397.4:c.506T>A	p.Leu169Ter	p.L169*	ENST00000282397	NM_002019.4	169	tTa/tAa	4/30	1	2	FACETS	0.793	0.72	0.869	1	0.987	1	SUBCLONAL	2	FALSE	1	0.275634037440144	2		353	572	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007693	45007693	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	55	288	0	ENST00000558401.1:c.140T>G	p.Val47Gly	p.V47G	ENST00000558401	NM_004048.2	47	gTg/gGg	2/4	0.275634037440144	1	FACETS	0.85	0.729	0.981	0.85	0.729	0.981	CLONAL	1	FALSE	0	0.275634037440144	1		288	405	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063364	67063364	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	96	311	0	ENST00000412916.2:c.54T>A	p.Phe18Leu	p.F18L	ENST00000412916		18	ttT/ttA	1/6	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.275634037440144	2		311	533	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992303	72992303	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1405980712	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	110	685	0	ENST00000268489.5:c.1742T>C	p.Val581Ala	p.V581A	ENST00000268489	NM_006885.3	581	gTg/gCg	2/10	1	2	FACETS	0.89	0.799	0.987	0.89	0.799	0.987	CLONAL	1	FALSE	1	0.275634037440144	2		685	897	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972415	81972415	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	129	352	0	ENST00000359376.3:c.3208G>A	p.Ala1070Thr	p.A1070T	ENST00000359376	NM_002661.3	1070	Gct/Act	29/33	0.275634037440144	1	FACETS	0.868	0.792	0.946	1	0.989	1	CLONAL	2	FALSE	0	0.275634037440144	1		352	465	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763496	59763496	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060501733	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	119	311	0	ENST00000259008.2:c.2606A>G	p.Gln869Arg	p.Q869R	ENST00000259008	NM_032043.2	869	cAg/cGg	19/20	0.275634037440144	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	0	0.275634037440144	1		311	522	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600362	10600362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1281598803	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	262	607	0	ENST00000171111.5:c.1493G>A	p.Arg498Gln	p.R498Q	ENST00000171111	NM_203500.1	498	cGa/cAa	4/6	1	2	FACETS	1	0.964	1	1	0.995	1	CLONAL	2	FALSE	1	0.275634037440144	2		607	917	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797135	42797135	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	237	711	0	ENST00000575354.2:c.3501del	p.Lys1168ArgfsTer13	p.K1168Rfs*13	ENST00000575354	NM_015125.3	1166	gCc/gc	15/20	1	2	FACETS	0.877	0.819	0.937	1	0.994	1	CLONAL	2	FALSE	1	0.275634037440144	2		711	980	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292821	62292822	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs769909059	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	124	323	0	ENST00000360203.5:c.287_289dup	p.Ala96dup	p.A96dup	ENST00000360203	NM_001283009.1	96	-/GCT	3/35	0.275634037440144	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	FALSE	1	0.275634037440144	3		323	453	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940817	49940817	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	155	637	0	ENST00000296474.3:c.226A>G	p.Asn76Asp	p.N76D	ENST00000296474	NM_002447.2	76	Aat/Gat	1/20	0.275634037440144	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	0	0.275634037440144	1		637	663	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361163	66361163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	48	270	0	ENST00000273854.3:c.1009G>A	p.Val337Ile	p.V337I	ENST00000273854	NM_004439.5	337	Gtc/Atc	4/18	0.275634037440144	1	FACETS	0.904	0.768	1	0.904	0.768	1	CLONAL	1	FALSE	0	0.275634037440144	1		270	332	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751242	57751242	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	88	270	0	ENST00000274289.3:c.1626-1G>C		p.X542_splice	ENST00000274289	NM_006622.3	542			1	2	FACETS	0.827	0.738	0.921	1	0.983	1	CLONAL	2	FALSE	1	0.275634037440144	2		270	386	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575490	67575490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148059720	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	108	282	0	ENST00000274335.5:c.563G>A	p.Arg188His	p.R188H	ENST00000274335		188	cGc/cAc	4/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.275634037440144	2		282	529	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372056	55372056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	32	347	0	ENST00000297316.4:c.746G>A	p.Gly249Asp	p.G249D	ENST00000297316	NM_022454.3	249	gGc/gAc	2/2	0.0986449611585969	4	FACETS	0.554	0.448	0.673	0.277	0.224	0.337	INDETERMINATE	1	FALSE	2	0.275634037440144	4		347	535	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27172631	27172631	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	130	410	0	ENST00000380036.4:c.646T>C	p.Trp216Arg	p.W216R	ENST00000380036	NM_000459.3	216	Tgg/Cgg	5/23	0.275634037440144	1	FACETS	0.77	0.702	0.841	1	0.987	1	SUBCLONAL	2	FALSE	0	0.275634037440144	1		410	528	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923357	36923357	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	159	535	0	ENST00000358127.4:c.905T>C	p.Val302Ala	p.V302A	ENST00000358127	NM_001280556.1	302	gTg/gCg	7/10	0.275634037440144	1	FACETS	0.871	0.803	0.942	1	0.991	1	CLONAL	2	FALSE	0	0.275634037440144	1		535	571	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759881	133759881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1310633113	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	98	696	0	ENST00000318560.5:c.2204C>T	p.Thr735Met	p.T735M	ENST00000318560	NM_005157.4	735	aCg/aTg	11/11	0.275634037440144	1	FACETS	0.914	0.816	1	0.914	0.816	1	CLONAL	1	FALSE	0	0.275634037440144	1		696	671	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759889	133759889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138167706	NA	P-0044406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	100	689	0	ENST00000318560.5:c.2212C>T	p.Arg738Trp	p.R738W	ENST00000318560	NM_005157.4	738	Cgg/Tgg	11/11	0.275634037440144	1	FACETS	0.901	0.806	1	0.901	0.806	1	CLONAL	1	FALSE	0	0.275634037440144	1		689	694	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553590	106553604	+	inframe_deletion	In_Frame_Del	DEL	GCGGGAACAGCCGCC	GCGGGAACAGCCGCC	-	novel	NA	P-0044447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	90	385	0	ENST00000369096.4:c.1555_1569del	p.Ala519_Ala523del	p.A519_A523del	ENST00000369096	NM_001198.3	519	GCGGGAACAGCCGCC/-	5/7	1	2	FACETS	0.822	0.733	0.916	0.822	0.733	0.916	CLONAL	1	TRUE	1	0.494215536016861	2		385	443	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061100	38061204	+	inframe_deletion	In_Frame_Del	DEL	GGTCCTTGCGGCTCTCAGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTGGC	GGTCCTTGCGGCTCTCAGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTGGC	-	novel	NA	P-0044548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	191	138	0	ENST00000250448.2:c.785_889del	p.Arg262_Asp296del	p.R262_D296del	ENST00000250448	NM_004496.3	262	cGCCAGAAGCGCTTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGGCGCCAAGGGCGGCCCTGAGAGCCGCAAGGACCcc/ccc	2/2	0.361213768685496	3	FACETS	1	0.95	1	1	0.995	1	CLONAL	4	TRUE	1	0.374311899568369	3		138	302	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618605	37618605	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	117	491	0	ENST00000447079.4:c.283del	p.Glu95ArgfsTer29	p.E95Rfs*29	ENST00000447079	NM_015083.1	94	aGg/ag	1/14	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.374311899568369	2		491	619	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667806	37667808	+	inframe_deletion	In_Frame_Del	DEL	TAC	TAC	-	novel	NA	P-0044548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	93	404	0	ENST00000447079.4:c.2692_2694del	p.Thr898del	p.T898del	ENST00000447079	NM_015083.1	897	atTACt/att	8/14	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.374311899568369	2		404	430	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361229	66361229	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	45	313	0	ENST00000273854.3:c.943C>G	p.His315Asp	p.H315D	ENST00000273854	NM_004439.5	315	Cac/Gac	4/18	0.217702846125928	2	FACETS	0.588	0.495	0.69	0.294	0.247	0.345	INDETERMINATE	1	TRUE	0	0.374311899568369	2		313	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0044549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	163	532	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.237017527568207	3	FACETS	1	0.983	1	0.812	0.751	0.874	CLONAL	2	TRUE	0	0.312711169298108	3		532	495	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731214	162731214	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	20	243	0	ENST00000367921.3:c.1069A>T	p.Met357Leu	p.M357L	ENST00000367921	NM_006182.2	357	Atg/Ttg	9/18	0.312711169298108	5	FACETS	0.628	0.481	0.801	0.209	0.16	0.267	SUBCLONAL	1	TRUE	2	0.312711169298108	5		243	299	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661785	227661785	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	53	511	0	ENST00000305123.5:c.1670C>A	p.Ala557Asp	p.A557D	ENST00000305123	NM_005544.2	557	gCc/gAc	1/2	0.312711169298108	8	FACETS	1	0.956	1			1	CLONAL	1	TRUE	NA	0.312711169298108	8		511	489	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0044571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	218	371	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.853	0.798	0.908	0.853	0.798	0.908	CLONAL	1	TRUE	1	0.845096359042238	2		371	605	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375045	31375045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745506485	NA	P-0044571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	377	450	1	ENST00000328111.2:c.442C>T	p.Arg148Trp	p.R148W	ENST00000328111	NM_006892.3	148	Cgg/Tgg	6/23	1	2	FACETS	0.996	0.95	1	0.996	0.95	1	CLONAL	1	TRUE	1	0.845096359042238	2		451	896	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720794	89720802	+	inframe_deletion	In_Frame_Del	DEL	TCTAGTACT	TCTAGTACT	-	novel	NA	P-0044571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	72	211	0	ENST00000371953.3:c.946_954del	p.Leu316_Leu318del	p.L316_L318del	ENST00000371953	NM_000314.4	315	taTCTAGTACTt/tat	8/9	0.845096359042238	1	FACETS	0.813	0.74	0.884	0.813	0.74	0.884	CLONAL	1	TRUE	0	0.845096359042238	1		211	121	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907805	76907806	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCCT	novel	NA	P-0044571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	144	107	0	ENST00000373344.5:c.4352_4355dup	p.Glu1453GlyfsTer15	p.E1453Gfs*15	ENST00000373344	NM_000489.3	1452	gag/gaAGGAg	15/35	1	1	FACETS	0.96	0.907	1	0.96	0.907	1	CLONAL	1	TRUE	0	0.845096359042238	1		107	205	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	175	582	2	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.484429406096511	1	FACETS	0.67	0.618	0.724	0.67	0.618	0.724	SUBCLONAL	1	TRUE	0	0.484429406096511	1		584	817	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0044800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	20	393	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.484429406096511	1	FACETS	0.17	0.129	0.218	0.17	0.129	0.218	SUBCLONAL	1	TRUE	0	0.484429406096511	1		393	368	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0044800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	58	730	1	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	0.484429406096511	1	FACETS	0.218	0.186	0.252	0.218	0.186	0.252	SUBCLONAL	1	TRUE	0	0.484429406096511	1		731	833	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0044800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	38	240	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	0.484429406096511	1	FACETS	0.39	0.323	0.463	0.39	0.323	0.463	SUBCLONAL	1	TRUE	0	0.484429406096511	1		241	305	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0044800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	156	577	6	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	0.484429406096511	1	FACETS	0.872	0.802	0.943	0.872	0.802	0.943	CLONAL	1	TRUE	0	0.484429406096511	1		583	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0044800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	401	657	0	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	0.484429406096511	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.484429406096511	1		657	912	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682399	52682400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	128	311	0	ENST00000394830.3:c.773dup	p.Asn258LysfsTer6	p.N258Kfs*6	ENST00000394830	NM_018313.4	258	aat/aaAt	8/30	0.484429406096511	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.484429406096511	1		311	363	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814253	76814253	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	20	177	0	ENST00000373344.5:c.6391C>T	p.Arg2131Ter	p.R2131*	ENST00000373344	NM_000489.3	2131	Cga/Tga	29/35	1	1	FACETS	0.242	0.185	0.308	0.242	0.185	0.308	SUBCLONAL	1	TRUE	0	0.484429406096511	1		177	259	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0044800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	121	439	3	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	0.484429406096511	1	FACETS	0.663	0.601	0.728	0.663	0.601	0.728	SUBCLONAL	1	TRUE	0	0.484429406096511	1		442	571	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141587	202141587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771150445	NA	P-0044800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	68	405	1	ENST00000358485.4:c.875G>A	p.Arg292Gln	p.R292Q	ENST00000358485	NM_001080125.1	292	cGg/cAg	7/9	0.484429406096511	1	FACETS	0.4	0.348	0.456	0.4	0.348	0.456	SUBCLONAL	1	TRUE	0	0.484429406096511	1		406	532	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200961	108200961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782310	NA	P-0044800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	115	335	1	ENST00000278616.4:c.7328G>A	p.Arg2443Gln	p.R2443Q	ENST00000278616	NM_000051.3	2443	cGa/cAa	50/63	0.484429406096511	1	FACETS	0.988	0.9	1	0.988	0.9	1	CLONAL	1	TRUE	0	0.484429406096511	1		336	364	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092714	27092714	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1392166633	NA	P-0044800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	33	343	0	ENST00000324856.7:c.2735C>T	p.Pro912Leu	p.P912L	ENST00000324856	NM_006015.4	912	cCg/cTg	9/20	0.484429406096511	1	FACETS	0.29	0.236	0.35	0.29	0.236	0.35	SUBCLONAL	1	TRUE	0	0.484429406096511	1		343	356	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896549	78896549	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774124294	NA	P-0044800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	402	762	3	ENST00000306801.3:c.2546G>A	p.Arg849His	p.R849H	ENST00000306801	NM_020761.2	849	cGc/cAc	22/34	0.484429406096511	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.484429406096511	1		765	917	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73047240	73047240	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	165	335	0	ENST00000356692.5:c.51del	p.Lys19ArgfsTer14	p.K19Rfs*14	ENST00000356692		16	aGg/ag	2/9	0.484429406096511	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.484429406096511	1		335	483	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858098	152858098	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782309279	NA	P-0044800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	34	386	0	ENST00000406277.2:c.517C>T	p.Arg173Trp	p.R173W	ENST00000406277	NM_152274.4	173	Cgg/Tgg	6/7	1	1	FACETS	0.18	0.146	0.218	0.18	0.146	0.218	SUBCLONAL	1	TRUE	0	0.484429406096511	1		386	592	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134305	2134305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762798984	NA	P-0044800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	386	850	1	ENST00000219476.3:c.4082G>A	p.Arg1361Gln	p.R1361Q	ENST00000219476	NM_000548.3	1361	cGa/cAa	34/42	0.484429406096511	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.484429406096511	1		851	859	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603021	48603021	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	139	259	0	ENST00000342988.3:c.1322G>A	p.Arg441His	p.R441H	ENST00000342988	NM_005359.5	441	cGt/cAt	11/12	0.484429406096511	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.484429406096511	1		259	392	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258094	16258094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	239	449	0	ENST00000375759.3:c.5359G>A	p.Ala1787Thr	p.A1787T	ENST00000375759	NM_015001.2	1787	Gca/Aca	11/15	0.484429406096511	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.484429406096511	1		449	579	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392019	118392019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	40	332	0	ENST00000534358.1:c.11530C>T	p.Arg3844Trp	p.R3844W	ENST00000534358	NM_005933.3	3844	Cgg/Tgg	35/36	0.484429406096511	1	FACETS	0.254	0.21	0.302	0.254	0.21	0.302	SUBCLONAL	1	TRUE	0	0.484429406096511	1		332	493	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143066	58143066	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786203856	NA	P-0044800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	53	771	0	ENST00000257904.6:c.718C>T	p.Arg240Ter	p.R240*	ENST00000257904	NM_000075.3	240	Cga/Tga	7/8	0.484429406096511	1	FACETS	0.193	0.163	0.225	0.193	0.163	0.225	SUBCLONAL	1	TRUE	0	0.484429406096511	1		771	861	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459430	40459430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775608800	NA	P-0044800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	95	549	0	ENST00000345506.4:c.1691C>T	p.Pro564Leu	p.P564L	ENST00000345506	NM_003152.3	564	cCg/cTg	15/20	0.484429406096511	1	FACETS	0.423	0.376	0.472	0.423	0.376	0.472	SUBCLONAL	1	TRUE	0	0.484429406096511	1		549	703	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39576687	39576687	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	33	206	0	ENST00000262039.4:c.977A>G	p.Gln326Arg	p.Q326R	ENST00000262039	NM_002647.2	326	cAa/cGa	9/25	0.484429406096511	1	FACETS	0.449	0.368	0.539	0.449	0.368	0.539	SUBCLONAL	1	TRUE	0	0.484429406096511	1		206	230	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217909	2217910	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0044800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	356	707	0	ENST00000398665.3:c.2686_2687del	p.Arg896GlyfsTer13	p.R896Gfs*13	ENST00000398665	NM_032482.2	895	GAg/g	22/28	0.484429406096511	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.484429406096511	1		707	817	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285039	15285039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	331	755	1	ENST00000263388.2:c.4576C>T	p.Arg1526Cys	p.R1526C	ENST00000263388	NM_000435.2	1526	Cgt/Tgt	25/33	0.484429406096511	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.484429406096511	1		756	806	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211354	36211355	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAG	rs201152143	NA	P-0044800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	221	610	0	ENST00000222270.7:c.1117_1119dup	p.Glu373dup	p.E373dup	ENST00000222270	NM_014727.1	373	aaa/aAAGaa	3/37	0.484429406096511	1	FACETS	0.948	0.886	1	0.948	0.886	1	CLONAL	1	TRUE	0	0.484429406096511	1		610	729	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224246	36224246	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs948721320	NA	P-0044800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	115	606	0	ENST00000222270.7:c.6796A>G	p.Ser2266Gly	p.S2266G	ENST00000222270	NM_014727.1	2266	Agt/Ggt	28/37	0.484429406096511	1	FACETS	0.568	0.513	0.627	0.568	0.513	0.627	SUBCLONAL	1	TRUE	0	0.484429406096511	1		606	633	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249789	39249789	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	113	372	0	ENST00000402219.2:c.1780C>T	p.Pro594Ser	p.P594S	ENST00000402219	NM_005633.3	594	Ccc/Tcc	10/23	0.484429406096511	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.484429406096511	1		372	350	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038190	30038190	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0044800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	169	338	0	ENST00000338641.4:c.364-1G>T		p.X122_splice	ENST00000338641	NM_000268.3	122			0.484429406096511	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.484429406096511	1		338	452	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575561	67575561	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	42	271	0	ENST00000274335.5:c.634G>T	p.Glu212Ter	p.E212*	ENST00000274335		212	Gaa/Taa	4/15	1	2	FACETS	0.411	0.343	0.486	0.411	0.343	0.486	SUBCLONAL	1	TRUE	1	0.484429406096511	2		271	422	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793363	242793363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	101	640	0	ENST00000334409.5:c.714del	p.Val239CysfsTer39	p.V239Cfs*39	ENST00000334409	NM_005018.2	238	ccC/cc	5/5	1	2	FACETS	0.89	0.795	0.991	0.89	0.795	0.991	CLONAL	1	TRUE	1	0.28	2		640	811	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	44	326	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.534	0.447	0.63	0.534	0.447	0.63	SUBCLONAL	1	TRUE	1	0.28	2		328	589	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	101	339	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.28	2		342	690	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	80	368	0	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.926	0.816	1	0.926	0.816	1	CLONAL	1	TRUE	1	0.28	2		368	617	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	117	399	2	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.796	0.721	0.874	1	0.986	1	SUBCLONAL	2	TRUE	1	0.28	2		401	525	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	52	300	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.784	0.668	0.91	0.784	0.668	0.91	CLONAL	1	TRUE	1	0.28	2		300	474	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	39	219	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.757	0.629	0.899	0.757	0.629	0.899	SUBCLONAL	1	TRUE	1	0.28	2		219	368	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	82	565	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.755	0.665	0.851	0.755	0.665	0.851	SUBCLONAL	1	TRUE	1	0.28	2		568	776	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	33	156	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.917	0.751	1	0.917	0.751	1	CLONAL	1	TRUE	1	0.28	2		156	257	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355266	15355266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770044101	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	54	274	0	ENST00000263377.2:c.2357C>T	p.Pro786Leu	p.P786L	ENST00000263377	NM_058243.2	786	cCg/cTg	13/20	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.28	2		274	352	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780068	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	118	578	0	ENST00000269305.4:c.472C>T	p.Arg158Cys	p.R158C	ENST00000269305	NM_001126112.2	158	Cgc/Tgc	5/11	1	2	FACETS	0.849	0.764	0.938	0.849	0.764	0.938	CLONAL	1	TRUE	1	0.28	2		578	993	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226294	2226294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	84	621	0	ENST00000326181.6:c.1907C>T	p.Thr636Met	p.T636M	ENST00000326181	NM_032271.2	636	aCg/aTg	20/21	1	2	FACETS	0.736	0.649	0.829	0.736	0.649	0.829	SUBCLONAL	1	TRUE	1	0.28	2		621	815	SUCCESS
APC	324	MSKCC	GRCh37	5	112154721	112154721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745918184	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	43	306	0	ENST00000257430.4:c.992C>T	p.Ser331Leu	p.S331L	ENST00000257430	NM_000038.5	331	tCg/tTg	10/16	1	2	FACETS	0.724	0.607	0.854	0.724	0.607	0.854	SUBCLONAL	1	TRUE	1	0.28	2		306	424	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265323	152265323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866869178	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	35	245	0	ENST00000206249.3:c.776G>A	p.Arg259Gln	p.R259Q	ENST00000206249	NM_000125.3	259	cGa/cAa	4/8	1	2	FACETS	0.665	0.546	0.799	0.665	0.546	0.799	SUBCLONAL	1	TRUE	1	0.28	2		245	376	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979986	7979987	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs746723399	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	100	579	0	ENST00000319144.4:c.1350dup	p.Leu451AlafsTer27	p.L451Afs*27	ENST00000319144	NM_001139.2	450	-/G	10/15	1	2	FACETS	0.832	0.742	0.927	0.832	0.742	0.927	CLONAL	1	TRUE	1	0.28	2		579	859	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413710	138413710	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	49	334	3	ENST00000289153.2:c.1810del	p.Arg604GlyfsTer4	p.R604Gfs*4	ENST00000289153	NM_006219.2	604	Cgg/gg	12/22	1	2	FACETS	0.595	0.504	0.696	0.595	0.504	0.696	SUBCLONAL	1	TRUE	1	0.28	2		337	588	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163307846	163307846	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61747498	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	30	278	0	ENST00000271452.3:c.472G>A	p.Ala158Thr	p.A158T	ENST00000271452	NM_145697.2	158	Gca/Aca	7/14	1	2	FACETS	0.459	0.369	0.561	0.459	0.369	0.561	SUBCLONAL	1	TRUE	1	0.28	2		278	467	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998128	169998128	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs753143066	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	135	389	3	ENST00000295797.4:c.826del	p.Thr276GlnfsTer7	p.T276Qfs*7	ENST00000295797	NM_002740.5	273	ttA/tt	9/18	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.28	2		392	707	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625303	69625303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1335560620	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	132	629	0	ENST00000334134.2:c.490C>T	p.Arg164Cys	p.R164C	ENST00000334134	NM_005247.2	164	Cgc/Tgc	3/3	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.28	2		629	889	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115272956	115272956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1178464540	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	77	481	0	ENST00000438362.2:c.1417C>T	p.Arg473Cys	p.R473C	ENST00000438362	NM_001242891.1	473	Cgt/Tgt	12/20	1	2	FACETS	0.77	0.676	0.872	0.77	0.676	0.872	SUBCLONAL	1	TRUE	1	0.28	2		481	714	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012386	152012386	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	26	257	1	ENST00000262189.6:c.427del	p.Ser143ValfsTer3	p.S143Vfs*3	ENST00000262189	NM_170606.2	143	Agt/gt	4/59	1	2	FACETS	0.497	0.393	0.615	0.497	0.393	0.615	SUBCLONAL	1	TRUE	1	0.28	2		258	374	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223614	36223614	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	99	675	1	ENST00000222270.7:c.6169del	p.Arg2057AlafsTer34	p.R2057Afs*34	ENST00000222270	NM_014727.1	2055	gCc/gc	28/37	1	2	FACETS	0.787	0.701	0.878	0.787	0.701	0.878	SUBCLONAL	1	TRUE	1	0.28	2		676	899	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352576	89352576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762710349	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	86	350	0	ENST00000301030.4:c.763C>T	p.Arg255Trp	p.R255W	ENST00000301030	NM_001256183.1	255	Cgg/Tgg	8/13	1	2	FACETS	0.966	0.855	1	0.966	0.855	1	CLONAL	1	TRUE	1	0.28	2		350	636	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431178	49431178	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs793888512	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	87	600	1	ENST00000301067.7:c.9961C>T	p.Arg3321Ter	p.R3321*	ENST00000301067	NM_003482.3	3321	Cga/Tga	34/54	1	2	FACETS	0.805	0.712	0.904	0.805	0.712	0.904	CLONAL	1	TRUE	1	0.28	2		601	772	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182662920	182662920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	39	308	0	ENST00000292782.4:c.742C>T	p.Arg248Cys	p.R248C	ENST00000292782	NM_020640.2	248	Cgc/Tgc	7/7	1	2	FACETS	0.493	0.408	0.588	0.493	0.408	0.588	SUBCLONAL	1	TRUE	1	0.28	2		308	565	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277992	41277992	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	40	269	0	ENST00000349496.5:c.1954+2T>C		p.X652_splice	ENST00000349496	NM_001904.3	652			1	2	FACETS	0.733	0.61	0.869	0.733	0.61	0.869	SUBCLONAL	1	TRUE	1	0.28	2		269	390	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877423	28877423	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750346448	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	73	407	0	ENST00000282397.4:c.3898G>A	p.Val1300Ile	p.V1300I	ENST00000282397	NM_002019.4	1300	Gtc/Atc	30/30	1	2	FACETS	0.766	0.669	0.87	0.766	0.669	0.87	SUBCLONAL	1	TRUE	1	0.28	2		407	681	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752799	57752800	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	38	198	0	ENST00000274289.3:c.1128dup	p.Asp377ArgfsTer7	p.D377Rfs*7	ENST00000274289	NM_006622.3	376	-/A	8/14	1	2	FACETS	0.73	0.604	0.869	0.73	0.604	0.869	SUBCLONAL	1	TRUE	1	0.28	2		198	372	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843553	3843553	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	62	369	0	ENST00000262367.5:c.1050del	p.Lys350AsnfsTer4	p.K350Nfs*4	ENST00000262367	NM_004380.2	350	aaA/aa	4/31	1	2	FACETS	0.638	0.55	0.734	0.638	0.55	0.734	SUBCLONAL	1	TRUE	1	0.28	2		369	694	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100793	8100793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	65	541	1	ENST00000346208.3:c.767G>A	p.Arg256Gln	p.R256Q	ENST00000346208		256	cGg/cAg	3/6	1	2	FACETS	0.633	0.548	0.725	0.633	0.548	0.725	SUBCLONAL	1	TRUE	1	0.28	2		542	734	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375668	118375668	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	52	314	0	ENST00000534358.1:c.9061A>C	p.Asn3021His	p.N3021H	ENST00000534358	NM_005933.3	3021	Aac/Cac	27/36	1	2	FACETS	0.693	0.59	0.806	0.693	0.59	0.806	SUBCLONAL	1	TRUE	1	0.28	2		314	536	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376499	118376499	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	35	282	0	ENST00000534358.1:c.9892T>C	p.Tyr3298His	p.Y3298H	ENST00000534358	NM_005933.3	3298	Tat/Cat	27/36	1	2	FACETS	0.67	0.55	0.805	0.67	0.55	0.805	SUBCLONAL	1	TRUE	1	0.28	2		282	373	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257248	133257248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774404704	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	59	348	0	ENST00000320574.5:c.230G>A	p.Arg77His	p.R77H	ENST00000320574	NM_006231.2	77	cGc/cAc	3/49	1	2	FACETS	0.72	0.62	0.83	0.72	0.62	0.83	SUBCLONAL	1	TRUE	1	0.28	2		348	585	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858692	9858693	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	39	337	0	ENST00000330684.3:c.2708dup	p.Asn903LysfsTer21	p.N903Kfs*21	ENST00000330684	NM_001134407.1	903	aac/aaAc	13/13	1	2	FACETS	0.583	0.483	0.694	0.583	0.483	0.694	SUBCLONAL	1	TRUE	1	0.28	2		337	478	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831731	72831731	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	83	388	0	ENST00000268489.5:c.4850C>A	p.Ser1617Tyr	p.S1617Y	ENST00000268489	NM_006885.3	1617	tCt/tAt	9/10	1	2	FACETS	0.988	0.873	1	0.988	0.873	1	CLONAL	1	TRUE	1	0.28	2		388	600	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337251	89337251	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	63	356	0	ENST00000301030.4:c.7780G>A	p.Val2594Met	p.V2594M	ENST00000301030	NM_001256183.1	2594	Gtg/Atg	12/13	1	2	FACETS	0.738	0.638	0.846	0.738	0.638	0.846	SUBCLONAL	1	TRUE	1	0.28	2		356	610	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677786	58677786	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	53	452	0	ENST00000305921.3:c.11T>C	p.Leu4Pro	p.L4P	ENST00000305921	NM_003620.3	4	cTg/cCg	1/6	1	2	FACETS	0.607	0.517	0.705	0.607	0.517	0.705	SUBCLONAL	1	TRUE	1	0.28	2		452	624	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741860	40741860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778561687	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	78	464	2	ENST00000392038.2:c.1112G>A	p.Arg371His	p.R371H	ENST00000392038	NM_001626.4	371	cGc/cAc	11/14	1	2	FACETS	0.843	0.741	0.953	0.843	0.741	0.953	CLONAL	1	TRUE	1	0.28	2		466	661	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484417	57484417	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	57	328	0	ENST00000371085.3:c.598T>C	p.Cys200Arg	p.C200R	ENST00000371085	NM_000516.4	200	Tgc/Cgc	8/13	1	2	FACETS	0.671	0.575	0.775	0.671	0.575	0.775	SUBCLONAL	1	TRUE	1	0.28	2		328	607	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626047	12626047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881007	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	67	340	0	ENST00000251849.4:c.1913C>T	p.Thr638Met	p.T638M	ENST00000251849	NM_002880.3	638	aCg/aTg	17/17	1	2	FACETS	0.819	0.712	0.935	0.819	0.712	0.935	CLONAL	1	TRUE	1	0.28	2		340	584	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067316	37067316	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	60	339	0	ENST00000231790.2:c.1228del	p.Ala410ProfsTer81	p.A410Pfs*81	ENST00000231790	NM_000249.3	409	caG/ca	12/19	1	2	FACETS	0.798	0.688	0.918	0.798	0.688	0.918	CLONAL	1	TRUE	1	0.28	2		339	537	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163746	47163746	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	47	334	0	ENST00000409792.3:c.2380T>C	p.Tyr794His	p.Y794H	ENST00000409792	NM_014159.6	794	Tac/Cac	3/21	1	2	FACETS	0.768	0.649	0.899	0.768	0.649	0.899	SUBCLONAL	1	TRUE	1	0.28	2		334	437	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947373	38947373	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	18	121	0	ENST00000357387.3:c.4307T>C	p.Ile1436Thr	p.I1436T	ENST00000357387	NM_152756.3	1436	aTa/aCa	32/38	1	2	FACETS	0.765	0.58	0.982	0.765	0.58	0.982	CLONAL	1	TRUE	1	0.28	2		121	168	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718159	117718159	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	49	356	0	ENST00000368508.3:c.698T>C	p.Ile233Thr	p.I233T	ENST00000368508	NM_002944.2	233	aTc/aCc	7/43	1	2	FACETS	0.578	0.488	0.676	0.578	0.488	0.676	SUBCLONAL	1	TRUE	1	0.28	2		356	606	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864366	151864366	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	58	294	0	ENST00000262189.6:c.9615C>G	p.His3205Gln	p.H3205Q	ENST00000262189	NM_170606.2	3205	caC/caG	42/59	1	2	FACETS	0.762	0.655	0.878	0.762	0.655	0.878	SUBCLONAL	1	TRUE	1	0.28	2		294	544	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231343	98231343	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	90	547	0	ENST00000331920.6:c.1940G>C	p.Ser647Thr	p.S647T	ENST00000331920	NM_000264.3	647	aGc/aCc	14/24	1	2	FACETS	0.743	0.658	0.834	0.743	0.658	0.834	SUBCLONAL	1	TRUE	1	0.28	2		547	865	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	50	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.180159418892375	1	FACETS	0.943	0.803	1	0.943	0.803	1	CLONAL	1	TRUE	0	0.246526863771937	1		485	377	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226550826	226550826	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0044992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	45	312	0	ENST00000366794.5:c.2822T>A	p.Leu941Ter	p.L941*	ENST00000366794	NM_001618.3	941	tTa/tAa	21/23	1	2	FACETS	0.732	0.615	0.861	0.732	0.615	0.861	SUBCLONAL	1	TRUE	1	0.246526863771937	2		312	499	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	22	367	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.217220141731457	4	FACETS		NA	1			1	NA	NA	FALSE	2	NA	4		367	697	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045056-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	26	714	1				ENST00000310581	NM_198253.2	-/1132			0.292789871675297	0	FACETS	0.38	0.308	0.46			1	INDETERMINATE	1	FALSE	0	0.570262040398694	0		715	103	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047507	49047507	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0045056-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	34	147	0	ENST00000267163.4:c.2501C>G	p.Ser834Ter	p.S834*	ENST00000267163	NM_000321.2	834	tCa/tGa	24/27	0.34089207908457	3	FACETS	0.952	0.788	1	0.317	0.262	0.377	INDETERMINATE	1	FALSE	0	0.570262040398694	3		147	161	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0045056-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	75	616	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.578451261839426	5	FACETS	1	0.954	1	0.392	0.345	0.442	CLONAL	1	FALSE	2	0.570262040398694	5		616	415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519985	NA	P-0045056-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	159	698	1	ENST00000269305.4:c.857A>T	p.Glu286Val	p.E286V	ENST00000269305	NM_001126112.2	286	gAa/gTa	8/11	0.578451261839426	5	FACETS	0.991	0.915	1	0.661	0.61	0.713	CLONAL	2	FALSE	2	0.570262040398694	5		699	522	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645970	215645970	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045056-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	65	491	0	ENST00000260947.4:c.628del	p.Thr210LeufsTer2	p.T210Lfs*2	ENST00000260947	NM_000465.2	210	Act/ct	4/11	0.578451261839426	1	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	FALSE	0	0.570262040398694	1		491	163	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136277	202136277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045056-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	54	462	0	ENST00000358485.4:c.521C>T	p.Ser174Leu	p.S174L	ENST00000358485	NM_001080125.1	174	tCa/tTa	3/9	0.434527219412805	2	FACETS	0.646	0.556	0.744	0.323	0.278	0.372	SUBCLONAL	1	FALSE	0	0.570262040398694	2		462	293	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47599183	47599183	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045056-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	190	635	0	ENST00000430070.2:c.417C>G	p.Asp139Glu	p.D139E	ENST00000430070	NM_018095.4	139	gaC/gaG	2/4	0.578451261839426	4	FACETS	0.911	0.848	0.976			1	CLONAL	2	FALSE	NA	0.570262040398694	4		635	574	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99472819	99472823	+	frameshift_variant	Frame_Shift_Del	DEL	GCTCT	GCTCT	-	novel	NA	P-0045056-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	55	570	0	ENST00000268035.6:c.2817_2821del	p.Leu940ArgfsTer19	p.L940Rfs*19	ENST00000268035	NM_000875.3	939	GCTCTg/g	14/21	0.578451261839426	1	FACETS	0.589	0.51	0.674	0.589	0.51	0.674	SUBCLONAL	1	FALSE	0	0.570262040398694	1		570	234	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701145	29701365	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	AACGTAATAGCATTAAGAAGATCGTGTGAAGCTTGCTTGCTTTCTTTTTTAAAATCAACTTAACATGGGCTCTTCACTAGTGACCCCTTCCCTGTCCTTGCCCTTTCCCCCCATGTTGTAATGCTGCACTTCCTGTTTTATAATGAACCCATCCGGTTTGCCATGTTGCCAGATGATCAACTCTTCGAAGCCTTGCCTAAATTTAATGCTGCCTTTTCTTT	AACGTAATAGCATTAAGAAGATCGTGTGAAGCTTGCTTGCTTTCTTTTTTAAAATCAACTTAACATGGGCTCTTCACTAGTGACCCCTTCCCTGTCCTTGCCCTTTCCCCCCATGTTGTAATGCTGCACTTCCTGTTTTATAATGAACCCATCCGGTTTGCCATGTTGCCAGATGATCAACTCTTCGAAGCCTTGCCTAAATTTAATGCTGCCTTTTCTTT	-	novel	NA	P-0045056-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	45	508	0	ENST00000356175.3:c.8432_*195del		p.*2811*	ENST00000356175	NM_000267.3	2810		57/57	0.578451261839426	4	FACETS	0.718	0.606	0.842			1	SUBCLONAL	1	FALSE	NA	0.570262040398694	4		508	345	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31015982	31015982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045056-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	55	697	0	ENST00000375687.4:c.304C>T	p.Pro102Ser	p.P102S	ENST00000375687	NM_015338.5	102	Cca/Tca	5/13	0.241534352816949	2	FACETS	0.546	0.469	0.63	0.273	0.234	0.315	INDETERMINATE	1	FALSE	0	0.570262040398694	2		697	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576865	7576865	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0045731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	398	451	2	ENST00000269305.4:c.981T>A	p.Tyr327Ter	p.Y327*	ENST00000269305	NM_001126112.2	327	taT/taA	9/11	0.626984917582433	2	FACETS	0.969	0.933	1	0.969	0.933	1	CLONAL	2	TRUE	0	0.626984917582433	2		453	655	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436076	49436076	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	139	489	0	ENST00000301067.7:c.5905C>G	p.Pro1969Ala	p.P1969A	ENST00000301067	NM_003482.3	1969	Ccc/Gcc	28/54	0.626984917582433	3	FACETS	0.839	0.765	0.916	0.42	0.382	0.458	CLONAL	1	TRUE	1	0.626984917582433	3		489	694	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975433	26975433	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	147	209	0	ENST00000381527.3:c.1059C>A	p.Tyr353Ter	p.Y353*	ENST00000381527	NM_001260.1	353	taC/taA	11/13	0.2721602846832	3	FACETS	1	0.976	1	0.583	0.535	0.633	INDETERMINATE	1	TRUE	1	0.626984917582433	3		209	528	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138095	64138095	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	65	516	0	ENST00000334205.4:c.2018G>T	p.Trp673Leu	p.W673L	ENST00000334205	NM_003942.2	673	tGg/tTg	16/17	0.213525140019476	3	FACETS	0.742	0.643	0.849	0.371	0.321	0.425	SUBCLONAL	1	TRUE	1	0.325926208764403	3		516	625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0045889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	125	663	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	0.222683185821655	2	FACETS	1	0.983	1	0.681	0.619	0.746	CLONAL	1	TRUE	0	0.325926208764403	2		663	563	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512342	38512342	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	109	443	0	ENST00000254066.5:c.1253A>T	p.Glu418Val	p.E418V	ENST00000254066	NM_000964.3	418	gAg/gTg	9/9	0.213525140019476	3	FACETS	1	0.982	1	0.724	0.653	0.799	CLONAL	1	TRUE	1	0.325926208764403	3		443	537	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140172	50140172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774218911	NA	P-0045889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	48	464	0	ENST00000246792.3:c.253G>A	p.Ala85Thr	p.A85T	ENST00000246792	NM_006270.3	85	Gcg/Acg	3/6	1	2	FACETS	0.604	0.51	0.706	0.604	0.51	0.706	SUBCLONAL	1	TRUE	1	0.325926208764403	2		464	488	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416141	29416141	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs753750497	NA	P-0045889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	72	414	0	ENST00000389048.3:c.4812C>A	p.Tyr1604Ter	p.Y1604*	ENST00000389048	NM_004304.4	1604	taC/taA	29/29	1	2	FACETS	0.799	0.699	0.907	0.799	0.699	0.907	CLONAL	1	TRUE	1	0.325926208764403	2		414	553	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156607	55156607	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	84	467	0	ENST00000257290.5:c.3008G>T	p.Trp1003Leu	p.W1003L	ENST00000257290	NM_006206.4	1003	tGg/tTg	22/23	1	2	FACETS	0.887	0.785	0.997	0.887	0.785	0.997	CLONAL	1	TRUE	1	0.325926208764403	2		467	581	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670657	86670657	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	33	224	0	ENST00000274376.6:c.1935T>G	p.Asp645Glu	p.D645E	ENST00000274376	NM_002890.2	645	gaT/gaG	15/25	0.286886067946903	1	FACETS	0.545	0.445	0.657	0.545	0.445	0.657	SUBCLONAL	1	TRUE	0	0.325926208764403	1		224	311	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710766	117710766	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	44	293	0	ENST00000368508.3:c.1506T>A	p.Phe502Leu	p.F502L	ENST00000368508	NM_002944.2	502	ttT/ttA	12/43	0.150487961086074	1	FACETS	0.611	0.513	0.718	0.611	0.513	0.718	INDETERMINATE	1	TRUE	0	0.325926208764403	1		293	370	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508470	106508470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1463222028	NA	P-0045889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	24	238	0	ENST00000359195.3:c.464C>T	p.Thr155Met	p.T155M	ENST00000359195	NM_002649.2	155	aCg/aTg	2/11	0.320346697005901	4	FACETS	0.62	0.486	0.774	0.31	0.243	0.387	SUBCLONAL	1	TRUE	2	0.325926208764403	4		238	315	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404598	8404598	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	104	254	0	ENST00000356435.5:c.4149G>T	p.Lys1383Asn	p.K1383N	ENST00000356435		1383	aaG/aaT	25/35	0.325926208764403	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.325926208764403	1		254	406	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504353	8504353	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	108	416	0	ENST00000356435.5:c.1730C>A	p.Pro577Gln	p.P577Q	ENST00000356435		577	cCa/cAa	12/35	0.325926208764403	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.325926208764403	1		416	544	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794838	242794838	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045889-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	73	615	0	ENST00000334409.5:c.371G>T	p.Gly124Val	p.G124V	ENST00000334409	NM_005018.2	124	gGg/gTg	2/5	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.27	2		615	538	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366990	118366990	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045889-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	45	393	3	ENST00000534358.1:c.5572C>T	p.Arg1858Ter	p.R1858*	ENST00000534358	NM_005933.3	1858	Cga/Tga	20/36	1	2	FACETS	0.714	0.6	0.839	0.714	0.6	0.839	SUBCLONAL	1	TRUE	1	0.27	2		396	467	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434078	49434078	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045889-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	58	565	1	ENST00000301067.7:c.7475G>T	p.Gly2492Val	p.G2492V	ENST00000301067	NM_003482.3	2492	gGg/gTg	31/54	1	2	FACETS	0.781	0.671	0.901	0.781	0.671	0.901	CLONAL	1	TRUE	1	0.27	2		566	550	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557373	29557373	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045889-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	25	225	0	ENST00000356175.3:c.3086del	p.Leu1029ProfsTer7	p.L1029Pfs*7	ENST00000356175	NM_000267.3	1029	cTc/cc	23/57	1	2	FACETS	0.65	0.513	0.806	0.65	0.513	0.806	SUBCLONAL	1	TRUE	1	0.27	2		225	285	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405971	49405971	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045889-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	77	465	0	ENST00000418115.1:c.167C>G	p.Ala56Gly	p.A56G	ENST00000418115	NM_001664.2	56	gCt/gGt	3/5	1	2	FACETS	0.989	0.869	1	0.989	0.869	1	CLONAL	1	TRUE	1	0.27	2		465	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0046090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	96	703	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.14	2		703	1134	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	54	367	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.14	2		367	724	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50820842	50820842	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	33	346	0	ENST00000398568.2:c.2017A>G	p.Thr673Ala	p.T673A	ENST00000398568	NM_001042412.1	673	Acc/Gcc	12/18	1	2	FACETS	0.816	0.663	0.989	0.816	0.663	0.989	CLONAL	1	TRUE	1	0.14	2		346	578	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157488271	157488271	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1358728441	NA	P-0046090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	37	480	0	ENST00000346085.5:c.2977C>T	p.Gln993Ter	p.Q993*	ENST00000346085	NM_020732.3	993	Cag/Tag	10/20	1	2	FACETS	0.762	0.626	0.914	0.762	0.626	0.914	CLONAL	1	TRUE	1	0.14	2		480	694	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971206	21971207	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	CCTG	novel	NA	P-0046090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	51	464	0	ENST00000304494.5:c.151-3_151dup	p.Val51AlafsTer70	p.V51Afs*70	ENST00000304494	NM_000077.4	51	gtc/gCAGGtc	2/3	0.14363645477866	1	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	0	0.14	1		464	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0046275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	14	568	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	1	2	FACETS	0.837	0.608	1	0.837	0.608	1	CLONAL	1	TRUE	1	0.22	2		568	152	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130427	29130427	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587781269	NA	P-0046275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	18	577	0	ENST00000328354.6:c.283C>T	p.Arg95Ter	p.R95*	ENST00000328354	NM_007194.3	95	Cga/Tga	2/15	1	2	FACETS	0.779	0.588	1	0.779	0.588	1	CLONAL	1	TRUE	1	0.22	2		577	210	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813324	102813324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377124814	NA	P-0046275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	20	588	1	ENST00000307046.8:c.365G>A	p.Arg122His	p.R122H	ENST00000307046	NM_001111285.1	122	cGt/cAt	3/4	1	2	FACETS	1	0.816	1	1	0.816	1	CLONAL	1	TRUE	1	0.22	2		589	170	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492685	56492686	+	splice_donor_variant	Splice_Site	DNP	GC	GC	AA	novel	NA	P-0046275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	14	313	0	ENST00000407977.2:c.252+1_252+2delinsTT		p.X84_splice	ENST00000407977		84			0.147782994118384	1	FACETS	1	0.796	1	1	0.796	1	CLONAL	1	TRUE	0	0.22	1		313	102	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540425	187540426	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	13	352	0	ENST00000441802.2:c.7314dup	p.Val2439CysfsTer3	p.V2439Cfs*3	ENST00000441802	NM_005245.3	2438	-/T	10/27	1	2	FACETS	0.762	0.546	1	0.762	0.546	1	CLONAL	1	TRUE	1	0.22	2		352	155	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227906	123227906	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	14	282	0	ENST00000218089.9:c.3617C>T	p.Pro1206Leu	p.P1206L	ENST00000218089	NM_001042749.1	1206	cCa/cTa	33/35	0.147782994118384	1	FACETS	0.892	0.65	1	0.892	0.65	1	CLONAL	1	TRUE	0	0.22	1		282	127	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0046877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	84	509	1				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		510	220	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141496	11141496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	75	621	0	ENST00000358026.2:c.3473C>T	p.Ala1158Val	p.A1158V	ENST00000358026	NM_001128849.1	1158	gCt/gTt	25/36	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		621	553	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204896	94204896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs185439615	NA	P-0046877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	34	259	0	ENST00000323929.3:c.689C>T	p.Pro230Leu	p.P230L	ENST00000323929	NM_005591.3	230	cCa/cTa	8/20	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		259	328	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586490	189586490	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	184	444	0	ENST00000264731.3:c.1114G>C	p.Asp372His	p.D372H	ENST00000264731	NM_003722.4	372	Gat/Cat	8/14	0.148786427928779	3	FACETS	0.947	0.875	1	0.631	0.583	0.681	INDETERMINATE	2	TRUE	0	0.255467753588835	3		444	858	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430992	181430992	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	111	551	0	ENST00000325404.1:c.844G>C	p.Glu282Gln	p.E282Q	ENST00000325404	NM_003106.3	282	Gag/Cag	1/1	0.148786427928779	3	FACETS	1	0.905	1	0.336	0.301	0.373	INDETERMINATE	1	TRUE	0	0.255467753588835	3		551	972	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437894	52437894	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	58	454	0	ENST00000460680.1:c.1267del	p.Thr423GlnfsTer7	p.T423Qfs*7	ENST00000460680	NM_004656.3	423	Aca/ca	13/17	1	2	FACETS	0.585	0.502	0.677	0.585	0.502	0.677	SUBCLONAL	1	TRUE	1	0.255467753588835	2		454	776	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0047013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	86	416	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.171517889580616	2	FACETS	1	0.96	1	0.594	0.526	0.666	CLONAL	1	TRUE	0	0.255467753588835	2		416	567	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129655	11129655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	74	445	0	ENST00000358026.2:c.2461G>A	p.Glu821Lys	p.E821K	ENST00000358026	NM_001128849.1	821	Gag/Aag	17/36	1	2	FACETS	0.708	0.619	0.805	0.708	0.619	0.805	SUBCLONAL	1	TRUE	1	0.255467753588835	2		445	818	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117081	193117081	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	123	274	0	ENST00000367435.3:c.814A>C	p.Asn272His	p.N272H	ENST00000367435	NM_024529.4	272	Aat/Cat	8/17	0.148786427928779	3	FACETS	0.829	0.751	0.911	0.553	0.501	0.607	INDETERMINATE	2	TRUE	0	0.255467753588835	3		274	655	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342128	70342128	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	68	423	0	ENST00000374080.3:c.1180C>A	p.Leu394Ile	p.L394I	ENST00000374080		394	Ctt/Att	8/45	1	2	FACETS	0.592	0.513	0.677	0.592	0.513	0.677	SUBCLONAL	1	TRUE	1	0.255467753588835	2		423	900	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578476	7578523	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGTGTGGAATCAACCCACAGCTGCACAGGGCAGGTCTTGGCCAGTT	GGGGTGTGGAATCAACCCACAGCTGCACAGGGCAGGTCTTGGCCAGTT	C	novel	NA	P-0047013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	68	592	0	ENST00000269305.4:c.407_454delinsG	p.Gln136ArgfsTer29	p.Q136Rfs*29	ENST00000269305	NM_001126112.2	136	cAACTGGCCAAGACCTGCCCTGTGCAGCTGTGGGTTGATTCCACACCCCcg/cGcg	5/11	1	2	FACETS	0.595	0.516	0.68	0.595	0.516	0.68	SUBCLONAL	1	TRUE	1	0.255467753588835	2		592	895	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058883	42058883	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121521-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	202	447	0	ENST00000219905.7:c.8603C>A	p.Pro2868His	p.P2868H	ENST00000219905	NM_001164273.1	2868	cCt/cAt	24/24	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	NA	1	0.770501241362903	2		447	514	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045901	26045901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771352320	NA	P-0121521-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	239	655	0	ENST00000540144.1:c.263C>T	p.Ser88Phe	p.S88F	ENST00000540144	NM_003531.2	88	tCt/tTt	1/1	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	NA	1	0.770501241362903	2		655	589	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513044	106513044	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0121521-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	154	430	0	ENST00000359195.3:c.2058A>T	p.Leu686Phe	p.L686F	ENST00000359195	NM_002649.2	686	ttA/ttT	3/11	0.770501241362903	4	FACETS	0.879	0.805	0.956	0.293	0.268	0.319	CLONAL	1	NA	1	0.770501241362903	4		430	805	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0047747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	75	371	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.196582042363338	4	FACETS	0.773	0.679	0.874	0.773	0.679	0.874	SUBCLONAL	2	TRUE	2	0.231529635485151	4		371	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882025	NA	P-0047747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	129	618	0	ENST00000269305.4:c.646G>T	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ttg	6/11	0.184493060736765	2	FACETS	0.751	0.681	0.824	0.751	0.681	0.824	SUBCLONAL	2	TRUE	0	0.231529635485151	2		618	742	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022684	12022684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745867456	NA	P-0047747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	148	893	3	ENST00000396373.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000396373	NM_001987.4	264	Cgc/Tgc	5/8	0.231529635485151	5	FACETS	0.901	0.826	0.98			1	CLONAL	3	TRUE	NA	0.231529635485151	5		896	637	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290231	15290231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	79	1078	0	ENST00000263388.2:c.3404G>A	p.Gly1135Asp	p.G1135D	ENST00000263388	NM_000435.2	1135	gGt/gAt	21/33	0.0782268793901963	4	FACETS	0.784	0.687	0.888	0.392	0.343	0.444	INDETERMINATE	1	TRUE	2	0.231529635485151	4		1078	1072	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426402	49426402	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	97	1022	0	ENST00000301067.7:c.12086T>G	p.Val4029Gly	p.V4029G	ENST00000301067	NM_003482.3	4029	gTa/gGa	39/54	0.203754005559325	3	FACETS	0.956	0.851	1	0.478	0.425	0.535	CLONAL	1	TRUE	1	0.231529635485151	3		1022	978	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435912	56435912	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	59	704	0	ENST00000407977.2:c.1225C>T	p.Gln409Ter	p.Q409*	ENST00000407977		409	Cag/Tag	9/10	0.231529635485151	2	FACETS	0.978	0.842	1	0.489	0.421	0.563	CLONAL	1	TRUE	0	0.231529635485151	2		704	521	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932792	49932792	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	94	829	0	ENST00000296474.3:c.3079G>C	p.Asp1027His	p.D1027H	ENST00000296474	NM_002447.2	1027	Gat/Cat	14/20	1	2	FACETS	0.954	0.848	1	0.954	0.848	1	CLONAL	1	TRUE	1	0.231529635485151	2		829	851	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0048095-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	99	304	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.657385379075902	3	FACETS	1	0.968	1	0.591	0.533	0.652	CLONAL	1	TRUE	1	0.658433990282187	3		304	338	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048095-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	142	812	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.635256533775304	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.658433990282187	4		812	304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579536	7579536	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567556930	NA	P-0048095-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	1334	859	0	ENST00000269305.4:c.151G>T	p.Glu51Ter	p.E51*	ENST00000269305	NM_001126112.2	51	Gaa/Taa	4/11	0.657385379075902	5	FACETS	0.989	0.975	1	0.989	0.975	1	CLONAL	5	TRUE	0	0.658433990282187	5		859	1629	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449778	8449778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533663469	NA	P-0048095-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	161	565	0	ENST00000356435.5:c.3935C>T	p.Ser1312Leu	p.S1312L	ENST00000356435		1312	tCa/tTa	23/35	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.658433990282187	2		565	479	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857148	9857148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048095-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	221	701	0	ENST00000330684.3:c.4253G>A	p.Gly1418Asp	p.G1418D	ENST00000330684	NM_001134407.1	1418	gGc/gAc	13/13	0.657385379075902	3	FACETS	1	0.964	1			1	CLONAL	1	TRUE	NA	0.658433990282187	3		701	848	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971375	13971375	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0048095-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	146	559	0	ENST00000405192.2:c.555-1G>C		p.X185_splice	ENST00000405192	NM_001163147.1	185			0.337388404665503	3	FACETS	1	0.951	1	0.525	0.482	0.571	INDETERMINATE	1	TRUE	1	0.658433990282187	3		559	561	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992288	72992288	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048095-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	893	792	0	ENST00000268489.5:c.1757G>A	p.Arg586Lys	p.R586K	ENST00000268489	NM_006885.3	586	aGg/aAg	2/10	0.657385379075902	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.658433990282187	3		792	1133	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39600606	39600606	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048095-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	83	238	0	ENST00000262039.4:c.1421A>T	p.Asp474Val	p.D474V	ENST00000262039	NM_002647.2	474	gAt/gTt	13/25	0.657385379075902	3	FACETS	0.851	0.767	0.935	0.851	0.767	0.935	CLONAL	2	TRUE	1	0.658433990282187	3		238	197	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617187	100617187	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048095-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	398	317	0	ENST00000308731.7:c.562C>T	p.Leu188Phe	p.L188F	ENST00000308731	NM_000061.2	188	Ctt/Ttt	7/19	0.604471103013942	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.658433990282187	2		317	521	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650137	93650137	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048095-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	330	551	0	ENST00000375746.1:c.1688G>A	p.Trp563Ter	p.W563*	ENST00000375746	NM_001174167.1	563	tGg/tAg	12/14	0.657385379075902	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.658433990282187	3		551	665	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730245	133730326	+	frameshift_variant	Frame_Shift_Del	DEL	CCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCC	CCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCC	-	novel	NA	P-0048095-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	383	616	0	ENST00000318560.5:c.311_392del	p.Thr104MetfsTer11	p.T104Mfs*11	ENST00000318560	NM_005157.4	104	aCCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCt/at	3/11	0.657385379075902	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.658433990282187	3		616	736	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332337	70332337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761821309	NA	P-0048097-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	163	690	0	ENST00000373644.4:c.242G>A	p.Arg81His	p.R81H	ENST00000373644	NM_030625.2	81	cGc/cAc	2/12	1	2	FACETS	0.98	0.905	1	0.98	0.905	1	CLONAL	1	TRUE	1	0.612783734650346	2		690	543	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479833	67479833	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048097-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	403	667	0	ENST00000327367.4:c.1140G>A	p.Trp380Ter	p.W380*	ENST00000327367	NM_005902.3	380	tgG/tgA	8/9	0.614652726246428	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.612783734650346	2		667	637	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149002	119149902	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGCAGGTACGGATCTAAACAGCGACTTTTTTCAGCTATGTAATAACCTTGGAAAATTCGGTATTATATAGCCTTTACTGATACAAGGGGTGGCCTGGCTTTTGGGGTTAGGTTTAAACTTTTACTTTTTTTTGATCTCTAGGAAATGTATTTTCTAGTAGATTAATATTTTAAGTATTTTCAGATGCATCTGTTACTATCTTTTGCTTCTTCTGCAGGAATCAGAAGGTCAGGGCTGTCCTTTCTGCCGATGTGAAATTAAAGGTACTGAACCCATCGTGGTAGATCCGTTTGATCCTAGAGGGAGTGGCAGCCTGTTGAGGCAAGGAGCAGAGGGAGCTCCCTCCCCAAATTATGATGATGATGATGATGAACGAGCTGATGATACTCTCTTCATGATGAAGGAATTGGCTGGTGCCAAGGTAAGATGGCAGTTTAGGAGACTGGCAAAATCCATTGTGAGTTGTCTTCTAAAGCCGTAAAACACTTAACGATATCCAAACTACAATGATAGGTAGTATTAATAGCTAATATTTATTGAGCATTTACTATATGACAGATATTGTGTTAAGCACTTTACTTGTTTTTTACTCAATCTTTACTACAGCCCTATGAGTACATACTACTATTATCCTTATTTAACAGATGAAGAAACTGAGGCACAAAGAGGTTAAGGAATTTGCCGAAGACCACACAGCTAGTAGGTTGAAGCATCTGTGAGCTGCATCTATGACCAGGCATTCCAGCTTAAGGCCCATGTTCTTACTGTCTGTATTTTTTAGGACTAAGACTTTATTCATATCTGTTGGTGGAGAATATGAGGGAGAAATAAAAGAACTGGACCCTCTTTTGCTAATGCAACTAGAATAAGTTCTGTTCCCTTTTTTTTTTTTTATTTTAA	TGGCAGGTACGGATCTAAACAGCGACTTTTTTCAGCTATGTAATAACCTTGGAAAATTCGGTATTATATAGCCTTTACTGATACAAGGGGTGGCCTGGCTTTTGGGGTTAGGTTTAAACTTTTACTTTTTTTTGATCTCTAGGAAATGTATTTTCTAGTAGATTAATATTTTAAGTATTTTCAGATGCATCTGTTACTATCTTTTGCTTCTTCTGCAGGAATCAGAAGGTCAGGGCTGTCCTTTCTGCCGATGTGAAATTAAAGGTACTGAACCCATCGTGGTAGATCCGTTTGATCCTAGAGGGAGTGGCAGCCTGTTGAGGCAAGGAGCAGAGGGAGCTCCCTCCCCAAATTATGATGATGATGATGATGAACGAGCTGATGATACTCTCTTCATGATGAAGGAATTGGCTGGTGCCAAGGTAAGATGGCAGTTTAGGAGACTGGCAAAATCCATTGTGAGTTGTCTTCTAAAGCCGTAAAACACTTAACGATATCCAAACTACAATGATAGGTAGTATTAATAGCTAATATTTATTGAGCATTTACTATATGACAGATATTGTGTTAAGCACTTTACTTGTTTTTTACTCAATCTTTACTACAGCCCTATGAGTACATACTACTATTATCCTTATTTAACAGATGAAGAAACTGAGGCACAAAGAGGTTAAGGAATTTGCCGAAGACCACACAGCTAGTAGGTTGAAGCATCTGTGAGCTGCATCTATGACCAGGCATTCCAGCTTAAGGCCCATGTTCTTACTGTCTGTATTTTTTAGGACTAAGACTTTATTCATATCTGTTGGTGGAGAATATGAGGGAGAAATAAAAGAACTGGACCCTCTTTTGCTAATGCAACTAGAATAAGTTCTGTTCCCTTTTTTTTTTTTTATTTTAA	-	novel	NA	P-0048097-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	72	522	0	ENST00000264033.4:c.1225_1431+482del		p.X409_splice	ENST00000264033	NM_005188.3	409		8-9/16	1	2	FACETS	0.519	0.455	0.588	0.519	0.455	0.588	SUBCLONAL	1	TRUE	1	0.612783734650346	2		522	453	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628518	90628518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs989223286	NA	P-0048097-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	96	790	0	ENST00000330062.3:c.1069G>A	p.Glu357Lys	p.E357K	ENST00000330062	NM_002168.2	357	Gag/Aag	8/11	0.13101296811572	6	FACETS	0.772	0.687	0.863			1	INDETERMINATE	1	TRUE	NA	0.612783734650346	6		790	903	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424453	47424453	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048097-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	651	721	0	ENST00000404338.3:c.2521C>A	p.His841Asn	p.H841N	ENST00000404338	NM_004491.4	841	Cat/Aat	1/6	0.614652726246428	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	1	0.612783734650346	4		721	1073	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38186952	38186952	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048097-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	101	521	0	ENST00000317025.8:c.1525C>A	p.Leu509Ile	p.L509I	ENST00000317025	NM_023034.1	509	Ctt/Att	6/24	0.261490860348006	1	FACETS	0.508	0.456	0.562	0.508	0.456	0.562	INDETERMINATE	1	TRUE	0	0.612783734650346	1		521	450	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741678	17741678	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	56	593	0	ENST00000250003.3:c.349C>A	p.Arg117Ser	p.R117S	ENST00000250003	NM_002478.4	117	Cgc/Agc	1/3	0.152365681639526	0	FACETS	0.824	0.711	0.945			1	INDETERMINATE	1	FALSE	0	0.313315040299294	0		593	298	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578465	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0048150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	128	871	0	ENST00000269305.4:c.465_466del	p.Val157ProfsTer23	p.V157Pfs*23	ENST00000269305	NM_001126112.2	155	acCCgc/acgc	5/11	0.317231561048816	1	FACETS	0.968	0.888	1	1	0.99	1	CLONAL	2	FALSE	0	0.313315040299294	1		871	356	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860839	151860839	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs182795390	NA	P-0048150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	20	493	0	ENST00000262189.6:c.9823A>G	p.Met3275Val	p.M3275V	ENST00000262189	NM_170606.2	3275	Atg/Gtg	43/59	0.111062047926774	3	FACETS	0.377	0.287	0.482	0.188	0.143	0.241	INDETERMINATE	1	FALSE	1	0.313315040299294	3		493	392	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740572	145740572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751616549	NA	P-0048339-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	84	617	0	ENST00000428558.2:c.1445G>A	p.Arg482His	p.R482H	ENST00000428558	NM_004260.3	482	cGc/cAc	8/22	0.371228866701116	7	FACETS	1	0.935	1	0.272	0.24	0.307	CLONAL	1	TRUE	3	0.371228866701116	7		617	801	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937282	76937286	+	frameshift_variant	Frame_Shift_Del	DEL	ATGAT	ATGAT	-	novel	NA	P-0048339-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	139	218	0	ENST00000373344.5:c.3462_3466del	p.Ser1155Ter	p.S1155*	ENST00000373344	NM_000489.3	1154	tcATCATct/tcct	9/35	0.337078925923201	2	FACETS	0.995	0.927	1			1	CLONAL	3	TRUE	NA	0.371228866701116	2		218	251	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0049058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	104	812	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.355717097027444	4	FACETS	1	0.937	1	0.354	0.317	0.394	CLONAL	1	TRUE	1	0.358603227561611	4		812	741	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443892	52443892	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0049058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	149	629	0	ENST00000460680.1:c.3G>A	p.Met1?	p.M1?	ENST00000460680	NM_004656.3	1	atG/atA	1/17	0.358603227561611	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.358603227561611	1		629	609	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279522	123279522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370877537	NA	P-0049058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	175	442	2	ENST00000358487.5:c.910G>A	p.Asp304Asn	p.D304N	ENST00000358487	NM_000141.4	304	Gac/Aac	7/18	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.358603227561611	2		444	684	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076736	72076736	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs769521243	NA	P-0049058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	64	371	0	ENST00000357731.5:c.761C>G	p.Ala254Gly	p.A254G	ENST00000357731	NM_173808.2	254	gCc/gGc	5/7	1	2	FACETS	0.725	0.629	0.829	0.725	0.629	0.829	SUBCLONAL	1	TRUE	1	0.358603227561611	2		371	492	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798355	42798355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	189	541	2	ENST00000575354.2:c.4226C>T	p.Ser1409Leu	p.S1409L	ENST00000575354	NM_015125.3	1409	tCg/tTg	18/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.358603227561611	2		543	870	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592163	67592164	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTAG	novel	NA	P-0049082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	21	194	0	ENST00000274335.5:c.1984_1985+3dup		p.S660fs	ENST00000274335		660	tct/tcTGTAGt	14/15	1	2	FACETS	0.741	0.571	0.938	0.741	0.571	0.938	CLONAL	1	TRUE	1	0.21	2		194	270	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163434	47163435	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0049082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	30	283	0	ENST00000409792.3:c.2691_2692del	p.Leu898GlufsTer17	p.L898Efs*17	ENST00000409792	NM_014159.6	897	ctCTtg/cttg	3/21	1	2	FACETS	0.907	0.732	1	0.907	0.732	1	CLONAL	1	TRUE	1	0.21	2		283	315	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597509	52597519	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTGAAAAAAG	TCTGAAAAAAG	-	novel	NA	P-0049082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	25	249	0	ENST00000394830.3:c.3801-10_3801del		p.X1267_splice	ENST00000394830	NM_018313.4	1267		25/30	1	2	FACETS	1	0.808	1	1	0.808	1	CLONAL	1	TRUE	1	0.21	2		249	233	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53254035	53254035	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	82	304	0	ENST00000375401.3:c.37G>T	p.Glu13Ter	p.E13*	ENST00000375401	NM_004187.3	13	Gag/Tag	1/26	0.0521708045575959	2	FACETS	1	0.936	1			1	INDETERMINATE	2	TRUE	NA	0.21	2		304	362	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0049440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	18	812	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.345	0.259	0.448	0.345	0.259	0.448	SUBCLONAL	1	TRUE	1	0.19	2		812	549	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0049440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	136	869	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.19	2		869	1225	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55334132	55334132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	44	453	0	ENST00000284073.2:c.29C>T	p.Ser10Leu	p.S10L	ENST00000284073	NM_138962.2	10	tCg/tTg	1/14	1	2	FACETS	0.579	0.484	0.685	0.579	0.484	0.685	SUBCLONAL	1	TRUE	1	0.19	2		453	800	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	24	714	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.922	0.723	1	0.922	0.723	1	CLONAL	1	TRUE	1	0.15	2		715	347	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0049440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	36	812	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.160250380140519	3	FACETS	0.992	0.815	1	0.496	0.407	0.596	CLONAL	1	TRUE	1	0.15	3		812	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0049440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	76	869	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.3	3	FACETS	1	0.951	1			1	CLONAL	1	TRUE	NA	0.15	3		869	924	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217918	2217918	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0049440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	65	986	1	ENST00000398665.3:c.2691+1G>A		p.X897_splice	ENST00000398665	NM_032482.2	897			1	2	FACETS	0.911	0.788	1	0.911	0.788	1	CLONAL	1	TRUE	1	0.15	2		987	951	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426379	49426379	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	123	1091	0	ENST00000301067.7:c.12109del	p.Ala4037ProfsTer13	p.A4037Pfs*13	ENST00000301067	NM_003482.3	4037	Gcc/cc	39/54	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.15	2		1091	1124	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942491	17942491	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	50	1058	0	ENST00000458235.1:c.2797A>C	p.Ile933Leu	p.I933L	ENST00000458235	NM_000215.3	933	Atc/Ctc	20/24	1	2	FACETS	0.7	0.592	0.82	0.7	0.592	0.82	SUBCLONAL	1	TRUE	1	0.15	2		1058	952	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970901	21970901	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs45476696	NA	P-0049942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	445	690	0	ENST00000304494.5:c.457G>T	p.Asp153Tyr	p.D153Y	ENST00000304494	NM_000077.4	153	Gac/Tac	2/3	0.240953810854191	3	FACETS	0.818	0.784	0.853	0.818	0.784	0.853	INDETERMINATE	2	TRUE	1	0.749816428210475	3		690	997	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0049942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	668	624	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.712102917495643	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.749816428210475	2		624	889	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584327	39584327	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	67	175	0	ENST00000262039.4:c.992C>G	p.Thr331Arg	p.T331R	ENST00000262039	NM_002647.2	331	aCa/aGa	10/25	0.725832031944293	3	FACETS	0.987	0.868	1	0.329	0.289	0.371	CLONAL	1	TRUE	0	0.749816428210475	3		175	249	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	490	477	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.223859573344204	4	FACETS	1	0.988	1	1	0.996	1	CLONAL	5	FALSE	0	0.223859573344204	4		477	1008	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841505	156841505	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145222195	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	297	793	0	ENST00000524377.1:c.808G>A	p.Asp270Asn	p.D270N	ENST00000524377	NM_002529.3	270	Gat/Aat	7/17	0.223859573344204	5	FACETS	0.879	0.829	0.931	1	0.988	1	CLONAL	4	FALSE	2	0.223859573344204	5		793	1008	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578193	28578193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs968020606	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	82	488	0	ENST00000241453.7:c.2978C>T	p.Ser993Leu	p.S993L	ENST00000241453	NM_004119.2	993	tCg/tTg	24/24	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.223859573344204	2		488	496	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476307	88476307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772244244	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	104	633	0	ENST00000360948.2:c.1825G>A	p.Asp609Asn	p.D609N	ENST00000360948	NM_001012338.2	609	Gat/Aat	15/19	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.223859573344204	2		633	620	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781386	135781386	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203549	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	109	653	1	ENST00000298552.3:c.1579C>T	p.Gln527Ter	p.Q527*	ENST00000298552	NM_001162426.1	527	Cag/Tag	15/23	0.223859573344204	3	FACETS	1	0.983	1	0.748	0.672	0.828	CLONAL	1	FALSE	1	0.223859573344204	3		654	724	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817359	39817359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142996574	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	148	508	0	ENST00000288319.7:c.204G>A	p.Met68Ile	p.M68I	ENST00000288319	NM_182918.3	68	atG/atA	2/10	0.223859573344204	3	FACETS	0.889	0.817	0.965	1	0.985	1	CLONAL	3	FALSE	1	0.223859573344204	3		508	551	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509235	106509235	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	458	651	0	ENST00000359195.3:c.1229G>A	p.Trp410Ter	p.W410*	ENST00000359195	NM_002649.2	410	tGg/tAg	2/11	0.223859573344204	8	FACETS	1	0.971	1	1	0.971	1	CLONAL	6	FALSE	2	0.223859573344204	8		651	1120	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424958105	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	64	372	1	ENST00000334344.6:c.940C>T	p.Arg314Cys	p.R314C	ENST00000334344	NM_152641.2	314	Cgt/Tgt	8/21	0.223859573344204	3	FACETS	1	0.956	1	0.625	0.541	0.714	CLONAL	1	FALSE	1	0.223859573344204	3		373	509	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481403	140481403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913357	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	127	381	0	ENST00000288602.6:c.1405G>A	p.Gly469Arg	p.G469R	ENST00000288602	NM_004333.4	469	Gga/Aga	11/18	0.223859573344204	8	FACETS	0.959	0.871	1	0.48	0.435	0.526	CLONAL	3	FALSE	2	0.223859573344204	8		381	659	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248423	212248423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771634130	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	64	356	0	ENST00000342788.4:c.3844C>T	p.Pro1282Ser	p.P1282S	ENST00000342788	NM_005235.2	1282	Cct/Tct	28/28	0.223859573344204	3	FACETS	0.759	0.659	0.866	0.759	0.659	0.866	SUBCLONAL	2	FALSE	1	0.223859573344204	3		356	419	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972909	55972909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	102	512	0	ENST00000263923.4:c.1481G>A	p.Gly494Glu	p.G494E	ENST00000263923	NM_002253.2	494	gGa/gAa	11/30	1	2	FACETS	0.817	0.732	0.905	1	0.984	1	CLONAL	2	FALSE	1	0.223859573344204	2		512	558	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295786	212295786	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751446160	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	104	530	0	ENST00000342788.4:c.2527G>A	p.Asp843Asn	p.D843N	ENST00000342788	NM_005235.2	843	Gat/Aat	21/28	0.223859573344204	3	FACETS	0.784	0.703	0.87	0.784	0.703	0.87	SUBCLONAL	2	FALSE	1	0.223859573344204	3		530	659	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048115	180048115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	253	894	0	ENST00000261937.6:c.2158G>A	p.Glu720Lys	p.E720K	ENST00000261937	NM_182925.4	720	Gaa/Aaa	14/30	0.223859573344204	5	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	FALSE	2	0.223859573344204	5		894	951	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804359	43804359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749391587	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	206	564	1	ENST00000372470.3:c.359G>A	p.Arg120Gln	p.R120Q	ENST00000372470	NM_005373.2	120	cGg/cAg	3/12	0.223859573344204	5	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	FALSE	2	0.223859573344204	5		565	724	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111995749	111995749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	227	431	0	ENST00000368678.4:c.1349G>A	p.Gly450Glu	p.G450E	ENST00000368678		450	gGa/gAa	12/13	0.223859573344204	3	FACETS	1	0.982	1	1	0.994	1	CLONAL	3	FALSE	1	0.223859573344204	3		431	667	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486824	56486824	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1023742896	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	129	545	2	ENST00000267101.3:c.1238C>T	p.Ser413Phe	p.S413F	ENST00000267101	NM_001982.3	413	tCc/tTc	11/28	0.223859573344204	3	FACETS	0.769	0.697	0.845	0.769	0.697	0.845	SUBCLONAL	2	FALSE	1	0.223859573344204	3		547	833	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086067	16086067	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	100	651	0	ENST00000281043.3:c.1243G>A	p.Glu415Lys	p.E415K	ENST00000281043	NM_005378.4	415	Gag/Aag	3/3	0.223859573344204	3	FACETS	1	0.98	1	0.73	0.653	0.813	CLONAL	1	FALSE	1	0.223859573344204	3		651	680	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576001	29576001	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	98	285	0	ENST00000356175.3:c.3975-1G>A		p.X1325_splice	ENST00000356175	NM_000267.3	1325			0.223859573344204	3	FACETS	0.912	0.821	1	1	0.979	1	CLONAL	3	FALSE	1	0.223859573344204	3		285	356	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295253	+	upstream_gene_variant	5'Flank	ONP	GAGG	GAGG	AAGA	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	168	483	0				ENST00000310581	NM_198253.2	-/1132			0.223859573344204	5	FACETS	0.884	0.817	0.953	1	0.98	1	CLONAL	4	FALSE	2	0.223859573344204	5		483	567	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576096	88576096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371590703	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	131	743	1	ENST00000360948.2:c.1577C>T	p.Pro526Leu	p.P526L	ENST00000360948	NM_001012338.2	526	cCg/cTg	13/19	1	2	FACETS	0.755	0.686	0.828	1	0.986	1	SUBCLONAL	2	FALSE	1	0.223859573344204	2		744	775	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158205	106158205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1383701111	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	52	370	0	ENST00000380013.4:c.3106C>T	p.His1036Tyr	p.H1036Y	ENST00000380013	NM_001127208.2	1036	Cac/Tac	3/11	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	FALSE	1	0.223859573344204	2		370	412	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256143	41256143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502358	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	113	472	0	ENST00000357654.3:c.437C>T	p.Ser146Phe	p.S146F	ENST00000357654	NM_007294.3	146	tCc/tTc	6/23	0.223859573344204	3	FACETS	1	0.983	1	0.735	0.661	0.812	CLONAL	1	FALSE	1	0.223859573344204	3		472	764	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431343	121431343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	146	444	0	ENST00000257555.6:c.547G>A	p.Gly183Arg	p.G183R	ENST00000257555		183	Gga/Aga	3/10	0.223859573344204	3	FACETS	1	0.939	1	1	0.989	1	CLONAL	3	FALSE	1	0.223859573344204	3		444	472	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164599	36164599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	226	747	0	ENST00000300305.3:c.1276C>T	p.Pro426Ser	p.P426S	ENST00000300305		426	Ccg/Tcg	8/8	0.223859573344204	3	FACETS	1	0.973	1	1	0.993	1	CLONAL	3	FALSE	1	0.223859573344204	3		747	697	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679365	29679366	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	97	473	0	ENST00000356175.3:c.7485_7486delinsTT	p.Arg2496Ter	p.R2496*	ENST00000356175	NM_000267.3	2495	ccCCga/ccTTga	50/57	0.223859573344204	3	FACETS	0.767	0.685	0.855	0.767	0.685	0.855	SUBCLONAL	2	FALSE	1	0.223859573344204	3		473	628	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188281	32188281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	142	972	0	ENST00000375023.3:c.1060G>A	p.Glu354Lys	p.E354K	ENST00000375023	NM_004557.3	354	Gag/Aag	6/30	0.223859573344204	3	FACETS	0.754	0.687	0.825	0.754	0.687	0.825	SUBCLONAL	2	FALSE	1	0.223859573344204	3		972	935	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873161	136873161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	138	387	0	ENST00000241393.3:c.337C>T	p.His113Tyr	p.H113Y	ENST00000241393	NM_003467.2	113	Cat/Tat	2/2	0.223859573344204	3	FACETS	1	0.927	1	1	0.988	1	CLONAL	3	FALSE	1	0.223859573344204	3		387	452	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597916	43597916	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	145	827	0	ENST00000355710.3:c.464C>T	p.Pro155Leu	p.P155L	ENST00000355710	NM_020975.4	155	cCa/cTa	3/20	0.223859573344204	3	FACETS	0.754	0.687	0.824	0.754	0.687	0.824	SUBCLONAL	2	FALSE	1	0.223859573344204	3		827	955	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769006	112769006	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	60	320	0	ENST00000369452.4:c.1285G>A	p.Val429Ile	p.V429I	ENST00000369452	NM_007373.3	429	Gtt/Att	7/9	0.223859573344204	3	FACETS	0.751	0.649	0.86	0.751	0.649	0.86	SUBCLONAL	2	FALSE	1	0.223859573344204	3		320	397	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977134	85977134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	97	316	0	ENST00000263360.6:c.736C>T	p.Leu246Phe	p.L246F	ENST00000263360	NM_003797.3	246	Ctt/Ttt	8/12	0.223859573344204	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	FALSE	1	0.223859573344204	3		316	411	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148947	119148948	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	94	472	0	ENST00000264033.4:c.1167_1168delinsAA	p.Asp390Asn	p.D390N	ENST00000264033	NM_005188.3	389	aaGGat/aaAAat	8/16	0.223859573344204	1	FACETS	0.783	0.7	0.871	1	0.982	1	SUBCLONAL	2	FALSE	0	0.223859573344204	1		472	476	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715774	18715774	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	131	291	0	ENST00000266497.5:c.3605C>G	p.Thr1202Ser	p.T1202S	ENST00000266497		1202	aCt/aGt	25/31	0.223859573344204	3	FACETS	1	0.945	1	1	0.988	1	CLONAL	3	FALSE	1	0.223859573344204	3		291	416	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245234	46245234	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	181	495	0	ENST00000334344.6:c.3328G>T	p.Gly1110Ter	p.G1110*	ENST00000334344	NM_152641.2	1110	Gga/Tga	15/21	0.223859573344204	3	FACETS	0.956	0.886	1	1	0.99	1	CLONAL	3	FALSE	1	0.223859573344204	3		495	627	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445952	49445952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	294	986	1	ENST00000301067.7:c.1514C>T	p.Pro505Leu	p.P505L	ENST00000301067	NM_003482.3	505	cCc/cTc	10/54	0.223859573344204	3	FACETS	1	0.96	1	1	0.994	1	CLONAL	3	FALSE	1	0.223859573344204	3		987	953	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576183	88576183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	102	698	1	ENST00000360948.2:c.1490G>A	p.Gly497Glu	p.G497E	ENST00000360948	NM_001012338.2	497	gGg/gAg	13/19	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.223859573344204	2		699	712	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576195	88576195	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	102	682	2	ENST00000360948.2:c.1478C>T	p.Ser493Leu	p.S493L	ENST00000360948	NM_001012338.2	493	tCa/tTa	13/19	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.223859573344204	2		684	681	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862752	9862752	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	189	621	2	ENST00000330684.3:c.2551G>A	p.Gly851Ser	p.G851S	ENST00000330684	NM_001134407.1	851	Ggc/Agc	12/13	0.223859573344204	3	FACETS	0.931	0.864	1	1	0.989	1	CLONAL	3	FALSE	1	0.223859573344204	3		623	672	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641677	23641677	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	162	459	0	ENST00000261584.4:c.1798T>G	p.Leu600Val	p.L600V	ENST00000261584	NM_024675.3	600	Tta/Gta	5/13	0.223859573344204	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	FALSE	1	0.223859573344204	3		459	666	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646443	23646443	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039479	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	223	551	1	ENST00000261584.4:c.1424C>T	p.Ser475Leu	p.S475L	ENST00000261584	NM_024675.3	475	tCa/tTa	4/13	0.223859573344204	3	FACETS	0.964	0.9	1	1	0.992	1	CLONAL	3	FALSE	1	0.223859573344204	3		552	766	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351875	89351875	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	180	803	0	ENST00000301030.4:c.1075C>T	p.Pro359Ser	p.P359S	ENST00000301030	NM_001256183.1	359	Cct/Tct	9/13	0.223859573344204	3	FACETS	0.861	0.794	0.932	0.861	0.794	0.932	CLONAL	2	FALSE	1	0.223859573344204	3		803	1038	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245881	41245881	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	83	481	0	ENST00000357654.3:c.1667A>G	p.Lys556Arg	p.K556R	ENST00000357654	NM_007294.3	556	aAa/aGa	10/23	0.223859573344204	3	FACETS	1	0.974	1	0.698	0.616	0.784	CLONAL	1	FALSE	1	0.223859573344204	3		481	591	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732896	74732897	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	125	477	1	ENST00000359995.5:c.346_347delinsAA	p.Gly116Lys	p.G116K	ENST00000359995	NM_001195427.1	116	GGa/AAa	1/3	0.223859573344204	6	FACETS	0.934	0.848	1	0.56	0.509	0.614	CLONAL	3	FALSE	1	0.223859573344204	6		478	577	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184643	7184643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1054595214	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	109	282	0	ENST00000302850.5:c.658C>T	p.Pro220Ser	p.P220S	ENST00000302850	NM_000208.2	220	Ccg/Tcg	3/22	0.103064485914215	5	FACETS	0.981	0.887	1	0.981	0.887	1	INDETERMINATE	3	FALSE	2	0.223859573344204	5		282	442	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254541	10254542	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	195	580	0	ENST00000340748.4:c.2968_2969delinsTT	p.Pro990Phe	p.P990F	ENST00000340748		990	CCc/TTc	28/40	0.103064485914215	5	FACETS	1	0.96	1	1	0.96	1	INDETERMINATE	3	FALSE	2	0.223859573344204	5		580	738	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690248	47690248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658187	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	178	403	0	ENST00000233146.2:c.1465G>A	p.Glu489Lys	p.E489K	ENST00000233146	NM_000251.2	489	Gaa/Aaa	9/16	0.223859573344204	3	FACETS	1	0.966	1	1	0.991	1	CLONAL	3	FALSE	1	0.223859573344204	3		403	551	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104616	209104616	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	186	509	0	ENST00000345146.2:c.962A>G	p.Lys321Arg	p.K321R	ENST00000345146	NM_005896.2	321	aAa/aGa	8/10	0.223859573344204	3	FACETS	0.978	0.907	1	1	0.99	1	CLONAL	3	FALSE	1	0.223859573344204	3		509	630	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483964	212483964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	64	443	1	ENST00000342788.4:c.2239C>T	p.Pro747Ser	p.P747S	ENST00000342788	NM_005235.2	747	Cct/Tct	19/28	0.223859573344204	3	FACETS	1	0.951	1	0.606	0.525	0.693	CLONAL	1	FALSE	1	0.223859573344204	3		444	525	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030004	36030004	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	257	765	0	ENST00000358208.4:c.1040-1G>A		p.X347_splice	ENST00000358208		347			0.103064485914215	5	FACETS	1	0.98	1	1	0.98	1	INDETERMINATE	3	FALSE	2	0.223859573344204	5		765	927	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743879	40743879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	185	545	0	ENST00000373198.4:c.3116C>T	p.Pro1039Leu	p.P1039L	ENST00000373198	NM_133170.3	1039	cCc/cTc	23/32	0.103064485914215	5	FACETS	0.883	0.817	0.953	0.883	0.817	0.953	INDETERMINATE	3	FALSE	2	0.223859573344204	5		545	833	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164282	47164283	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	78	313	0	ENST00000409792.3:c.1843_1844delinsTT	p.Pro615Leu	p.P615L	ENST00000409792	NM_014159.6	615	CCa/TTa	3/21	0.223859573344204	3	FACETS	0.934	0.824	1	0.934	0.824	1	CLONAL	2	FALSE	1	0.223859573344204	3		313	415	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670544	134670544	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774714501	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	259	801	1	ENST00000398015.3:c.455G>A	p.Gly152Glu	p.G152E	ENST00000398015	NM_004441.4	152	gGg/gAg	3/16	0.223859573344204	3	FACETS	1	0.962	1	1	0.994	1	CLONAL	3	FALSE	1	0.223859573344204	3		802	831	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156522	55156522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	111	616	0	ENST00000257290.5:c.2923C>T	p.Pro975Ser	p.P975S	ENST00000257290	NM_006206.4	975	Cct/Tct	22/23	1	2	FACETS	0.764	0.688	0.844	1	0.984	1	SUBCLONAL	2	FALSE	1	0.223859573344204	2		616	649	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156184	106156184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1472293244	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	71	388	0	ENST00000380013.4:c.1085C>T	p.Ala362Val	p.A362V	ENST00000380013	NM_001127208.2	362	gCt/gTt	3/11	1	2	FACETS	0.86	0.755	0.971	1	0.979	1	CLONAL	2	FALSE	1	0.223859573344204	2		388	369	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628136	187628136	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	145	651	0	ENST00000441802.2:c.2846T>A	p.Leu949Ter	p.L949*	ENST00000441802	NM_005245.3	949	tTa/tAa	2/27	1	2	FACETS	0.914	0.835	0.995	1	0.99	1	CLONAL	2	FALSE	1	0.223859573344204	2		651	709	SUCCESS
APC	324	MSKCC	GRCh37	5	112174113	112174113	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	132	328	0	ENST00000257430.4:c.2822A>G	p.Glu941Gly	p.E941G	ENST00000257430	NM_000038.5	941	gAa/gGa	16/16	0.223859573344204	5	FACETS	1	0.918	1	1	0.918	1	CLONAL	3	FALSE	2	0.223859573344204	5		328	522	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039516	180039516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	281	913	0	ENST00000261937.6:c.3527G>A	p.Arg1176Lys	p.R1176K	ENST00000261937	NM_182925.4	1176	aGg/aAg	26/30	0.223859573344204	5	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	FALSE	2	0.223859573344204	5		913	1018	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189083	32189084	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	70	620	1	ENST00000375023.3:c.470_471delinsAA	p.Arg157Gln	p.R157Q	ENST00000375023	NM_004557.3	157	cGG/cAA	4/30	0.223859573344204	3	FACETS	1	0.948	1	0.585	0.51	0.666	CLONAL	1	FALSE	1	0.223859573344204	3		621	594	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630039	117630039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	82	372	0	ENST00000368508.3:c.6487C>T	p.Pro2163Ser	p.P2163S	ENST00000368508	NM_002944.2	2163	Cca/Tca	41/43	0.223859573344204	3	FACETS	0.8	0.707	0.899	0.8	0.707	0.899	SUBCLONAL	2	FALSE	1	0.223859573344204	3		372	509	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117746771	117746771	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776963776	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	135	334	0	ENST00000368508.3:c.49C>T	p.Leu17Phe	p.L17F	ENST00000368508	NM_002944.2	17	Ctt/Ttt	1/43	0.223859573344204	3	FACETS	0.957	0.876	1	1	0.986	1	CLONAL	3	FALSE	1	0.223859573344204	3		334	467	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6439790	6439791	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	156	375	1	ENST00000356142.4:c.316_317delinsTT	p.Pro106Phe	p.P106F	ENST00000356142	NM_018890.3	106	CCt/TTt	5/7	0.223859573344204	5	FACETS	0.965	0.887	1	1	0.988	1	CLONAL	3	FALSE	3	0.223859573344204	5		376	643	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346607	81346607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	138	361	0	ENST00000222390.5:c.1346G>A	p.Gly449Glu	p.G449E	ENST00000222390	NM_000601.4	449	gGa/gAa	11/18	0.223859573344204	5	FACETS	0.998	0.913	1	1	0.987	1	CLONAL	3	FALSE	3	0.223859573344204	5		361	550	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339461	116339461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	151	380	1	ENST00000397752.3:c.323C>T	p.Ser108Leu	p.S108L	ENST00000397752	NM_000245.2	108	tCa/tTa	2/21	0.223859573344204	8	FACETS	1	0.971	1	0.566	0.519	0.615	CLONAL	3	FALSE	2	0.223859573344204	8		381	664	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206601	27206601	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	152	413	0	ENST00000380036.4:c.2386T>A	p.Phe796Ile	p.F796I	ENST00000380036	NM_000459.3	796	Ttc/Atc	15/23	0.223859573344204	3	FACETS	1	0.941	1	1	0.989	1	CLONAL	3	FALSE	1	0.223859573344204	3		413	491	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229688	98229688	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	79	225	0	ENST00000331920.6:c.2270T>G	p.Phe757Cys	p.F757C	ENST00000331920	NM_000264.3	757	tTt/tGt	15/24	0.223859573344204	3	FACETS	0.911	0.811	1	1	0.975	1	CLONAL	3	FALSE	1	0.223859573344204	3		225	287	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782165	135782166	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0050267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	143	477	0	ENST00000298552.3:c.1390_1391delinsAA	p.Gly464Asn	p.G464N	ENST00000298552	NM_001162426.1	464	GGt/AAt	14/23	0.223859573344204	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	FALSE	1	0.223859573344204	3		477	598	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0050314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	278	393	1	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.66651305126831	2	FACETS	0.998	0.957	1	0.998	0.957	1	CLONAL	2	TRUE	0	0.679178010318523	2		394	410	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0050314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	77	302	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	0.4829874863593	3	FACETS	0.734	0.647	0.826	0.367	0.323	0.413	SUBCLONAL	1	TRUE	1	0.679178010318523	3		302	414	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194670	29194670	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772256235	NA	P-0050314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	46	711	0	ENST00000240100.2:c.1058G>A	p.Arg353Gln	p.R353Q	ENST00000240100	NM_001394.6	353	cGg/cAg	4/4	0.679178010318523	1	FACETS	0.216	0.181	0.253	0.216	0.181	0.253	SUBCLONAL	1	TRUE	0	0.679178010318523	1		711	415	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245259	46245259	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	294	499	0	ENST00000334344.6:c.3353A>G	p.Gln1118Arg	p.Q1118R	ENST00000334344	NM_152641.2	1118	cAg/cGg	15/21	0.633416260131868	4	FACETS	0.914	0.864	0.965	0.914	0.864	0.965	CLONAL	2	TRUE	2	0.679178010318523	4		499	795	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431030	49431030	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	397	669	0	ENST00000301067.7:c.10109A>T	p.Gln3370Leu	p.Q3370L	ENST00000301067	NM_003482.3	3370	cAg/cTg	34/54	0.633416260131868	4	FACETS	0.959	0.915	1	0.959	0.915	1	CLONAL	2	TRUE	2	0.679178010318523	4		669	1023	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577588	7577602	+	inframe_deletion	In_Frame_Del	DEL	GGTGGTACAGTCAGA	GGTGGTACAGTCAGA	-	novel	NA	P-0050314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	426	534	0	ENST00000269305.4:c.679_693del	p.Ser227_Thr231del	p.S227_T231del	ENST00000269305	NM_001126112.2	227	TCTGACTGTACCACC/-	7/11	0.643086007754456	3	FACETS	0.941	0.912	0.97	0.941	0.912	0.97	CLONAL	3	TRUE	0	0.679178010318523	3		534	595	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965500	18966522	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTCGACCTCCTTTGACAGGTACGTCTTCTCCCATCACTGCCCCCTGTTCCCTGGTTGCCACCTGTGGCATCTTTATGAGCCCTCCCCGTCACTGTGGAGTGGGGTTCCCCACCCAGCTCTGCAAACTCAGGATGTCGGAGAGGCGGCCACAGCTGTGCGTGTCGCCAACCCCAAACCCTCCTCACAGGATGCAGAGCGCATTGAAAACGTTTGCCGTGGATGAGACCTCGGTGTCTGGCTACATCTACCACAAGCTGTTGGGCCACGAGGTGGAGGACGTAATCATCAAGTGCCAGCTGCCCAAGCGCTTCACGGCGCAGGGCCTCCCCGACCTCAACCACTCCCAGGTGCGCGCCGTCCTCAGCGCGCGGGGCCTCGCCCATGGGCCGGGACGCAAGCGGAGGCTGCCCCTAACGGCCGCTTGTATTGAAGGTTTATGCCGTGAAGACTGTGCTGCAAAGACCACTGAGCCTGATCCAGGGCCCGCCAGGCACGGGGAAGACGGTGACGTCGGCCACCATCGTCTACCACCTGGCCCGGCAAGGCAACGGGTAGGGCTGACACGGCCCTTGCGGGCAAGACCCGGGAGGGCTTTAGGGTGGCCAGATGGAAGGCCTGGTGCTGGGAGCCTTGGGCTCTGTCACACCGAAGAGAGCACGTGGCGGGTAGTGTCGCCATGGTGCCTACCGCTCTCTATGTGACATTATTCGTGTCAGCTCCAACCTTAGGATTGCATTTTAGTAACCAGGTCTGCTACTGGTTTAGAAAACTGGGGGCAGGGGGGGCATGGCTGCAGCAGCGTGAGTTCCGTGTGCGGCACTTTATAGTGTGGCGGGATGGTGCAAGTTCCAGCCTTGGCATTGCTTGCGGTGGGTAGAGCTGTGAAGCCTGGGCTGTCTGGATCTGAGCTCCTTCGGCATCGTGTCATTACTGCCTGTTAAAAATGTCAGGAGTTTAAGGCCAGCCTGAACAGGGTGAGACGTCTCTACAAAAAAAAAATTCAGAAATTAGCTGGGGGTAGT	AGTCGACCTCCTTTGACAGGTACGTCTTCTCCCATCACTGCCCCCTGTTCCCTGGTTGCCACCTGTGGCATCTTTATGAGCCCTCCCCGTCACTGTGGAGTGGGGTTCCCCACCCAGCTCTGCAAACTCAGGATGTCGGAGAGGCGGCCACAGCTGTGCGTGTCGCCAACCCCAAACCCTCCTCACAGGATGCAGAGCGCATTGAAAACGTTTGCCGTGGATGAGACCTCGGTGTCTGGCTACATCTACCACAAGCTGTTGGGCCACGAGGTGGAGGACGTAATCATCAAGTGCCAGCTGCCCAAGCGCTTCACGGCGCAGGGCCTCCCCGACCTCAACCACTCCCAGGTGCGCGCCGTCCTCAGCGCGCGGGGCCTCGCCCATGGGCCGGGACGCAAGCGGAGGCTGCCCCTAACGGCCGCTTGTATTGAAGGTTTATGCCGTGAAGACTGTGCTGCAAAGACCACTGAGCCTGATCCAGGGCCCGCCAGGCACGGGGAAGACGGTGACGTCGGCCACCATCGTCTACCACCTGGCCCGGCAAGGCAACGGGTAGGGCTGACACGGCCCTTGCGGGCAAGACCCGGGAGGGCTTTAGGGTGGCCAGATGGAAGGCCTGGTGCTGGGAGCCTTGGGCTCTGTCACACCGAAGAGAGCACGTGGCGGGTAGTGTCGCCATGGTGCCTACCGCTCTCTATGTGACATTATTCGTGTCAGCTCCAACCTTAGGATTGCATTTTAGTAACCAGGTCTGCTACTGGTTTAGAAAACTGGGGGCAGGGGGGGCATGGCTGCAGCAGCGTGAGTTCCGTGTGCGGCACTTTATAGTGTGGCGGGATGGTGCAAGTTCCAGCCTTGGCATTGCTTGCGGTGGGTAGAGCTGTGAAGCCTGGGCTGTCTGGATCTGAGCTCCTTCGGCATCGTGTCATTACTGCCTGTTAAAAATGTCAGGAGTTTAAGGCCAGCCTGAACAGGGTGAGACGTCTCTACAAAAAAAAAATTCAGAAATTAGCTGGGGGTAGT	-	novel	NA	P-0050314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	812	610	0	ENST00000262803.5:c.1247_1545-212del		p.X416_splice	ENST00000262803	NM_002911.3	416		9-11/24	0.679178010318523	10	FACETS	1	0.985	1			1	CLONAL	6	TRUE	NA	0.679178010318523	10		610	1452	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185041	32185055	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCCTGGTGGGGCGG	ATCCTGGTGGGGCGG	-	novel	NA	P-0050314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	297	532	0	ENST00000375023.3:c.1625-12_1627del		p.X542_splice	ENST00000375023	NM_004557.3	542		10/30	0.330397347639857	5	FACETS	1	0.992	1	0.828	0.784	0.872	INDETERMINATE	2	TRUE	2	0.679178010318523	5		532	711	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411504	63411504	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	454	668	0	ENST00000330258.3:c.1663G>T	p.Glu555Ter	p.E555*	ENST00000330258	NM_152424.3	555	Gag/Tag	2/2	0.55767309144411	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.679178010318523	4		668	1066	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610578	10610579	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	A	novel	NA	P-0050314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	407	760	0	ENST00000171111.5:c.131_132delinsT	p.Pro44LeufsTer24	p.P44Lfs*24	ENST00000171111	NM_203500.1	44	cCC/cT	2/6	0.677023756412834	2	FACETS	0.992	0.958	1	0.992	0.958	1	CLONAL	2	TRUE	0	0.679178010318523	2		760	604	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936096	178936096	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519940	NA	P-0050357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	17	437	0	ENST00000263967.3:c.1638G>T	p.Gln546His	p.Q546H	ENST00000263967	NM_006218.2	546	caG/caT	10/21	0.159398696709393	2	FACETS	0.316	0.235	0.413	0.158	0.117	0.207	SUBCLONAL	1	TRUE	0	0.253199195311807	2		437	425	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	53	714	1				ENST00000310581	NM_198253.2	-/1132			0.179790212246328	3	FACETS	0.875	0.746	1	0.292	0.248	0.339	CLONAL	1	TRUE	0	0.253199195311807	3		715	539	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539951	187539951	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs777631605	NA	P-0050357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	39	477	1	ENST00000441802.2:c.7789C>T	p.Arg2597Ter	p.R2597*	ENST00000441802	NM_005245.3	2597	Cga/Tga	10/27	0.185614101139836	2	FACETS	0.425	0.351	0.509	0.213	0.175	0.255	SUBCLONAL	1	TRUE	0	0.253199195311807	2		478	724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0050676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	174	635	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.261168321099472	3	FACETS	0.865	0.803	0.927	0.865	0.803	0.927	CLONAL	3	TRUE	0	0.328143625371044	3		635	476	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199803	108199812	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAAATGAA	GAAAAATGAA	-	novel	NA	P-0050676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	12	271	0	ENST00000278616.4:c.7146_7155del	p.Lys2383HisfsTer5	p.K2383Hfs*5	ENST00000278616	NM_000051.3	2382	gGAAAAATGAAg/gg	49/63	0.256455834040422	2	FACETS	0.804	0.572	1	0.402	0.286	0.541	CLONAL	1	TRUE	0	0.328143625371044	2		271	91	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0050707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	89	322	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.540899018165406	3	FACETS	1	0.98	1	0.723	0.649	0.8	CLONAL	1	TRUE	1	0.540899018165406	3		322	289	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586506	189586506	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs376910274	NA	P-0050707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	64	343	1	ENST00000264731.3:c.1129+1G>A		p.X377_splice	ENST00000264731	NM_003722.4	377			0.540899018165406	3	FACETS	0.999	0.872	1	0.499	0.436	0.567	CLONAL	1	TRUE	1	0.540899018165406	3		344	301	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0050707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	165	691	0	ENST00000269305.4:c.375+1G>C		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.517775272666973	2	FACETS	0.864	0.806	0.923	0.864	0.806	0.923	CLONAL	2	TRUE	0	0.540899018165406	2		691	353	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874622	35874622	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	24	518	0	ENST00000303115.3:c.778G>T	p.Ala260Ser	p.A260S	ENST00000303115	NM_002185.3	260	Gcc/Tcc	6/8	0.540899018165406	5	FACETS	0.379	0.297	0.475	0.126	0.099	0.159	SUBCLONAL	1	TRUE	2	0.540899018165406	5		518	424	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0050707-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	63	322	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.213455893132205	3	FACETS	1	0.958	1	0.635	0.551	0.726	CLONAL	1	TRUE	1	0.244693802428951	3		322	455	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586506	189586506	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs376910274	NA	P-0050707-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	51	343	1	ENST00000264731.3:c.1129+1G>A		p.X377_splice	ENST00000264731	NM_003722.4	377			0.213455893132205	3	FACETS	1	0.892	1	0.529	0.45	0.615	CLONAL	1	TRUE	1	0.244693802428951	3		344	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0050707-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	191	691	0	ENST00000269305.4:c.375+1G>C		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.239309684298434	2	FACETS	0.978	0.906	1	0.978	0.906	1	CLONAL	2	TRUE	0	0.244693802428951	2		691	798	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874622	35874622	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050707-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	46	518	0	ENST00000303115.3:c.778G>T	p.Ala260Ser	p.A260S	ENST00000303115	NM_002185.3	260	Gcc/Tcc	6/8	NA	2	FACETS	0.662	0.557	0.778			1	INDETERMINATE	1	TRUE	NA	0.244693802428951	2		518	568	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561756	55561756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376469897	NA	P-0050707-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	50	393	0	ENST00000288135.5:c.146G>A	p.Arg49His	p.R49H	ENST00000288135	NM_000222.2	49	cGc/cAc	2/21	0.244693802428951	5	FACETS	0.779	0.66	0.911	0.195	0.165	0.228	CLONAL	1	TRUE	1	0.244693802428951	5		393	717	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101154	41101154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200302453	NA	P-0050707-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	152	958	0	ENST00000373198.4:c.1202G>A	p.Arg401Gln	p.R401Q	ENST00000373198	NM_133170.3	401	cGg/cAg	8/32	0.213455893132205	3	FACETS	1	0.987	1	0.732	0.669	0.798	CLONAL	1	TRUE	1	0.244693802428951	3		958	953	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500511	99500511	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050707-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	67	1075	0	ENST00000268035.6:c.3944C>A	p.Pro1315Gln	p.P1315Q	ENST00000268035	NM_000875.3	1315	cCa/cAa	21/21	1	2	FACETS	0.538	0.466	0.616	0.538	0.466	0.616	SUBCLONAL	1	TRUE	1	0.244693802428951	2		1075	1018	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260599	10260599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050707-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	49	677	0	ENST00000340748.4:c.2263G>A	p.Glu755Lys	p.E755K	ENST00000340748		755	Gaa/Aaa	24/40	1	2	FACETS	0.585	0.494	0.685	0.585	0.494	0.685	SUBCLONAL	1	TRUE	1	0.244693802428951	2		677	685	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799511	72799511	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050707-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	58	774	0	ENST00000325599.8:c.1658C>G	p.Ser553Cys	p.S553C	ENST00000325599	NM_018130.2	553	tCt/tGt	11/11	1	2	FACETS	0.593	0.508	0.685	0.593	0.508	0.685	SUBCLONAL	1	TRUE	1	0.244693802428951	2		774	800	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0051739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	112	509	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.926	0.842	1	0.926	0.842	1	CLONAL	1	TRUE	1	0.701534230086121	2		510	345	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685307	89685307	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123317	NA	P-0051739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	131	196	0	ENST00000371953.3:c.202T>C	p.Tyr68His	p.Y68H	ENST00000371953	NM_000314.4	68	Tac/Cac	3/9	0.701534230086121	1	FACETS	0.925	0.858	0.993	0.925	0.858	0.993	CLONAL	1	TRUE	0	0.701534230086121	1		196	262	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411266	63411266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778813513	NA	P-0051739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	230	754	1	ENST00000330258.3:c.1901G>A	p.Arg634His	p.R634H	ENST00000330258	NM_152424.3	634	cGt/cAt	2/2	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.701534230086121	2		755	606	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135777022	135777022	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	202	552	0	ENST00000298552.3:c.2456A>C	p.Asn819Thr	p.N819T	ENST00000298552	NM_001162426.1	819	aAc/aCc	19/23	1	2	FACETS	0.908	0.846	0.972	0.908	0.846	0.972	CLONAL	1	TRUE	1	0.701534230086121	2		552	634	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0051856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	17	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		485	667	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913343	NA	P-0051856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	22	837	0	ENST00000269305.4:c.817C>A	p.Arg273Ser	p.R273S	ENST00000269305	NM_001126112.2	273	Cgt/Agt	8/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		837	977	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0051856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	77	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.158126164453409	2	FACETS	1	0.975	1	0.739	0.65	0.833	CLONAL	1	TRUE	0	0.206872273573815	2		485	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913343	NA	P-0051856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	102	837	0	ENST00000269305.4:c.817C>A	p.Arg273Ser	p.R273S	ENST00000269305	NM_001126112.2	273	Cgt/Agt	8/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.206872273573815	2		837	755	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746101	162746101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374058699	NA	P-0051856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	26	503	0	ENST00000367921.3:c.2224C>T	p.Arg742Trp	p.R742W	ENST00000367921	NM_006182.2	742	Cgg/Tgg	16/18	0.116522524418563	3	FACETS	0.568	0.449	0.706	0.284	0.224	0.353	INDETERMINATE	1	TRUE	1	0.206872273573815	3		503	488	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444337	49444337	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	140	906	0	ENST00000301067.7:c.3034G>T	p.Ala1012Ser	p.A1012S	ENST00000301067	NM_003482.3	1012	Gct/Tct	11/54	0.158126164453409	2	FACETS	0.913	0.833	0.997	0.913	0.833	0.997	CLONAL	2	TRUE	0	0.206872273573815	2		906	741	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597381	10597381	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	101	866	1	ENST00000171111.5:c.1822G>T	p.Val608Phe	p.V608F	ENST00000171111	NM_203500.1	608	Gtc/Ttc	6/6	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.206872273573815	2		867	822	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961079	55961079	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	86	833	0	ENST00000263923.4:c.2861C>A	p.Ala954Glu	p.A954E	ENST00000263923	NM_002253.2	954	gCa/gAa	21/30	1	2	FACETS	0.998	0.882	1	0.998	0.882	1	CLONAL	1	TRUE	1	0.206872273573815	2		833	833	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971182	21971182	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	61	523	0	ENST00000304494.5:c.176del	p.Val59GlyfsTer87	p.V59Gfs*87	ENST00000304494	NM_000077.4	59	gTg/gg	2/3	0.206872273573815	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.206872273573815	1		523	459	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356365	70356365	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	40	377	0	ENST00000374080.3:c.5260C>G	p.Pro1754Ala	p.P1754A	ENST00000374080		1754	Cct/Gct	37/45	0.139804427884341	2	FACETS	0.869	0.722	1			1	CLONAL	1	TRUE	NA	0.206872273573815	2		377	445	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383357	42383357	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs782709381	NA	P-0052139-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	56	561	0	ENST00000221972.3:c.377G>A	p.Arg126His	p.R126H	ENST00000221972	NM_021601.3	126	cGc/cAc	2/5	0.141575551891851	3	FACETS	0.568	0.485	0.659	0.189	0.161	0.22	INDETERMINATE	1	TRUE	0	0.275685830861811	3		561	814	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951168	48951168	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052139-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	136	337	13	ENST00000267163.4:c.1330C>T	p.Gln444Ter	p.Q444*	ENST00000267163	NM_000321.2	444	Cag/Tag	13/27	0.275685830861811	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.275685830861811	3		350	480	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934255	48934255	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052139-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	227	433	0	ENST00000267163.4:c.711del	p.Glu237AspfsTer27	p.E237Dfs*27	ENST00000267163	NM_000321.2	237	gAa/ga	7/27	0.275685830861811	3	FACETS	0.922	0.868	0.976	1	0.994	1	CLONAL	4	TRUE	1	0.275685830861811	3		433	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0052195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	481	599	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.717947053054232	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.717947053054232	1		599	815	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063715	67063715	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	155	211	0	ENST00000412916.2:c.164T>C	p.Ile55Thr	p.I55T	ENST00000412916		55	aTc/aCc	2/6	0.717947053054232	1	FACETS	0.992	0.929	1	0.992	0.929	1	CLONAL	1	TRUE	0	0.717947053054232	1		211	279	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271278	18271286	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGGCCTCA	CAGGCCTCA	-	novel	NA	P-0052195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	414	678	0	ENST00000222254.8:c.323-1_330del		p.X108_splice	ENST00000222254	NM_005027.3	108		3/16	1	2	FACETS	0.839	0.799	0.881	0.839	0.799	0.881	CLONAL	1	TRUE	1	0.717947053054232	2		678	1374	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522650	67522651	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0052195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	207	335	0	ENST00000274335.5:c.149dup	p.Glu51Ter	p.E51*	ENST00000274335		49	-/C	1/15	0.717947053054232	1	FACETS	0.88	0.828	0.932	0.88	0.828	0.932	CLONAL	1	TRUE	0	0.717947053054232	1		335	420	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0052330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	62	367	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.361606841844513	3	FACETS	0.714	0.617	0.82	0.357	0.308	0.41	SUBCLONAL	1	TRUE	1	0.361606841844513	3		367	567	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989642	68989642	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767992923	NA	P-0052330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	35	448	0	ENST00000288368.4:c.1580G>A	p.Arg527His	p.R527H	ENST00000288368	NM_024870.2	527	cGc/cAc	15/40	0.229830364614102	0	FACETS	0.302	0.247	0.363			1	SUBCLONAL	1	TRUE	0	0.361606841844513	0		448	409	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709048	117709048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	54	494	1	ENST00000368508.3:c.1909C>T	p.Pro637Ser	p.P637S	ENST00000368508	NM_002944.2	637	Cct/Tct	13/43	NA	2	FACETS	0.736	0.63	0.85			1	INDETERMINATE	1	TRUE	NA	0.361606841844513	2		495	406	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123156511	123156511	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	49	132	0	ENST00000218089.9:c.34A>T	p.Asn12Tyr	p.N12Y	ENST00000218089	NM_001042749.1	12	Aat/Tat	3/35	0.327928456313156	2	FACETS	1	0.929	1			1	CLONAL	1	TRUE	NA	0.361606841844513	2		132	236	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249092	55249092	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052366-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	68	660	0	ENST00000275493.2:c.2390G>C	p.Cys797Ser	p.C797S	ENST00000275493	NM_005228.3	797	tGc/tCc	20/28	0.631089344756392	7	FACETS	0.992	0.902	1	0.709	0.644	0.771	CLONAL	5	TRUE	0	0.631089344756392	7		660	112	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0052366-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	0	74	483	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	0.631089344756392	7	FACETS	1	0.99	1	1	0.99	1	CLONAL	8	TRUE	0	0.631089344756392	7		483	74	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790072	40790072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753667	NA	P-0052366-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	12	660	1	ENST00000373198.4:c.2659G>A	p.Ala887Thr	p.A887T	ENST00000373198	NM_133170.3	887	Gcc/Acc	18/32	0.635167040389706	1	FACETS	0.685	0.503	0.886	0.685	0.503	0.886	SUBCLONAL	1	TRUE	0	0.631089344756392	1		661	38	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855982	76855982	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	64	610	0	ENST00000373344.5:c.5618T>C	p.Phe1873Ser	p.F1873S	ENST00000373344	NM_000489.3	1873	tTc/tCc	23/35	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.425214944008845	2		610	208	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610009	43610032	+	protein_altering_variant	In_Frame_Del	DEL	CCTTCTGCATCCACTGCTACCACA	CCTTCTGCATCCACTGCTACCACA	TGC	novel	NA	P-0052498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	48	831	2	ENST00000355710.3:c.1961_1984delinsTGC	p.Ala654_Lys662delinsValGln	p.A654_K662delinsVQ	ENST00000355710	NM_020975.4	654	gCCTTCTGCATCCACTGCTACCACAag/gTGCag	11/20	NA	2	FACETS	1	0.865	1			1	INDETERMINATE	1	TRUE	NA	0.425214944008845	2		833	223	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	28	331	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.874	0.699	1	0.874	0.699	1	CLONAL	1	TRUE	1	0.174589344316231	2		331	367	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0052616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	66	588	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.174589344316231	1	FACETS	0.994	0.862	1	0.994	0.862	1	CLONAL	1	TRUE	0	0.174589344316231	1		588	694	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0052616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	24	219	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.174589344316231	1	FACETS	0.815	0.639	1	0.815	0.639	1	CLONAL	1	TRUE	0	0.174589344316231	1		219	308	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0052616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	66	565	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.174589344316231	2		568	678	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177584	56177584	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368201444	NA	P-0052616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	27	410	2	ENST00000399503.3:c.2557C>T	p.Arg853Cys	p.R853C	ENST00000399503	NM_005921.1	853	Cgt/Tgt	14/20	0.156595541132615	3	FACETS	0.749	0.595	0.925	0.374	0.297	0.463	CLONAL	1	TRUE	1	0.174589344316231	3		412	449	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333863	70333863	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs750883311	NA	P-0052616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	23	359	0	ENST00000373644.4:c.1768C>T	p.Arg590Ter	p.R590*	ENST00000373644	NM_030625.2	590	Cga/Tga	2/12	1	2	FACETS	0.621	0.484	0.781	0.621	0.484	0.781	SUBCLONAL	1	TRUE	1	0.174589344316231	2		359	424	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675571	86675571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1561325048	NA	P-0052616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	30	313	0	ENST00000274376.6:c.2513del	p.Asn838MetfsTer4	p.N838Mfs*4	ENST00000274376	NM_002890.2	836	gAa/ga	19/25	0.174589344316231	1	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	0	0.174589344316231	1		313	295	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491274	2491274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368302066	NA	P-0052616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	57	649	0	ENST00000355716.4:c.317G>A	p.Arg106His	p.R106H	ENST00000355716	NM_003820.2	106	cGc/cAc	4/8	1	2	FACETS	0.948	0.812	1	0.948	0.812	1	CLONAL	1	TRUE	1	0.174589344316231	2		649	689	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585423	29585423	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	95	603	0	ENST00000356175.3:c.4172G>T	p.Arg1391Ile	p.R1391I	ENST00000356175	NM_000267.3	1391	aGa/aTa	31/57	1	2	FACETS	0.766	0.682	0.856	1	0.981	1	SUBCLONAL	2	TRUE	1	0.174589344316231	2		603	710	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279324	38279324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774768179	NA	P-0052616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	56	652	0	ENST00000425967.3:c.1165G>A	p.Val389Ile	p.V389I	ENST00000425967	NM_001174067.1	389	Gtt/Att	9/19	1	2	FACETS	0.819	0.7	0.95	0.819	0.7	0.95	CLONAL	1	TRUE	1	0.174589344316231	2		652	783	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094347	27094347	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	61	457	0	ENST00000324856.7:c.3055G>C	p.Glu1019Gln	p.E1019Q	ENST00000324856	NM_006015.4	1019	Gag/Cag	11/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.174589344316231	2		457	561	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281837	39281837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374761537	NA	P-0052616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	32	522	0	ENST00000402219.2:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000402219	NM_005633.3	213	cGa/cAa	5/23	1	2	FACETS	0.639	0.517	0.777	0.639	0.517	0.777	SUBCLONAL	1	TRUE	1	0.174589344316231	2		522	574	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499486	89499486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373736475	NA	P-0052616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	36	424	0	ENST00000336596.2:c.2656G>A	p.Gly886Ser	p.G886S	ENST00000336596	NM_005233.5	886	Ggc/Agc	15/17	0.174589344316231	1	FACETS	0.892	0.734	1	0.892	0.734	1	CLONAL	1	TRUE	0	0.174589344316231	1		424	422	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846107	151846107	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	49	457	0	ENST00000262189.6:c.12905del	p.Pro4302LeufsTer24	p.P4302Lfs*24	ENST00000262189	NM_170606.2	4302	cCt/ct	52/59	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.174589344316231	2		457	554	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418998	116418998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369838973	NA	P-0052616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	30	229	1	ENST00000397752.3:c.3509G>A	p.Arg1170Gln	p.R1170Q	ENST00000397752	NM_000245.2	1170	cGa/cAa	17/21	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.174589344316231	2		230	256	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533390	29533390	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0052616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	16	223	0	ENST00000356175.3:c.1392+1G>T		p.X464_splice	ENST00000356175	NM_000267.3	464			1	2	FACETS	0.666	0.492	0.875	0.666	0.492	0.875	SUBCLONAL	1	TRUE	1	0.174589344316231	2		223	275	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790170	40790170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373191879	NA	P-0052616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	54	428	0	ENST00000373198.4:c.2561G>A	p.Arg854His	p.R854H	ENST00000373198	NM_133170.3	854	cGc/cAc	18/32	0.153427809795495	2	FACETS	1	0.919	1	0.557	0.476	0.646	CLONAL	1	TRUE	0	0.174589344316231	2		428	555	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012477	29012477	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	28	321	0	ENST00000282397.4:c.394G>T	p.Gly132Cys	p.G132C	ENST00000282397	NM_002019.4	132	Ggt/Tgt	4/30	1	2	FACETS	0.775	0.619	0.953	0.775	0.619	0.953	CLONAL	1	TRUE	1	0.174589344316231	2		321	414	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841460	156841460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	54	569	0	ENST00000524377.1:c.763A>C	p.Thr255Pro	p.T255P	ENST00000524377	NM_002529.3	255	Acc/Ccc	7/17	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.174589344316231	2		569	595	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137219	64137219	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	38	541	0	ENST00000334205.4:c.1651G>T	p.Asp551Tyr	p.D551Y	ENST00000334205	NM_003942.2	551	Gac/Tac	14/17	1	2	FACETS	0.724	0.598	0.866	0.724	0.598	0.866	SUBCLONAL	1	TRUE	1	0.174589344316231	2		541	601	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942229	71942229	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	30	506	0	ENST00000298229.2:c.1493G>T	p.Arg498Leu	p.R498L	ENST00000298229	NM_001567.3	498	cGc/cTc	12/28	1	2	FACETS	0.605	0.486	0.741	0.605	0.486	0.741	SUBCLONAL	1	TRUE	1	0.174589344316231	2		506	568	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687442	37687442	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	42	383	0	ENST00000447079.4:c.4346G>T	p.Gly1449Val	p.G1449V	ENST00000447079	NM_015083.1	1449	gGg/gTg	14/14	1	2	FACETS	0.996	0.832	1	0.996	0.832	1	CLONAL	1	TRUE	1	0.174589344316231	2		383	483	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510737	38510737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	31	383	1	ENST00000254066.5:c.991G>A	p.Ala331Thr	p.A331T	ENST00000254066	NM_000964.3	331	Gcc/Acc	7/9	1	2	FACETS	0.774	0.625	0.942	0.774	0.625	0.942	CLONAL	1	TRUE	1	0.174589344316231	2		384	459	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885829	59885829	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	27	364	0	ENST00000259008.2:c.917del	p.Asn306ThrfsTer32	p.N306Tfs*32	ENST00000259008	NM_032043.2	306	aAc/ac	7/20	1	2	FACETS	0.686	0.545	0.847	0.686	0.545	0.847	SUBCLONAL	1	TRUE	1	0.174589344316231	2		364	451	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207133	1207133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	74	662	2	ENST00000326873.7:c.221G>A	p.Arg74Lys	p.R74K	ENST00000326873	NM_000455.4	74	aGg/aAg	1/10	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.174589344316231	2		664	840	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288379	15288379	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	58	544	0	ENST00000263388.2:c.4360G>C	p.Asp1454His	p.D1454H	ENST00000263388	NM_000435.2	1454	Gac/Cac	24/33	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.174589344316231	2		544	648	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37061827	37061827	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs63750993	NA	P-0052616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	60	477	0	ENST00000231790.2:c.911A>T	p.Asp304Val	p.D304V	ENST00000231790	NM_000249.3	304	gAt/gTt	11/19	0.174589344316231	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.174589344316231	1		477	526	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55124978	55124978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	74	532	0	ENST00000257290.5:c.43C>T	p.Leu15Phe	p.L15F	ENST00000257290	NM_006206.4	15	Ctc/Ttc	2/23	0.174589344316231	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.174589344316231	1		532	594	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294508	1294508	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	48	381	0	ENST00000310581.5:c.493A>T	p.Ser165Cys	p.S165C	ENST00000310581	NM_198253.2	165	Agc/Tgc	2/16	0.156595541132615	3	FACETS	1	0.933	1	0.599	0.506	0.701	CLONAL	1	TRUE	1	0.174589344316231	3		381	499	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177474	56177474	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	30	382	0	ENST00000399503.3:c.2448del	p.Arg817GlufsTer5	p.R817Efs*5	ENST00000399503	NM_005921.1	816	tCc/tc	14/20	0.156595541132615	3	FACETS	0.867	0.698	1	0.433	0.349	0.53	CLONAL	1	TRUE	1	0.174589344316231	3		382	431	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177476	56177476	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0052616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	30	375	0	ENST00000399503.3:c.2449A>T	p.Arg817Ter	p.R817*	ENST00000399503	NM_005921.1	817	Aga/Tga	14/20	0.156595541132615	3	FACETS	0.869	0.7	1	0.434	0.35	0.531	CLONAL	1	TRUE	1	0.174589344316231	3		375	430	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170333	32170333	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	63	728	0	ENST00000375023.3:c.3275G>T	p.Gly1092Val	p.G1092V	ENST00000375023	NM_004557.3	1092	gGc/gTc	21/30	1	2	FACETS	0.922	0.796	1	0.922	0.796	1	CLONAL	1	TRUE	1	0.174589344316231	2		728	783	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38153392	38153392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	55	552	0	ENST00000317025.8:c.2837G>A	p.Cys946Tyr	p.C946Y	ENST00000317025	NM_023034.1	946	tGc/tAc	16/24	1	2	FACETS	0.955	0.816	1	0.955	0.816	1	CLONAL	1	TRUE	1	0.174589344316231	2		552	660	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0052616-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	51	355	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.804	0.682	0.938	0.804	0.682	0.938	CLONAL	1	TRUE	1	0.19	2		355	668	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218425	36218425	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555730957	NA	P-0052616-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	119	589	1	ENST00000222270.7:c.4204C>T	p.Arg1402Ter	p.R1402*	ENST00000222270	NM_014727.1	1402	Cga/Tga	16/37	1	2	FACETS	0.922	0.834	1	1	0.988	1	CLONAL	2	TRUE	1	0.19	2		590	679	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842432	68842432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052616-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	43	569	0	ENST00000261769.5:c.493G>A	p.Glu165Lys	p.E165K	ENST00000261769	NM_004360.3	165	Gaa/Aaa	4/16	1	2	FACETS	0.58	0.484	0.688	0.58	0.484	0.688	SUBCLONAL	1	TRUE	1	0.19	2		569	780	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0052625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1191	388	421	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.299561191722457	8	FACETS	1	0.978	1			1	CLONAL	3	TRUE	NA	0.29	8		421	1579	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0052625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	365	645	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.299720130840971	3	FACETS	0.889	0.844	0.934	0.889	0.844	0.934	CLONAL	3	TRUE	0	0.29	3		645	1081	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356353	66356353	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	130	310	0	ENST00000273854.3:c.1144G>T	p.Asp382Tyr	p.D382Y	ENST00000273854	NM_004439.5	382	Gac/Tac	5/18	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.419602115778482	2		310	539	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052954-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	47	714	1				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		715	148	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	186	863	7	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.385789962266414	2		870	748	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	130	471	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.385789962266414	2		471	608	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	344	565	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	1	0.385789962266414	2		568	752	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	168	730	1	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.385789962266414	2		731	741	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	66	363	1	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	0.632	0.549	0.722	0.632	0.549	0.722	SUBCLONAL	1	TRUE	1	0.385789962266414	2		364	541	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850705	63850705	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs201178069	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	47	423	0	ENST00000279873.7:c.1489del	p.Ile497Ter	p.I497*	ENST00000279873	NM_032199.2	495	Aaa/aa	10/10	1	2	FACETS	0.561	0.474	0.657	0.561	0.474	0.657	SUBCLONAL	1	TRUE	1	0.385789962266414	2		423	434	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685308	89685308	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876660634	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	57	222	0	ENST00000371953.3:c.203A>G	p.Tyr68Cys	p.Y68C	ENST00000371953	NM_000314.4	68	tAc/tGc	3/9	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.385789962266414	2		222	268	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	84	240	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.385789962266414	2		241	377	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943788	71943788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771815535	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	94	690	0	ENST00000298229.2:c.1831C>T	p.Arg611Cys	p.R611C	ENST00000298229	NM_001567.3	611	Cgc/Tgc	15/28	1	2	FACETS	0.627	0.558	0.701	0.627	0.558	0.701	SUBCLONAL	1	TRUE	1	0.385789962266414	2		690	777	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948755	71948755	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1565399032	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	166	946	6	ENST00000298229.2:c.3470del	p.Gly1157AspfsTer45	p.G1157Dfs*45	ENST00000298229	NM_001567.3	1156	cGg/cg	26/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.385789962266414	2		952	752	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219180	94219180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772423554	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	109	436	1	ENST00000323929.3:c.224G>A	p.Cys75Tyr	p.C75Y	ENST00000323929	NM_005591.3	75	tGc/tAc	4/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.385789962266414	2		437	463	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426672	49426672	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	63	497	0	ENST00000301067.7:c.11816A>T	p.Gln3939Leu	p.Q3939L	ENST00000301067	NM_003482.3	3939	cAg/cTg	39/54	1	2	FACETS	0.577	0.499	0.662	0.577	0.499	0.662	SUBCLONAL	1	TRUE	1	0.385789962266414	2		497	566	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447072	49447072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	140	505	0	ENST00000301067.7:c.872G>A	p.Cys291Tyr	p.C291Y	ENST00000301067	NM_003482.3	291	tGt/tAt	7/54	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.385789962266414	2		505	629	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	189	936	5	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.385789962266414	2		941	827	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519117	103519117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770975661	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	134	512	0	ENST00000355739.4:c.2455C>T	p.Arg819Trp	p.R819W	ENST00000355739	NM_000123.3	819	Cgg/Tgg	11/15	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.385789962266414	2		512	649	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021441	42021442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	116	489	3	ENST00000219905.7:c.3744dup	p.Glu1249ArgfsTer25	p.E1249Rfs*25	ENST00000219905	NM_001164273.1	1246	cga/cgAa	11/24	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.385789962266414	2		492	503	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472480	88472480	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	175	622	0	ENST00000360948.2:c.2075T>C	p.Leu692Pro	p.L692P	ENST00000360948	NM_001012338.2	692	cTa/cCa	16/19	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.385789962266414	2		622	649	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954698	17954698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs992942163	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	75	780	0	ENST00000458235.1:c.196G>A	p.Val66Met	p.V66M	ENST00000458235	NM_000215.3	66	Gtg/Atg	3/24	1	2	FACETS	0.516	0.452	0.586	0.516	0.452	0.586	SUBCLONAL	1	TRUE	1	0.385789962266414	2		780	753	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220868	36220868	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	48	250	0	ENST00000222270.7:c.4918C>A	p.Arg1640Ser	p.R1640S	ENST00000222270	NM_014727.1	1640	Cgc/Agc	23/37	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.385789962266414	2		250	208	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222925	36222925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746346674	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	192	896	1	ENST00000222270.7:c.5554G>A	p.Ala1852Thr	p.A1852T	ENST00000222270	NM_014727.1	1852	Gcc/Acc	27/37	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.385789962266414	2		897	840	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796882	42796883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761345552	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	174	909	1	ENST00000575354.2:c.3347dup	p.Ser1117LysfsTer34	p.S1117Kfs*34	ENST00000575354	NM_015125.3	1114	gcc/gCcc	14/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.385789962266414	2		910	858	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	164	897	3	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.385789962266414	2		900	744	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39725891	39725891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	92	357	0	ENST00000361337.2:c.762G>T	p.Glu254Asp	p.E254D	ENST00000361337	NM_003286.2	254	gaG/gaT	10/21	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.385789962266414	2		357	450	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292829	62292829	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1170676373	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	73	384	0	ENST00000360203.5:c.281C>T	p.Ala94Val	p.A94V	ENST00000360203	NM_001283009.1	94	gCt/gTt	3/35	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.385789962266414	2		384	307	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	133	336	3	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.385789962266414	2		339	497	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447429	12447429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573789959	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	75	621	0	ENST00000287820.6:c.668C>T	p.Ala223Val	p.A223V	ENST00000287820	NM_015869.4	223	gCg/gTg	5/7	0.385789962266414	2	FACETS	0.584	0.511	0.662	0.292	0.255	0.331	SUBCLONAL	1	TRUE	0	0.385789962266414	2		621	666	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165213	47165213	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	82	286	0	ENST00000409792.3:c.913del	p.Thr305GlnfsTer35	p.T305Qfs*35	ENST00000409792	NM_014159.6	305	Aca/ca	3/21	0.385789962266414	2	FACETS	1	0.961	1	0.595	0.529	0.666	CLONAL	1	TRUE	0	0.385789962266414	2		286	357	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247391	71247391	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	139	572	0	ENST00000318789.4:c.142G>A	p.Ala48Thr	p.A48T	ENST00000318789	NM_032682.5	48	Gca/Aca	6/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.385789962266414	2		572	642	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	145	409	1	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.385789962266414	2		410	573	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099427	157099432	+	inframe_deletion	In_Frame_Del	DEL	CAGCAG	CAGCAG	-	rs587779744	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	58	343	0	ENST00000346085.5:c.381_386del	p.Gln130_Gln131del	p.Q130_Q131del	ENST00000346085	NM_020732.3	122	CAGCAG/-	1/20	1	2	FACETS	0.828	0.715	0.951	0.828	0.715	0.951	CLONAL	1	TRUE	1	0.385789962266414	2		343	363	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391781	139391781	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	170	815	0	ENST00000277541.6:c.6410C>A	p.Pro2137His	p.P2137H	ENST00000277541	NM_017617.3	2137	cCc/cAc	34/34	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.385789962266414	2		815	734	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156719	20156719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	96	408	0	ENST00000379607.5:c.38G>A	p.Arg13His	p.R13H	ENST00000379607	NM_001412.3	13	cGc/cAc	2/7	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.385789962266414	2		408	428	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422384	47422384	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	111	478	3	ENST00000377045.4:c.23del	p.Pro8LeufsTer26	p.P8Lfs*26	ENST00000377045	NM_001654.4	6	ggC/gg	2/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.385789962266414	2		481	511	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354606	70354606	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	148	580	0	ENST00000374080.3:c.4771A>G	p.Asn1591Asp	p.N1591D	ENST00000374080		1591	Aat/Gat	35/45	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.385789962266414	2		580	660	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733513	85733513	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs387906350	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	94	465	1	ENST00000370580.1:c.499del	p.Ser167LeufsTer6	p.S167Lfs*6	ENST00000370580	NM_003921.4	167	Tct/ct	3/3	1	2	FACETS	0.934	0.836	1	0.934	0.836	1	CLONAL	1	TRUE	1	0.479415817211653	2		466	420	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793363	242793363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	111	640	0	ENST00000334409.5:c.714del	p.Val239CysfsTer39	p.V239Cfs*39	ENST00000334409	NM_005018.2	238	ccC/cc	5/5	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.479415817211653	2		640	441	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	203	339	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.472819928633928	2	FACETS	0.954	0.895	1	0.954	0.895	1	CLONAL	2	TRUE	0	0.479415817211653	2		342	444	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	44	509	1				ENST00000310581	NM_198253.2	-/1132			0.239992145080941	3	FACETS	0.764	0.653	0.881	0.509	0.435	0.587	INDETERMINATE	2	TRUE	0	0.479415817211653	3		510	149	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	127	570	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.479415817211653	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.479415817211653	1		570	349	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241895	133241895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483635586	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	103	634	0	ENST00000320574.5:c.2461C>T	p.Arg821Cys	p.R821C	ENST00000320574	NM_006231.2	821	Cgc/Tgc	21/49	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.479415817211653	2		634	406	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	141	358	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.479415817211653	1	FACETS	0.813	0.756	0.87	1	0.991	1	CLONAL	2	TRUE	0	0.479415817211653	1		358	275	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134252	11134252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	15	622	1	ENST00000358026.2:c.2918G>A	p.Arg973Gln	p.R973Q	ENST00000358026	NM_001128849.1	973	cGg/cAg	20/36	1	2	FACETS	0.127	0.092	0.169	0.127	0.092	0.169	SUBCLONAL	1	TRUE	1	0.479415817211653	2		623	493	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	120	560	2	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.479415817211653	2		562	458	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413214	139413214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	164	798	1	ENST00000277541.6:c.928G>A	p.Gly310Arg	p.G310R	ENST00000277541	NM_017617.3	310	Ggg/Agg	6/34	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.479415817211653	2		799	618	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291032	11291032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	117	433	0	ENST00000361445.4:c.2729G>A	p.Arg910Gln	p.R910Q	ENST00000361445	NM_004958.3	910	cGg/cAg	18/58	0.365443602485221	1	FACETS	0.959	0.873	1	0.959	0.873	1	CLONAL	1	TRUE	0	0.479415817211653	1		433	387	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	218	476	9	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	0.472819928633928	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.479415817211653	2		485	412	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	103	577	6	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	0.479415817211653	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.479415817211653	1		583	288	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259493	89259493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1293200426	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	97	444	0	ENST00000336596.2:c.637C>T	p.Pro213Ser	p.P213S	ENST00000336596	NM_005233.5	213	Cca/Tca	3/17	0.479415817211653	1	FACETS	0.908	0.817	1	0.908	0.817	1	CLONAL	1	TRUE	0	0.479415817211653	1		444	339	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217234	11217234	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1031980569	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	131	601	2	ENST00000361445.4:c.4444C>T	p.Arg1482Cys	p.R1482C	ENST00000361445	NM_004958.3	1482	Cgc/Tgc	30/58	0.365443602485221	1	FACETS	0.804	0.733	0.877	0.804	0.733	0.877	CLONAL	1	TRUE	0	0.479415817211653	1		603	517	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001438	29001438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1473309404	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	72	320	0	ENST00000282397.4:c.1294G>A	p.Glu432Lys	p.E432K	ENST00000282397	NM_002019.4	432	Gaa/Aaa	10/30	1	2	FACETS	0.803	0.706	0.907	0.803	0.706	0.907	CLONAL	1	TRUE	1	0.479415817211653	2		320	374	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610098	28610098	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	92	484	0	ENST00000241453.7:c.1392G>A	p.Trp464Ter	p.W464*	ENST00000241453	NM_004119.2	464	tgG/tgA	11/24	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.479415817211653	2		484	373	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533535	533535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	205	757	0	ENST00000451590.1:c.368G>A	p.Arg123His	p.R123H	ENST00000451590	NM_001130442.1	123	cGc/cAc	4/5	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.479415817211653	2		757	634	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271796	15271796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	126	803	0	ENST00000263388.2:c.6643C>T	p.Pro2215Ser	p.P2215S	ENST00000263388	NM_000435.2	2215	Cca/Tca	33/33	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.479415817211653	2		803	441	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120115	70120115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	23	95	0	ENST00000245479.2:c.1121del	p.Pro374ArgfsTer9	p.P374Rfs*9	ENST00000245479	NM_000346.3	373	Ccc/cc	3/3	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.479415817211653	2		95	71	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2957001	2957001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	103	578	1	ENST00000396946.4:c.2626G>A	p.Glu876Lys	p.E876K	ENST00000396946	NM_032415.4	876	Gaa/Aaa	20/25	0.365443602485221	1	FACETS	0.651	0.585	0.72	0.651	0.585	0.72	SUBCLONAL	1	TRUE	0	0.479415817211653	1		579	502	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060964	38060964	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35391958	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	74	255	0	ENST00000250448.2:c.1025C>T	p.Ala342Val	p.A342V	ENST00000250448	NM_004496.3	342	gCg/gTg	2/2	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.479415817211653	2		255	253	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849152	156849152	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs768180688	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	107	603	1	ENST00000524377.1:c.2044C>T	p.Arg682Cys	p.R682C	ENST00000524377	NM_002529.3	682	Cgt/Tgt	15/17	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.479415817211653	2		604	394	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450397	50450397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	151	504	0	ENST00000331340.3:c.581C>T	p.Thr194Met	p.T194M	ENST00000331340	NM_006060.4	194	aCg/aTg	5/8	0.479415817211653	3	FACETS	0.986	0.912	1	0.986	0.912	1	CLONAL	2	TRUE	1	0.479415817211653	3		504	396	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407962	139407962	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	130	682	0	ENST00000277541.6:c.2235G>A	p.Trp745Ter	p.W745*	ENST00000277541	NM_017617.3	745	tgG/tgA	14/34	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.479415817211653	2		682	460	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40739786	40739786	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1017033490	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	130	809	1	ENST00000392038.2:c.1439G>A	p.Arg480His	p.R480H	ENST00000392038	NM_001626.4	480	cGc/cAc	14/14	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.479415817211653	2		810	468	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384651	31384651	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	98	656	0	ENST00000328111.2:c.1359del	p.Leu454SerfsTer136	p.L454Sfs*136	ENST00000328111	NM_006892.3	451	gaG/ga	13/23	0.154853392850612	0	FACETS	0.553	0.497	0.611			1	INDETERMINATE	1	TRUE	0	0.479415817211653	0		656	385	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245060	46245060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	117	475	2	ENST00000334344.6:c.3154C>T	p.Pro1052Ser	p.P1052S	ENST00000334344	NM_152641.2	1052	Cct/Tct	15/21	1	2	FACETS	0.944	0.855	1	0.944	0.855	1	CLONAL	1	TRUE	1	0.479415817211653	2		477	517	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491682	120491683	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	95	363	0	ENST00000256646.2:c.2546_2547del	p.Lys849ArgfsTer6	p.K849Rfs*6	ENST00000256646	NM_024408.3	849	aAA/a	16/34	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.479415817211653	2		363	366	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954022	32954023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs397507419	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	71	437	11	ENST00000380152.3:c.9097dup	p.Thr3033AsnfsTer11	p.T3033Nfs*11	ENST00000380152		3030	aca/acAa	23/27	1	2	FACETS	0.854	0.75	0.964	0.854	0.75	0.964	CLONAL	1	TRUE	1	0.479415817211653	2		448	347	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082313	16082314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs780080562	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	90	713	5	ENST00000281043.3:c.134dup	p.Glu47GlyfsTer8	p.E47Gfs*8	ENST00000281043	NM_005378.4	43	acc/aCcc	2/3	1	2	FACETS	0.941	0.84	1	0.941	0.84	1	CLONAL	1	TRUE	1	0.479415817211653	2		718	399	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681120	117681120	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs748436511	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	66	429	0	ENST00000368508.3:c.3500del	p.Leu1167Ter	p.L1167*	ENST00000368508	NM_002944.2	1167	tTa/ta	23/43	1	2	FACETS	0.858	0.75	0.972	0.858	0.75	0.972	CLONAL	1	TRUE	1	0.479415817211653	2		429	321	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526976	31526976	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1485879154	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	227	624	0	ENST00000344624.3:c.64C>T	p.Arg22Ter	p.R22*	ENST00000344624		22	Cga/Tga	2/33	0.239992145080941	3	FACETS	0.993	0.932	1	0.662	0.621	0.704	INDETERMINATE	2	TRUE	0	0.479415817211653	3		624	591	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs753143066	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	85	542	2	ENST00000295797.4:c.826dup	p.Thr276AsnfsTer16	p.T276Nfs*16	ENST00000295797	NM_002740.5	273	tta/ttAa	9/18	1	2	FACETS	0.823	0.731	0.92	0.823	0.731	0.92	CLONAL	1	TRUE	1	0.479415817211653	2		544	431	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981315	68981315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866864487	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	72	283	0	ENST00000288368.4:c.1387C>T	p.Arg463Cys	p.R463C	ENST00000288368	NM_024870.2	463	Cgc/Tgc	12/40	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.479415817211653	2		283	291	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	rs267608078	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	45	519	0	ENST00000234420.5:c.3260_3261dup	p.Phe1088ProfsTer3	p.F1088Pfs*3	ENST00000234420	NM_000179.2	1085	acc/aCCcc	5/10	1	2	FACETS	0.432	0.363	0.507	0.432	0.363	0.507	SUBCLONAL	1	TRUE	1	0.479415817211653	2		519	435	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233240	69233240	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	56	336	0	ENST00000462284.1:c.1111del	p.Thr371LeufsTer2	p.T371Lfs*2	ENST00000462284	NM_002392.5	369	Aaa/aa	11/11	1	2	FACETS	0.934	0.809	1	0.934	0.809	1	CLONAL	1	TRUE	1	0.479415817211653	2		336	250	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435199	49435199	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	88	648	0	ENST00000301067.7:c.6354del	p.Ala2119LeufsTer25	p.A2119Lfs*25	ENST00000301067	NM_003482.3	2118	ccC/cc	31/54	0.27769843642817	4	FACETS	1	0.977	1	0.702	0.626	0.782	INDETERMINATE	1	TRUE	2	0.479415817211653	4		648	387	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	222	489	17	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	0.396510702254122	3	FACETS	0.905	0.855	0.954	1	0.992	1	CLONAL	3	TRUE	1	0.479415817211653	3		506	423	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912670	32912670	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398122776	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	80	442	0	ENST00000380152.3:c.4178C>T	p.Ala1393Val	p.A1393V	ENST00000380152		1393	gCg/gTg	11/27	1	2	FACETS	0.86	0.762	0.964	0.86	0.762	0.964	CLONAL	1	TRUE	1	0.479415817211653	2		442	388	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020726	37020726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs999324823	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	121	513	0	ENST00000358127.4:c.119G>A	p.Arg40Lys	p.R40K	ENST00000358127	NM_001280556.1	40	aGg/aAg	2/10	0.479415817211653	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.479415817211653	1		513	318	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781170	135781170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761959210	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	104	657	0	ENST00000298552.3:c.1795G>A	p.Gly599Arg	p.G599R	ENST00000298552	NM_001162426.1	599	Ggg/Agg	15/23	1	2	FACETS	0.971	0.874	1	0.971	0.874	1	CLONAL	1	TRUE	1	0.479415817211653	2		657	447	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607598	43607598	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752830820	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	104	929	2	ENST00000355710.3:c.1574G>A	p.Arg525Gln	p.R525Q	ENST00000355710	NM_020975.4	525	cGg/cAg	8/20	1	2	FACETS	0.947	0.853	1	0.947	0.853	1	CLONAL	1	TRUE	1	0.479415817211653	2		931	458	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686956	37686956	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750674097	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	104	438	0	ENST00000447079.4:c.3860C>T	p.Ser1287Phe	p.S1287F	ENST00000447079	NM_015083.1	1287	tCc/tTc	14/14	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.479415817211653	2		438	405	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189848	66189848	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	84	443	0	ENST00000273854.3:c.3098G>A	p.Gly1033Glu	p.G1033E	ENST00000273854	NM_004439.5	1033	gGa/gAa	18/18	0.129019266809325	0	FACETS	0.467	0.414	0.522			1	INDETERMINATE	1	TRUE	0	0.479415817211653	0		443	391	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729635	162729635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	122	543	1	ENST00000367921.3:c.721G>A	p.Asp241Asn	p.D241N	ENST00000367921	NM_006182.2	241	Gat/Aat	8/18	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.479415817211653	2		544	481	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729744	162729744	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750450749	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	125	563	1	ENST00000367921.3:c.830G>A	p.Arg277His	p.R277H	ENST00000367921	NM_006182.2	277	cGc/cAc	8/18	1	2	FACETS	0.988	0.898	1	0.988	0.898	1	CLONAL	1	TRUE	1	0.479415817211653	2		564	528	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298125	15298125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751284168	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	132	784	1	ENST00000263388.2:c.1631G>A	p.Arg544His	p.R544H	ENST00000263388	NM_000435.2	544	cGc/cAc	11/33	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.479415817211653	2		785	456	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428229	49428229	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs902898516	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	175	733	0	ENST00000301067.7:c.10471C>T	p.Arg3491Cys	p.R3491C	ENST00000301067	NM_003482.3	3491	Cgt/Tgt	37/54	0.27769843642817	4	FACETS	0.906	0.839	0.975	0.906	0.839	0.975	INDETERMINATE	2	TRUE	2	0.479415817211653	4		733	596	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149894	99149894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368448330	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	116	545	0	ENST00000074304.5:c.206C>T	p.Ala69Val	p.A69V	ENST00000074304	NM_001134224.1	69	gCg/gTg	5/26	1	2	FACETS	0.994	0.9	1	0.994	0.9	1	CLONAL	1	TRUE	1	0.479415817211653	2		545	487	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169988254	169988254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	40	378	2	ENST00000295797.4:c.496C>T	p.Arg166Cys	p.R166C	ENST00000295797	NM_002740.5	166	Cgc/Tgc	6/18	1	2	FACETS	0.461	0.384	0.547	0.461	0.384	0.547	SUBCLONAL	1	TRUE	1	0.479415817211653	2		380	362	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257943	19257943	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762715467	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	133	857	1	ENST00000162023.5:c.443C>T	p.Pro148Leu	p.P148L	ENST00000162023		148	cCg/cTg	9/13	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.479415817211653	2		858	437	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361190	66361190	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	90	397	0	ENST00000273854.3:c.982A>G	p.Thr328Ala	p.T328A	ENST00000273854	NM_004439.5	328	Acc/Gcc	4/18	0.129019266809325	0	FACETS	0.497	0.444	0.553			1	INDETERMINATE	1	TRUE	0	0.479415817211653	0		397	393	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370706	55370706	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	83	268	0	ENST00000297316.4:c.8G>T	p.Ser3Ile	p.S3I	ENST00000297316	NM_022454.3	3	aGc/aTc	1/2	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.479415817211653	2		268	256	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818237	43818237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1390710915	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	162	626	0	ENST00000372470.3:c.1702C>T	p.Leu568Phe	p.L568F	ENST00000372470	NM_005373.2	568	Ctt/Ttt	12/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.479415817211653	2		626	575	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778767	9778767	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	123	605	0	ENST00000377346.4:c.1036G>T	p.Gly346Trp	p.G346W	ENST00000377346	NM_005026.3	346	Ggg/Tgg	9/24	0.365443602485221	1	FACETS	0.873	0.795	0.954	0.873	0.795	0.954	CLONAL	1	TRUE	0	0.479415817211653	1		605	447	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937860	36937860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	106	880	0	ENST00000361632.4:c.976G>A	p.Glu326Lys	p.E326K	ENST00000361632		326	Gag/Aag	7/16	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.479415817211653	2		880	430	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512289	120512289	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	123	647	0	ENST00000256646.2:c.953G>C	p.Arg318Pro	p.R318P	ENST00000256646	NM_024408.3	318	cGc/cCc	6/34	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.479415817211653	2		647	504	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981141	201981141	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	177	726	1	ENST00000359651.3:c.220G>A	p.Asp74Asn	p.D74N	ENST00000359651		74	Gac/Aac	2/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.479415817211653	2		727	615	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652314	206652314	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	164	820	0	ENST00000367120.3:c.1021A>T	p.Lys341Ter	p.K341*	ENST00000367120	NM_014002.3	341	Aag/Tag	10/22	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.479415817211653	2		820	600	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850867	63850867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	139	425	0	ENST00000279873.7:c.1645C>T	p.Pro549Ser	p.P549S	ENST00000279873	NM_032199.2	549	Cca/Tca	10/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.479415817211653	2		425	462	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948335	71948335	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	119	821	0	ENST00000298229.2:c.3047A>T	p.Lys1016Ile	p.K1016I	ENST00000298229	NM_001567.3	1016	aAa/aTa	26/28	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.479415817211653	2		821	479	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948755	71948755	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs773081790	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	135	818	0	ENST00000298229.2:c.3467G>C	p.Arg1156Pro	p.R1156P	ENST00000298229	NM_001567.3	1156	cGg/cCg	26/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.479415817211653	2		818	453	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857553	57857553	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	95	583	0	ENST00000228682.2:c.79G>C	p.Ala27Pro	p.A27P	ENST00000228682	NM_005269.2	27	Gcc/Ccc	2/12	0.27769843642817	4	FACETS	1	0.977	1	0.675	0.605	0.75	INDETERMINATE	1	TRUE	2	0.479415817211653	4		583	434	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120789198	120789199	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	79	511	0	ENST00000257552.2:c.738_739delinsTT	p.Arg247Cys	p.R247C	ENST00000257552	NM_002442.3	246	ttCCgt/ttTTgt	11/15	1	2	FACETS	0.936	0.83	1	0.936	0.83	1	CLONAL	1	TRUE	1	0.479415817211653	2		511	352	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028397	42028397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	63	308	1	ENST00000219905.7:c.3935C>T	p.Ser1312Phe	p.S1312F	ENST00000219905	NM_001164273.1	1312	tCc/tTc	13/24	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.479415817211653	2		309	225	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823794	3823847	+	inframe_deletion	In_Frame_Del	DEL	ACTCATCGCCCCGCTGGATGACGGGAACTGGTTCTGTGGCAGAAACTGGCTCTG	ACTCATCGCCCCGCTGGATGACGGGAACTGGTTCTGTGGCAGAAACTGGCTCTG	-	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	261	671	0	ENST00000262367.5:c.2368_2421del	p.Gln790_Ser807del	p.Q790_S807del	ENST00000262367	NM_004380.2	790	CAGAGCCAGTTTCTGCCACAGAACCAGTTCCCGTCATCCAGCGGGGCGATGAGT/-	13/31	0.479415817211653	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.479415817211653	3		671	614	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821188	72821188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	118	583	0	ENST00000268489.5:c.10987G>A	p.Glu3663Lys	p.E3663K	ENST00000268489	NM_006885.3	3663	Gag/Aag	10/10	0.479415817211653	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.479415817211653	1		583	369	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827447	72827447	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	111	611	1	ENST00000268489.5:c.9134C>A	p.Ser3045Tyr	p.S3045Y	ENST00000268489	NM_006885.3	3045	tCc/tAc	9/10	0.479415817211653	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.479415817211653	1		612	350	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827738	72827738	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	101	572	0	ENST00000268489.5:c.8843G>A	p.Arg2948His	p.R2948H	ENST00000268489	NM_006885.3	2948	cGt/cAt	9/10	0.479415817211653	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.479415817211653	1		572	311	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980021	7980021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	148	702	0	ENST00000319144.4:c.1316G>A	p.Ser439Asn	p.S439N	ENST00000319144	NM_001139.2	439	aGc/aAc	10/15	0.479415817211653	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.479415817211653	1		702	375	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41219690	41219690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	94	419	0	ENST00000357654.3:c.5009G>A	p.Arg1670Lys	p.R1670K	ENST00000357654	NM_007294.3	1670	aGa/aAa	16/23	1	2	FACETS	0.954	0.854	1	0.954	0.854	1	CLONAL	1	TRUE	1	0.479415817211653	2		419	411	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554043	63554043	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	73	529	1	ENST00000307078.5:c.696G>T	p.Glu232Asp	p.E232D	ENST00000307078	NM_004655.3	232	gaG/gaT	2/11	1	2	FACETS	0.814	0.716	0.919	0.814	0.716	0.919	CLONAL	1	TRUE	1	0.479415817211653	2		530	374	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45423105	45423105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1341462958	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	65	291	1	ENST00000262160.6:c.23C>T	p.Thr8Met	p.T8M	ENST00000262160	NM_005901.5	8	aCg/aTg	2/11	1	2	FACETS	0.907	0.793	1	0.907	0.793	1	CLONAL	1	TRUE	1	0.479415817211653	2		292	299	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726598	41726599	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	126	672	1	ENST00000301178.4:c.143_144delinsAA	p.Arg48Gln	p.R48Q	ENST00000301178	NM_021913.4	48	cGG/cAA	2/20	1	2	FACETS	0.964	0.877	1	0.964	0.877	1	CLONAL	1	TRUE	1	0.479415817211653	2		673	545	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965158	25965158	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	94	602	0	ENST00000435504.4:c.4048G>A	p.Val1350Ile	p.V1350I	ENST00000435504		1350	Gta/Ata	13/13	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.479415817211653	2		602	377	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288542	198288542	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	74	422	0	ENST00000335508.6:c.185A>C	p.Glu62Ala	p.E62A	ENST00000335508	NM_012433.2	62	gAa/gCa	2/25	1	2	FACETS	0.784	0.689	0.884	0.784	0.689	0.884	SUBCLONAL	1	TRUE	1	0.479415817211653	2		422	394	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023823	31023823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	111	632	1	ENST00000375687.4:c.3308C>T	p.Ala1103Val	p.A1103V	ENST00000375687	NM_015338.5	1103	gCc/gTc	13/13	0.154853392850612	0	FACETS	0.673	0.611	0.737			1	INDETERMINATE	1	TRUE	0	0.479415817211653	0		633	358	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038261	30038262	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	82	463	0	ENST00000338641.4:c.434_435delinsTT	p.Ala145Val	p.A145V	ENST00000338641	NM_000268.3	145	gCC/gTT	4/16	1	2	FACETS	0.879	0.78	0.984	0.879	0.78	0.984	CLONAL	1	TRUE	1	0.479415817211653	2		463	389	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070339	37070354	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGCTTGTACCCCCC	GCAGCTTGTACCCCCC	-	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	54	426	0	ENST00000231790.2:c.1475_1490del	p.Ala492GlyfsTer11	p.A492Gfs*11	ENST00000231790	NM_000249.3	492	GCAGCTTGTACCCCCCgg/gg	13/19	0.479415817211653	1	FACETS	0.651	0.561	0.748	0.651	0.561	0.748	SUBCLONAL	1	TRUE	0	0.479415817211653	1		426	263	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584587	189584587	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	154	335	0	ENST00000264731.3:c.882+1G>A		p.X294_splice	ENST00000264731	NM_003722.4	294			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.479415817211653	2		335	498	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961301	1961301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	90	566	0	ENST00000382891.5:c.3089C>T	p.Ser1030Leu	p.S1030L	ENST00000382891	NM_133335.3	1030	tCg/tTg	17/22	0.479415817211653	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.479415817211653	1		566	276	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1962817	1962817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	99	486	0	ENST00000382891.5:c.3311C>T	p.Ala1104Val	p.A1104V	ENST00000382891	NM_133335.3	1104	gCg/gTg	18/22	0.479415817211653	1	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	0	0.479415817211653	1		486	314	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514316	149514316	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	68	485	0	ENST00000261799.4:c.628C>A	p.Gln210Lys	p.Q210K	ENST00000261799	NM_002609.3	210	Cag/Aag	4/23	0.472819928633928	2	FACETS	0.792	0.693	0.898	0.396	0.346	0.449	SUBCLONAL	1	TRUE	0	0.479415817211653	2		485	358	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163495	32163495	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	129	553	0	ENST00000375023.3:c.5731C>G	p.Pro1911Ala	p.P1911A	ENST00000375023	NM_004557.3	1911	Cct/Gct	30/30	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.479415817211653	2		553	499	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017497	112017497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	76	372	0	ENST00000368678.4:c.1016C>T	p.Thr339Ile	p.T339I	ENST00000368678		339	aCc/aTc	9/13	1	2	FACETS	0.893	0.789	1	0.893	0.789	1	CLONAL	1	TRUE	1	0.479415817211653	2		372	355	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706904	117706904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	115	477	0	ENST00000368508.3:c.2246G>A	p.Gly749Glu	p.G749E	ENST00000368508	NM_002944.2	749	gGg/gAg	15/43	1	2	FACETS	0.96	0.869	1	0.96	0.869	1	CLONAL	1	TRUE	1	0.479415817211653	2		477	500	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981768	70981769	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	108	732	1	ENST00000276594.2:c.327_328delinsAA	p.Glu110Lys	p.E110K	ENST00000276594	NM_024504.3	109	agGGaa/agAAaa	2/8	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.479415817211653	2		733	384	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976725	90976725	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs764823411	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	74	366	0	ENST00000265433.3:c.907A>G	p.Arg303Gly	p.R303G	ENST00000265433	NM_002485.4	303	Aga/Gga	8/16	1	2	FACETS	0.862	0.76	0.971	0.862	0.76	0.971	CLONAL	1	TRUE	1	0.479415817211653	2		366	358	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595365	141595365	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	159	689	0	ENST00000220592.5:c.68T>G	p.Phe23Cys	p.F23C	ENST00000220592	NM_012154.3	23	tTc/tGc	2/19	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.479415817211653	2		689	651	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054672	5054672	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	67	353	0	ENST00000381652.3:c.724C>A	p.Gln242Lys	p.Q242K	ENST00000381652	NM_004972.3	242	Caa/Aaa	7/25	0.479415817211653	1	FACETS	0.833	0.733	0.939	0.833	0.733	0.939	CLONAL	1	TRUE	0	0.479415817211653	1		353	255	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44733174	44733174	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	90	191	0	ENST00000377967.4:c.166C>A	p.Leu56Ile	p.L56I	ENST00000377967	NM_021140.2	56	Ctc/Atc	2/29	1	1	FACETS	0.78	0.711	0.849	1	0.985	1	SUBCLONAL	2	TRUE	0	0.479415817211653	1		191	183	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	507	509	1				ENST00000310581	NM_198253.2	-/1132			0.64377359180629	4	FACETS	1	0.996	1	1	0.996	1	CLONAL	4	TRUE	0	0.655270445249095	4		510	592	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	303	812	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.655270445249095	5	FACETS	0.923	0.877	0.97	0.923	0.877	0.97	CLONAL	3	TRUE	2	0.655270445249095	5		812	662	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11194408	11194408	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	163	458	0	ENST00000361445.4:c.5246G>C	p.Arg1749Pro	p.R1749P	ENST00000361445	NM_004958.3	1749	cGa/cCa	37/58	0.63685796184285	3	FACETS	1	0.975	1	0.567	0.523	0.613	CLONAL	1	TRUE	1	0.655270445249095	3		458	582	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202809	16202810	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	208	386	0	ENST00000375759.3:c.517_518delinsTT	p.Pro173Phe	p.P173F	ENST00000375759	NM_015001.2	173	CCt/TTt	3/15	0.63685796184285	3	FACETS	0.943	0.886	1	0.943	0.886	1	CLONAL	2	TRUE	1	0.655270445249095	3		386	447	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097788	27097789	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	87	381	0	ENST00000324856.7:c.3377_3378delinsTT	p.Ser1126Phe	p.S1126F	ENST00000324856	NM_006015.4	1126	tCC/tTT	12/20	0.63685796184285	3	FACETS	0.75	0.667	0.839	0.375	0.333	0.42	SUBCLONAL	1	TRUE	1	0.655270445249095	3		381	470	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461177	120461177	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	164	356	0	ENST00000256646.2:c.5782-1G>A		p.X1928_splice	ENST00000256646	NM_024408.3	1928			0.63685796184285	3	FACETS	0.936	0.873	1	0.936	0.873	1	CLONAL	2	TRUE	1	0.655270445249095	3		356	355	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852437	63852437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1362687523	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	124	521	1	ENST00000279873.7:c.3215C>T	p.Pro1072Leu	p.P1072L	ENST00000279873	NM_032199.2	1072	cCc/cTc	10/10	0.63685796184285	3	FACETS	0.844	0.766	0.926	0.422	0.383	0.463	CLONAL	1	TRUE	1	0.655270445249095	3		522	595	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534320	534320	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	99	379	0	ENST00000451590.1:c.3G>A	p.Met1?	p.M1?	ENST00000451590	NM_001130442.1	1	atG/atA	2/5	0.63685796184285	3	FACETS	0.983	0.884	1	0.492	0.442	0.544	CLONAL	1	TRUE	1	0.655270445249095	3		379	408	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943774	71943775	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	324	601	0	ENST00000298229.2:c.1817_1818delinsAA	p.Gly606Glu	p.G606E	ENST00000298229	NM_001567.3	606	gGG/gAA	15/28	0.63685796184285	3	FACETS	0.93	0.885	0.975	0.93	0.885	0.975	CLONAL	2	TRUE	1	0.655270445249095	3		601	706	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194200	94194200	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	66	238	0	ENST00000323929.3:c.1228G>C	p.Glu410Gln	p.E410Q	ENST00000323929	NM_005591.3	410	Gaa/Caa	12/20	0.63685796184285	3	FACETS	0.773	0.675	0.878	0.386	0.337	0.439	SUBCLONAL	1	TRUE	1	0.655270445249095	3		238	346	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219145	94219145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758112386	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	90	309	3	ENST00000323929.3:c.259C>T	p.Arg87Trp	p.R87W	ENST00000323929	NM_005591.3	87	Cgg/Tgg	4/20	0.63685796184285	3	FACETS	0.814	0.726	0.907	0.407	0.363	0.454	CLONAL	1	TRUE	1	0.655270445249095	3		312	448	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243524	46243524	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	92	260	0	ENST00000334344.6:c.1877C>T	p.Ser626Phe	p.S626F	ENST00000334344	NM_152641.2	626	tCt/tTt	14/21	0.63685796184285	3	FACETS	1	0.979	1	0.685	0.618	0.755	CLONAL	1	TRUE	1	0.655270445249095	3		260	272	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427045	49427045	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	147	599	0	ENST00000301067.7:c.11443C>T	p.Pro3815Ser	p.P3815S	ENST00000301067	NM_003482.3	3815	Cct/Tct	39/54	0.63685796184285	3	FACETS	1	0.937	1	0.513	0.47	0.557	CLONAL	1	TRUE	1	0.655270445249095	3		599	581	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431588	49431588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1305161243	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	187	661	0	ENST00000301067.7:c.9551C>T	p.Ser3184Phe	p.S3184F	ENST00000301067	NM_003482.3	3184	tCc/tTc	34/54	0.63685796184285	3	FACETS	1	0.939	1	0.508	0.47	0.547	CLONAL	1	TRUE	1	0.655270445249095	3		661	746	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864780	57864780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769216016	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	151	629	0	ENST00000228682.2:c.2257C>T	p.Leu753Phe	p.L753F	ENST00000228682	NM_005269.2	753	Ctt/Ttt	12/12	0.63685796184285	3	FACETS	0.897	0.822	0.975	0.449	0.411	0.488	CLONAL	1	TRUE	1	0.655270445249095	3		629	682	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112159	115112159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	168	567	0	ENST00000257566.3:c.1581G>A	p.Met527Ile	p.M527I	ENST00000257566	NM_016569.3	527	atG/atA	7/8	0.63685796184285	3	FACETS	0.96	0.885	1	0.48	0.442	0.519	CLONAL	1	TRUE	1	0.655270445249095	3		567	709	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194859	30194859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1186546402	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	105	360	0	ENST00000331968.5:c.286G>A	p.Gly96Arg	p.G96R	ENST00000331968	NM_002742.2	96	Gga/Aga	2/18	0.521708112690704	4	FACETS	1	0.903	1	0.502	0.452	0.556	CLONAL	1	TRUE	2	0.655270445249095	4		360	528	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609431	81609432	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	172	385	0	ENST00000298171.2:c.1029_1030delinsTT	p.Gln344Ter	p.Q344*	ENST00000298171	NM_000369.2	343	ttCCag/ttTTag	10/10	0.521708112690704	4	FACETS	0.911	0.846	0.977	0.911	0.846	0.977	CLONAL	2	TRUE	2	0.655270445249095	4		385	477	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557549	95557549	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	68	255	0	ENST00000393063.1:c.5518C>T	p.Pro1840Ser	p.P1840S	ENST00000393063	NM_030621.3	1840	Cca/Tca	26/28	0.521708112690704	4	FACETS	0.84	0.734	0.954	0.42	0.367	0.477	CLONAL	1	TRUE	2	0.655270445249095	4		255	409	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003147	42003147	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	117	483	0	ENST00000219905.7:c.2684C>G	p.Ser895Cys	p.S895C	ENST00000219905	NM_001164273.1	895	tCt/tGt	8/24	1	2	FACETS	0.829	0.753	0.907	0.829	0.753	0.907	CLONAL	1	TRUE	1	0.655270445249095	2		483	431	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457279	67457279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	154	617	0	ENST00000327367.4:c.253C>T	p.His85Tyr	p.H85Y	ENST00000327367	NM_005902.3	85	Cat/Tat	2/9	1	2	FACETS	0.829	0.763	0.898	0.829	0.763	0.898	CLONAL	1	TRUE	1	0.655270445249095	2		617	567	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126084	2126084	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1060504116	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	205	590	0	ENST00000219476.3:c.2655C>G	p.Ile885Met	p.I885M	ENST00000219476	NM_000548.3	885	atC/atG	24/42	0.10562971365674	3	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.655270445249095	3		590	776	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129622	2129623	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	433	763	1	ENST00000219476.3:c.3349_3350delinsAA	p.Gly1117Lys	p.G1117K	ENST00000219476	NM_000548.3	1117	GGg/AAg	29/42	0.10562971365674	3	FACETS	0.969	0.929	1			1	INDETERMINATE	2	TRUE	NA	0.655270445249095	3		764	905	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790414	3790415	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	107	378	1	ENST00000262367.5:c.4118_4119delinsTT	p.Pro1373Leu	p.P1373L	ENST00000262367	NM_004380.2	1373	cCC/cTT	24/31	0.63685796184285	3	FACETS	0.957	0.864	1	0.479	0.432	0.528	CLONAL	1	TRUE	1	0.655270445249095	3		379	453	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820627	3820627	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776803900	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	214	696	0	ENST00000262367.5:c.2824C>T	p.Pro942Ser	p.P942S	ENST00000262367	NM_004380.2	942	Cct/Tct	14/31	0.63685796184285	3	FACETS	1	0.94	1	0.505	0.47	0.542	CLONAL	1	TRUE	1	0.655270445249095	3		696	858	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50816356	50816356	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	89	274	0	ENST00000398568.2:c.1796A>T	p.Tyr599Phe	p.Y599F	ENST00000398568	NM_001042412.1	599	tAc/tTc	10/18	0.63685796184285	3	FACETS	1	0.896	1	0.501	0.448	0.557	CLONAL	1	TRUE	1	0.655270445249095	3		274	360	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346195	89346195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	200	379	0	ENST00000301030.4:c.6755G>A	p.Gly2252Glu	p.G2252E	ENST00000301030	NM_001256183.1	2252	gGg/gAg	9/13	0.655270445249095	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	1	0.655270445249095	3		379	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	368	625	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.63685796184285	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.655270445249095	3		625	735	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578450	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	216	766	2	ENST00000269305.4:c.480_481delinsTT	p.Met160_Ala161delinsIleSer	p.M160_A161delinsIS	ENST00000269305	NM_001126112.2	160	atGGcc/atTTcc	5/11	0.63685796184285	3	FACETS	0.975	0.907	1	0.487	0.453	0.522	CLONAL	1	TRUE	1	0.655270445249095	3		768	898	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654847	29654847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	55	245	0	ENST00000356175.3:c.5536C>T	p.Pro1846Ser	p.P1846S	ENST00000356175	NM_000267.3	1846	Ccg/Tcg	37/57	0.655270445249095	4	FACETS	0.803	0.69	0.925	0.402	0.345	0.463	CLONAL	1	TRUE	2	0.655270445249095	4		245	346	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436016	56436017	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	116	427	0	ENST00000407977.2:c.1120_1121delinsTT	p.Pro374Phe	p.P374F	ENST00000407977		374	CCc/TTc	9/10	0.655270445249095	4	FACETS	0.947	0.855	1	0.316	0.285	0.348	CLONAL	1	TRUE	1	0.655270445249095	4		427	619	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436116	56436116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258109670	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	157	568	0	ENST00000407977.2:c.1021C>T	p.Leu341Phe	p.L341F	ENST00000407977		341	Ctc/Ttc	9/10	0.655270445249095	4	FACETS	0.965	0.885	1	0.322	0.295	0.35	CLONAL	1	TRUE	1	0.655270445249095	4		568	822	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271901	15271901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	249	889	0	ENST00000263388.2:c.6538C>T	p.Pro2180Ser	p.P2180S	ENST00000263388	NM_000435.2	2180	Cct/Tct	33/33	0.521708112690704	4	FACETS	1	0.968	1	0.53	0.495	0.566	CLONAL	1	TRUE	2	0.655270445249095	4		889	1187	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281169	15281169	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	233	798	0	ENST00000263388.2:c.5087C>T	p.Pro1696Leu	p.P1696L	ENST00000263388	NM_000435.2	1696	cCc/cTc	27/33	0.521708112690704	4	FACETS	0.97	0.904	1	0.485	0.452	0.52	CLONAL	1	TRUE	2	0.655270445249095	4		798	1213	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285134	15285134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	238	716	3	ENST00000263388.2:c.4481G>A	p.Gly1494Asp	p.G1494D	ENST00000263388	NM_000435.2	1494	gGc/gAc	25/33	0.521708112690704	4	FACETS	1	0.945	1	0.507	0.473	0.543	CLONAL	1	TRUE	2	0.655270445249095	4		719	1185	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300123	15300123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568360640	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	252	679	0	ENST00000263388.2:c.1153G>A	p.Gly385Ser	p.G385S	ENST00000263388	NM_000435.2	385	Ggt/Agt	7/33	0.521708112690704	4	FACETS	1	0.987	1	0.608	0.569	0.648	CLONAL	1	TRUE	2	0.655270445249095	4		679	1047	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937682	17937682	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	389	552	0	ENST00000458235.1:c.3245C>T	p.Pro1082Leu	p.P1082L	ENST00000458235	NM_000215.3	1082	cCa/cTa	24/24	0.521708112690704	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.655270445249095	4		552	951	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726561	41726561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	151	519	0	ENST00000301178.4:c.106C>T	p.Pro36Ser	p.P36S	ENST00000301178	NM_021913.4	36	Ccc/Tcc	2/20	0.521708112690704	4	FACETS	0.951	0.87	1	0.476	0.435	0.518	CLONAL	1	TRUE	2	0.655270445249095	4		519	802	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794967	42794967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	201	656	0	ENST00000575354.2:c.2047C>T	p.Pro683Ser	p.P683S	ENST00000575354	NM_015125.3	683	Cct/Tct	10/20	0.521708112690704	4	FACETS	1	0.938	1	0.507	0.469	0.546	CLONAL	1	TRUE	2	0.655270445249095	4		656	1002	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795730	42795730	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs755709610	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	244	774	0	ENST00000575354.2:c.2719C>G	p.Gln907Glu	p.Q907E	ENST00000575354	NM_015125.3	907	Cag/Gag	11/20	0.521708112690704	4	FACETS	0.986	0.92	1	0.493	0.46	0.527	CLONAL	1	TRUE	2	0.655270445249095	4		774	1250	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919705	50919705	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	232	810	0	ENST00000440232.2:c.2873T>G	p.Leu958Arg	p.L958R	ENST00000440232	NM_002691.3	958	cTg/cGg	23/27	0.521708112690704	4	FACETS	1	0.954	1	0.515	0.48	0.552	CLONAL	1	TRUE	2	0.655270445249095	4		810	1138	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416519	29416519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	356	560	0	ENST00000389048.3:c.4434G>A	p.Met1478Ile	p.M1478I	ENST00000389048	NM_004304.4	1478	atG/atA	29/29	0.655270445249095	3	FACETS	0.98	0.936	1	0.98	0.936	1	CLONAL	2	TRUE	1	0.655270445249095	3		560	736	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605131	46605131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762678739	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	362	665	0	ENST00000263734.3:c.1348G>A	p.Glu450Lys	p.E450K	ENST00000263734	NM_001430.4	450	Gag/Aag	10/16	0.655270445249095	3	FACETS	0.928	0.886	0.971	0.928	0.886	0.971	CLONAL	2	TRUE	1	0.655270445249095	3		665	790	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607700	46607700	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766914476	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	377	662	0	ENST00000263734.3:c.1889C>T	p.Ser630Phe	p.S630F	ENST00000263734	NM_001430.4	630	tCc/tTc	12/16	0.655270445249095	3	FACETS	0.913	0.871	0.954	0.913	0.871	0.954	CLONAL	2	TRUE	1	0.655270445249095	3		662	837	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634668	158634668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1199234423	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	85	276	0	ENST00000263640.3:c.518C>T	p.Thr173Ile	p.T173I	ENST00000263640	NM_001105.4	173	aCc/aTc	5/11	0.63685796184285	3	FACETS	0.981	0.875	1	0.491	0.437	0.547	CLONAL	1	TRUE	1	0.655270445249095	3		276	351	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286809	212286809	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	59	284	0	ENST00000342788.4:c.2887A>T	p.Ser963Cys	p.S963C	ENST00000342788	NM_005235.2	963	Agt/Tgt	24/28	0.648399479642478	2	FACETS	0.682	0.593	0.778	0.341	0.296	0.389	SUBCLONAL	1	TRUE	0	0.655270445249095	2		284	264	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661879	227661879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	396	602	0	ENST00000305123.5:c.1576C>T	p.His526Tyr	p.H526Y	ENST00000305123	NM_005544.2	526	Cac/Tac	1/2	0.648399479642478	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.655270445249095	2		602	568	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546922	9546922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	138	389	0	ENST00000353224.5:c.1100C>T	p.Ser367Phe	p.S367F	ENST00000353224	NM_177990.2	367	tCc/tTc	5/10	0.405721074216377	5	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.655270445249095	5		389	613	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448558	89448558	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	114	416	1	ENST00000336596.2:c.1522C>T	p.Gln508Ter	p.Q508*	ENST00000336596	NM_005233.5	508	Caa/Taa	7/17	0.521708112690704	4	FACETS	0.857	0.773	0.946	0.429	0.386	0.473	CLONAL	1	TRUE	2	0.655270445249095	4		417	672	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205871	128205871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	94	367	0	ENST00000341105.2:c.4G>A	p.Glu2Lys	p.E2K	ENST00000341105	NM_032638.4	2	Gag/Aag	2/6	0.655270445249095	5	FACETS	1	0.904	1	0.338	0.301	0.377	CLONAL	1	TRUE	2	0.655270445249095	5		367	561	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506990	186506990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	90	184	0	ENST00000323963.5:c.1156C>T	p.Arg386Cys	p.R386C	ENST00000323963		386	Cgt/Tgt	11/11	0.655270445249095	5	FACETS	0.803	0.719	0.891	0.536	0.479	0.594	CLONAL	2	TRUE	2	0.655270445249095	5		184	339	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447110	187447111	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	515	560	1	ENST00000232014.4:c.1082_1083delinsTT	p.Ser361Phe	p.S361F	ENST00000232014	NM_001130845.1	361	tCC/tTT	5/10	0.655270445249095	5	FACETS	0.976	0.94	1	0.976	0.94	1	CLONAL	3	TRUE	2	0.655270445249095	5		561	1064	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217214	66217214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	90	368	0	ENST00000273854.3:c.2401C>T	p.Leu801Phe	p.L801F	ENST00000273854	NM_004439.5	801	Ctt/Ttt	14/18	0.63685796184285	3	FACETS	0.962	0.86	1	0.481	0.43	0.535	CLONAL	1	TRUE	1	0.655270445249095	3		368	379	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542643	187542643	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	109	313	0	ENST00000441802.2:c.5097T>A	p.Tyr1699Ter	p.Y1699*	ENST00000441802	NM_005245.3	1699	taT/taA	10/27	0.63685796184285	3	FACETS	1	0.919	1	0.509	0.46	0.56	CLONAL	1	TRUE	1	0.655270445249095	3		313	434	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630576	187630577	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	316	477	0	ENST00000441802.2:c.405dup	p.Arg136GlnfsTer9	p.R136Qfs*9	ENST00000441802	NM_005245.3	135	-/C	2/27	0.63685796184285	3	FACETS	0.949	0.902	0.995	0.949	0.902	0.995	CLONAL	2	TRUE	1	0.655270445249095	3		477	675	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189389	56189389	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	114	431	0	ENST00000399503.3:c.4421C>T	p.Pro1474Leu	p.P1474L	ENST00000399503	NM_005921.1	1474	cCt/cTt	20/20	0.521708112690704	4	FACETS	0.873	0.787	0.963	0.436	0.393	0.482	CLONAL	1	TRUE	2	0.655270445249095	4		431	660	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665371	176665400	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	TGGAGGGCCCCTTGGCTCAGTCAGAACTTG	TGGAGGGCCCCTTGGCTCAGTCAGAACTTG	-	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	191	342	0	ENST00000439151.2:c.4055_4084del	p.Leu1352_Gly1362delinsTer	p.L1352_G1362delins*	ENST00000439151	NM_022455.4	1352	tTGGAGGGCCCCTTGGCTCAGTCAGAACTTGga/tga	7/23	0.521708112690704	4	FACETS	0.859	0.799	0.919	0.859	0.799	0.919	CLONAL	2	TRUE	2	0.655270445249095	4		342	562	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053174	180053174	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	345	734	0	ENST00000261937.6:c.1195C>T	p.Leu399Phe	p.L399F	ENST00000261937	NM_182925.4	399	Ctc/Ttc	9/30	0.521708112690704	4	FACETS	0.942	0.895	0.99	0.942	0.895	0.99	CLONAL	2	TRUE	2	0.655270445249095	4		734	925	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045911	26045911	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	172	546	0	ENST00000540144.1:c.273G>A	p.Met91Ile	p.M91I	ENST00000540144	NM_003531.2	91	atG/atA	1/1	0.51306927877293	4	FACETS	1	0.978	1	0.388	0.358	0.42	CLONAL	1	TRUE	1	0.655270445249095	4		546	746	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197429	26197429	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	121	432	0	ENST00000356476.2:c.50C>A	p.Pro17Gln	p.P17Q	ENST00000356476		17	cCa/cAa	1/1	0.51306927877293	4	FACETS	1	0.968	1	0.383	0.347	0.42	CLONAL	1	TRUE	1	0.655270445249095	4		432	532	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671295	30671296	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	108	405	0	ENST00000376406.3:c.5581_5582delinsTT	p.Pro1861Leu	p.P1861L	ENST00000376406	NM_014641.2	1861	CCa/TTa	11/15	0.51306927877293	4	FACETS	1	0.969	1	0.394	0.355	0.434	CLONAL	1	TRUE	1	0.655270445249095	4		405	462	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658457	117658457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	125	390	0	ENST00000368508.3:c.5126G>A	p.Gly1709Asp	p.G1709D	ENST00000368508	NM_002944.2	1709	gGt/gAt	31/43	0.655270445249095	3	FACETS	1	0.934	1	0.516	0.469	0.564	CLONAL	1	TRUE	1	0.655270445249095	3		390	491	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710996	117710996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	80	203	0	ENST00000368508.3:c.1276C>T	p.Leu426Phe	p.L426F	ENST00000368508	NM_002944.2	426	Ctc/Ttc	12/43	0.655270445249095	3	FACETS	1	0.964	1	0.6	0.535	0.668	CLONAL	1	TRUE	1	0.655270445249095	3		203	270	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099852	157099852	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	261	483	0	ENST00000346085.5:c.789G>A	p.Met263Ile	p.M263I	ENST00000346085	NM_020732.3	263	atG/atA	1/20	0.655270445249095	3	FACETS	0.904	0.855	0.954	0.904	0.855	0.954	CLONAL	2	TRUE	1	0.655270445249095	3		483	585	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522005	157522005	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751387548	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	126	523	0	ENST00000346085.5:c.4277C>T	p.Pro1426Leu	p.P1426L	ENST00000346085	NM_020732.3	1426	cCc/cTc	18/20	0.655270445249095	3	FACETS	0.851	0.773	0.933	0.425	0.386	0.467	CLONAL	1	TRUE	1	0.655270445249095	3		523	600	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522095	157522095	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	329	514	1	ENST00000346085.5:c.4367C>T	p.Ser1456Phe	p.S1456F	ENST00000346085	NM_020732.3	1456	tCc/tTc	18/20	0.655270445249095	3	FACETS	0.999	0.953	1	0.999	0.953	1	CLONAL	2	TRUE	1	0.655270445249095	3		515	667	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522136	157522136	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	181	532	0	ENST00000346085.5:c.4408G>C	p.Asp1470His	p.D1470H	ENST00000346085	NM_020732.3	1470	Gat/Cat	18/20	0.655270445249095	3	FACETS	1	0.979	1	0.576	0.533	0.619	CLONAL	1	TRUE	1	0.655270445249095	3		532	637	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528216	157528216	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	139	452	0	ENST00000346085.5:c.5941C>T	p.Leu1981Phe	p.L1981F	ENST00000346085	NM_020732.3	1981	Ctt/Ttt	20/20	0.655270445249095	3	FACETS	1	0.963	1	0.546	0.5	0.594	CLONAL	1	TRUE	1	0.655270445249095	3		452	516	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983953	2983953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	400	637	1	ENST00000396946.4:c.577G>A	p.Glu193Lys	p.E193K	ENST00000396946	NM_032415.4	193	Gag/Aag	5/25	0.193717697867804	5	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.655270445249095	5		638	1038	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444414	50444414	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	128	319	0	ENST00000331340.3:c.344G>A	p.Gly115Glu	p.G115E	ENST00000331340	NM_006060.4	115	gGa/gAa	4/8	0.655270445249095	4	FACETS	1	0.962	1	0.553	0.503	0.605	CLONAL	1	TRUE	2	0.655270445249095	4		319	585	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878758	151878758	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1381665445	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	175	344	0	ENST00000262189.6:c.6187G>A	p.Ala2063Thr	p.A2063T	ENST00000262189	NM_170606.2	2063	Gca/Aca	36/59	0.63685796184285	3	FACETS	0.94	0.879	1	0.94	0.879	1	CLONAL	2	TRUE	1	0.655270445249095	3		344	377	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205252	38205252	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	175	657	0	ENST00000317025.8:c.438G>C	p.Lys146Asn	p.K146N	ENST00000317025	NM_023034.1	146	aaG/aaC	2/24	1	2	FACETS	0.808	0.747	0.871	0.808	0.747	0.871	CLONAL	1	TRUE	1	0.655270445249095	2		657	661	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864240	117864240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	213	346	0	ENST00000297338.2:c.1417C>T	p.Pro473Ser	p.P473S	ENST00000297338	NM_006265.2	473	Cct/Tct	11/14	0.655270445249095	3	FACETS	0.955	0.898	1	0.955	0.898	1	CLONAL	2	TRUE	1	0.655270445249095	3		346	452	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869692	117869692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1337189031	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	109	243	1	ENST00000297338.2:c.502C>T	p.Arg168Cys	p.R168C	ENST00000297338	NM_006265.2	168	Cgt/Tgt	6/14	0.655270445249095	3	FACETS	1	0.971	1	0.592	0.536	0.65	CLONAL	1	TRUE	1	0.655270445249095	3		244	373	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518073	8518073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1480778931	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	113	351	0	ENST00000356435.5:c.1318G>A	p.Glu440Lys	p.E440K	ENST00000356435		440	Gaa/Aaa	10/35	0.648399479642478	2	FACETS	0.958	0.871	1	0.479	0.435	0.524	CLONAL	1	TRUE	0	0.655270445249095	2		351	360	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169498	27169498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	231	424	0	ENST00000380036.4:c.499C>T	p.Arg167Trp	p.R167W	ENST00000380036	NM_000459.3	167	Cgg/Tgg	4/23	0.648399479642478	2	FACETS	0.996	0.949	1	0.996	0.949	1	CLONAL	2	TRUE	0	0.655270445249095	2		424	354	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211398	98211398	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	384	692	0	ENST00000331920.6:c.3757C>T	p.Gln1253Ter	p.Q1253*	ENST00000331920	NM_000264.3	1253	Caa/Taa	22/24	0.521708112690704	4	FACETS	0.999	0.952	1	0.999	0.952	1	CLONAL	2	TRUE	2	0.655270445249095	4		692	971	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242722	98242722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745669231	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	156	392	1	ENST00000331920.6:c.895C>T	p.Pro299Ser	p.P299S	ENST00000331920	NM_000264.3	299	Ccg/Tcg	6/24	0.521708112690704	4	FACETS	1	0.954	1	0.529	0.485	0.575	CLONAL	1	TRUE	2	0.655270445249095	4		393	745	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242737	98242738	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	272	426	0	ENST00000331920.6:c.879_880delinsTT	p.Arg294Cys	p.R294C	ENST00000331920	NM_000264.3	293	gaCCgc/gaTTgc	6/24	0.521708112690704	4	FACETS	0.984	0.929	1	0.984	0.929	1	CLONAL	2	TRUE	2	0.655270445249095	4		426	698	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912005	127912005	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	173	289	0	ENST00000373547.4:c.865C>T	p.Pro289Ser	p.P289S	ENST00000373547	NM_002721.4	289	Cca/Tca	7/7	0.521708112690704	4	FACETS	0.938	0.871	1	0.938	0.871	1	CLONAL	2	TRUE	2	0.655270445249095	4		289	466	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397713	139397736	+	inframe_deletion	In_Frame_Del	DEL	GGCACTCTGGAAGCACTGCGAGGA	GGCACTCTGGAAGCACTGCGAGGA	-	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	297	718	0	ENST00000277541.6:c.5065_5088del	p.Ser1689_Ala1696del	p.S1689_A1696del	ENST00000277541	NM_017617.3	1689	TCCTCGCAGTGCTTCCAGAGTGCC/-	27/34	0.521708112690704	4	FACETS	0.772	0.728	0.817	0.772	0.728	0.817	SUBCLONAL	2	TRUE	2	0.655270445249095	4		718	972	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418406	139418406	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1348892740	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	474	743	3	ENST00000277541.6:c.166C>T	p.Arg56Ter	p.R56*	ENST00000277541	NM_017617.3	56	Cga/Tga	3/34	0.521708112690704	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.655270445249095	4		746	1151	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820568	44820568	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	91	191	0	ENST00000377967.4:c.265G>A	p.Gly89Arg	p.G89R	ENST00000377967	NM_021140.2	89	Gga/Aga	3/29	0.655270445249095	2	FACETS	1	0.956	1			1	CLONAL	1	TRUE	NA	0.655270445249095	2		191	251	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410024	63410024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	147	295	0	ENST00000330258.3:c.3143C>T	p.Pro1048Leu	p.P1048L	ENST00000330258	NM_152424.3	1048	cCt/cTt	2/2	0.655270445249095	2	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.655270445249095	2		295	391	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099341	157099341	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587779741	NA	P-0053323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	21	326	0	ENST00000346085.5:c.278A>T	p.His93Leu	p.H93L	ENST00000346085	NM_020732.3	93	cAc/cTc	1/20	0.655270445249095	3	FACETS	0.251	0.193	0.319	0.126	0.096	0.16	SUBCLONAL	1	TRUE	1	0.655270445249095	3		326	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0053346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	258	599	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.335145321792665	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.335145321792665	2		599	706	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619172	37619172	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	19118	827	0	ENST00000447079.4:c.848C>A	p.Ser283Ter	p.S283*	ENST00000447079	NM_015083.1	283	tCg/tAg	1/14	0.335145321792665	112	FACETS	1	0.998	1			1	CLONAL	112	TRUE	NA	0.335145321792665	112		827	19802	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971115	21971133	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTCGGGTGAGAGTGGCG	GGGTCGGGTGAGAGTGGCG	-	rs730881674	NA	P-0053346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	31	287	0	ENST00000304494.5:c.225_243del	p.Ala76CysfsTer64	p.A76Cfs*64	ENST00000304494	NM_000077.4	75	ccCGCCACTCTCACCCGACCC/cc	2/3	1	2	FACETS	0.69	0.56	0.836	0.69	0.56	0.836	SUBCLONAL	1	TRUE	1	0.335145321792665	2		287	268	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649712	48649712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149753411	NA	P-0053346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	292	471	0	ENST00000376670.3:c.196G>A	p.Ala66Thr	p.A66T	ENST00000376670	NM_002049.3	66	Gct/Act	2/6	0.290730586814182	2	FACETS	1	0.968	1			1	CLONAL	3	TRUE	NA	0.335145321792665	2		471	568	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714471	40714471	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	345	592	0	ENST00000373198.4:c.3926A>T	p.Glu1309Val	p.E1309V	ENST00000373198	NM_133170.3	1309	gAg/gTg	29/32	0.335145321792665	5	FACETS	0.948	0.902	0.994			1	CLONAL	4	TRUE	NA	0.335145321792665	5		592	816	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	156	714	1				ENST00000310581	NM_198253.2	-/1132			0.349927919672015	1	FACETS	0.623	0.582	0.664	0.623	0.582	0.664	INDETERMINATE	1	TRUE	0	0.909777749442439	1		715	300	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0053430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	181	371	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.894428203358695	3	FACETS	1	0.929	1	0.501	0.464	0.538	CLONAL	1	TRUE	1	0.909777749442439	3		371	578	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295258	1295258	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0053430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	285	429	0				ENST00000310581	NM_198253.2	-/1132			0.349927919672015	1	FACETS	0.694	0.662	0.726	0.694	0.662	0.726	INDETERMINATE	1	TRUE	0	0.909777749442439	1		429	492	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246042	46246043	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0053430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	130	268	0	ENST00000334344.6:c.4137_4138del	p.His1379GlnfsTer10	p.H1379Qfs*10	ENST00000334344	NM_152641.2	1379	cAT/c	15/21	1	2	FACETS	0.999	0.923	1	0.999	0.923	1	CLONAL	1	TRUE	1	0.909777749442439	2		268	286	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641048	117641048	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	178	452	0	ENST00000368508.3:c.5923A>C	p.Ile1975Leu	p.I1975L	ENST00000368508	NM_002944.2	1975	Atc/Ctc	36/43	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.909777749442439	2		452	376	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0053772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	22	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.294629512953733	1	FACETS	1	0.817	1	1	0.817	1	CLONAL	1	TRUE	0	0.294629512953733	1		485	122	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0053772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	70	439	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.294629512953733	2		440	389	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591931	48591931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	14	369	1	ENST00000342988.3:c.1094G>A	p.Gly365Asp	p.G365D	ENST00000342988	NM_005359.5	365	gGt/gAt	9/12	1	2	FACETS	0.665	0.483	0.881	0.665	0.483	0.881	SUBCLONAL	1	TRUE	1	0.294629512953733	2		370	143	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519023	66519023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	43	458	0	ENST00000358598.2:c.304G>A	p.Ala102Thr	p.A102T	ENST00000358598	NM_212471.2	102	Gct/Act	3/11	1	2	FACETS	0.733	0.615	0.864	0.733	0.615	0.864	SUBCLONAL	1	TRUE	1	0.294629512953733	2		458	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0053841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	97	529	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.228091273667078	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.228091273667078	1		529	542	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664894	29664894	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1567617727	NA	P-0053841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	55	410	0	ENST00000356175.3:c.6637C>T	p.Gln2213Ter	p.Q2213*	ENST00000356175	NM_000267.3	2213	Caa/Taa	43/57	0.228091273667078	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.228091273667078	1		410	397	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431121	49431121	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	40	815	0	ENST00000301067.7:c.10018C>T	p.Gln3340Ter	p.Q3340*	ENST00000301067	NM_003482.3	3340	Cag/Tag	34/54	1	2	FACETS	0.667	0.553	0.793	0.667	0.553	0.793	SUBCLONAL	1	TRUE	1	0.228091273667078	2		815	526	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252059	226252059	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	27	332	0	ENST00000366813.1:c.7C>G	p.Arg3Gly	p.R3G	ENST00000366813		3	Cgt/Ggt	1/3	1	2	FACETS	0.711	0.566	0.876	0.711	0.566	0.876	SUBCLONAL	1	TRUE	1	0.228091273667078	2		332	333	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946435	2946435	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751651073	NA	P-0053841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	65	873	0	ENST00000396946.4:c.3302G>A	p.Arg1101His	p.R1101H	ENST00000396946	NM_032415.4	1101	cGc/cAc	25/25	0.228091273667078	1	FACETS	0.949	0.824	1	0.949	0.824	1	CLONAL	1	TRUE	0	0.228091273667078	1		873	532	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177896	56177896	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	30	533	1	ENST00000399503.3:c.2869C>T	p.Gln957Ter	p.Q957*	ENST00000399503	NM_005921.1	957	Caa/Taa	14/20	1	2	FACETS	0.461	0.371	0.565	0.461	0.371	0.565	SUBCLONAL	1	TRUE	1	0.228091273667078	2		534	570	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266577	41266577	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	49	483	0	ENST00000349496.5:c.374T>G	p.Leu125Trp	p.L125W	ENST00000349496	NM_001904.3	125	tTg/tGg	4/15	1	2	FACETS	0.858	0.727	1	0.858	0.727	1	CLONAL	1	TRUE	1	0.228091273667078	2		483	501	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	88	714	1				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.902	0.806	1			1	INDETERMINATE	1	TRUE	NA	0.567404221002669	2		715	344	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0054072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	108	433	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.567404221002669	2		434	364	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041737	14041737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	57	455	0	ENST00000311895.7:c.2284G>A	p.Asp762Asn	p.D762N	ENST00000311895	NM_005236.2	762	Gac/Aac	11/11	1	2	FACETS	0.459	0.394	0.529	0.459	0.394	0.529	SUBCLONAL	1	TRUE	1	0.567404221002669	2		455	438	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574959	41574959	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	novel	NA	P-0054072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	106	386	0	ENST00000263253.7:c.7244A>G	p.Ter2415TrpextTer30	p.*2415Wext*30	ENST00000263253	NM_001429.3	2415	tAg/tGg	31/31	1	2	FACETS	0.861	0.777	0.949	0.861	0.777	0.949	CLONAL	1	TRUE	1	0.567404221002669	2		386	434	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	109	564	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.944	0.849	1	0.944	0.849	1	CLONAL	1	TRUE	1	0.34	2		564	679	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	131	565	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.873	0.792	0.958	0.873	0.792	0.958	CLONAL	1	TRUE	1	0.34	2		568	883	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	136	936	5	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.862	0.783	0.945	0.862	0.783	0.945	CLONAL	1	TRUE	1	0.34	2		941	928	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	105	602	7	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.916	0.822	1	0.916	0.822	1	CLONAL	1	TRUE	1	0.34	2		609	674	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539564	187539564	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	80	570	0	ENST00000441802.2:c.8176C>T	p.Arg2726Ter	p.R2726*	ENST00000441802	NM_005245.3	2726	Cga/Tga	10/27	1	2	FACETS	0.77	0.678	0.868	0.77	0.678	0.868	SUBCLONAL	1	TRUE	1	0.34	2		570	611	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434367	121434367	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	122	795	5	ENST00000257555.6:c.1136del	p.Pro379LeufsTer5	p.P379Lfs*5	ENST00000257555		377	ctC/ct	6/10	1	2	FACETS	0.928	0.84	1	0.928	0.84	1	CLONAL	1	TRUE	1	0.34	2		800	773	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116254	209116254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369048275	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	73	399	1	ENST00000345146.2:c.22G>A	p.Gly8Ser	p.G8S	ENST00000345146	NM_005896.2	8	Ggt/Agt	3/10	1	2	FACETS	0.896	0.786	1	0.896	0.786	1	CLONAL	1	TRUE	1	0.34	2		400	479	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180367	32180367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1382129029	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	153	791	1	ENST00000375023.3:c.2564G>A	p.Arg855His	p.R855H	ENST00000375023	NM_004557.3	855	cGc/cAc	17/30	1	2	FACETS	0.98	0.897	1	0.98	0.897	1	CLONAL	1	TRUE	1	0.34	2		792	918	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982356	25982356	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	72	372	1	ENST00000435504.4:c.934C>T	p.Arg312Ter	p.R312*	ENST00000435504		312	Cga/Tga	9/13	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.34	2		373	412	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398279	25398279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894365	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	80	594	0	ENST00000311936.3:c.40G>A	p.Val14Ile	p.V14I	ENST00000311936	NM_004985.3	14	Gta/Ata	2/5	1	2	FACETS	0.78	0.688	0.88	0.78	0.688	0.88	SUBCLONAL	1	TRUE	1	0.34	2		594	603	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214615	5214615	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754694289	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	156	876	1	ENST00000357368.4:c.4451C>T	p.Ser1484Leu	p.S1484L	ENST00000357368	NM_002850.3	1484	tCg/tTg	29/38	1	2	FACETS	0.982	0.899	1	0.982	0.899	1	CLONAL	1	TRUE	1	0.34	2		877	934	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023769	27023769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	66	444	0	ENST00000324856.7:c.879del	p.Thr294ProfsTer69	p.T294Pfs*69	ENST00000324856	NM_006015.4	292	aCc/ac	1/20	1	2	FACETS	0.931	0.811	1	0.931	0.811	1	CLONAL	1	TRUE	1	0.34	2		444	417	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856093	68856093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121964878	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	134	747	1	ENST00000261769.5:c.1901C>T	p.Ala634Val	p.A634V	ENST00000261769	NM_004360.3	634	gCg/gTg	12/16	1	2	FACETS	0.934	0.849	1	0.934	0.849	1	CLONAL	1	TRUE	1	0.34	2		748	844	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38283643	38283643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs186746130	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	118	575	0	ENST00000425967.3:c.835G>A	p.Val279Met	p.V279M	ENST00000425967	NM_001174067.1	279	Gtg/Atg	7/19	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.34	2		575	627	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938407	76938407	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	124	425	1	ENST00000373344.5:c.2341C>T	p.Arg781Ter	p.R781*	ENST00000373344	NM_000489.3	781	Cga/Tga	9/35	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.34	1		426	462	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446324	187446324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs541016998	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	136	692	0	ENST00000232014.4:c.1364C>T	p.Thr455Met	p.T455M	ENST00000232014	NM_001130845.1	455	aCg/aTg	6/10	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.34	2		692	753	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873066	134873066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762457030	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	138	821	0	ENST00000398015.3:c.1370C>T	p.Pro457Leu	p.P457L	ENST00000398015	NM_004441.4	457	cCg/cTg	6/16	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.34	2		821	788	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202585	67202585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374915842	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	134	878	0	ENST00000312629.5:c.1394G>A	p.Arg465His	p.R465H	ENST00000312629	NM_003952.2	465	cGt/cAt	15/15	1	2	FACETS	0.958	0.87	1	0.958	0.87	1	CLONAL	1	TRUE	1	0.34	2		878	823	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540654	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	146	902	2	ENST00000269305.4:c.329G>A	p.Arg110His	p.R110H	ENST00000269305	NM_001126112.2	110	cGt/cAt	4/11	1	2	FACETS	0.903	0.824	0.986	0.903	0.824	0.986	CLONAL	1	TRUE	1	0.34	2		904	951	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249029	55249029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs483352806	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	119	753	0	ENST00000275493.2:c.2327G>A	p.Arg776His	p.R776H	ENST00000275493	NM_005228.3	776	cGc/cAc	20/28	1	2	FACETS	0.854	0.77	0.942	0.854	0.77	0.942	CLONAL	1	TRUE	1	0.34	2		753	820	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218979	193218979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500011	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	79	446	1	ENST00000367435.3:c.1537C>T	p.Arg513Trp	p.R513W	ENST00000367435	NM_024529.4	513	Cgg/Tgg	16/17	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.34	2		447	431	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457719	149457719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149911279	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	158	910	0	ENST00000286301.3:c.685G>A	p.Val229Ile	p.V229I	ENST00000286301	NM_005211.3	229	Gtt/Att	5/22	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.34	2		910	921	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	151	984	6	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	1	2	FACETS	0.951	0.869	1	0.951	0.869	1	CLONAL	1	TRUE	1	0.34	2		990	934	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954248	17954248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776850935	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	153	805	0	ENST00000458235.1:c.361C>T	p.Arg121Cys	p.R121C	ENST00000458235	NM_000215.3	121	Cgc/Tgc	4/24	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.34	2		805	862	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514694	103514694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs4150315	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	101	569	0	ENST00000355739.4:c.1195G>A	p.Glu399Lys	p.E399K	ENST00000355739	NM_000123.3	399	Gaa/Aaa	8/15	1	2	FACETS	0.954	0.854	1	0.954	0.854	1	CLONAL	1	TRUE	1	0.34	2		569	623	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212575	36212575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769208559	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	169	1045	0	ENST00000222270.7:c.2326C>T	p.Arg776Trp	p.R776W	ENST00000222270	NM_014727.1	776	Cgg/Tgg	3/37	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.34	2		1045	991	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444987	49444987	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	130	724	0	ENST00000301067.7:c.2479del	p.Gln827AsnfsTer103	p.Q827Nfs*103	ENST00000301067	NM_003482.3	827	Caa/aa	10/54	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.34	2		724	761	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858188	27858188	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	121	586	0	ENST00000359303.2:c.383C>T	p.Ala128Val	p.A128V	ENST00000359303	NM_003535.2	128	gCg/gTg	1/1	1	2	FACETS	0.97	0.877	1	0.97	0.877	1	CLONAL	1	TRUE	1	0.34	2		586	734	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420493	49420493	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs727503979	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	144	881	2	ENST00000301067.7:c.15256C>T	p.Arg5086Ter	p.R5086*	ENST00000301067	NM_003482.3	5086	Cga/Tga	48/54	1	2	FACETS	0.995	0.908	1	0.995	0.908	1	CLONAL	1	TRUE	1	0.34	2		883	851	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195544	102195544	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs922637067	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	111	664	0	ENST00000263464.3:c.304G>A	p.Val102Ile	p.V102I	ENST00000263464	NM_001165.4	102	Gtt/Att	2/9	1	2	FACETS	0.836	0.752	0.926	0.836	0.752	0.926	CLONAL	1	TRUE	1	0.34	2		664	781	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098425	11098425	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	27	469	0	ENST00000358026.2:c.947del	p.Pro316LeufsTer10	p.P316Lfs*10	ENST00000358026	NM_001128849.1	315	Ccc/cc	6/36	1	2	FACETS	0.359	0.285	0.444	0.359	0.285	0.444	SUBCLONAL	1	TRUE	1	0.34	2		469	442	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469969	25469969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1191462913	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	47	831	0	ENST00000264709.3:c.1073C>T	p.Thr358Met	p.T358M	ENST00000264709	NM_175629.2	358	aCg/aTg	9/23	1	2	FACETS	0.311	0.261	0.366	0.311	0.261	0.366	SUBCLONAL	1	TRUE	1	0.34	2		831	889	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915589	131915589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764784659	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	59	395	0	ENST00000265335.6:c.587G>A	p.Arg196His	p.R196H	ENST00000265335		196	cGt/cAt	5/25	1	2	FACETS	0.813	0.701	0.933	0.813	0.701	0.933	CLONAL	1	TRUE	1	0.34	2		395	427	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435697	110435697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745496477	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	74	427	2	ENST00000375856.3:c.2704C>T	p.Pro902Ser	p.P902S	ENST00000375856	NM_003749.2	902	Ccc/Tcc	1/2	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.34	2		429	393	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472553	88472553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	59	806	0	ENST00000360948.2:c.2002G>A	p.Val668Met	p.V668M	ENST00000360948	NM_001012338.2	668	Gtg/Atg	16/19	1	2	FACETS	0.458	0.393	0.529	0.458	0.393	0.529	SUBCLONAL	1	TRUE	1	0.34	2		806	758	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271704	38271704	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	166	1128	1	ENST00000425967.3:c.2245C>T	p.Arg749Cys	p.R749C	ENST00000425967	NM_001174067.1	749	Cgc/Tgc	17/19	1	2	FACETS	0.912	0.836	0.991	0.912	0.836	0.991	CLONAL	1	TRUE	1	0.34	2		1129	1071	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844416	156844416	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	170	1097	0	ENST00000524377.1:c.1251+1del		p.G417fs	ENST00000524377	NM_002529.3	417	Ggg/gg	10/17	1	2	FACETS	0.984	0.904	1	0.984	0.904	1	CLONAL	1	TRUE	1	0.34	2		1097	1016	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163298658	163298658	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755645930	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	126	768	3	ENST00000271452.3:c.298C>T	p.Arg100Trp	p.R100W	ENST00000271452	NM_145697.2	100	Cgg/Tgg	5/14	1	2	FACETS	0.971	0.88	1	0.971	0.88	1	CLONAL	1	TRUE	1	0.34	2		771	763	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410677	32410677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	102	623	4	ENST00000332351.3:c.1481C>T	p.Ala494Val	p.A494V	ENST00000332351	NM_024426.4	494	gCc/gTc	10/10	1	2	FACETS	0.852	0.763	0.947	0.852	0.763	0.947	CLONAL	1	TRUE	1	0.34	2		627	704	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446006	49446006	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778182231	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	186	1046	1	ENST00000301067.7:c.1460G>A	p.Arg487Gln	p.R487Q	ENST00000301067	NM_003482.3	487	cGg/cAg	10/54	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.34	2		1047	1083	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781928	3781928	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	100	563	0	ENST00000262367.5:c.4739del	p.Gly1580AlafsTer55	p.G1580Afs*55	ENST00000262367	NM_004380.2	1580	gGc/gc	29/31	1	2	FACETS	0.952	0.852	1	0.952	0.852	1	CLONAL	1	TRUE	1	0.34	2		563	618	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011227	12011227	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	80	496	0	ENST00000353533.5:c.633+1G>C		p.X211_splice	ENST00000353533	NM_003010.3	211			1	2	FACETS	0.97	0.857	1	0.97	0.857	1	CLONAL	1	TRUE	1	0.34	2		496	485	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40368045	40368045	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	156	808	0	ENST00000293328.3:c.1460C>T	p.Ala487Val	p.A487V	ENST00000293328	NM_012448.3	487	gCt/gTt	12/19	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.34	2		808	879	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40451807	40451807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1231666878	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	117	815	0	ENST00000345506.4:c.589C>T	p.Arg197Cys	p.R197C	ENST00000345506	NM_003152.3	197	Cgt/Tgt	7/20	1	2	FACETS	0.99	0.894	1	0.99	0.894	1	CLONAL	1	TRUE	1	0.34	2		815	695	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677960	58677961	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	37	302	0	ENST00000305921.3:c.185_186del	p.Glu62GlyfsTer27	p.E62Gfs*27	ENST00000305921	NM_003620.3	62	gAA/g	1/6	1	2	FACETS	0.777	0.644	0.925	0.777	0.644	0.925	CLONAL	1	TRUE	1	0.34	2		302	280	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858254	59858254	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs780020495	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	122	681	0	ENST00000259008.2:c.1741C>T	p.Arg581Ter	p.R581*	ENST00000259008	NM_032043.2	581	Cga/Tga	12/20	1	2	FACETS	0.957	0.865	1	0.957	0.865	1	CLONAL	1	TRUE	1	0.34	2		681	750	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967722	18967722	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	51	850	0	ENST00000262803.5:c.1861G>T	p.Gly621Cys	p.G621C	ENST00000262803	NM_002911.3	621	Ggt/Tgt	14/24	1	2	FACETS	0.35	0.297	0.41	0.35	0.297	0.41	SUBCLONAL	1	TRUE	1	0.34	2		850	856	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855786	45855786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	133	824	0	ENST00000391945.4:c.2024G>A	p.Gly675Asp	p.G675D	ENST00000391945	NM_000400.3	675	gGc/gAc	21/23	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.34	2		824	739	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637260	47637260	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	103	756	0	ENST00000233146.2:c.394G>T	p.Glu132Ter	p.E132*	ENST00000233146	NM_000251.2	132	Gaa/Taa	3/16	1	2	FACETS	0.802	0.718	0.892	0.802	0.718	0.892	CLONAL	1	TRUE	1	0.34	2		756	755	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21304023	21304023	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	125	640	0	ENST00000354336.3:c.802A>G	p.Arg268Gly	p.R268G	ENST00000354336	NM_005207.3	268	Agg/Ggg	3/3	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.34	2		640	716	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539446	187539447	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	109	589	0	ENST00000441802.2:c.8293_8294del	p.Leu2766Ter	p.L2766*	ENST00000441802	NM_005245.3	2765	AGt/t	10/27	1	2	FACETS	0.957	0.86	1	0.957	0.86	1	CLONAL	1	TRUE	1	0.34	2		589	670	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628364	86628364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	62	546	0	ENST00000274376.6:c.733C>T	p.Arg245Cys	p.R245C	ENST00000274376	NM_002890.2	245	Cgt/Tgt	3/25	1	2	FACETS	0.768	0.665	0.88	0.768	0.665	0.88	SUBCLONAL	1	TRUE	1	0.34	2		546	475	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968316	2968316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1012368675	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	133	841	2	ENST00000396946.4:c.1670G>A	p.Arg557His	p.R557H	ENST00000396946	NM_032415.4	557	cGc/cAc	13/25	1	2	FACETS	0.962	0.874	1	0.962	0.874	1	CLONAL	1	TRUE	1	0.34	2		843	813	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27203043	27203043	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	128	815	0	ENST00000380036.4:c.2139del	p.Phe713LeufsTer6	p.F713Lfs*6	ENST00000380036	NM_000459.3	712	aTt/at	13/23	1	2	FACETS	0.892	0.808	0.98	0.892	0.808	0.98	CLONAL	1	TRUE	1	0.34	2		815	844	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954220	48954237	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTAAATTTTTTACTTTT	GGTAAATTTTTTACTTTT	AAA	novel	NA	P-0054242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	101	282	1	ENST00000267163.4:c.1421_1421+17delinsAAA		p.X474_splice	ENST00000267163	NM_000321.2	474		15/27	0.432736350405282	2	FACETS	0.887	0.807	0.97	0.887	0.807	0.97	CLONAL	2	TRUE	0	0.43950928534947	2		283	259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579359	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587780066	NA	P-0054242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	373	1224	1	ENST00000269305.4:c.328del	p.Arg110ValfsTer13	p.R110Vfs*13	ENST00000269305	NM_001126112.2	110	Cgt/gt	4/11	0.432736350405282	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.43950928534947	2		1225	823	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579509	7579509	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	319	1151	0	ENST00000269305.4:c.178C>G	p.Pro60Ala	p.P60A	ENST00000269305	NM_001126112.2	60	Cca/Gca	4/11	0.432736350405282	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.43950928534947	2		1151	706	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579586	7579586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	270	954	0	ENST00000269305.4:c.101C>T	p.Pro34Leu	p.P34L	ENST00000269305	NM_001126112.2	34	cCc/cTc	4/11	0.432736350405282	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.43950928534947	2		954	608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579702	7579702	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	197	825	1	ENST00000269305.4:c.94C>A	p.Leu32Met	p.L32M	ENST00000269305	NM_001126112.2	32	Ctg/Atg	3/11	0.432736350405282	2	FACETS	0.879	0.821	0.938	0.879	0.821	0.938	CLONAL	2	TRUE	0	0.43950928534947	2		826	510	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0054242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	404	432	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.43950928534947	11	FACETS	1	0.982	1			1	CLONAL	6	TRUE	NA	0.43950928534947	11		432	869	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573118	64573118	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs772588551	NA	P-0054414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	284	467	0	ENST00000312049.6:c.1174G>T	p.Glu392Ter	p.E392*	ENST00000312049	NM_130799.2	392	Gag/Tag	8/10	0.876728638735146	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.876728638735146	1		467	364	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0054426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	249	439	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.98	1	1	0.996	1	CLONAL	3	TRUE	1	0.158360899384587	2		440	943	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0054426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	186	121	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.158360899384587	2	FACETS	0.961	0.892	1	1	0.993	1	CLONAL	4	TRUE	0	0.158360899384587	2		121	611	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0054426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	187	557	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	NA	2	FACETS	0.953	0.882	1			1	INDETERMINATE	3	TRUE	NA	0.158360899384587	2		559	826	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912186	114912186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	223	624	0	ENST00000543371.1:c.1256C>T	p.Ala419Val	p.A419V	ENST00000543371	NM_001198531.1	419	gCg/gTg	11/14	1	2	FACETS	1	0.964	1	1	0.995	1	CLONAL	3	TRUE	1	0.158360899384587	2		624	892	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265989	41266510	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACAT	TAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACAT	-	novel	NA	P-0054426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	104	203	0	ENST00000349496.5:c.14-26_309del		p.X5_splice	ENST00000349496	NM_001904.3	5		3-4/15	1	2	FACETS	0.957	0.866	1	1	0.991	1	CLONAL	4	TRUE	1	0.158360899384587	2		203	343	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277955	41277955	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	120	427	1	ENST00000349496.5:c.1919T>C	p.Leu640Pro	p.L640P	ENST00000349496	NM_001904.3	640	cTg/cCg	12/15	1	2	FACETS	0.853	0.773	0.938	1	0.991	1	CLONAL	3	TRUE	1	0.158360899384587	2		428	592	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84406221	84406221	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1027841598	NA	P-0054426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	106	450	0	ENST00000321945.7:c.5A>C	p.Glu2Ala	p.E2A	ENST00000321945	NM_139076.2	2	gAg/gCg	1/9	1	2	FACETS	1	0.973	1	1	0.99	1	CLONAL	2	TRUE	1	0.158360899384587	2		450	537	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251883	153251883	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0054426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	125	401	0	ENST00000281708.4:c.1122+1G>T		p.X374_splice	ENST00000281708	NM_033632.3	374			1	2	FACETS	0.98	0.891	1	1	0.992	1	CLONAL	3	TRUE	1	0.158360899384587	2		401	537	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980563	70980563	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	57	673	0	ENST00000276594.2:c.814A>C	p.Ser272Arg	p.S272R	ENST00000276594	NM_024504.3	272	Agt/Cgt	4/8	0.158360899384587	3	FACETS	0.745	0.637	0.864	0.372	0.318	0.432	SUBCLONAL	1	TRUE	1	0.158360899384587	3		673	1043	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	108	367	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.193906562087482	1	FACETS	0.902	0.813	0.996	0.902	0.813	0.996	INDETERMINATE	1	TRUE	0	0.377125639374292	1		367	515	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602354	28602354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1367367961	NA	P-0054675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	287	495	1	ENST00000241453.7:c.2014G>A	p.Glu672Lys	p.E672K	ENST00000241453	NM_004119.2	672	Gag/Aag	16/24	0.377125639374292	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.377125639374292	3		496	885	SUCCESS
APC	324	MSKCC	GRCh37	5	112174349	112174349	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	137	238	0	ENST00000257430.4:c.3058G>T	p.Glu1020Ter	p.E1020*	ENST00000257430	NM_000038.5	1020	Gaa/Taa	16/16	0.377125639374292	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	0	0.377125639374292	2		238	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577157	7577157	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0054675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	181	474	0	ENST00000269305.4:c.783-2A>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.377125639374292	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.377125639374292	1		474	646	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710635	114710635	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	114	459	0	ENST00000543371.1:c.122del	p.Leu41Ter	p.L41*	ENST00000543371	NM_001198531.1	40	gaT/ga	1/14	0.193906562087482	1	FACETS	0.731	0.659	0.807	0.731	0.659	0.807	INDETERMINATE	1	TRUE	0	0.377125639374292	1		459	671	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096022	11096022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745406632	NA	P-0054675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	267	801	0	ENST00000358026.2:c.296G>A	p.Arg99Gln	p.R99Q	ENST00000358026	NM_001128849.1	99	cGg/cAg	3/36	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.377125639374292	2		801	1284	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266693	41266693	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	69	402	0	ENST00000349496.5:c.490G>A	p.Asp164Asn	p.D164N	ENST00000349496	NM_001904.3	164	Gac/Aac	4/15	1	2	FACETS	0.602	0.524	0.686	0.602	0.524	0.686	SUBCLONAL	1	TRUE	1	0.377125639374292	2		402	608	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057690	180057690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767952525	NA	P-0054675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	460	833	1	ENST00000261937.6:c.265G>A	p.Ala89Thr	p.A89T	ENST00000261937	NM_182925.4	89	Gcc/Acc	3/30	0.377125639374292	2	FACETS	0.972	0.929	1	0.972	0.929	1	CLONAL	2	TRUE	0	0.377125639374292	2		834	1255	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	56	714	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.849	0.732	0.974	0.849	0.732	0.974	CLONAL	1	TRUE	1	0.425677831548982	2		715	310	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0054676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	77	433	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.425677831548982	2		434	287	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444688	78444688	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0054676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	144	463	0	ENST00000370768.2:c.1A>G	p.Met1?	p.M1?	ENST00000370768	NM_003902.3	1	Atg/Gtg	1/20	0.425677831548982	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.425677831548982	1		463	470	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101427	27101430	+	frameshift_variant	Frame_Shift_Del	DEL	CTAA	CTAA	-	novel	NA	P-0054676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	44	579	0	ENST00000324856.7:c.4712_4715del	p.Asn1571ThrfsTer40	p.N1571Tfs*40	ENST00000324856	NM_006015.4	1570	tCTAAc/tc	18/20	0.425677831548982	1	FACETS	0.34	0.285	0.401	0.34	0.285	0.401	SUBCLONAL	1	TRUE	0	0.425677831548982	1		579	479	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926599	59926599	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	58	375	0	ENST00000259008.2:c.398C>A	p.Thr133Asn	p.T133N	ENST00000259008	NM_032043.2	133	aCt/aAt	5/20	1	2	FACETS	0.946	0.82	1	0.946	0.82	1	CLONAL	1	TRUE	1	0.425677831548982	2		375	288	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791836	42791836	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	178	761	1	ENST00000575354.2:c.722T>C	p.Leu241Pro	p.L241P	ENST00000575354	NM_015125.3	241	cTg/cCg	5/20	0.425677831548982	1	FACETS	0.962	0.89	1	0.962	0.89	1	CLONAL	1	TRUE	0	0.425677831548982	1		762	684	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0054788-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	400	900	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	0.730467693739029	1	FACETS	0.943	0.909	0.978	0.943	0.909	0.978	CLONAL	1	TRUE	0	0.797712660132693	1		900	639	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920173	76920173	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054788-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	248	493	1	ENST00000373344.5:c.3904del	p.Arg1302GlufsTer44	p.R1302Efs*44	ENST00000373344	NM_000489.3	1302	Aga/ga	11/35	1	2	FACETS	0.961	0.905	1	0.961	0.905	1	CLONAL	1	TRUE	1	0.797712660132693	2		494	647	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17949122	17949122	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054788-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	445	826	0	ENST00000458235.1:c.1519C>A	p.Gln507Lys	p.Q507K	ENST00000458235	NM_000215.3	507	Cag/Aag	11/24	1	2	FACETS	0.984	0.941	1	0.984	0.941	1	CLONAL	1	TRUE	1	0.797712660132693	2		826	1134	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161398	55161398	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752633017	NA	P-0054788-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	58	516	0	ENST00000257290.5:c.3229G>A	p.Gly1077Ser	p.G1077S	ENST00000257290	NM_006206.4	1077	Ggc/Agc	23/23	1	2	FACETS	0.213	0.182	0.246	0.213	0.182	0.246	SUBCLONAL	1	TRUE	1	0.797712660132693	2		516	684	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404460	70404460	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054788-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	35	285	0	ENST00000373644.4:c.1974T>G	p.Asp658Glu	p.D658E	ENST00000373644	NM_030625.2	658	gaT/gaG	4/12	0.797712660132693	1	FACETS	0.209	0.172	0.25	0.209	0.172	0.25	SUBCLONAL	1	TRUE	0	0.797712660132693	1		285	252	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027825	48027825	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054788-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	40	300	0	ENST00000234420.5:c.2706del	p.Pro903LeufsTer3	p.P903Lfs*3	ENST00000234420	NM_000179.2	901	cgT/cg	4/10	0.797712660132693	1	FACETS	0.193	0.161	0.229	0.193	0.161	0.229	SUBCLONAL	1	TRUE	0	0.797712660132693	1		300	312	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027887	48028208	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAGACTGGACTTATTACTCCCAAAGCAGGCTTTGACTCTGATTATGACCAAGCTCTTGCTGACATAAGAGAAAATGAACAGAGCCTCCTGGAATACCTAGAGAAACAGCGCAACAGAATTGGCTGTAGGACCATAGTCTATTGGGGGATTGGTAGGAACCGTTACCAGCTGGAAATTCCTGAGAATTTCACCACTCGCAATTTGCCAGAAGAATACGAGTTGAAATCTACCAAGAAGGGCTGTAAACGATACTGGACCAAAACTATTGAAAAGAAGTTGGCTAATCTCATAAATGCTGAAGAACGGAGGGATGTATCATT	GAAAGACTGGACTTATTACTCCCAAAGCAGGCTTTGACTCTGATTATGACCAAGCTCTTGCTGACATAAGAGAAAATGAACAGAGCCTCCTGGAATACCTAGAGAAACAGCGCAACAGAATTGGCTGTAGGACCATAGTCTATTGGGGGATTGGTAGGAACCGTTACCAGCTGGAAATTCCTGAGAATTTCACCACTCGCAATTTGCCAGAAGAATACGAGTTGAAATCTACCAAGAAGGGCTGTAAACGATACTGGACCAAAACTATTGAAAAGAAGTTGGCTAATCTCATAAATGCTGAAGAACGGAGGGATGTATCATT	-	novel	NA	P-0054788-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	45	305	0	ENST00000234420.5:c.2768_3089del	p.Lys923ArgfsTer22	p.K923Rfs*22	ENST00000234420	NM_000179.2	922	cGAAAGACTGGACTTATTACTCCCAAAGCAGGCTTTGACTCTGATTATGACCAAGCTCTTGCTGACATAAGAGAAAATGAACAGAGCCTCCTGGAATACCTAGAGAAACAGCGCAACAGAATTGGCTGTAGGACCATAGTCTATTGGGGGATTGGTAGGAACCGTTACCAGCTGGAAATTCCTGAGAATTTCACCACTCGCAATTTGCCAGAAGAATACGAGTTGAAATCTACCAAGAAGGGCTGTAAACGATACTGGACCAAAACTATTGAAAAGAAGTTGGCTAATCTCATAAATGCTGAAGAACGGAGGGATGTATCATTg/cg	4/10	0.797712660132693	1	FACETS	0.206	0.173	0.241	0.206	0.173	0.241	SUBCLONAL	1	TRUE	0	0.797712660132693	1		305	330	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87338581	87338581	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054788-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	295	642	0	ENST00000277120.3:c.677C>G	p.Pro226Arg	p.P226R	ENST00000277120		226	cCt/cGt	7/19	1	2	FACETS	0.893	0.844	0.943	0.893	0.844	0.943	CLONAL	1	TRUE	1	0.797712660132693	2		642	828	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0054907-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	189	599	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.325040000854166	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.325040000854166	1		599	911	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0054907-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	44	452	0	ENST00000311936.3:c.34_35delinsCT	p.Gly12Leu	p.G12L	ENST00000311936	NM_004985.3	12	GGt/CTt	2/5	1	2	FACETS	0.771	0.649	0.906	0.771	0.649	0.906	CLONAL	1	TRUE	1	0.325040000854166	2		452	351	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	53	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.89	0.761	1	0.89	0.761	1	CLONAL	1	TRUE	1	0.299167489765748	2		485	398	SUCCESS
MET	4233	MSKCC	GRCh37	7	116399501	116399501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	82	508	0	ENST00000397752.3:c.2321G>A	p.Arg774Lys	p.R774K	ENST00000397752	NM_000245.2	774	aGa/aAa	10/21	1	2	FACETS	0.967	0.854	1	0.967	0.854	1	CLONAL	1	TRUE	1	0.299167489765748	2		508	567	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0055027-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	69	367	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.907	1	1	0.983	1	CLONAL	2	TRUE	1	0.243212664370697	2		367	274	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0055027-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	112	597	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.243212664370697	1	FACETS	1	0.972	1	1	0.99	1	CLONAL	2	TRUE	0	0.243212664370697	1		598	344	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591890	48591907	+	inframe_deletion	In_Frame_Del	DEL	TGGATACGTGGACCCTTC	TGGATACGTGGACCCTTC	-	novel	NA	P-0055027-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	88	423	0	ENST00000342988.3:c.1057_1074del	p.Tyr353_Gly358del	p.Y353_G358del	ENST00000342988	NM_005359.5	351	gaTGGATACGTGGACCCTTCt/gat	9/12	0.243212664370697	1	FACETS	1	0.972	1	1	0.988	1	CLONAL	2	TRUE	0	0.243212664370697	1		423	255	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0055049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	133	375	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	0.226626016840147	2	FACETS	0.82	0.748	0.895	0.82	0.748	0.895	CLONAL	2	FALSE	0	0.281637315954937	2		375	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579327	7579328	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	301	799	0	ENST00000269305.4:c.359dup	p.Ser121ValfsTer28	p.S121Vfs*28	ENST00000269305	NM_001126112.2	120	aag/aaAg	4/11	0.271056487230458	2	FACETS	0.957	0.901	1	0.957	0.901	1	CLONAL	2	FALSE	0	0.281637315954937	2		799	1117	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	200	488	4	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	0.918	0.858	0.978	0.918	0.858	0.978	CLONAL	1	TRUE	1	0.84	2		492	519	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	326	331	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.896	0.866	0.925	1	0.997	1	CLONAL	2	TRUE	1	0.84	2		331	433	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	325	582	2	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.84	2		584	644	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	223	812	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.953	0.895	1	0.953	0.895	1	CLONAL	1	TRUE	1	0.84	2		812	557	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850705	63850705	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs201178069	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	131	423	0	ENST00000279873.7:c.1489del	p.Ile497Ter	p.I497*	ENST00000279873	NM_032199.2	495	Aaa/aa	10/10	1	2	FACETS	0.864	0.793	0.936	0.864	0.793	0.936	CLONAL	1	TRUE	1	0.84	2		423	361	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	131	240	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.926	0.851	1	0.926	0.851	1	CLONAL	1	TRUE	1	0.84	2		241	337	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434367	121434367	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	244	795	5	ENST00000257555.6:c.1136del	p.Pro379LeufsTer5	p.P379Lfs*5	ENST00000257555		377	ctC/ct	6/10	1	2	FACETS	0.978	0.921	1	0.978	0.921	1	CLONAL	1	TRUE	1	0.84	2		800	594	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101267	27101268	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	222	444	0	ENST00000324856.7:c.4555dup	p.Gln1519ProfsTer13	p.Q1519Pfs*13	ENST00000324856	NM_006015.4	1517	gcc/gCcc	18/20	1	2	FACETS	0.952	0.894	1	0.952	0.894	1	CLONAL	1	TRUE	1	0.84	2		444	555	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660469	67660469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	184	394	1	ENST00000264010.4:c.1369C>T	p.Arg457Ter	p.R457*	ENST00000264010	NM_006565.3	457	Cga/Tga	8/12	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.84	2		395	437	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	207	565	4	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.84	2		569	490	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797278	42797278	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs968289754	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	215	786	1	ENST00000575354.2:c.3640C>T	p.Arg1214Ter	p.R1214*	ENST00000575354	NM_015125.3	1214	Cga/Tga	15/20	1	2	FACETS	0.943	0.884	1	0.943	0.884	1	CLONAL	1	TRUE	1	0.84	2		787	543	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720712	89720712	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	47	133	0	ENST00000371953.3:c.867del	p.Val290Ter	p.V290*	ENST00000371953	NM_000314.4	288	gAa/ga	8/9	1	2	FACETS	0.741	0.638	0.85	0.741	0.638	0.85	SUBCLONAL	1	TRUE	1	0.84	2		133	151	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143009	47143010	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	189	535	0	ENST00000409792.3:c.4953dup	p.Thr1652TyrfsTer14	p.T1652Yfs*14	ENST00000409792	NM_014159.6	1651	-/T	8/21	1	2	FACETS	0.775	0.72	0.83	0.775	0.72	0.83	SUBCLONAL	1	TRUE	1	0.84	2		535	581	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711908	89711910	+	inframe_deletion	In_Frame_Del	DEL	TAT	TAT	-	rs587780711	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	97	511	0	ENST00000371953.3:c.532_534del	p.Tyr178del	p.Y178del	ENST00000371953	NM_000314.4	176	TAT/-	6/9	1	2	FACETS	0.567	0.509	0.629	0.567	0.509	0.629	SUBCLONAL	1	TRUE	1	0.84	2		511	407	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247516	123247516	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519795	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	248	500	1	ENST00000358487.5:c.1975A>G	p.Lys659Glu	p.K659E	ENST00000358487	NM_000141.4	659	Aag/Gag	14/18	1	2	FACETS	0.948	0.893	1	0.948	0.893	1	CLONAL	1	TRUE	1	0.84	2		501	623	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466040	69466040	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	235	747	1	ENST00000227507.2:c.878T>A	p.Val293Glu	p.V293E	ENST00000227507	NM_053056.2	293	gTg/gAg	5/5	1	2	FACETS	0.873	0.82	0.927	0.873	0.82	0.927	CLONAL	1	TRUE	1	0.84	2		748	641	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	41	1159	0	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	0.129	0.106	0.153	0.129	0.106	0.153	SUBCLONAL	1	TRUE	1	0.84	2		1159	759	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626462	12626462	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs532786413	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	146	446	2	ENST00000251849.4:c.1687C>T	p.Arg563Ter	p.R563*	ENST00000251849	NM_002880.3	563	Cga/Tga	16/17	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.84	2		448	333	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644874	67644874	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	264	562	0	ENST00000264010.4:c.143del	p.Gly48ValfsTer14	p.G48Vfs*14	ENST00000264010	NM_006565.3	47	Ggg/gg	3/12	1	2	FACETS	0.972	0.917	1	0.972	0.917	1	CLONAL	1	TRUE	1	0.84	2		562	647	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797165	42797165	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	287	861	3	ENST00000575354.2:c.3532del	p.Gln1178ArgfsTer3	p.Q1178Rfs*3	ENST00000575354	NM_015125.3	1176	gCc/gc	15/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.84	2		864	681	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176710827	176710827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587784176	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	191	527	0	ENST00000439151.2:c.6049C>T	p.Arg2017Trp	p.R2017W	ENST00000439151	NM_022455.4	2017	Cgg/Tgg	20/23	1	2	FACETS	0.85	0.792	0.909	0.85	0.792	0.909	CLONAL	1	TRUE	1	0.84	2		527	535	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138924	64138924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1268525057	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	154	372	1	ENST00000334205.4:c.2291G>A	p.Arg764Gln	p.R764Q	ENST00000334205	NM_003942.2	764	cGa/cAa	17/17	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.84	2		373	363	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074276	8074276	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	234	476	0	ENST00000377482.5:c.383del	p.Pro128LeufsTer3	p.P128Lfs*3	ENST00000377482	NM_018948.3	128	cCt/ct	4/4	1	2	FACETS	0.976	0.918	1	0.976	0.918	1	CLONAL	1	TRUE	1	0.84	2		476	571	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023515	27023530	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCAACCACCAGTAC	CCCCAACCACCAGTAC	-	novel	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	191	529	0	ENST00000324856.7:c.621_636del	p.Phe207LeufsTer20	p.F207Lfs*20	ENST00000324856	NM_006015.4	207	ttCCCCAACCACCAGTAC/tt	1/20	1	2	FACETS	0.943	0.881	1	0.943	0.881	1	CLONAL	1	TRUE	1	0.84	2		529	482	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619216	43619216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777007074	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	245	640	1	ENST00000355710.3:c.2899G>A	p.Gly967Ser	p.G967S	ENST00000355710	NM_020975.4	967	Ggc/Agc	17/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.84	2		641	576	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620020	21620020	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	313	691	1	ENST00000382592.4:c.146C>T	p.Ala49Val	p.A49V	ENST00000382592	NM_014572.2	49	gCc/gTc	2/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.84	2		692	699	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103520608	103520608	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs886044319	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	78	227	0	ENST00000355739.4:c.2678+1G>A		p.X893_splice	ENST00000355739	NM_000123.3	893			1	2	FACETS	0.794	0.708	0.882	0.794	0.708	0.882	SUBCLONAL	1	TRUE	1	0.84	2		227	234	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636777	2636777	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	244	681	2	ENST00000342085.4:c.1226G>A	p.Gly409Asp	p.G409D	ENST00000342085	NM_002613.4	409	gGc/gAc	11/14	1	2	FACETS	0.906	0.852	0.961	0.906	0.852	0.961	CLONAL	1	TRUE	1	0.84	2		683	641	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550557	29550557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	23	263	2	ENST00000356175.3:c.1817G>A	p.Cys606Tyr	p.C606Y	ENST00000356175	NM_000267.3	606	tGc/tAc	16/57	1	2	FACETS	0.185	0.144	0.232	0.185	0.144	0.232	SUBCLONAL	1	TRUE	1	0.84	2		265	296	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272128	18272128	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1473370099	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	18	39	0	ENST00000222254.8:c.638C>T	p.Thr213Met	p.T213M	ENST00000222254	NM_005027.3	213	aCg/aTg	6/16	1	2	FACETS	0.794	0.621	0.98	0.794	0.621	0.98	CLONAL	1	TRUE	1	0.84	2		39	54	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219727	36219727	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	268	803	0	ENST00000222270.7:c.4624C>T	p.Gln1542Ter	p.Q1542*	ENST00000222270	NM_014727.1	1542	Cag/Tag	20/37	1	2	FACETS	0.901	0.85	0.953	0.901	0.85	0.953	CLONAL	1	TRUE	1	0.84	2		803	708	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62309644	62309644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	70	665	0	ENST00000360203.5:c.982G>A	p.Ala328Thr	p.A328T	ENST00000360203	NM_001283009.1	328	Gcc/Acc	12/35	1	2	FACETS	0.277	0.241	0.315	0.277	0.241	0.315	SUBCLONAL	1	TRUE	1	0.84	2		665	602	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71050166	71050166	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	177	401	0	ENST00000318789.4:c.1019A>G	p.Gln340Arg	p.Q340R	ENST00000318789	NM_032682.5	340	cAa/cGa	13/21	1	2	FACETS	0.947	0.882	1	0.947	0.882	1	CLONAL	1	TRUE	1	0.84	2		401	445	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274740	142274740	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757500301	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	118	349	14	ENST00000350721.4:c.2320del	p.Ile774TyrfsTer5	p.I774Yfs*5	ENST00000350721	NM_001184.3	774	Ata/ta	10/47	1	2	FACETS	0.93	0.852	1	0.93	0.852	1	CLONAL	1	TRUE	1	0.84	2		363	302	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196529	106196529	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	156	439	1	ENST00000380013.4:c.4865del	p.Leu1622Ter	p.L1622*	ENST00000380013	NM_001127208.2	1621	cTt/ct	11/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.84	2		440	328	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925324	131925324	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	37	98	0	ENST00000265335.6:c.1247A>C	p.Asn416Thr	p.N416T	ENST00000265335		416	aAt/aCt	9/25	1	2	FACETS	0.937	0.798	1	0.937	0.798	1	CLONAL	1	TRUE	1	0.84	2		98	94	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176683996	176683996	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	239	637	0	ENST00000439151.2:c.4813del	p.Arg1605GlyfsTer37	p.R1605Gfs*37	ENST00000439151	NM_022455.4	1604	Aaa/aa	13/23	1	2	FACETS	0.882	0.829	0.936	0.882	0.829	0.936	CLONAL	1	TRUE	1	0.84	2		637	645	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117650538	117650538	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	41	658	1	ENST00000368508.3:c.5320G>C	p.Ala1774Pro	p.A1774P	ENST00000368508	NM_002944.2	1774	Gct/Cct	32/43	1	2	FACETS	0.193	0.16	0.229	0.193	0.16	0.229	SUBCLONAL	1	TRUE	1	0.84	2		659	507	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841898	151841898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	195	367	0	ENST00000262189.6:c.14243C>T	p.Ala4748Val	p.A4748V	ENST00000262189	NM_170606.2	4748	gCa/gTa	55/59	0.0873242433916375	3	FACETS	1	0.99	1	0.687	0.642	0.732	INDETERMINATE	1	TRUE	1	0.84	3		367	480	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277159	38277159	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	265	760	0	ENST00000425967.3:c.1269del	p.Ser424ArgfsTer7	p.S424Rfs*7	ENST00000425967	NM_001174067.1	423	ggG/gg	10/19	1	2	FACETS	0.927	0.874	0.98	0.927	0.874	0.98	CLONAL	1	TRUE	1	0.84	2		760	681	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992996	68992996	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	154	360	0	ENST00000288368.4:c.1801G>T	p.Gly601Cys	p.G601C	ENST00000288368	NM_024870.2	601	Ggc/Tgc	17/40	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.84	2		360	364	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722761	49722761	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs62262682	NA	P-0055135-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	18	33	0	ENST00000449682.2:c.1478G>T	p.Arg493Leu	p.R493L	ENST00000449682	NM_020998.3	493	cGt/cTt	13/18	NA	3	FACETS	0.846	0.663	1	1	0.893	1	INDETERMINATE	3	TRUE	1	0.309019286351316	3		33	53	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202412	138202412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766108588	NA	P-0055135-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	131	723	0	ENST00000237289.4:c.2329G>A	p.Gly777Ser	p.G777S	ENST00000237289	NM_001270507.1	777	Ggc/Agc	9/9	0.197618944974193	4	FACETS	0.996	0.902	1			1	CLONAL	1	TRUE	NA	0.309019286351316	4		723	1114	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715678	30715678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039551	NA	P-0055135-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	114	530	1	ENST00000295754.5:c.1336G>A	p.Asp446Asn	p.D446N	ENST00000295754	NM_003242.5	446	Gat/Aat	5/7	1	2	FACETS	0.988	0.89	1	0.988	0.89	1	CLONAL	1	TRUE	1	0.309019286351316	2		531	747	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860657	151860657	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055135-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	165	797	0	ENST00000262189.6:c.10005G>A	p.Trp3335Ter	p.W3335*	ENST00000262189	NM_170606.2	3335	tgG/tgA	43/59	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.309019286351316	2		797	980	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0055265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	201	509	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.74240910438893	2		510	492	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0055265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	292	323	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.74240910438893	2		323	764	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445514	49445514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356632640	NA	P-0055265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	338	543	2	ENST00000301067.7:c.1952C>T	p.Ser651Leu	p.S651L	ENST00000301067	NM_003482.3	651	tCg/tTg	10/54	1	2	FACETS	0.948	0.899	0.998	0.948	0.899	0.998	CLONAL	1	TRUE	1	0.74240910438893	2		545	960	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729163	66729163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516792	NA	P-0055265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	407	594	1	ENST00000307102.5:c.371C>T	p.Pro124Leu	p.P124L	ENST00000307102	NM_002755.3	124	cCg/cTg	3/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.74240910438893	2		595	1072	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141518	11141519	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0055265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	490	712	2	ENST00000358026.2:c.3495_3496delinsTA	p.Gln1166Lys	p.Q1166K	ENST00000358026	NM_001128849.1	1165	ctCCag/ctTAag	25/36	0.1761333862266	2	FACETS	1	0.996	1	0.652	0.626	0.677	INDETERMINATE	1	TRUE	0	0.74240910438893	2		714	1013	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971187	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	323	462	1	ENST00000304494.5:c.171_172delinsTT	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	57	gcCCga/gcTTga	2/3	0.74240910438893	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.74240910438893	1		463	517	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0055265-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	130	509	1				ENST00000310581	NM_198253.2	-/1132			0.718573773193936	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.718573773193936	1		510	204	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0055265-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	220	323	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.718573773193936	2		323	599	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445514	49445514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356632640	NA	P-0055265-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	174	543	2	ENST00000301067.7:c.1952C>T	p.Ser651Leu	p.S651L	ENST00000301067	NM_003482.3	651	tCg/tTg	10/54	1	2	FACETS	0.895	0.83	0.962	0.895	0.83	0.962	CLONAL	1	TRUE	1	0.718573773193936	2		545	541	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729163	66729163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516792	NA	P-0055265-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	244	594	1	ENST00000307102.5:c.371C>T	p.Pro124Leu	p.P124L	ENST00000307102	NM_002755.3	124	cCg/cTg	3/11	1	2	FACETS	0.897	0.842	0.954	0.897	0.842	0.954	CLONAL	1	TRUE	1	0.718573773193936	2		595	757	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141518	11141519	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0055265-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	260	712	2	ENST00000358026.2:c.3495_3496delinsTA	p.Gln1166Lys	p.Q1166K	ENST00000358026	NM_001128849.1	1165	ctCCag/ctTAag	25/36	1	2	FACETS	0.993	0.935	1	0.993	0.935	1	CLONAL	1	TRUE	1	0.718573773193936	2		714	729	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971187	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055265-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	198	462	1	ENST00000304494.5:c.171_172delinsTT	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	57	gcCCga/gcTTga	2/3	0.718573773193936	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.718573773193936	1		463	313	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0055307-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	57	367	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.982	0.845	1	0.982	0.845	1	CLONAL	1	TRUE	1	0.276268485082217	2		367	420	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0055307-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	151	648	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	0.276268485082217	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.276268485082217	1		648	873	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578515	7578515	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1212996409	NA	P-0055307-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	139	615	1	ENST00000269305.4:c.415A>T	p.Lys139Ter	p.K139*	ENST00000269305	NM_001126112.2	139	Aag/Tag	5/11	0.276268485082217	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.276268485082217	1		616	788	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701263	43701263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1157211964	NA	P-0055307-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	56	549	0	ENST00000382044.4:c.5432C>T	p.Ala1811Val	p.A1811V	ENST00000382044	NM_001141980.1	1811	gCg/gTg	26/28	1	2	FACETS	0.541	0.463	0.627	0.541	0.463	0.627	SUBCLONAL	1	TRUE	1	0.276268485082217	2		549	749	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398299	25398299	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055307-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	53	234	0	ENST00000311936.3:c.20T>C	p.Val7Ala	p.V7A	ENST00000311936	NM_004985.3	7	gTg/gCg	2/5	1	2	FACETS	0.976	0.835	1	0.976	0.835	1	CLONAL	1	TRUE	1	0.276268485082217	2		234	393	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880219	37880220	+	missense_variant	Missense_Mutation	DNP	TT	TT	CC	rs121913469	NA	P-0055318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	159	616	0	ENST00000269571.5:c.2263_2264delinsCC	p.Leu755Pro	p.L755P	ENST00000269571		755	TTg/CCg	19/27	0.234491215199651	3	FACETS	0.962	0.883	1	0.962	0.883	1	CLONAL	2	TRUE	1	0.242330331787995	3		616	765	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880219	37880220	+	missense_variant	Missense_Mutation	DNP	TT	TT	CC	rs121913469	NA	P-0055318-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	350	616	0	ENST00000269571.5:c.2263_2264delinsCC	p.Leu755Pro	p.L755P	ENST00000269571		755	TTg/CCg	19/27	0.704704091863278	3	FACETS	0.849	0.809	0.89	0.849	0.809	0.89	CLONAL	2	TRUE	1	0.708084898795647	3		616	788	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143129653	143129653	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055318-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	49	446	0	ENST00000262992.4:c.997G>T	p.Gly333Ter	p.G333*	ENST00000262992	NM_001101669.1	333	Gga/Tga	12/24	0.365612516154678	3	FACETS	0.444	0.377	0.518	0.148	0.125	0.173	INDETERMINATE	1	TRUE	0	0.708084898795647	3		446	422	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10286249	10286250	+	missense_variant	Missense_Mutation	DNP	CG	CG	AT	novel	NA	P-0055318-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	132	626	2	ENST00000340748.4:c.566_567delinsAT	p.Ser189Tyr	p.S189Y	ENST00000340748		189	tCG/tAT	6/40	1	2	FACETS	0.558	0.508	0.611	0.558	0.508	0.611	SUBCLONAL	1	TRUE	1	0.708084898795647	2		628	668	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934268	39934268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055318-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	116	676	0	ENST00000378444.4:c.331G>A	p.Gly111Ser	p.G111S	ENST00000378444	NM_001123385.1	111	Ggc/Agc	4/15	0.476046799298094	3	FACETS	0.545	0.491	0.602	0.273	0.245	0.301	SUBCLONAL	1	TRUE	1	0.708084898795647	3		676	814	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6213787	6213787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747024697	NA	P-0055342-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	530	705	1	ENST00000252674.7:c.1429G>A	p.Glu477Lys	p.E477K	ENST00000252674	NM_005934.3	477	Gag/Aag	10/12	0.564806191032466	4	FACETS	0.856	0.827	0.884	0.856	0.827	0.884	CLONAL	3	TRUE	1	0.870893030787946	4		706	887	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0055399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	224	393	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.769599108912447	2	FACETS	0.897	0.856	0.936	0.897	0.856	0.936	CLONAL	2	TRUE	0	0.771092762714079	2		393	324	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274685	123274685	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	162	577	0	ENST00000358487.5:c.1233C>G	p.Ser411Arg	p.S411R	ENST00000358487	NM_000141.4	411	agC/agG	9/18	1	2	FACETS	0.479	0.439	0.52	0.479	0.439	0.52	SUBCLONAL	1	TRUE	1	0.771092762714079	2		577	877	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	272	173	0	ENST00000256196.4:c.68G>T	p.Gly23Val	p.G23V	ENST00000256196		23	gGc/gTc	1/6	0.767699847354044	2	FACETS	0.933	0.897	0.968	0.933	0.897	0.968	CLONAL	2	TRUE	0	0.771092762714079	2		173	378	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175836	24175837	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555881563	NA	P-0055399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	594	548	0	ENST00000263121.7:c.1066_1067del	p.Leu356AspfsTer4	p.L356Dfs*4	ENST00000263121	NM_003073.3	355	aCT/a	8/9	0.617199172440949	2	FACETS	0.881	0.857	0.906	0.881	0.857	0.906	CLONAL	2	TRUE	0	0.771092762714079	2		548	874	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442492	52442492	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	151	381	0	ENST00000460680.1:c.253C>G	p.Gln85Glu	p.Q85E	ENST00000460680	NM_004656.3	85	Cag/Gag	4/17	0.589379236932433	3	FACETS	0.659	0.602	0.717	0.329	0.301	0.359	SUBCLONAL	1	TRUE	1	0.771092762714079	3		381	824	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984117	2984117	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	193	490	0	ENST00000396946.4:c.413T>G	p.Leu138Arg	p.L138R	ENST00000396946	NM_032415.4	138	cTg/cGg	5/25	1	2	FACETS	0.601	0.557	0.647	0.601	0.557	0.647	SUBCLONAL	1	TRUE	1	0.771092762714079	2		490	833	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913226	39913228	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0055399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	49	246	0	ENST00000378444.4:c.4887_4889del	p.Asp1631del	p.D1631del	ENST00000378444	NM_001123385.1	1629	gaTGAc/gac	14/15	1	1	FACETS	0.173	0.146	0.202	0.173	0.146	0.202	SUBCLONAL	1	TRUE	0	0.771092762714079	1		246	451	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	167	949	18	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.525	0.483	0.569	0.525	0.483	0.569	SUBCLONAL	1	TRUE	1	0.803542599216413	2		967	791	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	65	331	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.337	0.293	0.385	0.337	0.293	0.385	SUBCLONAL	1	TRUE	1	0.803542599216413	2		331	480	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	96	309	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.573	0.514	0.635	0.573	0.514	0.635	SUBCLONAL	1	TRUE	1	0.803542599216413	2		309	417	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	119	444	0	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	1	2	FACETS	0.614	0.558	0.674	0.614	0.558	0.674	SUBCLONAL	1	TRUE	1	0.803542599216413	2		444	482	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	182	335	3	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.651	0.602	0.701	0.651	0.602	0.701	SUBCLONAL	1	TRUE	1	0.803542599216413	2		338	696	SUCCESS
AR	367	MSKCC	GRCh37	X	66766357	66766374	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGCGGCGGCGGC	GGCGGCGGCGGCGGCGGC	-	rs746853821	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	58	125	0	ENST00000374690.3:c.1403_1420del	p.Gly468_Gly473del	p.G468_G473del	ENST00000374690	NM_000044.3	457	GGCGGCGGCGGCGGCGGC/-	1/8	0.434095896509643	3	FACETS	0.71	0.615	0.812	0.355	0.307	0.406	INDETERMINATE	1	TRUE	1	0.803542599216413	3		125	285	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	206	756	4	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.534	0.495	0.574	0.534	0.495	0.574	SUBCLONAL	1	TRUE	1	0.803542599216413	2		760	961	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46543215	46543215	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	151	468	1	ENST00000262741.5:c.286del	p.Met96CysfsTer7	p.M96Cfs*7	ENST00000262741	NM_003629.3	96	Atg/tg	3/10	1	2	FACETS	0.598	0.548	0.649	0.598	0.548	0.649	SUBCLONAL	1	TRUE	1	0.803542599216413	2		469	629	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	297	471	4	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.803542599216413	2		475	672	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	183	778	11	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	0.464	0.428	0.502	0.464	0.428	0.502	SUBCLONAL	1	TRUE	1	0.803542599216413	2		789	981	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430775	78430775	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	144	472	0	ENST00000370768.2:c.614del	p.Gly205GlufsTer17	p.G205Efs*17	ENST00000370768	NM_003902.3	205	gGa/ga	8/20	1	2	FACETS	0.575	0.526	0.626	0.575	0.526	0.626	SUBCLONAL	1	TRUE	1	0.803542599216413	2		472	623	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097624	11097625	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1165714406	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	211	819	1	ENST00000358026.2:c.810dup	p.Gly271ArgfsTer16	p.G271Rfs*16	ENST00000358026	NM_001128849.1	268	-/C	5/36	1	2	FACETS	0.508	0.471	0.546	0.508	0.471	0.546	SUBCLONAL	1	TRUE	1	0.803542599216413	2		820	1034	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435128	110435129	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs772322568	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	44	525	0	ENST00000375856.3:c.3272dup	p.Lys1092GlufsTer233	p.K1092Efs*233	ENST00000375856	NM_003749.2	1091	ccg/ccCg	1/2	1	2	FACETS	0.14	0.117	0.166	0.14	0.117	0.166	SUBCLONAL	1	TRUE	1	0.803542599216413	2		525	781	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916726	178916726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772110575	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	68	326	1	ENST00000263967.3:c.113G>A	p.Arg38His	p.R38H	ENST00000263967	NM_006218.2	38	cGt/cAt	2/21	1	2	FACETS	0.548	0.48	0.619	0.548	0.48	0.619	SUBCLONAL	1	TRUE	1	0.803542599216413	2		327	309	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296203	15296204	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CA	CA	-	novel	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	227	758	0	ENST00000263388.2:c.2160_2161del	p.Cys720Ter	p.C720*	ENST00000263388	NM_000435.2	720	tgTGag/tgag	14/33	1	2	FACETS	0.573	0.534	0.613	0.573	0.534	0.613	SUBCLONAL	1	TRUE	1	0.803542599216413	2		758	986	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319854	8319854	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	100	382	0	ENST00000356435.5:c.5647C>T	p.Arg1883Ter	p.R1883*	ENST00000356435		1883	Cga/Tga	34/35	1	2	FACETS	0.521	0.467	0.577	0.521	0.467	0.577	SUBCLONAL	1	TRUE	1	0.803542599216413	2		382	478	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444378	49444378	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	210	673	2	ENST00000301067.7:c.2993del	p.Pro998LeufsTer2	p.P998Lfs*2	ENST00000301067	NM_003482.3	998	cCt/ct	11/54	1	2	FACETS	0.571	0.53	0.612	0.571	0.53	0.612	SUBCLONAL	1	TRUE	1	0.803542599216413	2		675	916	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942558	71942559	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	170	433	0	ENST00000298229.2:c.1516_1517del	p.Trp506GlufsTer45	p.W506Efs*45	ENST00000298229	NM_001567.3	505	cTG/c	13/28	1	2	FACETS	0.659	0.608	0.711	0.659	0.608	0.711	SUBCLONAL	1	TRUE	1	0.803542599216413	2		433	642	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519337	176519337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758837002	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	175	564	0	ENST00000292408.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000292408	NM_213647.1	248	cGg/cAg	7/18	1	2	FACETS	0.607	0.56	0.655	0.607	0.56	0.655	SUBCLONAL	1	TRUE	1	0.803542599216413	2		564	718	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829584	72829585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	52	631	0	ENST00000268489.5:c.6996dup	p.Cys2333MetfsTer2	p.C2333Mfs*2	ENST00000268489	NM_006885.3	2332	-/A	9/10	1	2	FACETS	0.17	0.144	0.199	0.17	0.144	0.199	SUBCLONAL	1	TRUE	1	0.803542599216413	2		631	760	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023715	27023716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	99	352	0	ENST00000324856.7:c.827dup	p.Gly277ArgfsTer123	p.G277Rfs*123	ENST00000324856	NM_006015.4	274	atg/atGg	1/20	1	2	FACETS	0.459	0.411	0.51	0.459	0.411	0.51	SUBCLONAL	1	TRUE	1	0.803542599216413	2		352	537	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092977	27092978	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	34	355	0	ENST00000324856.7:c.2910dup	p.Gly971TrpfsTer36	p.G971Wfs*36	ENST00000324856	NM_006015.4	970	ctt/cTtt	10/20	1	2	FACETS	0.175	0.143	0.212	0.175	0.143	0.212	SUBCLONAL	1	TRUE	1	0.803542599216413	2		355	483	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18649065	18649065	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	65	319	0	ENST00000266497.5:c.2744del	p.Asn915ThrfsTer24	p.N915Tfs*24	ENST00000266497		914	Aaa/aa	19/31	1	2	FACETS	0.548	0.479	0.622	0.548	0.479	0.622	SUBCLONAL	1	TRUE	1	0.803542599216413	2		319	295	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396233	396234	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769619638	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	224	848	0	ENST00000262320.3:c.792dup	p.Gly265ArgfsTer20	p.G265Rfs*20	ENST00000262320	NM_003502.3	264	-/C	2/11	1	2	FACETS	0.592	0.552	0.634	0.592	0.552	0.634	SUBCLONAL	1	TRUE	1	0.803542599216413	2		848	941	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609759	81609759	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	151	447	0	ENST00000298171.2:c.1357A>G	p.Met453Val	p.M453V	ENST00000298171	NM_000369.2	453	Atg/Gtg	10/10	1	2	FACETS	0.662	0.608	0.717	0.662	0.608	0.717	SUBCLONAL	1	TRUE	1	0.803542599216413	2		447	568	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408924	41408924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778928297	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	113	425	0	ENST00000373198.4:c.502G>A	p.Val168Ile	p.V168I	ENST00000373198	NM_133170.3	168	Gtc/Atc	4/32	1	2	FACETS	0.507	0.457	0.559	0.507	0.457	0.559	SUBCLONAL	1	TRUE	1	0.803542599216413	2		425	555	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301864	65301864	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	16	217	0	ENST00000342505.4:c.3175del	p.Tyr1059IlefsTer17	p.Y1059Ifs*17	ENST00000342505	NM_002227.2	1059	Tat/at	23/25	1	2	FACETS	0.131	0.096	0.172	0.131	0.096	0.172	SUBCLONAL	1	TRUE	1	0.803542599216413	2		217	304	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115269677	115269677	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	98	468	0	ENST00000438362.2:c.1529G>A	p.Cys510Tyr	p.C510Y	ENST00000438362	NM_001242891.1	510	tGt/tAt	13/20	1	2	FACETS	0.577	0.518	0.639	0.577	0.518	0.639	SUBCLONAL	1	TRUE	1	0.803542599216413	2		468	423	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720684	89720693	+	frameshift_variant	Frame_Shift_Del	DEL	TTCATACCAG	TTCATACCAG	-	novel	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	26	171	0	ENST00000371953.3:c.835_844del	p.Phe279AspfsTer9	p.F279Dfs*9	ENST00000371953	NM_000314.4	279	TTCATACCAGga/ga	8/9	1	2	FACETS	0.341	0.271	0.418	0.341	0.271	0.418	SUBCLONAL	1	TRUE	1	0.803542599216413	2		171	190	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948208	71948209	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	243	799	0	ENST00000298229.2:c.2926_2927dup	p.Pro977HisfsTer155	p.P977Hfs*155	ENST00000298229	NM_001567.3	974	gcc/gCCcc	26/28	1	2	FACETS	0.611	0.571	0.652	0.611	0.571	0.652	SUBCLONAL	1	TRUE	1	0.803542599216413	2		799	990	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136376	2136376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	214	648	3	ENST00000219476.3:c.4845G>A	p.Met1615Ile	p.M1615I	ENST00000219476	NM_000548.3	1615	atG/atA	37/42	1	2	FACETS	0.673	0.626	0.72	0.673	0.626	0.72	SUBCLONAL	1	TRUE	1	0.803542599216413	2		651	792	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917717	29917717	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	181	576	0	ENST00000389048.3:c.951A>T	p.Arg317Ser	p.R317S	ENST00000389048	NM_004304.4	317	agA/agT	3/29	1	2	FACETS	0.613	0.567	0.661	0.613	0.567	0.661	SUBCLONAL	1	TRUE	1	0.803542599216413	2		576	735	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268542	46268544	+	inframe_deletion	In_Frame_Del	DEL	CAG	CAG	-	novel	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	77	319	0	ENST00000371998.3:c.2938_2940del	p.Gln980del	p.Q980del	ENST00000371998		977	CAG/-	15/23	1	2	FACETS	0.531	0.469	0.596	0.531	0.469	0.596	SUBCLONAL	1	TRUE	1	0.803542599216413	2		319	361	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817379	39817379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	162	553	0	ENST00000288319.7:c.184G>A	p.Ala62Thr	p.A62T	ENST00000288319	NM_182918.3	62	Gcc/Acc	2/10	1	2	FACETS	0.574	0.527	0.621	0.574	0.527	0.621	SUBCLONAL	1	TRUE	1	0.803542599216413	2		553	703	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070395	37070395	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	95	284	0	ENST00000231790.2:c.1530G>T	p.Gln510His	p.Q510H	ENST00000231790	NM_000249.3	510	caG/caT	13/19	1	2	FACETS	0.551	0.493	0.612	0.551	0.493	0.612	SUBCLONAL	1	TRUE	1	0.803542599216413	2		284	429	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524446	187524446	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	163	541	1	ENST00000441802.2:c.11234G>A	p.Trp3745Ter	p.W3745*	ENST00000441802	NM_005245.3	3745	tGg/tAg	19/27	1	2	FACETS	0.53	0.487	0.575	0.53	0.487	0.575	SUBCLONAL	1	TRUE	1	0.803542599216413	2		542	765	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557211	187557211	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	140	455	0	ENST00000441802.2:c.4151C>A	p.Pro1384His	p.P1384H	ENST00000441802	NM_005245.3	1384	cCt/cAt	6/27	1	2	FACETS	0.574	0.525	0.626	0.574	0.525	0.626	SUBCLONAL	1	TRUE	1	0.803542599216413	2		455	607	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755518	57755518	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs775154027	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	40	381	0	ENST00000274289.3:c.269A>G	p.Lys90Arg	p.K90R	ENST00000274289	NM_006622.3	90	aAg/aGg	1/14	1	2	FACETS	0.204	0.169	0.243	0.204	0.169	0.243	SUBCLONAL	1	TRUE	1	0.803542599216413	2		381	488	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721820	176721820	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	133	467	0	ENST00000439151.2:c.7451C>A	p.Pro2484Gln	p.P2484Q	ENST00000439151	NM_022455.4	2484	cCa/cAa	23/23	1	2	FACETS	0.519	0.472	0.568	0.519	0.472	0.568	SUBCLONAL	1	TRUE	1	0.803542599216413	2		467	638	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981573	70981573	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	83	888	0	ENST00000276594.2:c.523A>G	p.Ser175Gly	p.S175G	ENST00000276594	NM_024504.3	175	Agc/Ggc	2/8	1	2	FACETS	0.19	0.167	0.215	0.19	0.167	0.215	SUBCLONAL	1	TRUE	1	0.803542599216413	2		888	1085	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929251	44929253	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0055406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	143	662	0	ENST00000377967.4:c.2353_2355del	p.Met785del	p.M785del	ENST00000377967	NM_021140.2	784	tTGAtg/ttg	17/29	0.434095896509643	3	FACETS	0.554	0.505	0.606	0.277	0.252	0.303	INDETERMINATE	1	TRUE	1	0.803542599216413	3		662	900	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	203	339	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.935	0.87	1	0.935	0.87	1	CLONAL	1	TRUE	1	0.610506987441969	2		342	711	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	201	368	0	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.931	0.866	0.998	0.931	0.866	0.998	CLONAL	1	TRUE	1	0.610506987441969	2		368	707	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	85	330	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.610506987441969	2	FACETS	1	0.971	1	0.613	0.552	0.677	CLONAL	1	TRUE	0	0.610506987441969	2		330	227	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914592	32914592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1799954	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	132	737	0	ENST00000380152.3:c.6100C>T	p.Arg2034Cys	p.R2034C	ENST00000380152		2034	Cgt/Tgt	11/27	0.610506987441969	2	FACETS	0.868	0.793	0.946	0.434	0.396	0.473	CLONAL	1	TRUE	0	0.610506987441969	2		737	498	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743993	41743993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	337	1347	1	ENST00000301178.4:c.928G>A	p.Ala310Thr	p.A310T	ENST00000301178	NM_021913.4	310	Gca/Aca	7/20	1	2	FACETS	0.98	0.927	1	0.98	0.927	1	CLONAL	1	TRUE	1	0.610506987441969	2		1348	1127	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736166	204736166	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	162	500	0	ENST00000302823.3:c.529del	p.Tyr177IlefsTer10	p.Y177Ifs*10	ENST00000302823	NM_005214.4	175	Ttt/tt	3/4	1	2	FACETS	0.91	0.839	0.983	0.91	0.839	0.983	CLONAL	1	TRUE	1	0.610506987441969	2		500	583	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097751	27097751	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	178	695	0	ENST00000324856.7:c.3344del	p.Pro1115GlnfsTer46	p.P1115Qfs*46	ENST00000324856	NM_006015.4	1114	Ccc/cc	12/20	1	2	FACETS	0.923	0.854	0.993	0.923	0.854	0.993	CLONAL	1	TRUE	1	0.610506987441969	2		695	632	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	145	504	3	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.644	0.588	0.702	0.644	0.588	0.702	SUBCLONAL	1	TRUE	1	0.610506987441969	2		507	738	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	243	918	0	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.942	0.882	1	0.942	0.882	1	CLONAL	1	TRUE	1	0.610506987441969	2		918	845	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509085	66509085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	76	383	0	ENST00000273854.3:c.242del	p.Asn81MetfsTer24	p.N81Mfs*24	ENST00000273854	NM_004439.5	81	aAt/at	2/18	1	2	FACETS	0.819	0.725	0.918	0.819	0.725	0.918	CLONAL	1	TRUE	1	0.610506987441969	2		383	304	SUCCESS
AR	367	MSKCC	GRCh37	X	66765149	66765151	+	inframe_deletion	In_Frame_Del	DEL	TGC	TGC	-	rs752055010	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	19	251	0	ENST00000374690.3:c.170_172del	p.Leu57del	p.L57del	ENST00000374690	NM_000044.3	54	tTGCtg/ttg	1/8	1	1	FACETS	0.267	0.204	0.34	0.267	0.204	0.34	SUBCLONAL	1	TRUE	0	0.610506987441969	1		251	162	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	114	406	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	0.610506987441969	2	FACETS	1	0.974	1	0.589	0.537	0.642	CLONAL	1	TRUE	0	0.610506987441969	2		406	317	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	330	1003	11	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.610506987441969	2		1014	1072	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521541	8521541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	122	594	0	ENST00000356435.5:c.697C>T	p.Arg233Cys	p.R233C	ENST00000356435		233	Cgt/Tgt	9/35	0.596832167647557	3	FACETS	0.775	0.702	0.852	0.258	0.234	0.284	SUBCLONAL	1	TRUE	0	0.610506987441969	3		594	673	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380283	25380283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913528	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	24	603	0	ENST00000311936.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000311936	NM_004985.3	59	Gca/Aca	3/5	1	2	FACETS	0.147	0.114	0.184	0.147	0.114	0.184	SUBCLONAL	1	TRUE	1	0.610506987441969	2		603	536	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257365	19257366	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	276	1272	0	ENST00000162023.5:c.767dup	p.Glu257ArgfsTer28	p.E257Rfs*28	ENST00000162023		256	cca/ccCa	11/13	1	2	FACETS	0.843	0.792	0.896	0.843	0.792	0.896	CLONAL	1	TRUE	1	0.610506987441969	2		1272	1072	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586503	189586503	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs143591434	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	24	454	1	ENST00000264731.3:c.1127G>A	p.Arg376His	p.R376H	ENST00000264731	NM_003722.4	376	cGc/cAc	8/14	0.610506987441969	2	FACETS	0.168	0.131	0.211	0.084	0.065	0.106	SUBCLONAL	1	TRUE	0	0.610506987441969	2		455	467	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671654	67671655	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	156	710	1	ENST00000264010.4:c.2070dup	p.Glu691ArgfsTer5	p.E691Rfs*5	ENST00000264010	NM_006565.3	688	gta/gtAa	12/12	1	2	FACETS	0.789	0.725	0.855	0.789	0.725	0.855	SUBCLONAL	1	TRUE	1	0.610506987441969	2		711	648	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015040	37015040	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756345939	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	221	861	3	ENST00000358127.4:c.364C>T	p.Arg122Trp	p.R122W	ENST00000358127	NM_001280556.1	122	Cgg/Tgg	3/10	0.596832167647557	3	FACETS	0.981	0.914	1	0.327	0.304	0.351	CLONAL	1	TRUE	0	0.610506987441969	3		864	963	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508557	106508557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	43	591	0	ENST00000359195.3:c.551G>A	p.Arg184His	p.R184H	ENST00000359195	NM_002649.2	184	cGc/cAc	2/11	0.593298347202153	3	FACETS	0.32	0.267	0.379	0.107	0.089	0.127	SUBCLONAL	1	TRUE	0	0.610506987441969	3		591	574	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800902	120800903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748469666	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	300	1152	3	ENST00000257552.2:c.345dup	p.Leu116AlafsTer15	p.L116Afs*15	ENST00000257552	NM_002442.3	115	-/G	6/15	1	2	FACETS	0.818	0.77	0.868	0.818	0.77	0.868	CLONAL	1	TRUE	1	0.610506987441969	2		1155	1201	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502386	186502386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs953593626	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	179	471	0	ENST00000323963.5:c.109G>A	p.Asp37Asn	p.D37N	ENST00000323963		37	Gat/Aat	3/11	0.610506987441969	2	FACETS	1	0.987	1	0.631	0.587	0.675	CLONAL	1	TRUE	0	0.610506987441969	2		471	465	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944516	71944516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293622519	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	114	778	0	ENST00000298229.2:c.2072G>A	p.Arg691Gln	p.R691Q	ENST00000298229	NM_001567.3	691	cGg/cAg	18/28	1	2	FACETS	0.421	0.378	0.466	0.421	0.378	0.466	SUBCLONAL	1	TRUE	1	0.610506987441969	2		778	888	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048698	180048698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771458044	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	327	1354	4	ENST00000261937.6:c.1864G>A	p.Ala622Thr	p.A622T	ENST00000261937	NM_182925.4	622	Gcc/Acc	13/30	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.610506987441969	2		1358	1045	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	250	1406	1	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	1	2	FACETS	0.675	0.63	0.721	0.675	0.63	0.721	SUBCLONAL	1	TRUE	1	0.610506987441969	2		1407	1214	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141568653	141568653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	96	1065	4	ENST00000220592.5:c.809C>T	p.Thr270Met	p.T270M	ENST00000220592	NM_012154.3	270	aCg/aTg	7/19	0.595035969196749	3	FACETS	0.341	0.302	0.382	0.114	0.1	0.128	SUBCLONAL	1	TRUE	0	0.610506987441969	3		1069	1205	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999104	100999104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779926918	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	294	1103	2	ENST00000325455.5:c.698C>T	p.Ala233Val	p.A233V	ENST00000325455	NM_001202474.3	233	gCg/gTg	1/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.610506987441969	2		1105	919	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434005	49434005	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	321	1356	3	ENST00000301067.7:c.7548del	p.Asn2517IlefsTer26	p.N2517Ifs*26	ENST00000301067	NM_003482.3	2516	ccC/cc	31/54	1	2	FACETS	0.903	0.852	0.954	0.903	0.852	0.954	CLONAL	1	TRUE	1	0.610506987441969	2		1359	1165	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007761	45007761	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	123	472	0	ENST00000558401.1:c.208G>T	p.Glu70Ter	p.E70*	ENST00000558401	NM_004048.2	70	Gag/Tag	2/4	1	2	FACETS	0.939	0.856	1	0.939	0.856	1	CLONAL	1	TRUE	1	0.610506987441969	2		472	429	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132814	152132815	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	219	880	0	ENST00000262189.6:c.57dup	p.Glu20ArgfsTer39	p.E20Rfs*39	ENST00000262189	NM_170606.2	19	-/C	1/59	NA	2	FACETS	0.625	0.581	0.672			1	INDETERMINATE	1	TRUE	NA	0.610506987441969	2		880	1147	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007845	45007846	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	34	471	0	ENST00000558401.1:c.293_294del	p.Tyr98CysfsTer16	p.Y98Cfs*16	ENST00000558401	NM_004048.2	98	TAt/t	2/4	1	2	FACETS	0.23	0.187	0.278	0.23	0.187	0.278	SUBCLONAL	1	TRUE	1	0.610506987441969	2		471	485	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40376882	40376882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766427008	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	192	729	2	ENST00000293328.3:c.290C>T	p.Thr97Met	p.T97M	ENST00000293328	NM_012448.3	97	aCg/aTg	4/19	1	2	FACETS	0.987	0.918	1	0.987	0.918	1	CLONAL	1	TRUE	1	0.610506987441969	2		731	637	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514688	103514688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	126	512	1	ENST00000355739.4:c.1189G>A	p.Asp397Asn	p.D397N	ENST00000355739	NM_000123.3	397	Gat/Aat	8/15	0.610506987441969	2	FACETS	0.928	0.846	1	0.464	0.423	0.506	CLONAL	1	TRUE	0	0.610506987441969	2		513	445	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249347	110249348	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1414	436	1463	0	ENST00000374672.4:c.1225_1226del	p.Lys409GlufsTer14	p.K409Efs*14	ENST00000374672	NM_004235.4	409	AAg/g	4/5	0.596832167647557	3	FACETS	1	0.958	1	0.336	0.319	0.353	CLONAL	1	TRUE	0	0.610506987441969	3		1463	1850	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112079	115112079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764962945	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	353	1385	1	ENST00000257566.3:c.1661C>T	p.Ser554Leu	p.S554L	ENST00000257566	NM_016569.3	554	tCg/tTg	7/8	1	2	FACETS	0.936	0.886	0.986	0.936	0.886	0.986	CLONAL	1	TRUE	1	0.610506987441969	2		1386	1236	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567664	226567664	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	228	916	1	ENST00000366794.5:c.1502C>T	p.Ala501Val	p.A501V	ENST00000366794	NM_001618.3	501	gCt/gTt	10/23	1	2	FACETS	0.965	0.902	1	0.965	0.902	1	CLONAL	1	TRUE	1	0.610506987441969	2		917	774	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244076	46244076	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	132	624	0	ENST00000334344.6:c.2173del	p.Gln725ArgfsTer33	p.Q725Rfs*33	ENST00000334344	NM_152641.2	724	Ccc/cc	15/21	1	2	FACETS	0.899	0.822	0.979	0.899	0.822	0.979	CLONAL	1	TRUE	1	0.610506987441969	2		624	481	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214145	36214145	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	352	1431	2	ENST00000222270.7:c.2975del	p.Gly992AlafsTer17	p.G992Afs*17	ENST00000222270	NM_014727.1	991	Ggg/gg	6/37	1	2	FACETS	0.904	0.855	0.953	0.904	0.855	0.953	CLONAL	1	TRUE	1	0.610506987441969	2		1433	1276	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807478	36807478	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199625181	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	292	1246	0	ENST00000373129.3:c.1186C>T	p.Arg396Trp	p.R396W	ENST00000373129	NM_032017.1	396	Cgg/Tgg	12/12	1	2	FACETS	0.906	0.853	0.96	0.906	0.853	0.96	CLONAL	1	TRUE	1	0.610506987441969	2		1246	1056	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307462	118307462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782414402	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	132	315	1	ENST00000534358.1:c.235G>A	p.Ala79Thr	p.A79T	ENST00000534358	NM_005933.3	79	Gcc/Acc	1/36	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.610506987441969	2		316	369	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230535	46230535	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	22	472	1	ENST00000334344.6:c.784G>T	p.Gly262Ter	p.G262*	ENST00000334344	NM_152641.2	262	Gga/Tga	8/21	1	2	FACETS	0.196	0.151	0.248	0.196	0.151	0.248	SUBCLONAL	1	TRUE	1	0.610506987441969	2		473	368	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029330	14029330	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs201514032	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	117	456	0	ENST00000311895.7:c.1541A>G	p.Tyr514Cys	p.Y514C	ENST00000311895	NM_005236.2	514	tAt/tGt	8/11	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.610506987441969	2		456	361	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993999	72993999	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	313	1132	0	ENST00000268489.5:c.46T>C	p.Cys16Arg	p.C16R	ENST00000268489	NM_006885.3	16	Tgc/Cgc	2/10	1	2	FACETS	0.992	0.937	1	0.992	0.937	1	CLONAL	1	TRUE	1	0.610506987441969	2		1132	1034	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246309	41246310	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	134	809	0	ENST00000357654.3:c.1238dup	p.Leu413PhefsTer6	p.L413Ffs*6	ENST00000357654	NM_007294.3	413	ttg/ttTg	10/23	1	2	FACETS	0.844	0.771	0.92	0.844	0.771	0.92	CLONAL	1	TRUE	1	0.610506987441969	2		809	520	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753479	42753480	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	364	1544	0	ENST00000222329.4:c.784_785del	p.Pro262SerfsTer46	p.P262Sfs*46	ENST00000222329	NM_006494.2	262	CCt/t	4/4	1	2	FACETS	0.935	0.886	0.985	0.935	0.886	0.985	CLONAL	1	TRUE	1	0.610506987441969	2		1544	1275	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497898	25497898	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	285	1221	0	ENST00000264709.3:c.551C>A	p.Pro184His	p.P184H	ENST00000264709	NM_175629.2	184	cCc/cAc	6/23	1	2	FACETS	0.978	0.921	1	0.978	0.921	1	CLONAL	1	TRUE	1	0.610506987441969	2		1221	955	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215661823	215661824	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1057517589	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	21	407	0	ENST00000260947.4:c.176_177del	p.Glu59AlafsTer8	p.E59Afs*8	ENST00000260947	NM_000465.2	59	gAG/g	2/11	1	2	FACETS	0.178	0.137	0.227	0.178	0.137	0.227	SUBCLONAL	1	TRUE	1	0.610506987441969	2		407	386	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659212	86659212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	49	264	0	ENST00000274376.6:c.1501G>A	p.Asp501Asn	p.D501N	ENST00000274376	NM_002890.2	501	Gat/Aat	11/25	1	2	FACETS	0.819	0.703	0.942	0.819	0.703	0.942	CLONAL	1	TRUE	1	0.610506987441969	2		264	196	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534416	140534417	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	168	530	0	ENST00000288602.6:c.496_497del	p.Arg166AspfsTer47	p.R166Dfs*47	ENST00000288602	NM_004333.4	166	AGg/g	3/18	0.593298347202153	3	FACETS	1	0.97	1	0.368	0.339	0.398	CLONAL	1	TRUE	0	0.610506987441969	3		530	651	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007062	152007062	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	331	472	0	ENST00000262189.6:c.838G>T	p.Gly280Trp	p.G280W	ENST00000262189	NM_170606.2	280	Ggg/Tgg	6/59	NA	2	FACETS	0.809	0.771	0.847			1	INDETERMINATE	2	TRUE	NA	0.610506987441969	2		472	670	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540152	23540152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769698076	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	123	337	0	ENST00000380871.4:c.251C>T	p.Pro84Leu	p.P84L	ENST00000380871	NM_006167.3	84	cCg/cTg	1/2	0.595035969196749	3	FACETS	0.939	0.853	1	0.313	0.284	0.344	CLONAL	1	TRUE	0	0.610506987441969	3		337	560	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908883	101908883	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	467	708	0	ENST00000374994.4:c.1248del	p.Ile417LeufsTer25	p.I417Lfs*25	ENST00000374994	NM_004612.2	416	tCc/tc	7/9	0.596832167647557	3	FACETS	0.913	0.883	0.943	0.913	0.883	0.943	CLONAL	3	TRUE	0	0.610506987441969	3		708	729	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	58	714	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.926	0.812	1	0.926	0.812	1	CLONAL	1	TRUE	1	0.75478300968775	2		715	166	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578184	7578184	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567551073	NA	P-0055472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	12	809	0	ENST00000269305.4:c.665del	p.Pro222ArgfsTer25	p.P222Rfs*25	ENST00000269305	NM_001126112.2	222	cCg/cg	6/11	0.75478300968775	1	FACETS	0.046	0.032	0.063	0.046	0.032	0.063	SUBCLONAL	1	TRUE	0	0.75478300968775	1		809	432	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641451	18641451	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	129	317	0	ENST00000266497.5:c.2450A>T	p.Gln817Leu	p.Q817L	ENST00000266497		817	cAa/cTa	17/31	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.75478300968775	2		317	336	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46588105	46588105	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	258	842	0	ENST00000263734.3:c.655C>A	p.Leu219Met	p.L219M	ENST00000263734	NM_001430.4	219	Ctg/Atg	6/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.75478300968775	2		842	681	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708572	43708572	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055646-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1365	366	566	0	ENST00000382044.4:c.4724A>G	p.Tyr1575Cys	p.Y1575C	ENST00000382044	NM_001141980.1	1575	tAc/tGc	22/28	0.668923012874396	4	FACETS	1	0.976	1	0.352	0.332	0.372	CLONAL	1	TRUE	1	0.668923012874396	4		566	1731	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	144	355	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.793	0.722	0.867	0.793	0.722	0.867	SUBCLONAL	1	TRUE	1	0.36	2		355	1009	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088788	27088788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	167	784	1	ENST00000324856.7:c.2402del	p.Gly801ValfsTer32	p.G801Vfs*32	ENST00000324856	NM_006015.4	799	caG/ca	7/20	1	2	FACETS	0.906	0.832	0.984	0.906	0.832	0.984	CLONAL	1	TRUE	1	0.36	2		785	1024	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	113	339	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.852	0.767	0.942	0.852	0.767	0.942	CLONAL	1	TRUE	1	0.36	2		342	737	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	71	371	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.924	0.809	1	0.924	0.809	1	CLONAL	1	TRUE	1	0.36	2		371	427	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020754	37020754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	125	701	1	ENST00000358127.4:c.91C>T	p.Arg31Trp	p.R31W	ENST00000358127	NM_001280556.1	31	Cgg/Tgg	2/10	1	2	FACETS	0.679	0.613	0.748	0.679	0.613	0.748	SUBCLONAL	1	TRUE	1	0.36	2		702	1023	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	43	235	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.3	1	FACETS	0.777	0.655	0.91	0.777	0.655	0.91	CLONAL	1	TRUE	0	0.36	1		235	252	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1447	261	1159	0	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	0.849	0.793	0.907	0.849	0.793	0.907	CLONAL	1	TRUE	1	0.36	2		1159	1708	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	77	51	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.36	2		51	400	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584583	52584583	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	191	886	2	ENST00000394830.3:c.4430del	p.Pro1477LeufsTer12	p.P1477Lfs*12	ENST00000394830	NM_018313.4	1477	cCt/ct	29/30	1	2	FACETS	0.895	0.827	0.967	0.895	0.827	0.967	CLONAL	1	TRUE	1	0.36	2		888	1185	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1292	130	737	1	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	1	2	FACETS	0.508	0.459	0.56	0.508	0.459	0.56	SUBCLONAL	1	TRUE	1	0.36	2		738	1422	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	159	664	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	1	2	FACETS	0.727	0.665	0.792	0.727	0.665	0.792	SUBCLONAL	1	TRUE	1	0.36	2		664	1215	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	98	456	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.897	0.802	0.998	0.897	0.802	0.998	CLONAL	1	TRUE	1	0.36	2		457	607	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216477	108216477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587782558	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	41	318	1	ENST00000278616.4:c.8432del	p.Lys2811SerfsTer46	p.K2811Sfs*46	ENST00000278616	NM_000051.3	2809	cAa/ca	58/63	1	2	FACETS	0.911	0.764	1	0.911	0.764	1	CLONAL	1	TRUE	1	0.36	2		319	250	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637699	52637700	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	87	419	0	ENST00000394830.3:c.2616dup	p.Ile873TyrfsTer2	p.I873Yfs*2	ENST00000394830	NM_018313.4	872	-/T	18/30	1	2	FACETS	0.935	0.83	1	0.935	0.83	1	CLONAL	1	TRUE	1	0.36	2		419	517	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72861878	72861878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201983708	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	103	623	0	ENST00000325599.8:c.1004G>A	p.Arg335His	p.R335H	ENST00000325599	NM_018130.2	335	cGc/cAc	9/11	1	2	FACETS	0.908	0.814	1	0.908	0.814	1	CLONAL	1	TRUE	1	0.36	2		623	630	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163553	32163554	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs777647776	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	167	760	6	ENST00000375023.3:c.5672dup	p.Gly1892ArgfsTer24	p.G1892Rfs*24	ENST00000375023	NM_004557.3	1891	ggc/ggGc	30/30	1	2	FACETS	0.746	0.684	0.812	0.746	0.684	0.812	SUBCLONAL	1	TRUE	1	0.36	2		766	1243	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835781	68835781	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060501215	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	162	786	0	ENST00000261769.5:c.377del	p.Pro126ArgfsTer89	p.P126Rfs*89	ENST00000261769	NM_004360.3	124	cgC/cg	3/16	1	2	FACETS	0.847	0.776	0.922	0.847	0.776	0.922	CLONAL	1	TRUE	1	0.36	2		786	1062	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412005	63412013	+	inframe_deletion	In_Frame_Del	DEL	CCTCTTCTT	CCTCTTCTT	-	rs587778022	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	109	935	0	ENST00000330258.3:c.1154_1162del	p.Glu385_Glu387del	p.E385_E387del	ENST00000330258	NM_152424.3	385	gAAGAAGAGGtg/gtg	2/2	1	2	FACETS	0.556	0.498	0.618	0.556	0.498	0.618	SUBCLONAL	1	TRUE	1	0.36	2		935	1089	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007689	45007690	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	99	387	0	ENST00000558401.1:c.137_138del	p.Tyr46CysfsTer10	p.Y46Cfs*10	ENST00000558401	NM_004048.2	46	TAt/t	2/4	1	2	FACETS	0.986	0.882	1	0.986	0.882	1	CLONAL	1	TRUE	1	0.36	2		387	558	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202732	128202732	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	223	1131	0	ENST00000341105.2:c.988C>T	p.Arg330Ter	p.R330*	ENST00000341105	NM_032638.4	330	Cga/Tga	4/6	1	2	FACETS	0.918	0.852	0.986	0.918	0.852	0.986	CLONAL	1	TRUE	1	0.36	2		1131	1350	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029072	14029072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763619616	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	54	267	1	ENST00000311895.7:c.1283C>T	p.Ala428Val	p.A428V	ENST00000311895	NM_005236.2	428	gCg/gTg	8/11	1	2	FACETS	0.796	0.682	0.919	0.796	0.682	0.919	CLONAL	1	TRUE	1	0.36	2		268	377	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458270	12458270	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	108	636	2	ENST00000287820.6:c.892del	p.Leu298CysfsTer38	p.L298Cfs*38	ENST00000287820	NM_015869.4	296	aCc/ac	6/7	1	2	FACETS	0.763	0.685	0.847	0.763	0.685	0.847	SUBCLONAL	1	TRUE	1	0.36	2		638	786	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630604	187630605	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	143	668	1	ENST00000441802.2:c.377dup	p.Asn126LysfsTer3	p.N126Kfs*3	ENST00000441802	NM_005245.3	126	aat/aaAt	2/27	NA	2	FACETS	0.884	0.805	0.966			1	INDETERMINATE	1	TRUE	NA	0.36	2		669	899	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434959	49434959	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555192751	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	193	1067	3	ENST00000301067.7:c.6594del	p.Tyr2199IlefsTer65	p.Y2199Ifs*65	ENST00000301067	NM_003482.3	2198	ccC/cc	31/54	1	2	FACETS	0.822	0.759	0.888	0.822	0.759	0.888	CLONAL	1	TRUE	1	0.36	2		1070	1304	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636722	2636724	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	139	760	2	ENST00000342085.4:c.1179_1181del	p.Ser394del	p.S394del	ENST00000342085	NM_002613.4	391	TCC/-	11/14	1	2	FACETS	0.745	0.677	0.816	0.745	0.677	0.816	SUBCLONAL	1	TRUE	1	0.36	2		762	1037	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525977	41525977	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	97	478	1	ENST00000263253.7:c.1256del	p.Asn419MetfsTer12	p.N419Mfs*12	ENST00000263253	NM_001429.3	418	Aaa/aa	5/31	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.36	2		479	537	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619323	1619323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761667569	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1225	151	1033	1	ENST00000344749.5:c.1318G>A	p.Ala440Thr	p.A440T	ENST00000344749	NM_001136139.2	440	Gca/Aca	15/19	1	2	FACETS	0.61	0.555	0.667	0.61	0.555	0.667	SUBCLONAL	1	TRUE	1	0.36	2		1034	1376	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438210	49438211	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1555194303	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	204	885	1	ENST00000301067.7:c.5058dup	p.Arg1687ThrfsTer4	p.R1687Tfs*4	ENST00000301067	NM_003482.3	1686	-/A	20/54	1	2	FACETS	0.819	0.758	0.884	0.819	0.758	0.884	CLONAL	1	TRUE	1	0.36	2		886	1383	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415845	49415845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	126	557	0	ENST00000301067.7:c.16502G>A	p.Arg5501Gln	p.R5501Q	ENST00000301067	NM_003482.3	5501	cGa/cAa	53/54	1	2	FACETS	0.999	0.906	1	0.999	0.906	1	CLONAL	1	TRUE	1	0.36	2		557	701	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242716	16242716	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	128	564	0	ENST00000375759.3:c.1342del	p.Thr448ProfsTer25	p.T448Pfs*25	ENST00000375759	NM_015001.2	446	gAa/ga	6/15	1	2	FACETS	0.93	0.843	1	0.93	0.843	1	CLONAL	1	TRUE	1	0.36	2		564	765	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262655	16262655	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375642545	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	129	659	0	ENST00000375759.3:c.9920G>A	p.Arg3307Gln	p.R3307Q	ENST00000375759	NM_015001.2	3307	cGg/cAg	11/15	1	2	FACETS	0.803	0.728	0.883	0.803	0.728	0.883	CLONAL	1	TRUE	1	0.36	2		659	892	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28595718	28595718	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	212	982	4	ENST00000253063.3:c.115C>T	p.Arg39Ter	p.R39*	ENST00000253063	NM_031459.4	39	Cga/Tga	2/10	1	2	FACETS	0.878	0.813	0.945	0.878	0.813	0.945	CLONAL	1	TRUE	1	0.36	2		986	1342	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66779584	66779584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	100	464	0	ENST00000307102.5:c.914G>A	p.Arg305Gln	p.R305Q	ENST00000307102	NM_002755.3	305	cGa/cAa	8/11	1	2	FACETS	0.89	0.797	0.99	0.89	0.797	0.99	CLONAL	1	TRUE	1	0.36	2		464	624	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223811	2223811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1314	235	1173	6	ENST00000326181.6:c.1109C>T	p.Ala370Val	p.A370V	ENST00000326181	NM_032271.2	370	gCg/gTg	12/21	1	2	FACETS	0.843	0.784	0.904	0.843	0.784	0.904	CLONAL	1	TRUE	1	0.36	2		1179	1549	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024572	14024572	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs746106147	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	53	331	0	ENST00000311895.7:c.798C>G	p.Ile266Met	p.I266M	ENST00000311895	NM_005236.2	266	atC/atG	5/11	1	2	FACETS	0.846	0.725	0.978	0.846	0.725	0.978	CLONAL	1	TRUE	1	0.36	2		331	348	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821998	72821998	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	124	581	1	ENST00000268489.5:c.10177C>T	p.Gln3393Ter	p.Q3393*	ENST00000268489	NM_006885.3	3393	Cag/Tag	10/10	1	2	FACETS	0.771	0.697	0.849	0.771	0.697	0.849	SUBCLONAL	1	TRUE	1	0.36	2		582	894	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042406	16042406	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	100	612	0	ENST00000268712.3:c.1268T>G	p.Leu423Arg	p.L423R	ENST00000268712	NM_006311.3	423	cTt/cGt	12/46	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.36	2		612	554	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229600	5229600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	41	127	0	ENST00000357368.4:c.2251G>A	p.Gly751Ser	p.G751S	ENST00000357368	NM_002850.3	751	Ggc/Agc	15/38	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.36	2		127	201	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349792	15349792	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	237	1143	2	ENST00000263377.2:c.3783-1G>T		p.X1261_splice	ENST00000263377	NM_058243.2	1261			1	2	FACETS	0.925	0.861	0.992	0.925	0.861	0.992	CLONAL	1	TRUE	1	0.36	2		1145	1423	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660300	227660300	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	201	792	2	ENST00000305123.5:c.3155A>C	p.Glu1052Ala	p.E1052A	ENST00000305123	NM_005544.2	1052	gAg/gCg	1/2	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.36	2		794	1063	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662260	227662260	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1205	265	1046	0	ENST00000305123.5:c.1195G>T	p.Gly399Cys	p.G399C	ENST00000305123	NM_005544.2	399	Ggc/Tgc	1/2	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.36	2		1046	1470	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023246	31023246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371903529	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	135	748	1	ENST00000375687.4:c.2731C>T	p.Pro911Ser	p.P911S	ENST00000375687	NM_015338.5	911	Ccc/Tcc	13/13	1	2	FACETS	0.796	0.723	0.873	0.796	0.723	0.873	SUBCLONAL	1	TRUE	1	0.36	2		749	942	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741453	39741453	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	88	406	0	ENST00000361337.2:c.1340C>A	p.Ala447Asp	p.A447D	ENST00000361337	NM_003286.2	447	gCt/gAt	14/21	1	2	FACETS	0.782	0.694	0.877	0.782	0.694	0.877	SUBCLONAL	1	TRUE	1	0.36	2		406	625	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169988255	169988255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1030581930	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	112	419	0	ENST00000295797.4:c.497G>A	p.Arg166His	p.R166H	ENST00000295797	NM_002740.5	166	cGc/cAc	6/18	1	2	FACETS	0.978	0.882	1	0.978	0.882	1	CLONAL	1	TRUE	1	0.36	2		419	636	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564702	55564702	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	73	573	0	ENST00000288135.5:c.590C>T	p.Ser197Leu	p.S197L	ENST00000288135	NM_000222.2	197	tCg/tTg	3/21	1	2	FACETS	0.538	0.47	0.612	0.538	0.47	0.612	SUBCLONAL	1	TRUE	1	0.36	2		573	754	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720852	176720852	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	120	514	1	ENST00000439151.2:c.6483G>T	p.Trp2161Cys	p.W2161C	ENST00000439151	NM_022455.4	2161	tgG/tgT	23/23	1	2	FACETS	0.92	0.831	1	0.92	0.831	1	CLONAL	1	TRUE	1	0.36	2		515	725	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180050990	180050990	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs762704129	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1289	216	1134	1	ENST00000261937.6:c.1493T>C	p.Val498Ala	p.V498A	ENST00000261937	NM_182925.4	498	gTg/gCg	11/30	1	2	FACETS	0.797	0.739	0.858	0.797	0.739	0.858	SUBCLONAL	1	TRUE	1	0.36	2		1135	1505	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798054	32798054	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	223	1024	0	ENST00000374899.4:c.1625T>C	p.Leu542Pro	p.L542P	ENST00000374899	NM_018833.2	542	cTg/cCg	9/12	1	2	FACETS	0.875	0.812	0.94	0.875	0.812	0.94	CLONAL	1	TRUE	1	0.36	2		1024	1416	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946403	2946403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1409	218	1181	0	ENST00000396946.4:c.3334G>A	p.Ala1112Thr	p.A1112T	ENST00000396946	NM_032415.4	1112	Gcc/Acc	25/25	1	2	FACETS	0.744	0.69	0.801	0.744	0.69	0.801	SUBCLONAL	1	TRUE	1	0.36	2		1181	1627	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523672	148523672	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	58	333	1	ENST00000320356.2:c.781A>T	p.Thr261Ser	p.T261S	ENST00000320356	NM_004456.4	261	Acc/Tcc	8/20	1	2	FACETS	0.716	0.616	0.824	0.716	0.616	0.824	SUBCLONAL	1	TRUE	1	0.36	2		334	450	SUCCESS
ATM	472	MSKCC	GRCh37	11	108159822	108159822	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	13	118	0	ENST00000278616.4:c.4231del	p.Ser1411AlafsTer40	p.S1411Afs*40	ENST00000278616	NM_000051.3	1410	Aaa/aa	28/63	1	2	FACETS	0.669	0.482	0.892	0.669	0.482	0.892	SUBCLONAL	1	TRUE	1	0.36	2		118	108	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678559	88678559	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764882745	NA	P-0055821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	200	628	0	ENST00000360948.2:c.977G>A	p.Arg326His	p.R326H	ENST00000360948	NM_001012338.2	326	cGt/cAt	9/19	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.861472890402423	2		628	457	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829164	72829164	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	359	976	1	ENST00000268489.5:c.7417C>T	p.Gln2473Ter	p.Q2473*	ENST00000268489	NM_006885.3	2473	Cag/Tag	9/10	0.823668026250263	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.861472890402423	1		977	464	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0055828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	19	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.637	0.483	0.819	0.637	0.483	0.819	SUBCLONAL	1	TRUE	1	0.17	2		485	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0055828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	80	599	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.17	2		599	756	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593405	48593405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519962	NA	P-0055828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	11	422	0	ENST00000342988.3:c.1156G>A	p.Gly386Ser	p.G386S	ENST00000342988	NM_005359.5	386	Ggt/Agt	10/12	1	2	FACETS	0.32	0.22	0.445	0.32	0.22	0.445	SUBCLONAL	1	TRUE	1	0.17	2		422	405	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028702	42028702	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	43	698	0	ENST00000219905.7:c.4240T>G	p.Ser1414Ala	p.S1414A	ENST00000219905	NM_001164273.1	1414	Tca/Gca	13/24	1	2	FACETS	0.846	0.707	1	0.846	0.707	1	CLONAL	1	TRUE	1	0.17	2		698	598	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056082-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	211	368	0	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	0.559231139462071	1	FACETS	0.856	0.8	0.914	0.856	0.8	0.914	CLONAL	1	TRUE	0	0.566337627486461	1		368	624	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0056082-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	289	518	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.520447461920058	2	FACETS	0.924	0.88	0.969	0.924	0.88	0.969	CLONAL	2	TRUE	0	0.566337627486461	2		518	552	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0056082-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	184	349	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.566337627486461	2		349	609	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575121	48575122	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056082-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	127	406	0	ENST00000342988.3:c.320dup	p.Asn107LysfsTer2	p.N107Kfs*2	ENST00000342988	NM_005359.5	105	-/A	3/12	0.566337627486461	1	FACETS	0.784	0.717	0.854	0.784	0.717	0.854	SUBCLONAL	1	TRUE	0	0.566337627486461	1		406	410	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494187	140494187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1158980679	NA	P-0056082-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	234	613	0	ENST00000288602.6:c.1061G>A	p.Arg354Gln	p.R354Q	ENST00000288602	NM_004333.4	354	cGa/cAa	8/18	0.566337627486461	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.566337627486461	1		613	588	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519504	137519505	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0056082-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	167	532	0	ENST00000367739.4:c.1132_1133dup	p.Ser378ArgfsTer6	p.S378Rfs*6	ENST00000367739	NM_000416.2	378	agt/agAGt	7/7	0.566337627486461	1	FACETS	0.846	0.783	0.91	0.846	0.783	0.91	CLONAL	1	TRUE	0	0.566337627486461	1		532	500	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029439	16029439	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056082-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	81	223	0	ENST00000268712.3:c.1591G>C	p.Glu531Gln	p.E531Q	ENST00000268712	NM_006311.3	531	Gaa/Caa	15/46	0.520447461920058	2	FACETS	1	0.898	1	0.504	0.449	0.561	CLONAL	1	TRUE	0	0.566337627486461	2		223	284	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376230	15376230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1483781735	NA	P-0056082-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	138	355	1	ENST00000263377.2:c.784G>A	p.Ala262Thr	p.A262T	ENST00000263377	NM_058243.2	262	Gct/Act	5/20	NA	2	FACETS	1	0.942	1			1	INDETERMINATE	1	TRUE	NA	0.566337627486461	2		356	471	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47600690	47600690	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056082-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	106	349	0	ENST00000263735.4:c.165T>A	p.Asn55Lys	p.N55K	ENST00000263735	NM_002354.2	55	aaT/aaA	2/9	1	2	FACETS	0.77	0.694	0.85	0.77	0.694	0.85	SUBCLONAL	1	TRUE	1	0.566337627486461	2		349	486	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947499	38947499	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056082-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	143	316	0	ENST00000357387.3:c.4181T>C	p.Leu1394Ser	p.L1394S	ENST00000357387	NM_152756.3	1394	tTa/tCa	32/38	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.566337627486461	2		316	446	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546419	46546419	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056082-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	158	345	0	ENST00000262741.5:c.110T>A	p.Leu37His	p.L37H	ENST00000262741	NM_003629.3	37	cTt/cAt	2/10	0.160480669158631	6	FACETS	0.937	0.862	1			1	INDETERMINATE	2	TRUE	NA	0.566337627486461	6		345	635	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223805	2223805	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056082-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	218	610	0	ENST00000326181.6:c.1103T>C	p.Ile368Thr	p.I368T	ENST00000326181	NM_032271.2	368	aTc/aCc	12/21	0.559231139462071	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.566337627486461	1		610	525	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274075	10274076	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0056082-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	205	638	0	ENST00000330684.3:c.193dup	p.Leu65ProfsTer73	p.L65Pfs*73	ENST00000330684	NM_001134407.1	65	ctg/cCtg	2/13	1	2	FACETS	0.985	0.917	1	0.985	0.917	1	CLONAL	1	TRUE	1	0.566337627486461	2		638	735	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38504598	38504598	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056082-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	199	595	0	ENST00000254066.5:c.209A>G	p.Glu70Gly	p.E70G	ENST00000254066	NM_000964.3	70	gAg/gGg	3/9	0.566337627486461	5	FACETS	1	0.962	1			1	CLONAL	1	TRUE	NA	0.566337627486461	5		595	1221	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404291	139404291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370797169	NA	P-0056082-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1231	124	770	2	ENST00000277541.6:c.2863C>T	p.Arg955Cys	p.R955C	ENST00000277541	NM_017617.3	955	Cgc/Tgc	18/34	0.566337627486461	4	FACETS	0.506	0.456	0.559	0.169	0.152	0.187	SUBCLONAL	1	TRUE	1	0.566337627486461	4		772	1355	SUCCESS
PHF6	84295	MSKCC	GRCh37	X	133559302	133559302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763271908	NA	P-0056082-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	105	204	0	ENST00000332070.3:c.1040G>A	p.Arg347Gln	p.R347Q	ENST00000332070	NM_032458.2	347	cGa/cAa	10/10	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.566337627486461	1		204	204	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0056303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	47	568	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.3	1	FACETS	0.417	0.351	0.49	0.417	0.351	0.49	SUBCLONAL	1	FALSE	0	0.3	1		569	638	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0056303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	84	324	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.170308072320444	2	FACETS	1	0.922	1	0.526	0.466	0.591	INDETERMINATE	1	FALSE	0	0.3	2		324	532	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	57	650	1	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.3	1	FACETS	0.541	0.464	0.625	0.541	0.464	0.625	SUBCLONAL	1	FALSE	0	0.3	1		651	597	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103828	47103828	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs976581260	NA	P-0056304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	184	467	0	ENST00000409792.3:c.6118C>T	p.Arg2040Ter	p.R2040*	ENST00000409792	NM_014159.6	2040	Cga/Tga	14/21	0.366566763440849	3	FACETS	0.911	0.851	0.972	0.607	0.567	0.648	CLONAL	2	TRUE	0	0.60837815354316	3		467	433	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246390	53246390	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	355	484	0	ENST00000375401.3:c.592C>T	p.Arg198Ter	p.R198*	ENST00000375401	NM_004187.3	198	Cga/Tga	5/26	0.47925150036443	2	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.60837815354316	2		484	563	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131327	202131327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	217	424	1	ENST00000358485.4:c.295G>A	p.Asp99Asn	p.D99N	ENST00000358485	NM_001080125.1	99	Gat/Aat	2/9	0.536253651865461	4	FACETS	0.787	0.734	0.841	0.787	0.734	0.841	SUBCLONAL	2	TRUE	2	0.60837815354316	4		425	729	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188236	10188236	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1559428107	NA	P-0056304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	330	739	1	ENST00000256474.2:c.381del	p.Leu128PhefsTer31	p.L128Ffs*31	ENST00000256474	NM_000551.3	127	Ggg/gg	2/3	0.366566763440849	3	FACETS	1	0.953	1	0.667	0.635	0.699	CLONAL	2	TRUE	0	0.60837815354316	3		740	707	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52676032	52676032	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	167	373	0	ENST00000394830.3:c.1025del	p.Leu342TyrfsTer20	p.L342Yfs*20	ENST00000394830	NM_018313.4	342	tTa/ta	11/30	0.495951621390082	2	FACETS	0.76	0.709	0.812	0.76	0.709	0.812	SUBCLONAL	2	TRUE	0	0.60837815354316	2		373	361	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519199	187519199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	129	646	0	ENST00000441802.2:c.12184C>T	p.Leu4062Phe	p.L4062F	ENST00000441802	NM_005245.3	4062	Ctc/Ttc	23/27	1	2	FACETS	0.803	0.732	0.877	0.803	0.732	0.877	CLONAL	1	TRUE	1	0.60837815354316	2		646	528	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0056319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	33	662	0	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		662	711	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	249	949	18	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.48	2		967	974	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	227	565	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.97	0.904	1	0.97	0.904	1	CLONAL	1	TRUE	1	0.48	2		568	975	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396233	396234	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769619638	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	185	848	0	ENST00000262320.3:c.792dup	p.Gly265ArgfsTer20	p.G265Rfs*20	ENST00000262320	NM_003502.3	264	-/C	2/11	1	2	FACETS	0.874	0.807	0.943	0.874	0.807	0.943	CLONAL	1	TRUE	1	0.48	2		848	882	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	82	456	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.887	0.788	0.993	0.887	0.788	0.993	CLONAL	1	TRUE	1	0.48	2		457	385	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	225	969	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.48	2		969	905	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	42	484	2	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.276	0.229	0.327	0.276	0.229	0.327	SUBCLONAL	1	TRUE	1	0.48	2		486	635	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023327	27023327	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	29	113	1	ENST00000324856.7:c.437del	p.Pro146GlnfsTer86	p.P146Qfs*86	ENST00000324856	NM_006015.4	145	Ccc/cc	1/20	1	2	FACETS	0.467	0.376	0.569	0.467	0.376	0.569	SUBCLONAL	1	TRUE	1	0.48	2		114	259	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144146	11144146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	233	860	0	ENST00000358026.2:c.3727C>T	p.Arg1243Trp	p.R1243W	ENST00000358026	NM_001128849.1	1243	Cgg/Tgg	26/36	1	2	FACETS	0.989	0.923	1	0.989	0.923	1	CLONAL	1	TRUE	1	0.48	2		860	982	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	248	835	1	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.48	2		836	981	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771932	135771932	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755396992	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	103	706	0	ENST00000298552.3:c.3185G>A	p.Arg1062Gln	p.R1062Q	ENST00000298552	NM_001162426.1	1062	cGg/cAg	23/23	1	2	FACETS	0.585	0.523	0.65	0.585	0.523	0.65	SUBCLONAL	1	TRUE	1	0.48	2		706	734	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354008	15354008	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	62	379	5	ENST00000263377.2:c.2872del	p.Leu958CysfsTer110	p.L958Cfs*110	ENST00000263377	NM_058243.2	958	Ctg/tg	14/20	1	2	FACETS	0.726	0.63	0.828	0.726	0.63	0.828	SUBCLONAL	1	TRUE	1	0.48	2		384	356	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542109	187542110	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1560943587	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	63	439	0	ENST00000441802.2:c.5630dup	p.Val1878CysfsTer8	p.V1878Cfs*8	ENST00000441802	NM_005245.3	1877	cct/ccCt	10/27	1	2	FACETS	0.645	0.56	0.737	0.645	0.56	0.737	SUBCLONAL	1	TRUE	1	0.48	2		439	407	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	61	582	4	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	0.444	0.383	0.511	0.444	0.383	0.511	SUBCLONAL	1	TRUE	1	0.48	2		586	572	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852118	63852118	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	154	684	0	ENST00000279873.7:c.2901del	p.Lys967AsnfsTer15	p.K967Nfs*15	ENST00000279873	NM_032199.2	966	Aaa/aa	10/10	1	2	FACETS	0.874	0.802	0.95	0.874	0.802	0.95	CLONAL	1	TRUE	1	0.48	2		684	734	SUCCESS
APC	324	MSKCC	GRCh37	5	112164611	112164611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587783034	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	74	293	1	ENST00000257430.4:c.1685C>T	p.Thr562Met	p.T562M	ENST00000257430	NM_000038.5	562	aCg/aTg	14/16	1	2	FACETS	0.907	0.8	1	0.907	0.8	1	CLONAL	1	TRUE	1	0.48	2		294	340	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426776	121426776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150513055	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	251	819	0	ENST00000257555.6:c.467C>T	p.Thr156Met	p.T156M	ENST00000257555		156	aCg/aTg	2/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.48	2		819	981	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806228	1806228	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868356240	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	237	910	1	ENST00000260795.2:c.1247G>A	p.Arg416His	p.R416H	ENST00000260795		416	cGc/cAc	8/17	1	2	FACETS	0.951	0.888	1	0.951	0.888	1	CLONAL	1	TRUE	1	0.48	2		911	1038	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270530	98270530	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs751977093	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	102	436	1	ENST00000331920.6:c.114del	p.Leu39CysfsTer41	p.L39Cfs*41	ENST00000331920	NM_000264.3	38	ggG/gg	1/24	1	2	FACETS	0.916	0.824	1	0.916	0.824	1	CLONAL	1	TRUE	1	0.48	2		437	464	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243801023	243801023	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	24	374	0	ENST00000263826.5:c.451T>G	p.Leu151Val	p.L151V	ENST00000263826	NM_005465.4	151	Ttg/Gtg	5/13	1	2	FACETS	0.272	0.213	0.34	0.272	0.213	0.34	SUBCLONAL	1	TRUE	1	0.48	2		374	368	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643942	52643943	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	102	402	0	ENST00000394830.3:c.1953dup	p.Ser652IlefsTer13	p.S652Ifs*13	ENST00000394830	NM_018313.4	651	-/A	17/30	1	2	FACETS	0.942	0.848	1	0.942	0.848	1	CLONAL	1	TRUE	1	0.48	2		402	451	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971324	13971324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752431857	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	216	562	0	ENST00000405192.2:c.605C>T	p.Thr202Met	p.T202M	ENST00000405192	NM_001163147.1	202	aCg/aTg	8/12	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.48	2		562	690	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188853	32188853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs192478549	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	204	1022	0	ENST00000375023.3:c.701G>A	p.Arg234Gln	p.R234Q	ENST00000375023	NM_004557.3	234	cGg/cAg	4/30	1	2	FACETS	0.944	0.877	1	0.944	0.877	1	CLONAL	1	TRUE	1	0.48	2		1022	900	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727429	66727429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	168	473	0	ENST00000307102.5:c.145C>T	p.Arg49Cys	p.R49C	ENST00000307102	NM_002755.3	49	Cgc/Tgc	2/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.48	2		473	620	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962529	100962529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767360879	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	105	374	0	ENST00000325455.5:c.1868G>A	p.Arg623His	p.R623H	ENST00000325455	NM_001202474.3	623	cGc/cAc	3/8	1	2	FACETS	0.742	0.666	0.821	0.742	0.666	0.821	SUBCLONAL	1	TRUE	1	0.48	2		374	590	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265479	152265479	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766779326	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	172	681	1	ENST00000206249.3:c.932C>T	p.Thr311Met	p.T311M	ENST00000206249	NM_000125.3	311	aCg/aTg	4/8	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.48	2		682	680	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738518	145738518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368611522	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	206	946	0	ENST00000428558.2:c.2467G>A	p.Glu823Lys	p.E823K	ENST00000428558	NM_004260.3	823	Gaa/Aaa	16/22	1	2	FACETS	0.939	0.872	1	0.939	0.872	1	CLONAL	1	TRUE	1	0.48	2		946	914	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144529	58144529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772079285	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	24	403	0	ENST00000257904.6:c.542G>A	p.Arg181Gln	p.R181Q	ENST00000257904	NM_000075.3	181	cGa/cAa	5/8	1	2	FACETS	0.242	0.189	0.303	0.242	0.189	0.303	SUBCLONAL	1	TRUE	1	0.48	2		403	414	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350062	81350062	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs759145490	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	79	288	0	ENST00000222390.5:c.1270C>T	p.Arg424Cys	p.R424C	ENST00000222390	NM_000601.4	424	Cgt/Tgt	10/18	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.48	2		288	304	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054540	42054541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	39	333	4	ENST00000219905.7:c.7731dup	p.Asp2578ArgfsTer45	p.D2578Rfs*45	ENST00000219905	NM_001164273.1	2575	aga/agAa	22/24	1	2	FACETS	0.388	0.321	0.462	0.388	0.321	0.462	SUBCLONAL	1	TRUE	1	0.48	2		337	419	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287500	46287500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457405698	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	108	380	0	ENST00000334344.6:c.5359C>T	p.Arg1787Cys	p.R1787C	ENST00000334344	NM_152641.2	1787	Cgc/Tgc	20/21	1	2	FACETS	0.918	0.828	1	0.918	0.828	1	CLONAL	1	TRUE	1	0.48	2		380	490	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307700	11307700	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	132	508	0	ENST00000361445.4:c.1207C>T	p.Arg403Ter	p.R403*	ENST00000361445	NM_004958.3	403	Cga/Tga	8/58	1	2	FACETS	0.955	0.87	1	0.955	0.87	1	CLONAL	1	TRUE	1	0.48	2		508	576	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113361	209113361	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765848107	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	90	320	0	ENST00000345146.2:c.146G>A	p.Arg49His	p.R49H	ENST00000345146	NM_005896.2	49	cGt/cAt	4/10	1	2	FACETS	0.954	0.852	1	0.954	0.852	1	CLONAL	1	TRUE	1	0.48	2		320	393	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967511	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	rs1349928568	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	20	300	0	ENST00000265433.3:c.1396dup	p.Arg466LysfsTer5	p.R466Kfs*5	ENST00000265433	NM_002485.4	466	agg/aAgg	10/16	1	2	FACETS	0.244	0.186	0.311	0.244	0.186	0.311	SUBCLONAL	1	TRUE	1	0.48	2		300	342	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	183	785	1	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	1	2	FACETS	0.895	0.827	0.966	0.895	0.827	0.966	CLONAL	1	TRUE	1	0.48	2		786	852	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950697	79950705	+	inframe_deletion	In_Frame_Del	DEL	GCTGCAGCG	GCTGCAGCG	-	rs758595508	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	25	314	1	ENST00000265081.6:c.162_170del	p.Ala60_Ala62del	p.A60_A62del	ENST00000265081	NM_002439.4	51	GCTGCAGCG/-	1/24	1	2	FACETS	0.264	0.208	0.329	0.264	0.208	0.329	SUBCLONAL	1	TRUE	1	0.48	2		315	394	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68290282	68290282	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs138727212	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	77	404	0	ENST00000487270.1:c.22C>T	p.Arg8Ter	p.R8*	ENST00000487270	NM_133509.3	8	Cga/Tga	2/11	1	2	FACETS	0.637	0.56	0.718	0.637	0.56	0.718	SUBCLONAL	1	TRUE	1	0.48	2		404	504	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214398	36214398	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs868041281	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	168	752	2	ENST00000222270.7:c.3057del	p.Gly1020AlafsTer4	p.G1020Afs*4	ENST00000222270	NM_014727.1	1018	Aaa/aa	7/37	1	2	FACETS	0.847	0.78	0.918	0.847	0.78	0.918	CLONAL	1	TRUE	1	0.48	2		754	826	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117524	4117524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371852537	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	75	342	2	ENST00000262948.5:c.196G>A	p.Glu66Lys	p.E66K	ENST00000262948	NM_030662.3	66	Gaa/Aaa	2/11	1	2	FACETS	0.97	0.858	1	0.97	0.858	1	CLONAL	1	TRUE	1	0.48	2		344	322	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750371	133750372	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	175	664	0	ENST00000318560.5:c.1206dup	p.Ile403HisfsTer42	p.I403Hfs*42	ENST00000318560	NM_005157.4	401	ttc/ttCc	7/11	1	2	FACETS	0.897	0.827	0.969	0.897	0.827	0.969	CLONAL	1	TRUE	1	0.48	2		664	813	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38184289	38184289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149768452	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	96	563	0	ENST00000317025.8:c.1667C>T	p.Thr556Met	p.T556M	ENST00000317025	NM_023034.1	556	aCg/aTg	7/24	1	2	FACETS	0.669	0.597	0.745	0.669	0.597	0.745	SUBCLONAL	1	TRUE	1	0.48	2		563	598	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154294	2154294	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243657106	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	283	1124	0	ENST00000434045.2:c.634C>T	p.Arg212Cys	p.R212C	ENST00000434045	NM_001127598.1	212	Cgt/Tgt	5/5	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.48	2		1124	1022	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	118	305	0	ENST00000256196.4:c.68del	p.Gly23AlafsTer18	p.G23Afs*18	ENST00000256196		23	gGc/gc	1/6	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.48	2		305	451	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436835	52436835	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755915077	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	174	835	1	ENST00000460680.1:c.1943C>T	p.Ala648Val	p.A648V	ENST00000460680	NM_004656.3	648	gCg/gTg	15/17	1	2	FACETS	0.857	0.79	0.927	0.857	0.79	0.927	CLONAL	1	TRUE	1	0.48	2		836	846	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541646	120541646	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167669994	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	238	826	0	ENST00000229340.5:c.211C>T	p.Arg71Cys	p.R71C	ENST00000229340	NM_006861.6	71	Cgc/Tgc	3/6	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.48	2		826	968	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532539	187532539	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	52	337	0	ENST00000441802.2:c.9853+1G>A		p.X3285_splice	ENST00000441802	NM_005245.3	3285			1	2	FACETS	0.703	0.602	0.813	0.703	0.602	0.813	SUBCLONAL	1	TRUE	1	0.48	2		337	308	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392858	118392858	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781866935	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	135	511	0	ENST00000534358.1:c.11890G>A	p.Ala3964Thr	p.A3964T	ENST00000534358	NM_005933.3	3964	Gcc/Acc	36/36	1	2	FACETS	0.922	0.841	1	0.922	0.841	1	CLONAL	1	TRUE	1	0.48	2		511	610	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793481	42793481	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs532264982	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	270	914	2	ENST00000575354.2:c.1283G>A	p.Arg428His	p.R428H	ENST00000575354	NM_015125.3	428	cGt/cAt	8/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.48	2		916	1019	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752786	42752786	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762382429	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	257	1097	2	ENST00000222329.4:c.1478G>A	p.Arg493His	p.R493H	ENST00000222329	NM_006494.2	493	cGc/cAc	4/4	1	2	FACETS	0.902	0.844	0.962	0.902	0.844	0.962	CLONAL	1	TRUE	1	0.48	2		1099	1187	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007713	45007713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148494241	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	119	353	0	ENST00000558401.1:c.160G>A	p.Asp54Asn	p.D54N	ENST00000558401	NM_004048.2	54	Gac/Aac	2/4	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.48	2		353	396	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267470	7267470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1240458376	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	207	695	0	ENST00000302850.5:c.538G>A	p.Glu180Lys	p.E180K	ENST00000302850	NM_000208.2	180	Gag/Aag	2/22	1	2	FACETS	0.994	0.923	1	0.994	0.923	1	CLONAL	1	TRUE	1	0.48	2		695	868	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120783979	120783979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112244011	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	100	1061	1	ENST00000257552.2:c.1006G>A	p.Ala336Thr	p.A336T	ENST00000257552	NM_002442.3	336	Gcc/Acc	13/15	1	2	FACETS	0.374	0.333	0.418	0.374	0.333	0.418	SUBCLONAL	1	TRUE	1	0.48	2		1062	1115	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650370	48650370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1317593957	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	258	515	0	ENST00000376670.3:c.340G>A	p.Glu114Lys	p.E114K	ENST00000376670	NM_002049.3	114	Gag/Aag	3/6	1	1	FACETS	0.781	0.74	0.822	1	0.994	1	SUBCLONAL	2	TRUE	0	0.48	1		515	523	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910632	50910632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1354117345	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	231	889	1	ENST00000440232.2:c.1735G>A	p.Glu579Lys	p.E579K	ENST00000440232	NM_002691.3	579	Gag/Aag	14/27	1	2	FACETS	0.936	0.873	1	0.936	0.873	1	CLONAL	1	TRUE	1	0.48	2		890	1028	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518050	176518050	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149737957	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	251	885	0	ENST00000292408.4:c.548G>A	p.Arg183His	p.R183H	ENST00000292408	NM_213647.1	183	cGc/cAc	5/18	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.48	2		885	975	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849833	156849833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758876909	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	126	784	0	ENST00000524377.1:c.2089G>A	p.Glu697Lys	p.E697K	ENST00000524377	NM_002529.3	697	Gag/Aag	16/17	1	2	FACETS	0.665	0.603	0.732	0.665	0.603	0.732	SUBCLONAL	1	TRUE	1	0.48	2		784	789	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264751	11264751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1384864432	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	157	727	1	ENST00000361445.4:c.3811G>A	p.Ala1271Thr	p.A1271T	ENST00000361445	NM_004958.3	1271	Gct/Act	26/58	1	2	FACETS	0.828	0.759	0.9	0.828	0.759	0.9	CLONAL	1	TRUE	1	0.48	2		728	790	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869486	102869486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755265524	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	178	514	1	ENST00000307046.8:c.155C>T	p.Thr52Met	p.T52M	ENST00000307046	NM_001111285.1	52	aCg/aTg	2/4	1	2	FACETS	0.993	0.917	1	0.993	0.917	1	CLONAL	1	TRUE	1	0.48	2		515	747	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944547	38944547	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	17	317	0	ENST00000357387.3:c.4913+1G>A		p.X1638_splice	ENST00000357387	NM_152756.3	1638			1	2	FACETS	0.245	0.183	0.319	0.245	0.183	0.319	SUBCLONAL	1	TRUE	1	0.48	2		317	289	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839711	27839711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747419710	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	118	668	1	ENST00000328488.2:c.383C>T	p.Ala128Val	p.A128V	ENST00000328488	NM_003533.2	128	gCg/gTg	1/1	1	2	FACETS	0.734	0.663	0.808	0.734	0.663	0.808	SUBCLONAL	1	TRUE	1	0.48	2		669	670	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486574	56486574	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	197	674	0	ENST00000267101.3:c.1153A>G	p.Asn385Asp	p.N385D	ENST00000267101	NM_001982.3	385	Aat/Gat	10/28	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.48	2		674	821	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156099	99156099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755959497	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	200	714	0	ENST00000074304.5:c.779G>A	p.Arg260Gln	p.R260Q	ENST00000074304	NM_001134224.1	260	cGg/cAg	10/26	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.48	2		714	788	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260036	16260036	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	204	816	0	ENST00000375759.3:c.7301C>A	p.Pro2434His	p.P2434H	ENST00000375759	NM_015001.2	2434	cCt/cAt	11/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.48	2		816	811	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165545	118165545	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	119	446	0	ENST00000369448.3:c.55T>A	p.Trp19Arg	p.W19R	ENST00000369448	NM_017709.3	19	Tgg/Agg	2/2	1	2	FACETS	0.978	0.887	1	0.978	0.887	1	CLONAL	1	TRUE	1	0.48	2		446	507	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849945	156849945	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755323716	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	82	833	0	ENST00000524377.1:c.2201C>T	p.Thr734Met	p.T734M	ENST00000524377	NM_002529.3	734	aCg/aTg	16/17	1	2	FACETS	0.414	0.364	0.467	0.414	0.364	0.467	SUBCLONAL	1	TRUE	1	0.48	2		833	826	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121652	108121652	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	129	470	0	ENST00000278616.4:c.1460T>A	p.Ile487Asn	p.I487N	ENST00000278616	NM_000051.3	487	aTt/aAt	10/63	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.48	2		470	514	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060775	38060775	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	85	1056	1	ENST00000250448.2:c.1214T>C	p.Leu405Pro	p.L405P	ENST00000250448	NM_004496.3	405	cTc/cCc	2/2	1	2	FACETS	0.315	0.277	0.356	0.315	0.277	0.356	SUBCLONAL	1	TRUE	1	0.48	2		1057	1124	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729098	66729098	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	116	609	0	ENST00000307102.5:c.306G>T	p.Glu102Asp	p.E102D	ENST00000307102	NM_002755.3	102	gaG/gaT	3/11	1	2	FACETS	0.781	0.705	0.86	0.781	0.705	0.86	SUBCLONAL	1	TRUE	1	0.48	2		609	619	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66737006	66737006	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	75	412	0	ENST00000307102.5:c.529C>A	p.Leu177Met	p.L177M	ENST00000307102	NM_002755.3	177	Ctg/Atg	5/11	1	2	FACETS	0.625	0.549	0.707	0.625	0.549	0.707	SUBCLONAL	1	TRUE	1	0.48	2		412	500	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354567	91354567	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	109	555	0	ENST00000355112.3:c.4007G>T	p.Arg1336Met	p.R1336M	ENST00000355112	NM_000057.2	1336	aGg/aTg	21/22	1	2	FACETS	0.798	0.719	0.882	0.798	0.719	0.882	SUBCLONAL	1	TRUE	1	0.48	2		555	569	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251094	99251094	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	49	667	1	ENST00000268035.6:c.398T>A	p.Leu133Gln	p.L133Q	ENST00000268035	NM_000875.3	133	cTg/cAg	2/21	1	2	FACETS	0.327	0.276	0.383	0.327	0.276	0.383	SUBCLONAL	1	TRUE	1	0.48	2		668	624	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346276	89346276	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1403325660	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	144	671	0	ENST00000301030.4:c.6674C>T	p.Thr2225Met	p.T2225M	ENST00000301030	NM_001256183.1	2225	aCg/aTg	9/13	1	2	FACETS	0.892	0.815	0.971	0.892	0.815	0.971	CLONAL	1	TRUE	1	0.48	2		671	673	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40864325	40864325	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	122	701	1	ENST00000428826.2:c.1383del	p.Thr462ProfsTer18	p.T462Pfs*18	ENST00000428826		461	ggG/gg	12/21	1	2	FACETS	0.653	0.591	0.72	0.653	0.591	0.72	SUBCLONAL	1	TRUE	1	0.48	2		702	778	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437613	56437613	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	115	461	0	ENST00000407977.2:c.850-1G>A		p.X284_splice	ENST00000407977		284			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.48	2		461	445	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120447	70120448	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	105	1001	0	ENST00000245479.2:c.1451_1452del	p.Ser484TrpfsTer93	p.S484Wfs*93	ENST00000245479	NM_000346.3	483	acCTct/acct	3/3	1	2	FACETS	0.379	0.338	0.423	0.379	0.338	0.423	SUBCLONAL	1	TRUE	1	0.48	2		1001	1154	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78704376	78704376	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	57	515	0	ENST00000306801.3:c.524T>C	p.Ile175Thr	p.I175T	ENST00000306801	NM_020761.2	175	aTc/aCc	5/34	1	2	FACETS	0.419	0.359	0.484	0.419	0.359	0.484	SUBCLONAL	1	TRUE	1	0.48	2		515	567	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765687	41765687	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1269282239	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	82	868	0	ENST00000301178.4:c.2563C>T	p.Leu855Phe	p.L855F	ENST00000301178	NM_021913.4	855	Ctc/Ttc	20/20	1	2	FACETS	0.388	0.341	0.439	0.388	0.341	0.439	SUBCLONAL	1	TRUE	1	0.48	2		868	880	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791560	42791560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	75	902	1	ENST00000575354.2:c.541C>T	p.Arg181Trp	p.R181W	ENST00000575354	NM_015125.3	181	Cgg/Tgg	4/20	1	2	FACETS	0.339	0.296	0.386	0.339	0.296	0.386	SUBCLONAL	1	TRUE	1	0.48	2		903	921	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082799	16082799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753047771	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	41	79	2	ENST00000281043.3:c.613G>A	p.Val205Met	p.V205M	ENST00000281043	NM_005378.4	205	Gtg/Atg	2/3	1	2	FACETS	0.817	0.688	0.958	0.817	0.688	0.958	CLONAL	1	TRUE	1	0.48	2		81	209	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707928	47707929	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	94	408	0	ENST00000233146.2:c.2552_2553del	p.Leu851ArgfsTer13	p.L851Rfs*13	ENST00000233146	NM_000251.2	851	cTT/c	15/16	1	2	FACETS	0.967	0.866	1	0.967	0.866	1	CLONAL	1	TRUE	1	0.48	2		408	405	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880899	134880899	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	105	713	0	ENST00000398015.3:c.1462A>T	p.Thr488Ser	p.T488S	ENST00000398015	NM_004441.4	488	Acc/Tcc	7/16	1	2	FACETS	0.657	0.589	0.729	0.657	0.589	0.729	SUBCLONAL	1	TRUE	1	0.48	2		713	666	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157581	106157581	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	57	338	1	ENST00000380013.4:c.2482T>C	p.Cys828Arg	p.C828R	ENST00000380013	NM_001127208.2	828	Tgc/Cgc	3/11	1	2	FACETS	0.854	0.739	0.978	0.854	0.739	0.978	CLONAL	1	TRUE	1	0.48	2		339	278	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120795	94120795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770806616	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	66	582	0	ENST00000369303.4:c.256C>T	p.Arg86Trp	p.R86W	ENST00000369303	NM_004440.3	86	Cgg/Tgg	3/17	1	2	FACETS	0.441	0.383	0.505	0.441	0.383	0.505	SUBCLONAL	1	TRUE	1	0.48	2		582	623	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781128	161781128	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	83	599	0	ENST00000366898.1:c.1277A>G	p.Glu426Gly	p.E426G	ENST00000366898	NM_004562.2	426	gAa/gGa	11/12	1	2	FACETS	0.473	0.417	0.533	0.473	0.417	0.533	SUBCLONAL	1	TRUE	1	0.48	2		599	731	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403117	116403117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199643166	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	89	457	1	ENST00000397752.3:c.2378G>A	p.Arg793His	p.R793H	ENST00000397752	NM_000245.2	793	cGc/cAc	11/21	1	2	FACETS	0.881	0.785	0.982	0.881	0.785	0.982	CLONAL	1	TRUE	1	0.48	2		458	421	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370753	55370753	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265488427	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	222	564	0	ENST00000297316.4:c.55G>A	p.Ala19Thr	p.A19T	ENST00000297316	NM_022454.3	19	Gcg/Acg	1/2	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.48	2		564	717	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595389	141595389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754981974	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	140	762	1	ENST00000220592.5:c.44C>T	p.Pro15Leu	p.P15L	ENST00000220592	NM_012154.3	15	cCg/cTg	2/19	1	2	FACETS	0.639	0.581	0.699	0.639	0.581	0.699	SUBCLONAL	1	TRUE	1	0.48	2		763	913	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934310	39934310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	33	391	0	ENST00000378444.4:c.289G>A	p.Gly97Ser	p.G97S	ENST00000378444	NM_001123385.1	97	Ggc/Agc	4/15	1	1	FACETS	0.251	0.204	0.304	0.251	0.204	0.304	SUBCLONAL	1	TRUE	0	0.48	1		391	416	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225983	53225983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1392496114	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	112	572	1	ENST00000375401.3:c.2866G>A	p.Ala956Thr	p.A956T	ENST00000375401	NM_004187.3	956	Gcg/Acg	19/26	1	1	FACETS	0.607	0.548	0.67	0.607	0.548	0.67	SUBCLONAL	1	TRUE	0	0.48	1		573	584	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412200	63412200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	209	536	0	ENST00000330258.3:c.967G>A	p.Asp323Asn	p.D323N	ENST00000330258	NM_152424.3	323	Gat/Aat	2/2	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.48	1		536	468	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341632	70341632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751188840	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	248	441	0	ENST00000374080.3:c.1067G>A	p.Arg356Gln	p.R356Q	ENST00000374080		356	cGg/cAg	7/45	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.48	1		441	530	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713129	30713129	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0056462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	26	282	0	ENST00000295754.5:c.455-1G>C		p.X152_splice	ENST00000295754	NM_003242.5	152			1	2	FACETS	0.356	0.282	0.441	0.356	0.282	0.441	SUBCLONAL	1	TRUE	1	0.48	2		282	304	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	203	582	2	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.474144470900701	2		584	820	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	130	326	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.742	0.674	0.814	0.742	0.674	0.814	SUBCLONAL	1	TRUE	1	0.474144470900701	2		328	739	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	226	.	.	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.474144470900701	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.474144470900701	1		0	659	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	132	368	0	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.858	0.781	0.939	0.858	0.781	0.939	CLONAL	1	TRUE	1	0.474144470900701	2		368	649	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023769	27023769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	76	444	0	ENST00000324856.7:c.879del	p.Thr294ProfsTer69	p.T294Pfs*69	ENST00000324856	NM_006015.4	292	aCc/ac	1/20	1	2	FACETS	0.689	0.607	0.778	0.689	0.607	0.778	SUBCLONAL	1	TRUE	1	0.474144470900701	2		444	465	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	154	1010	9	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.474144470900701	2		1019	630	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905772	50905772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854557	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	164	995	0	ENST00000440232.2:c.820G>A	p.Ala274Thr	p.A274T	ENST00000440232	NM_002691.3	274	Gcc/Acc	7/27	1	2	FACETS	0.963	0.887	1	0.963	0.887	1	CLONAL	1	TRUE	1	0.474144470900701	2		995	718	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948101	178948101	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	88	327	0	ENST00000263967.3:c.2873A>G	p.Gln958Arg	p.Q958R	ENST00000263967	NM_006218.2	958	cAg/cGg	20/21	0.438386793203958	3	FACETS	0.9	0.8	1	0.45	0.4	0.504	CLONAL	1	TRUE	1	0.474144470900701	3		327	510	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159110	24159110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779587990	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	103	557	1	ENST00000263121.7:c.782G>A	p.Arg261His	p.R261H	ENST00000263121	NM_003073.3	261	cGc/cAc	6/9	1	2	FACETS	0.871	0.783	0.963	0.871	0.783	0.963	CLONAL	1	TRUE	1	0.474144470900701	2		558	499	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610307	10610307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	204	1003	0	ENST00000171111.5:c.403C>T	p.Arg135Cys	p.R135C	ENST00000171111	NM_203500.1	135	Cgc/Tgc	2/6	1	2	FACETS	0.941	0.874	1	0.941	0.874	1	CLONAL	1	TRUE	1	0.474144470900701	2		1003	914	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948483	71948484	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	144	1170	4	ENST00000298229.2:c.3201dup	p.Ser1068GlnfsTer17	p.S1068Qfs*17	ENST00000298229	NM_001567.3	1065	-/C	26/28	1	2	FACETS	0.748	0.683	0.817	0.748	0.683	0.817	SUBCLONAL	1	TRUE	1	0.474144470900701	2		1174	812	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288789	15288789	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	46	190	0	ENST00000263388.2:c.3950del	p.Pro1317GlnfsTer103	p.P1317Qfs*103	ENST00000263388	NM_000435.2	1317	cCa/ca	24/33	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.474144470900701	2		190	185	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577103	7577103	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	222	827	1	ENST00000269305.4:c.835G>T	p.Gly279Trp	p.G279W	ENST00000269305	NM_001126112.2	279	Ggg/Tgg	8/11	0.474144470900701	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.474144470900701	1		828	648	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911651	134911651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	92	425	0	ENST00000398015.3:c.2116G>A	p.Asp706Asn	p.D706N	ENST00000398015	NM_004441.4	706	Gat/Aat	11/16	0.101189491427964	3	FACETS	0.947	0.844	1			1	INDETERMINATE	1	TRUE	NA	0.474144470900701	3		425	507	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123260369	123260369	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770309121	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	37	761	1	ENST00000358487.5:c.1532C>T	p.Ala511Val	p.A511V	ENST00000358487	NM_000141.4	511	gCg/gTg	11/18	0.474144470900701	1	FACETS	0.203	0.167	0.244	0.203	0.167	0.244	SUBCLONAL	1	TRUE	0	0.474144470900701	1		762	586	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875863	76875863	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	138	279	1	ENST00000373344.5:c.5272T>C	p.Tyr1758His	p.Y1758H	ENST00000373344	NM_000489.3	1758	Tat/Cat	20/35	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.474144470900701	1		280	322	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518160	8518160	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	120	559	0	ENST00000356435.5:c.1231C>G	p.Gln411Glu	p.Q411E	ENST00000356435		411	Caa/Gaa	10/35	0.474144470900701	1	FACETS	0.76	0.69	0.834	0.76	0.69	0.834	SUBCLONAL	1	TRUE	0	0.474144470900701	1		559	508	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865611	57865611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1027428919	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	176	997	2	ENST00000228682.2:c.3088G>A	p.Glu1030Lys	p.E1030K	ENST00000228682	NM_005269.2	1030	Gaa/Aaa	12/12	1	2	FACETS	0.901	0.831	0.974	0.901	0.831	0.974	CLONAL	1	TRUE	1	0.474144470900701	2		999	824	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661015	227661015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201133410	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	127	832	0	ENST00000305123.5:c.2440G>A	p.Asp814Asn	p.D814N	ENST00000305123	NM_005544.2	814	Gac/Aac	1/2	1	2	FACETS	0.742	0.673	0.815	0.742	0.673	0.815	SUBCLONAL	1	TRUE	1	0.474144470900701	2		832	722	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845550	151845550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753793539	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	169	799	0	ENST00000262189.6:c.13462G>A	p.Ala4488Thr	p.A4488T	ENST00000262189	NM_170606.2	4488	Gcc/Acc	52/59	1	2	FACETS	0.931	0.857	1	0.931	0.857	1	CLONAL	1	TRUE	1	0.474144470900701	2		799	766	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599927	10599928	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	191	902	0	ENST00000171111.5:c.1648dup	p.Met550AsnfsTer24	p.M550Nfs*24	ENST00000171111	NM_203500.1	550	atg/aAtg	5/6	1	2	FACETS	0.981	0.909	1	0.981	0.909	1	CLONAL	1	TRUE	1	0.474144470900701	2		902	821	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781641	9781641	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	129	908	0	ENST00000377346.4:c.1951C>A	p.Leu651Ile	p.L651I	ENST00000377346	NM_005026.3	651	Ctc/Atc	15/24	1	2	FACETS	0.683	0.619	0.75	0.683	0.619	0.75	SUBCLONAL	1	TRUE	1	0.474144470900701	2		908	797	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570877	226570877	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs552938819	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	99	565	0	ENST00000366794.5:c.1019G>A	p.Arg340Gln	p.R340Q	ENST00000366794	NM_001618.3	340	cGa/cAa	8/23	1	2	FACETS	0.759	0.68	0.843	0.759	0.68	0.843	SUBCLONAL	1	TRUE	1	0.474144470900701	2		565	550	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781401	3781401	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	144	835	0	ENST00000262367.5:c.4964T>C	p.Leu1655Pro	p.L1655P	ENST00000262367	NM_004380.2	1655	cTg/cCg	30/31	1	2	FACETS	0.926	0.847	1	0.926	0.847	1	CLONAL	1	TRUE	1	0.474144470900701	2		835	656	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298733	15298733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	146	958	0	ENST00000263388.2:c.1565G>A	p.Cys522Tyr	p.C522Y	ENST00000263388	NM_000435.2	522	tGc/tAc	10/33	1	2	FACETS	0.837	0.765	0.912	0.837	0.765	0.912	CLONAL	1	TRUE	1	0.474144470900701	2		958	736	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116188	209116188	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	119	442	0	ENST00000345146.2:c.88C>T	p.Leu30Phe	p.L30F	ENST00000345146	NM_005896.2	30	Ctc/Ttc	3/10	1	2	FACETS	0.873	0.791	0.959	0.873	0.791	0.959	CLONAL	1	TRUE	1	0.474144470900701	2		442	575	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024795	31024797	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1203207717	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	125	691	0	ENST00000375687.4:c.4285_4287del	p.Ser1429del	p.S1429del	ENST00000375687	NM_015338.5	1427	cCTTct/cct	13/13	1	2	FACETS	0.857	0.778	0.94	0.857	0.778	0.94	CLONAL	1	TRUE	1	0.474144470900701	2		691	615	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556683	41556683	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	154	610	0	ENST00000263253.7:c.3631del	p.Glu1211ArgfsTer16	p.E1211Rfs*16	ENST00000263253	NM_001429.3	1210	Ggg/gg	20/31	1	2	FACETS	0.964	0.885	1	0.964	0.885	1	CLONAL	1	TRUE	1	0.474144470900701	2		610	674	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37091957	37091981	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACATCTAATGTGTTTTCCAGAGTGA	ACATCTAATGTGTTTTCCAGAGTGA	-	novel	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	109	392	0	ENST00000231790.2:c.2104-19_2109del		p.X702_splice	ENST00000231790	NM_000249.3	702		19/19	0.474144470900701	1	FACETS	0.909	0.823	0.998	0.909	0.823	0.998	CLONAL	1	TRUE	0	0.474144470900701	1		392	386	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030305	180030305	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs758489407	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	194	951	2	ENST00000261937.6:c.3979C>T	p.Arg1327Ter	p.R1327*	ENST00000261937	NM_182925.4	1327	Cga/Tga	30/30	0.474144470900701	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.474144470900701	1		953	594	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815842	32815842	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	161	888	0	ENST00000354258.4:c.1774G>T	p.Glu592Ter	p.E592*	ENST00000354258	NM_000593.5	592	Gag/Tag	8/11	0.431093362265375	1	FACETS	0.766	0.705	0.83	0.766	0.705	0.83	SUBCLONAL	1	TRUE	0	0.474144470900701	1		888	676	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647488	117647488	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	113	490	0	ENST00000368508.3:c.5456C>A	p.Ser1819Tyr	p.S1819Y	ENST00000368508	NM_002944.2	1819	tCc/tAc	33/43	0.427481278652804	3	FACETS	0.892	0.804	0.985	0.446	0.402	0.493	CLONAL	1	TRUE	1	0.474144470900701	3		490	661	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099287	157099287	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	116	632	2	ENST00000346085.5:c.228del	p.Ala77ProfsTer34	p.A77Pfs*34	ENST00000346085	NM_020732.3	75	gCc/gc	1/20	0.427481278652804	3	FACETS	0.795	0.717	0.878	0.398	0.358	0.439	SUBCLONAL	1	TRUE	1	0.474144470900701	3		634	761	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981291	68981291	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	86	380	0	ENST00000288368.4:c.1363C>T	p.Pro455Ser	p.P455S	ENST00000288368	NM_024870.2	455	Cca/Tca	12/40	1	2	FACETS	0.73	0.648	0.817	0.73	0.648	0.817	SUBCLONAL	1	TRUE	1	0.474144470900701	2		380	497	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759686	133759686	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs61746126	NA	P-0056566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	104	513	0	ENST00000318560.5:c.2009A>G	p.Asn670Ser	p.N670S	ENST00000318560	NM_005157.4	670	aAt/aGt	11/11	0.444389894739895	3	FACETS	0.875	0.784	0.97	0.437	0.392	0.485	CLONAL	1	TRUE	1	0.439512565344058	3		513	660	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574000	7574000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	286	374	0	ENST00000269305.4:c.1027G>T	p.Glu343Ter	p.E343*	ENST00000269305	NM_001126112.2	343	Gag/Tag	10/11	0.444389894739895	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.439512565344058	2		374	603	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495511	56495511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	206	579	0	ENST00000267101.3:c.3701C>T	p.Ser1234Phe	p.S1234F	ENST00000267101	NM_001982.3	1234	tCt/tTt	28/28	0.407538529228098	4	FACETS	0.877	0.816	0.94	0.877	0.816	0.94	CLONAL	2	TRUE	2	0.439512565344058	4		579	769	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974756	21974756	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894097	NA	P-0056566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	124	505	0	ENST00000304494.5:c.71G>C	p.Arg24Pro	p.R24P	ENST00000304494	NM_000077.4	24	cGg/cCg	1/3	0.444389894739895	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	0	0.439512565344058	2		505	279	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667616	29667616	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1060500359	NA	P-0056566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	208	367	0	ENST00000356175.3:c.6952G>T	p.Glu2318Ter	p.E2318*	ENST00000356175	NM_000267.3	2318	Gaa/Taa	46/57	0.439512565344058	9	FACETS	0.985	0.912	1			1	CLONAL	2	TRUE	NA	0.439512565344058	9		367	1220	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624877	9624877	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	196	421	1	ENST00000353224.5:c.100G>T	p.Gly34Cys	p.G34C	ENST00000353224	NM_177990.2	34	Ggc/Tgc	3/10	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.439512565344058	2		422	681	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111429	56111429	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	17	348	0	ENST00000399503.3:c.29C>G	p.Ser10Trp	p.S10W	ENST00000399503	NM_005921.1	10	tCg/tGg	1/20	1	2	FACETS	0.342	0.256	0.445	0.342	0.256	0.445	SUBCLONAL	1	TRUE	1	0.439512565344058	2		348	226	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245861	41245861	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs80356898	NA	P-0056566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	208	331	0	ENST00000357654.3:c.1687C>G	p.Gln563Glu	p.Q563E	ENST00000357654	NM_007294.3	563	Cag/Gag	10/23	0.444389894739895	2	FACETS	0.99	0.929	1	0.99	0.929	1	CLONAL	2	TRUE	0	0.439512565344058	2		331	478	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867774	45867774	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	322	509	0	ENST00000391945.4:c.626A>G	p.Tyr209Cys	p.Y209C	ENST00000391945	NM_000400.3	209	tAc/tGc	8/23	0.407538529228098	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.439512565344058	4		509	966	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539727	187539727	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	35	515	0	ENST00000441802.2:c.8013C>G	p.Phe2671Leu	p.F2671L	ENST00000441802	NM_005245.3	2671	ttC/ttG	10/27	0.439785894970258	2	FACETS	0.489	0.401	0.586	0.244	0.2	0.293	SUBCLONAL	1	TRUE	0	0.439512565344058	2		515	326	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316060	11316060	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	106	410	0	ENST00000361445.4:c.694C>G	p.Gln232Glu	p.Q232E	ENST00000361445	NM_004958.3	232	Cag/Gag	5/58	0.345160986673692	3	FACETS	1	0.94	1	0.532	0.478	0.589	CLONAL	1	TRUE	1	0.439512565344058	3		410	553	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70412288	70412288	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs755298802	NA	P-0056566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	116	313	0	ENST00000373644.4:c.4398A>G	p.Ile1466Met	p.I1466M	ENST00000373644	NM_030625.2	1466	atA/atG	6/12	0.444389894739895	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	0	0.439512565344058	2		313	256	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439882	49439882	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	236	516	0	ENST00000301067.7:c.4659T>G	p.Cys1553Trp	p.C1553W	ENST00000301067	NM_003482.3	1553	tgT/tgG	17/54	0.407538529228098	4	FACETS	0.923	0.864	0.985	0.923	0.864	0.985	CLONAL	2	TRUE	2	0.439512565344058	4		516	837	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911181	32911181	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	183	372	0	ENST00000380152.3:c.2689G>C	p.Glu897Gln	p.E897Q	ENST00000380152		897	Gaa/Caa	11/27	0.444389894739895	3	FACETS	1	0.984	1			1	CLONAL	2	TRUE	NA	0.439512565344058	3		372	434	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816192	89816192	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1047919771	NA	P-0056566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	125	448	0	ENST00000389301.3:c.3185G>A	p.Gly1062Glu	p.G1062E	ENST00000389301	NM_000135.2	1062	gGg/gAg	32/43	0.444389894739895	3	FACETS	0.894	0.81	0.983	0.447	0.405	0.492	CLONAL	1	TRUE	1	0.439512565344058	3		448	776	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260675	1260675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144697790	NA	P-0056566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	99	491	0	ENST00000310581.5:c.2884C>T	p.Arg962Cys	p.R962C	ENST00000310581	NM_198253.2	962	Cgc/Tgc	12/16	0.4335415585695	4	FACETS	0.865	0.772	0.963	0.288	0.257	0.321	CLONAL	1	TRUE	1	0.439512565344058	4		491	750	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936023	44936023	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0056566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	120	168	0	ENST00000377967.4:c.2784C>G	p.Tyr928Ter	p.Y928*	ENST00000377967	NM_021140.2	928	taC/taG	18/29	1	1	FACETS	0.888	0.82	0.955	1	0.99	1	CLONAL	2	TRUE	0	0.439512565344058	1		168	240	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028821	47028841	+	frameshift_variant	Frame_Shift_Del	DEL	GTTCATATCCTCGCGAGTATG	GTTCATATCCTCGCGAGTATG	T	novel	NA	P-0056566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	155	0	0	ENST00000377604.3:c.125_145delinsT	p.Arg42LeufsTer8	p.R42Lfs*8	ENST00000377604	NM_001204468.1	42	cGTTCATATCCTCGCGAGTATGgc/cTgc	3/24	1	1	FACETS	0.756	0.702	0.811	1	0.99	1	SUBCLONAL	2	TRUE	0	0.439512565344058	1		0	364	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759686	133759686	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs61746126	NA	P-0056566-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	48	513	0	ENST00000318560.5:c.2009A>G	p.Asn670Ser	p.N670S	ENST00000318560	NM_005157.4	670	aAt/aGt	11/11	1	2	FACETS	0.792	0.672	0.923	0.792	0.672	0.923	CLONAL	1	TRUE	1	0.35343605681505	2		513	343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574000	7574000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056566-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	108	374	0	ENST00000269305.4:c.1027G>T	p.Glu343Ter	p.E343*	ENST00000269305	NM_001126112.2	343	Gag/Tag	10/11	0.296388655481879	2	FACETS	0.851	0.772	0.934	0.851	0.772	0.934	CLONAL	2	TRUE	0	0.35343605681505	2		374	359	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495511	56495511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056566-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	147	579	0	ENST00000267101.3:c.3701C>T	p.Ser1234Phe	p.S1234F	ENST00000267101	NM_001982.3	1234	tCt/tTt	28/28	0.287033454135813	4	FACETS	0.822	0.752	0.894	0.822	0.752	0.894	CLONAL	2	TRUE	2	0.35343605681505	4		579	685	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974756	21974756	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894097	NA	P-0056566-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	167	505	0	ENST00000304494.5:c.71G>C	p.Arg24Pro	p.R24P	ENST00000304494	NM_000077.4	24	cGg/cCg	1/3	NA	2	FACETS	0.982	0.91	1			1	INDETERMINATE	2	TRUE	NA	0.35343605681505	2		505	481	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667616	29667616	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1060500359	NA	P-0056566-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	93	367	0	ENST00000356175.3:c.6952G>T	p.Glu2318Ter	p.E2318*	ENST00000356175	NM_000267.3	2318	Gaa/Taa	46/57	0.35343605681505	7	FACETS	0.893	0.796	0.996			1	CLONAL	2	TRUE	NA	0.35343605681505	7		367	555	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624877	9624877	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056566-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	100	421	1	ENST00000353224.5:c.100G>T	p.Gly34Cys	p.G34C	ENST00000353224	NM_177990.2	34	Ggc/Tgc	3/10	0.31299597448596	2	FACETS	1	0.98	1	0.702	0.632	0.776	CLONAL	1	TRUE	0	0.35343605681505	2		422	403	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245861	41245861	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs80356898	NA	P-0056566-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	85	331	0	ENST00000357654.3:c.1687C>G	p.Gln563Glu	p.Q563E	ENST00000357654	NM_007294.3	563	Cag/Gag	10/23	0.224582477364553	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.35343605681505	1		331	279	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867774	45867774	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056566-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	157	509	0	ENST00000391945.4:c.626A>G	p.Tyr209Cys	p.Y209C	ENST00000391945	NM_000400.3	209	tAc/tGc	8/23	0.278961987873201	4	FACETS	1	0.975	1			1	CLONAL	2	TRUE	NA	0.35343605681505	4		509	528	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316060	11316060	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056566-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	52	410	0	ENST00000361445.4:c.694C>G	p.Gln232Glu	p.Q232E	ENST00000361445	NM_004958.3	232	Cag/Gag	5/58	0.159235965494051	2	FACETS	0.768	0.656	0.89	0.384	0.328	0.445	INDETERMINATE	1	TRUE	0	0.35343605681505	2		410	383	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70412288	70412288	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs755298802	NA	P-0056566-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	84	313	0	ENST00000373644.4:c.4398A>G	p.Ile1466Met	p.I1466M	ENST00000373644	NM_030625.2	1466	atA/atG	6/12	0.224582477364553	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.35343605681505	1		313	299	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439882	49439882	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056566-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	114	516	0	ENST00000301067.7:c.4659T>G	p.Cys1553Trp	p.C1553W	ENST00000301067	NM_003482.3	1553	tgT/tgG	17/54	0.287033454135813	4	FACETS	0.774	0.699	0.853	0.774	0.699	0.853	SUBCLONAL	2	TRUE	2	0.35343605681505	4		516	564	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911181	32911181	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056566-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	225	372	0	ENST00000380152.3:c.2689G>C	p.Glu897Gln	p.E897Q	ENST00000380152		897	Gaa/Caa	11/27	0.306105788446571	5	FACETS	0.912	0.857	0.967	0.912	0.857	0.967	CLONAL	4	TRUE	1	0.35343605681505	5		372	534	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816192	89816192	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1047919771	NA	P-0056566-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	42	448	0	ENST00000389301.3:c.3185G>A	p.Gly1062Glu	p.G1062E	ENST00000389301	NM_000135.2	1062	gGg/gAg	32/43	0.159235965494051	2	FACETS	0.59	0.493	0.697	0.295	0.246	0.349	INDETERMINATE	1	TRUE	0	0.35343605681505	2		448	403	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260675	1260675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144697790	NA	P-0056566-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	47	491	0	ENST00000310581.5:c.2884C>T	p.Arg962Cys	p.R962C	ENST00000310581	NM_198253.2	962	Cgc/Tgc	12/16	0.201758604218438	5	FACETS	0.851	0.719	0.997	0.17	0.143	0.2	INDETERMINATE	1	TRUE	0	0.35343605681505	5		491	478	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936023	44936023	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0056566-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	65	168	0	ENST00000377967.4:c.2784C>G	p.Tyr928Ter	p.Y928*	ENST00000377967	NM_021140.2	928	taC/taG	18/29	0.354719188210749	2	FACETS	0.915	0.807	1			1	CLONAL	2	TRUE	NA	0.35343605681505	2		168	201	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028821	47028841	+	frameshift_variant	Frame_Shift_Del	DEL	GTTCATATCCTCGCGAGTATG	GTTCATATCCTCGCGAGTATG	T	novel	NA	P-0056566-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	52	0	0	ENST00000377604.3:c.125_145delinsT	p.Arg42LeufsTer8	p.R42Lfs*8	ENST00000377604	NM_001204468.1	42	cGTTCATATCCTCGCGAGTATGgc/cTgc	3/24	1	1	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	0	0.35343605681505	1		0	228	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67624756	67624756	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056566-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	144	416	0	ENST00000272342.5:c.176G>A	p.Arg59Gln	p.R59Q	ENST00000272342	NM_019002.3	59	cGa/cAa	1/6	0.35343605681505	6	FACETS	1	0.947	1	0.524	0.479	0.571	CLONAL	2	TRUE	2	0.35343605681505	6		416	664	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022964	31022964	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056566-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	28	482	0	ENST00000375687.4:c.2449C>G	p.Leu817Val	p.L817V	ENST00000375687	NM_015338.5	817	Cta/Gta	13/13	0.354719188210749	3	FACETS	0.348	0.277	0.429	0.174	0.138	0.215	SUBCLONAL	1	TRUE	1	0.35343605681505	3		482	536	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941720	48941720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056670-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	97	245	0	ENST00000267163.4:c.1030C>T	p.Gln344Ter	p.Q344*	ENST00000267163	NM_000321.2	344	Cag/Tag	10/27	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.62094533691068	2		245	231	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953730	48953730	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs3092891	NA	P-0056670-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	80	191	0	ENST00000267163.4:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000267163	NM_000321.2	445	Cga/Tga	14/27	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.62094533691068	2		191	193	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593649	55593650	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCCAACACAACTTCCTTATGATCACAAATGGGAGTTTCC	novel	NA	P-0056816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	108	475	0	ENST00000288135.5:c.1717_1755dup	p.Pro573_Pro585dup	p.P573_P585dup	ENST00000288135	NM_000222.2	573	gac/gaCCCAACACAACTTCCTTATGATCACAAATGGGAGTTTCCc	11/21	1	2	FACETS	0.394	0.354	0.437	0.394	0.354	0.437	SUBCLONAL	1	TRUE	1	0.880636800256594	2		475	622	SUCCESS
APC	324	MSKCC	GRCh37	5	112155042	112155042	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs863225310	NA	P-0056873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	225	522	0	ENST00000257430.4:c.1312+1G>A		p.X438_splice	ENST00000257430	NM_000038.5	438			0.715269673587871	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.798838342598992	1		522	336	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214708	36214708	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	162	954	0	ENST00000222270.7:c.3134C>G	p.Pro1045Arg	p.P1045R	ENST00000222270	NM_014727.1	1045	cCa/cGa	8/37	0.50745075109807	1	FACETS	0.425	0.392	0.459	0.425	0.392	0.459	SUBCLONAL	1	TRUE	0	0.798838342598992	1		954	573	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332890	152332890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	208	491	0	ENST00000206249.3:c.1196C>T	p.Pro399Leu	p.P399L	ENST00000206249	NM_000125.3	399	cCa/cTa	5/8	1	2	FACETS	0.915	0.856	0.976	0.915	0.856	0.976	CLONAL	1	TRUE	1	0.798838342598992	2		491	569	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0056927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	72	812	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.270504023524834	2		812	494	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0056927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	132	371	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.270504023524834	3	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	1	0.270504023524834	3		371	537	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0056927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	80	331	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.270504023524834	2		331	412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934874	NA	P-0056927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	39	898	1	ENST00000269305.4:c.451C>A	p.Pro151Thr	p.P151T	ENST00000269305	NM_001126112.2	151	Ccc/Acc	5/11	1	2	FACETS	0.3	0.247	0.359	0.3	0.247	0.359	SUBCLONAL	1	TRUE	1	0.270504023524834	2		899	961	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750639	128750639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775522201	NA	P-0056927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	205	790	0	ENST00000377970.2:c.176C>T	p.Ala59Val	p.A59V	ENST00000377970	NM_002467.4	59	gCg/gTg	2/3	0.270504023524834	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.270504023524834	3		790	764	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115727	108115727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747727055	NA	P-0056927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	43	237	0	ENST00000278616.4:c.875C>T	p.Pro292Leu	p.P292L	ENST00000278616	NM_000051.3	292	cCg/cTg	7/63	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.270504023524834	2		237	220	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0056927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	161	482	1	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	0.270504023524834	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.270504023524834	2		483	556	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119808	70119808	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	111	671	0	ENST00000245479.2:c.811del	p.Arg271AlafsTer8	p.R271Afs*8	ENST00000245479	NM_000346.3	270	ttC/tt	3/3	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.270504023524834	2		671	690	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217148	66217148	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747385140	NA	P-0056927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	82	536	0	ENST00000273854.3:c.2467C>T	p.Arg823Trp	p.R823W	ENST00000273854	NM_004439.5	823	Cgg/Tgg	14/18	0.270504023524834	1	FACETS	0.921	0.814	1	0.921	0.814	1	CLONAL	1	TRUE	0	0.270504023524834	1		536	569	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134575	2134575	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	122	965	1	ENST00000219476.3:c.4352G>T	p.Arg1451Leu	p.R1451L	ENST00000219476	NM_000548.3	1451	cGc/cTc	34/42	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.270504023524834	2		966	896	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	47	714	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.781	0.664	0.909	0.781	0.664	0.909	CLONAL	1	TRUE	1	0.435917719869613	2		715	276	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0056933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	130	323	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.912	0.829	0.999	0.912	0.829	0.999	CLONAL	1	TRUE	1	0.435917719869613	2		323	654	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244997	46244997	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs868082376	NA	P-0056933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	121	754	1	ENST00000334344.6:c.3091C>T	p.Gln1031Ter	p.Q1031*	ENST00000334344	NM_152641.2	1031	Cag/Tag	15/21	0.388849069788789	1	FACETS	0.795	0.721	0.872	0.795	0.721	0.872	SUBCLONAL	1	TRUE	0	0.435917719869613	1		755	546	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100436	8100436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1220437638	NA	P-0056933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	173	1182	0	ENST00000346208.3:c.410C>T	p.Ser137Leu	p.S137L	ENST00000346208		137	tCg/tTg	3/6	1	2	FACETS	0.937	0.863	1	0.937	0.863	1	CLONAL	1	TRUE	1	0.435917719869613	2		1182	847	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820617	3820617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	118	1015	1	ENST00000262367.5:c.2834C>T	p.Ser945Leu	p.S945L	ENST00000262367	NM_004380.2	945	tCg/tTg	14/31	1	2	FACETS	0.585	0.527	0.646	0.585	0.527	0.646	SUBCLONAL	1	TRUE	1	0.435917719869613	2		1016	926	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976722	55976722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	31	542	0	ENST00000263923.4:c.1103G>A	p.Gly368Glu	p.G368E	ENST00000263923	NM_002253.2	368	gGa/gAa	9/30	1	2	FACETS	0.307	0.247	0.374	0.307	0.247	0.374	SUBCLONAL	1	TRUE	1	0.435917719869613	2		542	464	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099361	27099361	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	125	713	0	ENST00000324856.7:c.3598C>T	p.Gln1200Ter	p.Q1200*	ENST00000324856	NM_006015.4	1200	Cag/Tag	14/20	1	2	FACETS	0.888	0.805	0.974	0.888	0.805	0.974	CLONAL	1	TRUE	1	0.435917719869613	2		713	646	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212110	36212110	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	33	609	0	ENST00000222270.7:c.1861C>T	p.Pro621Ser	p.P621S	ENST00000222270	NM_014727.1	621	Cct/Tct	3/37	1	2	FACETS	0.389	0.317	0.471	0.389	0.317	0.471	SUBCLONAL	1	TRUE	1	0.435917719869613	2		609	389	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754689	41754689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349708742	NA	P-0056933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	45	989	1	ENST00000301178.4:c.1675G>A	p.Asp559Asn	p.D559N	ENST00000301178	NM_021913.4	559	Gac/Aac	14/20	1	2	FACETS	0.235	0.197	0.278	0.235	0.197	0.278	SUBCLONAL	1	TRUE	1	0.435917719869613	2		990	877	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691100	18691100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372642230	NA	P-0056933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	108	444	0	ENST00000266497.5:c.3211C>T	p.Pro1071Ser	p.P1071S	ENST00000266497		1071	Cct/Tct	23/31	0.435917719869613	3	FACETS	0.986	0.887	1	0.493	0.443	0.546	CLONAL	1	TRUE	1	0.435917719869613	3		444	612	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512245	120512245	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	73	765	0	ENST00000256646.2:c.997G>A	p.Asp333Asn	p.D333N	ENST00000256646	NM_024408.3	333	Gat/Aat	6/34	1	2	FACETS	0.52	0.455	0.591	0.52	0.455	0.591	SUBCLONAL	1	TRUE	1	0.435917719869613	2		765	644	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551798	150551799	+	missense_variant	Missense_Mutation	DNP	GT	GT	AA	novel	NA	P-0056933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	16	125	1	ENST00000369026.2:c.208_209delinsTT	p.Thr70Leu	p.T70L	ENST00000369026	NM_021960.4	70	ACg/TTg	1/3	1	2	FACETS	0.602	0.449	0.78	0.602	0.449	0.78	SUBCLONAL	1	TRUE	1	0.435917719869613	2		126	122	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324084	123324084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	45	578	0	ENST00000358487.5:c.386C>T	p.Ser129Leu	p.S129L	ENST00000358487	NM_000141.4	129	tCa/tTa	4/18	1	2	FACETS	0.346	0.29	0.408	0.346	0.29	0.408	SUBCLONAL	1	TRUE	1	0.435917719869613	2		578	596	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285660	46285660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	121	483	1	ENST00000334344.6:c.5020C>T	p.Pro1674Ser	p.P1674S	ENST00000334344	NM_152641.2	1674	Cct/Tct	17/21	0.388849069788789	1	FACETS	0.895	0.813	0.98	0.895	0.813	0.98	CLONAL	1	TRUE	0	0.435917719869613	1		484	485	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105533	30105533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	142	786	0	ENST00000331968.5:c.1153C>T	p.Pro385Ser	p.P385S	ENST00000331968	NM_002742.2	385	Cca/Tca	7/18	1	2	FACETS	0.83	0.757	0.906	0.83	0.757	0.906	CLONAL	1	TRUE	1	0.435917719869613	2		786	785	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560490	95560504	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAATCTGAGGGGATC	CAATCTGAGGGGATC	-	novel	NA	P-0056933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	65	544	0	ENST00000393063.1:c.5096-11_5099del		p.X1699_splice	ENST00000393063	NM_030621.3	1699		25/28	1	2	FACETS	0.565	0.49	0.646	0.565	0.49	0.646	SUBCLONAL	1	TRUE	1	0.435917719869613	2		544	528	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735442	40735442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs770955919	NA	P-0056933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	110	790	0	ENST00000373198.4:c.3431A>G	p.Asn1144Ser	p.N1144S	ENST00000373198	NM_133170.3	1144	aAc/aGc	25/32	1	2	FACETS	0.758	0.682	0.838	0.758	0.682	0.838	SUBCLONAL	1	TRUE	1	0.435917719869613	2		790	666	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176598	142176598	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0056933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	84	382	0	ENST00000350721.4:c.7504-1G>A		p.X2502_splice	ENST00000350721	NM_001184.3	2502			1	2	FACETS	0.911	0.809	1	0.911	0.809	1	CLONAL	1	TRUE	1	0.435917719869613	2		382	423	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542786	187542786	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	104	558	0	ENST00000441802.2:c.4954T>C	p.Ser1652Pro	p.S1652P	ENST00000441802	NM_005245.3	1652	Tct/Cct	10/27	1	2	FACETS	0.919	0.826	1	0.919	0.826	1	CLONAL	1	TRUE	1	0.435917719869613	2		558	519	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739737	41739737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	104	884	0	ENST00000242208.4:c.236C>T	p.Pro79Leu	p.P79L	ENST00000242208	NM_002192.2	79	cCc/cTc	2/3	0.116084165115019	5	FACETS	1	0.965	1	0.295	0.264	0.328	INDETERMINATE	1	TRUE	1	0.435917719869613	5		884	669	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397743	49397743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	50	559	0	ENST00000418115.1:c.481G>A	p.Ala161Thr	p.A161T	ENST00000418115	NM_001664.2	161	Gca/Aca	5/5	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.12	2		559	799	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956221	55956221	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs767542615	NA	P-0056953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	19	540	0	ENST00000263923.4:c.3094C>T	p.Arg1032Ter	p.R1032*	ENST00000263923	NM_002253.2	1032	Cga/Tga	23/30	1	2	FACETS	0.542	0.41	0.699	0.542	0.41	0.699	SUBCLONAL	1	TRUE	1	0.12	2		540	584	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696642	47696642	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519965	NA	P-0056953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	15	495	0	ENST00000347630.2:c.306C>G	p.Phe102Leu	p.F102L	ENST00000347630	NM_001007230.1	102	ttC/ttG	5/11	1	2	FACETS	0.383	0.279	0.511	0.383	0.279	0.511	SUBCLONAL	1	TRUE	1	0.12	2		495	652	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0056953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	48	679	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			1	2	FACETS	0.99	0.835	1	0.99	0.835	1	CLONAL	1	TRUE	1	0.12	2		679	808	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155392	185155392	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	24	408	0	ENST00000265026.3:c.633G>T	p.Leu211Phe	p.L211F	ENST00000265026	NM_004721.4	211	ttG/ttT	3/14	1	2	FACETS	0.937	0.733	1	0.937	0.733	1	CLONAL	1	TRUE	1	0.12	2		408	427	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510143	187510143	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754820384	NA	P-0056953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	47	546	0	ENST00000441802.2:c.13370A>G	p.Asn4457Ser	p.N4457S	ENST00000441802	NM_005245.3	4457	aAt/aGt	27/27	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.12	2		546	645	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0056972-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	121	309	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.696020002468574	1	FACETS	0.941	0.869	1	0.941	0.869	1	CLONAL	1	TRUE	0	0.696020002468574	1		309	241	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0056972-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	124	509	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.696020002468574	2		510	314	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0056972-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	164	323	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.978	0.905	1	0.978	0.905	1	CLONAL	1	TRUE	1	0.696020002468574	2		323	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0056972-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	24	706	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.696020002468574	1	FACETS	0.112	0.087	0.141	0.112	0.087	0.141	SUBCLONAL	1	TRUE	0	0.696020002468574	1		706	401	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946115	55946115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1560510770	NA	P-0056972-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	185	513	0	ENST00000263923.4:c.4064C>T	p.Pro1355Leu	p.P1355L	ENST00000263923	NM_002253.2	1355	cCt/cTt	30/30	1	2	FACETS	0.986	0.917	1	0.986	0.917	1	CLONAL	1	TRUE	1	0.696020002468574	2		513	539	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637715	23637715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45568339	NA	P-0056972-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	165	424	0	ENST00000261584.4:c.2590C>T	p.Pro864Ser	p.P864S	ENST00000261584	NM_024675.3	864	Cct/Tct	7/13	1	2	FACETS	0.982	0.909	1	0.982	0.909	1	CLONAL	1	TRUE	1	0.696020002468574	2		424	483	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303191	15303191	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs781622431	NA	P-0056972-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	219	756	0	ENST00000263388.2:c.337C>T	p.Arg113Ter	p.R113*	ENST00000263388	NM_000435.2	113	Cga/Tga	3/33	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.696020002468574	2		756	629	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970906	21970906	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501275	NA	P-0056972-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	204	655	0	ENST00000304494.5:c.452C>T	p.Pro151Leu	p.P151L	ENST00000304494	NM_000077.4	151	cCc/cTc	2/3	1	2	FACETS	0.952	0.888	1	0.952	0.888	1	CLONAL	1	TRUE	1	0.696020002468574	2		655	616	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755685	39755685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056972-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	208	626	0	ENST00000288319.7:c.1080G>A	p.Met360Ile	p.M360I	ENST00000288319	NM_182918.3	360	atG/atA	10/10	1	2	FACETS	0.941	0.878	1	0.941	0.878	1	CLONAL	1	TRUE	1	0.696020002468574	2		626	635	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814798	139814798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201857326	NA	P-0056972-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	233	681	0	ENST00000247668.2:c.791C>T	p.Ala264Val	p.A264V	ENST00000247668	NM_021138.3	264	gCg/gTg	8/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.696020002468574	2		681	652	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349200	11349200	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056972-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	150	668	0	ENST00000332029.2:c.136C>T	p.Pro46Ser	p.P46S	ENST00000332029	NM_003745.1	46	Ccg/Tcg	2/2	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.696020002468574	2		668	423	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99491855	99491855	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056972-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	219	593	0	ENST00000268035.6:c.3640C>T	p.Gln1214Ter	p.Q1214*	ENST00000268035	NM_000875.3	1214	Cag/Tag	20/21	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.696020002468574	2		593	603	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23640529	23640529	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056972-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	113	373	0	ENST00000261584.4:c.2582T>C	p.Leu861Ser	p.L861S	ENST00000261584	NM_024675.3	861	tTa/tCa	6/13	1	2	FACETS	0.89	0.809	0.973	0.89	0.809	0.973	CLONAL	1	TRUE	1	0.696020002468574	2		373	365	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743011	743011	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056972-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	57	396	0	ENST00000314574.4:c.967A>G	p.Ile323Val	p.I323V	ENST00000314574	NM_005433.3	323	Ata/Gta	8/12	1	2	FACETS	0.458	0.394	0.526	0.458	0.394	0.526	SUBCLONAL	1	TRUE	1	0.696020002468574	2		396	358	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743886	41743886	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747220380	NA	P-0056972-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	208	734	0	ENST00000301178.4:c.821G>A	p.Gly274Glu	p.G274E	ENST00000301178	NM_021913.4	274	gGa/gAa	7/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.696020002468574	2		734	576	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518915	187518915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs960026866	NA	P-0056972-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	175	493	0	ENST00000441802.2:c.12289C>T	p.Pro4097Ser	p.P4097S	ENST00000441802	NM_005245.3	4097	Ccc/Tcc	24/27	1	2	FACETS	0.833	0.771	0.896	0.833	0.771	0.896	CLONAL	1	TRUE	1	0.696020002468574	2		493	604	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864388	162864388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368134308	NA	P-0056972-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	178	531	0	ENST00000366898.1:c.125G>A	p.Arg42His	p.R42H	ENST00000366898	NM_004562.2	42	cGt/cAt	2/12	0.696020002468574	1	FACETS	0.99	0.929	1	0.99	0.929	1	CLONAL	1	TRUE	0	0.696020002468574	1		531	337	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342823	87342823	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056972-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	191	527	0	ENST00000277120.3:c.1108G>A	p.Asp370Asn	p.D370N	ENST00000277120		370	Gat/Aat	9/19	1	2	FACETS	0.977	0.909	1	0.977	0.909	1	CLONAL	1	TRUE	1	0.696020002468574	2		527	562	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240690	53240694	+	missense_variant	Missense_Mutation	ONP	GGGTT	GGGTT	AAGTG	novel	NA	P-0056972-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	136	292	0	ENST00000375401.3:c.1386_1390delinsCACTT	p.Pro464Ser	p.P464S	ENST00000375401	NM_004187.3	462	ctAACCCcc/ctCACTTcc	10/26	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.696020002468574	1		292	210	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876124	35876124	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057432-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	304	443	0	ENST00000303115.3:c.916T>G	p.Cys306Gly	p.C306G	ENST00000303115	NM_002185.3	306	Tgc/Ggc	8/8	0.276866213277117	2	FACETS	1	0.993	1	0.633	0.603	0.663	INDETERMINATE	1	TRUE	0	0.833466332012345	2		443	576	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118911	70118919	+	inframe_deletion	In_Frame_Del	DEL	GCGCGTGCA	GCGCGTGCA	-	novel	NA	P-0057523-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	95	837	0	ENST00000245479.2:c.485_493del	p.Arg162_Gln164del	p.R162_Q164del	ENST00000245479	NM_000346.3	161	ctGCGCGTGCAg/ctg	2/3	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.13	2		837	998	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729635	162729635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	316	543	1	ENST00000367921.3:c.721G>A	p.Asp241Asn	p.D241N	ENST00000367921	NM_006182.2	241	Gat/Aat	8/18	1	2	FACETS	0.945	0.895	0.995	0.945	0.895	0.995	CLONAL	1	TRUE	1	0.79	2		544	847	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	133	121	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.819	0.751	0.889	0.819	0.751	0.889	CLONAL	1	TRUE	1	0.79	2		121	411	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944516	71944516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293622519	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	334	778	0	ENST00000298229.2:c.2072G>A	p.Arg691Gln	p.R691Q	ENST00000298229	NM_001567.3	691	cGg/cAg	18/28	1	2	FACETS	0.944	0.895	0.993	0.944	0.895	0.993	CLONAL	1	TRUE	1	0.79	2		778	896	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782066	9782066	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	406	921	1	ENST00000377346.4:c.2089G>T	p.Asp697Tyr	p.D697Y	ENST00000377346	NM_005026.3	697	Gac/Tac	17/24	1	2	FACETS	0.922	0.879	0.966	0.922	0.879	0.966	CLONAL	1	TRUE	1	0.79	2		922	1115	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783338	9783338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	307	622	0	ENST00000377346.4:c.2582C>T	p.Ser861Phe	p.S861F	ENST00000377346	NM_005026.3	861	tCc/tTc	20/24	1	2	FACETS	0.922	0.872	0.972	0.922	0.872	0.972	CLONAL	1	TRUE	1	0.79	2		622	843	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784424	9784424	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145589432	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	288	521	0	ENST00000377346.4:c.2809G>A	p.Asp937Asn	p.D937N	ENST00000377346	NM_005026.3	937	Gac/Aac	22/24	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.79	2		521	709	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11313970	11313970	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	383	728	0	ENST00000361445.4:c.766A>C	p.Asn256His	p.N256H	ENST00000361445	NM_004958.3	256	Aat/Cat	6/58	1	2	FACETS	0.956	0.911	1	0.956	0.911	1	CLONAL	1	TRUE	1	0.79	2		728	1014	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797144	45797144	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	417	1080	0	ENST00000450313.1:c.1271T>G	p.Leu424Arg	p.L424R	ENST00000450313	NM_012222.2	424	cTa/cGa	13/16	1	2	FACETS	0.887	0.846	0.929	0.887	0.846	0.929	CLONAL	1	TRUE	1	0.79	2		1080	1190	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739117	46739117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	291	629	0	ENST00000371975.4:c.1466C>T	p.Ala489Val	p.A489V	ENST00000371975	NM_003579.3	489	gCc/gTc	13/18	1	2	FACETS	0.883	0.834	0.933	0.883	0.834	0.933	CLONAL	1	TRUE	1	0.79	2		629	834	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306939	65306939	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	132	412	0	ENST00000342505.4:c.2638G>T	p.Asp880Tyr	p.D880Y	ENST00000342505	NM_002227.2	880	Gac/Tac	19/25	1	2	FACETS	0.628	0.573	0.686	0.628	0.573	0.686	SUBCLONAL	1	TRUE	1	0.79	2		412	532	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873198	71873198	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	162	342	0	ENST00000357731.5:c.996C>A	p.Cys332Ter	p.C332*	ENST00000357731	NM_173808.2	332	tgC/tgA	7/7	1	2	FACETS	0.846	0.782	0.911	0.846	0.782	0.911	CLONAL	1	TRUE	1	0.79	2		342	485	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400981	72400981	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	129	219	1	ENST00000357731.5:c.190G>T	p.Asp64Tyr	p.D64Y	ENST00000357731	NM_173808.2	64	Gat/Tat	2/7	1	2	FACETS	0.93	0.854	1	0.93	0.854	1	CLONAL	1	TRUE	1	0.79	2		220	351	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262259	115262259	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	186	319	0	ENST00000438362.2:c.2295C>A	p.Phe765Leu	p.F765L	ENST00000438362	NM_001242891.1	765	ttC/ttA	18/20	1	2	FACETS	0.855	0.795	0.916	0.855	0.795	0.916	CLONAL	1	TRUE	1	0.79	2		319	551	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275368	115275368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	287	502	0	ENST00000438362.2:c.1045G>A	p.Asp349Asn	p.D349N	ENST00000438362	NM_001242891.1	349	Gat/Aat	10/20	1	2	FACETS	0.919	0.868	0.97	0.919	0.868	0.97	CLONAL	1	TRUE	1	0.79	2		502	791	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699483	117699483	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	192	356	0	ENST00000369458.3:c.158T>G	p.Ile53Ser	p.I53S	ENST00000369458	NM_024626.3	53	aTc/aGc	3/6	1	2	FACETS	0.887	0.826	0.949	0.887	0.826	0.949	CLONAL	1	TRUE	1	0.79	2		356	548	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161298214	161298214	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	204	411	0	ENST00000367975.2:c.106G>T	p.Glu36Ter	p.E36*	ENST00000367975	NM_003001.3	36	Gaa/Taa	3/6	1	2	FACETS	0.919	0.859	0.98	0.919	0.859	0.98	CLONAL	1	TRUE	1	0.79	2		411	562	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746003	162746003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs896311138	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	141	289	0	ENST00000367921.3:c.2126G>A	p.Arg709Gln	p.R709Q	ENST00000367921	NM_006182.2	709	cGa/cAa	16/18	1	2	FACETS	0.769	0.706	0.834	0.769	0.706	0.834	SUBCLONAL	1	TRUE	1	0.79	2		289	464	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218892	193218892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1225502334	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	79	186	0	ENST00000367435.3:c.1450C>T	p.Arg484Cys	p.R484C	ENST00000367435	NM_024529.4	484	Cgt/Tgt	16/17	1	2	FACETS	0.781	0.697	0.869	0.781	0.697	0.869	SUBCLONAL	1	TRUE	1	0.79	2		186	256	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983105	201983105	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	399	609	0	ENST00000359651.3:c.954G>T	p.Lys318Asn	p.K318N	ENST00000359651		318	aaG/aaT	7/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.79	2		609	969	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204501343	204501343	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	136	280	0	ENST00000367182.3:c.312G>T	p.Lys104Asn	p.K104N	ENST00000367182	NM_001278516.1	104	aaG/aaT	5/11	1	2	FACETS	0.737	0.675	0.801	0.737	0.675	0.801	SUBCLONAL	1	TRUE	1	0.79	2		280	467	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206646597	206646597	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	471	1075	1	ENST00000367120.3:c.27G>A	p.Trp9Ter	p.W9*	ENST00000367120	NM_014002.3	9	tgG/tgA	3/22	1	2	FACETS	0.91	0.87	0.95	0.91	0.87	0.95	CLONAL	1	TRUE	1	0.79	2		1076	1310	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206943189	206943189	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	196	346	0	ENST00000423557.1:c.429G>T	p.Lys143Asn	p.K143N	ENST00000423557	NM_000572.2	143	aaG/aaT	4/5	1	2	FACETS	0.909	0.848	0.971	0.909	0.848	0.971	CLONAL	1	TRUE	1	0.79	2		346	546	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226590079	226590079	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs768342881	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	239	454	0	ENST00000366794.5:c.122C>T	p.Ser41Leu	p.S41L	ENST00000366794	NM_001618.3	41	tCg/tTg	2/23	1	2	FACETS	0.956	0.898	1	0.956	0.898	1	CLONAL	1	TRUE	1	0.79	2		454	633	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828185	243828185	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	167	253	0	ENST00000263826.5:c.173A>C	p.Lys58Thr	p.K58T	ENST00000263826	NM_005465.4	58	aAa/aCa	3/13	1	2	FACETS	0.983	0.913	1	0.983	0.913	1	CLONAL	1	TRUE	1	0.79	2		253	430	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63662098	63662098	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	199	385	1	ENST00000279873.7:c.202C>A	p.Gln68Lys	p.Q68K	ENST00000279873	NM_032199.2	68	Caa/Aaa	2/10	0.721112481734921	2	FACETS	0.847	0.789	0.905			1	CLONAL	1	TRUE	NA	0.79	2		386	595	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332102	70332102	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs750698861	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	76	113	0	ENST00000373644.4:c.7C>T	p.Arg3Ter	p.R3*	ENST00000373644	NM_030625.2	3	Cga/Tga	2/12	0.721112481734921	2	FACETS	0.934	0.835	1			1	CLONAL	1	TRUE	NA	0.79	2		113	206	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332949	70332949	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	294	566	0	ENST00000373644.4:c.854C>A	p.Ser285Tyr	p.S285Y	ENST00000373644	NM_030625.2	285	tCt/tAt	2/12	0.721112481734921	2	FACETS	0.917	0.866	0.968			1	CLONAL	1	TRUE	NA	0.79	2		566	812	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70432771	70432771	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	190	360	0	ENST00000373644.4:c.4793G>T	p.Arg1598Ile	p.R1598I	ENST00000373644	NM_030625.2	1598	aGa/aTa	8/12	0.721112481734921	2	FACETS	0.868	0.808	0.929			1	CLONAL	1	TRUE	NA	0.79	2		360	554	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446128	70446128	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1349186385	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	196	358	0	ENST00000373644.4:c.5068C>T	p.Arg1690Ter	p.R1690*	ENST00000373644	NM_030625.2	1690	Cga/Tga	11/12	0.721112481734921	2	FACETS	0.933	0.87	0.996			1	CLONAL	1	TRUE	NA	0.79	2		358	532	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	219	376	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.721112481734921	1	FACETS	0.981	0.933	1	0.981	0.933	1	CLONAL	1	TRUE	0	0.79	1		376	342	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309845	104309845	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060501109	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	212	359	1	ENST00000369902.3:c.436C>T	p.Arg146Ter	p.R146*	ENST00000369902	NM_016169.3	146	Cga/Tga	3/12	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.79	2		360	508	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724144	112724144	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	121	221	0	ENST00000369452.4:c.28G>T	p.Asp10Tyr	p.D10Y	ENST00000369452	NM_007373.3	10	Gac/Tac	2/9	1	2	FACETS	0.826	0.754	0.9	0.826	0.754	0.9	CLONAL	1	TRUE	1	0.79	2		221	371	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724495	112724495	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	214	416	0	ENST00000369452.4:c.379G>T	p.Glu127Ter	p.E127*	ENST00000369452	NM_007373.3	127	Gaa/Taa	2/9	1	2	FACETS	0.921	0.862	0.982	0.921	0.862	0.982	CLONAL	1	TRUE	1	0.79	2		416	588	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769520	112769520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	234	476	0	ENST00000369452.4:c.1472G>A	p.Gly491Asp	p.G491D	ENST00000369452	NM_007373.3	491	gGt/gAt	8/9	1	2	FACETS	0.832	0.78	0.886	0.832	0.78	0.886	CLONAL	1	TRUE	1	0.79	2		476	712	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911535	114911535	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	143	272	0	ENST00000543371.1:c.1053G>T	p.Lys351Asn	p.K351N	ENST00000543371	NM_001198531.1	351	aaG/aaT	10/14	1	2	FACETS	0.921	0.849	0.995	0.921	0.849	0.995	CLONAL	1	TRUE	1	0.79	2		272	393	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14300963	14300963	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	277	469	0	ENST00000256196.4:c.535C>A	p.Gln179Lys	p.Q179K	ENST00000256196		179	Caa/Aaa	6/6	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.79	2		469	680	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410684	32410684	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	248	509	0	ENST00000332351.3:c.1474A>G	p.Lys492Glu	p.K492E	ENST00000332351	NM_024426.4	492	Aag/Gag	10/10	1	2	FACETS	0.907	0.853	0.963	0.907	0.853	0.963	CLONAL	1	TRUE	1	0.79	2		509	692	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200270	67200270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201348433	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	373	780	0	ENST00000312629.5:c.578G>A	p.Arg193Gln	p.R193Q	ENST00000312629	NM_003952.2	193	cGg/cAg	7/15	1	2	FACETS	0.919	0.875	0.965	0.919	0.875	0.965	CLONAL	1	TRUE	1	0.79	2		780	1027	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917607	94917607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	170	380	0	ENST00000536441.1:c.914C>T	p.Thr305Ile	p.T305I	ENST00000536441	NM_144665.3	305	aCt/aTt	6/10	1	2	FACETS	0.924	0.857	0.991	0.924	0.857	0.991	CLONAL	1	TRUE	1	0.79	2		380	466	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922293	100922293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149186732	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	102	207	0	ENST00000325455.5:c.2219G>A	p.Arg740Gln	p.R740Q	ENST00000325455	NM_001202474.3	740	cGa/cAa	5/8	1	2	FACETS	0.82	0.742	0.9	0.82	0.742	0.9	CLONAL	1	TRUE	1	0.79	2		207	315	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996859	100996859	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	235	424	0	ENST00000325455.5:c.1668A>C	p.Gln556His	p.Q556H	ENST00000325455	NM_001202474.3	556	caA/caC	2/8	1	2	FACETS	0.863	0.81	0.918	0.863	0.81	0.918	CLONAL	1	TRUE	1	0.79	2		424	689	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195500	102195500	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	215	316	0	ENST00000263464.3:c.260A>C	p.Lys87Thr	p.K87T	ENST00000263464	NM_001165.4	87	aAa/aCa	2/9	1	2	FACETS	0.9	0.842	0.959	0.9	0.842	0.959	CLONAL	1	TRUE	1	0.79	2		316	605	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201891	102201891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	100	232	0	ENST00000263464.3:c.1243G>T	p.Asp415Tyr	p.D415Y	ENST00000263464	NM_001165.4	415	Gat/Tat	6/9	1	2	FACETS	0.701	0.632	0.773	0.701	0.632	0.773	SUBCLONAL	1	TRUE	1	0.79	2		232	361	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098563	108098563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3218684	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	71	163	0	ENST00000278616.4:c.133C>T	p.Arg45Trp	p.R45W	ENST00000278616	NM_000051.3	45	Cgg/Tgg	3/63	1	2	FACETS	0.71	0.628	0.797	0.71	0.628	0.797	SUBCLONAL	1	TRUE	1	0.79	2		163	253	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	165	254	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.79	2		254	411	SUCCESS
ATM	472	MSKCC	GRCh37	11	108126981	108126981	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	298	488	0	ENST00000278616.4:c.2164T>G	p.Leu722Val	p.L722V	ENST00000278616	NM_000051.3	722	Ttg/Gtg	14/63	1	2	FACETS	0.916	0.866	0.966	0.916	0.866	0.966	CLONAL	1	TRUE	1	0.79	2		488	824	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155001	108155001	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	168	320	0	ENST00000278616.4:c.3794T>G	p.Phe1265Cys	p.F1265C	ENST00000278616	NM_000051.3	1265	tTt/tGt	26/63	1	2	FACETS	0.929	0.862	0.997	0.929	0.862	0.997	CLONAL	1	TRUE	1	0.79	2		320	458	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164078	108164078	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660003	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	82	125	0	ENST00000278616.4:c.4650G>T	p.Lys1550Asn	p.K1550N	ENST00000278616	NM_000051.3	1550	aaG/aaT	31/63	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.79	2		125	200	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186757	108186757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs864622251	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	207	332	0	ENST00000278616.4:c.6115G>A	p.Glu2039Lys	p.E2039K	ENST00000278616	NM_000051.3	2039	Gaa/Aaa	42/63	1	2	FACETS	0.884	0.826	0.943	0.884	0.826	0.943	CLONAL	1	TRUE	1	0.79	2		332	593	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199820	108199820	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	108	160	0	ENST00000278616.4:c.7162C>A	p.Leu2388Ile	p.L2388I	ENST00000278616	NM_000051.3	2388	Ctc/Atc	49/63	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.79	2		160	272	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203493	108203493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140263969	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	63	166	0	ENST00000278616.4:c.7793G>A	p.Arg2598Gln	p.R2598Q	ENST00000278616	NM_000051.3	2598	cGa/cAa	53/63	1	2	FACETS	0.81	0.712	0.911	0.81	0.712	0.911	CLONAL	1	TRUE	1	0.79	2		166	197	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216568	108216568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs767845728	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	133	215	0	ENST00000278616.4:c.8517C>A	p.Phe2839Leu	p.F2839L	ENST00000278616	NM_000051.3	2839	ttC/ttA	58/63	1	2	FACETS	0.881	0.809	0.955	0.881	0.809	0.955	CLONAL	1	TRUE	1	0.79	2		215	382	SUCCESS
CBL	867	MSKCC	GRCh37	11	119167659	119167659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	254	438	0	ENST00000264033.4:c.2068G>A	p.Glu690Lys	p.E690K	ENST00000264033	NM_005188.3	690	Gag/Aag	13/16	1	2	FACETS	0.95	0.894	1	0.95	0.894	1	CLONAL	1	TRUE	1	0.79	2		438	677	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419123	419123	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	149	209	0	ENST00000399788.2:c.3224G>T	p.Ser1075Ile	p.S1075I	ENST00000399788	NM_001042603.1	1075	aGc/aTc	22/28	1	2	FACETS	0.925	0.854	0.997	0.925	0.854	0.997	CLONAL	1	TRUE	1	0.79	2		209	408	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	459846	459846	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	358	671	0	ENST00000399788.2:c.1249G>T	p.Asp417Tyr	p.D417Y	ENST00000399788	NM_001042603.1	417	Gac/Tac	10/28	1	2	FACETS	0.871	0.827	0.915	0.871	0.827	0.915	CLONAL	1	TRUE	1	0.79	2		671	1041	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385236	4385236	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	243	565	0	ENST00000261254.3:c.261C>A	p.Phe87Leu	p.F87L	ENST00000261254	NM_001759.3	87	ttC/ttA	2/5	1	2	FACETS	0.851	0.799	0.904	0.851	0.799	0.904	CLONAL	1	TRUE	1	0.79	2		565	723	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871777	12871777	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	76	158	0	ENST00000228872.4:c.494A>C	p.Lys165Thr	p.K165T	ENST00000228872	NM_004064.3	165	aAa/aCa	2/3	1	2	FACETS	0.705	0.625	0.788	0.705	0.625	0.788	SUBCLONAL	1	TRUE	1	0.79	2		158	273	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435082	18435082	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	112	248	0	ENST00000266497.5:c.67G>T	p.Glu23Ter	p.E23*	ENST00000266497		23	Gaa/Taa	1/31	1	2	FACETS	0.819	0.745	0.896	0.819	0.745	0.896	CLONAL	1	TRUE	1	0.79	2		248	346	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435427	18435427	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	117	228	1	ENST00000266497.5:c.412G>T	p.Asp138Tyr	p.D138Y	ENST00000266497		138	Gat/Tat	1/31	1	2	FACETS	0.874	0.797	0.952	0.874	0.797	0.952	CLONAL	1	TRUE	1	0.79	2		229	339	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552608	18552608	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs760027403	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	177	287	1	ENST00000266497.5:c.2019G>T	p.Lys673Asn	p.K673N	ENST00000266497		673	aaG/aaT	14/31	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.79	2		288	448	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719961	18719961	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	138	266	0	ENST00000266497.5:c.3858G>T	p.Gln1286His	p.Q1286H	ENST00000266497		1286	caG/caT	27/31	1	2	FACETS	0.863	0.793	0.934	0.863	0.793	0.934	CLONAL	1	TRUE	1	0.79	2		266	405	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719983	18719983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1416966490	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	99	209	0	ENST00000266497.5:c.3880G>A	p.Val1294Ile	p.V1294I	ENST00000266497		1294	Gtt/Att	27/31	1	2	FACETS	0.811	0.733	0.892	0.811	0.733	0.892	CLONAL	1	TRUE	1	0.79	2		209	309	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298734	46298734	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	128	189	0	ENST00000334344.6:c.5381A>G	p.Glu1794Gly	p.E1794G	ENST00000334344	NM_152641.2	1794	gAa/gGa	21/21	1	2	FACETS	0.893	0.818	0.969	0.893	0.818	0.969	CLONAL	1	TRUE	1	0.79	2		189	363	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441765	49441765	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	314	566	0	ENST00000301067.7:c.4219T>G	p.Tyr1407Asp	p.Y1407D	ENST00000301067	NM_003482.3	1407	Tac/Gac	14/54	1	2	FACETS	0.962	0.912	1	0.962	0.912	1	CLONAL	1	TRUE	1	0.79	2		566	826	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480320	56480320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	201	319	0	ENST00000267101.3:c.427C>A	p.Leu143Met	p.L143M	ENST00000267101	NM_001982.3	143	Ctg/Atg	4/28	1	2	FACETS	0.969	0.906	1	0.969	0.906	1	CLONAL	1	TRUE	1	0.79	2		319	525	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490288	56490288	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1051947867	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	153	286	0	ENST00000267101.3:c.2057G>T	p.Ser686Ile	p.S686I	ENST00000267101	NM_001982.3	686	aGc/aTc	18/28	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.79	2		286	371	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102874103	102874103	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	112	231	0	ENST00000307046.8:c.57C>A	p.Phe19Leu	p.F19L	ENST00000307046	NM_001111285.1	19	ttC/ttA	1/4	1	2	FACETS	0.857	0.78	0.936	0.857	0.78	0.936	CLONAL	1	TRUE	1	0.79	2		231	331	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891037	112891037	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	147	265	0	ENST00000351677.2:c.371A>C	p.Lys124Thr	p.K124T	ENST00000351677	NM_002834.3	124	aAa/aCa	4/16	1	2	FACETS	0.912	0.842	0.984	0.912	0.842	0.984	CLONAL	1	TRUE	1	0.79	2		265	408	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	301	477	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	0.598452381923504	3	FACETS	1	0.988	1	0.578	0.546	0.611	CLONAL	1	TRUE	1	0.79	3		477	919	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26974623	26974623	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	208	431	1	ENST00000381527.3:c.967C>T	p.Arg323Ter	p.R323*	ENST00000381527	NM_001260.1	323	Cga/Tga	10/13	0.721112481734921	3	FACETS	0.91	0.847	0.976	0.455	0.423	0.488	CLONAL	1	TRUE	1	0.79	3		432	807	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597488	28597488	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs769640419	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	191	299	0	ENST00000241453.7:c.2417C>T	p.Ser806Leu	p.S806L	ENST00000241453	NM_004119.2	806	tCg/tTg	19/24	0.721112481734921	3	FACETS	0.98	0.91	1	0.49	0.455	0.527	CLONAL	1	TRUE	1	0.79	3		299	688	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28631538	28631538	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	324	338	0	ENST00000241453.7:c.430T>G	p.Phe144Val	p.F144V	ENST00000241453	NM_004119.2	144	Ttt/Gtt	4/24	0.721112481734921	3	FACETS	0.905	0.863	0.947	0.905	0.863	0.947	CLONAL	2	TRUE	1	0.79	3		338	632	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28883002	28883002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs115595062	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	207	438	0	ENST00000282397.4:c.3698C>T	p.Pro1233Leu	p.P1233L	ENST00000282397	NM_002019.4	1233	cCg/cTg	28/30	0.721112481734921	3	FACETS	0.869	0.808	0.932	0.435	0.404	0.466	CLONAL	1	TRUE	1	0.79	3		438	841	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28886180	28886180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	250	485	0	ENST00000282397.4:c.3442G>A	p.Ala1148Thr	p.A1148T	ENST00000282397	NM_002019.4	1148	Gca/Aca	26/30	0.721112481734921	3	FACETS	0.897	0.84	0.956	0.449	0.42	0.478	CLONAL	1	TRUE	1	0.79	3		485	984	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28886222	28886222	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	262	427	0	ENST00000282397.4:c.3400C>A	p.Leu1134Met	p.L1134M	ENST00000282397	NM_002019.4	1134	Ctg/Atg	26/30	0.721112481734921	3	FACETS	1	0.968	1	0.523	0.491	0.556	CLONAL	1	TRUE	1	0.79	3		427	885	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896448	28896448	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	168	290	0	ENST00000282397.4:c.3002C>A	p.Ser1001Tyr	p.S1001Y	ENST00000282397	NM_002019.4	1001	tCt/tAt	22/30	0.721112481734921	3	FACETS	0.93	0.858	1	0.465	0.429	0.502	CLONAL	1	TRUE	1	0.79	3		290	638	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008027	29008027	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	142	290	0	ENST00000282397.4:c.742C>A	p.Leu248Ile	p.L248I	ENST00000282397	NM_002019.4	248	Ctt/Att	6/30	0.721112481734921	3	FACETS	0.784	0.716	0.854	0.392	0.358	0.427	SUBCLONAL	1	TRUE	1	0.79	3		290	640	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008270	29008270	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	151	276	1	ENST00000282397.4:c.601G>T	p.Glu201Ter	p.E201*	ENST00000282397	NM_002019.4	201	Gaa/Taa	5/30	0.721112481734921	3	FACETS	0.836	0.767	0.908	0.418	0.383	0.454	CLONAL	1	TRUE	1	0.79	3		277	638	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912068	32912068	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	287	504	0	ENST00000380152.3:c.3576T>G	p.Phe1192Leu	p.F1192L	ENST00000380152		1192	ttT/ttG	11/27	0.721112481734921	3	FACETS	0.962	0.905	1	0.481	0.452	0.51	CLONAL	1	TRUE	1	0.79	3		504	1054	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913384	32913384	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	330	267	0	ENST00000380152.3:c.4892A>C	p.Lys1631Thr	p.K1631T	ENST00000380152		1631	aAa/aCa	11/27	0.721112481734921	3	FACETS	0.994	0.951	1	0.994	0.951	1	CLONAL	2	TRUE	1	0.79	3		267	586	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913729	32913729	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	127	277	0	ENST00000380152.3:c.5237C>A	p.Ser1746Tyr	p.S1746Y	ENST00000380152		1746	tCt/tAt	11/27	0.721112481734921	3	FACETS	0.828	0.753	0.905	0.414	0.376	0.453	CLONAL	1	TRUE	1	0.79	3		277	542	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914887	32914887	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	152	272	0	ENST00000380152.3:c.6395T>C	p.Leu2132Ser	p.L2132S	ENST00000380152		2132	tTa/tCa	11/27	0.721112481734921	3	FACETS	0.935	0.86	1	0.468	0.43	0.507	CLONAL	1	TRUE	1	0.79	3		272	574	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972645	32972645	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876658246	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	219	291	0	ENST00000380152.3:c.9995C>A	p.Ser3332Tyr	p.S3332Y	ENST00000380152		3332	tCt/tAt	27/27	0.721112481734921	3	FACETS	1	0.976	1	0.548	0.512	0.585	CLONAL	1	TRUE	1	0.79	3		291	706	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134681	41134681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	333	314	0	ENST00000379561.5:c.947G>A	p.Arg316Gln	p.R316Q	ENST00000379561	NM_002015.3	316	cGa/cAa	2/3	0.721112481734921	3	FACETS	0.912	0.87	0.953	0.912	0.87	0.953	CLONAL	2	TRUE	1	0.79	3		314	645	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134924	41134924	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	176	278	0	ENST00000379561.5:c.704C>A	p.Ser235Tyr	p.S235Y	ENST00000379561	NM_002015.3	235	tCt/tAt	2/3	0.721112481734921	3	FACETS	0.98	0.907	1	0.49	0.453	0.528	CLONAL	1	TRUE	1	0.79	3		278	634	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941657	48941657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1060503077	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	62	130	0	ENST00000267163.4:c.967G>T	p.Glu323Ter	p.E323*	ENST00000267163	NM_000321.2	323	Gaa/Taa	10/27	0.721112481734921	3	FACETS	0.852	0.744	0.967	0.426	0.372	0.484	CLONAL	1	TRUE	1	0.79	3		130	257	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954217	48954217	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	72	142	0	ENST00000267163.4:c.1418T>G	p.Phe473Cys	p.F473C	ENST00000267163	NM_000321.2	473	tTt/tGt	15/27	0.721112481734921	3	FACETS	0.748	0.658	0.843	0.374	0.329	0.422	SUBCLONAL	1	TRUE	1	0.79	3		142	340	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037919	49037919	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	136	306	0	ENST00000267163.4:c.2159A>C	p.Lys720Thr	p.K720T	ENST00000267163	NM_000321.2	720	aAa/aCa	21/27	0.721112481734921	3	FACETS	0.878	0.802	0.957	0.439	0.401	0.479	CLONAL	1	TRUE	1	0.79	3		306	547	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346413	73346413	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	95	165	0	ENST00000377767.4:c.1387G>T	p.Asp463Tyr	p.D463Y	ENST00000377767	NM_014953.3	463	Gac/Tac	10/21	0.721112481734921	3	FACETS	0.909	0.816	1	0.455	0.408	0.503	CLONAL	1	TRUE	1	0.79	3		165	369	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347916	73347916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139907646	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	10	220	0	ENST00000377767.4:c.1145G>A	p.Arg382Gln	p.R382Q	ENST00000377767	NM_014953.3	382	cGa/cAa	8/21	0.721112481734921	3	FACETS	0.078	0.052	0.111	0.039	0.026	0.056	SUBCLONAL	1	TRUE	1	0.79	3		220	453	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352340	73352340	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	170	387	0	ENST00000377767.4:c.565A>G	p.Ile189Val	p.I189V	ENST00000377767	NM_014953.3	189	Ata/Gta	3/21	0.721112481734921	3	FACETS	0.896	0.827	0.968	0.448	0.413	0.484	CLONAL	1	TRUE	1	0.79	3		387	670	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437782	110437782	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	357	888	0	ENST00000375856.3:c.619C>A	p.Leu207Met	p.L207M	ENST00000375856	NM_003749.2	207	Ctg/Atg	1/2	0.721112481734921	3	FACETS	0.965	0.914	1	0.483	0.457	0.509	CLONAL	1	TRUE	1	0.79	3		888	1306	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046482	30046482	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	253	507	0	ENST00000331968.5:c.2701G>T	p.Glu901Ter	p.E901*	ENST00000331968	NM_002742.2	901	Gaa/Taa	18/18	1	2	FACETS	0.907	0.853	0.962	0.907	0.853	0.962	CLONAL	1	TRUE	1	0.79	2		507	706	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068243	30068243	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	190	339	0	ENST00000331968.5:c.2156C>A	p.Pro719His	p.P719H	ENST00000331968	NM_002742.2	719	cCt/cAt	15/18	1	2	FACETS	0.892	0.831	0.955	0.892	0.831	0.955	CLONAL	1	TRUE	1	0.79	2		339	539	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871680	35871680	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	236	515	0	ENST00000216797.5:c.826A>C	p.Asn276His	p.N276H	ENST00000216797	NM_020529.2	276	Aac/Cac	5/6	1	2	FACETS	0.801	0.75	0.853	0.801	0.75	0.853	CLONAL	1	TRUE	1	0.79	2		515	746	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988565	36988565	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	441	1017	0	ENST00000354822.5:c.88A>C	p.Ile30Leu	p.I30L	ENST00000354822	NM_001079668.2	30	Atc/Ctc	2/3	1	2	FACETS	0.896	0.855	0.937	0.896	0.855	0.937	CLONAL	1	TRUE	1	0.79	2		1017	1246	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40683726	40683726	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	292	563	0	ENST00000249776.8:c.718G>T	p.Glu240Ter	p.E240*	ENST00000249776	NM_033286.3	240	Gaa/Taa	7/9	1	2	FACETS	0.844	0.796	0.892	0.844	0.796	0.892	CLONAL	1	TRUE	1	0.79	2		563	876	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724829	43724829	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	259	527	0	ENST00000382044.4:c.3238G>T	p.Glu1080Ter	p.E1080*	ENST00000382044	NM_001141980.1	1080	Gaa/Taa	17/28	1	2	FACETS	0.916	0.862	0.97	0.916	0.862	0.97	CLONAL	1	TRUE	1	0.79	2		527	716	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43766907	43766907	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765177854	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	118	218	1	ENST00000382044.4:c.1144G>A	p.Val382Ile	p.V382I	ENST00000382044	NM_001141980.1	382	Gtt/Att	10/28	1	2	FACETS	0.861	0.786	0.938	0.861	0.786	0.938	CLONAL	1	TRUE	1	0.79	2		219	347	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007743	45007743	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	156	273	0	ENST00000558401.1:c.190G>T	p.Glu64Ter	p.E64*	ENST00000558401	NM_004048.2	64	Gag/Tag	2/4	1	2	FACETS	0.902	0.834	0.971	0.902	0.834	0.971	CLONAL	1	TRUE	1	0.79	2		273	438	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007752	45007753	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	165	264	0	ENST00000558401.1:c.204dup	p.Val69SerfsTer21	p.V69Sfs*21	ENST00000558401	NM_004048.2	67	gaa/gAaa	2/4	1	2	FACETS	0.956	0.887	1	0.956	0.887	1	CLONAL	1	TRUE	1	0.79	2		264	437	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007894	45007895	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	138	194	0	ENST00000558401.1:c.343_344dup	p.Trp115CysfsTer31	p.W115Cfs*31	ENST00000558401	NM_004048.2	114	aag/aaGTg	2/4	1	2	FACETS	0.846	0.777	0.916	0.846	0.777	0.916	CLONAL	1	TRUE	1	0.79	2		194	413	SUCCESS
BLM	641	MSKCC	GRCh37	15	91290720	91290720	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs139282091	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	158	209	0	ENST00000355112.3:c.98C>T	p.Ser33Leu	p.S33L	ENST00000355112	NM_000057.2	33	tCa/tTa	2/22	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.79	2		209	396	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459939	99459939	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771230491	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	238	415	0	ENST00000268035.6:c.2035G>A	p.Asp679Asn	p.D679N	ENST00000268035	NM_000875.3	679	Gac/Aac	10/21	1	2	FACETS	0.98	0.921	1	0.98	0.921	1	CLONAL	1	TRUE	1	0.79	2		415	615	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	338190	338190	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs370661416	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	463	778	2	ENST00000262320.3:c.2521C>T	p.Arg841Ter	p.R841*	ENST00000262320	NM_003502.3	841	Cga/Tga	11/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.79	2		780	1096	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396560	396560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	376	793	0	ENST00000262320.3:c.466G>A	p.Val156Met	p.V156M	ENST00000262320	NM_003502.3	156	Gtg/Atg	2/11	1	2	FACETS	0.973	0.927	1	0.973	0.927	1	CLONAL	1	TRUE	1	0.79	2		793	978	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396689	396689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	347	621	0	ENST00000262320.3:c.337G>A	p.Asp113Asn	p.D113N	ENST00000262320	NM_003502.3	113	Gac/Aac	2/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.79	2		621	857	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3901011	3901011	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs11644721	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	194	326	0	ENST00000262367.5:c.86-1G>T		p.X29_splice	ENST00000262367	NM_004380.2	29			1	2	FACETS	0.963	0.899	1	0.963	0.899	1	CLONAL	1	TRUE	1	0.79	2		326	510	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857494	9857494	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	223	416	0	ENST00000330684.3:c.3907G>T	p.Asp1303Tyr	p.D1303Y	ENST00000330684	NM_001134407.1	1303	Gac/Tac	13/13	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.79	2		416	551	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041543	14041543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	225	371	0	ENST00000311895.7:c.2090C>A	p.Ser697Tyr	p.S697Y	ENST00000311895	NM_005236.2	697	tCt/tAt	11/11	1	2	FACETS	0.946	0.887	1	0.946	0.887	1	CLONAL	1	TRUE	1	0.79	2		371	602	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134484	30134484	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	260	630	1	ENST00000263025.4:c.47G>T	p.Arg16Ile	p.R16I	ENST00000263025	NM_002746.2	16	aGa/aTa	1/9	1	2	FACETS	0.988	0.932	1	0.988	0.932	1	CLONAL	1	TRUE	1	0.79	2		631	666	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50818342	50818342	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	139	256	0	ENST00000398568.2:c.1920A>C	p.Glu640Asp	p.E640D	ENST00000398568	NM_001042412.1	640	gaA/gaC	11/18	1	2	FACETS	0.931	0.857	1	0.931	0.857	1	CLONAL	1	TRUE	1	0.79	2		256	378	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842731	68842731	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	248	403	0	ENST00000261769.5:c.667G>T	p.Glu223Ter	p.E223*	ENST00000261769	NM_004360.3	223	Gaa/Taa	5/16	1	2	FACETS	0.888	0.835	0.943	0.888	0.835	0.943	CLONAL	1	TRUE	1	0.79	2		403	707	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992945	72992945	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs768546151	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	402	880	0	ENST00000268489.5:c.1100A>C	p.Lys367Thr	p.K367T	ENST00000268489	NM_006885.3	367	aAa/aCa	2/10	1	2	FACETS	0.901	0.858	0.944	0.901	0.858	0.944	CLONAL	1	TRUE	1	0.79	2		880	1130	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942162	81942162	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760308218	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	292	631	1	ENST00000359376.3:c.1699G>A	p.Glu567Lys	p.E567K	ENST00000359376	NM_002661.3	567	Gag/Aag	17/33	1	2	FACETS	0.963	0.91	1	0.963	0.91	1	CLONAL	1	TRUE	1	0.79	2		632	768	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81960697	81960697	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	227	543	0	ENST00000359376.3:c.2428G>T	p.Asp810Tyr	p.D810Y	ENST00000359376	NM_002661.3	810	Gac/Tac	23/33	1	2	FACETS	0.933	0.875	0.992	0.933	0.875	0.992	CLONAL	1	TRUE	1	0.79	2		543	616	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965174	81965174	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199703276	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	332	709	0	ENST00000359376.3:c.2654C>T	p.Pro885Leu	p.P885L	ENST00000359376	NM_002661.3	885	cCg/cTg	25/33	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.79	2		709	828	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972440	81972440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs891516801	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	237	503	0	ENST00000359376.3:c.3233G>A	p.Arg1078Gln	p.R1078Q	ENST00000359376	NM_002661.3	1078	cGa/cAa	29/33	1	2	FACETS	0.878	0.824	0.934	0.878	0.824	0.934	CLONAL	1	TRUE	1	0.79	2		503	683	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348674	89348674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs963622923	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	399	734	0	ENST00000301030.4:c.4276G>A	p.Glu1426Lys	p.E1426K	ENST00000301030	NM_001256183.1	1426	Gaa/Aaa	9/13	1	2	FACETS	0.905	0.862	0.949	0.905	0.862	0.949	CLONAL	1	TRUE	1	0.79	2		734	1116	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979514	7979514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141010860	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	286	602	1	ENST00000319144.4:c.1511C>T	p.Ala504Val	p.A504V	ENST00000319144	NM_001139.2	504	gCg/gTg	11/15	1	2	FACETS	0.895	0.845	0.946	0.895	0.845	0.946	CLONAL	1	TRUE	1	0.79	2		603	809	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984773	11984773	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	149	304	0	ENST00000353533.5:c.319G>T	p.Glu107Ter	p.E107*	ENST00000353533	NM_003010.3	107	Gaa/Taa	3/11	1	2	FACETS	0.896	0.827	0.967	0.896	0.827	0.967	CLONAL	1	TRUE	1	0.79	2		304	421	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011200	12011200	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	91	170	0	ENST00000353533.5:c.607G>T	p.Glu203Ter	p.E203*	ENST00000353533	NM_003010.3	203	Gaa/Taa	5/11	1	2	FACETS	0.866	0.78	0.955	0.866	0.78	0.955	CLONAL	1	TRUE	1	0.79	2		170	266	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15952232	15952232	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	342	671	0	ENST00000268712.3:c.6463G>T	p.Val2155Phe	p.V2155F	ENST00000268712	NM_006311.3	2155	Gtt/Ttt	41/46	1	2	FACETS	0.913	0.867	0.961	0.913	0.867	0.961	CLONAL	1	TRUE	1	0.79	2		671	948	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974924	15974924	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	211	346	0	ENST00000268712.3:c.3951A>C	p.Gln1317His	p.Q1317H	ENST00000268712	NM_006311.3	1317	caA/caC	30/46	1	2	FACETS	0.98	0.918	1	0.98	0.918	1	CLONAL	1	TRUE	1	0.79	2		346	545	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042448	16042448	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	210	361	0	ENST00000268712.3:c.1226A>C	p.Asp409Ala	p.D409A	ENST00000268712	NM_006311.3	409	gAt/gCt	12/46	1	2	FACETS	0.912	0.853	0.972	0.912	0.853	0.972	CLONAL	1	TRUE	1	0.79	2		361	583	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049796	16049796	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	193	267	0	ENST00000268712.3:c.976G>T	p.Glu326Ter	p.E326*	ENST00000268712	NM_006311.3	326	Gaa/Taa	10/46	1	2	FACETS	0.845	0.787	0.905	0.845	0.787	0.905	CLONAL	1	TRUE	1	0.79	2		267	578	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131205	17131205	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs757060348	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	438	954	0	ENST00000285071.4:c.247G>A	p.Glu83Lys	p.E83K	ENST00000285071	NM_144997.5	83	Gag/Aag	4/14	1	2	FACETS	0.964	0.921	1	0.964	0.921	1	CLONAL	1	TRUE	1	0.79	2		954	1150	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527518	29527518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	234	463	1	ENST00000356175.3:c.967G>A	p.Ala323Thr	p.A323T	ENST00000356175	NM_000267.3	323	Gcc/Acc	9/57	1	2	FACETS	0.843	0.79	0.897	0.843	0.79	0.897	CLONAL	1	TRUE	1	0.79	2		464	703	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533316	29533316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1466678870	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	152	209	0	ENST00000356175.3:c.1319G>A	p.Arg440Gln	p.R440Q	ENST00000356175	NM_000267.3	440	cGa/cAa	12/57	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.79	2		209	376	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554610	29554610	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060500317	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	117	230	0	ENST00000356175.3:c.2395A>G	p.Met799Val	p.M799V	ENST00000356175	NM_000267.3	799	Atg/Gtg	20/57	1	2	FACETS	0.832	0.759	0.908	0.832	0.759	0.908	CLONAL	1	TRUE	1	0.79	2		230	356	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684332	29684332	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	255	385	0	ENST00000356175.3:c.7852C>A	p.Leu2618Ile	p.L2618I	ENST00000356175	NM_000267.3	2618	Ctt/Att	53/57	1	2	FACETS	0.961	0.905	1	0.961	0.905	1	CLONAL	1	TRUE	1	0.79	2		385	672	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685556	29685556	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	196	346	0	ENST00000356175.3:c.7966T>G	p.Leu2656Val	p.L2656V	ENST00000356175	NM_000267.3	2656	Ttg/Gtg	54/57	1	2	FACETS	0.94	0.877	1	0.94	0.877	1	CLONAL	1	TRUE	1	0.79	2		346	528	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508177	38508177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749735817	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	270	331	0	ENST00000254066.5:c.485G>A	p.Arg162Gln	p.R162Q	ENST00000254066	NM_000964.3	162	cGa/cAa	5/9	1	2	FACETS	0.97	0.915	1	0.97	0.915	1	CLONAL	1	TRUE	1	0.79	2		331	705	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40500523	40500523	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	279	481	0	ENST00000264657.5:c.12G>A	p.Trp4Ter	p.W4*	ENST00000264657	NM_139276.2	4	tgG/tgA	2/24	1	2	FACETS	0.97	0.916	1	0.97	0.916	1	CLONAL	1	TRUE	1	0.79	2		481	728	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245866	41245866	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	198	382	2	ENST00000357654.3:c.1682C>A	p.Ser561Tyr	p.S561Y	ENST00000357654	NM_007294.3	561	tCt/tAt	10/23	1	2	FACETS	0.799	0.744	0.856	0.799	0.744	0.856	SUBCLONAL	1	TRUE	1	0.79	2		384	627	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688752	47688752	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	212	356	0	ENST00000347630.2:c.548A>G	p.Glu183Gly	p.E183G	ENST00000347630	NM_001007230.1	183	gAg/gGg	7/11	1	2	FACETS	0.927	0.867	0.988	0.927	0.867	0.988	CLONAL	1	TRUE	1	0.79	2		356	579	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440729	56440729	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	334	580	0	ENST00000407977.2:c.489G>T	p.Leu163Phe	p.L163F	ENST00000407977		163	ttG/ttT	5/10	1	2	FACETS	0.996	0.946	1	0.996	0.946	1	CLONAL	1	TRUE	1	0.79	2		580	849	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740542	58740542	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	225	456	0	ENST00000305921.3:c.1447A>C	p.Thr483Pro	p.T483P	ENST00000305921	NM_003620.3	483	Act/Cct	6/6	1	2	FACETS	0.882	0.826	0.939	0.882	0.826	0.939	CLONAL	1	TRUE	1	0.79	2		456	646	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519915	66519915	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	209	365	0	ENST00000358598.2:c.398A>C	p.Glu133Ala	p.E133A	ENST00000358598	NM_212471.2	133	gAa/gCa	4/11	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.79	2		365	527	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745793	745793	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	259	478	0	ENST00000314574.4:c.639A>C	p.Lys213Asn	p.K213N	ENST00000314574	NM_005433.3	213	aaA/aaC	6/12	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.79	2		478	649	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756746	756746	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	259	403	0	ENST00000314574.4:c.82A>C	p.Ser28Arg	p.S28R	ENST00000314574	NM_005433.3	28	Agt/Cgt	2/12	1	2	FACETS	0.857	0.806	0.909	0.857	0.806	0.909	CLONAL	1	TRUE	1	0.79	2		403	765	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570468	39570468	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs267605182	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	63	184	0	ENST00000262039.4:c.664C>T	p.Arg222Ter	p.R222*	ENST00000262039	NM_002647.2	222	Cga/Tga	6/25	1	2	FACETS	0.706	0.619	0.797	0.706	0.619	0.797	SUBCLONAL	1	TRUE	1	0.79	2		184	226	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637927	39637927	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	272	421	2	ENST00000262039.4:c.2344G>T	p.Glu782Ter	p.E782*	ENST00000262039	NM_002647.2	782	Gaa/Taa	22/25	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.79	2		423	674	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56402511	56402511	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	98	148	0	ENST00000348428.3:c.1553G>T	p.Arg518Ile	p.R518I	ENST00000348428	NM_006785.3	518	aGa/aTa	13/17	1	2	FACETS	0.973	0.883	1	0.973	0.883	1	CLONAL	1	TRUE	1	0.79	2		148	255	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244287	5244287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	484	1110	0	ENST00000357368.4:c.1195G>A	p.Glu399Lys	p.E399K	ENST00000357368	NM_002850.3	399	Gag/Aag	11/38	1	2	FACETS	0.903	0.864	0.942	0.903	0.864	0.942	CLONAL	1	TRUE	1	0.79	2		1110	1357	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267686	7267686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	351	528	0	ENST00000302850.5:c.322G>A	p.Val108Ile	p.V108I	ENST00000302850	NM_000208.2	108	Gtc/Atc	2/22	1	2	FACETS	0.971	0.923	1	0.971	0.923	1	CLONAL	1	TRUE	1	0.79	2		528	915	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281521	15281521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	411	839	0	ENST00000263388.2:c.4852G>A	p.Glu1618Lys	p.E1618K	ENST00000263388	NM_000435.2	1618	Gag/Aag	26/33	1	2	FACETS	0.983	0.939	1	0.983	0.939	1	CLONAL	1	TRUE	1	0.79	2		839	1058	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295132	15295132	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	440	841	0	ENST00000263388.2:c.2540A>C	p.Asp847Ala	p.D847A	ENST00000263388	NM_000435.2	847	gAt/gCt	16/33	1	2	FACETS	0.907	0.866	0.949	0.907	0.866	0.949	CLONAL	1	TRUE	1	0.79	2		841	1228	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302461	15302461	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	438	899	0	ENST00000263388.2:c.810C>A	p.Phe270Leu	p.F270L	ENST00000263388	NM_000435.2	270	ttC/ttA	6/33	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.79	2		899	1097	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793245	33793245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	105	178	0	ENST00000498907.2:c.76C>T	p.Pro26Ser	p.P26S	ENST00000498907	NM_004364.3	26	Ccc/Tcc	1/1	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.79	2		178	218	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222962	36222962	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs181607228	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	498	1225	2	ENST00000222270.7:c.5591G>A	p.Arg1864Gln	p.R1864Q	ENST00000222270	NM_014727.1	1864	cGa/cAa	27/37	1	2	FACETS	0.894	0.855	0.932	0.894	0.855	0.932	CLONAL	1	TRUE	1	0.79	2		1227	1411	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40744853	40744853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780894376	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	374	735	0	ENST00000392038.2:c.667G>A	p.Asp223Asn	p.D223N	ENST00000392038	NM_001626.4	223	Gac/Aac	8/14	1	2	FACETS	0.988	0.941	1	0.988	0.941	1	CLONAL	1	TRUE	1	0.79	2		735	958	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726744	41726744	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	404	891	0	ENST00000301178.4:c.289A>G	p.Ile97Val	p.I97V	ENST00000301178	NM_021913.4	97	Ata/Gta	2/20	1	2	FACETS	0.874	0.833	0.916	0.874	0.833	0.916	CLONAL	1	TRUE	1	0.79	2		891	1170	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792017	42792017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	474	816	0	ENST00000575354.2:c.821G>A	p.Arg274Gln	p.R274Q	ENST00000575354	NM_015125.3	274	cGa/cAa	6/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.79	2		816	1136	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719286	52719286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775654171	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	339	611	2	ENST00000322088.6:c.952C>T	p.Arg318Trp	p.R318W	ENST00000322088	NM_014225.5	318	Cgg/Tgg	8/15	1	2	FACETS	0.988	0.938	1	0.988	0.938	1	CLONAL	1	TRUE	1	0.79	2		613	869	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471102	25471102	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	380	786	0	ENST00000264709.3:c.659T>C	p.Val220Ala	p.V220A	ENST00000264709	NM_175629.2	220	gTc/gCc	7/23	1	2	FACETS	0.943	0.898	0.989	0.943	0.898	0.989	CLONAL	1	TRUE	1	0.79	2		786	1020	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978930	25978930	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	173	344	0	ENST00000435504.4:c.993C>A	p.Phe331Leu	p.F331L	ENST00000435504		331	ttC/ttA	10/13	1	2	FACETS	0.813	0.753	0.874	0.813	0.753	0.874	CLONAL	1	TRUE	1	0.79	2		344	539	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009097	27009097	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	120	201	0	ENST00000335756.4:c.33G>T	p.Glu11Asp	p.E11D	ENST00000335756	NM_001809.3	11	gaG/gaT	1/5	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.79	2		201	287	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249941	39249941	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	285	529	0	ENST00000402219.2:c.1628C>A	p.Ser543Tyr	p.S543Y	ENST00000402219	NM_005633.3	543	tCt/tAt	10/23	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.79	2		529	720	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278385	39278385	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	244	512	0	ENST00000402219.2:c.764T>G	p.Leu255Arg	p.L255R	ENST00000402219	NM_005633.3	255	cTt/cGt	6/23	1	2	FACETS	0.902	0.847	0.957	0.902	0.847	0.957	CLONAL	1	TRUE	1	0.79	2		512	685	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609693	46609693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	382	847	0	ENST00000263734.3:c.2417C>T	p.Thr806Ile	p.T806I	ENST00000263734	NM_001430.4	806	aCc/aTc	15/16	1	2	FACETS	0.841	0.799	0.883	0.841	0.799	0.883	CLONAL	1	TRUE	1	0.79	2		847	1150	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672784	47672784	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	190	366	0	ENST00000233146.2:c.1374A>T	p.Leu458Phe	p.L458F	ENST00000233146	NM_000251.2	458	ttA/ttT	8/16	1	2	FACETS	0.951	0.887	1	0.951	0.887	1	CLONAL	1	TRUE	1	0.79	2		366	506	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693876	47693876	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	155	277	0	ENST00000233146.2:c.1590A>C	p.Glu530Asp	p.E530D	ENST00000233146	NM_000251.2	530	gaA/gaC	10/16	1	2	FACETS	0.908	0.84	0.978	0.908	0.84	0.978	CLONAL	1	TRUE	1	0.79	2		277	432	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118926	61118926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	171	313	2	ENST00000295025.8:c.119G>A	p.Ser40Asn	p.S40N	ENST00000295025	NM_002908.2	40	aGc/aAc	2/11	1	2	FACETS	0.799	0.74	0.859	0.799	0.74	0.859	SUBCLONAL	1	TRUE	1	0.79	2		315	542	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118953	61118953	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	216	289	0	ENST00000295025.8:c.146C>A	p.Ser49Tyr	p.S49Y	ENST00000295025	NM_002908.2	49	tCt/tAt	2/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.79	2		289	515	SUCCESS
REL	5966	MSKCC	GRCh37	2	61128147	61128147	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1016724251	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	98	165	0	ENST00000295025.8:c.323G>A	p.Arg108Gln	p.R108Q	ENST00000295025	NM_002908.2	108	cGa/cAa	4/11	1	2	FACETS	0.745	0.672	0.821	0.745	0.672	0.821	SUBCLONAL	1	TRUE	1	0.79	2		165	333	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149488	61149488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	156	268	0	ENST00000295025.8:c.1678G>A	p.Asp560Asn	p.D560N	ENST00000295025	NM_002908.2	560	Gat/Aat	11/11	1	2	FACETS	0.934	0.864	1	0.934	0.864	1	CLONAL	1	TRUE	1	0.79	2		268	423	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715852	61715852	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	213	369	0	ENST00000401558.2:c.2077A>G	p.Lys693Glu	p.K693E	ENST00000401558	NM_003400.3	693	Aaa/Gaa	18/25	1	2	FACETS	0.999	0.936	1	0.999	0.936	1	CLONAL	1	TRUE	1	0.79	2		369	540	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	161	564	1	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	0.849	0.785	0.915	0.849	0.785	0.915	CLONAL	1	TRUE	1	0.79	2		565	480	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152295	99152295	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	179	284	0	ENST00000074304.5:c.374G>T	p.Arg125Ile	p.R125I	ENST00000074304	NM_001134224.1	125	aGa/aTa	6/26	1	2	FACETS	0.942	0.877	1	0.942	0.877	1	CLONAL	1	TRUE	1	0.79	2		284	481	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158595025	158595025	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	197	342	0	ENST00000263640.3:c.1322T>G	p.Phe441Cys	p.F441C	ENST00000263640	NM_001105.4	441	tTt/tGt	10/11	1	2	FACETS	0.837	0.78	0.895	0.837	0.78	0.895	CLONAL	1	TRUE	1	0.79	2		342	596	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719665	190719665	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	72	121	0	ENST00000441310.2:c.1667A>C	p.Lys556Thr	p.K556T	ENST00000441310	NM_000534.4	556	aAa/aCa	9/13	1	2	FACETS	0.98	0.875	1	0.98	0.875	1	CLONAL	1	TRUE	1	0.79	2		121	186	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131412	202131412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339962485	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	232	405	0	ENST00000358485.4:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000358485	NM_001080125.1	127	cGa/cAa	2/9	1	2	FACETS	0.964	0.906	1	0.964	0.906	1	CLONAL	1	TRUE	1	0.79	2		405	609	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248623	212248623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	255	471	0	ENST00000342788.4:c.3644C>T	p.Thr1215Ile	p.T1215I	ENST00000342788	NM_005235.2	1215	aCc/aTc	28/28	1	2	FACETS	0.933	0.878	0.988	0.933	0.878	0.988	CLONAL	1	TRUE	1	0.79	2		471	692	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248705	212248705	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	207	370	0	ENST00000342788.4:c.3562T>C	p.Tyr1188His	p.Y1188H	ENST00000342788	NM_005235.2	1188	Tat/Cat	28/28	1	2	FACETS	0.985	0.922	1	0.985	0.922	1	CLONAL	1	TRUE	1	0.79	2		370	532	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495254	212495254	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	166	421	0	ENST00000342788.4:c.2012T>C	p.Phe671Ser	p.F671S	ENST00000342788	NM_005235.2	671	tTt/tCt	17/28	1	2	FACETS	0.698	0.644	0.754	0.698	0.644	0.754	SUBCLONAL	1	TRUE	1	0.79	2		421	602	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652879	212652879	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1375692246	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	124	210	0	ENST00000342788.4:c.427C>A	p.Leu143Ile	p.L143I	ENST00000342788	NM_005235.2	143	Cta/Ata	4/28	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.79	2		210	291	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624870	9624870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs896197201	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	263	537	0	ENST00000353224.5:c.107C>T	p.Pro36Leu	p.P36L	ENST00000353224	NM_177990.2	36	cCc/cTc	3/10	1	2	FACETS	0.868	0.817	0.92	0.868	0.817	0.92	CLONAL	1	TRUE	1	0.79	2		537	767	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022592	31022592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs373221034	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	279	562	2	ENST00000375687.4:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000375687	NM_015338.5	693	Cga/Tga	13/13	1	2	FACETS	0.972	0.918	1	0.972	0.918	1	CLONAL	1	TRUE	1	0.79	2		564	727	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376766	31376766	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	342	623	1	ENST00000328111.2:c.761C>T	p.Ala254Val	p.A254V	ENST00000328111	NM_006892.3	254	gCt/gTt	7/23	1	2	FACETS	0.962	0.914	1	0.962	0.914	1	CLONAL	1	TRUE	1	0.79	2		624	900	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728729	39728729	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	117	212	1	ENST00000361337.2:c.1009G>T	p.Glu337Ter	p.E337*	ENST00000361337	NM_003286.2	337	Gaa/Taa	12/21	1	2	FACETS	0.892	0.815	0.972	0.892	0.815	0.972	CLONAL	1	TRUE	1	0.79	2		213	332	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268565	46268565	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs758347012	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	150	239	0	ENST00000371998.3:c.2952G>T	p.Met984Ile	p.M984I	ENST00000371998		984	atG/atT	15/23	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.79	2		239	362	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945705	54945705	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	194	475	0	ENST00000312783.6:c.865C>A	p.Leu289Ile	p.L289I	ENST00000312783	NM_198436.1	289	Ctc/Atc	9/10	1	2	FACETS	0.805	0.749	0.863	0.805	0.749	0.863	CLONAL	1	TRUE	1	0.79	2		475	610	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206833	36206833	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1555889984	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	299	457	0	ENST00000300305.3:c.679G>T	p.Glu227Ter	p.E227*	ENST00000300305		227	Gaa/Taa	6/8	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.79	2		457	746	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221721	22221721	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	45	85	0	ENST00000215832.6:c.10G>A	p.Ala4Thr	p.A4T	ENST00000215832	NM_002745.4	4	Gcg/Acg	1/9	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.79	2		85	110	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092931	29092931	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782268	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	222	371	0	ENST00000328354.6:c.1053G>T	p.Glu351Asp	p.E351D	ENST00000328354	NM_007194.3	351	gaG/gaT	10/15	1	2	FACETS	0.937	0.878	0.996	0.937	0.878	0.996	CLONAL	1	TRUE	1	0.79	2		371	600	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29115459	29115459	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	157	218	0	ENST00000328354.6:c.607G>T	p.Asp203Tyr	p.D203Y	ENST00000328354	NM_007194.3	203	Gat/Tat	5/15	1	2	FACETS	0.905	0.838	0.975	0.905	0.838	0.975	CLONAL	1	TRUE	1	0.79	2		218	439	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533773	41533773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	249	324	1	ENST00000263253.7:c.1739G>A	p.Arg580Gln	p.R580Q	ENST00000263253	NM_001429.3	580	cGa/cAa	8/31	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.79	2		325	627	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641905	12641905	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs755926381	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	123	222	0	ENST00000251849.4:c.844C>T	p.Arg282Ter	p.R282*	ENST00000251849	NM_002880.3	282	Cga/Tga	8/17	1	2	FACETS	0.885	0.809	0.962	0.885	0.809	0.962	CLONAL	1	TRUE	1	0.79	2		222	352	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267291	41267291	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	163	285	0	ENST00000349496.5:c.875A>C	p.Lys292Thr	p.K292T	ENST00000349496	NM_001904.3	292	aAa/aCa	6/15	1	2	FACETS	0.886	0.82	0.953	0.886	0.82	0.953	CLONAL	1	TRUE	1	0.79	2		285	466	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098816	47098816	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	391	763	0	ENST00000409792.3:c.6458A>C	p.Asp2153Ala	p.D2153A	ENST00000409792	NM_014159.6	2153	gAc/gCc	15/21	1	2	FACETS	0.936	0.892	0.982	0.936	0.892	0.982	CLONAL	1	TRUE	1	0.79	2		763	1057	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147533	47147533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	189	334	0	ENST00000409792.3:c.4793G>A	p.Arg1598Gln	p.R1598Q	ENST00000409792	NM_014159.6	1598	cGa/cAa	6/21	1	2	FACETS	0.929	0.866	0.993	0.929	0.866	0.993	CLONAL	1	TRUE	1	0.79	2		334	515	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162426	47162426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	184	298	0	ENST00000409792.3:c.3700G>A	p.Glu1234Lys	p.E1234K	ENST00000409792	NM_014159.6	1234	Gaa/Aaa	3/21	1	2	FACETS	0.881	0.819	0.943	0.881	0.819	0.943	CLONAL	1	TRUE	1	0.79	2		298	529	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163941	47163941	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	163	280	0	ENST00000409792.3:c.2185G>T	p.Glu729Ter	p.E729*	ENST00000409792	NM_014159.6	729	Gaa/Taa	3/21	1	2	FACETS	0.946	0.878	1	0.946	0.878	1	CLONAL	1	TRUE	1	0.79	2		280	436	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165406	47165406	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	186	323	1	ENST00000409792.3:c.720A>T	p.Glu240Asp	p.E240D	ENST00000409792	NM_014159.6	240	gaA/gaT	3/21	1	2	FACETS	0.874	0.813	0.936	0.874	0.813	0.936	CLONAL	1	TRUE	1	0.79	2		324	539	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610695	52610695	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	171	256	1	ENST00000394830.3:c.3478C>T	p.Arg1160Ter	p.R1160*	ENST00000394830	NM_018313.4	1160	Cga/Tga	23/30	0.721112481734921	1	FACETS	0.929	0.875	0.981	0.929	0.875	0.981	CLONAL	1	TRUE	0	0.79	1		257	282	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620542	52620542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	256	443	1	ENST00000394830.3:c.3211C>T	p.Arg1071Cys	p.R1071C	ENST00000394830	NM_018313.4	1071	Cgc/Tgc	21/30	0.721112481734921	1	FACETS	0.867	0.825	0.91	0.867	0.825	0.91	CLONAL	1	TRUE	0	0.79	1		444	452	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69986988	69986988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs994568417	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	223	464	1	ENST00000394351.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000394351	NM_000248.3	17	Gaa/Aaa	2/9	1	2	FACETS	0.922	0.865	0.981	0.922	0.865	0.981	CLONAL	1	TRUE	1	0.79	2		465	612	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990402	69990402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765051386	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	111	230	0	ENST00000394351.3:c.361G>A	p.Asp121Asn	p.D121N	ENST00000394351	NM_000248.3	121	Gat/Aat	4/9	1	2	FACETS	0.87	0.792	0.95	0.87	0.792	0.95	CLONAL	1	TRUE	1	0.79	2		230	323	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799799	72799799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779590242	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	274	465	1	ENST00000325599.8:c.1370C>T	p.Ser457Leu	p.S457L	ENST00000325599	NM_018130.2	457	tCg/tTg	11/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.79	2		466	685	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259477	89259477	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200567888	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	199	399	0	ENST00000336596.2:c.621G>T	p.Lys207Asn	p.K207N	ENST00000336596	NM_005233.5	207	aaG/aaT	3/17	1	2	FACETS	0.844	0.787	0.903	0.844	0.787	0.903	CLONAL	1	TRUE	1	0.79	2		399	597	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259557	89259557	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	158	338	0	ENST00000336596.2:c.701C>T	p.Ser234Phe	p.S234F	ENST00000336596	NM_005233.5	234	tCt/tTt	3/17	1	2	FACETS	0.832	0.768	0.897	0.832	0.768	0.897	CLONAL	1	TRUE	1	0.79	2		338	481	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480466	89480466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446890859	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	133	275	0	ENST00000336596.2:c.2303C>T	p.Ser768Leu	p.S768L	ENST00000336596	NM_005233.5	768	tCg/tTg	13/17	1	2	FACETS	0.922	0.848	0.999	0.922	0.848	0.999	CLONAL	1	TRUE	1	0.79	2		275	365	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720994	119720994	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	268	508	1	ENST00000316626.5:c.181G>A	p.Val61Met	p.V61M	ENST00000316626		61	Gtg/Atg	2/12	1	2	FACETS	0.924	0.871	0.978	0.924	0.871	0.978	CLONAL	1	TRUE	1	0.79	2		509	734	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119721018	119721018	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	303	533	0	ENST00000316626.5:c.157G>T	p.Glu53Ter	p.E53*	ENST00000316626		53	Gaa/Taa	2/12	1	2	FACETS	0.97	0.918	1	0.97	0.918	1	CLONAL	1	TRUE	1	0.79	2		533	791	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138423336	138423336	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	134	214	0	ENST00000289153.2:c.1531-1G>T		p.X511_splice	ENST00000289153	NM_006219.2	511			1	2	FACETS	0.912	0.838	0.987	0.912	0.838	0.987	CLONAL	1	TRUE	1	0.79	2		214	372	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453486	138453486	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	139	267	0	ENST00000289153.2:c.962G>T	p.Arg321Leu	p.R321L	ENST00000289153	NM_006219.2	321	cGa/cTa	5/22	1	2	FACETS	0.886	0.815	0.959	0.886	0.815	0.959	CLONAL	1	TRUE	1	0.79	2		267	397	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268419	142268419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs980426116	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	126	295	0	ENST00000350721.4:c.3073C>T	p.Arg1025Cys	p.R1025C	ENST00000350721	NM_001184.3	1025	Cgt/Tgt	15/47	1	2	FACETS	0.851	0.779	0.925	0.851	0.779	0.925	CLONAL	1	TRUE	1	0.79	2		295	375	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274749	142274749	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1232704868	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	154	272	0	ENST00000350721.4:c.2311A>C	p.Lys771Gln	p.K771Q	ENST00000350721	NM_001184.3	771	Aaa/Caa	10/47	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.79	2		272	390	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260150	149260150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761556137	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	224	548	0	ENST00000360632.3:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000360632	NM_015472.4	248	cGa/cAa	4/7	1	2	FACETS	0.892	0.835	0.949	0.892	0.835	0.949	CLONAL	1	TRUE	1	0.79	2		548	636	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916659	178916659	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	135	217	0	ENST00000263967.3:c.46A>G	p.Met16Val	p.M16V	ENST00000263967	NM_006218.2	16	Atg/Gtg	2/21	1	2	FACETS	0.888	0.816	0.962	0.888	0.816	0.962	CLONAL	1	TRUE	1	0.79	2		217	385	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916855	178916855	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	261	464	0	ENST00000263967.3:c.242A>C	p.Glu81Ala	p.E81A	ENST00000263967	NM_006218.2	81	gAa/gCa	2/21	1	2	FACETS	0.919	0.866	0.973	0.919	0.866	0.973	CLONAL	1	TRUE	1	0.79	2		464	719	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928106	178928106	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1242912405	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	187	359	0	ENST00000263967.3:c.1384A>G	p.Thr462Ala	p.T462A	ENST00000263967	NM_006218.2	462	Act/Gct	8/21	1	2	FACETS	0.873	0.813	0.935	0.873	0.813	0.935	CLONAL	1	TRUE	1	0.79	2		359	542	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182679095	182679095	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	119	363	0	ENST00000292782.4:c.439G>T	p.Glu147Ter	p.E147*	ENST00000292782	NM_020640.2	147	Gaa/Taa	4/7	1	2	FACETS	0.672	0.611	0.736	0.672	0.611	0.736	SUBCLONAL	1	TRUE	1	0.79	2		363	448	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182679145	182679145	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	103	304	0	ENST00000292782.4:c.390-1G>T		p.X130_splice	ENST00000292782	NM_020640.2	130			1	2	FACETS	0.716	0.647	0.789	0.716	0.647	0.789	SUBCLONAL	1	TRUE	1	0.79	2		304	364	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451439	187451439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	243	424	0	ENST00000232014.4:c.43G>A	p.Ala15Thr	p.A15T	ENST00000232014	NM_001130845.1	15	Gcc/Acc	3/10	1	2	FACETS	0.961	0.904	1	0.961	0.904	1	CLONAL	1	TRUE	1	0.79	2		424	640	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612028	189612028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs900140738	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	269	475	0	ENST00000264731.3:c.1780C>T	p.Arg594Ter	p.R594*	ENST00000264731	NM_003722.4	594	Cga/Tga	14/14	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.79	2		475	674	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957774	1957774	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	342	655	0	ENST00000382891.5:c.2740G>A	p.Glu914Lys	p.E914K	ENST00000382891	NM_133335.3	914	Gag/Aag	15/22	1	2	FACETS	0.953	0.904	1	0.953	0.904	1	CLONAL	1	TRUE	1	0.79	2		655	909	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131175	55131175	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	234	439	0	ENST00000257290.5:c.718A>G	p.Asn240Asp	p.N240D	ENST00000257290	NM_006206.4	240	Aat/Gat	5/23	1	2	FACETS	0.957	0.899	1	0.957	0.899	1	CLONAL	1	TRUE	1	0.79	2		439	619	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156540	55156540	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775205485	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	243	500	0	ENST00000257290.5:c.2941C>T	p.Arg981Cys	p.R981C	ENST00000257290	NM_006206.4	981	Cgt/Tgt	22/23	1	2	FACETS	0.866	0.813	0.921	0.866	0.813	0.921	CLONAL	1	TRUE	1	0.79	2		500	710	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594094	55594094	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs794726675	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	168	325	1	ENST00000288135.5:c.1879+1G>A		p.X627_splice	ENST00000288135	NM_000222.2	627			1	2	FACETS	0.975	0.906	1	0.975	0.906	1	CLONAL	1	TRUE	1	0.79	2		326	436	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55597510	55597510	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	175	320	0	ENST00000288135.5:c.2158G>T	p.Glu720Ter	p.E720*	ENST00000288135	NM_000222.2	720	Gag/Tag	15/21	1	2	FACETS	0.957	0.89	1	0.957	0.89	1	CLONAL	1	TRUE	1	0.79	2		320	463	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599298	55599298	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	216	369	0	ENST00000288135.5:c.2424T>G	p.Ile808Met	p.I808M	ENST00000288135	NM_000222.2	808	atT/atG	17/21	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.79	2		369	541	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968610	55968610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374980446	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	327	522	1	ENST00000263923.4:c.2053G>A	p.Glu685Lys	p.E685K	ENST00000263923	NM_002253.2	685	Gaa/Aaa	14/30	1	2	FACETS	0.926	0.878	0.975	0.926	0.878	0.975	CLONAL	1	TRUE	1	0.79	2		523	894	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972931	55972931	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	220	419	0	ENST00000263923.4:c.1459A>G	p.Ser487Gly	p.S487G	ENST00000263923	NM_002253.2	487	Agt/Ggt	11/30	1	2	FACETS	0.866	0.811	0.923	0.866	0.811	0.923	CLONAL	1	TRUE	1	0.79	2		419	643	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976936	55976936	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	200	305	1	ENST00000263923.4:c.977-1G>T		p.X326_splice	ENST00000263923	NM_002253.2	326			1	2	FACETS	0.999	0.934	1	0.999	0.934	1	CLONAL	1	TRUE	1	0.79	2		306	507	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189912	66189912	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	142	263	0	ENST00000273854.3:c.3034C>A	p.Leu1012Ile	p.L1012I	ENST00000273854	NM_004439.5	1012	Ctt/Att	18/18	1	2	FACETS	0.883	0.813	0.955	0.883	0.813	0.955	CLONAL	1	TRUE	1	0.79	2		263	407	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213774	66213774	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	152	283	0	ENST00000273854.3:c.2656G>T	p.Asp886Tyr	p.D886Y	ENST00000273854	NM_004439.5	886	Gat/Tat	15/18	1	2	FACETS	0.964	0.892	1	0.964	0.892	1	CLONAL	1	TRUE	1	0.79	2		283	399	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217159	66217159	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	244	402	0	ENST00000273854.3:c.2456T>C	p.Phe819Ser	p.F819S	ENST00000273854	NM_004439.5	819	tTt/tCt	14/18	1	2	FACETS	0.992	0.933	1	0.992	0.933	1	CLONAL	1	TRUE	1	0.79	2		402	623	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193889	106193889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395976555	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	166	253	0	ENST00000380013.4:c.4351C>T	p.Arg1451Trp	p.R1451W	ENST00000380013	NM_001127208.2	1451	Cgg/Tgg	10/11	1	2	FACETS	0.994	0.923	1	0.994	0.923	1	CLONAL	1	TRUE	1	0.79	2		253	423	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159134	143159134	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	105	217	0	ENST00000262992.4:c.719G>T	p.Arg240Ile	p.R240I	ENST00000262992	NM_001101669.1	240	aGa/aTa	10/24	1	2	FACETS	0.96	0.873	1	0.96	0.873	1	CLONAL	1	TRUE	1	0.79	2		217	277	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542692	187542692	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	217	334	0	ENST00000441802.2:c.5048G>T	p.Gly1683Val	p.G1683V	ENST00000441802	NM_005245.3	1683	gGg/gTg	10/27	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.79	2		334	537	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584475	187584475	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1163622953	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	124	258	0	ENST00000441802.2:c.3558C>A	p.Phe1186Leu	p.F1186L	ENST00000441802	NM_005245.3	1186	ttC/ttA	3/27	1	2	FACETS	0.83	0.759	0.904	0.83	0.759	0.904	CLONAL	1	TRUE	1	0.79	2		258	378	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628184	187628184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61733570	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	320	630	0	ENST00000441802.2:c.2798G>A	p.Arg933His	p.R933H	ENST00000441802	NM_005245.3	933	cGt/cAt	2/27	1	2	FACETS	0.919	0.87	0.968	0.919	0.87	0.968	CLONAL	1	TRUE	1	0.79	2		630	882	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629472	187629472	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	244	545	0	ENST00000441802.2:c.1510A>C	p.Asn504His	p.N504H	ENST00000441802	NM_005245.3	504	Aat/Cat	2/27	1	2	FACETS	0.851	0.799	0.904	0.851	0.799	0.904	CLONAL	1	TRUE	1	0.79	2		545	726	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950817	38950817	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	56	128	0	ENST00000357387.3:c.3133T>C	p.Phe1045Leu	p.F1045L	ENST00000357387	NM_152756.3	1045	Ttc/Ctc	31/38	1	2	FACETS	0.886	0.776	1	0.886	0.776	1	CLONAL	1	TRUE	1	0.79	2		128	160	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38960627	38960627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376491170	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	72	161	0	ENST00000357387.3:c.1724G>A	p.Arg575Gln	p.R575Q	ENST00000357387	NM_152756.3	575	cGa/cAa	20/38	1	2	FACETS	0.832	0.739	0.929	0.832	0.739	0.929	CLONAL	1	TRUE	1	0.79	2		161	219	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754855	57754855	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	142	253	0	ENST00000274289.3:c.335T>G	p.Ile112Ser	p.I112S	ENST00000274289	NM_006622.3	112	aTt/aGt	2/14	1	2	FACETS	0.982	0.907	1	0.982	0.907	1	CLONAL	1	TRUE	1	0.79	2		253	366	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576522	67576522	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	158	274	0	ENST00000274335.5:c.801T>G	p.Ile267Met	p.I267M	ENST00000274335		267	atT/atG	5/15	1	2	FACETS	0.915	0.847	0.985	0.915	0.847	0.985	CLONAL	1	TRUE	1	0.79	2		274	437	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682692	86682692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757298110	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	60	158	0	ENST00000274376.6:c.2897G>A	p.Arg966His	p.R966H	ENST00000274376	NM_002890.2	966	cGt/cAt	23/25	1	2	FACETS	0.759	0.665	0.859	0.759	0.665	0.859	SUBCLONAL	1	TRUE	1	0.79	2		158	200	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685209	86685209	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	97	146	0	ENST00000274376.6:c.2926-1G>T		p.X976_splice	ENST00000274376	NM_002890.2	976			1	2	FACETS	0.923	0.836	1	0.923	0.836	1	CLONAL	1	TRUE	1	0.79	2		146	266	SUCCESS
APC	324	MSKCC	GRCh37	5	112102048	112102048	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	67	219	0	ENST00000257430.4:c.161G>T	p.Ser54Ile	p.S54I	ENST00000257430	NM_000038.5	54	aGt/aTt	3/16	1	2	FACETS	0.695	0.612	0.783	0.695	0.612	0.783	SUBCLONAL	1	TRUE	1	0.79	2		219	244	SUCCESS
APC	324	MSKCC	GRCh37	5	112173912	112173912	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	140	291	0	ENST00000257430.4:c.2621C>A	p.Ser874Ter	p.S874*	ENST00000257430	NM_000038.5	874	tCa/tAa	16/16	1	2	FACETS	0.882	0.811	0.954	0.882	0.811	0.954	CLONAL	1	TRUE	1	0.79	2		291	402	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267600319	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	184	281	0	ENST00000257430.4:c.4199C>T	p.Ser1400Leu	p.S1400L	ENST00000257430	NM_000038.5	1400	tCg/tTg	16/16	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.79	2		281	466	SUCCESS
APC	324	MSKCC	GRCh37	5	112175921	112175921	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	89	148	0	ENST00000257430.4:c.4630G>T	p.Glu1544Ter	p.E1544*	ENST00000257430	NM_000038.5	1544	Gaa/Taa	16/16	1	2	FACETS	0.909	0.819	1	0.909	0.819	1	CLONAL	1	TRUE	1	0.79	2		148	248	SUCCESS
APC	324	MSKCC	GRCh37	5	112176873	112176873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	273	253	0	ENST00000257430.4:c.5582C>A	p.Ser1861Tyr	p.S1861Y	ENST00000257430	NM_000038.5	1861	tCt/tAt	16/16	1	2	FACETS	0.968	0.933	1	1	0.996	1	CLONAL	2	TRUE	1	0.79	2		253	357	SUCCESS
APC	324	MSKCC	GRCh37	5	112176882	112176882	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	133	260	0	ENST00000257430.4:c.5591C>A	p.Ser1864Tyr	p.S1864Y	ENST00000257430	NM_000038.5	1864	tCt/tAt	16/16	1	2	FACETS	0.965	0.888	1	0.965	0.888	1	CLONAL	1	TRUE	1	0.79	2		260	349	SUCCESS
APC	324	MSKCC	GRCh37	5	112177368	112177368	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	125	228	0	ENST00000257430.4:c.6077C>A	p.Ser2026Tyr	p.S2026Y	ENST00000257430	NM_000038.5	2026	tCt/tAt	16/16	1	2	FACETS	0.95	0.872	1	0.95	0.872	1	CLONAL	1	TRUE	1	0.79	2		228	333	SUCCESS
APC	324	MSKCC	GRCh37	5	112178000	112178000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768922431	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	165	462	0	ENST00000257430.4:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000257430	NM_000038.5	2237	Cga/Tga	16/16	1	2	FACETS	0.879	0.815	0.946	0.879	0.815	0.946	CLONAL	1	TRUE	1	0.79	2		462	475	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915058	131915058	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	196	351	1	ENST00000265335.6:c.415G>T	p.Glu139Ter	p.E139*	ENST00000265335		139	Gaa/Taa	4/25	1	2	FACETS	0.877	0.817	0.937	0.877	0.817	0.937	CLONAL	1	TRUE	1	0.79	2		352	566	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925500	131925500	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs867459964	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	139	209	0	ENST00000265335.6:c.1423C>A	p.Leu475Ile	p.L475I	ENST00000265335		475	Ctt/Att	9/25	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.79	2		209	338	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939718	131939718	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	141	230	0	ENST00000265335.6:c.2504A>C	p.Lys835Thr	p.K835T	ENST00000265335		835	aAa/aCa	15/25	1	2	FACETS	0.888	0.817	0.96	0.888	0.817	0.96	CLONAL	1	TRUE	1	0.79	2		230	402	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457707	149457707	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	368	731	0	ENST00000286301.3:c.697T>G	p.Phe233Val	p.F233V	ENST00000286301	NM_005211.3	233	Ttt/Gtt	5/22	1	2	FACETS	0.917	0.872	0.963	0.917	0.872	0.963	CLONAL	1	TRUE	1	0.79	2		731	1016	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504305	149504305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780819031	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	362	797	1	ENST00000261799.4:c.1897G>A	p.Val633Ile	p.V633I	ENST00000261799	NM_002609.3	633	Gtc/Atc	13/23	1	2	FACETS	0.854	0.811	0.898	0.854	0.811	0.898	CLONAL	1	TRUE	1	0.79	2		798	1073	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504382	149504382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	373	761	0	ENST00000261799.4:c.1820G>A	p.Gly607Asp	p.G607D	ENST00000261799	NM_002609.3	607	gGc/gAc	13/23	1	2	FACETS	0.965	0.918	1	0.965	0.918	1	CLONAL	1	TRUE	1	0.79	2		761	979	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562133	176562133	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	241	441	0	ENST00000439151.2:c.29G>T	p.Arg10Ile	p.R10I	ENST00000439151	NM_022455.4	10	aGa/aTa	2/23	1	2	FACETS	0.884	0.83	0.939	0.884	0.83	0.939	CLONAL	1	TRUE	1	0.79	2		441	690	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665317	176665317	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	196	313	0	ENST00000439151.2:c.4001C>A	p.Ser1334Tyr	p.S1334Y	ENST00000439151	NM_022455.4	1334	tCt/tAt	7/23	1	2	FACETS	0.971	0.907	1	0.971	0.907	1	CLONAL	1	TRUE	1	0.79	2		313	511	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057087	180057087	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	343	869	2	ENST00000261937.6:c.532C>T	p.Pro178Ser	p.P178S	ENST00000261937	NM_182925.4	178	Cca/Tca	5/30	1	2	FACETS	0.829	0.785	0.873	0.829	0.785	0.873	CLONAL	1	TRUE	1	0.79	2		871	1048	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490441	20490441	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	240	483	0	ENST00000346618.3:c.1178C>A	p.Ser393Tyr	p.S393Y	ENST00000346618	NM_001949.4	393	tCt/tAt	7/7	1	2	FACETS	0.843	0.79	0.896	0.843	0.79	0.896	CLONAL	1	TRUE	1	0.79	2		483	721	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940421	31940421	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	406	1021	1	ENST00000375333.2:c.454G>T	p.Glu152Ter	p.E152*	ENST00000375333	NM_032454.1	152	Gaa/Taa	3/8	1	2	FACETS	0.842	0.801	0.883	0.842	0.801	0.883	CLONAL	1	TRUE	1	0.79	2		1022	1221	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166902	32166902	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	494	1094	0	ENST00000375023.3:c.4336C>A	p.Pro1446Thr	p.P1446T	ENST00000375023	NM_004557.3	1446	Ccc/Acc	24/30	1	2	FACETS	0.93	0.89	0.97	0.93	0.89	0.97	CLONAL	1	TRUE	1	0.79	2		1094	1345	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64286793	64286793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	178	304	0	ENST00000370651.3:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000370651	NM_003463.4	3	cGa/cAa	2/6	1	2	FACETS	0.975	0.908	1	0.975	0.908	1	CLONAL	1	TRUE	1	0.79	2		304	462	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64290014	64290014	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	205	365	0	ENST00000370651.3:c.457C>T	p.Arg153Cys	p.R153C	ENST00000370651	NM_003463.4	153	Cgt/Tgt	6/6	1	2	FACETS	0.869	0.812	0.928	0.869	0.812	0.928	CLONAL	1	TRUE	1	0.79	2		365	597	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112029203	112029203	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	162	338	0	ENST00000368678.4:c.365C>T	p.Ala122Val	p.A122V	ENST00000368678		122	gCc/gTc	5/13	1	2	FACETS	0.842	0.779	0.907	0.842	0.779	0.907	CLONAL	1	TRUE	1	0.79	2		338	487	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662700	117662700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	178	347	0	ENST00000368508.3:c.4765G>A	p.Glu1589Lys	p.E1589K	ENST00000368508	NM_002944.2	1589	Gaa/Aaa	29/43	1	2	FACETS	0.891	0.828	0.955	0.891	0.828	0.955	CLONAL	1	TRUE	1	0.79	2		347	506	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715350	117715350	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1466068877	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	106	206	0	ENST00000368508.3:c.1139G>T	p.Arg380Ile	p.R380I	ENST00000368508	NM_002944.2	380	aGa/aTa	10/43	1	2	FACETS	0.886	0.805	0.969	0.886	0.805	0.969	CLONAL	1	TRUE	1	0.79	2		206	303	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117717404	117717404	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	114	268	0	ENST00000368508.3:c.803A>G	p.Glu268Gly	p.E268G	ENST00000368508	NM_002944.2	268	gAa/gGa	8/43	1	2	FACETS	0.761	0.692	0.833	0.761	0.692	0.833	SUBCLONAL	1	TRUE	1	0.79	2		268	379	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199623	138199623	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	193	325	0	ENST00000237289.4:c.1041A>C	p.Glu347Asp	p.E347D	ENST00000237289	NM_001270507.1	347	gaA/gaC	7/9	1	2	FACETS	0.973	0.909	1	0.973	0.909	1	CLONAL	1	TRUE	1	0.79	2		325	502	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163911	152163911	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	188	383	0	ENST00000206249.3:c.632G>T	p.Arg211Ile	p.R211I	ENST00000206249	NM_000125.3	211	aGa/aTa	2/8	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.79	2		383	473	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469898	157469898	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs794727977	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	308	641	0	ENST00000346085.5:c.2692C>T	p.Arg898Ter	p.R898*	ENST00000346085	NM_020732.3	898	Cga/Tga	9/20	1	2	FACETS	0.958	0.907	1	0.958	0.907	1	CLONAL	1	TRUE	1	0.79	2		641	814	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963878	2963878	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	332	662	1	ENST00000396946.4:c.1929C>A	p.Phe643Leu	p.F643L	ENST00000396946	NM_032415.4	643	ttC/ttA	15/25	0.721112481734921	3	FACETS	1	0.963	1			1	CLONAL	1	TRUE	NA	0.79	3		663	1145	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14027744	14027744	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	144	286	0	ENST00000405192.2:c.100T>G	p.Phe34Val	p.F34V	ENST00000405192	NM_001163147.1	34	Ttc/Gtc	3/12	1	2	FACETS	0.796	0.732	0.862	0.796	0.732	0.862	SUBCLONAL	1	TRUE	1	0.79	2		286	458	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14027749	14027749	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	142	280	0	ENST00000405192.2:c.95G>T	p.Arg32Ile	p.R32I	ENST00000405192	NM_001163147.1	32	aGa/aTa	3/12	1	2	FACETS	0.799	0.734	0.866	0.799	0.734	0.866	SUBCLONAL	1	TRUE	1	0.79	2		280	450	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509038	106509038	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	262	568	2	ENST00000359195.3:c.1032G>T	p.Lys344Asn	p.K344N	ENST00000359195	NM_002649.2	344	aaG/aaT	2/11	1	2	FACETS	0.895	0.843	0.948	0.895	0.843	0.948	CLONAL	1	TRUE	1	0.79	2		570	741	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513314	106513314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559655430	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	150	377	0	ENST00000359195.3:c.2218G>A	p.Glu740Lys	p.E740K	ENST00000359195	NM_002649.2	740	Gag/Aag	4/11	1	2	FACETS	0.971	0.898	1	0.971	0.898	1	CLONAL	1	TRUE	1	0.79	2		377	391	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523477	106523477	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	89	163	1	ENST00000359195.3:c.2630-1G>T		p.X877_splice	ENST00000359195	NM_002649.2	877			1	2	FACETS	0.92	0.829	1	0.92	0.829	1	CLONAL	1	TRUE	1	0.79	2		164	245	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523517	106523517	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	104	198	0	ENST00000359195.3:c.2669A>C	p.Lys890Thr	p.K890T	ENST00000359195	NM_002649.2	890	aAa/aCa	8/11	1	2	FACETS	0.847	0.768	0.928	0.847	0.768	0.928	CLONAL	1	TRUE	1	0.79	2		198	311	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526618	106526618	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	206	315	0	ENST00000359195.3:c.2911A>C	p.Asn971His	p.N971H	ENST00000359195	NM_002649.2	971	Aat/Cat	10/11	1	2	FACETS	0.969	0.907	1	0.969	0.907	1	CLONAL	1	TRUE	1	0.79	2		315	538	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398665	116398665	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1351264833	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	152	266	0	ENST00000397752.3:c.2255C>A	p.Ser752Tyr	p.S752Y	ENST00000397752	NM_000245.2	752	tCt/tAt	9/21	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.79	2		266	374	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846318	128846318	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	370	743	0	ENST00000249373.3:c.1154C>A	p.Ser385Tyr	p.S385Y	ENST00000249373	NM_005631.4	385	tCt/tAt	6/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.79	2		743	911	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514441	148514441	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	180	335	0	ENST00000320356.2:c.1283A>C	p.Asn428Thr	p.N428T	ENST00000320356	NM_004456.4	428	aAt/aCt	11/20	1	2	FACETS	0.833	0.773	0.894	0.833	0.773	0.894	CLONAL	1	TRUE	1	0.79	2		335	547	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849901	151849901	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	199	394	0	ENST00000262189.6:c.12415C>T	p.Arg4139Ter	p.R4139*	ENST00000262189	NM_170606.2	4139	Cga/Tga	49/59	1	2	FACETS	0.885	0.826	0.946	0.885	0.826	0.946	CLONAL	1	TRUE	1	0.79	2		394	569	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851373	151851373	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	222	419	0	ENST00000262189.6:c.12118C>A	p.Leu4040Ile	p.L4040I	ENST00000262189	NM_170606.2	4040	Ctt/Att	47/59	1	2	FACETS	0.901	0.844	0.959	0.901	0.844	0.959	CLONAL	1	TRUE	1	0.79	2		419	624	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873888	151873888	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	197	328	0	ENST00000262189.6:c.8650C>T	p.Arg2884Ter	p.R2884*	ENST00000262189	NM_170606.2	2884	Cga/Tga	38/59	1	2	FACETS	0.851	0.793	0.91	0.851	0.793	0.91	CLONAL	1	TRUE	1	0.79	2		328	586	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891566	151891566	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	181	338	0	ENST00000262189.6:c.4466A>C	p.Asp1489Ala	p.D1489A	ENST00000262189	NM_170606.2	1489	gAt/gCt	29/59	1	2	FACETS	0.937	0.872	1	0.937	0.872	1	CLONAL	1	TRUE	1	0.79	2		338	489	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945012	151945012	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	11	41	0	ENST00000262189.6:c.2507C>A	p.Ser836Tyr	p.S836Y	ENST00000262189	NM_170606.2	836	tCt/tAt	14/59	1	2	FACETS	0.398	0.279	0.539	0.398	0.279	0.539	SUBCLONAL	1	TRUE	1	0.79	2		41	70	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38134017	38134017	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs377462564	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	204	360	0	ENST00000317025.8:c.3869C>T	p.Ser1290Leu	p.S1290L	ENST00000317025	NM_023034.1	1290	tCg/tTg	23/24	0.721112481734921	4	FACETS	0.97	0.9	1			1	CLONAL	1	TRUE	NA	0.79	4		360	953	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146216	38146216	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	1046	686	0	ENST00000317025.8:c.3290G>A	p.Arg1097His	p.R1097H	ENST00000317025	NM_023034.1	1097	cGc/cAc	19/24	0.721112481734921	4	FACETS	0.939	0.918	0.961			1	CLONAL	3	TRUE	NA	0.79	4		686	1682	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162254	38162254	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	176	279	0	ENST00000317025.8:c.2462G>T	p.Arg821Ile	p.R821I	ENST00000317025	NM_023034.1	821	aGa/aTa	14/24	0.721112481734921	4	FACETS	0.957	0.883	1			1	CLONAL	1	TRUE	NA	0.79	4		279	833	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205681	38205681	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	788	458	0	ENST00000317025.8:c.9C>A	p.Phe3Leu	p.F3L	ENST00000317025	NM_023034.1	3	ttC/ttA	2/24	0.721112481734921	4	FACETS	0.954	0.929	0.978			1	CLONAL	3	TRUE	NA	0.79	4		458	1248	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129936	69129936	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	158	326	0	ENST00000288368.4:c.4690G>T	p.Asp1564Tyr	p.D1564Y	ENST00000288368	NM_024870.2	1564	Gat/Tat	38/40	1	2	FACETS	0.887	0.82	0.955	0.887	0.82	0.955	CLONAL	1	TRUE	1	0.79	2		326	451	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70967581	70967581	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	299	524	0	ENST00000276594.2:c.1442G>A	p.Arg481Gln	p.R481Q	ENST00000276594	NM_024504.3	481	cGa/cAa	7/8	1	2	FACETS	0.938	0.887	0.99	0.938	0.887	0.99	CLONAL	1	TRUE	1	0.79	2		524	807	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965872	90965872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775451862	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	122	220	0	ENST00000265433.3:c.1445G>A	p.Arg482Lys	p.R482K	ENST00000265433	NM_002485.4	482	aGa/aAa	11/16	1	2	FACETS	0.872	0.798	0.949	0.872	0.798	0.949	CLONAL	1	TRUE	1	0.79	2		220	354	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982702	90982702	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs372159380	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	146	300	0	ENST00000265433.3:c.786C>A	p.Phe262Leu	p.F262L	ENST00000265433	NM_002485.4	262	ttC/ttA	7/16	1	2	FACETS	0.852	0.784	0.921	0.852	0.784	0.921	CLONAL	1	TRUE	1	0.79	2		300	434	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752966	128752966	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	170	343	0	ENST00000377970.2:c.1127T>C	p.Val376Ala	p.V376A	ENST00000377970	NM_002467.4	376	gTc/gCc	3/3	1	2	FACETS	0.824	0.764	0.887	0.824	0.764	0.887	CLONAL	1	TRUE	1	0.79	2		343	522	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457400	5457400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1480335907	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	76	110	1	ENST00000381577.3:c.374G>A	p.Arg125Gln	p.R125Q	ENST00000381577	NM_014143.3	125	cGa/cAa	3/7	1	2	FACETS	0.962	0.861	1	0.962	0.861	1	CLONAL	1	TRUE	1	0.79	2		111	200	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319934	8319934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764537367	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	141	238	0	ENST00000356435.5:c.5567C>T	p.Thr1856Met	p.T1856M	ENST00000356435		1856	aCg/aTg	34/35	1	2	FACETS	0.954	0.88	1	0.954	0.88	1	CLONAL	1	TRUE	1	0.79	2		238	374	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528645	8528645	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	207	320	0	ENST00000356435.5:c.487T>G	p.Phe163Val	p.F163V	ENST00000356435		163	Ttc/Gtc	4/35	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.79	2		320	518	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971051	21971051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767642535	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	303	691	0	ENST00000304494.5:c.307C>T	p.Arg103Trp	p.R103W	ENST00000304494	NM_000077.4	103	Cgg/Tgg	2/3	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.79	2		691	731	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27183570	27183570	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	222	378	0	ENST00000380036.4:c.1144G>T	p.Glu382Ter	p.E382*	ENST00000380036	NM_000459.3	382	Gaa/Taa	8/23	1	2	FACETS	0.888	0.831	0.945	0.888	0.831	0.945	CLONAL	1	TRUE	1	0.79	2		378	633	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27192616	27192616	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	164	325	2	ENST00000380036.4:c.1619C>A	p.Ser540Tyr	p.S540Y	ENST00000380036	NM_000459.3	540	tCt/tAt	11/23	1	2	FACETS	0.849	0.786	0.914	0.849	0.786	0.914	CLONAL	1	TRUE	1	0.79	2		327	489	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206779	27206779	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	232	406	0	ENST00000380036.4:c.2564A>C	p.Lys855Thr	p.K855T	ENST00000380036	NM_000459.3	855	aAa/aCa	15/23	1	2	FACETS	0.989	0.929	1	0.989	0.929	1	CLONAL	1	TRUE	1	0.79	2		406	594	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336291	80336291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	158	333	0	ENST00000286548.4:c.1028C>T	p.Ala343Val	p.A343V	ENST00000286548	NM_002072.3	343	gCc/gTc	7/7	1	2	FACETS	0.881	0.815	0.949	0.881	0.815	0.949	CLONAL	1	TRUE	1	0.79	2		333	454	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482298	87482298	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	294	547	0	ENST00000277120.3:c.1585A>C	p.Asn529His	p.N529H	ENST00000277120		529	Aat/Cat	14/19	1	2	FACETS	0.998	0.944	1	0.998	0.944	1	CLONAL	1	TRUE	1	0.79	2		547	746	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248030	98248030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772368023	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	217	472	0	ENST00000331920.6:c.521C>T	p.Ala174Val	p.A174V	ENST00000331920	NM_000264.3	174	gCg/gTg	3/24	1	2	FACETS	0.852	0.796	0.908	0.852	0.796	0.908	CLONAL	1	TRUE	1	0.79	2		472	645	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900288	101900288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111854391	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	171	276	1	ENST00000374994.4:c.722C>T	p.Ser241Leu	p.S241L	ENST00000374994	NM_004612.2	241	tCg/tTg	4/9	1	2	FACETS	0.875	0.811	0.939	0.875	0.811	0.939	CLONAL	1	TRUE	1	0.79	2		277	495	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249860	110249860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770068428	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	381	948	0	ENST00000374672.4:c.815G>A	p.Arg272His	p.R272H	ENST00000374672	NM_004235.4	272	cGc/cAc	3/5	1	2	FACETS	0.975	0.929	1	0.975	0.929	1	CLONAL	1	TRUE	1	0.79	2		948	989	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779816	135779816	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768189353	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	221	341	0	ENST00000298552.3:c.2023G>A	p.Asp675Asn	p.D675N	ENST00000298552	NM_001162426.1	675	Gac/Aac	16/23	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.79	2		341	554	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801020	135801020	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	196	333	0	ENST00000298552.3:c.317A>C	p.Lys106Thr	p.K106T	ENST00000298552	NM_001162426.1	106	aAg/aCg	5/23	1	2	FACETS	0.884	0.825	0.946	0.884	0.825	0.946	CLONAL	1	TRUE	1	0.79	2		333	561	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15836765	15836765	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs775309730	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	258	209	0	ENST00000307771.7:c.827C>T	p.Ser276Leu	p.S276L	ENST00000307771	NM_005089.3	276	tCg/tTg	9/11	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.79	1		209	346	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53253955	53253955	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	357	406	0	ENST00000375401.3:c.117G>T	p.Glu39Asp	p.E39D	ENST00000375401	NM_004187.3	39	gaG/gaT	1/26	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.79	1		406	478	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412011	63412011	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	292	331	0	ENST00000330258.3:c.1156G>T	p.Glu386Ter	p.E386*	ENST00000330258	NM_152424.3	386	Gaa/Taa	2/2	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.79	1		331	399	SUCCESS
AR	367	MSKCC	GRCh37	X	66765792	66765792	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	489	658	0	ENST00000374690.3:c.804G>T	p.Met268Ile	p.M268I	ENST00000374690	NM_000044.3	268	atG/atT	1/8	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.79	1		658	676	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937357	76937357	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	179	160	0	ENST00000373344.5:c.3391A>G	p.Arg1131Gly	p.R1131G	ENST00000373344	NM_000489.3	1131	Aga/Gga	9/35	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.79	1		160	243	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615637	100615637	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	310	292	0	ENST00000308731.7:c.695A>G	p.Asp232Gly	p.D232G	ENST00000308731	NM_000061.2	232	gAt/gGt	8/19	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.79	1		292	403	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819769	81819769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	284	593	1	ENST00000359376.3:c.175G>A	p.Asp59Asn	p.D59N	ENST00000359376	NM_002661.3	59	Gac/Aac	2/33	1	2	FACETS	0.97	0.917	1	0.97	0.917	1	CLONAL	1	TRUE	1	0.79	2		594	741	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	45	488	4	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	0.786	0.661	0.923	0.786	0.661	0.923	CLONAL	1	TRUE	1	0.275991337654144	2		492	415	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	74	582	2	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.671	0.587	0.763	0.671	0.587	0.763	SUBCLONAL	1	TRUE	1	0.275991337654144	2		584	799	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	32	371	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.805	0.656	0.973	0.805	0.656	0.973	CLONAL	1	TRUE	1	0.275991337654144	2		371	288	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	83	560	2	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	0.666	0.587	0.752	0.666	0.587	0.752	SUBCLONAL	1	TRUE	1	0.275991337654144	2		562	903	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	78	456	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.924	0.82	1	1	0.983	1	CLONAL	2	TRUE	1	0.275991337654144	2		457	306	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	92	527	3	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.917	0.815	1	0.917	0.815	1	CLONAL	1	TRUE	1	0.275991337654144	2		530	727	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	21	351	1	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	2	FACETS	0.57	0.439	0.722	0.57	0.439	0.722	SUBCLONAL	1	TRUE	1	0.275991337654144	2		352	267	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385177	41385177	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201332786	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	186	701	0	ENST00000373198.4:c.784G>A	p.Val262Ile	p.V262I	ENST00000373198	NM_133170.3	262	Gtc/Atc	6/32	0.275991337654144	3	FACETS	0.908	0.839	0.979	0.908	0.839	0.979	CLONAL	2	TRUE	1	0.275991337654144	3		701	845	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	87	712	1	ENST00000324856.7:c.4555del	p.Gln1519ArgfsTer8	p.Q1519Rfs*8	ENST00000324856	NM_006015.4	1517	gCc/gc	18/20	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.275991337654144	2		713	561	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280109	66280109	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	22	336	0	ENST00000273854.3:c.1580C>T	p.Ala527Val	p.A527V	ENST00000273854	NM_004439.5	527	gCa/gTa	7/18	1	2	FACETS	0.514	0.399	0.648	0.514	0.399	0.648	SUBCLONAL	1	TRUE	1	0.275991337654144	2		336	310	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532517	63532517	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	109	836	2	ENST00000307078.5:c.2062del	p.Leu688Ter	p.L688*	ENST00000307078	NM_004655.3	688	Ctg/tg	8/11	1	2	FACETS	0.952	0.854	1	0.952	0.854	1	CLONAL	1	TRUE	1	0.275991337654144	2		838	830	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047906	180047906	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	134	920	0	ENST00000261937.6:c.2269G>A	p.Val757Ile	p.V757I	ENST00000261937	NM_182925.4	757	Gtc/Atc	15/30	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.275991337654144	2		920	932	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882049	36882050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs780753361	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	132	882	2	ENST00000358127.4:c.963dup	p.Ala322ArgfsTer19	p.A322Rfs*19	ENST00000358127	NM_001280556.1	321	-/C	8/10	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.275991337654144	2		884	893	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	33	413	3	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	0.892	0.73	1	0.892	0.73	1	CLONAL	1	TRUE	1	0.275991337654144	2		416	268	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	26	58	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.275991337654144	2		58	145	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262139	10262139	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	127	783	2	ENST00000340748.4:c.2152del	p.Met718CysfsTer59	p.M718Cfs*59	ENST00000340748		718	Atg/tg	23/40	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.275991337654144	2		785	877	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467434	66467434	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369606981	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	37	268	0	ENST00000273854.3:c.835G>A	p.Glu279Lys	p.E279K	ENST00000273854	NM_004439.5	279	Gaa/Aaa	3/18	1	2	FACETS	0.891	0.737	1	0.891	0.737	1	CLONAL	1	TRUE	1	0.275991337654144	2		268	301	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114816	108114817	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	67	503	0	ENST00000278616.4:c.640dup	p.Ser214PhefsTer40	p.S214Ffs*40	ENST00000278616	NM_000051.3	211	-/T	6/63	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.275991337654144	2		503	404	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076932	41076932	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	42	550	0	ENST00000373198.4:c.1488del	p.Phe498LeufsTer103	p.F498Lfs*103	ENST00000373198	NM_133170.3	496	ggG/gg	9/32	0.275991337654144	3	FACETS	0.691	0.577	0.818	0.346	0.288	0.409	SUBCLONAL	1	TRUE	1	0.275991337654144	3		550	501	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441974	6441974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	23	673	0	ENST00000356142.4:c.533C>T	p.Ala178Val	p.A178V	ENST00000356142	NM_018890.3	178	gCg/gTg	7/7	1	2	FACETS	0.201	0.155	0.253	0.201	0.155	0.253	SUBCLONAL	1	TRUE	1	0.275991337654144	2		673	831	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905061	50905061	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	89	707	2	ENST00000440232.2:c.347del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	115	Ccc/cc	4/27	1	2	FACETS	0.946	0.839	1	0.946	0.839	1	CLONAL	1	TRUE	1	0.275991337654144	2		709	682	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911288	29911288	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs45552635	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	27	534	0	ENST00000376809.5:c.587T>C	p.Leu196Pro	p.L196P	ENST00000376809	NM_002116.7	196	cTg/cCg	3/8	1	2	FACETS	0.543	0.432	0.67	0.543	0.432	0.67	SUBCLONAL	1	TRUE	1	0.275991337654144	2		534	360	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937480	32937480	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1135401923	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	59	610	0	ENST00000380152.3:c.8145del	p.Val2716TrpfsTer17	p.V2716Wfs*17	ENST00000380152		2714	cAa/ca	18/27	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.275991337654144	2		610	425	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534472	187534473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs749145480	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	59	370	0	ENST00000441802.2:c.9253dup	p.Leu3085ProfsTer2	p.L3085Pfs*2	ENST00000441802	NM_005245.3	3085	ctt/cCtt	13/27	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.275991337654144	2		370	427	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346792	89346792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765013102	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	62	465	2	ENST00000301030.4:c.6158C>T	p.Ala2053Val	p.A2053V	ENST00000301030	NM_001256183.1	2053	gCg/gTg	9/13	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.275991337654144	2		467	422	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324917	31324917	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	187	790	0	ENST00000412585.2:c.19del	p.Arg7GlufsTer13	p.R7Efs*13	ENST00000412585	NM_005514.6	7	Cga/ga	1/8	1	2	FACETS	0.89	0.824	0.959	1	0.992	1	CLONAL	2	TRUE	1	0.275991337654144	2		790	761	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874092	151874093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	64	587	0	ENST00000262189.6:c.8445dup	p.Ser2816IlefsTer6	p.S2816Ifs*6	ENST00000262189	NM_170606.2	2815	-/A	38/59	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.275991337654144	2		587	431	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231239	98231239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs570441437	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	139	739	0	ENST00000331920.6:c.2044C>T	p.Arg682Cys	p.R682C	ENST00000331920	NM_000264.3	682	Cgc/Tgc	14/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.275991337654144	2		739	890	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332620	153332620	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1190157909	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	45	466	0	ENST00000281708.4:c.336T>G	p.Asp112Glu	p.D112E	ENST00000281708	NM_033632.3	112	gaT/gaG	2/12	1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	1	0.275991337654144	2		466	324	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324132	31324132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41561215	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	31	502	3	ENST00000412585.2:c.431G>A	p.Gly144Asp	p.G144D	ENST00000412585	NM_005514.6	144	gGc/gAc	3/8	1	2	FACETS	0.476	0.384	0.58	0.476	0.384	0.58	SUBCLONAL	1	TRUE	1	0.275991337654144	2		505	472	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845684	151845684	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	80	577	0	ENST00000262189.6:c.13328A>G	p.Gln4443Arg	p.Q4443R	ENST00000262189	NM_170606.2	4443	cAg/cGg	52/59	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.275991337654144	2		577	520	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862826	9862826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	67	640	0	ENST00000330684.3:c.2477C>T	p.Ala826Val	p.A826V	ENST00000330684	NM_001134407.1	826	gCc/gTc	12/13	1	2	FACETS	0.754	0.655	0.861	0.754	0.655	0.861	SUBCLONAL	1	TRUE	1	0.275991337654144	2		640	644	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885938	111885939	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs751076276	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	42	609	0	ENST00000341259.2:c.1566dup	p.Glu523ArgfsTer23	p.E523Rfs*23	ENST00000341259	NM_005475.2	520	-/C	8/8	1	2	FACETS	0.469	0.391	0.556	0.469	0.391	0.556	SUBCLONAL	1	TRUE	1	0.275991337654144	2		609	649	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145736926	145736926	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs779070043	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	115	812	0	ENST00000428558.2:c.3515A>G	p.Tyr1172Cys	p.Y1172C	ENST00000428558	NM_004260.3	1172	tAc/tGc	22/22	0.275991337654144	3	FACETS	0.931	0.837	1	0.465	0.418	0.515	CLONAL	1	TRUE	1	0.275991337654144	3		812	1019	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246078881	246078881	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	100	618	0	ENST00000388985.4:c.764A>G	p.Asp255Gly	p.D255G	ENST00000388985		255	gAc/gGc	8/12	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.275991337654144	2		618	711	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447236	187447236	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	84	765	2	ENST00000232014.4:c.957del	p.Asn320MetfsTer4	p.N320Mfs*4	ENST00000232014	NM_001130845.1	319	ccC/cc	5/10	1	2	FACETS	0.783	0.691	0.882	0.783	0.691	0.882	SUBCLONAL	1	TRUE	1	0.275991337654144	2		767	777	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690357	117690357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	75	531	1	ENST00000369458.3:c.772G>A	p.Ala258Thr	p.A258T	ENST00000369458	NM_024626.3	258	Gct/Act	5/6	1	2	FACETS	0.954	0.837	1	0.954	0.837	1	CLONAL	1	TRUE	1	0.275991337654144	2		532	570	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800525	32800525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs865861257	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	54	944	0	ENST00000374899.4:c.1022C>T	p.Thr341Ile	p.T341I	ENST00000374899	NM_018833.2	341	aCc/aTc	6/12	1	2	FACETS	0.371	0.316	0.433	0.371	0.316	0.433	SUBCLONAL	1	TRUE	1	0.275991337654144	2		944	1054	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274213	10274213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1302734897	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	49	447	0	ENST00000330684.3:c.56G>A	p.Arg19His	p.R19H	ENST00000330684	NM_001134407.1	19	cGc/cAc	2/13	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.275991337654144	2		447	339	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661509	227661509	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs865937681	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	46	730	0	ENST00000305123.5:c.1946C>T	p.Pro649Leu	p.P649L	ENST00000305123	NM_005544.2	649	cCc/cTc	1/2	0.275991337654144	3	FACETS	0.497	0.417	0.586	0.249	0.208	0.293	SUBCLONAL	1	TRUE	1	0.275991337654144	3		730	763	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182121	11182121	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	49	742	0	ENST00000361445.4:c.6725A>G	p.His2242Arg	p.H2242R	ENST00000361445	NM_004958.3	2242	cAc/cGc	48/58	1	2	FACETS	0.411	0.346	0.482	0.411	0.346	0.482	SUBCLONAL	1	TRUE	1	0.275991337654144	2		742	865	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933687	36933687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	114	943	0	ENST00000361632.4:c.1712A>G	p.Asn571Ser	p.N571S	ENST00000361632		571	aAc/aGc	12/16	1	2	FACETS	0.948	0.853	1	0.948	0.853	1	CLONAL	1	TRUE	1	0.275991337654144	2		943	871	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812478	43812478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	78	537	0	ENST00000372470.3:c.1181C>T	p.Pro394Leu	p.P394L	ENST00000372470	NM_005373.2	394	cCa/cTa	8/12	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.275991337654144	2		537	559	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736412	85736412	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	52	411	0	ENST00000370580.1:c.235C>A	p.Leu79Met	p.L79M	ENST00000370580	NM_003921.4	79	Ctg/Atg	2/3	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.275991337654144	2		411	336	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120493347	120493347	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	80	498	0	ENST00000256646.2:c.2479G>A	p.Gly827Ser	p.G827S	ENST00000256646	NM_024408.3	827	Ggc/Agc	15/34	1	2	FACETS	0.96	0.846	1	0.96	0.846	1	CLONAL	1	TRUE	1	0.275991337654144	2		498	604	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551782	150551782	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	22	88	0	ENST00000369026.2:c.225G>C	p.Arg75Ser	p.R75S	ENST00000369026	NM_021960.4	75	agG/agC	1/3	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.275991337654144	2		88	137	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100634	8100634	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	120	807	0	ENST00000346208.3:c.608G>A	p.Gly203Asp	p.G203D	ENST00000346208		203	gGc/gAc	3/6	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.275991337654144	2		807	819	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710570	114710570	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	100	523	0	ENST00000543371.1:c.55A>T	p.Ile19Phe	p.I19F	ENST00000543371	NM_001198531.1	19	Att/Ttt	1/14	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.275991337654144	2		523	631	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256185	123256185	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	71	533	0	ENST00000358487.5:c.1724A>G	p.Tyr575Cys	p.Y575C	ENST00000358487	NM_000141.4	575	tAc/tGc	13/18	1	2	FACETS	0.895	0.782	1	0.895	0.782	1	CLONAL	1	TRUE	1	0.275991337654144	2		533	575	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427342	427342	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	40	632	0	ENST00000399788.2:c.2827G>T	p.Ala943Ser	p.A943S	ENST00000399788	NM_001042603.1	943	Gct/Tct	19/28	1	2	FACETS	0.433	0.358	0.516	0.433	0.358	0.516	SUBCLONAL	1	TRUE	1	0.275991337654144	2		632	670	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209007	133209007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs952583197	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	105	677	0	ENST00000320574.5:c.6224C>T	p.Thr2075Ile	p.T2075I	ENST00000320574	NM_006231.2	2075	aCa/aTa	45/49	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.275991337654144	2		677	751	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515133	103515133	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs778300706	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	31	285	0	ENST00000355739.4:c.1634A>G	p.Gln545Arg	p.Q545R	ENST00000355739	NM_000123.3	545	cAg/cGg	8/15	1	2	FACETS	0.902	0.733	1	0.902	0.733	1	CLONAL	1	TRUE	1	0.275991337654144	2		285	249	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830493	72830493	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	90	615	0	ENST00000268489.5:c.6088T>C	p.Tyr2030His	p.Y2030H	ENST00000268489	NM_006885.3	2030	Tac/Cac	9/10	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.275991337654144	2		615	613	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830531	72830531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	35	630	0	ENST00000268489.5:c.6050G>A	p.Arg2017Lys	p.R2017K	ENST00000268489	NM_006885.3	2017	aGg/aAg	9/10	1	2	FACETS	0.382	0.312	0.461	0.382	0.312	0.461	SUBCLONAL	1	TRUE	1	0.275991337654144	2		630	664	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347385	89347386	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	153	794	0	ENST00000301030.4:c.5564_5565del	p.Tyr1855TrpfsTer94	p.Y1855Wfs*94	ENST00000301030	NM_001256183.1	1855	tAT/t	9/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.275991337654144	2		794	943	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119686	70119686	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	88	703	0	ENST00000245479.2:c.688C>T	p.Gln230Ter	p.Q230*	ENST00000245479	NM_000346.3	230	Caa/Taa	3/3	1	2	FACETS	0.978	0.867	1	0.978	0.867	1	CLONAL	1	TRUE	1	0.275991337654144	2		703	652	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584376	39584376	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	40	346	0	ENST00000262039.4:c.1041G>C	p.Gln347His	p.Q347H	ENST00000262039	NM_002647.2	347	caG/caC	10/25	1	2	FACETS	0.914	0.763	1	0.914	0.763	1	CLONAL	1	TRUE	1	0.275991337654144	2		346	317	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372111	45372111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	64	547	0	ENST00000262160.6:c.1058G>A	p.Ser353Asn	p.S353N	ENST00000262160	NM_005901.5	353	aGt/aAt	9/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.275991337654144	2		547	368	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222981	5222981	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772298342	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	35	583	0	ENST00000357368.4:c.2822C>T	p.Ala941Val	p.A941V	ENST00000357368	NM_002850.3	941	gCc/gTc	18/38	1	2	FACETS	0.371	0.303	0.448	0.371	0.303	0.448	SUBCLONAL	1	TRUE	1	0.275991337654144	2		583	683	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7128967	7128967	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	47	306	0	ENST00000302850.5:c.2843-2A>T		p.X948_splice	ENST00000302850	NM_000208.2	948			1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.275991337654144	2		306	301	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212024	36212024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	160	1038	0	ENST00000222270.7:c.1775C>T	p.Thr592Ile	p.T592I	ENST00000222270	NM_014727.1	592	aCc/aTc	3/37	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.275991337654144	2		1038	1097	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221748	36221748	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	114	899	0	ENST00000222270.7:c.5417A>G	p.His1806Arg	p.H1806R	ENST00000222270	NM_014727.1	1806	cAc/cGc	26/37	1	2	FACETS	0.963	0.866	1	0.963	0.866	1	CLONAL	1	TRUE	1	0.275991337654144	2		899	858	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920477	50920477	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	89	643	0	ENST00000440232.2:c.3169C>A	p.Gln1057Lys	p.Q1057K	ENST00000440232	NM_002691.3	1057	Cag/Aag	26/27	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.275991337654144	2		643	587	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143269	30143269	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	50	611	0	ENST00000389048.3:c.257A>G	p.Glu86Gly	p.E86G	ENST00000389048	NM_004304.4	86	gAg/gGg	1/29	0.275991337654144	3	FACETS	0.618	0.524	0.723	0.309	0.262	0.362	SUBCLONAL	1	TRUE	1	0.275991337654144	3		611	667	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131286	202131286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	123	458	0	ENST00000358485.4:c.254G>A	p.Ser85Asn	p.S85N	ENST00000358485	NM_001080125.1	85	aGc/aAc	2/9	0.275991337654144	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.275991337654144	3		458	463	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285312	212285312	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	32	402	0	ENST00000342788.4:c.2989A>G	p.Ser997Gly	p.S997G	ENST00000342788	NM_005235.2	997	Agt/Ggt	25/28	0.275991337654144	3	FACETS	1	0.895	1	0.574	0.468	0.691	CLONAL	1	TRUE	1	0.275991337654144	3		402	230	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309905	30309905	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	188	649	0	ENST00000307677.4:c.117A>C	p.Glu39Asp	p.E39D	ENST00000307677	NM_138578.1	39	gaA/gaC	2/3	0.275991337654144	3	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	1	0.275991337654144	3		649	767	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57474027	57474027	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	31	273	0	ENST00000371085.3:c.244A>G	p.Ser82Gly	p.S82G	ENST00000371085	NM_000516.4	82	Agc/Ggc	3/13	0.275991337654144	3	FACETS	0.523	0.422	0.637	0.261	0.211	0.319	SUBCLONAL	1	TRUE	1	0.275991337654144	3		273	489	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928401	69928401	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	68	512	0	ENST00000352241.4:c.221G>T	p.Arg74Met	p.R74M	ENST00000352241	NM_198159.2	74	aGg/aTg	2/10	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.275991337654144	2		512	418	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215312	142215312	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1174152895	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	59	441	0	ENST00000350721.4:c.5789T>C	p.Val1930Ala	p.V1930A	ENST00000350721	NM_001184.3	1930	gTa/gCa	34/47	1	2	FACETS	0.822	0.708	0.946	0.822	0.708	0.946	CLONAL	1	TRUE	1	0.275991337654144	2		441	520	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447631	187447631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	66	720	0	ENST00000232014.4:c.562C>A	p.Leu188Met	p.L188M	ENST00000232014	NM_001130845.1	188	Ctg/Atg	5/10	1	2	FACETS	0.688	0.597	0.787	0.688	0.597	0.787	SUBCLONAL	1	TRUE	1	0.275991337654144	2		720	695	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189585628	189585628	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	19	407	0	ENST00000264731.3:c.889A>G	p.Thr297Ala	p.T297A	ENST00000264731	NM_003722.4	297	Act/Gct	7/14	1	2	FACETS	0.379	0.287	0.488	0.379	0.287	0.488	SUBCLONAL	1	TRUE	1	0.275991337654144	2		407	363	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1978211	1978211	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	45	762	0	ENST00000382891.5:c.3631A>G	p.Thr1211Ala	p.T1211A	ENST00000382891	NM_133335.3	1211	Acc/Gcc	21/22	1	2	FACETS	0.403	0.337	0.476	0.403	0.337	0.476	SUBCLONAL	1	TRUE	1	0.275991337654144	2		762	809	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561773	55561773	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	24	396	0	ENST00000288135.5:c.163A>G	p.Arg55Gly	p.R55G	ENST00000288135	NM_000222.2	55	Agg/Ggg	2/21	1	2	FACETS	0.386	0.302	0.483	0.386	0.302	0.483	SUBCLONAL	1	TRUE	1	0.275991337654144	2		396	451	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174866	56174866	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	22	358	0	ENST00000399503.3:c.2025A>C	p.Lys675Asn	p.K675N	ENST00000399503	NM_005921.1	675	aaA/aaC	11/20	1	2	FACETS	0.611	0.474	0.769	0.611	0.474	0.769	SUBCLONAL	1	TRUE	1	0.275991337654144	2		358	261	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576544	67576544	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	10	258	0	ENST00000274335.5:c.823T>A	p.Phe275Ile	p.F275I	ENST00000274335		275	Ttc/Atc	5/15	1	2	FACETS	0.366	0.248	0.515	0.366	0.248	0.515	SUBCLONAL	1	TRUE	1	0.275991337654144	2		258	198	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158581	26158581	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	35	607	0	ENST00000289316.2:c.184A>G	p.Ile62Val	p.I62V	ENST00000289316	NM_138720.2	62	Atc/Gtc	1/2	1	2	FACETS	0.45	0.368	0.543	0.45	0.368	0.543	SUBCLONAL	1	TRUE	1	0.275991337654144	2		607	563	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977556	2977556	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	85	661	0	ENST00000396946.4:c.1128G>T	p.Glu376Asp	p.E376D	ENST00000396946	NM_032415.4	376	gaG/gaT	8/25	1	2	FACETS	0.882	0.78	0.992	0.882	0.78	0.992	CLONAL	1	TRUE	1	0.275991337654144	2		661	698	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14027728	14027728	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	18	364	0	ENST00000405192.2:c.116T>A	p.Leu39Gln	p.L39Q	ENST00000405192	NM_001163147.1	39	cTg/cAg	3/12	1	2	FACETS	0.441	0.332	0.57	0.441	0.332	0.57	SUBCLONAL	1	TRUE	1	0.275991337654144	2		364	296	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133385	38133385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1254358650	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	51	357	0	ENST00000317025.8:c.4088C>T	p.Pro1363Leu	p.P1363L	ENST00000317025	NM_023034.1	1363	cCg/cTg	24/24	0.275991337654144	3	FACETS	1	0.89	1	0.527	0.449	0.612	CLONAL	1	TRUE	1	0.275991337654144	3		357	399	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864739	68864739	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	88	526	0	ENST00000288368.4:c.110A>G	p.Asp37Gly	p.D37G	ENST00000288368	NM_024870.2	37	gAc/gGc	1/40	0.275991337654144	3	FACETS	1	0.902	1	0.51	0.451	0.572	CLONAL	1	TRUE	1	0.275991337654144	3		526	712	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020405	69020405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	51	553	0	ENST00000288368.4:c.2777C>T	p.Ser926Phe	p.S926F	ENST00000288368	NM_024870.2	926	tCc/tTc	24/40	0.275991337654144	3	FACETS	0.848	0.721	0.987	0.424	0.36	0.494	CLONAL	1	TRUE	1	0.275991337654144	3		553	496	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5081806	5081806	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747381013	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	14	293	1	ENST00000381652.3:c.2516G>A	p.Arg839Gln	p.R839Q	ENST00000381652	NM_004972.3	839	cGg/cAg	19/25	1	2	FACETS	0.463	0.335	0.618	0.463	0.335	0.618	SUBCLONAL	1	TRUE	1	0.275991337654144	2		294	219	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815622	139815622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	85	689	0	ENST00000247668.2:c.1093C>T	p.Arg365Cys	p.R365C	ENST00000247668	NM_021138.3	365	Cgc/Tgc	9/11	1	2	FACETS	0.877	0.776	0.987	0.877	0.776	0.987	CLONAL	1	TRUE	1	0.275991337654144	2		689	702	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675859	30675861	+	missense_variant	Missense_Mutation	TNP	TCT	TCT	CCA	novel	NA	P-0058159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	67	799	1	ENST00000376406.3:c.2495_2497delinsTGG	p.Glu832_Arg833delinsValGly	p.E832_R833delinsVG	ENST00000376406	NM_014641.2	832	gAGAga/gTGGga	8/15	1	2	FACETS	0.634	0.55	0.725	0.634	0.55	0.725	SUBCLONAL	1	TRUE	1	0.275991337654144	2		800	766	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057302	30057302	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315496	NA	P-0058163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	324	277	0	ENST00000338641.4:c.784C>T	p.Arg262Ter	p.R262*	ENST00000338641	NM_000268.3	262	Cga/Tga	8/16	0.569909390739632	2	FACETS	0.997	0.954	1	0.997	0.954	1	CLONAL	2	TRUE	0	0.569909390739632	2		277	570	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160494	108160494	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369903995	NA	P-0058163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	62	315	0	ENST00000278616.4:c.4402G>A	p.Val1468Ile	p.V1468I	ENST00000278616	NM_000051.3	1468	Gtt/Att	29/63	0.569909390739632	2	FACETS	0.333	0.287	0.383	0.166	0.143	0.192	SUBCLONAL	1	TRUE	0	0.569909390739632	2		315	654	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0058177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	284	439	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.614716128804609	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	FALSE	0	0.614716128804609	3		440	393	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380350	14380350	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	170	249	0	ENST00000256196.4:c.67G>T	p.Gly23Cys	p.G23C	ENST00000256196		23	Ggc/Tgc	1/6	0.590752259174736	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	3	FALSE	0	0.614716128804609	3		249	239	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664915	138664915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs797044527	NA	P-0058177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	21	151	0	ENST00000330315.3:c.650C>T	p.Ser217Phe	p.S217F	ENST00000330315	NM_023067.3	217	tCc/tTc	1/1	0.614716128804609	8	FACETS	0.635	0.489	0.805	0.127	0.097	0.161	SUBCLONAL	1	FALSE	3	0.614716128804609	8		151	306	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086032	16086032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777508469	NA	P-0058177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	45	473	2	ENST00000281043.3:c.1208C>T	p.Thr403Met	p.T403M	ENST00000281043	NM_005378.4	403	aCg/aTg	3/3	0.468198432157296	4	FACETS	0.594	0.5	0.697	0.297	0.25	0.349	SUBCLONAL	1	FALSE	2	0.614716128804609	4		475	398	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477853	140477853	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs180177036	NA	P-0058177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	36	365	0	ENST00000288602.6:c.1455G>T	p.Leu485Phe	p.L485F	ENST00000288602	NM_004333.4	485	ttG/ttT	12/18	0.553435233887481	5	FACETS	0.837	0.692	0.998	0.279	0.23	0.333	CLONAL	1	FALSE	2	0.614716128804609	5		365	269	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188404	32188404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763926116	NA	P-0058177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	50	583	0	ENST00000375023.3:c.937G>A	p.Glu313Lys	p.E313K	ENST00000375023	NM_004557.3	313	Gaa/Aaa	6/30	0.614716128804609	4	FACETS	0.779	0.664	0.905	0.26	0.221	0.302	CLONAL	1	FALSE	1	0.614716128804609	4		583	337	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666393	206666393	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	210	574	0	ENST00000367120.3:c.1873G>T	p.Gly625Cys	p.G625C	ENST00000367120	NM_014002.3	625	Ggc/Tgc	19/22	0.468198432157296	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	FALSE	2	0.614716128804609	4		574	454	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795271	42795271	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	103	702	0	ENST00000575354.2:c.2351G>C	p.Gly784Ala	p.G784A	ENST00000575354	NM_015125.3	784	gGg/gCg	10/20	0.293502687224113	4	FACETS	0.762	0.689	0.838	0.508	0.459	0.559	INDETERMINATE	2	FALSE	1	0.614716128804609	4		702	355	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0058301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	73	879	0	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.209022827934502	2	FACETS	0.8	0.702	0.904	0.8	0.702	0.904	CLONAL	2	TRUE	0	0.210250823326001	2		879	434	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037966	49037966	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	37	296	0	ENST00000267163.4:c.2206C>T	p.Gln736Ter	p.Q736*	ENST00000267163	NM_000321.2	736	Cag/Tag	21/27	0.202968138069288	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	2	TRUE	0	0.210250823326001	2		296	169	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207064	1207065	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1131690917	NA	P-0058301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	111	573	0	ENST00000326873.7:c.157dup	p.Asp53GlyfsTer110	p.D53Gfs*110	ENST00000326873	NM_000455.4	51	atg/atGg	1/10	0.18950531346566	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	0	0.210250823326001	2		573	504	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239414	105239414	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781749630	NA	P-0058301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	87	751	0	ENST00000349310.3:c.973G>A	p.Asp325Asn	p.D325N	ENST00000349310	NM_001014432.1	325	Gac/Aac	12/15	0.0659342971309367	3	FACETS	1	0.975	1	0.697	0.617	0.782	INDETERMINATE	1	TRUE	1	0.210250823326001	3		751	656	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059116	42059116	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	28	586	0	ENST00000219905.7:c.8836G>C	p.Asp2946His	p.D2946H	ENST00000219905	NM_001164273.1	2946	Gat/Cat	24/24	0.202968138069288	2	FACETS	0.568	0.453	0.699	0.284	0.226	0.35	SUBCLONAL	1	TRUE	0	0.210250823326001	2		586	469	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2114403	2114403	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs45457694	NA	P-0058301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	33	625	1	ENST00000219476.3:c.1574A>G	p.Asn525Ser	p.N525S	ENST00000219476	NM_000548.3	525	aAc/aGc	15/42	0.18950531346566	2	FACETS	0.613	0.498	0.743	0.307	0.249	0.372	SUBCLONAL	1	TRUE	0	0.210250823326001	2		626	512	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559090	29559090	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0058301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	22	67	0	ENST00000356175.3:c.3198-1G>C		p.X1066_splice	ENST00000356175	NM_000267.3	1066			0.209022827934502	2	FACETS	1	0.794	1	1	0.794	1	CLONAL	2	TRUE	0	0.210250823326001	2		67	104	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532516	63532516	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	96	633	0	ENST00000307078.5:c.2063T>A	p.Leu688Gln	p.L688Q	ENST00000307078	NM_004655.3	688	cTg/cAg	8/11	0.135009378874868	4	FACETS	0.919	0.821	1	0.919	0.821	1	CLONAL	2	TRUE	2	0.210250823326001	4		633	601	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550304	39550304	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058301-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	74	469	0	ENST00000262039.4:c.415G>T	p.Gly139Trp	p.G139W	ENST00000262039	NM_002647.2	139	Ggg/Tgg	4/25	0.202968138069288	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	2	TRUE	0	0.210250823326001	2		469	344	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902529	1902533	+	missense_variant	Missense_Mutation	ONP	AAAGC	AAAGC	CAAGT	novel	NA	P-0058340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	338	891	0	ENST00000382891.5:c.148_152delinsCAAGT	p.Lys50_Ala51delinsGlnVal	p.K50_A51delinsQV	ENST00000382891	NM_133335.3	50	AAAGCc/CAAGTc	2/22	1	2	FACETS	0.906	0.856	0.956	0.906	0.856	0.956	CLONAL	1	FALSE	1	0.610754466192513	2		891	1222	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0058344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	48	444	0	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	1	2	FACETS	0.375	0.316	0.441	0.375	0.316	0.441	SUBCLONAL	1	TRUE	1	0.340996303749267	2		444	750	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0058344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	81	349	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	0.998	0.882	1	0.998	0.882	1	CLONAL	1	TRUE	1	0.340996303749267	2		349	476	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417925	32417925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1014605516	NA	P-0058344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	189	709	0	ENST00000332351.3:c.1127C>T	p.Pro376Leu	p.P376L	ENST00000332351	NM_024426.4	376	cCg/cTg	7/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.340996303749267	2		709	818	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042743	42042744	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	167	467	0	ENST00000219905.7:c.6939dup	p.Asp2314Ter	p.D2314*	ENST00000219905	NM_001164273.1	2313	gat/gaTt	17/24	1	2	FACETS	0.9	0.832	0.97	1	0.992	1	CLONAL	2	TRUE	1	0.340996303749267	2		467	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0058351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	190	879	0	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.22625121317205	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.22625121317205	1		879	1007	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680968	30680968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2517560	NA	P-0058351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1497	103	874	1	ENST00000376406.3:c.751G>A	p.Glu251Lys	p.E251K	ENST00000376406	NM_014641.2	251	Gaa/Aaa	5/15	0.22625121317205	8	FACETS	0.955	0.851	1			1	CLONAL	1	TRUE	NA	0.22625121317205	8		875	1600	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788618	3788618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398124146	NA	P-0058351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	139	551	0	ENST00000262367.5:c.4336C>T	p.Arg1446Cys	p.R1446C	ENST00000262367	NM_004380.2	1446	Cgc/Tgc	26/31	1	2	FACETS	0.784	0.714	0.857	1	0.987	1	SUBCLONAL	2	TRUE	1	0.22625121317205	2		551	784	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014214	70014214	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs150995386	NA	P-0058351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	178	809	0	ENST00000394351.3:c.1075G>C	p.Glu359Gln	p.E359Q	ENST00000394351	NM_000248.3	359	Gag/Cag	9/9	0.19484682716221	2	FACETS	0.762	0.701	0.825	0.762	0.701	0.825	SUBCLONAL	2	TRUE	0	0.22625121317205	2		809	1033	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61729414	61729414	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	75	527	0	ENST00000401558.2:c.333C>G	p.Ile111Met	p.I111M	ENST00000401558	NM_003400.3	111	atC/atG	5/25	0.191365122352345	3	FACETS	0.908	0.794	1	0.454	0.397	0.515	CLONAL	1	TRUE	1	0.22625121317205	3		527	813	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271219	26271219	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	60	648	0	ENST00000305910.3:c.394C>G	p.Arg132Gly	p.R132G	ENST00000305910	NM_003534.2	132	Cgt/Ggt	1/1	0.207997461228037	4	FACETS	0.695	0.597	0.802	0.232	0.199	0.268	SUBCLONAL	1	TRUE	1	0.22625121317205	4		648	936	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271321	26271321	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1171	119	892	0	ENST00000305910.3:c.292G>C	p.Glu98Gln	p.E98Q	ENST00000305910	NM_003534.2	98	Gag/Cag	1/1	0.207997461228037	4	FACETS	1	0.9	1	0.333	0.3	0.369	CLONAL	1	TRUE	1	0.22625121317205	4		892	1290	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303420	91303420	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	106	403	0	ENST00000355112.3:c.1131G>T	p.Glu377Asp	p.E377D	ENST00000355112	NM_000057.2	377	gaG/gaT	6/22	0.191365122352345	3	FACETS	0.874	0.785	0.967	0.874	0.785	0.967	CLONAL	2	TRUE	1	0.22625121317205	3		403	597	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259423	16259423	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	80	716	0	ENST00000375759.3:c.6688C>G	p.Pro2230Ala	p.P2230A	ENST00000375759	NM_015001.2	2230	Cca/Gca	11/15	1	2	FACETS	0.852	0.749	0.963	0.852	0.749	0.963	CLONAL	1	TRUE	1	0.22625121317205	2		716	830	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805025	43805025	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	85	925	0	ENST00000372470.3:c.475C>A	p.Pro159Thr	p.P159T	ENST00000372470	NM_005373.2	159	Cca/Aca	4/12	1	2	FACETS	0.798	0.704	0.899	0.798	0.704	0.899	SUBCLONAL	1	TRUE	1	0.22625121317205	2		925	942	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851798	63851798	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1246	84	820	1	ENST00000279873.7:c.2576G>T	p.Arg859Met	p.R859M	ENST00000279873	NM_032199.2	859	aGg/aTg	10/10	0.22625121317205	5	FACETS	0.748	0.658	0.845			1	SUBCLONAL	1	TRUE	NA	0.22625121317205	5		821	1330	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120361	70120361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1299	112	1013	0	ENST00000245479.2:c.1363G>A	p.Ala455Thr	p.A455T	ENST00000245479	NM_000346.3	455	Gcg/Acg	3/3	0.191365122352345	3	FACETS	0.781	0.7	0.868	0.391	0.35	0.434	SUBCLONAL	1	TRUE	1	0.22625121317205	3		1013	1411	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971687	18971687	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	122	1085	0	ENST00000262803.5:c.2353G>C	p.Ala785Pro	p.A785P	ENST00000262803	NM_002911.3	785	Gcc/Ccc	17/24	0.208547413412688	2	FACETS	0.966	0.872	1	0.483	0.436	0.534	CLONAL	1	TRUE	0	0.22625121317205	2		1085	1116	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944451	40944451	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs111367672	NA	P-0058351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	94	749	0	ENST00000373198.4:c.2051A>G	p.Asn684Ser	p.N684S	ENST00000373198	NM_133170.3	684	aAt/aGt	12/32	1	2	FACETS	0.992	0.881	1	0.992	0.881	1	CLONAL	1	TRUE	1	0.22625121317205	2		749	838	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538918	187538919	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0058351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	76	521	0	ENST00000441802.2:c.8821_8822del	p.Ser2941TyrfsTer5	p.S2941Yfs*5	ENST00000441802	NM_005245.3	2941	AGt/t	10/27	0.191365122352345	3	FACETS	0.976	0.855	1	0.488	0.427	0.554	CLONAL	1	TRUE	1	0.22625121317205	3		521	766	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057021	180057021	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	269	1234	0	ENST00000261937.6:c.598G>C	p.Asp200His	p.D200H	ENST00000261937	NM_182925.4	200	Gat/Cat	5/30	0.19484682716221	2	FACETS	0.92	0.862	0.98	0.92	0.862	0.98	CLONAL	2	TRUE	0	0.22625121317205	2		1234	1292	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38196107	38196107	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1410	86	737	1	ENST00000317025.8:c.694G>C	p.Asp232His	p.D232H	ENST00000317025	NM_023034.1	232	Gac/Cac	3/24	0.22625121317205	6	FACETS	0.738	0.65	0.833			1	SUBCLONAL	1	TRUE	NA	0.22625121317205	6		738	1496	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939496	68939496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1303990934	NA	P-0058351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	74	445	0	ENST00000288368.4:c.481C>T	p.Pro161Ser	p.P161S	ENST00000288368	NM_024870.2	161	Ccc/Tcc	5/40	0.208547413412688	2	FACETS	0.958	0.838	1	0.479	0.419	0.544	CLONAL	1	TRUE	0	0.22625121317205	2		445	683	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0058382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	220	367	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.594787054894094	3	FACETS	0.894	0.849	0.938	0.894	0.849	0.938	CLONAL	3	TRUE	0	0.594787054894094	3		367	358	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160434	108160436	+	inframe_deletion	In_Frame_Del	DEL	TTA	TTA	-	novel	NA	P-0058382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	183	369	0	ENST00000278616.4:c.4345_4347del	p.Leu1450del	p.L1450del	ENST00000278616	NM_000051.3	1448	TTA/-	29/63	NA	2	FACETS	1	0.959	1			1	INDETERMINATE	2	TRUE	NA	0.594787054894094	2		369	302	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62305446	62305446	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	137	679	0	ENST00000360203.5:c.919G>C	p.Gly307Arg	p.G307R	ENST00000360203	NM_001283009.1	307	Ggg/Cgg	10/35	0.542971871659782	4	FACETS	0.943	0.859	1	0.314	0.286	0.344	CLONAL	1	TRUE	1	0.594787054894094	4		679	779	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864648	68864648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	27	227	0	ENST00000288368.4:c.19G>A	p.Gly7Arg	p.G7R	ENST00000288368	NM_024870.2	7	Gga/Aga	1/40	0.318672858602518	1	FACETS	0.507	0.404	0.624	0.507	0.404	0.624	SUBCLONAL	1	TRUE	0	0.318672858602518	1		227	281	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631862	90631862	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	74	794	1	ENST00000330062.3:c.491G>A	p.Trp164Ter	p.W164*	ENST00000330062	NM_002168.2	164	tGg/tAg	4/11	1	2	FACETS	0.514	0.449	0.585	0.514	0.449	0.585	SUBCLONAL	1	TRUE	1	0.318672858602518	2		795	903	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861149	57861149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774058977	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	67	588	0	ENST00000228682.2:c.946G>A	p.Glu316Lys	p.E316K	ENST00000228682	NM_005269.2	316	Gaa/Aaa	9/12	1	2	FACETS	0.488	0.423	0.559	0.488	0.423	0.559	SUBCLONAL	1	TRUE	1	0.318672858602518	2		588	862	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556250	29556250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199474739	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	32	411	1	ENST00000356175.3:c.2617C>T	p.Arg873Cys	p.R873C	ENST00000356175	NM_000267.3	873	Cgt/Tgt	21/57	1	2	FACETS	0.346	0.28	0.421	0.346	0.28	0.421	SUBCLONAL	1	TRUE	1	0.318672858602518	2		412	581	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489247	2489247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	85	901	0	ENST00000355716.4:c.152C>T	p.Ser51Phe	p.S51F	ENST00000355716	NM_003820.2	51	tCc/tTc	2/8	0.318672858602518	1	FACETS	0.477	0.421	0.538	0.477	0.421	0.538	SUBCLONAL	1	TRUE	0	0.318672858602518	1		901	940	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130520	29130520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141568342	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	41	580	0	ENST00000328354.6:c.190G>A	p.Glu64Lys	p.E64K	ENST00000328354	NM_007194.3	64	Gag/Aag	2/15	0.318672858602518	1	FACETS	0.391	0.325	0.465	0.391	0.325	0.465	SUBCLONAL	1	TRUE	0	0.318672858602518	1		580	553	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261320	16261320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	85	729	0	ENST00000375759.3:c.8585C>T	p.Thr2862Ile	p.T2862I	ENST00000375759	NM_015001.2	2862	aCa/aTa	11/15	0.318672858602518	1	FACETS	0.633	0.56	0.712	0.633	0.56	0.712	SUBCLONAL	1	TRUE	0	0.318672858602518	1		729	708	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22408269	22408269	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	35	349	0	ENST00000344548.3:c.160G>A	p.Gly54Arg	p.G54R	ENST00000344548	NM_001039802.1	54	Gga/Aga	4/7	0.318672858602518	1	FACETS	0.434	0.356	0.523	0.434	0.356	0.523	SUBCLONAL	1	TRUE	0	0.318672858602518	1		349	425	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366674	40366674	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	54	553	0	ENST00000397332.2:c.523C>T	p.Pro175Ser	p.P175S	ENST00000397332	NM_001033082.2	175	Ccc/Tcc	2/3	0.318672858602518	1	FACETS	0.444	0.378	0.515	0.444	0.378	0.515	SUBCLONAL	1	TRUE	0	0.318672858602518	1		553	642	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946427	71946428	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	76	842	0	ENST00000298229.2:c.2591_2592delinsAT	p.Gly864Asp	p.G864D	ENST00000298229	NM_001567.3	864	gGC/gAT	23/28	0.318672858602518	1	FACETS	0.464	0.406	0.526	0.464	0.406	0.526	SUBCLONAL	1	TRUE	0	0.318672858602518	1		842	865	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426051	49426051	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774023846	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	82	1009	1	ENST00000301067.7:c.12437G>A	p.Gly4146Glu	p.G4146E	ENST00000301067	NM_003482.3	4146	gGg/gAg	39/54	1	2	FACETS	0.463	0.407	0.524	0.463	0.407	0.524	SUBCLONAL	1	TRUE	1	0.318672858602518	2		1010	1111	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986617	36986617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	30	300	0	ENST00000354822.5:c.1072C>T	p.Pro358Ser	p.P358S	ENST00000354822	NM_001079668.2	358	Ccg/Tcg	3/3	1	2	FACETS	0.467	0.376	0.57	0.467	0.376	0.57	SUBCLONAL	1	TRUE	1	0.318672858602518	2		300	403	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989174	41989174	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	59	538	0	ENST00000219905.7:c.1966G>A	p.Asp656Asn	p.D656N	ENST00000219905	NM_001164273.1	656	Gat/Aat	3/24	1	2	FACETS	0.532	0.457	0.614	0.532	0.457	0.614	SUBCLONAL	1	TRUE	1	0.318672858602518	2		538	696	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43739627	43739627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	50	389	0	ENST00000382044.4:c.2773G>A	p.Gly925Ser	p.G925S	ENST00000382044	NM_001141980.1	925	Ggt/Agt	13/28	1	2	FACETS	0.578	0.49	0.674	0.578	0.49	0.674	SUBCLONAL	1	TRUE	1	0.318672858602518	2		389	543	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2114289	2114289	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	153	858	0	ENST00000219476.3:c.1460C>G	p.Ser487Ter	p.S487*	ENST00000219476	NM_000548.3	487	tCa/tGa	15/42	0.318672858602518	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.318672858602518	1		858	777	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829938	72829938	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	72	702	0	ENST00000268489.5:c.6643C>T	p.Pro2215Ser	p.P2215S	ENST00000268489	NM_006885.3	2215	Cct/Tct	9/10	0.318672858602518	1	FACETS	0.543	0.474	0.617	0.543	0.474	0.617	SUBCLONAL	1	TRUE	0	0.318672858602518	1		702	700	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81891932	81891932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	63	536	0	ENST00000359376.3:c.402G>A	p.Met134Ile	p.M134I	ENST00000359376	NM_002661.3	134	atG/atA	4/33	0.318672858602518	1	FACETS	0.565	0.489	0.648	0.565	0.489	0.648	SUBCLONAL	1	TRUE	0	0.318672858602518	1		536	588	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627849	14627849	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	99	866	1	ENST00000254322.2:c.221G>A	p.Gly74Glu	p.G74E	ENST00000254322	NM_006145.1	74	gGg/gAg	2/3	1	2	FACETS	0.53	0.472	0.593	0.53	0.472	0.593	SUBCLONAL	1	TRUE	1	0.318672858602518	2		867	1172	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299817	15299817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	70	942	0	ENST00000263388.2:c.1361C>T	p.Thr454Ile	p.T454I	ENST00000263388	NM_000435.2	454	aCc/aTc	8/33	1	2	FACETS	0.395	0.343	0.452	0.395	0.343	0.452	SUBCLONAL	1	TRUE	1	0.318672858602518	2		942	1111	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792363	33792363	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	153	895	0	ENST00000498907.2:c.958G>T	p.Asp320Tyr	p.D320Y	ENST00000498907	NM_004364.3	320	Gac/Tac	1/1	1	2	FACETS	0.996	0.911	1	0.996	0.911	1	CLONAL	1	TRUE	1	0.318672858602518	2		895	964	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50143298	50143298	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	17	150	0	ENST00000246792.3:c.58G>A	p.Gly20Arg	p.G20R	ENST00000246792	NM_006270.3	20	Ggg/Agg	1/6	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.318672858602518	NA		150	239	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451857	29451857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	62	646	1	ENST00000389048.3:c.2708G>A	p.Gly903Glu	p.G903E	ENST00000389048	NM_004304.4	903	gGa/gAa	16/29	0.318672858602518	1	FACETS	0.488	0.421	0.561	0.488	0.421	0.561	SUBCLONAL	1	TRUE	0	0.318672858602518	1		647	670	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451870	29451870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	66	680	0	ENST00000389048.3:c.2695G>A	p.Gly899Ser	p.G899S	ENST00000389048	NM_004304.4	899	Ggt/Agt	16/29	0.318672858602518	1	FACETS	0.514	0.446	0.589	0.514	0.446	0.589	SUBCLONAL	1	TRUE	0	0.318672858602518	1		680	677	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053318	37053318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750012	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	38	326	0	ENST00000231790.2:c.553G>A	p.Val185Ile	p.V185I	ENST00000231790	NM_000249.3	185	Gta/Ata	7/19	0.318672858602518	1	FACETS	0.51	0.422	0.608	0.51	0.422	0.608	SUBCLONAL	1	TRUE	0	0.318672858602518	1		326	393	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437599	52437599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	70	844	0	ENST00000460680.1:c.1562G>A	p.Ser521Asn	p.S521N	ENST00000460680	NM_004656.3	521	aGc/aAc	13/17	0.318672858602518	1	FACETS	0.468	0.407	0.534	0.468	0.407	0.534	SUBCLONAL	1	TRUE	0	0.318672858602518	1		844	789	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52692301	52692301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542464402	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	50	415	0	ENST00000394830.3:c.559G>A	p.Glu187Lys	p.E187K	ENST00000394830	NM_018313.4	187	Gag/Aag	6/30	0.318672858602518	1	FACETS	0.553	0.469	0.645	0.553	0.469	0.645	SUBCLONAL	1	TRUE	0	0.318672858602518	1		415	477	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101744	71101744	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	37	242	0	ENST00000318789.4:c.454G>A	p.Glu152Lys	p.E152K	ENST00000318789	NM_032682.5	152	Gaa/Aaa	9/21	0.318672858602518	1	FACETS	0.514	0.424	0.614	0.514	0.424	0.614	SUBCLONAL	1	TRUE	0	0.318672858602518	1		242	380	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279253	142279253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	40	443	0	ENST00000350721.4:c.1393G>A	p.Ala465Thr	p.A465T	ENST00000350721	NM_001184.3	465	Gca/Aca	6/47	0.318672858602518	1	FACETS	0.455	0.378	0.541	0.455	0.378	0.541	SUBCLONAL	1	TRUE	0	0.318672858602518	1		443	464	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430516	181430516	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	49	566	0	ENST00000325404.1:c.368A>G	p.Asp123Gly	p.D123G	ENST00000325404	NM_003106.3	123	gAt/gGt	1/1	0.318672858602518	1	FACETS	0.446	0.377	0.521	0.446	0.377	0.521	SUBCLONAL	1	TRUE	0	0.318672858602518	1		566	580	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250888	153250888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	24	297	0	ENST00000281708.4:c.1172G>A	p.Gly391Asp	p.G391D	ENST00000281708	NM_033632.3	391	gGt/gAt	8/12	1	2	FACETS	0.475	0.373	0.593	0.475	0.373	0.593	SUBCLONAL	1	TRUE	1	0.318672858602518	2		297	317	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564492	86564492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200002693	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	82	774	0	ENST00000274376.6:c.224G>A	p.Gly75Glu	p.G75E	ENST00000274376	NM_002890.2	75	gGg/gAg	1/25	0.269231132193035	2	FACETS	0.562	0.494	0.635	0.281	0.247	0.318	SUBCLONAL	1	TRUE	0	0.318672858602518	2		774	916	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163410	32163410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	81	803	1	ENST00000375023.3:c.5816G>A	p.Gly1939Glu	p.G1939E	ENST00000375023	NM_004557.3	1939	gGg/gAg	30/30	0.318672858602518	1	FACETS	0.405	0.356	0.459	0.405	0.356	0.459	SUBCLONAL	1	TRUE	0	0.318672858602518	1		804	1054	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43742088	43742088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	94	765	1	ENST00000523873.1:c.77C>T	p.Ala26Val	p.A26V	ENST00000523873		26	gCt/gTt	2/8	0.318672858602518	1	FACETS	0.533	0.473	0.597	0.533	0.473	0.597	SUBCLONAL	1	TRUE	0	0.318672858602518	1		766	931	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391173	139391173	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	85	1167	0	ENST00000277541.6:c.7018C>T	p.Pro2340Ser	p.P2340S	ENST00000277541	NM_017617.3	2340	Ccc/Tcc	34/34	1	2	FACETS	0.441	0.388	0.498	0.441	0.388	0.498	SUBCLONAL	1	TRUE	1	0.318672858602518	2		1167	1209	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0058525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	30	304	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.653	0.526	0.798	0.653	0.526	0.798	SUBCLONAL	1	FALSE	1	0.206866317964856	2		304	444	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207077	1207077	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs121913319	NA	P-0058525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	114	951	2	ENST00000326873.7:c.169del	p.Glu57LysfsTer7	p.E57Kfs*7	ENST00000326873	NM_000455.4	55	ctG/ct	1/10	0.206866317964856	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	FALSE	0	0.206866317964856	1		953	967	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600326	10600326	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	88	661	0	ENST00000171111.5:c.1529C>T	p.Ala510Val	p.A510V	ENST00000171111	NM_203500.1	510	gCa/gTa	4/6	0.206866317964856	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	0	0.206866317964856	1		661	640	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141533	11141534	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0058525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	77	783	0	ENST00000358026.2:c.3512_3513del	p.Val1171AspfsTer4	p.V1171Dfs*4	ENST00000358026	NM_001128849.1	1170	acTGtg/actg	25/36	0.206866317964856	1	FACETS	0.895	0.785	1	0.895	0.785	1	CLONAL	1	FALSE	0	0.206866317964856	1		783	746	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170229	119170229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	32	243	0	ENST00000264033.4:c.2459C>T	p.Pro820Leu	p.P820L	ENST00000264033	NM_005188.3	820	cCc/cTc	16/16	1	2	FACETS	0.814	0.661	0.987	0.814	0.661	0.987	CLONAL	1	FALSE	1	0.206866317964856	2		243	380	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031666	69031666	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0058525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	41	303	0	ENST00000288368.4:c.3422-1G>C		p.X1141_splice	ENST00000288368	NM_024870.2	1141			1	2	FACETS	0.957	0.799	1	0.957	0.799	1	CLONAL	1	FALSE	1	0.206866317964856	2		303	414	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0058563-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	94	304	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.437921819993562	4	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	2	0.534018471086193	4		304	253	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220578	1220578	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0058563-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	141	827	0	ENST00000326873.7:c.598-2A>T		p.X200_splice	ENST00000326873	NM_000455.4	200			0.534018471086193	2	FACETS	0.904	0.839	0.969	0.904	0.839	0.969	CLONAL	2	TRUE	0	0.534018471086193	2		827	292	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696688	47696688	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519971	NA	P-0058563-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	145	568	0	ENST00000347630.2:c.260A>C	p.Tyr87Ser	p.Y87S	ENST00000347630	NM_001007230.1	87	tAc/tCc	5/11	0.534018471086193	3	FACETS	0.92	0.85	0.991	0.92	0.85	0.991	CLONAL	2	TRUE	1	0.534018471086193	3		568	374	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612160	43612161	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0058563-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	196	746	0	ENST00000355710.3:c.2265_2266delinsTT	p.Ala756Ser	p.A756S	ENST00000355710	NM_020975.4	755	gtGGcc/gtTTcc	12/20	0.534018471086193	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	3	TRUE	1	0.534018471086193	4		746	370	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57004232	57004232	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058563-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	49	913	0	ENST00000257254.3:c.247C>T	p.Pro83Ser	p.P83S	ENST00000257254		83	Ccc/Tcc	1/2	0.534018471086193	3	FACETS	0.711	0.605	0.826	0.356	0.302	0.413	SUBCLONAL	1	TRUE	1	0.534018471086193	3		913	327	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599943	10599944	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0058563-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	117	748	0	ENST00000171111.5:c.1632_1633delinsTT	p.Trp544_Thr545delinsCysSer	p.W544_T545delinsCS	ENST00000171111	NM_203500.1	544	tgGAct/tgTTct	5/6	0.534018471086193	2	FACETS	0.843	0.775	0.911	0.843	0.775	0.911	CLONAL	2	TRUE	0	0.534018471086193	2		748	260	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874253	151874253	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058563-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	55	523	0	ENST00000262189.6:c.8285C>T	p.Pro2762Leu	p.P2762L	ENST00000262189	NM_170606.2	2762	cCa/cTa	38/59	0.385547814748626	3	FACETS	1	0.885	1	0.514	0.444	0.589	CLONAL	1	TRUE	1	0.534018471086193	3		523	254	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845395	76845395	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058563-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	57	206	0	ENST00000373344.5:c.6126G>T	p.Gln2042His	p.Q2042H	ENST00000373344	NM_000489.3	2042	caG/caT	27/35	0.469752756207008	2	FACETS	0.97	0.865	1			1	CLONAL	2	TRUE	NA	0.534018471086193	2		206	110	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233124	69233124	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058563-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	104	688	0	ENST00000462284.1:c.991del	p.Leu331PhefsTer42	p.L331Ffs*42	ENST00000462284	NM_002392.5	330	gCc/gc	11/11	0.437921819993562	4	FACETS	0.776	0.701	0.855	0.776	0.701	0.855	SUBCLONAL	2	TRUE	2	0.534018471086193	4		688	385	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396574	396574	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058563-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	75	682	0	ENST00000262320.3:c.452A>T	p.Asp151Val	p.D151V	ENST00000262320	NM_003502.3	151	gAt/gTt	2/11	0.534018471086193	3	FACETS	0.989	0.872	1	0.494	0.436	0.556	CLONAL	1	TRUE	1	0.534018471086193	3		682	360	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1255435	1255435	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058563-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	139	743	0	ENST00000310581.5:c.3124C>A	p.Leu1042Ile	p.L1042I	ENST00000310581	NM_198253.2	1042	Ctc/Atc	14/16	0.437921819993562	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.534018471086193	4		743	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0058818-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	66	791	0	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	1	2	FACETS	0.776	0.672	0.888	0.776	0.672	0.888	SUBCLONAL	1	FALSE	1	0.231815402044346	2		791	734	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431734	49431734	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058818-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	113	937	0	ENST00000301067.7:c.9405del	p.Ile3136LeufsTer6	p.I3136Lfs*6	ENST00000301067	NM_003482.3	3135	acC/ac	34/54	0.144564807800945	3	FACETS	1	0.969	1	0.599	0.538	0.663	CLONAL	1	FALSE	1	0.231815402044346	3		937	908	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47684692	47684692	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058818-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	62	503	0	ENST00000347630.2:c.757G>T	p.Glu253Ter	p.E253*	ENST00000347630	NM_001007230.1	253	Gaa/Taa	9/11	1	2	FACETS	0.873	0.754	1	0.873	0.754	1	CLONAL	1	FALSE	1	0.231815402044346	2		503	613	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888058	81888058	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058818-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	78	513	0	ENST00000359376.3:c.203T>C	p.Met68Thr	p.M68T	ENST00000359376	NM_002661.3	68	aTg/aCg	3/33	0.144564807800945	3	FACETS	1	0.966	1	0.643	0.565	0.726	CLONAL	1	FALSE	1	0.231815402044346	3		513	584	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321634	30321635	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0058818-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	66	470	1	ENST00000322652.5:c.1489_1490delinsAT	p.Gly497Ile	p.G497I	ENST00000322652	NM_015355.2	497	GGc/ATc	13/16	0.209230017903205	3	FACETS	1	0.933	1			1	CLONAL	1	FALSE	NA	0.231815402044346	3		471	568	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627474	14627474	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058818-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	73	614	0	ENST00000254322.2:c.596A>G	p.Asn199Ser	p.N199S	ENST00000254322	NM_006145.1	199	aAc/aGc	2/3	0.144564807800945	3	FACETS	1	0.908	1	0.524	0.458	0.595	CLONAL	1	FALSE	1	0.231815402044346	3		614	671	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501560	149501567	+	frameshift_variant	Frame_Shift_Del	DEL	TGTCCATG	TGTCCATG	-	novel	NA	P-0058818-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	96	796	0	ENST00000261799.4:c.2220_2227del	p.Met741GlufsTer34	p.M741Efs*34	ENST00000261799	NM_002609.3	740	taCATGGACAtg/tatg	16/23	0.231815402044346	1	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	FALSE	0	0.231815402044346	1		796	725	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517933	8517933	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058818-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	55	609	0	ENST00000356435.5:c.1458A>T	p.Lys486Asn	p.K486N	ENST00000356435		486	aaA/aaT	10/35	0.175001178385938	2	FACETS	0.934	0.8	1	0.467	0.4	0.541	CLONAL	1	FALSE	0	0.231815402044346	2		609	508	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111502	8111503	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0058895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	64	395	0	ENST00000346208.3:c.990dup	p.Asn331GlufsTer21	p.N331Efs*21	ENST00000346208		330	agg/aGgg	5/6	1	2	FACETS	0.642	0.556	0.734	0.642	0.556	0.734	SUBCLONAL	1	TRUE	1	0.380781842562378	2		395	524	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165729	108165729	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs762083530	NA	P-0058895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	41	297	0	ENST00000278616.4:c.4852C>T	p.Arg1618Ter	p.R1618*	ENST00000278616	NM_000051.3	1618	Cga/Tga	32/63	0.380781842562378	1	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	0	0.380781842562378	1		297	161	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609380	39609380	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1370548557	NA	P-0058895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	44	247	0	ENST00000262039.4:c.1682G>A	p.Arg561His	p.R561H	ENST00000262039	NM_002647.2	561	cGc/cAc	15/25	1	2	FACETS	0.817	0.689	0.956	0.817	0.689	0.956	CLONAL	1	TRUE	1	0.380781842562378	2		247	283	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738590	43738590	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	26	308	0	ENST00000382044.4:c.3035T>C	p.Leu1012Pro	p.L1012P	ENST00000382044	NM_001141980.1	1012	cTg/cCg	14/28	1	2	FACETS	0.473	0.375	0.584	0.473	0.375	0.584	SUBCLONAL	1	TRUE	1	0.380781842562378	2		308	289	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0058899-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	69	378	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	0.246479354337671	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	0	0.246479354337671	1		378	369	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929073	44929073	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058899-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	55	316	0	ENST00000377967.4:c.2174del	p.Leu725Ter	p.L725*	ENST00000377967	NM_021140.2	725	Ttg/tg	17/29	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	1	0.246479354337671	2		316	399	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0058978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	56	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.807	0.698	0.923	1	0.972	1	CLONAL	2	FALSE	1	0.266947352842702	2		485	260	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0058978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	41	351	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	FALSE	1	0.266947352842702	2		351	287	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016615	12016615	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	23	431	0	ENST00000353533.5:c.751A>C	p.Ser251Arg	p.S251R	ENST00000353533	NM_003010.3	251	Agt/Cgt	7/11	0.266947352842702	1	FACETS	0.679	0.531	0.848	0.679	0.531	0.848	SUBCLONAL	1	FALSE	0	0.266947352842702	1		431	220	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575230	48575230	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	34	284	0	ENST00000342988.3:c.424+1del		p.D142fs	ENST00000342988	NM_005359.5	142	Gat/at	3/12	0.266947352842702	1	FACETS	0.99	0.815	1	0.99	0.815	1	CLONAL	1	FALSE	0	0.266947352842702	1		284	223	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0059019-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	50	416	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.2	2		416	369	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0059019-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	33	557	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.803	0.654	0.971	0.803	0.654	0.971	CLONAL	1	TRUE	1	0.2	2		559	411	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440904	56440904	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1458799446	NA	P-0059019-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	26	541	0	ENST00000407977.2:c.433C>T	p.Arg145Ter	p.R145*	ENST00000407977		145	Cga/Tga	4/10	1	2	FACETS	0.492	0.389	0.612	0.492	0.389	0.612	SUBCLONAL	1	TRUE	1	0.2	2		541	528	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492904	56492905	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0059019-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	42	503	0	ENST00000407977.2:c.33_34dup	p.Leu12ProfsTer7	p.L12Pfs*7	ENST00000407977		12	ctc/cCCtc	2/10	1	2	FACETS	0.685	0.571	0.812	0.685	0.571	0.812	SUBCLONAL	1	TRUE	1	0.2	2		503	613	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038875	12038875	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059019-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	38	500	0	ENST00000396373.4:c.1168A>C	p.Thr390Pro	p.T390P	ENST00000396373	NM_001987.4	390	Acc/Ccc	7/8	1	2	FACETS	0.896	0.741	1	0.896	0.741	1	CLONAL	1	TRUE	1	0.2	2		500	424	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039683	47039687	+	frameshift_variant	Frame_Shift_Del	DEL	GTTGA	GTTGA	-	novel	NA	P-0059019-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	33	267	0	ENST00000377604.3:c.1138_1142del	p.Glu380CysfsTer5	p.E380Cfs*5	ENST00000377604	NM_001204468.1	379	GTTGAg/g	11/24	1	1	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	0	0.2	1		267	269	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130336	11130336	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	141	587	0	ENST00000358026.2:c.2575A>G	p.Thr859Ala	p.T859A	ENST00000358026	NM_001128849.1	859	Acg/Gcg	18/36	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.628782389117004	2		587	412	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438488	52438501	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGCACGTCATCC	TCTGCACGTCATCC	-	novel	NA	P-0059185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	102	610	0	ENST00000460680.1:c.1218_1231del	p.Asp407HisfsTer6	p.D407Hfs*6	ENST00000460680	NM_004656.3	406	gaGGATGACGTGCAGAac/gaac	12/17	0.608381514279263	1	FACETS	0.775	0.703	0.849	0.775	0.703	0.849	SUBCLONAL	1	TRUE	0	0.628782389117004	1		610	287	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070577	67070578	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0059224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	215	613	0	ENST00000412916.2:c.207dup	p.Pro70SerfsTer13	p.P70Sfs*13	ENST00000412916		67	-/T	3/6	0.782370678015581	1	FACETS	0.956	0.907	1	0.956	0.907	1	CLONAL	1	TRUE	0	0.782370678015581	1		613	350	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266112	41266112	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913228	NA	P-0059224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	208	696	0	ENST00000349496.5:c.109T>G	p.Ser37Ala	p.S37A	ENST00000349496	NM_001904.3	37	Tct/Gct	3/15	1	2	FACETS	0.931	0.871	0.993	0.931	0.871	0.993	CLONAL	1	TRUE	1	0.782370678015581	2		696	571	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101234	27101235	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0059224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	378	811	0	ENST00000324856.7:c.4517dup	p.Tyr1506Ter	p.Y1506*	ENST00000324856	NM_006015.4	1506	tat/tAat	18/20	0.782370678015581	2	FACETS	0.996	0.967	1	0.996	0.967	1	CLONAL	2	TRUE	0	0.782370678015581	2		811	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0059351-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	201	433	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.327561674977376	2	FACETS	0.794	0.741	0.848	0.794	0.741	0.848	SUBCLONAL	2	TRUE	0	0.43732036513134	2		433	579	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615100	100615100	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782264410	NA	P-0059652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	30	270	0	ENST00000308731.7:c.815C>T	p.Ala272Val	p.A272V	ENST00000308731	NM_000061.2	272	gCa/gTa	9/19	1	2	FACETS	0.739	0.596	0.902	0.739	0.596	0.902	CLONAL	1	FALSE	1	0.205490011818539	2		270	395	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941690	48941690	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0059652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	52	243	0	ENST00000267163.4:c.1000A>T	p.Arg334Ter	p.R334*	ENST00000267163	NM_000321.2	334	Aga/Tga	10/27	0.205490011818539	3	FACETS	1	0.951	1	0.644	0.55	0.748	CLONAL	1	FALSE	1	0.205490011818539	3		243	433	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937983	76937983	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	63	452	0	ENST00000373344.5:c.2765del	p.Asp922ValfsTer48	p.D922Vfs*48	ENST00000373344	NM_000489.3	922	gAt/gt	9/35	0.205490011818539	3	FACETS	0.905	0.782	1	0.453	0.391	0.52	CLONAL	1	FALSE	1	0.205490011818539	3		452	747	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0059684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	285	309	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.686197960226862	3	FACETS	0.978	0.943	1	0.978	0.943	1	CLONAL	3	TRUE	0	0.704711954273102	3		309	373	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0059684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	188	367	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.704711954273102	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	1	0.704711954273102	3		367	356	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0059684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	101	228	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.704711954273102	2		228	234	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271819	15271819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765739997	NA	P-0059684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	41	840	0	ENST00000263388.2:c.6620G>A	p.Arg2207Gln	p.R2207Q	ENST00000263388	NM_000435.2	2207	cGg/cAg	33/33	1	2	FACETS	0.248	0.206	0.294	0.248	0.206	0.294	SUBCLONAL	1	TRUE	1	0.704711954273102	2		840	470	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0059684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	139	606	1	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	0.903	0.829	0.979	0.903	0.829	0.979	CLONAL	1	TRUE	1	0.704711954273102	2		607	437	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353860	40353860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238042644	NA	P-0059684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	22	545	0	ENST00000293328.3:c.2260G>A	p.Asp754Asn	p.D754N	ENST00000293328	NM_012448.3	754	Gat/Aat	19/19	1	2	FACETS	0.152	0.117	0.193	0.152	0.117	0.193	SUBCLONAL	1	TRUE	1	0.704711954273102	2		545	410	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217557	142217557	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1268253442	NA	P-0059684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	88	403	0	ENST00000350721.4:c.5440del	p.Arg1814GlufsTer10	p.R1814Efs*10	ENST00000350721	NM_001184.3	1814	Aga/ga	32/47	1	2	FACETS	0.788	0.705	0.874	0.788	0.705	0.874	SUBCLONAL	1	TRUE	1	0.704711954273102	2		403	317	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105892	27105892	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	169	729	1	ENST00000324856.7:c.5503C>T	p.Gln1835Ter	p.Q1835*	ENST00000324856	NM_006015.4	1835	Cag/Tag	20/20	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.704711954273102	2		730	477	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67646013	67646014	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs1470210640	NA	P-0059684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	121	456	4	ENST00000264010.4:c.950_951del	p.Thr317ArgfsTer91	p.T317Rfs*91	ENST00000264010	NM_006565.3	314	aAC/a	4/12	1	2	FACETS	0.753	0.685	0.824	0.753	0.685	0.824	SUBCLONAL	1	TRUE	1	0.704711954273102	2		460	456	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546324	46546324	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	113	478	0	ENST00000262741.5:c.205del	p.Asp69IlefsTer7	p.D69Ifs*7	ENST00000262741	NM_003629.3	69	Gat/at	2/10	1	2	FACETS	0.924	0.841	1	0.924	0.841	1	CLONAL	1	TRUE	1	0.704711954273102	2		478	347	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106074	27106074	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	127	760	0	ENST00000324856.7:c.5688del	p.Pro1898HisfsTer25	p.P1898Hfs*25	ENST00000324856	NM_006015.4	1895	gaG/ga	20/20	1	2	FACETS	0.801	0.731	0.874	0.801	0.731	0.874	CLONAL	1	TRUE	1	0.704711954273102	2		760	450	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433686	49433686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1236327026	NA	P-0059684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	132	751	0	ENST00000301067.7:c.7867G>A	p.Gly2623Arg	p.G2623R	ENST00000301067	NM_003482.3	2623	Gga/Aga	31/54	0.704711954273102	3	FACETS	0.781	0.71	0.854	0.39	0.355	0.427	SUBCLONAL	1	TRUE	1	0.704711954273102	3		751	649	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432923	432925	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1221939206	NA	P-0059684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	146	509	0	ENST00000399788.2:c.1991_1993del	p.Glu664del	p.E664del	ENST00000399788	NM_001042603.1	664	gAAGtg/gtg	15/28	0.704711954273102	3	FACETS	0.945	0.866	1	0.472	0.433	0.514	CLONAL	1	TRUE	1	0.704711954273102	3		509	593	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467810	66467810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370146960	NA	P-0059684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	133	535	0	ENST00000273854.3:c.459G>A	p.Met153Ile	p.M153I	ENST00000273854	NM_004439.5	153	atG/atA	3/18	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.704711954273102	2		535	334	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10789919	10789919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1391585643	NA	P-0059684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	50	430	0	ENST00000361367.2:c.1990C>T	p.Arg664Cys	p.R664C	ENST00000361367	NM_014633.3	664	Cgt/Tgt	16/25	1	2	FACETS	0.382	0.325	0.445	0.382	0.325	0.445	SUBCLONAL	1	TRUE	1	0.704711954273102	2		430	371	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678492	88678492	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	24	639	0	ENST00000360948.2:c.1044C>G	p.Ile348Met	p.I348M	ENST00000360948	NM_001012338.2	348	atC/atG	9/19	1	2	FACETS	0.212	0.166	0.264	0.212	0.166	0.264	SUBCLONAL	1	TRUE	1	0.704711954273102	2		639	322	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845703	68845703	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555515643	NA	P-0059684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	150	580	0	ENST00000261769.5:c.949T>C	p.Phe317Leu	p.F317L	ENST00000261769	NM_004360.3	317	Ttc/Ctc	7/16	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.704711954273102	2		580	422	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883243	37883243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886025	NA	P-0059684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	141	595	0	ENST00000269571.5:c.3146G>A	p.Ser1049Asn	p.S1049N	ENST00000269571		1049	aGc/aAc	25/27	1	2	FACETS	0.974	0.896	1	0.974	0.896	1	CLONAL	1	TRUE	1	0.704711954273102	2		595	411	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119929	70119929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769781671	NA	P-0059684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	129	683	0	ENST00000245479.2:c.931G>A	p.Gly311Ser	p.G311S	ENST00000245479	NM_000346.3	311	Ggc/Agc	3/3	1	2	FACETS	0.911	0.834	0.99	0.911	0.834	0.99	CLONAL	1	TRUE	1	0.704711954273102	2		683	402	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798851	42798851	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	128	667	0	ENST00000575354.2:c.4423A>G	p.Met1475Val	p.M1475V	ENST00000575354	NM_015125.3	1475	Atg/Gtg	19/20	1	2	FACETS	0.886	0.81	0.964	0.886	0.81	0.964	CLONAL	1	TRUE	1	0.704711954273102	2		667	410	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573039	41573039	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	142	771	0	ENST00000263253.7:c.5325del	p.Asn1776MetfsTer32	p.N1776Mfs*32	ENST00000263253	NM_001429.3	1775	aCc/ac	31/31	1	2	FACETS	0.944	0.868	1	0.944	0.868	1	CLONAL	1	TRUE	1	0.704711954273102	2		771	427	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437740	52437740	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770422186	NA	P-0059684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	73	630	0	ENST00000460680.1:c.1421C>T	p.Pro474Leu	p.P474L	ENST00000460680	NM_004656.3	474	cCg/cTg	13/17	1	2	FACETS	0.485	0.426	0.549	0.485	0.426	0.549	SUBCLONAL	1	TRUE	1	0.704711954273102	2		630	427	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793551	89793551	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	68	521	0	ENST00000336032.3:c.620A>C	p.Glu207Ala	p.E207A	ENST00000336032	NM_006813.2	207	gAg/gCg	2/2	1	2	FACETS	0.454	0.396	0.516	0.454	0.396	0.516	SUBCLONAL	1	TRUE	1	0.704711954273102	2		521	425	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873896	151873897	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0059684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	26	622	0	ENST00000262189.6:c.8641dup	p.Arg2881LysfsTer44	p.R2881Kfs*44	ENST00000262189	NM_170606.2	2881	aga/aAga	38/59	1	2	FACETS	0.159	0.125	0.197	0.159	0.125	0.197	SUBCLONAL	1	TRUE	1	0.704711954273102	2		622	465	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0060137-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	85	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.555	0.494	0.62	0.555	0.494	0.62	SUBCLONAL	1	TRUE	1	0.820682374193966	2		429	373	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0060137-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	243	384	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.820682374193966	2		384	585	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935538	13935538	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060137-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	274	561	0	ENST00000405192.2:c.1318G>A	p.Gly440Arg	p.G440R	ENST00000405192	NM_001163147.1	440	Ggg/Agg	12/12	1	2	FACETS	0.978	0.924	1	0.978	0.924	1	CLONAL	1	TRUE	1	0.820682374193966	2		561	683	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308353	15308353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060137-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	150	634	0	ENST00000263388.2:c.155G>A	p.Gly52Glu	p.G52E	ENST00000263388	NM_000435.2	52	gGa/gAa	2/33	1	2	FACETS	0.601	0.552	0.653	0.601	0.552	0.653	SUBCLONAL	1	TRUE	1	0.820682374193966	2		634	608	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43817921	43817921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1214203929	NA	P-0060137-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	289	671	0	ENST00000372470.3:c.1600G>A	p.Asp534Asn	p.D534N	ENST00000372470	NM_005373.2	534	Gac/Aac	11/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.820682374193966	2		671	663	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644486	18644486	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060137-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	124	334	0	ENST00000266497.5:c.2664T>A	p.Asp888Glu	p.D888E	ENST00000266497		888	gaT/gaA	18/31	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.820682374193966	2		334	299	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210605	5210605	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060137-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	163	717	0	ENST00000357368.4:c.5362G>T	p.Glu1788Ter	p.E1788*	ENST00000357368	NM_002850.3	1788	Gag/Tag	35/38	1	2	FACETS	0.538	0.495	0.583	0.538	0.495	0.583	SUBCLONAL	1	TRUE	1	0.820682374193966	2		717	738	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267672	198267672	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0060137-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	124	395	0	ENST00000335508.6:c.1806+1G>T		p.X602_splice	ENST00000335508	NM_012433.2	602			1	2	FACETS	0.835	0.764	0.908	0.835	0.764	0.908	CLONAL	1	TRUE	1	0.820682374193966	2		395	362	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095861	29095863	+	missense_variant	Missense_Mutation	TNP	TGC	TGC	GCA	novel	NA	P-0060137-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	179	476	0	ENST00000328354.6:c.971_973inv	p.Cys324_Lys325delinsLeuGln	p.C324_K325delinsLQ	ENST00000328354	NM_007194.3	324	tGCAag/tTGCag	9/15	1	2	FACETS	0.789	0.732	0.847	0.789	0.732	0.847	SUBCLONAL	1	TRUE	1	0.820682374193966	2		476	553	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531042	187531043	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0060137-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	244	512	0	ENST00000441802.2:c.9980_9981insG	p.Asp3327GlufsTer5	p.D3327Efs*5	ENST00000441802	NM_005245.3	3327	gat/gaGt	15/27	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.820682374193966	2		512	567	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184974	123184975	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060137-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	37	113	1	ENST00000218089.9:c.1021_1022insT	p.Gly341ValfsTer2	p.G341Vfs*2	ENST00000218089	NM_001042749.1	341	ggt/gTgt	12/35	1	1	FACETS	0.831	0.725	0.934	0.831	0.725	0.934	CLONAL	1	TRUE	0	0.820682374193966	1		114	64	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303751	65303751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	152	494	0	ENST00000342505.4:c.3004C>T	p.Arg1002Trp	p.R1002W	ENST00000342505	NM_002227.2	1002	Cgg/Tgg	22/25	0.2862771696822	3	FACETS	1	0.973	1	0.566	0.521	0.612	INDETERMINATE	1	TRUE	1	0.711701880282858	3		494	512	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692995	89692995	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	278	435	0	ENST00000371953.3:c.480del	p.Arg161GlufsTer6	p.R161Efs*6	ENST00000371953	NM_000314.4	160	aCc/ac	5/9	0.711701880282858	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.711701880282858	2		435	388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0060237-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	151	641	0	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	0.366507738137609	1	FACETS	0.867	0.796	0.942	0.867	0.796	0.942	CLONAL	1	TRUE	0	0.429851786571032	1		641	636	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57474013	57474014	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0060237-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	138	613	0	ENST00000371085.3:c.231_232insTG	p.Gln78CysfsTer23	p.Q78Cfs*23	ENST00000371085	NM_000516.4	77	ccg/ccGTg	3/13	1	2	FACETS	0.887	0.808	0.969	0.887	0.808	0.969	CLONAL	1	TRUE	1	0.429851786571032	2		613	724	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0060469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	351	324	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.354817967559317	6	FACETS	1	0.987	1	0.82	0.782	0.859	INDETERMINATE	3	TRUE	2	0.631450467917931	6		324	767	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096052	178096052	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	48	600	0	ENST00000397062.3:c.1279G>C	p.Glu427Gln	p.E427Q	ENST00000397062	NM_006164.4	427	Gag/Cag	5/5	0.136035916984859	3	FACETS	0.29	0.244	0.34	0.097	0.081	0.114	INDETERMINATE	1	TRUE	0	0.631450467917931	3		600	690	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974395	18974395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1322079562	NA	P-0060469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	179	537	0	ENST00000262803.5:c.2749C>T	p.Arg917Trp	p.R917W	ENST00000262803	NM_002911.3	917	Cgg/Tgg	19/24	0.136035916984859	3	FACETS	0.825	0.769	0.883	0.55	0.512	0.589	INDETERMINATE	2	TRUE	0	0.631450467917931	3		537	452	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955382	48955382	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0060469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	172	326	0	ENST00000267163.4:c.1499del		p.X500_splice	ENST00000267163	NM_000321.2	500			0.564809902620075	2	FACETS	0.876	0.823	0.929	0.876	0.823	0.929	CLONAL	2	TRUE	0	0.631450467917931	2		326	311	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032006	26032006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	125	760	0	ENST00000244661.2:c.283G>A	p.Glu95Lys	p.E95K	ENST00000244661	NM_003537.3	95	Gag/Aag	1/1	0.146587324986368	3	FACETS	0.685	0.621	0.754	0.228	0.207	0.252	INDETERMINATE	1	TRUE	0	0.631450467917931	3		760	760	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578515	7578516	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0060469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	287	665	0	ENST00000269305.4:c.414dup	p.Lys139GlnfsTer10	p.K139Qfs*10	ENST00000269305	NM_001126112.2	138	-/C	5/11	0.578188325238618	2	FACETS	0.812	0.772	0.851	0.812	0.772	0.851	CLONAL	2	TRUE	0	0.631450467917931	2		665	560	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733629	85733629	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	60	486	0	ENST00000370580.1:c.383G>C	p.Gly128Ala	p.G128A	ENST00000370580	NM_003921.4	128	gGa/gCa	3/3	0.529434901279086	2	FACETS	0.499	0.431	0.571	0.249	0.215	0.286	SUBCLONAL	1	TRUE	0	0.631450467917931	2		486	381	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957447	175957447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	121	441	0	ENST00000367669.3:c.1949C>T	p.Ser650Phe	p.S650F	ENST00000367669	NM_022457.5	650	tCc/tTc	17/20	0.631450467917931	4	FACETS	0.955	0.864	1	0.239	0.216	0.263	CLONAL	1	TRUE	0	0.631450467917931	4		441	655	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046683	42046683	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	49	473	0	ENST00000219905.7:c.7057G>C	p.Glu2353Gln	p.E2353Q	ENST00000219905	NM_001164273.1	2353	Gag/Cag	18/24	0.529434901279086	2	FACETS	0.378	0.32	0.44	0.189	0.16	0.22	SUBCLONAL	1	TRUE	0	0.631450467917931	2		473	411	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349157	11349157	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	39	617	0	ENST00000332029.2:c.179C>A	p.Ser60Ter	p.S60*	ENST00000332029	NM_003745.1	60	tCg/tAg	2/2	0.354817967559317	6	FACETS	0.435	0.36	0.52	0.109	0.09	0.13	INDETERMINATE	1	TRUE	2	0.631450467917931	6		617	642	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174889	56174889	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	343	459	0	ENST00000399503.3:c.2049del	p.Val684Ter	p.V684*	ENST00000399503	NM_005921.1	683	gTt/gt	11/20	0.515632219611805	3	FACETS	0.896	0.861	0.93	0.896	0.861	0.93	CLONAL	3	TRUE	0	0.631450467917931	3		459	532	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250796	26250796	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	94	668	0	ENST00000446824.2:c.38G>T	p.Gly13Val	p.G13V	ENST00000446824	NM_021018.2	13	gGc/gTc	1/1	0.146587324986368	3	FACETS	0.533	0.474	0.596	0.178	0.158	0.199	INDETERMINATE	1	TRUE	0	0.631450467917931	3		668	735	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686821	117686821	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	101	436	0	ENST00000368508.3:c.2896C>G	p.Gln966Glu	p.Q966E	ENST00000368508	NM_002944.2	966	Caa/Gaa	19/43	0.146587324986368	3	FACETS	1	0.906	1	0.336	0.302	0.371	INDETERMINATE	1	TRUE	0	0.631450467917931	3		436	418	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622174	162622174	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	89	593	0	ENST00000366898.1:c.523A>T	p.Thr175Ser	p.T175S	ENST00000366898	NM_004562.2	175	Acc/Tcc	4/12	0.146587324986368	3	FACETS	0.743	0.661	0.83	0.248	0.22	0.277	INDETERMINATE	1	TRUE	0	0.631450467917931	3		593	499	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864897	117864897	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	180	426	0	ENST00000297338.2:c.1212G>T	p.Arg404Ser	p.R404S	ENST00000297338	NM_006265.2	404	agG/agT	10/14	0.631450467917931	6	FACETS	1	0.979	1	0.393	0.362	0.426	CLONAL	1	TRUE	3	0.631450467917931	6		426	1094	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968167	68968167	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	30	384	0	ENST00000288368.4:c.1196G>C	p.Arg399Pro	p.R399P	ENST00000288368	NM_024870.2	399	cGa/cCa	10/40	0.566291439867419	3	FACETS	0.264	0.212	0.323	0.088	0.07	0.108	SUBCLONAL	1	TRUE	0	0.631450467917931	3		384	474	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399409	139399411	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	rs761020817	NA	P-0060486-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	189	652	1	ENST00000277541.6:c.4732_4734del	p.Val1578del	p.V1578del	ENST00000277541	NM_017617.3	1578	GTG/-	26/34	1	2	FACETS	0.88	0.817	0.946	0.88	0.817	0.946	CLONAL	1	TRUE	1	0.64	2		653	671	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176329	24176329	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060486-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	108	395	0	ENST00000263121.7:c.1120C>G	p.Arg374Gly	p.R374G	ENST00000263121	NM_003073.3	374	Cgg/Ggg	9/9	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.64	2		395	330	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274876	41274884	+	inframe_deletion	In_Frame_Del	DEL	CGTCTTGTT	CGTCTTGTT	-	novel	NA	P-0060486-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	156	485	0	ENST00000349496.5:c.1127_1135del	p.Arg376_Val378del	p.R376_V378del	ENST00000349496	NM_001904.3	376	CGTCTTGTT/-	8/15	1	2	FACETS	0.922	0.849	0.996	0.922	0.849	0.996	CLONAL	1	TRUE	1	0.64	2		485	529	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390780	139390781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGATGGCAGCG	novel	NA	P-0060486-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	180	836	0	ENST00000277541.6:c.7400_7410dup	p.Ser2471ArgfsTer10	p.S2471Rfs*10	ENST00000277541	NM_017617.3	2470	-/CGCTGCCATCC	34/34	1	2	FACETS	0.843	0.781	0.908	0.843	0.781	0.908	CLONAL	1	TRUE	1	0.64	2		836	667	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20153878	20153878	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060486-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	75	247	0	ENST00000379607.5:c.182T>G	p.Ile61Ser	p.I61S	ENST00000379607	NM_001412.3	61	aTc/aGc	3/7	0.3	1	FACETS	0.653	0.58	0.729	0.653	0.58	0.729	INDETERMINATE	1	TRUE	0	0.64	1		247	244	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0060527-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	231	509	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.741189142963252	2		510	509	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692993	89692993	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519724	NA	P-0060527-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	51	390	0	ENST00000371953.3:c.477G>T	p.Arg159Ser	p.R159S	ENST00000371953	NM_000314.4	159	agG/agT	5/9	0.741189142963252	1	FACETS	0.273	0.233	0.317	0.273	0.233	0.317	SUBCLONAL	1	TRUE	0	0.741189142963252	1		390	317	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210075	55210075	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060527-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20678	427	391	0	ENST00000275493.2:c.185T>G	p.Leu62Arg	p.L62R	ENST00000275493	NM_005228.3	62	cTt/cGt	2/28	0.741189142963252	39	FACETS	0.803	0.758	0.85	0.021	0.019	0.022	CLONAL	1	TRUE	0	0.741189142963252	39		391	21105	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233034	55233034	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060527-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20106	3002	502	0	ENST00000275493.2:c.1784G>A	p.Cys595Tyr	p.C595Y	ENST00000275493	NM_005228.3	595	tGc/tAc	15/28	0.741189142963252	39	FACETS	1	0.993	1	0.132	0.129	0.135	CLONAL	5	TRUE	0	0.741189142963252	39		502	23108	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221783	55221783	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060527-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24422	4186	710	1	ENST00000275493.2:c.827A>T	p.Gln276Leu	p.Q276L	ENST00000275493	NM_005228.3	276	cAg/cTg	7/28	0.741189142963252	39	FACETS	0.968	0.951	0.985	0.149	0.146	0.152	CLONAL	6	TRUE	0	0.741189142963252	39		711	28608	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945125	151945125	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1281477155	NA	P-0060527-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	20	278	0	ENST00000262189.6:c.2394T>A	p.His798Gln	p.H798Q	ENST00000262189	NM_170606.2	798	caT/caA	14/59	0.741189142963252	3	FACETS	0.188	0.143	0.241	0.094	0.071	0.121	SUBCLONAL	1	TRUE	1	0.741189142963252	3		278	393	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863449	57863449	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781683841	NA	P-0060587-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	158	565	5	ENST00000228682.2:c.1544G>A	p.Arg515Gln	p.R515Q	ENST00000228682	NM_005269.2	515	cGg/cAg	11/12	0.158456163789945	3	FACETS	0.992	0.913	1	0.496	0.456	0.537	INDETERMINATE	1	TRUE	1	0.752259766555953	3		570	583	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555309	106555309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060587-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	150	525	0	ENST00000369096.4:c.2426C>T	p.Pro809Leu	p.P809L	ENST00000369096	NM_001198.3	809	cCt/cTt	7/7	1	2	FACETS	0.807	0.743	0.873	0.807	0.743	0.873	CLONAL	1	TRUE	1	0.752259766555953	2		525	494	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	232	582	2	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.979	0.915	1	0.979	0.915	1	CLONAL	1	TRUE	1	0.55301251656292	2		584	857	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	149	399	2	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.945	0.868	1	0.945	0.868	1	CLONAL	1	TRUE	1	0.55301251656292	2		401	570	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	169	336	3	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	0.955	0.882	1	0.955	0.882	1	CLONAL	1	TRUE	1	0.55301251656292	2		339	640	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	93	121	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.55301251656292	2		121	303	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	193	471	4	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	0.91	0.844	0.978	0.91	0.844	0.978	CLONAL	1	TRUE	1	0.55301251656292	2		475	767	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	212	504	3	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.55301251656292	2		507	745	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	39	51	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.959	0.81	1	0.959	0.81	1	CLONAL	1	TRUE	1	0.55301251656292	2		51	147	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	62	484	2	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.281	0.242	0.324	0.281	0.242	0.324	SUBCLONAL	1	TRUE	1	0.55301251656292	2		486	798	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132522	11132522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778175819	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	63	623	1	ENST00000358026.2:c.2738C>T	p.Pro913Leu	p.P913L	ENST00000358026	NM_001128849.1	913	cCg/cTg	19/36	1	2	FACETS	0.272	0.235	0.313	0.272	0.235	0.313	SUBCLONAL	1	TRUE	1	0.55301251656292	2		624	837	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	122	417	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.992	0.903	1	0.992	0.903	1	CLONAL	1	TRUE	1	0.55301251656292	2		417	445	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	163	339	4	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.917	0.845	0.992	0.917	0.845	0.992	CLONAL	1	TRUE	1	0.55301251656292	2		343	643	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	128	499	1	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.647	0.587	0.709	0.647	0.587	0.709	SUBCLONAL	1	TRUE	1	0.55301251656292	2		500	716	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	41	500	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	0.206	0.171	0.246	0.206	0.171	0.246	SUBCLONAL	1	TRUE	1	0.55301251656292	2		500	719	SUCCESS
APC	324	MSKCC	GRCh37	5	112179431	112179431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622205	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	36	453	0	ENST00000257430.4:c.8140C>T	p.Arg2714Cys	p.R2714C	ENST00000257430	NM_000038.5	2714	Cgt/Tgt	16/16	1	2	FACETS	0.194	0.159	0.234	0.194	0.159	0.234	SUBCLONAL	1	TRUE	1	0.55301251656292	2		453	670	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003808	45003808	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	194	533	2	ENST00000558401.1:c.64C>T	p.Gln22Ter	p.Q22*	ENST00000558401	NM_004048.2	22	Cag/Tag	1/4	1	2	FACETS	0.893	0.828	0.96	0.893	0.828	0.96	CLONAL	1	TRUE	1	0.55301251656292	2		535	786	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	196	537	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	0.976	0.907	1	0.976	0.907	1	CLONAL	1	TRUE	1	0.55301251656292	2		537	726	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	159	561	5	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.761	0.698	0.825	0.761	0.698	0.825	SUBCLONAL	1	TRUE	1	0.55301251656292	2		566	756	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129329	152129329	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	167	483	3	ENST00000206249.3:c.287del	p.Gly96ValfsTer13	p.G96Vfs*13	ENST00000206249	NM_000125.3	94	ctG/ct	1/8	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.55301251656292	2		486	571	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892299	9892299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs796052549	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	164	500	1	ENST00000330684.3:c.2191G>A	p.Asp731Asn	p.D731N	ENST00000330684	NM_001134407.1	731	Gat/Aat	11/13	1	2	FACETS	0.995	0.918	1	0.995	0.918	1	CLONAL	1	TRUE	1	0.55301251656292	2		501	596	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	134	216	1	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.55301251656292	2		217	412	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993336	72993336	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	48	547	0	ENST00000268489.5:c.709C>T	p.Arg237Ter	p.R237*	ENST00000268489	NM_006885.3	237	Cga/Tga	2/10	1	2	FACETS	0.247	0.208	0.29	0.247	0.208	0.29	SUBCLONAL	1	TRUE	1	0.55301251656292	2		547	702	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116263	209116263	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	79	228	2	ENST00000345146.2:c.13del	p.Ile5SerfsTer7	p.I5Sfs*7	ENST00000345146	NM_005896.2	5	Atc/tc	3/10	1	2	FACETS	0.663	0.586	0.745	0.663	0.586	0.745	SUBCLONAL	1	TRUE	1	0.55301251656292	2		230	431	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997826	149997826	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	167	437	3	ENST00000253339.5:c.2641del	p.Asp881IlefsTer11	p.D881Ifs*11	ENST00000253339		881	Gat/at	5/7	1	2	FACETS	0.956	0.882	1	0.956	0.882	1	CLONAL	1	TRUE	1	0.55301251656292	2		440	632	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693003	89693003	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs786204900	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	96	209	0	ENST00000371953.3:c.491del	p.Lys164ArgfsTer3	p.K164Rfs*3	ENST00000371953	NM_000314.4	163	Aaa/aa	5/9	1	2	FACETS	0.853	0.765	0.945	0.853	0.765	0.945	CLONAL	1	TRUE	1	0.55301251656292	2		209	407	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349641	89349641	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs772267579	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	151	409	3	ENST00000301030.4:c.3309del	p.Asp1104MetfsTer214	p.D1104Mfs*214	ENST00000301030	NM_001256183.1	1103	aaA/aa	9/13	1	2	FACETS	0.929	0.853	1	0.929	0.853	1	CLONAL	1	TRUE	1	0.55301251656292	2		412	588	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564074	139564074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773216266	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	152	413	2	ENST00000308874.7:c.214G>A	p.Ala72Thr	p.A72T	ENST00000308874		72	Gcc/Acc	5/10	1	2	FACETS	0.998	0.917	1	0.998	0.917	1	CLONAL	1	TRUE	1	0.55301251656292	2		415	551	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905324	50905324	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	41	685	2	ENST00000440232.2:c.537del	p.Arg180GlyfsTer3	p.R180Gfs*3	ENST00000440232	NM_002691.3	178	Ggg/gg	5/27	1	2	FACETS	0.19	0.157	0.226	0.19	0.157	0.226	SUBCLONAL	1	TRUE	1	0.55301251656292	2		687	781	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670234	134670234	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764139128	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	157	428	1	ENST00000398015.3:c.145G>A	p.Asp49Asn	p.D49N	ENST00000398015	NM_004441.4	49	Gat/Aat	3/16	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.55301251656292	2		429	550	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815652	139815652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767258846	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	181	461	2	ENST00000247668.2:c.1123G>A	p.Ala375Thr	p.A375T	ENST00000247668	NM_021138.3	375	Gcc/Acc	9/11	1	2	FACETS	0.932	0.863	1	0.932	0.863	1	CLONAL	1	TRUE	1	0.55301251656292	2		463	702	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500414	99500414	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45526336	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	180	519	0	ENST00000268035.6:c.3847G>A	p.Glu1283Lys	p.E1283K	ENST00000268035	NM_000875.3	1283	Gag/Aag	21/21	1	2	FACETS	0.883	0.817	0.952	0.883	0.817	0.952	CLONAL	1	TRUE	1	0.55301251656292	2		519	737	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219725	36219725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568377293	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	44	559	1	ENST00000222270.7:c.4622C>T	p.Ala1541Val	p.A1541V	ENST00000222270	NM_014727.1	1541	gCg/gTg	20/37	1	2	FACETS	0.206	0.172	0.244	0.206	0.172	0.244	SUBCLONAL	1	TRUE	1	0.55301251656292	2		560	771	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357070	70357070	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773713291	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	206	603	3	ENST00000374080.3:c.5585G>A	p.Arg1862His	p.R1862H	ENST00000374080		1862	cGc/cAc	39/45	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.55301251656292	2		606	715	SUCCESS
PHF6	84295	MSKCC	GRCh37	X	133527637	133527637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267606359	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	128	263	0	ENST00000332070.3:c.347G>A	p.Arg116Gln	p.R116Q	ENST00000332070	NM_032458.2	116	cGa/cAa	4/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.55301251656292	2		263	399	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287212	33287213	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1268651006	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	163	514	2	ENST00000374542.5:c.1884dup	p.Cys629LeufsTer29	p.C629Lfs*29	ENST00000374542	NM_001141970.1	628	-/C	6/8	0.528730798375925	2	FACETS	0.713	0.655	0.773	0.356	0.327	0.387	SUBCLONAL	1	TRUE	0	0.55301251656292	2		516	827	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939479	71939479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775305188	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	216	678	5	ENST00000298229.2:c.334G>A	p.Ala112Thr	p.A112T	ENST00000298229	NM_001567.3	112	Gcc/Acc	3/28	1	2	FACETS	0.945	0.88	1	0.945	0.88	1	CLONAL	1	TRUE	1	0.55301251656292	2		683	827	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027453	48027453	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs876660037	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	169	392	1	ENST00000234420.5:c.2331G>A	p.Trp777Ter	p.W777*	ENST00000234420	NM_000179.2	777	tgG/tgA	4/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.55301251656292	2		393	567	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856028	151856028	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144222590	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	208	477	0	ENST00000262189.6:c.11590C>T	p.Arg3864Cys	p.R3864C	ENST00000262189	NM_170606.2	3864	Cgc/Tgc	44/59	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.55301251656292	2		477	690	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40469240	40469240	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs747667389	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	125	332	0	ENST00000264657.5:c.2104G>A	p.Ala702Thr	p.A702T	ENST00000264657	NM_139276.2	702	Gct/Act	22/24	1	2	FACETS	0.817	0.743	0.895	0.817	0.743	0.895	CLONAL	1	TRUE	1	0.55301251656292	2		332	553	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099431	27099431	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768377977	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	219	475	1	ENST00000324856.7:c.3668G>A	p.Arg1223His	p.R1223H	ENST00000324856	NM_006015.4	1223	cGc/cAc	14/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.55301251656292	2		476	712	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31025104	31025104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	166	443	0	ENST00000375687.4:c.4589C>T	p.Pro1530Leu	p.P1530L	ENST00000375687	NM_015338.5	1530	cCc/cTc	13/13	1	2	FACETS	0.957	0.883	1	0.957	0.883	1	CLONAL	1	TRUE	1	0.55301251656292	2		443	627	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435879	149435879	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs281860281	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	153	443	0	ENST00000286301.3:c.2345G>A	p.Arg782His	p.R782H	ENST00000286301	NM_005211.3	782	cGt/cAt	18/22	1	2	FACETS	0.943	0.866	1	0.943	0.866	1	CLONAL	1	TRUE	1	0.55301251656292	2		443	587	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619193	43619193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745650861	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	189	624	2	ENST00000355710.3:c.2876G>A	p.Arg959Gln	p.R959Q	ENST00000355710	NM_020975.4	959	cGg/cAg	17/20	1	2	FACETS	0.948	0.879	1	0.948	0.879	1	CLONAL	1	TRUE	1	0.55301251656292	2		626	721	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211569	46211569	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs896638040	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	109	186	1	ENST00000334344.6:c.535G>A	p.Val179Ile	p.V179I	ENST00000334344	NM_152641.2	179	Gta/Ata	5/21	1	2	FACETS	0.978	0.885	1	0.978	0.885	1	CLONAL	1	TRUE	1	0.55301251656292	2		187	403	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740357	46740359	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	185	502	0	ENST00000371975.4:c.1841_1843del	p.Lys614del	p.K614del	ENST00000371975	NM_003579.3	613	AAG/-	16/18	1	2	FACETS	0.91	0.843	0.98	0.91	0.843	0.98	CLONAL	1	TRUE	1	0.55301251656292	2		502	735	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512134	120512134	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	47	555	0	ENST00000256646.2:c.1108G>T	p.Gly370Cys	p.G370C	ENST00000256646	NM_024408.3	370	Ggt/Tgt	6/34	1	2	FACETS	0.2	0.168	0.235	0.2	0.168	0.235	SUBCLONAL	1	TRUE	1	0.55301251656292	2		555	851	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246258	46246258	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	32	429	0	ENST00000334344.6:c.4352C>A	p.Pro1451His	p.P1451H	ENST00000334344	NM_152641.2	1451	cCt/cAt	15/21	1	2	FACETS	0.185	0.15	0.226	0.185	0.15	0.226	SUBCLONAL	1	TRUE	1	0.55301251656292	2		429	624	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112353	115112353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	131	482	0	ENST00000257566.3:c.1387G>A	p.Ala463Thr	p.A463T	ENST00000257566	NM_016569.3	463	Gcg/Acg	7/8	1	2	FACETS	0.911	0.831	0.994	0.911	0.831	0.994	CLONAL	1	TRUE	1	0.55301251656292	2		482	520	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90634814	90634814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	200	484	1	ENST00000330062.3:c.178C>T	p.Arg60Cys	p.R60C	ENST00000330062	NM_002168.2	60	Cgt/Tgt	2/11	1	2	FACETS	0.955	0.888	1	0.955	0.888	1	CLONAL	1	TRUE	1	0.55301251656292	2		485	757	SUCCESS
BLM	641	MSKCC	GRCh37	15	91337406	91337406	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	62	110	2	ENST00000355112.3:c.3029A>G	p.Asp1010Gly	p.D1010G	ENST00000355112	NM_000057.2	1010	gAt/gGt	16/22	1	2	FACETS	0.776	0.676	0.882	0.776	0.676	0.882	SUBCLONAL	1	TRUE	1	0.55301251656292	2		112	289	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858267	59858267	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	129	210	2	ENST00000259008.2:c.1728del	p.Asn576LysfsTer14	p.N576Kfs*14	ENST00000259008	NM_032043.2	576	aaT/aa	12/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.55301251656292	2		212	437	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218424	36218424	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	131	485	0	ENST00000222270.7:c.4203G>A	p.Trp1401Ter	p.W1401*	ENST00000222270	NM_014727.1	1401	tgG/tgA	16/37	1	2	FACETS	0.806	0.734	0.881	0.806	0.734	0.881	CLONAL	1	TRUE	1	0.55301251656292	2		485	588	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423229	47423229	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	41	496	0	ENST00000404338.3:c.1297C>T	p.Arg433Ter	p.R433*	ENST00000404338	NM_004491.4	433	Cga/Tga	1/6	1	2	FACETS	0.208	0.172	0.248	0.208	0.172	0.248	SUBCLONAL	1	TRUE	1	0.55301251656292	2		496	713	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731529	47731529	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	110	365	0	ENST00000449228.1:c.263C>A	p.Ala88Asp	p.A88D	ENST00000449228	NM_001127240.2	88	gCt/gAt	2/4	1	2	FACETS	0.97	0.879	1	0.97	0.879	1	CLONAL	1	TRUE	1	0.55301251656292	2		365	410	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139908	50139908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373485975	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	162	432	1	ENST00000246792.3:c.421G>A	p.Gly141Arg	p.G141R	ENST00000246792	NM_006270.3	141	Ggg/Agg	4/6	1	2	FACETS	0.973	0.897	1	0.973	0.897	1	CLONAL	1	TRUE	1	0.55301251656292	2		433	602	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705527	47705528	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1573574188	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	137	290	0	ENST00000233146.2:c.2332dup	p.Cys778LeufsTer9	p.C778Lfs*9	ENST00000233146	NM_000251.2	776	gct/gcTt	14/16	1	2	FACETS	0.928	0.848	1	0.928	0.848	1	CLONAL	1	TRUE	1	0.55301251656292	2		290	534	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630567	67630567	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	120	227	0	ENST00000272342.5:c.758del	p.Lys253SerfsTer45	p.K253Sfs*45	ENST00000272342	NM_019002.3	251	acA/ac	5/6	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.55301251656292	2		227	389	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158595074	158595074	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1559028577	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	37	358	0	ENST00000263640.3:c.1273G>A	p.Glu425Lys	p.E425K	ENST00000263640	NM_001105.4	425	Gag/Aag	10/11	1	2	FACETS	0.242	0.199	0.291	0.242	0.199	0.291	SUBCLONAL	1	TRUE	1	0.55301251656292	2		358	552	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149537	202149538	+	splice_acceptor_variant	Splice_Site	INS	-	-	G	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	154	446	0	ENST00000358485.4:c.982dup		p.X328_splice	ENST00000358485	NM_001080125.1	328			1	2	FACETS	0.877	0.806	0.951	0.877	0.806	0.951	CLONAL	1	TRUE	1	0.55301251656292	2		446	635	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934270	49934270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	223	609	3	ENST00000296474.3:c.2237G>A	p.Ser746Asn	p.S746N	ENST00000296474	NM_002447.2	746	aGt/aAt	8/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.55301251656292	2		612	733	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63982041	63982041	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs371435328	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	50	552	0	ENST00000398590.3:c.2543A>G	p.Asn848Ser	p.N848S	ENST00000398590	NM_001177387.1	848	aAc/aGc	12/14	1	2	FACETS	0.222	0.188	0.26	0.222	0.188	0.26	SUBCLONAL	1	TRUE	1	0.55301251656292	2		552	814	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391220	89391220	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	27	332	0	ENST00000336596.2:c.1286G>A	p.Ser429Asn	p.S429N	ENST00000336596	NM_005233.5	429	aGc/aAc	5/17	1	2	FACETS	0.189	0.15	0.234	0.189	0.15	0.234	SUBCLONAL	1	TRUE	1	0.55301251656292	2		332	517	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448516	89448516	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	134	378	2	ENST00000336596.2:c.1480G>A	p.Val494Ile	p.V494I	ENST00000336596	NM_005233.5	494	Gtt/Att	7/17	1	2	FACETS	0.886	0.809	0.966	0.886	0.809	0.966	CLONAL	1	TRUE	1	0.55301251656292	2		380	547	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629355	187629355	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	178	528	2	ENST00000441802.2:c.1627T>C	p.Trp543Arg	p.W543R	ENST00000441802	NM_005245.3	543	Tgg/Cgg	2/27	1	2	FACETS	0.94	0.869	1	0.94	0.869	1	CLONAL	1	TRUE	1	0.55301251656292	2		530	685	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861061	35861061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398237911	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	139	391	0	ENST00000303115.3:c.190G>A	p.Val64Ile	p.V64I	ENST00000303115	NM_002185.3	64	Gtc/Atc	2/8	1	2	FACETS	0.934	0.855	1	0.934	0.855	1	CLONAL	1	TRUE	1	0.55301251656292	2		391	538	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178092	56178092	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	54	426	0	ENST00000399503.3:c.3065A>G	p.Gln1022Arg	p.Q1022R	ENST00000399503	NM_005921.1	1022	cAg/cGg	14/20	1	2	FACETS	0.314	0.268	0.365	0.314	0.268	0.365	SUBCLONAL	1	TRUE	1	0.55301251656292	2		426	621	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589521	67589596	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTTTAATCTTTCTAGGATCAAGTTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAAC	ATTTTAATCTTTCTAGGATCAAGTTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAAC	-	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	33	72	0	ENST00000274335.5:c.1300-15_1360del		p.X434_splice	ENST00000274335		434		10/15	1	2	FACETS	0.878	0.727	1	0.878	0.727	1	CLONAL	1	TRUE	1	0.55301251656292	2		72	136	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131893092	131893092	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	184	398	0	ENST00000265335.6:c.76A>G	p.Thr26Ala	p.T26A	ENST00000265335		26	Act/Gct	1/25	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.55301251656292	2		398	637	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31239472	31239472	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	67	719	0	ENST00000376228.5:c.247T>C	p.Tyr83His	p.Y83H	ENST00000376228	NM_002117.5	83	Tat/Cat	2/8	0.528730798375925	2	FACETS	0.252	0.218	0.289	0.126	0.109	0.145	SUBCLONAL	1	TRUE	0	0.55301251656292	2		719	961	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983848	2983848	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	133	378	1	ENST00000396946.4:c.682G>A	p.Glu228Lys	p.E228K	ENST00000396946	NM_032415.4	228	Gag/Aag	5/25	1	2	FACETS	0.864	0.788	0.943	0.864	0.788	0.943	CLONAL	1	TRUE	1	0.55301251656292	2		379	557	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945490	151945490	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	89	266	2	ENST00000262189.6:c.2029G>A	p.Val677Ile	p.V677I	ENST00000262189	NM_170606.2	677	Gta/Ata	14/59	1	2	FACETS	0.679	0.604	0.758	0.679	0.604	0.758	SUBCLONAL	1	TRUE	1	0.55301251656292	2		268	474	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194816	29194816	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	204	517	1	ENST00000240100.2:c.912G>T	p.Glu304Asp	p.E304D	ENST00000240100	NM_001394.6	304	gaG/gaT	4/4	1	2	FACETS	0.994	0.925	1	0.994	0.925	1	CLONAL	1	TRUE	1	0.55301251656292	2		518	742	SUCCESS
MTAP	4507	MSKCC	GRCh37	9	21854745	21854745	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	143	459	0	ENST00000380172.4:c.571del	p.Ala191ArgfsTer6	p.A191Rfs*6	ENST00000380172	NM_002451.3	189	tGg/tg	6/8	1	2	FACETS	0.799	0.731	0.871	0.799	0.731	0.871	SUBCLONAL	1	TRUE	1	0.55301251656292	2		459	647	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849200	76849200	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	113	249	0	ENST00000373344.5:c.6076A>T	p.Ile2026Phe	p.I2026F	ENST00000373344	NM_000489.3	2026	Att/Ttt	26/35	1	2	FACETS	0.931	0.843	1	0.931	0.843	1	CLONAL	1	TRUE	1	0.55301251656292	2		249	439	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0060640-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	1065	471	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.658083986088472	10	FACETS	0.964	0.951	0.977			1	CLONAL	10	TRUE	NA	0.658083986088472	10		471	1219	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524714	137524716	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs587776858	NA	P-0060640-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	94	442	0	ENST00000367739.4:c.653_655del	p.Glu218del	p.E218del	ENST00000367739	NM_000416.2	218	gAAGga/gga	5/7	0.352215104532013	6	FACETS	1	0.952	1	0.374	0.333	0.417	INDETERMINATE	1	TRUE	3	0.658083986088472	6		442	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579271	7579310	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CATTGAAGTCTCATGGAAGCCAGCCCCTCAGGGCAACTGA	CATTGAAGTCTCATGGAAGCCAGCCCCTCAGGGCAACTGA	-	novel	NA	P-0060640-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	738	371	0	ENST00000269305.4:c.375+2_375+41del		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.658083986088472	7	FACETS	0.986	0.968	1			1	CLONAL	7	TRUE	NA	0.658083986088472	7		371	860	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796833	57796833	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060640-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	317	552	0	ENST00000309042.7:c.1809G>C	p.Lys603Asn	p.K603N	ENST00000309042	NM_005612.4	603	aaG/aaC	4/4	0.658083986088472	3	FACETS	0.862	0.818	0.905	0.862	0.818	0.905	CLONAL	2	TRUE	1	0.658083986088472	3		552	743	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041167	47041167	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060640-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	137	567	0	ENST00000377604.3:c.1595C>G	p.Pro532Arg	p.P532R	ENST00000377604	NM_001204468.1	532	cCc/cGc	15/24	0.352215104532013	6	FACETS	0.858	0.779	0.942	0.286	0.259	0.314	INDETERMINATE	1	TRUE	3	0.658083986088472	6		567	1124	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285890	39285890	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060640-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	50	276	0	ENST00000402219.2:c.269C>T	p.Ala90Val	p.A90V	ENST00000402219	NM_005633.3	90	gCc/gTc	3/23	0.429182708903397	3	FACETS	1	0.906	1	0.534	0.46	0.613	CLONAL	1	TRUE	1	0.658083986088472	3		276	189	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421238	12421238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060640-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	154	425	0	ENST00000287820.6:c.118C>T	p.Pro40Ser	p.P40S	ENST00000287820	NM_015869.4	40	Ccc/Tcc	2/7	0.658083986088472	3	FACETS	1	0.932	1	0.508	0.467	0.551	CLONAL	1	TRUE	1	0.658083986088472	3		425	612	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900032	151900032	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060640-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	61	372	0	ENST00000262189.6:c.4079C>G	p.Pro1360Arg	p.P1360R	ENST00000262189	NM_170606.2	1360	cCt/cGt	26/59	0.658083986088472	3	FACETS	0.821	0.714	0.936	0.411	0.357	0.468	CLONAL	1	TRUE	1	0.658083986088472	3		372	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578281	7578281	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660254	NA	P-0060766-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	703	1084	2	ENST00000269305.4:c.568C>A	p.Pro190Thr	p.P190T	ENST00000269305	NM_001126112.2	190	Cct/Act	6/11	0.862490481560547	3	FACETS	0.973	0.958	0.987	0.973	0.958	0.987	CLONAL	3	TRUE	0	0.883869933200927	3		1086	786	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289167	33289167	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060766-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	695	690	0	ENST00000374542.5:c.385G>T	p.Glu129Ter	p.E129*	ENST00000374542	NM_001141970.1	129	Gag/Tag	3/8	0.862490481560547	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.883869933200927	3		690	752	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73649938	73649938	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750883928	NA	P-0060766-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	275	792	0	ENST00000377687.4:c.1288G>A	p.Ala430Thr	p.A430T	ENST00000377687	NM_001730.3	430	Gcc/Acc	4/4	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.883869933200927	2		792	594	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0060883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	262	515	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.463460056447899	4	FACETS	0.987	0.934	1	0.987	0.934	1	CLONAL	3	TRUE	1	0.461085482999548	4		515	561	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0060883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	105	504	3	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.380300675770602	3	FACETS	1	0.976	1	0.427	0.384	0.471	CLONAL	1	TRUE	0	0.461085482999548	3		507	438	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350062	81350062	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs759145490	NA	P-0060883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	27	288	0	ENST00000222390.5:c.1270C>T	p.Arg424Cys	p.R424C	ENST00000222390	NM_000601.4	424	Cgt/Tgt	10/18	1	2	FACETS	0.776	0.625	0.944	0.776	0.625	0.944	CLONAL	1	TRUE	1	0.461085482999548	2		288	151	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0060883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	142	430	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.463460056447899	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	2	0.461085482999548	4		430	413	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0060883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	214	470	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	0.463460056447899	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.461085482999548	2		470	400	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201099	108201099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759728261	NA	P-0060883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	155	397	0	ENST00000278616.4:c.7466C>T	p.Ser2489Phe	p.S2489F	ENST00000278616	NM_000051.3	2489	tCc/tTc	50/63	0.461085482999548	6	FACETS	1	0.976	1	0.575	0.529	0.622	CLONAL	2	TRUE	2	0.461085482999548	6		397	562	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609994	81609994	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750198847	NA	P-0060883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	65	538	1	ENST00000298171.2:c.1592G>A	p.Arg531Gln	p.R531Q	ENST00000298171	NM_000369.2	531	cGg/cAg	10/10	0.329146051939424	0	FACETS	0.47	0.411	0.534			1	SUBCLONAL	1	TRUE	0	0.461085482999548	0		539	323	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0060883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	124	451	0				ENST00000310581	NM_198253.2	-/1132			0.12856393194797	3	FACETS	1	0.967	1	0.735	0.676	0.796	INDETERMINATE	2	TRUE	0	0.461085482999548	3		451	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578247	7578247	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0060883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	195	592	0	ENST00000269305.4:c.602T>A	p.Leu201Ter	p.L201*	ENST00000269305	NM_001126112.2	201	tTg/tAg	6/11	0.463460056447899	3	FACETS	1	0.986	1	0.792	0.742	0.843	CLONAL	2	TRUE	0	0.461085482999548	3		592	438	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248599	212248599	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	23	560	0	ENST00000342788.4:c.3668A>C	p.Lys1223Thr	p.K1223T	ENST00000342788	NM_005235.2	1223	aAg/aCg	28/28	0.444488629611379	1	FACETS	0.236	0.184	0.297	0.236	0.184	0.297	SUBCLONAL	1	TRUE	0	0.461085482999548	1		560	325	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553441	106553441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746535819	NA	P-0060883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	183	499	0	ENST00000369096.4:c.1406C>T	p.Ser469Leu	p.S469L	ENST00000369096	NM_001198.3	469	tCg/tTg	5/7	0.103363648779809	5	FACETS	1	0.966	1			1	INDETERMINATE	3	TRUE	NA	0.461085482999548	5		499	425	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790129	40790129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	124	482	1	ENST00000373198.4:c.2602C>T	p.Pro868Ser	p.P868S	ENST00000373198	NM_133170.3	868	Ccc/Tcc	18/32	0.463460056447899	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.461085482999548	1		483	402	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213884	2213884	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	104	518	0	ENST00000398665.3:c.1696C>T	p.Gln566Ter	p.Q566*	ENST00000398665	NM_032482.2	566	Caa/Taa	18/28	0.12856393194797	3	FACETS	1	0.98	1	0.459	0.414	0.506	INDETERMINATE	1	TRUE	0	0.461085482999548	3		518	403	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99204042	99204042	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529481819	NA	P-0060883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	109	331	0	ENST00000074304.5:c.2905G>A	p.Glu969Lys	p.E969K	ENST00000074304	NM_001134224.1	969	Gaa/Aaa	26/26	0.463460056447899	4	FACETS	0.883	0.8	0.97	0.883	0.8	0.97	CLONAL	2	TRUE	2	0.461085482999548	4		331	391	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864126	57864126	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144673003	NA	P-0060883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	235	579	0	ENST00000228682.2:c.1603C>T	p.Pro535Ser	p.P535S	ENST00000228682	NM_005269.2	535	Ccc/Tcc	12/12	0.463460056447899	3	FACETS	1	0.987	1	0.773	0.728	0.818	CLONAL	2	TRUE	0	0.461085482999548	3		579	541	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645688	12645688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121434594	NA	P-0060883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	162	447	0	ENST00000251849.4:c.781C>T	p.Pro261Ser	p.P261S	ENST00000251849	NM_002880.3	261	Cct/Tct	7/17	0.463460056447899	4	FACETS	0.819	0.754	0.886	0.819	0.754	0.886	CLONAL	2	TRUE	2	0.461085482999548	4		447	627	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251206	115251206	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	72	433	0	ENST00000369535.4:c.520A>G	p.Ser174Gly	p.S174G	ENST00000369535	NM_002524.4	174	Agt/Ggt	5/7	0.463460056447899	4	FACETS	1	0.94	1	0.373	0.327	0.422	CLONAL	1	TRUE	1	0.461085482999548	4		433	408	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38787097	38787097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	169	464	0	ENST00000348513.6:c.896G>A	p.Arg299Lys	p.R299K	ENST00000348513	NM_003079.4	299	aGg/aAg	10/11	0.380109346356667	3	FACETS	1	0.983	1	0.779	0.726	0.833	CLONAL	2	TRUE	0	0.461085482999548	3		464	386	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244205	5244206	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0060883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	59	483	2	ENST00000357368.4:c.1276_1277delinsTT	p.Pro426Leu	p.P426L	ENST00000357368	NM_002850.3	426	CCg/TTg	11/38	0.221815683990259	0	FACETS	0.518	0.45	0.591			1	INDETERMINATE	1	TRUE	0	0.461085482999548	0		485	266	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422555	225422555	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	78	302	0	ENST00000264414.4:c.85T>G	p.Tyr29Asp	p.Y29D	ENST00000264414	NM_003590.4	29	Tat/Gat	2/16	0.463460056447899	4	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	TRUE	2	0.461085482999548	4		302	237	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008919	152008919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	151	369	0	ENST00000262189.6:c.703G>A	p.Asp235Asn	p.D235N	ENST00000262189	NM_170606.2	235	Gat/Aat	5/59	0.463460056447899	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.461085482999548	3		369	363	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852419	63852419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	108	458	0	ENST00000279873.7:c.3197C>T	p.Ser1066Leu	p.S1066L	ENST00000279873	NM_032199.2	1066	tCa/tTa	10/10	0.117295740148875	3	FACETS	1	0.98	1	0.672	0.607	0.74	INDETERMINATE	1	TRUE	1	0.461085482999548	3		458	429	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10777310	10777310	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	66	383	0	ENST00000361367.2:c.470A>G	p.Asn157Ser	p.N157S	ENST00000361367	NM_014633.3	157	aAt/aGt	4/25	0.461085482999548	5	FACETS	1	0.872	1	0.334	0.29	0.381	CLONAL	1	TRUE	2	0.461085482999548	5		383	483	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68973013	68973013	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	21	306	0	ENST00000288368.4:c.1338T>A	p.His446Gln	p.H446Q	ENST00000288368	NM_024870.2	446	caT/caA	11/40	0.463460056447899	1	FACETS	0.515	0.401	0.645	0.515	0.401	0.645	SUBCLONAL	1	TRUE	0	0.461085482999548	1		306	136	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033234	69033234	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	17	420	0	ENST00000288368.4:c.3674T>G	p.Leu1225Arg	p.L1225R	ENST00000288368	NM_024870.2	1225	cTt/cGt	30/40	0.463460056447899	1	FACETS	0.259	0.193	0.337	0.259	0.193	0.337	SUBCLONAL	1	TRUE	0	0.461085482999548	1		420	219	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226595568	226595568	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	54	579	0	ENST00000366794.5:c.63C>A	p.Cys21Ter	p.C21*	ENST00000366794	NM_001618.3	21	tgC/tgA	1/23	1	2	FACETS	0.491	0.419	0.57	0.491	0.419	0.57	SUBCLONAL	1	TRUE	1	0.385731193495936	2		579	570	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663752	241663752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	26	290	0	ENST00000366560.3:c.1375C>T	p.Leu459Phe	p.L459F	ENST00000366560	NM_000143.3	459	Ctc/Ttc	9/10	1	2	FACETS	0.402	0.319	0.498	0.402	0.319	0.498	SUBCLONAL	1	TRUE	1	0.385731193495936	2		290	335	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992604	72992604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	56	772	0	ENST00000268489.5:c.1441G>A	p.Glu481Lys	p.E481K	ENST00000268489	NM_006885.3	481	Gag/Aag	2/10	0.385731193495936	1	FACETS	0.357	0.305	0.413	0.357	0.305	0.413	SUBCLONAL	1	TRUE	0	0.385731193495936	1		772	657	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0061282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	265	708	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.236009181753912	2	FACETS	0.949	0.894	1	0.949	0.894	1	CLONAL	2	TRUE	0	0.385731193495936	2		708	724	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117578	4117578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1295043645	NA	P-0061282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	53	457	0	ENST00000262948.5:c.142G>A	p.Glu48Lys	p.E48K	ENST00000262948	NM_030662.3	48	Gag/Aag	2/11	0.340314108034991	2	FACETS	0.544	0.464	0.632	0.272	0.232	0.316	SUBCLONAL	1	TRUE	0	0.385731193495936	2		457	505	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442569	52442569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1298276806	NA	P-0061282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	84	617	1	ENST00000460680.1:c.176G>A	p.Arg59Gln	p.R59Q	ENST00000460680	NM_004656.3	59	cGg/cAg	4/17	1	2	FACETS	0.579	0.511	0.652	0.579	0.511	0.652	SUBCLONAL	1	TRUE	1	0.385731193495936	2		618	752	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590400	67590417	+	inframe_deletion	In_Frame_Del	DEL	AATGAAACCATAAAAATA	AATGAAACCATAAAAATA	-	novel	NA	P-0061282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	149	392	0	ENST00000274335.5:c.1462_1479del	p.Asn488_Ile493del	p.N488_I493del	ENST00000274335		488	AATGAAACCATAAAAATA/-	11/15	0.340314108034991	2	FACETS	0.812	0.747	0.878	0.812	0.747	0.878	CLONAL	2	TRUE	0	0.385731193495936	2		392	476	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714448	117714448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775340905	NA	P-0061282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	44	453	0	ENST00000368508.3:c.1201G>A	p.Glu401Lys	p.E401K	ENST00000368508	NM_002944.2	401	Gag/Aag	11/43	0.236009181753912	2	FACETS	0.454	0.38	0.535	0.227	0.19	0.268	SUBCLONAL	1	TRUE	0	0.385731193495936	2		453	503	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274894	38274894	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	79	545	0	ENST00000425967.3:c.1686A>C	p.Glu562Asp	p.E562D	ENST00000425967	NM_001174067.1	562	gaA/gaC	13/19	0.202018405279668	6	FACETS	0.804	0.705	0.91			1	INDETERMINATE	1	TRUE	NA	0.385731193495936	6		545	903	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578220	7578220	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061303-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	404	782	0	ENST00000269305.4:c.629del	p.Asn210ThrfsTer37	p.N210Tfs*37	ENST00000269305	NM_001126112.2	210	aAc/ac	6/11	0.568202518409287	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.568202518409287	2		782	668	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245118	46245118	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0061303-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	72	688	0	ENST00000334344.6:c.3212C>G	p.Ser1071Ter	p.S1071*	ENST00000334344	NM_152641.2	1071	tCa/tGa	15/21	0.543541086674535	4	FACETS	0.423	0.369	0.482	0.212	0.184	0.241	SUBCLONAL	1	TRUE	2	0.568202518409287	4		688	939	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40998378	40998378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061303-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	212	415	0	ENST00000267868.3:c.229G>A	p.Glu77Lys	p.E77K	ENST00000267868	NM_002875.4	77	Gag/Aag	4/10	0.568202518409287	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.568202518409287	3		415	458	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266221	41266221	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061303-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	460	592	0	ENST00000349496.5:c.218C>G	p.Ser73Cys	p.S73C	ENST00000349496	NM_001904.3	73	tCc/tGc	3/15	0.568202518409287	5	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	TRUE	2	0.568202518409287	5		592	983	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540805	187540805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061303-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	332	650	0	ENST00000441802.2:c.6935C>T	p.Ser2312Leu	p.S2312L	ENST00000441802	NM_005245.3	2312	tCa/tTa	10/27	0.276934450989807	5	FACETS	0.872	0.829	0.917	0.872	0.829	0.917	INDETERMINATE	3	TRUE	2	0.568202518409287	5		650	827	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0061430-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	128	384	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	0.93	0.847	1	0.93	0.847	1	CLONAL	1	TRUE	1	0.533426831678767	2		384	516	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101586	27101586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1420328983	NA	P-0061430-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	127	407	0	ENST00000324856.7:c.4868C>T	p.Ser1623Leu	p.S1623L	ENST00000324856	NM_006015.4	1623	tCg/tTg	18/20	1	2	FACETS	0.954	0.869	1	0.954	0.869	1	CLONAL	1	TRUE	1	0.533426831678767	2		407	499	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310551	65310551	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061430-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	101	404	0	ENST00000342505.4:c.2137G>T	p.Gly713Ter	p.G713*	ENST00000342505	NM_002227.2	713	Gga/Tga	16/25	1	2	FACETS	0.724	0.649	0.803	0.724	0.649	0.803	SUBCLONAL	1	TRUE	1	0.533426831678767	2		404	523	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727894	78727894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778029024	NA	P-0061430-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	61	321	0	ENST00000306801.3:c.739G>A	p.Glu247Lys	p.E247K	ENST00000306801	NM_020761.2	247	Gag/Aag	6/34	1	2	FACETS	0.484	0.418	0.555	0.484	0.418	0.555	SUBCLONAL	1	TRUE	1	0.533426831678767	2		321	473	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639155	176639155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061430-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	87	290	0	ENST00000439151.2:c.3755G>A	p.Gly1252Glu	p.G1252E	ENST00000439151	NM_022455.4	1252	gGa/gAa	5/23	1	2	FACETS	0.775	0.69	0.865	0.775	0.69	0.865	SUBCLONAL	1	TRUE	1	0.533426831678767	2		290	421	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310529	65310529	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061430-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	111	398	0	ENST00000342505.4:c.2159T>A	p.Leu720His	p.L720H	ENST00000342505	NM_002227.2	720	cTc/cAc	16/25	1	2	FACETS	0.766	0.691	0.845	0.766	0.691	0.845	SUBCLONAL	1	TRUE	1	0.533426831678767	2		398	543	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843721	156843721	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061430-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	61	509	0	ENST00000524377.1:c.1147T>A	p.Phe383Ile	p.F383I	ENST00000524377	NM_002529.3	383	Ttc/Atc	8/17	0.505066941775877	3	FACETS	0.327	0.281	0.378	0.109	0.093	0.126	SUBCLONAL	1	TRUE	0	0.533426831678767	3		509	885	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115693	108115693	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061430-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	26	239	0	ENST00000278616.4:c.841G>A	p.Glu281Lys	p.E281K	ENST00000278616	NM_000051.3	281	Gaa/Aaa	7/63	0.515503172625571	1	FACETS	0.319	0.254	0.393	0.319	0.254	0.393	SUBCLONAL	1	TRUE	0	0.533426831678767	1		239	224	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934507	9934507	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061430-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	133	277	0	ENST00000330684.3:c.1648C>G	p.Leu550Val	p.L550V	ENST00000330684	NM_001134407.1	550	Cta/Gta	7/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.533426831678767	2		277	382	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819651	81819651	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061430-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	142	350	0	ENST00000359376.3:c.57G>C	p.Lys19Asn	p.K19N	ENST00000359376	NM_002661.3	19	aaG/aaC	2/33	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.533426831678767	2		350	480	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752360	55752360	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061430-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	102	352	0	ENST00000284073.2:c.818T>C	p.Phe273Ser	p.F273S	ENST00000284073	NM_138962.2	273	tTc/tCc	12/14	1	2	FACETS	0.839	0.754	0.927	0.839	0.754	0.927	CLONAL	1	TRUE	1	0.533426831678767	2		352	456	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105651	11105651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061430-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	45	314	0	ENST00000358026.2:c.1567G>A	p.Glu523Lys	p.E523K	ENST00000358026	NM_001128849.1	523	Gag/Aag	9/36	0.43218127141868	3	FACETS	0.398	0.334	0.469	0.199	0.167	0.235	SUBCLONAL	1	TRUE	1	0.533426831678767	3		314	537	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39294764	39294771	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CATACCTC	CATACCTC	ATT	novel	NA	P-0061430-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	19	222	0	ENST00000402219.2:c.211_213+5delinsAAT		p.X71_splice	ENST00000402219	NM_005633.3	71		2/23	1	2	FACETS	0.233	0.176	0.299	0.233	0.176	0.299	SUBCLONAL	1	TRUE	1	0.533426831678767	2		222	306	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949977	44949978	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061430-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	74	221	0	ENST00000377967.4:c.3747dup	p.Lys1250Ter	p.K1250*	ENST00000377967	NM_021140.2	1249	tat/taTt	26/29	1	2	FACETS	0.802	0.707	0.902	0.802	0.707	0.902	CLONAL	1	TRUE	1	0.533426831678767	2		221	346	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966675	44966707	+	inframe_deletion	In_Frame_Del	DEL	TGAAGCAATGTCAGACATTGAGGGAAGCTCTCA	TGAAGCAATGTCAGACATTGAGGGAAGCTCTCA	-	novel	NA	P-0061430-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	96	236	0	ENST00000377967.4:c.3900_3932del	p.Lys1301_Ile1311del	p.K1301_I1311del	ENST00000377967	NM_021140.2	1300	cTGAAGCAATGTCAGACATTGAGGGAAGCTCTCAtt/ctt	27/29	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.533426831678767	2		236	313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577144	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	404	613	0	ENST00000269305.4:c.794T>G	p.Leu265Arg	p.L265R	ENST00000269305	NM_001126112.2	265	cTg/cGg	8/11	0.914395513432179	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.914395513432179	2		613	431	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022007	5022007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770579392	NA	P-0061453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	179	539	0	ENST00000381652.3:c.20C>T	p.Thr7Met	p.T7M	ENST00000381652	NM_004972.3	7	aCg/aTg	3/25	0.914395513432179	2	FACETS	0.837	0.779	0.895	0.418	0.389	0.448	CLONAL	1	TRUE	0	0.914395513432179	2		539	468	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444920	49444920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370492566	NA	P-0061453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1215	222	735	0	ENST00000301067.7:c.2546C>T	p.Ser849Leu	p.S849L	ENST00000301067	NM_003482.3	849	tCg/tTg	10/54	0.914395513432179	6	FACETS	0.956	0.887	1			1	CLONAL	1	TRUE	NA	0.914395513432179	6		735	1437	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557642	95557642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	468	593	0	ENST00000393063.1:c.5425G>A	p.Gly1809Arg	p.G1809R	ENST00000393063	NM_030621.3	1809	Ggg/Agg	26/28	0.914395513432179	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.914395513432179	2		593	508	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046702	42046702	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0061453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	464	566	0	ENST00000219905.7:c.7076C>G	p.Ser2359Ter	p.S2359*	ENST00000219905	NM_001164273.1	2359	tCa/tGa	18/24	0.914395513432179	3	FACETS	0.995	0.961	1	0.995	0.961	1	CLONAL	2	TRUE	1	0.914395513432179	3		566	743	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865360	40865360	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	421	567	0	ENST00000428826.2:c.1071C>A	p.Cys357Ter	p.C357*	ENST00000428826		357	tgC/tgA	11/21	0.808596318816405	4	FACETS	0.953	0.912	0.994	0.953	0.912	0.994	CLONAL	2	TRUE	2	0.914395513432179	4		567	925	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300186	15300186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	249	734	2	ENST00000263388.2:c.1090G>A	p.Ala364Thr	p.A364T	ENST00000263388	NM_000435.2	364	Gct/Act	7/33	1	2	FACETS	0.949	0.895	1	0.949	0.895	1	CLONAL	1	TRUE	1	0.914395513432179	2		736	574	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100924	41100924	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	219	693	0	ENST00000373198.4:c.1432G>C	p.Val478Leu	p.V478L	ENST00000373198	NM_133170.3	478	Gtg/Ctg	8/32	0.878315052858716	4	FACETS	0.902	0.839	0.967	0.451	0.419	0.484	CLONAL	1	TRUE	2	0.914395513432179	4		693	1017	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907781	76907781	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061453-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	503	293	0	ENST00000373344.5:c.4380del	p.Glu1461ArgfsTer29	p.E1461Rfs*29	ENST00000373344	NM_000489.3	1460	gaA/ga	15/35	0.914395513432179	2	FACETS	0.967	0.948	0.984			1	CLONAL	2	TRUE	NA	0.914395513432179	2		293	569	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947852	178947852	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	404	369	0	ENST00000263967.3:c.2727C>G	p.Phe909Leu	p.F909L	ENST00000263967	NM_006218.2	909	ttC/ttG	19/21	0.7192463837317	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	3	TRUE	1	0.78070121401847	4		369	614	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21630814	21630814	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	50	397	0	ENST00000421138.2:c.790G>A	p.Asp264Asn	p.D264N	ENST00000421138		264	Gat/Aat	8/16	0.687036915236109	4	FACETS	0.298	0.252	0.349	0.149	0.126	0.175	SUBCLONAL	1	TRUE	2	0.78070121401847	4		397	766	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578481	7578504	+	inframe_deletion	In_Frame_Del	DEL	GTGGAATCAACCCACAGCTGCACA	GTGGAATCAACCCACAGCTGCACA	-	novel	NA	P-0061473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	393	452	0	ENST00000269305.4:c.426_449del	p.Val143_Thr150del	p.V143_T150del	ENST00000269305	NM_001126112.2	142	ccTGTGCAGCTGTGGGTTGATTCCACa/cca	5/11	0.78070121401847	2	FACETS	0.896	0.866	0.925	0.896	0.866	0.925	CLONAL	2	TRUE	0	0.78070121401847	2		452	562	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316197	11316197	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	48	528	0	ENST00000361445.4:c.557A>C	p.Gln186Pro	p.Q186P	ENST00000361445	NM_004958.3	186	cAa/cCa	5/58	0.331416226238839	3	FACETS	0.826	0.701	0.964	0.413	0.35	0.482	CLONAL	1	FALSE	1	0.362041041551112	3		528	379	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671641	67671641	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	64	534	0	ENST00000264010.4:c.2050A>T	p.Ile684Phe	p.I684F	ENST00000264010	NM_006565.3	684	Att/Ttt	12/12	0.32558085731035	2	FACETS	1	0.951	1	0.593	0.518	0.673	CLONAL	1	FALSE	0	0.362041041551112	2		534	298	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971082	55971082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	36	473	0	ENST00000263923.4:c.1715C>T	p.Thr572Ile	p.T572I	ENST00000263923	NM_002253.2	572	aCt/aTt	13/30	0.362041041551112	3	FACETS	0.748	0.617	0.894	0.374	0.308	0.447	SUBCLONAL	1	FALSE	1	0.362041041551112	3		473	314	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923339	78923339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1441841406	NA	P-0061625-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	93	499	0	ENST00000306801.3:c.3362C>T	p.Thr1121Met	p.T1121M	ENST00000306801	NM_020761.2	1121	aCg/aTg	28/34	1	2	FACETS	0.56	0.499	0.624	0.56	0.499	0.624	SUBCLONAL	1	TRUE	1	0.622468329833313	2		499	534	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923135	48923135	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061625-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	30	257	0	ENST00000267163.4:c.583T>C	p.Trp195Arg	p.W195R	ENST00000267163	NM_000321.2	195	Tgg/Cgg	6/27	0.622468329833313	1	FACETS	0.492	0.402	0.59	0.492	0.402	0.59	SUBCLONAL	1	TRUE	0	0.622468329833313	1		257	135	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993466	72993466	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061625-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	28	614	0	ENST00000268489.5:c.579G>T	p.Gln193His	p.Q193H	ENST00000268489	NM_006885.3	193	caG/caT	2/10	0.622468329833313	1	FACETS	0.138	0.11	0.17	0.138	0.11	0.17	SUBCLONAL	1	TRUE	0	0.622468329833313	1		614	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0061756-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	238	737	1	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.272170506114537	2	FACETS	0.968	0.908	1	0.968	0.908	1	CLONAL	2	TRUE	0	0.355898883357935	2		738	691	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0061769-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	243	703	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.398942674038587	2	FACETS	0.889	0.836	0.942	0.889	0.836	0.942	CLONAL	2	TRUE	0	0.430020342885325	2		703	636	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0061769-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	169	393	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.42978443787754	2	FACETS	0.99	0.922	1	0.99	0.922	1	CLONAL	2	TRUE	0	0.430020342885325	2		393	397	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165600	185165600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763026193	NA	P-0061769-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	249	511	0	ENST00000265026.3:c.875C>T	p.Ala292Val	p.A292V	ENST00000265026	NM_004721.4	292	gCg/gTg	5/14	0.430020342885325	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.430020342885325	3		511	638	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175364	+	frameshift_variant	Frame_Shift_Del	DEL	GAATTTTCTTCAGGAGC	GAATTTTCTTCAGGAGC	-	novel	NA	P-0061769-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	228	600	0	ENST00000257430.4:c.4060_4076del	p.Phe1354IlefsTer15	p.F1354Ifs*15	ENST00000257430	NM_000038.5	1353	GAATTTTCTTCAGGAGCg/g	16/16	0.42978443787754	2	FACETS	0.969	0.911	1	0.969	0.911	1	CLONAL	2	TRUE	0	0.430020342885325	2		600	547	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508765	29508765	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061769-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	127	467	0	ENST00000356175.3:c.692T>C	p.Phe231Ser	p.F231S	ENST00000356175	NM_000267.3	231	tTt/tCt	7/57	0.398942674038587	2	FACETS	0.861	0.79	0.934	0.861	0.79	0.934	CLONAL	2	TRUE	0	0.430020342885325	2		467	343	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742731	39742731	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061769-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	139	680	0	ENST00000361337.2:c.1574T>A	p.Val525Glu	p.V525E	ENST00000361337	NM_003286.2	525	gTa/gAa	15/21	0.430020342885325	5	FACETS	1	0.958	1	0.364	0.331	0.399	CLONAL	1	TRUE	2	0.430020342885325	5		680	974	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031970	26031970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061769-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	83	924	0	ENST00000244661.2:c.319G>A	p.Asp107Asn	p.D107N	ENST00000244661	NM_003537.3	107	Gac/Aac	1/1	0.430020342885325	3	FACETS	0.449	0.395	0.508	0.15	0.131	0.17	SUBCLONAL	1	TRUE	0	0.430020342885325	3		924	1044	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860047	151860047	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061769-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	149	642	0	ENST00000262189.6:c.10615C>T	p.Leu3539Phe	p.L3539F	ENST00000262189	NM_170606.2	3539	Ctt/Ttt	43/59	0.430020342885325	3	FACETS	1	0.963	1	0.548	0.501	0.597	CLONAL	1	TRUE	1	0.430020342885325	3		642	768	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041442	47041442	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0061769-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	328	899	0	ENST00000377604.3:c.1785+1G>T		p.X595_splice	ENST00000377604	NM_001204468.1	595			0.413085627627056	4	FACETS	0.973	0.92	1			1	CLONAL	2	TRUE	NA	0.430020342885325	4		899	1121	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579415	7579415	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061811-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	186	647	0	ENST00000269305.4:c.272G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tGg/tAg	4/11	0.467843062718513	1	FACETS	0.929	0.861	0.998	0.929	0.861	0.998	CLONAL	1	TRUE	0	0.467843062718513	1		647	656	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0061811-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	313	595	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.461492049658639	3	FACETS	0.77	0.727	0.814	0.77	0.727	0.814	SUBCLONAL	2	TRUE	1	0.467843062718513	3		595	1072	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741426	17741426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061811-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	140	521	0	ENST00000250003.3:c.97C>T	p.Pro33Ser	p.P33S	ENST00000250003	NM_002478.4	33	Ccg/Tcg	1/3	1	2	FACETS	0.849	0.775	0.927	0.849	0.775	0.927	CLONAL	1	TRUE	1	0.467843062718513	2		521	705	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510786	120510786	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061811-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	162	477	0	ENST00000256646.2:c.1178A>G	p.Asn393Ser	p.N393S	ENST00000256646	NM_024408.3	393	aAc/aGc	7/34	1	2	FACETS	0.951	0.875	1	0.951	0.875	1	CLONAL	1	TRUE	1	0.467843062718513	2		477	728	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223598	36223598	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061811-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	234	746	0	ENST00000222270.7:c.6148A>T	p.Ser2050Cys	p.S2050C	ENST00000222270	NM_014727.1	2050	Agc/Tgc	28/37	1	2	FACETS	0.976	0.911	1	0.976	0.911	1	CLONAL	1	TRUE	1	0.467843062718513	2		746	1025	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054698	5054698	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061811-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	160	462	0	ENST00000381652.3:c.750G>C	p.Leu250Phe	p.L250F	ENST00000381652	NM_004972.3	250	ttG/ttC	7/25	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.467843062718513	2		462	638	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054711	5054711	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061811-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	158	451	0	ENST00000381652.3:c.763C>G	p.Leu255Val	p.L255V	ENST00000381652	NM_004972.3	255	Ctt/Gtt	7/25	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.467843062718513	2		451	612	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0061818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	204	645	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.421534350060365	1	FACETS	0.973	0.905	1	0.973	0.905	1	CLONAL	1	TRUE	0	0.421534350060365	1		645	785	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412375	139412375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1341448592	NA	P-0061818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	113	800	0	ENST00000277541.6:c.1270G>A	p.Glu424Lys	p.E424K	ENST00000277541	NM_017617.3	424	Gag/Aag	8/34	0.253538602718429	2	FACETS	0.569	0.511	0.631	0.285	0.255	0.316	SUBCLONAL	1	TRUE	0	0.421534350060365	2		800	942	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0061818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	99	336	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.898	0.805	0.997	0.898	0.805	0.997	CLONAL	1	TRUE	1	0.421534350060365	2		336	523	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573519	48573519	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	88	605	0	ENST00000342988.3:c.105del	p.Phe35LeufsTer10	p.F35Lfs*10	ENST00000342988	NM_005359.5	35	Ttt/tt	2/12	0.421534350060365	1	FACETS	0.598	0.531	0.669	0.598	0.531	0.669	SUBCLONAL	1	TRUE	0	0.421534350060365	1		605	551	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974797	21974798	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061818-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	361	821	0	ENST00000304494.5:c.29dup	p.Pro11AlafsTer4	p.P11Afs*4	ENST00000304494	NM_000077.4	10	gag/gaAg	1/3	0.365528552885822	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.421534350060365	2		821	844	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061830-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	223	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.577632756831858	5	FACETS	1	0.98	1	0.74	0.693	0.788	CLONAL	2	TRUE	2	0.577632756831858	5		485	649	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0061830-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	171	900	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.577632756831858	2		900	551	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653796	89653798	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs1554893765	NA	P-0061830-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	159	301	0	ENST00000371953.3:c.97_99del	p.Ile33del	p.I33del	ENST00000371953	NM_000314.4	32	ATT/-	2/9	0.577632756831858	2	FACETS	0.86	0.803	0.918	0.86	0.803	0.918	CLONAL	2	TRUE	0	0.577632756831858	2		301	320	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061836-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	41	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.195117807319611	1	FACETS	0.583	0.488	0.688	0.583	0.488	0.688	INDETERMINATE	1	TRUE	0	0.379833982841798	1		485	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578529	7578529	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs780442292	NA	P-0061836-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	128	612	0	ENST00000269305.4:c.401T>G	p.Phe134Cys	p.F134C	ENST00000269305	NM_001126112.2	134	tTt/tGt	5/11	0.379833982841798	1	FACETS	0.971	0.884	1	0.971	0.884	1	CLONAL	1	TRUE	0	0.379833982841798	1		612	562	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573430	48573430	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061836-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	96	497	0	ENST00000342988.3:c.14C>G	p.Ser5Cys	p.S5C	ENST00000342988	NM_005359.5	5	tCt/tGt	2/12	0.379833982841798	1	FACETS	0.973	0.872	1	0.973	0.872	1	CLONAL	1	TRUE	0	0.379833982841798	1		497	421	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265474	46265474	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061836-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	98	489	0	ENST00000371998.3:c.2344G>T	p.Asp782Tyr	p.D782Y	ENST00000371998		782	Gac/Tac	12/23	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.379833982841798	2		489	516	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736471	85736471	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061836-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	59	521	0	ENST00000370580.1:c.176C>G	p.Thr59Arg	p.T59R	ENST00000370580	NM_003921.4	59	aCa/aGa	2/3	0.195117807319611	1	FACETS	0.541	0.466	0.622	0.541	0.466	0.622	INDETERMINATE	1	TRUE	0	0.379833982841798	1		521	465	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165707	118165707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061836-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	39	748	0	ENST00000369448.3:c.217G>A	p.Gly73Ser	p.G73S	ENST00000369448	NM_017709.3	73	Ggc/Agc	2/2	0.195117807319611	1	FACETS	0.26	0.215	0.311	0.26	0.215	0.311	INDETERMINATE	1	TRUE	0	0.379833982841798	1		748	639	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717666	89717703	+	frameshift_variant	Frame_Shift_Del	DEL	CCCACACGACGGGAAGACAAGTTCATGTACTTTGAGTT	CCCACACGACGGGAAGACAAGTTCATGTACTTTGAGTT	-	novel	NA	P-0061836-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	33	514	0	ENST00000371953.3:c.694_731del	p.Thr232SerfsTer8	p.T232Sfs*8	ENST00000371953	NM_000314.4	231	CCCACACGACGGGAAGACAAGTTCATGTACTTTGAGTTc/c	7/9	0.379833982841798	1	FACETS	0.404	0.33	0.488	0.404	0.33	0.488	SUBCLONAL	1	TRUE	0	0.379833982841798	1		514	348	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349943	89349976	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGTTCCCACGGCTCCAGGCCCTTCCCAAAGTC	GCCGTTCCCACGGCTCCAGGCCCTTCCCAAAGTC	-	novel	NA	P-0061836-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	158	781	0	ENST00000301030.4:c.2974_3007del	p.Asp992ThrfsTer315	p.D992Tfs*315	ENST00000301030	NM_001256183.1	992	GACTTTGGGAAGGGCCTGGAGCCGTGGGAACGGCac/ac	9/13	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.379833982841798	2		781	799	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435703	56435703	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061836-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	141	680	0	ENST00000407977.2:c.1434del	p.Val479TrpfsTer23	p.V479Wfs*23	ENST00000407977		478	tcT/tc	9/10	1	2	FACETS	0.991	0.904	1	0.991	0.904	1	CLONAL	1	TRUE	1	0.379833982841798	2		680	749	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424826	47424826	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061836-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	98	693	1	ENST00000404338.3:c.2894A>T	p.Glu965Val	p.E965V	ENST00000404338	NM_004491.4	965	gAa/gTa	1/6	1	2	FACETS	0.758	0.676	0.844	0.758	0.676	0.844	SUBCLONAL	1	TRUE	1	0.379833982841798	2		694	681	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944443	40944443	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061836-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	89	616	0	ENST00000373198.4:c.2059T>G	p.Tyr687Asp	p.Y687D	ENST00000373198	NM_133170.3	687	Tac/Gac	12/32	1	2	FACETS	0.838	0.745	0.938	0.838	0.745	0.938	CLONAL	1	TRUE	1	0.379833982841798	2		616	559	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475482	12475482	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061836-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	147	644	0	ENST00000287820.6:c.1356C>A	p.Asn452Lys	p.N452K	ENST00000287820	NM_015869.4	452	aaC/aaA	7/7	0.195117807319611	1	FACETS	1	0.941	1	1	0.941	1	INDETERMINATE	1	TRUE	0	0.379833982841798	1		644	607	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188073	151188073	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061836-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	82	415	0	ENST00000262187.5:c.80T>C	p.Val27Ala	p.V27A	ENST00000262187	NM_005614.3	27	gTt/gCt	2/8	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.379833982841798	2		415	408	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741922	145741922	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1206707992	NA	P-0061836-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	166	740	0	ENST00000428558.2:c.581G>T	p.Cys194Phe	p.C194F	ENST00000428558	NM_004260.3	194	tGt/tTt	5/22	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.379833982841798	2		740	771	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741694	17741694	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061849-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	396	472	0	ENST00000250003.3:c.365T>G	p.Leu122Arg	p.L122R	ENST00000250003	NM_002478.4	122	cTg/cGg	1/3	0.702485390486232	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.702485390486232	2		472	507	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163648	32163648	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs764118051	NA	P-0061849-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	143	472	0	ENST00000375023.3:c.5578C>A	p.Arg1860Ser	p.R1860S	ENST00000375023	NM_004557.3	1860	Cgc/Agc	30/30	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.702485390486232	2		472	386	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730300	133730301	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0061849-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	150	387	0	ENST00000318560.5:c.369_370dup	p.Lys124ArgfsTer19	p.K124Rfs*19	ENST00000318560	NM_005157.4	122	-/GA	3/11	1	2	FACETS	0.771	0.708	0.836	0.771	0.708	0.836	SUBCLONAL	1	TRUE	1	0.702485390486232	2		387	554	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782329	NA	P-0061954-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	121	537	0	ENST00000269305.4:c.746G>C	p.Arg249Thr	p.R249T	ENST00000269305	NM_001126112.2	249	aGg/aCg	7/11	0.438413823833796	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.438413823833796	1		537	348	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249092	55249092	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061954-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	148	660	0	ENST00000275493.2:c.2390G>C	p.Cys797Ser	p.C797S	ENST00000275493	NM_005228.3	797	tGc/tCc	20/28	0.438413823833796	11	FACETS	0.76	0.692	0.832	0.138	0.125	0.152	SUBCLONAL	2	TRUE	0	0.438413823833796	11		660	1320	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174868	56174868	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061954-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	85	357	0	ENST00000399503.3:c.2028del	p.Gln677ArgfsTer8	p.Q677Rfs*8	ENST00000399503	NM_005921.1	676	cTt/ct	11/20	0.438413823833796	3	FACETS	1	0.976	1	0.459	0.409	0.512	CLONAL	1	TRUE	0	0.438413823833796	3		357	343	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249013	55249014	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACCCTGGCC	novel	NA	P-0061954-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	857	478	1	ENST00000275493.2:c.2315_2316insTGGCCACCC	p.Pro772_His773insGlyHisPro	p.P772_H773insGHP	ENST00000275493	NM_005228.3	771	aac/aACCCTGGCCac	20/28	0.438413823833796	11	FACETS	0.996	0.972	1	0.815	0.795	0.834	CLONAL	9	TRUE	0	0.438413823833796	11		479	1297	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0061969-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	433	534	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.515834249737801	6	FACETS	1	0.991	1	0.841	0.807	0.876	CLONAL	3	TRUE	2	0.695020021510125	6		534	885	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188296	32188296	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561687277	NA	P-0061969-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	286	852	0	ENST00000375023.3:c.1045G>A	p.Gly349Ser	p.G349S	ENST00000375023	NM_004557.3	349	Ggc/Agc	6/30	0.687791550293606	3	FACETS	1	0.984	1	0.561	0.528	0.595	CLONAL	1	TRUE	1	0.695020021510125	3		852	988	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576844	7577001	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTTAGTACCTGAAGGGTGAAATATTCTCCATCCAGTGGTTTCTTCTTTGGCTGGGGAGAGGAGCTGGTGTTGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAAGTGAATCTGAGGCATAACTGCACCCTTGGTCTCCTCCACCGCTTC	ACTTAGTACCTGAAGGGTGAAATATTCTCCATCCAGTGGTTTCTTCTTTGGCTGGGGAGAGGAGCTGGTGTTGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAAGTGAATCTGAGGCATAACTGCACCCTTGGTCTCCTCCACCGCTTC	-	novel	NA	P-0061969-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	186	668	0	ENST00000269305.4:c.919+18_993+9del		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	0.695020021510125	1	FACETS	0.978	0.919	1	0.978	0.919	1	CLONAL	1	TRUE	0	0.695020021510125	1		668	357	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793506	42793506	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061969-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	215	743	0	ENST00000575354.2:c.1308del	p.Ser436ArgfsTer36	p.S436Rfs*36	ENST00000575354	NM_015125.3	436	agT/ag	8/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.695020021510125	2		743	605	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0061991-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1380	1735	595	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		595	3115	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782620	NA	P-0061991-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	502	599	0	ENST00000269305.4:c.427G>A	p.Val143Met	p.V143M	ENST00000269305	NM_001126112.2	143	Gtg/Atg	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		599	892	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271368	18271368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061991-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1291	639	548	0	ENST00000222254.8:c.410G>A	p.Arg137Lys	p.R137K	ENST00000222254	NM_005027.3	137	aGg/aAg	3/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		548	1930	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934574	NA	P-0061997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	225	523	0	ENST00000269305.4:c.844C>G	p.Arg282Gly	p.R282G	ENST00000269305	NM_001126112.2	282	Cgg/Ggg	8/11	0.320080598350215	4	FACETS	0.847	0.792	0.904	1	0.989	1	CLONAL	3	TRUE	2	0.320080598350215	4		523	730	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0061997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	123	597	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.320080598350215	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.320080598350215	1		597	453	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274211	10274211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779149309	NA	P-0061997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	47	453	0	ENST00000330684.3:c.58G>A	p.Gly20Ser	p.G20S	ENST00000330684	NM_001134407.1	20	Ggt/Agt	2/13	1	2	FACETS	0.678	0.573	0.794	0.678	0.573	0.794	SUBCLONAL	1	TRUE	1	0.320080598350215	2		453	433	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625652	1625652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533848977	NA	P-0061997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	78	440	0	ENST00000344749.5:c.422C>T	p.Ser141Leu	p.S141L	ENST00000344749	NM_001136139.2	141	tCg/tTg	7/19	0.320080598350215	3	FACETS	1	0.948	1	0.57	0.502	0.642	CLONAL	1	TRUE	1	0.320080598350215	3		440	496	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0061997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	65	417	0				ENST00000310581	NM_198253.2	-/1132			0.296478571214075	4	FACETS	1	0.924	1	0.364	0.316	0.416	CLONAL	1	TRUE	1	0.320080598350215	4		417	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691003	NA	P-0061997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	96	387	0	ENST00000269305.4:c.96+1G>T		p.X32_splice	ENST00000269305	NM_001126112.2	32			0.320080598350215	4	FACETS	0.839	0.751	0.932	0.839	0.751	0.932	CLONAL	2	TRUE	2	0.320080598350215	4		387	472	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530142	212530143	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	254	436	0	ENST00000342788.4:c.1776dup	p.Cys593MetfsTer17	p.C593Mfs*17	ENST00000342788	NM_005235.2	592	-/A	15/28	NA	2	FACETS	1	0.948	1			1	INDETERMINATE	3	TRUE	NA	0.320080598350215	2		436	528	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957835	1957835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388626156	NA	P-0061997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	102	382	0	ENST00000382891.5:c.2801C>T	p.Ala934Val	p.A934V	ENST00000382891	NM_133335.3	934	gCg/gTg	15/22	0.320080598350215	3	FACETS	1	0.979	1	0.685	0.614	0.759	CLONAL	1	TRUE	1	0.320080598350215	3		382	540	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518034	69518034	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	63	389	0	ENST00000294312.3:c.331G>A	p.Gly111Arg	p.G111R	ENST00000294312	NM_005117.2	111	Ggg/Agg	2/3	0.280952318879557	4	FACETS	0.848	0.733	0.972	0.424	0.366	0.486	CLONAL	1	TRUE	2	0.320080598350215	4		389	613	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118391565	118391565	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	91	325	0	ENST00000534358.1:c.11478A>T	p.Leu3826Phe	p.L3826F	ENST00000534358	NM_005933.3	3826	ttA/ttT	34/36	1	2	FACETS	0.817	0.732	0.906	1	0.983	1	CLONAL	2	TRUE	1	0.320080598350215	2		325	348	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151191	202151192	+	missense_variant	Missense_Mutation	DNP	TA	TA	AT	novel	NA	P-0061997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	203	351	0	ENST00000358485.4:c.1491_1492delinsAT	p.Asp497_Ile498delinsGluPhe	p.D497_I498delinsEF	ENST00000358485	NM_001080125.1	497	gaTAtt/gaATtt	9/9	0.280966713255439	3	FACETS	1	0.983	1			1	CLONAL	3	TRUE	NA	0.320080598350215	3		351	435	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391747	139391747	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	139	500	0	ENST00000277541.6:c.6444C>G	p.Ser2148Arg	p.S2148R	ENST00000277541	NM_017617.3	2148	agC/agG	34/34	0.320080598350215	3	FACETS	1	0.984	1	0.69	0.629	0.754	CLONAL	1	TRUE	1	0.320080598350215	3		500	730	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0062006-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	174	712	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.601131616250736	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.601131616250736	1		712	360	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696461	47696461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062006-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	108	480	0	ENST00000347630.2:c.362G>A	p.Arg121Gln	p.R121Q	ENST00000347630	NM_001007230.1	121	cGg/cAg	6/11	0.601131616250736	1	FACETS	0.824	0.75	0.9	0.824	0.75	0.9	CLONAL	1	TRUE	0	0.601131616250736	1		480	305	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0062007-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	600	593	0	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.775676794435188	4	FACETS	1	0.996	1	1	0.996	1	CLONAL	4	TRUE	0	0.788691414668735	4		593	655	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954640	17954640	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1299325240	NA	P-0062007-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	194	602	1	ENST00000458235.1:c.254G>A	p.Ser85Asn	p.S85N	ENST00000458235	NM_000215.3	85	aGc/aAc	3/24	0.787649635982625	3	FACETS	1	0.985	1	0.607	0.565	0.65	CLONAL	1	TRUE	1	0.788691414668735	3		603	565	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145573	24145573	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062007-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	112	474	0	ENST00000263121.7:c.592C>A	p.Gln198Lys	p.Q198K	ENST00000263121	NM_003073.3	198	Cag/Aag	5/9	0.788691414668735	6	FACETS	0.887	0.798	0.982	0.222	0.199	0.246	CLONAL	1	TRUE	2	0.788691414668735	6		474	825	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288337	33288362	+	frameshift_variant	Frame_Shift_Del	DEL	CAACACAGGATCTGATAGTGCAGGGT	CAACACAGGATCTGATAGTGCAGGGT	-	novel	NA	P-0062007-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	410	622	0	ENST00000374542.5:c.1046_1071del	p.Asp349GlyfsTer17	p.D349Gfs*17	ENST00000374542	NM_001141970.1	349	gACCCTGCACTATCAGATCCTGTGTTG/g	4/8	0.787649635982625	3	FACETS	0.926	0.9	0.951	0.926	0.9	0.951	CLONAL	3	TRUE	0	0.788691414668735	3		622	522	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0062029-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	417	584	0	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	0.799418111309703	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.799418111309703	2		584	478	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348808	118348808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1131691799	NA	P-0062029-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	393	506	0	ENST00000534358.1:c.3461G>A	p.Arg1154Gln	p.R1154Q	ENST00000534358	NM_005933.3	1154	cGg/cAg	5/36	0.799418111309703	4	FACETS	0.948	0.905	0.992	0.632	0.603	0.661	CLONAL	2	TRUE	1	0.799418111309703	4		506	933	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0062032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	23	529	0	ENST00000269305.4:c.96+1G>A		p.X32_splice	ENST00000269305	NM_001126112.2	32			0.253673538743724	3	FACETS	1	0.86	1	0.564	0.444	0.699	CLONAL	1	TRUE	1	0.31	3		529	152	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670634	67670634	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	17	590	0	ENST00000264010.4:c.1879G>T	p.Glu627Ter	p.E627*	ENST00000264010	NM_006565.3	627	Gag/Tag	11/12	1	2	FACETS	0.587	0.439	0.76	0.587	0.439	0.76	SUBCLONAL	1	TRUE	1	0.31	2		590	187	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707667	176707668	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0062032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	31	635	0	ENST00000439151.2:c.5726_5727del	p.Ser1909Ter	p.S1909*	ENST00000439151	NM_022455.4	1908	gaCTct/gact	18/23	1	2	FACETS	0.971	0.791	1	0.971	0.791	1	CLONAL	1	TRUE	1	0.31	2		635	206	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100194	157101216	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CATGATGATGGGCCCCGGGGGCGGCGGGGCCGCGAGCCTCAGCAAGGCGGCCGCCGGCTCGGCGGCGGGGGGCTTCCAGCGCTTCGCCGGCCAGAACCAGCACCCGTCGGGGGCCACCCCGACCCTCAATCAGCTGCTCACCTCGCCCAGCCCCATGATGCGGAGCTACGGCGGCAGCTACCCCGAGTACAGCAGCCCCAGCGCGCCGCCGCCGCCGCCGTCGCAGCCCCAGTCCCAGGCGGCGGCGGCGGGGGCGGCGGCGGGCGGCCAGCAGGCGGCCGCGGGCATGGGCTTGGGCAAGGACATGGGCGCCCAGTACGCCGCTGCCAGCCCGGCCTGGGCGGCCGCGCAACAAAGGAGTCACCCGGCGATGAGCCCCGGCACCCCCGGACCGACCATGGGCAGATCCCAGGTAACCCTCGCGCCAGCCGGGCCTGCTTCCGCCCGGCGGCCTCGCCGCGCCGCGAGCCTGAGTTTCTTTCTTTGCCGCGTACTTTTCCCCGTCTTCCCGCGGGGGCGGCGGGGGCGCGGCGCCCAAAGCCATCTTGACGGGCGGCCGCCTCCCGCCGCGGTCGGGGCGCCCCGGGGGCCGGCGCGCTGTCCAGGCCTGGGAGGGCTTCGCCGGGCCGGGCCGGGCCGGGTGGCTTCTACCCCGCCGGCCCGCACCCGCGTCCCCCCCCTCCCCCAGGCCCGGGAACGCGAAGCGAGATCCCGAGGCGCCACCCGCGCGGTCGCCGTTTGGGGCGGCGGGGACCGTTCGGGTGCTTTTGTAACAAATAGGCTCTCCCGGCCAGGACGGCTGGGGCGAAGAGCCACCCGATCGGTTCTGGGAGCGCCCACAATGTGCTTTAACGGGGGAAAGAATGAGGAACTTTCTCACACCTTTAGCCACAGCACGTTCCCTCTTGGCTTCCGAGGTCCAGGCAGGGAAAATAGGTTAGCTTTGTGACAAGCGAGTGGGTTTTTCCTACTTAGGGAGAGCCATTCAGAGACACTCGGTGCGGGCTTCGAGCTCGAACGTTT	CATGATGATGGGCCCCGGGGGCGGCGGGGCCGCGAGCCTCAGCAAGGCGGCCGCCGGCTCGGCGGCGGGGGGCTTCCAGCGCTTCGCCGGCCAGAACCAGCACCCGTCGGGGGCCACCCCGACCCTCAATCAGCTGCTCACCTCGCCCAGCCCCATGATGCGGAGCTACGGCGGCAGCTACCCCGAGTACAGCAGCCCCAGCGCGCCGCCGCCGCCGCCGTCGCAGCCCCAGTCCCAGGCGGCGGCGGCGGGGGCGGCGGCGGGCGGCCAGCAGGCGGCCGCGGGCATGGGCTTGGGCAAGGACATGGGCGCCCAGTACGCCGCTGCCAGCCCGGCCTGGGCGGCCGCGCAACAAAGGAGTCACCCGGCGATGAGCCCCGGCACCCCCGGACCGACCATGGGCAGATCCCAGGTAACCCTCGCGCCAGCCGGGCCTGCTTCCGCCCGGCGGCCTCGCCGCGCCGCGAGCCTGAGTTTCTTTCTTTGCCGCGTACTTTTCCCCGTCTTCCCGCGGGGGCGGCGGGGGCGCGGCGCCCAAAGCCATCTTGACGGGCGGCCGCCTCCCGCCGCGGTCGGGGCGCCCCGGGGGCCGGCGCGCTGTCCAGGCCTGGGAGGGCTTCGCCGGGCCGGGCCGGGCCGGGTGGCTTCTACCCCGCCGGCCCGCACCCGCGTCCCCCCCCTCCCCCAGGCCCGGGAACGCGAAGCGAGATCCCGAGGCGCCACCCGCGCGGTCGCCGTTTGGGGCGGCGGGGACCGTTCGGGTGCTTTTGTAACAAATAGGCTCTCCCGGCCAGGACGGCTGGGGCGAAGAGCCACCCGATCGGTTCTGGGAGCGCCCACAATGTGCTTTAACGGGGGAAAGAATGAGGAACTTTCTCACACCTTTAGCCACAGCACGTTCCCTCTTGGCTTCCGAGGTCCAGGCAGGGAAAATAGGTTAGCTTTGTGACAAGCGAGTGGGTTTTTCCTACTTAGGGAGAGCCATTCAGAGACACTCGGTGCGGGCTTCGAGCTCGAACGTTT	-	novel	NA	P-0062032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	21	560	0	ENST00000346085.5:c.1131_1542+611del		p.X377_splice	ENST00000346085	NM_020732.3	377		1/20	1		FACETS		0.645	1				CLONAL	1	TRUE	1	0.31	2		560	163	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802635	135802635	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203343	NA	P-0062050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	211	308	0	ENST00000298552.3:c.163C>T	p.Gln55Ter	p.Q55*	ENST00000298552	NM_001162426.1	55	Cag/Tag	4/23	0.487639120984273	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	TRUE	0	0.487639120984273	3		308	347	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs121913468	NA	P-0062050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	133	313	0	ENST00000269571.5:c.2305G>A	p.Asp769Asn	p.D769N	ENST00000269571		769	Gac/Aac	19/27	0.487639120984273	4	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	2	0.487639120984273	4		313	394	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924206	11924206	+	start_lost	Translation_Start_Site	SNP	G	G	T	novel	NA	P-0062050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	103	542	0	ENST00000353533.5:c.3G>T	p.Met1?	p.M1?	ENST00000353533	NM_003010.3	1	atG/atT	1/11	0.487639120984273	4	FACETS	1	0.977	1	0.657	0.591	0.727	CLONAL	1	TRUE	2	0.487639120984273	4		542	478	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523515	41523515	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	83	360	0	ENST00000263253.7:c.931C>T	p.Gln311Ter	p.Q311*	ENST00000263253	NM_001429.3	311	Cag/Tag	4/31	0.334580994658748	4	FACETS	1	0.976	1	0.696	0.618	0.777	CLONAL	1	TRUE	2	0.487639120984273	4		360	364	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282666	1282666	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554041316	NA	P-0062050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	149	442	0	ENST00000310581.5:c.1647G>A	p.Met549Ile	p.M549I	ENST00000310581	NM_198253.2	549	atG/atA	3/16	0.467639544477347	2	FACETS	0.961	0.893	1	0.961	0.893	1	CLONAL	2	TRUE	0	0.487639120984273	2		442	318	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576397	67576397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	98	270	0	ENST00000274335.5:c.676C>T	p.Leu226Phe	p.L226F	ENST00000274335		226	Ctt/Ttt	5/15	0.467639544477347	2	FACETS	0.995	0.91	1	0.995	0.91	1	CLONAL	2	TRUE	0	0.487639120984273	2		270	202	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399401	139399401	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746431035	NA	P-0062052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	76	198	0	ENST00000277541.6:c.4742C>T	p.Pro1581Leu	p.P1581L	ENST00000277541	NM_017617.3	1581	cCg/cTg	26/34	0.252170092915319	3	FACETS	1	0.959	1	0.609	0.535	0.688	CLONAL	1	TRUE	1	0.256028996114774	3		198	550	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030201	180030201	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	93	174	0	ENST00000261937.6:c.4083C>A	p.Asn1361Lys	p.N1361K	ENST00000261937	NM_182925.4	1361	aaC/aaA	30/30	0.196560906057563	2	FACETS	1	0.98	1	0.746	0.666	0.831	CLONAL	1	TRUE	0	0.256028996114774	2		174	487	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62305336	62305336	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	39	181	0	ENST00000360203.5:c.809A>G	p.His270Arg	p.H270R	ENST00000360203	NM_001283009.1	270	cAt/cGt	10/35	0.256028996114774	4	FACETS	0.71	0.588	0.847	0.237	0.196	0.283	SUBCLONAL	1	TRUE	1	0.256028996114774	4		181	539	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439843	51439858	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGGACACCGCCTGT	GGGGGACACCGCCTGT	-	novel	NA	P-0062056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	129	307	0	ENST00000262662.1:c.409_424del	p.Gly137IlefsTer14	p.G137Ifs*14	ENST00000262662		136	aaGGGGGACACCGCCTGT/aa	4/4	0.67956373063846	1	FACETS	0.861	0.795	0.929	0.861	0.795	0.929	CLONAL	1	TRUE	0	0.67956373063846	1		307	291	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572947	41572956	+	frameshift_variant	Frame_Shift_Del	DEL	TGCTTGCCAG	TGCTTGCCAG	-	novel	NA	P-0062056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	159	423	0	ENST00000263253.7:c.5234_5243del	p.Ala1745ValfsTer14	p.A1745Vfs*14	ENST00000263253	NM_001429.3	1744	caTGCTTGCCAG/ca	31/31	1	2	FACETS	0.981	0.907	1	0.981	0.907	1	CLONAL	1	TRUE	1	0.67956373063846	2		423	477	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098601	47098601	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	154	401	0	ENST00000409792.3:c.6673del	p.Val2225TrpfsTer23	p.V2225Wfs*23	ENST00000409792	NM_014159.6	2225	Gtg/tg	15/21	0.67956373063846	1	FACETS	0.941	0.877	1	0.941	0.877	1	CLONAL	1	TRUE	0	0.67956373063846	1		401	318	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437558	52437598	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCTCCAAAAAGCACCTTGGAGATGTGGGAGGTGACAGGG	CCTCTCCAAAAAGCACCTTGGAGATGTGGGAGGTGACAGGG	-	novel	NA	P-0062056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	105	401	0	ENST00000460680.1:c.1563_1603del	p.Ser521ArgfsTer2	p.S521Rfs*2	ENST00000460680	NM_004656.3	521	agCCCTGTCACCTCCCACATCTCCAAGGTGCTTTTTGGAGAGGat/agat	13/17	0.67956373063846	1	FACETS	0.872	0.798	0.947	0.872	0.798	0.947	CLONAL	1	TRUE	0	0.67956373063846	1		401	234	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683698	162683698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs552077922	NA	P-0062056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	136	248	0	ENST00000366898.1:c.271G>A	p.Ala91Thr	p.A91T	ENST00000366898	NM_004562.2	91	Gcg/Acg	3/12	1	2	FACETS	0.964	0.885	1	0.964	0.885	1	CLONAL	1	TRUE	1	0.67956373063846	2		248	415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578284	7578284	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062068-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	229	764	1	ENST00000269305.4:c.565del	p.Ala189ProfsTer58	p.A189Pfs*58	ENST00000269305	NM_001126112.2	189	Gcc/cc	6/11	0.271519742185266	2	FACETS	0.98	0.915	1	0.98	0.915	1	CLONAL	2	TRUE	0	0.275573701197731	2		765	848	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449746	8449746	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1424143158	NA	P-0062068-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	126	484	0	ENST00000356435.5:c.3967C>T	p.Arg1323Cys	p.R1323C	ENST00000356435		1323	Cgc/Tgc	23/35	0.275573701197731	3	FACETS	0.944	0.859	1	0.944	0.859	1	CLONAL	2	TRUE	1	0.275573701197731	3		484	551	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024001	27024002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0062069-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	155	406	0	ENST00000324856.7:c.1113dup	p.Gln372AlafsTer28	p.Q372Afs*28	ENST00000324856	NM_006015.4	369	-/G	1/20	1	2	FACETS	0.97	0.894	1	1	0.992	1	CLONAL	2	TRUE	1	0.294137116483264	2		406	543	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062069-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	353	544	0	ENST00000397062.3:c.92G>A	p.Gly31Glu	p.G31E	ENST00000397062	NM_006164.4	31	gGa/gAa	2/5	0.294137116483264	3	FACETS	1	0.99	1	1	0.996	1	CLONAL	4	TRUE	0	0.294137116483264	3		544	623	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0062069-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	216	613	0	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	1	2	FACETS	1	0.938	1	1	0.994	1	CLONAL	2	TRUE	1	0.294137116483264	2		613	730	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781323	3781325	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0062069-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	244	820	0	ENST00000262367.5:c.5040_5042del	p.Leu1681del	p.L1681del	ENST00000262367	NM_004380.2	1680	tcCTTg/tcg	30/31	0.291107157981707	4	FACETS	0.938	0.876	1	0.626	0.584	0.669	CLONAL	2	TRUE	1	0.294137116483264	4		820	1144	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014284	70014284	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062069-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	223	600	0	ENST00000394351.3:c.1145C>G	p.Thr382Ser	p.T382S	ENST00000394351	NM_000248.3	382	aCc/aGc	9/9	1	2	FACETS	1	0.976	1	1	0.995	1	CLONAL	2	TRUE	1	0.294137116483264	2		600	697	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0062071-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	243	309	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.648581173166392	2	FACETS	0.966	0.92	1	0.966	0.92	1	CLONAL	2	TRUE	0	0.648581173166392	2		309	388	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0062071-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	193	453	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.648581173166392	2		453	462	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062071-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	190	549	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.648581173166392	2		549	575	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246445	105246445	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062071-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	137	595	0	ENST00000349310.3:c.155T>G	p.Leu52Arg	p.L52R	ENST00000349310	NM_001014432.1	52	cTc/cGc	4/15	1	2	FACETS	0.871	0.798	0.947	0.871	0.798	0.947	CLONAL	1	TRUE	1	0.648581173166392	2		595	485	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589557	67589562	+	inframe_deletion	In_Frame_Del	DEL	TAATAT	TAATAT	-	novel	NA	P-0062071-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	22	301	0	ENST00000274335.5:c.1321_1326del	p.Asn441_Ile442del	p.N441_I442del	ENST00000274335		440	gaTAATATt/gat	10/15	1	2	FACETS	0.216	0.167	0.273	0.216	0.167	0.273	SUBCLONAL	1	TRUE	1	0.648581173166392	2		301	314	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262429	39262429	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062071-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	136	464	0	ENST00000402219.2:c.998A>C	p.Glu333Ala	p.E333A	ENST00000402219	NM_005633.3	333	gAa/gCa	8/23	1	2	FACETS	0.91	0.833	0.989	0.91	0.833	0.989	CLONAL	1	TRUE	1	0.648581173166392	2		464	461	SUCCESS
APC	324	MSKCC	GRCh37	5	112176863	112176863	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1270783041	NA	P-0062080-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	123	555	0	ENST00000257430.4:c.5572C>T	p.Arg1858Ter	p.R1858*	ENST00000257430	NM_000038.5	1858	Cga/Tga	16/16	0.45775421554013	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.455387179048104	1		555	316	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422335	422335	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062080-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	121	501	0	ENST00000399788.2:c.2923G>T	p.Glu975Ter	p.E975*	ENST00000399788	NM_001042603.1	975	Gaa/Taa	20/28	0.455387179048104	5	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.455387179048104	5		501	650	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608255	100608255	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062080-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	120	250	0	ENST00000308731.7:c.1835A>G	p.Gln612Arg	p.Q612R	ENST00000308731	NM_000061.2	612	cAa/cGa	18/19	0.439973667537891	2	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.455387179048104	2		250	387	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022684	12022684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745867456	NA	P-0062083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	77	893	3	ENST00000396373.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000396373	NM_001987.4	264	Cgc/Tgc	5/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.125792128772252	2		896	932	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102192	27102193	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0062083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	52	548	0	ENST00000324856.7:c.5119dup	p.Ser1707LysfsTer20	p.S1707Kfs*20	ENST00000324856	NM_006015.4	1706	-/A	19/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.125792128772252	2		548	631	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103525	77103525	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	58	656	0	ENST00000356341.3:c.41C>T	p.Ala14Val	p.A14V	ENST00000356341	NM_002576.4	14	gCc/gTc	2/15	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.125792128772252	2		656	827	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631161	69631162	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0062083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	49	669	0	ENST00000334134.2:c.250_251delinsAA	p.Gly84Asn	p.G84N	ENST00000334134	NM_005247.2	84	GGc/AAc	2/3	1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	1	0.125792128772252	2		669	776	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61725922	61725922	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	56	472	0	ENST00000401558.2:c.645T>G	p.Asn215Lys	p.N215K	ENST00000401558	NM_003400.3	215	aaT/aaG	9/25	1	2	FACETS	0.824	0.707	0.953	1	0.971	1	CLONAL	2	TRUE	1	0.125792128772252	2		472	540	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29445395	29445395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	79	798	0	ENST00000544604.2:c.1226C>T	p.Ser409Phe	p.S409F	ENST00000544604	NM_001206998.1	409	tCc/tTc	8/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.125792128772252	2		798	940	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098670	47098670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143083979	NA	P-0062083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	52	827	0	ENST00000409792.3:c.6604C>T	p.Pro2202Ser	p.P2202S	ENST00000409792	NM_014159.6	2202	Cct/Tct	15/21	1	2	FACETS	0.846	0.718	0.988	0.846	0.718	0.988	CLONAL	1	TRUE	1	0.125792128772252	2		827	977	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124499135	124499135	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	28	418	0	ENST00000357628.3:c.578C>T	p.Ser193Phe	p.S193F	ENST00000357628	NM_015450.2	193	tCt/tTt	9/19	1	2	FACETS	0.869	0.694	1	0.869	0.694	1	CLONAL	1	TRUE	1	0.125792128772252	2		418	512	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124503565	124503565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	78	516	0	ENST00000357628.3:c.385G>A	p.Asp129Asn	p.D129N	ENST00000357628	NM_015450.2	129	Gac/Aac	8/19	1	2	FACETS	0.88	0.773	0.995	1	0.981	1	CLONAL	2	TRUE	1	0.125792128772252	2		516	705	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021732	69021732	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	48	548	2	ENST00000288368.4:c.3020A>G	p.Asp1007Gly	p.D1007G	ENST00000288368	NM_024870.2	1007	gAt/gGt	25/40	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.125792128772252	2		550	619	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974744	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAGCAGCGCCCGCA	CCTCCAGCAGCGCCCGCA	-	novel	NA	P-0062097-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	183	1338	0	ENST00000304494.5:c.83_100del	p.Val28_Glu33del	p.V28_E33del	ENST00000304494	NM_000077.4	28	gTGCGGGCGCTGCTGGAGGcg/gcg	1/3	0.43225207158954	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.43225207158954	1		1338	620	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518911	187518911	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062097-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	95	908	0	ENST00000441802.2:c.12293G>T	p.Cys4098Phe	p.C4098F	ENST00000441802	NM_005245.3	4098	tGt/tTt	24/27	0.43225207158954	1	FACETS	0.868	0.778	0.962	0.868	0.778	0.962	CLONAL	1	TRUE	0	0.43225207158954	1		908	397	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406408	70406408	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062097-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	31	988	0	ENST00000373644.4:c.3922C>T	p.Gln1308Ter	p.Q1308*	ENST00000373644	NM_030625.2	1308	Cag/Tag	4/12	0.178487686824309	0	FACETS	0.141	0.113	0.173			1	INDETERMINATE	1	TRUE	0	0.43225207158954	0		988	577	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235915	108235915	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062097-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	33	775	1	ENST00000278616.4:c.8957C>T	p.Ala2986Val	p.A2986V	ENST00000278616	NM_000051.3	2986	gCa/gTa	62/63	0.43225207158954	1	FACETS	0.224	0.182	0.272	0.224	0.182	0.272	SUBCLONAL	1	TRUE	0	0.43225207158954	1		776	534	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579718	7579734	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGTCTGAAAGACAAGA	AAGTCTGAAAGACAAGA	-	novel	NA	P-0062097-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	76	588	0	ENST00000269305.4:c.75-13_78del		p.X25_splice	ENST00000269305	NM_001126112.2	25		3/11	1	2	FACETS	0.731	0.643	0.825	0.731	0.643	0.825	SUBCLONAL	1	TRUE	1	0.43225207158954	2		588	481	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325949	30325949	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062097-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	27	733	0	ENST00000322652.5:c.2147A>C	p.Asn716Thr	p.N716T	ENST00000322652	NM_015355.2	716	aAc/aCc	16/16	1	2	FACETS	0.285	0.226	0.352	0.285	0.226	0.352	SUBCLONAL	1	TRUE	1	0.43225207158954	2		733	439	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10244971	10244971	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062097-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	26	714	0	ENST00000340748.4:c.4738G>T	p.Val1580Leu	p.V1580L	ENST00000340748		1580	Gtg/Ttg	39/40	1	2	FACETS	0.301	0.238	0.373	0.301	0.238	0.373	SUBCLONAL	1	TRUE	1	0.43225207158954	2		714	400	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68984792	68984792	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062097-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	51	632	0	ENST00000288368.4:c.1556G>T	p.Trp519Leu	p.W519L	ENST00000288368	NM_024870.2	519	tGg/tTg	14/40	0.43225207158954	3	FACETS	0.852	0.727	0.987	0.426	0.363	0.494	CLONAL	1	TRUE	1	0.43225207158954	3		632	337	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563422	87563422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062097-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	59	1048	0	ENST00000277120.3:c.1810G>A	p.Glu604Lys	p.E604K	ENST00000277120		604	Gag/Aag	16/19	0.43225207158954	1	FACETS	0.404	0.347	0.465	0.404	0.347	0.465	SUBCLONAL	1	TRUE	0	0.43225207158954	1		1048	530	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249765	110249765	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062097-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	49	1042	0	ENST00000374672.4:c.910G>C	p.Asp304His	p.D304H	ENST00000374672	NM_004235.4	304	Gac/Cac	3/5	0.43225207158954	2	FACETS	0.265	0.223	0.311	0.132	0.111	0.156	SUBCLONAL	1	TRUE	0	0.43225207158954	2		1042	856	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443684	49443691	+	frameshift_variant	Frame_Shift_Del	DEL	AGAGCCCA	AGAGCCCA	C	novel	NA	P-0062097-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	138	1014	0	ENST00000301067.7:c.3680_3687delinsG	p.Leu1227ArgfsTer101	p.L1227Rfs*101	ENST00000301067	NM_003482.3	1227	cTGGGCTCT/cG	11/54	1	2	FACETS	0.898	0.819	0.981	0.898	0.819	0.981	CLONAL	1	TRUE	1	0.43225207158954	2		1014	711	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0062106-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	24	117	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.391303063756068	1	FACETS	0.731	0.58	0.899	0.731	0.58	0.899	SUBCLONAL	1	TRUE	0	0.391303063756068	1		117	135	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0062106-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	146	439	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.318839702307288	2	FACETS	0.846	0.779	0.915	0.846	0.779	0.915	CLONAL	2	TRUE	0	0.391303063756068	2		440	441	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38964979	38964979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062106-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	48	345	0	ENST00000357387.3:c.1315C>T	p.Pro439Ser	p.P439S	ENST00000357387	NM_152756.3	439	Cct/Tct	16/38	0.234242639566798	3	FACETS	0.903	0.767	1	0.451	0.383	0.526	INDETERMINATE	1	TRUE	1	0.391303063756068	3		345	325	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0062107-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	77	532	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	0.905	0.792	1	0.905	0.792	1	CLONAL	1	TRUE	1	0.17	2		532	1001	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974762	21974762	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062107-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	90	595	0	ENST00000304494.5:c.65G>C	p.Arg22Pro	p.R22P	ENST00000304494	NM_000077.4	22	cGg/cCg	1/3	1	2	FACETS	0.961	0.85	1	0.961	0.85	1	CLONAL	1	TRUE	1	0.17	2		595	1102	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434378	49434378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062107-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	86	602	0	ENST00000301067.7:c.7175C>T	p.Pro2392Leu	p.P2392L	ENST00000301067	NM_003482.3	2392	cCt/cTt	31/54	1	2	FACETS	0.923	0.814	1	0.923	0.814	1	CLONAL	1	TRUE	1	0.17	2		602	1096	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914284	32914284	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062107-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	45	396	0	ENST00000380152.3:c.5793del	p.Gln1931HisfsTer32	p.Q1931Hfs*32	ENST00000380152		1931	cAa/ca	11/27	0.187170903300057	0	FACETS	0.842	0.713	0.982			1	CLONAL	2	TRUE	0	0.17	0		396	261	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267343	198267343	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062107-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	52	427	0	ENST00000335508.6:c.2014G>T	p.Ala672Ser	p.A672S	ENST00000335508	NM_012433.2	672	Gct/Tct	14/25	1	2	FACETS	0.946	0.804	1	0.946	0.804	1	CLONAL	1	TRUE	1	0.17	2		427	647	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221996	98221996	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062107-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	48	508	0	ENST00000331920.6:c.2773G>T	p.Ala925Ser	p.A925S	ENST00000331920	NM_000264.3	925	Gct/Tct	17/24	1	2	FACETS	0.69	0.581	0.81	0.69	0.581	0.81	SUBCLONAL	1	TRUE	1	0.17	2		508	819	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912818	100912818	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062107-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	26	302	0	ENST00000325455.5:c.2504T>A	p.Leu835Gln	p.L835Q	ENST00000325455	NM_001202474.3	835	cTa/cAa	7/8	1	2	FACETS	0.797	0.631	0.987	0.797	0.631	0.987	CLONAL	1	TRUE	1	0.17	2		302	384	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424431	49424431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062107-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	65	505	0	ENST00000301067.7:c.13792G>A	p.Gly4598Arg	p.G4598R	ENST00000301067	NM_003482.3	4598	Ggg/Agg	41/54	1	2	FACETS	0.944	0.817	1	0.944	0.817	1	CLONAL	1	TRUE	1	0.17	2		505	810	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557644	21557644	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062107-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	62	582	0	ENST00000382592.4:c.2201C>A	p.Ser734Tyr	p.S734Y	ENST00000382592	NM_014572.2	734	tCc/tAc	5/8	NA	2	FACETS	0.944	0.814	1			1	INDETERMINATE	1	TRUE	NA	0.17	2		582	773	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63965609	63965609	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs376789146	NA	P-0062107-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	41	442	0	ENST00000398590.3:c.518C>A	p.Ser173Tyr	p.S173Y	ENST00000398590	NM_001177387.1	173	tCc/tAc	6/14	1	2	FACETS	0.787	0.654	0.935	0.787	0.654	0.935	CLONAL	1	TRUE	1	0.17	2		442	613	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124493153	124493153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062107-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	21	287	0	ENST00000357628.3:c.742C>T	p.Leu248Phe	p.L248F	ENST00000357628	NM_015450.2	248	Ctt/Ttt	10/19	1	2	FACETS	0.958	0.739	1	0.958	0.739	1	CLONAL	1	TRUE	1	0.17	2		287	258	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70971006	70971006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062107-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	56	425	0	ENST00000276594.2:c.1255C>T	p.Leu419Phe	p.L419F	ENST00000276594	NM_024504.3	419	Ctc/Ttc	6/8	1	2	FACETS	0.973	0.833	1	0.973	0.833	1	CLONAL	1	TRUE	1	0.17	2		425	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0062107-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	191	532	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.325268015708249	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.325268015708249	2		532	548	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974762	21974762	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062107-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	155	595	0	ENST00000304494.5:c.65G>C	p.Arg22Pro	p.R22P	ENST00000304494	NM_000077.4	22	cGg/cCg	1/3	0.325268015708249	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.325268015708249	2		595	460	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434378	49434378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062107-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	177	602	0	ENST00000301067.7:c.7175C>T	p.Pro2392Leu	p.P2392L	ENST00000301067	NM_003482.3	2392	cCt/cTt	31/54	0.104038993631632	6	FACETS	0.883	0.817	0.952			1	INDETERMINATE	3	TRUE	NA	0.325268015708249	6		602	678	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914284	32914284	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062107-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	68	396	0	ENST00000380152.3:c.5793del	p.Gln1931HisfsTer32	p.Q1931Hfs*32	ENST00000380152		1931	cAa/ca	11/27	0.325268015708249	1	FACETS	1	0.913	1	1	0.984	1	CLONAL	2	TRUE	0	0.325268015708249	1		396	170	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267343	198267343	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062107-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	128	427	0	ENST00000335508.6:c.2014G>T	p.Ala672Ser	p.A672S	ENST00000335508	NM_012433.2	672	Gct/Tct	14/25	0.0900194070868328	4	FACETS	0.891	0.811	0.976	0.891	0.811	0.976	INDETERMINATE	2	TRUE	2	0.325268015708249	4		427	585	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221996	98221996	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062107-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	187	508	0	ENST00000331920.6:c.2773G>T	p.Ala925Ser	p.A925S	ENST00000331920	NM_000264.3	925	Gct/Tct	17/24	0.325268015708249	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.325268015708249	2		508	531	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912818	100912818	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062107-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	46	302	0	ENST00000325455.5:c.2504T>A	p.Leu835Gln	p.L835Q	ENST00000325455	NM_001202474.3	835	cTa/cAa	7/8	0.151789624458005	3	FACETS	1	0.88	1	0.349	0.295	0.408	INDETERMINATE	1	TRUE	0	0.325268015708249	3		302	314	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424431	49424431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062107-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	156	505	0	ENST00000301067.7:c.13792G>A	p.Gly4598Arg	p.G4598R	ENST00000301067	NM_003482.3	4598	Ggg/Agg	41/54	0.104038993631632	6	FACETS	0.913	0.84	0.988			1	INDETERMINATE	3	TRUE	NA	0.325268015708249	6		505	578	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557644	21557644	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062107-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	156	582	0	ENST00000382592.4:c.2201C>A	p.Ser734Tyr	p.S734Y	ENST00000382592	NM_014572.2	734	tCc/tAc	5/8	0.325268015708249	1	FACETS	0.849	0.784	0.916	1	0.991	1	CLONAL	2	TRUE	0	0.325268015708249	1		582	473	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63965609	63965609	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs376789146	NA	P-0062107-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	82	442	0	ENST00000398590.3:c.518C>A	p.Ser173Tyr	p.S173Y	ENST00000398590	NM_001177387.1	173	tCc/tAc	6/14	0.325268015708249	2	FACETS	1	0.971	1	0.65	0.576	0.727	CLONAL	1	TRUE	0	0.325268015708249	2		442	388	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124493153	124493153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062107-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	13	287	0	ENST00000357628.3:c.742C>T	p.Leu248Phe	p.L248F	ENST00000357628	NM_015450.2	248	Ctt/Ttt	10/19	0.118137923877907	3	FACETS	0.519	0.371	0.699	0.173	0.123	0.233	INDETERMINATE	1	TRUE	0	0.325268015708249	3		287	179	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70971006	70971006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062107-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	147	425	0	ENST00000276594.2:c.1255C>T	p.Leu419Phe	p.L419F	ENST00000276594	NM_024504.3	419	Ctc/Ttc	6/8	0.0900194070868328	4	FACETS	1	0.98	1	1	0.98	1	INDETERMINATE	2	TRUE	2	0.325268015708249	4		425	498	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94910922	94910922	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062107-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	30	294	0	ENST00000536441.1:c.1208G>T	p.Arg403Ile	p.R403I	ENST00000536441	NM_144665.3	403	aGa/aTa	8/10	0.151789624458005	3	FACETS	0.677	0.546	0.824	0.226	0.182	0.275	INDETERMINATE	1	TRUE	0	0.325268015708249	3		294	317	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426425	49427203	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGAGGAGGGTTGGACCCAGGGCTCCAGGGCTAGAAAAGTGTTGAAGAGGCTTTGCTGGCATGCCAGGGCCAAGTGCCACTTGCTGCTGCTGTTGTTGCTGAGGAGACAGTAAAGTTCGACTCTGGTTTAAAAGGCCCATCTGCTGCTGTTGCTGCTGCTGTTGAAACTGCTGCTGTTGTTGTTGCTGTTGCTGTTGTAGCTGCTGTTGCTGCTGTTGAAGCTGTTGCTGCTGCTGTTGTTGAAGCTGCTGCTGCTGTTGCTGCTGTTGAAGCTGTTGCTGCTGAAGTTGCTGTTGCTGTTGTAGCTGCTGCTGCTGCTGCTGCTGAAGTTGCTGTTGCTGTTGCAGCTGCTGCTGCTGCTGAAGCTGCTGTAAAGAGCCCATGGGCTGAGCGCTCAGTTTGGGCTGCCCACTGTGTGACATCAGACTCTGCTGAAGATGGGACAGCCCTGCCATGGACCCTTGCTGTTGGTGCTGTTGTTGCTGCTGCTGCTGCTGGGCTGTGACCAGCCTGTGTCCCATAAGGCCCTGACCCTGCTGTGCCAGCTGGGGGGAACTGAGCACCCGGGACTGGGTCATAAGCACCTGTCTGTGAGGGCCCTGGGGGCCCAAAGCTCCAGGGTGCTGCTGCTGCAACACAGCCACCTGGGCAGGGCCCAGCATGCCCTGGGGCCCCTGGGGTGGTTGAGGGGACAGCTGCTGGACCAGGAGGCCTTGGTGGCTGCTGGGAGGCATAAGGCCCTGGGGCTTGGGACCCAGAGCTTGGTTTGTCTGTACTC	CAGGAGGAGGGTTGGACCCAGGGCTCCAGGGCTAGAAAAGTGTTGAAGAGGCTTTGCTGGCATGCCAGGGCCAAGTGCCACTTGCTGCTGCTGTTGTTGCTGAGGAGACAGTAAAGTTCGACTCTGGTTTAAAAGGCCCATCTGCTGCTGTTGCTGCTGCTGTTGAAACTGCTGCTGTTGTTGTTGCTGTTGCTGTTGTAGCTGCTGTTGCTGCTGTTGAAGCTGTTGCTGCTGCTGTTGTTGAAGCTGCTGCTGCTGTTGCTGCTGTTGAAGCTGTTGCTGCTGAAGTTGCTGTTGCTGTTGTAGCTGCTGCTGCTGCTGCTGCTGAAGTTGCTGTTGCTGTTGCAGCTGCTGCTGCTGCTGAAGCTGCTGTAAAGAGCCCATGGGCTGAGCGCTCAGTTTGGGCTGCCCACTGTGTGACATCAGACTCTGCTGAAGATGGGACAGCCCTGCCATGGACCCTTGCTGTTGGTGCTGTTGTTGCTGCTGCTGCTGCTGGGCTGTGACCAGCCTGTGTCCCATAAGGCCCTGACCCTGCTGTGCCAGCTGGGGGGAACTGAGCACCCGGGACTGGGTCATAAGCACCTGTCTGTGAGGGCCCTGGGGGCCCAAAGCTCCAGGGTGCTGCTGCTGCAACACAGCCACCTGGGCAGGGCCCAGCATGCCCTGGGGCCCCTGGGGTGGTTGAGGGGACAGCTGCTGGACCAGGAGGCCTTGGTGGCTGCTGGGAGGCATAAGGCCCTGGGGCTTGGGACCCAGAGCTTGGTTTGTCTGTACTC	-	novel	NA	P-0062107-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	128	631	0	ENST00000301067.7:c.11285_12063del	p.Gly3762AspfsTer18	p.G3762Dfs*18	ENST00000301067	NM_003482.3	3762	gGAGTACAGACAAACCAAGCTCTGGGTCCCAAGCCCCAGGGCCTTATGCCTCCCAGCAGCCACCAAGGCCTCCTGGTCCAGCAGCTGTCCCCTCAACCACCCCAGGGGCCCCAGGGCATGCTGGGCCCTGCCCAGGTGGCTGTGTTGCAGCAGCAGCACCCTGGAGCTTTGGGCCCCCAGGGCCCTCACAGACAGGTGCTTATGACCCAGTCCCGGGTGCTCAGTTCCCCCCAGCTGGCACAGCAGGGTCAGGGCCTTATGGGACACAGGCTGGTCACAGCCCAGCAGCAGCAGCAGCAACAACAGCACCAACAGCAAGGGTCCATGGCAGGGCTGTCCCATCTTCAGCAGAGTCTGATGTCACACAGTGGGCAGCCCAAACTGAGCGCTCAGCCCATGGGCTCTTTACAGCAGCTTCAGCAGCAGCAGCAGCTGCAACAGCAACAGCAACTTCAGCAGCAGCAGCAGCAGCAGCTACAACAGCAACAGCAACTTCAGCAGCAACAGCTTCAACAGCAGCAACAGCAGCAGCAGCTTCAACAACAGCAGCAGCAACAGCTTCAACAGCAGCAACAGCAGCTACAACAGCAACAGCAACAACAACAGCAGCAGTTTCAACAGCAGCAGCAACAGCAGCAGATGGGCCTTTTAAACCAGAGTCGAACTTTACTGTCTCCTCAGCAACAACAGCAGCAGCAAGTGGCACTTGGCCCTGGCATGCCAGCAAAGCCTCTTCAACACTTTTCTAGCCCTGGAGCCCTGGGTCCAACCCTCCTCCTG/g	39/54	0.104038993631632	6	FACETS	0.967	0.878	1			1	INDETERMINATE	2	TRUE	NA	0.325268015708249	6		631	672	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432548	49432560	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCCTGGCAGAC	GGGCCTGGCAGAC	-	novel	NA	P-0062107-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	47	581	0	ENST00000301067.7:c.8579_8591del	p.Arg2860LeufsTer46	p.R2860Lfs*46	ENST00000301067	NM_003482.3	2860	cGTCTGCCAGGCCCt/ct	34/54	0.104038993631632	6	FACETS	0.738	0.622	0.867			1	INDETERMINATE	1	TRUE	NA	0.325268015708249	6		581	646	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917805	29917805	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062107-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	109	484	0	ENST00000389048.3:c.863G>C	p.Trp288Ser	p.W288S	ENST00000389048	NM_004304.4	288	tGg/tCg	3/29	0.0900194070868328	4	FACETS	0.782	0.704	0.864	0.782	0.704	0.864	INDETERMINATE	2	TRUE	2	0.325268015708249	4		484	568	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390947	89390947	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062107-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	33	390	0	ENST00000336596.2:c.1013A>C	p.Glu338Ala	p.E338A	ENST00000336596	NM_005233.5	338	gAg/gCg	5/17	0.175378009098657	3	FACETS	0.581	0.473	0.703	0.291	0.236	0.352	INDETERMINATE	1	TRUE	1	0.325268015708249	3		390	406	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670435	134670435	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062107-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	137	459	0	ENST00000398015.3:c.346G>T	p.Glu116Ter	p.E116*	ENST00000398015	NM_004441.4	116	Gag/Tag	3/16	0.325268015708249	5	FACETS	0.856	0.78	0.936	0.428	0.39	0.468	CLONAL	2	TRUE	1	0.325268015708249	5		459	732	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341641	70341641	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062107-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	38	263	0	ENST00000374080.3:c.1076T>C	p.Val359Ala	p.V359A	ENST00000374080		359	gTt/gCt	7/45	0.276252043649986	2	FACETS	0.73	0.606	0.868			1	SUBCLONAL	1	TRUE	NA	0.325268015708249	2		263	320	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981456	201981471	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTTCCTTCCTTGTCAG	CTTCCTTCCTTGTCAG	-	novel	NA	P-0062107-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	28	492	0	ENST00000359651.3:c.386-11_390del		p.X129_splice	ENST00000359651		129			0.175378009098657	3	FACETS	0.468	0.373	0.576	0.234	0.186	0.288	INDETERMINATE	1	TRUE	1	0.325268015708249	3		492	428	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0062115-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	426	421	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.43448424013337	5	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	2	0.43448424013337	5		421	986	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0062115-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	246	505	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	0.409074698385159	2	FACETS	0.909	0.856	0.963	0.909	0.856	0.963	CLONAL	2	TRUE	0	0.43448424013337	2		505	623	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685287	89685287	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs398123316	NA	P-0062115-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	131	289	0	ENST00000371953.3:c.182A>T	p.His61Leu	p.H61L	ENST00000371953	NM_000314.4	61	cAt/cTt	3/9	0.409074698385159	2	FACETS	0.798	0.732	0.865	0.798	0.732	0.865	SUBCLONAL	2	TRUE	0	0.43448424013337	2		289	378	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444927	49444927	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1439134461	NA	P-0062115-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	174	706	0	ENST00000301067.7:c.2539G>A	p.Glu847Lys	p.E847K	ENST00000301067	NM_003482.3	847	Gag/Aag	10/54	0.435881117830166	3	FACETS	0.982	0.903	1	0.491	0.451	0.532	CLONAL	1	TRUE	1	0.43448424013337	3		706	993	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386336	31386336	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062115-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	158	685	0	ENST00000328111.2:c.1561C>T	p.Pro521Ser	p.P521S	ENST00000328111	NM_006892.3	521	Ccc/Tcc	15/23	0.401121785908021	5	FACETS	0.974	0.891	1			1	CLONAL	1	TRUE	NA	0.43448424013337	5		685	1233	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940271	31940271	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062115-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	206	607	0	ENST00000375333.2:c.413C>G	p.Pro138Arg	p.P138R	ENST00000375333	NM_032454.1	138	cCt/cGt	2/8	0.435881117830166	4	FACETS	1	0.959	1	0.351	0.325	0.379	CLONAL	1	TRUE	1	0.43448424013337	4		607	1291	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0062125-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	176	416	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.488246279070026	1	FACETS	0.975	0.904	1	0.975	0.904	1	CLONAL	1	TRUE	0	0.488246279070026	1		416	559	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0062125-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	207	728	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.488246279070026	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.488246279070026	1		728	623	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0062125-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	221	531	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.488246279070026	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.488246279070026	1		531	578	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448310	56448310	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567880628	NA	P-0062125-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	231	628	0	ENST00000407977.2:c.337C>T	p.Arg113Ter	p.R113*	ENST00000407977		113	Cga/Tga	3/10	0.488246279070026	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.488246279070026	1		628	712	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0062125-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	178	633	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.488246279070026	1	FACETS	0.885	0.819	0.952	0.885	0.819	0.952	CLONAL	1	TRUE	0	0.488246279070026	1		633	623	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435095	49435095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062125-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	134	538	0	ENST00000301067.7:c.6458C>T	p.Pro2153Leu	p.P2153L	ENST00000301067	NM_003482.3	2153	cCt/cTt	31/54	0.488246279070026	1	FACETS	0.908	0.831	0.987	0.908	0.831	0.987	CLONAL	1	TRUE	0	0.488246279070026	1		538	457	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300869	137300869	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1384649916	NA	P-0062125-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	47	643	0	ENST00000481739.1:c.514C>T	p.Arg172Cys	p.R172C	ENST00000481739	NM_002957.4	172	Cgc/Tgc	4/10	1	2	FACETS	0.248	0.208	0.292	0.248	0.208	0.292	SUBCLONAL	1	TRUE	1	0.488246279070026	2		643	776	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338699	70338701	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0062125-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	125	206	0	ENST00000374080.3:c.98_99+1del		p.KEdel	ENST00000374080		32	aAGGag/aag	1/45	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.488246279070026	1		206	265	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0062128-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	78	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.934	0.823	1	0.934	0.823	1	CLONAL	1	TRUE	1	0.336040465568762	2		485	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578441	7578441	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062128-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	230	631	1	ENST00000269305.4:c.489C>A	p.Tyr163Ter	p.Y163*	ENST00000269305	NM_001126112.2	163	taC/taA	5/11	0.336040465568762	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.336040465568762	1		632	967	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220371	1220371	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0062128-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	141	532	1	ENST00000326873.7:c.465-1G>C		p.X155_splice	ENST00000326873	NM_000455.4	155			0.336040465568762	1	FACETS	0.891	0.812	0.973	0.891	0.812	0.973	CLONAL	1	TRUE	0	0.336040465568762	1		533	784	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356416	66356416	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062128-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	95	427	3	ENST00000273854.3:c.1081C>A	p.Pro361Thr	p.P361T	ENST00000273854	NM_004439.5	361	Cct/Act	5/18	1	2	FACETS	0.825	0.735	0.921	0.825	0.735	0.921	CLONAL	1	TRUE	1	0.336040465568762	2		430	685	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443866	52443866	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062128-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	241	553	0	ENST00000460680.1:c.29G>A	p.Ser10Asn	p.S10N	ENST00000460680	NM_004656.3	10	aGc/aAc	1/17	0.336040465568762	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.336040465568762	1		553	1115	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492503	50492503	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062128-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	127	446	0	ENST00000394963.4:c.1399A>T	p.Thr467Ser	p.T467S	ENST00000394963	NM_003076.4	467	Act/Tct	12/13	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.336040465568762	2		446	726	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074259	39074259	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062128-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	159	386	0	ENST00000357387.3:c.51del	p.Arg18GlyfsTer13	p.R18Gfs*13	ENST00000357387	NM_152756.3	17	ggG/gg	2/38	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.336040465568762	2		386	893	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372229	55372229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062128-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	100	562	1	ENST00000297316.4:c.919G>A	p.Gly307Ser	p.G307S	ENST00000297316	NM_022454.3	307	Ggc/Agc	2/2	0.242876893698517	3	FACETS	0.62	0.552	0.693	0.31	0.276	0.347	SUBCLONAL	1	TRUE	1	0.336040465568762	3		563	1121	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227867	123227867	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0062128-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	79	275	0	ENST00000218089.9:c.3579-1G>T		p.X1193_splice	ENST00000218089	NM_001042749.1	1193			1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.336040465568762	2		275	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519988	NA	P-0062146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	190	472	0	ENST00000269305.4:c.808T>C	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	Ttt/Ctt	8/11	0.331329044793366	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.349431531623307	2		472	482	SUCCESS
APC	324	MSKCC	GRCh37	5	112175346	112175350	+	frameshift_variant	Frame_Shift_Del	DEL	TTGAA	TTGAA	-	novel	NA	P-0062146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	144	456	0	ENST00000257430.4:c.4057_4061del	p.Glu1353PhefsTer20	p.E1353Ffs*20	ENST00000257430	NM_000038.5	1352	gTTGAA/g	16/16	0.349431531623307	2	FACETS	0.972	0.895	1	0.972	0.895	1	CLONAL	2	TRUE	0	0.349431531623307	2		456	424	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564507	55564507	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766253584	NA	P-0062146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	23	383	0	ENST00000288135.5:c.395C>T	p.Thr132Met	p.T132M	ENST00000288135	NM_000222.2	132	aCg/aTg	3/21	0.349431531623307	2	FACETS	0.368	0.286	0.462	0.184	0.143	0.231	SUBCLONAL	1	TRUE	0	0.349431531623307	2		383	358	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149626	202149626	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	88	516	0	ENST00000358485.4:c.1067A>T	p.Lys356Ile	p.K356I	ENST00000358485	NM_001080125.1	356	aAa/aTa	8/9	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.349431531623307	2		516	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0062150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	93	477	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.432065641688986	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.432065641688986	1		477	322	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639020	176639020	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	73	454	0	ENST00000439151.2:c.3620G>A	p.Arg1207Lys	p.R1207K	ENST00000439151	NM_022455.4	1207	aGa/aAa	5/23	1	2	FACETS	0.818	0.719	0.924	0.818	0.719	0.924	CLONAL	1	TRUE	1	0.432065641688986	2		454	413	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0062151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	109	509	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.765527537738762	2		510	257	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0062151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	26	812	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.275	0.218	0.339	0.275	0.218	0.339	SUBCLONAL	1	TRUE	1	0.765527537738762	2		812	247	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0062151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	140	634	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.926	0.852	1	0.926	0.852	1	CLONAL	1	TRUE	1	0.765527537738762	2		634	395	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374293	138374293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	77	527	0	ENST00000289153.2:c.3151G>A	p.Glu1051Lys	p.E1051K	ENST00000289153	NM_006219.2	1051	Gaa/Aaa	22/22	1	2	FACETS	0.492	0.434	0.554	0.492	0.434	0.554	SUBCLONAL	1	TRUE	1	0.765527537738762	2		527	409	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522449	187522449	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1342860045	NA	P-0062151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	148	435	0	ENST00000441802.2:c.11614C>T	p.Arg3872Ter	p.R3872*	ENST00000441802	NM_005245.3	3872	Cga/Tga	21/27	1	2	FACETS	0.984	0.909	1	0.984	0.909	1	CLONAL	1	TRUE	1	0.765527537738762	2		435	393	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806564	1806564	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	62	615	0	ENST00000260795.2:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000260795		427	tCc/tTc	9/17	1	2	FACETS	0.39	0.338	0.447	0.39	0.338	0.447	SUBCLONAL	1	TRUE	1	0.765527537738762	2		615	415	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845472	128845472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1428746507	NA	P-0062151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	140	579	1	ENST00000249373.3:c.769C>T	p.Arg257Trp	p.R257W	ENST00000249373	NM_005631.4	257	Cgg/Tgg	4/12	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.765527537738762	2		580	345	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740623	58740623	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs372024236	NA	P-0062151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	368	625	0	ENST00000305921.3:c.1528C>T	p.Gln510Ter	p.Q510*	ENST00000305921	NM_003620.3	510	Caa/Taa	6/6	0.765527537738762	2	FACETS	0.973	0.942	1	0.973	0.942	1	CLONAL	2	TRUE	0	0.765527537738762	2		625	494	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129972	55129972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	178	646	0	ENST00000257290.5:c.506C>T	p.Pro169Leu	p.P169L	ENST00000257290	NM_006206.4	169	cCt/cTt	4/23	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.765527537738762	2		646	457	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134460	2134460	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	42	845	0	ENST00000219476.3:c.4237G>A	p.Glu1413Lys	p.E1413K	ENST00000219476	NM_000548.3	1413	Gag/Aag	34/42	1	2	FACETS	0.214	0.178	0.254	0.214	0.178	0.254	SUBCLONAL	1	TRUE	1	0.765527537738762	2		845	512	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797350	45797350	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	231	837	0	ENST00000450313.1:c.1169T>G	p.Val390Gly	p.V390G	ENST00000450313	NM_012222.2	390	gTg/gGg	12/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.765527537738762	2		837	568	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175914307	175914307	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0062151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	90	347	0	ENST00000367669.3:c.2179-1G>A		p.X727_splice	ENST00000367669	NM_022457.5	727			1	2	FACETS	0.929	0.838	1	0.929	0.838	1	CLONAL	1	TRUE	1	0.765527537738762	2		347	253	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230561589	230561589	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0062151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	179	783	0				ENST00000391860	NM_001258311.1	-/409			1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.765527537738762	2		783	448	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620053	21620053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	143	621	0	ENST00000382592.4:c.113C>T	p.Pro38Leu	p.P38L	ENST00000382592	NM_014572.2	38	cCc/cTc	2/8	1	2	FACETS	0.999	0.922	1	0.999	0.922	1	CLONAL	1	TRUE	1	0.765527537738762	2		621	374	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2132460	2132460	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	116	435	0	ENST00000219476.3:c.3838C>T	p.Gln1280Ter	p.Q1280*	ENST00000219476	NM_000548.3	1280	Cag/Tag	32/42	1	2	FACETS	0.962	0.879	1	0.962	0.879	1	CLONAL	1	TRUE	1	0.765527537738762	2		435	315	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634343	23634344	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	novel	NA	P-0062151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	113	453	0	ENST00000261584.4:c.2942_2943delinsAA	p.Ser981Lys	p.S981K	ENST00000261584	NM_024675.3	981	aGT/aAA	9/13	1	2	FACETS	0.895	0.815	0.977	0.895	0.815	0.977	CLONAL	1	TRUE	1	0.765527537738762	2		453	330	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828384	72828385	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0062151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	175	699	0	ENST00000268489.5:c.8196_8197delinsTT	p.Arg2733Cys	p.R2733C	ENST00000268489	NM_006885.3	2732	tcCCgt/tcTTgt	9/10	1	2	FACETS	0.99	0.92	1	0.99	0.92	1	CLONAL	1	TRUE	1	0.765527537738762	2		699	462	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33680141	33680141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201150761	NA	P-0062151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	38	400	0	ENST00000308377.4:c.1940G>A	p.Arg647Gln	p.R647Q	ENST00000308377	NM_152270.3	647	cGa/cAa	5/5	0.765527537738762	2	FACETS	0.424	0.353	0.502	0.212	0.176	0.251	SUBCLONAL	1	TRUE	0	0.765527537738762	2		400	234	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38792338	38792338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	280	450	0	ENST00000348513.6:c.386C>T	p.Ser129Phe	p.S129F	ENST00000348513	NM_003079.4	129	tCt/tTt	7/11	0.765527537738762	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.765527537738762	2		450	359	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390342	56390342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	153	503	0	ENST00000348428.3:c.1081G>A	p.Ala361Thr	p.A361T	ENST00000348428	NM_006785.3	361	Gct/Act	10/17	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.765527537738762	2		503	358	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416788	29416789	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0062151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	139	479	0	ENST00000389048.3:c.4165-1_4165delinsAA		p.X1389_splice	ENST00000389048	NM_004304.4	1389		29/29	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.765527537738762	2		479	360	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248507	212248507	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	181	760	0	ENST00000342788.4:c.3760C>T	p.Gln1254Ter	p.Q1254*	ENST00000342788	NM_005235.2	1254	Cag/Tag	28/28	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.765527537738762	2		760	447	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793219	242793219	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	140	580	0	ENST00000334409.5:c.858G>A	p.Trp286Ter	p.W286*	ENST00000334409	NM_005018.2	286	tgG/tgA	5/5	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.765527537738762	2		580	356	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40828029	40828029	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0062151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	128	481	0	ENST00000373198.4:c.2400-1G>A		p.X800_splice	ENST00000373198	NM_133170.3	800			1	2	FACETS	0.998	0.917	1	0.998	0.917	1	CLONAL	1	TRUE	1	0.765527537738762	2		481	335	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268705	46268705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	192	664	0	ENST00000371998.3:c.2990C>T	p.Pro997Leu	p.P997L	ENST00000371998		997	cCc/cTc	16/23	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.765527537738762	2		664	485	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860416	42860416	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	155	499	0	ENST00000398585.3:c.461G>A	p.Gly154Glu	p.G154E	ENST00000398585	NM_001135099.1	154	gGg/gAg	5/14	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.765527537738762	2		499	364	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447788	187447789	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0062151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	176	670	1	ENST00000232014.4:c.404_405delinsTT	p.Ala135Val	p.A135V	ENST00000232014	NM_001130845.1	135	gCC/gTT	5/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.765527537738762	2		671	440	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517443	176517444	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0062151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	139	591	1	ENST00000292408.4:c.144_145delinsTT	p.Leu49Phe	p.L49F	ENST00000292408	NM_213647.1	48	gcCCtt/gcTTtt	3/18	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.765527537738762	2		592	356	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527882	157527883	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0062151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	147	638	0	ENST00000346085.5:c.5610_5611del	p.Ser1872HisfsTer7	p.S1872Hfs*7	ENST00000346085	NM_020732.3	1869	caAGag/caag	20/20	1	2	FACETS	0.877	0.808	0.948	0.877	0.808	0.948	CLONAL	1	TRUE	1	0.765527537738762	2		638	438	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835895	151835896	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0062151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	88	472	0	ENST00000262189.6:c.14628_14629delinsTT	p.Gln4877Ter	p.Q4877*	ENST00000262189	NM_170606.2	4876	atCCag/atTTag	58/59	1	2	FACETS	0.782	0.701	0.866	0.782	0.701	0.866	SUBCLONAL	1	TRUE	1	0.765527537738762	2		472	294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0062152-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	25	588	2	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	1	2	FACETS	0.15	0.118	0.188	0.15	0.118	0.188	SUBCLONAL	1	TRUE	1	0.804934170454846	2		590	413	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0062155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	11	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.537	0.37	0.746	0.537	0.37	0.746	SUBCLONAL	1	TRUE	1	0.13	2		485	315	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0062155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	28	613	2	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.65	0.517	0.802	0.65	0.517	0.802	SUBCLONAL	1	TRUE	1	0.13	2		615	663	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	183	529	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.995	0.931	1	0.995	0.931	1	CLONAL	1	TRUE	1	0.912830213592738	2		529	403	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513314	106513314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559655430	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	186	377	0	ENST00000359195.3:c.2218G>A	p.Glu740Lys	p.E740K	ENST00000359195	NM_002649.2	740	Gag/Aag	4/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.912830213592738	2		377	396	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322583	39322583	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	196	418	0	ENST00000373001.3:c.409A>C	p.Thr137Pro	p.T137P	ENST00000373001	NM_022157.3	137	Aca/Cca	2/7	0.50937846743348	4	FACETS	1	0.988	1	0.428	0.398	0.459	INDETERMINATE	1	TRUE	1	0.912830213592738	4		418	639	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322585	39322585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	201	448	0	ENST00000373001.3:c.407G>A	p.Gly136Glu	p.G136E	ENST00000373001	NM_022157.3	136	gGa/gAa	2/7	0.50937846743348	4	FACETS	1	0.987	1	0.424	0.394	0.454	INDETERMINATE	1	TRUE	1	0.912830213592738	4		448	663	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736316	243736316	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	229	413	0	ENST00000263826.5:c.731C>T	p.Ser244Phe	p.S244F	ENST00000263826	NM_005465.4	244	tCt/tTt	8/13	1	2	FACETS	0.972	0.916	1	0.972	0.916	1	CLONAL	1	TRUE	1	0.912830213592738	2		413	516	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933464	100933464	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	178	348	0	ENST00000325455.5:c.1926C>A	p.Phe642Leu	p.F642L	ENST00000325455	NM_001202474.3	642	ttC/ttA	4/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.912830213592738	2		348	365	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374399	118374399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	297	618	0	ENST00000534358.1:c.7792G>A	p.Asp2598Asn	p.D2598N	ENST00000534358	NM_005933.3	2598	Gac/Aac	27/36	0.912830213592738	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.912830213592738	1		618	330	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025536	1025536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	215	606	0	ENST00000358495.3:c.839C>T	p.Ser280Phe	p.S280F	ENST00000358495	NM_134424.2	280	tCc/tTc	9/12	1	2	FACETS	0.971	0.913	1	0.971	0.913	1	CLONAL	1	TRUE	1	0.912830213592738	2		606	485	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905387	11905387	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	164	396	0	ENST00000396373.4:c.37G>A	p.Glu13Lys	p.E13K	ENST00000396373	NM_001987.4	13	Gaa/Aaa	2/8	1	2	FACETS	0.961	0.894	1	0.961	0.894	1	CLONAL	1	TRUE	1	0.912830213592738	2		396	374	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434612	49434612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1401415779	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	261	645	0	ENST00000301067.7:c.6941C>T	p.Thr2314Ile	p.T2314I	ENST00000301067	NM_003482.3	2314	aCc/aTc	31/54	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.912830213592738	2		645	533	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434964	49434964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	250	618	0	ENST00000301067.7:c.6589C>T	p.Pro2197Ser	p.P2197S	ENST00000301067	NM_003482.3	2197	Ccc/Tcc	31/54	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.912830213592738	2		618	493	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636188	28636188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	189	414	0	ENST00000241453.7:c.184G>A	p.Asp62Asn	p.D62N	ENST00000241453	NM_004119.2	62	Gac/Aac	3/24	1	2	FACETS	0.965	0.903	1	0.965	0.903	1	CLONAL	1	TRUE	1	0.912830213592738	2		414	429	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951052	48951052	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	291	254	0	ENST00000267163.4:c.1216-2A>T		p.X406_splice	ENST00000267163	NM_000321.2	406			0.912830213592738	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.912830213592738	2		254	303	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675047	40675048	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	183	471	0	ENST00000249776.8:c.11_12delinsTT	p.Pro4Leu	p.P4L	ENST00000249776	NM_033286.3	4	cCC/cTT	1/9	0.837020510430576	1	FACETS	0.969	0.93	1	0.969	0.93	1	CLONAL	1	TRUE	0	0.912830213592738	1		471	225	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43767835	43767835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	230	486	0	ENST00000382044.4:c.1013C>T	p.Ser338Phe	p.S338F	ENST00000382044	NM_001141980.1	338	tCc/tTc	9/28	0.837020510430576	1	FACETS	0.965	0.93	0.996	0.965	0.93	0.996	CLONAL	1	TRUE	0	0.912830213592738	1		486	284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057519990	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	193	485	0	ENST00000269305.4:c.796G>T	p.Gly266Ter	p.G266*	ENST00000269305	NM_001126112.2	266	Gga/Tga	8/11	1	2	FACETS	0.968	0.906	1	0.968	0.906	1	CLONAL	1	TRUE	1	0.912830213592738	2		485	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578490	7578490	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	275	638	0	ENST00000269305.4:c.440T>C	p.Val147Ala	p.V147A	ENST00000269305	NM_001126112.2	147	gTt/gCt	5/11	1	2	FACETS	0.993	0.94	1	0.993	0.94	1	CLONAL	1	TRUE	1	0.912830213592738	2		638	607	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653044	29653044	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	227	485	0	ENST00000356175.3:c.4979A>C	p.Asn1660Thr	p.N1660T	ENST00000356175	NM_000267.3	1660	aAc/aCc	36/57	1	2	FACETS	0.973	0.916	1	0.973	0.916	1	CLONAL	1	TRUE	1	0.912830213592738	2		485	511	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216983	2216983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329819181	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	214	584	0	ENST00000398665.3:c.2438C>T	p.Pro813Leu	p.P813L	ENST00000398665	NM_032482.2	813	cCc/cTc	21/28	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.912830213592738	2		584	449	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117532	4117532	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	73	195	0	ENST00000262948.5:c.188A>G	p.Lys63Arg	p.K63R	ENST00000262948	NM_030662.3	63	aAg/aGg	2/11	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.912830213592738	2		195	154	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280072	18280072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	150	438	0	ENST00000222254.8:c.2155C>T	p.Pro719Ser	p.P719S	ENST00000222254	NM_005027.3	719	Ccg/Tcg	16/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.912830213592738	2		438	318	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214687	36214688	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	147	570	0	ENST00000222270.7:c.3113_3114delinsTT	p.Ala1038Val	p.A1038V	ENST00000222270	NM_014727.1	1038	gCC/gTT	8/37	1	2	FACETS	0.976	0.905	1	0.976	0.905	1	CLONAL	1	TRUE	1	0.912830213592738	2		570	330	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860794	45860794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762837634	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	264	742	0	ENST00000391945.4:c.1315G>A	p.Asp439Asn	p.D439N	ENST00000391945	NM_000400.3	439	Gac/Aac	14/23	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.912830213592738	2		742	533	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917048	50917048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs556196668	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	196	625	0	ENST00000440232.2:c.2300C>T	p.Ser767Leu	p.S767L	ENST00000440232	NM_002691.3	767	tCg/tTg	19/27	1	2	FACETS	0.967	0.906	1	0.967	0.906	1	CLONAL	1	TRUE	1	0.912830213592738	2		625	444	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921183	50921184	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	155	492	0	ENST00000440232.2:c.3303_3304delinsTT	p.Pro1102Ser	p.P1102S	ENST00000440232	NM_002691.3	1101	ccCCct/ccTTct	27/27	1	2	FACETS	0.984	0.915	1	0.984	0.915	1	CLONAL	1	TRUE	1	0.912830213592738	2		492	345	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738354	190738354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	192	363	0	ENST00000441310.2:c.2606G>A	p.Arg869Lys	p.R869K	ENST00000441310	NM_000534.4	869	aGa/aAa	12/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.912830213592738	2		363	402	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561124	9561124	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	216	451	0	ENST00000353224.5:c.658C>T	p.Gln220Ter	p.Q220*	ENST00000353224	NM_177990.2	220	Cag/Tag	4/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.912830213592738	2		451	441	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162873	47162873	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	232	442	0	ENST00000409792.3:c.3253C>T	p.Pro1085Ser	p.P1085S	ENST00000409792	NM_014159.6	1085	Cct/Tct	3/21	0.912830213592738	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.912830213592738	1		442	254	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447676	187447676	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	221	674	0	ENST00000232014.4:c.517C>T	p.Pro173Ser	p.P173S	ENST00000232014	NM_001130845.1	173	Cct/Tct	5/10	0.909310990241963	3	FACETS	0.965	0.901	1	0.482	0.45	0.515	CLONAL	1	TRUE	1	0.912830213592738	3		674	731	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201686	66201687	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	164	417	0	ENST00000273854.3:c.2815_2816delinsTT	p.Pro939Leu	p.P939L	ENST00000273854	NM_004439.5	939	CCa/TTa	16/18	1	2	FACETS	0.961	0.894	1	0.961	0.894	1	CLONAL	1	TRUE	1	0.912830213592738	2		417	374	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190766	106190766	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1193684921	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	163	367	0	ENST00000380013.4:c.4045-1G>A		p.X1349_splice	ENST00000380013	NM_001127208.2	1349			1	2	FACETS	0.925	0.86	0.991	0.925	0.86	0.991	CLONAL	1	TRUE	1	0.912830213592738	2		367	386	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961034	79961034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs966254697	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	198	467	0	ENST00000265081.6:c.431C>T	p.Ser144Phe	p.S144F	ENST00000265081	NM_002439.4	144	tCt/tTt	3/24	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.912830213592738	2		467	423	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499039	149499039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	206	473	0	ENST00000261799.4:c.2789C>T	p.Ser930Phe	p.S930F	ENST00000261799	NM_002609.3	930	tCc/tTc	20/23	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.912830213592738	2		473	441	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26046035	26046035	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	181	488	0	ENST00000540144.1:c.397G>A	p.Gly133Arg	p.G133R	ENST00000540144	NM_003531.2	133	Ggg/Agg	1/1	1	2	FACETS	0.901	0.841	0.963	0.901	0.841	0.963	CLONAL	1	TRUE	1	0.912830213592738	2		488	440	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967964	93967964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	178	398	0	ENST00000369303.4:c.1963C>T	p.Pro655Ser	p.P655S	ENST00000369303	NM_004440.3	655	Cca/Tca	11/17	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.912830213592738	2		398	383	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552940	106552941	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	240	681	0	ENST00000369096.4:c.905_906delinsAA	p.Arg302Gln	p.R302Q	ENST00000369096	NM_001198.3	302	cGG/cAA	5/7	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.912830213592738	2		681	517	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196881	138196882	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	209	468	0	ENST00000237289.4:c.543_544delinsAA	p.Met181_Ala182delinsIleThr	p.M181_A182delinsIT	ENST00000237289	NM_001270507.1	181	atGGcc/atAAcc	4/9	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.912830213592738	2		468	448	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55238896	55238897	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	114	265	0	ENST00000275493.2:c.1909_1910delinsTT	p.Pro637Leu	p.P637L	ENST00000275493	NM_005228.3	637	CCa/TTa	16/28	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.912830213592738	2		265	247	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843800	151843800	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	182	436	0	ENST00000262189.6:c.13915G>A	p.Glu4639Lys	p.E4639K	ENST00000262189	NM_170606.2	4639	Gag/Aag	53/59	1	2	FACETS	0.884	0.825	0.945	0.884	0.825	0.945	CLONAL	1	TRUE	1	0.912830213592738	2		436	451	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875031	151875031	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	427	393	0	ENST00000262189.6:c.7507C>T	p.Gln2503Ter	p.Q2503*	ENST00000262189	NM_170606.2	2503	Cag/Tag	38/59	1	2	FACETS	1	0.995	1	1	0.998	1	CLONAL	2	TRUE	1	0.912830213592738	2		393	454	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518312	8518312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1428808899	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	169	389	0	ENST00000356435.5:c.1079C>T	p.Pro360Leu	p.P360L	ENST00000356435		360	cCt/cTt	10/35	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.912830213592738	2		389	358	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528674	8528674	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	236	468	0	ENST00000356435.5:c.458C>G	p.Pro153Arg	p.P153R	ENST00000356435		153	cCg/cGg	4/35	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.912830213592738	2		468	507	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738163	133738164	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	150	344	0	ENST00000318560.5:c.563_564delinsTT	p.Ser188Phe	p.S188F	ENST00000318560	NM_005157.4	188	tCC/tTT	4/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.912830213592738	2		344	322	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564762	139564762	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	145	416	0	ENST00000308874.7:c.551G>A	p.Arg184Lys	p.R184K	ENST00000308874		184	aGg/aAg	7/10	1	2	FACETS	0.957	0.887	1	0.957	0.887	1	CLONAL	1	TRUE	1	0.912830213592738	2		416	332	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412308	63412309	+	missense_variant	Missense_Mutation	DNP	GG	GG	TA	novel	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	268	362	0	ENST00000330258.3:c.858_859delinsTA	p.Pro287Thr	p.P287T	ENST00000330258	NM_152424.3	286	agCCca/agTAca	2/2	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.912830213592738	1		362	295	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921184	50921184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757442072	NA	P-0062156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	150	476	0	ENST00000440232.2:c.3304C>T	p.Pro1102Ser	p.P1102S	ENST00000440232	NM_002691.3	1102	Cct/Tct	27/27	1	2	FACETS	0.975	0.905	1	0.975	0.905	1	CLONAL	1	TRUE	1	0.912830213592738	2		476	337	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0062162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	153	515	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.929	0.855	1	0.929	0.855	1	CLONAL	1	TRUE	1	0.63008161651241	2		515	523	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66779601	66779601	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	160	560	0	ENST00000307102.5:c.931T>C	p.Phe311Leu	p.F311L	ENST00000307102	NM_002755.3	311	Ttt/Ctt	8/11	1	2	FACETS	0.96	0.886	1	0.96	0.886	1	CLONAL	1	TRUE	1	0.63008161651241	2		560	529	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799174	88799174	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs200923715	NA	P-0062162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	135	609	0	ENST00000360948.2:c.211A>G	p.Ile71Val	p.I71V	ENST00000360948	NM_001012338.2	71	Atc/Gtc	2/19	1	2	FACETS	0.978	0.897	1	0.978	0.897	1	CLONAL	1	TRUE	1	0.63008161651241	2		609	438	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383722	42383722	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	121	609	0	ENST00000221972.3:c.497G>T	p.Arg166Met	p.R166M	ENST00000221972	NM_021601.3	166	aGg/aTg	3/5	1	2	FACETS	0.703	0.638	0.772	0.703	0.638	0.772	SUBCLONAL	1	TRUE	1	0.63008161651241	2		609	546	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637657	52637658	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0062162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	142	530	0	ENST00000394830.3:c.2658_2659insTG	p.Leu887CysfsTer29	p.L887Cfs*29	ENST00000394830	NM_018313.4	886	-/TG	18/30	0.63008161651241	1	FACETS	0.882	0.815	0.95	0.882	0.815	0.95	CLONAL	1	TRUE	0	0.63008161651241	1		530	350	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180835	106180837	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	novel	NA	P-0062162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	176	466	0	ENST00000380013.4:c.3866_3868del	p.Cys1289del	p.C1289del	ENST00000380013	NM_001127208.2	1288	gGTTgt/ggt	7/11	1	2	FACETS	0.928	0.859	0.999	0.928	0.859	0.999	CLONAL	1	TRUE	1	0.63008161651241	2		466	602	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0062164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	13	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.393	0.279	0.533	0.393	0.279	0.533	SUBCLONAL	1	TRUE	1	0.15	2		485	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0062164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	30	477	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.601	0.482	0.736	0.601	0.482	0.736	SUBCLONAL	1	TRUE	1	0.15	2		477	666	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	72	714	1				ENST00000310581	NM_198253.2	-/1132			0.365905448439437	1	FACETS	0.837	0.739	0.94	0.837	0.739	0.94	CLONAL	1	TRUE	0	0.47533579619221	1		715	276	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778878	9778878	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	52	650	0	ENST00000377346.4:c.1147G>T	p.Asp383Tyr	p.D383Y	ENST00000377346	NM_005026.3	383	Gac/Tac	9/24	0.439718018346848	1	FACETS	0.28	0.238	0.327	0.28	0.238	0.327	SUBCLONAL	1	TRUE	0	0.47533579619221	1		650	595	SUCCESS
MAD2L2	10459	MSKCC	GRCh37	1	11740621	11740621	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	26	609	0	ENST00000235310.3:c.38A>G	p.Gln13Arg	p.Q13R	ENST00000235310		13	cAa/cGa	4/11	0.439718018346848	1	FACETS	0.17	0.134	0.211	0.17	0.134	0.211	SUBCLONAL	1	TRUE	0	0.47533579619221	1		609	492	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796987	45796987	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	172	655	0	ENST00000450313.1:c.1343A>G	p.His448Arg	p.H448R	ENST00000450313	NM_012222.2	448	cAc/cGc	14/16	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.47533579619221	2		655	572	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241906	72241906	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	118	519	0	ENST00000357731.5:c.484G>T	p.Ala162Ser	p.A162S	ENST00000357731	NM_173808.2	162	Gcc/Tcc	3/7	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.47533579619221	2		519	429	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	92	408	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	1	2	FACETS	0.813	0.726	0.906	0.813	0.726	0.906	CLONAL	1	TRUE	1	0.47533579619221	2		408	476	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226573237	226573237	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	132	463	0	ENST00000366794.5:c.979A>G	p.Thr327Ala	p.T327A	ENST00000366794	NM_001618.3	327	Aca/Gca	7/23	0.465422149648461	3	FACETS	1	0.967	1	0.564	0.514	0.617	CLONAL	1	TRUE	1	0.47533579619221	3		463	609	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226595546	226595546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	149	501	0	ENST00000366794.5:c.85C>T	p.Pro29Ser	p.P29S	ENST00000366794	NM_001618.3	29	Ccc/Tcc	1/23	0.465422149648461	3	FACETS	1	0.981	1	0.624	0.572	0.678	CLONAL	1	TRUE	1	0.47533579619221	3		501	622	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230492967	230492967	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	117	562	0	ENST00000391860.1:c.87G>T	p.Met29Ile	p.M29I	ENST00000391860	NM_001258311.1	29	atG/atT	2/7	0.465422149648461	3	FACETS	1	0.955	1	0.547	0.495	0.602	CLONAL	1	TRUE	1	0.47533579619221	3		562	557	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607625	43607625	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	77	1073	0	ENST00000355710.3:c.1601T>A	p.Leu534Gln	p.L534Q	ENST00000355710	NM_020975.4	534	cTg/cAg	8/20	0.439718018346848	1	FACETS	0.398	0.35	0.451	0.398	0.35	0.451	SUBCLONAL	1	TRUE	0	0.47533579619221	1		1073	620	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622027	43622027	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	101	470	0	ENST00000355710.3:c.3044A>T	p.Tyr1015Phe	p.Y1015F	ENST00000355710	NM_020975.4	1015	tAc/tTc	19/20	0.439718018346848	1	FACETS	0.835	0.752	0.921	0.835	0.752	0.921	CLONAL	1	TRUE	0	0.47533579619221	1		470	388	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405505	70405505	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	68	555	0	ENST00000373644.4:c.3019A>G	p.Ile1007Val	p.I1007V	ENST00000373644	NM_030625.2	1007	Ata/Gta	4/12	0.324957940314867	1	FACETS	0.575	0.503	0.653	0.575	0.503	0.653	SUBCLONAL	1	TRUE	0	0.47533579619221	1		555	379	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32439188	32439188	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	33	436	0	ENST00000332351.3:c.885C>G	p.Tyr295Ter	p.Y295*	ENST00000332351	NM_024426.4	295	taC/taG	4/10	0.47533579619221	1	FACETS	0.437	0.358	0.526	0.437	0.358	0.526	SUBCLONAL	1	TRUE	0	0.47533579619221	1		436	242	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456332	32456332	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	95	561	0	ENST00000332351.3:c.560A>T	p.Gln187Leu	p.Q187L	ENST00000332351	NM_024426.4	187	cAg/cTg	1/10	0.47533579619221	1	FACETS	0.764	0.685	0.847	0.764	0.685	0.847	SUBCLONAL	1	TRUE	0	0.47533579619221	1		561	399	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94908726	94908726	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	57	406	0	ENST00000536441.1:c.1328A>G	p.Tyr443Cys	p.Y443C	ENST00000536441	NM_144665.3	443	tAt/tGt	9/10	0.391611952723743	1	FACETS	0.597	0.516	0.685	0.597	0.516	0.685	SUBCLONAL	1	TRUE	0	0.47533579619221	1		406	306	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996855	100996855	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	42	510	1	ENST00000325455.5:c.1672A>T	p.Ser558Cys	p.S558C	ENST00000325455	NM_001202474.3	558	Agc/Tgc	2/8	0.391611952723743	1	FACETS	0.397	0.333	0.469	0.397	0.333	0.469	SUBCLONAL	1	TRUE	0	0.47533579619221	1		511	339	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998876	100998876	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	78	609	0	ENST00000325455.5:c.926T>G	p.Leu309Arg	p.L309R	ENST00000325455	NM_001202474.3	309	cTg/cGg	1/8	0.391611952723743	1	FACETS	0.804	0.714	0.9	0.804	0.714	0.9	CLONAL	1	TRUE	0	0.47533579619221	1		609	311	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46215271	46215271	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	55	280	0	ENST00000334344.6:c.705+1G>T		p.X235_splice	ENST00000334344	NM_152641.2	235			1	2	FACETS	0.981	0.848	1	0.981	0.848	1	CLONAL	1	TRUE	1	0.47533579619221	2		280	236	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954373	48954373	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	120	356	0	ENST00000267163.4:c.1494T>A	p.Tyr498Ter	p.Y498*	ENST00000267163	NM_000321.2	498	taT/taA	16/27	0.392999730226663	2	FACETS	0.88	0.808	0.953	0.88	0.808	0.953	CLONAL	2	TRUE	0	0.47533579619221	2		356	287	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50731373	50731373	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1030667700	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	53	304	0	ENST00000307179.4:c.103A>G	p.Ser35Gly	p.S35G	ENST00000307179		35	Agt/Ggt	2/20	0.47533579619221	1	FACETS	0.837	0.724	0.958	0.837	0.724	0.958	CLONAL	1	TRUE	0	0.47533579619221	1		304	203	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341299	341299	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	70	404	0	ENST00000262320.3:c.2187-2A>T		p.X729_splice	ENST00000262320	NM_003502.3	729			1	2	FACETS	0.827	0.726	0.935	0.827	0.726	0.935	CLONAL	1	TRUE	1	0.47533579619221	2		404	356	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652204	3652204	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	100	602	0	ENST00000294008.3:c.865G>C	p.Glu289Gln	p.E289Q	ENST00000294008	NM_032444.2	289	Gag/Cag	4/15	1	2	FACETS	0.835	0.749	0.926	0.835	0.749	0.926	CLONAL	1	TRUE	1	0.47533579619221	2		602	504	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772198	68772198	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	79	439	0	ENST00000261769.5:c.49-2A>T		p.X17_splice	ENST00000261769	NM_004360.3	17			0.398816995481091	1	FACETS	0.853	0.758	0.953	0.853	0.758	0.953	CLONAL	1	TRUE	0	0.47533579619221	1		439	297	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992834	72992834	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	35	547	0	ENST00000268489.5:c.1211G>A	p.Gly404Asp	p.G404D	ENST00000268489	NM_006885.3	404	gGc/gAc	2/10	0.398816995481091	1	FACETS	0.313	0.256	0.376	0.313	0.256	0.376	SUBCLONAL	1	TRUE	0	0.47533579619221	1		547	359	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993638	72993638	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	62	770	0	ENST00000268489.5:c.407A>T	p.Gln136Leu	p.Q136L	ENST00000268489	NM_006885.3	136	cAg/cTg	2/10	0.398816995481091	1	FACETS	0.372	0.322	0.427	0.372	0.322	0.427	SUBCLONAL	1	TRUE	0	0.47533579619221	1		770	534	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349659	89349659	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	112	530	0	ENST00000301030.4:c.3291A>T	p.Glu1097Asp	p.E1097D	ENST00000301030	NM_001256183.1	1097	gaA/gaT	9/13	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.47533579619221	2		530	380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579494	7579494	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1555526721	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	189	720	0	ENST00000269305.4:c.193A>T	p.Arg65Ter	p.R65*	ENST00000269305	NM_001126112.2	65	Aga/Tga	4/11	0.392999730226663	2	FACETS	0.762	0.71	0.815	0.762	0.71	0.815	SUBCLONAL	2	TRUE	0	0.47533579619221	2		720	522	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983600	7983600	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	140	459	0	ENST00000319144.4:c.707T>A	p.Leu236Gln	p.L236Q	ENST00000319144	NM_001139.2	236	cTg/cAg	6/15	0.392999730226663	2	FACETS	0.769	0.708	0.831	0.769	0.708	0.831	SUBCLONAL	2	TRUE	0	0.47533579619221	2		459	383	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690570	33690570	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	119	579	0	ENST00000308377.4:c.257A>C	p.Gln86Pro	p.Q86P	ENST00000308377	NM_152270.3	86	cAg/cCg	2/5	1	2	FACETS	0.84	0.76	0.924	0.84	0.76	0.924	CLONAL	1	TRUE	1	0.47533579619221	2		579	596	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804406	46804406	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	141	536	0	ENST00000290295.7:c.602-1G>T		p.X201_splice	ENST00000290295	NM_006361.5	201			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.47533579619221	2		536	538	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761406	59761406	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	146	475	0	ENST00000259008.2:c.3001A>T	p.Ser1001Cys	p.S1001C	ENST00000259008	NM_032043.2	1001	Agc/Tgc	20/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.47533579619221	2		475	434	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533784	63533784	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1450569717	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	131	800	0	ENST00000307078.5:c.1370T>C	p.Val457Ala	p.V457A	ENST00000307078	NM_004655.3	457	gTa/gCa	6/11	1	2	FACETS	0.934	0.851	1	0.934	0.851	1	CLONAL	1	TRUE	1	0.47533579619221	2		800	590	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216278	2216278	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	104	572	0	ENST00000398665.3:c.1924-2A>G		p.X642_splice	ENST00000398665	NM_032482.2	642			0.391611952723743	1	FACETS	0.665	0.597	0.735	0.665	0.597	0.735	SUBCLONAL	1	TRUE	0	0.47533579619221	1		572	502	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10273354	10273354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748515801	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	56	367	0	ENST00000340748.4:c.949G>A	p.Glu317Lys	p.E317K	ENST00000340748		317	Gag/Aag	12/40	0.391611952723743	1	FACETS	0.471	0.405	0.543	0.471	0.405	0.543	SUBCLONAL	1	TRUE	0	0.47533579619221	1		367	381	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144114	11144114	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	102	651	0	ENST00000358026.2:c.3695G>A	p.Gly1232Asp	p.G1232D	ENST00000358026	NM_001128849.1	1232	gGc/gAc	26/36	0.391611952723743	1	FACETS	0.613	0.55	0.679	0.613	0.55	0.679	SUBCLONAL	1	TRUE	0	0.47533579619221	1		651	534	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295157	15295157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	60	600	1	ENST00000263388.2:c.2515G>A	p.Gly839Arg	p.G839R	ENST00000263388	NM_000435.2	839	Gga/Aga	16/33	0.391611952723743	1	FACETS	0.4	0.345	0.46	0.4	0.345	0.46	SUBCLONAL	1	TRUE	0	0.47533579619221	1		601	481	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218348	36218348	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	114	580	0	ENST00000222270.7:c.4127A>G	p.Tyr1376Cys	p.Y1376C	ENST00000222270	NM_014727.1	1376	tAc/tGc	16/37	1	2	FACETS	0.993	0.899	1	0.993	0.899	1	CLONAL	1	TRUE	1	0.47533579619221	2		580	483	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220058	36220058	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	140	761	0	ENST00000222270.7:c.4780-2A>G		p.X1594_splice	ENST00000222270	NM_014727.1	1594			1	2	FACETS	0.895	0.817	0.976	0.895	0.817	0.976	CLONAL	1	TRUE	1	0.47533579619221	2		761	658	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793405	42793405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	121	756	0	ENST00000575354.2:c.1207G>A	p.Ala403Thr	p.A403T	ENST00000575354	NM_015125.3	403	Gcc/Acc	8/20	1	2	FACETS	0.84	0.761	0.923	0.84	0.761	0.923	CLONAL	1	TRUE	1	0.47533579619221	2		756	606	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905271	50905271	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	173	789	0	ENST00000440232.2:c.479A>T	p.His160Leu	p.H160L	ENST00000440232	NM_002691.3	160	cAc/cTc	5/27	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.47533579619221	2		789	719	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182614	99182614	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	43	570	0	ENST00000074304.5:c.2417A>T	p.Gln806Leu	p.Q806L	ENST00000074304	NM_001134224.1	806	cAg/cTg	22/26	0.194332844411943	2	FACETS	0.363	0.303	0.429	0.181	0.151	0.215	INDETERMINATE	1	TRUE	0	0.47533579619221	2		570	499	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101035	41101035	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	89	613	0	ENST00000373198.4:c.1321A>C	p.Ile441Leu	p.I441L	ENST00000373198	NM_133170.3	441	Atc/Ctc	8/32	0.410840516532464	0	FACETS	0.459	0.409	0.512			1	SUBCLONAL	1	TRUE	0	0.47533579619221	0		613	428	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468406	89468406	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	87	401	0	ENST00000336596.2:c.1940A>T	p.Glu647Val	p.E647V	ENST00000336596	NM_005233.5	647	gAg/gTg	11/17	0.410840516532464	0	FACETS	0.722	0.648	0.799			1	SUBCLONAL	1	TRUE	0	0.47533579619221	0		401	266	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261592	142261592	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	86	381	0	ENST00000350721.4:c.3365A>G	p.Tyr1122Cys	p.Y1122C	ENST00000350721	NM_001184.3	1122	tAt/tGt	17/47	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.47533579619221	2		381	326	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430842	181430842	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs763171566	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	176	782	0	ENST00000325404.1:c.694A>T	p.Thr232Ser	p.T232S	ENST00000325404	NM_003106.3	232	Acc/Tcc	1/1	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.47533579619221	2		782	674	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526191	189526191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	142	724	0	ENST00000264731.3:c.455C>T	p.Pro152Leu	p.P152L	ENST00000264731	NM_003722.4	152	cCc/cTc	4/14	1	2	FACETS	0.996	0.911	1	0.996	0.911	1	CLONAL	1	TRUE	1	0.47533579619221	2		724	600	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955908	55955908	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	103	477	0	ENST00000263923.4:c.3254A>T	p.Gln1085Leu	p.Q1085L	ENST00000263923	NM_002253.2	1085	cAg/cTg	24/30	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.47533579619221	2		477	345	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979534	55979534	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	109	447	0	ENST00000263923.4:c.913T>C	p.Tyr305His	p.Y305H	ENST00000263923	NM_002253.2	305	Tac/Cac	7/30	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.47533579619221	2		447	372	SUCCESS
REST	5978	MSKCC	GRCh37	4	57786021	57786021	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1173497088	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	92	341	0	ENST00000309042.7:c.967A>G	p.Met323Val	p.M323V	ENST00000309042	NM_005612.4	323	Atg/Gtg	3/4	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.47533579619221	2		341	293	SUCCESS
ALB	213	MSKCC	GRCh37	4	74270094	74270094	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	106	395	0	ENST00000295897.4:c.50A>G	p.Tyr17Cys	p.Y17C	ENST00000295897	NM_000477.5	17	tAt/tGt	1/15	0.47533579619221	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.47533579619221	1		395	296	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143044531	143044531	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	62	387	0	ENST00000262992.4:c.1931A>T	p.Gln644Leu	p.Q644L	ENST00000262992	NM_001101669.1	644	cAg/cTg	18/24	0.47533579619221	1	FACETS	0.947	0.831	1	0.947	0.831	1	CLONAL	1	TRUE	0	0.47533579619221	1		387	210	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945048	38945048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	49	468	0	ENST00000357387.3:c.4756G>A	p.Ala1586Thr	p.A1586T	ENST00000357387	NM_152756.3	1586	Gct/Act	35/38	0.180549692849752	2	FACETS	0.454	0.385	0.53	0.227	0.192	0.265	INDETERMINATE	1	TRUE	0	0.47533579619221	2		468	454	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687113	176687113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	72	472	1	ENST00000439151.2:c.5090G>A	p.Arg1697Gln	p.R1697Q	ENST00000439151	NM_022455.4	1697	cGg/cAg	14/23	0.180549692849752	2	FACETS	0.602	0.527	0.683	0.301	0.263	0.342	INDETERMINATE	1	TRUE	0	0.47533579619221	2		473	503	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168650	32168650	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	193	543	0	ENST00000375023.3:c.4273C>A	p.Leu1425Met	p.L1425M	ENST00000375023	NM_004557.3	1425	Ctg/Atg	23/30	0.165944998225862	6	FACETS	1	0.97	1	0.721	0.669	0.775	INDETERMINATE	2	TRUE	3	0.47533579619221	6		543	732	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005246	150005246	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	210	621	0	ENST00000253339.5:c.979A>G	p.Arg327Gly	p.R327G	ENST00000253339		327	Aga/Gga	3/7	0.195187890827617	3	FACETS	1	0.975	1	0.719	0.674	0.764	INDETERMINATE	2	TRUE	0	0.47533579619221	3		621	507	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222658	157222658	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	52	622	0	ENST00000346085.5:c.1925A>T	p.Gln642Leu	p.Q642L	ENST00000346085	NM_020732.3	642	cAg/cTg	4/20	0.195187890827617	3	FACETS	0.411	0.349	0.479	0.137	0.116	0.16	INDETERMINATE	1	TRUE	0	0.47533579619221	3		622	659	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509313	106509313	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	97	612	0	ENST00000359195.3:c.1307G>C	p.Gly436Ala	p.G436A	ENST00000359195	NM_002649.2	436	gGt/gCt	2/11	1	2	FACETS	0.77	0.689	0.856	0.77	0.689	0.856	SUBCLONAL	1	TRUE	1	0.47533579619221	2		612	530	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859246	151859246	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	88	479	0	ENST00000262189.6:c.11416A>G	p.Lys3806Glu	p.K3806E	ENST00000262189	NM_170606.2	3806	Aag/Gag	43/59	1	2	FACETS	0.969	0.865	1	0.969	0.865	1	CLONAL	1	TRUE	1	0.47533579619221	2		479	382	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981288	68981288	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	22	309	0	ENST00000288368.4:c.1360A>T	p.Lys454Ter	p.K454*	ENST00000288368	NM_024870.2	454	Aaa/Taa	12/40	0.398816995481091	1	FACETS	0.418	0.326	0.522	0.418	0.326	0.522	SUBCLONAL	1	TRUE	0	0.47533579619221	1		309	169	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570352	87570352	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	134	712	0	ENST00000277120.3:c.2092T>A	p.Cys698Ser	p.C698S	ENST00000277120		698	Tgc/Agc	17/19	1	2	FACETS	0.972	0.887	1	0.972	0.887	1	CLONAL	1	TRUE	1	0.47533579619221	2		712	580	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15808622	15808622	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	109	351	0	ENST00000307771.7:c.4G>T	p.Ala2Ser	p.A2S	ENST00000307771	NM_005089.3	2	Gct/Tct	1/11	0.365905448439437	1	FACETS	0.922	0.836	1	0.922	0.836	1	CLONAL	1	TRUE	0	0.47533579619221	1		351	379	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918313	44918313	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	85	361	0	ENST00000377967.4:c.938A>C	p.Lys313Thr	p.K313T	ENST00000377967	NM_021140.2	313	aAa/aCa	11/29	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.47533579619221	2		361	286	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345213	70345213	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	43	497	0	ENST00000374080.3:c.2239A>T	p.Ser747Cys	p.S747C	ENST00000374080		747	Agc/Tgc	16/45	0.439718018346848	1	FACETS	0.293	0.245	0.347	0.293	0.245	0.347	SUBCLONAL	1	TRUE	0	0.47533579619221	1		497	470	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855929	76855929	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	15	432	0	ENST00000373344.5:c.5671C>A	p.Leu1891Ile	p.L1891I	ENST00000373344	NM_000489.3	1891	Cta/Ata	23/35	0.439718018346848	1	FACETS	0.186	0.135	0.246	0.186	0.135	0.246	SUBCLONAL	1	TRUE	0	0.47533579619221	1		432	259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0062166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	73	712	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	1	2	FACETS	0.584	0.509	0.664	0.584	0.509	0.664	SUBCLONAL	1	FALSE	1	0.3	2		712	834	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508473	106508473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370328855	NA	P-0062167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	179	514	0	ENST00000359195.3:c.467C>T	p.Ala156Val	p.A156V	ENST00000359195	NM_002649.2	156	gCg/gTg	2/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.784292717623904	2		514	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577098	7577098	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1567547687	NA	P-0062167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	470	537	0	ENST00000269305.4:c.840A>C	p.Arg280Ser	p.R280S	ENST00000269305	NM_001126112.2	280	agA/agC	8/11	0.767714997802274	2	FACETS	0.997	0.971	1	0.997	0.971	1	CLONAL	2	FALSE	0	0.784292717623904	2		537	601	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422279	47422279	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	185	522	0	ENST00000404338.3:c.347A>G	p.Tyr116Cys	p.Y116C	ENST00000404338	NM_004491.4	116	tAt/tGt	1/6	0.742514663637836	3	FACETS	0.937	0.868	1			1	CLONAL	1	FALSE	NA	0.784292717623904	3		522	701	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578204	7578204	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520001	NA	P-0062168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	41	624	0	ENST00000269305.4:c.645T>G	p.Ser215Arg	p.S215R	ENST00000269305	NM_001126112.2	215	agT/agG	6/11	1	2	FACETS	0.123	0.102	0.146	0.123	0.102	0.146	SUBCLONAL	1	TRUE	1	0.968435205505677	2		624	690	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348754	11348754	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	90	518	0	ENST00000332029.2:c.582C>G	p.Ile194Met	p.I194M	ENST00000332029	NM_003745.1	194	atC/atG	2/2	1	2	FACETS	0.294	0.26	0.329	0.294	0.26	0.329	SUBCLONAL	1	TRUE	1	0.968435205505677	2		518	633	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224211	36224263	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCGCCACCCCCTCCCCTGACGCTGGTGCTGAGCAGTGGGCCAGCCAGCCCG	CCCCGCCACCCCCTCCCCTGACGCTGGTGCTGAGCAGTGGGCCAGCCAGCCCG	-	novel	NA	P-0062168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	36	442	0	ENST00000222270.7:c.6769_6821del	p.Pro2257GlyfsTer28	p.P2257Gfs*28	ENST00000222270	NM_014727.1	2254	cCCCCGCCACCCCCTCCCCTGACGCTGGTGCTGAGCAGTGGGCCAGCCAGCCCG/c	28/37	1	2	FACETS	0.183	0.15	0.22	0.183	0.15	0.22	SUBCLONAL	1	TRUE	1	0.968435205505677	2		442	406	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0062170-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	105	304	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.223324814586365	3	FACETS	0.893	0.807	0.983	1	0.979	1	CLONAL	3	TRUE	1	0.223324814586365	3		304	390	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0062170-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	42	340	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.985	0.824	1	0.985	0.824	1	CLONAL	1	TRUE	1	0.223324814586365	2		340	382	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920413	114920413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767830105	NA	P-0062170-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	70	491	0	ENST00000543371.1:c.1354G>A	p.Gly452Arg	p.G452R	ENST00000543371	NM_001198531.1	452	Ggg/Agg	13/14	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.223324814586365	2		491	523	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920435	114920435	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062170-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	93	401	0	ENST00000543371.1:c.1376G>A	p.Trp459Ter	p.W459*	ENST00000543371	NM_001198531.1	459	tGg/tAg	13/14	1	2	FACETS	0.778	0.694	0.868	1	0.981	1	SUBCLONAL	2	TRUE	1	0.223324814586365	2		401	535	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701188	43701188	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062170-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	96	501	0	ENST00000382044.4:c.5507T>G	p.Val1836Gly	p.V1836G	ENST00000382044	NM_001141980.1	1836	gTc/gGc	26/28	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.223324814586365	2		501	702	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0062185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	151	515	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.933	0.86	1	0.933	0.86	1	CLONAL	1	TRUE	1	0.663036094248288	2		515	488	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0062185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	109	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.964	0.876	1	0.964	0.876	1	CLONAL	1	TRUE	1	0.663036094248288	2		429	341	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30323880	30323880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	131	265	0	ENST00000322652.5:c.1858C>T	p.His620Tyr	p.H620Y	ENST00000322652	NM_015355.2	620	Cat/Tat	15/16	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.663036094248288	2		265	381	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627662	14627664	+	frameshift_variant	Frame_Shift_Del	DEL	CAT	CAT	TA	novel	NA	P-0062185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	196	583	1	ENST00000254322.2:c.406_408delinsTA	p.Met136Ter	p.M136*	ENST00000254322	NM_006145.1	136	ATG/TA	2/3	1	2	FACETS	0.99	0.922	1	0.99	0.922	1	CLONAL	1	TRUE	1	0.663036094248288	2		584	597	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546862	9546862	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	186	571	0	ENST00000353224.5:c.1160C>T	p.Ser387Phe	p.S387F	ENST00000353224	NM_177990.2	387	tCc/tTc	5/10	1	2	FACETS	0.959	0.891	1	0.959	0.891	1	CLONAL	1	TRUE	1	0.663036094248288	2		571	585	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955960	55955960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs895270961	NA	P-0062185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	169	403	0	ENST00000263923.4:c.3202C>T	p.Pro1068Ser	p.P1068S	ENST00000263923	NM_002253.2	1068	Cct/Tct	24/30	1	2	FACETS	0.984	0.911	1	0.984	0.911	1	CLONAL	1	TRUE	1	0.663036094248288	2		403	518	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967835	93967835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138518092	NA	P-0062185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	177	377	0	ENST00000369303.4:c.2092G>A	p.Glu698Lys	p.E698K	ENST00000369303	NM_004440.3	698	Gaa/Aaa	11/17	0.663036094248288	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.663036094248288	1		377	324	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411809	116411809	+	intron_variant	Intron	SNP	C	C	T	novel	NA	P-0062185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	231	534	0	ENST00000397752.3:c.2888-94C>T		p.*963*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.663036094248288	2		534	662	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401024	139401025	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0062185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	187	513	0	ENST00000277541.6:c.3968_3969delinsTT	p.Ala1323Val	p.A1323V	ENST00000277541	NM_017617.3	1323	gCC/gTT	24/34	0.663036094248288	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.663036094248288	1		513	350	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608325	100608325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	126	412	0	ENST00000308731.7:c.1765G>A	p.Glu589Lys	p.E589K	ENST00000308731	NM_000061.2	589	Gaa/Aaa	18/19	1	2	FACETS	0.85	0.776	0.928	0.85	0.776	0.928	CLONAL	1	TRUE	1	0.663036094248288	2		412	447	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627662	14627662	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	195	584	0	ENST00000254322.2:c.408G>A	p.Met136Ile	p.M136I	ENST00000254322	NM_006145.1	136	atG/atA	2/3	1	2	FACETS	0.992	0.924	1	0.992	0.924	1	CLONAL	1	TRUE	1	0.663036094248288	2		584	593	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729094	66729099	+	inframe_deletion	In_Frame_Del	DEL	TGGAGA	TGGAGA	-	novel	NA	P-0062189-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	207	523	0	ENST00000307102.5:c.303_308del	p.Glu102_Ile103del	p.E102_I103del	ENST00000307102	NM_002755.3	101	cTGGAGAtc/ctc	3/11	0.3	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.32	2		523	635	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934576	NA	P-0062189-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	182	483	0	ENST00000269305.4:c.818G>C	p.Arg273Pro	p.R273P	ENST00000269305	NM_001126112.2	273	cGt/cCt	8/11	0.238884649826519	2	FACETS	0.88	0.816	0.947	0.88	0.816	0.947	CLONAL	2	TRUE	0	0.32	2		483	646	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216576	108216576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062189-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	56	382	0	ENST00000278616.4:c.8525C>T	p.Pro2842Leu	p.P2842L	ENST00000278616	NM_000051.3	2842	cCa/cTa	58/63	1	2	FACETS	0.829	0.712	0.956	0.829	0.712	0.956	CLONAL	1	TRUE	1	0.32	2		382	422	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560491	65560491	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062189-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	99	398	0	ENST00000358664.4:c.106A>G	p.Arg36Gly	p.R36G	ENST00000358664	NM_002382.4	36	Agg/Ggg	3/5	0.3	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	0	0.32	1		398	512	SUCCESS
APC	324	MSKCC	GRCh37	5	112178864	112178865	+	missense_variant	Missense_Mutation	DNP	CG	CG	GT	novel	NA	P-0062189-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	89	459	0	ENST00000257430.4:c.7573_7574delinsGT	p.Arg2525Val	p.R2525V	ENST00000257430	NM_000038.5	2525	CGc/GTc	16/16	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.32	2		459	540	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372409	55372409	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062189-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	71	620	0	ENST00000297316.4:c.1099C>G	p.Leu367Val	p.L367V	ENST00000297316	NM_022454.3	367	Ctg/Gtg	2/2	1	2	FACETS	0.888	0.776	1	0.888	0.776	1	CLONAL	1	TRUE	1	0.32	2		620	500	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939118	76939118	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062189-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	65	467	0	ENST00000373344.5:c.1630C>A	p.His544Asn	p.H544N	ENST00000373344	NM_000489.3	544	Cat/Aat	9/35	1	2	FACETS	0.67	0.581	0.767	0.67	0.581	0.767	SUBCLONAL	1	TRUE	1	0.32	2		467	606	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	224	563	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	0.967	0.905	1	0.967	0.905	1	CLONAL	1	TRUE	1	0.702075107574979	2		563	660	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920467	134920467	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	282	499	0	ENST00000398015.3:c.2282C>T	p.Ser761Phe	p.S761F	ENST00000398015	NM_004441.4	761	tCc/tTc	12/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.702075107574979	2		499	748	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636794	8636794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	173	450	0	ENST00000356435.5:c.115G>A	p.Gly39Arg	p.G39R	ENST00000356435		39	Gga/Aga	2/35	0.548837129284185	1	FACETS	0.635	0.589	0.682	0.635	0.589	0.682	SUBCLONAL	1	TRUE	0	0.702075107574979	1		450	504	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805121	43805121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	271	609	0	ENST00000372470.3:c.571G>A	p.Glu191Lys	p.E191K	ENST00000372470	NM_005373.2	191	Gaa/Aaa	4/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.702075107574979	2		609	732	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484287	8484287	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	154	436	0	ENST00000356435.5:c.3245C>T	p.Ser1082Leu	p.S1082L	ENST00000356435		1082	tCa/tTa	19/35	0.548837129284185	1	FACETS	0.607	0.56	0.655	0.607	0.56	0.655	SUBCLONAL	1	TRUE	0	0.702075107574979	1		436	469	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872696	136872696	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	260	627	0	ENST00000241393.3:c.802G>A	p.Glu268Lys	p.E268K	ENST00000241393	NM_003467.2	268	Gaa/Aaa	2/2	1	2	FACETS	0.961	0.904	1	0.961	0.904	1	CLONAL	1	TRUE	1	0.702075107574979	2		627	771	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610162	43610162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	473	624	0	ENST00000355710.3:c.2114C>T	p.Ser705Phe	p.S705F	ENST00000355710	NM_020975.4	705	tCc/tTc	11/20	0.702075107574979	3	FACETS	0.987	0.949	1	0.987	0.949	1	CLONAL	2	TRUE	1	0.702075107574979	3		624	922	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755732	39755732	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	230	497	1	ENST00000288319.7:c.1033G>A	p.Asp345Asn	p.D345N	ENST00000288319	NM_182918.3	345	Gac/Aac	10/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.702075107574979	2		498	614	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391340	139391340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1341934554	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	188	628	0	ENST00000277541.6:c.6851C>T	p.Thr2284Ile	p.T2284I	ENST00000277541	NM_017617.3	2284	aCc/aTc	34/34	0.548837129284185	1	FACETS	0.69	0.643	0.737	0.69	0.643	0.737	SUBCLONAL	1	TRUE	0	0.702075107574979	1		628	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574004	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	246	423	0	ENST00000269305.4:c.1023_1024delinsTT	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	341	ttCCga/ttTTga	10/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.702075107574979	2		423	573	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858306	9858306	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	224	529	0	ENST00000330684.3:c.3095C>T	p.Ser1032Phe	p.S1032F	ENST00000330684	NM_001134407.1	1032	tCc/tTc	13/13	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.702075107574979	2		529	638	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262096	10262096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	292	512	0	ENST00000340748.4:c.2195C>T	p.Ser732Phe	p.S732F	ENST00000340748		732	tCt/tTt	23/40	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.702075107574979	2		512	768	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043372	180043373	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	240	610	0	ENST00000261937.6:c.3213_3214delinsAA	p.Gly1072Ser	p.G1072S	ENST00000261937	NM_182925.4	1071	aaGGgc/aaAAgc	23/30	1	2	FACETS	0.919	0.862	0.978	0.919	0.862	0.978	CLONAL	1	TRUE	1	0.702075107574979	2		610	744	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268985	142268985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs911751877	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	170	300	0	ENST00000350721.4:c.2965C>T	p.Arg989Cys	p.R989C	ENST00000350721	NM_001184.3	989	Cgt/Tgt	14/47	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.702075107574979	2		300	464	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549127	87549127	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	195	477	0	ENST00000277120.3:c.1684G>A	p.Glu562Lys	p.E562K	ENST00000277120		562	Gaa/Aaa	15/19	0.548837129284185	1	FACETS	0.765	0.716	0.816	0.765	0.716	0.816	SUBCLONAL	1	TRUE	0	0.702075107574979	1		477	471	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504281	8504281	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1455551669	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	151	450	0	ENST00000356435.5:c.1802C>T	p.Ser601Leu	p.S601L	ENST00000356435		601	tCa/tTa	12/35	0.548837129284185	1	FACETS	0.639	0.589	0.689	0.639	0.589	0.689	SUBCLONAL	1	TRUE	0	0.702075107574979	1		450	437	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570097	212570097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	167	361	0	ENST00000342788.4:c.1144G>A	p.Glu382Lys	p.E382K	ENST00000342788	NM_005235.2	382	Gaa/Aaa	10/28	1	2	FACETS	0.942	0.872	1	0.942	0.872	1	CLONAL	1	TRUE	1	0.702075107574979	2		361	505	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371996	55371996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	192	550	0	ENST00000297316.4:c.686G>A	p.Gly229Asp	p.G229D	ENST00000297316	NM_022454.3	229	gGc/gAc	2/2	0.350612671406793	1	FACETS	0.796	0.745	0.848	0.796	0.745	0.848	INDETERMINATE	1	TRUE	0	0.702075107574979	1		550	446	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046590	30046590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	243	453	0	ENST00000331968.5:c.2593G>A	p.Asp865Asn	p.D865N	ENST00000331968	NM_002742.2	865	Gat/Aat	18/18	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.702075107574979	2		453	611	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082895	16082895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1412185126	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	129	382	0	ENST00000281043.3:c.709C>T	p.Pro237Ser	p.P237S	ENST00000281043	NM_005378.4	237	Ccg/Tcg	2/3	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.702075107574979	2		382	337	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981782	70981782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141129543	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	147	490	0	ENST00000276594.2:c.314C>T	p.Pro105Leu	p.P105L	ENST00000276594	NM_024504.3	105	cCc/cTc	2/8	0.350612671406793	1	FACETS	0.508	0.466	0.551	0.508	0.466	0.551	INDETERMINATE	1	TRUE	0	0.702075107574979	1		490	535	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521723	89521723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767387399	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	179	453	0	ENST00000336596.2:c.2800G>A	p.Gly934Ser	p.G934S	ENST00000336596	NM_005233.5	934	Ggt/Agt	16/17	1	2	FACETS	0.786	0.727	0.846	0.786	0.727	0.846	SUBCLONAL	1	TRUE	1	0.702075107574979	2		453	649	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245613	46245613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	262	525	0	ENST00000334344.6:c.3707C>T	p.Pro1236Leu	p.P1236L	ENST00000334344	NM_152641.2	1236	cCa/cTa	15/21	1	2	FACETS	0.957	0.9	1	0.957	0.9	1	CLONAL	1	TRUE	1	0.702075107574979	2		525	780	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665629	86665629	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	67	291	0	ENST00000274376.6:c.1611-1G>A		p.X537_splice	ENST00000274376	NM_002890.2	537			1	2	FACETS	0.785	0.691	0.884	0.785	0.691	0.884	SUBCLONAL	1	TRUE	1	0.702075107574979	2		291	243	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741958	162741958	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	298	516	0	ENST00000367921.3:c.1649G>A	p.Gly550Glu	p.G550E	ENST00000367921	NM_006182.2	550	gGa/gAa	13/18	0.381583461503707	1	FACETS	0.896	0.851	0.94	0.896	0.851	0.94	INDETERMINATE	1	TRUE	0	0.702075107574979	1		516	615	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055898	180055898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	187	473	0	ENST00000261937.6:c.1087C>T	p.Pro363Ser	p.P363S	ENST00000261937	NM_182925.4	363	Ccg/Tcg	8/30	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.702075107574979	2		473	532	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855609	45855609	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs758439420	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	268	593	0	ENST00000391945.4:c.2048G>A	p.Arg683Gln	p.R683Q	ENST00000391945	NM_000400.3	683	cGg/cAg	22/23	0.702075107574979	3	FACETS	1	0.974	1	0.533	0.501	0.567	CLONAL	1	TRUE	1	0.702075107574979	3		593	967	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211675	36211675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	223	638	0	ENST00000222270.7:c.1426C>T	p.Pro476Ser	p.P476S	ENST00000222270	NM_014727.1	476	Ccc/Tcc	3/37	0.702075107574979	3	FACETS	0.974	0.908	1	0.487	0.454	0.521	CLONAL	1	TRUE	1	0.702075107574979	3		638	881	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212113	36212113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757405245	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	116	284	0	ENST00000222270.7:c.1864C>T	p.Pro622Ser	p.P622S	ENST00000222270	NM_014727.1	622	Ccc/Tcc	3/37	0.702075107574979	3	FACETS	1	0.941	1	0.524	0.476	0.574	CLONAL	1	TRUE	1	0.702075107574979	3		284	426	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303107	15303107	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	261	666	0	ENST00000263388.2:c.343C>T	p.Pro115Ser	p.P115S	ENST00000263388	NM_000435.2	115	Cct/Tct	4/33	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.702075107574979	2		666	721	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221162	5221162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	296	619	0	ENST00000357368.4:c.3304C>T	p.Arg1102Cys	p.R1102C	ENST00000357368	NM_002850.3	1102	Cgc/Tgc	20/38	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.702075107574979	2		619	778	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061148	38061148	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1300427032	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	177	545	0	ENST00000250448.2:c.841G>A	p.Gly281Arg	p.G281R	ENST00000250448	NM_004496.3	281	Gga/Aga	2/2	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.702075107574979	2		545	471	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647482	23647482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1174443228	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	179	368	0	ENST00000261584.4:c.385C>T	p.Pro129Ser	p.P129S	ENST00000261584	NM_024675.3	129	Ccc/Tcc	4/13	1	2	FACETS	0.943	0.875	1	0.943	0.875	1	CLONAL	1	TRUE	1	0.702075107574979	2		368	541	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341712	8341712	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	106	446	0	ENST00000356435.5:c.4928G>A	p.Gly1643Glu	p.G1643E	ENST00000356435		1643	gGa/gAa	29/35	0.548837129284185	1	FACETS	0.513	0.464	0.564	0.513	0.464	0.564	SUBCLONAL	1	TRUE	0	0.702075107574979	1		446	382	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604509	43604509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763670106	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	443	517	0	ENST00000355710.3:c.1094C>T	p.Ser365Leu	p.S365L	ENST00000355710	NM_020975.4	365	tCg/tTg	6/20	0.702075107574979	3	FACETS	0.972	0.933	1	0.972	0.933	1	CLONAL	2	TRUE	1	0.702075107574979	3		517	877	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143350350	143350350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	79	183	0	ENST00000262992.4:c.112G>A	p.Glu38Lys	p.E38K	ENST00000262992	NM_001101669.1	38	Gaa/Aaa	3/24	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.702075107574979	2		183	219	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433682	149433682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	189	460	0	ENST00000286301.3:c.2869G>A	p.Gly957Arg	p.G957R	ENST00000286301	NM_005211.3	957	Ggg/Agg	22/22	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.702075107574979	2		460	497	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932904	49932904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	252	661	0	ENST00000296474.3:c.3040G>A	p.Gly1014Ser	p.G1014S	ENST00000296474	NM_002447.2	1014	Ggc/Agc	13/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.702075107574979	2		661	693	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209256	133209256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500801	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	187	582	0	ENST00000320574.5:c.6130C>T	p.Leu2044Phe	p.L2044F	ENST00000320574	NM_006231.2	2044	Ctt/Ttt	44/49	1	2	FACETS	0.93	0.864	0.997	0.93	0.864	0.997	CLONAL	1	TRUE	1	0.702075107574979	2		582	573	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437675	52437675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	222	538	0	ENST00000460680.1:c.1486G>A	p.Ala496Thr	p.A496T	ENST00000460680	NM_004656.3	496	Gcc/Acc	13/17	1	2	FACETS	0.94	0.879	1	0.94	0.879	1	CLONAL	1	TRUE	1	0.702075107574979	2		538	673	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995487	68995487	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	57	338	0	ENST00000288368.4:c.1891G>A	p.Glu631Lys	p.E631K	ENST00000288368	NM_024870.2	631	Gaa/Aaa	18/40	0.350612671406793	1	FACETS	0.329	0.284	0.378	0.329	0.284	0.378	INDETERMINATE	1	TRUE	0	0.702075107574979	1		338	320	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760671	59760671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	171	340	0	ENST00000259008.2:c.3736C>T	p.Pro1246Ser	p.P1246S	ENST00000259008	NM_032043.2	1246	Cct/Tct	20/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.702075107574979	2		340	439	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784346	9784346	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	215	502	0	ENST00000377346.4:c.2731G>A	p.Asp911Asn	p.D911N	ENST00000377346	NM_005026.3	911	Gat/Aat	22/24	1	2	FACETS	0.942	0.881	1	0.942	0.881	1	CLONAL	1	TRUE	1	0.702075107574979	2		502	650	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11269422	11269422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	218	473	0	ENST00000361445.4:c.3748G>A	p.Val1250Met	p.V1250M	ENST00000361445	NM_004958.3	1250	Gtg/Atg	25/58	1	2	FACETS	0.995	0.931	1	0.995	0.931	1	CLONAL	1	TRUE	1	0.702075107574979	2		473	624	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28600562	28600562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	216	473	0	ENST00000253063.3:c.913G>A	p.Glu305Lys	p.E305K	ENST00000253063	NM_031459.4	305	Gag/Aag	7/10	NA	2	FACETS	0.98	0.916	1			1	INDETERMINATE	1	TRUE	NA	0.702075107574979	2		473	628	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551357	150551381	+	frameshift_variant	Frame_Shift_Del	DEL	CCAACCCGTCGTAAGGTCTCCAGCG	CCAACCCGTCGTAAGGTCTCCAGCG	-	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	156	595	0	ENST00000369026.2:c.626_650del	p.Ala209GlyfsTer27	p.A209Gfs*27	ENST00000369026	NM_021960.4	209	gCGCTGGAGACCTTACGACGGGTTGGg/gg	1/3	NA	2	FACETS	0.622	0.571	0.676			1	INDETERMINATE	1	TRUE	NA	0.702075107574979	2		595	714	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230486825	230486825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766587228	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	112	453	0	ENST00000391860.1:c.428C>T	p.Pro143Leu	p.P143L	ENST00000391860	NM_001258311.1	143	cCc/cTc	3/7	0.381583461503707	1	FACETS	0.395	0.357	0.436	0.395	0.357	0.436	INDETERMINATE	1	TRUE	0	0.702075107574979	1		453	524	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112745407	112745407	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	83	358	0	ENST00000369452.4:c.725C>G	p.Thr242Arg	p.T242R	ENST00000369452	NM_007373.3	242	aCg/aGg	3/9	0.674809251818991	2	FACETS	0.556	0.493	0.623	0.278	0.246	0.312	SUBCLONAL	1	TRUE	0	0.702075107574979	2		358	425	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425614	49425614	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	235	637	0	ENST00000301067.7:c.12874C>T	p.Pro4292Ser	p.P4292S	ENST00000301067	NM_003482.3	4292	Cca/Tca	39/54	0.702075107574979	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.702075107574979	1		637	429	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95597845	95597845	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	134	341	0	ENST00000393063.1:c.438+1G>A		p.X146_splice	ENST00000393063	NM_030621.3	146			1	2	FACETS	0.936	0.858	1	0.936	0.858	1	CLONAL	1	TRUE	1	0.702075107574979	2		341	408	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749397	43749397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	108	376	0	ENST00000382044.4:c.1409C>T	p.Pro470Leu	p.P470L	ENST00000382044	NM_001141980.1	470	cCa/cTa	12/28	0.24357446782931	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.702075107574979	0		376	385	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478061	99478061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	161	430	0	ENST00000268035.6:c.2965C>T	p.Pro989Ser	p.P989S	ENST00000268035	NM_000875.3	989	Cct/Tct	16/21	0.204315003833516	2	FACETS	0.67	0.616	0.725	0.335	0.308	0.363	INDETERMINATE	1	TRUE	0	0.702075107574979	2		430	685	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799635	3799635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778840635	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	91	261	0	ENST00000262367.5:c.3829C>T	p.Pro1277Ser	p.P1277S	ENST00000262367	NM_004380.2	1277	Ccc/Tcc	21/31	1	2	FACETS	0.96	0.865	1	0.96	0.865	1	CLONAL	1	TRUE	1	0.702075107574979	2		261	270	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836635	89836635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	211	484	0	ENST00000389301.3:c.2255C>T	p.Thr752Ile	p.T752I	ENST00000389301	NM_000135.2	752	aCc/aTc	25/43	0.702075107574979	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.702075107574979	1		484	351	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679664	33679664	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	243	584	0	ENST00000308377.4:c.2417C>T	p.Pro806Leu	p.P806L	ENST00000308377	NM_152270.3	806	cCa/cTa	5/5	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.702075107574979	2		584	614	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350535	15350535	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	196	467	1	ENST00000263377.2:c.3380C>T	p.Pro1127Leu	p.P1127L	ENST00000263377	NM_058243.2	1127	cCc/cTc	16/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.702075107574979	2		468	525	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277969	18277969	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	236	436	0	ENST00000222254.8:c.1589C>T	p.Ser530Phe	p.S530F	ENST00000222254	NM_005027.3	530	tCc/tTc	13/16	0.702075107574979	3	FACETS	1	0.985	1	0.581	0.544	0.619	CLONAL	1	TRUE	1	0.702075107574979	3		436	782	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211675	36211676	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	225	638	0	ENST00000222270.7:c.1426_1427delinsTT	p.Pro476Phe	p.P476F	ENST00000222270	NM_014727.1	476	CCc/TTc	3/37	0.702075107574979	3	FACETS	0.983	0.917	1	0.491	0.458	0.526	CLONAL	1	TRUE	1	0.702075107574979	3		638	881	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505322	25505322	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	197	470	0	ENST00000264709.3:c.436C>T	p.Pro146Ser	p.P146S	ENST00000264709	NM_175629.2	146	Cct/Tct	4/23	1	2	FACETS	0.951	0.886	1	0.951	0.886	1	CLONAL	1	TRUE	1	0.702075107574979	2		470	590	SUCCESS
REL	5966	MSKCC	GRCh37	2	61144085	61144086	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	105	366	0	ENST00000295025.8:c.468_469delinsTT	p.Pro157Ser	p.P157S	ENST00000295025	NM_002908.2	156	ctCCct/ctTTct	5/11	1	2	FACETS	0.798	0.721	0.877	0.798	0.721	0.877	SUBCLONAL	1	TRUE	1	0.702075107574979	2		366	375	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732526	190732526	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	113	345	0	ENST00000441310.2:c.2344C>T	p.Leu782Phe	p.L782F	ENST00000441310	NM_000534.4	782	Ctt/Ttt	11/13	1	2	FACETS	0.984	0.897	1	0.984	0.897	1	CLONAL	1	TRUE	1	0.702075107574979	2		345	327	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589899	212589899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	211	391	0	ENST00000342788.4:c.643G>A	p.Glu215Lys	p.E215K	ENST00000342788	NM_005235.2	215	Gaa/Aaa	6/28	1	2	FACETS	0.951	0.888	1	0.951	0.888	1	CLONAL	1	TRUE	1	0.702075107574979	2		391	632	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561457	9561457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	295	526	0	ENST00000353224.5:c.325G>A	p.Asp109Asn	p.D109N	ENST00000353224	NM_177990.2	109	Gat/Aat	4/10	0.702075107574979	3	FACETS	1	0.946	1	0.502	0.473	0.533	CLONAL	1	TRUE	1	0.702075107574979	3		526	1130	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022862	31022863	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	255	612	1	ENST00000375687.4:c.2347_2348delinsTT	p.Pro783Leu	p.P783L	ENST00000375687	NM_015338.5	783	CCg/TTg	13/13	0.702075107574979	3	FACETS	1	0.938	1	0.501	0.469	0.533	CLONAL	1	TRUE	1	0.702075107574979	3		613	980	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755710	39755710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	219	509	0	ENST00000288319.7:c.1055G>A	p.Gly352Glu	p.G352E	ENST00000288319	NM_182918.3	352	gGa/gAa	10/10	1	2	FACETS	0.969	0.906	1	0.969	0.906	1	CLONAL	1	TRUE	1	0.702075107574979	2		509	644	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940637	49940637	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	233	550	0	ENST00000296474.3:c.406G>A	p.Gly136Ser	p.G136S	ENST00000296474	NM_002447.2	136	Ggc/Agc	1/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.702075107574979	2		550	635	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259329	89259329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1342457962	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	196	581	0	ENST00000336596.2:c.473G>A	p.Gly158Glu	p.G158E	ENST00000336596	NM_005233.5	158	gGg/gAg	3/17	1	2	FACETS	0.953	0.888	1	0.953	0.888	1	CLONAL	1	TRUE	1	0.702075107574979	2		581	586	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670821	134670822	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	232	507	0	ENST00000398015.3:c.732_733delinsAA	p.Glu245Lys	p.E245K	ENST00000398015	NM_004441.4	244	ggGGaa/ggAAaa	3/16	1	2	FACETS	0.972	0.911	1	0.972	0.911	1	CLONAL	1	TRUE	1	0.702075107574979	2		507	680	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456557	138456557	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	101	271	0	ENST00000289153.2:c.793C>T	p.Gln265Ter	p.Q265*	ENST00000289153	NM_006219.2	265	Cag/Tag	4/22	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.702075107574979	2		271	274	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146703	185146703	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1430375992	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	296	504	0	ENST00000265026.3:c.334G>A	p.Gly112Arg	p.G112R	ENST00000265026	NM_004721.4	112	Gga/Aga	2/14	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.702075107574979	2		504	838	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805519	1805519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199702395	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	198	539	0	ENST00000260795.2:c.1031C>T	p.Ser344Phe	p.S344F	ENST00000260795		344	tCt/tTt	7/17	0.310400788200895	1	FACETS	0.58	0.54	0.621	0.58	0.54	0.621	INDETERMINATE	1	TRUE	0	0.702075107574979	1		539	631	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127450	55127450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	323	529	0	ENST00000257290.5:c.238C>T	p.Leu80Phe	p.L80F	ENST00000257290	NM_006206.4	80	Ctt/Ttt	3/23	0.702075107574979	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.702075107574979	1		529	516	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029265	143029265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1287821311	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	112	273	0	ENST00000262992.4:c.2355G>A	p.Met785Ile	p.M785I	ENST00000262992	NM_001101669.1	785	atG/atA	21/24	1	2	FACETS	0.955	0.869	1	0.955	0.869	1	CLONAL	1	TRUE	1	0.702075107574979	2		273	334	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295782	1295782	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	322	648	0				ENST00000310581	NM_198253.2	-/1132			0.634510623671922	3	FACETS	1	0.989	1	0.588	0.556	0.621	CLONAL	1	TRUE	1	0.702075107574979	3		648	1054	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039580	180039580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762925852	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	230	503	0	ENST00000261937.6:c.3463G>A	p.Asp1155Asn	p.D1155N	ENST00000261937	NM_182925.4	1155	Gac/Aac	26/30	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.702075107574979	2		503	586	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680835	30680836	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	273	634	0	ENST00000376406.3:c.883_884delinsTT	p.Pro295Phe	p.P295F	ENST00000376406	NM_014641.2	295	CCt/TTt	5/15	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.702075107574979	2		634	770	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651954	36651954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	282	547	0	ENST00000244741.5:c.76G>A	p.Asp26Asn	p.D26N	ENST00000244741	NM_000389.4	26	Gac/Aac	2/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.702075107574979	2		547	742	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552879	106552888	+	frameshift_variant	Frame_Shift_Del	DEL	GACTTTAGAA	GACTTTAGAA	-	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	542	602	0	ENST00000369096.4:c.847_856del	p.Phe283ValfsTer25	p.F283Vfs*25	ENST00000369096	NM_001198.3	282	GACTTTAGAAga/ga	5/7	0.663480510895899	2	FACETS	0.903	0.875	0.931	0.903	0.875	0.931	CLONAL	2	TRUE	0	0.702075107574979	2		602	855	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467900	50467900	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	259	579	0	ENST00000331340.3:c.1135G>A	p.Ala379Thr	p.A379T	ENST00000331340	NM_006060.4	379	Gcc/Acc	8/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.702075107574979	2		579	647	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358994	81358994	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	166	400	0	ENST00000222390.5:c.967G>A	p.Gly323Arg	p.G323R	ENST00000222390	NM_000601.4	323	Gga/Aga	8/18	1	2	FACETS	0.827	0.764	0.892	0.827	0.764	0.892	CLONAL	1	TRUE	1	0.702075107574979	2		400	572	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509196	106509197	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	285	598	0	ENST00000359195.3:c.1190_1191delinsAA	p.Arg397Lys	p.R397K	ENST00000359195	NM_002649.2	397	aGG/aAA	2/11	1	2	FACETS	0.971	0.916	1	0.971	0.916	1	CLONAL	1	TRUE	1	0.702075107574979	2		598	836	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879232	151879233	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	271	584	0	ENST00000262189.6:c.5712_5713delinsTT	p.Pro1905Ser	p.P1905S	ENST00000262189	NM_170606.2	1904	acCCct/acTTct	36/59	1	2	FACETS	0.982	0.925	1	0.982	0.925	1	CLONAL	1	TRUE	1	0.702075107574979	2		584	786	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942864	68942864	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	199	488	0	ENST00000288368.4:c.676G>A	p.Glu226Lys	p.E226K	ENST00000288368	NM_024870.2	226	Gaa/Aaa	6/40	0.350612671406793	1	FACETS	0.695	0.65	0.742	0.695	0.65	0.742	INDETERMINATE	1	TRUE	0	0.702075107574979	1		488	529	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2073339	2073339	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	100	496	0	ENST00000349721.2:c.1874C>T	p.Pro625Leu	p.P625L	ENST00000349721	NM_003070.3	625	cCt/cTt	11/34	0.548837129284185	1	FACETS	0.381	0.342	0.423	0.381	0.342	0.423	SUBCLONAL	1	TRUE	0	0.702075107574979	1		496	485	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2161747	2161747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	176	440	0	ENST00000349721.2:c.4043G>A	p.Arg1348Lys	p.R1348K	ENST00000349721	NM_003070.3	1348	aGa/aAa	28/34	0.548837129284185	1	FACETS	0.736	0.685	0.788	0.736	0.685	0.788	SUBCLONAL	1	TRUE	0	0.702075107574979	1		440	442	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220564	98220564	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs886041943	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	214	451	0	ENST00000331920.6:c.2899G>T	p.Glu967Ter	p.E967*	ENST00000331920	NM_000264.3	967	Gag/Tag	18/24	0.548837129284185	1	FACETS	0.764	0.716	0.812	0.764	0.716	0.812	SUBCLONAL	1	TRUE	0	0.702075107574979	1		451	518	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391980	139391981	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	86	549	0	ENST00000277541.6:c.6210_6211delinsAA	p.Glu2071Lys	p.E2071K	ENST00000277541	NM_017617.3	2070	cgGGag/cgAAag	34/34	0.548837129284185	1	FACETS	0.395	0.351	0.441	0.395	0.351	0.441	SUBCLONAL	1	TRUE	0	0.702075107574979	1		549	403	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879232	151879232	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	270	583	0	ENST00000262189.6:c.5713C>T	p.Pro1905Ser	p.P1905S	ENST00000262189	NM_170606.2	1905	Cct/Tct	36/59	1	2	FACETS	0.985	0.928	1	0.985	0.928	1	CLONAL	1	TRUE	1	0.702075107574979	2		583	781	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432368	432374	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GATATCT	GATATCT	-	novel	NA	P-0062193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	34	200	2	ENST00000399788.2:c.2151-2_2155del		p.X717_splice	ENST00000399788	NM_001042603.1	717		16/28	1	2	FACETS	0.438	0.361	0.524	0.438	0.361	0.524	SUBCLONAL	1	TRUE	1	0.702075107574979	2		202	221	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0062194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	534	464	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.918964466160037	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.918964466160037	2		464	573	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145430	58145430	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894340	NA	P-0062194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	376	594	0	ENST00000257904.6:c.71G>T	p.Arg24Leu	p.R24L	ENST00000257904	NM_000075.3	24	cGt/cTt	2/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.918964466160037	2		594	779	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0062194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	276	335	0	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	0.918964466160037	2	FACETS	1	0.988	1	0.561	0.533	0.59	CLONAL	1	TRUE	0	0.918964466160037	2		335	535	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17349159	17349159	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs186768244	NA	P-0062195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	24	444	0	ENST00000375499.3:c.709C>G	p.Pro237Ala	p.P237A	ENST00000375499	NM_003000.2	237	Cca/Gca	7/8	1	2	FACETS	0.835	0.654	1	0.835	0.654	1	CLONAL	1	TRUE	1	0.13	2		444	442	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000090	30000091	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACTC	novel	NA	P-0062195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	22	405	0	ENST00000338641.4:c.103_104insACTC	p.Phe35TyrfsTer15	p.F35Yfs*15	ENST00000338641	NM_000268.3	35	ttc/tACTCtc	1/16	1	2	FACETS	0.953	0.739	1	0.953	0.739	1	CLONAL	1	TRUE	1	0.13	2		405	355	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163715	47163715	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	17	434	0	ENST00000409792.3:c.2411del	p.Leu804CysfsTer14	p.L804Cfs*14	ENST00000409792	NM_014159.6	804	tTg/tg	3/21	1	2	FACETS	1	0.784	1	1	0.784	1	CLONAL	1	TRUE	1	0.13	2		434	248	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0062196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	18	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.792	1	1	0.792	1	CLONAL	1	TRUE	1	0.11	2		485	309	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0062196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	11	376	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.58	0.399	0.806	0.58	0.399	0.806	SUBCLONAL	1	TRUE	1	0.11	2		376	345	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0062196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	19	375	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	1	0.766	1	1	0.766	1	CLONAL	1	TRUE	1	0.11	2		375	342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0062199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	25	.	.	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.128	0.1	0.16	0.128	0.1	0.16	SUBCLONAL	1	TRUE	1	0.445274233868335	2		0	879	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0062199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	148	409	1	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.985	0.902	1	0.985	0.902	1	CLONAL	1	TRUE	1	0.445274233868335	2		410	675	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0062199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	202	482	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.445274233868335	2		482	778	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190866	185190866	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1178695004	NA	P-0062199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	213	533	0	ENST00000265026.3:c.1747C>T	p.Arg583Ter	p.R583*	ENST00000265026	NM_004721.4	583	Cga/Tga	11/14	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.445274233868335	2		533	826	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692960	89692975	+	frameshift_variant	Frame_Shift_Del	DEL	ACAAGAGGCCCTAGAT	ACAAGAGGCCCTAGAT	GA	novel	NA	P-0062199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	421	411	2	ENST00000371953.3:c.444_459delinsGA	p.Gln149IlefsTer26	p.Q149Ifs*26	ENST00000371953	NM_000314.4	148	gcACAAGAGGCCCTAGAT/gcGA	5/9	0.445274233868335	3	FACETS	0.946	0.907	0.984	0.946	0.907	0.984	CLONAL	3	TRUE	0	0.445274233868335	3		413	815	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696425	47696425	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519967	NA	P-0062200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	129	431	0	ENST00000347630.2:c.398T>C	p.Phe133Ser	p.F133S	ENST00000347630	NM_001007230.1	133	tTc/tCc	6/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.55484660054695	2		431	398	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914547	32914547	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	140	546	0	ENST00000380152.3:c.6056del	p.Asn2019ThrfsTer21	p.N2019Tfs*21	ENST00000380152		2019	Aac/ac	11/27	0.55484660054695	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.55484660054695	1		546	329	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732900	74732900	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	173	455	0	ENST00000359995.5:c.343T>A	p.Tyr115Asn	p.Y115N	ENST00000359995	NM_001195427.1	115	Tac/Aac	1/3	0.443403867627244	3	FACETS	0.926	0.862	0.991	0.926	0.862	0.991	CLONAL	2	TRUE	1	0.55484660054695	3		455	430	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161807864	161807864	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	118	468	0	ENST00000366898.1:c.1129T>A	p.Cys377Ser	p.C377S	ENST00000366898	NM_004562.2	377	Tgc/Agc	10/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.55484660054695	2		468	372	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392071	81392071	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	83	369	0	ENST00000222390.5:c.206A>T	p.Gln69Leu	p.Q69L	ENST00000222390	NM_000601.4	69	cAa/cTa	2/18	0.498623205246724	5	FACETS	0.972	0.859	1	0.243	0.214	0.273	CLONAL	1	TRUE	1	0.55484660054695	5		369	564	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960122	151960139	+	inframe_deletion	In_Frame_Del	DEL	TGGTACTGATTTCATAAC	TGGTACTGATTTCATAAC	-	novel	NA	P-0062200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	17	297	0	ENST00000262189.6:c.1261_1278del	p.Val421_Pro426del	p.V421_P426del	ENST00000262189	NM_170606.2	421	GTTATGAAATCAGTACCA/-	9/59	NA	2	FACETS	0.215	0.16	0.28			1	INDETERMINATE	1	TRUE	NA	0.55484660054695	2		297	285	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224251	98224251	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	69	416	0	ENST00000331920.6:c.2590G>C	p.Glu864Gln	p.E864Q	ENST00000331920	NM_000264.3	864	Gaa/Caa	16/24	0.533838666296832	3	FACETS	0.673	0.588	0.765	0.337	0.294	0.383	SUBCLONAL	1	TRUE	1	0.55484660054695	3		416	472	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918292	44918292	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	60	142	0	ENST00000377967.4:c.917C>G	p.Ser306Cys	p.S306C	ENST00000377967	NM_021140.2	306	tCt/tGt	11/29	1	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.55484660054695	1		142	127	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514998	148515000	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs775039041	NA	P-0062207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	110	531	3	ENST00000320356.2:c.1209_1211del	p.Glu404del	p.E404del	ENST00000320356	NM_004456.4	403	gaAGAg/gag	10/20	0.383820350931009	4	FACETS	1	0.978	1	0.331	0.298	0.366	CLONAL	1	TRUE	0	0.376557401735669	4		534	607	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991961	72991961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1262542686	NA	P-0062207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	164	725	1	ENST00000268489.5:c.2084C>T	p.Pro695Leu	p.P695L	ENST00000268489	NM_006885.3	695	cCg/cTg	2/10	0.376557401735669	6	FACETS	0.975	0.897	1	0.488	0.448	0.529	CLONAL	2	TRUE	2	0.376557401735669	6		726	783	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392096	118392096	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	185	595	0	ENST00000534358.1:c.11607C>G	p.Ile3869Met	p.I3869M	ENST00000534358	NM_005933.3	3869	atC/atG	35/36	0.316755474613134	4	FACETS	0.905	0.838	0.975	0.453	0.419	0.488	CLONAL	2	TRUE	0	0.376557401735669	4		595	747	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993975	72993975	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1193072573	NA	P-0062207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	180	708	0	ENST00000268489.5:c.70T>C	p.Trp24Arg	p.W24R	ENST00000268489	NM_006885.3	24	Tgg/Cgg	2/10	0.376557401735669	6	FACETS	0.952	0.879	1	0.476	0.439	0.515	CLONAL	2	TRUE	2	0.376557401735669	6		708	880	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108559	8108559	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs532696717	NA	P-0062207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	181	676	0	ENST00000585124.1:c.836A>G	p.Asn279Ser	p.N279S	ENST00000585124	NM_004217.3	279	aAc/aGc	8/9	0.316755474613134	4	FACETS	0.97	0.898	1	0.485	0.449	0.523	CLONAL	2	TRUE	0	0.376557401735669	4		676	682	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33433466	33433466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1413648665	NA	P-0062207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	153	537	0	ENST00000345365.6:c.515C>T	p.Ala172Val	p.A172V	ENST00000345365	NM_002878.3	172	gCa/gTa	6/10	0.376557401735669	6	FACETS	0.784	0.717	0.854	0.392	0.358	0.427	SUBCLONAL	2	TRUE	2	0.376557401735669	6		537	909	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353784	15353784	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	102	401	0	ENST00000263377.2:c.3096G>C	p.Gln1032His	p.Q1032H	ENST00000263377	NM_058243.2	1032	caG/caC	14/20	0.316755474613134	4	FACETS	0.888	0.799	0.98	0.444	0.399	0.49	CLONAL	2	TRUE	0	0.376557401735669	4		401	420	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953172	17953172	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	172	629	1	ENST00000458235.1:c.814C>A	p.Arg272Ser	p.R272S	ENST00000458235	NM_000215.3	272	Cgc/Agc	6/24	0.316755474613134	4	FACETS	0.881	0.812	0.951	0.44	0.406	0.476	CLONAL	2	TRUE	0	0.376557401735669	4		630	714	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974307	18974307	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	164	622	0	ENST00000262803.5:c.2661C>G	p.His887Gln	p.H887Q	ENST00000262803	NM_002911.3	887	caC/caG	19/24	0.316755474613134	4	FACETS	0.854	0.786	0.925	0.427	0.393	0.463	CLONAL	2	TRUE	0	0.376557401735669	4		622	702	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324548	62324548	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1474203821	NA	P-0062207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1750	365	731	0	ENST00000360203.5:c.2904T>A	p.Cys968Ter	p.C968*	ENST00000360203	NM_001283009.1	968	tgT/tgA	30/35	0.376557401735669	16	FACETS	1	0.985	1	0.303	0.286	0.321	CLONAL	3	TRUE	5	0.376557401735669	16		731	2115	SUCCESS
ATR	545	MSKCC	GRCh37	3	142286920	142286920	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	76	322	0	ENST00000350721.4:c.136A>T	p.Thr46Ser	p.T46S	ENST00000350721	NM_001184.3	46	Aca/Tca	2/47	0.376557401735669	6	FACETS	0.813	0.716	0.917	0.271	0.238	0.306	CLONAL	2	TRUE	0	0.376557401735669	6		322	435	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157245	106157245	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	173	626	0	ENST00000380013.4:c.2146T>A	p.Ser716Thr	p.S716T	ENST00000380013	NM_001127208.2	716	Tca/Aca	3/11	0.376557401735669	6	FACETS	0.976	0.9	1	0.488	0.45	0.528	CLONAL	2	TRUE	2	0.376557401735669	6		626	825	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045846	26045846	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	212	942	0	ENST00000540144.1:c.208C>A	p.Arg70Ser	p.R70S	ENST00000540144	NM_003531.2	70	Cgc/Agc	1/1	0.376557401735669	6	FACETS	0.832	0.772	0.895	0.416	0.386	0.448	CLONAL	2	TRUE	2	0.376557401735669	6		942	1186	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426039	47426039	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	208	639	0	ENST00000377045.4:c.559C>A	p.Pro187Thr	p.P187T	ENST00000377045	NM_001654.4	187	Ccc/Acc	7/16	0.156444420046753	5	FACETS	0.907	0.847	0.969	0.907	0.847	0.969	INDETERMINATE	3	TRUE	2	0.376557401735669	5		639	635	SUCCESS
AR	367	MSKCC	GRCh37	X	66943603	66943603	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	160	546	0	ENST00000374690.3:c.2683A>C	p.Met895Leu	p.M895L	ENST00000374690	NM_000044.3	895	Atg/Ctg	8/8	0.332501694951493	4	FACETS	0.92	0.846	0.995			1	CLONAL	2	TRUE	NA	0.376557401735669	4		546	636	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341275	341275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219986773	NA	P-0062239-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	175	332	0	ENST00000262320.3:c.2209C>T	p.Arg737Trp	p.R737W	ENST00000262320	NM_003502.3	737	Cgg/Tgg	9/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.849039735105611	2		332	391	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274264	10274264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062240-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	40	418	0	ENST00000330684.3:c.5G>A	p.Gly2Asp	p.G2D	ENST00000330684	NM_001134407.1	2	gGc/gAc	2/13	1	2	FACETS	0.92	0.764	1	0.92	0.764	1	CLONAL	1	TRUE	1	0.184720411781938	2		418	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574035	7574035	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs867389695	NA	P-0062240-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	87	445	0	ENST00000269305.4:c.994-2A>G		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.184720411781938	2	FACETS	0.985	0.876	1	0.985	0.876	1	CLONAL	2	TRUE	0	0.184720411781938	2		445	478	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662196	227662196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062240-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	145	602	0	ENST00000305123.5:c.1259C>T	p.Pro420Leu	p.P420L	ENST00000305123	NM_005544.2	420	cCc/cTc	1/2	0.184720411781938	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.184720411781938	3		602	738	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643537	52643538	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0062240-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	37	420	0	ENST00000394830.3:c.2358dup	p.Val787CysfsTer9	p.V787Cfs*9	ENST00000394830	NM_018313.4	786	-/T	17/30	0.184720411781938	1	FACETS	0.701	0.577	0.839	0.701	0.577	0.839	SUBCLONAL	1	TRUE	0	0.184720411781938	1		420	519	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674263	86674263	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062240-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	32	419	0	ENST00000274376.6:c.2395G>T	p.Glu799Ter	p.E799*	ENST00000274376	NM_002890.2	799	Gag/Tag	18/25	0.184720411781938	2	FACETS	0.971	0.789	1	0.485	0.394	0.588	CLONAL	1	TRUE	0	0.184720411781938	2		419	357	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020744	37020744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062241-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	171	445	0	ENST00000358127.4:c.101C>T	p.Pro34Leu	p.P34L	ENST00000358127	NM_001280556.1	34	cCg/cTg	2/10	0.135246523677532	4	FACETS	0.992	0.926	1	0.992	0.926	1	INDETERMINATE	2	FALSE	2	0.855630796584354	4		445	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579318	7579330	+	frameshift_variant	Frame_Shift_Del	DEL	AGTCACAGACTTG	AGTCACAGACTTG	-	novel	NA	P-0062241-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	267	431	0	ENST00000269305.4:c.357_369del	p.Lys120AlafsTer46	p.K120Afs*46	ENST00000269305	NM_001126112.2	119	gcCAAGTCTGTGACT/gc	4/11	0.854720098407204	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	FALSE	0	0.855630796584354	2		431	299	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720424	89720755	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTTGAGTGAAGAAAAATCATGTGAATGAAAATGCAACAGATAACTCAGATTGCCTTATAATAGTCTTTGTGTTTACCTTTATTCAGAATATCAAATGATAGTTTATTTTGTTGACTTTTTGCAAATGTTTAACATAGGTGACAGATTTTCTTTTTTAAAAAAATAAAACATCATTAATTAAATATGTCATTTCATTTCTTTTTCTTTTCTTTTTTTTTTTTTTTAGGACAAAATGTTTCACTTTTGGGTAAATACATTCTTCATACCAGGACCAGAGGAAACCTCAGAAAAAGTAGAAAATGGAAGTCTATGTGATCAAGAAATCGATAGC	ATTTGAGTGAAGAAAAATCATGTGAATGAAAATGCAACAGATAACTCAGATTGCCTTATAATAGTCTTTGTGTTTACCTTTATTCAGAATATCAAATGATAGTTTATTTTGTTGACTTTTTGCAAATGTTTAACATAGGTGACAGATTTTCTTTTTTAAAAAAATAAAACATCATTAATTAAATATGTCATTTCATTTCTTTTTCTTTTCTTTTTTTTTTTTTTTAGGACAAAATGTTTCACTTTTGGGTAAATACATTCTTCATACCAGGACCAGAGGAAACCTCAGAAAAAGTAGAAAATGGAAGTCTATGTGATCAAGAAATCGATAGC	-	novel	NA	P-0062243-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	53	22	0	ENST00000371953.3:c.802-222_911del		p.X268_splice	ENST00000371953	NM_000314.4	268		8/9	0.736242312774122	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.736242312774122	1		22	69	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675091	40675091	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1197392495	NA	P-0062243-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	177	465	0	ENST00000249776.8:c.55T>C	p.Ser19Pro	p.S19P	ENST00000249776	NM_033286.3	19	Tct/Cct	1/9	0.736242312774122	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.736242312774122	1		465	290	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40477080	40477080	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0062243-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	136	422	0	ENST00000264657.5:c.1366-1G>T		p.X456_splice	ENST00000264657	NM_139276.2	456			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.736242312774122	2		422	349	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922755	44922755	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062243-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	92	473	0	ENST00000377967.4:c.1616C>G	p.Ser539Cys	p.S539C	ENST00000377967	NM_021140.2	539	tCt/tGt	16/29	0.468327196992105	1	FACETS	0.407	0.364	0.452	0.407	0.364	0.452	SUBCLONAL	1	TRUE	0	0.736242312774122	1		473	388	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019580	123019580	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062243-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	35	367	0	ENST00000355640.3:c.68T>C	p.Phe23Ser	p.F23S	ENST00000355640		23	tTt/tCt	2/7	0.263832969525417	3	FACETS	0.222	0.181	0.268	0.111	0.09	0.134	INDETERMINATE	1	TRUE	1	0.736242312774122	3		367	586	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882025	NA	P-0062244-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	202	618	0	ENST00000269305.4:c.646G>T	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ttg	6/11	0.676204572287734	1	FACETS	0.942	0.885	0.998	0.942	0.885	0.998	CLONAL	1	TRUE	0	0.676204572287734	1		618	420	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953730	48953730	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs3092891	NA	P-0062244-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	111	191	0	ENST00000267163.4:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000267163	NM_000321.2	445	Cga/Tga	14/27	0.676204572287734	1	FACETS	0.945	0.869	1	0.945	0.869	1	CLONAL	1	TRUE	0	0.676204572287734	1		191	230	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52693404	52693404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062244-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	56	531	0	ENST00000322088.6:c.55G>A	p.Glu19Lys	p.E19K	ENST00000322088	NM_014225.5	19	Gaa/Aaa	1/15	1	2	FACETS	0.217	0.185	0.252	0.217	0.185	0.252	SUBCLONAL	1	TRUE	1	0.676204572287734	2		531	763	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099170	157099170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1455171423	NA	P-0062244-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	93	467	0	ENST00000346085.5:c.107C>T	p.Ser36Phe	p.S36F	ENST00000346085	NM_020732.3	36	tCc/tTc	1/20	0.676204572287734	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.676204572287734	1		467	182	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47599071	47599071	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062244-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	203	574	0	ENST00000430070.2:c.529G>C	p.Glu177Gln	p.E177Q	ENST00000430070	NM_018095.4	177	Gag/Cag	2/4	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.676204572287734	2		574	588	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220041	133220041	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1258004616	NA	P-0062244-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	172	639	0	ENST00000320574.5:c.4396G>C	p.Glu1466Gln	p.E1466Q	ENST00000320574	NM_006231.2	1466	Gag/Cag	34/49	0.676204572287734	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.676204572287734	1		639	297	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241541	105241541	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062244-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	130	585	0	ENST00000349310.3:c.439A>T	p.Met147Leu	p.M147L	ENST00000349310	NM_001014432.1	147	Atg/Ttg	7/15	0.130900236405312	3	FACETS	1	0.981	1	0.629	0.576	0.684	INDETERMINATE	1	TRUE	1	0.676204572287734	3		585	409	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2107180	2107180	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0062244-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	148	544	0	ENST00000219476.3:c.848+1G>C		p.X283_splice	ENST00000219476	NM_000548.3	283			0.676204572287734	1	FACETS	0.92	0.855	0.985	0.92	0.855	0.985	CLONAL	1	TRUE	0	0.676204572287734	1		544	315	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783848	50783848	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062244-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	189	506	0	ENST00000398568.2:c.239C>G	p.Ala80Gly	p.A80G	ENST00000398568	NM_001042412.1	80	gCa/gGa	3/18	0.676204572287734	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.676204572287734	1		506	341	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883216	37883216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062244-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	163	529	0	ENST00000269571.5:c.3119G>A	p.Gly1040Glu	p.G1040E	ENST00000269571		1040	gGg/gAg	25/27	0.676204572287734	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.676204572287734	1		529	295	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732526	190732526	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062244-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	18	425	0	ENST00000441310.2:c.2344C>G	p.Leu782Val	p.L782V	ENST00000441310	NM_000534.4	782	Ctt/Gtt	11/13	0.676204572287734	1	FACETS	0.117	0.087	0.151	0.117	0.087	0.151	SUBCLONAL	1	TRUE	0	0.676204572287734	1		425	302	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103847	209103847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062244-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	21	430	0	ENST00000345146.2:c.1102G>A	p.Glu368Lys	p.E368K	ENST00000345146	NM_005896.2	368	Gag/Aag	9/10	0.676204572287734	1	FACETS	0.12	0.092	0.153	0.12	0.092	0.153	SUBCLONAL	1	TRUE	0	0.676204572287734	1		430	342	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916818	178916818	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062244-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	200	480	0	ENST00000263967.3:c.205A>G	p.Ile69Val	p.I69V	ENST00000263967	NM_006218.2	69	Att/Gtt	2/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.676204572287734	2		480	524	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0062251-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	13	304	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.184682411897046	3	FACETS	1	0.77	1	0.543	0.389	0.728	CLONAL	1	TRUE	1	0.19	3		304	138	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202797	128202797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062251-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	37	738	0	ENST00000341105.2:c.923G>A	p.Arg308Gln	p.R308Q	ENST00000341105	NM_032638.4	308	cGg/cAg	4/6	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.19	2		738	300	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608631	189608631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062251-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	21	583	0	ENST00000264731.3:c.1706G>T	p.Gly569Val	p.G569V	ENST00000264731	NM_003722.4	569	gGg/gTg	13/14	1	2	FACETS	0.945	0.73	1	0.945	0.73	1	CLONAL	1	TRUE	1	0.19	2		583	234	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671471	30671471	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062251-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	19	780	0	ENST00000376406.3:c.5489G>T	p.Gly1830Val	p.G1830V	ENST00000376406	NM_014641.2	1830	gGg/gTg	10/15	1	2	FACETS	0.704	0.535	0.903	0.704	0.535	0.903	CLONAL	1	TRUE	1	0.19	2		780	284	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124503463	124503463	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062251-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	18	590	0	ENST00000357628.3:c.487G>T	p.Asp163Tyr	p.D163Y	ENST00000357628	NM_015450.2	163	Gac/Tac	8/19	1	2	FACETS	0.846	0.638	1	0.846	0.638	1	CLONAL	1	TRUE	1	0.19	2		590	224	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595330	141595330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062251-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	16	707	1	ENST00000220592.5:c.103G>A	p.Gly35Arg	p.G35R	ENST00000220592	NM_012154.3	35	Ggg/Agg	2/19	1	2	FACETS	0.643	0.475	0.843	0.643	0.475	0.843	SUBCLONAL	1	TRUE	1	0.19	2		708	262	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080363	5080363	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062251-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	10	441	0	ENST00000381652.3:c.2266G>T	p.Ala756Ser	p.A756S	ENST00000381652	NM_004972.3	756	Gct/Tct	17/25	1	2	FACETS	0.797	0.543	1	0.797	0.543	1	CLONAL	1	TRUE	1	0.19	2		441	132	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074273	30074298	+	frameshift_variant	Frame_Shift_Del	DEL	CTGACATGAAGCGGCTTTCCATGGAG	CTGACATGAAGCGGCTTTCCATGGAG	-	novel	NA	P-0062252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	134	452	0	ENST00000338641.4:c.1535_1560del	p.Thr512AsnfsTer21	p.T512Nfs*21	ENST00000338641	NM_000268.3	512	aCTGACATGAAGCGGCTTTCCATGGAG/a	14/16	0.51825283052562	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.51825283052562	1		452	378	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0062253-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	102	309	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.610570535768885	3	FACETS	0.767	0.697	0.839	0.767	0.697	0.839	SUBCLONAL	2	TRUE	1	0.650353452972414	3		309	271	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0062253-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	80	393	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.650353452972414	2		393	216	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720805	89720808	+	frameshift_variant	Frame_Shift_Del	DEL	CTTT	CTTT	-	rs398123330	NA	P-0062253-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	23	126	0	ENST00000371953.3:c.956_959del	p.Thr319LysfsTer24	p.T319Kfs*24	ENST00000371953	NM_000314.4	319	aCTTTa/aa	8/9	0.610570535768885	3	FACETS	0.956	0.761	1	0.478	0.38	0.586	CLONAL	1	TRUE	1	0.650353452972414	3		126	98	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062253-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	91	455	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	1	2	FACETS	0.903	0.811	0.999	0.903	0.811	0.999	CLONAL	1	TRUE	1	0.650353452972414	2		455	310	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0062253-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	175	434	0	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.650353452972414	2		434	532	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514332	69514332	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062253-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	160	475	0	ENST00000294312.3:c.349G>T	p.Glu117Ter	p.E117*	ENST00000294312	NM_005117.2	117	Gag/Tag	3/3	1	2	FACETS	0.896	0.827	0.968	0.896	0.827	0.968	CLONAL	1	TRUE	1	0.650353452972414	2		475	549	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961964	41961964	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062253-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	141	525	0	ENST00000219905.7:c.874del	p.Val292SerfsTer37	p.V292Sfs*37	ENST00000219905	NM_001164273.1	291	cGg/cg	2/24	1	2	FACETS	0.799	0.731	0.868	0.799	0.731	0.868	SUBCLONAL	1	TRUE	1	0.650353452972414	2		525	543	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023727	31023727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531415735	NA	P-0062253-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	228	628	1	ENST00000375687.4:c.3212C>T	p.Ala1071Val	p.A1071V	ENST00000375687	NM_015338.5	1071	gCg/gTg	13/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.650353452972414	2		629	621	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638779	176638780	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs587784101	NA	P-0062253-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	146	536	0	ENST00000439151.2:c.3383_3384del	p.Ser1128PhefsTer2	p.S1128Ffs*2	ENST00000439151	NM_022455.4	1127	CTc/c	5/23	1	2	FACETS	0.77	0.706	0.837	0.77	0.706	0.837	SUBCLONAL	1	TRUE	1	0.650353452972414	2		536	583	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638711	176638712	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs797045812	NA	P-0062253-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	149	555	0	ENST00000439151.2:c.3316dup	p.Ser1106PhefsTer2	p.S1106Ffs*2	ENST00000439151	NM_022455.4	1104	cat/caTt	5/23	1	2	FACETS	0.794	0.729	0.862	0.794	0.729	0.862	SUBCLONAL	1	TRUE	1	0.650353452972414	2		555	577	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023326	27023332	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCCCA	GCCCCCA	-	novel	NA	P-0062253-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	170	511	0	ENST00000324856.7:c.435_441del	p.Pro146ThrfsTer84	p.P146Tfs*84	ENST00000324856	NM_006015.4	144	ccGCCCCCA/cc	1/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.650353452972414	2		511	506	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988467	41988468	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0062253-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	124	496	0	ENST00000219905.7:c.1260dup	p.Pro421SerfsTer12	p.P421Sfs*12	ENST00000219905	NM_001164273.1	420	gat/gaTt	3/24	1	2	FACETS	0.863	0.786	0.942	0.863	0.786	0.942	CLONAL	1	TRUE	1	0.650353452972414	2		496	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0062254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	295	617	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.55152970256128	2	FACETS	0.994	0.948	1	0.994	0.948	1	CLONAL	2	TRUE	0	0.55152970256128	2		617	538	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939032	48939033	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0062254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	81	196	0	ENST00000267163.4:c.869dup	p.Asn290LysfsTer20	p.N290Kfs*20	ENST00000267163	NM_000321.2	288	-/A	9/27	0.55152970256128	2	FACETS	0.825	0.745	0.906	0.825	0.745	0.906	CLONAL	2	TRUE	0	0.55152970256128	2		196	178	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299977	15299977	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	392	841	0	ENST00000263388.2:c.1201C>T	p.Pro401Ser	p.P401S	ENST00000263388	NM_000435.2	401	Ccc/Tcc	8/33	0.512946972705503	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	2	0.55152970256128	4		841	1091	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262726	16262726	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	387	706	0	ENST00000375759.3:c.9991G>C	p.Val3331Leu	p.V3331L	ENST00000375759	NM_015001.2	3331	Gtt/Ctt	11/15	0.55152970256128	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.55152970256128	3		706	855	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562442	21562442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	282	713	0	ENST00000382592.4:c.1477G>A	p.Ala493Thr	p.A493T	ENST00000382592	NM_014572.2	493	Gcg/Acg	4/8	0.477968507459329	5	FACETS	0.976	0.919	1	0.651	0.612	0.69	CLONAL	2	TRUE	2	0.55152970256128	5		713	957	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74001989	74001989	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	92	466	0	ENST00000318443.5:c.1505G>T	p.Gly502Val	p.G502V	ENST00000318443	NM_001024736.1	502	gGa/gTa	8/10	NA	2	FACETS	0.912	0.817	1			1	INDETERMINATE	1	TRUE	NA	0.55152970256128	2		466	366	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857047	9857047	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs568622613	NA	P-0062254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	114	542	0	ENST00000330684.3:c.4354C>A	p.Arg1452Ser	p.R1452S	ENST00000330684	NM_001134407.1	1452	Cgc/Agc	13/13	0.55152970256128	3	FACETS	1	0.934	1	0.52	0.47	0.572	CLONAL	1	TRUE	1	0.55152970256128	3		542	507	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660613	67660613	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	136	514	0	ENST00000264010.4:c.1513A>G	p.Arg505Gly	p.R505G	ENST00000264010	NM_006565.3	505	Aga/Gga	8/12	0.55152970256128	3	FACETS	1	0.931	1	0.512	0.466	0.559	CLONAL	1	TRUE	1	0.55152970256128	3		514	615	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428386	33428386	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	rs1597856297	NA	P-0062254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	294	608	0	ENST00000345365.6:c.739-2A>T		p.X247_splice	ENST00000345365	NM_002878.3	247			0.55152970256128	3	FACETS	0.994	0.942	1	0.994	0.942	1	CLONAL	2	TRUE	1	0.55152970256128	3		608	684	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107046	11107046	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	373	742	3	ENST00000358026.2:c.1751A>G	p.Lys584Arg	p.K584R	ENST00000358026	NM_001128849.1	584	aAg/aGg	10/36	0.512946972705503	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.55152970256128	4		745	1018	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17947980	17947980	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	143	556	0	ENST00000458235.1:c.1744C>G	p.Arg582Gly	p.R582G	ENST00000458235	NM_000215.3	582	Cgg/Ggg	13/24	0.512946972705503	4	FACETS	0.98	0.894	1	0.49	0.447	0.535	CLONAL	1	TRUE	2	0.55152970256128	4		556	821	SUCCESS
ALB	213	MSKCC	GRCh37	4	74282048	74282048	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	189	415	0	ENST00000295897.4:c.1268del	p.Gly423GlufsTer10	p.G423Efs*10	ENST00000295897	NM_000477.5	423	Gga/ga	10/15	0.528008835956649	3	FACETS	0.94	0.878	1	0.94	0.878	1	CLONAL	2	TRUE	1	0.55152970256128	3		415	465	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945034	151945034	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	28	164	0	ENST00000262189.6:c.2485G>A	p.Ala829Thr	p.A829T	ENST00000262189	NM_170606.2	829	Gct/Act	14/59	0.24537867400982	5	FACETS	0.716	0.575	0.877	0.239	0.191	0.293	INDETERMINATE	1	TRUE	2	0.55152970256128	5		164	259	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0062255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	69	228	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.233997744578271	3	FACETS	1	0.923	1	0.709	0.625	0.798	CLONAL	2	TRUE	0	0.287473315390015	3		228	258	SUCCESS
APC	324	MSKCC	GRCh37	5	112175147	112175147	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	79	478	0	ENST00000257430.4:c.3856G>T	p.Glu1286Ter	p.E1286*	ENST00000257430	NM_000038.5	1286	Gaa/Taa	16/16	0.287473315390015	3	FACETS	1	0.945	1	0.563	0.496	0.635	CLONAL	1	TRUE	1	0.287473315390015	3		478	558	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992916	72992916	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	64	567	0	ENST00000268489.5:c.1129G>A	p.Glu377Lys	p.E377K	ENST00000268489	NM_006885.3	377	Gaa/Aaa	2/10	0.257105565338978	3	FACETS	0.863	0.748	0.988	0.432	0.374	0.494	CLONAL	1	TRUE	1	0.287473315390015	3		567	590	SUCCESS
APC	324	MSKCC	GRCh37	5	112174176	112174177	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0062255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	117	449	0	ENST00000257430.4:c.2886dup	p.Ser963Ter	p.S963*	ENST00000257430	NM_000038.5	962	gat/gaTt	16/16	0.287473315390015	3	FACETS	0.956	0.867	1	0.956	0.867	1	CLONAL	2	TRUE	1	0.287473315390015	3		449	487	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10788021	10788021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	45	346	0	ENST00000361367.2:c.1670C>T	p.Ala557Val	p.A557V	ENST00000361367	NM_014633.3	557	gCt/gTt	13/25	0.287473315390015	3	FACETS	0.79	0.665	0.929	0.395	0.332	0.465	CLONAL	1	TRUE	1	0.287473315390015	3		346	453	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143007	7143007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151246790	NA	P-0062255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	88	613	0	ENST00000302850.5:c.2362G>A	p.Val788Met	p.V788M	ENST00000302850	NM_000208.2	788	Gtg/Atg	12/22	0.257105565338978	3	FACETS	1	0.906	1	0.513	0.454	0.575	CLONAL	1	TRUE	1	0.287473315390015	3		613	683	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	111	582	2	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.27045973905709	3	FACETS	1	0.943	1	0.537	0.482	0.595	CLONAL	1	TRUE	1	0.28	3		584	842	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	59	371	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.28	2		371	415	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911443	32911443	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359365	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	30	346	0	ENST00000380152.3:c.2957del	p.Asn986IlefsTer5	p.N986Ifs*5	ENST00000380152		984	gAa/ga	11/27	1	2	FACETS	0.687	0.555	0.836	0.687	0.555	0.836	SUBCLONAL	1	TRUE	1	0.28	2		346	312	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	215	565	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.848	0.789	0.908	1	0.993	1	CLONAL	2	TRUE	1	0.28	2		568	906	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	86	527	3	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.935	0.828	1	0.935	0.828	1	CLONAL	1	TRUE	1	0.28	2		530	657	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	85	674	0	ENST00000324856.7:c.5547_5548dup	p.Asp1850GlyfsTer34	p.D1850Gfs*34	ENST00000324856	NM_006015.4	1847	-/GG	20/20	1	2	FACETS	0.81	0.715	0.911	0.81	0.715	0.911	CLONAL	1	TRUE	1	0.28	2		674	750	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740216	162740216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775098890	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	98	539	0	ENST00000367921.3:c.1418G>A	p.Arg473His	p.R473H	ENST00000367921	NM_006182.2	473	cGc/cAc	12/18	1	2	FACETS	0.897	0.8	1	0.897	0.8	1	CLONAL	1	TRUE	1	0.28	2		539	780	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615036	43615036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1345166214	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	75	682	0	ENST00000355710.3:c.2450G>A	p.Arg817His	p.R817H	ENST00000355710	NM_020975.4	817	cGc/cAc	14/20	1	2	FACETS	0.884	0.775	1	0.884	0.775	1	CLONAL	1	TRUE	1	0.28	2		682	606	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202113	67202113	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	99	638	0	ENST00000312629.5:c.1216C>T	p.Pro406Ser	p.P406S	ENST00000312629	NM_003952.2	406	Ccc/Tcc	14/15	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.28	2		638	706	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945645	71945645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144781166	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	68	455	1	ENST00000298229.2:c.2401C>T	p.Arg801Cys	p.R801C	ENST00000298229	NM_001567.3	801	Cgc/Tgc	21/28	1	2	FACETS	0.795	0.692	0.907	0.795	0.692	0.907	CLONAL	1	TRUE	1	0.28	2		456	611	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170319	119170319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	93	519	0	ENST00000264033.4:c.2549C>T	p.Ala850Val	p.A850V	ENST00000264033	NM_005188.3	850	gCt/gTt	16/16	1	2	FACETS	0.833	0.741	0.933	0.833	0.741	0.933	CLONAL	1	TRUE	1	0.28	2		519	797	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298716	46298716	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	31	286	0	ENST00000334344.6:c.5364-1G>T		p.X1788_splice	ENST00000334344	NM_152641.2	1788			0.27045973905709	3	FACETS	0.668	0.54	0.812	0.334	0.27	0.406	SUBCLONAL	1	TRUE	1	0.28	3		286	378	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432347	49432347	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	225	700	0	ENST00000301067.7:c.8792del	p.Pro2931HisfsTer12	p.P2931Hfs*12	ENST00000301067	NM_003482.3	2931	cCa/ca	34/54	0.27045973905709	3	FACETS	0.919	0.856	0.984	0.919	0.856	0.984	CLONAL	2	TRUE	1	0.28	3		700	997	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120783958	120783958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253933590	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	81	600	0	ENST00000257552.2:c.1027G>A	p.Gly343Ser	p.G343S	ENST00000257552	NM_002442.3	343	Ggc/Agc	13/15	1	2	FACETS	0.907	0.799	1	0.907	0.799	1	CLONAL	1	TRUE	1	0.28	2		600	638	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243026	105243026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773971502	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	104	618	0	ENST00000349310.3:c.257G>A	p.Arg86His	p.R86H	ENST00000349310	NM_001014432.1	86	cGc/cAc	5/15	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.28	2		618	715	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052632	42052632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779811318	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	100	484	0	ENST00000219905.7:c.7303C>T	p.Arg2435Trp	p.R2435W	ENST00000219905	NM_001164273.1	2435	Cgg/Tgg	20/24	1	2	FACETS	0.803	0.717	0.896	0.803	0.717	0.896	CLONAL	1	TRUE	1	0.28	2		484	889	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396234	396234	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	125	542	1	ENST00000262320.3:c.792del	p.Gly265GlufsTer149	p.G265Efs*149	ENST00000262320	NM_003502.3	264	ccC/cc	2/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.28	2		543	679	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396247	396248	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	81	537	0	ENST00000262320.3:c.778_779del	p.Asp260ArgfsTer24	p.D260Rfs*24	ENST00000262320	NM_003502.3	260	GAc/c	2/11	1	2	FACETS	0.839	0.739	0.946	0.839	0.739	0.946	CLONAL	1	TRUE	1	0.28	2		537	690	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226338	2226338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	107	710	0	ENST00000326181.6:c.1951G>A	p.Val651Met	p.V651M	ENST00000326181	NM_032271.2	651	Gtg/Atg	20/21	1	2	FACETS	0.957	0.858	1	0.957	0.858	1	CLONAL	1	TRUE	1	0.28	2		710	799	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832224	72832224	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	91	622	0	ENST00000268489.5:c.4357C>A	p.Leu1453Met	p.L1453M	ENST00000268489	NM_006885.3	1453	Ctg/Atg	9/10	1	2	FACETS	0.948	0.842	1	0.948	0.842	1	CLONAL	1	TRUE	1	0.28	2		622	686	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81904511	81904511	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1189737304	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	43	294	0	ENST00000359376.3:c.624del	p.Lys208AsnfsTer55	p.K208Nfs*55	ENST00000359376	NM_002661.3	207	Aaa/aa	7/33	1	2	FACETS	0.835	0.7	0.983	0.835	0.7	0.983	CLONAL	1	TRUE	1	0.28	2		294	368	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346156	89346156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757094468	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	99	627	0	ENST00000301030.4:c.6794C>T	p.Ala2265Val	p.A2265V	ENST00000301030	NM_001256183.1	2265	gCc/gTc	9/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.28	2		627	624	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348973	89348973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144673419	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	90	646	0	ENST00000301030.4:c.3977C>T	p.Thr1326Met	p.T1326M	ENST00000301030	NM_001256183.1	1326	aCg/aTg	9/13	1	2	FACETS	0.856	0.759	0.959	0.856	0.759	0.959	CLONAL	1	TRUE	1	0.28	2		646	751	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371409680	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	163	574	0	ENST00000269305.4:c.848G>A	p.Arg283His	p.R283H	ENST00000269305	NM_001126112.2	283	cGc/cAc	8/11	1	2	FACETS	0.804	0.74	0.871	1	0.99	1	CLONAL	2	TRUE	1	0.28	2		574	724	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320886	30320889	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	novel	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	33	239	1	ENST00000322652.5:c.1297_1300del	p.Leu433IlefsTer22	p.L433Ifs*22	ENST00000322652	NM_015355.2	432	ttTCTC/tt	12/16	1	2	FACETS	0.746	0.609	0.899	0.746	0.609	0.899	SUBCLONAL	1	TRUE	1	0.28	2		240	316	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	81	430	0	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	0.984	0.868	1	0.984	0.868	1	CLONAL	1	TRUE	1	0.28	2		430	588	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	97	801	3	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.8	0.712	0.894	0.8	0.712	0.894	SUBCLONAL	1	TRUE	1	0.28	2		804	866	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238936	5238936	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	82	583	0	ENST00000357368.4:c.1843C>A	p.Gln615Lys	p.Q615K	ENST00000357368	NM_002850.3	615	Cag/Aag	13/38	1	2	FACETS	0.866	0.764	0.976	0.866	0.764	0.976	CLONAL	1	TRUE	1	0.28	2		583	676	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290217	15290217	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	124	815	1	ENST00000263388.2:c.3418C>A	p.Leu1140Ile	p.L1140I	ENST00000263388	NM_000435.2	1140	Ctc/Atc	21/33	1	2	FACETS	0.994	0.899	1	0.994	0.899	1	CLONAL	1	TRUE	1	0.28	2		816	891	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17389816	17389817	+	missense_variant	Missense_Mutation	DNP	GA	GA	CT	novel	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	95	572	1	ENST00000359435.4:c.949_950delinsCT	p.Glu317Leu	p.E317L	ENST00000359435	NM_001033549.1	317	GAg/CTg	9/9	1	2	FACETS	0.975	0.868	1	0.975	0.868	1	CLONAL	1	TRUE	1	0.28	2		573	696	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731520	47731520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	50	430	0	ENST00000449228.1:c.272G>A	p.Cys91Tyr	p.C91Y	ENST00000449228	NM_001127240.2	91	tGc/tAc	2/4	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.28	2		430	331	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149819	202149819	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	84	566	1	ENST00000358485.4:c.1264del	p.Asp422IlefsTer19	p.D422Ifs*19	ENST00000358485	NM_001080125.1	420	caG/ca	8/9	1	2	FACETS	0.923	0.816	1	0.923	0.816	1	CLONAL	1	TRUE	1	0.28	2		567	650	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732730	204732730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	81	466	0	ENST00000302823.3:c.65G>A	p.Cys22Tyr	p.C22Y	ENST00000302823	NM_005214.4	22	tGc/tAc	1/4	1	2	FACETS	0.806	0.71	0.909	0.806	0.71	0.909	CLONAL	1	TRUE	1	0.28	2		466	718	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794860	242794860	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	72	701	0	ENST00000334409.5:c.349G>T	p.Asp117Tyr	p.D117Y	ENST00000334409	NM_005018.2	117	Gac/Tac	2/5	0.123654213070395	3	FACETS	0.871	0.761	0.99			1	INDETERMINATE	1	TRUE	NA	0.28	3		701	673	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655413	45655413	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	111	607	0	ENST00000407780.3:c.439del	p.His147ThrfsTer15	p.H147Tfs*15	ENST00000407780	NM_001283052.1	147	Cac/ac	4/7	0.301553584231974	1	FACETS	0.94	0.846	1	0.94	0.846	1	CLONAL	1	TRUE	0	0.28	1		607	725	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183561	10183561	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs963501454	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	73	679	2	ENST00000256474.2:c.30G>T	p.Glu10Asp	p.E10D	ENST00000256474	NM_000551.3	10	gaG/gaT	1/3	1	2	FACETS	0.743	0.649	0.844	0.743	0.649	0.844	SUBCLONAL	1	TRUE	1	0.28	2		681	702	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998164	169998165	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	54	361	0	ENST00000295797.4:c.861dup	p.Glu288ArgfsTer4	p.E288Rfs*4	ENST00000295797	NM_002740.5	285	-/A	9/18	1	2	FACETS	0.784	0.67	0.908	0.784	0.67	0.908	CLONAL	1	TRUE	1	0.28	2		361	492	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186501419	186501419	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1560082706	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	68	369	0	ENST00000323963.5:c.20A>G	p.Asp7Gly	p.D7G	ENST00000323963		7	gAt/gGt	1/11	1	2	FACETS	0.915	0.797	1	0.915	0.797	1	CLONAL	1	TRUE	1	0.28	2		369	531	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972074	55972074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	93	455	0	ENST00000263923.4:c.1570G>A	p.Val524Met	p.V524M	ENST00000263923	NM_002253.2	524	Gtg/Atg	12/30	0.301553584231974	1	FACETS	0.96	0.855	1	0.96	0.855	1	CLONAL	1	TRUE	0	0.28	1		455	595	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	49	403	0	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	1	2	FACETS	0.734	0.622	0.857	0.734	0.622	0.857	SUBCLONAL	1	TRUE	1	0.28	2		403	477	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31405801	31405801	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	32	295	0	ENST00000344624.3:c.3977T>A	p.Met1326Lys	p.M1326K	ENST00000344624		1326	aTg/aAg	32/33	1	2	FACETS	0.61	0.495	0.739	0.61	0.495	0.739	SUBCLONAL	1	TRUE	1	0.28	2		295	375	SUCCESS
APC	324	MSKCC	GRCh37	5	112176739	112176740	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	30	349	0	ENST00000257430.4:c.5453dup	p.Asn1818LysfsTer2	p.N1818Kfs*2	ENST00000257430	NM_000038.5	1816	-/A	16/16	1	2	FACETS	0.487	0.392	0.595	0.487	0.392	0.595	SUBCLONAL	1	TRUE	1	0.28	2		349	440	SUCCESS
APC	324	MSKCC	GRCh37	5	112178001	112178001	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1299714632	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	67	466	0	ENST00000257430.4:c.6710G>A	p.Arg2237Gln	p.R2237Q	ENST00000257430	NM_000038.5	2237	cGa/cAa	16/16	1	2	FACETS	0.856	0.745	0.977	0.856	0.745	0.977	CLONAL	1	TRUE	1	0.28	2		466	559	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323362	31323363	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748204482	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	77	505	1	ENST00000412585.2:c.626dup	p.Thr211AspfsTer10	p.T211Dfs*10	ENST00000412585	NM_005514.6	209	cca/ccCa	4/8	1	2	FACETS	0.862	0.757	0.975	0.862	0.757	0.975	CLONAL	1	TRUE	1	0.28	2		506	638	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199888	138199888	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	111	697	0	ENST00000237289.4:c.1306G>T	p.Gly436Trp	p.G436W	ENST00000237289	NM_001270507.1	436	Ggg/Tgg	7/9	1	2	FACETS	0.956	0.859	1	0.956	0.859	1	CLONAL	1	TRUE	1	0.28	2		697	829	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023003	150023003	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	46	434	1	ENST00000253339.5:c.260C>T	p.Pro87Leu	p.P87L	ENST00000253339		87	cCa/cTa	1/7	1	2	FACETS	0.672	0.566	0.789	0.672	0.566	0.789	SUBCLONAL	1	TRUE	1	0.28	2		435	489	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522568	106522568	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs754441790	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	28	224	0	ENST00000359195.3:c.2545C>T	p.Arg849Ter	p.R849*	ENST00000359195	NM_002649.2	849	Cga/Tga	7/11	1	2	FACETS	0.719	0.577	0.881	0.719	0.577	0.881	SUBCLONAL	1	TRUE	1	0.28	2		224	278	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956823	68956823	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	38	390	0	ENST00000288368.4:c.941C>T	p.Thr314Ile	p.T314I	ENST00000288368	NM_024870.2	314	aCc/aTc	8/40	1	2	FACETS	0.557	0.46	0.666	0.557	0.46	0.666	SUBCLONAL	1	TRUE	1	0.28	2		390	487	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221935	98221935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201118857	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	98	553	0	ENST00000331920.6:c.2834G>A	p.Arg945Gln	p.R945Q	ENST00000331920	NM_000264.3	945	cGa/cAa	17/24	1	2	FACETS	0.899	0.801	1	0.899	0.801	1	CLONAL	1	TRUE	1	0.28	2		553	779	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391431	139391431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1163673587	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	110	750	0	ENST00000277541.6:c.6760G>A	p.Glu2254Lys	p.E2254K	ENST00000277541	NM_017617.3	2254	Gag/Aag	34/34	1	2	FACETS	0.997	0.896	1	0.997	0.896	1	CLONAL	1	TRUE	1	0.28	2		750	788	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230884	53230884	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	70	605	0	ENST00000375401.3:c.1909C>T	p.Arg637Trp	p.R637W	ENST00000375401	NM_004187.3	637	Cgg/Tgg	14/26	0.301553584231974	1	FACETS	0.768	0.67	0.873	0.768	0.67	0.873	SUBCLONAL	1	TRUE	0	0.28	1		605	560	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53241046	53241046	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	84	434	0	ENST00000375401.3:c.1165A>G	p.Thr389Ala	p.T389A	ENST00000375401	NM_004187.3	389	Acc/Gcc	9/26	0.301553584231974	1	FACETS	0.972	0.86	1	0.972	0.86	1	CLONAL	1	TRUE	0	0.28	1		434	531	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412344	63412344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs958633014	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	85	639	0	ENST00000330258.3:c.823G>A	p.Ala275Thr	p.A275T	ENST00000330258	NM_152424.3	275	Gcc/Acc	2/2	0.301553584231974	1	FACETS	0.919	0.814	1	0.919	0.814	1	CLONAL	1	TRUE	0	0.28	1		639	568	SUCCESS
AR	367	MSKCC	GRCh37	X	66941758	66941758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	67	420	1	ENST00000374690.3:c.2407del	p.Gln803ArgfsTer6	p.Q803Rfs*6	ENST00000374690	NM_000044.3	801	aCc/ac	6/8	0.301553584231974	1	FACETS	0.845	0.736	0.963	0.845	0.736	0.963	CLONAL	1	TRUE	0	0.28	1		421	487	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0062257-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	133	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.246808805903376	4	FACETS	0.977	0.893	1	0.977	0.893	1	CLONAL	2	TRUE	2	0.371060854639804	4		485	503	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0062257-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	145	423	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.36317730985453	3	FACETS	0.853	0.783	0.926	0.853	0.783	0.926	CLONAL	2	TRUE	1	0.371060854639804	3		423	543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0062257-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	213	529	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.335780180461832	2	FACETS	0.878	0.82	0.937	0.878	0.82	0.937	CLONAL	2	TRUE	0	0.371060854639804	2		529	654	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920413	114920413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767830105	NA	P-0062257-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	186	491	0	ENST00000543371.1:c.1354G>A	p.Gly452Arg	p.G452R	ENST00000543371	NM_001198531.1	452	Ggg/Agg	13/14	0.30228178363911	3	FACETS	0.87	0.807	0.936	0.87	0.807	0.936	CLONAL	2	TRUE	1	0.371060854639804	3		491	683	SUCCESS
APC	324	MSKCC	GRCh37	5	112175524	112175524	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062257-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	64	553	0	ENST00000257430.4:c.4233del	p.Ser1411ArgfsTer4	p.S1411Rfs*4	ENST00000257430	NM_000038.5	1411	agT/ag	16/16	0.36317730985453	3	FACETS	0.613	0.53	0.703	0.307	0.265	0.352	SUBCLONAL	1	TRUE	1	0.371060854639804	3		553	667	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591903	48591903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062257-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	84	596	0	ENST00000342988.3:c.1066C>T	p.Pro356Ser	p.P356S	ENST00000342988	NM_005359.5	356	Cct/Tct	9/12	0.371060854639804	1	FACETS	0.735	0.651	0.824	0.735	0.651	0.824	SUBCLONAL	1	TRUE	0	0.371060854639804	1		596	502	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0062258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	65	812	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.754	0.657	0.858	0.754	0.657	0.858	SUBCLONAL	1	TRUE	1	0.467092695482527	2		812	369	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0062258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	136	367	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.467092695482527	2		367	581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0062258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	58	568	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.416846360869838	1	FACETS	0.218	0.186	0.253	0.218	0.186	0.253	SUBCLONAL	1	TRUE	0	0.467092695482527	1		569	873	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0062258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	28	393	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.207	0.165	0.256	0.207	0.165	0.256	SUBCLONAL	1	TRUE	1	0.467092695482527	2		393	578	SUCCESS
APC	324	MSKCC	GRCh37	5	112162946	112162946	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1057517561	NA	P-0062258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	112	437	0	ENST00000257430.4:c.1548+2T>C		p.X516_splice	ENST00000257430	NM_000038.5	516			1	2	FACETS	0.931	0.841	1	0.931	0.841	1	CLONAL	1	TRUE	1	0.467092695482527	2		437	515	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631550	119631550	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0062258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	79	345	0	ENST00000316626.5:c.715+1G>A		p.X239_splice	ENST00000316626		239			1	2	FACETS	0.629	0.554	0.709	0.629	0.554	0.709	SUBCLONAL	1	TRUE	1	0.467092695482527	2		345	538	SUCCESS
APC	324	MSKCC	GRCh37	5	112175757	112175767	+	frameshift_variant	Frame_Shift_Del	DEL	TACATTTTGCC	TACATTTTGCC	-	novel	NA	P-0062258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	259	819	0	ENST00000257430.4:c.4466_4476del	p.Leu1489TyrfsTer21	p.L1489Yfs*21	ENST00000257430	NM_000038.5	1489	tTACATTTTGCC/t	16/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.467092695482527	2		819	1034	SUCCESS
AR	367	MSKCC	GRCh37	X	66765505	66765505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	70	917	0	ENST00000374690.3:c.517G>A	p.Gly173Ser	p.G173S	ENST00000374690	NM_000044.3	173	Ggc/Agc	1/8	0.17251652125134	3	FACETS	0.329	0.286	0.377	0.165	0.143	0.189	INDETERMINATE	1	TRUE	1	0.467092695482527	3		917	1123	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0062260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	343	711	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.749748451142863	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.751191121599074	2		711	434	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0062260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	232	484	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.748547213701166	3	FACETS	0.963	0.912	1	0.963	0.912	1	CLONAL	2	TRUE	1	0.751191121599074	3		484	441	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28607251	28607251	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	151	633	0	ENST00000253063.3:c.1381G>C	p.Glu461Gln	p.E461Q	ENST00000253063	NM_031459.4	461	Gag/Cag	10/10	0.732457356791038	5	FACETS	0.877	0.801	0.957	0.219	0.2	0.24	CLONAL	1	TRUE	1	0.751191121599074	5		633	975	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0062261-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	162	530	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.559007166359563	2		530	519	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855984	68855984	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121964877	NA	P-0062261-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	189	705	0	ENST00000261769.5:c.1792C>T	p.Arg598Ter	p.R598*	ENST00000261769	NM_004360.3	598	Cga/Tga	12/16	0.522318534578952	1	FACETS	0.892	0.831	0.955	0.892	0.831	0.955	CLONAL	1	TRUE	0	0.559007166359563	1		705	546	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915554	131915554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062261-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	91	316	0	ENST00000265335.6:c.552A>T	p.Arg184Ser	p.R184S	ENST00000265335		184	agA/agT	5/25	1	2	FACETS	0.885	0.792	0.982	0.885	0.792	0.982	CLONAL	1	TRUE	1	0.559007166359563	2		316	368	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0062261-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	186	471	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.579587424842001	2		471	608	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0062261-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	219	633	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.965	0.9	1	0.965	0.9	1	CLONAL	1	TRUE	1	0.579587424842001	2		633	783	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100583	67100583	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0062261-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	187	509	1	ENST00000412916.2:c.283-2A>G		p.X95_splice	ENST00000412916		95			0.579587424842001	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.579587424842001	1		510	414	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075203	16075203	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062261-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	197	674	0	ENST00000268712.3:c.349del	p.Ser117LeufsTer13	p.S117Lfs*13	ENST00000268712	NM_006311.3	117	Tct/ct	4/46	1	2	FACETS	0.925	0.859	0.993	0.925	0.859	0.993	CLONAL	1	TRUE	1	0.579587424842001	2		674	735	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0062262-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	161	703	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.218864200177305	2	FACETS	0.993	0.915	1	0.993	0.915	1	CLONAL	2	TRUE	0	0.277727208073549	2		703	584	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062262-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	129	714	1				ENST00000310581	NM_198253.2	-/1132			0.222592247858285	4	FACETS	0.916	0.837	0.997	0.916	0.837	0.997	CLONAL	3	TRUE	1	0.277727208073549	4		715	432	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866444	37866444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062262-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	135	807	0	ENST00000269571.5:c.749C>T	p.Ser250Phe	p.S250F	ENST00000269571		250	tCt/tTt	6/27	0.147154623660807	2	FACETS	0.817	0.745	0.892	0.817	0.745	0.892	INDETERMINATE	2	TRUE	0	0.277727208073549	2		807	595	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101327	27101327	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062262-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	98	831	0	ENST00000324856.7:c.4609C>T	p.Gln1537Ter	p.Q1537*	ENST00000324856	NM_006015.4	1537	Cag/Tag	18/20	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.277727208073549	2		831	652	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101181	27101181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062262-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	116	854	0	ENST00000324856.7:c.4463C>T	p.Ser1488Leu	p.S1488L	ENST00000324856	NM_006015.4	1488	tCa/tTa	18/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.277727208073549	2		854	643	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527839	157527839	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs771295398	NA	P-0062262-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	50	793	0	ENST00000346085.5:c.5564G>C	p.Arg1855Thr	p.R1855T	ENST00000346085	NM_020732.3	1855	aGa/aCa	20/20	1	2	FACETS	0.569	0.482	0.665	0.569	0.482	0.665	SUBCLONAL	1	TRUE	1	0.277727208073549	2		793	633	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435477	56435477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372129321	NA	P-0062262-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	145	823	0	ENST00000407977.2:c.1660C>T	p.Arg554Trp	p.R554W	ENST00000407977		554	Cgg/Tgg	9/10	0.147154623660807	2	FACETS	0.798	0.73	0.869	0.798	0.73	0.869	INDETERMINATE	2	TRUE	0	0.277727208073549	2		823	654	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923438	9923438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062262-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	41	655	0	ENST00000330684.3:c.1849G>A	p.Val617Met	p.V617M	ENST00000330684	NM_001134407.1	617	Gtg/Atg	9/13	1	2	FACETS	0.55	0.457	0.653	0.55	0.457	0.653	SUBCLONAL	1	TRUE	1	0.277727208073549	2		655	537	SUCCESS
ATR	545	MSKCC	GRCh37	3	142286936	142286936	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062262-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	40	337	0	ENST00000350721.4:c.120C>G	p.Phe40Leu	p.F40L	ENST00000350721	NM_001184.3	40	ttC/ttG	2/47	1	2	FACETS	0.862	0.719	1	0.862	0.719	1	CLONAL	1	TRUE	1	0.277727208073549	2		337	334	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5064995	5064995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768074072	NA	P-0062262-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	134	456	0	ENST00000381652.3:c.1169C>T	p.Pro390Leu	p.P390L	ENST00000381652	NM_004972.3	390	cCa/cTa	9/25	0.203008925373969	2	FACETS	0.939	0.858	1	0.939	0.858	1	CLONAL	2	TRUE	0	0.277727208073549	2		456	514	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331652	8331652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062262-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	122	597	0	ENST00000356435.5:c.5464G>A	p.Asp1822Asn	p.D1822N	ENST00000356435		1822	Gac/Aac	33/35	0.203008925373969	2	FACETS	0.868	0.789	0.951	0.868	0.789	0.951	CLONAL	2	TRUE	0	0.277727208073549	2		597	506	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028595	42028597	+	stop_gained	Nonsense_Mutation	TNP	CTC	CTC	TTT	novel	NA	P-0062262-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	95	826	0	ENST00000219905.7:c.4133_4135delinsTTT	p.Ser1378_Gln1379delinsPheTer	p.S1378_Q1379delinsF*	ENST00000219905	NM_001164273.1	1378	tCTCag/tTTTag	13/24	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.277727208073549	2		826	634	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0062264-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	115	367	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.944	0.855	1	0.944	0.855	1	CLONAL	1	TRUE	1	0.494106186757518	2		367	493	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971114	21971115	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGGTCGGGTGAGAGTGGCG	novel	NA	P-0062264-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	110	768	0	ENST00000304494.5:c.225_243dup	p.Val82ArgfsTer44	p.V82Rfs*44	ENST00000304494	NM_000077.4	81	-/CGCCACTCTCACCCGACCC	2/3	0.494106186757518	1	FACETS	0.392	0.352	0.435	0.392	0.352	0.435	SUBCLONAL	1	TRUE	0	0.494106186757518	1		768	855	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139332	108139332	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062264-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	132	434	0	ENST00000278616.4:c.2834A>C	p.His945Pro	p.H945P	ENST00000278616	NM_000051.3	945	cAt/cCt	18/63	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.494106186757518	2		434	528	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207138	1207140	+	frameshift_variant	Frame_Shift_Del	DEL	GCC	GCC	CA	novel	NA	P-0062264-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	507	672	0	ENST00000326873.7:c.226_228delinsCA	p.Ala76GlnfsTer20	p.A76Qfs*20	ENST00000326873	NM_000455.4	76	GCC/CA	1/10	0.494106186757518	2	FACETS	0.917	0.881	0.953	0.917	0.881	0.953	CLONAL	2	TRUE	0	0.494106186757518	2		672	1119	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164704	36164712	+	frameshift_variant	Frame_Shift_Del	DEL	CTTGCGACG	CTTGCGACG	A	novel	NA	P-0062264-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	312	816	0	ENST00000300305.3:c.1163_1171delinsT	p.Ser388PhefsTer209	p.S388Ffs*209	ENST00000300305		388	tCGTCGCAAGcg/tTcg	8/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.494106186757518	2		816	1198	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0062265-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	210	522	0	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	0.623702475374538	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.623702475374538	1		522	402	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970946	70970946	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062265-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	57	541	0	ENST00000276594.2:c.1315C>T	p.Arg439Ter	p.R439*	ENST00000276594	NM_024504.3	439	Cga/Tga	6/8	0.338537756427947	3	FACETS	0.328	0.281	0.38	0.109	0.093	0.127	INDETERMINATE	1	TRUE	0	0.623702475374538	3		541	731	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1721948	1721948	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062265-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	108	564	0	ENST00000378609.4:c.585C>A	p.Asp195Glu	p.D195E	ENST00000378609	NM_002074.3	195	gaC/gaA	9/12	1	2	FACETS	0.534	0.479	0.591	0.534	0.479	0.591	SUBCLONAL	1	TRUE	1	0.623702475374538	2		564	649	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760735	133760735	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs201683427	NA	P-0062265-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	102	616	0	ENST00000318560.5:c.3058G>C	p.Glu1020Gln	p.E1020Q	ENST00000318560	NM_005157.4	1020	Gag/Cag	11/11	0.429062384645866	1	FACETS	0.425	0.382	0.472	0.425	0.382	0.472	SUBCLONAL	1	TRUE	0	0.623702475374538	1		616	529	SUCCESS
APC	324	MSKCC	GRCh37	5	112174111	112174122	+	frameshift_variant	Frame_Shift_Del	DEL	GGAAAATTCAAA	GGAAAATTCAAA	ATGTTCAC	novel	NA	P-0062265-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	101	488	1	ENST00000257430.4:c.2820_2831delinsATGTTCAC	p.Glu941CysfsTer13	p.E941Cfs*13	ENST00000257430	NM_000038.5	940	tcGGAAAATTCAAAt/tcATGTTCACt	16/16	0.623702475374538	1	FACETS	0.785	0.712	0.86	0.785	0.712	0.86	SUBCLONAL	1	TRUE	0	0.623702475374538	1		489	284	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0062266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	185	471	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.361068722857515	2	FACETS	0.882	0.821	0.946	0.882	0.821	0.946	CLONAL	2	TRUE	0	0.386141247599636	2		471	543	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	16	564	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.119	0.087	0.158	0.119	0.087	0.158	SUBCLONAL	1	TRUE	1	0.386141247599636	2		564	694	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0062266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	100	540	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.782	0.7	0.87	0.782	0.7	0.87	SUBCLONAL	1	TRUE	1	0.386141247599636	2		540	662	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099397	27099397	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	84	540	0	ENST00000324856.7:c.3634C>T	p.Gln1212Ter	p.Q1212*	ENST00000324856	NM_006015.4	1212	Cag/Tag	14/20	1	2	FACETS	0.872	0.772	0.978	0.872	0.772	0.978	CLONAL	1	TRUE	1	0.386141247599636	2		540	499	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650737	67650737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	140	467	0	ENST00000264010.4:c.1042G>A	p.Glu348Lys	p.E348K	ENST00000264010	NM_006565.3	348	Gag/Aag	5/12	1	2	FACETS	0.979	0.892	1	0.979	0.892	1	CLONAL	1	TRUE	1	0.386141247599636	2		467	741	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524346	148524346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377467108	NA	P-0062266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	33	351	0	ENST00000320356.2:c.638G>A	p.Arg213His	p.R213H	ENST00000320356	NM_004456.4	213	cGc/cAc	7/20	0.361226281498265	3	FACETS	0.584	0.476	0.705	0.292	0.238	0.353	SUBCLONAL	1	TRUE	1	0.386141247599636	3		351	349	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831428	72831429	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0062266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	79	612	0	ENST00000268489.5:c.5152dup	p.Met1718AsnfsTer56	p.M1718Nfs*56	ENST00000268489	NM_006885.3	1718	atg/aAtg	9/10	1	2	FACETS	0.554	0.487	0.627	0.554	0.487	0.627	SUBCLONAL	1	TRUE	1	0.386141247599636	2		612	738	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514525	41514525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	33	454	0	ENST00000373198.4:c.136G>A	p.Ala46Thr	p.A46T	ENST00000373198	NM_133170.3	46	Gct/Act	2/32	1	2	FACETS	0.191	0.155	0.231	0.191	0.155	0.231	SUBCLONAL	1	TRUE	1	0.675722034491158	2		454	512	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514525	41514525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062267-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	27	454	0	ENST00000373198.4:c.136G>A	p.Ala46Thr	p.A46T	ENST00000373198	NM_133170.3	46	Gct/Act	2/32	0.230191015965044	1	FACETS	0.37	0.293	0.457	0.37	0.293	0.457	SUBCLONAL	1	TRUE	0	0.27	1		454	468	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864482	57864482	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	243	789	2	ENST00000228682.2:c.1959A>C	p.Arg653Ser	p.R653S	ENST00000228682	NM_005269.2	653	agA/agC	12/12	1	2	FACETS	0.999	0.934	1	0.999	0.934	1	CLONAL	1	TRUE	1	0.48955915211488	2		791	994	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50782593	50782594	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0062268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	222	578	1	ENST00000307179.4:c.2106_2107dup	p.Pro703LeufsTer12	p.P703Lfs*12	ENST00000307179		702	att/atTCt	14/20	0.48955915211488	2	FACETS	1	0.96	1	0.521	0.486	0.558	CLONAL	1	TRUE	0	0.48955915211488	2		579	870	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0062268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	196	635	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.159411463572505	3	FACETS	1	0.982	1	0.588	0.545	0.632	INDETERMINATE	1	TRUE	1	0.48955915211488	3		635	848	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0062268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	279	702	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.159411463572505	3	FACETS	1	0.991	1	0.646	0.607	0.686	INDETERMINATE	1	TRUE	1	0.48955915211488	3		702	1098	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968168	18968168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	165	511	1	ENST00000262803.5:c.2008G>A	p.Val670Met	p.V670M	ENST00000262803	NM_002911.3	670	Gtg/Atg	15/24	0.159411463572505	3	FACETS	1	0.959	1	0.533	0.49	0.578	INDETERMINATE	1	TRUE	1	0.48955915211488	3		512	787	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055897	180055897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768687155	NA	P-0062268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	155	540	2	ENST00000261937.6:c.1088C>T	p.Pro363Leu	p.P363L	ENST00000261937	NM_182925.4	363	cCg/cTg	8/30	0.156192999580462	0	FACETS	0.53	0.487	0.574			1	INDETERMINATE	1	TRUE	0	0.48955915211488	0		542	610	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0062269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	111	336	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.20457021520545	3	FACETS	0.95	0.861	1	0.95	0.861	1	INDETERMINATE	2	TRUE	1	0.343971660479571	3		336	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0062269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	178	500	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.343971660479571	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.343971660479571	1		500	738	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575152	48575152	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	86	379	0	ENST00000342988.3:c.346C>T	p.Gln116Ter	p.Q116*	ENST00000342988	NM_005359.5	116	Cag/Tag	3/12	0.343971660479571	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.343971660479571	1		379	402	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082811	16082811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	96	505	0	ENST00000281043.3:c.625C>T	p.Pro209Ser	p.P209S	ENST00000281043	NM_005378.4	209	Ccg/Tcg	2/3	1	2	FACETS	0.838	0.747	0.935	0.838	0.747	0.935	CLONAL	1	TRUE	1	0.343971660479571	2		505	666	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807450	36807450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	141	610	0	ENST00000373129.3:c.1214G>A	p.Gly405Asp	p.G405D	ENST00000373129	NM_032017.1	405	gGc/gAc	12/12	0.343971660479571	1	FACETS	0.947	0.864	1	0.947	0.864	1	CLONAL	1	TRUE	0	0.343971660479571	1		610	717	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90645531	90645538	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGTGGG	GAGGTGGG	-	novel	NA	P-0062269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	100	405	0	ENST00000330062.3:c.85_92del	p.Pro29AlafsTer25	p.P29Afs*25	ENST00000330062	NM_002168.2	29	CCCACCTCg/g	1/11	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.343971660479571	2		405	564	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0062270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	89	304	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA	2	FACETS	0.892	0.797	0.991			1	INDETERMINATE	2	TRUE	NA	0.276485145464179	2		304	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0062270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	70	568	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.276485145464179	1	FACETS	0.866	0.756	0.983	0.866	0.756	0.983	CLONAL	1	TRUE	0	0.276485145464179	1		569	504	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0062270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	95	466	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.276485145464179	2		466	498	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0062270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	74	487	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.276485145464179	1	FACETS	0.845	0.741	0.957	0.845	0.741	0.957	CLONAL	1	TRUE	0	0.276485145464179	1		487	546	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0062270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	74	121	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	NA	2	FACETS	0.776	0.684	0.873			1	INDETERMINATE	2	TRUE	NA	0.276485145464179	2		121	345	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519999	NA	P-0062270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	120	738	0	ENST00000269305.4:c.716A>G	p.Asn239Ser	p.N239S	ENST00000269305	NM_001126112.2	239	aAc/aGc	7/11	0.276485145464179	1	FACETS	0.789	0.717	0.864	1	0.986	1	SUBCLONAL	2	TRUE	0	0.276485145464179	1		738	474	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882099	36882099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199646937	NA	P-0062270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	60	514	0	ENST00000358127.4:c.914G>A	p.Arg305His	p.R305H	ENST00000358127	NM_001280556.1	305	cGt/cAt	8/10	0.273443964766968	2	FACETS	0.742	0.639	0.854	0.371	0.319	0.427	SUBCLONAL	1	TRUE	0	0.276485145464179	2		514	585	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70412277	70412277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	48	322	0	ENST00000373644.4:c.4387G>A	p.Ala1463Thr	p.A1463T	ENST00000373644	NM_030625.2	1463	Gca/Aca	6/12	1	2	FACETS	0.76	0.643	0.888	0.76	0.643	0.888	SUBCLONAL	1	TRUE	1	0.276485145464179	2		322	457	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032541	12032541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267604739	NA	P-0062270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	67	364	0	ENST00000353533.5:c.977C>T	p.Pro326Leu	p.P326L	ENST00000353533	NM_003010.3	326	cCg/cTg	9/11	0.276485145464179	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.276485145464179	1		364	349	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266963	41266963	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770795614	NA	P-0062270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	124	608	0	ENST00000349496.5:c.634C>T	p.Arg212Cys	p.R212C	ENST00000349496	NM_001904.3	212	Cgt/Tgt	5/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.276485145464179	2		608	745	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573312	41573312	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763290593	NA	P-0062270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	65	813	0	ENST00000263253.7:c.5597C>T	p.Pro1866Leu	p.P1866L	ENST00000263253	NM_001429.3	1866	cCg/cTg	31/31	1	2	FACETS	0.513	0.444	0.589	0.513	0.444	0.589	SUBCLONAL	1	TRUE	1	0.276485145464179	2		813	916	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784148	9784148	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	64	596	0	ENST00000377346.4:c.2716C>A	p.Gln906Lys	p.Q906K	ENST00000377346	NM_005026.3	906	Cag/Aag	21/24	1	2	FACETS	0.688	0.595	0.789	0.688	0.595	0.789	SUBCLONAL	1	TRUE	1	0.276485145464179	2		596	673	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436671	110436671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	96	683	0	ENST00000375856.3:c.1730C>A	p.Ser577Tyr	p.S577Y	ENST00000375856	NM_003749.2	577	tCc/tAc	1/2	0.276485145464179	4	FACETS	0.983	0.874	1	0.328	0.291	0.367	CLONAL	1	TRUE	1	0.276485145464179	4		683	902	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093446	30093446	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	15	288	0	ENST00000331968.5:c.1817G>T	p.Gly606Val	p.G606V	ENST00000331968	NM_002742.2	606	gGa/gTa	13/18	0.273443964766968	2	FACETS	0.502	0.368	0.664	0.251	0.184	0.332	SUBCLONAL	1	TRUE	0	0.276485145464179	2		288	216	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374429	31374429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	228	658	0	ENST00000328111.2:c.428C>T	p.Thr143Ile	p.T143I	ENST00000328111	NM_006892.3	143	aCc/aTc	5/23	0.0691176903406647	4	FACETS	1	0.964	1	1	0.964	1	INDETERMINATE	2	TRUE	2	0.276485145464179	4		658	1000	SUCCESS
APC	324	MSKCC	GRCh37	5	112176036	112176036	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	117	561	0	ENST00000257430.4:c.4746del	p.Met1583CysfsTer67	p.M1583Cfs*67	ENST00000257430	NM_000038.5	1582	gCc/gc	16/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.276485145464179	2		561	612	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864575	56864575	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	34	405	0	ENST00000519728.1:c.538A>G	p.Ile180Val	p.I180V	ENST00000519728	NM_002350.3	180	Att/Gtt	7/13	0.247817740106806	3	FACETS	0.546	0.445	0.659	0.273	0.222	0.33	SUBCLONAL	1	TRUE	1	0.276485145464179	3		405	513	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	34	510	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.72	0.587	0.869	0.72	0.587	0.869	SUBCLONAL	1	TRUE	1	0.18	2		510	525	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0062272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	34	616	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	1	2	FACETS	0.542	0.441	0.656	0.542	0.441	0.656	SUBCLONAL	1	TRUE	1	0.18	2		616	697	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	53	549	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.18	2		549	556	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0062272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	54	801	3	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.749	0.638	0.871	0.749	0.638	0.871	SUBCLONAL	1	TRUE	1	0.18	2		804	801	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0062272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	176	610	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.179381204480468	3	FACETS	0.838	0.772	0.906	1	0.984	1	CLONAL	3	TRUE	1	0.18	3		610	848	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0062272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	26	386	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	1	2	FACETS	0.935	0.742	1	0.935	0.742	1	CLONAL	1	TRUE	1	0.18	2		386	309	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	23	326	1	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.415	0.322	0.523	0.415	0.322	0.523	SUBCLONAL	1	TRUE	1	0.18	2		327	616	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871145	12871146	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs786201011	NA	P-0062272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	46	663	0	ENST00000228872.4:c.374_375del	p.Ser125Ter	p.S125*	ENST00000228872	NM_004064.3	124	aaCTct/aact	1/3	1	2	FACETS	0.782	0.657	0.92	0.782	0.657	0.92	CLONAL	1	TRUE	1	0.18	2		663	654	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437588	56437588	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	31	562	0	ENST00000407977.2:c.874C>T	p.His292Tyr	p.H292Y	ENST00000407977		292	Cat/Tat	8/10	1	2	FACETS	0.607	0.49	0.741	0.607	0.49	0.741	SUBCLONAL	1	TRUE	1	0.18	2		562	567	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489537	56489537	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	65	602	0	ENST00000267101.3:c.2002G>T	p.Gly668Trp	p.G668W	ENST00000267101	NM_001982.3	668	Ggg/Tgg	17/28	1	2	FACETS	0.931	0.806	1	0.931	0.806	1	CLONAL	1	TRUE	1	0.18	2		602	776	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354342	354342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375396918	NA	P-0062272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	56	524	0	ENST00000262320.3:c.1216G>A	p.Glu406Lys	p.E406K	ENST00000262320	NM_003502.3	406	Gag/Aag	5/11	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.18	2		524	563	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717718	89717719	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0062272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	33	381	0	ENST00000371953.3:c.743_744del	p.Pro248ArgfsTer4	p.P248Rfs*4	ENST00000371953	NM_000314.4	248	cCT/c	7/9	0.179381204480468	3	FACETS	0.763	0.62	0.924	0.381	0.31	0.462	CLONAL	1	TRUE	1	0.18	3		381	524	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056309	27056309	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	57	705	0	ENST00000324856.7:c.1307del	p.Gly436AlafsTer183	p.G436Afs*183	ENST00000324856	NM_006015.4	435	caG/ca	2/20	1	2	FACETS	0.81	0.693	0.938	0.81	0.693	0.938	CLONAL	1	TRUE	1	0.18	2		705	782	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100142	27100142	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	81	879	0	ENST00000324856.7:c.3938A>T	p.Asn1313Ile	p.N1313I	ENST00000324856	NM_006015.4	1313	aAc/aTc	16/20	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.18	2		879	833	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624275	89624276	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0062272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	63	300	0	ENST00000371953.3:c.49_50insT	p.Gln17LeufsTer27	p.Q17Lfs*27	ENST00000371953	NM_000314.4	17	caa/cTaa	1/9	0.179381204480468	3	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	1	0.18	3		300	345	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655410	67655410	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	36	470	0	ENST00000264010.4:c.1273C>A	p.His425Asn	p.H425N	ENST00000264010	NM_006565.3	425	Cac/Aac	7/12	1	2	FACETS	0.725	0.595	0.871	0.725	0.595	0.871	SUBCLONAL	1	TRUE	1	0.18	2		470	552	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89825110	89825110	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	67	619	0	ENST00000389301.3:c.2856G>T	p.Gln952His	p.Q952H	ENST00000389301	NM_000135.2	952	caG/caT	30/43	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.18	2		619	716	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592052	55592052	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	32	435	0	ENST00000288135.5:c.1376T>C	p.Val459Ala	p.V459A	ENST00000288135	NM_000222.2	459	gTg/gCg	9/21	1	2	FACETS	0.608	0.492	0.739	0.608	0.492	0.739	SUBCLONAL	1	TRUE	1	0.18	2		435	585	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589151	67589152	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0062272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	13	382	0	ENST00000274335.5:c.1141dup	p.Ile381AsnfsTer14	p.I381Nfs*14	ENST00000274335		380	tta/ttAa	9/15	1	2	FACETS	0.469	0.334	0.635	0.469	0.334	0.635	SUBCLONAL	1	TRUE	1	0.18	2		382	308	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721945	176721945	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	72	863	0	ENST00000439151.2:c.7576C>G	p.Pro2526Ala	p.P2526A	ENST00000439151	NM_022455.4	2526	Ccc/Gcc	23/23	1	2	FACETS	0.914	0.797	1	0.914	0.797	1	CLONAL	1	TRUE	1	0.18	2		863	875	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672864	30672864	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	81	852	0	ENST00000376406.3:c.4096A>C	p.Thr1366Pro	p.T1366P	ENST00000376406	NM_014641.2	1366	Act/Cct	10/15	1	2	FACETS	0.902	0.793	1	0.902	0.793	1	CLONAL	1	TRUE	1	0.18	2		852	998	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76953081	76953081	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	15	252	0	ENST00000373344.5:c.232C>T	p.Arg78Ter	p.R78*	ENST00000373344	NM_000489.3	78	Cga/Tga	4/35	1	2	FACETS	0.593	0.433	0.785	0.593	0.433	0.785	SUBCLONAL	1	TRUE	1	0.18	2		252	281	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39704920	39704920	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	44	494	0	ENST00000361337.2:c.265C>T	p.Arg89Ter	p.R89*	ENST00000361337	NM_003286.2	89	Cga/Tga	4/21	1	2	FACETS	0.888	0.743	1	0.888	0.743	1	CLONAL	1	TRUE	1	0.14	2		494	708	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2137891	2137891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45490993	NA	P-0062273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	53	798	0	ENST00000219476.3:c.5017G>A	p.Val1673Ile	p.V1673I	ENST00000219476	NM_000548.3	1673	Gtc/Atc	39/42	1	2	FACETS	0.851	0.723	0.991	0.851	0.723	0.991	CLONAL	1	TRUE	1	0.14	2		798	890	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223485	2223485	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	53	589	0	ENST00000398665.3:c.3596G>A	p.Arg1199Gln	p.R1199Q	ENST00000398665	NM_032482.2	1199	cGa/cAa	25/28	1	2	FACETS	0.966	0.822	1	0.966	0.822	1	CLONAL	1	TRUE	1	0.14	2		589	784	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879636	123879636	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	28	321	0	ENST00000330479.4:c.332C>T	p.Ser111Phe	p.S111F	ENST00000330479	NM_020382.3	111	tCc/tTc	4/9	1	2	FACETS	0.813	0.649	1	0.813	0.649	1	CLONAL	1	TRUE	1	0.14	2		321	492	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6222212	6222212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1237687182	NA	P-0062273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	57	834	0	ENST00000252674.7:c.1030G>A	p.Glu344Lys	p.E344K	ENST00000252674	NM_005934.3	344	Gag/Aag	6/12	1	2	FACETS	0.744	0.636	0.863	0.744	0.636	0.863	SUBCLONAL	1	TRUE	1	0.14	2		834	1094	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224067	39224067	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881032	NA	P-0062273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	34	317	0	ENST00000402219.2:c.3077G>A	p.Arg1026Lys	p.R1026K	ENST00000402219	NM_005633.3	1026	aGa/aAa	19/23	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.14	2		317	451	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519527	137519527	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	54	580	0	ENST00000367739.4:c.1111C>G	p.Leu371Val	p.L371V	ENST00000367739	NM_000416.2	371	Ctg/Gtg	7/7	1	2	FACETS	0.94	0.801	1	0.94	0.801	1	CLONAL	1	TRUE	1	0.14	2		580	821	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	24	471	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.782	0.613	0.977	0.782	0.613	0.977	CLONAL	1	TRUE	1	0.17	2		471	361	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857925	9857925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs534440095	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	30	622	0	ENST00000330684.3:c.3476G>A	p.Arg1159His	p.R1159H	ENST00000330684	NM_001134407.1	1159	cGc/cAc	13/13	1	2	FACETS	0.777	0.626	0.95	0.777	0.626	0.95	CLONAL	1	TRUE	1	0.17	2		622	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	27	529	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.861	0.685	1	0.861	0.685	1	CLONAL	1	TRUE	1	0.17	2		529	369	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216477	108216477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587782558	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	24	318	1	ENST00000278616.4:c.8432del	p.Lys2811SerfsTer46	p.K2811Sfs*46	ENST00000278616	NM_000051.3	2809	cAa/ca	58/63	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.17	2		319	228	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962529	100962529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767360879	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	30	374	0	ENST00000325455.5:c.1868G>A	p.Arg623His	p.R623H	ENST00000325455	NM_001202474.3	623	cGc/cAc	3/8	1	2	FACETS	0.978	0.788	1	0.978	0.788	1	CLONAL	1	TRUE	1	0.17	2		374	361	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259870	16259870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs186683366	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	35	590	0	ENST00000375759.3:c.7135G>A	p.Glu2379Lys	p.E2379K	ENST00000375759	NM_015001.2	2379	Gaa/Aaa	11/15	1	2	FACETS	0.812	0.665	0.978	0.812	0.665	0.978	CLONAL	1	TRUE	1	0.17	2		590	507	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532681	46532681	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201330473	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	29	428	0	ENST00000262741.5:c.397G>A	p.Val133Met	p.V133M	ENST00000262741	NM_003629.3	133	Gtg/Atg	4/10	1	2	FACETS	0.912	0.732	1	0.912	0.732	1	CLONAL	1	TRUE	1	0.17	2		428	374	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206667323	206667323	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs782670085	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	25	574	0	ENST00000367120.3:c.2116C>T	p.Arg706Trp	p.R706W	ENST00000367120	NM_014002.3	706	Cgg/Tgg	21/22	1	2	FACETS	0.732	0.576	0.911	0.732	0.576	0.911	CLONAL	1	TRUE	1	0.17	2		574	402	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100462	8100462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752779081	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	49	759	0	ENST00000346208.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000346208		146	Gcc/Acc	3/6	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.17	2		759	474	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143259	58143259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778187	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	20	415	0	ENST00000257904.6:c.661G>A	p.Asp221Asn	p.D221N	ENST00000257904	NM_000075.3	221	Gac/Aac	6/8	1	2	FACETS	0.761	0.582	0.971	0.761	0.582	0.971	CLONAL	1	TRUE	1	0.17	2		415	309	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126534	2126534	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45517268	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	32	617	0	ENST00000219476.3:c.2785G>A	p.Glu929Lys	p.E929K	ENST00000219476	NM_000548.3	929	Gag/Aag	25/42	1	2	FACETS	0.973	0.79	1	0.973	0.79	1	CLONAL	1	TRUE	1	0.17	2		617	387	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038692	14038692	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs760553358	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	17	274	0	ENST00000311895.7:c.2017G>A	p.Gly673Ser	p.G673S	ENST00000311895	NM_005236.2	673	Ggt/Agt	10/11	1	2	FACETS	0.613	0.457	0.8	0.613	0.457	0.8	SUBCLONAL	1	TRUE	1	0.17	2		274	326	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984472	72984472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781364785	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	28	545	0	ENST00000268489.5:c.3112G>A	p.Val1038Met	p.V1038M	ENST00000268489	NM_006885.3	1038	Gtg/Atg	3/10	1	2	FACETS	0.734	0.586	0.903	0.734	0.586	0.903	CLONAL	1	TRUE	1	0.17	2		545	449	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664546	29664547	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	40	442	0	ENST00000356175.3:c.6527_6528del	p.Phe2176CysfsTer44	p.F2176Cfs*44	ENST00000356175	NM_000267.3	2175	acTTtt/actt	42/57	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.17	2		442	386	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210729	2210729	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	28	709	0	ENST00000398665.3:c.1226G>A	p.Arg409His	p.R409H	ENST00000398665	NM_032482.2	409	cGc/cAc	14/28	1	2	FACETS	0.626	0.499	0.772	0.626	0.499	0.772	SUBCLONAL	1	TRUE	1	0.17	2		709	526	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032084	11032084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	30	767	0	ENST00000327064.4:c.1649G>A	p.Arg550Gln	p.R550Q	ENST00000327064	NM_199141.1	550	cGg/cAg	15/16	1	2	FACETS	0.691	0.555	0.845	0.691	0.555	0.845	SUBCLONAL	1	TRUE	1	0.17	2		767	511	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132635	11132635	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	23	549	0	ENST00000358026.2:c.2854del	p.Glu952LysfsTer5	p.E952Kfs*5	ENST00000358026	NM_001128849.1	951	Ggg/gg	19/36	1	2	FACETS	0.652	0.507	0.82	0.652	0.507	0.82	SUBCLONAL	1	TRUE	1	0.17	2		549	415	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214058	36214058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1385766471	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	29	630	1	ENST00000222270.7:c.2884C>T	p.Arg962Cys	p.R962C	ENST00000222270	NM_014727.1	962	Cgc/Tgc	6/37	1	2	FACETS	0.781	0.626	0.957	0.781	0.626	0.957	CLONAL	1	TRUE	1	0.17	2		631	437	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223001	36223002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	31	811	0	ENST00000222270.7:c.5636dup	p.Val1880CysfsTer92	p.V1880Cfs*92	ENST00000222270	NM_014727.1	1877	ttg/ttGg	27/37	1	2	FACETS	0.719	0.581	0.877	0.719	0.581	0.877	SUBCLONAL	1	TRUE	1	0.17	2		811	507	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425291	47425291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	23	579	0	ENST00000404338.3:c.3359G>A	p.Arg1120Gln	p.R1120Q	ENST00000404338	NM_004491.4	1120	cGg/cAg	1/6	1	2	FACETS	0.68	0.529	0.855	0.68	0.529	0.855	SUBCLONAL	1	TRUE	1	0.17	2		579	398	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	43	634	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	1	2	FACETS	0.973	0.814	1	0.973	0.814	1	CLONAL	1	TRUE	1	0.17	2		634	520	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464501	25464501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	39	539	0	ENST00000264709.3:c.2012C>T	p.Thr671Met	p.T671M	ENST00000264709	NM_175629.2	671	aCg/aTg	17/23	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.17	2		539	376	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637440	47637440	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	29	413	0	ENST00000233146.2:c.574del	p.Ile192SerfsTer22	p.I192Sfs*22	ENST00000233146	NM_000251.2	192	Atc/tc	3/16	1	2	FACETS	0.844	0.678	1	0.844	0.678	1	CLONAL	1	TRUE	1	0.17	2		413	404	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639697	47639697	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs878853824	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	14	296	0	ENST00000233146.2:c.790C>T	p.Gln264Ter	p.Q264*	ENST00000233146	NM_000251.2	264	Cag/Tag	4/16	1	2	FACETS	0.824	0.596	1	0.824	0.596	1	CLONAL	1	TRUE	1	0.17	2		296	200	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149655	61149655	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs767945446	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	19	364	0	ENST00000295025.8:c.1845A>T	p.Glu615Asp	p.E615D	ENST00000295025	NM_002908.2	615	gaA/gaT	11/11	1	2	FACETS	0.84	0.639	1	0.84	0.639	1	CLONAL	1	TRUE	1	0.17	2		364	266	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62320430	62320430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	29	453	0	ENST00000360203.5:c.1823G>A	p.Arg608Lys	p.R608K	ENST00000360203	NM_001283009.1	608	aGg/aAg	22/35	1	2	FACETS	1	0.804	1	1	0.804	1	CLONAL	1	TRUE	1	0.17	2		453	341	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21345975	21345975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs797045165	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	30	712	0	ENST00000215739.8:c.850C>T	p.Arg284Cys	p.R284C	ENST00000215739	NM_006767.3	284	Cgc/Tgc	9/21	1	2	FACETS	0.848	0.683	1	0.848	0.683	1	CLONAL	1	TRUE	1	0.17	2		712	416	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21345981	21345981	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773016962	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	21	692	0	ENST00000215739.8:c.856G>A	p.Gly286Arg	p.G286R	ENST00000215739	NM_006767.3	286	Ggg/Agg	9/21	1	2	FACETS	0.6	0.461	0.762	0.6	0.461	0.762	SUBCLONAL	1	TRUE	1	0.17	2		692	412	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29445404	29445404	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	24	689	0	ENST00000544604.2:c.1239del	p.Ala414ProfsTer38	p.A414Pfs*38	ENST00000544604	NM_001206998.1	412	aCc/ac	8/9	1	2	FACETS	0.632	0.494	0.791	0.632	0.494	0.791	SUBCLONAL	1	TRUE	1	0.17	2		689	447	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623099	52623099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	26	503	0	ENST00000394830.3:c.2952G>A	p.Trp984Ter	p.W984*	ENST00000394830	NM_018313.4	984	tgG/tgA	19/30	1	2	FACETS	0.767	0.607	0.95	0.767	0.607	0.95	CLONAL	1	TRUE	1	0.17	2		503	399	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468541	89468541	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	19	397	0	ENST00000336596.2:c.2074+1G>C		p.X692_splice	ENST00000336596	NM_005233.5	692			1	2	FACETS	0.677	0.514	0.87	0.677	0.514	0.87	SUBCLONAL	1	TRUE	1	0.17	2		397	330	SUCCESS
APC	324	MSKCC	GRCh37	5	112179211	112179212	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	28	526	0	ENST00000257430.4:c.7921_7922del	p.Lys2641AspfsTer12	p.K2641Dfs*12	ENST00000257430	NM_000038.5	2640	tcAAag/tcag	16/16	1	2	FACETS	0.888	0.71	1	0.888	0.71	1	CLONAL	1	TRUE	1	0.17	2		526	371	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	25	572	4	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	1	2	FACETS	0.778	0.613	0.968	0.778	0.613	0.968	CLONAL	1	TRUE	1	0.17	2		576	378	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138201288	138201288	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773168508	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	33	525	0	ENST00000237289.4:c.1987G>A	p.Gly663Ser	p.G663S	ENST00000237289	NM_001270507.1	663	Ggc/Agc	8/9	1	2	FACETS	0.961	0.783	1	0.961	0.783	1	CLONAL	1	TRUE	1	0.17	2		525	404	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418891	116418892	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	22	485	0	ENST00000397752.3:c.3402_3403del	p.Phe1134LeufsTer16	p.F1134Lfs*16	ENST00000397752	NM_000245.2	1134	ttTAgt/ttgt	17/21	1	2	FACETS	0.717	0.555	0.905	0.717	0.555	0.905	CLONAL	1	TRUE	1	0.17	2		485	361	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128848687	128848687	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1204546630	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	28	475	0	ENST00000249373.3:c.1352G>A	p.Arg451His	p.R451H	ENST00000249373	NM_005631.4	451	cGc/cAc	7/12	1	2	FACETS	0.958	0.766	1	0.958	0.766	1	CLONAL	1	TRUE	1	0.17	2		475	344	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534444	140534444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1258111302	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	33	435	0	ENST00000288602.6:c.469G>A	p.Val157Ile	p.V157I	ENST00000288602	NM_004333.4	157	Gtt/Att	3/18	1	2	FACETS	0.897	0.73	1	0.897	0.73	1	CLONAL	1	TRUE	1	0.17	2		435	433	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359987	87359987	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs200354354	NA	P-0062274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	25	377	0	ENST00000277120.3:c.1295C>T	p.Ser432Leu	p.S432L	ENST00000277120		432	tCg/tTg	11/19	1	2	FACETS	0.946	0.746	1	0.946	0.746	1	CLONAL	1	TRUE	1	0.17	2		377	311	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0062275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	88	304	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.365454198175333	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.365454198175333	3		304	255	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220703	1220703	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	46	575	0	ENST00000326873.7:c.721G>C	p.Ala241Pro	p.A241P	ENST00000326873	NM_000455.4	241	Gct/Cct	5/10	0.365454198175333	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.365454198175333	1		575	182	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012381	29012382	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0062275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	28	393	0	ENST00000282397.4:c.489dup	p.Asn164Ter	p.N164*	ENST00000282397	NM_002019.4	163	-/T	4/30	0.365454198175333	1	FACETS	0.712	0.574	0.865	0.712	0.574	0.865	SUBCLONAL	1	TRUE	0	0.365454198175333	1		393	176	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600530	10600530	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0062275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	52	646	0	ENST00000171111.5:c.1326-1G>T		p.X442_splice	ENST00000171111	NM_203500.1	442			0.365454198175333	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	0	0.365454198175333	1		646	217	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141406	11141406	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	45	561	0	ENST00000358026.2:c.3383G>A	p.Gly1128Glu	p.G1128E	ENST00000358026	NM_001128849.1	1128	gGa/gAa	25/36	0.365454198175333	1	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	0	0.365454198175333	1		561	192	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271589	15271589	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1177268940	NA	P-0062275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	56	713	0	ENST00000263388.2:c.6850A>T	p.Thr2284Ser	p.T2284S	ENST00000263388	NM_000435.2	2284	Act/Tct	33/33	0.365454198175333	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.365454198175333	1		713	218	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265454	198265454	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	26	308	0	ENST00000335508.6:c.2703A>T	p.Gln901His	p.Q901H	ENST00000335508	NM_012433.2	901	caA/caT	18/25	1	2	FACETS	0.644	0.513	0.793	0.644	0.513	0.793	SUBCLONAL	1	TRUE	1	0.365454198175333	2		308	221	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437431	52437431	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0062275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	36	624	0	ENST00000460680.1:c.1729+1G>A		p.X577_splice	ENST00000460680	NM_004656.3	577			0.365454198175333	1	FACETS	0.982	0.818	1	0.982	0.818	1	CLONAL	1	TRUE	0	0.365454198175333	1		624	164	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876229	35876229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	19	589	0	ENST00000303115.3:c.1021G>A	p.Gly341Arg	p.G341R	ENST00000303115	NM_002185.3	341	Gga/Aga	8/8	1	2	FACETS	0.389	0.296	0.499	0.389	0.296	0.499	SUBCLONAL	1	TRUE	1	0.365454198175333	2		589	267	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956785	68956785	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062275-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	64	396	0	ENST00000288368.4:c.903C>G	p.Asn301Lys	p.N301K	ENST00000288368	NM_024870.2	301	aaC/aaG	8/40	0.362384719773722	3	FACETS	0.908	0.798	1	0.908	0.798	1	CLONAL	2	TRUE	1	0.365454198175333	3		396	228	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564570	55564570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062276-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	33	523	1	ENST00000288135.5:c.458G>A	p.Gly153Glu	p.G153E	ENST00000288135	NM_000222.2	153	gGg/gAg	3/21	1	2	FACETS	0.653	0.532	0.79	0.653	0.532	0.79	SUBCLONAL	1	FALSE	1	0.25837714545579	2		524	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062276-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	30	509	0	ENST00000269305.4:c.1045G>A	p.Glu349Lys	p.E349K	ENST00000269305	NM_001126112.2	349	Gaa/Aaa	10/11	1	2	FACETS	0.586	0.472	0.716	0.586	0.472	0.716	SUBCLONAL	1	FALSE	1	0.25837714545579	2		509	396	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43742111	43742111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062276-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	32	512	0	ENST00000523873.1:c.100G>A	p.Gly34Arg	p.G34R	ENST00000523873		34	Ggg/Agg	2/8	0.239429871680456	2	FACETS	0.584	0.474	0.709	0.292	0.237	0.355	SUBCLONAL	1	FALSE	0	0.25837714545579	2		512	424	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	13	714	1				ENST00000310581	NM_198253.2	-/1132			0.259855595604987	0	FACETS	0.523	0.376	0.698			1	SUBCLONAL	1	FALSE	0	0.30748779031841	0		715	112	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0062277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	20	660	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.190113986015072	3	FACETS	0.598	0.458	0.761	0.299	0.229	0.381	SUBCLONAL	1	FALSE	1	0.30748779031841	3		660	251	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781467	135781467	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203537	NA	P-0062277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	36	662	0	ENST00000298552.3:c.1498C>T	p.Arg500Ter	p.R500*	ENST00000298552	NM_001162426.1	500	Cga/Tga	15/23	1	2	FACETS	0.861	0.711	1	0.861	0.711	1	CLONAL	1	FALSE	1	0.30748779031841	2		662	272	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557352	187557352	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0062277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	23	596	0	ENST00000441802.2:c.4010C>G	p.Ser1337Ter	p.S1337*	ENST00000441802	NM_005245.3	1337	tCa/tGa	6/27	0.283675521571133	1	FACETS	0.508	0.397	0.636	0.508	0.397	0.636	SUBCLONAL	1	FALSE	0	0.30748779031841	1		596	249	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222080	2222080	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	13	789	0	ENST00000398665.3:c.2912C>G	p.Ser971Cys	p.S971C	ENST00000398665	NM_032482.2	971	tCt/tGt	24/28	0.150636328968389	0	FACETS	0.26	0.185	0.351			1	INDETERMINATE	1	FALSE	0	0.30748779031841	0		789	225	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206661313	206661313	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	17	681	0	ENST00000367120.3:c.1679C>G	p.Ser560Cys	p.S560C	ENST00000367120	NM_014002.3	560	tCt/tGt	16/22	1	2	FACETS	0.358	0.267	0.466	0.358	0.267	0.466	SUBCLONAL	1	FALSE	1	0.30748779031841	2		681	309	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518423	69518423	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1396238386	NA	P-0062277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	12	412	0	ENST00000294312.3:c.222G>C	p.Gln74His	p.Q74H	ENST00000294312	NM_005117.2	74	caG/caC	1/3	1	2	FACETS	1	0.767	1	1	0.767	1	CLONAL	1	FALSE	1	0.30748779031841	2		412	72	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444861	49444861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	19	906	0	ENST00000301067.7:c.2605G>A	p.Glu869Lys	p.E869K	ENST00000301067	NM_003482.3	869	Gag/Aag	10/54	0.168371092693803	4	FACETS	0.438	0.332	0.563	0.219	0.166	0.282	INDETERMINATE	1	FALSE	2	0.30748779031841	4		906	369	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26927902	26927902	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	23	546	0	ENST00000381527.3:c.341C>G	p.Ser114Cys	p.S114C	ENST00000381527	NM_001260.1	114	tCt/tGt	4/13	1	2	FACETS	0.723	0.566	0.902	0.723	0.566	0.902	CLONAL	1	FALSE	1	0.30748779031841	2		546	207	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442077	52442077	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	24	640	0	ENST00000460680.1:c.272G>C	p.Cys91Ser	p.C91S	ENST00000460680	NM_004656.3	91	tGt/tCt	5/17	1	2	FACETS	0.41	0.321	0.512	0.41	0.321	0.512	SUBCLONAL	1	FALSE	1	0.30748779031841	2		640	381	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0062278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	109	355	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.797	0.717	0.882	0.797	0.717	0.882	SUBCLONAL	1	TRUE	1	0.420606036655992	2		355	650	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	95	331	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.694	0.618	0.774	0.694	0.618	0.774	SUBCLONAL	1	TRUE	1	0.420606036655992	2		331	651	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0062278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	124	453	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.420606036655992	2		453	517	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0062278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	58	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.841	0.727	0.964	0.841	0.727	0.964	CLONAL	1	TRUE	1	0.420606036655992	2		485	328	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798210	32798210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768337366	NA	P-0062278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	126	593	0	ENST00000374899.4:c.1469C>T	p.Thr490Met	p.T490M	ENST00000374899	NM_018833.2	490	aCg/aTg	9/12	1	2	FACETS	0.916	0.831	1	0.916	0.831	1	CLONAL	1	TRUE	1	0.420606036655992	2		593	654	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0062278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	109	476	9	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.894	0.805	0.987	0.894	0.805	0.987	CLONAL	1	TRUE	1	0.420606036655992	2		485	580	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0062278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	111	430	0	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.420606036655992	2		430	518	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0062278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	50	684	2	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	1	2	FACETS	0.321	0.271	0.376	0.321	0.271	0.376	SUBCLONAL	1	TRUE	1	0.420606036655992	2		686	741	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438316	110438317	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	rs532810290	NA	P-0062278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	50	635	0	ENST00000375856.3:c.82_84dup	p.Asn28dup	p.N28dup	ENST00000375856	NM_003749.2	28	-/AAC	1/2	1	2	FACETS	0.499	0.424	0.582	0.499	0.424	0.582	SUBCLONAL	1	TRUE	1	0.420606036655992	2		635	476	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0062278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	105	351	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.420606036655992	2		351	482	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744385	41744385	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	102	705	0	ENST00000301178.4:c.1010del	p.Pro337LeufsTer29	p.P337Lfs*29	ENST00000301178	NM_021913.4	335	ggC/gg	8/20	1	2	FACETS	0.94	0.844	1	0.94	0.844	1	CLONAL	1	TRUE	1	0.420606036655992	2		705	516	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0062278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	172	657	0	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.974	0.897	1	0.974	0.897	1	CLONAL	1	TRUE	1	0.420606036655992	2		657	840	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738645	145738645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764549158	NA	P-0062278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	114	786	0	ENST00000428558.2:c.2419C>T	p.Arg807Cys	p.R807C	ENST00000428558	NM_004260.3	807	Cgt/Tgt	15/22	1	2	FACETS	0.902	0.814	0.994	0.902	0.814	0.994	CLONAL	1	TRUE	1	0.420606036655992	2		786	601	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933223	100933223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1175582391	NA	P-0062278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	124	395	0	ENST00000325455.5:c.2167G>A	p.Glu723Lys	p.E723K	ENST00000325455	NM_001202474.3	723	Gag/Aag	4/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.420606036655992	2		395	508	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426821	121426821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765241951	NA	P-0062278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	124	643	0	ENST00000257555.6:c.512G>A	p.Arg171Gln	p.R171Q	ENST00000257555		171	cGa/cAa	2/10	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.420606036655992	2		643	587	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939465	36939465	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	159	745	0	ENST00000361632.4:c.385C>A	p.Leu129Ile	p.L129I	ENST00000361632		129	Ctc/Atc	4/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.420606036655992	2		745	703	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624292	89624299	+	frameshift_variant	Frame_Shift_Del	DEL	CTTAGACT	CTTAGACT	-	novel	NA	P-0062278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	140	331	0	ENST00000371953.3:c.66_73del	p.Leu23AspfsTer18	p.L23Dfs*18	ENST00000371953	NM_000314.4	22	gaCTTAGACTtg/gatg	1/9	0.420606036655992	2	FACETS	0.951	0.878	1	0.951	0.878	1	CLONAL	2	TRUE	0	0.420606036655992	2		331	350	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628408	21628408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780808359	NA	P-0062278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	59	264	0	ENST00000421138.2:c.1210C>T	p.Arg404Cys	p.R404C	ENST00000421138		404	Cgt/Tgt	11/16	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.420606036655992	2		264	262	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856115	111856115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226860826	NA	P-0062278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	114	741	0	ENST00000341259.2:c.166G>A	p.Ala56Thr	p.A56T	ENST00000341259	NM_005475.2	56	Gcg/Acg	2/8	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.420606036655992	2		741	515	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346970	73346970	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	84	334	0	ENST00000377767.4:c.1247T>G	p.Phe416Cys	p.F416C	ENST00000377767	NM_014953.3	416	tTt/tGt	9/21	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.420606036655992	2		334	359	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610354	10610354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1294214671	NA	P-0062278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	123	799	0	ENST00000171111.5:c.356G>A	p.Gly119Asp	p.G119D	ENST00000171111	NM_203500.1	119	gGc/gAc	2/6	1	2	FACETS	0.904	0.819	0.993	0.904	0.819	0.993	CLONAL	1	TRUE	1	0.420606036655992	2		799	647	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460543	149460543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372210450	NA	P-0062278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	120	738	0	ENST00000286301.3:c.94G>A	p.Val32Met	p.V32M	ENST00000286301	NM_005211.3	32	Gtg/Atg	3/22	1	2	FACETS	0.922	0.835	1	0.922	0.835	1	CLONAL	1	TRUE	1	0.420606036655992	2		738	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0062279-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	64	677	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.296458856656779	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.29	1		678	320	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0062279-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	32	367	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.296458856656779	1	FACETS	0.912	0.746	1	0.912	0.746	1	CLONAL	1	TRUE	0	0.29	1		367	207	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145753	11145753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062279-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	22	616	0	ENST00000358026.2:c.4115G>A	p.Arg1372His	p.R1372H	ENST00000358026	NM_001128849.1	1372	cGc/cAc	29/36	0.177595432651988	1	FACETS	0.397	0.307	0.501	0.397	0.307	0.501	SUBCLONAL	1	TRUE	0	0.29	1		616	327	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853112	151853112	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062279-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	41	393	0	ENST00000262189.6:c.11843A>G	p.Gln3948Arg	p.Q3948R	ENST00000262189	NM_170606.2	3948	cAg/cGg	46/59	1	2	FACETS	0.949	0.794	1	0.949	0.794	1	CLONAL	1	TRUE	1	0.29	2		393	298	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0062280-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	282	543	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.864008083885586	3	FACETS	0.816	0.774	0.857	0.544	0.516	0.571	CLONAL	2	TRUE	0	0.864008083885586	3		543	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934573	NA	P-0062280-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	205	429	1	ENST00000269305.4:c.722C>A	p.Ser241Tyr	p.S241Y	ENST00000269305	NM_001126112.2	241	tCc/tAc	7/11	0.864008083885586	3	FACETS	1	0.989	1	0.428	0.4	0.456	CLONAL	1	TRUE	0	0.864008083885586	3		430	529	SUCCESS
APC	324	MSKCC	GRCh37	5	112137036	112137036	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062280-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	245	363	0	ENST00000257430.4:c.790C>T	p.Gln264Ter	p.Q264*	ENST00000257430	NM_000038.5	264	Caa/Taa	8/16	0.864008083885586	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.864008083885586	1		363	270	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278407	39278407	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062280-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	122	288	1	ENST00000402219.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000402219	NM_005633.3	248	Cgc/Tgc	6/23	0.444680188533653	3	FACETS	1	0.983	1	0.652	0.598	0.707	INDETERMINATE	1	TRUE	1	0.864008083885586	3		289	310	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306956	65306956	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062280-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	230	493	0	ENST00000342505.4:c.2621T>G	p.Phe874Cys	p.F874C	ENST00000342505	NM_002227.2	874	tTc/tGc	19/25	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.864008083885586	2		493	481	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041144	29041144	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062280-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	106	434	0	ENST00000282397.4:c.284A>G	p.Asn95Ser	p.N95S	ENST00000282397	NM_002019.4	95	aAc/aGc	3/30	0.864008083885586	5	FACETS	0.484	0.433	0.539	0.121	0.108	0.135	SUBCLONAL	1	TRUE	1	0.864008083885586	5		434	1163	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124469379	124469379	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062280-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	57	279	0	ENST00000357628.3:c.1523G>C	p.Ser508Thr	p.S508T	ENST00000357628	NM_015450.2	508	aGt/aCt	16/19	1	2	FACETS	0.517	0.448	0.591	0.517	0.448	0.591	SUBCLONAL	1	TRUE	1	0.864008083885586	2		279	255	SUCCESS
AR	367	MSKCC	GRCh37	X	66863108	66863108	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1402718521	NA	P-0062280-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	180	226	0	ENST00000374690.3:c.1627G>T	p.Ala543Ser	p.A543S	ENST00000374690	NM_000044.3	543	Gcc/Tcc	2/8	0.686353523132541	3	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.864008083885586	3		226	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0062282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	37	624	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.500079935341062	2	FACETS	0.973	0.851	1	0.973	0.851	1	CLONAL	2	TRUE	0	0.613430612193442	2		624	62	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843495	3843495	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	33	582	2	ENST00000262367.5:c.1108C>T	p.Arg370Ter	p.R370*	ENST00000262367	NM_004380.2	370	Cga/Tga	4/31	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.613430612193442	2		584	81	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39657740	39657740	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	51	455	0	ENST00000361337.2:c.33G>C	p.Gln11His	p.Q11H	ENST00000361337	NM_003286.2	11	caG/caC	1/21	0.34494020676587	1	FACETS	0.763	0.663	0.868	0.763	0.663	0.868	INDETERMINATE	1	TRUE	0	0.613430612193442	1		455	151	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242680	46242681	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AATACCTCTCGACTTGCAGTAAATTAGCTCGTGGTGGAATCCTAAT	novel	NA	P-0062313-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	55	332	0	ENST00000334344.6:c.1687_1688insTAATACCTCTCGACTTGCAGTAAATTAGCTCGTGGTGGAATCCTAA	p.Thr563IlefsTer8	p.T563Ifs*8	ENST00000334344	NM_152641.2	548	gaa/gAATACCTCTCGACTTGCAGTAAATTAGCTCGTGGTGGAATCCTAATaa	13/21	1	2	FACETS	0.442	0.379	0.511	0.442	0.379	0.511	SUBCLONAL	1	TRUE	1	0.590673732128247	2		332	421	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100095	157100096	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0062313-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	287	888	2	ENST00000346085.5:c.1032_1033delinsAA	p.Ala345Thr	p.A345T	ENST00000346085	NM_020732.3	344	gcGGcg/gcAAcg	1/20	1	2	FACETS	0.979	0.921	1	0.979	0.921	1	CLONAL	1	TRUE	1	0.590673732128247	2		890	993	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	33	714	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.832	1	1	0.832	1	CLONAL	1	TRUE	1	0.55	2		715	120	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0062317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	57	371	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.55	2		371	203	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0062317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	31	683	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	1	2	FACETS	0.217	0.175	0.265	0.217	0.175	0.265	SUBCLONAL	1	TRUE	1	0.55	2		683	519	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73343052	73343052	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0062317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	19	295	0	ENST00000377767.4:c.1756-2A>G		p.X586_splice	ENST00000377767	NM_014953.3	586			1	2	FACETS	0.646	0.497	0.814	0.646	0.497	0.814	SUBCLONAL	1	TRUE	1	0.55	2		295	107	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463521	25463521	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0062317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	28	639	0	ENST00000264709.3:c.2161A>T	p.Lys721Ter	p.K721*	ENST00000264709	NM_175629.2	721	Aag/Tag	18/23	1	2	FACETS	0.269	0.215	0.331	0.269	0.215	0.331	SUBCLONAL	1	TRUE	1	0.55	2		639	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0062318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	200	635	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.341333401532918	2	FACETS	0.879	0.82	0.939	0.879	0.82	0.939	CLONAL	2	TRUE	0	0.399789567097857	2		635	569	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615014	43615014	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	143	656	0	ENST00000355710.3:c.2428G>T	p.Gly810Cys	p.G810C	ENST00000355710	NM_020975.4	810	Ggc/Tgc	14/20	0.173633476755041	3	FACETS	0.79	0.724	0.859	0.79	0.724	0.859	INDETERMINATE	2	TRUE	1	0.399789567097857	3		656	543	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94211949	94211949	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587782758	NA	P-0062318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	137	402	0	ENST00000323929.3:c.496C>G	p.Pro166Ala	p.P166A	ENST00000323929	NM_005591.3	166	Ccg/Gcg	6/20	0.33970891884753	3	FACETS	0.834	0.764	0.907	0.834	0.764	0.907	CLONAL	2	TRUE	1	0.399789567097857	3		402	493	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219475	5219475	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	143	543	0	ENST00000357368.4:c.3769T>G	p.Phe1257Val	p.F1257V	ENST00000357368	NM_002850.3	1257	Ttt/Gtt	23/38	0.341333401532918	2	FACETS	0.844	0.776	0.913	0.844	0.776	0.913	CLONAL	2	TRUE	0	0.399789567097857	2		543	424	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106922	11106931	+	frameshift_variant	Frame_Shift_Del	DEL	GACCAGAAGA	GACCAGAAGA	-	novel	NA	P-0062318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	169	612	0	ENST00000358026.2:c.1627_1636del	p.Asp543ArgfsTer67	p.D543Rfs*67	ENST00000358026	NM_001128849.1	543	GACCAGAAGAag/ag	10/36	0.341333401532918	2	FACETS	0.802	0.743	0.863	0.802	0.743	0.863	CLONAL	2	TRUE	0	0.399789567097857	2		612	527	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663346	227663346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024227751	NA	P-0062318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	126	604	0	ENST00000305123.5:c.109G>A	p.Glu37Lys	p.E37K	ENST00000305123	NM_005544.2	37	Gag/Aag	1/2	0.33970891884753	3	FACETS	0.85	0.775	0.927	0.85	0.775	0.927	CLONAL	2	TRUE	1	0.399789567097857	3		604	445	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292751	62292751	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	153	627	0	ENST00000360203.5:c.203C>G	p.Ser68Cys	p.S68C	ENST00000360203	NM_001283009.1	68	tCt/tGt	3/35	0.399789567097857	5	FACETS	0.765	0.701	0.833			1	SUBCLONAL	2	TRUE	NA	0.399789567097857	5		627	800	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30733020	30733020	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	169	623	1	ENST00000295754.5:c.1633G>C	p.Asp545His	p.D545H	ENST00000295754	NM_003242.5	545	Gac/Cac	7/7	0.341333401532918	2	FACETS	0.832	0.771	0.895	0.832	0.771	0.895	CLONAL	2	TRUE	0	0.399789567097857	2		624	508	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670792	134670792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	151	614	0	ENST00000398015.3:c.703C>T	p.Pro235Ser	p.P235S	ENST00000398015	NM_004441.4	235	Ccc/Tcc	3/16	0.33970891884753	3	FACETS	0.846	0.778	0.916	0.846	0.778	0.916	CLONAL	2	TRUE	1	0.399789567097857	3		614	536	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84390273	84390273	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs141624154	NA	P-0062318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	70	339	0	ENST00000321945.7:c.508A>C	p.Asn170His	p.N170H	ENST00000321945	NM_139076.2	170	Aat/Cat	6/9	0.33970891884753	3	FACETS	1	0.943	1	0.566	0.496	0.641	CLONAL	1	TRUE	1	0.399789567097857	3		339	371	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391156	89391156	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062319-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	111	536	0	ENST00000336596.2:c.1222G>A	p.Glu408Lys	p.E408K	ENST00000336596	NM_005233.5	408	Gag/Aag	5/17	0.552347039150744	4	FACETS	0.824	0.741	0.91			1	CLONAL	1	TRUE	NA	0.678318589673826	4		536	667	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610234	81610234	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062319-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	261	584	34	ENST00000298171.2:c.1832C>G	p.Pro611Arg	p.P611R	ENST00000298171	NM_000369.2	611	cCg/cGg	10/10	0.55134840048135	2	FACETS	0.774	0.735	0.813	0.774	0.735	0.813	SUBCLONAL	2	TRUE	0	0.678318589673826	2		618	497	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443625	52443625	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0062319-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	308	689	0	ENST00000460680.1:c.68-1G>T		p.X23_splice	ENST00000460680	NM_004656.3	23			0.55134840048135	2	FACETS	0.836	0.799	0.873	0.836	0.799	0.873	CLONAL	2	TRUE	0	0.678318589673826	2		689	543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0062320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	168	677	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.288179664039634	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	0	0.288179664039634	2		678	569	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468391	89468391	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	107	480	0	ENST00000336596.2:c.1925T>G	p.Leu642Arg	p.L642R	ENST00000336596	NM_005233.5	642	cTt/cGt	11/17	0.288179664039634	2	FACETS	0.888	0.802	0.978	0.888	0.802	0.978	CLONAL	2	TRUE	0	0.288179664039634	2		480	418	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245891	5245891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1045893958	NA	P-0062320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	195	827	0	ENST00000357368.4:c.884G>A	p.Arg295Gln	p.R295Q	ENST00000357368	NM_002850.3	295	cGg/cAg	10/38	0.288179664039634	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.288179664039634	2		827	658	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944965	31944965	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	150	628	0	ENST00000340398.3:c.136G>A	p.Val46Met	p.V46M	ENST00000340398	NM_001013699.2	46	Gtg/Atg	1/1	0.274800088367415	4	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	2	0.288179664039634	4		628	663	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309856	30309856	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	44	749	0	ENST00000307677.4:c.166T>A	p.Ser56Thr	p.S56T	ENST00000307677	NM_138578.1	56	Tcc/Acc	2/3	0.288179664039634	4	FACETS	0.448	0.374	0.53	0.224	0.187	0.265	SUBCLONAL	1	TRUE	2	0.288179664039634	4		749	878	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21348234	21348234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1162619671	NA	P-0062320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	200	1598	0	ENST00000215739.8:c.1375C>T	p.His459Tyr	p.H459Y	ENST00000215739	NM_006767.3	459	Cac/Tac	13/21	0.288179664039634	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.288179664039634	1		1598	1154	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294354	1294354	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	143	881	0	ENST00000310581.5:c.647T>G	p.Leu216Arg	p.L216R	ENST00000310581	NM_198253.2	216	cTg/cGg	2/16	0.176750456844181	4	FACETS	0.841	0.768	0.918	0.841	0.768	0.918	CLONAL	2	TRUE	2	0.288179664039634	4		881	760	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169117	32169117	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	154	811	0	ENST00000375023.3:c.3916C>G	p.Pro1306Ala	p.P1306A	ENST00000375023	NM_004557.3	1306	Cca/Gca	22/30	0.207868070366515	4	FACETS	0.842	0.771	0.916	0.842	0.771	0.916	CLONAL	2	TRUE	2	0.288179664039634	4		811	818	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578528	7578528	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	365	648	0	ENST00000269305.4:c.402T>A	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	ttT/ttA	5/11	NA	2	FACETS	0.99	0.958	1			1	INDETERMINATE	3	TRUE	NA	0.502704701660019	2		648	489	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258478	16258478	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	53	690	0	ENST00000375759.3:c.5743G>A	p.Glu1915Lys	p.E1915K	ENST00000375759	NM_015001.2	1915	Gaa/Aaa	11/15	NA	2	FACETS	0.365	0.311	0.425			1	INDETERMINATE	1	TRUE	NA	0.502704701660019	2		690	577	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574380	95574380	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	37	421	0	ENST00000393063.1:c.2487T>G	p.Ile829Met	p.I829M	ENST00000393063	NM_030621.3	829	atT/atG	17/28	0.337185577098956	3	FACETS	0.509	0.42	0.608	0.17	0.14	0.203	SUBCLONAL	1	TRUE	0	0.502704701660019	3		421	362	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24129365	24129365	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	67	458	0	ENST00000263121.7:c.9G>C	p.Met3Ile	p.M3I	ENST00000263121	NM_003073.3	3	atG/atC	1/9	0.468426449341403	3	FACETS	0.875	0.765	0.994	0.438	0.382	0.497	CLONAL	1	TRUE	1	0.502704701660019	3		458	381	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008488	70008488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	116	508	0	ENST00000394351.3:c.775C>T	p.Arg259Ter	p.R259*	ENST00000394351	NM_000248.3	259	Cga/Tga	8/9	0.502704701660019	6	FACETS	1	0.965	1	0.288	0.26	0.319	CLONAL	1	TRUE	2	0.502704701660019	6		508	802	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339480	81339480	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs746380080	NA	P-0062321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	35	404	0	ENST00000222390.5:c.1524G>T	p.Met508Ile	p.M508I	ENST00000222390	NM_000601.4	508	atG/atT	13/18	0.108784452343359	5	FACETS	0.643	0.527	0.772			1	INDETERMINATE	1	TRUE	NA	0.502704701660019	5		404	380	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70967539	70967539	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	41	395	0	ENST00000276594.2:c.1484C>G	p.Thr495Ser	p.T495S	ENST00000276594	NM_024504.3	495	aCt/aGt	7/8	0.351532468356449	3	FACETS	0.491	0.409	0.581	0.164	0.136	0.194	SUBCLONAL	1	TRUE	0	0.502704701660019	3		395	416	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246196	41246214	+	frameshift_variant	Frame_Shift_Del	DEL	GATTTGGAGTGAACTCTTT	GATTTGGAGTGAACTCTTT	TG	novel	NA	P-0062321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	272	500	1	ENST00000357654.3:c.1334_1352delinsCA	p.Glu445AlafsTer5	p.E445Afs*5	ENST00000357654	NM_007294.3	445	gAAAGAGTTCACTCCAAATCa/gCAa	10/23	0.511127058548726	3	FACETS	0.884	0.849	0.918	1	0.993	1	CLONAL	4	TRUE	0	0.502704701660019	3		501	383	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556065	29556067	+	inframe_deletion	In_Frame_Del	DEL	CCA	CCA	-	novel	NA	P-0062321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	75	366	0	ENST00000356175.3:c.2432_2434del	p.Thr811del	p.T811del	ENST00000356175	NM_000267.3	811	aCCAtt/att	21/57	0.511127058548726				0.965	1				CLONAL	1	TRUE	0	0.502704701660019	3		366	300	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0062322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	149	367	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.642575903275562	2		367	438	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0062322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	156	557	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.932	0.859	1	0.932	0.859	1	CLONAL	1	TRUE	1	0.642575903275562	2		559	521	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604748	48604748	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	190	600	0	ENST00000342988.3:c.1570T>C	p.Trp524Arg	p.W524R	ENST00000342988	NM_005359.5	524	Tgg/Cgg	12/12	0.642575903275562	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.642575903275562	1		600	397	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495478	56495478	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	273	719	0	ENST00000267101.3:c.3668A>T	p.Glu1223Val	p.E1223V	ENST00000267101	NM_001982.3	1223	gAg/gTg	28/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.642575903275562	2		719	779	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577111	7577112	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CACAAACACGCACCTCAAAGCTGTTCCGTCCCAGTAGATTA	novel	NA	P-0062322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	100	597	0	ENST00000269305.4:c.786_826dup	p.Ala276ValfsTer83	p.A276Vfs*83	ENST00000269305	NM_001126112.2	276	gcc/gTAATCTACTGGGACGGAACAGCTTTGAGGTGCGTGTTTGTGcc	8/11	0.642575903275562	1	FACETS	0.428	0.384	0.475	0.428	0.384	0.475	SUBCLONAL	1	TRUE	0	0.642575903275562	1		597	493	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0062323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	61	327	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.909	0.786	1	0.909	0.786	1	CLONAL	1	TRUE	1	0.277822499358347	2		327	483	SUCCESS
APC	324	MSKCC	GRCh37	5	112137036	112137036	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	54	363	0	ENST00000257430.4:c.790C>T	p.Gln264Ter	p.Q264*	ENST00000257430	NM_000038.5	264	Caa/Taa	8/16	1	2	FACETS	0.785	0.671	0.91	0.785	0.671	0.91	CLONAL	1	TRUE	1	0.277822499358347	2		363	495	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	80	566	0	ENST00000257430.4:c.4199C>A	p.Ser1400Ter	p.S1400*	ENST00000257430	NM_000038.5	1400	tCg/tAg	16/16	1	2	FACETS	0.83	0.73	0.937	0.83	0.73	0.937	CLONAL	1	TRUE	1	0.277822499358347	2		566	694	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624270	89624270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123324	NA	P-0062323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	48	255	0	ENST00000371953.3:c.44G>A	p.Arg15Lys	p.R15K	ENST00000371953	NM_000314.4	15	aGa/aAa	1/9	0.277822499358347	1	FACETS	0.921	0.783	1	0.921	0.783	1	CLONAL	1	TRUE	0	0.277822499358347	1		255	323	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236086	108236086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782292	NA	P-0062323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	70	330	1	ENST00000278616.4:c.9022C>T	p.Arg3008Cys	p.R3008C	ENST00000278616	NM_000051.3	3008	Cgt/Tgt	63/63	1	2	FACETS	0.701	0.61	0.799	0.701	0.61	0.799	SUBCLONAL	1	TRUE	1	0.277822499358347	2		331	719	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023048	27023091	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGCCGCCGGGCAGGAAAGCGAGGGCCCCGCCGTGGGGCCGCC	GCAGCCGCCGGGCAGGAAAGCGAGGGCCCCGCCGTGGGGCCGCC	-	novel	NA	P-0062323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	74	542	0	ENST00000324856.7:c.162_205del	p.Gln56LysfsTer40	p.Q56Kfs*40	ENST00000324856	NM_006015.4	52	GCAGCCGCCGGGCAGGAAAGCGAGGGCCCCGCCGTGGGGCCGCCg/g	1/20	1	2	FACETS	0.79	0.692	0.897	0.79	0.692	0.897	SUBCLONAL	1	TRUE	1	0.277822499358347	2		542	674	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368200	45368200	+	stop_lost	Nonstop_Mutation	SNP	A	A	T	novel	NA	P-0062323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	135	479	0	ENST00000262160.6:c.1402T>A	p.Ter468LysextTer8	p.*468Kext*8	ENST00000262160	NM_005901.5	468	Taa/Aaa	11/11	0.256032900295241	2	FACETS	0.789	0.719	0.861	0.789	0.719	0.861	SUBCLONAL	2	TRUE	0	0.277822499358347	2		479	616	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247174	153247174	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	130	422	0	ENST00000281708.4:c.1628G>C	p.Arg543Thr	p.R543T	ENST00000281708	NM_033632.3	543	aGa/aCa	10/12	0.256032900295241	2	FACETS	0.825	0.752	0.902	0.825	0.752	0.902	CLONAL	2	TRUE	0	0.277822499358347	2		422	567	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039204	49039204	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	62	383	0	ENST00000267163.4:c.2282T>C	p.Met761Thr	p.M761T	ENST00000267163	NM_000321.2	761	aTg/aCg	22/27	1	2	FACETS	0.847	0.732	0.971	0.847	0.732	0.971	CLONAL	1	TRUE	1	0.277822499358347	2		383	527	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120279	70120279	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	102	696	0	ENST00000245479.2:c.1281del	p.Tyr428ThrfsTer42	p.Y428Tfs*42	ENST00000245479	NM_000346.3	427	caC/ca	3/3	1	2	FACETS	0.961	0.86	1	0.961	0.86	1	CLONAL	1	TRUE	1	0.277822499358347	2		696	764	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375300	15375300	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	40	587	0	ENST00000263377.2:c.1127del	p.Phe376SerfsTer25	p.F376Sfs*25	ENST00000263377	NM_058243.2	376	tTc/tc	6/20	1	2	FACETS	0.399	0.331	0.476	0.399	0.331	0.476	SUBCLONAL	1	TRUE	1	0.277822499358347	2		587	721	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425371	47425371	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1420876999	NA	P-0062323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	55	620	0	ENST00000404338.3:c.3439C>T	p.Arg1147Cys	p.R1147C	ENST00000404338	NM_004491.4	1147	Cgc/Tgc	1/6	1	2	FACETS	0.502	0.429	0.584	0.502	0.429	0.584	SUBCLONAL	1	TRUE	1	0.277822499358347	2		620	788	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	208	509	1				ENST00000310581	NM_198253.2	-/1132			0.300178952347164	3	FACETS	0.862	0.807	0.918	1	0.989	1	CLONAL	3	TRUE	1	0.352169291831635	3		510	537	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	121	378	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	0.352169291831635	6	FACETS	0.89	0.806	0.979	0.445	0.403	0.49	CLONAL	2	TRUE	2	0.352169291831635	6		378	658	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076862	41076862	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs750249800	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	139	400	0	ENST00000373198.4:c.1558G>A	p.Glu520Lys	p.E520K	ENST00000373198	NM_133170.3	520	Gag/Aag	9/32	0.0730049916157633	3	FACETS	0.925	0.847	1			1	INDETERMINATE	2	TRUE	NA	0.352169291831635	3		400	502	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675456	30675456	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	258	724	0	ENST00000376406.3:c.2900C>T	p.Pro967Leu	p.P967L	ENST00000376406	NM_014641.2	967	cCa/cTa	8/15	0.352169291831635	5	FACETS	1	0.954	1	0.682	0.639	0.727	CLONAL	2	TRUE	2	0.352169291831635	5		724	1094	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976476	25976476	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	271	343	0	ENST00000435504.4:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000435504		357	Cga/Tga	11/13	0.316030911552107	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	4	TRUE	0	0.352169291831635	4		343	514	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256532	115256532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267606920	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	193	394	0	ENST00000369535.4:c.179G>A	p.Gly60Glu	p.G60E	ENST00000369535	NM_002524.4	60	gGa/gAa	3/7	0.352169291831635	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.352169291831635	3		394	581	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264696	1264696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532158398	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	84	620	0	ENST00000310581.5:c.2666G>A	p.Arg889Gln	p.R889Q	ENST00000310581	NM_198253.2	889	cGa/cAa	11/16	0.300178952347164	3	FACETS	0.956	0.845	1	0.478	0.422	0.537	CLONAL	1	TRUE	1	0.352169291831635	3		620	587	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466994	18466994	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773615749	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	107	357	0	ENST00000266497.5:c.1133G>A	p.Arg378Gln	p.R378Q	ENST00000266497		378	cGa/cAa	5/31	0.300178952347164	3	FACETS	0.889	0.804	0.978	0.889	0.804	0.978	CLONAL	2	TRUE	1	0.352169291831635	3		357	402	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295254	1295254	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	180	631	0				ENST00000310581	NM_198253.2	-/1132			0.300178952347164	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.352169291831635	3		631	530	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282583	1282583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1311034283	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	109	615	0	ENST00000310581.5:c.1730G>A	p.Arg577Gln	p.R577Q	ENST00000310581	NM_198253.2	577	cGg/cAg	3/16	0.300178952347164	3	FACETS	1	0.968	1	0.592	0.532	0.655	CLONAL	1	TRUE	1	0.352169291831635	3		615	615	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715885	61715885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777247294	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	286	395	0	ENST00000401558.2:c.2044C>T	p.Pro682Ser	p.P682S	ENST00000401558	NM_003400.3	682	Cct/Tct	18/25	0.316030911552107	4	FACETS	0.996	0.948	1	0.996	0.948	1	CLONAL	4	TRUE	0	0.352169291831635	4		395	551	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295241	1295241	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	68	602	0				ENST00000310581	NM_198253.2	-/1132			0.300178952347164	3	FACETS	0.844	0.735	0.962	0.422	0.367	0.481	CLONAL	1	TRUE	1	0.352169291831635	3		602	538	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961360	1961360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1047838051	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	190	519	0	ENST00000382891.5:c.3148G>A	p.Glu1050Lys	p.E1050K	ENST00000382891	NM_133335.3	1050	Gag/Aag	17/22	0.300178952347164	3	FACETS	0.984	0.914	1	0.984	0.914	1	CLONAL	2	TRUE	1	0.352169291831635	3		519	645	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858935	57858935	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	212	693	0	ENST00000228682.2:c.431G>A	p.Gly144Glu	p.G144E	ENST00000228682	NM_005269.2	144	gGg/gAg	5/12	0.352169291831635	3	FACETS	0.925	0.862	0.99	0.925	0.862	0.99	CLONAL	2	TRUE	1	0.352169291831635	3		693	765	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268741	46268741	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	234	643	0	ENST00000371998.3:c.3026C>T	p.Ser1009Phe	p.S1009F	ENST00000371998		1009	tCc/tTc	16/23	0.324762260733402	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.352169291831635	4		643	840	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976370	18976370	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1568284991	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	194	615	0	ENST00000262803.5:c.3020G>A	p.Gly1007Glu	p.G1007E	ENST00000262803	NM_002911.3	1007	gGg/gAg	22/24	0.283834543875891	3	FACETS	0.973	0.904	1	0.973	0.904	1	CLONAL	2	TRUE	1	0.352169291831635	3		615	666	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690637	33690637	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	163	604	1	ENST00000308377.4:c.190G>A	p.Ala64Thr	p.A64T	ENST00000308377	NM_152270.3	64	Gcc/Acc	2/5	0.283834543875891	3	FACETS	0.825	0.759	0.892	0.825	0.759	0.892	CLONAL	2	TRUE	1	0.352169291831635	3		605	660	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1720540	1720540	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	110	576	0	ENST00000378609.4:c.868G>T	p.Asp290Tyr	p.D290Y	ENST00000378609	NM_002074.3	290	Gac/Tac	10/12	0.352169291831635	3	FACETS	1	0.944	1	0.537	0.483	0.594	CLONAL	1	TRUE	1	0.352169291831635	3		576	684	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939410	36939410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	275	711	0	ENST00000361632.4:c.440G>A	p.Gly147Glu	p.G147E	ENST00000361632		147	gGa/gAa	4/16	0.352169291831635	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.352169291831635	3		711	871	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483206	120483206	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553196323	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	117	509	0	ENST00000256646.2:c.3155C>T	p.Pro1052Leu	p.P1052L	ENST00000256646	NM_024408.3	1052	cCc/cTc	19/34	0.352169291831635	3	FACETS	1	0.974	1	0.611	0.552	0.674	CLONAL	1	TRUE	1	0.352169291831635	3		509	639	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230492642	230492642	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	117	538	0	ENST00000391860.1:c.412C>T	p.Gln138Ter	p.Q138*	ENST00000391860	NM_001258311.1	138	Cag/Tag	2/7	0.352169291831635	6	FACETS	1	0.974	1	0.25	0.225	0.277	CLONAL	1	TRUE	1	0.352169291831635	6		538	906	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63817057	63817057	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	125	400	0	ENST00000279873.7:c.1028C>T	p.Pro343Leu	p.P343L	ENST00000279873	NM_032199.2	343	cCc/cTc	6/10	0.27904141083732	4	FACETS	0.841	0.764	0.921	0.841	0.764	0.921	CLONAL	2	TRUE	2	0.352169291831635	4		400	571	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588088	69588088	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	94	528	0	ENST00000168712.1:c.610C>T	p.Pro204Ser	p.P204S	ENST00000168712	NM_002007.2	204	Ccc/Tcc	3/3	0.283834543875891	3	FACETS	1	0.936	1	0.536	0.477	0.598	CLONAL	1	TRUE	1	0.352169291831635	3		528	586	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102094410	102094410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	101	493	0	ENST00000282441.5:c.1090C>T	p.Pro364Ser	p.P364S	ENST00000282441	NM_001130145.2	364	Cca/Tca	7/9	0.283834543875891	3	FACETS	1	0.966	1	0.593	0.531	0.658	CLONAL	1	TRUE	1	0.352169291831635	3		493	569	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243882	46243882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	175	540	0	ENST00000334344.6:c.1976C>T	p.Ser659Phe	p.S659F	ENST00000334344	NM_152641.2	659	tCt/tTt	15/21	0.352169291831635	3	FACETS	0.956	0.885	1	0.956	0.885	1	CLONAL	2	TRUE	1	0.352169291831635	3		540	611	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438697	49438697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1456158488	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	102	590	1	ENST00000301067.7:c.4793C>T	p.Ala1598Val	p.A1598V	ENST00000301067	NM_003482.3	1598	gCc/gTc	19/54	0.352169291831635	3	FACETS	0.941	0.842	1	0.47	0.421	0.523	CLONAL	1	TRUE	1	0.352169291831635	3		591	724	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112527	2112527	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs45493394	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	201	622	0	ENST00000219476.3:c.1287T>A	p.Tyr429Ter	p.Y429*	ENST00000219476	NM_000548.3	429	taT/taA	13/42	0.352169291831635	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.352169291831635	3		622	646	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858216	9858216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	243	625	0	ENST00000330684.3:c.3185C>T	p.Ser1062Leu	p.S1062L	ENST00000330684	NM_001134407.1	1062	tCa/tTa	13/13	0.352169291831635	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.352169291831635	3		625	757	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646303	23646303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373876101	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	208	574	0	ENST00000261584.4:c.1564C>T	p.Pro522Ser	p.P522S	ENST00000261584	NM_024675.3	522	Cca/Tca	4/13	0.352169291831635	3	FACETS	0.953	0.888	1	0.953	0.888	1	CLONAL	2	TRUE	1	0.352169291831635	3		574	729	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831169	72831170	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	179	640	0	ENST00000268489.5:c.5411_5412delinsAA	p.Ser1804Lys	p.S1804K	ENST00000268489	NM_006885.3	1804	aGT/aAA	9/10	0.344957819873564	2	FACETS	0.936	0.869	1	0.936	0.869	1	CLONAL	2	TRUE	0	0.352169291831635	2		640	543	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686983	37686983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs990242263	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	206	591	2	ENST00000447079.4:c.3887C>T	p.Ala1296Val	p.A1296V	ENST00000447079	NM_015083.1	1296	gCc/gTc	14/14	0.283834543875891	3	FACETS	0.986	0.918	1	0.986	0.918	1	CLONAL	2	TRUE	1	0.352169291831635	3		593	698	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61328036	61328036	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	48	151	0	ENST00000283752.5:c.220C>T	p.His74Tyr	p.H74Y	ENST00000283752	NM_006919.2	74	Cat/Tat	3/8	0.277327913727158	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	2	TRUE	0	0.352169291831635	2		151	134	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265730	10265730	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	108	510	0	ENST00000340748.4:c.1447T>A	p.Phe483Ile	p.F483I	ENST00000340748		483	Ttt/Att	19/40	0.300178952347164	3	FACETS	1	0.967	1	0.589	0.53	0.652	CLONAL	1	TRUE	1	0.352169291831635	3		510	612	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291220	10291220	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	111	645	2	ENST00000340748.4:c.251C>T	p.Ser84Phe	p.S84F	ENST00000340748		84	tCc/tTc	4/40	0.300178952347164	3	FACETS	1	0.93	1	0.521	0.469	0.577	CLONAL	1	TRUE	1	0.352169291831635	3		647	711	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143990	11143990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	163	545	0	ENST00000358026.2:c.3571C>T	p.His1191Tyr	p.H1191Y	ENST00000358026	NM_001128849.1	1191	Cac/Tac	26/36	0.352169291831635	2	FACETS	0.906	0.837	0.976	0.906	0.837	0.976	CLONAL	2	TRUE	0	0.352169291831635	2		545	511	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210895	36210895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs865950924	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	236	784	0	ENST00000222270.7:c.646C>T	p.Pro216Ser	p.P216S	ENST00000222270	NM_014727.1	216	Ccc/Tcc	3/37	0.352169291831635	5	FACETS	1	0.963	1	0.697	0.651	0.745	CLONAL	2	TRUE	2	0.352169291831635	5		784	979	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733273	40733273	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	164	575	0	ENST00000373198.4:c.3533T>C	p.Leu1178Pro	p.L1178P	ENST00000373198	NM_133170.3	1178	cTc/cCc	26/32	0.0730049916157633	3	FACETS	0.907	0.836	0.98			1	INDETERMINATE	2	TRUE	NA	0.352169291831635	3		575	604	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928909	49928909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	346	701	0	ENST00000296474.3:c.3457C>T	p.Pro1153Ser	p.P1153S	ENST00000296474	NM_002447.2	1153	Cct/Tct	16/20	0.352169291831635	5	FACETS	0.975	0.924	1	0.975	0.924	1	CLONAL	3	TRUE	2	0.352169291831635	5		701	1027	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940114	49940114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1382976247	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	224	732	0	ENST00000296474.3:c.929G>A	p.Gly310Glu	p.G310E	ENST00000296474	NM_002447.2	310	gGg/gAg	1/20	0.352169291831635	5	FACETS	0.935	0.87	1	0.623	0.58	0.668	CLONAL	2	TRUE	2	0.352169291831635	5		732	1040	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63973845	63973846	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	260	708	0	ENST00000398590.3:c.1206_1207delinsAA	p.Asp403Asn	p.D403N	ENST00000398590	NM_001177387.1	402	ccGGac/ccAAac	9/14	0.352169291831635	5	FACETS	0.856	0.803	0.909	0.856	0.803	0.909	CLONAL	3	TRUE	2	0.352169291831635	5		708	879	SUCCESS
ATR	545	MSKCC	GRCh37	3	142254964	142254964	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	110	260	0	ENST00000350721.4:c.3805C>T	p.Gln1269Ter	p.Q1269*	ENST00000350721	NM_001184.3	1269	Cag/Tag	20/47	0.290688300803821	4	FACETS	0.891	0.811	0.973	0.891	0.811	0.973	CLONAL	3	TRUE	1	0.352169291831635	4		260	316	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502416	186502416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	207	546	0	ENST00000323963.5:c.139G>A	p.Gly47Ser	p.G47S	ENST00000323963		47	Ggc/Agc	3/11	0.290688300803821	4	FACETS	1	0.978	1	0.744	0.693	0.797	CLONAL	2	TRUE	1	0.352169291831635	4		546	712	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447397	187447397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	289	739	0	ENST00000232014.4:c.796C>T	p.Pro266Ser	p.P266S	ENST00000232014	NM_001130845.1	266	Cca/Tca	5/10	0.290688300803821	4	FACETS	0.871	0.822	0.921	0.871	0.822	0.921	CLONAL	3	TRUE	1	0.352169291831635	4		739	849	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808371	1808371	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	286	835	0	ENST00000260795.2:c.2129G>A	p.Gly710Asp	p.G710D	ENST00000260795		710	gGc/gAc	15/17	0.300178952347164	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.352169291831635	3		835	860	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251203	251203	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1400219619	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	78	218	0	ENST00000264932.6:c.1648A>T	p.Lys550Ter	p.K550*	ENST00000264932	NM_004168.2	550	Aag/Tag	12/15	0.300178952347164	3	FACETS	1	0.916	1	1	0.916	1	CLONAL	2	TRUE	1	0.352169291831635	3		218	252	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950162	38950162	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780923070	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	88	569	0	ENST00000357387.3:c.3788C>T	p.Thr1263Ile	p.T1263I	ENST00000357387	NM_152756.3	1263	aCt/aTt	31/38	0.345603470286832	3	FACETS	0.921	0.817	1	0.461	0.408	0.517	CLONAL	1	TRUE	1	0.352169291831635	3		569	638	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177756	56177756	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	83	575	0	ENST00000399503.3:c.2729A>G	p.Lys910Arg	p.K910R	ENST00000399503	NM_005921.1	910	aAa/aGa	14/20	0.345603470286832	3	FACETS	0.834	0.736	0.938	0.417	0.368	0.469	CLONAL	1	TRUE	1	0.352169291831635	3		575	665	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048541	180048541	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	83	680	0	ENST00000261937.6:c.2020+1G>A		p.X674_splice	ENST00000261937	NM_182925.4	674			1	2	FACETS	0.798	0.705	0.897	0.798	0.705	0.897	SUBCLONAL	1	TRUE	1	0.352169291831635	2		680	591	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287880	33287881	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCTCCTCCTCTTCTTCTT	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	58	689	0	ENST00000374542.5:c.1355_1372dup	p.Glu452_Glu457dup	p.E452_E457dup	ENST00000374542	NM_001141970.1	452	gcc/gAAGAAGAAGAGGAGGAGGcc	5/8	0.352169291831635	5	FACETS	0.447	0.382	0.518	0.149	0.127	0.173	SUBCLONAL	1	TRUE	2	0.352169291831635	5		689	1126	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431629	6431629	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	309	225	0	ENST00000356142.4:c.182A>C	p.Gln61Pro	p.Q61P	ENST00000356142	NM_018890.3	61	cAa/cCa	3/7	0.352169291831635	11	FACETS	0.993	0.947	1	0.883	0.842	0.923	CLONAL	8	TRUE	2	0.352169291831635	11		225	571	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978779	13978779	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	783	495	0	ENST00000405192.2:c.328A>G	p.Lys110Glu	p.K110E	ENST00000405192	NM_001163147.1	110	Aaa/Gaa	6/12	0.352169291831635	11	FACETS	1	0.99	1	1	0.99	1	CLONAL	9	TRUE	2	0.352169291831635	11		495	1238	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345745	152345745	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs770438650	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	127	394	0	ENST00000359321.1:c.825T>G	p.Ser275Arg	p.S275R	ENST00000359321	NM_005431.1	275	agT/agG	3/3	0.352169291831635	6	FACETS	1	0.931	1	0.515	0.468	0.564	CLONAL	2	TRUE	2	0.352169291831635	6		394	597	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518115	8518115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	245	494	0	ENST00000356435.5:c.1276G>A	p.Ala426Thr	p.A426T	ENST00000356435		426	Gca/Aca	10/35	0.352169291831635	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.352169291831635	2		494	586	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971160	21971162	+	frameshift_variant	Frame_Shift_Del	DEL	GTG	GTG	TA	novel	NA	P-0062325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	310	636	1	ENST00000304494.5:c.196_198delinsTA	p.His66Ter	p.H66*	ENST00000304494	NM_000077.4	66	CAC/TA	2/3	0.352169291831635	2	FACETS	0.85	0.808	0.893	1	0.993	1	CLONAL	3	TRUE	0	0.352169291831635	2		637	690	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	71	714	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.716	0.629	0.807	0.716	0.629	0.807	SUBCLONAL	1	TRUE	1	0.595941033153626	2		715	333	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0062326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	304	634	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.375357495166153	3	FACETS	1	0.994	1	0.721	0.681	0.762	CLONAL	1	TRUE	1	0.595941033153626	3		634	918	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0062326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	231	561	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.595941033153626	2		561	764	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396633	30396633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	38	366	0	ENST00000331968.5:c.86C>T	p.Pro29Leu	p.P29L	ENST00000331968	NM_002742.2	29	cCa/cTa	1/18	0.595941033153626	1	FACETS	0.391	0.325	0.463	0.391	0.325	0.463	SUBCLONAL	1	TRUE	0	0.595941033153626	1		366	229	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679928	30679928	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	122	675	0	ENST00000376406.3:c.1791G>C	p.Lys597Asn	p.K597N	ENST00000376406	NM_014641.2	597	aaG/aaC	5/15	0.31111660808028	1	FACETS	0.409	0.37	0.45	0.409	0.37	0.45	INDETERMINATE	1	TRUE	0	0.595941033153626	1		675	703	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680263	30680263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	103	540	0	ENST00000376406.3:c.1456G>A	p.Glu486Lys	p.E486K	ENST00000376406	NM_014641.2	486	Gaa/Aaa	5/15	0.31111660808028	1	FACETS	0.38	0.34	0.422	0.38	0.34	0.422	INDETERMINATE	1	TRUE	0	0.595941033153626	1		540	639	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680590	30680590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1357602574	NA	P-0062326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	77	473	0	ENST00000376406.3:c.1129G>A	p.Asp377Asn	p.D377N	ENST00000376406	NM_014641.2	377	Gat/Aat	5/15	0.31111660808028	1	FACETS	0.356	0.313	0.402	0.356	0.313	0.402	INDETERMINATE	1	TRUE	0	0.595941033153626	1		473	509	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681071	30681071	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	91	458	0	ENST00000376406.3:c.648G>C	p.Leu216Phe	p.L216F	ENST00000376406	NM_014641.2	216	ttG/ttC	5/15	0.31111660808028	1	FACETS	0.369	0.328	0.413	0.369	0.328	0.413	INDETERMINATE	1	TRUE	0	0.595941033153626	1		458	581	SUCCESS
APC	324	MSKCC	GRCh37	5	112175358	112175358	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1554085480	NA	P-0062328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	210	460	0	ENST00000257430.4:c.4067C>G	p.Ser1356Ter	p.S1356*	ENST00000257430	NM_000038.5	1356	tCa/tGa	16/16	0.43714141083278	2	FACETS	0.867	0.812	0.924	0.867	0.812	0.924	CLONAL	2	TRUE	0	0.440147586764273	2		460	550	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0062328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	57	367	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.827	0.715	0.949	0.827	0.715	0.949	CLONAL	1	TRUE	1	0.440147586764273	2		367	313	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457303	67457303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768713596	NA	P-0062328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	155	722	0	ENST00000327367.4:c.277C>T	p.Arg93Ter	p.R93*	ENST00000327367	NM_005902.3	93	Cga/Tga	2/9	0.440147586764273	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.440147586764273	1		722	537	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29107991	29107991	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	84	411	0	ENST00000328354.6:c.698A>G	p.Glu233Gly	p.E233G	ENST00000328354	NM_007194.3	233	gAg/gGg	6/15	0.440147586764273	1	FACETS	0.919	0.819	1	0.919	0.819	1	CLONAL	1	TRUE	0	0.440147586764273	1		411	324	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884970	111884970	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	139	643	0	ENST00000341259.2:c.968T>G	p.Leu323Arg	p.L323R	ENST00000341259	NM_005475.2	323	cTa/cGa	5/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.440147586764273	2		643	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0062329-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	347	450	3	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.583840593376881	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.591212313361955	2		453	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0062331-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	135	703	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.199454733742604	3	FACETS	0.861	0.79	0.934	0.861	0.79	0.934	CLONAL	3	TRUE	0	0.289912062599005	3		703	413	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0062331-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	64	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.132177047754659	4	FACETS	0.823	0.717	0.937	0.823	0.717	0.937	INDETERMINATE	2	TRUE	2	0.289912062599005	4		485	346	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860053	57860053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200444628	NA	P-0062331-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	128	540	0	ENST00000228682.2:c.793C>T	p.Arg265Trp	p.R265W	ENST00000228682	NM_005269.2	265	Cgg/Tgg	8/12	0.289912062599005	6	FACETS	1	0.977	1	0.819	0.745	0.896	CLONAL	2	TRUE	3	0.289912062599005	6		540	568	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575186	48575186	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062331-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	84	332	0	ENST00000342988.3:c.380G>C	p.Cys127Ser	p.C127S	ENST00000342988	NM_005359.5	127	tGt/tCt	3/12	0.274589541805625	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	0	0.289912062599005	2		332	271	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0062332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	93	763	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.21	2		763	650	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200978	108200978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	56	441	0	ENST00000278616.4:c.7345G>A	p.Glu2449Lys	p.E2449K	ENST00000278616	NM_000051.3	2449	Gaa/Aaa	50/63	0.116656816152946	3	FACETS	0.963	0.825	1	0.481	0.412	0.557	INDETERMINATE	1	TRUE	1	0.21	3		441	612	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650756	67650756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	46	543	1	ENST00000264010.4:c.1061C>T	p.Ser354Phe	p.S354F	ENST00000264010	NM_006565.3	354	tCc/tTc	5/12	1	2	FACETS	0.659	0.554	0.775	0.659	0.554	0.775	SUBCLONAL	1	TRUE	1	0.21	2		544	665	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259406	89259406	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	68	634	0	ENST00000336596.2:c.550C>G	p.Gln184Glu	p.Q184E	ENST00000336596	NM_005233.5	184	Caa/Gaa	3/17	1	2	FACETS	0.93	0.809	1	0.93	0.809	1	CLONAL	1	TRUE	1	0.21	2		634	696	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388021	31388021	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	79	553	0	ENST00000328111.2:c.1822G>A	p.Glu608Lys	p.E608K	ENST00000328111	NM_006892.3	608	Gag/Aag	17/23	0.116656816152946	3	FACETS	1	0.956	1	0.595	0.523	0.672	INDETERMINATE	1	TRUE	1	0.21	3		553	699	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106946	27106946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	47	751	0	ENST00000324856.7:c.6557C>T	p.Ala2186Val	p.A2186V	ENST00000324856	NM_006015.4	2186	gCa/gTa	20/20	1	2	FACETS	0.566	0.476	0.666	0.566	0.476	0.666	SUBCLONAL	1	TRUE	1	0.21	2		751	791	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	73	480	0	ENST00000267101.3:c.273G>C	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atC	3/28	0.144792798795099	3	FACETS	1	0.952	1	0.592	0.517	0.672	CLONAL	1	TRUE	1	0.21	3		480	649	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679841	88679841	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0062332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	30	368	0	ENST00000360948.2:c.623-1G>A		p.X208_splice	ENST00000360948	NM_001012338.2	208			0.3	1	FACETS	0.807	0.651	0.982	0.807	0.651	0.982	CLONAL	1	TRUE	0	0.21	1		368	317	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114799823	114799823	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	41	358	0	ENST00000543371.1:c.490G>C	p.Gly164Arg	p.G164R	ENST00000543371	NM_001198531.1	164	Ggg/Cgg	5/14	1	2	FACETS	0.799	0.665	0.947	0.799	0.665	0.947	CLONAL	1	TRUE	1	0.21	2		358	489	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006808	62006808	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757407417	NA	P-0062332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	77	686	0	ENST00000392795.3:c.580G>A	p.Asp194Asn	p.D194N	ENST00000392795	NM_001039933.1	194	Gat/Aat	5/6	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.21	2		686	558	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575194	48575194	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	45	373	0	ENST00000342988.3:c.388C>G	p.Pro130Ala	p.P130A	ENST00000342988	NM_005359.5	130	Cca/Gca	3/12	0.296142001920318	1	FACETS	0.784	0.659	0.923	0.784	0.659	0.923	CLONAL	1	TRUE	0	0.21	1		373	489	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644690	134644690	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	49	511	0	ENST00000398015.3:c.91G>C	p.Glu31Gln	p.E31Q	ENST00000398015	NM_004441.4	31	Gag/Cag	2/16	1	2	FACETS	0.91	0.771	1	0.91	0.771	1	CLONAL	1	TRUE	1	0.21	2		511	513	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798880	135798880	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0062332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	68	452	0	ENST00000298552.3:c.364-1G>A		p.X122_splice	ENST00000298552	NM_001162426.1	122			0.3	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.21	1		452	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579575	7579575	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062333-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	88	692	0	ENST00000269305.4:c.112C>T	p.Gln38Ter	p.Q38*	ENST00000269305	NM_001126112.2	38	Caa/Taa	4/11	0.407055198086598	1	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	0	0.407055198086598	1		692	342	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0062333-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	85	324	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.958	0.851	1	0.958	0.851	1	CLONAL	1	TRUE	1	0.407055198086598	2		324	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0062333-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	30	663	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	0.407055198086598	1	FACETS	0.264	0.212	0.323	0.264	0.212	0.323	SUBCLONAL	1	TRUE	0	0.407055198086598	1		663	445	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0062333-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	134	323	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.86	0.789	0.931	1	0.99	1	CLONAL	2	TRUE	1	0.407055198086598	2		323	383	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0062333-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	114	340	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.155914797394236	6	FACETS	1	0.976	1			1	INDETERMINATE	2	TRUE	NA	0.407055198086598	6		340	414	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0062333-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	290	539	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	0.155914797394236	6	FACETS	0.981	0.93	1			1	INDETERMINATE	4	TRUE	NA	0.407055198086598	6		539	659	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0062333-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	169	622	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.86	0.797	0.924	1	0.992	1	CLONAL	2	TRUE	1	0.407055198086598	2		622	483	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395599	31395599	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908940	NA	P-0062333-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	166	676	1	ENST00000328111.2:c.2452G>A	p.Val818Met	p.V818M	ENST00000328111	NM_006892.3	818	Gtg/Atg	23/23	0.407055198086598	4	FACETS	1	0.989	1	0.498	0.458	0.54	CLONAL	1	TRUE	1	0.407055198086598	4		677	768	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711272	114711273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0062333-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	116	521	0	ENST00000543371.1:c.291dup	p.Pro98AlafsTer47	p.P98Afs*47	ENST00000543371	NM_001198531.1	96	aag/aaGg	3/14	1	2	FACETS	0.774	0.705	0.846	1	0.986	1	SUBCLONAL	2	TRUE	1	0.407055198086598	2		521	368	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591946	48591946	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062333-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	23	528	0	ENST00000342988.3:c.1109T>A	p.Val370Asp	p.V370D	ENST00000342988	NM_005359.5	370	gTc/gAc	9/12	0.407055198086598	1	FACETS	0.288	0.225	0.362	0.288	0.225	0.362	SUBCLONAL	1	TRUE	0	0.407055198086598	1		528	312	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6216464	6216464	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1279997160	NA	P-0062333-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	68	581	0	ENST00000252674.7:c.1259C>T	p.Ser420Leu	p.S420L	ENST00000252674	NM_005934.3	420	tCg/tTg	8/12	0.392977696858401	2	FACETS	0.886	0.775	1	0.443	0.387	0.503	CLONAL	1	TRUE	0	0.407055198086598	2		581	377	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446230	29446230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773583710	NA	P-0062333-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	80	654	0	ENST00000389048.3:c.3337C>T	p.Arg1113Trp	p.R1113W	ENST00000389048	NM_004304.4	1113	Cgg/Tgg	20/29	1	2	FACETS	0.804	0.71	0.904	0.804	0.71	0.904	CLONAL	1	TRUE	1	0.407055198086598	2		654	489	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0062340-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	123	421	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.192313286395215	3	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	1	0.23	3		421	580	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039440	47039440	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0062340-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	52	302	0	ENST00000377604.3:c.1062+1G>C		p.X354_splice	ENST00000377604	NM_001204468.1	354			0.0762617931023488	2	FACETS	0.866	0.751	0.988			1	INDETERMINATE	3	TRUE	NA	0.23	2		302	174	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518440	69518440	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1251637643	NA	P-0062340-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	14	345	0	ENST00000294312.3:c.205G>T	p.Asp69Tyr	p.D69Y	ENST00000294312	NM_005117.2	69	Gac/Tac	1/3	0.117769702524383	3	FACETS	1	0.737	1	0.506	0.368	0.671	INDETERMINATE	1	TRUE	1	0.23	3		345	134	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149440	61149440	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062340-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	35	558	0	ENST00000295025.8:c.1630A>G	p.Met544Val	p.M544V	ENST00000295025	NM_002908.2	544	Atg/Gtg	11/11	1	2	FACETS	0.643	0.527	0.774	0.643	0.527	0.774	SUBCLONAL	1	TRUE	1	0.23	2		558	473	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468433	89468433	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062340-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	30	469	0	ENST00000336596.2:c.1967A>T	p.Lys656Ile	p.K656I	ENST00000336596	NM_005233.5	656	aAa/aTa	11/17	0.3	1	FACETS	0.612	0.494	0.747	0.612	0.494	0.747	SUBCLONAL	1	TRUE	0	0.23	1		469	377	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	44	1247	7	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.202	0.168	0.239	0.202	0.168	0.239	SUBCLONAL	1	TRUE	1	0.649662073359329	2		1254	672	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	164	309	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.465421621956398	2	FACETS	0.784	0.733	0.835	0.784	0.733	0.835	SUBCLONAL	2	TRUE	0	0.649662073359329	2		309	322	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	8	349	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.146	0.093	0.213	0.146	0.093	0.213	SUBCLONAL	1	TRUE	1	0.649662073359329	2		349	169	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	229	595	1	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.649662073359329	2		596	622	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	48	560	2	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	0.254	0.214	0.298	0.254	0.214	0.298	SUBCLONAL	1	TRUE	1	0.649662073359329	2		562	582	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	206	489	17	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.649662073359329	2		506	428	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	168	335	3	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.746	0.688	0.807	0.746	0.688	0.807	SUBCLONAL	1	TRUE	1	0.649662073359329	2		338	693	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	210	471	4	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	0.981	0.916	1	0.981	0.916	1	CLONAL	1	TRUE	1	0.649662073359329	2		475	659	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270530	98270530	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs751977093	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	17	436	1	ENST00000331920.6:c.114del	p.Leu39CysfsTer41	p.L39Cfs*41	ENST00000331920	NM_000264.3	38	ggG/gg	1/24	1	2	FACETS	0.196	0.146	0.255	0.196	0.146	0.255	SUBCLONAL	1	TRUE	1	0.649662073359329	2		437	267	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67646013	67646014	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs1470210640	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	140	456	4	ENST00000264010.4:c.950_951del	p.Thr317ArgfsTer91	p.T317Rfs*91	ENST00000264010	NM_006565.3	314	aAC/a	4/12	1	2	FACETS	0.785	0.718	0.854	0.785	0.718	0.854	SUBCLONAL	1	TRUE	1	0.649662073359329	2		460	549	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	41	657	0	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.155	0.128	0.185	0.155	0.128	0.185	SUBCLONAL	1	TRUE	1	0.649662073359329	2		657	814	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	281	466	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	0.465421621956398	2	FACETS	0.795	0.756	0.834	0.795	0.756	0.834	SUBCLONAL	2	TRUE	0	0.649662073359329	2		466	544	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106078	27106078	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	201	644	0	ENST00000324856.7:c.5693del	p.Pro1898HisfsTer25	p.P1898Hfs*25	ENST00000324856	NM_006015.4	1897	Ccc/cc	20/20	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.649662073359329	2		644	607	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11177096	11177096	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878855328	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	99	339	0	ENST00000361445.4:c.6981G>A	p.Met2327Ile	p.M2327I	ENST00000361445	NM_004958.3	2327	atG/atA	50/58	1	2	FACETS	0.651	0.584	0.722	0.651	0.584	0.722	SUBCLONAL	1	TRUE	1	0.649662073359329	2		339	468	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777893	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	29	493	0	ENST00000361445.4:c.5930C>T	p.Thr1977Ile	p.T1977I	ENST00000361445	NM_004958.3	1977	aCa/aTa	43/58	1	2	FACETS	0.127	0.101	0.156	0.127	0.101	0.156	SUBCLONAL	1	TRUE	1	0.649662073359329	2		493	705	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	85	358	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	0.791	0.705	0.88	0.791	0.705	0.88	SUBCLONAL	1	TRUE	1	0.649662073359329	2		358	331	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	38	625	0	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.179	0.147	0.214	0.179	0.147	0.214	SUBCLONAL	1	TRUE	1	0.649662073359329	2		625	654	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952142	178952142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253171657	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	29	411	0	ENST00000263967.3:c.3197C>T	p.Ala1066Val	p.A1066V	ENST00000263967	NM_006218.2	1066	gCa/gTa	21/21	1	2	FACETS	0.22	0.176	0.27	0.22	0.176	0.27	SUBCLONAL	1	TRUE	1	0.649662073359329	2		411	406	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	130	395	4	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	1	2	FACETS	0.7	0.637	0.765	0.7	0.637	0.765	SUBCLONAL	1	TRUE	1	0.649662073359329	2		399	572	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692794	89692794	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121909238	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	22	214	0	ENST00000371953.3:c.278A>G	p.His93Arg	p.H93R	ENST00000371953	NM_000314.4	93	cAt/cGt	5/9	0.465421621956398	2	FACETS	0.306	0.238	0.385	0.153	0.119	0.193	SUBCLONAL	1	TRUE	0	0.649662073359329	2		214	221	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772950	135772951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs118203724	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	27	366	0	ENST00000298552.3:c.2672dup	p.Asn891LysfsTer13	p.N891Kfs*13	ENST00000298552	NM_001162426.1	891	aac/aaAc	21/23	1	2	FACETS	0.167	0.132	0.206	0.167	0.132	0.206	SUBCLONAL	1	TRUE	1	0.649662073359329	2		366	499	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057937	27057937	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	37	813	0	ENST00000324856.7:c.1650del	p.Tyr551ThrfsTer68	p.Y551Tfs*68	ENST00000324856	NM_006015.4	549	Ccc/cc	3/20	1	2	FACETS	0.162	0.132	0.194	0.162	0.132	0.194	SUBCLONAL	1	TRUE	1	0.649662073359329	2		813	705	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968597	55968597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34038364	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	193	477	1	ENST00000263923.4:c.2066C>T	p.Thr689Met	p.T689M	ENST00000263923	NM_002253.2	689	aCg/aTg	14/30	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.649662073359329	2		478	581	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106099	27106099	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	136	631	0	ENST00000324856.7:c.5710G>T	p.Glu1904Ter	p.E1904*	ENST00000324856	NM_006015.4	1904	Gaa/Taa	20/20	1	2	FACETS	0.693	0.632	0.757	0.693	0.632	0.757	SUBCLONAL	1	TRUE	1	0.649662073359329	2		631	604	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094309	193094309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748952219	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	36	353	0	ENST00000367435.3:c.199G>A	p.Val67Met	p.V67M	ENST00000367435	NM_024529.4	67	Gtg/Atg	2/17	0.649662073359329	3	FACETS	0.262	0.215	0.315	0.131	0.107	0.158	SUBCLONAL	1	TRUE	1	0.649662073359329	3		353	560	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444932	49444933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767415197	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	35	583	0	ENST00000301067.7:c.2533dup	p.Arg845ProfsTer3	p.R845Pfs*3	ENST00000301067	NM_003482.3	845	cgg/cCgg	10/54	1	2	FACETS	0.188	0.153	0.227	0.188	0.153	0.227	SUBCLONAL	1	TRUE	1	0.649662073359329	2		583	573	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	31	836	5	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	1	2	FACETS	0.169	0.136	0.207	0.169	0.136	0.207	SUBCLONAL	1	TRUE	1	0.649662073359329	2		841	564	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096205	2096205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	61	474	0	ENST00000219066.1:c.302C>T	p.Ala101Val	p.A101V	ENST00000219066	NM_002528.5	101	gCc/gTc	2/6	1	2	FACETS	0.437	0.378	0.501	0.437	0.378	0.501	SUBCLONAL	1	TRUE	1	0.649662073359329	2		474	430	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214866	36214866	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568372429	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	130	537	1	ENST00000222270.7:c.3296del	p.Gly1099AlafsTer83	p.G1099Afs*83	ENST00000222270	NM_014727.1	1098	Ggg/gg	8/37	1	2	FACETS	0.764	0.696	0.834	0.764	0.696	0.834	SUBCLONAL	1	TRUE	1	0.649662073359329	2		538	524	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639572	3639572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764254888	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	132	712	1	ENST00000294008.3:c.4067C>T	p.Pro1356Leu	p.P1356L	ENST00000294008	NM_032444.2	1356	cCg/cTg	12/15	1	2	FACETS	0.708	0.645	0.773	0.708	0.645	0.773	SUBCLONAL	1	TRUE	1	0.649662073359329	2		713	574	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210725	36210725	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	48	625	2	ENST00000222270.7:c.481del	p.Leu161PhefsTer6	p.L161Ffs*6	ENST00000222270	NM_014727.1	159	aCc/ac	3/37	1	2	FACETS	0.241	0.203	0.282	0.241	0.203	0.282	SUBCLONAL	1	TRUE	1	0.649662073359329	2		627	614	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52725466	52725466	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	40	627	0	ENST00000322088.6:c.1633C>T	p.Gln545Ter	p.Q545*	ENST00000322088	NM_014225.5	545	Cag/Tag	13/15	1	2	FACETS	0.194	0.16	0.231	0.194	0.16	0.231	SUBCLONAL	1	TRUE	1	0.649662073359329	2		627	636	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249413	110249413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	39	568	1	ENST00000374672.4:c.1160C>T	p.Ser387Leu	p.S387L	ENST00000374672	NM_004235.4	387	tCg/tTg	4/5	1	2	FACETS	0.19	0.157	0.228	0.19	0.157	0.228	SUBCLONAL	1	TRUE	1	0.649662073359329	2		569	631	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633218	3633218	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	38	727	0	ENST00000294008.3:c.5033del	p.Pro1678GlnfsTer37	p.P1678Qfs*37	ENST00000294008	NM_032444.2	1678	cCa/ca	14/15	1	2	FACETS	0.205	0.169	0.245	0.205	0.169	0.245	SUBCLONAL	1	TRUE	1	0.649662073359329	2		727	571	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536079	106536079	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	131	472	1	ENST00000369096.4:c.46G>A	p.Ala16Thr	p.A16T	ENST00000369096	NM_001198.3	16	Gcc/Acc	2/7	1	2	FACETS	0.754	0.687	0.823	0.754	0.687	0.823	SUBCLONAL	1	TRUE	1	0.649662073359329	2		473	535	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422380	47422380	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	91	457	0	ENST00000377045.4:c.17del	p.Gly6AlafsTer28	p.G6Afs*28	ENST00000377045	NM_001654.4	5	cGg/cg	2/16	1	2	FACETS	0.597	0.533	0.666	0.597	0.533	0.666	SUBCLONAL	1	TRUE	1	0.649662073359329	2		457	469	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504326	8504326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349236329	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	74	409	0	ENST00000356435.5:c.1757C>T	p.Ala586Val	p.A586V	ENST00000356435		586	gCt/gTt	12/35	1	2	FACETS	0.4	0.35	0.453	0.4	0.35	0.453	SUBCLONAL	1	TRUE	1	0.649662073359329	2		409	570	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303710	65303710	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	145	431	0	ENST00000342505.4:c.3045C>A	p.His1015Gln	p.H1015Q	ENST00000342505	NM_002227.2	1015	caC/caA	22/25	1	2	FACETS	0.718	0.657	0.781	0.718	0.657	0.781	SUBCLONAL	1	TRUE	1	0.649662073359329	2		431	622	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303729	65303729	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	140	469	1	ENST00000342505.4:c.3026T>A	p.Val1009Asp	p.V1009D	ENST00000342505	NM_002227.2	1009	gTc/gAc	22/25	1	2	FACETS	0.688	0.629	0.751	0.688	0.629	0.751	SUBCLONAL	1	TRUE	1	0.649662073359329	2		470	626	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653224	206653224	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782392890	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	50	654	1	ENST00000367120.3:c.1195G>A	p.Val399Ile	p.V399I	ENST00000367120	NM_014002.3	399	Gtc/Atc	11/22	0.649662073359329	3	FACETS	0.227	0.192	0.266	0.114	0.096	0.133	SUBCLONAL	1	TRUE	1	0.649662073359329	3		655	898	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555239	226555239	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	129	505	0	ENST00000366794.5:c.2348A>G	p.Asp783Gly	p.D783G	ENST00000366794	NM_001618.3	783	gAt/gGt	17/23	0.649662073359329	3	FACETS	0.669	0.607	0.735	0.335	0.303	0.368	SUBCLONAL	1	TRUE	1	0.649662073359329	3		505	786	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123260453	123260453	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	38	514	0	ENST00000358487.5:c.1448T>A	p.Leu483Gln	p.L483Q	ENST00000358487	NM_000141.4	483	cTg/cAg	11/18	0.465421621956398	2	FACETS	0.184	0.151	0.22	0.092	0.075	0.11	SUBCLONAL	1	TRUE	0	0.649662073359329	2		514	636	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864800	57864801	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	33	693	0	ENST00000228682.2:c.2279dup	p.Asn760LysfsTer15	p.N760Kfs*15	ENST00000228682	NM_005269.2	759	-/A	12/12	1	2	FACETS	0.178	0.144	0.216	0.178	0.144	0.216	SUBCLONAL	1	TRUE	1	0.649662073359329	2		693	570	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549455	21549455	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	161	532	0	ENST00000382592.4:c.2821A>C	p.Ser941Arg	p.S941R	ENST00000382592	NM_014572.2	941	Agc/Cgc	8/8	1	2	FACETS	0.876	0.808	0.946	0.876	0.808	0.946	CLONAL	1	TRUE	1	0.649662073359329	2		532	566	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660589	67660589	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	40	438	0	ENST00000264010.4:c.1489T>A	p.Cys497Ser	p.C497S	ENST00000264010	NM_006565.3	497	Tgt/Agt	8/12	1	2	FACETS	0.187	0.155	0.224	0.187	0.155	0.224	SUBCLONAL	1	TRUE	1	0.649662073359329	2		438	657	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976566	7976566	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	26	429	0	ENST00000319144.4:c.1826T>C	p.Leu609Pro	p.L609P	ENST00000319144	NM_001139.2	609	cTg/cCg	14/15	1	2	FACETS	0.179	0.142	0.223	0.179	0.142	0.223	SUBCLONAL	1	TRUE	1	0.649662073359329	2		429	446	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58733996	58733996	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	31	425	0	ENST00000305921.3:c.1054A>C	p.Asn352His	p.N352H	ENST00000305921	NM_003620.3	352	Aat/Cat	5/6	1	2	FACETS	0.164	0.132	0.2	0.164	0.132	0.2	SUBCLONAL	1	TRUE	1	0.649662073359329	2		425	582	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760904	59760904	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	80	413	0	ENST00000259008.2:c.3503A>G	p.Lys1168Arg	p.K1168R	ENST00000259008	NM_032043.2	1168	aAa/aGa	20/20	1	2	FACETS	0.731	0.649	0.817	0.731	0.649	0.817	SUBCLONAL	1	TRUE	1	0.649662073359329	2		413	337	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4097312	4097312	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	35	463	0	ENST00000262948.5:c.949G>T	p.Ala317Ser	p.A317S	ENST00000262948	NM_030662.3	317	Gcc/Tcc	8/11	1	2	FACETS	0.175	0.142	0.211	0.175	0.142	0.211	SUBCLONAL	1	TRUE	1	0.649662073359329	2		463	617	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228068	36228068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	143	672	0	ENST00000222270.7:c.7454G>A	p.Cys2485Tyr	p.C2485Y	ENST00000222270	NM_014727.1	2485	tGc/tAc	33/37	1	2	FACETS	0.778	0.712	0.846	0.778	0.712	0.846	SUBCLONAL	1	TRUE	1	0.649662073359329	2		672	566	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560857	9560857	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	49	534	0	ENST00000353224.5:c.925del	p.Gln309LysfsTer93	p.Q309Kfs*93	ENST00000353224	NM_177990.2	309	Caa/aa	4/10	1	2	FACETS	0.243	0.205	0.285	0.243	0.205	0.285	SUBCLONAL	1	TRUE	1	0.649662073359329	2		534	620	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62325770	62325770	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	136	529	0	ENST00000360203.5:c.3040del	p.Gln1014SerfsTer9	p.Q1014Sfs*9	ENST00000360203	NM_001283009.1	1013	gCc/gc	31/35	1	2	FACETS	0.811	0.742	0.883	0.811	0.742	0.883	CLONAL	1	TRUE	1	0.649662073359329	2		529	516	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21343095	21343095	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	197	500	0	ENST00000215739.8:c.527C>T	p.Ser176Leu	p.S176L	ENST00000215739	NM_006767.3	176	tCa/tTa	6/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.649662073359329	2		500	518	SUCCESS
REST	5978	MSKCC	GRCh37	4	57797935	57797935	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	25	504	0	ENST00000309042.7:c.2911T>C	p.Ser971Pro	p.S971P	ENST00000309042	NM_005612.4	971	Tca/Cca	4/4	1	2	FACETS	0.155	0.122	0.194	0.155	0.122	0.194	SUBCLONAL	1	TRUE	1	0.649662073359329	2		504	496	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630357	187630387	+	frameshift_variant	Frame_Shift_Del	DEL	TACCAGTTAACACTATCACACCACTGGTTGG	TACCAGTTAACACTATCACACCACTGGTTGG	-	novel	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	33	530	0	ENST00000441802.2:c.595_625del	p.Pro199AspfsTer5	p.P199Dfs*5	ENST00000441802	NM_005245.3	199	CCAACCAGTGGTGTGATAGTGTTAACTGGTAga/ga	2/27	1	2	FACETS	0.18	0.146	0.218	0.18	0.146	0.218	SUBCLONAL	1	TRUE	1	0.649662073359329	2		530	565	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922066	39922066	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	40	559	0	ENST00000378444.4:c.4106T>A	p.Ile1369Asn	p.I1369N	ENST00000378444	NM_001123385.1	1369	aTc/aAc	9/15	1	2	FACETS	0.186	0.154	0.222	0.186	0.154	0.222	SUBCLONAL	1	TRUE	1	0.649662073359329	2		559	662	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409811	63409811	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062341-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	33	540	0	ENST00000330258.3:c.3356C>G	p.Ser1119Cys	p.S1119C	ENST00000330258	NM_152424.3	1119	tCt/tGt	2/2	1	2	FACETS	0.199	0.161	0.241	0.199	0.161	0.241	SUBCLONAL	1	TRUE	1	0.649662073359329	2		540	511	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0062342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	42	812	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.200927738296335	3	FACETS	0.889	0.754	1	1	0.951	1	CLONAL	3	TRUE	1	0.209751263552959	3		812	166	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0062342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	142	532	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.161717912103333	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.209751263552959	2		532	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578194	7578194	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	141	448	0	ENST00000269305.4:c.655C>G	p.Pro219Ala	p.P219A	ENST00000269305	NM_001126112.2	219	Ccc/Gcc	6/11	0.161717912103333	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	0	0.209751263552959	2		448	648	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47594580	47594580	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	84	522	0	ENST00000430070.2:c.1507del	p.Asp503MetfsTer14	p.D503Mfs*14	ENST00000430070	NM_018095.4	503	Gat/at	4/4	0.200927738296335	3	FACETS	1	0.955	1	0.584	0.515	0.657	CLONAL	1	TRUE	1	0.209751263552959	3		522	758	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32806010	32806010	+	start_lost	Translation_Start_Site	SNP	T	T	C	rs775391251	NA	P-0062342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	64	392	0	ENST00000374899.4:c.1A>G	p.Met1?	p.M1?	ENST00000374899	NM_018833.2	1	Atg/Gtg	2/12	1	2	FACETS	0.961	0.832	1	0.961	0.832	1	CLONAL	1	TRUE	1	0.209751263552959	2		392	635	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0062343-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	185	433	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.975	1	1	0.994	1	CLONAL	2	TRUE	1	0.329430773411693	2		434	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0062343-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	464	532	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.329430773411693	2	FACETS	0.999	0.966	1	1	0.997	1	CLONAL	4	TRUE	0	0.329430773411693	2		532	705	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375562	40375562	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062343-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	54	550	0	ENST00000293328.3:c.388G>T	p.Ala130Ser	p.A130S	ENST00000293328	NM_012448.3	130	Gct/Tct	5/19	1	2	FACETS	0.553	0.472	0.642	0.553	0.472	0.642	SUBCLONAL	1	TRUE	1	0.329430773411693	2		550	593	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875862	76875863	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0062343-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	109	156	0	ENST00000373344.5:c.5272dup	p.Tyr1758LeufsTer6	p.Y1758Lfs*6	ENST00000373344	NM_000489.3	1758	tat/tTat		1	1	FACETS	0.985	0.912	1	1	0.992	1	CLONAL	3	TRUE	0	0.329430773411693	1		156	187	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345969	70345969	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062344-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	34	236	0	ENST00000374080.3:c.2506C>T	p.Leu836Phe	p.L836F	ENST00000374080		836	Ctt/Ttt	18/45	0.00918885060739516	2	FACETS	0.583	0.478	0.701			1	INDETERMINATE	1	TRUE	NA	0.39	2		236	299	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415193	109415193	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062344-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	119	486	0	ENST00000436639.2:c.84T>G	p.Ile28Met	p.I28M	ENST00000436639	NM_014454.2	28	atT/atG	1/10	1	2	FACETS	0.958	0.867	1	0.958	0.867	1	CLONAL	1	TRUE	1	0.39	2		486	637	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602688	10602688	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062348-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	99	718	0	ENST00000171111.5:c.890G>T	p.Cys297Phe	p.C297F	ENST00000171111	NM_203500.1	297	tGc/tTc	3/6	0.175487009466019	1	FACETS	0.849	0.76	0.944	1	0.984	1	CLONAL	2	TRUE	0	0.175487009466019	1		718	606	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486044	29486044	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062348-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	55	371	0	ENST00000356175.3:c.221del	p.Ala74ValfsTer11	p.A74Vfs*11	ENST00000356175	NM_000267.3	74	gCt/gt	3/57	1	2	FACETS	0.818	0.703	0.944	1	0.971	1	CLONAL	2	TRUE	1	0.175487009466019	2		371	383	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490345	29490346	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0062348-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	89	591	0	ENST00000356175.3:c.434_435del	p.Leu145GlnfsTer10	p.L145Qfs*10	ENST00000356175	NM_000267.3	144	TCt/t	4/57	1	2	FACETS	0.864	0.767	0.967	1	0.983	1	CLONAL	2	TRUE	1	0.175487009466019	2		591	587	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61323022	61323022	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062348-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	97	758	0	ENST00000283752.5:c.1042G>T	p.Ala348Ser	p.A348S	ENST00000283752	NM_006919.2	348	Gct/Tct	8/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.175487009466019	2		758	757	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219367	1219368	+	missense_variant	Missense_Mutation	DNP	TG	TG	CT	novel	NA	P-0062348-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	94	698	3	ENST00000326873.7:c.419_420delinsCT	p.Leu140Pro	p.L140P	ENST00000326873	NM_000455.4	140	cTG/cCT	3/10	0.175487009466019	1	FACETS	0.893	0.797	0.995	1	0.985	1	CLONAL	2	TRUE	0	0.175487009466019	1		701	547	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267568	7267568	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062348-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	109	662	0	ENST00000302850.5:c.440A>G	p.Glu147Gly	p.E147G	ENST00000302850	NM_000208.2	147	gAg/gGg	2/22	0.175487009466019	1	FACETS	0.967	0.871	1	1	0.988	1	CLONAL	2	TRUE	0	0.175487009466019	1		662	586	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275768	38275830	+	protein_altering_variant	In_Frame_Del	DEL	GAGGGTCTTCGGGAAGCTCATACTCAGAGACCCCTGCTAGCATGGGAGTCCCACTGGAGGAGA	GAGGGTCTTCGGGAAGCTCATACTCAGAGACCCCTGCTAGCATGGGAGTCCCACTGGAGGAGA	AGGAGG	novel	NA	P-0062348-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	75	747	1	ENST00000425967.3:c.1439_1501delinsCCTCCT	p.Leu480_Arg501delinsProSerCys	p.L480_R501delinsPSC	ENST00000425967	NM_001174067.1	480	cTCTCCTCCAGTGGGACTCCCATGCTAGCAGGGGTCTCTGAGTATGAGCTTCCCGAAGACCCTCgc/cCCTCCTgc	11/19	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.175487009466019	2		748	730	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0062349-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	57	471	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.271608791529589	4	FACETS	0.892	0.785	1	1	0.978	1	CLONAL	4	TRUE	2	0.287756509002316	4		471	143	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070608	67070608	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062349-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	27	472	0	ENST00000412916.2:c.232C>T	p.Arg78Ter	p.R78*	ENST00000412916		78	Cga/Tga	3/6	0.287756509002316	0	FACETS	0.846	0.681	1			1	CLONAL	1	TRUE	0	0.287756509002316	0		472	158	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028667	12028667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062349-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	27	393	0	ENST00000353533.5:c.870del	p.Trp291GlyfsTer27	p.W291Gfs*27	ENST00000353533	NM_003010.3	290	gtC/gt	8/11	0.287756509002316	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.287756509002316	1		393	117	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0062350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	431	416	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.704890609174698	3	FACETS	0.986	0.958	1	0.986	0.958	1	CLONAL	3	TRUE	0	0.704890609174698	3		416	559	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032093	11032093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062350-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	263	660	0	ENST00000327064.4:c.1658C>T	p.Ser553Phe	p.S553F	ENST00000327064	NM_199141.1	553	tCc/tTc	15/16	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.704890609174698	2		660	742	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0062351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	417	625	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.625142134423812	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.625142134423812	2		625	575	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408879	41408879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776612407	NA	P-0062351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	138	491	0	ENST00000373198.4:c.547C>T	p.Arg183Trp	p.R183W	ENST00000373198	NM_133170.3	183	Cgg/Tgg	4/32	0.582183304265721	4	FACETS	0.926	0.843	1	0.463	0.421	0.506	CLONAL	1	TRUE	2	0.625142134423812	4		491	775	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650367	48650367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782263736	NA	P-0062351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	221	359	0	ENST00000376670.3:c.337C>T	p.Arg113Cys	p.R113C	ENST00000376670	NM_002049.3	113	Cgc/Tgc	3/6	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.625142134423812	1		359	334	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386378	31386378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200193299	NA	P-0062351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	174	621	0	ENST00000328111.2:c.1603G>A	p.Val535Ile	p.V535I	ENST00000328111	NM_006892.3	535	Gtc/Atc	15/23	0.582183304265721	4	FACETS	0.918	0.845	0.995	0.459	0.422	0.498	CLONAL	1	TRUE	2	0.625142134423812	4		621	985	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146617	55146617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141047712	NA	P-0062351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	94	534	0	ENST00000257290.5:c.2291G>A	p.Arg764His	p.R764H	ENST00000257290	NM_006206.4	764	cGt/cAt	16/23	0.625142134423812	2	FACETS	0.859	0.772	0.951	0.43	0.386	0.476	CLONAL	1	TRUE	0	0.625142134423812	2		534	350	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741888	17741888	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	196	527	0	ENST00000250003.3:c.559G>A	p.Gly187Ser	p.G187S	ENST00000250003	NM_002478.4	187	Ggc/Agc	1/3	0.625142134423812	4	FACETS	1	0.985	1	0.413	0.383	0.445	CLONAL	1	TRUE	1	0.625142134423812	4		527	822	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939882	71939882	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	220	844	0	ENST00000298229.2:c.509C>G	p.Ala170Gly	p.A170G	ENST00000298229	NM_001567.3	170	gCt/gGt	4/28	0.625142134423812	4	FACETS	1	0.94	1	0.337	0.313	0.362	CLONAL	1	TRUE	1	0.625142134423812	4		844	1130	SUCCESS
ATM	472	MSKCC	GRCh37	11	108168083	108168083	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	78	456	0	ENST00000278616.4:c.4979A>G	p.Asn1660Ser	p.N1660S	ENST00000278616	NM_000051.3	1660	aAc/aGc	33/63	0.625142134423812	4	FACETS	0.805	0.709	0.907	0.268	0.236	0.303	CLONAL	1	TRUE	1	0.625142134423812	4		456	504	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714430	40714430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777325904	NA	P-0062351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	230	620	0	ENST00000373198.4:c.3967G>A	p.Val1323Ile	p.V1323I	ENST00000373198	NM_133170.3	1323	Gtc/Atc	29/32	0.582183304265721	4	FACETS	1	0.986	1	0.603	0.562	0.646	CLONAL	1	TRUE	2	0.625142134423812	4		620	991	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964478	93964478	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	109	471	0	ENST00000369303.4:c.2419G>C	p.Ala807Pro	p.A807P	ENST00000369303	NM_004440.3	807	Gcc/Ccc	14/17	0.625142134423812	4	FACETS	1	0.937	1	0.351	0.316	0.388	CLONAL	1	TRUE	1	0.625142134423812	4		471	538	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268766	41268766	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062357-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	252	484	0	ENST00000349496.5:c.1004A>T	p.Lys335Ile	p.K335I	ENST00000349496	NM_001904.3	335	aAa/aTa	7/15	0.522702722673985	2	FACETS	0.936	0.886	0.986	0.936	0.886	0.986	CLONAL	2	TRUE	0	0.522702722673985	2		484	515	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578408	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCTCAC	novel	NA	P-0062357-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	394	752	6	ENST00000269305.4:c.517_522dup	p.Val173_Arg174dup	p.V173_R174dup	ENST00000269305	NM_001126112.2	173	-/GTGAGG	5/11	0.522702722673985	2	FACETS	0.997	0.956	1	0.997	0.956	1	CLONAL	2	TRUE	0	0.522702722673985	2		758	756	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542569	187542569	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062357-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	206	575	1	ENST00000441802.2:c.5171C>G	p.Ala1724Gly	p.A1724G	ENST00000441802	NM_005245.3	1724	gCc/gGc	10/27	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.522702722673985	2		576	671	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056050	26056064	+	inframe_deletion	In_Frame_Del	DEL	CAACCTTGGGCTTAG	CAACCTTGGGCTTAG	-	novel	NA	P-0062357-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	121	602	1	ENST00000343677.2:c.593_607del	p.Ala198_Val202del	p.A198_V202del	ENST00000343677	NM_005319.3	198	gCTAAGCCCAAGGTTGtc/gtc	1/1	0.522702722673985	2	FACETS	0.757	0.685	0.831	0.378	0.342	0.416	SUBCLONAL	1	TRUE	0	0.522702722673985	2		603	612	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700315	117700315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062357-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	216	356	1	ENST00000368508.3:c.2504C>T	p.Ala835Val	p.A835V	ENST00000368508	NM_002944.2	835	gCt/gTt	17/43	0.522702722673985	2	FACETS	0.968	0.913	1	0.968	0.913	1	CLONAL	2	TRUE	0	0.522702722673985	2		357	427	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345737	152345737	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062357-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	31	311	0	ENST00000359321.1:c.833A>G	p.Glu278Gly	p.E278G	ENST00000359321	NM_005431.1	278	gAa/gGa	3/3	0.302212835797711	2	FACETS	0.359	0.291	0.437	0.18	0.145	0.219	INDETERMINATE	1	TRUE	0	0.522702722673985	2		311	330	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0062368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	186	324	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.466312369994975	5	FACETS	1	0.974	1	0.723	0.675	0.771	INDETERMINATE	2	TRUE	2	0.939060536211406	5		324	440	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578393	7578393	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876660821	NA	P-0062368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	432	713	0	ENST00000269305.4:c.537T>G	p.His179Gln	p.H179Q	ENST00000269305	NM_001126112.2	179	caT/caG	5/11	0.896542008426713	2	FACETS	0.956	0.938	0.973	0.956	0.938	0.973	CLONAL	2	TRUE	0	0.939060536211406	2		713	481	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560898	9560898	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767455314	NA	P-0062368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2428	219	597	1	ENST00000353224.5:c.884C>T	p.Pro295Leu	p.P295L	ENST00000353224	NM_177990.2	295	cCg/cTg	4/10	0.939060536211406	9	FACETS	0.755	0.699	0.815	0.094	0.087	0.102	SUBCLONAL	1	TRUE	1	0.939060536211406	9		598	2647	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772384	56772384	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	43	471	0	ENST00000337432.4:c.238G>C	p.Glu80Gln	p.E80Q	ENST00000337432	NM_058216.2	80	Gag/Cag	2/9	0.862058059516095	3	FACETS	0.248	0.207	0.294	0.124	0.103	0.147	SUBCLONAL	1	TRUE	1	0.939060536211406	3		471	542	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973979	55973979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762221907	NA	P-0062368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	29	578	1	ENST00000263923.4:c.1337C>T	p.Thr446Met	p.T446M	ENST00000263923	NM_002253.2	446	aCg/aTg	10/30	1	2	FACETS	0.173	0.139	0.212	0.173	0.139	0.212	SUBCLONAL	1	TRUE	1	0.939060536211406	2		579	357	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279766	46279766	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	194	540	0	ENST00000371998.3:c.3692G>C	p.Arg1231Thr	p.R1231T	ENST00000371998		1231	aGa/aCa	20/23	0.939060536211406	5	FACETS	0.95	0.878	1	0.317	0.292	0.342	CLONAL	1	TRUE	2	0.939060536211406	5		540	1048	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78931424	78931424	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	175	534	0	ENST00000306801.3:c.3371G>C	p.Gly1124Ala	p.G1124A	ENST00000306801	NM_020761.2	1124	gGa/gCa	29/34	0.862058059516095	3	FACETS	0.868	0.803	0.935	0.434	0.401	0.468	CLONAL	1	TRUE	1	0.939060536211406	3		534	631	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8338930	8338930	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1380382010	NA	P-0062368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	155	402	0	ENST00000356435.5:c.5371G>T	p.Asp1791Tyr	p.D1791Y	ENST00000356435		1791	Gat/Tat	32/35	1	2	FACETS	0.864	0.801	0.928	0.864	0.801	0.928	CLONAL	1	TRUE	1	0.939060536211406	2		402	382	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953974	32953974	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs80359156	NA	P-0062368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	96	316	0	ENST00000380152.3:c.9041C>G	p.Ser3014Ter	p.S3014*	ENST00000380152		3014	tCa/tGa	23/27	0.888448411581954	2	FACETS	0.828	0.75	0.907	0.414	0.375	0.454	CLONAL	1	TRUE	0	0.939060536211406	2		316	247	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405064	70405064	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	144	430	0	ENST00000373644.4:c.2578G>A	p.Glu860Lys	p.E860K	ENST00000373644	NM_030625.2	860	Gag/Aag	4/12	0.862058059516095	3	FACETS	0.903	0.829	0.98	0.452	0.414	0.49	CLONAL	1	TRUE	1	0.939060536211406	3		430	499	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77938071	77938071	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1975	229	461	0	ENST00000361507.4:c.647G>C	p.Arg216Thr	p.R216T	ENST00000361507	NM_080491.2	216	aGa/aCa	4/10	0.939060536211406	11	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.939060536211406	11		461	2204	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512292	38512292	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2144	1217	485	0	ENST00000254066.5:c.1203G>C	p.Glu401Asp	p.E401D	ENST00000254066	NM_000964.3	401	gaG/gaC	9/9	0.939060536211406	27	FACETS	0.982	0.955	1			1	CLONAL	10	TRUE	NA	0.939060536211406	27		485	3361	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583335	46583335	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	260	408	0	ENST00000263734.3:c.263A>T	p.Asp88Val	p.D88V	ENST00000263734	NM_001430.4	88	gAc/gTc	3/16	0.898875581303584	3	FACETS	0.962	0.917	1	0.962	0.917	1	CLONAL	2	TRUE	1	0.939060536211406	3		408	423	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096343	178096343	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	174	578	0	ENST00000397062.3:c.988C>G	p.Gln330Glu	p.Q330E	ENST00000397062	NM_006164.4	330	Caa/Gaa	5/5	0.896526924784588	3	FACETS	1	0.96	1	0.35	0.325	0.377	CLONAL	1	TRUE	0	0.939060536211406	3		578	518	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097203	178097203	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1371809729	NA	P-0062368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	168	396	0	ENST00000397062.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000397062	NM_006164.4	171	Cag/Tag	4/5	0.896526924784588	3	FACETS	0.891	0.823	0.961	0.297	0.274	0.321	CLONAL	1	TRUE	0	0.939060536211406	3		396	590	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626680	100626680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	27	371	0	ENST00000308731.7:c.250G>A	p.Glu84Lys	p.E84K	ENST00000308731	NM_000061.2	84	Gaa/Aaa	4/19	0.466312369994975	5	FACETS	0.317	0.252	0.392	0.106	0.084	0.131	INDETERMINATE	1	TRUE	2	0.939060536211406	5		371	437	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174395	11174395	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1085307113	NA	P-0062369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	161	408	0	ENST00000361445.4:c.7280T>A	p.Leu2427Gln	p.L2427Q	ENST00000361445	NM_004958.3	2427	cTg/cAg	53/58	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.61	2		408	472	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331922	81331922	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	51	294	0	ENST00000222390.5:c.2162del	p.Leu721Ter	p.L721*	ENST00000222390	NM_000601.4	721	tTa/ta	18/18	1	2	FACETS	0.995	0.862	1	0.995	0.862	1	CLONAL	1	TRUE	1	0.61	2		294	168	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0062370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	114	518	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.231681200455229	2	FACETS	0.936	0.85	1	0.936	0.85	1	CLONAL	2	TRUE	0	0.31	2		518	393	SUCCESS
APC	324	MSKCC	GRCh37	5	112175328	112175328	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0062370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	112	556	0	ENST00000257430.4:c.4037C>G	p.Ser1346Ter	p.S1346*	ENST00000257430	NM_000038.5	1346	tCa/tGa	16/16	0.243324538398779	2	FACETS	0.858	0.778	0.942	0.858	0.778	0.942	CLONAL	2	TRUE	0	0.31	2		556	421	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288980	33288980	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	45	673	0	ENST00000374542.5:c.572del	p.Leu191TrpfsTer38	p.L191Wfs*38	ENST00000374542	NM_001141970.1	191	tTg/tg	3/8	0.295662435861342	4	FACETS	0.598	0.502	0.705			1	SUBCLONAL	1	TRUE	NA	0.31	4		673	636	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261779	16261779	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	36	722	0	ENST00000375759.3:c.9044A>G	p.His3015Arg	p.H3015R	ENST00000375759	NM_015001.2	3015	cAt/cGt	11/15	1	2	FACETS	0.413	0.338	0.496	0.413	0.338	0.496	SUBCLONAL	1	TRUE	1	0.31	2		722	563	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120805887	120805887	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	48	674	0	ENST00000257552.2:c.191G>A	p.Gly64Asp	p.G64D	ENST00000257552	NM_002442.3	64	gGc/gAc	4/15	0.295662435861342	2	FACETS	0.556	0.47	0.651	0.278	0.235	0.326	SUBCLONAL	1	TRUE	0	0.31	2		674	557	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830620	72830655	+	inframe_deletion	In_Frame_Del	DEL	GGAGTCACACTCGAGCTTTTCCAGGTTCTCTCCCTG	GGAGTCACACTCGAGCTTTTCCAGGTTCTCTCCCTG	-	novel	NA	P-0062370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	35	582	0	ENST00000268489.5:c.5926_5961del	p.Gln1976_Ser1987del	p.Q1976_S1987del	ENST00000268489	NM_006885.3	1976	CAGGGAGAGAACCTGGAAAAGCTCGAGTGTGACTCC/-	9/10	1	2	FACETS	0.588	0.482	0.706	0.588	0.482	0.706	SUBCLONAL	1	TRUE	1	0.31	2		582	384	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99175955	99175955	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	35	425	0	ENST00000074304.5:c.1867C>A	p.Pro623Thr	p.P623T	ENST00000074304	NM_001134224.1	623	Cca/Aca	18/26	1	2	FACETS	0.549	0.45	0.66	0.549	0.45	0.66	SUBCLONAL	1	TRUE	1	0.31	2		425	411	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225495	26225495	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	55	949	0	ENST00000360408.1:c.113A>C	p.Lys38Thr	p.K38T	ENST00000360408	NM_003532.2	38	aAg/aCg	1/1	0.295662435861342	5	FACETS	0.596	0.508	0.693	0.298	0.254	0.347	SUBCLONAL	1	TRUE	3	0.31	5		949	872	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979251	93979251	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs369029096	NA	P-0062370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	34	477	0	ENST00000369303.4:c.1577A>G	p.Tyr526Cys	p.Y526C	ENST00000369303	NM_004440.3	526	tAc/tGc	7/17	0.295662435861342	3	FACETS	0.763	0.632	0.907	0.763	0.632	0.907	CLONAL	2	TRUE	1	0.31	3		477	166	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0062371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	307	340	1	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.762350497758358	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.76403495330385	2		341	383	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241882	72241882	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	102	443	0	ENST00000357731.5:c.508A>T	p.Ile170Phe	p.I170F	ENST00000357731	NM_173808.2	170	Att/Ttt	3/7	0.762350497758358	2	FACETS	0.567	0.509	0.627	0.283	0.254	0.314	SUBCLONAL	1	TRUE	0	0.76403495330385	2		443	471	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120479919	120479919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	112	551	0	ENST00000256646.2:c.3508G>A	p.Gly1170Arg	p.G1170R	ENST00000256646	NM_024408.3	1170	Gga/Aga	21/34	0.453128718443604	4	FACETS	0.762	0.686	0.842	0.381	0.343	0.421	INDETERMINATE	1	TRUE	2	0.76403495330385	4		551	679	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10781779	10781779	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	174	441	0	ENST00000361367.2:c.652C>G	p.Arg218Gly	p.R218G	ENST00000361367	NM_014633.3	218	Cgt/Ggt	6/25	0.762350497758358	3	FACETS	1	0.973	1	0.554	0.513	0.596	CLONAL	1	TRUE	1	0.76403495330385	3		441	568	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373919	118373919	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	69	508	0	ENST00000534358.1:c.7312G>C	p.Glu2438Gln	p.E2438Q	ENST00000534358	NM_005933.3	2438	Gaa/Caa	27/36	0.760916665864812	4	FACETS	0.496	0.431	0.565	0.124	0.107	0.142	SUBCLONAL	1	TRUE	0	0.76403495330385	4		508	643	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986694	36986694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1228608392	NA	P-0062371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	73	558	0	ENST00000354822.5:c.995C>T	p.Ala332Val	p.A332V	ENST00000354822	NM_001079668.2	332	gCg/gTg	3/3	0.762350497758358	2	FACETS	0.806	0.715	0.901	0.403	0.357	0.451	CLONAL	1	TRUE	0	0.76403495330385	2		558	237	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821096	72821100	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAC	CAGAC	-	novel	NA	P-0062371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	83	471	0	ENST00000268489.5:c.11075_11079del	p.Gly3692AspfsTer37	p.G3692Dfs*37	ENST00000268489	NM_006885.3	3692	gGTCTG/g	10/10	0.762350497758358	1	FACETS	0.442	0.394	0.492	0.442	0.394	0.492	SUBCLONAL	1	TRUE	0	0.76403495330385	1		471	304	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612352	1612352	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	190	609	0	ENST00000344749.5:c.1667G>T	p.Arg556Leu	p.R556L	ENST00000344749	NM_001136139.2	556	cGg/cTg	18/19	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.76403495330385	2		609	454	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277036	18277036	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	155	564	0	ENST00000222254.8:c.1483G>T	p.Gly495Cys	p.G495C	ENST00000222254	NM_005027.3	495	Ggc/Tgc	12/16	0.731762347567078	4	FACETS	0.98	0.899	1	0.49	0.449	0.533	CLONAL	1	TRUE	2	0.76403495330385	4		564	730	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139519	47139519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062372-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	122	447	0	ENST00000409792.3:c.5068G>A	p.Gly1690Arg	p.G1690R	ENST00000409792	NM_014159.6	1690	Gga/Aga	9/21	0.303049716923075	1	FACETS	0.779	0.705	0.857	0.779	0.705	0.857	SUBCLONAL	1	TRUE	0	0.37	1		447	690	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11999011	11999011	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062373-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	130	386	0	ENST00000353533.5:c.513G>C	p.Glu171Asp	p.E171D	ENST00000353533	NM_003010.3	171	gaG/gaC	4/11	0.394330215846107	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.394330215846107	1		386	367	SUCCESS
APC	324	MSKCC	GRCh37	5	112163677	112163677	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0062377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	95	436	0	ENST00000257430.4:c.1600A>T	p.Lys534Ter	p.K534*	ENST00000257430	NM_000038.5	534	Aaa/Taa	13/16	1	2	FACETS	0.792	0.707	0.881	0.792	0.707	0.881	SUBCLONAL	1	TRUE	1	0.465159057903853	2		436	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0062377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	227	543	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.465159057903853	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.465159057903853	1		543	676	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0062377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	187	647	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.465159057903853	2		647	797	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0062377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	260	613	2	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.247729198641721	3	FACETS	1	0.991	1	0.656	0.615	0.699	INDETERMINATE	1	TRUE	1	0.465159057903853	3		615	1050	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480412	89480412	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	136	515	0	ENST00000336596.2:c.2250del	p.Asn751ThrfsTer3	p.N751Tfs*3	ENST00000336596	NM_005233.5	750	cGg/cg	13/17	1	2	FACETS	0.845	0.77	0.924	0.845	0.77	0.924	CLONAL	1	TRUE	1	0.465159057903853	2		515	692	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541997	187541997	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	223	652	0	ENST00000441802.2:c.5743A>G	p.Ile1915Val	p.I1915V	ENST00000441802	NM_005245.3	1915	Att/Gtt	10/27	1	2	FACETS	0.982	0.915	1	0.982	0.915	1	CLONAL	1	TRUE	1	0.465159057903853	2		652	976	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2084101	2084101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062379-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	166	599	0	ENST00000349721.2:c.2431C>T	p.Arg811Cys	p.R811C	ENST00000349721	NM_003070.3	811	Cgt/Tgt	17/34	1	2	FACETS	0.527	0.485	0.571	0.527	0.485	0.571	SUBCLONAL	1	TRUE	1	0.78540688126621	2		599	802	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188197	10188197	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0062381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	90	538	0	ENST00000256474.2:c.341-1G>A		p.X114_splice	ENST00000256474	NM_000551.3	114			0.319833541590531	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.319833541590531	1		538	384	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675065	40675065	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	49	768	0	ENST00000249776.8:c.29A>C	p.Asp10Ala	p.D10A	ENST00000249776	NM_033286.3	10	gAc/gCc	1/9	1	2	FACETS	0.549	0.465	0.642	0.549	0.465	0.642	SUBCLONAL	1	TRUE	1	0.319833541590531	2		768	558	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46738390	46738390	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	71	904	0	ENST00000371975.4:c.1291G>C	p.Ala431Pro	p.A431P	ENST00000371975	NM_003579.3	431	Gcc/Ccc	12/18	1	2	FACETS	0.723	0.631	0.822	0.723	0.631	0.822	SUBCLONAL	1	TRUE	1	0.319833541590531	2		904	614	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550922	150550922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1560315852	NA	P-0062381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	170	835	0	ENST00000369026.2:c.734C>T	p.Ser245Leu	p.S245L	ENST00000369026	NM_021960.4	245	tCg/tTg	2/3	1	2	FACETS	0.985	0.905	1	0.985	0.905	1	CLONAL	1	TRUE	1	0.319833541590531	2		835	1079	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584514	52584514	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	85	843	0	ENST00000394830.3:c.4499C>A	p.Ser1500Ter	p.S1500*	ENST00000394830	NM_018313.4	1500	tCa/tAa	29/30	0.319833541590531	1	FACETS	0.867	0.769	0.972	0.867	0.769	0.972	CLONAL	1	TRUE	0	0.319833541590531	1		843	515	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663620	117663620	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	36	385	0	ENST00000368508.3:c.4612G>C	p.Asp1538His	p.D1538H	ENST00000368508	NM_002944.2	1538	Gat/Cat	28/43	1	2	FACETS	0.784	0.648	0.936	0.784	0.648	0.936	CLONAL	1	TRUE	1	0.319833541590531	2		385	287	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787810	135787810	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs118203450	NA	P-0062381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	44	590	0	ENST00000298552.3:c.772G>T	p.Glu258Ter	p.E258*	ENST00000298552	NM_001162426.1	258	Gag/Tag	9/23	0.319833541590531	1	FACETS	0.637	0.535	0.748	0.637	0.535	0.748	SUBCLONAL	1	TRUE	0	0.319833541590531	1		590	363	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061250	38061250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1459219194	NA	P-0062382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	72	818	0	ENST00000250448.2:c.739C>T	p.His247Tyr	p.H247Y	ENST00000250448	NM_004496.3	247	Cac/Tac	2/2	0.117504569035189	3	FACETS	1	0.957	1	0.602	0.529	0.68	INDETERMINATE	1	TRUE	1	0.367766105143448	3		818	385	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449492	32449503	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCCTTCCTACCT	GCCTTCCTACCT	-	novel	NA	P-0062382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	19	452	0	ENST00000332351.3:c.871_872+10del		p.X291_splice	ENST00000332351	NM_024426.4	291		3/10	1	2	FACETS	0.713	0.546	0.905	0.713	0.546	0.905	CLONAL	1	TRUE	1	0.367766105143448	2		452	145	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287237	46287237	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	52	690	0	ENST00000334344.6:c.5182A>G	p.Arg1728Gly	p.R1728G	ENST00000334344	NM_152641.2	1728	Aga/Gga	19/21	0.117504569035189	3	FACETS	0.943	0.806	1	0.472	0.403	0.546	INDETERMINATE	1	TRUE	1	0.367766105143448	3		690	355	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120783423	120783423	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1233704648	NA	P-0062382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	56	645	0	ENST00000257552.2:c.1060G>A	p.Ala354Thr	p.A354T	ENST00000257552	NM_002442.3	354	Gcc/Acc	14/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.367766105143448	2		645	233	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240657	133240657	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	22	649	0	ENST00000320574.5:c.2639C>G	p.Thr880Arg	p.T880R	ENST00000320574	NM_006231.2	880	aCg/aGg	23/49	1	2	FACETS	0.572	0.446	0.718	0.572	0.446	0.718	SUBCLONAL	1	TRUE	1	0.367766105143448	2		649	209	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99491933	99491933	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	33	683	0	ENST00000268035.6:c.3718A>G	p.Met1240Val	p.M1240V	ENST00000268035	NM_000875.3	1240	Atg/Gtg	20/21	1	2	FACETS	0.55	0.449	0.664	0.55	0.449	0.664	SUBCLONAL	1	TRUE	1	0.367766105143448	2		683	326	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223746	36223746	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746337039	NA	P-0062382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	34	927	0	ENST00000222270.7:c.6296C>T	p.Ala2099Val	p.A2099V	ENST00000222270	NM_014727.1	2099	gCa/gTa	28/37	1	2	FACETS	0.642	0.526	0.771	0.642	0.526	0.771	SUBCLONAL	1	TRUE	1	0.367766105143448	2		927	288	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877454	40877461	+	protein_altering_variant,splice_region_variant	In_Frame_Del	DEL	TGGAGGCA	TGGAGGCA	AATTC	novel	NA	P-0062382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	29	723	0	ENST00000373198.4:c.2235_2242delinsGAATT	p.Ala746_Thr748delinsAsnSer	p.A746_T748delinsNS	ENST00000373198	NM_133170.3	745	ggTGCCTCCAcc/ggGAATTcc	15/32	0.117504569035189	3	FACETS	0.664	0.535	0.811	0.332	0.267	0.406	INDETERMINATE	1	TRUE	1	0.367766105143448	3		723	281	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851876	134851876	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1576414758	NA	P-0062383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	25	779	0	ENST00000398015.3:c.1282A>C	p.Thr428Pro	p.T428P	ENST00000398015	NM_004441.4	428	Acc/Ccc	5/16	0.171549243505056	3	FACETS	1	0.904	1	0.636	0.503	0.786	CLONAL	1	FALSE	1	0.199317443793673	3		779	217	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	540	714	1				ENST00000310581	NM_198253.2	-/1132			0.831664619864711	3	FACETS	0.94	0.908	0.972	0.94	0.908	0.972	CLONAL	2	TRUE	1	0.831664619864711	3		715	978	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0062385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	619	617	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.830806375837704	2	FACETS	0.963	0.942	0.983	0.963	0.942	0.983	CLONAL	2	TRUE	0	0.831664619864711	2		617	773	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941720	48941720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	67	245	0	ENST00000267163.4:c.1030C>T	p.Gln344Ter	p.Q344*	ENST00000267163	NM_000321.2	344	Cag/Tag	10/27	0.831664619864711	1	FACETS	0.864	0.785	0.94	0.864	0.785	0.94	CLONAL	1	TRUE	0	0.831664619864711	1		245	109	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872219	45872219	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	434	702	0	ENST00000391945.4:c.215A>G	p.Tyr72Cys	p.Y72C	ENST00000391945	NM_000400.3	72	tAc/tGc	4/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.831664619864711	2		702	999	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872201	45872201	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	441	720	0	ENST00000391945.4:c.233C>G	p.Pro78Arg	p.P78R	ENST00000391945	NM_000400.3	78	cCa/cGa	4/23	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.831664619864711	2		720	990	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47491320	47491320	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	282	411	0	ENST00000404338.3:c.3901C>T	p.Gln1301Ter	p.Q1301*	ENST00000404338	NM_004491.4	1301	Caa/Taa	3/6	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.831664619864711	2		411	641	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111557	56111557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	405	615	0	ENST00000399503.3:c.157G>A	p.Glu53Lys	p.E53K	ENST00000399503	NM_005921.1	53	Gag/Aag	1/20	0.831664619864711	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.831664619864711	1		615	539	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120674	94120674	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	272	472	0	ENST00000369303.4:c.377A>C	p.Tyr126Ser	p.Y126S	ENST00000369303	NM_004440.3	126	tAc/tCc	3/17	1	2	FACETS	0.934	0.882	0.987	0.934	0.882	0.987	CLONAL	1	TRUE	1	0.831664619864711	2		472	700	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0062386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	215	634	0	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.471459818432527	2		634	861	SUCCESS
APC	324	MSKCC	GRCh37	5	112175749	112175756	+	frameshift_variant	Frame_Shift_Del	DEL	TACTTTAT	TACTTTAT	-	novel	NA	P-0062386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	140	635	0	ENST00000257430.4:c.4461_4468del	p.Leu1488PhefsTer23	p.L1488Ffs*23	ENST00000257430	NM_000038.5	1486	gaTACTTTATta/gata	16/16	0.457100208172966	1	FACETS	0.848	0.777	0.923	0.848	0.777	0.923	CLONAL	1	TRUE	0	0.471459818432527	1		635	535	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231416	46231416	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	133	450	0	ENST00000334344.6:c.1256T>A	p.Leu419His	p.L419H	ENST00000334344	NM_152641.2	419	cTc/cAc	10/21	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.471459818432527	2		450	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578230	7578230	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	179	662	0	ENST00000269305.4:c.619G>C	p.Asp207His	p.D207H	ENST00000269305	NM_001126112.2	207	Gat/Cat	6/11	1	2	FACETS	0.902	0.832	0.974	0.902	0.832	0.974	CLONAL	1	TRUE	1	0.471459818432527	2		662	842	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920392	134920392	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	129	641	0	ENST00000398015.3:c.2207C>A	p.Ala736Asp	p.A736D	ENST00000398015	NM_004441.4	736	gCt/gAt	12/16	1	2	FACETS	0.893	0.812	0.977	0.893	0.812	0.977	CLONAL	1	TRUE	1	0.471459818432527	2		641	613	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419998	152419998	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	160	572	0	ENST00000206249.3:c.1685A>G	p.Glu562Gly	p.E562G	ENST00000206249	NM_000125.3	562	gAg/gGg	8/8	1	2	FACETS	0.925	0.85	1	0.925	0.85	1	CLONAL	1	TRUE	1	0.471459818432527	2		572	734	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0062387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	57	349	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		349	114	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346157	89346158	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs878855327	NA	P-0062387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	8	737	0	ENST00000301030.4:c.6792dup	p.Ala2265ArgfsTer8	p.A2265Rfs*8	ENST00000301030	NM_001256183.1	2264	-/C	9/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		737	311	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577111	7577111	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786202082	NA	P-0062387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	135	667	1	ENST00000269305.4:c.827C>A	p.Ala276Asp	p.A276D	ENST00000269305	NM_001126112.2	276	gCc/gAc	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		668	251	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750600586	NA	P-0062388-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	46	737	1	ENST00000269305.4:c.413C>T	p.Ala138Val	p.A138V	ENST00000269305	NM_001126112.2	138	gCc/gTc	5/11	1	2	FACETS	0.286	0.24	0.336	0.286	0.24	0.336	SUBCLONAL	1	TRUE	1	0.499331489525907	2		738	645	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0062389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	22	351	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.508	0.393	0.642	0.508	0.393	0.642	SUBCLONAL	1	TRUE	1	0.19	2		351	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0062389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	78	666	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.19	2		666	789	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222006	1222006	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0062389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	47	390	0	ENST00000326873.7:c.920+1G>T		p.X307_splice	ENST00000326873	NM_000455.4	307			1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.19	2		390	458	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0062389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	13	294	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.556	0.396	0.751	0.556	0.396	0.751	SUBCLONAL	1	TRUE	1	0.19	2		294	246	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247901	59247925	+	frameshift_variant	Frame_Shift_Del	DEL	TCCAGCCGGGCGATTCTCTCCAGCT	TCCAGCCGGGCGATTCTCTCCAGCT	-	novel	NA	P-0062389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	52	661	0	ENST00000371222.2:c.818_842del	p.Lys273ArgfsTer4	p.K273Rfs*4	ENST00000371222	NM_002228.3	273	aAGCTGGAGAGAATCGCCCGGCTGGAg/ag	1/1	1	2	FACETS	0.629	0.534	0.734	0.629	0.534	0.734	SUBCLONAL	1	TRUE	1	0.19	2		661	870	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119434	193119434	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	36	345	0	ENST00000367435.3:c.829G>C	p.Asp277His	p.D277H	ENST00000367435	NM_024529.4	277	Gat/Cat	9/17	1	2	FACETS	0.743	0.61	0.892	0.743	0.61	0.892	SUBCLONAL	1	TRUE	1	0.19	2		345	510	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106019	8106019	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	65	571	0	ENST00000346208.3:c.839G>C	p.Gly280Ala	p.G280A	ENST00000346208		280	gGa/gCa	4/6	1	2	FACETS	0.749	0.647	0.859	0.749	0.647	0.859	SUBCLONAL	1	TRUE	1	0.19	2		571	914	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620375	43620375	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	59	483	0	ENST00000355710.3:c.2984G>T	p.Arg995Met	p.R995M	ENST00000355710	NM_020975.4	995	aGg/aTg	18/20	1	2	FACETS	0.86	0.739	0.993	0.86	0.739	0.993	CLONAL	1	TRUE	1	0.19	2		483	722	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456383	32456383	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	66	529	0	ENST00000332351.3:c.509del	p.Gly170AlafsTer116	p.G170Afs*116	ENST00000332351	NM_024426.4	170	gGc/gc	1/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.19	2		529	577	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160470	108160470	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1060501675	NA	P-0062389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	20	291	0	ENST00000278616.4:c.4378G>T	p.Ala1460Ser	p.A1460S	ENST00000278616	NM_000051.3	1460	Gct/Tct	29/63	1	2	FACETS	0.596	0.455	0.762	0.596	0.455	0.762	SUBCLONAL	1	TRUE	1	0.19	2		291	353	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868054	56868054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	76	584	0	ENST00000308159.5:c.1552G>A	p.Gly518Ser	p.G518S	ENST00000308159	NM_014669.4	518	Ggt/Agt	14/22	1	2	FACETS	0.912	0.799	1	0.912	0.799	1	CLONAL	1	TRUE	1	0.19	2		584	877	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993287	72993287	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	64	547	0	ENST00000268489.5:c.758del	p.Ser253ThrfsTer30	p.S253Tfs*30	ENST00000268489	NM_006885.3	253	aGc/ac	2/10	1	2	FACETS	0.879	0.76	1	0.879	0.76	1	CLONAL	1	TRUE	1	0.19	2		547	766	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456585	40456585	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	60	650	0	ENST00000345506.4:c.1295C>A	p.Ala432Glu	p.A432E	ENST00000345506	NM_003152.3	432	gCa/gAa	12/20	1	2	FACETS	0.688	0.591	0.794	0.688	0.591	0.794	SUBCLONAL	1	TRUE	1	0.19	2		650	918	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099221	4099221	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	49	526	0	ENST00000262948.5:c.897G>T	p.Arg299Ser	p.R299S	ENST00000262948	NM_030662.3	299	agG/agT	7/11	1	2	FACETS	0.938	0.794	1	0.938	0.794	1	CLONAL	1	TRUE	1	0.19	2		526	550	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262369	39262369	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	19	315	0	ENST00000402219.2:c.1058A>G	p.Tyr353Cys	p.Y353C	ENST00000402219	NM_005633.3	353	tAc/tGc	8/23	1	2	FACETS	0.651	0.494	0.836	0.651	0.494	0.836	SUBCLONAL	1	TRUE	1	0.19	2		315	307	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632225	215632225	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	28	331	0	ENST00000260947.4:c.1549G>C	p.Gly517Arg	p.G517R	ENST00000260947	NM_000465.2	517	Gga/Cga	6/11	1	2	FACETS	0.794	0.635	0.976	0.794	0.635	0.976	CLONAL	1	TRUE	1	0.19	2		331	371	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178715	32178715	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0062389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	33	428	0	ENST00000375023.3:c.2681-2A>T		p.X894_splice	ENST00000375023	NM_004557.3	894			1	2	FACETS	0.636	0.517	0.771	0.636	0.517	0.771	SUBCLONAL	1	TRUE	1	0.19	2		428	546	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41904987	41904987	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	52	573	0	ENST00000372991.4:c.560C>G	p.Ala187Gly	p.A187G	ENST00000372991	NM_001760.3	187	gCc/gGc	3/5	1	2	FACETS	0.632	0.536	0.738	0.632	0.536	0.738	SUBCLONAL	1	TRUE	1	0.19	2		573	866	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200296	138200296	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1430601409	NA	P-0062389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	60	671	0	ENST00000237289.4:c.1714C>T	p.Arg572Trp	p.R572W	ENST00000237289	NM_001270507.1	572	Cgg/Tgg	7/9	1	2	FACETS	0.738	0.634	0.851	0.738	0.634	0.851	SUBCLONAL	1	TRUE	1	0.19	2		671	856	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888198	112888198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121918453	NA	P-0062390-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	222	572	0	ENST00000351677.2:c.214G>A	p.Ala72Thr	p.A72T	ENST00000351677	NM_002834.3	72	Gcc/Acc	3/16	0.926023088175969	3	FACETS	0.879	0.82	0.939	0.44	0.41	0.47	CLONAL	1	TRUE	1	0.926023088175969	3		572	798	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275192	41275192	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062390-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	311	752	0	ENST00000349496.5:c.1358G>C	p.Arg453Pro	p.R453P	ENST00000349496	NM_001904.3	453	cGg/cCg	9/15	1	2	FACETS	0.943	0.896	0.991	0.943	0.896	0.991	CLONAL	1	TRUE	1	0.926023088175969	2		752	712	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921431	39921435	+	frameshift_variant	Frame_Shift_Del	DEL	GCCAG	GCCAG	A	novel	NA	P-0062390-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	298	606	0	ENST00000378444.4:c.4385_4389delinsT	p.Ala1462ValfsTer21	p.A1462Vfs*21	ENST00000378444	NM_001123385.1	1462	gCTGGC/gT	10/15	0.926023088175969	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.926023088175969	1		606	338	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0062391-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	333	425	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	0.354682720253822	4	FACETS	1	0.99	1	0.863	0.821	0.905	CLONAL	3	TRUE	0	0.354682720253822	4		425	737	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0062391-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	114	595	1	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.808	0.727	0.893	0.808	0.727	0.893	CLONAL	1	TRUE	1	0.354682720253822	2		596	796	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574030	7574030	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062391-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	194	484	0	ENST00000269305.4:c.997del	p.Arg333ValfsTer12	p.R333Vfs*12	ENST00000269305	NM_001126112.2	333	Cgt/gt	10/11	0.273539454953154	2	FACETS	0.845	0.786	0.906	0.845	0.786	0.906	CLONAL	2	TRUE	0	0.354682720253822	2		484	647	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630125	187630125	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs201488687	NA	P-0062391-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	195	766	0	ENST00000441802.2:c.857A>G	p.Asn286Ser	p.N286S	ENST00000441802	NM_005245.3	286	aAt/aGt	2/27	0.247879777752624	3	FACETS	1	0.989	1	0.708	0.656	0.763	CLONAL	1	TRUE	1	0.354682720253822	3		766	914	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90996769	90996786	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGGCAGCAGTTTCCA	GGCGGGCAGCAGTTTCCA	T	novel	NA	P-0062391-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	91	417	0	ENST00000265433.3:c.4_21delinsA	p.Trp2SerfsTer16	p.W2Sfs*16	ENST00000265433	NM_002485.4	2	TGGAAACTGCTGCCCGCC/A	1/16	0.247879777752624	3	FACETS	1	0.968	1	0.616	0.549	0.688	CLONAL	1	TRUE	1	0.354682720253822	3		417	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0062392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	397	647	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.844887353117976	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.844887353117976	2		647	453	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636974	176636974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138405802	NA	P-0062392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	161	626	0	ENST00000439151.2:c.1574G>A	p.Arg525Gln	p.R525Q	ENST00000439151	NM_022455.4	525	cGg/cAg	5/23	1	2	FACETS	0.918	0.852	0.986	0.918	0.852	0.986	CLONAL	1	TRUE	1	0.844887353117976	2		626	415	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322596	39322596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	317	518	0	ENST00000373001.3:c.396G>A	p.Met132Ile	p.M132I	ENST00000373001	NM_022157.3	132	atG/atA	2/7	0.844887353117976	7	FACETS	1	0.96	1			1	CLONAL	2	TRUE	NA	0.844887353117976	7		518	1143	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18762543	18762544	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGAAACACA	novel	NA	P-0062392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	76	280	0	ENST00000266497.5:c.4045_4053dup	p.His1349_Lys1351dup	p.H1349_K1351dup	ENST00000266497		1349	gtg/gTGAAACACAtg	29/31	0.798323754669892	4	FACETS	0.855	0.755	0.963	0.428	0.377	0.482	CLONAL	1	TRUE	2	0.844887353117976	4		280	388	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0062411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	74	416	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.230977450627982	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.230977450627982	1		416	493	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0062411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	61	573	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.725	0.624	0.834	0.725	0.624	0.834	SUBCLONAL	1	TRUE	1	0.230977450627982	2		573	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576858	7576858	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	100	645	0	ENST00000269305.4:c.988del	p.Leu330PhefsTer15	p.L330Ffs*15	ENST00000269305	NM_001126112.2	330	Ctt/tt	9/11	0.230977450627982	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.230977450627982	1		645	676	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030850	69030850	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150128151	NA	P-0062411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	69	459	0	ENST00000288368.4:c.3392C>T	p.Ser1131Leu	p.S1131L	ENST00000288368	NM_024870.2	1131	tCg/tTg	27/40	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.230977450627982	2		459	590	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760075	133760075	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1287213531	NA	P-0062411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	48	579	0	ENST00000318560.5:c.2398G>C	p.Asp800His	p.D800H	ENST00000318560	NM_005157.4	800	Gac/Cac	11/11	1	2	FACETS	0.804	0.68	0.941	0.804	0.68	0.941	CLONAL	1	TRUE	1	0.230977450627982	2		579	517	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578260	212578260	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs768893584	NA	P-0062412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	20	373	0	ENST00000342788.4:c.997G>T	p.Ala333Ser	p.A333S	ENST00000342788	NM_005235.2	333	Gct/Tct	8/28	0.480451262602551	3	FACETS	0.463	0.355	0.589	0.232	0.177	0.295	SUBCLONAL	1	TRUE	1	0.491194481137598	3		373	219	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097845	8097845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1315804209	NA	P-0062412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	84	683	0	ENST00000346208.3:c.227C>T	p.Pro76Leu	p.P76L	ENST00000346208		76	cCt/cTt	2/6	0.491194481137598	3	FACETS	0.834	0.738	0.935	0.417	0.369	0.468	CLONAL	1	TRUE	1	0.491194481137598	3		683	511	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891525	151891525	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	27	340	0	ENST00000262189.6:c.4507G>A	p.Gly1503Arg	p.G1503R	ENST00000262189	NM_170606.2	1503	Gga/Aga	29/59	0.378427176792184	5	FACETS	0.608	0.484	0.749	0.152	0.121	0.188	SUBCLONAL	1	TRUE	1	0.491194481137598	5		340	314	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0062413-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	241	433	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.995	0.934	1	0.995	0.934	1	CLONAL	1	TRUE	1	0.702257034226662	2		434	690	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0062413-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	370	529	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.702257034226662	2		529	936	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073475	8073477	+	inframe_deletion	In_Frame_Del	DEL	TAA	TAA	-	novel	NA	P-0062413-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	181	517	0	ENST00000377482.5:c.1182_1184del	p.Tyr395del	p.Y395del	ENST00000377482	NM_018948.3	394	taTTAc/tac	4/4	1	2	FACETS	0.601	0.555	0.65	0.601	0.555	0.65	SUBCLONAL	1	TRUE	1	0.702257034226662	2		517	857	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150931656	150931657	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0062413-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	138	402	0	ENST00000271640.5:c.2336_2337del	p.Tyr779Ter	p.Y779*	ENST00000271640	NM_001145415.1	778	gTA/g	15/22	1	2	FACETS	0.62	0.566	0.677	0.62	0.566	0.677	SUBCLONAL	1	TRUE	1	0.702257034226662	2		402	634	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497522	125497522	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062413-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	80	309	0	ENST00000428830.2:c.86del	p.Arg29LysfsTer2	p.R29Kfs*2	ENST00000428830	NM_001114121.2	29	aGa/aa	3/14	0.499691767133278	3	FACETS	0.956	0.849	1			1	CLONAL	1	TRUE	NA	0.702257034226662	3		309	322	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740527	58740528	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0062413-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	269	506	0	ENST00000305921.3:c.1435_1436dup	p.Lys480LeufsTer4	p.K480Lfs*4	ENST00000305921	NM_003620.3	478	tgc/tGCgc	6/6	1	2	FACETS	0.938	0.883	0.994	0.938	0.883	0.994	CLONAL	1	TRUE	1	0.702257034226662	2		506	817	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051169	128051169	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062413-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	200	664	0	ENST00000285398.2:c.154A>G	p.Lys52Glu	p.K52E	ENST00000285398	NM_000122.1	52	Aaa/Gaa	2/15	1	2	FACETS	0.549	0.508	0.592	0.549	0.508	0.592	SUBCLONAL	1	TRUE	1	0.702257034226662	2		664	1037	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391440	84391440	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062413-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	78	206	0	ENST00000321945.7:c.392T>G	p.Val131Gly	p.V131G	ENST00000321945	NM_139076.2	131	gTt/gGt	5/9	1	2	FACETS	0.829	0.737	0.924	0.829	0.737	0.924	CLONAL	1	TRUE	1	0.702257034226662	2		206	268	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778769	76778771	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0062413-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	111	212	0	ENST00000373344.5:c.6808_6810del	p.Glu2270del	p.E2270del	ENST00000373344	NM_000489.3	2270	GAA/-	31/35	1	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.702257034226662	1		212	169	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062414-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	88	714	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.81	0.723	0.901	0.81	0.723	0.901	CLONAL	1	TRUE	1	0.600139908280655	2		715	362	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0062414-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	107	371	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.929	0.84	1	0.929	0.84	1	CLONAL	1	TRUE	1	0.600139908280655	2		371	384	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927373	245927373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062414-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	189	489	0	ENST00000388985.4:c.1155G>A	p.Met385Ile	p.M385I	ENST00000388985		385	atG/atA	11/12	0.550339307131161	3	FACETS	0.967	0.895	1	0.483	0.447	0.521	CLONAL	1	TRUE	1	0.600139908280655	3		489	847	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374715	149374715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773592492	NA	P-0062414-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	142	498	0	ENST00000360632.3:c.379C>T	p.Pro127Ser	p.P127S	ENST00000360632	NM_015472.4	127	Ccc/Tcc	2/7	1	2	FACETS	0.893	0.818	0.97	0.893	0.818	0.97	CLONAL	1	TRUE	1	0.600139908280655	2		498	530	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97887421	97887421	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587779910	NA	P-0062414-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	169	445	0	ENST00000289081.3:c.943A>G	p.Ile315Val	p.I315V	ENST00000289081	NM_000136.2	315	Att/Gtt	10/15	1	2	FACETS	0.995	0.92	1	0.995	0.92	1	CLONAL	1	TRUE	1	0.600139908280655	2		445	566	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711879	89711880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0062415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	35	347	0	ENST00000371953.3:c.499dup	p.Thr167AsnfsTer13	p.T167Nfs*13	ENST00000371953	NM_000314.4	166	gta/gtAa	6/9	0.31032475474646	1	FACETS	0.906	0.751	1	0.906	0.751	1	CLONAL	1	TRUE	0	0.356660292547378	1		347	178	SUCCESS
H3C13	653604	MSKCC	GRCh37	1	149784839	149784839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1318402070	NA	P-0062415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	41	418	0	ENST00000331491.1:c.398G>A	p.Gly133Glu	p.G133E	ENST00000331491	NM_001123375.2	133	gGg/gAg	1/1	1	2	FACETS	0.827	0.693	0.974	0.827	0.693	0.974	CLONAL	1	TRUE	1	0.356660292547378	2		418	278	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392808	118392808	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	59	586	0	ENST00000534358.1:c.11840del	p.Tyr3947LeufsTer25	p.Y3947Lfs*25	ENST00000534358	NM_005933.3	3947	tAt/tt	36/36	1	2	FACETS	0.797	0.688	0.915	0.797	0.688	0.915	CLONAL	1	TRUE	1	0.356660292547378	2		586	415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577567	7577570	+	frameshift_variant	Frame_Shift_Del	DEL	ACAC	ACAC	-	novel	NA	P-0062415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	84	478	0	ENST00000269305.4:c.711_714del	p.Met237IlefsTer9	p.M237Ifs*9	ENST00000269305	NM_001126112.2	237	atGTGT/at	7/11	0.305544688755333	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.356660292547378	1		478	367	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38504686	38504687	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0062415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	71	533	0	ENST00000254066.5:c.299_300dup	p.Gly101MetfsTer36	p.G101Mfs*36	ENST00000254066	NM_000964.3	99	-/TA	3/9	1	2	FACETS	0.883	0.773	1	0.883	0.773	1	CLONAL	1	TRUE	1	0.356660292547378	2		533	451	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593474	48593480	+	frameshift_variant	Frame_Shift_Del	DEL	GTACAGA	GTACAGA	-	novel	NA	P-0062415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	67	451	0	ENST00000342988.3:c.1227_1233del	p.Gln410ThrfsTer3	p.Q410Tfs*3	ENST00000342988	NM_005359.5	409	GTACAGAgt/gt	10/12	0.356660292547378	1	FACETS	0.815	0.711	0.925	0.815	0.711	0.925	CLONAL	1	TRUE	0	0.356660292547378	1		451	379	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266850	18266851	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0062415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	54	598	0	ENST00000222254.8:c.164dup	p.Trp56LeufsTer14	p.W56Lfs*14	ENST00000222254	NM_005027.3	54	gtg/gtGg	2/16	0.305544688755333	1	FACETS	0.663	0.569	0.766	0.663	0.569	0.766	SUBCLONAL	1	TRUE	0	0.356660292547378	1		598	375	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157777	106157779	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0062415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	56	490	0	ENST00000380013.4:c.2679_2681del	p.Ser894del	p.S894del	ENST00000380013	NM_001127208.2	893	gCTTca/gca	3/11	1	2	FACETS	0.96	0.828	1	0.96	0.828	1	CLONAL	1	TRUE	1	0.356660292547378	2		490	327	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133748289	133748290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CATG	novel	NA	P-0062415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	74	447	0	ENST00000318560.5:c.951_954dup	p.Thr319HisfsTer64	p.T319Hfs*64	ENST00000318560	NM_005157.4	317	ttc/ttCATGc	6/11	0.305544688755333	1	FACETS	0.868	0.764	0.978	0.868	0.764	0.978	CLONAL	1	TRUE	0	0.356660292547378	1		447	393	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041621	47041621	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	70	709	0	ENST00000377604.3:c.1846G>T	p.Val616Phe	p.V616F	ENST00000377604	NM_001204468.1	616	Gtt/Ttt	17/24	1	2	FACETS	0.892	0.781	1	0.892	0.781	1	CLONAL	1	TRUE	1	0.356660292547378	2		709	440	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0062416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	46	367	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.226320626783823	2		367	345	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0062416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	113	439	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.226320626783823	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.226320626783823	1		440	648	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150913893	150913893	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	70	374	0	ENST00000271640.5:c.536A>T	p.Asp179Val	p.D179V	ENST00000271640	NM_001145415.1	179	gAt/gTt	5/22	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.226320626783823	2		374	579	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715628	30715628	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	87	467	0	ENST00000295754.5:c.1286T>A	p.Val429Asp	p.V429D	ENST00000295754	NM_003242.5	429	gTc/gAc	5/7	0.226320626783823	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.226320626783823	1		467	595	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0062417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	267	496	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.51507685062468	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.51507685062468	1		496	721	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54959348	54959348	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	10	205	0	ENST00000312783.6:c.352C>T	p.Gln118Ter	p.Q118*	ENST00000312783	NM_198436.1	118	Cag/Tag	5/10	1	2	FACETS	0.353	0.24	0.492	0.353	0.24	0.492	SUBCLONAL	1	TRUE	1	0.51507685062468	2		205	110	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007736	45007736	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1370797084	NA	P-0062417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	112	518	0	ENST00000558401.1:c.183G>C	p.Lys61Asn	p.K61N	ENST00000558401	NM_004048.2	61	aaG/aaC	2/4	1	2	FACETS	0.636	0.572	0.703	0.636	0.572	0.703	SUBCLONAL	1	TRUE	1	0.51507685062468	2		518	684	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120612002	120612002	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	27	160	0	ENST00000256646.2:c.19G>T	p.Ala7Ser	p.A7S	ENST00000256646	NM_024408.3	7	Gct/Tct	1/34	1	2	FACETS	0.481	0.385	0.59	0.481	0.385	0.59	SUBCLONAL	1	TRUE	1	0.51507685062468	2		160	218	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021929	246021929	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	64	485	0	ENST00000388985.4:c.945C>G	p.Ser315Arg	p.S315R	ENST00000388985		315	agC/agG	10/12	1	2	FACETS	0.327	0.283	0.376	0.327	0.283	0.376	SUBCLONAL	1	TRUE	1	0.51507685062468	2		485	759	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112745395	112745395	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	50	341	0	ENST00000369452.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000369452	NM_007373.3	238	tGt/tTt	3/9	0.42417153700015	1	FACETS	0.565	0.484	0.653	0.565	0.484	0.653	SUBCLONAL	1	TRUE	0	0.51507685062468	1		341	255	SUCCESS
EED	8726	MSKCC	GRCh37	11	85961390	85961390	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	141	522	0	ENST00000263360.6:c.167C>T	p.Pro56Leu	p.P56L	ENST00000263360	NM_003797.3	56	cCt/cTt	2/12	0.51507685062468	1	FACETS	0.795	0.729	0.864	0.795	0.729	0.864	SUBCLONAL	1	TRUE	0	0.51507685062468	1		522	511	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343408	118343408	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	59	637	0	ENST00000534358.1:c.1534C>A	p.Pro512Thr	p.P512T	ENST00000534358	NM_005933.3	512	Cca/Aca	3/36	0.51507685062468	1	FACETS	0.219	0.187	0.253	0.219	0.187	0.253	SUBCLONAL	1	TRUE	0	0.51507685062468	1		637	778	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033947	49033947	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs727504122	NA	P-0062417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	148	472	0	ENST00000267163.4:c.2084T>G	p.Met695Arg	p.M695R	ENST00000267163	NM_000321.2	695	aTg/aGg	20/27	0.51507685062468	1	FACETS	0.865	0.796	0.937	0.865	0.796	0.937	CLONAL	1	TRUE	0	0.51507685062468	1		472	493	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40500520	40500520	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	104	453	0	ENST00000264657.5:c.15T>G	p.Asn5Lys	p.N5K	ENST00000264657	NM_139276.2	5	aaT/aaG	2/24	1	2	FACETS	0.524	0.469	0.582	0.524	0.469	0.582	SUBCLONAL	1	TRUE	1	0.51507685062468	2		453	771	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591831	48591831	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	152	578	0	ENST00000342988.3:c.994G>T	p.Asp332Tyr	p.D332Y	ENST00000342988	NM_005359.5	332	Gat/Tat	9/12	1	2	FACETS	0.938	0.861	1	0.938	0.861	1	CLONAL	1	TRUE	1	0.51507685062468	2		578	629	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266737	142266737	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	49	343	0	ENST00000350721.4:c.3187G>T	p.Glu1063Ter	p.E1063*	ENST00000350721	NM_001184.3	1063	Gaa/Taa	16/47	0.51507685062468	4	FACETS	0.708	0.601	0.826	0.236	0.2	0.276	SUBCLONAL	1	TRUE	1	0.51507685062468	4		343	407	SUCCESS
REST	5978	MSKCC	GRCh37	4	57797704	57797704	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	44	577	0	ENST00000309042.7:c.2680C>G	p.Leu894Val	p.L894V	ENST00000309042	NM_005612.4	894	Ctt/Gtt	4/4	0.51507685062468	1	FACETS	0.17	0.141	0.201	0.17	0.141	0.201	SUBCLONAL	1	TRUE	0	0.51507685062468	1		577	748	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129882	69129882	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	101	611	0	ENST00000288368.4:c.4636A>T	p.Ile1546Phe	p.I1546F	ENST00000288368	NM_024870.2	1546	Atc/Ttc	38/40	1	2	FACETS	0.368	0.328	0.411	0.368	0.328	0.411	SUBCLONAL	1	TRUE	1	0.51507685062468	2		611	1066	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062418-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	49	714	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.912	0.77	1	0.912	0.77	1	CLONAL	1	TRUE	1	0.13	2		715	827	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0062418-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1225	49	634	0	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	1	2	FACETS	0.592	0.499	0.695	0.592	0.499	0.695	SUBCLONAL	1	TRUE	1	0.13	2		634	1274	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482437	56482437	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	14	666	0	ENST00000267101.3:c.985A>G	p.Lys329Glu	p.K329E	ENST00000267101	NM_001982.3	329	Aaa/Gaa	8/28	1	2	FACETS	0.251	0.18	0.337	0.251	0.18	0.337	SUBCLONAL	1	TRUE	1	0.16	2		666	698	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844172	68844172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	46	523	0	ENST00000261769.5:c.760G>A	p.Asp254Asn	p.D254N	ENST00000261769	NM_004360.3	254	Gat/Aat	6/16	1	2	FACETS	0.867	0.729	1	0.867	0.729	1	CLONAL	1	TRUE	1	0.16	2		523	663	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99472813	99472813	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	51	445	0	ENST00000268035.6:c.2809A>T	p.Ile937Phe	p.I937F	ENST00000268035	NM_000875.3	937	Atc/Ttc	14/21	1	2	FACETS	0.808	0.685	0.944	0.808	0.685	0.944	CLONAL	1	TRUE	1	0.16	2		445	789	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0062426-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	15	336	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.886	0.65	1	0.886	0.65	1	CLONAL	1	TRUE	1	0.180980988969744	2		336	187	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062426-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	26	566	0	ENST00000269305.4:c.376T>C	p.Tyr126His	p.Y126H	ENST00000269305	NM_001126112.2	126	Tac/Cac	5/11	0.180980988969744	1	FACETS	0.728	0.577	0.901	0.728	0.577	0.901	CLONAL	1	TRUE	0	0.180980988969744	1		566	359	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792732	33792737	+	inframe_deletion	In_Frame_Del	DEL	GCGGGT	GCGGGT	-	rs762459325	NA	P-0062426-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	8	561	1	ENST00000498907.2:c.584_589del	p.His195_Pro196del	p.H195_P196del	ENST00000498907	NM_004364.3	195	cACCCGCcg/ccg	1/1	0.126004980627888	3	FACETS	0.241	0.154	0.355	0.121	0.077	0.178	SUBCLONAL	1	TRUE	1	0.180980988969744	3		562	400	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132522	11132522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778175819	NA	P-0062426-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	46	623	1	ENST00000358026.2:c.2738C>T	p.Pro913Leu	p.P913L	ENST00000358026	NM_001128849.1	913	cCg/cTg	19/36	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.180980988969744	2		624	442	SUCCESS
ATR	545	MSKCC	GRCh37	3	142184069	142184069	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062426-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	12	210	0	ENST00000350721.4:c.6911C>A	p.Ala2304Asp	p.A2304D	ENST00000350721	NM_001184.3	2304	gCt/gAt	41/47	1	2	FACETS	1	0.795	1	1	0.795	1	CLONAL	1	TRUE	1	0.180980988969744	2		210	114	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974800	21974801	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0062426-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	23	654	0	ENST00000304494.5:c.26dup	p.Met9IlefsTer6	p.M9Ifs*6	ENST00000304494	NM_000077.4	9	atg/atTg	1/3	0.180980988969744	1	FACETS	0.608	0.474	0.764	0.608	0.474	0.764	SUBCLONAL	1	TRUE	0	0.180980988969744	1		654	380	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0062428-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	68	421	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.749	0.65	0.856	0.749	0.65	0.856	SUBCLONAL	1	TRUE	1	0.211869403090739	2		421	857	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062428-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	70	684	0	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	1	2	FACETS	0.696	0.605	0.794	0.696	0.605	0.794	SUBCLONAL	1	TRUE	1	0.211869403090739	2		684	950	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944264	81944264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1009796025	NA	P-0062429-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	205	500	0	ENST00000359376.3:c.1873G>A	p.Ala625Thr	p.A625T	ENST00000359376	NM_002661.3	625	Gcc/Acc	18/33	0.646396293149682	4	FACETS	1	0.947	1	0.341	0.316	0.367	CLONAL	1	TRUE	1	0.822305079954441	4		500	888	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577560	7577560	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520002	NA	P-0062429-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	384	516	0	ENST00000269305.4:c.721T>G	p.Ser241Ala	p.S241A	ENST00000269305	NM_001126112.2	241	Tcc/Gcc	7/11	0.70223249764493	2	FACETS	0.849	0.82	0.877	0.849	0.82	0.877	CLONAL	2	TRUE	0	0.822305079954441	2		516	550	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398260	25398260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062429-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	118	270	0	ENST00000311936.3:c.59C>T	p.Thr20Met	p.T20M	ENST00000311936	NM_004985.3	20	aCg/aTg	2/5	0.822305079954441	5	FACETS	0.814	0.735	0.899	0.271	0.245	0.3	CLONAL	1	TRUE	2	0.822305079954441	5		270	787	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0062454-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	13	703	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		703	238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578224	7578224	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1429743956	NA	P-0062455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	228	662	0	ENST00000269305.4:c.625A>T	p.Arg209Ter	p.R209*	ENST00000269305	NM_001126112.2	209	Aga/Tga	6/11	0.294001121014577	2	FACETS	0.983	0.919	1	0.983	0.919	1	CLONAL	2	TRUE	0	0.310621462072085	2		662	747	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0062455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	15	201	0	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	0.307548242042891	3	FACETS	0.996	0.737	1	0.498	0.368	0.651	CLONAL	1	TRUE	1	0.310621462072085	3		201	112	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138521	11138521	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	178	508	0	ENST00000358026.2:c.3277C>T	p.Arg1093Ter	p.R1093*	ENST00000358026	NM_001128849.1	1093	Cga/Tga	24/36	0.310621462072085	2	FACETS	0.939	0.87	1	0.939	0.87	1	CLONAL	2	TRUE	0	0.310621462072085	2		508	610	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954248	17954248	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	313	614	0	ENST00000458235.1:c.361C>A	p.Arg121Ser	p.R121S	ENST00000458235	NM_000215.3	121	Cgc/Agc	4/24	0.307018967335867	3	FACETS	0.967	0.916	1	0.967	0.916	1	CLONAL	3	TRUE	0	0.310621462072085	3		614	803	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0062456-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	250	635	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.3597298943309	4	FACETS	0.885	0.839	0.931	0.885	0.839	0.931	CLONAL	4	FALSE	0	0.414433026986314	4		635	482	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0062456-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	11	192	0	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	0.311364138478686	3	FACETS	0.509	0.353	0.699	0.254	0.176	0.35	SUBCLONAL	1	FALSE	1	0.414433026986314	3		192	126	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668619	52668619	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062456-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	37	317	0	ENST00000394830.3:c.1300C>T	p.Arg434Ter	p.R434*	ENST00000394830	NM_018313.4	434	Cga/Tga	12/30	0.311364138478686	3	FACETS	1	0.94	1	0.649	0.543	0.765	CLONAL	1	FALSE	1	0.414433026986314	3		317	166	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562336	21562336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765917652	NA	P-0062456-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	237	577	0	ENST00000382592.4:c.1583C>T	p.Ser528Leu	p.S528L	ENST00000382592	NM_014572.2	528	tCg/tTg	4/8	0.29268189334236	4	FACETS	0.863	0.811	0.916	1	0.991	1	CLONAL	3	FALSE	2	0.414433026986314	4		577	625	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006006	22006006	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749530069	NA	P-0062456-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	176	707	0	ENST00000276925.6:c.397C>T	p.Arg133Cys	p.R133C	ENST00000276925	NM_004936.3	133	Cgc/Tgc	2/2	0.311364138478686	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	FALSE	1	0.414433026986314	3		707	502	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1952922	1952922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1362563185	NA	P-0062456-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	65	551	0	ENST00000382891.5:c.2005G>A	p.Val669Met	p.V669M	ENST00000382891	NM_133335.3	669	Gtg/Atg	10/22	0.311364138478686	3	FACETS	0.821	0.714	0.937	0.411	0.357	0.469	CLONAL	1	FALSE	1	0.414433026986314	3		551	461	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524958	8524958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1462108267	NA	P-0062456-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	62	336	0	ENST00000356435.5:c.646C>T	p.Arg216Cys	p.R216C	ENST00000356435		216	Cgc/Tgc	7/35	0.311364138478686	3	FACETS	0.921	0.799	1	0.461	0.399	0.527	CLONAL	1	FALSE	1	0.414433026986314	3		336	392	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932184	39932184	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0062456-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	60	283	0	ENST00000378444.4:c.2415C>G	p.Tyr805Ter	p.Y805*	ENST00000378444	NM_001123385.1	805	taC/taG	4/15	0.295708364626461	2	FACETS	1	0.941	1			1	CLONAL	1	FALSE	NA	0.414433026986314	2		283	253	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0062457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	44	509	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.782284528933511	2		510	112	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0062457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	53	323	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.782284528933511	2		323	127	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513400	41513400	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	64	520	0	ENST00000263253.7:c.304C>T	p.Gln102Ter	p.Q102*	ENST00000263253	NM_001429.3	102	Caa/Taa	2/31	0.782284528933511	1	FACETS	0.996	0.906	1	0.996	0.906	1	CLONAL	1	TRUE	0	0.782284528933511	1		520	100	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805233	43805233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458939414	NA	P-0062457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	85	452	0	ENST00000372470.3:c.683G>A	p.Ser228Asn	p.S228N	ENST00000372470	NM_005373.2	228	aGt/aAt	4/12	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.782284528933511	2		452	200	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240343	41240343	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	13	282	0	ENST00000379561.5:c.7G>T	p.Glu3Ter	p.E3*	ENST00000379561	NM_002015.3	3	Gag/Tag	1/3	1	2	FACETS	0.209	0.149	0.281	0.209	0.149	0.281	SUBCLONAL	1	TRUE	1	0.782284528933511	2		282	159	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513286	44513286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763538177	NA	P-0062457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	168	466	0	ENST00000291552.4:c.649G>A	p.Gly217Ser	p.G217S	ENST00000291552	NM_006758.2	217	Ggt/Agt	8/8	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.782284528933511	2		466	411	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649557	48649557	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1478971085	NA	P-0062458-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	47	497	0	ENST00000376670.3:c.41C>T	p.Pro14Leu	p.P14L	ENST00000376670	NM_002049.3	14	cCc/cTc	2/6	1	2	FACETS	0.668	0.563	0.784	0.668	0.563	0.784	SUBCLONAL	1	TRUE	1	0.239224112922165	2		497	588	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250906	153250906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062458-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	8	311	0	ENST00000281708.4:c.1154C>T	p.Thr385Ile	p.T385I	ENST00000281708	NM_033632.3	385	aCa/aTa	8/12	1	2	FACETS	0.719	0.467	1	0.719	0.467	1	CLONAL	1	TRUE	1	0.239224112922165	2		311	93	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829055	72829055	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062458-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	75	538	1	ENST00000268489.5:c.7526del	p.Leu2509ProfsTer19	p.L2509Pfs*19	ENST00000268489	NM_006885.3	2509	cTc/cc	9/10	1	2	FACETS	0.902	0.79	1	0.902	0.79	1	CLONAL	1	TRUE	1	0.239224112922165	2		539	695	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923687	72923687	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062458-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	58	557	0	ENST00000268489.5:c.3391G>T	p.Glu1131Ter	p.E1131*	ENST00000268489	NM_006885.3	1131	Gag/Tag	4/10	1	2	FACETS	0.727	0.624	0.84	0.727	0.624	0.84	SUBCLONAL	1	TRUE	1	0.239224112922165	2		557	667	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578274	7578274	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062458-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	177	672	0	ENST00000269305.4:c.575del	p.Gln192ArgfsTer55	p.Q192Rfs*55	ENST00000269305	NM_001126112.2	192	cAg/cg	6/11	0.177809973502916	2	FACETS	0.97	0.895	1	0.97	0.895	1	CLONAL	2	TRUE	0	0.239224112922165	2		672	763	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062465-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	162	573	0	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	0.444907111327597	1	FACETS	0.99	0.913	1	0.99	0.913	1	CLONAL	1	TRUE	0	0.444907111327597	1		573	572	SUCCESS
APC	324	MSKCC	GRCh37	5	112175358	112175358	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1554085480	NA	P-0062465-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	102	460	0	ENST00000257430.4:c.4067C>G	p.Ser1356Ter	p.S1356*	ENST00000257430	NM_000038.5	1356	tCa/tGa	16/16	0.299250356736065	3	FACETS	0.961	0.862	1	0.481	0.431	0.534	CLONAL	1	TRUE	1	0.444907111327597	3		460	583	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971052	21971052	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062465-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	36	597	1	ENST00000579755.1:c.349G>A	p.Ala117Thr	p.A117T	ENST00000579755		117	Gcg/Acg	2/3	1	2	FACETS	0.276	0.226	0.332	0.276	0.226	0.332	SUBCLONAL	1	TRUE	1	0.444907111327597	2		598	587	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575376	64575376	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062465-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	204	727	0	ENST00000312049.6:c.641G>T	p.Gly214Val	p.G214V	ENST00000312049	NM_130799.2	214	gGt/gTt	3/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.444907111327597	2		727	831	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983128	7983128	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs143465858	NA	P-0062465-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	82	511	0	ENST00000319144.4:c.886C>A	p.Pro296Thr	p.P296T	ENST00000319144	NM_001139.2	296	Ccg/Acg	7/15	0.444907111327597	1	FACETS	0.871	0.775	0.972	0.871	0.775	0.972	CLONAL	1	TRUE	0	0.444907111327597	1		511	329	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253762	30253762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062465-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	121	555	0	ENST00000307677.4:c.692G>A	p.Ser231Asn	p.S231N	ENST00000307677	NM_138578.1	231	aGt/aAt	3/3	0.444907111327597	5	FACETS	0.742	0.668	0.82	0.185	0.167	0.205	SUBCLONAL	1	TRUE	1	0.444907111327597	5		555	1223	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151833968	151833968	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062465-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	135	515	0	ENST00000262189.6:c.14685C>G	p.His4895Gln	p.H4895Q	ENST00000262189	NM_170606.2	4895	caC/caG	59/59	0.444907111327597	3	FACETS	0.887	0.807	0.972	0.444	0.403	0.486	CLONAL	1	TRUE	1	0.444907111327597	3		515	836	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0062466-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	93	703	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.10008924178733	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		703	368	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752968	128752969	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGAGCGCCAGAGGAGGAACGAGC	novel	NA	P-0062466-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	48	627	0	ENST00000377970.2:c.1131_1154dup	p.Glu378_Leu385dup	p.E378_L385dup	ENST00000377970	NM_002467.4	378	ttg/tTGGAGCGCCAGAGGAGGAACGAGCtg	3/3	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		627	422	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091843	29091843	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555913901	NA	P-0062466-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	26	164	0	ENST00000328354.6:c.1114T>C	p.Ser372Pro	p.S372P	ENST00000328354	NM_007194.3	372	Tcc/Ccc	11/15	0.10008924178733	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		164	111	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755128667	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	84	740	0	ENST00000407977.2:c.1976dup	p.Pro660SerfsTer87	p.P660Sfs*87	ENST00000407977		659	ggt/ggGt	9/10	1	2	FACETS	0.557	0.492	0.628	0.557	0.492	0.628	SUBCLONAL	1	TRUE	1	0.389907507426646	2		740	773	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	146	355	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.389907507426646	2		355	744	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	66	949	18	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.623	0.542	0.712	0.623	0.542	0.712	SUBCLONAL	1	TRUE	1	0.389907507426646	2		967	543	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426123	138426123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217537873	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	61	369	0	ENST00000289153.2:c.1408G>A	p.Glu470Lys	p.E470K	ENST00000289153	NM_006219.2	470	Gaa/Aaa	9/22	1	2	FACETS	0.85	0.737	0.972	0.85	0.737	0.972	CLONAL	1	TRUE	1	0.389907507426646	2		369	368	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936096	178936096	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519940	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	20	437	0	ENST00000263967.3:c.1638G>T	p.Gln546His	p.Q546H	ENST00000263967	NM_006218.2	546	caG/caT	10/21	1	2	FACETS	0.39	0.298	0.497	0.39	0.298	0.497	SUBCLONAL	1	TRUE	1	0.389907507426646	2		437	263	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971156	21971156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	29	688	0	ENST00000304494.5:c.202G>A	p.Ala68Thr	p.A68T	ENST00000304494	NM_000077.4	68	Gcg/Acg	2/3	1	2	FACETS	0.293	0.235	0.36	0.293	0.235	0.36	SUBCLONAL	1	TRUE	1	0.389907507426646	2		688	507	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928078	178928080	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs587776933	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	21	461	0	ENST00000263967.3:c.1359_1361del	p.Glu453del	p.E453del	ENST00000263967	NM_006218.2	452	ttAGAa/tta	8/21	1	2	FACETS	0.263	0.202	0.334	0.263	0.202	0.334	SUBCLONAL	1	TRUE	1	0.389907507426646	2		461	410	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	74	488	4	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	0.603	0.527	0.683	0.603	0.527	0.683	SUBCLONAL	1	TRUE	1	0.389907507426646	2		492	630	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40486062	40486062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	59	480	0	ENST00000264657.5:c.803C>T	p.Thr268Met	p.T268M	ENST00000264657	NM_139276.2	268	aCg/aTg	9/24	1	2	FACETS	0.503	0.432	0.58	0.503	0.432	0.58	SUBCLONAL	1	TRUE	1	0.389907507426646	2		480	602	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733513	85733513	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs387906350	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	73	465	1	ENST00000370580.1:c.499del	p.Ser167LeufsTer6	p.S167Lfs*6	ENST00000370580	NM_003921.4	167	Tct/ct	3/3	1	2	FACETS	0.6	0.525	0.681	0.6	0.525	0.681	SUBCLONAL	1	TRUE	1	0.389907507426646	2		466	624	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221206	5221206	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200191658	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	67	607	1	ENST00000357368.4:c.3260C>T	p.Thr1087Met	p.T1087M	ENST00000357368	NM_002850.3	1087	aCg/aTg	20/38	1	2	FACETS	0.562	0.488	0.641	0.562	0.488	0.641	SUBCLONAL	1	TRUE	1	0.389907507426646	2		608	612	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466018	69466018	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	119	697	2	ENST00000227507.2:c.856A>G	p.Thr286Ala	p.T286A	ENST00000227507	NM_053056.2	286	Aca/Gca	5/5	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.389907507426646	2		699	577	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	108	863	7	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.967	0.87	1	0.967	0.87	1	CLONAL	1	TRUE	1	0.389907507426646	2		870	573	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793363	242793363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	34	640	0	ENST00000334409.5:c.714del	p.Val239CysfsTer39	p.V239Cfs*39	ENST00000334409	NM_005018.2	238	ccC/cc	5/5	1	2	FACETS	0.267	0.217	0.323	0.267	0.217	0.323	SUBCLONAL	1	TRUE	1	0.389907507426646	2		640	653	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216189	36216189	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	111	478	0	ENST00000222270.7:c.3602del	p.Pro1201ArgfsTer154	p.P1201Rfs*154	ENST00000222270	NM_014727.1	1199	ggC/gg	11/37	1	2	FACETS	0.888	0.8	0.981	0.888	0.8	0.981	CLONAL	1	TRUE	1	0.389907507426646	2		478	641	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998342	100998342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	15	512	0	ENST00000325455.5:c.1460G>A	p.Gly487Asp	p.G487D	ENST00000325455	NM_001202474.3	487	gGc/gAc	1/8	1	2	FACETS	0.298	0.218	0.395	0.298	0.218	0.395	SUBCLONAL	1	TRUE	1	0.389907507426646	2		512	258	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831345	89831346	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs878853663	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	40	597	1	ENST00000389301.3:c.2730_2731del	p.Trp911AspfsTer31	p.W911Dfs*31	ENST00000389301	NM_000135.2	910	ctCTgg/ctgg	28/43	1	2	FACETS	0.311	0.258	0.371	0.311	0.258	0.371	SUBCLONAL	1	TRUE	1	0.389907507426646	2		598	659	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357642	70357642	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	109	719	2	ENST00000374080.3:c.5898del	p.Ser1967AlafsTer19	p.S1967Afs*19	ENST00000374080		1965	Ccc/cc	41/45	1	2	FACETS	0.769	0.691	0.852	0.769	0.691	0.852	SUBCLONAL	1	TRUE	1	0.389907507426646	2		721	727	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692901	89692901	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs786204929	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	147	344	0	ENST00000371953.3:c.385G>T	p.Gly129Ter	p.G129*	ENST00000371953	NM_000314.4	129	Gga/Tga	5/9	0.389907507426646	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.389907507426646	2		344	335	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631641	119631641	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	46	365	0	ENST00000316626.5:c.625C>T	p.Arg209Ter	p.R209*	ENST00000316626		209	Cga/Tga	6/12	1	2	FACETS	0.54	0.455	0.633	0.54	0.455	0.633	SUBCLONAL	1	TRUE	1	0.389907507426646	2		365	437	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058066	27058066	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	110	567	0	ENST00000324856.7:c.1774del	p.Tyr592IlefsTer27	p.Y592Ifs*27	ENST00000324856	NM_006015.4	592	Tat/at	3/20	1	2	FACETS	0.903	0.813	0.998	0.903	0.813	0.998	CLONAL	1	TRUE	1	0.389907507426646	2		567	625	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514133	69514133	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	44	660	0	ENST00000294312.3:c.548T>C	p.Leu183Ser	p.L183S	ENST00000294312	NM_005117.2	183	tTg/tCg	3/3	1	2	FACETS	0.407	0.341	0.481	0.407	0.341	0.481	SUBCLONAL	1	TRUE	1	0.389907507426646	2		660	554	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942220	71942220	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	125	612	0	ENST00000298229.2:c.1484T>C	p.Leu495Pro	p.L495P	ENST00000298229	NM_001567.3	495	cTg/cCg	12/28	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.389907507426646	2		612	603	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434453	121434453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	59	698	0	ENST00000257555.6:c.1217C>T	p.Ala406Val	p.A406V	ENST00000257555		406	gCc/gTc	6/10	1	2	FACETS	0.48	0.412	0.553	0.48	0.412	0.553	SUBCLONAL	1	TRUE	1	0.389907507426646	2		698	631	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655465	67655466	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	131	453	0	ENST00000264010.4:c.1331_1332del	p.Thr444SerfsTer7	p.T444Sfs*7	ENST00000264010	NM_006565.3	443	gAC/g	7/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.389907507426646	2		453	525	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347795	89347795	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	32	680	0	ENST00000301030.4:c.5155A>G	p.Met1719Val	p.M1719V	ENST00000301030	NM_001256183.1	1719	Atg/Gtg	9/13	1	2	FACETS	0.261	0.211	0.318	0.261	0.211	0.318	SUBCLONAL	1	TRUE	1	0.389907507426646	2		680	628	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961310	15961310	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	57	517	0	ENST00000268712.3:c.6079del	p.Gln2027AsnfsTer22	p.Q2027Nfs*22	ENST00000268712	NM_006311.3	2027	Caa/aa	39/46	1	2	FACETS	0.412	0.353	0.477	0.412	0.353	0.477	SUBCLONAL	1	TRUE	1	0.389907507426646	2		517	709	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6222583	6222583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1360565477	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	110	617	0	ENST00000252674.7:c.659G>A	p.Arg220His	p.R220H	ENST00000252674	NM_005934.3	220	cGt/cAt	6/12	1	2	FACETS	0.936	0.843	1	0.936	0.843	1	CLONAL	1	TRUE	1	0.389907507426646	2		617	603	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383164	42383164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782467376	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	98	624	0	ENST00000221972.3:c.184G>A	p.Ala62Thr	p.A62T	ENST00000221972	NM_021601.3	62	Gcc/Acc	2/5	1	2	FACETS	0.849	0.759	0.945	0.849	0.759	0.945	CLONAL	1	TRUE	1	0.389907507426646	2		624	592	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147736	61147736	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs756078972	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	96	750	0	ENST00000295025.8:c.1046G>T	p.Gly349Val	p.G349V	ENST00000295025	NM_002908.2	349	gGt/gTt	10/11	1	2	FACETS	0.539	0.479	0.603	0.539	0.479	0.603	SUBCLONAL	1	TRUE	1	0.389907507426646	2		750	914	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736110	204736110	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756706504	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	82	543	0	ENST00000302823.3:c.467C>T	p.Pro156Leu	p.P156L	ENST00000302823	NM_005214.4	156	cCg/cTg	3/4	1	2	FACETS	0.645	0.569	0.727	0.645	0.569	0.727	SUBCLONAL	1	TRUE	1	0.389907507426646	2		543	652	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21348979	21348979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	110	735	0	ENST00000215739.8:c.1748G>A	p.Cys583Tyr	p.C583Y	ENST00000215739	NM_006767.3	583	tGc/tAc	15/21	1	2	FACETS	0.83	0.746	0.918	0.83	0.746	0.918	CLONAL	1	TRUE	1	0.389907507426646	2		735	680	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970957	55970957	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	55	475	2	ENST00000263923.4:c.1840G>A	p.Ala614Thr	p.A614T	ENST00000263923	NM_002253.2	614	Gcc/Acc	13/30	1	2	FACETS	0.588	0.503	0.68	0.588	0.503	0.68	SUBCLONAL	1	TRUE	1	0.389907507426646	2		477	480	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157757	106157757	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	117	526	0	ENST00000380013.4:c.2658G>T	p.Gln886His	p.Q886H	ENST00000380013	NM_001127208.2	886	caG/caT	3/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.389907507426646	2		526	544	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896390	151896390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369143780	NA	P-0062467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	54	415	0	ENST00000262189.6:c.4247C>T	p.Ser1416Leu	p.S1416L	ENST00000262189	NM_170606.2	1416	tCg/tTg	27/59	1	2	FACETS	0.674	0.577	0.779	0.674	0.577	0.779	SUBCLONAL	1	TRUE	1	0.389907507426646	2		415	411	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755128667	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	135	740	0	ENST00000407977.2:c.1976dup	p.Pro660SerfsTer87	p.P660Sfs*87	ENST00000407977		659	ggt/ggGt	9/10	1	2	FACETS	0.436	0.396	0.479	0.436	0.396	0.479	SUBCLONAL	1	TRUE	1	0.697627504429095	2		740	887	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16203146	16203146	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	65	441	0	ENST00000375759.3:c.854G>C	p.Ser285Thr	p.S285T	ENST00000375759	NM_015001.2	285	aGc/aCc	3/15	1	2	FACETS	0.271	0.235	0.311	0.271	0.235	0.311	SUBCLONAL	1	TRUE	1	0.697627504429095	2		441	687	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088788	27088788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	91	784	1	ENST00000324856.7:c.2402del	p.Gly801ValfsTer32	p.G801Vfs*32	ENST00000324856	NM_006015.4	799	caG/ca	7/20	1	2	FACETS	0.354	0.314	0.397	0.354	0.314	0.397	SUBCLONAL	1	TRUE	1	0.697627504429095	2		785	736	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	68	331	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.239	0.207	0.274	0.239	0.207	0.274	SUBCLONAL	1	TRUE	1	0.697627504429095	2		331	815	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429978	78429978	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	118	413	1	ENST00000370768.2:c.901del	p.Ile301TyrfsTer22	p.I301Yfs*22	ENST00000370768	NM_003902.3	301	Ata/ta	11/20	1	2	FACETS	0.561	0.507	0.617	0.561	0.507	0.617	SUBCLONAL	1	TRUE	1	0.697627504429095	2		414	603	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737052	162737052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765973930	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	99	505	1	ENST00000367921.3:c.1196G>A	p.Arg399Gln	p.R399Q	ENST00000367921	NM_006182.2	399	cGg/cAg	11/18	0.697627504429095	3	FACETS	0.387	0.345	0.432	0.194	0.172	0.216	SUBCLONAL	1	TRUE	1	0.697627504429095	3		506	989	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692844	89692844	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1114167629	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	26	129	0	ENST00000371953.3:c.328C>T	p.Gln110Ter	p.Q110*	ENST00000371953	NM_000314.4	110	Caa/Taa	5/9	1	2	FACETS	0.441	0.352	0.541	0.441	0.352	0.541	SUBCLONAL	1	TRUE	1	0.697627504429095	2		129	169	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	16	117	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.373	0.278	0.484	0.373	0.278	0.484	SUBCLONAL	1	TRUE	1	0.697627504429095	2		117	123	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941259	71941259	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	107	723	0	ENST00000298229.2:c.1034T>C	p.Leu345Pro	p.L345P	ENST00000298229	NM_001567.3	345	cTg/cCg	9/28	1	2	FACETS	0.314	0.281	0.349	0.314	0.281	0.349	SUBCLONAL	1	TRUE	1	0.697627504429095	2		723	978	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	119	773	6	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.415	0.374	0.458	0.415	0.374	0.458	SUBCLONAL	1	TRUE	1	0.697627504429095	2		779	822	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636382	21636382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	78	420	0	ENST00000421138.2:c.628G>A	p.Ala210Thr	p.A210T	ENST00000421138		210	Gca/Aca	7/16	1	2	FACETS	0.401	0.353	0.453	0.401	0.353	0.453	SUBCLONAL	1	TRUE	1	0.697627504429095	2		420	557	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	122	582	2	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.412	0.372	0.455	0.412	0.372	0.455	SUBCLONAL	1	TRUE	1	0.697627504429095	2		584	848	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434648	49434648	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	125	684	0	ENST00000301067.7:c.6905del	p.Pro2302GlnfsTer20	p.P2302Qfs*20	ENST00000301067	NM_003482.3	2302	cCa/ca	31/54	1	2	FACETS	0.427	0.386	0.47	0.427	0.386	0.47	SUBCLONAL	1	TRUE	1	0.697627504429095	2		684	840	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443730	49443730	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	139	514	0	ENST00000301067.7:c.3641G>T	p.Gly1214Val	p.G1214V	ENST00000301067	NM_003482.3	1214	gGt/gTt	11/54	1	2	FACETS	0.527	0.48	0.576	0.527	0.48	0.576	SUBCLONAL	1	TRUE	1	0.697627504429095	2		514	756	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493738	56493738	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	140	654	0	ENST00000267101.3:c.3054G>T	p.Glu1018Asp	p.E1018D	ENST00000267101	NM_001982.3	1018	gaG/gaT	25/28	1	2	FACETS	0.462	0.421	0.506	0.462	0.421	0.506	SUBCLONAL	1	TRUE	1	0.697627504429095	2		654	868	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785607	50785607	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	72	420	0	ENST00000398568.2:c.597G>T	p.Leu199Phe	p.L199F	ENST00000398568	NM_001042412.1	199	ttG/ttT	4/18	1	2	FACETS	0.298	0.26	0.339	0.298	0.26	0.339	SUBCLONAL	1	TRUE	1	0.697627504429095	2		420	693	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991949	72991949	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs753977275	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	84	529	1	ENST00000268489.5:c.2096del	p.Gly699AlafsTer125	p.G699Afs*125	ENST00000268489	NM_006885.3	699	gGc/gc	2/10	1	2	FACETS	0.339	0.299	0.381	0.339	0.299	0.381	SUBCLONAL	1	TRUE	1	0.697627504429095	2		530	711	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86545071	86545071	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	94	580	0	ENST00000262426.4:c.896C>A	p.Pro299His	p.P299H	ENST00000262426	NM_001451.2	299	cCc/cAc	1/2	1	2	FACETS	0.371	0.33	0.415	0.371	0.33	0.415	SUBCLONAL	1	TRUE	1	0.697627504429095	2		580	727	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351595	89351595	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	115	569	0	ENST00000301030.4:c.1355del	p.Asn452IlefsTer3	p.N452Ifs*3	ENST00000301030	NM_001256183.1	452	aAt/at	9/13	1	2	FACETS	0.376	0.338	0.416	0.376	0.338	0.416	SUBCLONAL	1	TRUE	1	0.697627504429095	2		569	877	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882019	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	28	625	1	ENST00000269305.4:c.455del	p.Pro152ArgfsTer18	p.P152Rfs*18	ENST00000269305	NM_001126112.2	152	cCg/cg	5/11	1	2	FACETS	0.09	0.071	0.111	0.09	0.071	0.111	SUBCLONAL	1	TRUE	1	0.697627504429095	2		626	896	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492936	56492936	+	start_lost	Translation_Start_Site	SNP	C	C	G	novel	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	142	395	0	ENST00000407977.2:c.3G>C	p.Met1?	p.M1?	ENST00000407977		1	atG/atC	2/10	1	2	FACETS	0.674	0.616	0.734	0.674	0.616	0.734	SUBCLONAL	1	TRUE	1	0.697627504429095	2		395	604	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117712	70117714	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs778226772	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	119	631	0	ENST00000245479.2:c.184_186del	p.Lys62del	p.K62del	ENST00000245479	NM_000346.3	60	ctGAAg/ctg	1/3	1	2	FACETS	0.429	0.387	0.473	0.429	0.387	0.473	SUBCLONAL	1	TRUE	1	0.697627504429095	2		631	795	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119246	3119249	+	frameshift_variant	Frame_Shift_Del	DEL	ACCT	ACCT	-	novel	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	97	619	0	ENST00000078429.4:c.781_784del	p.Tyr261ProfsTer49	p.Y261Pfs*49	ENST00000078429	NM_002067.2	260	ACCTac/ac	6/7	1	2	FACETS	0.358	0.319	0.4	0.358	0.319	0.4	SUBCLONAL	1	TRUE	1	0.697627504429095	2		619	776	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210713	5210713	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	87	663	0	ENST00000357368.4:c.5338A>G	p.Thr1780Ala	p.T1780A	ENST00000357368	NM_002850.3	1780	Acc/Gcc	34/38	1	2	FACETS	0.303	0.268	0.341	0.303	0.268	0.341	SUBCLONAL	1	TRUE	1	0.697627504429095	2		663	822	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	145	1247	7	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.475	0.433	0.519	0.475	0.433	0.519	SUBCLONAL	1	TRUE	1	0.697627504429095	2		1254	875	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214871	36214871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	69	495	3	ENST00000222270.7:c.3302del	p.Pro1101LeufsTer81	p.P1101Lfs*81	ENST00000222270	NM_014727.1	1099	ggC/gg	8/37	1	2	FACETS	0.325	0.283	0.37	0.325	0.283	0.37	SUBCLONAL	1	TRUE	1	0.697627504429095	2		498	609	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752695	42752695	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1366176199	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	77	566	2	ENST00000222329.4:c.1569del	p.Leu525SerfsTer6	p.L525Sfs*6	ENST00000222329	NM_006494.2	523	ggG/gg	4/4	1	2	FACETS	0.322	0.282	0.364	0.322	0.282	0.364	SUBCLONAL	1	TRUE	1	0.697627504429095	2		568	686	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	68	326	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.216	0.187	0.248	0.216	0.187	0.248	SUBCLONAL	1	TRUE	1	0.697627504429095	2		328	902	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662517	227662517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1393539515	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	146	554	0	ENST00000305123.5:c.938C>T	p.Pro313Leu	p.P313L	ENST00000305123	NM_005544.2	313	cCg/cTg	1/2	1	2	FACETS	0.533	0.486	0.581	0.533	0.486	0.581	SUBCLONAL	1	TRUE	1	0.697627504429095	2		554	786	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727191	40727191	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	79	537	0	ENST00000373198.4:c.3773G>T	p.Ser1258Ile	p.S1258I	ENST00000373198	NM_133170.3	1258	aGc/aTc	28/32	1	2	FACETS	0.315	0.276	0.356	0.315	0.276	0.356	SUBCLONAL	1	TRUE	1	0.697627504429095	2		537	720	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29279846	29279846	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	30	183	0	ENST00000544604.2:c.92del	p.Leu31ArgfsTer91	p.L31Rfs*91	ENST00000544604	NM_001206998.1	31	cTg/cg	1/9	1	2	FACETS	0.42	0.34	0.508	0.42	0.34	0.508	SUBCLONAL	1	TRUE	1	0.697627504429095	2		183	205	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035067	37035067	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777971423	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	75	496	0	ENST00000231790.2:c.29G>A	p.Arg10Gln	p.R10Q	ENST00000231790	NM_000249.3	10	cGg/cAg	1/19	1	2	FACETS	0.32	0.28	0.363	0.32	0.28	0.363	SUBCLONAL	1	TRUE	1	0.697627504429095	2		496	672	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	98	484	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.365	0.326	0.408	0.365	0.326	0.408	SUBCLONAL	1	TRUE	1	0.697627504429095	2		484	769	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749397	41749397	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	27	305	0	ENST00000226382.2:c.398T>G	p.Leu133Arg	p.L133R	ENST00000226382	NM_003924.3	133	cTg/cGg	2/3	1	2	FACETS	0.164	0.13	0.203	0.164	0.13	0.203	SUBCLONAL	1	TRUE	1	0.697627504429095	2		305	473	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604638	55604638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	119	515	1	ENST00000288135.5:c.2846C>T	p.Pro949Leu	p.P949L	ENST00000288135	NM_000222.2	949	cCc/cTc	21/21	1	2	FACETS	0.43	0.388	0.475	0.43	0.388	0.475	SUBCLONAL	1	TRUE	1	0.697627504429095	2		516	793	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531025	187531025	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	122	459	0	ENST00000441802.2:c.9998del	p.Pro3333LeufsTer43	p.P3333Lfs*43	ENST00000441802	NM_005245.3	3333	cCt/ct	15/27	1	2	FACETS	0.508	0.459	0.558	0.508	0.459	0.558	SUBCLONAL	1	TRUE	1	0.697627504429095	2		459	689	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	240502	240502	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369100772	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	15	78	1	ENST00000264932.6:c.1462G>A	p.Ala488Thr	p.A488T	ENST00000264932	NM_004168.2	488	Gct/Act	11/15	1	2	FACETS	0.374	0.276	0.489	0.374	0.276	0.489	SUBCLONAL	1	TRUE	1	0.697627504429095	2		79	115	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31466379	31466379	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	47	324	1	ENST00000344624.3:c.2376del	p.Lys792AsnfsTer7	p.K792Nfs*7	ENST00000344624		792	aaA/aa	16/33	1	2	FACETS	0.233	0.196	0.273	0.233	0.196	0.273	SUBCLONAL	1	TRUE	1	0.697627504429095	2		325	579	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589530	67589592	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTCTAGGATCAAGTTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATTACATGAATA	TTTCTAGGATCAAGTTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATTACATGAATA	-	novel	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	50	269	0	ENST00000274335.5:c.1300-6_1356del		p.X434_splice	ENST00000274335		434		10/15	1	2	FACETS	0.503	0.429	0.582	0.503	0.429	0.582	SUBCLONAL	1	TRUE	1	0.697627504429095	2		269	285	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322601	109322601	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	79	457	1	ENST00000436639.2:c.436G>T	p.Val146Leu	p.V146L	ENST00000436639	NM_014454.2	146	Gtg/Ttg	3/10	1	2	FACETS	0.385	0.339	0.435	0.385	0.339	0.435	SUBCLONAL	1	TRUE	1	0.697627504429095	2		458	588	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066731	5066731	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	12	313	0	ENST00000381652.3:c.1268A>T	p.Tyr423Phe	p.Y423F	ENST00000381652	NM_004972.3	423	tAt/tTt	10/25	1	2	FACETS	0.145	0.102	0.199	0.145	0.102	0.199	SUBCLONAL	1	TRUE	1	0.697627504429095	2		313	237	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139818357	139818357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	78	391	1	ENST00000247668.2:c.1192G>A	p.Gly398Ser	p.G398S	ENST00000247668	NM_021138.3	398	Ggc/Agc	10/11	1	2	FACETS	0.408	0.359	0.461	0.408	0.359	0.461	SUBCLONAL	1	TRUE	1	0.697627504429095	2		392	548	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20152120	20152120	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	84	296	0	ENST00000379607.5:c.210G>T	p.Trp70Cys	p.W70C	ENST00000379607	NM_001412.3	70	tgG/tgT	4/7	1	2	FACETS	0.602	0.535	0.673	0.602	0.535	0.673	SUBCLONAL	1	TRUE	1	0.697627504429095	2		296	400	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53253993	53253993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	126	525	0	ENST00000375401.3:c.79C>T	p.Pro27Ser	p.P27S	ENST00000375401	NM_004187.3	27	Cct/Tct	1/26	1	2	FACETS	0.515	0.466	0.565	0.515	0.466	0.565	SUBCLONAL	1	TRUE	1	0.697627504429095	2		525	702	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0062469-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	152	700	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.23772236835302	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.23772236835302	1		700	766	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0062469-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	51	304	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.196251940207673	2	FACETS	0.921	0.791	1	0.921	0.791	1	CLONAL	2	TRUE	0	0.23772236835302	2		304	233	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656798	45656798	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062469-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	66	579	0	ENST00000407780.3:c.358C>A	p.Leu120Met	p.L120M	ENST00000407780	NM_001283052.1	120	Ctg/Atg	3/7	1	2	FACETS	0.738	0.64	0.845	0.738	0.64	0.845	SUBCLONAL	1	TRUE	1	0.23772236835302	2		579	752	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521849	157521849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771056710	NA	P-0062469-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	63	619	0	ENST00000346085.5:c.4121G>A	p.Arg1374His	p.R1374H	ENST00000346085	NM_020732.3	1374	cGc/cAc	18/20	0.23772236835302	1	FACETS	0.729	0.63	0.836	0.729	0.63	0.836	SUBCLONAL	1	TRUE	0	0.23772236835302	1		619	641	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	47	309	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.899	0.763	1	0.899	0.763	1	CLONAL	1	TRUE	1	0.368175918338468	2		309	284	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	116	453	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.368175918338468	2		453	529	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339111	65339111	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	185	673	3	ENST00000342505.4:c.425del	p.Lys142ArgfsTer26	p.K142Rfs*26	ENST00000342505	NM_002227.2	142	aAg/ag	5/25	0.368175918338468	2	FACETS	0.88	0.818	0.944	0.88	0.818	0.944	CLONAL	2	TRUE	0	0.368175918338468	2		676	571	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	197	605	0	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	0.368175918338468	2	FACETS	0.964	0.899	1	0.964	0.899	1	CLONAL	2	TRUE	0	0.368175918338468	2		605	555	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189412	56189412	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	98	533	0	ENST00000399503.3:c.4444C>T	p.Arg1482Ter	p.R1482*	ENST00000399503	NM_005921.1	1482	Cga/Tga	20/20	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.368175918338468	2		533	513	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032794	30032794	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434259	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	98	571	0	ENST00000338641.4:c.169C>T	p.Arg57Ter	p.R57*	ENST00000338641	NM_000268.3	57	Cga/Tga	2/16	1	2	FACETS	0.986	0.882	1	0.986	0.882	1	CLONAL	1	TRUE	1	0.368175918338468	2		571	540	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416648	29416650	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs138827116	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	124	617	0	ENST00000389048.3:c.4303_4305del	p.Glu1435del	p.E1435del	ENST00000389048	NM_004304.4	1435	GAG/-	29/29	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.368175918338468	2		617	629	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	91	581	0	ENST00000397062.3:c.246A>T	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaT	2/5	1	2	FACETS	0.958	0.853	1	0.958	0.853	1	CLONAL	1	TRUE	1	0.368175918338468	2		581	516	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	110	444	0	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.368175918338468	2		444	575	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673750	176673750	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	96	475	0	ENST00000439151.2:c.4455del	p.Val1486Ter	p.V1486*	ENST00000439151	NM_022455.4	1484	Aaa/aa	10/23	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.368175918338468	2		475	467	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	105	687	3	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.368175918338468	2		690	562	SUCCESS
CBL	867	MSKCC	GRCh37	11	119077140	119077140	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1222275357	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	215	670	1	ENST00000264033.4:c.13G>A	p.Val5Met	p.V5M	ENST00000264033	NM_005188.3	5	Gtg/Atg	1/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.368175918338468	2		671	987	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570840	226570840	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	77	531	0	ENST00000366794.5:c.1056del	p.Lys352AsnfsTer29	p.K352Nfs*29	ENST00000366794	NM_001618.3	352	aaA/aa	8/23	1	2	FACETS	0.953	0.84	1	0.953	0.84	1	CLONAL	1	TRUE	1	0.368175918338468	2		531	439	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915588	131915588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769853458	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	47	356	0	ENST00000265335.6:c.586C>T	p.Arg196Cys	p.R196C	ENST00000265335		196	Cgt/Tgt	5/25	1	2	FACETS	0.874	0.742	1	0.874	0.742	1	CLONAL	1	TRUE	1	0.368175918338468	2		356	292	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	47	339	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.786	0.666	0.916	0.786	0.666	0.916	CLONAL	1	TRUE	1	0.368175918338468	2		342	325	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655479	67655479	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs769948988	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	53	524	1	ENST00000264010.4:c.1342C>T	p.Arg448Ter	p.R448*	ENST00000264010	NM_006565.3	448	Cga/Tga	7/12	1	2	FACETS	0.689	0.589	0.798	0.689	0.589	0.798	SUBCLONAL	1	TRUE	1	0.368175918338468	2		525	418	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300039	137300040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755912201	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	71	677	3	ENST00000481739.1:c.331dup	p.Leu111ProfsTer70	p.L111Pfs*70	ENST00000481739	NM_002957.4	108	-/C	3/10	1	2	FACETS	0.74	0.647	0.84	0.74	0.647	0.84	SUBCLONAL	1	TRUE	1	0.368175918338468	2		680	521	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646980	23646981	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	64	573	0	ENST00000261584.4:c.886dup	p.Met296AsnfsTer7	p.M296Nfs*7	ENST00000261584	NM_024675.3	296	atg/aAtg	4/13	1	2	FACETS	0.776	0.674	0.886	0.776	0.674	0.886	SUBCLONAL	1	TRUE	1	0.368175918338468	2		573	448	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231449	5231449	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	108	611	4	ENST00000357368.4:c.2027del	p.Pro676ArgfsTer134	p.P676Rfs*134	ENST00000357368	NM_002850.3	676	cCg/cg	14/38	0.178590588020942	1	FACETS	0.888	0.8	0.981	0.888	0.8	0.981	INDETERMINATE	1	TRUE	0	0.368175918338468	1		615	539	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876343	35876343	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200570812	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	103	592	0	ENST00000303115.3:c.1135G>A	p.Ala379Thr	p.A379T	ENST00000303115	NM_002185.3	379	Gcc/Acc	8/8	1	2	FACETS	0.992	0.89	1	0.992	0.89	1	CLONAL	1	TRUE	1	0.368175918338468	2		592	564	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630007	187630007	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	106	699	0	ENST00000441802.2:c.975G>A	p.Trp325Ter	p.W325*	ENST00000441802	NM_005245.3	325	tgG/tgA	2/27	1	2	FACETS	0.998	0.897	1	0.998	0.897	1	CLONAL	1	TRUE	1	0.368175918338468	2		699	577	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502298	157502298	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	108	662	0	ENST00000346085.5:c.3331G>A	p.Gly1111Arg	p.G1111R	ENST00000346085	NM_020732.3	1111	Ggg/Agg	12/20	1	2	FACETS	0.978	0.88	1	0.978	0.88	1	CLONAL	1	TRUE	1	0.368175918338468	2		662	600	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180600	32180600	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	88	438	0	ENST00000375023.3:c.2526+1G>A		p.X842_splice	ENST00000375023	NM_004557.3	842			1	2	FACETS	0.996	0.886	1	0.996	0.886	1	CLONAL	1	TRUE	1	0.368175918338468	2		438	480	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100887	27100887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	226	608	0	ENST00000324856.7:c.4169G>A	p.Ser1390Asn	p.S1390N	ENST00000324856	NM_006015.4	1390	aGc/aAc	18/20	0.368175918338468	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.368175918338468	2		608	564	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77934490	77934490	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	124	586	1	ENST00000361507.4:c.1535del	p.Pro512LeufsTer19	p.P512Lfs*19	ENST00000361507	NM_080491.2	512	cCt/ct	6/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.368175918338468	2		587	593	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425568	49425568	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	106	816	0	ENST00000301067.7:c.12920C>A	p.Pro4307His	p.P4307H	ENST00000301067	NM_003482.3	4307	cCc/cAc	39/54	0.202172641076204	1	FACETS	0.74	0.664	0.82	0.74	0.664	0.82	INDETERMINATE	1	TRUE	0	0.368175918338468	1		816	635	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544350	86544350	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	114	631	0	ENST00000262426.4:c.175A>G	p.Met59Val	p.M59V	ENST00000262426	NM_001451.2	59	Atg/Gtg	1/2	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.368175918338468	2		631	592	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446365	29446365	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	145	721	0	ENST00000389048.3:c.3202G>T	p.Ala1068Ser	p.A1068S	ENST00000389048	NM_004304.4	1068	Gcc/Tcc	20/29	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.368175918338468	2		721	733	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155437	99155438	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	106	468	0	ENST00000074304.5:c.666dup	p.Ser223IlefsTer17	p.S223Ifs*17	ENST00000074304	NM_001134224.1	221	-/A	9/26	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.368175918338468	2		468	519	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193572	99193572	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	122	633	0	ENST00000074304.5:c.2767C>T	p.Gln923Ter	p.Q923*	ENST00000074304	NM_001134224.1	923	Cag/Tag	25/26	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.368175918338468	2		633	601	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898825	134898825	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	60	473	0	ENST00000398015.3:c.1882+1G>A		p.X628_splice	ENST00000398015	NM_004441.4	628			1	2	FACETS	0.879	0.76	1	0.879	0.76	1	CLONAL	1	TRUE	1	0.368175918338468	2		473	371	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911436	134911436	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	98	573	0	ENST00000398015.3:c.1901A>G	p.Tyr634Cys	p.Y634C	ENST00000398015	NM_004441.4	634	tAc/tGc	11/16	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.368175918338468	2		573	474	SUCCESS
ATR	545	MSKCC	GRCh37	3	142297540	142297540	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	157	380	0	ENST00000350721.4:c.7del	p.Glu3AsnfsTer9	p.E3Nfs*9	ENST00000350721	NM_001184.3	3	Gaa/aa	1/47	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.368175918338468	2		380	609	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916653	178916653	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	46	412	0	ENST00000263967.3:c.40C>G	p.His14Asp	p.H14D	ENST00000263967	NM_006218.2	14	Cac/Gac	2/21	1	2	FACETS	0.722	0.61	0.845	0.722	0.61	0.845	SUBCLONAL	1	TRUE	1	0.368175918338468	2		412	346	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1918612	1918612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	60	425	1	ENST00000382891.5:c.775G>A	p.Ala259Thr	p.A259T	ENST00000382891	NM_133335.3	259	Gca/Aca	4/22	0.368175918338468	1	FACETS	0.702	0.607	0.804	0.702	0.607	0.804	SUBCLONAL	1	TRUE	0	0.368175918338468	1		426	379	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953614	38953614	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs767131444	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	19	383	0	ENST00000357387.3:c.2739T>A	p.Asp913Glu	p.D913E	ENST00000357387	NM_152756.3	913	gaT/gaA	28/38	1	2	FACETS	0.374	0.284	0.48	0.374	0.284	0.48	SUBCLONAL	1	TRUE	1	0.368175918338468	2		383	276	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179457	56179457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	57	479	0	ENST00000399503.3:c.3770G>A	p.Cys1257Tyr	p.C1257Y	ENST00000399503	NM_005921.1	1257	tGt/tAt	15/20	1	2	FACETS	0.808	0.696	0.93	0.808	0.696	0.93	CLONAL	1	TRUE	1	0.368175918338468	2		479	383	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194614	29194614	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761854287	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	109	686	1	ENST00000240100.2:c.1114G>A	p.Val372Met	p.V372M	ENST00000240100	NM_001394.6	372	Gtg/Atg	4/4	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.368175918338468	2		687	572	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566084	141566084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1308828307	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	87	548	1	ENST00000220592.5:c.1180G>A	p.Val394Ile	p.V394I	ENST00000220592	NM_012154.3	394	Gtc/Atc	10/19	1	2	FACETS	0.914	0.812	1	0.914	0.812	1	CLONAL	1	TRUE	1	0.368175918338468	2		549	517	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2123797	2123797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	100	689	1	ENST00000349721.2:c.3841C>T	p.Pro1281Ser	p.P1281S	ENST00000349721	NM_003070.3	1281	Ccc/Tcc	27/34	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.368175918338468	2		690	536	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5466769	5466769	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0062471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	64	611	0	ENST00000381577.3:c.791-1G>T		p.X264_splice	ENST00000381577	NM_014143.3	264			1	2	FACETS	0.727	0.631	0.831	0.727	0.631	0.831	SUBCLONAL	1	TRUE	1	0.368175918338468	2		611	478	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0062472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	56	309	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.18	2		309	589	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0062472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	17	349	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.836	0.625	1	0.836	0.625	1	CLONAL	1	TRUE	1	0.18	2		349	226	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0062472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	16	442	1	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	1	2	FACETS	0.231	0.17	0.306	0.231	0.17	0.306	SUBCLONAL	1	TRUE	1	0.18	2		443	769	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433117	49433118	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0062472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	39	592	0	ENST00000301067.7:c.8253_8254insT	p.Pro2752SerfsTer17	p.P2752Sfs*17	ENST00000301067	NM_003482.3	2751	-/T	33/54	1	2	FACETS	0.594	0.491	0.71	0.594	0.491	0.71	SUBCLONAL	1	TRUE	1	0.18	2		592	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062474-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	217	612	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.63276535703063	1	FACETS	0.773	0.724	0.822	0.773	0.724	0.822	SUBCLONAL	1	TRUE	0	0.669539596897036	1		612	558	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172472	108172472	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062474-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	81	366	0	ENST00000278616.4:c.5275C>G	p.Pro1759Ala	p.P1759A	ENST00000278616	NM_000051.3	1759	Cca/Gca	35/63	0.425141713602731	1	FACETS	0.348	0.308	0.392	0.348	0.308	0.392	SUBCLONAL	1	TRUE	0	0.669539596897036	1		366	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578224	7578224	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1429743956	NA	P-0062475-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	79	662	0	ENST00000269305.4:c.625A>T	p.Arg209Ter	p.R209*	ENST00000269305	NM_001126112.2	209	Aga/Tga	6/11	1	2	FACETS	0.468	0.411	0.53	0.468	0.411	0.53	SUBCLONAL	1	TRUE	1	0.4	2		662	844	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0062475-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	112	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.3	3	FACETS	1	0.98	1	0.671	0.606	0.738	CLONAL	1	TRUE	1	0.4	3		485	501	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986909	36986910	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCA	novel	NA	P-0062475-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	81	645	0	ENST00000354822.5:c.776_779dup	p.Gln260HisfsTer180	p.Q260Hfs*180	ENST00000354822	NM_001079668.2	260	cag/caTGCAg	3/3	1	2	FACETS	0.527	0.464	0.595	0.527	0.464	0.595	SUBCLONAL	1	TRUE	1	0.4	2		645	768	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0062478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	207	481	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.69099603969411	4	FACETS	0.987	0.915	1	0.493	0.457	0.531	CLONAL	1	TRUE	2	0.689487641342238	4		481	1028	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43817942	43817942	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1355	228	656	0	ENST00000372470.3:c.1621C>G	p.Gln541Glu	p.Q541E	ENST00000372470	NM_005373.2	541	Cag/Gag	11/12	0.689487641342238	7	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.689487641342238	7		656	1583	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437456	49437456	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	214	616	0	ENST00000301067.7:c.5429G>T	p.Gly1810Val	p.G1810V	ENST00000301067	NM_003482.3	1810	gGa/gTa	23/54	0.69099603969411	3	FACETS	1	0.932	1			1	CLONAL	1	TRUE	NA	0.689487641342238	3		616	834	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647121	23647121	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	161	563	1	ENST00000261584.4:c.746del	p.Pro249LeufsTer30	p.P249Lfs*30	ENST00000261584	NM_024675.3	249	cCt/ct	4/13	NA	2	FACETS	0.828	0.777	0.878			1	INDETERMINATE	2	TRUE	NA	0.689487641342238	2		564	282	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274098	18274098	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	224	629	0	ENST00000222254.8:c.1316T>C	p.Val439Ala	p.V439A	ENST00000222254	NM_005027.3	439	gTg/gCg	11/16	0.69099603969411	3	FACETS	1	0.939	1			1	CLONAL	1	TRUE	NA	0.689487641342238	3		629	868	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209230	36209230	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1759	97	909	0	ENST00000222270.7:c.310A>C	p.Ser104Arg	p.S104R	ENST00000222270	NM_014727.1	104	Agt/Cgt	1/37	0.69099603969411	5	FACETS	0.308	0.273	0.346	0.103	0.091	0.116	SUBCLONAL	1	TRUE	2	0.689487641342238	5		909	1856	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157546	106157546	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	154	514	0	ENST00000380013.4:c.2447A>T	p.Asn816Ile	p.N816I	ENST00000380013	NM_001127208.2	816	aAt/aTt	3/11	0.69099603969411	2	FACETS	1	0.96	1	0.529	0.489	0.57	CLONAL	1	TRUE	0	0.689487641342238	2		514	422	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753120	128753120	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1520	215	593	0	ENST00000377970.2:c.1281G>C	p.Lys427Asn	p.K427N	ENST00000377970	NM_002467.4	427	aaG/aaC	3/3	0.689487641342238	8	FACETS	1	0.973	1	0.184	0.17	0.198	CLONAL	1	TRUE	2	0.689487641342238	8		593	1735	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111061	193111061	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	42	459	0	ENST00000367435.3:c.594G>T	p.Lys198Asn	p.K198N	ENST00000367435	NM_024529.4	198	aaG/aaT	7/17	0.358469188016401	3	FACETS	0.906	0.76	1	0.453	0.38	0.533	CLONAL	1	TRUE	1	0.358469188016401	3		459	305	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674234	86674234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	114	403	0	ENST00000274376.6:c.2366G>A	p.Arg789Gln	p.R789Q	ENST00000274376	NM_002890.2	789	cGa/cAa	18/25	0.259994155854011	3	FACETS	1	0.976	1	0.804	0.734	0.876	CLONAL	2	TRUE	0	0.358469188016401	3		403	311	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270162	66270162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	115	496	0	ENST00000273854.3:c.1720G>A	p.Val574Ile	p.V574I	ENST00000273854	NM_004439.5	574	Gta/Ata	8/18	0.358469188016401	3	FACETS	0.941	0.855	1	0.941	0.855	1	CLONAL	2	TRUE	1	0.358469188016401	3		496	402	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652034	36652035	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0062479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	322	635	0	ENST00000244741.5:c.159dup	p.Val54CysfsTer9	p.V54Cfs*9	ENST00000244741	NM_000389.4	52	-/T	2/3	0.330967266895489	4	FACETS	1	0.976	1	0.785	0.746	0.825	CLONAL	3	TRUE	0	0.358469188016401	4		635	777	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0062479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	128	431	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	0.358469188016401	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.358469188016401	4		431	433	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360914	118360914	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	99	439	0	ENST00000534358.1:c.4646G>T	p.Trp1549Leu	p.W1549L	ENST00000534358	NM_005933.3	1549	tGg/tTg	13/36	0.358469188016401	3	FACETS	1	0.961	1	0.579	0.519	0.644	CLONAL	1	TRUE	1	0.358469188016401	3		439	562	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560493	65560493	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	147	479	0	ENST00000358664.4:c.104G>C	p.Arg35Pro	p.R35P	ENST00000358664	NM_002382.4	35	cGt/cCt	3/5	0.340393034791366	2	FACETS	0.888	0.817	0.96	0.888	0.817	0.96	CLONAL	2	TRUE	0	0.358469188016401	2		479	462	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778590	3778590	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	72	591	0	ENST00000262367.5:c.6458G>C	p.Gly2153Ala	p.G2153A	ENST00000262367	NM_004380.2	2153	gGt/gCt	31/31	0.358469188016401	3	FACETS	0.929	0.813	1	0.464	0.406	0.527	CLONAL	1	TRUE	1	0.358469188016401	3		591	510	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673788	37673788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1220664561	NA	P-0062479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	159	425	0	ENST00000447079.4:c.2942G>A	p.Arg981His	p.R981H	ENST00000447079	NM_015083.1	981	cGt/cAt	10/14	0.358469188016401	3	FACETS	1	0.979	1	0.771	0.714	0.831	CLONAL	2	TRUE	0	0.358469188016401	3		425	452	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221709	55221709	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	189	597	0	ENST00000275493.2:c.753C>A	p.Cys251Ter	p.C251*	ENST00000275493	NM_005228.3	251	tgC/tgA	7/28	0.358469188016401	3	FACETS	0.794	0.735	0.855	0.794	0.735	0.855	SUBCLONAL	2	TRUE	1	0.358469188016401	3		597	783	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860855	151860855	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	142	571	0	ENST00000262189.6:c.9807G>T	p.Gln3269His	p.Q3269H	ENST00000262189	NM_170606.2	3269	caG/caT	43/59	0.340393034791366	2	FACETS	0.886	0.814	0.96	0.886	0.814	0.96	CLONAL	2	TRUE	0	0.358469188016401	2		571	447	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930941	39930941	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	61	288	0	ENST00000378444.4:c.3000G>T	p.Met1000Ile	p.M1000I	ENST00000378444	NM_001123385.1	1000	atG/atT	5/15	1	2	FACETS	0.859	0.754	0.97	1	0.978	1	CLONAL	2	TRUE	1	0.358469188016401	2		288	198	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0062480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	236	544	0	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	0.493031227410364	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.498542419433808	2		544	460	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281250	15281250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184522923	NA	P-0062480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	125	676	0	ENST00000263388.2:c.5006G>A	p.Arg1669His	p.R1669H	ENST00000263388	NM_000435.2	1669	cGc/cAc	27/33	0.339313778132283	6	FACETS	1	0.982	1	0.338	0.306	0.372	CLONAL	1	TRUE	2	0.498542419433808	6		676	740	SUCCESS
APC	324	MSKCC	GRCh37	5	112154977	112154977	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	115	449	0	ENST00000257430.4:c.1248C>A	p.Tyr416Ter	p.Y416*	ENST00000257430	NM_000038.5	416	taC/taA	10/16	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.498542419433808	2		449	461	SUCCESS
APC	324	MSKCC	GRCh37	5	112175347	112175359	+	frameshift_variant	Frame_Shift_Del	DEL	TGAATTTTCTTCA	TGAATTTTCTTCA	CG	novel	NA	P-0062480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	101	494	1	ENST00000257430.4:c.4056_4068delinsCG	p.Glu1353GlyfsTer18	p.E1353Gfs*18	ENST00000257430	NM_000038.5	1352	gtTGAATTTTCTTCA/gtCG	16/16	1	2	FACETS	0.969	0.872	1	0.969	0.872	1	CLONAL	1	TRUE	1	0.498542419433808	2		495	418	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1691201	1691201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745456337	NA	P-0062481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	85	721	0	ENST00000378625.1:c.404G>A	p.Arg135Gln	p.R135Q	ENST00000378625	NM_001198994.1	135	cGa/cAa	4/14	0.156712761928355	3	FACETS	0.866	0.767	0.972	0.866	0.767	0.972	CLONAL	2	FALSE	1	0.186565793019038	3		721	575	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999603	100999603	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	43	741	0	ENST00000325455.5:c.199C>G	p.Gln67Glu	p.Q67E	ENST00000325455	NM_001202474.3	67	Cag/Gag	1/8	0.156712761928355	3	FACETS	0.903	0.755	1	0.452	0.377	0.534	CLONAL	1	FALSE	1	0.186565793019038	3		741	558	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68758676	68758676	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	67	579	0	ENST00000487270.1:c.832G>A	p.Asp278Asn	p.D278N	ENST00000487270	NM_133509.3	278	Gat/Aat	8/11	0.186565793019038	5	FACETS	1	0.972	1	0.746	0.648	0.852	CLONAL	1	FALSE	3	0.186565793019038	5		579	616	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0062481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	108	852	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.186565793019038	4	FACETS	1	0.971	1	0.806	0.726	0.891	CLONAL	2	FALSE	1	0.186565793019038	4		852	568	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176338	24176338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	36	404	0	ENST00000263121.7:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000263121	NM_003073.3	377	Cgt/Tgt	9/9	0.186565793019038	3	FACETS	1	0.946	1	0.715	0.59	0.854	CLONAL	1	FALSE	1	0.186565793019038	3		404	295	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565575	41565575	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	42	463	1	ENST00000263253.7:c.4241A>G	p.Tyr1414Cys	p.Y1414C	ENST00000263253	NM_001429.3	1414	tAt/tGt	26/31	0.186565793019038	3	FACETS	1	0.903	1	0.559	0.467	0.661	CLONAL	1	FALSE	1	0.186565793019038	3		464	440	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426083	138426083	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	41	346	0	ENST00000289153.2:c.1448C>T	p.Pro483Leu	p.P483L	ENST00000289153	NM_006219.2	483	cCa/cTa	9/22	0.150158906433314	3	FACETS	1	0.943	1	0.441	0.368	0.522	CLONAL	1	FALSE	0	0.186565793019038	3		346	363	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786421	135786421	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0062481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	129	496	0	ENST00000298552.3:c.1109C>G	p.Ser370Ter	p.S370*	ENST00000298552	NM_001162426.1	370	tCa/tGa	11/23	0.186565793019038	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	FALSE	1	0.186565793019038	4		496	473	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231065	53231065	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	171	333	0	ENST00000375401.3:c.1837G>T	p.Glu613Ter	p.E613*	ENST00000375401	NM_004187.3	613	Gag/Tag	13/26	0.186565793019038	4	FACETS	1	0.936	1			1	CLONAL	5	FALSE	NA	0.186565793019038	4		333	432	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218500	1218500	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1131690951	NA	P-0062482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	58	309	0	ENST00000326873.7:c.374+1A>G		p.X125_splice	ENST00000326873	NM_000455.4	125			1	2	FACETS	0.585	0.503	0.674	0.585	0.503	0.674	SUBCLONAL	1	TRUE	1	0.42	2		309	472	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835675	68835675	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	103	561	0	ENST00000261769.5:c.266T>C	p.Leu89Pro	p.L89P	ENST00000261769	NM_004360.3	89	cTa/cCa	3/16	1	2	FACETS	0.622	0.556	0.691	0.622	0.556	0.691	SUBCLONAL	1	TRUE	1	0.42	2		561	789	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0062483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	183	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.559657722782302	5	FACETS	1	0.987	1	0.833	0.778	0.889	CLONAL	2	TRUE	2	0.667602828624002	5		485	439	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0062483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	155	274	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.667602828624002	3	FACETS	0.963	0.885	1	0.482	0.442	0.523	CLONAL	1	TRUE	1	0.667602828624002	3		274	643	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433982	49433982	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760263014	NA	P-0062483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	172	786	0	ENST00000301067.7:c.7571C>T	p.Thr2524Met	p.T2524M	ENST00000301067	NM_003482.3	2524	aCg/aTg	31/54	0.559657722782302	5	FACETS	1	0.964	1	0.361	0.332	0.392	CLONAL	1	TRUE	2	0.667602828624002	5		786	951	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967993	93967993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	195	466	0	ENST00000369303.4:c.1934G>A	p.Gly645Asp	p.G645D	ENST00000369303	NM_004440.3	645	gGt/gAt	11/17	0.667602828624002	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.667602828624002	2		466	288	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	G	rs1131691003	NA	P-0062483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	235	505	2	ENST00000269305.4:c.96+1G>C		p.X32_splice	ENST00000269305	NM_001126112.2	32			NA	2	FACETS	0.983	0.938	1			1	INDETERMINATE	2	TRUE	NA	0.667602828624002	2		507	358	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761146	59761147	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs771654971	NA	P-0062483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	98	617	0	ENST00000259008.2:c.3260dup	p.Asn1087LysfsTer4	p.N1087Kfs*4	ENST00000259008	NM_032043.2	1087	aat/aaAt	20/20	0.621277502275151	4	FACETS	0.887	0.794	0.986	0.443	0.396	0.493	CLONAL	1	TRUE	2	0.667602828624002	4		617	552	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564520	55564520	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0062483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	136	616	0	ENST00000288135.5:c.408T>A	p.Cys136Ter	p.C136*	ENST00000288135	NM_000222.2	136	tgT/tgA	3/21	0.623392400541929	5	FACETS	0.985	0.896	1	0.328	0.298	0.36	CLONAL	1	TRUE	2	0.667602828624002	5		616	828	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540267	23540283	+	frameshift_variant	Frame_Shift_Del	DEL	TGCGGCCGCCTTGCCGC	TGCGGCCGCCTTGCCGC	-	novel	NA	P-0062483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	178	774	0	ENST00000380871.4:c.120_136del	p.Gln40HisfsTer62	p.Q40Hfs*62	ENST00000380871	NM_006167.3	40	caGCGGCAAGGCGGCCGCAcg/cacg	1/2	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.667602828624002	2		774	490	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0062484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	396	710	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.384329521479801	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.435141318225228	3		710	1099	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106861	27106861	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	190	667	0	ENST00000324856.7:c.6472C>T	p.Arg2158Ter	p.R2158*	ENST00000324856	NM_006015.4	2158	Cga/Tga	20/20	0.435141318225228	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.435141318225228	1		667	628	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025621	1025621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763842232	NA	P-0062484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	186	592	0	ENST00000358495.3:c.754G>A	p.Glu252Lys	p.E252K	ENST00000358495	NM_134424.2	252	Gag/Aag	9/12	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.435141318225228	2		592	835	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180964	108180964	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	72	349	0	ENST00000278616.4:c.5840C>G	p.Ser1947Cys	p.S1947C	ENST00000278616	NM_000051.3	1947	tCt/tGt	39/63	0.435141318225228	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.435141318225228	1		349	236	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839755	27839764	+	frameshift_variant	Frame_Shift_Del	DEL	AATGGCGCAC	AATGGCGCAC	-	novel	NA	P-0062484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	204	760	0	ENST00000328488.2:c.330_339del	p.Cys111ThrfsTer?	p.C111Tfs*?	ENST00000328488	NM_003533.2	110	ctGTGCGCCATT/ct	1/1	1	2	FACETS	0.925	0.857	0.995	0.925	0.857	0.995	CLONAL	1	TRUE	1	0.435141318225228	2		760	1014	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	91	714	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.804106420140126	2		715	213	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820810	36820810	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	132	344	0	ENST00000373129.3:c.567C>A	p.His189Gln	p.H189Q	ENST00000373129	NM_032017.1	189	caC/caA	6/12	1	2	FACETS	0.935	0.86	1	0.935	0.86	1	CLONAL	1	TRUE	1	0.804106420140126	2		344	351	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717721	89717721	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	114	240	0	ENST00000371953.3:c.746T>C	p.Val249Ala	p.V249A	ENST00000371953	NM_000314.4	249	gTg/gCg	7/9	0.804106420140126	1	FACETS	0.932	0.867	0.994	0.932	0.867	0.994	CLONAL	1	TRUE	0	0.804106420140126	1		240	182	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410687	63410687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	159	206	0	ENST00000330258.3:c.2480A>G	p.Glu827Gly	p.E827G	ENST00000330258	NM_152424.3	827	gAg/gGg	2/2	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.804106420140126	1		206	191	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230613	46230613	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	139	384	0	ENST00000334344.6:c.862C>T	p.Gln288Ter	p.Q288*	ENST00000334344	NM_152641.2	288	Cag/Tag	8/21	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.689843630539781	2		384	375	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105611	27105612	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0062487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	171	423	0	ENST00000324856.7:c.5225_5226del	p.Arg1742AsnfsTer13	p.R1742Nfs*13	ENST00000324856	NM_006015.4	1741	cAG/c	20/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.689843630539781	2		423	444	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624394	140624394	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1390903353	NA	P-0062487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	111	304	0	ENST00000288602.6:c.110C>T	p.Ser37Leu	p.S37L	ENST00000288602	NM_004333.4	37	tCg/tTg	1/18	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.689843630539781	2		304	263	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664876	138664876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	82	340	0	ENST00000330315.3:c.689C>T	p.Ala230Val	p.A230V	ENST00000330315	NM_023067.3	230	gCg/gTg	1/1	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.689843630539781	2		340	226	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0062487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	82	509	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.897	0.802	0.996	0.897	0.802	0.996	CLONAL	1	TRUE	1	0.689843630539781	2		510	265	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106521	27106522	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0062487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	161	525	0	ENST00000324856.7:c.6134_6135dup	p.Val2046LysfsTer90	p.V2046Kfs*90	ENST00000324856	NM_006015.4	2044	-/AA	20/20	1	2	FACETS	0.928	0.857	1	0.928	0.857	1	CLONAL	1	TRUE	1	0.689843630539781	2		525	503	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10800276	10800276	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143951897	NA	P-0062487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	44	439	0	ENST00000361367.2:c.3146G>A	p.Arg1049Gln	p.R1049Q	ENST00000361367	NM_014633.3	1049	cGa/cAa	25/25	0.689843630539781	1	FACETS	0.319	0.269	0.373	0.319	0.269	0.373	SUBCLONAL	1	TRUE	0	0.689843630539781	1		439	262	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422059	47422059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	80	445	0	ENST00000404338.3:c.127G>A	p.Val43Met	p.V43M	ENST00000404338	NM_004491.4	43	Gtg/Atg	1/6	1	2	FACETS	0.586	0.518	0.657	0.586	0.518	0.657	SUBCLONAL	1	TRUE	1	0.689843630539781	2		445	396	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38157072	38157072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	101	315	0	ENST00000317025.8:c.2648G>A	p.Ser883Asn	p.S883N	ENST00000317025	NM_023034.1	883	aGt/aAt	15/24	1	2	FACETS	0.942	0.852	1	0.942	0.852	1	CLONAL	1	TRUE	1	0.689843630539781	2		315	311	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189098	38189098	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	96	315	0	ENST00000317025.8:c.916C>G	p.Arg306Gly	p.R306G	ENST00000317025	NM_023034.1	306	Cga/Gga	5/24	1	2	FACETS	0.983	0.889	1	0.983	0.889	1	CLONAL	1	TRUE	1	0.689843630539781	2		315	283	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653796	89653804	+	inframe_deletion	In_Frame_Del	DEL	ATTATTGCT	ATTATTGCT	-	novel	NA	P-0062488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	33	230	0	ENST00000371953.3:c.96_104del	p.Ile32_Ala34del	p.I32_A34del	ENST00000371953	NM_000314.4	32	ATTATTGCT/-	2/9	0.243592444141557	2	FACETS	1	0.936	1	0.673	0.554	0.804	CLONAL	1	TRUE	0	0.263628828566224	2		230	186	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14031681	14031681	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766395322	NA	P-0062488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	48	312	0	ENST00000311895.7:c.1870C>T	p.Arg624Trp	p.R624W	ENST00000311895	NM_005236.2	624	Cgg/Tgg	9/11	0.263628828566224	2	FACETS	0.929	0.796	1	0.929	0.796	1	CLONAL	2	TRUE	0	0.263628828566224	2		312	196	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579383	7579384	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0062488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	99	552	0	ENST00000269305.4:c.303_304del	p.Lys101AsnfsTer47	p.K101Nfs*47	ENST00000269305	NM_001126112.2	101	aaAAcc/aacc	4/11	0.243592444141557	2	FACETS	0.882	0.792	0.976	0.882	0.792	0.976	CLONAL	2	TRUE	0	0.263628828566224	2		552	426	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676206	29676219	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	GTTAACAAACACAG	GTTAACAAACACAG	TGAC	novel	NA	P-0062488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	39	332	1	ENST00000356175.3:c.7195_7208delinsTGAC	p.Val2399Ter	p.V2399*	ENST00000356175	NM_000267.3	2399	GTTAACAAACACAGa/TGACa	48/57	0.243592444141557	2	FACETS	1	0.933	1	0.624	0.521	0.737	CLONAL	1	TRUE	0	0.263628828566224	2		333	237	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588982	67588982	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	56	380	0	ENST00000274335.5:c.1073G>C	p.Arg358Pro	p.R358P	ENST00000274335		358	cGa/cCa	8/15	0.243592444141557	2	FACETS	0.827	0.715	0.946	0.827	0.715	0.946	CLONAL	2	TRUE	0	0.263628828566224	2		380	257	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056440	26056440	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773914281	NA	P-0062488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	90	441	0	ENST00000343677.2:c.217G>A	p.Val73Met	p.V73M	ENST00000343677	NM_005319.3	73	Gtg/Atg	1/1	0.263628828566224	6	FACETS	1	0.925	1	0.699	0.623	0.781	CLONAL	2	TRUE	3	0.263628828566224	6		441	497	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552865	106552865	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	114	542	0	ENST00000369096.4:c.830A>G	p.Glu277Gly	p.E277G	ENST00000369096	NM_001198.3	277	gAa/gGa	5/7	0.263628828566224	6	FACETS	0.891	0.803	0.985	0.446	0.401	0.493	CLONAL	2	TRUE	2	0.263628828566224	6		542	741	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22008820	22008896	+	frameshift_variant	Frame_Shift_Del	DEL	GGTTGACTCCGTTGGGATCCGCGCCGGCTTCCAGGAGCTGTCGCACCTTCTCCACTAGTCCCCGCGCCGCGGCGCTG	GGTTGACTCCGTTGGGATCCGCGCCGGCTTCCAGGAGCTGTCGCACCTTCTCCACTAGTCCCCGCGCCGCGGCGCTG	-	novel	NA	P-0062488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	108	499	0	ENST00000276925.6:c.57_133del	p.Ser20PhefsTer41	p.S20Ffs*41	ENST00000276925	NM_004936.3	19	gcCAGCGCCGCGGCGCGGGGACTAGTGGAGAAGGTGCGACAGCTCCTGGAAGCCGGCGCGGATCCCAACGGAGTCAACCgt/gcgt	1/2	0.17302910077657	5	FACETS	1	0.965	1	0.77	0.694	0.849	CLONAL	2	TRUE	2	0.263628828566224	5		499	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0062489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3	311	677	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.933894447049603	4	FACETS	1	0.996	1	1	0.996	1	CLONAL	4	TRUE	0	0.933894447049603	4		678	314	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864778	37864778	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	199	364	0	ENST00000269571.5:c.430A>G	p.Ser144Gly	p.S144G	ENST00000269571		144	Agc/Ggc	3/27	0.933894447049603	5	FACETS	0.993	0.975	1	0.993	0.975	1	CLONAL	5	TRUE	0	0.933894447049603	5		364	206	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963095	38963095	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	87	289	0	ENST00000357387.3:c.1449G>C	p.Lys483Asn	p.K483N	ENST00000357387	NM_152756.3	483	aaG/aaC	17/38	0.50885823616638	6	FACETS	1	0.978	1	0.474	0.422	0.528	INDETERMINATE	1	TRUE	3	0.933894447049603	6		289	376	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245304	53245304	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	103	411	0	ENST00000375401.3:c.733A>T	p.Met245Leu	p.M245L	ENST00000375401	NM_004187.3	245	Atg/Ttg	6/26	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.933894447049603	2		411	207	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617628	100617628	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	81	312	0	ENST00000308731.7:c.441G>T	p.Trp147Cys	p.W147C	ENST00000308731	NM_000061.2	147	tgG/tgT	6/19	0.933894447049603	4	FACETS	0.895	0.793	1	0.298	0.264	0.334	CLONAL	1	TRUE	1	0.933894447049603	4		312	375	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242487	+	protein_altering_variant	In_Frame_Del	DEL	GAATTAAGAGAAGCAACATCTC	GAATTAAGAGAAGCAACATCTC	ATCT	novel	NA	P-0062489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	309	290	0	ENST00000275493.2:c.2236_2257delinsATCT	p.Glu746_Pro753delinsIleSer	p.E746_P753delinsIS	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCAACATCTCcg/ATCTcg	19/28	0.933894447049603	6	FACETS	1	0.989	1	1	0.989	1	CLONAL	4	TRUE	2	0.933894447049603	6		290	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0062491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	20	340	1	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		341	314	SUCCESS
AR	367	MSKCC	GRCh37	X	66765173	66765173	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs746341152	NA	P-0062491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	75	84	1	ENST00000374690.3:c.185A>T	p.Gln62Leu	p.Q62L	ENST00000374690	NM_000044.3	62	cAg/cTg	1/8	0.3	18	FACETS		NA	1			1	NA	NA	FALSE	0	NA	18		85	836	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062496-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	290	570	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.312337263492877	0	FACETS	0.893	0.85	0.935			1	CLONAL	2	TRUE	0	0.372630501975975	0		570	547	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027162	49027171	+	frameshift_variant	Frame_Shift_Del	DEL	AAGGACCGAG	AAGGACCGAG	-	novel	NA	P-0062496-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	84	358	0	ENST00000267163.4:c.1736_1745del	p.Arg579GlnfsTer29	p.R579Qfs*29	ENST00000267163	NM_000321.2	577	AAGGACCGAGaa/aa	18/27	0.372630501975975	0	FACETS	0.592	0.531	0.654			1	SUBCLONAL	2	TRUE	0	0.372630501975975	0		358	239	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845865	72845865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062496-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	252	586	0	ENST00000268489.5:c.3602G>A	p.Ser1201Asn	p.S1201N	ENST00000268489	NM_006885.3	1201	aGc/aAc	6/10	1	2	FACETS	0.838	0.787	0.891	1	0.994	1	CLONAL	2	TRUE	1	0.372630501975975	2		586	807	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917866	29917866	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062496-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	201	498	0	ENST00000389048.3:c.802T>A	p.Phe268Ile	p.F268I	ENST00000389048	NM_004304.4	268	Ttt/Att	3/29	0.351171395968526	1	FACETS	0.825	0.771	0.88	1	0.993	1	CLONAL	2	TRUE	0	0.372630501975975	1		498	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587780070	NA	P-0062497-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	301	633	0	ENST00000269305.4:c.535C>G	p.His179Asp	p.H179D	ENST00000269305	NM_001126112.2	179	Cat/Gat	5/11	0.696819151452512	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.69552929665781	2		633	408	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711308	114711308	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062497-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	158	323	0	ENST00000543371.1:c.323T>A	p.Ile108Asn	p.I108N	ENST00000543371	NM_001198531.1	108	aTc/aAc	3/14	0.696819151452512	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.69552929665781	2		323	213	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279538	1279538	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062497-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	169	466	0	ENST00000310581.5:c.1998C>G	p.Asn666Lys	p.N666K	ENST00000310581	NM_198253.2	666	aaC/aaG	5/16	0.597936827350185	4	FACETS	0.993	0.924	1	0.993	0.924	1	CLONAL	2	TRUE	2	0.69552929665781	4		466	415	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939367	76939367	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062497-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	243	419	0	ENST00000373344.5:c.1381G>T	p.Glu461Ter	p.E461*	ENST00000373344	NM_000489.3	461	Gaa/Taa	9/35	0.597936827350185	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.69552929665781	4		419	523	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	78	714	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.794	0.707	0.884	0.794	0.707	0.884	SUBCLONAL	1	TRUE	1	0.767924134189176	2		715	256	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923160	48923160	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776789	NA	P-0062498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	89	235	0	ENST00000267163.4:c.607+1G>A		p.X203_splice	ENST00000267163	NM_000321.2	203			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.767924134189176	2		235	207	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977639	2977639	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	105	350	0	ENST00000396946.4:c.1045C>T	p.Leu349Phe	p.L349F	ENST00000396946	NM_032415.4	349	Ctc/Ttc	8/25	1	2	FACETS	0.775	0.701	0.851	0.775	0.701	0.851	SUBCLONAL	1	TRUE	1	0.767924134189176	2		350	353	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	377	714	1				ENST00000310581	NM_198253.2	-/1132			0.372551250568224	5	FACETS	0.916	0.875	0.957	0.916	0.875	0.957	CLONAL	4	TRUE	1	0.416021516457979	5		715	803	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0062499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	168	605	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.416021516457979	2		605	660	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0062499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	136	552	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.416021516457979	2		552	636	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295247	1295247	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0062499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	350	545	0				ENST00000310581	NM_198253.2	-/1132			0.372551250568224	5	FACETS	0.936	0.893	0.979	0.936	0.893	0.979	CLONAL	4	TRUE	1	0.416021516457979	5		545	730	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47004903	47004903	+	intron_variant	Intron	SNP	C	C	T	novel	NA	P-0062499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	191	451	0	ENST00000377604.3:c.-126+19C>T		p.*42*	ENST00000377604	NM_001204468.1	-/163			1	1	FACETS	0.81	0.757	0.863	1	0.993	1	CLONAL	2	TRUE	0	0.416021516457979	1		451	449	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324917	31324917	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs776780353	NA	P-0062499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	179	611	0	ENST00000412585.2:c.19C>T	p.Arg7Ter	p.R7*	ENST00000412585	NM_005514.6	7	Cga/Tga	1/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.416021516457979	2		611	640	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955452	48955452	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0062499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	90	397	0	ENST00000267163.4:c.1568T>G	p.Leu523Ter	p.L523*	ENST00000267163	NM_000321.2	523	tTa/tGa	17/27	0.416021516457979	1	FACETS	0.941	0.842	1	0.941	0.842	1	CLONAL	1	TRUE	0	0.416021516457979	1		397	364	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102198795	102198795	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	113	333	0	ENST00000263464.3:c.966G>C	p.Leu322Phe	p.L322F	ENST00000263464	NM_001165.4	322	ttG/ttC	4/9	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.416021516457979	2		333	441	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50786466	50786466	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	80	384	0	ENST00000307179.4:c.2647G>C	p.Asp883His	p.D883H	ENST00000307179		883	Gat/Cat	16/20	1	2	FACETS	0.952	0.843	1	0.952	0.843	1	CLONAL	1	TRUE	1	0.416021516457979	2		384	404	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61722598	61722598	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	81	318	0	ENST00000401558.2:c.1039C>G	p.Leu347Val	p.L347V	ENST00000401558	NM_003400.3	347	Ctt/Gtt	11/25	1	2	FACETS	0.95	0.841	1	0.95	0.841	1	CLONAL	1	TRUE	1	0.416021516457979	2		318	410	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41521961	41521961	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1226998471	NA	P-0062499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	102	438	0	ENST00000263253.7:c.823C>G	p.Gln275Glu	p.Q275E	ENST00000263253	NM_001429.3	275	Cag/Gag	3/31	0.416021516457979	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.416021516457979	1		438	386	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673284	30673284	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	199	837	0	ENST00000376406.3:c.3676C>T	p.Gln1226Ter	p.Q1226*	ENST00000376406	NM_014641.2	1226	Cag/Tag	10/15	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.416021516457979	2		837	939	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124491962	124491962	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1444104997	NA	P-0062499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	73	345	0	ENST00000357628.3:c.913G>A	p.Val305Ile	p.V305I	ENST00000357628	NM_015450.2	305	Gtt/Att	11/19	1	2	FACETS	0.888	0.781	1	0.888	0.781	1	CLONAL	1	TRUE	1	0.416021516457979	2		345	395	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272374	38272374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	43	696	0	ENST00000425967.3:c.1993G>T	p.Asp665Tyr	p.D665Y	ENST00000425967	NM_001174067.1	665	Gac/Tac	15/19	0.416021516457979	1	FACETS	0.28	0.234	0.332	0.28	0.234	0.332	SUBCLONAL	1	TRUE	0	0.416021516457979	1		696	584	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	274	481	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.334321987656619	4	FACETS	0.836	0.787	0.886	0.836	0.787	0.886	INDETERMINATE	2	TRUE	2	0.610294370662571	4		481	865	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	340	714	1				ENST00000310581	NM_198253.2	-/1132			0.26917374732869	3	FACETS	1	0.98	1	0.699	0.667	0.732	INDETERMINATE	2	TRUE	0	0.610294370662571	3		715	693	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432377	78432377	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	55	323	0	ENST00000370768.2:c.473+1G>A		p.X158_splice	ENST00000370768	NM_003902.3	158			0.502578786860596	2	FACETS	0.485	0.416	0.559	0.242	0.208	0.28	SUBCLONAL	1	TRUE	0	0.610294370662571	2		323	372	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518370	204518370	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	269	568	0	ENST00000367182.3:c.1033G>C	p.Asp345His	p.D345H	ENST00000367182	NM_001278516.1	345	Gat/Cat	11/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.610294370662571	2		568	797	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720825	89720825	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	108	134	0	ENST00000371953.3:c.976G>C	p.Asp326His	p.D326H	ENST00000371953	NM_000314.4	326	Gac/Cac	8/9	0.577639722509197	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	0	0.610294370662571	2		134	177	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298733	46298733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	104	331	0	ENST00000334344.6:c.5380G>A	p.Glu1794Lys	p.E1794K	ENST00000334344	NM_152641.2	1794	Gaa/Aaa	21/21	0.610294370662571	4	FACETS	0.961	0.863	1	0.32	0.287	0.355	CLONAL	1	TRUE	1	0.610294370662571	4		331	571	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437376	110437376	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776945626	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	55	330	0	ENST00000375856.3:c.1025C>T	p.Ser342Leu	p.S342L	ENST00000375856	NM_003749.2	342	tCg/tTg	1/2	0.304646799583275	2	FACETS	0.455	0.39	0.525	0.228	0.195	0.263	INDETERMINATE	1	TRUE	0	0.610294370662571	2		330	396	SUCCESS
BLM	641	MSKCC	GRCh37	15	91341444	91341444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	43	277	0	ENST00000355112.3:c.3235G>A	p.Asp1079Asn	p.D1079N	ENST00000355112	NM_000057.2	1079	Gac/Aac	17/22	0.291979430185241	3	FACETS	0.456	0.382	0.538	0.228	0.191	0.269	INDETERMINATE	1	TRUE	1	0.610294370662571	3		277	403	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786752	3786752	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	238	422	0	ENST00000262367.5:c.4459C>G	p.His1487Asp	p.H1487D	ENST00000262367	NM_004380.2	1487	Cac/Gac	27/31	0.364796235180815	3	FACETS	0.788	0.74	0.837	0.788	0.74	0.837	INDETERMINATE	2	TRUE	1	0.610294370662571	3		422	646	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348567	89348567	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	348	571	0	ENST00000301030.4:c.4383G>C	p.Lys1461Asn	p.K1461N	ENST00000301030	NM_001256183.1	1461	aaG/aaC	9/13	0.364796235180815	3	FACETS	0.82	0.779	0.861	0.82	0.779	0.861	INDETERMINATE	2	TRUE	1	0.610294370662571	3		571	908	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877125	89877125	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	144	340	0	ENST00000389301.3:c.512G>A	p.Trp171Ter	p.W171*	ENST00000389301	NM_000135.2	171	tGg/tAg	5/43	0.364796235180815	3	FACETS	1	0.966	1	0.552	0.506	0.6	INDETERMINATE	1	TRUE	1	0.610294370662571	3		340	558	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882992	89882992	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1019317682	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	64	378	0	ENST00000389301.3:c.32C>T	p.Ser11Leu	p.S11L	ENST00000389301	NM_000135.2	11	tCg/tTg	1/43	0.364796235180815	3	FACETS	0.569	0.494	0.651	0.285	0.247	0.326	INDETERMINATE	1	TRUE	1	0.610294370662571	3		378	481	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217622	7217622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	269	502	0	ENST00000380728.2:c.305G>A	p.Arg102Gln	p.R102Q	ENST00000380728		102	cGa/cAa	4/11	0.610294370662571	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.610294370662571	1		502	541	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004838	16004838	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	245	538	0	ENST00000268712.3:c.2416G>T	p.Glu806Ter	p.E806*	ENST00000268712	NM_006311.3	806	Gaa/Taa	20/46	0.575810144901759	2	FACETS	0.813	0.769	0.857	0.813	0.769	0.857	CLONAL	2	TRUE	0	0.610294370662571	2		538	494	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866666	37866666	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757811990	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	354	655	0	ENST00000269571.5:c.833C>T	p.Thr278Met	p.T278M	ENST00000269571		278	aCg/aTg	7/27	0.334321987656619	4	FACETS	0.85	0.806	0.895	0.85	0.806	0.895	INDETERMINATE	2	TRUE	2	0.610294370662571	4		655	1099	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866686	37866686	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	352	613	0	ENST00000269571.5:c.853C>A	p.Pro285Thr	p.P285T	ENST00000269571		285	Ccc/Acc	7/27	0.334321987656619	4	FACETS	0.869	0.824	0.914	0.869	0.824	0.914	INDETERMINATE	2	TRUE	2	0.610294370662571	4		613	1069	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223153	1223153	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	212	569	0	ENST00000326873.7:c.1090C>G	p.Gln364Glu	p.Q364E	ENST00000326873	NM_000455.4	364	Cag/Gag	8/10	1	2	FACETS	0.841	0.783	0.901	0.841	0.783	0.901	CLONAL	1	TRUE	1	0.610294370662571	2		569	826	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10259603	10259603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	338	445	0	ENST00000340748.4:c.2629G>A	p.Glu877Lys	p.E877K	ENST00000340748		877	Gag/Aag	26/40	0.60120497715864	3	FACETS	0.97	0.924	1	0.97	0.924	1	CLONAL	2	TRUE	1	0.610294370662571	3		445	745	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872380	45872380	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	963	547	0	ENST00000391945.4:c.131C>G	p.Ser44Ter	p.S44*	ENST00000391945	NM_000400.3	44	tCa/tGa	3/23	0.610294370662571	5	FACETS	1	0.977	1	1	0.977	1	CLONAL	4	TRUE	1	0.610294370662571	5		547	1510	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141586	202141586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760898260	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	350	435	0	ENST00000358485.4:c.874C>T	p.Arg292Trp	p.R292W	ENST00000358485	NM_001080125.1	292	Cgg/Tgg	7/9	0.26917374732869	3	FACETS	1	0.991	1	0.764	0.731	0.797	INDETERMINATE	2	TRUE	0	0.610294370662571	3		435	653	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295699	212295699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776347334	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	291	437	0	ENST00000342788.4:c.2614G>A	p.Glu872Lys	p.E872K	ENST00000342788	NM_005235.2	872	Gaa/Aaa	21/28	0.26917374732869	3	FACETS	1	0.987	1	0.734	0.698	0.77	INDETERMINATE	2	TRUE	0	0.610294370662571	3		437	565	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371610	225371610	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	210	375	0	ENST00000264414.4:c.994G>C	p.Glu332Gln	p.E332Q	ENST00000264414	NM_003590.4	332	Gaa/Caa	7/16	0.26917374732869	3	FACETS	1	0.991	1	0.825	0.781	0.868	INDETERMINATE	2	TRUE	0	0.610294370662571	3		375	363	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024298	31024298	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	317	524	0	ENST00000375687.4:c.3783G>C	p.Lys1261Asn	p.K1261N	ENST00000375687	NM_015338.5	1261	aaG/aaC	13/13	0.610294370662571	4	FACETS	1	0.993	1	0.452	0.426	0.478	CLONAL	1	TRUE	1	0.610294370662571	4		524	1235	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31025091	31025091	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	318	468	0	ENST00000375687.4:c.4576G>A	p.Asp1526Asn	p.D1526N	ENST00000375687	NM_015338.5	1526	Gac/Aac	13/13	0.610294370662571	4	FACETS	1	0.992	1	0.438	0.413	0.464	CLONAL	1	TRUE	1	0.610294370662571	4		468	1276	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326261	62326261	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	309	577	0	ENST00000360203.5:c.3277G>C	p.Asp1093His	p.D1093H	ENST00000360203	NM_001283009.1	1093	Gac/Cac	32/35	0.29307534348315	4	FACETS	0.875	0.827	0.924	0.875	0.827	0.924	INDETERMINATE	2	TRUE	2	0.610294370662571	4		577	932	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436798	52436798	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	161	544	0	ENST00000460680.1:c.1980C>G	p.Phe660Leu	p.F660L	ENST00000460680	NM_004656.3	660	ttC/ttG	15/17	0.213837467916923	1	FACETS	0.589	0.543	0.638	0.589	0.543	0.638	INDETERMINATE	1	TRUE	0	0.610294370662571	1		544	622	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84393399	84393399	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	44	298	0	ENST00000321945.7:c.258G>C	p.Lys86Asn	p.K86N	ENST00000321945	NM_139076.2	86	aaG/aaC	4/9	0.339995277553908	3	FACETS	0.526	0.442	0.618	0.175	0.147	0.206	INDETERMINATE	1	TRUE	0	0.610294370662571	3		298	358	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	25	564	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.610294370662571	2	FACETS	0.188	0.147	0.234	0.094	0.073	0.117	SUBCLONAL	1	TRUE	0	0.610294370662571	2		564	436	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31483689	31483689	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	309	377	0	ENST00000344624.3:c.2043C>G	p.Phe681Leu	p.F681L	ENST00000344624		681	ttC/ttG	13/33	0.339995277553908	3	FACETS	1	0.991	1	0.776	0.74	0.811	INDETERMINATE	2	TRUE	0	0.610294370662571	3		377	568	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20483132	20483132	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	73	451	0	ENST00000346618.3:c.865G>A	p.Glu289Lys	p.E289K	ENST00000346618	NM_001949.4	289	Gag/Aag	4/7	0.329378339884471	2	FACETS	0.445	0.39	0.505	0.223	0.195	0.253	INDETERMINATE	1	TRUE	0	0.610294370662571	2		451	537	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197395	26197395	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	570	747	0	ENST00000356476.2:c.84G>C	p.Lys28Asn	p.K28N	ENST00000356476		28	aaG/aaC	1/1	0.329378339884471	2	FACETS	0.842	0.813	0.872	0.842	0.813	0.872	INDETERMINATE	2	TRUE	0	0.610294370662571	2		747	1109	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909253	41909253	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	84	462	0	ENST00000372991.4:c.135C>A	p.Phe45Leu	p.F45L	ENST00000372991	NM_001760.3	45	ttC/ttA	1/5	0.417084653650185	1	FACETS	0.364	0.322	0.408	0.364	0.322	0.408	SUBCLONAL	1	TRUE	0	0.610294370662571	1		462	526	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322590	109322590	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	196	382	0	ENST00000436639.2:c.447C>G	p.Phe149Leu	p.F149L	ENST00000436639	NM_014454.2	149	ttC/ttG	3/10	0.348836679260315	1	FACETS	0.911	0.851	0.971	0.911	0.851	0.971	INDETERMINATE	1	TRUE	0	0.610294370662571	1		382	490	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001345	150001345	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	98	508	0	ENST00000253339.5:c.2259G>C	p.Glu753Asp	p.E753D	ENST00000253339		753	gaG/gaC	4/7	0.348836679260315	1	FACETS	0.416	0.372	0.463	0.416	0.372	0.463	INDETERMINATE	1	TRUE	0	0.610294370662571	1		508	536	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151216551	151216551	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	149	236	0	ENST00000262187.5:c.47C>T	p.Ser16Phe	p.S16F	ENST00000262187	NM_005614.3	16	tCt/tTt	1/8	0.51822738302751	3	FACETS	0.954	0.885	1			1	CLONAL	2	TRUE	NA	0.610294370662571	3		236	334	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848547	151848547	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	290	402	0	ENST00000262189.6:c.12646G>T	p.Asp4216Tyr	p.D4216Y	ENST00000262189	NM_170606.2	4216	Gat/Tat	50/59	0.51822738302751	3	FACETS	0.953	0.903	1			1	CLONAL	2	TRUE	NA	0.610294370662571	3		402	651	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877100	151877100	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	368	502	0	ENST00000262189.6:c.7261C>G	p.Gln2421Glu	p.Q2421E	ENST00000262189	NM_170606.2	2421	Caa/Gaa	37/59	0.51822738302751	3	FACETS	0.934	0.89	0.977			1	CLONAL	2	TRUE	NA	0.610294370662571	3		502	843	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878206	151878206	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	386	591	0	ENST00000262189.6:c.6739C>T	p.Gln2247Ter	p.Q2247*	ENST00000262189	NM_170606.2	2247	Cag/Tag	36/59	0.51822738302751	3	FACETS	0.904	0.863	0.946			1	CLONAL	2	TRUE	NA	0.610294370662571	3		591	913	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878299	151878299	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	378	546	0	ENST00000262189.6:c.6646G>T	p.Val2216Phe	p.V2216F	ENST00000262189	NM_170606.2	2216	Gtc/Ttc	36/59	0.51822738302751	3	FACETS	0.956	0.912	0.999			1	CLONAL	2	TRUE	NA	0.610294370662571	3		546	846	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878326	151878326	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	375	543	0	ENST00000262189.6:c.6619C>T	p.Pro2207Ser	p.P2207S	ENST00000262189	NM_170606.2	2207	Cct/Tct	36/59	0.51822738302751	3	FACETS	0.934	0.891	0.977			1	CLONAL	2	TRUE	NA	0.610294370662571	3		543	859	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878785	151878785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	370	532	0	ENST00000262189.6:c.6160C>T	p.Gln2054Ter	p.Q2054*	ENST00000262189	NM_170606.2	2054	Cag/Tag	36/59	0.51822738302751	3	FACETS	0.952	0.908	0.996			1	CLONAL	2	TRUE	NA	0.610294370662571	3		532	831	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974792	21974792	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs141798398	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	551	664	1	ENST00000304494.5:c.35C>A	p.Ser12Ter	p.S12*	ENST00000304494	NM_000077.4	12	tCg/tAg	1/3	0.610294370662571	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.610294370662571	2		665	863	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942743	44942744	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	50	357	0	ENST00000377967.4:c.3327dup	p.Val1110CysfsTer41	p.V1110Cfs*41	ENST00000377967	NM_021140.2	1108	gct/gcTt	23/29	0.610294370662571	1	FACETS	0.323	0.274	0.375	0.323	0.274	0.375	SUBCLONAL	1	TRUE	0	0.610294370662571	1		357	353	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239971	53239971	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	312	508	0	ENST00000375401.3:c.1470C>G	p.Ile490Met	p.I490M	ENST00000375401	NM_004187.3	490	atC/atG	11/26	0.610294370662571	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.610294370662571	1		508	587	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0062502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	70	453	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.254807311184065	2		453	455	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	101	510	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.768	0.689	0.851	1	0.983	1	SUBCLONAL	2	TRUE	1	0.254807311184065	2		510	516	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100175	27100176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0062502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	87	584	1	ENST00000324856.7:c.3977dup	p.Gln1327AlafsTer11	p.Q1327Afs*11	ENST00000324856	NM_006015.4	1324	tac/taCc	16/20	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.254807311184065	2		585	675	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0062502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	86	471	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.254807311184065	2		471	471	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057781	27057781	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	109	611	0	ENST00000324856.7:c.1489C>T	p.Gln497Ter	p.Q497*	ENST00000324856	NM_006015.4	497	Caa/Taa	3/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.254807311184065	2		611	749	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692793	89692793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	52	247	0	ENST00000371953.3:c.277C>T	p.His93Tyr	p.H93Y	ENST00000371953	NM_000314.4	93	Cat/Tat	5/9	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.254807311184065	2		247	281	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225060	NA	P-0062502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	71	334	0	ENST00000263967.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000263967	NM_006218.2	104	cCa/cTa	2/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.254807311184065	2		334	458	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380346	14380346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	54	417	0	ENST00000256196.4:c.71G>A	p.Gly24Asp	p.G24D	ENST00000256196		24	gGc/gAc	1/6	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.254807311184065	2		417	394	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589552	67589552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	63	271	0	ENST00000274335.5:c.1315G>A	p.Glu439Lys	p.E439K	ENST00000274335		439	Gaa/Aaa	10/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.254807311184065	2		271	358	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127163	22127163	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	106	313	0	ENST00000215832.6:c.965A>T	p.Glu322Val	p.E322V	ENST00000215832	NM_002745.4	322	gAg/gTg	7/9	0.254807311184065	2	FACETS	0.974	0.879	1	0.974	0.879	1	CLONAL	2	TRUE	0	0.254807311184065	2		313	427	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588188	67588189	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0062502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	39	308	0	ENST00000274335.5:c.1019+1dup		p.R340fs	ENST00000274335		340	agg/aGgg	7/15	1	2	FACETS	0.793	0.658	0.943	0.793	0.658	0.943	CLONAL	1	TRUE	1	0.254807311184065	2		308	386	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937434	32937435	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0062503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	63	419	0	ENST00000380152.3:c.8100_8101dup	p.Ser2701TyrfsTer33	p.S2701Yfs*33	ENST00000380152		2699	aat/aATat	18/27	0.442218407529974	1	FACETS	0.976	0.866	1	0.976	0.866	1	CLONAL	1	TRUE	0	0.590791890656912	1		419	154	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578428	7578457	+	inframe_deletion	In_Frame_Del	DEL	GCTGTGACTGCTTGTAGATGGCCATGGCGC	GCTGTGACTGCTTGTAGATGGCCATGGCGC	-	novel	NA	P-0062503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	116	595	0	ENST00000269305.4:c.473_502del	p.Arg158_Gln167del	p.R158_Q167del	ENST00000269305	NM_001126112.2	158	cGCGCCATGGCCATCTACAAGCAGTCACAGCac/cac	5/11	0.590791890656912	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.590791890656912	1		595	270	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	257	714	1				ENST00000310581	NM_198253.2	-/1132			0.548652064300511	3	FACETS	0.942	0.892	0.993	0.942	0.892	0.993	CLONAL	2	TRUE	1	0.677359871544407	3		715	539	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0062504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	8	812	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.461983740558924	3	FACETS	0.198	0.127	0.289	0.099	0.063	0.145	SUBCLONAL	1	TRUE	1	0.677359871544407	3		812	160	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200024	123200024	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0062504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	63	152	0	ENST00000218089.9:c.2097-1G>A		p.X699_splice	ENST00000218089	NM_001042749.1	699			NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.677359871544407	2		152	140	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	284	521	0	ENST00000269571.5:c.829G>T	p.Asp277Tyr	p.D277Y	ENST00000269571		277	Gac/Tac	7/27	0.685904435700603	4	FACETS	1	0.964	1	0.519	0.487	0.553	CLONAL	1	TRUE	2	0.677359871544407	4		521	1354	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242757	66242757	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	196	354	0	ENST00000273854.3:c.1815G>T	p.Arg605Ser	p.R605S	ENST00000273854	NM_004439.5	605	agG/agT	9/18	0.317386510981393	3	FACETS	0.805	0.753	0.858	0.805	0.753	0.858	INDETERMINATE	2	TRUE	1	0.677359871544407	3		354	481	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981563	201981565	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TGG	TGG	-	rs995289305	NA	P-0062504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	22	411	0	ENST00000359651.3:c.478+1_478+3del		p.X160_splice	ENST00000359651		160		3/8	0.685904435700603	1	FACETS	0.175	0.136	0.221	0.175	0.136	0.221	SUBCLONAL	1	TRUE	0	0.677359871544407	1		411	245	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0062504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	214	367	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.560465407178417	4	FACETS	0.952	0.902	1	0.952	0.902	1	CLONAL	3	TRUE	1	0.677359871544407	4		367	371	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37863262	37863262	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs546886845	NA	P-0062504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	67	432	0	ENST00000269571.5:c.93G>T	p.Met31Ile	p.M31I	ENST00000269571		31	atG/atT	2/27	0.685904435700603	4	FACETS	0.274	0.237	0.315	0.137	0.118	0.158	SUBCLONAL	1	TRUE	2	0.677359871544407	4		432	1209	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211582	36211582	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	89	334	0	ENST00000222270.7:c.1333C>G	p.Pro445Ala	p.P445A	ENST00000222270	NM_014727.1	445	Cca/Gca	3/37	0.424852714645433	6	FACETS	0.774	0.686	0.869	0.194	0.171	0.218	SUBCLONAL	1	TRUE	2	0.677359871544407	6		334	799	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46587801	46587801	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1445965892	NA	P-0062504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	57	326	0	ENST00000263734.3:c.479A>C	p.Lys160Thr	p.K160T	ENST00000263734	NM_001430.4	160	aAa/aCa	5/16	0.489721836023516	4	FACETS	0.409	0.35	0.473	0.136	0.116	0.158	SUBCLONAL	1	TRUE	1	0.677359871544407	4		326	691	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513341	41513341	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0062504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	373	444	0	ENST00000263253.7:c.245C>G	p.Ser82Ter	p.S82*	ENST00000263253	NM_001429.3	82	tCa/tGa	2/31	0.596214435436785	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.677359871544407	3		444	702	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242849	142242849	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	135	335	0	ENST00000350721.4:c.4138G>C	p.Asp1380His	p.D1380H	ENST00000350721	NM_001184.3	1380	Gat/Cat	22/47	0.249190817426802	5	FACETS	0.804	0.735	0.875	0.536	0.49	0.583	INDETERMINATE	2	TRUE	2	0.677359871544407	5		335	500	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860778	151860778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	236	557	0	ENST00000262189.6:c.9884C>T	p.Thr3295Ile	p.T3295I	ENST00000262189	NM_170606.2	3295	aCt/aTt	43/59	0.30653476116	3	FACETS	1	0.99	1	0.649	0.608	0.69	INDETERMINATE	1	TRUE	1	0.677359871544407	3		557	719	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062566-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	62	714	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.828	0.721	0.942	0.828	0.721	0.942	CLONAL	1	TRUE	1	0.514602485418964	2		715	291	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0062566-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	141	433	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.514602485418964	2		434	527	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280115	142280115	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062566-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	121	455	0	ENST00000350721.4:c.1319C>T	p.Pro440Leu	p.P440L	ENST00000350721	NM_001184.3	440	cCt/cTt	5/47	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.514602485418964	2		455	467	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444576	78444830	+	coding_sequence_variant,5_prime_UTR_variant	In_Frame_Del	DEL	GCTCTCTGCAGTGCATCTTTGAAAGCGTCGTTAACTCCTCCACCACCACCGCCGCCACCACCGCCACCAGCTGAGCCAGAAGAGGGGGGAGGCACTGTTGAATAGTCTGCCATGGTTGCACTATAAGAGCCGCTGCCGCCTGTTCAGAGACTTCCTCTCAGCTAACAGCTAAGAAAGAAAGAAAATGGCGGCCGTCGAAGCTCTATTACATTCTTGCGCGACCATCGTGCCGTAAAGGGGCGGAGACTGAAGGAA	GCTCTCTGCAGTGCATCTTTGAAAGCGTCGTTAACTCCTCCACCACCACCGCCGCCACCACCGCCACCAGCTGAGCCAGAAGAGGGGGGAGGCACTGTTGAATAGTCTGCCATGGTTGCACTATAAGAGCCGCTGCCGCCTGTTCAGAGACTTCCTCTCAGCTAACAGCTAAGAAAGAAAGAAAATGGCGGCCGTCGAAGCTCTATTACATTCTTGCGCGACCATCGTGCCGTAAAGGGGCGGAGACTGAAGGAA	-	novel	NA	P-0062566-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	48	782	0				ENST00000370768	NM_003902.3	?-38/644		1/20	0.514602485418964	1	FACETS	0.44	0.374	0.512	0.44	0.374	0.512	SUBCLONAL	1	TRUE	0	0.514602485418964	1		782	315	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793077	42793078	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0062566-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	36	869	0	ENST00000575354.2:c.969_970del	p.Leu324GlufsTer82	p.L324Efs*82	ENST00000575354	NM_015125.3	323	ctCCtg/cttg	7/20	0.514602485418964	1	FACETS	0.278	0.228	0.333	0.278	0.228	0.333	SUBCLONAL	1	TRUE	0	0.514602485418964	1		869	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0062567-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	405	568	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.549553246015739	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.560099991850489	2		569	688	SUCCESS
APC	324	MSKCC	GRCh37	5	112175225	112175225	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062567-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	156	717	0	ENST00000257430.4:c.3934G>T	p.Gly1312Ter	p.G1312*	ENST00000257430	NM_000038.5	1312	Gga/Tga	16/16	1	2	FACETS	0.939	0.864	1	0.939	0.864	1	CLONAL	1	TRUE	1	0.560099991850489	2		717	593	SUCCESS
APC	324	MSKCC	GRCh37	5	112137024	112137024	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062567-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	118	487	0	ENST00000257430.4:c.778C>T	p.Gln260Ter	p.Q260*	ENST00000257430	NM_000038.5	260	Cag/Tag	8/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.560099991850489	2		487	392	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400765	72400765	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062567-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	38	508	0	ENST00000357731.5:c.406C>A	p.Gln136Lys	p.Q136K	ENST00000357731	NM_173808.2	136	Caa/Aaa	2/7	0.54588660510956	2	FACETS	0.334	0.276	0.399	0.167	0.138	0.2	SUBCLONAL	1	TRUE	0	0.560099991850489	2		508	406	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125499126	125499126	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0062567-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	113	608	0	ENST00000428830.2:c.290-1G>C		p.X97_splice	ENST00000428830	NM_001114121.2	97			0.505147182968242	4	FACETS	0.873	0.786	0.965	0.291	0.262	0.322	CLONAL	1	TRUE	1	0.560099991850489	4		608	721	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477812	140477812	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062567-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	116	577	0	ENST00000288602.6:c.1496A>G	p.Lys499Arg	p.K499R	ENST00000288602	NM_004333.4	499	aAa/aGa	12/18	0.525812425804688	3	FACETS	0.933	0.844	1	0.467	0.422	0.514	CLONAL	1	TRUE	1	0.560099991850489	3		577	568	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45800165	45800165	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587780088	NA	P-0062568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1297	198	846	1	ENST00000450313.1:c.55C>T	p.Arg19Ter	p.R19*	ENST00000450313	NM_012222.2	19	Cga/Tga	2/16	0.452346865897895	3	FACETS	0.725	0.669	0.783	0.362	0.334	0.392	SUBCLONAL	1	TRUE	1	0.447183511853399	3		847	1495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0062568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	552	938	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.403150853077574	2	FACETS	0.875	0.84	0.91	0.875	0.84	0.91	CLONAL	2	TRUE	0	0.447183511853399	2		938	1411	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56338830	56338879	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	CGGGGCGGGCGGGAGCCCCGGCAGTCCGGGGTCGCCGGCGAGGGCCATGT	CGGGGCGGGCGGGAGCCCCGGCAGTCCGGGGTCGCCGGCGAGGGCCATGT	-	novel	NA	P-0062568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	69	439	0	ENST00000348428.3:c.-44_6del		p.*15*	ENST00000348428	NM_006785.3	?-2/824		1/17	0.452346865897895	4	FACETS	0.571	0.496	0.652			1	SUBCLONAL	1	TRUE	NA	0.447183511853399	4		439	782	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754946	29754946	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs781677582	NA	P-0062568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	236	690	0	ENST00000389048.3:c.989A>G	p.Lys330Arg	p.K330R	ENST00000389048	NM_004304.4	330	aAg/aGg	4/29	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.447183511853399	2		690	1001	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47601142	47601142	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1617	183	655	0	ENST00000263735.4:c.380C>A	p.Thr127Lys	p.T127K	ENST00000263735	NM_002354.2	127	aCa/aAa	3/9	0.447183511853399	6	FACETS	0.861	0.792	0.935	0.172	0.158	0.187	CLONAL	1	TRUE	1	0.447183511853399	6		655	1800	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100959	41100959	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	289	817	0	ENST00000373198.4:c.1397A>C	p.Asn466Thr	p.N466T	ENST00000373198	NM_133170.3	466	aAc/aCc	8/32	0.276430048393192	3	FACETS	1	0.98	1	0.548	0.514	0.583	CLONAL	1	TRUE	1	0.447183511853399	3		817	1442	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474646	138474646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	163	583	0	ENST00000289153.2:c.347G>A	p.Cys116Tyr	p.C116Y	ENST00000289153	NM_006219.2	116	tGt/tAt	2/22	0.217181154345507	3	FACETS	0.994	0.913	1	0.497	0.456	0.54	INDETERMINATE	1	TRUE	1	0.447183511853399	3		583	897	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55570051	55570051	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	269	484	0	ENST00000288135.5:c.918A>C	p.Glu306Asp	p.E306D	ENST00000288135	NM_000222.2	306	gaA/gaC	5/21	0.359745353785722	2	FACETS	0.825	0.778	0.873	0.825	0.778	0.873	CLONAL	2	TRUE	0	0.447183511853399	2		484	729	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861055	35861055	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	281	567	0	ENST00000303115.3:c.184C>A	p.Pro62Thr	p.P62T	ENST00000303115	NM_002185.3	62	Cca/Aca	2/8	0.452346865897895	3	FACETS	1	0.993	1	0.706	0.663	0.75	CLONAL	1	TRUE	1	0.447183511853399	3		567	1089	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93953235	93953235	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	86	513	0	ENST00000369303.4:c.2906C>T	p.Thr969Ile	p.T969I	ENST00000369303	NM_004440.3	969	aCa/aTa	17/17	0.140400664423191	4	FACETS	0.753	0.666	0.847	0.188	0.166	0.212	INDETERMINATE	1	TRUE	0	0.447183511853399	4		513	739	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024001	27024002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0062569-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	64	406	0	ENST00000324856.7:c.1113dup	p.Gln372AlafsTer28	p.Q372Afs*28	ENST00000324856	NM_006015.4	369	-/G	1/20	0.239924536926202	1	FACETS	0.777	0.673	0.89	0.777	0.673	0.89	SUBCLONAL	1	TRUE	0	0.240256350646131	1		406	603	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0062571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	123	533	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.469002699918041	2		533	524	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0062571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	111	648	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	0.789	0.711	0.871	0.789	0.711	0.871	SUBCLONAL	1	TRUE	1	0.469002699918041	2		648	600	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514495	NA	P-0062571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	340	1079	0	ENST00000269305.4:c.542G>A	p.Arg181His	p.R181H	ENST00000269305	NM_001126112.2	181	cGc/cAc	5/11	0.469002699918041	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.469002699918041	1		1079	945	SUCCESS
APC	324	MSKCC	GRCh37	5	112175761	112175761	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	186	848	0	ENST00000257430.4:c.4473del	p.Phe1491LeufsTer16	p.F1491Lfs*16	ENST00000257430	NM_000038.5	1490	caT/ca	16/16	1	2	FACETS	0.93	0.86	1	0.93	0.86	1	CLONAL	1	TRUE	1	0.469002699918041	2		848	853	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0062571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	218	869	0	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	0.469002699918041	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.469002699918041	1		869	647	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736510	85736511	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs387906351	NA	P-0062571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	96	697	1	ENST00000370580.1:c.136dup	p.Ile46AsnfsTer4	p.I46Nfs*4	ENST00000370580	NM_003921.4	46	ata/aAta	2/3	1	2	FACETS	0.648	0.578	0.722	0.648	0.578	0.722	SUBCLONAL	1	TRUE	1	0.469002699918041	2		698	632	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440488	49440488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	270	986	0	ENST00000301067.7:c.4322G>A	p.Arg1441His	p.R1441H	ENST00000301067	NM_003482.3	1441	cGc/cAc	15/54	1	2	FACETS	0.999	0.936	1	0.999	0.936	1	CLONAL	1	TRUE	1	0.469002699918041	2		986	1153	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372308	55372308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs947668235	NA	P-0062571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	308	1160	0	ENST00000297316.4:c.998C>T	p.Pro333Leu	p.P333L	ENST00000297316	NM_022454.3	333	cCg/cTg	2/2	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.469002699918041	2		1160	1066	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0062572-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	270	899	0	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	0.741530653487223	4	FACETS	1	0.99	1	0.416	0.39	0.442	CLONAL	1	TRUE	1	0.739288213105356	4		899	1018	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0062572-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	695	.	.	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.741530653487223	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	1	0.739288213105356	4		0	998	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119792	17119792	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771653740	NA	P-0062572-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	222	753	1	ENST00000285071.4:c.1202G>A	p.Arg401His	p.R401H	ENST00000285071	NM_144997.5	401	cGc/cAc	11/14	0.741530653487223	4	FACETS	1	0.991	1	0.472	0.441	0.505	CLONAL	1	TRUE	1	0.739288213105356	4		754	737	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28624231	28624231	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0062572-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	140	696	0	ENST00000241453.7:c.742+1G>A		p.X248_splice	ENST00000241453	NM_004119.2	248			0.352445367060591	1	FACETS	0.728	0.673	0.784	0.728	0.673	0.784	INDETERMINATE	1	TRUE	0	0.739288213105356	1		696	328	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714540	52714540	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062572-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	681	816	0	ENST00000322088.6:c.298G>A	p.Glu100Lys	p.E100K	ENST00000322088	NM_014225.5	100	Gag/Aag	4/15	0.741530653487223	5	FACETS	0.965	0.939	0.99	1	0.997	1	CLONAL	4	TRUE	2	0.739288213105356	5		816	1007	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402561	20402561	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062572-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	143	802	1	ENST00000346618.3:c.98T>G	p.Met33Arg	p.M33R	ENST00000346618	NM_001949.4	33	aTg/aGg	1/7	0.54712827210942	4	FACETS	1	0.944	1	0.521	0.476	0.567	CLONAL	1	TRUE	2	0.739288213105356	4		803	646	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0062573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	11	564	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.739	1	1	0.739	1	CLONAL	1	FALSE	1	0.23222721413278	2		564	89	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0062573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	80	675	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.23222721413278	3	FACETS	1	0.93	1	1	0.979	1	CLONAL	4	FALSE	0	0.23222721413278	3		675	185	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0062573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	24	312	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	1	0.799	1	1	0.799	1	CLONAL	1	FALSE	1	0.23222721413278	2		313	204	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511329	157511329	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	93	672	0	ENST00000346085.5:c.3851del	p.Gly1284GlufsTer2	p.G1284Efs*2	ENST00000346085	NM_020732.3	1283	Ggg/gg	15/20	0.191130361168486	4	FACETS	1	0.945	1	1	0.945	1	CLONAL	3	FALSE	1	0.23222721413278	4		672	306	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240785	55240785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1417155613	NA	P-0062573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	116	809	0	ENST00000275493.2:c.2029C>T	p.Arg677Cys	p.R677C	ENST00000275493	NM_005228.3	677	Cgc/Tgc	17/28	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.23222721413278	2		809	680	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710595	114710597	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs754968616	NA	P-0062573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	73	768	0	ENST00000543371.1:c.85_87del	p.Glu29del	p.E29del	ENST00000543371	NM_001198531.1	27	cAGGag/cag	1/14	0.198833990239806	3	FACETS	1	0.888	1	1	0.888	1	CLONAL	2	FALSE	1	0.23222721413278	3		768	348	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589223	67589225	+	inframe_deletion	In_Frame_Del	DEL	TAA	TAA	-	novel	NA	P-0062573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	10	494	0	ENST00000274335.5:c.1214_1216del	p.Ile405del	p.I405del	ENST00000274335		404	tTAAta/tta	9/15	1	2	FACETS	1	0.71	1	1	0.71	1	CLONAL	1	FALSE	1	0.23222721413278	2		494	83	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638999	176638999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753389957	NA	P-0062573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	25	780	0	ENST00000439151.2:c.3599G>A	p.Arg1200Gln	p.R1200Q	ENST00000439151	NM_022455.4	1200	cGg/cAg	5/23	1	2	FACETS	0.916	0.725	1	0.916	0.725	1	CLONAL	1	FALSE	1	0.23222721413278	2		780	235	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051023	180051023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749803588	NA	P-0062573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	117	813	0	ENST00000261937.6:c.1460G>A	p.Arg487His	p.R487H	ENST00000261937	NM_182925.4	487	cGt/cAt	11/30	1	2	FACETS	0.825	0.745	0.908	1	0.986	1	CLONAL	2	FALSE	1	0.23222721413278	2		813	611	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332916	153332916	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1362274408	NA	P-0062573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	32	655	1	ENST00000281708.4:c.40C>T	p.Arg14Ter	p.R14*	ENST00000281708	NM_033632.3	14	Cga/Tga	2/12	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	FALSE	1	0.23222721413278	2		656	237	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753717	42753717	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587777006	NA	P-0062573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	150	963	0	ENST00000222329.4:c.547C>T	p.Arg183Ter	p.R183*	ENST00000222329	NM_006494.2	183	Cga/Tga	4/4	0.23222721413278	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	FALSE	2	0.23222721413278	4		963	673	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152357857	152357857	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759291002	NA	P-0062573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	33	413	0	ENST00000359321.1:c.50G>A	p.Arg17Gln	p.R17Q	ENST00000359321	NM_005431.1	17	cGa/cAa	2/3	1	2	FACETS	0.869	0.725	1	1	0.97	1	CLONAL	3	FALSE	1	0.23222721413278	2		413	109	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399363	139399363	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1213244424	NA	P-0062573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	118	798	0	ENST00000277541.6:c.4780C>T	p.Arg1594Trp	p.R1594W	ENST00000277541	NM_017617.3	1594	Cgg/Tgg	26/34	1	2	FACETS	0.921	0.834	1	1	0.988	1	CLONAL	2	FALSE	1	0.23222721413278	2		798	552	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0062573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	22	393	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.23222721413278	4	FACETS	1	0.84	1	0.721	0.568	0.891	CLONAL	2	FALSE	1	0.23222721413278	4		393	108	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350469	15350469	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0062573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	73	720	1	ENST00000263377.2:c.3445+1G>A		p.X1149_splice	ENST00000263377	NM_058243.2	1149			0.23222721413278	4	FACETS	0.829	0.728	0.938	0.829	0.728	0.938	CLONAL	2	FALSE	2	0.23222721413278	4		721	467	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691872	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs79375991	NA	P-0062573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	70	660	21	ENST00000295754.5:c.383del	p.Lys128SerfsTer35	p.K128Sfs*35	ENST00000295754	NM_003242.5	125	gAa/ga	3/7	0.23222721413278	3	FACETS	0.984	0.878	1	1	0.972	1	CLONAL	4	FALSE	0	0.23222721413278	3		681	171	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47594883	47594883	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs756343868	NA	P-0062573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	67	921	5	ENST00000430070.2:c.1204del	p.Glu402ArgfsTer27	p.E402Rfs*27	ENST00000430070	NM_018095.4	402	Gag/ag	4/4	1	2	FACETS	0.846	0.74	0.959	1	0.978	1	CLONAL	2	FALSE	1	0.23222721413278	2		926	341	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533907	533907	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1448375861	NA	P-0062573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	102	843	0	ENST00000451590.1:c.149C>T	p.Thr50Met	p.T50M	ENST00000451590	NM_001130442.1	50	aCg/aTg	3/5	1	2	FACETS	0.815	0.731	0.903	1	0.984	1	CLONAL	2	FALSE	1	0.23222721413278	2		843	539	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940240	71940240	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200692358	NA	P-0062573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	112	899	0	ENST00000298229.2:c.625C>T	p.Arg209Cys	p.R209C	ENST00000298229	NM_001567.3	209	Cgt/Tgt	5/28	1	2	FACETS	0.767	0.691	0.847	1	0.984	1	SUBCLONAL	2	FALSE	1	0.23222721413278	2		899	629	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041326	42041326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377364179	NA	P-0062573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	34	741	0	ENST00000219905.7:c.5521C>T	p.Arg1841Trp	p.R1841W	ENST00000219905	NM_001164273.1	1841	Cgg/Tgg	17/24	0.23222721413278	1	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	FALSE	0	0.23222721413278	1		741	226	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265144	10265144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753235229	NA	P-0062573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	118	798	0	ENST00000340748.4:c.1796C>T	p.Ala599Val	p.A599V	ENST00000340748		599	gCg/gTg	21/40	0.23222721413278	4	FACETS	0.949	0.857	1	0.949	0.857	1	CLONAL	2	FALSE	2	0.23222721413278	4		798	660	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256791	19256791	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781653583	NA	P-0062573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	96	678	0	ENST00000162023.5:c.922G>A	p.Gly308Ser	p.G308S	ENST00000162023		308	Ggc/Agc	13/13	0.23222721413278	4	FACETS	0.865	0.772	0.963	0.865	0.772	0.963	CLONAL	2	FALSE	2	0.23222721413278	4		678	589	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447753	187447753	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760727857	NA	P-0062573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	26	854	0	ENST00000232014.4:c.440G>A	p.Arg147Gln	p.R147Q	ENST00000232014	NM_001130845.1	147	cGg/cAg	5/10	0.170448288869915	1	FACETS	0.485	0.384	0.602	0.485	0.384	0.602	SUBCLONAL	1	FALSE	0	0.23222721413278	1		854	408	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520313	176520313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371352765	NA	P-0062573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	68	562	1	ENST00000292408.4:c.1232G>A	p.Arg411His	p.R411H	ENST00000292408	NM_213647.1	411	cGc/cAc	9/18	1	2	FACETS	0.854	0.748	0.967	1	0.978	1	CLONAL	2	FALSE	1	0.23222721413278	2		563	343	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2115922	2115922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	63	718	0	ENST00000349721.2:c.3557C>T	p.Ala1186Val	p.A1186V	ENST00000349721	NM_003070.3	1186	gCg/gTg	25/34	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.23222721413278	2		718	382	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240390	98240400	+	frameshift_variant	Frame_Shift_Del	DEL	TCAGGATGTCG	TCAGGATGTCG	-	novel	NA	P-0062573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	58	675	0	ENST00000331920.6:c.1284_1294del	p.Asp428GlufsTer5	p.D428Efs*5	ENST00000331920	NM_000264.3	428	gaCGACATCCTGAaa/gaaa	9/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.23222721413278	2		675	340	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750407	133750409	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0062573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	109	698	0	ENST00000318560.5:c.1242_1244del	p.Asn414del	p.N414del	ENST00000318560	NM_005157.4	413	tACAac/tac	7/11	1	2	FACETS	0.958	0.864	1	1	0.988	1	CLONAL	2	FALSE	1	0.23222721413278	2		698	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0062574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	29	439	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.28841101688445	6	FACETS	0.793	0.645	0.954	0.396	0.322	0.477	INDETERMINATE	2	FALSE	2	0.547657239152487	6		440	140	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784113	9784113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771951762	NA	P-0062574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	39	850	0	ENST00000377346.4:c.2681G>A	p.Arg894Gln	p.R894Q	ENST00000377346	NM_005026.3	894	cGg/cAg	21/24	0.552601776129146	4	FACETS	1	0.901	1	0.554	0.464	0.652	CLONAL	1	FALSE	2	0.547657239152487	4		850	199	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225365173	225365173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180155404	NA	P-0062574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	10	695	1	ENST00000264414.4:c.1517G>A	p.Arg506Gln	p.R506Q	ENST00000264414	NM_003590.4	506	cGg/cAg	11/16	0.552601776129146	1	FACETS	0.354	0.243	0.488	0.354	0.243	0.488	SUBCLONAL	1	FALSE	0	0.547657239152487	1		696	75	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270592	98270592	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1199437529	NA	P-0062574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	113	555	1	ENST00000331920.6:c.52A>G	p.Ser18Gly	p.S18G	ENST00000331920	NM_000264.3	18	Agc/Ggc	1/24	0.330961940937508	5	FACETS	0.789	0.709	0.874	0.263	0.236	0.292	SUBCLONAL	1	FALSE	2	0.547657239152487	5		556	953	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622119	43622120	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0062574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	46	855	0	ENST00000355710.3:c.3142dup	p.Leu1048ProfsTer11	p.L1048Pfs*11	ENST00000355710	NM_020975.4	1046	gcc/gCcc	19/20	0.547657239152487	5	FACETS	0.843	0.712	0.986	0.281	0.237	0.329	CLONAL	1	FALSE	2	0.547657239152487	5		855	363	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230459302	230459302	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1558189114	NA	P-0062574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	32	825	1	ENST00000391860.1:c.1099G>A	p.Ala367Thr	p.A367T	ENST00000391860	NM_001258311.1	367	Gcc/Acc	7/7	0.547657239152487	6	FACETS	0.8	0.651	0.967	0.2	0.162	0.242	CLONAL	1	FALSE	2	0.547657239152487	6		826	306	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246518385	246518385	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs146113064	NA	P-0062574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	20	639	1	ENST00000388985.4:c.176T>C	p.Leu59Pro	p.L59P	ENST00000388985		59	cTg/cCg	2/12	0.547657239152487	6	FACETS	1	0.903	1	0.339	0.262	0.425	CLONAL	1	FALSE	2	0.547657239152487	6		640	113	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426699	121426699	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	29	964	0	ENST00000257555.6:c.390G>T	p.Gln130His	p.Q130H	ENST00000257555		130	caG/caT	2/10	0.547657239152487	6	FACETS	1	0.872	1	0.539	0.442	0.642	CLONAL	2	FALSE	2	0.547657239152487	6		964	103	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273570	5273571	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0062574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	13	856	0	ENST00000357368.4:c.261_262insT	p.Gly88TrpfsTer15	p.G88Wfs*15	ENST00000357368	NM_002850.3	87	-/T	4/38	0.547657239152487	6	FACETS	0.659	0.472	0.884	0.22	0.157	0.295	SUBCLONAL	1	FALSE	3	0.547657239152487	6		856	151	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807375	1807375	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	78	877	0	ENST00000260795.2:c.1624C>A	p.Leu542Met	p.L542M	ENST00000260795		542	Ctg/Atg	11/17	0.390139955369617	6	FACETS	0.676	0.593	0.766	0.225	0.197	0.256	SUBCLONAL	1	FALSE	3	0.547657239152487	6		877	883	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032045	26032045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	22	1182	0	ENST00000244661.2:c.244G>A	p.Asp82Asn	p.D82N	ENST00000244661	NM_003537.3	82	Gat/Aat	1/1	0.455876760459202	5	FACETS	0.494	0.383	0.623	0.165	0.127	0.208	SUBCLONAL	1	FALSE	2	0.547657239152487	5		1182	296	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845632	151845632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	10	953	0	ENST00000262189.6:c.13380G>A	p.Met4460Ile	p.M4460I	ENST00000262189	NM_170606.2	4460	atG/atA	52/59	0.449789233865606	5	FACETS	0.723	0.495	1			1	CLONAL	1	FALSE	NA	0.547657239152487	5		953	92	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	48	714	1				ENST00000310581	NM_198253.2	-/1132			0.268889011826625	4	FACETS	0.795	0.684	0.912	0.795	0.684	0.912	INDETERMINATE	2	TRUE	2	0.58873302248926	4		715	163	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793881	NA	P-0062575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	214	859	0	ENST00000269305.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGg/gAg	8/11	0.521074425556862	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.58873302248926	2		859	350	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944562	40944562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868189942	NA	P-0062575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	169	335	1	ENST00000373198.4:c.1940C>T	p.Ser647Leu	p.S647L	ENST00000373198	NM_133170.3	647	tCg/tTg	12/32	0.500046747955956	4	FACETS	0.938	0.87	1	0.938	0.87	1	CLONAL	2	TRUE	2	0.58873302248926	4		336	486	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105617	27105617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528936858	NA	P-0062575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	27	810	0	ENST00000324856.7:c.5228C>T	p.Thr1743Met	p.T1743M	ENST00000324856	NM_006015.4	1743	aCg/aTg	20/20	0.58873302248926	2	FACETS	0.275	0.218	0.339	0.137	0.109	0.17	SUBCLONAL	1	TRUE	0	0.58873302248926	2		810	334	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027178	49027179	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0062575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	65	572	0	ENST00000267163.4:c.1746_1747insGA	p.Thr583GlufsTer29	p.T583Efs*29	ENST00000267163	NM_000321.2	582	cca/ccAGa	18/27	0.58873302248926	1	FACETS	0.89	0.789	0.995	0.89	0.789	0.995	CLONAL	1	TRUE	0	0.58873302248926	1		572	175	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771366	68771366	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	88	487	0	ENST00000261769.5:c.48G>C	p.Gln16His	p.Q16H	ENST00000261769	NM_004360.3	16	caG/caC	1/16	0.58873302248926	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.58873302248926	2		487	138	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80057465	80057465	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	116	554	0	ENST00000265081.6:c.1864G>C	p.Glu622Gln	p.E622Q	ENST00000265081	NM_002439.4	622	Gag/Cag	13/24	0.58873302248926	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	0	0.58873302248926	2		554	194	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0062576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	140	509	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.572688458447886	2		510	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0062576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	177	568	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.572688458447886	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.572688458447886	1		568	421	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2185868	2185868	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	127	602	0	ENST00000398665.3:c.140A>T	p.Glu47Val	p.E47V	ENST00000398665	NM_032482.2	47	gAa/gTa	3/28	1	2	FACETS	0.793	0.722	0.868	0.793	0.722	0.868	SUBCLONAL	1	TRUE	1	0.572688458447886	2		602	559	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0062576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	151	698	1	ENST00000257430.4:c.3919dup	p.Ile1307AsnfsTer8	p.I1307Nfs*8	ENST00000257430	NM_000038.5	1306	gaa/gAaa	16/16	1	2	FACETS	0.919	0.844	0.996	0.919	0.844	0.996	CLONAL	1	TRUE	1	0.572688458447886	2		699	574	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0062576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	113	327	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.953	0.865	1	0.953	0.865	1	CLONAL	1	TRUE	1	0.572688458447886	2		327	414	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981171	201981171	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	223	836	0	ENST00000359651.3:c.251del	p.Lys84SerfsTer71	p.K84Sfs*71	ENST00000359651		84	Aag/ag	2/8	0.572688458447886	3	FACETS	1	0.973	1	0.543	0.506	0.582	CLONAL	1	TRUE	1	0.572688458447886	3		836	922	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132515	11132515	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	194	935	0	ENST00000358026.2:c.2731G>A	p.Gly911Ser	p.G911S	ENST00000358026	NM_001128849.1	911	Ggc/Agc	19/36	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.572688458447886	2		935	672	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566874	212566874	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	187	779	0	ENST00000342788.4:c.1307T>C	p.Ile436Thr	p.I436T	ENST00000342788	NM_005235.2	436	aTc/aCc	12/28	1	2	FACETS	0.967	0.897	1	0.967	0.897	1	CLONAL	1	TRUE	1	0.572688458447886	2		779	675	SUCCESS
APC	324	MSKCC	GRCh37	5	112137043	112137043	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	100	555	0	ENST00000257430.4:c.797del	p.Val266GlyfsTer27	p.V266Gfs*27	ENST00000257430	NM_000038.5	266	gTg/gg	8/16	1	2	FACETS	0.774	0.695	0.857	0.774	0.695	0.857	SUBCLONAL	1	TRUE	1	0.572688458447886	2		555	451	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339742	116339742	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	186	774	0	ENST00000397752.3:c.604A>C	p.Asn202His	p.N202H	ENST00000397752	NM_000245.2	202	Aat/Cat	2/21	0.572688458447886	3	FACETS	1	0.957	1	0.525	0.485	0.566	CLONAL	1	TRUE	1	0.572688458447886	3		774	796	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845352	76845352	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	78	531	0	ENST00000373344.5:c.6169G>C	p.Ala2057Pro	p.A2057P	ENST00000373344	NM_000489.3	2057	Gct/Cct	27/35	0.289360326866085	3	FACETS	0.569	0.5	0.643	0.19	0.166	0.215	INDETERMINATE	1	TRUE	0	0.572688458447886	3		531	616	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527764	103527764	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062584-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	168	867	0	ENST00000355739.4:c.3072G>T	p.Arg1024Ser	p.R1024S	ENST00000355739	NM_000123.3	1024	agG/agT	15/15	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.421012301891035	2		867	773	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	103	714	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.909	0.82	1	0.909	0.82	1	CLONAL	1	TRUE	1	0.566339167784428	2		715	400	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720808	89720808	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs1114167667	NA	P-0062585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	28	197	0	ENST00000371953.3:c.959T>G	p.Leu320Ter	p.L320*	ENST00000371953	NM_000314.4	320	tTa/tGa	8/9	0.566339167784428	1	FACETS	0.639	0.521	0.767	0.639	0.521	0.767	SUBCLONAL	1	TRUE	0	0.566339167784428	1		197	111	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050948	49050948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	224	691	1	ENST00000267163.4:c.2632G>A	p.Asp878Asn	p.D878N	ENST00000267163	NM_000321.2	878	Gat/Aat	25/27	0.566339167784428	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.566339167784428	1		692	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578501	7578502	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0062585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	472	1045	0	ENST00000269305.4:c.428_429del	p.Val143AlafsTer5	p.V143Afs*5	ENST00000269305	NM_001126112.2	143	gTG/g	5/11	0.547022415995909	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.566339167784428	2		1045	822	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201564	133201564	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs538875477	NA	P-0062585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	189	936	0	ENST00000320574.5:c.6674G>A	p.Arg2225His	p.R2225H	ENST00000320574	NM_006231.2	2225	cGc/cAc	48/49	1	2	FACETS	0.962	0.892	1	0.962	0.892	1	CLONAL	1	TRUE	1	0.566339167784428	2		936	694	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0062586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	241	509	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.75516591571099	2		510	536	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0062586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	393	515	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.34131409121442	3	FACETS	0.838	0.801	0.876	0.838	0.801	0.876	INDETERMINATE	2	TRUE	1	0.75516591571099	3		515	855	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653814	89653814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780004	NA	P-0062586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	134	237	0	ENST00000371953.3:c.112C>T	p.Pro38Ser	p.P38S	ENST00000371953	NM_000314.4	38	Cct/Tct	2/9	0.726720328667449	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.75516591571099	1		237	220	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246102	46246102	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0062586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	333	510	0	ENST00000334344.6:c.4196T>A	p.Leu1399Ter	p.L1399*	ENST00000334344	NM_152641.2	1399	tTa/tAa	15/21	0.705514980007447	2	FACETS	0.942	0.909	0.975	0.942	0.909	0.975	CLONAL	2	TRUE	0	0.75516591571099	2		510	468	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191141	2191141	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	385	646	1	ENST00000398665.3:c.395C>T	p.Ser132Phe	p.S132F	ENST00000398665	NM_032482.2	132	tCc/tTc	5/28	1	2	FACETS	0.989	0.942	1	0.989	0.942	1	CLONAL	1	TRUE	1	0.75516591571099	2		647	1031	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0062586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	196	604	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.75516591571099	2		604	479	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156478	106156478	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376570662	NA	P-0062586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	359	604	0	ENST00000380013.4:c.1379C>T	p.Ser460Phe	p.S460F	ENST00000380013	NM_001127208.2	460	tCc/tTc	3/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.75516591571099	2		604	903	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980731	70980731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	250	432	0	ENST00000276594.2:c.737C>T	p.Ser246Phe	p.S246F	ENST00000276594	NM_024504.3	246	tCc/tTc	3/8	1	2	FACETS	0.999	0.94	1	0.999	0.94	1	CLONAL	1	TRUE	1	0.75516591571099	2		432	663	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675068	40675068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	282	543	0	ENST00000249776.8:c.32G>A	p.Arg11Lys	p.R11K	ENST00000249776	NM_033286.3	11	aGa/aAa	1/9	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.75516591571099	2		543	735	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641718	12641718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs5746220	NA	P-0062586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	418	615	0	ENST00000251849.4:c.923C>T	p.Pro308Leu	p.P308L	ENST00000251849	NM_002880.3	308	cCg/cTg	9/17	1	2	FACETS	0.943	0.899	0.987	0.943	0.899	0.987	CLONAL	1	TRUE	1	0.75516591571099	2		615	1174	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156402	106156402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1462029603	NA	P-0062586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	329	588	0	ENST00000380013.4:c.1303C>T	p.His435Tyr	p.H435Y	ENST00000380013	NM_001127208.2	435	Cac/Tac	3/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.75516591571099	2		588	854	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031702	69031702	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	230	426	0	ENST00000288368.4:c.3457G>A	p.Asp1153Asn	p.D1153N	ENST00000288368	NM_024870.2	1153	Gat/Aat	28/40	1	2	FACETS	0.94	0.881	1	0.94	0.881	1	CLONAL	1	TRUE	1	0.75516591571099	2		426	648	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256984	16256984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	357	610	0	ENST00000375759.3:c.4249G>A	p.Glu1417Lys	p.E1417K	ENST00000375759	NM_015001.2	1417	Gag/Aag	11/15	0.381756514551236	3	FACETS	1	0.992	1	0.616	0.584	0.648	INDETERMINATE	1	TRUE	1	0.75516591571099	3		610	1058	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572261	64572261	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs104894267	NA	P-0062586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	355	940	1	ENST00000312049.6:c.1378C>T	p.Arg460Ter	p.R460*	ENST00000312049	NM_130799.2	460	Cga/Tga	10/10	0.75516591571099	1	FACETS	0.977	0.937	1	0.977	0.937	1	CLONAL	1	TRUE	0	0.75516591571099	1		941	599	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906937	32906937	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793062	NA	P-0062586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	197	459	0	ENST00000380152.3:c.1322C>T	p.Thr441Ile	p.T441I	ENST00000380152		441	aCt/aTt	10/27	1	2	FACETS	0.84	0.782	0.9	0.84	0.782	0.9	CLONAL	1	TRUE	1	0.75516591571099	2		459	621	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43767865	43767865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	360	542	0	ENST00000382044.4:c.983C>T	p.Ser328Leu	p.S328L	ENST00000382044	NM_001141980.1	328	tCa/tTa	9/28	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.75516591571099	2		542	934	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945928	17945928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	333	686	0	ENST00000458235.1:c.2011G>A	p.Asp671Asn	p.D671N	ENST00000458235	NM_000215.3	671	Gac/Aac	15/24	1	2	FACETS	0.934	0.886	0.984	0.934	0.886	0.984	CLONAL	1	TRUE	1	0.75516591571099	2		686	944	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523110	25523111	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GT	GT	AA	novel	NA	P-0062586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	256	451	0	ENST00000264709.3:c.74_75delinsTT	p.Asp25Val	p.D25V	ENST00000264709	NM_175629.2	25	gAC/gTT	3/23	1	2	FACETS	0.938	0.882	0.994	0.938	0.882	0.994	CLONAL	1	TRUE	1	0.75516591571099	2		451	723	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294034	1294034	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	333	718	0	ENST00000310581.5:c.967C>T	p.Pro323Ser	p.P323S	ENST00000310581	NM_198253.2	323	Ccg/Tcg	2/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.75516591571099	2		718	870	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945139	38945139	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0062586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	207	338	0	ENST00000357387.3:c.4665T>A	p.Cys1555Ter	p.C1555*	ENST00000357387	NM_152756.3	1555	tgT/tgA	35/38	1	2	FACETS	0.934	0.873	0.997	0.934	0.873	0.997	CLONAL	1	TRUE	1	0.75516591571099	2		338	587	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0062587-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	28	228	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.692	0.554	0.85	0.692	0.554	0.85	SUBCLONAL	1	TRUE	1	0.24139528189467	2		228	335	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934824	49934824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062587-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	84	1103	0	ENST00000296474.3:c.2072C>T	p.Pro691Leu	p.P691L	ENST00000296474	NM_002447.2	691	cCc/cTc	7/20	1	2	FACETS	0.63	0.555	0.712	0.63	0.555	0.712	SUBCLONAL	1	TRUE	1	0.24139528189467	2		1103	1104	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045899	180045899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766043774	NA	P-0062587-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	57	949	1	ENST00000261937.6:c.2872G>A	p.Gly958Arg	p.G958R	ENST00000261937	NM_182925.4	958	Gga/Aga	21/30	0.158542822784908	0	FACETS	0.478	0.409	0.554			1	SUBCLONAL	1	TRUE	0	0.24139528189467	0		950	749	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291383	11291383	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	60	519	0	ENST00000361445.4:c.2623G>A	p.Glu875Lys	p.E875K	ENST00000361445	NM_004958.3	875	Gag/Aag	17/58	0.227917956591764	3	FACETS	1	0.945	1	0.591	0.512	0.676	CLONAL	1	FALSE	1	0.357024205542044	3		519	335	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481689	56481689	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	43	652	0	ENST00000267101.3:c.724G>C	p.Asp242His	p.D242H	ENST00000267101	NM_001982.3	242	Gac/Cac	6/28	0.234869186474066	4	FACETS	0.838	0.703	0.988	0.419	0.351	0.494	CLONAL	1	FALSE	2	0.357024205542044	4		652	390	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891019	112891019	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	35	373	0	ENST00000351677.2:c.353C>G	p.Ser118Cys	p.S118C	ENST00000351677	NM_002834.3	118	tCt/tGt	4/16	0.243063580676675	1	FACETS	0.942	0.782	1	0.942	0.782	1	CLONAL	1	FALSE	0	0.357024205542044	1		373	171	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891115	112891115	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	65	473	0	ENST00000351677.2:c.449C>G	p.Ser150Cys	p.S150C	ENST00000351677	NM_002834.3	150	tCt/tGt	4/16	0.243063580676675	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	0	0.357024205542044	1		473	278	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0062588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	257	471	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.357024205542044	4	FACETS	0.916	0.868	0.965	1	0.991	1	CLONAL	4	FALSE	1	0.357024205542044	4		471	533	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457593	67457593	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	59	679	0	ENST00000327367.4:c.403C>G	p.Leu135Val	p.L135V	ENST00000327367	NM_005902.3	135	Cta/Gta	3/9	1	2	FACETS	0.762	0.657	0.875	0.762	0.657	0.875	SUBCLONAL	1	FALSE	1	0.357024205542044	2		679	434	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835718	68835718	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	98	604	0	ENST00000261769.5:c.309G>A	p.Trp103Ter	p.W103*	ENST00000261769	NM_004360.3	103	tgG/tgA	3/16	0.357024205542044	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	0	0.357024205542044	1		604	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587782272	NA	P-0062588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	83	391	0	ENST00000269305.4:c.994-1G>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.357024205542044	3	FACETS	0.932	0.832	1	0.932	0.832	1	CLONAL	2	FALSE	1	0.357024205542044	3		391	294	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556367	29556367	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	51	489	0	ENST00000356175.3:c.2734C>T	p.Gln912Ter	p.Q912*	ENST00000356175	NM_000267.3	912	Caa/Taa	21/57	0.357024205542044	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	FALSE	0	0.357024205542044	1		489	203	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099252	4099252	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	54	579	1	ENST00000262948.5:c.866G>C	p.Gly289Ala	p.G289A	ENST00000262948	NM_030662.3	289	gGa/gCa	7/11	0.357024205542044	1	FACETS	0.796	0.684	0.917	0.796	0.684	0.917	CLONAL	1	FALSE	0	0.357024205542044	1		580	312	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280738	41280738	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	50	532	0	ENST00000349496.5:c.2251G>C	p.Asp751His	p.D751H	ENST00000349496	NM_001904.3	751	Gat/Cat	15/15	0.227917956591764	3	FACETS	0.866	0.737	1	0.433	0.368	0.504	CLONAL	1	FALSE	1	0.357024205542044	3		532	381	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0062588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	12	230	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	0.254468309109763	1	FACETS	0.552	0.392	0.745	0.552	0.392	0.745	SUBCLONAL	1	FALSE	0	0.357024205542044	1		230	100	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156716	106156716	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	32	558	0	ENST00000380013.4:c.1617G>C	p.Glu539Asp	p.E539D	ENST00000380013	NM_001127208.2	539	gaG/gaC	3/11	1	2	FACETS	0.594	0.483	0.718	0.594	0.483	0.718	SUBCLONAL	1	FALSE	1	0.357024205542044	2		558	302	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0062589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	40	453	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.289832257079363	2		453	255	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0062589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	14	367	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.779	0.568	1	0.779	0.568	1	CLONAL	1	TRUE	1	0.289832257079363	2		367	124	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101387	27101394	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTCTGC	CCCTCTGC	-	novel	NA	P-0062589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	14	501	1	ENST00000324856.7:c.4673_4680del	p.Ser1558CysfsTer11	p.S1558Cfs*11	ENST00000324856	NM_006015.4	1557	CCCTCTGCc/c	18/20	1	2	FACETS	0.517	0.374	0.688	0.517	0.374	0.688	SUBCLONAL	1	TRUE	1	0.289832257079363	2		502	187	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0062589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	41	1034	2	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	1	2	FACETS	0.7	0.584	0.829	0.7	0.584	0.829	SUBCLONAL	1	TRUE	1	0.289832257079363	2		1036	404	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692980	89692980	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1060500126	NA	P-0062589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	40	591	0	ENST00000371953.3:c.464A>C	p.Tyr155Ser	p.Y155S	ENST00000371953	NM_000314.4	155	tAt/tCt	5/9	0.259581332512739	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	2	TRUE	0	0.289832257079363	2		591	133	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446049	29446049	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	24	687	1	ENST00000544604.2:c.1883del	p.Pro628ArgfsTer38	p.P628Rfs*38	ENST00000544604	NM_001206998.1	627	tCc/tc	8/9	1	2	FACETS	0.781	0.616	0.97	0.781	0.616	0.97	CLONAL	1	TRUE	1	0.289832257079363	2		688	212	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0062590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	122	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.235830118472656	3	FACETS	0.988	0.904	1	0.988	0.904	1	CLONAL	3	TRUE	0	0.266425129719709	3		485	350	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171455	123171455	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	36	305	0	ENST00000218089.9:c.367C>T	p.Gln123Ter	p.Q123*	ENST00000218089	NM_001042749.1	123	Cag/Tag	6/35	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.266425129719709	2		305	240	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0062590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	56	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.266425129719709	2		429	301	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426787	49426787	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	188	776	0	ENST00000301067.7:c.11701C>T	p.Gln3901Ter	p.Q3901*	ENST00000301067	NM_003482.3	3901	Cag/Tag	39/54	0.235830118472656	3	FACETS	1	0.981	1	0.776	0.72	0.834	CLONAL	2	TRUE	0	0.266425129719709	3		776	687	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004664	16004664	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	90	588	0	ENST00000268712.3:c.2590C>T	p.Gln864Ter	p.Q864*	ENST00000268712	NM_006311.3	864	Cag/Tag	20/46	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.266425129719709	2		588	584	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077462	30077462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	44	540	0	ENST00000338641.4:c.1609G>A	p.Glu537Lys	p.E537K	ENST00000338641	NM_000268.3	537	Gag/Aag	15/16	1	2	FACETS	0.611	0.512	0.72	0.611	0.512	0.72	SUBCLONAL	1	TRUE	1	0.266425129719709	2		540	541	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802635	135802635	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203343	NA	P-0062590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	111	308	0	ENST00000298552.3:c.163C>T	p.Gln55Ter	p.Q55*	ENST00000298552	NM_001162426.1	55	Cag/Tag	4/23	0.266425129719709	2	FACETS	0.772	0.696	0.851	0.772	0.696	0.851	SUBCLONAL	2	TRUE	0	0.266425129719709	2		308	540	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949126	151949126	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	85	344	0	ENST00000262189.6:c.1519C>T	p.Gln507Ter	p.Q507*	ENST00000262189	NM_170606.2	507	Cag/Tag	11/59	0.163593130563922	2	FACETS	0.958	0.855	1	0.958	0.855	1	CLONAL	2	TRUE	0	0.266425129719709	2		344	333	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257889	19257889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1482048547	NA	P-0062590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	42	698	0	ENST00000162023.5:c.497G>A	p.Arg166His	p.R166H	ENST00000162023		166	cGc/cAc	9/13	1	2	FACETS	0.607	0.507	0.719	0.607	0.507	0.719	SUBCLONAL	1	TRUE	1	0.266425129719709	2		698	519	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831312	72831312	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	48	630	0	ENST00000268489.5:c.5269C>T	p.Gln1757Ter	p.Q1757*	ENST00000268489	NM_006885.3	1757	Cag/Tag	9/10	1	2	FACETS	0.711	0.601	0.832	0.711	0.601	0.832	SUBCLONAL	1	TRUE	1	0.266425129719709	2		630	507	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84406214	84406214	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	41	462	0	ENST00000321945.7:c.12G>C	p.Glu4Asp	p.E4D	ENST00000321945	NM_139076.2	4	gaG/gaC	1/9	1	2	FACETS	0.747	0.623	0.885	0.747	0.623	0.885	SUBCLONAL	1	TRUE	1	0.266425129719709	2		462	412	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714173	43714173	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0062590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	86	680	0	ENST00000382044.4:c.3980C>G	p.Ser1327Ter	p.S1327*	ENST00000382044	NM_001141980.1	1327	tCa/tGa	19/28	0.237830855409978	3	FACETS	0.978	0.865	1	0.489	0.432	0.55	CLONAL	1	TRUE	1	0.266425129719709	3		680	748	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857445	9857445	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	72	679	0	ENST00000330684.3:c.3956T>C	p.Leu1319Pro	p.L1319P	ENST00000330684	NM_001134407.1	1319	cTt/cCt	13/13	1	2	FACETS	0.981	0.858	1	0.981	0.858	1	CLONAL	1	TRUE	1	0.266425129719709	2		679	551	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687330	37687330	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	95	678	0	ENST00000447079.4:c.4234T>G	p.Leu1412Val	p.L1412V	ENST00000447079	NM_015083.1	1412	Tta/Gta	14/14	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.266425129719709	2		678	619	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40491383	40491383	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	75	509	0	ENST00000264657.5:c.417G>C	p.Glu139Asp	p.E139D	ENST00000264657	NM_139276.2	139	gaG/gaC	5/24	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.266425129719709	2		509	543	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098800	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCA	novel	NA	P-0062590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	85	502	0	ENST00000397062.3:c.243_245dup	p.Gly81_Glu82insAsp	p.G81_E82insD	ENST00000397062	NM_006164.4	82	gaa/gaTGAa	2/5	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.266425129719709	2		502	560	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162593	47162593	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	56	487	0	ENST00000409792.3:c.3533C>G	p.Ser1178Cys	p.S1178C	ENST00000409792	NM_014159.6	1178	tCt/tGt	3/21	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.266425129719709	2		487	390	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163148	47163148	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1054527589	NA	P-0062590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	60	436	0	ENST00000409792.3:c.2978C>T	p.Ser993Phe	p.S993F	ENST00000409792	NM_014159.6	993	tCt/tTt	3/21	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.266425129719709	2		436	393	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337223	89337223	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0062591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	162	703	0	ENST00000301030.4:c.7806+2T>C		p.X2602_splice	ENST00000301030	NM_001256183.1	2602			1	2	FACETS	0.996	0.926	1	0.996	0.926	1	CLONAL	1	FALSE	1	0.834072020347158	2		703	390	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39725954	39725954	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	131	583	0	ENST00000361337.2:c.825G>C	p.Arg275Ser	p.R275S	ENST00000361337	NM_003286.2	275	agG/agC	10/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.834072020347158	2		583	290	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467698	66467698	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753230187	NA	P-0000115-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	237	695	0	ENST00000273854.3:c.571C>T	p.Arg191Cys	p.R191C	ENST00000273854	NM_004439.5	191	Cgt/Tgt	3/18	0.608680897045808	2	FACETS	0.921	0.874	0.967	0.921	0.874	0.967	CLONAL	2	TRUE	0	0.624799780368882	2		695	412	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636817	8636817	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000115-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	168	671	0	ENST00000356435.5:c.92T>A	p.Val31Asp	p.V31D	ENST00000356435		31	gTt/gAt	2/35	1	2	FACETS	0.934	0.863	1	0.934	0.863	1	CLONAL	1	TRUE	1	0.624799780368882	2		671	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781504	NA	P-0000115-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	184	739	0	ENST00000269305.4:c.314G>A	p.Gly105Asp	p.G105D	ENST00000269305	NM_001126112.2	105	gGc/gAc	4/11	0.624799780368882	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.624799780368882	1		739	374	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123505203	123505203	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000115-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	375	873	0	ENST00000371139.4:c.349A>G	p.Ile117Val	p.I117V	ENST00000371139	NM_001114937.2	117	Ata/Gta	4/4	0.57810274604098	2	FACETS	0.815	0.78	0.851	0.815	0.78	0.851	CLONAL	2	TRUE	0	0.624799780368882	2		873	736	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46738426	46738426	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000115-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	191	738	0	ENST00000371975.4:c.1327A>G	p.Ser443Gly	p.S443G	ENST00000371975	NM_003579.3	443	Agt/Ggt	12/18	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.624799780368882	2		738	591	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421038	49421038	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000115-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	183	683	0	ENST00000301067.7:c.14711G>T	p.Arg4904Leu	p.R4904L	ENST00000301067	NM_003482.3	4904	cGa/cTa	48/54	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.624799780368882	2		683	514	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51504754	51504754	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000115-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	124	474	0	ENST00000260433.2:c.1026G>C	p.Glu342Asp	p.E342D	ENST00000260433		342	gaG/gaC	9/10	0.624799780368882	3	FACETS	1	0.952	1	0.535	0.487	0.585	CLONAL	1	TRUE	1	0.624799780368882	3		474	487	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805472	46805472	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000115-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	210	801	0	ENST00000290295.7:c.484T>A	p.Ser162Thr	p.S162T	ENST00000290295	NM_006361.5	162	Tcc/Acc	1/2	0.624799780368882	2	FACETS	1	0.987	1	0.608	0.569	0.647	CLONAL	1	TRUE	0	0.624799780368882	2		801	553	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753198	42753198	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs897260918	NA	P-0000115-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	210	825	0	ENST00000222329.4:c.1066G>A	p.Glu356Lys	p.E356K	ENST00000222329	NM_006494.2	356	Gag/Aag	4/4	0.608680897045808	2	FACETS	1	0.979	1	0.556	0.519	0.593	CLONAL	1	TRUE	0	0.624799780368882	2		825	605	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528943	157528957	+	inframe_deletion	In_Frame_Del	DEL	TGGATATCTCGATAT	TGGATATCTCGATAT	-	novel	NA	P-0000115-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	176	643	0	ENST00000346085.5:c.6668_6682del	p.Leu2223_Ser2228delinsPro	p.L2223_S2228delinsP	ENST00000346085	NM_020732.3	2223	cTGGATATCTCGATATca/cca	20/20	0.581054774181064	3	FACETS	1	0.963	1	0.533	0.493	0.576	CLONAL	1	TRUE	1	0.624799780368882	3		643	693	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120612003	120612004	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	rs372504208	NA	P-0001339-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	12	41	0	ENST00000256646.2:c.17_18del	p.Pro6ArgfsTer27	p.P6Rfs*27	ENST00000256646	NM_024408.3	6	cCC/c	1/34	0.369841974715383	5	FACETS	0.516	0.365	0.7	0.172	0.121	0.234	INDETERMINATE	1	TRUE	2	0.746149335481031	5		41	132	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451263	70451263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001339-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	177	397	0	ENST00000373644.4:c.6103C>T	p.His2035Tyr	p.H2035Y	ENST00000373644	NM_030625.2	2035	Cac/Tac	12/12	1	2	FACETS	0.744	0.688	0.801	0.744	0.688	0.801	SUBCLONAL	1	TRUE	1	0.746149335481031	2		397	638	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098680	2098680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1479698846	NA	P-0001339-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	292	408	0	ENST00000219476.3:c.64G>A	p.Gly22Arg	p.G22R	ENST00000219476	NM_000548.3	22	Gga/Aga	2/42	0.746149335481031	3	FACETS	0.968	0.911	1	0.484	0.455	0.514	CLONAL	1	TRUE	1	0.746149335481031	3		408	1110	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001396-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	36	372	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.288633228264424	3	FACETS	0.765	0.63	0.916	0.383	0.315	0.458	CLONAL	1	FALSE	1	0.288633228264424	3		372	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577524	7577524	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001396-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	63	675	0	ENST00000269305.4:c.757A>C	p.Thr253Pro	p.T253P	ENST00000269305	NM_001126112.2	253	Acc/Ccc	7/11	0.24831415149198	2	FACETS	0.859	0.752	0.973	0.859	0.752	0.973	CLONAL	2	FALSE	0	0.288633228264424	2		675	254	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687586	29687586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001396-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	43	674	2	ENST00000356175.3:c.8179G>A	p.Glu2727Lys	p.E2727K	ENST00000356175	NM_000267.3	2727	Gaa/Aaa	56/57	0.288633228264424	4	FACETS	0.853	0.714	1	0.284	0.238	0.336	CLONAL	1	FALSE	1	0.288633228264424	4		676	450	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691950	30691950	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001396-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	37	439	0	ENST00000295754.5:c.453del	p.Glu152AsnfsTer11	p.E152Nfs*11	ENST00000295754	NM_003242.5	151	gAa/ga	3/7	0.245210320328115	4	FACETS	1	0.946	1	0.697	0.579	0.827	CLONAL	1	FALSE	2	0.288633228264424	4		439	237	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40478169	40478169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1288968449	NA	P-0001396-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	32	638	1	ENST00000264657.5:c.1330G>A	p.Glu444Lys	p.E444K	ENST00000264657	NM_139276.2	444	Gag/Aag	15/24	1	2	FACETS	0.614	0.499	0.744	0.614	0.499	0.744	SUBCLONAL	1	FALSE	1	0.288633228264424	2		639	361	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001396-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	115	372	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.630915016377808	3	FACETS	0.926	0.838	1	0.463	0.419	0.509	CLONAL	1	TRUE	1	0.630915016377808	3		372	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577524	7577524	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001396-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	366	675	0	ENST00000269305.4:c.757A>C	p.Thr253Pro	p.T253P	ENST00000269305	NM_001126112.2	253	Acc/Ccc	7/11	0.630915016377808	2	FACETS	0.995	0.957	1	0.995	0.957	1	CLONAL	2	TRUE	0	0.630915016377808	2		675	583	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687586	29687586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001396-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	186	674	2	ENST00000356175.3:c.8179G>A	p.Glu2727Lys	p.E2727K	ENST00000356175	NM_000267.3	2727	Gaa/Aaa	56/57	0.630915016377808	5	FACETS	0.908	0.837	0.982	0.227	0.209	0.246	CLONAL	1	TRUE	1	0.630915016377808	5		676	1264	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691950	30691950	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001396-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	129	439	0	ENST00000295754.5:c.453del	p.Glu152AsnfsTer11	p.E152Nfs*11	ENST00000295754	NM_003242.5	151	gAa/ga	3/7	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.630915016377808	2		439	391	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40478169	40478169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1288968449	NA	P-0001396-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	199	638	1	ENST00000264657.5:c.1330G>A	p.Glu444Lys	p.E444K	ENST00000264657	NM_139276.2	444	Gag/Aag	15/24	0.620879978059464	3	FACETS	1	0.975	1	0.552	0.513	0.593	CLONAL	1	TRUE	1	0.630915016377808	3		639	751	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436042	49436042	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1164333482	NA	P-0001396-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	161	501	0	ENST00000301067.7:c.5939C>T	p.Thr1980Met	p.T1980M	ENST00000301067	NM_003482.3	1980	aCg/aTg	28/54	0.630915016377808	3	FACETS	1	0.981	1	0.603	0.556	0.651	CLONAL	1	TRUE	1	0.630915016377808	3		501	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0001531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	630	797	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.742268291097941	3	FACETS	1	0.998	1	1	0.998	1	CLONAL	3	TRUE	0	0.742268291097941	3		799	695	SUCCESS
APC	324	MSKCC	GRCh37	5	112175328	112175328	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0001531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	89	256	0	ENST00000257430.4:c.4037C>G	p.Ser1346Ter	p.S1346*	ENST00000257430	NM_000038.5	1346	tCa/tGa	16/16	0.467280030405809	5	FACETS	1	0.967	1			1	CLONAL	2	TRUE	NA	0.742268291097941	5		256	218	SUCCESS
APC	324	MSKCC	GRCh37	5	112175324	112175324	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1211642532	NA	P-0001531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	103	258	0	ENST00000257430.4:c.4033G>T	p.Glu1345Ter	p.E1345*	ENST00000257430	NM_000038.5	1345	Gaa/Taa	16/16	0.467280030405809	5	FACETS	0.931	0.854	1			1	CLONAL	3	TRUE	NA	0.742268291097941	5		258	210	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550460	29550460	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs763983337	NA	P-0001531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	94	218	0	ENST00000356175.3:c.1722-2A>G		p.X574_splice	ENST00000356175	NM_000267.3	574			0.742268291097941	3	FACETS	0.973	0.915	1	0.973	0.915	1	CLONAL	3	TRUE	0	0.742268291097941	3		218	119	SUCCESS
AR	367	MSKCC	GRCh37	X	66941796	66941796	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	117	269	0	ENST00000374690.3:c.2440T>G	p.Phe814Val	p.F814V	ENST00000374690	NM_000044.3	814	Ttc/Gtc	6/8	0.571316853070021	2	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.742268291097941	2		269	242	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0001822-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	365	316	0	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.694799867375078	1		316	569	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0001939-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	65	349	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.347318949650672	1	FACETS	0.706	0.621	0.796	0.706	0.621	0.796	SUBCLONAL	1	TRUE	0	0.576843971758103	1		349	227	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121074	3121074	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0001939-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	113	793	0	ENST00000078429.4:c.977C>G	p.Ser326Ter	p.S326*	ENST00000078429	NM_002067.2	326	tCa/tGa	7/7	0.438970848059534	1	FACETS	0.393	0.354	0.435	0.393	0.354	0.435	SUBCLONAL	1	TRUE	0	0.576843971758103	1		793	709	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40739804	40739804	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001939-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	148	984	0	ENST00000392038.2:c.1421C>G	p.Ser474Cys	p.S474C	ENST00000392038	NM_001626.4	474	tCc/tGc	14/14	0.438970848059534	1	FACETS	0.408	0.373	0.446	0.408	0.373	0.446	SUBCLONAL	1	TRUE	0	0.576843971758103	1		984	894	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176085811	176085812	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0001939-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	55	246	0	ENST00000367669.3:c.974_975del	p.Ile325AsnfsTer2	p.I325Nfs*2	ENST00000367669	NM_022457.5	325	aTT/a	9/20	0.576843971758103	3	FACETS	0.429	0.366	0.497	0.214	0.183	0.249	SUBCLONAL	1	TRUE	1	0.576843971758103	3		246	573	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936788	78936788	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001939-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	104	776	0	ENST00000306801.3:c.3870C>G	p.Ile1290Met	p.I1290M	ENST00000306801	NM_020761.2	1290	atC/atG	33/34	1	2	FACETS	0.42	0.376	0.468	0.42	0.376	0.468	SUBCLONAL	1	TRUE	1	0.576843971758103	2		776	858	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371726	55371726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001939-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	90	575	0	ENST00000297316.4:c.416C>T	p.Pro139Leu	p.P139L	ENST00000297316	NM_022454.3	139	cCg/cTg	2/2	0.208334227117484	3	FACETS	0.51	0.452	0.572	0.17	0.15	0.191	INDETERMINATE	1	TRUE	0	0.576843971758103	3		575	788	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	66	326	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.952	0.847	1	0.952	0.847	1	CLONAL	1	TRUE	1	0.877635077174507	2		326	158	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0002298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	135	327	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.927	0.854	1	0.927	0.854	1	CLONAL	1	TRUE	1	0.877635077174507	2		327	332	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791733	42791733	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	21	299	2	ENST00000575354.2:c.619T>C	p.Phe207Leu	p.F207L	ENST00000575354	NM_015125.3	207	Ttc/Ctc	5/20	0.877635077174507	1	FACETS	0.099	0.076	0.125	0.099	0.076	0.125	SUBCLONAL	1	TRUE	0	0.877635077174507	1		301	272	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798242	42798242	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	131	369	0	ENST00000575354.2:c.4195+1G>A		p.X1399_splice	ENST00000575354	NM_015125.3	1399			0.877635077174507	1	FACETS	0.722	0.672	0.771	0.722	0.672	0.771	SUBCLONAL	1	TRUE	0	0.877635077174507	1		369	232	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164782	36164782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752616540	NA	P-0002298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	139	332	1	ENST00000300305.3:c.1093G>A	p.Gly365Ser	p.G365S	ENST00000300305		365	Ggc/Agc	8/8	1	2	FACETS	0.825	0.759	0.892	0.825	0.759	0.892	CLONAL	1	TRUE	1	0.877635077174507	2		333	384	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0003185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	235	665	2	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	0.377758921948368	0	FACETS	0.904	0.857	0.951			1	CLONAL	2	FALSE	0	0.377758921948368	0		667	428	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111168	193111168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1452051467	NA	P-0003185-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	165	237	0	ENST00000367435.3:c.701G>A	p.Arg234Gln	p.R234Q	ENST00000367435	NM_024529.4	234	cGa/cAa	7/17	0.377758921948368	5	FACETS	0.839	0.771	0.909	0.419	0.385	0.455	CLONAL	2	FALSE	1	0.377758921948368	5		237	816	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0003940-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	77	651	0	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	1	2	FACETS	0.951	0.837	1	1	0.982	1	CLONAL	2	TRUE	1	0.16	2		651	506	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17355148	17355148	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs978525560	NA	P-0003940-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	118	339	0	ENST00000375499.3:c.370G>T	p.Val124Phe	p.V124F	ENST00000375499	NM_003000.2	124	Gtc/Ttc	4/8	0.3	4	FACETS	1	0.953	1			1	CLONAL	2	TRUE	NA	0.16	4		339	783	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527598	157527598	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1554237228	NA	P-0003940-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	73	230	0	ENST00000346085.5:c.5323A>T	p.Lys1775Ter	p.K1775*	ENST00000346085	NM_020732.3	1775	Aag/Tag	20/20	0.175545734348457	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.16	2		230	401	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2202730	2202730	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003940-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	75	420	0	ENST00000398665.3:c.739C>T	p.Pro247Ser	p.P247S	ENST00000398665	NM_032482.2	247	Cct/Tct	9/28	0.26351872698023	1	FACETS	0.825	0.724	0.932	1	0.979	1	CLONAL	2	TRUE	0	0.16	1		420	523	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196600	67196601	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0003940-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	80	265	0	ENST00000312629.5:c.131_132del	p.His44LeufsTer2	p.H44Lfs*2	ENST00000312629	NM_003952.2	43	ggACac/ggac	3/15	0.26351872698023	4	FACETS	1	0.958	1	0.605	0.532	0.685	CLONAL	1	TRUE	2	0.16	4		265	958	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	25	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.542	0.425	0.677	0.542	0.425	0.677	SUBCLONAL	1	TRUE	1	0.12	2		426	769	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743943	40743943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763964405	NA	P-0004188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	30	265	0	ENST00000373198.4:c.3052C>T	p.Arg1018Ter	p.R1018*	ENST00000373198	NM_133170.3	1018	Cga/Tga	23/32	1	2	FACETS	0.954	0.767	1	0.954	0.767	1	CLONAL	1	TRUE	1	0.12	2		265	524	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0004188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	40	343	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.815	0.675	0.972	0.815	0.675	0.972	CLONAL	1	TRUE	1	0.12	2		343	818	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439936	56439936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377765604	NA	P-0004188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	29	214	1	ENST00000407977.2:c.656G>A	p.Arg219His	p.R219H	ENST00000407977		219	cGc/cAc	6/10	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.12	2		215	414	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123789	11123789	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1555774786	NA	P-0004188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	42	346	1	ENST00000358026.2:c.2438+1G>A		p.X813_splice	ENST00000358026	NM_001128849.1	813			1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.12	2		347	669	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020103	123020103	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	54	274	0	ENST00000355640.3:c.591A>T	p.Gln197His	p.Q197H	ENST00000355640		197	caA/caT	2/7	1	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.12	1		274	602	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49423208	49423208	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	52	396	0	ENST00000301067.7:c.14051del	p.Pro4684LeufsTer113	p.P4684Lfs*113	ENST00000301067	NM_003482.3	4684	cCt/ct	43/54	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.12	2		396	808	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425865	49425865	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs146371387	NA	P-0004188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	51	428	0	ENST00000301067.7:c.12623del	p.Asn4208ThrfsTer7	p.N4208Tfs*7	ENST00000301067	NM_003482.3	4208	aAc/ac	39/54	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.12	2		428	717	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196880	108196880	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004188-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	42	316	0	ENST00000278616.4:c.6908del	p.Lys2303ArgfsTer7	p.K2303Rfs*7	ENST00000278616	NM_000051.3	2301	gcA/gc	47/63	1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	1	0.12	2		316	689	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	316	665	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.986	0.935	1	0.986	0.935	1	CLONAL	1	FALSE	1	0.817751533440445	2		665	784	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508472	106508472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	78	281	0	ENST00000359195.3:c.466G>A	p.Ala156Thr	p.A156T	ENST00000359195	NM_002649.2	156	Gcg/Acg	2/11	1	2	FACETS	0.805	0.718	0.895	0.805	0.718	0.895	CLONAL	1	FALSE	1	0.817751533440445	2		281	237	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	338	585	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.908	0.862	0.955	0.908	0.862	0.955	CLONAL	1	FALSE	1	0.817751533440445	2		590	910	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105715	27105717	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs765246223	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	94	389	0	ENST00000324856.7:c.5334_5336del	p.Glu1780del	p.E1780del	ENST00000324856	NM_006015.4	1776	GAA/-	20/20	1	2	FACETS	0.57	0.511	0.633	0.57	0.511	0.633	SUBCLONAL	1	FALSE	1	0.817751533440445	2		389	403	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955111	17955112	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755706305	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	258	849	1	ENST00000458235.1:c.115dup	p.Gln39ProfsTer13	p.Q39Pfs*13	ENST00000458235	NM_000215.3	39	cag/cCag	2/24	1	2	FACETS	0.741	0.695	0.787	0.741	0.695	0.787	SUBCLONAL	1	FALSE	1	0.817751533440445	2		850	852	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748399150	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	72	912	10	ENST00000220592.5:c.1806del	p.Ala603ProfsTer92	p.A603Pfs*92	ENST00000220592	NM_012154.3	602	ccC/cc	14/19	1	2	FACETS	0.172	0.15	0.197	0.172	0.15	0.197	SUBCLONAL	1	FALSE	1	0.817751533440445	2		922	1021	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922301	178922301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	224	377	1	ENST00000263967.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000263967	NM_006218.2	357	cGa/cAa	6/21	1	2	FACETS	0.989	0.929	1	0.989	0.929	1	CLONAL	1	FALSE	1	0.817751533440445	2		378	554	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776583	9776583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1224681360	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	319	850	1	ENST00000377346.4:c.686G>A	p.Arg229Gln	p.R229Q	ENST00000377346	NM_005026.3	229	cGg/cAg	6/24	1	2	FACETS	0.941	0.892	0.991	0.941	0.892	0.991	CLONAL	1	FALSE	1	0.817751533440445	2		851	829	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100934	27100934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	31	607	0	ENST00000324856.7:c.4216C>T	p.Pro1406Ser	p.P1406S	ENST00000324856	NM_006015.4	1406	Ccc/Tcc	18/20	1	2	FACETS	0.125	0.1	0.153	0.125	0.1	0.153	SUBCLONAL	1	FALSE	1	0.817751533440445	2		607	607	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911932	94911932	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	251	556	0	ENST00000536441.1:c.998T>C	p.Phe333Ser	p.F333S	ENST00000536441	NM_144665.3	333	tTt/tCt	7/10	1	2	FACETS	0.814	0.765	0.865	0.814	0.765	0.865	CLONAL	1	FALSE	1	0.817751533440445	2		556	754	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981721	101981721	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555075353	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	85	269	0	ENST00000282441.5:c.147del	p.Ala50ProfsTer24	p.A50Pfs*24	ENST00000282441	NM_001130145.2	48	Ccc/cc	1/9	1	2	FACETS	0.664	0.593	0.739	0.664	0.593	0.739	SUBCLONAL	1	FALSE	1	0.817751533440445	2		269	313	SUCCESS
ATM	472	MSKCC	GRCh37	11	108128310	108128310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778065	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	208	305	0	ENST00000278616.4:c.2353C>T	p.Arg785Cys	p.R785C	ENST00000278616	NM_000051.3	785	Cgt/Tgt	15/63	1	2	FACETS	0.963	0.902	1	0.963	0.902	1	CLONAL	1	FALSE	1	0.817751533440445	2		305	528	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420145	420145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564426386	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	210	441	0	ENST00000399788.2:c.3122C>T	p.Pro1041Leu	p.P1041L	ENST00000399788	NM_001042603.1	1041	cCg/cTg	21/28	NA	2	FACETS	0.859	0.803	0.916			1	INDETERMINATE	1	FALSE	NA	0.817751533440445	2		441	598	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434186	49434186	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370115365	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	337	1043	2	ENST00000301067.7:c.7367G>A	p.Arg2456His	p.R2456H	ENST00000301067	NM_003482.3	2456	cGc/cAc	31/54	1	2	FACETS	0.741	0.701	0.782	0.741	0.701	0.782	SUBCLONAL	1	FALSE	1	0.817751533440445	2		1045	1112	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555724	21555724	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753361598	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	272	731	1	ENST00000382592.4:c.2546G>A	p.Arg849Gln	p.R849Q	ENST00000382592	NM_014572.2	849	cGg/cAg	6/8	1	2	FACETS	0.91	0.858	0.962	0.91	0.858	0.962	CLONAL	1	FALSE	1	0.817751533440445	2		732	731	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562753	21562753	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339653606	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	25	374	0	ENST00000382592.4:c.1166C>T	p.Pro389Leu	p.P389L	ENST00000382592	NM_014572.2	389	cCg/cTg	4/8	1	2	FACETS	0.163	0.128	0.204	0.163	0.128	0.204	SUBCLONAL	1	FALSE	1	0.817751533440445	2		374	374	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528104	103528104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140930348	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	174	395	0	ENST00000355739.4:c.3412G>A	p.Val1138Met	p.V1138M	ENST00000355739	NM_000123.3	1138	Gtg/Atg	15/15	1	2	FACETS	0.958	0.892	1	0.958	0.892	1	CLONAL	1	FALSE	1	0.817751533440445	2		395	444	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052626	42052626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	277	451	1	ENST00000219905.7:c.7297C>T	p.Arg2433Trp	p.R2433W	ENST00000219905	NM_001164273.1	2433	Cgg/Tgg	20/24	1	2	FACETS	0.972	0.918	1	0.972	0.918	1	CLONAL	1	FALSE	1	0.817751533440445	2		452	697	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347159	347159	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750185512	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	292	891	0	ENST00000262320.3:c.1852G>A	p.Glu618Lys	p.E618K	ENST00000262320	NM_003502.3	618	Gag/Aag	7/11	1	2	FACETS	0.936	0.885	0.987	0.936	0.885	0.987	CLONAL	1	FALSE	1	0.817751533440445	2		891	763	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81939027	81939027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3935625	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	32	499	0	ENST00000359376.3:c.1382G>A	p.Arg461Gln	p.R461Q	ENST00000359376	NM_002661.3	461	cGa/cAa	15/33	1	2	FACETS	0.149	0.12	0.182	0.149	0.12	0.182	SUBCLONAL	1	FALSE	1	0.817751533440445	2		499	525	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944156	81944156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773800539	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	221	676	2	ENST00000359376.3:c.1765C>T	p.Arg589Cys	p.R589C	ENST00000359376	NM_002661.3	589	Cgc/Tgc	18/33	1	2	FACETS	0.821	0.769	0.875	0.821	0.769	0.875	CLONAL	1	FALSE	1	0.817751533440445	2		678	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514495	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	301	667	2	ENST00000269305.4:c.542G>A	p.Arg181His	p.R181H	ENST00000269305	NM_001126112.2	181	cGc/cAc	5/11	1	2	FACETS	0.978	0.926	1	0.978	0.926	1	CLONAL	1	FALSE	1	0.817751533440445	2		669	753	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974781	15974781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1454297938	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	203	405	0	ENST00000268712.3:c.4094G>A	p.Arg1365Gln	p.R1365Q	ENST00000268712	NM_006311.3	1365	cGg/cAg	30/46	1	2	FACETS	0.855	0.798	0.913	0.855	0.798	0.913	CLONAL	1	FALSE	1	0.817751533440445	2		405	581	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552152	29552152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199474738	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	95	276	0	ENST00000356175.3:c.1885G>A	p.Gly629Arg	p.G629R	ENST00000356175	NM_000267.3	629	Ggg/Agg	17/57	0.575020719876639	1	FACETS	0.66	0.601	0.72	0.66	0.601	0.72	SUBCLONAL	1	FALSE	0	0.817751533440445	1		276	208	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556373	29556373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765848298	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	37	490	0	ENST00000356175.3:c.2740C>T	p.Arg914Trp	p.R914W	ENST00000356175	NM_000267.3	914	Cgg/Tgg	21/57	0.575020719876639	1	FACETS	0.11	0.09	0.132	0.11	0.09	0.132	SUBCLONAL	1	FALSE	0	0.817751533440445	1		490	488	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879618	37879618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567911318	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	52	835	0	ENST00000269571.5:c.1993G>A	p.Val665Met	p.V665M	ENST00000269571		665	Gtg/Atg	17/27	1	2	FACETS	0.138	0.117	0.162	0.138	0.117	0.162	SUBCLONAL	1	FALSE	1	0.817751533440445	2		835	921	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530129	63530132	+	frameshift_variant	Frame_Shift_Del	DEL	AAGT	AAGT	-	novel	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	255	571	0	ENST00000307078.5:c.2303_2306del	p.Tyr768PhefsTer13	p.Y768Ffs*13	ENST00000307078	NM_004655.3	768	tACTTt/tt	10/11	1	2	FACETS	0.866	0.815	0.918	0.866	0.815	0.918	CLONAL	1	FALSE	1	0.817751533440445	2		571	720	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395746	45395746	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	138	346	1	ENST00000262160.6:c.388C>T	p.Arg130Ter	p.R130*	ENST00000262160	NM_005901.5	130	Cga/Tga	4/11	1	2	FACETS	0.659	0.603	0.717	0.659	0.603	0.717	SUBCLONAL	1	FALSE	1	0.817751533440445	2		347	512	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101031	4101031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375843855	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	136	604	0	ENST00000262948.5:c.691C>T	p.Arg231Cys	p.R231C	ENST00000262948	NM_030662.3	231	Cgc/Tgc	6/11	1	2	FACETS	0.603	0.55	0.657	0.603	0.55	0.657	SUBCLONAL	1	FALSE	1	0.817751533440445	2		604	552	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221156	5221156	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	320	818	1	ENST00000357368.4:c.3310A>G	p.Ser1104Gly	p.S1104G	ENST00000357368	NM_002850.3	1104	Agc/Ggc	20/38	1	2	FACETS	0.912	0.864	0.961	0.912	0.864	0.961	CLONAL	1	FALSE	1	0.817751533440445	2		819	858	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244020	5244020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752283871	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	48	846	0	ENST00000357368.4:c.1462G>A	p.Val488Met	p.V488M	ENST00000357368	NM_002850.3	488	Gtg/Atg	11/38	1	2	FACETS	0.132	0.111	0.156	0.132	0.111	0.156	SUBCLONAL	1	FALSE	1	0.817751533440445	2		846	888	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272146	15272146	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866716310	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	51	593	0	ENST00000263388.2:c.6293C>T	p.Thr2098Met	p.T2098M	ENST00000263388	NM_000435.2	2098	aCg/aTg	33/33	1	2	FACETS	0.189	0.16	0.221	0.189	0.16	0.221	SUBCLONAL	1	FALSE	1	0.817751533440445	2		593	659	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387420	17387420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757371052	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	255	789	0	ENST00000359435.4:c.686C>T	p.Thr229Met	p.T229M	ENST00000359435	NM_001033549.1	229	aCg/aTg	7/9	1	2	FACETS	0.745	0.699	0.792	0.745	0.699	0.792	SUBCLONAL	1	FALSE	1	0.817751533440445	2		789	837	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976896	18976896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1333445130	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	302	626	4	ENST00000262803.5:c.3281C>T	p.Ala1094Val	p.A1094V	ENST00000262803	NM_002911.3	1094	gCg/gTg	23/24	1	2	FACETS	0.923	0.874	0.973	0.923	0.874	0.973	CLONAL	1	FALSE	1	0.817751533440445	2		630	800	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744482	41744482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752081844	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	361	818	0	ENST00000301178.4:c.1102C>T	p.Arg368Trp	p.R368W	ENST00000301178	NM_021913.4	368	Cgg/Tgg	8/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.817751533440445	2		818	883	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383692	42383692	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202097187	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	252	676	0	ENST00000221972.3:c.467C>T	p.Ala156Val	p.A156V	ENST00000221972	NM_021601.3	156	gCg/gTg	3/5	1	2	FACETS	0.896	0.843	0.95	0.896	0.843	0.95	CLONAL	1	FALSE	1	0.817751533440445	2		676	688	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383707	42383707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782414774	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	247	623	1	ENST00000221972.3:c.482C>T	p.Thr161Met	p.T161M	ENST00000221972	NM_021601.3	161	aCg/aTg	3/5	1	2	FACETS	0.913	0.858	0.968	0.913	0.858	0.968	CLONAL	1	FALSE	1	0.817751533440445	2		624	662	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791308	42791308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573059625	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	370	841	1	ENST00000575354.2:c.368C>T	p.Pro123Leu	p.P123L	ENST00000575354	NM_015125.3	123	cCg/cTg	3/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.817751533440445	2		842	841	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919027	50919027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775310798	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	374	799	0	ENST00000440232.2:c.2764G>A	p.Val922Ile	p.V922I	ENST00000440232	NM_002691.3	922	Gtc/Atc	22/27	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.817751533440445	2		799	862	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716236	52716236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs945817997	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	225	690	0	ENST00000322088.6:c.680C>T	p.Ala227Val	p.A227V	ENST00000322088	NM_014225.5	227	gCg/gTg	6/15	1	2	FACETS	0.8	0.748	0.852	0.8	0.748	0.852	SUBCLONAL	1	FALSE	1	0.817751533440445	2		690	688	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262442	39262442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756679265	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	285	598	0	ENST00000402219.2:c.985G>A	p.Glu329Lys	p.E329K	ENST00000402219	NM_005633.3	329	Gaa/Aaa	8/23	0.780449456263562	2	FACETS	0.931	0.879	0.983	0.465	0.439	0.492	CLONAL	1	FALSE	0	0.817751533440445	2		598	749	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	249	437	6	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	0.780449456263562	2	FACETS	0.931	0.876	0.987	0.466	0.438	0.494	CLONAL	1	FALSE	0	0.817751533440445	2		443	654	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46252781	46252800	+	frameshift_variant	Frame_Shift_Del	DEL	GATTTTAAAGGAAACAGTAA	GATTTTAAAGGAAACAGTAA	-	novel	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	79	275	0	ENST00000371998.3:c.212_231del	p.Ile71ThrfsTer15	p.I71Tfs*15	ENST00000371998		70	gcGATTTTAAAGGAAACAGTAAga/gcga	4/23	1	2	FACETS	0.485	0.429	0.545	0.485	0.429	0.545	SUBCLONAL	1	FALSE	1	0.817751533440445	2		275	398	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655272	45655272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764295138	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	320	761	0	ENST00000407780.3:c.580C>T	p.Arg194Trp	p.R194W	ENST00000407780	NM_001283052.1	194	Cgg/Tgg	4/7	1	2	FACETS	0.901	0.853	0.949	0.901	0.853	0.949	CLONAL	1	FALSE	1	0.817751533440445	2		761	869	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442575	52442575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	194	444	0	ENST00000460680.1:c.170G>A	p.Arg57Gln	p.R57Q	ENST00000460680	NM_004656.3	57	cGg/cAg	4/17	1	2	FACETS	0.784	0.73	0.84	0.784	0.73	0.84	SUBCLONAL	1	FALSE	1	0.817751533440445	2		444	605	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921446	178921446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780572147	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	234	490	0	ENST00000263967.3:c.928C>T	p.Arg310Cys	p.R310C	ENST00000263967	NM_006218.2	310	Cgc/Tgc	5/21	1	2	FACETS	0.814	0.763	0.866	0.814	0.763	0.866	CLONAL	1	FALSE	1	0.817751533440445	2		490	703	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629129	187629129	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	45	517	0	ENST00000441802.2:c.1853A>G	p.Asn618Ser	p.N618S	ENST00000441802	NM_005245.3	618	aAc/aGc	2/27	1	2	FACETS	0.163	0.136	0.192	0.163	0.136	0.192	SUBCLONAL	1	FALSE	1	0.817751533440445	2		517	677	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456962	149456962	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764483518	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	196	497	0	ENST00000286301.3:c.766C>T	p.Arg256Cys	p.R256C	ENST00000286301	NM_005211.3	256	Cgt/Tgt	6/22	1	2	FACETS	0.862	0.804	0.922	0.862	0.804	0.922	CLONAL	1	FALSE	1	0.817751533440445	2		497	556	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401520	401520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751008894	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	201	449	0	ENST00000380956.4:c.842C>T	p.Thr281Met	p.T281M	ENST00000380956	NM_001195286.1	281	aCg/aTg	7/9	1	2	FACETS	0.979	0.916	1	0.979	0.916	1	CLONAL	1	FALSE	1	0.817751533440445	2		449	502	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138195987	138195987	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1409953541	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	69	155	0	ENST00000237289.4:c.301G>A	p.Gly101Ser	p.G101S	ENST00000237289	NM_001270507.1	101	Ggc/Agc	3/9	1	2	FACETS	0.796	0.705	0.891	0.796	0.705	0.891	SUBCLONAL	1	FALSE	1	0.817751533440445	2		155	212	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508401	106508401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760958737	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	120	317	0	ENST00000359195.3:c.395C>T	p.Pro132Leu	p.P132L	ENST00000359195	NM_002649.2	132	cCg/cTg	2/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	1	0.817751533440445	2		317	281	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38139044	38139044	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	220	572	1	ENST00000317025.8:c.3559C>T	p.Arg1187Ter	p.R1187*	ENST00000317025	NM_023034.1	1187	Cga/Tga	20/24	1	2	FACETS	0.688	0.642	0.735	0.688	0.642	0.735	SUBCLONAL	1	FALSE	1	0.817751533440445	2		573	782	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021699	69021699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779206847	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	223	472	0	ENST00000288368.4:c.2987C>T	p.Ala996Val	p.A996V	ENST00000288368	NM_024870.2	996	gCg/gTg	25/40	1	2	FACETS	0.858	0.803	0.913	0.858	0.803	0.913	CLONAL	1	FALSE	1	0.817751533440445	2		472	636	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971138	21971138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760640852	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	196	426	0	ENST00000304494.5:c.220G>A	p.Asp74Asn	p.D74N	ENST00000304494	NM_000077.4	74	Gac/Aac	2/3	1	2	FACETS	0.992	0.928	1	0.992	0.928	1	CLONAL	1	FALSE	1	0.817751533440445	2		426	483	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971179	21971179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs36204594	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	179	379	0	ENST00000304494.5:c.179C>T	p.Ala60Val	p.A60V	ENST00000304494	NM_000077.4	60	gCg/gTg	2/3	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	FALSE	1	0.817751533440445	2		379	436	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	197	382	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.817751533440445	2		382	451	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933871	39933871	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs865796679	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	279	409	1	ENST00000378444.4:c.728G>A	p.Arg243His	p.R243H	ENST00000378444	NM_001123385.1	243	cGc/cAc	4/15	1	1	FACETS	0.925	0.885	0.964	0.925	0.885	0.964	CLONAL	1	FALSE	0	0.817751533440445	1		410	436	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53241079	53241079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782110533	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	159	257	0	ENST00000375401.3:c.1132C>T	p.Arg378Trp	p.R378W	ENST00000375401	NM_004187.3	378	Cgg/Tgg	9/26	1	1	FACETS	0.737	0.688	0.785	0.737	0.688	0.785	SUBCLONAL	1	FALSE	0	0.817751533440445	1		257	312	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940000	76940000	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1311466929	NA	P-0004188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	22	257	0	ENST00000373344.5:c.748C>T	p.Arg250Ter	p.R250*	ENST00000373344	NM_000489.3	250	Cga/Tga	9/35	1	1	FACETS	0.083	0.064	0.105	0.083	0.064	0.105	SUBCLONAL	1	FALSE	0	0.817751533440445	1		257	383	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286830	33286830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775787032	NA	P-0004331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	30	187	0	ENST00000374542.5:c.2107C>T	p.Pro703Ser	p.P703S	ENST00000374542	NM_001141970.1	703	Cca/Tca	7/8	0.105457515622424	4	FACETS	0.71	0.572	0.866	0.355	0.286	0.433	INDETERMINATE	1	FALSE	2	0.275929050763779	4		187	391	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439913	51439914	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0004331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	10	114	0	ENST00000262662.1:c.480_481del	p.Ala161TrpfsTer23	p.A161Wfs*23	ENST00000262662		160	GGg/g	4/4	0.275929050763779	0	FACETS	0.292	0.197	0.41			1	SUBCLONAL	1	FALSE	0	0.275929050763779	0		114	180	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057194	30057198	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AATAA	AATAA	-	novel	NA	P-0004331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	106	325	0	ENST00000338641.4:c.678_682del	p.Asn226LysfsTer18	p.N226Kfs*18	ENST00000338641	NM_000268.3	226	AATAAa/a	8/16	0.275929050763779	0	FACETS	0.796	0.729	0.864			1	SUBCLONAL	3	FALSE	0	0.275929050763779	0		325	233	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0004494-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	97	188	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.227898755981736	4	FACETS	1	0.916	1	1	0.916	1	CLONAL	2	TRUE	2	0.227898755981736	4		188	509	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0004494-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	116	448	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.194927060490538	4	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	2	0.227898755981736	4		448	605	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0004494-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	14	489	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.227898755981736	2	FACETS	0.282	0.203	0.379	0.141	0.101	0.19	SUBCLONAL	1	TRUE	0	0.227898755981736	2		489	435	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0004494-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	111	409	1	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	0.194927060490538	4	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	2	0.227898755981736	4		410	560	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268383	198268383	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1172363633	NA	P-0004494-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	120	465	1	ENST00000335508.6:c.1645C>T	p.Arg549Cys	p.R549C	ENST00000335508	NM_012433.2	549	Cgt/Tgt	12/25	0.178032479816143	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.227898755981736	4		466	569	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457764	149457764	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004494-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	45	299	0	ENST00000286301.3:c.640C>T	p.Arg214Trp	p.R214W	ENST00000286301	NM_005211.3	214	Cgg/Tgg	5/22	0.227898755981736	4	FACETS	1	0.958	1	0.732	0.618	0.858	CLONAL	1	TRUE	2	0.227898755981736	4		299	331	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216611	108216611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201958469	NA	P-0004494-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	81	410	0	ENST00000278616.4:c.8560C>T	p.Arg2854Cys	p.R2854C	ENST00000278616	NM_000051.3	2854	Cgc/Tgc	58/63	0.194927060490538	4	FACETS	0.852	0.753	0.958	0.852	0.753	0.958	CLONAL	2	TRUE	2	0.227898755981736	4		410	512	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041046	29041046	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004494-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	108	370	0	ENST00000282397.4:c.382A>G	p.Ile128Val	p.I128V	ENST00000282397	NM_002019.4	128	Att/Gtt	3/30	0.203761746241922	3	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	1	0.227898755981736	3		370	494	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486104	29486104	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1555605404	NA	P-0004494-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	189	355	0	ENST00000356175.3:c.282del	p.Ala95LeufsTer8	p.A95Lfs*8	ENST00000356175	NM_000267.3	94	cTt/ct	3/57	0.227898755981736	3	FACETS	0.935	0.872	0.999	1	0.987	1	CLONAL	4	TRUE	0	0.227898755981736	3		355	494	SUCCESS
APC	324	MSKCC	GRCh37	5	112175595	112175613	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGTAAAACACCTCCACC	GAAGTAAAACACCTCCACC	-	novel	NA	P-0004494-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	98	536	1	ENST00000257430.4:c.4304_4322del	p.Arg1435AsnfsTer32	p.R1435Nfs*32	ENST00000257430	NM_000038.5	1435	aGAAGTAAAACACCTCCACCa/aa	16/16	0.227898755981736	4	FACETS	1	0.905	1	1	0.905	1	CLONAL	2	TRUE	2	0.227898755981736	4		537	522	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0005242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	365	442	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.640029988866371	3	FACETS	0.94	0.906	0.972	0.94	0.906	0.972	CLONAL	3	TRUE	0	0.640029988866371	3		442	534	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0005242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	298	219	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.640029988866371	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	3	TRUE	0	0.640029988866371	3		219	409	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255790	16255790	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	222	481	0	ENST00000375759.3:c.3055C>T	p.Gln1019Ter	p.Q1019*	ENST00000375759	NM_015001.2	1019	Cag/Tag	11/15	0.619644183208094	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.640029988866371	1		481	447	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105727	27105727	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772578230	NA	P-0005242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	244	462	2	ENST00000324856.7:c.5338G>A	p.Glu1780Lys	p.E1780K	ENST00000324856	NM_006015.4	1780	Gaa/Aaa	20/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.640029988866371	2		464	735	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936379	49936379	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	608	725	0	ENST00000296474.3:c.1469C>A	p.Ser490Ter	p.S490*	ENST00000296474	NM_002447.2	490	tCa/tAa	3/20	NA	2	FACETS	0.986	0.957	1			1	INDETERMINATE	2	TRUE	NA	0.640029988866371	2		725	963	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178143	56178143	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	176	427	2	ENST00000399503.3:c.3116C>A	p.Ser1039Ter	p.S1039*	ENST00000399503	NM_005921.1	1039	tCa/tAa	14/20	1	2	FACETS	0.893	0.826	0.961	0.893	0.826	0.961	CLONAL	1	TRUE	1	0.640029988866371	2		429	616	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874386	151874386	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	411	438	0	ENST00000262189.6:c.8152G>A	p.Glu2718Lys	p.E2718K	ENST00000262189	NM_170606.2	2718	Gaa/Aaa	38/59	0.544150889564305	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.640029988866371	3		438	811	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202720	133202720	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	284	590	0	ENST00000320574.5:c.6514G>C	p.Asp2172His	p.D2172H	ENST00000320574	NM_006231.2	2172	Gac/Cac	46/49	1	2	FACETS	0.897	0.845	0.951	0.897	0.845	0.951	CLONAL	1	TRUE	1	0.640029988866371	2		590	989	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237716	133237716	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	217	584	1	ENST00000320574.5:c.2899G>C	p.Glu967Gln	p.E967Q	ENST00000320574	NM_006231.2	967	Gag/Cag	25/49	1	2	FACETS	0.954	0.89	1	0.954	0.89	1	CLONAL	1	TRUE	1	0.640029988866371	2		585	711	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28901682	28901682	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005242-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	170	394	0	ENST00000282397.4:c.2713C>G	p.Leu905Val	p.L905V	ENST00000282397	NM_002019.4	905	Ctg/Gtg	20/30	1	2	FACETS	0.949	0.878	1	0.949	0.878	1	CLONAL	1	TRUE	1	0.640029988866371	2		394	560	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0005382-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	332	574	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	1	2	FACETS	0.943	0.895	0.991	0.943	0.895	0.991	CLONAL	1	TRUE	1	0.81430263455996	2		574	865	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256425	46256425	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1200320359	NA	P-0005382-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	93	548	0	ENST00000371998.3:c.653G>A	p.Arg218His	p.R218H	ENST00000371998		218	cGc/cAc	7/23	1	2	FACETS	0.286	0.254	0.321	0.286	0.254	0.321	SUBCLONAL	1	TRUE	1	0.81430263455996	2		548	798	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105258963	105258963	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005382-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	142	788	0	ENST00000349310.3:c.18T>G	p.Ile6Met	p.I6M	ENST00000349310	NM_001014432.1	6	atT/atG	3/15	1	2	FACETS	0.359	0.327	0.393	0.359	0.327	0.393	SUBCLONAL	1	TRUE	1	0.81430263455996	2		788	971	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557794	187557795	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005382-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	70	462	0	ENST00000441802.2:c.3916dup	p.Thr1306AsnfsTer16	p.T1306Nfs*16	ENST00000441802	NM_005245.3	1306	act/aAct	5/27	1	2	FACETS	0.249	0.217	0.284	0.249	0.217	0.284	SUBCLONAL	1	TRUE	1	0.81430263455996	2		462	690	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005459-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	99	326	0				ENST00000310581	NM_198253.2	-/1132			0.469621917925157	3	FACETS	0.938	0.85	1	0.938	0.85	1	CLONAL	2	TRUE	1	0.468808989747239	3		326	278	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625249	69625249	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781935233	NA	P-0005459-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	320	631	0	ENST00000334134.2:c.544G>A	p.Val182Met	p.V182M	ENST00000334134	NM_005247.2	182	Gtg/Atg	3/3	0.468808989747239	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.468808989747239	4		631	933	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117846	108117846	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005459-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	205	374	0	ENST00000278616.4:c.1057T>C	p.Cys353Arg	p.C353R	ENST00000278616	NM_000051.3	353	Tgt/Cgt	8/63	0.468808989747239	4	FACETS	0.973	0.907	1	0.973	0.907	1	CLONAL	2	TRUE	2	0.468808989747239	4		374	660	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474431	40474431	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs193922721	NA	P-0005459-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	290	475	0	ENST00000264657.5:c.1970A>G	p.Tyr657Cys	p.Y657C	ENST00000264657	NM_139276.2	657	tAt/tGt	21/24	0.468808989747239	4	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	2	0.468808989747239	4		475	904	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577409	7577572	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAAATCGGTAAGAGGTGGGCCCAGGGGTCAGAGGCAAGCAGAGGCTGGGGCACAGCAGGCCAGTGTGCAGGGTGGCAAGTGGCTCCTGACCTGGAGTCTTCCAGTGTGATGATGGTGAGGATGGGCCTCCGGTTCATGCCGCCCATGCAGGAACTGTTACACAT	GAAATCGGTAAGAGGTGGGCCCAGGGGTCAGAGGCAAGCAGAGGCTGGGGCACAGCAGGCCAGTGTGCAGGGTGGCAAGTGGCTCCTGACCTGGAGTCTTCCAGTGTGATGATGGTGAGGATGGGCCTCCGGTTCATGCCGCCCATGCAGGAACTGTTACACAT	-	novel	NA	P-0005459-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	117	256	0	ENST00000269305.4:c.709_782+90del		p.X237_splice	ENST00000269305	NM_001126112.2	237		7/11	0.469621917925157	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.468808989747239	2		256	224	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0006687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	258	889	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.383439756226533	1	FACETS	0.999	0.935	1	0.999	0.935	1	CLONAL	1	TRUE	0	0.383439756226533	1		889	1089	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836642	89836642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747723074	NA	P-0006687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1299	318	1225	0	ENST00000389301.3:c.2248G>A	p.Val750Met	p.V750M	ENST00000389301	NM_000135.2	750	Gtg/Atg	25/43	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.383439756226533	2		1225	1617	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266016	41266403	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	In_Frame_Del	DEL	GCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAAT	GCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAAT	-	novel	NA	P-0006687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	97	224	0	ENST00000349496.5:c.18_242-37del		p.A5_D81del	ENST00000349496	NM_001904.3	5		3/15	0.309897303737245	2	FACETS	1	0.982	1	0.744	0.67	0.821	CLONAL	1	TRUE	0	0.383439756226533	2		224	340	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231096	98231096	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	115	656	0	ENST00000331920.6:c.2187G>C	p.Lys729Asn	p.K729N	ENST00000331920	NM_000264.3	729	aaG/aaC	14/24	1	2	FACETS	0.618	0.556	0.685	0.618	0.556	0.685	SUBCLONAL	1	TRUE	1	0.383439756226533	2		656	970	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790455	3790455	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783490	NA	P-0006704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	155	488	1	ENST00000262367.5:c.4078C>T	p.Arg1360Ter	p.R1360*	ENST00000262367	NM_004380.2	1360	Cga/Tga	24/31	0.440360651679939	3	FACETS	1	0.946	1	0.522	0.478	0.568	CLONAL	1	TRUE	1	0.445125700106613	3		489	816	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0006704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	69	423	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.357590248253744	3	FACETS	0.795	0.694	0.903	0.397	0.347	0.452	CLONAL	1	TRUE	1	0.445125700106613	3		423	477	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482437	56482437	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	88	457	0	ENST00000267101.3:c.985A>G	p.Lys329Glu	p.K329E	ENST00000267101	NM_001982.3	329	Aaa/Gaa	8/28	0.357590248253744	3	FACETS	0.975	0.866	1	0.487	0.433	0.545	CLONAL	1	TRUE	1	0.445125700106613	3		457	496	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582302	119582302	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	232	480	0	ENST00000316626.5:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000316626		367	Cga/Tga	10/12	0.445125700106613	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.445125700106613	3		480	608	SUCCESS
APC	324	MSKCC	GRCh37	5	112174438	112174438	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs863225340	NA	P-0006704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	152	491	1	ENST00000257430.4:c.3147G>A	p.Trp1049Ter	p.W1049*	ENST00000257430	NM_000038.5	1049	tgG/tgA	16/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.445125700106613	2		492	556	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225411	26225411	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1241	262	792	0	ENST00000360408.1:c.29A>G	p.Lys10Arg	p.K10R	ENST00000360408	NM_003532.2	10	aAa/aGa	1/1	0.356241239897382	3	FACETS	0.958	0.895	1	0.479	0.447	0.511	CLONAL	1	TRUE	1	0.445125700106613	3		792	1503	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138083	64138083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777650305	NA	P-0006704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	151	365	0	ENST00000334205.4:c.2006G>A	p.Arg669Gln	p.R669Q	ENST00000334205	NM_003942.2	669	cGg/cAg	16/17	0.357590248253744	3	FACETS	0.967	0.884	1	0.483	0.442	0.527	CLONAL	1	TRUE	1	0.445125700106613	3		365	858	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344938	70344938	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	139	665	0	ENST00000374080.3:c.2168G>T	p.Gly723Val	p.G723V	ENST00000374080		723	gGg/gTg	15/45	0.221158537326124	3	FACETS	0.874	0.795	0.956			1	INDETERMINATE	1	TRUE	NA	0.445125700106613	3		665	874	SUCCESS
APC	324	MSKCC	GRCh37	5	112175508	112175509	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0006704-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	70	432	0	ENST00000257430.4:c.4219_4220del	p.Ser1407Ter	p.S1407*	ENST00000257430	NM_000038.5	1406	cAG/c	16/16	1	2	FACETS	0.681	0.595	0.773	0.681	0.595	0.773	SUBCLONAL	1	TRUE	1	0.445125700106613	2		432	462	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115712	8115875	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGGCCGCCCTCTCCAGACACATGTCCTCCCTGAGCCACATCTCG	CCCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGGCCGCCCTCTCCAGACACATGTCCTCCCTGAGCCACATCTCG	-	novel	NA	P-0006847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	98	313	0	ENST00000346208.3:c.1062_1225del	p.Thr355GlnfsTer97	p.T355Qfs*97	ENST00000346208		353	cCCCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGGCCGCCCTCTCCAGACACATGTCCTCCCTGAGCCACATCTCG/c	6/6	1	2	FACETS	0.533	0.476	0.594	0.533	0.476	0.594	SUBCLONAL	1	TRUE	1	0.522082711146087	2		313	704	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274827	38274827	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	205	284	0	ENST00000425967.3:c.1753G>C	p.Asp585His	p.D585H	ENST00000425967	NM_001174067.1	585	Gat/Cat	13/19	0.194590093284502	6	FACETS	0.84	0.779	0.902			1	INDETERMINATE	2	TRUE	NA	0.522082711146087	6		284	956	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057999	27058000	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCTCGACGCTCTC	novel	NA	P-0006847-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	77	197	0	ENST00000324856.7:c.1710_1723dup	p.Gln575ProfsTer49	p.Q575Pfs*49	ENST00000324856	NM_006015.4	569	-/CCCTCGACGCTCTC	3/20	1	2	FACETS	0.573	0.504	0.647	0.573	0.504	0.647	SUBCLONAL	1	TRUE	1	0.522082711146087	2		197	515	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0006859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	28	372	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.717	0.571	0.884	0.717	0.571	0.884	SUBCLONAL	1	TRUE	1	0.13	2		372	601	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0006859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	22	486	0	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	1	2	FACETS	0.451	0.348	0.572	0.451	0.348	0.572	SUBCLONAL	1	TRUE	1	0.13	2		486	750	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266486	41266486	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775104326	NA	P-0006859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	47	323	0	ENST00000349496.5:c.283C>T	p.Arg95Ter	p.R95*	ENST00000349496	NM_001904.3	95	Cga/Tga	4/15	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.13	2		323	700	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839983	27839983	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	69	692	0	ENST00000328488.2:c.111G>C	p.Lys37Asn	p.K37N	ENST00000328488	NM_003533.2	37	aaG/aaC	1/1	1	2	FACETS	0.976	0.847	1	0.976	0.847	1	CLONAL	1	TRUE	1	0.13	2		692	1088	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875722	56875722	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768650810	NA	P-0006859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	43	438	0	ENST00000308159.5:c.2326C>T	p.Arg776Ter	p.R776*	ENST00000308159	NM_014669.4	776	Cga/Tga	21/22	0.166500548874308	1	FACETS	0.786	0.656	0.931	0.786	0.656	0.931	CLONAL	1	TRUE	0	0.13	1		438	787	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842705	68842705	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	110	498	0	ENST00000261769.5:c.641T>A	p.Leu214Gln	p.L214Q	ENST00000261769	NM_004360.3	214	cTg/cAg	5/16	0.166500548874308	1	FACETS	0.991	0.891	1	1	0.988	1	CLONAL	2	TRUE	0	0.13	1		498	798	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969882	81969882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	44	480	1	ENST00000359376.3:c.2951G>A	p.Arg984His	p.R984H	ENST00000359376	NM_002661.3	984	cGc/cAc	27/33	0.166500548874308	1	FACETS	0.78	0.652	0.923	0.78	0.652	0.923	CLONAL	1	TRUE	0	0.13	1		481	811	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075200	16075200	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1240701348	NA	P-0006859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	32	309	0	ENST00000268712.3:c.352C>G	p.His118Asp	p.H118D	ENST00000268712	NM_006311.3	118	Cat/Gat	4/46	1	2	FACETS	0.859	0.696	1	0.859	0.696	1	CLONAL	1	TRUE	1	0.13	2		309	573	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375016	45375016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226662382	NA	P-0006859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	29	241	0	ENST00000262160.6:c.827C>T	p.Ser276Leu	p.S276L	ENST00000262160	NM_005901.5	276	tCg/tTg	8/11	1	2	FACETS	0.868	0.695	1	0.868	0.695	1	CLONAL	1	TRUE	1	0.13	2		241	514	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0006859-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	116	486	0	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	1	2	FACETS	0.962	0.869	1	0.962	0.869	1	CLONAL	1	TRUE	1	0.407526896911263	2		486	592	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875722	56875722	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768650810	NA	P-0006859-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	233	438	0	ENST00000308159.5:c.2326C>T	p.Arg776Ter	p.R776*	ENST00000308159	NM_014669.4	776	Cga/Tga	21/22	0.40194475270885	2	FACETS	0.991	0.932	1	0.991	0.932	1	CLONAL	2	TRUE	0	0.407526896911263	2		438	577	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842705	68842705	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006859-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	258	498	0	ENST00000261769.5:c.641T>A	p.Leu214Gln	p.L214Q	ENST00000261769	NM_004360.3	214	cTg/cAg	5/16	0.40194475270885	2	FACETS	0.956	0.901	1	0.956	0.901	1	CLONAL	2	TRUE	0	0.407526896911263	2		498	662	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089695	27089695	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006859-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	174	601	0	ENST00000324856.7:c.2651del	p.Cys884PhefsTer7	p.C884Ffs*7	ENST00000324856	NM_006015.4	884	tGt/tt	8/20	1	2	FACETS	0.969	0.893	1	0.969	0.893	1	CLONAL	1	TRUE	1	0.407526896911263	2		601	881	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244266	46244266	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006859-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	80	366	0	ENST00000334344.6:c.2360C>G	p.Thr787Ser	p.T787S	ENST00000334344	NM_152641.2	787	aCt/aGt	15/21	1	2	FACETS	0.872	0.771	0.98	0.872	0.771	0.98	CLONAL	1	TRUE	1	0.407526896911263	2		366	450	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610086	81610086	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006859-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	114	440	0	ENST00000298171.2:c.1684A>T	p.Ser562Cys	p.S562C	ENST00000298171	NM_000369.2	562	Agc/Tgc	10/10	1	2	FACETS	0.999	0.903	1	0.999	0.903	1	CLONAL	1	TRUE	1	0.407526896911263	2		440	560	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143999	11143999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1171822727	NA	P-0006859-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	153	542	1	ENST00000358026.2:c.3580G>A	p.Gly1194Arg	p.G1194R	ENST00000358026	NM_001128849.1	1194	Ggg/Agg	26/36	1	2	FACETS	0.996	0.913	1	0.996	0.913	1	CLONAL	1	TRUE	1	0.407526896911263	2		543	754	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165636	185165636	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006859-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	94	370	0	ENST00000265026.3:c.911T>C	p.Leu304Pro	p.L304P	ENST00000265026	NM_004721.4	304	cTc/cCc	5/14	1	2	FACETS	0.949	0.848	1	0.949	0.848	1	CLONAL	1	TRUE	1	0.407526896911263	2		370	486	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739626	41739626	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006859-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	106	384	0	ENST00000242208.4:c.347T>C	p.Leu116Pro	p.L116P	ENST00000242208	NM_002192.2	116	cTt/cCt	2/3	0.407526896911263	3	FACETS	1	0.908	1	0.506	0.454	0.56	CLONAL	1	TRUE	1	0.407526896911263	3		384	619	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73995319	73995319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148316620	NA	P-0006931-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	18	165	0	ENST00000318443.5:c.625C>T	p.Arg209Trp	p.R209W	ENST00000318443	NM_001024736.1	209	Cgg/Tgg	4/10	0.22318276133326	1	FACETS	0.517	0.391	0.665	0.517	0.391	0.665	SUBCLONAL	1	TRUE	0	0.309605097124806	1		165	190	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0007135-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	162	423	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.331110946219023	4	FACETS	1	0.989	1	0.747	0.688	0.808	CLONAL	1	TRUE	2	0.51901825574304	4		423	635	SUCCESS
APC	324	MSKCC	GRCh37	5	112175746	112175746	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007135-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	377	404	0	ENST00000257430.4:c.4455del	p.Asp1486IlefsTer21	p.D1486Ifs*21	ENST00000257430	NM_000038.5	1485	gcT/gc	16/16	0.51901825574304	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	0	0.51901825574304	3		404	594	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587781702	NA	P-0007135-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	234	449	2	ENST00000269305.4:c.920-1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.39901620006673	2	FACETS	0.784	0.737	0.831	0.784	0.737	0.831	SUBCLONAL	2	TRUE	0	0.51901825574304	2		451	575	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198283245	198283245	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007135-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	32	472	0	ENST00000335508.6:c.483G>C	p.Leu161Phe	p.L161F	ENST00000335508	NM_012433.2	161	ttG/ttC	5/25	0.432536501197065	4	FACETS	0.308	0.249	0.374	0.077	0.062	0.094	SUBCLONAL	1	TRUE	0	0.51901825574304	4		472	609	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298129	15298129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007135-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	40	507	2	ENST00000263388.2:c.1627G>A	p.Asp543Asn	p.D543N	ENST00000263388	NM_000435.2	543	Gat/Aat	11/33	0.406842124194909	4	FACETS	0.309	0.256	0.369	0.154	0.128	0.185	SUBCLONAL	1	TRUE	2	0.51901825574304	4		509	758	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs869025608	NA	P-0008404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	52	386	0	ENST00000307102.5:c.171G>T	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaT	2/11	0.411887373319995	5	FACETS	0.868	0.752	0.99	0.579	0.501	0.66	INDETERMINATE	2	TRUE	2	0.695527643425783	5		386	176	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921551	178921551	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	77	344	0	ENST00000263967.3:c.1033A>T	p.Asn345Tyr	p.N345Y	ENST00000263967	NM_006218.2	345	Aat/Tat	5/21	0.695527643425783	5	FACETS	0.935	0.857	1	1	0.978	1	CLONAL	4	TRUE	2	0.695527643425783	5		344	121	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578463	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371524413	NA	P-0008404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	69	654	0	ENST00000269305.4:c.467G>C	p.Arg156Pro	p.R156P	ENST00000269305	NM_001126112.2	156	cGc/cCc	5/11	0.691808380156145	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.695527643425783	2		654	91	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449671	187449671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	60	415	0	ENST00000232014.4:c.209G>A	p.Ser70Asn	p.S70N	ENST00000232014	NM_001130845.1	70	aGt/aAt	4/10	0.695527643425783	5	FACETS	0.933	0.83	1	0.933	0.83	1	CLONAL	3	TRUE	2	0.695527643425783	5		415	126	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202292	138202292	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	33	420	1	ENST00000237289.4:c.2209C>T	p.Gln737Ter	p.Q737*	ENST00000237289	NM_001270507.1	737	Cag/Tag	9/9	0.691808380156145	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	2	TRUE	0	0.695527643425783	2		421	46	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271208	38271208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765900637	NA	P-0008404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	39	491	0	ENST00000425967.3:c.2500G>A	p.Glu834Lys	p.E834K	ENST00000425967	NM_001174067.1	834	Gag/Aag	19/19	0.341999817580069	6	FACETS	1	0.933	1	0.791	0.673	0.915	INDETERMINATE	2	TRUE	3	0.695527643425783	6		491	113	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499623	18499623	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	79	513	4	ENST00000266497.5:c.1478T>A	p.Leu493Gln	p.L493Q	ENST00000266497		493	cTa/cAa	10/31	0.270136001579492	5	FACETS	1	0.927	1	0.697	0.624	0.773	INDETERMINATE	2	TRUE	2	0.695527643425783	5		517	222	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202293	133202293	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1220509815	NA	P-0008404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	34	610	0	ENST00000320574.5:c.6595A>T	p.Ile2199Phe	p.I2199F	ENST00000320574	NM_006231.2	2199	Atc/Ttc	47/49	0.695527643425783	2	FACETS	0.94	0.825	1	0.94	0.825	1	CLONAL	2	TRUE	0	0.695527643425783	2		610	52	SUCCESS
BLM	641	MSKCC	GRCh37	15	91337474	91337474	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	28	468	0	ENST00000355112.3:c.3097A>G	p.Ile1033Val	p.I1033V	ENST00000355112	NM_000057.2	1033	Ata/Gta	16/22	0.411887373319995	5	FACETS	1	0.855	1	0.356	0.288	0.432	INDETERMINATE	1	TRUE	2	0.695527643425783	5		468	154	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314616	30314616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	53	589	1	ENST00000262643.3:c.1165C>T	p.Leu389Phe	p.L389F	ENST00000262643	NM_001238.2	389	Ctc/Ttc	12/12	0.654274604964671	3	FACETS	0.925	0.842	1	0.925	0.842	1	CLONAL	3	TRUE	0	0.695527643425783	3		590	74	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220394	1220394	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	546	595	0	ENST00000326873.7:c.488del	p.Gly163AlafsTer124	p.G163Afs*124	ENST00000326873	NM_000455.4	163	Ggc/gc	4/10	0.654274604964671	3	FACETS	0.92	0.894	0.945	0.92	0.894	0.945	CLONAL	3	TRUE	0	0.695527643425783	3		595	767	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602570	10602587	+	frameshift_variant	Frame_Shift_Del	DEL	TCGGAAGTAGCCGCCCGC	TCGGAAGTAGCCGCCCGC	CCTT	novel	NA	P-0008404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	486	347	0	ENST00000171111.5:c.991_1008delinsAAGG	p.Ala331LysfsTer14	p.A331Kfs*14	ENST00000171111	NM_203500.1	331	GCGGGCGGCTACTTCCGA/AAGG	3/6	0.654274604964671	3	FACETS	0.892	0.864	0.918	0.892	0.864	0.918	CLONAL	3	TRUE	0	0.695527643425783	3		347	704	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs869025608	NA	P-0008404-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	179	386	0	ENST00000307102.5:c.171G>T	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaT	2/11	0.403205680816652	5	FACETS	1	0.975	1	0.739	0.687	0.793	CLONAL	2	TRUE	2	0.604642280235148	5		386	509	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921551	178921551	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008404-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	268	344	0	ENST00000263967.3:c.1033A>T	p.Asn345Tyr	p.N345Y	ENST00000263967	NM_006218.2	345	Aat/Tat	5/21	0.604642280235148	6	FACETS	0.999	0.95	1	0.999	0.95	1	CLONAL	4	TRUE	2	0.604642280235148	6		344	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578463	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371524413	NA	P-0008404-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	284	654	0	ENST00000269305.4:c.467G>C	p.Arg156Pro	p.R156P	ENST00000269305	NM_001126112.2	156	cGc/cCc	5/11	0.328918732293496	3	FACETS	1	0.992	1	0.806	0.768	0.844	INDETERMINATE	2	TRUE	0	0.604642280235148	3		654	506	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449671	187449671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008404-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	233	415	0	ENST00000232014.4:c.209G>A	p.Ser70Asn	p.S70N	ENST00000232014	NM_001130845.1	70	aGt/aAt	4/10	0.516562838005327	5	FACETS	0.872	0.82	0.924	0.872	0.82	0.924	CLONAL	3	TRUE	2	0.604642280235148	5		415	562	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202292	138202292	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008404-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	163	420	1	ENST00000237289.4:c.2209C>T	p.Gln737Ter	p.Q737*	ENST00000237289	NM_001270507.1	737	Cag/Tag	9/9	0.604642280235148	2	FACETS	0.835	0.78	0.889	0.835	0.78	0.889	CLONAL	2	TRUE	0	0.604642280235148	2		421	323	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271208	38271208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765900637	NA	P-0008404-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	149	491	0	ENST00000425967.3:c.2500G>A	p.Glu834Lys	p.E834K	ENST00000425967	NM_001174067.1	834	Gag/Aag	19/19	0.358007298681933	4	FACETS	0.897	0.827	0.968	0.897	0.827	0.968	INDETERMINATE	2	TRUE	2	0.604642280235148	4		491	441	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499623	18499623	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008404-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	200	513	4	ENST00000266497.5:c.1478T>A	p.Leu493Gln	p.L493Q	ENST00000266497		493	cTa/cAa	10/31	0.403205680816652	5	FACETS	1	0.987	1	0.818	0.765	0.872	CLONAL	2	TRUE	2	0.604642280235148	5		517	514	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202293	133202293	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1220509815	NA	P-0008404-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	238	610	0	ENST00000320574.5:c.6595A>T	p.Ile2199Phe	p.I2199F	ENST00000320574	NM_006231.2	2199	Atc/Ttc	47/49	0.557822765708335	2	FACETS	0.823	0.778	0.868	0.823	0.778	0.868	CLONAL	2	TRUE	0	0.604642280235148	2		610	478	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314616	30314616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008404-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	231	589	1	ENST00000262643.3:c.1165C>T	p.Leu389Phe	p.L389F	ENST00000262643	NM_001238.2	389	Ctc/Ttc	12/12	0.604642280235148	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.604642280235148	2		590	375	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220394	1220394	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008404-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	245	595	0	ENST00000326873.7:c.488del	p.Gly163AlafsTer124	p.G163Afs*124	ENST00000326873	NM_000455.4	163	Ggc/gc	4/10	0.604642280235148	2	FACETS	0.917	0.87	0.963	0.917	0.87	0.963	CLONAL	2	TRUE	0	0.604642280235148	2		595	442	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007635	45007635	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008404-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	118	230	0	ENST00000558401.1:c.82C>T	p.Gln28Ter	p.Q28*	ENST00000558401	NM_004048.2	28	Cag/Tag	2/4	0.577907921282599	2	FACETS	0.991	0.921	1	0.991	0.921	1	CLONAL	2	TRUE	0	0.604642280235148	2		230	197	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602587	10602587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1197443517	NA	P-0008404-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	222	543	1	ENST00000171111.5:c.991G>A	p.Ala331Thr	p.A331T	ENST00000171111	NM_203500.1	331	Gcg/Acg	3/6	0.604642280235148	2	FACETS	0.878	0.83	0.926	0.878	0.83	0.926	CLONAL	2	TRUE	0	0.604642280235148	2		544	418	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562517	95562517	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs369465519	NA	P-0008404-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	32	283	0	ENST00000393063.1:c.4740G>T	p.Gln1580His	p.Q1580H	ENST00000393063	NM_030621.3	1580	caG/caT	24/28	0.403205680816652	5	FACETS	0.662	0.539	0.8	0.221	0.179	0.267	SUBCLONAL	1	TRUE	2	0.604642280235148	5		283	305	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621908	1621910	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs550914200	NA	P-0008404-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	77	605	1	ENST00000344749.5:c.882_884del	p.Ser295del	p.S295del	ENST00000344749	NM_001136139.2	294	tcCTCa/tca	11/19	0.604642280235148	2	FACETS	0.567	0.5	0.639	0.284	0.25	0.32	SUBCLONAL	1	TRUE	0	0.604642280235148	2		606	449	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275420	38275420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369356672	NA	P-0008404-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	59	613	1	ENST00000425967.3:c.1613G>A	p.Arg538His	p.R538H	ENST00000425967	NM_001174067.1	538	cGt/cAt	12/19	0.358007298681933	4	FACETS	0.472	0.406	0.545	0.236	0.203	0.273	INDETERMINATE	1	TRUE	2	0.604642280235148	4		614	663	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602572	10602587	+	frameshift_variant	Frame_Shift_Del	DEL	GGAAGTAGCCGCCCGC	GGAAGTAGCCGCCCGC	CTT	novel	NA	P-0008404-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	223	583	2	ENST00000171111.5:c.991_1006delinsAAG	p.Ala331LysfsTer65	p.A331Kfs*65	ENST00000171111	NM_203500.1	331	GCGGGCGGCTACTTCCga/AAGga	3/6	0.604642280235148	2	FACETS	0.86	0.812	0.907	0.86	0.812	0.907	CLONAL	2	TRUE	0	0.604642280235148	2		585	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0008423-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	263	617	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.475900983802196	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.475900983802196	1		617	711	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376093	225376093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008423-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	127	566	1	ENST00000264414.4:c.861G>A	p.Met287Ile	p.M287I	ENST00000264414	NM_003590.4	287	atG/atA	6/16	1	2	FACETS	0.73	0.662	0.802	0.73	0.662	0.802	SUBCLONAL	1	TRUE	1	0.475900983802196	2		567	731	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498023	29498023	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs758860363	NA	P-0008423-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	194	586	1	ENST00000389048.3:c.1983C>A	p.Asn661Lys	p.N661K	ENST00000389048	NM_004304.4	661	aaC/aaA	11/29	1	2	FACETS	0.894	0.828	0.963	0.894	0.828	0.963	CLONAL	1	TRUE	1	0.475900983802196	2		587	912	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849655	68849655	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008423-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	175	392	0	ENST00000261769.5:c.1561del	p.Ile521Ter	p.I521*	ENST00000261769	NM_004360.3	520	Aaa/aa	10/16	0.475900983802196	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.475900983802196	1		392	528	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937580	32937611	+	frameshift_variant	Frame_Shift_Del	DEL	TGGTCAGAAGATTATTCTTCATGGAGCAGAAC	TGGTCAGAAGATTATTCTTCATGGAGCAGAAC	-	novel	NA	P-0008423-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	199	503	0	ENST00000380152.3:c.8245_8276del	p.Gln2749GlyfsTer4	p.Q2749Gfs*4	ENST00000380152		2747	gtTGGTCAGAAGATTATTCTTCATGGAGCAGAACtg/gttg	18/27	0.475900983802196	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.475900983802196	1		503	605	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009001-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	74	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.225526344980472	3	FACETS	1	0.944	1	0.571	0.5	0.648	CLONAL	1	TRUE	1	0.225526344980472	3		426	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578525	7578525	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519976	NA	P-0009001-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	173	1021	0	ENST00000269305.4:c.405C>G	p.Cys135Trp	p.C135W	ENST00000269305	NM_001126112.2	135	tgC/tgG	5/11	0.177824242044525	2	FACETS	1	0.987	1	0.698	0.641	0.757	CLONAL	1	TRUE	0	0.225526344980472	2		1021	1099	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928075	178928095	+	inframe_deletion	In_Frame_Del	DEL	ATTAGAAGATTTGCTGAACCC	ATTAGAAGATTTGCTGAACCC	-	novel	NA	P-0009001-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	38	577	0	ENST00000263967.3:c.1353_1373del	p.Leu452_Pro458del	p.L452_P458del	ENST00000263967	NM_006218.2	451	ggATTAGAAGATTTGCTGAACCCt/ggt	8/21	1	2	FACETS	0.623	0.514	0.745	0.623	0.514	0.745	SUBCLONAL	1	TRUE	1	0.225526344980472	2		577	541	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206756	36206757	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0009001-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	64	646	0	ENST00000300305.3:c.754_755dup	p.Leu253ProfsTer2	p.L253Pfs*2	ENST00000300305		252	tcc/tcTCc	6/8	1	2	FACETS	0.824	0.713	0.945	0.824	0.713	0.945	CLONAL	1	TRUE	1	0.225526344980472	2		646	689	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0009193-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	153	216	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.401380315393187	5	FACETS	0.983	0.934	1			1	CLONAL	6	TRUE	NA	0.401380315393187	5		216	207	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0009193-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	72	327	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.310145927966525	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	2	0.401380315393187	4		327	211	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939511	76939511	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009193-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	81	163	0	ENST00000373344.5:c.1237T>G	p.Leu413Val	p.L413V	ENST00000373344	NM_000489.3	413	Tta/Gta	9/35	0.238856770976549	2	FACETS	1	0.951	1			1	INDETERMINATE	3	TRUE	NA	0.401380315393187	2		163	128	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939518	76939518	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009193-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	85	158	0	ENST00000373344.5:c.1230A>T	p.Glu410Asp	p.E410D	ENST00000373344	NM_000489.3	410	gaA/gaT	9/35	0.238856770976549	2	FACETS	1	0.954	1			1	INDETERMINATE	3	TRUE	NA	0.401380315393187	2		158	134	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939725	76939725	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0009193-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	123	179	0	ENST00000373344.5:c.1023C>G	p.Tyr341Ter	p.Y341*	ENST00000373344	NM_000489.3	341	taC/taG	9/35	0.238856770976549	2	FACETS	0.923	0.871	0.972			1	INDETERMINATE	4	TRUE	NA	0.401380315393187	2		179	166	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40498589	40498589	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	328	478	0	ENST00000264657.5:c.271C>T	p.Gln91Ter	p.Q91*	ENST00000264657	NM_139276.2	91	Cag/Tag	3/24	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.677943254311917	2		478	898	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629895	187629895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531890135	NA	P-0009524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	314	456	0	ENST00000441802.2:c.1087G>A	p.Gly363Arg	p.G363R	ENST00000441802	NM_005245.3	363	Ggg/Agg	2/27	1	2	FACETS	0.982	0.929	1	0.982	0.929	1	CLONAL	1	TRUE	1	0.677943254311917	2		456	943	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372768	81372768	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	238	371	0	ENST00000222390.5:c.766G>T	p.Asp256Tyr	p.D256Y	ENST00000222390	NM_000601.4	256	Gat/Tat	7/18	1	2	FACETS	0.955	0.895	1	0.955	0.895	1	CLONAL	1	TRUE	1	0.677943254311917	2		371	735	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589556	67589591	+	inframe_deletion	In_Frame_Del	DEL	ATAATATTGAAGCTGTAGGGAAAAAATTACATGAAT	ATAATATTGAAGCTGTAGGGAAAAAATTACATGAAT	-	novel	NA	P-0009524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	160	344	0	ENST00000274335.5:c.1323_1358del	p.Ile442_Asn453del	p.I442_N453del	ENST00000274335		440	gATAATATTGAAGCTGTAGGGAAAAAATTACATGAATat/gat	10/15	1	2	FACETS	0.732	0.673	0.792	0.732	0.673	0.792	SUBCLONAL	1	TRUE	1	0.677943254311917	2		344	645	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101195	27101205	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCAAGGCAC	CAGCAAGGCAC	-	novel	NA	P-0009524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	227	442	0	ENST00000324856.7:c.4479_4489del	p.Gln1493HisfsTer6	p.Q1493Hfs*6	ENST00000324856	NM_006015.4	1493	CAGCAAGGCACc/c	18/20	1	2	FACETS	0.698	0.651	0.747	0.698	0.651	0.747	SUBCLONAL	1	TRUE	1	0.677943254311917	2		442	959	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615145	43615146	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0009524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	282	493	0	ENST00000355710.3:c.2562dup	p.Ala855CysfsTer30	p.A855Cfs*30	ENST00000355710	NM_020975.4	853	-/T	14/20	0.677943254311917	3	FACETS	0.956	0.898	1	0.478	0.449	0.508	CLONAL	1	TRUE	1	0.677943254311917	3		493	1165	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592122	67592140	+	protein_altering_variant	In_Frame_Del	DEL	TCTTGTCCGGGAGAGCAGT	TCTTGTCCGGGAGAGCAGT	ACTA	novel	NA	P-0009524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	222	398	0	ENST00000274335.5:c.1938_1956delinsACTA	p.Phe646_Ser652delinsLeuLeu	p.F646_S652delinsLL	ENST00000274335		646	ttTCTTGTCCGGGAGAGCAGT/ttACTA	14/15	1	2	FACETS	0.873	0.816	0.932	0.873	0.816	0.932	CLONAL	1	TRUE	1	0.677943254311917	2		398	750	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850290	128850292	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs758836898	NA	P-0009748-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	209	735	0	ENST00000249373.3:c.1556_1558del	p.Lys519del	p.K519del	ENST00000249373	NM_005631.4	518	gAGAag/gag	9/12	1	2	FACETS	0.977	0.907	1	0.977	0.907	1	CLONAL	1	TRUE	1	0.437373834414897	2		735	978	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971066	21971086	+	inframe_deletion	In_Frame_Del	DEL	GCAGCACCACCAGCGTGTCCA	GCAGCACCACCAGCGTGTCCA	-	novel	NA	P-0009748-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	101	575	0	ENST00000304494.5:c.272_292del	p.Leu91_Leu97del	p.L91_L97del	ENST00000304494	NM_000077.4	91	cTGGACACGCTGGTGGTGCTGCac/cac	2/3	0.437373834414897	1	FACETS	0.682	0.612	0.756	0.682	0.612	0.756	SUBCLONAL	1	TRUE	0	0.437373834414897	1		575	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0009791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	351	654	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.417413597672653	3	FACETS	0.84	0.803	0.877			1	CLONAL	3	TRUE	NA	0.523639434167271	3		654	671	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0009791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	230	308	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.523918329290843	3	FACETS	0.846	0.793	0.9	0.846	0.793	0.9	CLONAL	2	TRUE	1	0.523639434167271	3		308	655	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199553	16199553	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	86	509	3	ENST00000375759.3:c.326G>T	p.Gly109Val	p.G109V	ENST00000375759	NM_015001.2	109	gGa/gTa	2/15	1	2	FACETS	0.473	0.418	0.531	0.473	0.418	0.531	SUBCLONAL	1	TRUE	1	0.523639434167271	2		512	695	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671979	30671979	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	230	724	0	ENST00000376406.3:c.4981G>C	p.Glu1661Gln	p.E1661Q	ENST00000376406	NM_014641.2	1661	Gag/Cag	10/15	0.268953072695185	5	FACETS	1	0.989	1	0.438	0.408	0.47	INDETERMINATE	1	TRUE	2	0.523639434167271	5		724	1193	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137528150	137528150	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0009791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	91	518	1	ENST00000367739.4:c.150C>G	p.Tyr50Ter	p.Y50*	ENST00000367739	NM_000416.2	50	taC/taG	2/7	0.353767002512148	5	FACETS	0.558	0.493	0.626	0.186	0.164	0.209	SUBCLONAL	1	TRUE	2	0.523639434167271	5		519	1113	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229522	98229522	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	38	668	4	ENST00000331920.6:c.2436C>A	p.Tyr812Ter	p.Y812*	ENST00000331920	NM_000264.3	812	taC/taA	15/24	NA	2	FACETS	0.211	0.173	0.253			1	INDETERMINATE	1	TRUE	NA	0.523639434167271	2		672	689	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344720	118344720	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	158	629	0	ENST00000534358.1:c.2846C>G	p.Thr949Ser	p.T949S	ENST00000534358	NM_005933.3	949	aCt/aGt	3/36	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.523639434167271	2		629	546	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630670	90630670	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0009791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	104	695	0	ENST00000330062.3:c.815+1G>C		p.X272_splice	ENST00000330062	NM_002168.2	272			0.517805481075519	3	FACETS	0.521	0.466	0.58	0.261	0.233	0.29	SUBCLONAL	1	TRUE	1	0.523639434167271	3		695	962	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857771	9857771	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	233	742	0	ENST00000330684.3:c.3630C>A	p.Asn1210Lys	p.N1210K	ENST00000330684	NM_001134407.1	1210	aaC/aaA	13/13	0.417413597672653	3	FACETS	1	0.99	1			1	CLONAL	1	TRUE	NA	0.523639434167271	3		742	852	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371819	45371819	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	56	374	0	ENST00000262160.6:c.1172C>A	p.Ala391Asp	p.A391D	ENST00000262160	NM_005901.5	391	gCt/gAt	10/11	0.511584985820831	2	FACETS	0.465	0.399	0.537	0.232	0.199	0.269	SUBCLONAL	1	TRUE	0	0.523639434167271	2		374	460	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0010922-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	590	706	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	1	2	FACETS	0.923	0.889	0.958	0.923	0.889	0.958	CLONAL	1	TRUE	1	0.899208562603971	2		706	1421	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	173	326	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.978	0.913	1			1	INDETERMINATE	1	TRUE	NA	0.930956195629375	2		326	380	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0011009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	21	442	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.103	0.079	0.131	0.103	0.079	0.131	SUBCLONAL	1	TRUE	1	0.930956195629375	2		442	439	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0011009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	370	327	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.930956195629375	2		327	777	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791718	42791718	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1344635105	NA	P-0011009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	191	370	2	ENST00000575354.2:c.604C>T	p.Arg202Trp	p.R202W	ENST00000575354	NM_015125.3	202	Cgg/Tgg	5/20	0.930956195629375	1	FACETS	0.512	0.48	0.546	0.512	0.48	0.546	SUBCLONAL	1	TRUE	0	0.930956195629375	1		372	428	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791728	42791728	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	160	387	0	ENST00000575354.2:c.614A>G	p.Asn205Ser	p.N205S	ENST00000575354	NM_015125.3	205	aAt/aGt	5/20	0.930956195629375	1	FACETS	0.419	0.388	0.451	0.419	0.388	0.451	SUBCLONAL	1	TRUE	0	0.930956195629375	1		387	438	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217227	11217227	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	138	517	0	ENST00000361445.4:c.4451T>C	p.Leu1484Pro	p.L1484P	ENST00000361445	NM_004958.3	1484	cTc/cCc	30/58	0.930956195629375	1	FACETS	0.295	0.27	0.322	0.295	0.27	0.322	SUBCLONAL	1	TRUE	0	0.930956195629375	1		517	537	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78422333	78422334	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0011009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	246	298	0	ENST00000370768.2:c.1628dup	p.His543GlnfsTer24	p.H543Qfs*24	ENST00000370768	NM_003902.3	543	cac/caAc	17/20	0.930956195629375	1	FACETS	0.59	0.558	0.621	0.59	0.558	0.621	SUBCLONAL	1	TRUE	0	0.930956195629375	1		298	479	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972677	76972677	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	237	287	0	ENST00000373344.5:c.64del	p.Ala23HisfsTer18	p.A23Hfs*18	ENST00000373344	NM_000489.3	22	Ctt/tt	2/35	1	1	FACETS	0.387	0.362	0.411	0.387	0.362	0.411	SUBCLONAL	1	TRUE	0	0.930956195629375	1		287	704	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591131	67591148	+	inframe_deletion	In_Frame_Del	DEL	AGACGAGAGACCAATACT	AGACGAGAGACCAATACT	-	novel	NA	P-0011009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	75	288	0	ENST00000274335.5:c.1724_1741del	p.Lys575_Leu581delinsMet	p.K575_L581delinsM	ENST00000274335		575	aAGACGAGAGACCAATACTtg/atg	12/15	1	2	FACETS	0.254	0.222	0.288	0.254	0.222	0.288	SUBCLONAL	1	TRUE	1	0.930956195629375	2		288	634	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498424	89498424	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1176464192	NA	P-0011025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	214	344	1	ENST00000336596.2:c.2396G>A	p.Arg799His	p.R799H	ENST00000336596	NM_005233.5	799	cGc/cAc	14/17	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.343996708747459	2		345	1130	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15273367	15273367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1320	228	632	1	ENST00000263388.2:c.5822C>T	p.Ser1941Leu	p.S1941L	ENST00000263388	NM_000435.2	1941	tCa/tTa	32/33	1	2	FACETS	0.856	0.795	0.92	0.856	0.795	0.92	CLONAL	1	TRUE	1	0.343996708747459	2		633	1548	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678068	117678091	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AATACAAGCGACTATAGAGGAAAA	AATACAAGCGACTATAGAGGAAAA	-	novel	NA	P-0011025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	87	265	0	ENST00000368508.3:c.3855-13_3865del		p.X1285_splice	ENST00000368508	NM_002944.2	1285		25/43	0.290578843749908	0	FACETS	0.759	0.676	0.848			1	SUBCLONAL	1	TRUE	0	0.343996708747459	0		265	437	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479165	50479166	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0011025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	159	249	0	ENST00000394963.4:c.14_15del	p.Ala5GlyfsTer125	p.A5Gfs*125	ENST00000394963	NM_003076.4	5	GCg/g	1/13	0.343996708747459	1	FACETS	0.953	0.875	1	0.953	0.875	1	CLONAL	1	TRUE	0	0.343996708747459	1		249	803	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498424	89498424	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1176464192	NA	P-0011025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	123	344	1	ENST00000336596.2:c.2396G>A	p.Arg799His	p.R799H	ENST00000336596	NM_005233.5	799	cGc/cAc	14/17	1	2	FACETS	0.939	0.853	1	0.939	0.853	1	CLONAL	1	TRUE	1	0.508958090098441	2		345	515	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15273367	15273367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	216	632	1	ENST00000263388.2:c.5822C>T	p.Ser1941Leu	p.S1941L	ENST00000263388	NM_000435.2	1941	tCa/tTa	32/33	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.508958090098441	2		633	794	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678068	117678091	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AATACAAGCGACTATAGAGGAAAA	AATACAAGCGACTATAGAGGAAAA	-	novel	NA	P-0011025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	85	265	0	ENST00000368508.3:c.3855-13_3865del		p.X1285_splice	ENST00000368508	NM_002944.2	1285		25/43	0.508958090098441	1	FACETS	0.838	0.75	0.931	0.838	0.75	0.931	CLONAL	1	TRUE	0	0.508958090098441	1		265	297	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479165	50479166	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0011025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	87	249	0	ENST00000394963.4:c.14_15del	p.Ala5GlyfsTer125	p.A5Gfs*125	ENST00000394963	NM_003076.4	5	GCg/g	1/13	0.508958090098441	1	FACETS	0.904	0.81	1	0.904	0.81	1	CLONAL	1	TRUE	0	0.508958090098441	1		249	282	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638347	117638347	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519788	NA	P-0011025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	133	376	0	ENST00000368508.3:c.6094G>A	p.Gly2032Arg	p.G2032R	ENST00000368508	NM_002944.2	2032	Gga/Aga	38/43	NA	2	FACETS	0.975	0.89	1			1	INDETERMINATE	1	TRUE	NA	0.508958090098441	2		376	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0011027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	343	954	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.283726221165366	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.28	2		954	1015	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0011027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	140	185	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.3	3	FACETS	0.86	0.79	0.932	0.86	0.79	0.932	CLONAL	3	TRUE	0	0.28	3		185	442	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662409	227662409	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	54	262	0	ENST00000305123.5:c.1046C>T	p.Pro349Leu	p.P349L	ENST00000305123	NM_005544.2	349	cCc/cTc	1/2	0.3	5	FACETS	0.985	0.841	1			1	CLONAL	1	TRUE	NA	0.28	5		262	556	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420067	152420067	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141662120	NA	P-0011027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	77	431	2	ENST00000206249.3:c.1754C>T	p.Thr585Met	p.T585M	ENST00000206249	NM_000125.3	585	aCg/aTg	8/8	0.264448433413951	3	FACETS	0.909	0.798	1	0.454	0.399	0.514	CLONAL	1	TRUE	1	0.28	3		433	690	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207099	1207099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	222	450	0	ENST00000326873.7:c.187G>A	p.Val63Met	p.V63M	ENST00000326873	NM_000455.4	63	Gtg/Atg	1/10	0.294286819458146	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.28	2		450	724	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117911	70117920	+	frameshift_variant	Frame_Shift_Del	DEL	TACCCGCACT	TACCCGCACT	-	novel	NA	P-0011027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	111	243	0	ENST00000245479.2:c.380_389del	p.Tyr127CysfsTer17	p.Y127Cfs*17	ENST00000245479	NM_000346.3	127	TACCCGCACTtg/tg	1/3	0.160370903135903	3	FACETS	0.987	0.892	1	0.658	0.595	0.724	INDETERMINATE	2	TRUE	0	0.28	3		243	458	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653805	89653805	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659443	NA	P-0011416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	47	408	0	ENST00000371953.3:c.103A>G	p.Met35Val	p.M35V	ENST00000371953	NM_000314.4	35	Atg/Gtg	2/9	1	2	FACETS	0.705	0.594	0.826	0.705	0.594	0.826	SUBCLONAL	1	TRUE	1	0.247962226827837	2		408	538	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906916	32906919	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	rs80359277	NA	P-0011416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	31	278	1	ENST00000380152.3:c.1310_1313del	p.Lys437IlefsTer22	p.K437Ifs*22	ENST00000380152		434	aAAAGa/aa	10/27	0.171634572568695	1	FACETS	0.614	0.497	0.746	0.614	0.497	0.746	SUBCLONAL	1	TRUE	0	0.247962226827837	1		279	357	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120309	94120309	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	82	269	0	ENST00000369303.4:c.742A>G	p.Met248Val	p.M248V	ENST00000369303	NM_004440.3	248	Atg/Gtg	3/17	0.247962226827837	1	FACETS	0.614	0.54	0.693	0.614	0.54	0.693	SUBCLONAL	1	TRUE	0	0.247962226827837	1		269	944	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400800	56400800	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	57	220	0	ENST00000348428.3:c.1394G>C	p.Arg465Thr	p.R465T	ENST00000348428	NM_006785.3	465	aGg/aCg	11/17	1	2	FACETS	0.679	0.582	0.786	0.679	0.582	0.786	SUBCLONAL	1	TRUE	1	0.247962226827837	2		220	677	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162307	47162333	+	inframe_deletion	In_Frame_Del	DEL	TTGCTGATACGTGGTAGAAGGCTTTTC	TTGCTGATACGTGGTAGAAGGCTTTTC	-	novel	NA	P-0011416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	33	521	0	ENST00000409792.3:c.3793_3819del	p.Glu1265_Gln1273del	p.E1265_Q1273del	ENST00000409792	NM_014159.6	1265	GAAAAGCCTTCTACCACGTATCAGCAA/-	3/21	0.247962226827837	1	FACETS	0.425	0.345	0.515	0.425	0.345	0.515	SUBCLONAL	1	TRUE	0	0.247962226827837	1		521	549	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120309	94120309	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011416-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	20	269	0	ENST00000369303.4:c.742A>G	p.Met248Val	p.M248V	ENST00000369303	NM_004440.3	248	Atg/Gtg	3/17	1	2	FACETS	0.466	0.356	0.594	0.466	0.356	0.594	SUBCLONAL	1	TRUE	1	0.277841754523675	2		269	309	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400800	56400800	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011416-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	14	220	0	ENST00000348428.3:c.1394G>C	p.Arg465Thr	p.R465T	ENST00000348428	NM_006785.3	465	aGg/aCg	11/17	1	2	FACETS	0.361	0.261	0.483	0.361	0.261	0.483	SUBCLONAL	1	TRUE	1	0.277841754523675	2		220	279	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442579	52442579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1312611941	NA	P-0011416-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	22	406	0	ENST00000460680.1:c.166C>T	p.Arg56Cys	p.R56C	ENST00000460680	NM_004656.3	56	Cgc/Tgc	4/17	1	2	FACETS	0.394	0.305	0.498	0.394	0.305	0.498	SUBCLONAL	1	TRUE	1	0.277841754523675	2		406	402	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257234	16257234	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011416-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	49	564	0	ENST00000375759.3:c.4499T>C	p.Ile1500Thr	p.I1500T	ENST00000375759	NM_015001.2	1500	aTt/aCt	11/15	NA	2	FACETS	0.514	0.434	0.602			1	INDETERMINATE	1	TRUE	NA	0.277841754523675	2		564	686	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088696	27088712	+	frameshift_variant	Frame_Shift_Del	DEL	TCAGCCTTATCTCCGCG	TCAGCCTTATCTCCGCG	-	novel	NA	P-0011416-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	95	693	1	ENST00000324856.7:c.2313_2329del	p.Leu771PhefsTer40	p.L771Ffs*40	ENST00000324856	NM_006015.4	769	TCAGCCTTATCTCCGCGt/t	7/20	1	2	FACETS	0.924	0.823	1	0.924	0.823	1	CLONAL	1	TRUE	1	0.277841754523675	2		694	740	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278201	15278201	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011416-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	75	575	0	ENST00000263388.2:c.5221G>C	p.Ala1741Pro	p.A1741P	ENST00000263388	NM_000435.2	1741	Gct/Cct	29/33	0.277841754523675	1	FACETS	0.756	0.663	0.856	0.756	0.663	0.856	SUBCLONAL	1	TRUE	0	0.277841754523675	1		575	615	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183148	56183213	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TATCTGTCCTTATTTTTGTTTTTAACATACAAGGTCATTTGCTGTGTTTGTTGACAGGTGCCAATT	TATCTGTCCTTATTTTTGTTTTTAACATACAAGGTCATTTGCTGTGTTTGTTGACAGGTGCCAATT	ACCAG	novel	NA	P-0011416-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	21	345	1	ENST00000399503.3:c.4115-57_4123delinsACCAG		p.X1372_splice	ENST00000399503	NM_005921.1	1372		18/20	0.171668399200732	2	FACETS	0.389	0.299	0.494	0.194	0.149	0.247	SUBCLONAL	1	TRUE	0	0.277841754523675	2		346	389	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347812	70347812	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011416-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	52	270	0	ENST00000374080.3:c.3051G>C	p.Trp1017Cys	p.W1017C	ENST00000374080		1017	tgG/tgC	22/45	1	1	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	0	0.277841754523675	1		270	320	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578245	7578245	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780072	NA	P-0012114-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1195	67	816	1	ENST00000269305.4:c.604C>T	p.Arg202Cys	p.R202C	ENST00000269305	NM_001126112.2	202	Cgt/Tgt	6/11	0.142780124822936	2	FACETS	0.584	0.506	0.67	0.292	0.253	0.335	SUBCLONAL	1	TRUE	0	0.181718423949238	2		817	1262	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519992	NA	P-0012114-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	145	825	1	ENST00000269305.4:c.641A>T	p.His214Leu	p.H214L	ENST00000269305	NM_001126112.2	214	cAt/cTt	6/11	0.142780124822936	2	FACETS	1	0.981	1	0.649	0.591	0.711	CLONAL	1	TRUE	0	0.181718423949238	2		826	1229	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444401	50444401	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012895-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	342	730	1	ENST00000331340.3:c.331C>T	p.Arg111Ter	p.R111*	ENST00000331340	NM_006060.4	111	Cga/Tga	4/8	0.250919320447577	5	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	TRUE	2	0.250919320447577	5		731	1202	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793336	139793336	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012895-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	86	554	0	ENST00000247668.2:c.144G>T	p.Gln48His	p.Q48H	ENST00000247668	NM_021138.3	48	caG/caT	2/11	0.189010836977907	4	FACETS	0.954	0.842	1	0.477	0.421	0.537	CLONAL	1	TRUE	2	0.250919320447577	4		554	899	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50751282	50751282	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012895-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	191	583	0	ENST00000307179.4:c.421A>G	p.Thr141Ala	p.T141A	ENST00000307179		141	Aca/Gca	5/20	0.189010836977907	4	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	2	0.250919320447577	4		583	928	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0013160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	206	742	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	1	2	FACETS	0.841	0.787	0.896	1	0.995	1	CLONAL	3	TRUE	1	0.308027789103501	2		742	530	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185195118	185195118	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	52	671	1	ENST00000265026.3:c.2435G>T	p.Gly812Val	p.G812V	ENST00000265026	NM_004721.4	812	gGa/gTa	12/14	0.249923318532747	0	FACETS	0.431	0.367	0.502			1	SUBCLONAL	1	TRUE	0	0.308027789103501	0		672	542	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935283	36935283	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	260	1168	0	ENST00000361632.4:c.1444A>T	p.Asn482Tyr	p.N482Y	ENST00000361632		482	Aat/Tat	10/16	1	2	FACETS	1	0.987	1	1	0.996	1	CLONAL	2	TRUE	1	0.308027789103501	2		1168	727	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643632	52643632	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	92	467	0	ENST00000394830.3:c.2264T>A	p.Val755Asp	p.V755D	ENST00000394830	NM_018313.4	755	gTc/gAc	17/30	0.308027789103501	3	FACETS	0.831	0.742	0.923	0.554	0.495	0.616	CLONAL	2	TRUE	0	0.308027789103501	3		467	415	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0013538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	83	401	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.746	0.657	0.841	0.746	0.657	0.841	SUBCLONAL	1	TRUE	1	0.268391894050748	2		401	829	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593405	48593405	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	63	560	2	ENST00000342988.3:c.1156G>C	p.Gly386Arg	p.G386R	ENST00000342988	NM_005359.5	386	Ggt/Cgt	10/12	0.255057183553911	1	FACETS	0.587	0.507	0.674	0.587	0.507	0.674	SUBCLONAL	1	TRUE	0	0.268391894050748	1		562	692	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81902830	81902830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766422892	NA	P-0013538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	85	877	2	ENST00000359376.3:c.491G>A	p.Arg164Gln	p.R164Q	ENST00000359376	NM_002661.3	164	cGa/cAa	6/33	0.255057183553911	1	FACETS	0.509	0.449	0.574	0.509	0.449	0.574	SUBCLONAL	1	TRUE	0	0.268391894050748	1		879	1077	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117571	70117572	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0013538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	101	572	0	ENST00000245479.2:c.40dup	p.Gln14ProfsTer238	p.Q14Pfs*238	ENST00000245479	NM_000346.3	13	-/C	1/3	0.255057183553911	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.268391894050748	1		572	610	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918712	44918712	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	76	466	0	ENST00000377967.4:c.1194+1G>A		p.X398_splice	ENST00000377967	NM_021140.2	398			0.268391894050748	1	FACETS	0.761	0.668	0.862	0.761	0.668	0.862	SUBCLONAL	1	TRUE	0	0.268391894050748	1		466	644	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554625	29554626	+	splice_donor_variant	Splice_Site	INS	-	-	A	novel	NA	P-0013978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	56	353	2	ENST00000356175.3:c.2409+1_2409+2insA		p.X803_splice	ENST00000356175	NM_000267.3	803			1	2	FACETS	0.917	0.785	1	0.917	0.785	1	CLONAL	1	TRUE	1	0.19	2		355	643	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221302	1221302	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	93	470	1	ENST00000326873.7:c.827del	p.Gly276AlafsTer11	p.G276Afs*11	ENST00000326873	NM_000455.4	275	ccG/cc	6/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.19	2		471	761	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754979	29754979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	26	187	0	ENST00000389048.3:c.956C>T	p.Ser319Phe	p.S319F	ENST00000389048	NM_004304.4	319	tCc/tTc	4/29	1	2	FACETS	0.655	0.518	0.812	0.655	0.518	0.812	SUBCLONAL	1	TRUE	1	0.19	2		187	418	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524156	187524156	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	60	352	1	ENST00000441802.2:c.11383G>T	p.Glu3795Ter	p.E3795*	ENST00000441802	NM_005245.3	3795	Gaa/Taa	20/27	1	2	FACETS	0.834	0.718	0.962	0.834	0.718	0.962	CLONAL	1	TRUE	1	0.19	2		353	757	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593603	55593603	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913235	NA	P-0014307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	51	388	0	ENST00000288135.5:c.1669T>G	p.Trp557Gly	p.W557G	ENST00000288135	NM_000222.2	557	Tgg/Ggg	11/21	0.268898579386292	1	FACETS	0.574	0.487	0.669	0.574	0.487	0.669	SUBCLONAL	1	FALSE	0	0.268898579386292	1		388	572	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	36	197	0	ENST00000256196.4:c.68G>T	p.Gly23Val	p.G23V	ENST00000256196		23	gGc/gTc	1/6	0.268898579386292	1	FACETS	0.569	0.468	0.683	0.569	0.468	0.683	SUBCLONAL	1	FALSE	0	0.268898579386292	1		197	407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577519	7577527	+	inframe_deletion	In_Frame_Del	DEL	GATGGTGAG	GATGGTGAG	-	novel	NA	P-0014307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	86	574	0	ENST00000269305.4:c.754_762del	p.Leu252_Ile254del	p.L252_I254del	ENST00000269305	NM_001126112.2	252	CTCACCATC/-	7/11	0.176420702764825	2	FACETS	1	0.921	1	0.525	0.465	0.589	CLONAL	1	FALSE	0	0.268898579386292	2		574	609	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0014525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	513	781	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.292132779638618	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.29	2		781	1713	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880957	134880957	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	154	684	0	ENST00000398015.3:c.1520G>T	p.Arg507Leu	p.R507L	ENST00000398015	NM_004441.4	507	cGt/cTt	7/16	0.285669460798425	1	FACETS	0.982	0.898	1	0.982	0.898	1	CLONAL	1	TRUE	0	0.29	1		684	925	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913444	NA	P-0014525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	406	645	0	ENST00000275493.2:c.2582T>G	p.Leu861Arg	p.L861R	ENST00000275493	NM_005228.3	861	cTg/cGg	21/28	0.292132779638618	2	FACETS	0.996	0.947	1	0.996	0.947	1	CLONAL	2	TRUE	0	0.29	2		645	1405	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937066	48937068	+	stop_gained	Nonsense_Mutation	TNP	TAA	TAA	AAG	novel	NA	P-0014525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	100	424	1	ENST00000267163.4:c.834_836delinsAAG	p.Cys278_Lys279delinsTer	p.C278_K279delins*	ENST00000267163	NM_000321.2	278	tgTAAa/tgAAGa	8/27	0.304134760986588	1	FACETS	0.85	0.759	0.945	0.85	0.759	0.945	CLONAL	1	TRUE	0	0.29	1		425	694	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0014867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	28	112	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.462776576408605	3	FACETS	0.835	0.674	1	0.418	0.337	0.508	CLONAL	1	TRUE	1	0.48051969589841	3		112	173	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0014867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	221	500	11	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.306865677724018	2	FACETS	0.833	0.782	0.885	0.833	0.782	0.885	CLONAL	2	TRUE	0	0.48051969589841	2		511	552	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883551	37883551	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	76	683	0	ENST00000269571.5:c.3163G>T	p.Gly1055Cys	p.G1055C	ENST00000269571		1055	Ggc/Tgc	26/27	0.134574199383019	5	FACETS	0.955	0.839	1			1	INDETERMINATE	1	TRUE	NA	0.48051969589841	5		683	570	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	242	404	0	ENST00000346208.3:c.878T>G	p.Met293Arg	p.M293R	ENST00000346208		293	aTg/aGg	4/6	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.57	2		404	730	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354255	70354255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	204	573	0	ENST00000374080.3:c.4666G>A	p.Glu1556Lys	p.E1556K	ENST00000374080		1556	Gag/Aag	34/45	0.100022826283718	0	FACETS	0.364	0.338	0.391			1	INDETERMINATE	1	TRUE	0	0.57	0		573	846	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060780	38060797	+	inframe_deletion	In_Frame_Del	DEL	GTTGATGGAGAACGGGTG	GTTGATGGAGAACGGGTG	-	novel	NA	P-0014926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	323	835	0	ENST00000250448.2:c.1192_1209del	p.His398_Asn403del	p.H398_N403del	ENST00000250448	NM_004496.3	398	CACCCGTTCTCCATCAAC/-	2/2	1	2	FACETS	0.98	0.925	1	0.98	0.925	1	CLONAL	1	TRUE	1	0.57	2		835	1157	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061189	38061206	+	inframe_deletion	In_Frame_Del	DEL	TTGAAGCGCTTCTGGCGG	TTGAAGCGCTTCTGGCGG	-	novel	NA	P-0014926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	94	314	0	ENST00000250448.2:c.783_800del	p.Arg262_Lys267del	p.R262_K267del	ENST00000250448	NM_004496.3	261	cgCCGCCAGAAGCGCTTCAAg/cgg	2/2	1	2	FACETS	0.691	0.618	0.769	0.691	0.618	0.769	SUBCLONAL	1	TRUE	1	0.57	2		314	477	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226592	2226592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376766280	NA	P-0014926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	50	612	0	ENST00000398665.3:c.4072G>A	p.Gly1358Ser	p.G1358S	ENST00000398665	NM_032482.2	1358	Ggc/Agc	27/28	0.100022826283718	0	FACETS	0.103	0.086	0.12			1	INDETERMINATE	1	TRUE	0	0.57	0		612	735	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636989	176636989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	83	518	1	ENST00000439151.2:c.1589C>T	p.Pro530Leu	p.P530L	ENST00000439151	NM_022455.4	530	cCa/cTa	5/23	1	2	FACETS	0.336	0.295	0.379	0.336	0.295	0.379	SUBCLONAL	1	TRUE	1	0.57	2		519	868	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396278	139396278	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	210	603	1	ENST00000277541.6:c.5560C>A	p.Arg1854Ser	p.R1854S	ENST00000277541	NM_017617.3	1854	Cgc/Agc	30/34	1	2	FACETS	0.971	0.904	1	0.971	0.904	1	CLONAL	1	TRUE	1	0.57	2		604	759	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	104	462	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.294328131821651	2		462	555	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115904	8115904	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	124	532	0	ENST00000346208.3:c.1251del	p.Thr418ArgfsTer57	p.T418Rfs*57	ENST00000346208		417	aCc/ac	6/6	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.294328131821651	2		532	620	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0015289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	136	327	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.981	0.903	1	0.981	0.903	1	CLONAL	1	TRUE	1	0.755232040696084	2		327	367	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0015289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	408	556	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	1	2	FACETS	0.951	0.921	0.981	1	0.997	1	CLONAL	2	TRUE	1	0.755232040696084	2		556	568	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907602	76907602	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0015289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	244	361	0	ENST00000373344.5:c.4557+2T>G		p.X1519_splice	ENST00000373344	NM_000489.3	1519			1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.755232040696084	1		361	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579529	7579529	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658483	NA	P-0015437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	86	1154	2	ENST00000269305.4:c.158G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tGg/tAg	4/11	0.453604870994503	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.453604870994503	1		1156	274	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974821	15974821	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	29	636	0	ENST00000268712.3:c.4054del	p.His1352MetfsTer9	p.H1352Mfs*9	ENST00000268712	NM_006311.3	1352	Cat/at	30/46	0.453604870994503	1	FACETS	0.526	0.426	0.638	0.526	0.426	0.638	SUBCLONAL	1	TRUE	0	0.453604870994503	1		636	188	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	116	308	0	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	0.351773431512873	1	FACETS	0.906	0.819	0.997	0.906	0.819	0.997	CLONAL	1	TRUE	0	0.351773431512873	1		308	600	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780197	9780197	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751570218	NA	P-0016741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	171	534	2	ENST00000377346.4:c.1367C>T	p.Thr456Met	p.T456M	ENST00000377346	NM_005026.3	456	aCg/aTg	11/24	0.351773431512873	1	FACETS	0.852	0.784	0.924	0.852	0.784	0.924	CLONAL	1	TRUE	0	0.351773431512873	1		536	940	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0016741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	90	606	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.351773431512873	2		606	499	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260544	10260544	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1201583942	NA	P-0016741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	150	483	0	ENST00000340748.4:c.2318C>T	p.Pro773Leu	p.P773L	ENST00000340748		773	cCg/cTg	24/40	1	2	FACETS	0.86	0.785	0.938	0.86	0.785	0.938	CLONAL	1	TRUE	1	0.351773431512873	2		483	992	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216596	108216596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778080	NA	P-0016741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	52	262	0	ENST00000278616.4:c.8545C>T	p.Arg2849Ter	p.R2849*	ENST00000278616	NM_000051.3	2849	Cga/Tga	58/63	1	2	FACETS	0.741	0.633	0.859	0.741	0.633	0.859	SUBCLONAL	1	TRUE	1	0.351773431512873	2		262	399	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0016741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	86	462	0	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	0.309627961712804	3	FACETS	0.744	0.657	0.836	0.372	0.328	0.418	SUBCLONAL	1	TRUE	1	0.351773431512873	3		462	773	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	48	389	1	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	1	2	FACETS	0.982	0.836	1	0.982	0.836	1	CLONAL	1	TRUE	1	0.351773431512873	2		390	278	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158447	106158447	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	52	201	0	ENST00000380013.4:c.3353del	p.Asn1118IlefsTer19	p.N1118Ifs*19	ENST00000380013	NM_001127208.2	1116	atA/at	3/11	1	2	FACETS	0.692	0.591	0.803	0.692	0.591	0.803	SUBCLONAL	1	TRUE	1	0.351773431512873	2		201	427	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159109	24159109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1368176286	NA	P-0016741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	85	266	0	ENST00000263121.7:c.781C>T	p.Arg261Cys	p.R261C	ENST00000263121	NM_003073.3	261	Cgc/Tgc	6/9	1	2	FACETS	0.812	0.719	0.912	0.812	0.719	0.912	CLONAL	1	TRUE	1	0.351773431512873	2		266	595	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385182	41385182	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367872006	NA	P-0016741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	130	416	1	ENST00000373198.4:c.779G>A	p.Arg260Gln	p.R260Q	ENST00000373198	NM_133170.3	260	cGg/cAg	6/32	0.327816631812207	4	FACETS	0.915	0.828	1	0.305	0.276	0.336	CLONAL	1	TRUE	1	0.351773431512873	4		417	1092	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144026	11144026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	165	464	0	ENST00000358026.2:c.3607C>T	p.Arg1203Cys	p.R1203C	ENST00000358026	NM_001128849.1	1203	Cgc/Tgc	26/36	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.351773431512873	2		464	911	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38946656	38946657	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	rs1458580558	NA	P-0016741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	41	193	0	ENST00000357387.3:c.4315-3dup		p.X1439_splice	ENST00000357387	NM_152756.3	1439			1	2	FACETS	0.709	0.592	0.837	0.709	0.592	0.837	SUBCLONAL	1	TRUE	1	0.351773431512873	2		193	329	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	242	740	7	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.351773431512873	2		747	1362	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259043	16259043	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	117	357	1	ENST00000375759.3:c.6313del	p.Ala2105LeufsTer33	p.A2105Lfs*33	ENST00000375759	NM_015001.2	2103	aGg/ag	11/15	0.351773431512873	1	FACETS	0.909	0.822	1	0.909	0.822	1	CLONAL	1	TRUE	0	0.351773431512873	1		358	603	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850959	63850959	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	110	478	0	ENST00000279873.7:c.1737del	p.Cys580AlafsTer49	p.C580Afs*49	ENST00000279873	NM_032199.2	579	ctG/ct	10/10	1	2	FACETS	0.625	0.561	0.694	0.625	0.561	0.694	SUBCLONAL	1	TRUE	1	0.351773431512873	2		478	1000	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003788	45003788	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	81	261	0	ENST00000558401.1:c.44T>C	p.Leu15Pro	p.L15P	ENST00000558401	NM_004048.2	15	cTt/cCt	1/4	1	2	FACETS	0.919	0.812	1	0.919	0.812	1	CLONAL	1	TRUE	1	0.351773431512873	2		261	501	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993959	72993959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1244094531	NA	P-0016741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	130	455	0	ENST00000268489.5:c.86G>A	p.Ser29Asn	p.S29N	ENST00000268489	NM_006885.3	29	aGc/aAc	2/10	1	2	FACETS	0.942	0.854	1	0.942	0.854	1	CLONAL	1	TRUE	1	0.351773431512873	2		455	785	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40478139	40478139	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	155	471	0	ENST00000264657.5:c.1360C>A	p.Leu454Ile	p.L454I	ENST00000264657	NM_139276.2	454	Cta/Ata	15/24	0.309627961712804	3	FACETS	0.908	0.83	0.99	0.454	0.415	0.495	CLONAL	1	TRUE	1	0.351773431512873	3		471	1141	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4095439	4095441	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0016741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	134	581	0	ENST00000262948.5:c.991_993del	p.Pro331del	p.P331del	ENST00000262948	NM_030662.3	331	CCT/-	9/11	1	2	FACETS	0.669	0.607	0.736	0.669	0.607	0.736	SUBCLONAL	1	TRUE	1	0.351773431512873	2		581	1138	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350032	15350032	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	174	617	0	ENST00000263377.2:c.3620A>C	p.Gln1207Pro	p.Q1207P	ENST00000263377	NM_058243.2	1207	cAg/cCg	18/20	1	2	FACETS	0.896	0.824	0.972	0.896	0.824	0.972	CLONAL	1	TRUE	1	0.351773431512873	2		617	1104	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952496	17952496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	125	439	0	ENST00000458235.1:c.937G>A	p.Gly313Arg	p.G313R	ENST00000458235	NM_000215.3	313	Gga/Aga	7/24	1	2	FACETS	0.74	0.668	0.815	0.74	0.668	0.815	SUBCLONAL	1	TRUE	1	0.351773431512873	2		439	961	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220064	36220064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1232763910	NA	P-0016741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	156	804	4	ENST00000222270.7:c.4784C>T	p.Ala1595Val	p.A1595V	ENST00000222270	NM_014727.1	1595	gCg/gTg	22/37	1	2	FACETS	0.974	0.891	1	0.974	0.891	1	CLONAL	1	TRUE	1	0.351773431512873	2		808	911	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867536	45867536	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767916267	NA	P-0016741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	184	613	0	ENST00000391945.4:c.772C>T	p.Arg258Trp	p.R258W	ENST00000391945	NM_000400.3	258	Cgg/Tgg	9/23	1	2	FACETS	0.856	0.789	0.927	0.856	0.789	0.927	CLONAL	1	TRUE	1	0.351773431512873	2		613	1222	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	rs267608078	NA	P-0016741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	58	314	0	ENST00000234420.5:c.3260_3261dup	p.Phe1088ProfsTer3	p.F1088Pfs*3	ENST00000234420	NM_000179.2	1085	acc/aCCcc	5/10	1	2	FACETS	0.45	0.386	0.521	0.45	0.386	0.521	SUBCLONAL	1	TRUE	1	0.351773431512873	2		314	732	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021712	31021712	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	103	408	0	ENST00000375687.4:c.1711C>T	p.Pro571Ser	p.P571S	ENST00000375687	NM_015338.5	571	Ccc/Tcc	12/13	0.327816631812207	4	FACETS	0.73	0.651	0.813	0.243	0.217	0.271	SUBCLONAL	1	TRUE	1	0.351773431512873	4		408	1085	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818803	32818803	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs775370277	NA	P-0016741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	48	532	0	ENST00000354258.4:c.1148del	p.Gly383AspfsTer10	p.G383Dfs*10	ENST00000354258	NM_000593.5	383	gGa/ga	4/11	0.351773431512873	1	FACETS	0.256	0.216	0.302	0.256	0.216	0.302	SUBCLONAL	1	TRUE	0	0.351773431512873	1		532	877	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984022	2984022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753614569	NA	P-0016741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	154	361	1	ENST00000396946.4:c.508C>T	p.Arg170Cys	p.R170C	ENST00000396946	NM_032415.4	170	Cgc/Tgc	5/25	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.351773431512873	2		362	812	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98011519	98011519	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	119	401	1	ENST00000289081.3:c.55C>A	p.Leu19Ile	p.L19I	ENST00000289081	NM_000136.2	19	Ctt/Att	2/15	1	2	FACETS	0.773	0.697	0.853	0.773	0.697	0.853	SUBCLONAL	1	TRUE	1	0.351773431512873	2		402	875	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344973	70344973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756039521	NA	P-0016741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	90	493	0	ENST00000374080.3:c.2203G>A	p.Ala735Thr	p.A735T	ENST00000374080		735	Gcc/Acc	15/45	0.351773431512873	1	FACETS	0.575	0.51	0.645	0.575	0.51	0.645	SUBCLONAL	1	TRUE	0	0.351773431512873	1		493	733	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0017016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	226	326	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	1	2	FACETS	0.819	0.765	0.874	1	0.993	1	CLONAL	2	TRUE	1	0.36310976894495	2		326	760	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	748	860	0	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.36310976894495	2	FACETS	0.965	0.942	0.988	1	0.998	1	CLONAL	4	TRUE	0	0.36310976894495	2		860	1067	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597936	43597936	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	161	756	0	ENST00000355710.3:c.487del	p.Arg163GlyfsTer61	p.R163Gfs*61	ENST00000355710	NM_020975.4	162	Ccc/cc	3/20	0.36310976894495	1	FACETS	0.78	0.722	0.84	1	0.99	1	SUBCLONAL	2	TRUE	0	0.36310976894495	1		756	465	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918445	94918445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	223	513	0	ENST00000536441.1:c.737C>T	p.Ala246Val	p.A246V	ENST00000536441	NM_144665.3	246	gCa/gTa	5/10	1	2	FACETS	0.842	0.787	0.899	1	0.993	1	CLONAL	2	TRUE	1	0.36310976894495	2		513	729	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416383	49416384	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGATTTTCTCCCGCGGTTGGC	novel	NA	P-0017016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	28	366	0	ENST00000301067.7:c.16327_16328insGCCAACCGCGGGAGAAAATCT	p.Ile5442_Tyr5443insCysGlnProArgGluLysIle	p.I5442_Y5443insCQPREKI	ENST00000301067	NM_003482.3	5443	tac/tGCCAACCGCGGGAGAAAATCTac	51/54	1	2	FACETS	0.289	0.23	0.357	0.289	0.23	0.357	SUBCLONAL	1	TRUE	1	0.36310976894495	2		366	533	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681761	78681761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	244	524	1	ENST00000306801.3:c.469C>T	p.Arg157Trp	p.R157W	ENST00000306801	NM_020761.2	157	Cgg/Tgg	4/34	1	2	FACETS	0.991	0.931	1	1	0.995	1	CLONAL	2	TRUE	1	0.36310976894495	2		525	678	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129664	11129664	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0017016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	476	583	0	ENST00000358026.2:c.2470A>T	p.Lys824Ter	p.K824*	ENST00000358026	NM_001128849.1	824	Aag/Tag	17/36	1	2	FACETS	0.958	0.929	0.987	1	0.998	1	CLONAL	4	TRUE	1	0.36310976894495	2		583	684	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38135897	38135897	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	332	617	0	ENST00000317025.8:c.3794G>C	p.Cys1265Ser	p.C1265S	ENST00000317025	NM_023034.1	1265	tGt/tCt	22/24	1	2	FACETS	0.915	0.867	0.964	1	0.996	1	CLONAL	2	TRUE	1	0.36310976894495	2		617	999	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0017626-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	159	446	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.197558353375173	4	FACETS	0.8	0.733	0.869	0.8	0.733	0.869	SUBCLONAL	2	TRUE	2	0.281208518743074	4		446	906	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017626-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	130	693	1	ENST00000269305.4:c.475del	p.Ala159ProfsTer11	p.A159Pfs*11	ENST00000269305	NM_001126112.2	159	Gcc/cc	5/11	0.275451430510095	1	FACETS	0.905	0.821	0.994	0.905	0.821	0.994	CLONAL	1	TRUE	0	0.281208518743074	1		694	878	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851600	128851600	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017626-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	108	488	0	ENST00000249373.3:c.1925T>G	p.Val642Gly	p.V642G	ENST00000249373	NM_005631.4	642	gTg/gGg	11/12	0.197558353375173	4	FACETS	1	0.973	1	0.624	0.56	0.693	CLONAL	1	TRUE	2	0.281208518743074	4		488	788	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444259	50444259	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017626-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	71	546	0	ENST00000331340.3:c.189T>G	p.Ser63Arg	p.S63R	ENST00000331340	NM_006060.4	63	agT/agG	4/8	0.197558353375173	4	FACETS	0.666	0.58	0.76	0.333	0.29	0.38	SUBCLONAL	1	TRUE	2	0.281208518743074	4		546	971	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136831	55136832	+	missense_variant	Missense_Mutation	DNP	AA	AA	TT	novel	NA	P-0017933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	147	493	0	ENST00000257290.5:c.1153_1154inv	p.Lys385Leu	p.K385L	ENST00000257290	NM_006206.4	385	AAg/TTg	8/23	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		493	742	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591085	67591085	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519839	NA	P-0018721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	250	262	1	ENST00000274335.5:c.1678G>T	p.Asp560Tyr	p.D560Y	ENST00000274335		560	Gac/Tac	12/15	0.43280069778285	3	FACETS	0.935	0.879	0.992	0.935	0.879	0.992	CLONAL	2	TRUE	1	0.464223983758074	3		263	710	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	387	438	0	ENST00000269305.4:c.517G>C	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ctg	5/11	0.464223983758074	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.464223983758074	2		438	811	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0018721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	110	455	6	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	0.464223983758074	3	FACETS	0.709	0.637	0.786	0.355	0.318	0.393	SUBCLONAL	1	TRUE	1	0.464223983758074	3		461	823	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0018721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	259	281	0	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	0.464223983758074	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.464223983758074	3		281	554	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056342	27056343	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0018721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	112	354	0	ENST00000324856.7:c.1338_1339del	p.Gln449AlafsTer173	p.Q449Afs*173	ENST00000324856	NM_006015.4	446	tcTTat/tcat	2/20	0.241572662535027	3	FACETS	0.806	0.732	0.882	0.806	0.732	0.882	INDETERMINATE	2	TRUE	1	0.464223983758074	3		354	369	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112017	115112017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1156821376	NA	P-0018721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	121	564	3	ENST00000257566.3:c.1723G>A	p.Ala575Thr	p.A575T	ENST00000257566	NM_016569.3	575	Gcg/Acg	7/8	0.464223983758074	3	FACETS	0.486	0.438	0.538	0.243	0.219	0.269	SUBCLONAL	1	TRUE	1	0.464223983758074	3		567	1321	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303882	30303882	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	217	474	1	ENST00000262643.3:c.118C>T	p.Gln40Ter	p.Q40*	ENST00000262643	NM_001238.2	40	Cag/Tag	4/12	0.238651118339984	5	FACETS	1	0.989	1	0.446	0.414	0.479	INDETERMINATE	1	TRUE	2	0.464223983758074	5		475	1185	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213921	66213921	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	47	344	1	ENST00000273854.3:c.2509G>T	p.Gly837Ter	p.G837*	ENST00000273854	NM_004439.5	837	Gga/Tga	15/18	0.43280069778285	3	FACETS	0.383	0.323	0.45	0.192	0.161	0.225	SUBCLONAL	1	TRUE	1	0.464223983758074	3		345	651	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404331	139404331	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	138	544	0	ENST00000277541.6:c.2823C>G	p.Phe941Leu	p.F941L	ENST00000277541	NM_017617.3	941	ttC/ttG	18/34	1	2	FACETS	0.502	0.455	0.551	0.502	0.455	0.551	SUBCLONAL	1	TRUE	1	0.464223983758074	2		544	1185	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	37	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.864	0.71	1	0.864	0.71	1	CLONAL	1	TRUE	1	0.11	2		426	779	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0018972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	13	761	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.425	0.302	0.577	0.425	0.302	0.577	SUBCLONAL	1	TRUE	1	0.11	2		761	556	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971166	21971167	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	56	1168	0	ENST00000304494.5:c.191dup	p.Leu65AlafsTer55	p.L65Afs*55	ENST00000304494	NM_000077.4	64	ctg/ctTg	2/3	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.11	2		1168	765	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0018972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	18	1170	1	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.438	0.328	0.569	0.438	0.328	0.569	SUBCLONAL	1	TRUE	1	0.11	2		1171	748	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0019192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	93	442	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.28	0.249	0.313	0.28	0.249	0.313	SUBCLONAL	1	TRUE	1	0.969107009970502	2		442	686	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167804	56167804	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	85	519	0	ENST00000399503.3:c.1369del	p.Thr457GlnfsTer30	p.T457Qfs*30	ENST00000399503	NM_005921.1	457	Aca/ca	7/20	1	2	FACETS	0.332	0.294	0.373	0.332	0.294	0.373	SUBCLONAL	1	TRUE	1	0.969107009970502	2		519	528	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181757	56181758	+	splice_acceptor_variant	Splice_Site	INS	-	-	G	novel	NA	P-0019192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	63	392	0	ENST00000399503.3:c.3986dup		p.X1329_splice	ENST00000399503	NM_005921.1	1329			1	2	FACETS	0.335	0.291	0.383	0.335	0.291	0.383	SUBCLONAL	1	TRUE	1	0.969107009970502	2		392	388	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339328	70339328	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0019457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	45	475	0	ENST00000374080.3:c.204+1G>T		p.X68_splice	ENST00000374080		68			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		475	462	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39644783	39644783	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	49	552	0	ENST00000262039.4:c.2512A>T	p.Thr838Ser	p.T838S	ENST00000262039	NM_002647.2	838	Act/Tct	23/25	1	2	FACETS	0.703	0.595	0.823	0.703	0.595	0.823	SUBCLONAL	1	FALSE	1	0.232256821702111	2		552	600	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095944	178095944	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	53	512	0	ENST00000397062.3:c.1387G>T	p.Ala463Ser	p.A463S	ENST00000397062	NM_006164.4	463	Gct/Tct	5/5	1	2	FACETS	0.918	0.784	1	0.918	0.784	1	CLONAL	1	FALSE	1	0.232256821702111	2		512	497	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034457	123034457	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	49	688	0	ENST00000355640.3:c.1214A>C	p.Lys405Thr	p.K405T	ENST00000355640		405	aAa/aCa	6/7	1	2	FACETS	0.696	0.589	0.815	0.696	0.589	0.815	SUBCLONAL	1	FALSE	1	0.232256821702111	2		688	606	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0020088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	205	686	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.361174597882687	2		686	948	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635167	87635167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	129	479	2	ENST00000277120.3:c.2219G>A	p.Ser740Asn	p.S740N	ENST00000277120		740	aGc/aAc	18/19	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.361174597882687	2		481	696	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22405072	22405072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	56	384	0	ENST00000344548.3:c.101C>T	p.Pro34Leu	p.P34L	ENST00000344548	NM_001039802.1	34	cCg/cTg	3/7	1	2	FACETS	0.573	0.491	0.663	0.573	0.491	0.663	SUBCLONAL	1	TRUE	1	0.361174597882687	2		384	541	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265771	41266375	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACC	GCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACC	-	novel	NA	P-0020088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	78	43	0	ENST00000349496.5:c.13+199_242-70del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.36112758318884	2	FACETS	1	0.973	1	1	0.989	1	CLONAL	4	TRUE	0	0.361174597882687	2		43	99	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749442	41749442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1476963248	NA	P-0020088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	119	436	1	ENST00000226382.2:c.353C>T	p.Ala118Val	p.A118V	ENST00000226382	NM_003924.3	118	gCg/gTg	2/3	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.361174597882687	2		437	629	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589590	67589604	+	inframe_deletion	In_Frame_Del	DEL	ATATAACACTCAGTT	ATATAACACTCAGTT	-	novel	NA	P-0020088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	208	495	0	ENST00000274335.5:c.1353_1367del	p.Glu451_Phe456delinsAsp	p.E451_F456delinsD	ENST00000274335		451	gaATATAACACTCAGTTt/gat	10/15	0.211058999835107	3	FACETS	1	0.953	1	0.685	0.638	0.732	INDETERMINATE	2	TRUE	0	0.361174597882687	3		495	662	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0020088-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	244	686	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.3110017708362	1	FACETS	1	0.941	1	1	0.941	1	INDETERMINATE	1	TRUE	0	0.521391914464575	1		686	691	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635167	87635167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020088-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	356	479	2	ENST00000277120.3:c.2219G>A	p.Ser740Asn	p.S740N	ENST00000277120		740	aGc/aAc	18/19	0.295302198825346	2	FACETS	0.902	0.861	0.943	0.902	0.861	0.943	INDETERMINATE	2	TRUE	0	0.521391914464575	2		481	757	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22405072	22405072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020088-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	87	384	0	ENST00000344548.3:c.101C>T	p.Pro34Leu	p.P34L	ENST00000344548	NM_001039802.1	34	cCg/cTg	3/7	0.3110017708362	1	FACETS	0.914	0.82	1	0.914	0.82	1	INDETERMINATE	1	TRUE	0	0.521391914464575	1		384	270	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265771	41266375	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACC	GCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACC	-	novel	NA	P-0020088-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	110	43	0	ENST00000349496.5:c.13+199_242-70del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.521391914464575	2	FACETS	1	0.949	1	1	0.991	1	CLONAL	3	TRUE	0	0.521391914464575	2		43	140	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749442	41749442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1476963248	NA	P-0020088-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	204	436	1	ENST00000226382.2:c.353C>T	p.Ala118Val	p.A118V	ENST00000226382	NM_003924.3	118	gCg/gTg	2/3	0.348270826260253	1	FACETS	0.898	0.837	0.961	0.898	0.837	0.961	CLONAL	1	TRUE	0	0.521391914464575	1		437	644	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589590	67589604	+	inframe_deletion	In_Frame_Del	DEL	ATATAACACTCAGTT	ATATAACACTCAGTT	-	novel	NA	P-0020088-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	147	495	0	ENST00000274335.5:c.1353_1367del	p.Glu451_Phe456delinsAsp	p.E451_F456delinsD	ENST00000274335		451	gaATATAACACTCAGTTt/gat	10/15	0.28414929911871	3	FACETS	1	0.972	1	0.731	0.679	0.785	INDETERMINATE	2	TRUE	0	0.521391914464575	3		495	324	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115967	8115995	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	TGGTCACCGCCATGGGTTAGAGCCCTGCT	TGGTCACCGCCATGGGTTAGAGCCCTGCT	-	novel	NA	P-0020544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	37	571	0	ENST00000346208.3:c.1313_*9del		p.*438*	ENST00000346208		438		6/6	1	2	FACETS	0.642	0.53	0.766	0.642	0.53	0.766	SUBCLONAL	1	FALSE	1	0.327392415870154	2		571	352	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737624	145737624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1287050785	NA	P-0020544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	150	1261	1	ENST00000428558.2:c.3139G>A	p.Glu1047Lys	p.E1047K	ENST00000428558	NM_004260.3	1047	Gag/Aag	19/22	1	2	FACETS	0.946	0.864	1	0.946	0.864	1	CLONAL	1	FALSE	1	0.327392415870154	2		1262	969	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	161	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.389105400123987	2		426	760	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36814336	36814336	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	37	714	0	ENST00000373129.3:c.704G>A	p.Gly235Glu	p.G235E	ENST00000373129	NM_032017.1	235	gGg/gAg	8/12	0.389105400123987	1	FACETS	0.212	0.174	0.255	0.212	0.174	0.255	SUBCLONAL	1	TRUE	0	0.389105400123987	1		714	722	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414679	56414679	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	76	613	1	ENST00000348428.3:c.2080G>A	p.Gly694Arg	p.G694R	ENST00000348428	NM_006785.3	694	Gga/Aga	17/17	1	2	FACETS	0.542	0.475	0.614	0.542	0.475	0.614	SUBCLONAL	1	TRUE	1	0.389105400123987	2		614	721	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222901	5222901	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	96	290	0	ENST00000357368.4:c.2902G>T	p.Ala968Ser	p.A968S	ENST00000357368	NM_002850.3	968	Gcc/Tcc	18/38	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.389105400123987	2		290	440	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955070	17955070	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1296361489	NA	P-0020613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	112	809	2	ENST00000458235.1:c.157C>A	p.Leu53Met	p.L53M	ENST00000458235	NM_000215.3	53	Ctg/Atg	2/24	1	2	FACETS	0.61	0.548	0.676	0.61	0.548	0.676	SUBCLONAL	1	TRUE	1	0.389105400123987	2		811	944	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197539	106197540	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	115	443	0	ENST00000380013.4:c.5875dup	p.Thr1959AsnfsTer56	p.T1959Nfs*56	ENST00000380013	NM_001127208.2	1958	gaa/gAaa	11/11	0.389105400123987	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.389105400123987	1		443	448	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	35	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.298	0.243	0.359	0.298	0.243	0.359	SUBCLONAL	1	TRUE	1	0.363518374148233	2		298	647	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0020646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	33	665	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.191	0.154	0.232	0.191	0.154	0.232	SUBCLONAL	1	TRUE	1	0.363518374148233	2		665	952	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0020970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	324	954	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.597882917799267	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.597882917799267	1		954	589	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557272	29557278	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATATAGG	ATATAGG	-	novel	NA	P-0020970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	106	408	0	ENST00000356175.3:c.2991-6_2991del		p.X997_splice	ENST00000356175	NM_000267.3	997		23/57	0.597882917799267	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.597882917799267	1		408	184	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244831	41244831	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs876659072	NA	P-0020970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	274	800	0	ENST00000357654.3:c.2717del	p.Lys906ArgfsTer94	p.K906Rfs*94	ENST00000357654	NM_007294.3	906	aAg/ag	10/23	0.597882917799267	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.597882917799267	1		800	514	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0021076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	101	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.154425061222396	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	3	FALSE	1	0.154425061222396	4		298	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0021147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	458	797	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.548661160156753	2		799	727	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0021147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	127	309	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.137495453993931	3	FACETS	1	0.985	1	0.706	0.645	0.769	INDETERMINATE	1	TRUE	1	0.548661160156753	3		309	418	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220064	36220064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1232763910	NA	P-0021147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	57	804	4	ENST00000222270.7:c.4784C>T	p.Ala1595Val	p.A1595V	ENST00000222270	NM_014727.1	1595	gCg/gTg	22/37	0.550641803328594	3	FACETS	0.314	0.268	0.364	0.157	0.134	0.182	SUBCLONAL	1	TRUE	1	0.548661160156753	3		808	843	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0021147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	95	402	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	0.137495453993931	3	FACETS	1	0.955	1	0.56	0.502	0.621	INDETERMINATE	1	TRUE	1	0.548661160156753	3		402	394	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663299	227663301	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs753296153	NA	P-0021147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	183	586	0	ENST00000305123.5:c.154_156del	p.Lys52del	p.K52del	ENST00000305123	NM_005544.2	52	AAG/-	1/2	0.333989421909739	3	FACETS	1	0.98	1	0.584	0.54	0.629	CLONAL	1	TRUE	1	0.548661160156753	3		586	728	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598132	55598132	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	88	547	1	ENST00000288135.5:c.2329G>A	p.Ala777Thr	p.A777T	ENST00000288135	NM_000222.2	777	Gca/Aca	16/21	0.269129511293215	4	FACETS	0.789	0.699	0.884	0.263	0.233	0.295	INDETERMINATE	1	TRUE	1	0.548661160156753	4		548	630	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110251222	110251222	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756574707	NA	P-0021147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	44	873	0	ENST00000374672.4:c.115G>A	p.Ala39Thr	p.A39T	ENST00000374672	NM_004235.4	39	Gcc/Acc	2/5	0.413220060236427	2	FACETS	0.212	0.177	0.252	0.106	0.088	0.126	SUBCLONAL	1	TRUE	0	0.548661160156753	2		873	755	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0021149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	125	112	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.872500607363422	3	FACETS	0.953	0.887	1	0.635	0.591	0.679	CLONAL	2	TRUE	0	0.872500607363422	3		112	216	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0021149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	813	556	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.872500607363422	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.872500607363422	3		556	862	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637689	52637689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	249	629	1	ENST00000394830.3:c.2627G>A	p.Arg876His	p.R876H	ENST00000394830	NM_018313.4	876	cGt/cAt	18/30	1	2	FACETS	0.956	0.901	1	0.956	0.901	1	CLONAL	1	TRUE	1	0.872500607363422	2		630	597	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273849	18273851	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0021149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	649	678	0	ENST00000222254.8:c.1184_1186del	p.Phe395del	p.F395del	ENST00000222254	NM_005027.3	394	acCTTc/acc	10/16	0.872500607363422	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.872500607363422	3		678	1023	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021299	31021299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	237	547	0	ENST00000375687.4:c.1298C>T	p.Ala433Val	p.A433V	ENST00000375687	NM_015338.5	433	gCa/gTa	12/13	0.872500607363422	3	FACETS	1	0.94	1	0.335	0.313	0.357	CLONAL	1	TRUE	0	0.872500607363422	3		547	777	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375973	8375973	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	153	383	0	ENST00000356435.5:c.4624A>C	p.Asn1542His	p.N1542H	ENST00000356435		1542	Aac/Cac	28/35	0.872500607363422	3	FACETS	0.969	0.892	1	0.484	0.446	0.524	CLONAL	1	TRUE	1	0.872500607363422	3		383	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0021221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	371	954	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.383214970268053	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	0	0.383214970268053	3		954	745	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0021221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	96	327	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.383214970268053	4	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	2	0.383214970268053	4		327	322	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120479957	120479957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	223	704	0	ENST00000256646.2:c.3470C>T	p.Pro1157Leu	p.P1157L	ENST00000256646	NM_024408.3	1157	cCc/cTc	21/34	0.383214970268053	5	FACETS	1	0.979	1	0.747	0.697	0.798	CLONAL	2	TRUE	2	0.383214970268053	5		704	818	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102196022	102196022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	46	322	0	ENST00000263464.3:c.782C>T	p.Thr261Ile	p.T261I	ENST00000263464	NM_001165.4	261	aCa/aTa	2/9	0.383214970268053	4	FACETS	0.796	0.672	0.933	0.398	0.336	0.467	CLONAL	1	TRUE	2	0.383214970268053	4		322	417	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117440	4117440	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	184	827	0	ENST00000262948.5:c.280T>C	p.Ser94Pro	p.S94P	ENST00000262948	NM_030662.3	94	Tcg/Ccg	2/11	0.383214970268053	4	FACETS	0.997	0.924	1	0.997	0.924	1	CLONAL	2	TRUE	2	0.383214970268053	4		827	666	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934190	39934190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146403660	NA	P-0021221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	196	858	0	ENST00000378444.4:c.409G>A	p.Val137Ile	p.V137I	ENST00000378444	NM_001123385.1	137	Gtc/Atc	4/15	0.383214970268053	3	FACETS	0.966	0.899	1			1	CLONAL	2	TRUE	NA	0.383214970268053	3		858	631	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907699	76907699	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0021221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	222	637	1	ENST00000373344.5:c.4462A>T	p.Lys1488Ter	p.K1488*	ENST00000373344	NM_000489.3	1488	Aaa/Taa	15/35	0.383214970268053	3	FACETS	0.955	0.892	1	0.955	0.892	1	CLONAL	2	TRUE	1	0.383214970268053	3		638	723	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	213	372	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.92776080164408	2		372	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0021320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	24	1055	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	0.92776080164408	1	FACETS	0.049	0.038	0.061	0.049	0.038	0.061	SUBCLONAL	1	TRUE	0	0.92776080164408	1		1055	570	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961321	54961321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs2230743	NA	P-0021320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	218	836	0	ENST00000312783.6:c.311C>T	p.Ser104Leu	p.S104L	ENST00000312783	NM_198436.1	104	tCg/tTg	4/10	1	2	FACETS	0.689	0.644	0.735	0.689	0.644	0.735	SUBCLONAL	1	TRUE	1	0.92776080164408	2		836	682	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939109	48939109	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0021320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	263	600	2	ENST00000267163.4:c.939+2T>A		p.X313_splice	ENST00000267163	NM_000321.2	313			0.92776080164408	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.92776080164408	1		602	290	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871674	35871674	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	40	787	2	ENST00000216797.5:c.832C>T	p.Gln278Ter	p.Q278*	ENST00000216797	NM_020529.2	278	Cag/Tag	5/6	1	2	FACETS	0.142	0.117	0.169	0.142	0.117	0.169	SUBCLONAL	1	TRUE	1	0.92776080164408	2		789	608	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457614	67457614	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253901433	NA	P-0021320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	319	979	2	ENST00000327367.4:c.424C>T	p.Arg142Cys	p.R142C	ENST00000327367	NM_005902.3	142	Cgc/Tgc	3/9	1	2	FACETS	0.87	0.826	0.916	0.87	0.826	0.916	CLONAL	1	TRUE	1	0.92776080164408	2		981	790	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935696	15935696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	30	622	0	ENST00000268712.3:c.7237C>T	p.Pro2413Ser	p.P2413S	ENST00000268712	NM_006311.3	2413	Cct/Tct	46/46	0.911484176593194	1	FACETS	0.11	0.089	0.135	0.11	0.089	0.135	SUBCLONAL	1	TRUE	0	0.92776080164408	1		622	314	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212428	36212428	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	411	1133	0	ENST00000222270.7:c.2179C>G	p.Leu727Val	p.L727V	ENST00000222270	NM_014727.1	727	Ctg/Gtg	3/37	1	2	FACETS	0.955	0.913	0.997	0.955	0.913	0.997	CLONAL	1	TRUE	1	0.92776080164408	2		1133	928	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665213	138665213	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	483	1142	1	ENST00000330315.3:c.352G>C	p.Glu118Gln	p.E118Q	ENST00000330315	NM_023067.3	118	Gag/Cag	1/1	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.92776080164408	2		1143	1018	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55270261	55270261	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	304	980	0	ENST00000275493.2:c.3214G>C	p.Asp1072His	p.D1072H	ENST00000275493	NM_005228.3	1072	Gac/Cac	27/28	1	2	FACETS	0.833	0.788	0.878	0.833	0.788	0.878	CLONAL	1	TRUE	1	0.92776080164408	2		980	787	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439637	140439637	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	314	703	0	ENST00000288602.6:c.2102G>C	p.Arg701Thr	p.R701T	ENST00000288602	NM_004333.4	701	aGa/aCa	17/18	1	2	FACETS	0.947	0.899	0.994	0.947	0.899	0.994	CLONAL	1	TRUE	1	0.92776080164408	2		703	715	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	530	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.470097063155767	4	FACETS	0.963	0.928	0.999	0.963	0.928	0.999	CLONAL	3	TRUE	1	0.513419737614762	4		426	1081	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0021536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	47	112	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.51175919898578	2	FACETS	1	0.875	1	0.511	0.438	0.59	CLONAL	1	TRUE	0	0.513419737614762	2		112	179	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577123	7577123	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876660333	NA	P-0021536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	314	419	0	ENST00000269305.4:c.815T>G	p.Val272Gly	p.V272G	ENST00000269305	NM_001126112.2	272	gTg/gGg	8/11	0.505677759707119	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.513419737614762	2		419	589	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190872	185190872	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	52	898	1	ENST00000265026.3:c.1753C>T	p.Arg585Ter	p.R585*	ENST00000265026	NM_004721.4	585	Cga/Tga	11/14	0.508207331694304	3	FACETS	0.289	0.245	0.338	0.145	0.122	0.169	SUBCLONAL	1	TRUE	1	0.513419737614762	3		899	880	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258977	16258977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751501193	NA	P-0021536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	166	480	1	ENST00000375759.3:c.6242G>A	p.Arg2081Gln	p.R2081Q	ENST00000375759	NM_015001.2	2081	cGa/cAa	11/15	1	2	FACETS	0.981	0.905	1	0.981	0.905	1	CLONAL	1	TRUE	1	0.513419737614762	2		481	659	SUCCESS
APC	324	MSKCC	GRCh37	5	112175074	112175074	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	131	144	0	ENST00000257430.4:c.3784del	p.Tyr1262IlefsTer3	p.Y1262Ifs*3	ENST00000257430	NM_000038.5	1261	acT/ac	16/16	0.513419737614762	2	FACETS	0.985	0.913	1	0.985	0.913	1	CLONAL	2	TRUE	0	0.513419737614762	2		144	259	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524304	176524304	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	329	410	0	ENST00000292408.4:c.2165T>A	p.Met722Lys	p.M722K	ENST00000292408	NM_213647.1	722	aTg/aAg	17/18	0.513419737614762	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.513419737614762	2		410	533	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411496	63411497	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0021536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	388	509	0	ENST00000330258.3:c.1670_1671del	p.Glu557GlyfsTer22	p.E557Gfs*22	ENST00000330258	NM_152424.3	557	gAG/g	2/2	0.433827580797394	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.513419737614762	4		509	1023	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021536-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	79	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	FALSE	1	0.257925549166903	2		426	599	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0021536-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	9	112	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.332	0.22	0.476	0.332	0.22	0.476	SUBCLONAL	1	FALSE	1	0.257925549166903	2		112	210	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577123	7577123	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876660333	NA	P-0021536-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	77	419	0	ENST00000269305.4:c.815T>G	p.Val272Gly	p.V272G	ENST00000269305	NM_001126112.2	272	gTg/gGg	8/11	1	2	FACETS	0.877	0.77	0.992	0.877	0.77	0.992	CLONAL	1	FALSE	1	0.257925549166903	2		419	681	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258977	16258977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751501193	NA	P-0021536-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	48	480	1	ENST00000375759.3:c.6242G>A	p.Arg2081Gln	p.R2081Q	ENST00000375759	NM_015001.2	2081	cGa/cAa	11/15	0.257925549166903	1	FACETS	0.409	0.344	0.48	0.409	0.344	0.48	SUBCLONAL	1	FALSE	0	0.257925549166903	1		481	793	SUCCESS
APC	324	MSKCC	GRCh37	5	112175074	112175074	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021536-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	22	144	0	ENST00000257430.4:c.3784del	p.Tyr1262IlefsTer3	p.Y1262Ifs*3	ENST00000257430	NM_000038.5	1261	acT/ac	16/16	1	2	FACETS	0.84	0.655	1	0.84	0.655	1	CLONAL	1	FALSE	1	0.257925549166903	2		144	203	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524304	176524304	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021536-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	82	410	0	ENST00000292408.4:c.2165T>A	p.Met722Lys	p.M722K	ENST00000292408	NM_213647.1	722	aTg/aAg	17/18	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	FALSE	1	0.257925549166903	2		410	613	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411496	63411497	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0021536-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	81	509	0	ENST00000330258.3:c.1670_1671del	p.Glu557GlyfsTer22	p.E557Gfs*22	ENST00000330258	NM_152424.3	557	gAG/g	2/2	1	2	FACETS	0.709	0.623	0.801	0.709	0.623	0.801	SUBCLONAL	1	FALSE	1	0.257925549166903	2		509	886	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	445	1119	1	ENST00000269305.4:c.383del	p.Pro128LeufsTer42	p.P128Lfs*42	ENST00000269305	NM_001126112.2	128	cCt/ct	5/11	0.654571663725097	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.654571663725097	1		1120	818	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433714	49433715	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGAGGGCGTAGTGG	novel	NA	P-0021782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	385	1207	0	ENST00000301067.7:c.7825_7838dup	p.Ser2614HisfsTer82	p.S2614Hfs*82	ENST00000301067	NM_003482.3	2613	ccg/ccCCACTACGCCCTCCg	31/54	0.654571663725097	4	FACETS	1	0.993	1	0.642	0.608	0.676	CLONAL	1	TRUE	2	0.654571663725097	4		1207	1517	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981793	70981793	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1603	1858	1116	0	ENST00000276594.2:c.303G>T	p.Trp101Cys	p.W101C	ENST00000276594	NM_024504.3	101	tgG/tgT	2/8	0.654571663725097	10	FACETS	0.989	0.97	1	0.989	0.97	1	CLONAL	6	TRUE	4	0.654571663725097	10		1116	3461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0021787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	145	564	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.180412336068952	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	0	0.180412336068952	2		564	781	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555240	226555240	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	32	744	0	ENST00000366794.5:c.2347G>C	p.Asp783His	p.D783H	ENST00000366794	NM_001618.3	783	Gat/Cat	17/23	0.180412336068952	3	FACETS	0.658	0.533	0.8	0.329	0.266	0.4	SUBCLONAL	1	TRUE	1	0.180412336068952	3		744	588	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506678	103506678	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1279673720	NA	P-0021787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	25	423	0	ENST00000355739.4:c.421A>G	p.Asn141Asp	p.N141D	ENST00000355739	NM_000123.3	141	Aac/Gac	4/15	0.180412336068952	3	FACETS	0.889	0.701	1	0.444	0.35	0.553	CLONAL	1	TRUE	1	0.180412336068952	3		423	340	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574790	95574790	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	19	486	0	ENST00000393063.1:c.2307C>A	p.Tyr769Ter	p.Y769*	ENST00000393063	NM_030621.3	769	taC/taA	16/28	0.180412336068952	3	FACETS	0.617	0.468	0.794	0.309	0.234	0.397	SUBCLONAL	1	TRUE	1	0.180412336068952	3		486	372	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880984	37880985	+	inframe_insertion	In_Frame_Ins	INS	-	-	TACGTGATGGCT	rs397516977	NA	P-0022097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	443	756	0	ENST00000269571.5:c.2314_2325dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/TACGTGATGGCT	20/27	0.419985159220016	3	FACETS	0.835	0.796	0.874	0.835	0.796	0.874	CLONAL	2	TRUE	1	0.497465230046802	3		756	1332	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	461396	461396	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	79	503	0	ENST00000399788.2:c.1124C>G	p.Ser375Cys	p.S375C	ENST00000399788	NM_001042603.1	375	tCt/tGt	9/28	0.423053883669063	1	FACETS	0.488	0.43	0.55	0.488	0.43	0.55	SUBCLONAL	1	TRUE	0	0.497465230046802	1		503	489	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30103718	30103718	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	1090	573	2	ENST00000331968.5:c.1220T>C	p.Met407Thr	p.M407T	ENST00000331968	NM_002742.2	407	aTg/aCg	8/18	0.497465230046802	8	FACETS	1	0.989	1			1	CLONAL	7	TRUE	NA	0.497465230046802	8		575	1538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577045	7577045	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	328	742	0	ENST00000269305.4:c.893del	p.Glu298GlyfsTer47	p.E298Gfs*47	ENST00000269305	NM_001126112.2	298	gAg/gg	8/11	0.497465230046802	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.497465230046802	1		742	672	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546098	41546098	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763211430	NA	P-0022097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	51	602	0	ENST00000263253.7:c.2713C>A	p.Pro905Thr	p.P905T	ENST00000263253	NM_001429.3	905	Cct/Act	14/31	0.280290430245184	2	FACETS	0.278	0.235	0.325	0.139	0.117	0.163	INDETERMINATE	1	TRUE	0	0.497465230046802	2		602	738	SUCCESS
APC	324	MSKCC	GRCh37	5	112173885	112173885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	338	371	0	ENST00000257430.4:c.2594C>T	p.Pro865Leu	p.P865L	ENST00000257430	NM_000038.5	865	cCa/cTa	16/16	0.497465230046802	3	FACETS	0.876	0.836	0.915	1	0.994	1	CLONAL	3	TRUE	1	0.497465230046802	3		371	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0022396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	462	723	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.822092440557611	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.822092440557611	2		723	525	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537975	212537975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267599192	NA	P-0022396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	50	454	0	ENST00000342788.4:c.1630C>T	p.Arg544Trp	p.R544W	ENST00000342788	NM_005235.2	544	Cgg/Tgg	14/28	0.821701094251656	4	FACETS	0.434	0.368	0.506	0.145	0.122	0.169	SUBCLONAL	1	TRUE	1	0.822092440557611	4		454	511	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189066	38189066	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2889	287	843	0	ENST00000317025.8:c.948G>C	p.Gln316His	p.Q316H	ENST00000317025	NM_023034.1	316	caG/caC	5/24	0.822092440557611	12	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.822092440557611	12		843	3176	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	111	309	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.112786725070591	3	FACETS	1	0.976	1	0.623	0.565	0.683	INDETERMINATE	1	TRUE	1	0.6	3		309	386	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	147	723	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.976	0.897	1	0.976	0.897	1	CLONAL	1	TRUE	1	0.6	2		723	502	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	86	532	1	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	1	2	FACETS	0.992	0.888	1	0.992	0.888	1	CLONAL	1	TRUE	1	0.6	2		533	289	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	186	701	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.112786725070591	3	FACETS	1	0.968	1	0.541	0.501	0.583	INDETERMINATE	1	TRUE	1	0.6	3		701	745	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291067	11291067	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	70	666	0	ENST00000361445.4:c.2694G>T	p.Lys898Asn	p.K898N	ENST00000361445	NM_004958.3	898	aaG/aaT	18/58	0.3	1	FACETS	0.333	0.291	0.379	0.333	0.291	0.379	INDETERMINATE	1	TRUE	0	0.6	1		666	490	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317000	11317000	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	49	411	0	ENST00000361445.4:c.494G>T	p.Arg165Ile	p.R165I	ENST00000361445	NM_004958.3	165	aGa/aTa	4/58	0.3	1	FACETS	0.372	0.317	0.433	0.372	0.317	0.433	INDETERMINATE	1	TRUE	0	0.6	1		411	307	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256692	16256692	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	32	614	0	ENST00000375759.3:c.3957G>T	p.Gln1319His	p.Q1319H	ENST00000375759	NM_015001.2	1319	caG/caT	11/15	1	2	FACETS	0.256	0.208	0.311	0.256	0.208	0.311	SUBCLONAL	1	TRUE	1	0.6	2		614	416	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257959	16257959	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	120	616	0	ENST00000375759.3:c.5224T>C	p.Phe1742Leu	p.F1742L	ENST00000375759	NM_015001.2	1742	Ttt/Ctt	11/15	1	2	FACETS	0.948	0.863	1	0.948	0.863	1	CLONAL	1	TRUE	1	0.6	2		616	422	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260803	16260803	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150899650	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	125	593	1	ENST00000375759.3:c.8068G>A	p.Val2690Met	p.V2690M	ENST00000375759	NM_015001.2	2690	Gtg/Atg	11/15	1	2	FACETS	0.92	0.838	1	0.92	0.838	1	CLONAL	1	TRUE	1	0.6	2		594	453	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088709	27088709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373690941	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	180	775	2	ENST00000324856.7:c.2318C>T	p.Pro773Leu	p.P773L	ENST00000324856	NM_006015.4	773	cCg/cTg	7/20	1	2	FACETS	0.992	0.919	1	0.992	0.919	1	CLONAL	1	TRUE	1	0.6	2		777	605	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101301	27101301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746264786	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	138	727	0	ENST00000324856.7:c.4583G>A	p.Arg1528Gln	p.R1528Q	ENST00000324856	NM_006015.4	1528	cGa/cAa	18/20	1	2	FACETS	0.991	0.909	1	0.991	0.909	1	CLONAL	1	TRUE	1	0.6	2		727	464	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39317318	39317318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	120	638	1	ENST00000373001.3:c.868G>A	p.Asp290Asn	p.D290N	ENST00000373001	NM_022157.3	290	Gat/Aat	5/7	1	2	FACETS	0.871	0.792	0.954	0.871	0.792	0.954	CLONAL	1	TRUE	1	0.6	2		639	459	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322577	39322577	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	116	657	0	ENST00000373001.3:c.415G>T	p.Ala139Ser	p.A139S	ENST00000373001	NM_022157.3	139	Gca/Tca	2/7	1	2	FACETS	0.885	0.803	0.97	0.885	0.803	0.97	CLONAL	1	TRUE	1	0.6	2		657	437	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46714211	46714211	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	145	596	0	ENST00000371975.4:c.31G>A	p.Ala11Thr	p.A11T	ENST00000371975	NM_003579.3	11	Gcc/Acc	2/18	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.6	2		596	475	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439681	51439681	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	64	501	0	ENST00000262662.1:c.246C>A	p.Phe82Leu	p.F82L	ENST00000262662		82	ttC/ttA	4/4	1	2	FACETS	0.484	0.42	0.553	0.484	0.42	0.553	SUBCLONAL	1	TRUE	1	0.6	2		501	441	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444592	78444592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	140	466	2	ENST00000370768.2:c.97G>T	p.Asp33Tyr	p.D33Y	ENST00000370768	NM_003902.3	33	Gat/Tat	1/20	1	2	FACETS	0.922	0.845	1	0.922	0.845	1	CLONAL	1	TRUE	1	0.6	2		468	506	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497768	120497768	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781902176	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	59	595	4	ENST00000256646.2:c.2114G>A	p.Arg705His	p.R705H	ENST00000256646	NM_024408.3	705	cGc/cAc	13/34	1	2	FACETS	0.358	0.307	0.412	0.358	0.307	0.412	SUBCLONAL	1	TRUE	1	0.6	2		599	550	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874163	155874163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs977405637	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	207	735	1	ENST00000368323.3:c.368G>A	p.Arg123His	p.R123H	ENST00000368323	NM_006912.5	123	cGt/cAt	5/6	1	2	FACETS	0.996	0.928	1	0.996	0.928	1	CLONAL	1	TRUE	1	0.6	2		736	693	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874172	155874172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753425443	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	190	742	2	ENST00000368323.3:c.359G>A	p.Arg120Gln	p.R120Q	ENST00000368323	NM_006912.5	120	cGa/cAa	5/6	1	2	FACETS	0.94	0.872	1	0.94	0.872	1	CLONAL	1	TRUE	1	0.6	2		744	674	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729614	162729614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773580613	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	103	598	0	ENST00000367921.3:c.700G>A	p.Asp234Asn	p.D234N	ENST00000367921	NM_006182.2	234	Gat/Aat	8/18	1	2	FACETS	0.844	0.76	0.93	0.844	0.76	0.93	CLONAL	1	TRUE	1	0.6	2		598	407	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111074	193111074	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	86	412	0	ENST00000367435.3:c.607G>T	p.Asp203Tyr	p.D203Y	ENST00000367435	NM_024529.4	203	Gat/Tat	7/17	1	2	FACETS	0.952	0.852	1	0.952	0.852	1	CLONAL	1	TRUE	1	0.6	2		412	301	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111167	193111167	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	114	493	0	ENST00000367435.3:c.700C>T	p.Arg234Ter	p.R234*	ENST00000367435	NM_024529.4	234	Cga/Tga	7/17	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.6	2		493	351	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204512023	204512023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	110	518	0	ENST00000367182.3:c.623G>A	p.Ser208Asn	p.S208N	ENST00000367182	NM_001278516.1	208	aGc/aAc	8/11	1	2	FACETS	0.896	0.812	0.985	0.896	0.812	0.985	CLONAL	1	TRUE	1	0.6	2		518	409	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226568877	226568877	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	113	601	0	ENST00000366794.5:c.1192C>A	p.Leu398Ile	p.L398I	ENST00000366794	NM_001618.3	398	Ctc/Atc	9/23	1	2	FACETS	0.812	0.735	0.892	0.812	0.735	0.892	CLONAL	1	TRUE	1	0.6	2		601	464	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716095	243716095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	156	739	1	ENST00000263826.5:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000263826	NM_005465.4	367	Cga/Tga	10/13	1	2	FACETS	0.85	0.781	0.921	0.85	0.781	0.921	CLONAL	1	TRUE	1	0.6	2		740	612	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63662041	63662041	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs371476471	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	190	522	0	ENST00000279873.7:c.145A>G	p.Lys49Glu	p.K49E	ENST00000279873	NM_032199.2	49	Aag/Gag	2/10	0.3	4	FACETS	0.883	0.821	0.946			1	INDETERMINATE	2	TRUE	NA	0.6	4		522	574	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63760071	63760071	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751880754	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	126	374	1	ENST00000279873.7:c.724G>A	p.Asp242Asn	p.D242N	ENST00000279873	NM_032199.2	242	Gat/Aat	4/10	0.3	4	FACETS	0.804	0.734	0.876			1	INDETERMINATE	2	TRUE	NA	0.6	4		375	418	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63817029	63817029	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	116	338	0	ENST00000279873.7:c.1000G>A	p.Glu334Lys	p.E334K	ENST00000279873	NM_032199.2	334	Gaa/Aaa	6/10	0.3	4	FACETS	0.791	0.719	0.865			1	INDETERMINATE	2	TRUE	NA	0.6	4		338	391	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63817076	63817076	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	23	236	0	ENST00000279873.7:c.1047G>T	p.Gln349His	p.Q349H	ENST00000279873	NM_032199.2	349	caG/caT	6/10	0.3	4	FACETS	0.463	0.361	0.58			1	INDETERMINATE	1	TRUE	NA	0.6	4		236	265	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850636	63850636	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	72	372	1	ENST00000279873.7:c.1414G>T	p.Glu472Ter	p.E472*	ENST00000279873	NM_032199.2	472	Gaa/Taa	10/10	0.3	4	FACETS	0.967	0.849	1			1	INDETERMINATE	1	TRUE	NA	0.6	4		373	397	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450596	70450596	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	154	574	0	ENST00000373644.4:c.5440del	p.Ser1814ValfsTer9	p.S1814Vfs*9	ENST00000373644	NM_030625.2	1812	gtA/gt	12/12	1	2	FACETS	0.982	0.904	1	0.982	0.904	1	CLONAL	1	TRUE	1	0.6	2		574	523	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720741	89720741	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs371387815	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	13	185	1	ENST00000371953.3:c.892C>T	p.Gln298Ter	p.Q298*	ENST00000371953	NM_000314.4	298	Caa/Taa	8/9	1	2	FACETS	0.31	0.222	0.415	0.31	0.222	0.415	SUBCLONAL	1	TRUE	1	0.6	2		186	140	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258033	123258033	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	111	744	0	ENST00000358487.5:c.1648C>A	p.Leu550Ile	p.L550I	ENST00000358487	NM_000141.4	550	Ctt/Att	12/18	1	2	FACETS	0.845	0.764	0.928	0.845	0.764	0.928	CLONAL	1	TRUE	1	0.6	2		744	438	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279681	123279681	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	53	392	1	ENST00000358487.5:c.751C>T	p.Arg251Ter	p.R251*	ENST00000358487	NM_000141.4	251	Cga/Tga	7/18	1	2	FACETS	0.603	0.518	0.695	0.603	0.518	0.695	SUBCLONAL	1	TRUE	1	0.6	2		393	293	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154880	2154880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761163170	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	158	664	0	ENST00000434045.2:c.341G>A	p.Arg114His	p.R114H	ENST00000434045	NM_001127598.1	114	cGt/cAt	4/5	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.6	2		664	467	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456678	32456678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	97	444	1	ENST00000332351.3:c.214G>A	p.Asp72Asn	p.D72N	ENST00000332351	NM_024426.4	72	Gac/Aac	1/10	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.6	2		445	300	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132779	64132779	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776640922	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	97	616	3	ENST00000334205.4:c.913G>A	p.Asp305Asn	p.D305N	ENST00000334205	NM_003942.2	305	Gat/Aat	9/17	1	2	FACETS	0.865	0.777	0.956	0.865	0.777	0.956	CLONAL	1	TRUE	1	0.6	2		619	374	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577332	64577332	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1470227348	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	57	712	0	ENST00000312049.6:c.250T>C	p.Ser84Pro	p.S84P	ENST00000312049	NM_130799.2	84	Tct/Cct	2/10	1	2	FACETS	0.443	0.381	0.51	0.443	0.381	0.51	SUBCLONAL	1	TRUE	1	0.6	2		712	429	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514320	69514320	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	52	561	0	ENST00000294312.3:c.361G>C	p.Ala121Pro	p.A121P	ENST00000294312	NM_005117.2	121	Gct/Cct	3/3	1	2	FACETS	0.492	0.421	0.57	0.492	0.421	0.57	SUBCLONAL	1	TRUE	1	0.6	2		561	352	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047231	77047231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	169	629	1	ENST00000356341.3:c.1313G>A	p.Arg438Gln	p.R438Q	ENST00000356341	NM_002576.4	438	cGa/cAa	13/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.6	2		630	524	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94169032	94169032	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1264567817	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	127	595	0	ENST00000323929.3:c.1960G>T	p.Asp654Tyr	p.D654Y	ENST00000323929	NM_005591.3	654	Gac/Tac	18/20	1	2	FACETS	0.989	0.903	1	0.989	0.903	1	CLONAL	1	TRUE	1	0.6	2		595	428	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94923009	94923009	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	193	780	0	ENST00000536441.1:c.459A>C	p.Lys153Asn	p.K153N	ENST00000536441	NM_144665.3	153	aaA/aaC	4/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.6	2		780	623	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962516	100962516	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	135	613	0	ENST00000325455.5:c.1881C>A	p.Cys627Ter	p.C627*	ENST00000325455	NM_001202474.3	627	tgC/tgA	3/8	1	2	FACETS	0.865	0.791	0.943	0.865	0.791	0.943	CLONAL	1	TRUE	1	0.6	2		613	520	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996761	100996761	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	49	591	0	ENST00000325455.5:c.1766T>C	p.Val589Ala	p.V589A	ENST00000325455	NM_001202474.3	589	gTc/gCc	2/8	1	2	FACETS	0.403	0.342	0.47	0.403	0.342	0.47	SUBCLONAL	1	TRUE	1	0.6	2		591	405	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998793	100998793	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	53	632	0	ENST00000325455.5:c.1009A>C	p.Ser337Arg	p.S337R	ENST00000325455	NM_001202474.3	337	Agc/Cgc	1/8	1	2	FACETS	0.423	0.361	0.49	0.423	0.361	0.49	SUBCLONAL	1	TRUE	1	0.6	2		632	418	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195344	102195344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1220112786	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	178	564	1	ENST00000263464.3:c.104C>T	p.Thr35Met	p.T35M	ENST00000263464	NM_001165.4	35	aCg/aTg	2/9	1	2	FACETS	0.957	0.886	1	0.957	0.886	1	CLONAL	1	TRUE	1	0.6	2		565	620	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170554	108170554	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	130	567	2	ENST00000278616.4:c.5119G>T	p.Glu1707Ter	p.E1707*	ENST00000278616	NM_000051.3	1707	Gaa/Taa	34/63	1	2	FACETS	0.93	0.849	1	0.93	0.849	1	CLONAL	1	TRUE	1	0.6	2		569	466	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199820	108199820	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	106	420	0	ENST00000278616.4:c.7162C>T	p.Leu2388Phe	p.L2388F	ENST00000278616	NM_000051.3	2388	Ctc/Ttc	49/63	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.6	2		420	338	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199875	108199875	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs771994581	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	49	368	0	ENST00000278616.4:c.7217A>G	p.Lys2406Arg	p.K2406R	ENST00000278616	NM_000051.3	2406	aAa/aGa	49/63	1	2	FACETS	0.519	0.441	0.602	0.519	0.441	0.602	SUBCLONAL	1	TRUE	1	0.6	2		368	315	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416777	416777	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs373294922	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	81	388	0	ENST00000399788.2:c.3773A>G	p.Asp1258Gly	p.D1258G	ENST00000399788	NM_001042603.1	1258	gAt/gGt	23/28	0.3	2	FACETS	0.854	0.76	0.954			1	INDETERMINATE	1	TRUE	NA	0.6	2		388	316	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427295	427295	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	131	629	0	ENST00000399788.2:c.2874G>T	p.Lys958Asn	p.K958N	ENST00000399788	NM_001042603.1	958	aaG/aaT	19/28	0.3	2	FACETS	0.812	0.74	0.886			1	INDETERMINATE	1	TRUE	NA	0.6	2		629	538	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435382	18435382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	39	461	0	ENST00000266497.5:c.367G>A	p.Glu123Lys	p.E123K	ENST00000266497		123	Gaa/Aaa	1/31	0.3	2	FACETS	0.396	0.329	0.471			1	INDETERMINATE	1	TRUE	NA	0.6	2		461	328	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21623997	21623997	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759728105	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	73	322	0	ENST00000421138.2:c.1703C>T	p.Ser568Leu	p.S568L	ENST00000421138		568	tCg/tTg	15/16	0.3	2	FACETS	0.839	0.741	0.942			1	INDETERMINATE	1	TRUE	NA	0.6	2		322	290	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624504	21624504	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	214	785	0	ENST00000421138.2:c.1525A>C	p.Lys509Gln	p.K509Q	ENST00000421138		509	Aaa/Caa	14/16	0.3	2	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.6	2		785	688	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21627911	21627911	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs770499904	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	145	700	2	ENST00000421138.2:c.1219C>T	p.Arg407Ter	p.R407*	ENST00000421138		407	Cga/Tga	12/16	0.3	2	FACETS	0.926	0.85	1			1	INDETERMINATE	1	TRUE	NA	0.6	2		702	522	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233157	46233157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	33	437	0	ENST00000334344.6:c.1376C>T	p.Pro459Leu	p.P459L	ENST00000334344	NM_152641.2	459	cCt/cTt	11/21	0.112786725070591	3	FACETS	0.354	0.288	0.428	0.177	0.144	0.214	INDETERMINATE	1	TRUE	1	0.6	3		437	404	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416612	49416612	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	160	656	0	ENST00000301067.7:c.16099A>G	p.Thr5367Ala	p.T5367A	ENST00000301067	NM_003482.3	5367	Acc/Gcc	51/54	0.112786725070591	3	FACETS	1	0.984	1	0.628	0.579	0.679	INDETERMINATE	1	TRUE	1	0.6	3		656	552	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420778	49420778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1427665021	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	51	647	0	ENST00000301067.7:c.14971C>T	p.Arg4991Trp	p.R4991W	ENST00000301067	NM_003482.3	4991	Cgg/Tgg	48/54	0.112786725070591	3	FACETS	0.469	0.399	0.546	0.235	0.199	0.273	INDETERMINATE	1	TRUE	1	0.6	3		647	471	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495747	56495747	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	134	570	0	ENST00000267101.3:c.3937C>A	p.Leu1313Ile	p.L1313I	ENST00000267101	NM_001982.3	1313	Cta/Ata	28/28	0.112786725070591	3	FACETS	1	0.977	1	0.601	0.55	0.654	INDETERMINATE	1	TRUE	1	0.6	3		570	483	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864187	57864187	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	65	617	0	ENST00000228682.2:c.1664T>C	p.Val555Ala	p.V555A	ENST00000228682	NM_005269.2	555	gTc/gCc	12/12	0.112786725070591	3	FACETS	0.674	0.586	0.768	0.337	0.293	0.384	INDETERMINATE	1	TRUE	1	0.6	3		617	418	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864193	57864193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746398371	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	128	614	2	ENST00000228682.2:c.1670G>A	p.Arg557His	p.R557H	ENST00000228682	NM_005269.2	557	cGc/cAc	12/12	0.112786725070591	3	FACETS	1	0.984	1	0.675	0.617	0.734	INDETERMINATE	1	TRUE	1	0.6	3		616	411	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233378	69233378	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	96	484	0	ENST00000462284.1:c.1243G>T	p.Glu415Ter	p.E415*	ENST00000462284	NM_002392.5	415	Gaa/Taa	11/11	1	2	FACETS	0.889	0.799	0.983	0.889	0.799	0.983	CLONAL	1	TRUE	1	0.6	2		484	360	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112892416	112892416	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1488672907	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	73	657	1	ENST00000351677.2:c.574G>T	p.Asp192Tyr	p.D192Y	ENST00000351677	NM_002834.3	192	Gat/Tat	5/16	1	2	FACETS	0.494	0.433	0.559	0.494	0.433	0.559	SUBCLONAL	1	TRUE	1	0.6	2		658	493	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112508	115112508	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755311630	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	32	634	0	ENST00000257566.3:c.1232C>T	p.Ala411Val	p.A411V	ENST00000257566	NM_016569.3	411	gCg/gTg	7/8	1	2	FACETS	0.216	0.175	0.263	0.216	0.175	0.263	SUBCLONAL	1	TRUE	1	0.6	2		634	493	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117311	115117311	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	128	512	0	ENST00000257566.3:c.863A>C	p.Lys288Thr	p.K288T	ENST00000257566	NM_016569.3	288	aAg/aCg	4/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.6	2		512	368	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800928	120800928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1337094477	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	148	601	2	ENST00000257552.2:c.320G>A	p.Arg107Gln	p.R107Q	ENST00000257552	NM_002442.3	107	cGa/cAa	6/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.6	2		603	467	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133208920	133208920	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	48	607	0	ENST00000320574.5:c.6311T>G	p.Phe2104Cys	p.F2104C	ENST00000320574	NM_006231.2	2104	tTc/tGc	45/49	1	2	FACETS	0.39	0.33	0.456	0.39	0.33	0.456	SUBCLONAL	1	TRUE	1	0.6	2		607	410	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210831	133210831	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	68	914	0	ENST00000320574.5:c.5945T>G	p.Ile1982Ser	p.I1982S	ENST00000320574	NM_006231.2	1982	aTt/aGt	43/49	1	2	FACETS	0.425	0.37	0.485	0.425	0.37	0.485	SUBCLONAL	1	TRUE	1	0.6	2		914	533	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214650	133214650	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	138	579	0	ENST00000320574.5:c.5628G>T	p.Lys1876Asn	p.K1876N	ENST00000320574	NM_006231.2	1876	aaG/aaT	41/49	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.6	2		579	418	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623524	28623524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371030554	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	89	499	0	ENST00000241453.7:c.1033G>A	p.Val345Ile	p.V345I	ENST00000241453	NM_004119.2	345	Gta/Ata	8/24	0.183501993152667	3	FACETS	1	0.952	1	0.557	0.498	0.619	INDETERMINATE	1	TRUE	1	0.6	3		499	346	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32899248	32899248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375125172	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	74	478	1	ENST00000380152.3:c.352C>T	p.Arg118Cys	p.R118C	ENST00000380152		118	Cgc/Tgc	4/27	0.183501993152667	3	FACETS	0.699	0.614	0.79	0.349	0.307	0.395	INDETERMINATE	1	TRUE	1	0.6	3		479	459	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900639	32900639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41293469	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	117	484	1	ENST00000380152.3:c.520C>T	p.Arg174Cys	p.R174C	ENST00000380152		174	Cgt/Tgt	7/27	0.183501993152667	3	FACETS	1	0.98	1	0.642	0.584	0.702	INDETERMINATE	1	TRUE	1	0.6	3		485	395	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911500	32911500	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555283008	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	153	571	0	ENST00000380152.3:c.3008A>G	p.His1003Arg	p.H1003R	ENST00000380152		1003	cAc/cGc	11/27	0.183501993152667	3	FACETS	1	0.987	1	0.695	0.641	0.751	INDETERMINATE	1	TRUE	1	0.6	3		571	477	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912546	32912546	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs80358655	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	215	671	0	ENST00000380152.3:c.4054G>T	p.Asp1352Tyr	p.D1352Y	ENST00000380152		1352	Gat/Tat	11/27	0.183501993152667	3	FACETS	0.751	0.703	0.801	0.751	0.703	0.801	INDETERMINATE	2	TRUE	1	0.6	3		671	620	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914232	32914232	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	78	642	0	ENST00000380152.3:c.5740A>G	p.Ser1914Gly	p.S1914G	ENST00000380152		1914	Agc/Ggc	11/27	0.183501993152667	3	FACETS	0.635	0.559	0.717	0.318	0.279	0.359	INDETERMINATE	1	TRUE	1	0.6	3		642	532	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32920978	32920978	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs80358920	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	76	575	2	ENST00000380152.3:c.6952C>T	p.Arg2318Ter	p.R2318*	ENST00000380152		2318	Cga/Tga	13/27	0.183501993152667	3	FACETS	0.585	0.514	0.662	0.292	0.257	0.331	INDETERMINATE	1	TRUE	1	0.6	3		577	563	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335535	73335535	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	219	624	0	ENST00000377767.4:c.2636A>G	p.Asp879Gly	p.D879G	ENST00000377767	NM_014953.3	879	gAc/gGc	19/21	0.183501993152667	3	FACETS	0.777	0.727	0.827	0.777	0.727	0.827	INDETERMINATE	2	TRUE	1	0.6	3		624	611	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515335	103515335	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	103	428	0	ENST00000355739.4:c.1836G>T	p.Glu612Asp	p.E612D	ENST00000355739	NM_000123.3	612	gaG/gaT	8/15	0.183501993152667	3	FACETS	1	0.97	1	0.598	0.54	0.659	INDETERMINATE	1	TRUE	1	0.6	3		428	373	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066828	30066828	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	119	683	1	ENST00000331968.5:c.2303C>A	p.Ser768Tyr	p.S768Y	ENST00000331968	NM_002742.2	768	tCt/tAt	16/18	1	2	FACETS	0.881	0.801	0.965	0.881	0.801	0.965	CLONAL	1	TRUE	1	0.6	2		684	450	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135304	30135304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	125	642	0	ENST00000331968.5:c.514C>T	p.Arg172Cys	p.R172C	ENST00000331968	NM_002742.2	172	Cgt/Tgt	3/18	1	2	FACETS	0.875	0.797	0.956	0.875	0.797	0.956	CLONAL	1	TRUE	1	0.6	2		642	476	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135325	30135325	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	143	659	0	ENST00000331968.5:c.493G>T	p.Glu165Ter	p.E165*	ENST00000331968	NM_002742.2	165	Gaa/Taa	3/18	1	2	FACETS	0.959	0.88	1	0.959	0.88	1	CLONAL	1	TRUE	1	0.6	2		659	497	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582984	95582984	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	106	462	0	ENST00000393063.1:c.1558A>C	p.Ser520Arg	p.S520R	ENST00000393063	NM_030621.3	520	Agt/Cgt	11/28	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.6	2		462	337	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590756	95590756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746886465	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	119	532	0	ENST00000393063.1:c.1153C>T	p.Arg385Cys	p.R385C	ENST00000393063	NM_030621.3	385	Cgc/Tgc	9/28	1	2	FACETS	0.972	0.885	1	0.972	0.885	1	CLONAL	1	TRUE	1	0.6	2		532	408	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005631	42005631	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	45	482	0	ENST00000219905.7:c.3367G>T	p.Glu1123Ter	p.E1123*	ENST00000219905	NM_001164273.1	1123	Gaa/Taa	9/24	1	2	FACETS	0.5	0.422	0.585	0.5	0.422	0.585	SUBCLONAL	1	TRUE	1	0.6	2		482	300	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042302	42042302	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	65	664	0	ENST00000219905.7:c.6497C>A	p.Ser2166Tyr	p.S2166Y	ENST00000219905	NM_001164273.1	2166	tCt/tAt	17/24	1	2	FACETS	0.5	0.435	0.571	0.5	0.435	0.571	SUBCLONAL	1	TRUE	1	0.6	2		664	433	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707804	43707804	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	85	782	0	ENST00000382044.4:c.5077A>C	p.Thr1693Pro	p.T1693P	ENST00000382044	NM_001141980.1	1693	Aca/Cca	23/28	1	2	FACETS	0.462	0.409	0.519	0.462	0.409	0.519	SUBCLONAL	1	TRUE	1	0.6	2		782	613	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714141	43714141	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	183	801	0	ENST00000382044.4:c.4012G>T	p.Gly1338Ter	p.G1338*	ENST00000382044	NM_001141980.1	1338	Gga/Tga	19/28	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.6	2		801	602	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784525	43784525	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1048972918	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	174	722	1	ENST00000382044.4:c.149G>A	p.Arg50Gln	p.R50Q	ENST00000382044	NM_001141980.1	50	cGa/cAa	2/28	1	2	FACETS	0.919	0.85	0.991	0.919	0.85	0.991	CLONAL	1	TRUE	1	0.6	2		723	631	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007642	45007642	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	115	388	0	ENST00000558401.1:c.89A>G	p.Tyr30Cys	p.Y30C	ENST00000558401	NM_004048.2	30	tAc/tGc	2/4	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.6	2		388	339	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007791	45007791	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	112	595	0	ENST00000558401.1:c.238T>C	p.Trp80Arg	p.W80R	ENST00000558401	NM_004048.2	80	Tgg/Cgg	2/4	1	2	FACETS	0.784	0.709	0.863	0.784	0.709	0.863	SUBCLONAL	1	TRUE	1	0.6	2		595	476	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007876	45007876	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	156	544	0	ENST00000558401.1:c.323C>A	p.Ser108Ter	p.S108*	ENST00000558401	NM_004048.2	108	tCa/tAa	2/4	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.6	2		544	491	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669589	88669589	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	109	448	0	ENST00000360948.2:c.1309G>T	p.Gly437Ter	p.G437*	ENST00000360948	NM_001012338.2	437	Gga/Tga	12/19	1	2	FACETS	0.966	0.876	1	0.966	0.876	1	CLONAL	1	TRUE	1	0.6	2		448	376	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679272	88679272	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	43	648	0	ENST00000360948.2:c.766-1G>A		p.X256_splice	ENST00000360948	NM_001012338.2	256			1	2	FACETS	0.345	0.288	0.407	0.345	0.288	0.407	SUBCLONAL	1	TRUE	1	0.6	2		648	416	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799180	88799180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	123	740	0	ENST00000360948.2:c.205G>A	p.Ala69Thr	p.A69T	ENST00000360948	NM_001012338.2	69	Gcc/Acc	2/19	1	2	FACETS	0.974	0.888	1	0.974	0.888	1	CLONAL	1	TRUE	1	0.6	2		740	421	SUCCESS
BLM	641	MSKCC	GRCh37	15	91290717	91290717	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	98	424	0	ENST00000355112.3:c.95T>G	p.Phe32Cys	p.F32C	ENST00000355112	NM_000057.2	32	tTt/tGt	2/22	1	2	FACETS	0.915	0.824	1	0.915	0.824	1	CLONAL	1	TRUE	1	0.6	2		424	357	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303958	91303958	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	87	704	1	ENST00000355112.3:c.1355A>G	p.Glu452Gly	p.E452G	ENST00000355112	NM_000057.2	452	gAg/gGg	7/22	1	2	FACETS	0.556	0.493	0.622	0.556	0.493	0.622	SUBCLONAL	1	TRUE	1	0.6	2		705	522	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396626	396626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143341222	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	145	634	0	ENST00000262320.3:c.400G>A	p.Glu134Lys	p.E134K	ENST00000262320	NM_003502.3	134	Gag/Aag	2/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.6	2		634	432	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126107	2126107	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs796053491	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	178	775	0	ENST00000219476.3:c.2678T>C	p.Ile893Thr	p.I893T	ENST00000219476	NM_000548.3	893	aTa/aCa	24/42	1	2	FACETS	0.996	0.923	1	0.996	0.923	1	CLONAL	1	TRUE	1	0.6	2		775	596	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136735	2136735	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs377129517	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	143	825	0	ENST00000219476.3:c.4852G>A	p.Val1618Ile	p.V1618I	ENST00000219476	NM_000548.3	1618	Gtc/Atc	38/42	1	2	FACETS	0.951	0.873	1	0.951	0.873	1	CLONAL	1	TRUE	1	0.6	2		825	501	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644516	3644516	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1367749586	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	163	796	1	ENST00000294008.3:c.2098G>A	p.Gly700Arg	p.G700R	ENST00000294008	NM_032444.2	700	Ggg/Agg	10/15	1	2	FACETS	0.909	0.838	0.982	0.909	0.838	0.982	CLONAL	1	TRUE	1	0.6	2		797	598	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857706	9857706	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	84	485	0	ENST00000330684.3:c.3695C>T	p.Ser1232Phe	p.S1232F	ENST00000330684	NM_001134407.1	1232	tCc/tTc	13/13	1	2	FACETS	0.952	0.851	1	0.952	0.851	1	CLONAL	1	TRUE	1	0.6	2		485	294	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916198	9916198	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	51	631	1	ENST00000330684.3:c.2091C>A	p.Asn697Lys	p.N697K	ENST00000330684	NM_001134407.1	697	aaC/aaA	10/13	1	2	FACETS	0.466	0.397	0.54	0.466	0.397	0.54	SUBCLONAL	1	TRUE	1	0.6	2		632	365	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916260	9916260	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	35	504	0	ENST00000330684.3:c.2029T>G	p.Ser677Ala	p.S677A	ENST00000330684	NM_001134407.1	677	Tcc/Gcc	10/13	1	2	FACETS	0.398	0.327	0.477	0.398	0.327	0.477	SUBCLONAL	1	TRUE	1	0.6	2		504	293	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14022054	14022054	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	148	587	0	ENST00000311895.7:c.754T>G	p.Leu252Val	p.L252V	ENST00000311895	NM_005236.2	252	Tta/Gta	4/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.6	2		587	454	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029183	14029183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	95	373	0	ENST00000311895.7:c.1394C>T	p.Ser465Phe	p.S465F	ENST00000311895	NM_005236.2	465	tCt/tTt	8/11	1	2	FACETS	0.954	0.858	1	0.954	0.858	1	CLONAL	1	TRUE	1	0.6	2		373	332	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645297	67645297	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	119	559	2	ENST00000264010.4:c.562G>T	p.Asp188Tyr	p.D188Y	ENST00000264010	NM_006565.3	188	Gat/Tat	3/12	1	2	FACETS	0.938	0.853	1	0.938	0.853	1	CLONAL	1	TRUE	1	0.6	2		561	423	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993212	72993212	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	223	834	0	ENST00000268489.5:c.833G>T	p.Arg278Met	p.R278M	ENST00000268489	NM_006885.3	278	aGg/aTg	2/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.6	2		834	652	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81939108	81939108	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	81	475	0	ENST00000359376.3:c.1463A>C	p.Asp488Ala	p.D488A	ENST00000359376	NM_002661.3	488	gAc/gCc	15/33	1	2	FACETS	0.857	0.762	0.957	0.857	0.762	0.957	CLONAL	1	TRUE	1	0.6	2		475	315	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990399	81990399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199530350	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	186	715	0	ENST00000359376.3:c.3670C>T	p.Arg1224Cys	p.R1224C	ENST00000359376	NM_002661.3	1224	Cgc/Tgc	32/33	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.6	2		715	516	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349604	89349604	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs924589358	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	199	907	1	ENST00000301030.4:c.3346G>A	p.Ala1116Thr	p.A1116T	ENST00000301030	NM_001256183.1	1116	Gca/Aca	9/13	1	2	FACETS	0.995	0.925	1	0.995	0.925	1	CLONAL	1	TRUE	1	0.6	2		908	667	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350407	89350407	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	200	881	0	ENST00000301030.4:c.2543C>A	p.Ser848Ter	p.S848*	ENST00000301030	NM_001256183.1	848	tCa/tAa	9/13	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.6	2		881	636	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350882	89350882	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751750670	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	257	1072	1	ENST00000301030.4:c.2068G>A	p.Asp690Asn	p.D690N	ENST00000301030	NM_001256183.1	690	Gat/Aat	9/13	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.6	2		1073	841	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216782	7216782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324992597	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	99	549	1	ENST00000380728.2:c.641C>T	p.Ser214Leu	p.S214L	ENST00000380728		214	tCg/tTg	8/11	1	2	FACETS	0.912	0.821	1	0.912	0.821	1	CLONAL	1	TRUE	1	0.6	2		550	362	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	132	751	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	1	2	FACETS	0.924	0.845	1	0.924	0.845	1	CLONAL	1	TRUE	1	0.6	2		751	476	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16056687	16056687	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs767188997	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	156	605	2	ENST00000268712.3:c.755A>C	p.Lys252Thr	p.K252T	ENST00000268712	NM_006311.3	252	aAa/aCa	7/46	1	2	FACETS	0.947	0.872	1	0.947	0.872	1	CLONAL	1	TRUE	1	0.6	2		607	549	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528158	29528158	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs149739570	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	152	799	0	ENST00000356175.3:c.1166A>G	p.His389Arg	p.H389R	ENST00000356175	NM_000267.3	389	cAc/cGc	10/57	1	2	FACETS	0.937	0.861	1	0.937	0.861	1	CLONAL	1	TRUE	1	0.6	2		799	541	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627509	37627509	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs371684674	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	145	609	2	ENST00000447079.4:c.1424C>A	p.Ser475Tyr	p.S475Y	ENST00000447079	NM_015083.1	475	tCt/tAt	2/14	1	2	FACETS	0.94	0.863	1	0.94	0.863	1	CLONAL	1	TRUE	1	0.6	2		611	514	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37680983	37680983	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	144	571	0	ENST00000447079.4:c.3152G>A	p.Arg1051Gln	p.R1051Q	ENST00000447079	NM_015083.1	1051	cGa/cAa	12/14	1	2	FACETS	0.918	0.842	0.996	0.918	0.842	0.996	CLONAL	1	TRUE	1	0.6	2		571	523	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38504619	38504619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1240210247	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	102	773	1	ENST00000254066.5:c.230C>T	p.Ser77Leu	p.S77L	ENST00000254066	NM_000964.3	77	tCg/tTg	3/9	1	2	FACETS	0.588	0.527	0.653	0.588	0.527	0.653	SUBCLONAL	1	TRUE	1	0.6	2		774	578	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40857132	40857132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316478374	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	145	632	0	ENST00000428826.2:c.1909G>A	p.Glu637Lys	p.E637K	ENST00000428826		637	Gaa/Aaa	17/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.6	2		632	447	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244866	41244866	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	156	693	0	ENST00000357654.3:c.2682A>C	p.Lys894Asn	p.K894N	ENST00000357654	NM_007294.3	894	aaA/aaC	10/23	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.6	2		693	506	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246409	41246409	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs876659193	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	144	810	0	ENST00000357654.3:c.1139A>C	p.Gln380Pro	p.Q380P	ENST00000357654	NM_007294.3	380	cAg/cCg	10/23	1	2	FACETS	0.954	0.876	1	0.954	0.876	1	CLONAL	1	TRUE	1	0.6	2		810	503	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699412	47699412	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	85	446	0	ENST00000347630.2:c.96C>A	p.Phe32Leu	p.F32L	ENST00000347630	NM_001007230.1	32	ttC/ttA	4/11	1	2	FACETS	0.846	0.754	0.942	0.846	0.754	0.942	CLONAL	1	TRUE	1	0.6	2		446	335	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677945	58677945	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770413280	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	43	320	1	ENST00000305921.3:c.170C>T	p.Ala57Val	p.A57V	ENST00000305921	NM_003620.3	57	gCc/gTc	1/6	1	2	FACETS	0.571	0.481	0.669	0.571	0.481	0.669	SUBCLONAL	1	TRUE	1	0.6	2		321	251	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761219	59761219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs575998972	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	189	846	0	ENST00000259008.2:c.3188C>T	p.Ser1063Leu	p.S1063L	ENST00000259008	NM_032043.2	1063	tCg/tTg	20/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.6	2		846	622	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761357	59761357	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747907706	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	134	703	1	ENST00000259008.2:c.3050C>T	p.Pro1017Leu	p.P1017L	ENST00000259008	NM_032043.2	1017	cCg/cTg	20/20	1	2	FACETS	0.946	0.866	1	0.946	0.866	1	CLONAL	1	TRUE	1	0.6	2		704	472	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007506	62007506	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	135	732	0	ENST00000392795.3:c.361T>C	p.Tyr121His	p.Y121H	ENST00000392795	NM_001039933.1	121	Tac/Cac	3/6	1	2	FACETS	0.891	0.815	0.97	0.891	0.815	0.97	CLONAL	1	TRUE	1	0.6	2		732	505	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372094	45372094	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	136	743	0	ENST00000262160.6:c.1075A>G	p.Ser359Gly	p.S359G	ENST00000262160	NM_005901.5	359	Agc/Ggc	9/11	1	2	FACETS	0.933	0.854	1	0.933	0.854	1	CLONAL	1	TRUE	1	0.6	2		743	486	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45377685	45377685	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	76	427	0	ENST00000262160.6:c.744A>C	p.Glu248Asp	p.E248D	ENST00000262160	NM_005901.5	248	gaA/gaC	7/11	1	2	FACETS	0.844	0.748	0.946	0.844	0.748	0.946	CLONAL	1	TRUE	1	0.6	2		427	300	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604736	48604736	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	131	559	0	ENST00000342988.3:c.1558G>T	p.Glu520Ter	p.E520*	ENST00000342988	NM_005359.5	520	Gaa/Taa	12/12	1	2	FACETS	0.906	0.827	0.987	0.906	0.827	0.987	CLONAL	1	TRUE	1	0.6	2		559	482	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226642	1226642	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	68	473	0	ENST00000326873.7:c.1298A>G	p.Gln433Arg	p.Q433R	ENST00000326873	NM_000455.4	433	cAg/cGg	9/10	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.6	2		473	204	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211143	2211143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	60	807	1	ENST00000398665.3:c.1397G>A	p.Ser466Asn	p.S466N	ENST00000398665	NM_032482.2	466	aGc/aAc	15/28	1	2	FACETS	0.387	0.333	0.445	0.387	0.333	0.445	SUBCLONAL	1	TRUE	1	0.6	2		808	517	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117529	4117529	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1135401787	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	58	248	0	ENST00000262948.5:c.191T>C	p.Val64Ala	p.V64A	ENST00000262948	NM_030662.3	64	gTc/gCc	2/11	1	2	FACETS	0.997	0.87	1	0.997	0.87	1	CLONAL	1	TRUE	1	0.6	2		248	194	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214663	5214663	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	32	792	0	ENST00000357368.4:c.4403T>C	p.Leu1468Pro	p.L1468P	ENST00000357368	NM_002850.3	1468	cTg/cCg	29/38	1	2	FACETS	0.226	0.183	0.275	0.226	0.183	0.275	SUBCLONAL	1	TRUE	1	0.6	2		792	472	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220080	5220080	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375875548	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	100	669	2	ENST00000357368.4:c.3635G>A	p.Arg1212His	p.R1212H	ENST00000357368	NM_002850.3	1212	cGc/cAc	22/38	1	2	FACETS	0.923	0.832	1	0.923	0.832	1	CLONAL	1	TRUE	1	0.6	2		671	361	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10267124	10267124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751093624	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	155	696	1	ENST00000340748.4:c.1294G>A	p.Glu432Lys	p.E432K	ENST00000340748		432	Gaa/Aaa	17/40	1	2	FACETS	0.886	0.815	0.96	0.886	0.815	0.96	CLONAL	1	TRUE	1	0.6	2		697	583	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106922	11106922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	174	746	0	ENST00000358026.2:c.1627G>A	p.Asp543Asn	p.D543N	ENST00000358026	NM_001128849.1	543	Gac/Aac	10/36	1	2	FACETS	0.976	0.904	1	0.976	0.904	1	CLONAL	1	TRUE	1	0.6	2		746	594	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144518	11144518	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765989895	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	154	577	1	ENST00000358026.2:c.3850G>A	p.Asp1284Asn	p.D1284N	ENST00000358026	NM_001128849.1	1284	Gac/Aac	27/36	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.6	2		578	462	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954299	17954299	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	86	576	0	ENST00000458235.1:c.310T>G	p.Phe104Val	p.F104V	ENST00000458235	NM_000215.3	104	Ttt/Gtt	4/24	1	2	FACETS	0.821	0.733	0.915	0.821	0.733	0.915	CLONAL	1	TRUE	1	0.6	2		576	349	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273041	18273041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	166	773	1	ENST00000222254.8:c.931C>T	p.Pro311Ser	p.P311S	ENST00000222254	NM_005027.3	311	Ccg/Tcg	8/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.6	2		774	530	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313208	30313208	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	132	779	1	ENST00000262643.3:c.902C>A	p.Ala301Asp	p.A301D	ENST00000262643	NM_001238.2	301	gCt/gAt	10/12	1	2	FACETS	0.818	0.746	0.893	0.818	0.746	0.893	CLONAL	1	TRUE	1	0.6	2		780	538	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218664	36218664	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	133	774	0	ENST00000222270.7:c.4368C>A	p.Phe1456Leu	p.F1456L	ENST00000222270	NM_014727.1	1456	ttC/ttA	17/37	1	2	FACETS	0.947	0.866	1	0.947	0.866	1	CLONAL	1	TRUE	1	0.6	2		774	468	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229346	36229346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1452431678	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	159	591	3	ENST00000222270.7:c.8036G>A	p.Arg2679His	p.R2679H	ENST00000222270	NM_014727.1	2679	cGc/cAc	37/37	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.6	2		594	517	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229444	36229444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	66	530	0	ENST00000222270.7:c.8134C>T	p.Arg2712Trp	p.R2712W	ENST00000222270	NM_014727.1	2712	Cgg/Tgg	37/37	1	2	FACETS	0.685	0.599	0.777	0.685	0.599	0.777	SUBCLONAL	1	TRUE	1	0.6	2		530	321	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763489	41763489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201238916	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	116	594	0	ENST00000301178.4:c.2288G>A	p.Arg763His	p.R763H	ENST00000301178	NM_021913.4	763	cGc/cAc	19/20	1	2	FACETS	0.883	0.801	0.968	0.883	0.801	0.968	CLONAL	1	TRUE	1	0.6	2		594	438	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383653	42383653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555843732	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	108	662	0	ENST00000221972.3:c.428G>A	p.Arg143Gln	p.R143Q	ENST00000221972	NM_021601.3	143	cGa/cAa	3/5	1	2	FACETS	0.925	0.838	1	0.925	0.838	1	CLONAL	1	TRUE	1	0.6	2		662	389	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753836	42753836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1250639908	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	87	904	2	ENST00000222329.4:c.428G>A	p.Arg143His	p.R143H	ENST00000222329	NM_006494.2	143	cGc/cAc	4/4	1	2	FACETS	0.446	0.395	0.501	0.446	0.395	0.501	SUBCLONAL	1	TRUE	1	0.6	2		906	650	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793222	42793222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	145	735	0	ENST00000575354.2:c.1114G>A	p.Ala372Thr	p.A372T	ENST00000575354	NM_015125.3	372	Gcg/Acg	7/20	1	2	FACETS	0.9	0.826	0.977	0.9	0.826	0.977	CLONAL	1	TRUE	1	0.6	2		735	537	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797894	42797894	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1314616216	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	49	718	3	ENST00000575354.2:c.3946G>T	p.Gly1316Trp	p.G1316W	ENST00000575354	NM_015125.3	1316	Ggg/Tgg	16/20	1	2	FACETS	0.365	0.31	0.427	0.365	0.31	0.427	SUBCLONAL	1	TRUE	1	0.6	2		721	447	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860760	45860760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146632315	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	57	745	2	ENST00000391945.4:c.1349G>A	p.Arg450His	p.R450H	ENST00000391945	NM_000400.3	450	cGt/cAt	14/23	1	2	FACETS	0.497	0.428	0.572	0.497	0.428	0.572	SUBCLONAL	1	TRUE	1	0.6	2		747	382	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868194	45868194	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1032384332	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	62	752	1	ENST00000391945.4:c.496C>T	p.Arg166Cys	p.R166C	ENST00000391945	NM_000400.3	166	Cgt/Tgt	7/23	1	2	FACETS	0.44	0.38	0.504	0.44	0.38	0.504	SUBCLONAL	1	TRUE	1	0.6	2		753	470	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716301	52716301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	104	645	1	ENST00000322088.6:c.745C>T	p.Arg249Cys	p.R249C	ENST00000322088	NM_014225.5	249	Cgc/Tgc	6/15	1	2	FACETS	0.91	0.822	1	0.91	0.822	1	CLONAL	1	TRUE	1	0.6	2		646	381	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085680	16085680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776847158	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	79	742	0	ENST00000281043.3:c.856C>T	p.Arg286Cys	p.R286C	ENST00000281043	NM_005378.4	286	Cgt/Tgt	3/3	1	2	FACETS	0.474	0.418	0.535	0.474	0.418	0.535	SUBCLONAL	1	TRUE	1	0.6	2		742	555	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086001	16086001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	170	604	0	ENST00000281043.3:c.1177C>T	p.Arg393Cys	p.R393C	ENST00000281043	NM_005378.4	393	Cgc/Tgc	3/3	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.6	2		604	541	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25498386	25498386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1274769751	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	118	575	0	ENST00000264709.3:c.475G>A	p.Glu159Lys	p.E159K	ENST00000264709	NM_175629.2	159	Gaa/Aaa	5/23	1	2	FACETS	0.906	0.824	0.992	0.906	0.824	0.992	CLONAL	1	TRUE	1	0.6	2		575	434	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523076	25523076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	137	680	0	ENST00000264709.3:c.109G>A	p.Glu37Lys	p.E37K	ENST00000264709	NM_175629.2	37	Gag/Aag	3/23	1	2	FACETS	0.945	0.866	1	0.945	0.866	1	CLONAL	1	TRUE	1	0.6	2		680	483	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966873	25966873	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1271466699	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	115	645	2	ENST00000435504.4:c.2333del	p.Pro778GlnfsTer21	p.P778Qfs*21	ENST00000435504		778	cCa/ca	13/13	1	2	FACETS	0.833	0.755	0.915	0.833	0.755	0.915	CLONAL	1	TRUE	1	0.6	2		647	460	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967231	25967231	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	114	539	0	ENST00000435504.4:c.1975G>T	p.Asp659Tyr	p.D659Y	ENST00000435504		659	Gac/Tac	13/13	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.6	2		539	368	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982356	25982356	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	89	311	0	ENST00000435504.4:c.934C>T	p.Arg312Ter	p.R312*	ENST00000435504		312	Cga/Tga	9/13	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.6	2		311	279	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068387	26068387	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	57	605	0	ENST00000435504.4:c.103C>A	p.Leu35Ile	p.L35I	ENST00000435504		35	Ctt/Att	2/13	1	2	FACETS	0.344	0.295	0.398	0.344	0.295	0.398	SUBCLONAL	1	TRUE	1	0.6	2		605	552	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101038	26101038	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	126	630	0	ENST00000435504.4:c.54G>T	p.Lys18Asn	p.K18N	ENST00000435504		18	aaG/aaT	1/13	1	2	FACETS	0.83	0.756	0.907	0.83	0.756	0.907	CLONAL	1	TRUE	1	0.6	2		630	506	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456525	29456525	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	52	843	0	ENST00000389048.3:c.2393A>G	p.Asn798Ser	p.N798S	ENST00000389048	NM_004304.4	798	aAc/aGc	14/29	1	2	FACETS	0.305	0.259	0.355	0.305	0.259	0.355	SUBCLONAL	1	TRUE	1	0.6	2		843	568	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143132	30143132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1262491330	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	80	720	0	ENST00000389048.3:c.394G>A	p.Val132Met	p.V132M	ENST00000389048	NM_004304.4	132	Gtg/Atg	1/29	1	2	FACETS	0.796	0.707	0.89	0.796	0.707	0.89	SUBCLONAL	1	TRUE	1	0.6	2		720	335	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39240688	39240688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	65	651	0	ENST00000402219.2:c.2080C>T	p.Arg694Trp	p.R694W	ENST00000402219	NM_005633.3	694	Cgg/Tgg	13/23	1	2	FACETS	0.466	0.405	0.532	0.466	0.405	0.532	SUBCLONAL	1	TRUE	1	0.6	2		651	465	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656970	47656970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757276241	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	145	496	0	ENST00000233146.2:c.1166G>A	p.Arg389Gln	p.R389Q	ENST00000233146	NM_000251.2	389	cGa/cAa	7/16	1	2	FACETS	0.999	0.918	1	0.999	0.918	1	CLONAL	1	TRUE	1	0.6	2		496	484	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698180	47698180	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63751411	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	94	520	0	ENST00000233146.2:c.1738G>T	p.Glu580Ter	p.E580*	ENST00000233146	NM_000251.2	580	Gaa/Taa	11/16	1	2	FACETS	0.744	0.666	0.826	0.744	0.666	0.826	SUBCLONAL	1	TRUE	1	0.6	2		520	421	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703539	47703539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1203462814	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	129	694	1	ENST00000233146.2:c.2039G>A	p.Arg680Gln	p.R680Q	ENST00000233146	NM_000251.2	680	cGa/cAa	13/16	1	2	FACETS	0.984	0.899	1	0.984	0.899	1	CLONAL	1	TRUE	1	0.6	2		695	437	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47709930	47709930	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	70	505	0	ENST00000233146.2:c.2647A>C	p.Ile883Leu	p.I883L	ENST00000233146	NM_000251.2	883	Att/Ctt	16/16	1	2	FACETS	0.527	0.461	0.598	0.527	0.461	0.598	SUBCLONAL	1	TRUE	1	0.6	2		505	443	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47710035	47710035	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	94	446	0	ENST00000233146.2:c.2752A>C	p.Lys918Gln	p.K918Q	ENST00000233146	NM_000251.2	918	Aag/Cag	16/16	1	2	FACETS	0.906	0.813	1	0.906	0.813	1	CLONAL	1	TRUE	1	0.6	2		446	346	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026616	48026616	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	109	531	0	ENST00000234420.5:c.1494G>T	p.Lys498Asn	p.K498N	ENST00000234420	NM_000179.2	498	aaG/aaT	4/10	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.6	2		531	354	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149342	61149342	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	111	486	0	ENST00000295025.8:c.1532A>G	p.Asn511Ser	p.N511S	ENST00000295025	NM_002908.2	511	aAt/aGt	11/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.6	2		486	329	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266136	198266136	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	131	512	0	ENST00000335508.6:c.2484A>C	p.Arg828Ser	p.R828S	ENST00000335508	NM_012433.2	828	agA/agC	17/25	0.112786725070591	3	FACETS	1	0.977	1	0.604	0.552	0.658	INDETERMINATE	1	TRUE	1	0.6	3		512	470	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141632	202141632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764461240	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	130	578	0	ENST00000358485.4:c.920G>A	p.Arg307Gln	p.R307Q	ENST00000358485	NM_001080125.1	307	cGg/cAg	7/9	0.112786725070591	3	FACETS	1	0.965	1	0.556	0.507	0.606	INDETERMINATE	1	TRUE	1	0.6	3		578	507	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251876	212251876	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1553519044	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	41	312	0	ENST00000342788.4:c.3184-1G>T		p.X1062_splice	ENST00000342788	NM_005235.2	1062			0.112786725070591	3	FACETS	0.689	0.577	0.81	0.344	0.288	0.405	INDETERMINATE	1	TRUE	1	0.6	3		312	258	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285182	212285182	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	110	565	0	ENST00000342788.4:c.3119G>T	p.Arg1040Ile	p.R1040I	ENST00000342788	NM_005235.2	1040	aGa/aTa	25/28	0.112786725070591	3	FACETS	1	0.975	1	0.613	0.555	0.673	INDETERMINATE	1	TRUE	1	0.6	3		565	389	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495220	212495220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	189	654	0	ENST00000342788.4:c.2046G>T	p.Lys682Asn	p.K682N	ENST00000342788	NM_005235.2	682	aaG/aaT	17/28	0.112786725070591	3	FACETS	1	0.99	1	0.694	0.645	0.744	INDETERMINATE	1	TRUE	1	0.6	3		654	590	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225343000	225343000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371342121	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	227	888	2	ENST00000264414.4:c.2092G>A	p.Asp698Asn	p.D698N	ENST00000264414	NM_003590.4	698	Gac/Aac	15/16	0.112786725070591	3	FACETS	1	0.985	1	0.59	0.55	0.63	INDETERMINATE	1	TRUE	1	0.6	3		890	834	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422393	225422393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1417750087	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	169	642	0	ENST00000264414.4:c.247G>A	p.Glu83Lys	p.E83K	ENST00000264414	NM_003590.4	83	Gaa/Aaa	2/16	0.112786725070591	3	FACETS	1	0.982	1	0.605	0.559	0.653	INDETERMINATE	1	TRUE	1	0.6	3		642	605	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662061	227662061	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1466090544	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	112	674	0	ENST00000305123.5:c.1394A>G	p.Tyr465Cys	p.Y465C	ENST00000305123	NM_005544.2	465	tAt/tGt	1/2	0.112786725070591	3	FACETS	1	0.944	1	0.531	0.48	0.584	INDETERMINATE	1	TRUE	1	0.6	3		674	457	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662637	227662637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755496379	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	131	620	0	ENST00000305123.5:c.818C>T	p.Ser273Leu	p.S273L	ENST00000305123	NM_005544.2	273	tCg/tTg	1/2	0.112786725070591	3	FACETS	1	0.96	1	0.545	0.497	0.595	INDETERMINATE	1	TRUE	1	0.6	3		620	521	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523271	9523271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775109543	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	78	621	1	ENST00000353224.5:c.1966C>T	p.Arg656Trp	p.R656W	ENST00000353224	NM_177990.2	656	Cgg/Tgg	9/10	1	2	FACETS	0.398	0.349	0.45	0.398	0.349	0.45	SUBCLONAL	1	TRUE	1	0.6	2		622	654	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538366	9538366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	95	497	0	ENST00000353224.5:c.1632G>T	p.Gln544His	p.Q544H	ENST00000353224	NM_177990.2	544	caG/caT	7/10	1	2	FACETS	0.814	0.73	0.902	0.814	0.73	0.902	CLONAL	1	TRUE	1	0.6	2		497	389	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31015953	31015953	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745960978	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	53	494	1	ENST00000375687.4:c.275G>A	p.Arg92His	p.R92H	ENST00000375687	NM_015338.5	92	cGc/cAc	5/13	1	2	FACETS	0.535	0.459	0.618	0.535	0.459	0.618	SUBCLONAL	1	TRUE	1	0.6	2		495	330	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024947	31024947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	153	637	1	ENST00000375687.4:c.4432G>A	p.Ala1478Thr	p.A1478T	ENST00000375687	NM_015338.5	1478	Gca/Aca	13/13	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.6	2		638	467	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710547	40710547	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	149	707	0	ENST00000373198.4:c.4304A>G	p.Asn1435Ser	p.N1435S	ENST00000373198	NM_133170.3	1435	aAc/aGc	31/32	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.6	2		707	473	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743943	40743943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763964405	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	66	265	0	ENST00000373198.4:c.3052C>T	p.Arg1018Ter	p.R1018*	ENST00000373198	NM_133170.3	1018	Cga/Tga	23/32	1	2	FACETS	0.534	0.465	0.608	0.534	0.465	0.608	SUBCLONAL	1	TRUE	1	0.6	2		265	412	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827900	40827900	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	131	698	0	ENST00000373198.4:c.2528C>A	p.Ser843Tyr	p.S843Y	ENST00000373198	NM_133170.3	843	tCt/tAt	17/32	1	2	FACETS	0.88	0.804	0.96	0.88	0.804	0.96	CLONAL	1	TRUE	1	0.6	2		698	496	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911144	40911144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776134993	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	115	603	1	ENST00000373198.4:c.2161C>T	p.Arg721Cys	p.R721C	ENST00000373198	NM_133170.3	721	Cgt/Tgt	13/32	1	2	FACETS	0.998	0.908	1	0.998	0.908	1	CLONAL	1	TRUE	1	0.6	2		604	384	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944424	40944424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	115	763	0	ENST00000373198.4:c.2078C>A	p.Pro693His	p.P693H	ENST00000373198	NM_133170.3	693	cCt/cAt	12/32	1	2	FACETS	0.755	0.683	0.83	0.755	0.683	0.83	SUBCLONAL	1	TRUE	1	0.6	2		763	508	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076862	41076862	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs750249800	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	76	559	2	ENST00000373198.4:c.1558G>A	p.Glu520Lys	p.E520K	ENST00000373198	NM_133170.3	520	Gag/Aag	9/32	1	2	FACETS	0.812	0.719	0.91	0.812	0.719	0.91	CLONAL	1	TRUE	1	0.6	2		561	312	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268443	46268443	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	70	520	0	ENST00000371998.3:c.2830G>T	p.Asp944Tyr	p.D944Y	ENST00000371998		944	Gat/Tat	15/23	1	2	FACETS	0.654	0.573	0.739	0.654	0.573	0.739	SUBCLONAL	1	TRUE	1	0.6	2		520	357	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775499	39775499	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	157	764	2	ENST00000288319.7:c.521A>G	p.Asp174Gly	p.D174G	ENST00000288319	NM_182918.3	174	gAc/gGc	4/10	0.112786725070591	3	FACETS	1	0.986	1	0.657	0.605	0.709	INDETERMINATE	1	TRUE	1	0.6	3		766	518	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42842584	42842584	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147233451	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	73	725	2	ENST00000398585.3:c.1273G>A	p.Glu425Lys	p.E425K	ENST00000398585	NM_001135099.1	425	Gag/Aag	11/14	0.112786725070591	3	FACETS	0.621	0.545	0.704	0.311	0.272	0.352	INDETERMINATE	1	TRUE	1	0.6	3		727	509	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095890	29095890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555915471	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	57	720	0	ENST00000328354.6:c.944G>A	p.Gly315Glu	p.G315E	ENST00000328354	NM_007194.3	315	gGg/gAg	9/15	1	2	FACETS	0.339	0.291	0.392	0.339	0.291	0.392	SUBCLONAL	1	TRUE	1	0.6	2		720	560	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37628873	37628873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	138	698	1	ENST00000249071.6:c.193G>A	p.Asp65Asn	p.D65N	ENST00000249071	NM_002872.4	65	Gac/Aac	3/7	1	2	FACETS	0.922	0.844	1	0.922	0.844	1	CLONAL	1	TRUE	1	0.6	2		699	499	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546153	41546153	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	71	456	0	ENST00000263253.7:c.2768C>A	p.Ser923Tyr	p.S923Y	ENST00000263253	NM_001429.3	923	tCt/tAt	14/31	1	2	FACETS	0.548	0.48	0.621	0.548	0.48	0.621	SUBCLONAL	1	TRUE	1	0.6	2		456	432	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	90	362	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	1	2	FACETS	0.968	0.868	1	0.968	0.868	1	CLONAL	1	TRUE	1	0.6	2		362	310	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266655	41266655	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200968230	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	157	581	1	ENST00000349496.5:c.452G>A	p.Arg151His	p.R151H	ENST00000349496	NM_001904.3	151	cGt/cAt	4/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.6	2		582	492	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058692	47058692	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	146	728	0	ENST00000409792.3:c.7586A>G	p.Asp2529Gly	p.D2529G	ENST00000409792	NM_014159.6	2529	gAc/gGc	21/21	1	2	FACETS	0.871	0.799	0.945	0.871	0.799	0.945	CLONAL	1	TRUE	1	0.6	2		728	559	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162080	47162080	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	26	505	0	ENST00000409792.3:c.4046T>G	p.Phe1349Cys	p.F1349C	ENST00000409792	NM_014159.6	1349	tTt/tGt	3/21	1	2	FACETS	0.246	0.194	0.304	0.246	0.194	0.304	SUBCLONAL	1	TRUE	1	0.6	2		505	353	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637738	52637738	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	105	611	0	ENST00000394830.3:c.2578G>T	p.Glu860Ter	p.E860*	ENST00000394830	NM_018313.4	860	Gaa/Taa	18/30	1	2	FACETS	0.871	0.786	0.959	0.871	0.786	0.959	CLONAL	1	TRUE	1	0.6	2		611	402	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026810	71026810	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	116	473	0	ENST00000318789.4:c.1412C>A	p.Ala471Glu	p.A471E	ENST00000318789	NM_032682.5	471	gCa/gAa	16/21	1	2	FACETS	0.979	0.89	1	0.979	0.89	1	CLONAL	1	TRUE	1	0.6	2		473	395	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665096	138665096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758370933	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	56	308	0	ENST00000330315.3:c.469C>T	p.Pro157Ser	p.P157S	ENST00000330315	NM_023067.3	157	Ccc/Tcc	1/1	0.112786725070591	3	FACETS	1	0.93	1	0.557	0.483	0.635	INDETERMINATE	1	TRUE	1	0.6	3		308	218	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917555	178917555	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	160	603	0	ENST00000263967.3:c.430C>A	p.Leu144Met	p.L144M	ENST00000263967	NM_006218.2	144	Ctg/Atg	3/21	0.112786725070591	3	FACETS	1	0.988	1	0.702	0.648	0.757	INDETERMINATE	1	TRUE	1	0.6	3		603	494	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921533	178921533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	108	520	0	ENST00000263967.3:c.1015C>T	p.Leu339Phe	p.L339F	ENST00000263967	NM_006218.2	339	Ctt/Ttt	5/21	0.112786725070591	3	FACETS	1	0.955	1	0.548	0.495	0.603	INDETERMINATE	1	TRUE	1	0.6	3		520	427	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665375	182665375	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	103	508	0	ENST00000292782.4:c.566G>A	p.Arg189Lys	p.R189K	ENST00000292782	NM_020640.2	189	aGa/aAa	5/7	0.112786725070591	3	FACETS	1	0.933	1	0.523	0.471	0.577	INDETERMINATE	1	TRUE	1	0.6	3		508	427	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440346	187440346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	86	640	0	ENST00000232014.4:c.2021G>A	p.Arg674Gln	p.R674Q	ENST00000232014	NM_001130845.1	674	cGa/cAa	10/10	0.112786725070591	3	FACETS	0.621	0.55	0.697	0.311	0.275	0.349	INDETERMINATE	1	TRUE	1	0.6	3		640	600	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902755	1902755	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	81	783	0	ENST00000382891.5:c.374A>C	p.Lys125Thr	p.K125T	ENST00000382891	NM_133335.3	125	aAg/aCg	2/22	1	2	FACETS	0.438	0.386	0.494	0.438	0.386	0.494	SUBCLONAL	1	TRUE	1	0.6	2		783	616	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561767	55561767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780349712	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	105	511	1	ENST00000288135.5:c.157G>A	p.Glu53Lys	p.E53K	ENST00000288135	NM_000222.2	53	Gag/Aag	2/21	1	2	FACETS	0.928	0.839	1	0.928	0.839	1	CLONAL	1	TRUE	1	0.6	2		512	377	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589752	55589752	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	90	422	0	ENST00000288135.5:c.1234A>C	p.Lys412Gln	p.K412Q	ENST00000288135	NM_000222.2	412	Aaa/Caa	8/21	1	2	FACETS	0.987	0.886	1	0.987	0.886	1	CLONAL	1	TRUE	1	0.6	2		422	304	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599320	55599320	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913506	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	139	643	0	ENST00000288135.5:c.2446G>T	p.Asp816Tyr	p.D816Y	ENST00000288135	NM_000222.2	816	Gac/Tac	17/21	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.6	2		643	459	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955616	55955616	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	93	611	0	ENST00000263923.4:c.3329A>C	p.Lys1110Thr	p.K1110T	ENST00000263923	NM_002253.2	1110	aAg/aCg	25/30	1	2	FACETS	0.809	0.725	0.898	0.809	0.725	0.898	CLONAL	1	TRUE	1	0.6	2		611	383	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972940	55972940	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	160	810	0	ENST00000263923.4:c.1450G>T	p.Glu484Ter	p.E484*	ENST00000263923	NM_002253.2	484	Gaa/Taa	11/30	1	2	FACETS	0.929	0.856	1	0.929	0.856	1	CLONAL	1	TRUE	1	0.6	2		810	574	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270111	66270111	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs539707153	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	136	517	1	ENST00000273854.3:c.1771G>A	p.Gly591Ser	p.G591S	ENST00000273854	NM_004439.5	591	Ggc/Agc	8/18	1	2	FACETS	0.865	0.791	0.942	0.865	0.791	0.942	CLONAL	1	TRUE	1	0.6	2		518	524	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467874	66467874	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	124	498	0	ENST00000273854.3:c.395T>G	p.Phe132Cys	p.F132C	ENST00000273854	NM_004439.5	132	tTt/tGt	3/18	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.6	2		498	403	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535365	66535365	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	144	704	0	ENST00000273854.3:c.96C>A	p.Tyr32Ter	p.Y32*	ENST00000273854	NM_004439.5	32	taC/taA	1/18	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.6	2		704	472	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157311	106157311	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	143	611	2	ENST00000380013.4:c.2212C>A	p.Leu738Ile	p.L738I	ENST00000380013	NM_001127208.2	738	Ctc/Atc	3/11	0.183501993152667	3	FACETS	1	0.971	1	0.565	0.518	0.615	INDETERMINATE	1	TRUE	1	0.6	3		613	548	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193749	106193749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs552345702	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	29	329	0	ENST00000380013.4:c.4211G>A	p.Arg1404Gln	p.R1404Q	ENST00000380013	NM_001127208.2	1404	cGa/cAa	10/11	0.183501993152667	3	FACETS	0.42	0.338	0.513	0.21	0.169	0.257	INDETERMINATE	1	TRUE	1	0.6	3		329	299	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197030	106197030	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs572196470	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	72	393	0	ENST00000380013.4:c.5363A>G	p.Asp1788Gly	p.D1788G	ENST00000380013	NM_001127208.2	1788	gAc/gGc	11/11	0.183501993152667	3	FACETS	1	0.962	1	0.609	0.539	0.683	INDETERMINATE	1	TRUE	1	0.6	3		393	256	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197563	106197563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745668941	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	135	487	0	ENST00000380013.4:c.5896C>T	p.Arg1966Cys	p.R1966C	ENST00000380013	NM_001127208.2	1966	Cgt/Tgt	11/11	0.183501993152667	3	FACETS	1	0.98	1	0.618	0.566	0.673	INDETERMINATE	1	TRUE	1	0.6	3		487	473	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	173	716	1	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	0.183501993152667	3	FACETS	1	0.977	1	0.574	0.53	0.619	INDETERMINATE	1	TRUE	1	0.6	3		717	653	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518086	187518086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200185840	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	158	663	2	ENST00000441802.2:c.12608G>A	p.Arg4203His	p.R4203H	ENST00000441802	NM_005245.3	4203	cGt/cAt	25/27	0.183501993152667	3	FACETS	1	0.981	1	0.607	0.559	0.656	INDETERMINATE	1	TRUE	1	0.6	3		665	564	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542509	187542509	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	71	655	0	ENST00000441802.2:c.5231G>T	p.Gly1744Val	p.G1744V	ENST00000441802	NM_005245.3	1744	gGt/gTt	10/27	0.183501993152667	3	FACETS	0.596	0.521	0.677	0.298	0.26	0.339	INDETERMINATE	1	TRUE	1	0.6	3		655	516	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549409	187549409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs562017880	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	217	732	0	ENST00000441802.2:c.4709G>A	p.Arg1570Gln	p.R1570Q	ENST00000441802	NM_005245.3	1570	cGg/cAg	9/27	0.183501993152667	3	FACETS	1	0.988	1	0.629	0.587	0.673	INDETERMINATE	1	TRUE	1	0.6	3		732	747	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629661	187629661	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	105	658	1	ENST00000441802.2:c.1321A>C	p.Ser441Arg	p.S441R	ENST00000441802	NM_005245.3	441	Agt/Cgt	2/27	0.183501993152667	3	FACETS	0.673	0.604	0.747	0.337	0.302	0.374	INDETERMINATE	1	TRUE	1	0.6	3		659	676	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630967	187630967	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	86	612	0	ENST00000441802.2:c.15G>T	p.Leu5Phe	p.L5F	ENST00000441802	NM_005245.3	5	ttG/ttT	2/27	0.183501993152667	3	FACETS	0.61	0.54	0.685	0.305	0.27	0.343	INDETERMINATE	1	TRUE	1	0.6	3		612	611	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294255	1294255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1174718400	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	124	686	0	ENST00000310581.5:c.746C>T	p.Thr249Met	p.T249M	ENST00000310581	NM_198253.2	249	aCg/aTg	2/16	1	2	FACETS	0.933	0.85	1	0.933	0.85	1	CLONAL	1	TRUE	1	0.6	2		686	443	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294532	1294532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1360708027	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	97	642	1	ENST00000310581.5:c.469G>A	p.Ala157Thr	p.A157T	ENST00000310581	NM_198253.2	157	Gcg/Acg	2/16	1	2	FACETS	0.948	0.854	1	0.948	0.854	1	CLONAL	1	TRUE	1	0.6	2		643	341	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515239	31515239	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1478716580	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	136	861	0	ENST00000344624.3:c.1146G>T	p.Lys382Asn	p.K382N	ENST00000344624		382	aaG/aaT	5/33	0.112786725070591	3	FACETS	0.808	0.736	0.884	0.404	0.368	0.442	INDETERMINATE	1	TRUE	1	0.6	3		861	729	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950669	38950669	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	95	539	0	ENST00000357387.3:c.3281T>C	p.Val1094Ala	p.V1094A	ENST00000357387	NM_152756.3	1094	gTg/gCg	31/38	0.112786725070591	3	FACETS	1	0.958	1	0.564	0.506	0.624	INDETERMINATE	1	TRUE	1	0.6	3		539	365	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963141	38963141	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs749429040	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	81	281	0	ENST00000357387.3:c.1403G>A	p.Arg468Gln	p.R468Q	ENST00000357387	NM_152756.3	468	cGa/cAa	17/38	0.112786725070591	3	FACETS	1	0.976	1	0.686	0.612	0.762	INDETERMINATE	1	TRUE	1	0.6	3		281	256	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982073	38982073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	136	627	0	ENST00000357387.3:c.649G>A	p.Asp217Asn	p.D217N	ENST00000357387	NM_152756.3	217	Gat/Aat	8/38	0.112786725070591	3	FACETS	1	0.966	1	0.556	0.508	0.606	INDETERMINATE	1	TRUE	1	0.6	3		627	530	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170985	56170985	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	105	387	0	ENST00000399503.3:c.1813A>C	p.Asn605His	p.N605H	ENST00000399503	NM_005921.1	605	Aat/Cat	10/20	0.112786725070591	3	FACETS	0.756	0.686	0.827	0.756	0.686	0.827	INDETERMINATE	2	TRUE	1	0.6	3		387	301	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751565	57751565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	134	403	0	ENST00000274289.3:c.1426G>A	p.Ala476Thr	p.A476T	ENST00000274289	NM_006622.3	476	Gca/Aca	11/14	0.112786725070591	3	FACETS	1	0.984	1	0.666	0.61	0.724	INDETERMINATE	1	TRUE	1	0.6	3		403	436	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	129	310	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	0.112786725070591	3	FACETS	1	0.985	1	0.685	0.627	0.745	INDETERMINATE	1	TRUE	1	0.6	3		310	408	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627297	86627297	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	123	486	0	ENST00000274376.6:c.672G>T	p.Met224Ile	p.M224I	ENST00000274376	NM_002890.2	224	atG/atT	2/25	0.112786725070591	3	FACETS	1	0.982	1	0.66	0.602	0.719	INDETERMINATE	1	TRUE	1	0.6	3		486	404	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672759	86672759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	134	484	1	ENST00000274376.6:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000274376	NM_002890.2	749	cGa/cAa	17/25	0.112786725070591	3	FACETS	1	0.986	1	0.708	0.649	0.769	INDETERMINATE	1	TRUE	1	0.6	3		485	410	SUCCESS
APC	324	MSKCC	GRCh37	5	112116503	112116503	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	38	409	0	ENST00000257430.4:c.548A>G	p.Asp183Gly	p.D183G	ENST00000257430	NM_000038.5	183	gAt/gGt	6/16	0.112786725070591	3	FACETS	0.554	0.46	0.659	0.277	0.23	0.33	INDETERMINATE	1	TRUE	1	0.6	3		409	297	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	126	308	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.112786725070591	3	FACETS	1	0.983	1	0.672	0.614	0.732	INDETERMINATE	1	TRUE	1	0.6	3		308	406	SUCCESS
APC	324	MSKCC	GRCh37	5	112175814	112175814	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	40	353	0	ENST00000257430.4:c.4523C>A	p.Ala1508Asp	p.A1508D	ENST00000257430	NM_000038.5	1508	gCt/gAt	16/16	0.112786725070591	3	FACETS	0.51	0.425	0.604	0.255	0.212	0.302	INDETERMINATE	1	TRUE	1	0.6	3		353	340	SUCCESS
APC	324	MSKCC	GRCh37	5	112179524	112179524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779809	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	107	479	1	ENST00000257430.4:c.8233C>T	p.Pro2745Ser	p.P2745S	ENST00000257430	NM_000038.5	2745	Cct/Tct	16/16	0.112786725070591	3	FACETS	1	0.974	1	0.61	0.552	0.671	INDETERMINATE	1	TRUE	1	0.6	3		480	380	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460545	149460545	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	140	725	0	ENST00000286301.3:c.92T>C	p.Val31Ala	p.V31A	ENST00000286301	NM_005211.3	31	gTc/gCc	3/22	1	2	FACETS	0.989	0.907	1	0.989	0.907	1	CLONAL	1	TRUE	1	0.6	2		725	472	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562906	176562906	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	85	697	0	ENST00000439151.2:c.802G>T	p.Glu268Ter	p.E268*	ENST00000439151	NM_022455.4	268	Gaa/Taa	2/23	1	2	FACETS	0.501	0.444	0.563	0.501	0.444	0.563	SUBCLONAL	1	TRUE	1	0.6	2		697	565	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637607	176637607	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	119	693	0	ENST00000439151.2:c.2207C>A	p.Ser736Tyr	p.S736Y	ENST00000439151	NM_022455.4	736	tCt/tAt	5/23	1	2	FACETS	0.883	0.803	0.967	0.883	0.803	0.967	CLONAL	1	TRUE	1	0.6	2		693	449	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046722	180046722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768562688	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	126	799	1	ENST00000261937.6:c.2590G>A	p.Ala864Thr	p.A864T	ENST00000261937	NM_182925.4	864	Gct/Act	18/30	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.6	2		800	417	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056376	180056376	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	92	748	0	ENST00000261937.6:c.868G>T	p.Glu290Ter	p.E290*	ENST00000261937	NM_182925.4	290	Gaa/Taa	7/30	1	2	FACETS	0.813	0.728	0.903	0.813	0.728	0.903	CLONAL	1	TRUE	1	0.6	2		748	377	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777880	27777880	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	95	438	0	ENST00000369163.2:c.29A>C	p.Lys10Thr	p.K10T	ENST00000369163	NM_003536.2	10	aAg/aCg	1/1	0.3	4	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.6	4		438	339	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673706	30673706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	172	694	0	ENST00000376406.3:c.3254G>A	p.Gly1085Glu	p.G1085E	ENST00000376406	NM_014641.2	1085	gGg/gAg	10/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.6	2		694	538	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188007	32188007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1227961128	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	121	865	0	ENST00000375023.3:c.1214C>T	p.Ala405Val	p.A405V	ENST00000375023	NM_004557.3	405	gCc/gTc	7/30	1	2	FACETS	0.919	0.836	1	0.919	0.836	1	CLONAL	1	TRUE	1	0.6	2		865	439	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803500	32803500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550712305	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	175	764	0	ENST00000374899.4:c.659G>A	p.Arg220Gln	p.R220Q	ENST00000374899	NM_018833.2	220	cGa/cAa	4/12	1	2	FACETS	0.982	0.909	1	0.982	0.909	1	CLONAL	1	TRUE	1	0.6	2		764	594	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547352	106547352	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs548550985	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	59	591	0	ENST00000369096.4:c.589C>A	p.Leu197Ile	p.L197I	ENST00000369096	NM_001198.3	197	Ctt/Att	4/7	0.112786725070591	3	FACETS	0.47	0.404	0.541	0.235	0.202	0.271	INDETERMINATE	1	TRUE	1	0.6	3		591	544	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553668	106553668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1261004652	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	137	459	0	ENST00000369096.4:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000369096	NM_001198.3	545	Gaa/Aaa	5/7	0.112786725070591	3	FACETS	1	0.986	1	0.689	0.632	0.747	INDETERMINATE	1	TRUE	1	0.6	3		459	431	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642495	117642495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs9489124	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	191	741	1	ENST00000368508.3:c.5704G>A	p.Glu1902Lys	p.E1902K	ENST00000368508	NM_002944.2	1902	Gaa/Aaa	35/43	0.112786725070591	3	FACETS	1	0.982	1	0.589	0.546	0.633	INDETERMINATE	1	TRUE	1	0.6	3		742	703	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663679	117663679	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	51	534	0	ENST00000368508.3:c.4553A>G	p.Glu1518Gly	p.E1518G	ENST00000368508	NM_002944.2	1518	gAa/gGa	28/43	0.112786725070591	3	FACETS	0.472	0.402	0.55	0.236	0.201	0.275	INDETERMINATE	1	TRUE	1	0.6	3		534	468	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704541	117704541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	23	588	0	ENST00000368508.3:c.2435C>T	p.Thr812Ile	p.T812I	ENST00000368508	NM_002944.2	812	aCc/aTc	16/43	0.112786725070591	3	FACETS	0.217	0.168	0.273	0.108	0.084	0.137	INDETERMINATE	1	TRUE	1	0.6	3		588	460	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023160	150023160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	145	698	1	ENST00000253339.5:c.103C>T	p.Arg35Trp	p.R35W	ENST00000253339		35	Cgg/Tgg	1/7	0.112786725070591	3	FACETS	1	0.986	1	0.673	0.618	0.729	INDETERMINATE	1	TRUE	1	0.6	3		699	467	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528673	157528673	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1226524520	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	90	652	0	ENST00000346085.5:c.6398C>T	p.Ala2133Val	p.A2133V	ENST00000346085	NM_020732.3	2133	gCg/gTg	20/20	0.112786725070591	3	FACETS	0.661	0.587	0.739	0.331	0.293	0.37	INDETERMINATE	1	TRUE	1	0.6	3		652	590	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729313	41729313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	133	555	0	ENST00000242208.4:c.1216G>A	p.Asp406Asn	p.D406N	ENST00000242208	NM_002192.2	406	Gat/Aat	3/3	1	2	FACETS	0.96	0.878	1	0.96	0.878	1	CLONAL	1	TRUE	1	0.6	2		555	462	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459493	50459493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	102	479	0	ENST00000331340.3:c.782C>A	p.Ser261Tyr	p.S261Y	ENST00000331340	NM_006060.4	261	tCt/tAt	7/8	1	2	FACETS	0.876	0.79	0.966	0.876	0.79	0.966	CLONAL	1	TRUE	1	0.6	2		479	388	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242511	55242511	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs121913418	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	33	470	2	ENST00000275493.2:c.2281G>A	p.Asp761Asn	p.D761N	ENST00000275493	NM_005228.3	761	Gat/Aat	19/28	1	2	FACETS	0.317	0.258	0.383	0.317	0.258	0.383	SUBCLONAL	1	TRUE	1	0.6	2		472	347	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508472	106508472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	42	281	0	ENST00000359195.3:c.466G>A	p.Ala156Thr	p.A156T	ENST00000359195	NM_002649.2	156	Gcg/Acg	2/11	1	2	FACETS	0.795	0.674	0.926	0.795	0.674	0.926	CLONAL	1	TRUE	1	0.6	2		281	176	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509747	106509747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761655879	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	129	617	2	ENST00000359195.3:c.1741G>A	p.Glu581Lys	p.E581K	ENST00000359195	NM_002649.2	581	Gaa/Aaa	2/11	1	2	FACETS	0.927	0.846	1	0.927	0.846	1	CLONAL	1	TRUE	1	0.6	2		619	464	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520000	106520000	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs759433704	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	99	444	0	ENST00000359195.3:c.2428C>A	p.Pro810Thr	p.P810T	ENST00000359195	NM_002649.2	810	Cca/Aca	6/11	1	2	FACETS	0.871	0.784	0.962	0.871	0.784	0.962	CLONAL	1	TRUE	1	0.6	2		444	379	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845484	128845484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755698791	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	165	749	1	ENST00000249373.3:c.781C>T	p.Arg261Cys	p.R261C	ENST00000249373	NM_005631.4	261	Cgc/Tgc	4/12	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.6	2		750	541	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850942	128850942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs989582182	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	100	572	0	ENST00000249373.3:c.1789G>A	p.Asp597Asn	p.D597N	ENST00000249373	NM_005631.4	597	Gac/Aac	10/12	1	2	FACETS	0.894	0.805	0.986	0.894	0.805	0.986	CLONAL	1	TRUE	1	0.6	2		572	373	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543665	148543665	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	59	569	0	ENST00000320356.2:c.143A>G	p.Lys48Arg	p.K48R	ENST00000320356	NM_004456.4	48	aAa/aGa	3/20	1	2	FACETS	0.336	0.288	0.387	0.336	0.288	0.387	SUBCLONAL	1	TRUE	1	0.6	2		569	586	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874337	151874337	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	63	606	1	ENST00000262189.6:c.8201C>A	p.Thr2734Asn	p.T2734N	ENST00000262189	NM_170606.2	2734	aCt/aAt	38/59	1	2	FACETS	0.475	0.412	0.543	0.475	0.412	0.543	SUBCLONAL	1	TRUE	1	0.6	2		607	442	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874613	151874613	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	55	520	0	ENST00000262189.6:c.7925C>A	p.Ser2642Tyr	p.S2642Y	ENST00000262189	NM_170606.2	2642	tCt/tAt	38/59	1	2	FACETS	0.531	0.457	0.612	0.531	0.457	0.612	SUBCLONAL	1	TRUE	1	0.6	2		520	345	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884466	151884466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1435892915	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	136	543	0	ENST00000262189.6:c.4889C>T	p.Ser1630Leu	p.S1630L	ENST00000262189	NM_170606.2	1630	tCg/tTg	33/59	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.6	2		543	436	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38157028	38157028	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	149	797	1	ENST00000317025.8:c.2692C>T	p.Arg898Cys	p.R898C	ENST00000317025	NM_023034.1	898	Cgt/Tgt	15/24	1	2	FACETS	0.842	0.772	0.914	0.842	0.772	0.914	CLONAL	1	TRUE	1	0.6	2		798	590	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187215	38187215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763425861	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	232	976	2	ENST00000317025.8:c.1262G>A	p.Arg421Gln	p.R421Q	ENST00000317025	NM_023034.1	421	cGa/cAa	6/24	1	2	FACETS	0.894	0.835	0.954	0.894	0.835	0.954	CLONAL	1	TRUE	1	0.6	2		978	865	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187408	38187408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243215593	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	116	537	1	ENST00000317025.8:c.1069C>T	p.Arg357Trp	p.R357W	ENST00000317025	NM_023034.1	357	Cgg/Tgg	6/24	1	2	FACETS	0.899	0.816	0.985	0.899	0.816	0.985	CLONAL	1	TRUE	1	0.6	2		538	430	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922561	56922561	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	170	684	0	ENST00000519728.1:c.1431A>C	p.Lys477Asn	p.K477N	ENST00000519728	NM_002350.3	477	aaA/aaC	13/13	1	2	FACETS	0.977	0.903	1	0.977	0.903	1	CLONAL	1	TRUE	1	0.6	2		684	580	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992764	68992764	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs769067107	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	31	770	1	ENST00000288368.4:c.1729C>T	p.Arg577Ter	p.R577*	ENST00000288368	NM_024870.2	577	Cga/Tga	16/40	1	2	FACETS	0.174	0.14	0.213	0.174	0.14	0.213	SUBCLONAL	1	TRUE	1	0.6	2		771	594	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009351	69009351	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	160	581	1	ENST00000288368.4:c.2468A>G	p.Tyr823Cys	p.Y823C	ENST00000288368	NM_024870.2	823	tAt/tGt	22/40	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.6	2		582	517	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69012039	69012039	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	157	710	0	ENST00000288368.4:c.2676A>C	p.Arg892Ser	p.R892S	ENST00000288368	NM_024870.2	892	agA/agC	23/40	1	2	FACETS	0.839	0.771	0.909	0.839	0.771	0.909	CLONAL	1	TRUE	1	0.6	2		710	624	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69012076	69012076	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	74	504	0	ENST00000288368.4:c.2713A>C	p.Lys905Gln	p.K905Q	ENST00000288368	NM_024870.2	905	Aag/Cag	23/40	1	2	FACETS	0.62	0.545	0.699	0.62	0.545	0.699	SUBCLONAL	1	TRUE	1	0.6	2		504	398	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028029	69028029	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	133	694	0	ENST00000288368.4:c.3188A>C	p.Lys1063Thr	p.K1063T	ENST00000288368	NM_024870.2	1063	aAg/aCg	26/40	1	2	FACETS	0.992	0.908	1	0.992	0.908	1	CLONAL	1	TRUE	1	0.6	2		694	447	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058531	69058531	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	196	819	1	ENST00000288368.4:c.4175C>A	p.Pro1392His	p.P1392H	ENST00000288368	NM_024870.2	1392	cCt/cAt	34/40	1	2	FACETS	0.952	0.885	1	0.952	0.885	1	CLONAL	1	TRUE	1	0.6	2		820	686	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066787	5066787	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs560489093	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	47	246	0	ENST00000381652.3:c.1324G>A	p.Glu442Lys	p.E442K	ENST00000381652	NM_004972.3	442	Gag/Aag	10/25	1	2	FACETS	0.927	0.796	1	0.927	0.796	1	CLONAL	1	TRUE	1	0.6	2		246	169	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528648	8528648	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	74	501	1	ENST00000356435.5:c.484G>T	p.Asp162Tyr	p.D162Y	ENST00000356435		162	Gat/Tat	4/35	1	2	FACETS	0.468	0.41	0.53	0.468	0.41	0.53	SUBCLONAL	1	TRUE	1	0.6	2		502	527	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840615	36840615	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1282780266	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	64	597	1	ENST00000358127.4:c.1118G>A	p.Ser373Asn	p.S373N	ENST00000358127	NM_001280556.1	373	aGc/aAc	10/10	1	2	FACETS	0.513	0.445	0.585	0.513	0.445	0.585	SUBCLONAL	1	TRUE	1	0.6	2		598	416	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002648	37002648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	97	500	1	ENST00000358127.4:c.601G>A	p.Glu201Lys	p.E201K	ENST00000358127	NM_001280556.1	201	Gaa/Aaa	5/10	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.6	2		501	322	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229567	98229567	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs778260156	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	131	613	1	ENST00000331920.6:c.2391C>A	p.Tyr797Ter	p.Y797*	ENST00000331920	NM_000264.3	797	taC/taA	15/24	1	2	FACETS	0.912	0.833	0.993	0.912	0.833	0.993	CLONAL	1	TRUE	1	0.6	2		614	479	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268704	98268704	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774822170	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	122	464	1	ENST00000331920.6:c.379G>A	p.Glu127Lys	p.E127K	ENST00000331920	NM_000264.3	127	Gag/Aag	2/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.6	2		465	362	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249765	110249765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1059912	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	157	708	0	ENST00000374672.4:c.910G>A	p.Asp304Asn	p.D304N	ENST00000374672	NM_004235.4	304	Gac/Aac	3/5	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.6	2		708	478	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750417	133750417	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	44	681	0	ENST00000318560.5:c.1248C>A	p.Phe416Leu	p.F416L	ENST00000318560	NM_005157.4	416	ttC/ttA	7/11	1	2	FACETS	0.306	0.256	0.36	0.306	0.256	0.36	SUBCLONAL	1	TRUE	1	0.6	2		681	480	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759442	133759442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754252285	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	130	676	3	ENST00000318560.5:c.1765C>T	p.Arg589Cys	p.R589C	ENST00000318560	NM_005157.4	589	Cgc/Tgc	11/11	1	2	FACETS	0.92	0.84	1	0.92	0.84	1	CLONAL	1	TRUE	1	0.6	2		679	471	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759527	133759527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	88	743	2	ENST00000318560.5:c.1850G>A	p.Arg617His	p.R617H	ENST00000318560	NM_005157.4	617	cGc/cAc	11/11	1	2	FACETS	0.639	0.569	0.714	0.639	0.569	0.714	SUBCLONAL	1	TRUE	1	0.6	2		745	459	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778026	135778026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1336228562	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	74	636	2	ENST00000298552.3:c.2357G>A	p.Arg786Gln	p.R786Q	ENST00000298552	NM_001162426.1	786	cGa/cAa	18/23	1	2	FACETS	0.454	0.398	0.515	0.454	0.398	0.515	SUBCLONAL	1	TRUE	1	0.6	2		638	543	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778098	135778098	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	186	693	0	ENST00000298552.3:c.2285A>C	p.Asn762Thr	p.N762T	ENST00000298552	NM_001162426.1	762	aAt/aCt	18/23	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.6	2		693	565	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787720	135787720	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770653972	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	70	626	0	ENST00000298552.3:c.862C>T	p.Arg288Cys	p.R288C	ENST00000298552	NM_001162426.1	288	Cgt/Tgt	9/23	1	2	FACETS	0.458	0.4	0.521	0.458	0.4	0.521	SUBCLONAL	1	TRUE	1	0.6	2		626	509	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796804	135796804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223799508	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	79	507	2	ENST00000298552.3:c.683G>A	p.Arg228Gln	p.R228Q	ENST00000298552	NM_001162426.1	228	cGa/cAa	8/23	1	2	FACETS	0.872	0.775	0.974	0.872	0.775	0.974	CLONAL	1	TRUE	1	0.6	2		509	302	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797258	135797258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514834	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	18	402	1	ENST00000298552.3:c.611G>A	p.Arg204His	p.R204H	ENST00000298552	NM_001162426.1	204	cGt/cAt	7/23	1	2	FACETS	0.188	0.141	0.243	0.188	0.141	0.243	SUBCLONAL	1	TRUE	1	0.6	2		403	320	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931828	39931828	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	146	330	0	ENST00000378444.4:c.2771T>G	p.Phe924Cys	p.F924C	ENST00000378444	NM_001123385.1	924	tTt/tGt	4/15	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.6	1		330	245	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929227	44929227	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	118	336	0	ENST00000377967.4:c.2327A>G	p.Asp776Gly	p.D776G	ENST00000377967	NM_021140.2	776	gAc/gGc	17/29	1	1	FACETS	0.915	0.838	0.993	0.915	0.838	0.993	CLONAL	1	TRUE	0	0.6	1		336	301	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412094	63412094	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374751715	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	109	540	1	ENST00000330258.3:c.1073G>A	p.Arg358Gln	p.R358Q	ENST00000330258	NM_152424.3	358	cGa/cAa	2/2	1	1	FACETS	0.737	0.669	0.808	0.737	0.669	0.808	SUBCLONAL	1	TRUE	0	0.6	1		541	345	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874295	76874295	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	176	328	0	ENST00000373344.5:c.5427G>T	p.Glu1809Asp	p.E1809D	ENST00000373344	NM_000489.3	1809	gaG/gaT	21/35	1	1	FACETS	0.758	0.717	0.797	1	0.993	1	SUBCLONAL	2	TRUE	0	0.6	1		328	271	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939761	76939761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	202	387	0	ENST00000373344.5:c.987G>T	p.Lys329Asn	p.K329N	ENST00000373344	NM_000489.3	329	aaG/aaT	9/35	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.6	1		387	345	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76954099	76954099	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	167	356	0	ENST00000373344.5:c.152G>A	p.Gly51Glu	p.G51E	ENST00000373344	NM_000489.3	51	gGa/gAa	3/35	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.6	1		356	288	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020225	123020225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	207	378	0	ENST00000355640.3:c.713G>A	p.Arg238Gln	p.R238Q	ENST00000355640		238	cGa/cAa	2/7	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.6	1		378	324	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217381	123217381	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	170	296	1	ENST00000218089.9:c.3035G>A	p.Arg1012Gln	p.R1012Q	ENST00000218089	NM_001042749.1	1012	cGa/cAa	29/35	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.6	1		297	292	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6036981	6036981	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777286241	NA	P-0023271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	121	671	0	ENST00000265849.7:c.779C>T	p.Ser260Phe	p.S260F	ENST00000265849	NM_000535.5	260	tCc/tTc	7/15	1	2	FACETS	0.785	0.712	0.86	0.785	0.712	0.86	SUBCLONAL	1	TRUE	1	0.6	2		671	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0023364-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	455	819	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.48619222766347	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.513161497179241	2		819	852	SUCCESS
APC	324	MSKCC	GRCh37	5	112137081	112137081	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1554076225	NA	P-0023364-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	256	344	1	ENST00000257430.4:c.834+1G>A		p.X278_splice	ENST00000257430	NM_000038.5	278			0.508293349163003	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	3	TRUE	0	0.513161497179241	3		345	414	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64126884	64126886	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0023364-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	469	922	0	ENST00000334205.4:c.91_93del	p.Glu31del	p.E31del	ENST00000334205	NM_003942.2	30	gtGGAg/gtg	2/17	0.513262237010109	3	FACETS	0.941	0.9	0.981	0.941	0.9	0.981	CLONAL	2	TRUE	1	0.513161497179241	3		922	1221	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348565	89348565	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023364-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	263	970	1	ENST00000301030.4:c.4385G>T	p.Arg1462Ile	p.R1462I	ENST00000301030	NM_001256183.1	1462	aGa/aTa	9/13	0.513262237010109	3	FACETS	1	0.949	1	0.508	0.475	0.542	CLONAL	1	TRUE	1	0.513161497179241	3		971	1267	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247112	153247255	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TATGATTCATCAGGAGAGCATTTAAGGGAGAGATAAGAGATCTTACCTGTAATGAATAGACTCTATTAGTATGCCCCTGCAACGTGTGTAGACAGGTTTCAGTCTCTGGATCCCACACCTTTACCATAAAATCATATGCTCCAC	TATGATTCATCAGGAGAGCATTTAAGGGAGAGATAAGAGATCTTACCTGTAATGAATAGACTCTATTAGTATGCCCCTGCAACGTGTGTAGACAGGTTTCAGTCTCTGGATCCCACACCTTTACCATAAAATCATATGCTCCAC	-	novel	NA	P-0023364-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	45	149	0	ENST00000281708.4:c.1547_1644+46del		p.X516_splice	ENST00000281708	NM_033632.3	516		10/12	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.513161497179241	2		149	134	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950860	32950860	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023364-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	145	523	0	ENST00000380152.3:c.8686C>G	p.Arg2896Gly	p.R2896G	ENST00000380152		2896	Cgt/Ggt	21/27	0.513262237010109	4	FACETS	0.962	0.877	1	0.481	0.438	0.525	CLONAL	1	TRUE	2	0.513161497179241	4		523	889	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115973	8115974	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0023797-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	52	459	0	ENST00000346208.3:c.1319_1320del	p.Thr440SerfsTer66	p.T440Sfs*66	ENST00000346208		440	aCC/a	6/6	0.126837086014474	3	FACETS	0.761	0.655	0.874	0.761	0.655	0.874	INDETERMINATE	2	TRUE	1	0.359897949191198	3		459	224	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336157	73336157	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023797-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	33	407	0	ENST00000377767.4:c.2246T>C	p.Met749Thr	p.M749T	ENST00000377767	NM_014953.3	749	aTg/aCg	17/21	0.359897949191198	1	FACETS	0.958	0.791	1	0.958	0.791	1	CLONAL	1	TRUE	0	0.359897949191198	1		407	157	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570416	95570416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023797-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	67	367	0	ENST00000393063.1:c.3317C>T	p.Ser1106Phe	p.S1106F	ENST00000393063	NM_030621.3	1106	tCt/tTt	22/28	0.359898787984012	3	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	1	0.359897949191198	3		367	201	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42026719	42026719	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0023797-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	28	322	0	ENST00000219905.7:c.3844-1G>T		p.X1282_splice	ENST00000219905	NM_001164273.1	1282			1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.359897949191198	2		322	120	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400015	49400015	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023797-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	47	384	1	ENST00000418115.1:c.322C>A	p.Pro108Thr	p.P108T	ENST00000418115	NM_001664.2	108	Ccc/Acc	4/5	0.344599295928998	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.359897949191198	1		385	191	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0023908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	155	510	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.749485405054153	2	FACETS	0.962	0.912	1	0.962	0.912	1	CLONAL	2	TRUE	0	0.749485405054153	2		510	215	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0024223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	458	675	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.256791611475299	5	FACETS	1	0.971	1			1	CLONAL	5	TRUE	NA	0.256791611475299	5		675	974	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243789	41243792	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	rs80357868	NA	P-0024223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	179	766	0	ENST00000357654.3:c.3756_3759del	p.Ser1253ArgfsTer10	p.S1253Rfs*10	ENST00000357654	NM_007294.3	1252	ctGTCT/ct	10/23	0.256791611475299	2	FACETS	0.952	0.88	1	0.952	0.88	1	CLONAL	2	TRUE	0	0.256791611475299	2		766	732	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311669	30311669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	206	730	0	ENST00000262643.3:c.523C>T	p.Arg175Trp	p.R175W	ENST00000262643	NM_001238.2	175	Cgg/Tgg	7/12	0.256791611475299	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.256791611475299	3		730	851	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211767	36211768	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0024223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1247	141	1139	0	ENST00000222270.7:c.1520dup	p.Glu508GlyfsTer42	p.E508Gfs*42	ENST00000222270	NM_014727.1	506	-/C	3/37	0.256791611475299	4	FACETS	0.994	0.903	1			1	CLONAL	1	TRUE	NA	0.256791611475299	4		1139	1388	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214704	36214704	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	84	705	2	ENST00000222270.7:c.3130G>A	p.Gly1044Ser	p.G1044S	ENST00000222270	NM_014727.1	1044	Ggc/Agc	8/37	0.256791611475299	4	FACETS	0.985	0.869	1			1	CLONAL	1	TRUE	NA	0.256791611475299	4		707	835	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279295	142279295	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	157	535	0	ENST00000350721.4:c.1351A>T	p.Ile451Phe	p.I451F	ENST00000350721	NM_001184.3	451	Att/Ttt	6/47	0.256791611475299	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.256791611475299	4		535	677	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645118	86645118	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	106	575	1	ENST00000274376.6:c.1190A>C	p.Gln397Pro	p.Q397P	ENST00000274376	NM_002890.2	397	cAg/cCg	8/25	0.256791611475299	4	FACETS	0.907	0.815	1	0.907	0.815	1	CLONAL	2	TRUE	2	0.256791611475299	4		576	572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	255	805	0	ENST00000269305.4:c.742del	p.Arg248GlyfsTer97	p.R248Gfs*97	ENST00000269305	NM_001126112.2	248	Cgg/gg	7/11	0.440792748218398	2	FACETS	0.834	0.785	0.883	0.834	0.785	0.883	CLONAL	2	TRUE	0	0.45255851337425	2		805	676	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952211	17952211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1420054751	NA	P-0024831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	121	656	0	ENST00000458235.1:c.1129C>T	p.His377Tyr	p.H377Y	ENST00000458235	NM_000215.3	377	Cac/Tac	8/24	1	2	FACETS	0.885	0.802	0.973	0.885	0.802	0.973	CLONAL	1	TRUE	1	0.45255851337425	2		656	604	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793421	242793421	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	141	847	0	ENST00000334409.5:c.656T>G	p.Phe219Cys	p.F219C	ENST00000334409	NM_005018.2	219	tTc/tGc	5/5	1	2	FACETS	0.869	0.793	0.949	0.869	0.793	0.949	CLONAL	1	TRUE	1	0.45255851337425	2		847	717	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662780	117662780	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	63	300	0	ENST00000368508.3:c.4685A>C	p.Gln1562Pro	p.Q1562P	ENST00000368508	NM_002944.2	1562	cAg/cCg	29/43	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.45255851337425	NA		300	300	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279339	38279339	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	297	907	3	ENST00000425967.3:c.1150T>C	p.Ser384Pro	p.S384P	ENST00000425967	NM_001174067.1	384	Tct/Cct	9/19	0.308880673577782	4	FACETS	0.994	0.938	1			1	CLONAL	2	TRUE	NA	0.45255851337425	4		910	959	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412460	63412460	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	111	974	1	ENST00000330258.3:c.707G>T	p.Gly236Val	p.G236V	ENST00000330258	NM_152424.3	236	gGg/gTg	2/2	0.45255851337425	2	FACETS	0.756	0.681	0.835	0.378	0.34	0.418	SUBCLONAL	1	TRUE	0	0.45255851337425	2		975	649	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024831-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	280	805	0	ENST00000269305.4:c.742del	p.Arg248GlyfsTer97	p.R248Gfs*97	ENST00000269305	NM_001126112.2	248	Cgg/gg	7/11	0.413677513619632	2	FACETS	0.92	0.869	0.971	0.92	0.869	0.971	CLONAL	2	TRUE	0	0.413677513619632	2		805	736	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952211	17952211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1420054751	NA	P-0024831-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	99	656	0	ENST00000458235.1:c.1129C>T	p.His377Tyr	p.H377Y	ENST00000458235	NM_000215.3	377	Cac/Tac	8/24	0.413471860819445	3	FACETS	0.856	0.765	0.953	0.428	0.382	0.477	CLONAL	1	TRUE	1	0.413677513619632	3		656	675	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793421	242793421	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024831-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	120	847	0	ENST00000334409.5:c.656T>G	p.Phe219Cys	p.F219C	ENST00000334409	NM_005018.2	219	tTc/tGc	5/5	0.284879540551179	3	FACETS	0.977	0.883	1	0.488	0.441	0.538	CLONAL	1	TRUE	1	0.413677513619632	3		847	717	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662780	117662780	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024831-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	56	300	0	ENST00000368508.3:c.4685A>C	p.Gln1562Pro	p.Q1562P	ENST00000368508	NM_002944.2	1562	cAg/cCg	29/43	1	2	FACETS	0.93	0.803	1	0.93	0.803	1	CLONAL	1	TRUE	1	0.413677513619632	2		300	291	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279339	38279339	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024831-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	307	907	3	ENST00000425967.3:c.1150T>C	p.Ser384Pro	p.S384P	ENST00000425967	NM_001174067.1	384	Tct/Cct	9/19	0.413677513619632	4	FACETS	1	0.984	1	0.739	0.698	0.781	CLONAL	2	TRUE	1	0.413677513619632	4		910	946	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412460	63412460	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024831-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	161	974	1	ENST00000330258.3:c.707G>T	p.Gly236Val	p.G236V	ENST00000330258	NM_152424.3	236	gGg/gTg	2/2	0.413677513619632	2	FACETS	1	0.949	1	0.522	0.479	0.566	CLONAL	1	TRUE	0	0.413677513619632	2		975	746	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0025425-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	759	686	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.928244412025119	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	1	0.928244412025119	3		686	1033	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112910784	112910784	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025425-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	87	401	0	ENST00000351677.2:c.793C>T	p.Arg265Ter	p.R265*	ENST00000351677	NM_002834.3	265	Cga/Tga	7/16	1	2	FACETS	0.412	0.366	0.461	0.412	0.366	0.461	SUBCLONAL	1	TRUE	1	0.928244412025119	2		401	455	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610682	81610682	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025425-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	45	276	0	ENST00000298171.2:c.2280G>A	p.Met760Ile	p.M760I	ENST00000298171	NM_000369.2	760	atG/atA	10/10	1	2	FACETS	0.356	0.301	0.417	0.356	0.301	0.417	SUBCLONAL	1	TRUE	1	0.928244412025119	2		276	272	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0026275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	872	819	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.769072602925579	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.769072602925579	2		819	1123	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339499	81339499	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1562873352	NA	P-0026275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	170	718	0	ENST00000222390.5:c.1505G>C	p.Arg502Pro	p.R502P	ENST00000222390	NM_000601.4	502	cGa/cCa	13/18	0.723354883747566	2	FACETS	0.56	0.515	0.606	0.28	0.257	0.303	SUBCLONAL	1	TRUE	0	0.769072602925579	2		718	790	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0026305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	108	797	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.28882882371902	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.28882882371902	1		799	556	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0026305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	72	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.28882882371902	2		298	460	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913384	NA	P-0026305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	106	279	0	ENST00000304494.5:c.262G>T	p.Glu88Ter	p.E88*	ENST00000304494	NM_000077.4	88	Gag/Tag	2/3	0.28882882371902	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.28882882371902	1		279	503	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123260396	123260396	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	33	292	0	ENST00000358487.5:c.1505G>C	p.Gly502Ala	p.G502A	ENST00000358487	NM_000141.4	502	gGa/gCa	11/18	NA	2	FACETS	0.399	0.324	0.484			1	INDETERMINATE	1	TRUE	NA	0.28882882371902	2		292	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577564	7577564	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057522275	NA	P-0026371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	57	496	0	ENST00000269305.4:c.717C>G	p.Asn239Lys	p.N239K	ENST00000269305	NM_001126112.2	239	aaC/aaG	7/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		496	660	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577572	7577572	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	61	487	0	ENST00000269305.4:c.709A>C	p.Met237Leu	p.M237L	ENST00000269305	NM_001126112.2	237	Atg/Ctg	7/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		487	644	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242482	+	protein_altering_variant	In_Frame_Del	DEL	GAATTAAGAGAAGCAAC	GAATTAAGAGAAGCAAC	AT	rs727504402	NA	P-0026371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	31	453	2	ENST00000275493.2:c.2236_2252delinsAT	p.Glu746_Thr751delinsIle	p.E746_T751delinsI	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCAACa/ATa	19/28	0.191199202443666	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		455	643	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631102	69631102	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121917704	NA	P-0027020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	130	570	1	ENST00000334134.2:c.310C>T	p.Arg104Ter	p.R104*	ENST00000334134	NM_005247.2	104	Cga/Tga	2/3	1	2	FACETS	0.936	0.851	1	0.936	0.851	1	CLONAL	1	TRUE	1	0.443709162587791	2		571	626	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0027020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	211	423	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.444229325586751	3	FACETS	0.964	0.901	1	0.964	0.901	1	CLONAL	2	TRUE	1	0.443709162587791	3		423	603	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47205368	47205368	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	156	473	0	ENST00000409792.3:c.47A>G	p.Tyr16Cys	p.Y16C	ENST00000409792	NM_014159.6	16	tAc/tGc	1/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.443709162587791	2		473	584	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655479	67655479	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs769948988	NA	P-0027020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	246	481	0	ENST00000264010.4:c.1342C>T	p.Arg448Ter	p.R448*	ENST00000264010	NM_006565.3	448	Cga/Tga	7/12	0.444229325586751	3	FACETS	0.964	0.905	1	0.964	0.905	1	CLONAL	2	TRUE	1	0.443709162587791	3		481	703	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873686	35873727	+	inframe_deletion	In_Frame_Del	DEL	CTCGAGGCGGATCTCCTGCAGCTCCTTGACCATCTGCTCGTA	CTCGAGGCGGATCTCCTGCAGCTCCTTGACCATCTGCTCGTA	-	novel	NA	P-0027020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	210	444	0	ENST00000216797.5:c.124_165del	p.Tyr42_Glu55del	p.Y42_E55del	ENST00000216797	NM_020529.2	42	TACGAGCAGATGGTCAAGGAGCTGCAGGAGATCCGCCTCGAG/-	1/6	0.443709162587791	2	FACETS	0.854	0.8	0.91	0.854	0.8	0.91	CLONAL	2	TRUE	0	0.443709162587791	2		444	554	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578562	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGTACTGTAGGA	GAGTACTGTAGGA	-	novel	NA	P-0027020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	346	706	0	ENST00000269305.4:c.376-8_380del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	NA	2	FACETS	0.892	0.848	0.937			1	INDETERMINATE	2	TRUE	NA	0.443709162587791	2		706	874	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436082	56436083	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0027020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	106	471	0	ENST00000407977.2:c.1054dup	p.His352ProfsTer91	p.H352Pfs*91	ENST00000407977		352	cac/cCac	9/10	0.444229325586751	1	FACETS	0.892	0.805	0.982	0.892	0.805	0.982	CLONAL	1	TRUE	0	0.443709162587791	1		471	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0027049-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	571	571	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.445590355283377	3	FACETS	0.888	0.858	0.919	0.888	0.858	0.919	CLONAL	3	TRUE	0	0.503076779137914	3		571	1066	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0027049-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	81	564	1	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.208939071489604	2	FACETS	1	0.967	1	0.61	0.544	0.678	INDETERMINATE	1	TRUE	0	0.503076779137914	2		565	264	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591083	67591084	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGA	novel	NA	P-0027049-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	53	283	0	ENST00000274335.5:c.1677_1679dup	p.Asp560dup	p.D560dup	ENST00000274335		560	att/atTGAt	12/15	0.503076779137914	2	FACETS	0.836	0.734	0.94	0.836	0.734	0.94	CLONAL	2	TRUE	0	0.503076779137914	2		283	126	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987368	2987368	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775081227	NA	P-0027049-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	98	592	0	ENST00000396946.4:c.61G>A	p.Ala21Thr	p.A21T	ENST00000396946	NM_032415.4	21	Gcc/Acc	3/25	0.217088999322352	0	FACETS	0.276	0.246	0.308			1	INDETERMINATE	1	TRUE	0	0.503076779137914	0		592	701	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39311710	39311710	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs151267022	NA	P-0027444-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	151	258	0	ENST00000373001.3:c.949A>G	p.Ile317Val	p.I317V	ENST00000373001	NM_022157.3	317	Att/Gtt	6/7	0.251016820851322	1	FACETS	0.894	0.816	0.977	0.894	0.816	0.977	CLONAL	1	TRUE	0	0.25408871819893	1		258	1160	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927440	245927440	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027444-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	69	207	0	ENST00000388985.4:c.1088C>A	p.Pro363Gln	p.P363Q	ENST00000388985		363	cCa/cAa	11/12	1	2	FACETS	0.495	0.429	0.566	0.495	0.429	0.566	SUBCLONAL	1	TRUE	1	0.25408871819893	2		207	1098	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347066	347117	+	frameshift_variant	Frame_Shift_Del	DEL	TCCTGCGGTGCCTGCTGATCTCCTTTTCCCCCTCAATGATCCACTGCATGAT	TCCTGCGGTGCCTGCTGATCTCCTTTTCCCCCTCAATGATCCACTGCATGAT	-	novel	NA	P-0027444-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	133	329	0	ENST00000262320.3:c.1894_1945del	p.Ile632ProfsTer56	p.I632Pfs*56	ENST00000262320	NM_003502.3	632	ATCATGCAGTGGATCATTGAGGGGGAAAAGGAGATCAGCAGGCACCGCAGGAcc/cc	7/11	0.25408871819893	1	FACETS	0.813	0.737	0.894	0.813	0.737	0.894	CLONAL	1	TRUE	0	0.25408871819893	1		329	1124	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779519	3779519	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027444-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1324	301	334	1	ENST00000262367.5:c.5529C>A	p.Cys1843Ter	p.C1843*	ENST00000262367	NM_004380.2	1843	tgC/tgA	31/31	0.25408871819893	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.25408871819893	1		335	1625	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66521051	66521051	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0027444-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	37	66	0	ENST00000358598.2:c.503-2A>C		p.X168_splice	ENST00000358598	NM_212471.2	168			0.25408871819893	1	FACETS	0.792	0.655	0.944	0.792	0.655	0.944	CLONAL	1	TRUE	0	0.25408871819893	1		66	321	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718120	117718120	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754066414	NA	P-0027444-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	97	200	0	ENST00000368508.3:c.737C>T	p.Thr246Ile	p.T246I	ENST00000368508	NM_002944.2	246	aCc/aTc	7/43	0.161402480322355	2	FACETS	0.901	0.803	1	0.451	0.401	0.504	CLONAL	1	TRUE	0	0.25408871819893	2		200	847	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0027598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	149	497	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.458792175429033	1	FACETS	0.889	0.816	0.964	0.889	0.816	0.964	CLONAL	1	TRUE	0	0.458792175429033	1		497	563	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948136	178948136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	135	334	0	ENST00000263967.3:c.2908G>A	p.Glu970Lys	p.E970K	ENST00000263967	NM_006218.2	970	Gaa/Aaa	20/21	1	2	FACETS	0.924	0.842	1	0.924	0.842	1	CLONAL	1	TRUE	1	0.458792175429033	2		334	637	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0027610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	115	327	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.454708263008603	3	FACETS	1	0.97	1	0.586	0.532	0.644	CLONAL	1	TRUE	1	0.558768322645008	3		327	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0027610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	840	686	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.559498693367303	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.558768322645008	3		686	1175	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589625	67589627	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	novel	NA	P-0027610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	99	424	0	ENST00000274335.5:c.1390_1392del	p.Asp464del	p.D464del	ENST00000274335		463	tATGat/tat	10/15	0.527960312277429	3	FACETS	0.635	0.567	0.707	0.317	0.283	0.354	SUBCLONAL	1	TRUE	1	0.558768322645008	3		424	714	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891535	76891535	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	223	507	1	ENST00000373344.5:c.4570G>T	p.Glu1524Ter	p.E1524*	ENST00000373344	NM_000489.3	1524	Gaa/Taa	16/35	0.344189095163957	3	FACETS	1	0.989	1	0.652	0.609	0.697	CLONAL	1	TRUE	1	0.558768322645008	3		508	783	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519980	NA	P-0027661-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	177	747	0	ENST00000269305.4:c.528C>G	p.Cys176Trp	p.C176W	ENST00000269305	NM_001126112.2	176	tgC/tgG	5/11	0.509225758663877	1	FACETS	0.919	0.852	0.987	0.919	0.852	0.987	CLONAL	1	TRUE	0	0.509225758663877	1		747	564	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376188	15376188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772107398	NA	P-0027661-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	52	474	0	ENST00000263377.2:c.826G>A	p.Ala276Thr	p.A276T	ENST00000263377	NM_058243.2	276	Gcg/Acg	5/20	0.509225758663877	1	FACETS	0.402	0.343	0.466	0.402	0.343	0.466	SUBCLONAL	1	TRUE	0	0.509225758663877	1		474	379	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163498	108163498	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027661-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	37	502	0	ENST00000278616.4:c.4589A>C	p.Glu1530Ala	p.E1530A	ENST00000278616	NM_000051.3	1530	gAg/gCg	30/63	0.509225758663877	1	FACETS	0.311	0.257	0.372	0.311	0.257	0.372	SUBCLONAL	1	TRUE	0	0.509225758663877	1		502	348	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573567	48573567	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0027661-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	64	504	0	ENST00000342988.3:c.151A>T	p.Lys51Ter	p.K51*	ENST00000342988	NM_005359.5	51	Aaa/Taa	2/12	0.509225758663877	1	FACETS	0.483	0.42	0.551	0.483	0.42	0.551	SUBCLONAL	1	TRUE	0	0.509225758663877	1		504	388	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659189	86659189	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0027661-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	49	350	0	ENST00000274376.6:c.1478T>G	p.Leu493Ter	p.L493*	ENST00000274376	NM_002890.2	493	tTa/tGa	11/25	0.509225758663877	1	FACETS	0.496	0.423	0.576	0.496	0.423	0.576	SUBCLONAL	1	TRUE	0	0.509225758663877	1		350	289	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150933660	150933660	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027661-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	48	563	0	ENST00000271640.5:c.3122A>C	p.Lys1041Thr	p.K1041T	ENST00000271640	NM_001145415.1	1041	aAg/aCg	16/22	1	2	FACETS	0.307	0.259	0.36	0.307	0.259	0.36	SUBCLONAL	1	TRUE	1	0.509225758663877	2		563	615	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38793757	38793758	+	missense_variant	Missense_Mutation	DNP	CT	CT	AC	novel	NA	P-0027661-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	101	517	2	ENST00000348513.6:c.223_224delinsGT	p.Arg75Val	p.R75V	ENST00000348513	NM_003079.4	75	AGg/GTg	5/11	0.218668793331482	5	FACETS	0.673	0.6	0.751			1	INDETERMINATE	1	TRUE	NA	0.509225758663877	5		519	1039	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790025	40790025	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027661-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	68	657	0	ENST00000373198.4:c.2706A>C	p.Arg902Ser	p.R902S	ENST00000373198	NM_133170.3	902	agA/agC	18/32	0.371866431521651	1	FACETS	0.315	0.274	0.36	0.315	0.274	0.36	SUBCLONAL	1	TRUE	0	0.509225758663877	1		657	632	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272085	142272085	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027661-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	60	365	0	ENST00000350721.4:c.2789A>G	p.Lys930Arg	p.K930R	ENST00000350721	NM_001184.3	930	aAg/aGg	13/47	1	2	FACETS	0.459	0.396	0.528	0.459	0.396	0.528	SUBCLONAL	1	TRUE	1	0.509225758663877	2		365	513	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198069	185198069	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027661-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	69	534	0	ENST00000265026.3:c.2551G>C	p.Glu851Gln	p.E851Q	ENST00000265026	NM_004721.4	851	Gag/Cag	13/14	1	2	FACETS	0.396	0.344	0.451	0.396	0.344	0.451	SUBCLONAL	1	TRUE	1	0.509225758663877	2		534	685	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164828	32164828	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027661-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	54	555	0	ENST00000375023.3:c.5074A>C	p.Thr1692Pro	p.T1692P	ENST00000375023	NM_004557.3	1692	Act/Cct	28/30	0.507013639156746	2	FACETS	0.328	0.28	0.382	0.164	0.14	0.191	SUBCLONAL	1	TRUE	0	0.509225758663877	2		555	646	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224498	53224498	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027661-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	77	343	0	ENST00000375401.3:c.3215A>T	p.Glu1072Val	p.E1072V	ENST00000375401	NM_004187.3	1072	gAg/gTg	21/26	1	1	FACETS	0.794	0.705	0.887	0.794	0.705	0.887	SUBCLONAL	1	TRUE	0	0.509225758663877	1		343	284	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360522	70360522	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027661-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	26	293	0	ENST00000374080.3:c.6082A>C	p.Ser2028Arg	p.S2028R	ENST00000374080		2028	Agt/Cgt	42/45	1	1	FACETS	0.18	0.142	0.224	0.18	0.142	0.224	SUBCLONAL	1	TRUE	0	0.509225758663877	1		293	422	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0027662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	82	764	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.18714821122419	2		764	748	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0027662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	56	308	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.9	0.77	1	0.9	0.77	1	CLONAL	1	FALSE	1	0.18714821122419	2		308	665	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073647	8073647	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	58	395	0	ENST00000377482.5:c.1012C>G	p.Leu338Val	p.L338V	ENST00000377482	NM_018948.3	338	Ctt/Gtt	4/4	1	2	FACETS	0.929	0.798	1	0.929	0.798	1	CLONAL	1	FALSE	1	0.18714821122419	2		395	667	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551366	150551366	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	121	672	0	ENST00000369026.2:c.641G>C	p.Arg214Pro	p.R214P	ENST00000369026	NM_021960.4	214	cGa/cCa	1/3	0.186360693621774	3	FACETS	1	0.962	1	0.569	0.513	0.629	CLONAL	1	FALSE	1	0.18714821122419	3		672	1242	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235861	108235861	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	60	406	0	ENST00000278616.4:c.8903T>G	p.Leu2968Trp	p.L2968W	ENST00000278616	NM_000051.3	2968	tTg/tGg	62/63	0.186360693621774	3	FACETS	0.818	0.703	0.944	0.409	0.351	0.472	CLONAL	1	FALSE	1	0.18714821122419	3		406	857	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954319	48954319	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	108	351	0	ENST00000267163.4:c.1440C>A	p.Asn480Lys	p.N480K	ENST00000267163	NM_000321.2	480	aaC/aaA	16/27	0.18714821122419	5	FACETS	0.867	0.778	0.963	0.578	0.518	0.642	CLONAL	2	FALSE	2	0.18714821122419	5		351	852	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201059	NA	P-0027662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	190	598	0	ENST00000269305.4:c.856G>T	p.Glu286Ter	p.E286*	ENST00000269305	NM_001126112.2	286	Gaa/Taa	8/11	0.18714821122419	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	FALSE	0	0.18714821122419	2		598	944	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632241	215632241	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs371785856	NA	P-0027662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	55	367	0	ENST00000260947.4:c.1533G>T	p.Lys511Asn	p.K511N	ENST00000260947	NM_000465.2	511	aaG/aaT	6/11	0.186360693621774	3	FACETS	0.866	0.74	1	0.433	0.37	0.503	CLONAL	1	FALSE	1	0.18714821122419	3		367	742	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319334	62319334	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1352	80	573	0	ENST00000360203.5:c.1526A>C	p.His509Pro	p.H509P	ENST00000360203	NM_001283009.1	509	cAc/cCc	18/35	0.18714821122419	6	FACETS	0.82	0.719	0.93	0.164	0.143	0.186	CLONAL	1	FALSE	1	0.18714821122419	6		573	1432	SUCCESS
APC	324	MSKCC	GRCh37	5	112090669	112090669	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	52	401	0	ENST00000257430.4:c.82G>T	p.Glu28Ter	p.E28*	ENST00000257430	NM_000038.5	28	Gaa/Taa	2/16	1	2	FACETS	0.81	0.689	0.944	0.81	0.689	0.944	CLONAL	1	FALSE	1	0.18714821122419	2		401	686	SUCCESS
APC	324	MSKCC	GRCh37	5	112173783	112173783	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0027662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	60	319	0	ENST00000257430.4:c.2492T>A	p.Leu831Ter	p.L831*	ENST00000257430	NM_000038.5	831	tTa/tAa	16/16	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	FALSE	1	0.18714821122419	2		319	577	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450405	50450405	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1271463285	NA	P-0027662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	103	354	0	ENST00000331340.3:c.589G>A	p.Val197Ile	p.V197I	ENST00000331340	NM_006060.4	197	Gtt/Att	5/8	0.18714821122419	5	FACETS	1	0.941	1	0.715	0.641	0.794	CLONAL	2	FALSE	2	0.18714821122419	5		354	657	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884798	151884798	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0027662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	55	309	0	ENST00000262189.6:c.4793+2T>A		p.X1598_splice	ENST00000262189	NM_170606.2	1598			0.186360693621774	3	FACETS	0.971	0.83	1	0.485	0.415	0.563	CLONAL	1	FALSE	1	0.18714821122419	3		309	662	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050744	5050744	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	153	451	0	ENST00000381652.3:c.527A>T	p.Glu176Val	p.E176V	ENST00000381652	NM_004972.3	176	gAa/gTa	6/25	0.186360693621774	3	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	FALSE	1	0.18714821122419	3		451	882	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781504	NA	P-0027709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	113	869	0	ENST00000269305.4:c.314G>T	p.Gly105Val	p.G105V	ENST00000269305	NM_001126112.2	105	gGc/gTc	4/11	0.228549059205271	1	FACETS	0.929	0.835	1	0.929	0.835	1	CLONAL	1	TRUE	0	0.233024615559216	1		869	922	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508754	38508754	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	65	564	0	ENST00000254066.5:c.802A>T	p.Ile268Phe	p.I268F	ENST00000254066	NM_000964.3	268	Atc/Ttc	6/9	1	2	FACETS	0.769	0.666	0.882	0.769	0.666	0.882	SUBCLONAL	1	TRUE	1	0.233024615559216	2		564	725	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630587	187630587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770123806	NA	P-0027709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	83	688	0	ENST00000441802.2:c.395G>A	p.Arg132Gln	p.R132Q	ENST00000441802	NM_005245.3	132	cGa/cAa	2/27	1	2	FACETS	0.873	0.769	0.984	0.873	0.769	0.984	CLONAL	1	TRUE	1	0.233024615559216	2		688	816	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955132	17955132	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	99	869	1	ENST00000458235.1:c.95C>A	p.Ala32Asp	p.A32D	ENST00000458235	NM_000215.3	32	gCt/gAt	2/24	1	2	FACETS	0.872	0.777	0.974	0.872	0.777	0.974	CLONAL	1	TRUE	1	0.233024615559216	2		870	974	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176118146	176118146	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	40	360	0	ENST00000367669.3:c.827G>T	p.Arg276Ile	p.R276I	ENST00000367669	NM_022457.5	276	aGa/aTa	6/20	1	2	FACETS	0.718	0.597	0.854	0.718	0.597	0.854	SUBCLONAL	1	TRUE	1	0.233024615559216	2		360	478	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097648	8097648	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	76	307	0	ENST00000346208.3:c.30G>T	p.Trp10Cys	p.W10C	ENST00000346208		10	tgG/tgT	2/6	1	2	FACETS	0.916	0.809	1	1	0.982	1	CLONAL	2	TRUE	1	0.233024615559216	2		307	356	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741493	17741493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	63	722	1	ENST00000250003.3:c.164C>A	p.Ala55Glu	p.A55E	ENST00000250003	NM_002478.4	55	gCg/gAg	1/3	0.233024615559216	1	FACETS	0.609	0.526	0.7	0.609	0.526	0.7	SUBCLONAL	1	TRUE	0	0.233024615559216	1		723	784	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202072	67202072	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	124	789	0	ENST00000312629.5:c.1175C>G	p.Pro392Arg	p.P392R	ENST00000312629	NM_003952.2	392	cCg/cGg	14/15	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.233024615559216	2		789	997	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123552	108123552	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	33	468	0	ENST00000278616.4:c.1811C>A	p.Pro604His	p.P604H	ENST00000278616	NM_000051.3	604	cCt/cAt	12/63	1	2	FACETS	0.45	0.366	0.546	0.45	0.366	0.546	SUBCLONAL	1	TRUE	1	0.233024615559216	2		468	629	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433086	49433086	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	153	837	0	ENST00000301067.7:c.8285G>T	p.Gly2762Val	p.G2762V	ENST00000301067	NM_003482.3	2762	gGg/gTg	33/54	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.233024615559216	2		837	891	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001457	29001458	+	splice_acceptor_variant,intron_variant	Splice_Site	DNP	TG	TG	CT	novel	NA	P-0027709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	29	271	0	ENST00000282397.4:c.1277-3_1277-2delinsAG		p.X426_splice	ENST00000282397	NM_002019.4	426			1	2	FACETS	0.549	0.44	0.674	0.549	0.44	0.674	SUBCLONAL	1	TRUE	1	0.233024615559216	2		271	453	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281871	49281871	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs200853229	NA	P-0027709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	83	653	0	ENST00000282018.3:c.918C>A	p.Tyr306Ter	p.Y306*	ENST00000282018	NM_020377.2	306	taC/taA	1/1	1	2	FACETS	0.793	0.699	0.895	0.793	0.699	0.895	SUBCLONAL	1	TRUE	1	0.233024615559216	2		653	898	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81534636	81534636	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	44	671	1	ENST00000298171.2:c.281C>T	p.Ser94Leu	p.S94L	ENST00000298171	NM_000369.2	94	tCa/tTa	3/10	1	2	FACETS	0.567	0.474	0.67	0.567	0.474	0.67	SUBCLONAL	1	TRUE	1	0.233024615559216	2		672	666	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572475	95572475	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	80	538	0	ENST00000393063.1:c.2890G>T	p.Glu964Ter	p.E964*	ENST00000393063	NM_030621.3	964	Gag/Tag	19/28	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.233024615559216	2		538	673	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640500	3640500	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	77	806	0	ENST00000294008.3:c.3139G>T	p.Gly1047Trp	p.G1047W	ENST00000294008	NM_032444.2	1047	Ggg/Tgg	12/15	1	2	FACETS	0.693	0.607	0.787	0.693	0.607	0.787	SUBCLONAL	1	TRUE	1	0.233024615559216	2		806	953	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511548	38511548	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	104	605	0	ENST00000254066.5:c.1046A>G	p.Asp349Gly	p.D349G	ENST00000254066	NM_000964.3	349	gAc/gGc	8/9	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.233024615559216	2		605	794	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743344	743344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1341514002	NA	P-0027709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	107	620	0	ENST00000314574.4:c.796G>A	p.Ala266Thr	p.A266T	ENST00000314574	NM_005433.3	266	Gca/Aca	7/12	1	2	FACETS	0.999	0.895	1	0.999	0.895	1	CLONAL	1	TRUE	1	0.233024615559216	2		620	919	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220895	36220895	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	39	247	0	ENST00000222270.7:c.4945G>T	p.Ala1649Ser	p.A1649S	ENST00000222270	NM_014727.1	1649	Gcc/Tcc	23/37	1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	1	0.233024615559216	2		247	328	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791754	42791754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	59	706	2	ENST00000575354.2:c.640C>T	p.His214Tyr	p.H214Y	ENST00000575354	NM_015125.3	214	Cac/Tac	5/20	1	2	FACETS	0.587	0.503	0.678	0.587	0.503	0.678	SUBCLONAL	1	TRUE	1	0.233024615559216	2		708	863	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906412	50906412	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	51	810	2	ENST00000440232.2:c.1073G>T	p.Arg358Leu	p.R358L	ENST00000440232	NM_002691.3	358	cGg/cTg	9/27	1	2	FACETS	0.487	0.412	0.569	0.487	0.412	0.569	SUBCLONAL	1	TRUE	1	0.233024615559216	2		812	899	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543739	29543739	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	53	530	1	ENST00000389048.3:c.1424C>T	p.Pro475Leu	p.P475L	ENST00000389048	NM_004304.4	475	cCt/cTt	7/29	1	2	FACETS	0.772	0.658	0.897	0.772	0.658	0.897	SUBCLONAL	1	TRUE	1	0.233024615559216	2		531	589	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793293	242793293	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	53	876	1	ENST00000334409.5:c.784C>A	p.Pro262Thr	p.P262T	ENST00000334409	NM_005018.2	262	Ccc/Acc	5/5	1	2	FACETS	0.451	0.383	0.526	0.451	0.383	0.526	SUBCLONAL	1	TRUE	1	0.233024615559216	2		877	1009	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851573	134851573	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	73	566	0	ENST00000398015.3:c.979C>A	p.Arg327Ser	p.R327S	ENST00000398015	NM_004441.4	327	Cgc/Agc	5/16	0.233024615559216	1	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	0	0.233024615559216	1		566	537	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474638	138474638	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	49	668	0	ENST00000289153.2:c.355G>C	p.Gly119Arg	p.G119R	ENST00000289153	NM_006219.2	119	Ggg/Cgg	2/22	1	2	FACETS	0.515	0.435	0.604	0.515	0.435	0.604	SUBCLONAL	1	TRUE	1	0.233024615559216	2		668	816	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976570	55976570	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	56	491	0	ENST00000263923.4:c.1255G>T	p.Val419Phe	p.V419F	ENST00000263923	NM_002253.2	419	Gtc/Ttc	9/30	1	2	FACETS	0.941	0.807	1	0.941	0.807	1	CLONAL	1	TRUE	1	0.233024615559216	2		491	511	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029312	143029312	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	26	377	0	ENST00000262992.4:c.2308A>T	p.Asn770Tyr	p.N770Y	ENST00000262992	NM_001101669.1	770	Aat/Tat	21/24	1	2	FACETS	0.453	0.358	0.562	0.453	0.358	0.562	SUBCLONAL	1	TRUE	1	0.233024615559216	2		377	493	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876334	35876334	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1261225210	NA	P-0027709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	74	557	1	ENST00000303115.3:c.1126G>T	p.Ala376Ser	p.A376S	ENST00000303115	NM_002185.3	376	Gca/Tca	8/8	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.233024615559216	2		558	626	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721296	176721296	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	62	412	0	ENST00000439151.2:c.6927G>T	p.Leu2309Phe	p.L2309F	ENST00000439151	NM_022455.4	2309	ttG/ttT	23/23	0.233024615559216	3	FACETS	0.934	0.807	1	0.467	0.403	0.537	CLONAL	1	TRUE	1	0.233024615559216	3		412	636	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412033	116412049	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTCCAGAAGGTATAT	TTTTCCAGAAGGTATAT	-	novel	NA	P-0027826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	573	871	1	ENST00000397752.3:c.3020_3028+8del		p.X1007_splice	ENST00000397752	NM_000245.2	1007		14/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		872	1400	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0027826-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	310	954	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.612719670774435	2	FACETS	0.954	0.913	0.994	0.954	0.913	0.994	CLONAL	2	TRUE	0	0.635817290949035	2		954	511	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178641	108178641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775036118	NA	P-0027826-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	223	188	0	ENST00000278616.4:c.5692C>T	p.Arg1898Ter	p.R1898*	ENST00000278616	NM_000051.3	1898	Cga/Tga	38/63	0.635817290949035	6	FACETS	0.914	0.863	0.964	0.914	0.863	0.964	CLONAL	4	TRUE	2	0.635817290949035	6		188	436	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155445	47155445	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0027826-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	198	309	0	ENST00000409792.3:c.4636A>T	p.Arg1546Ter	p.R1546*	ENST00000409792	NM_014159.6	1546	Aga/Tga	5/21	0.612719670774435	2	FACETS	0.967	0.916	1	0.967	0.916	1	CLONAL	2	TRUE	0	0.635817290949035	2		309	322	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046294	69046294	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1436851943	NA	P-0027826-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	156	239	0	ENST00000288368.4:c.3767A>G	p.Asp1256Gly	p.D1256G	ENST00000288368	NM_024870.2	1256	gAt/gGt	32/40	0.637842209264349	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.635817290949035	3		239	307	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0027860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	49	764	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.420235459495211	1	FACETS	0.383	0.324	0.447	0.383	0.324	0.447	SUBCLONAL	1	TRUE	0	0.420235459495211	1		764	481	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170399	119170399	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	66	532	1	ENST00000264033.4:c.2629G>T	p.Ala877Ser	p.A877S	ENST00000264033	NM_005188.3	877	Gct/Tct	16/16	0.212894745425215	1	FACETS	0.405	0.352	0.464	0.405	0.352	0.464	INDETERMINATE	1	TRUE	0	0.420235459495211	1		533	612	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0027860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	178	575	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.420235459495211	1	FACETS	0.946	0.875	1	0.946	0.875	1	CLONAL	1	TRUE	0	0.420235459495211	1		575	707	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0027860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	225	657	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.420235459495211	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.420235459495211	1		657	697	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390186	89390186	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	136	407	0	ENST00000336596.2:c.935G>T	p.Arg312Leu	p.R312L	ENST00000336596	NM_005233.5	312	cGg/cTg	4/17	0.420235459495211	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.420235459495211	1		407	480	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191218	185191218	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	54	419	0	ENST00000265026.3:c.2099C>T	p.Ser700Phe	p.S700F	ENST00000265026	NM_004721.4	700	tCc/tTc	11/14	0.420235459495211	1	FACETS	0.466	0.398	0.539	0.466	0.398	0.539	SUBCLONAL	1	TRUE	0	0.420235459495211	1		419	436	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970900	21970900	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0027860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	166	692	0	ENST00000304494.5:c.457+1G>T		p.X153_splice	ENST00000304494	NM_000077.4	153			0.420235459495211	1	FACETS	0.975	0.899	1	0.975	0.899	1	CLONAL	1	TRUE	0	0.420235459495211	1		692	640	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	191	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.394115966813847	3	FACETS	0.969	0.902	1	0.969	0.902	1	CLONAL	2	TRUE	1	0.425326066843598	3		426	562	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577555	7577555	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	348	581	0	ENST00000269305.4:c.726C>A	p.Cys242Ter	p.C242*	ENST00000269305	NM_001126112.2	242	tgC/tgA	7/11	0.426126304750971	3	FACETS	0.98	0.936	1	0.98	0.936	1	CLONAL	3	TRUE	0	0.425326066843598	3		581	675	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151216555	151216648	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	GGTAGCCCAGGATCGCGATCTTCCGGGACTTGGACTGCGGCATCTTGGCGGCCTCCTCAGCCCCGGCCCAACCACATCAACCGCGGCGGCGGTG	GGTAGCCCAGGATCGCGATCTTCCGGGACTTGGACTGCGGCATCTTGGCGGCCTCCTCAGCCCCGGCCCAACCACATCAACCGCGGCGGCGGTG	AGTA	novel	NA	P-0028207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	10	243	0	ENST00000262187.5:c.-51_43delinsTACT		p.*17*	ENST00000262187	NM_005614.3	?-15/184		1/8	1	2	FACETS	0.235	0.159	0.331	0.235	0.159	0.331	SUBCLONAL	1	TRUE	1	0.425326066843598	2		243	200	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0028262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	501	335	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.771538222332137	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	1	0.771538222332137	4		335	747	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346311	73346311	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	29	308	0	ENST00000377767.4:c.1489A>C	p.Asn497His	p.N497H	ENST00000377767	NM_014953.3	497	Aat/Cat	10/21	1	2	FACETS	0.175	0.14	0.215	0.175	0.14	0.215	SUBCLONAL	1	TRUE	1	0.771538222332137	2		308	430	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259288	36259292	+	protein_altering_variant	In_Frame_Del	DEL	GCCAG	GCCAG	CA	novel	NA	P-0028262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	286	268	1	ENST00000300305.3:c.199_203delinsTG	p.Leu67_Ala68delinsCys	p.L67_A68delinsC	ENST00000300305		67	CTGGCc/TGc	3/8	0.771538222332137	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.771538222332137	3		269	486	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225060	NA	P-0028283-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	367	492	0	ENST00000263967.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000263967	NM_006218.2	104	cCa/cTa	2/21	0.600108987948431	3	FACETS	0.841	0.807	0.875	0.841	0.807	0.875	CLONAL	3	TRUE	0	0.600108987948431	3		492	630	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738607	43738608	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0028283-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	246	488	0	ENST00000382044.4:c.3017_3018del	p.Glu1006ValfsTer13	p.E1006Vfs*13	ENST00000382044	NM_001141980.1	1006	gAG/g	14/28	0.528600204861464	2	FACETS	0.815	0.771	0.859	0.815	0.771	0.859	CLONAL	2	TRUE	0	0.600108987948431	2		488	503	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285201	15285201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028283-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	225	823	0	ENST00000263388.2:c.4414G>A	p.Glu1472Lys	p.E1472K	ENST00000263388	NM_000435.2	1472	Gag/Aag	25/33	0.598613577296779	3	FACETS	0.874	0.813	0.936	0.437	0.406	0.468	CLONAL	1	TRUE	1	0.600108987948431	3		823	1116	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123025153	123025153	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028283-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	115	370	0	ENST00000355640.3:c.1043T>A	p.Leu348His	p.L348H	ENST00000355640		348	cTt/cAt	4/7	1	2	FACETS	0.867	0.786	0.951	0.867	0.786	0.951	CLONAL	1	TRUE	1	0.600108987948431	2		370	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0028570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	140	796	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.545784572085557	3	FACETS	0.552	0.501	0.605	0.184	0.167	0.202	SUBCLONAL	1	TRUE	0	0.545784572085557	3		796	1184	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519975	NA	P-0028570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	1032	864	0	ENST00000269305.4:c.403T>G	p.Cys135Gly	p.C135G	ENST00000269305	NM_001126112.2	135	Tgc/Ggc	5/11	0.545784572085557	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.545784572085557	3		864	1476	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417436	139417436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182763411	NA	P-0028570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	130	645	4	ENST00000277541.6:c.608G>A	p.Arg203His	p.R203H	ENST00000277541	NM_017617.3	203	cGc/cAc	4/34	1	2	FACETS	0.598	0.542	0.656	0.598	0.542	0.656	SUBCLONAL	1	TRUE	1	0.545784572085557	2		649	797	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791489	42791489	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	114	673	0	ENST00000575354.2:c.470C>G	p.Ser157Cys	p.S157C	ENST00000575354	NM_015125.3	157	tCt/tGt	4/20	1	2	FACETS	0.454	0.408	0.502	0.454	0.408	0.502	SUBCLONAL	1	TRUE	1	0.545784572085557	2		673	921	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795523	42795523	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	138	774	0	ENST00000575354.2:c.2603C>A	p.Pro868Gln	p.P868Q	ENST00000575354	NM_015125.3	868	cCg/cAg	10/20	0.149055390813665	3	FACETS	0.568	0.516	0.623	0.284	0.258	0.312	INDETERMINATE	1	TRUE	1	0.545784572085557	3		774	1133	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796856	42796856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	140	844	1	ENST00000575354.2:c.3314C>T	p.Ser1105Leu	p.S1105L	ENST00000575354	NM_015125.3	1105	tCa/tTa	14/20	0.149055390813665	3	FACETS	0.592	0.538	0.649	0.296	0.269	0.325	INDETERMINATE	1	TRUE	1	0.545784572085557	3		845	1103	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098689	178098909	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTTAAACCTGCCATAACTTTCCCAAGAACTGAGTACTCTGTACCTGGGAGTAGTTGGCAGATCCACTGGTTTCTGACTGGATGTGCTGGGCTGGCTGAATTGGGAGAAATTCACCTGTCTCTTCATCTAGTTGTAACTGAGCGAAAAAGGCTTTCTCTTGCTCCTTTTGGAGTTGTTCTTGTCTTTCCTTTTCAAGTTTTTTCTGTTTTTCCAGCTCATA	CCTTAAACCTGCCATAACTTTCCCAAGAACTGAGTACTCTGTACCTGGGAGTAGTTGGCAGATCCACTGGTTTCTGACTGGATGTGCTGGGCTGGCTGAATTGGGAGAAATTCACCTGTCTCTTCATCTAGTTGTAACTGAGCGAAAAAGGCTTTCTCTTGCTCCTTTTGGAGTTGTTCTTGTCTTTCCTTTTCAAGTTTTTTCTGTTTTTCCAGCTCATA	-	novel	NA	P-0028570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	38	272	0	ENST00000397062.3:c.136_312+44del		p.X46_splice	ENST00000397062	NM_006164.4	46		2/5	0.215448937906265	3	FACETS	0.47	0.389	0.56	0.235	0.194	0.28	INDETERMINATE	1	TRUE	1	0.545784572085557	3		272	377	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538787	23538787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	64	439	0	ENST00000380871.4:c.652C>T	p.Pro218Ser	p.P218S	ENST00000380871	NM_006167.3	218	Cct/Tct	2/2	0.398114902624399	1	FACETS	0.344	0.298	0.393	0.344	0.298	0.393	SUBCLONAL	1	TRUE	0	0.545784572085557	1		439	496	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261640	16261640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1014687757	NA	P-0028570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	119	607	1	ENST00000375759.3:c.8905G>A	p.Glu2969Lys	p.E2969K	ENST00000375759	NM_015001.2	2969	Gag/Aag	11/15	0.196427579413966	5	FACETS	0.681	0.613	0.753			1	INDETERMINATE	1	TRUE	NA	0.545784572085557	5		608	1165	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46271087	46271087	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	86	554	0	ENST00000371998.3:c.3211G>T	p.Glu1071Ter	p.E1071*	ENST00000371998		1071	Gaa/Taa	17/23	1	2	FACETS	0.332	0.293	0.374	0.332	0.293	0.374	SUBCLONAL	1	TRUE	1	0.545784572085557	2		554	949	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443857	52443883	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CCTGGGTCGCTCTCCAGCTCCAGCCAG	CCTGGGTCGCTCTCCAGCTCCAGCCAG	-	novel	NA	P-0028570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	112	653	0	ENST00000460680.1:c.12_37+1del		p.X4_splice	ENST00000460680	NM_004656.3	4		1/17	0.545784572085557	1	FACETS	0.499	0.45	0.551	0.499	0.45	0.551	SUBCLONAL	1	TRUE	0	0.545784572085557	1		653	598	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31483689	31483689	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	45	412	0	ENST00000344624.3:c.2043C>G	p.Phe681Leu	p.F681L	ENST00000344624		681	ttC/ttG	13/33	NA	2	FACETS	0.233	0.195	0.275			1	INDETERMINATE	1	TRUE	NA	0.545784572085557	2		412	708	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180049840	180049840	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0028570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	64	715	0	ENST00000261937.6:c.1549-1G>A		p.X517_splice	ENST00000261937	NM_182925.4	517			0.545784572085557	2	FACETS	0.289	0.25	0.332	0.145	0.125	0.166	SUBCLONAL	1	TRUE	0	0.545784572085557	2		715	811	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332699	153332699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780061054	NA	P-0028570-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	246	440	0	ENST00000281708.4:c.257C>T	p.Ser86Leu	p.S86L	ENST00000281708	NM_033632.3	86	tCg/tTg	2/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.794427845778444	2		440	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0028570-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	303	796	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.794427845778444	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.794427845778444	1		796	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0028570-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	10	556	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.794427845778444	1	FACETS	0.038	0.025	0.054	0.038	0.025	0.054	SUBCLONAL	1	TRUE	0	0.794427845778444	1		556	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519975	NA	P-0028570-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	381	864	0	ENST00000269305.4:c.403T>G	p.Cys135Gly	p.C135G	ENST00000269305	NM_001126112.2	135	Tgc/Ggc	5/11	0.794427845778444	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.794427845778444	1		864	488	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417436	139417436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182763411	NA	P-0028570-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	327	645	4	ENST00000277541.6:c.608G>A	p.Arg203His	p.R203H	ENST00000277541	NM_017617.3	203	cGc/cAc	4/34	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.794427845778444	2		649	752	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791489	42791489	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028570-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	309	673	0	ENST00000575354.2:c.470C>G	p.Ser157Cys	p.S157C	ENST00000575354	NM_015125.3	157	tCt/tGt	4/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.794427845778444	2		673	699	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795523	42795523	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028570-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	326	774	0	ENST00000575354.2:c.2603C>A	p.Pro868Gln	p.P868Q	ENST00000575354	NM_015125.3	868	cCg/cAg	10/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.794427845778444	2		774	717	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796856	42796856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028570-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	348	844	1	ENST00000575354.2:c.3314C>T	p.Ser1105Leu	p.S1105L	ENST00000575354	NM_015125.3	1105	tCa/tTa	14/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.794427845778444	2		845	853	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098689	178098909	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTTAAACCTGCCATAACTTTCCCAAGAACTGAGTACTCTGTACCTGGGAGTAGTTGGCAGATCCACTGGTTTCTGACTGGATGTGCTGGGCTGGCTGAATTGGGAGAAATTCACCTGTCTCTTCATCTAGTTGTAACTGAGCGAAAAAGGCTTTCTCTTGCTCCTTTTGGAGTTGTTCTTGTCTTTCCTTTTCAAGTTTTTTCTGTTTTTCCAGCTCATA	CCTTAAACCTGCCATAACTTTCCCAAGAACTGAGTACTCTGTACCTGGGAGTAGTTGGCAGATCCACTGGTTTCTGACTGGATGTGCTGGGCTGGCTGAATTGGGAGAAATTCACCTGTCTCTTCATCTAGTTGTAACTGAGCGAAAAAGGCTTTCTCTTGCTCCTTTTGGAGTTGTTCTTGTCTTTCCTTTTCAAGTTTTTTCTGTTTTTCCAGCTCATA	-	novel	NA	P-0028570-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	98	272	0	ENST00000397062.3:c.136_312+44del		p.X46_splice	ENST00000397062	NM_006164.4	46		2/5	0.794427845778444	3	FACETS	1	0.964	1	0.573	0.517	0.63	CLONAL	1	TRUE	1	0.794427845778444	3		272	301	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538787	23538787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028570-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	166	439	0	ENST00000380871.4:c.652C>T	p.Pro218Ser	p.P218S	ENST00000380871	NM_006167.3	218	Cct/Tct	2/2	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.794427845778444	2		439	382	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438735	49438736	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAGTACTG	novel	NA	P-0028570-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	244	513	0	ENST00000301067.7:c.4747_4754dup	p.Arg1586SerfsTer10	p.R1586Sfs*10	ENST00000301067	NM_003482.3	1585	ttt/ttCAGTACTTt	19/54	1	2	FACETS	0.848	0.796	0.902	0.848	0.796	0.902	CLONAL	1	TRUE	1	0.794427845778444	2		513	724	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36934823	36934823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145256322	NA	P-0028675-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	51	281	0	ENST00000361632.4:c.1510G>A	p.Val504Met	p.V504M	ENST00000361632		504	Gtg/Atg	11/16	0.781584932556661	2	FACETS	0.811	0.703	0.924	0.405	0.351	0.462	CLONAL	1	TRUE	0	0.781584932556661	2		281	161	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578474	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028675-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	216	458	2	ENST00000269305.4:c.456del	p.Gly154AlafsTer16	p.G154Afs*16	ENST00000269305	NM_001126112.2	152	ccG/cc	5/11	0.769567232268238	2	FACETS	0.886	0.845	0.925	0.886	0.845	0.925	CLONAL	2	TRUE	0	0.781584932556661	2		460	312	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026757	6026758	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs863224498	NA	P-0028675-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	19	147	0	ENST00000265849.7:c.1638_1639del	p.Ser547ArgfsTer14	p.S547Rfs*14	ENST00000265849	NM_000535.5	546	ttTTca/ttca	11/15	0.781584932556661	4	FACETS	0.841	0.649	1	0.28	0.216	0.353	CLONAL	1	TRUE	1	0.781584932556661	4		147	103	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0028691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	472	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.704506798466609	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	1	0.704506798466609	3		298	735	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0028691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	979	686	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.704506798466609	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.704506798466609	3		686	1221	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030465	49030466	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0028691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	309	255	10	ENST00000267163.4:c.1941_1942del	p.Ser648ThrfsTer4	p.S648Tfs*4	ENST00000267163	NM_000321.2	647	cTT/c	19/27	0.704506798466609	3	FACETS	0.986	0.953	1	0.986	0.953	1	CLONAL	3	TRUE	0	0.704506798466609	3		265	401	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245912902	245912902	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1331325646	NA	P-0028691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	117	242	0	ENST00000388985.4:c.1250T>G	p.Leu417Arg	p.L417R	ENST00000388985		417	cTt/cGt	12/12	0.447576016798211	3	FACETS	0.989	0.898	1			1	CLONAL	1	TRUE	NA	0.704506798466609	3		242	454	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137029	64137029	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	259	632	0	ENST00000334205.4:c.1540G>C	p.Val514Leu	p.V514L	ENST00000334205	NM_003942.2	514	Gtg/Ctg	13/17	0.704506798466609	2	FACETS	1	0.971	1	0.524	0.494	0.556	CLONAL	1	TRUE	0	0.704506798466609	2		632	701	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436585	110436585	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	299	725	1	ENST00000375856.3:c.1816T>C	p.Ser606Pro	p.S606P	ENST00000375856	NM_003749.2	606	Tcg/Ccg	1/2	0.659455946673086	4	FACETS	1	0.966	1			1	CLONAL	1	TRUE	NA	0.704506798466609	4		726	1391	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510189	149510189	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	200	517	0	ENST00000261799.4:c.1280C>T	p.Pro427Leu	p.P427L	ENST00000261799	NM_002609.3	427	cCt/cTt	9/23	0.704506798466609	3	FACETS	0.94	0.872	1	0.47	0.436	0.505	CLONAL	1	TRUE	1	0.704506798466609	3		517	817	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956723	68956723	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs750933833	NA	P-0029290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	119	418	0	ENST00000288368.4:c.841C>T	p.Arg281Trp	p.R281W	ENST00000288368	NM_024870.2	281	Cgg/Tgg	8/40	0.103572096284722	4	FACETS	0.862	0.78	0.948	0.862	0.78	0.948	INDETERMINATE	2	TRUE	2	0.279530632358842	4		418	632	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971192	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCGCT	GGGCGCT	-	novel	NA	P-0029290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	57	334	0	ENST00000304494.5:c.166_172del	p.Ser56GlufsTer88	p.S56Efs*88	ENST00000304494	NM_000077.4	56	AGCGCCCga/ga	2/3	0.279530632358842	1	FACETS	0.833	0.717	0.96	0.833	0.717	0.96	CLONAL	1	TRUE	0	0.279530632358842	1		334	421	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998718	100998718	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	115	650	0	ENST00000325455.5:c.1084G>A	p.Ala362Thr	p.A362T	ENST00000325455	NM_001202474.3	362	Gcg/Acg	1/8	0.0974970452341952	3	FACETS	1	0.904	1	0.503	0.452	0.556	INDETERMINATE	1	TRUE	1	0.279530632358842	3		650	933	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610554	81610554	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	47	380	0	ENST00000298171.2:c.2152G>T	p.Asp718Tyr	p.D718Y	ENST00000298171	NM_000369.2	718	Gat/Tat	10/10	0.279530632358842	2	FACETS	0.678	0.572	0.795	0.339	0.286	0.398	SUBCLONAL	1	TRUE	0	0.279530632358842	2		380	496	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90645587	90645597	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGAGCGAGC	GCAGAGCGAGC	-	novel	NA	P-0029290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	41	88	0	ENST00000330062.3:c.26_36del	p.Arg9GlnfsTer44	p.R9Qfs*44	ENST00000330062	NM_002168.2	9	cGCTCGCTCTGC/c	1/11	0.267464673409811	3	FACETS	1	0.955	1	0.727	0.611	0.854	CLONAL	1	TRUE	1	0.279530632358842	3		88	230	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056547	26056547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749161844	NA	P-0029290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	31	214	0	ENST00000343677.2:c.110G>A	p.Gly37Asp	p.G37D	ENST00000343677	NM_005319.3	37	gGt/gAt	1/1	0.14415923345935	4	FACETS	0.85	0.688	1	0.425	0.344	0.516	INDETERMINATE	1	TRUE	2	0.279530632358842	4		214	334	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622516	158622516	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906589	NA	P-0029293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	59	487	0	ENST00000263640.3:c.983G>A	p.Gly328Glu	p.G328E	ENST00000263640	NM_001105.4	328	gGg/gAg	8/11	1	2	FACETS	0.454	0.391	0.522	0.454	0.391	0.522	SUBCLONAL	1	TRUE	1	0.566464112405669	2		487	459	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397639	139397639	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	191	744	0	ENST00000277541.6:c.5162T>G	p.Val1721Gly	p.V1721G	ENST00000277541	NM_017617.3	1721	gTg/gGg	27/34	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.566464112405669	2		744	609	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390904	139390908	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGT	CAGGT	ACTG	novel	NA	P-0029293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	198	928	2	ENST00000277541.6:c.7283_7287delinsCAGT	p.His2428ProfsTer7	p.H2428Pfs*7	ENST00000277541	NM_017617.3	2428	cACCTG/cCAGT	34/34	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.566464112405669	2		930	621	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029610-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	27	326	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.804	1	1	0.804	1	CLONAL	1	TRUE	1	0.310171757189654	2		326	174	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929428	44929429	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0029610-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	89	323	0	ENST00000377967.4:c.2530dup	p.Leu844ProfsTer2	p.L844Pfs*2	ENST00000377967	NM_021140.2	843	agc/agCc	17/29	1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.310171757189654	1		323	327	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864519	57864519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs572181120	NA	P-0029610-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	29	659	1	ENST00000228682.2:c.1996C>T	p.Pro666Ser	p.P666S	ENST00000228682	NM_005269.2	666	Cca/Tca	12/12	1	2	FACETS	0.348	0.279	0.428	0.348	0.279	0.428	SUBCLONAL	1	TRUE	1	0.310171757189654	2		660	537	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853200	68853201	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0030800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	285	608	0	ENST00000261769.5:c.1585_1586del	p.Thr529CysfsTer7	p.T529Cfs*7	ENST00000261769	NM_004360.3	528	gAC/g	11/16	0.350301766360512	3	FACETS	0.887	0.841	0.933			1	CLONAL	3	TRUE	NA	0.418369885911419	3		608	619	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197599	106197599	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555385319	NA	P-0030800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	168	455	0	ENST00000380013.4:c.5932G>A	p.Val1978Met	p.V1978M	ENST00000380013	NM_001127208.2	1978	Gtg/Atg	11/11	0.342133125634592	4	FACETS	0.89	0.821	0.961	0.89	0.821	0.961	CLONAL	2	TRUE	2	0.418369885911419	4		455	640	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542593	187542593	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	213	533	0	ENST00000441802.2:c.5147C>G	p.Ser1716Cys	p.S1716C	ENST00000441802	NM_005245.3	1716	tCt/tGt	10/27	0.342133125634592	4	FACETS	0.946	0.882	1	0.946	0.882	1	CLONAL	2	TRUE	2	0.418369885911419	4		533	763	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462501	92462501	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	264	617	2	ENST00000265734.4:c.137G>A	p.Arg46Gln	p.R46Q	ENST00000265734	NM_001259.6	46	cGg/cAg	2/8	0.363560956286441	3	FACETS	0.923	0.868	0.979	0.923	0.868	0.979	CLONAL	2	TRUE	1	0.418369885911419	3		619	827	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820290	139820290	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	270	695	0	ENST00000247668.2:c.1443G>C	p.Lys481Asn	p.K481N	ENST00000247668	NM_021138.3	481	aaG/aaC	11/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.418369885911419	NA		695	995	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0031215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	451	676	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.720735140311795	3	FACETS	0.988	0.964	1	0.988	0.964	1	CLONAL	3	TRUE	0	0.762903856227983	3		676	551	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215609829	215609829	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	85	539	0	ENST00000260947.4:c.1865T>C	p.Leu622Pro	p.L622P	ENST00000260947	NM_000465.2	622	cTt/cCt	9/11	0.762903856227983	6	FACETS	0.627	0.553	0.706	0.157	0.138	0.177	SUBCLONAL	1	TRUE	2	0.762903856227983	6		539	898	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197343	26197343	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	93	483	0	ENST00000356476.2:c.136A>C	p.Thr46Pro	p.T46P	ENST00000356476		46	Acg/Ccg	1/1	0.762903856227983	4	FACETS	0.707	0.629	0.789	0.236	0.209	0.263	SUBCLONAL	1	TRUE	1	0.762903856227983	4		483	608	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0031240-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	38	761	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.3	3	FACETS	0.422	0.348	0.506	0.211	0.174	0.253	SUBCLONAL	1	TRUE	1	0.27	3		761	757	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0031240-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	15	442	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.712	0.524	0.936	0.712	0.524	0.936	CLONAL	1	TRUE	1	0.27	2		442	156	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0031240-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	116	685	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.27	2		685	757	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063346	67063346	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031240-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	37	518	0	ENST00000412916.2:c.36C>G	p.Phe12Leu	p.F12L	ENST00000412916		12	ttC/ttG	1/6	1	2	FACETS	0.428	0.351	0.513	0.428	0.351	0.513	SUBCLONAL	1	TRUE	1	0.27	2		518	641	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663346	227663346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024227751	NA	P-0031240-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	61	544	0	ENST00000305123.5:c.109G>A	p.Glu37Lys	p.E37K	ENST00000305123	NM_005544.2	37	Gag/Aag	1/2	1	2	FACETS	0.672	0.579	0.774	0.672	0.579	0.774	SUBCLONAL	1	TRUE	1	0.27	2		544	672	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163720	32163720	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031240-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	58	577	0	ENST00000375023.3:c.5506G>T	p.Glu1836Ter	p.E1836*	ENST00000375023	NM_004557.3	1836	Gag/Tag	30/30	0.148634513079638	2	FACETS	0.548	0.47	0.634	0.274	0.235	0.317	INDETERMINATE	1	TRUE	0	0.27	2		577	784	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436189	110436189	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1360944265	NA	P-0031240-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	52	664	0	ENST00000375856.3:c.2212G>A	p.Glu738Lys	p.E738K	ENST00000375856	NM_003749.2	738	Gag/Aag	1/2	1	2	FACETS	0.489	0.415	0.571	0.489	0.415	0.571	SUBCLONAL	1	TRUE	1	0.27	2		664	787	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205277	61205277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031240-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	40	477	0	ENST00000301761.2:c.217G>A	p.Glu73Lys	p.E73K	ENST00000301761	NM_017841.2	73	Gag/Aag	2/4	1	2	FACETS	0.509	0.422	0.606	0.509	0.422	0.606	SUBCLONAL	1	TRUE	1	0.27	2		477	582	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300137	137300137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540273274	NA	P-0031240-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	51	665	4	ENST00000481739.1:c.422G>A	p.Arg141His	p.R141H	ENST00000481739	NM_002957.4	141	cGc/cAc	3/10	1	2	FACETS	0.499	0.423	0.583	0.499	0.423	0.583	SUBCLONAL	1	TRUE	1	0.27	2		669	757	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814825	139814825	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031240-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	88	654	0	ENST00000247668.2:c.818A>C	p.Glu273Ala	p.E273A	ENST00000247668	NM_021138.3	273	gAg/gCg	8/11	1	2	FACETS	0.781	0.691	0.877	0.781	0.691	0.877	SUBCLONAL	1	TRUE	1	0.27	2		654	835	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245750	46245750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031240-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	39	615	0	ENST00000334344.6:c.3844G>A	p.Asp1282Asn	p.D1282N	ENST00000334344	NM_152641.2	1282	Gat/Aat	15/21	1	2	FACETS	0.427	0.353	0.51	0.427	0.353	0.51	SUBCLONAL	1	TRUE	1	0.27	2		615	677	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434435	49434435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1459498988	NA	P-0031240-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	44	689	0	ENST00000301067.7:c.7118C>T	p.Ser2373Phe	p.S2373F	ENST00000301067	NM_003482.3	2373	tCc/tTc	31/54	1	2	FACETS	0.37	0.309	0.438	0.37	0.309	0.438	SUBCLONAL	1	TRUE	1	0.27	2		689	880	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026377	48026377	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs762814792	NA	P-0031240-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	36	613	0	ENST00000234420.5:c.1255C>T	p.Gln419Ter	p.Q419*	ENST00000234420	NM_000179.2	419	Cag/Tag	4/10	1	2	FACETS	0.404	0.331	0.486	0.404	0.331	0.486	SUBCLONAL	1	TRUE	1	0.27	2		613	660	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102837	71102837	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031240-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	39	546	0	ENST00000318789.4:c.370C>G	p.Gln124Glu	p.Q124E	ENST00000318789	NM_032682.5	124	Cag/Gag	8/21	1	2	FACETS	0.384	0.317	0.459	0.384	0.317	0.459	SUBCLONAL	1	TRUE	1	0.27	2		546	752	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198198	185198198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031240-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	56	542	0	ENST00000265026.3:c.2680G>A	p.Glu894Lys	p.E894K	ENST00000265026	NM_004721.4	894	Gag/Aag	13/14	1	2	FACETS	0.616	0.527	0.714	0.616	0.527	0.714	SUBCLONAL	1	TRUE	1	0.27	2		542	673	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165288	32165288	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs754599630	NA	P-0031240-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	79	603	0	ENST00000375023.3:c.4840G>C	p.Glu1614Gln	p.E1614Q	ENST00000375023	NM_004557.3	1614	Gag/Cag	27/30	0.148634513079638	2	FACETS	0.764	0.671	0.864	0.382	0.335	0.432	INDETERMINATE	1	TRUE	0	0.27	2		603	766	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907692	76907692	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031240-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	44	468	0	ENST00000373344.5:c.4469G>C	p.Arg1490Thr	p.R1490T	ENST00000373344	NM_000489.3	1490	aGa/aCa	15/35	1	2	FACETS	0.608	0.509	0.717	0.608	0.509	0.717	SUBCLONAL	1	TRUE	1	0.27	2		468	536	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830288	72830288	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	25	409	0	ENST00000268489.5:c.6293C>T	p.Ser2098Leu	p.S2098L	ENST00000268489	NM_006885.3	2098	tCg/tTg	9/10	1	2	FACETS	0.978	0.769	1	0.978	0.769	1	CLONAL	1	TRUE	1	0.11	2		409	465	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224594	108224594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658519	NA	P-0031298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	29	380	0	ENST00000278616.4:c.8773G>A	p.Gly2925Ser	p.G2925S	ENST00000278616	NM_000051.3	2925	Ggt/Agt	60/63	1	2	FACETS	0.969	0.776	1	0.969	0.776	1	CLONAL	1	TRUE	1	0.11	2		380	544	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875920	76875920	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	297	206	0	ENST00000373344.5:c.5215C>T	p.Arg1739Ter	p.R1739*	ENST00000373344	NM_000489.3	1739	Cga/Tga	20/35	0.820864406751548	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.865370004504738	2		206	313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573956	7573977	+	frameshift_variant	Frame_Shift_Del	DEL	CTTCCCAGCCTGGGCATCCTTG	CTTCCCAGCCTGGGCATCCTTG	-	novel	NA	P-0031601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	362	423	0	ENST00000269305.4:c.1050_1071del	p.Lys351SerfsTer12	p.K351Sfs*12	ENST00000269305	NM_001126112.2	350	ctCAAGGATGCCCAGGCTGGGAAG/ct	10/11	0.845740787726536	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.865370004504738	2		423	411	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739438	145739439	+	missense_variant	Missense_Mutation	DNP	GG	GG	CC	novel	NA	P-0031601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	96	468	1	ENST00000428558.2:c.1931_1932inv	p.Ala644Gly	p.A644G	ENST00000428558	NM_004260.3	644	gCC/gGG	12/22	0.701895848246586	5	FACETS	0.663	0.59	0.74	0.221	0.196	0.247	SUBCLONAL	1	TRUE	2	0.865370004504738	5		469	769	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739439	145739439	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	92	455	0	ENST00000428558.2:c.1931C>G	p.Ala644Gly	p.A644G	ENST00000428558	NM_004260.3	644	gCc/gGc	12/22	0.701895848246586	5	FACETS	0.65	0.577	0.727	0.217	0.192	0.243	SUBCLONAL	1	TRUE	2	0.865370004504738	5		455	752	SUCCESS
ATR	545	MSKCC	GRCh37	3	142185254	142185254	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	55	386	0	ENST00000350721.4:c.6809T>A	p.Leu2270His	p.L2270H	ENST00000350721	NM_001184.3	2270	cTt/cAt	40/47	0.453629520126888	4	FACETS	0.55	0.47	0.638	0.183	0.156	0.213	SUBCLONAL	1	TRUE	1	0.453629520126888	4		386	641	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0031772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	154	836	0	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	0.16013026709562	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.247583337436315	1		836	1061	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61197631	61197631	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs775763888	NA	P-0031772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	56	441	0	ENST00000301761.2:c.13A>G	p.Thr5Ala	p.T5A	ENST00000301761	NM_017841.2	5	Aca/Gca	1/4	1	2	FACETS	0.55	0.47	0.638	0.55	0.47	0.638	SUBCLONAL	1	TRUE	1	0.247583337436315	2		441	822	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70411679	70411679	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	38	429	0	ENST00000373644.4:c.4353A>T	p.Glu1451Asp	p.E1451D	ENST00000373644	NM_030625.2	1451	gaA/gaT	5/12	1	2	FACETS	0.44	0.363	0.528	0.44	0.363	0.528	SUBCLONAL	1	TRUE	1	0.247583337436315	2		429	697	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426722	212426722	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	41	423	0	ENST00000342788.4:c.2393T>C	p.Leu798Pro	p.L798P	ENST00000342788	NM_005235.2	798	cTt/cCt	20/28	1	2	FACETS	0.484	0.402	0.575	0.484	0.402	0.575	SUBCLONAL	1	TRUE	1	0.247583337436315	2		423	685	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589020	67589025	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	ACACTA	ACACTA	-	novel	NA	P-0031772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	18	227	0	ENST00000274335.5:c.1112_1117del	p.Thr371_Leu372del	p.T371_L372del	ENST00000274335		371	ACACTA/-	8/15	0.227075558696465	1	FACETS	0.455	0.342	0.588	0.455	0.342	0.588	SUBCLONAL	1	TRUE	0	0.247583337436315	1		227	280	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180351	27180351	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	25	328	0	ENST00000380036.4:c.1015C>A	p.Gln339Lys	p.Q339K	ENST00000380036	NM_000459.3	339	Cag/Aag	7/23	0.227075558696465	1	FACETS	0.377	0.297	0.471	0.377	0.297	0.471	SUBCLONAL	1	TRUE	0	0.247583337436315	1		328	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0032093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	771	797	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.490682376896314	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	4	TRUE	0	0.49677859719644	4		799	1107	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0032093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	334	574	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	0.499297906445035	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.49677859719644	3		574	819	SUCCESS
APC	324	MSKCC	GRCh37	5	112179309	112179309	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs539168162	NA	P-0032093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	102	356	0	ENST00000257430.4:c.8018G>C	p.Arg2673Thr	p.R2673T	ENST00000257430	NM_000038.5	2673	aGa/aCa	16/16	0.499297906445035	3	FACETS	1	0.951	1	0.549	0.493	0.607	CLONAL	1	TRUE	1	0.49677859719644	3		356	467	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141549486	141549486	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	142	500	0	ENST00000220592.5:c.2102G>C	p.Gly701Ala	p.G701A	ENST00000220592	NM_012154.3	701	gGg/gCg	16/19	0.311675937398862	5	FACETS	1	0.981	1	0.424	0.386	0.463	CLONAL	1	TRUE	2	0.49677859719644	5		500	785	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740487	145740551	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGCAGCCTGGCCTCAGCCCAGCCTCAGCCCTGGCAGCCACGCTCACCAGACAGGATCCGCATGA	CTGCAGCCTGGCCTCAGCCCAGCCTCAGCCCTGGCAGCCACGCTCACCAGACAGGATCCGCATGA	-	novel	NA	P-0032093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1312	354	703	0	ENST00000428558.2:c.1466_1484-31del		p.X489_splice	ENST00000428558	NM_004260.3	489		8/22	0.49677859719644	7	FACETS	0.959	0.906	1			1	CLONAL	2	TRUE	NA	0.49677859719644	7		703	1666	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923342	9923342	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397514557	NA	P-0032100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	102	476	0	ENST00000330684.3:c.1945C>G	p.Leu649Val	p.L649V	ENST00000330684	NM_001134407.1	649	Ctg/Gtg	9/13	0.466998021297544	4	FACETS	0.962	0.861	1	0.481	0.43	0.534	CLONAL	1	TRUE	2	0.475668941166477	4		476	658	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117383	115117383	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	93	344	0	ENST00000257566.3:c.791del	p.Pro264LeufsTer18	p.P264Lfs*18	ENST00000257566	NM_016569.3	264	cCt/ct	4/8	0.476015602089774	3	FACETS	1	0.937	1	0.534	0.477	0.594	CLONAL	1	TRUE	1	0.475668941166477	3		344	453	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434971	110434971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	165	794	2	ENST00000375856.3:c.3430C>T	p.Arg1144Cys	p.R1144C	ENST00000375856	NM_003749.2	1144	Cgc/Tgc	1/2	1	2	FACETS	0.984	0.906	1	0.984	0.906	1	CLONAL	1	TRUE	1	0.475668941166477	2		796	705	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845659	68845660	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0032100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	266	485	0	ENST00000261769.5:c.907_908del	p.Thr303HisfsTer7	p.T303Hfs*7	ENST00000261769	NM_004360.3	302	tAC/t	7/16	0.466970047422334	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.475668941166477	2		485	555	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349199	15349199	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	85	393	0	ENST00000263377.2:c.4078A>T	p.Asn1360Tyr	p.N1360Y	ENST00000263377	NM_058243.2	1360	Aat/Tat	20/20	0.476015602089774	3	FACETS	0.852	0.756	0.956	0.426	0.378	0.478	CLONAL	1	TRUE	1	0.475668941166477	3		393	519	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196433	106196433	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs368705448	NA	P-0032100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	115	368	0	ENST00000380013.4:c.4766A>G	p.Tyr1589Cys	p.Y1589C	ENST00000380013	NM_001127208.2	1589	tAt/tGt	11/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.475668941166477	2		368	421	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570311	87570311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285612169	NA	P-0032100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	200	485	1	ENST00000277120.3:c.2051C>T	p.Ala684Val	p.A684V	ENST00000277120		684	gCg/gTg	17/19	0.455592267970069	5	FACETS	0.958	0.89	1	0.639	0.593	0.685	CLONAL	2	TRUE	2	0.475668941166477	5		486	752	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484441	57484441	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	76	400	0	ENST00000371085.3:c.624del	p.Phe208LeufsTer34	p.F208Lfs*34	ENST00000371085	NM_000516.4	208	Ttt/tt	8/13	0.466998021297544	4	FACETS	0.712	0.625	0.807	0.356	0.312	0.404	SUBCLONAL	1	TRUE	2	0.475668941166477	4		400	662	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606469	93606469	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	119	608	0	ENST00000375746.1:c.289G>C	p.Asp97His	p.D97H	ENST00000375746	NM_001174167.1	97	Gat/Cat	2/14	0.455592267970069	5	FACETS	0.955	0.861	1	0.318	0.287	0.352	CLONAL	1	TRUE	2	0.475668941166477	5		608	898	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955538	48955538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913303	NA	P-0032264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	45	293	0	ENST00000267163.4:c.1654C>T	p.Arg552Ter	p.R552*	ENST00000267163	NM_000321.2	552	Cga/Tga	17/27	0.3	1	FACETS	0.895	0.757	1	0.895	0.757	1	CLONAL	1	FALSE	0	0.3	1		293	285	SUCCESS
APC	324	MSKCC	GRCh37	5	112179624	112179624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	16	260	1	ENST00000257430.4:c.8333C>T	p.Ala2778Val	p.A2778V	ENST00000257430	NM_000038.5	2778	gCt/gTt	16/16	1	2	FACETS	0.363	0.268	0.477	0.363	0.268	0.477	SUBCLONAL	1	FALSE	1	0.3	2		261	294	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089764	27089765	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	58	373	0	ENST00000324856.7:c.2721dup	p.Ile908TyrfsTer28	p.I908Yfs*28	ENST00000324856	NM_006015.4	907	tct/tcTt	8/20	1	2	FACETS	0.844	0.727	0.972	0.844	0.727	0.972	CLONAL	1	FALSE	1	0.3	2		373	458	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281768	49281768	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148425155	NA	P-0032266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	259	508	0	ENST00000282018.3:c.815C>T	p.Thr272Met	p.T272M	ENST00000282018	NM_020377.2	272	aCg/aTg	1/1	0.62186321960817	3	FACETS	0.995	0.932	1	0.498	0.466	0.53	CLONAL	1	TRUE	1	0.637376432115636	3		508	1077	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49724690	49724690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	139	332	0	ENST00000449682.2:c.499G>A	p.Glu167Lys	p.E167K	ENST00000449682	NM_020998.3	167	Gaa/Aaa	5/18	0.62186321960817	3	FACETS	0.862	0.787	0.941	0.431	0.393	0.471	CLONAL	1	TRUE	1	0.637376432115636	3		332	667	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89355072	89355072	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	182	347	0	ENST00000301030.4:c.608C>T	p.Thr203Met	p.T203M	ENST00000301030	NM_001256183.1	203	aCg/aTg	7/13	0.62186321960817	3	FACETS	1	0.953	1	0.52	0.481	0.561	CLONAL	1	TRUE	1	0.637376432115636	3		347	724	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	159	430	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.934	0.859	1	0.934	0.859	1	CLONAL	1	TRUE	1	0.50750498950509	2		431	671	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	163	505	4	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.93	0.856	1	0.93	0.856	1	CLONAL	1	TRUE	1	0.50750498950509	2		509	691	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	159	132	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.50750498950509	2		132	611	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564515	55564515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754738766	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	133	492	1	ENST00000288135.5:c.403C>T	p.Arg135Cys	p.R135C	ENST00000288135	NM_000222.2	135	Cgc/Tgc	3/21	1	2	FACETS	0.872	0.795	0.953	0.872	0.795	0.953	CLONAL	1	TRUE	1	0.50750498950509	2		493	601	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	89	556	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.345564573014138	1	FACETS	0.353	0.313	0.396	0.353	0.313	0.396	SUBCLONAL	1	TRUE	0	0.50750498950509	1		562	741	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	94	462	0	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	1	2	FACETS	0.52	0.462	0.581	0.52	0.462	0.581	SUBCLONAL	1	TRUE	1	0.50750498950509	2		462	713	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784404	9784404	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	245	591	0	ENST00000377346.4:c.2789T>C	p.Val930Ala	p.V930A	ENST00000377346	NM_005026.3	930	gTc/gCc	22/24	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.50750498950509	2		591	887	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11168277	11168277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	69	570	0	ENST00000361445.4:c.7595C>T	p.Ala2532Val	p.A2532V	ENST00000361445	NM_004958.3	2532	gCg/gTg	57/58	NA	2	FACETS	0.327	0.284	0.374			1	INDETERMINATE	1	TRUE	NA	0.50750498950509	2		570	832	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190747	11190747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759603938	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	137	656	1	ENST00000361445.4:c.5452C>T	p.Arg1818Cys	p.R1818C	ENST00000361445	NM_004958.3	1818	Cgt/Tgt	39/58	NA	2	FACETS	0.629	0.572	0.688			1	INDETERMINATE	1	TRUE	NA	0.50750498950509	2		657	859	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256633	16256634	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	160	421	0	ENST00000375759.3:c.3899_3900del	p.Ile1300AsnfsTer10	p.I1300Nfs*10	ENST00000375759	NM_015001.2	1300	ATa/a	11/15	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.50750498950509	2		421	554	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932103	36932103	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	147	446	0	ENST00000361632.4:c.2366A>G	p.Asn789Ser	p.N789S	ENST00000361632		789	aAc/aGc	16/16	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.50750498950509	2		446	574	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932353	36932353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	282	687	1	ENST00000361632.4:c.2116C>T	p.Pro706Ser	p.P706S	ENST00000361632		706	Ccg/Tcg	16/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.50750498950509	2		688	1053	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251236	115251236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	173	547	0	ENST00000369535.4:c.490C>T	p.Arg164Cys	p.R164C	ENST00000369535	NM_002524.4	164	Cgc/Tgc	5/7	1	2	FACETS	0.76	0.7	0.823	0.76	0.7	0.823	SUBCLONAL	1	TRUE	1	0.50750498950509	2		547	897	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851325	156851325	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201891311	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	113	582	0	ENST00000524377.1:c.2282G>A	p.Arg761Gln	p.R761Q	ENST00000524377	NM_002529.3	761	cGg/cAg	17/17	1	2	FACETS	0.591	0.531	0.653	0.591	0.531	0.653	SUBCLONAL	1	TRUE	1	0.50750498950509	2		582	754	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729671	162729671	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376303676	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	166	461	1	ENST00000367921.3:c.757G>A	p.Gly253Ser	p.G253S	ENST00000367921	NM_006182.2	253	Ggc/Agc	8/18	1	2	FACETS	0.907	0.835	0.982	0.907	0.835	0.982	CLONAL	1	TRUE	1	0.50750498950509	2		462	721	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70441195	70441195	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	138	521	0	ENST00000373644.4:c.4864C>T	p.Arg1622Ter	p.R1622*	ENST00000373644	NM_030625.2	1622	Cga/Tga	9/12	0.255104077525354	1	FACETS	0.504	0.458	0.551	0.504	0.458	0.551	INDETERMINATE	1	TRUE	0	0.50750498950509	1		521	806	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685298	89685298	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	124	324	0	ENST00000371953.3:c.193T>C	p.Tyr65His	p.Y65H	ENST00000371953	NM_000314.4	65	Tac/Cac	3/9	0.255104077525354	1	FACETS	0.649	0.589	0.711	0.649	0.589	0.711	INDETERMINATE	1	TRUE	0	0.50750498950509	1		324	562	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693003	89693003	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs786204900	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	54	317	0	ENST00000371953.3:c.491del	p.Lys164ArgfsTer3	p.K164Rfs*3	ENST00000371953	NM_000314.4	163	Aaa/aa	5/9	0.255104077525354	1	FACETS	0.34	0.291	0.394	0.34	0.291	0.394	INDETERMINATE	1	TRUE	0	0.50750498950509	1		317	467	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373348	118373348	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	115	436	0	ENST00000534358.1:c.6741T>A	p.Asp2247Glu	p.D2247E	ENST00000534358	NM_005933.3	2247	gaT/gaA	27/36	1	2	FACETS	0.582	0.524	0.643	0.582	0.524	0.643	SUBCLONAL	1	TRUE	1	0.50750498950509	2		436	779	SUCCESS
CBL	867	MSKCC	GRCh37	11	119145604	119145604	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	93	383	1	ENST00000264033.4:c.815del	p.Leu272Ter	p.L272*	ENST00000264033	NM_005188.3	270	gcT/gc	5/16	1	2	FACETS	0.537	0.478	0.601	0.537	0.478	0.601	SUBCLONAL	1	TRUE	1	0.50750498950509	2		384	682	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	317	425	5	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	NA	2	FACETS	0.868	0.824	0.911			1	INDETERMINATE	2	TRUE	NA	0.50750498950509	2		430	720	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628513	21628513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	201	540	0	ENST00000421138.2:c.1105G>A	p.Val369Met	p.V369M	ENST00000421138		369	Gtg/Atg	11/16	1	2	FACETS	0.944	0.876	1	0.944	0.876	1	CLONAL	1	TRUE	1	0.50750498950509	2		540	839	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424180	49424180	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	181	412	0	ENST00000301067.7:c.13882C>T	p.Pro4628Ser	p.P4628S	ENST00000301067	NM_003482.3	4628	Ccc/Tcc	42/54	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.50750498950509	2		412	649	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446151	49446151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	271	641	0	ENST00000301067.7:c.1315C>T	p.Pro439Ser	p.P439S	ENST00000301067	NM_003482.3	439	Cca/Tca	10/54	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.50750498950509	2		641	1045	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447925	49447925	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	125	333	0	ENST00000301067.7:c.511-2A>G		p.X171_splice	ENST00000301067	NM_003482.3	171			1	2	FACETS	0.958	0.872	1	0.958	0.872	1	CLONAL	1	TRUE	1	0.50750498950509	2		333	514	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877335	28877335	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750851829	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	137	453	0	ENST00000282397.4:c.3986C>T	p.Ser1329Leu	p.S1329L	ENST00000282397	NM_002019.4	1329	tCg/tTg	30/30	0.50750498950509	1	FACETS	0.884	0.81	0.96	0.884	0.81	0.96	CLONAL	1	TRUE	0	0.50750498950509	1		453	456	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061063	38061064	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	97	201	0	ENST00000250448.2:c.925dup	p.Leu309ProfsTer106	p.L309Pfs*106	ENST00000250448	NM_004496.3	309	ctc/cCtc	2/2	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.50750498950509	2		201	335	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562347	95562347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140875148	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	69	367	0	ENST00000393063.1:c.4910C>T	p.Ser1637Leu	p.S1637L	ENST00000393063	NM_030621.3	1637	tCg/tTg	24/28	NA	2	FACETS	0.424	0.369	0.484			1	INDETERMINATE	1	TRUE	NA	0.50750498950509	2		367	641	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562994	95562995	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCC	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	105	353	0	ENST00000393063.1:c.4260_4262dup	p.Glu1420dup	p.E1420dup	ENST00000393063	NM_030621.3	1420	gat/gaGGAt	24/28	NA	2	FACETS	0.683	0.613	0.757			1	INDETERMINATE	1	TRUE	NA	0.50750498950509	2		353	606	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022990	33022990	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	42	337	0	ENST00000300177.4:c.104del	p.Pro35ArgfsTer49	p.P35Rfs*49	ENST00000300177	NM_001191322.1	33	atC/at	2/2	0.345564573014138	1	FACETS	0.32	0.267	0.378	0.32	0.267	0.378	SUBCLONAL	1	TRUE	0	0.50750498950509	1		337	386	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42026766	42026766	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1567050204	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	166	386	0	ENST00000219905.7:c.3890T>C	p.Leu1297Ser	p.L1297S	ENST00000219905	NM_001164273.1	1297	tTg/tCg	12/24	0.345564573014138	1	FACETS	0.759	0.7	0.82	0.759	0.7	0.82	SUBCLONAL	1	TRUE	0	0.50750498950509	1		386	643	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478609	99478609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1330526325	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	87	422	0	ENST00000268035.6:c.3251G>A	p.Arg1084Gln	p.R1084Q	ENST00000268035	NM_000875.3	1084	cGg/cAg	17/21	0.255104077525354	1	FACETS	0.396	0.351	0.445	0.396	0.351	0.445	INDETERMINATE	1	TRUE	0	0.50750498950509	1		422	646	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106666	2106666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772558666	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	248	628	0	ENST00000219476.3:c.670G>A	p.Ala224Thr	p.A224T	ENST00000219476	NM_000548.3	224	Gcc/Acc	8/42	0.345564573014138	1	FACETS	0.953	0.895	1	0.953	0.895	1	CLONAL	1	TRUE	0	0.50750498950509	1		628	765	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110762	2110762	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	139	813	0	ENST00000219476.3:c.1067T>C	p.Val356Ala	p.V356A	ENST00000219476	NM_000548.3	356	gTg/gCg	11/42	0.345564573014138	1	FACETS	0.422	0.384	0.463	0.422	0.384	0.463	SUBCLONAL	1	TRUE	0	0.50750498950509	1		813	968	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777952	3777952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	392	967	1	ENST00000262367.5:c.7096C>T	p.Arg2366Trp	p.R2366W	ENST00000262367	NM_004380.2	2366	Cgg/Tgg	31/31	0.345564573014138	1	FACETS	0.985	0.937	1	0.985	0.937	1	CLONAL	1	TRUE	0	0.50750498950509	1		968	1170	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032332	10032332	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	43	372	0	ENST00000330684.3:c.491A>G	p.Asp164Gly	p.D164G	ENST00000330684	NM_001134407.1	164	gAt/gGt	3/13	0.345564573014138	1	FACETS	0.276	0.231	0.326	0.276	0.231	0.326	SUBCLONAL	1	TRUE	0	0.50750498950509	1		372	458	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041627	14041627	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	175	420	0	ENST00000311895.7:c.2174A>C	p.Glu725Ala	p.E725A	ENST00000311895	NM_005236.2	725	gAg/gCg	11/11	0.345564573014138	1	FACETS	0.912	0.845	0.981	0.912	0.845	0.981	CLONAL	1	TRUE	0	0.50750498950509	1		420	564	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771325	68771325	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1064793079	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	45	227	0	ENST00000261769.5:c.7C>A	p.Pro3Thr	p.P3T	ENST00000261769	NM_004360.3	3	Cct/Act	1/16	0.345564573014138	1	FACETS	0.408	0.344	0.478	0.408	0.344	0.478	SUBCLONAL	1	TRUE	0	0.50750498950509	1		227	324	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828963	72828963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	110	636	0	ENST00000268489.5:c.7618C>T	p.Pro2540Ser	p.P2540S	ENST00000268489	NM_006885.3	2540	Ccg/Tcg	9/10	0.345564573014138	1	FACETS	0.408	0.367	0.453	0.408	0.367	0.453	SUBCLONAL	1	TRUE	0	0.50750498950509	1		636	792	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830233	72830234	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	68	351	0	ENST00000268489.5:c.6347dup	p.Gln2117AlafsTer39	p.Q2117Afs*39	ENST00000268489	NM_006885.3	2116	ccg/ccCg	9/10	0.345564573014138	1	FACETS	0.475	0.415	0.54	0.475	0.415	0.54	SUBCLONAL	1	TRUE	0	0.50750498950509	1		351	421	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993581	72993581	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	215	558	1	ENST00000268489.5:c.464del	p.Gly155AlafsTer17	p.G155Afs*17	ENST00000268489	NM_006885.3	155	gGc/gc	2/10	0.345564573014138	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.50750498950509	1		559	632	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805947	89805947	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200215131	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	76	431	2	ENST00000389301.3:c.3949C>T	p.Arg1317Trp	p.R1317W	ENST00000389301	NM_000135.2	1317	Cgg/Tgg	40/43	0.345564573014138	1	FACETS	0.381	0.334	0.431	0.381	0.334	0.431	SUBCLONAL	1	TRUE	0	0.50750498950509	1		433	587	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217850	7217850	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	271	699	3	ENST00000380728.2:c.161del	p.Lys54ArgfsTer9	p.K54Rfs*9	ENST00000380728		54	aAg/ag	3/11	NA	2	FACETS	0.842	0.789	0.896			1	INDETERMINATE	1	TRUE	NA	0.50750498950509	2		702	1269	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217872	7217875	+	frameshift_variant	Frame_Shift_Del	DEL	CTTC	CTTC	-	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	243	612	1	ENST00000380728.2:c.136_139del	p.Glu46AsnfsTer16	p.E46Nfs*16	ENST00000380728		46	GAAGaa/aa	3/11	NA	2	FACETS	0.891	0.832	0.951			1	INDETERMINATE	1	TRUE	NA	0.50750498950509	2		613	1075	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691039	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	230	694	0	ENST00000269305.4:c.919+1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.50750498950509	1	FACETS	0.937	0.877	0.998	0.937	0.877	0.998	CLONAL	1	TRUE	0	0.50750498950509	1		694	722	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487532	38487532	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	89	492	0	ENST00000254066.5:c.62T>C	p.Val21Ala	p.V21A	ENST00000254066	NM_000964.3	21	gTg/gCg	2/9	0.345564573014138	1	FACETS	0.395	0.35	0.443	0.395	0.35	0.443	SUBCLONAL	1	TRUE	0	0.50750498950509	1		492	663	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359707	40359707	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	118	462	0	ENST00000293328.3:c.1946G>A	p.Arg649Lys	p.R649K	ENST00000293328	NM_012448.3	649	aGa/aAa	16/19	0.345564573014138	1	FACETS	0.481	0.434	0.53	0.481	0.434	0.53	SUBCLONAL	1	TRUE	0	0.50750498950509	1		462	722	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40461469	40461469	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	212	774	0	ENST00000345506.4:c.2189G>C	p.Cys730Ser	p.C730S	ENST00000345506	NM_003152.3	730	tGc/tCc	19/20	0.345564573014138	1	FACETS	0.67	0.622	0.719	0.67	0.622	0.719	SUBCLONAL	1	TRUE	0	0.50750498950509	1		774	931	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58701096	58701096	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	103	505	0	ENST00000305921.3:c.687A>C	p.Glu229Asp	p.E229D	ENST00000305921	NM_003620.3	229	gaA/gaC	2/6	0.345564573014138	1	FACETS	0.429	0.384	0.477	0.429	0.384	0.477	SUBCLONAL	1	TRUE	0	0.50750498950509	1		505	706	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59937249	59937249	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555618429	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	81	437	0	ENST00000259008.2:c.113G>A	p.Ser38Asn	p.S38N	ENST00000259008	NM_032043.2	38	aGc/aAc	3/20	0.345564573014138	1	FACETS	0.389	0.343	0.439	0.389	0.343	0.439	SUBCLONAL	1	TRUE	0	0.50750498950509	1		437	612	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214637	5214637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757423838	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	206	679	0	ENST00000357368.4:c.4429C>T	p.Arg1477Cys	p.R1477C	ENST00000357368	NM_002850.3	1477	Cgt/Tgt	29/38	1	2	FACETS	0.886	0.823	0.952	0.886	0.823	0.952	CLONAL	1	TRUE	1	0.50750498950509	2		679	916	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222730	5222731	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs756013055	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	96	514	2	ENST00000357368.4:c.3072dup	p.Val1025ArgfsTer34	p.V1025Rfs*34	ENST00000357368	NM_002850.3	1024	-/C	18/38	1	2	FACETS	0.518	0.461	0.578	0.518	0.461	0.578	SUBCLONAL	1	TRUE	1	0.50750498950509	2		516	731	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135028	11135028	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555779989	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	224	564	0	ENST00000358026.2:c.2995G>A	p.Asp999Asn	p.D999N	ENST00000358026	NM_001128849.1	999	Gac/Aac	21/36	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.50750498950509	2		564	827	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218138	36218138	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	150	376	0	ENST00000222270.7:c.4085A>C	p.His1362Pro	p.H1362P	ENST00000222270	NM_014727.1	1362	cAc/cCc	15/37	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.50750498950509	2		376	572	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753149	42753151	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs199960550	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	199	573	8	ENST00000222329.4:c.1113_1115del	p.Ser373del	p.S373del	ENST00000222329	NM_006494.2	371	tcTTCc/tcc	4/4	1	2	FACETS	0.854	0.792	0.919	0.854	0.792	0.919	CLONAL	1	TRUE	1	0.50750498950509	2		581	918	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753644	42753644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759092904	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	249	693	1	ENST00000222329.4:c.620G>A	p.Arg207Gln	p.R207Q	ENST00000222329	NM_006494.2	207	cGa/cAa	4/4	1	2	FACETS	0.994	0.93	1	0.994	0.93	1	CLONAL	1	TRUE	1	0.50750498950509	2		694	987	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793116	42793117	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	114	729	0	ENST00000575354.2:c.1012dup	p.Ala338GlyfsTer69	p.A338Gfs*69	ENST00000575354	NM_015125.3	336	-/G	7/20	1	2	FACETS	0.404	0.363	0.448	0.404	0.363	0.448	SUBCLONAL	1	TRUE	1	0.50750498950509	2		729	1111	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902166	50902166	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	134	506	0	ENST00000440232.2:c.62del	p.Gly21AlafsTer20	p.G21Afs*20	ENST00000440232	NM_002691.3	20	Ggg/gg	2/27	1	2	FACETS	0.789	0.719	0.863	0.789	0.719	0.863	SUBCLONAL	1	TRUE	1	0.50750498950509	2		506	669	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918125	50918127	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs763850764	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	76	675	0	ENST00000440232.2:c.2446_2448del	p.Ser816del	p.S816del	ENST00000440232	NM_002691.3	814	ttCTCc/ttc	20/27	1	2	FACETS	0.299	0.261	0.34	0.299	0.261	0.34	SUBCLONAL	1	TRUE	1	0.50750498950509	2		675	1001	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719125	52719125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771769470	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	107	504	2	ENST00000322088.6:c.901G>A	p.Ala301Thr	p.A301T	ENST00000322088	NM_014225.5	301	Gca/Aca	7/15	1	2	FACETS	0.519	0.465	0.577	0.519	0.465	0.577	SUBCLONAL	1	TRUE	1	0.50750498950509	2		506	812	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222492	39222492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	222	665	0	ENST00000402219.2:c.3118G>A	p.Val1040Ile	p.V1040I	ENST00000402219	NM_005633.3	1040	Gtt/Att	20/23	NA	2	FACETS	0.809	0.753	0.868			1	INDETERMINATE	1	TRUE	NA	0.50750498950509	2		665	1081	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919674	96919674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140860906	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	151	475	0	ENST00000258439.3:c.589C>T	p.Arg197Cys	p.R197C	ENST00000258439	NM_001193304.2	197	Cgc/Tgc	4/4	1	2	FACETS	0.861	0.789	0.936	0.861	0.789	0.936	CLONAL	1	TRUE	1	0.50750498950509	2		475	691	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095986	178095986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201871588	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	145	468	0	ENST00000397062.3:c.1345C>T	p.Arg449Cys	p.R449C	ENST00000397062	NM_006164.4	449	Cgc/Tgc	5/5	1	2	FACETS	0.849	0.777	0.925	0.849	0.777	0.925	CLONAL	1	TRUE	1	0.50750498950509	2		468	673	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178129297	178129297	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	86	415	0	ENST00000397062.3:c.8A>T	p.Asp3Val	p.D3V	ENST00000397062	NM_006164.4	3	gAc/gTc	1/5	1	2	FACETS	0.586	0.519	0.658	0.586	0.519	0.658	SUBCLONAL	1	TRUE	1	0.50750498950509	2		415	578	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682399	52682400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	65	466	0	ENST00000394830.3:c.773dup	p.Asn258LysfsTer6	p.N258Kfs*6	ENST00000394830	NM_018313.4	258	aat/aaAt	8/30	1	2	FACETS	0.291	0.251	0.334	0.291	0.251	0.334	SUBCLONAL	1	TRUE	1	0.50750498950509	2		466	881	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445018	89445018	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	47	425	0	ENST00000336596.2:c.1338T>G	p.Asp446Glu	p.D446E	ENST00000336596	NM_005233.5	446	gaT/gaG	6/17	1	2	FACETS	0.277	0.233	0.326	0.277	0.233	0.326	SUBCLONAL	1	TRUE	1	0.50750498950509	2		425	668	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	221	338	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.50750498950509	2		338	642	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540134	187540134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1560939993	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	99	409	0	ENST00000441802.2:c.7606G>A	p.Ala2536Thr	p.A2536T	ENST00000441802	NM_005245.3	2536	Gcc/Acc	10/27	0.388600219547785	1	FACETS	0.491	0.439	0.546	0.491	0.439	0.546	SUBCLONAL	1	TRUE	0	0.50750498950509	1		409	593	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278901	1278901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772441504	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	174	545	3	ENST00000310581.5:c.2141C>T	p.Thr714Met	p.T714M	ENST00000310581	NM_198253.2	714	aCg/aTg	6/16	1	2	FACETS	0.872	0.805	0.943	0.872	0.805	0.943	CLONAL	1	TRUE	1	0.50750498950509	2		548	786	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752795	57752795	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	124	345	0	ENST00000274289.3:c.1133A>G	p.Lys378Arg	p.K378R	ENST00000274289	NM_006622.3	378	aAa/aGa	8/14	1	2	FACETS	0.856	0.777	0.938	0.856	0.777	0.938	CLONAL	1	TRUE	1	0.50750498950509	2		345	571	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066722	94066722	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	214	497	1	ENST00000369303.4:c.1037C>T	p.Thr346Ile	p.T346I	ENST00000369303	NM_004440.3	346	aCa/aTa	5/17	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.50750498950509	2		498	794	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528546	157528546	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	271	615	0	ENST00000346085.5:c.6271A>G	p.Ile2091Val	p.I2091V	ENST00000346085	NM_020732.3	2091	Atc/Gtc	20/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.50750498950509	2		615	985	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6036958	6036958	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	178	411	0	ENST00000265849.7:c.802del	p.Tyr268ThrfsTer39	p.Y268Tfs*39	ENST00000265849	NM_000535.5	268	Tac/ac	7/15	1	2	FACETS	0.853	0.787	0.922	0.853	0.787	0.922	CLONAL	1	TRUE	1	0.50750498950509	2		411	822	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482927	140482927	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	266	198	1	ENST00000288602.6:c.1208del	p.Pro403LeufsTer8	p.P403Lfs*8	ENST00000288602	NM_004333.4	403	cCt/ct	10/18	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.50750498950509	2		199	887	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845959	151845959	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	131	628	0	ENST00000262189.6:c.13053del	p.Lys4351AsnfsTer5	p.K4351Nfs*5	ENST00000262189	NM_170606.2	4351	aaA/aa	52/59	1	2	FACETS	0.529	0.479	0.581	0.529	0.479	0.581	SUBCLONAL	1	TRUE	1	0.50750498950509	2		628	976	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877811	151877812	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	157	293	0	ENST00000262189.6:c.7133_7134del	p.Thr2378ArgfsTer11	p.T2378Rfs*11	ENST00000262189	NM_170606.2	2378	aCA/a	36/59	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.50750498950509	2		293	532	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340356	8340356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs553232071	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	160	414	0	ENST00000356435.5:c.5240G>A	p.Arg1747His	p.R1747H	ENST00000356435		1747	cGt/cAt	31/35	1	2	FACETS	0.919	0.845	0.996	0.919	0.845	0.996	CLONAL	1	TRUE	1	0.50750498950509	2		414	686	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341261	8341261	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759691127	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	133	290	0	ENST00000356435.5:c.4955C>T	p.Ala1652Val	p.A1652V	ENST00000356435		1652	gCc/gTc	30/35	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.50750498950509	2		290	466	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882049	36882050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs780753361	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	201	648	0	ENST00000358127.4:c.963dup	p.Ala322ArgfsTer19	p.A322Rfs*19	ENST00000358127	NM_001280556.1	321	-/C	8/10	1	2	FACETS	0.921	0.855	0.99	0.921	0.855	0.99	CLONAL	1	TRUE	1	0.50750498950509	2		648	860	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249372	110249372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	372	911	5	ENST00000374672.4:c.1201G>A	p.Ala401Thr	p.A401T	ENST00000374672	NM_004235.4	401	Gcg/Acg	4/5	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.50750498950509	2		916	1368	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730335	133730335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	211	464	0	ENST00000318560.5:c.401G>A	p.Arg134His	p.R134H	ENST00000318560	NM_005157.4	134	cGc/cAc	3/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.50750498950509	2		464	700	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759912	133759913	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	192	624	0	ENST00000318560.5:c.2236_2237del	p.Gln746ValfsTer2	p.Q746Vfs*2	ENST00000318560	NM_005157.4	745	agACag/agag	11/11	1	2	FACETS	0.926	0.858	0.997	0.926	0.858	0.997	CLONAL	1	TRUE	1	0.50750498950509	2		624	817	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760447	133760447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771729224	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	169	541	1	ENST00000318560.5:c.2770G>A	p.Gly924Arg	p.G924R	ENST00000318560	NM_005157.4	924	Ggg/Agg	11/11	1	2	FACETS	0.982	0.906	1	0.982	0.906	1	CLONAL	1	TRUE	1	0.50750498950509	2		542	678	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293658	137293658	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	223	782	0	ENST00000481739.1:c.213del	p.Met72TrpfsTer27	p.M72Wfs*27	ENST00000481739	NM_002957.4	70	tCc/tc	2/10	1	2	FACETS	0.795	0.74	0.853	0.795	0.74	0.853	SUBCLONAL	1	TRUE	1	0.50750498950509	2		782	1105	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923001	39923001	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	237	313	0	ENST00000378444.4:c.3707A>G	p.Glu1236Gly	p.E1236G	ENST00000378444	NM_001123385.1	1236	gAa/gGa	8/15	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.50750498950509	1		313	490	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161392	55161392	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767697835	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	117	421	0	ENST00000257290.5:c.3223G>A	p.Asp1075Asn	p.D1075N	ENST00000257290	NM_006206.4	1075	Gac/Aac	23/23	1	2	FACETS	0.766	0.692	0.843	0.766	0.692	0.843	SUBCLONAL	1	TRUE	1	0.50750498950509	2		421	602	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492897	56492898	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	C	novel	NA	P-0032288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	98	297	0	ENST00000407977.2:c.41_42delinsG	p.Pro14ArgfsTer4	p.P14Rfs*4	ENST00000407977		14	cCC/cG	2/10	0.345564573014138	1	FACETS	0.816	0.735	0.901	0.816	0.735	0.901	CLONAL	1	TRUE	0	0.50750498950509	1		297	353	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112593	115112593	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	73	681	0	ENST00000257566.3:c.1147G>A	p.Glu383Lys	p.E383K	ENST00000257566	NM_016569.3	383	Gag/Aag	7/8	1	2	FACETS	0.284	0.247	0.324	0.284	0.247	0.324	SUBCLONAL	1	TRUE	1	0.500110218645246	2		681	1028	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772264	68772265	+	stop_gained,inframe_insertion	Nonsense_Mutation	INS	-	-	GTA	novel	NA	P-0032331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	233	691	0	ENST00000261769.5:c.115_116insAGT	p.Thr38_Phe39insTer	p.T38_F39ins*	ENST00000261769	NM_004360.3	38	acg/acGTAg	2/16	0.500110218645246	1	FACETS	0.977	0.916	1	0.977	0.916	1	CLONAL	1	TRUE	0	0.500110218645246	1		691	715	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916923	178916929	+	protein_altering_variant	In_Frame_Del	DEL	CCAGTAG	CCAGTAG	GTGT	novel	NA	P-0032331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	161	380	2	ENST00000263967.3:c.310_316delinsGTGT	p.Pro104_Gly106delinsValCys	p.P104_G106delinsVC	ENST00000263967	NM_006218.2	104	CCAGTAGgc/GTGTgc	2/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.500110218645246	2		382	618	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0032344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	277	764	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.723807556278825	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.723807556278825	3		764	446	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0032344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	407	387	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.431756150198263	3	FACETS	0.877	0.848	0.905	1	0.996	1	INDETERMINATE	3	TRUE	1	0.723807556278825	3		388	582	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696708	47696708	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	350	410	1	ENST00000347630.2:c.240C>G	p.Ser80Arg	p.S80R	ENST00000347630	NM_001007230.1	80	agC/agG	5/11	0.723807556278825	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.723807556278825	2		411	430	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs149680468	NA	P-0032344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	193	272	0	ENST00000281708.4:c.1513C>A	p.Arg505Ser	p.R505S	ENST00000281708	NM_033632.3	505	Cgc/Agc	10/12	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.723807556278825	2		272	457	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395108	139395108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371414501	NA	P-0032353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	8	608	1	ENST00000277541.6:c.5830G>A	p.Ala1944Thr	p.A1944T	ENST00000277541	NM_017617.3	1944	Gcc/Acc	31/34	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		609	314	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0032353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	8	439	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		439	200	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	594	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.868714368138274	2	FACETS	0.989	0.97	1	0.989	0.97	1	CLONAL	2	TRUE	0	0.87564463800126	2		298	686	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555687605	NA	P-0032364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	240	319	0	ENST00000342988.3:c.1610A>G	p.Asp537Gly	p.D537G	ENST00000342988	NM_005359.5	537	gAc/gGc	12/12	0.87564463800126	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.87564463800126	1		319	284	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518512	204518512	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	229	314	0	ENST00000367182.3:c.1175T>A	p.Val392Glu	p.V392E	ENST00000367182	NM_001278516.1	392	gTg/gAg	11/11	0.30185420283178	5	FACETS	0.763	0.713	0.814			1	INDETERMINATE	2	TRUE	NA	0.87564463800126	5		314	793	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038231	30038231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	297	448	0	ENST00000338641.4:c.404C>T	p.Pro135Leu	p.P135L	ENST00000338641	NM_000268.3	135	cCt/cTt	4/16	0.706921162900267	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.706921162900267	2		448	391	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144027	11144027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770680174	NA	P-0032956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	1614	499	0	ENST00000358026.2:c.3608G>A	p.Arg1203His	p.R1203H	ENST00000358026	NM_001128849.1	1203	cGc/cAc	26/36	0.706921162900267	12	FACETS	1	0.995	1			1	CLONAL	10	TRUE	NA	0.706921162900267	12		499	2034	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576878	7576878	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	667	628	0	ENST00000269305.4:c.968del	p.Leu323ArgfsTer22	p.L323Rfs*22	ENST00000269305	NM_001126112.2	323	cTg/cg	9/11	0.706921162900267	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	4	TRUE	0	0.706921162900267	4		628	798	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546887	9546887	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	102	428	0	ENST00000353224.5:c.1135A>G	p.Lys379Glu	p.K379E	ENST00000353224	NM_177990.2	379	Aaa/Gaa	5/10	0.706921162900267	5	FACETS	0.824	0.737	0.916			1	CLONAL	1	TRUE	NA	0.706921162900267	5		428	722	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	26	571	0	ENST00000269305.4:c.859G>T	p.Glu287Ter	p.E287*	ENST00000269305	NM_001126112.2	287	Gag/Tag	8/11	1	2	FACETS	0.319	0.252	0.396	0.319	0.252	0.396	SUBCLONAL	1	TRUE	1	0.37	2		571	441	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441261	52441261	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	20	466	0	ENST00000460680.1:c.509T>G	p.Phe170Cys	p.F170C	ENST00000460680	NM_004656.3	170	tTt/tGt	7/17	1	2	FACETS	0.339	0.259	0.433	0.339	0.259	0.433	SUBCLONAL	1	TRUE	1	0.37	2		466	319	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564615	55564615	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs149092990	NA	P-0033005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	22	558	0	ENST00000288135.5:c.503C>A	p.Ala168Glu	p.A168E	ENST00000288135	NM_000222.2	168	gCg/gAg	3/21	1	2	FACETS	0.347	0.268	0.438	0.347	0.268	0.438	SUBCLONAL	1	TRUE	1	0.37	2		558	343	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481403	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0033005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	8	468	1	ENST00000288602.6:c.1405_1406delinsAT	p.Gly469Ile	p.G469I	ENST00000288602	NM_004333.4	469	GGa/ATa	11/18	1	2	FACETS	0.156	0.099	0.229	0.156	0.099	0.229	SUBCLONAL	1	TRUE	1	0.37	2		469	278	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0033091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	110	442	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.442548459113306	2		442	441	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725042	89725042	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1085308041	NA	P-0033091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	49	173	0	ENST00000371953.3:c.1027-2A>G		p.X343_splice	ENST00000371953	NM_000314.4	343			1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.442548459113306	2		173	195	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0033091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	124	128	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.94	0.853	1	0.94	0.853	1	CLONAL	1	TRUE	1	0.442548459113306	2		128	596	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781467	135781467	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203537	NA	P-0033091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	169	688	2	ENST00000298552.3:c.1498C>T	p.Arg500Ter	p.R500*	ENST00000298552	NM_001162426.1	500	Cga/Tga	15/23	0.442548459113306	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.442548459113306	1		690	592	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437701	49437701	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555194045	NA	P-0033091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	279	960	1	ENST00000301067.7:c.5269C>T	p.Arg1757Ter	p.R1757*	ENST00000301067	NM_003482.3	1757	Cga/Tga	22/54	1	2	FACETS	0.967	0.907	1	0.967	0.907	1	CLONAL	1	TRUE	1	0.442548459113306	2		961	1304	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624270	89624270	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs398123324	NA	P-0033091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	125	485	0	ENST00000371953.3:c.44G>C	p.Arg15Thr	p.R15T	ENST00000371953	NM_000314.4	15	aGa/aCa	1/9	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.442548459113306	2		485	456	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058083	27058087	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTC	CCCTC	-	novel	NA	P-0033091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	138	543	0	ENST00000324856.7:c.1792_1796del	p.Pro598ThrfsTer23	p.P598Tfs*23	ENST00000324856	NM_006015.4	597	ttCCCTCca/ttca	3/20	1	2	FACETS	0.955	0.871	1	0.955	0.871	1	CLONAL	1	TRUE	1	0.442548459113306	2		543	653	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852472	63852472	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	213	757	0	ENST00000279873.7:c.3250G>C	p.Gly1084Arg	p.G1084R	ENST00000279873	NM_032199.2	1084	Ggg/Cgg	10/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.442548459113306	2		757	822	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645437	67645438	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0033091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	112	630	0	ENST00000264010.4:c.703_704del	p.Gly235SerfsTer6	p.G235Sfs*6	ENST00000264010	NM_006565.3	234	gaGGgt/gagt	3/12	1	2	FACETS	0.977	0.883	1	0.977	0.883	1	CLONAL	1	TRUE	1	0.442548459113306	2		630	518	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197376	26197376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	124	598	0	ENST00000356476.2:c.103G>A	p.Gly35Ser	p.G35S	ENST00000356476		35	Ggc/Agc	1/1	1	2	FACETS	0.942	0.855	1	0.942	0.855	1	CLONAL	1	TRUE	1	0.442548459113306	2		598	595	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0033104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	47	665	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.69662403692501	1	FACETS	0.109	0.091	0.128	0.109	0.091	0.128	SUBCLONAL	1	TRUE	0	0.769010547193743	1		665	691	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	530	559	0	ENST00000269305.4:c.379T>C	p.Ser127Pro	p.S127P	ENST00000269305	NM_001126112.2	127	Tcc/Ccc	5/11	0.69662403692501	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.769010547193743	1		559	723	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0033104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	67	77	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	0.769010547193743	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.769010547193743	1		77	89	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556457	29556457	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	463	431	0	ENST00000356175.3:c.2824del	p.Ser942AlafsTer12	p.S942Afs*12	ENST00000356175	NM_000267.3	942	Agc/gc	21/57	0.769010547193743	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.769010547193743	2		431	597	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0033151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	85	473	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.619765001637754	2		473	250	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0033151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	587	636	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.619765001637754	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.619765001637754	2		636	926	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0033151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	129	470	2	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	0.619765001637754	1	FACETS	0.865	0.795	0.937	0.865	0.795	0.937	CLONAL	1	TRUE	0	0.619765001637754	1		472	332	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0033151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	205	419	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.619765001637754	2		419	578	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0033151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	187	451	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.619765001637754	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.619765001637754	1		451	352	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549725	187549725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199516712	NA	P-0033151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	152	529	0	ENST00000441802.2:c.4516C>T	p.Arg1506Cys	p.R1506C	ENST00000441802	NM_005245.3	1506	Cgt/Tgt	8/27	1	2	FACETS	0.791	0.726	0.858	0.791	0.726	0.858	SUBCLONAL	1	TRUE	1	0.619765001637754	2		529	620	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353815	15353815	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780028668	NA	P-0033151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	101	453	0	ENST00000263377.2:c.3065C>T	p.Pro1022Leu	p.P1022L	ENST00000263377	NM_058243.2	1022	cCg/cTg	14/20	1	2	FACETS	0.888	0.801	0.979	0.888	0.801	0.979	CLONAL	1	TRUE	1	0.619765001637754	2		453	367	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190770	11190770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757173592	NA	P-0033151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	207	662	0	ENST00000361445.4:c.5429C>T	p.Ala1810Val	p.A1810V	ENST00000361445	NM_004958.3	1810	gCc/gTc	39/58	0.619765001637754	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.619765001637754	1		662	427	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137252	64137252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1398636953	NA	P-0033151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	196	594	1	ENST00000334205.4:c.1684C>T	p.Pro562Ser	p.P562S	ENST00000334205	NM_003942.2	562	Ccc/Tcc	14/17	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.619765001637754	2		595	590	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256147	133256147	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	234	642	0	ENST00000320574.5:c.514C>T	p.Pro172Ser	p.P172S	ENST00000320574	NM_006231.2	172	Cct/Tct	6/49	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.619765001637754	2		642	682	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658900	3658901	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	220	644	2	ENST00000294008.3:c.65_66delinsTT	p.Ala22Val	p.A22V	ENST00000294008	NM_032444.2	22	gCC/gTT	2/15	1	2	FACETS	0.934	0.872	0.998	0.934	0.872	0.998	CLONAL	1	TRUE	1	0.619765001637754	2		646	760	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991699	25991699	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	244	618	0	ENST00000435504.4:c.543A>T	p.Gln181His	p.Q181H	ENST00000435504		181	caA/caT	7/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.619765001637754	2		618	749	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98011440	98011441	+	missense_variant	Missense_Mutation	DNP	AG	AG	GA	novel	NA	P-0033151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	172	627	1	ENST00000289081.3:c.133_134delinsTC	p.Leu45Ser	p.L45S	ENST00000289081	NM_000136.2	45	CTa/TCa	2/15	1	2	FACETS	0.88	0.813	0.949	0.88	0.813	0.949	CLONAL	1	TRUE	1	0.619765001637754	2		628	631	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032069	10032069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868215122	NA	P-0033480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	102	701	0	ENST00000330684.3:c.754G>A	p.Asp252Asn	p.D252N	ENST00000330684	NM_001134407.1	252	Gat/Aat	3/13	0.369468612744017	1	FACETS	0.401	0.358	0.446	0.401	0.358	0.446	SUBCLONAL	1	FALSE	0	0.465077933478844	1		701	840	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448624	89448624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	63	633	0	ENST00000336596.2:c.1588C>T	p.Pro530Ser	p.P530S	ENST00000336596	NM_005233.5	530	Cca/Tca	7/17	1	2	FACETS	0.268	0.23	0.308	0.268	0.23	0.308	SUBCLONAL	1	FALSE	1	0.465077933478844	2		633	1012	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426973	70426973	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	257	521	0	ENST00000373644.4:c.4633A>G	p.Asn1545Asp	p.N1545D	ENST00000373644	NM_030625.2	1545	Aat/Gat	7/12	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.465077933478844	2		521	879	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518658	103518658	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	72	382	0	ENST00000355739.4:c.2246C>T	p.Ser749Leu	p.S749L	ENST00000355739	NM_000123.3	749	tCa/tTa	10/15	0.284208083165254	1	FACETS	0.482	0.422	0.546	0.482	0.422	0.546	SUBCLONAL	1	FALSE	0	0.465077933478844	1		382	493	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267496	198267496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764445898	NA	P-0033510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	217	566	0	ENST00000335508.6:c.1861G>A	p.Asp621Asn	p.D621N	ENST00000335508	NM_012433.2	621	Gat/Aat	14/25	1	2	FACETS	0.999	0.937	1	0.999	0.937	1	CLONAL	1	TRUE	1	0.79011461884145	2		566	550	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0033530-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	150	319	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.906	0.835	0.978	0.906	0.835	0.978	CLONAL	1	TRUE	1	0.736127681262278	2		319	450	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711281	114711281	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033530-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	169	455	0	ENST00000543371.1:c.296C>G	p.Pro99Arg	p.P99R	ENST00000543371	NM_001198531.1	99	cCg/cGg	3/14	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.736127681262278	2		455	376	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144880	47144880	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033530-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	151	526	0	ENST00000409792.3:c.4873C>T	p.Arg1625Cys	p.R1625C	ENST00000409792	NM_014159.6	1625	Cgt/Tgt	7/21	1	2	FACETS	0.935	0.862	1	0.935	0.862	1	CLONAL	1	TRUE	1	0.736127681262278	2		526	439	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523516	41523516	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033530-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	185	640	1	ENST00000263253.7:c.932A>C	p.Gln311Pro	p.Q311P	ENST00000263253	NM_001429.3	311	cAg/cCg	4/31	1	2	FACETS	0.972	0.905	1	0.972	0.905	1	CLONAL	1	TRUE	1	0.736127681262278	2		641	517	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125235	47125235	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033530-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	179	584	0	ENST00000409792.3:c.6035T>G	p.Leu2012Arg	p.L2012R	ENST00000409792	NM_014159.6	2012	cTc/cGc	12/21	1	2	FACETS	0.939	0.872	1	0.939	0.872	1	CLONAL	1	TRUE	1	0.736127681262278	2		584	518	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411892	116411968	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTGTTTTAAGATCTGGGCAGTGAATTAGTTCGCTACGATGCAAGAGTACACACTCCTCATTTGGATAGGCTTGTAA	TCTGTTTTAAGATCTGGGCAGTGAATTAGTTCGCTACGATGCAAGAGTACACACTCCTCATTTGGATAGGCTTGTAA	-	novel	NA	P-0033530-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	619	821	0	ENST00000397752.3:c.2888-11_2953del		p.X963_splice	ENST00000397752	NM_000245.2	963		14/21	0.736127681262278	3	FACETS	1	0.995	1	0.626	0.601	0.65	CLONAL	1	TRUE	1	0.736127681262278	3		821	1839	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6222556	6222566	+	frameshift_variant	Frame_Shift_Del	DEL	GTGTCCTTGGA	GTGTCCTTGGA	-	novel	NA	P-0033530-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	136	915	0	ENST00000252674.7:c.676_686del	p.Ser226LeufsTer117	p.S226Lfs*117	ENST00000252674	NM_005934.3	226	TCCAAGGACACc/c	6/12	1	2	FACETS	0.878	0.805	0.952	0.878	0.805	0.952	CLONAL	1	TRUE	1	0.736127681262278	2		915	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578484	7578485	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1064793929	NA	P-0033718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	242	799	0	ENST00000269305.4:c.445dup	p.Ser149PhefsTer32	p.S149Ffs*32	ENST00000269305	NM_001126112.2	149	tcc/tTcc	5/11	0.263530481625942	3	FACETS	1	0.977	1	0.723	0.677	0.769	CLONAL	2	TRUE	0	0.338073385956592	3		799	772	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618887	37618887	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	340	636	0	ENST00000447079.4:c.565del	p.Glu189SerfsTer2	p.E189Sfs*2	ENST00000447079	NM_015083.1	188	cGg/cg	1/14	0.338073385956592	5	FACETS	1	0.982	1			1	CLONAL	4	TRUE	NA	0.338073385956592	5		636	716	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100342	157100342	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1178936568	NA	P-0033718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	19	206	0	ENST00000346085.5:c.1279A>T	p.Ser427Cys	p.S427C	ENST00000346085	NM_020732.3	427	Agc/Tgc	1/20	0.338073385956592	5	FACETS	0.528	0.4	0.678	0.176	0.133	0.226	SUBCLONAL	1	TRUE	2	0.338073385956592	5		206	321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0033826-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	517	670	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.73837051803182	3	FACETS	0.975	0.952	0.997	0.975	0.952	0.997	CLONAL	3	TRUE	0	0.761271424640719	3		670	641	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626123	12626123	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs80338797	NA	P-0033826-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	138	391	0	ENST00000251849.4:c.1837C>G	p.Leu613Val	p.L613V	ENST00000251849	NM_002880.3	613	Cta/Gta	17/17	0.431563473584053	3	FACETS	1	0.984	1	0.645	0.593	0.698	INDETERMINATE	1	TRUE	1	0.761271424640719	3		391	388	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033826-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	122	264	0	ENST00000256196.4:c.68G>A	p.Gly23Asp	p.G23D	ENST00000256196		23	gGc/gAc	1/6	0.429628876924279	4	FACETS	0.932	0.855	1	0.932	0.855	1	INDETERMINATE	2	TRUE	2	0.761271424640719	4		264	303	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37665987	37665987	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033826-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	168	480	0	ENST00000447079.4:c.2639T>C	p.Leu880Pro	p.L880P	ENST00000447079	NM_015083.1	880	cTt/cCt	7/14	0.476860528278528	3	FACETS	0.939	0.866	1	0.469	0.433	0.507	CLONAL	1	TRUE	1	0.761271424640719	3		480	649	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0034409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	234	372	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.840630701181845	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.842126818840056	2		372	266	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	362	462	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.777713801204771	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.842126818840056	4		462	770	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0034409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	374	524	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.840630701181845	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.842126818840056	2		524	427	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472594	88472594	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	159	389	0	ENST00000360948.2:c.1961C>A	p.Ser654Tyr	p.S654Y	ENST00000360948	NM_001012338.2	654	tCc/tAc	16/19	0.761595807847945	3	FACETS	1	0.967	1	0.543	0.501	0.586	CLONAL	1	TRUE	1	0.842126818840056	3		389	494	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0034409-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	121	372	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.193223992931376	3	FACETS	1	0.981	1	0.669	0.607	0.734	INDETERMINATE	1	TRUE	1	0.401430886711906	3		372	541	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034409-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	79	522	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.495	0.435	0.56	0.495	0.435	0.56	SUBCLONAL	1	TRUE	1	0.401430886711906	2		522	795	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0034409-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	188	524	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.193223992931376	3	FACETS	1	0.989	1	0.701	0.649	0.755	INDETERMINATE	1	TRUE	1	0.401430886711906	3		524	802	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370951	55370951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034409-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	68	568	0	ENST00000297316.4:c.253C>T	p.Arg85Trp	p.R85W	ENST00000297316	NM_022454.3	85	Cgg/Tgg	1/2	1	2	FACETS	0.384	0.333	0.439	0.384	0.333	0.439	SUBCLONAL	1	TRUE	1	0.401430886711906	2		568	883	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670015	86670016	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034409-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	53	325	0	ENST00000274376.6:c.1815dup	p.Leu606ThrfsTer8	p.L606Tfs*8	ENST00000274376	NM_002890.2	604	-/A	14/25	0.177376221973141	4	FACETS	0.728	0.621	0.845	0.364	0.31	0.423	INDETERMINATE	1	TRUE	2	0.401430886711906	4		325	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0034442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	323	586	1	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.505823021161581	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.624079897018959	1		587	610	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888722	76888725	+	frameshift_variant	Frame_Shift_Del	DEL	TTTC	TTTC	-	novel	NA	P-0034442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	216	559	0	ENST00000373344.5:c.5104_5107del	p.Glu1702TyrfsTer22	p.E1702Yfs*22	ENST00000373344	NM_000489.3	1702	GAAAta/ta	19/35	0.183113084966065	5	FACETS	0.985	0.921	1	0.657	0.614	0.701	INDETERMINATE	2	TRUE	2	0.624079897018959	5		559	680	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089123	37089125	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs63751247	NA	P-0034935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	332	484	0	ENST00000231790.2:c.1852_1854del	p.Lys618del	p.K618del	ENST00000231790	NM_000249.3	615	ctGAAg/ctg	16/19	0.597460276490275	2	FACETS	0.867	0.827	0.906	0.867	0.827	0.906	CLONAL	2	TRUE	0	0.597460276490275	2		484	641	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0034935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	173	423	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	NA	2	FACETS	0.951	0.88	1			1	INDETERMINATE	1	TRUE	NA	0.597460276490275	2		423	609	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0034935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	107	349	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.948	0.858	1	0.948	0.858	1	CLONAL	1	TRUE	1	0.597460276490275	2		349	378	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115780	8115780	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	191	489	1	ENST00000346208.3:c.1131del	p.Val378CysfsTer26	p.V378Cfs*26	ENST00000346208		376	Aaa/aa	6/6	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.597460276490275	2		490	635	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266110	41266110	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	220	332	0	ENST00000349496.5:c.107A>C	p.His36Pro	p.H36P	ENST00000349496	NM_001904.3	36	cAt/cCt	3/15	0.597460276490275	2	FACETS	0.942	0.892	0.991	0.942	0.892	0.991	CLONAL	2	TRUE	0	0.597460276490275	2		332	391	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717769	89717770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	83	325	0	ENST00000371953.3:c.800dup	p.Asp268GlyfsTer30	p.D268Gfs*30	ENST00000371953	NM_000314.4	265	cta/ctAa	7/9	1	2	FACETS	0.724	0.643	0.809	0.724	0.643	0.809	SUBCLONAL	1	TRUE	1	0.597460276490275	2		325	384	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106336	27106337	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0034935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	216	685	0	ENST00000324856.7:c.5952_5953del	p.Ser1985GlnfsTer13	p.S1985Qfs*13	ENST00000324856	NM_006015.4	1983	TGt/t	20/20	1	2	FACETS	0.923	0.861	0.988	0.923	0.861	0.988	CLONAL	1	TRUE	1	0.597460276490275	2		685	783	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0034935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	120	423	3	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	0.83	0.754	0.909	0.83	0.754	0.909	CLONAL	1	TRUE	1	0.597460276490275	2		426	484	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	136	469	0	ENST00000330684.3:c.4021A>G	p.Ser1341Gly	p.S1341G	ENST00000330684	NM_001134407.1	1341	Agc/Ggc	13/13	1	2	FACETS	0.893	0.816	0.972	0.893	0.816	0.972	CLONAL	1	TRUE	1	0.597460276490275	2		469	510	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245587	41245587	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357522	NA	P-0034935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	353	838	7	ENST00000357654.3:c.1961del	p.Lys654SerfsTer47	p.K654Sfs*47	ENST00000357654	NM_007294.3	654	aAg/ag	10/23	1	2	FACETS	0.961	0.911	1	0.961	0.911	1	CLONAL	1	TRUE	1	0.597460276490275	2		845	1229	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539018	187539018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374444088	NA	P-0034935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	216	583	0	ENST00000441802.2:c.8722G>A	p.Val2908Ile	p.V2908I	ENST00000441802	NM_005245.3	2908	Gtc/Atc	10/27	1	2	FACETS	0.98	0.914	1	0.98	0.914	1	CLONAL	1	TRUE	1	0.597460276490275	2		583	738	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0034935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	174	443	2	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.597460276490275	2		445	577	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0034935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	212	217	0	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.597460276490275	2		217	668	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717663	89717663	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554825186	NA	P-0034935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	190	529	0	ENST00000371953.3:c.688G>T	p.Gly230Ter	p.G230*	ENST00000371953	NM_000314.4	230	Gga/Tga	7/9	1	2	FACETS	0.971	0.902	1	0.971	0.902	1	CLONAL	1	TRUE	1	0.597460276490275	2		529	655	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944381	131944382	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs748536322	NA	P-0034935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	82	196	1	ENST00000265335.6:c.2801dup	p.Asn934LysfsTer10	p.N934Kfs*10	ENST00000265335		931	-/A	17/25	1	2	FACETS	0.991	0.885	1	0.991	0.885	1	CLONAL	1	TRUE	1	0.597460276490275	2		197	277	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151290	202151290	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	188	450	0	ENST00000358485.4:c.1596del	p.Lys532AsnfsTer73	p.K532Nfs*73	ENST00000358485	NM_001080125.1	530	agA/ag	9/9	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.597460276490275	2		450	611	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41489075	41489076	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555902247	NA	P-0034935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	162	431	0	ENST00000263253.7:c.70_71del	p.Ser24GlyfsTer14	p.S24Gfs*14	ENST00000263253	NM_001429.3	23	CTc/c	1/31	1	2	FACETS	0.875	0.806	0.946	0.875	0.806	0.946	CLONAL	1	TRUE	1	0.597460276490275	2		431	620	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911172	29911172	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	71	352	0	ENST00000376809.5:c.471G>A	p.Trp157Ter	p.W157*	ENST00000376809	NM_002116.7	157	tgG/tgA	3/8	0.597460276490275	2	FACETS	0.994	0.88	1	0.497	0.44	0.557	CLONAL	1	TRUE	0	0.597460276490275	2		352	239	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0034935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	303	666	1	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.858	0.808	0.909	0.858	0.808	0.909	CLONAL	1	TRUE	1	0.597460276490275	2		667	1182	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139079	50139079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs925989732	NA	P-0034935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	245	650	1	ENST00000246792.3:c.484G>A	p.Ala162Thr	p.A162T	ENST00000246792	NM_006270.3	162	Gcc/Acc	5/6	1	2	FACETS	0.988	0.926	1	0.988	0.926	1	CLONAL	1	TRUE	1	0.597460276490275	2		651	830	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998316	100998316	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	31	85	0	ENST00000325455.5:c.1486C>T	p.Pro496Ser	p.P496S	ENST00000325455	NM_001202474.3	496	Ccc/Tcc	1/8	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.597460276490275	2		85	100	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262438	16262438	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	104	362	1	ENST00000375759.3:c.9703A>G	p.Lys3235Glu	p.K3235E	ENST00000375759	NM_015001.2	3235	Aag/Gag	11/15	1	2	FACETS	0.975	0.882	1	0.975	0.882	1	CLONAL	1	TRUE	1	0.597460276490275	2		363	357	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241032	133241032	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs762395135	NA	P-0034935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	200	502	0	ENST00000320574.5:c.2485A>G	p.Met829Val	p.M829V	ENST00000320574	NM_006231.2	829	Atg/Gtg	22/49	1	2	FACETS	0.95	0.883	1	0.95	0.883	1	CLONAL	1	TRUE	1	0.597460276490275	2		502	705	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66777509	66777509	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	180	585	1	ENST00000307102.5:c.879del	p.Arg295GlyfsTer23	p.R295Gfs*23	ENST00000307102	NM_002755.3	292	aCc/ac	7/11	1	2	FACETS	0.825	0.763	0.89	0.825	0.763	0.89	CLONAL	1	TRUE	1	0.597460276490275	2		586	730	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980315	7980316	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0034935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	161	444	0	ENST00000319144.4:c.1267dup	p.Leu423ProfsTer26	p.L423Pfs*26	ENST00000319144	NM_001139.2	423	ctc/cCtc	9/15	1	2	FACETS	0.924	0.852	0.999	0.924	0.852	0.999	CLONAL	1	TRUE	1	0.597460276490275	2		444	583	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372131	45372131	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	200	532	2	ENST00000262160.6:c.1038del	p.Phe346LeufsTer5	p.F346Lfs*5	ENST00000262160	NM_005901.5	346	ttT/tt	9/11	1	2	FACETS	0.951	0.884	1	0.951	0.884	1	CLONAL	1	TRUE	1	0.597460276490275	2		534	704	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051628	128051628	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0034935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	205	647	0	ENST00000285398.2:c.28+2T>C		p.X10_splice	ENST00000285398	NM_000122.1	10			1	2	FACETS	0.903	0.84	0.968	0.903	0.84	0.968	CLONAL	1	TRUE	1	0.597460276490275	2		647	760	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056568	26056568	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	195	241	1	ENST00000343677.2:c.89del	p.Gly30ValfsTer33	p.G30Vfs*33	ENST00000343677	NM_005319.3	30	gGt/gt	1/1	0.597460276490275	2	FACETS	0.943	0.89	0.996	0.943	0.89	0.996	CLONAL	2	TRUE	0	0.597460276490275	2		242	346	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476781	140476781	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	196	587	0	ENST00000288602.6:c.1625A>G	p.His542Arg	p.H542R	ENST00000288602	NM_004333.4	542	cAt/cGt	13/18	1	2	FACETS	0.981	0.912	1	0.981	0.912	1	CLONAL	1	TRUE	1	0.597460276490275	2		587	669	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970950	21970951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs749588877	NA	P-0034935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	312	847	1	ENST00000304494.5:c.407dup	p.Thr137HisfsTer5	p.T137Hfs*5	ENST00000304494	NM_000077.4	136	ggc/ggGc	2/3	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.597460276490275	2		848	1001	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0035144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	621	510	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.60081104034788	4	FACETS	0.923	0.901	0.945	0.923	0.901	0.945	CLONAL	4	FALSE	0	0.678353149783975	4		510	832	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716326	52716326	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	388	660	0	ENST00000322088.6:c.770G>T	p.Trp257Leu	p.W257L	ENST00000322088	NM_014225.5	257	tGg/tTg	6/15	0.268789643369361	6	FACETS	1	0.987	1	0.812	0.776	0.848	INDETERMINATE	3	FALSE	2	0.678353149783975	6		660	830	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578258	+	frameshift_variant	Frame_Shift_Del	DEL	ACTCCACACGCAAATTTCCTTCC	ACTCCACACGCAAATTTCCTTCC	-	novel	NA	P-0035338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	240	608	0	ENST00000269305.4:c.591_613del	p.Glu198PhefsTer3	p.E198Ffs*3	ENST00000269305	NM_001126112.2	197	gtGGAAGGAAATTTGCGTGTGGAGTat/gtat	6/11	0.668045880542671	2	FACETS	0.898	0.854	0.941	0.898	0.854	0.941	CLONAL	2	TRUE	0	0.668045880542671	2		608	400	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133821	55133821	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	125	457	0	ENST00000257290.5:c.1034C>A	p.Pro345His	p.P345H	ENST00000257290	NM_006206.4	345	cCc/cAc	7/23	0.668045880542671	2	FACETS	1	0.965	1	0.55	0.504	0.597	CLONAL	1	TRUE	0	0.668045880542671	2		457	340	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	131	496	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.917	0.837	0.999	0.917	0.837	0.999	CLONAL	1	TRUE	1	0.589307220565538	2		496	485	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	122	430	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.589307220565538	2		431	398	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	78	441	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.854	0.758	0.955	0.854	0.758	0.955	CLONAL	1	TRUE	1	0.589307220565538	2		441	310	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	262	516	1	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.589307220565538	2		517	675	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993581	72993581	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	146	558	1	ENST00000268489.5:c.464del	p.Gly155AlafsTer17	p.G155Afs*17	ENST00000268489	NM_006885.3	155	gGc/gc	2/10	1	2	FACETS	0.894	0.82	0.971	0.894	0.82	0.971	CLONAL	1	TRUE	1	0.589307220565538	2		559	554	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	142	443	2	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.994	0.912	1	0.994	0.912	1	CLONAL	1	TRUE	1	0.589307220565538	2		445	485	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151290	202151290	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	179	450	0	ENST00000358485.4:c.1596del	p.Lys532AsnfsTer73	p.K532Nfs*73	ENST00000358485	NM_001080125.1	530	agA/ag	9/9	1	2	FACETS	0.963	0.892	1	0.963	0.892	1	CLONAL	1	TRUE	1	0.589307220565538	2		450	631	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258440	16258440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1440008576	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	162	556	0	ENST00000375759.3:c.5705G>A	p.Arg1902Gln	p.R1902Q	ENST00000375759	NM_015001.2	1902	cGg/cAg	11/15	1	2	FACETS	0.884	0.814	0.956	0.884	0.814	0.956	CLONAL	1	TRUE	1	0.589307220565538	2		556	622	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023769	27023769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	141	292	2	ENST00000324856.7:c.879del	p.Thr294ProfsTer69	p.T294Pfs*69	ENST00000324856	NM_006015.4	292	aCc/ac	1/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.589307220565538	2		294	445	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023827	27023827	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	86	291	0	ENST00000324856.7:c.936del	p.Gly314AlafsTer49	p.G314Afs*49	ENST00000324856	NM_006015.4	311	taC/ta	1/20	1	2	FACETS	0.832	0.742	0.926	0.832	0.742	0.926	CLONAL	1	TRUE	1	0.589307220565538	2		291	351	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	69	554	0	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	0.43	0.374	0.489	0.43	0.374	0.489	SUBCLONAL	1	TRUE	1	0.589307220565538	2		554	545	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193181550	193181550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	82	357	0	ENST00000367435.3:c.1097C>T	p.Ala366Val	p.A366V	ENST00000367435	NM_024529.4	366	gCa/gTa	13/17	1	2	FACETS	0.63	0.558	0.706	0.63	0.558	0.706	SUBCLONAL	1	TRUE	1	0.589307220565538	2		357	442	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405964	70405964	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	42	644	0	ENST00000373644.4:c.3478A>G	p.Lys1160Glu	p.K1160E	ENST00000373644	NM_030625.2	1160	Aaa/Gaa	4/12	1	2	FACETS	0.23	0.192	0.273	0.23	0.192	0.273	SUBCLONAL	1	TRUE	1	0.589307220565538	2		644	619	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456821	32456821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs992227366	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	174	586	1	ENST00000332351.3:c.71G>A	p.Cys24Tyr	p.C24Y	ENST00000332351	NM_024426.4	24	tGc/tAc	1/10	1	2	FACETS	0.978	0.905	1	0.978	0.905	1	CLONAL	1	TRUE	1	0.589307220565538	2		587	604	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64126762	64126762	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	174	629	0	ENST00000334205.4:c.55G>T	p.Ala19Ser	p.A19S	ENST00000334205	NM_003942.2	19	Gcc/Tcc	1/17	1	2	FACETS	0.936	0.865	1	0.936	0.865	1	CLONAL	1	TRUE	1	0.589307220565538	2		629	631	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200877	67200877	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	142	598	2	ENST00000312629.5:c.870del	p.Tyr291ThrfsTer14	p.Y291Tfs*14	ENST00000312629	NM_003952.2	289	Ccc/cc	10/15	1	2	FACETS	0.745	0.681	0.812	0.745	0.681	0.812	SUBCLONAL	1	TRUE	1	0.589307220565538	2		600	647	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466019	69466019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	190	755	0	ENST00000227507.2:c.857C>T	p.Thr286Ile	p.T286I	ENST00000227507	NM_053056.2	286	aCa/aTa	5/5	1	2	FACETS	0.879	0.814	0.945	0.879	0.814	0.945	CLONAL	1	TRUE	1	0.589307220565538	2		755	734	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945372	71945372	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773625159	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	258	877	1	ENST00000298229.2:c.2260G>A	p.Glu754Lys	p.E754K	ENST00000298229	NM_001567.3	754	Gag/Aag	20/28	1	2	FACETS	0.86	0.806	0.916	0.86	0.806	0.916	CLONAL	1	TRUE	1	0.589307220565538	2		878	1018	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948548	71948548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349798484	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	221	775	0	ENST00000298229.2:c.3260G>A	p.Gly1087Asp	p.G1087D	ENST00000298229	NM_001567.3	1087	gGc/gAc	26/28	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.589307220565538	2		775	733	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219106	94219109	+	frameshift_variant	Frame_Shift_Del	DEL	TGAC	TGAC	-	rs1555017184	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	97	335	0	ENST00000323929.3:c.295_298del	p.Val99ThrfsTer10	p.V99Tfs*10	ENST00000323929	NM_005591.3	99	GTCAac/ac	4/20	1	2	FACETS	0.776	0.696	0.86	0.776	0.696	0.86	SUBCLONAL	1	TRUE	1	0.589307220565538	2		335	424	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195706	102195706	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	115	425	0	ENST00000263464.3:c.466G>A	p.Ala156Thr	p.A156T	ENST00000263464	NM_001165.4	156	Gcc/Acc	2/9	1	2	FACETS	0.858	0.778	0.941	0.858	0.778	0.941	CLONAL	1	TRUE	1	0.589307220565538	2		425	455	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344955	118344955	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	85	238	1	ENST00000534358.1:c.3086del	p.Lys1029ArgfsTer65	p.K1029Rfs*65	ENST00000534358	NM_005933.3	1027	ctA/ct	3/36	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.589307220565538	2		239	280	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	92	337	0	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.811	0.726	0.9	0.811	0.726	0.9	CLONAL	1	TRUE	1	0.589307220565538	2		337	385	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416675	416676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	123	429	0	ENST00000399788.2:c.3874dup	p.Thr1292AsnfsTer2	p.T1292Nfs*2	ENST00000399788	NM_001042603.1	1292	act/aAct	23/28	NA	2	FACETS	0.875	0.796	0.957			1	INDETERMINATE	1	TRUE	NA	0.589307220565538	2		429	477	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111886024	111886024	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201102821	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	33	569	0	ENST00000341259.2:c.1646G>A	p.Arg549Gln	p.R549Q	ENST00000341259	NM_005475.2	549	cGa/cAa	8/8	1	2	FACETS	0.216	0.175	0.262	0.216	0.175	0.262	SUBCLONAL	1	TRUE	1	0.589307220565538	2		569	519	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	194	671	9	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.931	0.865	1	0.931	0.865	1	CLONAL	1	TRUE	1	0.589307220565538	2		680	707	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434367	121434367	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	207	734	2	ENST00000257555.6:c.1136del	p.Pro379LeufsTer5	p.P379Lfs*5	ENST00000257555		377	ctC/ct	6/10	1	2	FACETS	0.957	0.891	1	0.957	0.891	1	CLONAL	1	TRUE	1	0.589307220565538	2		736	734	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549116	21549116	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	151	591	0	ENST00000382592.4:c.3160C>T	p.Arg1054Ter	p.R1054*	ENST00000382592	NM_014572.2	1054	Cga/Tga	8/8	1	2	FACETS	0.848	0.779	0.921	0.848	0.779	0.921	CLONAL	1	TRUE	1	0.589307220565538	2		591	604	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519181	103519181	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	116	369	0	ENST00000355739.4:c.2519T>G	p.Phe840Cys	p.F840C	ENST00000355739	NM_000123.3	840	tTt/tGt	11/15	1	2	FACETS	0.845	0.766	0.927	0.845	0.766	0.927	CLONAL	1	TRUE	1	0.589307220565538	2		369	466	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435219	110435219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746894027	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	158	491	1	ENST00000375856.3:c.3182C>T	p.Ser1061Leu	p.S1061L	ENST00000375856	NM_003749.2	1061	tCg/tTg	1/2	1	2	FACETS	0.98	0.904	1	0.98	0.904	1	CLONAL	1	TRUE	1	0.589307220565538	2		492	547	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438396	110438396	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	31	38	0	ENST00000375856.3:c.5C>T	p.Ala2Val	p.A2V	ENST00000375856	NM_003749.2	2	gCg/gTg	1/2	1	2	FACETS	0.809	0.686	0.933	1	0.96	1	CLONAL	2	TRUE	1	0.589307220565538	2		38	65	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246445	105246445	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	184	646	0	ENST00000349310.3:c.155T>G	p.Leu52Arg	p.L52R	ENST00000349310	NM_001014432.1	52	cTc/cGc	4/15	1	2	FACETS	0.834	0.771	0.898	0.834	0.771	0.898	CLONAL	1	TRUE	1	0.589307220565538	2		646	749	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473707	67473707	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	178	588	0	ENST00000327367.4:c.787C>A	p.Pro263Thr	p.P263T	ENST00000327367	NM_005902.3	263	Ccc/Acc	6/9	1	2	FACETS	0.947	0.877	1	0.947	0.877	1	CLONAL	1	TRUE	1	0.589307220565538	2		588	638	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99460051	99460051	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	156	400	1	ENST00000268035.6:c.2147C>T	p.Ala716Val	p.A716V	ENST00000268035	NM_000875.3	716	gCt/gTt	10/21	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.589307220565538	2		401	527	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347093	347093	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	271	944	3	ENST00000262320.3:c.1918del	p.Glu640LysfsTer65	p.E640Kfs*65	ENST00000262320	NM_003502.3	640	Gaa/aa	7/11	1	2	FACETS	0.873	0.819	0.928	0.873	0.819	0.928	CLONAL	1	TRUE	1	0.589307220565538	2		947	1054	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347983	347983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760961378	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	252	926	5	ENST00000262320.3:c.1523del	p.Gly508ValfsTer197	p.G508Vfs*197	ENST00000262320	NM_003502.3	508	gGt/gt	6/11	1	2	FACETS	0.936	0.877	0.996	0.936	0.877	0.996	CLONAL	1	TRUE	1	0.589307220565538	2		931	914	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973703	15973703	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	193	504	0	ENST00000268712.3:c.4289T>C	p.Val1430Ala	p.V1430A	ENST00000268712	NM_006311.3	1430	gTa/gCa	31/46	1	2	FACETS	0.991	0.921	1	0.991	0.921	1	CLONAL	1	TRUE	1	0.589307220565538	2		504	661	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131219	17131219	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1555611377	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	284	809	0	ENST00000285071.4:c.233del	p.Lys78SerfsTer52	p.K78Sfs*52	ENST00000285071	NM_144997.5	78	aAg/ag	4/14	1	2	FACETS	0.951	0.894	1	0.951	0.894	1	CLONAL	1	TRUE	1	0.589307220565538	2		809	1014	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883774	37883774	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	222	854	1	ENST00000269571.5:c.3391del	p.Leu1131Ter	p.L1131*	ENST00000269571		1129	gCc/gc	26/27	1	2	FACETS	0.881	0.822	0.942	0.881	0.822	0.942	CLONAL	1	TRUE	1	0.589307220565538	2		855	855	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485708	40485708	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs869312887	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	167	514	0	ENST00000264657.5:c.1032G>C	p.Gln344His	p.Q344H	ENST00000264657	NM_139276.2	344	caG/caC	10/24	1	2	FACETS	0.846	0.78	0.914	0.846	0.78	0.914	CLONAL	1	TRUE	1	0.589307220565538	2		514	670	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752444	55752444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1422545682	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	270	882	1	ENST00000284073.2:c.902C>T	p.Ala301Val	p.A301V	ENST00000284073	NM_138962.2	301	gCg/gTg	12/14	0.57784373156808	2	FACETS	0.89	0.835	0.946	0.445	0.417	0.473	CLONAL	1	TRUE	0	0.589307220565538	2		883	1030	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438269	56438281	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTGATGGCCCA	GGCTGATGGCCCA	-	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	320	677	0	ENST00000407977.2:c.712_724del	p.Trp238SerfsTer177	p.W238Sfs*177	ENST00000407977		238	TGGGCCATCAGCCag/ag	7/10	0.57784373156808	2	FACETS	0.874	0.834	0.915	0.874	0.834	0.915	CLONAL	2	TRUE	0	0.589307220565538	2		677	621	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774157	56774157	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	152	533	0	ENST00000337432.4:c.508G>A	p.Val170Ile	p.V170I	ENST00000337432	NM_058216.2	170	Gta/Ata	3/9	0.57784373156808	2	FACETS	0.928	0.853	1	0.464	0.426	0.503	CLONAL	1	TRUE	0	0.589307220565538	2		533	556	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	279	655	3	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	0.57784373156808	2	FACETS	1	0.973	1	0.528	0.497	0.56	CLONAL	1	TRUE	0	0.589307220565538	2		658	897	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533939	63533940	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs771001164	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	118	401	2	ENST00000307078.5:c.1214_1215del	p.Glu405GlyfsTer56	p.E405Gfs*56	ENST00000307078	NM_004655.3	405	gAG/g	6/11	0.57784373156808	2	FACETS	0.965	0.878	1	0.482	0.439	0.528	CLONAL	1	TRUE	0	0.589307220565538	2		403	415	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119910	70119910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1297203260	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	162	465	1	ENST00000245479.2:c.916del	p.Val306CysfsTer77	p.V306Cfs*77	ENST00000245479	NM_000346.3	304	ccG/cc	3/3	0.57784373156808	2	FACETS	0.977	0.901	1	0.488	0.45	0.527	CLONAL	1	TRUE	0	0.589307220565538	2		466	563	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374902	45374902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	153	591	0	ENST00000262160.6:c.941G>A	p.Gly314Asp	p.G314D	ENST00000262160	NM_005901.5	314	gGt/gAt	8/11	1	2	FACETS	0.833	0.765	0.904	0.833	0.765	0.904	CLONAL	1	TRUE	1	0.589307220565538	2		591	623	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56411576	56411576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	101	306	0	ENST00000348428.3:c.1760C>T	p.Pro587Leu	p.P587L	ENST00000348428	NM_006785.3	587	cCa/cTa	15/17	1	2	FACETS	0.974	0.879	1	0.974	0.879	1	CLONAL	1	TRUE	1	0.589307220565538	2		306	352	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619131	1619132	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	222	692	0	ENST00000344749.5:c.1428_1429del	p.Arg477AlafsTer35	p.R477Afs*35	ENST00000344749	NM_001136139.2	476	tcTCgg/tcgg	16/19	1	2	FACETS	0.965	0.901	1	0.965	0.901	1	CLONAL	1	TRUE	1	0.589307220565538	2		692	781	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231399	5231399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568688962	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	252	772	3	ENST00000357368.4:c.2077C>T	p.Arg693Cys	p.R693C	ENST00000357368	NM_002850.3	693	Cgc/Tgc	14/38	1	2	FACETS	0.949	0.89	1	0.949	0.89	1	CLONAL	1	TRUE	1	0.589307220565538	2		775	901	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300082	15300082	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs112788166	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	188	619	0	ENST00000263388.2:c.1192+2T>C		p.X398_splice	ENST00000263388	NM_000435.2	398			1	2	FACETS	0.992	0.921	1	0.992	0.921	1	CLONAL	1	TRUE	1	0.589307220565538	2		619	643	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211183	36211183	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	359	1086	4	ENST00000222270.7:c.939del	p.Val314Ter	p.V314*	ENST00000222270	NM_014727.1	312	Aaa/aa	3/37	1	2	FACETS	0.953	0.902	1	0.953	0.902	1	CLONAL	1	TRUE	1	0.589307220565538	2		1090	1279	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40739829	40739829	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	298	835	0	ENST00000392038.2:c.1396C>A	p.Gln466Lys	p.Q466K	ENST00000392038	NM_001626.4	466	Cag/Aag	14/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.589307220565538	2		835	934	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	114	474	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.589307220565538	2		474	352	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799299	42799300	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1158987717	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	62	363	1	ENST00000575354.2:c.4790dup	p.Pro1598ThrfsTer16	p.P1598Tfs*16	ENST00000575354	NM_015125.3	1595	tcc/tCcc	20/20	1	2	FACETS	0.67	0.583	0.763	0.67	0.583	0.763	SUBCLONAL	1	TRUE	1	0.589307220565538	2		364	314	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139882	50139882	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	228	807	0	ENST00000246792.3:c.447G>T	p.Gln149His	p.Q149H	ENST00000246792	NM_006270.3	149	caG/caT	4/6	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.589307220565538	2		807	767	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719066	52719066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568595903	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	153	568	0	ENST00000322088.6:c.842C>T	p.Thr281Ile	p.T281I	ENST00000322088	NM_014225.5	281	aCa/aTa	7/15	1	2	FACETS	0.951	0.875	1	0.951	0.875	1	CLONAL	1	TRUE	1	0.589307220565538	2		568	546	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605080	46605080	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	203	850	0	ENST00000263734.3:c.1301del	p.Pro434ArgfsTer9	p.P434Rfs*9	ENST00000263734	NM_001430.4	433	Ccc/cc	10/16	1	2	FACETS	0.82	0.762	0.881	0.82	0.762	0.881	CLONAL	1	TRUE	1	0.589307220565538	2		850	840	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705562	47705562	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	112	406	0	ENST00000233146.2:c.2362A>T	p.Thr788Ser	p.T788S	ENST00000233146	NM_000251.2	788	Act/Tct	14/16	1	2	FACETS	0.948	0.86	1	0.948	0.86	1	CLONAL	1	TRUE	1	0.589307220565538	2		406	401	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570070	212570070	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745408040	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	132	483	0	ENST00000342788.4:c.1171G>A	p.Val391Ile	p.V391I	ENST00000342788	NM_005235.2	391	Gtc/Atc	10/28	1	2	FACETS	0.833	0.76	0.909	0.833	0.76	0.909	CLONAL	1	TRUE	1	0.589307220565538	2		483	538	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662194	227662194	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	147	572	0	ENST00000305123.5:c.1261A>G	p.Ser421Gly	p.S421G	ENST00000305123	NM_005544.2	421	Agc/Ggc	1/2	1	2	FACETS	0.857	0.786	0.931	0.857	0.786	0.931	CLONAL	1	TRUE	1	0.589307220565538	2		572	582	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795103	242795104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768249210	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	167	837	1	ENST00000334409.5:c.105dup	p.Thr36HisfsTer70	p.T36Hfs*70	ENST00000334409	NM_005018.2	35	-/C	2/5	1	2	FACETS	0.657	0.604	0.712	0.657	0.604	0.712	SUBCLONAL	1	TRUE	1	0.589307220565538	2		838	863	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	23	246	0	ENST00000375687.4:c.1933_1934dup	p.Gly646ValfsTer58	p.G646Vfs*58	ENST00000375687	NM_015338.5	642	-/GG	13/13	1	2	FACETS	0.485	0.381	0.602	0.485	0.381	0.602	SUBCLONAL	1	TRUE	1	0.589307220565538	2		246	161	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100974	41100974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1259827929	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	154	582	0	ENST00000373198.4:c.1382G>A	p.Arg461Gln	p.R461Q	ENST00000373198	NM_133170.3	461	cGa/cAa	8/32	1	2	FACETS	0.887	0.816	0.961	0.887	0.816	0.961	CLONAL	1	TRUE	1	0.589307220565538	2		582	589	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574689	41574689	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	261	870	2	ENST00000263253.7:c.6974C>A	p.Ser2325Tyr	p.S2325Y	ENST00000263253	NM_001429.3	2325	tCc/tAc	31/31	1	2	FACETS	0.934	0.877	0.994	0.934	0.877	0.994	CLONAL	1	TRUE	1	0.589307220565538	2		872	948	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455623	189455623	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	140	447	0	ENST00000264731.3:c.157G>T	p.Glu53Ter	p.E53*	ENST00000264731	NM_003722.4	53	Gag/Tag	2/14	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.589307220565538	2		447	429	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131182	55131182	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	33	583	0	ENST00000257290.5:c.725T>C	p.Val242Ala	p.V242A	ENST00000257290	NM_006206.4	242	gTg/gCg	5/23	1	2	FACETS	0.22	0.178	0.266	0.22	0.178	0.266	SUBCLONAL	1	TRUE	1	0.589307220565538	2		583	510	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602911	55602911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753419764	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	115	211	1	ENST00000288135.5:c.2621C>T	p.Pro874Leu	p.P874L	ENST00000288135	NM_000222.2	874	cCg/cTg	19/21	1	2	FACETS	0.957	0.869	1	0.957	0.869	1	CLONAL	1	TRUE	1	0.589307220565538	2		212	408	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84403315	84403315	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs770769937	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	27	331	0	ENST00000321945.7:c.170A>G	p.Tyr57Cys	p.Y57C	ENST00000321945	NM_139076.2	57	tAt/tGt	2/9	1	2	FACETS	0.196	0.155	0.242	0.196	0.155	0.242	SUBCLONAL	1	TRUE	1	0.589307220565538	2		331	468	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	213	537	2	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	0.851	0.792	0.912	0.851	0.792	0.912	CLONAL	1	TRUE	1	0.589307220565538	2		539	849	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517818	187517819	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	31	363	0	ENST00000441802.2:c.12875_12876del	p.Val4292AlafsTer27	p.V4292Afs*27	ENST00000441802	NM_005245.3	4292	gTG/g	25/27	1	2	FACETS	0.235	0.189	0.286	0.235	0.189	0.286	SUBCLONAL	1	TRUE	1	0.589307220565538	2		363	448	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	188	585	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.997	0.926	1	0.997	0.926	1	CLONAL	1	TRUE	1	0.589307220565538	2		590	640	SUCCESS
APC	324	MSKCC	GRCh37	5	112116506	112116506	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1257143633	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	70	261	0	ENST00000257430.4:c.551T>C	p.Met184Thr	p.M184T	ENST00000257430	NM_000038.5	184	aTg/aCg	6/16	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.589307220565538	2		261	226	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638731	176638731	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151165525	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	221	671	0	ENST00000439151.2:c.3331G>A	p.Asp1111Asn	p.D1111N	ENST00000439151	NM_022455.4	1111	Gat/Aat	5/23	1	2	FACETS	0.984	0.919	1	0.984	0.919	1	CLONAL	1	TRUE	1	0.589307220565538	2		671	762	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553356	106553356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	127	406	0	ENST00000369096.4:c.1321C>T	p.Pro441Ser	p.P441S	ENST00000369096	NM_001198.3	441	Ccg/Tcg	5/7	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.589307220565538	2		406	416	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341865	8341865	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	113	644	0	ENST00000356435.5:c.4775G>T	p.Arg1592Met	p.R1592M	ENST00000356435		1592	aGg/aTg	29/35	1	2	FACETS	0.634	0.572	0.699	0.634	0.572	0.699	SUBCLONAL	1	TRUE	1	0.589307220565538	2		644	605	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624493	93624493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1276980680	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	80	298	0	ENST00000375746.1:c.584G>A	p.Arg195Gln	p.R195Q	ENST00000375746	NM_001174167.1	195	cGa/cAa	4/14	1	2	FACETS	0.973	0.867	1	0.973	0.867	1	CLONAL	1	TRUE	1	0.589307220565538	2		298	279	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328378	137328380	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs763369916	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	209	834	0	ENST00000481739.1:c.1315_1317del	p.Phe439del	p.F439del	ENST00000481739	NM_002957.4	436	cTCTtc/ctc	10/10	1	2	FACETS	0.78	0.725	0.838	0.78	0.725	0.838	SUBCLONAL	1	TRUE	1	0.589307220565538	2		834	909	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400303	139400303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs553328686	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	207	716	0	ENST00000277541.6:c.4045G>A	p.Ala1349Thr	p.A1349T	ENST00000277541	NM_017617.3	1349	Gct/Act	25/34	1	2	FACETS	0.962	0.896	1	0.962	0.896	1	CLONAL	1	TRUE	1	0.589307220565538	2		716	730	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041265	47041265	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1556779896	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	238	857	0	ENST00000377604.3:c.1693C>T	p.Pro565Ser	p.P565S	ENST00000377604	NM_001204468.1	565	Cct/Tct	15/24	1	2	FACETS	0.991	0.928	1	0.991	0.928	1	CLONAL	1	TRUE	1	0.589307220565538	2		857	815	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	35	736	3	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	1	2	FACETS	0.176	0.144	0.213	0.176	0.144	0.213	SUBCLONAL	1	TRUE	1	0.589307220565538	2		739	674	SUCCESS
AR	367	MSKCC	GRCh37	X	66765155	66765155	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs868709351	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	11	343	0	ENST00000374690.3:c.167T>A	p.Leu56Gln	p.L56Q	ENST00000374690	NM_000044.3	56	cTg/cAg	1/8	1	2	FACETS	0.184	0.127	0.255	0.184	0.127	0.255	SUBCLONAL	1	TRUE	1	0.589307220565538	2		343	203	SUCCESS
AR	367	MSKCC	GRCh37	X	66765475	66765475	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1234341494	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	186	830	0	ENST00000374690.3:c.487A>G	p.Thr163Ala	p.T163A	ENST00000374690	NM_000044.3	163	Acg/Gcg	1/8	1	2	FACETS	0.893	0.827	0.961	0.893	0.827	0.961	CLONAL	1	TRUE	1	0.589307220565538	2		830	707	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776354	76776354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	117	660	0	ENST00000373344.5:c.7112C>T	p.Ala2371Val	p.A2371V	ENST00000373344	NM_000489.3	2371	gCg/gTg	34/35	1	2	FACETS	0.793	0.718	0.87	0.793	0.718	0.87	SUBCLONAL	1	TRUE	1	0.589307220565538	2		660	501	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	172	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.467938450830309	4	FACETS	0.919	0.866	0.971	1	0.989	1	CLONAL	4	FALSE	1	0.494021668239448	4		426	283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934874	NA	P-0035585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	982	836	0	ENST00000269305.4:c.451C>A	p.Pro151Thr	p.P151T	ENST00000269305	NM_001126112.2	151	Ccc/Acc	5/11	0.494021668239448	2	FACETS	0.926	0.915	0.937	1	0.999	1	CLONAL	4	FALSE	0	0.494021668239448	2		836	1073	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0035585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	191	349	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.494021668239448	3	FACETS	1	0.97	1	1	0.994	1	CLONAL	4	FALSE	0	0.494021668239448	3		349	238	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964491	70964491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1447674775	NA	P-0035585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	557	880	3	ENST00000276594.2:c.1537G>A	p.Gly513Arg	p.G513R	ENST00000276594	NM_024504.3	513	Ggg/Agg	8/8	0.376162253520445	4	FACETS	0.891	0.862	0.92	1	0.996	1	CLONAL	4	FALSE	1	0.494021668239448	4		883	945	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669586	88669586	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	203	645	0	ENST00000360948.2:c.1312C>A	p.Leu438Ile	p.L438I	ENST00000360948	NM_001012338.2	438	Ctt/Att	12/19	1	2	FACETS	0.928	0.871	0.985	1	0.994	1	CLONAL	2	FALSE	1	0.494021668239448	2		645	443	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400116	41400116	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	620	704	0	ENST00000373198.4:c.643G>T	p.Ala215Ser	p.A215S	ENST00000373198	NM_133170.3	215	Gct/Tct	5/32	0.494021668239448	9	FACETS	1	0.975	1	1	0.975	1	CLONAL	6	FALSE	3	0.494021668239448	9		704	1132	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0035700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	58	442	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.835	0.729	0.947	0.835	0.729	0.947	CLONAL	1	TRUE	1	0.690980439590351	2		442	201	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923745	72923746	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	172	570	0	ENST00000268489.5:c.3332dup	p.His1112AlafsTer43	p.H1112Afs*43	ENST00000268489	NM_006885.3	1111	aag/aaAg	4/10	1	2	FACETS	0.982	0.911	1	0.982	0.911	1	CLONAL	1	TRUE	1	0.690980439590351	2		570	507	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882953	89882953	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	32	82	0	ENST00000389301.3:c.71A>G	p.Glu24Gly	p.E24G	ENST00000389301	NM_000135.2	24	gAg/gGg	1/43	1	2	FACETS	0.858	0.713	1	0.858	0.713	1	CLONAL	1	TRUE	1	0.690980439590351	2		82	108	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39002697	39002697	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	114	396	0	ENST00000357387.3:c.332T>C	p.Ile111Thr	p.I111T	ENST00000357387	NM_152756.3	111	aTc/aCc	5/38	1	2	FACETS	0.976	0.889	1	0.976	0.889	1	CLONAL	1	TRUE	1	0.690980439590351	2		396	338	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0035891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	307	715	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.8744019333173	1	FACETS	0.943	0.909	0.976	0.943	0.909	0.976	CLONAL	1	TRUE	0	0.8744019333173	1		715	419	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399486	139399486	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	420	910	0	ENST00000277541.6:c.4657G>T	p.Glu1553Ter	p.E1553*	ENST00000277541	NM_017617.3	1553	Gag/Tag	26/34	0.487488639510502	1	FACETS	0.747	0.718	0.775	0.747	0.718	0.775	INDETERMINATE	1	TRUE	0	0.8744019333173	1		910	724	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128018806	128018806	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	70	403	0	ENST00000285398.2:c.2062A>G	p.Lys688Glu	p.K688E	ENST00000285398	NM_000122.1	688	Aag/Gag	13/15	0.631625441156393	4	FACETS	0.445	0.387	0.507	0.222	0.193	0.254	SUBCLONAL	1	TRUE	2	0.8744019333173	4		403	675	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226595610	226595611	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0035891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	211	542	0	ENST00000366794.5:c.20_21del	p.Lys7ThrfsTer38	p.K7Tfs*38	ENST00000366794	NM_001618.3	7	aAG/a	1/23	1	2	FACETS	0.899	0.842	0.956	0.899	0.842	0.956	CLONAL	1	TRUE	1	0.8744019333173	2		542	537	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627221	12627221	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	67	422	0	ENST00000251849.4:c.1495T>C	p.Ser499Pro	p.S499P	ENST00000251849	NM_002880.3	499	Tct/Cct	14/17	0.845721013557066	3	FACETS	0.274	0.237	0.313	0.137	0.118	0.157	SUBCLONAL	1	TRUE	1	0.8744019333173	3		422	805	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916643	178916669	+	inframe_deletion	In_Frame_Del	DEL	GTGGGGCATCCACTTGATGCCCCCAAG	GTGGGGCATCCACTTGATGCCCCCAAG	-	novel	NA	P-0035891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	184	260	0	ENST00000263967.3:c.30_56del	p.Trp11_Arg19del	p.W11_R19del	ENST00000263967	NM_006218.2	10	ctGTGGGGCATCCACTTGATGCCCCCAAGa/cta	2/21	0.845721013557066	3	FACETS	0.792	0.742	0.842	0.792	0.742	0.842	SUBCLONAL	2	TRUE	1	0.8744019333173	3		260	382	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007052	152007052	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	73	292	0	ENST00000262189.6:c.848A>G	p.Glu283Gly	p.E283G	ENST00000262189	NM_170606.2	283	gAa/gGa	6/59	1	2	FACETS	0.446	0.393	0.504	0.446	0.393	0.504	SUBCLONAL	1	TRUE	1	0.8744019333173	2		292	374	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571867	64571867	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	60	1053	1	ENST00000312049.6:c.1772A>T	p.Lys591Ile	p.K591I	ENST00000312049	NM_130799.2	591	aAa/aTa	10/10	1	2	FACETS	0.117	0.1	0.136	0.117	0.1	0.136	SUBCLONAL	1	TRUE	1	0.8744019333173	2		1054	1171	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822132	72822132	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	23	646	0	ENST00000268489.5:c.10043T>A	p.Leu3348Gln	p.L3348Q	ENST00000268489	NM_006885.3	3348	cTg/cAg	10/10	0.8744019333173	1	FACETS	0.164	0.129	0.205	0.164	0.129	0.205	SUBCLONAL	1	TRUE	0	0.8744019333173	1		646	180	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883641	37883641	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	54	926	0	ENST00000269571.5:c.3253G>T	p.Val1085Leu	p.V1085L	ENST00000269571		1085	Gta/Tta	26/27	0.8744019333173	3	FACETS	0.169	0.144	0.197	0.085	0.072	0.099	SUBCLONAL	1	TRUE	1	0.8744019333173	3		926	1049	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs753143066	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	177	822	7	ENST00000295797.4:c.826dup	p.Thr276AsnfsTer16	p.T276Nfs*16	ENST00000295797	NM_002740.5	273	tta/ttAa	9/18	1	2	FACETS	0.848	0.78	0.918	1	0.991	1	CLONAL	2	TRUE	1	0.19	2		829	1099	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	378	556	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.986	1	1	0.997	1	CLONAL	4	TRUE	1	0.19	2		562	918	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	194	851	5	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.888	0.82	0.958	1	0.992	1	CLONAL	2	TRUE	1	0.19	2		856	1150	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807363	3807364	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	112	379	0	ENST00000262367.5:c.3623dup	p.Gln1209ThrfsTer25	p.Q1209Tfs*25	ENST00000262367	NM_004380.2	1208	cca/ccCa	19/31	1	2	FACETS	1	0.937	1	1	0.989	1	CLONAL	2	TRUE	1	0.19	2		379	561	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	123	217	0	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.894	0.809	0.983	1	0.988	1	CLONAL	2	TRUE	1	0.19	2		217	724	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	190	666	1	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.828	0.764	0.895	1	0.991	1	CLONAL	2	TRUE	1	0.19	2		667	1208	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	168	585	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.989	0.909	1	1	0.992	1	CLONAL	2	TRUE	1	0.19	2		590	894	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782032	9782032	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	118	680	0	ENST00000377346.4:c.2059del		p.X687_splice	ENST00000377346	NM_005026.3	687			1	2	FACETS	0.785	0.708	0.866	1	0.985	1	SUBCLONAL	2	TRUE	1	0.19	2		680	791	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024011	27024011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1259199322	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	33	84	1	ENST00000324856.7:c.1117C>T	p.Pro373Ser	p.P373S	ENST00000324856	NM_006015.4	373	Ccg/Tcg	1/20	1	2	FACETS	1	0.838	1	1	0.972	1	CLONAL	3	TRUE	1	0.19	2		85	115	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599271	28599271	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs770146088	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	216	916	0	ENST00000253063.3:c.722del	p.Pro241GlnfsTer6	p.P241Qfs*6	ENST00000253063	NM_031459.4	239	agC/ag	5/10	1	2	FACETS	0.954	0.885	1	1	0.993	1	CLONAL	2	TRUE	1	0.19	2		916	1192	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933540	36933540	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3917997	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	186	757	1	ENST00000361632.4:c.1747C>T	p.Arg583Cys	p.R583C	ENST00000361632		583	Cgt/Tgt	13/16	1	2	FACETS	0.95	0.876	1	1	0.992	1	CLONAL	2	TRUE	1	0.19	2		758	1031	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	191	853	7	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	0.93	0.859	1	1	0.992	1	CLONAL	2	TRUE	1	0.19	2		860	1081	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439881	51439881	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	73	332	0	ENST00000262662.1:c.446G>T	p.Arg149Met	p.R149M	ENST00000262662		149	aGg/aTg	4/4	1	2	FACETS	0.755	0.662	0.855	1	0.975	1	SUBCLONAL	2	TRUE	1	0.19	2		332	509	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107230	193107230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	43	346	0	ENST00000367435.3:c.439C>T	p.Arg147Cys	p.R147C	ENST00000367435	NM_024529.4	147	Cgc/Tgc	6/17	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.19	2		346	319	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567294	226567294	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	148	732	0	ENST00000366794.5:c.1592C>G	p.Ala531Gly	p.A531G	ENST00000366794	NM_001618.3	531	gCa/gGa	11/23	1	2	FACETS	0.921	0.841	1	1	0.99	1	CLONAL	2	TRUE	1	0.19	2		732	846	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681275	88681275	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	163	689	1	ENST00000372037.3:c.1167-2A>G		p.X389_splice	ENST00000372037	NM_004329.2	389			1	2	FACETS	0.992	0.911	1	1	0.992	1	CLONAL	2	TRUE	1	0.19	2		690	865	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8246261	8246261	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	119	444	0	ENST00000335790.3:c.373G>A	p.Val125Met	p.V125M	ENST00000335790	NM_002315.2	125	Gtg/Atg	4/4	1	2	FACETS	1	0.957	1	1	0.99	1	CLONAL	2	TRUE	1	0.19	2		444	570	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	461435	461435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	138	592	0	ENST00000399788.2:c.1085C>T	p.Thr362Ile	p.T362I	ENST00000399788	NM_001042603.1	362	aCa/aTa	9/28	1	2	FACETS	0.931	0.848	1	1	0.99	1	CLONAL	2	TRUE	1	0.19	2		592	780	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926927	112926927	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs994514579	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	115	584	0	ENST00000351677.2:c.1547T>C	p.Met516Thr	p.M516T	ENST00000351677	NM_002834.3	516	aTg/aCg	13/16	0.31638900994084	2	FACETS	0.759	0.684	0.839			1	SUBCLONAL	2	TRUE	NA	0.19	2		584	797	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112283	115112283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1018135320	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	51	172	0	ENST00000257566.3:c.1457C>T	p.Thr486Met	p.T486M	ENST00000257566	NM_016569.3	486	aCg/aTg	7/8	0.31638900994084	2	FACETS	1	0.941	1			1	CLONAL	2	TRUE	NA	0.19	2		172	226	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118693	115118693	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	132	633	0	ENST00000257566.3:c.648del	p.Lys216AsnfsTer27	p.K216Nfs*27	ENST00000257566	NM_016569.3	216	aaA/aa	2/8	0.31638900994084	2	FACETS	0.85	0.772	0.933			1	CLONAL	2	TRUE	NA	0.19	2		633	817	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118929	115118929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	82	404	0	ENST00000257566.3:c.412G>A	p.Val138Met	p.V138M	ENST00000257566	NM_016569.3	138	Gtg/Atg	2/8	0.31638900994084	2	FACETS	0.916	0.811	1			1	CLONAL	2	TRUE	NA	0.19	2		404	471	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28644683	28644683	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	164	820	0	ENST00000241453.7:c.110del	p.Leu37Ter	p.L37*	ENST00000241453	NM_004119.2	37	tTa/ta	2/24	1	2	FACETS	1	0.919	1	1	0.992	1	CLONAL	2	TRUE	1	0.19	2		820	863	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134507	41134507	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	164	634	0	ENST00000379561.5:c.1121T>C	p.Leu374Pro	p.L374P	ENST00000379561	NM_002015.3	374	cTt/cCt	2/3	1	2	FACETS	1	0.941	1	1	0.992	1	CLONAL	2	TRUE	1	0.19	2		634	838	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878061	48878062	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1131690852	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	60	211	0	ENST00000267163.4:c.19dup	p.Arg7ProfsTer24	p.R7Pfs*24	ENST00000267163	NM_000321.2	5	acc/aCcc	1/27	1	2	FACETS	0.757	0.654	0.868	1	0.97	1	SUBCLONAL	2	TRUE	1	0.19	2		211	417	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033865	49033865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369755801	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	116	527	0	ENST00000267163.4:c.2002C>T	p.Arg668Cys	p.R668C	ENST00000267163	NM_000321.2	668	Cgc/Tgc	20/27	1	2	FACETS	0.886	0.8	0.977	1	0.987	1	CLONAL	2	TRUE	1	0.19	2		527	689	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437427	110437427	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	67	500	0	ENST00000375856.3:c.974A>G	p.His325Arg	p.H325R	ENST00000375856	NM_003749.2	325	cAc/cGc	1/2	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.19	2		500	665	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690618	88690618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149623569	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	96	415	1	ENST00000360948.2:c.412C>T	p.Arg138Trp	p.R138W	ENST00000360948	NM_001012338.2	138	Cgg/Tgg	5/19	1	2	FACETS	0.961	0.859	1	1	0.986	1	CLONAL	2	TRUE	1	0.19	2		416	526	SUCCESS
BLM	641	MSKCC	GRCh37	15	91337587	91337587	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	69	283	0	ENST00000355112.3:c.3210G>T	p.Lys1070Asn	p.K1070N	ENST00000355112	NM_000057.2	1070	aaG/aaT	16/22	1	2	FACETS	1	0.934	1	1	0.983	1	CLONAL	2	TRUE	1	0.19	2		283	330	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637562	23637562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374736398	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	151	551	0	ENST00000261584.4:c.2743G>A	p.Ala915Thr	p.A915T	ENST00000261584	NM_024675.3	915	Gca/Aca	7/13	1	2	FACETS	1	0.919	1	1	0.991	1	CLONAL	2	TRUE	1	0.19	2		551	791	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847215	68847215	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	122	472	0	ENST00000261769.5:c.1138-1G>A		p.X380_splice	ENST00000261769	NM_004360.3	380			1	2	FACETS	1	0.959	1	1	0.99	1	CLONAL	2	TRUE	1	0.19	2		472	583	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346158	89346158	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs878855327	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	62	317	0	ENST00000301030.4:c.6792del	p.Ala2265ProfsTer72	p.A2265Pfs*72	ENST00000301030	NM_001256183.1	2264	ccC/cc	9/13	1	2	FACETS	1	0.911	1	1	0.981	1	CLONAL	2	TRUE	1	0.19	2		317	308	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805074	89805074	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs74977201	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	211	695	0	ENST00000389301.3:c.4303G>A	p.Ala1435Thr	p.A1435T	ENST00000389301	NM_000135.2	1435	Gcc/Acc	43/43	1	2	FACETS	1	0.95	1	1	0.994	1	CLONAL	2	TRUE	1	0.19	2		695	1079	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805351	89805351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149851163	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	150	605	0	ENST00000389301.3:c.4199G>A	p.Arg1400His	p.R1400H	ENST00000389301	NM_000135.2	1400	cGt/cAt	42/43	1	2	FACETS	0.873	0.798	0.952	1	0.99	1	CLONAL	2	TRUE	1	0.19	2		605	904	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131409	17131409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs539468848	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	163	657	2	ENST00000285071.4:c.43G>A	p.Gly15Ser	p.G15S	ENST00000285071	NM_144997.5	15	Ggc/Agc	4/14	1	2	FACETS	1	0.94	1	1	0.992	1	CLONAL	2	TRUE	1	0.19	2		659	834	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	226	905	3	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	1	0.969	1	1	0.994	1	CLONAL	2	TRUE	1	0.19	2		908	1109	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453399	40453399	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs759027671	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	259	896	16	ENST00000345506.4:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000345506	NM_003152.3	366	Ccc/cc	10/20	1	2	FACETS	1	0.976	1	1	0.995	1	CLONAL	2	TRUE	1	0.19	2		912	1256	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47679279	47679279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1399168977	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	98	543	0	ENST00000347630.2:c.928G>A	p.Asp310Asn	p.D310N	ENST00000347630	NM_001007230.1	310	Gac/Aac	10/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.19	2		543	786	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	169	312	4	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	1	0.971	1	1	0.993	1	CLONAL	2	TRUE	1	0.19	2		316	797	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627322	14627322	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1417674736	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	254	970	2	ENST00000254322.2:c.748G>A	p.Asp250Asn	p.D250N	ENST00000254322	NM_006145.1	250	Gat/Aat	2/3	1	2	FACETS	1	0.935	1	1	0.995	1	CLONAL	2	TRUE	1	0.19	2		972	1336	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272337	15272337	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs771517374	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	222	974	8	ENST00000263388.2:c.6102del	p.Gly2035ValfsTer50	p.G2035Vfs*50	ENST00000263388	NM_000435.2	2034	ccC/cc	33/33	1	2	FACETS	0.982	0.913	1	1	0.994	1	CLONAL	2	TRUE	1	0.19	2		982	1190	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214866	36214866	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568372429	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	176	875	4	ENST00000222270.7:c.3296del	p.Gly1099AlafsTer83	p.G1099Afs*83	ENST00000222270	NM_014727.1	1098	Ggg/gg	8/37	1	2	FACETS	0.828	0.761	0.897	1	0.991	1	CLONAL	2	TRUE	1	0.19	2		879	1119	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222828	36222828	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	293	926	1	ENST00000222270.7:c.5462del	p.Pro1821HisfsTer74	p.P1821Hfs*74	ENST00000222270	NM_014727.1	1819	gaC/ga	27/37	1	2	FACETS	1	0.979	1	1	0.996	1	CLONAL	2	TRUE	1	0.19	2		927	1412	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799051	42799051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	297	1019	0	ENST00000575354.2:c.4535G>A	p.Arg1512His	p.R1512H	ENST00000575354	NM_015125.3	1512	cGt/cAt	20/20	1	2	FACETS	1	0.979	1	1	0.996	1	CLONAL	2	TRUE	1	0.19	2		1019	1431	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905891	50905891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755550936	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	193	953	1	ENST00000440232.2:c.863C>T	p.Ala288Val	p.A288V	ENST00000440232	NM_002691.3	288	gCg/gTg	8/27	1	2	FACETS	0.902	0.833	0.974	1	0.992	1	CLONAL	2	TRUE	1	0.19	2		954	1126	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	178	725	2	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	0.942	0.867	1	1	0.992	1	CLONAL	2	TRUE	1	0.19	2		727	995	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467434	25467434	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	141	659	0	ENST00000264709.3:c.1642A>G	p.Met548Val	p.M548V	ENST00000264709	NM_175629.2	548	Atg/Gtg	14/23	1	2	FACETS	0.886	0.807	0.968	1	0.989	1	CLONAL	2	TRUE	1	0.19	2		659	838	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416647	29416647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201129468	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	99	518	0	ENST00000389048.3:c.4306C>T	p.Arg1436Cys	p.R1436C	ENST00000389048	NM_004304.4	1436	Cgc/Tgc	29/29	1	2	FACETS	0.868	0.777	0.966	1	0.985	1	CLONAL	2	TRUE	1	0.19	2		518	600	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693887	47693887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778523	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	88	475	0	ENST00000233146.2:c.1601G>A	p.Arg534His	p.R534H	ENST00000233146	NM_000251.2	534	cGt/cAt	10/16	1	2	FACETS	0.93	0.827	1	1	0.984	1	CLONAL	2	TRUE	1	0.19	2		475	498	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027494	48027494	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755587950	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	36	462	0	ENST00000234420.5:c.2372G>A	p.Arg791His	p.R791H	ENST00000234420	NM_000179.2	791	cGt/cAt	4/10	1	2	FACETS	0.563	0.461	0.678	0.563	0.461	0.678	SUBCLONAL	1	TRUE	1	0.19	2		462	673	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646085	215646085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	138	808	5	ENST00000260947.4:c.513del	p.Asp172MetfsTer40	p.D172Mfs*40	ENST00000260947	NM_000465.2	171	aaA/aa	4/11	1	2	FACETS	0.897	0.816	0.981	1	0.989	1	CLONAL	2	TRUE	1	0.19	2		813	810	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385068	31385068	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	201	809	1	ENST00000328111.2:c.1453C>T	p.Arg485Ter	p.R485*	ENST00000328111	NM_006892.3	485	Cga/Tga	14/23	1	2	FACETS	0.954	0.883	1	1	0.993	1	CLONAL	2	TRUE	1	0.19	2		810	1109	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164716	36164716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285485702	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	223	836	0	ENST00000300305.3:c.1159G>A	p.Gly387Ser	p.G387S	ENST00000300305		387	Ggc/Agc	8/8	1	2	FACETS	1	0.946	1	1	0.994	1	CLONAL	2	TRUE	1	0.19	2		836	1150	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513272	41513272	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	83	643	0	ENST00000263253.7:c.176G>A	p.Gly59Asp	p.G59D	ENST00000263253	NM_001429.3	59	gGt/gAt	2/31	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.19	2		643	736	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533742	41533742	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	112	638	0	ENST00000263253.7:c.1708C>T	p.Gln570Ter	p.Q570*	ENST00000263253	NM_001429.3	570	Cag/Tag	8/31	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.19	2		638	877	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436311	52436311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773230722	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	149	585	0	ENST00000460680.1:c.2183G>A	p.Arg728His	p.R728H	ENST00000460680	NM_004656.3	728	cGc/cAc	17/17	1	2	FACETS	0.961	0.879	1	1	0.991	1	CLONAL	2	TRUE	1	0.19	2		585	816	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204623	128204623	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	149	689	3	ENST00000341105.2:c.818del	p.Gly273AspfsTer53	p.G273Dfs*53	ENST00000341105	NM_032638.4	273	gGa/ga	3/6	1	2	FACETS	0.828	0.756	0.904	1	0.989	1	CLONAL	2	TRUE	1	0.19	2		692	947	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608610	189608610	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	168	711	0	ENST00000264731.3:c.1685T>C	p.Leu562Pro	p.L562P	ENST00000264731	NM_003722.4	562	cTg/cCg	13/14	1	2	FACETS	0.98	0.901	1	1	0.992	1	CLONAL	2	TRUE	1	0.19	2		711	902	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	223684	223684	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1057523165	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	101	434	0	ENST00000264932.6:c.150+1G>A		p.X50_splice	ENST00000264932	NM_004168.2	50			1	2	FACETS	1	0.939	1	1	0.988	1	CLONAL	2	TRUE	1	0.19	2		434	499	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945700	38945700	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	83	415	0	ENST00000357387.3:c.4526A>G	p.Asp1509Gly	p.D1509G	ENST00000357387	NM_152756.3	1509	gAc/gGc	34/38	1	2	FACETS	0.914	0.809	1	1	0.983	1	CLONAL	2	TRUE	1	0.19	2		415	478	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944382	131944382	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs748536322	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	62	221	4	ENST00000265335.6:c.2801del	p.Asn934IlefsTer6	p.N934Ifs*6	ENST00000265335		932	Aaa/aa	17/25	1	2	FACETS	1	0.911	1	1	0.981	1	CLONAL	2	TRUE	1	0.19	2		225	308	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131945054	131945054	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	66	326	0	ENST00000265335.6:c.3002T>C	p.Met1001Thr	p.M1001T	ENST00000265335		1001	aTg/aCg	19/25	1	2	FACETS	0.856	0.746	0.974	1	0.977	1	CLONAL	2	TRUE	1	0.19	2		326	406	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289130	33289130	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	228	725	0	ENST00000374542.5:c.422del	p.Lys141ArgfsTer3	p.K141Rfs*3	ENST00000374542	NM_001141970.1	141	aAg/ag	3/8	1	2	FACETS	1	0.952	1	1	0.994	1	CLONAL	2	TRUE	1	0.19	2		725	1166	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100414	157100414	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1438676618	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	12	40	0	ENST00000346085.5:c.1351T>C	p.Ser451Pro	p.S451P	ENST00000346085	NM_020732.3	451	Tcg/Ccg	1/20	1	2	FACETS	1	0.836	1	1	0.836	1	CLONAL	1	TRUE	1	0.19	2		40	97	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	52	676	0	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.585	0.497	0.683	0.585	0.497	0.683	SUBCLONAL	1	TRUE	1	0.19	2		676	935	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538873	23538873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	141	575	1	ENST00000380871.4:c.566G>A	p.Gly189Glu	p.G189E	ENST00000380871	NM_006167.3	189	gGa/gAa	2/2	0.31638900994084	3	FACETS	0.896	0.816	0.98	0.896	0.816	0.98	CLONAL	2	TRUE	1	0.19	3		576	907	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540372	23540372	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1403765240	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	89	391	0	ENST00000380871.4:c.31del	p.Glu11ArgfsTer66	p.E11Rfs*66	ENST00000380871	NM_006167.3	11	Gag/ag	1/2	0.31638900994084	3	FACETS	0.781	0.693	0.875	0.781	0.693	0.875	SUBCLONAL	2	TRUE	1	0.19	3		391	657	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992742	68992742	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	90	815	1	ENST00000288368.4:c.1707G>T	p.Met569Ile	p.M569I	ENST00000288368	NM_024870.2	569	atG/atT	16/40	0.31638900994084	3	FACETS	0.759	0.674	0.851	0.759	0.674	0.851	SUBCLONAL	2	TRUE	1	0.19	3		816	683	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971023	21971023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782797	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	130	610	1	ENST00000304494.5:c.335G>A	p.Arg112His	p.R112H	ENST00000304494	NM_000077.4	112	cGt/cAt	2/3	1	2	FACETS	0.899	0.816	0.986	1	0.989	1	CLONAL	2	TRUE	1	0.19	2		611	761	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169499	27169499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573385848	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	133	648	2	ENST00000380036.4:c.500G>A	p.Arg167Gln	p.R167Q	ENST00000380036	NM_000459.3	167	cGg/cAg	4/23	1	2	FACETS	0.938	0.853	1	1	0.99	1	CLONAL	2	TRUE	1	0.19	2		650	746	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27183482	27183482	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	100	486	0	ENST00000380036.4:c.1056A>G	p.Ile352Met	p.I352M	ENST00000380036	NM_000459.3	352	atA/atG	8/23	1	2	FACETS	0.911	0.815	1	1	0.986	1	CLONAL	2	TRUE	1	0.19	2		486	578	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966633	36966633	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	164	701	0	ENST00000358127.4:c.693del	p.Gln231HisfsTer47	p.Q231Hfs*47	ENST00000358127	NM_001280556.1	231	caG/ca	6/10	1	2	FACETS	1	0.948	1	1	0.992	1	CLONAL	2	TRUE	1	0.19	2		701	829	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566440	139566446	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGGAC	CCCGGAC	-	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	168	895	0	ENST00000308874.7:c.704_710del	p.Asp235AlafsTer17	p.D235Afs*17	ENST00000308874		233	ctCCCGGAC/ct	9/10	1	2	FACETS	0.845	0.776	0.918	1	0.99	1	CLONAL	2	TRUE	1	0.19	2		895	1046	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932085	39932085	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	240	870	0	ENST00000378444.4:c.2514del	p.Lys839SerfsTer17	p.K839Sfs*17	ENST00000378444	NM_001123385.1	838	ccC/cc	4/15	0.31638900994084	2	FACETS	1	0.969	1			1	CLONAL	2	TRUE	NA	0.19	2		870	1187	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227982	53227982	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1556840029	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	220	873	1	ENST00000375401.3:c.2332C>T	p.Arg778Ter	p.R778*	ENST00000375401	NM_004187.3	778	Cga/Tga	16/26	0.0968253974904152	0	FACETS	0.846	0.787	0.908			1	INDETERMINATE	2	TRUE	0	0.19	0		874	1108	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240761	53240761	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs781819495	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	163	772	0	ENST00000375401.3:c.1319A>G	p.Tyr440Cys	p.Y440C	ENST00000375401	NM_004187.3	440	tAt/tGt	10/26	0.0968253974904152	0	FACETS	0.705	0.647	0.767			1	INDETERMINATE	2	TRUE	0	0.19	0		772	985	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246393	53246393	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	199	913	0	ENST00000375401.3:c.589del	p.Leu197TyrfsTer37	p.L197Yfs*37	ENST00000375401	NM_004187.3	197	Cta/ta	5/26	0.0968253974904152	0	FACETS	0.718	0.664	0.775			1	INDETERMINATE	2	TRUE	0	0.19	0		913	1181	SUCCESS
AR	367	MSKCC	GRCh37	X	66941722	66941722	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	153	742	0	ENST00000374690.3:c.2366G>T	p.Arg789Met	p.R789M	ENST00000374690	NM_000044.3	789	aGg/aTg	6/8	0.0968253974904152	0	FACETS	0.676	0.618	0.737			1	INDETERMINATE	2	TRUE	0	0.19	0		742	965	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611138	100611138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868978699	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	136	706	1	ENST00000308731.7:c.1468C>T	p.Arg490Cys	p.R490C	ENST00000308731	NM_000061.2	490	Cgc/Tgc	15/19	0.0968253974904152	0	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	0	0.19	0		707	865	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993831	72993831	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	108	524	2	ENST00000268489.5:c.214del	p.Ser72ProfsTer37	p.S72Pfs*37	ENST00000268489	NM_006885.3	72	Tcc/cc	2/10	1	2	FACETS	1	0.918	1	1	0.988	1	CLONAL	2	TRUE	1	0.19	2		526	556	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279861	46279866	+	inframe_deletion	In_Frame_Del	DEL	CAGCAA	CAGCAA	-	rs748517056	NA	P-0035892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	40	390	3	ENST00000371998.3:c.3810_3815del	p.Gln1275_Gln1276del	p.Q1275_Q1276del	ENST00000371998		1263	CAGCAA/-	20/23	1	2	FACETS	0.883	0.733	1	0.883	0.733	1	CLONAL	1	TRUE	1	0.19	2		393	477	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007825	45007825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	110	399	2	ENST00000558401.1:c.276del	p.Thr93LeufsTer10	p.T93Lfs*10	ENST00000558401	NM_004048.2	91	aCc/ac	2/4	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.431758418385722	2		401	365	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	109	132	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.765	0.695	0.837	1	0.985	1	SUBCLONAL	2	TRUE	1	0.431758418385722	2		132	330	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	254	556	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.431758418385722	2	FACETS	0.904	0.86	0.947	1	0.994	1	CLONAL	3	TRUE	0	0.431758418385722	2		562	434	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	81	516	1	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.92	0.815	1	0.92	0.815	1	CLONAL	1	TRUE	1	0.431758418385722	2		517	408	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570293	87570293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202111708	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	101	346	0	ENST00000277120.3:c.2033C>T	p.Ala678Val	p.A678V	ENST00000277120		678	gCg/gTg	17/19	1	2	FACETS	0.845	0.766	0.925	1	0.986	1	CLONAL	2	TRUE	1	0.431758418385722	2		346	277	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216596	108216596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778080	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	80	262	0	ENST00000278616.4:c.8545C>T	p.Arg2849Ter	p.R2849*	ENST00000278616	NM_000051.3	2849	Cga/Tga	58/63	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.431758418385722	2		262	273	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	92	216	1	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	0.778	0.701	0.857	1	0.983	1	SUBCLONAL	2	TRUE	1	0.431758418385722	2		217	274	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	21	388	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	0.29	0.223	0.368	0.29	0.223	0.368	SUBCLONAL	1	TRUE	1	0.431758418385722	2		388	336	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924336	112924336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507536	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	135	343	0	ENST00000351677.2:c.1282G>A	p.Val428Met	p.V428M	ENST00000351677	NM_002834.3	428	Gtg/Atg	11/16	0.267814218110326	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.431758418385722	1		343	405	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249360	153249361	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	43	286	0	ENST00000281708.4:c.1417dup	p.Arg473LysfsTer4	p.R473Kfs*4	ENST00000281708	NM_033632.3	473	aga/aAga	9/12	1	2	FACETS	0.724	0.61	0.85	0.724	0.61	0.85	SUBCLONAL	1	TRUE	1	0.431758418385722	2		286	275	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440904	56440904	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1458799446	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	260	632	1	ENST00000407977.2:c.433C>T	p.Arg145Ter	p.R145*	ENST00000407977		145	Cga/Tga	4/10	0.431758418385722	2	FACETS	1	0.983	1	1	0.995	1	CLONAL	3	TRUE	0	0.431758418385722	2		633	382	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	50	405	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.726	0.619	0.842	0.726	0.619	0.842	SUBCLONAL	1	TRUE	1	0.431758418385722	2		405	319	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241722	55241722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1051753269	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	138	343	1	ENST00000275493.2:c.2170G>A	p.Gly724Ser	p.G724S	ENST00000275493	NM_005228.3	724	Ggc/Agc	18/28	0.42163423565839	3	FACETS	0.964	0.887	1	0.964	0.887	1	CLONAL	2	TRUE	1	0.431758418385722	3		344	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138729528	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	17	424	0	ENST00000269305.4:c.523C>T	p.Arg175Cys	p.R175C	ENST00000269305	NM_001126112.2	175	Cgc/Tgc	5/11	1	2	FACETS	0.207	0.154	0.271	0.207	0.154	0.271	SUBCLONAL	1	TRUE	1	0.431758418385722	2		424	380	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392039	81392039	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757576097	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	110	258	0	ENST00000222390.5:c.238C>T	p.Leu80Phe	p.L80F	ENST00000222390	NM_000601.4	80	Ctt/Ttt	2/18	0.42163423565839	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.431758418385722	3		258	280	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220339	98220339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772406487	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	63	220	0	ENST00000331920.6:c.3124G>A	p.Val1042Met	p.V1042M	ENST00000331920	NM_000264.3	1042	Gtg/Atg	18/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.431758418385722	2		220	216	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926248	112926248	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs121918468	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	121	346	1	ENST00000351677.2:c.1381G>A	p.Ala461Thr	p.A461T	ENST00000351677	NM_002834.3	461	Gct/Act	12/16	0.267814218110326	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.431758418385722	1		347	415	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485115	57485115	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754097818	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	60	233	0	ENST00000371085.3:c.949C>T	p.Arg317Cys	p.R317C	ENST00000371085	NM_000516.4	317	Cgc/Tgc	11/13	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.431758418385722	2		233	242	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224163	98224163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138154222	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	81	235	1	ENST00000331920.6:c.2678G>A	p.Arg893His	p.R893H	ENST00000331920	NM_000264.3	893	cGc/cAc	16/24	1	2	FACETS	0.816	0.731	0.903	1	0.982	1	CLONAL	2	TRUE	1	0.431758418385722	2		236	230	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007901	45007901	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	62	236	0	ENST00000558401.1:c.346+2T>C		p.X116_splice	ENST00000558401	NM_004048.2	116			1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.431758418385722	2		236	256	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097625	11097625	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	108	521	1	ENST00000358026.2:c.810del	p.Met272CysfsTer31	p.M272Cfs*31	ENST00000358026	NM_001128849.1	269	Ccc/cc	5/36	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.431758418385722	2		522	430	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662939	52662939	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	90	320	0	ENST00000394830.3:c.1414C>T	p.Arg472Ter	p.R472*	ENST00000394830	NM_018313.4	472	Cga/Tga	13/30	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.431758418385722	2		320	310	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37045935	37045935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750781	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	106	334	0	ENST00000231790.2:c.350C>T	p.Thr117Met	p.T117M	ENST00000231790	NM_000249.3	117	aCg/aTg	4/19	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.431758418385722	2		334	376	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464537	25464537	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752434188	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	94	420	1	ENST00000264709.3:c.1976G>A	p.Arg659His	p.R659H	ENST00000264709	NM_175629.2	659	cGc/cAc	17/23	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.431758418385722	2		421	393	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118924	70118926	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	141	453	0	ENST00000245479.2:c.499_501del	p.Lys167del	p.K167del	ENST00000245479	NM_000346.3	166	AAG/-	2/3	0.431758418385722	2	FACETS	0.798	0.735	0.864	0.798	0.735	0.864	SUBCLONAL	2	TRUE	0	0.431758418385722	2		453	409	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120460319	120460319	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1446995271	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	120	398	0	ENST00000256646.2:c.5996del	p.Asn1999MetfsTer32	p.N1999Mfs*32	ENST00000256646	NM_024408.3	1999	aAt/at	33/34	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.431758418385722	2		398	417	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288503	15288503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	26	139	0	ENST00000263388.2:c.4236G>A	p.Trp1412Ter	p.W1412*	ENST00000263388	NM_000435.2	1412	tgG/tgA	24/33	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.431758418385722	2		139	92	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521385	187521385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426195084	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	80	337	2	ENST00000441802.2:c.11770C>T	p.Arg3924Cys	p.R3924C	ENST00000441802	NM_005245.3	3924	Cgc/Tgc	22/27	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.431758418385722	2		339	280	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105715	27105717	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs765246223	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	45	389	0	ENST00000324856.7:c.5334_5336del	p.Glu1780del	p.E1780del	ENST00000324856	NM_006015.4	1776	GAA/-	20/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.431758418385722	2		389	166	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974782	21974782	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs138677674	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	34	117	0	ENST00000304494.5:c.45G>A	p.Trp15Ter	p.W15*	ENST00000304494	NM_000077.4	15	tgG/tgA	1/3	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.431758418385722	2		117	118	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123616	108123616	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	71	281	0	ENST00000278616.4:c.1880del	p.Phe627SerfsTer22	p.F627Sfs*22	ENST00000278616	NM_000051.3	625	aaT/aa	12/63	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.431758418385722	2		281	278	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263192	115263192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	138	395	0	ENST00000438362.2:c.2158C>T	p.Arg720Cys	p.R720C	ENST00000438362	NM_001242891.1	720	Cgc/Tgc	17/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.431758418385722	2		395	458	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266046	41266046	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	31	163	0	ENST00000349496.5:c.43G>A	p.Glu15Lys	p.E15K	ENST00000349496	NM_001904.3	15	Gaa/Aaa	3/15	1	2	FACETS	0.798	0.652	0.959	0.798	0.652	0.959	CLONAL	1	TRUE	1	0.431758418385722	2		163	180	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361098	70361103	+	inframe_deletion	In_Frame_Del	DEL	CAGCAG	CAGCAG	-	rs766775649	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	26	144	0	ENST00000374080.3:c.6303_6308del	p.Gln2114_Gln2115del	p.Q2114_Q2115del	ENST00000374080		2096	CAGCAG/-	43/45	1	1	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	0	0.431758418385722	1		144	84	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753452	42753452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	111	476	0	ENST00000222329.4:c.812C>T	p.Thr271Met	p.T271M	ENST00000222329	NM_006494.2	271	aCg/aTg	4/4	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.431758418385722	2		476	373	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031690	69031690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371787029	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	80	332	0	ENST00000288368.4:c.3445C>T	p.Arg1149Cys	p.R1149C	ENST00000288368	NM_024870.2	1149	Cgc/Tgc	28/40	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.431758418385722	2		332	305	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058342	42058342	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201470885	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	59	195	0	ENST00000219905.7:c.8062G>A	p.Val2688Ile	p.V2688I	ENST00000219905	NM_001164273.1	2688	Gtc/Atc	24/24	1	2	FACETS	0.776	0.681	0.876	1	0.974	1	SUBCLONAL	2	TRUE	1	0.431758418385722	2		195	176	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434958	49434959	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1555192751	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	48	305	0	ENST00000301067.7:c.6594dup	p.Tyr2199LeufsTer3	p.Y2199Lfs*3	ENST00000301067	NM_003482.3	2198	-/C	31/54	0.152662764983692	4	FACETS	0.808	0.692	0.932	0.808	0.692	0.932	INDETERMINATE	2	TRUE	2	0.431758418385722	4		305	197	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023743	27023744	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	58	212	0	ENST00000324856.7:c.854dup	p.Thr286AsnfsTer114	p.T286Nfs*114	ENST00000324856	NM_006015.4	283	-/G	1/20	1	2	FACETS	0.988	0.856	1	0.988	0.856	1	CLONAL	1	TRUE	1	0.431758418385722	2		212	272	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096155	71096155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1450448594	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	68	198	1	ENST00000318789.4:c.602G>A	p.Arg201His	p.R201H	ENST00000318789	NM_032682.5	201	cGc/cAc	10/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.431758418385722	2		199	216	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406432	70406432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779743688	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	124	474	2	ENST00000373644.4:c.3946G>A	p.Asp1316Asn	p.D1316N	ENST00000373644	NM_030625.2	1316	Gat/Aat	4/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.431758418385722	2		476	431	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562118	21562118	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	238	672	1	ENST00000382592.4:c.1801G>A	p.Ala601Thr	p.A601T	ENST00000382592	NM_014572.2	601	Gcc/Acc	4/8	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.431758418385722	2		673	780	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944606	32944606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	118	431	0	ENST00000380152.3:c.8399C>T	p.Pro2800Leu	p.P2800L	ENST00000380152		2800	cCt/cTt	19/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.431758418385722	2		431	434	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789607	3789607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369991761	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	88	262	0	ENST00000262367.5:c.4252G>A	p.Gly1418Ser	p.G1418S	ENST00000262367	NM_004380.2	1418	Ggc/Agc	25/31	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.431758418385722	2		262	312	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993516	72993516	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772845316	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	111	401	0	ENST00000268489.5:c.529G>A	p.Ala177Thr	p.A177T	ENST00000268489	NM_006885.3	177	Gcg/Acg	2/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.431758418385722	2		401	383	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533887	63533887	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	161	261	0	ENST00000307078.5:c.1267del	p.Leu423SerfsTer35	p.L423Sfs*35	ENST00000307078	NM_004655.3	423	Ctc/tc	6/11	0.431758418385722	2	FACETS	1	0.95	1	1	0.992	1	CLONAL	3	TRUE	0	0.431758418385722	2		261	247	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144134	11144134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs75911614	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	70	380	0	ENST00000358026.2:c.3715T>C	p.Ser1239Pro	p.S1239P	ENST00000358026	NM_001128849.1	1239	Tcc/Ccc	26/36	1	2	FACETS	0.943	0.827	1	0.943	0.827	1	CLONAL	1	TRUE	1	0.431758418385722	2		380	344	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945723	17945723	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199774111	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	118	472	1	ENST00000458235.1:c.2137G>A	p.Ala713Thr	p.A713T	ENST00000458235	NM_000215.3	713	Gcc/Acc	16/24	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.431758418385722	2		473	401	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214058	36214058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1385766471	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	160	789	0	ENST00000222270.7:c.2884C>T	p.Arg962Cys	p.R962C	ENST00000222270	NM_014727.1	962	Cgc/Tgc	6/37	1	2	FACETS	0.814	0.754	0.877	1	0.991	1	CLONAL	2	TRUE	1	0.431758418385722	2		789	455	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967317	25967317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767307523	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	63	240	0	ENST00000435504.4:c.1889C>T	p.Pro630Leu	p.P630L	ENST00000435504		630	cCg/cTg	13/13	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.431758418385722	2		240	231	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262596	39262596	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs766965165	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	98	305	1	ENST00000402219.2:c.910C>T	p.Arg304Ter	p.R304*	ENST00000402219	NM_005633.3	304	Cga/Tga	7/23	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.431758418385722	2		306	314	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719490	61719490	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	40	365	0	ENST00000401558.2:c.1693G>A	p.Val565Ile	p.V565I	ENST00000401558	NM_003400.3	565	Gta/Ata	15/25	1	2	FACETS	0.626	0.522	0.74	0.626	0.522	0.74	SUBCLONAL	1	TRUE	1	0.431758418385722	2		365	296	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149819	202149819	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	88	428	0	ENST00000358485.4:c.1264del	p.Asp422IlefsTer19	p.D422Ifs*19	ENST00000358485	NM_001080125.1	420	caG/ca	8/9	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.431758418385722	2		428	336	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248579	212248579	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	148	384	0	ENST00000342788.4:c.3688C>T	p.Pro1230Ser	p.P1230S	ENST00000342788	NM_005235.2	1230	Cca/Tca	28/28	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.431758418385722	2		384	498	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024754	31024755	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	80	386	0	ENST00000375687.4:c.4243dup	p.Arg1415ProfsTer9	p.R1415Pfs*9	ENST00000375687	NM_015338.5	1413	-/C	13/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.431758418385722	2		386	257	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582342	119582342	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	114	244	1	ENST00000316626.5:c.1059del	p.Phe353LeufsTer?	p.F353Lfs*?	ENST00000316626		353	ttT/tt	10/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.431758418385722	2		245	412	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031963	26031963	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	51	268	1	ENST00000244661.2:c.326A>G	p.Asn109Ser	p.N109S	ENST00000244661	NM_003537.3	109	aAc/aGc	1/1	1	2	FACETS	0.949	0.814	1	0.949	0.814	1	CLONAL	1	TRUE	1	0.431758418385722	2		269	249	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056050	26056050	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764601216	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	67	240	0	ENST00000343677.2:c.607G>A	p.Val203Ile	p.V203I	ENST00000343677	NM_005319.3	203	Gtc/Atc	1/1	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.431758418385722	2		240	284	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55272966	55272966	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775345513	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	96	334	0	ENST00000275493.2:c.3289G>A	p.Val1097Ile	p.V1097I	ENST00000275493	NM_005228.3	1097	Gtt/Att	28/28	0.42163423565839	3	FACETS	1	0.98	1	0.702	0.63	0.777	CLONAL	1	TRUE	1	0.431758418385722	3		334	385	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613633	100613633	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	21	200	1	ENST00000308731.7:c.946A>G	p.Thr316Ala	p.T316A	ENST00000308731	NM_000061.2	316	Aca/Gca	11/19	1	1	FACETS	0.345	0.266	0.436	0.345	0.266	0.436	SUBCLONAL	1	TRUE	0	0.431758418385722	1		201	221	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397742	49397742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552757	NA	P-0036203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	214	467	1	ENST00000418115.1:c.482C>T	p.Ala161Val	p.A161V	ENST00000418115	NM_001664.2	161	gCa/gTa	5/5	0.296870423727967	3	FACETS	0.885	0.823	0.949	0.885	0.823	0.949	CLONAL	2	TRUE	1	0.29	3		468	955	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549706	187549706	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	97	330	0	ENST00000441802.2:c.4535G>T	p.Gly1512Val	p.G1512V	ENST00000441802	NM_005245.3	1512	gGc/gTc	8/27	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.29	2		330	620	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932717	39932717	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	134	459	0	ENST00000378444.4:c.1882G>C	p.Ala628Pro	p.A628P	ENST00000378444	NM_001123385.1	628	Gca/Cca	4/15	0.0189664709224937	2	FACETS	0.93	0.85	1			1	INDETERMINATE	2	TRUE	NA	0.29	2		459	497	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250047	53250047	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	80	274	0	ENST00000375401.3:c.202C>T	p.Arg68Ter	p.R68*	ENST00000375401	NM_004187.3	68	Cga/Tga	2/26	0.203481946601718	2	FACETS	1	0.959	1			1	CLONAL	1	TRUE	NA	0.29	2		274	461	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0036203-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	115	686	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.299457393483651	2	FACETS	1	0.951	1	0.543	0.49	0.599	CLONAL	1	TRUE	0	0.32	2		686	662	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397742	49397742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552757	NA	P-0036203-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	237	467	1	ENST00000418115.1:c.482C>T	p.Ala161Val	p.A161V	ENST00000418115	NM_001664.2	161	gCa/gTa	5/5	0.30161539214578	3	FACETS	0.928	0.867	0.99	0.928	0.867	0.99	CLONAL	2	TRUE	1	0.32	3		468	926	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549706	187549706	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036203-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	71	330	0	ENST00000441802.2:c.4535G>T	p.Gly1512Val	p.G1512V	ENST00000441802	NM_005245.3	1512	gGc/gTc	8/27	1	2	FACETS	0.898	0.786	1	0.898	0.786	1	CLONAL	1	TRUE	1	0.32	2		330	494	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932717	39932717	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036203-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	147	459	0	ENST00000378444.4:c.1882G>C	p.Ala628Pro	p.A628P	ENST00000378444	NM_001123385.1	628	Gca/Cca	4/15	0.30161539214578	2	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.32	2		459	646	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250047	53250047	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036203-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	110	274	0	ENST00000375401.3:c.202C>T	p.Arg68Ter	p.R68*	ENST00000375401	NM_004187.3	68	Cga/Tga	2/26	0.30161539214578	2	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.32	2		274	529	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357643	70357643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036203-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	116	460	0	ENST00000374080.3:c.5894C>T	p.Pro1965Leu	p.P1965L	ENST00000374080		1965	cCc/cTc	41/45	0.30161539214578	2	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.32	2		460	581	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033352	48033352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750949	NA	P-0036203-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	49	299	0	ENST00000234420.5:c.3656C>T	p.Thr1219Ile	p.T1219I	ENST00000234420	NM_000179.2	1219	aCt/aTt	8/10	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.32	2		299	264	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650842	93650842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036203-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	115	344	0	ENST00000375746.1:c.1768C>T	p.Arg590Trp	p.R590W	ENST00000375746	NM_001174167.1	590	Cgg/Tgg	13/14	0.275760717250091	3	FACETS	0.935	0.848	1	0.623	0.565	0.684	CLONAL	2	TRUE	0	0.32	3		344	446	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524995	187524995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1484600496	NA	P-0036203-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	69	490	0	ENST00000441802.2:c.10685G>A	p.Gly3562Asp	p.G3562D	ENST00000441802	NM_005245.3	3562	gGc/gAc	19/27	1	2	FACETS	0.769	0.67	0.875	0.769	0.67	0.875	SUBCLONAL	1	TRUE	1	0.32	2		490	561	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247533	123247533	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036203-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	59	391	0	ENST00000358487.5:c.1958A>G	p.Asn653Ser	p.N653S	ENST00000358487	NM_000141.4	653	aAt/aGt	14/18	0.270398519833237	3	FACETS	0.741	0.638	0.854	0.371	0.319	0.427	SUBCLONAL	1	TRUE	1	0.32	3		391	577	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741859	17741859	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036203-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	24	135	0	ENST00000250003.3:c.530C>T	p.Ala177Val	p.A177V	ENST00000250003	NM_002478.4	177	gCc/gTc	1/3	0.30161539214578	3	FACETS	0.972	0.768	1	0.486	0.384	0.602	CLONAL	1	TRUE	1	0.32	3		135	179	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374229	118374229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036203-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	45	320	1	ENST00000534358.1:c.7622C>T	p.Ala2541Val	p.A2541V	ENST00000534358	NM_005933.3	2541	gCc/gTc	27/36	0.299457393483651	2	FACETS	0.783	0.66	0.918	0.392	0.33	0.459	CLONAL	1	TRUE	0	0.32	2		321	359	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58700995	58700995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036203-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	106	500	0	ENST00000305921.3:c.586G>A	p.Val196Ile	p.V196I	ENST00000305921	NM_003620.3	196	Gtt/Att	2/6	0.277110566985892	3	FACETS	0.92	0.825	1	0.46	0.412	0.511	CLONAL	1	TRUE	1	0.32	3		500	835	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033714	48033714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036203-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	46	309	0	ENST00000234420.5:c.3925C>T	p.Pro1309Ser	p.P1309S	ENST00000234420	NM_000179.2	1309	Cca/Tca	9/10	1	2	FACETS	0.985	0.834	1	0.985	0.834	1	CLONAL	1	TRUE	1	0.32	2		309	292	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630665	158630665	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036203-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	15	227	2	ENST00000263640.3:c.578G>A	p.Gly193Asp	p.G193D	ENST00000263640	NM_001105.4	193	gGc/gAc	6/11	1	2	FACETS	0.32	0.233	0.424	0.32	0.233	0.424	SUBCLONAL	1	TRUE	1	0.32	2		229	293	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182680	38182680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036203-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	82	437	0	ENST00000396334.3:c.833C>T	p.Pro278Leu	p.P278L	ENST00000396334	NM_002468.4	278	cCc/cTc	5/5	0.30161539214578	3	FACETS	0.776	0.684	0.875	0.388	0.342	0.438	SUBCLONAL	1	TRUE	1	0.32	3		437	766	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503727	186503727	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036203-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	85	314	0	ENST00000323963.5:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000323963		135	tGc/tAc	5/11	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.32	2		314	502	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803094	32803094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036203-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	124	478	1	ENST00000374899.4:c.782G>A	p.Ser261Asn	p.S261N	ENST00000374899	NM_018833.2	261	aGt/aAt	5/12	0.30161539214578	2	FACETS	1	0.973	1	0.598	0.542	0.657	CLONAL	1	TRUE	0	0.32	2		479	648	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739917	41739917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036203-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	60	397	0	ENST00000242208.4:c.56G>A	p.Arg19Lys	p.R19K	ENST00000242208	NM_002192.2	19	aGg/aAg	2/3	0.231638244631012	5	FACETS	0.789	0.679	0.91	0.263	0.226	0.304	CLONAL	1	TRUE	2	0.32	5		397	703	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344916	70344916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036203-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	38	319	0	ENST00000374080.3:c.2146G>A	p.Glu716Lys	p.E716K	ENST00000374080		716	Gag/Aag	15/45	0.30161539214578	2	FACETS	0.514	0.425	0.614			1	SUBCLONAL	1	TRUE	NA	0.32	2		319	462	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0036230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	215	434	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.385799646641495	1	FACETS	0.7	0.653	0.747	0.7	0.653	0.747	SUBCLONAL	1	TRUE	0	0.628880446193494	1		434	670	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	281	132	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.912	0.869	0.954	1	0.996	1	CLONAL	2	TRUE	1	0.628880446193494	2		132	490	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0036230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	285	551	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.628880446193494	2	FACETS	0.964	0.921	1	0.964	0.921	1	CLONAL	2	TRUE	0	0.628880446193494	2		551	470	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0036230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	176	701	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.998	0.925	1	0.998	0.925	1	CLONAL	1	TRUE	1	0.628880446193494	2		701	561	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	90	197	0	ENST00000256196.4:c.68G>T	p.Gly23Val	p.G23V	ENST00000256196		23	gGc/gTc	1/6	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.628880446193494	2		197	234	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023769	27023769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	121	292	2	ENST00000324856.7:c.879del	p.Thr294ProfsTer69	p.T294Pfs*69	ENST00000324856	NM_006015.4	292	aCc/ac	1/20	1	2	FACETS	0.905	0.825	0.989	0.905	0.825	0.989	CLONAL	1	TRUE	1	0.628880446193494	2		294	425	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0036230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	129	534	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.230243156790817	0	FACETS	0.321	0.292	0.35			1	INDETERMINATE	1	TRUE	0	0.628880446193494	0		534	475	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	165	503	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.988	0.914	1	0.988	0.914	1	CLONAL	1	TRUE	1	0.628880446193494	2		503	531	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353819	15353819	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	109	410	2	ENST00000263377.2:c.3061del	p.His1021IlefsTer47	p.H1021Ifs*47	ENST00000263377	NM_058243.2	1021	Cat/at	14/20	1	2	FACETS	0.719	0.649	0.793	0.719	0.649	0.793	SUBCLONAL	1	TRUE	1	0.628880446193494	2		412	482	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0036230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	146	443	2	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.918	0.843	0.995	0.918	0.843	0.995	CLONAL	1	TRUE	1	0.628880446193494	2		445	506	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023860	27023861	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0036230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	69	128	0	ENST00000324856.7:c.971dup	p.Ala325ArgfsTer75	p.A325Rfs*75	ENST00000324856	NM_006015.4	322	-/G	1/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.628880446193494	2		128	183	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612735	228612735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	249	640	1	ENST00000366696.1:c.292G>A	p.Glu98Lys	p.E98K	ENST00000366696	NM_003493.2	98	Gag/Aag	1/1	0.628880446193494	3	FACETS	1	0.976	1	0.542	0.507	0.577	CLONAL	1	TRUE	1	0.628880446193494	3		641	961	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442811	442811	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	139	392	2	ENST00000399788.2:c.1495del	p.Glu499SerfsTer19	p.E499Sfs*19	ENST00000399788	NM_001042603.1	499	Gag/ag	12/28	1	2	FACETS	0.969	0.89	1	0.969	0.89	1	CLONAL	1	TRUE	1	0.628880446193494	2		394	456	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853195	68853195	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886039590	NA	P-0036230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	214	479	0	ENST00000261769.5:c.1578G>A	p.Trp526Ter	p.W526*	ENST00000261769	NM_004360.3	526	tgG/tgA	11/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.628880446193494	2		479	655	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508253	106508253	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	115	338	1	ENST00000359195.3:c.247G>A	p.Val83Met	p.V83M	ENST00000359195	NM_002649.2	83	Gtg/Atg	2/11	1	2	FACETS	0.883	0.802	0.968	0.883	0.802	0.968	CLONAL	1	TRUE	1	0.628880446193494	2		339	414	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864218	57864218	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	209	572	4	ENST00000228682.2:c.1700del	p.Pro567LeufsTer46	p.P567Lfs*46	ENST00000228682	NM_005269.2	565	ttC/tt	12/12	1	2	FACETS	0.982	0.916	1	0.982	0.916	1	CLONAL	1	TRUE	1	0.628880446193494	2		576	677	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99812464	99812465	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	98	350	0	ENST00000280892.6:c.204dup	p.Lys69Ter	p.K69*	ENST00000280892	NM_001130678.1	68	-/T	3/7	1	2	FACETS	0.947	0.854	1	0.947	0.854	1	CLONAL	1	TRUE	1	0.628880446193494	2		350	329	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812279	43812279	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	233	565	0	ENST00000372470.3:c.1144C>A	p.Pro382Thr	p.P382T	ENST00000372470	NM_005373.2	382	Cct/Act	7/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.628880446193494	2		565	707	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944483	71944483	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0036230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	208	602	0	ENST00000298229.2:c.2041-2A>G		p.X681_splice	ENST00000298229	NM_001567.3	681			1	2	FACETS	0.998	0.931	1	0.998	0.931	1	CLONAL	1	TRUE	1	0.628880446193494	2		602	663	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944752	71944752	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	279	706	0	ENST00000298229.2:c.2176G>T	p.Glu726Ter	p.E726*	ENST00000298229	NM_001567.3	726	Gag/Tag	19/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.628880446193494	2		706	796	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392695	118392695	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	221	542	0	ENST00000534358.1:c.11727T>A	p.Asn3909Lys	p.N3909K	ENST00000534358	NM_005933.3	3909	aaT/aaA	36/36	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.628880446193494	2		542	641	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727463	66727463	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	179	486	0	ENST00000307102.5:c.179T>C	p.Val60Ala	p.V60A	ENST00000307102	NM_002755.3	60	gTg/gCg	2/11	1	2	FACETS	0.955	0.885	1	0.955	0.885	1	CLONAL	1	TRUE	1	0.628880446193494	2		486	596	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630743	90630743	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1418478547	NA	P-0036230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	246	600	0	ENST00000330062.3:c.743T>C	p.Met248Thr	p.M248T	ENST00000330062	NM_002168.2	248	aTg/aCg	6/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.628880446193494	2		600	733	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828912	72828913	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0036230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	233	659	0	ENST00000268489.5:c.7668_7669del	p.Gln2557GlufsTer21	p.Q2557Efs*21	ENST00000268489	NM_006885.3	2556	gcGCag/gcag	9/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.628880446193494	2		659	662	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946238	81946238	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	212	579	1	ENST00000359376.3:c.1971G>T	p.Glu657Asp	p.E657D	ENST00000359376	NM_002661.3	657	gaG/gaT	19/33	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.628880446193494	2		580	633	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357183	89357183	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	199	669	0	ENST00000301030.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000301030	NM_001256183.1	151	Ccc/Tcc	6/13	1	2	FACETS	0.732	0.678	0.787	0.732	0.678	0.787	SUBCLONAL	1	TRUE	1	0.628880446193494	2		669	865	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935795	15935795	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	136	409	0	ENST00000268712.3:c.7138T>C	p.Ser2380Pro	p.S2380P	ENST00000268712	NM_006311.3	2380	Tca/Cca	46/46	1	2	FACETS	0.957	0.877	1	0.957	0.877	1	CLONAL	1	TRUE	1	0.628880446193494	2		409	452	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553459	29553459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	182	433	0	ENST00000356175.3:c.2008G>A	p.Ala670Thr	p.A670T	ENST00000356175	NM_000267.3	670	Gca/Aca	18/57	1	2	FACETS	0.934	0.866	1	0.934	0.866	1	CLONAL	1	TRUE	1	0.628880446193494	2		433	620	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276833	15276833	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	241	674	0	ENST00000263388.2:c.5432A>T	p.Asp1811Val	p.D1811V	ENST00000263388	NM_000435.2	1811	gAt/gTt	30/33	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.628880446193494	2		674	719	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051596	30051596	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	186	408	0	ENST00000338641.4:c.530A>G	p.Tyr177Cys	p.Y177C	ENST00000338641	NM_000268.3	177	tAt/tGt	6/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.628880446193494	2		408	551	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659171	86659171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	14	226	0	ENST00000274376.6:c.1460G>A	p.Gly487Glu	p.G487E	ENST00000274376	NM_002890.2	487	gGa/gAa	11/25	0.220815038502938	1	FACETS	0.129	0.093	0.173	0.129	0.093	0.173	INDETERMINATE	1	TRUE	0	0.684246745476899	1		226	208	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458639	120458640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036433-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	110	429	0	ENST00000256646.2:c.6705dup	p.Gly2236TrpfsTer8	p.G2236Wfs*8	ENST00000256646	NM_024408.3	2235	-/T	34/34	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.395005480584331	2		429	535	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862174	68862174	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036433-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	112	398	0	ENST00000261769.5:c.2262C>A	p.Tyr754Ter	p.Y754*	ENST00000261769	NM_004360.3	754	taC/taA	14/16	0.395005480584331	1	FACETS	0.892	0.806	0.983	0.892	0.806	0.983	CLONAL	1	TRUE	0	0.395005480584331	1		398	510	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0036570-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	35	365	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.158503246913313	3	FACETS	1	0.896	1	0.566	0.466	0.677	CLONAL	1	TRUE	1	0.250257681348233	3		365	278	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577529	7577529	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs730882027	NA	P-0036570-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	73	673	0	ENST00000269305.4:c.752T>A	p.Ile251Asn	p.I251N	ENST00000269305	NM_001126112.2	251	aTc/aAc	7/11	0.250257681348233	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.250257681348233	1		673	466	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304162	65304162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367582687	NA	P-0036570-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	29	559	0	ENST00000342505.4:c.2953G>A	p.Val985Ile	p.V985I	ENST00000342505	NM_002227.2	985	Gtt/Att	21/25	1	2	FACETS	0.68	0.546	0.831	0.68	0.546	0.831	SUBCLONAL	1	TRUE	1	0.250257681348233	2		559	341	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135626	64135626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1187689165	NA	P-0036570-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	90	784	0	ENST00000334205.4:c.1094C>T	p.Ser365Phe	p.S365F	ENST00000334205	NM_003942.2	365	tCc/tTc	10/17	0.158503246913313	3	FACETS	1	0.978	1	0.725	0.645	0.811	CLONAL	1	TRUE	1	0.250257681348233	3		784	558	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0036916-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	171	764	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.813	0.752	0.877	0.813	0.752	0.877	CLONAL	1	TRUE	1	0.68043637176233	2		764	618	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0036916-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	212	315	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.68043637176233	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.68043637176233	2		315	307	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0036916-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	234	383	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.223878857933308	1	FACETS	0.684	0.642	0.728	0.684	0.642	0.728	INDETERMINATE	1	TRUE	0	0.68043637176233	1		383	663	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604756	48604756	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036916-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	160	279	0	ENST00000342988.3:c.1578A>C	p.Glu526Asp	p.E526D	ENST00000342988	NM_005359.5	526	gaA/gaC	12/12	0.68043637176233	1	FACETS	0.83	0.771	0.889	0.83	0.771	0.889	CLONAL	1	TRUE	0	0.68043637176233	1		279	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0036916-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	273	391	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	0.596078713966733	1	FACETS	0.999	0.949	1	0.999	0.949	1	CLONAL	1	TRUE	0	0.68043637176233	1		391	530	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247224	153247224	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036916-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	160	235	0	ENST00000281708.4:c.1578G>T	p.Trp526Cys	p.W526C	ENST00000281708	NM_033632.3	526	tgG/tgT	10/12	0.39735175322856	1	FACETS	0.768	0.712	0.825	0.768	0.712	0.825	INDETERMINATE	1	TRUE	0	0.68043637176233	1		235	404	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718145	117718145	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036916-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	253	418	0	ENST00000368508.3:c.712A>C	p.Lys238Gln	p.K238Q	ENST00000368508	NM_002944.2	238	Aaa/Caa	7/43	1	2	FACETS	0.908	0.852	0.965	0.908	0.852	0.965	CLONAL	1	TRUE	1	0.68043637176233	2		418	819	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1959731	1959731	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1416347752	NA	P-0036933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	15	206	0	ENST00000382891.5:c.2953G>A	p.Glu985Lys	p.E985K	ENST00000382891	NM_133335.3	985	Gag/Aag	16/22	1	2	FACETS	0.562	0.411	0.743	0.562	0.411	0.743	SUBCLONAL	1	TRUE	1	0.205452638834071	2		206	260	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373112	118373112	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0036933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	18	171	0	ENST00000534358.1:c.6506-1G>A		p.X2169_splice	ENST00000534358	NM_005933.3	2169			0.205452638834071	2	FACETS	0.903	0.683	1	0.452	0.341	0.581	CLONAL	1	TRUE	0	0.205452638834071	2		171	194	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435164	56435164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	29	319	0	ENST00000407977.2:c.1973G>A	p.Gly658Glu	p.G658E	ENST00000407977		658	gGg/gAg	9/10	1	2	FACETS	0.763	0.613	0.934	0.763	0.613	0.934	CLONAL	1	TRUE	1	0.205452638834071	2		319	370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0037029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	387	564	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.360723327597923	3	FACETS	1	0.994	1	0.819	0.786	0.852	INDETERMINATE	2	TRUE	0	0.601810251432641	3		564	681	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204499930	204499930	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	131	539	0	ENST00000367182.3:c.272C>T	p.Ser91Phe	p.S91F	ENST00000367182	NM_001278516.1	91	tCc/tTc	4/11	0.534793901878331	4	FACETS	0.894	0.812	0.981	0.298	0.27	0.327	CLONAL	1	TRUE	1	0.601810251432641	4		539	780	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16235839	16235839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766201418	NA	P-0037029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	50	591	0	ENST00000375759.3:c.905G>A	p.Ser302Asn	p.S302N	ENST00000375759	NM_015001.2	302	aGt/aAt	4/15	1	2	FACETS	0.249	0.211	0.291	0.249	0.211	0.291	SUBCLONAL	1	TRUE	1	0.601810251432641	2		591	667	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109833	115109833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753103762	NA	P-0037029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	132	393	0	ENST00000257566.3:c.2045C>T	p.Ala682Val	p.A682V	ENST00000257566	NM_016569.3	682	gCc/gTc	8/8	0.540498933697336	3	FACETS	1	0.968	1	0.563	0.514	0.614	CLONAL	1	TRUE	1	0.601810251432641	3		393	507	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004232	29004232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763071731	NA	P-0037029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	151	448	1	ENST00000282397.4:c.1061G>A	p.Arg354Gln	p.R354Q	ENST00000282397	NM_002019.4	354	cGg/cAg	8/30	0.602024638818355	4	FACETS	0.862	0.788	0.94	0.287	0.262	0.314	CLONAL	1	TRUE	1	0.601810251432641	4		449	932	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	15	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.308	0.224	0.41	0.308	0.224	0.41	SUBCLONAL	1	TRUE	1	0.16	2		426	609	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439926	56439927	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0037093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	48	387	0	ENST00000407977.2:c.665dup	p.Cys222TrpfsTer37	p.C222Wfs*37	ENST00000407977		222	tgc/tgGc	6/10	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.16	2		387	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0037095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	148	722	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.346150532246126	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.346150532246126	1		722	666	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448564	89448564	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1184230536	NA	P-0037095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	67	578	0	ENST00000336596.2:c.1528C>T	p.Arg510Ter	p.R510*	ENST00000336596	NM_005233.5	510	Cga/Tga	7/17	1	2	FACETS	0.667	0.58	0.762	0.667	0.58	0.762	SUBCLONAL	1	TRUE	1	0.346150532246126	2		578	580	SUCCESS
APC	324	MSKCC	GRCh37	5	112174835	112174835	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0037095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	37	318	0	ENST00000257430.4:c.3544A>T	p.Lys1182Ter	p.K1182*	ENST00000257430	NM_000038.5	1182	Aaa/Taa	16/16	1	2	FACETS	0.701	0.58	0.835	0.701	0.58	0.835	SUBCLONAL	1	TRUE	1	0.346150532246126	2		318	305	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273146	115273146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	79	538	0	ENST00000438362.2:c.1312G>A	p.Glu438Lys	p.E438K	ENST00000438362	NM_001242891.1	438	Gag/Aag	11/20	0.292129849111738	2	FACETS	0.74	0.651	0.835	0.37	0.325	0.418	SUBCLONAL	1	TRUE	0	0.346150532246126	2		538	617	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578200	28578200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573326027	NA	P-0037095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	192	523	0	ENST00000241453.7:c.2971G>A	p.Glu991Lys	p.E991K	ENST00000241453	NM_004119.2	991	Gaa/Aaa	24/24	0.346150532246126	3	FACETS	0.897	0.833	0.964	0.897	0.833	0.964	CLONAL	2	TRUE	1	0.346150532246126	3		523	725	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	48	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.726	0.613	0.851	0.726	0.613	0.851	SUBCLONAL	1	TRUE	1	0.22	2		426	601	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440713	56440713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779337229	NA	P-0037098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	87	732	0	ENST00000407977.2:c.505G>A	p.Ala169Thr	p.A169T	ENST00000407977		169	Gct/Act	5/10	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.22	2		732	726	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38966777	38966780	+	frameshift_variant	Frame_Shift_Del	DEL	CTAA	CTAA	-	novel	NA	P-0037098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	18	272	0	ENST00000357387.3:c.1262_1265del	p.Val421GlufsTer6	p.V421Efs*6	ENST00000357387	NM_152756.3	421	gTTAGa/ga	15/38	1	2	FACETS	0.494	0.372	0.64	0.494	0.372	0.64	SUBCLONAL	1	TRUE	1	0.22	2		272	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579410	7579410	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567556123	NA	P-0037098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	68	773	0	ENST00000269305.4:c.277del	p.Leu93CysfsTer30	p.L93Cfs*30	ENST00000269305	NM_001126112.2	93	Ctg/tg	4/11	1	2	FACETS	0.766	0.665	0.876	0.766	0.665	0.876	SUBCLONAL	1	TRUE	1	0.22	2		773	807	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457309	67457309	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	64	745	0	ENST00000327367.4:c.283C>A	p.Pro95Thr	p.P95T	ENST00000327367	NM_005902.3	95	Cca/Aca	2/9	1	2	FACETS	0.693	0.599	0.796	0.693	0.599	0.796	SUBCLONAL	1	TRUE	1	0.22	2		745	839	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280081	66280081	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0037098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	38	433	0	ENST00000273854.3:c.1608T>A	p.Tyr536Ter	p.Y536*	ENST00000273854	NM_004439.5	536	taT/taA	7/18	1	2	FACETS	0.708	0.585	0.846	0.708	0.585	0.846	SUBCLONAL	1	TRUE	1	0.22	2		433	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0037100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	184	617	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.203987450352275	2	FACETS	1	0.989	1	0.724	0.668	0.781	CLONAL	1	TRUE	0	0.292916399644475	2		617	868	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800960	18800960	+	stop_lost	Nonstop_Mutation	SNP	T	T	A	novel	NA	P-0037100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	52	336	0	ENST00000266497.5:c.4336T>A	p.Ter1446ArgextTer4	p.*1446Rext*4	ENST00000266497		1446	Tga/Aga	31/31	0.292916399644475	3	FACETS	0.733	0.624	0.853	0.367	0.312	0.427	SUBCLONAL	1	TRUE	1	0.292916399644475	3		336	555	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678377	88678377	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	164	983	0	ENST00000360948.2:c.1159G>T	p.Ala387Ser	p.A387S	ENST00000360948	NM_001012338.2	387	Gcc/Tcc	9/19	0.240281662255199	3	FACETS	0.949	0.869	1	0.474	0.434	0.517	CLONAL	1	TRUE	1	0.292916399644475	3		983	1353	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259484	89259484	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	54	513	3	ENST00000336596.2:c.628G>T	p.Ala210Ser	p.A210S	ENST00000336596	NM_005233.5	210	Gct/Tct	3/17	1	2	FACETS	0.569	0.485	0.661	0.569	0.485	0.661	SUBCLONAL	1	TRUE	1	0.292916399644475	2		516	648	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750461	41750461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	67	547	0	ENST00000226382.2:c.167G>A	p.Gly56Asp	p.G56D	ENST00000226382	NM_003924.3	56	gGc/gAc	1/3	0.114113665948234	3	FACETS	1	0.882	1	0.507	0.441	0.578	INDETERMINATE	1	TRUE	1	0.292916399644475	3		547	517	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047216	180047216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	118	861	5	ENST00000261937.6:c.2499C>A	p.Tyr833Ter	p.Y833*	ENST00000261937	NM_182925.4	833	taC/taA	17/30	1	2	FACETS	0.934	0.842	1	0.934	0.842	1	CLONAL	1	TRUE	1	0.292916399644475	2		866	863	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0037104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	53	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.370073128412815	2		298	270	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957847	1957847	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200311175	NA	P-0037104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	114	641	0	ENST00000382891.5:c.2813C>T	p.Pro938Leu	p.P938L	ENST00000382891	NM_133335.3	938	cCg/cTg	15/22	1	2	FACETS	0.853	0.769	0.943	0.853	0.769	0.943	CLONAL	1	TRUE	1	0.370073128412815	2		641	722	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604700	48604700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	84	436	0	ENST00000342988.3:c.1522G>A	p.Gly508Ser	p.G508S	ENST00000342988	NM_005359.5	508	Ggc/Agc	12/12	0.370073128412815	1	FACETS	0.992	0.882	1	0.992	0.882	1	CLONAL	1	TRUE	0	0.370073128412815	1		436	373	SUCCESS
APC	324	MSKCC	GRCh37	5	112175170	112175191	+	frameshift_variant	Frame_Shift_Del	DEL	ACAGGAAGCAGATTCTGCTAAT	ACAGGAAGCAGATTCTGCTAAT	-	novel	NA	P-0037104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	34	253	0	ENST00000257430.4:c.3881_3902del	p.Gln1294ProfsTer4	p.Q1294Pfs*4	ENST00000257430	NM_000038.5	1293	acACAGGAAGCAGATTCTGCTAAT/ac	16/16	0.360828161051007	2	FACETS	0.772	0.645	0.908	0.772	0.645	0.908	CLONAL	2	TRUE	0	0.370073128412815	2		253	119	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858566	27858566	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	41	299	0	ENST00000359303.2:c.5C>G	p.Ala2Gly	p.A2G	ENST00000359303	NM_003535.2	2	gCc/gGc	1/1	1	2	FACETS	0.827	0.693	0.974	0.827	0.693	0.974	CLONAL	1	TRUE	1	0.370073128412815	2		299	268	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0037106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	311	434	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.62715666397715	2		434	786	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0037106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	171	171	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.62715666397715	2		171	437	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692896	89692896	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs398123322	NA	P-0037106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	168	456	0	ENST00000371953.3:c.380G>T	p.Gly127Val	p.G127V	ENST00000371953	NM_000314.4	127	gGa/gTa	5/9	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.62715666397715	2		456	402	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0037106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	136	494	2	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.62715666397715	2		496	394	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0037106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	266	501	0	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.62715666397715	2		501	594	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099035	27099035	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	251	500	0	ENST00000324856.7:c.3451del	p.Ser1151AlafsTer10	p.S1151Afs*10	ENST00000324856	NM_006015.4	1151	Agc/gc	13/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.62715666397715	2		500	656	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468434	120468434	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0037106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	269	535	0	ENST00000256646.2:c.4006-1G>T		p.X1336_splice	ENST00000256646	NM_024408.3	1336			1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.62715666397715	2		535	666	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711969	89711969	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	153	482	0	ENST00000371953.3:c.587A>C	p.His196Pro	p.H196P	ENST00000371953	NM_000314.4	196	cAc/cCc	6/9	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.62715666397715	2		482	448	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466036	69466038	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	novel	NA	P-0037106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	336	815	0	ENST00000227507.2:c.875_877del	p.Asp292del	p.D292del	ENST00000227507	NM_053056.2	292	GAC/-	5/5	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.62715666397715	2		815	865	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252751	133252751	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	264	535	1	ENST00000320574.5:c.949A>G	p.Ile317Val	p.I317V	ENST00000320574	NM_006231.2	317	Att/Gtt	10/49	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.62715666397715	2		536	648	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670670	67670670	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	275	467	0	ENST00000264010.4:c.1915C>T	p.Gln639Ter	p.Q639*	ENST00000264010	NM_006565.3	639	Cag/Tag	11/12	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.62715666397715	2		467	676	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481781	40481781	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	179	381	0	ENST00000264657.5:c.1123G>C	p.Val375Leu	p.V375L	ENST00000264657	NM_139276.2	375	Gtt/Ctt	12/24	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.62715666397715	2		381	483	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	592	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.584499219377511	3	FACETS	0.98	0.952	1			1	CLONAL	3	TRUE	NA	0.584499219377511	3		426	890	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0037111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	41	235	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	1	2	FACETS	0.653	0.549	0.765	0.653	0.549	0.765	SUBCLONAL	1	TRUE	1	0.584499219377511	2		235	215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0037111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	520	694	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.515653626283441	3	FACETS	0.836	0.807	0.865	0.836	0.807	0.865	CLONAL	3	TRUE	0	0.584499219377511	3		694	917	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593469	48593470	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTTTG	novel	NA	P-0037111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	191	393	0	ENST00000342988.3:c.1221_1225dup	p.Val409AlafsTer8	p.V409Afs*8	ENST00000342988	NM_005359.5	407	gtc/gtCTTTGc	10/12	0.431852636336165	2	FACETS	1	0.991	1	0.715	0.668	0.762	CLONAL	1	TRUE	0	0.584499219377511	2		393	457	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267350	41267350	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	113	205	0	ENST00000349496.5:c.934A>C	p.Lys312Gln	p.K312Q	ENST00000349496	NM_001904.3	312	Aag/Cag	6/15	0.455978481960556	2	FACETS	0.809	0.744	0.875	0.809	0.744	0.875	CLONAL	2	TRUE	0	0.584499219377511	2		205	239	SUCCESS
APC	324	MSKCC	GRCh37	5	112162803	112162803	+	splice_acceptor_variant	Splice_Site	DEL	A	A	-	novel	NA	P-0037111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	51	318	0	ENST00000257430.4:c.1409-2del		p.X470_splice	ENST00000257430	NM_000038.5	470			1	2	FACETS	0.669	0.573	0.772	0.669	0.573	0.772	SUBCLONAL	1	TRUE	1	0.584499219377511	2		318	261	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437606	56437606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886926322	NA	P-0037123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	168	414	0	ENST00000407977.2:c.856C>T	p.Arg286Trp	p.R286W	ENST00000407977		286	Cgg/Tgg	8/10	0.455507419341212	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.455507419341212	1		414	488	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473719	67473719	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	290	606	0	ENST00000327367.4:c.799G>T	p.Glu267Ter	p.E267*	ENST00000327367	NM_005902.3	267	Gag/Tag	6/9	0.455507419341212	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.455507419341212	1		606	725	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578289	7578289	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	228	619	0	ENST00000269305.4:c.560del	p.Gly187ValfsTer60	p.G187Vfs*60	ENST00000269305	NM_001126112.2	187	gGt/gt	6/11	0.455507419341212	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.455507419341212	1		619	611	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205820	108205820	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	160	397	0	ENST00000278616.4:c.8135G>A	p.Arg2712Lys	p.R2712K	ENST00000278616	NM_000051.3	2712	aGg/aAg	55/63	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.455507419341212	2		397	582	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	309	414	2	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	0.215980229437189	3	FACETS	0.835	0.792	0.879	0.835	0.792	0.879	INDETERMINATE	2	TRUE	1	0.648270632425708	3		416	756	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	74	306	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.352151759825802	1	FACETS	0.266	0.232	0.301	0.266	0.232	0.301	INDETERMINATE	1	TRUE	0	0.648270632425708	1		306	581	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	236	665	2	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	1	2	FACETS	0.813	0.759	0.867	0.813	0.759	0.867	CLONAL	1	TRUE	1	0.648270632425708	2		667	896	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864218	57864218	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	151	572	4	ENST00000228682.2:c.1700del	p.Pro567LeufsTer46	p.P567Lfs*46	ENST00000228682	NM_005269.2	565	ttC/tt	12/12	0.352151759825802	1	FACETS	0.811	0.751	0.873	0.811	0.751	0.873	INDETERMINATE	1	TRUE	0	0.648270632425708	1		576	388	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935634	13935634	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	85	506	1	ENST00000405192.2:c.1222C>T	p.Arg408Cys	p.R408C	ENST00000405192	NM_001163147.1	408	Cgt/Tgt	12/12	1	2	FACETS	0.473	0.419	0.531	0.473	0.419	0.531	SUBCLONAL	1	TRUE	1	0.648270632425708	2		507	554	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25368390	25368390	+	intron_variant	Intron	DEL	T	T	-	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	51	462	0	ENST00000311936.3:c.451-5545del		p.*151*	ENST00000311936	NM_004985.3	185/189			0.648270632425708	1	FACETS	0.278	0.237	0.323	0.278	0.237	0.323	SUBCLONAL	1	TRUE	0	0.648270632425708	1		462	382	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646981	23646981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	97	893	2	ENST00000261584.4:c.886del	p.Met296Ter	p.M296*	ENST00000261584	NM_024675.3	296	Atg/tg	4/13	0.215980229437189	3	FACETS	0.372	0.33	0.416	0.186	0.165	0.208	INDETERMINATE	1	TRUE	1	0.648270632425708	3		895	1066	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526061	189526061	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	154	375	0	ENST00000264731.3:c.325C>T	p.Pro109Ser	p.P109S	ENST00000264731	NM_003722.4	109	Cca/Tca	4/14	0.215980229437189	3	FACETS	1	0.984	1	0.641	0.591	0.692	INDETERMINATE	1	TRUE	1	0.648270632425708	3		375	491	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120115	70120115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	16	147	0	ENST00000245479.2:c.1121del	p.Pro374ArgfsTer9	p.P374Rfs*9	ENST00000245479	NM_000346.3	373	Ccc/cc	3/3	0.313828699532283	1	FACETS	0.283	0.211	0.366	0.283	0.211	0.366	INDETERMINATE	1	TRUE	0	0.648270632425708	1		147	118	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512041	148512041	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	38	328	1	ENST00000320356.2:c.1637A>T	p.Asn546Ile	p.N546I	ENST00000320356	NM_004456.4	546	aAt/aTt	14/20	1	2	FACETS	0.239	0.197	0.286	0.239	0.197	0.286	SUBCLONAL	1	TRUE	1	0.648270632425708	2		329	490	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029511	16029511	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	205	500	0	ENST00000268712.3:c.1519C>T	p.Arg507Ter	p.R507*	ENST00000268712	NM_006311.3	507	Cga/Tga	15/46	0.313828699532283	1	FACETS	0.784	0.733	0.836	0.784	0.733	0.836	INDETERMINATE	1	TRUE	0	0.648270632425708	1		500	545	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521544	8521544	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	162	420	0	ENST00000356435.5:c.694C>T	p.Arg232Cys	p.R232C	ENST00000356435		232	Cgc/Tgc	9/35	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.648270632425708	2		420	461	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193602	99193602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1271977013	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	44	399	0	ENST00000074304.5:c.2797C>T	p.Arg933Cys	p.R933C	ENST00000074304	NM_001134224.1	933	Cgc/Tgc	25/26	1	2	FACETS	0.369	0.31	0.434	0.369	0.31	0.434	SUBCLONAL	1	TRUE	1	0.648270632425708	2		399	368	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492897	8492897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544419494	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	99	620	0	ENST00000356435.5:c.2432G>A	p.Arg811His	p.R811H	ENST00000356435		811	cGc/cAc	16/35	1	2	FACETS	0.341	0.304	0.381	0.341	0.304	0.381	SUBCLONAL	1	TRUE	1	0.648270632425708	2		620	895	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752695	42752695	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1366176199	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	154	722	5	ENST00000222329.4:c.1569del	p.Leu525SerfsTer6	p.L525Sfs*6	ENST00000222329	NM_006494.2	523	ggG/gg	4/4	0.425013973835232	1	FACETS	0.722	0.666	0.778	0.722	0.666	0.778	SUBCLONAL	1	TRUE	0	0.648270632425708	1		727	445	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444236	49444238	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	170	1002	1	ENST00000301067.7:c.3133_3135del	p.Pro1045del	p.P1045del	ENST00000301067	NM_003482.3	1045	CCT/-	11/54	0.352151759825802	1	FACETS	0.45	0.415	0.488	0.45	0.415	0.488	INDETERMINATE	1	TRUE	0	0.648270632425708	1		1003	787	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041262	29041262	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	36	523	0	ENST00000282397.4:c.166del	p.Glu56LysfsTer12	p.E56Kfs*12	ENST00000282397	NM_002019.4	56	Gaa/aa	3/30	0.21766722060647	3	FACETS	0.277	0.227	0.334	0.139	0.113	0.167	INDETERMINATE	1	TRUE	1	0.648270632425708	3		523	530	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494665	2494665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779181014	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	112	701	0	ENST00000355716.4:c.805G>A	p.Val269Met	p.V269M	ENST00000355716	NM_003820.2	269	Gtg/Atg	8/8	0.425013973835232	1	FACETS	0.475	0.429	0.523	0.475	0.429	0.523	SUBCLONAL	1	TRUE	0	0.648270632425708	1		701	492	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937983	36937983	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	122	904	0	ENST00000361632.4:c.853del	p.Leu285SerfsTer43	p.L285Sfs*43	ENST00000361632		285	Ctc/tc	7/16	0.425013973835232	1	FACETS	0.461	0.418	0.506	0.461	0.418	0.506	SUBCLONAL	1	TRUE	0	0.648270632425708	1		904	552	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910259	50910259	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1043752384	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	210	682	1	ENST00000440232.2:c.1514G>A	p.Arg505His	p.R505H	ENST00000440232	NM_002691.3	505	cGc/cAc	13/27	0.425013973835232	1	FACETS	0.839	0.786	0.892	0.839	0.786	0.892	CLONAL	1	TRUE	0	0.648270632425708	1		683	522	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164655	36164655	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	89	766	0	ENST00000300305.3:c.1220A>G	p.Tyr407Cys	p.Y407C	ENST00000300305		407	tAc/tGc	8/8	1	2	FACETS	0.436	0.387	0.488	0.436	0.387	0.488	SUBCLONAL	1	TRUE	1	0.648270632425708	2		766	630	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879229	151879229	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763438739	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	200	588	0	ENST00000262189.6:c.5716C>T	p.Arg1906Ter	p.R1906*	ENST00000262189	NM_170606.2	1906	Cga/Tga	36/59	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.648270632425708	2		588	539	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1956968	1956968	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143360610	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	89	651	3	ENST00000382891.5:c.2419G>A	p.Ala807Thr	p.A807T	ENST00000382891	NM_133335.3	807	Gcc/Acc	13/22	1	2	FACETS	0.387	0.343	0.434	0.387	0.343	0.434	SUBCLONAL	1	TRUE	1	0.648270632425708	2		654	709	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218452	5218452	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753143589	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	85	791	0	ENST00000357368.4:c.4027C>T	p.Arg1343Cys	p.R1343C	ENST00000357368	NM_002850.3	1343	Cgc/Tgc	25/38	0.425013973835232	1	FACETS	0.29	0.256	0.326	0.29	0.256	0.326	SUBCLONAL	1	TRUE	0	0.648270632425708	1		791	611	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004348	150004348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766836005	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	176	579	0	ENST00000253339.5:c.1877G>A	p.Arg626Gln	p.R626Q	ENST00000253339		626	cGa/cAa	3/7	1	2	FACETS	0.83	0.768	0.895	0.83	0.768	0.895	CLONAL	1	TRUE	1	0.648270632425708	2		579	654	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444617	187444617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs545063119	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	289	622	1	ENST00000232014.4:c.1610C>T	p.Thr537Met	p.T537M	ENST00000232014	NM_001130845.1	537	aCg/aTg	7/10	0.215980229437189	3	FACETS	0.841	0.796	0.886	0.841	0.796	0.886	INDETERMINATE	2	TRUE	1	0.648270632425708	3		623	702	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629493	187629493	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	202	753	0	ENST00000441802.2:c.1489T>C	p.Tyr497His	p.Y497H	ENST00000441802	NM_005245.3	497	Tac/Cac	2/27	1	2	FACETS	0.83	0.771	0.89	0.83	0.771	0.89	CLONAL	1	TRUE	1	0.648270632425708	2		753	751	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707981	43707981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	292	854	0	ENST00000382044.4:c.4900C>T	p.Arg1634Trp	p.R1634W	ENST00000382044	NM_001141980.1	1634	Cgg/Tgg	23/28	0.648270632425708	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.648270632425708	1		854	594	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023190	27023190	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	49	144	0	ENST00000324856.7:c.296A>G	p.Asp99Gly	p.D99G	ENST00000324856	NM_006015.4	99	gAc/gGc	1/20	0.425013973835232	1	FACETS	0.73	0.633	0.831	0.73	0.633	0.831	SUBCLONAL	1	TRUE	0	0.648270632425708	1		144	140	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228613004	228613004	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375918041	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	160	427	0	ENST00000366696.1:c.23C>T	p.Ala8Val	p.A8V	ENST00000366696	NM_003493.2	8	gCg/gTg	1/1	0.32796505195502	3	FACETS	1	0.983	1	0.615	0.568	0.665	INDETERMINATE	1	TRUE	1	0.648270632425708	3		427	531	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404659	70404659	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	67	567	0	ENST00000373644.4:c.2173G>T	p.Asp725Tyr	p.D725Y	ENST00000373644	NM_030625.2	725	Gat/Tat	4/12	0.425013973835232	1	FACETS	0.283	0.246	0.323	0.283	0.246	0.323	SUBCLONAL	1	TRUE	0	0.648270632425708	1		567	494	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137854	64137854	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs755881487	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	344	1069	1	ENST00000334205.4:c.1955G>A	p.Arg652Gln	p.R652Q	ENST00000334205	NM_003942.2	652	cGa/cAa	15/17	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.648270632425708	2		1070	984	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94163079	94163079	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	56	514	0	ENST00000323929.3:c.2068G>A	p.Glu690Lys	p.E690K	ENST00000323929	NM_005591.3	690	Gag/Aag	19/20	1	2	FACETS	0.296	0.253	0.343	0.296	0.253	0.343	SUBCLONAL	1	TRUE	1	0.648270632425708	2		514	584	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156155	119156155	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	39	620	0	ENST00000264033.4:c.1820A>T	p.Asp607Val	p.D607V	ENST00000264033	NM_005188.3	607	gAt/gTt	11/16	1	2	FACETS	0.169	0.139	0.202	0.169	0.139	0.202	SUBCLONAL	1	TRUE	1	0.648270632425708	2		620	713	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427986	49427986	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	73	772	0	ENST00000301067.7:c.10604A>G	p.His3535Arg	p.H3535R	ENST00000301067	NM_003482.3	3535	cAc/cGc	38/54	0.352151759825802	1	FACETS	0.235	0.205	0.267	0.235	0.205	0.267	INDETERMINATE	1	TRUE	0	0.648270632425708	1		772	647	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445668	49445668	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	117	1008	0	ENST00000301067.7:c.1798T>A	p.Phe600Ile	p.F600I	ENST00000301067	NM_003482.3	600	Ttc/Atc	10/54	0.352151759825802	1	FACETS	0.299	0.269	0.33	0.299	0.269	0.33	INDETERMINATE	1	TRUE	0	0.648270632425708	1		1008	816	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864151	57864151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	219	581	0	ENST00000228682.2:c.1628G>A	p.Ser543Asn	p.S543N	ENST00000228682	NM_005269.2	543	aGc/aAc	12/12	0.352151759825802	1	FACETS	0.938	0.882	0.994	0.938	0.882	0.994	INDETERMINATE	1	TRUE	0	0.648270632425708	1		581	487	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864787	57864787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	61	663	0	ENST00000228682.2:c.2264C>A	p.Pro755His	p.P755H	ENST00000228682	NM_005269.2	755	cCt/cAt	12/12	0.352151759825802	1	FACETS	0.274	0.236	0.314	0.274	0.236	0.314	INDETERMINATE	1	TRUE	0	0.648270632425708	1		663	465	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888304	112888304	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	145	494	0	ENST00000351677.2:c.320C>A	p.Pro107His	p.P107H	ENST00000351677	NM_002834.3	107	cCt/cAt	3/16	0.352151759825802	1	FACETS	0.722	0.665	0.78	0.722	0.665	0.78	INDETERMINATE	1	TRUE	0	0.648270632425708	1		494	419	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050876	49050876	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	42	318	0	ENST00000267163.4:c.2560A>T	p.Asn854Tyr	p.N854Y	ENST00000267163	NM_000321.2	854	Aac/Tac	25/27	0.648270632425708	1	FACETS	0.368	0.309	0.432	0.368	0.309	0.432	SUBCLONAL	1	TRUE	0	0.648270632425708	1		318	238	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724596	43724597	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	370	1051	0	ENST00000382044.4:c.3470_3471del	p.Ile1157ArgfsTer27	p.I1157Rfs*27	ENST00000382044	NM_001141980.1	1157	aTA/a	17/28	0.648270632425708	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.648270632425708	1		1051	747	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994608	73994608	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	134	923	0	ENST00000318443.5:c.92T>C	p.Val31Ala	p.V31A	ENST00000318443	NM_001024736.1	31	gTc/gCc	3/10	1	2	FACETS	0.505	0.459	0.554	0.505	0.459	0.554	SUBCLONAL	1	TRUE	1	0.648270632425708	2		923	818	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676143	29676143	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	42	345	0	ENST00000356175.3:c.7132A>G	p.Arg2378Gly	p.R2378G	ENST00000356175	NM_000267.3	2378	Agg/Ggg	48/57	0.313828699532283	1	FACETS	0.264	0.221	0.311	0.264	0.221	0.311	INDETERMINATE	1	TRUE	0	0.648270632425708	1		345	332	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485736	40485736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776115471	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	190	544	0	ENST00000264657.5:c.1004G>A	p.Arg335Gln	p.R335Q	ENST00000264657	NM_139276.2	335	cGg/cAg	10/24	0.313828699532283	1	FACETS	0.741	0.69	0.792	0.741	0.69	0.792	INDETERMINATE	1	TRUE	0	0.648270632425708	1		544	535	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966793	18966793	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	94	784	0	ENST00000262803.5:c.1604A>G	p.His535Arg	p.H535R	ENST00000262803	NM_002911.3	535	cAc/cGc	12/24	0.425013973835232	1	FACETS	0.241	0.214	0.27	0.241	0.214	0.27	SUBCLONAL	1	TRUE	0	0.648270632425708	1		784	813	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312916	30312916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146040933	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	85	654	0	ENST00000262643.3:c.719G>A	p.Arg240His	p.R240H	ENST00000262643	NM_001238.2	240	cGt/cAt	9/12	0.425013973835232	1	FACETS	0.346	0.307	0.388	0.346	0.307	0.388	SUBCLONAL	1	TRUE	0	0.648270632425708	1		654	512	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156917	89156917	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	91	631	0	ENST00000336596.2:c.19A>G	p.Ile7Val	p.I7V	ENST00000336596	NM_005233.5	7	Atc/Gtc	1/17	0.215980229437189	3	FACETS	0.966	0.864	1	0.483	0.432	0.537	INDETERMINATE	1	TRUE	1	0.648270632425708	3		631	385	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177024	56177024	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	168	511	0	ENST00000399503.3:c.2294T>C	p.Leu765Ser	p.L765S	ENST00000399503	NM_005921.1	765	tTg/tCg	13/20	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.648270632425708	2		511	511	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671558	30671558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	77	775	0	ENST00000376406.3:c.5402del	p.Pro1801ArgfsTer15	p.P1801Rfs*15	ENST00000376406	NM_014641.2	1801	cCg/cg	10/15	1	2	FACETS	0.273	0.239	0.31	0.273	0.239	0.31	SUBCLONAL	1	TRUE	1	0.648270632425708	2		775	869	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405904	157405904	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	65	501	0	ENST00000346085.5:c.2146G>T	p.Ala716Ser	p.A716S	ENST00000346085	NM_020732.3	716	Gcg/Tcg	6/20	1	2	FACETS	0.396	0.343	0.452	0.396	0.343	0.452	SUBCLONAL	1	TRUE	1	0.648270632425708	2		501	507	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189012	38189012	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	99	973	1	ENST00000317025.8:c.1002A>T	p.Lys334Asn	p.K334N	ENST00000317025	NM_023034.1	334	aaA/aaT	5/24	1	2	FACETS	0.349	0.311	0.39	0.349	0.311	0.39	SUBCLONAL	1	TRUE	1	0.648270632425708	2		974	875	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956762	68956762	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	61	703	1	ENST00000288368.4:c.880T>C	p.Tyr294His	p.Y294H	ENST00000288368	NM_024870.2	294	Tac/Cac	8/40	0.376748395676439	3	FACETS	0.232	0.199	0.268	0.116	0.099	0.134	INDETERMINATE	1	TRUE	1	0.648270632425708	3		704	1074	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141569579	141569582	+	frameshift_variant	Frame_Shift_Del	DEL	ACAA	ACAA	-	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	215	623	0	ENST00000220592.5:c.702_705del	p.Cys235LysfsTer15	p.C235Kfs*15	ENST00000220592	NM_012154.3	234	gtTTGT/gt	6/19	0.376748395676439	3	FACETS	0.945	0.879	1	0.473	0.439	0.507	INDETERMINATE	1	TRUE	1	0.648270632425708	3		623	929	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738400	145738400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781636798	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	90	807	0	ENST00000428558.2:c.2585C>T	p.Ser862Leu	p.S862L	ENST00000428558	NM_004260.3	862	tCg/tTg	16/22	0.376748395676439	3	FACETS	0.371	0.328	0.417	0.185	0.164	0.209	INDETERMINATE	1	TRUE	1	0.648270632425708	3		807	992	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524963	8524963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	43	346	1	ENST00000356435.5:c.641G>A	p.Gly214Asp	p.G214D	ENST00000356435		214	gGc/gAc	7/35	1	2	FACETS	0.238	0.198	0.281	0.238	0.198	0.281	SUBCLONAL	1	TRUE	1	0.648270632425708	2		347	558	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912266	97912266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373270404	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	154	444	1	ENST00000289081.3:c.625C>T	p.Arg209Cys	p.R209C	ENST00000289081	NM_000136.2	209	Cgt/Tgt	7/15	0.21766722060647	3	FACETS	1	0.955	1	0.529	0.486	0.573	INDETERMINATE	1	TRUE	1	0.648270632425708	3		445	595	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932791	39932791	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	356	494	0	ENST00000378444.4:c.1808C>G	p.Ala603Gly	p.A603G	ENST00000378444	NM_001123385.1	603	gCc/gGc	4/15	1	1	FACETS	0.768	0.743	0.793	1	0.997	1	SUBCLONAL	2	TRUE	0	0.648270632425708	1		494	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577152	7577154	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	ACC	ACC	-	rs1567548347	NA	P-0037128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	177	536	0	ENST00000269305.4:c.784_786del	p.Gly262del	p.G262del	ENST00000269305	NM_001126112.2	262	GGT/-	8/11	0.293085467678172	2	FACETS	0.853	0.793	0.914	1	0.987	1	CLONAL	3	FALSE	0	0.293085467678172	2		536	472	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453092	140453092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	42	315	0	ENST00000288602.6:c.1843G>A	p.Gly615Arg	p.G615R	ENST00000288602	NM_004333.4	615	Gga/Aga	15/18	0.293085467678172	3	FACETS	1	0.933	1	0.407	0.342	0.479	CLONAL	1	FALSE	0	0.293085467678172	3		315	269	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932106	36932111	+	frameshift_variant	Frame_Shift_Del	DEL	TCATAG	TCATAG	CT	novel	NA	P-0037128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	58	484	1	ENST00000361632.4:c.2358_2363delinsAG	p.Tyr787GlyfsTer14	p.Y787Gfs*14	ENST00000361632		786	tcCTATGAg/tcAGg	16/16	0.293085467678172	5	FACETS	0.877	0.758	1	0.877	0.758	1	CLONAL	2	FALSE	3	0.293085467678172	5		485	325	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215907	41215907	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs80357418	NA	P-0037128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	161	449	0	ENST00000357654.3:c.5136G>A	p.Trp1712Ter	p.W1712*	ENST00000357654	NM_007294.3	1712	tgG/tgA	17/23	0.293085467678172	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	FALSE	0	0.293085467678172	2		449	504	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480483	89480483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	12	332	1	ENST00000336596.2:c.2320G>A	p.Asp774Asn	p.D774N	ENST00000336596	NM_005233.5	774	Gac/Aac	13/17	0.149029321169679	0	FACETS	0.369	0.26	0.502			1	INDETERMINATE	1	FALSE	0	0.293085467678172	0		333	157	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27190556	27190556	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373235916	NA	P-0037128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	63	638	1	ENST00000380036.4:c.1357G>A	p.Val453Met	p.V453M	ENST00000380036	NM_000459.3	453	Gtg/Atg	10/23	0.263877653733166	0	FACETS	0.781	0.679	0.892			1	SUBCLONAL	1	FALSE	0	0.293085467678172	0		639	389	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643261	38643261	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	33	516	0	ENST00000299084.4:c.731A>C	p.Glu244Ala	p.E244A	ENST00000299084	NM_152594.2	244	gAg/gCg	7/7	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		516	497	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593603	55593603	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913235	NA	P-0037133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	150	388	0	ENST00000288135.5:c.1669T>G	p.Trp557Gly	p.W557G	ENST00000288135	NM_000222.2	557	Tgg/Ggg	11/21	0.443649581946932	3	FACETS	0.904	0.833	0.977	0.904	0.833	0.977	CLONAL	2	TRUE	1	0.443649581946932	3		388	457	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0037170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	247	372	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.760568250250045	2	FACETS	0.991	0.954	1	0.991	0.954	1	CLONAL	2	TRUE	0	0.776164738693867	2		372	321	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0037170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	134	171	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.995	0.916	1	0.995	0.916	1	CLONAL	1	TRUE	1	0.776164738693867	2		171	347	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244133	133244133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759398253	NA	P-0037170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	247	409	1	ENST00000320574.5:c.2275C>T	p.Arg759Cys	p.R759C	ENST00000320574	NM_006231.2	759	Cgt/Tgt	20/49	1	2	FACETS	0.943	0.887	1	0.943	0.887	1	CLONAL	1	TRUE	1	0.776164738693867	2		410	675	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16247378	16247378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772371033	NA	P-0037170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	69	156	1	ENST00000375759.3:c.1649G>A	p.Arg550His	p.R550H	ENST00000375759	NM_015001.2	550	cGc/cAc	9/15	1	2	FACETS	0.819	0.725	0.918	0.819	0.725	0.918	CLONAL	1	TRUE	1	0.776164738693867	2		157	217	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106865	27106882	+	inframe_deletion	In_Frame_Del	DEL	AGAACCCGGTGTGCCGGG	AGAACCCGGTGTGCCGGG	-	novel	NA	P-0037170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	167	443	0	ENST00000324856.7:c.6479_6496del	p.Asn2160_Glu2165del	p.N2160_E2165del	ENST00000324856	NM_006015.4	2159	aAGAACCCGGTGTGCCGGGag/aag	20/20	1	2	FACETS	0.771	0.713	0.831	0.771	0.713	0.831	SUBCLONAL	1	TRUE	1	0.776164738693867	2		443	558	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022937	33022937	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	170	284	0	ENST00000300177.4:c.46G>T	p.Gly16Trp	p.G16W	ENST00000300177	NM_001191322.1	16	Ggg/Tgg	2/2	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.776164738693867	2		284	413	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266828	18266828	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	322	563	0	ENST00000222254.8:c.139G>T	p.Gly47Cys	p.G47C	ENST00000222254	NM_005027.3	47	Ggc/Tgc	2/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.776164738693867	2		563	801	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211857	36211881	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCCGTGTCATCAAGACACCCCGG	CTCCCGTGTCATCAAGACACCCCGG	-	novel	NA	P-0037170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	358	848	0	ENST00000222270.7:c.1609_1633del	p.Ser537AspfsTer60	p.S537Dfs*60	ENST00000222270	NM_014727.1	536	tcCTCCCGTGTCATCAAGACACCCCGG/tc	3/37	1	2	FACETS	0.847	0.804	0.891	0.847	0.804	0.891	CLONAL	1	TRUE	1	0.776164738693867	2		848	1089	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0037179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	32	516	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	0.997	0.819	1	1	0.962	1	CLONAL	2	TRUE	1	0.19	2		516	169	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982992	201982992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	13	660	0	ENST00000359651.3:c.841G>A	p.Asp281Asn	p.D281N	ENST00000359651		281	Gac/Aac	7/8	1	2	FACETS	0.681	0.486	0.917	0.681	0.486	0.917	SUBCLONAL	1	TRUE	1	0.19	2		660	201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	177	620	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.125730128662098	3	FACETS	1	0.98	1	0.792	0.73	0.855	CLONAL	2	TRUE	0	0.202116446669938	3		620	812	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171974	32171974	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	45	546	0	ENST00000375023.3:c.3058A>T	p.Thr1020Ser	p.T1020S	ENST00000375023	NM_004557.3	1020	Act/Tct	19/30	0.202116446669938	3	FACETS	0.738	0.619	0.871	0.369	0.309	0.436	SUBCLONAL	1	TRUE	1	0.202116446669938	3		546	664	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0037194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	90	423	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.240828333796285	3	FACETS	1	0.971	1	0.826	0.74	0.916	CLONAL	2	TRUE	0	0.249825628895188	3		423	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0037194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	163	510	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.236966519350296	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.249825628895188	2		510	624	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0037194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	58	529	1	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.249825628895188	5	FACETS	1	0.967	1	0.493	0.424	0.567	CLONAL	1	TRUE	2	0.249825628895188	5		530	432	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743930	41743930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141302305	NA	P-0037194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	221	732	0	ENST00000301178.4:c.865G>A	p.Val289Met	p.V289M	ENST00000301178	NM_021913.4	289	Gtg/Atg	7/20	0.229159230361877	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.249825628895188	3		732	925	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	155	489	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	0.249825628895188	2	FACETS	0.972	0.893	1	0.972	0.893	1	CLONAL	2	TRUE	0	0.249825628895188	2		489	638	SUCCESS
APC	324	MSKCC	GRCh37	5	112174241	112174241	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1254176854	NA	P-0037194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	53	410	1	ENST00000257430.4:c.2950G>T	p.Glu984Ter	p.E984*	ENST00000257430	NM_000038.5	984	Gaa/Taa	16/16	0.249825628895188	3	FACETS	0.801	0.687	0.923	0.801	0.687	0.923	CLONAL	2	TRUE	1	0.249825628895188	3		411	298	SUCCESS
APC	324	MSKCC	GRCh37	5	112175657	112175657	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0037194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	51	347	0	ENST00000257430.4:c.4366A>T	p.Lys1456Ter	p.K1456*	ENST00000257430	NM_000038.5	1456	Aaa/Taa	16/16	0.249825628895188	3	FACETS	1	0.933	1	0.587	0.5	0.682	CLONAL	1	TRUE	1	0.249825628895188	3		347	391	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138137	64138137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	260	630	0	ENST00000334205.4:c.2060C>T	p.Thr687Met	p.T687M	ENST00000334205	NM_003942.2	687	aCg/aTg	16/17	0.249825628895188	3	FACETS	0.905	0.85	0.962	1	0.992	1	CLONAL	3	TRUE	1	0.249825628895188	3		630	862	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157488275	157488275	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377351099	NA	P-0037194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	124	449	1	ENST00000346085.5:c.2981C>T	p.Ala994Val	p.A994V	ENST00000346085	NM_020732.3	994	gCg/gTg	10/20	0.0736297329853677	4	FACETS	0.977	0.886	1	0.977	0.886	1	INDETERMINATE	2	TRUE	2	0.249825628895188	4		450	635	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132863	152132865	+	inframe_deletion	In_Frame_Del	DEL	CGA	CGA	-	novel	NA	P-0037194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	136	415	0	ENST00000262189.6:c.7_9del	p.Ser3del	p.S3del	ENST00000262189	NM_170606.2	3	TCG/-	1/59	0.0736297329853677	4	FACETS	0.945	0.865	1	1	0.986	1	INDETERMINATE	3	TRUE	2	0.249825628895188	4		415	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0037195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	533	790	6	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	0.493083003657708	3	FACETS	0.935	0.903	0.967	0.935	0.903	0.967	CLONAL	3	TRUE	0	0.50935636628805	3		796	936	SUCCESS
APC	324	MSKCC	GRCh37	5	112173429	112173429	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	164	419	0	ENST00000257430.4:c.2138C>A	p.Ser713Ter	p.S713*	ENST00000257430	NM_000038.5	713	tCa/tAa	16/16	0.487023082949563	2	FACETS	0.91	0.848	0.971	0.91	0.848	0.971	CLONAL	2	TRUE	0	0.50935636628805	2		419	354	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982395	201982395	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	172	771	0	ENST00000359651.3:c.774G>A	p.Trp258Ter	p.W258*	ENST00000359651		258	tgG/tgA	6/8	0.441477532659764	3	FACETS	0.885	0.814	0.959	0.443	0.407	0.48	CLONAL	1	TRUE	1	0.50935636628805	3		771	957	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133603	55133603	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	97	561	1	ENST00000257290.5:c.907A>C	p.Lys303Gln	p.K303Q	ENST00000257290	NM_006206.4	303	Aag/Cag	6/23	0.50935636628805	2	FACETS	0.762	0.682	0.846	0.381	0.341	0.423	SUBCLONAL	1	TRUE	0	0.50935636628805	2		562	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0037220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	157	510	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.339602497968757	1	FACETS	0.96	0.88	1	0.96	0.88	1	CLONAL	1	TRUE	0	0.339602497968757	1		510	800	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0037220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	79	185	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.339602497968757	2		185	426	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0037220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	79	455	6	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.736	0.648	0.831	0.736	0.648	0.831	SUBCLONAL	1	TRUE	1	0.339602497968757	2		461	632	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0037220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	321	371	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.23922076342178	3	FACETS	1	0.992	1	0.832	0.788	0.876	CLONAL	2	TRUE	0	0.339602497968757	3		371	886	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473708	67473708	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	271	612	13	ENST00000327367.4:c.788C>A	p.Pro263His	p.P263H	ENST00000327367	NM_005902.3	263	cCc/cAc	6/9	0.339602497968757	1	FACETS	0.758	0.713	0.804	1	0.994	1	SUBCLONAL	2	TRUE	0	0.339602497968757	1		625	874	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316117	11316117	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	72	610	8	ENST00000361445.4:c.637C>T	p.Leu213Phe	p.L213F	ENST00000361445	NM_004958.3	213	Ctt/Ttt	5/58	0.339602497968757	1	FACETS	0.405	0.353	0.462	0.405	0.353	0.462	SUBCLONAL	1	TRUE	0	0.339602497968757	1		618	869	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422902	45422903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AACAC	novel	NA	P-0037220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	98	417	5	ENST00000262160.6:c.221_225dup	p.Thr76ValfsTer14	p.T76Vfs*14	ENST00000262160	NM_005901.5	75	-/GTGTT	2/11	0.339602497968757	1	FACETS	0.897	0.803	0.997	0.897	0.803	0.997	CLONAL	1	TRUE	0	0.339602497968757	1		422	534	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46602909	46602909	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	151	768	18	ENST00000263734.3:c.967G>T	p.Gly323Trp	p.G323W	ENST00000263734	NM_001430.4	323	Ggg/Tgg	8/16	1	2	FACETS	0.867	0.791	0.946	0.867	0.791	0.946	CLONAL	1	TRUE	1	0.339602497968757	2		786	1026	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961048	55961048	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	190	691	9	ENST00000263923.4:c.2892C>G	p.Asp964Glu	p.D964E	ENST00000263923	NM_002253.2	964	gaC/gaG	21/30	0.339602497968757	1	FACETS	0.974	0.9	1	0.974	0.9	1	CLONAL	1	TRUE	0	0.339602497968757	1		700	954	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852008	128852008	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	167	788	11	ENST00000249373.3:c.2080C>A	p.Pro694Thr	p.P694T	ENST00000249373	NM_005631.4	694	Cct/Act	12/12	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.339602497968757	2		799	968	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127951982	127951982	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	161	621	9	ENST00000373547.4:c.16C>A	p.Leu6Met	p.L6M	ENST00000373547	NM_002721.4	6	Ctg/Atg	1/7	1	2	FACETS	0.956	0.876	1	0.956	0.876	1	CLONAL	1	TRUE	1	0.339602497968757	2		630	992	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139414015	139414015	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	178	531	14	ENST00000277541.6:c.745T>G	p.Phe249Val	p.F249V	ENST00000277541	NM_017617.3	249	Ttc/Gtc	5/34	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.339602497968757	2		545	983	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725042	89725042	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1085308041	NA	P-0037240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	33	173	0	ENST00000371953.3:c.1027-2A>G		p.X343_splice	ENST00000371953	NM_000314.4	343			1	2	FACETS	0.773	0.635	0.926	1	0.95	1	CLONAL	2	TRUE	1	0.212370797734711	2		173	201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	65	559	0	ENST00000269305.4:c.379T>C	p.Ser127Pro	p.S127P	ENST00000269305	NM_001126112.2	127	Tcc/Ccc	5/11	1	2	FACETS	0.656	0.567	0.753	0.656	0.567	0.753	SUBCLONAL	1	TRUE	1	0.212370797734711	2		559	933	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100175	27100176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0037240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	129	403	0	ENST00000324856.7:c.3977dup	p.Gln1327AlafsTer11	p.Q1327Afs*11	ENST00000324856	NM_006015.4	1324	tac/taCc	16/20	0.212370797734711	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	2	TRUE	0	0.212370797734711	2		403	602	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0037240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	55	372	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	0.909	0.777	1	0.909	0.777	1	CLONAL	1	TRUE	1	0.212370797734711	2		372	570	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645156	67645156	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	68	527	2	ENST00000264010.4:c.421G>T	p.Glu141Ter	p.E141*	ENST00000264010	NM_006565.3	141	Gaa/Taa	3/12	1	2	FACETS	0.946	0.822	1	0.946	0.822	1	CLONAL	1	TRUE	1	0.212370797734711	2		529	677	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685269	89685269	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs786203847	NA	P-0037240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	32	224	0	ENST00000371953.3:c.165-1G>A		p.X55_splice	ENST00000371953	NM_000314.4	55			1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.212370797734711	2		224	226	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410988	31410988	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	75	435	0	ENST00000344624.3:c.3532C>G	p.Arg1178Gly	p.R1178G	ENST00000344624		1178	Cga/Gga	28/33	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.212370797734711	2		435	696	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591078	67591110	+	inframe_deletion	In_Frame_Del	DEL	AGAAATTGACAAACGTATGAACAGCATTAAACC	AGAAATTGACAAACGTATGAACAGCATTAAACC	-	novel	NA	P-0037240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	40	211	0	ENST00000274335.5:c.1674_1706del	p.Glu558_Pro568del	p.E558_P568del	ENST00000274335		557	cgAGAAATTGACAAACGTATGAACAGCATTAAACCa/cga	12/15	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.212370797734711	2		211	309	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593236	67593247	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTAGGGTGGACG	CTAGGGTGGACG	-	novel	NA	P-0037240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	36	214	0	ENST00000274335.5:c.1986-4_1993del		p.X662_splice	ENST00000274335		662		15/15	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.212370797734711	2		214	304	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0037242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	164	636	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.969	0.894	1	0.969	0.894	1	CLONAL	1	TRUE	1	0.599203129030765	2		636	565	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878115	48878117	+	inframe_deletion	In_Frame_Del	DEL	CCG	CCG	-	rs587778823	NA	P-0037242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	11	89	0	ENST00000267163.4:c.78_80del	p.Pro29del	p.P29del	ENST00000267163	NM_000321.2	23	CCG/-	1/27	0.599203129030765	3	FACETS	0.293	0.202	0.404	0.146	0.101	0.202	SUBCLONAL	1	TRUE	1	0.599203129030765	3		89	163	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578217	7578218	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0037242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	353	555	0	ENST00000269305.4:c.631_632del	p.Thr211PhefsTer4	p.T211Ffs*4	ENST00000269305	NM_001126112.2	211	ACt/t	6/11	0.599203129030765	2	FACETS	0.988	0.948	1	0.988	0.948	1	CLONAL	2	TRUE	0	0.599203129030765	2		555	596	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400909	72400909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	72	424	0	ENST00000357731.5:c.262G>T	p.Asp88Tyr	p.D88Y	ENST00000357731	NM_173808.2	88	Gat/Tat	2/7	0.459170424497902	1	FACETS	0.65	0.575	0.729	0.65	0.575	0.729	SUBCLONAL	1	TRUE	0	0.599203129030765	1		424	259	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575696	48575696	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1555685248	NA	P-0037242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	72	562	0	ENST00000342988.3:c.454+2T>C		p.X152_splice	ENST00000342988	NM_005359.5	152			0.599203129030765	1	FACETS	0.92	0.821	1	0.92	0.821	1	CLONAL	1	TRUE	0	0.599203129030765	1		562	183	SUCCESS
APC	324	MSKCC	GRCh37	5	112175511	112175511	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	195	369	0	ENST00000257430.4:c.4220del	p.Ser1407MetfsTer8	p.S1407Mfs*8	ENST00000257430	NM_000038.5	1407	aGt/at	16/16	0.596510155729608	2	FACETS	0.995	0.941	1	0.995	0.941	1	CLONAL	2	TRUE	0	0.599203129030765	2		369	327	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170270	32170270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187627302	NA	P-0037242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	183	631	2	ENST00000375023.3:c.3338G>A	p.Arg1113His	p.R1113H	ENST00000375023	NM_004557.3	1113	cGc/cAc	21/30	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.599203129030765	2		633	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519998	NA	P-0037262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	417	477	0	ENST00000269305.4:c.581T>C	p.Leu194Pro	p.L194P	ENST00000269305	NM_001126112.2	194	cTt/cCt	6/11	0.625017660634713	2	FACETS	0.975	0.94	1	0.975	0.94	1	CLONAL	2	TRUE	0	0.625017660634713	2		477	684	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575199	48575199	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0037262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	122	340	1	ENST00000342988.3:c.393T>A	p.Tyr131Ter	p.Y131*	ENST00000342988	NM_005359.5	131	taT/taA	3/12	0.613370211464694	1	FACETS	0.938	0.863	1	0.938	0.863	1	CLONAL	1	TRUE	0	0.625017660634713	1		341	286	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798440	42798440	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	225	564	3	ENST00000575354.2:c.4311del	p.Phe1437LeufsTer17	p.F1437Lfs*17	ENST00000575354	NM_015125.3	1437	ttC/tt	18/20	0.625017660634713	2	FACETS	1	0.949	1	0.508	0.475	0.542	CLONAL	1	TRUE	0	0.625017660634713	2		567	708	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909523	50909523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	481	573	1	ENST00000440232.2:c.1327C>T	p.Arg443Trp	p.R443W	ENST00000440232	NM_002691.3	443	Cgg/Tgg	11/27	0.625017660634713	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.625017660634713	2		574	742	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483910	212483910	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	98	424	1	ENST00000342788.4:c.2293T>C	p.Phe765Leu	p.F765L	ENST00000342788	NM_005235.2	765	Ttc/Ctc	19/28	0.625017660634713	3	FACETS	0.792	0.709	0.879	0.396	0.354	0.44	SUBCLONAL	1	TRUE	1	0.625017660634713	3		425	520	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396889	139396889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777962754	NA	P-0037262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	171	364	2	ENST00000277541.6:c.5219C>T	p.Ala1740Val	p.A1740V	ENST00000277541	NM_017617.3	1740	gCg/gTg	28/34	0.625017660634713	3	FACETS	1	0.966	1	0.542	0.5	0.585	CLONAL	1	TRUE	1	0.625017660634713	3		366	663	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0037264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	42	442	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.317412660285524	3	FACETS	0.47	0.391	0.557	0.235	0.195	0.279	SUBCLONAL	1	TRUE	1	0.317412660285524	3		442	653	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	71	388	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	0.317412660285524	3	FACETS	0.946	0.827	1	0.473	0.413	0.537	CLONAL	1	TRUE	1	0.317412660285524	3		388	548	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114224	115114225	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0037264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	309	721	0	ENST00000257566.3:c.992dup	p.Glu332GlyfsTer6	p.E332Gfs*6	ENST00000257566	NM_016569.3	331	aag/aaAg	6/8	0.195520152026469	4	FACETS	1	0.991	1	0.822	0.776	0.869	CLONAL	2	TRUE	1	0.317412660285524	4		721	1040	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842676	68842677	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0037264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	245	671	0	ENST00000261769.5:c.615dup	p.Ile206TyrfsTer3	p.I206Yfs*3	ENST00000261769	NM_004360.3	204	-/T	5/16	0.317412660285524	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.317412660285524	2		671	673	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206763	36206764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGGGTTGGGCGT	novel	NA	P-0037264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	170	576	0	ENST00000300305.3:c.736_748dup	p.Arg250HisfsTer15	p.R250Hfs*15	ENST00000300305		250	cgt/cACGCCCAACCCTCgt	6/8	0.195520152026469	4	FACETS	0.827	0.761	0.896	0.551	0.507	0.597	CLONAL	2	TRUE	1	0.317412660285524	4		576	853	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0037286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	129	372	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.426034359688598	2		372	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0037298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	302	866	0	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		866	615	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	28	326	0				ENST00000310581	NM_198253.2	-/1132			0.24316270223994	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.24316270223994	1		326	152	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0037309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	45	441	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.24316270223994	2		441	326	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381541	81381541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	27	285	0	ENST00000222390.5:c.520G>A	p.Glu174Lys	p.E174K	ENST00000222390	NM_000601.4	174	Gaa/Aaa	5/18	1	2	FACETS	0.673	0.536	0.829	0.673	0.536	0.829	SUBCLONAL	1	TRUE	1	0.24316270223994	2		285	330	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058361	42058361	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	43	314	0	ENST00000219905.7:c.8081C>T	p.Ser2694Phe	p.S2694F	ENST00000219905	NM_001164273.1	2694	tCc/tTc	24/24	1	2	FACETS	0.985	0.827	1	0.985	0.827	1	CLONAL	1	TRUE	1	0.24316270223994	2		314	359	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121909229	NA	P-0037309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	26	416	0	ENST00000371953.3:c.389G>T	p.Arg130Leu	p.R130L	ENST00000371953	NM_000314.4	130	cGa/cTa	5/9	0.24316270223994	1	FACETS	0.585	0.464	0.724	0.585	0.464	0.724	SUBCLONAL	1	TRUE	0	0.24316270223994	1		416	321	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027128	49027128	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs794727199	NA	P-0037309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	28	258	0	ENST00000267163.4:c.1696-1G>A		p.X566_splice	ENST00000267163	NM_000321.2	566			1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.24316270223994	2		258	224	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260146	10260146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751754286	NA	P-0037309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	60	505	0	ENST00000340748.4:c.2521G>A	p.Glu841Lys	p.E841K	ENST00000340748		841	Gaa/Aaa	25/40	1	2	FACETS	0.783	0.674	0.902	0.783	0.674	0.902	CLONAL	1	TRUE	1	0.24316270223994	2		505	630	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912075	56912075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	66	562	0	ENST00000519728.1:c.1303G>A	p.Glu435Lys	p.E435K	ENST00000519728	NM_002350.3	435	Gaa/Aaa	12/13	1	2	FACETS	0.891	0.774	1	0.891	0.774	1	CLONAL	1	TRUE	1	0.24316270223994	2		562	609	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484270	8484270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867884876	NA	P-0037309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	38	513	0	ENST00000356435.5:c.3262C>T	p.Arg1088Cys	p.R1088C	ENST00000356435		1088	Cgt/Tgt	19/35	0.24316270223994	1	FACETS	0.492	0.406	0.588	0.492	0.406	0.588	SUBCLONAL	1	TRUE	0	0.24316270223994	1		513	558	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612211	189612211	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	60	434	1	ENST00000264731.3:c.1963C>T	p.Arg655Ter	p.R655*	ENST00000264731	NM_003722.4	655	Cga/Tga	14/14	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.24316270223994	2		435	445	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202911	27202911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	38	461	0	ENST00000380036.4:c.2003C>T	p.Ser668Phe	p.S668F	ENST00000380036	NM_000459.3	668	tCt/tTt	13/23	0.24316270223994	1	FACETS	0.637	0.527	0.76	0.637	0.527	0.76	SUBCLONAL	1	TRUE	0	0.24316270223994	1		461	431	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494688	2494688	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	43	507	1	ENST00000355716.4:c.828C>A	p.Phe276Leu	p.F276L	ENST00000355716	NM_003820.2	276	ttC/ttA	8/8	1	2	FACETS	0.826	0.692	0.975	0.826	0.692	0.975	CLONAL	1	TRUE	1	0.24316270223994	2		508	428	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300515	11300515	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	47	767	0	ENST00000361445.4:c.1631C>T	p.Ser544Phe	p.S544F	ENST00000361445	NM_004958.3	544	tCc/tTc	11/58	1	2	FACETS	0.552	0.465	0.649	0.552	0.465	0.649	SUBCLONAL	1	TRUE	1	0.24316270223994	2		767	700	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259673	16259673	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	74	429	0	ENST00000375759.3:c.6938C>T	p.Pro2313Leu	p.P2313L	ENST00000375759	NM_015001.2	2313	cCa/cTa	11/15	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.24316270223994	2		429	411	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933758	36933758	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	42	559	0	ENST00000361632.4:c.1641G>A	p.Trp547Ter	p.W547*	ENST00000361632		547	tgG/tgA	12/16	1	2	FACETS	0.62	0.517	0.735	0.62	0.517	0.735	SUBCLONAL	1	TRUE	1	0.24316270223994	2		559	557	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156836701	156836701	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0037309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	55	647	0	ENST00000524377.1:c.360-1G>A		p.X120_splice	ENST00000524377	NM_002529.3	120			1	2	FACETS	0.73	0.624	0.846	0.73	0.624	0.846	SUBCLONAL	1	TRUE	1	0.24316270223994	2		647	620	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845973	156845973	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	47	532	1	ENST00000524377.1:c.1603G>A	p.Glu535Lys	p.E535K	ENST00000524377	NM_002529.3	535	Gag/Aag	13/17	1	2	FACETS	0.822	0.694	0.963	0.822	0.694	0.963	CLONAL	1	TRUE	1	0.24316270223994	2		533	470	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134332	2134333	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0037309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	57	714	0	ENST00000219476.3:c.4109_4110delinsTT	p.Pro1370Leu	p.P1370L	ENST00000219476	NM_000548.3	1370	cCC/cTT	34/42	1	2	FACETS	0.779	0.668	0.9	0.779	0.668	0.9	SUBCLONAL	1	TRUE	1	0.24316270223994	2		714	602	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678043	58678043	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1456766576	NA	P-0037309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	40	167	0	ENST00000305921.3:c.268C>T	p.Arg90Cys	p.R90C	ENST00000305921	NM_003620.3	90	Cgc/Tgc	1/6	1	2	FACETS	0.889	0.748	1	1	0.966	1	CLONAL	2	TRUE	1	0.24316270223994	2		167	185	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561213	9561213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	57	423	1	ENST00000353224.5:c.569C>T	p.Ser190Phe	p.S190F	ENST00000353224	NM_177990.2	190	tCc/tTc	4/10	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.24316270223994	2		424	458	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266105	41266110	+	inframe_deletion	In_Frame_Del	DEL	AATCCA	AATCCA	-	novel	NA	P-0037309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	29	252	0	ENST00000349496.5:c.102_107del	p.Ile35_His36del	p.I35_H36del	ENST00000349496	NM_001904.3	34	ggAATCCAt/ggt	3/15	1	2	FACETS	0.741	0.595	0.905	0.741	0.595	0.905	CLONAL	1	TRUE	1	0.24316270223994	2		252	322	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638630	176638630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	105	543	0	ENST00000439151.2:c.3230C>T	p.Ser1077Leu	p.S1077L	ENST00000439151	NM_022455.4	1077	tCa/tTa	5/23	0.24316270223994	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.24316270223994	1		543	618	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816819	32816839	+	frameshift_variant	Frame_Shift_Del	DEL	CCACTGCTTACAGCCCCACTG	CCACTGCTTACAGCCCCACTG	ACTT	novel	NA	P-0037309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	95	569	1	ENST00000354258.4:c.1485_1505delinsAAGT	p.Gly497GlufsTer38	p.G497Efs*38	ENST00000354258	NM_000593.5	495	acCAGTGGGGCTGTAAGCAGTGGg/acAAGTg	6/11	0.143947816348409	2	FACETS	1	0.969	1	0.623	0.555	0.695	INDETERMINATE	1	TRUE	0	0.24316270223994	2		570	627	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700271	117700271	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764329833	NA	P-0037309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	22	402	0	ENST00000368508.3:c.2548C>T	p.Gln850Ter	p.Q850*	ENST00000368508	NM_002944.2	850	Caa/Taa	17/43	0.24316270223994	1	FACETS	0.501	0.389	0.632	0.501	0.389	0.632	SUBCLONAL	1	TRUE	0	0.24316270223994	1		402	317	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522431	157522431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	48	574	0	ENST00000346085.5:c.4703C>T	p.Ser1568Phe	p.S1568F	ENST00000346085	NM_020732.3	1568	tCt/tTt	18/20	0.24316270223994	1	FACETS	0.654	0.553	0.766	0.654	0.553	0.766	SUBCLONAL	1	TRUE	0	0.24316270223994	1		574	530	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207611	29207611	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1474424761	NA	P-0037309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	29	400	0	ENST00000240100.2:c.185T>A	p.Leu62Gln	p.L62Q	ENST00000240100	NM_001394.6	62	cTa/cAa	1/4	1	2	FACETS	0.593	0.476	0.727	0.593	0.476	0.727	SUBCLONAL	1	TRUE	1	0.24316270223994	2		400	402	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814887	139814887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	34	601	1	ENST00000247668.2:c.880G>A	p.Glu294Lys	p.E294K	ENST00000247668	NM_021138.3	294	Gag/Aag	8/11	0.24316270223994	1	FACETS	0.426	0.347	0.515	0.426	0.347	0.515	SUBCLONAL	1	TRUE	0	0.24316270223994	1		602	577	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940120	31940123	+	missense_variant	Missense_Mutation	ONP	GAAG	GAAG	AAAT	novel	NA	P-0037309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	141	679	0	ENST00000375333.2:c.262_265delinsAAAT	p.Glu88_Asp89delinsLysTyr	p.E88_D89delinsKY	ENST00000375333	NM_032454.1	88	GAAGac/AAATac	2/8	0.143947816348409	2	FACETS	0.869	0.794	0.948	0.869	0.794	0.948	INDETERMINATE	2	TRUE	0	0.24316270223994	2		679	667	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0037377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	76	372	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.429535257772619	2		372	317	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0037377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	84	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.745	0.66	0.836	0.745	0.66	0.836	SUBCLONAL	1	TRUE	1	0.429535257772619	2		298	525	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44520605	44520605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	61	193	0	ENST00000291552.4:c.157C>T	p.Arg53Cys	p.R53C	ENST00000291552	NM_006758.2	53	Cgt/Tgt	3/8	1	2	FACETS	0.879	0.764	1	0.879	0.764	1	CLONAL	1	TRUE	1	0.429535257772619	2		193	323	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910331	29910331	+	start_lost	Translation_Start_Site	SNP	A	A	T	novel	NA	P-0037377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	75	435	0	ENST00000376809.5:c.1A>T	p.Met1?	p.M1?	ENST00000376809	NM_002116.7	1	Atg/Ttg	1/8	1	2	FACETS	0.462	0.404	0.524	0.462	0.404	0.524	SUBCLONAL	1	TRUE	1	0.429535257772619	2		435	756	SUCCESS
APC	324	MSKCC	GRCh37	5	112174236	112174236	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	190	263	0	ENST00000257430.4:c.2945C>A	p.Ser982Ter	p.S982*	ENST00000257430	NM_000038.5	982	tCg/tAg	16/16	0.429535257772619	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	0	0.429535257772619	2		263	439	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114901076	114901076	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1247712690	NA	P-0037377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	75	299	0	ENST00000543371.1:c.685+1G>A		p.X229_splice	ENST00000543371	NM_001198531.1	229			1	2	FACETS	0.992	0.876	1	0.992	0.876	1	CLONAL	1	TRUE	1	0.429535257772619	2		299	352	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456321	32456321	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756501972	NA	P-0037377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	189	447	0	ENST00000332351.3:c.571G>A	p.Gly191Ser	p.G191S	ENST00000332351	NM_024426.4	191	Ggc/Agc	1/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.429535257772619	2		447	724	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0037383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	156	434	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.476589361269915	2		434	622	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0037383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	213	816	6	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.953	0.886	1	0.953	0.886	1	CLONAL	1	TRUE	1	0.476589361269915	2		822	938	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0037383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	269	695	7	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.786	0.741	0.832	1	0.994	1	SUBCLONAL	2	TRUE	1	0.476589361269915	2		702	718	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0037383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	122	701	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.795	0.72	0.874	0.795	0.72	0.874	SUBCLONAL	1	TRUE	1	0.476589361269915	2		701	644	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0037383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	235	655	3	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.476589361269915	2		658	885	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534411	140534411	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	140	337	0	ENST00000288602.6:c.502G>T	p.Val168Leu	p.V168L	ENST00000288602	NM_004333.4	168	Gtg/Ttg	3/18	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.476589361269915	2		337	570	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121909229	NA	P-0037383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	217	415	0	ENST00000371953.3:c.389G>C	p.Arg130Pro	p.R130P	ENST00000371953	NM_000314.4	130	cGa/cCa	5/9	0.476589361269915	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.476589361269915	2		415	451	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160588	56160588	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	58	204	0	ENST00000399503.3:c.862C>T	p.Arg288Ter	p.R288*	ENST00000399503	NM_005921.1	288	Cga/Tga	4/20	1	2	FACETS	0.845	0.732	0.966	0.845	0.732	0.966	CLONAL	1	TRUE	1	0.476589361269915	2		204	288	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	87	291	2	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.476589361269915	2		293	347	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446270	187446270	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	149	617	2	ENST00000232014.4:c.1418del	p.Pro473ArgfsTer117	p.P473Rfs*117	ENST00000232014	NM_001130845.1	473	cCg/cg	6/10	1	2	FACETS	0.804	0.735	0.875	0.804	0.735	0.875	CLONAL	1	TRUE	1	0.476589361269915	2		619	778	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217556	142217557	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1268253442	NA	P-0037383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	30	481	1	ENST00000350721.4:c.5440dup	p.Arg1814LysfsTer8	p.R1814Kfs*8	ENST00000350721	NM_001184.3	1814	aga/aAga	32/47	1	2	FACETS	0.258	0.207	0.316	0.258	0.207	0.316	SUBCLONAL	1	TRUE	1	0.476589361269915	2		482	488	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152357788	152357788	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs777753452	NA	P-0037383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	71	925	0	ENST00000359321.1:c.119A>G	p.His40Arg	p.H40R	ENST00000359321	NM_005431.1	40	cAt/cGt	2/3	1	2	FACETS	0.76	0.667	0.86	0.76	0.667	0.86	SUBCLONAL	1	TRUE	1	0.476589361269915	2		925	392	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380350	14380350	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	102	178	0	ENST00000256196.4:c.67G>T	p.Gly23Cys	p.G23C	ENST00000256196		23	Ggc/Tgc	1/6	1	2	FACETS	0.762	0.691	0.834	1	0.985	1	SUBCLONAL	2	TRUE	1	0.476589361269915	2		178	281	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600496	43600496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178140696	NA	P-0037383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	197	516	0	ENST00000355710.3:c.722C>T	p.Ala241Val	p.A241V	ENST00000355710	NM_020975.4	241	gCc/gTc	4/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.476589361269915	2		516	693	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432575	49432575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1285381948	NA	P-0037383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	135	666	0	ENST00000301067.7:c.8564C>T	p.Ala2855Val	p.A2855V	ENST00000301067	NM_003482.3	2855	gCg/gTg	34/54	1	2	FACETS	0.758	0.69	0.83	0.758	0.69	0.83	SUBCLONAL	1	TRUE	1	0.476589361269915	2		666	747	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222308	53222309	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0037383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	190	856	0	ENST00000375401.3:c.4523dup	p.Ala1509CysfsTer75	p.A1509Cfs*75	ENST00000375401	NM_004187.3	1508	cct/ccCt	26/26	1	2	FACETS	0.954	0.883	1	0.954	0.883	1	CLONAL	1	TRUE	1	0.476589361269915	2		856	836	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662453	67662453	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs879255516	NA	P-0037383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	227	590	0	ENST00000264010.4:c.1699C>T	p.Arg567Trp	p.R567W	ENST00000264010	NM_006565.3	567	Cgg/Tgg	9/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.476589361269915	2		590	876	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106207	27106207	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	161	540	0	ENST00000324856.7:c.5819del	p.Pro1940HisfsTer16	p.P1940Hfs*16	ENST00000324856	NM_006015.4	1940	Cca/ca	20/20	1	2	FACETS	0.988	0.909	1	0.988	0.909	1	CLONAL	1	TRUE	1	0.476589361269915	2		540	684	SUCCESS
ATR	545	MSKCC	GRCh37	3	142171980	142171980	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	34	525	0	ENST00000350721.4:c.7751T>C	p.Val2584Ala	p.V2584A	ENST00000350721	NM_001184.3	2584	gTc/gCc	46/47	1	2	FACETS	0.287	0.234	0.346	0.287	0.234	0.346	SUBCLONAL	1	TRUE	1	0.476589361269915	2		525	498	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178471	56178471	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	59	262	0	ENST00000399503.3:c.3447del	p.Phe1149LeufsTer23	p.F1149Lfs*23	ENST00000399503	NM_005921.1	1148	acT/ac	14/20	1	2	FACETS	0.963	0.837	1	0.963	0.837	1	CLONAL	1	TRUE	1	0.476589361269915	2		262	257	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0037403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	83	327	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.987	0.882	1	0.987	0.882	1	CLONAL	1	TRUE	1	0.585730768433881	2		327	287	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1427441061	NA	P-0037403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	384	559	0	ENST00000269305.4:c.560-2A>G		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.585730768433881	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.585730768433881	2		559	560	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937309	76937309	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0037403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	132	253	0	ENST00000373344.5:c.3439A>T	p.Lys1147Ter	p.K1147*	ENST00000373344	NM_000489.3	1147	Aag/Tag	9/35	1	1	FACETS	0.852	0.803	0.899	1	0.992	1	CLONAL	2	TRUE	0	0.585730768433881	1		253	187	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418947	116418947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	73	302	0	ENST00000397752.3:c.3458C>T	p.Pro1153Leu	p.P1153L	ENST00000397752	NM_000245.2	1153	cCg/cTg	17/21	NA	2	FACETS	0.931	0.822	1			1	INDETERMINATE	1	FALSE	NA	0.517404553062463	2		302	303	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625186	69625186	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs547457011	NA	P-0037421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	122	746	0	ENST00000334134.2:c.607G>A	p.Gly203Ser	p.G203S	ENST00000334134	NM_005247.2	203	Ggt/Agt	3/3	0.468306436855543	4	FACETS	0.708	0.639	0.782			1	SUBCLONAL	1	FALSE	NA	0.517404553062463	4		746	1010	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448690	49448690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	75	406	1	ENST00000301067.7:c.169G>A	p.Asp57Asn	p.D57N	ENST00000301067	NM_003482.3	57	Gac/Aac	2/54	0.517404553062463	3	FACETS	0.676	0.593	0.764			1	SUBCLONAL	1	FALSE	NA	0.517404553062463	3		407	540	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618688	37618688	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	301	423	0	ENST00000447079.4:c.365del	p.Leu122TyrfsTer2	p.L122Yfs*2	ENST00000447079	NM_015083.1	122	Tta/ta	1/14	0.517404553062463	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	FALSE	0	0.517404553062463	2		423	549	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032042	26032042	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	85	355	0	ENST00000244661.2:c.247C>G	p.Leu83Val	p.L83V	ENST00000244661	NM_003537.3	83	Ctt/Gtt	1/1	0.499895491879082	4	FACETS	0.811	0.717	0.91	0.27	0.239	0.304	CLONAL	1	FALSE	1	0.517404553062463	4		355	615	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	21	326	0				ENST00000310581	NM_198253.2	-/1132			0.444304384636036	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.877833649420484	0		326	50	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0037422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	54	327	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.925	0.812	1	0.925	0.812	1	CLONAL	1	FALSE	1	0.877833649420484	2		327	133	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413070	139413072	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0037422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	166	589	0	ENST00000277541.6:c.1070_1072del	p.Phe357del	p.F357del	ENST00000277541	NM_017617.3	357	tTCTac/tac	6/34	0.790609534476209	1	FACETS	0.877	0.831	0.921	0.877	0.831	0.921	CLONAL	1	FALSE	0	0.877833649420484	1		589	242	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030384	49030384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554834063	NA	P-0037422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	41	310	1	ENST00000267163.4:c.1859C>T	p.Thr620Met	p.T620M	ENST00000267163	NM_000321.2	620	aCg/aTg	19/27	1	2	FACETS	0.89	0.764	1	0.89	0.764	1	CLONAL	1	FALSE	1	0.877833649420484	2		311	105	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428586	78428586	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	84	483	0	ENST00000370768.2:c.1213C>T	p.Gln405Ter	p.Q405*	ENST00000370768	NM_003902.3	405	Cag/Tag	14/20	0.877833649420484	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	0	0.877833649420484	1		483	107	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157470057	157470057	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554226145	NA	P-0037422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	40	357	0	ENST00000346085.5:c.2851C>T	p.Gln951Ter	p.Q951*	ENST00000346085	NM_020732.3	951	Cag/Tag	9/20	1	2	FACETS	0.949	0.816	1	0.949	0.816	1	CLONAL	1	FALSE	1	0.877833649420484	2		357	96	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798857	42798862	+	inframe_deletion	In_Frame_Del	DEL	CTCTTT	CTCTTT	-	novel	NA	P-0037422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	243	861	0	ENST00000575354.2:c.4430_4435del	p.Leu1477_Phe1478del	p.L1477_F1478del	ENST00000575354	NM_015125.3	1477	CTCTTT/-	19/20	NA	2	FACETS	0.899	0.866	0.929			1	INDETERMINATE	2	FALSE	NA	0.877833649420484	2		861	308	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900649	32900650	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0037423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	29	519	0	ENST00000380152.3:c.530_531insGA	p.His179AsnfsTer7	p.H179Nfs*7	ENST00000380152		177	cca/ccGAa	7/27	0.3	0	FACETS	0.796	0.646	0.963			1	CLONAL	1	FALSE	0	0.3	0		519	170	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467810	50467810	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs765032404	NA	P-0037423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	42	460	0	ENST00000331340.3:c.1045C>A	p.Gln349Lys	p.Q349K	ENST00000331340	NM_006060.4	349	Cag/Aag	8/8	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	FALSE	1	0.3	2		460	263	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243045	105243045	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1733	364	634	0	ENST00000349310.3:c.238T>C	p.Trp80Arg	p.W80R	ENST00000349310	NM_001014432.1	80	Tgg/Cgg	5/15	1	2	FACETS	0.946	0.893	1	1	0.996	1	CLONAL	2	FALSE	1	0.183569170973373	2		634	2097	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061312	38061312	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1329067081	NA	P-0037427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1640	238	780	0	ENST00000250448.2:c.677A>G	p.Asp226Gly	p.D226G	ENST00000250448	NM_004496.3	226	gAc/gGc	2/2	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.183569170973373	2		780	1878	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039225	49039225	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	15	508	0	ENST00000267163.4:c.2303T>C	p.Ile768Thr	p.I768T	ENST00000267163	NM_000321.2	768	aTt/aCt	22/27	0.178488336503215	0	FACETS	1	0.761	1			1	CLONAL	1	FALSE	0	0.183569170973373	0		508	129	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061164	38061193	+	inframe_deletion	In_Frame_Del	DEL	GCCGGCCCCCGGCTGCTTCTCGCACTTGAA	GCCGGCCCCCGGCTGCTTCTCGCACTTGAA	-	novel	NA	P-0037427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	75	322	0	ENST00000250448.2:c.796_825del	p.Phe266_Gly275del	p.F266_G275del	ENST00000250448	NM_004496.3	266	TTCAAGTGCGAGAAGCAGCCGGGGGCCGGC/-	2/2	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	FALSE	1	0.183569170973373	2		322	812	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574517	41574517	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1258	125	751	0	ENST00000263253.7:c.6802C>T	p.Gln2268Ter	p.Q2268*	ENST00000263253	NM_001429.3	2268	Cag/Tag	31/31	0.183569170973373	1	FACETS	0.894	0.807	0.987	0.894	0.807	0.987	CLONAL	1	FALSE	0	0.183569170973373	1		751	1383	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752356	57752356	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	88	420	0	ENST00000274289.3:c.1217C>A	p.Ser406Ter	p.S406*	ENST00000274289	NM_006622.3	406	tCa/tAa	9/14	1	2	FACETS	0.816	0.725	0.913	0.816	0.725	0.913	CLONAL	1	TRUE	1	0.409396508119846	2		420	527	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982043	70982043	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1278278618	NA	P-0037450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	49	648	3	ENST00000276594.2:c.53C>T	p.Pro18Leu	p.P18L	ENST00000276594	NM_024504.3	18	cCg/cTg	2/8	0.377152147597025	1	FACETS	0.3	0.254	0.352	0.3	0.254	0.352	SUBCLONAL	1	TRUE	0	0.409396508119846	1		651	634	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	135	326	0				ENST00000310581	NM_198253.2	-/1132			0.523391074215425	5	FACETS	0.925	0.871	0.978	1	0.985	1	CLONAL	5	TRUE	1	0.523391074215425	5		326	199	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0037451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	520	954	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.523391074215425	7	FACETS	1	0.99	1			1	CLONAL	7	TRUE	NA	0.523391074215425	7		954	638	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426753	212426753	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	80	481	0	ENST00000342788.4:c.2362C>A	p.Leu788Met	p.L788M	ENST00000342788	NM_005235.2	788	Ctg/Atg	20/28	0.523391074215425	3	FACETS	0.969	0.858	1	0.485	0.429	0.544	CLONAL	1	TRUE	1	0.523391074215425	3		481	398	SUCCESS
APC	324	MSKCC	GRCh37	5	112154934	112154934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878853416	NA	P-0037451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	162	559	1	ENST00000257430.4:c.1205G>A	p.Arg402His	p.R402H	ENST00000257430	NM_000038.5	402	cGt/cAt	10/16	0.523391074215425	4	FACETS	0.881	0.814	0.951	0.588	0.542	0.634	CLONAL	2	TRUE	1	0.523391074215425	4		560	535	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037483-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	261	677	1	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	0.676498131413496	4	FACETS	0.955	0.901	1	0.955	0.901	1	CLONAL	2	FALSE	2	0.676498131413496	4		678	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764146326	NA	P-0037483-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	208	744	1	ENST00000269305.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000269305	NM_001126112.2	281	Gac/Aac	8/11	0.676498131413496	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	0	0.676498131413496	1		745	375	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205050	128205050	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037483-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	115	742	0	ENST00000341105.2:c.391G>A	p.Ala131Thr	p.A131T	ENST00000341105	NM_032638.4	131	Gct/Act	3/6	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.676498131413496	2		742	291	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226806	2226806	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037483-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	109	444	0	ENST00000398665.3:c.4286C>G	p.Ser1429Cys	p.S1429C	ENST00000398665	NM_032482.2	1429	tCt/tGt	27/28	0.144290580522415	4	FACETS	0.806	0.732	0.883	0.806	0.732	0.883	INDETERMINATE	2	FALSE	2	0.676498131413496	4		444	335	SUCCESS
APC	324	MSKCC	GRCh37	5	112175230	112175233	+	frameshift_variant	Frame_Shift_Del	DEL	TAGG	TAGG	-	novel	NA	P-0037483-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	103	266	0	ENST00000257430.4:c.3940_3943del	p.Arg1314GlnfsTer6	p.R1314Qfs*6	ENST00000257430	NM_000038.5	1313	acTAGG/ac	16/16	0.676153184319537	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	FALSE	0	0.676498131413496	2		266	151	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0037506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	351	1951	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.641188252757432	2	FACETS	0.931	0.894	0.967	0.931	0.894	0.967	CLONAL	2	TRUE	0	0.665082862615027	2		1952	567	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	50	347	1	ENST00000263967.3:c.333G>T	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaT	2/21	0.546674733895728	3	FACETS	0.419	0.356	0.489	0.21	0.178	0.245	SUBCLONAL	1	TRUE	1	0.665082862615027	3		348	478	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114791	108114791	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	118	452	0	ENST00000278616.4:c.608A>G	p.Asp203Gly	p.D203G	ENST00000278616	NM_000051.3	203	gAc/gGc	6/63	0.2348775289715	4	FACETS	0.798	0.721	0.88	0.2	0.18	0.22	INDETERMINATE	1	TRUE	0	0.665082862615027	4		452	740	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701885	43701885	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	46	237	0	ENST00000382044.4:c.5360C>T	p.Ala1787Val	p.A1787V	ENST00000382044	NM_001141980.1	1787	gCa/gTa	25/28	0.641188252757432	2	FACETS	0.466	0.394	0.544	0.233	0.197	0.272	SUBCLONAL	1	TRUE	0	0.665082862615027	2		237	297	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650563	48650563	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	47	655	0	ENST00000376670.3:c.533G>C	p.Ser178Thr	p.S178T	ENST00000376670	NM_002049.3	178	aGc/aCc	3/6	0.665082862615027	1	FACETS	0.286	0.242	0.334	0.286	0.242	0.334	SUBCLONAL	1	TRUE	0	0.665082862615027	1		655	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579406	7579406	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0037511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	545	551	0	ENST00000269305.4:c.281C>G	p.Ser94Ter	p.S94*	ENST00000269305	NM_001126112.2	94	tCa/tGa	4/11	0.583911575901469	2	FACETS	0.838	0.807	0.868	0.838	0.807	0.868	CLONAL	2	TRUE	0	0.594766214931012	2		551	1094	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664910	138664910	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	89	118	0	ENST00000330315.3:c.655C>G	p.Gln219Glu	p.Q219E	ENST00000330315	NM_023067.3	219	Cag/Gag	1/1	0.594766214931012	3	FACETS	0.415	0.367	0.467	0.208	0.183	0.234	SUBCLONAL	1	TRUE	1	0.594766214931012	3		118	935	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851423	156851423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2090	391	532	0	ENST00000524377.1:c.2380G>A	p.Val794Ile	p.V794I	ENST00000524377	NM_002529.3	794	Gtc/Atc	17/17	0.255160083342851	6	FACETS	1	0.989	1	0.193	0.182	0.205	INDETERMINATE	1	TRUE	0	0.594766214931012	6		532	2481	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939101	48939179	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCAGAGGTAATCTGAAAGGAAATTTAATAAAATATTAATGTTTTGAGACTGTGGAGGGAGGATAATTGTCTAACTTTC	TCCAGAGGTAATCTGAAAGGAAATTTAATAAAATATTAATGTTTTGAGACTGTGGAGGGAGGATAATTGTCTAACTTTC	-	novel	NA	P-0037511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	27	230	0	ENST00000267163.4:c.934_939+73del		p.X312_splice	ENST00000267163	NM_000321.2	312		9/27	0.594766214931012	1	FACETS	0.75	0.615	0.896	0.75	0.615	0.896	SUBCLONAL	1	TRUE	0	0.594766214931012	1		230	85	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	109	473	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.601244861023733	2		473	348	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027128	49027128	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs794727199	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	107	258	0	ENST00000267163.4:c.1696-1G>A		p.X566_splice	ENST00000267163	NM_000321.2	566			1	2	FACETS	0.937	0.848	1	0.937	0.848	1	CLONAL	1	TRUE	1	0.601244861023733	2		258	380	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662453	117662453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	152	417	0	ENST00000368508.3:c.4924G>A	p.Glu1642Lys	p.E1642K	ENST00000368508	NM_002944.2	1642	Gaa/Aaa	30/43	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.601244861023733	2		417	461	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390806	139390806	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767435492	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	231	561	0	ENST00000277541.6:c.7385C>T	p.Pro2462Leu	p.P2462L	ENST00000277541	NM_017617.3	2462	cCc/cTc	34/34	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.601244861023733	2		561	727	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037486	12037486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	110	299	0	ENST00000396373.4:c.1117C>T	p.Pro373Ser	p.P373S	ENST00000396373	NM_001987.4	373	Ccc/Tcc	6/8	1	2	FACETS	0.96	0.871	1	0.96	0.871	1	CLONAL	1	TRUE	1	0.601244861023733	2		299	381	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89825073	89825073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	193	357	0	ENST00000389301.3:c.2893C>T	p.Pro965Ser	p.P965S	ENST00000389301	NM_000135.2	965	Cct/Tct	30/43	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.601244861023733	2		357	542	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520017	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	205	526	0	ENST00000326873.7:c.647C>T	p.Ser216Phe	p.S216F	ENST00000326873	NM_000455.4	216	tCc/tTc	5/10	0.601244861023733	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.601244861023733	1		526	443	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129884	55129884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs574683248	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	215	521	1	ENST00000257290.5:c.418G>A	p.Val140Met	p.V140M	ENST00000257290	NM_006206.4	140	Gtg/Atg	4/23	1	2	FACETS	0.964	0.899	1	0.964	0.899	1	CLONAL	1	TRUE	1	0.601244861023733	2		522	742	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686868	117686868	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	108	247	0	ENST00000368508.3:c.2849C>T	p.Ser950Phe	p.S950F	ENST00000368508	NM_002944.2	950	tCt/tTt	19/43	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.601244861023733	2		247	329	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348912	11348912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765480579	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	102	228	0	ENST00000332029.2:c.424G>A	p.Glu142Lys	p.E142K	ENST00000332029	NM_003745.1	142	Gag/Aag	2/2	1	2	FACETS	0.842	0.759	0.929	0.842	0.759	0.929	CLONAL	1	TRUE	1	0.601244861023733	2		228	403	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118782	115118782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	198	400	0	ENST00000257566.3:c.559C>T	p.His187Tyr	p.H187Y	ENST00000257566	NM_016569.3	187	Cac/Tac	2/8	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.601244861023733	2		400	651	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514110	69514110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1264857484	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	199	466	0	ENST00000294312.3:c.571C>T	p.Pro191Ser	p.P191S	ENST00000294312	NM_005117.2	191	Ccc/Tcc	3/3	1	2	FACETS	0.994	0.925	1	0.994	0.925	1	CLONAL	1	TRUE	1	0.601244861023733	2		466	666	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467924	50467924	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	101	297	0	ENST00000331340.3:c.1159G>C	p.Glu387Gln	p.E387Q	ENST00000331340	NM_006060.4	387	Gag/Cag	8/8	1	2	FACETS	0.96	0.866	1	0.96	0.866	1	CLONAL	1	TRUE	1	0.601244861023733	2		297	350	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795364	42795364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	52	402	1	ENST00000575354.2:c.2444C>T	p.Ala815Val	p.A815V	ENST00000575354	NM_015125.3	815	gCc/gTc	10/20	0.354022254318636	2	FACETS	0.453	0.387	0.525	0.226	0.193	0.263	INDETERMINATE	1	TRUE	0	0.601244861023733	2		403	382	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964193	28964193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	133	292	0	ENST00000282397.4:c.1709G>A	p.Gly570Glu	p.G570E	ENST00000282397	NM_002019.4	570	gGa/gAa	13/30	1	2	FACETS	0.994	0.91	1	0.994	0.91	1	CLONAL	1	TRUE	1	0.601244861023733	2		292	445	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560043	29560043	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs868450405	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	224	208	0	ENST00000356175.3:c.3520C>T	p.Gln1174Ter	p.Q1174*	ENST00000356175	NM_000267.3	1174	Cag/Tag	27/57	0.601244861023733	2	FACETS	0.978	0.928	1	0.978	0.928	1	CLONAL	2	TRUE	0	0.601244861023733	2		208	381	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439656	140439656	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	109	279	0	ENST00000288602.6:c.2083G>C	p.Glu695Gln	p.E695Q	ENST00000288602	NM_004333.4	695	Gag/Cag	17/18	1	2	FACETS	0.98	0.888	1	0.98	0.888	1	CLONAL	1	TRUE	1	0.601244861023733	2		279	370	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864462	56864462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	214	467	0	ENST00000308159.5:c.950C>T	p.Pro317Leu	p.P317L	ENST00000308159	NM_014669.4	317	cCt/cTt	10/22	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.601244861023733	2		467	696	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533950	63533950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	90	225	0	ENST00000307078.5:c.1204G>A	p.Glu402Lys	p.E402K	ENST00000307078	NM_004655.3	402	Gaa/Aaa	6/11	0.601244861023733	2	FACETS	0.96	0.861	1	0.48	0.43	0.531	CLONAL	1	TRUE	0	0.601244861023733	2		225	312	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435092	56435092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	378	494	0	ENST00000407977.2:c.2045C>T	p.Pro682Leu	p.P682L	ENST00000407977		682	cCc/cTc	9/10	0.601244861023733	2	FACETS	0.973	0.935	1	0.973	0.935	1	CLONAL	2	TRUE	0	0.601244861023733	2		494	646	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93968002	93968002	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs766856886	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	123	301	0	ENST00000369303.4:c.1925G>A	p.Gly642Glu	p.G642E	ENST00000369303	NM_004440.3	642	gGa/gAa	11/17	1	2	FACETS	0.919	0.838	1	0.919	0.838	1	CLONAL	1	TRUE	1	0.601244861023733	2		301	445	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627698	37627698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	420	529	0	ENST00000447079.4:c.1613C>T	p.Pro538Leu	p.P538L	ENST00000447079	NM_015083.1	538	cCt/cTt	2/14	0.601244861023733	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.601244861023733	2		529	698	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267442	7267442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	366	432	0	ENST00000302850.5:c.566C>T	p.Thr189Ile	p.T189I	ENST00000302850	NM_000208.2	189	aCc/aTc	2/22	0.545769521349054	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.601244861023733	3		432	770	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246274	41246274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1260879887	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	394	499	0	ENST00000357654.3:c.1274C>T	p.Ser425Phe	p.S425F	ENST00000357654	NM_007294.3	425	tCt/tTt	10/23	0.601244861023733	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.601244861023733	2		499	654	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609036	43609036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	145	468	0	ENST00000355710.3:c.1792G>A	p.Glu598Lys	p.E598K	ENST00000355710	NM_020975.4	598	Gag/Aag	10/20	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.601244861023733	2		468	468	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054879	5054879	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	86	274	0	ENST00000381652.3:c.931G>T	p.Glu311Ter	p.E311*	ENST00000381652	NM_004972.3	311	Gaa/Taa	7/25	0.601244861023733	1	FACETS	0.893	0.805	0.984	0.893	0.805	0.984	CLONAL	1	TRUE	0	0.601244861023733	1		274	224	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535355	66535355	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	120	339	2	ENST00000273854.3:c.106C>T	p.Arg36Ter	p.R36*	ENST00000273854	NM_004439.5	36	Cga/Tga	1/18	1	2	FACETS	0.964	0.878	1	0.964	0.878	1	CLONAL	1	TRUE	1	0.601244861023733	2		341	414	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523340	9523340	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	140	360	0	ENST00000353224.5:c.1897G>A	p.Val633Met	p.V633M	ENST00000353224	NM_177990.2	633	Gtg/Atg	9/10	1	2	FACETS	0.889	0.814	0.966	0.889	0.814	0.966	CLONAL	1	TRUE	1	0.601244861023733	2		360	524	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213999	36213999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774513604	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	79	631	0	ENST00000222270.7:c.2825G>A	p.Gly942Glu	p.G942E	ENST00000222270	NM_014727.1	942	gGa/gAa	6/37	0.354022254318636	2	FACETS	0.319	0.28	0.362	0.16	0.14	0.181	INDETERMINATE	1	TRUE	0	0.601244861023733	2		631	823	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097809	27097809	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	127	279	0	ENST00000324856.7:c.3398C>T	p.Pro1133Leu	p.P1133L	ENST00000324856	NM_006015.4	1133	cCc/cTc	12/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.601244861023733	2		279	398	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805086	89805086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	191	416	0	ENST00000389301.3:c.4291G>A	p.Glu1431Lys	p.E1431K	ENST00000389301	NM_000135.2	1431	Gag/Aag	43/43	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.601244861023733	2		416	624	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11022897	11022897	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	308	641	0	ENST00000327064.4:c.596C>T	p.Ser199Leu	p.S199L	ENST00000327064	NM_199141.1	199	tCg/tTg	5/16	0.545769521349054	3	FACETS	1	0.974	1	0.53	0.499	0.562	CLONAL	1	TRUE	1	0.601244861023733	3		641	1257	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379775	17379775	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	81	658	0	ENST00000359435.4:c.160G>A	p.Glu54Lys	p.E54K	ENST00000359435	NM_001033549.1	54	Gag/Aag	2/9	0.545769521349054	3	FACETS	0.317	0.278	0.358	0.158	0.139	0.179	SUBCLONAL	1	TRUE	1	0.601244861023733	3		658	1107	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858295	9858295	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	164	361	0	ENST00000330684.3:c.3106G>A	p.Glu1036Lys	p.E1036K	ENST00000330684	NM_001134407.1	1036	Gag/Aag	13/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.601244861023733	2		361	482	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158595041	158595041	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1262652803	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	121	327	0	ENST00000263640.3:c.1306C>T	p.Pro436Ser	p.P436S	ENST00000263640	NM_001105.4	436	Ccc/Tcc	10/11	1	2	FACETS	0.862	0.784	0.943	0.862	0.784	0.943	CLONAL	1	TRUE	1	0.601244861023733	2		327	467	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264623	11264623	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	244	386	0	ENST00000361445.4:c.3939G>T	p.Met1313Ile	p.M1313I	ENST00000361445	NM_004958.3	1313	atG/atT	26/58	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.601244861023733	2		386	624	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256184	16256184	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	209	441	0	ENST00000375759.3:c.3449C>G	p.Ser1150Ter	p.S1150*	ENST00000375759	NM_015001.2	1150	tCa/tGa	11/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.601244861023733	2		441	621	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262177	16262177	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	64	211	0	ENST00000375759.3:c.9442C>T	p.Pro3148Ser	p.P3148S	ENST00000375759	NM_015001.2	3148	Cct/Tct	11/15	1	2	FACETS	0.963	0.846	1	0.963	0.846	1	CLONAL	1	TRUE	1	0.601244861023733	2		211	221	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885815	23885815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	197	306	0	ENST00000374561.5:c.103G>A	p.Glu35Lys	p.E35K	ENST00000374561	NM_002167.4	35	Gag/Aag	1/3	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.601244861023733	2		306	508	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058620	72058620	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	227	363	0	ENST00000357731.5:c.820C>T	p.Gln274Ter	p.Q274*	ENST00000357731	NM_173808.2	274	Caa/Taa	6/7	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.601244861023733	2		363	653	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724433	162724433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	148	418	0	ENST00000367921.3:c.205G>A	p.Asp69Asn	p.D69N	ENST00000367921	NM_006182.2	69	Gat/Aat	5/18	1	2	FACETS	0.967	0.889	1	0.967	0.889	1	CLONAL	1	TRUE	1	0.601244861023733	2		418	509	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100561	8100561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	193	480	0	ENST00000346208.3:c.535G>A	p.Asp179Asn	p.D179N	ENST00000346208		179	Gac/Aac	3/6	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.601244861023733	2		480	540	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77069999	77069999	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	80	408	0	ENST00000356341.3:c.541G>A	p.Asp181Asn	p.D181N	ENST00000356341	NM_002576.4	181	Gat/Aat	6/15	1	2	FACETS	0.368	0.323	0.415	0.368	0.323	0.415	SUBCLONAL	1	TRUE	1	0.601244861023733	2		408	724	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151884	108151884	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370602633	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	149	289	0	ENST00000278616.4:c.3565C>T	p.Leu1189Phe	p.L1189F	ENST00000278616	NM_000051.3	1189	Ctt/Ttt	24/63	0.601244861023733	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.601244861023733	1		289	339	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416189	416189	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	145	313	0	ENST00000399788.2:c.3997C>G	p.Arg1333Gly	p.R1333G	ENST00000399788	NM_001042603.1	1333	Cga/Gga	24/28	1	2	FACETS	0.908	0.833	0.986	0.908	0.833	0.986	CLONAL	1	TRUE	1	0.601244861023733	2		313	531	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037486	12037487	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	110	302	0	ENST00000396373.4:c.1117_1118delinsTT	p.Pro373Phe	p.P373F	ENST00000396373	NM_001987.4	373	CCc/TTc	6/8	1	2	FACETS	0.96	0.871	1	0.96	0.871	1	CLONAL	1	TRUE	1	0.601244861023733	2		302	381	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435736	49435736	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	202	567	0	ENST00000301067.7:c.6147G>T	p.Trp2049Cys	p.W2049C	ENST00000301067	NM_003482.3	2049	tgG/tgT	29/54	1	2	FACETS	0.982	0.915	1	0.982	0.915	1	CLONAL	1	TRUE	1	0.601244861023733	2		567	684	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438623	49438623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754087735	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	191	514	0	ENST00000301067.7:c.4867G>A	p.Glu1623Lys	p.E1623K	ENST00000301067	NM_003482.3	1623	Gag/Aag	19/54	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.601244861023733	2		514	632	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859405	57859405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	134	351	0	ENST00000228682.2:c.550G>A	p.Asp184Asn	p.D184N	ENST00000228682	NM_005269.2	184	Gac/Aac	6/12	1	2	FACETS	0.913	0.835	0.994	0.913	0.835	0.994	CLONAL	1	TRUE	1	0.601244861023733	2		351	488	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947630	+	splice_donor_variant	Splice_Site	DNP	GT	GT	AA	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	87	228	1	ENST00000267163.4:c.1215+1_1215+2delinsAA		p.X405_splice	ENST00000267163	NM_000321.2	405			1	2	FACETS	0.931	0.833	1	0.931	0.833	1	CLONAL	1	TRUE	1	0.601244861023733	2		229	311	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562562	95562563	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	98	272	1	ENST00000393063.1:c.4694_4695delinsTT	p.Ala1565Val	p.A1565V	ENST00000393063	NM_030621.3	1565	gCC/gTT	24/28	0.601244861023733	3	FACETS	0.793	0.709	0.881	0.396	0.354	0.441	SUBCLONAL	1	TRUE	1	0.601244861023733	3		273	535	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701095	43701095	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	115	305	0	ENST00000382044.4:c.5600G>A	p.Trp1867Ter	p.W1867*	ENST00000382044	NM_001141980.1	1867	tGg/tAg	26/28	1	2	FACETS	0.89	0.807	0.975	0.89	0.807	0.975	CLONAL	1	TRUE	1	0.601244861023733	2		305	430	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354561	91354561	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	114	347	0	ENST00000355112.3:c.4001G>C	p.Arg1334Thr	p.R1334T	ENST00000355112	NM_000057.2	1334	aGg/aCg	21/22	1	2	FACETS	0.731	0.661	0.804	0.731	0.661	0.804	SUBCLONAL	1	TRUE	1	0.601244861023733	2		347	519	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486238	99486238	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	191	452	0	ENST00000268035.6:c.3544G>A	p.Glu1182Lys	p.E1182K	ENST00000268035	NM_000875.3	1182	Gag/Aag	19/21	1	2	FACETS	0.988	0.918	1	0.988	0.918	1	CLONAL	1	TRUE	1	0.601244861023733	2		452	643	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993129	72993129	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	274	626	1	ENST00000268489.5:c.916C>T	p.Arg306Ter	p.R306*	ENST00000268489	NM_006885.3	306	Cga/Tga	2/10	1	2	FACETS	0.966	0.908	1	0.966	0.908	1	CLONAL	1	TRUE	1	0.601244861023733	2		627	944	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350444	89350444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1160170926	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	389	751	0	ENST00000301030.4:c.2506G>A	p.Asp836Asn	p.D836N	ENST00000301030	NM_001256183.1	836	Gat/Aat	9/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.601244861023733	2		751	1190	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577067	7577067	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	528	578	0	ENST00000269305.4:c.871A>T	p.Lys291Ter	p.K291*	ENST00000269305	NM_001126112.2	291	Aag/Tag	8/11	0.601244861023733	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.601244861023733	2		578	876	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883664	37883664	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	395	557	0	ENST00000269571.5:c.3276G>T	p.Met1092Ile	p.M1092I	ENST00000269571		1092	atG/atT	26/27	0.601244861023733	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.601244861023733	2		557	643	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56787254	56787254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	460	433	0	ENST00000337432.4:c.740C>T	p.Pro247Leu	p.P247L	ENST00000337432	NM_058216.2	247	cCa/cTa	5/9	0.601244861023733	2	FACETS	0.954	0.919	0.989	0.954	0.919	0.989	CLONAL	2	TRUE	0	0.601244861023733	2		433	802	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208019	5208019	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	193	531	0	ENST00000357368.4:c.5692G>C	p.Glu1898Gln	p.E1898Q	ENST00000357368	NM_002850.3	1898	Gag/Cag	37/38	0.545769521349054	3	FACETS	0.966	0.895	1	0.483	0.447	0.52	CLONAL	1	TRUE	1	0.601244861023733	3		531	864	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243989	5243989	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	210	460	0	ENST00000357368.4:c.1493C>T	p.Thr498Ile	p.T498I	ENST00000357368	NM_002850.3	498	aCc/aTc	11/38	0.545769521349054	3	FACETS	1	0.962	1	0.525	0.488	0.563	CLONAL	1	TRUE	1	0.601244861023733	3		460	865	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166232	7166233	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	221	480	0	ENST00000302850.5:c.1793_1794delinsTT	p.Thr598Ile	p.T598I	ENST00000302850	NM_000208.2	598	aCC/aTT	8/22	0.545769521349054	3	FACETS	1	0.94	1	0.505	0.47	0.541	CLONAL	1	TRUE	1	0.601244861023733	3		480	947	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265022	10265022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316701284	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	159	426	0	ENST00000340748.4:c.1918G>A	p.Asp640Asn	p.D640N	ENST00000340748		640	Gac/Aac	21/40	0.545769521349054	3	FACETS	0.9	0.827	0.977	0.45	0.413	0.489	CLONAL	1	TRUE	1	0.601244861023733	3		426	764	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097266	11097266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1210836682	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	144	491	0	ENST00000358026.2:c.757C>T	p.His253Tyr	p.H253Y	ENST00000358026	NM_001128849.1	253	Cat/Tat	4/36	0.545769521349054	3	FACETS	0.884	0.808	0.963	0.442	0.404	0.482	CLONAL	1	TRUE	1	0.601244861023733	3		491	705	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276302	15276302	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	236	552	0	ENST00000263388.2:c.5692G>T	p.Asp1898Tyr	p.D1898Y	ENST00000263388	NM_000435.2	1898	Gac/Tac	31/33	0.545769521349054	3	FACETS	1	0.94	1	0.503	0.47	0.538	CLONAL	1	TRUE	1	0.601244861023733	3		552	1014	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211616	36211616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	68	384	0	ENST00000222270.7:c.1367C>T	p.Ser456Phe	p.S456F	ENST00000222270	NM_014727.1	456	tCc/tTc	3/37	0.354022254318636	2	FACETS	0.553	0.483	0.628	0.277	0.241	0.314	INDETERMINATE	1	TRUE	0	0.601244861023733	2		384	409	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213342	36213342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	98	596	0	ENST00000222270.7:c.2539G>A	p.Glu847Lys	p.E847K	ENST00000222270	NM_014727.1	847	Gag/Aag	4/37	0.354022254318636	2	FACETS	0.35	0.311	0.391	0.175	0.155	0.196	INDETERMINATE	1	TRUE	0	0.601244861023733	2		596	932	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213977	36213977	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	85	640	0	ENST00000222270.7:c.2803G>T	p.Glu935Ter	p.E935*	ENST00000222270	NM_014727.1	935	Gaa/Taa	6/37	0.354022254318636	2	FACETS	0.337	0.297	0.379	0.168	0.148	0.19	INDETERMINATE	1	TRUE	0	0.601244861023733	2		640	840	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216639	36216639	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	95	432	0	ENST00000222270.7:c.3805G>C	p.Glu1269Gln	p.E1269Q	ENST00000222270	NM_014727.1	1269	Gag/Cag	13/37	0.354022254318636	2	FACETS	0.447	0.398	0.499	0.223	0.199	0.25	INDETERMINATE	1	TRUE	0	0.601244861023733	2		432	707	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795429	42795429	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1210506844	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	57	412	0	ENST00000575354.2:c.2509C>T	p.Gln837Ter	p.Q837*	ENST00000575354	NM_015125.3	837	Cag/Tag	10/20	0.354022254318636	2	FACETS	0.482	0.415	0.555	0.241	0.207	0.278	INDETERMINATE	1	TRUE	0	0.601244861023733	2		412	393	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868104	45868104	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	83	542	0	ENST00000391945.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000391945	NM_000400.3	196	Cga/Tga	7/23	0.354022254318636	2	FACETS	0.396	0.349	0.446	0.198	0.174	0.223	INDETERMINATE	1	TRUE	0	0.601244861023733	2		542	697	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871896	45871896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	72	410	0	ENST00000391945.4:c.352C>T	p.His118Tyr	p.H118Y	ENST00000391945	NM_000400.3	118	Cac/Tac	5/23	0.354022254318636	2	FACETS	0.399	0.349	0.454	0.2	0.174	0.227	INDETERMINATE	1	TRUE	0	0.601244861023733	2		410	600	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104653	209104653	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	149	426	0	ENST00000345146.2:c.925C>A	p.His309Asn	p.H309N	ENST00000345146	NM_005896.2	309	Cac/Aac	8/10	1	2	FACETS	0.921	0.847	0.999	0.921	0.847	0.999	CLONAL	1	TRUE	1	0.601244861023733	2		426	538	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368479	225368479	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	178	384	0	ENST00000264414.4:c.1267C>A	p.Gln423Lys	p.Q423K	ENST00000264414	NM_003590.4	423	Caa/Aaa	9/16	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.601244861023733	2		384	583	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101032	41101032	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	181	455	0	ENST00000373198.4:c.1324C>T	p.Gln442Ter	p.Q442*	ENST00000373198	NM_133170.3	442	Cag/Tag	8/32	NA	2	FACETS	0.959	0.889	1			1	INDETERMINATE	1	TRUE	NA	0.601244861023733	2		455	628	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268488	46268488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	106	316	0	ENST00000371998.3:c.2875C>T	p.Pro959Ser	p.P959S	ENST00000371998		959	Ccc/Tcc	15/23	1	2	FACETS	0.836	0.754	0.92	0.836	0.754	0.92	CLONAL	1	TRUE	1	0.601244861023733	2		316	422	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715660	30715660	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	130	249	0	ENST00000295754.5:c.1318G>C	p.Glu440Gln	p.E440Q	ENST00000295754	NM_003242.5	440	Gag/Cag	5/7	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.601244861023733	2		249	395	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277976	41277976	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	78	277	0	ENST00000349496.5:c.1940G>A	p.Arg647Lys	p.R647K	ENST00000349496	NM_001904.3	647	aGg/aAg	12/15	1	2	FACETS	0.782	0.692	0.876	0.782	0.692	0.876	SUBCLONAL	1	TRUE	1	0.601244861023733	2		277	332	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277990	41277990	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	79	285	0	ENST00000349496.5:c.1954G>A	p.Ala652Thr	p.A652T	ENST00000349496	NM_001904.3	652	Gcg/Acg	12/15	1	2	FACETS	0.784	0.696	0.878	0.784	0.696	0.878	SUBCLONAL	1	TRUE	1	0.601244861023733	2		285	335	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49724700	49724701	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	136	392	1	ENST00000449682.2:c.488_489delinsAA	p.Arg163Gln	p.R163Q	ENST00000449682	NM_020998.3	163	cGG/cAA	5/18	1	2	FACETS	0.912	0.835	0.992	0.912	0.835	0.992	CLONAL	1	TRUE	1	0.601244861023733	2		393	496	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801217	1801217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886042775	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	208	564	0	ENST00000260795.2:c.346C>T	p.Arg116Cys	p.R116C	ENST00000260795		116	Cgc/Tgc	2/17	1	2	FACETS	0.969	0.903	1	0.969	0.903	1	CLONAL	1	TRUE	1	0.601244861023733	2		564	714	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517756	187517756	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	76	215	0	ENST00000441802.2:c.12938del	p.Pro4313LeufsTer36	p.P4313Lfs*36	ENST00000441802	NM_005245.3	4313	cCt/ct	25/27	1	2	FACETS	0.984	0.874	1	0.984	0.874	1	CLONAL	1	TRUE	1	0.601244861023733	2		215	257	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630455	187630455	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	227	641	0	ENST00000441802.2:c.527C>T	p.Ala176Val	p.A176V	ENST00000441802	NM_005245.3	176	gCa/gTa	2/27	1	2	FACETS	0.906	0.846	0.968	0.906	0.846	0.968	CLONAL	1	TRUE	1	0.601244861023733	2		641	833	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80037345	80037345	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	95	220	0	ENST00000265081.6:c.1631A>G	p.Asn544Ser	p.N544S	ENST00000265081	NM_002439.4	544	aAt/aGt	11/24	1	2	FACETS	0.911	0.819	1	0.911	0.819	1	CLONAL	1	TRUE	1	0.601244861023733	2		220	347	SUCCESS
APC	324	MSKCC	GRCh37	5	112178640	112178640	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1489688452	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	136	337	0	ENST00000257430.4:c.7349C>T	p.Pro2450Leu	p.P2450L	ENST00000257430	NM_000038.5	2450	cCa/cTa	16/16	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.601244861023733	2		337	450	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672587	30672587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	189	557	0	ENST00000376406.3:c.4373C>T	p.Ser1458Phe	p.S1458F	ENST00000376406	NM_014641.2	1458	tCc/tTc	10/15	1	2	FACETS	0.943	0.875	1	0.943	0.875	1	CLONAL	1	TRUE	1	0.601244861023733	2		557	667	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120233	94120233	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	114	300	0	ENST00000369303.4:c.818G>A	p.Gly273Glu	p.G273E	ENST00000369303	NM_004440.3	273	gGa/gAa	3/17	1	2	FACETS	0.985	0.895	1	0.985	0.895	1	CLONAL	1	TRUE	1	0.601244861023733	2		300	385	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519551	137519551	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	136	319	0	ENST00000367739.4:c.1087C>T	p.Pro363Ser	p.P363S	ENST00000367739	NM_000416.2	363	Cct/Tct	7/7	1	2	FACETS	0.875	0.8	0.953	0.875	0.8	0.953	CLONAL	1	TRUE	1	0.601244861023733	2		319	517	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099176	157099176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264221880	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	98	205	0	ENST00000346085.5:c.113C>T	p.Ser38Phe	p.S38F	ENST00000346085	NM_020732.3	38	tCc/tTc	1/20	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.601244861023733	2		205	318	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845708	151845708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	188	468	0	ENST00000262189.6:c.13304G>A	p.Trp4435Ter	p.W4435*	ENST00000262189	NM_170606.2	4435	tGg/tAg	52/59	1	2	FACETS	0.997	0.926	1	0.997	0.926	1	CLONAL	1	TRUE	1	0.601244861023733	2		468	627	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851409	151851409	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	197	383	0	ENST00000262189.6:c.12082C>T	p.Pro4028Ser	p.P4028S	ENST00000262189	NM_170606.2	4028	Cct/Tct	47/59	1	2	FACETS	0.957	0.889	1	0.957	0.889	1	CLONAL	1	TRUE	1	0.601244861023733	2		383	685	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874533	151874533	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	159	348	0	ENST00000262189.6:c.8005G>T	p.Glu2669Ter	p.E2669*	ENST00000262189	NM_170606.2	2669	Gaa/Taa	38/59	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.601244861023733	2		348	525	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285944	38285944	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1169416110	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	153	345	0	ENST00000425967.3:c.467C>T	p.Pro156Leu	p.P156L	ENST00000425967	NM_001174067.1	156	cCc/cTc	5/19	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.601244861023733	2		345	463	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8338964	8338964	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	139	373	0	ENST00000356435.5:c.5337G>T	p.Met1779Ile	p.M1779I	ENST00000356435		1779	atG/atT	32/35	0.601244861023733	1	FACETS	0.836	0.769	0.904	0.836	0.769	0.904	CLONAL	1	TRUE	0	0.601244861023733	1		373	387	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500885	8500885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1193645875	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	190	451	0	ENST00000356435.5:c.1997C>T	p.Pro666Leu	p.P666L	ENST00000356435		666	cCt/cTt	13/35	0.601244861023733	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.601244861023733	1		451	409	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776126	135776126	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	143	352	0	ENST00000298552.3:c.2601G>C	p.Gln867His	p.Q867H	ENST00000298552	NM_001162426.1	867	caG/caC	20/23	1	2	FACETS	0.92	0.844	0.999	0.92	0.844	0.999	CLONAL	1	TRUE	1	0.601244861023733	2		352	517	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396202	139396203	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	149	458	0	ENST00000277541.6:c.5635_5636delinsTT	p.Pro1879Phe	p.P1879F	ENST00000277541	NM_017617.3	1879	CCt/TTt	30/34	1	2	FACETS	0.876	0.804	0.95	0.876	0.804	0.95	CLONAL	1	TRUE	1	0.601244861023733	2		458	566	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410335	63410365	+	frameshift_variant	Frame_Shift_Del	DEL	ACTGTCTCGGCTCCATTCTCCTTCTTCCTCC	ACTGTCTCGGCTCCATTCTCCTTCTTCCTCC	CTG	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	209	615	2	ENST00000330258.3:c.2802_2832delinsCAG	p.Glu934AspfsTer33	p.E934Dfs*33	ENST00000330258	NM_152424.3	934	gaGGAGGAAGAAGGAGAATGGAGCCGAGACAGT/gaCAG	2/2	NA	2	FACETS	0.904	0.842	0.968			1	INDETERMINATE	1	TRUE	NA	0.601244861023733	2		617	769	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343544	70343544	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	209	501	0	ENST00000374080.3:c.1718T>A	p.Phe573Tyr	p.F573Y	ENST00000374080		573	tTt/tAt	12/45	0.601244861023733	1	FACETS	0.988	0.927	1	0.988	0.927	1	CLONAL	1	TRUE	0	0.601244861023733	1		501	492	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039402	49039402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1158706854	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	184	503	0	ENST00000267163.4:c.2387C>T	p.Pro796Leu	p.P796L	ENST00000267163	NM_000321.2	796	cCc/cTc	23/27	1	2	FACETS	0.836	0.774	0.9	0.836	0.774	0.9	CLONAL	1	TRUE	1	0.601244861023733	2		503	732	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166233	7166233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772521737	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	221	472	0	ENST00000302850.5:c.1793C>T	p.Thr598Ile	p.T598I	ENST00000302850	NM_000208.2	598	aCc/aTc	8/22	0.545769521349054	3	FACETS	1	0.943	1	0.507	0.472	0.543	CLONAL	1	TRUE	1	0.601244861023733	3		472	943	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039401	49039401	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs869264218	NA	P-0037515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	183	500	0	ENST00000267163.4:c.2388del	p.Leu797TyrfsTer13	p.L797Yfs*13	ENST00000267163	NM_000321.2	796	Ccc/cc	23/27	1	2	FACETS	0.825	0.763	0.889	0.825	0.763	0.889	CLONAL	1	TRUE	1	0.601244861023733	2		500	738	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	146	326	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.997	0.923	1	0.997	0.923	1	CLONAL	1	TRUE	1	0.837005548061242	2		326	350	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0037523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	167	265	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.837005548061242	1	FACETS	0.768	0.721	0.815	0.768	0.721	0.815	SUBCLONAL	1	TRUE	0	0.837005548061242	1		265	302	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220274	55220274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14163	17072	575	1	ENST00000275493.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000275493	NM_005228.3	222	Cgc/Tgc	6/28	0.837005548061242	41	FACETS	0.984	0.977	0.99			1	CLONAL	23	TRUE	NA	0.837005548061242	41		576	31235	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0037523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23999	7137	588	2	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.837005548061242	41	FACETS	1	0.998	1			1	CLONAL	9	TRUE	NA	0.837005548061242	41		590	31136	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117753	70117753	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	322	514	0	ENST00000245479.2:c.221G>C	p.Arg74Pro	p.R74P	ENST00000245479	NM_000346.3	74	cGc/cCc	1/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.837005548061242	2		514	745	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0037581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	96	676	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.244109782638446	1	FACETS	0.906	0.807	1	0.906	0.807	1	CLONAL	1	FALSE	0	0.244109782638446	1		676	762	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	131	598	4	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.774	0.702	0.849	0.774	0.702	0.849	SUBCLONAL	1	TRUE	1	0.416101523815935	2		602	814	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0037611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	82	423	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.751	0.664	0.844	0.751	0.664	0.844	SUBCLONAL	1	TRUE	1	0.416101523815935	2		423	525	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	100	676	0	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.582	0.519	0.649	0.582	0.519	0.649	SUBCLONAL	1	TRUE	1	0.416101523815935	2		676	826	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214058	36214058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1385766471	NA	P-0037611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	159	789	0	ENST00000222270.7:c.2884C>T	p.Arg962Cys	p.R962C	ENST00000222270	NM_014727.1	962	Cgc/Tgc	6/37	1	2	FACETS	0.759	0.695	0.826	0.759	0.695	0.826	SUBCLONAL	1	TRUE	1	0.416101523815935	2		789	1007	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443612	29443612	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	57	623	0	ENST00000389048.3:c.3605del	p.Gly1202GlufsTer56	p.G1202Efs*56	ENST00000389048	NM_004304.4	1202	gGa/ga	23/29	1	2	FACETS	0.278	0.237	0.322	0.278	0.237	0.322	SUBCLONAL	1	TRUE	1	0.416101523815935	2		623	987	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589605	67589616	+	inframe_deletion	In_Frame_Del	DEL	TCAAGAAAAAAG	TCAAGAAAAAAG	-	novel	NA	P-0037611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	59	252	0	ENST00000274335.5:c.1370_1381del	p.Gln457_Ser460del	p.Q457_S460del	ENST00000274335		456	ttTCAAGAAAAAAGt/ttt	10/15	1	2	FACETS	0.933	0.809	1	0.933	0.809	1	CLONAL	1	TRUE	1	0.416101523815935	2		252	304	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942053	71942053	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	109	637	2	ENST00000298229.2:c.1322del	p.Asn441ThrfsTer2	p.N441Tfs*2	ENST00000298229	NM_001567.3	439	ccA/cc	12/28	1	2	FACETS	0.596	0.535	0.661	0.596	0.535	0.661	SUBCLONAL	1	TRUE	1	0.416101523815935	2		639	879	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316397	14316397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782457908	NA	P-0037611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	31	474	0	ENST00000256196.4:c.208G>A	p.Ala70Thr	p.A70T	ENST00000256196		70	Gca/Aca	3/6	1	2	FACETS	0.336	0.272	0.41	0.336	0.272	0.41	SUBCLONAL	1	TRUE	1	0.416101523815935	2		474	443	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107184	11107186	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs1484395538	NA	P-0037611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	140	542	0	ENST00000358026.2:c.1778_1780del	p.Glu593del	p.E593del	ENST00000358026	NM_001128849.1	592	gcAGAa/gca	11/36	1	2	FACETS	0.758	0.69	0.829	0.758	0.69	0.829	SUBCLONAL	1	TRUE	1	0.416101523815935	2		542	888	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087939	27087939	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	161	636	0	ENST00000324856.7:c.2227del	p.Gln743AsnfsTer90	p.Q743Nfs*90	ENST00000324856	NM_006015.4	742	aaC/aa	6/20	1	2	FACETS	0.909	0.835	0.987	0.909	0.835	0.987	CLONAL	1	TRUE	1	0.416101523815935	2		636	851	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720674	89720674	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs886044679	NA	P-0037611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	108	224	0	ENST00000371953.3:c.827del	p.Asn276IlefsTer15	p.N276Ifs*15	ENST00000371953	NM_000314.4	275	gtA/gt	8/9	0.416101523815935	1	FACETS	0.8	0.731	0.87	1	0.987	1	SUBCLONAL	2	TRUE	0	0.416101523815935	1		224	257	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944169	71944169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148045527	NA	P-0037611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	144	564	0	ENST00000298229.2:c.2002C>T	p.Arg668Trp	p.R668W	ENST00000298229	NM_001567.3	668	Cgg/Tgg	17/28	1	2	FACETS	0.971	0.887	1	0.971	0.887	1	CLONAL	1	TRUE	1	0.416101523815935	2		564	713	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828809	26828809	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	72	238	0	ENST00000381527.3:c.31A>C	p.Ser11Arg	p.S11R	ENST00000381527	NM_001260.1	11	Agc/Cgc	1/13	1	2	FACETS	0.759	0.665	0.859	0.759	0.665	0.859	SUBCLONAL	1	TRUE	1	0.416101523815935	2		238	456	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26970492	26970492	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0037611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	17	231	0	ENST00000381527.3:c.860+1G>A		p.X287_splice	ENST00000381527	NM_001260.1	287			1	2	FACETS	0.399	0.298	0.517	0.399	0.298	0.517	SUBCLONAL	1	TRUE	1	0.416101523815935	2		231	205	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654720	67654720	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	113	448	0	ENST00000264010.4:c.1207G>A	p.Gly403Arg	p.G403R	ENST00000264010	NM_006565.3	403	Ggg/Agg	6/12	1	2	FACETS	0.93	0.839	1	0.93	0.839	1	CLONAL	1	TRUE	1	0.416101523815935	2		448	584	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625599	1625599	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1281758564	NA	P-0037611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	154	633	3	ENST00000344749.5:c.475C>T	p.Arg159Trp	p.R159W	ENST00000344749	NM_001136139.2	159	Cgg/Tgg	7/19	1	2	FACETS	0.846	0.774	0.921	0.846	0.774	0.921	CLONAL	1	TRUE	1	0.416101523815935	2		636	875	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628361	187628361	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1203002890	NA	P-0037611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	141	760	1	ENST00000441802.2:c.2621C>T	p.Thr874Met	p.T874M	ENST00000441802	NM_005245.3	874	aCg/aTg	2/27	1	2	FACETS	0.584	0.531	0.64	0.584	0.531	0.64	SUBCLONAL	1	TRUE	1	0.416101523815935	2		761	1160	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588086	67588086	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0037611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	56	250	0	ENST00000274335.5:c.917-1G>A		p.X306_splice	ENST00000274335		306			1	2	FACETS	0.931	0.804	1	0.931	0.804	1	CLONAL	1	TRUE	1	0.416101523815935	2		250	289	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189031	38189031	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	95	718	0	ENST00000317025.8:c.983G>C	p.Arg328Pro	p.R328P	ENST00000317025	NM_023034.1	328	cGa/cCa	5/24	0.402560820912235	3	FACETS	0.592	0.526	0.662	0.296	0.263	0.331	SUBCLONAL	1	TRUE	1	0.416101523815935	3		718	932	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499808	8499808	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	145	537	0	ENST00000356435.5:c.2161G>A	p.Glu721Lys	p.E721K	ENST00000356435		721	Gag/Aag	14/35	0.393860747285307	2	FACETS	0.926	0.846	1	0.463	0.423	0.505	CLONAL	1	TRUE	0	0.416101523815935	2		537	753	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	56	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.118923215296549	5	FACETS	1	0.938	1			1	INDETERMINATE	2	TRUE	NA	0.329200517117812	5		426	222	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225552	133225552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs535074635	NA	P-0037613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	72	449	0	ENST00000320574.5:c.4112G>A	p.Arg1371Gln	p.R1371Q	ENST00000320574	NM_006231.2	1371	cGa/cAa	32/49	0.329200517117812	4	FACETS	1	0.939	1	1	0.939	1	CLONAL	3	TRUE	1	0.329200517117812	4		449	180	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099070	27099070	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	35	382	0	ENST00000324856.7:c.3486del	p.Pro1163GlnfsTer17	p.P1163Qfs*17	ENST00000324856	NM_006015.4	1162	ccA/cc	13/20	0.329200517117812	5	FACETS	1	0.95	1	0.499	0.413	0.595	CLONAL	1	TRUE	2	0.329200517117812	5		382	212	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604661	48604663	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0037613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	21	267	0	ENST00000342988.3:c.1484_1486del	p.Leu495del	p.L495del	ENST00000342988	NM_005359.5	495	CTT/-	12/12	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.329200517117812	2		267	93	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839732	27839732	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1452025102	NA	P-0037613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	29	379	2	ENST00000328488.2:c.362T>C	p.Met121Thr	p.M121T	ENST00000328488	NM_003533.2	121	aTg/aCg	1/1	0.23934548896348	5	FACETS	1	0.901	1	0.399	0.322	0.485	CLONAL	1	TRUE	2	0.329200517117812	5		381	220	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212161	36212161	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1296215893	NA	P-0037617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	224	375	0	ENST00000222270.7:c.1912G>C	p.Ala638Pro	p.A638P	ENST00000222270	NM_014727.1	638	Gcc/Ccc	3/37	0.493848902444936	3	FACETS	1	0.991	1	0.69	0.644	0.737	CLONAL	1	TRUE	1	0.493848902444936	3		375	820	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509045	106509045	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	41	363	0	ENST00000359195.3:c.1039G>T	p.Glu347Ter	p.E347*	ENST00000359195	NM_002649.2	347	Gag/Tag	2/11	0.493848902444936	3	FACETS	0.34	0.282	0.404	0.17	0.141	0.202	SUBCLONAL	1	TRUE	1	0.493848902444936	3		363	609	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780068	NA	P-0037637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	148	813	1	ENST00000269305.4:c.472C>T	p.Arg158Cys	p.R158C	ENST00000269305	NM_001126112.2	158	Cgc/Tgc	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		814	251	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3824659	3824659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775229806	NA	P-0037637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	69	642	1	ENST00000262367.5:c.2194G>A	p.Val732Ile	p.V732I	ENST00000262367	NM_004380.2	732	Gtc/Atc	12/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		643	399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578447	+	frameshift_variant	Frame_Shift_Del	DEL	GCTTGTAGATG	GCTTGTAGATG	-	novel	NA	P-0037637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	135	767	0	ENST00000269305.4:c.483_493del	p.Ile162ValfsTer15	p.I162Vfs*15	ENST00000269305	NM_001126112.2	161	gcCATCTACAAGCag/gcag	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		767	238	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448433	49448433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1301033353	NA	P-0037637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	114	658	0	ENST00000301067.7:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000301067	NM_003482.3	93	cGg/cAg	3/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		658	393	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748907	41748907	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	46	559	0	ENST00000301178.4:c.1432G>T	p.Glu478Ter	p.E478*	ENST00000301178	NM_021913.4	478	Gag/Tag	11/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		559	211	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750473	41750473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	29	638	0	ENST00000226382.2:c.155G>A	p.Gly52Glu	p.G52E	ENST00000226382	NM_003924.3	52	gGg/gAg	1/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		638	149	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0037668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	66	751	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.291484673418072	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.291484673418072	1		751	349	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446341	29446342	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0037668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	72	601	1	ENST00000389048.3:c.3225_3226delinsAA	p.Ser1075_Pro1076delinsArgThr	p.S1075_P1076delinsRT	ENST00000389048	NM_004304.4	1075	agCCct/agAAct	20/29	0.291484673418072	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.291484673418072	1		602	364	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038275	30038275	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0037669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	132	277	0	ENST00000338641.4:c.447+1G>A		p.X149_splice	ENST00000338641	NM_000268.3	149			0.766465620052294	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.769663574752302	1		277	190	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189834	11189834	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	155	363	0	ENST00000361445.4:c.5675T>C	p.Ile1892Thr	p.I1892T	ENST00000361445	NM_004958.3	1892	aTc/aCc	40/58	0.766465620052294	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.769663574752302	1		363	244	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724465	112724465	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	25	431	1	ENST00000369452.4:c.349T>C	p.Ser117Pro	p.S117P	ENST00000369452	NM_007373.3	117	Tca/Cca	2/9	1	2	FACETS	0.154	0.12	0.192	0.154	0.12	0.192	SUBCLONAL	1	TRUE	1	0.769663574752302	2		432	423	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352570	89352570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	167	357	1	ENST00000301030.4:c.769G>A	p.Gly257Arg	p.G257R	ENST00000301030	NM_001256183.1	257	Gga/Aga	8/13	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.769663574752302	2		358	427	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175890	24175890	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	127	251	0	ENST00000263121.7:c.1118G>A	p.Arg373Lys	p.R373K	ENST00000263121	NM_003073.3	373	aGg/aAg	8/9	0.766465620052294	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.769663574752302	1		251	195	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0037671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	48	278	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.19	2		278	459	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77070006	77070006	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs866570863	NA	P-0037671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	40	336	0	ENST00000356341.3:c.534T>G	p.Asp178Glu	p.D178E	ENST00000356341	NM_002576.4	178	gaT/gaG	6/15	1	2	FACETS	0.628	0.521	0.749	0.628	0.521	0.749	SUBCLONAL	1	TRUE	1	0.19	2		336	670	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913255	NA	P-0037671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	98	465	0	ENST00000369535.4:c.183A>C	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caC	3/7	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.19	2		465	893	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692892	89692892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554898129	NA	P-0037671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	46	231	0	ENST00000371953.3:c.376G>A	p.Ala126Thr	p.A126T	ENST00000371953	NM_000314.4	126	Gct/Act	5/9	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.19	2		231	378	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711876	89711876	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs786204863	NA	P-0037671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	30	283	0	ENST00000371953.3:c.494G>T	p.Gly165Val	p.G165V	ENST00000371953	NM_000314.4	165	gGa/gTa	6/9	1	2	FACETS	0.835	0.673	1	0.835	0.673	1	CLONAL	1	TRUE	1	0.19	2		283	378	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223229	36223229	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749130618	NA	P-0037671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	78	701	0	ENST00000222270.7:c.5779C>T	p.Arg1927Trp	p.R1927W	ENST00000222270	NM_014727.1	1927	Cgg/Tgg	28/37	1	2	FACETS	0.752	0.659	0.853	0.752	0.659	0.853	SUBCLONAL	1	TRUE	1	0.19	2		701	1092	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416692	29416692	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	30	339	0	ENST00000389048.3:c.4261del	p.Val1421PhefsTer56	p.V1421Ffs*56	ENST00000389048	NM_004304.4	1421	Gtt/tt	29/29	1	2	FACETS	0.734	0.591	0.897	0.734	0.591	0.897	SUBCLONAL	1	TRUE	1	0.19	2		339	430	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039207	49039208	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0037671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	42	332	0	ENST00000267163.4:c.2288_2289del	p.Arg763ThrfsTer31	p.R763Tfs*31	ENST00000267163	NM_000321.2	762	cAG/c	22/27	1	2	FACETS	0.813	0.678	0.963	0.813	0.678	0.963	CLONAL	1	TRUE	1	0.19	2		332	544	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221355	2221355	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	43	461	0	ENST00000326181.6:c.441+1del		p.G147fs	ENST00000326181	NM_032271.2	147	Ggg/gg	6/21	1	2	FACETS	0.662	0.552	0.784	0.662	0.552	0.784	SUBCLONAL	1	TRUE	1	0.19	2		461	684	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679334	29679334	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	24	249	0	ENST00000356175.3:c.7454C>T	p.Ala2485Val	p.A2485V	ENST00000356175	NM_000267.3	2485	gCc/gTc	50/57	1	2	FACETS	0.555	0.434	0.695	0.555	0.434	0.695	SUBCLONAL	1	TRUE	1	0.19	2		249	455	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10259591	10259591	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs746143694	NA	P-0037671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	61	496	0	ENST00000340748.4:c.2641A>G	p.Lys881Glu	p.K881E	ENST00000340748		881	Aaa/Gaa	26/40	1	2	FACETS	0.831	0.715	0.957	0.831	0.715	0.957	CLONAL	1	TRUE	1	0.19	2		496	773	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222286	39222286	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	69	367	0	ENST00000402219.2:c.3324T>G	p.Asp1108Glu	p.D1108E	ENST00000402219	NM_005633.3	1108	gaT/gaG	20/23	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.19	2		367	637	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264272	46264272	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	35	224	0	ENST00000371998.3:c.1319C>G	p.Ala440Gly	p.A440G	ENST00000371998		440	gCt/gGt	11/23	1	2	FACETS	0.957	0.785	1	0.957	0.785	1	CLONAL	1	TRUE	1	0.19	2		224	385	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433552	138433552	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	26	219	0	ENST00000289153.2:c.1060A>G	p.Arg354Gly	p.R354G	ENST00000289153	NM_006219.2	354	Agg/Ggg	7/22	1	2	FACETS	1	0.81	1	1	0.81	1	CLONAL	1	TRUE	1	0.19	2		219	268	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591031	67591033	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs1370788402	NA	P-0037671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	18	135	0	ENST00000274335.5:c.1630_1632del	p.Arg544del	p.R544del	ENST00000274335		542	AGA/-	12/15	1	2	FACETS	0.89	0.672	1	0.89	0.672	1	CLONAL	1	TRUE	1	0.19	2		135	213	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940520	31940520	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1292507674	NA	P-0037671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	47	424	0	ENST00000375333.2:c.553G>A	p.Ala185Thr	p.A185T	ENST00000375333	NM_032454.1	185	Gcc/Acc	3/8	1	2	FACETS	0.638	0.536	0.75	0.638	0.536	0.75	SUBCLONAL	1	TRUE	1	0.19	2		424	776	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859267	151859267	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	53	335	0	ENST00000262189.6:c.11395T>C	p.Cys3799Arg	p.C3799R	ENST00000262189	NM_170606.2	3799	Tgt/Cgt	43/59	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.19	2		335	500	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058542	69058542	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	34	463	1	ENST00000288368.4:c.4190del	p.Asn1397MetfsTer16	p.N1397Mfs*16	ENST00000288368	NM_024870.2	1396	Aaa/aa	34/40	1	2	FACETS	0.555	0.452	0.671	0.555	0.452	0.671	SUBCLONAL	1	TRUE	1	0.19	2		464	645	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39935711	39935711	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1435258487	NA	P-0037671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	33	317	0	ENST00000378444.4:c.161A>G	p.Asn54Ser	p.N54S	ENST00000378444	NM_001123385.1	54	aAc/aGc	3/15	1	2	FACETS	0.685	0.557	0.83	0.685	0.557	0.83	SUBCLONAL	1	TRUE	1	0.19	2		317	507	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411207	63411207	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	57	481	0	ENST00000330258.3:c.1960T>G	p.Tyr654Asp	p.Y654D	ENST00000330258	NM_152424.3	654	Tat/Gat	2/2	1	2	FACETS	0.875	0.749	1	0.875	0.749	1	CLONAL	1	TRUE	1	0.19	2		481	686	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939495	76939495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557142053	NA	P-0037671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	61	465	0	ENST00000373344.5:c.1253G>A	p.Arg418Gln	p.R418Q	ENST00000373344	NM_000489.3	418	cGa/cAa	9/35	1	2	FACETS	0.963	0.83	1	0.963	0.83	1	CLONAL	1	TRUE	1	0.19	2		465	667	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0037676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	272	413	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.237095198813395	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.27	2		413	909	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30061032	30061032	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	88	317	0	ENST00000338641.4:c.866del	p.Lys289SerfsTer7	p.K289Sfs*7	ENST00000338641	NM_000268.3	288	tcA/tc	9/16	0.29484598528988	1	FACETS	0.888	0.787	0.995	0.888	0.787	0.995	CLONAL	1	TRUE	0	0.27	1		317	635	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613405	100613405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs918787974	NA	P-0037676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	80	708	0	ENST00000308731.7:c.995G>A	p.Arg332His	p.R332H	ENST00000308731	NM_000061.2	332	cGt/cAt	12/19	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.27	2		708	568	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227911	123227911	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	48	242	0	ENST00000218089.9:c.3622G>A	p.Val1208Met	p.V1208M	ENST00000218089	NM_001042749.1	1208	Gtg/Atg	33/35	1	2	FACETS	0.869	0.736	1	0.869	0.736	1	CLONAL	1	TRUE	1	0.27	2		242	409	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	105	143	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	0.345178940711032	3	FACETS	0.933	0.851	1	0.933	0.851	1	CLONAL	3	TRUE	0	0.345178940711032	3		143	255	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578499	7578499	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs786203071	NA	P-0037682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	139	581	0	ENST00000269305.4:c.431A>C	p.Gln144Pro	p.Q144P	ENST00000269305	NM_001126112.2	144	cAg/cCg	5/11	0.345178940711032	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.345178940711032	1		581	636	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107749	30107749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760459161	NA	P-0037682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	65	399	0	ENST00000331968.5:c.931C>T	p.Arg311Cys	p.R311C	ENST00000331968	NM_002742.2	311	Cgt/Tgt	6/18	1	2	FACETS	0.765	0.665	0.874	0.765	0.665	0.874	SUBCLONAL	1	TRUE	1	0.345178940711032	2		399	492	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913579	32913579	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1135401904	NA	P-0037682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	191	253	0	ENST00000380152.3:c.5087G>T	p.Gly1696Val	p.G1696V	ENST00000380152		1696	gGa/gTa	11/27	0.345178940711032	5	FACETS	0.907	0.848	0.967	0.907	0.848	0.967	CLONAL	4	TRUE	1	0.345178940711032	5		253	463	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188197	10188197	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0037695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	33	498	0	ENST00000256474.2:c.341-1G>T		p.X114_splice	ENST00000256474	NM_000551.3	114			1	2	FACETS	0.764	0.622	0.926	0.764	0.622	0.926	CLONAL	1	TRUE	1	0.17	2		498	508	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610695	52610695	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	18	380	3	ENST00000394830.3:c.3478C>T	p.Arg1160Ter	p.R1160*	ENST00000394830	NM_018313.4	1160	Cga/Tga	23/30	1	2	FACETS	0.66	0.496	0.853	0.66	0.496	0.853	SUBCLONAL	1	TRUE	1	0.17	2		383	321	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794816	242794816	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	50	608	0	ENST00000334409.5:c.393G>T	p.Lys131Asn	p.K131N	ENST00000334409	NM_005018.2	131	aaG/aaT	2/5	0.3	2	FACETS	1	0.954	1			1	CLONAL	1	TRUE	NA	0.17	2		608	439	SUCCESS
APC	324	MSKCC	GRCh37	5	112154742	112154742	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	44	472	0	ENST00000257430.4:c.1013C>G	p.Ser338Cys	p.S338C	ENST00000257430	NM_000038.5	338	tCt/tGt	10/16	0.125762381670864	3	FACETS	1	0.903	1	0.555	0.465	0.654	CLONAL	1	TRUE	1	0.17	3		472	506	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678138	58678138	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	400	653	0	ENST00000305921.3:c.363G>A	p.Trp121Ter	p.W121*	ENST00000305921	NM_003620.3	121	tgG/tgA	1/6	0.706299201518109	3	FACETS	0.985	0.935	1	0.493	0.467	0.518	CLONAL	1	TRUE	1	0.706299201518109	3		653	1556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0037701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	222	797	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.618637440234796	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.623763592768207	1		799	476	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521487	8521487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758577045	NA	P-0037701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	219	675	0	ENST00000356435.5:c.751G>A	p.Gly251Arg	p.G251R	ENST00000356435		251	Gga/Aga	9/35	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.623763592768207	2		675	646	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40371842	40371842	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	236	936	0	ENST00000293328.3:c.569C>T	p.Ala190Val	p.A190V	ENST00000293328	NM_012448.3	190	gCc/gTc	6/19	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.623763592768207	2		936	732	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688815	47688815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	144	408	0	ENST00000347630.2:c.485G>A	p.Ser162Asn	p.S162N	ENST00000347630	NM_001007230.1	162	aGt/aAt	7/11	1	2	FACETS	0.987	0.907	1	0.987	0.907	1	CLONAL	1	TRUE	1	0.623763592768207	2		408	468	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953735	48953735	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0037702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	226	224	0	ENST00000267163.4:c.1338C>G	p.Tyr446Ter	p.Y446*	ENST00000267163	NM_000321.2	446	taC/taG	14/27	0.728240682899379	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.749518231481302	2		224	301	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057520008	NA	P-0037702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	1176	664	0	ENST00000269305.4:c.613T>A	p.Tyr205Asn	p.Y205N	ENST00000269305	NM_001126112.2	205	Tat/Aat	6/11	NA	2	FACETS	1	0.998	1			1	INDETERMINATE	2	TRUE	NA	0.749518231481302	2		664	1409	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456497	89456497	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs762801053	NA	P-0037702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	255	407	0	ENST00000336596.2:c.1673T>C	p.Val558Ala	p.V558A	ENST00000336596	NM_005233.5	558	gTt/gCt	8/17	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.749518231481302	2		407	626	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0037744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	240	797	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.601582128488363	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.601582128488363	1		799	486	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245380	153245380	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	165	594	0	ENST00000281708.4:c.1811A>C	p.Lys604Thr	p.K604T	ENST00000281708	NM_033632.3	604	aAa/aCa	11/12	0.104542555313643	3	FACETS	1	0.979	1	0.587	0.541	0.634	INDETERMINATE	1	TRUE	1	0.601582128488363	3		594	608	SUCCESS
APC	324	MSKCC	GRCh37	5	112175162	112175162	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561588104	NA	P-0037744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	54	245	0	ENST00000257430.4:c.3871C>T	p.Gln1291Ter	p.Q1291*	ENST00000257430	NM_000038.5	1291	Cag/Tag	16/16	1	2	FACETS	0.911	0.79	1	0.911	0.79	1	CLONAL	1	TRUE	1	0.601582128488363	2		245	197	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0037744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	140	449	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.601582128488363	2		449	456	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251901	153251901	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	118	416	0	ENST00000281708.4:c.1105G>T	p.Glu369Ter	p.E369*	ENST00000281708	NM_033632.3	369	Gaa/Taa	7/12	0.104542555313643	3	FACETS	1	0.983	1	0.68	0.62	0.743	INDETERMINATE	1	TRUE	1	0.601582128488363	3		416	375	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978444	2978444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	200	695	0	ENST00000396946.4:c.886G>A	p.Asp296Asn	p.D296N	ENST00000396946	NM_032415.4	296	Gac/Aac	7/25	1	2	FACETS	0.873	0.811	0.936	0.873	0.811	0.936	CLONAL	1	TRUE	1	0.601582128488363	2		695	762	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0037748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	105	442	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.268379556335763	2		442	762	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485837	57485837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	118	519	0	ENST00000371085.3:c.1138C>T	p.Arg380Cys	p.R380C	ENST00000371085	NM_000516.4	380	Cgt/Tgt	13/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.268379556335763	2		519	768	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855903	68855903	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0037748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	77	420	0	ENST00000261769.5:c.1712-1G>A		p.X571_splice	ENST00000261769	NM_004360.3	571			0.268379556335763	1	FACETS	0.998	0.878	1	0.998	0.878	1	CLONAL	1	TRUE	0	0.268379556335763	1		420	498	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2185853	2185853	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0037748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	65	701	0	ENST00000398665.3:c.126-1G>C		p.X42_splice	ENST00000398665	NM_032482.2	42			1	2	FACETS	0.429	0.371	0.494	0.429	0.371	0.494	SUBCLONAL	1	TRUE	1	0.268379556335763	2		701	1128	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577093	7577100	+	frameshift_variant	Frame_Shift_Del	DEL	CGGTCTCT	CGGTCTCT	-	novel	NA	P-0037768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	372	853	1	ENST00000269305.4:c.838_845del	p.Arg280AlafsTer23	p.R280Afs*23	ENST00000269305	NM_001126112.2	280	AGAGACCGg/g	8/11	0.605686195181439	1	FACETS	0.882	0.84	0.924	0.882	0.84	0.924	CLONAL	1	TRUE	0	0.627265529288183	1		854	923	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581154	48581154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	198	351	0	ENST00000342988.3:c.458C>T	p.Pro153Leu	p.P153L	ENST00000342988	NM_005359.5	153	cCa/cTa	5/12	1	2	FACETS	0.959	0.893	1	0.959	0.893	1	CLONAL	1	TRUE	1	0.627265529288183	2		351	658	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985352	60985352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	427	836	1	ENST00000333681.4:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000333681		183	cGg/cAg	2/3	1	2	FACETS	0.917	0.873	0.962	0.917	0.873	0.962	CLONAL	1	TRUE	1	0.627265529288183	2		837	1484	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814142	76814142	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	117	302	0	ENST00000373344.5:c.6502C>T	p.Gln2168Ter	p.Q2168*	ENST00000373344	NM_000489.3	2168	Cag/Tag	29/35	0.627265529288183	1	FACETS	0.895	0.821	0.971	0.895	0.821	0.971	CLONAL	1	TRUE	0	0.627265529288183	1		302	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577150	7577150	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	329	650	1	ENST00000269305.4:c.788del	p.Asn263IlefsTer82	p.N263Ifs*82	ENST00000269305	NM_001126112.2	263	aAt/at	8/11	0.77657218232021	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.778106782455199	1		651	515	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376727	31376727	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	322	617	0	ENST00000328111.2:c.722C>T	p.Ala241Val	p.A241V	ENST00000328111	NM_006892.3	241	gCc/gTc	7/23	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.778106782455199	2		617	761	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900274	32900274	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	149	369	0	ENST00000380152.3:c.462A>C	p.Gln154His	p.Q154H	ENST00000380152		154	caA/caC	5/27	1	2	FACETS	0.674	0.619	0.732	0.674	0.619	0.732	SUBCLONAL	1	TRUE	1	0.778106782455199	2		369	568	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0037795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	43	315	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		315	163	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0037795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	436	500	11	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		511	558	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0037795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	45	349	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		349	153	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471048	8471048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	37	368	0	ENST00000356435.5:c.3451C>T	p.Arg1151Cys	p.R1151C	ENST00000356435		1151	Cgc/Tgc	20/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		368	206	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134018	41134018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144016210	NA	P-0037795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1314	155	572	0	ENST00000379561.5:c.1610G>A	p.Arg537His	p.R537H	ENST00000379561	NM_002015.3	537	cGt/cAt	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		572	1469	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437749	49437760	+	inframe_deletion	In_Frame_Del	DEL	CGGCGCCCTCTG	CGGCGCCCTCTG	-	novel	NA	P-0037795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	39	639	1	ENST00000301067.7:c.5210_5221del	p.Ala1737_Ala1740del	p.A1737_A1740del	ENST00000301067	NM_003482.3	1737	gCAGAGGGCGCCGtg/gtg	22/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		640	491	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434489	121434489	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	203	996	0	ENST00000257555.6:c.1253A>T	p.Glu418Val	p.E418V	ENST00000257555		418	gAg/gTg	6/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		996	506	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36217156	36217156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771289674	NA	P-0037795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	271	871	0	ENST00000222270.7:c.3905G>A	p.Arg1302His	p.R1302H	ENST00000222270	NM_014727.1	1302	cGc/cAc	14/37	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		871	679	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061220	38061225	+	inframe_deletion	In_Frame_Del	DEL	CGTTCT	CGTTCT	-	novel	NA	P-0037801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	282	557	0	ENST00000250448.2:c.764_769del	p.Glu255_Asn256del	p.E255_N256del	ENST00000250448	NM_004496.3	255	gAGAACGgc/ggc	2/2	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	FALSE	1	0.507630117808826	2		557	754	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244949	133244949	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	544	776	0	ENST00000320574.5:c.2166G>T	p.Arg722Ser	p.R722S	ENST00000320574	NM_006231.2	722	agG/agT	19/49	0.364559665074577	3	FACETS	0.958	0.92	0.997	0.958	0.92	0.997	CLONAL	2	FALSE	1	0.507630117808826	3		776	1402	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966754	18966754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568279022	NA	P-0037801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	313	903	0	ENST00000262803.5:c.1565C>T	p.Pro522Leu	p.P522L	ENST00000262803	NM_002911.3	522	cCg/cTg	12/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.507630117808826	2		903	1191	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262362	16262362	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	122	390	0	ENST00000375759.3:c.9627G>T	p.Gln3209His	p.Q3209H	ENST00000375759	NM_015001.2	3209	caG/caT	11/15	1	2	FACETS	0.923	0.838	1	0.923	0.838	1	CLONAL	1	FALSE	1	0.507630117808826	2		390	521	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057790	27057790	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	195	917	0	ENST00000324856.7:c.1498T>G	p.Tyr500Asp	p.Y500D	ENST00000324856	NM_006015.4	500	Tat/Gat	3/20	1	2	FACETS	0.58	0.535	0.626	0.58	0.535	0.626	SUBCLONAL	1	FALSE	1	0.507630117808826	2		917	1325	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106704	27106707	+	frameshift_variant	Frame_Shift_Del	DEL	CCTG	CCTG	-	novel	NA	P-0037801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	243	658	0	ENST00000324856.7:c.6315_6318del	p.Leu2106AlafsTer28	p.L2106Afs*28	ENST00000324856	NM_006015.4	2105	acCCTG/ac	20/20	1	2	FACETS	0.964	0.901	1	0.964	0.901	1	CLONAL	1	FALSE	1	0.507630117808826	2		658	993	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3113328	3113336	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GCCAATGCG	GCCAATGCG	TC	novel	NA	P-0037801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	297	615	2	ENST00000078429.4:c.322_330delinsTC	p.Ala108SerfsTer3	p.A108Sfs*3	ENST00000078429	NM_002067.2	108	GCCAATGCG/TC	3/7	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	FALSE	1	0.507630117808826	2		617	870	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522214	157522214	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	234	743	0	ENST00000346085.5:c.4486A>C	p.Thr1496Pro	p.T1496P	ENST00000346085	NM_020732.3	1496	Aca/Cca	18/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.507630117808826	2		743	903	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	176	632	2	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	1	2	FACETS	0.983	0.903	1	0.983	0.903	1	CLONAL	1	TRUE	1	0.283344442814226	2		634	1264	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715678	30715678	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	136	331	1	ENST00000295754.5:c.1336G>T	p.Asp446Tyr	p.D446Y	ENST00000295754	NM_003242.5	446	Gat/Tat	5/7	0.236639550874325	2	FACETS	1	0.986	1	0.743	0.677	0.812	CLONAL	1	TRUE	0	0.283344442814226	2		332	646	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846037	68846037	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0037821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	138	673	0	ENST00000261769.5:c.1009-1G>A		p.X337_splice	ENST00000261769	NM_004360.3	337			1	2	FACETS	0.87	0.79	0.954	0.87	0.79	0.954	CLONAL	1	TRUE	1	0.283344442814226	2		673	1120	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526205	189526205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	105	727	0	ENST00000264731.3:c.469G>A	p.Asp157Asn	p.D157N	ENST00000264731	NM_003722.4	157	Gat/Aat	4/14	1	2	FACETS	0.583	0.521	0.65	0.583	0.521	0.65	SUBCLONAL	1	TRUE	1	0.283344442814226	2		727	1271	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202887	16202887	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	128	609	0	ENST00000375759.3:c.595C>A	p.Pro199Thr	p.P199T	ENST00000375759	NM_015001.2	199	Ccc/Acc	3/15	1	2	FACETS	0.852	0.771	0.938	0.852	0.771	0.938	CLONAL	1	TRUE	1	0.283344442814226	2		609	1060	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023217	27023218	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0037821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	63	139	0	ENST00000324856.7:c.323_324insT	p.Arg110Ter	p.R110*	ENST00000324856	NM_006015.4	108	ggc/ggTc	1/20	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.283344442814226	2		139	425	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101343	27101343	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1242	160	754	0	ENST00000324856.7:c.4626del	p.Gly1543AlafsTer22	p.G1543Afs*22	ENST00000324856	NM_006015.4	1542	gAa/ga	18/20	1	2	FACETS	0.806	0.736	0.878	0.806	0.736	0.878	CLONAL	1	TRUE	1	0.283344442814226	2		754	1402	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989415	7989415	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	151	848	1	ENST00000319144.4:c.271G>A	p.Ala91Thr	p.A91T	ENST00000319144	NM_001139.2	91	Gcc/Acc	2/15	1	2	FACETS	0.781	0.712	0.854	0.781	0.712	0.854	SUBCLONAL	1	TRUE	1	0.283344442814226	2		849	1365	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212548	36212548	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1349	193	934	0	ENST00000222270.7:c.2299C>T	p.Gln767Ter	p.Q767*	ENST00000222270	NM_014727.1	767	Cag/Tag	3/37	1	2	FACETS	0.883	0.815	0.956	0.883	0.815	0.956	CLONAL	1	TRUE	1	0.283344442814226	2		934	1542	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921566	178921566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793349	NA	P-0037869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	100	256	0	ENST00000263967.3:c.1048G>A	p.Asp350Asn	p.D350N	ENST00000263967	NM_006218.2	350	Gac/Aac	5/21	1	2	FACETS	0.924	0.835	1	0.924	0.835	1	CLONAL	1	TRUE	1	0.680695844844735	2		256	318	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	46	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.925	0.783	1	0.925	0.783	1	CLONAL	1	TRUE	1	0.313698009463879	2		426	317	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0037880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	32	188	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	0.836	0.682	1	0.836	0.682	1	CLONAL	1	TRUE	1	0.313698009463879	2		188	244	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248601	59248602	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0037880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	61	571	0	ENST00000371222.2:c.140_141dup	p.Ser48GlyfsTer3	p.S48Gfs*3	ENST00000371222	NM_002228.3	47	-/GG	1/1	1	2	FACETS	0.794	0.686	0.911	0.794	0.686	0.911	CLONAL	1	TRUE	1	0.313698009463879	2		571	490	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724450	112724450	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	40	325	0	ENST00000369452.4:c.334A>G	p.Ile112Val	p.I112V	ENST00000369452	NM_007373.3	112	Ata/Gta	2/9	1	2	FACETS	0.82	0.684	0.97	0.82	0.684	0.97	CLONAL	1	TRUE	1	0.313698009463879	2		325	311	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712533	43712533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	64	468	2	ENST00000382044.4:c.4651G>A	p.Ala1551Thr	p.A1551T	ENST00000382044	NM_001141980.1	1551	Gcc/Acc	21/28	1	2	FACETS	0.891	0.773	1	0.891	0.773	1	CLONAL	1	TRUE	1	0.313698009463879	2		470	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579558	7579596	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAAATCATCCATTGCTTGGGACGGCAAGGGGGACTGTAG	CAAATCATCCATTGCTTGGGACGGCAAGGGGGACTGTAG	-	novel	NA	P-0037880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	72	503	0	ENST00000269305.4:c.97-6_129del		p.X33_splice	ENST00000269305	NM_001126112.2	33		4/11	0.287511744415147	2	FACETS	1	0.973	1	0.706	0.622	0.796	CLONAL	1	TRUE	0	0.313698009463879	2		503	325	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391441	84391441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1560574598	NA	P-0037880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	29	207	0	ENST00000321945.7:c.391G>A	p.Val131Ile	p.V131I	ENST00000321945	NM_139076.2	131	Gtt/Att	5/9	1	2	FACETS	0.84	0.679	1	0.84	0.679	1	CLONAL	1	TRUE	1	0.313698009463879	2		207	220	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045856	26045929	+	frameshift_variant	Frame_Shift_Del	DEL	GAGAAATCGCCCAGGACTTCAAAACCGACCTGCGTTTCCAGAGCTCTGCGGTGATGGCGCTGCAGGAGGCTTGT	GAGAAATCGCCCAGGACTTCAAAACCGACCTGCGTTTCCAGAGCTCTGCGGTGATGGCGCTGCAGGAGGCTTGT	-	novel	NA	P-0037880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	38	337	0	ENST00000540144.1:c.221_294del	p.Glu74GlyfsTer18	p.E74Gfs*18	ENST00000540144	NM_003531.2	73	cGAGAAATCGCCCAGGACTTCAAAACCGACCTGCGTTTCCAGAGCTCTGCGGTGATGGCGCTGCAGGAGGCTTGT/c	1/1	0.305904784611116	3	FACETS	0.787	0.652	0.937	0.394	0.326	0.469	CLONAL	1	TRUE	1	0.313698009463879	3		337	356	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039834	47039834	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	145	319	0	ENST00000377604.3:c.1177G>T	p.Glu393Ter	p.E393*	ENST00000377604	NM_001204468.1	393	Gaa/Taa	12/24	0.313698009463879	2	FACETS	0.997	0.926	1			1	CLONAL	3	TRUE	NA	0.313698009463879	2		319	309	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0037945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	136	617	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.296458719796224	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.296458719796224	1		617	626	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149550	202149559	+	frameshift_variant	Frame_Shift_Del	DEL	ACGACCTTTG	ACGACCTTTG	-	novel	NA	P-0037945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	85	403	0	ENST00000358485.4:c.992_1001del	p.Thr331LysfsTer15	p.T331Kfs*15	ENST00000358485	NM_001080125.1	331	ACGACCTTTGaa/aa	8/9	0.296458719796224	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.296458719796224	1		403	437	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	150	326	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.922	0.854	0.99	0.922	0.854	0.99	CLONAL	1	TRUE	1	0.904020516467503	2		326	360	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0037977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	217	327	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.904020516467503	2		327	473	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884777	111884777	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	265	725	0	ENST00000341259.2:c.866T>C	p.Val289Ala	p.V289A	ENST00000341259	NM_005475.2	289	gTg/gCg	4/8	1	2	FACETS	0.875	0.826	0.925	0.875	0.826	0.925	CLONAL	1	TRUE	1	0.904020516467503	2		725	670	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562894	21562894	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	303	700	1	ENST00000382592.4:c.1025G>A	p.Ser342Asn	p.S342N	ENST00000382592	NM_014572.2	342	aGc/aAc	4/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.904020516467503	2		701	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578179	7578179	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	205	511	0	ENST00000269305.4:c.670G>T	p.Glu224Ter	p.E224*	ENST00000269305	NM_001126112.2	224	Gag/Tag	6/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.439251448037561	2		511	902	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0038014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	115	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.439251448037561	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.439251448037561	1		298	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0038014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	282	598	4	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.439251448037561	2		602	1132	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0038014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	105	309	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.998	0.899	1	0.998	0.899	1	CLONAL	1	TRUE	1	0.439251448037561	2		309	479	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	94	283	0	ENST00000342988.3:c.1610A>C	p.Asp537Ala	p.D537A	ENST00000342988	NM_005359.5	537	gAc/gCc	12/12	0.439251448037561	1	FACETS	0.908	0.814	1	0.908	0.814	1	CLONAL	1	TRUE	0	0.439251448037561	1		283	368	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004721	150004721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1034620976	NA	P-0038014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	114	434	0	ENST00000253339.5:c.1504C>T	p.Arg502Cys	p.R502C	ENST00000253339		502	Cgt/Tgt	3/7	0.134511907019261	0	FACETS	0.476	0.429	0.525			1	INDETERMINATE	1	TRUE	0	0.439251448037561	0		434	612	SUCCESS
APC	324	MSKCC	GRCh37	5	112175036	112175037	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0038014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	50	164	0	ENST00000257430.4:c.3746dup	p.Cys1249TrpfsTer7	p.C1249Wfs*7	ENST00000257430	NM_000038.5	1249	tgc/tGgc	16/16	1	2	FACETS	0.869	0.743	1	0.869	0.743	1	CLONAL	1	TRUE	1	0.439251448037561	2		164	262	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193154	11193154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471906651	NA	P-0038014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	175	443	0	ENST00000361445.4:c.5347G>A	p.Asp1783Asn	p.D1783N	ENST00000361445	NM_004958.3	1783	Gac/Aac	38/58	0.439251448037561	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.439251448037561	1		443	514	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114799817	114799817	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	143	407	0	ENST00000543371.1:c.484C>T	p.Gln162Ter	p.Q162*	ENST00000543371	NM_001198531.1	162	Cag/Tag	5/14	1	2	FACETS	0.883	0.807	0.964	0.883	0.807	0.964	CLONAL	1	TRUE	1	0.439251448037561	2		407	737	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231290	46231290	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	104	255	0	ENST00000334344.6:c.1133del	p.Leu378TrpfsTer13	p.L378Wfs*13	ENST00000334344	NM_152641.2	377	aTt/at	10/21	1	2	FACETS	0.921	0.828	1	0.921	0.828	1	CLONAL	1	TRUE	1	0.439251448037561	2		255	514	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213553	2213553	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	191	615	0	ENST00000398665.3:c.1573C>G	p.Leu525Val	p.L525V	ENST00000398665	NM_032482.2	525	Ctc/Gtc	17/28	1	2	FACETS	0.996	0.922	1	0.996	0.922	1	CLONAL	1	TRUE	1	0.439251448037561	2		615	873	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344204	118344204	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	48	566	0	ENST00000534358.1:c.2330C>G	p.Ser777Cys	p.S777C	ENST00000534358	NM_005933.3	777	tCt/tGt	3/36	1	2	FACETS	0.385	0.324	0.452	0.385	0.324	0.452	SUBCLONAL	1	TRUE	1	0.335261903940724	2		566	744	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230533	46230533	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0038256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	27	414	0	ENST00000334344.6:c.782C>G	p.Ser261Ter	p.S261*	ENST00000334344	NM_152641.2	261	tCa/tGa	8/21	0.335261903940724	1	FACETS	0.271	0.215	0.335	0.271	0.215	0.335	SUBCLONAL	1	TRUE	0	0.335261903940724	1		414	495	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243951	46243951	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0038256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	54	466	0	ENST00000334344.6:c.2045C>G	p.Ser682Ter	p.S682*	ENST00000334344	NM_152641.2	682	tCa/tGa	15/21	0.335261903940724	1	FACETS	0.511	0.436	0.592	0.511	0.436	0.592	SUBCLONAL	1	TRUE	0	0.335261903940724	1		466	525	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135315	2135315	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	55	626	0	ENST00000219476.3:c.4654G>C	p.Glu1552Gln	p.E1552Q	ENST00000219476	NM_000548.3	1552	Gaa/Caa	36/42	1	2	FACETS	0.463	0.396	0.538	0.463	0.396	0.538	SUBCLONAL	1	TRUE	1	0.335261903940724	2		626	708	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610210	10610210	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	291	821	0	ENST00000171111.5:c.500T>A	p.Val167Asp	p.V167D	ENST00000171111	NM_203500.1	167	gTt/gAt	2/6	0.335261903940724	2	FACETS	0.983	0.927	1	0.983	0.927	1	CLONAL	2	TRUE	0	0.335261903940724	2		821	883	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55597566	55597566	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	99	445	0	ENST00000288135.5:c.2214A>C	p.Lys738Asn	p.K738N	ENST00000288135	NM_000222.2	738	aaA/aaC	15/21	1	2	FACETS	0.954	0.853	1	0.954	0.853	1	CLONAL	1	TRUE	1	0.335261903940724	2		445	619	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180603	56180603	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269929971	NA	P-0038256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	70	400	0	ENST00000399503.3:c.3932G>A	p.Gly1311Glu	p.G1311E	ENST00000399503	NM_005921.1	1311	gGa/gAa	16/20	1	2	FACETS	0.776	0.678	0.882	0.776	0.678	0.882	SUBCLONAL	1	TRUE	1	0.335261903940724	2		400	538	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	69	326	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.83	0.726	0.94	1	0.978	1	CLONAL	2	TRUE	1	0.22	2		326	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577520	7577520	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	224	580	0	ENST00000269305.4:c.761T>A	p.Ile254Asn	p.I254N	ENST00000269305	NM_001126112.2	254	aTc/aAc	7/11	0.293361568207575	2	FACETS	0.936	0.875	0.999	1	0.991	1	CLONAL	3	TRUE	0	0.22	2		580	725	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945615	206945615	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0038376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	60	434	0	ENST00000423557.1:c.165+1G>T		p.X55_splice	ENST00000423557	NM_000572.2	55			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.22	2		434	418	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979529	7979529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768784091	NA	P-0038376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	51	622	1	ENST00000319144.4:c.1496G>A	p.Arg499His	p.R499H	ENST00000319144	NM_001139.2	499	cGc/cAc	11/15	0.293361568207575	2	FACETS	0.706	0.599	0.823	0.353	0.299	0.412	SUBCLONAL	1	TRUE	0	0.22	2		623	657	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317070	11317070	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766996808	NA	P-0038376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	55	603	1	ENST00000361445.4:c.424G>A	p.Ala142Thr	p.A142T	ENST00000361445	NM_004958.3	142	Gct/Act	4/58	1	2	FACETS	0.708	0.605	0.822	0.708	0.605	0.822	SUBCLONAL	1	TRUE	1	0.22	2		604	706	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780566	56780566	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	42	467	0	ENST00000337432.4:c.581A>G	p.Lys194Arg	p.K194R	ENST00000337432	NM_058216.2	194	aAa/aGa	4/9	1	2	FACETS	0.718	0.599	0.85	0.718	0.599	0.85	SUBCLONAL	1	TRUE	1	0.22	2		467	532	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149818	202149819	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0038376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	96	595	0	ENST00000358485.4:c.1259_1260del	p.Gln420ArgfsTer3	p.Q420Rfs*3	ENST00000358485	NM_001080125.1	420	cAG/c	8/9	0.3	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.22	1		595	532	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933633	49933633	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	68	816	0	ENST00000296474.3:c.2644T>G	p.Phe882Val	p.F882V	ENST00000296474	NM_002447.2	882	Ttt/Gtt	10/20	1	2	FACETS	0.85	0.739	0.971	0.85	0.739	0.971	CLONAL	1	TRUE	1	0.22	2		816	727	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915187	131915188	+	missense_variant	Missense_Mutation	DNP	GC	GC	CT	novel	NA	P-0038376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	35	446	1	ENST00000265335.6:c.544_545delinsCT	p.Ala182Leu	p.A182L	ENST00000265335		182	GCa/CTa	4/25	1	2	FACETS	0.692	0.567	0.832	0.692	0.567	0.832	SUBCLONAL	1	TRUE	1	0.22	2		447	460	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176684029	176684029	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	137	609	1	ENST00000439151.2:c.4843T>A	p.Tyr1615Asn	p.Y1615N	ENST00000439151	NM_022455.4	1615	Tac/Aac	13/23	1	2	FACETS	0.852	0.776	0.931	1	0.989	1	CLONAL	2	TRUE	1	0.22	2		610	731	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271350	26271350	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	59	529	0	ENST00000305910.3:c.263C>G	p.Ser88Cys	p.S88C	ENST00000305910	NM_003534.2	88	tCc/tGc	1/1	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.22	2		529	475	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175882	24175882	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	27	438	0	ENST00000263121.7:c.1110G>T	p.Arg370Ser	p.R370S	ENST00000263121	NM_003073.3	370	agG/agT	8/9	1	2	FACETS	0.357	0.283	0.442	0.357	0.283	0.442	SUBCLONAL	1	FALSE	1	0.3	2		438	504	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	17	326	0				ENST00000310581	NM_198253.2	-/1132			0.342106317297851	0	FACETS	0.485	0.365	0.624			1	SUBCLONAL	1	TRUE	0	0.338690887277428	0		326	137	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175882	24175882	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	94	438	0	ENST00000263121.7:c.1110G>T	p.Arg370Ser	p.R370S	ENST00000263121	NM_003073.3	370	agG/agT	8/9	0.275746911595049	3	FACETS	1	0.98	1	0.723	0.646	0.803	CLONAL	1	TRUE	1	0.338690887277428	3		438	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0038613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	223	690	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.339600444814899	4	FACETS	1	0.973	1	0.721	0.673	0.771	CLONAL	2	TRUE	1	0.338690887277428	4		690	815	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056283	26056283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1459637809	NA	P-0038613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1204	145	528	0	ENST00000343677.2:c.374G>A	p.Gly125Glu	p.G125E	ENST00000343677	NM_005319.3	125	gGa/gAa	1/1	0.338690887277428	15	FACETS	1	0.923	1			1	CLONAL	2	TRUE	NA	0.338690887277428	15		528	1349	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732535	74732535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	49	163	0	ENST00000359995.5:c.374G>A	p.Arg125His	p.R125H	ENST00000359995	NM_001195427.1	125	cGt/cAt	2/3	0.23211882591734	4	FACETS	1	0.964	1	0.748	0.639	0.866	CLONAL	1	TRUE	2	0.338690887277428	4		163	259	SUCCESS
APC	324	MSKCC	GRCh37	5	112175930	112175930	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	54	222	0	ENST00000257430.4:c.4639G>T	p.Glu1547Ter	p.E1547*	ENST00000257430	NM_000038.5	1547	Gaa/Taa	16/16	0.342106317297851	3	FACETS	0.905	0.784	1	0.905	0.784	1	CLONAL	2	TRUE	1	0.338690887277428	3		222	206	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247174	153247174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	54	259	0	ENST00000281708.4:c.1628G>A	p.Arg543Lys	p.R543K	ENST00000281708	NM_033632.3	543	aGa/aAa	10/12	0.154949456953543	4	FACETS	1	0.862	1	0.503	0.431	0.582	INDETERMINATE	1	TRUE	2	0.338690887277428	4		259	424	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224531	108224531	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	33	321	0	ENST00000278616.4:c.8710G>C	p.Glu2904Gln	p.E2904Q	ENST00000278616	NM_000051.3	2904	Gag/Cag	60/63	0.204646689136335	4	FACETS	0.864	0.706	1	0.432	0.353	0.521	CLONAL	1	TRUE	2	0.338690887277428	4		321	302	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572904	41572904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	86	628	0	ENST00000263253.7:c.5189C>T	p.Ser1730Phe	p.S1730F	ENST00000263253	NM_001429.3	1730	tCt/tTt	31/31	0.275746911595049	3	FACETS	0.988	0.875	1	0.494	0.437	0.554	CLONAL	1	TRUE	1	0.338690887277428	3		628	601	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406383	70406383	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149145995	NA	P-0038613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	72	691	0	ENST00000373644.4:c.3897G>C	p.Leu1299Phe	p.L1299F	ENST00000373644	NM_030625.2	1299	ttG/ttC	4/12	0.154949456953543	4	FACETS	0.884	0.772	1	0.442	0.386	0.502	INDETERMINATE	1	TRUE	2	0.338690887277428	4		691	644	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94908721	94908721	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1390641197	NA	P-0038613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	58	613	0	ENST00000536441.1:c.1333G>C	p.Glu445Gln	p.E445Q	ENST00000536441	NM_144665.3	445	Gag/Cag	9/10	0.204646689136335	4	FACETS	0.488	0.418	0.565	0.244	0.209	0.283	SUBCLONAL	1	TRUE	2	0.338690887277428	4		613	939	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236158	108236159	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGAAT	novel	NA	P-0038613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	73	625	0	ENST00000278616.4:c.9096_9100dup	p.Leu3034Ter	p.L3034*	ENST00000278616	NM_000051.3	3032	gtg/gTGAATtg	63/63	0.204646689136335	4	FACETS	0.954	0.835	1	0.477	0.417	0.541	CLONAL	1	TRUE	2	0.338690887277428	4		625	605	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835613	68835613	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0038613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	186	544	0	ENST00000261769.5:c.204T>A	p.Tyr68Ter	p.Y68*	ENST00000261769	NM_004360.3	68	taT/taA	3/16	0.283766355448778	3	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.338690887277428	3		544	518	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158595023	158595023	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	63	424	0	ENST00000263640.3:c.1324G>T	p.Glu442Ter	p.E442*	ENST00000263640	NM_001105.4	442	Gaa/Taa	10/11	0.283766355448778	3	FACETS	1	0.909	1			1	CLONAL	1	TRUE	NA	0.338690887277428	3		424	410	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714460	40714460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775362831	NA	P-0038613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	15	397	2	ENST00000373198.4:c.3937G>A	p.Gly1313Arg	p.G1313R	ENST00000373198	NM_133170.3	1313	Ggg/Agg	29/32	0.342106317297851	0	FACETS	0.248	0.181	0.328			1	SUBCLONAL	1	TRUE	0	0.338690887277428	0		399	236	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114271	143114271	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	46	353	0	ENST00000262992.4:c.1150C>G	p.Leu384Val	p.L384V	ENST00000262992	NM_001101669.1	384	Cta/Gta	13/24	0.154949456953543	4	FACETS	0.872	0.736	1	0.436	0.368	0.511	INDETERMINATE	1	TRUE	2	0.338690887277428	4		353	417	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38153408	38153408	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	101	571	0	ENST00000317025.8:c.2821G>C	p.Glu941Gln	p.E941Q	ENST00000317025	NM_023034.1	941	Gaa/Caa	16/24	0.338690887277428	9	FACETS	1	0.961	1			1	CLONAL	1	TRUE	NA	0.338690887277428	9		571	1112	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0038720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	301	675	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA	2	FACETS	0.93	0.881	0.98			1	INDETERMINATE	1	TRUE	NA	0.838466835485784	2		675	772	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346798	89346798	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0038720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	265	590	1	ENST00000301030.4:c.6152C>G	p.Ser2051Ter	p.S2051*	ENST00000301030	NM_001256183.1	2051	tCa/tGa	9/13	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.838466835485784	2		591	617	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405630	139405630	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	463	836	0	ENST00000277541.6:c.2561C>G	p.Ser854Cys	p.S854C	ENST00000277541	NM_017617.3	854	tCc/tGc	16/34	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.838466835485784	2		836	1019	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340408	8340408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775122610	NA	P-0038720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	318	625	1	ENST00000356435.5:c.5188C>T	p.Arg1730Trp	p.R1730W	ENST00000356435		1730	Cgg/Tgg	31/35	0.8297200998617	3	FACETS	0.978	0.923	1			1	CLONAL	1	TRUE	NA	0.838466835485784	3		626	1101	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350918	89350918	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	461	930	0	ENST00000301030.4:c.2032C>G	p.Leu678Val	p.L678V	ENST00000301030	NM_001256183.1	678	Ctt/Gtt	9/13	1	2	FACETS	0.955	0.915	0.997	0.955	0.915	0.997	CLONAL	1	TRUE	1	0.838466835485784	2		930	1151	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326100	62326100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772175599	NA	P-0038720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	66	727	2	ENST00000360203.5:c.3116C>T	p.Pro1039Leu	p.P1039L	ENST00000360203	NM_001283009.1	1039	cCt/cTt	32/35	1	2	FACETS	0.176	0.152	0.202	0.176	0.152	0.202	SUBCLONAL	1	TRUE	1	0.838466835485784	2		729	894	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183700	10183700	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	339	601	0	ENST00000256474.2:c.169G>T	p.Gly57Trp	p.G57W	ENST00000256474	NM_000551.3	57	Ggg/Tgg	1/3	0.830019782106294	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.838466835485784	1		601	445	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55260503	55260503	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	286	698	0	ENST00000275493.2:c.2670C>G	p.Ile890Met	p.I890M	ENST00000275493	NM_005228.3	890	atC/atG	22/28	1	2	FACETS	0.961	0.909	1	0.961	0.909	1	CLONAL	1	TRUE	1	0.838466835485784	2		698	710	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188059	151188059	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	139	587	0	ENST00000262187.5:c.94G>C	p.Val32Leu	p.V32L	ENST00000262187	NM_005614.3	32	Gtg/Ctg	2/8	1	2	FACETS	0.543	0.496	0.592	0.543	0.496	0.592	SUBCLONAL	1	TRUE	1	0.838466835485784	2		587	611	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128432026	128432127	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAATAAAAGTTCTTATATAATAAACTAAATATATAAATCTCAAATTAAGAATTAAAATCATTTCCATTTACCTGATTGCTTAGAATTTCTTTCTTTCCACTG	AAATAAAAGTTCTTATATAATAAACTAAATATATAAATCTCAAATTAAGAATTAAAATCATTTCCATTTACCTGATTGCTTAGAATTTCTTTCTTTCCACTG	-	novel	NA	P-0038720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	138	214	0	ENST00000265960.3:c.319_349+71del		p.X107_splice	ENST00000265960	NM_001006617.1	107		3/12	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.838466835485784	2		214	283	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	153	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.521661550879057	2		426	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0038793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	152	482	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	0.521661550879057	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.521661550879057	1		482	408	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031750	36031750	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879255268	NA	P-0038793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	161	511	1	ENST00000358208.4:c.1579G>A	p.Glu527Lys	p.E527K	ENST00000358208		527	Gag/Aag	12/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.521661550879057	2		512	525	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971175	21971182	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCGCCA	CTCCGCCA	-	novel	NA	P-0038793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	134	242	0	ENST00000304494.5:c.176_183del	p.Val59AlafsTer58	p.V59Afs*58	ENST00000304494	NM_000077.4	59	gTGGCGGAG/g	2/3	0.521661550879057	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.521661550879057	1		242	297	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0038803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	143	163	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.769440732746385	2	FACETS	0.963	0.913	1	0.963	0.913	1	CLONAL	2	TRUE	0	0.769440732746385	2		163	193	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0038803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	1474	442	0	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	0.769440732746385	9	FACETS	0.958	0.942	0.975			1	CLONAL	7	TRUE	NA	0.769440732746385	9		442	2109	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129378	2129378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368095502	NA	P-0038803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	345	597	0	ENST00000219476.3:c.3233G>A	p.Arg1078Gln	p.R1078Q	ENST00000219476	NM_000548.3	1078	cGg/cAg	28/42	0.769440732746385	3	FACETS	0.919	0.869	0.971	0.46	0.434	0.486	CLONAL	1	TRUE	1	0.769440732746385	3		597	1351	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923594	39923594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	29	255	0	ENST00000378444.4:c.3497C>T	p.Ser1166Phe	p.S1166F	ENST00000378444	NM_001123385.1	1166	tCt/tTt	7/15	1	1	FACETS	0.107	0.086	0.132	0.107	0.086	0.132	SUBCLONAL	1	TRUE	0	0.769440732746385	1		255	432	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739873	41739873	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1261664857	NA	P-0038803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	210	421	0	ENST00000242208.4:c.100G>A	p.Asp34Asn	p.D34N	ENST00000242208	NM_002192.2	34	Gac/Aac	2/3	0.769440732746385	4	FACETS	0.92	0.854	0.988	0.307	0.284	0.33	CLONAL	1	TRUE	1	0.769440732746385	4		421	1050	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602358	28602358	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1958	151	388	0	ENST00000241453.7:c.2010C>G	p.Ser670Arg	p.S670R	ENST00000241453	NM_004119.2	670	agC/agG	16/24	0.769440732746385	8	FACETS	0.616	0.56	0.675	0.088	0.08	0.097	SUBCLONAL	1	TRUE	1	0.769440732746385	8		388	2109	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578464	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGGTG	novel	NA	P-0038803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	908	720	0	ENST00000269305.4:c.462_466dup	p.Arg156ProfsTer16	p.R156Pfs*16	ENST00000269305	NM_001126112.2	156	cgc/cCACCCgc	5/11	0.769440732746385	2	FACETS	0.935	0.915	0.955	0.935	0.915	0.955	CLONAL	2	TRUE	0	0.769440732746385	2		720	1262	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412529	63412530	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0038803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	551	281	0	ENST00000330258.3:c.637_638insGG	p.Gln213ArgfsTer70	p.Q213Rfs*70	ENST00000330258	NM_152424.3	213	cag/cGGag	2/2	0.739548173173272	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.769440732746385	2		281	633	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934874	NA	P-0038881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	253	836	0	ENST00000269305.4:c.451C>A	p.Pro151Thr	p.P151T	ENST00000269305	NM_001126112.2	151	Ccc/Acc	5/11	0.566425030837978	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.566425030837978	1		836	603	SUCCESS
APC	324	MSKCC	GRCh37	5	112170747	112170747	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1561568632	NA	P-0038881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	119	513	0	ENST00000257430.4:c.1847del	p.Leu616TrpfsTer14	p.L616Wfs*14	ENST00000257430	NM_000038.5	615	Ttt/tt	15/16	0.561696140129782	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.566425030837978	1		513	286	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202232	138202232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561168863	NA	P-0038881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	111	548	0	ENST00000237289.4:c.2149G>A	p.Ala717Thr	p.A717T	ENST00000237289	NM_001270507.1	717	Gcc/Acc	9/9	1	2	FACETS	0.873	0.79	0.96	0.873	0.79	0.96	CLONAL	1	TRUE	1	0.566425030837978	2		548	449	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662382	227662382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	168	661	0	ENST00000305123.5:c.1073G>A	p.Arg358Gln	p.R358Q	ENST00000305123	NM_005544.2	358	cGg/cAg	1/2	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.566425030837978	2		661	526	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29115452	29115452	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759734429	NA	P-0038881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	45	327	0	ENST00000328354.6:c.614C>T	p.Thr205Ile	p.T205I	ENST00000328354	NM_007194.3	205	aCt/aTt	5/15	1	2	FACETS	0.509	0.43	0.596	0.509	0.43	0.596	SUBCLONAL	1	TRUE	1	0.566425030837978	2		327	312	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516878	187516878	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	22	484	0	ENST00000441802.2:c.13103T>G	p.Leu4368Arg	p.L4368R	ENST00000441802	NM_005245.3	4368	cTg/cGg	26/27	1	2	FACETS	0.212	0.164	0.268	0.212	0.164	0.268	SUBCLONAL	1	TRUE	1	0.566425030837978	2		484	366	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516883	187516883	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	21	493	0	ENST00000441802.2:c.13098G>T	p.Gln4366His	p.Q4366H	ENST00000441802	NM_005245.3	4366	caG/caT	26/27	1	2	FACETS	0.194	0.148	0.246	0.194	0.148	0.246	SUBCLONAL	1	TRUE	1	0.566425030837978	2		493	383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0039226-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	12	797	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.563	0.393	0.773	0.563	0.393	0.773	SUBCLONAL	1	TRUE	1	0.09	2		799	474	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937863	36937868	+	inframe_deletion	In_Frame_Del	DEL	GGCTGG	GGCTGG	-	novel	NA	P-0039226-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	12	0	0	ENST00000361632.4:c.968_973del	p.Pro323_Ser324del	p.P323_S324del	ENST00000361632		323	cCCAGCCtg/ctg	7/16	1	2	FACETS	0.687	0.481	0.943	0.687	0.481	0.943	SUBCLONAL	1	TRUE	1	0.09	2		0	388	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061186	38061186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039226-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	16	501	0	ENST00000250448.2:c.803G>A	p.Cys268Tyr	p.C268Y	ENST00000250448	NM_004496.3	268	tGc/tAc	2/2	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.09	2		501	306	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705430	43705430	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039226-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	10	0	0	ENST00000382044.4:c.5192A>G	p.Lys1731Arg	p.K1731R	ENST00000382044	NM_001141980.1	1731	aAg/aGg	24/28	1	2	FACETS	0.524	0.353	0.741	0.524	0.353	0.741	SUBCLONAL	1	TRUE	1	0.09	2		0	424	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246559	41246559	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039226-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	11	0	0	ENST00000357654.3:c.989del	p.Asp330ValfsTer11	p.D330Vfs*11	ENST00000357654	NM_007294.3	330	gAt/gt	10/23	1	2	FACETS	0.484	0.333	0.674	0.484	0.333	0.674	SUBCLONAL	1	TRUE	1	0.09	2		0	505	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781846	3781848	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0039269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	226	550	9	ENST00000262367.5:c.4819_4821del	p.Lys1607del	p.K1607del	ENST00000262367	NM_004380.2	1607	AAG/-	29/31	1	2	FACETS	0.771	0.719	0.825	0.771	0.719	0.825	SUBCLONAL	1	TRUE	1	0.662946772051128	2		559	884	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579481	7579482	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0039269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	511	601	9	ENST00000269305.4:c.205_206del	p.Ala69CysfsTer79	p.A69Cfs*79	ENST00000269305	NM_001126112.2	69	GCt/t	4/11	0.626135830865795	2	FACETS	0.955	0.924	0.986	0.955	0.924	0.986	CLONAL	2	TRUE	0	0.662946772051128	2		610	807	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519996	NA	P-0039292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	428	631	0	ENST00000269305.4:c.395A>T	p.Lys132Met	p.K132M	ENST00000269305	NM_001126112.2	132	aAg/aTg	5/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.62933608683082	NA		631	670	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967464	38967464	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs376772272	NA	P-0039292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	87	348	0	ENST00000357387.3:c.1126A>G	p.Ile376Val	p.I376V	ENST00000357387	NM_152756.3	376	Att/Gtt	13/38	0.592555655003	5	FACETS	1	0.953	1	0.38	0.337	0.425	CLONAL	1	FALSE	2	0.62933608683082	5		348	472	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422165	81422165	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	110	440	0	ENST00000298171.2:c.141C>G	p.Ile47Met	p.I47M	ENST00000298171	NM_000369.2	47	atC/atG	1/10	0.629379024247745	3	FACETS	0.948	0.856	1	0.474	0.428	0.522	CLONAL	1	FALSE	1	0.62933608683082	3		440	485	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472553	88472553	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	104	536	0	ENST00000360948.2:c.2002G>C	p.Val668Leu	p.V668L	ENST00000360948	NM_001012338.2	668	Gtg/Ctg	16/19	0.629379024247745	3	FACETS	0.983	0.886	1	0.492	0.443	0.543	CLONAL	1	FALSE	1	0.62933608683082	3		536	442	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441357	149441357	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs370659554	NA	P-0039292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	163	583	0	ENST00000286301.3:c.1682A>T	p.Tyr561Phe	p.Y561F	ENST00000286301	NM_005211.3	561	tAt/tTt	12/22	0.629379024247745	3	FACETS	1	0.958	1	0.53	0.488	0.574	CLONAL	1	FALSE	1	0.62933608683082	3		583	642	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922240	39922240	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	104	378	0	ENST00000378444.4:c.3932G>T	p.Cys1311Phe	p.C1311F	ENST00000378444	NM_001123385.1	1311	tGc/tTc	9/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.62933608683082	2		378	278	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0039375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	82	686	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.781	0.687	0.883	0.781	0.687	0.883	SUBCLONAL	1	FALSE	1	0.215044276082022	2		686	976	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440109	49440109	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	90	838	0	ENST00000301067.7:c.4517C>A	p.Thr1506Asn	p.T1506N	ENST00000301067	NM_003482.3	1506	aCc/aAc	16/54	1	2	FACETS	0.79	0.699	0.887	0.79	0.699	0.887	SUBCLONAL	1	FALSE	1	0.215044276082022	2		838	1060	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993470	72993470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	96	886	1	ENST00000268489.5:c.575C>T	p.Pro192Leu	p.P192L	ENST00000268489	NM_006885.3	192	cCg/cTg	2/10	1	2	FACETS	0.812	0.721	0.909	0.812	0.721	0.909	CLONAL	1	FALSE	1	0.215044276082022	2		887	1100	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579415	7579416	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	106	879	1	ENST00000269305.4:c.271dup	p.Trp91LeufsTer58	p.W91Lfs*58	ENST00000269305	NM_001126112.2	91	tgg/tTgg	4/11	0.215044276082022	1	FACETS	0.88	0.787	0.978	0.88	0.787	0.978	CLONAL	1	FALSE	0	0.215044276082022	1		880	1000	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440958	56440976	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGCCTGCAGAGGCACACA	GAGCCTGCAGAGGCACACA	-	novel	NA	P-0039375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	51	684	0	ENST00000407977.2:c.376-15_379del		p.X126_splice	ENST00000407977		126		4/10	0.215044276082022	1	FACETS	0.502	0.425	0.586	0.502	0.425	0.586	SUBCLONAL	1	FALSE	0	0.215044276082022	1		684	844	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0039408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	360	372	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.299071244277932	6	FACETS	1	0.976	1	1	0.976	1	CLONAL	5	TRUE	1	0.28	6		372	776	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0039408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	350	687	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.28	2		688	1077	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242475	55242475	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057520037	NA	P-0039408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	78	363	0	ENST00000275493.2:c.2245G>C	p.Glu749Gln	p.E749Q	ENST00000275493	NM_005228.3	749	Gaa/Caa	19/28	0.214451683341801	4	FACETS	0.966	0.849	1	0.483	0.424	0.547	CLONAL	1	TRUE	2	0.28	4		363	738	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4123815	4123815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	230	423	0	ENST00000262948.5:c.58G>A	p.Glu20Lys	p.E20K	ENST00000262948	NM_030662.3	20	Gag/Aag	1/11	0.291555895512766	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.28	3		423	849	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518640	69518640	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	88	563	0	ENST00000294312.3:c.5G>A	p.Arg2Gln	p.R2Q	ENST00000294312	NM_005117.2	2	cGg/cAg	1/3	0.214451683341801	4	FACETS	0.755	0.667	0.849	0.377	0.333	0.425	SUBCLONAL	1	TRUE	2	0.28	4		563	1066	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0039432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	36	675	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.99	0.814	1	0.99	0.814	1	CLONAL	1	TRUE	1	0.17	2		675	428	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	74	632	2	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.17	2		634	597	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028657	12028657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	27	406	0	ENST00000353533.5:c.860G>A	p.Arg287His	p.R287H	ENST00000353533	NM_003010.3	287	cGc/cAc	8/11	1	2	FACETS	0.79	0.628	0.975	0.79	0.628	0.975	CLONAL	1	TRUE	1	0.17	2		406	402	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	119	326	0				ENST00000310581	NM_198253.2	-/1132			0.367191233469257	4	FACETS	1	0.982	1	0.46	0.416	0.506	CLONAL	1	TRUE	1	0.401448706975147	4		326	602	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0039448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	43	675	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.298	0.249	0.354	0.298	0.249	0.354	SUBCLONAL	1	TRUE	1	0.401448706975147	2		675	718	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138135	2138135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201206500	NA	P-0039448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	186	899	2	ENST00000219476.3:c.5155G>A	p.Ala1719Thr	p.A1719T	ENST00000219476	NM_000548.3	1719	Gca/Aca	40/42	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.401448706975147	2		901	872	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840003	27840003	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	48	469	0	ENST00000328488.2:c.91C>A	p.Pro31Thr	p.P31T	ENST00000328488	NM_003533.2	31	Ccg/Acg	1/1	0.256384926853121	4	FACETS	0.512	0.432	0.601	0.171	0.144	0.201	SUBCLONAL	1	TRUE	1	0.401448706975147	4		469	654	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578490	7578490	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	545	956	1	ENST00000269305.4:c.440T>A	p.Val147Asp	p.V147D	ENST00000269305	NM_001126112.2	147	gTt/gAt	5/11	0.401448706975147	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.401448706975147	2		957	1278	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120366	94120366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1216099858	NA	P-0039448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	51	286	0	ENST00000369303.4:c.685G>A	p.Glu229Lys	p.E229K	ENST00000369303	NM_004440.3	229	Gag/Aag	3/17	1	2	FACETS	0.658	0.561	0.764	0.658	0.561	0.764	SUBCLONAL	1	TRUE	1	0.401448706975147	2		286	386	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542708	187542708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	33	410	0	ENST00000441802.2:c.5032G>A	p.Glu1678Lys	p.E1678K	ENST00000441802	NM_005245.3	1678	Gaa/Aaa	10/27	1	2	FACETS	0.369	0.3	0.447	0.369	0.3	0.447	SUBCLONAL	1	TRUE	1	0.401448706975147	2		410	445	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255316	16255316	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	60	496	0	ENST00000375759.3:c.2581A>C	p.Lys861Gln	p.K861Q	ENST00000375759	NM_015001.2	861	Aaa/Caa	11/15	0.23356748680619	2	FACETS	0.384	0.33	0.443	0.192	0.165	0.222	INDETERMINATE	1	TRUE	0	0.401448706975147	2		496	779	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656340	18656340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1225421850	NA	P-0039448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	82	397	0	ENST00000266497.5:c.3019G>A	p.Asp1007Asn	p.D1007N	ENST00000266497		1007	Gat/Aat	21/31	0.157680346104259	5	FACETS	1	0.971	1	0.443	0.392	0.498	INDETERMINATE	1	TRUE	2	0.401448706975147	5		397	492	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476312	88476312	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	49	707	1	ENST00000360948.2:c.1820G>A	p.Cys607Tyr	p.C607Y	ENST00000360948	NM_001012338.2	607	tGc/tAc	15/19	1	2	FACETS	0.349	0.294	0.409	0.349	0.294	0.409	SUBCLONAL	1	TRUE	1	0.401448706975147	2		708	700	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647160	2647160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	35	514	0	ENST00000342085.4:c.1438G>A	p.Glu480Lys	p.E480K	ENST00000342085	NM_002613.4	480	Gaa/Aaa	13/14	1	2	FACETS	0.285	0.233	0.344	0.285	0.233	0.344	SUBCLONAL	1	TRUE	1	0.401448706975147	2		514	612	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971355	15971355	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	118	693	0	ENST00000268712.3:c.4594A>G	p.Lys1532Glu	p.K1532E	ENST00000268712	NM_006311.3	1532	Aag/Gag	32/46	1	2	FACETS	0.771	0.696	0.851	0.771	0.696	0.851	SUBCLONAL	1	TRUE	1	0.401448706975147	2		693	762	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068439	16068439	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	11	113	0	ENST00000268712.3:c.472T>A	p.Ser158Thr	p.S158T	ENST00000268712	NM_006311.3	158	Tct/Act	5/46	1	2	FACETS	0.397	0.275	0.547	0.397	0.275	0.547	SUBCLONAL	1	TRUE	1	0.401448706975147	2		113	138	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222142	2222142	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1197	69	886	1	ENST00000398665.3:c.2974G>A	p.Ala992Thr	p.A992T	ENST00000398665	NM_032482.2	992	Gca/Aca	24/28	0.157680346104259	5	FACETS	0.435	0.377	0.498	0.145	0.125	0.166	INDETERMINATE	1	TRUE	2	0.401448706975147	5		887	1266	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026091	48026092	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAACAAGCAACT	novel	NA	P-0039448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	54	421	0	ENST00000234420.5:c.971_982dup	p.Lys324_Thr327dup	p.K324_T327dup	ENST00000234420	NM_000179.2	324	-/AAACAAGCAACT	4/10	0.292374597405769	5	FACETS	0.806	0.688	0.934	0.269	0.229	0.312	CLONAL	1	TRUE	2	0.401448706975147	5		421	535	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980856	40980856	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0039448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	61	591	0	ENST00000373198.4:c.1630A>T	p.Lys544Ter	p.K544*	ENST00000373198	NM_133170.3	544	Aag/Tag	10/32	0.298449519249991	4	FACETS	0.432	0.371	0.498	0.216	0.185	0.249	SUBCLONAL	1	TRUE	2	0.401448706975147	4		591	986	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156591	55156591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	221	624	0	ENST00000257290.5:c.2992G>A	p.Asp998Asn	p.D998N	ENST00000257290	NM_006206.4	998	Gac/Aac	22/23	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.401448706975147	2		624	753	SUCCESS
APC	324	MSKCC	GRCh37	5	112175964	112175964	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	21	273	0	ENST00000257430.4:c.4673A>T	p.Asp1558Val	p.D1558V	ENST00000257430	NM_000038.5	1558	gAt/gTt	16/16	0.124789535275604	6	FACETS	0.58	0.447	0.736			1	INDETERMINATE	1	TRUE	NA	0.401448706975147	6		273	325	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497410	149497410	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	45	554	0	ENST00000261799.4:c.2908T>A	p.Tyr970Asn	p.Y970N	ENST00000261799	NM_002609.3	970	Tac/Aac	22/23	0.401448706975147	1	FACETS	0.309	0.259	0.364	0.309	0.259	0.364	SUBCLONAL	1	TRUE	0	0.401448706975147	1		554	580	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928823	44928823	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0039448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	74	305	0	ENST00000377967.4:c.1926del		p.X642_splice	ENST00000377967	NM_021140.2	642			0.124789535275604	6	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.401448706975147	6		305	478	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040799	47040802	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	AGGT	AGGT	C	novel	NA	P-0039448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	174	810	0	ENST00000377604.3:c.1434_1435+2delinsC		p.X478_splice	ENST00000377604	NM_001204468.1	478		13/24	0.124789535275604	6	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.401448706975147	6		810	1164	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0039503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	174	727	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	1	2	FACETS	0.964	0.889	1	0.964	0.889	1	CLONAL	1	TRUE	1	0.462723675032737	2		727	780	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0039503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	59	458	0	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	1	2	FACETS	0.483	0.416	0.556	0.483	0.416	0.556	SUBCLONAL	1	TRUE	1	0.462723675032737	2		458	528	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307316	118307316	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs9332745	NA	P-0039503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	14	14	0	ENST00000534358.1:c.89C>G	p.Ala30Gly	p.A30G	ENST00000534358	NM_005933.3	30	gCc/gGc	1/36	0.462723675032737	1	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	0	0.462723675032737	1		14	35	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248319	59248319	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	23	207	0	ENST00000371222.2:c.424A>C	p.Met142Leu	p.M142L	ENST00000371222	NM_002228.3	142	Atg/Ctg	1/1	1	2	FACETS	0.558	0.438	0.695	0.558	0.438	0.695	SUBCLONAL	1	TRUE	1	0.462723675032737	2		207	178	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344150	118344150	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	120	536	0	ENST00000534358.1:c.2276G>A	p.Ser759Asn	p.S759N	ENST00000534358	NM_005933.3	759	aGt/aAt	3/36	NA	2	FACETS	0.753	0.681	0.829			1	INDETERMINATE	1	TRUE	NA	0.462723675032737	2		536	689	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774200	56774200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	77	372	0	ENST00000337432.4:c.551C>A	p.Ala184Glu	p.A184E	ENST00000337432	NM_058216.2	184	gCa/gAa	3/9	1	2	FACETS	0.83	0.732	0.934	0.83	0.732	0.934	CLONAL	1	TRUE	1	0.462723675032737	2		372	401	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	220	598	4	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.91	0.849	0.973	1	0.994	1	CLONAL	2	TRUE	1	0.29439837847692	2		602	821	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	152	423	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.275501399365082	3	FACETS	0.838	0.768	0.911	0.838	0.768	0.911	CLONAL	2	TRUE	1	0.29439837847692	3		423	707	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	310	556	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.956	1	1	0.996	1	CLONAL	2	TRUE	1	0.29439837847692	2		562	1038	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	150	1951	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.97	0.885	1	0.97	0.885	1	CLONAL	1	TRUE	1	0.29439837847692	2		1952	1051	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	89	460	6	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	0.275501399365082	3	FACETS	0.803	0.711	0.901	0.401	0.355	0.451	CLONAL	1	TRUE	1	0.29439837847692	3		466	864	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	94	606	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.854	0.759	0.954	0.854	0.759	0.954	CLONAL	1	TRUE	1	0.29439837847692	2		606	748	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	98	531	3	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	0.261336049086886	1	FACETS	0.822	0.733	0.915	0.822	0.733	0.915	CLONAL	1	TRUE	0	0.29439837847692	1		534	691	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73340177	73340177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35017269	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	55	280	0	ENST00000377767.4:c.1903C>T	p.Pro635Ser	p.P635S	ENST00000377767	NM_014953.3	635	Cct/Tct	15/21	1	2	FACETS	0.941	0.808	1	0.941	0.808	1	CLONAL	1	TRUE	1	0.29439837847692	2		280	397	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	55	285	1	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	1	2	FACETS	0.965	0.829	1	0.965	0.829	1	CLONAL	1	TRUE	1	0.29439837847692	2		286	387	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636729	8636729	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	49	329	0	ENST00000356435.5:c.180del	p.Gly61GlufsTer11	p.G61Efs*11	ENST00000356435		60	aaA/aa	2/35	1	2	FACETS	0.81	0.687	0.944	0.81	0.687	0.944	CLONAL	1	TRUE	1	0.29439837847692	2		329	411	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	136	987	5	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.808	0.733	0.888	0.808	0.733	0.888	CLONAL	1	TRUE	1	0.29439837847692	2		992	1143	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	136	601	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.29439837847692	2		601	798	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216476	108216477	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587782558	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	40	206	0	ENST00000278616.4:c.8432dup	p.Ser2812ValfsTer3	p.S2812Vfs*3	ENST00000278616	NM_000051.3	2809	caa/cAaa	58/63	1	2	FACETS	0.912	0.761	1	0.912	0.761	1	CLONAL	1	TRUE	1	0.29439837847692	2		206	298	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976790	2976790	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1053219257	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	145	1040	0	ENST00000396946.4:c.1222C>T	p.Arg408Cys	p.R408C	ENST00000396946	NM_032415.4	408	Cgc/Tgc	9/25	1	2	FACETS	0.822	0.748	0.899	0.822	0.748	0.899	CLONAL	1	TRUE	1	0.29439837847692	2		1040	1199	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257144	19257144	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	89	715	0	ENST00000162023.5:c.819del	p.Thr274ProfsTer?	p.T274Pfs*?	ENST00000162023		273	ccC/cc	12/13	1	2	FACETS	0.761	0.675	0.855	0.761	0.675	0.855	SUBCLONAL	1	TRUE	1	0.29439837847692	2		715	794	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760024	133760024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	166	1094	1	ENST00000318560.5:c.2352del	p.Arg785GlyfsTer3	p.R785Gfs*3	ENST00000318560	NM_005157.4	783	Ccc/cc	11/11	1	2	FACETS	0.868	0.795	0.945	0.868	0.795	0.945	CLONAL	1	TRUE	1	0.29439837847692	2		1095	1299	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043349	6043349	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781716	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	59	338	0	ENST00000265849.7:c.325del	p.Glu109LysfsTer3	p.E109Kfs*3	ENST00000265849	NM_000535.5	109	Gaa/aa	4/15	1	2	FACETS	0.917	0.791	1	0.917	0.791	1	CLONAL	1	TRUE	1	0.29439837847692	2		338	437	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526209	189526210	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1462944177	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	106	794	0	ENST00000264731.3:c.480_481del	p.Pro161IlefsTer36	p.P161Ifs*36	ENST00000264731	NM_003722.4	158	gCT/g	4/14	1	2	FACETS	0.723	0.647	0.804	0.723	0.647	0.804	SUBCLONAL	1	TRUE	1	0.29439837847692	2		794	996	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885295	111885295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148636776	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	209	689	1	ENST00000341259.2:c.1183G>A	p.Glu395Lys	p.E395K	ENST00000341259	NM_005475.2	395	Gag/Aag	6/8	0.275501399365082	3	FACETS	0.905	0.841	0.971	0.905	0.841	0.971	CLONAL	2	TRUE	1	0.29439837847692	3		690	900	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430488	181430488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	138	862	0	ENST00000325404.1:c.340C>T	p.Arg114Trp	p.R114W	ENST00000325404	NM_003106.3	114	Cgg/Tgg	1/1	1	2	FACETS	0.938	0.853	1	0.938	0.853	1	CLONAL	1	TRUE	1	0.29439837847692	2		862	999	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111484	8111484	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs757598199	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	139	687	0	ENST00000346208.3:c.970A>G	p.Thr324Ala	p.T324A	ENST00000346208		324	Aca/Gca	5/6	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.29439837847692	2		687	883	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990429	81990429	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	116	644	0	ENST00000359376.3:c.3700G>T	p.Glu1234Ter	p.E1234*	ENST00000359376	NM_002661.3	1234	Gag/Tag	32/33	1	2	FACETS	0.926	0.834	1	0.926	0.834	1	CLONAL	1	TRUE	1	0.29439837847692	2		644	851	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899231	78899231	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200514795	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	121	634	0	ENST00000306801.3:c.2870C>T	p.Thr957Met	p.T957M	ENST00000306801	NM_020761.2	957	aCg/aTg	24/34	1	2	FACETS	0.976	0.882	1	0.976	0.882	1	CLONAL	1	TRUE	1	0.29439837847692	2		634	842	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328444	137328444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780219731	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	147	801	2	ENST00000481739.1:c.1373C>T	p.Pro458Leu	p.P458L	ENST00000481739	NM_002957.4	458	cCg/cTg	10/10	1	2	FACETS	0.947	0.863	1	0.947	0.863	1	CLONAL	1	TRUE	1	0.29439837847692	2		803	1055	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795003	242795003	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764200391	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	190	1177	2	ENST00000334409.5:c.206G>A	p.Arg69His	p.R69H	ENST00000334409	NM_005018.2	69	cGc/cAc	2/5	1	2	FACETS	0.954	0.88	1	0.954	0.88	1	CLONAL	1	TRUE	1	0.29439837847692	2		1179	1353	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417946	32417946	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	117	604	0	ENST00000332351.3:c.1106G>C	p.Arg369Pro	p.R369P	ENST00000332351	NM_024426.4	369	cGa/cCa	7/10	0.29439837847692	2	FACETS	1	0.963	1	0.567	0.512	0.625	CLONAL	1	TRUE	0	0.29439837847692	2		604	701	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056397	180056397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368167894	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	129	806	4	ENST00000261937.6:c.847C>T	p.Arg283Cys	p.R283C	ENST00000261937	NM_182925.4	283	Cgc/Tgc	7/30	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.29439837847692	2		810	849	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967090	18967091	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	126	920	0	ENST00000262803.5:c.1814_1815dup	p.Leu606SerfsTer3	p.L606Sfs*3	ENST00000262803	NM_002911.3	602	gca/gcAGa	13/24	1	2	FACETS	0.785	0.709	0.865	0.785	0.709	0.865	SUBCLONAL	1	TRUE	1	0.29439837847692	2		920	1091	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445203	49445203	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	152	956	3	ENST00000301067.7:c.2263del	p.Arg755GlyfsTer175	p.R755Gfs*175	ENST00000301067	NM_003482.3	755	Cgg/gg	10/54	0.275501399365082	3	FACETS	0.897	0.818	0.981	0.449	0.409	0.491	CLONAL	1	TRUE	1	0.29439837847692	3		959	1320	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845189	151845189	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201742813	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	103	563	3	ENST00000262189.6:c.13823G>A	p.Arg4608His	p.R4608H	ENST00000262189	NM_170606.2	4608	cGc/cAc	52/59	1	2	FACETS	0.955	0.855	1	0.955	0.855	1	CLONAL	1	TRUE	1	0.29439837847692	2		566	733	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986523	36986523	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1330324860	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	134	883	0	ENST00000354822.5:c.1166C>T	p.Thr389Ile	p.T389I	ENST00000354822	NM_001079668.2	389	aCc/aTc	3/3	1	2	FACETS	0.844	0.765	0.927	0.844	0.765	0.927	CLONAL	1	TRUE	1	0.29439837847692	2		883	1079	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244243	5244243	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1390768500	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	120	898	1	ENST00000357368.4:c.1239del	p.Ser414AlafsTer30	p.S414Afs*30	ENST00000357368	NM_002850.3	413	ccC/cc	11/38	1	2	FACETS	0.814	0.733	0.899	0.814	0.733	0.899	CLONAL	1	TRUE	1	0.29439837847692	2		899	1002	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212815	27212815	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1307510192	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	142	841	1	ENST00000380036.4:c.2797G>A	p.Ala933Thr	p.A933T	ENST00000380036	NM_000459.3	933	Gcg/Acg	17/23	1	2	FACETS	0.907	0.825	0.993	0.907	0.825	0.993	CLONAL	1	TRUE	1	0.29439837847692	2		842	1064	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481463	20481463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	48	296	0	ENST00000346618.3:c.532C>T	p.Arg178Trp	p.R178W	ENST00000346618	NM_001949.4	178	Cgg/Tgg	3/7	1	2	FACETS	0.748	0.633	0.874	0.748	0.633	0.874	SUBCLONAL	1	TRUE	1	0.29439837847692	2		296	436	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962899	2962899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3735134	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	206	931	0	ENST00000396946.4:c.2009C>T	p.Thr670Met	p.T670M	ENST00000396946	NM_032415.4	670	aCg/aTg	16/25	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.29439837847692	2		931	1167	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643536	38643536	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373477920	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	118	645	0	ENST00000299084.4:c.1006G>A	p.Val336Ile	p.V336I	ENST00000299084	NM_152594.2	336	Gta/Ata	7/7	1	2	FACETS	0.987	0.891	1	0.987	0.891	1	CLONAL	1	TRUE	1	0.29439837847692	2		645	812	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518224	103518224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376753356	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	43	271	0	ENST00000355739.4:c.2162C>T	p.Ala721Val	p.A721V	ENST00000355739	NM_000123.3	721	gCg/gTg	9/15	1	2	FACETS	0.79	0.662	0.93	0.79	0.662	0.93	CLONAL	1	TRUE	1	0.29439837847692	2		271	370	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1977089	1977089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	169	898	0	ENST00000382891.5:c.3583G>A	p.Ala1195Thr	p.A1195T	ENST00000382891	NM_133335.3	1195	Gcc/Acc	20/22	1	2	FACETS	0.965	0.885	1	0.965	0.885	1	CLONAL	1	TRUE	1	0.29439837847692	2		898	1190	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262222	115262222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	83	395	0	ENST00000438362.2:c.2332G>A	p.Ala778Thr	p.A778T	ENST00000438362	NM_001242891.1	778	Gcc/Acc	18/20	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.29439837847692	2		395	554	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11172923	11172923	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	120	569	0	ENST00000361445.4:c.7352C>T	p.Ala2451Val	p.A2451V	ENST00000361445	NM_004958.3	2451	gCt/gTt	54/58	1	2	FACETS	0.967	0.873	1	0.967	0.873	1	CLONAL	1	TRUE	1	0.29439837847692	2		569	843	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598315	28598315	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	163	995	0	ENST00000253063.3:c.287T>C	p.Leu96Pro	p.L96P	ENST00000253063	NM_031459.4	96	cTg/cCg	3/10	1	2	FACETS	0.899	0.823	0.978	0.899	0.823	0.978	CLONAL	1	TRUE	1	0.29439837847692	2		995	1232	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219148	94219148	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763902512	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	70	487	0	ENST00000323929.3:c.256G>A	p.Asp86Asn	p.D86N	ENST00000323929	NM_005591.3	86	Gat/Aat	4/20	1	2	FACETS	0.752	0.656	0.857	0.752	0.656	0.857	SUBCLONAL	1	TRUE	1	0.29439837847692	2		487	632	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143302	108143302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	59	382	0	ENST00000278616.4:c.3121G>A	p.Ala1041Thr	p.A1041T	ENST00000278616	NM_000051.3	1041	Gcc/Acc	21/63	1	2	FACETS	0.726	0.625	0.836	0.726	0.625	0.836	SUBCLONAL	1	TRUE	1	0.29439837847692	2		382	552	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50490678	50490678	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	230	639	2	ENST00000394963.4:c.1315G>A	p.Glu439Lys	p.E439K	ENST00000394963	NM_003076.4	439	Gag/Aag	11/13	0.275501399365082	3	FACETS	0.988	0.922	1	0.988	0.922	1	CLONAL	2	TRUE	1	0.29439837847692	3		641	907	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001907	29001907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	67	417	0	ENST00000282397.4:c.1258G>A	p.Ala420Thr	p.A420T	ENST00000282397	NM_002019.4	420	Gcc/Acc	9/30	1	2	FACETS	0.729	0.634	0.833	0.729	0.634	0.833	SUBCLONAL	1	TRUE	1	0.29439837847692	2		417	624	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643791	38643791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752958999	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	125	797	0	ENST00000299084.4:c.1261G>A	p.Val421Ile	p.V421I	ENST00000299084	NM_152594.2	421	Gtc/Atc	7/7	1	2	FACETS	0.837	0.756	0.922	0.837	0.756	0.922	CLONAL	1	TRUE	1	0.29439837847692	2		797	1015	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708590	43708593	+	frameshift_variant	Frame_Shift_Del	DEL	TCCT	TCCT	-	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	105	580	2	ENST00000382044.4:c.4703_4706del	p.Lys1568SerfsTer33	p.K1568Sfs*33	ENST00000382044	NM_001141980.1	1568	aAGGAg/ag	22/28	1	2	FACETS	0.897	0.804	0.997	0.897	0.804	0.997	CLONAL	1	TRUE	1	0.29439837847692	2		582	795	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396233	396234	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769619638	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	120	720	0	ENST00000262320.3:c.792dup	p.Gly265ArgfsTer20	p.G265Rfs*20	ENST00000262320	NM_003502.3	264	-/C	2/11	1	2	FACETS	0.833	0.751	0.919	0.833	0.751	0.919	CLONAL	1	TRUE	1	0.29439837847692	2		720	979	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032276	10032276	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587780353	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	119	679	0	ENST00000330684.3:c.547T>A	p.Phe183Ile	p.F183I	ENST00000330684	NM_001134407.1	183	Ttc/Atc	3/13	1	2	FACETS	0.957	0.863	1	0.957	0.863	1	CLONAL	1	TRUE	1	0.29439837847692	2		679	845	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50811837	50811837	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	80	416	0	ENST00000398568.2:c.1114T>C	p.Trp372Arg	p.W372R	ENST00000398568	NM_001042412.1	372	Tgg/Cgg	7/18	1	2	FACETS	0.909	0.801	1	0.909	0.801	1	CLONAL	1	TRUE	1	0.29439837847692	2		416	598	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831029	72831029	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	75	502	0	ENST00000268489.5:c.5552C>A	p.Pro1851Gln	p.P1851Q	ENST00000268489	NM_006885.3	1851	cCg/cAg	9/10	1	2	FACETS	0.817	0.716	0.925	0.817	0.716	0.925	CLONAL	1	TRUE	1	0.29439837847692	2		502	624	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559872	29559872	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375845704	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	72	312	0	ENST00000356175.3:c.3469G>A	p.Val1157Ile	p.V1157I	ENST00000356175	NM_000267.3	1157	Gta/Ata	26/57	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.29439837847692	2		312	452	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117562	70117562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	148	796	1	ENST00000245479.2:c.30G>A	p.Met10Ile	p.M10I	ENST00000245479	NM_000346.3	10	atG/atA	1/3	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.29439837847692	2		797	926	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78519466	78519466	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	113	569	0	ENST00000306801.3:c.37C>A	p.Leu13Met	p.L13M	ENST00000306801	NM_020761.2	13	Ctg/Atg	1/34	1	2	FACETS	0.955	0.859	1	0.955	0.859	1	CLONAL	1	TRUE	1	0.29439837847692	2		569	804	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220995	36220995	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	316	664	1	ENST00000222270.7:c.5045G>T	p.Cys1682Phe	p.C1682F	ENST00000222270	NM_014727.1	1682	tGc/tTc	23/37	0.288280896052951	4	FACETS	0.91	0.86	0.961	0.91	0.86	0.961	CLONAL	3	TRUE	1	0.29439837847692	4		665	1018	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223460	36223460	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1444	162	1052	0	ENST00000222270.7:c.6010C>T	p.Gln2004Ter	p.Q2004*	ENST00000222270	NM_014727.1	2004	Cag/Tag	28/37	0.288280896052951	4	FACETS	0.887	0.811	0.967	0.296	0.27	0.323	CLONAL	1	TRUE	1	0.29439837847692	4		1052	1606	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40744816	40744816	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	161	824	0	ENST00000392038.2:c.704del	p.Gly235ValfsTer73	p.G235Vfs*73	ENST00000392038	NM_001626.4	235	gGt/gt	8/14	0.288280896052951	4	FACETS	1	0.947	1	0.35	0.319	0.381	CLONAL	1	TRUE	1	0.29439837847692	4		824	1350	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799130	42799131	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1405	160	975	1	ENST00000575354.2:c.4620dup	p.Thr1541HisfsTer18	p.T1541Hfs*18	ENST00000575354	NM_015125.3	1538	-/C	20/20	0.288280896052951	4	FACETS	0.899	0.821	0.981	0.3	0.273	0.327	CLONAL	1	TRUE	1	0.29439837847692	4		976	1565	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729868	47729868	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	162	776	0	ENST00000449228.1:c.521del	p.Pro174GlnfsTer55	p.P174Qfs*55	ENST00000449228	NM_001127240.2	174	cCa/ca	3/4	0.288280896052951	4	FACETS	1	0.951	1	0.352	0.322	0.384	CLONAL	1	TRUE	1	0.29439837847692	4		776	1348	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50138888	50138888	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1241	579	1129	0	ENST00000246792.3:c.602G>T	p.Ser201Ile	p.S201I	ENST00000246792	NM_006270.3	201	aGc/aTc	6/6	0.288280896052951	4	FACETS	0.932	0.895	0.971	0.932	0.895	0.971	CLONAL	3	TRUE	1	0.29439837847692	4		1129	1820	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877373	40877373	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs370061295	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	101	582	0	ENST00000373198.4:c.2323A>G	p.Met775Val	p.M775V	ENST00000373198	NM_133170.3	775	Atg/Gtg	15/32	0.261336049086886	1	FACETS	0.771	0.689	0.858	0.771	0.689	0.858	SUBCLONAL	1	TRUE	0	0.29439837847692	1		582	759	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484797	57484797	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	114	679	0	ENST00000371085.3:c.777G>T	p.Glu259Asp	p.E259D	ENST00000371085	NM_000516.4	259	gaG/gaT	10/13	1	2	FACETS	0.925	0.833	1	0.925	0.833	1	CLONAL	1	TRUE	1	0.29439837847692	2		679	837	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266901	41266903	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	72	387	0	ENST00000349496.5:c.575_577del	p.Pro192del	p.P192del	ENST00000349496	NM_001904.3	191	tCTCct/tct	5/15	1	2	FACETS	0.899	0.787	1	0.899	0.787	1	CLONAL	1	TRUE	1	0.29439837847692	2		387	544	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799850	72799850	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	78	513	0	ENST00000325599.8:c.1319A>G	p.His440Arg	p.H440R	ENST00000325599	NM_018130.2	440	cAt/cGt	11/11	1	2	FACETS	0.833	0.732	0.941	0.833	0.732	0.941	CLONAL	1	TRUE	1	0.29439837847692	2		513	636	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750842	57750842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	63	366	0	ENST00000274289.3:c.1762G>T	p.Asp588Tyr	p.D588Y	ENST00000274289	NM_006622.3	588	Gat/Tat	13/14	1	2	FACETS	0.851	0.737	0.974	0.851	0.737	0.974	CLONAL	1	TRUE	1	0.29439837847692	2		366	503	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456977	149456977	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	74	449	0	ENST00000286301.3:c.751G>T	p.Asp251Tyr	p.D251Y	ENST00000286301	NM_005211.3	251	Gac/Tac	6/22	1	2	FACETS	0.823	0.721	0.933	0.823	0.721	0.933	CLONAL	1	TRUE	1	0.29439837847692	2		449	611	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959020	2959020	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	115	682	0	ENST00000396946.4:c.2496A>G	p.Ile832Met	p.I832M	ENST00000396946	NM_032415.4	832	atA/atG	18/25	1	2	FACETS	0.956	0.861	1	0.956	0.861	1	CLONAL	1	TRUE	1	0.29439837847692	2		682	817	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508870	106508870	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	100	557	0	ENST00000359195.3:c.864A>C	p.Lys288Asn	p.K288N	ENST00000359195	NM_002649.2	288	aaA/aaC	2/11	1	2	FACETS	0.928	0.829	1	0.928	0.829	1	CLONAL	1	TRUE	1	0.29439837847692	2		557	732	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925131	81925131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1382212475	NA	P-0039600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	179	571	1	ENST00000359376.3:c.922G>A	p.Ala308Thr	p.A308T	ENST00000359376	NM_002661.3	308	Gcg/Acg	11/33	0.201824886584533	4	FACETS	0.819	0.755	0.884	0.819	0.755	0.884	INDETERMINATE	2	TRUE	2	0.344201119008031	4		572	854	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023174	48023174	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs63751077	NA	P-0039600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	191	430	0	ENST00000234420.5:c.599C>G	p.Ser200Ter	p.S200*	ENST00000234420	NM_000179.2	200	tCa/tGa	3/10	0.344201119008031	3	FACETS	0.933	0.866	1	0.933	0.866	1	CLONAL	2	TRUE	1	0.344201119008031	3		430	697	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0039601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	63	401	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.786	0.681	0.899	0.786	0.681	0.899	SUBCLONAL	1	TRUE	1	0.333321701070858	2		401	481	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564515	55564515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754738766	NA	P-0039601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	108	492	1	ENST00000288135.5:c.403C>T	p.Arg135Cys	p.R135C	ENST00000288135	NM_000222.2	135	Cgc/Tgc	3/21	1	2	FACETS	0.938	0.842	1	0.938	0.842	1	CLONAL	1	TRUE	1	0.333321701070858	2		493	691	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378558	25378558	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1135401776	NA	P-0039601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	74	369	1	ENST00000311936.3:c.440A>G	p.Lys147Arg	p.K147R	ENST00000311936	NM_004985.3	147	aAg/aGg	4/5	1	2	FACETS	0.908	0.797	1	0.908	0.797	1	CLONAL	1	TRUE	1	0.333321701070858	2		370	489	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226102	2226102	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	197	804	3	ENST00000326181.6:c.1799G>C	p.Gly600Ala	p.G600A	ENST00000326181	NM_032271.2	600	gGc/gCc	19/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.333321701070858	2		807	1063	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	30	326	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.694	0.561	0.845	0.694	0.561	0.845	SUBCLONAL	1	TRUE	1	0.29	2		326	298	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395529	116395529	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	38	555	0	ENST00000397752.3:c.1822G>C	p.Glu608Gln	p.E608Q	ENST00000397752	NM_000245.2	608	Gag/Cag	6/21	0.286508975721487	3	FACETS	0.674	0.557	0.805	0.337	0.278	0.403	SUBCLONAL	1	TRUE	1	0.29	3		555	445	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730799	40730799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	72	802	0	ENST00000373198.4:c.3736G>A	p.Glu1246Lys	p.E1246K	ENST00000373198	NM_133170.3	1246	Gaa/Aaa	27/32	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.29	2		802	474	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465606	99465606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	35	717	0	ENST00000268035.6:c.2431G>A	p.Glu811Lys	p.E811K	ENST00000268035	NM_000875.3	811	Gag/Aag	11/21	1	2	FACETS	0.494	0.404	0.594	0.494	0.404	0.594	SUBCLONAL	1	TRUE	1	0.29	2		717	489	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969327	44969327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	17	196	0	ENST00000377967.4:c.4009G>A	p.Glu1337Lys	p.E1337K	ENST00000377967	NM_021140.2	1337	Gag/Aag	28/29	0.299629436711116	2	FACETS	0.888	0.669	1			1	CLONAL	1	TRUE	NA	0.29	2		196	132	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057961	27057961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	33	704	0	ENST00000324856.7:c.1669C>T	p.Gln557Ter	p.Q557*	ENST00000324856	NM_006015.4	557	Cag/Tag	3/20	1	2	FACETS	0.551	0.449	0.666	0.551	0.449	0.666	SUBCLONAL	1	TRUE	1	0.29	2		704	413	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576858	7576858	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	102	701	0	ENST00000269305.4:c.988del	p.Leu330PhefsTer15	p.L330Ffs*15	ENST00000269305	NM_001126112.2	330	Ctt/tt	9/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.29	2		701	562	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940022	49940022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760389915	NA	P-0039666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	94	869	0	ENST00000296474.3:c.1021G>A	p.Glu341Lys	p.E341K	ENST00000296474	NM_002447.2	341	Gag/Aag	1/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.29	2		869	535	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932926	39932926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	37	388	0	ENST00000378444.4:c.1673C>T	p.Ser558Leu	p.S558L	ENST00000378444	NM_001123385.1	558	tCa/tTa	4/15	0.299629436711116	2	FACETS	1	0.912	1			1	CLONAL	1	TRUE	NA	0.29	2		388	220	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435975	110435975	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	43	857	0	ENST00000375856.3:c.2426C>G	p.Ser809Cys	p.S809C	ENST00000375856	NM_003749.2	809	tCc/tGc	1/2	1	2	FACETS	0.493	0.411	0.583	0.493	0.411	0.583	SUBCLONAL	1	TRUE	1	0.29	2		857	602	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184360	7184360	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	48	792	0	ENST00000302850.5:c.941A>T	p.Glu314Val	p.E314V	ENST00000302850	NM_000208.2	314	gAg/gTg	3/22	1	2	FACETS	0.49	0.414	0.575	0.49	0.414	0.575	SUBCLONAL	1	TRUE	1	0.29	2		792	675	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976501	18976501	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	42	967	0	ENST00000262803.5:c.3151C>G	p.Gln1051Glu	p.Q1051E	ENST00000262803	NM_002911.3	1051	Cag/Gag	22/24	1	2	FACETS	0.512	0.427	0.607	0.512	0.427	0.607	SUBCLONAL	1	TRUE	1	0.29	2		967	566	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940475	49940475	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	106	917	0	ENST00000296474.3:c.568G>C	p.Glu190Gln	p.E190Q	ENST00000296474	NM_002447.2	190	Gag/Cag	1/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.29	2		917	646	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779150	135779169	+	frameshift_variant	Frame_Shift_Del	DEL	TGCAGTAAAAGCAACTGGTC	TGCAGTAAAAGCAACTGGTC	-	novel	NA	P-0039666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	50	610	0	ENST00000298552.3:c.2077_2096del	p.Asp693GlnfsTer6	p.D693Qfs*6	ENST00000298552	NM_001162426.1	693	GACCAGTTGCTTTTACTGCAc/c	17/23	0.188360473199197	2	FACETS	0.745	0.633	0.868	0.372	0.316	0.434	SUBCLONAL	1	TRUE	0	0.29	2		610	463	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981170	201981170	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	53	928	0	ENST00000359651.3:c.249C>G	p.Asn83Lys	p.N83K	ENST00000359651		83	aaC/aaG	2/8	1	2	FACETS	0.555	0.473	0.646	0.555	0.473	0.646	SUBCLONAL	1	TRUE	1	0.29	2		928	658	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900653	3900653	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	44	754	0	ENST00000262367.5:c.443C>G	p.Ser148Cys	p.S148C	ENST00000262367	NM_004380.2	148	tCc/tGc	2/31	1	2	FACETS	0.67	0.562	0.789	0.67	0.562	0.789	SUBCLONAL	1	TRUE	1	0.29	2		754	453	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991902	72991902	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	38	674	0	ENST00000268489.5:c.2143C>G	p.Arg715Gly	p.R715G	ENST00000268489	NM_006885.3	715	Cga/Gga	2/10	1	2	FACETS	0.413	0.341	0.495	0.413	0.341	0.495	SUBCLONAL	1	TRUE	1	0.29	2		674	634	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281879	142281881	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0039666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	31	581	0	ENST00000350721.4:c.363_365del	p.Lys122del	p.K122del	ENST00000350721	NM_001184.3	121	aaGAAa/aaa	4/47	1	2	FACETS	0.453	0.366	0.552	0.453	0.366	0.552	SUBCLONAL	1	TRUE	1	0.29	2		581	472	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039666-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	110	326	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.939	0.852	1	0.939	0.852	1	CLONAL	1	TRUE	1	0.645724459952347	2		326	363	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395529	116395529	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039666-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	125	555	0	ENST00000397752.3:c.1822G>C	p.Glu608Gln	p.E608Q	ENST00000397752	NM_000245.2	608	Gag/Cag	6/21	0.645724459952347	6	FACETS	1	0.965	1			1	CLONAL	1	TRUE	NA	0.645724459952347	6		555	780	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730799	40730799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039666-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	167	802	0	ENST00000373198.4:c.3736G>A	p.Glu1246Lys	p.E1246K	ENST00000373198	NM_133170.3	1246	Gaa/Aaa	27/32	0.563313885443231	1	FACETS	0.675	0.624	0.727	0.675	0.624	0.727	SUBCLONAL	1	TRUE	0	0.645724459952347	1		802	519	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465606	99465606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039666-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	188	717	0	ENST00000268035.6:c.2431G>A	p.Glu811Lys	p.E811K	ENST00000268035	NM_000875.3	811	Gag/Aag	11/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.645724459952347	2		717	495	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969327	44969327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039666-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	209	196	0	ENST00000377967.4:c.4009G>A	p.Glu1337Lys	p.E1337K	ENST00000377967	NM_021140.2	1337	Gag/Aag	28/29	0.647374088192781	2	FACETS	0.86	0.829	0.888			1	CLONAL	3	TRUE	NA	0.645724459952347	2		196	251	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057961	27057961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039666-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	278	704	0	ENST00000324856.7:c.1669C>T	p.Gln557Ter	p.Q557*	ENST00000324856	NM_006015.4	557	Cag/Tag	3/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.645724459952347	2		704	802	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576858	7576858	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039666-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	407	701	0	ENST00000269305.4:c.988del	p.Leu330PhefsTer15	p.L330Ffs*15	ENST00000269305	NM_001126112.2	330	Ctt/tt	9/11	0.647374088192781	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.645724459952347	2		701	630	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940022	49940022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760389915	NA	P-0039666-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	608	869	0	ENST00000296474.3:c.1021G>A	p.Glu341Lys	p.E341K	ENST00000296474	NM_002447.2	341	Gag/Aag	1/20	0.647374088192781	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.645724459952347	2		869	844	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932926	39932926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039666-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	226	388	0	ENST00000378444.4:c.1673C>T	p.Ser558Leu	p.S558L	ENST00000378444	NM_001123385.1	558	tCa/tTa	4/15	0.591604615626241	2	FACETS	1	0.992	1			1	CLONAL	1	TRUE	NA	0.645724459952347	2		388	510	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080656	5080656	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs769318116	NA	P-0039666-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	167	320	0	ENST00000381652.3:c.2407C>T	p.Arg803Ter	p.R803*	ENST00000381652	NM_004972.3	803	Cga/Tga	18/25	0.647374088192781	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.645724459952347	2		320	241	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435975	110435975	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039666-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	189	857	0	ENST00000375856.3:c.2426C>G	p.Ser809Cys	p.S809C	ENST00000375856	NM_003749.2	809	tCc/tGc	1/2	NA	2	FACETS	0.866	0.803	0.93			1	INDETERMINATE	1	TRUE	NA	0.645724459952347	2		857	676	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184360	7184360	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039666-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	217	792	0	ENST00000302850.5:c.941A>T	p.Glu314Val	p.E314V	ENST00000302850	NM_000208.2	314	gAg/gTg	3/22	0.645198016903071	3	FACETS	0.97	0.902	1	0.485	0.451	0.52	CLONAL	1	TRUE	1	0.645724459952347	3		792	917	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976501	18976501	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039666-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	275	967	0	ENST00000262803.5:c.3151C>G	p.Gln1051Glu	p.Q1051E	ENST00000262803	NM_002911.3	1051	Cag/Gag	22/24	0.428285707833925	3	FACETS	0.984	0.924	1			1	CLONAL	1	TRUE	NA	0.645724459952347	3		967	1145	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940475	49940475	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039666-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	618	917	0	ENST00000296474.3:c.568G>C	p.Glu190Gln	p.E190Q	ENST00000296474	NM_002447.2	190	Gag/Cag	1/20	0.647374088192781	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.645724459952347	2		917	915	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779150	135779169	+	frameshift_variant	Frame_Shift_Del	DEL	TGCAGTAAAAGCAACTGGTC	TGCAGTAAAAGCAACTGGTC	-	novel	NA	P-0039666-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	224	610	0	ENST00000298552.3:c.2077_2096del	p.Asp693GlnfsTer6	p.D693Qfs*6	ENST00000298552	NM_001162426.1	693	GACCAGTTGCTTTTACTGCAc/c	17/23	0.647374088192781	2	FACETS	0.848	0.803	0.893	0.848	0.803	0.893	CLONAL	2	TRUE	0	0.645724459952347	2		610	409	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118656	11118656	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039666-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	251	705	1	ENST00000358026.2:c.2080G>T	p.Asp694Tyr	p.D694Y	ENST00000358026	NM_001128849.1	694	Gac/Tac	14/36	0.645198016903071	3	FACETS	0.949	0.887	1	0.474	0.443	0.506	CLONAL	1	TRUE	1	0.645724459952347	3		706	1084	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11172463	11172463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776222414	NA	P-0039666-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	304	656	1	ENST00000358026.2:c.5011C>T	p.Arg1671Cys	p.R1671C	ENST00000358026	NM_001128849.1	1671	Cgc/Tgc	36/36	0.645198016903071	3	FACETS	1	0.986	1	0.571	0.538	0.605	CLONAL	1	TRUE	1	0.645724459952347	3		657	1090	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118948	61118948	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039666-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	139	341	0	ENST00000295025.8:c.143del	p.Pro48LeufsTer6	p.P48Lfs*6	ENST00000295025	NM_002908.2	47	taC/ta	2/11	0.647374088192781	3	FACETS	0.938	0.857	1	0.469	0.428	0.512	CLONAL	1	TRUE	1	0.645724459952347	3		341	607	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182681729	182681729	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039666-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	196	403	0	ENST00000292782.4:c.329G>C	p.Arg110Thr	p.R110T	ENST00000292782	NM_020640.2	110	aGa/aCa	3/7	0.647374088192781	2	FACETS	1	0.97	1	0.536	0.5	0.574	CLONAL	1	TRUE	0	0.645724459952347	2		403	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0039691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	102	571	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.46665607431873	3	FACETS	0.874	0.783	0.97	0.437	0.391	0.485	CLONAL	1	FALSE	1	0.46665607431873	3		571	617	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0039691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	53	278	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.46665607431873	NA		278	509	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0039691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	148	423	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.46665607431873	NA		423	519	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0039691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	58	231	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.46665607431873	3	FACETS	0.989	0.856	1	0.494	0.428	0.566	CLONAL	1	FALSE	1	0.46665607431873	3		231	310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0039691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	123	617	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.46665607431873	3	FACETS	1	0.986	1	0.739	0.673	0.807	CLONAL	1	FALSE	1	0.46665607431873	3		617	440	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0039691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	151	216	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.46665607431873	4	FACETS	1	0.953	1	1	0.953	1	CLONAL	4	FALSE	0	0.46665607431873	4		216	234	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694712	176694712	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	127	393	0	ENST00000439151.2:c.5296C>T	p.Arg1766Ter	p.R1766*	ENST00000439151	NM_022455.4	1766	Cga/Tga	15/23	0.46665607431873	4	FACETS	1	0.984	1	0.355	0.323	0.389	CLONAL	1	FALSE	0	0.46665607431873	4		393	562	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798846	135798846	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs118203381	NA	P-0039691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	30	260	0	ENST00000298552.3:c.397G>A	p.Val133Ile	p.V133I	ENST00000298552	NM_001162426.1	133	Gtc/Atc	6/23	0.259940746288714	5	FACETS	0.588	0.474	0.717	0.196	0.158	0.239	INDETERMINATE	1	FALSE	2	0.46665607431873	5		260	372	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309846	104309846	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764847917	NA	P-0039691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	45	331	2	ENST00000369902.3:c.437G>A	p.Arg146Gln	p.R146Q	ENST00000369902	NM_016169.3	146	cGa/cAa	3/12	0.259940746288714	5	FACETS	0.771	0.649	0.906	0.257	0.216	0.302	INDETERMINATE	1	FALSE	2	0.46665607431873	5		333	425	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710655	114710655	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	177	391	0	ENST00000543371.1:c.140C>G	p.Ser47Cys	p.S47C	ENST00000543371	NM_001198531.1	47	tCt/tGt	1/14	0.259940746288714	5	FACETS	1	0.965	1	0.713	0.66	0.767	INDETERMINATE	2	FALSE	2	0.46665607431873	5		391	603	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678038	58678038	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs777761218	NA	P-0039691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	47	275	0	ENST00000305921.3:c.263C>G	p.Pro88Arg	p.P88R	ENST00000305921	NM_003620.3	88	cCt/cGt	1/6	0.46665607431873	3	FACETS	0.726	0.615	0.848	0.363	0.307	0.424	SUBCLONAL	1	FALSE	1	0.46665607431873	3		275	342	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575098	48575098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	47	288	0	ENST00000342988.3:c.292C>T	p.Leu98Phe	p.L98F	ENST00000342988	NM_005359.5	98	Ctc/Ttc	3/12	0.437608381109669	2	FACETS	0.586	0.496	0.684	0.293	0.248	0.342	SUBCLONAL	1	FALSE	0	0.46665607431873	2		288	344	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204849	128204849	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	82	485	1	ENST00000341105.2:c.592G>A	p.Ala198Thr	p.A198T	ENST00000341105	NM_032638.4	198	Gcg/Acg	3/6	1	2	FACETS	0.633	0.559	0.712	0.633	0.559	0.712	SUBCLONAL	1	FALSE	1	0.46665607431873	2		486	555	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258974	153258975	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	31	234	0	ENST00000281708.4:c.840dup	p.Ile281HisfsTer6	p.I281Hfs*6	ENST00000281708	NM_033632.3	280	-/C	5/12	0.46665607431873	3	FACETS	0.697	0.567	0.843	0.349	0.283	0.422	SUBCLONAL	1	FALSE	1	0.46665607431873	3		234	235	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831324	72831324	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	62	347	0	ENST00000268489.5:c.5257C>T	p.Gln1753Ter	p.Q1753*	ENST00000268489	NM_006885.3	1753	Caa/Taa	9/10	0.39554277784056	2	FACETS	0.977	0.85	1	0.488	0.425	0.557	CLONAL	1	TRUE	0	0.39554277784056	2		347	321	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120116	70120116	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs112211472	NA	P-0039694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	19	104	0	ENST00000245479.2:c.1118C>G	p.Pro373Arg	p.P373R	ENST00000245479	NM_000346.3	373	cCc/cGc	3/3	0.39554277784056	3	FACETS	1	0.777	1	0.336	0.259	0.425	CLONAL	1	TRUE	0	0.39554277784056	3		104	114	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928063	178928080	+	inframe_deletion	In_Frame_Del	DEL	AGTACCTCATGGATTAGA	AGTACCTCATGGATTAGA	-	novel	NA	P-0039694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	148	459	0	ENST00000263967.3:c.1343_1360del	p.Val448_Glu453del	p.V448_E453del	ENST00000263967	NM_006218.2	447	ccAGTACCTCATGGATTAGAa/cca	8/21	0.303411301935409	4	FACETS	0.845	0.775	0.918	0.845	0.775	0.918	CLONAL	2	TRUE	2	0.39554277784056	4		459	618	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157186	106157186	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	65	382	0	ENST00000380013.4:c.2087C>G	p.Ser696Cys	p.S696C	ENST00000380013	NM_001127208.2	696	tCc/tGc	3/11	0.202484193965294	5	FACETS	0.996	0.864	1	0.332	0.288	0.379	INDETERMINATE	1	TRUE	2	0.39554277784056	5		382	526	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271281	26271281	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	40	474	0	ENST00000305910.3:c.332G>C	p.Cys111Ser	p.C111S	ENST00000305910	NM_003534.2	111	tGt/tCt	1/1	0.232638595125624	5	FACETS	0.533	0.442	0.634	0.178	0.147	0.212	INDETERMINATE	1	TRUE	2	0.39554277784056	5		474	605	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	15	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		298	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0039724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	20	654	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		654	687	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	81	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.466172149699913	1	FACETS	0.768	0.69	0.849	0.768	0.69	0.849	SUBCLONAL	1	TRUE	0	0.65392254634123	1		298	217	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023140	27023155	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCGGCGGCGGCGGA	TGGCGGCGGCGGCGGA	-	novel	NA	P-0039733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	166	38	0	ENST00000324856.7:c.246_261del	p.Gly83ProfsTer13	p.G83Pfs*13	ENST00000324856	NM_006015.4	82	ggTGGCGGCGGCGGCGGA/gg	1/20	0.64667886049042	1	FACETS	0.829	0.794	0.862	1	0.994	1	CLONAL	2	TRUE	0	0.65392254634123	1		38	206	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578196	7578196	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	284	605	0	ENST00000269305.4:c.653T>A	p.Val218Glu	p.V218E	ENST00000269305	NM_001126112.2	218	gTg/gAg	6/11	0.734335132751803	1	FACETS	0.995	0.95	1	0.995	0.95	1	CLONAL	1	TRUE	0	0.753748499976609	1		605	472	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984705	11984705	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0039751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	65	198	0	ENST00000353533.5:c.251C>G	p.Ser84Ter	p.S84*	ENST00000353533	NM_003010.3	84	tCa/tGa	3/11	0.734335132751803	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	0	0.753748499976609	1		198	107	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578188	7578188	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201592	NA	P-0039772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	466	660	0	ENST00000269305.4:c.661G>T	p.Glu221Ter	p.E221*	ENST00000269305	NM_001126112.2	221	Gag/Tag	6/11	0.629272343856133	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.629272343856133	2		660	712	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589149	67589151	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	novel	NA	P-0039772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	93	269	0	ENST00000274335.5:c.1138_1140del	p.Leu380del	p.L380del	ENST00000274335		379	aaATTa/aaa	9/15	0.559335326686653	4	FACETS	0.898	0.811	0.989	0.898	0.811	0.989	CLONAL	2	TRUE	2	0.629272343856133	4		269	268	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696345	47696345	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	285	402	0	ENST00000347630.2:c.478G>A	p.Glu160Lys	p.E160K	ENST00000347630	NM_001007230.1	160	Gag/Aag	6/11	0.629272343856133	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.629272343856133	4		402	683	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023818	27023818	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0039772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	409	379	0	ENST00000324856.7:c.924C>G	p.Tyr308Ter	p.Y308*	ENST00000324856	NM_006015.4	308	taC/taG	1/20	0.614042977433747	4	FACETS	0.997	0.968	1	0.997	0.968	1	CLONAL	4	TRUE	0	0.629272343856133	4		379	531	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192429	138192429	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	102	239	0	ENST00000237289.4:c.65G>C	p.Arg22Pro	p.R22P	ENST00000237289	NM_001270507.1	22	cGg/cCg	2/9	0.629272343856133	3	FACETS	1	0.959	1	0.559	0.504	0.617	CLONAL	1	TRUE	1	0.629272343856133	3		239	381	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0039775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	104	441	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.245887392029887	4	FACETS	0.917	0.826	1	0.917	0.826	1	CLONAL	2	TRUE	2	0.334149399509402	4		441	453	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5465595	5465595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148141792	NA	P-0039775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	113	229	0	ENST00000381577.3:c.779G>A	p.Arg260His	p.R260H	ENST00000381577	NM_014143.3	260	cGt/cAt	5/7	0.245887392029887	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.334149399509402	4		229	380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587782289	NA	P-0039775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	216	611	0	ENST00000269305.4:c.706T>A	p.Tyr236Asn	p.Y236N	ENST00000269305	NM_001126112.2	236	Tac/Aac	7/11	0.307236986398422	2	FACETS	0.922	0.861	0.985	0.922	0.861	0.985	CLONAL	2	TRUE	0	0.334149399509402	2		611	701	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220023	5220023	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1690	255	791	1	ENST00000357368.4:c.3692T>A	p.Phe1231Tyr	p.F1231Y	ENST00000357368	NM_002850.3	1231	tTc/tAc	22/38	0.334149399509402	10	FACETS	0.917	0.854	0.982	0.229	0.213	0.246	CLONAL	2	TRUE	2	0.334149399509402	10		792	1945	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0039783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	194	651	0	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	1	2	FACETS	0.836	0.775	0.9	0.836	0.775	0.9	CLONAL	1	TRUE	1	0.559050697003944	2		651	830	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445302	49445302	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	89	900	1	ENST00000301067.7:c.2164G>T	p.Glu722Ter	p.E722*	ENST00000301067	NM_003482.3	722	Gag/Tag	10/54	0.377057322972193	1	FACETS	0.235	0.207	0.264	0.235	0.207	0.264	SUBCLONAL	1	TRUE	0	0.559050697003944	1		901	977	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420564	49420564	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	95	618	0	ENST00000301067.7:c.15185G>C	p.Cys5062Ser	p.C5062S	ENST00000301067	NM_003482.3	5062	tGt/tCt	48/54	0.377057322972193	1	FACETS	0.354	0.315	0.396	0.354	0.315	0.396	SUBCLONAL	1	TRUE	0	0.559050697003944	1		618	691	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412330	139412330	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	235	737	0	ENST00000277541.6:c.1315del	p.Gln439SerfsTer192	p.Q439Sfs*192	ENST00000277541	NM_017617.3	439	Cag/ag	8/34	1	2	FACETS	0.878	0.819	0.937	0.878	0.819	0.937	CLONAL	1	TRUE	1	0.559050697003944	2		737	958	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374293	138374293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	69	518	0	ENST00000289153.2:c.3151G>A	p.Glu1051Lys	p.E1051K	ENST00000289153	NM_006219.2	1051	Gaa/Aaa	22/22	1	2	FACETS	0.698	0.608	0.795	0.698	0.608	0.795	SUBCLONAL	1	TRUE	1	0.313331699040595	2		518	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0039786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	167	709	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.293996688083474	2	FACETS	0.864	0.797	0.933	0.864	0.797	0.933	CLONAL	2	TRUE	0	0.313331699040595	2		709	617	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473722	67473722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs794727798	NA	P-0039786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	151	637	0	ENST00000327367.4:c.802C>T	p.Arg268Cys	p.R268C	ENST00000327367	NM_005902.3	268	Cgc/Tgc	6/9	0.313331699040595	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.313331699040595	1		637	646	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248599	212248599	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1281587425	NA	P-0039786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	129	473	0	ENST00000342788.4:c.3668A>G	p.Lys1223Arg	p.K1223R	ENST00000342788	NM_005235.2	1223	aAg/aGg	28/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.313331699040595	2		473	621	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39318104	39318104	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	80	497	1	ENST00000373001.3:c.698T>C	p.Val233Ala	p.V233A	ENST00000373001	NM_022157.3	233	gTg/gCg	4/7	0.313331699040595	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.313331699040595	1		498	413	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691182	18691182	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	57	358	0	ENST00000266497.5:c.3293T>C	p.Leu1098Pro	p.L1098P	ENST00000266497		1098	cTt/cCt	23/31	0.313331699040595	2	FACETS	1	0.866	1	0.503	0.433	0.578	CLONAL	1	TRUE	0	0.313331699040595	2		358	362	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587437	29587438	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs1555618821	NA	P-0039786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	102	305	0	ENST00000356175.3:c.4419_4420del	p.His1473GlnfsTer7	p.H1473Qfs*7	ENST00000356175	NM_000267.3	1473	cAT/c	33/57	0.293996688083474	2	FACETS	0.818	0.737	0.902	0.818	0.737	0.902	CLONAL	2	TRUE	0	0.313331699040595	2		305	398	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543923	41543923	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	47	586	1	ENST00000263253.7:c.2214G>C	p.Gln738His	p.Q738H	ENST00000263253	NM_001429.3	738	caG/caC	12/31	0.313331699040595	1	FACETS	0.396	0.333	0.465	0.396	0.333	0.465	SUBCLONAL	1	TRUE	0	0.313331699040595	1		587	639	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517964	8517964	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	64	310	0	ENST00000356435.5:c.1427T>G	p.Ile476Ser	p.I476S	ENST00000356435		476	aTc/aGc	10/35	0.313331699040595	1	FACETS	0.965	0.84	1	0.965	0.84	1	CLONAL	1	TRUE	0	0.313331699040595	1		310	357	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870813	12870814	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0039802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	132	358	0	ENST00000228872.4:c.41_42del	p.Glu14AlafsTer110	p.E14Afs*110	ENST00000228872	NM_004064.3	14	GAg/g	1/3	0.367904786755211	7	FACETS	0.89	0.816	0.965	0.593	0.544	0.644	CLONAL	4	TRUE	1	0.367904786755211	7		358	387	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878278	151878279	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	117	952	0	ENST00000262189.6:c.6666dup	p.Ala2223SerfsTer13	p.A2223Sfs*13	ENST00000262189	NM_170606.2	2222	-/A	36/59	0.329914684798157	4	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	2	0.367904786755211	4		952	414	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	11	326	0				ENST00000310581	NM_198253.2	-/1132			0.351587632774892	0	FACETS	0.276	0.192	0.378			1	SUBCLONAL	1	TRUE	0	0.433820917482169	0		326	104	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0039829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	73	652	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	0.589	0.516	0.669	0.589	0.516	0.669	SUBCLONAL	1	TRUE	1	0.433820917482169	2		652	571	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480341	56480341	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	61	461	0	ENST00000267101.3:c.448G>C	p.Glu150Gln	p.E150Q	ENST00000267101	NM_001982.3	150	Gag/Cag	4/28	0.333706449753785	4	FACETS	0.752	0.649	0.864	0.376	0.324	0.432	SUBCLONAL	1	TRUE	2	0.433820917482169	4		461	536	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	27	392	0	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	1	2	FACETS	0.368	0.293	0.454	0.368	0.293	0.454	SUBCLONAL	1	TRUE	1	0.433820917482169	2		392	338	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	109	607	0	ENST00000267101.3:c.273G>A	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atA	3/28	0.333706449753785	4	FACETS	0.994	0.893	1	0.497	0.446	0.551	CLONAL	1	TRUE	2	0.433820917482169	4		607	725	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	338190	338190	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs370661416	NA	P-0039829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	43	651	0	ENST00000262320.3:c.2521C>T	p.Arg841Ter	p.R841*	ENST00000262320	NM_003502.3	841	Cga/Tga	11/11	1	2	FACETS	0.455	0.381	0.537	0.455	0.381	0.537	SUBCLONAL	1	TRUE	1	0.433820917482169	2		651	436	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482861	67482861	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567005581	NA	P-0039829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	44	416	0	ENST00000327367.4:c.1265C>A	p.Ser422Tyr	p.S422Y	ENST00000327367	NM_005902.3	422	tCc/tAc	9/9	1	2	FACETS	0.466	0.391	0.549	0.466	0.391	0.549	SUBCLONAL	1	TRUE	1	0.433820917482169	2		416	435	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347917	73347917	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs202067860	NA	P-0039829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	30	257	0	ENST00000377767.4:c.1144C>T	p.Arg382Ter	p.R382*	ENST00000377767	NM_014953.3	382	Cga/Tga	8/21	0.310863005400095	4	FACETS	0.665	0.538	0.81	0.333	0.269	0.405	SUBCLONAL	1	TRUE	2	0.433820917482169	4		257	298	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922817	44922826	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGCCTGCC	CCTGCCTGCC	-	novel	NA	P-0039829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	26	208	0	ENST00000377967.4:c.1679_1688del	p.Pro560LeufsTer30	p.P560Lfs*30	ENST00000377967	NM_021140.2	560	CCTGCCTGCCct/ct	16/29	1	1	FACETS	0.489	0.39	0.601	0.489	0.39	0.601	SUBCLONAL	1	TRUE	0	0.433820917482169	1		208	192	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540391	187540391	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0039829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	25	402	0	ENST00000441802.2:c.7349C>G	p.Ser2450Ter	p.S2450*	ENST00000441802	NM_005245.3	2450	tCa/tGa	10/27	1	2	FACETS	0.397	0.314	0.493	0.397	0.314	0.493	SUBCLONAL	1	TRUE	1	0.433820917482169	2		402	290	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041603	47041603	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	29	357	0	ENST00000377604.3:c.1831del	p.Glu611ArgfsTer93	p.E611Rfs*93	ENST00000377604	NM_001204468.1	610	Ggg/gg	17/24	1	1	FACETS	0.501	0.405	0.609	0.501	0.405	0.609	SUBCLONAL	1	TRUE	0	0.433820917482169	1		357	209	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729222	66729222	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	45	477	0	ENST00000307102.5:c.430G>C	p.Glu144Gln	p.E144Q	ENST00000307102	NM_002755.3	144	Gag/Cag	3/11	1	2	FACETS	0.596	0.503	0.699	0.596	0.503	0.699	SUBCLONAL	1	TRUE	1	0.433820917482169	2		477	348	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798378	42798378	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778167932	NA	P-0039829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	59	703	0	ENST00000575354.2:c.4249C>T	p.Arg1417Cys	p.R1417C	ENST00000575354	NM_015125.3	1417	Cgc/Tgc	18/20	0.20160524934893	3	FACETS	0.671	0.578	0.772	0.336	0.289	0.386	INDETERMINATE	1	TRUE	1	0.433820917482169	3		703	493	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938440	76938440	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	36	226	0	ENST00000373344.5:c.2308C>G	p.Gln770Glu	p.Q770E	ENST00000373344	NM_000489.3	770	Cag/Gag	9/35	0.179212971613799	2	FACETS	0.612	0.506	0.731			1	INDETERMINATE	1	TRUE	NA	0.433820917482169	2		226	271	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200485	67200485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	65	683	0	ENST00000312629.5:c.679C>T	p.His227Tyr	p.H227Y	ENST00000312629	NM_003952.2	227	Cac/Tac	8/15	0.310863005400095	4	FACETS	0.693	0.601	0.793	0.347	0.3	0.397	SUBCLONAL	1	TRUE	2	0.433820917482169	4		683	620	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186507007	186507007	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	26	209	0	ENST00000323963.5:c.1173C>G	p.Phe391Leu	p.F391L	ENST00000323963		391	ttC/ttG	11/11	0.255493230696731	3	FACETS	0.462	0.366	0.571	0.231	0.183	0.286	INDETERMINATE	1	TRUE	1	0.433820917482169	3		209	316	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200625	67200625	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	48	755	0	ENST00000312629.5:c.736C>A	p.His246Asn	p.H246N	ENST00000312629	NM_003952.2	246	Cac/Aac	9/15	0.310863005400095	4	FACETS	0.51	0.43	0.598	0.255	0.215	0.299	SUBCLONAL	1	TRUE	2	0.433820917482169	4		755	622	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201481	67201481	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	65	703	0	ENST00000312629.5:c.922C>A	p.Pro308Thr	p.P308T	ENST00000312629	NM_003952.2	308	Ccc/Acc	11/15	0.310863005400095	4	FACETS	0.632	0.547	0.724	0.316	0.273	0.362	SUBCLONAL	1	TRUE	2	0.433820917482169	4		703	680	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201734	67201734	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	46	523	0	ENST00000312629.5:c.1035C>G	p.Phe345Leu	p.F345L	ENST00000312629	NM_003952.2	345	ttC/ttG	12/15	0.310863005400095	4	FACETS	0.655	0.552	0.769	0.328	0.276	0.385	SUBCLONAL	1	TRUE	2	0.433820917482169	4		523	464	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170440	108170440	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0039829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	27	230	0	ENST00000278616.4:c.5006-1G>C		p.X1669_splice	ENST00000278616	NM_000051.3	1669			0.205159971308637	4	FACETS	0.574	0.457	0.707	0.287	0.228	0.354	INDETERMINATE	1	TRUE	2	0.433820917482169	4		230	311	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172389	108172389	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	42	363	0	ENST00000278616.4:c.5192C>T	p.Ser1731Leu	p.S1731L	ENST00000278616	NM_000051.3	1731	tCa/tTa	35/63	0.205159971308637	4	FACETS	0.612	0.511	0.723	0.306	0.255	0.362	INDETERMINATE	1	TRUE	2	0.433820917482169	4		363	454	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487185	56487185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777498890	NA	P-0039829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	60	436	0	ENST00000267101.3:c.1331G>A	p.Arg444Gln	p.R444Q	ENST00000267101	NM_001982.3	444	cGa/cAa	12/28	0.333706449753785	4	FACETS	0.715	0.616	0.822	0.357	0.308	0.411	SUBCLONAL	1	TRUE	2	0.433820917482169	4		436	555	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010560	48010560	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587779920	NA	P-0039829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	24	316	0	ENST00000234420.5:c.188C>A	p.Ser63Tyr	p.S63Y	ENST00000234420	NM_000179.2	63	tCc/tAc	1/10	1	2	FACETS	0.477	0.375	0.593	0.477	0.375	0.593	SUBCLONAL	1	TRUE	1	0.433820917482169	2		316	232	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39690066	39690066	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	24	212	0	ENST00000361337.2:c.91C>G	p.Arg31Gly	p.R31G	ENST00000361337	NM_003286.2	31	Cga/Gga	3/21	1	2	FACETS	0.356	0.279	0.444	0.356	0.279	0.444	SUBCLONAL	1	TRUE	1	0.433820917482169	2		212	311	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419961	41419961	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	23	525	0	ENST00000373198.4:c.360G>C	p.Leu120Phe	p.L120F	ENST00000373198	NM_133170.3	120	ttG/ttC	3/32	0.394954778979282	0	FACETS	0.17	0.132	0.213			1	SUBCLONAL	1	TRUE	0	0.433820917482169	0		525	354	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178941944	178941944	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	45	343	0	ENST00000263967.3:c.2263C>G	p.Leu755Val	p.L755V	ENST00000263967	NM_006218.2	755	Cta/Gta	15/21	0.255493230696731	3	FACETS	0.542	0.455	0.637	0.271	0.227	0.319	INDETERMINATE	1	TRUE	1	0.433820917482169	3		343	466	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541358	187541358	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs367573644	NA	P-0039829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	24	303	0	ENST00000441802.2:c.6382C>G	p.Gln2128Glu	p.Q2128E	ENST00000441802	NM_005245.3	2128	Caa/Gaa	10/27	1	2	FACETS	0.457	0.359	0.569	0.457	0.359	0.569	SUBCLONAL	1	TRUE	1	0.433820917482169	2		303	242	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509431	149509431	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	46	679	0	ENST00000261799.4:c.1468G>C	p.Glu490Gln	p.E490Q	ENST00000261799	NM_002609.3	490	Gag/Cag	10/23	1	2	FACETS	0.347	0.292	0.408	0.347	0.292	0.408	SUBCLONAL	1	TRUE	1	0.433820917482169	2		679	611	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277050	38277050	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0039829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	22	425	0	ENST00000425967.3:c.1377+1G>T		p.X459_splice	ENST00000425967	NM_001174067.1	459			1	2	FACETS	0.327	0.253	0.413	0.327	0.253	0.413	SUBCLONAL	1	TRUE	1	0.433820917482169	2		425	310	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741802	145741802	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs746487281	NA	P-0039829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	79	700	0	ENST00000428558.2:c.701C>G	p.Ser234Cys	p.S234C	ENST00000428558	NM_004260.3	234	tCc/tGc	5/22	1	2	FACETS	0.76	0.671	0.856	0.76	0.671	0.856	SUBCLONAL	1	TRUE	1	0.433820917482169	2		700	479	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	143	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.375217444927729	3	FACETS	0.897	0.823	0.974	0.897	0.823	0.974	CLONAL	2	TRUE	1	0.376529701448061	3		426	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0039833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	618	797	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.376529701448061	4	FACETS	0.944	0.917	0.971	1	0.996	1	CLONAL	5	TRUE	0	0.376529701448061	4		799	957	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005429	29005429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372354806	NA	P-0039833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	109	271	0	ENST00000282397.4:c.832G>A	p.Val278Ile	p.V278I	ENST00000282397	NM_002019.4	278	Gta/Ata	7/30	0.376529701448061	6	FACETS	0.887	0.799	0.98	0.444	0.399	0.49	CLONAL	2	TRUE	2	0.376529701448061	6		271	572	SUCCESS
APC	324	MSKCC	GRCh37	5	112175217	112175217	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	110	188	0	ENST00000257430.4:c.3929del	p.Lys1310ArgfsTer11	p.K1310Rfs*11	ENST00000257430	NM_000038.5	1309	gAa/ga	16/16	0.376529701448061	4	FACETS	0.898	0.825	0.97	0.898	0.825	0.97	CLONAL	4	TRUE	0	0.376529701448061	4		188	224	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014180	14014180	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	156	476	0	ENST00000311895.7:c.158G>T	p.Cys53Phe	p.C53F	ENST00000311895	NM_005236.2	53	tGc/tTc	1/11	0.156531324767363	6	FACETS	0.882	0.812	0.954	0.882	0.812	0.954	INDETERMINATE	3	TRUE	3	0.376529701448061	6		476	549	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257943	19257943	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762715467	NA	P-0039833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	271	843	0	ENST00000162023.5:c.443C>T	p.Pro148Leu	p.P148L	ENST00000162023		148	cCg/cTg	9/13	0.0756403580593934	4	FACETS	0.893	0.837	0.949	0.893	0.837	0.949	INDETERMINATE	2	TRUE	2	0.376529701448061	4		843	1110	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010562	48010562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587779921	NA	P-0039833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	72	285	0	ENST00000234420.5:c.190G>A	p.Ala64Thr	p.A64T	ENST00000234420	NM_000179.2	64	Gcg/Acg	1/10	0.292206249534064	3	FACETS	0.988	0.866	1	0.494	0.433	0.56	CLONAL	1	TRUE	1	0.376529701448061	3		285	460	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336664	81336664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	16	210	0	ENST00000222390.5:c.1558G>A	p.Gly520Arg	p.G520R	ENST00000222390	NM_000601.4	520	Gga/Aga	14/18	1	2	FACETS	0.694	0.513	0.91	0.694	0.513	0.91	SUBCLONAL	1	TRUE	1	0.18	2		210	256	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0039930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	329	500	11	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.87912216032618	1	FACETS	0.69	0.659	0.721	0.69	0.659	0.721	SUBCLONAL	1	TRUE	0	0.87912216032618	1		511	608	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602493	10602493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	127	422	0	ENST00000171111.5:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000171111	NM_203500.1	362	cGg/cAg	3/6	0.87912216032618	1	FACETS	0.299	0.272	0.328	0.299	0.272	0.328	SUBCLONAL	1	TRUE	0	0.87912216032618	1		422	541	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118941	115118941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	201	193	1	ENST00000257566.3:c.400C>T	p.Pro134Ser	p.P134S	ENST00000257566	NM_016569.3	134	Cct/Tct	2/8	0.87912216032618	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.87912216032618	1		194	242	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692847	89692847	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123321	NA	P-0039930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	159	136	7	ENST00000371953.3:c.331T>C	p.Trp111Arg	p.W111R	ENST00000371953	NM_000314.4	111	Tgg/Cgg	5/9	0.87912216032618	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.87912216032618	1		143	196	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942562	71942562	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	355	305	7	ENST00000298229.2:c.1518G>A	p.Trp506Ter	p.W506*	ENST00000298229	NM_001567.3	506	tgG/tgA	13/28	0.87912216032618	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.87912216032618	1		312	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579328	7579328	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	144	487	0	ENST00000269305.4:c.359A>G	p.Lys120Arg	p.K120R	ENST00000269305	NM_001126112.2	120	aAg/aGg	4/11	0.87912216032618	1	FACETS	0.295	0.27	0.322	0.295	0.27	0.322	SUBCLONAL	1	TRUE	0	0.87912216032618	1		487	622	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81902896	81902896	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	86	315	0	ENST00000359376.3:c.557A>C	p.Lys186Thr	p.K186T	ENST00000359376	NM_002661.3	186	aAg/aCg	6/33	0.87912216032618	1	FACETS	0.258	0.229	0.289	0.258	0.229	0.289	SUBCLONAL	1	TRUE	0	0.87912216032618	1		315	425	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039194	49039194	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	110	339	0	ENST00000267163.4:c.2272T>C	p.Ser758Pro	p.S758P	ENST00000267163	NM_000321.2	758	Tcg/Ccg	22/27	0.738791603367494	0	FACETS		NA	1			1	NA	1	TRUE	0	0.87912216032618	0		339	175	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321586	30321586	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	78	222	0	ENST00000322652.5:c.1441C>T	p.His481Tyr	p.H481Y	ENST00000322652	NM_015355.2	481	Cat/Tat	13/16	0.87912216032618	1	FACETS	0.333	0.295	0.372	0.333	0.295	0.372	SUBCLONAL	1	TRUE	0	0.87912216032618	1		222	299	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581229	48581229	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs377767331	NA	P-0039934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	123	517	0	ENST00000342988.3:c.533C>G	p.Ser178Ter	p.S178*	ENST00000342988	NM_005359.5	178	tCa/tGa	5/12	0.449200497858898	2	FACETS	0.946	0.858	1	0.473	0.429	0.519	CLONAL	1	TRUE	0	0.449200497858898	2		517	579	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	221	518	1	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	0.368100269619528	2	FACETS	0.771	0.722	0.821	0.771	0.722	0.821	SUBCLONAL	2	TRUE	0	0.449200497858898	2		519	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0039934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	436	796	2	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.449200497858898	2	FACETS	0.971	0.929	1	0.971	0.929	1	CLONAL	2	TRUE	0	0.449200497858898	2		798	1000	SUCCESS
APC	324	MSKCC	GRCh37	5	112155043	112155043	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0039934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	293	378	0	ENST00000257430.4:c.1312+2T>G		p.X438_splice	ENST00000257430	NM_000038.5	438			0.398900909455192	3	FACETS	0.873	0.829	0.917	0.873	0.829	0.917	CLONAL	3	TRUE	0	0.449200497858898	3		378	610	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937187	36937187	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	67	778	2	ENST00000361632.4:c.1132T>C	p.Ser378Pro	p.S378P	ENST00000361632		378	Tca/Cca	9/16	1	2	FACETS	0.308	0.266	0.353	0.308	0.266	0.353	SUBCLONAL	1	TRUE	1	0.449200497858898	2		780	969	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119045	70119045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	185	626	1	ENST00000245479.2:c.617C>T	p.Ala206Val	p.A206V	ENST00000245479	NM_000346.3	206	gCg/gTg	2/3	0.436601904426571	3	FACETS	1	0.948	1	0.517	0.477	0.558	CLONAL	1	TRUE	1	0.449200497858898	3		627	976	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378641	25378641	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	143	416	0	ENST00000311936.3:c.357T>G	p.Asp119Glu	p.D119E	ENST00000311936	NM_004985.3	119	gaT/gaG	4/5	0.329218003256742	3	FACETS	0.837	0.769	0.907	0.837	0.769	0.907	CLONAL	2	TRUE	1	0.449200497858898	3		416	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764146326	NA	P-0039936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	198	721	0	ENST00000269305.4:c.841G>T	p.Asp281Tyr	p.D281Y	ENST00000269305	NM_001126112.2	281	Gac/Tac	8/11	0.24460119673104	2	FACETS	1	0.99	1	0.708	0.657	0.761	CLONAL	1	TRUE	0	0.349953872885677	2		721	799	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0039936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	28	170	0	ENST00000349496.5:c.101G>A	p.Gly34Glu	p.G34E	ENST00000349496	NM_001904.3	34	gGa/gAa	3/15	1	2	FACETS	0.506	0.405	0.621	0.506	0.405	0.621	SUBCLONAL	1	TRUE	1	0.349953872885677	2		170	316	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022499	12022499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200351280	NA	P-0039936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	78	620	0	ENST00000396373.4:c.605G>A	p.Arg202Gln	p.R202Q	ENST00000396373	NM_001987.4	202	cGg/cAg	5/8	0.232823554100808	3	FACETS	0.808	0.71	0.913	0.404	0.355	0.457	CLONAL	1	TRUE	1	0.349953872885677	3		620	648	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873158	71873158	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	37	315	1	ENST00000357731.5:c.1036T>A	p.Phe346Ile	p.F346I	ENST00000357731	NM_173808.2	346	Ttc/Atc	7/7	0.226660998758631	3	FACETS	0.634	0.523	0.757	0.211	0.174	0.253	SUBCLONAL	1	TRUE	0	0.349953872885677	3		316	392	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039967-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	60	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.22	2		298	505	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0039967-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	10	764	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.186	0.125	0.263	0.186	0.125	0.263	SUBCLONAL	1	TRUE	1	0.22	2		764	490	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984927	101984927	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039967-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	32	336	0	ENST00000282441.5:c.374C>G	p.Ala125Gly	p.A125G	ENST00000282441	NM_001130145.2	125	gCt/gGt	2/9	1	2	FACETS	0.722	0.586	0.875	0.722	0.586	0.875	SUBCLONAL	1	TRUE	1	0.22	2		336	403	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974696	21974697	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039967-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	46	476	0	ENST00000304494.5:c.130dup	p.Tyr44LeufsTer76	p.Y44Lfs*76	ENST00000304494	NM_000077.4	44	tac/tTac	1/3	1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	1	0.22	2		476	417	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158504	26158504	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039967-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	27	520	0	ENST00000289316.2:c.107A>G	p.Glu36Gly	p.E36G	ENST00000289316	NM_138720.2	36	gAg/gGg	1/2	1	2	FACETS	0.47	0.373	0.582	0.47	0.373	0.582	SUBCLONAL	1	TRUE	1	0.22	2		520	522	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954221	48954221	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0039971-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	47	192	0	ENST00000267163.4:c.1421+1G>A		p.X474_splice	ENST00000267163	NM_000321.2	474			0.694691914416497	1	FACETS	0.92	0.807	1	0.92	0.807	1	CLONAL	1	TRUE	0	0.694691914416497	1		192	96	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940370	49940370	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039971-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	294	617	0	ENST00000296474.3:c.673G>C	p.Ala225Pro	p.A225P	ENST00000296474	NM_002447.2	225	Gcc/Ccc	1/20	0.694691914416497	3	FACETS	1	0.959	1	0.511	0.481	0.542	CLONAL	1	TRUE	1	0.694691914416497	3		617	1115	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7590608	7590710	+	splice_donor_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	GCCCCAGCGATTTTCCCGAGCTGAAAATACACGGAGCCGAGAGCCCGTGACTCAGAGAGGACTCATCAAGTTCAGTCAGGAGCTTACCCAATCCAGGGAAGCG	GCCCCAGCGATTTTCCCGAGCTGAAAATACACGGAGCCGAGAGCCCGTGACTCAGAGAGGACTCATCAAGTTCAGTCAGGAGCTTACCCAATCCAGGGAAGCG	TCGC	novel	NA	P-0039971-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	256	490	3	ENST00000269305.4:c.-44_-29+87delinsGCGA		p.X15_splice	ENST00000269305	NM_001126112.2	15		1/11	0.694691914416497	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.694691914416497	1		493	466	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24135758	24135758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	96	457	0	ENST00000263121.7:c.245C>T	p.Thr82Met	p.T82M	ENST00000263121	NM_003073.3	82	aCg/aTg	3/9	0.320666345902482	3	FACETS	1	0.98	1	0.719	0.644	0.798	CLONAL	1	TRUE	1	0.347540967533073	3		457	451	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421039	49421039	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123721	NA	P-0039981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	152	539	1	ENST00000301067.7:c.14710C>T	p.Arg4904Ter	p.R4904*	ENST00000301067	NM_003482.3	4904	Cga/Tga	48/54	0.347540967533073	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.347540967533073	2		540	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578548	7578553	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GGGAGT	GGGAGT	-	novel	NA	P-0039981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	187	934	0	ENST00000269305.4:c.377_382del	p.Tyr126_Pro128delinsSer	p.Y126_P128delinsS	ENST00000269305	NM_001126112.2	126	tACTCCCct/tct	5/11	0.347540967533073	2	FACETS	0.807	0.748	0.867	0.807	0.748	0.867	CLONAL	2	TRUE	0	0.347540967533073	2		934	667	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222748	5222748	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	207	767	0	ENST00000357368.4:c.3055G>T	p.Gly1019Cys	p.G1019C	ENST00000357368	NM_002850.3	1019	Ggc/Tgc	18/38	0.327724604238522	3	FACETS	0.917	0.854	0.983	0.917	0.854	0.983	CLONAL	2	TRUE	1	0.347540967533073	3		767	762	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245359	153245359	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	129	464	0	ENST00000281708.4:c.1832del	p.Gly611AspfsTer17	p.G611Dfs*17	ENST00000281708	NM_033632.3	611	gGa/ga	11/12	0.34722865847421	3	FACETS	0.884	0.806	0.964	0.884	0.806	0.964	CLONAL	2	TRUE	1	0.347540967533073	3		464	493	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258742	16258742	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	52	508	0	ENST00000375759.3:c.6007G>T	p.Glu2003Ter	p.E2003*	ENST00000375759	NM_015001.2	2003	Gaa/Taa	11/15	1	2	FACETS	0.823	0.702	0.955	0.823	0.702	0.955	CLONAL	1	TRUE	1	0.285385854722504	2		508	443	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109323510	109323511	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0039997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	56	544	0	ENST00000436639.2:c.314_315dup	p.Gly106ArgfsTer41	p.G106Rfs*41	ENST00000436639	NM_014454.2	105	-/AG	2/10	1	2	FACETS	0.445	0.38	0.515	0.445	0.38	0.515	SUBCLONAL	1	TRUE	1	0.401798577243498	2		544	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0040007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	494	797	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.672423230396942	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.68420394736088	2		799	658	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211656	5211656	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	174	774	0	ENST00000357368.4:c.5179A>T	p.Ile1727Phe	p.I1727F	ENST00000357368	NM_002850.3	1727	Atc/Ttc	33/38	1	2	FACETS	0.982	0.911	1	0.982	0.911	1	CLONAL	1	TRUE	1	0.68420394736088	2		774	518	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136330	202136330	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	16	469	0	ENST00000358485.4:c.574C>G	p.Leu192Val	p.L192V	ENST00000358485	NM_001080125.1	192	Ctg/Gtg	3/9	0.571370101885994	1	FACETS	0.159	0.117	0.208	0.159	0.117	0.208	SUBCLONAL	1	TRUE	0	0.68420394736088	1		469	194	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842397	68842398	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0040009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	173	637	0	ENST00000261769.5:c.463_464del	p.Asp155LeufsTer12	p.D155Lfs*12	ENST00000261769	NM_004360.3	153	aAG/a	4/16	0.386904082769422	1	FACETS	0.938	0.865	1	0.938	0.865	1	CLONAL	1	FALSE	0	0.386904082769422	1		637	769	SUCCESS
REL	5966	MSKCC	GRCh37	2	61128218	61128218	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	68	183	0	ENST00000295025.8:c.394G>T	p.Val132Phe	p.V132F	ENST00000295025	NM_002908.2	132	Gtc/Ttc	4/11	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	FALSE	1	0.386904082769422	2		183	346	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197241	26197241	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	134	602	0	ENST00000356476.2:c.238A>C	p.Lys80Gln	p.K80Q	ENST00000356476		80	Aag/Cag	1/1	1	2	FACETS	0.988	0.899	1	0.988	0.899	1	CLONAL	1	FALSE	1	0.386904082769422	2		602	701	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579406	7579406	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	231	790	0	ENST00000269305.4:c.281C>A	p.Ser94Ter	p.S94*	ENST00000269305	NM_001126112.2	94	tCa/tAa	4/11	0.509691019378707	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.509691019378707	1		790	604	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897445	78897445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334868419	NA	P-0040032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	57	713	0	ENST00000306801.3:c.2780G>A	p.Arg927Gln	p.R927Q	ENST00000306801	NM_020761.2	927	cGg/cAg	23/34	0.393299100160572	3	FACETS	0.261	0.223	0.303	0.131	0.111	0.152	SUBCLONAL	1	TRUE	1	0.509691019378707	3		713	1075	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143226689	143226689	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs149208667	NA	P-0040032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	97	310	0	ENST00000262992.4:c.425G>A	p.Arg142Gln	p.R142Q	ENST00000262992	NM_001101669.1	142	cGa/cAa	7/24	0.509691019378707	1	FACETS	0.854	0.77	0.942	0.854	0.77	0.942	CLONAL	1	TRUE	0	0.509691019378707	1		310	332	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143273	58143273	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	40	336	2	ENST00000257904.6:c.647G>C	p.Gly216Ala	p.G216A	ENST00000257904	NM_000075.3	216	gGa/gCa	6/8	1	2	FACETS	0.424	0.353	0.503	0.424	0.353	0.503	SUBCLONAL	1	TRUE	1	0.509691019378707	2		338	370	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70442624	70442624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755430373	NA	P-0040032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	96	476	0	ENST00000373644.4:c.4946G>A	p.Arg1649Gln	p.R1649Q	ENST00000373644	NM_030625.2	1649	cGg/cAg	10/12	1	2	FACETS	0.678	0.605	0.754	0.678	0.605	0.754	SUBCLONAL	1	TRUE	1	0.509691019378707	2		476	556	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	465622	465622	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2724	171	563	0	ENST00000399788.2:c.754G>T	p.Ala252Ser	p.A252S	ENST00000399788	NM_001042603.1	252	Gca/Tca	6/28	0.509691019378707	12	FACETS	0.822	0.752	0.897			1	CLONAL	1	TRUE	NA	0.509691019378707	12		563	2895	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18439796	18439796	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	29	339	0	ENST00000266497.5:c.694A>C	p.Ile232Leu	p.I232L	ENST00000266497		232	Att/Ctt	2/31	0.178433660323004	2	FACETS	0.211	0.169	0.26	0.106	0.084	0.13	INDETERMINATE	1	TRUE	0	0.509691019378707	2		339	539	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436322	110436322	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	104	331	0	ENST00000375856.3:c.2079G>T	p.Arg693Ser	p.R693S	ENST00000375856	NM_003749.2	693	agG/agT	1/2	1	2	FACETS	0.779	0.709	0.85	1	0.986	1	SUBCLONAL	2	TRUE	1	0.509691019378707	2		331	262	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987012	36987012	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	176	582	0	ENST00000354822.5:c.677G>T	p.Ser226Ile	p.S226I	ENST00000354822	NM_001079668.2	226	aGc/aTc	3/3	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.509691019378707	2		582	644	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534319	63534549	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCTCTCGGATCTGCTGCAGGCGCTCCTCCAGGCTGTGGCGGCTCTCCAACTCCAGCTTCAGCTTTTCCAGCCTCGAGATCAGCTCAGCTGCAAAGGTGGCGGGTTCCACGGGGGTCATCTCCTTGGGCAGGCGGTGGGTTCTCTACAGGACGTGGAAAGGAAAGGGAGGAGGCACGTTCAGCAGGCTAGGTGGGCGGTGGCTTGGCCGGAGCTTCCCGCACCAGGCGCTG	ACCTCTCGGATCTGCTGCAGGCGCTCCTCCAGGCTGTGGCGGCTCTCCAACTCCAGCTTCAGCTTTTCCAGCCTCGAGATCAGCTCAGCTGCAAAGGTGGCGGGTTCCACGGGGGTCATCTCCTTGGGCAGGCGGTGGGTTCTCTACAGGACGTGGAAAGGAAAGGGAGGAGGCACGTTCAGCAGGCTAGGTGGGCGGTGGCTTGGCCGGAGCTTCCCGCACCAGGCGCTG	-	novel	NA	P-0040032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	108	693	0	ENST00000307078.5:c.1060-88_1200+2del		p.X354_splice	ENST00000307078	NM_004655.3	354		5/11	0.509691019378707	1	FACETS	0.62	0.559	0.685	0.62	0.559	0.685	SUBCLONAL	1	TRUE	0	0.509691019378707	1		693	509	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982038	70982038	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040034-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	55	852	0	ENST00000276594.2:c.58G>A	p.Glu20Lys	p.E20K	ENST00000276594	NM_024504.3	20	Gag/Aag	2/8	0.392241731747764	4	FACETS	0.641	0.55	0.739	0.16	0.137	0.185	INDETERMINATE	1	TRUE	0	0.801325762556395	4		852	386	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578487	7578488	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAACCC	novel	NA	P-0040034-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	133	959	0	ENST00000269305.4:c.437_442dup	p.Val147_Asp148insGlyVal	p.V147_D148insGV	ENST00000269305	NM_001126112.2	148	gat/gGGGTTGat	5/11	0.801325762556395	2	FACETS	0.826	0.775	0.874	0.826	0.775	0.874	CLONAL	2	TRUE	0	0.801325762556395	2		959	201	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36940993	36940993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040034-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	38	633	0	ENST00000361632.4:c.346G>A	p.Glu116Lys	p.E116K	ENST00000361632		116	Gag/Aag	3/16	0.477477362430226	3	FACETS	0.531	0.442	0.63	0.266	0.221	0.315	INDETERMINATE	1	TRUE	1	0.801325762556395	3		633	250	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210420	2210420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763560759	NA	P-0040034-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	39	770	1	ENST00000398665.3:c.1027C>T	p.Arg343Cys	p.R343C	ENST00000398665	NM_032482.2	343	Cgc/Tgc	13/28	0.580228915498976	3	FACETS	0.509	0.424	0.602	0.254	0.212	0.301	SUBCLONAL	1	TRUE	1	0.801325762556395	3		771	268	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0040039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	95	551	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.2730554737396	2		551	576	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs121913292	NA	P-0040039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	40	491	0	ENST00000371953.3:c.389del	p.Arg130GlnfsTer4	p.R130Qfs*4	ENST00000371953	NM_000314.4	130	cGa/ca	5/9	1	2	FACETS	0.509	0.422	0.606	0.509	0.422	0.606	SUBCLONAL	1	TRUE	1	0.2730554737396	2		491	576	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279674	123279674	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs77543610	NA	P-0040039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	70	415	0	ENST00000358487.5:c.758C>G	p.Pro253Arg	p.P253R	ENST00000358487	NM_000141.4	253	cCt/cGt	7/18	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.2730554737396	2		415	448	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591145	67591154	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TACTTGATGT	TACTTGATGT	-	novel	NA	P-0040039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	21	322	0	ENST00000274335.5:c.1738_1745+2del		p.X580_splice	ENST00000274335		580		12/15	0.217639561027274	3	FACETS	0.454	0.349	0.577	0.227	0.174	0.289	SUBCLONAL	1	TRUE	1	0.2730554737396	3		322	385	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971114	21971115	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGGTCGGGTGAGAGTGGCG	novel	NA	P-0040039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	79	681	0	ENST00000304494.5:c.225_243dup	p.Val82ArgfsTer44	p.V82Rfs*44	ENST00000304494	NM_000077.4	81	-/CGCCACTCTCACCCGACCC	2/3	0.190753598755564	2	FACETS	0.721	0.634	0.816	0.361	0.317	0.408	SUBCLONAL	1	TRUE	0	0.2730554737396	2		681	802	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278886	1278886	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	145	714	3	ENST00000310581.5:c.2156C>A	p.Thr719Asn	p.T719N	ENST00000310581	NM_198253.2	719	aCc/aAc	6/16	0.217639561027274	3	FACETS	1	0.982	1	0.646	0.589	0.706	CLONAL	1	TRUE	1	0.2730554737396	3		717	934	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591265	67591265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	72	455	0	ENST00000274335.5:c.1763G>A	p.Gly588Asp	p.G588D	ENST00000274335		588	gGt/gAt	13/15	0.217639561027274	3	FACETS	1	0.879	1	0.503	0.439	0.571	CLONAL	1	TRUE	1	0.2730554737396	3		455	596	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371753	55371761	+	inframe_deletion	In_Frame_Del	DEL	TGAAGCGGG	TGAAGCGGG	-	novel	NA	P-0040039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	34	461	0	ENST00000297316.4:c.445_453del	p.Lys149_Val151del	p.K149_V151del	ENST00000297316	NM_022454.3	148	cTGAAGCGGGtg/ctg	2/2	1	2	FACETS	0.397	0.323	0.481	0.397	0.323	0.481	SUBCLONAL	1	TRUE	1	0.2730554737396	2		461	627	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	197	381	1	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.869	0.811	0.929	0.869	0.811	0.929	CLONAL	1	TRUE	1	0.83	2		382	546	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	236	494	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.92	0.865	0.977	0.92	0.865	0.977	CLONAL	1	TRUE	1	0.83	2		494	618	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	246	723	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.935	0.88	0.991	0.935	0.88	0.991	CLONAL	1	TRUE	1	0.83	2		723	634	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440904	56440904	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1458799446	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	314	632	1	ENST00000407977.2:c.433C>T	p.Arg145Ter	p.R145*	ENST00000407977		145	Cga/Tga	4/10	1	2	FACETS	0.983	0.932	1	0.983	0.932	1	CLONAL	1	TRUE	1	0.83	2		633	770	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913403	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	166	312	0	ENST00000349496.5:c.110C>A	p.Ser37Tyr	p.S37Y	ENST00000349496	NM_001904.3	37	tCt/tAt	3/15	1	2	FACETS	0.995	0.925	1	0.995	0.925	1	CLONAL	1	TRUE	1	0.83	2		312	402	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106094	8106094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	196	428	0	ENST00000346208.3:c.914G>A	p.Arg305Gln	p.R305Q	ENST00000346208		305	cGa/cAa	4/6	1	2	FACETS	0.914	0.853	0.975	0.914	0.853	0.975	CLONAL	1	TRUE	1	0.83	2		428	517	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	115	317	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	0.815	0.743	0.889	0.815	0.743	0.889	CLONAL	1	TRUE	1	0.83	2		317	340	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	178	346	1	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	1	2	FACETS	0.964	0.898	1	0.964	0.898	1	CLONAL	1	TRUE	1	0.83	2		347	445	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068357	26068357	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	128	280	0	ENST00000435504.4:c.133G>T	p.Glu45Ter	p.E45*	ENST00000435504		45	Gaa/Taa	2/13	1	2	FACETS	0.871	0.799	0.945	0.871	0.799	0.945	CLONAL	1	TRUE	1	0.83	2		280	354	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720870	89720870	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1554825652	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	177	276	1	ENST00000371953.3:c.1021T>G	p.Phe341Val	p.F341V	ENST00000371953	NM_000314.4	341	Ttt/Gtt	8/9	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.83	2		277	423	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	251	426	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.83	2		426	602	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001303	29001303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201407326	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	149	239	0	ENST00000282397.4:c.1429G>A	p.Glu477Lys	p.E477K	ENST00000282397	NM_002019.4	477	Gaa/Aaa	10/30	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.83	2		239	324	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259962	16259962	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	317	560	0	ENST00000375759.3:c.7227G>T	p.Glu2409Asp	p.E2409D	ENST00000375759	NM_015001.2	2409	gaG/gaT	11/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.83	2		560	715	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987413	2987413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	197	365	0	ENST00000396946.4:c.16C>T	p.Pro6Ser	p.P6S	ENST00000396946	NM_032415.4	6	Cca/Tca	3/25	1	2	FACETS	0.959	0.897	1	0.959	0.897	1	CLONAL	1	TRUE	1	0.83	2		365	495	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996829	100996829	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	109	479	0	ENST00000325455.5:c.1698T>G	p.Ile566Met	p.I566M	ENST00000325455	NM_001202474.3	566	atT/atG	2/8	1	2	FACETS	0.464	0.418	0.513	0.464	0.418	0.513	SUBCLONAL	1	TRUE	1	0.83	2		479	566	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280068	66280068	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	111	208	0	ENST00000273854.3:c.1621C>T	p.Arg541Ter	p.R541*	ENST00000273854	NM_004439.5	541	Cga/Tga	7/18	1	2	FACETS	0.955	0.873	1	0.955	0.873	1	CLONAL	1	TRUE	1	0.83	2		208	280	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	179	653	0	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	0.762	0.707	0.819	0.762	0.707	0.819	SUBCLONAL	1	TRUE	1	0.83	2		653	566	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134594	41134594	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	153	360	0	ENST00000379561.5:c.1034C>A	p.Ser345Tyr	p.S345Y	ENST00000379561	NM_002015.3	345	tCt/tAt	2/3	1	2	FACETS	0.789	0.728	0.852	0.789	0.728	0.852	SUBCLONAL	1	TRUE	1	0.83	2		360	467	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88677032	88677032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782400	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	149	289	0	ENST00000372037.3:c.817C>T	p.Arg273Ter	p.R273*	ENST00000372037	NM_004329.2	273	Cga/Tga	9/13	1	2	FACETS	0.96	0.888	1	0.96	0.888	1	CLONAL	1	TRUE	1	0.83	2		289	374	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250046	53250046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1569282235	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	266	601	0	ENST00000375401.3:c.203G>A	p.Arg68Gln	p.R68Q	ENST00000375401	NM_004187.3	68	cGa/cAa	2/26	1	2	FACETS	0.817	0.769	0.865	0.817	0.769	0.865	CLONAL	1	TRUE	1	0.83	2		601	785	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858746	9858746	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	129	270	0	ENST00000330684.3:c.2655C>A	p.Phe885Leu	p.F885L	ENST00000330684	NM_001134407.1	885	ttC/ttA	13/13	1	2	FACETS	0.984	0.905	1	0.984	0.905	1	CLONAL	1	TRUE	1	0.83	2		270	316	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690814	89690814	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	110	244	0	ENST00000371953.3:c.221G>T	p.Arg74Ile	p.R74I	ENST00000371953	NM_000314.4	74	aGa/aTa	4/9	1	2	FACETS	0.878	0.8	0.958	0.878	0.8	0.958	CLONAL	1	TRUE	1	0.83	2		244	302	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685312	86685312	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	171	121	0	ENST00000274376.6:c.3028C>T	p.Arg1010Ter	p.R1010*	ENST00000274376	NM_002890.2	1010	Cga/Tga	24/25	1	2	FACETS	1	0.989	1	1	0.995	1	CLONAL	2	TRUE	1	0.83	2		121	193	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636719	176636719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140095431	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	189	336	0	ENST00000439151.2:c.1319G>A	p.Arg440Gln	p.R440Q	ENST00000439151	NM_022455.4	440	cGa/cAa	5/23	1	2	FACETS	0.951	0.887	1	0.951	0.887	1	CLONAL	1	TRUE	1	0.83	2		336	479	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845627	63845627	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	95	169	0	ENST00000279873.7:c.1366G>T	p.Glu456Ter	p.E456*	ENST00000279873	NM_032199.2	456	Gaa/Taa	9/10	1	2	FACETS	0.987	0.896	1	0.987	0.896	1	CLONAL	1	TRUE	1	0.83	2		169	232	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827580	72827580	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	304	601	0	ENST00000268489.5:c.9001G>T	p.Glu3001Ter	p.E3001*	ENST00000268489	NM_006885.3	3001	Gaa/Taa	9/10	1	2	FACETS	0.949	0.899	1	0.949	0.899	1	CLONAL	1	TRUE	1	0.83	2		601	772	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317559	1317559	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	170	380	0	ENST00000400841.2:c.506A>G	p.Asn169Ser	p.N169S	ENST00000400841		169	aAc/aGc	5/6	1	2	FACETS	0.881	0.818	0.945	0.881	0.818	0.945	CLONAL	1	TRUE	1	0.83	2		380	465	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736142	204736142	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	158	310	0	ENST00000302823.3:c.499C>A	p.Leu167Ile	p.L167I	ENST00000302823	NM_005214.4	167	Ctt/Att	3/4	1	2	FACETS	0.863	0.799	0.929	0.863	0.799	0.929	CLONAL	1	TRUE	1	0.83	2		310	441	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262885	46262885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761607812	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	228	362	1	ENST00000371998.3:c.1058G>A	p.Arg353Gln	p.R353Q	ENST00000371998		353	cGa/cAa	10/23	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.83	2		363	518	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165729	108165729	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs762083530	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	19	294	0	ENST00000278616.4:c.4852C>T	p.Arg1618Ter	p.R1618*	ENST00000278616	NM_000051.3	1618	Cga/Tga	32/63	1	2	FACETS	0.131	0.099	0.169	0.131	0.099	0.169	SUBCLONAL	1	TRUE	1	0.83	2		294	350	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	461462	461462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	95	383	0	ENST00000399788.2:c.1058G>A	p.Gly353Glu	p.G353E	ENST00000399788	NM_001042603.1	353	gGa/gAa	9/28	0.3	2	FACETS	0.43	0.384	0.479			1	INDETERMINATE	1	TRUE	NA	0.83	2		383	532	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134924	41134924	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	115	283	0	ENST00000379561.5:c.704C>A	p.Ser235Tyr	p.S235Y	ENST00000379561	NM_002015.3	235	tCt/tAt	2/3	1	2	FACETS	0.801	0.73	0.874	0.801	0.73	0.874	CLONAL	1	TRUE	1	0.83	2		283	346	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890120	76890120	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	26	413	0	ENST00000373344.5:c.4774C>A	p.Leu1592Ile	p.L1592I	ENST00000373344	NM_000489.3	1592	Ctt/Att	17/35	1	2	FACETS	0.144	0.114	0.179	0.144	0.114	0.179	SUBCLONAL	1	TRUE	1	0.83	2		413	435	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064380	30064380	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	227	454	0	ENST00000338641.4:c.944C>A	p.Ser315Tyr	p.S315Y	ENST00000338641	NM_000268.3	315	tCt/tAt	10/16	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.83	2		454	544	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355047	73355047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	123	371	0	ENST00000377767.4:c.323G>A	p.Arg108His	p.R108H	ENST00000377767	NM_014953.3	108	cGc/cAc	2/21	1	2	FACETS	0.805	0.736	0.877	0.805	0.736	0.877	CLONAL	1	TRUE	1	0.83	2		371	368	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182679046	182679046	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	26	295	0	ENST00000292782.4:c.488A>G	p.Asn163Ser	p.N163S	ENST00000292782	NM_020640.2	163	aAt/aGt	4/7	1	2	FACETS	0.188	0.149	0.233	0.188	0.149	0.233	SUBCLONAL	1	TRUE	1	0.83	2		295	333	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007719	45007719	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	285	274	0	ENST00000558401.1:c.166G>T	p.Glu56Ter	p.E56*	ENST00000558401	NM_004048.2	56	Gaa/Taa	2/4	1	2	FACETS	0.962	0.93	0.992	1	0.997	1	CLONAL	2	TRUE	1	0.83	2		274	357	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958874	38958874	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	68	200	0	ENST00000357387.3:c.2238C>A	p.Phe746Leu	p.F746L	ENST00000357387	NM_152756.3	746	ttC/ttA	23/38	1	2	FACETS	0.755	0.667	0.847	0.755	0.667	0.847	SUBCLONAL	1	TRUE	1	0.83	2		200	217	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264407	46264407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529456958	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	189	348	1	ENST00000371998.3:c.1454G>A	p.Arg485His	p.R485H	ENST00000371998		485	cGt/cAt	11/23	1	2	FACETS	0.959	0.895	1	0.959	0.895	1	CLONAL	1	TRUE	1	0.83	2		349	475	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749576	41749576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771047905	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	354	614	0	ENST00000301178.4:c.1501C>T	p.Arg501Cys	p.R501C	ENST00000301178	NM_021913.4	501	Cgc/Tgc	12/20	1	2	FACETS	0.951	0.904	0.998	0.951	0.904	0.998	CLONAL	1	TRUE	1	0.83	2		614	897	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619124	43619124	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	224	476	0	ENST00000355710.3:c.2807C>A	p.Ser936Tyr	p.S936Y	ENST00000355710	NM_020975.4	936	tCt/tAt	17/20	1	2	FACETS	0.964	0.905	1	0.964	0.905	1	CLONAL	1	TRUE	1	0.83	2		476	560	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911583	131911583	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	107	247	0	ENST00000265335.6:c.328G>T	p.Glu110Ter	p.E110*	ENST00000265335		110	Gaa/Taa	3/25	1	2	FACETS	0.745	0.675	0.817	0.745	0.675	0.817	SUBCLONAL	1	TRUE	1	0.83	2		247	346	SUCCESS
APC	324	MSKCC	GRCh37	5	112175924	112175924	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	116	188	0	ENST00000257430.4:c.4633T>G	p.Ser1545Ala	p.S1545A	ENST00000257430	NM_000038.5	1545	Tca/Gca	16/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.83	2		188	257	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300870	137300870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1174764642	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	414	675	1	ENST00000481739.1:c.515G>A	p.Arg172His	p.R172H	ENST00000481739	NM_002957.4	172	cGc/cAc	4/10	1	2	FACETS	0.999	0.954	1	0.999	0.954	1	CLONAL	1	TRUE	1	0.83	2		676	999	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158129	106158129	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs770136804	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	18	275	1	ENST00000380013.4:c.3030G>T	p.Glu1010Asp	p.E1010D	ENST00000380013	NM_001127208.2	1010	gaG/gaT	3/11	1	2	FACETS	0.135	0.101	0.175	0.135	0.101	0.175	SUBCLONAL	1	TRUE	1	0.83	2		276	321	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423427	116423427	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	15	263	0	ENST00000397752.3:c.3702C>A	p.Tyr1234Ter	p.Y1234*	ENST00000397752	NM_000245.2	1234	taC/taA	19/21	1	2	FACETS	0.121	0.088	0.161	0.121	0.088	0.161	SUBCLONAL	1	TRUE	1	0.83	2		263	298	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131183	202131183	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	98	231	0	ENST00000358485.4:c.152-1G>T		p.X51_splice	ENST00000358485	NM_001080125.1	51			1	2	FACETS	0.859	0.778	0.942	0.859	0.778	0.942	CLONAL	1	TRUE	1	0.83	2		231	275	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28605706	28605706	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143630873	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	255	587	0	ENST00000253063.3:c.1310G>A	p.Arg437Gln	p.R437Q	ENST00000253063	NM_031459.4	437	cGa/cAa	9/10	1	2	FACETS	0.905	0.852	0.959	0.905	0.852	0.959	CLONAL	1	TRUE	1	0.83	2		587	679	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43773135	43773135	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	233	538	0	ENST00000382044.4:c.457G>T	p.Glu153Ter	p.E153*	ENST00000382044	NM_001141980.1	153	Gaa/Taa	5/28	1	2	FACETS	0.832	0.78	0.885	0.832	0.78	0.885	CLONAL	1	TRUE	1	0.83	2		538	675	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286951	33286951	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1453165364	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	219	540	0	ENST00000374542.5:c.1986G>T	p.Lys662Asn	p.K662N	ENST00000374542	NM_001141970.1	662	aaG/aaT	7/8	1	2	FACETS	0.846	0.792	0.901	0.846	0.792	0.901	CLONAL	1	TRUE	1	0.83	2		540	624	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779545	3779545	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	449	972	0	ENST00000262367.5:c.5503G>T	p.Glu1835Ter	p.E1835*	ENST00000262367	NM_004380.2	1835	Gaa/Taa	31/31	1	2	FACETS	0.902	0.862	0.943	0.902	0.862	0.943	CLONAL	1	TRUE	1	0.83	2		972	1199	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400336	225400336	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	88	149	0	ENST00000264414.4:c.287C>A	p.Ser96Ter	p.S96*	ENST00000264414	NM_003590.4	96	tCa/tAa	3/16	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.83	2		149	201	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608234	28608234	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	210	450	0	ENST00000241453.7:c.1822G>T	p.Glu608Ter	p.E608*	ENST00000241453	NM_004119.2	608	Gaa/Taa	14/24	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.83	2		450	469	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256940	16256940	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	248	490	0	ENST00000375759.3:c.4205C>A	p.Ser1402Tyr	p.S1402Y	ENST00000375759	NM_015001.2	1402	tCt/tAt	11/15	1	2	FACETS	0.837	0.786	0.888	0.837	0.786	0.888	CLONAL	1	TRUE	1	0.83	2		490	714	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22413222	22413222	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	38	92	0	ENST00000344548.3:c.349A>G	p.Ile117Val	p.I117V	ENST00000344548	NM_001039802.1	117	Att/Gtt	6/7	1	2	FACETS	0.715	0.604	0.834	0.715	0.604	0.834	SUBCLONAL	1	TRUE	1	0.83	2		92	128	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873204	71873204	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	147	386	0	ENST00000357731.5:c.990C>A	p.Phe330Leu	p.F330L	ENST00000357731	NM_173808.2	330	ttC/ttA	7/7	1	2	FACETS	0.894	0.826	0.965	0.894	0.826	0.965	CLONAL	1	TRUE	1	0.83	2		386	396	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577215	64577215	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	359	697	2	ENST00000312049.6:c.367G>A	p.Asp123Asn	p.D123N	ENST00000312049	NM_130799.2	123	Gat/Aat	2/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.83	2		699	864	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497558	125497558	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	16	223	0	ENST00000428830.2:c.122A>G	p.Asp41Gly	p.D41G	ENST00000428830	NM_001114121.2	41	gAt/gGt	3/14	1	2	FACETS	0.129	0.095	0.17	0.129	0.095	0.17	SUBCLONAL	1	TRUE	1	0.83	2		223	299	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420510	49420510	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	292	614	0	ENST00000301067.7:c.15239T>C	p.Val5080Ala	p.V5080A	ENST00000301067	NM_003482.3	5080	gTg/gCg	48/54	1	2	FACETS	0.971	0.919	1	0.971	0.919	1	CLONAL	1	TRUE	1	0.83	2		614	725	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426758	49426758	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	122	295	0	ENST00000301067.7:c.11730G>T	p.Gln3910His	p.Q3910H	ENST00000301067	NM_003482.3	3910	caG/caT	39/54	1	2	FACETS	0.867	0.794	0.942	0.867	0.794	0.942	CLONAL	1	TRUE	1	0.83	2		295	339	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50488303	50488303	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs750857733	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	263	425	0	ENST00000394963.4:c.1217C>A	p.Ser406Tyr	p.S406Y	ENST00000394963	NM_003076.4	406	tCt/tAt	10/13	1	2	FACETS	0.975	0.92	1	0.975	0.92	1	CLONAL	1	TRUE	1	0.83	2		425	650	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931823	28931823	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	129	241	2	ENST00000282397.4:c.2117-1G>T		p.X706_splice	ENST00000282397	NM_002019.4	706			1	2	FACETS	0.925	0.85	1	0.925	0.85	1	CLONAL	1	TRUE	1	0.83	2		243	336	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893334	32893334	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	151	291	0	ENST00000380152.3:c.188A>G	p.Lys63Arg	p.K63R	ENST00000380152		63	aAa/aGa	3/27	1	2	FACETS	0.953	0.882	1	0.953	0.882	1	CLONAL	1	TRUE	1	0.83	2		291	382	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944669	32944669	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	85	359	0	ENST00000380152.3:c.8462T>G	p.Ile2821Ser	p.I2821S	ENST00000380152		2821	aTt/aGt	19/27	1	2	FACETS	0.415	0.367	0.465	0.415	0.367	0.465	SUBCLONAL	1	TRUE	1	0.83	2		359	494	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788582	3788582	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	178	328	0	ENST00000262367.5:c.4372T>G	p.Leu1458Val	p.L1458V	ENST00000262367	NM_004380.2	1458	Tta/Gta	26/31	1	2	FACETS	0.92	0.857	0.985	0.92	0.857	0.985	CLONAL	1	TRUE	1	0.83	2		328	466	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89833553	89833553	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	161	331	0	ENST00000389301.3:c.2597A>C	p.Lys866Thr	p.K866T	ENST00000389301	NM_000135.2	866	aAa/aCa	27/43	1	2	FACETS	0.992	0.922	1	0.992	0.922	1	CLONAL	1	TRUE	1	0.83	2		331	391	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40447704	40447704	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	291	510	0	ENST00000345506.4:c.443T>G	p.Phe148Cys	p.F148C	ENST00000345506	NM_003152.3	148	tTt/tGt	6/20	1	2	FACETS	0.957	0.905	1	0.957	0.905	1	CLONAL	1	TRUE	1	0.83	2		510	733	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39613922	39613922	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	112	209	0	ENST00000262039.4:c.1839+1G>T		p.X613_splice	ENST00000262039	NM_002647.2	613			1	2	FACETS	0.918	0.838	1	0.918	0.838	1	CLONAL	1	TRUE	1	0.83	2		209	294	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951134	17951134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs745373403	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	341	580	0	ENST00000458235.1:c.1159A>G	p.Asn387Asp	p.N387D	ENST00000458235	NM_000215.3	387	Aac/Gac	9/24	1	2	FACETS	0.989	0.94	1	0.989	0.94	1	CLONAL	1	TRUE	1	0.83	2		580	831	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212425	36212425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	100	700	0	ENST00000222270.7:c.2176G>A	p.Ala726Thr	p.A726T	ENST00000222270	NM_014727.1	726	Gct/Act	3/37	1	2	FACETS	0.256	0.228	0.285	0.256	0.228	0.285	SUBCLONAL	1	TRUE	1	0.83	2		700	943	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867752	45867752	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	381	896	0	ENST00000391945.4:c.648G>T	p.Lys216Asn	p.K216N	ENST00000391945	NM_000400.3	216	aaG/aaT	8/23	1	2	FACETS	0.953	0.908	0.999	0.953	0.908	0.999	CLONAL	1	TRUE	1	0.83	2		896	963	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213125	39213125	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	419	849	0	ENST00000402219.2:c.3842A>G	p.Glu1281Gly	p.E1281G	ENST00000402219	NM_005633.3	1281	gAa/gGa	23/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.83	2		849	971	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026864	71026864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1251323482	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	81	247	1	ENST00000318789.4:c.1358C>T	p.Ala453Val	p.A453V	ENST00000318789	NM_032682.5	453	gCg/gTg	16/21	1	2	FACETS	0.824	0.737	0.913	0.824	0.737	0.913	CLONAL	1	TRUE	1	0.83	2		248	237	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188318	142188318	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	149	330	0	ENST00000350721.4:c.6413T>G	p.Phe2138Cys	p.F2138C	ENST00000350721	NM_001184.3	2138	tTt/tGt	38/47	1	2	FACETS	0.965	0.893	1	0.965	0.893	1	CLONAL	1	TRUE	1	0.83	2		330	372	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553645	106553645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752218761	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	165	352	1	ENST00000369096.4:c.1610C>T	p.Ala537Val	p.A537V	ENST00000369096	NM_001198.3	537	gCg/gTg	5/7	1	2	FACETS	0.878	0.814	0.943	0.878	0.814	0.943	CLONAL	1	TRUE	1	0.83	2		353	453	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677843	117677843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	42	213	0	ENST00000368508.3:c.4090G>A	p.Asp1364Asn	p.D1364N	ENST00000368508	NM_002944.2	1364	Gat/Aat	25/43	1	2	FACETS	0.383	0.322	0.451	0.383	0.322	0.451	SUBCLONAL	1	TRUE	1	0.83	2		213	264	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709180	117709180	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1330973277	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	120	269	0	ENST00000368508.3:c.1777G>T	p.Asp593Tyr	p.D593Y	ENST00000368508	NM_002944.2	593	Gat/Tat	13/43	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.83	2		269	273	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331622	8331622	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	213	413	0	ENST00000356435.5:c.5494G>T	p.Glu1832Ter	p.E1832*	ENST00000356435		1832	Gaa/Taa	33/35	1	2	FACETS	0.959	0.899	1	0.959	0.899	1	CLONAL	1	TRUE	1	0.83	2		413	535	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485786	8485786	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	105	240	0	ENST00000356435.5:c.3031T>G	p.Phe1011Val	p.F1011V	ENST00000356435		1011	Ttc/Gtc	17/35	1	2	FACETS	0.866	0.787	0.948	0.866	0.787	0.948	CLONAL	1	TRUE	1	0.83	2		240	292	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796793	135796793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	141	256	0	ENST00000298552.3:c.694G>A	p.Glu232Lys	p.E232K	ENST00000298552	NM_001162426.1	232	Gaa/Aaa	8/23	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.83	2		256	337	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314934	1314934	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	223	449	0	ENST00000400841.2:c.727A>C	p.Met243Leu	p.M243L	ENST00000400841		243	Atg/Ctg	6/6	1	2	FACETS	0.912	0.856	0.97	0.912	0.856	0.97	CLONAL	1	TRUE	1	0.83	2		449	589	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814197	76814197	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	17	289	0	ENST00000373344.5:c.6447C>A	p.Phe2149Leu	p.F2149L	ENST00000373344	NM_000489.3	2149	ttC/ttA	29/35	1	2	FACETS	0.125	0.093	0.164	0.125	0.093	0.164	SUBCLONAL	1	TRUE	1	0.83	2		289	327	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73995286	73995286	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765808662	NA	P-0040086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	16	49	0	ENST00000318443.5:c.592G>A	p.Glu198Lys	p.E198K	ENST00000318443	NM_001024736.1	198	Gag/Aag	4/10	1	2	FACETS	0.559	0.423	0.711	0.559	0.423	0.711	SUBCLONAL	1	TRUE	1	0.83	2		49	69	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696450	47696450	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	74	469	0	ENST00000347630.2:c.373T>A	p.Phe125Ile	p.F125I	ENST00000347630	NM_001007230.1	125	Ttt/Att	6/11	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.186732792341772	2		469	780	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39251241	39251241	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	55	475	2	ENST00000402219.2:c.1112A>T	p.Glu371Val	p.E371V	ENST00000402219	NM_005633.3	371	gAa/gTa	9/23	1	2	FACETS	0.856	0.731	0.993	0.856	0.731	0.993	CLONAL	1	TRUE	1	0.186732792341772	2		477	688	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984130	2984130	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	150	473	0	ENST00000396946.4:c.400G>A	p.Glu134Lys	p.E134K	ENST00000396946	NM_032415.4	134	Gag/Aag	5/25	0.186732792341772	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	1	0.186732792341772	3		473	844	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0040094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	434	954	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.615352554895281	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	FALSE	0	0.616885950496223	3		954	591	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121438948	121438948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146855738	NA	P-0040094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	258	787	0	ENST00000257555.6:c.1849G>A	p.Val617Ile	p.V617I	ENST00000257555		617	Gtc/Atc	10/10	0.415500007715074	5	FACETS	0.837	0.79	0.886	0.837	0.79	0.886	CLONAL	3	FALSE	2	0.616885950496223	5		787	641	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251911	153251911	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	160	328	0	ENST00000281708.4:c.1095G>T	p.Trp365Cys	p.W365C	ENST00000281708	NM_033632.3	365	tgG/tgT	7/12	0.582500019787977	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	3	FALSE	0	0.616885950496223	3		328	224	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366884	15366884	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	136	330	0	ENST00000263377.2:c.1742G>C	p.Ser581Thr	p.S581T	ENST00000263377	NM_058243.2	581	aGc/aCc	9/20	0.616885950496223	9	FACETS	1	0.941	1	0.348	0.316	0.38	CLONAL	2	FALSE	3	0.616885950496223	9		330	668	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0040098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	132	685	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.924	0.841	1	0.924	0.841	1	CLONAL	1	TRUE	1	0.406803851461265	2		685	702	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177874	56177875	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0040098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	74	395	0	ENST00000399503.3:c.2849_2850del	p.Glu950AlafsTer53	p.E950Afs*53	ENST00000399503	NM_005921.1	949	acAGag/acag	14/20	1	2	FACETS	0.868	0.764	0.98	0.868	0.764	0.98	CLONAL	1	TRUE	1	0.406803851461265	2		395	419	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793316	242793316	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	215	1033	0	ENST00000334409.5:c.761C>T	p.Pro254Leu	p.P254L	ENST00000334409	NM_005018.2	254	cCt/cTt	5/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.406803851461265	2		1033	914	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858702	9858702	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	66	385	0	ENST00000330684.3:c.2699C>T	p.Ser900Leu	p.S900L	ENST00000330684	NM_001134407.1	900	tCa/tTa	13/13	0.387718196736266	3	FACETS	0.836	0.728	0.953	0.418	0.364	0.477	CLONAL	1	TRUE	1	0.406803851461265	3		385	467	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115056	3115056	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	141	731	0	ENST00000078429.4:c.591G>T	p.Glu197Asp	p.E197D	ENST00000078429	NM_002067.2	197	gaG/gaT	4/7	0.406803851461265	1	FACETS	0.991	0.908	1	0.991	0.908	1	CLONAL	1	TRUE	0	0.406803851461265	1		731	557	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916948	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	novel	NA	P-0040098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	79	352	0	ENST00000263967.3:c.333_335del	p.Lys111_Ile112delinsAsn	p.K111_I112delinsN	ENST00000263967	NM_006218.2	111	aaGATc/aac	2/21	1	2	FACETS	0.993	0.879	1	0.993	0.879	1	CLONAL	1	TRUE	1	0.406803851461265	2		352	391	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161696	56161696	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0040098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	86	391	0	ENST00000399503.3:c.1193C>G	p.Ser398Ter	p.S398*	ENST00000399503	NM_005921.1	398	tCa/tGa	6/20	1	2	FACETS	0.881	0.782	0.986	0.881	0.782	0.986	CLONAL	1	TRUE	1	0.406803851461265	2		391	480	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227941	53227949	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCACTGCG	CTCACTGCG	-	novel	NA	P-0040098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	137	837	0	ENST00000375401.3:c.2365_2368+5del		p.X789_splice	ENST00000375401	NM_004187.3	789		16/26	0.406803851461265	1	FACETS	0.849	0.775	0.927	0.849	0.775	0.927	CLONAL	1	TRUE	0	0.406803851461265	1		837	632	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	89	390	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	0.24352179899368	1	FACETS	0.936	0.837	1	1	0.985	1	CLONAL	2	TRUE	0	0.24352179899368	1		390	343	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007825	45007825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	55	399	2	ENST00000558401.1:c.276del	p.Thr93LeufsTer10	p.T93Lfs*10	ENST00000558401	NM_004048.2	91	aCc/ac	2/4	0.24352179899368	1	FACETS	0.972	0.834	1	0.972	0.834	1	CLONAL	1	TRUE	0	0.24352179899368	1		401	408	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	90	764	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.24352179899368	1	FACETS	0.927	0.83	1	1	0.985	1	CLONAL	2	TRUE	0	0.24352179899368	1		764	350	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	96	816	6	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	0.243214847650744	4	FACETS	0.909	0.808	1	0.303	0.269	0.339	CLONAL	1	TRUE	1	0.24352179899368	4		822	1079	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	71	413	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	0.24352179899368	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.24352179899368	1		413	390	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	161	556	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.939	1	1	0.992	1	CLONAL	2	TRUE	1	0.24352179899368	2		562	646	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	156	851	5	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.893	0.82	0.97	1	0.991	1	CLONAL	2	TRUE	1	0.24352179899368	2		856	717	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	45	460	6	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	0.243214847650744	4	FACETS	0.748	0.628	0.882	0.249	0.209	0.294	SUBCLONAL	1	TRUE	1	0.24352179899368	4		466	614	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	142	389	1	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	1	2	FACETS	0.93	0.856	1	1	0.993	1	CLONAL	3	TRUE	1	0.24352179899368	2		390	418	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	135	419	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.24352179899368	1	FACETS	0.892	0.82	0.965	1	0.992	1	CLONAL	3	TRUE	0	0.24352179899368	1		419	364	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	109	601	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	0.178161864798116	1	FACETS	0.819	0.739	0.902	1	0.986	1	CLONAL	2	TRUE	0	0.24352179899368	1		601	480	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736166	204736166	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	85	135	0	ENST00000302823.3:c.529del	p.Tyr177IlefsTer10	p.Y177Ifs*10	ENST00000302823	NM_005214.4	175	Ttt/tt	3/4	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.24352179899368	2		135	476	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	123	325	1	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	0.913	0.829	1	1	0.989	1	CLONAL	2	TRUE	1	0.24352179899368	2		326	553	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332273	70332273	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	30	445	1	ENST00000373644.4:c.184del	p.Thr62GlnfsTer13	p.T62Qfs*13	ENST00000373644	NM_030625.2	60	Aaa/aa	2/12	1	2	FACETS	0.613	0.494	0.748	0.613	0.494	0.748	SUBCLONAL	1	TRUE	1	0.24352179899368	2		446	402	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287315	46287315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1565642121	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	82	465	0	ENST00000334344.6:c.5260C>T	p.Arg1754Ter	p.R1754*	ENST00000334344	NM_152641.2	1754	Cga/Tga	19/21	0.243214847650744	4	FACETS	1	0.977	1	0.496	0.438	0.558	CLONAL	1	TRUE	1	0.24352179899368	4		465	563	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276860	15276861	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs753725730	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	84	735	3	ENST00000263388.2:c.5404dup	p.Ala1802GlyfsTer8	p.A1802Gfs*8	ENST00000263388	NM_000435.2	1802	gct/gGct	30/33	1	2	FACETS	0.888	0.783	1	0.888	0.783	1	CLONAL	1	TRUE	1	0.24352179899368	2		738	777	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161939	47161939	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	25	363	0	ENST00000409792.3:c.4187del	p.Asn1396MetfsTer16	p.N1396Mfs*16	ENST00000409792	NM_014159.6	1396	aAt/at	3/21	0.24352179899368	1	FACETS	0.751	0.594	0.93	0.751	0.594	0.93	CLONAL	1	TRUE	0	0.24352179899368	1		363	240	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211461	46211461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	84	165	1	ENST00000334344.6:c.427C>T	p.Arg143Cys	p.R143C	ENST00000334344	NM_152641.2	143	Cgt/Tgt	5/21	0.243214847650744	4	FACETS	0.993	0.894	1	1	0.977	1	CLONAL	4	TRUE	1	0.24352179899368	4		166	216	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850945	128850945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762491039	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	130	570	0	ENST00000249373.3:c.1792G>A	p.Gly598Arg	p.G598R	ENST00000249373	NM_005631.4	598	Ggg/Agg	10/12	1	2	FACETS	0.94	0.856	1	1	0.99	1	CLONAL	2	TRUE	1	0.24352179899368	2		570	568	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73342925	73342925	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs774491006	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	20	156	0	ENST00000377767.4:c.1881del	p.Ala629LeufsTer2	p.A629Lfs*2	ENST00000377767	NM_014953.3	627	aaA/aa	14/21	0.13912147697655	4	FACETS	1	0.86	1	0.587	0.452	0.743	INDETERMINATE	1	TRUE	2	0.24352179899368	4		156	174	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44733177	44733177	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	91	610	0	ENST00000377967.4:c.169T>C	p.Phe57Leu	p.F57L	ENST00000377967	NM_021140.2	57	Ttt/Ctt	2/29	0.24352179899368	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.24352179899368	1		610	549	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396234	396234	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	70	750	4	ENST00000262320.3:c.792del	p.Gly265GlufsTer149	p.G265Efs*149	ENST00000262320	NM_003502.3	264	ccC/cc	2/11	1	2	FACETS	0.791	0.689	0.901	0.791	0.689	0.901	CLONAL	1	TRUE	1	0.24352179899368	2		754	727	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050833	5050833	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	48	405	0	ENST00000381652.3:c.614+2T>C		p.X205_splice	ENST00000381652	NM_004972.3	205			0.178161864798116	1	FACETS	0.811	0.687	0.947	0.811	0.687	0.947	CLONAL	1	TRUE	0	0.24352179899368	1		405	427	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647657	3647657	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs774532876	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	97	843	3	ENST00000294008.3:c.1406del	p.Pro469HisfsTer4	p.P469Hfs*4	ENST00000294008	NM_032444.2	469	cCa/ca	7/15	1	2	FACETS	0.865	0.77	0.967	0.865	0.77	0.967	CLONAL	1	TRUE	1	0.24352179899368	2		846	921	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993351	72993351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752231847	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	204	779	1	ENST00000268489.5:c.694C>T	p.Arg232Cys	p.R232C	ENST00000268489	NM_006885.3	232	Cgc/Tgc	2/10	1	2	FACETS	0.99	0.92	1	1	0.994	1	CLONAL	2	TRUE	1	0.24352179899368	2		780	846	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444378	49444378	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	142	720	2	ENST00000301067.7:c.2993del	p.Pro998LeufsTer2	p.P998Lfs*2	ENST00000301067	NM_003482.3	998	cCt/ct	11/54	0.243214847650744	4	FACETS	0.954	0.871	1	0.636	0.58	0.695	CLONAL	2	TRUE	1	0.24352179899368	4		722	760	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376248	15376248	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	96	627	2	ENST00000263377.2:c.766del	p.Gln256SerfsTer27	p.Q256Sfs*27	ENST00000263377	NM_058243.2	256	Cag/ag	5/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.24352179899368	2		629	532	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932400	36932400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764345289	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	140	665	1	ENST00000361632.4:c.2069C>T	p.Thr690Met	p.T690M	ENST00000361632		690	aCg/aTg	16/16	1	2	FACETS	0.847	0.773	0.924	1	0.989	1	CLONAL	2	TRUE	1	0.24352179899368	2		666	679	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817720	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	102	474	5	ENST00000262367.5:c.3250dup	p.Ile1084AsnfsTer3	p.I1084Nfs*3	ENST00000262367	NM_004380.2	1084	atc/aAtc		1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.24352179899368	2		479	586	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123260369	123260369	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770309121	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	57	588	2	ENST00000358487.5:c.1532C>T	p.Ala511Val	p.A511V	ENST00000358487	NM_000141.4	511	gCg/gTg	11/18	1	2	FACETS	0.662	0.567	0.766	0.662	0.567	0.766	SUBCLONAL	1	TRUE	1	0.24352179899368	2		590	707	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970916	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	97	365	0	ENST00000265081.6:c.1147_1148del	p.Lys383GlyfsTer20	p.K383Gfs*20	ENST00000265081	NM_002439.4	381	AAa/a	7/24	1	2	FACETS	0.862	0.772	0.957	1	0.985	1	CLONAL	2	TRUE	1	0.24352179899368	2		365	462	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478781	57478781	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769546153	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	117	466	0	ENST00000371085.3:c.367G>A	p.Glu123Lys	p.E123K	ENST00000371085	NM_000516.4	123	Gag/Aag	5/13	0.178161864798116	1	FACETS	0.911	0.827	0.999	1	0.988	1	CLONAL	2	TRUE	0	0.24352179899368	1		466	463	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739893	145739893	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377298374	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	70	645	2	ENST00000428558.2:c.1637C>T	p.Pro546Leu	p.P546L	ENST00000428558	NM_004260.3	546	cCg/cTg	10/22	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.24352179899368	2		647	556	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037492	12037492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	43	395	0	ENST00000396373.4:c.1123G>A	p.Gly375Arg	p.G375R	ENST00000396373	NM_001987.4	375	Gga/Aga	6/8	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.24352179899368	NA		395	503	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090086	37090086	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63751310	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	163	543	2	ENST00000231790.2:c.1975C>T	p.Arg659Ter	p.R659*	ENST00000231790	NM_000249.3	659	Cga/Tga	17/19	0.24352179899368	1	FACETS	0.903	0.837	0.97	1	0.994	1	CLONAL	3	TRUE	0	0.24352179899368	1		545	434	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945604	71945604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	40	640	0	ENST00000298229.2:c.2360G>A	p.Ser787Asn	p.S787N	ENST00000298229	NM_001567.3	787	aGc/aAc	21/28	0.24352179899368	1	FACETS	0.495	0.41	0.589	0.495	0.41	0.589	SUBCLONAL	1	TRUE	0	0.24352179899368	1		640	583	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486803	56486803	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	144	620	0	ENST00000267101.3:c.1217T>C	p.Met406Thr	p.M406T	ENST00000267101	NM_001982.3	406	aTg/aCg	11/28	0.243214847650744	4	FACETS	0.854	0.779	0.933	0.569	0.519	0.622	CLONAL	2	TRUE	1	0.24352179899368	4		620	861	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562564	21562564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1452154404	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	42	228	0	ENST00000382592.4:c.1355C>T	p.Pro452Leu	p.P452L	ENST00000382592	NM_014572.2	452	cCg/cTg	4/8	0.13912147697655	4	FACETS	0.928	0.782	1	0.928	0.782	1	INDETERMINATE	2	TRUE	2	0.24352179899368	4		228	231	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912870	32912870	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	23	268	0	ENST00000380152.3:c.4381del	p.Ser1461ProfsTer2	p.S1461Pfs*2	ENST00000380152		1460	Ttt/tt	11/27	0.13912147697655	4	FACETS	1	0.811	1	0.52	0.407	0.649	INDETERMINATE	1	TRUE	2	0.24352179899368	4		268	226	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630434	90630434	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	173	623	0	ENST00000330062.3:c.877A>G	p.Met293Val	p.M293V	ENST00000330062	NM_002168.2	293	Atg/Gtg	7/11	0.24352179899368	1	FACETS	0.981	0.907	1	1	0.993	1	CLONAL	2	TRUE	0	0.24352179899368	1		623	636	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343582	343582	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	73	722	0	ENST00000262320.3:c.2092del	p.His698ThrfsTer7	p.H698Tfs*7	ENST00000262320	NM_003502.3	698	Cac/ac	8/11	1	2	FACETS	0.669	0.584	0.762	0.669	0.584	0.762	SUBCLONAL	1	TRUE	1	0.24352179899368	2		722	896	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900335	3900335	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199768244	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	144	686	0	ENST00000262367.5:c.761C>T	p.Ala254Val	p.A254V	ENST00000262367	NM_004380.2	254	gCg/gTg	2/31	1	2	FACETS	0.805	0.735	0.877	1	0.988	1	CLONAL	2	TRUE	1	0.24352179899368	2		686	735	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134499	30134499	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	35	298	1	ENST00000263025.4:c.32del	p.Gly11AlafsTer21	p.G11Afs*21	ENST00000263025	NM_002746.2	11	gGc/gc	1/9	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.24352179899368	2		299	276	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973799	15973799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	120	453	2	ENST00000268712.3:c.4193C>T	p.Ala1398Val	p.A1398V	ENST00000268712	NM_006311.3	1398	gCc/gTc	31/46	1	2	FACETS	1	0.929	1	1	0.99	1	CLONAL	2	TRUE	1	0.24352179899368	2		455	480	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40457682	40457682	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	51	626	0	ENST00000345506.4:c.1435A>G	p.Thr479Ala	p.T479A	ENST00000345506	NM_003152.3	479	Acg/Gcg	13/20	1	2	FACETS	0.587	0.498	0.686	0.587	0.498	0.686	SUBCLONAL	1	TRUE	1	0.24352179899368	2		626	713	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677806	58677806	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	60	610	0	ENST00000305921.3:c.31G>A	p.Val11Ile	p.V11I	ENST00000305921	NM_003620.3	11	Gtc/Atc	1/6	1	2	FACETS	0.782	0.673	0.901	0.782	0.673	0.901	CLONAL	1	TRUE	1	0.24352179899368	2		610	630	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208330	5208330	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	167	772	1	ENST00000357368.4:c.5560del	p.Glu1854ArgfsTer59	p.E1854Rfs*59	ENST00000357368	NM_002850.3	1854	Gag/ag	36/38	1	2	FACETS	0.901	0.83	0.976	1	0.991	1	CLONAL	2	TRUE	1	0.24352179899368	2		773	761	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223287	5223287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758410040	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	194	778	0	ENST00000357368.4:c.2516C>T	p.Ser839Leu	p.S839L	ENST00000357368	NM_002850.3	839	tCg/tTg	18/38	1	2	FACETS	1	0.976	1	1	0.994	1	CLONAL	2	TRUE	1	0.24352179899368	2		778	715	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627664	14627664	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753013282	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	70	665	0	ENST00000254322.2:c.406A>G	p.Met136Val	p.M136V	ENST00000254322	NM_006145.1	136	Atg/Gtg	2/3	1	2	FACETS	0.947	0.826	1	0.947	0.826	1	CLONAL	1	TRUE	1	0.24352179899368	2		665	607	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855832	45855832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761085729	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	193	755	0	ENST00000391945.4:c.1978G>A	p.Ala660Thr	p.A660T	ENST00000391945	NM_000400.3	660	Gcg/Acg	21/23	1	2	FACETS	0.939	0.87	1	1	0.993	1	CLONAL	2	TRUE	1	0.24352179899368	2		755	844	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754967	29754969	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	117	586	0	ENST00000389048.3:c.966_968del	p.Leu323del	p.L323del	ENST00000389048	NM_004304.4	322	ctTCTc/ctc	4/29	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.24352179899368	2		586	647	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172080	99172080	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	54	619	0	ENST00000074304.5:c.1646T>C	p.Leu549Pro	p.L549P	ENST00000074304	NM_001134224.1	549	cTg/cCg	17/26	1	2	FACETS	0.662	0.564	0.769	0.662	0.564	0.769	SUBCLONAL	1	TRUE	1	0.24352179899368	2		619	670	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39725894	39725894	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	41	428	1	ENST00000361337.2:c.765A>T	p.Glu255Asp	p.E255D	ENST00000361337	NM_003286.2	255	gaA/gaT	10/21	0.178161864798116	1	FACETS	0.621	0.517	0.737	0.621	0.517	0.737	SUBCLONAL	1	TRUE	0	0.24352179899368	1		429	476	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574718	41574718	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780778684	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	75	819	1	ENST00000263253.7:c.7003C>T	p.Pro2335Ser	p.P2335S	ENST00000263253	NM_001429.3	2335	Cct/Tct	31/31	0.24352179899368	1	FACETS	0.706	0.618	0.801	0.706	0.618	0.801	SUBCLONAL	1	TRUE	0	0.24352179899368	1		820	766	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176486	142176486	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	58	411	0	ENST00000350721.4:c.7615A>G	p.Thr2539Ala	p.T2539A	ENST00000350721	NM_001184.3	2539	Aca/Gca	45/47	0.24352179899368	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.24352179899368	1		411	379	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279124	142279124	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	37	287	0	ENST00000350721.4:c.1522T>C	p.Ser508Pro	p.S508P	ENST00000350721	NM_001184.3	508	Tct/Cct	6/47	0.24352179899368	1	FACETS	0.794	0.657	0.947	0.794	0.657	0.947	CLONAL	1	TRUE	0	0.24352179899368	1		287	336	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806576	1806576	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	86	715	0	ENST00000260795.2:c.1292T>C	p.Met431Thr	p.M431T	ENST00000260795		431	aTg/aCg	9/17	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.24352179899368	2		715	680	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807381	1807381	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762781471	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	74	696	0	ENST00000260795.2:c.1630G>A	p.Ala544Thr	p.A544T	ENST00000260795		544	Gcc/Acc	11/17	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.24352179899368	2		696	598	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749424	41749424	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	59	487	0	ENST00000226382.2:c.371A>G	p.Asp124Gly	p.D124G	ENST00000226382	NM_003924.3	124	gAc/gGc	2/3	1	2	FACETS	0.886	0.763	1	0.886	0.763	1	CLONAL	1	TRUE	1	0.24352179899368	2		487	547	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955571	55955571	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1380184007	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	42	424	0	ENST00000263923.4:c.3374T>C	p.Met1125Thr	p.M1125T	ENST00000263923	NM_002253.2	1125	aTg/aCg	25/30	1	2	FACETS	0.713	0.595	0.843	0.713	0.595	0.843	SUBCLONAL	1	TRUE	1	0.24352179899368	2		424	484	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383659	84383659	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	118	432	0	ENST00000321945.7:c.1193A>C	p.Lys398Thr	p.K398T	ENST00000321945	NM_139076.2	398	aAg/aCg	9/9	1	2	FACETS	0.983	0.892	1	1	0.989	1	CLONAL	2	TRUE	1	0.24352179899368	2		432	493	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157863	106157863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	29	392	2	ENST00000380013.4:c.2764C>T	p.His922Tyr	p.H922Y	ENST00000380013	NM_001127208.2	922	Cat/Tat	3/11	1	2	FACETS	0.781	0.628	0.954	0.781	0.628	0.954	CLONAL	1	TRUE	1	0.24352179899368	2		394	305	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31401588	31401588	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	171	551	0	ENST00000344624.3:c.4076G>T	p.Arg1359Ile	p.R1359I	ENST00000344624		1359	aGa/aTa	33/33	1	2	FACETS	0.99	0.914	1	1	0.992	1	CLONAL	2	TRUE	1	0.24352179899368	2		551	709	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876506	35876506	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	124	598	0	ENST00000303115.3:c.1298A>G	p.Gln433Arg	p.Q433R	ENST00000303115	NM_002185.3	433	cAg/cGg	8/8	1	2	FACETS	0.914	0.83	1	1	0.989	1	CLONAL	2	TRUE	1	0.24352179899368	2		598	557	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402725	20402726	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	117	427	0	ENST00000346618.3:c.267dup	p.Gly90ArgfsTer77	p.G90Rfs*77	ENST00000346618	NM_001949.4	88	gcc/gCcc	1/7	1	2	FACETS	0.969	0.878	1	1	0.989	1	CLONAL	2	TRUE	1	0.24352179899368	2		427	496	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967948	93967948	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	107	459	0	ENST00000369303.4:c.1979T>G	p.Val660Gly	p.V660G	ENST00000369303	NM_004440.3	660	gTt/gGt	11/17	1	2	FACETS	0.981	0.885	1	1	0.988	1	CLONAL	2	TRUE	1	0.24352179899368	2		459	448	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536107	106536107	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779091345	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	75	347	0	ENST00000369096.4:c.74G>T	p.Arg25Met	p.R25M	ENST00000369096	NM_001198.3	25	aGg/aTg	2/7	1	2	FACETS	0.888	0.783	0.998	1	0.981	1	CLONAL	2	TRUE	1	0.24352179899368	2		347	347	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976700	2976700	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	153	570	1	ENST00000396946.4:c.1312C>A	p.Leu438Ile	p.L438I	ENST00000396946	NM_032415.4	438	Ctc/Atc	9/25	1	2	FACETS	1	0.977	1	1	0.993	1	CLONAL	2	TRUE	1	0.24352179899368	2		571	539	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467717	50467717	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	151	724	0	ENST00000331340.3:c.952G>A	p.Ala318Thr	p.A318T	ENST00000331340	NM_006060.4	318	Gcc/Acc	8/8	1	2	FACETS	0.932	0.855	1	1	0.991	1	CLONAL	2	TRUE	1	0.24352179899368	2		724	665	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845625	128845625	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	85	416	0	ENST00000249373.3:c.920+2T>C		p.X307_splice	ENST00000249373	NM_005631.4	307			1	2	FACETS	0.907	0.807	1	1	0.984	1	CLONAL	2	TRUE	1	0.24352179899368	2		416	385	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38186934	38186934	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	43	594	0	ENST00000317025.8:c.1543del	p.Asp515MetfsTer21	p.D515Mfs*21	ENST00000317025	NM_023034.1	515	Gat/at	6/24	1	2	FACETS	0.654	0.547	0.773	0.654	0.547	0.773	SUBCLONAL	1	TRUE	1	0.24352179899368	2		594	540	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141582948	141582948	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	210	709	0	ENST00000220592.5:c.299T>C	p.Leu100Pro	p.L100P	ENST00000220592	NM_012154.3	100	cTa/cCa	3/19	1	2	FACETS	1	0.936	1	1	0.994	1	CLONAL	2	TRUE	1	0.24352179899368	2		709	857	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741253	145741253	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs533978275	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	91	789	0	ENST00000428558.2:c.1153A>G	p.Lys385Glu	p.K385E	ENST00000428558	NM_004260.3	385	Aag/Gag	6/22	1	2	FACETS	0.981	0.871	1	0.981	0.871	1	CLONAL	1	TRUE	1	0.24352179899368	2		789	762	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760907	133760907	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	102	810	0	ENST00000318560.5:c.3230T>C	p.Met1077Thr	p.M1077T	ENST00000318560	NM_005157.4	1077	aTg/aCg	11/11	0.178161864798116	1	FACETS	0.859	0.768	0.957	0.859	0.768	0.957	CLONAL	1	TRUE	0	0.24352179899368	1		810	856	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393439	139393439	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	154	668	0	ENST00000277541.6:c.6092C>A	p.Ala2031Asp	p.A2031D	ENST00000277541	NM_017617.3	2031	gCc/gAc	33/34	0.178161864798116	1	FACETS	0.824	0.756	0.895	1	0.99	1	CLONAL	2	TRUE	0	0.24352179899368	1		668	674	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409748	139409748	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	93	680	0	ENST00000277541.6:c.2008T>C	p.Tyr670His	p.Y670H	ENST00000277541	NM_017617.3	670	Tac/Cac	12/34	0.178161864798116	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.24352179899368	1		680	642	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44919375	44919375	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	43	362	0	ENST00000377967.4:c.1303C>T	p.Gln435Ter	p.Q435*	ENST00000377967	NM_021140.2	435	Cag/Tag	13/29	0.24352179899368	1	FACETS	0.896	0.753	1	0.896	0.753	1	CLONAL	1	TRUE	0	0.24352179899368	1		362	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0040126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	293	954	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.430802810593164	2	FACETS	0.958	0.908	1	0.958	0.908	1	CLONAL	2	TRUE	0	0.455995968853541	2		954	671	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442080	52442080	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	141	524	0	ENST00000460680.1:c.269C>G	p.Ser90Cys	p.S90C	ENST00000460680	NM_004656.3	90	tCt/tGt	5/17	1	2	FACETS	0.943	0.861	1	0.943	0.861	1	CLONAL	1	TRUE	1	0.455995968853541	2		524	656	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236676	236676	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	163	335	0	ENST00000264932.6:c.1394G>T	p.Arg465Leu	p.R465L	ENST00000264932	NM_004168.2	465	cGg/cTg	10/15	0.449767097705117	3	FACETS	0.89	0.824	0.959	0.89	0.824	0.959	CLONAL	2	TRUE	1	0.455995968853541	3		335	493	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226561922	226561929	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATAACCTC	ATAACCTC	-	novel	NA	P-0040126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	30	284	0	ENST00000366794.5:c.2068_2070+5del		p.X690_splice	ENST00000366794	NM_001618.3	690		14/23	0.455995968853541	3	FACETS	0.358	0.288	0.438	0.179	0.144	0.219	SUBCLONAL	1	TRUE	1	0.455995968853541	3		284	451	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514037	69514037	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	38	501	0	ENST00000294312.3:c.644A>T	p.Glu215Val	p.E215V	ENST00000294312	NM_005117.2	215	gAg/gTg	3/3	1	2	FACETS	0.276	0.227	0.33	0.276	0.227	0.33	SUBCLONAL	1	TRUE	1	0.455995968853541	2		501	604	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17949071	17949071	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0040126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	135	548	0	ENST00000458235.1:c.1569+1G>A		p.X523_splice	ENST00000458235	NM_000215.3	523			0.449767097705117	3	FACETS	0.973	0.886	1	0.487	0.443	0.533	CLONAL	1	TRUE	1	0.455995968853541	3		548	747	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607512	46607512	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	69	761	0	ENST00000263734.3:c.1701G>C	p.Met567Ile	p.M567I	ENST00000263734	NM_001430.4	567	atG/atC	12/16	0.455995968853541	3	FACETS	0.355	0.308	0.407	0.178	0.154	0.204	SUBCLONAL	1	TRUE	1	0.455995968853541	3		761	1046	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118912	61118912	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	64	376	0	ENST00000295025.8:c.105T>G	p.Ile35Met	p.I35M	ENST00000295025	NM_002908.2	35	atT/atG	2/11	0.208386782229578	4	FACETS	0.705	0.61	0.807	0.352	0.305	0.404	INDETERMINATE	1	TRUE	2	0.455995968853541	4		376	580	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652204	36652204	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	82	639	0	ENST00000244741.5:c.326A>G	p.Asp109Gly	p.D109G	ENST00000244741	NM_000389.4	109	gAc/gGc	2/3	0.455995968853541	4	FACETS	0.449	0.395	0.509	0.15	0.131	0.17	SUBCLONAL	1	TRUE	1	0.455995968853541	4		639	1165	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413253	139413253	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	88	581	0	ENST00000277541.6:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000277541	NM_017617.3	297	Gac/Tac	6/34	0.430802810593164	2	FACETS	0.513	0.454	0.576	0.256	0.227	0.288	SUBCLONAL	1	TRUE	0	0.455995968853541	2		581	753	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183764	10183764	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs5030804	NA	P-0040167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	228	676	0	ENST00000256474.2:c.233A>G	p.Asn78Ser	p.N78S	ENST00000256474	NM_000551.3	78	aAt/aGt	1/3	0.502058155928684	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.502058155928684	1		676	671	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537897	212537898	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AT	novel	NA	P-0040167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	101	552	0	ENST00000342788.4:c.1707_1708delinsAT	p.Cys569_His570delinsTer	p.C569_H570delins*	ENST00000342788	NM_005235.2	569	tgCCat/tgATat	14/28	1	2	FACETS	0.721	0.646	0.8	0.721	0.646	0.8	SUBCLONAL	1	TRUE	1	0.502058155928684	2		552	558	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163371	47163371	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	51	368	0	ENST00000409792.3:c.2755G>T	p.Glu919Ter	p.E919*	ENST00000409792	NM_014159.6	919	Gag/Tag	3/21	0.502058155928684	1	FACETS	0.951	0.824	1	0.951	0.824	1	CLONAL	1	TRUE	0	0.502058155928684	1		368	160	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713654	52713654	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	152	568	0	ENST00000394830.3:c.74del	p.Ser25LeufsTer20	p.S25Lfs*20	ENST00000394830	NM_018313.4	25	tCt/tt	2/30	0.502058155928684	1	FACETS	0.986	0.909	1	0.986	0.909	1	CLONAL	1	TRUE	0	0.502058155928684	1		568	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0040207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	197	834	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.302121224813521	1	FACETS	1	0.97	1	1	0.97	1	INDETERMINATE	1	TRUE	0	0.59	1		834	445	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939102	36939102	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	113	958	0	ENST00000361632.4:c.607G>T	p.Val203Leu	p.V203L	ENST00000361632		203	Gtg/Ttg	5/16	1	2	FACETS	0.704	0.636	0.776	0.704	0.636	0.776	SUBCLONAL	1	TRUE	1	0.59	2		958	544	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0040226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	304	308	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.806409668772977	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.806409668772977	2		308	366	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246004	41246004	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	164	757	0	ENST00000357654.3:c.1544A>T	p.Glu515Val	p.E515V	ENST00000357654	NM_007294.3	515	gAg/gTg	10/23	1	2	FACETS	0.57	0.525	0.618	0.57	0.525	0.618	SUBCLONAL	1	TRUE	1	0.806409668772977	2		757	713	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630059	187630059	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	128	616	0	ENST00000441802.2:c.923C>A	p.Ser308Tyr	p.S308Y	ENST00000441802	NM_005245.3	308	tCc/tAc	2/27	0.556853386240818	3	FACETS	0.537	0.486	0.59	0.268	0.243	0.295	SUBCLONAL	1	TRUE	1	0.806409668772977	3		616	830	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673592	30673592	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	175	833	0	ENST00000376406.3:c.3368C>G	p.Ala1123Gly	p.A1123G	ENST00000376406	NM_014641.2	1123	gCt/gGt	10/15	1	2	FACETS	0.472	0.434	0.511	0.472	0.434	0.511	SUBCLONAL	1	TRUE	1	0.806409668772977	2		833	920	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0040228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	41	372	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.814	0.68	0.961	0.814	0.68	0.961	CLONAL	1	TRUE	1	0.31	2		372	325	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0040228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	48	265	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.763	0.646	0.891	0.763	0.646	0.891	SUBCLONAL	1	TRUE	1	0.31	2		265	406	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0040228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	12	200	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.186	0.13	0.256	0.186	0.13	0.256	SUBCLONAL	1	TRUE	1	0.31	2		201	416	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0040228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	81	434	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.884	0.78	0.996	0.884	0.78	0.996	CLONAL	1	TRUE	1	0.31	2		434	591	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0040228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	104	556	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.993	0.89	1	0.993	0.89	1	CLONAL	1	TRUE	1	0.31	2		562	676	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0040228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	18	128	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.28	0.21	0.363	0.28	0.21	0.363	SUBCLONAL	1	TRUE	1	0.31	2		128	415	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	46	474	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.724	0.611	0.848	0.724	0.611	0.848	SUBCLONAL	1	TRUE	1	0.31	2		474	410	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0040228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	86	312	4	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	0.972	0.861	1	0.972	0.861	1	CLONAL	1	TRUE	1	0.31	2		316	571	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	35	325	1	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	0.385	0.315	0.465	0.385	0.315	0.465	SUBCLONAL	1	TRUE	1	0.31	2		326	586	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0040228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	16	241	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	1	2	FACETS	0.25	0.184	0.329	0.25	0.184	0.329	SUBCLONAL	1	TRUE	1	0.31	2		241	413	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177584	56177584	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368201444	NA	P-0040228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	73	248	0	ENST00000399503.3:c.2557C>T	p.Arg853Cys	p.R853C	ENST00000399503	NM_005921.1	853	Cgt/Tgt	14/20	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.31	2		248	444	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092740	27092740	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1557611083	NA	P-0040228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	74	288	0	ENST00000324856.7:c.2765del	p.Gly922AlafsTer2	p.G922Afs*2	ENST00000324856	NM_006015.4	921	Ggg/gg	9/20	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.31	2		288	438	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286237	66286238	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	35	163	0	ENST00000273854.3:c.1448dup	p.Asn483LysfsTer21	p.N483Kfs*21	ENST00000273854	NM_004439.5	483	aac/aaAc	6/18	1	2	FACETS	0.763	0.628	0.914	0.763	0.628	0.914	CLONAL	1	TRUE	1	0.31	2		163	296	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523708	148523708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520183	NA	P-0040228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	40	142	0	ENST00000320356.2:c.745G>A	p.Glu249Lys	p.E249K	ENST00000320356	NM_004456.4	249	Gaa/Aaa	8/20	1	2	FACETS	0.89	0.743	1	0.89	0.743	1	CLONAL	1	TRUE	1	0.31	2		142	290	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100999	41100999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1371429276	NA	P-0040228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	87	579	1	ENST00000373198.4:c.1357C>T	p.Arg453Cys	p.R453C	ENST00000373198	NM_133170.3	453	Cgc/Tgc	8/32	1	2	FACETS	0.92	0.816	1	0.92	0.816	1	CLONAL	1	TRUE	1	0.31	2		580	610	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955111	17955112	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755706305	NA	P-0040228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	103	849	1	ENST00000458235.1:c.115dup	p.Gln39ProfsTer13	p.Q39Pfs*13	ENST00000458235	NM_000215.3	39	cag/cCag	2/24	1	2	FACETS	0.784	0.701	0.872	0.784	0.701	0.872	SUBCLONAL	1	TRUE	1	0.31	2		850	848	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991949	72991949	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs753977275	NA	P-0040228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	75	515	3	ENST00000268489.5:c.2096del	p.Gly699AlafsTer125	p.G699Afs*125	ENST00000268489	NM_006885.3	699	gGc/gc	2/10	1	2	FACETS	0.774	0.679	0.877	0.774	0.679	0.877	SUBCLONAL	1	TRUE	1	0.31	2		518	625	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	137	827	2	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.31	2		829	785	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0040228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	58	283	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	1	2	FACETS	0.947	0.817	1	0.947	0.817	1	CLONAL	1	TRUE	1	0.31	2		283	395	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637062	93637062	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369986984	NA	P-0040228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	91	410	0	ENST00000375746.1:c.1112C>T	p.Thr371Met	p.T371M	ENST00000375746	NM_001174167.1	371	aCg/aTg	9/14	1	2	FACETS	0.932	0.828	1	0.932	0.828	1	CLONAL	1	TRUE	1	0.31	2		410	630	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587160	189587160	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs941268998	NA	P-0040228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	53	210	0	ENST00000264731.3:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000264731	NM_003722.4	393	Cga/Tga	9/14	1	2	FACETS	0.872	0.746	1	0.872	0.746	1	CLONAL	1	TRUE	1	0.31	2		210	392	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112421	115112421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200038495	NA	P-0040228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	79	653	0	ENST00000257566.3:c.1319C>T	p.Ala440Val	p.A440V	ENST00000257566	NM_016569.3	440	gCc/gTc	7/8	1	2	FACETS	0.781	0.687	0.881	0.781	0.687	0.881	SUBCLONAL	1	TRUE	1	0.31	2		653	653	SUCCESS
AR	367	MSKCC	GRCh37	X	66765979	66765979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	117	838	0	ENST00000374690.3:c.991G>A	p.Ala331Thr	p.A331T	ENST00000374690	NM_000044.3	331	Gct/Act	1/8	1	2	FACETS	0.893	0.805	0.987	0.893	0.805	0.987	CLONAL	1	TRUE	1	0.31	2		838	845	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760529	133760529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371656033	NA	P-0040228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	116	872	1	ENST00000318560.5:c.2852C>T	p.Pro951Leu	p.P951L	ENST00000318560	NM_005157.4	951	cCg/cTg	11/11	1	2	FACETS	0.995	0.897	1	0.995	0.897	1	CLONAL	1	TRUE	1	0.31	2		873	752	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670711	86670711	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	21	68	0	ENST00000274376.6:c.1989G>T	p.Lys663Asn	p.K663N	ENST00000274376	NM_002890.2	663	aaG/aaT	15/25	1	2	FACETS	0.88	0.683	1	0.88	0.683	1	CLONAL	1	TRUE	1	0.31	2		68	154	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711975	89711975	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	59	187	0	ENST00000371953.3:c.593T>G	p.Met198Arg	p.M198R	ENST00000371953	NM_000314.4	198	aTg/aGg	6/9	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.31	2		187	363	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819186	3819186	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	56	439	0	ENST00000262367.5:c.3049C>A	p.Pro1017Thr	p.P1017T	ENST00000262367	NM_004380.2	1017	Ccc/Acc	15/31	1	2	FACETS	0.645	0.553	0.746	0.645	0.553	0.746	SUBCLONAL	1	TRUE	1	0.31	2		439	560	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830109	72830109	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	110	496	0	ENST00000268489.5:c.6472C>T	p.Arg2158Ter	p.R2158*	ENST00000268489	NM_006885.3	2158	Cga/Tga	9/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.31	2		496	643	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11015744	11015744	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	70	396	1	ENST00000327064.4:c.338C>T	p.Thr113Ile	p.T113I	ENST00000327064	NM_199141.1	113	aCa/aTa	2/16	1	2	FACETS	0.978	0.855	1	0.978	0.855	1	CLONAL	1	TRUE	1	0.31	2		397	462	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753288	42753288	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	147	1001	1	ENST00000222329.4:c.976C>A	p.Leu326Ile	p.L326I	ENST00000222329	NM_006494.2	326	Ctc/Atc	4/4	1	2	FACETS	0.983	0.897	1	0.983	0.897	1	CLONAL	1	TRUE	1	0.31	2		1002	965	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385156	41385156	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	124	650	0	ENST00000373198.4:c.805A>G	p.Ile269Val	p.I269V	ENST00000373198	NM_133170.3	269	Atc/Gtc	6/32	1	2	FACETS	0.959	0.868	1	0.959	0.868	1	CLONAL	1	TRUE	1	0.31	2		650	834	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437657	52437657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	107	732	0	ENST00000460680.1:c.1504G>A	p.Ala502Thr	p.A502T	ENST00000460680	NM_004656.3	502	Gct/Act	13/17	1	2	FACETS	0.955	0.857	1	0.955	0.857	1	CLONAL	1	TRUE	1	0.31	2		732	723	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931323	131931323	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	82	233	0	ENST00000265335.6:c.2028A>C	p.Glu676Asp	p.E676D	ENST00000265335		676	gaA/gaC	13/25	1	2	FACETS	0.976	0.863	1	0.976	0.863	1	CLONAL	1	TRUE	1	0.31	2		233	542	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982311	201982312	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	353	777	0	ENST00000359651.3:c.692dup	p.Arg233SerfsTer2	p.R233Sfs*2	ENST00000359651		230	-/G	6/8	0.402669381599353	2	FACETS	0.989	0.941	1	0.989	0.941	1	CLONAL	2	TRUE	0	0.402669381599353	2		777	886	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	41	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.238871046857479	4	FACETS	0.755	0.634	0.888	0.755	0.634	0.888	SUBCLONAL	2	TRUE	2	0.280279619540409	4		426	248	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295795	212295795	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369248674	NA	P-0040248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	69	543	0	ENST00000342788.4:c.2518G>A	p.Val840Ile	p.V840I	ENST00000342788	NM_005235.2	840	Gtt/Att	21/28	NA	2	FACETS	0.837	0.743	0.935			1	INDETERMINATE	3	TRUE	NA	0.280279619540409	2		543	196	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713818	30713818	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	56	667	0	ENST00000295754.5:c.1143G>C	p.Lys381Asn	p.K381N	ENST00000295754	NM_003242.5	381	aaG/aaC	4/7	0.208052425269986	3	FACETS	1	0.894	1	0.69	0.599	0.787	CLONAL	2	TRUE	0	0.280279619540409	3		667	220	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0040256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	154	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.333871971172198	6	FACETS	1	0.943	1			1	CLONAL	3	TRUE	NA	0.333871971172198	6		298	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0040256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	88	709	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.328059011433522	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	0	0.333871971172198	2		709	254	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	339	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.322348596882904	6	FACETS	0.959	0.918	1	0.959	0.918	1	CLONAL	6	TRUE	0	0.322348596882904	6		426	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0040257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	222	781	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.322348596882904	2	FACETS	0.978	0.915	1	0.978	0.915	1	CLONAL	2	TRUE	0	0.322348596882904	2		781	704	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0040262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	235	293	0	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	1	2	FACETS	0.969	0.914	1	0.969	0.914	1	CLONAL	1	TRUE	1	0.925515178198669	2		293	524	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075157	16075157	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	275	344	0	ENST00000268712.3:c.395C>G	p.Pro132Arg	p.P132R	ENST00000268712	NM_006311.3	132	cCg/cGg	4/46	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.925515178198669	2		344	558	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052559	42052563	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	GAGTG	GAGTG	A	novel	NA	P-0040262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	251	395	0	ENST00000219905.7:c.7230_7234delinsA	p.Trp2410Ter	p.W2410*	ENST00000219905	NM_001164273.1	2410	tgGAGTGac/tgAac	20/24	1	2	FACETS	0.897	0.845	0.948	0.897	0.845	0.948	CLONAL	1	TRUE	1	0.925515178198669	2		395	605	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	177	326	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.962	0.895	1	0.962	0.895	1	CLONAL	1	TRUE	1	0.819904396852113	2		326	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0040299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	552	911	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.819904396852113	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.819904396852113	1		911	696	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023964	31023964	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773823004	NA	P-0040299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	121	684	0	ENST00000375687.4:c.3449G>A	p.Gly1150Glu	p.G1150E	ENST00000375687	NM_015338.5	1150	gGa/gAa	13/13	0.812978197490124	4	FACETS	0.441	0.397	0.488	0.147	0.132	0.163	SUBCLONAL	1	TRUE	1	0.819904396852113	4		684	1218	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872380	45872380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	366	773	0	ENST00000391945.4:c.131C>T	p.Ser44Leu	p.S44L	ENST00000391945	NM_000400.3	44	tCa/tTa	3/23	1	2	FACETS	0.964	0.918	1	0.964	0.918	1	CLONAL	1	TRUE	1	0.819904396852113	2		773	926	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425983	49425983	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	310	977	0	ENST00000301067.7:c.12505G>A	p.Gly4169Arg	p.G4169R	ENST00000301067	NM_003482.3	4169	Ggg/Agg	39/54	1	2	FACETS	0.898	0.85	0.947	0.898	0.85	0.947	CLONAL	1	TRUE	1	0.819904396852113	2		977	842	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786770	3786770	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	527	551	0	ENST00000262367.5:c.4441G>C	p.Asp1481His	p.D1481H	ENST00000262367	NM_004380.2	1481	Gat/Cat	27/31	0.819904396852113	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.819904396852113	2		551	628	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857702	9857703	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0040299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	404	502	0	ENST00000330684.3:c.3698_3699delinsAA	p.Pro1233Gln	p.P1233Q	ENST00000330684	NM_001134407.1	1233	cCC/cAA	13/13	0.819904396852113	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.819904396852113	2		502	464	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849404	68849420	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTCTGCTCTCTAGGGC	TTTCTGCTCTCTAGGGC	-	novel	NA	P-0040299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	374	493	0	ENST00000261769.5:c.1321-12_1325del		p.X441_splice	ENST00000261769	NM_004360.3	441		10/16	0.315441051487968	3	FACETS	0.981	0.957	1			1	INDETERMINATE	3	TRUE	NA	0.819904396852113	3		493	437	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251475	10251475	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	374	695	0	ENST00000340748.4:c.3457G>C	p.Glu1153Gln	p.E1153Q	ENST00000340748		1153	Gag/Cag	31/40	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.819904396852113	2		695	903	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42870072	42870072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	216	707	1	ENST00000398585.3:c.100G>A	p.Asp34Asn	p.D34N	ENST00000398585	NM_001135099.1	34	Gat/Aat	2/14	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.819904396852113	2		708	495	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87322817	87322817	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	33	384	0	ENST00000277120.3:c.418T>A	p.Leu140Met	p.L140M	ENST00000277120		140	Ttg/Atg	5/19	1	2	FACETS	0.345	0.283	0.415	0.345	0.283	0.415	SUBCLONAL	1	TRUE	1	0.819904396852113	2		384	233	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0040354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	128	797	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.369223658197778	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.369223658197778	1		799	473	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	26	142	1	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	0.348998257355403	2	FACETS	1	0.914	1	0.634	0.512	0.769	CLONAL	1	TRUE	0	0.369223658197778	2		143	111	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0040354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	66	185	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.365818973667358	2	FACETS	0.876	0.774	0.983	0.876	0.774	0.983	CLONAL	2	TRUE	0	0.369223658197778	2		185	204	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380279	25380279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	72	304	0	ENST00000311936.3:c.179G>A	p.Gly60Asp	p.G60D	ENST00000311936	NM_004985.3	60	gGt/gAt	3/5	1	2	FACETS	0.931	0.817	1	0.931	0.817	1	CLONAL	1	TRUE	1	0.369223658197778	2		304	419	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391521	84391521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542570943	NA	P-0040354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	58	223	0	ENST00000321945.7:c.311G>A	p.Arg104His	p.R104H	ENST00000321945	NM_139076.2	104	cGt/cAt	5/9	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.369223658197778	2		223	299	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0040391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	59	441	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.912	1	1	0.985	1	CLONAL	4	FALSE	1	0.0900813117649761	2		441	306	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36814361	36814361	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	157	868	1	ENST00000373129.3:c.679G>T	p.Gly227Trp	p.G227W	ENST00000373129	NM_032017.1	227	Ggg/Tgg	8/12	0.0900813117649761	1	FACETS	1	0.972	1	1	0.994	1	CLONAL	3	FALSE	0	0.0900813117649761	1		869	971	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587780070	NA	P-0040410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	345	541	0	ENST00000269305.4:c.535C>A	p.His179Asn	p.H179N	ENST00000269305	NM_001126112.2	179	Cat/Aat	5/11	0.779529517935415	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.779529517935415	1		541	517	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732941	74732941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	109	123	0	ENST00000359995.5:c.302G>A	p.Ser101Asn	p.S101N	ENST00000359995	NM_001195427.1	101	aGc/aAc	1/3	0.702561086667726	3	FACETS	0.82	0.752	0.889	0.547	0.501	0.593	CLONAL	2	TRUE	0	0.779529517935415	3		123	237	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538967	23538976	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGGTGGGC	CCAGGTGGGC	-	novel	NA	P-0040410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	273	595	0	ENST00000380871.4:c.463_472del	p.Ala155ProfsTer11	p.A155Pfs*11	ENST00000380871	NM_006167.3	155	GCCCACCTGGcc/cc	2/2	0.779529517935415	1	FACETS	0.855	0.813	0.896	0.855	0.813	0.896	CLONAL	1	TRUE	0	0.779529517935415	1		595	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0040444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	483	657	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.799962212343212	1	FACETS	0.965	0.933	0.996	0.965	0.933	0.996	CLONAL	1	TRUE	0	0.799962212343212	1		657	751	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685282	86685282	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	201	229	0	ENST00000274376.6:c.2998G>T	p.Glu1000Ter	p.E1000*	ENST00000274376	NM_002890.2	1000	Gag/Tag	24/25	0.799962212343212	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.799962212343212	1		229	279	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	164	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.335205201140544	3	FACETS	0.863	0.797	0.93	0.863	0.797	0.93	CLONAL	2	TRUE	1	0.435964337249723	3		426	531	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512041	148512041	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	84	328	1	ENST00000320356.2:c.1637A>T	p.Asn546Ile	p.N546I	ENST00000320356	NM_004456.4	546	aAt/aTt	14/20	1	2	FACETS	0.874	0.775	0.978	0.874	0.775	0.978	CLONAL	1	TRUE	1	0.435964337249723	2		329	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0040447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	168	661	0	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.435964337249723	1	FACETS	0.985	0.909	1	0.985	0.909	1	CLONAL	1	TRUE	0	0.435964337249723	1		661	612	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524486	44524486	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	65	240	0	ENST00000291552.4:c.71T>C	p.Ile24Thr	p.I24T	ENST00000291552	NM_006758.2	24	aTt/aCt	2/8	1	2	FACETS	0.941	0.822	1	0.941	0.822	1	CLONAL	1	TRUE	1	0.435964337249723	2		240	317	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691945	30691945	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	21	332	1	ENST00000295754.5:c.447C>A	p.Phe149Leu	p.F149L	ENST00000295754	NM_003242.5	149	ttC/ttA	3/7	0.435964337249723	1	FACETS	0.238	0.183	0.302	0.238	0.183	0.302	SUBCLONAL	1	TRUE	0	0.435964337249723	1		333	317	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0040496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	128	326	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.430802751042268	2		326	586	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0040496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	166	281	0	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	0.430802751042268	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.430802751042268	2		281	376	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0040496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	184	696	2	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.858	0.791	0.927	0.858	0.791	0.927	CLONAL	1	TRUE	1	0.430802751042268	2		698	996	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115594	108115594	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730881336	NA	P-0040496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	107	427	0	ENST00000278616.4:c.742C>T	p.Arg248Ter	p.R248*	ENST00000278616	NM_000051.3	248	Cga/Tga	7/63	1	2	FACETS	0.771	0.693	0.854	0.771	0.693	0.854	SUBCLONAL	1	TRUE	1	0.430802751042268	2		427	644	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508260	106508260	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	79	376	0	ENST00000359195.3:c.254C>T	p.Ala85Val	p.A85V	ENST00000359195	NM_002649.2	85	gCg/gTg	2/11	1	2	FACETS	0.886	0.783	0.995	0.886	0.783	0.995	CLONAL	1	TRUE	1	0.430802751042268	2		376	414	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982102	201982103	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTCA	novel	NA	P-0040496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	227	880	0	ENST00000359651.3:c.627_630dup	p.Asp211LeufsTer7	p.D211Lfs*7	ENST00000359651		209	tcc/tcCTCAc	5/8	0.430802751042268	1	FACETS	0.766	0.713	0.82	0.766	0.713	0.82	SUBCLONAL	1	TRUE	0	0.430802751042268	1		880	1080	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186613	108186613	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	106	342	0	ENST00000278616.4:c.6070G>C	p.Gly2024Arg	p.G2024R	ENST00000278616	NM_000051.3	2024	Ggg/Cgg	41/63	1	2	FACETS	0.939	0.845	1	0.939	0.845	1	CLONAL	1	TRUE	1	0.430802751042268	2		342	524	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458552	12458552	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	210	663	0	ENST00000287820.6:c.1169A>C	p.Asp390Ala	p.D390A	ENST00000287820	NM_015869.4	390	gAc/gCc	6/7	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.430802751042268	2		663	910	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943672	71943672	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	122	545	0	ENST00000298229.2:c.1715G>C	p.Arg572Thr	p.R572T	ENST00000298229	NM_001567.3	572	aGg/aCg	15/28	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.31646118465491	2		545	550	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964483	93964483	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	45	493	0	ENST00000369303.4:c.2414C>A	p.Pro805His	p.P805H	ENST00000369303	NM_004440.3	805	cCc/cAc	14/17	1	2	FACETS	0.867	0.734	1	0.867	0.734	1	CLONAL	1	TRUE	1	0.37597489286089	2		493	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577587	7577605	+	frameshift_variant	Frame_Shift_Del	DEL	TGGTGGTACAGTCAGAGCC	TGGTGGTACAGTCAGAGCC	-	novel	NA	P-0040518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	181	550	1	ENST00000269305.4:c.676_694del	p.Gly226SerfsTer15	p.G226Sfs*15	ENST00000269305	NM_001126112.2	226	GGCTCTGACTGTACCACCAtc/tc	7/11	0.37597489286089	0	FACETS	0.693	0.655	0.73			1	SUBCLONAL	3	TRUE	0	0.37597489286089	0		551	289	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0040524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	146	372	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.942	0.868	1	0.942	0.868	1	CLONAL	1	TRUE	1	0.745211327066878	2		372	416	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	259	522	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.978	0.921	1	0.978	0.921	1	CLONAL	1	TRUE	1	0.745211327066878	2		522	711	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570301	87570301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	261	642	0	ENST00000277120.3:c.2041G>A	p.Val681Ile	p.V681I	ENST00000277120		681	Gtc/Atc	17/19	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.745211327066878	2		642	678	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50815287	50815287	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779388734	NA	P-0040524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	227	556	0	ENST00000398568.2:c.1640C>T	p.Pro547Leu	p.P547L	ENST00000398568	NM_001042412.1	547	cCg/cTg	9/18	1	2	FACETS	0.884	0.828	0.942	0.884	0.828	0.942	CLONAL	1	TRUE	1	0.745211327066878	2		556	689	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	26	326	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.791	0.626	0.982	0.791	0.626	0.982	CLONAL	1	TRUE	1	0.15	2		326	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0040539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	54	757	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.15	2		757	712	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444878	49444878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747921601	NA	P-0040539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	46	861	0	ENST00000301067.7:c.2588G>A	p.Arg863Gln	p.R863Q	ENST00000301067	NM_003482.3	863	cGg/cAg	10/54	1	2	FACETS	0.759	0.637	0.894	0.759	0.637	0.894	SUBCLONAL	1	TRUE	1	0.15	2		861	808	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061321	38061321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	60	884	0	ENST00000250448.2:c.668C>T	p.Ser223Phe	p.S223F	ENST00000250448	NM_004496.3	223	tCc/tTc	2/2	1	2	FACETS	0.936	0.804	1	0.936	0.804	1	CLONAL	1	TRUE	1	0.15	2		884	855	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684109	29684109	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0040539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	28	502	0	ENST00000356175.3:c.7806+1G>C		p.X2602_splice	ENST00000356175	NM_000267.3	2602			1	2	FACETS	0.679	0.541	0.837	0.679	0.541	0.837	SUBCLONAL	1	TRUE	1	0.15	2		502	550	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	263	571	0	ENST00000269305.4:c.859G>T	p.Glu287Ter	p.E287*	ENST00000269305	NM_001126112.2	287	Gag/Tag	8/11	0.245721391740159	2	FACETS	0.87	0.818	0.924	0.87	0.818	0.924	CLONAL	2	TRUE	0	0.346594874867334	2		571	872	SUCCESS
APC	324	MSKCC	GRCh37	5	112175240	112175240	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	32	185	0	ENST00000257430.4:c.3949G>T	p.Glu1317Ter	p.E1317*	ENST00000257430	NM_000038.5	1317	Gaa/Taa	16/16	1	2	FACETS	0.736	0.6	0.887	0.736	0.6	0.887	SUBCLONAL	1	TRUE	1	0.346594874867334	2		185	251	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193181198	193181198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	32	204	1	ENST00000367435.3:c.1034C>T	p.Ser345Phe	p.S345F	ENST00000367435	NM_024529.4	345	tCt/tTt	12/17	0.160144477889991	4	FACETS	0.727	0.591	0.88	0.364	0.295	0.44	INDETERMINATE	1	TRUE	2	0.346594874867334	4		205	342	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884869	134884869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1261079719	NA	P-0040545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	159	358	3	ENST00000398015.3:c.1645G>A	p.Gly549Arg	p.G549R	ENST00000398015	NM_004441.4	549	Ggg/Agg	8/16	0.222298444964989	4	FACETS	0.852	0.783	0.924	0.852	0.783	0.924	CLONAL	2	TRUE	2	0.346594874867334	4		361	725	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419867	41419867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1569159161	NA	P-0040545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	62	442	1	ENST00000373198.4:c.454G>A	p.Ala152Thr	p.A152T	ENST00000373198	NM_133170.3	152	Gcc/Acc	3/32	0.346594874867334	5	FACETS	0.634	0.546	0.73	0.211	0.182	0.244	SUBCLONAL	1	TRUE	2	0.346594874867334	5		443	858	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956704	93956704	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0040545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	22	217	0	ENST00000369303.4:c.2533-1G>A		p.X845_splice	ENST00000369303	NM_004440.3	845			0.27884991836945	3	FACETS	0.496	0.385	0.626	0.248	0.192	0.313	SUBCLONAL	1	TRUE	1	0.346594874867334	3		217	300	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679799	88679799	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1467942640	NA	P-0040545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	141	436	0	ENST00000360948.2:c.664C>T	p.Arg222Ter	p.R222*	ENST00000360948	NM_001012338.2	222	Cga/Tga	7/19	0.27884991836945	3	FACETS	1	0.987	1	0.742	0.678	0.809	CLONAL	1	TRUE	1	0.346594874867334	3		436	643	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499670	8499670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	31	330	0	ENST00000356435.5:c.2299G>A	p.Asp767Asn	p.D767N	ENST00000356435		767	Gat/Aat	14/35	0.264835724121619	3	FACETS	0.421	0.339	0.513	0.14	0.113	0.171	SUBCLONAL	1	TRUE	0	0.346594874867334	3		330	499	SUCCESS
APC	324	MSKCC	GRCh37	5	112173932	112173932	+	frameshift_variant	Frame_Shift_Ins	INS	T	T	CTA	novel	NA	P-0040545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	64	291	0	ENST00000257430.4:c.2641delinsCTA	p.Ser881LeufsTer36	p.S881Lfs*36	ENST00000257430	NM_000038.5	881	Tcc/CTAcc	16/16	1	2	FACETS	0.888	0.772	1	0.888	0.772	1	CLONAL	1	TRUE	1	0.346594874867334	2		291	416	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	101	434	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.926	0.831	1	0.926	0.831	1	CLONAL	1	TRUE	1	0.449801454333642	2		434	485	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	136	132	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.852	0.784	0.92	1	0.99	1	CLONAL	2	TRUE	1	0.449801454333642	2		132	355	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	120	381	1	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.958	0.868	1	0.958	0.868	1	CLONAL	1	TRUE	1	0.449801454333642	2		382	557	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	78	556	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.57	0.501	0.644	0.57	0.501	0.644	SUBCLONAL	1	TRUE	1	0.449801454333642	2		562	608	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	81	666	1	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.456	0.401	0.516	0.456	0.401	0.516	SUBCLONAL	1	TRUE	1	0.449801454333642	2		667	789	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143994	11143994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	134	476	0	ENST00000358026.2:c.3575G>A	p.Arg1192His	p.R1192H	ENST00000358026	NM_001128849.1	1192	cGc/cAc	26/36	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.449801454333642	2		476	575	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552144	29552144	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	51	184	0	ENST00000356175.3:c.1882del	p.Tyr628ThrfsTer3	p.Y628Tfs*3	ENST00000356175	NM_000267.3	626	cTt/ct	17/57	1	2	FACETS	0.961	0.825	1	0.961	0.825	1	CLONAL	1	TRUE	1	0.449801454333642	2		184	236	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	59	339	2	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.711	0.614	0.815	0.711	0.614	0.815	SUBCLONAL	1	TRUE	1	0.449801454333642	2		341	369	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	126	541	0	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	1	2	FACETS	0.82	0.744	0.9	0.82	0.744	0.9	CLONAL	1	TRUE	1	0.449801454333642	2		541	683	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1627369	1627369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35936626	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	143	513	0	ENST00000344749.5:c.355G>A	p.Gly119Ser	p.G119S	ENST00000344749	NM_001136139.2	119	Ggc/Agc	6/19	1	2	FACETS	0.941	0.86	1	0.941	0.86	1	CLONAL	1	TRUE	1	0.449801454333642	2		513	676	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291473	10291473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61750053	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	88	445	0	ENST00000340748.4:c.206G>A	p.Arg69His	p.R69H	ENST00000340748		69	cGt/cAt	3/40	1	2	FACETS	0.725	0.643	0.811	0.725	0.643	0.811	SUBCLONAL	1	TRUE	1	0.449801454333642	2		445	540	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467448	25467448	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1164367418	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	65	521	1	ENST00000264709.3:c.1628del	p.Gly543AlafsTer108	p.G543Afs*108	ENST00000264709	NM_175629.2	543	gGc/gc	14/23	1	2	FACETS	0.441	0.382	0.505	0.441	0.382	0.505	SUBCLONAL	1	TRUE	1	0.449801454333642	2		522	656	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753099	42753099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	137	572	2	ENST00000222329.4:c.1165C>T	p.Arg389Trp	p.R389W	ENST00000222329	NM_006494.2	389	Cgg/Tgg	4/4	1	2	FACETS	0.943	0.86	1	0.943	0.86	1	CLONAL	1	TRUE	1	0.449801454333642	2		574	646	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271362	26271362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781608741	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	60	365	0	ENST00000305910.3:c.251G>A	p.Arg84His	p.R84H	ENST00000305910	NM_003534.2	84	cGc/cAc	1/1	1	2	FACETS	0.53	0.457	0.61	0.53	0.457	0.61	SUBCLONAL	1	TRUE	1	0.449801454333642	2		365	503	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073425	8073426	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs775750077	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	60	354	0	ENST00000377482.5:c.1233dup	p.Arg412Ter	p.R412*	ENST00000377482	NM_018948.3	411	-/T	4/4	1	2	FACETS	0.64	0.553	0.734	0.64	0.553	0.734	SUBCLONAL	1	TRUE	1	0.449801454333642	2		354	417	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260290	16260290	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755142962	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	55	428	0	ENST00000375759.3:c.7559del	p.Pro2520GlnfsTer15	p.P2520Qfs*15	ENST00000375759	NM_015001.2	2519	Ccc/cc	11/15	1	2	FACETS	0.594	0.509	0.685	0.594	0.509	0.685	SUBCLONAL	1	TRUE	1	0.449801454333642	2		428	412	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653866	89653866	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	46	259	0	ENST00000371953.3:c.164+1del		p.R55fs	ENST00000371953	NM_000314.4	55	aGg/ag	2/9	1	2	FACETS	0.849	0.721	0.987	0.849	0.721	0.987	CLONAL	1	TRUE	1	0.449801454333642	2		259	241	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724286	112724286	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	118	376	0	ENST00000369452.4:c.170C>A	p.Ser57Tyr	p.S57Y	ENST00000369452	NM_007373.3	57	tCc/tAc	2/9	1	2	FACETS	0.934	0.845	1	0.934	0.845	1	CLONAL	1	TRUE	1	0.449801454333642	2		376	562	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574518	64574518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	139	568	2	ENST00000312049.6:c.877C>T	p.Pro293Ser	p.P293S	ENST00000312049	NM_130799.2	293	Cct/Tct	6/10	1	2	FACETS	0.941	0.859	1	0.941	0.859	1	CLONAL	1	TRUE	1	0.449801454333642	2		570	657	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118845	115118845	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	82	316	1	ENST00000257566.3:c.496C>A	p.His166Asn	p.H166N	ENST00000257566	NM_016569.3	166	Cac/Aac	2/8	1	2	FACETS	0.803	0.711	0.901	0.803	0.711	0.901	CLONAL	1	TRUE	1	0.449801454333642	2		317	454	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676159	29676159	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	68	216	0	ENST00000356175.3:c.7148C>A	p.Ala2383Asp	p.A2383D	ENST00000356175	NM_000267.3	2383	gCt/gAt	48/57	1	2	FACETS	0.988	0.867	1	0.988	0.867	1	CLONAL	1	TRUE	1	0.449801454333642	2		216	306	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684371	29684372	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	70	326	0	ENST00000356175.3:c.7892_7893del	p.Lys2631SerfsTer7	p.K2631Sfs*7	ENST00000356175	NM_000267.3	2631	AAa/a	53/57	1	2	FACETS	0.769	0.673	0.871	0.769	0.673	0.871	SUBCLONAL	1	TRUE	1	0.449801454333642	2		326	405	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054405	13054405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1200295838	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	138	475	0	ENST00000316448.5:c.1015G>A	p.Ala339Thr	p.A339T	ENST00000316448	NM_004343.3	339	Gct/Act	8/9	1	2	FACETS	0.889	0.811	0.971	0.889	0.811	0.971	CLONAL	1	TRUE	1	0.449801454333642	2		475	690	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714699	52714699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1359743267	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	119	477	2	ENST00000322088.6:c.457G>A	p.Val153Ile	p.V153I	ENST00000322088	NM_014225.5	153	Gtc/Atc	4/15	1	2	FACETS	0.827	0.748	0.91	0.827	0.748	0.91	CLONAL	1	TRUE	1	0.449801454333642	2		479	640	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185051	99185051	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	87	316	0	ENST00000074304.5:c.2453T>C	p.Leu818Ser	p.L818S	ENST00000074304	NM_001134224.1	818	tTa/tCa	23/26	1	2	FACETS	0.811	0.721	0.907	0.811	0.721	0.907	CLONAL	1	TRUE	1	0.449801454333642	2		316	477	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104653	209104653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	97	349	0	ENST00000345146.2:c.925C>T	p.His309Tyr	p.H309Y	ENST00000345146	NM_005896.2	309	Cac/Tac	8/10	1	2	FACETS	0.918	0.822	1	0.918	0.822	1	CLONAL	1	TRUE	1	0.449801454333642	2		349	470	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920060	1920060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770171601	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	104	542	0	ENST00000382891.5:c.1120G>A	p.Ala374Thr	p.A374T	ENST00000382891	NM_133335.3	374	Gca/Aca	5/22	0.449801454333642	1	FACETS	0.747	0.672	0.825	0.747	0.672	0.825	SUBCLONAL	1	TRUE	0	0.449801454333642	1		542	480	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244130	153244151	+	frameshift_variant	Frame_Shift_Del	DEL	CTGATCCGCCACACAACTCCCC	CTGATCCGCCACACAACTCCCC	-	novel	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	98	357	0	ENST00000281708.4:c.2006_2027del	p.Gly669GlufsTer31	p.G669Efs*31	ENST00000281708	NM_033632.3	669	gGGGGAGTTGTGTGGCGGATCAGa/ga	12/12	1	2	FACETS	0.877	0.785	0.973	0.877	0.785	0.973	CLONAL	1	TRUE	1	0.449801454333642	2		357	497	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629954	187629954	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	146	579	0	ENST00000441802.2:c.1028C>G	p.Thr343Ser	p.T343S	ENST00000441802	NM_005245.3	343	aCt/aGt	2/27	1	2	FACETS	0.949	0.868	1	0.949	0.868	1	CLONAL	1	TRUE	1	0.449801454333642	2		579	684	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589532	67589558	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTAGGATCAAGTTGTCAAAGAAGATA	TCTAGGATCAAGTTGTCAAAGAAGATA	-	novel	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	13	137	0	ENST00000274335.5:c.1300-5_1321del		p.X434_splice	ENST00000274335		434		10/15	1	2	FACETS	0.462	0.332	0.619	0.462	0.332	0.619	SUBCLONAL	1	TRUE	1	0.449801454333642	2		137	125	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672599	30672599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	101	518	0	ENST00000376406.3:c.4361A>G	p.Glu1454Gly	p.E1454G	ENST00000376406	NM_014641.2	1454	gAg/gGg	10/15	1	2	FACETS	0.805	0.721	0.893	0.805	0.721	0.893	CLONAL	1	TRUE	1	0.449801454333642	2		518	558	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133296	38133296	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	119	443	0	ENST00000317025.8:c.4177del	p.Ala1393ProfsTer30	p.A1393Pfs*30	ENST00000317025	NM_023034.1	1393	Gcc/cc	24/24	1	2	FACETS	0.967	0.877	1	0.967	0.877	1	CLONAL	1	TRUE	1	0.449801454333642	2		443	547	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187221	38187222	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	78	559	2	ENST00000317025.8:c.1255dup	p.Thr419AsnfsTer28	p.T419Nfs*28	ENST00000317025	NM_023034.1	419	acc/aAcc	6/24	1	2	FACETS	0.427	0.375	0.484	0.427	0.375	0.484	SUBCLONAL	1	TRUE	1	0.449801454333642	2		561	812	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227672	53227672	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	89	417	0	ENST00000375401.3:c.2516G>T	p.Gly839Val	p.G839V	ENST00000375401	NM_004187.3	839	gGc/gTc	17/26	1	2	FACETS	0.716	0.636	0.8	0.716	0.636	0.8	SUBCLONAL	1	TRUE	1	0.449801454333642	2		417	553	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246332	53246332	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	133	508	0	ENST00000375401.3:c.650A>G	p.Gln217Arg	p.Q217R	ENST00000375401	NM_004187.3	217	cAg/cGg	5/26	1	2	FACETS	0.999	0.911	1	0.999	0.911	1	CLONAL	1	TRUE	1	0.449801454333642	2		508	592	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	435	326	0				ENST00000310581	NM_198253.2	-/1132			0.590442595220811	6	FACETS	1	0.976	1	1	0.976	1	CLONAL	4	TRUE	2	0.590442595220811	6		326	788	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482369	56482369	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	47	781	0	ENST00000267101.3:c.917C>G	p.Pro306Arg	p.P306R	ENST00000267101	NM_001982.3	306	cCt/cGt	8/28	0.590442595220811	3	FACETS	0.437	0.369	0.512	0.218	0.184	0.256	SUBCLONAL	1	TRUE	1	0.590442595220811	3		781	472	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127665	64127665	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1291878532	NA	P-0040586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	49	942	2	ENST00000334205.4:c.158C>T	p.Ala53Val	p.A53V	ENST00000334205	NM_003942.2	53	gCg/gTg	3/17	0.205796355040231	5	FACETS	0.322	0.272	0.378	0.107	0.09	0.126	INDETERMINATE	1	TRUE	2	0.590442595220811	5		944	971	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117150	7117150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146490822	NA	P-0040586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	36	865	2	ENST00000302850.5:c.4066G>A	p.Glu1356Lys	p.E1356K	ENST00000302850	NM_000208.2	1356	Gag/Aag	22/22	0.590442595220811	3	FACETS	0.22	0.18	0.265	0.11	0.09	0.133	SUBCLONAL	1	TRUE	1	0.590442595220811	3		867	719	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879855	37879855	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1604	360	854	0	ENST00000269571.5:c.2150A>T	p.Glu717Val	p.E717V	ENST00000269571		717	gAg/gTg	18/27	0.590442595220811	8	FACETS	0.86	0.812	0.91			1	CLONAL	2	TRUE	NA	0.590442595220811	8		854	1964	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868168	45868168	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	54	1036	0	ENST00000391945.4:c.522C>G	p.Ile174Met	p.I174M	ENST00000391945	NM_000400.3	174	atC/atG	7/23	0.471917231599721	3	FACETS	0.337	0.287	0.391	0.112	0.095	0.131	SUBCLONAL	1	TRUE	0	0.590442595220811	3		1036	704	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618928	37618928	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1389471686	NA	P-0040586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	73	706	1	ENST00000447079.4:c.604C>T	p.Arg202Ter	p.R202*	ENST00000447079	NM_015083.1	202	Cga/Tga	1/14	0.590442595220811	8	FACETS	0.738	0.644	0.841			1	SUBCLONAL	1	TRUE	NA	0.590442595220811	8		707	928	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643566	38643578	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAATGTTAGGG	GAAAATGTTAGGG	-	novel	NA	P-0040586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	35	741	0	ENST00000299084.4:c.1044_1056del	p.Gly350MetfsTer52	p.G350Mfs*52	ENST00000299084	NM_152594.2	346	GAAAATGTTAGGGga/ga	7/7	1	2	FACETS	0.406	0.334	0.486	0.406	0.334	0.486	SUBCLONAL	1	TRUE	1	0.590442595220811	2		741	292	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864936	57864936	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1050431269	NA	P-0040586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	49	953	0	ENST00000228682.2:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000228682	NM_005269.2	805	Cga/Tga	12/12	0.590442595220811	3	FACETS	0.363	0.306	0.424	0.181	0.153	0.212	SUBCLONAL	1	TRUE	1	0.590442595220811	3		953	593	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711887	89711887	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	29	509	1	ENST00000371953.3:c.505C>T	p.Pro169Ser	p.P169S	ENST00000371953	NM_000314.4	169	Ccc/Tcc	6/9	0.471917231599721	3	FACETS	0.612	0.494	0.743	0.204	0.164	0.248	SUBCLONAL	1	TRUE	0	0.590442595220811	3		510	208	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17349186	17349186	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	70	675	0	ENST00000375499.3:c.682G>T	p.Glu228Ter	p.E228*	ENST00000375499	NM_003000.2	228	Gag/Tag	7/8	0.333934099719981	5	FACETS	0.797	0.696	0.906	0.266	0.232	0.302	INDETERMINATE	1	TRUE	2	0.590442595220811	5		675	561	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690362	117690362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	72	688	0	ENST00000369458.3:c.767C>T	p.Ser256Leu	p.S256L	ENST00000369458	NM_024626.3	256	tCa/tTa	5/6	0.333934099719981	5	FACETS	0.832	0.727	0.944	0.277	0.242	0.315	INDETERMINATE	1	TRUE	2	0.590442595220811	5		688	553	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551990	150551990	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	101	616	0	ENST00000369026.2:c.17G>C	p.Arg6Thr	p.R6T	ENST00000369026	NM_021960.4	6	aGa/aCa	1/3	0.590442595220811	7	FACETS	0.841	0.75	0.938	0.168	0.15	0.188	CLONAL	1	TRUE	2	0.590442595220811	7		616	1007	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118937	115118938	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0040586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	14	350	1	ENST00000257566.3:c.403_404delinsAT	p.Pro135Ile	p.P135I	ENST00000257566	NM_016569.3	135	CCa/ATa	2/8	0.25351726452193	3	FACETS	0.389	0.282	0.517	0.13	0.094	0.173	INDETERMINATE	1	TRUE	0	0.590442595220811	3		351	158	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910723	32910723	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507282	NA	P-0040586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	24	557	0	ENST00000380152.3:c.2231C>T	p.Ser744Leu	p.S744L	ENST00000380152		744	tCa/tTa	11/27	0.590442595220811	3	FACETS	0.393	0.308	0.49	0.196	0.154	0.245	SUBCLONAL	1	TRUE	1	0.590442595220811	3		557	268	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923090	48923090	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0040586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	102	380	0	ENST00000267163.4:c.540-2A>G		p.X180_splice	ENST00000267163	NM_000321.2	180			0.582118449344766	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	0	0.590442595220811	3		380	138	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107922	30107922	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	53	601	0	ENST00000331968.5:c.885C>A	p.Phe295Leu	p.F295L	ENST00000331968	NM_002742.2	295	ttC/ttA	5/18	0.370324300578388	4	FACETS	0.55	0.469	0.639	0.275	0.234	0.32	SUBCLONAL	1	TRUE	2	0.590442595220811	4		601	519	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108018	30108018	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	54	735	0	ENST00000331968.5:c.789G>C	p.Leu263Phe	p.L263F	ENST00000331968	NM_002742.2	263	ttG/ttC	5/18	0.370324300578388	4	FACETS	0.494	0.421	0.573	0.247	0.21	0.287	SUBCLONAL	1	TRUE	2	0.590442595220811	4		735	589	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100633	67100633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	43	653	0	ENST00000412916.2:c.331A>G	p.Lys111Glu	p.K111E	ENST00000412916		111	Aaa/Gaa	4/6	0.590442595220811	2	FACETS	0.287	0.24	0.339	0.143	0.12	0.17	SUBCLONAL	1	TRUE	0	0.590442595220811	2		653	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579410	7579410	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	86	914	0	ENST00000269305.4:c.277C>G	p.Leu93Val	p.L93V	ENST00000269305	NM_001126112.2	93	Ctg/Gtg	4/11	0.417000005452531	5	FACETS	0.58	0.512	0.653	0.193	0.17	0.218	SUBCLONAL	1	TRUE	2	0.590442595220811	5		914	947	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867571	45867571	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	56	1064	0	ENST00000391945.4:c.737C>G	p.Ser246Cys	p.S246C	ENST00000391945	NM_000400.3	246	tCc/tGc	9/23	0.471917231599721	3	FACETS	0.332	0.283	0.385	0.111	0.094	0.129	SUBCLONAL	1	TRUE	0	0.590442595220811	3		1064	741	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281189	46281189	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs142561017	NA	P-0040586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	52	701	0	ENST00000371998.3:c.3986C>G	p.Ser1329Cys	p.S1329C	ENST00000371998		1329	tCt/tGt	21/23	0.370701546306365	5	FACETS	0.547	0.465	0.637	0.182	0.155	0.213	SUBCLONAL	1	TRUE	2	0.590442595220811	5		701	607	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1976629	1976629	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	39	808	1	ENST00000382891.5:c.3412C>T	p.Arg1138Ter	p.R1138*	ENST00000382891	NM_133335.3	1138	Cga/Tga	19/22	0.370701546306365	5	FACETS	0.436	0.361	0.521	0.145	0.12	0.174	SUBCLONAL	1	TRUE	2	0.590442595220811	5		809	571	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048716	180048716	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	31	921	0	ENST00000261937.6:c.1846T>C	p.Phe616Leu	p.F616L	ENST00000261937	NM_182925.4	616	Ttc/Ctc	13/30	0.590442595220811	3	FACETS	0.232	0.187	0.283	0.116	0.093	0.142	SUBCLONAL	1	TRUE	1	0.590442595220811	3		921	587	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942774	68942774	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	93	646	0	ENST00000288368.4:c.586G>C	p.Ala196Pro	p.A196P	ENST00000288368	NM_024870.2	196	Gca/Cca	6/40	0.479115689719979	2	FACETS	0.746	0.668	0.829	0.373	0.334	0.415	SUBCLONAL	1	TRUE	0	0.590442595220811	2		646	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0040587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	411	797	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.475918044354006	2	FACETS	0.812	0.776	0.849	0.812	0.776	0.849	CLONAL	2	TRUE	0	0.502515177173484	2		799	1007	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475140	40475140	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	79	698	0	ENST00000264657.5:c.1770T>G	p.Ser590Arg	p.S590R	ENST00000264657	NM_139276.2	590	agT/agG	20/24	0.320626202380246	3	FACETS	0.395	0.346	0.447	0.197	0.173	0.224	SUBCLONAL	1	TRUE	1	0.502515177173484	3		698	997	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937323	76937323	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	66	272	0	ENST00000373344.5:c.3425C>T	p.Ser1142Leu	p.S1142L	ENST00000373344	NM_000489.3	1142	tCa/tTa	9/35	1	1	FACETS	0.813	0.714	0.916	0.813	0.714	0.916	CLONAL	1	TRUE	0	0.502515177173484	1		272	242	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040604-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	90	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.777	0.694	0.865	0.777	0.694	0.865	SUBCLONAL	1	TRUE	1	0.581723831162772	2		426	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0040604-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	196	564	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.543925471640364	1	FACETS	0.996	0.931	1	0.996	0.931	1	CLONAL	1	TRUE	0	0.581723831162772	1		564	480	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0040614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	144	371	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.913	0.837	0.991	0.913	0.837	0.991	CLONAL	1	TRUE	1	0.591879693512972	2		371	533	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602565	10602565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	239	667	0	ENST00000171111.5:c.1013C>T	p.Ser338Leu	p.S338L	ENST00000171111	NM_203500.1	338	tCg/tTg	3/6	0.591879693512972	1	FACETS	0.96	0.904	1	0.96	0.904	1	CLONAL	1	TRUE	0	0.591879693512972	1		667	592	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732985	30732985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	172	470	1	ENST00000295754.5:c.1598G>A	p.Cys533Tyr	p.C533Y	ENST00000295754	NM_003242.5	533	tGt/tAt	7/7	0.591879693512972	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.591879693512972	1		471	398	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728630	190728630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770849733	NA	P-0040614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	201	498	0	ENST00000441310.2:c.2018C>T	p.Ser673Phe	p.S673F	ENST00000441310	NM_000534.4	673	tCt/tTt	10/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.591879693512972	2		498	609	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481403	140481403	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913357	NA	P-0040614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	150	365	0	ENST00000288602.6:c.1405G>C	p.Gly469Arg	p.G469R	ENST00000288602	NM_004333.4	469	Gga/Cga	11/18	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.591879693512972	2		365	480	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11293543	11293543	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	134	401	0	ENST00000361445.4:c.2333C>G	p.Ala778Gly	p.A778G	ENST00000361445	NM_004958.3	778	gCa/gGa	15/58	1	2	FACETS	0.891	0.815	0.971	0.891	0.815	0.971	CLONAL	1	TRUE	1	0.591879693512972	2		401	508	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10305509	10305509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257821053	NA	P-0040614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	25	466	1	ENST00000340748.4:c.67G>A	p.Asp23Asn	p.D23N	ENST00000340748		23	Gat/Aat	1/40	0.591879693512972	1	FACETS	0.142	0.112	0.178	0.142	0.112	0.178	SUBCLONAL	1	TRUE	0	0.591879693512972	1		467	418	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602464	10602464	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	254	665	0	ENST00000171111.5:c.1114G>T	p.Gly372Trp	p.G372W	ENST00000171111	NM_203500.1	372	Ggg/Tgg	3/6	0.591879693512972	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.591879693512972	1		665	561	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105552	11105552	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	243	633	0	ENST00000358026.2:c.1468C>G	p.His490Asp	p.H490D	ENST00000358026	NM_001128849.1	490	Cac/Gac	9/36	0.591879693512972	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.591879693512972	1		633	548	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113366	209113366	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1553603130	NA	P-0040614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	109	272	0	ENST00000345146.2:c.141G>C	p.Glu47Asp	p.E47D	ENST00000345146	NM_005896.2	47	gaG/gaC	4/10	1	2	FACETS	0.94	0.851	1	0.94	0.851	1	CLONAL	1	TRUE	1	0.591879693512972	2		272	392	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252935	36252935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	138	457	0	ENST00000300305.3:c.427G>A	p.Glu143Lys	p.E143K	ENST00000300305		143	Gag/Aag	4/8	1	2	FACETS	0.967	0.886	1	0.967	0.886	1	CLONAL	1	TRUE	1	0.591879693512972	2		457	482	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8733822	8733822	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	195	516	0	ENST00000356435.5:c.22C>A	p.Leu8Met	p.L8M	ENST00000356435		8	Ctg/Atg	1/35	0.591879693512972	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.591879693512972	1		516	452	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224206	98224206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750373573	NA	P-0040614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	137	404	0	ENST00000331920.6:c.2635G>A	p.Asp879Asn	p.D879N	ENST00000331920	NM_000264.3	879	Gat/Aat	16/24	1	2	FACETS	0.985	0.903	1	0.985	0.903	1	CLONAL	1	TRUE	1	0.591879693512972	2		404	470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0040615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	184	954	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.268790710485724	2		954	916	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942835	68942835	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	45	672	2	ENST00000288368.4:c.647G>T	p.Arg216Ile	p.R216I	ENST00000288368	NM_024870.2	216	aGa/aTa	6/40	1	2	FACETS	0.388	0.325	0.458	0.388	0.325	0.458	SUBCLONAL	1	TRUE	1	0.268790710485724	2		674	863	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0040631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	392	797	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.795563072812225	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.795563072812225	1		799	584	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	139	441	0	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	0.596177434818602	1	FACETS	0.364	0.333	0.397	0.364	0.333	0.397	SUBCLONAL	1	TRUE	0	0.795563072812225	1		441	578	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115952	8115953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0040633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	145	544	0	ENST00000346208.3:c.1300dup	p.His434ProfsTer73	p.H434Pfs*73	ENST00000346208		433	cac/caCc	6/6	0.628527402515389	6	FACETS	0.887	0.813	0.964	0.355	0.325	0.386	CLONAL	2	TRUE	1	0.65309012652485	6		544	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577157	7577157	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0040637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	99	397	0	ENST00000269305.4:c.783-2A>C		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	0.969	0.865	1	0.969	0.865	1	CLONAL	1	TRUE	1	0.28	2		397	730	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857315	68857316	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0040637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	27	301	0	ENST00000261769.5:c.1950_1951insTA	p.Ile651Ter	p.I651*	ENST00000261769	NM_004360.3	650	-/TA	13/16	1	2	FACETS	0.438	0.348	0.542	0.438	0.348	0.542	SUBCLONAL	1	TRUE	1	0.28	2		301	440	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186507050	186507050	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	17	177	0	ENST00000323963.5:c.1216C>T	p.Leu406Phe	p.L406F	ENST00000323963		406	Ctt/Ttt	11/11	1	2	FACETS	0.502	0.375	0.652	0.502	0.375	0.652	SUBCLONAL	1	TRUE	1	0.28	2		177	242	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	270	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.720898795887172	3	FACETS	0.909	0.861	0.956	0.909	0.861	0.956	CLONAL	2	TRUE	1	0.729382316155329	3		426	556	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604701	48604701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555687572	NA	P-0040658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	148	308	0	ENST00000342988.3:c.1523G>A	p.Gly508Asp	p.G508D	ENST00000342988	NM_005359.5	508	gGc/gAc	12/12	0.646619464350177	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.729382316155329	1		308	249	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222727	5222727	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746980740	NA	P-0040658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	167	484	0	ENST00000357368.4:c.3076C>T	p.Arg1026Cys	p.R1026C	ENST00000357368	NM_002850.3	1026	Cgc/Tgc	18/38	1	2	FACETS	0.944	0.875	1	0.944	0.875	1	CLONAL	1	TRUE	1	0.729382316155329	2		484	485	SUCCESS
APC	324	MSKCC	GRCh37	5	112175952	112175952	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587783031	NA	P-0040658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	63	175	0	ENST00000257430.4:c.4666del	p.Thr1556LeufsTer9	p.T1556Lfs*9	ENST00000257430	NM_000038.5	1554	gAa/ga	16/16	1	2	FACETS	0.723	0.633	0.818	0.723	0.633	0.818	SUBCLONAL	1	TRUE	1	0.729382316155329	2		175	239	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873016	134873016	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	141	441	0	ENST00000398015.3:c.1320G>T	p.Met440Ile	p.M440I	ENST00000398015	NM_004441.4	440	atG/atT	6/16	1	2	FACETS	0.903	0.831	0.978	0.903	0.831	0.978	CLONAL	1	TRUE	1	0.729382316155329	2		441	428	SUCCESS
APC	324	MSKCC	GRCh37	5	112174307	112174308	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATAAAATACA	novel	NA	P-0040658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	84	232	0	ENST00000257430.4:c.3017_3026dup	p.His1009GlnfsTer2	p.H1009Qfs*2	ENST00000257430	NM_000038.5	1006	cat/cATAAAATACAat	16/16	1	2	FACETS	0.75	0.67	0.835	0.75	0.67	0.835	SUBCLONAL	1	TRUE	1	0.729382316155329	2		232	307	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647536	117647536	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	141	414	0	ENST00000368508.3:c.5408G>A	p.Trp1803Ter	p.W1803*	ENST00000368508	NM_002944.2	1803	tGg/tAg	33/43	1	2	FACETS	0.895	0.823	0.969	0.895	0.823	0.969	CLONAL	1	TRUE	1	0.729382316155329	2		414	432	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	166	326	0				ENST00000310581	NM_198253.2	-/1132			0.32314821256806	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	FALSE	0	0.349269167367914	2		326	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780071	NA	P-0040669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	257	491	0	ENST00000269305.4:c.580C>T	p.Leu194Phe	p.L194F	ENST00000269305	NM_001126112.2	194	Ctt/Ttt	6/11	0.32314821256806	2	FACETS	0.967	0.909	1	0.967	0.909	1	CLONAL	2	FALSE	0	0.349269167367914	2		491	761	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488700	212488700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	57	347	1	ENST00000342788.4:c.2149G>A	p.Glu717Lys	p.E717K	ENST00000342788	NM_005235.2	717	Gag/Aag	18/28	0.244858638820159	0	FACETS	0.382	0.328	0.441			1	SUBCLONAL	1	FALSE	0	0.349269167367914	0		348	556	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645255	67645255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	100	526	0	ENST00000264010.4:c.520G>A	p.Glu174Lys	p.E174K	ENST00000264010	NM_006565.3	174	Gag/Aag	3/12	NA	2	FACETS	0.645	0.575	0.719			1	INDETERMINATE	1	FALSE	NA	0.349269167367914	2		526	888	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534506	140534506	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	34	368	0	ENST00000288602.6:c.407C>T	p.Ser136Leu	p.S136L	ENST00000288602	NM_004333.4	136	tCa/tTa	3/18	1	2	FACETS	0.301	0.245	0.364	0.301	0.245	0.364	SUBCLONAL	1	FALSE	1	0.349269167367914	2		368	647	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562247	21562247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143741195	NA	P-0040669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	127	651	0	ENST00000382592.4:c.1672C>T	p.Arg558Cys	p.R558C	ENST00000382592	NM_014572.2	558	Cgc/Tgc	4/8	0.19369049103072	2	FACETS	0.743	0.672	0.818	0.371	0.336	0.409	INDETERMINATE	1	FALSE	0	0.349269167367914	2		651	979	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939096	48939096	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1214283717	NA	P-0040669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	135	181	0	ENST00000267163.4:c.928G>T	p.Gly310Ter	p.G310*	ENST00000267163	NM_000321.2	310	Gga/Tga	9/27	0.349269167367914	3	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	FALSE	1	0.349269167367914	3		181	444	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713301	43713301	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	73	704	0	ENST00000382044.4:c.4172G>C	p.Arg1391Thr	p.R1391T	ENST00000382044	NM_001141980.1	1391	aGa/aCa	20/28	0.349269167367914	1	FACETS	0.393	0.343	0.447	0.393	0.343	0.447	SUBCLONAL	1	FALSE	0	0.349269167367914	1		704	878	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713326	43713326	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	85	735	0	ENST00000382044.4:c.4147G>T	p.Asp1383Tyr	p.D1383Y	ENST00000382044	NM_001141980.1	1383	Gat/Tat	20/28	0.349269167367914	1	FACETS	0.426	0.376	0.48	0.426	0.376	0.48	SUBCLONAL	1	FALSE	0	0.349269167367914	1		735	943	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5078363	5078363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	46	322	0	ENST00000381652.3:c.2050G>A	p.Glu684Lys	p.E684K	ENST00000381652	NM_004972.3	684	Gaa/Aaa	16/25	NA	2	FACETS	0.501	0.421	0.588			1	INDETERMINATE	1	FALSE	NA	0.349269167367914	2		322	526	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0040670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	13	441	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.429	0.304	0.582	0.429	0.304	0.582	SUBCLONAL	1	TRUE	1	0.14	2		441	433	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959088	2959088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	46	246	0	ENST00000396946.4:c.2428G>A	p.Asp810Asn	p.D810N	ENST00000396946	NM_032415.4	810	Gac/Aac	18/25	1	2	FACETS	0.915	0.769	1	0.915	0.769	1	CLONAL	1	TRUE	1	0.14	2		246	718	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0040671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	214	830	0	ENST00000269305.4:c.376-1del		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.532246848577835	3	FACETS	0.989	0.933	1	0.66	0.622	0.697	CLONAL	2	TRUE	0	0.682628045658494	3		830	425	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156578	55156578	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	14	531	2	ENST00000257290.5:c.2979C>A	p.Tyr993Ter	p.Y993*	ENST00000257290	NM_006206.4	993	taC/taA	22/23	0.425016300176706	1	FACETS	0.16	0.116	0.213	0.16	0.116	0.213	SUBCLONAL	1	TRUE	0	0.682628045658494	1		533	169	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061140	38061187	+	inframe_deletion	In_Frame_Del	DEL	CCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCA	CCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCA	-	novel	NA	P-0040672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	139	158	1	ENST00000250448.2:c.802_849del	p.Cys268_Gly283del	p.C268_G283del	ENST00000250448	NM_004496.3	268	TGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGG/-	2/2	0.244056691071661	5	FACETS	1	0.97	1	1	0.989	1	CLONAL	4	TRUE	2	0.403082885736347	5		159	257	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145736846	145736846	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	227	732	0	ENST00000428558.2:c.3595G>C	p.Ala1199Pro	p.A1199P	ENST00000428558	NM_004260.3	1199	Gcc/Ccc	22/22	0.403082885736347	9	FACETS	0.945	0.878	1	0.27	0.251	0.29	CLONAL	2	TRUE	2	0.403082885736347	9		732	1436	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0040703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	194	561	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	0.584333234423206	1	FACETS	0.794	0.741	0.847	0.794	0.741	0.847	SUBCLONAL	1	TRUE	0	0.650652881813833	1		561	507	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0040749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	26	675	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.240674294805844	1	FACETS	0.113	0.088	0.14	0.113	0.088	0.14	INDETERMINATE	1	TRUE	0	0.55199830296302	1		675	606	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828602	72828603	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	44	816	0	ENST00000268489.5:c.7978dup	p.Tyr2660LeufsTer68	p.Y2660Lfs*68	ENST00000268489	NM_006885.3	2660	tat/tTat	9/10	0.55199830296302	1	FACETS	0.274	0.229	0.322	0.274	0.229	0.322	SUBCLONAL	1	TRUE	0	0.55199830296302	1		816	422	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413278	139413278	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0040749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	176	862	0	ENST00000277541.6:c.866-2A>T		p.X289_splice	ENST00000277541	NM_017617.3	289			1	2	FACETS	0.986	0.912	1	0.986	0.912	1	CLONAL	1	TRUE	1	0.55199830296302	2		862	647	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089060	37089060	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs915595144	NA	P-0040752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	79	445	0	ENST00000231790.2:c.1782G>C	p.Glu594Asp	p.E594D	ENST00000231790	NM_000249.3	594	gaG/gaC	16/19	0.221385525488645	2	FACETS	0.975	0.857	1	0.487	0.428	0.551	CLONAL	1	TRUE	0	0.221385525488645	2		445	732	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520000	NA	P-0040752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1250	321	1166	0	ENST00000269305.4:c.452C>A	p.Pro151His	p.P151H	ENST00000269305	NM_001126112.2	151	cCc/cAc	5/11	0.169434844879035	2	FACETS	0.923	0.869	0.978	0.923	0.869	0.978	CLONAL	2	TRUE	0	0.221385525488645	2		1166	1571	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444900	49444900	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1301	120	863	0	ENST00000301067.7:c.2566G>C	p.Glu856Gln	p.E856Q	ENST00000301067	NM_003482.3	856	Gag/Cag	10/54	0.208370013906887	3	FACETS	0.847	0.762	0.938	0.424	0.381	0.469	CLONAL	1	TRUE	1	0.221385525488645	3		863	1421	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238203	133238203	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0040752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	94	666	0	ENST00000320574.5:c.2774C>G	p.Ser925Ter	p.S925*	ENST00000320574	NM_006231.2	925	tCa/tGa	24/49	0.177600193794704	2	FACETS	0.85	0.755	0.952	0.425	0.377	0.476	CLONAL	1	TRUE	0	0.221385525488645	2		666	999	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884174	151884787	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTCTAGGACAAAGTAAAATGCAAGATGTTTCTAGACATCTAGGGAATCTTCATGTTGTGGGTCATCATAGACAAAAATTAGTTAAGCTACCTTTCTATTGCAGTTAAAAAAAAAAAAGGTATTGCACATGTGAAAATGTTGGTAAAACAGAAATAATATATTCATGGCTTACCAGGGAATTCTTCCTTTAAGTTGGGGAAATTAATATTGGTGTAGAGAACTGGGGCAACAGTTGCCATTTCACCCAGAGCCTCCTCTTTCTCCCACTTAAGCGTGCTTCTCTGGGCATTCGACATTGTGTCATTTTCTCCTTCCACAGTGGGAGCTGATGATGTCCAAGAGTTGTTAGGATCACTTGCCATTGGATTAAAGGCTGAATTTTTATCCCTGGGAAAAAATAAATATCTTTACTTTATGAACATAAAATAACTTCTTAATATATGTTCAAGTATAGCTTTCATTAAAACCTATTACAAAACAGTTAAAAGTAACATATTTATAGCAAAAGCCACAATAAACGCAACATACAATAATATCATACACAATCATTTAAGCAGACTAATTTATATATAAATCAAACAGAAATTAGTGCAATTTAAGTTTCCATAGAAAA	GGTCTAGGACAAAGTAAAATGCAAGATGTTTCTAGACATCTAGGGAATCTTCATGTTGTGGGTCATCATAGACAAAAATTAGTTAAGCTACCTTTCTATTGCAGTTAAAAAAAAAAAAGGTATTGCACATGTGAAAATGTTGGTAAAACAGAAATAATATATTCATGGCTTACCAGGGAATTCTTCCTTTAAGTTGGGGAAATTAATATTGGTGTAGAGAACTGGGGCAACAGTTGCCATTTCACCCAGAGCCTCCTCTTTCTCCCACTTAAGCGTGCTTCTCTGGGCATTCGACATTGTGTCATTTTCTCCTTCCACAGTGGGAGCTGATGATGTCCAAGAGTTGTTAGGATCACTTGCCATTGGATTAAAGGCTGAATTTTTATCCCTGGGAAAAAATAAATATCTTTACTTTATGAACATAAAATAACTTCTTAATATATGTTCAAGTATAGCTTTCATTAAAACCTATTACAAAACAGTTAAAAGTAACATATTTATAGCAAAAGCCACAATAAACGCAACATACAATAATATCATACACAATCATTTAAGCAGACTAATTTATATATAAATCAAACAGAAATTAGTGCAATTTAAGTTTCCATAGAAAA	-	novel	NA	P-0040752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	82	23	0	ENST00000262189.6:c.4793+13_5008+173del		p.X1598_splice	ENST00000262189	NM_170606.2	1598		33/59	0.169434844879035	2	FACETS	0.998	0.933	1	1	0.99	1	CLONAL	7	TRUE	0	0.221385525488645	2		23	106	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148891	119148891	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs267606706	NA	P-0040781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	11	292	1	ENST00000264033.4:c.1111T>C	p.Tyr371His	p.Y371H	ENST00000264033	NM_005188.3	371	Tac/Cac	8/16	0.462936767922474	1	FACETS	0.125	0.086	0.174	0.125	0.086	0.174	SUBCLONAL	1	TRUE	0	0.462936767922474	1		293	292	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440923	52440923	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	139	562	0	ENST00000460680.1:c.581G>A	p.Gly194Glu	p.G194E	ENST00000460680	NM_004656.3	194	gGg/gAg	8/17	0.462936767922474	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.462936767922474	1		562	415	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607614	46607614	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	139	839	0	ENST00000263734.3:c.1803C>G	p.His601Gln	p.H601Q	ENST00000263734	NM_001430.4	601	caC/caG	12/16	1	2	FACETS	0.808	0.737	0.883	0.808	0.737	0.883	CLONAL	1	TRUE	1	0.462936767922474	2		839	743	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0040797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	692	701	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.480972590629456	5	FACETS	1	0.996	1	0.898	0.873	0.923	CLONAL	4	TRUE	0	0.480972590629456	5		701	1103	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249510	153249510	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1157879635	NA	P-0040797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	200	605	1	ENST00000281708.4:c.1268G>T	p.Gly423Val	p.G423V	ENST00000281708	NM_033632.3	423	gGa/gTa	9/12	0.121996287828282	6	FACETS	0.916	0.854	0.979	0.916	0.854	0.979	INDETERMINATE	3	TRUE	3	0.480972590629456	6		606	594	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477106	67477106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1348033858	NA	P-0040797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	89	724	1	ENST00000327367.4:c.913G>A	p.Ala305Thr	p.A305T	ENST00000327367	NM_005902.3	305	Gca/Aca	7/9	1	2	FACETS	0.606	0.538	0.678	0.606	0.538	0.678	SUBCLONAL	1	TRUE	1	0.480972590629456	2		725	611	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678382	88678382	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	160	970	0	ENST00000360948.2:c.1154del	p.Gly385AlafsTer29	p.G385Afs*29	ENST00000360948	NM_001012338.2	385	gGc/gc	9/19	1	2	FACETS	0.749	0.687	0.814	0.749	0.687	0.814	SUBCLONAL	1	TRUE	1	0.480972590629456	2		970	888	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577166	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTACTCAGGAT	CTACTCAGGAT	-	novel	NA	P-0040797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	394	652	0	ENST00000269305.4:c.783-11_783-1del		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.421286879008947	3	FACETS	0.927	0.889	0.964			1	CLONAL	3	TRUE	NA	0.480972590629456	3		652	731	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0040801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	143	764	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.944	0.872	1	0.944	0.872	1	CLONAL	1	TRUE	1	0.832217788751133	2		764	364	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438170	56438171	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0040801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	353	1119	0	ENST00000407977.2:c.822_823del	p.Ile274MetfsTer7	p.I274Mfs*7	ENST00000407977		274	atCTgt/atgt	7/10	0.832217788751133	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.832217788751133	1		1119	452	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0040812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	258	686	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.469543834359085	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	FALSE	1	0.469543834359085	3		686	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934573	NA	P-0040812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	226	629	0	ENST00000269305.4:c.722C>A	p.Ser241Tyr	p.S241Y	ENST00000269305	NM_001126112.2	241	tCc/tAc	7/11	0.164717060212613	6	FACETS	1	0.986	1			1	INDETERMINATE	3	FALSE	NA	0.469543834359085	6		629	535	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156731	20156731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	180	426	0	ENST00000379607.5:c.26G>A	p.Gly9Asp	p.G9D	ENST00000379607	NM_001412.3	9	gGt/gAt	2/7	NA	2	FACETS	0.98	0.917	1			1	INDETERMINATE	2	FALSE	NA	0.469543834359085	2		426	391	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	159	112	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.443908551399944	2	FACETS	0.803	0.743	0.864	0.803	0.743	0.864	CLONAL	2	TRUE	0	0.443908551399944	2		112	446	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	256	306	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.907	0.848	0.969	0.907	0.848	0.969	CLONAL	1	TRUE	1	0.443908551399944	2		306	1271	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	168	496	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.867	0.797	0.94	0.867	0.797	0.94	CLONAL	1	TRUE	1	0.443908551399944	2		496	873	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	99	132	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.818	0.733	0.909	0.818	0.733	0.909	CLONAL	1	TRUE	1	0.443908551399944	2		132	545	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482927	140482927	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	206	198	1	ENST00000288602.6:c.1208del	p.Pro403LeufsTer8	p.P403Lfs*8	ENST00000288602	NM_004333.4	403	cCt/ct	10/18	1	2	FACETS	0.972	0.902	1	0.972	0.902	1	CLONAL	1	TRUE	1	0.443908551399944	2		199	955	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	242	128	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.443908551399944	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.443908551399944	2		128	510	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	185	217	0	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.985	0.911	1	0.985	0.911	1	CLONAL	1	TRUE	1	0.443908551399944	2		217	846	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	197	585	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.87	0.805	0.937	0.87	0.805	0.937	CLONAL	1	TRUE	1	0.443908551399944	2		590	1020	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736166	204736166	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	35	135	0	ENST00000302823.3:c.529del	p.Tyr177IlefsTer10	p.Y177Ifs*10	ENST00000302823	NM_005214.4	175	Ttt/tt	3/4	NA	2	FACETS	0.243	0.198	0.293			1	INDETERMINATE	1	TRUE	NA	0.443908551399944	2		135	650	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024505	16024505	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	182	195	0	ENST00000268712.3:c.1713del	p.Arg572GlufsTer18	p.R572Efs*18	ENST00000268712	NM_006311.3	571	ggG/gg	16/46	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.443908551399944	2		195	801	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965666	90965666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	93	129	0	ENST00000265433.3:c.1651del	p.Arg551GlyfsTer8	p.R551Gfs*8	ENST00000265433	NM_002485.4	551	Agg/gg	11/16	1	2	FACETS	0.767	0.684	0.856	0.767	0.684	0.856	SUBCLONAL	1	TRUE	1	0.443908551399944	2		129	546	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	241	316	0	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	0.963	0.898	1	0.963	0.898	1	CLONAL	1	TRUE	1	0.443908551399944	2		316	1128	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	66	252	3	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	NA	2	FACETS	0.356	0.308	0.408			1	INDETERMINATE	1	TRUE	NA	0.443908551399944	2		255	836	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716154	243716154	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	189	240	0	ENST00000263826.5:c.1040A>G	p.Tyr347Cys	p.Y347C	ENST00000263826	NM_005465.4	347	tAc/tGc	10/13	1	2	FACETS	0.907	0.838	0.978	0.907	0.838	0.978	CLONAL	1	TRUE	1	0.443908551399944	2		240	939	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	250	307	0	ENST00000227507.2:c.859C>G	p.Pro287Ala	p.P287A	ENST00000227507	NM_053056.2	287	Ccc/Gcc	5/5	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.443908551399944	2		307	1086	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268793	98268793	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1554708751	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	158	229	0	ENST00000331920.6:c.290del	p.Asn97ThrfsTer20	p.N97Tfs*20	ENST00000331920	NM_000264.3	97	aAc/ac	2/24	1	2	FACETS	0.852	0.781	0.925	0.852	0.781	0.925	CLONAL	1	TRUE	1	0.443908551399944	2		229	836	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255142	16255143	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	rs764595221	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	183	182	3	ENST00000375759.3:c.2417_2418del	p.Arg806ThrfsTer14	p.R806Tfs*14	ENST00000375759	NM_015001.2	803	GAg/g	11/15	0.244788842225209	3	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.443908551399944	3		185	779	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469772	157469772	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	200	260	0	ENST00000346085.5:c.2570del	p.Pro857GlnfsTer57	p.P857Qfs*57	ENST00000346085	NM_020732.3	856	Ccc/cc	9/20	NA	2	FACETS	0.895	0.829	0.963			1	INDETERMINATE	1	TRUE	NA	0.443908551399944	2		260	1007	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670282	134670282	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748807854	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	130	172	0	ENST00000398015.3:c.193G>A	p.Glu65Lys	p.E65K	ENST00000398015	NM_004441.4	65	Gag/Aag	3/16	0.183272309181584	1	FACETS	0.761	0.692	0.832	0.761	0.692	0.832	INDETERMINATE	1	TRUE	0	0.443908551399944	1		172	599	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	238	304	1	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	0.364926491758021	3	FACETS	1	0.97	1			1	CLONAL	1	TRUE	NA	0.443908551399944	3		305	1224	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151254	202151254	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	120	134	0	ENST00000358485.4:c.1557del	p.Lys520AsnfsTer10	p.K520Nfs*10	ENST00000358485	NM_001080125.1	518	atG/at	9/9	NA	2	FACETS	0.855	0.774	0.941			1	INDETERMINATE	1	TRUE	NA	0.443908551399944	2		134	632	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612890	228612890	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757564822	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	177	224	0	ENST00000366696.1:c.137C>T	p.Thr46Met	p.T46M	ENST00000366696	NM_003493.2	46	aCg/aTg	1/1	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.443908551399944	2		224	716	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512370	38512370	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567767560	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	135	241	0	ENST00000254066.5:c.1286del	p.Gly429ValfsTer214	p.G429Vfs*214	ENST00000254066	NM_000964.3	427	ccG/cc	9/9	1	2	FACETS	0.607	0.551	0.666	0.607	0.551	0.666	SUBCLONAL	1	TRUE	1	0.443908551399944	2		241	1002	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615539	43615539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1451004715	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	139	198	1	ENST00000355710.3:c.2618G>A	p.Arg873Gln	p.R873Q	ENST00000355710	NM_020975.4	873	cGg/cAg	15/20	0.183272309181584	1	FACETS	0.616	0.561	0.674	0.616	0.561	0.674	INDETERMINATE	1	TRUE	0	0.443908551399944	1		199	791	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210440	36210440	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	200	230	1	ENST00000222270.7:c.433C>T	p.Arg145Ter	p.R145*	ENST00000222270	NM_014727.1	145	Cga/Tga	2/37	1	2	FACETS	0.996	0.923	1	0.996	0.923	1	CLONAL	1	TRUE	1	0.443908551399944	2		231	905	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589588	67589590	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	80	79	0	ENST00000274335.5:c.1351_1353del	p.Glu451del	p.E451del	ENST00000274335		451	GAA/-	10/15	1	2	FACETS	0.797	0.705	0.896	0.797	0.705	0.896	SUBCLONAL	1	TRUE	1	0.443908551399944	2		79	452	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748399150	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1399	261	912	10	ENST00000220592.5:c.1806del	p.Ala603ProfsTer92	p.A603Pfs*92	ENST00000220592	NM_012154.3	602	ccC/cc	14/19	0.443908551399944	3	FACETS	0.866	0.808	0.925	0.433	0.404	0.463	CLONAL	1	TRUE	1	0.443908551399944	3		922	1660	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097039	11097039	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	309	341	0	ENST00000358026.2:c.530T>C	p.Leu177Pro	p.L177P	ENST00000358026	NM_001128849.1	177	cTg/cCg	4/36	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.443908551399944	2		341	1262	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106366	27106366	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	410	218	0	ENST00000324856.7:c.5979del	p.Phe1993LeufsTer22	p.F1993Lfs*22	ENST00000324856	NM_006015.4	1993	Ttt/tt	20/20	NA	2	FACETS	0.978	0.935	1			1	INDETERMINATE	2	TRUE	NA	0.443908551399944	2		218	944	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993737	72993737	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	143	221	0	ENST00000268489.5:c.308G>C	p.Arg103Pro	p.R103P	ENST00000268489	NM_006885.3	103	cGc/cCc	2/10	1	2	FACETS	0.999	0.913	1	0.999	0.913	1	CLONAL	1	TRUE	1	0.443908551399944	2		221	645	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214714	36214714	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	194	240	0	ENST00000222270.7:c.3145del	p.Ala1049ArgfsTer133	p.A1049Rfs*133	ENST00000222270	NM_014727.1	1047	cGg/cg	8/37	1	2	FACETS	0.991	0.918	1	0.991	0.918	1	CLONAL	1	TRUE	1	0.443908551399944	2		240	882	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561430	141561430	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	310	200	0	ENST00000220592.5:c.1375del	p.Gln459SerfsTer9	p.Q459Sfs*9	ENST00000220592	NM_012154.3	459	Cag/ag	11/19	0.443908551399944	3	FACETS	0.868	0.82	0.917	0.868	0.82	0.917	CLONAL	2	TRUE	1	0.443908551399944	3		200	983	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484207	8484207	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773612496	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	183	162	0	ENST00000356435.5:c.3325C>T	p.Arg1109Cys	p.R1109C	ENST00000356435		1109	Cgt/Tgt	19/35	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.443908551399944	2		162	795	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754705	42754705	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381524812	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	102	88	0	ENST00000222329.4:c.35C>T	p.Pro12Leu	p.P12L	ENST00000222329	NM_006494.2	12	cCg/cTg	2/4	1	2	FACETS	0.896	0.804	0.992	0.896	0.804	0.992	CLONAL	1	TRUE	1	0.443908551399944	2		88	513	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514615	44514615	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	190	191	0	ENST00000291552.4:c.541C>A	p.Leu181Met	p.L181M	ENST00000291552	NM_006758.2	181	Ctg/Atg	7/8	1	2	FACETS	0.986	0.913	1	0.986	0.913	1	CLONAL	1	TRUE	1	0.443908551399944	2		191	868	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776633	9776633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	218	290	0	ENST00000377346.4:c.736A>G	p.Arg246Gly	p.R246G	ENST00000377346	NM_005026.3	246	Agg/Ggg	6/24	0.443908551399944	2	FACETS	0.84	0.78	0.902	0.42	0.39	0.451	CLONAL	1	TRUE	0	0.443908551399944	2		290	1169	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187715	11187715	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	209	222	0	ENST00000361445.4:c.6182del	p.Gly2061AlafsTer5	p.G2061Afs*5	ENST00000361445	NM_004958.3	2061	gGc/gc	44/58	0.443908551399944	2	FACETS	1	0.968	1	0.536	0.498	0.575	CLONAL	1	TRUE	0	0.443908551399944	2		222	878	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188516	11188516	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	164	172	1	ENST00000361445.4:c.5905C>A	p.Pro1969Thr	p.P1969T	ENST00000361445	NM_004958.3	1969	Ccc/Acc	42/58	0.443908551399944	2	FACETS	1	0.957	1	0.529	0.487	0.573	CLONAL	1	TRUE	0	0.443908551399944	2		173	698	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107222	27107222	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs962329524	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	159	151	0	ENST00000324856.7:c.6833T>C	p.Val2278Ala	p.V2278A	ENST00000324856	NM_006015.4	2278	gTa/gCa	20/20	NA	2	FACETS	0.998	0.917	1			1	INDETERMINATE	1	TRUE	NA	0.443908551399944	2		151	718	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933426	36933426	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	252	264	0	ENST00000361632.4:c.1861C>A	p.Pro621Thr	p.P621T	ENST00000361632		621	Cca/Aca	13/16	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.443908551399944	2		264	1024	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310440	65310440	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	121	163	0	ENST00000342505.4:c.2248C>T	p.Gln750Ter	p.Q750*	ENST00000342505	NM_002227.2	750	Caa/Taa	16/25	1	2	FACETS	0.845	0.765	0.929	0.845	0.765	0.929	CLONAL	1	TRUE	1	0.443908551399944	2		163	645	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125496722	125496722	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1350704599	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	108	149	0	ENST00000428830.2:c.59A>G	p.Tyr20Cys	p.Y20C	ENST00000428830	NM_001114121.2	20	tAt/tGt	2/14	1	2	FACETS	0.925	0.834	1	0.925	0.834	1	CLONAL	1	TRUE	1	0.443908551399944	2		149	526	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420675	49420675	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	211	237	0	ENST00000301067.7:c.15074T>C	p.Val5025Ala	p.V5025A	ENST00000301067	NM_003482.3	5025	gTa/gCa	48/54	1	2	FACETS	0.944	0.877	1	0.944	0.877	1	CLONAL	1	TRUE	1	0.443908551399944	2		237	1007	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864295	57864295	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	58	271	0	ENST00000228682.2:c.1772C>T	p.Ala591Val	p.A591V	ENST00000228682	NM_005269.2	591	gCa/gTa	12/12	1	2	FACETS	0.285	0.244	0.33	0.285	0.244	0.33	SUBCLONAL	1	TRUE	1	0.443908551399944	2		271	918	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237607	133237607	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	210	205	0	ENST00000320574.5:c.3008A>G	p.Tyr1003Cys	p.Y1003C	ENST00000320574	NM_006231.2	1003	tAt/tGt	25/49	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.443908551399944	2		205	800	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257854	133257854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561834381	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	133	186	0	ENST00000320574.5:c.74C>T	p.Ala25Val	p.A25V	ENST00000320574	NM_006231.2	25	gCc/gTc	2/49	1	2	FACETS	0.904	0.823	0.989	0.904	0.823	0.989	CLONAL	1	TRUE	1	0.443908551399944	2		186	663	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562888	21562888	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	252	304	0	ENST00000382592.4:c.1031del	p.Pro344ArgfsTer89	p.P344Rfs*89	ENST00000382592	NM_014572.2	344	cCg/cg	4/8	NA	2	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.443908551399944	2		304	1056	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518158	103518158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	105	128	0	ENST00000355739.4:c.2096G>A	p.Ser699Asn	p.S699N	ENST00000355739	NM_000123.3	699	aGc/aAc	9/15	NA	2	FACETS	0.931	0.838	1			1	INDETERMINATE	1	TRUE	NA	0.443908551399944	2		128	508	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610569	81610569	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	110	160	0	ENST00000298171.2:c.2167A>G	p.Lys723Glu	p.K723E	ENST00000298171	NM_000369.2	723	Aag/Gag	10/10	1	2	FACETS	0.862	0.777	0.952	0.862	0.777	0.952	CLONAL	1	TRUE	1	0.443908551399944	2		160	575	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021470	42021472	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	rs758651564	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	184	194	0	ENST00000219905.7:c.3775_3777del	p.Ser1259del	p.S1259del	ENST00000219905	NM_001164273.1	1256	TCC/-	11/24	1	2	FACETS	0.961	0.888	1	0.961	0.888	1	CLONAL	1	TRUE	1	0.443908551399944	2		194	863	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43699652	43699652	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	154	233	0	ENST00000382044.4:c.5863T>C	p.Cys1955Arg	p.C1955R	ENST00000382044	NM_001141980.1	1955	Tgc/Cgc	28/28	1	2	FACETS	0.931	0.854	1	0.931	0.854	1	CLONAL	1	TRUE	1	0.443908551399944	2		233	745	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351215	89351215	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs143817649	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	245	272	0	ENST00000301030.4:c.1735T>C	p.Tyr579His	p.Y579H	ENST00000301030	NM_001256183.1	579	Tac/Cac	9/13	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.443908551399944	2		272	1056	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89862413	89862413	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs760513588	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	182	268	0	ENST00000389301.3:c.907A>G	p.Ser303Gly	p.S303G	ENST00000389301	NM_000135.2	303	Agt/Ggt	11/43	NA	2	FACETS	0.914	0.844	0.987			1	INDETERMINATE	1	TRUE	NA	0.443908551399944	2		268	897	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679288	29679288	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	105	149	0	ENST00000356175.3:c.7408A>G	p.Thr2470Ala	p.T2470A	ENST00000356175	NM_000267.3	2470	Act/Gct	50/57	1	2	FACETS	0.915	0.823	1	0.915	0.823	1	CLONAL	1	TRUE	1	0.443908551399944	2		149	517	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627389	37627389	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	200	253	0	ENST00000447079.4:c.1304T>G	p.Val435Gly	p.V435G	ENST00000447079	NM_015083.1	435	gTa/gGa	2/14	1	2	FACETS	0.866	0.802	0.933	0.866	0.802	0.933	CLONAL	1	TRUE	1	0.443908551399944	2		253	1040	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872109	37872109	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	293	349	0	ENST00000269571.5:c.1430T>C	p.Val477Ala	p.V477A	ENST00000269571		477	gTg/gCg	12/27	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.443908551399944	2		349	1273	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5258088	5258088	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	87	221	0	ENST00000357368.4:c.646T>C	p.Cys216Arg	p.C216R	ENST00000357368	NM_002850.3	216	Tgt/Cgt	8/38	NA	2	FACETS	0.499	0.441	0.561			1	INDETERMINATE	1	TRUE	NA	0.443908551399944	2		221	786	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248653	10248653	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	174	205	0	ENST00000340748.4:c.4100T>C	p.Val1367Ala	p.V1367A	ENST00000340748		1367	gTg/gCg	35/40	1	2	FACETS	0.943	0.869	1	0.943	0.869	1	CLONAL	1	TRUE	1	0.443908551399944	2		205	831	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376247	15376248	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs780128218	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	105	238	0	ENST00000263377.2:c.766dup	p.Gln256ProfsTer46	p.Q256Pfs*46	ENST00000263377	NM_058243.2	256	cag/cCag	5/20	1	2	FACETS	0.539	0.483	0.6	0.539	0.483	0.6	SUBCLONAL	1	TRUE	1	0.443908551399944	2		238	877	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266852	18266852	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	232	207	0	ENST00000222254.8:c.163G>T	p.Gly55Cys	p.G55C	ENST00000222254	NM_005027.3	55	Ggc/Tgc	2/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.443908551399944	2		207	942	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212131	36212131	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	99	175	2	ENST00000222270.7:c.1886del	p.Pro629ArgfsTer31	p.P629Rfs*31	ENST00000222270	NM_014727.1	628	Ccc/cc	3/37	1	2	FACETS	0.723	0.646	0.804	0.723	0.646	0.804	SUBCLONAL	1	TRUE	1	0.443908551399944	2		177	617	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905121	50905121	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	214	388	0	ENST00000440232.2:c.403T>C	p.Phe135Leu	p.F135L	ENST00000440232	NM_002691.3	135	Ttc/Ctc	4/27	1	2	FACETS	0.814	0.755	0.875	0.814	0.755	0.875	CLONAL	1	TRUE	1	0.443908551399944	2		388	1185	SUCCESS
ALK	238	MSKCC	GRCh37	2	29541220	29541220	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	133	162	0	ENST00000389048.3:c.1597A>G	p.Thr533Ala	p.T533A	ENST00000389048	NM_004304.4	533	Aca/Gca	8/29	1	2	FACETS	0.773	0.703	0.847	0.773	0.703	0.847	SUBCLONAL	1	TRUE	1	0.443908551399944	2		162	775	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422401	225422401	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	42	150	0	ENST00000264414.4:c.239T>C	p.Val80Ala	p.V80A	ENST00000264414	NM_003590.4	80	gTt/gCt	2/16	1	2	FACETS	0.307	0.256	0.364	0.307	0.256	0.364	SUBCLONAL	1	TRUE	1	0.443908551399944	2		150	616	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661228	227661228	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	251	292	0	ENST00000305123.5:c.2227A>G	p.Thr743Ala	p.T743A	ENST00000305123	NM_005544.2	743	Acc/Gcc	1/2	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.443908551399944	2		292	1096	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662586	227662586	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	133	227	0	ENST00000305123.5:c.869A>G	p.Asn290Ser	p.N290S	ENST00000305123	NM_005544.2	290	aAc/aGc	1/2	1	2	FACETS	0.795	0.722	0.871	0.795	0.722	0.871	SUBCLONAL	1	TRUE	1	0.443908551399944	2		227	754	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24135832	24135832	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	189	184	0	ENST00000263121.7:c.319T>A	p.Tyr107Asn	p.Y107N	ENST00000263121	NM_003073.3	107	Tac/Aac	3/9	0.364926491758021	3	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.443908551399944	3		184	813	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627366	37627366	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1235	211	356	0	ENST00000249071.6:c.353A>G	p.Asp118Gly	p.D118G	ENST00000249071	NM_002872.4	118	gAc/gGc	5/7	NA	2	FACETS	0.657	0.609	0.708			1	INDETERMINATE	1	TRUE	NA	0.443908551399944	2		356	1446	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12647768	12647768	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	45	162	0	ENST00000251849.4:c.612T>A	p.Ser204Arg	p.S204R	ENST00000251849	NM_002880.3	204	agT/agA	6/17	1	2	FACETS	0.278	0.232	0.328	0.278	0.232	0.328	SUBCLONAL	1	TRUE	1	0.443908551399944	2		162	730	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37059025	37059025	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	129	151	0	ENST00000231790.2:c.822del	p.Ala275ProfsTer2	p.A275Pfs*2	ENST00000231790	NM_000249.3	273	agA/ag	10/19	1	2	FACETS	0.871	0.792	0.955	0.871	0.792	0.955	CLONAL	1	TRUE	1	0.443908551399944	2		151	667	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405963	49405963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	212	226	0	ENST00000418115.1:c.175G>A	p.Asp59Asn	p.D59N	ENST00000418115	NM_001664.2	59	Gac/Aac	3/5	1	2	FACETS	0.958	0.89	1	0.958	0.89	1	CLONAL	1	TRUE	1	0.443908551399944	2		226	997	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242836	142242836	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	135	154	0	ENST00000350721.4:c.4151T>C	p.Val1384Ala	p.V1384A	ENST00000350721	NM_001184.3	1384	gTg/gCg	22/47	1	2	FACETS	0.962	0.877	1	0.962	0.877	1	CLONAL	1	TRUE	1	0.443908551399944	2		154	632	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589588	67589592	+	protein_altering_variant	In_Frame_Del	DEL	GAATA	GAATA	TT	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	81	84	0	ENST00000274335.5:c.1351_1355delinsTT	p.Glu451_Tyr452delinsPhe	p.E451_Y452delinsF	ENST00000274335		451	GAATAt/TTt	10/15	1	2	FACETS	0.78	0.689	0.876	0.78	0.689	0.876	SUBCLONAL	1	TRUE	1	0.443908551399944	2		84	468	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180049811	180049811	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	237	335	1	ENST00000261937.6:c.1577C>T	p.Ala526Val	p.A526V	ENST00000261937	NM_182925.4	526	gCc/gTc	12/30	0.246954455342631	0	FACETS	0.628	0.586	0.67			1	INDETERMINATE	1	TRUE	0	0.443908551399944	0		336	946	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109321766	109321766	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	256	219	0	ENST00000436639.2:c.657del	p.Lys219AsnfsTer5	p.K219Nfs*5	ENST00000436639	NM_014454.2	219	aaA/aa	4/10	NA	2	FACETS	0.977	0.914	1			1	INDETERMINATE	1	TRUE	NA	0.443908551399944	2		219	1180	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415267	109415267	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	235	266	0	ENST00000436639.2:c.10G>T	p.Gly4Ter	p.G4*	ENST00000436639	NM_014454.2	4	Gga/Tga	1/10	NA	2	FACETS	1	0.94	1			1	INDETERMINATE	1	TRUE	NA	0.443908551399944	2		266	1050	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959031	2959031	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1306775800	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	163	233	0	ENST00000396946.4:c.2485A>G	p.Met829Val	p.M829V	ENST00000396946	NM_032415.4	829	Atg/Gtg	18/25	1	2	FACETS	0.888	0.816	0.963	0.888	0.816	0.963	CLONAL	1	TRUE	1	0.443908551399944	2		233	827	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441968	6441968	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554264268	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	234	274	0	ENST00000356142.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000356142	NM_018890.3	176	tGc/tAc	7/7	1	2	FACETS	0.969	0.904	1	0.969	0.904	1	CLONAL	1	TRUE	1	0.443908551399944	2		274	1088	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56860228	56860228	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	176	202	0	ENST00000519728.1:c.230T>G	p.Ile77Ser	p.I77S	ENST00000519728	NM_002350.3	77	aTc/aGc	4/13	1	2	FACETS	0.954	0.88	1	0.954	0.88	1	CLONAL	1	TRUE	1	0.443908551399944	2		202	831	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141569599	141569599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	147	160	0	ENST00000220592.5:c.685C>T	p.Pro229Ser	p.P229S	ENST00000220592	NM_012154.3	229	Cca/Tca	6/19	0.443908551399944	3	FACETS	1	0.947	1	0.524	0.479	0.571	CLONAL	1	TRUE	1	0.443908551399944	3		160	772	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250409	110250409	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	244	265	0	ENST00000374672.4:c.266C>T	p.Ala89Val	p.A89V	ENST00000374672	NM_004235.4	89	gCg/gTg	3/5	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.443908551399944	2		265	1070	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915865	127915865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	156	187	1	ENST00000373547.4:c.616G>A	p.Ala206Thr	p.A206T	ENST00000373547	NM_002721.4	206	Gct/Act	6/7	1	2	FACETS	0.899	0.824	0.977	0.899	0.824	0.977	CLONAL	1	TRUE	1	0.443908551399944	2		188	782	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300071	137300071	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	205	335	0	ENST00000481739.1:c.356T>C	p.Val119Ala	p.V119A	ENST00000481739	NM_002957.4	119	gTc/gCc	3/10	1	2	FACETS	0.766	0.71	0.826	0.766	0.71	0.826	SUBCLONAL	1	TRUE	1	0.443908551399944	2		335	1205	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137320966	137320966	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	234	307	0	ENST00000481739.1:c.923T>C	p.Leu308Pro	p.L308P	ENST00000481739	NM_002957.4	308	cTg/cCg	7/10	1	2	FACETS	0.912	0.85	0.976	0.912	0.85	0.976	CLONAL	1	TRUE	1	0.443908551399944	2		307	1156	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589592	67589592	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	81	82	0	ENST00000274335.5:c.1355A>T	p.Tyr452Phe	p.Y452F	ENST00000274335		452	tAt/tTt	10/15	1	2	FACETS	0.795	0.703	0.893	0.795	0.703	0.893	SUBCLONAL	1	TRUE	1	0.443908551399944	2		82	459	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	132	326	0				ENST00000310581	NM_198253.2	-/1132			0.545151180373073	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.545151180373073	1		326	316	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0040827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	455	789	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.545151180373073	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.545151180373073	1		789	942	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	95	819	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.939	0.834	1	0.939	0.834	1	CLONAL	1	TRUE	1	0.2	2		819	1012	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	113	954	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.965	0.866	1	0.965	0.866	1	CLONAL	1	TRUE	1	0.2	2		954	1171	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	95	551	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.876	0.783	0.976	1	0.984	1	CLONAL	2	TRUE	1	0.2	2		551	542	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	49	723	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.658	0.556	0.771	0.658	0.556	0.771	SUBCLONAL	1	TRUE	1	0.2	2		723	745	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956220	55956220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190050670	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	51	558	0	ENST00000263923.4:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000263923	NM_002253.2	1032	cGa/cAa	23/30	1	2	FACETS	0.682	0.578	0.796	0.682	0.578	0.796	SUBCLONAL	1	TRUE	1	0.2	2		558	748	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	106	701	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.2	2		701	804	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	50	516	1	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.726	0.615	0.848	0.726	0.615	0.848	SUBCLONAL	1	TRUE	1	0.2	2		517	689	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	36	310	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.2	2		310	307	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549725	187549725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199516712	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	55	529	0	ENST00000441802.2:c.4516C>T	p.Arg1506Cys	p.R1506C	ENST00000441802	NM_005245.3	1506	Cgt/Tgt	8/27	1	2	FACETS	0.967	0.827	1	0.967	0.827	1	CLONAL	1	TRUE	1	0.2	2		529	569	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	83	905	3	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.819	0.72	0.924	0.819	0.72	0.924	CLONAL	1	TRUE	1	0.2	2		908	1014	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613405	100613405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs918787974	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	50	708	0	ENST00000308731.7:c.995G>A	p.Arg332His	p.R332H	ENST00000308731	NM_000061.2	332	cGt/cAt	12/19	1	2	FACETS	0.71	0.601	0.83	0.71	0.601	0.83	SUBCLONAL	1	TRUE	1	0.2	2		708	704	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	48	653	0	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	0.756	0.638	0.886	0.756	0.638	0.886	SUBCLONAL	1	TRUE	1	0.2	2		653	635	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073308	8073308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780544753	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	41	418	0	ENST00000377482.5:c.1351G>A	p.Val451Met	p.V451M	ENST00000377482	NM_018948.3	451	Gtg/Atg	4/4	1	2	FACETS	0.709	0.59	0.842	0.709	0.59	0.842	SUBCLONAL	1	TRUE	1	0.2	2		418	578	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778926	9778926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765972601	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	75	748	1	ENST00000377346.4:c.1195G>A	p.Glu399Lys	p.E399K	ENST00000377346	NM_005026.3	399	Gag/Aag	9/24	1	2	FACETS	0.807	0.706	0.917	0.807	0.706	0.917	CLONAL	1	TRUE	1	0.2	2		749	929	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169361	11169361	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519777	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	36	533	0	ENST00000361445.4:c.7514G>A	p.Arg2505Gln	p.R2505Q	ENST00000361445	NM_004958.3	2505	cGa/cAa	56/58	1	2	FACETS	0.604	0.495	0.726	0.604	0.495	0.726	SUBCLONAL	1	TRUE	1	0.2	2		533	596	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186751	11186751	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752458445	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	63	628	0	ENST00000361445.4:c.6454C>T	p.Arg2152Cys	p.R2152C	ENST00000361445	NM_004958.3	2152	Cgc/Tgc	46/58	1	2	FACETS	0.885	0.764	1	0.885	0.764	1	CLONAL	1	TRUE	1	0.2	2		628	712	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11308061	11308061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200901835	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	80	911	0	ENST00000361445.4:c.931C>T	p.Arg311Cys	p.R311C	ENST00000361445	NM_004958.3	311	Cgt/Tgt	7/58	1	2	FACETS	0.691	0.606	0.783	0.691	0.606	0.783	SUBCLONAL	1	TRUE	1	0.2	2		911	1158	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245981	16245981	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758108044	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	45	404	1	ENST00000375759.3:c.1604G>A	p.Arg535Gln	p.R535Q	ENST00000375759	NM_015001.2	535	cGa/cAa	8/15	1	2	FACETS	0.739	0.62	0.871	0.739	0.62	0.871	SUBCLONAL	1	TRUE	1	0.2	2		405	609	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262660	16262660	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748733011	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	68	483	0	ENST00000375759.3:c.9925G>A	p.Gly3309Ser	p.G3309S	ENST00000375759	NM_015001.2	3309	Ggc/Agc	11/15	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.2	2		483	600	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101099	27101099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	85	860	0	ENST00000324856.7:c.4381C>T	p.Arg1461Ter	p.R1461*	ENST00000324856	NM_006015.4	1461	Cga/Tga	18/20	1	2	FACETS	0.868	0.766	0.979	0.868	0.766	0.979	CLONAL	1	TRUE	1	0.2	2		860	979	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101511	27101511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748573855	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	97	996	0	ENST00000324856.7:c.4793G>A	p.Arg1598His	p.R1598H	ENST00000324856	NM_006015.4	1598	cGc/cAc	18/20	1	2	FACETS	0.887	0.789	0.993	0.887	0.789	0.993	CLONAL	1	TRUE	1	0.2	2		996	1093	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	48	540	0	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	1	2	FACETS	0.738	0.623	0.866	0.738	0.623	0.866	SUBCLONAL	1	TRUE	1	0.2	2		540	650	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105607	27105607	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	45	624	0	ENST00000324856.7:c.5218G>T	p.Gly1740Ter	p.G1740*	ENST00000324856	NM_006015.4	1740	Gga/Tga	20/20	1	2	FACETS	0.652	0.547	0.769	0.652	0.547	0.769	SUBCLONAL	1	TRUE	1	0.2	2		624	690	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106328	27106328	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748000514	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	60	789	1	ENST00000324856.7:c.5939G>A	p.Arg1980His	p.R1980H	ENST00000324856	NM_006015.4	1980	cGc/cAc	20/20	1	2	FACETS	0.744	0.64	0.859	0.744	0.64	0.859	SUBCLONAL	1	TRUE	1	0.2	2		790	806	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107144	27107144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	84	631	0	ENST00000324856.7:c.6755C>T	p.Thr2252Ile	p.T2252I	ENST00000324856	NM_006015.4	2252	aCt/aTt	20/20	1	2	FACETS	0.992	0.875	1	0.992	0.875	1	CLONAL	1	TRUE	1	0.2	2		631	847	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46512247	46512247	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765089522	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	52	519	0	ENST00000262741.5:c.992G>A	p.Gly331Glu	p.G331E	ENST00000262741	NM_003629.3	331	gGa/gAa	8/10	1	2	FACETS	0.824	0.701	0.96	0.824	0.701	0.96	CLONAL	1	TRUE	1	0.2	2		519	631	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740333	46740333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	47	684	0	ENST00000371975.4:c.1813G>A	p.Ala605Thr	p.A605T	ENST00000371975	NM_003579.3	605	Gcc/Acc	16/18	1	2	FACETS	0.556	0.468	0.654	0.556	0.468	0.654	SUBCLONAL	1	TRUE	1	0.2	2		684	845	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65312344	65312344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	52	613	0	ENST00000342505.4:c.1975C>T	p.Arg659Cys	p.R659C	ENST00000342505	NM_002227.2	659	Cgc/Tgc	14/25	1	2	FACETS	0.704	0.598	0.82	0.704	0.598	0.82	SUBCLONAL	1	TRUE	1	0.2	2		613	739	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321246	65321246	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773295685	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	64	628	3	ENST00000342505.4:c.1594C>T	p.Arg532Cys	p.R532C	ENST00000342505	NM_002227.2	532	Cgc/Tgc	11/25	1	2	FACETS	0.775	0.67	0.89	0.775	0.67	0.89	SUBCLONAL	1	TRUE	1	0.2	2		631	826	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428511	78428511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408536007	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	14	529	0	ENST00000370768.2:c.1288C>T	p.Arg430Cys	p.R430C	ENST00000370768	NM_003902.3	430	Cgt/Tgt	14/20	1	2	FACETS	0.246	0.176	0.33	0.246	0.176	0.33	SUBCLONAL	1	TRUE	1	0.2	2		529	570	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429957	78429957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	53	433	1	ENST00000370768.2:c.922C>T	p.Arg308Cys	p.R308C	ENST00000370768	NM_003902.3	308	Cgc/Tgc	11/20	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.2	2		434	471	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251226	115251226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	50	524	0	ENST00000369535.4:c.500G>A	p.Arg167Gln	p.R167Q	ENST00000369535	NM_002524.4	167	cGa/cAa	5/7	1	2	FACETS	0.804	0.681	0.939	0.804	0.681	0.939	CLONAL	1	TRUE	1	0.2	2		524	622	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115267948	115267948	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	33	431	0	ENST00000438362.2:c.1785C>A	p.Phe595Leu	p.F595L	ENST00000438362	NM_001242891.1	595	ttC/ttA	15/20	1	2	FACETS	0.621	0.505	0.753	0.621	0.505	0.753	SUBCLONAL	1	TRUE	1	0.2	2		431	531	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280138	115280138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	38	487	0	ENST00000438362.2:c.494C>T	p.Ala165Val	p.A165V	ENST00000438362	NM_001242891.1	165	gCc/gTc	5/20	1	2	FACETS	0.515	0.424	0.617	0.515	0.424	0.617	SUBCLONAL	1	TRUE	1	0.2	2		487	738	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165692	118165692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771057074	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	46	470	0	ENST00000369448.3:c.202G>A	p.Asp68Asn	p.D68N	ENST00000369448	NM_017709.3	68	Gac/Aac	2/2	1	2	FACETS	0.821	0.691	0.965	0.821	0.691	0.965	CLONAL	1	TRUE	1	0.2	2		470	560	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462942	120462942	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	73	566	1	ENST00000256646.2:c.5389G>A	p.Ala1797Thr	p.A1797T	ENST00000256646	NM_024408.3	1797	Gca/Aca	30/34	1	2	FACETS	0.975	0.852	1	0.975	0.852	1	CLONAL	1	TRUE	1	0.2	2		567	749	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120479946	120479946	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782313621	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	75	707	0	ENST00000256646.2:c.3481G>A	p.Gly1161Arg	p.G1161R	ENST00000256646	NM_024408.3	1161	Ggg/Agg	21/34	1	2	FACETS	0.817	0.714	0.928	0.817	0.714	0.928	CLONAL	1	TRUE	1	0.2	2		707	918	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480064	120480064	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	72	547	0	ENST00000256646.2:c.3363G>T	p.Gln1121His	p.Q1121H	ENST00000256646	NM_024408.3	1121	caG/caT	21/34	1	2	FACETS	0.978	0.854	1	0.978	0.854	1	CLONAL	1	TRUE	1	0.2	2		547	736	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484331	120484331	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	41	445	0	ENST00000256646.2:c.2799C>A	p.Phe933Leu	p.F933L	ENST00000256646	NM_024408.3	933	ttC/ttA	18/34	1	2	FACETS	0.761	0.633	0.903	0.761	0.633	0.903	CLONAL	1	TRUE	1	0.2	2		445	539	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120502048	120502048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1352414422	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	35	454	0	ENST00000256646.2:c.1993C>T	p.Arg665Cys	p.R665C	ENST00000256646	NM_024408.3	665	Cgc/Tgc	12/34	1	2	FACETS	0.688	0.563	0.828	0.688	0.563	0.828	SUBCLONAL	1	TRUE	1	0.2	2		454	509	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874263	155874263	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1557960039	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	134	666	0	ENST00000368323.3:c.268A>G	p.Met90Val	p.M90V	ENST00000368323	NM_006912.5	90	Atg/Gtg	5/6	1	2	FACETS	0.87	0.791	0.953	1	0.989	1	CLONAL	2	TRUE	1	0.2	2		666	770	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838017	156838017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	77	996	1	ENST00000524377.1:c.550G>A	p.Ala184Thr	p.A184T	ENST00000524377	NM_002529.3	184	Gcc/Acc	5/17	1	2	FACETS	0.689	0.603	0.782	0.689	0.603	0.782	SUBCLONAL	1	TRUE	1	0.2	2		997	1118	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843688	156843688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754611476	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	83	1113	1	ENST00000524377.1:c.1114G>A	p.Ala372Thr	p.A372T	ENST00000524377	NM_002529.3	372	Gcc/Acc	8/17	1	2	FACETS	0.718	0.632	0.811	0.718	0.632	0.811	SUBCLONAL	1	TRUE	1	0.2	2		1114	1156	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156848984	156848984	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1381516878	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	73	911	0	ENST00000524377.1:c.1876C>T	p.Gln626Ter	p.Q626*	ENST00000524377	NM_002529.3	626	Cag/Tag	15/17	1	2	FACETS	0.841	0.734	0.957	0.841	0.734	0.957	CLONAL	1	TRUE	1	0.2	2		911	868	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724611	162724611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149507401	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	53	531	0	ENST00000367921.3:c.383G>A	p.Arg128His	p.R128H	ENST00000367921	NM_006182.2	128	cGc/cAc	5/18	1	2	FACETS	0.81	0.69	0.942	0.81	0.69	0.942	CLONAL	1	TRUE	1	0.2	2		531	654	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132997	176132997	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs746336083	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	35	419	0	ENST00000367669.3:c.596G>T	p.Arg199Ile	p.R199I	ENST00000367669	NM_022457.5	199	aGa/aTa	4/20	1	2	FACETS	0.731	0.598	0.879	0.731	0.598	0.879	SUBCLONAL	1	TRUE	1	0.2	2		419	479	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206943235	206943235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760677075	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	52	369	0	ENST00000423557.1:c.383G>A	p.Arg128Gln	p.R128Q	ENST00000423557	NM_000572.2	128	cGa/cAa	4/5	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.2	2		369	515	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612638	228612638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146830002	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	75	758	1	ENST00000366696.1:c.389G>A	p.Arg130His	p.R130H	ENST00000366696	NM_003493.2	130	cGt/cAt	1/1	1	2	FACETS	0.88	0.77	1	0.88	0.77	1	CLONAL	1	TRUE	1	0.2	2		759	852	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667401	241667401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749316923	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	51	596	0	ENST00000366560.3:c.1049G>A	p.Arg350Gln	p.R350Q	ENST00000366560	NM_000143.3	350	cGg/cAg	7/10	1	2	FACETS	0.691	0.586	0.807	0.691	0.586	0.807	SUBCLONAL	1	TRUE	1	0.2	2		596	738	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243668610	243668610	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	36	419	0	ENST00000263826.5:c.1381G>A	p.Asp461Asn	p.D461N	ENST00000263826	NM_005465.4	461	Gac/Aac	13/13	1	2	FACETS	0.656	0.538	0.788	0.656	0.538	0.788	SUBCLONAL	1	TRUE	1	0.2	2		419	549	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243708889	243708889	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	35	428	0	ENST00000263826.5:c.1174G>T	p.Gly392Ter	p.G392*	ENST00000263826	NM_005465.4	392	Gga/Tga	11/13	1	2	FACETS	0.875	0.718	1	0.875	0.718	1	CLONAL	1	TRUE	1	0.2	2		428	400	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097643	8097643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	34	247	0	ENST00000346208.3:c.25C>T	p.Arg9Cys	p.R9C	ENST00000346208		9	Cgc/Tgc	2/6	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.2	2		247	282	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106042	8106042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	64	614	0	ENST00000346208.3:c.862G>A	p.Gly288Arg	p.G288R	ENST00000346208		288	Ggg/Agg	4/6	1	2	FACETS	0.774	0.669	0.889	0.774	0.669	0.889	SUBCLONAL	1	TRUE	1	0.2	2		614	827	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606811	43606811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775842917	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	73	1052	2	ENST00000355710.3:c.1420C>T	p.Arg474Trp	p.R474W	ENST00000355710	NM_020975.4	474	Cgg/Tgg	7/20	1	2	FACETS	0.735	0.641	0.837	0.735	0.641	0.837	SUBCLONAL	1	TRUE	1	0.2	2		1054	993	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615084	43615084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782636	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	86	870	0	ENST00000355710.3:c.2498G>A	p.Arg833His	p.R833H	ENST00000355710	NM_020975.4	833	cGc/cAc	14/20	1	2	FACETS	0.965	0.852	1	0.965	0.852	1	CLONAL	1	TRUE	1	0.2	2		870	891	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851586	63851586	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	65	695	0	ENST00000279873.7:c.2364C>A	p.Phe788Leu	p.F788L	ENST00000279873	NM_032199.2	788	ttC/ttA	10/10	1	2	FACETS	0.837	0.724	0.959	0.837	0.724	0.959	CLONAL	1	TRUE	1	0.2	2		695	777	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851828	63851828	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs201944744	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	76	722	0	ENST00000279873.7:c.2606C>A	p.Ser869Tyr	p.S869Y	ENST00000279873	NM_032199.2	869	tCt/tAt	10/10	1	2	FACETS	0.907	0.794	1	0.907	0.794	1	CLONAL	1	TRUE	1	0.2	2		722	838	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852262	63852262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178738385	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	67	690	1	ENST00000279873.7:c.3040C>T	p.Arg1014Cys	p.R1014C	ENST00000279873	NM_032199.2	1014	Cgc/Tgc	10/10	1	2	FACETS	0.777	0.674	0.89	0.777	0.674	0.89	SUBCLONAL	1	TRUE	1	0.2	2		691	862	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332272	70332273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1446158817	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	49	488	1	ENST00000373644.4:c.184dup	p.Thr62AsnfsTer4	p.T62Nfs*4	ENST00000373644	NM_030625.2	59	-/A	2/12	1	2	FACETS	0.854	0.723	0.998	0.854	0.723	0.998	CLONAL	1	TRUE	1	0.2	2		489	574	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332565	70332565	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs185830524	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	44	694	0	ENST00000373644.4:c.470C>T	p.Ser157Leu	p.S157L	ENST00000373644	NM_030625.2	157	tCg/tTg	2/12	1	2	FACETS	0.684	0.573	0.808	0.684	0.573	0.808	SUBCLONAL	1	TRUE	1	0.2	2		694	643	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406214	70406214	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	73	782	0	ENST00000373644.4:c.3728A>C	p.Lys1243Thr	p.K1243T	ENST00000373644	NM_030625.2	1243	aAa/aCa	4/12	1	2	FACETS	0.942	0.823	1	0.942	0.823	1	CLONAL	1	TRUE	1	0.2	2		782	775	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70412277	70412277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	33	302	0	ENST00000373644.4:c.4387G>A	p.Ala1463Thr	p.A1463T	ENST00000373644	NM_030625.2	1463	Gca/Aca	6/12	1	2	FACETS	0.948	0.774	1	0.948	0.774	1	CLONAL	1	TRUE	1	0.2	2		302	348	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70432653	70432653	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	27	409	0	ENST00000373644.4:c.4675C>T	p.Arg1559Cys	p.R1559C	ENST00000373644	NM_030625.2	1559	Cgt/Tgt	8/12	1	2	FACETS	0.804	0.64	0.99	0.804	0.64	0.99	CLONAL	1	TRUE	1	0.2	2		409	336	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450691	70450691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368896189	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	71	590	0	ENST00000373644.4:c.5531C>T	p.Ala1844Val	p.A1844V	ENST00000373644	NM_030625.2	1844	gCa/gTa	12/12	1	2	FACETS	0.902	0.786	1	0.902	0.786	1	CLONAL	1	TRUE	1	0.2	2		590	787	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624270	89624270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123324	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	58	410	0	ENST00000371953.3:c.44G>A	p.Arg15Lys	p.R15K	ENST00000371953	NM_000314.4	15	aGa/aAa	1/9	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.2	2		410	509	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	72	286	1	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.2	2		287	551	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156699	2156699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs975030738	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	89	916	0	ENST00000434045.2:c.223G>A	p.Ala75Thr	p.A75T	ENST00000434045	NM_001127598.1	75	Gcc/Acc	3/5	1	2	FACETS	0.854	0.755	0.96	0.854	0.755	0.96	CLONAL	1	TRUE	1	0.2	2		916	1042	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251941	8251941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	92	903	3	ENST00000335790.3:c.136G>A	p.Glu46Lys	p.E46K	ENST00000335790	NM_002315.2	46	Gaa/Aaa	2/4	1	2	FACETS	0.977	0.866	1	0.977	0.866	1	CLONAL	1	TRUE	1	0.2	2		906	942	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132927	64132927	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145356210	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	71	709	0	ENST00000334205.4:c.1061G>A	p.Arg354Gln	p.R354Q	ENST00000334205	NM_003942.2	354	cGa/cAa	9/17	1	2	FACETS	0.952	0.83	1	0.952	0.83	1	CLONAL	1	TRUE	1	0.2	2		709	746	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137241	64137241	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	51	719	0	ENST00000334205.4:c.1673G>A	p.Arg558Gln	p.R558Q	ENST00000334205	NM_003942.2	558	cGg/cAg	14/17	1	2	FACETS	0.52	0.44	0.608	0.52	0.44	0.608	SUBCLONAL	1	TRUE	1	0.2	2		719	981	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941049	71941049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373511105	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	67	1025	1	ENST00000298229.2:c.925G>A	p.Val309Met	p.V309M	ENST00000298229	NM_001567.3	309	Gtg/Atg	8/28	1	2	FACETS	0.636	0.551	0.728	0.636	0.551	0.728	SUBCLONAL	1	TRUE	1	0.2	2		1026	1054	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948365	71948365	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	154	1122	0	ENST00000298229.2:c.3077T>G	p.Leu1026Arg	p.L1026R	ENST00000298229	NM_001567.3	1026	cTt/cGt	26/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.2	2		1122	1234	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999798	100999798	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	29	745	0	ENST00000325455.5:c.4A>C	p.Thr2Pro	p.T2P	ENST00000325455	NM_001202474.3	2	Act/Cct	1/8	1	2	FACETS	0.505	0.404	0.621	0.505	0.404	0.621	SUBCLONAL	1	TRUE	1	0.2	2		745	574	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165730	108165730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765759912	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	22	403	0	ENST00000278616.4:c.4853G>A	p.Arg1618Gln	p.R1618Q	ENST00000278616	NM_000051.3	1618	cGa/cAa	32/63	1	2	FACETS	0.5	0.387	0.632	0.5	0.387	0.632	SUBCLONAL	1	TRUE	1	0.2	2		403	440	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188249	108188249	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1057517120	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	22	243	0	ENST00000278616.4:c.6347+1G>A		p.X2116_splice	ENST00000278616	NM_000051.3	2116			1	2	FACETS	0.978	0.761	1	0.978	0.761	1	CLONAL	1	TRUE	1	0.2	2		243	225	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111958593	111958593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555186772	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	38	596	0	ENST00000375549.3:c.65G>A	p.Arg22Gln	p.R22Q	ENST00000375549	NM_003002.3	22	cGa/cAa	2/4	1	2	FACETS	0.564	0.465	0.675	0.564	0.465	0.675	SUBCLONAL	1	TRUE	1	0.2	2		596	674	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342548	118342548	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	19	311	0	ENST00000534358.1:c.674C>A	p.Pro225His	p.P225H	ENST00000534358	NM_005933.3	225	cCt/cAt	3/36	1	2	FACETS	0.676	0.513	0.867	0.676	0.513	0.867	SUBCLONAL	1	TRUE	1	0.2	2		311	281	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343875	118343875	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	65	541	0	ENST00000534358.1:c.2001T>G	p.Phe667Leu	p.F667L	ENST00000534358	NM_005933.3	667	ttT/ttG	3/36	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.2	2		541	637	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362582	118362582	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	37	506	0	ENST00000534358.1:c.4943A>C	p.Lys1648Thr	p.K1648T	ENST00000534358	NM_005933.3	1648	aAg/aCg	15/36	1	2	FACETS	0.556	0.457	0.668	0.556	0.457	0.668	SUBCLONAL	1	TRUE	1	0.2	2		506	665	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	459809	459809	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	82	763	0	ENST00000399788.2:c.1286G>T	p.Arg429Ile	p.R429I	ENST00000399788	NM_001042603.1	429	aGa/aTa	10/28	0.3	1	FACETS	0.78	0.686	0.881	0.78	0.686	0.881	SUBCLONAL	1	TRUE	0	0.2	1		763	946	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385250	4385250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	77	602	0	ENST00000261254.3:c.275C>T	p.Pro92Leu	p.P92L	ENST00000261254	NM_001759.3	92	cCg/cTg	2/5	0.3	1	FACETS	0.814	0.714	0.923	0.814	0.714	0.923	CLONAL	1	TRUE	0	0.2	1		602	851	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022522	12022522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762232508	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	94	785	0	ENST00000396373.4:c.628C>T	p.Arg210Cys	p.R210C	ENST00000396373	NM_001987.4	210	Cgc/Tgc	5/8	0.208431526915204	4	FACETS	1	0.974	1	0.667	0.593	0.747	CLONAL	1	TRUE	2	0.2	4		785	845	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022819	12022819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465114480	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	57	664	1	ENST00000396373.4:c.925C>T	p.Arg309Trp	p.R309W	ENST00000396373	NM_001987.4	309	Cgg/Tgg	5/8	0.208431526915204	4	FACETS	1	0.927	1	0.565	0.485	0.653	CLONAL	1	TRUE	2	0.2	4		665	605	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435082	18435082	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	68	448	0	ENST00000266497.5:c.67G>T	p.Glu23Ter	p.E23*	ENST00000266497		23	Gaa/Taa	1/31	0.0914294749029332	3	FACETS	0.926	0.809	1	0.926	0.809	1	INDETERMINATE	2	TRUE	1	0.2	3		448	404	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435293	18435293	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	65	434	0	ENST00000266497.5:c.278G>A	p.Ser93Asn	p.S93N	ENST00000266497		93	aGc/aAc	1/31	0.0914294749029332	3	FACETS	0.833	0.725	0.95	0.833	0.725	0.95	INDETERMINATE	2	TRUE	1	0.2	3		434	429	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656263	18656263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762092026	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	52	569	0	ENST00000266497.5:c.2942G>A	p.Arg981His	p.R981H	ENST00000266497		981	cGc/cAc	21/31	0.0914294749029332	3	FACETS	1	0.884	1	0.523	0.445	0.608	INDETERMINATE	1	TRUE	1	0.2	3		569	547	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46215235	46215235	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	20	299	0	ENST00000334344.6:c.670G>A	p.Glu224Lys	p.E224K	ENST00000334344	NM_152641.2	224	Gaa/Aaa	6/21	0.0914294749029332	3	FACETS	0.663	0.506	0.846	0.331	0.253	0.423	INDETERMINATE	1	TRUE	1	0.2	3		299	332	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244530	46244530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	55	607	1	ENST00000334344.6:c.2624G>A	p.Gly875Glu	p.G875E	ENST00000334344	NM_152641.2	875	gGa/gAa	15/21	0.0914294749029332	3	FACETS	0.925	0.79	1	0.463	0.395	0.537	INDETERMINATE	1	TRUE	1	0.2	3		608	654	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416443	49416443	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	86	724	0	ENST00000301067.7:c.16268T>C	p.Val5423Ala	p.V5423A	ENST00000301067	NM_003482.3	5423	gTt/gCt	51/54	0.0914294749029332	3	FACETS	1	0.949	1	0.569	0.502	0.64	INDETERMINATE	1	TRUE	1	0.2	3		724	832	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432375	49432375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751964761	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	87	894	2	ENST00000301067.7:c.8764C>T	p.Arg2922Trp	p.R2922W	ENST00000301067	NM_003482.3	2922	Cgg/Tgg	34/54	0.0914294749029332	3	FACETS	0.958	0.846	1	0.479	0.423	0.539	INDETERMINATE	1	TRUE	1	0.2	3		896	999	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433649	49433649	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200359477	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	124	1145	2	ENST00000301067.7:c.7904G>A	p.Arg2635Gln	p.R2635Q	ENST00000301067	NM_003482.3	2635	cGa/cAa	31/54	0.0914294749029332	3	FACETS	1	0.941	1	0.53	0.477	0.585	INDETERMINATE	1	TRUE	1	0.2	3		1147	1288	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434774	49434774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746355138	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	95	977	0	ENST00000301067.7:c.6779G>A	p.Ser2260Asn	p.S2260N	ENST00000301067	NM_003482.3	2260	aGc/aAc	31/54	0.0914294749029332	3	FACETS	0.902	0.8	1	0.451	0.4	0.505	INDETERMINATE	1	TRUE	1	0.2	3		977	1159	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434965	49434965	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	53	733	0	ENST00000301067.7:c.6588T>G	p.Tyr2196Ter	p.Y2196*	ENST00000301067	NM_003482.3	2196	taT/taG	31/54	0.0914294749029332	3	FACETS	0.795	0.677	0.926	0.398	0.338	0.463	INDETERMINATE	1	TRUE	1	0.2	3		733	733	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436643	49436643	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	78	821	0	ENST00000301067.7:c.5663C>T	p.Ser1888Phe	p.S1888F	ENST00000301067	NM_003482.3	1888	tCc/tTc	26/54	0.0914294749029332	3	FACETS	0.972	0.852	1	0.486	0.426	0.551	INDETERMINATE	1	TRUE	1	0.2	3		821	883	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487212	56487212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144549266	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	55	662	1	ENST00000267101.3:c.1358G>A	p.Arg453His	p.R453H	ENST00000267101	NM_001982.3	453	cGt/cAt	12/28	0.0914294749029332	3	FACETS	0.821	0.701	0.953	0.41	0.35	0.477	INDETERMINATE	1	TRUE	1	0.2	3		663	737	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864148	57864148	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766159479	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	93	652	0	ENST00000228682.2:c.1625G>A	p.Arg542His	p.R542H	ENST00000228682	NM_005269.2	542	cGc/cAc	12/12	0.0914294749029332	3	FACETS	1	0.968	1	0.625	0.555	0.699	INDETERMINATE	1	TRUE	1	0.2	3		652	819	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864355	57864355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765569651	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	76	889	0	ENST00000228682.2:c.1832G>A	p.Arg611Gln	p.R611Q	ENST00000228682	NM_005269.2	611	cGg/cAg	12/12	0.0914294749029332	3	FACETS	1	0.898	1	0.514	0.45	0.583	INDETERMINATE	1	TRUE	1	0.2	3		889	813	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69214108	69214108	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	34	326	0	ENST00000462284.1:c.312A>C	p.Lys104Asn	p.K104N	ENST00000462284	NM_002392.5	104	aaA/aaC	5/11	0.0914294749029332	3	FACETS	1	0.88	1	0.55	0.45	0.662	INDETERMINATE	1	TRUE	1	0.2	3		326	340	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233525	69233525	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	29	475	0	ENST00000462284.1:c.1390C>A	p.Leu464Ile	p.L464I	ENST00000462284	NM_002392.5	464	Ctt/Att	11/11	0.0914294749029332	3	FACETS	0.685	0.549	0.84	0.342	0.274	0.42	INDETERMINATE	1	TRUE	1	0.2	3		475	466	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813361	102813361	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1280732914	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	53	622	0	ENST00000307046.8:c.328G>A	p.Ala110Thr	p.A110T	ENST00000307046	NM_001111285.1	110	Gca/Aca	3/4	0.0914294749029332	3	FACETS	0.796	0.678	0.927	0.398	0.339	0.464	INDETERMINATE	1	TRUE	1	0.2	3		622	732	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856364	111856364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	14	60	0	ENST00000341259.2:c.415C>T	p.Arg139Cys	p.R139C	ENST00000341259	NM_005475.2	139	Cgc/Tgc	2/8	0.0914294749029332	3	FACETS	1	0.779	1	0.542	0.394	0.719	INDETERMINATE	1	TRUE	1	0.2	3		60	142	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112892395	112892395	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	47	536	0	ENST00000351677.2:c.553G>T	p.Glu185Ter	p.E185*	ENST00000351677	NM_002834.3	185	Gaa/Taa	5/16	0.0914294749029332	3	FACETS	0.841	0.708	0.987	0.42	0.354	0.494	INDETERMINATE	1	TRUE	1	0.2	3		536	615	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112602	115112602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs865915137	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	105	996	1	ENST00000257566.3:c.1138G>A	p.Glu380Lys	p.E380K	ENST00000257566	NM_016569.3	380	Gag/Aag	7/8	0.0914294749029332	3	FACETS	1	0.918	1	0.516	0.461	0.574	INDETERMINATE	1	TRUE	1	0.2	3		997	1120	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115397	115115397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866796237	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	62	682	0	ENST00000257566.3:c.929G>A	p.Arg310Gln	p.R310Q	ENST00000257566	NM_016569.3	310	cGa/cAa	5/8	0.0914294749029332	3	FACETS	0.796	0.686	0.916	0.398	0.343	0.458	INDETERMINATE	1	TRUE	1	0.2	3		682	857	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117422	115117422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151047347	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	32	434	0	ENST00000257566.3:c.752G>A	p.Arg251Gln	p.R251Q	ENST00000257566	NM_016569.3	251	cGg/cAg	4/8	0.0914294749029332	3	FACETS	0.782	0.634	0.949	0.391	0.317	0.475	INDETERMINATE	1	TRUE	1	0.2	3		434	450	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434070	121434070	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766770471	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	67	656	1	ENST00000257555.6:c.961C>T	p.Arg321Cys	p.R321C	ENST00000257555		321	Cgc/Tgc	5/10	0.0914294749029332	3	FACETS	1	0.896	1	0.518	0.45	0.593	INDETERMINATE	1	TRUE	1	0.2	3		657	711	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123875312	123875312	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	54	514	0	ENST00000330479.4:c.268G>T	p.Gly90Ter	p.G90*	ENST00000330479	NM_020382.3	90	Gga/Tga	3/9	0.0914294749029332	3	FACETS	0.918	0.783	1	0.459	0.391	0.533	INDETERMINATE	1	TRUE	1	0.2	3		514	647	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212495	133212495	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879254168	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	51	517	0	ENST00000320574.5:c.5794C>T	p.Arg1932Cys	p.R1932C	ENST00000320574	NM_006231.2	1932	Cgt/Tgt	42/49	0.0914294749029332	3	FACETS	0.938	0.797	1	0.469	0.398	0.547	INDETERMINATE	1	TRUE	1	0.2	3		517	598	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225525	133225525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762090058	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	57	680	0	ENST00000320574.5:c.4139C>T	p.Ser1380Leu	p.S1380L	ENST00000320574	NM_006231.2	1380	tCg/tTg	32/49	0.0914294749029332	3	FACETS	0.793	0.679	0.918	0.396	0.339	0.459	INDETERMINATE	1	TRUE	1	0.2	3		680	791	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133236035	133236035	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762140272	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	55	638	0	ENST00000320574.5:c.3121C>T	p.Arg1041Trp	p.R1041W	ENST00000320574	NM_006231.2	1041	Cgg/Tgg	26/49	0.0914294749029332	3	FACETS	0.833	0.712	0.967	0.417	0.356	0.484	INDETERMINATE	1	TRUE	1	0.2	3		638	726	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240670	133240670	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1208731306	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	62	690	0	ENST00000320574.5:c.2626T>G	p.Phe876Val	p.F876V	ENST00000320574	NM_006231.2	876	Ttt/Gtt	23/49	0.0914294749029332	3	FACETS	0.855	0.737	0.983	0.427	0.368	0.492	INDETERMINATE	1	TRUE	1	0.2	3		690	798	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	94	587	0	ENST00000320574.5:c.1231G>C	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ctg	13/49	0.0914294749029332	3	FACETS	0.93	0.829	1	0.93	0.829	1	INDETERMINATE	2	TRUE	1	0.2	3		587	556	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549394	21549394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148935054	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	44	663	1	ENST00000382592.4:c.2882G>A	p.Arg961Gln	p.R961Q	ENST00000382592	NM_014572.2	961	cGg/cAg	8/8	1	2	FACETS	0.681	0.57	0.805	0.681	0.57	0.805	SUBCLONAL	1	TRUE	1	0.2	2		664	646	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563413	21563413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150428840	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	126	1034	2	ENST00000382592.4:c.506G>A	p.Arg169Gln	p.R169Q	ENST00000382592	NM_014572.2	169	cGg/cAg	4/8	1	2	FACETS	0.992	0.896	1	0.992	0.896	1	CLONAL	1	TRUE	1	0.2	2		1036	1270	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975407	26975407	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs981705610	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	43	494	0	ENST00000381527.3:c.1033G>A	p.Val345Ile	p.V345I	ENST00000381527	NM_001260.1	345	Gtt/Att	11/13	1	2	FACETS	0.848	0.71	1	0.848	0.71	1	CLONAL	1	TRUE	1	0.2	2		494	507	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578253	28578253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144397269	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	82	628	0	ENST00000241453.7:c.2918G>A	p.Arg973Gln	p.R973Q	ENST00000241453	NM_004119.2	973	cGa/cAa	24/24	1	2	FACETS	0.999	0.88	1	0.999	0.88	1	CLONAL	1	TRUE	1	0.2	2		628	821	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597546	28597546	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1474119276	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	53	617	0	ENST00000241453.7:c.2359G>T	p.Asp787Tyr	p.D787Y	ENST00000241453	NM_004119.2	787	Gat/Tat	19/24	1	2	FACETS	0.709	0.603	0.825	0.709	0.603	0.825	SUBCLONAL	1	TRUE	1	0.2	2		617	748	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622521	28622521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	37	488	0	ENST00000241453.7:c.1096G>T	p.Glu366Ter	p.E366*	ENST00000241453	NM_004119.2	366	Gag/Tag	9/24	1	2	FACETS	0.72	0.593	0.862	0.72	0.593	0.862	SUBCLONAL	1	TRUE	1	0.2	2		488	514	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623592	28623592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	54	561	0	ENST00000241453.7:c.965G>T	p.Arg322Ile	p.R322I	ENST00000241453	NM_004119.2	322	aGa/aTa	8/24	1	2	FACETS	0.906	0.773	1	0.906	0.773	1	CLONAL	1	TRUE	1	0.2	2		561	596	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907459	32907459	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	27	328	0	ENST00000380152.3:c.1844A>C	p.Asn615Thr	p.N615T	ENST00000380152		615	aAc/aCc	10/27	1	2	FACETS	0.754	0.6	0.93	0.754	0.6	0.93	CLONAL	1	TRUE	1	0.2	2		328	358	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911247	32911247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs431825298	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	54	638	0	ENST00000380152.3:c.2755G>A	p.Glu919Lys	p.E919K	ENST00000380152		919	Gaa/Aaa	11/27	1	2	FACETS	0.931	0.795	1	0.931	0.795	1	CLONAL	1	TRUE	1	0.2	2		638	580	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911328	32911328	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs80358534	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	41	603	0	ENST00000380152.3:c.2836G>T	p.Asp946Tyr	p.D946Y	ENST00000380152		946	Gat/Tat	11/27	1	2	FACETS	0.817	0.68	0.969	0.817	0.68	0.969	CLONAL	1	TRUE	1	0.2	2		603	502	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914091	32914091	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	40	555	0	ENST00000380152.3:c.5599A>G	p.Thr1867Ala	p.T1867A	ENST00000380152		1867	Aca/Gca	11/27	1	2	FACETS	0.837	0.695	0.994	0.837	0.695	0.994	CLONAL	1	TRUE	1	0.2	2		555	478	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914893	32914893	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	39	443	0	ENST00000380152.3:c.6401A>G	p.Asn2134Ser	p.N2134S	ENST00000380152		2134	aAt/aGt	11/27	1	2	FACETS	0.951	0.789	1	0.951	0.789	1	CLONAL	1	TRUE	1	0.2	2		443	410	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134523	41134523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263390525	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	46	559	0	ENST00000379561.5:c.1105G>A	p.Glu369Lys	p.E369K	ENST00000379561	NM_002015.3	369	Gaa/Aaa	2/3	1	2	FACETS	0.806	0.678	0.947	0.806	0.678	0.947	CLONAL	1	TRUE	1	0.2	2		559	571	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73340168	73340168	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs770832001	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	37	343	0	ENST00000377767.4:c.1912C>T	p.Arg638Ter	p.R638*	ENST00000377767	NM_014953.3	638	Cga/Tga	15/21	1	2	FACETS	1	0.83	1	1	0.83	1	CLONAL	1	TRUE	1	0.2	2		343	368	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514495	103514495	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	40	313	0	ENST00000355739.4:c.996G>T	p.Glu332Asp	p.E332D	ENST00000355739	NM_000123.3	332	gaG/gaT	8/15	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.2	2		313	367	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514895	103514895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	42	446	0	ENST00000355739.4:c.1396G>A	p.Glu466Lys	p.E466K	ENST00000355739	NM_000123.3	466	Gag/Aag	8/15	1	2	FACETS	0.868	0.724	1	0.868	0.724	1	CLONAL	1	TRUE	1	0.2	2		446	484	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515036	103515036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775996769	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	34	419	0	ENST00000355739.4:c.1537G>A	p.Ala513Thr	p.A513T	ENST00000355739	NM_000123.3	513	Gca/Aca	8/15	1	2	FACETS	0.785	0.641	0.947	0.785	0.641	0.947	CLONAL	1	TRUE	1	0.2	2		419	433	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434842	110434842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	64	688	0	ENST00000375856.3:c.3559G>A	p.Glu1187Lys	p.E1187K	ENST00000375856	NM_003749.2	1187	Gag/Aag	1/2	1	2	FACETS	0.696	0.601	0.799	0.696	0.601	0.799	SUBCLONAL	1	TRUE	1	0.2	2		688	920	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435606	110435606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	47	277	0	ENST00000375856.3:c.2795C>T	p.Ser932Leu	p.S932L	ENST00000375856	NM_003749.2	932	tCg/tTg	1/2	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.2	2		277	435	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436662	110436662	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1172028943	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	114	957	2	ENST00000375856.3:c.1739C>T	p.Thr580Met	p.T580M	ENST00000375856	NM_003749.2	580	aCg/aTg	1/2	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.2	2		959	1123	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046638	30046638	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1419328188	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	60	597	0	ENST00000331968.5:c.2545C>T	p.Arg849Ter	p.R849*	ENST00000331968	NM_002742.2	849	Cga/Tga	18/18	0.0914294749029332	3	FACETS	0.917	0.789	1	0.458	0.394	0.528	INDETERMINATE	1	TRUE	1	0.2	3		597	720	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066913	30066913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	58	645	1	ENST00000331968.5:c.2218C>T	p.Arg740Trp	p.R740W	ENST00000331968	NM_002742.2	740	Cgg/Tgg	16/18	0.0914294749029332	3	FACETS	0.863	0.74	0.998	0.432	0.37	0.499	INDETERMINATE	1	TRUE	1	0.2	3		646	739	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068315	30068315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141649026	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	35	404	0	ENST00000331968.5:c.2084G>A	p.Arg695Gln	p.R695Q	ENST00000331968	NM_002742.2	695	cGg/cAg	15/18	0.0914294749029332	3	FACETS	0.904	0.741	1	0.452	0.37	0.544	INDETERMINATE	1	TRUE	1	0.2	3		404	426	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988308	36988309	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776709	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	37	463	0	ENST00000354822.5:c.344dup	p.Tyr116LeufsTer323	p.Y116Lfs*323	ENST00000354822	NM_001079668.2	115	ggc/ggGc	2/3	0.0914294749029332	3	FACETS	0.644	0.53	0.773	0.322	0.265	0.387	INDETERMINATE	1	TRUE	1	0.2	3		463	632	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65569030	65569030	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	31	508	0	ENST00000358664.4:c.28G>A	p.Glu10Lys	p.E10K	ENST00000358664	NM_002382.4	10	Gag/Aag	1/5	0.0914294749029332	3	FACETS	0.556	0.449	0.679	0.278	0.224	0.34	INDETERMINATE	1	TRUE	1	0.2	3		508	613	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68290283	68290283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867530891	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	38	472	0	ENST00000487270.1:c.23G>A	p.Arg8Gln	p.R8Q	ENST00000487270	NM_133509.3	8	cGa/cAa	2/11	0.0914294749029332	3	FACETS	0.789	0.651	0.943	0.394	0.325	0.472	INDETERMINATE	1	TRUE	1	0.2	3		472	530	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353842	68353842	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	67	470	0	ENST00000487270.1:c.677G>A	p.Gly226Asp	p.G226D	ENST00000487270	NM_133509.3	226	gGc/gAc	7/11	0.0914294749029332	3	FACETS	1	0.955	1	0.618	0.537	0.706	INDETERMINATE	1	TRUE	1	0.2	3		470	596	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609554	81609554	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	52	554	0	ENST00000298171.2:c.1152T>G	p.His384Gln	p.H384Q	ENST00000298171	NM_000369.2	384	caT/caG	10/10	0.0914294749029332	3	FACETS	0.88	0.748	1	0.44	0.374	0.513	INDETERMINATE	1	TRUE	1	0.2	3		554	650	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610143	81610143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	45	436	0	ENST00000298171.2:c.1741G>A	p.Ala581Thr	p.A581T	ENST00000298171	NM_000369.2	581	Gca/Aca	10/10	0.0914294749029332	3	FACETS	0.939	0.789	1	0.47	0.394	0.553	INDETERMINATE	1	TRUE	1	0.2	3		436	527	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571498	95571498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	61	452	1	ENST00000393063.1:c.3179G>A	p.Arg1060His	p.R1060H	ENST00000393063	NM_030621.3	1060	cGc/cAc	21/28	0.0914294749029332	3	FACETS	0.907	0.781	1	0.453	0.39	0.522	INDETERMINATE	1	TRUE	1	0.2	3		453	740	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95592924	95592924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755944755	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	27	426	0	ENST00000393063.1:c.896C>T	p.Ser299Leu	p.S299L	ENST00000393063	NM_030621.3	299	tCg/tTg	8/28	0.0914294749029332	3	FACETS	0.832	0.662	1	0.416	0.331	0.513	INDETERMINATE	1	TRUE	1	0.2	3		426	357	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95595941	95595941	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749484792	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	31	466	0	ENST00000393063.1:c.602G>A	p.Arg201His	p.R201H	ENST00000393063	NM_030621.3	201	cGc/cAc	7/28	0.0914294749029332	3	FACETS	0.735	0.594	0.895	0.367	0.297	0.448	INDETERMINATE	1	TRUE	1	0.2	3		466	464	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614595	38614595	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	40	589	0	ENST00000299084.4:c.361G>T	p.Glu121Ter	p.E121*	ENST00000299084	NM_152594.2	121	Gag/Tag	3/7	1	2	FACETS	0.897	0.746	1	0.897	0.746	1	CLONAL	1	TRUE	1	0.2	2		589	446	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054042	42054042	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	17	360	0	ENST00000219905.7:c.7504C>A	p.Leu2502Ile	p.L2502I	ENST00000219905	NM_001164273.1	2502	Ctt/Att	21/24	1	2	FACETS	0.503	0.375	0.656	0.503	0.375	0.656	SUBCLONAL	1	TRUE	1	0.2	2		360	338	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707822	43707822	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs746063219	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	69	829	1	ENST00000382044.4:c.5059C>T	p.Arg1687Ter	p.R1687*	ENST00000382044	NM_001141980.1	1687	Cga/Tga	23/28	1	2	FACETS	0.637	0.552	0.728	0.637	0.552	0.728	SUBCLONAL	1	TRUE	1	0.2	2		830	1084	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748923	43748923	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774605101	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	114	966	0	ENST00000382044.4:c.1883C>T	p.Ser628Leu	p.S628L	ENST00000382044	NM_001141980.1	628	tCg/tTg	12/28	1	2	FACETS	0.916	0.823	1	0.916	0.823	1	CLONAL	1	TRUE	1	0.2	2		966	1244	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457330	67457330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	100	765	0	ENST00000327367.4:c.304G>A	p.Glu102Lys	p.E102K	ENST00000327367	NM_005902.3	102	Gag/Aag	2/9	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.2	2		765	919	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73995416	73995416	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	66	513	0	ENST00000318443.5:c.722G>T	p.Arg241Ile	p.R241I	ENST00000318443	NM_001024736.1	241	aGa/aTa	4/10	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.2	2		513	585	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726698	88726698	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375475747	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	116	526	0	ENST00000360948.2:c.346C>T	p.Arg116Trp	p.R116W	ENST00000360948	NM_001012338.2	116	Cgg/Tgg	4/19	1	2	FACETS	0.895	0.808	0.986	1	0.987	1	CLONAL	2	TRUE	1	0.2	2		526	648	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628529	90628529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1220662107	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	70	850	0	ENST00000330062.3:c.1058G>A	p.Arg353His	p.R353H	ENST00000330062	NM_002168.2	353	cGc/cAc	8/11	1	2	FACETS	0.828	0.721	0.945	0.828	0.721	0.945	CLONAL	1	TRUE	1	0.2	2		850	845	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628548	90628548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767061831	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	75	843	2	ENST00000330062.3:c.1039G>A	p.Ala347Thr	p.A347T	ENST00000330062	NM_002168.2	347	Gct/Act	8/11	1	2	FACETS	0.862	0.754	0.979	0.862	0.754	0.979	CLONAL	1	TRUE	1	0.2	2		845	870	SUCCESS
BLM	641	MSKCC	GRCh37	15	91290720	91290720	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs139282091	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	20	327	0	ENST00000355112.3:c.98C>T	p.Ser33Leu	p.S33L	ENST00000355112	NM_000057.2	33	tCa/tTa	2/22	1	2	FACETS	0.539	0.412	0.689	0.539	0.412	0.689	SUBCLONAL	1	TRUE	1	0.2	2		327	371	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250976	99250976	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776250673	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	75	711	0	ENST00000268035.6:c.280G>A	p.Glu94Lys	p.E94K	ENST00000268035	NM_000875.3	94	Gag/Aag	2/21	1	2	FACETS	0.878	0.768	0.997	0.878	0.768	0.997	CLONAL	1	TRUE	1	0.2	2		711	854	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251057	99251057	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555434208	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	52	697	0	ENST00000268035.6:c.361G>A	p.Glu121Lys	p.E121K	ENST00000268035	NM_000875.3	121	Gag/Aag	2/21	1	2	FACETS	0.696	0.591	0.812	0.696	0.591	0.812	SUBCLONAL	1	TRUE	1	0.2	2		697	747	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465390	99465390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145300307	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	43	487	0	ENST00000268035.6:c.2215C>T	p.Arg739Trp	p.R739W	ENST00000268035	NM_000875.3	739	Cgg/Tgg	11/21	1	2	FACETS	0.798	0.667	0.943	0.798	0.667	0.943	CLONAL	1	TRUE	1	0.2	2		487	539	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500303	99500303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61740868	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	50	779	1	ENST00000268035.6:c.3736C>T	p.Arg1246Cys	p.R1246C	ENST00000268035	NM_000875.3	1246	Cgc/Tgc	21/21	1	2	FACETS	0.657	0.556	0.769	0.657	0.556	0.769	SUBCLONAL	1	TRUE	1	0.2	2		780	761	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343707	343707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758124815	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	83	1002	1	ENST00000262320.3:c.1967C>T	p.Thr656Met	p.T656M	ENST00000262320	NM_003502.3	656	aCg/aTg	8/11	1	2	FACETS	0.766	0.674	0.866	0.766	0.674	0.866	SUBCLONAL	1	TRUE	1	0.2	2		1003	1083	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094713	2094713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748576083	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	100	931	1	ENST00000219066.1:c.467C>T	p.Ala156Val	p.A156V	ENST00000219066	NM_002528.5	156	gCg/gTg	3/6	1	2	FACETS	0.883	0.787	0.987	0.883	0.787	0.987	CLONAL	1	TRUE	1	0.2	2		932	1132	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134391	2134391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397515033	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	110	994	1	ENST00000219476.3:c.4168G>A	p.Glu1390Lys	p.E1390K	ENST00000219476	NM_000548.3	1390	Gag/Aag	34/42	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.2	2		995	1040	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3645613	3645613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200807331	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	73	809	0	ENST00000294008.3:c.2006G>A	p.Arg669His	p.R669H	ENST00000294008	NM_032444.2	669	cGc/cAc	9/15	1	2	FACETS	0.731	0.638	0.833	0.731	0.638	0.833	SUBCLONAL	1	TRUE	1	0.2	2		809	998	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778977	3778977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745551441	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	39	718	0	ENST00000262367.5:c.6071C>T	p.Ala2024Val	p.A2024V	ENST00000262367	NM_004380.2	2024	gCg/gTg	31/31	1	2	FACETS	0.679	0.562	0.811	0.679	0.562	0.811	SUBCLONAL	1	TRUE	1	0.2	2		718	574	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823855	3823855	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs117910358	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	70	844	2	ENST00000262367.5:c.2360C>T	p.Ala787Val	p.A787V	ENST00000262367	NM_004380.2	787	gCg/gTg	13/31	1	2	FACETS	0.723	0.629	0.826	0.723	0.629	0.826	SUBCLONAL	1	TRUE	1	0.2	2		846	968	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832792	3832792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	65	611	0	ENST00000262367.5:c.1466G>A	p.Gly489Glu	p.G489E	ENST00000262367	NM_004380.2	489	gGa/gAa	6/31	1	2	FACETS	0.849	0.735	0.973	0.849	0.735	0.973	CLONAL	1	TRUE	1	0.2	2		611	766	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843447	3843447	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783461	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	39	539	0	ENST00000262367.5:c.1156C>T	p.Arg386Ter	p.R386*	ENST00000262367	NM_004380.2	386	Cga/Tga	4/31	1	2	FACETS	0.534	0.441	0.638	0.534	0.441	0.638	SUBCLONAL	1	TRUE	1	0.2	2		539	730	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032401	10032404	+	missense_variant	Missense_Mutation	ONP	GTCG	GTCG	ATCA	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	28	413	0	ENST00000330684.3:c.419_422delinsTGAT	p.Pro140_Thr141delinsLeuMet	p.P140_T141delinsLM	ENST00000330684	NM_001134407.1	140	cCGACg/cTGATg	3/13	1	2	FACETS	0.645	0.515	0.794	0.645	0.515	0.794	SUBCLONAL	1	TRUE	1	0.2	2		413	434	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23635373	23635373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502786	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	54	700	0	ENST00000261584.4:c.2791C>T	p.Leu931Phe	p.L931F	ENST00000261584	NM_024675.3	931	Ctc/Ttc	8/13	1	2	FACETS	0.703	0.599	0.817	0.703	0.599	0.817	SUBCLONAL	1	TRUE	1	0.2	2		700	768	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646205	23646205	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	54	544	0	ENST00000261584.4:c.1662A>T	p.Glu554Asp	p.E554D	ENST00000261584	NM_024675.3	554	gaA/gaT	4/13	1	2	FACETS	0.802	0.684	0.932	0.802	0.684	0.932	CLONAL	1	TRUE	1	0.2	2		544	673	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646797	23646797	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	68	774	0	ENST00000261584.4:c.1070C>A	p.Ser357Tyr	p.S357Y	ENST00000261584	NM_024675.3	357	tCt/tAt	4/13	1	2	FACETS	0.796	0.691	0.91	0.796	0.691	0.91	CLONAL	1	TRUE	1	0.2	2		774	854	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650710	67650710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243010179	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	78	689	0	ENST00000264010.4:c.1015C>T	p.Arg339Trp	p.R339W	ENST00000264010	NM_006565.3	339	Cgg/Tgg	5/12	1	2	FACETS	0.762	0.667	0.864	0.762	0.667	0.864	SUBCLONAL	1	TRUE	1	0.2	2		689	1024	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863691	68863691	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	48	493	0	ENST00000261769.5:c.2430T>G	p.Phe810Leu	p.F810L	ENST00000261769	NM_004360.3	810	ttT/ttG	15/16	1	2	FACETS	0.768	0.648	0.9	0.768	0.648	0.9	SUBCLONAL	1	TRUE	1	0.2	2		493	625	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829497	72829497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761486040	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	76	693	0	ENST00000268489.5:c.7084G>A	p.Asp2362Asn	p.D2362N	ENST00000268489	NM_006885.3	2362	Gac/Aac	9/10	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.2	2		693	723	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829641	72829641	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	56	769	0	ENST00000268489.5:c.6940G>T	p.Glu2314Ter	p.E2314*	ENST00000268489	NM_006885.3	2314	Gag/Tag	9/10	1	2	FACETS	0.677	0.579	0.785	0.677	0.579	0.785	SUBCLONAL	1	TRUE	1	0.2	2		769	827	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830892	72830892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150923130	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	62	654	0	ENST00000268489.5:c.5689G>A	p.Glu1897Lys	p.E1897K	ENST00000268489	NM_006885.3	1897	Gag/Aag	9/10	1	2	FACETS	0.826	0.712	0.949	0.826	0.712	0.949	CLONAL	1	TRUE	1	0.2	2		654	751	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830958	72830958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393698686	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	40	572	1	ENST00000268489.5:c.5623G>A	p.Glu1875Lys	p.E1875K	ENST00000268489	NM_006885.3	1875	Gaa/Aaa	9/10	1	2	FACETS	0.729	0.605	0.867	0.729	0.605	0.867	SUBCLONAL	1	TRUE	1	0.2	2		573	549	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832571	72832571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764024381	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	53	431	0	ENST00000268489.5:c.4010G>A	p.Ser1337Asn	p.S1337N	ENST00000268489	NM_006885.3	1337	aGc/aAc	9/10	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.2	2		431	467	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992208	72992208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761739295	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	80	862	1	ENST00000268489.5:c.1837G>A	p.Asp613Asn	p.D613N	ENST00000268489	NM_006885.3	613	Gat/Aat	2/10	1	2	FACETS	0.887	0.779	1	0.887	0.779	1	CLONAL	1	TRUE	1	0.2	2		863	902	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993279	72993279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764820053	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	89	997	1	ENST00000268489.5:c.766G>A	p.Val256Ile	p.V256I	ENST00000268489	NM_006885.3	256	Gta/Ata	2/10	1	2	FACETS	0.718	0.635	0.808	0.718	0.635	0.808	SUBCLONAL	1	TRUE	1	0.2	2		998	1239	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993567	72993567	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780566431	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	46	761	0	ENST00000268489.5:c.478G>A	p.Gly160Ser	p.G160S	ENST00000268489	NM_006885.3	160	Ggc/Agc	2/10	1	2	FACETS	0.618	0.519	0.728	0.618	0.519	0.728	SUBCLONAL	1	TRUE	1	0.2	2		761	744	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348200	89348200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	101	907	0	ENST00000301030.4:c.4750G>A	p.Glu1584Lys	p.E1584K	ENST00000301030	NM_001256183.1	1584	Gag/Aag	9/13	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.2	2		907	914	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89806506	89806506	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	54	479	0	ENST00000389301.3:c.3830G>T	p.Ser1277Ile	p.S1277I	ENST00000389301	NM_000135.2	1277	aGc/aTc	39/43	1	2	FACETS	0.868	0.741	1	0.868	0.741	1	CLONAL	1	TRUE	1	0.2	2		479	622	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857867	89857867	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148473140	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	58	808	3	ENST00000389301.3:c.1303C>T	p.Arg435Cys	p.R435C	ENST00000389301	NM_000135.2	435	Cgc/Tgc	14/43	1	2	FACETS	0.675	0.579	0.781	0.675	0.579	0.781	SUBCLONAL	1	TRUE	1	0.2	2		811	859	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217414	7217414	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	65	677	0	ENST00000380728.2:c.382C>A	p.Leu128Ile	p.L128I	ENST00000380728		128	Ctc/Atc	5/11	1	2	FACETS	0.893	0.773	1	0.893	0.773	1	CLONAL	1	TRUE	1	0.2	2		677	728	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958211	11958211	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	24	402	0	ENST00000353533.5:c.121C>T	p.Arg41Cys	p.R41C	ENST00000353533	NM_003010.3	41	Cgc/Tgc	2/11	1	2	FACETS	0.642	0.503	0.802	0.642	0.503	0.802	SUBCLONAL	1	TRUE	1	0.2	2		402	374	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028639	12028639	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	38	484	0	ENST00000353533.5:c.842G>A	p.Arg281Gln	p.R281Q	ENST00000353533	NM_003010.3	281	cGa/cAa	8/11	1	2	FACETS	0.655	0.541	0.784	0.655	0.541	0.784	SUBCLONAL	1	TRUE	1	0.2	2		484	580	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049799	16049799	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	38	459	0	ENST00000268712.3:c.973A>C	p.Ile325Leu	p.I325L	ENST00000268712	NM_006311.3	325	Ata/Cta	10/46	1	2	FACETS	0.83	0.686	0.99	0.83	0.686	0.99	CLONAL	1	TRUE	1	0.2	2		459	458	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559876	29559876	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	29	354	0	ENST00000356175.3:c.3473A>G	p.Asp1158Gly	p.D1158G	ENST00000356175	NM_000267.3	1158	gAc/gGc	26/57	1	2	FACETS	0.682	0.547	0.836	0.682	0.547	0.836	SUBCLONAL	1	TRUE	1	0.2	2		354	425	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588752	29588752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867955218	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	30	344	0	ENST00000356175.3:c.4538G>A	p.Arg1513Gln	p.R1513Q	ENST00000356175	NM_000267.3	1513	cGa/cAa	34/57	1	2	FACETS	0.642	0.517	0.785	0.642	0.517	0.785	SUBCLONAL	1	TRUE	1	0.2	2		344	467	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618410	37618410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	35	511	0	ENST00000447079.4:c.86G>A	p.Ser29Asn	p.S29N	ENST00000447079	NM_015083.1	29	aGc/aAc	1/14	1	2	FACETS	0.665	0.545	0.801	0.665	0.545	0.801	SUBCLONAL	1	TRUE	1	0.2	2		511	526	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627835	37627835	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	76	684	0	ENST00000447079.4:c.1750T>G	p.Leu584Val	p.L584V	ENST00000447079	NM_015083.1	584	Ttg/Gtg	2/14	1	2	FACETS	0.812	0.71	0.922	0.812	0.71	0.922	CLONAL	1	TRUE	1	0.2	2		684	936	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676315	37676315	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201479472	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	99	690	0	ENST00000447079.4:c.3070G>A	p.Glu1024Lys	p.E1024K	ENST00000447079	NM_015083.1	1024	Gaa/Aaa	11/14	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.2	2		690	880	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881392	37881392	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	193	900	0	ENST00000269571.5:c.2584A>G	p.Thr862Ala	p.T862A	ENST00000269571		862	Aca/Gca	21/27	1	2	FACETS	0.873	0.806	0.942	1	0.992	1	CLONAL	2	TRUE	1	0.2	2		900	1106	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883719	37883719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143958183	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	69	1005	0	ENST00000269571.5:c.3331C>T	p.Arg1111Trp	p.R1111W	ENST00000269571		1111	Cgg/Tgg	26/27	1	2	FACETS	0.617	0.536	0.706	0.617	0.536	0.706	SUBCLONAL	1	TRUE	1	0.2	2		1005	1118	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441476	40441476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	70	783	1	ENST00000345506.4:c.47G>A	p.Arg16His	p.R16H	ENST00000345506	NM_003152.3	16	cGc/cAc	3/20	1	2	FACETS	0.943	0.822	1	0.943	0.822	1	CLONAL	1	TRUE	1	0.2	2		784	742	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40461406	40461406	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	91	818	0	ENST00000345506.4:c.2126C>A	p.Ala709Glu	p.A709E	ENST00000345506	NM_003152.3	709	gCa/gAa	19/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.2	2		818	791	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489466	40489466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	63	600	0	ENST00000264657.5:c.784C>T	p.Arg262Trp	p.R262W	ENST00000264657	NM_139276.2	262	Cgg/Tgg	8/24	1	2	FACETS	0.722	0.623	0.83	0.722	0.623	0.83	SUBCLONAL	1	TRUE	1	0.2	2		600	873	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234450	41234450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs4986849	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	46	538	0	ENST00000357654.3:c.4328G>A	p.Arg1443Gln	p.R1443Q	ENST00000357654	NM_007294.3	1443	cGa/cAa	12/23	1	2	FACETS	0.646	0.543	0.761	0.646	0.543	0.761	SUBCLONAL	1	TRUE	1	0.2	2		538	712	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699348	47699348	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	36	491	0	ENST00000347630.2:c.160A>C	p.Ser54Arg	p.S54R	ENST00000347630	NM_001007230.1	54	Agt/Cgt	4/11	1	2	FACETS	0.702	0.576	0.843	0.702	0.576	0.843	SUBCLONAL	1	TRUE	1	0.2	2		491	513	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780637	56780637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	37	675	0	ENST00000337432.4:c.652G>A	p.Glu218Lys	p.E218K	ENST00000337432	NM_058216.2	218	Gag/Aag	4/9	1	2	FACETS	0.542	0.445	0.65	0.542	0.445	0.65	SUBCLONAL	1	TRUE	1	0.2	2		675	683	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780650	56780650	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	37	637	0	ENST00000337432.4:c.665A>G	p.Gln222Arg	p.Q222R	ENST00000337432	NM_058216.2	222	cAa/cGa	4/9	1	2	FACETS	0.561	0.462	0.674	0.561	0.462	0.674	SUBCLONAL	1	TRUE	1	0.2	2		637	659	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740837	58740837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200809297	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	95	604	0	ENST00000305921.3:c.1742G>A	p.Arg581Gln	p.R581Q	ENST00000305921	NM_003620.3	581	cGa/cAa	6/6	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.2	2		604	809	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770824	59770824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45572934	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	42	468	0	ENST00000259008.2:c.2542C>T	p.Arg848Cys	p.R848C	ENST00000259008	NM_032043.2	848	Cgc/Tgc	18/20	1	2	FACETS	1	0.836	1	1	0.836	1	CLONAL	1	TRUE	1	0.2	2		468	420	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530163	63530163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145007501	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	66	602	1	ENST00000307078.5:c.2272G>A	p.Ala758Thr	p.A758T	ENST00000307078	NM_004655.3	758	Gcg/Acg	10/11	1	2	FACETS	0.753	0.652	0.863	0.753	0.652	0.863	SUBCLONAL	1	TRUE	1	0.2	2		603	876	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526514	66526514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	51	502	0	ENST00000358598.2:c.1070G>A	p.Arg357His	p.R357H	ENST00000358598	NM_212471.2	357	cGt/cAt	11/11	1	2	FACETS	0.662	0.562	0.774	0.662	0.562	0.774	SUBCLONAL	1	TRUE	1	0.2	2		502	770	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78811795	78811795	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	56	527	0	ENST00000306801.3:c.1210C>T	p.Arg404Trp	p.R404W	ENST00000306801	NM_020761.2	404	Cgg/Tgg	10/34	1	2	FACETS	0.809	0.692	0.937	0.809	0.692	0.937	CLONAL	1	TRUE	1	0.2	2		527	692	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867626	78867626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781190662	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	108	983	1	ENST00000306801.3:c.2362C>T	p.Arg788Cys	p.R788C	ENST00000306801	NM_020761.2	788	Cgc/Tgc	20/34	1	2	FACETS	0.969	0.868	1	0.969	0.868	1	CLONAL	1	TRUE	1	0.2	2		984	1114	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78931513	78931513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750857501	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	71	765	0	ENST00000306801.3:c.3460C>T	p.Arg1154Cys	p.R1154C	ENST00000306801	NM_020761.2	1154	Cgt/Tgt	29/34	1	2	FACETS	0.893	0.778	1	0.893	0.778	1	CLONAL	1	TRUE	1	0.2	2		765	795	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395686	45395686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200841904	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	34	414	1	ENST00000262160.6:c.448G>A	p.Glu150Lys	p.E150K	ENST00000262160	NM_005901.5	150	Gaa/Aaa	4/11	1	2	FACETS	0.66	0.539	0.797	0.66	0.539	0.797	SUBCLONAL	1	TRUE	1	0.2	2		415	515	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45423021	45423021	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	29	409	0	ENST00000262160.6:c.107A>G	p.Gln36Arg	p.Q36R	ENST00000262160	NM_005901.5	36	cAg/cGg	2/11	1	2	FACETS	0.55	0.441	0.676	0.55	0.441	0.676	SUBCLONAL	1	TRUE	1	0.2	2		409	527	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390363	56390363	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs902013273	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	39	399	0	ENST00000348428.3:c.1102G>A	p.Glu368Lys	p.E368K	ENST00000348428	NM_006785.3	368	Gaa/Aaa	10/17	1	2	FACETS	0.973	0.807	1	0.973	0.807	1	CLONAL	1	TRUE	1	0.2	2		399	401	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60795959	60795959	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748122615	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	48	573	2	ENST00000333681.4:c.619C>T	p.Arg207Trp	p.R207W	ENST00000333681		207	Cgg/Tgg	3/3	1	2	FACETS	0.563	0.474	0.661	0.563	0.474	0.661	SUBCLONAL	1	TRUE	1	0.2	2		575	853	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220701	1220701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	100	819	4	ENST00000326873.7:c.719C>T	p.Ser240Leu	p.S240L	ENST00000326873	NM_000455.4	240	tCg/tTg	5/10	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.2	2		823	924	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632108	1632108	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	76	858	0	ENST00000344749.5:c.227G>T	p.Ser76Ile	p.S76I	ENST00000344749	NM_001136139.2	76	aGc/aTc	5/19	1	2	FACETS	0.878	0.768	0.996	0.878	0.768	0.996	CLONAL	1	TRUE	1	0.2	2		858	866	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210773	2210773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745490701	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	76	720	2	ENST00000398665.3:c.1270C>T	p.Arg424Trp	p.R424W	ENST00000398665	NM_032482.2	424	Cgg/Tgg	14/28	1	2	FACETS	0.844	0.739	0.958	0.844	0.739	0.958	CLONAL	1	TRUE	1	0.2	2		722	900	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216388	2216388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753135719	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	65	898	0	ENST00000398665.3:c.2032G>A	p.Ala678Thr	p.A678T	ENST00000398665	NM_032482.2	678	Gcc/Acc	20/28	1	2	FACETS	0.758	0.656	0.87	0.758	0.656	0.87	SUBCLONAL	1	TRUE	1	0.2	2		898	857	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226316	2226316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376487667	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	74	980	1	ENST00000398665.3:c.3796G>A	p.Ala1266Thr	p.A1266T	ENST00000398665	NM_032482.2	1266	Gcc/Acc	27/28	1	2	FACETS	0.675	0.589	0.769	0.675	0.589	0.769	SUBCLONAL	1	TRUE	1	0.2	2		981	1096	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115036	3115036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1317391449	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	101	964	0	ENST00000078429.4:c.571G>A	p.Glu191Lys	p.E191K	ENST00000078429	NM_002067.2	191	Gag/Aag	4/7	1	2	FACETS	0.885	0.789	0.988	0.885	0.789	0.988	CLONAL	1	TRUE	1	0.2	2		964	1141	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215422	5215422	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	61	668	0	ENST00000357368.4:c.4196C>T	p.Ser1399Phe	p.S1399F	ENST00000357368	NM_002850.3	1399	tCc/tTc	28/38	1	2	FACETS	0.806	0.694	0.928	0.806	0.694	0.928	CLONAL	1	TRUE	1	0.2	2		668	757	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231588	5231588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772048652	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	53	379	0	ENST00000357368.4:c.1888G>A	p.Val630Met	p.V630M	ENST00000357368	NM_002850.3	630	Gtg/Atg	14/38	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.2	2		379	522	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5239059	5239059	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768636218	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	139	764	0	ENST00000357368.4:c.1720G>A	p.Asp574Asn	p.D574N	ENST00000357368	NM_002850.3	574	Gac/Aac	13/38	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.2	2		764	1099	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265024	5265024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1054150595	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	60	684	0	ENST00000357368.4:c.563G>A	p.Arg188Gln	p.R188Q	ENST00000357368	NM_002850.3	188	cGa/cAa	5/38	1	2	FACETS	0.73	0.627	0.842	0.73	0.627	0.842	SUBCLONAL	1	TRUE	1	0.2	2		684	822	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117159	7117159	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs74495977	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	64	805	0	ENST00000302850.5:c.4057C>T	p.Arg1353Trp	p.R1353W	ENST00000302850	NM_000208.2	1353	Cgg/Tgg	22/22	1	2	FACETS	0.69	0.596	0.793	0.69	0.596	0.793	SUBCLONAL	1	TRUE	1	0.2	2		805	927	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7163154	7163154	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	83	782	0	ENST00000302850.5:c.1918C>A	p.Leu640Met	p.L640M	ENST00000302850	NM_000208.2	640	Ctg/Atg	9/22	1	2	FACETS	0.741	0.652	0.837	0.741	0.652	0.837	SUBCLONAL	1	TRUE	1	0.2	2		782	1120	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10244971	10244971	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	49	671	1	ENST00000340748.4:c.4738G>A	p.Val1580Met	p.V1580M	ENST00000340748		1580	Gtg/Atg	39/40	1	2	FACETS	0.674	0.569	0.789	0.674	0.569	0.789	SUBCLONAL	1	TRUE	1	0.2	2		672	727	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10286250	10286250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781646588	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	64	742	0	ENST00000340748.4:c.566C>T	p.Ser189Leu	p.S189L	ENST00000340748		189	tCg/tTg	6/40	1	2	FACETS	0.632	0.546	0.727	0.632	0.546	0.727	SUBCLONAL	1	TRUE	1	0.2	2		742	1012	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100004	11100004	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555756272	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	68	761	1	ENST00000358026.2:c.1130G>A	p.Arg377His	p.R377H	ENST00000358026	NM_001128849.1	377	cGc/cAc	7/36	1	2	FACETS	0.769	0.668	0.88	0.769	0.668	0.88	SUBCLONAL	1	TRUE	1	0.2	2		762	884	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169474	11169474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555795341	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	93	784	0	ENST00000358026.2:c.4640G>A	p.Arg1547His	p.R1547H	ENST00000358026	NM_001128849.1	1547	cGc/cAc	33/36	1	2	FACETS	0.997	0.885	1	0.997	0.885	1	CLONAL	1	TRUE	1	0.2	2		784	933	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170837	11170837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374648988	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	77	750	0	ENST00000358026.2:c.4981G>A	p.Asp1661Asn	p.D1661N	ENST00000358026	NM_001128849.1	1661	Gat/Aat	35/36	1	2	FACETS	0.856	0.75	0.97	0.856	0.75	0.97	CLONAL	1	TRUE	1	0.2	2		750	900	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054535	13054535	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	48	441	0	ENST00000316448.5:c.1062G>T	p.Glu354Asp	p.E354D	ENST00000316448	NM_004343.3	354	gaG/gaT	9/9	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.2	2		441	433	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626895	14626895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143320658	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	91	833	0	ENST00000254322.2:c.880C>T	p.Arg294Trp	p.R294W	ENST00000254322	NM_006145.1	294	Cgg/Tgg	3/3	1	2	FACETS	0.944	0.836	1	0.944	0.836	1	CLONAL	1	TRUE	1	0.2	2		833	964	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271769	15271769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	80	1116	0	ENST00000263388.2:c.6670G>A	p.Ala2224Thr	p.A2224T	ENST00000263388	NM_000435.2	2224	Gct/Act	33/33	1	2	FACETS	0.745	0.654	0.843	0.745	0.654	0.843	SUBCLONAL	1	TRUE	1	0.2	2		1116	1074	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276764	15276764	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202027632	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	92	888	1	ENST00000263388.2:c.5501G>A	p.Arg1834Gln	p.R1834Q	ENST00000263388	NM_000435.2	1834	cGg/cAg	30/33	1	2	FACETS	0.833	0.738	0.935	0.833	0.738	0.935	CLONAL	1	TRUE	1	0.2	2		889	1104	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296403	15296403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs10406745	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	86	990	3	ENST00000263388.2:c.2039G>A	p.Arg680His	p.R680H	ENST00000263388	NM_000435.2	680	cGc/cAc	13/33	1	2	FACETS	0.708	0.624	0.799	0.708	0.624	0.799	SUBCLONAL	1	TRUE	1	0.2	2		993	1214	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367867	15367867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1454979767	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	92	912	1	ENST00000263377.2:c.1459G>A	p.Asp487Asn	p.D487N	ENST00000263377	NM_058243.2	487	Gac/Aac	8/20	1	2	FACETS	0.84	0.744	0.943	0.84	0.744	0.943	CLONAL	1	TRUE	1	0.2	2		913	1095	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15379843	15379843	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	31	367	0	ENST00000263377.2:c.296A>C	p.Lys99Thr	p.K99T	ENST00000263377	NM_058243.2	99	aAg/aCg	3/20	1	2	FACETS	0.812	0.657	0.987	0.812	0.657	0.987	CLONAL	1	TRUE	1	0.2	2		367	382	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945726	17945726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178958564	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	106	958	0	ENST00000458235.1:c.2134G>A	p.Gly712Ser	p.G712S	ENST00000458235	NM_000215.3	712	Ggc/Agc	16/24	1	2	FACETS	0.975	0.872	1	0.975	0.872	1	CLONAL	1	TRUE	1	0.2	2		958	1087	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946851	17946851	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	151	691	0	ENST00000458235.1:c.1796T>C	p.Val599Ala	p.V599A	ENST00000458235	NM_000215.3	599	gTg/gCg	14/24	1	2	FACETS	0.941	0.861	1	1	0.991	1	CLONAL	2	TRUE	1	0.2	2		691	802	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948867	17948867	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	141	746	0	ENST00000458235.1:c.1575G>T	p.Glu525Asp	p.E525D	ENST00000458235	NM_000215.3	525	gaG/gaT	12/24	1	2	FACETS	0.882	0.804	0.964	1	0.989	1	CLONAL	2	TRUE	1	0.2	2		746	799	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273915	18273915	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	59	781	0	ENST00000222254.8:c.1248G>T	p.Lys416Asn	p.K416N	ENST00000222254	NM_005027.3	416	aaG/aaT	10/16	1	2	FACETS	0.664	0.569	0.767	0.664	0.569	0.767	SUBCLONAL	1	TRUE	1	0.2	2		781	889	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279935	18279935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	89	785	2	ENST00000222254.8:c.2018C>T	p.Thr673Met	p.T673M	ENST00000222254	NM_005027.3	673	aCg/aTg	16/16	1	2	FACETS	0.83	0.734	0.934	0.83	0.734	0.934	CLONAL	1	TRUE	1	0.2	2		787	1072	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976372	18976372	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	112	955	0	ENST00000262803.5:c.3022C>T	p.Arg1008Ter	p.R1008*	ENST00000262803	NM_002911.3	1008	Cga/Tga	22/24	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.2	2		955	1032	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258640	19258640	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs533071900	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	54	680	0	ENST00000162023.5:c.260C>T	p.Thr87Met	p.T87M	ENST00000162023		87	aCg/aTg	8/13	1	2	FACETS	0.799	0.681	0.928	0.799	0.681	0.928	CLONAL	1	TRUE	1	0.2	2		680	676	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260102	19260102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371035718	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	63	942	3	ENST00000162023.5:c.191G>A	p.Arg64His	p.R64H	ENST00000162023		64	cGt/cAt	7/13	1	2	FACETS	0.525	0.452	0.604	0.525	0.452	0.604	SUBCLONAL	1	TRUE	1	0.2	2		945	1201	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210808	36210808	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	95	1045	1	ENST00000222270.7:c.559G>T	p.Glu187Ter	p.E187*	ENST00000222270	NM_014727.1	187	Gaa/Taa	3/37	1	2	FACETS	0.81	0.719	0.907	0.81	0.719	0.907	CLONAL	1	TRUE	1	0.2	2		1046	1173	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227815	36227815	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	82	962	0	ENST00000222270.7:c.7300G>A	p.Ala2434Thr	p.A2434T	ENST00000222270	NM_014727.1	2434	Gcg/Acg	32/37	1	2	FACETS	0.777	0.683	0.879	0.777	0.683	0.879	SUBCLONAL	1	TRUE	1	0.2	2		962	1055	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726544	41726544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs891614619	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	64	636	0	ENST00000301178.4:c.89C>T	p.Thr30Met	p.T30M	ENST00000301178	NM_021913.4	30	aCg/aTg	2/20	1	2	FACETS	0.951	0.823	1	0.951	0.823	1	CLONAL	1	TRUE	1	0.2	2		636	673	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752675	42752675	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	52	785	0	ENST00000222329.4:c.1589T>C	p.Val530Ala	p.V530A	ENST00000222329	NM_006494.2	530	gTg/gCg	4/4	1	2	FACETS	0.638	0.542	0.744	0.638	0.542	0.744	SUBCLONAL	1	TRUE	1	0.2	2		785	815	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752763	42752763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760204780	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	90	981	1	ENST00000222329.4:c.1501G>A	p.Ala501Thr	p.A501T	ENST00000222329	NM_006494.2	501	Gct/Act	4/4	1	2	FACETS	0.886	0.784	0.995	0.886	0.784	0.995	CLONAL	1	TRUE	1	0.2	2		982	1016	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793336	42793336	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	52	832	0	ENST00000575354.2:c.1138G>A	p.Val380Met	p.V380M	ENST00000575354	NM_015125.3	380	Gtg/Atg	8/20	1	2	FACETS	0.635	0.539	0.741	0.635	0.539	0.741	SUBCLONAL	1	TRUE	1	0.2	2		832	819	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795241	42795241	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs574832764	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	67	941	0	ENST00000575354.2:c.2321C>T	p.Ala774Val	p.A774V	ENST00000575354	NM_015125.3	774	gCg/gTg	10/20	1	2	FACETS	0.813	0.705	0.93	0.813	0.705	0.93	CLONAL	1	TRUE	1	0.2	2		941	824	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795423	42795423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	59	769	0	ENST00000575354.2:c.2503C>T	p.Gln835Ter	p.Q835*	ENST00000575354	NM_015125.3	835	Cag/Tag	10/20	1	2	FACETS	0.915	0.786	1	0.915	0.786	1	CLONAL	1	TRUE	1	0.2	2		769	645	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45864811	45864811	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	117	1098	0	ENST00000391945.4:c.1208T>G	p.Phe403Cys	p.F403C	ENST00000391945	NM_000400.3	403	tTt/tGt	12/23	1	2	FACETS	0.916	0.824	1	0.916	0.824	1	CLONAL	1	TRUE	1	0.2	2		1098	1277	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909674	50909674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199700312	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	108	938	0	ENST00000440232.2:c.1394G>A	p.Arg465Gln	p.R465Q	ENST00000440232	NM_002691.3	465	cGg/cAg	12/27	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.2	2		938	1072	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918795	50918795	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777468034	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	81	939	1	ENST00000440232.2:c.2665C>T	p.Arg889Cys	p.R889C	ENST00000440232	NM_002691.3	889	Cgc/Tgc	21/27	1	2	FACETS	0.774	0.68	0.875	0.774	0.68	0.875	SUBCLONAL	1	TRUE	1	0.2	2		940	1047	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705255	52705255	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	81	645	0	ENST00000322088.6:c.137G>T	p.Arg46Met	p.R46M	ENST00000322088	NM_014225.5	46	aGg/aTg	2/15	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.2	2		645	798	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466773	25466773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1431156021	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	68	616	0	ENST00000264709.3:c.1930G>A	p.Ala644Thr	p.A644T	ENST00000264709	NM_175629.2	644	Gct/Act	16/23	1	2	FACETS	0.855	0.743	0.977	0.855	0.743	0.977	CLONAL	1	TRUE	1	0.2	2		616	795	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467047	25467047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	78	789	1	ENST00000264709.3:c.1828G>A	p.Ala610Thr	p.A610T	ENST00000264709	NM_175629.2	610	Gct/Act	15/23	1	2	FACETS	0.876	0.769	0.993	0.876	0.769	0.993	CLONAL	1	TRUE	1	0.2	2		790	890	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015097	27015097	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	37	487	0	ENST00000335756.4:c.199T>G	p.Phe67Val	p.F67V	ENST00000335756	NM_001809.3	67	Ttc/Gtc	2/5	1	2	FACETS	0.545	0.448	0.654	0.545	0.448	0.654	SUBCLONAL	1	TRUE	1	0.2	2		487	679	SUCCESS
ALK	238	MSKCC	GRCh37	2	29420510	29420510	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758127441	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	57	463	0	ENST00000389048.3:c.3971C>T	p.Ser1324Phe	p.S1324F	ENST00000389048	NM_004304.4	1324	tCt/tTt	27/29	1	2	FACETS	0.886	0.76	1	0.886	0.76	1	CLONAL	1	TRUE	1	0.2	2		463	643	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498318	29498318	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	79	611	0	ENST00000389048.3:c.1862C>T	p.Ala621Val	p.A621V	ENST00000389048	NM_004304.4	621	gCc/gTc	10/29	1	2	FACETS	0.986	0.866	1	0.986	0.866	1	CLONAL	1	TRUE	1	0.2	2		611	801	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607453	46607453	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150597114	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	72	1054	0	ENST00000263734.3:c.1642G>A	p.Glu548Lys	p.E548K	ENST00000263734	NM_001430.4	548	Gag/Aag	12/16	1	2	FACETS	0.62	0.54	0.707	0.62	0.54	0.707	SUBCLONAL	1	TRUE	1	0.2	2		1054	1161	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657021	47657021	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146567853	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	33	369	0	ENST00000233146.2:c.1217G>A	p.Arg406Gln	p.R406Q	ENST00000233146	NM_000251.2	406	cGa/cAa	7/16	1	2	FACETS	0.769	0.626	0.93	0.769	0.626	0.93	CLONAL	1	TRUE	1	0.2	2		369	429	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47709939	47709939	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1230083633	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	23	356	0	ENST00000233146.2:c.2656G>A	p.Glu886Lys	p.E886K	ENST00000233146	NM_000251.2	886	Gag/Aag	16/16	1	2	FACETS	0.568	0.442	0.714	0.568	0.442	0.714	SUBCLONAL	1	TRUE	1	0.2	2		356	405	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026606	48026606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1358771617	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	34	489	0	ENST00000234420.5:c.1484G>A	p.Arg495Gln	p.R495Q	ENST00000234420	NM_000179.2	495	cGa/cAa	4/10	1	2	FACETS	0.778	0.636	0.938	0.778	0.636	0.938	CLONAL	1	TRUE	1	0.2	2		489	437	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032168	48032169	+	splice_donor_variant,intron_variant	Splice_Site	DNP	TG	TG	CA	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	51	294	0	ENST00000234420.5:c.3556+2_3556+3inv		p.X1186_splice	ENST00000234420	NM_000179.2	1186			1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.2	2		294	429	SUCCESS
REL	5966	MSKCC	GRCh37	2	61128147	61128147	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1016724251	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	38	294	0	ENST00000295025.8:c.323G>A	p.Arg108Gln	p.R108Q	ENST00000295025	NM_002908.2	108	cGa/cAa	4/11	1	2	FACETS	0.792	0.654	0.945	0.792	0.654	0.945	CLONAL	1	TRUE	1	0.2	2		294	480	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919611	96919611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746291260	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	60	626	0	ENST00000258439.3:c.652G>A	p.Glu218Lys	p.E218K	ENST00000258439	NM_001193304.2	218	Gag/Aag	4/4	1	2	FACETS	0.87	0.748	1	0.87	0.748	1	CLONAL	1	TRUE	1	0.2	2		626	690	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99163079	99163079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1403218618	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	63	572	0	ENST00000074304.5:c.1085C>T	p.Ala362Val	p.A362V	ENST00000074304	NM_001134224.1	362	gCg/gTg	13/26	1	2	FACETS	0.831	0.718	0.955	0.831	0.718	0.955	CLONAL	1	TRUE	1	0.2	2		572	758	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872492	136872492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	25	365	0	ENST00000241393.3:c.1006G>A	p.Gly336Arg	p.G336R	ENST00000241393	NM_003467.2	336	Gga/Aga	2/2	1	2	FACETS	0.551	0.433	0.686	0.551	0.433	0.686	SUBCLONAL	1	TRUE	1	0.2	2		365	454	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634767	158634767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	36	423	1	ENST00000263640.3:c.419G>A	p.Cys140Tyr	p.C140Y	ENST00000263640	NM_001105.4	140	tGc/tAc	5/11	1	2	FACETS	0.651	0.534	0.782	0.651	0.534	0.782	SUBCLONAL	1	TRUE	1	0.2	2		424	553	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096649	178096649	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	26	312	0	ENST00000397062.3:c.682T>G	p.Phe228Val	p.F228V	ENST00000397062	NM_006164.4	228	Ttt/Gtt	5/5	1	2	FACETS	0.708	0.561	0.877	0.708	0.561	0.877	SUBCLONAL	1	TRUE	1	0.2	2		312	367	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719032	190719032	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	44	257	0	ENST00000441310.2:c.1034C>A	p.Ser345Tyr	p.S345Y	ENST00000441310	NM_000534.4	345	tCt/tAt	9/13	1	2	FACETS	0.884	0.747	1	1	0.968	1	CLONAL	2	TRUE	1	0.2	2		257	249	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257714	198257714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	29	336	0	ENST00000335508.6:c.3738G>A	p.Met1246Ile	p.M1246I	ENST00000335508	NM_012433.2	1246	atG/atA	24/25	1	2	FACETS	0.788	0.633	0.964	0.788	0.633	0.964	CLONAL	1	TRUE	1	0.2	2		336	368	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274548	198274548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778869024	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	65	653	1	ENST00000335508.6:c.850G>A	p.Ala284Thr	p.A284T	ENST00000335508	NM_012433.2	284	Gca/Aca	7/25	1	2	FACETS	0.763	0.66	0.875	0.763	0.66	0.875	SUBCLONAL	1	TRUE	1	0.2	2		654	852	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198283309	198283309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	26	471	0	ENST00000335508.6:c.419G>A	p.Gly140Glu	p.G140E	ENST00000335508	NM_012433.2	140	gGg/gAg	5/25	1	2	FACETS	0.564	0.446	0.7	0.564	0.446	0.7	SUBCLONAL	1	TRUE	1	0.2	2		471	461	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131412	202131412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339962485	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	61	587	0	ENST00000358485.4:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000358485	NM_001080125.1	127	cGa/cAa	2/9	1	2	FACETS	0.949	0.818	1	0.949	0.818	1	CLONAL	1	TRUE	1	0.2	2		587	643	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136279	202136279	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	58	549	0	ENST00000358485.4:c.523G>T	p.Glu175Ter	p.E175*	ENST00000358485	NM_001080125.1	175	Gaa/Taa	3/9	1	2	FACETS	0.863	0.741	0.997	0.863	0.741	0.997	CLONAL	1	TRUE	1	0.2	2		549	672	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735643	204735643	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	25	471	0	ENST00000302823.3:c.444G>T	p.Gln148His	p.Q148H	ENST00000302823	NM_005214.4	148	caG/caT	2/4	1	2	FACETS	0.546	0.429	0.68	0.546	0.429	0.68	SUBCLONAL	1	TRUE	1	0.2	2		471	458	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293194	212293194	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	34	391	0	ENST00000342788.4:c.2658G>T	p.Trp886Cys	p.W886C	ENST00000342788	NM_005235.2	886	tgG/tgT	22/28	1	2	FACETS	0.8	0.654	0.965	0.8	0.654	0.965	CLONAL	1	TRUE	1	0.2	2		391	425	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295729	212295729	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	77	635	0	ENST00000342788.4:c.2584T>G	p.Phe862Val	p.F862V	ENST00000342788	NM_005235.2	862	Ttt/Gtt	21/28	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.2	2		635	688	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543828	212543828	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371593463	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	85	402	1	ENST00000342788.4:c.1571G>A	p.Arg524His	p.R524H	ENST00000342788	NM_005235.2	524	cGc/cAc	13/28	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.2	2		403	827	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215617226	215617226	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777937955	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	19	348	0	ENST00000260947.4:c.1622C>T	p.Ser541Leu	p.S541L	ENST00000260947	NM_000465.2	541	tCg/tTg	7/11	1	2	FACETS	0.635	0.482	0.816	0.635	0.482	0.816	SUBCLONAL	1	TRUE	1	0.2	2		348	299	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645592	215645592	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs752869298	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	46	726	0	ENST00000260947.4:c.1006T>C	p.Cys336Arg	p.C336R	ENST00000260947	NM_000465.2	336	Tgt/Cgt	4/11	1	2	FACETS	0.629	0.529	0.741	0.629	0.529	0.741	SUBCLONAL	1	TRUE	1	0.2	2		726	731	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437265	220437265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1224525818	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	102	1118	1	ENST00000243786.2:c.169C>T	p.Arg57Trp	p.R57W	ENST00000243786	NM_002191.3	57	Cgg/Tgg	1/2	1	2	FACETS	0.873	0.779	0.974	0.873	0.779	0.974	CLONAL	1	TRUE	1	0.2	2		1119	1168	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437275	220437275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370513243	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	101	1115	1	ENST00000243786.2:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000243786	NM_002191.3	60	cGa/cAa	1/2	1	2	FACETS	0.831	0.741	0.928	0.831	0.741	0.928	CLONAL	1	TRUE	1	0.2	2		1116	1215	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422458	225422458	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	35	483	2	ENST00000264414.4:c.182C>T	p.Ala61Val	p.A61V	ENST00000264414	NM_003590.4	61	gCa/gTa	2/16	1	2	FACETS	0.676	0.553	0.814	0.676	0.553	0.814	SUBCLONAL	1	TRUE	1	0.2	2		485	518	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661564	227661564	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	48	849	0	ENST00000305123.5:c.1891G>T	p.Asp631Tyr	p.D631Y	ENST00000305123	NM_005544.2	631	Gac/Tac	1/2	1	2	FACETS	0.626	0.528	0.735	0.626	0.528	0.735	SUBCLONAL	1	TRUE	1	0.2	2		849	767	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662349	227662349	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1295685737	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	51	742	0	ENST00000305123.5:c.1106T>C	p.Leu369Pro	p.L369P	ENST00000305123	NM_005544.2	369	cTc/cCc	1/2	1	2	FACETS	0.684	0.58	0.798	0.684	0.58	0.798	SUBCLONAL	1	TRUE	1	0.2	2		742	746	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662792	227662792	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	111	834	0	ENST00000305123.5:c.663C>A	p.Phe221Leu	p.F221L	ENST00000305123	NM_005544.2	221	ttC/ttA	1/2	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.2	2		834	1009	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561352	9561352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773981325	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	33	543	0	ENST00000353224.5:c.430G>A	p.Glu144Lys	p.E144K	ENST00000353224	NM_177990.2	144	Gaa/Aaa	4/10	1	2	FACETS	0.527	0.428	0.639	0.527	0.428	0.639	SUBCLONAL	1	TRUE	1	0.2	2		543	626	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31372582	31372582	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751017290	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	57	735	0	ENST00000328111.2:c.223G>A	p.Asp75Asn	p.D75N	ENST00000328111	NM_006892.3	75	Gac/Aac	4/23	1	2	FACETS	0.706	0.605	0.818	0.706	0.605	0.818	SUBCLONAL	1	TRUE	1	0.2	2		735	807	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386409	31386409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572676072	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	77	725	0	ENST00000328111.2:c.1634G>A	p.Arg545His	p.R545H	ENST00000328111	NM_006892.3	545	cGc/cAc	15/23	1	2	FACETS	0.817	0.716	0.927	0.817	0.716	0.927	CLONAL	1	TRUE	1	0.2	2		725	942	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728762	39728762	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	50	490	0	ENST00000361337.2:c.1042G>T	p.Glu348Ter	p.E348*	ENST00000361337	NM_003286.2	348	Gag/Tag	12/21	1	2	FACETS	0.943	0.8	1	0.943	0.8	1	CLONAL	1	TRUE	1	0.2	2		490	530	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741455	39741455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	47	484	0	ENST00000361337.2:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000361337	NM_003286.2	448	Cgg/Tgg	14/21	1	2	FACETS	0.721	0.607	0.847	0.721	0.607	0.847	SUBCLONAL	1	TRUE	1	0.2	2		484	652	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757416	40757416	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	98	659	0	ENST00000373198.4:c.2882A>G	p.Tyr961Cys	p.Y961C	ENST00000373198	NM_133170.3	961	tAc/tGc	20/32	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.2	2		659	942	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944419	40944419	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	57	584	0	ENST00000373198.4:c.2083C>A	p.Leu695Ile	p.L695I	ENST00000373198	NM_133170.3	695	Ctc/Atc	12/32	1	2	FACETS	0.774	0.663	0.896	0.774	0.663	0.896	SUBCLONAL	1	TRUE	1	0.2	2		584	736	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46255889	46255889	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	22	349	0	ENST00000371998.3:c.501G>T	p.Lys167Asn	p.K167N	ENST00000371998		167	aaG/aaT	6/23	1	2	FACETS	0.701	0.543	0.883	0.701	0.543	0.883	SUBCLONAL	1	TRUE	1	0.2	2		349	314	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268333	46268333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747268479	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	44	472	0	ENST00000371998.3:c.2720G>A	p.Arg907Gln	p.R907Q	ENST00000371998		907	cGa/cAa	15/23	1	2	FACETS	0.776	0.65	0.916	0.776	0.65	0.916	CLONAL	1	TRUE	1	0.2	2		472	567	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484414	57484414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	72	565	0	ENST00000371085.3:c.595C>T	p.Arg199Cys	p.R199C	ENST00000371085	NM_000516.4	199	Cgc/Tgc	8/13	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.2	2		565	675	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485873	57485873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397514456	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	55	430	0	ENST00000371085.3:c.1174G>A	p.Glu392Lys	p.E392K	ENST00000371085	NM_000516.4	392	Gag/Aag	13/13	1	2	FACETS	0.927	0.793	1	0.927	0.793	1	CLONAL	1	TRUE	1	0.2	2		430	593	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319038	62319038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219409480	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	124	1021	1	ENST00000360203.5:c.1396G>A	p.Glu466Lys	p.E466K	ENST00000360203	NM_001283009.1	466	Gag/Aag	17/35	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.2	2		1022	1165	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324513	62324513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123018	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	121	999	2	ENST00000360203.5:c.2869C>T	p.Arg957Trp	p.R957W	ENST00000360203	NM_001283009.1	957	Cgg/Tgg	30/35	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.2	2		1001	1137	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326704	62326704	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	92	1181	1	ENST00000360203.5:c.3523G>T	p.Gly1175Trp	p.G1175W	ENST00000360203	NM_001283009.1	1175	Ggg/Tgg	34/35	1	2	FACETS	0.794	0.704	0.892	0.794	0.704	0.892	SUBCLONAL	1	TRUE	1	0.2	2		1182	1158	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143232	24143232	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	71	854	0	ENST00000263121.7:c.464G>A	p.Arg155His	p.R155H	ENST00000263121	NM_003073.3	155	cGc/cAc	4/9	1	2	FACETS	0.691	0.601	0.789	0.691	0.601	0.789	SUBCLONAL	1	TRUE	1	0.2	2		854	1027	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167489	24167489	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	100	833	0	ENST00000263121.7:c.873G>T	p.Glu291Asp	p.E291D	ENST00000263121	NM_003073.3	291	gaG/gaT	7/9	1	2	FACETS	0.973	0.867	1	0.973	0.867	1	CLONAL	1	TRUE	1	0.2	2		833	1028	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29106023	29106023	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587782152	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	27	355	0	ENST00000328354.6:c.817G>T	p.Glu273Ter	p.E273*	ENST00000328354	NM_007194.3	273	Gaa/Taa	7/15	1	2	FACETS	0.56	0.445	0.693	0.56	0.445	0.693	SUBCLONAL	1	TRUE	1	0.2	2		355	482	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051621	30051621	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	27	453	0	ENST00000338641.4:c.555G>T	p.Glu185Asp	p.E185D	ENST00000338641	NM_000268.3	185	gaG/gaT	6/16	1	2	FACETS	0.504	0.4	0.623	0.504	0.4	0.623	SUBCLONAL	1	TRUE	1	0.2	2		453	536	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523507	41523507	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778261	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	49	550	0	ENST00000263253.7:c.923C>T	p.Pro308Leu	p.P308L	ENST00000263253	NM_001429.3	308	cCg/cTg	4/31	1	2	FACETS	0.845	0.715	0.988	0.845	0.715	0.988	CLONAL	1	TRUE	1	0.2	2		550	580	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545781	41545781	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	51	637	0	ENST00000263253.7:c.2396C>A	p.Ser799Tyr	p.S799Y	ENST00000263253	NM_001429.3	799	tCt/tAt	14/31	1	2	FACETS	0.661	0.56	0.772	0.661	0.56	0.772	SUBCLONAL	1	TRUE	1	0.2	2		637	772	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548259	41548259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	28	385	0	ENST00000263253.7:c.3047G>A	p.Ser1016Asn	p.S1016N	ENST00000263253	NM_001429.3	1016	aGc/aAc	16/31	1	2	FACETS	0.538	0.429	0.663	0.538	0.429	0.663	SUBCLONAL	1	TRUE	1	0.2	2		385	520	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566561	41566561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753948138	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	33	376	0	ENST00000263253.7:c.4438G>A	p.Val1480Ile	p.V1480I	ENST00000263253	NM_001429.3	1480	Gtc/Atc	27/31	1	2	FACETS	0.642	0.522	0.778	0.642	0.522	0.778	SUBCLONAL	1	TRUE	1	0.2	2		376	514	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447395	12447395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	55	574	0	ENST00000287820.6:c.634C>T	p.Arg212Trp	p.R212W	ENST00000287820	NM_015869.4	212	Cgg/Tgg	5/7	1	2	FACETS	0.744	0.635	0.864	0.744	0.635	0.864	SUBCLONAL	1	TRUE	1	0.2	2		574	739	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729875	30729875	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1553631693	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	33	370	1	ENST00000295754.5:c.1397-1G>A		p.X466_splice	ENST00000295754	NM_003242.5	466			1	2	FACETS	0.771	0.628	0.932	0.771	0.628	0.932	CLONAL	1	TRUE	1	0.2	2		371	428	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275291	41275291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750554859	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	52	492	0	ENST00000349496.5:c.1457G>A	p.Arg486His	p.R486H	ENST00000349496	NM_001904.3	486	cGc/cAc	9/15	1	2	FACETS	0.875	0.745	1	0.875	0.745	1	CLONAL	1	TRUE	1	0.2	2		492	594	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275649	41275649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	49	476	0	ENST00000349496.5:c.1544G>A	p.Arg515Gln	p.R515Q	ENST00000349496	NM_001904.3	515	cGa/cAa	10/15	1	2	FACETS	0.777	0.657	0.909	0.777	0.657	0.909	CLONAL	1	TRUE	1	0.2	2		476	631	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278087	41278087	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	46	415	0	ENST00000349496.5:c.1963G>A	p.Ala655Thr	p.A655T	ENST00000349496	NM_001904.3	655	Gca/Aca	13/15	1	2	FACETS	0.964	0.813	1	0.964	0.813	1	CLONAL	1	TRUE	1	0.2	2		415	477	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47061275	47061275	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	51	488	0	ENST00000409792.3:c.7406A>G	p.Lys2469Arg	p.K2469R	ENST00000409792	NM_014159.6	2469	aAa/aGa	19/21	1	2	FACETS	0.77	0.654	0.899	0.77	0.654	0.899	SUBCLONAL	1	TRUE	1	0.2	2		488	662	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163758	47163758	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	26	478	0	ENST00000409792.3:c.2368G>T	p.Asp790Tyr	p.D790Y	ENST00000409792	NM_014159.6	790	Gat/Tat	3/21	1	2	FACETS	0.55	0.434	0.682	0.55	0.434	0.682	SUBCLONAL	1	TRUE	1	0.2	2		478	473	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164477	47164477	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1445389349	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	35	431	0	ENST00000409792.3:c.1649G>A	p.Ser550Asn	p.S550N	ENST00000409792	NM_014159.6	550	aGt/aAt	3/21	1	2	FACETS	0.862	0.707	1	0.862	0.707	1	CLONAL	1	TRUE	1	0.2	2		431	406	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49929190	49929190	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs55856544	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	102	776	0	ENST00000296474.3:c.3352+1G>A		p.X1118_splice	ENST00000296474	NM_002447.2	1118			1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.2	2		776	978	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934723	49934723	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	76	733	0	ENST00000296474.3:c.2173C>A	p.Leu725Met	p.L725M	ENST00000296474	NM_002447.2	725	Ctg/Atg	7/20	1	2	FACETS	0.886	0.776	1	0.886	0.776	1	CLONAL	1	TRUE	1	0.2	2		733	858	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940814	49940814	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756348422	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	90	821	0	ENST00000296474.3:c.229C>T	p.Arg77Cys	p.R77C	ENST00000296474	NM_002447.2	77	Cgc/Tgc	1/20	1	2	FACETS	0.93	0.823	1	0.93	0.823	1	CLONAL	1	TRUE	1	0.2	2		821	968	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651490	52651490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	57	570	1	ENST00000394830.3:c.1606C>T	p.Pro536Ser	p.P536S	ENST00000394830	NM_018313.4	536	Cca/Tca	15/30	1	2	FACETS	0.888	0.761	1	0.888	0.761	1	CLONAL	1	TRUE	1	0.2	2		571	642	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52677265	52677265	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs374515597	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	66	561	0	ENST00000394830.3:c.994C>T	p.Arg332Cys	p.R332C	ENST00000394830	NM_018313.4	332	Cgt/Tgt	10/30	1	2	FACETS	0.842	0.729	0.964	0.842	0.729	0.964	CLONAL	1	TRUE	1	0.2	2		561	784	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021818	71021818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869025203	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	15	235	1	ENST00000318789.4:c.1540C>T	p.Arg514Cys	p.R514C	ENST00000318789	NM_032682.5	514	Cgt/Tgt	18/21	1	2	FACETS	0.543	0.397	0.72	0.543	0.397	0.72	SUBCLONAL	1	TRUE	1	0.2	2		236	276	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026184	71026184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	40	329	0	ENST00000318789.4:c.1438G>A	p.Glu480Lys	p.E480K	ENST00000318789	NM_032682.5	480	Gaa/Aaa	17/21	1	2	FACETS	0.821	0.682	0.976	0.821	0.682	0.976	CLONAL	1	TRUE	1	0.2	2		329	487	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799481	72799481	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144498351	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	64	742	1	ENST00000325599.8:c.1688G>A	p.Arg563His	p.R563H	ENST00000325599	NM_018130.2	563	cGc/cAc	11/11	1	2	FACETS	0.699	0.603	0.803	0.699	0.603	0.803	SUBCLONAL	1	TRUE	1	0.2	2		743	916	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89444996	89444996	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	42	476	2	ENST00000336596.2:c.1316C>A	p.Pro439His	p.P439H	ENST00000336596	NM_005233.5	439	cCt/cAt	6/17	1	2	FACETS	0.674	0.562	0.799	0.674	0.562	0.799	SUBCLONAL	1	TRUE	1	0.2	2		478	623	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445111	89445111	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	31	344	0	ENST00000336596.2:c.1431G>T	p.Lys477Asn	p.K477N	ENST00000336596	NM_005233.5	477	aaG/aaT	6/17	1	2	FACETS	0.876	0.709	1	0.876	0.709	1	CLONAL	1	TRUE	1	0.2	2		344	354	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468516	89468516	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1453560937	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	59	347	0	ENST00000336596.2:c.2050C>T	p.Arg684Ter	p.R684*	ENST00000336596	NM_005233.5	684	Cga/Tga	11/17	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.2	2		347	482	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498444	89498444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	33	370	0	ENST00000336596.2:c.2416G>A	p.Asp806Asn	p.D806N	ENST00000336596	NM_005233.5	806	Gat/Aat	14/17	1	2	FACETS	0.745	0.606	0.901	0.745	0.606	0.901	CLONAL	1	TRUE	1	0.2	2		370	443	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204594	128204594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148024280	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	69	829	0	ENST00000341105.2:c.847C>T	p.Arg283Cys	p.R283C	ENST00000341105	NM_032638.4	283	Cgc/Tgc	3/6	1	2	FACETS	0.723	0.627	0.826	0.723	0.627	0.826	SUBCLONAL	1	TRUE	1	0.2	2		829	955	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670340	134670340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415689583	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	42	441	1	ENST00000398015.3:c.251G>A	p.Arg84His	p.R84H	ENST00000398015	NM_004441.4	84	cGc/cAc	3/16	1	2	FACETS	0.759	0.633	0.9	0.759	0.633	0.9	SUBCLONAL	1	TRUE	1	0.2	2		442	553	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670615	134670615	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781004053	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	80	815	0	ENST00000398015.3:c.526G>A	p.Ala176Thr	p.A176T	ENST00000398015	NM_004441.4	176	Gct/Act	3/16	1	2	FACETS	0.76	0.667	0.861	0.76	0.667	0.861	SUBCLONAL	1	TRUE	1	0.2	2		815	1052	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417934	138417934	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1194965901	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	36	360	0	ENST00000289153.2:c.1585C>T	p.Arg529Ter	p.R529*	ENST00000289153	NM_006219.2	529	Cga/Tga	11/22	1	2	FACETS	0.833	0.685	0.999	0.833	0.685	0.999	CLONAL	1	TRUE	1	0.2	2		360	432	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188288	142188288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1470834016	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	36	423	0	ENST00000350721.4:c.6443G>A	p.Arg2148Gln	p.R2148Q	ENST00000350721	NM_001184.3	2148	cGa/cAa	38/47	1	2	FACETS	0.859	0.707	1	0.859	0.707	1	CLONAL	1	TRUE	1	0.2	2		423	419	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188397	142188397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1169255490	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	26	377	0	ENST00000350721.4:c.6334C>T	p.Arg2112Cys	p.R2112C	ENST00000350721	NM_001184.3	2112	Cgt/Tgt	38/47	1	2	FACETS	0.762	0.604	0.944	0.762	0.604	0.944	CLONAL	1	TRUE	1	0.2	2		377	341	SUCCESS
ATR	545	MSKCC	GRCh37	3	142216024	142216024	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	57	384	0	ENST00000350721.4:c.5569T>G	p.Leu1857Val	p.L1857V	ENST00000350721	NM_001184.3	1857	Tta/Gta	33/47	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.2	2		384	409	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226828	142226828	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	41	465	0	ENST00000350721.4:c.4976A>C	p.Glu1659Ala	p.E1659A	ENST00000350721	NM_001184.3	1659	gAa/gCa	28/47	1	2	FACETS	0.787	0.655	0.934	0.787	0.655	0.934	CLONAL	1	TRUE	1	0.2	2		465	521	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281762	142281762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	38	687	0	ENST00000350721.4:c.482G>A	p.Arg161Lys	p.R161K	ENST00000350721	NM_001184.3	161	aGa/aAa	4/47	1	2	FACETS	0.693	0.572	0.829	0.693	0.572	0.829	SUBCLONAL	1	TRUE	1	0.2	2		687	548	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260151	149260151	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1307297959	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	48	584	1	ENST00000360632.3:c.742C>T	p.Arg248Ter	p.R248*	ENST00000360632	NM_015472.4	248	Cga/Tga	4/7	1	2	FACETS	0.839	0.709	0.983	0.839	0.709	0.983	CLONAL	1	TRUE	1	0.2	2		585	572	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170020841	170020841	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	21	266	0	ENST00000295797.4:c.1717A>G	p.Lys573Glu	p.K573E	ENST00000295797	NM_002740.5	573	Aag/Gag	18/18	1	2	FACETS	0.753	0.58	0.953	0.753	0.58	0.953	CLONAL	1	TRUE	1	0.2	2		266	279	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922301	178922301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	65	377	1	ENST00000263967.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000263967	NM_006218.2	357	cGa/cAa	6/21	1	2	FACETS	0.778	0.677	0.886	1	0.974	1	SUBCLONAL	2	TRUE	1	0.2	2		378	418	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951934	178951934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	46	497	0	ENST00000263967.3:c.2989C>T	p.Leu997Phe	p.L997F	ENST00000263967	NM_006218.2	997	Ctc/Ttc	21/21	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.2	2		497	454	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431053	181431053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1226834656	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	47	832	1	ENST00000325404.1:c.905C>T	p.Pro302Leu	p.P302L	ENST00000325404	NM_003106.3	302	cCg/cTg	1/1	1	2	FACETS	0.537	0.451	0.631	0.537	0.451	0.631	SUBCLONAL	1	TRUE	1	0.2	2		833	876	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442763	187442763	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	57	600	0	ENST00000232014.4:c.1943A>G	p.His648Arg	p.H648R	ENST00000232014	NM_001130845.1	648	cAc/cGc	9/10	1	2	FACETS	0.856	0.733	0.99	0.856	0.733	0.99	CLONAL	1	TRUE	1	0.2	2		600	666	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446301	187446301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374228382	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	54	726	0	ENST00000232014.4:c.1387G>A	p.Glu463Lys	p.E463K	ENST00000232014	NM_001130845.1	463	Gag/Aag	6/10	1	2	FACETS	0.703	0.599	0.817	0.703	0.599	0.817	SUBCLONAL	1	TRUE	1	0.2	2		726	768	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446976	187446976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369842677	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	79	882	2	ENST00000232014.4:c.1217G>A	p.Arg406Gln	p.R406Q	ENST00000232014	NM_001130845.1	406	cGa/cAa	5/10	1	2	FACETS	0.818	0.717	0.926	0.818	0.717	0.926	CLONAL	1	TRUE	1	0.2	2		884	966	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447384	187447384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780987785	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	78	724	0	ENST00000232014.4:c.809G>A	p.Arg270Gln	p.R270Q	ENST00000232014	NM_001130845.1	270	cGa/cAa	5/10	1	2	FACETS	0.934	0.82	1	0.934	0.82	1	CLONAL	1	TRUE	1	0.2	2		724	835	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455614	189455614	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	43	558	0	ENST00000264731.3:c.148C>A	p.Leu50Ile	p.L50I	ENST00000264731	NM_003722.4	50	Ctc/Atc	2/14	1	2	FACETS	0.819	0.685	0.968	0.819	0.685	0.968	CLONAL	1	TRUE	1	0.2	2		558	525	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612028	189612028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs900140738	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	54	550	1	ENST00000264731.3:c.1780C>T	p.Arg594Ter	p.R594*	ENST00000264731	NM_003722.4	594	Cga/Tga	14/14	1	2	FACETS	0.865	0.738	1	0.865	0.738	1	CLONAL	1	TRUE	1	0.2	2		551	624	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612035	189612035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773237715	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	62	590	3	ENST00000264731.3:c.1787C>T	p.Ala596Val	p.A596V	ENST00000264731	NM_003722.4	596	gCg/gTg	14/14	1	2	FACETS	0.969	0.836	1	0.969	0.836	1	CLONAL	1	TRUE	1	0.2	2		593	640	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612268	189612268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs972760958	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	51	484	0	ENST00000264731.3:c.2020C>T	p.Arg674Cys	p.R674C	ENST00000264731	NM_003722.4	674	Cgc/Tgc	14/14	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.2	2		484	493	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806243	1806243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778355	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	65	763	0	ENST00000260795.2:c.1262G>A	p.Arg421Gln	p.R421Q	ENST00000260795		421	cGa/cAa	8/17	1	2	FACETS	0.786	0.68	0.901	0.786	0.68	0.901	CLONAL	1	TRUE	1	0.2	2		763	827	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806668	1806668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771872811	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	80	1014	0	ENST00000260795.2:c.1384G>A	p.Asp462Asn	p.D462N	ENST00000260795		462	Gac/Aac	9/17	1	2	FACETS	0.743	0.652	0.841	0.743	0.652	0.841	SUBCLONAL	1	TRUE	1	0.2	2		1014	1077	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902664	1902664	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	95	863	1	ENST00000382891.5:c.283G>A	p.Asp95Asn	p.D95N	ENST00000382891	NM_133335.3	95	Gat/Aat	2/22	1	2	FACETS	0.815	0.724	0.914	0.815	0.724	0.914	CLONAL	1	TRUE	1	0.2	2		864	1165	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1936914	1936914	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	65	642	0	ENST00000382891.5:c.1599G>T	p.Gln533His	p.Q533H	ENST00000382891	NM_133335.3	533	caG/caT	7/22	1	2	FACETS	0.85	0.735	0.974	0.85	0.735	0.974	CLONAL	1	TRUE	1	0.2	2		642	765	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1956914	1956914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	92	830	0	ENST00000382891.5:c.2365C>T	p.Pro789Ser	p.P789S	ENST00000382891	NM_133335.3	789	Ccc/Tcc	13/22	1	2	FACETS	0.796	0.705	0.893	0.796	0.705	0.893	SUBCLONAL	1	TRUE	1	0.2	2		830	1156	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1978254	1978254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754405808	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	74	912	2	ENST00000382891.5:c.3674C>T	p.Thr1225Met	p.T1225M	ENST00000382891	NM_133335.3	1225	aCg/aTg	21/22	1	2	FACETS	0.595	0.519	0.678	0.595	0.519	0.678	SUBCLONAL	1	TRUE	1	0.2	2		914	1244	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980413	1980413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1373	76	1145	0	ENST00000382891.5:c.3875C>T	p.Ser1292Leu	p.S1292L	ENST00000382891	NM_133335.3	1292	tCg/tTg	22/22	1	2	FACETS	0.524	0.458	0.597	0.524	0.458	0.597	SUBCLONAL	1	TRUE	1	0.2	2		1145	1449	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748270	41748270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1338837491	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	124	846	0	ENST00000226382.2:c.499G>A	p.Ala167Thr	p.A167T	ENST00000226382	NM_003924.3	167	Gcc/Acc	3/3	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.2	2		846	1128	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141125	55141125	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	29	362	0	ENST00000257290.5:c.1771G>T	p.Asp591Tyr	p.D591Y	ENST00000257290	NM_006206.4	591	Gat/Tat	12/23	1	2	FACETS	0.649	0.52	0.795	0.649	0.52	0.795	SUBCLONAL	1	TRUE	1	0.2	2		362	447	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152120	55152120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745464928	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	60	726	0	ENST00000257290.5:c.2552C>T	p.Ser851Leu	p.S851L	ENST00000257290	NM_006206.4	851	tCg/tTg	18/23	1	2	FACETS	0.663	0.57	0.765	0.663	0.57	0.765	SUBCLONAL	1	TRUE	1	0.2	2		726	905	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161380	55161380	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376544204	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	49	597	1	ENST00000257290.5:c.3211G>A	p.Asp1071Asn	p.D1071N	ENST00000257290	NM_006206.4	1071	Gac/Aac	23/23	1	2	FACETS	0.731	0.618	0.856	0.731	0.618	0.856	SUBCLONAL	1	TRUE	1	0.2	2		598	670	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598166	55598166	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	46	383	0	ENST00000288135.5:c.2361+2T>C		p.X787_splice	ENST00000288135	NM_000222.2	787			1	2	FACETS	0.996	0.839	1	0.996	0.839	1	CLONAL	1	TRUE	1	0.2	2		383	462	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602719	55602719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752695117	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	41	467	1	ENST00000288135.5:c.2540C>T	p.Thr847Met	p.T847M	ENST00000288135	NM_000222.2	847	aCg/aTg	18/21	1	2	FACETS	0.812	0.676	0.963	0.812	0.676	0.963	CLONAL	1	TRUE	1	0.2	2		468	505	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958795	55958795	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	59	584	0	ENST00000263923.4:c.3058G>A	p.Ala1020Thr	p.A1020T	ENST00000263923	NM_002253.2	1020	Gca/Aca	22/30	1	2	FACETS	0.789	0.677	0.911	0.789	0.677	0.911	CLONAL	1	TRUE	1	0.2	2		584	748	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509127	66509127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145126637	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	20	399	0	ENST00000273854.3:c.200G>A	p.Arg67His	p.R67H	ENST00000273854	NM_004439.5	67	cGc/cAc	2/18	1	2	FACETS	0.571	0.436	0.73	0.571	0.436	0.73	SUBCLONAL	1	TRUE	1	0.2	2		399	350	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99802232	99802232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200243582	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	10	98	0	ENST00000280892.6:c.661G>A	p.Ala221Thr	p.A221T	ENST00000280892	NM_001130678.1	221	Gca/Aca	7/7	1	2	FACETS	0.901	0.614	1	0.901	0.614	1	CLONAL	1	TRUE	1	0.2	2		98	111	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808294	99808294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	34	430	0	ENST00000280892.6:c.395G>A	p.Arg132Gln	p.R132Q	ENST00000280892	NM_001130678.1	132	cGa/cAa	5/7	1	2	FACETS	0.744	0.608	0.898	0.744	0.608	0.898	SUBCLONAL	1	TRUE	1	0.2	2		430	457	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094807	143094807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	41	346	0	ENST00000262992.4:c.1337C>A	p.Ser446Tyr	p.S446Y	ENST00000262992	NM_001101669.1	446	tCt/tAt	14/24	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.2	2		346	329	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245500	153245500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1304288466	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	43	554	1	ENST00000281708.4:c.1691G>A	p.Arg564His	p.R564H	ENST00000281708	NM_033632.3	564	cGt/cAt	11/12	1	2	FACETS	0.686	0.573	0.812	0.686	0.573	0.812	SUBCLONAL	1	TRUE	1	0.2	2		555	627	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249411	153249411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	47	555	0	ENST00000281708.4:c.1367C>T	p.Thr456Ile	p.T456I	ENST00000281708	NM_033632.3	456	aCc/aTc	9/12	1	2	FACETS	0.763	0.643	0.896	0.763	0.643	0.896	SUBCLONAL	1	TRUE	1	0.2	2		555	616	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517822	187517822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	43	396	0	ENST00000441802.2:c.12872C>T	p.Ser4291Phe	p.S4291F	ENST00000441802	NM_005245.3	4291	tCt/tTt	25/27	1	2	FACETS	0.919	0.769	1	0.919	0.769	1	CLONAL	1	TRUE	1	0.2	2		396	468	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521114	187521114	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760053140	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	48	568	0	ENST00000441802.2:c.12041C>T	p.Thr4014Met	p.T4014M	ENST00000441802	NM_005245.3	4014	aCg/aTg	22/27	1	2	FACETS	0.786	0.663	0.921	0.786	0.663	0.921	CLONAL	1	TRUE	1	0.2	2		568	611	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534281	187534281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	57	542	0	ENST00000441802.2:c.9445G>A	p.Ala3149Thr	p.A3149T	ENST00000441802	NM_005245.3	3149	Gcc/Acc	13/27	1	2	FACETS	0.839	0.719	0.971	0.839	0.719	0.971	CLONAL	1	TRUE	1	0.2	2		542	679	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542164	187542164	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	28	501	1	ENST00000441802.2:c.5576C>A	p.Ala1859Asp	p.A1859D	ENST00000441802	NM_005245.3	1859	gCt/gAt	10/27	1	2	FACETS	0.718	0.574	0.883	0.718	0.574	0.883	SUBCLONAL	1	TRUE	1	0.2	2		502	390	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549832	187549832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371598532	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	41	472	1	ENST00000441802.2:c.4409C>T	p.Ala1470Val	p.A1470V	ENST00000441802	NM_005245.3	1470	gCg/gTg	8/27	1	2	FACETS	0.804	0.669	0.954	0.804	0.669	0.954	CLONAL	1	TRUE	1	0.2	2		473	510	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628071	187628071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	87	769	0	ENST00000441802.2:c.2911G>A	p.Glu971Lys	p.E971K	ENST00000441802	NM_005245.3	971	Gaa/Aaa	2/27	1	2	FACETS	0.928	0.82	1	0.928	0.82	1	CLONAL	1	TRUE	1	0.2	2		769	938	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628879	187628879	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	60	681	0	ENST00000441802.2:c.2103T>G	p.Asp701Glu	p.D701E	ENST00000441802	NM_005245.3	701	gaT/gaG	2/27	1	2	FACETS	0.748	0.643	0.863	0.748	0.643	0.863	SUBCLONAL	1	TRUE	1	0.2	2		681	802	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	223625	223625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752532780	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	62	467	0	ENST00000264932.6:c.92G>A	p.Arg31Gln	p.R31Q	ENST00000264932	NM_004168.2	31	cGa/cAa	2/15	1	2	FACETS	0.9	0.776	1	0.9	0.776	1	CLONAL	1	TRUE	1	0.2	2		467	689	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233601	233601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	33	481	0	ENST00000264932.6:c.905G>A	p.Gly302Asp	p.G302D	ENST00000264932	NM_004168.2	302	gGt/gAt	8/15	1	2	FACETS	0.699	0.569	0.846	0.699	0.569	0.846	SUBCLONAL	1	TRUE	1	0.2	2		481	472	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236696	236696	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143798161	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	60	322	2	ENST00000264932.6:c.1414G>A	p.Glu472Lys	p.E472K	ENST00000264932	NM_004168.2	472	Gaa/Aaa	10/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.2	2		324	440	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293551	1293551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	111	1043	2	ENST00000310581.5:c.1450G>A	p.Glu484Lys	p.E484K	ENST00000310581	NM_198253.2	484	Gaa/Aaa	2/16	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.2	2		1045	1062	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449442	31449442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766022493	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	57	556	2	ENST00000344624.3:c.2767C>T	p.Arg923Trp	p.R923W	ENST00000344624		923	Cgg/Tgg	19/33	1	2	FACETS	0.847	0.726	0.98	0.847	0.726	0.98	CLONAL	1	TRUE	1	0.2	2		558	673	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515145	31515145	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1202201920	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	83	855	0	ENST00000344624.3:c.1240C>T	p.Arg414Ter	p.R414*	ENST00000344624		414	Cga/Tga	5/33	1	2	FACETS	0.856	0.753	0.966	0.856	0.753	0.966	CLONAL	1	TRUE	1	0.2	2		855	970	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38981988	38981988	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263964007	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	47	480	0	ENST00000357387.3:c.734G>A	p.Arg245Gln	p.R245Q	ENST00000357387	NM_152756.3	245	cGa/cAa	8/38	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.2	2		480	409	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174921	56174921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1263184187	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	27	349	0	ENST00000399503.3:c.2080G>A	p.Ala694Thr	p.A694T	ENST00000399503	NM_005921.1	694	Gcc/Acc	11/20	1	2	FACETS	0.668	0.531	0.825	0.668	0.531	0.825	SUBCLONAL	1	TRUE	1	0.2	2		349	404	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753174	57753174	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	31	377	0	ENST00000274289.3:c.842A>T	p.Glu281Val	p.E281V	ENST00000274289	NM_006622.3	281	gAa/gTa	7/14	1	2	FACETS	0.871	0.705	1	0.871	0.705	1	CLONAL	1	TRUE	1	0.2	2		377	356	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589010	67589010	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	40	309	0	ENST00000274335.5:c.1101T>G	p.Asp367Glu	p.D367E	ENST00000274335		367	gaT/gaG	8/15	1	2	FACETS	0.778	0.651	0.918	1	0.958	1	CLONAL	2	TRUE	1	0.2	2		309	257	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628398	86628398	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	23	321	0	ENST00000274376.6:c.767A>G	p.Tyr256Cys	p.Y256C	ENST00000274376	NM_002890.2	256	tAc/tGc	3/25	1	2	FACETS	0.83	0.649	1	0.83	0.649	1	CLONAL	1	TRUE	1	0.2	2		321	277	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649000	86649000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755634472	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	20	353	0	ENST00000274376.6:c.1280G>A	p.Arg427Gln	p.R427Q	ENST00000274376	NM_002890.2	427	cGa/cAa	9/25	1	2	FACETS	0.551	0.421	0.704	0.551	0.421	0.704	SUBCLONAL	1	TRUE	1	0.2	2		353	363	SUCCESS
APC	324	MSKCC	GRCh37	5	112177697	112177697	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs780856653	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	30	388	0	ENST00000257430.4:c.6406C>A	p.Leu2136Ile	p.L2136I	ENST00000257430	NM_000038.5	2136	Ctt/Att	16/16	1	2	FACETS	0.847	0.683	1	0.847	0.683	1	CLONAL	1	TRUE	1	0.2	2		388	354	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924484	131924484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	43	443	0	ENST00000265335.6:c.1157G>A	p.Gly386Glu	p.G386E	ENST00000265335		386	gGa/gAa	8/25	1	2	FACETS	0.892	0.747	1	0.892	0.747	1	CLONAL	1	TRUE	1	0.2	2		443	482	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460516	149460516	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	74	875	3	ENST00000286301.3:c.121C>T	p.Arg41Ter	p.R41*	ENST00000286301	NM_005211.3	41	Cga/Tga	3/22	1	2	FACETS	0.832	0.727	0.946	0.832	0.727	0.946	CLONAL	1	TRUE	1	0.2	2		878	889	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176516607	176516607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545721160	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	47	715	0	ENST00000292408.4:c.4C>T	p.Arg2Trp	p.R2W	ENST00000292408	NM_213647.1	2	Cgg/Tgg	2/18	1	2	FACETS	0.517	0.435	0.609	0.517	0.435	0.609	SUBCLONAL	1	TRUE	1	0.2	2		715	909	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030329	180030329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142322370	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	91	903	1	ENST00000261937.6:c.3955C>T	p.Arg1319Trp	p.R1319W	ENST00000261937	NM_182925.4	1319	Cgg/Tgg	30/30	1	2	FACETS	0.836	0.74	0.938	0.836	0.74	0.938	CLONAL	1	TRUE	1	0.2	2		904	1089	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197474	26197474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	26	316	0	ENST00000356476.2:c.5C>T	p.Ala2Val	p.A2V	ENST00000356476		2	gCt/gTt	1/1	1	2	FACETS	0.922	0.732	1	0.922	0.732	1	CLONAL	1	TRUE	1	0.2	2		316	282	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680247	30680247	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	93	918	1	ENST00000376406.3:c.1472C>A	p.Pro491His	p.P491H	ENST00000376406	NM_014641.2	491	cCt/cAt	5/15	1	2	FACETS	0.882	0.783	0.989	0.882	0.783	0.989	CLONAL	1	TRUE	1	0.2	2		919	1054	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680721	30680721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61748586	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	61	659	2	ENST00000376406.3:c.998C>T	p.Ala333Val	p.A333V	ENST00000376406	NM_014641.2	333	gCg/gTg	5/15	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.2	2		661	589	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139217	37139217	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	59	603	0	ENST00000373509.5:c.557A>G	p.Asp186Gly	p.D186G	ENST00000373509	NM_002648.3	186	gAc/gGc	4/6	1	2	FACETS	0.928	0.798	1	0.928	0.798	1	CLONAL	1	TRUE	1	0.2	2		603	636	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745295	43745295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs933893718	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	94	815	1	ENST00000523873.1:c.208G>A	p.Glu70Lys	p.E70K	ENST00000523873		70	Gag/Aag	3/8	1	2	FACETS	0.957	0.85	1	0.957	0.85	1	CLONAL	1	TRUE	1	0.2	2		816	982	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790697	89790697	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	118	1047	0	ENST00000336032.3:c.84C>A	p.Tyr28Ter	p.Y28*	ENST00000336032	NM_006813.2	28	taC/taA	1/2	1	2	FACETS	0.992	0.892	1	0.992	0.892	1	CLONAL	1	TRUE	1	0.2	2		1047	1190	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964377	93964377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	27	457	1	ENST00000369303.4:c.2520G>A	p.Met840Ile	p.M840I	ENST00000369303	NM_004440.3	840	atG/atA	14/17	1	2	FACETS	0.571	0.453	0.706	0.571	0.453	0.706	SUBCLONAL	1	TRUE	1	0.2	2		458	473	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020831	112020831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770159855	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	48	449	0	ENST00000368678.4:c.740C>T	p.Ser247Leu	p.S247L	ENST00000368678		247	tCg/tTg	8/13	1	2	FACETS	0.692	0.583	0.811	0.692	0.583	0.811	SUBCLONAL	1	TRUE	1	0.2	2		449	694	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662397	117662397	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	31	620	0	ENST00000368508.3:c.4980G>T	p.Glu1660Asp	p.E1660D	ENST00000368508	NM_002944.2	1660	gaG/gaT	30/43	1	2	FACETS	0.57	0.46	0.695	0.57	0.46	0.695	SUBCLONAL	1	TRUE	1	0.2	2		620	544	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678001	117678001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs62430836	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	43	576	0	ENST00000368508.3:c.3932G>A	p.Arg1311Gln	p.R1311Q	ENST00000368508	NM_002944.2	1311	cGa/cAa	25/43	1	2	FACETS	0.819	0.685	0.968	0.819	0.685	0.968	CLONAL	1	TRUE	1	0.2	2		576	525	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704494	117704494	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	27	422	0	ENST00000368508.3:c.2482T>C	p.Phe828Leu	p.F828L	ENST00000368508	NM_002944.2	828	Ttt/Ctt	16/43	1	2	FACETS	0.682	0.542	0.842	0.682	0.542	0.842	SUBCLONAL	1	TRUE	1	0.2	2		422	396	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708055	117708055	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	42	479	0	ENST00000368508.3:c.2122T>C	p.Ser708Pro	p.S708P	ENST00000368508	NM_002944.2	708	Tca/Cca	14/43	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.2	2		479	406	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709050	117709050	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	71	560	0	ENST00000368508.3:c.1907T>C	p.Val636Ala	p.V636A	ENST00000368508	NM_002944.2	636	gTa/gCa	13/43	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.2	2		560	665	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725528	117725528	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	56	499	0	ENST00000368508.3:c.353G>T	p.Arg118Leu	p.R118L	ENST00000368508	NM_002944.2	118	cGa/cTa	5/43	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.2	2		499	560	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149982926	149982926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777519756	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	40	477	0	ENST00000253339.5:c.3332C>T	p.Ser1111Leu	p.S1111L	ENST00000253339		1111	tCg/tTg	7/7	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.2	2		477	372	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005414	150005414	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	40	571	0	ENST00000253339.5:c.811A>C	p.Asn271His	p.N271H	ENST00000253339		271	Aac/Cac	3/7	1	2	FACETS	0.514	0.426	0.613	0.514	0.426	0.613	SUBCLONAL	1	TRUE	1	0.2	2		571	778	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332821	152332821	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	64	579	0	ENST00000206249.3:c.1127T>C	p.Val376Ala	p.V376A	ENST00000206249	NM_000125.3	376	gTc/gCc	5/8	1	2	FACETS	0.895	0.774	1	0.895	0.774	1	CLONAL	1	TRUE	1	0.2	2		579	715	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527808	157527808	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766931727	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	31	568	0	ENST00000346085.5:c.5533C>T	p.Arg1845Cys	p.R1845C	ENST00000346085	NM_020732.3	1845	Cgc/Tgc	20/20	1	2	FACETS	0.531	0.428	0.648	0.531	0.428	0.648	SUBCLONAL	1	TRUE	1	0.2	2		568	584	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55209991	55209991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144158123	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	71	427	0	ENST00000275493.2:c.101C>T	p.Thr34Met	p.T34M	ENST00000275493	NM_005228.3	34	aCg/aTg	2/28	0.0914294749029332	3	FACETS	1	0.972	1	0.729	0.637	0.827	INDETERMINATE	1	TRUE	1	0.2	3		427	536	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227938	55227938	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	43	433	0	ENST00000275493.2:c.1405T>G	p.Leu469Val	p.L469V	ENST00000275493	NM_005228.3	469	Ttg/Gtg	12/28	0.0914294749029332	3	FACETS	0.99	0.828	1	0.495	0.414	0.584	INDETERMINATE	1	TRUE	1	0.2	3		433	478	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331991	81331991	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	28	372	0	ENST00000222390.5:c.2093C>A	p.Ala698Asp	p.A698D	ENST00000222390	NM_000601.4	698	gCc/gAc	18/18	0.0914294749029332	3	FACETS	0.792	0.633	0.973	0.396	0.316	0.487	INDETERMINATE	1	TRUE	1	0.2	3		372	389	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335040	81335040	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751819844	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	33	417	0	ENST00000222390.5:c.1787C>T	p.Thr596Met	p.T596M	ENST00000222390	NM_000601.4	596	aCg/aTg	16/18	0.0914294749029332	3	FACETS	0.908	0.739	1	0.454	0.369	0.549	INDETERMINATE	1	TRUE	1	0.2	3		417	400	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381489	81381489	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	59	427	0	ENST00000222390.5:c.572C>T	p.Thr191Ile	p.T191I	ENST00000222390	NM_000601.4	191	aCa/aTa	5/18	0.0914294749029332	3	FACETS	1	0.956	1	0.646	0.557	0.744	INDETERMINATE	1	TRUE	1	0.2	3		427	502	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92404119	92404119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761377867	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	37	460	2	ENST00000265734.4:c.260G>A	p.Arg87Gln	p.R87Q	ENST00000265734	NM_001259.6	87	cGa/cAa	3/8	0.0914294749029332	3	FACETS	0.898	0.741	1	0.449	0.37	0.538	INDETERMINATE	1	TRUE	1	0.2	3		462	453	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508284	106508284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	40	436	0	ENST00000359195.3:c.278C>T	p.Pro93Leu	p.P93L	ENST00000359195	NM_002649.2	93	cCg/cTg	2/11	0.0914294749029332	3	FACETS	0.882	0.732	1	0.441	0.366	0.524	INDETERMINATE	1	TRUE	1	0.2	3		436	499	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508535	106508535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	19	422	0	ENST00000359195.3:c.529C>T	p.Arg177Cys	p.R177C	ENST00000359195	NM_002649.2	177	Cgc/Tgc	2/11	0.0914294749029332	3	FACETS	0.645	0.489	0.829	0.323	0.244	0.415	INDETERMINATE	1	TRUE	1	0.2	3		422	324	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524619	106524619	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	30	269	0	ENST00000359195.3:c.2780G>T	p.Arg927Ile	p.R927I	ENST00000359195	NM_002649.2	927	aGa/aTa	9/11	0.0914294749029332	3	FACETS	1	0.899	1	0.594	0.48	0.722	INDETERMINATE	1	TRUE	1	0.2	3		269	278	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545618	106545618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	35	547	0	ENST00000359195.3:c.3095C>T	p.Ser1032Phe	p.S1032F	ENST00000359195	NM_002649.2	1032	tCc/tTc	11/11	0.0914294749029332	3	FACETS	0.659	0.539	0.795	0.33	0.269	0.398	INDETERMINATE	1	TRUE	1	0.2	3		547	584	SUCCESS
MET	4233	MSKCC	GRCh37	7	116414127	116414127	+	intron_variant	Intron	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	21	1078	0	ENST00000397752.3:c.3029-808G>A		p.*1010*	ENST00000397752	NM_000245.2	-/1390			0.0914294749029332	3	FACETS	0.246	0.188	0.315	0.123	0.094	0.158	INDETERMINATE	1	TRUE	1	0.2	3		1078	938	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850275	128850275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	92	853	0	ENST00000249373.3:c.1538C>T	p.Pro513Leu	p.P513L	ENST00000249373	NM_005631.4	513	cCg/cTg	9/12	0.0914294749029332	3	FACETS	0.985	0.874	1	0.493	0.437	0.553	INDETERMINATE	1	TRUE	1	0.2	3		853	1027	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494257	140494257	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	78	939	0	ENST00000288602.6:c.991C>A	p.Leu331Ile	p.L331I	ENST00000288602	NM_004333.4	331	Ctc/Atc	8/18	0.0914294749029332	3	FACETS	0.725	0.635	0.822	0.362	0.317	0.411	INDETERMINATE	1	TRUE	1	0.2	3		939	1184	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140500228	140500228	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs547693139	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	79	657	1	ENST00000288602.6:c.914C>T	p.Ala305Val	p.A305V	ENST00000288602	NM_004333.4	305	gCg/gTg	7/18	0.0914294749029332	3	FACETS	0.964	0.847	1	0.482	0.423	0.546	INDETERMINATE	1	TRUE	1	0.2	3		658	901	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859595	151859595	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	54	558	0	ENST00000262189.6:c.11067C>A	p.Phe3689Leu	p.F3689L	ENST00000262189	NM_170606.2	3689	ttC/ttA	43/59	0.0914294749029332	3	FACETS	1	0.881	1	0.518	0.442	0.601	INDETERMINATE	1	TRUE	1	0.2	3		558	573	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38194888	38194888	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	82	751	1	ENST00000317025.8:c.845C>A	p.Pro282His	p.P282H	ENST00000317025	NM_023034.1	282	cCt/cAt	4/24	1	2	FACETS	0.801	0.704	0.905	0.801	0.704	0.905	CLONAL	1	TRUE	1	0.2	2		752	1024	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275843	38275843	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781608303	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	84	754	0	ENST00000425967.3:c.1426C>T	p.Arg476Trp	p.R476W	ENST00000425967	NM_001174067.1	476	Cgg/Tgg	11/19	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.2	2		754	825	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002940	69002940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	50	303	0	ENST00000288368.4:c.2240G>A	p.Arg747Gln	p.R747Q	ENST00000288368	NM_024870.2	747	cGg/cAg	20/40	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.2	2		303	474	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70967582	70967582	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	65	703	0	ENST00000276594.2:c.1441C>T	p.Arg481Ter	p.R481*	ENST00000276594	NM_024504.3	481	Cga/Tga	7/8	1	2	FACETS	0.895	0.775	1	0.895	0.775	1	CLONAL	1	TRUE	1	0.2	2		703	726	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859872	117859872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	26	280	1	ENST00000297338.2:c.1763C>T	p.Thr588Met	p.T588M	ENST00000297338	NM_006265.2	588	aCg/aTg	14/14	1	2	FACETS	0.726	0.575	0.899	0.726	0.575	0.899	SUBCLONAL	1	TRUE	1	0.2	2		281	358	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117874111	117874111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	22	417	0	ENST00000297338.2:c.343C>T	p.His115Tyr	p.H115Y	ENST00000297338	NM_006265.2	115	Cat/Tat	4/14	1	2	FACETS	0.584	0.452	0.737	0.584	0.452	0.737	SUBCLONAL	1	TRUE	1	0.2	2		417	377	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738491	145738491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1260068103	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	64	927	1	ENST00000428558.2:c.2494G>A	p.Val832Met	p.V832M	ENST00000428558	NM_004260.3	832	Gtg/Atg	16/22	1	2	FACETS	0.726	0.627	0.834	0.726	0.627	0.834	SUBCLONAL	1	TRUE	1	0.2	2		928	881	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5029797	5029797	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1438069581	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	23	467	0	ENST00000381652.3:c.241T>C	p.Tyr81His	p.Y81H	ENST00000381652	NM_004972.3	81	Tat/Cat	4/25	1	2	FACETS	0.56	0.436	0.704	0.56	0.436	0.704	SUBCLONAL	1	TRUE	1	0.2	2		467	411	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072541	5072541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368927897	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	27	454	0	ENST00000381652.3:c.1691G>A	p.Arg564Gln	p.R564Q	ENST00000381652	NM_004972.3	564	cGa/cAa	13/25	1	2	FACETS	0.552	0.438	0.683	0.552	0.438	0.683	SUBCLONAL	1	TRUE	1	0.2	2		454	489	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341787	8341787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	57	629	1	ENST00000356435.5:c.4853C>T	p.Thr1618Ile	p.T1618I	ENST00000356435		1618	aCc/aTc	29/35	1	2	FACETS	0.861	0.738	0.996	0.861	0.738	0.996	CLONAL	1	TRUE	1	0.2	2		630	662	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484372	8484372	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	71	345	0	ENST00000356435.5:c.3160T>G	p.Tyr1054Asp	p.Y1054D	ENST00000356435		1054	Tat/Gat	19/35	1	2	FACETS	0.892	0.782	1	1	0.98	1	CLONAL	2	TRUE	1	0.2	2		345	398	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633353	8633353	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	59	572	1	ENST00000356435.5:c.316G>T	p.Glu106Ter	p.E106*	ENST00000356435		106	Gaa/Taa	3/35	1	2	FACETS	0.919	0.79	1	0.919	0.79	1	CLONAL	1	TRUE	1	0.2	2		573	642	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185580	27185580	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	96	757	0	ENST00000380036.4:c.1280A>G	p.Asn427Ser	p.N427S	ENST00000380036	NM_000459.3	427	aAc/aGc	9/23	1	2	FACETS	0.891	0.791	0.997	0.891	0.791	0.997	CLONAL	1	TRUE	1	0.2	2		757	1078	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80343492	80343492	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	49	504	1	ENST00000286548.4:c.827A>C	p.Lys276Thr	p.K276T	ENST00000286548	NM_002072.3	276	aAa/aCa	6/7	1	2	FACETS	0.923	0.782	1	0.923	0.782	1	CLONAL	1	TRUE	1	0.2	2		505	531	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317081	87317081	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201490630	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	38	427	0	ENST00000277120.3:c.220G>A	p.Ala74Thr	p.A74T	ENST00000277120		74	Gca/Aca	3/19	1	2	FACETS	0.675	0.557	0.807	0.675	0.557	0.807	SUBCLONAL	1	TRUE	1	0.2	2		427	563	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635191	87635191	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367769334	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	78	664	0	ENST00000277120.3:c.2243C>T	p.Thr748Met	p.T748M	ENST00000277120		748	aCg/aTg	18/19	1	2	FACETS	0.854	0.749	0.968	0.854	0.749	0.968	CLONAL	1	TRUE	1	0.2	2		664	913	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650170	93650170	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs201765057	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	46	452	0	ENST00000375746.1:c.1721G>A	p.Arg574Gln	p.R574Q	ENST00000375746	NM_001174167.1	574	cGa/cAa	12/14	1	2	FACETS	0.873	0.735	1	0.873	0.735	1	CLONAL	1	TRUE	1	0.2	2		452	527	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93657818	93657818	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	49	470	0	ENST00000375746.1:c.1844A>G	p.Asn615Ser	p.N615S	ENST00000375746	NM_001174167.1	615	aAc/aGc	14/14	1	2	FACETS	0.76	0.642	0.889	0.76	0.642	0.889	SUBCLONAL	1	TRUE	1	0.2	2		470	645	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215892	98215892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769691754	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	72	687	0	ENST00000331920.6:c.3317C>T	p.Thr1106Met	p.T1106M	ENST00000331920	NM_000264.3	1106	aCg/aTg	20/24	1	2	FACETS	0.739	0.644	0.842	0.739	0.644	0.842	SUBCLONAL	1	TRUE	1	0.2	2		687	974	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220390	98220390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	72	632	0	ENST00000331920.6:c.3073C>T	p.Arg1025Cys	p.R1025C	ENST00000331920	NM_000264.3	1025	Cgc/Tgc	18/24	1	2	FACETS	0.94	0.82	1	0.94	0.82	1	CLONAL	1	TRUE	1	0.2	2		632	766	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232209	98232209	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs960630296	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	40	403	0	ENST00000331920.6:c.1733C>T	p.Ala578Val	p.A578V	ENST00000331920	NM_000264.3	578	gCg/gTg	13/24	1	2	FACETS	0.86	0.715	1	0.86	0.715	1	CLONAL	1	TRUE	1	0.2	2		403	465	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347977	128347977	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs746222671	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	96	826	0	ENST00000265960.3:c.528G>T	p.Lys176Asn	p.K176N	ENST00000265960	NM_001006617.1	176	aaG/aaT	5/12	1	2	FACETS	0.87	0.773	0.974	0.87	0.773	0.974	CLONAL	1	TRUE	1	0.2	2		826	1103	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759812	133759812	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766513552	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	68	806	2	ENST00000318560.5:c.2135G>A	p.Arg712His	p.R712H	ENST00000318560	NM_005157.4	712	cGc/cAc	11/11	1	2	FACETS	0.889	0.772	1	0.889	0.772	1	CLONAL	1	TRUE	1	0.2	2		808	765	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135777046	135777046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761281095	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	72	636	1	ENST00000298552.3:c.2432G>A	p.Arg811Gln	p.R811Q	ENST00000298552	NM_001162426.1	811	cGg/cAg	19/23	1	2	FACETS	0.835	0.728	0.951	0.835	0.728	0.951	CLONAL	1	TRUE	1	0.2	2		637	862	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391890	139391890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	84	985	6	ENST00000277541.6:c.6301G>A	p.Ala2101Thr	p.A2101T	ENST00000277541	NM_017617.3	2101	Gca/Aca	34/34	1	2	FACETS	0.802	0.706	0.904	0.802	0.706	0.904	CLONAL	1	TRUE	1	0.2	2		991	1048	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399546	139399546	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764136623	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	51	684	1	ENST00000277541.6:c.4597G>A	p.Asp1533Asn	p.D1533N	ENST00000277541	NM_017617.3	1533	Gac/Aac	26/34	1	2	FACETS	0.685	0.581	0.8	0.685	0.581	0.8	SUBCLONAL	1	TRUE	1	0.2	2		685	744	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402764	139402764	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758471372	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	115	946	1	ENST00000277541.6:c.3245G>A	p.Arg1082His	p.R1082H	ENST00000277541	NM_017617.3	1082	cGc/cAc	20/34	1	2	FACETS	0.945	0.849	1	0.945	0.849	1	CLONAL	1	TRUE	1	0.2	2		947	1217	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566734	139566734	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144969763	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	71	925	0	ENST00000308874.7:c.818C>T	p.Ser273Leu	p.S273L	ENST00000308874		273	tCg/tTg	10/10	1	2	FACETS	0.723	0.629	0.825	0.723	0.629	0.825	SUBCLONAL	1	TRUE	1	0.2	2		925	982	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802531	139802531	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1193747361	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	85	778	0	ENST00000247668.2:c.376G>A	p.Glu126Lys	p.E126K	ENST00000247668	NM_021138.3	126	Gaa/Aaa	5/11	1	2	FACETS	0.871	0.768	0.982	0.871	0.768	0.982	CLONAL	1	TRUE	1	0.2	2		778	976	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814793	139814793	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	64	839	0	ENST00000247668.2:c.786C>A	p.Ser262Arg	p.S262R	ENST00000247668	NM_021138.3	262	agC/agA	8/11	1	2	FACETS	0.616	0.532	0.708	0.616	0.532	0.708	SUBCLONAL	1	TRUE	1	0.2	2		839	1039	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321286	1321286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780766655	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	73	545	1	ENST00000400841.2:c.469G>A	p.Asp157Asn	p.D157N	ENST00000400841		157	Gac/Aac	4/6	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.2	2		546	641	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841136	15841136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	38	552	0	ENST00000307771.7:c.1220C>T	p.Ser407Phe	p.S407F	ENST00000307771	NM_005089.3	407	tCt/tTt	11/11	1	2	FACETS	0.548	0.452	0.657	0.548	0.452	0.657	SUBCLONAL	1	TRUE	1	0.2	2		552	693	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20150342	20150342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	37	427	0	ENST00000379607.5:c.295G>A	p.Glu99Lys	p.E99K	ENST00000379607	NM_001412.3	99	Gaa/Aaa	5/7	1	2	FACETS	0.782	0.645	0.936	0.782	0.645	0.936	CLONAL	1	TRUE	1	0.2	2		427	473	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918695	44918695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746746824	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	84	481	0	ENST00000377967.4:c.1178G>A	p.Arg393Gln	p.R393Q	ENST00000377967	NM_021140.2	393	cGa/cAa	12/29	1	2	FACETS	0.761	0.673	0.854	1	0.978	1	SUBCLONAL	2	TRUE	1	0.2	2		481	552	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928852	44928852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750754452	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	90	445	1	ENST00000377967.4:c.1952C>T	p.Ser651Leu	p.S651L	ENST00000377967	NM_021140.2	651	tCg/tTg	17/29	1	2	FACETS	0.936	0.833	1	1	0.985	1	CLONAL	2	TRUE	1	0.2	2		446	481	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426521	47426521	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	58	872	1	ENST00000377045.4:c.864G>T	p.Lys288Asn	p.K288N	ENST00000377045	NM_001654.4	288	aaG/aaT	9/16	1	2	FACETS	0.635	0.544	0.734	0.635	0.544	0.734	SUBCLONAL	1	TRUE	1	0.2	2		873	914	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651658	48651658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	72	891	0	ENST00000376670.3:c.824G>A	p.Gly275Glu	p.G275E	ENST00000376670	NM_002049.3	275	gGg/gAg	5/6	1	2	FACETS	0.655	0.57	0.747	0.655	0.57	0.747	SUBCLONAL	1	TRUE	1	0.2	2		891	1099	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222493	53222493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556832633	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	80	877	0	ENST00000375401.3:c.4339G>A	p.Gly1447Arg	p.G1447R	ENST00000375401	NM_004187.3	1447	Ggg/Agg	26/26	1	2	FACETS	0.796	0.699	0.901	0.796	0.699	0.901	CLONAL	1	TRUE	1	0.2	2		877	1005	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223894	53223894	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	89	1082	0	ENST00000375401.3:c.3465G>T	p.Gln1155His	p.Q1155H	ENST00000375401	NM_004187.3	1155	caG/caT	23/26	1	2	FACETS	0.823	0.728	0.926	0.823	0.728	0.926	CLONAL	1	TRUE	1	0.2	2		1082	1081	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228015	53228015	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	84	914	0	ENST00000375401.3:c.2299G>A	p.Ala767Thr	p.A767T	ENST00000375401	NM_004187.3	767	Gct/Act	16/26	1	2	FACETS	0.797	0.702	0.899	0.797	0.702	0.899	SUBCLONAL	1	TRUE	1	0.2	2		914	1054	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228018	53228018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199422238	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	88	919	0	ENST00000375401.3:c.2296C>T	p.Arg766Trp	p.R766W	ENST00000375401	NM_004187.3	766	Cgg/Tgg	16/26	1	2	FACETS	0.829	0.732	0.932	0.829	0.732	0.932	CLONAL	1	TRUE	1	0.2	2		919	1062	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245080	53245080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1428740468	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	66	827	0	ENST00000375401.3:c.860C>T	p.Ser287Leu	p.S287L	ENST00000375401	NM_004187.3	287	tCg/tTg	7/26	1	2	FACETS	0.719	0.622	0.824	0.719	0.622	0.824	SUBCLONAL	1	TRUE	1	0.2	2		827	918	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412029	63412029	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754922124	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	53	858	0	ENST00000330258.3:c.1138G>A	p.Glu380Lys	p.E380K	ENST00000330258	NM_152424.3	380	Gag/Aag	2/2	1	2	FACETS	0.693	0.589	0.807	0.693	0.589	0.807	SUBCLONAL	1	TRUE	1	0.2	2		858	765	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412637	63412637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779222316	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	86	793	1	ENST00000330258.3:c.530G>A	p.Arg177His	p.R177H	ENST00000330258	NM_152424.3	177	cGc/cAc	2/2	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.2	2		794	819	SUCCESS
AR	367	MSKCC	GRCh37	X	66765122	66765122	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	45	665	1	ENST00000374690.3:c.134C>T	p.Ala45Val	p.A45V	ENST00000374690	NM_000044.3	45	gCg/gTg	1/8	1	2	FACETS	0.643	0.539	0.758	0.643	0.539	0.758	SUBCLONAL	1	TRUE	1	0.2	2		666	700	SUCCESS
AR	367	MSKCC	GRCh37	X	66765551	66765551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1455444688	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	85	967	1	ENST00000374690.3:c.563C>T	p.Ala188Val	p.A188V	ENST00000374690	NM_000044.3	188	gCc/gTc	1/8	1	2	FACETS	0.78	0.687	0.88	0.78	0.687	0.88	SUBCLONAL	1	TRUE	1	0.2	2		968	1090	SUCCESS
AR	367	MSKCC	GRCh37	X	66905884	66905884	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	29	474	0	ENST00000374690.3:c.1801G>A	p.Asp601Asn	p.D601N	ENST00000374690	NM_000044.3	601	Gat/Aat	3/8	1	2	FACETS	0.637	0.511	0.782	0.637	0.511	0.782	SUBCLONAL	1	TRUE	1	0.2	2		474	455	SUCCESS
AR	367	MSKCC	GRCh37	X	66942700	66942700	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs200801099	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	46	538	0	ENST00000374690.3:c.2481C>A	p.Phe827Leu	p.F827L	ENST00000374690	NM_000044.3	827	ttC/ttA	7/8	1	2	FACETS	0.723	0.608	0.851	0.723	0.608	0.851	SUBCLONAL	1	TRUE	1	0.2	2		538	636	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344959	70344959	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	60	814	0	ENST00000374080.3:c.2189G>A	p.Arg730Gln	p.R730Q	ENST00000374080		730	cGa/cAa	15/45	1	2	FACETS	0.596	0.512	0.688	0.596	0.512	0.688	SUBCLONAL	1	TRUE	1	0.2	2		814	1007	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354667	70354667	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1569482153	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	70	743	1	ENST00000374080.3:c.4832G>A	p.Arg1611His	p.R1611H	ENST00000374080		1611	cGt/cAt	35/45	1	2	FACETS	0.726	0.631	0.829	0.726	0.631	0.829	SUBCLONAL	1	TRUE	1	0.2	2		744	964	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829787	76829787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057517948	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	50	722	0	ENST00000373344.5:c.6254G>A	p.Arg2085His	p.R2085H	ENST00000373344	NM_000489.3	2085	cGt/cAt	28/35	1	2	FACETS	0.763	0.647	0.892	0.763	0.647	0.892	SUBCLONAL	1	TRUE	1	0.2	2		722	655	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829824	76829824	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	37	533	0	ENST00000373344.5:c.6218-1G>T		p.X2073_splice	ENST00000373344	NM_000489.3	2073			1	2	FACETS	0.761	0.627	0.912	0.761	0.627	0.912	CLONAL	1	TRUE	1	0.2	2		533	486	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907620	76907620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	40	528	0	ENST00000373344.5:c.4541G>A	p.Arg1514Gln	p.R1514Q	ENST00000373344	NM_000489.3	1514	cGa/cAa	15/35	1	2	FACETS	0.611	0.506	0.728	0.611	0.506	0.728	SUBCLONAL	1	TRUE	1	0.2	2		528	655	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937173	76937173	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	50	676	0	ENST00000373344.5:c.3575G>T	p.Ser1192Ile	p.S1192I	ENST00000373344	NM_000489.3	1192	aGc/aTc	9/35	1	2	FACETS	0.817	0.692	0.954	0.817	0.692	0.954	CLONAL	1	TRUE	1	0.2	2		676	612	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938304	76938304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	34	672	1	ENST00000373344.5:c.2444C>T	p.Ser815Phe	p.S815F	ENST00000373344	NM_000489.3	815	tCt/tTt	9/35	1	2	FACETS	0.634	0.517	0.766	0.634	0.517	0.766	SUBCLONAL	1	TRUE	1	0.2	2		673	536	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938640	76938640	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	73	651	0	ENST00000373344.5:c.2108C>A	p.Ser703Tyr	p.S703Y	ENST00000373344	NM_000489.3	703	tCt/tAt	9/35	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.2	2		651	569	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939697	76939697	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	45	780	0	ENST00000373344.5:c.1051G>T	p.Glu351Ter	p.E351*	ENST00000373344	NM_000489.3	351	Gag/Tag	9/35	1	2	FACETS	0.67	0.562	0.79	0.67	0.562	0.79	SUBCLONAL	1	TRUE	1	0.2	2		780	672	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940066	76940066	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	41	636	0	ENST00000373344.5:c.682A>T	p.Asn228Tyr	p.N228Y	ENST00000373344	NM_000489.3	228	Aac/Tac	9/35	1	2	FACETS	0.597	0.496	0.71	0.597	0.496	0.71	SUBCLONAL	1	TRUE	1	0.2	2		636	687	SUCCESS
BTK	695	MSKCC	GRCh37	X	100609652	100609652	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	107	522	1	ENST00000308731.7:c.1597G>T	p.Gly533Ter	p.G533*	ENST00000308731	NM_000061.2	533	Gga/Tga	16/19	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.2	2		523	734	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615095	100615095	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	39	575	0	ENST00000308731.7:c.820G>T	p.Asp274Tyr	p.D274Y	ENST00000308731	NM_000061.2	274	Gac/Tac	9/19	1	2	FACETS	0.663	0.549	0.791	0.663	0.549	0.791	SUBCLONAL	1	TRUE	1	0.2	2		575	588	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615626	100615626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782467781	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	48	642	1	ENST00000308731.7:c.706C>T	p.Arg236Trp	p.R236W	ENST00000308731	NM_000061.2	236	Cgg/Tgg	8/19	1	2	FACETS	0.689	0.581	0.808	0.689	0.581	0.808	SUBCLONAL	1	TRUE	1	0.2	2		643	697	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020196	123020196	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	56	774	1	ENST00000355640.3:c.684C>A	p.Phe228Leu	p.F228L	ENST00000355640		228	ttC/ttA	2/7	1	2	FACETS	0.613	0.523	0.711	0.613	0.523	0.711	SUBCLONAL	1	TRUE	1	0.2	2		775	914	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020278	123020278	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	41	666	0	ENST00000355640.3:c.766C>A	p.Leu256Ile	p.L256I	ENST00000355640		256	Ctt/Att	2/7	1	2	FACETS	0.722	0.6	0.857	0.722	0.6	0.857	SUBCLONAL	1	TRUE	1	0.2	2		666	568	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176490	123176490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	27	327	0	ENST00000218089.9:c.457G>A	p.Asp153Asn	p.D153N	ENST00000218089	NM_001042749.1	153	Gat/Aat	7/35	1	2	FACETS	0.74	0.589	0.912	0.74	0.589	0.912	CLONAL	1	TRUE	1	0.2	2		327	365	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032168	48032168	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	51	294	0	ENST00000234420.5:c.3556+2T>C		p.X1186_splice	ENST00000234420	NM_000179.2	1186			1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.2	2		294	429	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799050	42799050	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	70	1047	0	ENST00000575354.2:c.4534C>T	p.Arg1512Cys	p.R1512C	ENST00000575354	NM_015125.3	1512	Cgt/Tgt	20/20	1	2	FACETS	0.635	0.552	0.726	0.635	0.552	0.726	SUBCLONAL	1	TRUE	1	0.2	2		1047	1102	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	16	326	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.477	0.353	0.625	0.477	0.353	0.625	SUBCLONAL	1	TRUE	1	0.294088364686105	2		326	228	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0040837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	60	819	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.294088364686105	3	FACETS	0.652	0.561	0.751	0.326	0.28	0.376	SUBCLONAL	1	TRUE	1	0.294088364686105	3		819	718	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0040837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	236	441	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.294088364686105	6	FACETS	1	0.969	1	1	0.969	1	CLONAL	4	TRUE	2	0.294088364686105	6		441	608	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736308	243736308	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754990008	NA	P-0040837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	137	476	0	ENST00000263826.5:c.739C>T	p.Arg247Cys	p.R247C	ENST00000263826	NM_005465.4	247	Cgc/Tgc	8/13	0.185419937898802	4	FACETS	0.901	0.822	0.984	0.901	0.822	0.984	CLONAL	2	TRUE	2	0.294088364686105	4		476	669	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353866	15353866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	116	655	0	ENST00000263377.2:c.3014C>T	p.Ser1005Phe	p.S1005F	ENST00000263377	NM_058243.2	1005	tCc/tTc	14/20	0.185419937898802	4	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	2	0.294088364686105	4		655	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579321	7579322	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs587780067	NA	P-0040837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	175	670	0	ENST00000269305.4:c.365_366del	p.Val122AspfsTer26	p.V122Dfs*26	ENST00000269305	NM_001126112.2	122	gTG/g	4/11	0.294088364686105	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.294088364686105	3		670	619	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895608	28895608	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0040837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	33	449	0	ENST00000282397.4:c.3166A>T	p.Lys1056Ter	p.K1056*	ENST00000282397	NM_002019.4	1056	Aaa/Taa	23/30	1	2	FACETS	0.605	0.493	0.731	0.605	0.493	0.731	SUBCLONAL	1	TRUE	1	0.294088364686105	2		449	371	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906673	32906673	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769368098	NA	P-0040837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	43	517	0	ENST00000380152.3:c.1058C>T	p.Ser353Leu	p.S353L	ENST00000380152		353	tCa/tTa	10/27	1	2	FACETS	0.892	0.749	1	0.892	0.749	1	CLONAL	1	TRUE	1	0.294088364686105	2		517	328	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435447	110435447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762592279	NA	P-0040837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	93	522	0	ENST00000375856.3:c.2954C>T	p.Ser985Phe	p.S985F	ENST00000375856	NM_003749.2	985	tCc/tTc	1/2	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.294088364686105	2		522	545	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822441	72822441	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	195	1000	0	ENST00000268489.5:c.9734A>C	p.Lys3245Thr	p.K3245T	ENST00000268489	NM_006885.3	3245	aAg/aCg	10/10	0.231870152167157	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	0	0.294088364686105	2		1000	663	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627812	37627812	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	35	726	0	ENST00000447079.4:c.1727T>C	p.Val576Ala	p.V576A	ENST00000447079	NM_015083.1	576	gTt/gCt	2/14	0.294088364686105	3	FACETS	0.416	0.339	0.501	0.208	0.169	0.251	SUBCLONAL	1	TRUE	1	0.294088364686105	3		726	657	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113262	209113262	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	117	416	0	ENST00000345146.2:c.245G>C	p.Arg82Thr	p.R82T	ENST00000345146	NM_005896.2	82	aGg/aCg	4/10	0.294088364686105	3	FACETS	1	0.908	1	1	0.908	1	CLONAL	2	TRUE	1	0.294088364686105	3		416	456	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149437066	149437066	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0040837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	48	730	0	ENST00000286301.3:c.2221+1G>A		p.X741_splice	ENST00000286301	NM_005211.3	741			1	2	FACETS	0.631	0.534	0.739	0.631	0.534	0.739	SUBCLONAL	1	TRUE	1	0.294088364686105	2		730	517	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416881	121416881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	326	908	2	ENST00000257555.6:c.310G>A	p.Val104Met	p.V104M	ENST00000257555		104	Gtg/Atg	1/10	1	2	FACETS	0.996	0.944	1	0.996	0.944	1	CLONAL	1	TRUE	1	0.752493474352673	2		910	870	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	113	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.315625609504219	3	FACETS	1	0.957	1	0.724	0.659	0.791	CLONAL	2	TRUE	0	0.356444078100409	3		426	344	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0040868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	55	442	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.664	0.569	0.767	0.664	0.569	0.767	SUBCLONAL	1	TRUE	1	0.356444078100409	2		442	465	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0040868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	50	163	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.350857858702592	3	FACETS	0.762	0.654	0.877	0.762	0.654	0.877	SUBCLONAL	2	TRUE	1	0.356444078100409	3		163	217	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0040868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	46	286	1	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	0.78	0.659	0.911	0.78	0.659	0.911	CLONAL	1	TRUE	1	0.356444078100409	2		287	331	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197505	106197506	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	45	238	0	ENST00000380013.4:c.5844dup	p.Val1949SerfsTer7	p.V1949Sfs*7	ENST00000380013	NM_001127208.2	1946	-/A	11/11	1	2	FACETS	0.73	0.615	0.855	0.73	0.615	0.855	SUBCLONAL	1	TRUE	1	0.356444078100409	2		238	346	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732969	30732969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893810	NA	P-0040868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	179	293	0	ENST00000295754.5:c.1582C>T	p.Arg528Cys	p.R528C	ENST00000295754	NM_003242.5	528	Cgt/Tgt	7/7	0.324592998883949	2	FACETS	0.975	0.906	1	0.975	0.906	1	CLONAL	2	TRUE	0	0.356444078100409	2		293	515	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249456	153249456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	50	331	0	ENST00000281708.4:c.1322G>A	p.Arg441Gln	p.R441Q	ENST00000281708	NM_033632.3	441	cGg/cAg	9/12	1	2	FACETS	0.748	0.637	0.87	0.748	0.637	0.87	SUBCLONAL	1	TRUE	1	0.356444078100409	2		331	375	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979357	93979357	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	37	240	0	ENST00000369303.4:c.1471T>C	p.Ser491Pro	p.S491P	ENST00000369303	NM_004440.3	491	Tca/Cca	7/17	0.314207486176347	2	FACETS	0.887	0.737	1	0.444	0.368	0.527	CLONAL	1	TRUE	0	0.356444078100409	2		240	234	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605868	46605868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745977062	NA	P-0040868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	110	478	1	ENST00000263734.3:c.1516G>A	p.Ala506Thr	p.A506T	ENST00000263734	NM_001430.4	506	Gcc/Acc	11/16	1	2	FACETS	0.837	0.753	0.927	0.837	0.753	0.927	CLONAL	1	TRUE	1	0.356444078100409	2		479	737	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977952	131977952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201810	NA	P-0040868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	124	281	0	ENST00000265335.6:c.3835C>T	p.Arg1279Cys	p.R1279C	ENST00000265335		1279	Cgt/Tgt	25/25	0.350857858702592	3	FACETS	0.876	0.798	0.957	0.876	0.798	0.957	CLONAL	2	TRUE	1	0.356444078100409	3		281	468	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861813	57861813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142822754	NA	P-0040868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	109	491	0	ENST00000228682.2:c.1114C>T	p.Arg372Cys	p.R372C	ENST00000228682	NM_005269.2	372	Cgc/Tgc	10/12	0.315625609504219	3	FACETS	0.802	0.719	0.889	0.267	0.239	0.297	CLONAL	1	TRUE	0	0.356444078100409	3		491	899	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246653	41246653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	170	377	1	ENST00000357654.3:c.895G>A	p.Val299Ile	p.V299I	ENST00000357654	NM_007294.3	299	Gta/Ata	10/23	0.31438244157646	3	FACETS	0.952	0.88	1	0.952	0.88	1	CLONAL	2	TRUE	1	0.356444078100409	3		378	590	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665369	182665369	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	29	116	0	ENST00000292782.4:c.572A>G	p.Lys191Arg	p.K191R	ENST00000292782	NM_020640.2	191	aAa/aGa	5/7	1	2	FACETS	0.83	0.672	1	0.83	0.672	1	CLONAL	1	TRUE	1	0.356444078100409	2		116	196	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675693	30675693	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	170	554	0	ENST00000376406.3:c.2663A>G	p.Glu888Gly	p.E888G	ENST00000376406	NM_014641.2	888	gAg/gGg	8/15	0.337042598071422	3	FACETS	1	0.969	1	0.554	0.509	0.601	CLONAL	1	TRUE	1	0.356444078100409	3		554	1015	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222457	53222457	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782179560	NA	P-0040868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	311	717	3	ENST00000375401.3:c.4375C>T	p.Arg1459Trp	p.R1459W	ENST00000375401	NM_004187.3	1459	Cgg/Tgg	26/26	0.31438244157646	3	FACETS	0.868	0.819	0.919	0.868	0.819	0.919	CLONAL	2	TRUE	1	0.356444078100409	3		720	1184	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0040884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	109	442	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.927	0.838	1	0.927	0.838	1	CLONAL	1	TRUE	1	0.535468434982963	2		442	439	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0040884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	180	567	2	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.91	0.841	0.981	0.91	0.841	0.981	CLONAL	1	TRUE	1	0.535468434982963	2		569	739	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0040884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	199	556	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.942	0.875	1	0.942	0.875	1	CLONAL	1	TRUE	1	0.535468434982963	2		562	789	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0040884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	188	585	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.983	0.912	1	0.983	0.912	1	CLONAL	1	TRUE	1	0.535468434982963	2		590	714	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720671	89720671	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587782607	NA	P-0040884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	38	165	0	ENST00000371953.3:c.822G>A	p.Trp274Ter	p.W274*	ENST00000371953	NM_000314.4	274	tgG/tgA	8/9	0.535468434982963	3	FACETS	0.706	0.587	0.836	0.353	0.293	0.418	SUBCLONAL	1	TRUE	1	0.535468434982963	3		165	255	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16022738	16022738	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	114	362	0	ENST00000268712.3:c.1914del	p.Gly639ValfsTer2	p.G639Vfs*2	ENST00000268712	NM_006311.3	638	aaA/aa	17/46	1	2	FACETS	0.902	0.817	0.991	0.902	0.817	0.991	CLONAL	1	TRUE	1	0.535468434982963	2		362	472	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149355	119149356	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATG	rs397507494	NA	P-0040884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	85	389	0	ENST00000264033.4:c.1380_1382dup	p.Asp460dup	p.D460dup	ENST00000264033	NM_005188.3	460	tat/tATGat	9/16	1	2	FACETS	0.712	0.632	0.796	0.712	0.632	0.796	SUBCLONAL	1	TRUE	1	0.535468434982963	2		389	446	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881488	48881489	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0040884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	100	228	0	ENST00000267163.4:c.219_220dup	p.Ala74GlufsTer4	p.A74Efs*4	ENST00000267163	NM_000321.2	70	-/AG	2/27	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.535468434982963	2		228	342	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188297	32188297	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs753855314	NA	P-0040884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	210	661	0	ENST00000375023.3:c.1044del	p.Gly349AlafsTer49	p.G349Afs*49	ENST00000375023	NM_004557.3	348	ggC/gg	6/30	1	2	FACETS	0.91	0.846	0.976	0.91	0.846	0.976	CLONAL	1	TRUE	1	0.535468434982963	2		661	862	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416544	29416544	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	169	511	1	ENST00000389048.3:c.4409C>T	p.Ala1470Val	p.A1470V	ENST00000389048	NM_004304.4	1470	gCc/gTc	29/29	1	2	FACETS	0.904	0.834	0.977	0.904	0.834	0.977	CLONAL	1	TRUE	1	0.535468434982963	2		512	698	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651132	206651132	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	221	613	0	ENST00000367120.3:c.742G>T	p.Gly248Cys	p.G248C	ENST00000367120	NM_014002.3	248	Ggt/Tgt	8/22	0.511111978628703	4	FACETS	1	0.975	1	0.367	0.341	0.394	CLONAL	1	TRUE	1	0.535468434982963	4		613	1151	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573978	41573978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	184	522	1	ENST00000263253.7:c.6263G>A	p.Arg2088Gln	p.R2088Q	ENST00000263253	NM_001429.3	2088	cGg/cAg	31/31	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.535468434982963	2		523	678	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944132	71944134	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs746559845	NA	P-0040884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	54	571	0	ENST00000298229.2:c.1967_1969del	p.Ser656del	p.S656del	ENST00000298229	NM_001567.3	655	atCTCc/atc	17/28	1	2	FACETS	0.277	0.236	0.322	0.277	0.236	0.322	SUBCLONAL	1	TRUE	1	0.535468434982963	2		571	729	SUCCESS
MET	4233	MSKCC	GRCh37	7	116414204	116414205	+	intron_variant	Intron	DEL	AA	AA	-	novel	NA	P-0040884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	112	565	2	ENST00000397752.3:c.3029-722_3029-721del		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.636	0.573	0.702	0.636	0.573	0.702	SUBCLONAL	1	TRUE	1	0.535468434982963	2		567	658	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201522	133201522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs190813054	NA	P-0040884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	202	643	0	ENST00000320574.5:c.6716C>T	p.Ala2239Val	p.A2239V	ENST00000320574	NM_006231.2	2239	gCg/gTg	48/49	1	2	FACETS	0.934	0.867	1	0.934	0.867	1	CLONAL	1	TRUE	1	0.535468434982963	2		643	808	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372287	55372288	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1170462661	NA	P-0040884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	166	582	0	ENST00000297316.4:c.983dup	p.Gly331ArgfsTer34	p.G331Rfs*34	ENST00000297316	NM_022454.3	326	cac/caCc	2/2	1	2	FACETS	0.845	0.778	0.914	0.845	0.778	0.914	CLONAL	1	TRUE	1	0.535468434982963	2		582	734	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418183	139418183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750539322	NA	P-0040884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	197	618	0	ENST00000277541.6:c.389C>T	p.Pro130Leu	p.P130L	ENST00000277541	NM_017617.3	130	cCg/cTg	3/34	1	2	FACETS	0.88	0.816	0.946	0.88	0.816	0.946	CLONAL	1	TRUE	1	0.535468434982963	2		618	836	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179449	56179451	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0040884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	77	288	0	ENST00000399503.3:c.3767_3769del	p.Ser1256del	p.S1256del	ENST00000399503	NM_005921.1	1254	ttTTCt/ttt	15/20	1	2	FACETS	0.801	0.708	0.9	0.801	0.708	0.9	CLONAL	1	TRUE	1	0.535468434982963	2		288	359	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94211982	94211982	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782512	NA	P-0040884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	164	406	0	ENST00000323929.3:c.463C>T	p.Arg155Cys	p.R155C	ENST00000323929	NM_005591.3	155	Cgt/Tgt	6/20	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.535468434982963	2		406	602	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219204	133219204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	202	582	0	ENST00000320574.5:c.4840G>A	p.Ala1614Thr	p.A1614T	ENST00000320574	NM_006231.2	1614	Gct/Act	37/49	1	2	FACETS	0.96	0.892	1	0.96	0.892	1	CLONAL	1	TRUE	1	0.535468434982963	2		582	786	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293074	91293075	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	42	418	0	ENST00000355112.3:c.582dup	p.Lys195Ter	p.K195*	ENST00000355112	NM_000057.2	192	-/T	3/22	1	2	FACETS	0.268	0.223	0.318	0.268	0.223	0.318	SUBCLONAL	1	TRUE	1	0.535468434982963	2		418	585	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830179	72830180	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCTGGTAGAGTTGGGC	novel	NA	P-0040884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	121	506	0	ENST00000268489.5:c.6385_6401dup	p.His2134GlnfsTer48	p.H2134Qfs*48	ENST00000268489	NM_006885.3	2134	cat/caGCCCAACTCTACCAGCAt	9/10	1	2	FACETS	0.701	0.634	0.77	0.701	0.634	0.77	SUBCLONAL	1	TRUE	1	0.535468434982963	2		506	645	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991590	72991590	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	217	652	0	ENST00000268489.5:c.2455C>A	p.Leu819Ile	p.L819I	ENST00000268489	NM_006885.3	819	Ctc/Atc	2/10	1	2	FACETS	0.927	0.864	0.993	0.927	0.864	0.993	CLONAL	1	TRUE	1	0.535468434982963	2		652	874	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212200	36212200	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	185	576	0	ENST00000222270.7:c.1951C>T	p.Gln651Ter	p.Q651*	ENST00000222270	NM_014727.1	651	Cag/Tag	3/37	1	2	FACETS	0.897	0.83	0.967	0.897	0.83	0.967	CLONAL	1	TRUE	1	0.535468434982963	2		576	770	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753837	42753837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368169058	NA	P-0040884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	230	714	1	ENST00000222329.4:c.427C>T	p.Arg143Cys	p.R143C	ENST00000222329	NM_006494.2	143	Cgc/Tgc	4/4	1	2	FACETS	0.97	0.905	1	0.97	0.905	1	CLONAL	1	TRUE	1	0.535468434982963	2		715	886	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794009	42794009	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	192	602	0	ENST00000575354.2:c.1370G>T	p.Gly457Val	p.G457V	ENST00000575354	NM_015125.3	457	gGc/gTc	9/20	1	2	FACETS	0.865	0.801	0.931	0.865	0.801	0.931	CLONAL	1	TRUE	1	0.535468434982963	2		602	829	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795440	39795440	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	198	558	0	ENST00000288319.7:c.280G>A	p.Val94Met	p.V94M	ENST00000288319	NM_182918.3	94	Gtg/Atg	3/10	1	2	FACETS	0.98	0.91	1	0.98	0.91	1	CLONAL	1	TRUE	1	0.535468434982963	2		558	755	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755786	57755786	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0040884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	131	450	0	ENST00000274289.3:c.1A>G	p.Met1?	p.M1?	ENST00000274289	NM_006622.3	1	Atg/Gtg	1/14	1	2	FACETS	0.894	0.815	0.977	0.894	0.815	0.977	CLONAL	1	TRUE	1	0.535468434982963	2		450	547	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570361	87570361	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	54	645	0	ENST00000277120.3:c.2104del	p.Glu702ArgfsTer5	p.E702Rfs*5	ENST00000277120		701	Ggg/gg	17/19	1	2	FACETS	0.252	0.215	0.294	0.252	0.215	0.294	SUBCLONAL	1	TRUE	1	0.535468434982963	2		645	799	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0040893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	108	370	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.984	0.89	1	0.984	0.89	1	CLONAL	1	TRUE	1	0.554435183102996	2		370	396	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602911	55602911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753419764	NA	P-0040893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	113	211	1	ENST00000288135.5:c.2621C>T	p.Pro874Leu	p.P874L	ENST00000288135	NM_000222.2	874	cCg/cTg	19/21	1	2	FACETS	0.791	0.715	0.871	0.791	0.715	0.871	SUBCLONAL	1	TRUE	1	0.554435183102996	2		212	515	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0040893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	15	171	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.124	0.09	0.166	0.124	0.09	0.166	SUBCLONAL	1	TRUE	1	0.554435183102996	2		171	435	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0040893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	11	170	0	ENST00000349496.5:c.101G>A	p.Gly34Glu	p.G34E	ENST00000349496	NM_001904.3	34	gGa/gAa	3/15	1	2	FACETS	0.091	0.062	0.127	0.091	0.062	0.127	SUBCLONAL	1	TRUE	1	0.554435183102996	2		170	435	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0040893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	13	413	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.097	0.068	0.132	0.097	0.068	0.132	SUBCLONAL	1	TRUE	1	0.554435183102996	2		413	485	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0040893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	19	166	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	0.156	0.118	0.201	0.156	0.118	0.201	SUBCLONAL	1	TRUE	1	0.554435183102996	2		166	439	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0040893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	33	249	0	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	1	2	FACETS	0.196	0.159	0.239	0.196	0.159	0.239	SUBCLONAL	1	TRUE	1	0.554435183102996	2		249	606	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654643	67654643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs968244943	NA	P-0040893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	192	258	0	ENST00000264010.4:c.1130G>A	p.Arg377His	p.R377H	ENST00000264010	NM_006565.3	377	cGt/cAt	6/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.554435183102996	2		258	630	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997697	149997697	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs145871963	NA	P-0040893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	29	184	0	ENST00000253339.5:c.2770C>T	p.Arg924Ter	p.R924*	ENST00000253339		924	Cga/Tga	5/7	1	2	FACETS	0.285	0.229	0.349	0.285	0.229	0.349	SUBCLONAL	1	TRUE	1	0.554435183102996	2		184	367	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426808	121426808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371759652	NA	P-0040893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	176	295	2	ENST00000257555.6:c.499G>A	p.Val167Ile	p.V167I	ENST00000257555		167	Gtc/Atc	2/10	1	2	FACETS	0.963	0.891	1	0.963	0.891	1	CLONAL	1	TRUE	1	0.554435183102996	2		297	659	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624260	89624262	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	novel	NA	P-0040893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	105	120	0	ENST00000371953.3:c.36_38del	p.Asn12del	p.N12del	ENST00000371953	NM_000314.4	12	AAC/-	1/9	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.554435183102996	2		120	302	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591137	67591142	+	inframe_deletion	In_Frame_Del	DEL	GAGACC	GAGACC	-	novel	NA	P-0040893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	63	160	0	ENST00000274335.5:c.1730_1735del	p.Arg577_Gln579delinsLys	p.R577_Q579delinsK	ENST00000274335		577	aGAGACCaa/aaa	12/15	1	2	FACETS	0.832	0.727	0.944	0.832	0.727	0.944	CLONAL	1	TRUE	1	0.554435183102996	2		160	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0040931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	248	836	0	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	0.307958792363481	3	FACETS	1	0.982	1			1	CLONAL	2	FALSE	NA	0.307958792363481	3		836	825	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0041069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	304	473	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.847135976734086	2		473	675	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0041069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	402	441	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.847135976734086	3	FACETS	0.988	0.95	1	0.988	0.95	1	CLONAL	2	TRUE	1	0.847135976734086	3		441	684	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436907	49436907	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	413	882	0	ENST00000301067.7:c.5596C>T	p.Pro1866Ser	p.P1866S	ENST00000301067	NM_003482.3	1866	Cca/Tca	25/54	1	2	FACETS	0.98	0.936	1	0.98	0.936	1	CLONAL	1	TRUE	1	0.847135976734086	2		882	995	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243766	41243766	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	rs397507219	NA	P-0041069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	245	566	0	ENST00000357654.3:c.3782T>G	p.Leu1261Ter	p.L1261*	ENST00000357654	NM_007294.3	1261	tTa/tGa	10/23	1	2	FACETS	0.901	0.848	0.955	0.901	0.848	0.955	CLONAL	1	TRUE	1	0.847135976734086	2		566	642	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724050	61724051	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	205	407	0	ENST00000401558.2:c.851dup	p.Thr285AsnfsTer30	p.T285Nfs*30	ENST00000401558	NM_003400.3	284	gta/gtTa	10/25	1	2	FACETS	0.978	0.916	1	0.978	0.916	1	CLONAL	1	TRUE	1	0.847135976734086	2		407	495	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0041069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	182	473	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.997	0.931	1	0.997	0.931	1	CLONAL	1	TRUE	1	0.852848898548381	2		473	428	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0041069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	202	441	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.852848898548381	3	FACETS	0.889	0.838	0.94	0.889	0.838	0.94	CLONAL	2	TRUE	1	0.852848898548381	3		441	380	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436907	49436907	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	303	882	0	ENST00000301067.7:c.5596C>T	p.Pro1866Ser	p.P1866S	ENST00000301067	NM_003482.3	1866	Cca/Tca	25/54	1	2	FACETS	0.992	0.941	1	0.992	0.941	1	CLONAL	1	TRUE	1	0.852848898548381	2		882	716	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243766	41243766	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	rs397507219	NA	P-0041069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	123	566	0	ENST00000357654.3:c.3782T>G	p.Leu1261Ter	p.L1261*	ENST00000357654	NM_007294.3	1261	tTa/tGa	10/23	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.852848898548381	2		566	284	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724050	61724051	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	118	407	0	ENST00000401558.2:c.851dup	p.Thr285AsnfsTer30	p.T285Nfs*30	ENST00000401558	NM_003400.3	284	gta/gtTa	10/25	1	2	FACETS	0.925	0.848	1	0.925	0.848	1	CLONAL	1	TRUE	1	0.852848898548381	2		407	299	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598362	28598362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770770051	NA	P-0041069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	302	496	1	ENST00000253063.3:c.334C>T	p.Arg112Cys	p.R112C	ENST00000253063	NM_031459.4	112	Cgc/Tgc	3/10	1	2	FACETS	0.944	0.895	0.994	0.944	0.895	0.994	CLONAL	1	TRUE	1	0.852848898548381	2		497	750	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	76	326	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.868	0.764	0.978	0.868	0.764	0.978	CLONAL	1	TRUE	1	0.407442518177389	2		326	430	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0041473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	125	441	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.407442518177389	4	FACETS	1	0.959	1	0.723	0.661	0.788	CLONAL	2	TRUE	1	0.407442518177389	4		441	398	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086010	16086010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	146	592	0	ENST00000281043.3:c.1186G>A	p.Asp396Asn	p.D396N	ENST00000281043	NM_005378.4	396	Gac/Aac	3/3	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.407442518177389	2		592	695	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230641	46230641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	58	542	0	ENST00000334344.6:c.890C>T	p.Ser297Phe	p.S297F	ENST00000334344	NM_152641.2	297	tCc/tTc	8/21	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.407442518177389	2		542	232	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0041473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	61	390	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.407442518177389	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.407442518177389	1		390	196	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874636	35874636	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	51	439	0	ENST00000303115.3:c.792G>A	p.Trp264Ter	p.W264*	ENST00000303115	NM_002185.3	264	tgG/tgA	6/8	1	2	FACETS	0.897	0.768	1	0.897	0.768	1	CLONAL	1	TRUE	1	0.407442518177389	2		439	279	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544088	18544088	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	40	365	0	ENST00000266497.5:c.1905G>A	p.Met635Ile	p.M635I	ENST00000266497		635	atG/atA	13/31	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.407442518177389	2		365	158	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891006	112891006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	27	349	0	ENST00000351677.2:c.340C>T	p.His114Tyr	p.H114Y	ENST00000351677	NM_002834.3	114	Cat/Tat	4/16	1	2	FACETS	0.818	0.658	0.997	0.818	0.658	0.997	CLONAL	1	TRUE	1	0.407442518177389	2		349	162	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575139	64575139	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	69	563	0	ENST00000312049.6:c.668T>G	p.Leu223Arg	p.L223R	ENST00000312049	NM_130799.2	223	cTg/cGg	4/10	0.373158671098446	3	FACETS	1	0.968	1	0.664	0.583	0.75	CLONAL	1	TRUE	1	0.407442518177389	3		563	307	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868354	56868356	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	GGT	GGT	-	novel	NA	P-0041473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	35	332	0	ENST00000308159.5:c.1737+1_1737+3del		p.X579_splice	ENST00000308159	NM_014669.4	579		15/22	0.155913426687828	1	FACETS	0.554	0.457	0.662	0.554	0.457	0.662	INDETERMINATE	1	TRUE	0	0.407442518177389	1		332	247	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046361	128046361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	61	537	1	ENST00000285398.2:c.902C>T	p.Ser301Phe	p.S301F	ENST00000285398	NM_000122.1	301	tCt/tTt	7/15	1	2	FACETS	0.79	0.685	0.904	0.79	0.685	0.904	CLONAL	1	TRUE	1	0.407442518177389	2		538	379	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394366	162394367	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	36	420	1	ENST00000366898.1:c.701_702delinsAA	p.Arg234Gln	p.R234Q	ENST00000366898	NM_004562.2	234	cGG/cAA	6/12	0.155913426687828	1	FACETS	0.501	0.413	0.598	0.501	0.413	0.598	INDETERMINATE	1	TRUE	0	0.407442518177389	1		421	281	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444407	50444407	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	96	459	1	ENST00000331340.3:c.337C>T	p.Pro113Ser	p.P113S	ENST00000331340	NM_006060.4	113	Cct/Tct	4/8	0.194487453027179	4	FACETS	1	0.977	1	0.678	0.607	0.754	INDETERMINATE	1	TRUE	2	0.407442518177389	4		460	489	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339499	81339499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	67	515	1	ENST00000222390.5:c.1505G>A	p.Arg502Gln	p.R502Q	ENST00000222390	NM_000601.4	502	cGa/cAa	13/18	0.194487453027179	4	FACETS	1	0.962	1	0.639	0.559	0.726	INDETERMINATE	1	TRUE	2	0.407442518177389	4		516	362	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968073	68968073	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	27	441	0	ENST00000288368.4:c.1102T>A	p.Leu368Ile	p.L368I	ENST00000288368	NM_024870.2	368	Tta/Ata	10/40	0.259180996027554	1	FACETS	0.577	0.463	0.705	0.577	0.463	0.705	SUBCLONAL	1	TRUE	0	0.407442518177389	1		441	183	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411662	63411662	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	95	404	1	ENST00000330258.3:c.1505G>A	p.Gly502Glu	p.G502E	ENST00000330258	NM_152424.3	502	gGa/gAa	2/2	1	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.407442518177389	1		405	256	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020185	123020185	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	92	329	0	ENST00000355640.3:c.673C>T	p.Pro225Ser	p.P225S	ENST00000355640		225	Cct/Tct	2/7	1	1	FACETS	0.799	0.724	0.876	1	0.985	1	SUBCLONAL	2	TRUE	0	0.407442518177389	1		329	225	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115952	8115953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0041508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	307	544	0	ENST00000346208.3:c.1300dup	p.His434ProfsTer73	p.H434Pfs*73	ENST00000346208		433	cac/caCc	6/6	1	2	FACETS	0.912	0.863	0.962	0.912	0.863	0.962	CLONAL	1	TRUE	1	0.801481194366485	2		544	840	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0042238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	85	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.277551161810091	3	FACETS	1	0.971	1	0.651	0.578	0.729	CLONAL	1	TRUE	1	0.34	3		426	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0042238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	218	954	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.248605919534617	2	FACETS	0.857	0.8	0.916	0.857	0.8	0.916	CLONAL	2	TRUE	0	0.34	2		954	748	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14015990	14015990	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	47	340	0	ENST00000311895.7:c.310G>C	p.Gly104Arg	p.G104R	ENST00000311895	NM_005236.2	104	Ggt/Cgt	2/11	0.109380436389037	5	FACETS	1	0.905	1	0.275	0.232	0.321	INDETERMINATE	1	TRUE	1	0.34	5		340	380	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647280	23647280	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	82	619	0	ENST00000261584.4:c.587G>C	p.Arg196Thr	p.R196T	ENST00000261584	NM_024675.3	196	aGa/aCa	4/13	0.109380436389037	5	FACETS	1	0.95	1	0.286	0.252	0.323	INDETERMINATE	1	TRUE	1	0.34	5		619	636	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952344	17952344	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	182	1086	1	ENST00000458235.1:c.996C>A	p.Phe332Leu	p.F332L	ENST00000458235	NM_000215.3	332	ttC/ttA	8/24	0.135927167210736	4	FACETS	1	0.988	1	0.711	0.655	0.769	INDETERMINATE	1	TRUE	2	0.34	4		1087	1009	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586422	189586422	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	128	602	0	ENST00000264731.3:c.1046G>T	p.Gly349Val	p.G349V	ENST00000264731	NM_003722.4	349	gGa/gTa	8/14	1	2	FACETS	0.883	0.8	0.97	0.883	0.8	0.97	CLONAL	1	TRUE	1	0.356258707669948	2		602	814	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098959	178098959	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519921	NA	P-0043061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	71	288	0	ENST00000397062.3:c.86A>G	p.Asp29Gly	p.D29G	ENST00000397062	NM_006164.4	29	gAt/gGt	2/5	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.356258707669948	2		288	380	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908876	101908876	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs387906697	NA	P-0043061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	206	642	0	ENST00000374994.4:c.1240C>T	p.Arg414Ter	p.R414*	ENST00000374994	NM_004612.2	414	Cga/Tga	7/9	0.356258707669948	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.356258707669948	1		642	751	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276378	115276378	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs749941097	NA	P-0043061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	70	438	0	ENST00000438362.2:c.950T>C	p.Ile317Thr	p.I317T	ENST00000438362	NM_001242891.1	317	aTc/aCc	9/20	1	2	FACETS	0.929	0.813	1	0.929	0.813	1	CLONAL	1	TRUE	1	0.356258707669948	2		438	423	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562742	21562743	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	rs1309929430	NA	P-0043061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	115	494	4	ENST00000382592.4:c.1176_1177del	p.His393ArgfsTer6	p.H393Rfs*6	ENST00000382592	NM_014572.2	392	gcGCac/gcac	4/8	0.356258707669948	1	FACETS	0.988	0.894	1	0.988	0.894	1	CLONAL	1	TRUE	0	0.356258707669948	1		498	537	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908231	28908231	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	117	566	1	ENST00000282397.4:c.2524G>T	p.Val842Phe	p.V842F	ENST00000282397	NM_002019.4	842	Gtt/Ttt	18/30	0.356258707669948	1	FACETS	0.813	0.734	0.896	0.813	0.734	0.896	CLONAL	1	TRUE	0	0.356258707669948	1		567	664	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128201252	128201252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs942714895	NA	P-0043061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	248	770	3	ENST00000265960.3:c.1483G>A	p.Ala495Thr	p.A495T	ENST00000265960	NM_001006617.1	495	Gct/Act	12/12	0.356258707669948	1	FACETS	0.797	0.749	0.846	1	0.994	1	SUBCLONAL	2	TRUE	0	0.356258707669948	1		773	718	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	35	414	2	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.76	0.622	0.915	0.76	0.622	0.915	CLONAL	1	TRUE	1	0.18	2		416	512	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	16	303	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.597	0.44	0.783	0.597	0.44	0.783	SUBCLONAL	1	TRUE	1	0.18	2		304	298	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	48	496	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.844	0.712	0.989	0.844	0.712	0.989	CLONAL	1	TRUE	1	0.18	2		496	632	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056342	27056343	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	24	354	0	ENST00000324856.7:c.1338_1339del	p.Gln449AlafsTer173	p.Q449Afs*173	ENST00000324856	NM_006015.4	446	tcTTat/tcat	2/20	1	2	FACETS	0.751	0.589	0.939	0.751	0.589	0.939	CLONAL	1	TRUE	1	0.18	2		354	355	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	53	696	2	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.737	0.627	0.858	0.737	0.627	0.858	SUBCLONAL	1	TRUE	1	0.18	2		698	799	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	99	742	0	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.18	2		742	764	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145550	24145550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	58	633	2	ENST00000263121.7:c.569G>A	p.Arg190Gln	p.R190Q	ENST00000263121	NM_003073.3	190	cGg/cAg	5/9	1	2	FACETS	0.797	0.683	0.921	0.797	0.683	0.921	CLONAL	1	TRUE	1	0.18	2		635	809	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	60	554	2	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	0.73	0.627	0.843	0.73	0.627	0.843	SUBCLONAL	1	TRUE	1	0.18	2		556	913	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	20	301	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	0.71	0.543	0.906	0.71	0.543	0.906	CLONAL	1	TRUE	1	0.18	2		301	313	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46527638	46527638	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	38	414	2	ENST00000262741.5:c.727C>T	p.Arg243Ter	p.R243*	ENST00000262741	NM_003629.3	243	Cga/Tga	6/10	1	2	FACETS	0.75	0.619	0.897	0.75	0.619	0.897	SUBCLONAL	1	TRUE	1	0.18	2		416	563	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074255	8074255	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	39	440	0	ENST00000377482.5:c.404del	p.Asn135ThrfsTer40	p.N135Tfs*40	ENST00000377482	NM_018948.3	135	aAc/ac	4/4	1	2	FACETS	0.795	0.658	0.948	0.795	0.658	0.948	CLONAL	1	TRUE	1	0.18	2		440	545	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508725	106508725	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	54	521	1	ENST00000359195.3:c.723del	p.Gly242AlafsTer17	p.G242Afs*17	ENST00000359195	NM_002649.2	240	aCc/ac	2/11	1	2	FACETS	0.993	0.848	1	0.993	0.848	1	CLONAL	1	TRUE	1	0.18	2		522	604	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165282	47165283	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	32	317	0	ENST00000409792.3:c.843dup	p.Glu282ArgfsTer9	p.E282Rfs*9	ENST00000409792	NM_014159.6	281	-/A	3/21	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.18	2		317	305	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736474	85736474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	28	311	0	ENST00000370580.1:c.173G>A	p.Arg58Gln	p.R58Q	ENST00000370580	NM_003921.4	58	cGa/cAa	2/3	1	2	FACETS	0.81	0.647	0.996	0.81	0.647	0.996	CLONAL	1	TRUE	1	0.18	2		311	384	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501488	149501488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771923448	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	80	810	0	ENST00000261799.4:c.2299G>A	p.Glu767Lys	p.E767K	ENST00000261799	NM_002609.3	767	Gag/Aag	16/23	1	2	FACETS	0.985	0.866	1	0.985	0.866	1	CLONAL	1	TRUE	1	0.18	2		810	902	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	56	861	3	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	1	2	FACETS	0.644	0.55	0.748	0.644	0.55	0.748	SUBCLONAL	1	TRUE	1	0.18	2		864	966	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120043	70120043	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	12	38	0	ENST00000245479.2:c.1049del	p.Pro350HisfsTer33	p.P350Hfs*33	ENST00000245479	NM_000346.3	349	Ccc/cc	3/3	1	2	FACETS	1	0.784	1	1	0.911	1	CLONAL	2	TRUE	1	0.18	2		38	60	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531777	46531779	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	35	331	0	ENST00000262741.5:c.568_570del	p.Glu190del	p.E190del	ENST00000262741	NM_003629.3	190	GAG/-	5/10	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.18	2		331	340	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202350	138202351	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775280214	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	39	631	1	ENST00000237289.4:c.2274dup	p.Lys759GlnfsTer10	p.K759Qfs*10	ENST00000237289	NM_001270507.1	756	gac/gaCc	9/9	1	2	FACETS	0.683	0.565	0.816	0.683	0.565	0.816	SUBCLONAL	1	TRUE	1	0.18	2		632	634	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120806011	120806011	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	60	674	1	ENST00000257552.2:c.166del	p.Leu56Ter	p.L56*	ENST00000257552	NM_002442.3	56	Ctg/tg	3/15	1	2	FACETS	0.801	0.689	0.924	0.801	0.689	0.924	CLONAL	1	TRUE	1	0.18	2		675	832	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438655	49438655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1268188754	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	67	683	1	ENST00000301067.7:c.4835G>A	p.Arg1612His	p.R1612H	ENST00000301067	NM_003482.3	1612	cGc/cAc	19/54	1	2	FACETS	0.883	0.766	1	0.883	0.766	1	CLONAL	1	TRUE	1	0.18	2		684	843	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357122	89357122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200994100	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	62	667	1	ENST00000301030.4:c.512G>A	p.Arg171His	p.R171H	ENST00000301030	NM_001256183.1	171	cGc/cAc	6/13	1	2	FACETS	0.756	0.651	0.871	0.756	0.651	0.871	SUBCLONAL	1	TRUE	1	0.18	2		668	911	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508683	106508683	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1490061702	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	51	482	2	ENST00000359195.3:c.677G>A	p.Arg226His	p.R226H	ENST00000359195	NM_002649.2	226	cGc/cAc	2/11	1	2	FACETS	0.927	0.788	1	0.927	0.788	1	CLONAL	1	TRUE	1	0.18	2		484	611	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670697	67670697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749826586	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	40	550	0	ENST00000264010.4:c.1942G>A	p.Ala648Thr	p.A648T	ENST00000264010	NM_006565.3	648	Gcc/Acc	11/12	1	2	FACETS	0.655	0.542	0.78	0.655	0.542	0.78	SUBCLONAL	1	TRUE	1	0.18	2		550	679	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524749	187524749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372461501	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	70	698	0	ENST00000441802.2:c.10931C>T	p.Ala3644Val	p.A3644V	ENST00000441802	NM_005245.3	3644	gCg/gTg	19/27	1	2	FACETS	0.911	0.792	1	0.911	0.792	1	CLONAL	1	TRUE	1	0.18	2		698	854	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100286	8100286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241255776	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	37	705	0	ENST00000346208.3:c.260C>T	p.Pro87Leu	p.P87L	ENST00000346208		87	cCg/cTg	3/6	1	2	FACETS	0.61	0.501	0.732	0.61	0.501	0.732	SUBCLONAL	1	TRUE	1	0.18	2		705	674	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639380	3639380	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs781663547	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	68	744	0	ENST00000294008.3:c.4259del	p.Pro1420GlnfsTer30	p.P1420Qfs*30	ENST00000294008	NM_032444.2	1420	cCa/ca	12/15	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.18	2		744	736	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430801	78430801	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	50	510	0	ENST00000370768.2:c.588G>T	p.Lys196Asn	p.K196N	ENST00000370768	NM_003902.3	196	aaG/aaT	8/20	1	2	FACETS	0.923	0.782	1	0.923	0.782	1	CLONAL	1	TRUE	1	0.18	2		510	602	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332642	70332642	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1473362793	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	45	515	0	ENST00000373644.4:c.547G>A	p.Gly183Ser	p.G183S	ENST00000373644	NM_030625.2	183	Ggt/Agt	2/12	1	2	FACETS	0.945	0.794	1	0.945	0.794	1	CLONAL	1	TRUE	1	0.18	2		515	529	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110190	8110190	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761178783	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	38	565	0	ENST00000585124.1:c.415C>T	p.Arg139Cys	p.R139C	ENST00000585124	NM_004217.3	139	Cgt/Tgt	6/9	1	2	FACETS	0.663	0.547	0.793	0.663	0.547	0.793	SUBCLONAL	1	TRUE	1	0.18	2		565	637	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676225	29676225	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	34	346	0	ENST00000356175.3:c.7214del	p.Cys2405LeufsTer6	p.C2405Lfs*6	ENST00000356175	NM_000267.3	2405	tGt/tt	48/57	1	2	FACETS	1	0.836	1	1	0.836	1	CLONAL	1	TRUE	1	0.18	2		346	369	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145704	11145704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	76	701	3	ENST00000358026.2:c.4066C>T	p.Arg1356Trp	p.R1356W	ENST00000358026	NM_001128849.1	1356	Cgg/Tgg	29/36	1	2	FACETS	0.959	0.839	1	0.959	0.839	1	CLONAL	1	TRUE	1	0.18	2		704	881	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31015938	31015938	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	39	359	0	ENST00000375687.4:c.260C>T	p.Ala87Val	p.A87V	ENST00000375687	NM_015338.5	87	gCc/gTc	5/13	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.18	2		359	417	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37622772	37622772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	61	762	0	ENST00000249071.6:c.520C>T	p.Arg174Trp	p.R174W	ENST00000249071	NM_002872.4	174	Cgg/Tgg	6/7	1	2	FACETS	0.683	0.587	0.788	0.683	0.587	0.788	SUBCLONAL	1	TRUE	1	0.18	2		762	992	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807996	1807996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	65	883	2	ENST00000260795.2:c.1972G>A	p.Val658Met	p.V658M	ENST00000260795		658	Gtg/Atg	14/17	1	2	FACETS	0.774	0.669	0.888	0.774	0.669	0.888	SUBCLONAL	1	TRUE	1	0.18	2		885	933	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974264	2974264	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	40	590	0	ENST00000396946.4:c.1342-1G>T		p.X448_splice	ENST00000396946	NM_032415.4	448			1	2	FACETS	0.646	0.535	0.77	0.646	0.535	0.77	SUBCLONAL	1	TRUE	1	0.18	2		590	688	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509435	106509435	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	49	530	0	ENST00000359195.3:c.1429C>A	p.Arg477Ser	p.R477S	ENST00000359195	NM_002649.2	477	Cgt/Agt	2/11	1	2	FACETS	0.885	0.749	1	0.885	0.749	1	CLONAL	1	TRUE	1	0.18	2		530	615	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140508767	140508767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746348396	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	51	446	0	ENST00000288602.6:c.533G>A	p.Arg178Gln	p.R178Q	ENST00000288602	NM_004333.4	178	cGa/cAa	4/18	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.18	2		446	440	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336316	80336316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1412853649	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	41	381	0	ENST00000286548.4:c.1003G>A	p.Glu335Lys	p.E335K	ENST00000286548	NM_002072.3	335	Gag/Aag	7/7	1	2	FACETS	0.864	0.719	1	0.864	0.719	1	CLONAL	1	TRUE	1	0.18	2		381	527	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399314	139399314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554727837	NA	P-0043177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	79	775	1	ENST00000277541.6:c.4829C>T	p.Ala1610Val	p.A1610V	ENST00000277541	NM_017617.3	1610	gCa/gTa	26/34	1	2	FACETS	0.857	0.752	0.971	0.857	0.752	0.971	CLONAL	1	TRUE	1	0.18	2		776	1024	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0043177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	24	413	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.858	0.672	1	0.858	0.672	1	CLONAL	1	TRUE	1	0.12	2		413	466	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	22	619	1	ENST00000324856.7:c.4555del	p.Gln1519ArgfsTer8	p.Q1519Rfs*8	ENST00000324856	NM_006015.4	1517	gCc/gc	18/20	1	2	FACETS	1	0.802	1	1	0.802	1	CLONAL	1	TRUE	1	0.12	2		620	353	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106732	27106732	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	22	600	0	ENST00000324856.7:c.6343C>T	p.Gln2115Ter	p.Q2115*	ENST00000324856	NM_006015.4	2115	Cag/Tag	20/20	1	2	FACETS	0.973	0.753	1	0.973	0.753	1	CLONAL	1	TRUE	1	0.12	2		600	377	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246597	46246597	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	10	180	0	ENST00000334344.6:c.4691C>A	p.Thr1564Asn	p.T1564N	ENST00000334344	NM_152641.2	1564	aCt/aAt	15/21	1	2	FACETS	0.963	0.654	1	0.963	0.654	1	CLONAL	1	TRUE	1	0.12	2		180	173	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420460	49420460	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	23	613	0	ENST00000301067.7:c.15289C>T	p.Arg5097Ter	p.R5097*	ENST00000301067	NM_003482.3	5097	Cga/Tga	48/54	1	2	FACETS	0.93	0.724	1	0.93	0.724	1	CLONAL	1	TRUE	1	0.12	2		613	412	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937017	48937017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752342013	NA	P-0043177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	26	369	0	ENST00000267163.4:c.785G>A	p.Arg262Gln	p.R262Q	ENST00000267163	NM_000321.2	262	cGg/cAg	8/27	0.0996483579010375	3	FACETS	1	0.802	1	0.507	0.401	0.629	CLONAL	1	TRUE	1	0.12	3		369	453	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641340	23641340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141458731	NA	P-0043177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	25	659	0	ENST00000261584.4:c.2135C>T	p.Ala712Val	p.A712V	ENST00000261584	NM_024675.3	712	gCg/gTg	5/13	0.0996483579010375	0	FACETS	0.817	0.643	1			1	CLONAL	1	TRUE	0	0.12	0		659	449	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702332	47702332	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	20	337	0	ENST00000233146.2:c.1929del	p.Val644PhefsTer41	p.V644Ffs*41	ENST00000233146	NM_000251.2	643	gAa/ga	12/16	1	2	FACETS	0.887	0.677	1	0.887	0.677	1	CLONAL	1	TRUE	1	0.12	2		337	376	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645099	86645099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1305400293	NA	P-0043177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	24	326	0	ENST00000274376.6:c.1171C>T	p.Arg391Trp	p.R391W	ENST00000274376	NM_002890.2	391	Cgg/Tgg	8/25	0.0996483579010375	3	FACETS	1	0.84	1	0.545	0.427	0.682	CLONAL	1	TRUE	1	0.12	3		326	389	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874147	151874148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs747256476	NA	P-0043334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	290	565	7	ENST00000262189.6:c.8390dup	p.Glu2798GlyfsTer11	p.E2798Gfs*11	ENST00000262189	NM_170606.2	2797	aag/aaAg	38/59	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.378661138972659	NA		572	650	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	218	326	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.378661138972659	NA		326	550	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717661	89717661	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0043334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	387	599	0	ENST00000371953.3:c.686C>G	p.Ser229Ter	p.S229*	ENST00000371953	NM_000314.4	229	tCa/tGa	7/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.378661138972659	NA		599	674	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0043334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	623	480	3	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.378661138972659	NA		483	832	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577093	7577093	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882008	NA	P-0043334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	653	783	0	ENST00000269305.4:c.845G>C	p.Arg282Pro	p.R282P	ENST00000269305	NM_001126112.2	282	cGg/cCg	8/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.378661138972659	NA		783	888	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934133	39934133	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	400	695	1	ENST00000378444.4:c.466C>T	p.Gln156Ter	p.Q156*	ENST00000378444	NM_001123385.1	156	Caa/Taa	4/15	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.378661138972659	NA		696	1464	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38991131	38991131	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0043334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	329	500	0	ENST00000357387.3:c.503C>G	p.Ser168Ter	p.S168*	ENST00000357387	NM_152756.3	168	tCa/tGa	7/38	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.378661138972659	NA		500	957	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11318615	11318615	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	190	520	0	ENST00000361445.4:c.198A>T	p.Gln66His	p.Q66H	ENST00000361445	NM_004958.3	66	caA/caT	3/58	0.378661138972659	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.378661138972659	1		520	768	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201930	102201930	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	147	360	0	ENST00000263464.3:c.1282A>G	p.Arg428Gly	p.R428G	ENST00000263464	NM_001165.4	428	Agg/Ggg	6/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.378661138972659	NA		360	564	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189493	56189493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769426596	NA	P-0043334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	327	447	0	ENST00000399503.3:c.4525C>T	p.Arg1509Cys	p.R1509C	ENST00000399503	NM_005921.1	1509	Cgt/Tgt	20/20	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.378661138972659	NA		447	491	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732969	30732969	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	45	348	0	ENST00000295754.5:c.1582C>G	p.Arg528Gly	p.R528G	ENST00000295754	NM_003242.5	528	Cgt/Ggt	7/7	1	2	FACETS	0.794	0.671	0.928	0.794	0.671	0.928	CLONAL	1	FALSE	1	0.396436942411362	2		348	286	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40477076	40477076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	59	376	2	ENST00000264657.5:c.1369C>T	p.His457Tyr	p.H457Y	ENST00000264657	NM_139276.2	457	Cac/Tac	16/24	1	2	FACETS	0.863	0.746	0.988	0.863	0.746	0.988	CLONAL	1	FALSE	1	0.396436942411362	2		378	345	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262335	46262335	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs955693886	NA	P-0043937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	15	341	0	ENST00000371998.3:c.919C>G	p.Leu307Val	p.L307V	ENST00000371998		307	Cta/Gta	9/23	1	2	FACETS	0.382	0.28	0.504	0.382	0.28	0.504	SUBCLONAL	1	FALSE	1	0.396436942411362	2		341	198	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051625	30051625	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0043937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	37	273	0	ENST00000338641.4:c.559A>T	p.Arg187Ter	p.R187*	ENST00000338641	NM_000268.3	187	Aga/Tga	6/16	0.373538281006521	1	FACETS	0.645	0.536	0.765	0.645	0.536	0.765	SUBCLONAL	1	FALSE	0	0.396436942411362	1		273	232	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144849	47144849	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	30	293	0	ENST00000409792.3:c.4904G>T	p.Cys1635Phe	p.C1635F	ENST00000409792	NM_014159.6	1635	tGt/tTt	7/21	1	2	FACETS	0.784	0.637	0.948	0.784	0.637	0.948	CLONAL	1	FALSE	1	0.396436942411362	2		293	193	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044362-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	80	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.918	0.81	1	0.918	0.81	1	CLONAL	1	TRUE	1	0.33	2		298	528	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040995	47040995	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044362-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	112	393	0	ENST00000377604.3:c.1525C>T	p.Gln509Ter	p.Q509*	ENST00000377604	NM_001204468.1	509	Caa/Taa	14/24	1	1	FACETS	0.817	0.743	0.893	1	0.987	1	CLONAL	2	TRUE	0	0.33	1		393	347	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989476	7989476	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044362-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	83	692	0	ENST00000319144.4:c.210C>A	p.His70Gln	p.H70Q	ENST00000319144	NM_001139.2	70	caC/caA	2/15	1	2	FACETS	0.87	0.769	0.978	0.87	0.769	0.978	CLONAL	1	TRUE	1	0.33	2		692	578	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187558069	187558069	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0044362-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	88	454	0	ENST00000441802.2:c.3643-1G>T		p.X1215_splice	ENST00000441802	NM_005245.3	1215			1	2	FACETS	0.932	0.828	1	0.932	0.828	1	CLONAL	1	TRUE	1	0.33	2		454	572	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958165	2958165	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044362-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	111	599	0	ENST00000396946.4:c.2567A>T	p.Glu856Val	p.E856V	ENST00000396946	NM_032415.4	856	gAg/gTg	19/25	0.128915348217356	3	FACETS	1	0.973	1	0.615	0.554	0.68	INDETERMINATE	1	TRUE	1	0.33	3		599	637	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332041	81332041	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044362-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	139	418	0	ENST00000222390.5:c.2043A>T	p.Gln681His	p.Q681H	ENST00000222390	NM_000601.4	681	caA/caT	18/18	0.128915348217356	3	FACETS	1	0.984	1	0.685	0.625	0.749	INDETERMINATE	1	TRUE	1	0.33	3		418	716	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1327781	1327781	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044362-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	89	443	0	ENST00000400841.2:c.100A>T	p.Ile34Phe	p.I34F	ENST00000400841		34	Atc/Ttc	2/6	1	1	FACETS	0.845	0.751	0.945	0.845	0.751	0.945	CLONAL	1	TRUE	0	0.33	1		443	533	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0044808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	192	300	1	ENST00000374690.3:c.2105T>A	p.Leu702His	p.L702H	ENST00000374690	NM_000044.3	702	cTc/cAc	4/8	1	1	FACETS	0.697	0.651	0.743	0.697	0.651	0.743	SUBCLONAL	1	TRUE	0	0.731382955800961	1		301	478	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831069	72831069	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	247	468	0	ENST00000268489.5:c.5512C>T	p.Gln1838Ter	p.Q1838*	ENST00000268489	NM_006885.3	1838	Cag/Tag	9/10	0.634153034535046	3	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.731382955800961	3		468	862	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634326	23634328	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0044808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	265	478	0	ENST00000261584.4:c.2958_2960del	p.Asp986_Gln987delinsGlu	p.D986_Q987delinsE	ENST00000261584	NM_024675.3	986	gaTCAa/gaa	9/13	1	2	FACETS	0.884	0.831	0.937	0.884	0.831	0.937	CLONAL	1	TRUE	1	0.731382955800961	2		478	820	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226314	2226314	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	488	994	0	ENST00000398665.3:c.3794C>G	p.Ser1265Cys	p.S1265C	ENST00000398665	NM_032482.2	1265	tCc/tGc	27/28	0.731382955800961	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.731382955800961	1		994	844	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793309	33793330	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	GGCCGACTCCATGGGGGAGTTA	GGCCGACTCCATGGGGGAGTTA	-	novel	NA	P-0044808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	76	225	1	ENST00000498907.2:c.-10_12del		p.*4*	ENST00000498907	NM_004364.3	?-4/358		1/1	1	2	FACETS	0.617	0.545	0.692	0.617	0.545	0.692	SUBCLONAL	1	TRUE	1	0.731382955800961	2		226	337	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671666	30671666	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	189	715	0	ENST00000376406.3:c.5294A>T	p.Glu1765Val	p.E1765V	ENST00000376406	NM_014641.2	1765	gAa/gTa	10/15	1	2	FACETS	0.524	0.484	0.566	0.524	0.484	0.566	SUBCLONAL	1	TRUE	1	0.731382955800961	2		715	986	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862890	117862903	+	frameshift_variant	Frame_Shift_Del	DEL	TTTCTCCTTCTCTT	TTTCTCCTTCTCTT	-	novel	NA	P-0044808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	259	412	0	ENST00000297338.2:c.1574_1587del	p.Lys525ArgfsTer7	p.K525Rfs*7	ENST00000297338	NM_006265.2	525	aAAGAGAAGGAGAAA/a	12/14	0.571782112363569	4	FACETS	0.75	0.705	0.797			1	SUBCLONAL	2	TRUE	NA	0.731382955800961	4		412	817	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	129	326	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.66	2		326	353	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0044816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	253	679	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	0.993	0.933	1	0.993	0.933	1	CLONAL	1	TRUE	1	0.66	2		679	772	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799059	42799059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	91	932	1	ENST00000575354.2:c.4543C>T	p.Arg1515Cys	p.R1515C	ENST00000575354	NM_015125.3	1515	Cgc/Tgc	20/20	0.668868699890047	1	FACETS	0.269	0.238	0.301	0.269	0.238	0.301	SUBCLONAL	1	TRUE	0	0.66	1		933	688	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0044919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	350	564	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.304487030144011	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.32	3		564	766	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551215	29551215	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs777414641	NA	P-0044919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	59	469	0	ENST00000389048.3:c.1414+1G>A		p.X472_splice	ENST00000389048	NM_004304.4	472			0.304487030144011	3	FACETS	0.861	0.741	0.99	0.43	0.37	0.495	CLONAL	1	TRUE	1	0.32	3		469	497	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968017	18968155	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGTGGCCAGGTGGTGTCCTGTGCATCCTGGGGCCCCTACTTCCTTGCTAGTGTGTGTTGAGGCTGATTCACACCTGAGCTTCTTGACTTGTGGGGGCCCCTGTTCCTACAGCTGATCCTTGTAGGCGACCACTGCCAG	CTGTGGCCAGGTGGTGTCCTGTGCATCCTGGGGCCCCTACTTCCTTGCTAGTGTGTGTTGAGGCTGATTCACACCTGAGCTTCTTGACTTGTGGGGGCCCCTGTTCCTACAGCTGATCCTTGTAGGCGACCACTGCCAG	-	novel	NA	P-0044919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	44	253	0	ENST00000262803.5:c.1969-109_1998del		p.X657_splice	ENST00000262803	NM_002911.3	657		15/24	0.289526644455735	4	FACETS	1	0.955	1			1	CLONAL	1	TRUE	NA	0.32	4		253	258	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067818	30067818	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	44	316	0	ENST00000338641.4:c.1003G>A	p.Glu335Lys	p.E335K	ENST00000338641	NM_000268.3	335	Gag/Aag	11/16	0.273724059848343	2	FACETS	0.899	0.757	1	0.449	0.378	0.527	CLONAL	1	TRUE	0	0.32	2		316	306	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860758	151860758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	63	425	0	ENST00000262189.6:c.9904C>T	p.Pro3302Ser	p.P3302S	ENST00000262189	NM_170606.2	3302	Ccc/Tcc	43/59	0.296643602363179	4	FACETS	0.909	0.786	1	0.454	0.393	0.521	CLONAL	1	TRUE	2	0.32	4		425	572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0046201-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	293	565	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.443163816327573	2	FACETS	0.928	0.879	0.977	0.928	0.879	0.977	CLONAL	2	TRUE	0	0.449999985380887	2		565	702	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012389	29012389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161996687	NA	P-0046201-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	37	419	0	ENST00000282397.4:c.482C>T	p.Thr161Met	p.T161M	ENST00000282397	NM_002019.4	161	aCg/aTg	4/30	0.297176065320941	5	FACETS	0.452	0.371	0.542	0.151	0.123	0.181	SUBCLONAL	1	TRUE	2	0.449999985380887	5		419	610	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849054	156849054	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786205449	NA	P-0046201-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	42	543	0	ENST00000524377.1:c.1946G>A	p.Arg649Gln	p.R649Q	ENST00000524377	NM_002529.3	649	cGg/cAg	15/17	1	2	FACETS	0.264	0.219	0.313	0.264	0.219	0.313	SUBCLONAL	1	TRUE	1	0.449999985380887	2		543	708	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436026	56436026	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771831816	NA	P-0046201-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	320	648	1	ENST00000407977.2:c.1111C>T	p.Arg371Ter	p.R371*	ENST00000407977		371	Cga/Tga	9/10	0.444769290492172	2	FACETS	0.961	0.913	1	0.961	0.913	1	CLONAL	2	TRUE	0	0.449999985380887	2		649	740	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916120	9916120	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0046201-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	242	391	0	ENST00000330684.3:c.2168+1G>A		p.X723_splice	ENST00000330684	NM_001134407.1	723			0.443163816327573	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.449999985380887	2		391	492	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64289166	64289166	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046201-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	78	322	0	ENST00000370651.3:c.334C>T	p.Pro112Ser	p.P112S	ENST00000370651	NM_003463.4	112	Cca/Tca	5/6	0.119289286629586	4	FACETS	0.808	0.717	0.904	0.808	0.717	0.904	INDETERMINATE	2	TRUE	2	0.449999985380887	4		322	311	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916942	178916944	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	novel	NA	P-0046201-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	19	367	0	ENST00000263967.3:c.330_332del	p.Lys111del	p.K111del	ENST00000263967	NM_006218.2	110	gAAAag/gag	2/21	0.444769290492172	2	FACETS	0.367	0.279	0.47	0.184	0.139	0.235	SUBCLONAL	1	TRUE	0	0.449999985380887	2		367	230	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735356	204735356	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046201-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	33	539	0	ENST00000302823.3:c.157A>G	p.Ile53Val	p.I53V	ENST00000302823	NM_005214.4	53	Atc/Gtc	2/4	0.268843723893909	2	FACETS	0.222	0.18	0.27	0.111	0.09	0.135	INDETERMINATE	1	TRUE	0	0.449999985380887	2		539	660	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98011447	98011447	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046201-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	42	435	0	ENST00000289081.3:c.127G>C	p.Glu43Gln	p.E43Q	ENST00000289081	NM_000136.2	43	Gag/Cag	2/15	0.16646789539383	3	FACETS	0.492	0.41	0.582	0.246	0.205	0.291	INDETERMINATE	1	TRUE	1	0.449999985380887	3		435	465	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0046983-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	177	686	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.981	0.909	1	0.981	0.909	1	CLONAL	1	TRUE	1	0.641057896438337	2		686	563	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226349	133226349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046983-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	165	523	0	ENST00000320574.5:c.3709G>A	p.Glu1237Lys	p.E1237K	ENST00000320574	NM_006231.2	1237	Gag/Aag	30/49	1	2	FACETS	0.776	0.715	0.84	0.776	0.715	0.84	SUBCLONAL	1	TRUE	1	0.641057896438337	2		523	663	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877366	28877366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1392528455	NA	P-0046983-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	358	431	0	ENST00000282397.4:c.3955G>A	p.Ala1319Thr	p.A1319T	ENST00000282397	NM_002019.4	1319	Gcg/Acg	30/30	0.641057896438337	3	FACETS	0.953	0.909	0.997	0.953	0.909	0.997	CLONAL	2	TRUE	1	0.641057896438337	3		431	774	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0046983-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	367	675	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.640578495907039	2	FACETS	0.932	0.895	0.969	0.932	0.895	0.969	CLONAL	2	TRUE	0	0.641057896438337	2		675	614	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533793	63533793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046983-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	279	628	0	ENST00000307078.5:c.1361C>T	p.Ser454Phe	p.S454F	ENST00000307078	NM_004655.3	454	tCt/tTt	6/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.641057896438337	2		628	826	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368252	45368252	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046983-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	188	378	0	ENST00000262160.6:c.1350C>G	p.Asp450Glu	p.D450E	ENST00000262160	NM_005901.5	450	gaC/gaG	11/11	0.641057896438337	1	FACETS	0.999	0.936	1	0.999	0.936	1	CLONAL	1	TRUE	0	0.641057896438337	1		378	399	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046983-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	208	508	0	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	0.641057896438337	1	FACETS	0.932	0.875	0.99	0.932	0.875	0.99	CLONAL	1	TRUE	0	0.641057896438337	1		508	473	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139010	50139010	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046983-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	219	570	0	ENST00000246792.3:c.553C>A	p.Gln185Lys	p.Q185K	ENST00000246792	NM_006270.3	185	Cag/Aag	5/6	1	2	FACETS	0.992	0.927	1	0.992	0.927	1	CLONAL	1	TRUE	1	0.641057896438337	2		570	689	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662283	227662283	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046983-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	484	632	0	ENST00000305123.5:c.1172G>C	p.Ser391Thr	p.S391T	ENST00000305123	NM_005544.2	391	aGt/aCt	1/2	0.641057896438337	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.641057896438337	3		632	976	SUCCESS
APC	324	MSKCC	GRCh37	5	112175551	112175552	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0046983-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	187	542	0	ENST00000257430.4:c.4260_4261del	p.Ser1421Ter	p.S1421*	ENST00000257430	NM_000038.5	1420	ccCAgt/ccgt	16/16	0.641057896438337	1	FACETS	0.875	0.817	0.934	0.875	0.817	0.934	CLONAL	1	TRUE	0	0.641057896438337	1		542	453	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172008	32172008	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046983-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	208	517	0	ENST00000375023.3:c.3024C>A	p.Asp1008Glu	p.D1008E	ENST00000375023	NM_004557.3	1008	gaC/gaA	19/30	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.641057896438337	2		517	646	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265313	152265313	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046983-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	139	375	0	ENST00000206249.3:c.766C>T	p.Arg256Ter	p.R256*	ENST00000206249	NM_000125.3	256	Cga/Tga	4/8	1	2	FACETS	0.951	0.873	1	0.951	0.873	1	CLONAL	1	TRUE	1	0.641057896438337	2		375	456	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526976	31526976	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1485879154	NA	P-0046983-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	193	448	0	ENST00000344624.3:c.64C>T	p.Arg22Ter	p.R22*	ENST00000344624		22	Cga/Tga	2/33	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.641057896438337	2		448	586	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	461486	461486	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046983-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	138	254	0	ENST00000399788.2:c.1034G>C	p.Cys345Ser	p.C345S	ENST00000399788	NM_001042603.1	345	tGt/tCt	9/28	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.641057896438337	2		254	393	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858648	9858648	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046983-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	181	568	0	ENST00000330684.3:c.2753C>G	p.Pro918Arg	p.P918R	ENST00000330684	NM_001134407.1	918	cCc/cGc	13/13	1	2	FACETS	0.856	0.792	0.921	0.856	0.792	0.921	CLONAL	1	TRUE	1	0.641057896438337	2		568	660	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026783	48026783	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881791	NA	P-0046983-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	215	480	0	ENST00000234420.5:c.1661G>A	p.Arg554His	p.R554H	ENST00000234420	NM_000179.2	554	cGt/cAt	4/10	0.641057896438337	3	FACETS	0.916	0.852	0.982	0.458	0.426	0.491	CLONAL	1	TRUE	1	0.641057896438337	3		480	967	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1932456	1932456	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046983-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	178	406	0	ENST00000382891.5:c.1514A>C	p.Lys505Thr	p.K505T	ENST00000382891	NM_133335.3	505	aAg/aCg	6/22	1	2	FACETS	0.904	0.838	0.973	0.904	0.838	0.973	CLONAL	1	TRUE	1	0.641057896438337	2		406	614	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0046983-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	116	686	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.446375601411913	1	FACETS	0.994	0.904	1	0.994	0.904	1	CLONAL	1	TRUE	0	0.446375601411913	1		686	406	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226349	133226349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046983-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	105	523	0	ENST00000320574.5:c.3709G>A	p.Glu1237Lys	p.E1237K	ENST00000320574	NM_006231.2	1237	Gag/Aag	30/49	1	2	FACETS	0.828	0.744	0.917	0.828	0.744	0.917	CLONAL	1	TRUE	1	0.446375601411913	2		523	568	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877366	28877366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1392528455	NA	P-0046983-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	135	431	0	ENST00000282397.4:c.3955G>A	p.Ala1319Thr	p.A1319T	ENST00000282397	NM_002019.4	1319	Gcg/Acg	30/30	1	2	FACETS	0.944	0.86	1	0.944	0.86	1	CLONAL	1	TRUE	1	0.446375601411913	2		431	641	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972432	32972432	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046983-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	117	544	0	ENST00000380152.3:c.9782A>G	p.Asp3261Gly	p.D3261G	ENST00000380152		3261	gAc/gGc	27/27	1	2	FACETS	0.837	0.757	0.922	0.837	0.757	0.922	CLONAL	1	TRUE	1	0.446375601411913	2		544	626	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0046983-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	102	675	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.446375601411913	1	FACETS	0.87	0.784	0.96	0.87	0.784	0.96	CLONAL	1	TRUE	0	0.446375601411913	1		675	408	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533793	63533793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046983-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	126	628	0	ENST00000307078.5:c.1361C>T	p.Ser454Phe	p.S454F	ENST00000307078	NM_004655.3	454	tCt/tTt	6/11	1	2	FACETS	0.873	0.792	0.957	0.873	0.792	0.957	CLONAL	1	TRUE	1	0.446375601411913	2		628	647	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368252	45368252	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046983-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	141	378	0	ENST00000262160.6:c.1350C>G	p.Asp450Glu	p.D450E	ENST00000262160	NM_005901.5	450	gaC/gaG	11/11	0.446375601411913	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.446375601411913	1		378	381	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046983-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	120	508	0	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	0.446375601411913	1	FACETS	0.93	0.846	1	0.93	0.846	1	CLONAL	1	TRUE	0	0.446375601411913	1		508	449	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139010	50139010	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046983-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	120	570	0	ENST00000246792.3:c.553C>A	p.Gln185Lys	p.Q185K	ENST00000246792	NM_006270.3	185	Cag/Aag	5/6	1	2	FACETS	0.924	0.837	1	0.924	0.837	1	CLONAL	1	TRUE	1	0.446375601411913	2		570	582	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662283	227662283	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046983-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	126	632	0	ENST00000305123.5:c.1172G>C	p.Ser391Thr	p.S391T	ENST00000305123	NM_005544.2	391	aGt/aCt	1/2	1	2	FACETS	0.867	0.787	0.951	0.867	0.787	0.951	CLONAL	1	TRUE	1	0.446375601411913	2		632	651	SUCCESS
APC	324	MSKCC	GRCh37	5	112175551	112175552	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0046983-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	137	542	0	ENST00000257430.4:c.4260_4261del	p.Ser1421Ter	p.S1421*	ENST00000257430	NM_000038.5	1420	ccCAgt/ccgt	16/16	0.446375601411913	1	FACETS	0.929	0.85	1	0.929	0.85	1	CLONAL	1	TRUE	0	0.446375601411913	1		542	513	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172008	32172008	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046983-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	253	517	0	ENST00000375023.3:c.3024C>A	p.Asp1008Glu	p.D1008E	ENST00000375023	NM_004557.3	1008	gaC/gaA	19/30	0.43592968188536	2	FACETS	0.984	0.929	1	0.984	0.929	1	CLONAL	2	TRUE	0	0.446375601411913	2		517	576	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265313	152265313	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046983-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	85	375	0	ENST00000206249.3:c.766C>T	p.Arg256Ter	p.R256*	ENST00000206249	NM_000125.3	256	Cga/Tga	4/8	1	2	FACETS	0.972	0.864	1	0.972	0.864	1	CLONAL	1	TRUE	1	0.446375601411913	2		375	392	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0047181-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	202	387	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.510282895191921	3	FACETS	0.943	0.882	1			1	CLONAL	2	TRUE	NA	0.510282895191921	3		388	527	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207118	1207118	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047181-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	341	529	0	ENST00000326873.7:c.206C>A	p.Ser69Ter	p.S69*	ENST00000326873	NM_000455.4	69	tCg/tAg	1/10	0.503387248582159	2	FACETS	0.901	0.858	0.943	0.901	0.858	0.943	CLONAL	2	TRUE	0	0.510282895191921	2		529	742	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274541	198274541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047181-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	147	503	0	ENST00000335508.6:c.857C>T	p.Ser286Phe	p.S286F	ENST00000335508	NM_012433.2	286	tCc/tTc	7/25	1	2	FACETS	0.847	0.775	0.922	0.847	0.775	0.922	CLONAL	1	TRUE	1	0.510282895191921	2		503	680	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054395	42054396	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047181-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	104	394	0	ENST00000219905.7:c.7585dup	p.Arg2529LysfsTer9	p.R2529Kfs*9	ENST00000219905	NM_001164273.1	2527	caa/cAaa	22/24	1	2	FACETS	0.759	0.682	0.84	0.759	0.682	0.84	SUBCLONAL	1	TRUE	1	0.510282895191921	2		394	537	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259196	89259196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047181-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	175	500	0	ENST00000336596.2:c.340G>A	p.Gly114Arg	p.G114R	ENST00000336596	NM_005233.5	114	Gga/Aga	3/17	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.510282895191921	2		500	651	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227925	123227925	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047181-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	81	325	0	ENST00000218089.9:c.3636G>C	p.Met1212Ile	p.M1212I	ENST00000218089	NM_001042749.1	1212	atG/atC	33/35	1	2	FACETS	0.735	0.65	0.825	0.735	0.65	0.825	SUBCLONAL	1	TRUE	1	0.510282895191921	2		325	432	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923802	39923808	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCTGG	CCTCTGG	-	novel	NA	P-0047718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	73	601	0	ENST00000378444.4:c.3283_3289del	p.Pro1095ThrfsTer16	p.P1095Tfs*16	ENST00000378444	NM_001123385.1	1095	CCAGAGGac/ac	7/15	1	2	FACETS	0.929	0.811	1	0.929	0.811	1	CLONAL	1	TRUE	1	0.17	2		601	924	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0047733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	424	672	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.110965724825754	5	FACETS	0.897	0.859	0.936			1	INDETERMINATE	4	TRUE	NA	0.402244309900464	5		672	942	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481601	40481601	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	155	559	0	ENST00000264657.5:c.1204G>C	p.Gly402Arg	p.G402R	ENST00000264657	NM_139276.2	402	Ggc/Cgc	13/24	0.344136762829289	4	FACETS	1	0.962	1	0.272	0.249	0.297	CLONAL	1	TRUE	0	0.402244309900464	4		559	992	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40497650	40497650	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	466	529	0	ENST00000264657.5:c.299A>G	p.Glu100Gly	p.E100G	ENST00000264657	NM_139276.2	100	gAg/gGg	4/24	0.344136762829289	4	FACETS	0.886	0.851	0.92	0.886	0.851	0.92	CLONAL	4	TRUE	0	0.402244309900464	4		529	917	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480499	57480499	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	126	322	0	ENST00000371085.3:c.494G>C	p.Arg165Pro	p.R165P	ENST00000371085	NM_000516.4	165	cGc/cCc	6/13	0.342932763887371	3	FACETS	0.774	0.705	0.846	0.516	0.47	0.564	SUBCLONAL	2	TRUE	0	0.402244309900464	3		322	486	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396917	139396928	+	inframe_deletion	In_Frame_Del	DEL	GCGGGGGCGGCT	GCGGGGGCGGCT	-	novel	NA	P-0047733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	105	540	0	ENST00000277541.6:c.5180_5191del	p.Glu1727_Pro1731delinsAla	p.E1727_P1731delinsA	ENST00000277541	NM_017617.3	1727	gAGCCGCCCCCGCcg/gcg	28/34	0.264250480512636	4	FACETS	0.865	0.775	0.962	0.433	0.387	0.481	CLONAL	1	TRUE	2	0.402244309900464	4		540	846	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	119	414	2	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.781702487888262	2		416	252	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	123	845	0	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.781702487888262	2		845	300	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438316	110438317	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	rs532810290	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	45	409	0	ENST00000375856.3:c.82_84dup	p.Asn28dup	p.N28dup	ENST00000375856	NM_003749.2	28	-/AAC	1/2	1	2	FACETS	0.496	0.421	0.578	0.496	0.421	0.578	SUBCLONAL	1	TRUE	1	0.781702487888262	2		409	232	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169085	119169085	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146517083	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	74	686	0	ENST00000264033.4:c.2269G>A	p.Ala757Thr	p.A757T	ENST00000264033	NM_005188.3	757	Gca/Aca	15/16	1	2	FACETS	0.731	0.648	0.818	0.731	0.648	0.818	SUBCLONAL	1	TRUE	1	0.781702487888262	2		686	259	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533905	63533905	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	20	684	0	ENST00000307078.5:c.1249del	p.Ala417ArgfsTer41	p.A417Rfs*41	ENST00000307078	NM_004655.3	417	Gcg/cg	6/11	1	2	FACETS	0.181	0.138	0.231	0.181	0.138	0.231	SUBCLONAL	1	TRUE	1	0.781702487888262	2		684	283	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	154	828	2	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.781702487888262	2		830	343	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931452	131931452	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507178	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	89	534	10	ENST00000265335.6:c.2165del	p.Lys722ArgfsTer14	p.K722Rfs*14	ENST00000265335		719	ctA/ct	13/25	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.781702487888262	2		544	225	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	350	574	26	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	0.781702487888262	4	FACETS	0.992	0.955	1	0.992	0.955	1	CLONAL	3	TRUE	1	0.781702487888262	4		600	536	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55569954	55569954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138585275	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	71	478	0	ENST00000288135.5:c.821C>T	p.Thr274Met	p.T274M	ENST00000288135	NM_000222.2	274	aCg/aTg	5/21	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.781702487888262	2		478	168	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	132	719	3	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.781702487888262	2		722	309	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	62	613	10	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.901	0.795	1	0.901	0.795	1	CLONAL	1	TRUE	1	0.781702487888262	2		623	176	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	68	527	0	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.619	0.544	0.699	0.619	0.544	0.699	SUBCLONAL	1	TRUE	1	0.781702487888262	2		527	281	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790455	3790455	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783490	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	133	488	1	ENST00000262367.5:c.4078C>T	p.Arg1360Ter	p.R1360*	ENST00000262367	NM_004380.2	1360	Cga/Tga	24/31	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.781702487888262	2		489	293	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670755	67670755	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	17	575	0	ENST00000264010.4:c.1999+1G>A		p.X667_splice	ENST00000264010	NM_006565.3	667			1	2	FACETS	0.145	0.107	0.189	0.145	0.107	0.189	SUBCLONAL	1	TRUE	1	0.781702487888262	2		575	301	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748480	43748480	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395807781	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	124	554	0	ENST00000523873.1:c.434G>A	p.Arg145Gln	p.R145Q	ENST00000523873		145	cGa/cAa	6/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.781702487888262	2		554	284	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164563	36164563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1340631548	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	61	625	0	ENST00000300305.3:c.1312G>A	p.Gly438Ser	p.G438S	ENST00000300305		438	Ggc/Agc	8/8	0.781702487888262	3	FACETS	0.646	0.561	0.738	0.323	0.28	0.369	SUBCLONAL	1	TRUE	1	0.781702487888262	3		625	336	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041375	42041375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764277967	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	120	712	0	ENST00000219905.7:c.5570C>T	p.Ser1857Leu	p.S1857L	ENST00000219905	NM_001164273.1	1857	tCg/tTg	17/24	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.781702487888262	2		712	262	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181311	123181311	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs774761933	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	75	194	0	ENST00000218089.9:c.775C>T	p.Arg259Ter	p.R259*	ENST00000218089	NM_001042749.1	259	Cga/Tga	9/35	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.781702487888262	1		194	82	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217623	7217623	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	114	602	0	ENST00000380728.2:c.304C>T	p.Arg102Ter	p.R102*	ENST00000380728		102	Cga/Tga	4/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.781702487888262	2		602	272	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856520	45856520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751318902	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	182	772	0	ENST00000391945.4:c.1738G>A	p.Ala580Thr	p.A580T	ENST00000391945	NM_000400.3	580	Gcc/Acc	18/23	0.166347364720192	4	FACETS	1	0.984	1	1	0.984	1	INDETERMINATE	2	TRUE	2	0.781702487888262	4		772	360	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128848687	128848687	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1204546630	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	95	589	0	ENST00000249373.3:c.1352G>A	p.Arg451His	p.R451H	ENST00000249373	NM_005631.4	451	cGc/cAc	7/12	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.781702487888262	2		589	226	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980558	1980559	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs752037034	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	107	861	16	ENST00000382891.5:c.4028dup	p.Glu1344ArgfsTer91	p.E1344Rfs*91	ENST00000382891	NM_133335.3	1340	-/C	22/22	1	2	FACETS	0.916	0.833	1	0.916	0.833	1	CLONAL	1	TRUE	1	0.781702487888262	2		877	299	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874147	151874148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs747256476	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	71	565	7	ENST00000262189.6:c.8390dup	p.Glu2798GlyfsTer11	p.E2798Gfs*11	ENST00000262189	NM_170606.2	2797	aag/aaAg	38/59	1	2	FACETS	0.882	0.784	0.984	0.882	0.784	0.984	CLONAL	1	TRUE	1	0.781702487888262	2		572	206	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	148	306	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.781702487888262	2		306	335	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609084	43609086	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs377767399	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	116	942	0	ENST00000355710.3:c.1846_1848del	p.Glu616del	p.E616del	ENST00000355710	NM_020975.4	614	GAG/-	10/20	0.781702487888262	3	FACETS	1	0.915	1	0.503	0.457	0.551	CLONAL	1	TRUE	1	0.781702487888262	3		942	410	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048667	180048667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749960761	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	108	822	1	ENST00000261937.6:c.1895G>A	p.Arg632His	p.R632H	ENST00000261937	NM_182925.4	632	cGc/cAc	13/30	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.781702487888262	2		823	229	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445149	49445149	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	133	991	2	ENST00000301067.7:c.2317del	p.Gln773SerfsTer157	p.Q773Sfs*157	ENST00000301067	NM_003482.3	773	Cag/ag	10/54	1	2	FACETS	0.94	0.864	1	0.94	0.864	1	CLONAL	1	TRUE	1	0.781702487888262	2		993	362	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942852	68942852	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	47	623	0	ENST00000288368.4:c.664G>A	p.Glu222Lys	p.E222K	ENST00000288368	NM_024870.2	222	Gaa/Aaa	6/40	0.781702487888262	3	FACETS	0.764	0.651	0.885	0.382	0.325	0.443	SUBCLONAL	1	TRUE	1	0.781702487888262	3		623	219	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099262	4099262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730880523	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	94	739	1	ENST00000262948.5:c.856G>A	p.Gly286Arg	p.G286R	ENST00000262948	NM_030662.3	286	Ggg/Agg	7/11	0.166347364720192	4	FACETS	0.952	0.864	1	0.952	0.864	1	INDETERMINATE	2	TRUE	2	0.781702487888262	4		740	225	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245026	41245026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80357337	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	95	587	0	ENST00000357654.3:c.2522G>A	p.Arg841Gln	p.R841Q	ENST00000357654	NM_007294.3	841	cGg/cAg	10/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.781702487888262	2		587	190	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106558	27106558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	163	867	0	ENST00000324856.7:c.6169C>T	p.Arg2057Trp	p.R2057W	ENST00000324856	NM_006015.4	2057	Cgg/Tgg	20/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.781702487888262	2		867	327	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155386	106155386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1238868376	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	71	604	0	ENST00000380013.4:c.287G>A	p.Arg96His	p.R96H	ENST00000380013	NM_001127208.2	96	cGc/cAc	3/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.781702487888262	2		604	151	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508786	31508786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	105	472	0	ENST00000344624.3:c.1529G>A	p.Arg510His	p.R510H	ENST00000344624		510	cGc/cAc	7/33	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.781702487888262	2		472	224	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996257	73996257	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775475628	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	15	122	0	ENST00000318443.5:c.991C>T	p.Arg331Cys	p.R331C	ENST00000318443	NM_001024736.1	331	Cgt/Tgt	5/10	1	2	FACETS	1	0.779	1	1	0.779	1	CLONAL	1	TRUE	1	0.781702487888262	2		122	38	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106592	27106592	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	131	812	0	ENST00000324856.7:c.6203C>T	p.Ser2068Leu	p.S2068L	ENST00000324856	NM_006015.4	2068	tCg/tTg	20/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.781702487888262	2		812	318	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8113505	8113505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	16	475	0	ENST00000585124.1:c.38G>A	p.Gly13Asp	p.G13D	ENST00000585124	NM_004217.3	13	gGc/gAc	2/9	1	2	FACETS	0.155	0.114	0.204	0.155	0.114	0.204	SUBCLONAL	1	TRUE	1	0.781702487888262	2		475	264	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958480	90958480	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	52	403	0	ENST00000265433.3:c.1958del	p.Lys653SerfsTer4	p.K653Sfs*4	ENST00000265433	NM_002485.4	653	aAg/ag	13/16	0.781702487888262	3	FACETS	1	0.899	1	0.523	0.453	0.597	CLONAL	1	TRUE	1	0.781702487888262	3		403	177	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491375	2491375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760189429	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	150	811	0	ENST00000355716.4:c.418G>A	p.Ala140Thr	p.A140T	ENST00000355716	NM_003820.2	140	Gct/Act	4/8	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.781702487888262	2		811	317	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748014	72748014	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1364690756	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	104	721	1	ENST00000357731.5:c.164C>T	p.Thr55Met	p.T55M	ENST00000357731	NM_173808.2	55	aCg/aTg	1/7	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.781702487888262	2		722	236	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468261	120468261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587735797	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	111	870	0	ENST00000256646.2:c.4178G>A	p.Arg1393His	p.R1393H	ENST00000256646	NM_024408.3	1393	cGc/cAc	25/34	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.781702487888262	2		870	248	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552736	18552736	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	31	594	0	ENST00000266497.5:c.2147G>T	p.Trp716Leu	p.W716L	ENST00000266497		716	tGg/tTg	14/31	1	2	FACETS	0.601	0.494	0.717	0.601	0.494	0.717	SUBCLONAL	1	TRUE	1	0.781702487888262	2		594	132	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591612	38591612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057518150	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	53	389	0	ENST00000299084.4:c.71G>A	p.Arg24Gln	p.R24Q	ENST00000299084	NM_152594.2	24	cGa/cAa	2/7	1	2	FACETS	0.788	0.685	0.897	0.788	0.685	0.897	SUBCLONAL	1	TRUE	1	0.781702487888262	2		389	172	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130308	2130308	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1555511520	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	144	767	0	ENST00000219476.3:c.3540G>T	p.Lys1180Asn	p.K1180N	ENST00000219476	NM_000548.3	1180	aaG/aaT	30/42	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.781702487888262	2		767	355	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81941300	81941300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369542682	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	120	527	0	ENST00000359376.3:c.1478G>A	p.Arg493Gln	p.R493Q	ENST00000359376	NM_002661.3	493	cGg/cAg	16/33	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.781702487888262	2		527	261	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621149	1621149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376498623	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	115	795	0	ENST00000344749.5:c.997G>A	p.Gly333Ser	p.G333S	ENST00000344749	NM_001136139.2	333	Ggc/Agc	12/19	0.166347364720192	4	FACETS	0.95	0.87	1	0.95	0.87	1	INDETERMINATE	2	TRUE	2	0.781702487888262	4		795	276	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250476	10250476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	142	712	0	ENST00000340748.4:c.3776G>A	p.Arg1259Gln	p.R1259Q	ENST00000340748		1259	cGg/cAg	33/40	0.166347364720192	4	FACETS	1	0.945	1	1	0.945	1	INDETERMINATE	2	TRUE	2	0.781702487888262	4		712	316	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635692	47635692	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	55	372	0	ENST00000233146.2:c.364A>T	p.Lys122Ter	p.K122*	ENST00000233146	NM_000251.2	122	Aag/Tag	2/16	1	2	FACETS	0.932	0.816	1	0.932	0.816	1	CLONAL	1	TRUE	1	0.781702487888262	2		372	151	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169361	99169361	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1392799869	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	123	654	0	ENST00000074304.5:c.1291C>T	p.Arg431Trp	p.R431W	ENST00000074304	NM_001134224.1	431	Cgg/Tgg	15/26	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.781702487888262	2		654	279	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713480	40713480	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	90	733	0	ENST00000373198.4:c.4035G>T	p.Gln1345His	p.Q1345H	ENST00000373198	NM_133170.3	1345	caG/caT	30/32	0.781702487888262	4	FACETS	0.972	0.868	1	0.324	0.289	0.361	CLONAL	1	TRUE	1	0.781702487888262	4		733	422	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566433	41566433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769217956	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	75	538	0	ENST00000263253.7:c.4310C>T	p.Ala1437Val	p.A1437V	ENST00000263253	NM_001429.3	1437	gCa/gTa	27/31	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.781702487888262	2		538	188	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949022	44949022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	43	233	0	ENST00000377967.4:c.3583C>T	p.Pro1195Ser	p.P1195S	ENST00000377967	NM_021140.2	1195	Ccc/Tcc	25/29	1	1	FACETS	0.918	0.811	1	0.918	0.811	1	CLONAL	1	TRUE	0	0.781702487888262	1		233	73	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	148	607	0	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.781702487888262	2		607	360	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1688545	1688545	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1015720948	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	83	623	0	ENST00000378625.1:c.779+1G>A		p.X260_splice	ENST00000378625	NM_001198994.1	260			1	2	FACETS	0.756	0.675	0.84	0.756	0.675	0.84	SUBCLONAL	1	TRUE	1	0.781702487888262	2		623	281	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957495	175957495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750125741	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	68	540	0	ENST00000367669.3:c.1901G>A	p.Arg634His	p.R634H	ENST00000367669	NM_022457.5	634	cGt/cAt	17/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.781702487888262	2		540	143	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557604	95557604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	54	610	0	ENST00000393063.1:c.5463G>A	p.Met1821Ile	p.M1821I	ENST00000393063	NM_030621.3	1821	atG/atA	26/28	1	2	FACETS	0.709	0.614	0.808	0.709	0.614	0.808	SUBCLONAL	1	TRUE	1	0.781702487888262	2		610	195	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122913	7122913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749951195	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	12	628	0	ENST00000302850.5:c.3346C>T	p.Arg1116Cys	p.R1116C	ENST00000302850	NM_000208.2	1116	Cgt/Tgt	18/22	0.166347364720192	4	FACETS	0.235	0.165	0.321	0.117	0.082	0.161	INDETERMINATE	1	TRUE	2	0.781702487888262	4		628	233	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101923	11101923	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502063	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	105	794	0	ENST00000358026.2:c.1343G>A	p.Arg448His	p.R448H	ENST00000358026	NM_001128849.1	448	cGc/cAc	8/36	0.166347364720192	4	FACETS	1	0.983	1	0.727	0.659	0.798	INDETERMINATE	1	TRUE	2	0.781702487888262	4		794	329	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145672	11145672	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746533073	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	102	776	0	ENST00000358026.2:c.4034C>T	p.Ser1345Leu	p.S1345L	ENST00000358026	NM_001128849.1	1345	tCg/tTg	29/36	0.166347364720192	4	FACETS	0.855	0.777	0.935	0.855	0.777	0.935	INDETERMINATE	2	TRUE	2	0.781702487888262	4		776	272	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990481	69990481	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs201247895	NA	P-0048166-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	65	394	0	ENST00000394351.3:c.440C>T	p.Thr147Met	p.T147M	ENST00000394351	NM_000248.3	147	aCg/aTg	4/9	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.781702487888262	2		394	151	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736385	85736385	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs770819167	NA	P-0049043-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	29	625	0	ENST00000370580.1:c.262C>T	p.Arg88Ter	p.R88*	ENST00000370580	NM_003921.4	88	Cga/Tga	2/3	1	2	FACETS	1	0.891	1	1	0.966	1	CLONAL	2	TRUE	1	0.434393194003336	2		625	62	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0049948-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	338	665	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.514903680957199	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.524067655700307	2		665	643	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030797	69030797	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049948-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	387	369	1	ENST00000288368.4:c.3339C>G	p.Ser1113Arg	p.S1113R	ENST00000288368	NM_024870.2	1113	agC/agG	27/40	0.417872581464787	3	FACETS	1	0.986	1			1	CLONAL	3	TRUE	NA	0.524067655700307	3		370	593	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0049948-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	349	401	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.524067655700307	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	3	TRUE	1	0.524067655700307	4		401	670	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423113	47423113	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs368594699	NA	P-0049948-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	409	559	0	ENST00000404338.3:c.1181T>C	p.Ile394Thr	p.I394T	ENST00000404338	NM_004491.4	394	aTt/aCt	1/6	0.487571662133246	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.524067655700307	4		559	1082	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523699	148523699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049948-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	157	407	0	ENST00000320356.2:c.754C>T	p.Leu252Phe	p.L252F	ENST00000320356	NM_004456.4	252	Ctc/Ttc	8/20	0.487571662133246	4	FACETS	1	0.971	1	0.564	0.517	0.613	CLONAL	1	TRUE	2	0.524067655700307	4		407	810	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68999990	68999990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049948-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	68	491	0	ENST00000288368.4:c.2059C>T	p.Leu687Phe	p.L687F	ENST00000288368	NM_024870.2	687	Ctt/Ttt	19/40	0.417872581464787	3	FACETS	0.486	0.422	0.555			1	SUBCLONAL	1	TRUE	NA	0.524067655700307	3		491	674	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091340	193091340	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050023-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	38	385	0	ENST00000367435.3:c.10G>A	p.Val4Met	p.V4M	ENST00000367435	NM_024529.4	4	Gtg/Atg	1/17	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.14	2		385	444	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244664	46244664	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555155026	NA	P-0050023-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	58	580	0	ENST00000334344.6:c.2758C>T	p.Gln920Ter	p.Q920*	ENST00000334344	NM_152641.2	920	Cag/Tag	15/21	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.14	2		580	787	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109958	115109958	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050023-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	25	546	0	ENST00000257566.3:c.1920C>A	p.Tyr640Ter	p.Y640*	ENST00000257566	NM_016569.3	640	taC/taA	8/8	1	2	FACETS	0.897	0.707	1	0.897	0.707	1	CLONAL	1	TRUE	1	0.14	2		546	398	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655480	67655480	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050023-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	14	345	0	ENST00000264010.4:c.1343G>T	p.Arg448Leu	p.R448L	ENST00000264010	NM_006565.3	448	cGa/cTa	7/12	1	2	FACETS	0.36	0.258	0.483	0.36	0.258	0.483	SUBCLONAL	1	TRUE	1	0.14	2		345	556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0050023-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	28	573	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	1	2	FACETS	0.576	0.458	0.71	0.576	0.458	0.71	SUBCLONAL	1	TRUE	1	0.14	2		573	695	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805398	46805399	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0050023-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	35	530	0	ENST00000290295.7:c.557dup	p.Glu187ArgfsTer23	p.E187Rfs*23	ENST00000290295	NM_006361.5	186	gga/ggGa	1/2	1	2	FACETS	0.796	0.651	0.96	0.796	0.651	0.96	CLONAL	1	TRUE	1	0.14	2		530	628	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860887	45860887	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0050023-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	59	632	0	ENST00000391945.4:c.1307+1G>A		p.X436_splice	ENST00000391945	NM_000400.3	436			1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.14	2		632	614	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436923	29436923	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050023-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	28	448	0	ENST00000389048.3:c.3670C>A	p.Leu1224Met	p.L1224M	ENST00000389048	NM_004304.4	1224	Ctg/Atg	24/29	1	2	FACETS	0.73	0.582	0.9	0.73	0.582	0.9	SUBCLONAL	1	TRUE	1	0.14	2		448	548	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162176	47162176	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050023-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	41	447	0	ENST00000409792.3:c.3950G>T	p.Gly1317Val	p.G1317V	ENST00000409792	NM_014159.6	1317	gGg/gTg	3/21	1	2	FACETS	0.984	0.819	1	0.984	0.819	1	CLONAL	1	TRUE	1	0.14	2		447	595	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133775	55133775	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050023-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	29	414	0	ENST00000257290.5:c.988C>A	p.His330Asn	p.H330N	ENST00000257290	NM_006206.4	330	Cat/Aat	7/23	1	2	FACETS	0.786	0.63	0.965	0.786	0.63	0.965	CLONAL	1	TRUE	1	0.14	2		414	527	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715464	117715464	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050023-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	20	338	1	ENST00000368508.3:c.1025G>T	p.Gly342Val	p.G342V	ENST00000368508	NM_002944.2	342	gGa/gTa	10/43	1	2	FACETS	0.744	0.568	0.951	0.744	0.568	0.951	CLONAL	1	TRUE	1	0.14	2		339	384	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436084	51436084	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050023-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	27	0	0	ENST00000262662.1:c.44G>T	p.Arg15Met	p.R15M	ENST00000262662		15	aGg/aTg	3/4	1	2	FACETS	0.648	0.514	0.802	0.648	0.514	0.802	SUBCLONAL	1	TRUE	1	0.14	2		0	595	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920771	100920771	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050023-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	15	0	0	ENST00000325455.5:c.2377T>A	p.Ser793Thr	p.S793T	ENST00000325455	NM_001202474.3	793	Tca/Aca	6/8	1	2	FACETS	0.52	0.379	0.691	0.52	0.379	0.691	SUBCLONAL	1	TRUE	1	0.14	2		0	412	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599874	10599874	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050023-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	21	0	0	ENST00000171111.5:c.1702G>T	p.Val568Phe	p.V568F	ENST00000171111	NM_203500.1	568	Gtc/Ttc	5/6	1	2	FACETS	0.502	0.385	0.639	0.502	0.385	0.639	SUBCLONAL	1	TRUE	1	0.14	2		0	598	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291542	15291542	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1242208956	NA	P-0050023-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	17	0	0	ENST00000263388.2:c.3092G>T	p.Arg1031Leu	p.R1031L	ENST00000263388	NM_000435.2	1031	cGc/cTc	19/33	1	2	FACETS	0.473	0.352	0.619	0.473	0.352	0.619	SUBCLONAL	1	TRUE	1	0.14	2		0	513	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73343030	73343030	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050023-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	11	0	0	ENST00000377767.4:c.1776A>T	p.Glu592Asp	p.E592D	ENST00000377767	NM_014953.3	592	gaA/gaT	14/21	1	2	FACETS	0.419	0.288	0.583	0.419	0.288	0.583	SUBCLONAL	1	TRUE	1	0.14	2		0	375	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260837	16260837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050023-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	23	0	0	ENST00000375759.3:c.8102C>T	p.Thr2701Met	p.T2701M	ENST00000375759	NM_015001.2	2701	aCg/aTg	11/15	1	2	FACETS	0.418	0.324	0.528	0.418	0.324	0.528	SUBCLONAL	1	TRUE	1	0.14	2		0	786	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281745	46281745	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050023-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	16	0	0	ENST00000371998.3:c.4192A>G	p.Ser1398Gly	p.S1398G	ENST00000371998		1398	Agc/Ggc	22/23	1	2	FACETS	0.414	0.305	0.546	0.414	0.305	0.546	SUBCLONAL	1	TRUE	1	0.14	2		0	552	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335921	73335921	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050023-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	16	0	0	ENST00000377767.4:c.2374G>C	p.Ala792Pro	p.A792P	ENST00000377767	NM_014953.3	792	Gct/Cct	18/21	1	2	FACETS	0.407	0.3	0.537	0.407	0.3	0.537	SUBCLONAL	1	TRUE	1	0.14	2		0	561	SUCCESS
ATR	545	MSKCC	GRCh37	3	142172026	142172026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050023-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	9	0	0	ENST00000350721.4:c.7705G>A	p.Val2569Met	p.V2569M	ENST00000350721	NM_001184.3	2569	Gtg/Atg	46/47	1	2	FACETS	0.327	0.215	0.471	0.327	0.215	0.471	SUBCLONAL	1	TRUE	1	0.14	2		0	393	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874031	123874031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1447464550	NA	P-0050023-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	11	0	0	ENST00000330479.4:c.62C>T	p.Ala21Val	p.A21V	ENST00000330479	NM_020382.3	21	gCg/gTg	2/9	1	2	FACETS	0.327	0.224	0.455	0.327	0.224	0.455	SUBCLONAL	1	TRUE	1	0.14	2		0	481	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373892	118373892	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050023-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	14	0	0	ENST00000534358.1:c.7285A>G	p.Arg2429Gly	p.R2429G	ENST00000534358	NM_005933.3	2429	Aga/Gga	27/36	1	2	FACETS	0.322	0.231	0.432	0.322	0.231	0.432	SUBCLONAL	1	TRUE	1	0.14	2		0	622	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163310199	163310199	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050023-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	6	0	0	ENST00000271452.3:c.652G>T	p.Glu218Ter	p.E218*	ENST00000271452	NM_145697.2	218	Gag/Tag	9/14	1	2	FACETS	0.192	0.114	0.299	0.192	0.114	0.299	SUBCLONAL	1	TRUE	1	0.14	2		0	446	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193565	99193565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051440-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	140	411	0	ENST00000074304.5:c.2760G>A	p.Met920Ile	p.M920I	ENST00000074304	NM_001134224.1	920	atG/atA	25/26	0.452081762098178	1	FACETS	0.293	0.267	0.319	0.293	0.267	0.319	INDETERMINATE	1	TRUE	0	0.870511603270199	1		411	621	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845609	63845609	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	135	289	0	ENST00000279873.7:c.1351del	p.Ser451AlafsTer28	p.S451Afs*28	ENST00000279873	NM_032199.2	450	Aaa/aa	9/10	1	2	FACETS	0.956	0.88	1	0.956	0.88	1	CLONAL	1	TRUE	1	0.789180335965619	2		289	358	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858452	9858452	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	248	536	0	ENST00000330684.3:c.2949A>T	p.Gln983His	p.Q983H	ENST00000330684	NM_001134407.1	983	caA/caT	13/13	1	2	FACETS	0.955	0.899	1	0.955	0.899	1	CLONAL	1	TRUE	1	0.789180335965619	2		536	658	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845218	128845218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750931655	NA	P-0051558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	128	623	0	ENST00000249373.3:c.712G>A	p.Gly238Arg	p.G238R	ENST00000249373	NM_005631.4	238	Ggg/Agg	3/12	NA	2	FACETS	0.461	0.419	0.506			1	INDETERMINATE	1	TRUE	NA	0.789180335965619	2		623	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0051721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	318	797	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.186217423023525	3	FACETS	1	0.994	1	0.482	0.454	0.51	INDETERMINATE	1	TRUE	0	0.396904733797177	3		799	1329	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0051721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	100	423	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.396904733797177	4	FACETS	1	0.962	1	0.752	0.68	0.827	CLONAL	2	TRUE	1	0.396904733797177	4		423	312	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670340	134670340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415689583	NA	P-0051721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	98	441	1	ENST00000398015.3:c.251G>A	p.Arg84His	p.R84H	ENST00000398015	NM_004441.4	84	cGc/cAc	3/16	0.135081700573001	3	FACETS	0.773	0.689	0.862	0.386	0.344	0.431	INDETERMINATE	1	TRUE	1	0.396904733797177	3		442	766	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274114	10274114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	266	754	1	ENST00000330684.3:c.155G>A	p.Arg52Gln	p.R52Q	ENST00000330684	NM_001134407.1	52	cGa/cAa	2/13	0.219525701794992	4	FACETS	1	0.992	1	0.698	0.653	0.744	INDETERMINATE	1	TRUE	2	0.396904733797177	4		755	1341	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913382	32913382	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1555283980	NA	P-0053329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	64	459	1	ENST00000380152.3:c.4894del	p.Ser1632ValfsTer4	p.S1632Vfs*4	ENST00000380152		1630	tcA/tc	11/27	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.603242038747735	2		460	170	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727949	78727949	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	177	629	0	ENST00000306801.3:c.794C>T	p.Ser265Phe	p.S265F	ENST00000306801	NM_020761.2	265	tCc/tTc	6/34	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.603242038747735	2		629	443	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097176	11097176	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	366	842	1	ENST00000358026.2:c.667C>T	p.Pro223Ser	p.P223S	ENST00000358026	NM_001128849.1	223	Ccc/Tcc	4/36	0.603242038747735	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.603242038747735	3		843	671	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405027	405027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568315642	NA	P-0053329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	113	402	0	ENST00000380956.4:c.1109C>T	p.Ala370Val	p.A370V	ENST00000380956	NM_001195286.1	370	gCg/gTg	8/9	0.55437430838569	4	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.603242038747735	4		402	479	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202412	138202412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766108588	NA	P-0055135-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	178	784	0	ENST00000237289.4:c.2329G>A	p.Gly777Ser	p.G777S	ENST00000237289	NM_001270507.1	777	Ggc/Agc	9/9	0.284711177187033	4	FACETS	1	0.986	1	0.444	0.409	0.481	CLONAL	1	TRUE	1	0.338955291451634	4		784	1055	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715678	30715678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039551	NA	P-0055135-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	107	688	0	ENST00000295754.5:c.1336G>A	p.Asp446Asn	p.D446N	ENST00000295754	NM_003242.5	446	Gat/Aat	5/7	1	2	FACETS	0.868	0.779	0.963	0.868	0.779	0.963	CLONAL	1	TRUE	1	0.338955291451634	2		688	727	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860657	151860657	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055135-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	186	885	2	ENST00000262189.6:c.10005G>A	p.Trp3335Ter	p.W3335*	ENST00000262189	NM_170606.2	3335	tgG/tgA	43/59	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.338955291451634	2		887	944	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057559-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	46	326	0				ENST00000310581	NM_198253.2	-/1132			0.234176351059077	0	FACETS	0.678	0.584	0.776			1	INDETERMINATE	1	TRUE	0	0.495834475291407	0		326	138	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423229	47423229	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057559-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	185	478	0	ENST00000404338.3:c.1297C>T	p.Arg433Ter	p.R433*	ENST00000404338	NM_004491.4	433	Cga/Tga	1/6	0.302698016989073	4	FACETS	0.974	0.905	1	0.974	0.905	1	CLONAL	2	TRUE	2	0.495834475291407	4		478	573	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440881	52440881	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057559-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	199	491	0	ENST00000460680.1:c.623G>C	p.Arg208Pro	p.R208P	ENST00000460680	NM_004656.3	208	cGg/cCg	8/17	NA	2	FACETS	0.884	0.829	0.94			1	INDETERMINATE	2	TRUE	NA	0.495834475291407	2		491	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0058083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	63	464	0	ENST00000269305.4:c.97-1G>A		p.X33_splice	ENST00000269305	NM_001126112.2	33			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.239849769920187	2		464	437	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230468718	230468757	+	frameshift_variant	Frame_Shift_Del	DEL	GTCAGCATGGACAGTGGGAGGCCGGTGCAGTCACTCTTCC	GTCAGCATGGACAGTGGGAGGCCGGTGCAGTCACTCTTCC	-	novel	NA	P-0058083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	48	620	0	ENST00000391860.1:c.761_800del	p.Arg254ProfsTer16	p.R254Pfs*16	ENST00000391860	NM_001258311.1	254	cGGAAGAGTGACTGCACCGGCCTCCCACTGTCCATGCTGACc/cc	5/7	0.219775227927906	2	FACETS	0.689	0.582	0.807	0.344	0.291	0.404	SUBCLONAL	1	TRUE	0	0.239849769920187	2		620	581	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244710	41244711	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0058083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	75	561	0	ENST00000357654.3:c.2837_2838del	p.Ile946LysfsTer5	p.I946Kfs*5	ENST00000357654	NM_007294.3	946	aTC/a	10/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.239849769920187	2		561	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0058179-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	328	485	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.534463030138637	3	FACETS	0.925	0.886	0.963	0.925	0.886	0.963	CLONAL	3	FALSE	0	0.559258544998461	3		485	541	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528895	157528895	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs763772159	NA	P-0058179-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	93	401	0	ENST00000346085.5:c.6620G>C	p.Arg2207Thr	p.R2207T	ENST00000346085	NM_020732.3	2207	aGa/aCa	20/20	1	2	FACETS	0.932	0.836	1	0.932	0.836	1	CLONAL	1	FALSE	1	0.559258544998461	2		401	357	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651995	36651995	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058179-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	420	458	0	ENST00000244741.5:c.119del	p.Gly40AlafsTer108	p.G40Afs*108	ENST00000244741	NM_000389.4	39	gcG/gc	2/3	0.559258544998461	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	FALSE	1	0.559258544998461	4		458	730	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100093	157100117	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCGGCGGCGGCAGCAGCAGGAG	GCGGCGGCGGCGGCAGCAGCAGGAG	-	novel	NA	P-0058179-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	46	506	1	ENST00000346085.5:c.1044_1068del	p.Ala350MetfsTer11	p.A350Mfs*11	ENST00000346085	NM_020732.3	344	GCGGCGGCGGCGGCAGCAGCAGGAGgc/gc	1/20	1	2	FACETS	0.588	0.498	0.685	0.588	0.498	0.685	SUBCLONAL	1	FALSE	1	0.559258544998461	2		507	280	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0058179-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	200	473	0				ENST00000310581	NM_198253.2	-/1132			0.559258544998461	4	FACETS	0.898	0.844	0.952	1	0.991	1	CLONAL	3	FALSE	2	0.559258544998461	4		473	414	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420107	41420107	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0058179-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	83	328	0	ENST00000373198.4:c.215-1G>A		p.X72_splice	ENST00000373198	NM_133170.3	72			0.481525194659395	5	FACETS	1	0.935	1	0.361	0.319	0.405	CLONAL	1	FALSE	2	0.559258544998461	5		328	504	SUCCESS
ATM	472	MSKCC	GRCh37	11	108128236	108128236	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058179-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	56	216	0	ENST00000278616.4:c.2279T>C	p.Ile760Thr	p.I760T	ENST00000278616	NM_000051.3	760	aTc/aCc	15/63	0.449311211601306	4	FACETS	0.958	0.825	1	0.479	0.412	0.551	CLONAL	1	FALSE	2	0.559258544998461	4		216	326	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385192	4385192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058179-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	131	271	0	ENST00000261254.3:c.217G>A	p.Glu73Lys	p.E73K	ENST00000261254	NM_001759.3	73	Gaa/Aaa	2/5	0.559258544998461	4	FACETS	0.863	0.79	0.939	0.863	0.79	0.939	CLONAL	2	FALSE	2	0.559258544998461	4		271	423	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129422	2129422	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058179-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	78	419	0	ENST00000219476.3:c.3277G>C	p.Glu1093Gln	p.E1093Q	ENST00000219476	NM_000548.3	1093	Gag/Cag	28/42	0.559258544998461	3	FACETS	0.908	0.803	1	0.454	0.401	0.51	CLONAL	1	FALSE	1	0.559258544998461	3		419	393	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879854	37879854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058179-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	502	605	0	ENST00000269571.5:c.2149G>C	p.Glu717Gln	p.E717Q	ENST00000269571		717	Gag/Cag	18/27	0.559258544998461	5	FACETS	1	0.977	1	1	0.977	1	CLONAL	4	FALSE	1	0.559258544998461	5		605	815	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191232	2191232	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058179-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	67	380	0	ENST00000398665.3:c.486G>C	p.Leu162Phe	p.L162F	ENST00000398665	NM_032482.2	162	ttG/ttC	5/28	0.449311211601306	4	FACETS	0.828	0.722	0.943	0.414	0.361	0.472	CLONAL	1	FALSE	2	0.559258544998461	4		380	451	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426813	212426813	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058179-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	151	321	0	ENST00000342788.4:c.2302G>A	p.Glu768Lys	p.E768K	ENST00000342788	NM_005235.2	768	Gaa/Aaa	20/28	0.449311211601306	4	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	FALSE	2	0.559258544998461	4		321	418	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436403	52436403	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058179-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	235	438	0	ENST00000460680.1:c.2091del	p.Val698CysfsTer38	p.V698Cfs*38	ENST00000460680	NM_004656.3	697	tcC/tc	17/17	0.559258544998461	5	FACETS	1	0.985	1			1	CLONAL	2	FALSE	NA	0.559258544998461	5		438	668	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629376	187629376	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs888101917	NA	P-0058179-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	211	486	0	ENST00000441802.2:c.1606C>G	p.Leu536Val	p.L536V	ENST00000441802	NM_005245.3	536	Ctg/Gtg	2/27	0.449311211601306	4	FACETS	0.941	0.879	1	0.941	0.879	1	CLONAL	2	FALSE	2	0.559258544998461	4		486	625	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527786	157527786	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058179-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	116	394	0	ENST00000346085.5:c.5511G>C	p.Lys1837Asn	p.K1837N	ENST00000346085	NM_020732.3	1837	aaG/aaC	20/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	FALSE	1	0.559258544998461	2		394	400	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56910937	56910937	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058179-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	85	345	0	ENST00000519728.1:c.1083G>C	p.Lys361Asn	p.K361N	ENST00000519728	NM_002350.3	361	aaG/aaC	11/13	0.559258544998461	3	FACETS	0.905	0.804	1	0.452	0.402	0.506	CLONAL	1	FALSE	1	0.559258544998461	3		345	430	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194134	94194134	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058179-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	63	210	0	ENST00000323929.3:c.1294C>T	p.Leu432Phe	p.L432F	ENST00000323929	NM_005591.3	432	Ctt/Ttt	12/20	0.449311211601306	4	FACETS	1	0.952	1	0.602	0.525	0.683	CLONAL	1	FALSE	2	0.559258544998461	4		210	292	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38792204	38792204	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058179-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	82	284	0	ENST00000348513.6:c.520C>G	p.Gln174Glu	p.Q174E	ENST00000348513	NM_003079.4	174	Cag/Gag	7/11	0.559258544998461	4	FACETS	0.913	0.807	1	0.304	0.269	0.342	CLONAL	1	FALSE	1	0.559258544998461	4		284	501	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61305230	61305230	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0058179-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	64	280	0	ENST00000341074.5:c.896T>A	p.Leu299Ter	p.L299*	ENST00000341074	NM_002974.2	299	tTg/tAg	8/8	0.529014442431779	3	FACETS	0.976	0.852	1	0.325	0.284	0.37	CLONAL	1	FALSE	0	0.559258544998461	3		280	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0060212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	111	539	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.387209858979397	1	FACETS	0.901	0.814	0.993	0.901	0.814	0.993	CLONAL	1	TRUE	0	0.387209858979397	1		539	513	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098816	178098816	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	11	488	0	ENST00000397062.3:c.229G>C	p.Asp77His	p.D77H	ENST00000397062	NM_006164.4	77	Gat/Cat	2/5	1	2	FACETS	0.114	0.078	0.159	0.114	0.078	0.159	SUBCLONAL	1	TRUE	1	0.387209858979397	2		488	499	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216947	7216947	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	85	621	0	ENST00000380728.2:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000380728		192	Cag/Tag	7/11	0.387209858979397	1	FACETS	0.797	0.708	0.892	0.797	0.708	0.892	SUBCLONAL	1	TRUE	0	0.387209858979397	1		621	444	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584725	187584725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	131	613	0	ENST00000441802.2:c.3308C>T	p.Ser1103Phe	p.S1103F	ENST00000441802	NM_005245.3	1103	tCc/tTc	3/27	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.387209858979397	2		613	605	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870630	40870630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777571053	NA	P-0060212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	81	491	0	ENST00000428826.2:c.773G>A	p.Arg258Gln	p.R258Q	ENST00000428826		258	cGa/cAa	9/21	1	2	FACETS	0.896	0.792	1	0.896	0.792	1	CLONAL	1	TRUE	1	0.387209858979397	2		491	467	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983083	201983084	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0060212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	188	655	0	ENST00000359651.3:c.934dup	p.Ala312GlyfsTer159	p.A312Gfs*159	ENST00000359651		311	gtg/gtGg	7/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.387209858979397	2		655	724	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73637989	73637989	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	167	357	0	ENST00000377687.4:c.1163C>G	p.Ser388Cys	p.S388C	ENST00000377687	NM_001730.3	388	tCt/tGt	3/4	1	2	FACETS	1	0.97	1	1	0.993	1	CLONAL	2	TRUE	1	0.387209858979397	2		357	400	SUCCESS
YES1	7525	MSKCC	GRCh37	18	742957	742957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1434151124	NA	P-0060212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	58	296	0	ENST00000314574.4:c.1021G>A	p.Glu341Lys	p.E341K	ENST00000314574	NM_005433.3	341	Gaa/Aaa	8/12	0.341075785379719	2	FACETS	1	0.966	1	0.684	0.595	0.778	CLONAL	1	TRUE	0	0.387209858979397	2		296	219	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668691	52668691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060327-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	201	299	0	ENST00000394830.3:c.1228C>T	p.His410Tyr	p.H410Y	ENST00000394830	NM_018313.4	410	Cat/Tat	12/30	0.853771421967011	3	FACETS	0.957	0.89	1	0.479	0.445	0.513	CLONAL	1	TRUE	1	0.853771421967011	3		299	702	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033249	69033249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs114811202	NA	P-0060327-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	213	382	0	ENST00000288368.4:c.3689G>A	p.Arg1230Gln	p.R1230Q	ENST00000288368	NM_024870.2	1230	cGg/cAg	30/40	0.80214147672815	4	FACETS	1	0.97	1	0.538	0.501	0.577	CLONAL	1	TRUE	2	0.853771421967011	4		382	859	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609923	81609923	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060327-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	848	557	0	ENST00000298171.2:c.1521A>T	p.Leu507Phe	p.L507F	ENST00000298171	NM_000369.2	507	ttA/ttT	10/10	0.84723370852709	5	FACETS	0.976	0.948	1	0.976	0.948	1	CLONAL	3	TRUE	2	0.853771421967011	5		557	1548	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919773	50919773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060327-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	278	524	0	ENST00000440232.2:c.2941G>A	p.Ala981Thr	p.A981T	ENST00000440232	NM_002691.3	981	Gct/Act	23/27	0.741268992296494	4	FACETS	1	0.973	1	0.531	0.499	0.565	CLONAL	1	TRUE	2	0.853771421967011	4		524	1136	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726026	61726027	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0060327-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	143	264	0	ENST00000401558.2:c.612_613del	p.Gln204HisfsTer39	p.Q204Hfs*39	ENST00000401558	NM_003400.3	204	caGAta/cata	8/25	1	2	FACETS	0.875	0.807	0.944	0.875	0.807	0.944	CLONAL	1	TRUE	1	0.853771421967011	2		264	383	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060422-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	25	326	0				ENST00000310581	NM_198253.2	-/1132			0.282931996352153	0	FACETS	0.975	0.779	1			1	CLONAL	1	TRUE	0	0.282931996352153	0		326	130	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39623721	39623721	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060422-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	23	493	0	ENST00000262039.4:c.2128A>T	p.Ser710Cys	p.S710C	ENST00000262039	NM_002647.2	710	Agt/Tgt	20/25	0.282931996352153	2	FACETS	0.392	0.305	0.493	0.196	0.152	0.247	SUBCLONAL	1	TRUE	0	0.282931996352153	2		493	415	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858492	9858492	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148669437	NA	P-0060422-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	23	664	0	ENST00000330684.3:c.2909G>A	p.Arg970Gln	p.R970Q	ENST00000330684	NM_001134407.1	970	cGg/cAg	13/13	0.282931996352153	1	FACETS	0.473	0.369	0.593	0.473	0.369	0.593	SUBCLONAL	1	TRUE	0	0.282931996352153	1		664	295	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123722	11123722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263140481	NA	P-0060422-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	185	680	1	ENST00000358026.2:c.2372C>T	p.Ala791Val	p.A791V	ENST00000358026	NM_001128849.1	791	gCg/gTg	16/36	0.282931996352153	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.282931996352153	2		681	602	SUCCESS
AXL	558	MSKCC	GRCh37	19	41725363	41725363	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060422-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	58	645	0	ENST00000301178.4:c.66G>T	p.Trp22Cys	p.W22C	ENST00000301178	NM_021913.4	22	tgG/tgT	1/20	0.198662520712849	1	FACETS	0.637	0.547	0.734	0.637	0.547	0.734	SUBCLONAL	1	TRUE	0	0.282931996352153	1		645	553	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183637	10183637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060422-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	144	794	2	ENST00000256474.2:c.106G>A	p.Glu36Lys	p.E36K	ENST00000256474	NM_000551.3	36	Gag/Aag	1/3	0.264086199517432	4	FACETS	0.876	0.8	0.956	0.876	0.8	0.956	CLONAL	2	TRUE	2	0.282931996352153	4		796	745	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664933	138664933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060422-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	85	561	0	ENST00000330315.3:c.632C>T	p.Ser211Leu	p.S211L	ENST00000330315	NM_023067.3	211	tCa/tTa	1/1	0.282931996352153	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	TRUE	0	0.282931996352153	2		561	289	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941653	48941653	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0060971-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	222	240	0	ENST00000267163.4:c.963C>G	p.Tyr321Ter	p.Y321*	ENST00000267163	NM_000321.2	321	taC/taG	10/27	0.956506578673779	1	FACETS	0.998	0.974	1	0.998	0.974	1	CLONAL	1	TRUE	0	0.959899953267553	1		240	241	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060971-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	376	362	0	ENST00000269305.4:c.713del	p.Cys238LeufsTer9	p.C238Lfs*9	ENST00000269305	NM_001126112.2	238	tGt/tt	7/11	0.94864176841118	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.959899953267553	1		362	391	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061088-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	238	326	0				ENST00000310581	NM_198253.2	-/1132			0.45089046329499	5	FACETS	1	0.974	1	0.792	0.747	0.838	CLONAL	3	TRUE	1	0.474144438903402	5		326	542	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0061088-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	188	486	0	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	0.474144438903402	3	FACETS	0.885	0.824	0.948	0.885	0.824	0.948	CLONAL	2	TRUE	1	0.474144438903402	3		486	554	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133761036	133761036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1456042173	NA	P-0061088-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	108	509	0	ENST00000318560.5:c.3359C>T	p.Ser1120Leu	p.S1120L	ENST00000318560	NM_005157.4	1120	tCg/tTg	11/11	0.17078259965527	5	FACETS	1	0.957	1	0.374	0.336	0.415	INDETERMINATE	1	TRUE	2	0.474144438903402	5		509	694	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332699	153332699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780061054	NA	P-0061088-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	323	440	0	ENST00000281708.4:c.257C>T	p.Ser86Leu	p.S86L	ENST00000281708	NM_033632.3	86	tCg/tTg	2/12	0.453974831584573	4	FACETS	0.931	0.886	0.977	0.931	0.886	0.977	CLONAL	3	TRUE	1	0.474144438903402	4		440	719	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030426	49030426	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061088-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	298	460	0	ENST00000267163.4:c.1901C>A	p.Ser634Ter	p.S634*	ENST00000267163	NM_000321.2	634	tCa/tAa	19/27	0.0787236898243724	6	FACETS	1	0.985	1			1	INDETERMINATE	4	TRUE	NA	0.474144438903402	6		460	565	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39708741	39708741	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061088-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	117	323	0	ENST00000361337.2:c.352G>C	p.Asp118His	p.D118H	ENST00000361337	NM_003286.2	118	Gat/Cat	6/21	0.330625309390711	4	FACETS	1	0.983	1	0.708	0.641	0.777	CLONAL	1	TRUE	2	0.474144438903402	4		323	514	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480341	56480341	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061088-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	223	461	0	ENST00000267101.3:c.448G>C	p.Glu150Gln	p.E150Q	ENST00000267101	NM_001982.3	150	Gag/Cag	4/28	0.474144438903402	3	FACETS	0.998	0.936	1	0.998	0.936	1	CLONAL	2	TRUE	1	0.474144438903402	3		461	583	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984408	201984408	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0061088-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	692	545	0	ENST00000359651.3:c.1073C>G	p.Ser358Ter	p.S358*	ENST00000359651		358	tCa/tGa	8/8	0.474144438903402	4	FACETS	1	0.996	1	1	0.996	1	CLONAL	4	TRUE	0	0.474144438903402	4		545	962	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026622	6026622	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061088-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	99	502	0	ENST00000265849.7:c.1774C>G	p.Gln592Glu	p.Q592E	ENST00000265849	NM_000535.5	592	Caa/Gaa	11/15	0.465698066438124	3	FACETS	0.835	0.746	0.928	0.417	0.373	0.464	CLONAL	1	TRUE	1	0.474144438903402	3		502	619	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132787	152132787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061088-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	78	429	0	ENST00000262189.6:c.85C>T	p.Pro29Ser	p.P29S	ENST00000262189	NM_170606.2	29	Ccc/Tcc	1/59	0.465698066438124	3	FACETS	0.822	0.725	0.927	0.411	0.362	0.464	CLONAL	1	TRUE	1	0.474144438903402	3		429	495	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039462	49039462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061088-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	289	447	0	ENST00000267163.4:c.2447C>T	p.Ser816Leu	p.S816L	ENST00000267163	NM_000321.2	816	tCa/tTa	23/27	0.0787236898243724	6	FACETS	0.995	0.945	1			1	INDETERMINATE	4	TRUE	NA	0.474144438903402	6		447	597	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366970	40366970	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369326949	NA	P-0061088-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	143	695	0	ENST00000397332.2:c.227G>A	p.Gly76Asp	p.G76D	ENST00000397332	NM_001033082.2	76	gGc/gAc	2/3	0.432343918071282	4	FACETS	0.69	0.628	0.757	0.173	0.156	0.19	SUBCLONAL	1	TRUE	0	0.474144438903402	4		695	1288	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223125	5223125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748343733	NA	P-0061088-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	117	706	0	ENST00000357368.4:c.2678C>T	p.Ser893Leu	p.S893L	ENST00000357368	NM_002850.3	893	tCa/tTa	18/38	0.465698066438124	3	FACETS	0.898	0.811	0.99	0.449	0.405	0.495	CLONAL	1	TRUE	1	0.474144438903402	3		706	680	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92252372	92252372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061088-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	46	273	0	ENST00000265734.4:c.676G>A	p.Asp226Asn	p.D226N	ENST00000265734	NM_001259.6	226	Gat/Aat	6/8	0.465698066438124	3	FACETS	0.79	0.668	0.922	0.395	0.334	0.461	CLONAL	1	TRUE	1	0.474144438903402	3		273	304	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651474	52651474	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061088-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	37	422	0	ENST00000394830.3:c.1622G>C	p.Arg541Thr	p.R541T	ENST00000394830	NM_018313.4	541	aGa/aCa	15/30	0.330625309390711	4	FACETS	0.34	0.279	0.408	0.17	0.139	0.204	SUBCLONAL	1	TRUE	2	0.474144438903402	4		422	677	SUCCESS
RET	5979	MSKCC	GRCh37	10	43614996	43614996	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs79658334	NA	P-0061118-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	153	505	0	ENST00000355710.3:c.2410G>T	p.Val804Leu	p.V804L	ENST00000355710	NM_020975.4	804	Gtg/Ttg	14/20	0.482978636599995	1	FACETS	0.763	0.71	0.815	1	0.991	1	SUBCLONAL	2	TRUE	0	0.482978636599995	1		505	315	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342973	118342973	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061118-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	169	593	0	ENST00000534358.1:c.1099A>T	p.Thr367Ser	p.T367S	ENST00000534358	NM_005933.3	367	Aca/Tca	3/36	1	2	FACETS	0.821	0.764	0.88	1	0.992	1	CLONAL	2	TRUE	1	0.482978636599995	2		593	426	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244425	5244425	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061118-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	183	537	0	ENST00000357368.4:c.1057G>C	p.Asp353His	p.D353H	ENST00000357368	NM_002850.3	353	Gac/Cac	11/38	1	2	FACETS	0.873	0.815	0.932	1	0.993	1	CLONAL	2	TRUE	1	0.482978636599995	2		537	434	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275050	41275050	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061118-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	172	572	0	ENST00000349496.5:c.1216del	p.Val406PhefsTer9	p.V406Ffs*9	ENST00000349496	NM_001904.3	406	Gtt/tt	9/15	1	2	FACETS	0.844	0.786	0.903	1	0.992	1	CLONAL	2	TRUE	1	0.482978636599995	2		572	422	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692791	89692791	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1114167623	NA	P-0061239-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	46	91	0	ENST00000371953.3:c.275A>G	p.Asp92Gly	p.D92G	ENST00000371953	NM_000314.4	92	gAc/gGc	5/9	0.361198052009469	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.361198052009469	1		91	177	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577573	7577573	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061239-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	62	198	0	ENST00000269305.4:c.708C>A	p.Tyr236Ter	p.Y236*	ENST00000269305	NM_001126112.2	236	taC/taA	7/11	0.361198052009469	1	FACETS	0.882	0.767	1	0.882	0.767	1	CLONAL	1	TRUE	0	0.361198052009469	1		198	319	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985677	60985677	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061239-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	74	296	0	ENST00000333681.4:c.223C>G	p.Pro75Ala	p.P75A	ENST00000333681		75	Ccg/Gcg	2/3	0.361198052009469	1	FACETS	0.973	0.858	1	0.973	0.858	1	CLONAL	1	TRUE	0	0.361198052009469	1		296	345	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260172	149260172	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061239-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	81	180	0	ENST00000360632.3:c.721C>T	p.Gln241Ter	p.Q241*	ENST00000360632	NM_015472.4	241	Cag/Tag	4/7	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.361198052009469	2		180	429	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032039	26032039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061239-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	115	376	0	ENST00000244661.2:c.250C>T	p.Arg84Cys	p.R84C	ENST00000244661	NM_003537.3	84	Cgc/Tgc	1/1	1	2	FACETS	0.98	0.884	1	0.98	0.884	1	CLONAL	1	TRUE	1	0.361198052009469	2		376	650	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878256	151878256	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0061239-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	106	232	0	ENST00000262189.6:c.6689C>G	p.Ser2230Ter	p.S2230*	ENST00000262189	NM_170606.2	2230	tCa/tGa	36/59	0.196192208908943	1	FACETS	1	0.931	1	1	0.931	1	INDETERMINATE	1	TRUE	0	0.361198052009469	1		232	462	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692967	89693087	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCCCTAGATTTCTATGGGGAAGTAAGGACCAGAGACAAAAAGGTAAGTTATTTTTTGATGTTTTTCCTTTCCTCTTCCTGGATCTGAGAATTTATTGGAAAACAGATTTTGGGTTTCTTTT	GCCCTAGATTTCTATGGGGAAGTAAGGACCAGAGACAAAAAGGTAAGTTATTTTTTGATGTTTTTCCTTTCCTCTTCCTGGATCTGAGAATTTATTGGAAAACAGATTTTGGGTTTCTTTT	-	novel	NA	P-0061267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	67	352	0	ENST00000371953.3:c.451_492+79del		p.X151_splice	ENST00000371953	NM_000314.4	151		5/9	0.719961212490595	1	FACETS	0.291	0.253	0.331	0.291	0.253	0.331	SUBCLONAL	1	TRUE	0	0.719961212490595	1		352	410	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039385	49039385	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs794727372	NA	P-0061267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	415	414	0	ENST00000267163.4:c.2370C>A	p.Tyr790Ter	p.Y790*	ENST00000267163	NM_000321.2	790	taC/taA	23/27	0.719961212490595	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.719961212490595	1		414	705	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634452	23634452	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0061267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	274	288	0	ENST00000261584.4:c.2835-1G>T		p.X945_splice	ENST00000261584	NM_024675.3	945			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.719961212490595	2		288	728	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578422	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCGCCTCACAACCTCCGT	CAGCGCCTCACAACCTCCGT	-	novel	NA	P-0061267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	428	501	0	ENST00000269305.4:c.508_527del	p.Thr170ProfsTer4	p.T170Pfs*4	ENST00000269305	NM_001126112.2	170	ACGGAGGTTGTGAGGCGCTGc/c	5/11	0.719961212490595	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.719961212490595	1		501	743	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734194	58734194	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1344	357	344	0	ENST00000305921.3:c.1252C>G	p.Pro418Ala	p.P418A	ENST00000305921	NM_003620.3	418	Cca/Gca	5/6	0.719961212490595	4	FACETS	1	0.947	1	0.334	0.315	0.354	CLONAL	1	TRUE	1	0.719961212490595	4		344	1701	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026845	48026845	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	404	457	0	ENST00000234420.5:c.1723G>A	p.Asp575Asn	p.D575N	ENST00000234420	NM_000179.2	575	Gat/Aat	4/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.719961212490595	2		457	1093	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641232	12641232	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	589	346	0	ENST00000251849.4:c.1066G>C	p.Gly356Arg	p.G356R	ENST00000251849	NM_002880.3	356	Ggg/Cgg	10/17	0.719961212490595	3	FACETS	0.989	0.955	1	0.989	0.955	1	CLONAL	2	TRUE	1	0.719961212490595	3		346	1125	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259208	89259208	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	310	424	0	ENST00000336596.2:c.352G>C	p.Glu118Gln	p.E118Q	ENST00000336596	NM_005233.5	118	Gag/Cag	3/17	NA	2	FACETS	1	0.953	1			1	INDETERMINATE	1	TRUE	NA	0.719961212490595	2		424	855	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964370	70964370	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	67	299	0	ENST00000276594.2:c.1658A>T	p.Lys553Ile	p.K553I	ENST00000276594	NM_024504.3	553	aAa/aTa	8/8	0.719961212490595	3	FACETS	0.25	0.216	0.287	0.125	0.108	0.144	SUBCLONAL	1	TRUE	1	0.719961212490595	3		299	1012	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0061296-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	122	387	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.26061417414028	3	FACETS	1	0.951	1	0.708	0.646	0.772	CLONAL	2	TRUE	0	0.352925066702561	3		388	383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0061296-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	117	557	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.229445479536708	2	FACETS	1	0.975	1	0.615	0.557	0.676	CLONAL	1	TRUE	0	0.352925066702561	2		557	539	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011200	12011200	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061296-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	72	317	0	ENST00000353533.5:c.607G>T	p.Glu203Ter	p.E203*	ENST00000353533	NM_003010.3	203	Gaa/Taa	5/11	0.229445479536708	2	FACETS	0.75	0.663	0.842	0.75	0.663	0.842	SUBCLONAL	2	TRUE	0	0.352925066702561	2		317	272	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436044	116436044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061296-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	143	575	0	ENST00000397752.3:c.4039G>A	p.Glu1347Lys	p.E1347K	ENST00000397752	NM_000245.2	1347	Gag/Aag	21/21	0.352925066702561	3	FACETS	1	0.969	1	0.57	0.519	0.622	CLONAL	1	TRUE	1	0.352925066702561	3		575	837	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974769	21974769	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs760065045	NA	P-0061296-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	136	609	0	ENST00000304494.5:c.58G>C	p.Ala20Pro	p.A20P	ENST00000304494	NM_000077.4	20	Gcg/Ccg	1/3	0.352925066702561	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.352925066702561	1		609	615	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400095	41400095	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061296-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	45	437	0	ENST00000373198.4:c.664C>A	p.His222Asn	p.H222N	ENST00000373198	NM_133170.3	222	Cat/Aat	5/32	1	2	FACETS	0.518	0.435	0.61	0.518	0.435	0.61	SUBCLONAL	1	TRUE	1	0.352925066702561	2		437	492	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724635	112724635	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061296-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	59	456	0	ENST00000369452.4:c.519G>C	p.Met173Ile	p.M173I	ENST00000369452	NM_007373.3	173	atG/atC	2/9	1	2	FACETS	0.596	0.513	0.687	0.596	0.513	0.687	SUBCLONAL	1	TRUE	1	0.352925066702561	2		456	561	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125496666	125496666	+	start_lost	Translation_Start_Site	SNP	G	G	T	novel	NA	P-0061296-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	97	476	0	ENST00000428830.2:c.3G>T	p.Met1?	p.M1?	ENST00000428830	NM_001114121.2	1	atG/atT	2/14	0.352925066702561	3	FACETS	1	0.908	1	0.509	0.454	0.567	CLONAL	1	TRUE	1	0.352925066702561	3		476	635	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856242	111856242	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061296-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	62	501	0	ENST00000341259.2:c.293C>G	p.Ala98Gly	p.A98G	ENST00000341259	NM_005475.2	98	gCc/gGc	2/8	0.287461473955909	2	FACETS	0.665	0.575	0.763	0.333	0.287	0.382	SUBCLONAL	1	TRUE	0	0.352925066702561	2		501	528	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618944	37618944	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750404979	NA	P-0061296-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	222	610	1	ENST00000447079.4:c.620C>T	p.Pro207Leu	p.P207L	ENST00000447079	NM_015083.1	207	cCc/cTc	1/14	0.150439539736269	4	FACETS	0.926	0.863	0.991	0.926	0.863	0.991	INDETERMINATE	2	TRUE	2	0.352925066702561	4		611	919	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2180756	2180756	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0061296-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	50	238	0	ENST00000398665.3:c.125+1G>A		p.X42_splice	ENST00000398665	NM_032482.2	42			0.352925066702561	1	FACETS	0.915	0.783	1	0.915	0.783	1	CLONAL	1	TRUE	0	0.352925066702561	1		238	255	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156393	106156393	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061296-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	99	581	0	ENST00000380013.4:c.1294G>C	p.Glu432Gln	p.E432Q	ENST00000380013	NM_001127208.2	432	Gaa/Caa	3/11	1	2	FACETS	0.896	0.801	0.997	0.896	0.801	0.997	CLONAL	1	TRUE	1	0.352925066702561	2		581	626	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631179	176631179	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061296-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	161	554	0	ENST00000439151.2:c.1122G>C	p.Glu374Asp	p.E374D	ENST00000439151	NM_022455.4	374	gaG/gaC	4/23	0.352925066702561	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.352925066702561	1		554	574	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517906	8517906	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061296-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	22	390	0	ENST00000356435.5:c.1485del	p.Phe495LeufsTer26	p.F495Lfs*26	ENST00000356435		495	ttT/tt	10/35	0.352925066702561	1	FACETS	0.238	0.183	0.301	0.238	0.183	0.301	SUBCLONAL	1	TRUE	0	0.352925066702561	1		390	432	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221313	1221314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs121913321	NA	P-0061433-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	115	497	0	ENST00000326873.7:c.842dup	p.Leu282AlafsTer3	p.L282Afs*3	ENST00000326873	NM_000455.4	279	ggc/ggCc	6/10	0.307543327645783	2	FACETS	0.956	0.87	1	0.956	0.87	1	CLONAL	2	TRUE	0	0.326857839738862	2		497	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0061433-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	153	654	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.326857839738862	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.326857839738862	2		654	426	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0061433-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	92	278	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.326857839738862	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	0	0.326857839738862	2		278	267	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600011	10600029	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGCATAGATACAGTTGT	GCAGCATAGATACAGTTGT	-	novel	NA	P-0061433-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	107	478	0	ENST00000171111.5:c.1547_1565del	p.His516LeufsTer10	p.H516Lfs*10	ENST00000171111	NM_203500.1	516	cACAACTGTATCTATGCTGCt/ct	5/6	0.307543327645783	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	2	TRUE	0	0.326857839738862	2		478	325	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134230	11134230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1227826852	NA	P-0061433-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	92	386	0	ENST00000358026.2:c.2896C>T	p.Arg966Trp	p.R966W	ENST00000358026	NM_001128849.1	966	Cgg/Tgg	20/36	0.307543327645783	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.326857839738862	2		386	244	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261830	16261830	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061433-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	115	593	0	ENST00000375759.3:c.9095G>C	p.Gly3032Ala	p.G3032A	ENST00000375759	NM_015001.2	3032	gGg/gCg	11/15	0.307543327645783	2	FACETS	0.961	0.875	1	0.961	0.875	1	CLONAL	2	TRUE	0	0.326857839738862	2		593	366	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981845	201981845	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061433-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	127	488	0	ENST00000359651.3:c.556G>T	p.Ala186Ser	p.A186S	ENST00000359651		186	Gca/Tca	4/8	0.28711941060319	3	FACETS	0.916	0.841	0.992	0.916	0.841	0.992	CLONAL	3	TRUE	0	0.326857839738862	3		488	329	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748068	41748068	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061433-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	61	274	0	ENST00000226382.2:c.701del	p.Gly234AlafsTer75	p.G234Afs*75	ENST00000226382	NM_003924.3	234	gGc/gc	3/3	0.307543327645783	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.326857839738862	2		274	157	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554942	106554942	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061433-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	73	438	0	ENST00000369096.4:c.2059C>T	p.His687Tyr	p.H687Y	ENST00000369096	NM_001198.3	687	Cac/Tac	7/7	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.326857839738862	2		438	360	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2083346	2083346	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0061433-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	131	263	0	ENST00000349721.2:c.2349-1G>T		p.X783_splice	ENST00000349721	NM_003070.3	783			0.250266302740662	3	FACETS	0.981	0.904	1			1	CLONAL	3	TRUE	NA	0.326857839738862	3		263	317	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034491	47034491	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061433-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	46	333	0	ENST00000377604.3:c.576G>C	p.Gln192His	p.Q192H	ENST00000377604	NM_001204468.1	192	caG/caC	6/24	0.243407500368375	1	FACETS	0.961	0.816	1	0.961	0.816	1	CLONAL	1	TRUE	0	0.326857839738862	1		333	245	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0061471-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	139	566	0	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.349110901658604	2	FACETS	0.901	0.827	0.977	0.901	0.827	0.977	CLONAL	2	TRUE	0	0.349110901658604	2		566	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574005	7574005	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061471-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	114	378	0	ENST00000269305.4:c.1022T>C	p.Phe341Ser	p.F341S	ENST00000269305	NM_001126112.2	341	tTc/tCc	10/11	0.2950052808144	2	FACETS	0.902	0.821	0.986	0.902	0.821	0.986	CLONAL	2	TRUE	0	0.349110901658604	2		378	362	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2208944	2208944	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061471-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	97	301	0	ENST00000398665.3:c.974A>G	p.Tyr325Cys	p.Y325C	ENST00000398665	NM_032482.2	325	tAt/tGt	12/28	0.349110901658604	2	FACETS	0.945	0.854	1	0.945	0.854	1	CLONAL	2	TRUE	0	0.349110901658604	2		301	294	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426127	47426127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061471-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	104	539	0	ENST00000377045.4:c.647C>G	p.Pro216Arg	p.P216R	ENST00000377045	NM_001654.4	216	cCc/cGc	7/16	1	2	FACETS	0.821	0.742	0.903	1	0.986	1	CLONAL	2	TRUE	1	0.349110901658604	2		539	363	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047494	49047494	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0061471-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	90	117	0	ENST00000267163.4:c.2490-2A>T		p.X830_splice	ENST00000267163	NM_000321.2	830			0.349110901658604	2	FACETS	0.993	0.908	1	1	0.985	1	CLONAL	3	TRUE	0	0.349110901658604	2		117	173	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414266	32414266	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061471-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	143	341	0	ENST00000332351.3:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000332351	NM_024426.4	429	Gaa/Taa	8/10	0.331334833923873	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.349110901658604	2		341	380	SUCCESS
MAD2L2	10459	MSKCC	GRCh37	1	11740433	11740433	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061471-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	36	476	0	ENST00000235310.3:c.136A>C	p.Lys46Gln	p.K46Q	ENST00000235310		46	Aag/Cag	5/11	0.17553573675784	3	FACETS	0.592	0.487	0.71	0.197	0.162	0.237	INDETERMINATE	1	TRUE	0	0.349110901658604	3		476	409	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429829	78429830	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0061471-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	34	432	0	ENST00000370768.2:c.958_959del	p.Glu320LysfsTer30	p.E320Kfs*30	ENST00000370768	NM_003902.3	320	GAa/a	12/20	0.17553573675784	3	FACETS	0.496	0.405	0.599	0.165	0.135	0.2	INDETERMINATE	1	TRUE	0	0.349110901658604	3		432	461	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163298057	163298057	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061471-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	104	277	0	ENST00000271452.3:c.238G>T	p.Glu80Ter	p.E80*	ENST00000271452	NM_145697.2	80	Gaa/Taa	4/14	0.349110901658604	5	FACETS	1	0.952	1	0.727	0.656	0.802	CLONAL	2	TRUE	2	0.349110901658604	5		277	416	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223046	1223046	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1405959130	NA	P-0061471-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	146	587	0	ENST00000326873.7:c.983C>G	p.Thr328Ser	p.T328S	ENST00000326873	NM_000455.4	328	aCc/aGc	8/10	0.349110901658604	2	FACETS	0.944	0.869	1	0.944	0.869	1	CLONAL	2	TRUE	0	0.349110901658604	2		587	443	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498383	89498383	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061471-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	84	338	0	ENST00000336596.2:c.2355G>T	p.Lys785Asn	p.K785N	ENST00000336596	NM_005233.5	785	aaG/aaT	14/17	0.349110901658604	2	FACETS	0.847	0.757	0.941	0.847	0.757	0.941	CLONAL	2	TRUE	0	0.349110901658604	2		338	284	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048885	180048886	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0061471-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	95	486	0	ENST00000261937.6:c.1676_1677delinsAA	p.Thr559Lys	p.T559K	ENST00000261937	NM_182925.4	559	aCC/aAA	13/30	0.267761768438948	3	FACETS	1	0.98	1	0.726	0.65	0.807	CLONAL	1	TRUE	1	0.349110901658604	3		486	440	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965330	68965330	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0061471-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	68	279	0	ENST00000288368.4:c.944-2A>T		p.X315_splice	ENST00000288368	NM_024870.2	315			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.349110901658604	2		279	297	SUCCESS
H3C13	653604	MSKCC	GRCh37	1	149784837	149784837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061471-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	32	398	0	ENST00000331491.1:c.400G>A	p.Glu134Lys	p.E134K	ENST00000331491	NM_001123375.2	134	Gag/Aag	1/1	0.349110901658604	5	FACETS	0.673	0.546	0.816	0.224	0.182	0.272	SUBCLONAL	1	TRUE	2	0.349110901658604	5		398	415	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0061471-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	142	566	0	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.350481325484375	1	FACETS	0.847	0.773	0.924	0.847	0.773	0.924	CLONAL	1	TRUE	0	0.373503341751736	1		566	730	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574005	7574005	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061471-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	122	378	0	ENST00000269305.4:c.1022T>C	p.Phe341Ser	p.F341S	ENST00000269305	NM_001126112.2	341	tTc/tCc	10/11	0.373503341751736	1	FACETS	0.902	0.818	0.99	0.902	0.818	0.99	CLONAL	1	TRUE	0	0.373503341751736	1		378	589	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2208944	2208944	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061471-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	69	301	0	ENST00000398665.3:c.974A>G	p.Tyr325Cys	p.Y325C	ENST00000398665	NM_032482.2	325	tAt/tGt	12/28	0.350481325484375	1	FACETS	0.799	0.7	0.905	0.799	0.7	0.905	CLONAL	1	TRUE	0	0.373503341751736	1		301	376	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426127	47426127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061471-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	149	539	0	ENST00000377045.4:c.647C>G	p.Pro216Arg	p.P216R	ENST00000377045	NM_001654.4	216	cCc/cGc	7/16	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.373503341751736	2		539	778	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047494	49047494	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0061471-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	51	117	0	ENST00000267163.4:c.2490-2A>T		p.X830_splice	ENST00000267163	NM_000321.2	830			0.373503341751736	1	FACETS	0.978	0.841	1	0.978	0.841	1	CLONAL	1	TRUE	0	0.373503341751736	1		117	227	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414266	32414266	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061471-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	128	341	0	ENST00000332351.3:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000332351	NM_024426.4	429	Gaa/Taa	8/10	0.373503341751736	1	FACETS	0.978	0.89	1	0.978	0.89	1	CLONAL	1	TRUE	0	0.373503341751736	1		341	570	SUCCESS
MAD2L2	10459	MSKCC	GRCh37	1	11740433	11740433	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061471-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	124	476	0	ENST00000235310.3:c.136A>C	p.Lys46Gln	p.K46Q	ENST00000235310		46	Aag/Cag	5/11	1	2	FACETS	0.896	0.811	0.985	0.896	0.811	0.985	CLONAL	1	TRUE	1	0.373503341751736	2		476	741	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429829	78429830	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0061471-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	86	432	0	ENST00000370768.2:c.958_959del	p.Glu320LysfsTer30	p.E320Kfs*30	ENST00000370768	NM_003902.3	320	GAa/a	12/20	1	2	FACETS	0.843	0.748	0.945	0.843	0.748	0.945	CLONAL	1	TRUE	1	0.373503341751736	2		432	546	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163298057	163298057	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061471-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	58	277	0	ENST00000271452.3:c.238G>T	p.Glu80Ter	p.E80*	ENST00000271452	NM_145697.2	80	Gaa/Taa	4/14	0.353653882077207	3	FACETS	0.901	0.777	1	0.451	0.388	0.518	CLONAL	1	TRUE	1	0.373503341751736	3		277	409	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223046	1223046	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1405959130	NA	P-0061471-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	138	587	0	ENST00000326873.7:c.983C>G	p.Thr328Ser	p.T328S	ENST00000326873	NM_000455.4	328	aCc/aGc	8/10	0.350481325484375	1	FACETS	0.814	0.742	0.89	0.814	0.742	0.89	CLONAL	1	TRUE	0	0.373503341751736	1		587	738	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498383	89498383	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061471-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	77	338	0	ENST00000336596.2:c.2355G>T	p.Lys785Asn	p.K785N	ENST00000336596	NM_005233.5	785	aaG/aaT	14/17	0.373503341751736	1	FACETS	0.791	0.697	0.89	0.791	0.697	0.89	SUBCLONAL	1	TRUE	0	0.373503341751736	1		338	424	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048885	180048886	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0061471-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	124	486	0	ENST00000261937.6:c.1676_1677delinsAA	p.Thr559Lys	p.T559K	ENST00000261937	NM_182925.4	559	aCC/aAA	13/30	1	2	FACETS	0.835	0.756	0.919	0.835	0.756	0.919	CLONAL	1	TRUE	1	0.373503341751736	2		486	795	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965330	68965330	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0061471-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	64	279	0	ENST00000288368.4:c.944-2A>T		p.X315_splice	ENST00000288368	NM_024870.2	315			1	2	FACETS	0.993	0.865	1	0.993	0.865	1	CLONAL	1	TRUE	1	0.373503341751736	2		279	345	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0061483-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	285	475	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.505317419437318	3	FACETS	1	0.973	1	0.696	0.658	0.733	CLONAL	2	TRUE	0	0.505317419437318	3		475	677	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468919	25468919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061483-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	85	324	0	ENST00000264709.3:c.1444G>A	p.Glu482Lys	p.E482K	ENST00000264709	NM_175629.2	482	Gag/Aag	12/23	0.505317419437318	3	FACETS	0.939	0.833	1	0.469	0.416	0.525	CLONAL	1	TRUE	1	0.505317419437318	3		324	449	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954339	48954339	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061483-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	87	215	0	ENST00000267163.4:c.1460T>C	p.Leu487Ser	p.L487S	ENST00000267163	NM_000321.2	487	tTg/tCg	16/27	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.505317419437318	2		215	312	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497404	149497404	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1411722144	NA	P-0061483-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	81	368	0	ENST00000261799.4:c.2914C>A	p.Gln972Lys	p.Q972K	ENST00000261799	NM_002609.3	972	Cag/Aag	22/23	0.45200814026288	4	FACETS	0.839	0.74	0.945	0.42	0.37	0.473	CLONAL	1	TRUE	2	0.505317419437318	4		368	575	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860159	57860159	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061521-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	84	614	0	ENST00000228682.2:c.899C>A	p.Pro300Gln	p.P300Q	ENST00000228682	NM_005269.2	300	cCa/cAa	8/12	1	2	FACETS	0.768	0.687	0.854	0.768	0.687	0.854	SUBCLONAL	1	TRUE	1	0.756580255523363	2		614	289	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941653	48941653	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0061590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	21	240	0	ENST00000267163.4:c.963C>G	p.Tyr321Ter	p.Y321*	ENST00000267163	NM_000321.2	321	taC/taG	10/27	1	2	FACETS	0.459	0.354	0.581	0.459	0.354	0.581	SUBCLONAL	1	TRUE	1	0.34274309172714	2		240	267	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	87	326	0				ENST00000310581	NM_198253.2	-/1132			0.261363772633149	4	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	2	0.34274309172714	4		326	320	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313266	65313266	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	160	517	0	ENST00000342505.4:c.1848G>C	p.Lys616Asn	p.K616N	ENST00000342505	NM_002227.2	616	aaG/aaC	13/25	0.128883411357252	3	FACETS	1	0.94	1	0.681	0.629	0.736	INDETERMINATE	2	TRUE	0	0.34274309172714	3		517	535	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633620	69633620	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	35	563	0	ENST00000334134.2:c.82G>C	p.Asp28His	p.D28H	ENST00000334134	NM_005247.2	28	Gat/Cat	1/3	1	2	FACETS	0.584	0.479	0.7	0.584	0.479	0.7	SUBCLONAL	1	TRUE	1	0.34274309172714	2		563	350	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0061590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	51	548	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	0.132144177980158	5	FACETS	0.828	0.704	0.965	0.276	0.234	0.322	INDETERMINATE	1	TRUE	2	0.34274309172714	5		548	544	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589364	28589364	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	88	428	0	ENST00000241453.7:c.2683G>C	p.Asp895His	p.D895H	ENST00000241453	NM_004119.2	895	Gat/Cat	22/24	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.34274309172714	2		428	446	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912570	32912570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	99	476	0	ENST00000380152.3:c.4078G>A	p.Asp1360Asn	p.D1360N	ENST00000380152		1360	Gat/Aat	11/27	1	2	FACETS	0.92	0.822	1	0.92	0.822	1	CLONAL	1	TRUE	1	0.34274309172714	2		476	628	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574002	7574002	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs375338359	NA	P-0061590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	149	494	0	ENST00000269305.4:c.1025G>C	p.Arg342Pro	p.R342P	ENST00000269305	NM_001126112.2	342	cGa/cCa	10/11	0.247231549535264	3	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	1	0.34274309172714	3		494	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0061590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	116	598	4	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.247231549535264	3	FACETS	1	0.967	1	0.582	0.525	0.642	CLONAL	1	TRUE	1	0.34274309172714	3		602	681	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004564	16004564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	163	606	0	ENST00000268712.3:c.2690G>A	p.Arg897Lys	p.R897K	ENST00000268712	NM_006311.3	897	aGa/aAa	20/46	0.247231549535264	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	1	0.34274309172714	3		606	534	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573485	48573485	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	78	579	0	ENST00000342988.3:c.69G>C	p.Leu23Phe	p.L23F	ENST00000342988	NM_005359.5	23	ttG/ttC	2/12	0.337325447468105	2	FACETS	0.935	0.824	1	0.467	0.412	0.527	CLONAL	1	TRUE	0	0.34274309172714	2		579	487	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222503	2222503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	146	657	0	ENST00000398665.3:c.3335C>T	p.Ser1112Phe	p.S1112F	ENST00000398665	NM_032482.2	1112	tCc/tTc	24/28	0.34274309172714	4	FACETS	0.873	0.799	0.95	0.582	0.533	0.634	CLONAL	2	TRUE	1	0.34274309172714	4		657	655	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353939	15353947	+	inframe_deletion	In_Frame_Del	DEL	GGGGTGGTG	GGGGTGGTG	-	rs758265124	NA	P-0061590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	67	311	0	ENST00000263377.2:c.2933_2941del	p.Pro978_Pro980del	p.P978_P980del	ENST00000263377	NM_058243.2	978	cCACCACCCCag/cag	14/20	0.34274309172714	4	FACETS	0.987	0.867	1	0.658	0.578	0.742	CLONAL	2	TRUE	1	0.34274309172714	4		311	266	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172141	99172141	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	89	792	0	ENST00000074304.5:c.1707C>G	p.Cys569Trp	p.C569W	ENST00000074304	NM_001134224.1	569	tgC/tgG	17/26	0.247231549535264	3	FACETS	1	0.894	1	0.504	0.447	0.564	CLONAL	1	TRUE	1	0.34274309172714	3		792	604	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172143	99172143	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	94	801	0	ENST00000074304.5:c.1709C>T	p.Thr570Ile	p.T570I	ENST00000074304	NM_001134224.1	570	aCc/aTc	17/26	0.247231549535264	3	FACETS	1	0.923	1	0.522	0.465	0.583	CLONAL	1	TRUE	1	0.34274309172714	3		801	615	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37091976	37091976	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0061590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	77	504	0	ENST00000231790.2:c.2104-1G>C		p.X702_splice	ENST00000231790	NM_000249.3	702			0.34274309172714	7	FACETS	1	0.931	1	0.182	0.159	0.207	CLONAL	1	TRUE	1	0.34274309172714	7		504	764	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197187	26197187	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	226	865	0	ENST00000356476.2:c.292G>C	p.Glu98Gln	p.E98Q	ENST00000356476		98	Gag/Cag	1/1	0.217141045147838	4	FACETS	0.983	0.917	1	0.983	0.917	1	CLONAL	2	TRUE	2	0.34274309172714	4		865	901	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005546	150005546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	84	668	0	ENST00000253339.5:c.679C>T	p.His227Tyr	p.H227Y	ENST00000253339		227	Cac/Tac	3/7	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.34274309172714	2		668	486	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509849	106509849	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	163	575	0	ENST00000359195.3:c.1843G>T	p.Glu615Ter	p.E615*	ENST00000359195	NM_002649.2	615	Gaa/Taa	2/11	0.132144177980158	5	FACETS	1	0.977	1	0.772	0.711	0.834	INDETERMINATE	2	TRUE	2	0.34274309172714	5		575	622	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845113	128845113	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	113	670	0	ENST00000249373.3:c.607C>T	p.Pro203Ser	p.P203S	ENST00000249373	NM_005631.4	203	Ccc/Tcc	3/12	0.132144177980158	5	FACETS	0.885	0.799	0.975	0.59	0.533	0.65	INDETERMINATE	2	TRUE	2	0.34274309172714	5		670	564	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922109	39922109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780712297	NA	P-0061590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	117	638	0	ENST00000378444.4:c.4063G>A	p.Glu1355Lys	p.E1355K	ENST00000378444	NM_001123385.1	1355	Gag/Aag	9/15	0.34274309172714	3	FACETS	1	0.967	1	0.387	0.349	0.427	CLONAL	1	TRUE	0	0.34274309172714	3		638	689	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0061598-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	71	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.153402288976471	3	FACETS	0.984	0.864	1	0.984	0.864	1	CLONAL	2	TRUE	1	0.206685783404315	3		426	385	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830790	3830790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061598-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	61	643	0	ENST00000262367.5:c.1766G>A	p.Arg589Lys	p.R589K	ENST00000262367	NM_004380.2	589	aGg/aAg	8/31	0.153402288976471	3	FACETS	1	0.87	1	0.505	0.435	0.581	CLONAL	1	TRUE	1	0.206685783404315	3		643	645	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235258	235258	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0061598-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	21	348	0	ENST00000264932.6:c.1065-1G>C		p.X355_splice	ENST00000264932	NM_004168.2	355			1	2	FACETS	0.594	0.457	0.754	0.594	0.457	0.754	SUBCLONAL	1	TRUE	1	0.206685783404315	2		348	342	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983321	149983327	+	frameshift_variant	Frame_Shift_Del	DEL	AGGACTG	AGGACTG	-	novel	NA	P-0061598-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	28	502	0	ENST00000253339.5:c.2931_2937del	p.Ser978LysfsTer17	p.S978Kfs*17	ENST00000253339		977	ctCAGTCCT/ct	7/7	1	2	FACETS	0.546	0.436	0.673	0.546	0.436	0.673	SUBCLONAL	1	TRUE	1	0.206685783404315	2		502	496	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151947012	151947012	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061598-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	26	371	0	ENST00000262189.6:c.1762C>T	p.Gln588Ter	p.Q588*	ENST00000262189	NM_170606.2	588	Cag/Tag	13/59	1	2	FACETS	0.615	0.487	0.763	0.615	0.487	0.763	SUBCLONAL	1	TRUE	1	0.206685783404315	2		371	409	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0061635-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	77	372	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.989	0.87	1	0.989	0.87	1	CLONAL	1	TRUE	1	0.289858374477163	2		372	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578529	7578529	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061635-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	78	545	0	ENST00000269305.4:c.401T>C	p.Phe134Ser	p.F134S	ENST00000269305	NM_001126112.2	134	tTt/tCt	5/11	0.289858374477163	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.289858374477163	1		545	418	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447775	187447775	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779270221	NA	P-0061635-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	89	533	0	ENST00000232014.4:c.418C>T	p.Arg140Cys	p.R140C	ENST00000232014	NM_001130845.1	140	Cgt/Tgt	5/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.289858374477163	2		533	560	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630782	67630782	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061635-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	43	457	0	ENST00000272342.5:c.968A>T	p.Lys323Ile	p.K323I	ENST00000272342	NM_019002.3	323	aAa/aTa	5/6	1	2	FACETS	0.544	0.455	0.644	0.544	0.455	0.644	SUBCLONAL	1	TRUE	1	0.289858374477163	2		457	545	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945424	151945424	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061635-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	58	325	0	ENST00000262189.6:c.2095T>G	p.Leu699Val	p.L699V	ENST00000262189	NM_170606.2	699	Tta/Gta	14/59	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.289858374477163	2		325	391	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0061711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	277	446	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.407583525021151	6	FACETS	1	0.965	1	1	0.965	1	CLONAL	3	TRUE	3	0.407583525021151	6		446	797	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538922	187538922	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	173	459	0	ENST00000441802.2:c.8818T>G	p.Leu2940Val	p.L2940V	ENST00000441802	NM_005245.3	2940	Tta/Gta	10/27	0.407583525021151	2	FACETS	0.987	0.919	1	0.987	0.919	1	CLONAL	2	TRUE	0	0.407583525021151	2		459	430	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038519	47038519	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	162	231	0	ENST00000377604.3:c.681del	p.Phe227LeufsTer39	p.F227Lfs*39	ENST00000377604	NM_001204468.1	227	ttC/tt	8/24	0.255942157793954	2	FACETS	0.892	0.836	0.948			1	CLONAL	3	TRUE	NA	0.407583525021151	2		231	297	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152864456	152864456	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	81	193	1	ENST00000406277.2:c.70G>C	p.Val24Leu	p.V24L	ENST00000406277	NM_152274.4	24	Gtg/Ctg	3/7	0.255942157793954		FACETS		0.691	0.859				SUBCLONAL	2	TRUE	NA	0.407583525021151	2		194	257	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029395	16029395	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0061712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	180	184	0	ENST00000268712.3:c.1634+1G>A		p.X545_splice	ENST00000268712	NM_006311.3	545			0.651358338898021	3	FACETS	0.883	0.831	0.935	0.883	0.831	0.935	CLONAL	2	TRUE	1	0.921823711196815	3		184	323	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111462	8111463	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	408	532	0	ENST00000346208.3:c.949dup	p.Cys317LeufsTer35	p.C317Lfs*35	ENST00000346208		316	-/T	5/6	0.788667912923756	4	FACETS	0.798	0.761	0.835			1	SUBCLONAL	2	TRUE	NA	0.921823711196815	4		532	1066	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222062	2222062	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	88	677	0	ENST00000398665.3:c.2894T>C	p.Leu965Ser	p.L965S	ENST00000398665	NM_032482.2	965	tTg/tCg	24/28	1	2	FACETS	0.197	0.174	0.222	0.197	0.174	0.222	SUBCLONAL	1	TRUE	1	0.921823711196815	2		677	968	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377241	118377241	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782228819	NA	P-0061782-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	62	600	0	ENST00000534358.1:c.10634G>A	p.Arg3545Gln	p.R3545Q	ENST00000534358	NM_005933.3	3545	cGg/cAg	27/36	1	2	FACETS	0.62	0.534	0.714	0.62	0.534	0.714	SUBCLONAL	1	TRUE	1	0.249963207429727	2		600	800	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66777356	66777356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061782-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	48	496	0	ENST00000307102.5:c.722C>T	p.Ser241Phe	p.S241F	ENST00000307102	NM_002755.3	241	tCt/tTt	7/11	1	2	FACETS	0.558	0.471	0.655	0.558	0.471	0.655	SUBCLONAL	1	TRUE	1	0.249963207429727	2		496	688	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0061782-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	157	216	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.249963207429727	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.249963207429727	1		216	776	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247862	10247862	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061782-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	55	619	0	ENST00000340748.4:c.4340C>A	p.Ser1447Ter	p.S1447*	ENST00000340748		1447	tCa/tAa	36/40	1	2	FACETS	0.612	0.523	0.71	0.612	0.523	0.71	SUBCLONAL	1	TRUE	1	0.249963207429727	2		619	719	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217475	142217475	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061782-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	43	308	0	ENST00000350721.4:c.5522G>C	p.Arg1841Thr	p.R1841T	ENST00000350721	NM_001184.3	1841	aGa/aCa	32/47	1	2	FACETS	0.754	0.632	0.89	0.754	0.632	0.89	SUBCLONAL	1	TRUE	1	0.249963207429727	2		308	456	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876205	35876205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061782-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	44	522	0	ENST00000303115.3:c.997G>A	p.Glu333Lys	p.E333K	ENST00000303115	NM_002185.3	333	Gaa/Aaa	8/8	0.184433897200677	4	FACETS	0.508	0.425	0.601	0.169	0.141	0.201	SUBCLONAL	1	TRUE	1	0.249963207429727	4		522	866	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038466	180038466	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061782-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	47	523	0	ENST00000261937.6:c.3551T>C	p.Val1184Ala	p.V1184A	ENST00000261937	NM_182925.4	1184	gTc/gCc	27/30	0.249963207429727	1	FACETS	0.609	0.514	0.715	0.609	0.514	0.715	SUBCLONAL	1	TRUE	0	0.249963207429727	1		523	540	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268891	55268891	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061782-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	69	599	0	ENST00000275493.2:c.2957G>C	p.Arg986Thr	p.R986T	ENST00000275493	NM_005228.3	986	aGa/aCa	25/28	1	2	FACETS	0.664	0.577	0.759	0.664	0.577	0.759	SUBCLONAL	1	TRUE	1	0.249963207429727	2		599	831	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2161878	2161878	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764576819	NA	P-0061782-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	47	467	0	ENST00000349721.2:c.4174G>A	p.Asp1392Asn	p.D1392N	ENST00000349721	NM_003070.3	1392	Gat/Aat	28/34	0.249963207429727	1	FACETS	0.627	0.529	0.735	0.627	0.529	0.735	SUBCLONAL	1	TRUE	0	0.249963207429727	1		467	525	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0061812-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	204	557	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.279006572584029	2	FACETS	0.951	0.885	1	0.951	0.885	1	CLONAL	2	TRUE	0	0.290576040458206	2		557	738	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0061812-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	126	278	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.287175966487594	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.290576040458206	2		278	404	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220433	1220433	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061812-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	304	580	0	ENST00000326873.7:c.526G>T	p.Asp176Tyr	p.D176Y	ENST00000326873	NM_000455.4	176	Gac/Tac	4/10	0.28740884316831	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	0	0.290576040458206	3		580	774	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837920	156837920	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061812-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	182	615	0	ENST00000524377.1:c.453C>A	p.His151Gln	p.H151Q	ENST00000524377	NM_002529.3	151	caC/caA	5/17	0.24888424134989	3	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	1	0.290576040458206	3		615	705	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449566	187449566	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061812-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	238	596	0	ENST00000232014.4:c.314T>C	p.Val105Ala	p.V105A	ENST00000232014	NM_001130845.1	105	gTg/gCg	4/10	0.130238951716466	5	FACETS	1	0.979	1	0.741	0.692	0.792	INDETERMINATE	2	TRUE	2	0.290576040458206	5		596	1058	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231671	66231671	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1427787527	NA	P-0061812-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	39	397	2	ENST00000273854.3:c.2029A>G	p.Ile677Val	p.I677V	ENST00000273854	NM_004439.5	677	Att/Gtt	11/18	0.24888424134989	3	FACETS	1	0.901	1	0.559	0.466	0.662	CLONAL	1	TRUE	1	0.290576040458206	3		399	275	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0061833-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	22	636	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		636	261	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	151	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.217405443353621	3	FACETS	0.956	0.889	1	1	0.992	1	CLONAL	4	TRUE	1	0.286795350208355	3		298	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0061856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	337	617	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.286795350208355	1	FACETS	0.897	0.86	0.934	1	0.997	1	CLONAL	4	TRUE	0	0.286795350208355	1		617	561	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0061856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	76	242	0	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	1	FACETS	1	0.892	1	1	0.985	1	CLONAL	2	TRUE	0	0.286795350208355	1		242	227	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171462	123171462	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0061856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	115	94	0	ENST00000218089.9:c.374C>G	p.Ser125Ter	p.S125*	ENST00000218089	NM_001042749.1	125	tCa/tGa	6/35	1	1	FACETS	0.987	0.922	1	1	0.993	1	CLONAL	4	TRUE	0	0.286795350208355	1		94	174	SUCCESS
AR	367	MSKCC	GRCh37	X	66765148	66765149	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	rs752055010	NA	P-0061856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	36	238	0	ENST00000374690.3:c.170_172dup	p.Leu57dup	p.L57dup	ENST00000374690	NM_000044.3	57	ttg/tTGCtg	1/8	1	1	FACETS	0.889	0.735	1	0.889	0.735	1	CLONAL	1	TRUE	0	0.286795350208355	1		238	242	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44894182	44894182	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	131	100	0	ENST00000377967.4:c.571C>T	p.Gln191Ter	p.Q191*	ENST00000377967	NM_021140.2	191	Cag/Tag	7/29	1	1	FACETS	0.993	0.932	1	1	0.994	1	CLONAL	4	TRUE	0	0.286795350208355	1		100	197	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984425	201984426	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	401	657	0	ENST00000359651.3:c.1092dup	p.Glu365ArgfsTer106	p.E365Rfs*106	ENST00000359651		364	gaa/gAaa	8/8	0.2557007828214	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	3	TRUE	0	0.286795350208355	2		657	859	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778441	3778452	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGCTGCTGCT	GCTGCTGCTGCT	AA	novel	NA	P-0061856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	280	886	4	ENST00000262367.5:c.6596_6607delinsTT	p.Gln2199LeufsTer100	p.Q2199Lfs*100	ENST00000262367	NM_004380.2	2199	cAGCAGCAGCAGCaa/cTTaa	31/31	0.286795350208355	0	FACETS	0.738	0.699	0.777			1	SUBCLONAL	3	TRUE	0	0.286795350208355	0		890	629	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0061871-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	98	372	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.526	0.471	0.585	0.526	0.471	0.585	SUBCLONAL	1	TRUE	1	0.692508266065284	2		372	538	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518496	204518496	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061871-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1770	138	489	0	ENST00000367182.3:c.1159G>C	p.Asp387His	p.D387H	ENST00000367182	NM_001278516.1	387	Gat/Cat	11/11	0.692508266065284	6	FACETS	0.498	0.451	0.548			1	SUBCLONAL	1	TRUE	NA	0.692508266065284	6		489	1908	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658609	206658609	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061871-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1627	103	440	0	ENST00000367120.3:c.1582G>C	p.Val528Leu	p.V528L	ENST00000367120	NM_014002.3	528	Gtg/Ctg	15/22	0.692508266065284	6	FACETS	0.41	0.365	0.458			1	SUBCLONAL	1	TRUE	NA	0.692508266065284	6		440	1730	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842402	68842417	+	frameshift_variant	Frame_Shift_Del	DEL	GACTGGGTTATTCCTC	GACTGGGTTATTCCTC	-	novel	NA	P-0061871-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	115	465	0	ENST00000261769.5:c.463_478del	p.Asp155ProfsTer55	p.D155Pfs*55	ENST00000261769	NM_004360.3	155	GACTGGGTTATTCCTCcc/cc	4/16	0.339168072515481	1	FACETS	0.392	0.354	0.432	0.392	0.354	0.432	INDETERMINATE	1	TRUE	0	0.692508266065284	1		465	554	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0061886-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	15	450	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.182	0.132	0.243	0.182	0.132	0.243	SUBCLONAL	1	TRUE	1	0.24	2		450	687	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0061886-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	30	278	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.749	0.604	0.912	0.749	0.604	0.912	CLONAL	1	TRUE	1	0.24	2		278	334	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0061886-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	45	370	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.24	2		370	318	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0061887-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	195	372	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.621811656907	2		372	605	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061887-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	194	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.580223780472396	3	FACETS	0.899	0.841	0.957	0.899	0.841	0.957	CLONAL	2	TRUE	1	0.621811656907	3		298	455	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252940	36252940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061887-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	198	412	0	ENST00000300305.3:c.422C>T	p.Ser141Leu	p.S141L	ENST00000300305		141	tCg/tTg	4/8	1	2	FACETS	0.956	0.89	1	0.956	0.89	1	CLONAL	1	TRUE	1	0.621811656907	2		412	666	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602543	10602543	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061887-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	204	552	0	ENST00000171111.5:c.1035C>A	p.Tyr345Ter	p.Y345*	ENST00000171111	NM_203500.1	345	taC/taA	3/6	0.621811656907	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.621811656907	1		552	428	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443675	29443675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1034835558	NA	P-0061890-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	44	521	2	ENST00000389048.3:c.3542G>A	p.Arg1181His	p.R1181H	ENST00000389048	NM_004304.4	1181	cGc/cAc	23/29	0.215523402997962	1	FACETS	0.642	0.54	0.754	0.642	0.54	0.754	SUBCLONAL	1	TRUE	0	0.33	1		523	347	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523501	106523501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373006568	NA	P-0061890-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	33	379	0	ENST00000359195.3:c.2653G>A	p.Ala885Thr	p.A885T	ENST00000359195	NM_002649.2	885	Gcc/Acc	8/11	0.175266576929402	3	FACETS	0.552	0.449	0.668	0.276	0.224	0.334	INDETERMINATE	1	TRUE	1	0.33	3		379	422	SUCCESS
APC	324	MSKCC	GRCh37	5	112162807	112162807	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061890-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	54	359	0	ENST00000257430.4:c.1411G>T	p.Gly471Ter	p.G471*	ENST00000257430	NM_000038.5	471	Gga/Tga	12/16	0.230055268627102	3	FACETS	0.96	0.823	1	0.48	0.411	0.555	CLONAL	1	TRUE	1	0.33	3		359	397	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162722916	162722916	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061890-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	25	473	0	ENST00000367921.3:c.114del	p.Gly39AlafsTer45	p.G39Afs*45	ENST00000367921	NM_006182.2	38	ggA/gg	4/18	1	2	FACETS	0.376	0.296	0.468	0.376	0.296	0.468	SUBCLONAL	1	TRUE	1	0.33	2		473	403	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	55	326	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.971	0.838	1	0.971	0.838	1	CLONAL	1	TRUE	1	0.417876473564361	2		326	271	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0061896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	244	639	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	0.417876473564361	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.417876473564361	3		639	658	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942839	44942839	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	105	467	0	ENST00000377967.4:c.3419G>A	p.Gly1140Glu	p.G1140E	ENST00000377967	NM_021140.2	1140	gGg/gAg	23/29	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.417876473564361	2		467	440	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531855	41531855	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	129	502	0	ENST00000263253.7:c.1567C>T	p.Gln523Ter	p.Q523*	ENST00000263253	NM_001429.3	523	Caa/Taa	7/31	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.417876473564361	2		502	588	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425674	49425677	+	frameshift_variant	Frame_Shift_Del	DEL	CTGT	CTGT	-	novel	NA	P-0061896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	127	681	0	ENST00000301067.7:c.12811_12814del	p.Thr4271AlafsTer6	p.T4271Afs*6	ENST00000301067	NM_003482.3	4271	ACAGgc/gc	39/54	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.417876473564361	2		681	594	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651881	36651903	+	frameshift_variant,start_lost	Frame_Shift_Del	DEL	GTCAGAACCGGCTGGGGATGTCC	GTCAGAACCGGCTGGGGATGTCC	-	rs1295208193	NA	P-0061896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	34	635	0	ENST00000244741.5:c.12_34del	p.Ala5_?12	p.A5_?12	ENST00000244741	NM_000389.4	1	atGTCAGAACCGGCTGGGGATGTCCgt/atgt	2/3	1	2	FACETS	0.266	0.217	0.322	0.266	0.217	0.322	SUBCLONAL	1	TRUE	1	0.417876473564361	2		635	611	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427360	49427360	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	107	689	0	ENST00000301067.7:c.11128G>C	p.Gly3710Arg	p.G3710R	ENST00000301067	NM_003482.3	3710	Gga/Cga	39/54	1	2	FACETS	0.947	0.852	1	0.947	0.852	1	CLONAL	1	TRUE	1	0.417876473564361	2		689	541	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129198	2129198	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0061909-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	137	899	0	ENST00000219476.3:c.3131+1G>T		p.X1044_splice	ENST00000219476	NM_000548.3	1044			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		899	373	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	43	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.241630247546567	2		298	329	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0061913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	49	432	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.241630247546567	1	FACETS	0.845	0.717	0.985	0.845	0.717	0.985	CLONAL	1	TRUE	0	0.241630247546567	1		432	422	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247812	59247813	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0061913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	64	487	0	ENST00000371222.2:c.930_931del	p.Lys311SerfsTer6	p.K311Sfs*6	ENST00000371222	NM_002228.3	310	caGAaa/caaa	1/1	1	2	FACETS	0.78	0.675	0.895	0.78	0.675	0.895	SUBCLONAL	1	TRUE	1	0.241630247546567	2		487	679	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589535	67589535	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1403833564	NA	P-0061913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	41	227	0	ENST00000274335.5:c.1300-2A>G		p.X434_splice	ENST00000274335		434			0.241630247546567	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	0	0.241630247546567	1		227	267	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907504	32907504	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80358479	NA	P-0061913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	93	388	0	ENST00000380152.3:c.1889C>T	p.Thr630Ile	p.T630I	ENST00000380152		630	aCa/aTa	10/27	0.204795813069659	3	FACETS	0.879	0.784	0.978	0.879	0.784	0.978	CLONAL	2	TRUE	1	0.241630247546567	3		388	491	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450756	70450756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767435262	NA	P-0061913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	67	530	2	ENST00000373644.4:c.5596G>A	p.Ala1866Thr	p.A1866T	ENST00000373644	NM_030625.2	1866	Gca/Aca	12/12	1	2	FACETS	0.882	0.766	1	0.882	0.766	1	CLONAL	1	TRUE	1	0.241630247546567	2		532	629	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492871	56492872	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0061913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	39	492	0	ENST00000407977.2:c.67dup	p.Ala23GlyfsTer17	p.A23Gfs*17	ENST00000407977		23	gca/gGca	2/10	0.241630247546567	1	FACETS	0.617	0.511	0.735	0.617	0.511	0.735	SUBCLONAL	1	TRUE	0	0.241630247546567	1		492	460	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271492	26271492	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	59	634	1	ENST00000305910.3:c.121C>G	p.Arg41Gly	p.R41G	ENST00000305910	NM_003534.2	41	Cgc/Ggc	1/1	1	2	FACETS	0.795	0.684	0.917	0.795	0.684	0.917	CLONAL	1	TRUE	1	0.241630247546567	2		635	614	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055761	152055761	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0061913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	54	247	0	ENST00000262189.6:c.162-1G>C		p.X54_splice	ENST00000262189	NM_170606.2	54			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.241630247546567	2		247	310	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0061931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	33	370	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.948	0.774	1	0.948	0.774	1	CLONAL	1	TRUE	1	0.2	2		370	348	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243045	105243045	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	42	634	0	ENST00000349310.3:c.238T>C	p.Trp80Arg	p.W80R	ENST00000349310	NM_001014432.1	80	Tgg/Cgg	5/15	1	2	FACETS	0.687	0.573	0.815	0.687	0.573	0.815	SUBCLONAL	1	TRUE	1	0.2	2		634	611	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339230	70339230	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs199469667	NA	P-0061931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	8	330	0	ENST00000374080.3:c.107T>G	p.Leu36Arg	p.L36R	ENST00000374080		36	cTg/cGg	2/45	1	2	FACETS	0.205	0.131	0.302	0.205	0.131	0.302	SUBCLONAL	1	TRUE	1	0.2	2		330	390	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692980	89692980	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060500126	NA	P-0061931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	27	419	0	ENST00000371953.3:c.464A>G	p.Tyr155Cys	p.Y155C	ENST00000371953	NM_000314.4	155	tAt/tGt	5/9	1	2	FACETS	0.73	0.581	0.9	0.73	0.581	0.9	SUBCLONAL	1	TRUE	1	0.2	2		419	370	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591111	67591137	+	inframe_deletion	In_Frame_Del	DEL	AGACCTTATCCAGCTGAGAAAGACGAG	AGACCTTATCCAGCTGAGAAAGACGAG	-	novel	NA	P-0061931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	35	432	0	ENST00000274335.5:c.1709_1735del	p.Leu570_Asp578del	p.L570_D578del	ENST00000274335		568	ccAGACCTTATCCAGCTGAGAAAGACGAGa/cca	12/15	1	2	FACETS	0.835	0.685	1	0.835	0.685	1	CLONAL	1	TRUE	1	0.2	2		432	419	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105988	27105989	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0061931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	102	626	0	ENST00000324856.7:c.5599_5600insTA	p.Pro1867LeufsTer17	p.P1867Lfs*17	ENST00000324856	NM_006015.4	1867	cct/cTAct	20/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.2	2		626	711	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	98	845	0	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	0.863	0.768	0.964	0.863	0.768	0.964	CLONAL	1	FALSE	1	0.232760614504776	2		845	976	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510155	120510155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	80	617	0	ENST00000256646.2:c.1354C>T	p.Arg452Cys	p.R452C	ENST00000256646	NM_024408.3	452	Cgt/Tgt	8/34	0.191594786128524	3	FACETS	0.928	0.816	1	0.464	0.408	0.525	CLONAL	1	FALSE	1	0.232760614504776	3		617	827	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656600	3656600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs575953567	NA	P-0061939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	100	680	2	ENST00000294008.3:c.635G>A	p.Arg212Gln	p.R212Q	ENST00000294008	NM_032444.2	212	cGa/cAa	3/15	0.115179766604021	3	FACETS	0.981	0.875	1	0.49	0.437	0.547	INDETERMINATE	1	FALSE	1	0.232760614504776	3		682	978	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0061939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	177	737	0	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	0.190032719341503	3	FACETS	0.881	0.811	0.953	0.881	0.811	0.953	CLONAL	2	FALSE	1	0.232760614504776	3		737	964	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0061939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	72	691	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.190032719341503	3	FACETS	0.832	0.726	0.947	0.416	0.363	0.474	CLONAL	1	FALSE	1	0.232760614504776	3		691	830	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276903	15276903	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0061939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	88	623	0	ENST00000263388.2:c.5363-1G>T		p.X1788_splice	ENST00000263388	NM_000435.2	1788			0.232760614504776	3	FACETS	1	0.887	1	0.501	0.443	0.563	CLONAL	1	FALSE	1	0.232760614504776	3		623	842	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561254	9561254	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	111	539	0	ENST00000353224.5:c.528G>T	p.Lys176Asn	p.K176N	ENST00000353224	NM_177990.2	176	aaG/aaT	4/10	0.232760614504776	4	FACETS	1	0.979	1	0.339	0.304	0.376	CLONAL	1	FALSE	0	0.232760614504776	4		539	868	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961059	55961059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530419081	NA	P-0061939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	61	500	0	ENST00000263923.4:c.2881C>T	p.Arg961Trp	p.R961W	ENST00000263923	NM_002253.2	961	Cgg/Tgg	21/30	0.232760614504776	3	FACETS	0.945	0.815	1	0.473	0.407	0.544	CLONAL	1	FALSE	1	0.232760614504776	3		500	619	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738424	145738424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1167531855	NA	P-0061939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	83	798	0	ENST00000428558.2:c.2561C>G	p.Thr854Ser	p.T854S	ENST00000428558	NM_004260.3	854	aCc/aGc	16/22	0.232760614504776	5	FACETS	0.876	0.771	0.99	0.292	0.257	0.33	CLONAL	1	FALSE	2	0.232760614504776	5		798	1098	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0061940-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	38	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.654	0.541	0.779	0.654	0.541	0.779	SUBCLONAL	1	TRUE	1	0.29	2		426	401	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0061940-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	22	442	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.624	0.485	0.785	0.624	0.485	0.785	SUBCLONAL	1	TRUE	1	0.29	2		442	243	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0061940-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	31	371	1	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	0.717	0.582	0.87	0.717	0.582	0.87	SUBCLONAL	1	TRUE	1	0.29	2		372	298	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246482	105246482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061940-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	165	471	0	ENST00000349310.3:c.118G>A	p.Glu40Lys	p.E40K	ENST00000349310	NM_001014432.1	40	Gag/Aag	4/15	1	2	FACETS	0.885	0.816	0.956	1	0.991	1	CLONAL	2	TRUE	1	0.29	2		471	643	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422257	47422257	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1324454897	NA	P-0061940-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	95	541	0	ENST00000404338.3:c.325C>T	p.Arg109Ter	p.R109*	ENST00000404338	NM_004491.4	109	Cga/Tga	1/6	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.29	2		541	648	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057665	27057666	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0061940-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	194	620	0	ENST00000324856.7:c.1377dup	p.Ser460GlnfsTer163	p.S460Qfs*163	ENST00000324856	NM_006015.4	458	ggc/ggCc	3/20	0.237208643348181	2	FACETS	0.952	0.884	1	0.952	0.884	1	CLONAL	2	TRUE	0	0.29	2		620	703	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs753143066	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	185	822	7	ENST00000295797.4:c.826dup	p.Thr276AsnfsTer16	p.T276Nfs*16	ENST00000295797	NM_002740.5	273	tta/ttAa	9/18	1	2	FACETS	0.874	0.812	0.938	0.874	0.812	0.938	CLONAL	1	TRUE	1	0.707705526813784	2		829	598	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	216	434	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.707705526813784	2		434	535	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	475	132	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.952	0.922	0.982	1	0.998	1	CLONAL	2	TRUE	1	0.707705526813784	2		132	705	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	237	598	4	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.933	0.875	0.992	0.933	0.875	0.992	CLONAL	1	TRUE	1	0.707705526813784	2		602	718	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156720	20156720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	204	319	0	ENST00000379607.5:c.37C>T	p.Arg13Cys	p.R13C	ENST00000379607	NM_001412.3	13	Cgc/Tgc	2/7	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.707705526813784	2		319	564	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	474	381	1	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.707705526813784	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.707705526813784	2		382	619	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852248	63852248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145564601	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	264	591	0	ENST00000279873.7:c.3026C>T	p.Ala1009Val	p.A1009V	ENST00000279873	NM_032199.2	1009	gCg/gTg	10/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.707705526813784	2		591	657	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	214	816	6	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.929	0.868	0.991	0.929	0.868	0.991	CLONAL	1	TRUE	1	0.707705526813784	2		822	651	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913237	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	198	453	0	ENST00000369535.4:c.35G>T	p.Gly12Val	p.G12V	ENST00000369535	NM_002524.4	12	gGt/gTt	2/7	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.707705526813784	2		453	558	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370236	40370236	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs761761205	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	139	675	5	ENST00000293328.3:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000293328	NM_012448.3	368	Cag/ag	9/19	1	2	FACETS	0.602	0.55	0.657	0.602	0.55	0.657	SUBCLONAL	1	TRUE	1	0.707705526813784	2		680	652	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660808	227660810	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	rs747646240	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	211	777	16	ENST00000305123.5:c.2645_2647del	p.Gln882del	p.Q882del	ENST00000305123	NM_005544.2	882	cAGCcc/ccc	1/2	1	2	FACETS	0.898	0.838	0.959	0.898	0.838	0.959	CLONAL	1	TRUE	1	0.707705526813784	2		793	664	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567647	226567647	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	129	748	1	ENST00000366794.5:c.1519del	p.Ser507AlafsTer17	p.S507Afs*17	ENST00000366794	NM_001618.3	507	Agc/gc	10/23	1	2	FACETS	0.495	0.449	0.544	0.495	0.449	0.544	SUBCLONAL	1	TRUE	1	0.707705526813784	2		749	736	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	162	619	1	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.707705526813784	2		620	451	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905324	50905324	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	206	792	1	ENST00000440232.2:c.537del	p.Arg180GlyfsTer3	p.R180Gfs*3	ENST00000440232	NM_002691.3	178	Ggg/gg	5/27	1	2	FACETS	0.782	0.728	0.838	0.782	0.728	0.838	SUBCLONAL	1	TRUE	1	0.707705526813784	2		793	744	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856209	111856209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	144	613	1	ENST00000341259.2:c.260G>A	p.Arg87His	p.R87H	ENST00000341259	NM_005475.2	87	cGc/cAc	2/8	1	2	FACETS	0.938	0.863	1	0.938	0.863	1	CLONAL	1	TRUE	1	0.707705526813784	2		614	434	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	179	695	7	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.76	0.703	0.818	0.76	0.703	0.818	SUBCLONAL	1	TRUE	1	0.707705526813784	2		702	666	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916730	178916730	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	213	393	0	ENST00000263967.3:c.117G>T	p.Glu39Asp	p.E39D	ENST00000263967	NM_006218.2	39	gaG/gaT	2/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.707705526813784	2		393	561	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943789	71943789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773085707	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	184	594	1	ENST00000298229.2:c.1832G>A	p.Arg611His	p.R611H	ENST00000298229	NM_001567.3	611	cGc/cAc	15/28	1	2	FACETS	0.748	0.693	0.805	0.748	0.693	0.805	SUBCLONAL	1	TRUE	1	0.707705526813784	2		595	695	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	93	720	0	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	1	2	FACETS	0.419	0.372	0.468	0.419	0.372	0.468	SUBCLONAL	1	TRUE	1	0.707705526813784	2		720	628	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863054	56863054	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1266824391	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	204	383	0	ENST00000519728.1:c.327del	p.Glu110LysfsTer15	p.E110Kfs*15	ENST00000519728	NM_002350.3	107	acA/ac	5/13	1	2	FACETS	0.979	0.914	1	0.979	0.914	1	CLONAL	1	TRUE	1	0.707705526813784	2		383	589	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216189	36216189	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	237	639	2	ENST00000222270.7:c.3602del	p.Pro1201ArgfsTer154	p.P1201Rfs*154	ENST00000222270	NM_014727.1	1199	ggC/gg	11/37	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.707705526813784	2		641	627	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989105	41989105	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	272	419	0	ENST00000219905.7:c.1897G>T	p.Gly633Ter	p.G633*	ENST00000219905	NM_001164273.1	633	Gga/Tga	3/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.707705526813784	2		419	691	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466019	69466019	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	224	740	0	ENST00000227507.2:c.857C>G	p.Thr286Arg	p.T286R	ENST00000227507	NM_053056.2	286	aCa/aGa	5/5	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.707705526813784	2		740	630	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856094	111856094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs895574020	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	180	691	1	ENST00000341259.2:c.145G>A	p.Ala49Thr	p.A49T	ENST00000341259	NM_005475.2	49	Gcc/Acc	2/8	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.707705526813784	2		692	499	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415891	49415891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	264	639	0	ENST00000301067.7:c.16456G>A	p.Val5486Met	p.V5486M	ENST00000301067	NM_003482.3	5486	Gtg/Atg	53/54	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.707705526813784	2		639	717	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502705	149502705	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138008832	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	212	656	0	ENST00000261799.4:c.2083C>T	p.Arg695Cys	p.R695C	ENST00000261799	NM_002609.3	695	Cgc/Tgc	15/23	1	2	FACETS	0.977	0.914	1	0.977	0.914	1	CLONAL	1	TRUE	1	0.707705526813784	2		656	613	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143993	11143993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568509370	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	227	639	0	ENST00000358026.2:c.3574C>T	p.Arg1192Cys	p.R1192C	ENST00000358026	NM_001128849.1	1192	Cgc/Tgc	26/36	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.707705526813784	2		639	630	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952145	178952149	+	frameshift_variant	Frame_Shift_Del	DEL	TGAAC	TGAAC	-	novel	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	147	402	0	ENST00000263967.3:c.3204_*1del		p.LN1067fs	ENST00000263967	NM_006218.2	1067	tTGAAC/t	21/21	1	2	FACETS	0.815	0.748	0.883	0.815	0.748	0.883	CLONAL	1	TRUE	1	0.707705526813784	2		402	510	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206943232	206943232	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	243	550	1	ENST00000423557.1:c.386T>G	p.Phe129Cys	p.F129C	ENST00000423557	NM_000572.2	129	tTt/tGt	4/5	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.707705526813784	2		551	657	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434921	110434921	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	40	825	5	ENST00000375856.3:c.3480del	p.Val1161CysfsTer98	p.V1161Cfs*98	ENST00000375856	NM_003749.2	1160	ccC/cc	1/2	1	2	FACETS	0.165	0.136	0.196	0.165	0.136	0.196	SUBCLONAL	1	TRUE	1	0.707705526813784	2		830	687	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632437	3632437	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs956924993	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	221	683	0	ENST00000294008.3:c.5411A>G	p.His1804Arg	p.H1804R	ENST00000294008	NM_032444.2	1804	cAc/cGc	15/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.707705526813784	2		683	597	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786818	3786818	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	185	465	0	ENST00000262367.5:c.4395-2A>G		p.X1465_splice	ENST00000262367	NM_004380.2	1465			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.707705526813784	2		465	488	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134269	11134269	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	42	542	0	ENST00000358026.2:c.2935C>T	p.Arg979Ter	p.R979*	ENST00000358026	NM_001128849.1	979	Cga/Tga	20/36	1	2	FACETS	0.216	0.18	0.256	0.216	0.18	0.256	SUBCLONAL	1	TRUE	1	0.707705526813784	2		542	549	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249927	39249927	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs397517149	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	262	457	0	ENST00000402219.2:c.1642A>C	p.Ser548Arg	p.S548R	ENST00000402219	NM_005633.3	548	Agt/Cgt	10/23	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.707705526813784	2		457	697	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713651	30713651	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769750420	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	245	764	1	ENST00000295754.5:c.976G>A	p.Ala326Thr	p.A326T	ENST00000295754	NM_003242.5	326	Gcc/Acc	4/7	1	2	FACETS	0.986	0.927	1	0.986	0.927	1	CLONAL	1	TRUE	1	0.707705526813784	2		765	702	SUCCESS
ALB	213	MSKCC	GRCh37	4	74279260	74279260	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	218	497	0	ENST00000295897.4:c.967C>T	p.Pro323Ser	p.P323S	ENST00000295897	NM_000477.5	323	Cct/Tct	8/15	1	2	FACETS	0.84	0.785	0.898	0.84	0.785	0.898	CLONAL	1	TRUE	1	0.707705526813784	2		497	733	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591122	67591149	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTGAGAAAGACGAGAGACCAATACTT	AGCTGAGAAAGACGAGAGACCAATACTT	-	novel	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	205	385	0	ENST00000274335.5:c.1715_1742del	p.Gln572ArgfsTer4	p.Q572Rfs*4	ENST00000274335		572	cAGCTGAGAAAGACGAGAGACCAATACTTg/cg	12/15	1	2	FACETS	0.914	0.852	0.977	0.914	0.852	0.977	CLONAL	1	TRUE	1	0.707705526813784	2		385	634	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457776	149457776	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	225	630	2	ENST00000286301.3:c.628G>A	p.Ala210Thr	p.A210T	ENST00000286301	NM_005211.3	210	Gca/Aca	5/22	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.707705526813784	2		632	630	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860912	151860912	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	206	418	0	ENST00000262189.6:c.9751-1G>T		p.X3251_splice	ENST00000262189	NM_170606.2	3251			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.707705526813784	2		418	527	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538829	23538829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	196	577	0	ENST00000380871.4:c.610G>A	p.Ala204Thr	p.A204T	ENST00000380871	NM_006167.3	204	Gcc/Acc	2/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.707705526813784	2		577	487	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760871	133760871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	230	644	0	ENST00000318560.5:c.3194del	p.Thr1065SerfsTer4	p.T1065Sfs*4	ENST00000318560	NM_005157.4	1065	aCg/ag	11/11	0.707705526813784	2	FACETS	1	0.948	1	0.506	0.475	0.538	CLONAL	1	TRUE	0	0.707705526813784	2		644	642	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986676	36986676	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754318871	NA	P-0061943-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	102	625	0	ENST00000354822.5:c.1013G>A	p.Ser338Asn	p.S338N	ENST00000354822	NM_001079668.2	338	aGc/aAc	3/3	0.359348277420348	3	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	TRUE	1	0.363611907300964	3		625	324	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729180	66729180	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061943-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	172	645	0	ENST00000307102.5:c.388T>A	p.Tyr130Asn	p.Y130N	ENST00000307102	NM_002755.3	130	Tat/Aat	3/11	0.359348277420348	3	FACETS	0.954	0.883	1	0.954	0.883	1	CLONAL	2	TRUE	1	0.363611907300964	3		645	586	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0061943-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	153	539	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.360268292013088	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	0	0.363611907300964	2		539	411	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031748	36031749	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061943-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	87	624	0	ENST00000358208.4:c.1577_1578insA	p.Glu527ArgfsTer49	p.E527Rfs*49	ENST00000358208		526	acc/acAc	12/12	0.359348277420348	3	FACETS	0.973	0.863	1	0.487	0.431	0.546	CLONAL	1	TRUE	1	0.363611907300964	3		624	581	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564515	55564515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754738766	NA	P-0061943-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	66	492	1	ENST00000288135.5:c.403C>T	p.Arg135Cys	p.R135C	ENST00000288135	NM_000222.2	135	Cgc/Tgc	3/21	0.359348277420348	3	FACETS	0.86	0.748	0.981	0.43	0.374	0.491	CLONAL	1	TRUE	1	0.363611907300964	3		493	499	SUCCESS
APC	324	MSKCC	GRCh37	5	112175912	112175912	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201801	NA	P-0061943-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	181	554	0	ENST00000257430.4:c.4621C>T	p.Gln1541Ter	p.Q1541*	ENST00000257430	NM_000038.5	1541	Cag/Tag	16/16	0.360268292013088	2	FACETS	0.968	0.901	1	0.968	0.901	1	CLONAL	2	TRUE	0	0.363611907300964	2		554	514	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0061944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	175	476	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.703346872997095	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.703346872997095	1		476	308	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0061944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	157	163	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.703346872997095	2		163	433	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0061944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	88	441	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.78	0.698	0.865	0.78	0.698	0.865	SUBCLONAL	1	TRUE	1	0.703346872997095	2		441	321	SUCCESS
APC	324	MSKCC	GRCh37	5	112175171	112175171	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085373	NA	P-0061944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	125	481	0	ENST00000257430.4:c.3880C>T	p.Gln1294Ter	p.Q1294*	ENST00000257430	NM_000038.5	1294	Cag/Tag	16/16	1	2	FACETS	0.85	0.776	0.927	0.85	0.776	0.927	CLONAL	1	TRUE	1	0.703346872997095	2		481	418	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055919	180055919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1368679940	NA	P-0061944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	201	488	0	ENST00000261937.6:c.1066G>A	p.Val356Met	p.V356M	ENST00000261937	NM_182925.4	356	Gtg/Atg	8/30	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.703346872997095	2		488	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578181	7578192	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCTCATAG	GGCGGCTCATAG	-	rs876660749	NA	P-0061944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	250	580	0	ENST00000269305.4:c.657_668del	p.Tyr220_Pro223del	p.Y220_P223del	ENST00000269305	NM_001126112.2	219	ccCTATGAGCCGCCt/cct	6/11	0.698904879703217	1	FACETS	0.935	0.885	0.984	0.935	0.885	0.984	CLONAL	1	TRUE	0	0.703346872997095	1		580	493	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061945-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	292	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.529434184741253	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.546166638005502	3		298	669	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0061945-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	205	796	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.538405842213128	1	FACETS	0.966	0.903	1	0.966	0.903	1	CLONAL	1	TRUE	0	0.546166638005502	1		796	565	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573639	48573639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061945-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	111	480	0	ENST00000342988.3:c.223C>T	p.Gln75Ter	p.Q75*	ENST00000342988	NM_005359.5	75	Cag/Tag	2/12	0.538405842213128	1	FACETS	0.882	0.802	0.964	0.882	0.802	0.964	CLONAL	1	TRUE	0	0.546166638005502	1		480	335	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419852	41419853	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAAAGT	novel	NA	P-0061945-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	231	475	0	ENST00000373198.4:c.463_468dup	p.Thr155_Phe156dup	p.T155_F156dup	ENST00000373198	NM_133170.3	155	-/ACTTTC	3/32	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.546166638005502	2		475	835	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061946-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	24	143	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	0.409771063226265	2	FACETS	0.239	0.187	0.3	0.12	0.093	0.15	SUBCLONAL	1	TRUE	0	0.468487467576301	2		143	428	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0061946-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	254	662	0	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	0.468487467576301	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.468487467576301	2		662	506	SUCCESS
APC	324	MSKCC	GRCh37	5	112173926	112173926	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060503287	NA	P-0061946-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	182	542	0	ENST00000257430.4:c.2635C>T	p.Gln879Ter	p.Q879*	ENST00000257430	NM_000038.5	879	Cag/Tag	16/16	0.409771063226265	2	FACETS	0.914	0.854	0.975	0.914	0.854	0.975	CLONAL	2	TRUE	0	0.468487467576301	2		542	425	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102107	27102107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061946-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	215	539	0	ENST00000324856.7:c.5033C>T	p.Ser1678Phe	p.S1678F	ENST00000324856	NM_006015.4	1678	tCt/tTt	19/20	0.468487467576301	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.468487467576301	3		539	498	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739716	41739716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749750926	NA	P-0061946-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	83	523	0	ENST00000242208.4:c.257C>T	p.Ala86Val	p.A86V	ENST00000242208	NM_002192.2	86	gCg/gTg	2/3	0.468487467576301	8	FACETS	0.917	0.808	1	0.153	0.134	0.173	CLONAL	1	TRUE	2	0.468487467576301	8		523	929	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	116	494	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.53	2		494	382	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	137	522	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.859	0.784	0.937	0.859	0.784	0.937	CLONAL	1	TRUE	1	0.53	2		522	602	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	65	551	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.915	0.802	1	0.915	0.802	1	CLONAL	1	TRUE	1	0.53	2		551	268	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	175	510	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.965	0.892	1	0.965	0.892	1	CLONAL	1	TRUE	1	0.53	2		510	684	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	98	413	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.53	2		413	346	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	39	723	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.244	0.202	0.292	0.244	0.202	0.292	SUBCLONAL	1	TRUE	1	0.53	2		723	603	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487277	56487277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035001455	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	230	435	0	ENST00000267101.3:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000267101	NM_001982.3	475	Cgg/Tgg	12/28	1	2	FACETS	0.808	0.76	0.856	1	0.994	1	CLONAL	2	TRUE	1	0.53	2		435	537	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	125	532	1	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	1	2	FACETS	0.895	0.814	0.98	0.895	0.814	0.98	CLONAL	1	TRUE	1	0.53	2		533	527	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720877	89720877	+	splice_donor_variant	Splice_Site	SNP	T	T	G	rs1114167624	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	37	180	0	ENST00000371953.3:c.1026+2T>G		p.X342_splice	ENST00000371953	NM_000314.4	342			1	2	FACETS	0.702	0.584	0.83	0.702	0.584	0.83	SUBCLONAL	1	TRUE	1	0.53	2		180	199	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148504761	148504761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397515548	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	94	275	0	ENST00000320356.2:c.2233G>A	p.Glu745Lys	p.E745K	ENST00000320356	NM_004456.4	745	Gaa/Aaa	20/20	1	2	FACETS	0.859	0.769	0.953	0.859	0.769	0.953	CLONAL	1	TRUE	1	0.53	2		275	413	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636210	87636210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs957713208	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	131	423	0	ENST00000277120.3:c.2375G>A	p.Arg792His	p.R792H	ENST00000277120		792	cGc/cAc	19/19	1	2	FACETS	0.863	0.786	0.943	0.863	0.786	0.943	CLONAL	1	TRUE	1	0.53	2		423	573	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674234	86674234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	97	283	0	ENST00000274376.6:c.2366G>A	p.Arg789Gln	p.R789Q	ENST00000274376	NM_002890.2	789	cGa/cAa	18/25	1	2	FACETS	0.953	0.857	1	0.953	0.857	1	CLONAL	1	TRUE	1	0.53	2		283	384	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672371	86672371	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	105	307	0	ENST00000274376.6:c.2173G>T	p.Glu725Ter	p.E725*	ENST00000274376	NM_002890.2	725	Gaa/Taa	16/25	1	2	FACETS	0.996	0.899	1	0.996	0.899	1	CLONAL	1	TRUE	1	0.53	2		307	398	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285871	87285871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408094711	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	102	392	0	ENST00000277120.3:c.208G>A	p.Glu70Lys	p.E70K	ENST00000277120		70	Gaa/Aaa	2/19	1	2	FACETS	0.828	0.744	0.916	0.828	0.744	0.916	CLONAL	1	TRUE	1	0.53	2		392	465	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520177	9520177	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	110	429	0	ENST00000353224.5:c.2092C>T	p.Pro698Ser	p.P698S	ENST00000353224	NM_177990.2	698	Cca/Tca	10/10	1	2	FACETS	0.798	0.72	0.88	0.798	0.72	0.88	SUBCLONAL	1	TRUE	1	0.53	2		429	520	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383281	31383281	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751976489	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	169	478	0	ENST00000328111.2:c.1193G>A	p.Arg398His	p.R398H	ENST00000328111	NM_006892.3	398	cGc/cAc	11/23	1	2	FACETS	0.88	0.811	0.951	0.88	0.811	0.951	CLONAL	1	TRUE	1	0.53	2		478	725	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164855	47164855	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424607930	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	118	401	0	ENST00000409792.3:c.1271G>A	p.Arg424Gln	p.R424Q	ENST00000409792	NM_014159.6	424	cGa/cAa	3/21	1	2	FACETS	0.97	0.881	1	0.97	0.881	1	CLONAL	1	TRUE	1	0.53	2		401	459	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265007	198265007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773349667	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	139	409	0	ENST00000335508.6:c.2870G>A	p.Arg957Gln	p.R957Q	ENST00000335508	NM_012433.2	957	cGa/cAa	19/25	1	2	FACETS	0.928	0.849	1	0.928	0.849	1	CLONAL	1	TRUE	1	0.53	2		409	565	SUCCESS
AR	367	MSKCC	GRCh37	X	66905935	66905935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218564193	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	94	348	0	ENST00000374690.3:c.1852C>T	p.Arg618Trp	p.R618W	ENST00000374690	NM_000044.3	618	Cgg/Tgg	3/8	1	2	FACETS	0.917	0.822	1	0.917	0.822	1	CLONAL	1	TRUE	1	0.53	2		348	387	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836855	151836855	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	114	340	0	ENST00000262189.6:c.14365C>T	p.Arg4789Ter	p.R4789*	ENST00000262189	NM_170606.2	4789	Cga/Tga	56/59	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.53	2		340	421	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427983	49427983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866777837	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	137	447	1	ENST00000301067.7:c.10607G>A	p.Arg3536His	p.R3536H	ENST00000301067	NM_003482.3	3536	cGc/cAc	38/54	1	2	FACETS	0.907	0.829	0.989	0.907	0.829	0.989	CLONAL	1	TRUE	1	0.53	2		448	570	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134681	41134681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	132	417	0	ENST00000379561.5:c.947G>A	p.Arg316Gln	p.R316Q	ENST00000379561	NM_002015.3	316	cGa/cAa	2/3	1	2	FACETS	0.981	0.895	1	0.981	0.895	1	CLONAL	1	TRUE	1	0.53	2		417	508	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007331	143007331	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	73	272	0	ENST00000262992.4:c.2453G>T	p.Arg818Ile	p.R818I	ENST00000262992	NM_001101669.1	818	aGa/aTa	22/24	1	2	FACETS	0.97	0.857	1	0.97	0.857	1	CLONAL	1	TRUE	1	0.53	2		272	284	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911881	94911881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1489329660	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	72	291	0	ENST00000536441.1:c.1049G>A	p.Arg350Gln	p.R350Q	ENST00000536441	NM_144665.3	350	cGa/cAa	7/10	1	2	FACETS	0.947	0.836	1	0.947	0.836	1	CLONAL	1	TRUE	1	0.53	2		291	287	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241033	39241033	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	58	307	0	ENST00000402219.2:c.2038G>T	p.Glu680Ter	p.E680*	ENST00000402219	NM_005633.3	680	Gaa/Taa	12/23	1	2	FACETS	0.842	0.73	0.961	0.842	0.73	0.961	CLONAL	1	TRUE	1	0.53	2		307	260	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850642	63850642	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	126	405	0	ENST00000279873.7:c.1420G>T	p.Glu474Ter	p.E474*	ENST00000279873	NM_032199.2	474	Gaa/Taa	10/10	1	2	FACETS	0.961	0.875	1	0.961	0.875	1	CLONAL	1	TRUE	1	0.53	2		405	495	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856060	45856060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913024	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	148	477	0	ENST00000391945.4:c.1846C>T	p.Arg616Trp	p.R616W	ENST00000391945	NM_000400.3	616	Cgg/Tgg	20/23	1	2	FACETS	0.916	0.839	0.995	0.916	0.839	0.995	CLONAL	1	TRUE	1	0.53	2		477	610	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907143	32907143	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs80358438	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	70	449	0	ENST00000380152.3:c.1528G>T	p.Glu510Ter	p.E510*	ENST00000380152		510	Gaa/Taa	10/27	1	2	FACETS	0.805	0.707	0.909	0.805	0.707	0.909	CLONAL	1	TRUE	1	0.53	2		449	328	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127805	47127805	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	138	329	0	ENST00000409792.3:c.5278-1G>T		p.X1760_splice	ENST00000409792	NM_014159.6	1760			1	2	FACETS	0.895	0.818	0.975	0.895	0.818	0.975	CLONAL	1	TRUE	1	0.53	2		329	582	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881387	111881387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1429573443	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	134	432	0	ENST00000393256.3:c.65C>T	p.Ala22Val	p.A22V	ENST00000393256	NM_006538.4	22	gCg/gTg	2/4	1	2	FACETS	0.919	0.839	1	0.919	0.839	1	CLONAL	1	TRUE	1	0.53	2		432	550	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614584	38614584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749378713	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	59	276	0	ENST00000299084.4:c.350G>A	p.Arg117Gln	p.R117Q	ENST00000299084	NM_152594.2	117	cGa/cAa	3/7	1	2	FACETS	0.901	0.784	1	0.901	0.784	1	CLONAL	1	TRUE	1	0.53	2		276	247	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524362	187524362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766902640	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	163	413	1	ENST00000441802.2:c.11318G>A	p.Arg3773His	p.R3773H	ENST00000441802	NM_005245.3	3773	cGc/cAc	19/27	1	2	FACETS	0.917	0.844	0.992	0.917	0.844	0.992	CLONAL	1	TRUE	1	0.53	2		414	671	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508328	106508328	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769318398	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	87	495	0	ENST00000359195.3:c.322G>A	p.Glu108Lys	p.E108K	ENST00000359195	NM_002649.2	108	Gag/Aag	2/11	1	2	FACETS	0.634	0.563	0.709	0.634	0.563	0.709	SUBCLONAL	1	TRUE	1	0.53	2		495	518	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	59	423	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.84	0.73	0.958	0.84	0.73	0.958	CLONAL	1	TRUE	1	0.53	2		423	265	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335147	65335147	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	115	380	0	ENST00000342505.4:c.494A>C	p.Asp165Ala	p.D165A	ENST00000342505	NM_002227.2	165	gAt/gCt	6/25	1	2	FACETS	0.986	0.895	1	0.986	0.895	1	CLONAL	1	TRUE	1	0.53	2		380	440	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274722	123274722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1219597593	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	140	405	0	ENST00000358487.5:c.1196G>A	p.Arg399Gln	p.R399Q	ENST00000358487	NM_000141.4	399	cGa/cAa	9/18	1	2	FACETS	0.895	0.819	0.975	0.895	0.819	0.975	CLONAL	1	TRUE	1	0.53	2		405	590	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47599403	47599403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201283706	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	121	473	0	ENST00000430070.2:c.197C>T	p.Ser66Leu	p.S66L	ENST00000430070	NM_018095.4	66	tCg/tTg	2/4	1	2	FACETS	0.807	0.731	0.886	0.807	0.731	0.886	CLONAL	1	TRUE	1	0.53	2		473	566	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151865	108151865	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	63	310	0	ENST00000278616.4:c.3546G>T	p.Glu1182Asp	p.E1182D	ENST00000278616	NM_000051.3	1182	gaG/gaT	24/63	1	2	FACETS	0.755	0.657	0.859	0.755	0.657	0.859	SUBCLONAL	1	TRUE	1	0.53	2		310	315	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103513904	103513904	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	68	335	0	ENST00000355739.4:c.720G>T	p.Lys240Asn	p.K240N	ENST00000355739	NM_000123.3	240	aaG/aaT	7/15	1	2	FACETS	0.773	0.677	0.875	0.773	0.677	0.875	SUBCLONAL	1	TRUE	1	0.53	2		335	332	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135361	30135361	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	131	359	0	ENST00000331968.5:c.457T>G	p.Ser153Ala	p.S153A	ENST00000331968	NM_002742.2	153	Tca/Gca	3/18	1	2	FACETS	0.947	0.864	1	0.947	0.864	1	CLONAL	1	TRUE	1	0.53	2		359	522	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690740	33690740	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	137	407	0	ENST00000308377.4:c.87A>C	p.Glu29Asp	p.E29D	ENST00000308377	NM_152270.3	29	gaA/gaC	2/5	1	2	FACETS	0.998	0.913	1	0.998	0.913	1	CLONAL	1	TRUE	1	0.53	2		407	518	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756768	756768	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	140	430	0	ENST00000314574.4:c.60T>G	p.Asn20Lys	p.N20K	ENST00000314574	NM_005433.3	20	aaT/aaG	2/12	1	2	FACETS	0.982	0.899	1	0.982	0.899	1	CLONAL	1	TRUE	1	0.53	2		430	538	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050436	13050436	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	160	396	0	ENST00000316448.5:c.388A>G	p.Ile130Val	p.I130V	ENST00000316448	NM_004343.3	130	Atc/Gtc	3/9	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.53	2		396	586	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713606	52713606	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1453215498	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	34	396	0	ENST00000394830.3:c.122T>G	p.Leu41Arg	p.L41R	ENST00000394830	NM_018313.4	41	cTt/cGt	2/30	1	2	FACETS	0.263	0.214	0.318	0.263	0.214	0.318	SUBCLONAL	1	TRUE	1	0.53	2		396	488	SUCCESS
REST	5978	MSKCC	GRCh37	4	57777358	57777358	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	161	414	0	ENST00000309042.7:c.554A>C	p.Lys185Thr	p.K185T	ENST00000309042	NM_005612.4	185	aAa/aCa	2/4	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.53	2		414	583	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796404	57796404	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	124	442	0	ENST00000309042.7:c.1380G>T	p.Lys460Asn	p.K460N	ENST00000309042	NM_005612.4	460	aaG/aaT	4/4	1	2	FACETS	0.998	0.909	1	0.998	0.909	1	CLONAL	1	TRUE	1	0.53	2		442	469	SUCCESS
APC	324	MSKCC	GRCh37	5	112177949	112177949	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs374464049	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	136	422	0	ENST00000257430.4:c.6658A>G	p.Asn2220Asp	p.N2220D	ENST00000257430	NM_000038.5	2220	Aac/Gac	16/16	1	2	FACETS	0.995	0.91	1	0.995	0.91	1	CLONAL	1	TRUE	1	0.53	2		422	516	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866699	117866699	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	74	317	0	ENST00000297338.2:c.946A>G	p.Thr316Ala	p.T316A	ENST00000297338	NM_006265.2	316	Aca/Gca	9/14	1	2	FACETS	0.934	0.826	1	0.934	0.826	1	CLONAL	1	TRUE	1	0.53	2		317	299	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376635	8376635	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	118	346	0	ENST00000356435.5:c.4478A>C	p.Tyr1493Ser	p.Y1493S	ENST00000356435		1493	tAt/tCt	27/35	1	2	FACETS	0.924	0.838	1	0.924	0.838	1	CLONAL	1	TRUE	1	0.53	2		346	482	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215881	98215881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs911494100	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	117	343	0	ENST00000331920.6:c.3328G>A	p.Asp1110Asn	p.D1110N	ENST00000331920	NM_000264.3	1110	Gac/Aac	20/24	1	2	FACETS	0.88	0.797	0.966	0.88	0.797	0.966	CLONAL	1	TRUE	1	0.53	2		343	502	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907644	76907644	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs181244850	NA	P-0061947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	122	374	0	ENST00000373344.5:c.4517G>T	p.Arg1506Leu	p.R1506L	ENST00000373344	NM_000489.3	1506	cGt/cTt	15/35	1	2	FACETS	0.982	0.893	1	0.982	0.893	1	CLONAL	1	TRUE	1	0.53	2		374	469	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692922	89692922	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201044	NA	P-0061948-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	181	405	0	ENST00000371953.3:c.406T>C	p.Cys136Arg	p.C136R	ENST00000371953	NM_000314.4	136	Tgt/Cgt	5/9	0.534122994369455	3	FACETS	0.839	0.78	0.899	0.839	0.78	0.899	CLONAL	2	TRUE	1	0.534122994369455	3		405	512	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692949	89692950	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0061948-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	129	411	0	ENST00000371953.3:c.434_435insAT	p.Phe145LeufsTer3	p.F145Lfs*3	ENST00000371953	NM_000314.4	145	ttt/tTAtt	5/9	0.534122994369455	3	FACETS	1	0.963	1	0.555	0.506	0.607	CLONAL	1	TRUE	1	0.534122994369455	3		411	551	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68292293	68292293	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs577027561	NA	P-0061948-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	84	322	0	ENST00000487270.1:c.197C>T	p.Thr66Met	p.T66M	ENST00000487270	NM_133509.3	66	aCg/aTg	3/11	0.482804749422899	4	FACETS	0.865	0.765	0.971	0.432	0.382	0.486	CLONAL	1	TRUE	2	0.534122994369455	4		322	558	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589425	67590101	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTCGTAATTACATAATTGCAATTTTAAAGATGTTTCCATGTCAGCTATTTTGTTAAACAATTGTTATTTGATTAAATACCTTATCCATTGAATTTATTTTAATCTTTCTAGGATCAAGTTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACACTCAGTTTCAAGAAAAAAGTCGAGAATATGATAGATTATATGAAGAATATACCCGCACATCCCAGGTGAGTTTTCTATGAAAATCAGATTAAAAAATAAGAGTTCTAAACTTTTAAAGACTAACATGGAAAAAAGAATTTAAAAGGTTGAGTTTTTACGAATGAGGTGGGGGTGAGAGCATTTATTTGTGAATCATTGTTGATTATTCTAGTGTAATATCTCTAAAGCTTTAAACCAAAAATTTTAAGTATCAGAATAATAAATTAAGTTCACGTGATAACTGAAGCAGTCACTGAGTTTCAAGTTGATTTAATTCGTGATAGAAGGATCCTGTTTAGATTGGAAGTTAGTAATAACTGGAAGTTTCACAGACTTGTCTAATCCCTGAAATGGAGATTTAGGCATTAATATATATCCTACCATGAAAAGGAAGGGCTATATACTGCTGTGCTTTTCTAGACCCTTATTCTTCACTGGTCACTCATGTATCTGGGAATGCCAGAG	ACTCGTAATTACATAATTGCAATTTTAAAGATGTTTCCATGTCAGCTATTTTGTTAAACAATTGTTATTTGATTAAATACCTTATCCATTGAATTTATTTTAATCTTTCTAGGATCAAGTTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACACTCAGTTTCAAGAAAAAAGTCGAGAATATGATAGATTATATGAAGAATATACCCGCACATCCCAGGTGAGTTTTCTATGAAAATCAGATTAAAAAATAAGAGTTCTAAACTTTTAAAGACTAACATGGAAAAAAGAATTTAAAAGGTTGAGTTTTTACGAATGAGGTGGGGGTGAGAGCATTTATTTGTGAATCATTGTTGATTATTCTAGTGTAATATCTCTAAAGCTTTAAACCAAAAATTTTAAGTATCAGAATAATAAATTAAGTTCACGTGATAACTGAAGCAGTCACTGAGTTTCAAGTTGATTTAATTCGTGATAGAAGGATCCTGTTTAGATTGGAAGTTAGTAATAACTGGAAGTTTCACAGACTTGTCTAATCCCTGAAATGGAGATTTAGGCATTAATATATATCCTACCATGAAAAGGAAGGGCTATATACTGCTGTGCTTTTCTAGACCCTTATTCTTCACTGGTCACTCATGTATCTGGGAATGCCAGAG	-	novel	NA	P-0061948-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	27	270	0	ENST00000274335.5:c.1300-112_1426-263del		p.X434_splice	ENST00000274335		434		10/15	1	2	FACETS	0.475	0.38	0.582	0.475	0.38	0.582	SUBCLONAL	1	TRUE	1	0.534122994369455	2		270	213	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0061949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	319	675	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.844002226621285	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.844002226621285	2		675	356	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0061949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	168	574	26	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	0.926	0.86	0.992	0.926	0.86	0.992	CLONAL	1	TRUE	1	0.844002226621285	2		600	430	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0061949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	130	423	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.31761861108841	4	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	2	TRUE	2	0.844002226621285	4		423	249	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11210203	11210203	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	219	410	0	ENST00000361445.4:c.4550C>T	p.Ala1517Val	p.A1517V	ENST00000361445	NM_004958.3	1517	gCt/gTt	31/58	0.245626835047922	4	FACETS	1	0.948	1	1	0.948	1	INDETERMINATE	2	TRUE	2	0.844002226621285	4		410	475	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612975	228612975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs551314787	NA	P-0061949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	237	777	0	ENST00000366696.1:c.52C>T	p.Arg18Cys	p.R18C	ENST00000366696	NM_003493.2	18	Cgc/Tgc	1/1	0.836766717750577	3	FACETS	1	0.967	1	0.525	0.491	0.559	CLONAL	1	TRUE	1	0.844002226621285	3		777	761	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828125	243828125	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	60	296	0	ENST00000263826.5:c.233A>G	p.Gln78Arg	p.Q78R	ENST00000263826	NM_005465.4	78	cAg/cGg	3/13	0.836766717750577	3	FACETS	1	0.931	1	0.546	0.479	0.617	CLONAL	1	TRUE	1	0.844002226621285	3		296	185	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025826	1025826	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1054640166	NA	P-0061949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	22	642	0	ENST00000358495.3:c.704C>T	p.Ala235Val	p.A235V	ENST00000358495	NM_134424.2	235	gCg/gTg	8/12	1	2	FACETS	0.129	0.099	0.163	0.129	0.099	0.163	SUBCLONAL	1	TRUE	1	0.844002226621285	2		642	404	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881489	48881490	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs587778862	NA	P-0061949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	153	331	0	ENST00000267163.4:c.219_220del	p.Arg73SerfsTer36	p.R73Sfs*36	ENST00000267163	NM_000321.2	71	AGa/a	2/27	0.167640448164609	3	FACETS	1	0.987	1	0.664	0.615	0.714	INDETERMINATE	1	TRUE	1	0.844002226621285	3		331	388	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030368	49030368	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	100	369	2	ENST00000267163.4:c.1848del	p.Gly617ValfsTer6	p.G617Vfs*6	ENST00000267163	NM_000321.2	615	Aaa/aa	19/27	0.167640448164609	3	FACETS	1	0.98	1	0.658	0.598	0.72	INDETERMINATE	1	TRUE	1	0.844002226621285	3		371	256	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0061949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	115	470	2	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	0.225054931900156	3	FACETS	1	0.961	1	0.55	0.501	0.601	INDETERMINATE	1	TRUE	1	0.844002226621285	3		472	352	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0061949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	219	556	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.225054931900156	3	FACETS	0.782	0.736	0.828	0.782	0.736	0.828	INDETERMINATE	2	TRUE	1	0.844002226621285	3		562	472	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031541	11031541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1160510813	NA	P-0061949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	215	740	0	ENST00000327064.4:c.1456G>A	p.Gly486Ser	p.G486S	ENST00000327064	NM_199141.1	486	Ggc/Agc	13/16	0.195254400547221	4	FACETS	0.893	0.838	0.949	0.893	0.838	0.949	INDETERMINATE	2	TRUE	2	0.844002226621285	4		740	526	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0061949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	177	785	1	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	0.245626835047922	4	FACETS	1	0.989	1	0.704	0.653	0.757	INDETERMINATE	1	TRUE	2	0.844002226621285	4		786	549	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400310	225400310	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	133	329	0	ENST00000264414.4:c.313C>G	p.Leu105Val	p.L105V	ENST00000264414	NM_003590.4	105	Cta/Gta	3/16	1	2	FACETS	0.955	0.88	1	0.955	0.88	1	CLONAL	1	TRUE	1	0.844002226621285	2		329	330	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660361	227660361	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199755602	NA	P-0061949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	91	543	0	ENST00000305123.5:c.3094G>A	p.Ala1032Thr	p.A1032T	ENST00000305123	NM_005544.2	1032	Gct/Act	1/2	1	2	FACETS	0.922	0.833	1	0.922	0.833	1	CLONAL	1	TRUE	1	0.844002226621285	2		543	234	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495657	72495657	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	176	426	0	ENST00000477973.2:c.415A>T	p.Thr139Ser	p.T139S	ENST00000477973	NM_012234.5	139	Acc/Tcc	1/4	0.412707229034842	4	FACETS	0.927	0.864	0.99	0.927	0.864	0.99	INDETERMINATE	2	TRUE	2	0.844002226621285	4		426	415	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0061949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	185	231	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.974	0.909	1	0.974	0.909	1	CLONAL	1	TRUE	1	0.844002226621285	2		231	450	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422384	47422384	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	47	422	0	ENST00000377045.4:c.23del	p.Pro8LeufsTer26	p.P8Lfs*26	ENST00000377045	NM_001654.4	6	ggC/gg	2/16	0.501780980821707	1	FACETS	0.233	0.198	0.272	0.233	0.198	0.272	INDETERMINATE	1	TRUE	0	0.844002226621285	1		422	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0121494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	80	426	0	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	0.273012363968419	3	FACETS	0.946	0.833	1	0.473	0.416	0.534	CLONAL	1	NA	1	0.288979202490317	3		426	670	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922924	39922935	+	inframe_deletion	In_Frame_Del	DEL	CCCTTTTCCTGC	CCCTTTTCCTGC	-	novel	NA	P-0121494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	61	438	0	ENST00000378444.4:c.3773_3784del	p.Gly1258_Arg1261del	p.G1258_R1261del	ENST00000378444	NM_001123385.1	1258	gGCAGGAAAAGGGca/gca	8/15	1	2	FACETS	0.78	0.674	0.896	0.78	0.674	0.896	SUBCLONAL	1	NA	1	0.288979202490317	2		438	541	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922940	39922965	+	frameshift_variant	Frame_Shift_Del	DEL	TTTCTCTTCAGTGATGTTAGTCCCCT	TTTCTCTTCAGTGATGTTAGTCCCCT	AAA	novel	NA	P-0121494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	61	435	0	ENST00000378444.4:c.3743_3768delinsTTT	p.Gln1248LeufsTer21	p.Q1248Lfs*21	ENST00000378444	NM_001123385.1	1248	cAGGGGACTAACATCACTGAAGAGAAA/cTTT	8/15	1	2	FACETS	0.779	0.672	0.895	0.779	0.672	0.895	SUBCLONAL	1	NA	1	0.288979202490317	2		435	542	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0061951-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	20	387	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.802	1	1	0.802	1	CLONAL	1	TRUE	1	0.17	2		388	224	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0061951-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	34	510	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	1	0.834	1	1	0.834	1	CLONAL	1	TRUE	1	0.17	2		510	392	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0061951-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	25	492	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	1	2	FACETS	0.86	0.678	1	0.86	0.678	1	CLONAL	1	TRUE	1	0.17	2		492	342	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602722	10602722	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs773547929	NA	P-0061951-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	25	733	1	ENST00000171111.5:c.856C>T	p.Gln286Ter	p.Q286*	ENST00000171111	NM_203500.1	286	Cag/Tag	3/6	1	2	FACETS	0.687	0.541	0.856	0.687	0.541	0.856	SUBCLONAL	1	TRUE	1	0.17	2		734	428	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21345927	21345927	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061951-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	27	692	0	ENST00000215739.8:c.802A>T	p.Ile268Phe	p.I268F	ENST00000215739	NM_006767.3	268	Atc/Ttc	9/21	1	2	FACETS	0.76	0.604	0.938	0.76	0.604	0.938	CLONAL	1	TRUE	1	0.17	2		692	418	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950714	79950730	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCGCAGCGGCCGCAG	GGCCGCAGCGGCCGCAG	-	novel	NA	P-0061951-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	21	599	0	ENST00000265081.6:c.168_184del	p.Ala58ProfsTer21	p.A58Pfs*21	ENST00000265081	NM_002439.4	56	gcGGCCGCAGCGGCCGCAGcg/gccg	1/24	1	2	FACETS	0.625	0.481	0.795	0.625	0.481	0.795	SUBCLONAL	1	TRUE	1	0.17	2		599	395	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0061955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	171	473	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.609194072008463	2		473	448	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0061955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	77	764	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.609194072008463	3	FACETS	1	0.926	1	0.53	0.47	0.594	CLONAL	1	TRUE	1	0.609194072008463	3		764	311	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098951	178098953	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0061955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	178	492	0	ENST00000397062.3:c.92_94del	p.Gly31del	p.G31del	ENST00000397062	NM_006164.4	31	gGAGta/gta	2/5	1	2	FACETS	0.989	0.916	1	0.989	0.916	1	CLONAL	1	TRUE	1	0.609194072008463	2		492	591	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434142	49434142	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057518571	NA	P-0061955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	231	732	0	ENST00000301067.7:c.7411C>T	p.Arg2471Ter	p.R2471*	ENST00000301067	NM_003482.3	2471	Cga/Tga	31/54	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.609194072008463	2		732	758	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295547	1295547	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215810	NA	P-0061955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	243	922	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.609194072008463	2		922	717	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023224	27023225	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0061955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	164	579	0	ENST00000324856.7:c.333dup	p.Ala112ArgfsTer5	p.A112Rfs*5	ENST00000324856	NM_006015.4	110	-/C	1/20	0.609194072008463	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.609194072008463	1		579	367	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204696	108204696	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs775136925	NA	P-0061955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	127	234	0	ENST00000278616.4:c.8010+1G>C		p.X2670_splice	ENST00000278616	NM_000051.3	2670			0.609194072008463	1	FACETS	0.954	0.878	1	0.954	0.878	1	CLONAL	1	TRUE	0	0.609194072008463	1		234	304	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446781	49446781	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	235	782	0	ENST00000301067.7:c.1029C>A	p.Tyr343Ter	p.Y343*	ENST00000301067	NM_003482.3	343	taC/taA	8/54	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.609194072008463	2		782	743	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044402	5044402	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0061955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	234	296	0	ENST00000381652.3:c.351-1G>C		p.X117_splice	ENST00000381652	NM_004972.3	117			0.609194072008463	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.609194072008463	2		296	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0061956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	192	571	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.259555760383019	4	FACETS	0.894	0.827	0.962	0.894	0.827	0.962	CLONAL	2	TRUE	2	0.322541901570152	4		571	881	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577035	7577036	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0061956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	230	508	0	ENST00000269305.4:c.902dup	p.Gly302ArgfsTer4	p.G302Rfs*4	ENST00000269305	NM_001126112.2	301	cca/ccCa	8/11	0.259555760383019	4	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	2	0.322541901570152	4		508	942	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793382	18793382	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs77070108	NA	P-0061956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	61	281	0	ENST00000266497.5:c.4079C>T	p.Ala1360Val	p.A1360V	ENST00000266497		1360	gCg/gTg	30/31	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.322541901570152	2		281	342	SUCCESS
APC	324	MSKCC	GRCh37	5	112136985	112136985	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	73	282	0	ENST00000257430.4:c.739C>T	p.Gln247Ter	p.Q247*	ENST00000257430	NM_000038.5	247	Cag/Tag	8/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.322541901570152	2		282	383	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111965609	111965609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	25	31	0	ENST00000375549.3:c.395C>T	p.Ser132Leu	p.S132L	ENST00000375549	NM_003002.3	132	tCa/tTa	4/4	0.306334852410198	2	FACETS	1	0.819	1	1	0.819	1	CLONAL	2	TRUE	0	0.322541901570152	2		31	77	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356402	70356402	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	107	477	0	ENST00000374080.3:c.5297C>G	p.Pro1766Arg	p.P1766R	ENST00000374080		1766	cCc/cGc	37/45	0.294404439176723	3	FACETS	0.951	0.853	1			1	CLONAL	1	TRUE	NA	0.322541901570152	3		477	810	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0061957-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	122	665	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.526843694449613	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.542427688179303	1		665	315	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0061957-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	80	315	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	1	2	FACETS	0.886	0.786	0.991	0.886	0.786	0.991	CLONAL	1	TRUE	1	0.542427688179303	2		315	333	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508977	106508977	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760224981	NA	P-0061957-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	101	598	0	ENST00000359195.3:c.971C>T	p.Pro324Leu	p.P324L	ENST00000359195	NM_002649.2	324	cCa/cTa	2/11	0.465035122289822	3	FACETS	0.672	0.601	0.748	0.336	0.3	0.374	SUBCLONAL	1	TRUE	1	0.542427688179303	3		598	704	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922241	100922241	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061957-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	46	304	0	ENST00000325455.5:c.2271C>A	p.Ser757Arg	p.S757R	ENST00000325455	NM_001202474.3	757	agC/agA	5/8	1	2	FACETS	0.874	0.746	1	0.874	0.746	1	CLONAL	1	TRUE	1	0.542427688179303	2		304	194	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047264	128047264	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs56116802	NA	P-0061957-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	97	504	0	ENST00000285398.2:c.657+1G>A		p.X219_splice	ENST00000285398	NM_000122.1	219			1	2	FACETS	0.858	0.77	0.95	0.858	0.77	0.95	CLONAL	1	TRUE	1	0.542427688179303	2		504	417	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266645	41266645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061957-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	134	484	0	ENST00000349496.5:c.442C>T	p.Leu148Phe	p.L148F	ENST00000349496	NM_001904.3	148	Ctt/Ttt	4/15	0.25714635006164	3	FACETS	0.851	0.782	0.921	0.851	0.782	0.921	INDETERMINATE	2	TRUE	1	0.542427688179303	3		484	369	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499416	89499416	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061957-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	39	544	0	ENST00000336596.2:c.2586G>T	p.Gln862His	p.Q862H	ENST00000336596	NM_005233.5	862	caG/caT	15/17	0.25714635006164	3	FACETS	0.369	0.306	0.44	0.185	0.153	0.22	INDETERMINATE	1	TRUE	1	0.542427688179303	3		544	495	SUCCESS
APC	324	MSKCC	GRCh37	5	112175112	112175113	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0061957-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	48	459	0	ENST00000257430.4:c.3822_3823dup	p.Ser1275IlefsTer14	p.S1275Ifs*14	ENST00000257430	NM_000038.5	1274	tgt/tgTAt	16/16	1	2	FACETS	0.705	0.601	0.817	0.705	0.601	0.817	SUBCLONAL	1	TRUE	1	0.542427688179303	2		459	251	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0061958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	923	701	0	ENST00000269305.4:c.920-2A>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.843974040174847	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.845873901046525	3		701	1027	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421555	32421555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	317	579	1	ENST00000332351.3:c.1037C>T	p.Thr346Met	p.T346M	ENST00000332351	NM_024426.4	346	aCg/aTg	6/10	0.502071370652572	5	FACETS	0.949	0.898	1	0.633	0.599	0.667	INDETERMINATE	2	TRUE	2	0.845873901046525	5		580	896	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256792	16256792	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	456	571	0	ENST00000375759.3:c.4057G>A	p.Val1353Met	p.V1353M	ENST00000375759	NM_015001.2	1353	Gtg/Atg	11/15	0.502071370652572	5	FACETS	0.921	0.885	0.957	0.921	0.885	0.957	INDETERMINATE	3	TRUE	2	0.845873901046525	5		571	885	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106966	27106966	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	299	700	0	ENST00000324856.7:c.6577G>T	p.Gly2193Cys	p.G2193C	ENST00000324856	NM_006015.4	2193	Ggc/Tgc	20/20	0.502071370652572	5	FACETS	1	0.994	1	0.491	0.463	0.521	INDETERMINATE	1	TRUE	2	0.845873901046525	5		700	1088	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65349159	65349159	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0061958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	268	401	0	ENST00000342505.4:c.7-1G>T		p.X3_splice	ENST00000342505	NM_002227.2	3			0.502071370652572	5	FACETS	0.99	0.934	1	0.66	0.622	0.699	INDETERMINATE	2	TRUE	2	0.845873901046525	5		401	726	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669398	241669398	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	320	345	0	ENST00000366560.3:c.809A>T	p.Tyr270Phe	p.Y270F	ENST00000366560	NM_000143.3	270	tAt/tTt	6/10	0.502071370652572	5	FACETS	0.917	0.874	0.96	0.917	0.874	0.96	INDETERMINATE	3	TRUE	2	0.845873901046525	5		345	624	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934153	48934157	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GGGAA	GGGAA	-	novel	NA	P-0061958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	141	109	0	ENST00000267163.4:c.609_613del	p.Glu204IlefsTer6	p.E204Ifs*6	ENST00000267163	NM_000321.2	203	gGGGAA/g	7/27	0.845873901046525	2	FACETS	0.969	0.926	1	0.969	0.926	1	CLONAL	2	TRUE	0	0.845873901046525	2		109	172	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570167	95570167	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	305	475	0	ENST00000393063.1:c.3566A>G	p.Tyr1189Cys	p.Y1189C	ENST00000393063	NM_030621.3	1189	tAt/tGt	22/28	0.502071370652572	5	FACETS	1	0.984	1	0.726	0.688	0.765	INDETERMINATE	2	TRUE	2	0.845873901046525	5		475	751	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128016966	128016966	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	253	569	0	ENST00000285398.2:c.2123A>T	p.Glu708Val	p.E708V	ENST00000285398	NM_000122.1	708	gAg/gTg	14/15	0.442327335239782	5	FACETS	1	0.993	1	0.497	0.465	0.529	INDETERMINATE	1	TRUE	2	0.845873901046525	5		569	911	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	147	326	0				ENST00000310581	NM_198253.2	-/1132			0.269428900112182	5	FACETS	0.837	0.767	0.91	0.837	0.767	0.91	CLONAL	3	TRUE	2	0.269428900112182	5		326	610	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004922	150004922	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	98	642	0	ENST00000253339.5:c.1303C>T	p.Gln435Ter	p.Q435*	ENST00000253339		435	Cag/Tag	3/7	0.269428900112182	3	FACETS	1	0.937	1	0.537	0.478	0.599	CLONAL	1	TRUE	1	0.269428900112182	3		642	769	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0061959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	201	597	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.265333082996002	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.269428900112182	2		597	628	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742640	39742640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	145	554	0	ENST00000361337.2:c.1483G>A	p.Glu495Lys	p.E495K	ENST00000361337	NM_003286.2	495	Gaa/Aaa	15/21	0.193815985852568	4	FACETS	0.999	0.913	1	0.999	0.913	1	CLONAL	2	TRUE	2	0.269428900112182	4		554	684	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649694	206649694	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	79	692	0	ENST00000367120.3:c.529G>C	p.Glu177Gln	p.E177Q	ENST00000367120	NM_014002.3	177	Gag/Cag	6/22	0.23395026761737	4	FACETS	0.959	0.843	1	0.32	0.281	0.362	CLONAL	1	TRUE	1	0.269428900112182	4		692	776	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425385	49425386	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	666	805	0	ENST00000301067.7:c.13102dup	p.Thr4368AsnfsTer4	p.T4368Nfs*4	ENST00000301067	NM_003482.3	4368	acc/aAcc	39/54	0.269428900112182	9	FACETS	0.977	0.944	1	0.977	0.944	1	CLONAL	7	TRUE	2	0.269428900112182	9		805	1405	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808916	1808916	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	79	875	0	ENST00000260795.2:c.2348C>T	p.Ser783Leu	p.S783L	ENST00000260795		783	tCa/tTa	17/17	0.193815985852568	4	FACETS	0.835	0.733	0.946	0.418	0.366	0.473	CLONAL	1	TRUE	2	0.269428900112182	4		875	891	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775433	39775433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168532464	NA	P-0061959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	82	636	0	ENST00000288319.7:c.587G>A	p.Arg196Lys	p.R196K	ENST00000288319	NM_182918.3	196	aGa/aAa	4/10	0.269428900112182	3	FACETS	1	0.919	1	0.526	0.464	0.593	CLONAL	1	TRUE	1	0.269428900112182	3		636	656	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72897392	72897392	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	66	605	0	ENST00000325599.8:c.100G>C	p.Glu34Gln	p.E34Q	ENST00000325599	NM_018130.2	34	Gag/Cag	1/11	0.269428900112182	3	FACETS	0.949	0.824	1	0.474	0.412	0.542	CLONAL	1	TRUE	1	0.269428900112182	3		605	586	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702337	47702337	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs267607982	NA	P-0061959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	46	272	0	ENST00000233146.2:c.1933C>T	p.Gln645Ter	p.Q645*	ENST00000233146	NM_000251.2	645	Caa/Taa	12/16	0.269428900112182	5	FACETS	0.807	0.679	0.949	0.269	0.226	0.317	CLONAL	1	TRUE	2	0.269428900112182	5		272	594	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098790	47098790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	91	691	0	ENST00000409792.3:c.6484C>T	p.His2162Tyr	p.H2162Y	ENST00000409792	NM_014159.6	2162	Cat/Tat	15/21	0.269428900112182	3	FACETS	1	0.925	1	0.527	0.468	0.591	CLONAL	1	TRUE	1	0.269428900112182	3		691	727	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155410	106155410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	61	403	0	ENST00000380013.4:c.311C>T	p.Ser104Phe	p.S104F	ENST00000380013	NM_001127208.2	104	tCt/tTt	3/11	0.193815985852568	4	FACETS	0.924	0.797	1	0.462	0.398	0.532	CLONAL	1	TRUE	2	0.269428900112182	4		403	622	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204512070	204512070	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	43	261	0	ENST00000367182.3:c.670C>G	p.Gln224Glu	p.Q224E	ENST00000367182	NM_001278516.1	224	Cag/Gag	8/11	0.23395026761737	4	FACETS	0.812	0.679	0.959	0.271	0.226	0.32	CLONAL	1	TRUE	1	0.269428900112182	4		261	499	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94169046	94169046	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0061959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	42	187	0	ENST00000323929.3:c.1946C>G	p.Ser649Ter	p.S649*	ENST00000323929	NM_005591.3	649	tCa/tGa	18/20	0.269428900112182	3	FACETS	0.871	0.729	1	0.436	0.364	0.515	CLONAL	1	TRUE	1	0.269428900112182	3		187	406	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352458	118352458	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	57	366	0	ENST00000534358.1:c.3663G>C	p.Lys1221Asn	p.K1221N	ENST00000534358	NM_005933.3	1221	aaG/aaC	7/36	0.269428900112182	3	FACETS	0.949	0.815	1	0.474	0.407	0.548	CLONAL	1	TRUE	1	0.269428900112182	3		366	506	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434411	110434411	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	57	663	0	ENST00000375856.3:c.3990G>C	p.Leu1330Phe	p.L1330F	ENST00000375856	NM_003749.2	1330	ttG/ttC	1/2	0.256365839191507	3	FACETS	0.828	0.71	0.956	0.276	0.236	0.319	CLONAL	1	TRUE	0	0.269428900112182	3		663	580	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422058	81422058	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	66	623	0	ENST00000298171.2:c.34C>G	p.Leu12Val	p.L12V	ENST00000298171	NM_000369.2	12	Ctg/Gtg	1/10	1	2	FACETS	0.884	0.768	1	0.884	0.768	1	CLONAL	1	TRUE	1	0.269428900112182	2		623	554	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250826	99250826	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	73	716	0	ENST00000268035.6:c.130C>T	p.Gln44Ter	p.Q44*	ENST00000268035	NM_000875.3	44	Cag/Tag	2/21	0.269428900112182	3	FACETS	1	0.875	1	0.5	0.437	0.567	CLONAL	1	TRUE	1	0.269428900112182	3		716	615	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982858	7982858	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0061959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	69	684	0	ENST00000319144.4:c.928-1G>A		p.X310_splice	ENST00000319144	NM_001139.2	310			0.265333082996002	2	FACETS	0.968	0.845	1	0.484	0.422	0.551	CLONAL	1	TRUE	0	0.269428900112182	2		684	529	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899266	78899266	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	99	637	0	ENST00000306801.3:c.2905C>A	p.Gln969Lys	p.Q969K	ENST00000306801	NM_020761.2	969	Cag/Aag	24/34	0.269428900112182	4	FACETS	1	0.964	1	0.297	0.265	0.332	CLONAL	1	TRUE	0	0.269428900112182	4		637	784	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371718	45371718	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	67	309	0	ENST00000262160.6:c.1273G>C	p.Glu425Gln	p.E425Q	ENST00000262160	NM_005901.5	425	Gaa/Caa	10/11	1	2	FACETS	0.975	0.849	1	0.975	0.849	1	CLONAL	1	TRUE	1	0.269428900112182	2		309	510	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566730	212566730	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs959924017	NA	P-0061959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	88	353	0	ENST00000342788.4:c.1451G>C	p.Arg484Thr	p.R484T	ENST00000342788	NM_005235.2	484	aGa/aCa	12/28	0.269428900112182	3	FACETS	1	0.966	1	0.616	0.546	0.69	CLONAL	1	TRUE	1	0.269428900112182	3		353	602	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623247	52623247	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	112	412	0	ENST00000394830.3:c.2804C>G	p.Ser935Cys	p.S935C	ENST00000394830	NM_018313.4	935	tCt/tGt	19/30	0.269428900112182	3	FACETS	0.865	0.781	0.954	0.865	0.781	0.954	CLONAL	2	TRUE	1	0.269428900112182	3		412	545	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146541	185146541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759834442	NA	P-0061959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	105	635	0	ENST00000265026.3:c.172G>A	p.Glu58Lys	p.E58K	ENST00000265026	NM_004721.4	58	Gag/Aag	2/14	0.269428900112182	3	FACETS	1	0.98	1	0.696	0.625	0.772	CLONAL	1	TRUE	1	0.269428900112182	3		635	635	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980380	1980380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	130	592	0	ENST00000382891.5:c.3842C>T	p.Pro1281Leu	p.P1281L	ENST00000382891	NM_133335.3	1281	cCt/cTt	22/22	0.193815985852568	4	FACETS	1	0.915	1	1	0.915	1	CLONAL	2	TRUE	2	0.269428900112182	4		592	609	SUCCESS
APC	324	MSKCC	GRCh37	5	112137026	112137026	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	58	303	0	ENST00000257430.4:c.780G>C	p.Gln260His	p.Q260H	ENST00000257430	NM_000038.5	260	caG/caC	8/16	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.269428900112182	2		303	363	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938124	76938124	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	151	130	0	ENST00000373344.5:c.2624C>T	p.Ser875Leu	p.S875L	ENST00000373344	NM_000489.3	875	tCa/tTa	9/35	0.269428900112182	2	FACETS	1	0.953	1			1	CLONAL	3	TRUE	NA	0.269428900112182	2		130	360	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091716	29091716	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	23	30	0	ENST00000328354.6:c.1241G>C	p.Gly414Ala	p.G414A	ENST00000328354	NM_007194.3	414	gGa/gCa	11/15	0.269428900112182	4	FACETS	0.942	0.779	1	1	0.946	1	CLONAL	5	TRUE	1	0.269428900112182	4		30	46	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0061961-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	287	434	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.594965888118432	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.594965888118432	3		434	620	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0061961-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	85	370	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.594965888118432	3	FACETS	0.774	0.687	0.867	0.387	0.343	0.434	SUBCLONAL	1	TRUE	1	0.594965888118432	3		370	479	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712018	89712018	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs727504114	NA	P-0061961-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	186	350	1	ENST00000371953.3:c.634+2T>C		p.X212_splice	ENST00000371953	NM_000314.4	212			0.594965888118432	3	FACETS	0.97	0.908	1	0.97	0.908	1	CLONAL	2	TRUE	1	0.594965888118432	3		351	418	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46597542	46597542	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061961-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	130	429	0	ENST00000262741.5:c.83T>G	p.Phe28Cys	p.F28C	ENST00000262741	NM_003629.3	28	tTt/tGt	1/10	0.543157158714487	3	FACETS	0.996	0.908	1			1	CLONAL	1	TRUE	NA	0.594965888118432	3		429	569	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631186	67631186	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061961-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	70	175	0	ENST00000272342.5:c.1372G>A	p.Asp458Asn	p.D458N	ENST00000272342	NM_019002.3	458	Gat/Aat	5/6	0.594965888118432	3	FACETS	0.925	0.813	1	0.463	0.406	0.523	CLONAL	1	TRUE	1	0.594965888118432	3		175	330	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592166	67592167	+	stop_gained,inframe_insertion	Nonsense_Mutation	INS	-	-	AGTGTA	novel	NA	P-0061961-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	206	405	0	ENST00000274335.5:c.1983_1985+3dup		p.V661VV*	ENST00000274335		661	gta/gtAGTGTAa	14/15	0.594965888118432	3	FACETS	0.874	0.818	0.93	0.874	0.818	0.93	CLONAL	2	TRUE	1	0.594965888118432	3		405	514	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144148	55144148	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519700	NA	P-0061964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	192	375	0	ENST00000257290.5:c.1977C>G	p.Asn659Lys	p.N659K	ENST00000257290	NM_006206.4	659	aaC/aaG	14/23	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.679035646720592	2		375	536	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602619	10602619	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1239985410	NA	P-0061965-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	121	650	0	ENST00000171111.5:c.959G>T	p.Arg320Leu	p.R320L	ENST00000171111	NM_203500.1	320	cGg/cTg	3/6	0.193462045165071	2	FACETS	0.977	0.885	1	0.488	0.442	0.537	INDETERMINATE	1	FALSE	0	0.400311283243077	2		650	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0061965-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	175	577	0	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	0.172807421966326	4	FACETS	0.886	0.818	0.956	0.443	0.409	0.478	INDETERMINATE	2	FALSE	0	0.400311283243077	4		577	691	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864186	117864186	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0061965-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	30	424	0	ENST00000297338.2:c.1470+1G>A		p.X490_splice	ENST00000297338	NM_006265.2	490			0.172741755417273	3	FACETS	0.471	0.379	0.575	0.235	0.189	0.288	INDETERMINATE	1	FALSE	1	0.400311283243077	3		424	382	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564809	86564809	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0061965-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	88	602	0	ENST00000274376.6:c.539+2T>A		p.X180_splice	ENST00000274376	NM_002890.2	180			0.223191828446525	2	FACETS	0.788	0.7	0.882	0.394	0.35	0.441	INDETERMINATE	1	FALSE	0	0.400311283243077	2		602	558	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121438955	121438955	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061965-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	97	578	0	ENST00000257555.6:c.1856A>G	p.Glu619Gly	p.E619G	ENST00000257555		619	gAg/gGg	10/10	0.177639730938463	3	FACETS	0.934	0.834	1	0.467	0.417	0.52	INDETERMINATE	1	FALSE	1	0.400311283243077	3		578	623	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121438963	121438963	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061965-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	96	586	0	ENST00000257555.6:c.1864A>T	p.Ile622Phe	p.I622F	ENST00000257555		622	Atc/Ttc	10/10	0.177639730938463	3	FACETS	0.955	0.852	1	0.477	0.426	0.532	INDETERMINATE	1	FALSE	1	0.400311283243077	3		586	603	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959398	26959398	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061965-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	25	423	0	ENST00000381527.3:c.565G>A	p.Asp189Asn	p.D189N	ENST00000381527	NM_001260.1	189	Gat/Aat	6/13	0.400311283243077	1	FACETS	0.555	0.441	0.684	0.555	0.441	0.684	SUBCLONAL	1	FALSE	0	0.400311283243077	1		423	180	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654737	29654737	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs771529172	NA	P-0061965-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	183	546	0	ENST00000356175.3:c.5426G>T	p.Arg1809Leu	p.R1809L	ENST00000356175	NM_000267.3	1809	cGc/cTc	37/57	0.206711651851266	3	FACETS	1	0.989	1	0.471	0.435	0.508	INDETERMINATE	1	FALSE	0	0.400311283243077	3		546	777	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416497	29416497	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061965-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	50	649	0	ENST00000389048.3:c.4456C>A	p.Pro1486Thr	p.P1486T	ENST00000389048	NM_004304.4	1486	Cct/Act	29/29	1	2	FACETS	0.436	0.369	0.509	0.436	0.369	0.509	SUBCLONAL	1	FALSE	1	0.400311283243077	2		649	573	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917833	29917833	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061965-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	93	491	0	ENST00000389048.3:c.835C>A	p.Pro279Thr	p.P279T	ENST00000389048	NM_004304.4	279	Cca/Aca	3/29	1	2	FACETS	0.954	0.852	1	0.954	0.852	1	CLONAL	1	FALSE	1	0.400311283243077	2		491	487	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660420	227660420	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061965-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	47	669	0	ENST00000305123.5:c.3035A>G	p.Tyr1012Cys	p.Y1012C	ENST00000305123	NM_005544.2	1012	tAt/tGt	1/2	1	2	FACETS	0.427	0.36	0.501	0.427	0.36	0.501	SUBCLONAL	1	FALSE	1	0.400311283243077	2		669	550	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355266	81355266	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061965-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	77	431	0	ENST00000222390.5:c.1108C>A	p.Pro370Thr	p.P370T	ENST00000222390	NM_000601.4	370	Cca/Aca	9/18	0.211779887429354	2	FACETS	1	0.962	1	0.607	0.537	0.68	INDETERMINATE	1	FALSE	0	0.400311283243077	2		431	317	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045755	47045755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782214369	NA	P-0061965-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	102	726	0	ENST00000377604.3:c.2636G>A	p.Arg879His	p.R879H	ENST00000377604	NM_001204468.1	879	cGc/cAc	23/24	1	2	FACETS	0.693	0.62	0.771	0.693	0.62	0.771	SUBCLONAL	1	FALSE	1	0.400311283243077	2		726	735	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341578	70341578	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061965-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	92	563	0	ENST00000374080.3:c.1013C>A	p.Thr338Asn	p.T338N	ENST00000374080		338	aCt/aAt	7/45	1	2	FACETS	0.66	0.587	0.739	0.66	0.587	0.739	SUBCLONAL	1	FALSE	1	0.400311283243077	2		563	696	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100093	27100093	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	111	716	0	ENST00000324856.7:c.3889G>A	p.Glu1297Lys	p.E1297K	ENST00000324856	NM_006015.4	1297	Gag/Aag	16/20	0.538630734298146	1	FACETS	0.575	0.519	0.634	0.575	0.519	0.634	SUBCLONAL	1	TRUE	0	0.538630734298146	1		716	524	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100456	8100457	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0061966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	95	711	0	ENST00000346208.3:c.430_431delinsCT	p.Gly144Leu	p.G144L	ENST00000346208		144	GGc/CTc	3/6	0.263762302563077	2	FACETS	0.487	0.433	0.544	0.243	0.216	0.272	INDETERMINATE	1	TRUE	0	0.538630734298146	2		711	725	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115760	8115760	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	81	538	0	ENST00000346208.3:c.1106C>G	p.Ser369Cys	p.S369C	ENST00000346208		369	tCt/tGt	6/6	0.263762302563077	2	FACETS	0.484	0.427	0.546	0.242	0.213	0.273	INDETERMINATE	1	TRUE	0	0.538630734298146	2		538	621	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450915	70450915	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	75	569	0	ENST00000373644.4:c.5755G>C	p.Glu1919Gln	p.E1919Q	ENST00000373644	NM_030625.2	1919	Gag/Cag	12/12	0.263762302563077	2	FACETS	0.47	0.412	0.533	0.235	0.206	0.267	INDETERMINATE	1	TRUE	0	0.538630734298146	2		569	592	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719890	18719890	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	31	277	0	ENST00000266497.5:c.3787C>A	p.His1263Asn	p.H1263N	ENST00000266497		1263	Cat/Aat	27/31	0.105022773078527	6	FACETS	0.602	0.487	0.733			1	INDETERMINATE	1	TRUE	NA	0.538630734298146	6		277	397	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240308	41240308	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	65	429	0	ENST00000379561.5:c.42C>G	p.Phe14Leu	p.F14L	ENST00000379561	NM_002015.3	14	ttC/ttG	1/3	0.538630734298146	1	FACETS	0.604	0.528	0.685	0.604	0.528	0.685	SUBCLONAL	1	TRUE	0	0.538630734298146	1		429	292	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343642	343642	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	92	563	0	ENST00000262320.3:c.2032C>G	p.Gln678Glu	p.Q678E	ENST00000262320	NM_003502.3	678	Cag/Gag	8/11	1	2	FACETS	0.57	0.507	0.637	0.57	0.507	0.637	SUBCLONAL	1	TRUE	1	0.538630734298146	2		563	599	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135277	2135277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	66	523	0	ENST00000219476.3:c.4616C>T	p.Ser1539Leu	p.S1539L	ENST00000219476	NM_000548.3	1539	tCa/tTa	36/42	1	2	FACETS	0.494	0.429	0.564	0.494	0.429	0.564	SUBCLONAL	1	TRUE	1	0.538630734298146	2		523	496	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273897	10273897	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1458256024	NA	P-0061966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	62	508	0	ENST00000330684.3:c.372C>G	p.Ile124Met	p.I124M	ENST00000330684	NM_001134407.1	124	atC/atG	2/13	1	2	FACETS	0.451	0.39	0.518	0.451	0.39	0.518	SUBCLONAL	1	TRUE	1	0.538630734298146	2		508	510	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783770	50783770	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	46	448	0	ENST00000398568.2:c.161C>T	p.Ser54Phe	p.S54F	ENST00000398568	NM_001042412.1	54	tCt/tTt	3/18	0.330480160334816	1	FACETS	0.301	0.254	0.354	0.301	0.254	0.354	SUBCLONAL	1	TRUE	0	0.538630734298146	1		448	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579378	7579383	+	frameshift_variant	Frame_Shift_Del	DEL	GTAGGT	GTAGGT	C	novel	NA	P-0061966-T01-IM7	NA	A	A	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	149	604	0	ENST00000269305.4:c.304_309delinsG	p.Thr102AlafsTer45	p.T102Afs*45	ENST00000269305	NM_001126112.2	102	ACCTAC/G	4/11	0.538630734298146	1	FACETS	0.919	0.847	0.992	0.919	0.847	0.992	CLONAL	1	TRUE	0	0.538630734298146	1		604	440	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78831682	78831682	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	55	475	0	ENST00000306801.3:c.1491G>C	p.Lys497Asn	p.K497N	ENST00000306801	NM_020761.2	497	aaG/aaC	13/34	0.538630734298146	1	FACETS	0.426	0.366	0.491	0.426	0.366	0.491	SUBCLONAL	1	TRUE	0	0.538630734298146	1		475	350	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030079	36030079	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs751597996	NA	P-0061966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	52	393	0	ENST00000358208.4:c.1114C>T	p.Gln372Ter	p.Q372*	ENST00000358208		372	Cag/Tag	9/12	0.538630734298146	5	FACETS	0.579	0.492	0.674	0.193	0.164	0.225	SUBCLONAL	1	TRUE	2	0.538630734298146	5		393	603	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306560	41306560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	54	410	0	ENST00000373198.4:c.1099G>A	p.Glu367Lys	p.E367K	ENST00000373198	NM_133170.3	367	Gag/Aag	7/32	0.538630734298146	5	FACETS	0.553	0.472	0.643	0.184	0.157	0.215	SUBCLONAL	1	TRUE	2	0.538630734298146	5		410	655	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913283	NA	P-0061966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	68	409	0	ENST00000263967.3:c.3129G>T	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atT	21/21	1	2	FACETS	0.48	0.418	0.547	0.48	0.418	0.547	SUBCLONAL	1	TRUE	1	0.538630734298146	2		409	526	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590995	67590995	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	50	307	0	ENST00000274335.5:c.1588A>C	p.Lys530Gln	p.K530Q	ENST00000274335		530	Aag/Cag	12/15	0.538630734298146	1	FACETS	0.424	0.361	0.492	0.424	0.361	0.492	SUBCLONAL	1	TRUE	0	0.538630734298146	1		307	320	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250614	26250614	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	125	789	0	ENST00000446824.2:c.220G>C	p.Glu74Gln	p.E74Q	ENST00000446824	NM_021018.2	74	Gag/Cag	1/1	0.538630734298146	1	FACETS	0.551	0.5	0.604	0.551	0.5	0.604	SUBCLONAL	1	TRUE	0	0.538630734298146	1		789	616	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969185	93969185	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	122	404	1	ENST00000369303.4:c.1811G>T	p.Gly604Val	p.G604V	ENST00000369303	NM_004440.3	604	gGc/gTc	10/17	0.330480160334816	1	FACETS	0.851	0.777	0.928	0.851	0.777	0.928	CLONAL	1	TRUE	0	0.538630734298146	1		405	389	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663605	117663605	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	74	256	0	ENST00000368508.3:c.4627T>G	p.Leu1543Val	p.L1543V	ENST00000368508	NM_002944.2	1543	Tta/Gta	28/43	0.330480160334816	1	FACETS	0.823	0.73	0.919	0.823	0.73	0.919	CLONAL	1	TRUE	0	0.538630734298146	1		256	244	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372430	55372430	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	68	594	0	ENST00000297316.4:c.1120G>C	p.Glu374Gln	p.E374Q	ENST00000297316	NM_022454.3	374	Gag/Cag	2/2	0.538630734298146	4	FACETS	0.467	0.406	0.535	0.156	0.135	0.179	SUBCLONAL	1	TRUE	1	0.538630734298146	4		594	831	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117875402	117875402	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	67	379	0	ENST00000297338.2:c.241G>C	p.Ala81Pro	p.A81P	ENST00000297338	NM_006265.2	81	Gca/Cca	3/14	0.538630734298146	4	FACETS	0.543	0.471	0.621	0.181	0.157	0.207	SUBCLONAL	1	TRUE	1	0.538630734298146	4		379	705	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499697	8499697	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	73	497	0	ENST00000356435.5:c.2272G>A	p.Glu758Lys	p.E758K	ENST00000356435		758	Gag/Aag	14/35	1	2	FACETS	0.504	0.441	0.571	0.504	0.441	0.571	SUBCLONAL	1	TRUE	1	0.538630734298146	2		497	538	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0061967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	341	372	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.768071624965634	2	FACETS	0.944	0.914	0.973	0.944	0.914	0.973	CLONAL	2	TRUE	0	0.811552854529693	2		372	445	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67197052	67197052	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	404	444	0	ENST00000312629.5:c.295A>G	p.Lys99Glu	p.K99E	ENST00000312629	NM_003952.2	99	Aaa/Gaa	4/15	0.767208042314555	3	FACETS	0.979	0.94	1	0.979	0.94	1	CLONAL	2	TRUE	1	0.811552854529693	3		444	715	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041898	42041898	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	179	557	0	ENST00000219905.7:c.6095del	p.Leu2032TrpfsTer70	p.L2032Wfs*70	ENST00000219905	NM_001164273.1	2031	caT/ca	17/24	0.773903232782312	2	FACETS	0.857	0.796	0.919	0.428	0.398	0.46	CLONAL	1	TRUE	0	0.811552854529693	2		557	515	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51503150	51503150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	196	480	0	ENST00000260433.2:c.1367G>A	p.Arg456Lys	p.R456K	ENST00000260433		456	aGa/aAa	10/10	0.811552854529693	3	FACETS	1	0.932	1	0.501	0.466	0.538	CLONAL	1	TRUE	1	0.811552854529693	3		480	677	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830321	72830321	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1464698105	NA	P-0061967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	477	644	0	ENST00000268489.5:c.6260A>T	p.Gln2087Leu	p.Q2087L	ENST00000268489	NM_006885.3	2087	cAg/cTg	9/10	0.767208042314555	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.811552854529693	3		644	811	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346071	89346071	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	61	130	0	ENST00000301030.4:c.6879C>A	p.Asp2293Glu	p.D2293E	ENST00000301030	NM_001256183.1	2293	gaC/gaA	9/13	0.767208042314555	3	FACETS	1	0.952	1	0.587	0.516	0.661	CLONAL	1	TRUE	1	0.811552854529693	3		130	180	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574019	7574020	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	348	393	0	ENST00000269305.4:c.1007dup	p.Arg337AlafsTer10	p.R337Afs*10	ENST00000269305	NM_001126112.2	336	gag/gaAg	10/11	0.757218850864317	2	FACETS	0.91	0.88	0.94	0.91	0.88	0.94	CLONAL	2	TRUE	0	0.811552854529693	2		393	471	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16097859	16097860	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0061967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	145	218	0	ENST00000268712.3:c.24dup	p.Asn9GlnfsTer34	p.N9Qfs*34	ENST00000268712	NM_006311.3	8	-/C	2/46	0.757218850864317	2	FACETS	0.889	0.841	0.934	0.889	0.841	0.934	CLONAL	2	TRUE	0	0.811552854529693	2		218	201	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733058	74733058	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	177	543	1	ENST00000359995.5:c.185T>C	p.Phe62Ser	p.F62S	ENST00000359995	NM_001195427.1	62	tTt/tCt	1/3	0.768071624965634	2	FACETS	0.823	0.764	0.884	0.412	0.382	0.442	CLONAL	1	TRUE	0	0.811552854529693	2		544	530	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626928	14626934	+	frameshift_variant	Frame_Shift_Del	DEL	CGGGTAT	CGGGTAT	-	novel	NA	P-0061967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	261	626	0	ENST00000254322.2:c.841_847del	p.Ile281SerfsTer38	p.I281Sfs*38	ENST00000254322	NM_006145.1	281	ATACCCGtc/tc	3/3	0.747305116597603	4	FACETS	0.99	0.927	1	0.495	0.463	0.528	CLONAL	1	TRUE	2	0.811552854529693	4		626	1177	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278398	39278398	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	79	335	0	ENST00000402219.2:c.751G>T	p.Asp251Tyr	p.D251Y	ENST00000402219	NM_005633.3	251	Gat/Tat	6/23	0.811552854529693	3	FACETS	1	0.937	1	0.537	0.478	0.597	CLONAL	1	TRUE	1	0.811552854529693	3		335	255	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504298	186504298	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	203	286	0	ENST00000323963.5:c.635T>G	p.Leu212Trp	p.L212W	ENST00000323963		212	tTg/tGg	7/11	0.768071624965634	2	FACETS	0.89	0.85	0.928	0.89	0.85	0.928	CLONAL	2	TRUE	0	0.811552854529693	2		286	281	SUCCESS
REST	5978	MSKCC	GRCh37	4	57777588	57777588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	363	515	0	ENST00000309042.7:c.784C>T	p.His262Tyr	p.H262Y	ENST00000309042	NM_005612.4	262	Cac/Tac	2/4	0.767208042314555	3	FACETS	0.791	0.755	0.828	0.791	0.755	0.828	SUBCLONAL	2	TRUE	1	0.811552854529693	3		515	795	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538337	187538337	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	104	381	0	ENST00000441802.2:c.8897A>C	p.Gln2966Pro	p.Q2966P	ENST00000441802	NM_005245.3	2966	cAg/cCg	11/27	0.747305116597603	4	FACETS	0.871	0.783	0.964	0.436	0.391	0.482	CLONAL	1	TRUE	2	0.811552854529693	4		381	533	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101612	27101612	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	216	606	0	ENST00000324856.7:c.4899del	p.Met1634Ter	p.M1634*	ENST00000324856	NM_006015.4	1632	Ccc/cc	18/20	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.417917307601066	2		606	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578418	7578418	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	224	615	0	ENST00000269305.4:c.512A>G	p.Glu171Gly	p.E171G	ENST00000269305	NM_001126112.2	171	gAg/gGg	5/11	0.326545144789436	2	FACETS	0.782	0.732	0.834	0.782	0.732	0.834	SUBCLONAL	2	TRUE	0	0.417917307601066	2		615	685	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185819	32185819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145916093	NA	P-0061968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	99	426	0	ENST00000375023.3:c.1577C>T	p.Ala526Val	p.A526V	ENST00000375023	NM_004557.3	526	gCg/gTg	9/30	0.372589419644659	3	FACETS	0.881	0.788	0.981	0.441	0.394	0.491	CLONAL	1	TRUE	1	0.417917307601066	3		426	650	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022899	27022899	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	228	499	0	ENST00000324856.7:c.5C>G	p.Ala2Gly	p.A2G	ENST00000324856	NM_006015.4	2	gCc/gGc	1/20	0.330978356722473	3	FACETS	0.912	0.854	0.972	0.912	0.854	0.972	CLONAL	2	TRUE	1	0.417917307601066	3		499	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579368	7579368	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	192	513	0	ENST00000269305.4:c.319del	p.Tyr107ThrfsTer16	p.Y107Tfs*16	ENST00000269305	NM_001126112.2	107	Tac/ac	4/11	0.25309961771545	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.25309961771545	2		513	669	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532695	187532695	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316346360	NA	P-0061969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	63	510	0	ENST00000441802.2:c.9698G>A	p.Arg3233His	p.R3233H	ENST00000441802	NM_005245.3	3233	cGt/cAt	14/27	1	2	FACETS	0.92	0.797	1	0.92	0.797	1	CLONAL	1	TRUE	1	0.25309961771545	2		510	541	SUCCESS
REST	5978	MSKCC	GRCh37	4	57777681	57777682	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0061969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	42	320	0	ENST00000309042.7:c.877_878delinsAG	p.Gln293Arg	p.Q293R	ENST00000309042	NM_005612.4	293	CAg/AGg	2/4	0.11688344462825	3	FACETS	0.865	0.723	1	0.288	0.241	0.341	INDETERMINATE	1	TRUE	0	0.25309961771545	3		320	432	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356311	66356311	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1021419209	NA	P-0061969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	40	517	1	ENST00000273854.3:c.1186A>G	p.Lys396Glu	p.K396E	ENST00000273854	NM_004439.5	396	Aag/Gag	5/18	0.11688344462825	3	FACETS	0.559	0.463	0.666	0.186	0.154	0.222	INDETERMINATE	1	TRUE	0	0.25309961771545	3		518	637	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123199786	123199786	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	58	250	0	ENST00000218089.9:c.2086G>A	p.Ala696Thr	p.A696T	ENST00000218089	NM_001042749.1	696	Gct/Act	21/35	0.181640841199473	3	FACETS	0.939	0.814	1	0.939	0.814	1	CLONAL	2	TRUE	1	0.25309961771545	3		250	275	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246482	105246482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	75	471	0	ENST00000349310.3:c.118G>A	p.Glu40Lys	p.E40K	ENST00000349310	NM_001014432.1	40	Gag/Aag	4/15	1	2	FACETS	0.951	0.834	1	0.951	0.834	1	CLONAL	1	TRUE	1	0.2771763726765	2		471	569	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0061972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	56	349	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.988	0.849	1	0.988	0.849	1	CLONAL	1	TRUE	1	0.2771763726765	2		349	409	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266112	41266112	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913228	NA	P-0061972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	78	465	0	ENST00000349496.5:c.109T>G	p.Ser37Ala	p.S37A	ENST00000349496	NM_001904.3	37	Tct/Gct	3/15	1	2	FACETS	0.841	0.739	0.951	0.841	0.739	0.951	CLONAL	1	TRUE	1	0.2771763726765	2		465	669	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988037	85988037	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs947096920	NA	P-0061972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	34	394	0	ENST00000263360.6:c.982A>G	p.Ile328Val	p.I328V	ENST00000263360	NM_003797.3	328	Att/Gtt	10/12	1	2	FACETS	0.549	0.448	0.662	0.549	0.448	0.662	SUBCLONAL	1	TRUE	1	0.2771763726765	2		394	447	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087358	27087359	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCAA	novel	NA	P-0061972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	66	436	0	ENST00000324856.7:c.1934_1937dup	p.Asp647AsnfsTer3	p.D647Nfs*3	ENST00000324856	NM_006015.4	644	-/TCAA	5/20	1	2	FACETS	0.809	0.702	0.924	0.809	0.702	0.924	CLONAL	1	TRUE	1	0.2771763726765	2		436	589	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0061973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	147	797	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.70221651941836	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.70221651941836	1		799	224	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	52	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.163861098745652	4	FACETS	1	0.968	1	0.741	0.643	0.845	INDETERMINATE	1	TRUE	2	0.70221651941836	4		298	170	SUCCESS
APC	324	MSKCC	GRCh37	5	112174096	112174096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs137854575	NA	P-0061973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	54	483	0	ENST00000257430.4:c.2805C>A	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	taC/taA	16/16	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.70221651941836	2		483	140	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221711	55221711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760101437	NA	P-0061973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	11	576	0	ENST00000275493.2:c.755G>A	p.Arg252His	p.R252H	ENST00000275493	NM_005228.3	252	cGc/cAc	7/28	1	2	FACETS	0.093	0.064	0.13	0.093	0.064	0.13	SUBCLONAL	1	TRUE	1	0.70221651941836	2		576	337	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984147	2984147	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	84	458	0	ENST00000396946.4:c.383C>T	p.Thr128Met	p.T128M	ENST00000396946	NM_032415.4	128	aCg/aTg	5/25	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.70221651941836	2		458	209	SUCCESS
APC	324	MSKCC	GRCh37	5	112176018	112176018	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	47	521	0	ENST00000257430.4:c.4728del	p.Glu1577AsnfsTer73	p.E1577Nfs*73	ENST00000257430	NM_000038.5	1576	gAa/ga	16/16	1	2	FACETS	0.802	0.688	0.922	0.802	0.688	0.922	CLONAL	1	TRUE	1	0.70221651941836	2		521	167	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778831	9778831	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375873391	NA	P-0061973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	155	676	0	ENST00000377346.4:c.1100C>T	p.Ser367Leu	p.S367L	ENST00000377346	NM_005026.3	367	tCg/tTg	9/24	0.70221651941836	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.70221651941836	1		676	250	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116197	67116197	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753789494	NA	P-0061973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	90	437	0	ENST00000412916.2:c.481C>T	p.Arg161Trp	p.R161W	ENST00000412916		161	Cgg/Tgg	5/6	1	2	FACETS	0.932	0.838	1	0.932	0.838	1	CLONAL	1	TRUE	1	0.70221651941836	2		437	275	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105798	27105798	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	11	563	0	ENST00000324856.7:c.5409G>T	p.Glu1803Asp	p.E1803D	ENST00000324856	NM_006015.4	1803	gaG/gaT	20/20	0.70221651941836	1	FACETS	0.151	0.104	0.208	0.151	0.104	0.208	SUBCLONAL	1	TRUE	0	0.70221651941836	1		563	135	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390160	89390160	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	54	462	0	ENST00000336596.2:c.909C>A	p.Asn303Lys	p.N303K	ENST00000336596	NM_005233.5	303	aaC/aaA	4/17	1	2	FACETS	0.805	0.699	0.918	0.805	0.699	0.918	CLONAL	1	TRUE	1	0.70221651941836	2		462	191	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0061974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	145	473	0				ENST00000310581	NM_198253.2	-/1132			0.362505242267474	5	FACETS	1	0.967	1	1	0.967	1	CLONAL	3	TRUE	2	0.437000639697127	5		473	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0061974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	227	752	0	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	0.369802871448427	3	FACETS	0.859	0.81	0.909	0.859	0.81	0.909	CLONAL	3	TRUE	0	0.437000639697127	3		752	491	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981851	201981852	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0061974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	90	641	0	ENST00000359651.3:c.567dup	p.Ser190LeufsTer6	p.S190Lfs*6	ENST00000359651		188	gcc/gCcc	4/8	0.365456038177288	4	FACETS	1	0.948	1	0.555	0.494	0.62	CLONAL	1	TRUE	2	0.437000639697127	4		641	533	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604332	189604332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763644058	NA	P-0061974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	190	541	0	ENST00000264731.3:c.1499G>A	p.Gly500Glu	p.G500E	ENST00000264731	NM_003722.4	500	gGa/gAa	11/14	0.362505242267474	5	FACETS	1	0.954	1	0.691	0.641	0.743	CLONAL	2	TRUE	2	0.437000639697127	5		541	694	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316131	11316131	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	209	598	0	ENST00000361445.4:c.623G>A	p.Gly208Glu	p.G208E	ENST00000361445	NM_004958.3	208	gGa/gAa	5/58	0.347864294049669	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	2	0.437000639697127	4		598	641	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220119	5220119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755452432	NA	P-0061974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	159	638	0	ENST00000357368.4:c.3596C>T	p.Ser1199Leu	p.S1199L	ENST00000357368	NM_002850.3	1199	tCg/tTg	22/38	0.37055297169162	5	FACETS	0.853	0.788	0.919	0.853	0.788	0.919	CLONAL	3	TRUE	2	0.437000639697127	5		638	471	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984122	201984356	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCTGGGCACGGTTACAGGCCAGTGTAGGGAAAGAGCTTCTGCTTGCCAGTGTGAAGAACAGAGGAGTTTAGGAAGTGTGAGTCAGGCTCAGCTTAGTCAGGCAGAGACCAGTGGGCATGGGTTACCTGGGGGTAACGCGGGCCAGGTGGGCGGGCTGGCAGCCTGGGGCCCATTTCCTGCCAAAGCACCTCTGACCATCCTTCTCTTCACCCAGGTACTACTACAAACGGGAGA	TCCTGGGCACGGTTACAGGCCAGTGTAGGGAAAGAGCTTCTGCTTGCCAGTGTGAAGAACAGAGGAGTTTAGGAAGTGTGAGTCAGGCTCAGCTTAGTCAGGCAGAGACCAGTGGGCATGGGTTACCTGGGGGTAACGCGGGCCAGGTGGGCGGGCTGGCAGCCTGGGGCCCATTTCCTGCCAAAGCACCTCTGACCATCCTTCTCTTCACCCAGGTACTACTACAAACGGGAGA	-	novel	NA	P-0061974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	57	69	0	ENST00000359651.3:c.1002-209_1027del		p.X334_splice	ENST00000359651		334		8/8	0.365456038177288	4	FACETS	0.91	0.814	1	1	0.981	1	CLONAL	4	TRUE	2	0.437000639697127	4		69	103	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097751	8097751	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	181	668	0	ENST00000346208.3:c.133G>C	p.Glu45Gln	p.E45Q	ENST00000346208		45	Gag/Cag	2/6	0.437155227783571	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.437000639697127	3		668	493	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606668	43606668	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	91	724	1	ENST00000355710.3:c.1277G>C	p.Cys426Ser	p.C426S	ENST00000355710	NM_020975.4	426	tGt/tCt	7/20	0.437155227783571	3	FACETS	0.9	0.801	1	0.45	0.4	0.503	CLONAL	1	TRUE	1	0.437000639697127	3		725	564	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312686	91312686	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	68	323	0	ENST00000355112.3:c.2425C>G	p.Gln809Glu	p.Q809E	ENST00000355112	NM_000057.2	809	Caa/Gaa	12/22	0.395045499192779	3	FACETS	0.87	0.759	0.988	0.435	0.379	0.494	CLONAL	1	TRUE	1	0.437000639697127	3		323	436	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212126	142212126	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	143	334	0	ENST00000350721.4:c.5926C>G	p.Leu1976Val	p.L1976V	ENST00000350721	NM_001184.3	1976	Ctt/Gtt	35/47	0.362505242267474	5	FACETS	0.957	0.877	1	0.638	0.584	0.694	CLONAL	2	TRUE	2	0.437000639697127	5		334	566	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604322	189604322	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	204	558	0	ENST00000264731.3:c.1489G>A	p.Asp497Asn	p.D497N	ENST00000264731	NM_003722.4	497	Gat/Aat	11/14	0.362505242267474	5	FACETS	1	0.961	1	0.698	0.649	0.748	CLONAL	2	TRUE	2	0.437000639697127	5		558	738	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943789	71943789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773085707	NA	P-0061975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	84	594	1	ENST00000298229.2:c.1832G>A	p.Arg611His	p.R611H	ENST00000298229	NM_001567.3	611	cGc/cAc	15/28	1	2	FACETS	0.481	0.424	0.541	0.481	0.424	0.541	SUBCLONAL	1	TRUE	1	0.509526733217809	2		595	686	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0061975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	121	701	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.509526733217809	2		701	461	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0061975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	61	529	1	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.509526733217809	2		530	209	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0061975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	157	349	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.509526733217809	2		349	471	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	60	420	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.503	0.434	0.578	0.503	0.434	0.578	SUBCLONAL	1	TRUE	1	0.509526733217809	2		420	468	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717615	89717615	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909227	NA	P-0061975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	217	354	0	ENST00000371953.3:c.640C>T	p.Gln214Ter	p.Q214*	ENST00000371953	NM_000314.4	214	Cag/Tag	7/9	0.500298984344319	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.509526733217809	3		354	474	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630626	158630626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912678	NA	P-0061975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	184	418	0	ENST00000263640.3:c.617G>A	p.Arg206His	p.R206H	ENST00000263640	NM_001105.4	206	cGc/cAc	6/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.509526733217809	2		418	543	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371810	55371831	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGCCCCGAGGGCGGCCGCGT	TGGGCCCCGAGGGCGGCCGCGT	-	novel	NA	P-0061975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	32	585	0	ENST00000297316.4:c.500_521del	p.Leu167ArgfsTer213	p.L167Rfs*213	ENST00000297316	NM_022454.3	167	cTGGGCCCCGAGGGCGGCCGCGTg/cg	2/2	1	2	FACETS	0.316	0.256	0.383	0.316	0.256	0.383	SUBCLONAL	1	TRUE	1	0.509526733217809	2		585	398	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101068	27101068	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	128	533	2	ENST00000324856.7:c.4354del	p.Gln1452ArgfsTer29	p.Q1452Rfs*29	ENST00000324856	NM_006015.4	1450	ggC/gg	18/20	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.509526733217809	2		535	496	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928080	178928080	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	38	382	0	ENST00000263967.3:c.1358A>G	p.Glu453Gly	p.E453G	ENST00000263967	NM_006218.2	453	gAa/gGa	8/21	1	2	FACETS	0.439	0.363	0.522	0.439	0.363	0.522	SUBCLONAL	1	TRUE	1	0.509526733217809	2		382	340	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11227537	11227537	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	43	384	0	ENST00000361445.4:c.4291G>A	p.Gly1431Arg	p.G1431R	ENST00000361445	NM_004958.3	1431	Gga/Aga	29/58	1	2	FACETS	0.298	0.249	0.352	0.298	0.249	0.352	SUBCLONAL	1	TRUE	1	0.509526733217809	2		384	567	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371849	55371850	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0061975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	103	573	0	ENST00000297316.4:c.541dup	p.Leu181ProfsTer184	p.L181Pfs*184	ENST00000297316	NM_022454.3	180	ggc/ggCc	2/2	1	2	FACETS	0.991	0.893	1	0.991	0.893	1	CLONAL	1	TRUE	1	0.509526733217809	2		573	408	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746003	162746003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs896311138	NA	P-0061975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	111	520	0	ENST00000367921.3:c.2126G>A	p.Arg709Gln	p.R709Q	ENST00000367921	NM_006182.2	709	cGa/cAa	16/18	1	2	FACETS	0.824	0.743	0.908	0.824	0.743	0.908	CLONAL	1	TRUE	1	0.509526733217809	2		520	529	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs112445441	NA	P-0061975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	99	282	0	ENST00000311936.3:c.38G>T	p.Gly13Val	p.G13V	ENST00000311936	NM_004985.3	13	gGc/gTc	2/5	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.509526733217809	2		282	338	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099077	27099077	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	307	653	1	ENST00000324856.7:c.3494del	p.Pro1165GlnfsTer15	p.P1165Qfs*15	ENST00000324856	NM_006015.4	1165	Cca/ca	13/20	1	2	FACETS	0.863	0.819	0.907	1	0.996	1	CLONAL	2	TRUE	1	0.509526733217809	2		654	698	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712017	89712018	+	splice_donor_variant	Splice_Site	DNP	GT	GT	TC	novel	NA	P-0061975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	77	339	1	ENST00000371953.3:c.634+1_634+2delinsTC		p.X212_splice	ENST00000371953	NM_000314.4	212			0.500298984344319	3	FACETS	0.939	0.828	1	0.469	0.414	0.528	CLONAL	1	TRUE	1	0.509526733217809	3		340	404	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94910881	94910881	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0061975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	81	348	0	ENST00000536441.1:c.1247+2T>A		p.X416_splice	ENST00000536441	NM_144665.3	416			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.509526733217809	2		348	284	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103510743	103510743	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	72	421	0	ENST00000355739.4:c.647G>T	p.Arg216Ile	p.R216I	ENST00000355739	NM_000123.3	216	aGa/aTa	6/15	1	2	FACETS	0.854	0.747	0.969	0.854	0.747	0.969	CLONAL	1	TRUE	1	0.311175916898459	2		421	542	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362500	40362500	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219718677	NA	P-0061976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	60	439	0	ENST00000293328.3:c.1696C>T	p.Arg566Trp	p.R566W	ENST00000293328	NM_012448.3	566	Cgg/Tgg	14/19	1	2	FACETS	0.755	0.651	0.867	0.755	0.651	0.867	SUBCLONAL	1	TRUE	1	0.311175916898459	2		439	511	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202911	16202911	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	66	526	0	ENST00000375759.3:c.619G>A	p.Glu207Lys	p.E207K	ENST00000375759	NM_015001.2	207	Gag/Aag	3/15	0.311175916898459	1	FACETS	0.882	0.769	1	0.882	0.769	1	CLONAL	1	TRUE	0	0.311175916898459	1		526	406	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134270	2134270	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	45	683	0	ENST00000219476.3:c.4048del	p.Glu1350ArgfsTer33	p.E1350Rfs*33	ENST00000219476	NM_000548.3	1349	gcG/gc	34/42	0.311175916898459	1	FACETS	0.708	0.597	0.83	0.708	0.597	0.83	SUBCLONAL	1	TRUE	0	0.311175916898459	1		683	345	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652106	36652107	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	69	628	0	ENST00000244741.5:c.229dup	p.Tyr77LeufsTer12	p.Y77Lfs*12	ENST00000244741	NM_000389.4	76	-/T	2/3	0.311175916898459	1	FACETS	0.898	0.785	1	0.898	0.785	1	CLONAL	1	TRUE	0	0.311175916898459	1		628	417	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577546	64577549	+	protein_altering_variant	In_Frame_Del	DEL	CGGG	CGGG	T	novel	NA	P-0061976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	51	497	0	ENST00000312049.6:c.33_36delinsA	p.Phe11_Pro12delinsLeu	p.F11_P12delinsL	ENST00000312049	NM_130799.2	11	ttCCCG/ttA	2/10	0.311175916898459	1	FACETS	0.941	0.806	1	0.941	0.806	1	CLONAL	1	TRUE	0	0.311175916898459	1		497	294	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0061977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	118	231	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.298660214073178	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.3	1		231	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0061977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	177	1951	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.771	0.712	0.833	1	0.99	1	SUBCLONAL	2	TRUE	1	0.3	2		1952	765	SUCCESS
APC	324	MSKCC	GRCh37	5	112175419	112175419	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0061977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	89	517	0	ENST00000257430.4:c.4128T>A	p.Tyr1376Ter	p.Y1376*	ENST00000257430	NM_000038.5	1376	taT/taA	16/16	1	2	FACETS	0.913	0.81	1	0.913	0.81	1	CLONAL	1	TRUE	1	0.3	2		517	650	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371942	55371942	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	62	692	0	ENST00000297316.4:c.632C>T	p.Ala211Val	p.A211V	ENST00000297316	NM_022454.3	211	gCg/gTg	2/2	1	2	FACETS	0.53	0.457	0.61	0.53	0.457	0.61	SUBCLONAL	1	TRUE	1	0.3	2		692	780	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037475	12037475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs724159946	NA	P-0061977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	150	526	0	ENST00000396373.4:c.1106G>A	p.Arg369Gln	p.R369Q	ENST00000396373	NM_001987.4	369	cGg/cAg	6/8	0.168017259389957	4	FACETS	1	0.985	1	0.69	0.63	0.753	INDETERMINATE	1	TRUE	2	0.3	4		526	942	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563267	21563267	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1365471980	NA	P-0061977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	71	745	0	ENST00000382592.4:c.652G>A	p.Gly218Arg	p.G218R	ENST00000382592	NM_014572.2	218	Gga/Aga	4/8	0.193995151992963	3	FACETS	0.515	0.448	0.588	0.172	0.149	0.196	SUBCLONAL	1	TRUE	0	0.3	3		745	1057	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0061978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	496	372	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.861172593187752	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.861172593187752	2		372	562	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258036	123258036	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	189	313	0	ENST00000358487.5:c.1645A>G	p.Asn549Asp	p.N549D	ENST00000358487	NM_000141.4	549	Aat/Gat	12/18	0.861172593187752	2	FACETS	1	0.956	1	0.514	0.481	0.547	CLONAL	1	TRUE	0	0.861172593187752	2		313	427	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0061978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	340	370	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.861172593187752	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.861172593187752	2		370	394	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907692	111907692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775080943	NA	P-0061978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	444	402	0	ENST00000393256.3:c.466G>A	p.Gly156Arg	p.G156R	ENST00000393256	NM_006538.4	156	Gga/Aga	3/4	0.861172593187752	2	FACETS	0.986	0.963	1	0.986	0.963	1	CLONAL	2	TRUE	0	0.861172593187752	2		402	523	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976488	25976488	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	375	307	0	ENST00000435504.4:c.1057C>T	p.Gln353Ter	p.Q353*	ENST00000435504		353	Cag/Tag	11/13	0.861172593187752	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.861172593187752	2		307	434	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0061978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	343	234	0	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	0.861172593187752	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.861172593187752	2		234	383	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342400	70342400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	204	432	0	ENST00000374080.3:c.1291C>T	p.Arg431Trp	p.R431W	ENST00000374080		431	Cgg/Tgg	9/45	1	2	FACETS	0.874	0.817	0.932	0.874	0.817	0.932	CLONAL	1	TRUE	1	0.861172593187752	2		432	542	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829029	72829030	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	342	558	0	ENST00000268489.5:c.7551dup	p.Gln2518SerfsTer16	p.Q2518Sfs*16	ENST00000268489	NM_006885.3	2517	-/T	9/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.861172593187752	2		558	687	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550473	29550473	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199474774	NA	P-0061978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	141	310	0	ENST00000356175.3:c.1733T>C	p.Leu578Pro	p.L578P	ENST00000356175	NM_000267.3	578	cTt/cCt	16/57	1	2	FACETS	0.917	0.847	0.989	0.917	0.847	0.989	CLONAL	1	TRUE	1	0.861172593187752	2		310	357	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657356	29657356	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	216	391	0	ENST00000356175.3:c.5589T>G	p.Phe1863Leu	p.F1863L	ENST00000356175	NM_000267.3	1863	ttT/ttG	38/57	1	2	FACETS	0.954	0.895	1	0.954	0.895	1	CLONAL	1	TRUE	1	0.861172593187752	2		391	526	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220144	36220173	+	inframe_deletion	In_Frame_Del	DEL	AACGACGGCTCCCTCAAGAATGTGCATGCT	AACGACGGCTCCCTCAAGAATGTGCATGCT	-	novel	NA	P-0061978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	287	525	0	ENST00000222270.7:c.4864_4893del	p.Asn1622_Ala1631del	p.N1622_A1631del	ENST00000222270	NM_014727.1	1622	AACGACGGCTCCCTCAAGAATGTGCATGCT/-	22/37	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.861172593187752	2		525	665	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391067	89391067	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	266	420	0	ENST00000336596.2:c.1133C>G	p.Pro378Arg	p.P378R	ENST00000336596	NM_005233.5	378	cCa/cGa	5/17	1	2	FACETS	0.976	0.922	1	0.976	0.922	1	CLONAL	1	TRUE	1	0.861172593187752	2		420	633	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0061979-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	105	441	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.56	2		441	363	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	101	326	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.472940198537826	2		326	416	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0061980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	69	219	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.472940198537826	2		219	290	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462171	120462171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1296823228	NA	P-0061980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	218	581	0	ENST00000256646.2:c.5545G>A	p.Glu1849Lys	p.E1849K	ENST00000256646	NM_024408.3	1849	Gaa/Aaa	31/34	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.472940198537826	2		581	757	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31381390	31381390	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	110	278	0	ENST00000328111.2:c.1115C>T	p.Ser372Leu	p.S372L	ENST00000328111	NM_006892.3	372	tCa/tTa	10/23	1	2	FACETS	0.992	0.896	1	0.992	0.896	1	CLONAL	1	TRUE	1	0.472940198537826	2		278	469	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090482	37090482	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	157	372	0	ENST00000231790.2:c.2077G>C	p.Glu693Gln	p.E693Q	ENST00000231790	NM_000249.3	693	Gag/Cag	18/19	0.472940198537826	3	FACETS	0.986	0.903	1	0.493	0.451	0.536	CLONAL	1	TRUE	1	0.472940198537826	3		372	833	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652353	48652353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1340713003	NA	P-0061980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	194	659	0	ENST00000376670.3:c.1024G>A	p.Gly342Ser	p.G342S	ENST00000376670	NM_002049.3	342	Ggt/Agt	6/6	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.472940198537826	2		659	790	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786887	135786887	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554817388	NA	P-0061980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	153	404	0	ENST00000298552.3:c.982C>T	p.Gln328Ter	p.Q328*	ENST00000298552	NM_001162426.1	328	Cag/Tag	10/23	0.472940198537826	1	FACETS	0.952	0.876	1	0.952	0.876	1	CLONAL	1	TRUE	0	0.472940198537826	1		404	519	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981084	201981084	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0061980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	153	434	0	ENST00000359651.3:c.164-1G>C		p.X55_splice	ENST00000359651		55			1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.472940198537826	2		434	470	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941221	36941221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754120929	NA	P-0061980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	39	546	0	ENST00000361632.4:c.118G>A	p.Asp40Asn	p.D40N	ENST00000361632		40	Gat/Aat	3/16	1	2	FACETS	0.235	0.194	0.281	0.235	0.194	0.281	SUBCLONAL	1	TRUE	1	0.472940198537826	2		546	703	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104668	209104668	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	144	481	0	ENST00000345146.2:c.910G>C	p.Glu304Gln	p.E304Q	ENST00000345146	NM_005896.2	304	Gaa/Caa	8/10	0.217435940672896	1	FACETS	0.728	0.666	0.792	0.728	0.666	0.792	INDETERMINATE	1	TRUE	0	0.472940198537826	1		481	639	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467057	25467057	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	122	626	0	ENST00000264709.3:c.1818G>C	p.Gln606His	p.Q606H	ENST00000264709	NM_175629.2	606	caG/caC	15/23	0.217435940672896	1	FACETS	0.596	0.54	0.655	0.596	0.54	0.655	INDETERMINATE	1	TRUE	0	0.472940198537826	1		626	661	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057709	27057709	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	209	597	0	ENST00000324856.7:c.1417C>T	p.Gln473Ter	p.Q473*	ENST00000324856	NM_006015.4	473	Cag/Tag	3/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.472940198537826	2		597	859	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462162	120462162	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	211	557	0	ENST00000256646.2:c.5554G>C	p.Glu1852Gln	p.E1852Q	ENST00000256646	NM_024408.3	1852	Gag/Cag	31/34	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.472940198537826	2		557	746	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478785	56478785	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	134	392	0	ENST00000267101.3:c.241C>G	p.Arg81Gly	p.R81G	ENST00000267101	NM_001982.3	81	Cga/Gga	3/28	1	2	FACETS	0.898	0.818	0.981	0.898	0.818	0.981	CLONAL	1	TRUE	1	0.472940198537826	2		392	631	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467104	99467104	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0061980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	137	401	0	ENST00000268035.6:c.2486-1G>C		p.X829_splice	ENST00000268035	NM_000875.3	829			1	2	FACETS	0.975	0.891	1	0.975	0.891	1	CLONAL	1	TRUE	1	0.472940198537826	2		401	594	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139648	202139648	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	180	415	0	ENST00000358485.4:c.809C>A	p.Ser270Tyr	p.S270Y	ENST00000358485	NM_001080125.1	270	tCt/tAt	6/9	0.217435940672896	1	FACETS	0.842	0.779	0.907	0.842	0.779	0.907	INDETERMINATE	1	TRUE	0	0.472940198537826	1		415	690	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510086	187510086	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	140	525	0	ENST00000441802.2:c.13427C>A	p.Ser4476Tyr	p.S4476Y	ENST00000441802	NM_005245.3	4476	tCt/tAt	27/27	1	2	FACETS	0.878	0.802	0.958	0.878	0.802	0.958	CLONAL	1	TRUE	1	0.472940198537826	2		525	674	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141567217	141567217	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	173	537	0	ENST00000220592.5:c.997G>C	p.Glu333Gln	p.E333Q	ENST00000220592	NM_012154.3	333	Gag/Cag	8/19	1	2	FACETS	0.953	0.878	1	0.953	0.878	1	CLONAL	1	TRUE	1	0.472940198537826	2		537	768	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212850	27212850	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	182	478	0	ENST00000380036.4:c.2832C>A	p.Phe944Leu	p.F944L	ENST00000380036	NM_000459.3	944	ttC/ttA	17/23	0.472940198537826	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.472940198537826	1		478	562	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341204	70341204	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	198	632	0	ENST00000374080.3:c.763C>A	p.Leu255Met	p.L255M	ENST00000374080		255	Ctg/Atg	6/45	1	2	FACETS	0.917	0.85	0.987	0.917	0.85	0.987	CLONAL	1	TRUE	1	0.472940198537826	2		632	913	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121151	11121155	+	missense_variant	Missense_Mutation	ONP	GAGAG	GAGAG	AAGAT	novel	NA	P-0061980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	158	510	0	ENST00000358026.2:c.2218_2222delinsAAGAT	p.Glu740_Arg741delinsLysIle	p.E740_R741delinsKI	ENST00000358026	NM_001128849.1	740	GAGAGa/AAGATa	15/36	1	2	FACETS	0.975	0.896	1	0.975	0.896	1	CLONAL	1	TRUE	1	0.472940198537826	2		510	685	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0061981-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	100	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.251838684202715	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	1	0.25137124581072	3		426	410	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980418	201980419	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061981-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	82	613	0	ENST00000359651.3:c.155dup	p.Thr54TyrfsTer38	p.T54Yfs*38	ENST00000359651		52	gag/gAag	1/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.25137124581072	2		613	494	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0061981-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	217	574	1	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	0.25137124581072	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	3	TRUE	0	0.25137124581072	3		575	631	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395101	139395101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777423973	NA	P-0061981-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	95	650	4	ENST00000277541.6:c.5837G>A	p.Arg1946His	p.R1946H	ENST00000277541	NM_017617.3	1946	cGc/cAc	31/34	0.251838684202715	3	FACETS	0.915	0.818	1	0.915	0.818	1	CLONAL	2	TRUE	1	0.25137124581072	3		654	465	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593607	55593610	+	protein_altering_variant	In_Frame_Del	DEL	AGGT	AGGT	G	novel	NA	P-0061982-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	100	404	0	ENST00000288135.5:c.1673_1676delinsG	p.Lys558_Val559delinsSer	p.K558_V559delinsS	ENST00000288135	NM_000222.2	558	aAGGTt/aGt	11/21	1	2	FACETS	0.886	0.792	0.985	0.886	0.792	0.985	CLONAL	1	TRUE	1	0.336026730904134	2		404	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0061983-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	124	694	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	1	2	FACETS	0.993	0.901	1	1	0.989	1	CLONAL	2	TRUE	1	0.19	2		694	657	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909634	76909634	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061983-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	30	163	0	ENST00000373344.5:c.4271A>G	p.Lys1424Arg	p.K1424R	ENST00000373344	NM_000489.3	1424	aAa/aGa	14/35	1	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.19	1		163	191	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981167	201981168	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061983-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	51	578	0	ENST00000359651.3:c.248dup	p.Asn83LysfsTer9	p.N83Kfs*9	ENST00000359651		82	-/A	2/8	1	2	FACETS	0.765	0.649	0.893	0.765	0.649	0.893	SUBCLONAL	1	TRUE	1	0.19	2		578	702	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416459	49416459	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061983-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	40	507	0	ENST00000301067.7:c.16252G>C	p.Glu5418Gln	p.E5418Q	ENST00000301067	NM_003482.3	5418	Gaa/Caa	51/54	1	2	FACETS	0.564	0.467	0.672	0.564	0.467	0.672	SUBCLONAL	1	TRUE	1	0.19	2		507	747	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346912	70346912	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760933452	NA	P-0061983-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	21	223	0	ENST00000374080.3:c.2779G>A	p.Val927Met	p.V927M	ENST00000374080		927	Gtg/Atg	20/45	1	1	FACETS	0.617	0.475	0.783	0.617	0.475	0.783	SUBCLONAL	1	TRUE	0	0.19	1		223	324	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927689	131927689	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061983-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	15	274	0	ENST00000265335.6:c.1756G>C	p.Glu586Gln	p.E586Q	ENST00000265335		586	Gaa/Caa	11/25	1	2	FACETS	0.528	0.386	0.7	0.528	0.386	0.7	SUBCLONAL	1	TRUE	1	0.19	2		274	299	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206578	108206578	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	58	376	0	ENST00000278616.4:c.8158G>T	p.Asp2720Tyr	p.D2720Y	ENST00000278616	NM_000051.3	2720	Gat/Tat	56/63	0.228371266548901	1	FACETS	0.975	0.839	1	0.975	0.839	1	CLONAL	1	TRUE	0	0.21	1		376	507	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240285	41240285	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	80	448	0	ENST00000379561.5:c.65C>G	p.Ser22Trp	p.S22W	ENST00000379561	NM_002015.3	22	tCg/tGg	1/3	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.21	2		448	751	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31238074	31238075	+	missense_variant	Missense_Mutation	DNP	CT	CT	AC	novel	NA	P-0061984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	10	29	0	ENST00000376228.5:c.807_808delinsGT	p.Ala270Ser	p.A270S	ENST00000376228	NM_002117.5	269	gcAGct/gcGTct	4/8	1	2	FACETS	0.821	0.568	1	1	0.865	1	CLONAL	2	TRUE	1	0.21	2		29	58	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981543	201981544	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0061984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	145	514	0	ENST00000359651.3:c.460dup	p.Leu154ProfsTer7	p.L154Pfs*7	ENST00000359651		153	gcc/gCcc	3/8	0.190203995378794	3	FACETS	0.914	0.834	0.997	0.914	0.834	0.997	CLONAL	2	TRUE	1	0.21	3		514	835	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106319	27106319	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	87	621	0	ENST00000324856.7:c.5931del	p.Ala1978ProfsTer37	p.A1978Pfs*37	ENST00000324856	NM_006015.4	1977	cTt/ct	20/20	1	2	FACETS	0.922	0.815	1	0.922	0.815	1	CLONAL	1	TRUE	1	0.21	2		621	899	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40880886	40880886	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	74	432	0	ENST00000428826.2:c.74G>T	p.Arg25Leu	p.R25L	ENST00000428826		25	cGa/cTa	3/21	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.21	2		432	647	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197472	26197472	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1214166794	NA	P-0061984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	104	637	0	ENST00000356476.2:c.7C>T	p.Arg3Cys	p.R3C	ENST00000356476		3	Cgt/Tgt	1/1	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.21	2		637	975	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44920573	44920574	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0061984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	36	245	0	ENST00000377967.4:c.1335_1336dup	p.Ser446PhefsTer25	p.S446Ffs*25	ENST00000377967	NM_021140.2	445	act/acTTt	14/29	1	2	FACETS	0.797	0.656	0.956	0.797	0.656	0.956	CLONAL	1	TRUE	1	0.21	2		245	430	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0061994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	55	473	0				ENST00000310581	NM_198253.2	-/1132			0.447125885449476	1	FACETS	0.868	0.757	0.985	0.868	0.757	0.985	CLONAL	1	TRUE	0	0.538253000757366	1		473	172	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	167	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.533128006707459	3	FACETS	0.977	0.909	1	0.977	0.909	1	CLONAL	2	TRUE	1	0.538253000757366	3		298	403	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546784	9546784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1252319558	NA	P-0061994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	105	585	0	ENST00000353224.5:c.1238C>T	p.Pro413Leu	p.P413L	ENST00000353224	NM_177990.2	413	cCg/cTg	5/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.538253000757366	2		585	344	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633489	69633489	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1409151454	NA	P-0061994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	21	500	0	ENST00000334134.2:c.213C>A	p.Ser71Arg	p.S71R	ENST00000334134	NM_005247.2	71	agC/agA	1/3	1	2	FACETS	0.328	0.253	0.415	0.328	0.253	0.415	SUBCLONAL	1	TRUE	1	0.538253000757366	2		500	238	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921547	178921549	+	missense_variant	Missense_Mutation	TNP	CGT	CGT	TTC	novel	NA	P-0061994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	51	303	0	ENST00000263967.3:c.1029_1031delinsTTC	p.Val344Ser	p.V344S	ENST00000263967	NM_006218.2	343	taCGTg/taTTCg	5/21	1	2	FACETS	0.707	0.606	0.816	0.707	0.606	0.816	SUBCLONAL	1	TRUE	1	0.538253000757366	2		303	268	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1685058	1685058	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061995-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	93	416	0	ENST00000378625.1:c.1567G>T	p.Ala523Ser	p.A523S	ENST00000378625	NM_001198994.1	523	Gca/Tca	13/14	0.250632181908706	5	FACETS	1	0.967	1			1	INDETERMINATE	1	FALSE	NA	0.441472163736828	5		416	573	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800942	243800942	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061995-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	74	300	0	ENST00000263826.5:c.532A>T	p.Ile178Phe	p.I178F	ENST00000263826	NM_005465.4	178	Att/Ttt	5/13	0.291794321909395	5	FACETS	1	0.926	1	0.706	0.626	0.791	CLONAL	2	FALSE	2	0.441472163736828	5		300	263	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982331	201982332	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0061996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	114	631	0	ENST00000359651.3:c.715dup	p.Asp239GlyfsTer62	p.D239Gfs*62	ENST00000359651		237	aag/aaGg	6/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.361522535216945	2		631	574	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258036	123258036	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	56	313	0	ENST00000358487.5:c.1645A>G	p.Asn549Asp	p.N549D	ENST00000358487	NM_000141.4	549	Aat/Gat	12/18	1	2	FACETS	0.865	0.745	0.996	0.865	0.745	0.996	CLONAL	1	TRUE	1	0.361522535216945	2		313	358	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410605	32410605	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0061996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	94	457	0	ENST00000332351.3:c.1553G>C	p.Ter518SerextTer22	p.*518Sext*22	ENST00000332351	NM_024426.4	518	tGa/tCa	10/10	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.361522535216945	2		457	520	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196935	108196935	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	90	361	1	ENST00000278616.4:c.6958G>A	p.Asp2320Asn	p.D2320N	ENST00000278616	NM_000051.3	2320	Gat/Aat	47/63	1	2	FACETS	0.954	0.849	1	0.954	0.849	1	CLONAL	1	TRUE	1	0.361522535216945	2		362	522	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15976751	15976751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	47	331	0	ENST00000268712.3:c.3803C>T	p.Pro1268Leu	p.P1268L	ENST00000268712	NM_006311.3	1268	cCg/cTg	28/46	0.361522535216945	1	FACETS	0.696	0.59	0.811	0.696	0.59	0.811	SUBCLONAL	1	TRUE	0	0.361522535216945	1		331	306	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246443	10246443	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	69	490	0	ENST00000340748.4:c.4694T>G	p.Leu1565Arg	p.L1565R	ENST00000340748		1565	cTc/cGc	38/40	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.361522535216945	2		490	352	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273219	18273219	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	96	622	0	ENST00000222254.8:c.1012G>A	p.Glu338Lys	p.E338K	ENST00000222254	NM_005027.3	338	Gag/Aag	9/16	1	2	FACETS	0.959	0.856	1	0.959	0.856	1	CLONAL	1	TRUE	1	0.361522535216945	2		622	554	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62305435	62305435	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	105	548	0	ENST00000360203.5:c.908C>G	p.Ser303Cys	p.S303C	ENST00000360203	NM_001283009.1	303	tCc/tGc	10/35	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.361522535216945	2		548	432	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712614	52712614	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0061996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	74	281	0	ENST00000394830.3:c.139-1G>C		p.X47_splice	ENST00000394830	NM_018313.4	47			0.361522535216945	1	FACETS	0.958	0.845	1	0.958	0.845	1	CLONAL	1	TRUE	0	0.361522535216945	1		281	350	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71050185	71050185	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	112	399	0	ENST00000318789.4:c.1000G>A	p.Asp334Asn	p.D334N	ENST00000318789	NM_032682.5	334	Gac/Aac	13/21	0.361522535216945	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.361522535216945	1		399	460	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916957	178916959	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0061996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	77	310	0	ENST00000263967.3:c.344_346del	p.Arg115_Glu116delinsGln	p.R115_E116delinsQ	ENST00000263967	NM_006218.2	115	cGAGaa/caa	2/21	1	2	FACETS	0.932	0.821	1	0.932	0.821	1	CLONAL	1	TRUE	1	0.361522535216945	2		310	457	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217163	66217163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	92	410	0	ENST00000273854.3:c.2452G>A	p.Asp818Asn	p.D818N	ENST00000273854	NM_004439.5	818	Gac/Aac	14/18	1	2	FACETS	0.901	0.802	1	0.901	0.802	1	CLONAL	1	TRUE	1	0.361522535216945	2		410	565	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288219	33288219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202099332	NA	P-0061996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	91	566	1	ENST00000374542.5:c.1189C>T	p.Arg397Trp	p.R397W	ENST00000374542	NM_001141970.1	397	Cgg/Tgg	4/8	1	2	FACETS	0.925	0.824	1	0.925	0.824	1	CLONAL	1	TRUE	1	0.361522535216945	2		567	544	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289545	33289545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1436067809	NA	P-0061996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	70	498	0	ENST00000374542.5:c.158C>T	p.Ser53Leu	p.S53L	ENST00000374542	NM_001141970.1	53	tCg/tTg	2/8	1	2	FACETS	0.988	0.866	1	0.988	0.866	1	CLONAL	1	TRUE	1	0.361522535216945	2		498	392	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138800	37138800	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	85	650	0	ENST00000373509.5:c.233G>A	p.Gly78Glu	p.G78E	ENST00000373509	NM_002648.3	78	gGa/gAa	3/6	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.361522535216945	2		650	356	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509254	106509254	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	85	545	0	ENST00000359195.3:c.1248C>A	p.Phe416Leu	p.F416L	ENST00000359195	NM_002649.2	416	ttC/ttA	2/11	1	2	FACETS	0.886	0.785	0.993	0.886	0.785	0.993	CLONAL	1	TRUE	1	0.361522535216945	2		545	531	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0061998-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	12	335	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	1	2	FACETS	0.145	0.101	0.199	0.145	0.101	0.199	SUBCLONAL	1	TRUE	1	0.334024183877059	2		335	497	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266709	198266709	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061999-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	102	392	0	ENST00000335508.6:c.2223G>C	p.Lys741Asn	p.K741N	ENST00000335508	NM_012433.2	741	aaG/aaC	15/25	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.389287722373753	2		392	503	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427058	49427059	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061999-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	125	624	0	ENST00000301067.7:c.11429dup	p.Leu3810PhefsTer202	p.L3810Ffs*202	ENST00000301067	NM_003482.3	3810	ttg/ttTg	39/54	1	2	FACETS	0.924	0.838	1	0.924	0.838	1	CLONAL	1	TRUE	1	0.389287722373753	2		624	695	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672225	30672225	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061999-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	182	800	0	ENST00000376406.3:c.4735C>T	p.Gln1579Ter	p.Q1579*	ENST00000376406	NM_014641.2	1579	Cag/Tag	10/15	1	2	FACETS	0.891	0.821	0.963	0.891	0.821	0.963	CLONAL	1	TRUE	1	0.389287722373753	2		800	1050	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389407	8389407	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061999-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	71	284	0	ENST00000356435.5:c.4211G>A	p.Gly1404Glu	p.G1404E	ENST00000356435		1404	gGg/gAg	26/35	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.389287722373753	2		284	357	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	58	326	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.45575810402882	2		326	252	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447282	187447284	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1350754735	NA	P-0062000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	40	607	0	ENST00000232014.4:c.909_911del	p.Glu304del	p.E304del	ENST00000232014	NM_001130845.1	303	gaAGAg/gag	5/10	0.391744430807102	3	FACETS	0.346	0.287	0.412	0.173	0.143	0.206	SUBCLONAL	1	TRUE	1	0.45575810402882	3		607	623	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098615	47098625	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGCAGAAAG	GGGGCAGAAAG	-	novel	NA	P-0062000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	107	680	0	ENST00000409792.3:c.6649_6659del	p.Leu2217SerfsTer25	p.L2217Sfs*25	ENST00000409792	NM_014159.6	2217	CTTTCTGCCCCt/t	15/21	0.45575810402882	1	FACETS	0.867	0.784	0.955	0.867	0.784	0.955	CLONAL	1	TRUE	0	0.45575810402882	1		680	418	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439852	52439852	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0062000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	141	516	0	ENST00000460680.1:c.860C>G	p.Ser287Ter	p.S287*	ENST00000460680	NM_004656.3	287	tCa/tGa	10/17	0.45575810402882	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.45575810402882	1		516	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0062001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	191	828	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.418961102604777	2	FACETS	0.814	0.76	0.869	0.814	0.76	0.869	CLONAL	2	TRUE	0	0.491845306164703	2		828	477	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875645	35875645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201449880	NA	P-0062001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	49	375	0	ENST00000303115.3:c.832G>A	p.Asp278Asn	p.D278N	ENST00000303115	NM_002185.3	278	Gat/Aat	7/8	0.145606335384225	1	FACETS	0.33	0.28	0.386	0.33	0.28	0.386	INDETERMINATE	1	TRUE	0	0.491845306164703	1		375	455	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457269	89457269	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	57	357	0	ENST00000336596.2:c.1750G>A	p.Gly584Ser	p.G584S	ENST00000336596	NM_005233.5	584	Ggc/Agc	9/17	0.491845306164703	1	FACETS	0.519	0.447	0.596	0.519	0.447	0.596	SUBCLONAL	1	TRUE	0	0.491845306164703	1		357	337	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431662	6431662	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	78	289	0	ENST00000356142.4:c.215A>G	p.Tyr72Cys	p.Y72C	ENST00000356142	NM_018890.3	72	tAt/tGt	3/7	0.186293850795383	4	FACETS	0.883	0.777	0.996	0.441	0.388	0.498	INDETERMINATE	1	TRUE	2	0.491845306164703	4		289	536	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242482	55242506	+	protein_altering_variant	In_Frame_Del	DEL	CATCTCCGAAAGCCAACAAGGAAAT	CATCTCCGAAAGCCAACAAGGAAAT	G	novel	NA	P-0062001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	90	403	0	ENST00000275493.2:c.2252_2276delinsG	p.Thr751_Ile759delinsSer	p.T751_I759delinsS	ENST00000275493	NM_005228.3	751	aCATCTCCGAAAGCCAACAAGGAAATc/aGc	19/28	0.346498285844305	1	FACETS	0.695	0.621	0.773	0.695	0.621	0.773	SUBCLONAL	1	TRUE	0	0.491845306164703	1		403	397	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	62	326	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.968	0.844	1	0.968	0.844	1	CLONAL	1	TRUE	1	0.470967662582675	2		326	272	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332699	153332699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780061054	NA	P-0062011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	131	440	0	ENST00000281708.4:c.257C>T	p.Ser86Leu	p.S86L	ENST00000281708	NM_033632.3	86	tCg/tTg	2/12	0.470967662582675	1	FACETS	0.982	0.899	1	0.982	0.899	1	CLONAL	1	TRUE	0	0.470967662582675	1		440	433	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645693	12645693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397516827	NA	P-0062011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	133	347	0	ENST00000251849.4:c.776C>T	p.Ser259Phe	p.S259F	ENST00000251849	NM_002880.3	259	tCc/tTc	7/17	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.470967662582675	2		347	461	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553761	106553761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	134	366	0	ENST00000369096.4:c.1726G>A	p.Glu576Lys	p.E576K	ENST00000369096	NM_001198.3	576	Gaa/Aaa	5/7	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.470967662582675	2		366	543	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956220	55956220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190050670	NA	P-0062011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	111	558	0	ENST00000263923.4:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000263923	NM_002253.2	1032	cGa/cAa	23/30	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.470967662582675	2		558	438	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	84	142	1	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	0.470967662582675	1	FACETS	0.819	0.73	0.913	0.819	0.73	0.913	CLONAL	1	TRUE	0	0.470967662582675	1		143	333	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375964	8375964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144763077	NA	P-0062011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	105	321	0	ENST00000356435.5:c.4633G>A	p.Asp1545Asn	p.D1545N	ENST00000356435		1545	Gat/Aat	28/35	0.470967662582675	1	FACETS	0.977	0.884	1	0.977	0.884	1	CLONAL	1	TRUE	0	0.470967662582675	1		321	349	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553249	106553249	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1415765117	NA	P-0062011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	129	493	0	ENST00000369096.4:c.1214C>T	p.Ser405Leu	p.S405L	ENST00000369096	NM_001198.3	405	tCg/tTg	5/7	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.470967662582675	2		493	545	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509625	106509625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	114	466	0	ENST00000359195.3:c.1619G>A	p.Gly540Glu	p.G540E	ENST00000359195	NM_002649.2	540	gGg/gAg	2/11	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.470967662582675	2		466	483	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512350	149512350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754790326	NA	P-0062011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	125	411	0	ENST00000261799.4:c.1090G>A	p.Glu364Lys	p.E364K	ENST00000261799	NM_002609.3	364	Gaa/Aaa	7/23	1	2	FACETS	0.983	0.894	1	0.983	0.894	1	CLONAL	1	TRUE	1	0.470967662582675	2		411	540	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241948	39241948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	98	225	0	ENST00000402219.2:c.1898C>T	p.Ser633Phe	p.S633F	ENST00000402219	NM_005633.3	633	tCc/tTc	11/23	1	2	FACETS	0.939	0.843	1	0.939	0.843	1	CLONAL	1	TRUE	1	0.470967662582675	2		225	443	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501563	149501563	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	128	340	0	ENST00000261799.4:c.2224G>A	p.Asp742Asn	p.D742N	ENST00000261799	NM_002609.3	742	Gac/Aac	16/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.470967662582675	2		340	452	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856039	45856039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372960848	NA	P-0062011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	115	341	0	ENST00000391945.4:c.1867G>A	p.Val623Ile	p.V623I	ENST00000391945	NM_000400.3	623	Gtc/Atc	20/23	0.266185438877788	1	FACETS	0.948	0.861	1	0.948	0.861	1	INDETERMINATE	1	TRUE	0	0.470967662582675	1		341	394	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239421	123239421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764959117	NA	P-0062011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	64	424	0	ENST00000358487.5:c.2416G>A	p.Glu806Lys	p.E806K	ENST00000358487	NM_000141.4	806	Gaa/Aaa	18/18	0.266185438877788	1	FACETS	0.427	0.37	0.488	0.427	0.37	0.488	INDETERMINATE	1	TRUE	0	0.470967662582675	1		424	487	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963978	2963978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	112	463	0	ENST00000396946.4:c.1829C>T	p.Ser610Phe	p.S610F	ENST00000396946	NM_032415.4	610	tCc/tTc	15/25	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.470967662582675	2		463	466	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68999973	68999973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	195	312	0	ENST00000288368.4:c.2042C>T	p.Pro681Leu	p.P681L	ENST00000288368	NM_024870.2	681	cCa/cTa	19/40	0.470967662582675	3	FACETS	0.917	0.855	0.98	0.917	0.855	0.98	CLONAL	2	TRUE	1	0.470967662582675	3		312	558	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0062011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	125	334	0	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.470967662582675	2		334	491	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805094	43805094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	122	413	0	ENST00000372470.3:c.544C>T	p.Pro182Ser	p.P182S	ENST00000372470	NM_005373.2	182	Ccc/Tcc	4/12	0.470967662582675	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.470967662582675	1		413	372	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041143	29041143	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	136	333	0	ENST00000282397.4:c.285C>A	p.Asn95Lys	p.N95K	ENST00000282397	NM_002019.4	95	aaC/aaA	3/30	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.470967662582675	2		333	566	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519022	103519022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201666781	NA	P-0062011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	100	304	0	ENST00000355739.4:c.2360C>T	p.Pro787Leu	p.P787L	ENST00000355739	NM_000123.3	787	cCc/cTc	11/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.470967662582675	2		304	375	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654712	29654712	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	117	386	0	ENST00000356175.3:c.5401C>T	p.Gln1801Ter	p.Q1801*	ENST00000356175	NM_000267.3	1801	Cag/Tag	37/57	1	2	FACETS	0.986	0.893	1	0.986	0.893	1	CLONAL	1	TRUE	1	0.470967662582675	2		386	504	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758786	41758786	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140047155	NA	P-0062011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	73	391	0	ENST00000301178.4:c.1840C>T	p.Pro614Ser	p.P614S	ENST00000301178	NM_021913.4	614	Cca/Tca	16/20	0.266185438877788	1	FACETS	0.56	0.492	0.633	0.56	0.492	0.633	INDETERMINATE	1	TRUE	0	0.470967662582675	1		391	423	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560881	9560881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	137	443	0	ENST00000353224.5:c.901G>A	p.Ala301Thr	p.A301T	ENST00000353224	NM_177990.2	301	Gca/Aca	4/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.470967662582675	2		443	505	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394081	31394081	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	91	236	0	ENST00000328111.2:c.2368C>T	p.Pro790Ser	p.P790S	ENST00000328111	NM_006892.3	790	Cct/Tct	22/23	1	2	FACETS	0.933	0.834	1	0.933	0.834	1	CLONAL	1	TRUE	1	0.470967662582675	2		236	414	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076922	41076922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	99	281	0	ENST00000373198.4:c.1498G>A	p.Glu500Lys	p.E500K	ENST00000373198	NM_133170.3	500	Gag/Aag	9/32	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.470967662582675	2		281	385	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455563	189455563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	108	269	0	ENST00000264731.3:c.97G>A	p.Glu33Lys	p.E33K	ENST00000264731	NM_003722.4	33	Gaa/Aaa	2/14	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.470967662582675	2		269	450	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149452973	149452973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	111	405	0	ENST00000286301.3:c.973G>A	p.Val325Met	p.V325M	ENST00000286301	NM_005211.3	325	Gtg/Atg	7/22	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.470967662582675	2		405	466	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460581	149460582	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0062011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	97	422	0	ENST00000286301.3:c.55_56delinsAA	p.Gly19Lys	p.G19K	ENST00000286301	NM_005211.3	19	GGa/AAa	3/22	1	2	FACETS	0.926	0.83	1	0.926	0.83	1	CLONAL	1	TRUE	1	0.470967662582675	2		422	445	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120311	94120311	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	146	360	0	ENST00000369303.4:c.740G>A	p.Arg247Lys	p.R247K	ENST00000369303	NM_004440.3	247	aGg/aAg	3/17	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.470967662582675	2		360	522	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197313	27197313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	85	264	0	ENST00000380036.4:c.1625G>A	p.Gly542Glu	p.G542E	ENST00000380036	NM_000459.3	542	gGa/gAa	12/23	0.470967662582675	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.470967662582675	1		264	267	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966611	36966611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs984035588	NA	P-0062012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	308	478	0	ENST00000358127.4:c.715C>T	p.Arg239Cys	p.R239C	ENST00000358127	NM_001280556.1	239	Cgc/Tgc	6/10	0.752727673480382	6	FACETS	1	0.958	1	0.407	0.384	0.43	CLONAL	2	TRUE	1	0.752727673480382	6		478	1008	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594204	55594204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	69	374	0	ENST00000288135.5:c.1907C>T	p.Ala636Val	p.A636V	ENST00000288135	NM_000222.2	636	gCc/gTc	13/21	0.72064559614421	4	FACETS	0.607	0.53	0.691	0.304	0.265	0.346	SUBCLONAL	1	TRUE	2	0.752727673480382	4		374	529	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932358	36932358	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	156	639	0	ENST00000361632.4:c.2111del	p.Lys704ArgfsTer98	p.K704Rfs*98	ENST00000361632		704	aAg/ag	16/16	0.566343514180974	5	FACETS	0.843	0.771	0.918			1	CLONAL	1	TRUE	NA	0.752727673480382	5		639	1047	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46512295	46512295	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	132	444	0	ENST00000262741.5:c.944G>A	p.Trp315Ter	p.W315*	ENST00000262741	NM_003629.3	315	tGg/tAg	8/10	0.754070513589717	2	FACETS	0.835	0.765	0.907	0.418	0.382	0.454	CLONAL	1	TRUE	0	0.752727673480382	2		444	420	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252137	226252137	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	66	174	0	ENST00000366813.1:c.85A>T	p.Ser29Cys	p.S29C	ENST00000366813		29	Agt/Tgt	1/3	0.754070513589717	4	FACETS	0.778	0.678	0.885	0.259	0.226	0.295	SUBCLONAL	1	TRUE	1	0.752727673480382	4		174	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578414	7578427	+	frameshift_variant	Frame_Shift_Del	DEL	AACCTCCGTCATGT	AACCTCCGTCATGT	-	novel	NA	P-0062012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	458	577	0	ENST00000269305.4:c.503_516del	p.His168ArgfsTer8	p.H168Rfs*8	ENST00000269305	NM_001126112.2	168	cACATGACGGAGGTT/c	5/11	0.754070513589717	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.752727673480382	2		577	577	SUCCESS
APC	324	MSKCC	GRCh37	5	112151221	112151263	+	frameshift_variant	Frame_Shift_Del	DEL	AGCCAGTGTTTTGAGTTCTAGTAGCACACACTCTGCACCTCGA	AGCCAGTGTTTTGAGTTCTAGTAGCACACACTCTGCACCTCGA	-	novel	NA	P-0062012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	90	356	0	ENST00000257430.4:c.866_908del	p.Ala289GlyfsTer2	p.A289Gfs*2	ENST00000257430	NM_000038.5	288	acAGCCAGTGTTTTGAGTTCTAGTAGCACACACTCTGCACCTCGA/ac	9/16	0.754070513589717	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.752727673480382	1		356	140	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0062013-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	95	309	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.282213160010735	3	FACETS	1	0.968	1	0.614	0.548	0.685	CLONAL	1	TRUE	1	0.3157225545969	3		309	567	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26978211	26978211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1448365337	NA	P-0062013-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	57	270	1	ENST00000381527.3:c.1388G>A	p.Arg463Gln	p.R463Q	ENST00000381527	NM_001260.1	463	cGg/cAg	13/13	0.3157225545969	5	FACETS	1	0.944	1	0.399	0.343	0.461	CLONAL	1	TRUE	2	0.3157225545969	5		271	444	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117878	70117888	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCAGGCGGC	GCGCAGGCGGC	-	novel	NA	P-0062013-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	314	552	0	ENST00000245479.2:c.353_363del	p.Ala118GlufsTer130	p.A118Efs*130	ENST00000245479	NM_000346.3	116	GCGCAGGCGGCg/g	1/3	0.3157225545969	5	FACETS	0.984	0.938	1	0.984	0.938	1	CLONAL	5	TRUE	0	0.3157225545969	5		552	596	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635569	47635569	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062013-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	173	295	0	ENST00000233146.2:c.241A>G	p.Ser81Gly	p.S81G	ENST00000233146	NM_000251.2	81	Agt/Ggt	2/16	0.3157225545969	4	FACETS	1	0.95	1	1	0.95	1	CLONAL	3	TRUE	1	0.3157225545969	4		295	468	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125352	47125352	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062013-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	80	530	0	ENST00000409792.3:c.5918C>T	p.Pro1973Leu	p.P1973L	ENST00000409792	NM_014159.6	1973	cCt/cTt	12/21	0.3157225545969	4	FACETS	1	0.888	1	0.336	0.296	0.38	CLONAL	1	TRUE	1	0.3157225545969	4		530	661	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0062013-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	190	701	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.3157225545969	4	FACETS	0.987	0.919	1	0.987	0.919	1	CLONAL	3	TRUE	1	0.3157225545969	4		701	535	SUCCESS
APC	324	MSKCC	GRCh37	5	112175755	112175756	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0062013-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	159	523	0	ENST00000257430.4:c.4466dup	p.Leu1489PhefsTer25	p.L1489Ffs*25	ENST00000257430	NM_000038.5	1488	-/T	16/16	0.282213160010735	3	FACETS	0.947	0.871	1	0.947	0.871	1	CLONAL	2	TRUE	1	0.3157225545969	3		523	616	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845101	128845101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201246258	NA	P-0062013-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	68	463	0	ENST00000249373.3:c.595C>T	p.Arg199Trp	p.R199W	ENST00000249373	NM_005631.4	199	Cgg/Tgg	3/12	0.309508799576455	4	FACETS	0.895	0.779	1	0.448	0.389	0.511	CLONAL	1	TRUE	2	0.3157225545969	4		463	633	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0062015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	74	636	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.929	0.813	1	0.929	0.813	1	CLONAL	1	TRUE	1	0.24	2		636	664	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0062015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	68	450	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	0.824	0.716	0.94	0.824	0.716	0.94	CLONAL	1	TRUE	1	0.24	2		450	688	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30061039	30061039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754093587	NA	P-0062015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	61	332	0	ENST00000338641.4:c.871C>T	p.Arg291Cys	p.R291C	ENST00000338641	NM_000268.3	291	Cgt/Tgt	9/16	0.0878768317519047	3	FACETS	0.99	0.854	1	0.495	0.427	0.569	INDETERMINATE	1	TRUE	1	0.24	3		332	575	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612992	228612992	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1410959088	NA	P-0062015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	128	690	1	ENST00000366696.1:c.35C>T	p.Thr12Met	p.T12M	ENST00000366696	NM_003493.2	12	aCg/aTg	1/1	0.281623105927318	3	FACETS	1	0.975	1	0.612	0.554	0.674	CLONAL	1	TRUE	1	0.24	3		691	976	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007643	45007653	+	frameshift_variant	Frame_Shift_Del	DEL	CTCACGTCATC	CTCACGTCATC	-	novel	NA	P-0062015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	38	482	0	ENST00000558401.1:c.91_101del	p.His33GlufsTer20	p.H33Efs*20	ENST00000558401	NM_004048.2	30	taCTCACGTCATCca/taca	2/4	1	2	FACETS	0.464	0.382	0.555	0.464	0.382	0.555	SUBCLONAL	1	TRUE	1	0.24	2		482	683	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832400	72832400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	85	528	0	ENST00000268489.5:c.4181C>T	p.Ser1394Leu	p.S1394L	ENST00000268489	NM_006885.3	1394	tCa/tTa	9/10	1	2	FACETS	0.899	0.794	1	0.899	0.794	1	CLONAL	1	TRUE	1	0.24	2		528	788	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806125	1806125	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	81	531	0	ENST00000260795.2:c.1144G>A	p.Gly382Ser	p.G382S	ENST00000260795		382	Ggc/Agc	8/17	1	2	FACETS	0.852	0.75	0.962	0.852	0.75	0.962	CLONAL	1	TRUE	1	0.24	2		531	792	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0062016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	141	486	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.289982167405015	2	FACETS	0.97	0.889	1	0.97	0.889	1	CLONAL	2	TRUE	0	0.28	2		486	519	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0062016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	52	410	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.301188247336745	3	FACETS	0.903	0.77	1	0.451	0.385	0.525	CLONAL	1	TRUE	1	0.28	3		410	469	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880957	134880957	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770406411	NA	P-0062016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	67	380	0	ENST00000398015.3:c.1520G>A	p.Arg507His	p.R507H	ENST00000398015	NM_004441.4	507	cGt/cAt	7/16	0.289982167405015	2	FACETS	0.979	0.852	1	0.489	0.426	0.558	CLONAL	1	TRUE	0	0.28	2		380	489	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295774	212295774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754127388	NA	P-0062016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	51	341	0	ENST00000342788.4:c.2539C>T	p.Arg847Cys	p.R847C	ENST00000342788	NM_005235.2	847	Cgt/Tgt	21/28	0.260703779650223	3	FACETS	0.95	0.809	1	0.475	0.404	0.553	CLONAL	1	TRUE	1	0.28	3		341	437	SUCCESS
APC	324	MSKCC	GRCh37	5	112174454	112174455	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0062016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	119	409	0	ENST00000257430.4:c.3164dup	p.Ile1056AsnfsTer4	p.I1056Nfs*4	ENST00000257430	NM_000038.5	1055	ata/aTta	16/16	0.301188247336745	3	FACETS	0.981	0.89	1	0.981	0.89	1	CLONAL	2	TRUE	1	0.28	3		409	494	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447410	12447410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766913119	NA	P-0062017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	242	480	0	ENST00000287820.6:c.649G>A	p.Glu217Lys	p.E217K	ENST00000287820	NM_015869.4	217	Gag/Aag	5/7	0.907802282457119	6	FACETS	1	0.961	1	0.261	0.243	0.28	CLONAL	1	TRUE	2	0.907802282457119	6		480	1438	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942733	48942733	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	231	276	0	ENST00000267163.4:c.1121del	p.Pro374GlnfsTer6	p.P374Qfs*6	ENST00000267163	NM_000321.2	374	Cca/ca	11/27	0.907802282457119	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.907802282457119	2		276	246	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46543236	46543236	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	90	337	0	ENST00000262741.5:c.265G>T	p.Val89Phe	p.V89F	ENST00000262741	NM_003629.3	89	Gtc/Ttc	3/10	1	2	FACETS	0.762	0.677	0.853	0.762	0.677	0.853	SUBCLONAL	1	TRUE	1	0.373082341158366	2		337	633	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49280978	49280978	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	82	343	0	ENST00000282018.3:c.25C>A	p.Gln9Lys	p.Q9K	ENST00000282018	NM_020377.2	9	Caa/Aaa	1/1	0.373082341158366	1	FACETS	0.939	0.833	1	0.939	0.833	1	CLONAL	1	TRUE	0	0.373082341158366	1		343	381	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519063	103519063	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	128	382	0	ENST00000355739.4:c.2401G>C	p.Asp801His	p.D801H	ENST00000355739	NM_000123.3	801	Gat/Cat	11/15	0.373082341158366	3	FACETS	0.928	0.841	1	0.309	0.28	0.341	CLONAL	1	TRUE	0	0.373082341158366	3		382	877	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579390	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGAAGGGACAGAAGATGACAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCC	novel	NA	P-0062019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	98	560	0	ENST00000269305.4:c.246_297dup	p.Gln100GlyfsTer66	p.Q100Gfs*66	ENST00000269305	NM_001126112.2	99	-/GGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTGTCATCTTCTGTCCCTTCC	4/11	0.373082341158366	1	FACETS	0.43	0.382	0.48	0.43	0.382	0.48	SUBCLONAL	1	TRUE	0	0.373082341158366	1		560	995	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778804	76778804	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	31	378	0	ENST00000373344.5:c.6775G>T	p.Asp2259Tyr	p.D2259Y	ENST00000373344	NM_000489.3	2259	Gac/Tac	31/35	0.143672617179503	0	FACETS	0.329	0.266	0.399			1	INDETERMINATE	1	TRUE	0	0.373082341158366	0		378	317	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0062020-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	120	365	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.3	3	FACETS	0.806	0.73	0.885	0.806	0.73	0.885	CLONAL	2	FALSE	1	0.3	3		365	571	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0062020-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	68	486	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	1	2	FACETS	0.657	0.571	0.75	0.657	0.571	0.75	SUBCLONAL	1	FALSE	1	0.3	2		486	690	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0062025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	57	423	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.199079380873183	4	FACETS	0.875	0.755	1	0.875	0.755	1	CLONAL	2	TRUE	2	0.230264188600395	4		423	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0062025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	130	1951	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.230264188600395	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.230264188600395	2		1952	464	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0062025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	47	188	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.230264188600395	2		188	372	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276765	15276765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs550464740	NA	P-0062025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	132	639	0	ENST00000263388.2:c.5500C>T	p.Arg1834Trp	p.R1834W	ENST00000263388	NM_000435.2	1834	Cgg/Tgg	30/33	0.201064218413534	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.230264188600395	3		639	559	SUCCESS
APC	324	MSKCC	GRCh37	5	112175772	112175772	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	40	551	0	ENST00000257430.4:c.4483del	p.Ser1495ValfsTer12	p.S1495Vfs*12	ENST00000257430	NM_000038.5	1494	gAa/ga	16/16	1	2	FACETS	0.712	0.591	0.846	0.712	0.591	0.846	SUBCLONAL	1	TRUE	1	0.230264188600395	2		551	488	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399227	139399227	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	47	498	0	ENST00000277541.6:c.4916C>T	p.Ala1639Val	p.A1639V	ENST00000277541	NM_017617.3	1639	gCc/gTc	26/34	0.230264188600395	7	FACETS	1	0.864	1	0.257	0.216	0.302	CLONAL	1	TRUE	3	0.230264188600395	7		498	626	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245380	153245380	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	85	594	0	ENST00000281708.4:c.1811A>C	p.Lys604Thr	p.K604T	ENST00000281708	NM_033632.3	604	aAa/aCa	11/12	0.201064218413534	3	FACETS	0.964	0.857	1	0.964	0.857	1	CLONAL	2	TRUE	1	0.230264188600395	3		594	427	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109702	115109702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1218875641	NA	P-0062025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	115	548	0	ENST00000257566.3:c.2176C>T	p.Arg726Trp	p.R726W	ENST00000257566	NM_016569.3	726	Cgg/Tgg	8/8	0.199079380873183	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	2	0.230264188600395	4		548	561	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133763	2133763	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	47	604	0	ENST00000219476.3:c.3951G>T	p.Leu1317Phe	p.L1317F	ENST00000219476	NM_000548.3	1317	ttG/ttT	33/42	0.201064218413534	3	FACETS	0.905	0.764	1	0.453	0.382	0.531	CLONAL	1	TRUE	1	0.230264188600395	3		604	503	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793122	33793122	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	80	521	0	ENST00000498907.2:c.199T>A	p.Tyr67Asn	p.Y67N	ENST00000498907	NM_004364.3	67	Tac/Aac	1/1	0.201064218413534	3	FACETS	0.983	0.871	1	0.983	0.871	1	CLONAL	2	TRUE	1	0.230264188600395	3		521	394	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106162500	106162500	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	43	270	0	ENST00000380013.4:c.3414A>T	p.Gln1138His	p.Q1138H	ENST00000380013	NM_001127208.2	1138	caA/caT	4/11	0.201064218413534	3	FACETS	1	0.948	1	0.672	0.565	0.789	CLONAL	1	TRUE	1	0.230264188600395	3		270	310	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259065	153259065	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	49	418	0	ENST00000281708.4:c.750del	p.Leu250PhefsTer4	p.L250Ffs*4	ENST00000281708	NM_033632.3	250	ttG/tt	5/12	0.201064218413534	3	FACETS	1	0.951	1	0.654	0.555	0.761	CLONAL	1	TRUE	1	0.230264188600395	3		418	363	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952151	76952151	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062025-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	46	305	0	ENST00000373344.5:c.284A>G	p.Glu95Gly	p.E95G	ENST00000373344	NM_000489.3	95	gAa/gGa	5/35	0.152307243982503	4	FACETS	1	0.953	1	0.683	0.577	0.799	CLONAL	1	TRUE	2	0.230264188600395	4		305	360	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0062026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	23	401	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.54	0.421	0.678	0.54	0.421	0.678	SUBCLONAL	1	TRUE	1	0.27727830297054	2		401	307	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207162	1207162	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs137853076	NA	P-0062026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	65	473	0	ENST00000326873.7:c.250A>T	p.Lys84Ter	p.K84*	ENST00000326873	NM_000455.4	84	Aag/Tag	1/10	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.27727830297054	2		473	429	SUCCESS
APC	324	MSKCC	GRCh37	5	112102985	112102985	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs774416950	NA	P-0062026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	47	403	0	ENST00000257430.4:c.320C>G	p.Ser107Cys	p.S107C	ENST00000257430	NM_000038.5	107	tCt/tGt	4/16	0.27727830297054	1	FACETS	0.636	0.537	0.745	0.636	0.537	0.745	SUBCLONAL	1	TRUE	0	0.27727830297054	1		403	459	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376220	225376220	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs773074706	NA	P-0062027-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	31	459	0	ENST00000264414.4:c.734T>C	p.Ile245Thr	p.I245T	ENST00000264414	NM_003590.4	245	aTa/aCa	6/16	1	2	FACETS	0.846	0.689	1	0.846	0.689	1	CLONAL	1	FALSE	1	0.324249810091006	2		459	226	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0062030-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	70	537	1	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.20534641304819	1	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	0	0.20534641304819	1		538	590	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380276	+	missense_variant	Missense_Mutation	DNP	TT	TT	CC	novel	NA	P-0062030-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	76	460	0	ENST00000311936.3:c.182_183delinsGG	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAA/cGG	3/5	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.20534641304819	2		460	698	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	247	527	0	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.924	0.869	0.98	0.924	0.869	0.98	CLONAL	1	TRUE	1	0.796853425198292	2		527	671	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	190	434	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.796853425198292	2		434	474	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	199	132	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.789	0.735	0.845	0.789	0.735	0.845	SUBCLONAL	1	TRUE	1	0.796853425198292	2		132	633	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422384	47422384	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	32	422	0	ENST00000377045.4:c.23del	p.Pro8LeufsTer26	p.P8Lfs*26	ENST00000377045	NM_001654.4	6	ggC/gg	2/16	1	2	FACETS	0.181	0.147	0.22	0.181	0.147	0.22	SUBCLONAL	1	TRUE	1	0.796853425198292	2		422	443	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	111	370	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.834	0.759	0.912	0.834	0.759	0.912	CLONAL	1	TRUE	1	0.796853425198292	2		370	334	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	85	516	1	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.321	0.284	0.361	0.321	0.284	0.361	SUBCLONAL	1	TRUE	1	0.796853425198292	2		517	664	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913476	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	155	331	0	ENST00000358487.5:c.1647T>G	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaG	12/18	1	2	FACETS	0.987	0.915	1	0.987	0.915	1	CLONAL	1	TRUE	1	0.796853425198292	2		331	394	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11177098	11177098	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	21	419	0	ENST00000361445.4:c.6979A>G	p.Met2327Val	p.M2327V	ENST00000361445	NM_004958.3	2327	Atg/Gtg	50/58	0.719354238529849	2	FACETS	0.102	0.078	0.13	0.051	0.039	0.065	SUBCLONAL	1	TRUE	0	0.796853425198292	2		419	517	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560514	65560514	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	425	447	0	ENST00000358664.4:c.83A>G	p.His28Arg	p.H28R	ENST00000358664	NM_002382.4	28	cAt/cGt	3/5	0.722317822854851	2	FACETS	0.879	0.85	0.906	0.879	0.85	0.906	CLONAL	2	TRUE	0	0.796853425198292	2		447	607	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103755	47103756	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	73	552	0	ENST00000409792.3:c.6190_6191del	p.Asp2064ProfsTer8	p.D2064Pfs*8	ENST00000409792	NM_014159.6	2064	GAc/c	14/21	1	2	FACETS	0.251	0.219	0.286	0.251	0.219	0.286	SUBCLONAL	1	TRUE	1	0.796853425198292	2		552	730	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	139	851	5	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.544	0.497	0.594	0.544	0.497	0.594	SUBCLONAL	1	TRUE	1	0.796853425198292	2		856	641	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902196	50902196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3218772	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	158	486	0	ENST00000440232.2:c.88C>T	p.Arg30Trp	p.R30W	ENST00000440232	NM_002691.3	30	Cgg/Tgg	2/27	1	2	FACETS	0.91	0.842	0.979	0.91	0.842	0.979	CLONAL	1	TRUE	1	0.796853425198292	2		486	436	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115780	8115780	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	37	489	1	ENST00000346208.3:c.1131del	p.Val378CysfsTer26	p.V378Cfs*26	ENST00000346208		376	Aaa/aa	6/6	1	2	FACETS	0.13	0.107	0.157	0.13	0.107	0.157	SUBCLONAL	1	TRUE	1	0.796853425198292	2		490	713	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622516	158622516	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906589	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	86	487	0	ENST00000263640.3:c.983G>A	p.Gly328Glu	p.G328E	ENST00000263640	NM_001105.4	328	gGg/gAg	8/11	1	2	FACETS	0.486	0.432	0.544	0.486	0.432	0.544	SUBCLONAL	1	TRUE	1	0.796853425198292	2		487	444	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732740	204732741	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	127	452	0	ENST00000302823.3:c.81dup	p.Leu28SerfsTer32	p.L28Sfs*32	ENST00000302823	NM_005214.4	25	-/T	1/4	1	2	FACETS	0.509	0.462	0.558	0.509	0.462	0.558	SUBCLONAL	1	TRUE	1	0.796853425198292	2		452	626	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807363	3807364	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	146	379	0	ENST00000262367.5:c.3623dup	p.Gln1209ThrfsTer25	p.Q1209Tfs*25	ENST00000262367	NM_004380.2	1208	cca/ccCa	19/31	1	2	FACETS	0.737	0.677	0.799	0.737	0.677	0.799	SUBCLONAL	1	TRUE	1	0.796853425198292	2		379	497	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262685	16262685	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564799201	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	35	497	0	ENST00000375759.3:c.9950C>T	p.Pro3317Leu	p.P3317L	ENST00000375759	NM_015001.2	3317	cCg/cTg	11/15	NA	2	FACETS	0.171	0.14	0.206			1	INDETERMINATE	1	TRUE	NA	0.796853425198292	2		497	514	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405954	157405954	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	130	543	0	ENST00000346085.5:c.2201del	p.Gly734AlafsTer11	p.G734Afs*11	ENST00000346085	NM_020732.3	732	ccG/cc	6/20	1	2	FACETS	0.536	0.487	0.586	0.536	0.487	0.586	SUBCLONAL	1	TRUE	1	0.796853425198292	2		543	609	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339110	65339111	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	203	548	3	ENST00000342505.4:c.425dup	p.Ile143AspfsTer9	p.I143Dfs*9	ENST00000342505	NM_002227.2	142	aag/aaAg	5/25	1	2	FACETS	0.754	0.702	0.807	0.754	0.702	0.807	SUBCLONAL	1	TRUE	1	0.796853425198292	2		551	676	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591135	67591135	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	168	409	0	ENST00000274335.5:c.1728del	p.Arg577GlufsTer5	p.R577Efs*5	ENST00000274335		576	acG/ac	12/15	1	2	FACETS	0.893	0.828	0.96	0.893	0.828	0.96	CLONAL	1	TRUE	1	0.796853425198292	2		409	472	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570293	87570293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202111708	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	145	346	0	ENST00000277120.3:c.2033C>T	p.Ala678Val	p.A678V	ENST00000277120		678	gCg/gTg	17/19	1	2	FACETS	0.66	0.606	0.717	0.66	0.606	0.717	SUBCLONAL	1	TRUE	1	0.796853425198292	2		346	551	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351031	89351031	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	34	458	0	ENST00000301030.4:c.1919del	p.Asn640ThrfsTer13	p.N640Tfs*13	ENST00000301030	NM_001256183.1	640	aAc/ac	9/13	1	2	FACETS	0.14	0.114	0.17	0.14	0.114	0.17	SUBCLONAL	1	TRUE	1	0.796853425198292	2		458	610	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1623951	1623951	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs374988827	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	25	337	0	ENST00000344749.5:c.548C>T	p.Ser183Leu	p.S183L	ENST00000344749	NM_001136139.2	183	tCg/tTg	8/19	1	2	FACETS	0.149	0.117	0.186	0.149	0.117	0.186	SUBCLONAL	1	TRUE	1	0.796853425198292	2		337	420	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	60	460	6	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.308	0.265	0.354	0.308	0.265	0.354	SUBCLONAL	1	TRUE	1	0.796853425198292	2		466	489	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056244	27056251	+	frameshift_variant	Frame_Shift_Del	DEL	GGACATGG	GGACATGG	-	novel	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	423	576	0	ENST00000324856.7:c.1241_1248del	p.Gly414ValfsTer206	p.G414Vfs*206	ENST00000324856	NM_006015.4	414	GGACATGGg/g	2/20	1	2	FACETS	0.891	0.862	0.918	1	0.997	1	CLONAL	2	TRUE	1	0.796853425198292	2		576	596	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150933382	150933382	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1220025296	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	37	571	4	ENST00000271640.5:c.2849del	p.Pro950GlnfsTer16	p.P950Qfs*16	ENST00000271640	NM_001145415.1	948	caC/ca	16/22	1	2	FACETS	0.174	0.143	0.209	0.174	0.143	0.209	SUBCLONAL	1	TRUE	1	0.796853425198292	2		575	533	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226580017	226580017	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	82	378	0	ENST00000366794.5:c.287-2A>G		p.X96_splice	ENST00000366794	NM_001618.3	96			0.730076709648511	3	FACETS	0.426	0.376	0.481	0.213	0.188	0.241	SUBCLONAL	1	TRUE	1	0.796853425198292	3		378	675	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692843	89692843	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	40	146	0	ENST00000371953.3:c.328del	p.Gln110AsnfsTer3	p.Q110Nfs*3	ENST00000371953	NM_000314.4	109	gaC/ga	5/9	1	2	FACETS	0.947	0.811	1	0.947	0.811	1	CLONAL	1	TRUE	1	0.796853425198292	2		146	106	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589770	69589770	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1454619366	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	219	866	0	ENST00000168712.1:c.83del	p.Gly28AlafsTer99	p.G28Afs*99	ENST00000168712	NM_002007.2	28	gGc/gc	1/3	1	2	FACETS	0.951	0.891	1	0.951	0.891	1	CLONAL	1	TRUE	1	0.796853425198292	2		866	578	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949103	71949104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	121	658	0	ENST00000298229.2:c.3573dup	p.Arg1192AlafsTer23	p.R1192Afs*23	ENST00000298229	NM_001567.3	1190	-/G	27/28	1	2	FACETS	0.512	0.464	0.563	0.512	0.464	0.563	SUBCLONAL	1	TRUE	1	0.796853425198292	2		658	593	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944878	31944878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141415515	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	74	308	0	ENST00000340398.3:c.223G>A	p.Ala75Thr	p.A75T	ENST00000340398	NM_001013699.2	75	Gcg/Acg	1/1	1	2	FACETS	0.506	0.446	0.57	0.506	0.446	0.57	SUBCLONAL	1	TRUE	1	0.796853425198292	2		308	367	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434431	49434431	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	205	607	0	ENST00000301067.7:c.7122C>G	p.Tyr2374Ter	p.Y2374*	ENST00000301067	NM_003482.3	2374	taC/taG	31/54	1	2	FACETS	0.976	0.914	1	0.976	0.914	1	CLONAL	1	TRUE	1	0.796853425198292	2		607	527	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420225	88420225	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	33	504	0	ENST00000360948.2:c.2461T>C	p.Tyr821His	p.Y821H	ENST00000360948	NM_001012338.2	821	Tac/Cac	19/19	1	2	FACETS	0.151	0.122	0.184	0.151	0.122	0.184	SUBCLONAL	1	TRUE	1	0.796853425198292	2		504	548	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831898	72831899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	196	564	0	ENST00000268489.5:c.4681_4682dup	p.Val1562Ter	p.V1562*	ENST00000268489	NM_006885.3	1561	cta/ctCTa	9/10	1	2	FACETS	0.819	0.762	0.876	0.819	0.762	0.876	CLONAL	1	TRUE	1	0.796853425198292	2		564	601	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982848	7982848	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	24	503	0	ENST00000319144.4:c.937A>G	p.Ile313Val	p.I313V	ENST00000319144	NM_001139.2	313	Att/Gtt	8/15	1	2	FACETS	0.138	0.107	0.173	0.138	0.107	0.173	SUBCLONAL	1	TRUE	1	0.796853425198292	2		503	437	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38792285	38792285	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	29	420	0	ENST00000348513.6:c.439A>G	p.Ser147Gly	p.S147G	ENST00000348513	NM_003079.4	147	Agt/Ggt	7/11	1	2	FACETS	0.16	0.128	0.197	0.16	0.128	0.197	SUBCLONAL	1	TRUE	1	0.796853425198292	2		420	454	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184402	7184402	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	205	473	0	ENST00000302850.5:c.899G>A	p.Gly300Asp	p.G300D	ENST00000302850	NM_000208.2	300	gGc/gAc	3/22	1	2	FACETS	0.878	0.82	0.937	0.878	0.82	0.937	CLONAL	1	TRUE	1	0.796853425198292	2		473	586	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225360629	225360629	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	25	365	0	ENST00000264414.4:c.1762C>T	p.Arg588Trp	p.R588W	ENST00000264414	NM_003590.4	588	Cgg/Tgg	13/16	1	2	FACETS	0.151	0.118	0.188	0.151	0.118	0.188	SUBCLONAL	1	TRUE	1	0.796853425198292	2		365	416	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400133	41400133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	170	445	0	ENST00000373198.4:c.626C>T	p.Ala209Val	p.A209V	ENST00000373198	NM_133170.3	209	gCc/gTc	5/32	1	2	FACETS	0.813	0.753	0.874	0.813	0.753	0.874	CLONAL	1	TRUE	1	0.796853425198292	2		445	525	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165694	47165694	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	102	562	0	ENST00000409792.3:c.432del	p.Phe144LeufsTer8	p.F144Lfs*8	ENST00000409792	NM_014159.6	144	ttT/tt	3/21	1	2	FACETS	0.452	0.405	0.501	0.452	0.405	0.501	SUBCLONAL	1	TRUE	1	0.796853425198292	2		562	567	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268334	142268334	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	17	251	0	ENST00000350721.4:c.3158T>G	p.Leu1053Arg	p.L1053R	ENST00000350721	NM_001184.3	1053	cTt/cGt	15/47	1	2	FACETS	0.168	0.125	0.219	0.168	0.125	0.219	SUBCLONAL	1	TRUE	1	0.796853425198292	2		251	254	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591148	67591149	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0062033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	158	389	0	ENST00000274335.5:c.1741_1742del	p.Leu581AspfsTer20	p.L581Dfs*20	ENST00000274335		581	TTg/g	12/15	1	2	FACETS	0.899	0.832	0.968	0.899	0.832	0.968	CLONAL	1	TRUE	1	0.796853425198292	2		389	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0062034-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	345	1055	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	0.509204192833475	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	3	TRUE	0	0.50535474683792	3		1055	570	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445273	29445273	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs113994091	NA	P-0062034-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	92	634	0	ENST00000389048.3:c.3452C>T	p.Thr1151Met	p.T1151M	ENST00000389048	NM_004304.4	1151	aCg/aTg	22/29	0.509204192833475	4	FACETS	0.989	0.881	1	0.247	0.22	0.276	CLONAL	1	TRUE	0	0.50535474683792	4		634	554	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0062035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	36	401	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.771	0.635	0.923	0.771	0.635	0.923	CLONAL	1	TRUE	1	0.26	2		401	359	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223063	1223097	+	frameshift_variant	Frame_Shift_Del	DEL	AGCATGACTGTGGTGCCGTACTTGGAGGACCTGCA	AGCATGACTGTGGTGCCGTACTTGGAGGACCTGCA	-	novel	NA	P-0062035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	81	603	0	ENST00000326873.7:c.1000_1034del	p.Ser334ArgfsTer14	p.S334Rfs*14	ENST00000326873	NM_000455.4	334	AGCATGACTGTGGTGCCGTACTTGGAGGACCTGCAc/c	8/10	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.26	2		603	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0062037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	529	828	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.553450686615521	3	FACETS	0.891	0.862	0.92	0.891	0.862	0.92	CLONAL	3	TRUE	0	0.602131556407185	3		828	855	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098973	178098973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	390	489	0	ENST00000397062.3:c.72G>C	p.Trp24Cys	p.W24C	ENST00000397062	NM_006164.4	24	tgG/tgC	2/5	0.525186147975102	3	FACETS	0.897	0.856	0.939	0.897	0.856	0.939	CLONAL	2	TRUE	1	0.602131556407185	3		489	939	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90971041	90971041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200297914	NA	P-0062037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	93	569	0	ENST00000265433.3:c.1036G>A	p.Val346Met	p.V346M	ENST00000265433	NM_002485.4	346	Gtg/Atg	9/16	0.602131556407185	3	FACETS	0.365	0.323	0.41	0.183	0.161	0.205	SUBCLONAL	1	TRUE	1	0.602131556407185	3		569	1101	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022423	12022423	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	161	1029	0	ENST00000396373.4:c.529G>T	p.Glu177Ter	p.E177*	ENST00000396373	NM_001987.4	177	Gaa/Taa	5/8	0.297847352680628	1	FACETS	0.451	0.414	0.49	0.451	0.414	0.49	INDETERMINATE	1	TRUE	0	0.602131556407185	1		1029	829	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971060	21971060	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	284	700	0	ENST00000304494.5:c.298del	p.Ala100ProfsTer46	p.A100Pfs*46	ENST00000304494	NM_000077.4	100	Gcc/cc	2/3	0.602131556407185	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.602131556407185	1		700	547	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953979	131953979	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	276	216	0	ENST00000265335.6:c.3382C>G	p.Leu1128Val	p.L1128V	ENST00000265335		1128	Ctt/Gtt	21/25	0.548205934124248	2	FACETS	0.87	0.827	0.913	0.87	0.827	0.913	CLONAL	2	TRUE	0	0.602131556407185	2		216	527	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023738	27023757	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGGCGGGGGAACTCCCCA	GCCGGCGGGGGAACTCCCCA	-	novel	NA	P-0062037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	173	762	0	ENST00000324856.7:c.847_866del	p.Gly283HisfsTer110	p.G283Hfs*110	ENST00000324856	NM_006015.4	282	GCCGGCGGGGGAACTCCCCAg/g	1/20	0.297847352680628	1	FACETS	0.84	0.78	0.901	0.84	0.78	0.901	INDETERMINATE	1	TRUE	0	0.602131556407185	1		762	478	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729730	162729730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	413	771	0	ENST00000367921.3:c.816G>A	p.Met272Ile	p.M272I	ENST00000367921	NM_006182.2	272	atG/atA	8/18	0.300808181726995	3	FACETS	0.851	0.812	0.89	0.851	0.812	0.89	INDETERMINATE	2	TRUE	1	0.602131556407185	3		771	1049	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737133	162737133	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	225	694	0	ENST00000367921.3:c.1277A>C	p.Gln426Pro	p.Q426P	ENST00000367921	NM_006182.2	426	cAg/cCg	11/18	0.300808181726995	3	FACETS	1	0.966	1	0.529	0.493	0.566	INDETERMINATE	1	TRUE	1	0.602131556407185	3		694	919	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998276	100998276	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	161	623	0	ENST00000325455.5:c.1526C>A	p.Pro509His	p.P509H	ENST00000325455	NM_001202474.3	509	cCc/cAc	1/8	0.548205934124248	2	FACETS	0.828	0.773	0.883	0.828	0.773	0.883	CLONAL	2	TRUE	0	0.602131556407185	2		623	323	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226300	2226300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	259	865	0	ENST00000326181.6:c.1915del	p.Leu639CysfsTer27	p.L639Cfs*27	ENST00000326181	NM_032271.2	638	aCc/ac	20/21	0.297847352680628	1	FACETS	0.855	0.805	0.906	0.855	0.805	0.906	INDETERMINATE	1	TRUE	0	0.602131556407185	1		865	703	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56402469	56402469	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	205	319	0	ENST00000348428.3:c.1511C>T	p.Ser504Phe	p.S504F	ENST00000348428	NM_006785.3	504	tCt/tTt	13/17	0.602131556407185	1	FACETS	0.969	0.908	1	0.969	0.908	1	CLONAL	1	TRUE	0	0.602131556407185	1		319	491	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425290	47425290	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178800275	NA	P-0062037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	303	784	0	ENST00000404338.3:c.3358C>T	p.Arg1120Trp	p.R1120W	ENST00000404338	NM_004491.4	1120	Cgg/Tgg	1/6	0.297847352680628	1	FACETS	0.893	0.845	0.941	0.893	0.845	0.941	INDETERMINATE	1	TRUE	0	0.602131556407185	1		784	788	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723442	52723442	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	230	574	0	ENST00000322088.6:c.1303G>T	p.Gly435Ter	p.G435*	ENST00000322088	NM_014225.5	435	Gga/Tga	11/15	0.297847352680628	1	FACETS	0.95	0.893	1	0.95	0.893	1	INDETERMINATE	1	TRUE	0	0.602131556407185	1		574	562	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155369	99155369	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	231	551	0	ENST00000074304.5:c.595G>T	p.Asp199Tyr	p.D199Y	ENST00000074304	NM_001134224.1	199	Gat/Tat	9/26	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.602131556407185	2		551	708	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543673	9543673	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0062037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	183	503	0	ENST00000353224.5:c.1483-2A>T		p.X495_splice	ENST00000353224	NM_177990.2	495			0.353566773391932	1	FACETS	0.74	0.687	0.794	0.74	0.687	0.794	INDETERMINATE	1	TRUE	0	0.602131556407185	1		503	574	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332904	153332914	+	frameshift_variant	Frame_Shift_Del	DEL	AGCCTCCAGTT	AGCCTCCAGTT	-	novel	NA	P-0062037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	278	611	0	ENST00000281708.4:c.42_52del	p.Thr15SerfsTer4	p.T15Sfs*4	ENST00000281708	NM_033632.3	14	cgAACTGGAGGCTct/cgct	2/12	0.602131556407185	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.602131556407185	1		611	611	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691022	NA	P-0062038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	535	520	0	ENST00000269305.4:c.1024del	p.Arg342GlufsTer3	p.R342Efs*3	ENST00000269305	NM_001126112.2	342	Cga/ga	10/11	0.726751130654789	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.726751130654789	2		520	720	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201089	108201089	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779865	NA	P-0062038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	473	483	0	ENST00000278616.4:c.7456C>T	p.Arg2486Ter	p.R2486*	ENST00000278616	NM_000051.3	2486	Cga/Tga	50/63	0.726751130654789	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.726751130654789	2		483	638	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246198	41246198	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	511	542	0	ENST00000357654.3:c.1350A>T	p.Lys450Asn	p.K450N	ENST00000357654	NM_007294.3	450	aaA/aaT	10/23	0.726751130654789	4	FACETS	0.965	0.926	1	0.965	0.926	1	CLONAL	2	TRUE	2	0.726751130654789	4		542	1258	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120498	70120499	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0062038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	1032	733	0	ENST00000245479.2:c.1503dup	p.Val502ArgfsTer76	p.V502Rfs*76	ENST00000245479	NM_000346.3	500	-/C	3/3	0.726751130654789	4	FACETS	0.982	0.959	1	0.982	0.959	1	CLONAL	3	TRUE	1	0.726751130654789	4		733	1665	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0062039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	70	442	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.598747667367577	2		442	228	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0062039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	613	235	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	0.598747667367577	3	FACETS	0.97	0.943	0.997	0.97	0.943	0.997	CLONAL	3	TRUE	0	0.598747667367577	3		235	914	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020768	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs926053251	NA	P-0062039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	28	684	0	ENST00000358127.4:c.77T>G	p.Val26Gly	p.V26G	ENST00000358127	NM_001280556.1	26	gTt/gGt	2/10	1	2	FACETS	0.127	0.101	0.157	0.127	0.101	0.157	SUBCLONAL	1	TRUE	1	0.598747667367577	2		684	735	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501195	NA	P-0062039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	191	789	0	ENST00000269305.4:c.313G>A	p.Gly105Ser	p.G105S	ENST00000269305	NM_001126112.2	105	Ggc/Agc	4/11	0.577998565346442	1	FACETS	0.863	0.805	0.922	0.863	0.805	0.922	CLONAL	1	TRUE	0	0.598747667367577	1		789	518	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647725	2647725	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	189	634	0	ENST00000342085.4:c.1628G>A	p.Trp543Ter	p.W543*	ENST00000342085	NM_002613.4	543	tGg/tAg	14/14	1	2	FACETS	0.832	0.771	0.895	0.832	0.771	0.895	CLONAL	1	TRUE	1	0.598747667367577	2		634	759	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692902	89692903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0062039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	137	436	0	ENST00000371953.3:c.387_388dup	p.Arg130HisfsTer5	p.R130Hfs*5	ENST00000371953	NM_000314.4	129	gga/ggACa	5/9	0.537809688189874	2	FACETS	0.82	0.761	0.879	0.82	0.761	0.879	CLONAL	2	TRUE	0	0.598747667367577	2		436	279	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913615	32913615	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	94	469	0	ENST00000380152.3:c.5123C>A	p.Ala1708Glu	p.A1708E	ENST00000380152		1708	gCa/gAa	11/27	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.598747667367577	2		469	297	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149344	61149344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs541714900	NA	P-0062039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	200	692	0	ENST00000295025.8:c.1534C>T	p.Pro512Ser	p.P512S	ENST00000295025	NM_002908.2	512	Cca/Tca	11/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.598747667367577	2		692	589	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861006	35861006	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200464578	NA	P-0062039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	262	613	0	ENST00000303115.3:c.135G>T	p.Gln45His	p.Q45H	ENST00000303115	NM_002185.3	45	caG/caT	2/8	0.598747667367577	3	FACETS	0.92	0.869	0.972	0.92	0.869	0.972	CLONAL	2	TRUE	1	0.598747667367577	3		613	618	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878944	151878944	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	69	644	0	ENST00000262189.6:c.6001G>C	p.Ala2001Pro	p.A2001P	ENST00000262189	NM_170606.2	2001	Gct/Cct	36/59	1	2	FACETS	0.433	0.379	0.491	0.433	0.379	0.491	SUBCLONAL	1	TRUE	1	0.796280467783058	2		644	400	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782329	NA	P-0062051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	31	379	0	ENST00000269305.4:c.746G>C	p.Arg249Thr	p.R249T	ENST00000269305	NM_001126112.2	249	aGg/aCg	7/11	1	2	FACETS	0.786	0.638	0.951	0.786	0.638	0.951	CLONAL	1	FALSE	1	0.3	2		379	263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0062053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	187	722	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.577636015785122	2	FACETS	0.984	0.928	1	0.984	0.928	1	CLONAL	2	TRUE	0	0.577636015785122	2		722	329	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037969	49037969	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	rs587778868	NA	P-0062053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	41	188	0	ENST00000267163.4:c.2209G>T	p.Glu737Ter	p.E737*	ENST00000267163	NM_000321.2	737	Gag/Tag	21/27	0.495182136771138	1	FACETS	0.834	0.712	0.962	0.834	0.712	0.962	CLONAL	1	TRUE	0	0.577636015785122	1		188	121	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931631	39931631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	58	335	0	ENST00000378444.4:c.2968C>A	p.Gln990Lys	p.Q990K	ENST00000378444	NM_001123385.1	990	Cag/Aag	4/15	NA	2	FACETS	0.596	0.515	0.683			1	INDETERMINATE	1	TRUE	NA	0.577636015785122	2		335	337	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584488	39584488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs375465653	NA	P-0062053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	118	256	0	ENST00000262039.4:c.1153C>T	p.Arg385Ter	p.R385*	ENST00000262039	NM_002647.2	385	Cga/Tga	10/25	0.531643598407995	2	FACETS	0.716	0.648	0.787	0.358	0.324	0.394	SUBCLONAL	1	TRUE	0	0.577636015785122	2		256	571	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785814	50785814	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	46	144	0	ENST00000398568.2:c.804C>G	p.Asp268Glu	p.D268E	ENST00000398568	NM_001042412.1	268	gaC/gaG	4/18	0.577636015785122	1	FACETS	0.871	0.752	0.996	0.871	0.752	0.996	CLONAL	1	TRUE	0	0.577636015785122	1		144	130	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272929	11272929	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	109	284	0	ENST00000361445.4:c.3322G>C	p.Asp1108His	p.D1108H	ENST00000361445	NM_004958.3	1108	Gat/Cat	22/58	1	2	FACETS	0.866	0.782	0.952	0.866	0.782	0.952	CLONAL	1	TRUE	1	0.577636015785122	2		284	436	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276846	123276846	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	146	300	0	ENST00000358487.5:c.1071G>T	p.Leu357Phe	p.L357F	ENST00000358487	NM_000141.4	357	ttG/ttT	8/18	0.197390754357037	6	FACETS	1	0.976	1	0.771	0.709	0.835	INDETERMINATE	2	TRUE	3	0.577636015785122	6		300	471	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537914	212537914	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	120	285	0	ENST00000342788.4:c.1691A>C	p.Asp564Ala	p.D564A	ENST00000342788	NM_005235.2	564	gAt/gCt	14/28	0.577636015785122	2	FACETS	1	0.92	1	0.505	0.46	0.552	CLONAL	1	TRUE	0	0.577636015785122	2		285	411	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662962	227662962	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	119	334	0	ENST00000305123.5:c.493C>A	p.Gln165Lys	p.Q165K	ENST00000305123	NM_005544.2	165	Caa/Aaa	1/2	0.108533588669633	6	FACETS	0.899	0.816	0.986			1	INDETERMINATE	2	TRUE	NA	0.577636015785122	6		334	494	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586397	189586397	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	29	304	0	ENST00000264731.3:c.1021G>C	p.Glu341Gln	p.E341Q	ENST00000264731	NM_003722.4	341	Gag/Cag	8/14	0.567996182169099	4	FACETS	0.28	0.224	0.345	0.07	0.056	0.087	SUBCLONAL	1	TRUE	0	0.577636015785122	4		304	565	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979561	55979561	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1212024668	NA	P-0062053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	113	245	0	ENST00000263923.4:c.886G>T	p.Gly296Cys	p.G296C	ENST00000263923	NM_002253.2	296	Ggt/Tgt	7/30	0.565672852212472	2	FACETS	1	0.974	1	0.596	0.543	0.651	CLONAL	1	TRUE	0	0.577636015785122	2		245	328	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142950015	142950015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1354348566	NA	P-0062053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	70	245	0	ENST00000262992.4:c.2695G>A	p.Ala899Thr	p.A899T	ENST00000262992	NM_001101669.1	899	Gct/Act	24/24	1	2	FACETS	0.943	0.832	1	0.943	0.832	1	CLONAL	1	TRUE	1	0.577636015785122	2		245	257	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523713	148523713	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	56	257	0	ENST00000320356.2:c.740T>A	p.Leu247His	p.L247H	ENST00000320356	NM_004456.4	247	cTc/cAc	8/20	0.337253244224253	1	FACETS	0.592	0.513	0.676	0.592	0.513	0.676	INDETERMINATE	1	TRUE	0	0.577636015785122	1		257	233	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411809	63411809	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	117	352	0	ENST00000330258.3:c.1358T>A	p.Leu453His	p.L453H	ENST00000330258	NM_152424.3	453	cTt/cAt	2/2	0.577636015785122	3	FACETS	1	0.921	1	0.509	0.461	0.559	CLONAL	1	TRUE	1	0.577636015785122	3		352	513	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421903	49421904	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	G	novel	NA	P-0062053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	94	352	0	ENST00000301067.7:c.14403_14404delinsC	p.Ala4802GlnfsTer6	p.A4802Qfs*6	ENST00000301067	NM_003482.3	4801	gtGGca/gtCca	46/54	0.496246283667044	4	FACETS	0.965	0.861	1			1	CLONAL	1	TRUE	NA	0.577636015785122	4		352	532	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610073	43610084	+	protein_altering_variant	In_Frame_Ins	INS	CTTCCGGAGGCC	CTTCCGGAGGCC	TCCATCTCCAAAAAGTCATCT	novel	NA	P-0062053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	88	446	0	ENST00000355710.3:c.2025_2036delinsTCCATCTCCAAAAAGTCATCT	p.Phe676_Pro679delinsProSerProLysSerHisLeu	p.F676_P679delinsPSPKSHL	ENST00000355710	NM_020975.4	675	acCTTCCGGAGGCCc/acTCCATCTCCAAAAAGTCATCTc	11/20	0.510736197430168	4	FACETS	0.805	0.714	0.902	0.403	0.357	0.451	CLONAL	1	TRUE	2	0.577636015785122	4		446	597	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0062057-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	68	345	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.2061434532938	3	FACETS	0.852	0.744	0.968	0.852	0.744	0.968	CLONAL	2	TRUE	1	0.2061434532938	3		345	427	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062057-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	76	373	1	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.2061434532938	2		374	514	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857531	68857531	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs876661120	NA	P-0062057-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	45	257	0	ENST00000261769.5:c.2164+2T>C		p.X722_splice	ENST00000261769	NM_004360.3	722			0.2061434532938	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.2061434532938	1		257	328	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948712	71948712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374001069	NA	P-0062057-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	42	559	0	ENST00000298229.2:c.3424C>T	p.Arg1142Cys	p.R1142C	ENST00000298229	NM_001567.3	1142	Cgc/Tgc	26/28	0.104351249693545	1	FACETS	0.662	0.552	0.784	0.662	0.552	0.784	INDETERMINATE	1	TRUE	0	0.2061434532938	1		559	552	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138645	55138669	+	frameshift_variant	Frame_Shift_Del	DEL	CGCTTCCTGATATTGAGTGGATGAT	CGCTTCCTGATATTGAGTGGATGAT	-	novel	NA	P-0062057-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	28	262	0	ENST00000257290.5:c.1322_1346del	p.Pro441HisfsTer40	p.P441Hfs*40	ENST00000257290	NM_006206.4	441	cCGCTTCCTGATATTGAGTGGATGATa/ca	9/23	0.2061434532938	1	FACETS	0.626	0.5	0.77	0.626	0.5	0.77	SUBCLONAL	1	TRUE	0	0.2061434532938	1		262	389	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510024	187510024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs183728932	NA	P-0062057-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	25	367	0	ENST00000441802.2:c.13489G>A	p.Asp4497Asn	p.D4497N	ENST00000441802	NM_005245.3	4497	Gat/Aat	27/27	0.2061434532938	1	FACETS	0.455	0.358	0.568	0.455	0.358	0.568	SUBCLONAL	1	TRUE	0	0.2061434532938	1		367	478	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627237	86627237	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0062057-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	37	326	0	ENST00000274376.6:c.612T>A	p.Tyr204Ter	p.Y204*	ENST00000274376	NM_002890.2	204	taT/taA	2/25	0.205925672866517	2	FACETS	0.767	0.632	0.918	0.384	0.316	0.459	CLONAL	1	TRUE	0	0.2061434532938	2		326	468	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0062066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	104	319	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.836	0.753	0.923	0.836	0.753	0.923	CLONAL	1	TRUE	1	0.550379118909254	2		319	452	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0062066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	252	372	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.53778510780482	4	FACETS	0.997	0.938	1	0.665	0.625	0.705	CLONAL	2	TRUE	1	0.550379118909254	4		372	712	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578179	7578179	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	260	511	0	ENST00000269305.4:c.670G>T	p.Glu224Ter	p.E224*	ENST00000269305	NM_001126112.2	224	Gag/Tag	6/11	0.490599085345713	2	FACETS	0.859	0.813	0.905	0.859	0.813	0.905	CLONAL	2	TRUE	0	0.550379118909254	2		511	550	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983276	15983276	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0062066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	176	402	0	ENST00000268712.3:c.3501+2T>G		p.X1167_splice	ENST00000268712	NM_006311.3	1167			0.490599085345713	2	FACETS	0.869	0.813	0.925	0.869	0.813	0.925	CLONAL	2	TRUE	0	0.550379118909254	2		402	368	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839963	27839963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	194	915	0	ENST00000328488.2:c.131C>T	p.Pro44Leu	p.P44L	ENST00000328488	NM_003533.2	44	cCc/cTc	1/1	1	2	FACETS	0.994	0.923	1	0.994	0.923	1	CLONAL	1	TRUE	1	0.550379118909254	2		915	709	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80646076	80646076	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	24	139	0	ENST00000286548.4:c.76G>C	p.Glu26Gln	p.E26Q	ENST00000286548	NM_002072.3	26	Gag/Cag	1/7	1	2	FACETS	0.89	0.713	1	0.89	0.713	1	CLONAL	1	TRUE	1	0.550379118909254	2		139	98	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0062067-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	138	824	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.447548491121083	6	FACETS	0.856	0.78	0.934	0.428	0.39	0.467	CLONAL	2	TRUE	2	0.447548491121083	6		824	683	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0062067-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	288	365	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.447548491121083	6	FACETS	1	0.976	1	1	0.994	1	CLONAL	5	TRUE	2	0.447548491121083	6		365	473	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176470	123176470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062067-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	35	415	0	ENST00000218089.9:c.437G>A	p.Arg146Gln	p.R146Q	ENST00000218089	NM_001042749.1	146	cGa/cAa	7/35	0.188675194948944	5	FACETS	1	0.862	1	0.351	0.289	0.42	INDETERMINATE	1	TRUE	2	0.447548491121083	5		415	248	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574002	7574006	+	frameshift_variant	Frame_Shift_Del	DEL	CGGAA	CGGAA	-	novel	NA	P-0062067-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	156	662	0	ENST00000269305.4:c.1021_1025del	p.Phe341ArgfsTer4	p.F341Rfs*4	ENST00000269305	NM_001126112.2	341	TTCCGa/a	10/11	0.454061636708002	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.447548491121083	2		662	310	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170011227	170011227	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062067-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	48	542	0	ENST00000295797.4:c.1348A>T	p.Arg450Trp	p.R450W	ENST00000295797	NM_002740.5	450	Agg/Tgg	14/18	0.248713980028108	5	FACETS	0.924	0.783	1	0.308	0.261	0.36	INDETERMINATE	1	TRUE	2	0.447548491121083	5		542	388	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981908	70981908	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062067-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	36	902	0	ENST00000276594.2:c.188C>A	p.Ala63Asp	p.A63D	ENST00000276594	NM_024504.3	63	gCc/gAc	2/8	0.454061636708002	1	FACETS	0.333	0.274	0.399	0.333	0.274	0.399	SUBCLONAL	1	TRUE	0	0.447548491121083	1		902	375	SUCCESS
APC	324	MSKCC	GRCh37	5	112175879	112175880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0062076-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	163	672	0	ENST00000257430.4:c.4592dup	p.Asn1531LysfsTer2	p.N1531Kfs*2	ENST00000257430	NM_000038.5	1530	gaa/gAaa	16/16	0.687529666024394	1	FACETS	0.923	0.862	0.985	0.923	0.862	0.985	CLONAL	1	TRUE	0	0.687529666024394	1		672	337	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508065	106508065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1326957848	NA	P-0062076-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	126	631	0	ENST00000359195.3:c.59G>A	p.Arg20His	p.R20H	ENST00000359195	NM_002649.2	20	cGc/cAc	2/11	0.686013339825414	3	FACETS	1	0.93	1	0.512	0.466	0.559	CLONAL	1	TRUE	1	0.687529666024394	3		631	481	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839697	27839697	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062076-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	171	752	0	ENST00000328488.2:c.397G>A	p.Gly133Arg	p.G133R	ENST00000328488	NM_003533.2	133	Ggg/Agg	1/1	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.687529666024394	2		752	456	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391636	139391638	+	missense_variant	Missense_Mutation	TNP	GTC	GTC	ATT	novel	NA	P-0062076-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	121	814	0	ENST00000277541.6:c.6553_6555delinsAAT	p.Asp2185Asn	p.D2185N	ENST00000277541	NM_017617.3	2185	GAC/AAT	34/34	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.687529666024394	2		814	345	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191492	10191492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397516444	NA	P-0062078-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	112	529	0	ENST00000256474.2:c.485G>A	p.Cys162Tyr	p.C162Y	ENST00000256474	NM_000551.3	162	tGc/tAc	3/3	0.436466947244871	1	FACETS	0.892	0.807	0.98	0.892	0.807	0.98	CLONAL	1	TRUE	0	0.436466947244871	1		529	450	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439162	52439162	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062078-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	114	662	0	ENST00000460680.1:c.1080del	p.Leu361Ter	p.L361*	ENST00000460680	NM_004656.3	360	ttT/tt	11/17	0.436466947244871	1	FACETS	0.898	0.813	0.985	0.898	0.813	0.985	CLONAL	1	TRUE	0	0.436466947244871	1		662	455	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851168	63851168	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062078-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	183	765	0	ENST00000279873.7:c.1946T>C	p.Leu649Pro	p.L649P	ENST00000279873	NM_032199.2	649	cTt/cCt	10/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.436466947244871	2		765	775	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156310	106156311	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	C	novel	NA	P-0062078-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	185	814	0	ENST00000380013.4:c.1211_1212delinsC	p.Leu404SerfsTer23	p.L404Sfs*23	ENST00000380013	NM_001127208.2	404	tTG/tC	3/11	1	2	FACETS	0.972	0.898	1	0.972	0.898	1	CLONAL	1	TRUE	1	0.436466947244871	2		814	872	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294235	11294235	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs746242022	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	152	524	0	ENST00000361445.4:c.2296del	p.Arg766AspfsTer11	p.R766Dfs*11	ENST00000361445	NM_004958.3	766	Cga/ga	14/58	1	2	FACETS	0.995	0.91	1	0.995	0.91	1	CLONAL	1	TRUE	1	0.338252829963078	2		524	903	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	181	645	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.338252829963078	2		646	1028	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106078	27106078	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	90	672	0	ENST00000324856.7:c.5693del	p.Pro1898HisfsTer25	p.P1898Hfs*25	ENST00000324856	NM_006015.4	1897	Ccc/cc	20/20	1	2	FACETS	0.509	0.45	0.572	0.509	0.45	0.572	SUBCLONAL	1	TRUE	1	0.338252829963078	2		672	1045	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932859	36932859	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	166	616	0	ENST00000361632.4:c.2012G>A	p.Gly671Asp	p.G671D	ENST00000361632		671	gGc/gAc	15/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.338252829963078	2		616	879	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120469123	120469123	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs746314617	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	156	420	0	ENST00000256646.2:c.4004C>G	p.Pro1335Arg	p.P1335R	ENST00000256646	NM_024408.3	1335	cCg/cGg	24/34	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.338252829963078	2		420	821	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193172983	193172983	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	114	393	0	ENST00000367435.3:c.1030+1G>A		p.X344_splice	ENST00000367435	NM_024529.4	344			1	2	FACETS	0.997	0.899	1	0.997	0.899	1	CLONAL	1	TRUE	1	0.338252829963078	2		393	676	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231487256	231487256	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	142	490	1	ENST00000295050.7:c.663del	p.Gly222AlafsTer7	p.G222Afs*7	ENST00000295050	NM_032018.5	219	tcA/tc	4/5	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.338252829963078	2		491	726	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692897	89692897	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	61	350	0	ENST00000371953.3:c.383del	p.Lys128ArgfsTer6	p.K128Rfs*6	ENST00000371953	NM_000314.4	127	ggA/gg	5/9	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.338252829963078	2		350	351	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	66	303	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.918	0.8	1	0.918	0.8	1	CLONAL	1	TRUE	1	0.338252829963078	2		304	425	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310879	123310879	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1164513666	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	178	574	1	ENST00000358487.5:c.549del	p.Asn184ThrfsTer9	p.N184Tfs*9	ENST00000358487	NM_000141.4	183	ggG/gg	5/18	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.338252829963078	2		575	1048	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577512	64577512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	146	608	0	ENST00000312049.6:c.70G>A	p.Ala24Thr	p.A24T	ENST00000312049	NM_130799.2	24	Gct/Act	2/10	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.338252829963078	2		608	801	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948208	71948208	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	81	638	0	ENST00000298229.2:c.2920G>C	p.Ala974Pro	p.A974P	ENST00000298229	NM_001567.3	974	Gcc/Ccc	26/28	1	2	FACETS	0.489	0.43	0.553	0.489	0.43	0.553	SUBCLONAL	1	TRUE	1	0.338252829963078	2		638	979	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865628	57865628	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	194	694	0	ENST00000228682.2:c.3109del	p.Leu1037TrpfsTer23	p.L1037Wfs*23	ENST00000228682	NM_005269.2	1035	aaC/aa	12/12	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.338252829963078	2		694	1012	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	65	567	2	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.381	0.329	0.438	0.381	0.329	0.438	SUBCLONAL	1	TRUE	1	0.338252829963078	2		569	1009	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437355	121437355	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	164	615	0	ENST00000257555.6:c.1693C>A	p.Leu565Ile	p.L565I	ENST00000257555		565	Ctc/Atc	9/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.338252829963078	2		615	865	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991334	41991334	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	26	458	0	ENST00000219905.7:c.2165T>C	p.Val722Ala	p.V722A	ENST00000219905	NM_001164273.1	722	gTg/gCg	5/24	1	2	FACETS	0.32	0.253	0.398	0.32	0.253	0.398	SUBCLONAL	1	TRUE	1	0.338252829963078	2		458	480	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	146	390	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.338252829963078	2		390	831	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007825	45007825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	155	399	2	ENST00000558401.1:c.276del	p.Thr93LeufsTer10	p.T93Lfs*10	ENST00000558401	NM_004048.2	91	aCc/ac	2/4	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.338252829963078	2		401	843	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799280	88799280	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	123	432	0	ENST00000360948.2:c.105T>A	p.Asn35Lys	p.N35K	ENST00000360948	NM_001012338.2	35	aaT/aaA	2/19	1	2	FACETS	0.98	0.887	1	0.98	0.887	1	CLONAL	1	TRUE	1	0.338252829963078	2		432	742	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	132	496	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.756	0.685	0.831	0.756	0.685	0.831	SUBCLONAL	1	TRUE	1	0.338252829963078	2		496	1032	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	157	308	0	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.338252829963078	2		308	921	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573009	7573009	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs876658982	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	57	522	0	ENST00000269305.4:c.1101-1G>A		p.X367_splice	ENST00000269305	NM_001126112.2	367			1	2	FACETS	0.397	0.339	0.46	0.397	0.339	0.46	SUBCLONAL	1	TRUE	1	0.338252829963078	2		522	849	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587781525	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	155	602	0	ENST00000269305.4:c.842A>G	p.Asp281Gly	p.D281G	ENST00000269305	NM_001126112.2	281	gAc/gGc	8/11	1	2	FACETS	0.885	0.81	0.965	0.885	0.81	0.965	CLONAL	1	TRUE	1	0.338252829963078	2		602	1035	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320963	30320963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371166327	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	76	379	1	ENST00000322652.5:c.1373G>A	p.Arg458His	p.R458H	ENST00000322652	NM_015355.2	458	cGc/cAc	12/16	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.338252829963078	2		380	437	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362218	40362218	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	102	522	0	ENST00000293328.3:c.1877G>A	p.Gly626Asp	p.G626D	ENST00000293328	NM_012448.3	626	gGc/gAc	15/19	1	2	FACETS	0.7	0.625	0.779	0.7	0.625	0.779	SUBCLONAL	1	TRUE	1	0.338252829963078	2		522	862	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	157	491	1	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.338252829963078	2		492	836	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120031	70120031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	73	272	0	ENST00000245479.2:c.1037del	p.Pro346ArgfsTer37	p.P346Rfs*37	ENST00000245479	NM_000346.3	345	Ccc/cc	3/3	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.338252829963078	2		272	380	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897434	78897434	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	208	756	0	ENST00000306801.3:c.2773del	p.Arg925GlyfsTer48	p.R925Gfs*48	ENST00000306801	NM_020761.2	923	ttC/tt	23/34	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.338252829963078	2		756	1178	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3113463	3113463	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	86	527	1	ENST00000078429.4:c.457C>A	p.Leu153Ile	p.L153I	ENST00000078429	NM_002067.2	153	Ctc/Atc	3/7	1	2	FACETS	0.622	0.55	0.7	0.622	0.55	0.7	SUBCLONAL	1	TRUE	1	0.338252829963078	2		528	817	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238945	5238945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745665862	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	161	601	1	ENST00000357368.4:c.1834C>T	p.Arg612Cys	p.R612C	ENST00000357368	NM_002850.3	612	Cgc/Tgc	13/38	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.338252829963078	2		602	873	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10259654	10259654	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs62621087	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	157	387	0	ENST00000340748.4:c.2578G>A	p.Gly860Arg	p.G860R	ENST00000340748		860	Ggg/Agg	26/40	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.338252829963078	2		387	734	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262139	10262139	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	190	602	6	ENST00000340748.4:c.2152del	p.Met718CysfsTer59	p.M718Cfs*59	ENST00000340748		718	Atg/tg	23/40	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.338252829963078	2		608	1027	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276755	15276755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138265894	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	187	710	0	ENST00000263388.2:c.5510G>A	p.Arg1837His	p.R1837H	ENST00000263388	NM_000435.2	1837	cGt/cAt	30/33	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.338252829963078	2		710	1026	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367902	15367902	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	70	558	0	ENST00000263377.2:c.1424del	p.Pro475LeufsTer109	p.P475Lfs*109	ENST00000263377	NM_058243.2	475	cCt/ct	8/20	1	2	FACETS	0.522	0.454	0.595	0.522	0.454	0.595	SUBCLONAL	1	TRUE	1	0.338252829963078	2		558	793	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223760	36223760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1165953081	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	63	761	0	ENST00000222270.7:c.6310C>T	p.Arg2104Trp	p.R2104W	ENST00000222270	NM_014727.1	2104	Cgg/Tgg	28/37	1	2	FACETS	0.365	0.314	0.42	0.365	0.314	0.42	SUBCLONAL	1	TRUE	1	0.338252829963078	2		761	1021	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858943	45858943	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	41	412	0	ENST00000391945.4:c.1523T>G	p.Phe508Cys	p.F508C	ENST00000391945	NM_000400.3	508	tTt/tGt	16/23	1	2	FACETS	0.308	0.256	0.367	0.308	0.256	0.367	SUBCLONAL	1	TRUE	1	0.338252829963078	2		412	786	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470603	25470603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	155	578	0	ENST00000264709.3:c.871G>A	p.Gly291Ser	p.G291S	ENST00000264709	NM_175629.2	291	Ggc/Agc	8/23	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.338252829963078	2		578	793	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661596	227661596	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	209	721	0	ENST00000305123.5:c.1859C>T	p.Ala620Val	p.A620V	ENST00000305123	NM_005544.2	620	gCc/gTc	1/2	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.338252829963078	2		721	1007	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793269	242793269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1381223113	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	49	620	0	ENST00000334409.5:c.808G>A	p.Gly270Ser	p.G270S	ENST00000334409	NM_005018.2	270	Ggc/Agc	5/5	1	2	FACETS	0.347	0.292	0.407	0.347	0.292	0.407	SUBCLONAL	1	TRUE	1	0.338252829963078	2		620	836	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	133	430	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	0.338252829963078	2	FACETS	0.938	0.852	1	0.469	0.426	0.515	CLONAL	1	TRUE	0	0.338252829963078	2		431	838	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070349	37070349	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs63750855	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	154	517	1	ENST00000231790.2:c.1489del	p.Arg497GlyfsTer11	p.R497Gfs*11	ENST00000231790	NM_000249.3	495	aCc/ac	13/19	0.338252829963078	2	FACETS	1	0.948	1	0.524	0.479	0.571	CLONAL	1	TRUE	0	0.338252829963078	2		518	869	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	329	450	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.338252829963078	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.338252829963078	2		450	884	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014157	70014157	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	191	504	0	ENST00000394351.3:c.1018A>G	p.Thr340Ala	p.T340A	ENST00000394351	NM_000248.3	340	Act/Gct	9/9	0.338252829963078	2	FACETS	1	0.973	1	0.557	0.514	0.601	CLONAL	1	TRUE	0	0.338252829963078	2		504	1014	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71019915	71019915	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs142371797	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	142	508	0	ENST00000318789.4:c.1694A>G	p.Tyr565Cys	p.Y565C	ENST00000318789	NM_032682.5	565	tAc/tGc	19/21	0.338252829963078	2	FACETS	1	0.932	1	0.513	0.467	0.56	CLONAL	1	TRUE	0	0.338252829963078	2		508	819	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73046212	73046212	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	97	432	0	ENST00000356692.5:c.24G>T	p.Glu8Asp	p.E8D	ENST00000356692		8	gaG/gaT	1/9	0.338252829963078	2	FACETS	0.945	0.844	1	0.472	0.422	0.526	CLONAL	1	TRUE	0	0.338252829963078	2		432	607	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664761	138664761	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs797044528	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	97	398	2	ENST00000330315.3:c.804del	p.Gly269AlafsTer2	p.G269Afs*2	ENST00000330315	NM_023067.3	268	ccC/cc	1/1	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.338252829963078	2		400	517	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs753143066	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	96	822	7	ENST00000295797.4:c.826dup	p.Thr276AsnfsTer16	p.T276Nfs*16	ENST00000295797	NM_002740.5	273	tta/ttAa	9/18	1	2	FACETS	0.927	0.828	1	0.927	0.828	1	CLONAL	1	TRUE	1	0.338252829963078	2		829	612	SUCCESS
REST	5978	MSKCC	GRCh37	4	57777088	57777088	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	152	497	0	ENST00000309042.7:c.284A>C	p.Glu95Ala	p.E95A	ENST00000309042	NM_005612.4	95	gAg/gCg	2/4	1	2	FACETS	0.973	0.889	1	0.973	0.889	1	CLONAL	1	TRUE	1	0.338252829963078	2		497	924	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	104	564	1	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.338252829963078	2		565	547	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584618	187584618	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	40	538	0	ENST00000441802.2:c.3415A>G	p.Thr1139Ala	p.T1139A	ENST00000441802	NM_005245.3	1139	Aca/Gca	3/27	1	2	FACETS	0.308	0.255	0.367	0.308	0.255	0.367	SUBCLONAL	1	TRUE	1	0.338252829963078	2		538	768	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236628	236628	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201139275	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	111	342	0	ENST00000264932.6:c.1346C>T	p.Ala449Val	p.A449V	ENST00000264932	NM_004168.2	449	gCc/gTc	10/15	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.338252829963078	2		342	654	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295851	1295851	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	200	872	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.338252829963078	2		872	1126	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752812	57752812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	58	429	0	ENST00000274289.3:c.1116del	p.Phe372LeufsTer31	p.F372Lfs*31	ENST00000274289	NM_006622.3	372	ttT/tt	8/14	1	2	FACETS	0.601	0.516	0.693	0.601	0.516	0.693	SUBCLONAL	1	TRUE	1	0.338252829963078	2		429	571	SUCCESS
APC	324	MSKCC	GRCh37	5	112176192	112176192	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370433763	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	175	516	0	ENST00000257430.4:c.4901C>T	p.Pro1634Leu	p.P1634L	ENST00000257430	NM_000038.5	1634	cCg/cTg	16/16	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.338252829963078	2		516	1017	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522414	176522414	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	164	650	0	ENST00000292408.4:c.1603A>G	p.Asn535Asp	p.N535D	ENST00000292408	NM_213647.1	535	Aac/Gac	12/18	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.338252829963078	2		650	877	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910770	29910770	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	159	523	0	ENST00000376809.5:c.310A>G	p.Thr104Ala	p.T104A	ENST00000376809	NM_002116.7	104	Acc/Gcc	2/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.338252829963078	2		523	753	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129060	152129060	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	140	532	0	ENST00000206249.3:c.13C>A	p.Leu5Ile	p.L5I	ENST00000206249	NM_000125.3	5	Ctc/Atc	1/8	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.338252829963078	2		532	766	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129397	152129397	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	61	582	0	ENST00000206249.3:c.350T>C	p.Leu117Pro	p.L117P	ENST00000206249	NM_000125.3	117	cTg/cCg	1/8	1	2	FACETS	0.48	0.413	0.553	0.48	0.413	0.553	SUBCLONAL	1	TRUE	1	0.338252829963078	2		582	751	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860130	151860130	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	137	651	0	ENST00000262189.6:c.10532G>A	p.Gly3511Asp	p.G3511D	ENST00000262189	NM_170606.2	3511	gGc/gAc	43/59	1	2	FACETS	0.851	0.773	0.933	0.851	0.773	0.933	CLONAL	1	TRUE	1	0.338252829963078	2		651	952	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	151	859	5	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	0.823	0.751	0.898	0.823	0.751	0.898	CLONAL	1	TRUE	1	0.338252829963078	2		864	1085	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062081-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	123	505	4	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.769	0.694	0.848	0.769	0.694	0.848	SUBCLONAL	1	TRUE	1	0.338252829963078	2		509	946	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0062082-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	19	372	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.548	0.415	0.705	0.548	0.415	0.705	SUBCLONAL	1	TRUE	1	0.19	2		372	365	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0062082-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	12	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.538	0.377	0.735	0.538	0.377	0.735	SUBCLONAL	1	TRUE	1	0.19	2		298	235	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0062082-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	57	616	0	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.19	2		616	521	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141507	11141507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062082-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	50	599	0	ENST00000358026.2:c.3484G>A	p.Gly1162Ser	p.G1162S	ENST00000358026	NM_001128849.1	1162	Ggc/Agc	25/36	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.19	2		599	460	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224214	36224214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774855256	NA	P-0062082-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	35	526	0	ENST00000222270.7:c.6764C>T	p.Pro2255Leu	p.P2255L	ENST00000222270	NM_014727.1	2255	cCg/cTg	28/37	0.3	5	FACETS	1	0.915	1	0.403	0.33	0.484	CLONAL	1	TRUE	2	0.19	5		526	392	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911143	40911143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370795038	NA	P-0062082-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	25	304	2	ENST00000373198.4:c.2162G>A	p.Arg721His	p.R721H	ENST00000373198	NM_133170.3	721	cGt/cAt	13/32	0.108932929184322	5	FACETS	1	0.908	1	0.326	0.258	0.405	INDETERMINATE	1	TRUE	1	0.19	5		306	259	SUCCESS
ALB	213	MSKCC	GRCh37	4	74274354	74274354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764279820	NA	P-0062082-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	29	506	0	ENST00000295897.4:c.314G>A	p.Arg105His	p.R105H	ENST00000295897	NM_000477.5	105	cGt/cAt	4/15	1	2	FACETS	0.832	0.668	1	0.832	0.668	1	CLONAL	1	TRUE	1	0.19	2		506	367	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0062082-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	28	200	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.556	0.443	0.685	0.556	0.443	0.685	SUBCLONAL	1	TRUE	1	0.19	2		201	530	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103868	209103868	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1160632942	NA	P-0062113-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	30	457	0	ENST00000345146.2:c.1081G>T	p.Glu361Ter	p.E361*	ENST00000345146	NM_005896.2	361	Gaa/Taa	9/10	0.624055522625239	2	FACETS	0.173	0.139	0.212	0.087	0.069	0.106	SUBCLONAL	1	TRUE	0	0.666235379532495	2		457	520	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63898353	63898353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062113-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	183	508	0	ENST00000398590.3:c.79G>A	p.Ala27Thr	p.A27T	ENST00000398590	NM_001177387.1	27	Gcc/Acc	3/14	0.217774316235678	1	FACETS	0.532	0.493	0.573	0.532	0.493	0.573	INDETERMINATE	1	TRUE	0	0.666235379532495	1		508	688	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856008	151856008	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062113-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	63	492	0	ENST00000262189.6:c.11610G>C	p.Lys3870Asn	p.K3870N	ENST00000262189	NM_170606.2	3870	aaG/aaC	44/59	1	2	FACETS	0.284	0.245	0.326	0.284	0.245	0.326	SUBCLONAL	1	TRUE	1	0.666235379532495	2		492	666	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577098	7577099	+	missense_variant	Missense_Mutation	DNP	TC	TC	GT	novel	NA	P-0062153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	372	545	0	ENST00000269305.4:c.839_840delinsAC	p.Arg280Asn	p.R280N	ENST00000269305	NM_001126112.2	280	aGA/aAC	8/11	0.856255158720219	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.856255158720219	2		545	407	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937897	76937897	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	349	268	0	ENST00000373344.5:c.2851del	p.Thr951ProfsTer19	p.T951Pfs*19	ENST00000373344	NM_000489.3	951	Acc/cc	9/35	0.624788672160895	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.856255158720219	2		268	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0062154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	319	516	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.507936947932911	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	0	0.507936947932911	3		516	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0062157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	109	722	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.385051638054596	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.385051638054596	1		722	389	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740263	162740263	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs752778008	NA	P-0062157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	113	428	0	ENST00000367921.3:c.1465C>T	p.Arg489Ter	p.R489*	ENST00000367921	NM_006182.2	489	Cga/Tga	12/18	1	2	FACETS	0.996	0.899	1	0.996	0.899	1	CLONAL	1	TRUE	1	0.385051638054596	2		428	589	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0062157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	85	636	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.924	0.819	1	0.924	0.819	1	CLONAL	1	TRUE	1	0.385051638054596	2		636	478	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148727	20148727	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0062157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	62	228	0	ENST00000379607.5:c.338-2A>C		p.X113_splice	ENST00000379607	NM_001412.3	113			1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.385051638054596	2		228	298	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260211	149260211	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	114	434	0	ENST00000360632.3:c.682C>G	p.Gln228Glu	p.Q228E	ENST00000360632	NM_015472.4	228	Cag/Gag	4/7	0.280045766489052	4	FACETS	0.899	0.814	0.987	0.899	0.814	0.987	CLONAL	2	TRUE	2	0.387815799383662	4		434	454	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0062174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	65	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.724	0.631	0.822	0.724	0.631	0.822	SUBCLONAL	1	TRUE	1	0.533024019537986	2		298	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934573	NA	P-0062174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	182	629	0	ENST00000269305.4:c.722C>A	p.Ser241Tyr	p.S241Y	ENST00000269305	NM_001126112.2	241	tCc/tAc	7/11	0.533024019537986	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.533024019537986	1		629	445	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0062174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	180	163	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.932	0.861	1	0.932	0.861	1	CLONAL	1	TRUE	1	0.533024019537986	2		163	725	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0062174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	166	309	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.945	0.871	1	0.945	0.871	1	CLONAL	1	TRUE	1	0.533024019537986	2		309	659	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474041	29474041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs78723472	NA	P-0062174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	189	604	0	ENST00000389048.3:c.2134G>A	p.Val712Met	p.V712M	ENST00000389048	NM_004304.4	712	Gtg/Atg	12/29	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.533024019537986	2		604	642	SUCCESS
APC	324	MSKCC	GRCh37	5	112175751	112175752	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1114167577	NA	P-0062174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	160	575	0	ENST00000257430.4:c.4463dup	p.Leu1488PhefsTer26	p.L1488Ffs*26	ENST00000257430	NM_000038.5	1487	act/acTt	16/16	1	2	FACETS	0.844	0.776	0.915	0.844	0.776	0.915	CLONAL	1	TRUE	1	0.533024019537986	2		575	711	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913293	NA	P-0062174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	89	413	0	ENST00000371953.3:c.517C>A	p.Arg173Ser	p.R173S	ENST00000371953	NM_000314.4	173	Cgc/Agc	6/9	0.533024019537986	1	FACETS	0.745	0.666	0.826	0.745	0.666	0.826	SUBCLONAL	1	TRUE	0	0.533024019537986	1		413	329	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119849	70119849	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	48	542	0	ENST00000245479.2:c.852del	p.Asn285ThrfsTer98	p.N285Tfs*98	ENST00000245479	NM_000346.3	284	tCc/tc	3/3	1	2	FACETS	0.302	0.254	0.354	0.302	0.254	0.354	SUBCLONAL	1	TRUE	1	0.533024019537986	2		542	597	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438545	52438545	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1553645146	NA	P-0062175-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	90	633	0	ENST00000460680.1:c.1174C>T	p.Gln392Ter	p.Q392*	ENST00000460680	NM_004656.3	392	Cag/Tag	12/17	0.192567617562115	1	FACETS	0.519	0.461	0.581	0.519	0.461	0.581	INDETERMINATE	1	TRUE	0	0.409219718200114	1		633	674	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588991	67588991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062175-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	127	566	0	ENST00000274335.5:c.1082C>T	p.Ser361Phe	p.S361F	ENST00000274335		361	tCt/tTt	8/15	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.409219718200114	2		566	605	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001395	150001395	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062175-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	154	581	0	ENST00000253339.5:c.2209C>T	p.Arg737Ter	p.R737*	ENST00000253339		737	Cga/Tga	4/7	0.409219718200114	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.409219718200114	1		581	548	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557407	21557407	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062175-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	143	579	0	ENST00000382592.4:c.2438G>T	p.Cys813Phe	p.C813F	ENST00000382592	NM_014572.2	813	tGc/tTc	5/8	0.409219718200114	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.409219718200114	1		579	516	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441961	52441973	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CACTGCAGCCTAC	CACTGCAGCCTAC	-	novel	NA	P-0062175-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	124	502	0	ENST00000460680.1:c.375+1_375+13del		p.X125_splice	ENST00000460680	NM_004656.3	125			0.192567617562115	1	FACETS	0.823	0.747	0.902	0.823	0.747	0.902	INDETERMINATE	1	TRUE	0	0.409219718200114	1		502	586	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0062176-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	92	670	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.30542616250166	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.30542616250166	1		670	440	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246251	46246252	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0062176-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	129	540	0	ENST00000334344.6:c.4345_4346del	p.Asn1449TrpfsTer53	p.N1449Wfs*53	ENST00000334344	NM_152641.2	1449	AAt/t	15/21	0.30542616250166	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.30542616250166	2		540	401	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0062177-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	114	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.820244334887581	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.820244334887581	3		426	167	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0062177-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	125	497	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	0.820244334887581	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.820244334887581	3		497	195	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749500	41749500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062177-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	66	411	0	ENST00000226382.2:c.295C>T	p.Arg99Trp	p.R99W	ENST00000226382	NM_003924.3	99	Cgg/Tgg	2/3	0.820244334887581	3	FACETS	1	0.922	1	0.53	0.467	0.596	CLONAL	1	TRUE	1	0.820244334887581	3		411	214	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575209	48575209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767326	NA	P-0062177-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	74	293	0	ENST00000342988.3:c.403C>T	p.Arg135Ter	p.R135*	ENST00000342988	NM_005359.5	135	Cga/Tga	3/12	0.820244334887581	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.820244334887581	2		293	87	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0062177-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	151	443	0	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.820244334887581	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.820244334887581	2		443	173	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21348507	21348507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201159165	NA	P-0062177-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	58	678	0	ENST00000215739.8:c.1564G>A	p.Glu522Lys	p.E522K	ENST00000215739	NM_006767.3	522	Gag/Aag	14/21	0.820244334887581	3	FACETS	0.739	0.64	0.844	0.369	0.32	0.422	SUBCLONAL	1	TRUE	1	0.820244334887581	3		678	270	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54956521	54956521	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062177-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	41	393	0	ENST00000312783.6:c.673C>G	p.Leu225Val	p.L225V	ENST00000312783	NM_198436.1	225	Ctt/Gtt	7/10	0.820244334887581	7	FACETS	1	0.94	1	0.255	0.214	0.3	CLONAL	1	TRUE	2	0.820244334887581	7		393	239	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590707	189590707	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062177-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	261	572	0	ENST00000264731.3:c.1272G>T	p.Met424Ile	p.M424I	ENST00000264731	NM_003722.4	424	atG/atT	10/14	0.820244334887581	4	FACETS	0.993	0.95	1	0.993	0.95	1	CLONAL	3	TRUE	1	0.820244334887581	4		572	389	SUCCESS
APC	324	MSKCC	GRCh37	5	112175474	112175475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAAC	novel	NA	P-0062177-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	72	518	0	ENST00000257430.4:c.4183_4184insAAAC	p.Ser1395LysfsTer4	p.S1395Kfs*4	ENST00000257430	NM_000038.5	1395	agt/aAAACgt	16/16	0.820244334887581	3	FACETS	0.971	0.859	1	0.485	0.429	0.544	CLONAL	1	TRUE	1	0.820244334887581	3		518	255	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359611	40359611	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062178-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	98	334	0	ENST00000293328.3:c.2042A>T	p.Lys681Ile	p.K681I	ENST00000293328	NM_012448.3	681	aAa/aTa	16/19	1	2	FACETS	0.891	0.798	0.988	0.891	0.798	0.988	CLONAL	1	TRUE	1	0.457427501413121	2		334	481	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867523	35867523	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062178-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	221	342	0	ENST00000303115.3:c.337G>C	p.Glu113Gln	p.E113Q	ENST00000303115	NM_002185.3	113	Gaa/Caa	3/8	0.457427501413121	6	FACETS	1	0.982	1	0.575	0.537	0.615	CLONAL	2	TRUE	2	0.457427501413121	6		342	804	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0062179-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	218	476	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.374997866195942	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.374997866195942	2		476	571	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480306	89480306	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062179-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	63	398	1	ENST00000336596.2:c.2143G>A	p.Asp715Asn	p.D715N	ENST00000336596	NM_005233.5	715	Gat/Aat	13/17	0.36480927304574	3	FACETS	0.813	0.704	0.93	0.406	0.352	0.465	CLONAL	1	TRUE	1	0.374997866195942	3		399	491	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422494	47422494	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062179-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	117	521	0	ENST00000404338.3:c.562C>T	p.Leu188Phe	p.L188F	ENST00000404338	NM_004491.4	188	Ctt/Ttt	1/6	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.374997866195942	2		521	608	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0062180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	46	764	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.882	0.747	1	0.882	0.747	1	CLONAL	1	TRUE	1	0.33	2		764	316	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0062180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	73	293	0	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	1	2	FACETS	0.569	0.496	0.647	0.569	0.496	0.647	SUBCLONAL	1	TRUE	1	0.33	2		293	778	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057691	27057691	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	87	547	0	ENST00000324856.7:c.1399C>T	p.Gln467Ter	p.Q467*	ENST00000324856	NM_006015.4	467	Cag/Tag	3/20	1	2	FACETS	0.579	0.511	0.651	0.579	0.511	0.651	SUBCLONAL	1	TRUE	1	0.33	2		547	911	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121912580	NA	P-0062180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	14	383	0	ENST00000342988.3:c.1157G>T	p.Gly386Val	p.G386V	ENST00000342988	NM_005359.5	386	gGt/gTt	10/12	0.3	1	FACETS	0.146	0.105	0.197	0.146	0.105	0.197	SUBCLONAL	1	TRUE	0	0.33	1		383	484	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120806851	120806851	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	67	642	0	ENST00000257552.2:c.44C>T	p.Ser15Leu	p.S15L	ENST00000257552	NM_002442.3	15	tCg/tTg	1/15	1	2	FACETS	0.575	0.499	0.658	0.575	0.499	0.658	SUBCLONAL	1	TRUE	1	0.33	2		642	706	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813296	102813296	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	67	528	0	ENST00000307046.8:c.393G>C	p.Lys131Asn	p.K131N	ENST00000307046	NM_001111285.1	131	aaG/aaC	3/4	1	2	FACETS	0.494	0.428	0.565	0.494	0.428	0.565	SUBCLONAL	1	TRUE	1	0.33	2		528	822	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61323099	61323099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559175012	NA	P-0062180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	116	555	0	ENST00000283752.5:c.965G>A	p.Gly322Asp	p.G322D	ENST00000283752	NM_006919.2	322	gGt/gAt	8/8	0.3	1	FACETS	0.765	0.69	0.845	0.765	0.69	0.845	SUBCLONAL	1	TRUE	0	0.33	1		555	767	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1905942	1905942	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0062180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	76	336	0	ENST00000382891.5:c.598-1G>T		p.X200_splice	ENST00000382891	NM_133335.3	200			1	2	FACETS	0.765	0.672	0.866	0.765	0.672	0.866	SUBCLONAL	1	TRUE	1	0.33	2		336	602	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0062181-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	73	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.944	0.833	1	0.944	0.833	1	CLONAL	1	TRUE	1	0.500627375273227	2		298	309	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425677	49425677	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062181-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	159	570	0	ENST00000301067.7:c.12811A>G	p.Thr4271Ala	p.T4271A	ENST00000301067	NM_003482.3	4271	Aca/Gca	39/54	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.500627375273227	2		570	579	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931847	39931847	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0062181-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	128	427	0	ENST00000378444.4:c.2752del	p.Gln918LysfsTer18	p.Q918Kfs*18	ENST00000378444	NM_001123385.1	918	Caa/aa	4/15	0.418498293087893	1	FACETS	0.915	0.836	0.996	0.915	0.836	0.996	CLONAL	1	TRUE	0	0.500627375273227	1		427	419	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0062187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	16	326	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.954	0.717	1	0.954	0.717	1	CLONAL	1	FALSE	1	0.372697845961409	2		326	90	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0062187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	66	727	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.372697845961409	3	FACETS	0.917	0.808	1	0.917	0.808	1	CLONAL	2	FALSE	1	0.372697845961409	3		727	229	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	78	518	1	ENST00000269305.4:c.853G>T	p.Glu285Ter	p.E285*	ENST00000269305	NM_001126112.2	285	Gag/Tag	8/11	0.372697845961409	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	FALSE	1	0.372697845961409	3		519	207	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929157	44929157	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0062187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	72	391	0	ENST00000377967.4:c.2257C>T	p.Gln753Ter	p.Q753*	ENST00000377967	NM_021140.2	753	Cag/Tag	17/29	0.340214554450104	5	FACETS	1	0.96	1	1	0.96	1	CLONAL	4	FALSE	1	0.372697845961409	5		391	134	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267597	7267597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	31	451	0	ENST00000302850.5:c.411G>A	p.Met137Ile	p.M137I	ENST00000302850	NM_000208.2	137	atG/atA	2/22	0.372697845961409	5	FACETS	1	0.945	1	0.75	0.613	0.901	CLONAL	1	FALSE	3	0.372697845961409	5		451	173	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0062187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	55	652	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.368598614802146	2	FACETS	0.789	0.686	0.897	0.789	0.686	0.897	SUBCLONAL	2	FALSE	0	0.372697845961409	2		652	187	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942845	44942845	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	17	334	0	ENST00000377967.4:c.3425G>C	p.Arg1142Thr	p.R1142T	ENST00000377967	NM_021140.2	1142	aGa/aCa	23/29	0.340214554450104	5	FACETS	1	0.848	1	0.296	0.223	0.381	CLONAL	1	FALSE	1	0.372697845961409	5		334	120	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37628012	37628012	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	19	460	0	ENST00000249071.6:c.248C>T	p.Ser83Phe	p.S83F	ENST00000249071	NM_002872.4	83	tCc/tTc	4/7	0.372414884693579	3	FACETS	0.672	0.513	0.857	0.336	0.256	0.429	SUBCLONAL	1	FALSE	1	0.372697845961409	3		460	180	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481466	40481466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193922717	NA	P-0062187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	52	452	0	ENST00000264657.5:c.1243G>A	p.Glu415Lys	p.E415K	ENST00000264657	NM_139276.2	415	Gag/Aag	14/24	0.372697845961409	3	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	FALSE	1	0.372697845961409	3		452	146	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513354	106513354	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	10	351	0	ENST00000359195.3:c.2258C>G	p.Ser753Cys	p.S753C	ENST00000359195	NM_002649.2	753	tCt/tGt	4/11	0.372697845961409	3	FACETS	0.558	0.381	0.779	0.279	0.19	0.39	SUBCLONAL	1	FALSE	1	0.372697845961409	3		351	114	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315366	30315366	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	16	366	1	ENST00000322652.5:c.1051C>G	p.Gln351Glu	p.Q351E	ENST00000322652	NM_015355.2	351	Cag/Gag	10/16	0.372697845961409	3	FACETS	0.926	0.693	1	0.463	0.346	0.599	CLONAL	1	FALSE	1	0.372697845961409	3		367	110	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981488	201981489	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0062187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	68	441	0	ENST00000359651.3:c.403dup	p.Glu135GlyfsTer7	p.E135Gfs*7	ENST00000359651		134	-/G	3/8	0.372697845961409	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	3	FALSE	0	0.372697845961409	3		441	130	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120995	115120995	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	51	462	0	ENST00000257566.3:c.11C>G	p.Ser4Cys	p.S4C	ENST00000257566	NM_016569.3	4	tCc/tGc	1/8	0.30500524221042	4	FACETS	0.866	0.745	0.995	0.866	0.745	0.995	CLONAL	2	FALSE	2	0.372697845961409	4		462	217	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793290	33793290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555742325	NA	P-0062187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	56	370	0	ENST00000498907.2:c.31C>T	p.Pro11Ser	p.P11S	ENST00000498907	NM_004364.3	11	Ccg/Tcg	1/1	0.372697845961409	5	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	FALSE	3	0.372697845961409	5		370	191	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051208	128051208	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	28	510	0	ENST00000285398.2:c.115C>A	p.Pro39Thr	p.P39T	ENST00000285398	NM_000122.1	39	Ccc/Acc	2/15	0.372697845961409	5	FACETS	0.786	0.63	0.964	0.197	0.157	0.241	CLONAL	1	FALSE	1	0.372697845961409	5		510	298	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62322181	62322181	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753525041	NA	P-0062187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	66	384	0	ENST00000360203.5:c.2437G>A	p.Glu813Lys	p.E813K	ENST00000360203	NM_001283009.1	813	Gag/Aag	27/35	0.372697845961409	4	FACETS	0.959	0.852	1	1	0.975	1	CLONAL	3	FALSE	2	0.372697845961409	4		384	169	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670302	134670302	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	36	446	0	ENST00000398015.3:c.213G>A	p.Trp71Ter	p.W71*	ENST00000398015	NM_004441.4	71	tgG/tgA	3/16	0.372697845961409	3	FACETS	1	0.932	1	0.63	0.523	0.746	CLONAL	1	FALSE	1	0.372697845961409	3		446	182	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144390280	144390280	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	42	443	0	ENST00000262995.4:c.2113G>A	p.Glu705Lys	p.E705K	ENST00000262995	NM_207123.2	705	Gaa/Aaa	11/11	0.372697845961409	3	FACETS	1	0.892	1	1	0.892	1	CLONAL	2	FALSE	1	0.372697845961409	3		443	127	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	893126	893126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759352780	NA	P-0062187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	35	345	0	ENST00000166345.3:c.13G>A	p.Val5Met	p.V5M	ENST00000166345	NM_004237.3	5	Gtg/Atg	1/13	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	FALSE	1	0.372697845961409	2		345	162	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	908509	908509	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	49	436	0	ENST00000166345.3:c.799G>A	p.Gly267Ser	p.G267S	ENST00000166345	NM_004237.3	267	Ggc/Agc	9/13	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	1	0.372697845961409	2		436	220	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622190	117622190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs565633598	NA	P-0062187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	11	307	1	ENST00000368508.3:c.6680A>G	p.Tyr2227Cys	p.Y2227C	ENST00000368508	NM_002944.2	2227	tAt/tGt	42/43	0.234559652072826	2	FACETS	0.952	0.694	1	0.952	0.694	1	CLONAL	2	FALSE	0	0.372697845961409	2		308	31	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781210	161781210	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746922936	NA	P-0062187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	19	358	0	ENST00000366898.1:c.1195G>A	p.Glu399Lys	p.E399K	ENST00000366898	NM_004562.2	399	Gag/Aag	11/12	0.234559652072826	2	FACETS	0.637	0.487	0.811	0.319	0.243	0.406	SUBCLONAL	1	FALSE	0	0.372697845961409	2		358	160	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975495	13975495	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	53	419	0	ENST00000405192.2:c.392G>T	p.Gly131Val	p.G131V	ENST00000405192	NM_001163147.1	131	gGa/gTa	7/12	0.372697845961409	3	FACETS	1	0.873	1	1	0.873	1	CLONAL	2	FALSE	1	0.372697845961409	3		419	168	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860550	151860550	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0062187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	39	567	0	ENST00000262189.6:c.10112C>G	p.Ser3371Ter	p.S3371*	ENST00000262189	NM_170606.2	3371	tCa/tGa	43/59	0.372697845961409	3	FACETS	0.766	0.645	0.897	0.766	0.645	0.897	SUBCLONAL	2	FALSE	1	0.372697845961409	3		567	162	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413904	139413904	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	81	422	0	ENST00000277541.6:c.856G>C	p.Glu286Gln	p.E286Q	ENST00000277541	NM_017617.3	286	Gag/Cag	5/34	0.368598614802146	2	FACETS	0.957	0.858	1	0.957	0.858	1	CLONAL	2	FALSE	0	0.372697845961409	2		422	227	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0062188-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	176	319	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.65858914767528	2		319	530	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0062188-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	143	675	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.824	0.756	0.895	0.824	0.756	0.895	CLONAL	1	TRUE	1	0.65858914767528	2		675	527	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0062188-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	248	390	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.65858914767528	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.65858914767528	1		390	471	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678783	52678784	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0062188-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	98	222	0	ENST00000394830.3:c.835dup	p.Ile279AsnfsTer8	p.I279Nfs*8	ENST00000394830	NM_018313.4	279	ata/aAta	9/30	0.65858914767528	1	FACETS	0.786	0.713	0.86	0.786	0.713	0.86	SUBCLONAL	1	TRUE	0	0.65858914767528	1		222	254	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0062188-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	205	383	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.65858914767528	2		383	563	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158326	108158326	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0062188-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	130	273	0	ENST00000278616.4:c.3994-1G>A		p.X1332_splice	ENST00000278616	NM_000051.3	1332			1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.65858914767528	2		273	388	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216092	7216092	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	187	479	0	ENST00000380728.2:c.967C>T	p.Arg323Ter	p.R323*	ENST00000380728		323	Cga/Tga	11/11	0.830116285275579	3	FACETS	0.919	0.852	0.988	0.459	0.426	0.494	CLONAL	1	TRUE	1	0.830116285275579	3		479	694	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0062201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	258	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.721311013697556	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.830116285275579	4		298	540	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440092	99440092	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	176	404	0	ENST00000268035.6:c.1060A>G	p.Thr354Ala	p.T354A	ENST00000268035	NM_000875.3	354	Acc/Gcc	4/21	1	2	FACETS	0.982	0.915	1	0.982	0.915	1	CLONAL	1	TRUE	1	0.830116285275579	2		404	432	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411669	63411669	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	222	498	0	ENST00000330258.3:c.1498T>C	p.Tyr500His	p.Y500H	ENST00000330258	NM_152424.3	500	Tac/Cac	2/2	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.830116285275579	2		498	506	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0062202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	310	675	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.954	0.906	1	1	0.996	1	CLONAL	2	TRUE	1	0.45	2		675	722	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392634	118392634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555053677	NA	P-0062202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	87	391	0	ENST00000534358.1:c.11666G>A	p.Arg3889Gln	p.R3889Q	ENST00000534358	NM_005933.3	3889	cGa/cAa	36/36	1	2	FACETS	0.646	0.572	0.724	0.646	0.572	0.724	SUBCLONAL	1	TRUE	1	0.45	2		391	599	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210181	123210181	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0062202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	156	287	0	ENST00000218089.9:c.2534-1G>C		p.X845_splice	ENST00000218089	NM_001042749.1	845			1	2	FACETS	0.776	0.717	0.836	1	0.99	1	SUBCLONAL	2	TRUE	1	0.45	2		287	447	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872207	45872207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	76	493	0	ENST00000391945.4:c.227C>T	p.Thr76Ile	p.T76I	ENST00000391945	NM_000400.3	76	aCt/aTt	4/23	1	2	FACETS	0.463	0.405	0.525	0.463	0.405	0.525	SUBCLONAL	1	TRUE	1	0.45	2		493	730	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988809	41988809	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	105	406	0	ENST00000219905.7:c.1601C>T	p.Ser534Leu	p.S534L	ENST00000219905	NM_001164273.1	534	tCa/tTa	3/24	1	2	FACETS	0.776	0.697	0.86	0.776	0.697	0.86	SUBCLONAL	1	TRUE	1	0.45	2		406	601	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521451	187521451	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0062202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	66	404	0	ENST00000441802.2:c.11704C>G	p.Gln3902Glu	p.Q3902E	ENST00000441802	NM_005245.3	3902	Cag/Gag	22/27	1	2	FACETS	0.558	0.485	0.637	0.558	0.485	0.637	SUBCLONAL	1	TRUE	1	0.45	2		404	526	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016261	150016261	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	33	294	0	ENST00000253339.5:c.445G>C	p.Glu149Gln	p.E149Q	ENST00000253339		149	Gag/Cag	2/7	1	2	FACETS	0.327	0.266	0.396	0.327	0.266	0.396	SUBCLONAL	1	TRUE	1	0.45	2		294	448	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413091	63413091	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	121	391	0	ENST00000330258.3:c.76G>T	p.Glu26Ter	p.E26*	ENST00000330258	NM_152424.3	26	Gaa/Taa	2/2	1	2	FACETS	0.873	0.791	0.959	0.873	0.791	0.959	CLONAL	1	TRUE	1	0.45	2		391	616	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	377	819	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.561803010118748	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.575713368187455	2		819	623	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176478	142176478	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	205	420	0	ENST00000350721.4:c.7623G>T	p.Arg2541Ser	p.R2541S	ENST00000350721	NM_001184.3	2541	agG/agT	45/47	0.234038111970676	5	FACETS	1	0.962	1	0.698	0.651	0.746	INDETERMINATE	2	TRUE	2	0.575713368187455	5		420	634	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	234	265	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.575713368187455	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.575713368187455	2		265	366	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971000	21971000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	407	659	0	ENST00000304494.5:c.358G>T	p.Glu120Ter	p.E120*	ENST00000304494	NM_000077.4	120	Gag/Tag	2/3	0.575713368187455	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.575713368187455	2		659	655	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530064	212530064	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	120	533	0	ENST00000342788.4:c.1855C>T	p.Pro619Ser	p.P619S	ENST00000342788	NM_005235.2	619	Cca/Tca	15/28	1	2	FACETS	0.757	0.686	0.831	0.757	0.686	0.831	SUBCLONAL	1	TRUE	1	0.575713368187455	2		533	551	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281344	49281344	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202077345	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	291	551	0	ENST00000282018.3:c.391G>A	p.Val131Met	p.V131M	ENST00000282018	NM_020377.2	131	Gtg/Atg	1/1	0.561803010118748	2	FACETS	0.89	0.846	0.933	0.89	0.846	0.933	CLONAL	2	TRUE	0	0.575713368187455	2		551	568	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462682	29462682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	234	546	0	ENST00000389048.3:c.2219G>A	p.Gly740Glu	p.G740E	ENST00000389048	NM_004304.4	740	gGa/gAa	13/29	0.268818833773238	3	FACETS	0.826	0.775	0.877	0.826	0.775	0.877	INDETERMINATE	2	TRUE	1	0.575713368187455	3		546	634	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265367	152265367	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	208	556	0	ENST00000206249.3:c.820G>T	p.Gly274Trp	p.G274W	ENST00000206249	NM_000125.3	274	Ggg/Tgg	4/8	0.268818833773238	3	FACETS	1	0.992	1	0.737	0.688	0.788	INDETERMINATE	1	TRUE	1	0.575713368187455	3		556	631	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1735885	1735885	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	203	459	0	ENST00000378609.4:c.403G>T	p.Val135Leu	p.V135L	ENST00000378609	NM_002074.3	135	Gtg/Ttg	7/12	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.575713368187455	2		459	538	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851402	156851402	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	174	561	0	ENST00000524377.1:c.2359G>T	p.Ala787Ser	p.A787S	ENST00000524377	NM_002529.3	787	Gca/Tca	17/17	1	2	FACETS	0.939	0.868	1	0.939	0.868	1	CLONAL	1	TRUE	1	0.575713368187455	2		561	644	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326616	161326616	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	118	372	0	ENST00000367975.2:c.391G>T	p.Gly131Trp	p.G131W	ENST00000367975	NM_003001.3	131	Ggg/Tgg	5/6	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.575713368187455	2		372	372	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003790	57003790	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	292	642	0	ENST00000257254.3:c.689G>C	p.Gly230Ala	p.G230A	ENST00000257254		230	gGc/gCc	1/2	0.208281257072767	5	FACETS	1	0.99	1	0.81	0.766	0.855	INDETERMINATE	2	TRUE	2	0.575713368187455	5		642	778	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123704	46123704	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	273	502	0	ENST00000334344.6:c.85A>G	p.Ser29Gly	p.S29G	ENST00000334344	NM_152641.2	29	Agc/Ggc	1/21	0.56153529752832	3	FACETS	0.932	0.881	0.984	0.932	0.881	0.984	CLONAL	2	TRUE	1	0.575713368187455	3		502	655	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420591	49420592	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	304	701	0	ENST00000301067.7:c.15157dup	p.Asp5053GlyfsTer19	p.D5053Gfs*19	ENST00000301067	NM_003482.3	5053	gac/gGac	48/54	0.56153529752832	3	FACETS	0.84	0.795	0.885	0.84	0.795	0.885	CLONAL	2	TRUE	1	0.575713368187455	3		701	810	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060578	38060578	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	373	737	0	ENST00000250448.2:c.1411A>T	p.Thr471Ser	p.T471S	ENST00000250448	NM_004496.3	471	Act/Tct	2/2	0.56153529752832	3	FACETS	0.956	0.911	1	0.956	0.911	1	CLONAL	2	TRUE	1	0.575713368187455	3		737	873	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640316	3640316	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	444	601	0	ENST00000294008.3:c.3323A>C	p.Glu1108Ala	p.E1108A	ENST00000294008	NM_032444.2	1108	gAg/gCg	12/15	0.558490715668304	4	FACETS	0.94	0.903	0.977	0.94	0.903	0.977	CLONAL	3	TRUE	1	0.575713368187455	4		601	862	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274252	10274252	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	121	448	0	ENST00000330684.3:c.17A>G	p.Tyr6Cys	p.Y6C	ENST00000330684	NM_001134407.1	6	tAt/tGt	2/13	0.56153529752832	3	FACETS	0.898	0.813	0.986	0.449	0.406	0.493	CLONAL	1	TRUE	1	0.575713368187455	3		448	603	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86545100	86545100	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	278	608	0	ENST00000262426.4:c.925C>A	p.Leu309Met	p.L309M	ENST00000262426	NM_001451.2	309	Ctg/Atg	1/2	0.232502305437308	3	FACETS	1	0.967	1	0.685	0.649	0.721	INDETERMINATE	2	TRUE	0	0.575713368187455	3		608	605	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579483	7579483	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	392	745	0	ENST00000269305.4:c.204G>T	p.Glu68Asp	p.E68D	ENST00000269305	NM_001126112.2	68	gaG/gaT	4/11	0.561803010118748	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.575713368187455	2		745	670	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61305265	61305265	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1178840981	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	34	237	0	ENST00000341074.5:c.861C>G	p.Phe287Leu	p.F287L	ENST00000341074	NM_002974.2	287	ttC/ttG	8/8	0.268818833773238	3	FACETS	0.65	0.535	0.778	0.325	0.267	0.389	INDETERMINATE	1	TRUE	1	0.575713368187455	3		237	234	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250915	10250915	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	116	492	0	ENST00000340748.4:c.3565G>C	p.Glu1189Gln	p.E1189Q	ENST00000340748		1189	Gag/Cag	32/40	0.137223019916068	5	FACETS	0.754	0.683	0.828	0.377	0.341	0.414	INDETERMINATE	2	TRUE	1	0.575713368187455	5		492	498	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098347	11098347	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs750547893	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	156	541	0	ENST00000358026.2:c.865A>G	p.Met289Val	p.M289V	ENST00000358026	NM_001128849.1	289	Atg/Gtg	6/36	0.137223019916068	5	FACETS	0.833	0.766	0.903	0.417	0.383	0.452	INDETERMINATE	2	TRUE	1	0.575713368187455	5		541	606	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339030	225339030	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	147	392	0	ENST00000264414.4:c.2239G>T	p.Gly747Ter	p.G747*	ENST00000264414	NM_003590.4	747	Gga/Tga	16/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.575713368187455	2		392	469	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017854	31017854	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	233	388	0	ENST00000375687.4:c.716C>T	p.Thr239Ile	p.T239I	ENST00000375687	NM_015338.5	239	aCa/aTa	8/13	0.425226298226834	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.575713368187455	4		388	595	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670849	134670849	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	143	528	0	ENST00000398015.3:c.760A>T	p.Thr254Ser	p.T254S	ENST00000398015	NM_004441.4	254	Acc/Tcc	3/16	0.234038111970676	5	FACETS	1	0.973	1	0.388	0.354	0.424	INDETERMINATE	1	TRUE	2	0.575713368187455	5		528	795	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504402	186504402	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	174	358	0	ENST00000323963.5:c.739A>G	p.Ile247Val	p.I247V	ENST00000323963		247	Atc/Gtc	7/11	0.234038111970676	5	FACETS	1	0.969	1	0.721	0.668	0.774	INDETERMINATE	2	TRUE	2	0.575713368187455	5		358	521	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524553	187524553	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	227	482	0	ENST00000441802.2:c.11127del	p.Lys3709AsnfsTer11	p.K3709Nfs*11	ENST00000441802	NM_005245.3	3709	aaA/aa	19/27	0.561803010118748	2	FACETS	0.808	0.761	0.855	0.808	0.761	0.855	CLONAL	2	TRUE	0	0.575713368187455	2		482	488	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963120	38963120	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	218	394	0	ENST00000357387.3:c.1424G>C	p.Cys475Ser	p.C475S	ENST00000357387	NM_152756.3	475	tGt/tCt	17/38	0.575713368187455	5	FACETS	0.825	0.769	0.883	0.55	0.512	0.589	CLONAL	2	TRUE	2	0.575713368187455	5		394	855	SUCCESS
APC	324	MSKCC	GRCh37	5	112174791	112174791	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	337	532	0	ENST00000257430.4:c.3500A>C	p.Asn1167Thr	p.N1167T	ENST00000257430	NM_000038.5	1167	aAt/aCt	16/16	0.561803010118748	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.575713368187455	2		532	561	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677798	117677798	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1248711517	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	187	402	0	ENST00000368508.3:c.4135A>G	p.Met1379Val	p.M1379V	ENST00000368508	NM_002944.2	1379	Atg/Gtg	25/43	0.268818833773238	3	FACETS	0.9	0.84	0.96	0.9	0.84	0.96	INDETERMINATE	2	TRUE	1	0.575713368187455	3		402	465	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161970029	161970029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751095098	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	122	413	0	ENST00000366898.1:c.940C>T	p.Arg314Trp	p.R314W	ENST00000366898	NM_004562.2	314	Cgg/Tgg	9/12	0.268818833773238	3	FACETS	1	0.959	1	0.549	0.499	0.601	INDETERMINATE	1	TRUE	1	0.575713368187455	3		413	497	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140549976	140549976	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	246	365	0	ENST00000288602.6:c.175G>T	p.Glu59Ter	p.E59*	ENST00000288602	NM_004333.4	59	Gaa/Taa	2/18	0.56153529752832	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.575713368187455	3		365	538	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213524	27213525	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	272	431	0	ENST00000380036.4:c.2924dup	p.Asn975LysfsTer46	p.N975Kfs*46	ENST00000380036	NM_000459.3	974	gaa/gAaa	18/23	0.575713368187455	2	FACETS	0.997	0.95	1	0.997	0.95	1	CLONAL	2	TRUE	0	0.575713368187455	2		431	474	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939954	76939954	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	164	264	0	ENST00000373344.5:c.794G>T	p.Cys265Phe	p.C265F	ENST00000373344	NM_000489.3	265	tGc/tTc	9/35	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.575713368187455	1		264	291	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0062204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	14	426	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.717	0.517	0.961	0.717	0.517	0.961	CLONAL	1	TRUE	1	0.11	2		426	355	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0062204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	19	761	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.577	0.436	0.744	0.577	0.436	0.744	SUBCLONAL	1	TRUE	1	0.11	2		761	599	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0062204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	20	476	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.648	0.494	0.83	0.648	0.494	0.83	SUBCLONAL	1	TRUE	1	0.11	2		476	561	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710553	114710554	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGCCA	novel	NA	P-0062204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	34	509	0	ENST00000543371.1:c.39_43dup	p.Asn15ThrfsTer6	p.N15Tfs*6	ENST00000543371	NM_001198531.1	13	ggc/ggCGCCAc	1/14	1	2	FACETS	0.975	0.795	1	0.975	0.795	1	CLONAL	1	TRUE	1	0.11	2		509	634	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564973	226564973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	75	502	0	ENST00000366794.5:c.1777G>C	p.Gly593Arg	p.G593R	ENST00000366794	NM_001618.3	593	Ggt/Cgt	13/23	0.145530305427804	5	FACETS	0.844	0.738	0.96	0.211	0.184	0.24	CLONAL	1	TRUE	1	0.217838689876592	5		502	1082	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0062206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	151	311	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.217838689876592	2	FACETS	0.905	0.828	0.985	0.905	0.828	0.985	CLONAL	2	TRUE	0	0.217838689876592	2		311	766	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857784	9857784	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	66	679	0	ENST00000330684.3:c.3617G>C	p.Arg1206Pro	p.R1206P	ENST00000330684	NM_001134407.1	1206	cGa/cCa	13/13	0.136867221021616	3	FACETS	0.654	0.566	0.751	0.327	0.283	0.376	SUBCLONAL	1	TRUE	1	0.217838689876592	3		679	1027	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688784	47688808	+	frameshift_variant	Frame_Shift_Del	DEL	GCCAGAAATGTTGACAGAATCTTGC	GCCAGAAATGTTGACAGAATCTTGC	-	novel	NA	P-0062206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	155	373	0	ENST00000347630.2:c.492_516del	p.Gln165ArgfsTer4	p.Q165Rfs*4	ENST00000347630	NM_001007230.1	164	gtGCAAGATTCTGTCAACATTTCTGGC/gt	7/11	0.183933488068979	4	FACETS	1	0.924	1	0.505	0.462	0.55	CLONAL	2	TRUE	0	0.217838689876592	4		373	858	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	896831	896831	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	63	514	0	ENST00000166345.3:c.310G>A	p.Glu104Lys	p.E104K	ENST00000166345	NM_004237.3	104	Gaa/Aaa	3/13	0.217838689876592	0	FACETS	0.551	0.475	0.634			1	SUBCLONAL	1	TRUE	0	0.217838689876592	0		514	821	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198272771	198272771	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	99	371	0	ENST00000335508.6:c.1190G>A	p.Arg397His	p.R397H	ENST00000335508	NM_012433.2	397	cGc/cAc	9/25	1	2	FACETS	0.814	0.729	0.904	0.814	0.729	0.904	CLONAL	1	TRUE	1	0.464233560131741	2		371	524	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089620	27089620	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1217715911	NA	P-0062208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	137	626	0	ENST00000324856.7:c.2576G>C	p.Ser859Thr	p.S859T	ENST00000324856	NM_006015.4	859	aGt/aCt	8/20	0.464233560131741	1	FACETS	0.899	0.823	0.978	0.899	0.823	0.978	CLONAL	1	TRUE	0	0.464233560131741	1		626	504	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992148	11992148	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	283	498	0	ENST00000396373.4:c.238A>G	p.Arg80Gly	p.R80G	ENST00000396373	NM_001987.4	80	Agg/Ggg	3/8	0.464233560131741	3	FACETS	0.876	0.826	0.928	0.876	0.826	0.928	CLONAL	2	TRUE	1	0.464233560131741	3		498	857	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431193	49431193	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	294	686	0	ENST00000301067.7:c.9946G>C	p.Gly3316Arg	p.G3316R	ENST00000301067	NM_003482.3	3316	Ggt/Cgt	34/54	0.464233560131741	3	FACETS	0.922	0.871	0.974	0.922	0.871	0.974	CLONAL	2	TRUE	1	0.464233560131741	3		686	846	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183864	10183864	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	83	445	0	ENST00000256474.2:c.333C>A	p.Ser111Arg	p.S111R	ENST00000256474	NM_000551.3	111	agC/agA	1/3	0.432193658657247	1	FACETS	0.756	0.672	0.845	0.756	0.672	0.845	SUBCLONAL	1	TRUE	0	0.464233560131741	1		445	363	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637697	52637697	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0062208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	98	326	0	ENST00000394830.3:c.2619del	p.Ile875PhefsTer40	p.I875Ffs*40	ENST00000394830	NM_018313.4	873	atT/at	18/30	0.432193658657247	1	FACETS	0.795	0.714	0.879	0.795	0.714	0.879	SUBCLONAL	1	TRUE	0	0.464233560131741	1		326	408	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000366	42000366	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0062209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	72	406	0	ENST00000219905.7:c.2385G>A	p.Trp795Ter	p.W795*	ENST00000219905	NM_001164273.1	795	tgG/tgA	7/24	1	2	FACETS	0.767	0.67	0.873	0.767	0.67	0.873	SUBCLONAL	1	TRUE	1	0.26	2		406	722	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094321	193094321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	111	489	0	ENST00000367435.3:c.211C>T	p.His71Tyr	p.H71Y	ENST00000367435	NM_024529.4	71	Cat/Tat	2/17	0.224680247701843	3	FACETS	1	0.976	1	0.641	0.576	0.709	CLONAL	1	TRUE	1	0.26	3		489	753	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021360	42021360	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0062209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	76	532	0	ENST00000219905.7:c.3658-2A>G		p.X1220_splice	ENST00000219905	NM_001164273.1	1220			1	2	FACETS	0.783	0.686	0.887	0.783	0.686	0.887	SUBCLONAL	1	TRUE	1	0.26	2		532	747	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0062209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	95	387	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.26	2		388	576	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448552	89448552	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	110	618	0	ENST00000336596.2:c.1516G>T	p.Val506Leu	p.V506L	ENST00000336596	NM_005233.5	506	Gta/Tta	7/17	1	2	FACETS	0.892	0.8	0.989	0.892	0.8	0.989	CLONAL	1	TRUE	1	0.26	2		618	949	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81340830	81340830	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0062209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	55	229	0	ENST00000222390.5:c.1411G>C	p.Gly471Arg	p.G471R	ENST00000222390	NM_000601.4	471	Ggt/Cgt	12/18	1	2	FACETS	0.998	0.856	1	0.998	0.856	1	CLONAL	1	TRUE	1	0.26	2		229	424	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938041	76938041	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0062209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	83	577	0	ENST00000373344.5:c.2707del	p.Glu903AsnfsTer2	p.E903Nfs*2	ENST00000373344	NM_000489.3	903	Gaa/aa	9/35	1	2	FACETS	0.762	0.671	0.859	0.762	0.671	0.859	SUBCLONAL	1	TRUE	1	0.26	2		577	838	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0062210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	281	567	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	0.453697738306986	4	FACETS	0.925	0.871	0.979	0.925	0.871	0.979	CLONAL	2	TRUE	2	0.521126709713309	4		567	887	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061207	38061207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	319	788	0	ENST00000250448.2:c.782G>A	p.Arg261His	p.R261H	ENST00000250448	NM_004496.3	261	cGc/cAc	2/2	0.212797753928535	6	FACETS	0.936	0.887	0.987	0.936	0.887	0.987	INDETERMINATE	3	TRUE	3	0.521126709713309	6		788	890	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204515968	204515968	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0062210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	195	342	0	ENST00000367182.3:c.866C>A	p.Ser289Tyr	p.S289Y	ENST00000367182	NM_001278516.1	289	tCc/tAc	10/11	0.491836676406332	3	FACETS	0.953	0.89	1	0.953	0.89	1	CLONAL	2	TRUE	1	0.521126709713309	3		342	495	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060805	38060805	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0062210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	361	840	1	ENST00000250448.2:c.1184C>A	p.Ser395Tyr	p.S395Y	ENST00000250448	NM_004496.3	395	tCc/tAc	2/2	0.212797753928535	6	FACETS	0.927	0.881	0.974	0.927	0.881	0.974	INDETERMINATE	3	TRUE	3	0.521126709713309	6		841	1017	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030884	36030884	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0062210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	276	630	1	ENST00000358208.4:c.1163G>A	p.Arg388Gln	p.R388Q	ENST00000358208		388	cGg/cAg	10/12	0.453697738306986	4	FACETS	0.942	0.887	0.998	0.942	0.887	0.998	CLONAL	2	TRUE	2	0.521126709713309	4		631	855	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577466	64577466	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062211-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	462	828	0	ENST00000312049.6:c.116T>G	p.Leu39Trp	p.L39W	ENST00000312049	NM_130799.2	39	tTg/tGg	2/10	0.867984296252658	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.867984296252658	1		828	560	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939651	76939651	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0062211-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	354	694	0	ENST00000373344.5:c.1097T>G	p.Met366Arg	p.M366R	ENST00000373344	NM_000489.3	366	aTg/aGg	9/35	0.867984296252658	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.867984296252658	1		694	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0062212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	292	954	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.900583969679397	4	FACETS	0.994	0.977	1	0.994	0.977	1	CLONAL	4	FALSE	0	0.911540082240442	4		954	308	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631102	69631102	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121917704	NA	P-0062212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	66	570	1	ENST00000334134.2:c.310C>T	p.Arg104Ter	p.R104*	ENST00000334134	NM_005247.2	104	Cga/Tga	2/3	0.320420458096358	1	FACETS	0.536	0.478	0.595	0.536	0.478	0.595	INDETERMINATE	1	FALSE	0	0.911540082240442	1		571	147	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487154	56487154	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0062212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	282	507	0	ENST00000267101.3:c.1300A>G	p.Lys434Glu	p.K434E	ENST00000267101	NM_001982.3	434	Aag/Gag	12/28	0.911540082240442	6	FACETS	0.954	0.905	1	0.954	0.905	1	CLONAL	3	FALSE	3	0.911540082240442	6		507	610	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423424	47423424	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0062212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	846	521	0	ENST00000404338.3:c.1492G>T	p.Glu498Ter	p.E498*	ENST00000404338	NM_004491.4	498	Gaa/Taa	1/6	0.911540082240442	8	FACETS	0.997	0.99	1	1	0.999	1	CLONAL	8	FALSE	1	0.911540082240442	8		521	869	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000514-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	167	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.522636416060276	5	FACETS	1	0.979	1	0.768	0.711	0.826	CLONAL	2	TRUE	2	0.520964374933279	5		336	496	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0000514-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	140	311	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.437220879232097	3	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.520964374933279	3		311	459	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771321	68771321	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs878854691	NA	P-0000514-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	102	156	0	ENST00000261769.5:c.3G>A	p.Met1?	p.M1?	ENST00000261769	NM_004360.3	1	atG/atA	1/16	0.488895357830743	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.520964374933279	2		156	174	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0000836-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	221	365	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		365	981	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0001293-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	327	562	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.470214215267008	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.470214215267008	1		562	900	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012397	176012397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001293-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	123	494	0	ENST00000367669.3:c.1537G>A	p.Glu513Lys	p.E513K	ENST00000367669	NM_022457.5	513	Gag/Aag	14/20	0.248799380858452	1	FACETS	0.388	0.35	0.428	0.388	0.35	0.428	INDETERMINATE	1	TRUE	0	0.470214215267008	1		494	1032	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032271	26032271	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1278314228	NA	P-0001293-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	56	115	0	ENST00000244661.2:c.18G>C	p.Gln6His	p.Q6H	ENST00000244661	NM_003537.3	6	caG/caC	1/1	0.267528159727732	3	FACETS	1	0.943	1	0.588	0.509	0.673	INDETERMINATE	1	TRUE	1	0.470214215267008	3		115	250	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184956	32184956	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001293-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	243	547	0	ENST00000375023.3:c.1712G>C	p.Gly571Ala	p.G571A	ENST00000375023	NM_004557.3	571	gGa/gCa	10/30	0.470214215267008	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.470214215267008	1		547	676	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215854	98215854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001293-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	173	335	0	ENST00000331920.6:c.3355C>G	p.Leu1119Val	p.L1119V	ENST00000331920	NM_000264.3	1119	Ctg/Gtg	20/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.470214215267008	2		335	675	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001396-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	191	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.688456985100111	3	FACETS	1	0.944	1	0.51	0.473	0.549	CLONAL	1	TRUE	1	0.688456985100111	3		336	731	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577524	7577524	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001396-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	404	563	0	ENST00000269305.4:c.757A>C	p.Thr253Pro	p.T253P	ENST00000269305	NM_001126112.2	253	Acc/Ccc	7/11	0.688456985100111	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.688456985100111	2		563	580	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40478169	40478169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1288968449	NA	P-0001396-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	105	364	0	ENST00000264657.5:c.1330G>A	p.Glu444Lys	p.E444K	ENST00000264657	NM_139276.2	444	Gag/Aag	15/24	0.688456985100111	3	FACETS	0.768	0.69	0.849	0.384	0.345	0.425	SUBCLONAL	1	TRUE	1	0.688456985100111	3		364	534	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687586	29687586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001396-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	199	509	0	ENST00000356175.3:c.8179G>A	p.Glu2727Lys	p.E2727K	ENST00000356175	NM_000267.3	2727	Gaa/Aaa	56/57	0.688456985100111	4	FACETS	0.943	0.873	1			1	CLONAL	1	TRUE	NA	0.688456985100111	4		509	1035	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691950	30691950	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001396-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	165	546	0	ENST00000295754.5:c.453del	p.Glu152AsnfsTer11	p.E152Nfs*11	ENST00000295754	NM_003242.5	151	gAa/ga	3/7	1	2	FACETS	0.978	0.906	1	0.978	0.906	1	CLONAL	1	TRUE	1	0.688456985100111	2		546	490	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001847-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	29	345	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.803	0.664	0.952	0.803	0.664	0.952	CLONAL	1	TRUE	1	0.820325911659458	2		345	88	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001847-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	281	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.973	0.92	1	0.973	0.92	1	CLONAL	1	TRUE	1	0.820325911659458	2		336	704	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0001847-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	221	562	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.942	0.884	1	0.942	0.884	1	CLONAL	1	TRUE	1	0.820325911659458	2		562	572	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637717	52637717	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001847-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	291	283	0	ENST00000394830.3:c.2599G>T	p.Glu867Ter	p.E867*	ENST00000394830	NM_018313.4	867	Gaa/Taa	18/30	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.820325911659458	2		283	686	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619135	43619135	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001847-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	225	247	2	ENST00000355710.3:c.2818C>A	p.Leu940Met	p.L940M	ENST00000355710	NM_020975.4	940	Ctg/Atg	17/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.820325911659458	2		249	489	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481845	56481845	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1354914975	NA	P-0001847-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	271	309	0	ENST00000267101.3:c.773G>A	p.Arg258His	p.R258H	ENST00000267101	NM_001982.3	258	cGc/cAc	7/28	1	2	FACETS	0.983	0.929	1	0.983	0.929	1	CLONAL	1	TRUE	1	0.820325911659458	2		309	672	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756569	756569	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001847-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	201	216	0	ENST00000314574.4:c.259G>C	p.Ala87Pro	p.A87P	ENST00000314574	NM_005433.3	87	Gct/Cct	2/12	1	2	FACETS	0.952	0.89	1	0.952	0.89	1	CLONAL	1	TRUE	1	0.820325911659458	2		216	515	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798210	42798211	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0001847-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	158	216	0	ENST00000575354.2:c.4166_4167del	p.Ser1389LeufsTer51	p.S1389Lfs*51	ENST00000575354	NM_015125.3	1388	ggCTct/ggct	17/20	0.820325911659458	1	FACETS	0.884	0.832	0.935	0.884	0.832	0.935	CLONAL	1	TRUE	0	0.820325911659458	1		216	257	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0002538-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	384	484	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.667543633116044	2		484	538	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42790947	42790947	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002538-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	187	846	0	ENST00000575354.2:c.92C>G	p.Ser31Cys	p.S31C	ENST00000575354	NM_015125.3	31	tCt/tGt	2/20	0.634100912980193	4	FACETS	0.88	0.812	0.95	0.44	0.406	0.475	CLONAL	1	TRUE	2	0.667543633116044	4		846	1062	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213965	2213965	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002538-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	192	785	0	ENST00000398665.3:c.1777C>G	p.Arg593Gly	p.R593G	ENST00000398665	NM_032482.2	593	Cgc/Ggc	18/28	0.667377246124398	2	FACETS	1	0.977	1	0.552	0.515	0.59	CLONAL	1	TRUE	0	0.667543633116044	2		785	521	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805425	32805426	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0002538-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	158	803	0	ENST00000374899.4:c.496_497delinsTT	p.Glu166Leu	p.E166L	ENST00000374899	NM_018833.2	166	GAg/TTg	3/12	0.667377246124398	5	FACETS	0.853	0.78	0.929	0.284	0.26	0.31	CLONAL	1	TRUE	2	0.667543633116044	5		803	1111	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120551	94120551	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002538-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	95	398	0	ENST00000369303.4:c.500T>G	p.Leu167Arg	p.L167R	ENST00000369303	NM_004440.3	167	cTt/cGt	3/17	0.667377246124398	5	FACETS	0.917	0.818	1			1	CLONAL	1	TRUE	NA	0.667543633116044	5		398	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0002804-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	498	627	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.549013891375477	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.549013891375477	2		628	865	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0002804-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	96	289	2	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.549013891375477	2		291	349	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818836	32818836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1226281975	NA	P-0002804-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	232	636	0	ENST00000354258.4:c.1115G>A	p.Arg372Gln	p.R372Q	ENST00000354258	NM_000593.5	372	cGa/cAa	4/11	0.549013891375477	3	FACETS	0.945	0.88	1	0.472	0.44	0.506	CLONAL	1	TRUE	1	0.549013891375477	3		636	1140	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	139	411	0	ENST00000269305.4:c.560-1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.249047280769318	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.249047280769318	1		411	818	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962834	2962834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778151	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	51	515	0	ENST00000396946.4:c.2074G>A	p.Val692Met	p.V692M	ENST00000396946	NM_032415.4	692	Gtg/Atg	16/25	1	2	FACETS	0.446	0.378	0.522	0.446	0.378	0.522	SUBCLONAL	1	TRUE	1	0.249047280769318	2		515	918	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475063	40475063	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	104	641	0	ENST00000264657.5:c.1847A>G	p.Glu616Gly	p.E616G	ENST00000264657	NM_139276.2	616	gAa/gGa	20/24	1	2	FACETS	0.696	0.621	0.776	0.696	0.621	0.776	SUBCLONAL	1	TRUE	1	0.249047280769318	2		641	1200	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495239	212495239	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	161	414	0	ENST00000342788.4:c.2027G>T	p.Arg676Ile	p.R676I	ENST00000342788	NM_005235.2	676	aGa/aTa	17/28	0.249047280769318	3	FACETS	0.895	0.822	0.972	0.895	0.822	0.972	CLONAL	2	TRUE	1	0.249047280769318	3		414	812	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370719	225370719	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	181	410	0	ENST00000264414.4:c.1160A>T	p.Tyr387Phe	p.Y387F	ENST00000264414	NM_003590.4	387	tAc/tTc	8/16	0.249047280769318	3	FACETS	0.965	0.891	1	0.965	0.891	1	CLONAL	2	TRUE	1	0.249047280769318	3		410	847	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972913	55972913	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	57	412	1	ENST00000263923.4:c.1477G>T	p.Gly493Ter	p.G493*	ENST00000263923	NM_002253.2	493	Gga/Tga	11/30	1	2	FACETS	0.627	0.537	0.726	0.627	0.537	0.726	SUBCLONAL	1	TRUE	1	0.249047280769318	2		413	730	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56171080	56171080	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	72	324	0	ENST00000399503.3:c.1908C>G	p.Cys636Trp	p.C636W	ENST00000399503	NM_005921.1	636	tgC/tgG	10/20	1	2	FACETS	0.884	0.772	1	0.884	0.772	1	CLONAL	1	TRUE	1	0.249047280769318	2		324	654	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289543	33289543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	105	402	0	ENST00000374542.5:c.160G>T	p.Gly54Cys	p.G54C	ENST00000374542	NM_001141970.1	54	Ggc/Tgc	2/8	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.249047280769318	2		402	840	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609870	117609870	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1406518415	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	58	557	0	ENST00000368508.3:c.6829C>G	p.Leu2277Val	p.L2277V	ENST00000368508	NM_002944.2	2277	Ctt/Gtt	43/43	1	2	FACETS	0.512	0.438	0.592	0.512	0.438	0.592	SUBCLONAL	1	TRUE	1	0.249047280769318	2		557	910	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730031	41730031	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1244	162	802	0	ENST00000242208.4:c.498G>C	p.Arg166Ser	p.R166S	ENST00000242208	NM_002192.2	166	agG/agC	3/3	1	2	FACETS	0.925	0.846	1	0.925	0.846	1	CLONAL	1	TRUE	1	0.249047280769318	2		802	1406	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92354968	92354968	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	116	371	0	ENST00000265734.4:c.509A>G	p.Tyr170Cys	p.Y170C	ENST00000265734	NM_001259.6	170	tAt/tGt	4/8	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.249047280769318	2		371	822	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151932979	151932979	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	17	52	0	ENST00000262189.6:c.2692G>C	p.Gly898Arg	p.G898R	ENST00000262189	NM_170606.2	898	Ggt/Cgt	16/59	1	2	FACETS	1	0.802	1	1	0.802	1	CLONAL	1	TRUE	1	0.249047280769318	2		52	127	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852044	63852044	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	40	297	0	ENST00000279873.7:c.2822A>C	p.Gln941Pro	p.Q941P	ENST00000279873	NM_032199.2	941	cAg/cCg	10/10	1	2	FACETS	0.668	0.555	0.794	0.668	0.555	0.794	SUBCLONAL	1	TRUE	1	0.249047280769318	2		297	481	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852655	63852655	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	108	370	0	ENST00000279873.7:c.3433G>T	p.Ala1145Ser	p.A1145S	ENST00000279873	NM_032199.2	1145	Gct/Tct	10/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.249047280769318	2		370	757	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659795	88659795	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	34	314	0	ENST00000372037.3:c.442G>A	p.Asp148Asn	p.D148N	ENST00000372037	NM_004329.2	148	Gat/Aat	7/13	1	2	FACETS	0.453	0.369	0.548	0.453	0.369	0.548	SUBCLONAL	1	TRUE	1	0.249047280769318	2		314	603	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742473	17742473	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1288774741	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	59	629	1	ENST00000250003.3:c.655G>A	p.Gly219Ser	p.G219S	ENST00000250003	NM_002478.4	219	Ggc/Agc	2/3	1	2	FACETS	0.601	0.515	0.694	0.601	0.515	0.694	SUBCLONAL	1	TRUE	1	0.249047280769318	2		630	789	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32438037	32438037	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	53	468	0	ENST00000332351.3:c.1000A>C	p.Asn334His	p.N334H	ENST00000332351	NM_024426.4	334	Aac/Cac	5/10	1	2	FACETS	0.49	0.416	0.571	0.49	0.416	0.571	SUBCLONAL	1	TRUE	1	0.249047280769318	2		468	869	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129169	64129169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746466314	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	74	449	0	ENST00000334205.4:c.707C>T	p.Ser236Leu	p.S236L	ENST00000334205	NM_003942.2	236	tCg/tTg	7/17	1	2	FACETS	0.853	0.746	0.968	0.853	0.746	0.968	CLONAL	1	TRUE	1	0.249047280769318	2		449	697	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573210	64573210	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	77	506	0	ENST00000312049.6:c.1082A>G	p.Tyr361Cys	p.Y361C	ENST00000312049	NM_130799.2	361	tAc/tGc	8/10	1	2	FACETS	0.765	0.671	0.867	0.765	0.671	0.867	SUBCLONAL	1	TRUE	1	0.249047280769318	2		506	808	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376287	118376287	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	89	658	0	ENST00000534358.1:c.9680C>G	p.Ser3227Cys	p.S3227C	ENST00000534358	NM_005933.3	3227	tCt/tGt	27/36	1	2	FACETS	0.671	0.593	0.755	0.671	0.593	0.755	SUBCLONAL	1	TRUE	1	0.249047280769318	2		658	1065	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404932	404932	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	71	433	0	ENST00000399788.2:c.4262G>T	p.Arg1421Leu	p.R1421L	ENST00000399788	NM_001042603.1	1421	cGg/cTg	26/28	1	2	FACETS	0.732	0.638	0.834	0.732	0.638	0.834	SUBCLONAL	1	TRUE	1	0.249047280769318	2		433	779	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435020	49435020	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	28	299	0	ENST00000301067.7:c.6533G>T	p.Gly2178Val	p.G2178V	ENST00000301067	NM_003482.3	2178	gGa/gTa	31/54	1	2	FACETS	0.59	0.472	0.725	0.59	0.472	0.725	SUBCLONAL	1	TRUE	1	0.249047280769318	2		299	381	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112127	115112127	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	51	555	0	ENST00000257566.3:c.1613G>T	p.Gly538Val	p.G538V	ENST00000257566	NM_016569.3	538	gGc/gTc	7/8	1	2	FACETS	0.526	0.446	0.615	0.526	0.446	0.615	SUBCLONAL	1	TRUE	1	0.249047280769318	2		555	778	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133234453	133234453	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	80	383	0	ENST00000320574.5:c.3378+1G>T		p.X1126_splice	ENST00000320574	NM_006231.2	1126			1	2	FACETS	0.841	0.74	0.95	0.841	0.74	0.95	CLONAL	1	TRUE	1	0.249047280769318	2		383	764	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008059	29008059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	72	411	0	ENST00000282397.4:c.710C>T	p.Pro237Leu	p.P237L	ENST00000282397	NM_002019.4	237	cCa/cTa	6/30	0.249047280769318	1	FACETS	0.786	0.687	0.893	0.786	0.687	0.893	SUBCLONAL	1	TRUE	0	0.249047280769318	1		411	644	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008333	29008333	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	81	412	0	ENST00000282397.4:c.538G>T	p.Asp180Tyr	p.D180Y	ENST00000282397	NM_002019.4	180	Gat/Tat	5/30	0.249047280769318	1	FACETS	0.873	0.77	0.985	0.873	0.77	0.985	CLONAL	1	TRUE	0	0.249047280769318	1		412	652	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059085	42059085	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	210	815	0	ENST00000219905.7:c.8805G>T	p.Lys2935Asn	p.K2935N	ENST00000219905	NM_001164273.1	2935	aaG/aaT	24/24	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.249047280769318	2		815	1274	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528177	29528177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	100	292	0	ENST00000356175.3:c.1185G>T	p.Lys395Asn	p.K395N	ENST00000356175	NM_000267.3	395	aaG/aaT	10/57	0.0632840547010258	3	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.249047280769318	3		292	647	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557943	29557943	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1555614652	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	30	244	0	ENST00000356175.3:c.3197G>T	p.Arg1066Ile	p.R1066I	ENST00000356175	NM_000267.3	1066	aGa/aTa	24/57	0.0632840547010258	3	FACETS	0.548	0.441	0.671			1	INDETERMINATE	1	TRUE	NA	0.249047280769318	3		244	494	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585461	29585461	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	97	357	0	ENST00000356175.3:c.4210G>T	p.Gly1404Trp	p.G1404W	ENST00000356175	NM_000267.3	1404	Ggg/Tgg	31/57	0.0632840547010258	3	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.249047280769318	3		357	609	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599993	10599993	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	93	564	0	ENST00000171111.5:c.1583A>C	p.Gln528Pro	p.Q528P	ENST00000171111	NM_203500.1	528	cAg/cCg	5/6	0.249047280769318	1	FACETS	0.768	0.682	0.86	0.768	0.682	0.86	SUBCLONAL	1	TRUE	0	0.249047280769318	1		564	851	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308066	30308066	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs776946024	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	88	428	0	ENST00000262643.3:c.203G>T	p.Cys68Phe	p.C68F	ENST00000262643	NM_001238.2	68	tGt/tTt	5/12	0.0632840547010258	3	FACETS	0.919	0.813	1			1	INDETERMINATE	1	TRUE	NA	0.249047280769318	3		428	865	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308356	30308356	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	80	512	0	ENST00000262643.3:c.370G>T	p.Glu124Ter	p.E124*	ENST00000262643	NM_001238.2	124	Gaa/Taa	6/12	0.0632840547010258	3	FACETS	0.706	0.62	0.799			1	INDETERMINATE	1	TRUE	NA	0.249047280769318	3		512	1023	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944509	40944509	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	101	556	0	ENST00000373198.4:c.1993G>T	p.Ala665Ser	p.A665S	ENST00000373198	NM_133170.3	665	Gct/Tct	12/32	1	2	FACETS	0.952	0.85	1	0.952	0.85	1	CLONAL	1	TRUE	1	0.249047280769318	2		556	852	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419951	41419951	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	104	517	0	ENST00000373198.4:c.370G>T	p.Val124Leu	p.V124L	ENST00000373198	NM_133170.3	124	Gtg/Ttg	3/32	1	2	FACETS	0.948	0.848	1	0.948	0.848	1	CLONAL	1	TRUE	1	0.249047280769318	2		517	881	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411621	63411621	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	129	314	0	ENST00000330258.3:c.1546G>C	p.Glu516Gln	p.E516Q	ENST00000330258	NM_152424.3	516	Gag/Cag	2/2	1	1	FACETS	0.828	0.754	0.905	1	0.988	1	CLONAL	2	TRUE	0	0.249047280769318	1		314	548	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344937	70344937	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	129	363	0	ENST00000374080.3:c.2167G>C	p.Gly723Arg	p.G723R	ENST00000374080		723	Ggg/Cgg	15/45	1	1	FACETS	0.838	0.763	0.916	1	0.988	1	CLONAL	2	TRUE	0	0.249047280769318	1		363	541	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964751	15964751	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	153	467	0	ENST00000268712.3:c.5845del	p.Glu1949AsnfsTer27	p.E1949Nfs*27	ENST00000268712	NM_006311.3	1949	Gaa/aa	37/46	0.249047280769318	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.249047280769318	1		467	902	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449776	8449778	+	stop_gained	Nonsense_Mutation	TNP	GTG	GTG	TTT	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	132	409	2	ENST00000356435.5:c.3935_3937delinsAAA	p.Ser1312_His1313delinsTer	p.S1312_H1313delins*	ENST00000356435		1312	tCACac/tAAAac	23/35	0.20785023399335	2	FACETS	1	0.983	1	0.687	0.624	0.754	CLONAL	1	TRUE	0	0.249047280769318	2		411	771	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857926	9857927	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0004863-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	42	414	0	ENST00000330684.3:c.3474_3475delinsAG	p.Phe1158_Arg1159delinsLeuGly	p.F1158_R1159delinsLG	ENST00000330684	NM_001134407.1	1158	ttCCgc/ttAGgc	13/13	1	2	FACETS	0.485	0.404	0.576	0.485	0.404	0.576	SUBCLONAL	1	TRUE	1	0.249047280769318	2		414	695	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	235	698	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.653732036857615	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.655166031531601	1		698	456	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754890	29754890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370848188	NA	P-0005145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	170	363	0	ENST00000389048.3:c.1045G>A	p.Val349Ile	p.V349I	ENST00000389048	NM_004304.4	349	Gtc/Atc	4/29	1	2	FACETS	0.977	0.905	1	0.977	0.905	1	CLONAL	1	TRUE	1	0.655166031531601	2		363	531	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313231	65313231	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	157	352	0	ENST00000342505.4:c.1883A>C	p.His628Pro	p.H628P	ENST00000342505	NM_002227.2	628	cAc/cCc	13/25	1	2	FACETS	0.865	0.797	0.935	0.865	0.797	0.935	CLONAL	1	TRUE	1	0.655166031531601	2		352	554	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167795	56167795	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	186	346	0	ENST00000399503.3:c.1360G>A	p.Glu454Lys	p.E454K	ENST00000399503	NM_005921.1	454	Gaa/Aaa	7/20	0.655166031531601	3	FACETS	1	0.963	1	0.532	0.492	0.572	CLONAL	1	TRUE	1	0.655166031531601	3		346	709	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482843	67482843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	200	416	0	ENST00000327367.4:c.1247C>T	p.Ser416Phe	p.S416F	ENST00000327367	NM_005902.3	416	tCc/tTc	9/9	1	2	FACETS	0.963	0.897	1	0.963	0.897	1	CLONAL	1	TRUE	1	0.655166031531601	2		416	634	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313222	30313222	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	212	474	0	ENST00000262643.3:c.916C>A	p.His306Asn	p.H306N	ENST00000262643	NM_001238.2	306	Cat/Aat	10/12	1	2	FACETS	0.985	0.92	1	0.985	0.92	1	CLONAL	1	TRUE	1	0.655166031531601	2		474	657	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797301	135797301	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	101	219	0	ENST00000298552.3:c.568del	p.Arg190AlafsTer20	p.R190Afs*20	ENST00000298552	NM_001162426.1	190	Cgc/gc	7/23	1	2	FACETS	0.909	0.821	1	0.909	0.821	1	CLONAL	1	TRUE	1	0.655166031531601	2		219	339	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115252290	115252290	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	174	349	0	ENST00000369535.4:c.350A>G	p.Lys117Arg	p.K117R	ENST00000369535	NM_002524.4	117	aAg/aGg	4/7	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.655166031531601	2		349	491	SUCCESS
RET	5979	MSKCC	GRCh37	10	43598035	43598035	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	265	551	3	ENST00000355710.3:c.583T>A	p.Phe195Ile	p.F195I	ENST00000355710	NM_020975.4	195	Ttc/Atc	3/20	1	2	FACETS	0.994	0.935	1	0.994	0.935	1	CLONAL	1	TRUE	1	0.655166031531601	2		554	814	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42002946	42002946	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	177	409	1	ENST00000219905.7:c.2483A>T	p.Asp828Val	p.D828V	ENST00000219905	NM_001164273.1	828	gAt/gTt	8/24	1	2	FACETS	0.927	0.859	0.997	0.927	0.859	0.997	CLONAL	1	TRUE	1	0.655166031531601	2		410	583	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028677	12028677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	159	334	0	ENST00000353533.5:c.880G>A	p.Gly294Arg	p.G294R	ENST00000353533	NM_003010.3	294	Ggg/Agg	8/11	0.655166031531601	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.655166031531601	1		334	324	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69032522	69032522	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0005145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	189	379	0	ENST00000288368.4:c.3595+1G>A		p.X1199_splice	ENST00000288368	NM_024870.2	1199			0.642317488952807	4	FACETS	0.963	0.889	1	0.321	0.296	0.347	CLONAL	1	TRUE	1	0.655166031531601	4		379	992	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033216	69033216	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	214	432	0	ENST00000288368.4:c.3656A>G	p.Lys1219Arg	p.K1219R	ENST00000288368	NM_024870.2	1219	aAg/aGg	30/40	0.642317488952807	4	FACETS	1	0.963	1	0.352	0.327	0.378	CLONAL	1	TRUE	1	0.655166031531601	4		432	1023	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650814	93650814	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	140	295	0	ENST00000375746.1:c.1740A>C	p.Glu580Asp	p.E580D	ENST00000375746	NM_001174167.1	580	gaA/gaC	13/14	1	2	FACETS	0.954	0.876	1	0.954	0.876	1	CLONAL	1	TRUE	1	0.655166031531601	2		295	448	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0005382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	428	478	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	1	2	FACETS	0.995	0.949	1	0.995	0.949	1	CLONAL	1	TRUE	1	0.73	2		478	1179	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106593	27106593	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	273	1006	1	ENST00000324856.7:c.6207del	p.Gln2070SerfsTer65	p.Q2070Sfs*65	ENST00000324856	NM_006015.4	2068	tcG/tc	20/20	1	2	FACETS	0.931	0.874	0.988	0.931	0.874	0.988	CLONAL	1	TRUE	1	0.586150253778233	2		1007	1001	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215772	98215772	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1398400648	NA	P-0006921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	210	603	0	ENST00000331920.6:c.3437A>G	p.Asp1146Gly	p.D1146G	ENST00000331920	NM_000264.3	1146	gAc/gGc	20/24	0.586150253778233	2	FACETS	1	0.949	1	0.51	0.476	0.546	CLONAL	1	TRUE	0	0.586150253778233	2		603	702	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090083	37090083	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	209	585	0	ENST00000231790.2:c.1972C>G	p.Leu658Val	p.L658V	ENST00000231790	NM_000249.3	658	Ctt/Gtt	17/19	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.586150253778233	2		585	686	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936069	49936069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	263	921	0	ENST00000296474.3:c.1601G>A	p.Gly534Glu	p.G534E	ENST00000296474	NM_002447.2	534	gGg/gAg	4/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.586150253778233	2		921	832	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003746	45003746	+	start_lost	Translation_Start_Site	SNP	T	T	G	rs1057519879	NA	P-0006921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	166	634	0	ENST00000558401.1:c.2T>G	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	aTg/aGg	1/4	1	2	FACETS	0.877	0.808	0.948	0.877	0.808	0.948	CLONAL	1	TRUE	1	0.586150253778233	2		634	646	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102116	27102116	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	178	753	0	ENST00000324856.7:c.5042T>C	p.Leu1681Pro	p.L1681P	ENST00000324856	NM_006015.4	1681	cTg/cCg	19/20	1	2	FACETS	0.815	0.753	0.88	0.815	0.753	0.88	CLONAL	1	TRUE	1	0.586150253778233	2		753	745	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120508129	120508129	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	234	623	0	ENST00000256646.2:c.1628A>C	p.Asn543Thr	p.N543T	ENST00000256646	NM_024408.3	543	aAt/aCt	10/34	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.586150253778233	2		623	709	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175794	176175795	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	185	626	0	ENST00000367669.3:c.320_321insT	p.Ser108GlnfsTer34	p.S108Qfs*34	ENST00000367669	NM_022457.5	107	ggc/ggTc	1/20	0.586150253778233	3	FACETS	1	0.925	1	0.5	0.462	0.539	CLONAL	1	TRUE	1	0.586150253778233	3		626	816	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557677	95557677	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	179	657	0	ENST00000393063.1:c.5390A>C	p.Glu1797Ala	p.E1797A	ENST00000393063	NM_030621.3	1797	gAg/gCg	26/28	1	2	FACETS	0.973	0.901	1	0.973	0.901	1	CLONAL	1	TRUE	1	0.586150253778233	2		657	628	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614527	38614527	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	155	494	0	ENST00000299084.4:c.293A>C	p.Lys98Thr	p.K98T	ENST00000299084	NM_152594.2	98	aAg/aCg	3/7	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.586150253778233	2		494	425	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041020	42041020	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	256	872	0	ENST00000219905.7:c.5398T>G	p.Leu1800Val	p.L1800V	ENST00000219905	NM_001164273.1	1800	Tta/Gta	16/24	1	2	FACETS	0.981	0.921	1	0.981	0.921	1	CLONAL	1	TRUE	1	0.586150253778233	2		872	890	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701234	43701234	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	298	847	0	ENST00000382044.4:c.5461T>G	p.Phe1821Val	p.F1821V	ENST00000382044	NM_001141980.1	1821	Ttc/Gtc	26/28	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.586150253778233	2		847	902	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136273	2136273	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	99	864	0	ENST00000219476.3:c.4742T>A	p.Leu1581His	p.L1581H	ENST00000219476	NM_000548.3	1581	cTc/cAc	37/42	1	2	FACETS	0.421	0.376	0.47	0.421	0.376	0.47	SUBCLONAL	1	TRUE	1	0.586150253778233	2		864	802	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14016011	14016011	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	174	561	0	ENST00000311895.7:c.331A>C	p.Ser111Arg	p.S111R	ENST00000311895	NM_005236.2	111	Agt/Cgt	2/11	1	2	FACETS	0.925	0.855	0.997	0.925	0.855	0.997	CLONAL	1	TRUE	1	0.586150253778233	2		561	642	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641653	23641653	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	220	659	0	ENST00000261584.4:c.1822A>G	p.Ser608Gly	p.S608G	ENST00000261584	NM_024675.3	608	Agt/Ggt	5/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.586150253778233	2		659	715	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650792	37650792	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	50	601	0	ENST00000447079.4:c.2264T>G	p.Leu755Arg	p.L755R	ENST00000447079	NM_015083.1	755	cTg/cGg	5/14	1	2	FACETS	0.245	0.208	0.287	0.245	0.208	0.287	SUBCLONAL	1	TRUE	1	0.586150253778233	2		601	695	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414961	56414961	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	156	631	0	ENST00000348428.3:c.2362T>G	p.Ser788Ala	p.S788A	ENST00000348428	NM_006785.3	788	Tca/Gca	17/17	1	2	FACETS	0.81	0.744	0.879	0.81	0.744	0.879	CLONAL	1	TRUE	1	0.586150253778233	2		631	657	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211246	36211246	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	304	878	0	ENST00000222270.7:c.997G>T	p.Glu333Ter	p.E333*	ENST00000222270	NM_014727.1	333	Gag/Tag	3/37	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.586150253778233	2		878	953	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225338962	225338962	+	stop_lost	Nonstop_Mutation	SNP	T	T	G	novel	NA	P-0006921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	126	565	0	ENST00000264414.4:c.2307A>C	p.Ter769TyrextTer22	p.*769Yext*22	ENST00000264414	NM_003590.4	769	taA/taC	16/16	1	2	FACETS	0.855	0.778	0.934	0.855	0.778	0.934	CLONAL	1	TRUE	1	0.586150253778233	2		565	503	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574619	41574619	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	306	988	0	ENST00000263253.7:c.6904T>C	p.Ser2302Pro	p.S2302P	ENST00000263253	NM_001429.3	2302	Tct/Cct	31/31	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.586150253778233	2		988	955	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939827	49939827	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	231	742	0	ENST00000296474.3:c.1216T>G	p.Phe406Val	p.F406V	ENST00000296474	NM_002447.2	406	Ttt/Gtt	1/20	1	2	FACETS	0.994	0.929	1	0.994	0.929	1	CLONAL	1	TRUE	1	0.586150253778233	2		742	793	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531031	187531031	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	116	749	0	ENST00000441802.2:c.9992A>C	p.Asn3331Thr	p.N3331T	ENST00000441802	NM_005245.3	3331	aAt/aCt	15/27	1	2	FACETS	0.513	0.463	0.567	0.513	0.463	0.567	SUBCLONAL	1	TRUE	1	0.586150253778233	2		749	771	SUCCESS
APC	324	MSKCC	GRCh37	5	112177885	112177886	+	missense_variant	Missense_Mutation	DNP	GA	GA	TG	novel	NA	P-0006921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	189	661	0	ENST00000257430.4:c.6594_6595delinsTG	p.Leu2198_Ile2199delinsPheVal	p.L2198_I2199delinsFV	ENST00000257430	NM_000038.5	2198	ttGAtt/ttTGtt	16/16	1	2	FACETS	0.859	0.796	0.924	0.859	0.796	0.924	CLONAL	1	TRUE	1	0.586150253778233	2		661	751	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638430	117638430	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	224	722	0	ENST00000368508.3:c.6011T>G	p.Phe2004Cys	p.F2004C	ENST00000368508	NM_002944.2	2004	tTt/tGt	38/43	0.586150253778233	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.586150253778233	1		722	527	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	512	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.305519978685533	3	FACETS	0.831	0.796	0.866	0.831	0.796	0.866	INDETERMINATE	2	TRUE	1	0.570011394040581	3		473	1389	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0007512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	509	358	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.570011394040581	2		359	1533	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0007512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	414	349	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.291779080297938	1	FACETS	0.856	0.816	0.897	0.856	0.816	0.897	INDETERMINATE	1	TRUE	0	0.570011394040581	1		349	1213	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484610	57484610	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007512-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	337	222	0	ENST00000371085.3:c.694C>T	p.Arg232Cys	p.R232C	ENST00000371085	NM_000516.4	232	Cgc/Tgc	9/13	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.570011394040581	2		222	1006	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0007866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	267	484	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.326196054385063	3	FACETS	0.908	0.859	0.958	0.908	0.859	0.958	CLONAL	3	TRUE	0	0.383423281799443	3		484	609	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0007866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	40	201	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.368562295353352	3	FACETS	1	0.944	1	0.821	0.704	0.941	CLONAL	2	TRUE	0	0.383423281799443	3		201	101	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200723	128200723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	298	764	0	ENST00000341105.2:c.1082G>A	p.Arg361His	p.R361H	ENST00000341105	NM_032638.4	361	cGc/cAc	5/6	0.305391279836264	4	FACETS	0.919	0.87	0.969	1	0.993	1	CLONAL	3	TRUE	2	0.383423281799443	4		764	780	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735547	40735547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756810336	NA	P-0007866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	404	534	0	ENST00000373198.4:c.3326G>A	p.Arg1109Gln	p.R1109Q	ENST00000373198	NM_133170.3	1109	cGg/cAg	25/32	0.383423281799443	8	FACETS	1	0.986	1	0.89	0.851	0.928	CLONAL	5	TRUE	2	0.383423281799443	8		534	849	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281149	46281149	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0007866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	61	411	0	ENST00000371998.3:c.3947-1G>A		p.X1316_splice	ENST00000371998		1316			0.383423281799443	14	FACETS	0.837	0.722	0.963	0.152	0.131	0.176	CLONAL	2	TRUE	3	0.383423281799443	14		411	627	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784292	43784292	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	67	567	1	ENST00000382044.4:c.194A>T	p.Asp65Val	p.D65V	ENST00000382044	NM_001141980.1	65	gAt/gTt	3/28	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.383423281799443	2		568	276	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609727	117609727	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	37	550	0	ENST00000368508.3:c.6972C>A	p.Cys2324Ter	p.C2324*	ENST00000368508	NM_002944.2	2324	tgC/tgA	43/43	0.383423281799443	4	FACETS	0.534	0.44	0.64	0.267	0.22	0.32	SUBCLONAL	1	TRUE	2	0.383423281799443	4		550	500	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349990	15349990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762877879	NA	P-0008008-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	47	503	2	ENST00000263377.2:c.3662G>A	p.Ser1221Asn	p.S1221N	ENST00000263377	NM_058243.2	1221	aGc/aAc	18/20	0.256663383758421	1	FACETS	0.349	0.294	0.41	0.349	0.294	0.41	SUBCLONAL	1	TRUE	0	0.39	1		505	556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0008846-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	45	699	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.994	0.84	1	0.994	0.84	1	CLONAL	1	FALSE	1	0.309110901496473	2		699	293	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119091	70119092	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CACT	novel	NA	P-0008846-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	9	602	0	ENST00000245479.2:c.665_668dup	p.Pro224LeufsTer29	p.P224Lfs*29	ENST00000245479	NM_000346.3	221	-/CACT	2/3	1	2	FACETS	0.197	0.13	0.284	0.197	0.13	0.284	SUBCLONAL	1	FALSE	1	0.309110901496473	2		602	295	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419923	+	missense_variant	Missense_Mutation	DNP	TA	TA	CC	novel	NA	P-0008846-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	8	615	0	ENST00000206249.3:c.1609_1610delinsCC	p.Tyr537Pro	p.Y537P	ENST00000206249	NM_000125.3	537	TAt/CCt	8/8	1	2	FACETS	0.165	0.106	0.243	0.165	0.106	0.243	SUBCLONAL	1	FALSE	1	0.309110901496473	2		615	313	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0009193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	63	562	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.214346463013184	2		562	406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0009193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	335	760	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			NA	2	FACETS	1	0.987	1			1	INDETERMINATE	3	TRUE	NA	0.214346463013184	2		760	933	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939511	76939511	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	31	352	0	ENST00000373344.5:c.1237T>G	p.Leu413Val	p.L413V	ENST00000373344	NM_000489.3	413	Tta/Gta	9/35	1	1	FACETS	0.541	0.437	0.66	0.541	0.437	0.66	SUBCLONAL	1	TRUE	0	0.214346463013184	1		352	477	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939518	76939518	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	32	360	0	ENST00000373344.5:c.1230A>T	p.Glu410Asp	p.E410D	ENST00000373344	NM_000489.3	410	gaA/gaT	9/35	1	1	FACETS	0.583	0.473	0.708	0.583	0.473	0.708	SUBCLONAL	1	TRUE	0	0.214346463013184	1		360	457	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939725	76939725	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0009193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	31	395	0	ENST00000373344.5:c.1023C>G	p.Tyr341Ter	p.Y341*	ENST00000373344	NM_000489.3	341	taC/taG	9/35	1	1	FACETS	0.534	0.431	0.65	0.534	0.431	0.65	SUBCLONAL	1	TRUE	0	0.214346463013184	1		395	484	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937602	76937602	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	51	321	0	ENST00000373344.5:c.3146del	p.Ile1049LysfsTer69	p.I1049Kfs*69	ENST00000373344	NM_000489.3	1049	aTa/aa	9/35	1	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.214346463013184	1		321	291	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0009202-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	524	456	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.509069034960719	2	FACETS	0.972	0.936	1	0.972	0.936	1	CLONAL	2	TRUE	0	0.506368127267352	2		456	1065	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748132	72748132	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009202-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	310	641	0	ENST00000357731.5:c.46T>G	p.Trp16Gly	p.W16G	ENST00000357731	NM_173808.2	16	Tgg/Ggg	1/7	0.509069034960719	2	FACETS	1	0.994	1	0.713	0.674	0.752	CLONAL	1	TRUE	0	0.506368127267352	2		641	859	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729635	162729635	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009202-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	263	708	0	ENST00000367921.3:c.721G>C	p.Asp241His	p.D241H	ENST00000367921	NM_006182.2	241	Gat/Cat	8/18	0.364633496301568	6	FACETS	1	0.992	1	0.472	0.441	0.504	CLONAL	1	TRUE	3	0.506368127267352	6		708	1477	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437170	121437170	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009202-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	113	730	0	ENST00000257555.6:c.1601C>G	p.Ala534Gly	p.A534G	ENST00000257555		534	gCc/gGc	8/10	0.509069034960719	3	FACETS	0.459	0.412	0.51	0.23	0.206	0.255	SUBCLONAL	1	TRUE	1	0.506368127267352	3		730	1218	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212555	133212555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009202-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	391	601	0	ENST00000320574.5:c.5734G>A	p.Glu1912Lys	p.E1912K	ENST00000320574	NM_006231.2	1912	Gaa/Aaa	42/49	0.509069034960719	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.506368127267352	3		601	934	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680659	88680659	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009202-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	168	441	0	ENST00000360948.2:c.598T>C	p.Phe200Leu	p.F200L	ENST00000360948	NM_001012338.2	200	Ttc/Ctc	6/19	0.509069034960719	4	FACETS	0.939	0.862	1	0.313	0.287	0.34	CLONAL	1	TRUE	1	0.506368127267352	4		441	1065	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467868	99467868	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009202-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	259	624	0	ENST00000268035.6:c.2737A>T	p.Asn913Tyr	p.N913Y	ENST00000268035	NM_000875.3	913	Aat/Tat	13/21	0.509069034960719	4	FACETS	1	0.985	1	0.393	0.367	0.419	CLONAL	1	TRUE	1	0.506368127267352	4		624	1308	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867265	68867265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121964872	NA	P-0009202-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	602	615	0	ENST00000261769.5:c.2512A>G	p.Ser838Gly	p.S838G	ENST00000261769	NM_004360.3	838	Agc/Ggc	16/16	0.281307635253745	5	FACETS	0.996	0.96	1	0.996	0.96	1	INDETERMINATE	3	TRUE	2	0.506368127267352	5		615	1400	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819671	81819671	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009202-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	388	606	0	ENST00000359376.3:c.77C>A	p.Thr26Lys	p.T26K	ENST00000359376	NM_002661.3	26	aCg/aAg	2/33	0.281307635253745	5	FACETS	0.835	0.794	0.875	0.835	0.794	0.875	INDETERMINATE	3	TRUE	2	0.506368127267352	5		606	1077	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346165	89346165	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009202-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	374	765	0	ENST00000301030.4:c.6785G>C	p.Gly2262Ala	p.G2262A	ENST00000301030	NM_001256183.1	2262	gGc/gCc	9/13	0.281307635253745	5	FACETS	0.936	0.887	0.985	0.624	0.591	0.657	INDETERMINATE	2	TRUE	2	0.506368127267352	5		765	1389	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667819	37667819	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009202-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	100	485	0	ENST00000447079.4:c.2704C>G	p.Arg902Gly	p.R902G	ENST00000447079	NM_015083.1	902	Cga/Gga	8/14	0.281307635253745	5	FACETS	0.739	0.659	0.824	0.246	0.219	0.275	INDETERMINATE	1	TRUE	2	0.506368127267352	5		485	941	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218443	36218444	+	missense_variant	Missense_Mutation	DNP	GC	GC	TA	novel	NA	P-0009202-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	201	668	1	ENST00000222270.7:c.4222_4223delinsTA	p.Ala1408Tyr	p.A1408Y	ENST00000222270	NM_014727.1	1408	GCc/TAc	16/37	0.509069034960719	4	FACETS	0.904	0.836	0.975	0.226	0.209	0.244	CLONAL	1	TRUE	0	0.506368127267352	4		669	1323	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086008	16086008	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009202-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	415	623	0	ENST00000281043.3:c.1184A>T	p.Asn395Ile	p.N395I	ENST00000281043	NM_005378.4	395	aAc/aTc	3/3	0.278427227152414	5	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.506368127267352	5		623	1235	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031910	26031910	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs199881140	NA	P-0009202-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1410	265	770	0	ENST00000244661.2:c.379C>G	p.Leu127Val	p.L127V	ENST00000244661	NM_003537.3	127	Ctc/Gtc	1/1	0.509069034960719	4	FACETS	0.941	0.879	1	0.314	0.293	0.335	CLONAL	1	TRUE	1	0.506368127267352	4		770	1675	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170249	32170249	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009202-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	824	756	0	ENST00000375023.3:c.3359A>C	p.Tyr1120Ser	p.Y1120S	ENST00000375023	NM_004557.3	1120	tAt/tCt	21/30	0.509069034960719	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	1	0.506368127267352	4		756	1586	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157454284	157454284	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554301240	NA	P-0009202-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	45	587	0	ENST00000346085.5:c.2494C>T	p.Gln832Ter	p.Q832*	ENST00000346085	NM_020732.3	832	Cag/Tag	8/20	0.509069034960719	3	FACETS	0.247	0.207	0.293	0.124	0.103	0.147	SUBCLONAL	1	TRUE	1	0.506368127267352	3		587	900	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431596	6431596	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009202-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	34	248	0	ENST00000356142.4:c.149C>A	p.Pro50Gln	p.P50Q	ENST00000356142	NM_018890.3	50	cCg/cAg	3/7	0.358065973520817	4	FACETS	0.473	0.386	0.57	0.236	0.193	0.285	SUBCLONAL	1	TRUE	2	0.506368127267352	4		248	428	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417493	139417494	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	A	novel	NA	P-0009202-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	705	797	0	ENST00000277541.6:c.550_551delinsT	p.Gln184Ter	p.Q184*	ENST00000277541	NM_017617.3	184	CAg/Tg	4/34	0.509069034960719	3	FACETS	0.964	0.936	0.992	0.964	0.936	0.992	CLONAL	3	TRUE	0	0.506368127267352	3		797	1207	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034416	47034416	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0009748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	285	515	0	ENST00000377604.3:c.503-2A>T		p.X168_splice	ENST00000377604	NM_001204468.1	168			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.373834216048585	2		515	1411	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992135	72992135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1589	346	743	0	ENST00000268489.5:c.1910G>A	p.Gly637Glu	p.G637E	ENST00000268489	NM_006885.3	637	gGg/gAg	2/10	1	2	FACETS	0.957	0.902	1	0.957	0.902	1	CLONAL	1	TRUE	1	0.373834216048585	2		743	1935	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717730	89717731	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0009748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	154	295	0	ENST00000371953.3:c.757_758del	p.Ile253GlnfsTer44	p.I253Qfs*44	ENST00000371953	NM_000314.4	252	gAT/g	7/9	0.369488302723403	1	FACETS	0.852	0.781	0.927	0.852	0.781	0.927	CLONAL	1	TRUE	0	0.373834216048585	1		295	786	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974745	21974747	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	novel	NA	P-0009748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	144	310	0	ENST00000304494.5:c.80_82del	p.Glu27del	p.E27del	ENST00000304494	NM_000077.4	27	gAGGtg/gtg	1/3	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.373834216048585	2		310	678	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0010341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	233	735	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.586008725867842	1	FACETS	0.858	0.805	0.912	0.858	0.805	0.912	CLONAL	1	TRUE	0	0.586008725867842	1		735	655	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0010341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	151	290	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.821	0.753	0.891	0.821	0.753	0.891	CLONAL	1	TRUE	1	0.586008725867842	2		290	628	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175528	108175528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs376603775	NA	P-0010341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	182	319	0	ENST00000278616.4:c.5623C>T	p.Arg1875Ter	p.R1875*	ENST00000278616	NM_000051.3	1875	Cga/Tga	37/63	1	2	FACETS	0.847	0.784	0.913	0.847	0.784	0.913	CLONAL	1	TRUE	1	0.586008725867842	2		319	733	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954221	48954238	+	splice_donor_variant,intron_variant	Splice_Site	DEL	GTAAATTTTTTACTTTTA	GTAAATTTTTTACTTTTA	-	novel	NA	P-0010341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	365	527	0	ENST00000267163.4:c.1421+6_1421+23del		p.X474_splice	ENST00000267163	NM_000321.2	474			0.564722523008761	2	FACETS	1	0.982	1	0.536	0.508	0.564	CLONAL	1	TRUE	0	0.586008725867842	2		527	1162	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231377	46231377	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010341-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	183	368	0	ENST00000334344.6:c.1217A>G	p.His406Arg	p.H406R	ENST00000334344	NM_152641.2	406	cAt/cGt	10/21	1	2	FACETS	0.931	0.862	1	0.931	0.862	1	CLONAL	1	TRUE	1	0.586008725867842	2		368	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0010640-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	332	644	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.315069580355153	2	FACETS	1	0.993	1	0.672	0.635	0.71	CLONAL	1	TRUE	0	0.421855217459171	2		645	1171	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242486	+	inframe_deletion	In_Frame_Del	DEL	TTAAGAGAAGCAACATCT	TTAAGAGAAGCAACATCT	-	rs121913440	NA	P-0010640-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	198	420	0	ENST00000275493.2:c.2239_2256del	p.Leu747_Ser752del	p.L747_S752del	ENST00000275493	NM_005228.3	747	TTAAGAGAAGCAACATCT/-	19/28	0.421855217459171	5	FACETS	1	0.97	1	0.365	0.337	0.395	CLONAL	1	TRUE	2	0.421855217459171	5		420	1398	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984952	101984952	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1384754271	NA	P-0010640-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	145	211	1	ENST00000282441.5:c.399G>T	p.Gln133His	p.Q133H	ENST00000282441	NM_001130145.2	133	caG/caT	2/9	0.294454981285432	3	FACETS	0.829	0.761	0.899	0.829	0.761	0.899	CLONAL	2	TRUE	1	0.421855217459171	3		212	502	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0010703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	12	152	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.09	0.063	0.123	0.09	0.063	0.123	SUBCLONAL	1	FALSE	1	0.937607409957027	2		152	285	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0010703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	18	328	1	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.063	0.047	0.083	0.063	0.047	0.083	SUBCLONAL	1	FALSE	1	0.937607409957027	2		329	607	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561764	55561764	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913505	NA	P-0011037-T10-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	174	414	0	ENST00000288135.5:c.154G>A	p.Asp52Asn	p.D52N	ENST00000288135	NM_000222.2	52	Gac/Aac	2/21	1	2	FACETS	0.988	0.917	1	0.988	0.917	1	CLONAL	1	TRUE	1	0.71	2		414	496	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638326	117638326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752085591	NA	P-0011037-T10-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	180	511	0	ENST00000368508.3:c.6115C>T	p.Arg2039Cys	p.R2039C	ENST00000368508	NM_002944.2	2039	Cgt/Tgt	38/43	1	2	FACETS	0.939	0.872	1	0.939	0.872	1	CLONAL	1	TRUE	1	0.71	2		511	540	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22405002	22405002	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011037-T10-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	29	79	0	ENST00000344548.3:c.31G>C	p.Asp11His	p.D11H	ENST00000344548	NM_001039802.1	11	Gat/Cat	3/7	1	2	FACETS	0.801	0.658	0.955	0.801	0.658	0.955	CLONAL	1	TRUE	1	0.71	2		79	102	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0011593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	81	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.229334391787632	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.22	1		336	607	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352766	70352766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866231134	NA	P-0011593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	128	572	0	ENST00000374080.3:c.4487G>A	p.Arg1496His	p.R1496H	ENST00000374080		1496	cGc/cAc	32/45	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.22	2		572	1082	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220528	123220528	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	93	538	1	ENST00000218089.9:c.3185G>A	p.Gly1062Glu	p.G1062E	ENST00000218089	NM_001042749.1	1062	gGa/gAa	30/35	1	2	FACETS	0.673	0.596	0.756	0.673	0.596	0.756	SUBCLONAL	1	TRUE	1	0.22	2		539	1256	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845624	68845649	+	frameshift_variant	Frame_Shift_Del	DEL	CGATGATGTGAACACCTACAATGCCG	CGATGATGTGAACACCTACAATGCCG	-	novel	NA	P-0011593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	70	309	0	ENST00000261769.5:c.871_896del	p.Asp291HisfsTer11	p.D291Hfs*11	ENST00000261769	NM_004360.3	290	gaCGATGATGTGAACACCTACAATGCCGcc/gacc	7/16	0.3	1	FACETS	0.881	0.768	1	0.881	0.768	1	CLONAL	1	TRUE	0	0.22	1		309	643	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341575	89341575	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	32	249	0	ENST00000301030.4:c.7495del	p.Glu2499SerfsTer3	p.E2499Sfs*3	ENST00000301030	NM_001256183.1	2499	Gag/ag	10/13	0.3	1	FACETS	0.618	0.501	0.75	0.618	0.501	0.75	SUBCLONAL	1	TRUE	0	0.22	1		249	419	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138135	2138135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201206500	NA	P-0012146-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	147	790	1	ENST00000219476.3:c.5155G>A	p.Ala1719Thr	p.A1719T	ENST00000219476	NM_000548.3	1719	Gca/Aca	40/42	0.473297920430205	4	FACETS	0.87	0.793	0.951	0.29	0.264	0.317	CLONAL	1	TRUE	1	0.479269173789429	4		791	1043	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012146-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	173	698	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.479269173789429	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.479269173789429	1		698	525	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227959	123227959	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012146-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	143	838	2	ENST00000218089.9:c.3670G>A	p.Glu1224Lys	p.E1224K	ENST00000218089	NM_001042749.1	1224	Gag/Aag	33/35	1	2	FACETS	0.896	0.819	0.976	0.896	0.819	0.976	CLONAL	1	TRUE	1	0.479269173789429	2		840	666	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849512	68849512	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012146-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	199	810	0	ENST00000261769.5:c.1416del	p.Val473SerfsTer8	p.V473Sfs*8	ENST00000261769	NM_004360.3	472	aCc/ac	10/16	0.479269173789429	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.479269173789429	1		810	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0013006-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	467	456	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.726878784564943	2		456	1212	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0013006-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	210	522	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	1	2	FACETS	0.986	0.922	1	0.986	0.922	1	CLONAL	1	TRUE	1	0.726878784564943	2		522	586	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612187	189612187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1051829008	NA	P-0013006-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	319	639	0	ENST00000264731.3:c.1939C>T	p.Arg647Cys	p.R647C	ENST00000264731	NM_003722.4	647	Cgc/Tgc	14/14	1	2	FACETS	0.995	0.943	1	0.995	0.943	1	CLONAL	1	TRUE	1	0.726878784564943	2		639	882	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781425	3781425	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013006-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	39	373	0	ENST00000262367.5:c.4940C>A	p.Pro1647His	p.P1647H	ENST00000262367	NM_004380.2	1647	cCc/cAc	30/31	1	2	FACETS	0.207	0.171	0.247	0.207	0.171	0.247	SUBCLONAL	1	TRUE	1	0.726878784564943	2		373	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0013796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	215	845	0	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	0.194691575120772	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	3	TRUE	0	0.194691575120772	3		845	782	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880219	37880220	+	missense_variant	Missense_Mutation	DNP	TT	TT	CC	rs121913469	NA	P-0013796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	139	463	3	ENST00000269571.5:c.2263_2264delinsCC	p.Leu755Pro	p.L755P	ENST00000269571		755	TTg/CCg	19/27	0.194691575120772	3	FACETS	1	0.98	1	0.83	0.758	0.906	CLONAL	2	TRUE	0	0.194691575120772	3		466	629	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097256	178097256	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	101	430	0	ENST00000397062.3:c.458G>A	p.Ser153Asn	p.S153N	ENST00000397062	NM_006164.4	153	aGc/aAc	4/5	0.194691575120772	5	FACETS	1	0.921	1	0.69	0.617	0.766	CLONAL	2	TRUE	2	0.194691575120772	5		430	648	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271300	1271300	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	74	450	0	ENST00000310581.5:c.2402C>A	p.Ala801Asp	p.A801D	ENST00000310581	NM_198253.2	801	gCc/gAc	8/16	0.179148157704798	3	FACETS	0.764	0.67	0.865	0.509	0.446	0.577	SUBCLONAL	2	TRUE	0	0.194691575120772	3		450	546	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0013878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	144	529	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.720013336186345	6	FACETS	0.842	0.766	0.922	0.168	0.153	0.185	CLONAL	1	TRUE	1	0.720013336186345	6		529	1159	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0013878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	309	635	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	1	2	FACETS	0.909	0.859	0.96	0.909	0.859	0.96	CLONAL	1	TRUE	1	0.720013336186345	2		635	944	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285087	15285087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763870059	NA	P-0013878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	183	455	1	ENST00000263388.2:c.4528C>T	p.Arg1510Cys	p.R1510C	ENST00000263388	NM_000435.2	1510	Cgc/Tgc	25/33	1	2	FACETS	0.983	0.915	1	0.983	0.915	1	CLONAL	1	TRUE	1	0.720013336186345	2		456	517	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945988	17945988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747131454	NA	P-0013878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	265	735	1	ENST00000458235.1:c.1951C>T	p.Arg651Trp	p.R651W	ENST00000458235	NM_000215.3	651	Cgg/Tgg	15/24	1	2	FACETS	0.933	0.878	0.989	0.933	0.878	0.989	CLONAL	1	TRUE	1	0.720013336186345	2		736	789	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872581	136872581	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	552	1257	3	ENST00000241393.3:c.917G>A	p.Gly306Glu	p.G306E	ENST00000241393	NM_003467.2	306	gGa/gAa	2/2	1	2	FACETS	0.964	0.925	1	0.964	0.925	1	CLONAL	1	TRUE	1	0.720013336186345	2		1260	1590	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686351	30686351	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	258	382	0	ENST00000295754.5:c.207C>G	p.Ser69Arg	p.S69R	ENST00000295754	NM_003242.5	69	agC/agG	2/7	0.720013336186345	1	FACETS	0.901	0.854	0.948	0.901	0.854	0.948	CLONAL	1	TRUE	0	0.720013336186345	1		382	509	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910797	29910797	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs41559912	NA	P-0013878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	550	719	0	ENST00000376809.5:c.337G>T	p.Glu113Ter	p.E113*	ENST00000376809	NM_002116.7	113	Gag/Tag	2/8	0.720013336186345	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.720013336186345	2		719	759	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593618	55593662	+	inframe_deletion	In_Frame_Del	DEL	GAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTT	GAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTT	-	novel	NA	P-0014184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	111	520	0	ENST00000288135.5:c.1684_1728del	p.Glu562_Leu576del	p.E562_L576del	ENST00000288135	NM_000222.2	562	GAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTT/-	11/21	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.622498661263915	2		520	305	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894229	NA	P-0014370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	204	561	1	ENST00000451590.1:c.34G>T	p.Gly12Cys	p.G12C	ENST00000451590	NM_001130442.1	12	Ggc/Tgc	2/5	0.3	4	FACETS	0.987	0.921	1			1	CLONAL	4	TRUE	NA	0.2	4		562	620	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061121	38061137	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCCTTGGCGCCGCTG	CGCCCTTGGCGCCGCTG	-	novel	NA	P-0014370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	22	127	0	ENST00000250448.2:c.852_868del	p.Ser285ProfsTer2	p.S285Pfs*2	ENST00000250448	NM_004496.3	284	ggCAGCGGCGCCAAGGGCGgc/gggc	2/2	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.2	2		127	149	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774932	73774932	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	49	490	0	ENST00000254810.4:c.241A>G	p.Thr81Ala	p.T81A	ENST00000254810	NM_005324.3	81	Acc/Gcc	3/4	1	2	FACETS	0.81	0.685	0.947	0.81	0.685	0.947	CLONAL	1	TRUE	1	0.2	2		490	605	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022400	31022400	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	17	165	0	ENST00000375687.4:c.1885G>T	p.Gly629Cys	p.G629C	ENST00000375687	NM_015338.5	629	Ggt/Tgt	13/13	1	2	FACETS	0.829	0.621	1	0.829	0.621	1	CLONAL	1	TRUE	1	0.2	2		165	205	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541903	187541905	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1455163228	NA	P-0014370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	43	465	0	ENST00000441802.2:c.5835_5837del	p.Arg1945del	p.R1945del	ENST00000441802	NM_005245.3	1945	agAAGc/agc	10/27	0.3	2	FACETS	0.785	0.656	0.928			1	CLONAL	1	TRUE	NA	0.2	2		465	548	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227797	53227798	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0014370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	59	621	0	ENST00000375401.3:c.2390_2391del	p.Leu797ArgfsTer3	p.L797Rfs*3	ENST00000375401	NM_004187.3	797	cTA/c	17/26	0.0803839175587995	0	FACETS	0.743	0.639	0.857			1	INDETERMINATE	1	TRUE	0	0.2	0		621	635	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014483-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	68	698	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.364	0.316	0.417	0.364	0.316	0.417	SUBCLONAL	1	TRUE	1	0.398161253583296	2		698	938	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680655	88680655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142726068	NA	P-0014483-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	140	601	0	ENST00000360948.2:c.602G>A	p.Arg201His	p.R201H	ENST00000360948	NM_001012338.2	201	cGc/cAc	6/19	0.398161253583296	3	FACETS	0.912	0.83	0.998	0.456	0.415	0.499	CLONAL	1	TRUE	1	0.398161253583296	3		601	925	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576888	7576888	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0014483-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	224	676	1	ENST00000269305.4:c.958A>T	p.Lys320Ter	p.K320*	ENST00000269305	NM_001126112.2	320	Aag/Tag	9/11	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.398161253583296	2		677	867	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794714	120794714	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014483-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	357	685	2	ENST00000257552.2:c.643G>C	p.Gly215Arg	p.G215R	ENST00000257552	NM_002442.3	215	Ggc/Cgc	9/15	0.398161253583296	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.398161253583296	3		687	1034	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176504	142176504	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1196005889	NA	P-0014483-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	145	559	0	ENST00000350721.4:c.7597C>T	p.Arg2533Ter	p.R2533*	ENST00000350721	NM_001184.3	2533	Cga/Tga	45/47	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.398161253583296	2		559	725	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152571	56152572	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0014483-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	126	417	0	ENST00000399503.3:c.629dup	p.Val211CysfsTer9	p.V211Cfs*9	ENST00000399503	NM_005921.1	209	-/C	2/20	0.394373024530567	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.398161253583296	1		417	506	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476337	88476338	+	missense_variant	Missense_Mutation	DNP	GC	GC	TG	novel	NA	P-0014483-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	179	781	2	ENST00000360948.2:c.1794_1795delinsCA	p.Glu598_His599delinsAspAsn	p.E598_H599delinsDN	ENST00000360948	NM_001012338.2	598	gaGCac/gaCAac	15/19	0.398161253583296	3	FACETS	0.944	0.869	1	0.472	0.434	0.512	CLONAL	1	TRUE	1	0.398161253583296	3		783	1142	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578224	7578224	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1429743956	NA	P-0014640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	299	863	2	ENST00000269305.4:c.625A>T	p.Arg209Ter	p.R209*	ENST00000269305	NM_001126112.2	209	Aga/Tga	6/11	0.52502763133463	1	FACETS	0.945	0.892	0.998	0.945	0.892	0.998	CLONAL	1	TRUE	0	0.52502763133463	1		865	889	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741946	17741946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	46	416	0	ENST00000250003.3:c.617G>T	p.Cys206Phe	p.C206F	ENST00000250003	NM_002478.4	206	tGc/tTc	1/3	0.309076968424792	1	FACETS	0.303	0.255	0.355	0.303	0.255	0.355	INDETERMINATE	1	TRUE	0	0.52502763133463	1		416	427	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086199	16086199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	236	649	2	ENST00000281043.3:c.1375G>A	p.Glu459Lys	p.E459K	ENST00000281043	NM_005378.4	459	Gaa/Aaa	3/3	1	2	FACETS	0.975	0.911	1	0.975	0.911	1	CLONAL	1	TRUE	1	0.52502763133463	2		651	922	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	protein_altering_variant	In_Frame_Ins	INS	-	-	GTT	rs1554350347	NA	P-0014640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	288	576	0	ENST00000275493.2:c.2308_2309insGTT	p.Asp770delinsGlyTyr	p.D770delinsGY	ENST00000275493	NM_005228.3	770	gac/gGTTac	20/28	0.242919659529945	3	FACETS	0.795	0.75	0.841	0.795	0.75	0.841	INDETERMINATE	2	TRUE	1	0.52502763133463	3		576	871	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577563	64577563	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	133	364	31	ENST00000312049.6:c.19C>T	p.Gln7Ter	p.Q7*	ENST00000312049	NM_130799.2	7	Cag/Tag	2/10	0.694956344690087	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.694956344690087	1		395	247	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158150	47158202	+	frameshift_variant	Frame_Shift_Del	DEL	CACATGCTATTTCACCTTGAGCTCTTTCATCTTTAGAAAGAGGTGTACACTCA	CACATGCTATTTCACCTTGAGCTCTTTCATCTTTAGAAAGAGGTGTACACTCA	-	novel	NA	P-0015330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	89	678	0	ENST00000409792.3:c.4497_4549del	p.Cys1499TrpfsTer6	p.C1499Wfs*6	ENST00000409792	NM_014159.6	1499	tgTGAGTGTACACCTCTTTCTAAAGATGAAAGAGCTCAAGGTGAAATAGCATGTGgg/tggg	4/21	1	2	FACETS	0.511	0.455	0.571	0.511	0.455	0.571	SUBCLONAL	1	TRUE	1	0.694956344690087	2		678	501	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287330	33287330	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	140	592	0	ENST00000374542.5:c.1767del	p.Arg590GlyfsTer12	p.R590Gfs*12	ENST00000374542	NM_001141970.1	589	tcC/tc	6/8	0.653798223172538	1	FACETS	0.589	0.541	0.639	0.589	0.541	0.639	SUBCLONAL	1	TRUE	0	0.694956344690087	1		592	446	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0015673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	30	429	0	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	1	2	FACETS	0.163	0.13	0.2	0.163	0.13	0.2	SUBCLONAL	1	TRUE	1	0.31	2		429	1191	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533552	533552	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	623	479	0	ENST00000451590.1:c.351G>T	p.Lys117Asn	p.K117N	ENST00000451590	NM_001130442.1	117	aaG/aaT	4/5	1	2	FACETS	1	0.995	1	1	0.998	1	CLONAL	2	TRUE	1	0.31	2		479	1658	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152095	55152106	+	inframe_deletion	In_Frame_Del	DEL	ATCATGCATGAT	ATCATGCATGAT	-	rs121913267	NA	P-0016902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	141	599	0	ENST00000257290.5:c.2527_2538del	p.Ile843_Asp846del	p.I843_D846del	ENST00000257290	NM_006206.4	843	ATCATGCATGAT/-	18/23	1	2	FACETS	0.774	0.706	0.845	0.774	0.706	0.845	SUBCLONAL	1	TRUE	1	0.491134222972763	2		599	742	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0016929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	138	434	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.803	0.733	0.876	0.803	0.733	0.876	CLONAL	1	TRUE	1	0.548794265444506	2		434	626	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115720	8115720	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	178	473	0	ENST00000346208.3:c.1066A>G	p.Met356Val	p.M356V	ENST00000346208		356	Atg/Gtg	6/6	1	2	FACETS	0.863	0.797	0.931	0.863	0.797	0.931	CLONAL	1	TRUE	1	0.548794265444506	2		473	752	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100669	67100669	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	168	465	0	ENST00000412916.2:c.367G>C	p.Gly123Arg	p.G123R	ENST00000412916		123	Ggc/Cgc	4/6	0.548794265444506	1	FACETS	0.876	0.812	0.943	0.876	0.812	0.943	CLONAL	1	TRUE	0	0.548794265444506	1		465	507	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652067	36652067	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016989-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	313	876	0	ENST00000244741.5:c.189del	p.Phe63LeufsTer85	p.F63Lfs*85	ENST00000244741	NM_000389.4	63	ttC/tt	2/3	1	2	FACETS	0.951	0.898	1	0.951	0.898	1	CLONAL	1	TRUE	1	0.623382030243351	2		876	1056	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790828	89790829	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0016989-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	252	741	0	ENST00000336032.3:c.216_217del	p.Ala74SerfsTer133	p.A74Sfs*133	ENST00000336032	NM_006813.2	72	cCT/c	1/2	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.623382030243351	2		741	807	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856020	68856020	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016989-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	65	714	1	ENST00000261769.5:c.1828C>A	p.Gln610Lys	p.Q610K	ENST00000261769	NM_004360.3	610	Cag/Aag	12/16	0.325754628052875	1	FACETS	0.191	0.165	0.22	0.191	0.165	0.22	INDETERMINATE	1	TRUE	0	0.623382030243351	1		715	750	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295186	1295187	+	upstream_gene_variant	5'Flank	INS	-	-	GGGGCCGCGGAAAGGAAGGGGA	novel	NA	P-0016989-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	32	145	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.458	0.374	0.552	0.458	0.374	0.552	SUBCLONAL	1	TRUE	1	0.623382030243351	2		145	224	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651968	36651972	+	frameshift_variant	Frame_Shift_Del	DEL	GAGCC	GAGCC	-	novel	NA	P-0016989-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	302	744	0	ENST00000244741.5:c.91_95del	p.Ser31ArgfsTer3	p.S31Rfs*3	ENST00000244741	NM_000389.4	30	ctGAGCCgc/ctgc	2/3	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.623382030243351	2		744	913	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007411	45007799	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATGAGGGAAAGATACCAAGTCACGGTTTATTCTTCAAAATGGAGGTGGCTTGTTGGGAAGGTGGAAGCTCATTTGGCCAGAGTGGAAATGGAATTGGGAGAAATCGATGACCAAATGTAAACACTTGGTGCCTGATATAGCTTGACACCAAGTTAGCCCCAAGTGAAATACCCTGGCAATATTAATGTGTCTTTTCCCGATATTCCTCAGGTACTCCAAAGATTCAGGTTTACTCACGTCATCCAGCAGAGAATGGAAAGTCAAATTTCCTGAATTGCTATGTGTCTGGGTTTCATCCATCCGACATTGAAGTTGACTTACTGAAGAATGGAGAGAGAATTGAAAAAGTGGAGCATTCAGACTTGTCTTTCAGCAAGGACTGGTCTTTC	ATGAGGGAAAGATACCAAGTCACGGTTTATTCTTCAAAATGGAGGTGGCTTGTTGGGAAGGTGGAAGCTCATTTGGCCAGAGTGGAAATGGAATTGGGAGAAATCGATGACCAAATGTAAACACTTGGTGCCTGATATAGCTTGACACCAAGTTAGCCCCAAGTGAAATACCCTGGCAATATTAATGTGTCTTTTCCCGATATTCCTCAGGTACTCCAAAGATTCAGGTTTACTCACGTCATCCAGCAGAGAATGGAAAGTCAAATTTCCTGAATTGCTATGTGTCTGGGTTTCATCCATCCGACATTGAAGTTGACTTACTGAAGAATGGAGAGAGAATTGAAAAAGTGGAGCATTCAGACTTGTCTTTCAGCAAGGACTGGTCTTTC	-	novel	NA	P-0017382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	102	13	0	ENST00000558401.1:c.68-210_246del		p.X23_splice	ENST00000558401	NM_004048.2	23		2/4	0.370839920286355	2	FACETS	1	0.983	1	0.699	0.635	0.764	CLONAL	1	TRUE	0	0.544747796942963	2		13	268	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280016	18280016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778763290	NA	P-0017382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	163	483	1	ENST00000222254.8:c.2099C>T	p.Ser700Leu	p.S700L	ENST00000222254	NM_005027.3	700	tCg/tTg	16/16	1	2	FACETS	0.962	0.887	1	0.962	0.887	1	CLONAL	1	TRUE	1	0.544747796942963	2		484	622	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170815004	170815004	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	97	302	0	ENST00000296930.5:c.52C>G	p.Leu18Val	p.L18V	ENST00000296930	NM_002520.6	18	Ctt/Gtt	1/11	1	2	FACETS	0.83	0.745	0.92	0.83	0.745	0.92	CLONAL	1	TRUE	1	0.544747796942963	2		302	429	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805594	32805594	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	56	966	0	ENST00000374899.4:c.417G>A	p.Trp139Ter	p.W139*	ENST00000374899	NM_018833.2	139	tgG/tgA	2/12	1	2	FACETS	0.2	0.17	0.232	0.2	0.17	0.232	SUBCLONAL	1	TRUE	1	0.544747796942963	2		966	1030	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0017699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	190	548	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.919	0.852	0.988	0.919	0.852	0.988	CLONAL	1	TRUE	1	0.558650489132712	2		548	740	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273012	55273012	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs755330584	NA	P-0017699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	265	605	0	ENST00000275493.2:c.3335A>G	p.Asn1112Ser	p.N1112S	ENST00000275493	NM_005228.3	1112	aAt/aGt	28/28	0.558650489132712	3	FACETS	0.911	0.853	0.972	0.456	0.426	0.486	CLONAL	1	TRUE	1	0.558650489132712	3		605	1332	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003766	45003767	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0017699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	142	379	0	ENST00000558401.1:c.22_23delinsAA	p.Ala8Asn	p.A8N	ENST00000558401	NM_004048.2	8	GCt/AAt	1/4	1	2	FACETS	0.873	0.799	0.95	0.873	0.799	0.95	CLONAL	1	TRUE	1	0.558650489132712	2		379	582	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100619	67100619	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	277	515	0	ENST00000412916.2:c.317T>G	p.Val106Gly	p.V106G	ENST00000412916		106	gTc/gGc	4/6	0.558650489132712	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.558650489132712	1		515	685	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47679332	47679339	+	frameshift_variant	Frame_Shift_Del	DEL	GCATCCTC	GCATCCTC	-	novel	NA	P-0017699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	363	466	1	ENST00000347630.2:c.868_875del	p.Glu290ProfsTer4	p.E290Pfs*4	ENST00000347630	NM_001007230.1	290	GAGGATGCc/c	10/11	0.558650489132712	2	FACETS	0.973	0.932	1	0.973	0.932	1	CLONAL	2	TRUE	0	0.558650489132712	2		467	668	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161210	56161210	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	546	558	0	ENST00000399503.3:c.1079T>G	p.Phe360Cys	p.F360C	ENST00000399503	NM_005921.1	360	tTt/tGt	5/20	0.558650489132712	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.558650489132712	3		558	1186	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181813	56181815	+	inframe_deletion	In_Frame_Del	DEL	TTA	TTA	-	novel	NA	P-0017699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	234	511	0	ENST00000399503.3:c.4040_4042del	p.Ile1347del	p.I1347del	ENST00000399503	NM_005921.1	1346	gTTAtt/gtt	17/20	0.558650489132712	3	FACETS	1	0.974	1	0.541	0.505	0.579	CLONAL	1	TRUE	1	0.558650489132712	3		511	990	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0018097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	500	644	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.958	0.917	1	0.958	0.917	1	CLONAL	1	TRUE	1	0.720096963778985	2		645	1449	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0018097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	188	562	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.944	0.879	1	0.944	0.879	1	CLONAL	1	TRUE	1	0.720096963778985	2		562	553	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937602	76937602	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	220	321	0	ENST00000373344.5:c.3146del	p.Ile1049LysfsTer69	p.I1049Kfs*69	ENST00000373344	NM_000489.3	1049	aTa/aa	9/35	0.371842134022031	1	FACETS	0.601	0.562	0.64	0.601	0.562	0.64	INDETERMINATE	1	TRUE	0	0.720096963778985	1		321	651	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720857	89720857	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs786201816	NA	P-0018097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	278	347	0	ENST00000371953.3:c.1008C>G	p.Tyr336Ter	p.Y336*	ENST00000371953	NM_000314.4	336	taC/taG	8/9	0.609937410468856	1	FACETS	0.887	0.842	0.932	0.887	0.842	0.932	CLONAL	1	TRUE	0	0.720096963778985	1		347	557	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285703	46285703	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0018097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	219	281	0	ENST00000334344.6:c.5061+2T>C		p.X1687_splice	ENST00000334344	NM_152641.2	1687			1	2	FACETS	0.95	0.889	1	0.95	0.889	1	CLONAL	1	TRUE	1	0.720096963778985	2		281	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579394	7579394	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1245723119	NA	P-0018097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	472	582	2	ENST00000269305.4:c.293C>T	p.Pro98Leu	p.P98L	ENST00000269305	NM_001126112.2	98	cCt/cTt	4/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.720096963778985	2		584	1211	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0018105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	188	411	0	ENST00000269305.4:c.560-1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.303666567409511	3	FACETS	0.872	0.806	0.941	0.872	0.806	0.941	CLONAL	2	TRUE	1	0.26	3		411	937	SUCCESS
APC	324	MSKCC	GRCh37	5	112175147	112175147	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	47	196	1	ENST00000257430.4:c.3856G>T	p.Glu1286Ter	p.E1286*	ENST00000257430	NM_000038.5	1286	Gaa/Taa	16/16	1	2	FACETS	0.977	0.827	1	0.977	0.827	1	CLONAL	1	TRUE	1	0.26	2		197	370	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550419	39550419	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	84	225	0	ENST00000262039.4:c.530A>G	p.Lys177Arg	p.K177R	ENST00000262039	NM_002647.2	177	aAg/aGg	4/25	0.178773444419217	4	FACETS	0.794	0.703	0.89	0.529	0.468	0.594	SUBCLONAL	2	TRUE	1	0.26	4		225	513	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306568	41306568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	123	662	0	ENST00000373198.4:c.1091G>A	p.Arg364Gln	p.R364Q	ENST00000373198	NM_133170.3	364	cGa/cAa	7/32	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.168691061102882	2		662	1167	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	81	294	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.786	0.693	0.885	1	0.979	1	SUBCLONAL	2	TRUE	1	0.168691061102882	2		294	611	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578538	7578538	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1131691037	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1414	236	1060	0	ENST00000269305.4:c.392A>T	p.Asn131Ile	p.N131I	ENST00000269305	NM_001126112.2	131	aAc/aTc	5/11	0.168691061102882	1	FACETS	0.776	0.722	0.833	1	0.992	1	SUBCLONAL	2	TRUE	0	0.168691061102882	1		1060	1650	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911144	40911144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776134993	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	101	605	0	ENST00000373198.4:c.2161C>T	p.Arg721Cys	p.R721C	ENST00000373198	NM_133170.3	721	Cgt/Tgt	13/32	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.168691061102882	2		605	1117	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612205	189612205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	123	574	0	ENST00000264731.3:c.1957C>T	p.Pro653Ser	p.P653S	ENST00000264731	NM_003722.4	653	Cca/Tca	14/14	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.168691061102882	2		574	992	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982072	93982072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1334631229	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	97	577	0	ENST00000369303.4:c.1393G>A	p.Glu465Lys	p.E465K	ENST00000369303	NM_004440.3	465	Gaa/Aaa	6/17	0.168691061102882	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.168691061102882	1		577	928	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813334	102813334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1430553116	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	47	492	0	ENST00000307046.8:c.355C>T	p.Arg119Cys	p.R119C	ENST00000307046	NM_001111285.1	119	Cgc/Tgc	3/4	1	2	FACETS	0.608	0.511	0.716	0.608	0.511	0.716	SUBCLONAL	1	TRUE	1	0.168691061102882	2		492	916	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156501	55156501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	43	511	1	ENST00000257290.5:c.2902G>A	p.Asp968Asn	p.D968N	ENST00000257290	NM_006206.4	968	Gac/Aac	22/23	1	2	FACETS	0.611	0.51	0.725	0.611	0.51	0.725	SUBCLONAL	1	TRUE	1	0.168691061102882	2		512	834	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383301	4383301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	148	665	1	ENST00000261254.3:c.95C>T	p.Thr32Ile	p.T32I	ENST00000261254	NM_001759.3	32	aCc/aTc	1/5	1	2	FACETS	0.822	0.75	0.898	1	0.989	1	CLONAL	2	TRUE	1	0.168691061102882	2		666	1067	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25459872	25459872	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs750597155	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1264	88	808	2	ENST00000264709.3:c.2411C>T	p.Pro804Leu	p.P804L	ENST00000264709	NM_175629.2	804	cCg/cTg	21/23	1	2	FACETS	0.772	0.681	0.869	0.772	0.681	0.869	SUBCLONAL	1	TRUE	1	0.168691061102882	2		810	1352	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259197	89259197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	81	409	0	ENST00000336596.2:c.341G>A	p.Gly114Glu	p.G114E	ENST00000336596	NM_005233.5	114	gGa/gAa	3/17	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.168691061102882	2		409	703	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056973	180056973	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1272	172	876	0	ENST00000261937.6:c.646C>T	p.Leu216Phe	p.L216F	ENST00000261937	NM_182925.4	216	Ctt/Ttt	5/30	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.168691061102882	2		876	1444	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997434	149997434	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1257	191	967	1	ENST00000253339.5:c.2845C>T	p.Pro949Ser	p.P949S	ENST00000253339		949	Cct/Tct	6/7	0.168691061102882	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.168691061102882	1		968	1448	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552696	18552696	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1023238256	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	84	739	2	ENST00000266497.5:c.2107G>A	p.Glu703Lys	p.E703K	ENST00000266497		703	Gaa/Aaa	14/31	1	2	FACETS	0.85	0.748	0.959	0.85	0.748	0.959	CLONAL	1	TRUE	1	0.168691061102882	2		741	1172	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149242	119149242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779039234	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	220	620	0	ENST00000264033.4:c.1250C>T	p.Pro417Leu	p.P417L	ENST00000264033	NM_005188.3	417	cCt/cTt	9/16	0.168691061102882	1	FACETS	1	0.979	1	1	0.994	1	CLONAL	2	TRUE	0	0.168691061102882	1		620	1056	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476403	88476403	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	41	499	0	ENST00000360948.2:c.1729C>T	p.Pro577Ser	p.P577S	ENST00000360948	NM_001012338.2	577	Ccc/Tcc	15/19	1	2	FACETS	0.63	0.523	0.749	0.63	0.523	0.749	SUBCLONAL	1	TRUE	1	0.168691061102882	2		499	772	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074244	8074244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	168	618	0	ENST00000377482.5:c.415C>T	p.Leu139Phe	p.L139F	ENST00000377482	NM_018948.3	139	Ctt/Ttt	4/4	0.168691061102882	3	FACETS	0.909	0.834	0.988	0.909	0.834	0.988	CLONAL	2	TRUE	1	0.168691061102882	3		618	1188	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941241	36941241	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	123	672	0	ENST00000361632.4:c.98C>T	p.Ala33Val	p.A33V	ENST00000361632		33	gCc/gTc	3/16	0.168691061102882	3	FACETS	1	0.972	1	0.604	0.544	0.667	CLONAL	1	TRUE	1	0.168691061102882	3		672	1309	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805789	43805789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1307494831	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	213	626	0	ENST00000372470.3:c.845G>A	p.Gly282Glu	p.G282E	ENST00000372470	NM_005373.2	282	gGa/gAa	5/12	0.168691061102882	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.168691061102882	3		626	1185	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273015	115273015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	131	757	0	ENST00000438362.2:c.1358C>T	p.Ala453Val	p.A453V	ENST00000438362	NM_001242891.1	453	gCt/gTt	12/20	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.168691061102882	2		757	1236	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246498710	246498710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	132	665	0	ENST00000388985.4:c.295C>T	p.Pro99Ser	p.P99S	ENST00000388985		99	Cca/Tca	3/12	0.168691061102882	3	FACETS	0.773	0.7	0.85			1	SUBCLONAL	2	TRUE	NA	0.168691061102882	3		665	1098	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258061	123258061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358630379	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	132	816	1	ENST00000358487.5:c.1620G>A	p.Met540Ile	p.M540I	ENST00000358487	NM_000141.4	540	atG/atA	12/18	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.168691061102882	2		817	1267	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948727	71948727	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	147	639	0	ENST00000298229.2:c.3439C>T	p.Pro1147Ser	p.P1147S	ENST00000298229	NM_001567.3	1147	Cca/Tca	26/28	0.168691061102882	2	FACETS	0.827	0.754	0.904	0.827	0.754	0.904	CLONAL	2	TRUE	0	0.168691061102882	2		639	1054	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18576924	18576924	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	124	778	0	ENST00000266497.5:c.2332C>G	p.Leu778Val	p.L778V	ENST00000266497		778	Cta/Gta	16/31	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.168691061102882	2		778	1183	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120810	115120810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1469975580	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	71	311	0	ENST00000257566.3:c.196G>A	p.Asp66Asn	p.D66N	ENST00000257566	NM_016569.3	66	Gat/Aat	1/8	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.168691061102882	2		311	609	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431499	121431499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	53	608	0	ENST00000257555.6:c.703G>A	p.Glu235Lys	p.E235K	ENST00000257555		235	Gag/Aag	3/10	1	2	FACETS	0.602	0.511	0.702	0.602	0.511	0.702	SUBCLONAL	1	TRUE	1	0.168691061102882	2		608	1044	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257848	133257848	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	135	545	0	ENST00000320574.5:c.80C>T	p.Ser27Phe	p.S27F	ENST00000320574	NM_006231.2	27	tCc/tTc	2/49	1	2	FACETS	0.898	0.816	0.985	1	0.989	1	CLONAL	2	TRUE	1	0.168691061102882	2		545	891	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912304	32912304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	52	517	0	ENST00000380152.3:c.3812C>T	p.Ser1271Leu	p.S1271L	ENST00000380152		1271	tCa/tTa	11/27	1	2	FACETS	0.625	0.53	0.729	0.625	0.53	0.729	SUBCLONAL	1	TRUE	1	0.168691061102882	2		517	987	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708450	43708450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	61	678	2	ENST00000382044.4:c.4846C>T	p.Leu1616Phe	p.L1616F	ENST00000382044	NM_001141980.1	1616	Ctt/Ttt	22/28	1	2	FACETS	0.667	0.573	0.769	0.667	0.573	0.769	SUBCLONAL	1	TRUE	1	0.168691061102882	2		680	1085	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096136	2096136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	78	629	0	ENST00000219066.1:c.371C>T	p.Pro124Leu	p.P124L	ENST00000219066	NM_002528.5	124	cCc/cTc	2/6	1	2	FACETS	0.833	0.73	0.945	0.833	0.73	0.945	CLONAL	1	TRUE	1	0.168691061102882	2		629	1110	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2215914	2215914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1463	80	849	0	ENST00000326181.6:c.116C>T	p.Ser39Leu	p.S39L	ENST00000326181	NM_032271.2	39	tCa/tTa	3/21	1	2	FACETS	0.615	0.539	0.697	0.615	0.539	0.697	SUBCLONAL	1	TRUE	1	0.168691061102882	2		849	1543	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816292	89816292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	70	442	0	ENST00000389301.3:c.3085G>A	p.Glu1029Lys	p.E1029K	ENST00000389301	NM_000135.2	1029	Gag/Aag	32/43	1	2	FACETS	0.951	0.827	1	0.951	0.827	1	CLONAL	1	TRUE	1	0.168691061102882	2		442	873	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1314	227	995	1	ENST00000269305.4:c.376-1G>C		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.168691061102882	1	FACETS	0.8	0.743	0.859	1	0.992	1	SUBCLONAL	2	TRUE	0	0.168691061102882	1		996	1541	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110201	8110201	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	180	708	1	ENST00000585124.1:c.404C>T	p.Pro135Leu	p.P135L	ENST00000585124	NM_004217.3	135	cCc/cTc	6/9	0.168691061102882	1	FACETS	0.796	0.733	0.863	1	0.99	1	SUBCLONAL	2	TRUE	0	0.168691061102882	1		709	1227	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559858	29559858	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	97	352	0	ENST00000356175.3:c.3455T>G	p.Leu1152Ter	p.L1152*	ENST00000356175	NM_000267.3	1152	tTa/tGa	26/57	0.168691061102882	1	FACETS	0.76	0.678	0.847	1	0.981	1	SUBCLONAL	2	TRUE	0	0.168691061102882	1		352	693	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40476791	40476791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	91	728	1	ENST00000264657.5:c.1538C>T	p.Ser513Phe	p.S513F	ENST00000264657	NM_139276.2	513	tCc/tTc	17/24	0.168691061102882	1	FACETS	0.864	0.764	0.97	0.864	0.764	0.97	CLONAL	1	TRUE	0	0.168691061102882	1		729	1144	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125476	7125476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1311	103	837	0	ENST00000302850.5:c.3076C>T	p.Leu1026Phe	p.L1026F	ENST00000302850	NM_000208.2	1026	Ctt/Ttt	17/22	1	2	FACETS	0.864	0.77	0.964	0.864	0.77	0.964	CLONAL	1	TRUE	1	0.168691061102882	2		837	1414	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267900	7267901	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	62	368	3	ENST00000302850.5:c.107_108delinsTT	p.Pro36Leu	p.P36L	ENST00000302850	NM_000208.2	36	cCC/cTT	2/22	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.168691061102882	2		371	677	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272128	15272128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408330704	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	164	554	1	ENST00000263388.2:c.6311C>T	p.Ser2104Leu	p.S2104L	ENST00000263388	NM_000435.2	2104	tCg/tTg	33/33	1	2	FACETS	0.962	0.882	1	1	0.992	1	CLONAL	2	TRUE	1	0.168691061102882	2		555	1011	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223145	36223145	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1559	186	1049	3	ENST00000222270.7:c.5695C>T	p.Pro1899Ser	p.P1899S	ENST00000222270	NM_014727.1	1899	Ccc/Tcc	28/37	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.168691061102882	2		1052	1745	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605111	46605111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748180336	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	135	743	1	ENST00000263734.3:c.1328G>A	p.Arg443Lys	p.R443K	ENST00000263734	NM_001430.4	443	aGg/aAg	10/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.168691061102882	2		744	1197	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285261	212285261	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	63	650	0	ENST00000342788.4:c.3040G>A	p.Glu1014Lys	p.E1014K	ENST00000342788	NM_005235.2	1014	Gaa/Aaa	25/28	1	2	FACETS	0.708	0.61	0.815	0.708	0.61	0.815	SUBCLONAL	1	TRUE	1	0.168691061102882	2		650	1055	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546830	9546830	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781148117	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	74	281	0	ENST00000353224.5:c.1192G>A	p.Ala398Thr	p.A398T	ENST00000353224	NM_177990.2	398	Gct/Act	5/10	1	2	FACETS	0.766	0.671	0.867	1	0.976	1	SUBCLONAL	2	TRUE	1	0.168691061102882	2		281	573	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265061	46265061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1229549236	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	125	567	1	ENST00000371998.3:c.1931C>T	p.Ser644Leu	p.S644L	ENST00000371998		644	tCa/tTa	12/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.168691061102882	2		568	1169	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545963	41545963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1493	200	991	0	ENST00000263253.7:c.2578C>T	p.Pro860Ser	p.P860S	ENST00000263253	NM_001429.3	860	Cca/Tca	14/31	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.168691061102882	2		991	1693	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940066	49940066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	80	663	0	ENST00000296474.3:c.977C>T	p.Ser326Phe	p.S326F	ENST00000296474	NM_002447.2	326	tCc/tTc	1/20	1	2	FACETS	0.867	0.761	0.982	0.867	0.761	0.982	CLONAL	1	TRUE	1	0.168691061102882	2		663	1094	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266689	142266689	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	72	708	0	ENST00000350721.4:c.3235T>A	p.Leu1079Ile	p.L1079I	ENST00000350721	NM_001184.3	1079	Tta/Ata	16/47	1	2	FACETS	0.794	0.692	0.905	0.794	0.692	0.905	CLONAL	1	TRUE	1	0.168691061102882	2		708	1075	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586493	189586493	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	47	473	0	ENST00000264731.3:c.1117G>A	p.Gly373Ser	p.G373S	ENST00000264731	NM_003722.4	373	Ggt/Agt	8/14	1	2	FACETS	0.73	0.615	0.859	0.73	0.615	0.859	SUBCLONAL	1	TRUE	1	0.168691061102882	2		473	763	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953820	55953820	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	61	729	2	ENST00000263923.4:c.3616G>A	p.Glu1206Lys	p.E1206K	ENST00000263923	NM_002253.2	1206	Gaa/Aaa	27/30	1	2	FACETS	0.599	0.515	0.692	0.599	0.515	0.692	SUBCLONAL	1	TRUE	1	0.168691061102882	2		731	1207	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31401603	31401603	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	156	717	0	ENST00000344624.3:c.4061A>C	p.Glu1354Ala	p.E1354A	ENST00000344624		1354	gAa/gCa	33/33	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.168691061102882	2		717	1334	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31511284	31511284	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1273	145	770	0	ENST00000344624.3:c.1291-1G>A		p.X431_splice	ENST00000344624		431			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.168691061102882	2		770	1418	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923703	131923704	+	missense_variant	Missense_Mutation	DNP	TG	TG	AT	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	106	714	1	ENST00000265335.6:c.973_974delinsAT	p.Cys325Ile	p.C325I	ENST00000265335		325	TGt/ATt	7/25	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.168691061102882	2		715	1133	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517544	176517544	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1261	169	769	1	ENST00000292408.4:c.245G>A	p.Trp82Ter	p.W82*	ENST00000292408	NM_213647.1	82	tGg/tAg	3/18	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.168691061102882	2		770	1430	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322430	31322430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs956809791	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	51	506	0	ENST00000412585.2:c.1025G>A	p.Gly342Glu	p.G342E	ENST00000412585	NM_005514.6	342	gGg/gAg	6/8	1	2	FACETS	0.719	0.609	0.84	0.719	0.609	0.84	SUBCLONAL	1	TRUE	1	0.168691061102882	2		506	841	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679148	117679148	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1459800881	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	125	595	0	ENST00000368508.3:c.3673G>A	p.Asp1225Asn	p.D1225N	ENST00000368508	NM_002944.2	1225	Gat/Aat	24/43	0.168691061102882	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.168691061102882	1		595	915	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709105	117709105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	130	599	0	ENST00000368508.3:c.1852G>A	p.Asp618Asn	p.D618N	ENST00000368508	NM_002944.2	618	Gac/Aac	13/43	0.168691061102882	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.168691061102882	1		599	1107	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265554	152265554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	119	579	0	ENST00000206249.3:c.1007C>T	p.Pro336Leu	p.P336L	ENST00000206249	NM_000125.3	336	cCc/cTc	4/8	0.168691061102882	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.168691061102882	1		579	977	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140549963	140549963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	68	649	0	ENST00000288602.6:c.188C>T	p.Ala63Val	p.A63V	ENST00000288602	NM_004333.4	63	gCc/gTc	2/18	1	2	FACETS	0.713	0.618	0.816	0.713	0.618	0.816	SUBCLONAL	1	TRUE	1	0.168691061102882	2		649	1131	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879010	151879010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	73	519	0	ENST00000262189.6:c.5935C>T	p.Pro1979Ser	p.P1979S	ENST00000262189	NM_170606.2	1979	Ccc/Tcc	36/59	1	2	FACETS	0.818	0.713	0.932	0.818	0.713	0.932	CLONAL	1	TRUE	1	0.168691061102882	2		519	1058	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981348	68981348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	105	577	0	ENST00000288368.4:c.1420G>A	p.Glu474Lys	p.E474K	ENST00000288368	NM_024870.2	474	Gag/Aag	12/40	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.168691061102882	2		577	865	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486156	8486156	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	86	498	0	ENST00000356435.5:c.2661G>T	p.Lys887Asn	p.K887N	ENST00000356435		887	aaG/aaT	17/35	0.168691061102882	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.168691061102882	1		498	812	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974720	21974721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs398123152	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	74	360	1	ENST00000304494.5:c.106dup	p.Ala36GlyfsTer8	p.A36Gfs*8	ENST00000304494	NM_000077.4	36	gcg/gGcg	1/3	0.168691061102882	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.168691061102882	1		361	563	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220435	98220435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	66	679	0	ENST00000331920.6:c.3028C>T	p.Pro1010Ser	p.P1010S	ENST00000331920	NM_000264.3	1010	Ccc/Tcc	18/24	1	2	FACETS	0.647	0.559	0.742	0.647	0.559	0.742	SUBCLONAL	1	TRUE	1	0.168691061102882	2		679	1210	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	175	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	NA	2	FACETS	0.862	0.801	0.924			1	INDETERMINATE	2	TRUE	NA	0.424044274041854	2		336	479	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118704	115118706	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0019579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	249	580	2	ENST00000257566.3:c.635_637del	p.Asn212del	p.N212del	ENST00000257566	NM_016569.3	212	aACAtt/att	2/8	0.424044274041854	3	FACETS	0.96	0.902	1	0.96	0.902	1	CLONAL	2	TRUE	1	0.424044274041854	3		582	741	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246498775	246498775	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	196	543	0	ENST00000388985.4:c.230A>G	p.Lys77Arg	p.K77R	ENST00000388985		77	aAa/aGa	3/12	0.243352142745789	5	FACETS	0.973	0.903	1	0.649	0.602	0.697	INDETERMINATE	2	TRUE	2	0.424044274041854	5		543	777	SUCCESS
RET	5979	MSKCC	GRCh37	10	43614987	43614987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1364361946	NA	P-0019579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	77	620	0	ENST00000355710.3:c.2401C>T	p.Leu801Phe	p.L801F	ENST00000355710	NM_020975.4	801	Ctc/Ttc	14/20	0.406716959997961	3	FACETS	0.742	0.652	0.839	0.371	0.326	0.42	SUBCLONAL	1	TRUE	1	0.424044274041854	3		620	593	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579417	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	GGAG	GGAG	-	novel	NA	P-0019579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	302	820	2	ENST00000269305.4:c.267_270del	p.Ser90GlyfsTer32	p.S90Gfs*32	ENST00000269305	NM_001126112.2	89	ccCTCC/cc	4/11	0.423505654575541	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.424044274041854	2		822	702	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374327	81374327	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	94	382	0	ENST00000222390.5:c.735C>G	p.Phe245Leu	p.F245L	ENST00000222390	NM_000601.4	245	ttC/ttG	6/18	0.424044274041854	3	FACETS	0.997	0.89	1	0.498	0.445	0.556	CLONAL	1	TRUE	1	0.424044274041854	3		382	539	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	62	345	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.85	0.739	0.97	0.85	0.739	0.97	CLONAL	1	TRUE	1	0.437849685539192	2		345	333	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413084	139413084	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	110	626	0	ENST00000277541.6:c.1058G>C	p.Arg353Pro	p.R353P	ENST00000277541	NM_017617.3	353	cGt/cCt	6/34	1	2	FACETS	0.902	0.813	0.996	0.902	0.813	0.996	CLONAL	1	TRUE	1	0.437849685539192	2		626	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578266	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs942158624	NA	P-0020593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	230	765	0	ENST00000269305.4:c.583A>T	p.Ile195Phe	p.I195F	ENST00000269305	NM_001126112.2	195	Atc/Ttc	6/11	0.437994621213135	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.437994621213135	1		765	753	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509676	106509676	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139426517	NA	P-0020593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	79	586	1	ENST00000359195.3:c.1670C>T	p.Ala557Val	p.A557V	ENST00000359195	NM_002649.2	557	gCg/gTg	2/11	0.215958869026367	1	FACETS	0.499	0.439	0.562	0.499	0.439	0.562	INDETERMINATE	1	TRUE	0	0.437994621213135	1		587	565	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426544	49426544	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555188379	NA	P-0020593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	329	1053	17	ENST00000301067.7:c.11944C>T	p.Arg3982Ter	p.R3982*	ENST00000301067	NM_003482.3	3982	Cga/Tga	39/54	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.437994621213135	2		1070	1315	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115386	115115386	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	364	725	0	ENST00000257566.3:c.940del	p.Arg314GlufsTer9	p.R314Efs*9	ENST00000257566	NM_016569.3	314	Aga/ga	5/8	0.388150488489883	3	FACETS	0.949	0.902	0.998			1	CLONAL	2	TRUE	NA	0.437994621213135	3		725	1067	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721024	176721024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	143	560	0	ENST00000439151.2:c.6655C>T	p.Arg2219Cys	p.R2219C	ENST00000439151	NM_022455.4	2219	Cgt/Tgt	23/23	0.451534514144068	3	FACETS	1	0.952	1	0.532	0.485	0.58	CLONAL	1	TRUE	1	0.451534514144068	3		560	730	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948572	54948572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373550419	NA	P-0020624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	47	522	2	ENST00000312783.6:c.746C>T	p.Ser249Leu	p.S249L	ENST00000312783	NM_198436.1	249	tCg/tTg	8/10	0.451534514144068	3	FACETS	0.746	0.632	0.871	0.373	0.316	0.436	SUBCLONAL	1	TRUE	1	0.451534514144068	3		524	342	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089484	27089484	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	165	697	0	ENST00000324856.7:c.2440A>G	p.Asn814Asp	p.N814D	ENST00000324856	NM_006015.4	814	Aac/Gac	8/20	0.248571364924941	3	FACETS	1	0.983	1	0.623	0.573	0.675	INDETERMINATE	1	TRUE	1	0.451534514144068	3		697	719	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721024	176721024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	167	560	0	ENST00000439151.2:c.6655C>T	p.Arg2219Cys	p.R2219C	ENST00000439151	NM_022455.4	2219	Cgt/Tgt	23/23	1	2	FACETS	0.915	0.85	0.982	0.915	0.85	0.982	CLONAL	1	FALSE	1	0.850445725855882	2		560	429	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089484	27089484	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	218	697	0	ENST00000324856.7:c.2440A>G	p.Asn814Asp	p.N814D	ENST00000324856	NM_006015.4	814	Aac/Gac	8/20	1	2	FACETS	0.887	0.831	0.944	0.887	0.831	0.944	CLONAL	1	FALSE	1	0.850445725855882	2		697	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0021221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	760	644	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.873367280449143	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.873367280449143	2		645	838	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0021221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	165	562	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.873367280449143	2		562	377	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934190	39934190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146403660	NA	P-0021221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	304	1116	1	ENST00000378444.4:c.409G>A	p.Val137Ile	p.V137I	ENST00000378444	NM_001123385.1	137	Gtc/Atc	4/15	0.644646663621492	1	FACETS	0.668	0.636	0.7	0.668	0.636	0.7	SUBCLONAL	1	TRUE	0	0.873367280449143	1		1117	587	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120479957	120479957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	347	968	0	ENST00000256646.2:c.3470C>T	p.Pro1157Leu	p.P1157L	ENST00000256646	NM_024408.3	1157	cCc/cTc	21/34	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.873367280449143	2		968	726	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117440	4117440	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	264	869	0	ENST00000262948.5:c.280T>C	p.Ser94Pro	p.S94P	ENST00000262948	NM_030662.3	94	Tcg/Ccg	2/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.873367280449143	2		869	531	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907699	76907699	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0021221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	436	1214	0	ENST00000373344.5:c.4462A>T	p.Lys1488Ter	p.K1488*	ENST00000373344	NM_000489.3	1488	Aaa/Taa	15/35	0.325207764715354	1	FACETS	0.573	0.549	0.598	0.573	0.549	0.598	INDETERMINATE	1	TRUE	0	0.873367280449143	1		1214	981	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436679	110436679	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	243	914	0	ENST00000375856.3:c.1722G>T	p.Arg574Ser	p.R574S	ENST00000375856	NM_003749.2	574	agG/agT	1/2	0.448152347960126	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.448152347960126	1		914	775	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862143	68862150	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAGGAT	CAGAGGAT	-	novel	NA	P-0021659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	200	686	0	ENST00000261769.5:c.2231_2238del	p.Pro744ArgfsTer10	p.P744Rfs*10	ENST00000261769	NM_004360.3	744	cCAGAGGAT/c	14/16	0.448152347960126	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.448152347960126	1		686	670	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0021747-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	63	519	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.3	1	FACETS	0.793	0.685	0.91	0.793	0.685	0.91	CLONAL	1	TRUE	0	0.21	1		519	677	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786740	3786740	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021747-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	36	0	0	ENST00000262367.5:c.4471C>G	p.Gln1491Glu	p.Q1491E	ENST00000262367	NM_004380.2	1491	Caa/Gaa	27/31	1	2	FACETS	0.466	0.382	0.561	0.466	0.382	0.561	SUBCLONAL	1	TRUE	1	0.21	2		0	736	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577152	7577154	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	ACC	ACC	-	rs1567548347	NA	P-0021794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	89	648	0	ENST00000269305.4:c.784_786del	p.Gly262del	p.G262del	ENST00000269305	NM_001126112.2	262	GGT/-	8/11	0.294448595757022	1	FACETS	0.7	0.622	0.785	0.7	0.622	0.785	SUBCLONAL	1	TRUE	0	0.333475537697668	1		648	635	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851193	63851193	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	84	647	0	ENST00000279873.7:c.1971C>G	p.Phe657Leu	p.F657L	ENST00000279873	NM_032199.2	657	ttC/ttG	10/10	1	2	FACETS	0.627	0.553	0.707	0.627	0.553	0.707	SUBCLONAL	1	TRUE	1	0.333475537697668	2		647	803	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911154	32911154	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	78	526	0	ENST00000380152.3:c.2663del	p.Asn888IlefsTer7	p.N888Ifs*7	ENST00000380152		888	Aat/at	11/27	0.333475537697668	1	FACETS	0.836	0.738	0.942	0.836	0.738	0.942	CLONAL	1	TRUE	0	0.333475537697668	1		526	466	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675514	40675514	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	96	586	0	ENST00000249776.8:c.295C>T	p.Gln99Ter	p.Q99*	ENST00000249776	NM_033286.3	99	Cag/Tag	2/9	1	2	FACETS	0.795	0.709	0.888	0.795	0.709	0.888	SUBCLONAL	1	TRUE	1	0.333475537697668	2		586	724	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793361	42793361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	132	775	1	ENST00000575354.2:c.1163G>A	p.Gly388Asp	p.G388D	ENST00000575354	NM_015125.3	388	gGc/gAc	8/20	1	2	FACETS	0.902	0.818	0.99	0.902	0.818	0.99	CLONAL	1	TRUE	1	0.333475537697668	2		776	878	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466874	57466874	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	128	633	0	ENST00000371085.3:c.93G>C	p.Gln31His	p.Q31H	ENST00000371085	NM_000516.4	31	caG/caC	1/13	0.269042105067845	3	FACETS	0.841	0.761	0.926			1	CLONAL	1	TRUE	NA	0.333475537697668	3		633	1065	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244148	153244148	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	144	756	0	ENST00000281708.4:c.2009del	p.Gly670GlufsTer37	p.G670Efs*37	ENST00000281708	NM_033632.3	670	gGa/ga	12/12	0.333475537697668	1	FACETS	0.801	0.731	0.876	0.801	0.731	0.876	CLONAL	1	TRUE	0	0.333475537697668	1		756	898	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0022121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	21	368	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	0.317	0.243	0.403	0.317	0.243	0.403	SUBCLONAL	1	TRUE	1	0.290946939834934	2		368	456	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879229	151879229	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763438739	NA	P-0022121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	74	578	2	ENST00000262189.6:c.5716C>T	p.Arg1906Ter	p.R1906*	ENST00000262189	NM_170606.2	1906	Cga/Tga	36/59	0.237709046854236	3	FACETS	0.752	0.657	0.854	0.376	0.328	0.427	SUBCLONAL	1	TRUE	1	0.290946939834934	3		580	775	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291798	15291798	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs759991207	NA	P-0022121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	76	790	0	ENST00000263388.2:c.2968G>C	p.Glu990Gln	p.E990Q	ENST00000263388	NM_000435.2	990	Gag/Cag	18/33	1	2	FACETS	0.598	0.524	0.679	0.598	0.524	0.679	SUBCLONAL	1	TRUE	1	0.290946939834934	2		790	873	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176330	24176331	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0022121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	257	586	0	ENST00000263121.7:c.1121_1122insC	p.Met375AspfsTer70	p.M375Dfs*70	ENST00000263121	NM_003073.3	374	cgg/cgCg	9/9	0.290946939834934	0	FACETS	0.904	0.859	0.948			1	CLONAL	3	TRUE	0	0.290946939834934	0		586	462	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067935	30067944	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGGTGATTT	CTGGTGATTT	-	novel	NA	P-0022121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	171	506	0	ENST00000338641.4:c.1122+1_1122+10del		p.X374_splice	ENST00000338641	NM_000268.3	374		11/16	0.290946939834934	0	FACETS	0.725	0.677	0.775			1	SUBCLONAL	3	TRUE	0	0.290946939834934	0		506	383	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407502	407502	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	78	510	0	ENST00000380956.4:c.1260C>G	p.Asn420Lys	p.N420K	ENST00000380956	NM_001195286.1	420	aaC/aaG	9/9	1	2	FACETS	0.924	0.813	1	0.924	0.813	1	CLONAL	1	TRUE	1	0.290946939834934	2		510	580	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874476	151874476	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	69	543	0	ENST00000262189.6:c.8062A>C	p.Lys2688Gln	p.K2688Q	ENST00000262189	NM_170606.2	2688	Aaa/Caa	38/59	0.237709046854236	3	FACETS	0.837	0.729	0.954	0.419	0.364	0.477	CLONAL	1	TRUE	1	0.290946939834934	3		543	649	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528737	8528737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	181	427	0	ENST00000356435.5:c.395C>T	p.Pro132Leu	p.P132L	ENST00000356435		132	cCa/cTa	4/35	1	2	FACETS	1	0.985	1	1	0.994	1	CLONAL	2	TRUE	1	0.290946939834934	2		427	512	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185243	123185243	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	57	650	0	ENST00000218089.9:c.1195del	p.Gln399ArgfsTer26	p.Q399Rfs*26	ENST00000218089	NM_001042749.1	399	Cag/ag	13/35	0.290946939834934	5	FACETS	0.612	0.524	0.71	0.153	0.131	0.178	SUBCLONAL	1	TRUE	1	0.290946939834934	5		650	919	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0022951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	85	450	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.948	0.842	1	0.948	0.842	1	CLONAL	1	TRUE	1	0.39679891066689	2		450	452	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0022951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	103	511	1	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	0.919	0.825	1	0.919	0.825	1	CLONAL	1	TRUE	1	0.39679891066689	2		512	565	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0022951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	44	663	0	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	1	2	FACETS	0.373	0.312	0.441	0.373	0.312	0.441	SUBCLONAL	1	TRUE	1	0.39679891066689	2		663	594	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307913	11307913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557482604	NA	P-0022951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	136	539	1	ENST00000361445.4:c.1079G>A	p.Arg360Gln	p.R360Q	ENST00000361445	NM_004958.3	360	cGg/cAg	7/58	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.39679891066689	2		540	671	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572651	64572651	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	141	686	0	ENST00000312049.6:c.1205C>A	p.Ser402Tyr	p.S402Y	ENST00000312049	NM_130799.2	402	tCc/tAc	9/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.39679891066689	2		686	651	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56367665	56367673	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTCACAGA	TTTCACAGA	-	novel	NA	P-0022951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	56	164	0	ENST00000348428.3:c.499-6_501del		p.X167_splice	ENST00000348428	NM_006785.3	167		4/17	1	2	FACETS	0.893	0.77	1	0.893	0.77	1	CLONAL	1	TRUE	1	0.39679891066689	2		164	316	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030641	47030646	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	CAGCCA	CAGCCA	ATCCTGCTGAGGATGCAGCATGCTGAGGATGCTG	novel	NA	P-0022951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	109	448	0	ENST00000377604.3:c.416_421delinsATCCTGCTGAGGATGCAGCATGCTGAGGATGCTG	p.Ala139AspfsTer9	p.A139Dfs*9	ENST00000377604	NM_001204468.1	139	gCAGCCAct/gATCCTGCTGAGGATGCAGCATGCTGAGGATGCTGct	4/24	1	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.39679891066689	1		448	325	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0022951-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	112	450	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.586	0.527	0.649	0.586	0.527	0.649	SUBCLONAL	1	FALSE	1	0.508814023199465	2		450	751	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0022951-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	128	511	1	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	0.722	0.655	0.792	0.722	0.655	0.792	SUBCLONAL	1	FALSE	1	0.508814023199465	2		512	697	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307913	11307913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557482604	NA	P-0022951-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	144	539	1	ENST00000361445.4:c.1079G>A	p.Arg360Gln	p.R360Q	ENST00000361445	NM_004958.3	360	cGg/cAg	7/58	NA	2	FACETS	0.737	0.673	0.804			1	INDETERMINATE	1	FALSE	NA	0.508814023199465	2		540	768	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572651	64572651	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022951-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	210	686	0	ENST00000312049.6:c.1205C>A	p.Ser402Tyr	p.S402Y	ENST00000312049	NM_130799.2	402	tCc/tAc	9/10	1	2	FACETS	0.827	0.768	0.888	0.827	0.768	0.888	CLONAL	1	FALSE	1	0.508814023199465	2		686	998	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56367665	56367673	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTCACAGA	TTTCACAGA	-	novel	NA	P-0022951-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	60	164	0	ENST00000348428.3:c.499-6_501del		p.X167_splice	ENST00000348428	NM_006785.3	167		4/17	1	2	FACETS	0.842	0.732	0.96	0.842	0.732	0.96	CLONAL	1	FALSE	1	0.508814023199465	2		164	280	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030641	47030646	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	CAGCCA	CAGCCA	ATCCTGCTGAGGATGCAGCATGCTGAGGATGCTG	novel	NA	P-0022951-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	134	448	0	ENST00000377604.3:c.416_421delinsATCCTGCTGAGGATGCAGCATGCTGAGGATGCTG	p.Ala139AspfsTer9	p.A139Dfs*9	ENST00000377604	NM_001204468.1	139	gCAGCCAct/gATCCTGCTGAGGATGCAGCATGCTGAGGATGCTGct	4/24	1	1	FACETS	0.785	0.718	0.855	0.785	0.718	0.855	SUBCLONAL	1	FALSE	0	0.508814023199465	1		448	500	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466022	69466022	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022951-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	214	952	0	ENST00000227507.2:c.860C>G	p.Pro287Arg	p.P287R	ENST00000227507	NM_053056.2	287	cCc/cGc	5/5	1	2	FACETS	0.721	0.669	0.775	0.721	0.669	0.775	SUBCLONAL	1	FALSE	1	0.508814023199465	2		952	1167	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023746-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	245	345	0				ENST00000310581	NM_198253.2	-/1132			0.334013272033751	6	FACETS	1	0.987	1	0.73	0.697	0.762	INDETERMINATE	4	FALSE	0	0.771009496382249	6		345	369	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0023746-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	287	800	1	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.544425476259035	5	FACETS	1	0.981	1	0.721	0.682	0.761	CLONAL	2	FALSE	2	0.771009496382249	5		801	742	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794690	42794690	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023746-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	111	924	1	ENST00000575354.2:c.1770C>A	p.Phe590Leu	p.F590L	ENST00000575354	NM_015125.3	590	ttC/ttA	10/20	0.771009496382249	6	FACETS	1	0.907	1	0.252	0.226	0.279	CLONAL	1	FALSE	2	0.771009496382249	6		925	726	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982329	201982330	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0023746-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	303	936	0	ENST00000359651.3:c.709_710dup	p.Gly238ArgfsTer17	p.G238Rfs*17	ENST00000359651		236	-/AA	6/8	0.771009496382249	2	FACETS	1	0.994	1	0.681	0.649	0.713	CLONAL	1	FALSE	0	0.771009496382249	2		936	577	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426279	49426279	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023746-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	205	928	0	ENST00000301067.7:c.12209C>T	p.Ser4070Phe	p.S4070F	ENST00000301067	NM_003482.3	4070	tCt/tTt	39/54	0.702390613105883	4	FACETS	1	0.988	1	0.644	0.599	0.69	CLONAL	1	FALSE	2	0.771009496382249	4		928	731	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426355	49426355	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023746-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	203	979	0	ENST00000301067.7:c.12133C>T	p.Gln4045Ter	p.Q4045*	ENST00000301067	NM_003482.3	4045	Cag/Tag	39/54	0.702390613105883	4	FACETS	1	0.986	1	0.623	0.579	0.668	CLONAL	1	FALSE	2	0.771009496382249	4		979	749	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426526	49426526	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023746-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	228	1071	1	ENST00000301067.7:c.11962C>T	p.Gln3988Ter	p.Q3988*	ENST00000301067	NM_003482.3	3988	Cag/Tag	39/54	0.702390613105883	4	FACETS	1	0.977	1	0.552	0.515	0.591	CLONAL	1	FALSE	2	0.771009496382249	4		1072	948	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426531	49426531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023746-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	241	1067	0	ENST00000301067.7:c.11957C>T	p.Ser3986Phe	p.S3986F	ENST00000301067	NM_003482.3	3986	tCt/tTt	39/54	0.702390613105883	4	FACETS	1	0.983	1	0.572	0.534	0.611	CLONAL	1	FALSE	2	0.771009496382249	4		1067	968	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426595	49426595	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023746-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	246	1182	0	ENST00000301067.7:c.11893C>T	p.Gln3965Ter	p.Q3965*	ENST00000301067	NM_003482.3	3965	Cag/Tag	39/54	0.702390613105883	4	FACETS	1	0.969	1	0.53	0.495	0.566	CLONAL	1	FALSE	2	0.771009496382249	4		1182	1066	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426751	49426751	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023746-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	261	1120	0	ENST00000301067.7:c.11737C>T	p.Gln3913Ter	p.Q3913*	ENST00000301067	NM_003482.3	3913	Cag/Tag	39/54	0.702390613105883	4	FACETS	1	0.989	1	0.615	0.577	0.654	CLONAL	1	FALSE	2	0.771009496382249	4		1120	975	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116176	67116176	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023746-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	119	667	0	ENST00000412916.2:c.460G>C	p.Glu154Gln	p.E154Q	ENST00000412916		154	Gaa/Caa	5/6	0.771009496382249	5	FACETS	1	0.934	1	0.347	0.314	0.382	CLONAL	1	FALSE	2	0.771009496382249	5		667	639	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14628969	14628969	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023746-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	256	1163	0	ENST00000254322.2:c.193G>C	p.Asp65His	p.D65H	ENST00000254322	NM_006145.1	65	Gac/Cac	1/3	0.765937961121377	4	FACETS	1	0.992	1	0.706	0.663	0.75	CLONAL	1	FALSE	2	0.771009496382249	4		1163	833	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541890	187541891	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023746-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	441	912	0	ENST00000441802.2:c.5849dup	p.Thr1951AsnfsTer3	p.T1951Nfs*3	ENST00000441802	NM_005245.3	1950	cta/ctTa	10/27	0.771009496382249	3	FACETS	0.97	0.933	1	0.97	0.933	1	CLONAL	2	FALSE	1	0.771009496382249	3		912	817	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176490	123176490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023746-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	72	227	0	ENST00000218089.9:c.457G>A	p.Asp153Asn	p.D153N	ENST00000218089	NM_001042749.1	153	Gat/Aat	7/35	0.771009496382249	2	FACETS	0.798	0.708	0.893			1	SUBCLONAL	1	FALSE	NA	0.771009496382249	2		227	234	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627478	14627478	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023746-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	168	618	2	ENST00000254322.2:c.592C>T	p.Arg198Ter	p.R198*	ENST00000254322	NM_006145.1	198	Cga/Tga	2/3	0.765937961121377	4	FACETS	1	0.988	1	0.694	0.642	0.748	CLONAL	1	FALSE	2	0.771009496382249	4		620	556	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852289	128852289	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023746-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	94	813	0	ENST00000249373.3:c.2361C>G	p.Phe787Leu	p.F787L	ENST00000249373	NM_005631.4	787	ttC/ttG	12/12	0.153128951137923	6	FACETS	1	0.971	1	0.422	0.376	0.469	INDETERMINATE	1	FALSE	3	0.771009496382249	6		813	490	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916735	48916735	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023746-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	41	343	0	ENST00000267163.4:c.265G>A	p.Gly89Arg	p.G89R	ENST00000267163	NM_000321.2	89	Gga/Aga	3/27	0.59112551283703	4	FACETS	0.622	0.52	0.733	0.311	0.26	0.367	SUBCLONAL	1	FALSE	2	0.771009496382249	4		343	303	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857607	78858078	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGCCATCTGCCTGGAGCAGCTCAACGACCCGCACCCCTTGCTGCGCCAGTGGGTGGCCATCTGCCTCGGCAGGATCTGGCAGAACTTCGACTCGGCGAGGTGGTGCGGCGTGAGGGACAGCGCTCATGAGAAGCTCTACAGCCTCCTCTCCGACCCCATTCCCGAGGTGAGTCAGGCGGGGGCTCAGAGTCCAGTCCTCCTGGCTGCCGACTGCGGGGGTAAGGCAGAGGTCTGCTCGCGTGCGGGTGTGGCCGGCCACGTGTCCAGGAACTTCAGGGGCTGCACGCTAATAAGAGTAGGACAGTGGGACCTTGGTGAGAAGAGAACCACACCACTGGGGATTTTGCACCCAGGCCCAGAGTGCGCTCCCGGGGACAGTGGCACAGCTGCAAGCGGGGGTCCCAGAGGGAACCTCAGAGGCAGGGGTCACGTGCTCGCTGTCCGGGTGCCGCTCTGCGTCCTCACTGTGGCC	TGCCATCTGCCTGGAGCAGCTCAACGACCCGCACCCCTTGCTGCGCCAGTGGGTGGCCATCTGCCTCGGCAGGATCTGGCAGAACTTCGACTCGGCGAGGTGGTGCGGCGTGAGGGACAGCGCTCATGAGAAGCTCTACAGCCTCCTCTCCGACCCCATTCCCGAGGTGAGTCAGGCGGGGGCTCAGAGTCCAGTCCTCCTGGCTGCCGACTGCGGGGGTAAGGCAGAGGTCTGCTCGCGTGCGGGTGTGGCCGGCCACGTGTCCAGGAACTTCAGGGGCTGCACGCTAATAAGAGTAGGACAGTGGGACCTTGGTGAGAAGAGAACCACACCACTGGGGATTTTGCACCCAGGCCCAGAGTGCGCTCCCGGGGACAGTGGCACAGCTGCAAGCGGGGGTCCCAGAGGGAACCTCAGAGGCAGGGGTCACGTGCTCGCTGTCCGGGTGCCGCTCTGCGTCCTCACTGTGGCC	-	novel	NA	P-0023746-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	115	848	0	ENST00000306801.3:c.1680_1842+309del		p.X560_splice	ENST00000306801	NM_020761.2	560		16/34	0.564125139722679	6	FACETS	1	0.966	1	0.289	0.26	0.319	CLONAL	1	FALSE	2	0.771009496382249	6		848	656	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631369	67631369	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023746-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	118	591	0	ENST00000272342.5:c.1555G>A	p.Glu519Lys	p.E519K	ENST00000272342	NM_019002.3	519	Gaa/Aaa	5/6	0.661401028740236	4	FACETS	1	0.974	1	0.604	0.548	0.661	CLONAL	1	FALSE	2	0.771009496382249	4		591	449	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151615	55151615	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023746-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	80	521	0	ENST00000257290.5:c.2401C>A	p.Gln801Lys	p.Q801K	ENST00000257290	NM_006206.4	801	Caa/Aaa	17/23	0.771009496382249	3	FACETS	0.659	0.583	0.741	0.33	0.291	0.371	SUBCLONAL	1	FALSE	1	0.771009496382249	3		521	436	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778143	27778143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023746-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	150	1308	0	ENST00000369163.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000369163	NM_003536.2	98	Gag/Aag	1/1	0.265123276588139	6	FACETS	1	0.953	1	0.177	0.162	0.194	INDETERMINATE	1	FALSE	0	0.771009496382249	6		1308	929	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675495	30675495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023746-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	132	1038	0	ENST00000376406.3:c.2861G>A	p.Gly954Glu	p.G954E	ENST00000376406	NM_014641.2	954	gGg/gAg	8/15	0.265123276588139	6	FACETS	1	0.976	1	0.202	0.183	0.221	INDETERMINATE	1	FALSE	0	0.771009496382249	6		1038	719	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0024836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	246	735	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.261798577904936	2	FACETS	0.808	0.755	0.862	0.808	0.755	0.862	CLONAL	2	TRUE	0	0.3	2		735	1015	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259903	16259903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	62	459	2	ENST00000375759.3:c.7168C>T	p.Pro2390Ser	p.P2390S	ENST00000375759	NM_015001.2	2390	Ccc/Tcc	11/15	1	2	FACETS	0.502	0.433	0.578	0.502	0.433	0.578	SUBCLONAL	1	TRUE	1	0.3	2		461	823	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785662	50785662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	75	532	1	ENST00000398568.2:c.652G>A	p.Gly218Ser	p.G218S	ENST00000398568	NM_001042412.1	218	Ggt/Agt	4/18	1	2	FACETS	0.548	0.479	0.623	0.548	0.479	0.623	SUBCLONAL	1	TRUE	1	0.3	2		533	912	SUCCESS
APC	324	MSKCC	GRCh37	5	112175564	112175565	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0024836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	89	275	0	ENST00000257430.4:c.4275_4276dup	p.Ser1426IlefsTer48	p.S1426Ifs*48	ENST00000257430	NM_000038.5	1425	gat/gATat	16/16	0.3	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.3	1		275	430	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251882	153251884	+	splice_donor_variant,coding_sequence_variant	Splice_Site	TNP	ACC	ACC	TCA	novel	NA	P-0024836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	48	430	0	ENST00000281708.4:c.1122_1122+2delinsTGA		p.X374_splice	ENST00000281708	NM_033632.3	374		7/12	1	2	FACETS	0.464	0.391	0.544	0.464	0.391	0.544	SUBCLONAL	1	TRUE	1	0.3	2		430	690	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0025356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	137	735	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.286800401699899	1	FACETS	0.932	0.848	1	0.932	0.848	1	CLONAL	1	TRUE	0	0.313535705488093	1		735	791	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0025356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	120	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.88	0.794	0.971	0.88	0.794	0.971	CLONAL	1	TRUE	1	0.313535705488093	2		485	870	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	90	387	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.286800401699899	1	FACETS	0.888	0.79	0.992	0.888	0.79	0.992	CLONAL	1	TRUE	0	0.313535705488093	1		387	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0025538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	713	456	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.820373226527345	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.820373226527345	3		456	769	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0025657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	64	419	1	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.218353740018599	1	FACETS	0.525	0.455	0.6	0.525	0.455	0.6	INDETERMINATE	1	TRUE	0	0.406414070693177	1		420	478	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221708	22221709	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCG	rs751880548	NA	P-0025657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	15	56	1	ENST00000215832.6:c.20_22dup	p.Ala7dup	p.A7dup	ENST00000215832	NM_002745.4	7	ggc/gCGGgc	1/9	1	2	FACETS	0.802	0.596	1	0.802	0.596	1	CLONAL	1	TRUE	1	0.406414070693177	2		57	92	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861055	35861055	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	37	403	0	ENST00000303115.3:c.184C>A	p.Pro62Thr	p.P62T	ENST00000303115	NM_002185.3	62	Cca/Aca	2/8	1	2	FACETS	0.275	0.226	0.33	0.275	0.226	0.33	SUBCLONAL	1	TRUE	1	0.406414070693177	2		403	663	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073643	8073643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746627277	NA	P-0025657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	35	384	1	ENST00000377482.5:c.1016C>T	p.Pro339Leu	p.P339L	ENST00000377482	NM_018948.3	339	cCg/cTg	4/4	1	2	FACETS	0.279	0.228	0.336	0.279	0.228	0.336	SUBCLONAL	1	TRUE	1	0.406414070693177	2		385	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578209	7578209	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	125	680	0	ENST00000269305.4:c.640C>G	p.His214Asp	p.H214D	ENST00000269305	NM_001126112.2	214	Cat/Gat	6/11	1	2	FACETS	0.65	0.587	0.716	0.65	0.587	0.716	SUBCLONAL	1	TRUE	1	0.406414070693177	2		680	947	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411879	116411900	+	splice_region_variant,intron_variant	Splice_Region	DEL	CTCTTTCTTTCTCTCTGTTTTA	CTCTTTCTTTCTCTCTGTTTTA	-	novel	NA	P-0025657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1241	1694	894	0	ENST00000397752.3:c.2888-24_2888-3del		p.X963_splice	ENST00000397752	NM_000245.2	963			0.406414070693177	7	FACETS	0.954	0.936	0.973			1	CLONAL	6	TRUE	NA	0.406414070693177	7		894	2935	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0025802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	360	642	1	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.670262883306656	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.675721098589775	2		643	516	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643380	38643380	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	134	398	0	ENST00000299084.4:c.850A>G	p.Lys284Glu	p.K284E	ENST00000299084	NM_152594.2	284	Aaa/Gaa	7/7	0.45969488906083	4	FACETS	0.947	0.871	1	0.947	0.871	1	CLONAL	2	TRUE	2	0.675721098589775	4		398	351	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492899	56492899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1409912837	NA	P-0025802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	66	214	0	ENST00000407977.2:c.40C>T	p.Pro14Ser	p.P14S	ENST00000407977		14	Ccc/Tcc	2/10	0.675721098589775	3	FACETS	0.998	0.876	1	0.333	0.292	0.376	CLONAL	1	TRUE	0	0.675721098589775	3		214	262	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577564	7577564	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057522275	NA	P-0026371-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	301	548	0	ENST00000269305.4:c.717C>G	p.Asn239Lys	p.N239K	ENST00000269305	NM_001126112.2	239	aaC/aaG	7/11	0.502297436137852	2	FACETS	0.869	0.827	0.912	0.869	0.827	0.912	CLONAL	2	TRUE	0	0.572261421945746	2		548	605	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577572	7577572	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026371-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	317	541	0	ENST00000269305.4:c.709A>C	p.Met237Leu	p.M237L	ENST00000269305	NM_001126112.2	237	Atg/Ctg	7/11	0.502297436137852	2	FACETS	0.898	0.856	0.94	0.898	0.856	0.94	CLONAL	2	TRUE	0	0.572261421945746	2		541	617	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242482	+	protein_altering_variant	In_Frame_Del	DEL	GAATTAAGAGAAGCAAC	GAATTAAGAGAAGCAAC	AT	rs727504402	NA	P-0026371-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	242	368	1	ENST00000275493.2:c.2236_2252delinsAT	p.Glu746_Thr751delinsIle	p.E746_T751delinsI	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCAACa/ATa	19/28	0.572261421945746	4	FACETS	0.995	0.935	1	0.664	0.623	0.704	CLONAL	2	TRUE	1	0.572261421945746	4		369	668	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822439	72822439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026371-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	55	793	0	ENST00000268489.5:c.9736G>A	p.Ala3246Thr	p.A3246T	ENST00000268489	NM_006885.3	3246	Gca/Aca	10/10	NA	2	FACETS	0.208	0.177	0.242			1	INDETERMINATE	1	TRUE	NA	0.572261421945746	2		793	923	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593689	215593689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026371-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	113	377	0	ENST00000260947.4:c.2045C>T	p.Thr682Ile	p.T682I	ENST00000260947	NM_000465.2	682	aCc/aTc	11/11	0.160951491279237	1	FACETS	0.589	0.532	0.647	0.589	0.532	0.647	INDETERMINATE	1	TRUE	0	0.572261421945746	1		377	479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0027025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	355	599	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	0.430725787242122	2	FACETS	0.903	0.858	0.948	0.903	0.858	0.948	CLONAL	2	TRUE	0	0.430725787242122	2		599	913	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971039	21971040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0027025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	266	422	0	ENST00000304494.5:c.318dup	p.Arg107AlafsTer13	p.R107Afs*13	ENST00000304494	NM_000077.4	106	-/G	2/3	0.379466375091888	2	FACETS	0.896	0.845	0.948	0.896	0.845	0.948	CLONAL	2	TRUE	0	0.430725787242122	2		422	689	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	187	543	0	ENST00000324856.7:c.666C>A	p.Tyr222Ter	p.Y222*	ENST00000324856	NM_006015.4	222	taC/taA	1/20	1	2	FACETS	0.911	0.842	0.983	0.911	0.842	0.983	CLONAL	1	TRUE	1	0.430725787242122	2		543	953	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929084	32929099	+	frameshift_variant	Frame_Shift_Del	DEL	ATCTGACTTTGGAAAA	ATCTGACTTTGGAAAA	-	novel	NA	P-0027025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	74	511	0	ENST00000380152.3:c.7098_7113del	p.Thr2367GlnfsTer4	p.T2367Qfs*4	ENST00000380152		2365	cATCTGACTTTGGAAAAa/ca	14/27	1	2	FACETS	0.41	0.358	0.466	0.41	0.358	0.466	SUBCLONAL	1	TRUE	1	0.430725787242122	2		511	839	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435669	110435669	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910525456	NA	P-0027025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	203	504	1	ENST00000375856.3:c.2732C>T	p.Pro911Leu	p.P911L	ENST00000375856	NM_003749.2	911	cCg/cTg	1/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.430725787242122	2		505	810	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95597861	95597861	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	76	473	0	ENST00000393063.1:c.423G>C	p.Glu141Asp	p.E141D	ENST00000393063	NM_030621.3	141	gaG/gaC	5/28	1	2	FACETS	0.455	0.399	0.516	0.455	0.399	0.516	SUBCLONAL	1	TRUE	1	0.430725787242122	2		473	775	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454546	99454546	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	48	422	0	ENST00000268035.6:c.1465G>T	p.Glu489Ter	p.E489*	ENST00000268035	NM_000875.3	489	Gaa/Taa	7/21	0.379406090776418	2	FACETS	0.321	0.271	0.377	0.161	0.135	0.189	SUBCLONAL	1	TRUE	0	0.430725787242122	2		422	694	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113810	11113810	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	81	624	0	ENST00000358026.2:c.1918G>T	p.Glu640Ter	p.E640*	ENST00000358026	NM_001128849.1	640	Gag/Tag	12/36	0.379406090776418	2	FACETS	0.462	0.406	0.522	0.231	0.203	0.261	SUBCLONAL	1	TRUE	0	0.430725787242122	2		624	814	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983095	149983095	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	98	552	0	ENST00000253339.5:c.3163G>T	p.Glu1055Ter	p.E1055*	ENST00000253339		1055	Gaa/Taa	7/7	0.156530504981164	3	FACETS	0.559	0.497	0.624	0.186	0.165	0.208	INDETERMINATE	1	TRUE	0	0.430725787242122	3		552	990	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55225370	55225370	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	202	468	1	ENST00000275493.2:c.1222C>T	p.Gln408Ter	p.Q408*	ENST00000275493	NM_005228.3	408	Cag/Tag	11/28	0.273826721714662	3	FACETS	1	0.959	1	0.525	0.486	0.566	CLONAL	1	TRUE	1	0.430725787242122	3		469	1085	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0027826-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	208	644	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.493665017801189	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.493665017801189	1		645	523	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178641	108178641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775036118	NA	P-0027826-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	144	329	2	ENST00000278616.4:c.5692C>T	p.Arg1898Ter	p.R1898*	ENST00000278616	NM_000051.3	1898	Cga/Tga	38/63	0.153988142626246	3	FACETS	1	0.987	1	0.726	0.666	0.788	INDETERMINATE	1	TRUE	1	0.493665017801189	3		331	501	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155445	47155445	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0027826-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	159	467	0	ENST00000409792.3:c.4636A>T	p.Arg1546Ter	p.R1546*	ENST00000409792	NM_014159.6	1546	Aga/Tga	5/21	0.493665017801189	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.493665017801189	1		467	404	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046294	69046294	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1436851943	NA	P-0027826-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	96	367	0	ENST00000288368.4:c.3767A>G	p.Asp1256Gly	p.D1256G	ENST00000288368	NM_024870.2	1256	gAt/gGt	32/40	1	2	FACETS	0.88	0.788	0.976	0.88	0.788	0.976	CLONAL	1	TRUE	1	0.493665017801189	2		367	442	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0027898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	153	734	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		734	725	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063335	67063368	+	frameshift_variant	Frame_Shift_Del	DEL	AGAAGCAAGTTCGAGAACGAGGAGTTTTTTAGGA	AGAAGCAAGTTCGAGAACGAGGAGTTTTTTAGGA	-	novel	NA	P-0027898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	18	226	0	ENST00000412916.2:c.27_60del	p.Arg9SerfsTer2	p.R9Sfs*2	ENST00000412916		9	AGAAGCAAGTTCGAGAACGAGGAGTTTTTTAGGAag/ag	1/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		226	314	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846076	68846076	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	197	667	0	ENST00000261769.5:c.1048del	p.Leu350PhefsTer6	p.L350Ffs*6	ENST00000261769	NM_004360.3	349	gaC/ga	8/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		667	896	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	136	277	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.978	0.891	1	0.978	0.891	1	CLONAL	1	TRUE	1	0.414520861759268	2		277	671	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	199	650	3	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.997	0.924	1	0.997	0.924	1	CLONAL	1	TRUE	1	0.414520861759268	2		653	963	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	163	431	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.414520861759268	2		437	749	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	196	715	1	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.808	0.747	0.872	0.808	0.747	0.872	CLONAL	1	TRUE	1	0.414520861759268	2		716	1170	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885632	23885632	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	142	414	1	ENST00000374561.5:c.286del	p.His96ThrfsTer30	p.H96Tfs*30	ENST00000374561	NM_002167.4	96	Cac/ac	1/3	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.414520861759268	2		415	602	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	94	341	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	0.774	0.69	0.863	0.774	0.69	0.863	SUBCLONAL	1	TRUE	1	0.414520861759268	2		341	586	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	396	581	7	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.894	0.852	0.937	1	0.996	1	CLONAL	2	TRUE	1	0.414520861759268	2		588	1068	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	225	331	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.414520861759268	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.414520861759268	2		331	534	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435300	110435302	+	inframe_deletion	In_Frame_Del	DEL	GGT	GGT	-	rs765493638	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	73	225	2	ENST00000375856.3:c.3099_3101del	p.Pro1036del	p.P1036del	ENST00000375856	NM_003749.2	1033	ccACCg/ccg	1/2	1	2	FACETS	0.922	0.811	1	0.922	0.811	1	CLONAL	1	TRUE	1	0.414520861759268	2		227	382	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	126	443	7	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.913	0.828	1	0.913	0.828	1	CLONAL	1	TRUE	1	0.414520861759268	2		450	666	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	148	593	0	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	1	2	FACETS	0.802	0.733	0.875	0.802	0.733	0.875	CLONAL	1	TRUE	1	0.414520861759268	2		593	890	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72891538	72891538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs529764235	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	172	340	0	ENST00000325599.8:c.224G>A	p.Arg75His	p.R75H	ENST00000325599	NM_018130.2	75	cGc/cAc	3/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.414520861759268	2		340	745	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900984	114900984	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778855667	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	189	565	1	ENST00000543371.1:c.598del	p.Leu200SerfsTer25	p.L200Sfs*25	ENST00000543371	NM_001198531.1	198	caC/ca	6/14	1	2	FACETS	0.893	0.825	0.964	0.893	0.825	0.964	CLONAL	1	TRUE	1	0.414520861759268	2		566	1021	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	167	502	1	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.978	0.899	1	0.978	0.899	1	CLONAL	1	TRUE	1	0.414520861759268	2		503	824	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980034	7980034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369807670	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	241	678	1	ENST00000319144.4:c.1303G>A	p.Val435Ile	p.V435I	ENST00000319144	NM_001139.2	435	Gtc/Atc	10/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.414520861759268	2		679	1127	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662458	227662458	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	136	472	2	ENST00000305123.5:c.997G>A	p.Glu333Lys	p.E333K	ENST00000305123	NM_005544.2	333	Gaa/Aaa	1/2	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.414520861759268	2		474	646	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274217	5274217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	178	484	0	ENST00000357368.4:c.230G>A	p.Arg77His	p.R77H	ENST00000357368	NM_002850.3	77	cGc/cAc	3/38	1	2	FACETS	0.906	0.835	0.98	0.906	0.835	0.98	CLONAL	1	TRUE	1	0.414520861759268	2		484	948	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222191	2222191	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs778747333	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	190	675	0	ENST00000398665.3:c.3023C>G	p.Ser1008Cys	p.S1008C	ENST00000398665	NM_032482.2	1008	tCc/tGc	24/28	1	2	FACETS	0.972	0.899	1	0.972	0.899	1	CLONAL	1	TRUE	1	0.414520861759268	2		675	943	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434182	12434182	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776687	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	199	476	1	ENST00000287820.6:c.556del	p.Ser186ValfsTer47	p.S186Vfs*47	ENST00000287820	NM_015869.4	184	Aaa/aa	4/7	0.414520861759268	2	FACETS	1	0.977	1	0.561	0.521	0.604	CLONAL	1	TRUE	0	0.414520861759268	2		477	855	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007806	45007807	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	133	473	0	ENST00000558401.1:c.253_254del	p.Leu85ValfsTer4	p.L85Vfs*4	ENST00000558401	NM_004048.2	85	TTg/g	2/4	0.414520861759268	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.414520861759268	1		473	502	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739024	145739024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371818842	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	216	551	0	ENST00000428558.2:c.2131G>A	p.Glu711Lys	p.E711K	ENST00000428558	NM_004260.3	711	Gag/Aag	13/22	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.414520861759268	2		551	972	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060955	38060955	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	94	332	0	ENST00000250448.2:c.1034del	p.Gly345AlafsTer5	p.G345Afs*5	ENST00000250448	NM_004496.3	345	gGc/gc	2/2	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.414520861759268	2		332	445	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940522	131940522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375315737	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	133	362	0	ENST00000265335.6:c.2549G>A	p.Arg850His	p.R850H	ENST00000265335		850	cGt/cAt	16/25	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.414520861759268	2		362	599	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40743886	40743886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434593	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	152	510	3	ENST00000392038.2:c.821G>A	p.Arg274His	p.R274H	ENST00000392038	NM_001626.4	274	cGc/cAc	9/14	1	2	FACETS	0.892	0.816	0.971	0.892	0.816	0.971	CLONAL	1	TRUE	1	0.414520861759268	2		513	822	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857379	9857380	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	130	404	0	ENST00000330684.3:c.4021dup	p.Ser1341LysfsTer25	p.S1341Kfs*25	ENST00000330684	NM_001134407.1	1341	agc/aAgc	13/13	1	2	FACETS	0.983	0.894	1	0.983	0.894	1	CLONAL	1	TRUE	1	0.414520861759268	2		404	638	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86668002	86668002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769775990	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	94	334	0	ENST00000274376.6:c.1766G>A	p.Arg589His	p.R589H	ENST00000274376	NM_002890.2	589	cGc/cAc	13/25	1	2	FACETS	0.888	0.792	0.988	0.888	0.792	0.988	CLONAL	1	TRUE	1	0.414520861759268	2		334	511	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259381	16259381	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	118	356	0	ENST00000375759.3:c.6646G>A	p.Ala2216Thr	p.A2216T	ENST00000375759	NM_015001.2	2216	Gct/Act	11/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.414520861759268	2		356	495	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483203	120483204	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	151	398	1	ENST00000256646.2:c.3157dup	p.Leu1053ProfsTer21	p.L1053Pfs*21	ENST00000256646	NM_024408.3	1053	ctg/cCtg	19/34	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.414520861759268	2		399	666	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444018	49444018	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	178	559	0	ENST00000301067.7:c.3353T>C	p.Leu1118Pro	p.L1118P	ENST00000301067	NM_003482.3	1118	cTa/cCa	11/54	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.414520861759268	2		559	815	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864847	57864847	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	176	607	0	ENST00000228682.2:c.2324C>A	p.Pro775His	p.P775H	ENST00000228682	NM_005269.2	775	cCc/cAc	12/12	1	2	FACETS	0.985	0.908	1	0.985	0.908	1	CLONAL	1	TRUE	1	0.414520861759268	2		607	862	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865628	57865628	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	250	735	0	ENST00000228682.2:c.3109del	p.Leu1037TrpfsTer23	p.L1037Wfs*23	ENST00000228682	NM_005269.2	1035	aaC/aa	12/12	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.414520861759268	2		735	1185	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504578	103504578	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	124	382	0	ENST00000355739.4:c.204del	p.Arg69GlufsTer15	p.R69Efs*15	ENST00000355739	NM_000123.3	67	Ttt/tt	2/15	1	2	FACETS	0.918	0.832	1	0.918	0.832	1	CLONAL	1	TRUE	1	0.414520861759268	2		382	652	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138478	2138478	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138831802	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	269	673	1	ENST00000219476.3:c.5291G>A	p.Ser1764Asn	p.S1764N	ENST00000219476	NM_000548.3	1764	aGc/aAc	42/42	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.414520861759268	2		674	1128	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868140	56868140	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	154	500	1	ENST00000308159.5:c.1638G>T	p.Glu546Asp	p.E546D	ENST00000308159	NM_014669.4	546	gaG/gaT	14/22	1	2	FACETS	0.835	0.764	0.909	0.835	0.764	0.909	CLONAL	1	TRUE	1	0.414520861759268	2		501	890	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245725	41245725	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs397508911	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	161	590	2	ENST00000357654.3:c.1823del	p.Lys608ArgfsTer4	p.K608Rfs*4	ENST00000357654	NM_007294.3	608	aAg/ag	10/23	1	2	FACETS	0.944	0.866	1	0.944	0.866	1	CLONAL	1	TRUE	1	0.414520861759268	2		592	823	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545653	63545653	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	163	470	0	ENST00000307078.5:c.941T>C	p.Met314Thr	p.M314T	ENST00000307078	NM_004655.3	314	aTg/aCg	3/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.414520861759268	2		470	703	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56367746	56367746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	169	420	1	ENST00000348428.3:c.572G>A	p.Arg191Gln	p.R191Q	ENST00000348428	NM_006785.3	191	cGa/cAa	4/17	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.414520861759268	2		421	713	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56376709	56376709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	82	469	0	ENST00000348428.3:c.749C>T	p.Ala250Val	p.A250V	ENST00000348428	NM_006785.3	250	gCt/gTt	5/17	1	2	FACETS	0.469	0.413	0.53	0.469	0.413	0.53	SUBCLONAL	1	TRUE	1	0.414520861759268	2		469	843	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298137	15298137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200317373	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	233	571	0	ENST00000263388.2:c.1619C>T	p.Thr540Met	p.T540M	ENST00000263388	NM_000435.2	540	aCg/aTg	11/33	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.414520861759268	2		571	993	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219922	36219922	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	192	607	0	ENST00000222270.7:c.4724T>C	p.Leu1575Pro	p.L1575P	ENST00000222270	NM_014727.1	1575	cTg/cCg	21/37	1	2	FACETS	0.96	0.888	1	0.96	0.888	1	CLONAL	1	TRUE	1	0.414520861759268	2		607	965	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471122	25471122	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	176	435	0	ENST00000264709.3:c.640-1G>T		p.X214_splice	ENST00000264709	NM_175629.2	214			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.414520861759268	2		435	755	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149670	202149670	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	122	507	0	ENST00000358485.4:c.1111T>G	p.Cys371Gly	p.C371G	ENST00000358485	NM_001080125.1	371	Tgc/Ggc	8/9	1	2	FACETS	0.813	0.736	0.895	0.813	0.736	0.895	CLONAL	1	TRUE	1	0.414520861759268	2		507	724	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225365203	225365203	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1559348578	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	110	274	0	ENST00000264414.4:c.1487T>C	p.Val496Ala	p.V496A	ENST00000264414	NM_003590.4	496	gTa/gCa	11/16	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.414520861759268	2		274	513	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793314	242793314	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	242	631	0	ENST00000334409.5:c.763A>G	p.Ser255Gly	p.S255G	ENST00000334409	NM_005018.2	255	Agc/Ggc	5/5	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.414520861759268	2		631	947	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022502	31022502	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs775538653	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	66	299	0	ENST00000375687.4:c.1987A>G	p.Ser663Gly	p.S663G	ENST00000375687	NM_015338.5	663	Agc/Ggc	13/13	1	2	FACETS	0.834	0.727	0.948	0.834	0.727	0.948	CLONAL	1	TRUE	1	0.414520861759268	2		299	382	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710625	40710625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	181	546	0	ENST00000373198.4:c.4226C>T	p.Ala1409Val	p.A1409V	ENST00000373198	NM_133170.3	1409	gCc/gTc	31/32	1	2	FACETS	0.946	0.873	1	0.946	0.873	1	CLONAL	1	TRUE	1	0.414520861759268	2		546	923	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206863	36206863	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	129	402	0	ENST00000300305.3:c.649G>T	p.Gly217Trp	p.G217W	ENST00000300305		217	Ggg/Tgg	6/8	1	2	FACETS	0.994	0.904	1	0.994	0.904	1	CLONAL	1	TRUE	1	0.414520861759268	2		402	626	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513409	41513409	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	172	537	4	ENST00000263253.7:c.313G>A	p.Ala105Thr	p.A105T	ENST00000263253	NM_001429.3	105	Gcc/Acc	2/31	1	2	FACETS	0.967	0.891	1	0.967	0.891	1	CLONAL	1	TRUE	1	0.414520861759268	2		541	858	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523641	41523641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	233	638	3	ENST00000263253.7:c.1057C>T	p.Arg353Cys	p.R353C	ENST00000263253	NM_001429.3	353	Cgc/Tgc	4/31	1	2	FACETS	0.983	0.916	1	0.983	0.916	1	CLONAL	1	TRUE	1	0.414520861759268	2		641	1144	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332739	153332739	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	143	468	0	ENST00000281708.4:c.217del	p.Gln73SerfsTer15	p.Q73Sfs*15	ENST00000281708	NM_033632.3	73	Cag/ag	2/12	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.414520861759268	2		468	676	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540104	187540105	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	121	346	0	ENST00000441802.2:c.7635_7636del	p.Gly2546ThrfsTer9	p.G2546Tfs*9	ENST00000441802	NM_005245.3	2545	agAGga/agga	10/27	1	2	FACETS	0.973	0.882	1	0.973	0.882	1	CLONAL	1	TRUE	1	0.414520861759268	2		346	600	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520223	176520223	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	179	598	0	ENST00000292408.4:c.1142C>A	p.Ala381Asp	p.A381D	ENST00000292408	NM_213647.1	381	gCt/gAt	9/18	1	2	FACETS	0.962	0.887	1	0.962	0.887	1	CLONAL	1	TRUE	1	0.414520861759268	2		598	898	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706902	117706902	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	142	466	0	ENST00000368508.3:c.2248del	p.Ala750LeufsTer2	p.A750Lfs*2	ENST00000368508	NM_002944.2	750	Gct/ct	15/43	1	2	FACETS	0.877	0.8	0.958	0.877	0.8	0.958	CLONAL	1	TRUE	1	0.414520861759268	2		466	781	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450321	50450321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	168	541	0	ENST00000331340.3:c.505G>A	p.Gly169Arg	p.G169R	ENST00000331340	NM_006060.4	169	Ggg/Agg	5/8	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.414520861759268	2		541	791	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221814	55221815	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	252	715	0	ENST00000275493.2:c.861dup	p.Gly288TrpfsTer11	p.G288Wfs*11	ENST00000275493	NM_005228.3	286	-/T	7/28	1	2	FACETS	0.992	0.927	1	0.992	0.927	1	CLONAL	1	TRUE	1	0.414520861759268	2		715	1226	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540214	23540219	+	inframe_deletion	In_Frame_Del	DEL	CTCTGG	CTCTGG	-	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	33	328	1	ENST00000380871.4:c.184_189del	p.Pro62_Glu63del	p.P62_E63del	ENST00000380871	NM_006167.3	62	CCAGAG/-	1/2	1	2	FACETS	0.369	0.3	0.446	0.369	0.3	0.446	SUBCLONAL	1	TRUE	1	0.414520861759268	2		329	432	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563503	87563503	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	180	648	0	ENST00000277120.3:c.1891A>G	p.Met631Val	p.M631V	ENST00000277120		631	Atg/Gtg	16/19	1	2	FACETS	0.892	0.822	0.964	0.892	0.822	0.964	CLONAL	1	TRUE	1	0.414520861759268	2		648	974	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755916	133755916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766145624	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	183	538	1	ENST00000318560.5:c.1543G>A	p.Val515Ile	p.V515I	ENST00000318560	NM_005157.4	515	Gtc/Atc	10/11	1	2	FACETS	0.929	0.858	1	0.929	0.858	1	CLONAL	1	TRUE	1	0.414520861759268	2		539	950	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390589	139390589	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	252	740	1	ENST00000277541.6:c.7602G>T	p.Glu2534Asp	p.E2534D	ENST00000277541	NM_017617.3	2534	gaG/gaT	34/34	1	2	FACETS	0.993	0.928	1	0.993	0.928	1	CLONAL	1	TRUE	1	0.414520861759268	2		741	1224	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929475	44929475	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	196	275	0	ENST00000377967.4:c.2575A>G	p.Met859Val	p.M859V	ENST00000377967	NM_021140.2	859	Atg/Gtg	17/29	1	1	FACETS	0.822	0.77	0.875	1	0.993	1	CLONAL	2	TRUE	0	0.414520861759268	1		275	456	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338703	70338703	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	127	274	0	ENST00000374080.3:c.99G>T	p.Glu33Asp	p.E33D	ENST00000374080		33	gaG/gaT	1/45	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.414520861759268	1		274	346	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490609	56490610	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0028074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	53	472	2	ENST00000267101.3:c.2253_2254delinsAT	p.Ser752Cys	p.S752C	ENST00000267101	NM_001982.3	751	caGAgt/caATgt	19/28	1	2	FACETS	0.315	0.268	0.367	0.315	0.268	0.367	SUBCLONAL	1	TRUE	1	0.47963178410813	2		474	701	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434713	110434713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	55	624	0	ENST00000375856.3:c.3688G>A	p.Gly1230Ser	p.G1230S	ENST00000375856	NM_003749.2	1230	Ggt/Agt	1/2	1	2	FACETS	0.266	0.226	0.309	0.266	0.226	0.309	SUBCLONAL	1	TRUE	1	0.47963178410813	2		624	863	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577092	7577093	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGGTCTCTCCCAGGACAGGCACAAACA	novel	NA	P-0028074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	207	705	0	ENST00000269305.4:c.819_845dup	p.Val274_Arg282dup	p.V274_R282dup	ENST00000269305	NM_001126112.2	274	cgg/cgTGTTTGTGCCTGTCCTGGGAGAGACCGg	8/11	0.47963178410813	1	FACETS	0.684	0.634	0.734	0.684	0.634	0.734	SUBCLONAL	1	TRUE	0	0.47963178410813	1		705	960	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0028074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	158	337	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	0.47963178410813	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.47963178410813	1		337	436	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940510	29940510	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	208	577	0	ENST00000389048.3:c.721T>A	p.Phe241Ile	p.F241I	ENST00000389048	NM_004304.4	241	Ttt/Att	2/29	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.47963178410813	2		577	785	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275138	41275138	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	85	330	0	ENST00000349496.5:c.1304A>C	p.Lys435Thr	p.K435T	ENST00000349496	NM_001904.3	435	aAg/aCg	9/15	1	2	FACETS	0.686	0.608	0.769	0.686	0.608	0.769	SUBCLONAL	1	TRUE	1	0.47963178410813	2		330	517	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008521	70008521	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876657699	NA	P-0028074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	52	507	0	ENST00000394351.3:c.808C>T	p.Arg270Ter	p.R270*	ENST00000394351	NM_000248.3	270	Cga/Tga	8/9	1	2	FACETS	0.244	0.206	0.285	0.244	0.206	0.285	SUBCLONAL	1	TRUE	1	0.47963178410813	2		507	890	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259362	89259362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	142	512	0	ENST00000336596.2:c.506G>A	p.Arg169Lys	p.R169K	ENST00000336596	NM_005233.5	169	aGa/aAa	3/17	1	2	FACETS	0.867	0.792	0.945	0.867	0.792	0.945	CLONAL	1	TRUE	1	0.47963178410813	2		512	683	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0028074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	163	466	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.47963178410813	1	FACETS	0.938	0.866	1	0.938	0.866	1	CLONAL	1	TRUE	0	0.47963178410813	1		466	551	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0028142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	45	295	3	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		298	214	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	121	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.832	0.754	0.913	0.832	0.754	0.913	CLONAL	1	TRUE	1	0.5	2		473	582	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	230	900	2	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.89	0.829	0.952	0.89	0.829	0.952	CLONAL	1	TRUE	1	0.5	2		902	1034	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946225	81946225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1325870340	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	136	545	0	ENST00000359376.3:c.1958G>A	p.Arg653His	p.R653H	ENST00000359376	NM_002661.3	653	cGc/cAc	19/33	1	2	FACETS	0.876	0.799	0.956	0.876	0.799	0.956	CLONAL	1	TRUE	1	0.5	2		545	621	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968322	2968323	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762770988	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	183	774	0	ENST00000396946.4:c.1663dup	p.Arg555ProfsTer38	p.R555Pfs*38	ENST00000396946	NM_032415.4	555	cgg/cCgg	13/25	1	2	FACETS	0.892	0.824	0.962	0.892	0.824	0.962	CLONAL	1	TRUE	1	0.5	2		774	821	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099103	27099103	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	106	444	0	ENST00000324856.7:c.3524del	p.Pro1175HisfsTer5	p.P1175Hfs*5	ENST00000324856	NM_006015.4	1173	atC/at	13/20	1	2	FACETS	0.808	0.727	0.893	0.808	0.727	0.893	CLONAL	1	TRUE	1	0.5	2		444	525	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	170	718	3	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.966	0.891	1	0.966	0.891	1	CLONAL	1	TRUE	1	0.5	2		721	704	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316397	14316397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782457908	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	125	573	1	ENST00000256196.4:c.208G>A	p.Ala70Thr	p.A70T	ENST00000256196		70	Gca/Aca	3/6	1	2	FACETS	0.876	0.796	0.959	0.876	0.796	0.959	CLONAL	1	TRUE	1	0.5	2		574	571	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	272	867	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.5	2		867	1047	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	157	551	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.952	0.874	1	0.952	0.874	1	CLONAL	1	TRUE	1	0.5	2		552	660	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15976868	15976868	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139458532	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	129	470	0	ENST00000268712.3:c.3686G>A	p.Arg1229Gln	p.R1229Q	ENST00000268712	NM_006311.3	1229	cGa/cAa	28/46	1	2	FACETS	0.925	0.842	1	0.925	0.842	1	CLONAL	1	TRUE	1	0.5	2		470	558	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511578	66511578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	132	387	0	ENST00000358598.2:c.38G>A	p.Arg13His	p.R13H	ENST00000358598	NM_212471.2	13	cGc/cAc	2/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.5	2		387	468	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602530	10602530	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777308626	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	215	694	0	ENST00000171111.5:c.1048G>A	p.Gly350Ser	p.G350S	ENST00000171111	NM_203500.1	350	Ggc/Agc	3/6	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.5	2		694	808	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589168	67589168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	71	323	0	ENST00000274335.5:c.1156C>T	p.Arg386Ter	p.R386*	ENST00000274335		386	Cga/Tga	9/15	0.0905242471877237	3	FACETS	1	0.953	1	0.584	0.514	0.658	INDETERMINATE	1	TRUE	1	0.5	3		323	304	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	72	265	2	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.5	2		267	282	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639700	47639700	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs267607934	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	112	348	0	ENST00000233146.2:c.792+1G>A		p.X264_splice	ENST00000233146	NM_000251.2	264			1	2	FACETS	0.945	0.855	1	0.945	0.855	1	CLONAL	1	TRUE	1	0.5	2		348	474	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562285	21562285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749940600	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	263	910	1	ENST00000382592.4:c.1634G>A	p.Arg545His	p.R545H	ENST00000382592	NM_014572.2	545	cGt/cAt	4/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.5	2		911	974	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169083	32169083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1056526093	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	229	858	1	ENST00000375023.3:c.3950G>A	p.Arg1317Gln	p.R1317Q	ENST00000375023	NM_004557.3	1317	cGg/cAg	22/30	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.5	2		859	818	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564969	226564969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776941221	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	150	549	0	ENST00000366794.5:c.1781C>T	p.Thr594Met	p.T594M	ENST00000366794	NM_001618.3	594	aCg/aTg	13/23	1	2	FACETS	0.806	0.738	0.878	0.806	0.738	0.878	CLONAL	1	TRUE	1	0.5	2		549	744	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221305	2221305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376879458	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	203	881	0	ENST00000326181.6:c.389G>A	p.Cys130Tyr	p.C130Y	ENST00000326181	NM_032271.2	130	tGc/tAc	6/21	1	2	FACETS	0.894	0.83	0.961	0.894	0.83	0.961	CLONAL	1	TRUE	1	0.5	2		881	908	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437606	56437606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886926322	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	106	401	0	ENST00000407977.2:c.856C>T	p.Arg286Trp	p.R286W	ENST00000407977		286	Cgg/Tgg	8/10	1	2	FACETS	0.924	0.833	1	0.924	0.833	1	CLONAL	1	TRUE	1	0.5	2		401	459	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027676	48027678	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs587782858	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	70	340	0	ENST00000234420.5:c.2561_2563del	p.Lys854del	p.K854del	ENST00000234420	NM_000179.2	852	AAG/-	4/10	1	2	FACETS	0.709	0.621	0.803	0.709	0.621	0.803	SUBCLONAL	1	TRUE	1	0.5	2		340	395	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62009575	62009575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs114330958	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	204	630	3	ENST00000392795.3:c.47C>T	p.Ala16Val	p.A16V	ENST00000392795	NM_001039933.1	16	gCg/gTg	1/6	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.5	2		633	781	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609673	46609673	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	190	749	2	ENST00000263734.3:c.2402del	p.Pro801HisfsTer39	p.P801Hfs*39	ENST00000263734	NM_001430.4	799	ttC/tt	15/16	1	2	FACETS	0.939	0.87	1	0.939	0.87	1	CLONAL	1	TRUE	1	0.5	2		751	809	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223858	36223858	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	209	974	5	ENST00000222270.7:c.6413del	p.Pro2138ArgfsTer15	p.P2138Rfs*15	ENST00000222270	NM_014727.1	2136	ctC/ct	28/37	1	2	FACETS	0.859	0.798	0.923	0.859	0.798	0.923	CLONAL	1	TRUE	1	0.5	2		979	973	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211118	36211118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200835025	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	250	1067	3	ENST00000222270.7:c.869G>A	p.Arg290His	p.R290H	ENST00000222270	NM_014727.1	290	cGt/cAt	3/37	1	2	FACETS	0.912	0.853	0.974	0.912	0.853	0.974	CLONAL	1	TRUE	1	0.5	2		1070	1096	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223103	1223103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782058	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	218	693	1	ENST00000326873.7:c.1040C>T	p.Ala347Val	p.A347V	ENST00000326873	NM_000455.4	347	gCg/gTg	8/10	1	2	FACETS	0.947	0.881	1	0.947	0.881	1	CLONAL	1	TRUE	1	0.5	2		694	921	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201692	66201692	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753118521	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	146	556	1	ENST00000273854.3:c.2810G>A	p.Arg937His	p.R937H	ENST00000273854	NM_004439.5	937	cGt/cAt	16/18	1	2	FACETS	0.911	0.834	0.991	0.911	0.834	0.991	CLONAL	1	TRUE	1	0.5	2		557	641	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101271	4101271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776316565	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	188	692	0	ENST00000262948.5:c.536G>A	p.Arg179Gln	p.R179Q	ENST00000262948	NM_030662.3	179	cGg/cAg	5/11	1	2	FACETS	0.978	0.906	1	0.978	0.906	1	CLONAL	1	TRUE	1	0.5	2		692	769	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46252683	46252683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372533478	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	102	351	0	ENST00000371998.3:c.112C>T	p.Arg38Trp	p.R38W	ENST00000371998		38	Cgg/Tgg	4/23	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.5	2		351	405	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300125	15300125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201917592	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	231	808	3	ENST00000263388.2:c.1151C>T	p.Thr384Met	p.T384M	ENST00000263388	NM_000435.2	384	aCg/aTg	7/33	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.5	2		811	888	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241496	105241496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	207	783	1	ENST00000349310.3:c.484G>A	p.Gly162Ser	p.G162S	ENST00000349310	NM_001014432.1	162	Ggc/Agc	7/15	1	2	FACETS	0.945	0.878	1	0.945	0.878	1	CLONAL	1	TRUE	1	0.5	2		784	876	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087557	27087557	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	186	747	0	ENST00000324856.7:c.2131T>G	p.Ser711Ala	p.S711A	ENST00000324856	NM_006015.4	711	Tca/Gca	5/20	1	2	FACETS	0.876	0.81	0.945	0.876	0.81	0.945	CLONAL	1	TRUE	1	0.5	2		747	849	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597882	43597882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	255	942	0	ENST00000355710.3:c.430C>T	p.Arg144Cys	p.R144C	ENST00000355710	NM_020975.4	144	Cgc/Tgc	3/20	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.5	2		942	1013	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136025	64136025	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	232	874	1	ENST00000334205.4:c.1286G>A	p.Arg429His	p.R429H	ENST00000334205	NM_003942.2	429	cGc/cAc	11/17	1	2	FACETS	0.982	0.917	1	0.982	0.917	1	CLONAL	1	TRUE	1	0.5	2		875	945	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67197058	67197058	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	77	383	0	ENST00000312629.5:c.301C>A	p.Leu101Ile	p.L101I	ENST00000312629	NM_003952.2	101	Cta/Ata	4/15	1	2	FACETS	0.703	0.62	0.792	0.703	0.62	0.792	SUBCLONAL	1	TRUE	1	0.5	2		383	438	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438527	49438527	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	163	654	0	ENST00000301067.7:c.4963G>A	p.Gly1655Ser	p.G1655S	ENST00000301067	NM_003482.3	1655	Ggt/Agt	19/54	1	2	FACETS	0.782	0.718	0.848	0.782	0.718	0.848	SUBCLONAL	1	TRUE	1	0.5	2		654	834	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111855955	111855956	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	56	585	0	ENST00000341259.2:c.9dup	p.Pro4AlafsTer28	p.P4Afs*28	ENST00000341259	NM_005475.2	2	-/G	2/8	1	2	FACETS	0.301	0.257	0.349	0.301	0.257	0.349	SUBCLONAL	1	TRUE	1	0.5	2		585	744	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109680	115109680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	251	877	0	ENST00000257566.3:c.2198C>T	p.Ala733Val	p.A733V	ENST00000257566	NM_016569.3	733	gCc/gTc	8/8	1	2	FACETS	0.964	0.902	1	0.964	0.902	1	CLONAL	1	TRUE	1	0.5	2		877	1042	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453453	40453453	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	200	880	2	ENST00000345506.4:c.1154del	p.Asn385MetfsTer13	p.N385Mfs*13	ENST00000345506	NM_003152.3	384	Aaa/aa	10/20	1	2	FACETS	0.815	0.756	0.878	0.815	0.756	0.878	CLONAL	1	TRUE	1	0.5	2		882	981	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208058	5208058	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	85	579	0	ENST00000357368.4:c.5653G>T	p.Gly1885Cys	p.G1885C	ENST00000357368	NM_002850.3	1885	Ggc/Tgc	37/38	1	2	FACETS	0.751	0.666	0.84	0.751	0.666	0.84	SUBCLONAL	1	TRUE	1	0.5	2		579	453	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693948	47693948	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs267607969	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	77	328	0	ENST00000233146.2:c.1661+1G>T		p.X554_splice	ENST00000233146	NM_000251.2	554			1	2	FACETS	0.898	0.794	1	0.898	0.794	1	CLONAL	1	TRUE	1	0.5	2		328	343	SUCCESS
ATR	545	MSKCC	GRCh37	3	142297525	142297525	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	137	539	1	ENST00000350721.4:c.22C>A	p.Leu8Met	p.L8M	ENST00000350721	NM_001184.3	8	Ctg/Atg	1/47	1	2	FACETS	0.961	0.878	1	0.961	0.878	1	CLONAL	1	TRUE	1	0.5	2		540	570	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958855	55958855	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	142	442	0	ENST00000263923.4:c.2998C>A	p.Leu1000Met	p.L1000M	ENST00000263923	NM_002253.2	1000	Ctg/Atg	22/30	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.5	2		442	539	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197300	106197300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776598022	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	74	360	0	ENST00000380013.4:c.5633G>A	p.Arg1878His	p.R1878H	ENST00000380013	NM_001127208.2	1878	cGt/cAt	11/11	1	2	FACETS	0.791	0.697	0.892	0.791	0.697	0.892	SUBCLONAL	1	TRUE	1	0.5	2		360	374	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530978	187530978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376075512	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	161	528	0	ENST00000441802.2:c.10045G>A	p.Val3349Ile	p.V3349I	ENST00000441802	NM_005245.3	3349	Gtt/Att	15/27	1	2	FACETS	0.948	0.873	1	0.948	0.873	1	CLONAL	1	TRUE	1	0.5	2		528	679	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754876	57754876	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	92	431	0	ENST00000274289.3:c.314A>T	p.Asn105Ile	p.N105I	ENST00000274289	NM_006622.3	105	aAc/aTc	2/14	0.0905242471877237	3	FACETS	0.913	0.814	1	0.456	0.407	0.509	INDETERMINATE	1	TRUE	1	0.5	3		431	504	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591130	67591131	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGG	novel	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	74	308	0	ENST00000274335.5:c.1725_1726insGAG	p.Lys575_Thr576insGlu	p.K575_T576insE	ENST00000274335		575	aag/aAGGag	12/15	0.0905242471877237	3	FACETS	1	0.895	1	0.508	0.448	0.573	INDETERMINATE	1	TRUE	1	0.5	3		308	364	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86658452	86658452	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	44	192	0	ENST00000274376.6:c.1421del	p.Asn474ThrfsTer9	p.N474Tfs*9	ENST00000274376	NM_002890.2	473	Aaa/aa	10/25	0.0905242471877237	3	FACETS	0.991	0.839	1	0.495	0.419	0.578	INDETERMINATE	1	TRUE	1	0.5	3		192	222	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488375	20488375	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	128	492	0	ENST00000346618.3:c.1031G>T	p.Gly344Val	p.G344V	ENST00000346618	NM_001949.4	344	gGg/gTg	6/7	1	2	FACETS	0.923	0.84	1	0.923	0.84	1	CLONAL	1	TRUE	1	0.5	2		492	555	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29195975	29195975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	191	718	1	ENST00000240100.2:c.623C>T	p.Ala208Val	p.A208V	ENST00000240100	NM_001394.6	208	gCc/gTc	3/4	1	2	FACETS	0.899	0.832	0.968	0.899	0.832	0.968	CLONAL	1	TRUE	1	0.5	2		719	850	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	594	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.760832313061375	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.760832313061375	2		485	637	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040962	47040962	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782623757	NA	P-0029765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	413	684	1	ENST00000377604.3:c.1492C>T	p.Arg498Cys	p.R498C	ENST00000377604	NM_001204468.1	498	Cgc/Tgc	14/24	0.678641376372683	4	FACETS	0.924	0.883	0.967	0.924	0.883	0.967	CLONAL	2	TRUE	2	0.760832313061375	4		685	1034	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	177	345	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.928	0.865	0.991	0.928	0.865	0.991	CLONAL	1	TRUE	1	0.902203684576521	2		345	423	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692818	89692818	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1339631701	NA	P-0030152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	58	288	0	ENST00000371953.3:c.302T>C	p.Ile101Thr	p.I101T	ENST00000371953	NM_000314.4	101	aTc/aCc	5/9	0.902203684576521	1	FACETS	0.338	0.294	0.384	0.338	0.294	0.384	SUBCLONAL	1	TRUE	0	0.902203684576521	1		288	209	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591247	67591247	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0030152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	246	423	0	ENST00000274335.5:c.1746-1G>A		p.X582_splice	ENST00000274335		582			1	2	FACETS	0.859	0.808	0.91	0.859	0.808	0.91	CLONAL	1	TRUE	1	0.902203684576521	2		423	635	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653815	89653815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	14	487	0	ENST00000371953.3:c.113C>T	p.Pro38Leu	p.P38L	ENST00000371953	NM_000314.4	38	cCt/cTt	2/9	0.902203684576521	1	FACETS	0.069	0.049	0.093	0.069	0.049	0.093	SUBCLONAL	1	TRUE	0	0.902203684576521	1		487	247	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399152	139399152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	364	685	0	ENST00000277541.6:c.4991G>A	p.Arg1664Lys	p.R1664K	ENST00000277541	NM_017617.3	1664	aGg/aAg	26/34	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.902203684576521	2		685	790	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215239	123215240	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	222	345	0	ENST00000218089.9:c.2788dup	p.Met930AsnfsTer8	p.M930Nfs*8	ENST00000218089	NM_001042749.1	929	gaa/gAaa	28/35	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.902203684576521	2		345	481	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577578	7577578	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	315	499	0	ENST00000269305.4:c.703A>G	p.Asn235Asp	p.N235D	ENST00000269305	NM_001126112.2	235	Aac/Gac	7/11	0.796028214722749	2	FACETS	0.936	0.904	0.966	0.936	0.904	0.966	CLONAL	2	TRUE	0	0.811049362815945	2		499	415	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976790	2976790	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	369	663	0	ENST00000396946.4:c.1222C>A	p.Arg408Ser	p.R408S	ENST00000396946	NM_032415.4	408	Cgc/Agc	9/25	0.717306995677219	3	FACETS	0.92	0.881	0.959	0.92	0.881	0.959	CLONAL	2	TRUE	1	0.811049362815945	3		663	695	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434415	49434415	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	527	611	0	ENST00000301067.7:c.7138C>T	p.Gln2380Ter	p.Q2380*	ENST00000301067	NM_003482.3	2380	Cag/Tag	31/54	0.811049362815945	3	FACETS	0.976	0.955	0.995	0.976	0.955	0.995	CLONAL	3	TRUE	0	0.811049362815945	3		611	624	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964187	28964187	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1206561200	NA	P-0030192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	187	350	0	ENST00000282397.4:c.1715A>T	p.Asp572Val	p.D572V	ENST00000282397	NM_002019.4	572	gAc/gTc	13/30	0.794822646137405	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.811049362815945	2		350	230	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436772	110436772	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767955504	NA	P-0030192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1374	120	714	1	ENST00000375856.3:c.1629G>A	p.Met543Ile	p.M543I	ENST00000375856	NM_003749.2	543	atG/atA	1/2	0.811049362815945	6	FACETS	0.519	0.467	0.575			1	SUBCLONAL	1	TRUE	NA	0.811049362815945	6		715	1494	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437486	110437486	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	95	520	0	ENST00000375856.3:c.915G>T	p.Lys305Asn	p.K305N	ENST00000375856	NM_003749.2	305	aaG/aaT	1/2	0.811049362815945	6	FACETS	0.487	0.432	0.546			1	SUBCLONAL	1	TRUE	NA	0.811049362815945	6		520	1261	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437970	110437970	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs994486330	NA	P-0030192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	16	126	0	ENST00000375856.3:c.431G>C	p.Ser144Thr	p.S144T	ENST00000375856	NM_003749.2	144	aGc/aCc	1/2	0.811049362815945	6	FACETS	0.426	0.315	0.558			1	SUBCLONAL	1	TRUE	NA	0.811049362815945	6		126	243	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724651	43724651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	190	626	1	ENST00000382044.4:c.3416C>T	p.Thr1139Ile	p.T1139I	ENST00000382044	NM_001141980.1	1139	aCt/aTt	17/28	1	2	FACETS	0.924	0.862	0.988	0.924	0.862	0.988	CLONAL	1	TRUE	1	0.811049362815945	2		627	507	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99491831	99491831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772355972	NA	P-0030192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	97	390	0	ENST00000268035.6:c.3616G>A	p.Ala1206Thr	p.A1206T	ENST00000268035	NM_000875.3	1206	Gcc/Acc	20/21	0.811049362815945	3	FACETS	0.773	0.693	0.857	0.386	0.346	0.429	SUBCLONAL	1	TRUE	1	0.811049362815945	3		390	435	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81902877	81902877	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	368	441	0	ENST00000359376.3:c.538G>A	p.Ala180Thr	p.A180T	ENST00000359376	NM_002661.3	180	Gcc/Acc	6/33	0.451522679157484	5	FACETS	0.9	0.86	0.94	0.9	0.86	0.94	INDETERMINATE	3	TRUE	2	0.811049362815945	5		441	745	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223256	41223256	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs80358008	NA	P-0030192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	66	380	0	ENST00000357654.3:c.4676-1G>C		p.X1559_splice	ENST00000357654	NM_007294.3	1559			NA	2	FACETS	0.464	0.405	0.527			1	INDETERMINATE	1	TRUE	NA	0.811049362815945	2		380	351	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808007	1808007	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	286	760	1	ENST00000260795.2:c.1983G>T	p.Met661Ile	p.M661I	ENST00000260795		661	atG/atT	14/17	0.480165858471313	4	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.811049362815945	4		761	888	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226149	226149	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	472	713	1	ENST00000264932.6:c.608C>A	p.Thr203Asn	p.T203N	ENST00000264932	NM_004168.2	203	aCc/aAc	5/15	0.196200658748651	1	FACETS	1	0.997	1	1	0.997	1	INDETERMINATE	1	TRUE	0	0.811049362815945	1		714	572	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021741	69021741	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	256	454	0	ENST00000288368.4:c.3029G>T	p.Gly1010Val	p.G1010V	ENST00000288368	NM_024870.2	1010	gGt/gTt	25/40	0.293453964129323	5	FACETS	1	0.987	1	0.772	0.729	0.816	INDETERMINATE	2	TRUE	2	0.811049362815945	5		454	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0030650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	330	584	0	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.625312123678414	1	FACETS	0.803	0.774	0.83	1	0.996	1	CLONAL	2	TRUE	0	0.625312123678414	1		584	452	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325082	39325082	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	277	404	0	ENST00000373001.3:c.237G>C	p.Lys79Asn	p.K79N	ENST00000373001	NM_022157.3	79	aaG/aaC	1/7	NA	2	FACETS	0.968	0.911	1			1	INDETERMINATE	1	TRUE	NA	0.635336051484463	2		404	901	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750998	128750998	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1439970381	NA	P-0031769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	199	349	0	ENST00000377970.2:c.535C>T	p.Pro179Ser	p.P179S	ENST00000377970	NM_002467.4	179	Ccc/Tcc	2/3	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.635336051484463	2		349	608	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79974778	79974778	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	68	789	0	ENST00000265081.6:c.1206T>G	p.Phe402Leu	p.F402L	ENST00000265081	NM_002439.4	402	ttT/ttG	8/24	1	2	FACETS	0.336	0.291	0.386	0.336	0.291	0.386	SUBCLONAL	1	FALSE	1	0.341479434279675	2		789	1184	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878689	151878689	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	52	473	0	ENST00000262189.6:c.6256del	p.Ser2086LeufsTer20	p.S2086Lfs*20	ENST00000262189	NM_170606.2	2086	Tct/ct	36/59	1	2	FACETS	0.495	0.421	0.577	0.495	0.421	0.577	SUBCLONAL	1	FALSE	1	0.341479434279675	2		473	615	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0031813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	551	548	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.405058383234489	2	FACETS	0.989	0.957	1	1	0.997	1	CLONAL	3	TRUE	0	0.405058383234489	2		548	917	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0031813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	151	553	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.397785974129536	3	FACETS	0.964	0.889	1	0.964	0.889	1	CLONAL	2	TRUE	1	0.405058383234489	3		553	465	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431634	6431634	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	228	530	0	ENST00000356142.4:c.187G>C	p.Asp63His	p.D63H	ENST00000356142	NM_018890.3	63	Gat/Cat	3/7	0.32532549236237	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	2	0.405058383234489	4		530	770	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	231	534	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	0.396382284745886	3	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	1	0.405058383234489	3		534	684	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913355	NA	P-0031813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	157	479	0	ENST00000288602.6:c.1406G>T	p.Gly469Val	p.G469V	ENST00000288602	NM_004333.4	469	gGa/gTa	11/18	0.32532549236237	4	FACETS	0.908	0.835	0.983	0.908	0.835	0.983	CLONAL	2	TRUE	2	0.405058383234489	4		479	600	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777893	NA	P-0031813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	150	586	0	ENST00000361445.4:c.5930C>T	p.Thr1977Ile	p.T1977I	ENST00000361445	NM_004958.3	1977	aCa/aTa	43/58	1	2	FACETS	0.961	0.879	1	0.961	0.879	1	CLONAL	1	TRUE	1	0.405058383234489	2		586	771	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549228	226549228	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	144	452	0	ENST00000366794.5:c.2978A>G	p.Asp993Gly	p.D993G	ENST00000366794	NM_001618.3	993	gAt/gGt	23/23	0.405058383234489	6	FACETS	1	0.981	1	0.258	0.235	0.283	CLONAL	1	TRUE	1	0.405058383234489	6		452	997	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807504	1807504	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1048418015	NA	P-0031813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	184	827	3	ENST00000260795.2:c.1673C>T	p.Ala558Val	p.A558V	ENST00000260795		558	gCg/gTg	12/17	1	2	FACETS	0.959	0.886	1	0.959	0.886	1	CLONAL	1	TRUE	1	0.405058383234489	2		830	947	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413913	139413913	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	152	839	0	ENST00000277541.6:c.847T>C	p.Cys283Arg	p.C283R	ENST00000277541	NM_017617.3	283	Tgc/Cgc	5/34	1	2	FACETS	0.92	0.842	1	0.92	0.842	1	CLONAL	1	TRUE	1	0.405058383234489	2		839	816	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480522	123480522	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	252	595	0	ENST00000371139.4:c.30A>C	p.Lys10Asn	p.K10N	ENST00000371139	NM_001114937.2	10	aaA/aaC	1/4	0.255390643655623	4	FACETS	0.937	0.878	0.998	0.937	0.878	0.998	CLONAL	2	TRUE	2	0.405058383234489	4		595	933	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0031816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	267	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.661602081610279	5	FACETS	1	0.982	1	0.732	0.691	0.774	CLONAL	2	TRUE	2	0.729275738789822	5		336	698	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0031816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	122	268	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.729275738789822	2	FACETS	0.88	0.823	0.936	0.88	0.823	0.936	CLONAL	2	TRUE	0	0.729275738789822	2		268	190	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0031816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	579	666	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.729275738789822	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.729275738789822	2		666	786	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941685	48941685	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs763184576	NA	P-0031816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	127	225	0	ENST00000267163.4:c.995A>G	p.Asp332Gly	p.D332G	ENST00000267163	NM_000321.2	332	gAt/gGt	10/27	0.729275738789822	2	FACETS	0.962	0.905	1	0.962	0.905	1	CLONAL	2	TRUE	0	0.729275738789822	2		225	181	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12043157	12043158	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	184	247	0	ENST00000353533.5:c.1044dup	p.Thr349TyrfsTer4	p.T349Yfs*4	ENST00000353533	NM_003010.3	348	ctt/cTtt	10/11	0.729275738789822	2	FACETS	0.934	0.887	0.98	0.934	0.887	0.98	CLONAL	2	TRUE	0	0.729275738789822	2		247	270	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457191	25457191	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1480791034	NA	P-0031816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	144	711	0	ENST00000264709.3:c.2696G>C	p.Arg899Pro	p.R899P	ENST00000264709	NM_175629.2	899	cGc/cCc	23/23	0.728404399935118	3	FACETS	0.582	0.53	0.636	0.291	0.265	0.318	SUBCLONAL	1	TRUE	1	0.729275738789822	3		711	926	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069351	30069351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	88	754	0	ENST00000338641.4:c.1216G>A	p.Glu406Lys	p.E406K	ENST00000338641	NM_000268.3	406	Gag/Aag	12/16	0.300669541454754	3	FACETS	0.433	0.383	0.486	0.216	0.191	0.243	INDETERMINATE	1	TRUE	1	0.729275738789822	3		754	761	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265419	152265419	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	69	535	0	ENST00000206249.3:c.872T>G	p.Leu291Arg	p.L291R	ENST00000206249	NM_000125.3	291	cTt/cGt	4/8	0.556628241144435	4	FACETS	0.386	0.335	0.441	0.193	0.167	0.221	SUBCLONAL	1	TRUE	2	0.729275738789822	4		535	848	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845659	68845660	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0032100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	83	648	0	ENST00000261769.5:c.907_908del	p.Thr303HisfsTer7	p.T303Hfs*7	ENST00000261769	NM_004360.3	302	tAC/t	7/16	0.216023547424887	2	FACETS	1	0.969	1	0.647	0.571	0.727	CLONAL	1	FALSE	0	0.216023547424887	2		648	594	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570311	87570311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285612169	NA	P-0032100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	79	504	1	ENST00000277120.3:c.2051C>T	p.Ala684Val	p.A684V	ENST00000277120		684	gCg/gTg	17/19	0.191388866845295	5	FACETS	0.769	0.676	0.868	0.512	0.451	0.579	SUBCLONAL	2	FALSE	2	0.216023547424887	5		505	630	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0032148-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	114	503	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.200569275424361	4	FACETS	0.985	0.892	1	0.985	0.892	1	CLONAL	3	TRUE	1	0.200569275424361	4		503	462	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859399	57859399	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032148-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	53	551	0	ENST00000228682.2:c.544G>C	p.Glu182Gln	p.E182Q	ENST00000228682	NM_005269.2	182	Gag/Cag	6/12	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.200569275424361	2		551	418	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781791	3781791	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	48	535	0	ENST00000262367.5:c.4876G>T	p.Glu1626Ter	p.E1626*	ENST00000262367	NM_004380.2	1626	Gag/Tag	29/31	0.174371706109731	1	FACETS	0.551	0.467	0.644	0.551	0.467	0.644	INDETERMINATE	1	TRUE	0	0.346898086409966	1		535	415	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3113463	3113463	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	43	456	0	ENST00000078429.4:c.457C>G	p.Leu153Val	p.L153V	ENST00000078429	NM_002067.2	153	Ctc/Gtc	3/7	1	2	FACETS	0.571	0.478	0.674	0.571	0.478	0.674	SUBCLONAL	1	TRUE	1	0.346898086409966	2		456	434	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061163	38061175	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCGGCCCCCGG	CGCCGGCCCCCGG	-	novel	NA	P-0032547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	51	192	0	ENST00000250448.2:c.814_826del	p.Pro272AlafsTer45	p.P272Afs*45	ENST00000250448	NM_004496.3	272	CCGGGGGCCGGCGgc/gc	2/2	1	2	FACETS	0.778	0.671	0.891	1	0.969	1	SUBCLONAL	2	TRUE	1	0.346898086409966	2		192	189	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390346	118390346	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	119	587	0	ENST00000534358.1:c.11160G>C	p.Leu3720Phe	p.L3720F	ENST00000534358	NM_005933.3	3720	ttG/ttC	32/36	0.346898086409966	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.346898086409966	1		587	545	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907371	32907371	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	84	334	0	ENST00000380152.3:c.1759del	p.Thr587GlnfsTer27	p.T587Qfs*27	ENST00000380152		586	Aaa/aa	10/27	0.346898086409966	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.346898086409966	1		334	362	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151174438	151174438	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	38	288	0	ENST00000262187.5:c.256T>A	p.Ser86Thr	p.S86T	ENST00000262187	NM_005614.3	86	Tct/Act	4/8	0.306907413229597	3	FACETS	0.583	0.482	0.696	0.194	0.16	0.232	SUBCLONAL	1	TRUE	0	0.346898086409966	3		288	441	SUCCESS
AR	367	MSKCC	GRCh37	X	66765127	66765127	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	64	388	4	ENST00000374690.3:c.139G>A	p.Ala47Thr	p.A47T	ENST00000374690	NM_000044.3	47	Gca/Aca	1/8	0.248197263464729	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.346898086409966	1		392	279	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0032833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	79	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.186676641125038	3	FACETS	0.874	0.774	0.979	0.874	0.774	0.979	CLONAL	2	TRUE	1	0.285445691479615	3		336	362	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0032833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	78	503	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.269640055242544	4	FACETS	1	0.969	1	0.662	0.582	0.746	CLONAL	1	TRUE	2	0.285445691479615	4		503	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0032983-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	16	644	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.761	0.565	0.993	0.761	0.565	0.993	CLONAL	1	TRUE	1	0.232384745163062	2		645	181	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0032983-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	13	564	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	0.232384745163062	2	FACETS	0.965	0.707	1	0.965	0.707	1	CLONAL	2	TRUE	0	0.232384745163062	2		564	58	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059204	27059204	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0032983-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	21	383	0	ENST00000324856.7:c.1841C>G	p.Ser614Ter	p.S614*	ENST00000324856	NM_006015.4	614	tCa/tGa	4/20	1	2	FACETS	0.766	0.598	0.955	1	0.924	1	CLONAL	2	TRUE	1	0.232384745163062	2		383	118	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974792	21974792	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs141798398	NA	P-0033031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	16	150	0	ENST00000304494.5:c.35C>A	p.Ser12Ter	p.S12*	ENST00000304494	NM_000077.4	12	tCg/tAg	1/3	0.351336255484982	1	FACETS	0.799	0.6	1	0.799	0.6	1	CLONAL	1	TRUE	0	0.351336255484982	1		150	94	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057520000	NA	P-0033031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	114	725	0	ENST00000269305.4:c.452C>G	p.Pro151Arg	p.P151R	ENST00000269305	NM_001126112.2	151	cCc/cGc	5/11	0.309788673131046	2	FACETS	0.826	0.75	0.904	0.826	0.75	0.904	CLONAL	2	TRUE	0	0.351336255484982	2		725	393	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491475	18491475	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	48	267	0	ENST00000266497.5:c.1388A>T	p.Lys463Ile	p.K463I	ENST00000266497		463	aAa/aTa	8/31	0.216340106061393	4	FACETS	0.901	0.771	1	0.901	0.771	1	CLONAL	2	TRUE	2	0.351336255484982	4		267	205	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735489	204735489	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	51	359	0	ENST00000302823.3:c.290T>G	p.Phe97Cys	p.F97C	ENST00000302823	NM_005214.4	97	tTc/tGc	2/4	0.196153916957825	5	FACETS	1	0.963	1	0.483	0.413	0.559	INDETERMINATE	1	TRUE	2	0.351336255484982	5		359	306	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0033856-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	156	499	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	0.906524445993782	3	FACETS	0.8	0.736	0.867			1	SUBCLONAL	1	TRUE	NA	0.969696498509197	3		499	597	SUCCESS
APC	324	MSKCC	GRCh37	5	112175141	112175141	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033856-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	367	606	0	ENST00000257430.4:c.3850G>T	p.Glu1284Ter	p.E1284*	ENST00000257430	NM_000038.5	1284	Gaa/Taa	16/16	0.742374099613264	4	FACETS	1	0.996	1	0.875	0.854	0.895	CLONAL	3	TRUE	0	0.969696498509197	4		606	426	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372173	55372173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033856-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	154	886	0	ENST00000297316.4:c.863C>T	p.Ala288Val	p.A288V	ENST00000297316	NM_022454.3	288	gCg/gTg	2/2	0.942426460416663	3	FACETS	0.949	0.875	1	0.474	0.437	0.513	CLONAL	1	TRUE	1	0.969696498509197	3		886	497	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252869	36252869	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033856-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	123	519	0	ENST00000300305.3:c.493G>C	p.Gly165Arg	p.G165R	ENST00000300305		165	Ggt/Cgt	4/8	0.732909435730551	3	FACETS	0.506	0.457	0.556	0.253	0.228	0.278	SUBCLONAL	1	TRUE	1	0.969696498509197	3		519	745	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119086	70119086	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033856-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	174	797	0	ENST00000245479.2:c.658G>T	p.Glu220Ter	p.E220*	ENST00000245479	NM_000346.3	220	Gag/Tag	2/3	0.969696498509197	3	FACETS	0.857	0.792	0.923	0.428	0.396	0.462	CLONAL	1	TRUE	1	0.969696498509197	3		797	622	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0034063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	99	277	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.21479281447443	3	FACETS	0.875	0.787	0.967	1	0.977	1	CLONAL	3	TRUE	1	0.21479281447443	3		277	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0034063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	142	484	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.21479281447443	2	FACETS	1	0.963	1	1	0.99	1	CLONAL	3	TRUE	0	0.21479281447443	2		484	408	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866359	37866359	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	27	488	0	ENST00000269571.5:c.664G>T	p.Gly222Cys	p.G222C	ENST00000269571		222	Ggt/Tgt	6/27	0.21479281447443	2	FACETS	0.764	0.609	0.941	0.382	0.304	0.471	CLONAL	1	TRUE	0	0.21479281447443	2		488	329	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640660	3640660	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	87	621	0	ENST00000294008.3:c.2979G>T	p.Glu993Asp	p.E993D	ENST00000294008	NM_032444.2	993	gaG/gaT	12/15	0.21479281447443	4	FACETS	0.754	0.667	0.845	0.502	0.445	0.564	SUBCLONAL	2	TRUE	1	0.21479281447443	4		621	653	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143479	30143479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542229113	NA	P-0034063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	21	224	0	ENST00000389048.3:c.47C>T	p.Thr16Met	p.T16M	ENST00000389048	NM_004304.4	16	aCg/aTg	1/29	0.21479281447443	1	FACETS	1	0.833	1	1	0.833	1	CLONAL	1	TRUE	0	0.21479281447443	1		224	160	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612188	189612188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774550896	NA	P-0034063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	33	400	0	ENST00000264731.3:c.1940G>A	p.Arg647His	p.R647H	ENST00000264731	NM_003722.4	647	cGc/cAc	14/14	0.191070451707654	4	FACETS	0.835	0.68	1	0.418	0.34	0.505	CLONAL	1	TRUE	2	0.21479281447443	4		400	447	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245512	153245512	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	100	289	0	ENST00000281708.4:c.1679A>T	p.Asp560Val	p.D560V	ENST00000281708	NM_033632.3	560	gAt/gTt	11/12	0.21479281447443	3	FACETS	1	0.904	1	1	0.983	1	CLONAL	3	TRUE	1	0.21479281447443	3		289	343	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031930	26031930	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	65	225	0	ENST00000244661.2:c.359T>C	p.Ile120Thr	p.I120T	ENST00000244661	NM_003537.3	120	aTt/aCt	1/1	0.191070451707654	4	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	2	0.21479281447443	4		225	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0034131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	700	699	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.715182800739752	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.715182800739752	2		699	928	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589579	67589593	+	inframe_deletion	In_Frame_Del	DEL	AAATTACATGAATAT	AAATTACATGAATAT	-	novel	NA	P-0034131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	226	251	0	ENST00000274335.5:c.1344_1358del	p.Lys448_Tyr452del	p.K448_Y452del	ENST00000274335		448	AAATTACATGAATAT/-	10/15	0.715182800739752	2	FACETS	0.991	0.947	1	0.991	0.947	1	CLONAL	2	TRUE	0	0.715182800739752	2		251	319	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073570	8073571	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0034131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	250	413	1	ENST00000377482.5:c.1088dup	p.Leu364ThrfsTer12	p.L364Tfs*12	ENST00000377482	NM_018948.3	363	gca/gcCa	4/4	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.715182800739752	2		414	676	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720675	89720675	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	70	194	0	ENST00000371953.3:c.826A>G	p.Asn276Asp	p.N276D	ENST00000371953	NM_000314.4	276	Aat/Gat	8/9	0.715182800739752	1	FACETS	0.925	0.834	1	0.925	0.834	1	CLONAL	1	TRUE	0	0.715182800739752	1		194	136	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806573	1806573	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	120	539	0	ENST00000260795.2:c.1289C>T	p.Ser430Phe	p.S430F	ENST00000260795		430	tCc/tTc	9/17	1	2	FACETS	0.413	0.373	0.456	0.413	0.373	0.456	SUBCLONAL	1	TRUE	1	0.715182800739752	2		539	812	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0034231-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	349	503	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.233484236079895	14	FACETS	1	0.968	1	1	0.968	1	CLONAL	10	TRUE	4	0.233484236079895	14		503	706	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0034231-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	137	845	0	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	0.211618818562106	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.233484236079895	2		845	489	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637781	176637781	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034231-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	65	656	0	ENST00000439151.2:c.2381A>T	p.His794Leu	p.H794L	ENST00000439151	NM_022455.4	794	cAc/cTc	5/23	1	2	FACETS	0.8	0.698	0.909	1	0.975	1	CLONAL	2	TRUE	1	0.233484236079895	2		656	348	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117874101	117874101	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034231-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	46	406	0	ENST00000297338.2:c.353A>G	p.Asp118Gly	p.D118G	ENST00000297338	NM_006265.2	118	gAt/gGt	4/14	0.216396287680285	3	FACETS	0.9	0.771	1	1	0.957	1	CLONAL	3	TRUE	1	0.233484236079895	3		406	163	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0034322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	68	456	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.16	2		456	737	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481696	56481696	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	44	787	0	ENST00000267101.3:c.731T>C	p.Phe244Ser	p.F244S	ENST00000267101	NM_001982.3	244	tTt/tCt	6/28	1	2	FACETS	0.694	0.581	0.821	0.694	0.581	0.821	SUBCLONAL	1	TRUE	1	0.16	2		787	792	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371690	225371690	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	38	546	0	ENST00000264414.4:c.914G>T	p.Arg305Leu	p.R305L	ENST00000264414	NM_003590.4	305	cGt/cTt	7/16	1	2	FACETS	0.895	0.739	1	0.895	0.739	1	CLONAL	1	TRUE	1	0.16	2		546	531	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0034328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	172	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.229072086546238	4	FACETS	0.98	0.906	1	0.98	0.906	1	INDETERMINATE	2	TRUE	2	0.392052816228113	4		336	623	SUCCESS
ATM	472	MSKCC	GRCh37	11	108168089	108168089	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	94	385	0	ENST00000278616.4:c.4985C>A	p.Thr1662Asn	p.T1662N	ENST00000278616	NM_000051.3	1662	aCt/aAt	33/63	0.392052816228113	5	FACETS	1	0.947	1	0.369	0.328	0.412	CLONAL	1	TRUE	2	0.392052816228113	5		385	688	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579312	7579319	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CGTGCAAG	CGTGCAAG	-	novel	NA	P-0034328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	261	443	0	ENST00000269305.4:c.368_375del	p.Thr123IlefsTer23	p.T123Ifs*23	ENST00000269305	NM_001126112.2	123	aCTTGCACG/a	4/11	0.392052816228113	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.392052816228113	2		443	577	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619220	37619221	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0034328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	111	447	0	ENST00000447079.4:c.899_900del	p.Arg300IlefsTer6	p.R300Ifs*6	ENST00000447079	NM_015083.1	299	cAG/c	1/14	0.392052816228113	6	FACETS	1	0.939	1			1	CLONAL	1	TRUE	NA	0.392052816228113	6		447	948	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182132	99182132	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	182	406	0	ENST00000074304.5:c.2197A>G	p.Ser733Gly	p.S733G	ENST00000074304	NM_001134224.1	733	Agc/Ggc	21/26	0.263703804579305	4	FACETS	0.97	0.899	1	0.97	0.899	1	CLONAL	2	TRUE	2	0.392052816228113	4		406	666	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151948034	151948034	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	86	501	0	ENST00000262189.6:c.1639del	p.Glu547LysfsTer65	p.E547Kfs*65	ENST00000262189	NM_170606.2	547	Gaa/aa	12/59	0.392052816228113	3	FACETS	0.757	0.67	0.851	0.379	0.335	0.426	SUBCLONAL	1	TRUE	1	0.392052816228113	3		501	693	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072578	5072579	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0034328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	78	366	0	ENST00000381652.3:c.1729_1730del	p.Glu577SerfsTer8	p.E577Sfs*8	ENST00000381652	NM_004972.3	576	acAGaa/acaa	13/25	0.392052816228113	1	FACETS	0.884	0.782	0.991	0.884	0.782	0.991	CLONAL	1	TRUE	0	0.392052816228113	1		366	362	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891179	101891179	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	72	387	0	ENST00000374994.4:c.140C>A	p.Thr47Asn	p.T47N	ENST00000374994	NM_004612.2	47	aCt/aAt	2/9	0.167182935846294	4	FACETS	0.552	0.481	0.629	0.276	0.24	0.315	INDETERMINATE	1	TRUE	2	0.392052816228113	4		387	927	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0034500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	105	335	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.215114881139827	3	FACETS	1	0.971	1	0.801	0.722	0.882	CLONAL	2	TRUE	0	0.231752176037116	3		335	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0034500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	151	572	0	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.206037345073727	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.231752176037116	2		572	599	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168695	32168695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143103753	NA	P-0034500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	56	597	0	ENST00000375023.3:c.4228C>T	p.Arg1410Cys	p.R1410C	ENST00000375023	NM_004557.3	1410	Cgc/Tgc	23/30	0.231752176037116	5	FACETS	0.85	0.727	0.986	0.283	0.242	0.329	CLONAL	1	TRUE	2	0.231752176037116	5		597	766	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026137	71026138	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	126	487	0	ENST00000318789.4:c.1484dup	p.Thr496HisfsTer21	p.T496Hfs*21	ENST00000318789	NM_032682.5	495	ttc/ttTc	17/21	0.18104984151512	3	FACETS	0.786	0.712	0.864	0.786	0.712	0.864	SUBCLONAL	2	TRUE	1	0.231752176037116	3		487	772	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672294	30672294	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	90	758	0	ENST00000376406.3:c.4666A>G	p.Thr1556Ala	p.T1556A	ENST00000376406	NM_014641.2	1556	Act/Gct	10/15	0.231752176037116	5	FACETS	1	0.896	1	0.338	0.299	0.38	CLONAL	1	TRUE	2	0.231752176037116	5		758	1033	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772893	135772894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0034500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	168	666	0	ENST00000298552.3:c.2728_2729dup	p.Leu910PhefsTer22	p.L910Ffs*22	ENST00000298552	NM_001162426.1	910	ttg/ttTTg	21/23	0.21801476729779	2	FACETS	0.963	0.887	1	0.963	0.887	1	CLONAL	2	TRUE	0	0.231752176037116	2		666	753	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720676	89720676	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	10	246	0	ENST00000371953.3:c.827A>C	p.Asn276Thr	p.N276T	ENST00000371953	NM_000314.4	276	aAt/aCt	8/9	0.47259834742856	1	FACETS	0.175	0.118	0.246	0.175	0.118	0.246	SUBCLONAL	1	TRUE	0	0.47259834742856	1		246	185	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs11575997	NA	P-0035019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	346	429	0	ENST00000269305.4:c.993+1G>T		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.39704947698952	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	3	TRUE	0	0.39704947698952	3		429	691	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570070	212570070	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745408040	NA	P-0035019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	242	358	2	ENST00000342788.4:c.1171G>A	p.Val391Ile	p.V391I	ENST00000342788	NM_005235.2	391	Gtc/Atc	10/28	0.367428351854248	3	FACETS	0.854	0.805	0.904	0.854	0.805	0.904	CLONAL	3	TRUE	0	0.39704947698952	3		360	570	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738485	145738485	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767722327	NA	P-0035019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	147	426	0	ENST00000428558.2:c.2500G>A	p.Ala834Thr	p.A834T	ENST00000428558	NM_004260.3	834	Gcc/Acc	16/22	0.39704947698952	5	FACETS	0.764	0.698	0.833	0.382	0.349	0.417	SUBCLONAL	2	TRUE	1	0.39704947698952	5		426	773	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670739	134670739	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	65	390	0	ENST00000398015.3:c.650C>A	p.Ser217Tyr	p.S217Y	ENST00000398015	NM_004441.4	217	tCt/tAt	3/16	NA	2	FACETS	0.736	0.64	0.839			1	INDETERMINATE	1	TRUE	NA	0.39704947698952	2		390	445	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	263	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.16248016220052	3	FACETS	0.908	0.861	0.956	0.908	0.861	0.956	INDETERMINATE	3	TRUE	0	0.440217177420327	3		473	535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934874	NA	P-0035585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	313	725	2	ENST00000269305.4:c.451C>A	p.Pro151Thr	p.P151T	ENST00000269305	NM_001126112.2	151	Ccc/Acc	5/11	0.440217177420327	1	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	0	0.440217177420327	1		727	483	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0035585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	59	283	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.440217177420327	2		284	218	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964491	70964491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1447674775	NA	P-0035585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	201	629	1	ENST00000276594.2:c.1537G>A	p.Gly513Arg	p.G513R	ENST00000276594	NM_024504.3	513	Ggg/Agg	8/8	0.440217177420327	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.440217177420327	3		630	485	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669586	88669586	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	102	300	0	ENST00000360948.2:c.1312C>A	p.Leu438Ile	p.L438I	ENST00000360948	NM_001012338.2	438	Ctt/Att	12/19	0.440217177420327	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.440217177420327	3		300	237	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400116	41400116	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	282	479	0	ENST00000373198.4:c.643G>T	p.Ala215Ser	p.A215S	ENST00000373198	NM_133170.3	215	Gct/Tct	5/32	0.440217177420327	6	FACETS	1	0.972	1	0.828	0.786	0.87	CLONAL	4	TRUE	1	0.440217177420327	6		479	582	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39762962	39762962	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	22	269	0	ENST00000288319.7:c.874C>A	p.Pro292Thr	p.P292T	ENST00000288319	NM_182918.3	292	Cct/Act	9/10	0.181548386702396	3	FACETS	0.512	0.398	0.644	0.171	0.132	0.215	INDETERMINATE	1	TRUE	0	0.440217177420327	3		269	238	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	179	672	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.875	0.81	0.942	0.875	0.81	0.942	CLONAL	1	TRUE	1	0.624455907646663	2		672	655	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	104	364	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.893	0.807	0.983	0.893	0.807	0.983	CLONAL	1	TRUE	1	0.624455907646663	2		364	373	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	264	555	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.97	0.925	1	1	0.996	1	CLONAL	2	TRUE	1	0.624455907646663	2		555	436	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941657	48941657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1060503077	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	80	248	0	ENST00000267163.4:c.967G>T	p.Glu323Ter	p.E323*	ENST00000267163	NM_000321.2	323	Gaa/Taa	10/27	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.624455907646663	2		248	240	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	139	544	0	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	1	2	FACETS	0.909	0.833	0.987	0.909	0.833	0.987	CLONAL	1	TRUE	1	0.624455907646663	2		544	490	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953115	81953115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1336595726	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	104	386	0	ENST00000359376.3:c.2081G>A	p.Arg694His	p.R694H	ENST00000359376	NM_002661.3	694	cGc/cAc	20/33	1	2	FACETS	0.872	0.787	0.96	0.872	0.787	0.96	CLONAL	1	TRUE	1	0.624455907646663	2		386	382	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349892	15349892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1427595023	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	217	807	0	ENST00000263377.2:c.3760C>T	p.Arg1254Trp	p.R1254W	ENST00000263377	NM_058243.2	1254	Cgg/Tgg	18/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.624455907646663	2		807	626	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448552	89448552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	147	589	0	ENST00000336596.2:c.1516G>A	p.Val506Ile	p.V506I	ENST00000336596	NM_005233.5	506	Gta/Ata	7/17	1	2	FACETS	0.907	0.833	0.983	0.907	0.833	0.983	CLONAL	1	TRUE	1	0.624455907646663	2		589	519	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214592	5214592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369295620	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	70	780	0	ENST00000357368.4:c.4474C>T	p.Arg1492Trp	p.R1492W	ENST00000357368	NM_002850.3	1492	Cgg/Tgg	29/38	1	2	FACETS	0.32	0.279	0.365	0.32	0.279	0.365	SUBCLONAL	1	TRUE	1	0.624455907646663	2		780	700	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247767	10247767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781301028	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	257	827	0	ENST00000340748.4:c.4435G>A	p.Val1479Met	p.V1479M	ENST00000340748		1479	Gtg/Atg	36/40	1	2	FACETS	0.976	0.917	1	0.976	0.917	1	CLONAL	1	TRUE	1	0.624455907646663	2		827	843	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443675	29443675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1034835558	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	188	676	0	ENST00000389048.3:c.3542G>A	p.Arg1181His	p.R1181H	ENST00000389048	NM_004304.4	1181	cGc/cAc	23/29	1	2	FACETS	0.883	0.819	0.949	0.883	0.819	0.949	CLONAL	1	TRUE	1	0.624455907646663	2		676	682	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885299	111885299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200936167	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	153	656	0	ENST00000341259.2:c.1187C>T	p.Thr396Met	p.T396M	ENST00000341259	NM_005475.2	396	aCg/aTg	6/8	1	2	FACETS	0.822	0.755	0.891	0.822	0.755	0.891	CLONAL	1	TRUE	1	0.624455907646663	2		656	596	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411923	116411923	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs34589476	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	280	983	1	ENST00000397752.3:c.2908C>T	p.Arg970Cys	p.R970C	ENST00000397752	NM_000245.2	970	Cgc/Tgc	14/21	1	2	FACETS	0.993	0.935	1	0.993	0.935	1	CLONAL	1	TRUE	1	0.624455907646663	2		984	903	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460516	149460516	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	254	765	2	ENST00000286301.3:c.121C>T	p.Arg41Ter	p.R41*	ENST00000286301	NM_005211.3	41	Cga/Tga	3/22	1	2	FACETS	0.987	0.927	1	0.987	0.927	1	CLONAL	1	TRUE	1	0.624455907646663	2		767	824	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866439	42866439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61735791	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	348	994	1	ENST00000398585.3:c.193G>A	p.Ala65Thr	p.A65T	ENST00000398585	NM_001135099.1	65	Gca/Aca	3/14	1	2	FACETS	0.941	0.891	0.991	0.941	0.891	0.991	CLONAL	1	TRUE	1	0.624455907646663	2		995	1185	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345955	70345955	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	176	634	0	ENST00000374080.3:c.2492C>T	p.Ala831Val	p.A831V	ENST00000374080		831	gCt/gTt	18/45	1	2	FACETS	0.895	0.828	0.964	0.895	0.828	0.964	CLONAL	1	TRUE	1	0.624455907646663	2		634	630	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057302	30057302	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315496	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	110	400	0	ENST00000338641.4:c.784C>T	p.Arg262Ter	p.R262*	ENST00000338641	NM_000268.3	262	Cga/Tga	8/16	1	2	FACETS	0.745	0.673	0.82	0.745	0.673	0.82	SUBCLONAL	1	TRUE	1	0.624455907646663	2		400	473	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650881	93650881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200438123	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	188	502	0	ENST00000375746.1:c.1807G>A	p.Asp603Asn	p.D603N	ENST00000375746	NM_001174167.1	603	Gat/Aat	13/14	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.624455907646663	2		502	573	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015293	128015293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770995913	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	157	493	0	ENST00000285398.2:c.2228G>A	p.Arg743His	p.R743H	ENST00000285398	NM_000122.1	743	cGc/cAc	15/15	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.624455907646663	2		493	495	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108185	209108185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751364381	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	126	489	1	ENST00000345146.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000345146	NM_005896.2	222	Cgt/Tgt	6/10	1	2	FACETS	0.915	0.835	0.998	0.915	0.835	0.998	CLONAL	1	TRUE	1	0.624455907646663	2		490	441	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638899	176638899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750922390	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	231	611	1	ENST00000439151.2:c.3499C>T	p.Arg1167Cys	p.R1167C	ENST00000439151	NM_022455.4	1167	Cgc/Tgc	5/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.624455907646663	2		612	695	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823855	3823855	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs117910358	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	69	729	1	ENST00000262367.5:c.2360C>T	p.Ala787Val	p.A787V	ENST00000262367	NM_004380.2	787	gCg/gTg	13/31	1	2	FACETS	0.266	0.231	0.304	0.266	0.231	0.304	SUBCLONAL	1	TRUE	1	0.624455907646663	2		730	830	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909629	76909629	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs919106518	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	142	729	1	ENST00000373344.5:c.4276C>T	p.Arg1426Ter	p.R1426*	ENST00000373344	NM_000489.3	1426	Cga/Tga	14/35	1	2	FACETS	0.77	0.704	0.838	0.77	0.704	0.838	SUBCLONAL	1	TRUE	1	0.624455907646663	2		730	591	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675248	176675248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201483724	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	114	290	2	ENST00000439151.2:c.4564G>A	p.Asp1522Asn	p.D1522N	ENST00000439151	NM_022455.4	1522	Gat/Aat	11/23	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.624455907646663	2		292	344	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021817	71021817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs797045586	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	73	257	0	ENST00000318789.4:c.1541G>A	p.Arg514His	p.R514H	ENST00000318789	NM_032682.5	514	cGt/cAt	18/21	1	2	FACETS	0.903	0.799	1	0.903	0.799	1	CLONAL	1	TRUE	1	0.624455907646663	2		257	259	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629583	187629583	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs201582617	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	250	737	0	ENST00000441802.2:c.1399G>T	p.Ala467Ser	p.A467S	ENST00000441802	NM_005245.3	467	Gcg/Tcg	2/27	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.624455907646663	2		737	765	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711081	61711081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs996736538	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	103	419	0	ENST00000401558.2:c.2668G>A	p.Ala890Thr	p.A890T	ENST00000401558	NM_003400.3	890	Gca/Aca	21/25	1	2	FACETS	0.991	0.896	1	0.991	0.896	1	CLONAL	1	TRUE	1	0.624455907646663	2		419	333	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138570	2138570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45517423	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	98	850	3	ENST00000219476.3:c.5383C>T	p.Arg1795Cys	p.R1795C	ENST00000219476	NM_000548.3	1795	Cgc/Tgc	42/42	1	2	FACETS	0.36	0.32	0.402	0.36	0.32	0.402	SUBCLONAL	1	TRUE	1	0.624455907646663	2		853	873	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968595	55968595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199504669	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	55	675	0	ENST00000263923.4:c.2068G>A	p.Ala690Thr	p.A690T	ENST00000263923	NM_002253.2	690	Gca/Aca	14/30	1	2	FACETS	0.234	0.2	0.272	0.234	0.2	0.272	SUBCLONAL	1	TRUE	1	0.624455907646663	2		675	752	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980426	7980426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759484732	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	292	833	0	ENST00000319144.4:c.1157G>A	p.Arg386His	p.R386H	ENST00000319144	NM_001139.2	386	cGc/cAc	9/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.624455907646663	2		833	854	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675823	30675823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	234	995	0	ENST00000376406.3:c.2533G>A	p.Asp845Asn	p.D845N	ENST00000376406	NM_014641.2	845	Gat/Aat	8/15	1	2	FACETS	0.761	0.71	0.813	0.761	0.71	0.813	SUBCLONAL	1	TRUE	1	0.624455907646663	2		995	985	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467675	50467675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759124417	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	146	541	0	ENST00000331340.3:c.910G>A	p.Glu304Lys	p.E304K	ENST00000331340	NM_006060.4	304	Gaa/Aaa	8/8	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.624455907646663	2		541	446	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638456	176638456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750354456	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	197	820	0	ENST00000439151.2:c.3056G>A	p.Arg1019His	p.R1019H	ENST00000439151	NM_022455.4	1019	cGc/cAc	5/23	1	2	FACETS	0.817	0.759	0.878	0.817	0.759	0.878	CLONAL	1	TRUE	1	0.624455907646663	2		820	772	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740216	162740216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775098890	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	153	510	1	ENST00000367921.3:c.1418G>A	p.Arg473His	p.R473H	ENST00000367921	NM_006182.2	473	cGc/cAc	12/18	1	2	FACETS	0.906	0.833	0.98	0.906	0.833	0.98	CLONAL	1	TRUE	1	0.624455907646663	2		511	541	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846040	128846040	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	253	973	1	ENST00000249373.3:c.970G>A	p.Ala324Thr	p.A324T	ENST00000249373	NM_005631.4	324	Gcc/Acc	5/12	1	2	FACETS	0.833	0.78	0.887	0.833	0.78	0.887	CLONAL	1	TRUE	1	0.624455907646663	2		974	973	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	121	266	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	0.624455907646663	2	FACETS	0.916	0.834	1	0.458	0.417	0.501	CLONAL	1	TRUE	0	0.624455907646663	2		266	423	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127447	55127447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1333247214	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	200	657	0	ENST00000257290.5:c.235G>A	p.Gly79Ser	p.G79S	ENST00000257290	NM_006206.4	79	Ggc/Agc	3/23	1	2	FACETS	0.855	0.795	0.918	0.855	0.795	0.918	CLONAL	1	TRUE	1	0.624455907646663	2		657	749	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7174624	7174624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771406570	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	238	713	1	ENST00000302850.5:c.1093G>A	p.Gly365Arg	p.G365R	ENST00000302850	NM_000208.2	365	Ggg/Agg	4/22	1	2	FACETS	0.965	0.904	1	0.965	0.904	1	CLONAL	1	TRUE	1	0.624455907646663	2		714	790	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061208	38061208	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	222	685	0	ENST00000250448.2:c.781C>A	p.Arg261Ser	p.R261S	ENST00000250448	NM_004496.3	261	Cgc/Agc	2/2	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.624455907646663	2		685	681	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725295	49725295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760608948	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	206	606	0	ENST00000449682.2:c.130C>T	p.Arg44Trp	p.R44W	ENST00000449682	NM_020998.3	44	Cgg/Tgg	2/18	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.624455907646663	2		606	620	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149982884	149982884	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1327531500	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	99	506	0	ENST00000253339.5:c.3374G>A	p.Arg1125His	p.R1125H	ENST00000253339		1125	cGc/cAc	7/7	1	2	FACETS	0.843	0.759	0.931	0.843	0.759	0.931	CLONAL	1	TRUE	1	0.624455907646663	2		506	376	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65323452	65323452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765489448	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	189	522	0	ENST00000342505.4:c.1345G>A	p.Ala449Thr	p.A449T	ENST00000342505	NM_002227.2	449	Gcc/Acc	10/25	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.624455907646663	2		522	581	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888121	81888121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762900860	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	163	564	2	ENST00000359376.3:c.266G>A	p.Arg89His	p.R89H	ENST00000359376	NM_002661.3	89	cGc/cAc	3/33	1	2	FACETS	0.919	0.848	0.992	0.919	0.848	0.992	CLONAL	1	TRUE	1	0.624455907646663	2		566	568	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874604	35874604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137868226	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	150	575	1	ENST00000303115.3:c.760G>A	p.Ala254Thr	p.A254T	ENST00000303115	NM_002185.3	254	Gct/Act	6/8	1	2	FACETS	0.831	0.763	0.902	0.831	0.763	0.902	CLONAL	1	TRUE	1	0.624455907646663	2		576	578	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047329	128047329	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748503195	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	187	508	0	ENST00000285398.2:c.593G>A	p.Arg198His	p.R198H	ENST00000285398	NM_000122.1	198	cGc/cAc	5/15	1	2	FACETS	0.975	0.906	1	0.975	0.906	1	CLONAL	1	TRUE	1	0.624455907646663	2		508	614	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136070	64136070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	188	729	0	ENST00000334205.4:c.1331G>A	p.Arg444His	p.R444H	ENST00000334205	NM_003942.2	444	cGc/cAc	11/17	1	2	FACETS	0.953	0.885	1	0.953	0.885	1	CLONAL	1	TRUE	1	0.624455907646663	2		729	632	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279645	18279645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	173	652	2	ENST00000222254.8:c.1918C>T	p.Arg640Trp	p.R640W	ENST00000222254	NM_005027.3	640	Cgg/Tgg	15/16	1	2	FACETS	0.741	0.683	0.8	0.741	0.683	0.8	SUBCLONAL	1	TRUE	1	0.624455907646663	2		654	748	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421519	32421519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	270	671	0	ENST00000332351.3:c.1073C>T	p.Thr358Met	p.T358M	ENST00000332351	NM_024426.4	358	aCg/aTg	6/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.624455907646663	2		671	787	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592099	67592099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	100	269	0	ENST00000274335.5:c.1915C>T	p.Arg639Ter	p.R639*	ENST00000274335		639	Cga/Tga	14/15	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.624455907646663	2		269	312	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491390	18491390	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1377942847	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	86	251	2	ENST00000266497.5:c.1309del	p.Ile437TyrfsTer5	p.I437Yfs*5	ENST00000266497		435	Aaa/aa	8/31	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.624455907646663	2		253	273	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243232	123243232	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	273	925	0	ENST00000358487.5:c.2281C>A	p.Leu761Ile	p.L761I	ENST00000358487	NM_000141.4	761	Ctc/Atc	17/18	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.624455907646663	2		925	854	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748509	43748509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371177206	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	119	384	0	ENST00000523873.1:c.463C>T	p.Arg155Cys	p.R155C	ENST00000523873		155	Cgc/Tgc	6/8	1	2	FACETS	0.916	0.834	1	0.916	0.834	1	CLONAL	1	TRUE	1	0.624455907646663	2		384	416	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510723	38510723	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752501819	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	140	516	0	ENST00000254066.5:c.977C>T	p.Thr326Met	p.T326M	ENST00000254066	NM_000964.3	326	aCg/aTg	7/9	1	2	FACETS	0.881	0.807	0.957	0.881	0.807	0.957	CLONAL	1	TRUE	1	0.624455907646663	2		516	509	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131895051	131895051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370769989	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	85	283	0	ENST00000265335.6:c.205G>A	p.Asp69Asn	p.D69N	ENST00000265335		69	Gat/Aat	2/25	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.624455907646663	2		283	266	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205756	108205756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531980488	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	116	365	0	ENST00000278616.4:c.8071C>T	p.Arg2691Cys	p.R2691C	ENST00000278616	NM_000051.3	2691	Cgc/Tgc	55/63	0.624455907646663	2	FACETS	1	0.969	1	0.57	0.52	0.621	CLONAL	1	TRUE	0	0.624455907646663	2		365	326	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132465	11132465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	260	838	1	ENST00000358026.2:c.2681C>T	p.Thr894Met	p.T894M	ENST00000358026	NM_001128849.1	894	aCg/aTg	19/36	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.624455907646663	2		839	810	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596068	43596068	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537523906	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	215	769	1	ENST00000355710.3:c.235C>T	p.Arg79Trp	p.R79W	ENST00000355710	NM_020975.4	79	Cgg/Tgg	2/20	1	2	FACETS	0.954	0.89	1	0.954	0.89	1	CLONAL	1	TRUE	1	0.624455907646663	2		770	722	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951085	17951085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	235	690	1	ENST00000458235.1:c.1208G>A	p.Arg403His	p.R403H	ENST00000458235	NM_000215.3	403	cGc/cAc	9/24	1	2	FACETS	0.901	0.843	0.961	0.901	0.843	0.961	CLONAL	1	TRUE	1	0.624455907646663	2		691	835	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617397	43617397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	154	522	0	ENST00000355710.3:c.2734C>T	p.Arg912Trp	p.R912W	ENST00000355710	NM_020975.4	912	Cgg/Tgg	16/20	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.624455907646663	2		522	487	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830751	72830751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761415382	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	235	699	0	ENST00000268489.5:c.5830G>A	p.Ala1944Thr	p.A1944T	ENST00000268489	NM_006885.3	1944	Gcc/Acc	9/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.624455907646663	2		699	706	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561436	9561436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757167550	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	178	563	0	ENST00000353224.5:c.346G>A	p.Gly116Ser	p.G116S	ENST00000353224	NM_177990.2	116	Ggt/Agt	4/10	1	2	FACETS	0.998	0.926	1	0.998	0.926	1	CLONAL	1	TRUE	1	0.624455907646663	2		563	571	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033753	48033753	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1553333707	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	79	305	0	ENST00000234420.5:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000234420	NM_000179.2	1322	Gaa/Taa	9/10	1	2	FACETS	0.955	0.851	1	0.955	0.851	1	CLONAL	1	TRUE	1	0.624455907646663	2		305	265	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047800	128047800	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	136	478	0	ENST00000285398.2:c.521G>T	p.Arg174Ile	p.R174I	ENST00000285398	NM_000122.1	174	aGa/aTa	4/15	1	2	FACETS	0.994	0.912	1	0.994	0.912	1	CLONAL	1	TRUE	1	0.624455907646663	2		478	438	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372746	81372746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	123	383	0	ENST00000222390.5:c.788C>T	p.Pro263Leu	p.P263L	ENST00000222390	NM_000601.4	263	cCc/cTc	7/18	1	2	FACETS	0.94	0.857	1	0.94	0.857	1	CLONAL	1	TRUE	1	0.624455907646663	2		383	419	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856365	111856365	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750857643	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	107	201	0	ENST00000341259.2:c.416G>A	p.Arg139His	p.R139H	ENST00000341259	NM_005475.2	139	cGc/cAc	2/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.624455907646663	2		201	319	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851891	134851891	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs769821589	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	168	526	0	ENST00000398015.3:c.1297G>A	p.Ala433Thr	p.A433T	ENST00000398015	NM_004441.4	433	Gcc/Acc	5/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.624455907646663	2		526	505	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238951	5238951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237159914	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	151	515	0	ENST00000357368.4:c.1828C>T	p.Arg610Trp	p.R610W	ENST00000357368	NM_002850.3	610	Cgg/Tgg	13/38	1	2	FACETS	0.977	0.9	1	0.977	0.9	1	CLONAL	1	TRUE	1	0.624455907646663	2		515	495	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739881	145739881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764297840	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	214	796	0	ENST00000428558.2:c.1649C>T	p.Ala550Val	p.A550V	ENST00000428558	NM_004260.3	550	gCg/gTg	10/22	1	2	FACETS	0.94	0.877	1	0.94	0.877	1	CLONAL	1	TRUE	1	0.624455907646663	2		796	729	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240450	98240450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370354759	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	177	501	1	ENST00000331920.6:c.1234G>A	p.Ala412Thr	p.A412T	ENST00000331920	NM_000264.3	412	Gca/Aca	9/24	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.624455907646663	2		502	537	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164451	36164451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	105	437	2	ENST00000300305.3:c.1424C>T	p.Ala475Val	p.A475V	ENST00000300305		475	gCc/gTc	8/8	1	2	FACETS	0.983	0.891	1	0.983	0.891	1	CLONAL	1	TRUE	1	0.624455907646663	2		439	342	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808989	1808989	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	rs121913103	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	89	450	0	ENST00000260795.2:c.2421A>G	p.Ter807TrpextTer101	p.*807Wext*101	ENST00000260795		807	tgA/tgG	17/17	1	2	FACETS	0.754	0.673	0.839	0.754	0.673	0.839	SUBCLONAL	1	TRUE	1	0.624455907646663	2		450	378	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101031	4101031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375843855	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	191	603	0	ENST00000262948.5:c.691C>T	p.Arg231Cys	p.R231C	ENST00000262948	NM_030662.3	231	Cgc/Tgc	6/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.624455907646663	2		603	551	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759406	133759406	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1371645607	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	44	746	2	ENST00000318560.5:c.1729C>T	p.Arg577Ter	p.R577*	ENST00000318560	NM_005157.4	577	Cga/Tga	11/11	1	2	FACETS	0.183	0.153	0.217	0.183	0.153	0.217	SUBCLONAL	1	TRUE	1	0.624455907646663	2		748	770	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052636	42052636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1054243525	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	202	567	0	ENST00000219905.7:c.7307G>A	p.Arg2436His	p.R2436H	ENST00000219905	NM_001164273.1	2436	cGt/cAt	20/24	1	2	FACETS	0.924	0.86	0.99	0.924	0.86	0.99	CLONAL	1	TRUE	1	0.624455907646663	2		567	700	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40368097	40368097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555548681	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	86	659	2	ENST00000293328.3:c.1408G>A	p.Val470Ile	p.V470I	ENST00000293328	NM_012448.3	470	Gtt/Att	12/19	1	2	FACETS	0.356	0.314	0.4	0.356	0.314	0.4	SUBCLONAL	1	TRUE	1	0.624455907646663	2		661	774	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533680	63533680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	202	678	1	ENST00000307078.5:c.1474G>A	p.Ala492Thr	p.A492T	ENST00000307078	NM_004655.3	492	Gcc/Acc	6/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.624455907646663	2		679	545	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201885	152201885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778449608	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	157	377	1	ENST00000206249.3:c.739G>A	p.Glu247Lys	p.E247K	ENST00000206249	NM_000125.3	247	Gaa/Aaa	3/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.624455907646663	2		378	422	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059183	27059183	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	151	457	0	ENST00000324856.7:c.1820C>A	p.Ser607Ter	p.S607*	ENST00000324856	NM_006015.4	607	tCa/tAa	4/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.624455907646663	2		457	450	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265025	5265025	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	93	771	0	ENST00000357368.4:c.562C>T	p.Arg188Ter	p.R188*	ENST00000357368	NM_002850.3	188	Cga/Tga	5/38	1	2	FACETS	0.358	0.318	0.402	0.358	0.318	0.402	SUBCLONAL	1	TRUE	1	0.624455907646663	2		771	831	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279531	1279531	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372140951	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	214	1053	0	ENST00000310581.5:c.2005C>T	p.Arg669Trp	p.R669W	ENST00000310581	NM_198253.2	669	Cgg/Tgg	5/16	1	2	FACETS	0.735	0.683	0.788	0.735	0.683	0.788	SUBCLONAL	1	TRUE	1	0.624455907646663	2		1053	933	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214666	5214666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs116660613	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	297	923	0	ENST00000357368.4:c.4400C>T	p.Pro1467Leu	p.P1467L	ENST00000357368	NM_002850.3	1467	cCg/cTg	29/38	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.624455907646663	2		923	950	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524347	187524347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773283301	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	60	504	1	ENST00000441802.2:c.11333C>T	p.Ala3778Val	p.A3778V	ENST00000441802	NM_005245.3	3778	gCg/gTg	19/27	1	2	FACETS	0.334	0.287	0.384	0.334	0.287	0.384	SUBCLONAL	1	TRUE	1	0.624455907646663	2		505	576	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728765	39728765	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	122	411	0	ENST00000361337.2:c.1045A>G	p.Arg349Gly	p.R349G	ENST00000361337	NM_003286.2	349	Agg/Ggg	12/21	1	2	FACETS	0.894	0.814	0.977	0.894	0.814	0.977	CLONAL	1	TRUE	1	0.624455907646663	2		411	437	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224539	123224539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	142	705	0	ENST00000218089.9:c.3392G>T	p.Arg1131Ile	p.R1131I	ENST00000218089	NM_001042749.1	1131	aGa/aTa	31/35	1	2	FACETS	0.699	0.638	0.761	0.699	0.638	0.761	SUBCLONAL	1	TRUE	1	0.624455907646663	2		705	651	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508932	106508932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	125	445	0	ENST00000359195.3:c.926C>T	p.Thr309Met	p.T309M	ENST00000359195	NM_002649.2	309	aCg/aTg	2/11	1	2	FACETS	0.965	0.881	1	0.965	0.881	1	CLONAL	1	TRUE	1	0.624455907646663	2		445	415	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912175	29912175	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs41547331	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	18	224	0	ENST00000376809.5:c.895+1G>A		p.X299_splice	ENST00000376809	NM_002116.7	299			1	2	FACETS	0.28	0.211	0.36	0.28	0.211	0.36	SUBCLONAL	1	TRUE	1	0.624455907646663	2		224	206	SUCCESS
BTK	695	MSKCC	GRCh37	X	100609658	100609658	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782740486	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	172	493	1	ENST00000308731.7:c.1591G>A	p.Asp531Asn	p.D531N	ENST00000308731	NM_000061.2	531	Gat/Aat	16/19	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.624455907646663	2		494	539	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448601	89448601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775665893	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	168	613	2	ENST00000336596.2:c.1565G>A	p.Arg522His	p.R522H	ENST00000336596	NM_005233.5	522	cGc/cAc	7/17	1	2	FACETS	0.897	0.828	0.967	0.897	0.828	0.967	CLONAL	1	TRUE	1	0.624455907646663	2		615	600	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652248	48652248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057518396	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	53	722	0	ENST00000376670.3:c.919C>T	p.Arg307Cys	p.R307C	ENST00000376670	NM_002049.3	307	Cgc/Tgc	6/6	1	2	FACETS	0.224	0.19	0.261	0.224	0.19	0.261	SUBCLONAL	1	TRUE	1	0.624455907646663	2		722	757	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176614	56176614	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	127	394	0	ENST00000399503.3:c.2164G>T	p.Glu722Ter	p.E722*	ENST00000399503	NM_005921.1	722	Gaa/Taa	12/20	1	2	FACETS	0.944	0.862	1	0.944	0.862	1	CLONAL	1	TRUE	1	0.624455907646663	2		394	431	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427465	427465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769625142	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	179	700	1	ENST00000399788.2:c.2704C>T	p.Arg902Trp	p.R902W	ENST00000399788	NM_001042603.1	902	Cgg/Tgg	19/28	1	2	FACETS	0.678	0.626	0.733	0.678	0.626	0.733	SUBCLONAL	1	TRUE	1	0.624455907646663	2		701	845	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520205	176520205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766563138	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	290	1032	0	ENST00000292408.4:c.1124C>T	p.Ser375Leu	p.S375L	ENST00000292408	NM_213647.1	375	tCg/tTg	9/18	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.624455907646663	2		1032	906	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528936	157528936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1390972891	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	211	593	1	ENST00000346085.5:c.6661C>T	p.Arg2221Trp	p.R2221W	ENST00000346085	NM_020732.3	2221	Cgg/Tgg	20/20	1	2	FACETS	0.989	0.923	1	0.989	0.923	1	CLONAL	1	TRUE	1	0.624455907646663	2		594	683	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245501	153245501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1024060344	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	147	508	0	ENST00000281708.4:c.1690C>T	p.Arg564Cys	p.R564C	ENST00000281708	NM_033632.3	564	Cgt/Tgt	11/12	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.624455907646663	2		508	458	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911141	29911141	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	114	742	0	ENST00000376809.5:c.440A>G	p.Tyr147Cys	p.Y147C	ENST00000376809	NM_002116.7	147	tAc/tGc	3/8	1	2	FACETS	0.658	0.594	0.725	0.658	0.594	0.725	SUBCLONAL	1	TRUE	1	0.624455907646663	2		742	555	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720871	89720871	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	158	382	0	ENST00000371953.3:c.1022T>G	p.Phe341Cys	p.F341C	ENST00000371953	NM_000314.4	341	tTt/tGt	8/9	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.624455907646663	2		382	478	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100283	8100283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	211	716	0	ENST00000346208.3:c.257G>A	p.Arg86His	p.R86H	ENST00000346208		86	cGc/cAc	3/6	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.624455907646663	2		716	631	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984022	2984022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753614569	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	205	730	1	ENST00000396946.4:c.508C>T	p.Arg170Cys	p.R170C	ENST00000396946	NM_032415.4	170	Cgc/Tgc	5/25	1	2	FACETS	0.933	0.868	0.999	0.933	0.868	0.999	CLONAL	1	TRUE	1	0.624455907646663	2		731	704	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371710	89371710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764805663	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	261	848	0	ENST00000301030.4:c.130C>T	p.Arg44Cys	p.R44C	ENST00000301030	NM_001256183.1	44	Cgt/Tgt	4/13	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.624455907646663	2		848	795	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136030	64136030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1380280944	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	265	800	1	ENST00000334205.4:c.1291C>T	p.Arg431Cys	p.R431C	ENST00000334205	NM_003942.2	431	Cgc/Tgc	11/17	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.624455907646663	2		801	812	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553485	106553485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	97	414	0	ENST00000369096.4:c.1450C>T	p.Pro484Ser	p.P484S	ENST00000369096	NM_001198.3	484	Ccc/Tcc	5/7	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.624455907646663	2		414	294	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112328	115112328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1438073122	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	23	464	3	ENST00000257566.3:c.1412G>A	p.Arg471His	p.R471H	ENST00000257566	NM_016569.3	471	cGc/cAc	7/8	1	2	FACETS	0.2	0.155	0.251	0.2	0.155	0.251	SUBCLONAL	1	TRUE	1	0.624455907646663	2		467	369	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100906	41100906	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs560503250	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	154	630	1	ENST00000373198.4:c.1450G>A	p.Val484Ile	p.V484I	ENST00000373198	NM_133170.3	484	Gtt/Att	8/32	1	2	FACETS	0.903	0.831	0.978	0.903	0.831	0.978	CLONAL	1	TRUE	1	0.624455907646663	2		631	546	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942193	71942193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749091098	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	226	790	0	ENST00000298229.2:c.1457G>A	p.Arg486His	p.R486H	ENST00000298229	NM_001567.3	486	cGc/cAc	12/28	0.624455907646663	2	FACETS	0.985	0.921	1	0.492	0.46	0.525	CLONAL	1	TRUE	0	0.624455907646663	2		790	735	SUCCESS
APC	324	MSKCC	GRCh37	5	112177368	112177368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	99	341	1	ENST00000257430.4:c.6077C>T	p.Ser2026Phe	p.S2026F	ENST00000257430	NM_000038.5	2026	tCt/tTt	16/16	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.624455907646663	2		342	301	SUCCESS
APC	324	MSKCC	GRCh37	5	112178864	112178864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774952444	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	72	408	0	ENST00000257430.4:c.7573C>T	p.Arg2525Cys	p.R2525C	ENST00000257430	NM_000038.5	2525	Cgc/Tgc	16/16	1	2	FACETS	0.705	0.621	0.795	0.705	0.621	0.795	SUBCLONAL	1	TRUE	1	0.624455907646663	2		408	327	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393421	139393421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	279	879	1	ENST00000277541.6:c.6110C>T	p.Ala2037Val	p.A2037V	ENST00000277541	NM_017617.3	2037	gCc/gTc	33/34	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.624455907646663	2		880	880	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760790	133760790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367600262	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	43	857	1	ENST00000318560.5:c.3113C>T	p.Ala1038Val	p.A1038V	ENST00000318560	NM_005157.4	1038	gCg/gTg	11/11	1	2	FACETS	0.194	0.161	0.23	0.194	0.161	0.23	SUBCLONAL	1	TRUE	1	0.624455907646663	2		858	711	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937356	76937356	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	154	581	0	ENST00000373344.5:c.3392G>T	p.Arg1131Ile	p.R1131I	ENST00000373344	NM_000489.3	1131	aGa/aTa	9/35	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.624455907646663	2		581	432	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4090609	4090609	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751040819	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	141	642	2	ENST00000262948.5:c.1190G>A	p.Arg397His	p.R397H	ENST00000262948	NM_030662.3	397	cGc/cAc	11/11	1	2	FACETS	0.727	0.665	0.792	0.727	0.665	0.792	SUBCLONAL	1	TRUE	1	0.624455907646663	2		644	621	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934222	39934222	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1358504792	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	219	847	0	ENST00000378444.4:c.377C>T	p.Pro126Leu	p.P126L	ENST00000378444	NM_001123385.1	126	cCg/cTg	4/15	1	2	FACETS	0.699	0.65	0.749	0.699	0.65	0.749	SUBCLONAL	1	TRUE	1	0.624455907646663	2		847	1004	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028136	48028136	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782324	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	116	364	1	ENST00000234420.5:c.3014G>A	p.Arg1005Gln	p.R1005Q	ENST00000234420	NM_000179.2	1005	cGa/cAa	4/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.624455907646663	2		365	344	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348106	89348106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	323	1070	0	ENST00000301030.4:c.4844C>T	p.Ser1615Phe	p.S1615F	ENST00000301030	NM_001256183.1	1615	tCc/tTc	9/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.624455907646663	2		1070	933	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344548	118344548	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	143	397	0	ENST00000534358.1:c.2674A>G	p.Lys892Glu	p.K892E	ENST00000534358	NM_005933.3	892	Aaa/Gaa	3/36	0.624455907646663	2	FACETS	1	0.925	1	0.503	0.462	0.545	CLONAL	1	TRUE	0	0.624455907646663	2		397	455	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754303	57754303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	144	593	0	ENST00000274289.3:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000274289	NM_006622.3	183	cGa/cAa	4/14	1	2	FACETS	0.812	0.744	0.883	0.812	0.744	0.883	CLONAL	1	TRUE	1	0.624455907646663	2		593	568	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40376874	40376874	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199894785	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	174	532	2	ENST00000293328.3:c.298C>T	p.Arg100Cys	p.R100C	ENST00000293328	NM_012448.3	100	Cgc/Tgc	4/19	1	2	FACETS	0.905	0.837	0.975	0.905	0.837	0.975	CLONAL	1	TRUE	1	0.624455907646663	2		534	616	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046722	180046722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768562688	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	53	981	0	ENST00000261937.6:c.2590G>A	p.Ala864Thr	p.A864T	ENST00000261937	NM_182925.4	864	Gct/Act	18/30	1	2	FACETS	0.173	0.146	0.202	0.173	0.146	0.202	SUBCLONAL	1	TRUE	1	0.624455907646663	2		981	983	SUCCESS
MET	4233	MSKCC	GRCh37	7	116414341	116414341	+	intron_variant	Intron	SNP	G	G	A	rs929061044	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	252	927	0	ENST00000397752.3:c.3029-594G>A		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.624455907646663	2		927	779	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377048	118377048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	131	420	0	ENST00000534358.1:c.10441C>T	p.Pro3481Ser	p.P3481S	ENST00000534358	NM_005933.3	3481	Ccc/Tcc	27/36	0.624455907646663	2	FACETS	0.992	0.908	1	0.496	0.454	0.539	CLONAL	1	TRUE	0	0.624455907646663	2		420	423	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670085	86670085	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	55	379	0	ENST00000274376.6:c.1882A>C	p.Thr628Pro	p.T628P	ENST00000274376	NM_002890.2	628	Act/Cct	14/25	1	2	FACETS	0.359	0.308	0.416	0.359	0.308	0.416	SUBCLONAL	1	TRUE	1	0.624455907646663	2		379	490	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495826	56495826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	79	366	0	ENST00000267101.3:c.4016C>T	p.Ala1339Val	p.A1339V	ENST00000267101	NM_001982.3	1339	gCc/gTc	28/28	1	2	FACETS	0.806	0.715	0.901	0.806	0.715	0.901	CLONAL	1	TRUE	1	0.624455907646663	2		366	314	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627218	37627218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375280392	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	194	564	1	ENST00000447079.4:c.1133G>A	p.Arg378His	p.R378H	ENST00000447079	NM_015083.1	378	cGc/cAc	2/14	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.624455907646663	2		565	579	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519712	137519712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560014238	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	91	423	0	ENST00000367739.4:c.926C>T	p.Thr309Met	p.T309M	ENST00000367739	NM_000416.2	309	aCg/aTg	7/7	1	2	FACETS	0.842	0.755	0.934	0.842	0.755	0.934	CLONAL	1	TRUE	1	0.624455907646663	2		423	346	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984079	2984079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	191	588	1	ENST00000396946.4:c.451G>A	p.Glu151Lys	p.E151K	ENST00000396946	NM_032415.4	151	Gag/Aag	5/25	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.624455907646663	2		589	610	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226035	133226035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200398117	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	252	810	1	ENST00000320574.5:c.3862G>A	p.Ala1288Thr	p.A1288T	ENST00000320574	NM_006231.2	1288	Gcc/Acc	31/49	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.624455907646663	2		811	777	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281668	49281668	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201815757	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	274	944	2	ENST00000282018.3:c.715C>T	p.Arg239Trp	p.R239W	ENST00000282018	NM_020377.2	239	Cgg/Tgg	1/1	1	2	FACETS	0.883	0.83	0.937	0.883	0.83	0.937	CLONAL	1	TRUE	1	0.624455907646663	2		946	994	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211883	36211883	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202218975	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	376	1209	1	ENST00000222270.7:c.1634G>A	p.Arg545Gln	p.R545Q	ENST00000222270	NM_014727.1	545	cGa/cAa	3/37	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.624455907646663	2		1210	1187	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39690130	39690130	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	65	234	0	ENST00000361337.2:c.155G>T	p.Ser52Ile	p.S52I	ENST00000361337	NM_003286.2	52	aGt/aTt	3/21	1	2	FACETS	0.82	0.719	0.926	0.82	0.719	0.926	CLONAL	1	TRUE	1	0.624455907646663	2		234	254	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3113452	3113452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	242	689	0	ENST00000078429.4:c.446G>A	p.Arg149His	p.R149H	ENST00000078429	NM_002067.2	149	cGc/cAc	3/7	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.624455907646663	2		689	746	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285167	15285167	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs940480447	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	348	1069	2	ENST00000263388.2:c.4448G>A	p.Arg1483His	p.R1483H	ENST00000263388	NM_000435.2	1483	cGc/cAc	25/33	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.624455907646663	2		1071	1060	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250311	110250311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753267332	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	249	929	0	ENST00000374672.4:c.364G>A	p.Ala122Thr	p.A122T	ENST00000374672	NM_004235.4	122	Gcc/Acc	3/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.624455907646663	2		929	740	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348978	11348978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774980003	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	308	754	0	ENST00000332029.2:c.358G>A	p.Ala120Thr	p.A120T	ENST00000332029	NM_003745.1	120	Gcc/Acc	2/2	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.624455907646663	2		754	849	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041379	47041379	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	267	846	0	ENST00000377604.3:c.1723G>A	p.Asp575Asn	p.D575N	ENST00000377604	NM_001204468.1	575	Gat/Aat	16/24	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.624455907646663	2		846	751	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226080	2226080	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1397292006	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	290	967	1	ENST00000326181.6:c.1777C>T	p.Arg593Trp	p.R593W	ENST00000326181	NM_032271.2	593	Cgg/Tgg	19/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.624455907646663	2		968	907	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40857171	40857171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1287411309	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	71	419	0	ENST00000428826.2:c.1870G>A	p.Gly624Arg	p.G624R	ENST00000428826		624	Gga/Aga	17/21	1	2	FACETS	0.492	0.431	0.558	0.492	0.431	0.558	SUBCLONAL	1	TRUE	1	0.624455907646663	2		419	462	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250360	10250360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	75	321	0	ENST00000340748.4:c.3892G>A	p.Val1298Met	p.V1298M	ENST00000340748		1298	Gtg/Atg	33/40	1	2	FACETS	0.73	0.645	0.82	0.73	0.645	0.82	SUBCLONAL	1	TRUE	1	0.624455907646663	2		321	329	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511205	148511205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	175	523	2	ENST00000320356.2:c.1697G>A	p.Arg566His	p.R566H	ENST00000320356	NM_004456.4	566	cGc/cAc	15/20	1	2	FACETS	0.733	0.676	0.791	0.733	0.676	0.791	SUBCLONAL	1	TRUE	1	0.624455907646663	2		525	765	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399488	139399488	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748862853	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	69	982	1	ENST00000277541.6:c.4655C>T	p.Ala1552Val	p.A1552V	ENST00000277541	NM_017617.3	1552	gCg/gTg	26/34	1	2	FACETS	0.198	0.171	0.226	0.198	0.171	0.226	SUBCLONAL	1	TRUE	1	0.624455907646663	2		983	1118	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533512	63533512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367624903	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	254	923	1	ENST00000307078.5:c.1642G>A	p.Glu548Lys	p.E548K	ENST00000307078	NM_004655.3	548	Gag/Aag	6/11	1	2	FACETS	0.935	0.877	0.994	0.935	0.877	0.994	CLONAL	1	TRUE	1	0.624455907646663	2		924	870	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245300	41245300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	250	919	0	ENST00000357654.3:c.2248C>T	p.Leu750Phe	p.L750F	ENST00000357654	NM_007294.3	750	Ctc/Ttc	10/23	1	2	FACETS	0.98	0.919	1	0.98	0.919	1	CLONAL	1	TRUE	1	0.624455907646663	2		919	817	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212815	27212815	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1307510192	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	260	808	1	ENST00000380036.4:c.2797G>A	p.Ala933Thr	p.A933T	ENST00000380036	NM_000459.3	933	Gcg/Acg	17/23	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.624455907646663	2		809	800	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020732	37020732	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	143	562	3	ENST00000358127.4:c.113G>A	p.Arg38His	p.R38H	ENST00000358127	NM_001280556.1	38	cGc/cAc	2/10	1	2	FACETS	0.859	0.788	0.933	0.859	0.788	0.933	CLONAL	1	TRUE	1	0.624455907646663	2		565	533	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931411	131931411	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772468452	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	51	424	0	ENST00000265335.6:c.2116C>T	p.Arg706Ter	p.R706*	ENST00000265335		706	Cga/Tga	13/25	1	2	FACETS	0.365	0.311	0.425	0.365	0.311	0.425	SUBCLONAL	1	TRUE	1	0.624455907646663	2		424	447	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564680	86564680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775315018	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	215	702	0	ENST00000274376.6:c.412C>T	p.Pro138Ser	p.P138S	ENST00000274376	NM_002890.2	138	Ccc/Tcc	1/25	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.624455907646663	2		702	662	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445125	49445125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs565042425	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	213	777	2	ENST00000301067.7:c.2341G>A	p.Ala781Thr	p.A781T	ENST00000301067	NM_003482.3	781	Gct/Act	10/54	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.624455907646663	2		779	664	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657076	45657076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770959767	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	24	417	1	ENST00000407780.3:c.80C>T	p.Ala27Val	p.A27V	ENST00000407780	NM_001283052.1	27	gCg/gTg	3/7	1	2	FACETS	0.187	0.146	0.234	0.187	0.146	0.234	SUBCLONAL	1	TRUE	1	0.624455907646663	2		418	412	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867301	45867301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1269826858	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	210	988	0	ENST00000391945.4:c.892G>A	p.Ala298Thr	p.A298T	ENST00000391945	NM_000400.3	298	Gcc/Acc	10/23	1	2	FACETS	0.734	0.682	0.788	0.734	0.682	0.788	SUBCLONAL	1	TRUE	1	0.624455907646663	2		988	916	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116170	67116170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761036715	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	186	474	0	ENST00000412916.2:c.454G>A	p.Glu152Lys	p.E152K	ENST00000412916		152	Gaa/Aaa	5/6	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.624455907646663	2		474	563	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40368072	40368072	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555548678	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	108	737	1	ENST00000293328.3:c.1433C>T	p.Ala478Val	p.A478V	ENST00000293328	NM_012448.3	478	gCg/gTg	12/19	1	2	FACETS	0.393	0.352	0.437	0.393	0.352	0.437	SUBCLONAL	1	TRUE	1	0.624455907646663	2		738	880	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927471	178927471	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	125	533	0	ENST00000263967.3:c.1234C>T	p.Arg412Ter	p.R412*	ENST00000263967	NM_006218.2	412	Cga/Tga	7/21	1	2	FACETS	0.886	0.807	0.967	0.886	0.807	0.967	CLONAL	1	TRUE	1	0.624455907646663	2		533	452	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649273	23649273	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs200048921	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	136	444	0	ENST00000261584.4:c.109C>T	p.Arg37Cys	p.R37C	ENST00000261584	NM_024675.3	37	Cgt/Tgt	3/13	1	2	FACETS	0.981	0.899	1	0.981	0.899	1	CLONAL	1	TRUE	1	0.624455907646663	2		444	444	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622622	158622622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	194	579	0	ENST00000263640.3:c.877G>A	p.Asp293Asn	p.D293N	ENST00000263640	NM_001105.4	293	Gac/Aac	8/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.624455907646663	2		579	542	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292463	15292463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	315	969	1	ENST00000263388.2:c.2716G>A	p.Ala906Thr	p.A906T	ENST00000263388	NM_000435.2	906	Gcc/Acc	17/33	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.624455907646663	2		970	953	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639963	3639963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142008398	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	268	972	1	ENST00000294008.3:c.3676C>T	p.Arg1226Trp	p.R1226W	ENST00000294008	NM_032444.2	1226	Cgg/Tgg	12/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.624455907646663	2		973	832	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573507	48573507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	63	298	0	ENST00000342988.3:c.91G>A	p.Glu31Lys	p.E31K	ENST00000342988	NM_005359.5	31	Gag/Aag	2/12	1	2	FACETS	0.885	0.776	1	0.885	0.776	1	CLONAL	1	TRUE	1	0.624455907646663	2		298	228	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635202	87635202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1170229422	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	180	616	1	ENST00000277120.3:c.2254G>A	p.Val752Ile	p.V752I	ENST00000277120		752	Gtc/Atc	18/19	1	2	FACETS	0.857	0.793	0.922	0.857	0.793	0.922	CLONAL	1	TRUE	1	0.624455907646663	2		617	673	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604643	43604643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	202	723	0	ENST00000355710.3:c.1228C>T	p.Leu410Phe	p.L410F	ENST00000355710	NM_020975.4	410	Ctc/Ttc	6/20	1	2	FACETS	0.891	0.829	0.955	0.891	0.829	0.955	CLONAL	1	TRUE	1	0.624455907646663	2		723	726	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139408993	139408993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746313097	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	303	919	3	ENST00000277541.6:c.2176G>A	p.Val726Ile	p.V726I	ENST00000277541	NM_017617.3	726	Gtc/Atc	13/34	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.624455907646663	2		922	932	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851906	63851906	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	32	562	0	ENST00000279873.7:c.2684C>T	p.Ala895Val	p.A895V	ENST00000279873	NM_032199.2	895	gCg/gTg	10/10	1	2	FACETS	0.174	0.141	0.212	0.174	0.141	0.212	SUBCLONAL	1	TRUE	1	0.624455907646663	2		562	589	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598311	28598311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1480732926	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	372	984	0	ENST00000253063.3:c.283C>T	p.Arg95Cys	p.R95C	ENST00000253063	NM_031459.4	95	Cgc/Tgc	3/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.624455907646663	2		984	1077	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170804	11170804	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1306144699	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	247	699	0	ENST00000358026.2:c.4948C>T	p.Arg1650Ter	p.R1650*	ENST00000358026	NM_001128849.1	1650	Cga/Tga	35/36	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.624455907646663	2		699	773	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528243	157528243	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs797045283	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	54	644	0	ENST00000346085.5:c.5968C>T	p.Arg1990Ter	p.R1990*	ENST00000346085	NM_020732.3	1990	Cga/Tga	20/20	1	2	FACETS	0.277	0.236	0.322	0.277	0.236	0.322	SUBCLONAL	1	TRUE	1	0.624455907646663	2		644	625	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664524	29664524	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	211	655	0	ENST00000356175.3:c.6503C>A	p.Pro2168His	p.P2168H	ENST00000356175	NM_000267.3	2168	cCt/cAt	42/57	1	2	FACETS	0.994	0.927	1	0.994	0.927	1	CLONAL	1	TRUE	1	0.624455907646663	2		655	680	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160646	56160646	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343464548	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	28	357	1	ENST00000399503.3:c.920G>A	p.Arg307His	p.R307H	ENST00000399503	NM_005921.1	307	cGt/cAt	4/20	1	2	FACETS	0.222	0.177	0.273	0.222	0.177	0.273	SUBCLONAL	1	TRUE	1	0.624455907646663	2		358	404	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723074	52723074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	160	565	0	ENST00000322088.6:c.1259G>A	p.Arg420Gln	p.R420Q	ENST00000322088	NM_014225.5	420	cGg/cAg	10/15	1	2	FACETS	0.932	0.859	1	0.932	0.859	1	CLONAL	1	TRUE	1	0.624455907646663	2		565	550	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122297	2122297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45517215	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	355	987	1	ENST00000219476.3:c.2153G>A	p.Arg718His	p.R718H	ENST00000219476	NM_000548.3	718	cGc/cAc	20/42	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.624455907646663	2		988	1021	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374685	118374685	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	101	409	0	ENST00000534358.1:c.8078C>A	p.Ser2693Tyr	p.S2693Y	ENST00000534358	NM_005933.3	2693	tCt/tAt	27/36	0.624455907646663	2	FACETS	0.896	0.808	0.987	0.448	0.404	0.494	CLONAL	1	TRUE	0	0.624455907646663	2		409	361	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867477	35867477	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	74	306	0	ENST00000303115.3:c.291G>T	p.Lys97Asn	p.K97N	ENST00000303115	NM_002185.3	97	aaG/aaT	3/8	1	2	FACETS	0.956	0.848	1	0.956	0.848	1	CLONAL	1	TRUE	1	0.624455907646663	2		306	248	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169345	11169345	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	142	460	0	ENST00000361445.4:c.7528+2T>C		p.X2510_splice	ENST00000361445	NM_004958.3	2510			1	2	FACETS	0.938	0.861	1	0.938	0.861	1	CLONAL	1	TRUE	1	0.624455907646663	2		460	485	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272460	11272460	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	181	525	0	ENST00000361445.4:c.3470A>G	p.His1157Arg	p.H1157R	ENST00000361445	NM_004958.3	1157	cAc/cGc	23/58	1	2	FACETS	0.929	0.861	0.999	0.929	0.861	0.999	CLONAL	1	TRUE	1	0.624455907646663	2		525	624	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202759	16202759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375675403	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	40	521	1	ENST00000375759.3:c.467C>T	p.Thr156Met	p.T156M	ENST00000375759	NM_015001.2	156	aCg/aTg	3/15	1	2	FACETS	0.28	0.233	0.333	0.28	0.233	0.333	SUBCLONAL	1	TRUE	1	0.624455907646663	2		522	457	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256472	16256472	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	201	673	0	ENST00000375759.3:c.3737G>T	p.Arg1246Ile	p.R1246I	ENST00000375759	NM_015001.2	1246	aGa/aTa	11/15	1	2	FACETS	0.945	0.88	1	0.945	0.88	1	CLONAL	1	TRUE	1	0.624455907646663	2		673	681	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261895	16261895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777145562	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	169	552	1	ENST00000375759.3:c.9160G>A	p.Ala3054Thr	p.A3054T	ENST00000375759	NM_015001.2	3054	Gcc/Acc	11/15	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.624455907646663	2		553	529	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023637	27023637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	220	751	0	ENST00000324856.7:c.743G>A	p.Gly248Asp	p.G248D	ENST00000324856	NM_006015.4	248	gGc/gAc	1/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.624455907646663	2		751	679	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087566	27087566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	40	751	0	ENST00000324856.7:c.2140C>T	p.Leu714Phe	p.L714F	ENST00000324856	NM_006015.4	714	Ctc/Ttc	5/20	1	2	FACETS	0.166	0.137	0.198	0.166	0.137	0.198	SUBCLONAL	1	TRUE	1	0.624455907646663	2		751	774	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099436	27099436	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	162	583	0	ENST00000324856.7:c.3673T>C	p.Ser1225Pro	p.S1225P	ENST00000324856	NM_006015.4	1225	Tcc/Ccc	14/20	1	2	FACETS	0.928	0.856	1	0.928	0.856	1	CLONAL	1	TRUE	1	0.624455907646663	2		583	559	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105775	27105775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	149	514	0	ENST00000324856.7:c.5386C>T	p.Pro1796Ser	p.P1796S	ENST00000324856	NM_006015.4	1796	Cca/Tca	20/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.624455907646663	2		514	423	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932037	36932037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	148	693	1	ENST00000361632.4:c.2432G>A	p.Cys811Tyr	p.C811Y	ENST00000361632		811	tGt/tAt	16/16	1	2	FACETS	0.785	0.72	0.853	0.785	0.72	0.853	SUBCLONAL	1	TRUE	1	0.624455907646663	2		694	604	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939054	36939054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	261	808	1	ENST00000361632.4:c.655C>T	p.Leu219Phe	p.L219F	ENST00000361632		219	Ctt/Ttt	5/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.624455907646663	2		809	785	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805227	43805227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	154	749	0	ENST00000372470.3:c.677C>T	p.Ser226Phe	p.S226F	ENST00000372470	NM_005373.2	226	tCc/tTc	4/12	1	2	FACETS	0.697	0.639	0.757	0.697	0.639	0.757	SUBCLONAL	1	TRUE	1	0.624455907646663	2		749	708	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798295	45798295	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	200	754	0	ENST00000450313.1:c.641G>C	p.Gly214Ala	p.G214A	ENST00000450313	NM_012222.2	214	gGc/gCc	8/16	1	2	FACETS	0.93	0.865	0.996	0.93	0.865	0.996	CLONAL	1	TRUE	1	0.624455907646663	2		754	689	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546387	46546387	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	96	474	0	ENST00000262741.5:c.142G>A	p.Ala48Thr	p.A48T	ENST00000262741	NM_003629.3	48	Gca/Aca	2/10	1	2	FACETS	0.587	0.524	0.653	0.587	0.524	0.653	SUBCLONAL	1	TRUE	1	0.624455907646663	2		474	524	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332758	65332758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	124	492	0	ENST00000342505.4:c.781G>A	p.Val261Met	p.V261M	ENST00000342505	NM_002227.2	261	Gtg/Atg	7/25	1	2	FACETS	0.858	0.781	0.937	0.858	0.781	0.937	CLONAL	1	TRUE	1	0.624455907646663	2		492	463	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736465	85736465	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	126	463	0	ENST00000370580.1:c.182G>T	p.Ser61Ile	p.S61I	ENST00000370580	NM_003921.4	61	aGt/aTt	2/3	1	2	FACETS	0.807	0.735	0.882	0.807	0.735	0.882	CLONAL	1	TRUE	1	0.624455907646663	2		463	500	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273206	115273206	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	149	538	0	ENST00000438362.2:c.1252A>G	p.Met418Val	p.M418V	ENST00000438362	NM_001242891.1	418	Atg/Gtg	11/20	1	2	FACETS	0.986	0.908	1	0.986	0.908	1	CLONAL	1	TRUE	1	0.624455907646663	2		538	484	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695773	117695773	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs768183667	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	163	509	0	ENST00000369458.3:c.664A>G	p.Thr222Ala	p.T222A	ENST00000369458	NM_024626.3	222	Aca/Gca	4/6	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.624455907646663	2		509	520	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838329	156838329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1228967598	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	291	1058	0	ENST00000524377.1:c.607G>A	p.Ala203Thr	p.A203T	ENST00000524377	NM_002529.3	203	Gcc/Acc	6/17	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.624455907646663	2		1058	912	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849143	156849143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775191394	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	203	941	1	ENST00000524377.1:c.2035G>A	p.Asp679Asn	p.D679N	ENST00000524377	NM_002529.3	679	Gac/Aac	15/17	1	2	FACETS	0.709	0.658	0.762	0.709	0.658	0.762	SUBCLONAL	1	TRUE	1	0.624455907646663	2		942	917	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724599	162724599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	28	538	0	ENST00000367921.3:c.371G>A	p.Arg124Gln	p.R124Q	ENST00000367921	NM_006182.2	124	cGg/cAg	5/18	1	2	FACETS	0.178	0.141	0.219	0.178	0.141	0.219	SUBCLONAL	1	TRUE	1	0.624455907646663	2		538	505	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163297304	163297304	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	154	614	0	ENST00000271452.3:c.150G>T	p.Met50Ile	p.M50I	ENST00000271452	NM_145697.2	50	atG/atT	3/14	1	2	FACETS	0.92	0.847	0.996	0.92	0.847	0.996	CLONAL	1	TRUE	1	0.624455907646663	2		614	536	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163307820	163307820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139996430	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	53	310	0	ENST00000271452.3:c.446C>T	p.Ala149Val	p.A149V	ENST00000271452	NM_145697.2	149	gCg/gTg	7/14	1	2	FACETS	0.633	0.545	0.729	0.633	0.545	0.729	SUBCLONAL	1	TRUE	1	0.624455907646663	2		310	268	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163313637	163313637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	29	155	0	ENST00000271452.3:c.784G>A	p.Val262Ile	p.V262I	ENST00000271452	NM_145697.2	262	Gtc/Atc	10/14	1	2	FACETS	0.693	0.565	0.834	0.693	0.565	0.834	SUBCLONAL	1	TRUE	1	0.624455907646663	2		155	134	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015444	176015444	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	39	412	0	ENST00000367669.3:c.1294G>T	p.Asp432Tyr	p.D432Y	ENST00000367669	NM_022457.5	432	Gat/Tat	12/20	1	2	FACETS	0.319	0.264	0.379	0.319	0.264	0.379	SUBCLONAL	1	TRUE	1	0.624455907646663	2		412	392	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570853	226570853	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	154	559	0	ENST00000366794.5:c.1043T>C	p.Leu348Ser	p.L348S	ENST00000366794	NM_001618.3	348	tTg/tCg	8/23	1	2	FACETS	0.83	0.763	0.9	0.83	0.763	0.9	CLONAL	1	TRUE	1	0.624455907646663	2		559	594	SUCCESS
FH	2271	MSKCC	GRCh37	1	241677006	241677006	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	98	401	0	ENST00000366560.3:c.275T>C	p.Val92Ala	p.V92A	ENST00000366560	NM_000143.3	92	gTt/gCt	3/10	1	2	FACETS	0.767	0.689	0.849	0.767	0.689	0.849	SUBCLONAL	1	TRUE	1	0.624455907646663	2		401	409	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243778453	243778453	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767433650	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	103	383	0	ENST00000263826.5:c.572C>T	p.Ala191Val	p.A191V	ENST00000263826	NM_005465.4	191	gCa/gTa	6/13	1	2	FACETS	0.861	0.777	0.949	0.861	0.777	0.949	CLONAL	1	TRUE	1	0.624455907646663	2		383	383	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100684	8100684	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	203	814	0	ENST00000346208.3:c.658A>G	p.Thr220Ala	p.T220A	ENST00000346208		220	Acc/Gcc	3/6	1	2	FACETS	0.941	0.876	1	0.941	0.876	1	CLONAL	1	TRUE	1	0.624455907646663	2		814	691	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106097	8106097	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	118	439	1	ENST00000346208.3:c.917G>T	p.Arg306Met	p.R306M	ENST00000346208		306	aGg/aTg	4/6	1	2	FACETS	0.714	0.647	0.785	0.714	0.647	0.785	SUBCLONAL	1	TRUE	1	0.624455907646663	2		440	529	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596006	43596006	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	243	816	0	ENST00000355710.3:c.173A>G	p.Asp58Gly	p.D58G	ENST00000355710	NM_020975.4	58	gAc/gGc	2/20	1	2	FACETS	0.943	0.884	1	0.943	0.884	1	CLONAL	1	TRUE	1	0.624455907646663	2		816	825	SUCCESS
RET	5979	MSKCC	GRCh37	10	43613826	43613826	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	174	849	0	ENST00000355710.3:c.2290G>C	p.Ala764Pro	p.A764P	ENST00000355710	NM_020975.4	764	Gcc/Ccc	13/20	1	2	FACETS	0.665	0.613	0.719	0.665	0.613	0.719	SUBCLONAL	1	TRUE	1	0.624455907646663	2		849	838	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405030	70405030	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1480841047	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	137	613	0	ENST00000373644.4:c.2544T>G	p.Ser848Arg	p.S848R	ENST00000373644	NM_030625.2	848	agT/agG	4/12	1	2	FACETS	0.879	0.805	0.956	0.879	0.805	0.956	CLONAL	1	TRUE	1	0.624455907646663	2		613	499	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710631	114710631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	99	412	0	ENST00000543371.1:c.116G>T	p.Arg39Met	p.R39M	ENST00000543371	NM_001198531.1	39	aGg/aTg	1/14	1	2	FACETS	0.759	0.682	0.839	0.759	0.682	0.839	SUBCLONAL	1	TRUE	1	0.624455907646663	2		412	418	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258056	123258056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	58	681	0	ENST00000358487.5:c.1625G>A	p.Gly542Glu	p.G542E	ENST00000358487	NM_000141.4	542	gGg/gAg	12/18	1	2	FACETS	0.295	0.253	0.341	0.295	0.253	0.341	SUBCLONAL	1	TRUE	1	0.624455907646663	2		681	629	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123260408	123260408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	239	641	2	ENST00000358487.5:c.1493C>T	p.Ala498Val	p.A498V	ENST00000358487	NM_000141.4	498	gCg/gTg	11/18	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.624455907646663	2		643	731	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741372	17741372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	326	1023	2	ENST00000250003.3:c.43G>A	p.Ala15Thr	p.A15T	ENST00000250003	NM_002478.4	15	Gcc/Acc	1/3	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.624455907646663	2		1025	1044	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741756	17741756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	196	762	2	ENST00000250003.3:c.427C>T	p.Arg143Trp	p.R143W	ENST00000250003	NM_002478.4	143	Cgg/Tgg	1/3	1	2	FACETS	0.765	0.709	0.822	0.765	0.709	0.822	SUBCLONAL	1	TRUE	1	0.624455907646663	2		764	821	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741786	17741786	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	235	643	1	ENST00000250003.3:c.457G>A	p.Ala153Thr	p.A153T	ENST00000250003	NM_002478.4	153	Gcc/Acc	1/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.624455907646663	2		644	705	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741871	17741871	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	65	239	0	ENST00000250003.3:c.542C>A	p.Pro181Gln	p.P181Q	ENST00000250003	NM_002478.4	181	cCg/cAg	1/3	1	2	FACETS	0.934	0.821	1	0.934	0.821	1	CLONAL	1	TRUE	1	0.624455907646663	2		239	223	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414215	32414215	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	128	434	0	ENST00000332351.3:c.1336A>G	p.Thr446Ala	p.T446A	ENST00000332351	NM_024426.4	446	Aca/Gca	8/10	1	2	FACETS	0.818	0.746	0.894	0.818	0.746	0.894	CLONAL	1	TRUE	1	0.624455907646663	2		434	501	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571865	64571865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	355	1171	0	ENST00000312049.6:c.1774G>A	p.Val592Met	p.V592M	ENST00000312049	NM_130799.2	592	Gtg/Atg	10/10	1	2	FACETS	0.924	0.875	0.973	0.924	0.875	0.973	CLONAL	1	TRUE	1	0.624455907646663	2		1171	1231	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198851	67198851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373631670	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	37	420	1	ENST00000312629.5:c.322C>T	p.Arg108Cys	p.R108C	ENST00000312629	NM_003952.2	108	Cgc/Tgc	5/15	0.624455907646663	2	FACETS	0.236	0.194	0.283	0.118	0.097	0.142	SUBCLONAL	1	TRUE	0	0.624455907646663	2		421	503	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200498	67200498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	254	762	2	ENST00000312629.5:c.692G>A	p.Gly231Asp	p.G231D	ENST00000312629	NM_003952.2	231	gGc/gAc	8/15	0.624455907646663	2	FACETS	1	0.982	1	0.555	0.522	0.589	CLONAL	1	TRUE	0	0.624455907646663	2		764	733	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202536	67202536	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	221	918	0	ENST00000312629.5:c.1345C>A	p.Pro449Thr	p.P449T	ENST00000312629	NM_003952.2	449	Cca/Aca	15/15	0.624455907646663	2	FACETS	0.833	0.776	0.891	0.416	0.388	0.446	CLONAL	1	TRUE	0	0.624455907646663	2		918	850	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941889	71941889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	187	799	1	ENST00000298229.2:c.1247C>T	p.Ser416Phe	p.S416F	ENST00000298229	NM_001567.3	416	tCc/tTc	11/28	0.624455907646663	2	FACETS	0.754	0.698	0.813	0.377	0.349	0.407	SUBCLONAL	1	TRUE	0	0.624455907646663	2		800	794	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942214	71942214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253875635	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	174	680	0	ENST00000298229.2:c.1478C>T	p.Thr493Met	p.T493M	ENST00000298229	NM_001567.3	493	aCg/aTg	12/28	0.624455907646663	2	FACETS	0.945	0.874	1	0.472	0.437	0.509	CLONAL	1	TRUE	0	0.624455907646663	2		680	590	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94170382	94170382	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	129	410	0	ENST00000323929.3:c.1887G>T	p.Gln629His	p.Q629H	ENST00000323929	NM_005591.3	629	caG/caT	17/20	0.624455907646663	2	FACETS	1	0.924	1	0.505	0.462	0.55	CLONAL	1	TRUE	0	0.624455907646663	2		410	409	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94906459	94906459	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	311	546	0	ENST00000536441.1:c.1439T>G	p.Leu480Arg	p.L480R	ENST00000536441	NM_144665.3	480	cTt/cGt	10/10	0.624455907646663	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.624455907646663	2		546	479	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102094365	102094365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770645607	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	131	432	0	ENST00000282441.5:c.1045C>T	p.Arg349Cys	p.R349C	ENST00000282441	NM_001130145.2	349	Cgt/Tgt	7/9	0.624455907646663	2	FACETS	0.992	0.908	1	0.496	0.454	0.539	CLONAL	1	TRUE	0	0.624455907646663	2		432	423	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124585	108124585	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs141175037	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	108	410	0	ENST00000278616.4:c.1943T>C	p.Val648Ala	p.V648A	ENST00000278616	NM_000051.3	648	gTa/gCa	13/63	0.624455907646663	2	FACETS	1	0.964	1	0.56	0.509	0.612	CLONAL	1	TRUE	0	0.624455907646663	2		410	309	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139169	108139169	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	179	746	0	ENST00000278616.4:c.2671T>C	p.Ser891Pro	p.S891P	ENST00000278616	NM_000051.3	891	Tca/Cca	18/63	0.624455907646663	2	FACETS	0.941	0.872	1	0.471	0.436	0.506	CLONAL	1	TRUE	0	0.624455907646663	2		746	609	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360889	118360889	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	206	486	0	ENST00000534358.1:c.4621C>A	p.Pro1541Thr	p.P1541T	ENST00000534358	NM_005933.3	1541	Cca/Aca	13/36	0.624455907646663	2	FACETS	1	0.974	1	0.543	0.507	0.581	CLONAL	1	TRUE	0	0.624455907646663	2		486	607	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374070	118374070	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	142	446	0	ENST00000534358.1:c.7463A>G	p.Asp2488Gly	p.D2488G	ENST00000534358	NM_005933.3	2488	gAt/gGt	27/36	0.624455907646663	2	FACETS	1	0.943	1	0.516	0.474	0.559	CLONAL	1	TRUE	0	0.624455907646663	2		446	441	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380686	118380686	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	104	308	1	ENST00000534358.1:c.10924G>A	p.Glu3642Lys	p.E3642K	ENST00000534358	NM_005933.3	3642	Gaa/Aaa	30/36	0.624455907646663	2	FACETS	0.98	0.887	1	0.49	0.443	0.538	CLONAL	1	TRUE	0	0.624455907646663	2		309	340	SUCCESS
CBL	867	MSKCC	GRCh37	11	119167708	119167708	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	226	611	0	ENST00000264033.4:c.2117G>T	p.Arg706Met	p.R706M	ENST00000264033	NM_005188.3	706	aGg/aTg	13/16	0.624455907646663	2	FACETS	1	0.964	1	0.522	0.489	0.557	CLONAL	1	TRUE	0	0.624455907646663	2		611	693	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125496671	125496671	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	117	355	0	ENST00000428830.2:c.8T>C	p.Val3Ala	p.V3A	ENST00000428830	NM_001114121.2	3	gTg/gCg	2/14	0.624455907646663	2	FACETS	0.886	0.805	0.97	0.443	0.402	0.485	CLONAL	1	TRUE	0	0.624455907646663	2		355	423	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125499319	125499319	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	139	580	0	ENST00000428830.2:c.388G>T	p.Asp130Tyr	p.D130Y	ENST00000428830	NM_001114121.2	130	Gat/Tat	5/14	0.624455907646663	2	FACETS	0.918	0.841	0.997	0.459	0.42	0.499	CLONAL	1	TRUE	0	0.624455907646663	2		580	485	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417057	417057	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	166	496	0	ENST00000399788.2:c.3493A>T	p.Ile1165Phe	p.I1165F	ENST00000399788	NM_001042603.1	1165	Att/Ttt	23/28	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.624455907646663	2		496	525	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420129	420129	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	209	530	1	ENST00000399788.2:c.3138G>T	p.Gln1046His	p.Q1046H	ENST00000399788	NM_001042603.1	1046	caG/caT	21/28	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.624455907646663	2		531	639	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426478	49426478	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	415	1183	0	ENST00000301067.7:c.12010A>C	p.Lys4004Gln	p.K4004Q	ENST00000301067	NM_003482.3	4004	Aag/Cag	39/54	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.624455907646663	2		1183	1270	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426871	49426871	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	175	574	0	ENST00000301067.7:c.11617C>A	p.Leu3873Met	p.L3873M	ENST00000301067	NM_003482.3	3873	Ctg/Atg	39/54	1	2	FACETS	0.956	0.886	1	0.956	0.886	1	CLONAL	1	TRUE	1	0.624455907646663	2		574	586	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427217	49427217	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	297	1051	0	ENST00000301067.7:c.11271G>T	p.Gln3757His	p.Q3757H	ENST00000301067	NM_003482.3	3757	caG/caT	39/54	1	2	FACETS	0.971	0.915	1	0.971	0.915	1	CLONAL	1	TRUE	1	0.624455907646663	2		1051	980	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432110	49432110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764280781	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	271	960	0	ENST00000301067.7:c.9029C>T	p.Ala3010Val	p.A3010V	ENST00000301067	NM_003482.3	3010	gCt/gTt	34/54	1	2	FACETS	0.949	0.892	1	0.949	0.892	1	CLONAL	1	TRUE	1	0.624455907646663	2		960	915	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490602	56490602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	157	514	0	ENST00000267101.3:c.2246G>A	p.Gly749Glu	p.G749E	ENST00000267101	NM_001982.3	749	gGa/gAa	19/28	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.624455907646663	2		514	499	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493738	56493738	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	136	510	0	ENST00000267101.3:c.3054G>T	p.Glu1018Asp	p.E1018D	ENST00000267101	NM_001982.3	1018	gaG/gaT	25/28	1	2	FACETS	0.947	0.868	1	0.947	0.868	1	CLONAL	1	TRUE	1	0.624455907646663	2		510	460	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856124	111856124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168055611	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	267	739	2	ENST00000341259.2:c.175C>T	p.Arg59Cys	p.R59C	ENST00000341259	NM_005475.2	59	Cgc/Tgc	2/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.624455907646663	2		741	833	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856554	111856554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs953545115	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	158	453	0	ENST00000341259.2:c.605G>A	p.Arg202His	p.R202H	ENST00000341259	NM_005475.2	202	cGc/cAc	2/8	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.624455907646663	2		453	488	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112022	115112022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773504740	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	268	919	1	ENST00000257566.3:c.1718C>T	p.Ala573Val	p.A573V	ENST00000257566	NM_016569.3	573	gCg/gTg	7/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.624455907646663	2		920	792	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112472	115112472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145432134	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	280	899	0	ENST00000257566.3:c.1268G>A	p.Arg423Gln	p.R423Q	ENST00000257566	NM_016569.3	423	cGg/cAg	7/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.624455907646663	2		899	867	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120535095	120535095	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	266	752	0	ENST00000229340.5:c.560T>C	p.Val187Ala	p.V187A	ENST00000229340	NM_006861.6	187	gTg/gCg	6/6	1	2	FACETS	0.974	0.915	1	0.974	0.915	1	CLONAL	1	TRUE	1	0.624455907646663	2		752	875	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536617	120536617	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	157	750	0	ENST00000229340.5:c.475G>T	p.Glu159Ter	p.E159*	ENST00000229340	NM_006861.6	159	Gag/Tag	5/6	1	2	FACETS	0.662	0.607	0.719	0.662	0.607	0.719	SUBCLONAL	1	TRUE	1	0.624455907646663	2		750	760	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434086	121434086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369764257	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	213	594	2	ENST00000257555.6:c.977C>T	p.Ala326Val	p.A326V	ENST00000257555		326	gCg/gTg	5/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.624455907646663	2		596	652	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123892066	123892066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	130	417	0	ENST00000330479.4:c.875G>A	p.Arg292His	p.R292H	ENST00000330479	NM_020382.3	292	cGc/cAc	8/9	1	2	FACETS	0.982	0.898	1	0.982	0.898	1	CLONAL	1	TRUE	1	0.624455907646663	2		417	424	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214670	133214670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138231414	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	213	602	1	ENST00000320574.5:c.5608C>T	p.Arg1870Cys	p.R1870C	ENST00000320574	NM_006231.2	1870	Cgc/Tgc	41/49	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.624455907646663	2		603	645	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252020	133252020	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs761203384	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	265	842	1	ENST00000320574.5:c.1190A>G	p.Tyr397Cys	p.Y397C	ENST00000320574	NM_006231.2	397	tAc/tGc	12/49	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.624455907646663	2		843	809	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619889	21619889	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	165	572	0	ENST00000382592.4:c.277A>G	p.Thr93Ala	p.T93A	ENST00000382592	NM_014572.2	93	Acc/Gcc	2/8	1	2	FACETS	0.929	0.858	1	0.929	0.858	1	CLONAL	1	TRUE	1	0.624455907646663	2		572	569	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597571	28597571	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	242	748	0	ENST00000241453.7:c.2334G>T	p.Glu778Asp	p.E778D	ENST00000241453	NM_004119.2	778	gaG/gaT	19/24	1	2	FACETS	0.892	0.835	0.95	0.892	0.835	0.95	CLONAL	1	TRUE	1	0.624455907646663	2		748	869	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602352	28602352	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	204	600	0	ENST00000241453.7:c.2016G>T	p.Glu672Asp	p.E672D	ENST00000241453	NM_004119.2	672	gaG/gaT	16/24	1	2	FACETS	0.909	0.846	0.973	0.909	0.846	0.973	CLONAL	1	TRUE	1	0.624455907646663	2		600	719	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877404	28877404	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	203	482	0	ENST00000282397.4:c.3917G>T	p.Arg1306Met	p.R1306M	ENST00000282397	NM_002019.4	1306	aGg/aTg	30/30	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.624455907646663	2		482	638	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28903839	28903839	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	149	695	0	ENST00000282397.4:c.2620G>T	p.Ala874Ser	p.A874S	ENST00000282397	NM_002019.4	874	Gct/Tct	19/30	1	2	FACETS	0.667	0.611	0.726	0.667	0.611	0.726	SUBCLONAL	1	TRUE	1	0.624455907646663	2		695	715	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912163	32912163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	206	818	5	ENST00000380152.3:c.3671G>A	p.Gly1224Asp	p.G1224D	ENST00000380152		1224	gGc/gAc	11/27	1	2	FACETS	0.944	0.879	1	0.944	0.879	1	CLONAL	1	TRUE	1	0.624455907646663	2		823	699	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913269	32913269	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	149	518	2	ENST00000380152.3:c.4777G>T	p.Glu1593Ter	p.E1593*	ENST00000380152		1593	Gaa/Taa	11/27	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.624455907646663	2		520	461	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514009	103514009	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	89	447	0	ENST00000355739.4:c.825G>T	p.Glu275Asp	p.E275D	ENST00000355739	NM_000123.3	275	gaG/gaT	7/15	1	2	FACETS	0.841	0.752	0.933	0.841	0.752	0.933	CLONAL	1	TRUE	1	0.624455907646663	2		447	339	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514877	103514877	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	91	306	0	ENST00000355739.4:c.1378A>C	p.Ser460Arg	p.S460R	ENST00000355739	NM_000123.3	460	Agc/Cgc	8/15	1	2	FACETS	0.962	0.864	1	0.962	0.864	1	CLONAL	1	TRUE	1	0.624455907646663	2		306	303	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435294	110435294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	171	448	0	ENST00000375856.3:c.3107C>T	p.Pro1036Leu	p.P1036L	ENST00000375856	NM_003749.2	1036	cCg/cTg	1/2	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.624455907646663	2		448	472	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560445	95560445	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	117	557	0	ENST00000393063.1:c.5144T>C	p.Leu1715Pro	p.L1715P	ENST00000393063	NM_030621.3	1715	cTc/cCc	25/28	1	2	FACETS	0.666	0.602	0.732	0.666	0.602	0.732	SUBCLONAL	1	TRUE	1	0.624455907646663	2		557	563	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95563031	95563031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776416084	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	45	333	0	ENST00000393063.1:c.4226C>T	p.Ala1409Val	p.A1409V	ENST00000393063	NM_030621.3	1409	gCg/gTg	24/28	1	2	FACETS	0.459	0.387	0.537	0.459	0.387	0.537	SUBCLONAL	1	TRUE	1	0.624455907646663	2		333	314	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95593084	95593084	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	133	412	0	ENST00000393063.1:c.736T>C	p.Tyr246His	p.Y246H	ENST00000393063	NM_030621.3	246	Tat/Cat	8/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.624455907646663	2		412	362	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028624	42028624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1274154364	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	207	709	1	ENST00000219905.7:c.4162C>T	p.Pro1388Ser	p.P1388S	ENST00000219905	NM_001164273.1	1388	Cct/Tct	13/24	1	2	FACETS	0.907	0.845	0.971	0.907	0.845	0.971	CLONAL	1	TRUE	1	0.624455907646663	2		710	731	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028686	42028686	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	164	677	0	ENST00000219905.7:c.4224G>C	p.Met1408Ile	p.M1408I	ENST00000219905	NM_001164273.1	1408	atG/atC	13/24	1	2	FACETS	0.962	0.889	1	0.962	0.889	1	CLONAL	1	TRUE	1	0.624455907646663	2		677	546	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041065	42041065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1202147554	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	261	794	0	ENST00000219905.7:c.5443C>T	p.His1815Tyr	p.H1815Y	ENST00000219905	NM_001164273.1	1815	Cat/Tat	16/24	1	2	FACETS	0.999	0.939	1	0.999	0.939	1	CLONAL	1	TRUE	1	0.624455907646663	2		794	837	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054471	42054471	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769432234	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	104	436	0	ENST00000219905.7:c.7655C>A	p.Ser2552Tyr	p.S2552Y	ENST00000219905	NM_001164273.1	2552	tCt/tAt	22/24	1	2	FACETS	0.879	0.794	0.967	0.879	0.794	0.967	CLONAL	1	TRUE	1	0.624455907646663	2		436	379	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701285	43701285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	47	444	0	ENST00000382044.4:c.5410G>A	p.Ala1804Thr	p.A1804T	ENST00000382044	NM_001141980.1	1804	Gct/Act	26/28	1	2	FACETS	0.319	0.269	0.374	0.319	0.269	0.374	SUBCLONAL	1	TRUE	1	0.624455907646663	2		444	472	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714135	43714135	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200761797	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	319	974	1	ENST00000382044.4:c.4018G>A	p.Gly1340Arg	p.G1340R	ENST00000382044	NM_001141980.1	1340	Gga/Aga	19/28	1	2	FACETS	0.977	0.923	1	0.977	0.923	1	CLONAL	1	TRUE	1	0.624455907646663	2		975	1046	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43772162	43772162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	259	814	0	ENST00000382044.4:c.553G>A	p.Asp185Asn	p.D185N	ENST00000382044	NM_001141980.1	185	Gat/Aat	6/28	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.624455907646663	2		814	829	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007735	45007735	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	131	465	0	ENST00000558401.1:c.182A>C	p.Lys61Thr	p.K61T	ENST00000558401	NM_004048.2	61	aAg/aCg	2/4	1	2	FACETS	0.992	0.908	1	0.992	0.908	1	CLONAL	1	TRUE	1	0.624455907646663	2		465	423	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477127	67477127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750756638	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	253	722	0	ENST00000327367.4:c.934G>A	p.Ala312Thr	p.A312T	ENST00000327367	NM_005902.3	312	Gct/Act	7/9	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.624455907646663	2		722	770	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996221	73996221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	166	533	1	ENST00000318443.5:c.955G>A	p.Ala319Thr	p.A319T	ENST00000318443	NM_001024736.1	319	Gca/Aca	5/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.624455907646663	2		534	498	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456466	99456466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764375938	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	57	450	1	ENST00000268035.6:c.1783C>T	p.Arg595Cys	p.R595C	ENST00000268035	NM_000875.3	595	Cgt/Tgt	8/21	1	2	FACETS	0.368	0.316	0.425	0.368	0.316	0.425	SUBCLONAL	1	TRUE	1	0.624455907646663	2		451	496	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467887	99467887	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	122	343	0	ENST00000268035.6:c.2756C>A	p.Pro919His	p.P919H	ENST00000268035	NM_000875.3	919	cCt/cAt	13/21	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.624455907646663	2		343	381	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478122	99478122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1470161328	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	185	509	1	ENST00000268035.6:c.3026C>T	p.Ser1009Leu	p.S1009L	ENST00000268035	NM_000875.3	1009	tCg/tTg	16/21	1	2	FACETS	0.948	0.88	1	0.948	0.88	1	CLONAL	1	TRUE	1	0.624455907646663	2		510	625	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094737	2094737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750992242	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	272	1040	1	ENST00000219066.1:c.443C>T	p.Ala148Val	p.A148V	ENST00000219066	NM_002528.5	148	gCg/gTg	3/6	1	2	FACETS	0.837	0.786	0.889	0.837	0.786	0.889	CLONAL	1	TRUE	1	0.624455907646663	2		1041	1041	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104399	2104399	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	291	839	0	ENST00000219476.3:c.439A>G	p.Thr147Ala	p.T147A	ENST00000219476	NM_000548.3	147	Aca/Gca	5/42	1	2	FACETS	0.989	0.933	1	0.989	0.933	1	CLONAL	1	TRUE	1	0.624455907646663	2		839	942	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2105422	2105422	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	253	753	0	ENST00000219476.3:c.501G>A	p.Trp167Ter	p.W167*	ENST00000219476	NM_000548.3	167	tgG/tgA	6/42	1	2	FACETS	0.993	0.932	1	0.993	0.932	1	CLONAL	1	TRUE	1	0.624455907646663	2		753	816	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136747	2136747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769913589	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	281	878	0	ENST00000219476.3:c.4864G>A	p.Ala1622Thr	p.A1622T	ENST00000219476	NM_000548.3	1622	Gcc/Acc	38/42	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.624455907646663	2		878	860	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779671	3779671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	147	913	1	ENST00000262367.5:c.5377C>T	p.Pro1793Ser	p.P1793S	ENST00000262367	NM_004380.2	1793	Cca/Tca	31/31	1	2	FACETS	0.597	0.545	0.651	0.597	0.545	0.651	SUBCLONAL	1	TRUE	1	0.624455907646663	2		914	789	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781324	3781324	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	308	1047	0	ENST00000262367.5:c.5041T>G	p.Leu1681Val	p.L1681V	ENST00000262367	NM_004380.2	1681	Ttg/Gtg	30/31	1	2	FACETS	0.938	0.885	0.992	0.938	0.885	0.992	CLONAL	1	TRUE	1	0.624455907646663	2		1047	1052	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789672	3789672	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	135	502	0	ENST00000262367.5:c.4187T>G	p.Leu1396Arg	p.L1396R	ENST00000262367	NM_004380.2	1396	cTg/cGg	25/31	1	2	FACETS	0.899	0.823	0.978	0.899	0.823	0.978	CLONAL	1	TRUE	1	0.624455907646663	2		502	481	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807853	3807853	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	115	505	0	ENST00000262367.5:c.3566T>A	p.Ile1189Asn	p.I1189N	ENST00000262367	NM_004380.2	1189	aTt/aAt	18/31	1	2	FACETS	0.782	0.709	0.859	0.782	0.709	0.859	SUBCLONAL	1	TRUE	1	0.624455907646663	2		505	471	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843396	3843396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	140	425	0	ENST00000262367.5:c.1207G>A	p.Ala403Thr	p.A403T	ENST00000262367	NM_004380.2	403	Gcc/Acc	4/31	1	2	FACETS	0.936	0.859	1	0.936	0.859	1	CLONAL	1	TRUE	1	0.624455907646663	2		425	479	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041900	14041900	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	23	404	0	ENST00000311895.7:c.2447T>C	p.Leu816Pro	p.L816P	ENST00000311895	NM_005236.2	816	cTg/cCg	11/11	1	2	FACETS	0.186	0.144	0.234	0.186	0.144	0.234	SUBCLONAL	1	TRUE	1	0.624455907646663	2		404	397	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641347	23641347	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730881887	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	221	878	0	ENST00000261584.4:c.2128A>G	p.Thr710Ala	p.T710A	ENST00000261584	NM_024675.3	710	Acg/Gcg	5/13	1	2	FACETS	0.957	0.893	1	0.957	0.893	1	CLONAL	1	TRUE	1	0.624455907646663	2		878	740	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646401	23646401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	246	729	0	ENST00000261584.4:c.1466C>T	p.Ser489Phe	p.S489F	ENST00000261584	NM_024675.3	489	tCt/tTt	4/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.624455907646663	2		729	754	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50810134	50810134	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	143	489	0	ENST00000398568.2:c.958T>C	p.Ser320Pro	p.S320P	ENST00000398568	NM_001042412.1	320	Tca/Cca	6/18	1	2	FACETS	0.968	0.889	1	0.968	0.889	1	CLONAL	1	TRUE	1	0.624455907646663	2		489	473	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50811834	50811834	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	135	473	0	ENST00000398568.2:c.1111A>G	p.Thr371Ala	p.T371A	ENST00000398568	NM_001042412.1	371	Aca/Gca	7/18	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.624455907646663	2		473	425	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56792506	56792506	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	201	568	0	ENST00000308159.5:c.236A>G	p.Glu79Gly	p.E79G	ENST00000308159	NM_014669.4	79	gAg/gGg	3/22	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.624455907646663	2		568	630	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645132	67645132	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	214	658	1	ENST00000264010.4:c.397G>T	p.Glu133Ter	p.E133*	ENST00000264010	NM_006565.3	133	Gaa/Taa	3/12	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.624455907646663	2		659	680	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670686	67670686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	148	549	1	ENST00000264010.4:c.1931C>T	p.Ala644Val	p.A644V	ENST00000264010	NM_006565.3	644	gCc/gTc	11/12	1	2	FACETS	0.893	0.82	0.968	0.893	0.82	0.968	CLONAL	1	TRUE	1	0.624455907646663	2		550	531	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835755	68835755	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	39	634	0	ENST00000261769.5:c.346C>A	p.Leu116Met	p.L116M	ENST00000261769	NM_004360.3	116	Ctg/Atg	3/16	1	2	FACETS	0.174	0.144	0.209	0.174	0.144	0.209	SUBCLONAL	1	TRUE	1	0.624455907646663	2		634	716	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821590	72821590	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	48	195	0	ENST00000268489.5:c.10585T>C	p.Tyr3529His	p.Y3529H	ENST00000268489	NM_006885.3	3529	Tac/Cac	10/10	1	2	FACETS	0.943	0.812	1	0.943	0.812	1	CLONAL	1	TRUE	1	0.624455907646663	2		195	163	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830568	72830568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368676441	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	105	757	1	ENST00000268489.5:c.6013G>A	p.Val2005Ile	p.V2005I	ENST00000268489	NM_006885.3	2005	Gtt/Att	9/10	1	2	FACETS	0.419	0.375	0.466	0.419	0.375	0.466	SUBCLONAL	1	TRUE	1	0.624455907646663	2		758	802	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830682	72830682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	209	762	0	ENST00000268489.5:c.5899G>A	p.Val1967Met	p.V1967M	ENST00000268489	NM_006885.3	1967	Gtg/Atg	9/10	1	2	FACETS	0.827	0.77	0.887	0.827	0.77	0.887	CLONAL	1	TRUE	1	0.624455907646663	2		762	809	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830919	72830919	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	193	582	1	ENST00000268489.5:c.5662G>T	p.Glu1888Ter	p.E1888*	ENST00000268489	NM_006885.3	1888	Gaa/Taa	9/10	1	2	FACETS	0.95	0.882	1	0.95	0.882	1	CLONAL	1	TRUE	1	0.624455907646663	2		583	651	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993974	72993974	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	254	894	1	ENST00000268489.5:c.71G>A	p.Trp24Ter	p.W24*	ENST00000268489	NM_006885.3	24	tGg/tAg	2/10	1	2	FACETS	0.931	0.873	0.99	0.931	0.873	0.99	CLONAL	1	TRUE	1	0.624455907646663	2		895	874	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965233	81965233	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	183	585	0	ENST00000359376.3:c.2713G>A	p.Glu905Lys	p.E905K	ENST00000359376	NM_002661.3	905	Gag/Aag	25/33	1	2	FACETS	0.967	0.897	1	0.967	0.897	1	CLONAL	1	TRUE	1	0.624455907646663	2		585	606	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341577	89341577	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1052222126	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	119	524	0	ENST00000301030.4:c.7493C>T	p.Ala2498Val	p.A2498V	ENST00000301030	NM_001256183.1	2498	gCg/gTg	10/13	1	2	FACETS	0.845	0.768	0.925	0.845	0.768	0.925	CLONAL	1	TRUE	1	0.624455907646663	2		524	451	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346973	89346973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773403872	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	87	386	0	ENST00000301030.4:c.5977C>T	p.Arg1993Cys	p.R1993C	ENST00000301030	NM_001256183.1	1993	Cgt/Tgt	9/13	1	2	FACETS	0.785	0.701	0.874	0.785	0.701	0.874	SUBCLONAL	1	TRUE	1	0.624455907646663	2		386	355	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347764	89347764	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1353936075	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	149	663	0	ENST00000301030.4:c.5186C>T	p.Ala1729Val	p.A1729V	ENST00000301030	NM_001256183.1	1729	gCc/gTc	9/13	1	2	FACETS	0.817	0.75	0.887	0.817	0.75	0.887	CLONAL	1	TRUE	1	0.624455907646663	2		663	584	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349681	89349681	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	81	1066	0	ENST00000301030.4:c.3269C>A	p.Ala1090Asp	p.A1090D	ENST00000301030	NM_001256183.1	1090	gCt/gAt	9/13	1	2	FACETS	0.257	0.226	0.291	0.257	0.226	0.291	SUBCLONAL	1	TRUE	1	0.624455907646663	2		1066	1008	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838214	89838214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	124	550	0	ENST00000389301.3:c.2023G>A	p.Ala675Thr	p.A675T	ENST00000389301	NM_000135.2	675	Gca/Aca	23/43	1	2	FACETS	0.714	0.649	0.783	0.714	0.649	0.783	SUBCLONAL	1	TRUE	1	0.624455907646663	2		550	556	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984220	7984220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	125	616	0	ENST00000319144.4:c.509G>A	p.Arg170His	p.R170H	ENST00000319144	NM_001139.2	170	cGc/cAc	4/15	1	2	FACETS	0.652	0.592	0.715	0.652	0.592	0.715	SUBCLONAL	1	TRUE	1	0.624455907646663	2		616	614	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044572	12044572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1177038824	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	149	563	0	ENST00000353533.5:c.1195G>A	p.Asp399Asn	p.D399N	ENST00000353533	NM_003010.3	399	Gat/Aat	11/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.624455907646663	2		563	450	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483145	29483145	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs886039548	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	119	433	1	ENST00000356175.3:c.204+1G>T		p.X68_splice	ENST00000356175	NM_000267.3	68			1	2	FACETS	0.914	0.832	0.999	0.914	0.832	0.999	CLONAL	1	TRUE	1	0.624455907646663	2		434	417	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528504	29528504	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs267606603	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	93	508	0	ENST00000356175.3:c.1260+1G>A		p.X420_splice	ENST00000356175	NM_000267.3	420			1	2	FACETS	0.686	0.614	0.763	0.686	0.614	0.763	SUBCLONAL	1	TRUE	1	0.624455907646663	2		508	434	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562776	29562776	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	138	529	0	ENST00000356175.3:c.3856A>C	p.Thr1286Pro	p.T1286P	ENST00000356175	NM_000267.3	1286	Aca/Cca	28/57	1	2	FACETS	0.872	0.798	0.948	0.872	0.798	0.948	CLONAL	1	TRUE	1	0.624455907646663	2		529	507	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664840	29664840	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs757736155	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	23	442	0	ENST00000356175.3:c.6583T>C	p.Cys2195Arg	p.C2195R	ENST00000356175	NM_000267.3	2195	Tgc/Cgc	43/57	1	2	FACETS	0.21	0.164	0.265	0.21	0.164	0.265	SUBCLONAL	1	TRUE	1	0.624455907646663	2		442	350	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325796	30325796	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	81	328	0	ENST00000322652.5:c.1994A>T	p.Asp665Val	p.D665V	ENST00000322652	NM_015355.2	665	gAc/gTc	16/16	1	2	FACETS	0.901	0.803	1	0.901	0.803	1	CLONAL	1	TRUE	1	0.624455907646663	2		328	288	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428041	33428041	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555566990	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	32	624	0	ENST00000345365.6:c.918G>T	p.Gln306His	p.Q306H	ENST00000345365	NM_002878.3	306	caG/caT	10/10	1	2	FACETS	0.17	0.137	0.207	0.17	0.137	0.207	SUBCLONAL	1	TRUE	1	0.624455907646663	2		624	604	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627771	37627771	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	285	733	0	ENST00000447079.4:c.1686G>T	p.Gln562His	p.Q562H	ENST00000447079	NM_015083.1	562	caG/caT	2/14	1	2	FACETS	0.966	0.91	1	0.966	0.91	1	CLONAL	1	TRUE	1	0.624455907646663	2		733	945	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37865670	37865670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	76	616	0	ENST00000269571.5:c.539C>T	p.Ala180Val	p.A180V	ENST00000269571		180	gCt/gTt	4/27	1	2	FACETS	0.371	0.325	0.42	0.371	0.325	0.42	SUBCLONAL	1	TRUE	1	0.624455907646663	2		616	656	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881124	37881124	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	235	857	1	ENST00000269571.5:c.2453G>A	p.Gly818Asp	p.G818D	ENST00000269571		818	gGc/gAc	20/27	1	2	FACETS	0.955	0.894	1	0.955	0.894	1	CLONAL	1	TRUE	1	0.624455907646663	2		858	788	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508695	38508695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200827868	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	145	803	0	ENST00000254066.5:c.743G>A	p.Gly248Asp	p.G248D	ENST00000254066	NM_000964.3	248	gGc/gAc	6/9	1	2	FACETS	0.597	0.545	0.651	0.597	0.545	0.651	SUBCLONAL	1	TRUE	1	0.624455907646663	2		803	778	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508713	38508713	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	225	723	0	ENST00000254066.5:c.761T>C	p.Ile254Thr	p.I254T	ENST00000254066	NM_000964.3	254	aTc/aCc	6/9	1	2	FACETS	0.982	0.918	1	0.982	0.918	1	CLONAL	1	TRUE	1	0.624455907646663	2		723	734	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865388	40865388	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	215	856	0	ENST00000428826.2:c.1043C>G	p.Ala348Gly	p.A348G	ENST00000428826		348	gCc/gGc	11/21	1	2	FACETS	0.841	0.783	0.9	0.841	0.783	0.9	CLONAL	1	TRUE	1	0.624455907646663	2		856	819	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805827	46805827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	152	586	1	ENST00000290295.7:c.129G>A	p.Met43Ile	p.M43I	ENST00000290295	NM_006361.5	43	atG/atA	1/2	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.624455907646663	2		587	485	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696719	47696719	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	139	492	1	ENST00000347630.2:c.229G>T	p.Asp77Tyr	p.D77Y	ENST00000347630	NM_001007230.1	77	Gat/Tat	5/11	1	2	FACETS	0.945	0.867	1	0.945	0.867	1	CLONAL	1	TRUE	1	0.624455907646663	2		493	471	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696725	47696725	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	82	458	0	ENST00000347630.2:c.223G>T	p.Gly75Trp	p.G75W	ENST00000347630	NM_001007230.1	75	Ggg/Tgg	5/11	1	2	FACETS	0.616	0.546	0.691	0.616	0.546	0.691	SUBCLONAL	1	TRUE	1	0.624455907646663	2		458	426	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752363	55752363	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745388891	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	58	970	2	ENST00000284073.2:c.821C>T	p.Pro274Leu	p.P274L	ENST00000284073	NM_138962.2	274	cCg/cTg	12/14	1	2	FACETS	0.197	0.168	0.228	0.197	0.168	0.228	SUBCLONAL	1	TRUE	1	0.624455907646663	2		972	943	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763214	59763214	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	196	671	0	ENST00000259008.2:c.2888T>C	p.Ile963Thr	p.I963T	ENST00000259008	NM_032043.2	963	aTc/aCc	19/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.624455907646663	2		671	579	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59924575	59924575	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	109	359	0	ENST00000259008.2:c.514A>C	p.Lys172Gln	p.K172Q	ENST00000259008	NM_032043.2	172	Aaa/Caa	6/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.624455907646663	2		359	322	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554433	63554433	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	207	683	0	ENST00000307078.5:c.306G>T	p.Glu102Asp	p.E102D	ENST00000307078	NM_004655.3	102	gaG/gaT	2/11	1	2	FACETS	0.957	0.892	1	0.957	0.892	1	CLONAL	1	TRUE	1	0.624455907646663	2		683	693	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66525064	66525064	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	132	459	0	ENST00000358598.2:c.823C>T	p.Gln275Ter	p.Q275*	ENST00000358598	NM_212471.2	275	Cag/Tag	9/11	1	2	FACETS	0.935	0.856	1	0.935	0.856	1	CLONAL	1	TRUE	1	0.624455907646663	2		459	452	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39595526	39595526	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	59	243	0	ENST00000262039.4:c.1412T>C	p.Leu471Pro	p.L471P	ENST00000262039	NM_002647.2	471	cTg/cCg	12/25	1	2	FACETS	0.974	0.852	1	0.974	0.852	1	CLONAL	1	TRUE	1	0.624455907646663	2		243	194	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45377680	45377680	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	36	217	0	ENST00000262160.6:c.749C>A	p.Ser250Tyr	p.S250Y	ENST00000262160	NM_005901.5	250	tCt/tAt	7/11	1	2	FACETS	0.73	0.609	0.861	0.73	0.609	0.861	SUBCLONAL	1	TRUE	1	0.624455907646663	2		217	158	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45391492	45391492	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	78	378	0	ENST00000262160.6:c.668C>A	p.Pro223His	p.P223H	ENST00000262160	NM_005901.5	223	cCt/cAt	6/11	1	2	FACETS	0.704	0.623	0.789	0.704	0.623	0.789	SUBCLONAL	1	TRUE	1	0.624455907646663	2		378	355	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219336	1219336	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	48	895	0	ENST00000326873.7:c.388G>A	p.Glu130Lys	p.E130K	ENST00000326873	NM_000455.4	130	Gag/Aag	3/10	1	2	FACETS	0.174	0.146	0.204	0.174	0.146	0.204	SUBCLONAL	1	TRUE	1	0.624455907646663	2		895	885	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1650223	1650223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	274	904	0	ENST00000344749.5:c.25C>T	p.Pro9Ser	p.P9S	ENST00000344749	NM_001136139.2	9	Cct/Tct	2/19	1	2	FACETS	0.916	0.861	0.972	0.916	0.861	0.972	CLONAL	1	TRUE	1	0.624455907646663	2		904	958	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2221981	2221981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	76	749	0	ENST00000398665.3:c.2813C>T	p.Ser938Phe	p.S938F	ENST00000398665	NM_032482.2	938	tCc/tTc	24/28	1	2	FACETS	0.333	0.292	0.378	0.333	0.292	0.378	SUBCLONAL	1	TRUE	1	0.624455907646663	2		749	730	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3113446	3113446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1035292287	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	246	716	1	ENST00000078429.4:c.440G>A	p.Arg147His	p.R147H	ENST00000078429	NM_002067.2	147	cGc/cAc	3/7	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.624455907646663	2		717	750	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4090612	4090612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs117945277	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	209	676	1	ENST00000262948.5:c.1187C>T	p.Thr396Met	p.T396M	ENST00000262948	NM_030662.3	396	aCg/aTg	11/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.624455907646663	2		677	649	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214595	5214595	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	223	807	0	ENST00000357368.4:c.4471A>G	p.Thr1491Ala	p.T1491A	ENST00000357368	NM_002850.3	1491	Acg/Gcg	29/38	1	2	FACETS	0.988	0.923	1	0.988	0.923	1	CLONAL	1	TRUE	1	0.624455907646663	2		807	723	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122941	7122941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	290	973	1	ENST00000302850.5:c.3318G>A	p.Met1106Ile	p.M1106I	ENST00000302850	NM_000208.2	1106	atG/atA	18/22	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.624455907646663	2		974	863	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602296	10602296	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs934945819	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	252	920	2	ENST00000171111.5:c.1282G>A	p.Val428Ile	p.V428I	ENST00000171111	NM_203500.1	428	Gtc/Atc	3/6	1	2	FACETS	0.911	0.854	0.969	0.911	0.854	0.969	CLONAL	1	TRUE	1	0.624455907646663	2		922	886	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296128	15296128	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1481559244	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	303	991	0	ENST00000263388.2:c.2236G>A	p.Gly746Ser	p.G746S	ENST00000263388	NM_000435.2	746	Ggt/Agt	14/33	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.624455907646663	2		991	921	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302292	15302292	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs767905805	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	289	1000	0	ENST00000263388.2:c.979G>T	p.Ala327Ser	p.A327S	ENST00000263388	NM_000435.2	327	Gcc/Tcc	6/33	1	2	FACETS	0.961	0.906	1	0.961	0.906	1	CLONAL	1	TRUE	1	0.624455907646663	2		1000	963	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271331	18271331	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753702580	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	248	865	1	ENST00000222254.8:c.373C>T	p.Pro125Ser	p.P125S	ENST00000222254	NM_005027.3	125	Ccc/Tcc	3/16	1	2	FACETS	0.87	0.815	0.927	0.87	0.815	0.927	CLONAL	1	TRUE	1	0.624455907646663	2		866	913	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271740	18271740	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561325993	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	276	906	0	ENST00000222254.8:c.427G>A	p.Glu143Lys	p.E143K	ENST00000222254	NM_005027.3	143	Gaa/Aaa	4/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.624455907646663	2		906	857	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968220	18968220	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	224	776	0	ENST00000262803.5:c.2060G>A	p.Arg687His	p.R687H	ENST00000262803	NM_002911.3	687	cGc/cAc	15/24	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.624455907646663	2		776	709	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212451	36212451	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	175	920	1	ENST00000222270.7:c.2202G>T	p.Gln734His	p.Q734H	ENST00000222270	NM_014727.1	734	caG/caT	3/37	1	2	FACETS	0.63	0.581	0.682	0.63	0.581	0.682	SUBCLONAL	1	TRUE	1	0.624455907646663	2		921	889	SUCCESS
AXL	558	MSKCC	GRCh37	19	41759588	41759588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769826822	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	226	771	0	ENST00000301178.4:c.2011C>T	p.Arg671Trp	p.R671W	ENST00000301178	NM_021913.4	671	Cgg/Tgg	17/20	1	2	FACETS	0.934	0.873	0.997	0.934	0.873	0.997	CLONAL	1	TRUE	1	0.624455907646663	2		771	775	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753650	42753650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1053655	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	200	870	1	ENST00000222329.4:c.614G>A	p.Arg205His	p.R205H	ENST00000222329	NM_006494.2	205	cGc/cAc	4/4	1	2	FACETS	0.973	0.906	1	0.973	0.906	1	CLONAL	1	TRUE	1	0.624455907646663	2		871	658	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796472	42796472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367725186	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	271	1044	7	ENST00000575354.2:c.3029C>T	p.Ala1010Val	p.A1010V	ENST00000575354	NM_015125.3	1010	gCg/gTg	13/20	1	2	FACETS	0.956	0.899	1	0.956	0.899	1	CLONAL	1	TRUE	1	0.624455907646663	2		1051	908	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799213	42799213	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	193	786	0	ENST00000575354.2:c.4697C>A	p.Ser1566Tyr	p.S1566Y	ENST00000575354	NM_015125.3	1566	tCt/tAt	20/20	1	2	FACETS	0.93	0.864	0.997	0.93	0.864	0.997	CLONAL	1	TRUE	1	0.624455907646663	2		786	665	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855762	45855762	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	44	635	0	ENST00000391945.4:c.2046+2T>C		p.X682_splice	ENST00000391945	NM_000400.3	682			1	2	FACETS	0.278	0.233	0.328	0.278	0.233	0.328	SUBCLONAL	1	TRUE	1	0.624455907646663	2		635	507	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856347	45856347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	228	804	0	ENST00000391945.4:c.1825G>A	p.Asp609Asn	p.D609N	ENST00000391945	NM_000400.3	609	Gac/Aac	19/23	1	2	FACETS	0.952	0.89	1	0.952	0.89	1	CLONAL	1	TRUE	1	0.624455907646663	2		804	767	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868350	45868350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765679315	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	345	981	0	ENST00000391945.4:c.427C>T	p.Arg143Trp	p.R143W	ENST00000391945	NM_000400.3	143	Cgg/Tgg	6/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.624455907646663	2		981	1063	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905282	50905282	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	56	1109	0	ENST00000440232.2:c.490C>A	p.Leu164Met	p.L164M	ENST00000440232	NM_002691.3	164	Ctg/Atg	5/27	1	2	FACETS	0.178	0.152	0.207	0.178	0.152	0.207	SUBCLONAL	1	TRUE	1	0.624455907646663	2		1109	1008	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505435	25505435	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	54	735	0	ENST00000264709.3:c.323G>A	p.Gly108Glu	p.G108E	ENST00000264709	NM_175629.2	108	gGg/gAg	4/23	1	2	FACETS	0.307	0.262	0.356	0.307	0.262	0.356	SUBCLONAL	1	TRUE	1	0.624455907646663	2		735	564	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973194	25973194	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	134	552	1	ENST00000435504.4:c.1231T>C	p.Ser411Pro	p.S411P	ENST00000435504		411	Tcc/Ccc	12/13	1	2	FACETS	0.787	0.719	0.859	0.787	0.719	0.859	SUBCLONAL	1	TRUE	1	0.624455907646663	2		553	545	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416458	29416458	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	245	997	1	ENST00000389048.3:c.4495C>T	p.Pro1499Ser	p.P1499S	ENST00000389048	NM_004304.4	1499	Ccc/Tcc	29/29	1	2	FACETS	0.783	0.732	0.836	0.783	0.732	0.836	SUBCLONAL	1	TRUE	1	0.624455907646663	2		998	1002	SUCCESS
ALK	238	MSKCC	GRCh37	2	29448336	29448336	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	331	1150	0	ENST00000389048.3:c.3163A>G	p.Ile1055Val	p.I1055V	ENST00000389048	NM_004304.4	1055	Atc/Gtc	19/29	1	2	FACETS	0.96	0.908	1	0.96	0.908	1	CLONAL	1	TRUE	1	0.624455907646663	2		1150	1104	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451780	29451780	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	225	736	0	ENST00000389048.3:c.2785T>A	p.Ser929Thr	p.S929T	ENST00000389048	NM_004304.4	929	Tcc/Acc	16/29	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.624455907646663	2		736	667	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455216	29455216	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	172	737	1	ENST00000389048.3:c.2586G>T	p.Glu862Asp	p.E862D	ENST00000389048	NM_004304.4	862	gaG/gaT	15/29	1	2	FACETS	0.788	0.727	0.851	0.788	0.727	0.851	SUBCLONAL	1	TRUE	1	0.624455907646663	2		738	699	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754809	29754809	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	175	546	0	ENST00000389048.3:c.1126C>A	p.Leu376Ile	p.L376I	ENST00000389048	NM_004304.4	376	Ctc/Atc	4/29	1	2	FACETS	0.961	0.89	1	0.961	0.89	1	CLONAL	1	TRUE	1	0.624455907646663	2		546	583	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46588190	46588190	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148453283	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	193	639	0	ENST00000263734.3:c.740G>A	p.Arg247His	p.R247H	ENST00000263734	NM_001430.4	247	cGc/cAc	6/16	1	2	FACETS	0.902	0.838	0.969	0.902	0.838	0.969	CLONAL	1	TRUE	1	0.624455907646663	2		639	685	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027095	48027095	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	156	461	0	ENST00000234420.5:c.1973T>C	p.Val658Ala	p.V658A	ENST00000234420	NM_000179.2	658	gTg/gCg	4/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.624455907646663	2		461	465	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711089	61711089	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	122	447	0	ENST00000401558.2:c.2660G>T	p.Arg887Met	p.R887M	ENST00000401558	NM_003400.3	887	aGg/aTg	21/25	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.624455907646663	2		447	363	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634786	158634786	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765195676	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	91	373	0	ENST00000263640.3:c.400G>A	p.Ala134Thr	p.A134T	ENST00000263640	NM_001105.4	134	Gca/Aca	5/11	1	2	FACETS	0.692	0.618	0.77	0.692	0.618	0.77	SUBCLONAL	1	TRUE	1	0.624455907646663	2		373	421	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149771	202149771	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	141	725	1	ENST00000358485.4:c.1212C>A	p.Cys404Ter	p.C404*	ENST00000358485	NM_001080125.1	404	tgC/tgA	8/9	1	2	FACETS	0.614	0.56	0.671	0.614	0.56	0.671	SUBCLONAL	1	TRUE	1	0.624455907646663	2		726	735	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285245	212285245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	108	591	0	ENST00000342788.4:c.3056C>T	p.Ala1019Val	p.A1019V	ENST00000342788	NM_005235.2	1019	gCt/gTt	25/28	1	2	FACETS	0.858	0.776	0.944	0.858	0.776	0.944	CLONAL	1	TRUE	1	0.624455907646663	2		591	403	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286748	212286748	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1239361918	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	75	407	0	ENST00000342788.4:c.2948G>T	p.Arg983Ile	p.R983I	ENST00000342788	NM_005235.2	983	aGa/aTa	24/28	1	2	FACETS	0.543	0.478	0.613	0.543	0.478	0.613	SUBCLONAL	1	TRUE	1	0.624455907646663	2		407	442	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812158	212812158	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	86	299	0	ENST00000342788.4:c.418A>T	p.Thr140Ser	p.T140S	ENST00000342788	NM_005235.2	140	Aca/Tca	3/28	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.624455907646663	2		299	264	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403235	213403235	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	164	492	0	ENST00000342788.4:c.20T>G	p.Leu7Arg	p.L7R	ENST00000342788	NM_005235.2	7	cTt/cGt	1/28	1	2	FACETS	0.993	0.918	1	0.993	0.918	1	CLONAL	1	TRUE	1	0.624455907646663	2		492	529	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339063	225339063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	118	434	0	ENST00000264414.4:c.2206C>T	p.Pro736Ser	p.P736S	ENST00000264414	NM_003590.4	736	Cca/Tca	16/16	1	2	FACETS	0.881	0.801	0.964	0.881	0.801	0.964	CLONAL	1	TRUE	1	0.624455907646663	2		434	429	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661501	227661501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780995783	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	224	871	0	ENST00000305123.5:c.1954C>T	p.Arg652Cys	p.R652C	ENST00000305123	NM_005544.2	652	Cgc/Tgc	1/2	1	2	FACETS	0.944	0.882	1	0.944	0.882	1	CLONAL	1	TRUE	1	0.624455907646663	2		871	760	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538301	9538301	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	58	594	1	ENST00000353224.5:c.1697A>G	p.His566Arg	p.H566R	ENST00000353224	NM_177990.2	566	cAc/cGc	7/10	1	2	FACETS	0.274	0.234	0.316	0.274	0.234	0.316	SUBCLONAL	1	TRUE	1	0.624455907646663	2		595	679	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31020766	31020766	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	79	234	0	ENST00000375687.4:c.1063T>G	p.Phe355Val	p.F355V	ENST00000375687	NM_015338.5	355	Ttt/Gtt	11/13	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.624455907646663	2		234	233	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022696	31022696	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	35	640	0	ENST00000375687.4:c.2181G>T	p.Glu727Asp	p.E727D	ENST00000375687	NM_015338.5	727	gaG/gaT	13/13	1	2	FACETS	0.211	0.172	0.255	0.211	0.172	0.255	SUBCLONAL	1	TRUE	1	0.624455907646663	2		640	531	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375127	31375127	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	206	861	0	ENST00000328111.2:c.524A>G	p.Glu175Gly	p.E175G	ENST00000328111	NM_006892.3	175	gAg/gGg	6/23	1	2	FACETS	0.815	0.757	0.874	0.815	0.757	0.874	CLONAL	1	TRUE	1	0.624455907646663	2		861	810	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388084	31388084	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	96	361	0	ENST00000328111.2:c.1885A>G	p.Arg629Gly	p.R629G	ENST00000328111	NM_006892.3	629	Agg/Ggg	17/23	1	2	FACETS	0.886	0.797	0.979	0.886	0.797	0.979	CLONAL	1	TRUE	1	0.624455907646663	2		361	347	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36024652	36024652	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	280	955	1	ENST00000358208.4:c.641G>A	p.Gly214Asp	p.G214D	ENST00000358208		214	gGc/gAc	6/12	1	2	FACETS	0.93	0.875	0.987	0.93	0.875	0.987	CLONAL	1	TRUE	1	0.624455907646663	2		956	964	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980785	40980785	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	160	643	0	ENST00000373198.4:c.1701G>T	p.Lys567Asn	p.K567N	ENST00000373198	NM_133170.3	567	aaG/aaT	10/32	1	2	FACETS	0.796	0.732	0.862	0.796	0.732	0.862	SUBCLONAL	1	TRUE	1	0.624455907646663	2		643	644	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485852	57485852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	148	443	1	ENST00000371085.3:c.1153C>T	p.Arg385Cys	p.R385C	ENST00000371085	NM_000516.4	385	Cgc/Tgc	13/13	1	2	FACETS	0.942	0.867	1	0.942	0.867	1	CLONAL	1	TRUE	1	0.624455907646663	2		444	503	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42842589	42842589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758880900	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	261	789	0	ENST00000398585.3:c.1268C>T	p.Ala423Val	p.A423V	ENST00000398585	NM_001135099.1	423	gCc/gTc	11/14	1	2	FACETS	0.994	0.934	1	0.994	0.934	1	CLONAL	1	TRUE	1	0.624455907646663	2		789	841	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37061940	37061940	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	138	427	0	ENST00000231790.2:c.1024A>G	p.Met342Val	p.M342V	ENST00000231790	NM_000249.3	342	Atg/Gtg	11/19	1	2	FACETS	0.971	0.891	1	0.971	0.891	1	CLONAL	1	TRUE	1	0.624455907646663	2		427	455	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662965	52662965	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	152	586	0	ENST00000394830.3:c.1388A>T	p.Asn463Ile	p.N463I	ENST00000394830	NM_018313.4	463	aAt/aTt	13/30	1	2	FACETS	0.953	0.877	1	0.953	0.877	1	CLONAL	1	TRUE	1	0.624455907646663	2		586	511	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026807	71026807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	86	285	0	ENST00000318789.4:c.1415C>A	p.Ser472Tyr	p.S472Y	ENST00000318789	NM_032682.5	472	tCt/tAt	16/21	1	2	FACETS	0.95	0.85	1	0.95	0.85	1	CLONAL	1	TRUE	1	0.624455907646663	2		285	290	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102787	71102787	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	98	310	0	ENST00000318789.4:c.420G>T	p.Gln140His	p.Q140H	ENST00000318789	NM_032682.5	140	caG/caT	8/21	1	2	FACETS	0.951	0.858	1	0.951	0.858	1	CLONAL	1	TRUE	1	0.624455907646663	2		310	330	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799437	72799437	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	198	690	0	ENST00000325599.8:c.1732T>C	p.Ter578ArgextTer9	p.*578Rext*9	ENST00000325599	NM_018130.2	578	Tga/Cga	11/11	1	2	FACETS	0.977	0.909	1	0.977	0.909	1	CLONAL	1	TRUE	1	0.624455907646663	2		690	649	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259409	89259409	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	167	693	0	ENST00000336596.2:c.553G>A	p.Asp185Asn	p.D185N	ENST00000336596	NM_005233.5	185	Gat/Aat	3/17	1	2	FACETS	0.989	0.914	1	0.989	0.914	1	CLONAL	1	TRUE	1	0.624455907646663	2		693	541	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462381	89462381	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	151	590	0	ENST00000336596.2:c.1853C>T	p.Ala618Val	p.A618V	ENST00000336596	NM_005233.5	618	gCc/gTc	10/17	1	2	FACETS	0.864	0.794	0.936	0.864	0.794	0.936	CLONAL	1	TRUE	1	0.624455907646663	2		590	560	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499516	89499516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773476878	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	94	372	2	ENST00000336596.2:c.2686G>A	p.Ala896Thr	p.A896T	ENST00000336596	NM_005233.5	896	Gca/Aca	15/17	1	2	FACETS	0.715	0.64	0.794	0.715	0.64	0.794	SUBCLONAL	1	TRUE	1	0.624455907646663	2		374	421	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119666149	119666149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762056483	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	105	449	0	ENST00000316626.5:c.332G>A	p.Arg111Gln	p.R111Q	ENST00000316626		111	cGa/cAa	3/12	1	2	FACETS	0.899	0.813	0.989	0.899	0.813	0.989	CLONAL	1	TRUE	1	0.624455907646663	2		449	374	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880987	134880987	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	196	586	0	ENST00000398015.3:c.1550T>C	p.Phe517Ser	p.F517S	ENST00000398015	NM_004441.4	517	tTc/tCc	7/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.624455907646663	2		586	587	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188177	142188177	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	72	304	0	ENST00000350721.4:c.6552+2T>C		p.X2184_splice	ENST00000350721	NM_001184.3	2184			1	2	FACETS	0.919	0.813	1	0.919	0.813	1	CLONAL	1	TRUE	1	0.624455907646663	2		304	251	SUCCESS
ATR	545	MSKCC	GRCh37	3	142224008	142224008	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	221	759	0	ENST00000350721.4:c.5169C>G	p.Asp1723Glu	p.D1723E	ENST00000350721	NM_001184.3	1723	gaC/gaG	29/47	1	2	FACETS	0.938	0.875	1	0.938	0.875	1	CLONAL	1	TRUE	1	0.624455907646663	2		759	755	SUCCESS
ATR	545	MSKCC	GRCh37	3	142224078	142224078	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	168	649	0	ENST00000350721.4:c.5099C>T	p.Pro1700Leu	p.P1700L	ENST00000350721	NM_001184.3	1700	cCa/cTa	29/47	1	2	FACETS	0.79	0.728	0.854	0.79	0.728	0.854	SUBCLONAL	1	TRUE	1	0.624455907646663	2		649	681	SUCCESS
ATR	545	MSKCC	GRCh37	3	142285004	142285004	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	167	520	0	ENST00000350721.4:c.251T>C	p.Val84Ala	p.V84A	ENST00000350721	NM_001184.3	84	gTa/gCa	3/47	1	2	FACETS	0.969	0.896	1	0.969	0.896	1	CLONAL	1	TRUE	1	0.624455907646663	2		520	552	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182662949	182662949	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	151	506	0	ENST00000292782.4:c.713T>C	p.Val238Ala	p.V238A	ENST00000292782	NM_020640.2	238	gTt/gCt	7/7	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.624455907646663	2		506	457	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665381	182665381	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	58	231	0	ENST00000292782.4:c.560A>T	p.Asn187Ile	p.N187I	ENST00000292782	NM_020640.2	187	aAt/aTt	5/7	1	2	FACETS	0.88	0.767	1	0.88	0.767	1	CLONAL	1	TRUE	1	0.624455907646663	2		231	211	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443331	187443331	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	142	433	1	ENST00000232014.4:c.1795G>A	p.Glu599Lys	p.E599K	ENST00000232014	NM_001130845.1	599	Gag/Aag	8/10	1	2	FACETS	0.93	0.853	1	0.93	0.853	1	CLONAL	1	TRUE	1	0.624455907646663	2		434	489	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806222	1806222	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	243	835	0	ENST00000260795.2:c.1241T>G	p.Ile414Ser	p.I414S	ENST00000260795		414	aTc/aGc	8/17	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.624455907646663	2		835	777	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1918616	1918616	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	145	402	0	ENST00000382891.5:c.779G>A	p.Arg260His	p.R260H	ENST00000382891	NM_133335.3	260	cGc/cAc	4/22	1	2	FACETS	0.898	0.825	0.974	0.898	0.825	0.974	CLONAL	1	TRUE	1	0.624455907646663	2		402	517	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133763	55133763	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	159	535	0	ENST00000257290.5:c.976G>A	p.Ala326Thr	p.A326T	ENST00000257290	NM_006206.4	326	Gct/Act	7/23	1	2	FACETS	0.968	0.893	1	0.968	0.893	1	CLONAL	1	TRUE	1	0.624455907646663	2		535	526	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564654	55564654	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	235	650	0	ENST00000288135.5:c.542G>A	p.Arg181Gln	p.R181Q	ENST00000288135	NM_000222.2	181	cGg/cAg	3/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.624455907646663	2		650	677	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594204	55594204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	104	511	0	ENST00000288135.5:c.1907C>T	p.Ala636Val	p.A636V	ENST00000288135	NM_000222.2	636	gCc/gTc	13/21	1	2	FACETS	0.808	0.729	0.891	0.808	0.729	0.891	CLONAL	1	TRUE	1	0.624455907646663	2		511	412	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604629	55604629	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779103998	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	205	573	0	ENST00000288135.5:c.2837G>A	p.Arg946Gln	p.R946Q	ENST00000288135	NM_000222.2	946	cGa/cAa	21/21	1	2	FACETS	0.896	0.834	0.96	0.896	0.834	0.96	CLONAL	1	TRUE	1	0.624455907646663	2		573	733	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968171	55968171	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	121	484	0	ENST00000263923.4:c.2159G>T	p.Arg720Leu	p.R720L	ENST00000263923	NM_002253.2	720	cGg/cTg	15/30	1	2	FACETS	0.797	0.725	0.873	0.797	0.725	0.873	SUBCLONAL	1	TRUE	1	0.624455907646663	2		484	486	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970915	55970915	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	152	694	0	ENST00000263923.4:c.1882G>A	p.Glu628Lys	p.E628K	ENST00000263923	NM_002253.2	628	Gag/Aag	13/30	1	2	FACETS	0.797	0.732	0.864	0.797	0.732	0.864	SUBCLONAL	1	TRUE	1	0.624455907646663	2		694	611	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356262	66356262	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs769625548	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	209	663	0	ENST00000273854.3:c.1235T>C	p.Val412Ala	p.V412A	ENST00000273854	NM_004439.5	412	gTc/gCc	5/18	1	2	FACETS	0.986	0.919	1	0.986	0.919	1	CLONAL	1	TRUE	1	0.624455907646663	2		663	679	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467401	66467401	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	76	345	0	ENST00000273854.3:c.868A>G	p.Met290Val	p.M290V	ENST00000273854	NM_004439.5	290	Atg/Gtg	3/18	1	2	FACETS	0.879	0.78	0.983	0.879	0.78	0.983	CLONAL	1	TRUE	1	0.624455907646663	2		345	277	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143324126	143324126	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	18	346	0	ENST00000262992.4:c.337A>G	p.Thr113Ala	p.T113A	ENST00000262992	NM_001101669.1	113	Aca/Gca	5/24	1	2	FACETS	0.17	0.127	0.22	0.17	0.127	0.22	SUBCLONAL	1	TRUE	1	0.624455907646663	2		346	339	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518308	187518308	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	57	277	0	ENST00000441802.2:c.12386A>G	p.Asp4129Gly	p.D4129G	ENST00000441802	NM_005245.3	4129	gAc/gGc	25/27	1	2	FACETS	0.774	0.671	0.882	0.774	0.671	0.882	SUBCLONAL	1	TRUE	1	0.624455907646663	2		277	236	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539108	187539108	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	165	719	0	ENST00000441802.2:c.8632G>T	p.Glu2878Ter	p.E2878*	ENST00000441802	NM_005245.3	2878	Gaa/Taa	10/27	1	2	FACETS	0.921	0.85	0.993	0.921	0.85	0.993	CLONAL	1	TRUE	1	0.624455907646663	2		719	574	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542393	187542393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs572509773	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	120	454	0	ENST00000441802.2:c.5347G>A	p.Val1783Met	p.V1783M	ENST00000441802	NM_005245.3	1783	Gtg/Atg	10/27	1	2	FACETS	0.922	0.839	1	0.922	0.839	1	CLONAL	1	TRUE	1	0.624455907646663	2		454	417	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542456	187542456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371394820	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	122	527	0	ENST00000441802.2:c.5284G>A	p.Ala1762Thr	p.A1762T	ENST00000441802	NM_005245.3	1762	Gcg/Acg	10/27	1	2	FACETS	0.849	0.773	0.929	0.849	0.773	0.929	CLONAL	1	TRUE	1	0.624455907646663	2		527	460	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629663	187629663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	67	807	1	ENST00000441802.2:c.1319C>T	p.Thr440Ile	p.T440I	ENST00000441802	NM_005245.3	440	aCa/aTa	2/27	1	2	FACETS	0.264	0.229	0.302	0.264	0.229	0.302	SUBCLONAL	1	TRUE	1	0.624455907646663	2		808	813	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1266595	1266595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	189	502	0	ENST00000310581.5:c.2638G>A	p.Ala880Thr	p.A880T	ENST00000310581	NM_198253.2	880	Gcg/Acg	10/16	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.624455907646663	2		502	594	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294307	1294307	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	238	956	1	ENST00000310581.5:c.694C>A	p.Leu232Met	p.L232M	ENST00000310581	NM_198253.2	232	Ctg/Atg	2/16	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.624455907646663	2		957	744	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31407011	31407011	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	177	715	0	ENST00000344624.3:c.3896C>A	p.Thr1299Asn	p.T1299N	ENST00000344624		1299	aCt/aAt	31/33	1	2	FACETS	0.979	0.907	1	0.979	0.907	1	CLONAL	1	TRUE	1	0.624455907646663	2		715	579	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31521307	31521307	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	205	620	0	ENST00000344624.3:c.870G>T	p.Glu290Asp	p.E290D	ENST00000344624		290	gaG/gaT	3/33	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.624455907646663	2		620	599	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967462	38967462	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	100	363	0	ENST00000357387.3:c.1128T>G	p.Ile376Met	p.I376M	ENST00000357387	NM_152756.3	376	atT/atG	13/38	1	2	FACETS	0.882	0.795	0.973	0.882	0.795	0.973	CLONAL	1	TRUE	1	0.624455907646663	2		363	363	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39002764	39002764	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748219571	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	55	340	0	ENST00000357387.3:c.265C>T	p.Arg89Trp	p.R89W	ENST00000357387	NM_152756.3	89	Cgg/Tgg	5/38	1	2	FACETS	0.549	0.472	0.632	0.549	0.472	0.632	SUBCLONAL	1	TRUE	1	0.624455907646663	2		340	321	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176927	56176927	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	45	359	0	ENST00000399503.3:c.2197G>A	p.Gly733Ser	p.G733S	ENST00000399503	NM_005921.1	733	Ggt/Agt	13/20	1	2	FACETS	0.477	0.403	0.558	0.477	0.403	0.558	SUBCLONAL	1	TRUE	1	0.624455907646663	2		359	302	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753133	57753133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749015923	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	109	452	0	ENST00000274289.3:c.883G>A	p.Ala295Thr	p.A295T	ENST00000274289	NM_006622.3	295	Gca/Aca	7/14	1	2	FACETS	0.959	0.87	1	0.959	0.87	1	CLONAL	1	TRUE	1	0.624455907646663	2		452	364	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589547	67589547	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	46	163	0	ENST00000274335.5:c.1310T>A	p.Val437Asp	p.V437D	ENST00000274335		437	gTc/gAc	10/15	1	2	FACETS	0.938	0.805	1	0.938	0.805	1	CLONAL	1	TRUE	1	0.624455907646663	2		163	157	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591317	67591317	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	77	306	0	ENST00000274335.5:c.1814+1G>C		p.X605_splice	ENST00000274335		605			1	2	FACETS	0.819	0.726	0.917	0.819	0.726	0.917	CLONAL	1	TRUE	1	0.624455907646663	2		306	301	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961106	79961106	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	194	686	0	ENST00000265081.6:c.503A>C	p.Asp168Ala	p.D168A	ENST00000265081	NM_002439.4	168	gAt/gCt	3/24	1	2	FACETS	0.983	0.914	1	0.983	0.914	1	CLONAL	1	TRUE	1	0.624455907646663	2		686	632	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80150098	80150098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	154	619	0	ENST00000265081.6:c.2963C>T	p.Ala988Val	p.A988V	ENST00000265081	NM_002439.4	988	gCc/gTc	21/24	1	2	FACETS	0.988	0.911	1	0.988	0.911	1	CLONAL	1	TRUE	1	0.624455907646663	2		619	499	SUCCESS
APC	324	MSKCC	GRCh37	5	112178943	112178943	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	93	364	1	ENST00000257430.4:c.7652A>G	p.His2551Arg	p.H2551R	ENST00000257430	NM_000038.5	2551	cAc/cGc	16/16	1	2	FACETS	0.993	0.894	1	0.993	0.894	1	CLONAL	1	TRUE	1	0.624455907646663	2		365	300	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915178	131915179	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs786201531	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	150	616	0	ENST00000265335.6:c.541dup	p.Ser181PhefsTer7	p.S181Ffs*7	ENST00000265335		179	att/aTtt	4/25	1	2	FACETS	0.888	0.816	0.962	0.888	0.816	0.962	CLONAL	1	TRUE	1	0.624455907646663	2		616	541	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131951715	131951715	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	53	243	0	ENST00000265335.6:c.3057A>C	p.Gln1019His	p.Q1019H	ENST00000265335		1019	caA/caC	20/25	1	2	FACETS	0.824	0.712	0.943	0.824	0.712	0.943	CLONAL	1	TRUE	1	0.624455907646663	2		243	206	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636821	176636821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	146	540	1	ENST00000439151.2:c.1421G>A	p.Gly474Asp	p.G474D	ENST00000439151	NM_022455.4	474	gGc/gAc	5/23	1	2	FACETS	0.856	0.786	0.93	0.856	0.786	0.93	CLONAL	1	TRUE	1	0.624455907646663	2		541	546	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637225	176637225	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771243523	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	70	743	0	ENST00000439151.2:c.1825C>T	p.Pro609Ser	p.P609S	ENST00000439151	NM_022455.4	609	Ccc/Tcc	5/23	1	2	FACETS	0.286	0.249	0.326	0.286	0.249	0.326	SUBCLONAL	1	TRUE	1	0.624455907646663	2		743	784	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858506	27858506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1311110530	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	119	432	0	ENST00000359303.2:c.65C>T	p.Ala22Val	p.A22V	ENST00000359303	NM_003535.2	22	gCc/gTc	1/1	1	2	FACETS	0.943	0.859	1	0.943	0.859	1	CLONAL	1	TRUE	1	0.624455907646663	2		432	404	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912379	29912379	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	117	713	1	ENST00000376809.5:c.998G>T	p.Arg333Met	p.R333M	ENST00000376809	NM_002116.7	333	aGg/aTg	5/8	1	2	FACETS	0.581	0.525	0.64	0.581	0.525	0.64	SUBCLONAL	1	TRUE	1	0.624455907646663	2		714	645	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805712	32805712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760254380	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	205	772	0	ENST00000374899.4:c.299G>A	p.Ser100Asn	p.S100N	ENST00000374899	NM_018833.2	100	aGc/aAc	2/12	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.624455907646663	2		772	634	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793708	89793709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	68	387	0	ENST00000336032.3:c.782dup	p.Asn261LysfsTer12	p.N261Kfs*12	ENST00000336032	NM_006813.2	259	-/A	2/2	1	2	FACETS	0.631	0.553	0.715	0.631	0.553	0.715	SUBCLONAL	1	TRUE	1	0.624455907646663	2		387	345	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974412	93974412	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	83	331	0	ENST00000369303.4:c.1642G>A	p.Val548Ile	p.V548I	ENST00000369303	NM_004440.3	548	Gtc/Atc	8/17	1	2	FACETS	0.923	0.824	1	0.923	0.824	1	CLONAL	1	TRUE	1	0.624455907646663	2		331	288	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068129	94068129	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	76	200	0	ENST00000369303.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000369303	NM_004440.3	278	cCc/cTc	4/17	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.624455907646663	2		200	189	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112025235	112025235	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	203	604	0	ENST00000368678.4:c.514A>G	p.Thr172Ala	p.T172A	ENST00000368678		172	Acc/Gcc	6/13	1	2	FACETS	0.959	0.893	1	0.959	0.893	1	CLONAL	1	TRUE	1	0.624455907646663	2		604	678	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112029204	112029204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	99	389	0	ENST00000368678.4:c.364G>A	p.Ala122Thr	p.A122T	ENST00000368678		122	Gcc/Acc	5/13	1	2	FACETS	0.898	0.809	0.991	0.898	0.809	0.991	CLONAL	1	TRUE	1	0.624455907646663	2		389	353	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641081	117641081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766115237	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	187	682	1	ENST00000368508.3:c.5890G>A	p.Ala1964Thr	p.A1964T	ENST00000368508	NM_002944.2	1964	Gca/Aca	36/43	1	2	FACETS	0.983	0.913	1	0.983	0.913	1	CLONAL	1	TRUE	1	0.624455907646663	2		683	609	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647572	117647572	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	162	643	0	ENST00000368508.3:c.5372G>T	p.Ser1791Ile	p.S1791I	ENST00000368508	NM_002944.2	1791	aGc/aTc	33/43	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.624455907646663	2		643	517	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663630	117663631	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs776274768	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	132	540	0	ENST00000368508.3:c.4601dup	p.Asn1534LysfsTer21	p.N1534Kfs*21	ENST00000368508	NM_002944.2	1534	aat/aaAt	28/43	1	2	FACETS	0.734	0.669	0.802	0.734	0.669	0.802	SUBCLONAL	1	TRUE	1	0.624455907646663	2		540	576	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683963	117683963	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	166	700	0	ENST00000368508.3:c.3184G>T	p.Glu1062Ter	p.E1062*	ENST00000368508	NM_002944.2	1062	Gaa/Taa	21/43	1	2	FACETS	0.936	0.865	1	0.936	0.865	1	CLONAL	1	TRUE	1	0.624455907646663	2		700	568	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129171	152129171	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	236	866	0	ENST00000206249.3:c.124G>T	p.Val42Leu	p.V42L	ENST00000206249	NM_000125.3	42	Gtg/Ttg	1/8	1	2	FACETS	0.945	0.884	1	0.945	0.884	1	CLONAL	1	TRUE	1	0.624455907646663	2		866	800	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099152	157099152	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	88	500	0	ENST00000346085.5:c.89G>T	p.Ser30Ile	p.S30I	ENST00000346085	NM_020732.3	30	aGc/aTc	1/20	1	2	FACETS	0.671	0.598	0.748	0.671	0.598	0.748	SUBCLONAL	1	TRUE	1	0.624455907646663	2		500	420	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525086	157525086	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	134	333	0	ENST00000346085.5:c.4981C>A	p.Leu1661Ile	p.L1661I	ENST00000346085	NM_020732.3	1661	Ctt/Att	19/20	1	2	FACETS	0.993	0.91	1	0.993	0.91	1	CLONAL	1	TRUE	1	0.624455907646663	2		333	432	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683555	162683555	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	130	558	0	ENST00000366898.1:c.412+2T>C		p.X138_splice	ENST00000366898	NM_004562.2	138			1	2	FACETS	0.851	0.777	0.929	0.851	0.777	0.929	CLONAL	1	TRUE	1	0.624455907646663	2		558	489	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444357	50444357	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	78	410	0	ENST00000331340.3:c.287A>G	p.His96Arg	p.H96R	ENST00000331340	NM_006060.4	96	cAc/cGc	4/8	1	2	FACETS	0.564	0.497	0.635	0.564	0.497	0.635	SUBCLONAL	1	TRUE	1	0.624455907646663	2		410	443	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459547	50459547	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	97	278	0	ENST00000331340.3:c.836C>A	p.Pro279His	p.P279H	ENST00000331340	NM_006060.4	279	cCt/cAt	7/8	1	2	FACETS	0.847	0.761	0.936	0.847	0.761	0.936	CLONAL	1	TRUE	1	0.624455907646663	2		278	367	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92300795	92300795	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	100	367	0	ENST00000265734.4:c.592A>G	p.Thr198Ala	p.T198A	ENST00000265734	NM_001259.6	198	Acc/Gcc	5/8	1	2	FACETS	0.887	0.8	0.978	0.887	0.8	0.978	CLONAL	1	TRUE	1	0.624455907646663	2		367	361	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545573	106545573	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	79	523	0	ENST00000359195.3:c.3050A>G	p.Tyr1017Cys	p.Y1017C	ENST00000359195	NM_002649.2	1017	tAt/tGt	11/11	1	2	FACETS	0.749	0.664	0.838	0.749	0.664	0.838	SUBCLONAL	1	TRUE	1	0.624455907646663	2		523	338	SUCCESS
MET	4233	MSKCC	GRCh37	7	116414030	116414030	+	intron_variant	Intron	SNP	T	T	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	19	1208	1	ENST00000397752.3:c.3029-905T>C		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.069	0.051	0.089	0.069	0.051	0.089	SUBCLONAL	1	TRUE	1	0.624455907646663	2		1209	887	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418886	116418886	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs745437003	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	110	418	0	ENST00000397752.3:c.3397G>T	p.Asp1133Tyr	p.D1133Y	ENST00000397752	NM_000245.2	1133	Gat/Tat	17/21	1	2	FACETS	0.863	0.782	0.948	0.863	0.782	0.948	CLONAL	1	TRUE	1	0.624455907646663	2		418	408	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829111	128829111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	26	64	0	ENST00000249373.3:c.119G>A	p.Gly40Glu	p.G40E	ENST00000249373	NM_005631.4	40	gGg/gAg	1/12	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.624455907646663	2		64	60	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506220	148506220	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	203	480	0	ENST00000320356.2:c.2138T>C	p.Ile713Thr	p.I713T	ENST00000320356	NM_004456.4	713	aTa/aCa	19/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.624455907646663	2		480	617	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864462	151864462	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	110	347	0	ENST00000262189.6:c.9519T>A	p.Asn3173Lys	p.N3173K	ENST00000262189	NM_170606.2	3173	aaT/aaA	42/59	1	2	FACETS	0.973	0.883	1	0.973	0.883	1	CLONAL	1	TRUE	1	0.624455907646663	2		347	362	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874604	151874604	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	151	480	1	ENST00000262189.6:c.7934T>C	p.Val2645Ala	p.V2645A	ENST00000262189	NM_170606.2	2645	gTc/gCc	38/59	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.624455907646663	2		481	424	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874767	151874767	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	118	421	0	ENST00000262189.6:c.7771G>T	p.Gly2591Ter	p.G2591*	ENST00000262189	NM_170606.2	2591	Gga/Tga	38/59	1	2	FACETS	0.859	0.78	0.941	0.859	0.78	0.941	CLONAL	1	TRUE	1	0.624455907646663	2		421	440	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878377	151878377	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	207	720	0	ENST00000262189.6:c.6568T>C	p.Phe2190Leu	p.F2190L	ENST00000262189	NM_170606.2	2190	Ttt/Ctt	36/59	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.624455907646663	2		720	659	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945396	151945396	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	176	780	1	ENST00000262189.6:c.2123C>A	p.Ser708Ter	p.S708*	ENST00000262189	NM_170606.2	708	tCa/tAa	14/59	1	2	FACETS	0.909	0.841	0.979	0.909	0.841	0.979	CLONAL	1	TRUE	1	0.624455907646663	2		781	620	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207497	29207497	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	22	668	0	ENST00000240100.2:c.299G>C	p.Gly100Ala	p.G100A	ENST00000240100	NM_001394.6	100	gGc/gCc	1/4	0.624455907646663	1	FACETS	0.145	0.112	0.183	0.145	0.112	0.183	SUBCLONAL	1	TRUE	0	0.624455907646663	1		668	334	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162192	38162192	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	31	464	0	ENST00000317025.8:c.2524T>A	p.Ser842Thr	p.S842T	ENST00000317025	NM_023034.1	842	Tcc/Acc	14/24	0.624455907646663	1	FACETS	0.217	0.175	0.263	0.217	0.175	0.263	SUBCLONAL	1	TRUE	0	0.624455907646663	1		464	315	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38173512	38173512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777597698	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	166	646	0	ENST00000317025.8:c.1904G>A	p.Arg635His	p.R635H	ENST00000317025	NM_023034.1	635	cGc/cAc	10/24	0.624455907646663	1	FACETS	0.802	0.744	0.861	0.802	0.744	0.861	CLONAL	1	TRUE	0	0.624455907646663	1		646	456	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863304	56863304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141769918	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	104	538	0	ENST00000519728.1:c.448G>A	p.Ala150Thr	p.A150T	ENST00000519728	NM_002350.3	150	Gct/Act	6/13	1	2	FACETS	0.55	0.493	0.609	0.55	0.493	0.609	SUBCLONAL	1	TRUE	1	0.624455907646663	2		538	606	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864528	56864528	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	159	610	1	ENST00000519728.1:c.491G>A	p.Ser164Asn	p.S164N	ENST00000519728	NM_002350.3	164	aGc/aAc	7/13	1	2	FACETS	0.875	0.806	0.946	0.875	0.806	0.946	CLONAL	1	TRUE	1	0.624455907646663	2		611	582	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950476	68950476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1406399796	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	164	509	0	ENST00000288368.4:c.788G>A	p.Arg263Gln	p.R263Q	ENST00000288368	NM_024870.2	263	cGg/cAg	7/40	1	2	FACETS	0.958	0.885	1	0.958	0.885	1	CLONAL	1	TRUE	1	0.624455907646663	2		509	548	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028049	69028049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	145	589	0	ENST00000288368.4:c.3208C>T	p.Pro1070Ser	p.P1070S	ENST00000288368	NM_024870.2	1070	Cca/Tca	26/40	1	2	FACETS	0.992	0.912	1	0.992	0.912	1	CLONAL	1	TRUE	1	0.624455907646663	2		589	468	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981483	70981483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	350	1141	1	ENST00000276594.2:c.613G>A	p.Val205Ile	p.V205I	ENST00000276594	NM_024504.3	205	Gtt/Att	2/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.624455907646663	2		1142	1053	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981559	70981559	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	291	1241	2	ENST00000276594.2:c.537G>T	p.Glu179Asp	p.E179D	ENST00000276594	NM_024504.3	179	gaG/gaT	2/8	1	2	FACETS	0.797	0.75	0.846	0.797	0.75	0.846	SUBCLONAL	1	TRUE	1	0.624455907646663	2		1243	1169	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90990463	90990463	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	84	530	0	ENST00000265433.3:c.569C>A	p.Pro190His	p.P190H	ENST00000265433	NM_002485.4	190	cCt/cAt	5/16	1	2	FACETS	0.725	0.645	0.81	0.725	0.645	0.81	SUBCLONAL	1	TRUE	1	0.624455907646663	2		530	371	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141567330	141567330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	164	543	1	ENST00000220592.5:c.884C>T	p.Pro295Leu	p.P295L	ENST00000220592	NM_012154.3	295	cCg/cTg	8/19	1	2	FACETS	0.973	0.899	1	0.973	0.899	1	CLONAL	1	TRUE	1	0.624455907646663	2		544	540	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737127	145737127	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	147	819	0	ENST00000428558.2:c.3439C>A	p.Leu1147Met	p.L1147M	ENST00000428558	NM_004260.3	1147	Ctg/Atg	21/22	1	2	FACETS	0.628	0.574	0.684	0.628	0.574	0.684	SUBCLONAL	1	TRUE	1	0.624455907646663	2		819	750	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739320	145739320	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1483958590	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	273	789	0	ENST00000428558.2:c.2050A>G	p.Thr684Ala	p.T684A	ENST00000428558	NM_004260.3	684	Aca/Gca	12/22	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.624455907646663	2		789	808	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5064916	5064916	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	74	469	0	ENST00000381652.3:c.1090T>C	p.Ser364Pro	p.S364P	ENST00000381652	NM_004972.3	364	Tct/Cct	9/25	1	2	FACETS	0.568	0.5	0.642	0.568	0.5	0.642	SUBCLONAL	1	TRUE	1	0.624455907646663	2		469	417	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123066	5123066	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	111	600	0	ENST00000381652.3:c.3122G>T	p.Gly1041Val	p.G1041V	ENST00000381652	NM_004972.3	1041	gGa/gTa	23/25	1	2	FACETS	0.626	0.564	0.691	0.626	0.564	0.691	SUBCLONAL	1	TRUE	1	0.624455907646663	2		600	568	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5557701	5557701	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	28	646	0	ENST00000397747.3:c.715A>G	p.Thr239Ala	p.T239A	ENST00000397747	NM_025239.3	239	Aca/Gca	5/7	1	2	FACETS	0.16	0.127	0.198	0.16	0.127	0.198	SUBCLONAL	1	TRUE	1	0.624455907646663	2		646	560	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5557710	5557710	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	135	591	0	ENST00000397747.3:c.724G>T	p.Ala242Ser	p.A242S	ENST00000397747	NM_025239.3	242	Gcc/Tcc	5/7	1	2	FACETS	0.779	0.711	0.85	0.779	0.711	0.85	SUBCLONAL	1	TRUE	1	0.624455907646663	2		591	555	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341892	8341892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	166	673	1	ENST00000356435.5:c.4748G>A	p.Gly1583Asp	p.G1583D	ENST00000356435		1583	gGc/gAc	29/35	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.624455907646663	2		674	516	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484203	8484203	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775510240	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	226	683	1	ENST00000356435.5:c.3329C>T	p.Thr1110Ile	p.T1110I	ENST00000356435		1110	aCc/aTc	19/35	1	2	FACETS	0.959	0.896	1	0.959	0.896	1	CLONAL	1	TRUE	1	0.624455907646663	2		684	755	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006036	22006036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167893458	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	106	896	2	ENST00000276925.6:c.367C>T	p.Arg123Trp	p.R123W	ENST00000276925	NM_004936.3	123	Cgg/Tgg	2/2	1	2	FACETS	0.433	0.388	0.481	0.433	0.388	0.481	SUBCLONAL	1	TRUE	1	0.624455907646663	2		898	784	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212870	27212870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	95	737	3	ENST00000380036.4:c.2852G>A	p.Gly951Asp	p.G951D	ENST00000380036	NM_000459.3	951	gGc/gAc	17/23	1	2	FACETS	0.365	0.325	0.409	0.365	0.325	0.409	SUBCLONAL	1	TRUE	1	0.624455907646663	2		740	833	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409509	80409509	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	172	711	0	ENST00000286548.4:c.606-1G>T		p.X202_splice	ENST00000286548	NM_002072.3	202			1	2	FACETS	0.975	0.903	1	0.975	0.903	1	CLONAL	1	TRUE	1	0.624455907646663	2		711	565	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97869451	97869451	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	257	885	0	ENST00000289081.3:c.1430C>G	p.Thr477Arg	p.T477R	ENST00000289081	NM_000136.2	477	aCa/aGa	14/15	1	2	FACETS	0.935	0.878	0.994	0.935	0.878	0.994	CLONAL	1	TRUE	1	0.624455907646663	2		885	880	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98009734	98009734	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	122	431	0	ENST00000289081.3:c.230A>C	p.Asn77Thr	p.N77T	ENST00000289081	NM_000136.2	77	aAt/aCt	3/15	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.624455907646663	2		431	381	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242701	98242701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs547776340	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	185	559	1	ENST00000331920.6:c.916G>A	p.Ala306Thr	p.A306T	ENST00000331920	NM_000264.3	306	Gcc/Acc	6/24	1	2	FACETS	0.965	0.896	1	0.965	0.896	1	CLONAL	1	TRUE	1	0.624455907646663	2		560	614	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248045	98248045	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	208	672	0	ENST00000331920.6:c.506T>C	p.Val169Ala	p.V169A	ENST00000331920	NM_000264.3	169	gTc/gCc	3/24	1	2	FACETS	0.92	0.857	0.985	0.92	0.857	0.985	CLONAL	1	TRUE	1	0.624455907646663	2		672	724	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891320	101891320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	177	686	0	ENST00000374994.4:c.281C>A	p.Ser94Tyr	p.S94Y	ENST00000374994	NM_004612.2	94	tCt/tAt	2/9	1	2	FACETS	0.884	0.818	0.952	0.884	0.818	0.952	CLONAL	1	TRUE	1	0.624455907646663	2		686	641	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249417	110249417	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	377	1352	2	ENST00000374672.4:c.1156C>T	p.Arg386Ter	p.R386*	ENST00000374672	NM_004235.4	386	Cga/Tga	4/5	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.624455907646663	2		1354	1196	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249873	110249873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	60	849	0	ENST00000374672.4:c.802G>A	p.Gly268Ser	p.G268S	ENST00000374672	NM_004235.4	268	Ggc/Agc	3/5	1	2	FACETS	0.294	0.253	0.339	0.294	0.253	0.339	SUBCLONAL	1	TRUE	1	0.624455907646663	2		849	653	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781486	135781486	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	142	434	0	ENST00000298552.3:c.1479G>T	p.Glu493Asp	p.E493D	ENST00000298552	NM_001162426.1	493	gaG/gaT	15/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.624455907646663	2		434	416	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393425	139393425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542300217	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	281	860	1	ENST00000277541.6:c.6106G>A	p.Ala2036Thr	p.A2036T	ENST00000277541	NM_017617.3	2036	Gcc/Acc	33/34	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.624455907646663	2		861	852	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395128	139395128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	331	948	1	ENST00000277541.6:c.5810G>A	p.Arg1937His	p.R1937H	ENST00000277541	NM_017617.3	1937	cGc/cAc	31/34	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.624455907646663	2		949	949	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395239	139395239	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	292	885	0	ENST00000277541.6:c.5699G>T	p.Ser1900Ile	p.S1900I	ENST00000277541	NM_017617.3	1900	aGc/aTc	31/34	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.624455907646663	2		885	836	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400136	139400136	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	317	1102	1	ENST00000277541.6:c.4212G>T	p.Glu1404Asp	p.E1404D	ENST00000277541	NM_017617.3	1404	gaG/gaT	25/34	1	2	FACETS	0.983	0.929	1	0.983	0.929	1	CLONAL	1	TRUE	1	0.624455907646663	2		1103	1033	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401261	139401261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777189816	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	69	1042	0	ENST00000277541.6:c.3808G>A	p.Glu1270Lys	p.E1270K	ENST00000277541	NM_017617.3	1270	Gag/Aag	23/34	1	2	FACETS	0.212	0.184	0.243	0.212	0.184	0.243	SUBCLONAL	1	TRUE	1	0.624455907646663	2		1042	1043	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417611	139417611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388726872	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	371	1063	2	ENST00000277541.6:c.433G>A	p.Ala145Thr	p.A145T	ENST00000277541	NM_017617.3	145	Gcc/Acc	4/34	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.624455907646663	2		1065	1045	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566454	139566454	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	268	999	0	ENST00000308874.7:c.713G>A	p.Ser238Asn	p.S238N	ENST00000308874		238	aGc/aAc	9/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.624455907646663	2		999	827	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814825	139814825	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	263	822	0	ENST00000247668.2:c.818A>G	p.Glu273Gly	p.E273G	ENST00000247668	NM_021138.3	273	gAg/gGg	8/11	1	2	FACETS	0.992	0.932	1	0.992	0.932	1	CLONAL	1	TRUE	1	0.624455907646663	2		822	849	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814843	139814843	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201077633	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	277	845	0	ENST00000247668.2:c.836C>T	p.Thr279Met	p.T279M	ENST00000247668	NM_021138.3	279	aCg/aTg	8/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.624455907646663	2		845	844	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20153882	20153882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	133	518	1	ENST00000379607.5:c.178C>T	p.His60Tyr	p.H60Y	ENST00000379607	NM_001412.3	60	Cac/Tac	3/7	1	2	FACETS	0.914	0.836	0.995	0.914	0.836	0.995	CLONAL	1	TRUE	1	0.624455907646663	2		519	466	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911652	39911652	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	144	527	0	ENST00000378444.4:c.4978C>T	p.Pro1660Ser	p.P1660S	ENST00000378444	NM_001123385.1	1660	Cca/Tca	15/15	1	2	FACETS	0.857	0.786	0.931	0.857	0.786	0.931	CLONAL	1	TRUE	1	0.624455907646663	2		527	538	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44919382	44919382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	135	458	0	ENST00000377967.4:c.1310C>T	p.Ala437Val	p.A437V	ENST00000377967	NM_021140.2	437	gCc/gTc	13/29	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.624455907646663	2		458	412	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041197	47041197	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	324	1008	1	ENST00000377604.3:c.1625C>A	p.Pro542His	p.P542H	ENST00000377604	NM_001204468.1	542	cCt/cAt	15/24	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.624455907646663	2		1009	1013	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223485	53223485	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782288948	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	205	757	0	ENST00000375401.3:c.3874G>A	p.Ala1292Thr	p.A1292T	ENST00000375401	NM_004187.3	1292	Gcc/Acc	23/26	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.624455907646663	2		757	651	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223605	53223605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	136	758	1	ENST00000375401.3:c.3754C>T	p.Arg1252Cys	p.R1252C	ENST00000375401	NM_004187.3	1252	Cgc/Tgc	23/26	1	2	FACETS	0.713	0.65	0.778	0.713	0.65	0.778	SUBCLONAL	1	TRUE	1	0.624455907646663	2		759	611	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411503	63411503	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	191	950	0	ENST00000330258.3:c.1664A>G	p.Glu555Gly	p.E555G	ENST00000330258	NM_152424.3	555	gAg/gGg	2/2	1	2	FACETS	0.806	0.747	0.867	0.806	0.747	0.867	CLONAL	1	TRUE	1	0.624455907646663	2		950	759	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338654	70338654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	239	669	0	ENST00000374080.3:c.50C>T	p.Pro17Leu	p.P17L	ENST00000374080		17	cCg/cTg	1/45	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.624455907646663	2		669	699	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340838	70340838	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	120	620	0	ENST00000374080.3:c.571A>G	p.Thr191Ala	p.T191A	ENST00000374080		191	Acc/Gcc	5/45	1	2	FACETS	0.718	0.651	0.788	0.718	0.651	0.788	SUBCLONAL	1	TRUE	1	0.624455907646663	2		620	535	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343004	70343004	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	200	701	0	ENST00000374080.3:c.1545G>T	p.Lys515Asn	p.K515N	ENST00000374080		515	aaG/aaT	11/45	1	2	FACETS	0.835	0.776	0.896	0.835	0.776	0.896	CLONAL	1	TRUE	1	0.624455907646663	2		701	767	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347751	70347751	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556336381	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	110	516	0	ENST00000374080.3:c.2990G>A	p.Cys997Tyr	p.C997Y	ENST00000374080		997	tGc/tAc	22/45	1	2	FACETS	0.665	0.599	0.733	0.665	0.599	0.733	SUBCLONAL	1	TRUE	1	0.624455907646663	2		516	530	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829818	76829818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1440854109	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	102	506	0	ENST00000373344.5:c.6223G>A	p.Gly2075Arg	p.G2075R	ENST00000373344	NM_000489.3	2075	Ggg/Agg	28/35	1	2	FACETS	0.77	0.694	0.851	0.77	0.694	0.851	SUBCLONAL	1	TRUE	1	0.624455907646663	2		506	424	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76931779	76931779	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	69	526	1	ENST00000373344.5:c.3751T>C	p.Ser1251Pro	p.S1251P	ENST00000373344	NM_000489.3	1251	Tct/Cct	10/35	1	2	FACETS	0.415	0.362	0.473	0.415	0.362	0.473	SUBCLONAL	1	TRUE	1	0.624455907646663	2		527	532	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938093	76938093	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	247	840	0	ENST00000373344.5:c.2655A>C	p.Arg885Ser	p.R885S	ENST00000373344	NM_000489.3	885	agA/agC	9/35	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.624455907646663	2		840	722	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944391	76944391	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	125	562	0	ENST00000373344.5:c.514A>G	p.Thr172Ala	p.T172A	ENST00000373344	NM_000489.3	172	Act/Gct	7/35	1	2	FACETS	0.834	0.76	0.912	0.834	0.76	0.912	CLONAL	1	TRUE	1	0.624455907646663	2		562	480	SUCCESS
BTK	695	MSKCC	GRCh37	X	100604895	100604895	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	139	471	0	ENST00000308731.7:c.1958A>G	p.Asp653Gly	p.D653G	ENST00000308731	NM_000061.2	653	gAt/gGt	19/19	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.624455907646663	2		471	435	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197789	123197789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	140	616	0	ENST00000218089.9:c.1913C>T	p.Ala638Val	p.A638V	ENST00000218089	NM_001042749.1	638	gCa/gTa	20/35	1	2	FACETS	0.944	0.866	1	0.944	0.866	1	CLONAL	1	TRUE	1	0.624455907646663	2		616	475	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227876	123227876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868559404	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	80	345	0	ENST00000218089.9:c.3587G>A	p.Gly1196Asp	p.G1196D	ENST00000218089	NM_001042749.1	1196	gGc/gAc	33/35	1	2	FACETS	0.803	0.714	0.897	0.803	0.714	0.897	CLONAL	1	TRUE	1	0.624455907646663	2		345	319	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152864487	152864487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	17	73	0	ENST00000406277.2:c.41G>A	p.Gly14Asp	p.G14D	ENST00000406277	NM_152274.4	14	gGc/gAc	2/7	NA		FACETS		NA	1				INDETERMINATE	NA	TRUE	NA	0.624455907646663	NA		73	63	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141568623	141568623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	208	727	0	ENST00000220592.5:c.839G>A	p.Arg280His	p.R280H	ENST00000220592	NM_012154.3	280	cGc/cAc	7/19	1	2	FACETS	0.892	0.83	0.955	0.892	0.83	0.955	CLONAL	1	TRUE	1	0.624455907646663	2		727	747	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849299	89849299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374490484	NA	P-0036175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	143	669	0	ENST00000389301.3:c.1594G>A	p.Glu532Lys	p.E532K	ENST00000389301	NM_000135.2	532	Gag/Aag	17/43	0.492999485544019	1	FACETS	0.86	0.789	0.934	0.86	0.789	0.934	CLONAL	1	TRUE	0	0.492999485544019	1		669	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7577078	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTAGGAAAGAGGCAAGGAAAGGTGATAAAAGTGAATCTGAGGCATAACTGCACCCTTGGTCTCCTCCACCGCTTCTTGTCCTGCTTGCTTACCTCGCTTAGTGCTCCCTGGGGGCAGCTCGTGGTGAGGCTCCCCTTTCTTGCGGAGATTCT	CTAGGAAAGAGGCAAGGAAAGGTGATAAAAGTGAATCTGAGGCATAACTGCACCCTTGGTCTCCTCCACCGCTTCTTGTCCTGCTTGCTTACCTCGCTTAGTGCTCCCTGGGGGCAGCTCGTGGTGAGGCTCCCCTTTCTTGCGGAGATTCT	-	novel	NA	P-0036175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	213	750	0	ENST00000269305.4:c.860_920-1del		p.X287_splice	ENST00000269305	NM_001126112.2	287		8/11	0.492999485544019	1	FACETS	0.944	0.881	1	0.944	0.881	1	CLONAL	1	TRUE	0	0.492999485544019	1		750	690	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0036364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	24	507	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.551	0.43	0.692	0.551	0.43	0.692	SUBCLONAL	1	TRUE	1	0.14	2		507	622	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396851	139396851	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	40	520	0	ENST00000277541.6:c.5257G>A	p.Gly1753Arg	p.G1753R	ENST00000277541	NM_017617.3	1753	Ggg/Agg	28/34	1	2	FACETS	0.766	0.635	0.913	0.766	0.635	0.913	CLONAL	1	TRUE	1	0.14	2		520	746	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120351	70120352	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	66	881	0	ENST00000245479.2:c.1354dup	p.Tyr452LeufsTer126	p.Y452Lfs*126	ENST00000245479	NM_000346.3	451	-/T	3/3	1	2	FACETS	0.844	0.73	0.968	0.844	0.73	0.968	CLONAL	1	TRUE	1	0.14	2		881	1117	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482393	56482393	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	45	548	0	ENST00000267101.3:c.941A>T	p.Lys314Ile	p.K314I	ENST00000267101	NM_001982.3	314	aAa/aTa	8/28	1	2	FACETS	0.968	0.812	1	0.968	0.812	1	CLONAL	1	TRUE	1	0.14	2		548	664	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577084	7577084	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121912667	NA	P-0036542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	131	685	0	ENST00000269305.4:c.854A>T	p.Glu285Val	p.E285V	ENST00000269305	NM_001126112.2	285	gAg/gTg	8/11	0.343394778520359	1	FACETS	0.888	0.807	0.973	0.888	0.807	0.973	CLONAL	1	TRUE	0	0.343394778520359	1		685	712	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913836	32913837	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359507	NA	P-0036542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	39	440	2	ENST00000380152.3:c.5351dup	p.Asn1784LysfsTer3	p.N1784Kfs*3	ENST00000380152		1782	caa/cAaa	11/27	0.343394778520359	1	FACETS	0.836	0.699	0.986	0.836	0.699	0.986	CLONAL	1	TRUE	0	0.343394778520359	1		442	225	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115267929	115267929	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1322231550	NA	P-0036542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	63	525	0	ENST00000438362.2:c.1804C>G	p.Leu602Val	p.L602V	ENST00000438362	NM_001242891.1	602	Ctg/Gtg	15/20	1	2	FACETS	0.851	0.739	0.973	0.851	0.739	0.973	CLONAL	1	TRUE	1	0.343394778520359	2		525	431	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618716	37618719	+	frameshift_variant	Frame_Shift_Del	DEL	AAAA	AAAA	-	novel	NA	P-0036570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	145	412	0	ENST00000447079.4:c.394_397del	p.Lys132AlafsTer11	p.K132Afs*11	ENST00000447079	NM_015083.1	131	gAAAAa/ga	1/14	0.783646912684763	1	FACETS	0.954	0.895	1	0.954	0.895	1	CLONAL	1	TRUE	0	0.783646912684763	1		412	236	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520008	NA	P-0036570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	309	622	0	ENST00000269305.4:c.613T>C	p.Tyr205His	p.Y205H	ENST00000269305	NM_001126112.2	205	Tat/Cat	6/11	0.783646912684763	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.783646912684763	1		622	430	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	62	301	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	0.804	0.709	0.903	0.804	0.709	0.903	CLONAL	1	TRUE	1	0.876428388297641	2		301	176	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0036584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	687	792	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.808478229015699	2	FACETS	0.976	0.959	0.993	0.976	0.959	0.993	CLONAL	2	TRUE	0	0.876428388297641	2		793	803	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0036584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	256	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.845857004640777	3	FACETS	0.839	0.795	0.882	0.839	0.795	0.882	CLONAL	2	TRUE	1	0.876428388297641	3		485	501	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214604	5214604	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs116515629	NA	P-0036584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	302	743	2	ENST00000357368.4:c.4462G>A	p.Val1488Ile	p.V1488I	ENST00000357368	NM_002850.3	1488	Gtc/Atc	29/38	0.845857004640777	3	FACETS	0.939	0.886	0.994	0.47	0.443	0.497	CLONAL	1	TRUE	1	0.876428388297641	3		745	1055	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	123	530	0	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	1	2	FACETS	0.83	0.761	0.902	0.83	0.761	0.902	CLONAL	1	TRUE	1	0.876428388297641	2		530	338	SUCCESS
APC	324	MSKCC	GRCh37	5	112175153	112175153	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	97	266	0	ENST00000257430.4:c.3862G>T	p.Gly1288Ter	p.G1288*	ENST00000257430	NM_000038.5	1288	Gga/Tga	16/16	0.809291208745417	2	FACETS	0.851	0.798	0.901	0.851	0.798	0.901	CLONAL	2	TRUE	0	0.876428388297641	2		266	130	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100451	8100451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266983268	NA	P-0036584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	272	735	0	ENST00000346208.3:c.425C>T	p.Ser142Leu	p.S142L	ENST00000346208		142	tCg/tTg	3/6	0.845857004640777	3	FACETS	0.82	0.77	0.872	0.41	0.385	0.436	CLONAL	1	TRUE	1	0.876428388297641	3		735	1088	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41228557	41228557	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	299	711	0	ENST00000357654.3:c.4432G>C	p.Glu1478Gln	p.E1478Q	ENST00000357654	NM_007294.3	1478	Gag/Cag	13/23	0.616338964122759	4	FACETS	0.912	0.865	0.96	0.912	0.865	0.96	CLONAL	2	TRUE	2	0.876428388297641	4		711	702	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896433	151896433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	82	465	0	ENST00000262189.6:c.4204G>A	p.Gly1402Ser	p.G1402S	ENST00000262189	NM_170606.2	1402	Ggt/Agt	27/59	0.845857004640777	3	FACETS	0.813	0.723	0.907	0.407	0.361	0.454	CLONAL	1	TRUE	1	0.876428388297641	3		465	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0036600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	256	806	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.422540273617138	2	FACETS	0.965	0.91	1	0.965	0.91	1	CLONAL	2	TRUE	0	0.422540273617138	2		806	628	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212230	5212230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367918810	NA	P-0036600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	125	741	1	ENST00000357368.4:c.4801G>A	p.Val1601Ile	p.V1601I	ENST00000357368	NM_002850.3	1601	Gtc/Atc	32/38	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.422540273617138	2		742	558	SUCCESS
APC	324	MSKCC	GRCh37	5	112137081	112137081	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0036600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	122	351	0	ENST00000257430.4:c.834+1G>C		p.X278_splice	ENST00000257430	NM_000038.5	278			0.422540273617138	2	FACETS	0.878	0.804	0.953	0.878	0.804	0.953	CLONAL	2	TRUE	0	0.422540273617138	2		351	329	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134451	30134459	+	inframe_deletion	In_Frame_Del	DEL	TCCCCCGGG	TCCCCCGGG	-	novel	NA	P-0036600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	67	665	0	ENST00000263025.4:c.72_80del	p.Pro25_Glu27del	p.P25_E27del	ENST00000263025	NM_002746.2	24	gtCCCGGGGGAg/gtg	1/9	1	2	FACETS	0.61	0.531	0.695	0.61	0.531	0.695	SUBCLONAL	1	TRUE	1	0.422540273617138	2		665	520	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226620	1226620	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782687	NA	P-0036600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	75	524	0	ENST00000326873.7:c.1276C>T	p.Arg426Trp	p.R426W	ENST00000326873	NM_000455.4	426	Cgg/Tgg	9/10	1	2	FACETS	0.949	0.837	1	0.949	0.837	1	CLONAL	1	TRUE	1	0.422540273617138	2		524	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0036622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	147	456	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.244748015997743	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	2	TRUE	0	0.244748015997743	2		456	595	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0036622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	99	266	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	0.244748015997743	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	0	0.244748015997743	2		266	390	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849800	156849800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41358549	NA	P-0036622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	174	377	0	ENST00000524377.1:c.2056C>T	p.Arg686Cys	p.R686C	ENST00000524377	NM_002529.3	686	Cgc/Tgc	16/17	0.244748015997743	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	3	TRUE	1	0.244748015997743	4		377	560	SUCCESS
APC	324	MSKCC	GRCh37	5	112174266	112174267	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	99	262	0	ENST00000257430.4:c.2976dup	p.Lys993Ter	p.K993*	ENST00000257430	NM_000038.5	992	agt/agTt	16/16	0.244748015997743	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	1	0.244748015997743	3		262	414	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258607	16258607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753287056	NA	P-0036622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	41	322	0	ENST00000375759.3:c.5872C>T	p.Arg1958Trp	p.R1958W	ENST00000375759	NM_015001.2	1958	Cgg/Tgg	11/15	1	2	FACETS	0.928	0.775	1	0.928	0.775	1	CLONAL	1	TRUE	1	0.244748015997743	2		322	361	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456353	99456353	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371466243	NA	P-0036622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	120	275	1	ENST00000268035.6:c.1670C>T	p.Pro557Leu	p.P557L	ENST00000268035	NM_000875.3	557	cCg/cTg	8/21	0.244748015997743	4	FACETS	0.935	0.851	1	0.935	0.851	1	CLONAL	3	TRUE	1	0.244748015997743	4		276	435	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024045	31024045	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	61	427	0	ENST00000375687.4:c.3531del	p.Leu1178CysfsTer39	p.L1178Cfs*39	ENST00000375687	NM_015338.5	1177	cTt/ct	13/13	0.244748015997743	8	FACETS	0.927	0.797	1	0.154	0.132	0.178	CLONAL	1	TRUE	2	0.244748015997743	8		427	933	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542714	187542714	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	63	355	0	ENST00000441802.2:c.5026C>G	p.Leu1676Val	p.L1676V	ENST00000441802	NM_005245.3	1676	Ctt/Gtt	10/27	0.219200539175967	3	FACETS	1	0.943	1	0.584	0.505	0.668	CLONAL	1	TRUE	1	0.244748015997743	3		355	495	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584629	187584629	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	60	402	0	ENST00000441802.2:c.3404A>C	p.Asn1135Thr	p.N1135T	ENST00000441802	NM_005245.3	1135	aAt/aCt	3/27	0.219200539175967	3	FACETS	1	0.904	1	0.53	0.457	0.61	CLONAL	1	TRUE	1	0.244748015997743	3		402	519	SUCCESS
APC	324	MSKCC	GRCh37	5	112175405	112175415	+	frameshift_variant	Frame_Shift_Del	DEL	CCACCTGAACA	CCACCTGAACA	-	novel	NA	P-0036622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	40	217	0	ENST00000257430.4:c.4115_4125del	p.Pro1372LeufsTer10	p.P1372Lfs*10	ENST00000257430	NM_000038.5	1372	CCACCTGAACAc/c	16/16	0.244748015997743	3	FACETS	1	0.909	1	0.57	0.475	0.674	CLONAL	1	TRUE	1	0.244748015997743	3		217	322	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163566	32163566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	68	360	0	ENST00000375023.3:c.5660C>T	p.Ala1887Val	p.A1887V	ENST00000375023	NM_004557.3	1887	gCt/gTt	30/30	0.244748015997743	3	FACETS	1	0.919	1	0.539	0.469	0.614	CLONAL	1	TRUE	1	0.244748015997743	3		360	579	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0036724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	400	800	0	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.377168518117645	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.402794158609926	2		800	984	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265445	152265445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149490424	NA	P-0036724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	107	512	1	ENST00000206249.3:c.898C>T	p.Arg300Cys	p.R300C	ENST00000206249	NM_000125.3	300	Cgc/Tgc	4/8	1	2	FACETS	0.922	0.83	1	0.922	0.83	1	CLONAL	1	TRUE	1	0.402794158609926	2		513	576	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666636	206666636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782318549	NA	P-0036724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	144	607	0	ENST00000367120.3:c.1970G>A	p.Arg657Gln	p.R657Q	ENST00000367120	NM_014002.3	657	cGa/cAa	20/22	0.402794158609926	1	FACETS	0.86	0.786	0.937	0.86	0.786	0.937	CLONAL	1	TRUE	0	0.402794158609926	1		607	664	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114905796	114905796	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1414161688	NA	P-0036724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	108	486	1	ENST00000543371.1:c.815C>T	p.Thr272Met	p.T272M	ENST00000543371	NM_001198531.1	272	aCg/aTg	8/14	1	2	FACETS	0.841	0.756	0.93	0.841	0.756	0.93	CLONAL	1	TRUE	1	0.402794158609926	2		487	638	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056833	102056833	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	75	420	0	ENST00000282441.5:c.773G>A	p.Trp258Ter	p.W258*	ENST00000282441	NM_001130145.2	258	tGg/tAg	4/9	1	2	FACETS	0.922	0.812	1	0.922	0.812	1	CLONAL	1	TRUE	1	0.402794158609926	2		420	404	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46266506	46266506	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	98	359	0	ENST00000371998.3:c.2493del	p.Gln832LysfsTer8	p.Q832Kfs*8	ENST00000371998		831	Ttt/tt	13/23	0.136944997242583	4	FACETS	0.758	0.68	0.841	0.758	0.68	0.841	INDETERMINATE	2	TRUE	2	0.402794158609926	4		359	450	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946331	55946331	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0036724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	46	262	0	ENST00000263923.4:c.3849-1G>C		p.X1283_splice	ENST00000263923	NM_002253.2	1283			1	2	FACETS	0.828	0.702	0.965	0.828	0.702	0.965	CLONAL	1	TRUE	1	0.402794158609926	2		262	276	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249471	153249471	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	98	622	0	ENST00000281708.4:c.1307G>T	p.Ser436Ile	p.S436I	ENST00000281708	NM_033632.3	436	aGt/aTt	9/12	1	2	FACETS	0.87	0.779	0.968	0.87	0.779	0.968	CLONAL	1	TRUE	1	0.402794158609926	2		622	559	SUCCESS
APC	324	MSKCC	GRCh37	5	112175158	112175158	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	90	229	0	ENST00000257430.4:c.3867del	p.Cys1289Ter	p.C1289*	ENST00000257430	NM_000038.5	1289	tgT/tg	16/16	0.377168518117645	2	FACETS	0.989	0.894	1	0.989	0.894	1	CLONAL	2	TRUE	0	0.402794158609926	2		229	226	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0036966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	480	562	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.80843733272984	1	FACETS	0.992	0.961	1	0.992	0.961	1	CLONAL	1	TRUE	0	0.80843733272984	1		562	713	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912815	100912815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1000609240	NA	P-0036966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	128	374	0	ENST00000325455.5:c.2507G>A	p.Arg836Gln	p.R836Q	ENST00000325455	NM_001202474.3	836	cGa/cAa	7/8	0.772541873509325	3	FACETS	0.729	0.663	0.798	0.364	0.331	0.399	SUBCLONAL	1	TRUE	1	0.80843733272984	3		374	610	SUCCESS
APC	324	MSKCC	GRCh37	5	112173644	112173644	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	103	326	0	ENST00000257430.4:c.2353C>G	p.His785Asp	p.H785D	ENST00000257430	NM_000038.5	785	Cat/Gat	16/16	1	2	FACETS	0.681	0.615	0.75	0.681	0.615	0.75	SUBCLONAL	1	TRUE	1	0.80843733272984	2		326	374	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180049755	180049755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776380290	NA	P-0036966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	373	586	0	ENST00000261937.6:c.1633C>T	p.Arg545Trp	p.R545W	ENST00000261937	NM_182925.4	545	Cgg/Tgg	12/30	1	2	FACETS	0.995	0.948	1	0.995	0.948	1	CLONAL	1	TRUE	1	0.80843733272984	2		586	927	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751158	128751158	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3362	342	497	0	ENST00000377970.2:c.695C>A	p.Ser232Tyr	p.S232Y	ENST00000377970	NM_002467.4	232	tCt/tAt	2/3	0.80843733272984	11	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.80843733272984	11		497	3704	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0037007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	39	529	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.479817710975978	3	FACETS	0.37	0.306	0.441	0.185	0.153	0.221	SUBCLONAL	1	TRUE	1	0.502059295721873	3		529	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0037007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	395	575	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.433153517986653	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.502059295721873	2		575	774	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0037007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	17	437	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.479817710975978	3	FACETS	0.187	0.139	0.245	0.094	0.069	0.123	SUBCLONAL	1	TRUE	1	0.502059295721873	3		437	452	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604764	48604765	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs377767376	NA	P-0037007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	22	351	0	ENST00000342988.3:c.1587dup	p.His530ThrfsTer47	p.H530Tfs*47	ENST00000342988	NM_005359.5	529	tta/ttAa	12/12	1	2	FACETS	0.241	0.187	0.305	0.241	0.187	0.305	SUBCLONAL	1	TRUE	1	0.502059295721873	2		351	363	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111508	8111508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	138	523	1	ENST00000346208.3:c.994G>A	p.Ala332Thr	p.A332T	ENST00000346208		332	Gcc/Acc	5/6	0.479817710975978	3	FACETS	1	0.913	1	0.501	0.456	0.547	CLONAL	1	TRUE	1	0.502059295721873	3		524	687	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914070	32914070	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs431825332	NA	P-0037007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	73	454	0	ENST00000380152.3:c.5578A>G	p.Lys1860Glu	p.K1860E	ENST00000380152		1860	Aaa/Gaa	11/27	0.303317945496687	6	FACETS	0.871	0.762	0.989			1	CLONAL	1	TRUE	NA	0.502059295721873	6		454	669	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227653	36227653	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0037007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	307	513	0	ENST00000222270.7:c.7222A>T	p.Lys2408Ter	p.K2408*	ENST00000222270	NM_014727.1	2408	Aaa/Taa	31/37	0.44612708167394	3	FACETS	0.97	0.918	1	0.97	0.918	1	CLONAL	2	TRUE	1	0.502059295721873	3		513	789	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032003	26032003	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	70	325	0	ENST00000244661.2:c.286G>C	p.Ala96Pro	p.A96P	ENST00000244661	NM_003537.3	96	Gct/Cct	1/1	0.479817710975978	3	FACETS	0.784	0.686	0.889	0.392	0.343	0.445	SUBCLONAL	1	TRUE	1	0.502059295721873	3		325	445	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0037027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	334	548	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.0352194702957394	3	FACETS	1	0.987	1			1	INDETERMINATE	4	TRUE	NA	0.267386634547368	3		548	649	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579443	7579444	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0037027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	174	647	0	ENST00000269305.4:c.243_244del	p.Pro82GlyfsTer66	p.P82Gfs*66	ENST00000269305	NM_001126112.2	81	acACcg/accg	4/11	0.267386634547368	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.267386634547368	2		647	616	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907714	111907714	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs376024148	NA	P-0037027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	92	441	0	ENST00000393256.3:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000393256	NM_006538.4	163	tAt/tGt	3/4	0.267386634547368	3	FACETS	0.754	0.672	0.841	0.754	0.672	0.841	SUBCLONAL	2	TRUE	1	0.267386634547368	3		441	517	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636339	87636339	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	56	670	0	ENST00000277120.3:c.2504A>G	p.Asp835Gly	p.D835G	ENST00000277120		835	gAc/gGc	19/19	0.267386634547368	3	FACETS	0.824	0.706	0.954	0.412	0.353	0.477	CLONAL	1	TRUE	1	0.267386634547368	3		670	576	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	163	583	0	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	1	2	FACETS	0.969	0.893	1	1	0.994	1	CLONAL	3	FALSE	1	0.179434731457646	2		583	625	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	87	431	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.871	0.777	0.97	1	0.988	1	CLONAL	3	FALSE	1	0.179434731457646	2		437	371	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	271	564	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	0.179434731457646	2	FACETS	1	0.982	1	1	0.997	1	CLONAL	7	FALSE	0	0.179434731457646	2		564	412	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434187	49434187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754060706	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	277	840	0	ENST00000301067.7:c.7366C>T	p.Arg2456Cys	p.R2456C	ENST00000301067	NM_003482.3	2456	Cgc/Tgc	31/54	0.179434731457646	4	FACETS	0.951	0.895	1	1	0.995	1	CLONAL	4	FALSE	2	0.179434731457646	4		840	957	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016264	150016264	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	146	579	1	ENST00000253339.5:c.442C>T	p.Arg148Ter	p.R148*	ENST00000253339		148	Cga/Tga	2/7	0.179434731457646	3	FACETS	1	0.95	1	1	0.989	1	CLONAL	3	FALSE	1	0.179434731457646	3		580	563	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	66	373	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	1	0.9	1	1	0.985	1	CLONAL	3	FALSE	1	0.179434731457646	2		373	239	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	11	353	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.681	0.471	0.941	0.681	0.471	0.941	SUBCLONAL	1	FALSE	1	0.179434731457646	2		354	180	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085942	16085942	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	136	526	0	ENST00000281043.3:c.1118G>A	p.Arg373Gln	p.R373Q	ENST00000281043	NM_005378.4	373	cGa/cAa	3/3	1	2	FACETS	1	0.926	1	1	0.993	1	CLONAL	3	FALSE	1	0.179434731457646	2		526	499	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729843	41729843	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138819536	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	25	477	1	ENST00000242208.4:c.686G>A	p.Arg229Gln	p.R229Q	ENST00000242208	NM_002192.2	229	cGg/cAg	3/3	1	2	FACETS	0.618	0.486	0.77	0.618	0.486	0.77	SUBCLONAL	1	FALSE	1	0.179434731457646	2		478	451	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	96	310	1	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	1	0.95	1	1	0.99	1	CLONAL	3	FALSE	1	0.179434731457646	2		311	327	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821959	72821960	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762108866	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	88	380	1	ENST00000268489.5:c.10215dup	p.Gly3406ArgfsTer25	p.G3406Rfs*25	ENST00000268489	NM_006885.3	3405	-/C	10/10	1	2	FACETS	1	0.957	1	1	0.987	1	CLONAL	2	FALSE	1	0.179434731457646	2		381	426	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841178	15841178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753128407	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	109	306	0	ENST00000307771.7:c.1262G>A	p.Arg421Gln	p.R421Q	ENST00000307771	NM_005089.3	421	cGa/cAa	11/11	1	2	FACETS	1	0.918	1	1	0.991	1	CLONAL	3	FALSE	1	0.179434731457646	2		306	399	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022498	12022498	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs567885519	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	222	684	0	ENST00000396373.4:c.604C>T	p.Arg202Trp	p.R202W	ENST00000396373	NM_001987.4	202	Cgg/Tgg	5/8	0.179434731457646	3	FACETS	0.925	0.867	0.983	1	0.993	1	CLONAL	5	FALSE	0	0.179434731457646	3		684	583	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514780	44514780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769567889	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	213	524	1	ENST00000291552.4:c.467G>A	p.Arg156His	p.R156H	ENST00000291552	NM_006758.2	156	cGt/cAt	6/8	1	2	FACETS	1	0.938	1	1	0.995	1	CLONAL	3	FALSE	1	0.179434731457646	2		525	786	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022535	12022535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159947	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	164	662	0	ENST00000396373.4:c.641C>T	p.Pro214Leu	p.P214L	ENST00000396373	NM_001987.4	214	cCg/cTg	5/8	0.179434731457646	3	FACETS	1	0.972	1	1	0.99	1	CLONAL	4	FALSE	0	0.179434731457646	3		662	454	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184465	7184465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329693158	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	249	673	0	ENST00000302850.5:c.836G>A	p.Arg279His	p.R279H	ENST00000302850	NM_000208.2	279	cGc/cAc	3/22	1	2	FACETS	1	0.954	1	1	0.996	1	CLONAL	3	FALSE	1	0.179434731457646	2		673	905	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354667	70354667	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1569482153	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	164	589	0	ENST00000374080.3:c.4832G>A	p.Arg1611His	p.R1611H	ENST00000374080		1611	cGt/cAt	35/45	1	2	FACETS	1	0.924	1	1	0.994	1	CLONAL	3	FALSE	1	0.179434731457646	2		589	608	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172027	32172027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1417982489	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	187	657	0	ENST00000375023.3:c.3005G>A	p.Arg1002His	p.R1002H	ENST00000375023	NM_004557.3	1002	cGc/cAc	19/30	0.179434731457646	3	FACETS	1	0.976	1	1	0.992	1	CLONAL	3	FALSE	1	0.179434731457646	3		657	675	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513259	44513259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	229	418	2	ENST00000291552.4:c.676C>T	p.Arg226Cys	p.R226C	ENST00000291552	NM_006758.2	226	Cgt/Tgt	8/8	1	2	FACETS	1	0.935	1	1	0.995	1	CLONAL	3	FALSE	1	0.179434731457646	2		420	850	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346714	225346714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	66	617	0	ENST00000264414.4:c.1924C>T	p.Arg642Trp	p.R642W	ENST00000264414	NM_003590.4	642	Cgg/Tgg	14/16	1	2	FACETS	0.991	0.865	1	1	0.981	1	CLONAL	2	FALSE	1	0.179434731457646	2		617	371	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057594	180057594	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371804364	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	231	815	3	ENST00000261937.6:c.361G>A	p.Glu121Lys	p.E121K	ENST00000261937	NM_182925.4	121	Gag/Aag	3/30	1	2	FACETS	1	0.954	1	1	0.995	1	CLONAL	3	FALSE	1	0.179434731457646	2		818	837	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522741	67522741	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	74	265	0	ENST00000274335.5:c.244del	p.Ile82SerfsTer32	p.I82Sfs*32	ENST00000274335		80	Aaa/aa	1/15	1	2	FACETS	1	0.942	1	1	0.987	1	CLONAL	3	FALSE	1	0.179434731457646	2		265	250	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143191881	143191881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs184155869	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	108	548	0	ENST00000262992.4:c.550G>A	p.Val184Met	p.V184M	ENST00000262992	NM_001101669.1	184	Gtg/Atg	8/24	1	2	FACETS	1	0.971	1	1	0.99	1	CLONAL	2	FALSE	1	0.179434731457646	2		548	500	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458270	12458270	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	174	654	1	ENST00000287820.6:c.892del	p.Leu298CysfsTer38	p.L298Cfs*38	ENST00000287820	NM_015869.4	296	aCc/ac	6/7	1	2	FACETS	0.982	0.908	1	1	0.994	1	CLONAL	3	FALSE	1	0.179434731457646	2		655	658	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717712	89717712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782350	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	72	502	0	ENST00000371953.3:c.737C>T	p.Pro246Leu	p.P246L	ENST00000371953	NM_000314.4	246	cCg/cTg	7/9	1	2	FACETS	0.904	0.797	1	1	0.986	1	CLONAL	3	FALSE	1	0.179434731457646	2		502	296	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221243	1221243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	100	647	1	ENST00000326873.7:c.766G>A	p.Glu256Lys	p.E256K	ENST00000326873	NM_000455.4	256	Gaa/Aaa	6/10	1	2	FACETS	0.839	0.75	0.934	1	0.984	1	CLONAL	2	FALSE	1	0.179434731457646	2		648	664	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86648978	86648978	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	61	310	0	ENST00000274376.6:c.1261del	p.Asp421ThrfsTer3	p.D421Tfs*3	ENST00000274376	NM_002890.2	420	Ggg/gg	9/25	1	2	FACETS	1	0.933	1	1	0.985	1	CLONAL	3	FALSE	1	0.179434731457646	2		310	206	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097688	27097688	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	152	598	1	ENST00000324856.7:c.3281del	p.Lys1094SerfsTer67	p.K1094Sfs*67	ENST00000324856	NM_006015.4	1093	Aaa/aa	12/20	1	2	FACETS	1	0.937	1	1	0.993	1	CLONAL	3	FALSE	1	0.179434731457646	2		599	553	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224189	36224189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376011791	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	182	464	0	ENST00000222270.7:c.6739G>A	p.Gly2247Arg	p.G2247R	ENST00000222270	NM_014727.1	2247	Gga/Aga	28/37	1	2	FACETS	1	0.968	1	1	0.994	1	CLONAL	3	FALSE	1	0.179434731457646	2		464	627	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350054	70350054	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs966195679	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	106	415	0	ENST00000374080.3:c.4037G>A	p.Arg1346His	p.R1346H	ENST00000374080		1346	cGc/cAc	28/45	1	2	FACETS	0.867	0.782	0.957	1	0.99	1	CLONAL	3	FALSE	1	0.179434731457646	2		415	454	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777960	3777960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1266123570	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	316	860	0	ENST00000262367.5:c.7088C>T	p.Pro2363Leu	p.P2363L	ENST00000262367	NM_004380.2	2363	cCg/cTg	31/31	1	2	FACETS	1	0.948	1	1	0.997	1	CLONAL	3	FALSE	1	0.179434731457646	2		860	1168	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953633	32953633	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359732	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	50	472	1	ENST00000380152.3:c.8940del	p.Glu2981LysfsTer7	p.E2981Kfs*7	ENST00000380152		2978	tcA/tc	22/27	1	2	FACETS	0.906	0.779	1	1	0.98	1	CLONAL	3	FALSE	1	0.179434731457646	2		473	205	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212138	36212138	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1258696516	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	99	341	0	ENST00000222270.7:c.1893del	p.Ser632ProfsTer28	p.S632Pfs*28	ENST00000222270	NM_014727.1	630	gCc/gc	3/37	1	2	FACETS	1	0.944	1	1	0.99	1	CLONAL	3	FALSE	1	0.179434731457646	2		341	344	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940571	71940571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760513714	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	244	707	0	ENST00000298229.2:c.722C>T	p.Ser241Leu	p.S241L	ENST00000298229	NM_001567.3	241	tCg/tTg	6/28	1	2	FACETS	1	0.946	1	1	0.996	1	CLONAL	3	FALSE	1	0.179434731457646	2		707	896	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052635	42052635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	169	573	0	ENST00000219905.7:c.7306C>T	p.Arg2436Cys	p.R2436C	ENST00000219905	NM_001164273.1	2436	Cgt/Tgt	20/24	1	2	FACETS	0.906	0.835	0.979	1	0.994	1	CLONAL	3	FALSE	1	0.179434731457646	2		573	693	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324202	31324202	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs41556417	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	15	203	0	ENST00000412585.2:c.361A>T	p.Ser121Cys	p.S121C	ENST00000412585	NM_005514.6	121	Agc/Tgc	3/8	0.179434731457646	3	FACETS	1	0.839	1	0.607	0.447	0.798	CLONAL	1	FALSE	1	0.179434731457646	3		203	150	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827589	72827589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343025200	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	152	754	0	ENST00000268489.5:c.8992C>T	p.Arg2998Trp	p.R2998W	ENST00000268489	NM_006885.3	2998	Cgg/Tgg	9/10	1	2	FACETS	0.905	0.831	0.982	1	0.993	1	CLONAL	3	FALSE	1	0.179434731457646	2		754	624	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563285	21563285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1207863433	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	230	662	1	ENST00000382592.4:c.634G>A	p.Val212Met	p.V212M	ENST00000382592	NM_014572.2	212	Gtg/Atg	4/8	1	2	FACETS	0.996	0.93	1	1	0.995	1	CLONAL	3	FALSE	1	0.179434731457646	2		663	858	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47643569	47643569	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs267607940	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	70	429	0	ENST00000233146.2:c.1076+1G>A		p.X359_splice	ENST00000233146	NM_000251.2	359			1	2	FACETS	1	0.934	1	1	0.987	1	CLONAL	3	FALSE	1	0.179434731457646	2		429	240	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798286	45798286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147754007	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	202	603	0	ENST00000450313.1:c.650G>A	p.Arg217His	p.R217H	ENST00000450313	NM_012222.2	217	cGc/cAc	8/16	1	2	FACETS	1	0.957	1	1	0.995	1	CLONAL	3	FALSE	1	0.179434731457646	2		603	722	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872243	45872243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773453200	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	138	771	0	ENST00000391945.4:c.191C>T	p.Pro64Leu	p.P64L	ENST00000391945	NM_000400.3	64	cCg/cTg	4/23	1	2	FACETS	0.855	0.777	0.936	1	0.989	1	CLONAL	2	FALSE	1	0.179434731457646	2		771	900	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231833	36231833	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	198	628	1	ENST00000300305.3:c.551C>T	p.Pro184Leu	p.P184L	ENST00000300305		184	cCg/cTg	5/8	1	2	FACETS	0.904	0.839	0.971	1	0.994	1	CLONAL	3	FALSE	1	0.179434731457646	2		629	814	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781466	3781468	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs1555471931	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	18	407	0	ENST00000262367.5:c.4897_4899del	p.Phe1633del	p.F1633del	ENST00000262367	NM_004380.2	1633	TTC/-	30/31	1	2	FACETS	0.643	0.484	0.831	0.643	0.484	0.831	SUBCLONAL	1	FALSE	1	0.179434731457646	2		407	312	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220637	2220637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750885564	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	221	587	0	ENST00000326181.6:c.254G>A	p.Arg85His	p.R85H	ENST00000326181	NM_032271.2	85	cGc/cAc	5/21	1	2	FACETS	1	0.977	1	1	0.995	1	CLONAL	3	FALSE	1	0.179434731457646	2		587	746	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797413	42797413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555772579	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	240	696	0	ENST00000575354.2:c.3775G>A	p.Ala1259Thr	p.A1259T	ENST00000575354	NM_015125.3	1259	Gcc/Acc	15/20	1	2	FACETS	1	0.976	1	1	0.996	1	CLONAL	3	FALSE	1	0.179434731457646	2		696	823	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184785	32184785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11963697	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	157	645	0	ENST00000375023.3:c.1798G>A	p.Val600Ile	p.V600I	ENST00000375023	NM_004557.3	600	Gtt/Att	11/30	0.179434731457646	3	FACETS	0.97	0.892	1	1	0.988	1	CLONAL	3	FALSE	1	0.179434731457646	3		645	655	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858551	9858551	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	101	708	0	ENST00000330684.3:c.2850G>T	p.Gln950His	p.Q950H	ENST00000330684	NM_001134407.1	950	caG/caT	13/13	1	2	FACETS	1	0.935	1	1	0.99	1	CLONAL	3	FALSE	1	0.179434731457646	2		708	358	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354291	70354291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1218546722	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	262	723	1	ENST00000374080.3:c.4702G>A	p.Gly1568Ser	p.G1568S	ENST00000374080		1568	Ggc/Agc	34/45	1	2	FACETS	1	0.964	1	1	0.996	1	CLONAL	3	FALSE	1	0.179434731457646	2		724	937	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058530	72058530	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	46	584	0	ENST00000357731.5:c.910G>T	p.Gly304Cys	p.G304C	ENST00000357731	NM_173808.2	304	Ggc/Tgc	6/7	1	2	FACETS	0.868	0.73	1	0.868	0.73	1	CLONAL	1	FALSE	1	0.179434731457646	2		584	591	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239405	123239405	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	88	486	0	ENST00000358487.5:c.2432A>G	p.Gln811Arg	p.Q811R	ENST00000358487	NM_000141.4	811	cAg/cGg	18/18	1	2	FACETS	1	0.951	1	1	0.989	1	CLONAL	3	FALSE	1	0.179434731457646	2		486	296	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192701	94192701	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	88	630	0	ENST00000323929.3:c.1373T>C	p.Val458Ala	p.V458A	ENST00000323929	NM_005591.3	458	gTa/gCa	13/20	1	2	FACETS	1	0.934	1	1	0.989	1	CLONAL	3	FALSE	1	0.179434731457646	2		630	309	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374468	118374468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	121	578	0	ENST00000534358.1:c.7861C>T	p.Arg2621Cys	p.R2621C	ENST00000534358	NM_005933.3	2621	Cgt/Tgt	27/36	1	2	FACETS	0.861	0.782	0.944	1	0.991	1	CLONAL	3	FALSE	1	0.179434731457646	2		578	522	SUCCESS
CBL	867	MSKCC	GRCh37	11	119167630	119167630	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs768065878	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	24	481	0	ENST00000264033.4:c.2039C>A	p.Pro680His	p.P680H	ENST00000264033	NM_005188.3	680	cCt/cAt	13/16	1	2	FACETS	0.741	0.581	0.926	0.741	0.581	0.926	CLONAL	1	FALSE	1	0.179434731457646	2		481	361	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445202	49445202	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776110112	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	219	626	2	ENST00000301067.7:c.2264G>A	p.Arg755Gln	p.R755Q	ENST00000301067	NM_003482.3	755	cGg/cAg	10/54	0.179434731457646	4	FACETS	1	0.981	1	1	0.993	1	CLONAL	3	FALSE	2	0.179434731457646	4		628	845	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202759	133202759	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs5745067	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	164	585	0	ENST00000320574.5:c.6475C>T	p.Arg2159Cys	p.R2159C	ENST00000320574	NM_006231.2	2159	Cgc/Tgc	46/49	0.179434731457646	4	FACETS	1	0.977	1	1	0.991	1	CLONAL	3	FALSE	2	0.179434731457646	4		585	620	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292759	91292759	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	101	627	1	ENST00000355112.3:c.261G>T	p.Lys87Asn	p.K87N	ENST00000355112	NM_000057.2	87	aaG/aaT	3/22	1	2	FACETS	1	0.941	1	1	0.99	1	CLONAL	3	FALSE	1	0.179434731457646	2		628	354	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500304	99500304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45512296	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	158	678	0	ENST00000268035.6:c.3737G>A	p.Arg1246His	p.R1246H	ENST00000268035	NM_000875.3	1246	cGc/cAc	21/21	1	2	FACETS	0.85	0.781	0.921	1	0.993	1	CLONAL	3	FALSE	1	0.179434731457646	2		678	691	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579885	7579885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs535274413	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	71	643	1	ENST00000269305.4:c.28G>A	p.Val10Ile	p.V10I	ENST00000269305	NM_001126112.2	10	Gtc/Atc	2/11	0.179434731457646	2	FACETS	0.934	0.814	1	0.467	0.407	0.533	CLONAL	1	FALSE	0	0.179434731457646	2		644	847	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212348	5212348	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	211	676	0	ENST00000357368.4:c.4769G>T	p.Ser1590Ile	p.S1590I	ENST00000357368	NM_002850.3	1590	aGt/aTt	31/38	1	2	FACETS	1	0.975	1	1	0.995	1	CLONAL	3	FALSE	1	0.179434731457646	2		676	716	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138623	11138623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	138	541	0	ENST00000358026.2:c.3379G>A	p.Asp1127Asn	p.D1127N	ENST00000358026	NM_001128849.1	1127	Gat/Aat	24/36	1	2	FACETS	1	0.945	1	1	0.993	1	CLONAL	3	FALSE	1	0.179434731457646	2		541	492	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298024	15298024	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769773673	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	277	858	0	ENST00000263388.2:c.1732C>T	p.Arg578Cys	p.R578C	ENST00000263388	NM_000435.2	578	Cgc/Tgc	11/33	1	2	FACETS	1	0.979	1	1	0.996	1	CLONAL	3	FALSE	1	0.179434731457646	2		858	947	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349622	15349622	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	216	747	0	ENST00000263377.2:c.3952del	p.Gln1318SerfsTer30	p.Q1318Sfs*30	ENST00000263377	NM_058243.2	1318	Cag/ag	19/20	1	2	FACETS	1	0.957	1	1	0.995	1	CLONAL	3	FALSE	1	0.179434731457646	2		747	775	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912856	50912856	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777542518	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	214	684	0	ENST00000440232.2:c.2087G>A	p.Ser696Asn	p.S696N	ENST00000440232	NM_002691.3	696	aGc/aAc	17/27	1	2	FACETS	1	0.964	1	1	0.995	1	CLONAL	3	FALSE	1	0.179434731457646	2		684	757	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723446	52723446	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	140	579	0	ENST00000322088.6:c.1307T>C	p.Val436Ala	p.V436A	ENST00000322088	NM_014225.5	436	gTg/gCg	11/15	1	2	FACETS	0.978	0.895	1	1	0.993	1	CLONAL	3	FALSE	1	0.179434731457646	2		579	532	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635679	47635679	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	95	564	1	ENST00000233146.2:c.351G>A	p.Trp117Ter	p.W117*	ENST00000233146	NM_000251.2	117	tgG/tgA	2/16	1	2	FACETS	0.922	0.832	1	1	0.99	1	CLONAL	4	FALSE	1	0.179434731457646	2		565	287	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659952	227659952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	198	658	0	ENST00000305123.5:c.3503G>A	p.Gly1168Glu	p.G1168E	ENST00000305123	NM_005544.2	1168	gGg/gAg	1/2	1	2	FACETS	1	0.965	1	1	0.995	1	CLONAL	3	FALSE	1	0.179434731457646	2		658	693	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662847	227662847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	51	701	1	ENST00000305123.5:c.608C>T	p.Ala203Val	p.A203V	ENST00000305123	NM_005544.2	203	gCc/gTc	1/2	1	2	FACETS	0.745	0.632	0.87	0.745	0.632	0.87	SUBCLONAL	1	FALSE	1	0.179434731457646	2		702	763	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62305416	62305416	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	194	575	0	ENST00000360203.5:c.889C>T	p.Pro297Ser	p.P297S	ENST00000360203	NM_001283009.1	297	Ccg/Tcg	10/35	0.104257974973679	0	FACETS	0.806	0.748	0.866			1	INDETERMINATE	3	FALSE	0	0.179434731457646	0		575	734	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71064745	71064745	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	103	438	2	ENST00000318789.4:c.929G>A	p.Trp310Ter	p.W310*	ENST00000318789	NM_032682.5	310	tGg/tAg	12/21	1	2	FACETS	0.884	0.796	0.976	1	0.99	1	CLONAL	3	FALSE	1	0.179434731457646	2		440	433	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180824	106180826	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	91	448	0	ENST00000380013.4:c.3854_3856del	p.Phe1285del	p.F1285del	ENST00000380013	NM_001127208.2	1284	tcCTTc/tcc	7/11	1	2	FACETS	0.961	0.86	1	1	0.989	1	CLONAL	3	FALSE	1	0.179434731457646	2		448	352	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659222	86659225	+	frameshift_variant	Frame_Shift_Del	DEL	TTAT	TTAT	-	novel	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	50	319	0	ENST00000274376.6:c.1517_1520del	p.Tyr506LeufsTer13	p.Y506Lfs*13	ENST00000274376	NM_002890.2	504	cTTATt/ct	11/25	1	2	FACETS	1	0.887	1	1	0.981	1	CLONAL	3	FALSE	1	0.179434731457646	2		319	180	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675296	176675296	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	31	383	0	ENST00000439151.2:c.4612G>T	p.Gly1538Ter	p.G1538*	ENST00000439151	NM_022455.4	1538	Gga/Tga	11/23	1	2	FACETS	0.759	0.614	0.925	0.759	0.614	0.925	CLONAL	1	FALSE	1	0.179434731457646	2		383	455	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339673	116339673	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753697730	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	110	493	0	ENST00000397752.3:c.535G>A	p.Ala179Thr	p.A179T	ENST00000397752	NM_000245.2	179	Gcc/Acc	2/21	1	2	FACETS	0.881	0.796	0.97	1	0.99	1	CLONAL	3	FALSE	1	0.179434731457646	2		493	464	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372505	55372505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	288	902	0	ENST00000297316.4:c.1195G>A	p.Val399Met	p.V399M	ENST00000297316	NM_022454.3	399	Gtg/Atg	2/2	1	2	FACETS	0.967	0.91	1	1	0.996	1	CLONAL	3	FALSE	1	0.179434731457646	2		902	1106	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136850	69136850	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	141	407	0	ENST00000288368.4:c.4764G>T	p.Gln1588His	p.Q1588H	ENST00000288368	NM_024870.2	1588	caG/caT	39/40	1	2	FACETS	0.977	0.895	1	1	0.993	1	CLONAL	3	FALSE	1	0.179434731457646	2		407	536	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738322	145738322	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1564792721	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	214	812	0	ENST00000428558.2:c.2663A>G	p.Gln888Arg	p.Q888R	ENST00000428558	NM_004260.3	888	cAa/cGa	16/22	1	2	FACETS	1	0.932	1	1	0.995	1	CLONAL	3	FALSE	1	0.179434731457646	2		812	795	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759863	133759863	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768245401	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	48	711	1	ENST00000318560.5:c.2186C>T	p.Thr729Met	p.T729M	ENST00000318560	NM_005157.4	729	aCg/aTg	11/11	0.104257974973679	0	FACETS	0.672	0.567	0.788			1	INDETERMINATE	1	FALSE	0	0.179434731457646	0		712	653	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652243	48652244	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0037042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	125	611	0	ENST00000376670.3:c.917dup	p.Asn306LysfsTer38	p.N306Kfs*38	ENST00000376670	NM_002049.3	305	cga/cgAa	6/6	1	2	FACETS	1	0.965	1	1	0.991	1	CLONAL	2	FALSE	1	0.179434731457646	2		611	617	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0037044-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	582	572	0	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.299744513673349	5	FACETS	1	0.994	1			1	INDETERMINATE	4	TRUE	NA	0.645863398128224	5		572	820	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633551	69633551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037044-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4604	131	0	0	ENST00000334134.2:c.151G>A	p.Ala51Thr	p.A51T	ENST00000334134	NM_005247.2	51	Gcc/Acc	1/3	0.645863398128224	25	FACETS	0.722	0.651	0.798			1	SUBCLONAL	1	TRUE	NA	0.645863398128224	25		0	4735	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376430	118376430	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037044-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	178	712	0	ENST00000534358.1:c.9823G>T	p.Gly3275Trp	p.G3275W	ENST00000534358	NM_005933.3	3275	Ggg/Tgg	27/36	0.64649437399372	3	FACETS	0.999	0.923	1	0.499	0.461	0.539	CLONAL	1	TRUE	1	0.645863398128224	3		712	730	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911675	32911675	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037044-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	127	511	0	ENST00000380152.3:c.3183G>T	p.Lys1061Asn	p.K1061N	ENST00000380152		1061	aaG/aaT	11/27	0.64649437399372	2	FACETS	1	0.972	1	0.568	0.521	0.617	CLONAL	1	TRUE	0	0.645863398128224	2		511	346	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265534	152265535	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAA	novel	NA	P-0037044-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	332	605	2	ENST00000206249.3:c.989_990insAGA	p.Glu330dup	p.E330dup	ENST00000206249	NM_000125.3	330	-/GAA	4/8	0.64649437399372	4	FACETS	1	0.978	1	0.702	0.666	0.737	CLONAL	2	TRUE	1	0.645863398128224	4		607	804	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502222	186502222	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037044-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	144	525	0	ENST00000323963.5:c.31G>A	p.Glu11Lys	p.E11K	ENST00000323963		11	Gaa/Aaa	2/11	0.64649437399372	2	FACETS	1	0.96	1	0.533	0.491	0.577	CLONAL	1	TRUE	0	0.645863398128224	2		525	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0037081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	269	525	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.75985640388966	1	FACETS	0.967	0.922	1	0.967	0.922	1	CLONAL	1	TRUE	0	0.75985640388966	1		525	454	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969370	44969371	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0037081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	170	342	1	ENST00000377967.4:c.4052_4053delinsTT	p.Arg1351Leu	p.R1351L	ENST00000377967	NM_021140.2	1351	cGA/cTT	28/29	0.75985640388966	1	FACETS	0.944	0.888	0.999	0.944	0.888	0.999	CLONAL	1	TRUE	0	0.75985640388966	1		343	294	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	110	345	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.976	1	1	0.991	1	CLONAL	2	TRUE	1	0.432638271732463	2		345	219	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850341	128850341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121918347	NA	P-0037090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	139	499	0	ENST00000249373.3:c.1604G>T	p.Trp535Leu	p.W535L	ENST00000249373	NM_005631.4	535	tGg/tTg	9/12	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.432638271732463	2		499	624	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860747	3860747	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	92	359	0	ENST00000262367.5:c.832C>T	p.Gln278Ter	p.Q278*	ENST00000262367	NM_004380.2	278	Cag/Tag	3/31	1	2	FACETS	0.913	0.815	1	0.913	0.815	1	CLONAL	1	TRUE	1	0.432638271732463	2		359	466	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026154	71026154	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	222	363	0	ENST00000318789.4:c.1468G>T	p.Glu490Ter	p.E490*	ENST00000318789	NM_032682.5	490	Gag/Tag	17/21	1	2	FACETS	0.908	0.852	0.965	1	0.994	1	CLONAL	2	TRUE	1	0.432638271732463	2		363	565	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148544299	148544299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	305	397	0	ENST00000320356.2:c.92G>A	p.Arg31Lys	p.R31K	ENST00000320356	NM_004456.4	31	aGg/aAg	2/20	1	2	FACETS	0.979	0.929	1	1	0.996	1	CLONAL	2	TRUE	1	0.432638271732463	2		397	720	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	100	345	0				ENST00000310581	NM_198253.2	-/1132			0.494994434637841	1	FACETS	0.812	0.739	0.887	0.812	0.739	0.887	CLONAL	1	TRUE	0	0.663603752002861	1		345	248	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0037103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	312	699	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.663603752002861	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.663603752002861	1		699	566	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0037103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	45	206	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.472809627113604	1	FACETS	0.392	0.333	0.457	0.392	0.333	0.457	SUBCLONAL	1	TRUE	0	0.663603752002861	1		206	231	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101007	41101007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375946335	NA	P-0037103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	150	520	0	ENST00000373198.4:c.1349G>A	p.Arg450Gln	p.R450Q	ENST00000373198	NM_133170.3	450	cGa/cAa	8/32	1	2	FACETS	0.829	0.762	0.899	0.829	0.762	0.899	CLONAL	1	TRUE	1	0.663603752002861	2		520	545	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719107	52719107	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	198	579	0	ENST00000322088.6:c.883G>A	p.Glu295Lys	p.E295K	ENST00000322088	NM_014225.5	295	Gag/Aag	7/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.663603752002861	2		579	559	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928076	178928084	+	inframe_deletion	In_Frame_Del	DEL	TTAGAAGAT	TTAGAAGAT	-	novel	NA	P-0037103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	367	504	0	ENST00000263967.3:c.1356_1364del	p.Glu453_Leu455del	p.E453_L455del	ENST00000263967	NM_006218.2	452	TTAGAAGAT/-	8/21	0.492635862840467	4	FACETS	1	0.984	1	0.712	0.679	0.746	CLONAL	2	TRUE	1	0.663603752002861	4		504	861	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137727	64137727	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	212	777	0	ENST00000334205.4:c.1828C>T	p.Gln610Ter	p.Q610*	ENST00000334205	NM_003942.2	610	Cag/Tag	15/17	0.427711922434241	1	FACETS	0.607	0.566	0.649	0.607	0.566	0.649	SUBCLONAL	1	TRUE	0	0.663603752002861	1		777	703	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258563	16258563	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	176	396	0	ENST00000375759.3:c.5828C>G	p.Ala1943Gly	p.A1943G	ENST00000375759	NM_015001.2	1943	gCg/gGg	11/15	0.436181979547806	3	FACETS	1	0.99	1			1	CLONAL	1	TRUE	NA	0.663603752002861	3		396	486	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989422	7989422	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs779456276	NA	P-0037103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	30	598	0	ENST00000319144.4:c.264G>T	p.Gln88His	p.Q88H	ENST00000319144	NM_001139.2	88	caG/caT	2/15	0.663603752002861	1	FACETS	0.134	0.108	0.164	0.134	0.108	0.164	SUBCLONAL	1	TRUE	0	0.663603752002861	1		598	450	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564752	86564753	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CATT	novel	NA	P-0037103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	137	595	0	ENST00000274376.6:c.486_487insTTCA	p.Glu163PhefsTer18	p.E163Ffs*18	ENST00000274376	NM_002890.2	162	cca/cCATTca	1/25	0.493171191542963	1	FACETS	0.471	0.43	0.514	0.471	0.43	0.514	SUBCLONAL	1	TRUE	0	0.663603752002861	1		595	586	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627278	86627278	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	149	396	0	ENST00000274376.6:c.655del	p.Ser219HisfsTer6	p.S219Hfs*6	ENST00000274376	NM_002890.2	218	cTt/ct	2/25	0.493171191542963	1	FACETS	0.606	0.558	0.656	0.606	0.558	0.656	SUBCLONAL	1	TRUE	0	0.663603752002861	1		396	495	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	228	345	0				ENST00000310581	NM_198253.2	-/1132			0.546402803698277	1	FACETS	0.745	0.707	0.784	0.745	0.707	0.784	SUBCLONAL	1	TRUE	0	0.86544191009562	1		345	401	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0037112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	425	666	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.810077393999551	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.86544191009562	1		666	543	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717629	89717629	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1554825165	NA	P-0037112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	268	419	0	ENST00000371953.3:c.654C>A	p.Cys218Ter	p.C218*	ENST00000371953	NM_000314.4	218	tgC/tgA	7/9	0.86544191009562	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.86544191009562	1		419	341	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22153396	22153396	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	244	409	0	ENST00000215832.6:c.514C>T	p.Arg172Cys	p.R172C	ENST00000215832	NM_002745.4	172	Cgt/Tgt	4/9	NA	2	FACETS	0.991	0.934	1			1	INDETERMINATE	1	TRUE	NA	0.86544191009562	2		409	569	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493452	56493452	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	92	428	0	ENST00000267101.3:c.2860A>T	p.Ile954Phe	p.I954F	ENST00000267101	NM_001982.3	954	Att/Ttt	24/28	1	2	FACETS	0.894	0.798	0.995	0.894	0.798	0.995	CLONAL	1	TRUE	1	0.447663929838753	2		428	460	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191499	10191500	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	novel	NA	P-0037119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	127	509	0	ENST00000256474.2:c.495_497dup	p.Val166dup	p.V166dup	ENST00000256474	NM_000551.3	166	-/GTT	3/3	0.447663929838753	1	FACETS	0.983	0.897	1	0.983	0.897	1	CLONAL	1	TRUE	0	0.447663929838753	1		509	448	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807150	1807150	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs762079212	NA	P-0037119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	151	873	0	ENST00000260795.2:c.1481T>C	p.Ile494Thr	p.I494T	ENST00000260795		494	aTt/aCt	10/17	1	2	FACETS	0.904	0.828	0.984	0.904	0.828	0.984	CLONAL	1	TRUE	1	0.447663929838753	2		873	746	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581157	48581157	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1555685624	NA	P-0040956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	104	309	0	ENST00000342988.3:c.461C>G	p.Ser154Ter	p.S154*	ENST00000342988	NM_005359.5	154	tCa/tGa	5/12	0.72773331043718	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.72773331043718	1		309	154	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812293	212812293	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569995088	NA	P-0040956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	121	362	0	ENST00000342788.4:c.283C>T	p.Arg95Cys	p.R95C	ENST00000342788	NM_005235.2	95	Cgt/Tgt	3/28	1	2	FACETS	0.836	0.762	0.912	0.836	0.762	0.912	CLONAL	1	TRUE	1	0.72773331043718	2		362	398	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332619	153332619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	101	410	1	ENST00000281708.4:c.337G>A	p.Glu113Lys	p.E113K	ENST00000281708	NM_033632.3	113	Gag/Aag	2/12	1	2	FACETS	0.637	0.572	0.704	0.637	0.572	0.704	SUBCLONAL	1	TRUE	1	0.72773331043718	2		411	436	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627760	14627760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	259	735	0	ENST00000254322.2:c.310G>A	p.Glu104Lys	p.E104K	ENST00000254322	NM_006145.1	104	Gag/Aag	2/3	1	2	FACETS	0.954	0.898	1	0.954	0.898	1	CLONAL	1	TRUE	1	0.72773331043718	2		735	746	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906804	32906804	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760815829	NA	P-0040956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	252	694	2	ENST00000380152.3:c.1189C>T	p.Gln397Ter	p.Q397*	ENST00000380152		397	Caa/Taa	10/27	1	2	FACETS	0.973	0.915	1	0.973	0.915	1	CLONAL	1	TRUE	1	0.72773331043718	2		696	712	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839802	27839802	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	201	624	0	ENST00000328488.2:c.292G>C	p.Glu98Gln	p.E98Q	ENST00000328488	NM_003533.2	98	Gag/Cag	1/1	0.624364447650288	3	FACETS	1	0.986	1	0.405	0.377	0.434	CLONAL	1	TRUE	0	0.72773331043718	3		624	620	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220564	98220564	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	137	494	0	ENST00000331920.6:c.2899G>A	p.Glu967Lys	p.E967K	ENST00000331920	NM_000264.3	967	Gag/Aag	18/24	1	2	FACETS	0.932	0.856	1	0.932	0.856	1	CLONAL	1	TRUE	1	0.72773331043718	2		494	404	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420241	49420241	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	281	755	0	ENST00000301067.7:c.15508C>T	p.Gln5170Ter	p.Q5170*	ENST00000301067	NM_003482.3	5170	Cag/Tag	48/54	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.72773331043718	2		755	752	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43817889	43817889	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	225	502	0	ENST00000372470.3:c.1568G>C	p.Arg523Thr	p.R523T	ENST00000372470	NM_005373.2	523	aGa/aCa	11/12	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.72773331043718	2		502	524	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94170347	94170347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	125	306	0	ENST00000323929.3:c.1922C>T	p.Ser641Leu	p.S641L	ENST00000323929	NM_005591.3	641	tCa/tTa	17/20	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.72773331043718	2		306	332	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420640	49420640	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	223	709	0	ENST00000301067.7:c.15109G>A	p.Glu5037Lys	p.E5037K	ENST00000301067	NM_003482.3	5037	Gag/Aag	48/54	1	2	FACETS	0.937	0.877	0.998	0.937	0.877	0.998	CLONAL	1	TRUE	1	0.72773331043718	2		709	654	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421666	49421666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	249	664	0	ENST00000301067.7:c.14563G>A	p.Asp4855Asn	p.D4855N	ENST00000301067	NM_003482.3	4855	Gat/Aat	47/54	1	2	FACETS	0.891	0.836	0.947	0.891	0.836	0.947	CLONAL	1	TRUE	1	0.72773331043718	2		664	768	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435743	49435752	+	frameshift_variant	Frame_Shift_Del	DEL	TTCATGATTT	TTCATGATTT	-	novel	NA	P-0040956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	242	658	0	ENST00000301067.7:c.6131_6140del	p.Gln2044ArgfsTer47	p.Q2044Rfs*47	ENST00000301067	NM_003482.3	2044	cAAATCATGAAg/cg	29/54	1	2	FACETS	0.937	0.879	0.995	0.937	0.879	0.995	CLONAL	1	TRUE	1	0.72773331043718	2		658	710	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422121	81422121	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	130	559	0	ENST00000298171.2:c.97C>G	p.Gln33Glu	p.Q33E	ENST00000298171	NM_000369.2	33	Cag/Gag	1/10	0.72773331043718	3	FACETS	0.567	0.514	0.623	0.284	0.257	0.312	SUBCLONAL	1	TRUE	1	0.72773331043718	3		559	859	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41276071	41276071	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	186	518	0	ENST00000357654.3:c.43A>T	p.Ile15Phe	p.I15F	ENST00000357654	NM_007294.3	15	Att/Ttt	2/23	1	2	FACETS	0.954	0.887	1	0.954	0.887	1	CLONAL	1	TRUE	1	0.72773331043718	2		518	536	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96931001	96931001	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	191	493	0	ENST00000258439.3:c.119C>G	p.Ser40Cys	p.S40C	ENST00000258439	NM_001193304.2	40	tCt/tGt	2/4	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.72773331043718	2		493	513	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114206	73114206	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	190	387	0	ENST00000356692.5:c.842C>A	p.Ser281Ter	p.S281*	ENST00000356692		281	tCa/tAa	8/9	0.72773331043718	1	FACETS	0.977	0.921	1	0.977	0.921	1	CLONAL	1	TRUE	0	0.72773331043718	1		387	340	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114701	73114701	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	155	400	0	ENST00000356692.5:c.1082C>G	p.Ser361Cys	p.S361C	ENST00000356692		361	tCt/tGt	9/9	0.72773331043718	1	FACETS	0.993	0.93	1	0.993	0.93	1	CLONAL	1	TRUE	0	0.72773331043718	1		400	273	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947226	178947226	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	100	187	0	ENST00000263967.3:c.2662G>C	p.Glu888Gln	p.E888Q	ENST00000263967	NM_006218.2	888	Gaa/Caa	18/21	0.72773331043718	3	FACETS	1	0.94	1	0.529	0.477	0.584	CLONAL	1	TRUE	1	0.72773331043718	3		187	354	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6045603	6045603	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	163	293	0	ENST00000265849.7:c.83C>G	p.Ser28Cys	p.S28C	ENST00000265849	NM_000535.5	28	tCt/tGt	2/15	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.72773331043718	2		293	448	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994269	21994269	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	241	689	0	ENST00000579755.1:c.62G>T	p.Arg21Met	p.R21M	ENST00000579755		21	aGg/aTg	1/3	0.72773331043718				0.919	1				CLONAL	1	TRUE	1	0.72773331043718	3		689	919	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158124	27158124	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	416	472	0	ENST00000380036.4:c.348G>T	p.Met116Ile	p.M116I	ENST00000380036	NM_000459.3	116	atG/atT	2/23	0.72773331043718	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.72773331043718	3		472	725	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760382	133760382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	198	736	0	ENST00000318560.5:c.2705C>T	p.Pro902Leu	p.P902L	ENST00000318560	NM_005157.4	902	cCa/cTa	11/11	0.609471015152781	3	FACETS	1	0.965	1	0.53	0.493	0.569	CLONAL	1	TRUE	1	0.72773331043718	3		736	700	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412609	139412609	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	256	670	0	ENST00000277541.6:c.1235A>T	p.Asp412Val	p.D412V	ENST00000277541	NM_017617.3	412	gAc/gTc	7/34	0.72773331043718	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.72773331043718	1		670	413	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692988	89692998	+	protein_altering_variant	In_Frame_Del	DEL	GTAAGGACCAG	GTAAGGACCAG	AT	novel	NA	P-0040972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	201	371	0	ENST00000371953.3:c.472_482delinsAT	p.Val158_Arg161delinsIle	p.V158_R161delinsI	ENST00000371953	NM_000314.4	158	GTAAGGACCAGa/ATa	5/9	0.578350443597767	2	FACETS	0.839	0.789	0.89	0.839	0.789	0.89	CLONAL	2	TRUE	0	0.578350443597767	2		371	414	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038599	14038599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	156	332	0	ENST00000311895.7:c.1924G>A	p.Val642Ile	p.V642I	ENST00000311895	NM_005236.2	642	Gtc/Atc	10/11	0.180882541300462	6	FACETS	1	0.979	1	0.785	0.724	0.848	INDETERMINATE	2	TRUE	3	0.578350443597767	6		332	494	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665757	29665757	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs772295894	NA	P-0040972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	196	262	0	ENST00000356175.3:c.6792C>G	p.Tyr2264Ter	p.Y2264*	ENST00000356175	NM_000267.3	2264	taC/taG	45/57	0.45652837032758	4	FACETS	0.981	0.916	1	0.981	0.916	1	CLONAL	2	TRUE	2	0.578350443597767	4		262	545	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778749	76778749	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	173	354	0	ENST00000373344.5:c.6830A>C	p.Glu2277Ala	p.E2277A	ENST00000373344	NM_000489.3	2277	gAg/gCg	31/35	0.525887676934415	2	FACETS	0.857	0.802	0.912	0.857	0.802	0.912	CLONAL	2	TRUE	0	0.578350443597767	2		354	349	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566716	212566716	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	26	273	0	ENST00000342788.4:c.1465G>T	p.Asp489Tyr	p.D489Y	ENST00000342788	NM_005235.2	489	Gac/Tac	12/28	0.237870558636152	2	FACETS	0.942	0.76	1	0.942	0.76	1	CLONAL	2	FALSE	0	0.237870558636152	2		273	116	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793165	42793165	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1135401823	NA	P-0040975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	36	790	0	ENST00000575354.2:c.1057C>T	p.Arg353Ter	p.R353*	ENST00000575354	NM_015125.3	353	Cga/Tga	7/20	0.237870558636152	4	FACETS	0.552	0.452	0.664	0.184	0.15	0.222	SUBCLONAL	1	FALSE	1	0.237870558636152	4		790	679	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187467	32187467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1255759249	NA	P-0040975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	51	675	3	ENST00000375023.3:c.1412G>A	p.Arg471His	p.R471H	ENST00000375023	NM_004557.3	471	cGt/cAt	8/30	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	FALSE	1	0.237870558636152	2		678	427	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883969	37883969	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14349	1897	673	0	ENST00000269571.5:c.3440C>A	p.Pro1147His	p.P1147H	ENST00000269571		1147	cCc/cAc	27/27	0.237870558636152	91	FACETS	1	0.991	1			1	CLONAL	11	FALSE	NA	0.237870558636152	91		673	16246	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523097	25523097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	88	496	0	ENST00000264709.3:c.88G>A	p.Glu30Lys	p.E30K	ENST00000264709	NM_175629.2	30	Gag/Aag	3/23	0.237870558636152	2	FACETS	0.941	0.84	1	0.941	0.84	1	CLONAL	2	FALSE	0	0.237870558636152	2		496	393	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460572	8460572	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0040975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	15	316	0	ENST00000356435.5:c.3715-1G>C		p.X1239_splice	ENST00000356435		1239			1	2	FACETS	0.65	0.477	0.857	0.65	0.477	0.857	SUBCLONAL	1	FALSE	1	0.237870558636152	2		316	194	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974830	15974830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	128	407	0	ENST00000268712.3:c.4045C>T	p.Arg1349Cys	p.R1349C	ENST00000268712	NM_006311.3	1349	Cgt/Tgt	30/46	0.472809564165042	4	FACETS	1	0.971	1	0.388	0.353	0.426	CLONAL	1	TRUE	1	0.537059024476873	4		407	629	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456486	29456486	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	113	676	0	ENST00000389048.3:c.2432T>A	p.Val811Glu	p.V811E	ENST00000389048	NM_004304.4	811	gTg/gAg	14/29	0.272675761468377	4	FACETS	0.714	0.642	0.791	0.357	0.321	0.396	INDETERMINATE	1	TRUE	2	0.537059024476873	4		676	906	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0041054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	35	431	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	0.832	0.681	1	0.832	0.681	1	CLONAL	1	TRUE	1	0.16	2		431	526	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0041054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	33	304	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.16	2		304	376	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37622790	37622790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	59	700	0	ENST00000249071.6:c.502G>A	p.Val168Met	p.V168M	ENST00000249071	NM_002872.4	168	Gtg/Atg	6/7	1	2	FACETS	0.847	0.727	0.978	0.847	0.727	0.978	CLONAL	1	TRUE	1	0.16	2		700	871	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058747	180058748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755445139	NA	P-0041062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	97	726	4	ENST00000261937.6:c.89dup	p.Thr31AspfsTer15	p.T31Dfs*15	ENST00000261937	NM_182925.4	30	ccg/ccCg	2/30	NA	2	FACETS	0.989	0.89	1			1	INDETERMINATE	1	TRUE	NA	0.571960650685363	2		730	343	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618716	37618719	+	frameshift_variant	Frame_Shift_Del	DEL	AAAA	AAAA	-	novel	NA	P-0041062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	107	412	0	ENST00000447079.4:c.394_397del	p.Lys132AlafsTer11	p.K132Afs*11	ENST00000447079	NM_015083.1	131	gAAAAa/ga	1/14	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.571960650685363	2		412	351	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462214	120462214	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	79	437	0	ENST00000256646.2:c.5502G>T	p.Leu1834Phe	p.L1834F	ENST00000256646	NM_024408.3	1834	ttG/ttT	31/34	0.53845728182768	5	FACETS	1	0.945	1			1	CLONAL	1	TRUE	NA	0.571960650685363	5		437	458	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619280	37619281	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0041062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	151	473	0	ENST00000447079.4:c.957_958del	p.Tyr319Ter	p.Y319*	ENST00000447079	NM_015083.1	319	tAC/t	1/14	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.571960650685363	2		473	411	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	100	345	0				ENST00000310581	NM_198253.2	-/1132			0.290498646585931	1	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	0	0.290498646585931	1		345	580	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555057	106555057	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs940196192	NA	P-0041068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	210	609	0	ENST00000369096.4:c.2174G>A	p.Arg725Gln	p.R725Q	ENST00000369096	NM_001198.3	725	cGa/cAa	7/7	0.281050369120779	2	FACETS	0.935	0.871	1	0.935	0.871	1	CLONAL	2	TRUE	0	0.290498646585931	2		609	773	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230613	46230613	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	132	502	0	ENST00000334344.6:c.862C>T	p.Gln288Ter	p.Q288*	ENST00000334344	NM_152641.2	288	Cag/Tag	8/21	0.116886561889618	3	FACETS	1	0.97	1			1	INDETERMINATE	2	TRUE	NA	0.290498646585931	3		502	459	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658412	117658412	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	100	668	0	ENST00000368508.3:c.5171C>T	p.Ser1724Leu	p.S1724L	ENST00000368508	NM_002944.2	1724	tCa/tTa	31/43	0.281050369120779	2	FACETS	0.918	0.827	1	0.918	0.827	1	CLONAL	2	TRUE	0	0.290498646585931	2		668	375	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524329	148524329	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	155	393	0	ENST00000320356.2:c.655C>T	p.Pro219Ser	p.P219S	ENST00000320356	NM_004456.4	219	Cct/Tct	7/20	0.290498646585931	6	FACETS	1	0.971	1	0.874	0.81	0.939	CLONAL	4	TRUE	1	0.290498646585931	6		393	386	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857458	9857458	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759696882	NA	P-0041068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	88	644	0	ENST00000330684.3:c.3943G>A	p.Asp1315Asn	p.D1315N	ENST00000330684	NM_001134407.1	1315	Gac/Aac	13/13	0.281050369120779	2	FACETS	1	0.894	1	0.504	0.447	0.565	CLONAL	1	TRUE	0	0.290498646585931	2		644	601	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156495	55156495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	74	462	0	ENST00000257290.5:c.2896C>T	p.His966Tyr	p.H966Y	ENST00000257290	NM_006206.4	966	Cac/Tac	22/23	1	2	FACETS	0.93	0.815	1	0.93	0.815	1	CLONAL	1	TRUE	1	0.290498646585931	2		462	548	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123159736	123159736	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1251136516	NA	P-0041068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	31	414	0	ENST00000218089.9:c.91G>A	p.Glu31Lys	p.E31K	ENST00000218089	NM_001042749.1	31	Gaa/Aaa	4/35	0.225206049594795	3	FACETS	0.759	0.615	0.921	0.38	0.307	0.461	CLONAL	1	TRUE	1	0.290498646585931	3		414	322	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197366	94197366	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766182900	NA	P-0041068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	105	628	0	ENST00000323929.3:c.1138C>T	p.Arg380Cys	p.R380C	ENST00000323929	NM_005591.3	380	Cgc/Tgc	11/20	0.24897157587014	2	FACETS	0.85	0.767	0.938	0.85	0.767	0.938	CLONAL	2	TRUE	0	0.290498646585931	2		628	425	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319898	8319898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	97	412	0	ENST00000356435.5:c.5603G>A	p.Gly1868Glu	p.G1868E	ENST00000356435		1868	gGa/gAa	34/35	0.24897157587014	2	FACETS	1	0.981	1	0.744	0.667	0.825	CLONAL	1	TRUE	0	0.290498646585931	2		412	449	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98009731	98009731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	29	387	0	ENST00000289081.3:c.233C>T	p.Pro78Leu	p.P78L	ENST00000289081	NM_000136.2	78	cCt/cTt	3/15	1	2	FACETS	0.723	0.582	0.883	0.723	0.582	0.883	SUBCLONAL	1	TRUE	1	0.290498646585931	2		387	276	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012419	29012419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867762505	NA	P-0041068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	43	651	0	ENST00000282397.4:c.452G>A	p.Gly151Glu	p.G151E	ENST00000282397	NM_002019.4	151	gGa/gAa	4/30	0.290498646585931	1	FACETS	0.534	0.447	0.63	0.534	0.447	0.63	SUBCLONAL	1	TRUE	0	0.290498646585931	1		651	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs11575997	NA	P-0041068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	204	429	0	ENST00000269305.4:c.993+1G>T		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.281050369120779	2	FACETS	0.896	0.833	0.961	0.896	0.833	0.961	CLONAL	2	TRUE	0	0.290498646585931	2		429	784	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128246829	128246829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1389464216	NA	P-0041068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	104	687	0	ENST00000265960.3:c.1100C>T	p.Ser367Leu	p.S367L	ENST00000265960	NM_001006617.1	367	tCg/tTg	9/12	1	2	FACETS	0.876	0.784	0.974	0.876	0.784	0.974	CLONAL	1	TRUE	1	0.290498646585931	2		687	817	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298782	46298782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	74	437	0	ENST00000334344.6:c.5429C>T	p.Thr1810Ile	p.T1810I	ENST00000334344	NM_152641.2	1810	aCc/aTc	21/21	0.116886561889618	3	FACETS	0.947	0.837	1			1	INDETERMINATE	2	TRUE	NA	0.290498646585931	3		437	308	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548940	29548940	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	33	425	0	ENST00000356175.3:c.1714G>T	p.Glu572Ter	p.E572*	ENST00000356175	NM_000267.3	572	Gag/Tag	15/57	0.281050369120779	2	FACETS	1	0.871	1	0.538	0.442	0.645	CLONAL	1	TRUE	0	0.290498646585931	2		425	211	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646270	3646270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780697002	NA	P-0041068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	146	997	0	ENST00000294008.3:c.1808C>T	p.Ser603Leu	p.S603L	ENST00000294008	NM_032444.2	603	tCg/tTg	8/15	0.290498646585931	1	FACETS	0.921	0.84	1	0.921	0.84	1	CLONAL	1	TRUE	0	0.290498646585931	1		997	933	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325151	39325152	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0041068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	266	837	3	ENST00000373001.3:c.167dup	p.Ala57ArgfsTer2	p.A57Rfs*2	ENST00000373001	NM_022157.3	56	ggc/ggGc	1/7	0.290498646585931	3	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	1	0.290498646585931	3		840	1044	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557720	21557720	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	147	817	0	ENST00000382592.4:c.2125C>T	p.Gln709Ter	p.Q709*	ENST00000382592	NM_014572.2	709	Cag/Tag	5/8	0.290498646585931	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.290498646585931	1		817	849	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562373	21562373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	145	789	0	ENST00000382592.4:c.1546C>T	p.Pro516Ser	p.P516S	ENST00000382592	NM_014572.2	516	Ccg/Tcg	4/8	0.290498646585931	1	FACETS	0.999	0.912	1	0.999	0.912	1	CLONAL	1	TRUE	0	0.290498646585931	1		789	854	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857889	9857889	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	110	705	0	ENST00000330684.3:c.3512C>T	p.Pro1171Leu	p.P1171L	ENST00000330684	NM_001134407.1	1171	cCc/cTc	13/13	0.281050369120779	2	FACETS	0.883	0.792	0.978	0.441	0.396	0.489	CLONAL	1	TRUE	0	0.290498646585931	2		705	858	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273870	10273870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	188	873	0	ENST00000330684.3:c.399G>A	p.Met133Ile	p.M133I	ENST00000330684	NM_001134407.1	133	atG/atA	2/13	0.281050369120779	2	FACETS	1	0.985	1	0.637	0.588	0.688	CLONAL	1	TRUE	0	0.290498646585931	2		873	1016	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925108	81925108	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764885126	NA	P-0041068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	187	592	0	ENST00000359376.3:c.899G>A	p.Ser300Asn	p.S300N	ENST00000359376	NM_002661.3	300	aGc/aAc	11/33	0.281050369120779	2	FACETS	0.889	0.824	0.957	0.889	0.824	0.957	CLONAL	2	TRUE	0	0.290498646585931	2		592	724	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222900	5222900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747443047	NA	P-0041068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	152	727	0	ENST00000357368.4:c.2903C>T	p.Ala968Val	p.A968V	ENST00000357368	NM_002850.3	968	gCc/gTc	18/38	0.286766915228707	3	FACETS	1	0.979	1	0.615	0.561	0.67	CLONAL	1	TRUE	1	0.290498646585931	3		727	975	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367899	15367899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	140	1010	0	ENST00000263377.2:c.1427C>T	p.Pro476Leu	p.P476L	ENST00000263377	NM_058243.2	476	cCc/cTc	8/20	0.286766915228707	3	FACETS	0.956	0.868	1	0.478	0.434	0.524	CLONAL	1	TRUE	1	0.290498646585931	3		1010	1155	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46588162	46588162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1202845001	NA	P-0041068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	102	831	0	ENST00000263734.3:c.712C>T	p.Pro238Ser	p.P238S	ENST00000263734	NM_001430.4	238	Ccc/Tcc	6/16	1	2	FACETS	0.925	0.827	1	0.925	0.827	1	CLONAL	1	TRUE	1	0.290498646585931	2		831	759	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324279	62324279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770018942	NA	P-0041068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	337	1052	1	ENST00000360203.5:c.2774C>T	p.Ser925Phe	p.S925F	ENST00000360203	NM_001283009.1	925	tCc/tTc	29/35	0.246135051536345	2	FACETS	0.988	0.935	1	0.988	0.935	1	CLONAL	2	TRUE	0	0.290498646585931	2		1053	1174	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806210	1806210	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	154	964	0	ENST00000260795.2:c.1229C>T	p.Thr410Ile	p.T410I	ENST00000260795		410	aCc/aTc	8/17	1	2	FACETS	0.969	0.886	1	0.969	0.886	1	CLONAL	1	TRUE	1	0.290498646585931	2		964	1094	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139721	55139721	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	78	489	0	ENST00000257290.5:c.1382C>T	p.Ser461Phe	p.S461F	ENST00000257290	NM_006206.4	461	tCc/tTc	10/23	1	2	FACETS	0.891	0.783	1	0.891	0.783	1	CLONAL	1	TRUE	1	0.290498646585931	2		489	603	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946149	55946149	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	72	409	0	ENST00000263923.4:c.4030C>T	p.Gln1344Ter	p.Q1344*	ENST00000263923	NM_002253.2	1344	Cag/Tag	30/30	1	2	FACETS	0.892	0.78	1	0.892	0.78	1	CLONAL	1	TRUE	1	0.290498646585931	2		409	556	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271241	38271241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	143	1028	0	ENST00000425967.3:c.2467G>A	p.Glu823Lys	p.E823K	ENST00000425967	NM_001174067.1	823	Gag/Aag	19/19	0.290498646585931	1	FACETS	0.873	0.795	0.955	0.873	0.795	0.955	CLONAL	1	TRUE	0	0.290498646585931	1		1028	964	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564657	139564657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	208	1131	0	ENST00000308874.7:c.446C>T	p.Pro149Leu	p.P149L	ENST00000308874		149	cCc/cTc	7/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.290498646585931	2		1131	1290	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0041122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	17	304	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	0.212	0.157	0.277	0.212	0.157	0.277	SUBCLONAL	1	TRUE	1	0.326858067540804	2		304	491	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913471	NA	P-0041122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	50	789	0	ENST00000269571.5:c.2329G>C	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ctg	20/27	1	2	FACETS	0.305	0.258	0.358	0.305	0.258	0.358	SUBCLONAL	1	TRUE	1	0.326858067540804	2		789	1003	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609813	81609813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs925961475	NA	P-0041122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	37	360	1	ENST00000298171.2:c.1411G>A	p.Ala471Thr	p.A471T	ENST00000298171	NM_000369.2	471	Gcc/Acc	10/10	1	2	FACETS	0.511	0.421	0.612	0.511	0.421	0.612	SUBCLONAL	1	TRUE	1	0.326858067540804	2		361	443	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643808	38643808	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	79	679	0	ENST00000299084.4:c.1278C>A	p.Cys426Ter	p.C426*	ENST00000299084	NM_152594.2	426	tgC/tgA	7/7	1	2	FACETS	0.558	0.489	0.631	0.558	0.489	0.631	SUBCLONAL	1	TRUE	1	0.326858067540804	2		679	867	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	67	345	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.841	0.733	0.958	0.841	0.733	0.958	CLONAL	1	TRUE	1	0.348511944458212	2		345	457	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	25	306	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	0.0544352156953047	3	FACETS	0.334	0.263	0.417	0.167	0.131	0.209	INDETERMINATE	1	TRUE	1	0.348511944458212	3		306	504	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180653	32180653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	119	696	0	ENST00000375023.3:c.2474C>T	p.Pro825Leu	p.P825L	ENST00000375023	NM_004557.3	825	cCt/cTt	16/30	1	2	FACETS	0.791	0.714	0.873	0.791	0.714	0.873	SUBCLONAL	1	TRUE	1	0.348511944458212	2		696	863	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560902	9560902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756198440	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	46	573	0	ENST00000353224.5:c.880G>A	p.Glu294Lys	p.E294K	ENST00000353224	NM_177990.2	294	Gaa/Aaa	4/10	1	2	FACETS	0.388	0.326	0.457	0.388	0.326	0.457	SUBCLONAL	1	TRUE	1	0.348511944458212	2		573	680	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549725	187549725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199516712	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	29	455	2	ENST00000441802.2:c.4516C>T	p.Arg1506Cys	p.R1506C	ENST00000441802	NM_005245.3	1506	Cgt/Tgt	8/27	1	2	FACETS	0.323	0.258	0.396	0.323	0.258	0.396	SUBCLONAL	1	TRUE	1	0.348511944458212	2		457	516	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517724	187517724	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	14	235	0	ENST00000441802.2:c.12970C>T	p.Gln4324Ter	p.Q4324*	ENST00000441802	NM_005245.3	4324	Cag/Tag	25/27	1	2	FACETS	0.338	0.244	0.451	0.338	0.244	0.451	SUBCLONAL	1	TRUE	1	0.348511944458212	2		235	238	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442854	187442854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867576130	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	28	418	0	ENST00000232014.4:c.1852C>T	p.Arg618Cys	p.R618C	ENST00000232014	NM_001130845.1	618	Cgt/Tgt	9/10	1	2	FACETS	0.311	0.248	0.383	0.311	0.248	0.383	SUBCLONAL	1	TRUE	1	0.348511944458212	2		418	517	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681434	88681434	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782496	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	52	641	0	ENST00000372037.3:c.1324C>T	p.Arg442Cys	p.R442C	ENST00000372037	NM_004329.2	442	Cgt/Tgt	11/13	1	2	FACETS	0.373	0.317	0.436	0.373	0.317	0.436	SUBCLONAL	1	TRUE	1	0.348511944458212	2		641	799	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164832	47164832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1017636782	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	57	311	0	ENST00000409792.3:c.1294C>T	p.Arg432Cys	p.R432C	ENST00000409792	NM_014159.6	432	Cgt/Tgt	3/21	1	2	FACETS	0.79	0.68	0.91	0.79	0.68	0.91	CLONAL	1	TRUE	1	0.348511944458212	2		311	414	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031973	26031973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	51	376	0	ENST00000244661.2:c.316G>A	p.Glu106Lys	p.E106K	ENST00000244661	NM_003537.3	106	Gag/Aag	1/1	1	2	FACETS	0.555	0.472	0.647	0.555	0.472	0.647	SUBCLONAL	1	TRUE	1	0.348511944458212	2		376	527	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089494	27089494	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	52	727	0	ENST00000324856.7:c.2450C>T	p.Ala817Val	p.A817V	ENST00000324856	NM_006015.4	817	gCc/gTc	8/20	0.348511944458212	3	FACETS	0.358	0.304	0.419	0.179	0.152	0.21	SUBCLONAL	1	TRUE	1	0.348511944458212	3		727	978	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201807	102201807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	79	411	0	ENST00000263464.3:c.1159G>A	p.Glu387Lys	p.E387K	ENST00000263464	NM_001165.4	387	Gaa/Aaa	6/9	1	2	FACETS	0.988	0.872	1	0.988	0.872	1	CLONAL	1	TRUE	1	0.348511944458212	2		411	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578479	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	71	917	3	ENST00000269305.4:c.451_452delinsTT	p.Pro151Phe	p.P151F	ENST00000269305	NM_001126112.2	151	CCc/TTc	5/11	1	2	FACETS	0.388	0.337	0.443	0.388	0.337	0.443	SUBCLONAL	1	TRUE	1	0.348511944458212	2		920	1050	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462683	29462683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766541301	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	75	710	0	ENST00000389048.3:c.2218G>A	p.Gly740Arg	p.G740R	ENST00000389048	NM_004304.4	740	Gga/Aga	13/29	0.0544352156953047	3	FACETS	0.567	0.495	0.644	0.283	0.247	0.322	INDETERMINATE	1	TRUE	1	0.348511944458212	3		710	892	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577527	7577527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	110	688	0	ENST00000269305.4:c.754C>T	p.Leu252Phe	p.L252F	ENST00000269305	NM_001126112.2	252	Ctc/Ttc	7/11	1	2	FACETS	0.758	0.68	0.84	0.758	0.68	0.84	SUBCLONAL	1	TRUE	1	0.348511944458212	2		688	833	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740479	58740479	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	56	547	0	ENST00000305921.3:c.1384C>T	p.Gln462Ter	p.Q462*	ENST00000305921	NM_003620.3	462	Caa/Taa	6/6	1	2	FACETS	0.446	0.382	0.517	0.446	0.382	0.517	SUBCLONAL	1	TRUE	1	0.348511944458212	2		547	720	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781428	135781428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	58	557	1	ENST00000298552.3:c.1537C>T	p.Pro513Ser	p.P513S	ENST00000298552	NM_001162426.1	513	Cca/Tca	15/23	1	2	FACETS	0.528	0.453	0.61	0.528	0.453	0.61	SUBCLONAL	1	TRUE	1	0.348511944458212	2		558	630	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235849	108235849	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	63	403	0	ENST00000278616.4:c.8891C>T	p.Pro2964Leu	p.P2964L	ENST00000278616	NM_000051.3	2964	cCt/cTt	62/63	1	2	FACETS	0.654	0.566	0.749	0.654	0.566	0.749	SUBCLONAL	1	TRUE	1	0.348511944458212	2		403	553	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874140	155874140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	205	629	1	ENST00000368323.3:c.391C>T	p.Leu131Phe	p.L131F	ENST00000368323	NM_006912.5	131	Ctt/Ttt	5/6	0.348511944458212	3	FACETS	1	0.989	1	0.678	0.628	0.729	CLONAL	1	TRUE	1	0.348511944458212	3		630	1019	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257832	198257832	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	35	494	0	ENST00000335508.6:c.3620C>T	p.Ser1207Leu	p.S1207L	ENST00000335508	NM_012433.2	1207	tCg/tTg	24/25	0.0544352156953047	3	FACETS	0.339	0.277	0.409	0.169	0.138	0.205	INDETERMINATE	1	TRUE	1	0.348511944458212	3		494	696	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845580	151845580	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1287135873	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	93	697	1	ENST00000262189.6:c.13432C>T	p.Arg4478Ter	p.R4478*	ENST00000262189	NM_170606.2	4478	Cga/Tga	52/59	0.0878752219269328	4	FACETS	0.735	0.652	0.824	0.368	0.326	0.412	INDETERMINATE	1	TRUE	2	0.348511944458212	4		698	979	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858006	9858006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	35	606	0	ENST00000330684.3:c.3395C>T	p.Pro1132Leu	p.P1132L	ENST00000330684	NM_001134407.1	1132	cCa/cTa	13/13	1	2	FACETS	0.327	0.267	0.395	0.327	0.267	0.395	SUBCLONAL	1	TRUE	1	0.348511944458212	2		606	614	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578476	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	131	929	1	ENST00000269305.4:c.454_455delinsTT	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	CCg/TTg	5/11	1	2	FACETS	0.733	0.664	0.806	0.733	0.664	0.806	SUBCLONAL	1	TRUE	1	0.348511944458212	2		930	1026	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445316	49445316	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	84	956	0	ENST00000301067.7:c.2150C>T	p.Ser717Phe	p.S717F	ENST00000301067	NM_003482.3	717	tCc/tTc	10/54	1	2	FACETS	0.464	0.409	0.524	0.464	0.409	0.524	SUBCLONAL	1	TRUE	1	0.348511944458212	2		956	1038	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211700	36211700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	58	679	1	ENST00000222270.7:c.1451C>T	p.Ala484Val	p.A484V	ENST00000222270	NM_014727.1	484	gCt/gTt	3/37	0.0544352156953047	3	FACETS	0.495	0.424	0.572	0.247	0.212	0.286	INDETERMINATE	1	TRUE	1	0.348511944458212	3		680	790	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25462077	25462077	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752626029	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	41	536	1	ENST00000264709.3:c.2330C>T	p.Pro777Leu	p.P777L	ENST00000264709	NM_175629.2	777	cCt/cTt	20/23	0.0544352156953047	3	FACETS	0.371	0.308	0.442	0.186	0.154	0.221	INDETERMINATE	1	TRUE	1	0.348511944458212	3		537	744	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867383	68867383	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	38	434	0	ENST00000261769.5:c.2630G>A	p.Gly877Glu	p.G877E	ENST00000261769	NM_004360.3	877	gGa/gAa	16/16	1	2	FACETS	0.377	0.311	0.451	0.377	0.311	0.451	SUBCLONAL	1	TRUE	1	0.348511944458212	2		434	579	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708103	117708103	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	27	521	0	ENST00000368508.3:c.2074A>C	p.Asn692His	p.N692H	ENST00000368508	NM_002944.2	692	Aat/Cat	14/43	1	2	FACETS	0.326	0.258	0.403	0.326	0.258	0.403	SUBCLONAL	1	TRUE	1	0.348511944458212	2		521	476	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46277748	46277748	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	103	322	0	ENST00000371998.3:c.3547-1G>A		p.X1183_splice	ENST00000371998		1183			0.0878752219269328	4	FACETS	0.837	0.753	0.926	0.837	0.753	0.926	INDETERMINATE	2	TRUE	2	0.348511944458212	4		322	476	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856028	151856028	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144222590	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	48	496	0	ENST00000262189.6:c.11590C>T	p.Arg3864Cys	p.R3864C	ENST00000262189	NM_170606.2	3864	Cgc/Tgc	44/59	0.0878752219269328	4	FACETS	0.454	0.382	0.533	0.227	0.191	0.267	INDETERMINATE	1	TRUE	2	0.348511944458212	4		496	819	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478828	56478828	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	75	824	1	ENST00000267101.3:c.284C>T	p.Ser95Phe	p.S95F	ENST00000267101	NM_001982.3	95	tCt/tTt	3/28	1	2	FACETS	0.47	0.411	0.534	0.47	0.411	0.534	SUBCLONAL	1	TRUE	1	0.348511944458212	2		825	916	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983076	201983076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293525214	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	55	813	1	ENST00000359651.3:c.925G>A	p.Glu309Lys	p.E309K	ENST00000359651		309	Gag/Aag	7/8	0.348511944458212	3	FACETS	0.38	0.323	0.442	0.19	0.161	0.221	SUBCLONAL	1	TRUE	1	0.348511944458212	3		814	976	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94922971	94922971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	37	409	0	ENST00000536441.1:c.497C>T	p.Pro166Leu	p.P166L	ENST00000536441	NM_144665.3	166	cCt/cTt	4/10	1	2	FACETS	0.457	0.376	0.547	0.457	0.376	0.547	SUBCLONAL	1	TRUE	1	0.348511944458212	2		409	465	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909956	100909956	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	44	421	0	ENST00000325455.5:c.2693C>T	p.Ser898Phe	p.S898F	ENST00000325455	NM_001202474.3	898	tCc/tTc	8/8	1	2	FACETS	0.488	0.409	0.576	0.488	0.409	0.576	SUBCLONAL	1	TRUE	1	0.348511944458212	2		421	517	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122745	108122745	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	23	351	0	ENST00000278616.4:c.1789C>T	p.Pro597Ser	p.P597S	ENST00000278616	NM_000051.3	597	Cca/Tca	11/63	1	2	FACETS	0.292	0.227	0.368	0.292	0.227	0.368	SUBCLONAL	1	TRUE	1	0.348511944458212	2		351	452	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347623	118347623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	104	587	0	ENST00000534358.1:c.3260C>T	p.Pro1087Leu	p.P1087L	ENST00000534358	NM_005933.3	1087	cCt/cTt	4/36	1	2	FACETS	0.784	0.702	0.871	0.784	0.702	0.871	SUBCLONAL	1	TRUE	1	0.348511944458212	2		587	761	SUCCESS
CBL	867	MSKCC	GRCh37	11	119145624	119145624	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	42	420	0	ENST00000264033.4:c.830T>G	p.Val277Gly	p.V277G	ENST00000264033	NM_005188.3	277	gTg/gGg	5/16	1	2	FACETS	0.47	0.392	0.556	0.47	0.392	0.556	SUBCLONAL	1	TRUE	1	0.348511944458212	2		420	513	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475168	475168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	52	608	1	ENST00000399788.2:c.469C>T	p.Leu157Phe	p.L157F	ENST00000399788	NM_001042603.1	157	Ctt/Ttt	4/28	1	2	FACETS	0.445	0.378	0.518	0.445	0.378	0.518	SUBCLONAL	1	TRUE	1	0.348511944458212	2		609	671	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245520	46245520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	30	395	0	ENST00000334344.6:c.3614G>A	p.Gly1205Glu	p.G1205E	ENST00000334344	NM_152641.2	1205	gGa/gAa	15/21	1	2	FACETS	0.453	0.365	0.553	0.453	0.365	0.553	SUBCLONAL	1	TRUE	1	0.348511944458212	2		395	380	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433095	49433095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	76	808	0	ENST00000301067.7:c.8276C>T	p.Pro2759Leu	p.P2759L	ENST00000301067	NM_003482.3	2759	cCc/cTc	33/54	1	2	FACETS	0.525	0.459	0.596	0.525	0.459	0.596	SUBCLONAL	1	TRUE	1	0.348511944458212	2		808	831	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445955	49445955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	66	906	0	ENST00000301067.7:c.1511C>T	p.Ser504Phe	p.S504F	ENST00000301067	NM_003482.3	504	tCt/tTt	10/54	1	2	FACETS	0.378	0.327	0.433	0.378	0.327	0.433	SUBCLONAL	1	TRUE	1	0.348511944458212	2		906	1003	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811738	102811738	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1490271682	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	44	704	0	ENST00000307046.8:c.446G>A	p.Arg149Lys	p.R149K	ENST00000307046	NM_001111285.1	149	aGg/aAg	4/4	1	2	FACETS	0.341	0.285	0.404	0.341	0.285	0.404	SUBCLONAL	1	TRUE	1	0.348511944458212	2		704	740	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590964	95590965	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	34	254	1	ENST00000393063.1:c.944_945delinsTT	p.Pro315Leu	p.P315L	ENST00000393063	NM_030621.3	315	cCC/cTT	9/28	1	2	FACETS	0.697	0.572	0.836	0.697	0.572	0.836	SUBCLONAL	1	TRUE	1	0.348511944458212	2		255	280	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996008	73996008	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	117	789	0	ENST00000318443.5:c.742G>A	p.Glu248Lys	p.E248K	ENST00000318443	NM_001024736.1	248	Gag/Aag	5/10	1	2	FACETS	0.775	0.699	0.857	0.775	0.699	0.857	SUBCLONAL	1	TRUE	1	0.348511944458212	2		789	866	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690600	88690600	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	37	462	0	ENST00000360948.2:c.430T>G	p.Trp144Gly	p.W144G	ENST00000360948	NM_001012338.2	144	Tgg/Ggg	5/19	1	2	FACETS	0.321	0.264	0.386	0.321	0.264	0.386	SUBCLONAL	1	TRUE	1	0.348511944458212	2		462	661	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292923	91292923	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	50	535	0	ENST00000355112.3:c.425G>C	p.Ser142Thr	p.S142T	ENST00000355112	NM_000057.2	142	aGt/aCt	3/22	1	2	FACETS	0.419	0.355	0.491	0.419	0.355	0.491	SUBCLONAL	1	TRUE	1	0.348511944458212	2		535	684	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136841	2136842	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	42	748	1	ENST00000219476.3:c.4958_4959delinsTT	p.Ser1653Phe	p.S1653F	ENST00000219476	NM_000548.3	1653	tCC/tTT	38/42	1	2	FACETS	0.297	0.247	0.353	0.297	0.247	0.353	SUBCLONAL	1	TRUE	1	0.348511944458212	2		749	812	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923284	9923284	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	36	501	0	ENST00000330684.3:c.2003A>G	p.Lys668Arg	p.K668R	ENST00000330684	NM_001134407.1	668	aAa/aGa	9/13	1	2	FACETS	0.383	0.314	0.46	0.383	0.314	0.46	SUBCLONAL	1	TRUE	1	0.348511944458212	2		501	540	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50830331	50830331	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	35	503	0	ENST00000398568.2:c.2774C>T	p.Ser925Phe	p.S925F	ENST00000398568	NM_001042412.1	925	tCc/tTc	18/18	1	2	FACETS	0.349	0.285	0.421	0.349	0.285	0.421	SUBCLONAL	1	TRUE	1	0.348511944458212	2		503	576	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957140	81957140	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	40	622	0	ENST00000359376.3:c.2358T>G	p.Asp786Glu	p.D786E	ENST00000359376	NM_002661.3	786	gaT/gaG	22/33	1	2	FACETS	0.344	0.285	0.41	0.344	0.285	0.41	SUBCLONAL	1	TRUE	1	0.348511944458212	2		622	667	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965170	81965171	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	54	684	1	ENST00000359376.3:c.2650_2651delinsTT	p.Pro884Phe	p.P884F	ENST00000359376	NM_002661.3	884	CCt/TTt	25/33	1	2	FACETS	0.384	0.326	0.446	0.384	0.326	0.446	SUBCLONAL	1	TRUE	1	0.348511944458212	2		685	808	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108345	8108346	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	42	654	1	ENST00000585124.1:c.878_879delinsTT	p.Pro293Leu	p.P293L	ENST00000585124	NM_004217.3	293	cCC/cTT	9/9	1	2	FACETS	0.312	0.26	0.371	0.312	0.26	0.371	SUBCLONAL	1	TRUE	1	0.348511944458212	2		655	772	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191155	2191156	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	127	824	1	ENST00000398665.3:c.409_410delinsAA	p.Gly137Lys	p.G137K	ENST00000398665	NM_032482.2	137	GGg/AAg	5/28	1	2	FACETS	0.707	0.639	0.778	0.707	0.639	0.778	SUBCLONAL	1	TRUE	1	0.348511944458212	2		825	1031	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207670	2207671	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	94	684	0	ENST00000398665.3:c.954_955delinsTT	p.Arg319Cys	p.R319C	ENST00000398665	NM_032482.2	318	gaCCgc/gaTTgc	11/28	1	2	FACETS	0.659	0.586	0.738	0.659	0.586	0.738	SUBCLONAL	1	TRUE	1	0.348511944458212	2		684	818	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222732	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	60	714	1	ENST00000357368.4:c.3071_3072delinsTT	p.Pro1024Leu	p.P1024L	ENST00000357368	NM_002850.3	1024	cCC/cTT	18/38	1	2	FACETS	0.413	0.355	0.477	0.413	0.355	0.477	SUBCLONAL	1	TRUE	1	0.348511944458212	2		715	833	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122666	7122666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	60	695	1	ENST00000302850.5:c.3488G>A	p.Arg1163Lys	p.R1163K	ENST00000302850	NM_000208.2	1163	aGa/aAa	19/22	1	2	FACETS	0.369	0.316	0.426	0.369	0.316	0.426	SUBCLONAL	1	TRUE	1	0.348511944458212	2		696	934	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252833	10252833	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	68	754	0	ENST00000340748.4:c.3132G>A	p.Trp1044Ter	p.W1044*	ENST00000340748		1044	tgG/tgA	29/40	1	2	FACETS	0.435	0.377	0.497	0.435	0.377	0.497	SUBCLONAL	1	TRUE	1	0.348511944458212	2		754	898	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295259	15295260	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	123	821	0	ENST00000263388.2:c.2412_2413delinsTT	p.Pro805Ser	p.P805S	ENST00000263388	NM_000435.2	804	ggCCca/ggTTca	16/33	0.0544352156953047	3	FACETS	0.745	0.672	0.822	0.372	0.336	0.411	INDETERMINATE	1	TRUE	1	0.348511944458212	3		821	1113	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298793	15298793	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778571943	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	66	844	0	ENST00000263388.2:c.1505C>T	p.Ser502Phe	p.S502F	ENST00000263388	NM_000435.2	502	tCc/tTc	10/33	0.0544352156953047	3	FACETS	0.447	0.387	0.513	0.224	0.193	0.257	INDETERMINATE	1	TRUE	1	0.348511944458212	3		844	994	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355231	15355231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	66	748	0	ENST00000263377.2:c.2392C>T	p.Pro798Ser	p.P798S	ENST00000263377	NM_058243.2	798	Cca/Tca	13/20	0.0544352156953047	3	FACETS	0.517	0.447	0.592	0.258	0.223	0.296	INDETERMINATE	1	TRUE	1	0.348511944458212	3		748	861	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976518	18976519	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	133	870	1	ENST00000262803.5:c.3168_3169delinsAA	p.Gly1057Ser	p.G1057S	ENST00000262803	NM_002911.3	1056	caGGgc/caAAgc	22/24	0.0544352156953047	3	FACETS	0.846	0.766	0.929	0.423	0.383	0.465	INDETERMINATE	1	TRUE	1	0.348511944458212	3		871	1060	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209089	36209089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	11	83	0	ENST00000222270.7:c.169G>A	p.Gly57Ser	p.G57S	ENST00000222270	NM_014727.1	57	Ggc/Agc	1/37	0.0544352156953047	3	FACETS	0.414	0.286	0.572	0.207	0.143	0.286	INDETERMINATE	1	TRUE	1	0.348511944458212	3		83	179	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902162	50902163	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	105	733	0	ENST00000440232.2:c.54_55delinsTT	p.Arg19Cys	p.R19C	ENST00000440232	NM_002691.3	18	gcCCgt/gcTTgt	2/27	0.0544352156953047	3	FACETS	0.782	0.7	0.869	0.391	0.35	0.435	INDETERMINATE	1	TRUE	1	0.348511944458212	3		733	905	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52725449	52725449	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	68	675	0	ENST00000322088.6:c.1616A>T	p.Asn539Ile	p.N539I	ENST00000322088	NM_014225.5	539	aAt/aTt	13/15	0.0544352156953047	3	FACETS	0.466	0.404	0.534	0.233	0.202	0.267	INDETERMINATE	1	TRUE	1	0.348511944458212	3		675	983	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467169	25467170	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	46	616	0	ENST00000264709.3:c.1705_1706delinsTT	p.Pro569Leu	p.P569L	ENST00000264709	NM_175629.2	569	CCg/TTg	15/23	0.0544352156953047	3	FACETS	0.453	0.381	0.534	0.227	0.19	0.267	INDETERMINATE	1	TRUE	1	0.348511944458212	3		616	684	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149158	61149158	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	70	405	0	ENST00000295025.8:c.1348C>T	p.Pro450Ser	p.P450S	ENST00000295025	NM_002908.2	450	Cct/Tct	11/11	0.0544352156953047	3	FACETS	0.911	0.795	1	0.455	0.397	0.518	INDETERMINATE	1	TRUE	1	0.348511944458212	3		405	518	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046310	128046310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1423048236	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	130	532	0	ENST00000285398.2:c.953C>T	p.Pro318Leu	p.P318L	ENST00000285398	NM_000122.1	318	cCc/cTc	7/15	0.0544352156953047	3	FACETS	1	0.929	1	0.514	0.466	0.565	INDETERMINATE	1	TRUE	1	0.348511944458212	3		532	852	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104650	209104650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773327968	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	110	586	1	ENST00000345146.2:c.928G>A	p.Gly310Arg	p.G310R	ENST00000345146	NM_005896.2	310	Ggg/Agg	8/10	1	2	FACETS	0.842	0.756	0.932	0.842	0.756	0.932	CLONAL	1	TRUE	1	0.348511944458212	2		587	750	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215633976	215633976	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	31	391	0	ENST00000260947.4:c.1375C>T	p.His459Tyr	p.H459Y	ENST00000260947	NM_000465.2	459	Cat/Tat	5/11	1	2	FACETS	0.342	0.276	0.417	0.342	0.276	0.417	SUBCLONAL	1	TRUE	1	0.348511944458212	2		391	520	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215674192	215674192	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879254280	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	69	721	0	ENST00000260947.4:c.102G>A	p.Trp34Ter	p.W34*	ENST00000260947	NM_000465.2	34	tgG/tgA	1/11	1	2	FACETS	0.466	0.405	0.533	0.466	0.405	0.533	SUBCLONAL	1	TRUE	1	0.348511944458212	2		721	849	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437311	220437311	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	66	512	1	ENST00000243786.2:c.215C>T	p.Ser72Phe	p.S72F	ENST00000243786	NM_002191.3	72	tCt/tTt	1/2	1	2	FACETS	0.37	0.32	0.425	0.37	0.32	0.425	SUBCLONAL	1	TRUE	1	0.348511944458212	2		513	1023	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024152	31024152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	104	686	0	ENST00000375687.4:c.3637C>T	p.Leu1213Phe	p.L1213F	ENST00000375687	NM_015338.5	1213	Ctc/Ttc	13/13	1	2	FACETS	0.77	0.689	0.856	0.77	0.689	0.856	SUBCLONAL	1	TRUE	1	0.348511944458212	2		686	775	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070361	37070361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	35	422	2	ENST00000231790.2:c.1496G>A	p.Arg499Lys	p.R499K	ENST00000231790	NM_000249.3	499	aGg/aAg	13/19	1	2	FACETS	0.363	0.297	0.438	0.363	0.297	0.438	SUBCLONAL	1	TRUE	1	0.348511944458212	2		424	553	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103707	47103707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	36	479	0	ENST00000409792.3:c.6239C>T	p.Ser2080Phe	p.S2080F	ENST00000409792	NM_014159.6	2080	tCc/tTc	14/21	1	2	FACETS	0.361	0.296	0.434	0.361	0.296	0.434	SUBCLONAL	1	TRUE	1	0.348511944458212	2		479	573	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259472	89259472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	42	539	1	ENST00000336596.2:c.616G>A	p.Val206Met	p.V206M	ENST00000336596	NM_005233.5	206	Gtg/Atg	3/17	1	2	FACETS	0.383	0.319	0.455	0.383	0.319	0.455	SUBCLONAL	1	TRUE	1	0.348511944458212	2		540	629	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390143	89390143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	96	361	0	ENST00000336596.2:c.892G>A	p.Glu298Lys	p.E298K	ENST00000336596	NM_005233.5	298	Gaa/Aaa	4/17	1	2	FACETS	0.939	0.838	1	0.939	0.838	1	CLONAL	1	TRUE	1	0.348511944458212	2		361	587	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607162	189607162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	49	706	0	ENST00000264731.3:c.1541G>A	p.Gly514Glu	p.G514E	ENST00000264731	NM_003722.4	514	gGa/gAa	12/14	1	2	FACETS	0.346	0.292	0.406	0.346	0.292	0.406	SUBCLONAL	1	TRUE	1	0.348511944458212	2		706	813	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749481	41749481	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	53	558	0	ENST00000226382.2:c.314T>A	p.Phe105Tyr	p.F105Y	ENST00000226382	NM_003924.3	105	tTc/tAc	2/3	1	2	FACETS	0.42	0.357	0.488	0.42	0.357	0.488	SUBCLONAL	1	TRUE	1	0.348511944458212	2		558	725	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189876	66189876	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	55	475	0	ENST00000273854.3:c.3070C>T	p.Gln1024Ter	p.Q1024*	ENST00000273854	NM_004439.5	1024	Caa/Taa	18/18	1	2	FACETS	0.489	0.418	0.568	0.489	0.418	0.568	SUBCLONAL	1	TRUE	1	0.348511944458212	2		475	645	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79968172	79968172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	69	492	1	ENST00000265081.6:c.902G>A	p.Gly301Glu	p.G301E	ENST00000265081	NM_002439.4	301	gGa/gAa	5/24	1	2	FACETS	0.622	0.541	0.709	0.622	0.541	0.709	SUBCLONAL	1	TRUE	1	0.348511944458212	2		493	637	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819759	170819759	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	24	222	0	ENST00000296930.5:c.398T>G	p.Val133Gly	p.V133G	ENST00000296930	NM_002520.6	133	gTg/gGg	5/11	1	2	FACETS	0.536	0.421	0.667	0.536	0.421	0.667	SUBCLONAL	1	TRUE	1	0.348511944458212	2		222	257	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673437	30673437	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	83	571	1	ENST00000376406.3:c.3523G>A	p.Asp1175Asn	p.D1175N	ENST00000376406	NM_014641.2	1175	Gac/Aac	10/15	1	2	FACETS	0.717	0.633	0.808	0.717	0.633	0.808	SUBCLONAL	1	TRUE	1	0.348511944458212	2		572	664	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324929	31324929	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750982109	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	58	898	1	ENST00000412585.2:c.7G>A	p.Val3Ile	p.V3I	ENST00000412585	NM_005514.6	3	Gtc/Atc	1/8	1	2	FACETS	0.309	0.265	0.359	0.309	0.265	0.359	SUBCLONAL	1	TRUE	1	0.348511944458212	2		899	1076	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166749	32166749	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	63	874	0	ENST00000375023.3:c.4489C>T	p.Pro1497Ser	p.P1497S	ENST00000375023	NM_004557.3	1497	Ccc/Tcc	24/30	1	2	FACETS	0.338	0.291	0.389	0.338	0.291	0.389	SUBCLONAL	1	TRUE	1	0.348511944458212	2		874	1070	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181617	32181617	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	68	767	0	ENST00000375023.3:c.2168G>A	p.Gly723Glu	p.G723E	ENST00000375023	NM_004557.3	723	gGa/gAa	14/30	1	2	FACETS	0.386	0.335	0.442	0.386	0.335	0.442	SUBCLONAL	1	TRUE	1	0.348511944458212	2		767	1010	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187905	32187905	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	48	724	1	ENST00000375023.3:c.1315+1G>A		p.X439_splice	ENST00000375023	NM_004557.3	439			1	2	FACETS	0.315	0.265	0.37	0.315	0.265	0.37	SUBCLONAL	1	TRUE	1	0.348511944458212	2		725	874	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969186	93969186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	28	363	0	ENST00000369303.4:c.1810G>A	p.Gly604Ser	p.G604S	ENST00000369303	NM_004440.3	604	Ggc/Agc	10/17	1	2	FACETS	0.386	0.308	0.475	0.386	0.308	0.475	SUBCLONAL	1	TRUE	1	0.348511944458212	2		363	416	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553656	106553656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	41	461	0	ENST00000369096.4:c.1621C>T	p.Pro541Ser	p.P541S	ENST00000369096	NM_001198.3	541	Ccc/Tcc	5/7	1	2	FACETS	0.44	0.366	0.522	0.44	0.366	0.522	SUBCLONAL	1	TRUE	1	0.348511944458212	2		461	535	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528909	157528909	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371461578	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	98	650	0	ENST00000346085.5:c.6634C>T	p.Arg2212Cys	p.R2212C	ENST00000346085	NM_020732.3	2212	Cgc/Tgc	20/20	1	2	FACETS	0.684	0.61	0.763	0.684	0.61	0.763	SUBCLONAL	1	TRUE	1	0.348511944458212	2		650	822	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55231515	55231516	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	77	512	1	ENST00000275493.2:c.1721_1722delinsAA	p.Arg574Gln	p.R574Q	ENST00000275493	NM_005228.3	574	cGG/cAA	14/28	0.0878752219269328	4	FACETS	0.844	0.741	0.955	0.422	0.37	0.478	INDETERMINATE	1	TRUE	2	0.348511944458212	4		513	706	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55260518	55260518	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	59	535	0	ENST00000275493.2:c.2685T>G	p.Ser895Arg	p.S895R	ENST00000275493	NM_005228.3	895	agT/agG	22/28	0.0878752219269328	4	FACETS	0.65	0.559	0.751	0.325	0.279	0.376	INDETERMINATE	1	TRUE	2	0.348511944458212	4		535	702	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508200	106508200	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	79	416	0	ENST00000359195.3:c.194G>A	p.Gly65Asp	p.G65D	ENST00000359195	NM_002649.2	65	gGc/gAc	2/11	0.0878752219269328	4	FACETS	1	0.964	1	0.625	0.551	0.704	INDETERMINATE	1	TRUE	2	0.348511944458212	4		416	489	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540147	23540148	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	47	304	1	ENST00000380871.4:c.255_256delinsAA	p.Glu86Lys	p.E86K	ENST00000380871	NM_006167.3	85	gaGGag/gaAAag	1/2	1	2	FACETS	0.623	0.526	0.729	0.623	0.526	0.729	SUBCLONAL	1	TRUE	1	0.348511944458212	2		305	433	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864750	68864750	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	43	604	0	ENST00000288368.4:c.121A>C	p.Thr41Pro	p.T41P	ENST00000288368	NM_024870.2	41	Acg/Ccg	1/40	1	2	FACETS	0.395	0.33	0.468	0.395	0.33	0.468	SUBCLONAL	1	TRUE	1	0.348511944458212	2		604	624	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971100	21971101	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AT	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	156	515	1	ENST00000579755.1:c.300_301delinsAT	p.Cys100_Pro101delinsTer	p.C100_P101delins*	ENST00000579755		100	tgCCcg/tgATcg	2/3	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.348511944458212	2		516	611	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911602	39911603	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	47	310	1	ENST00000378444.4:c.5027_5028delinsTT	p.Ser1676Phe	p.S1676F	ENST00000378444	NM_001123385.1	1676	tCC/tTT	15/15	0.109761352661667	2	FACETS	0.585	0.494	0.685			1	INDETERMINATE	1	TRUE	NA	0.348511944458212	2		311	461	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200043	123200043	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	13	152	0	ENST00000218089.9:c.2115G>C	p.Lys705Asn	p.K705N	ENST00000218089	NM_001042749.1	705	aaG/aaC	22/35	0.109761352661667	2	FACETS	0.429	0.306	0.577			1	INDETERMINATE	1	TRUE	NA	0.348511944458212	2		152	174	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0041176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	312	696	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.364915925035053	3	FACETS	1	0.971	1	0.687	0.653	0.722	CLONAL	2	FALSE	0	0.563104100019551	3		696	689	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416797	121416797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1320041799	NA	P-0041176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	119	1053	1	ENST00000257555.6:c.226G>A	p.Asp76Asn	p.D76N	ENST00000257555		76	Gac/Aac	1/10	0.24282423415606	0	FACETS	0.199	0.179	0.22			1	INDETERMINATE	1	FALSE	0	0.563104100019551	0		1054	928	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435570	110435570	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	53	646	0	ENST00000375856.3:c.2831C>G	p.Ser944Trp	p.S944W	ENST00000375856	NM_003749.2	944	tCg/tGg	1/2	1	2	FACETS	0.359	0.306	0.417	0.359	0.306	0.417	SUBCLONAL	1	FALSE	1	0.563104100019551	2		646	525	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508656	38508656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	517	733	1	ENST00000254066.5:c.704G>A	p.Cys235Tyr	p.C235Y	ENST00000254066	NM_000964.3	235	tGc/tAc	6/9	0.687925610648254	2	FACETS	0.895	0.87	0.92	1	0.997	1	CLONAL	3	TRUE	0	0.54	2		734	713	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0041178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	121	565	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	0.187165707067932	1	FACETS	0.816	0.739	0.897	1	0.987	1	CLONAL	2	TRUE	0	0.216715397432433	1		565	610	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610608	52610609	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	54	405	1	ENST00000394830.3:c.3564dup	p.Glu1189ArgfsTer6	p.E1189Rfs*6	ENST00000394830	NM_018313.4	1188	-/A	23/30	0.205356459573172	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.216715397432433	1		406	396	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981504	55981504	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	56	410	0	ENST00000263923.4:c.433A>G	p.Thr145Ala	p.T145A	ENST00000263923	NM_002253.2	145	Act/Gct	4/30	0.205356459573172	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.216715397432433	1		410	375	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0041193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	1257	529	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.745534385854394	7	FACETS	0.992	0.981	1			1	CLONAL	7	TRUE	NA	0.745534385854394	7		529	1391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0041193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	293	775	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.745534385854394	1	FACETS	0.934	0.89	0.977	0.934	0.89	0.977	CLONAL	1	TRUE	0	0.745534385854394	1		775	528	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	193	345	0				ENST00000310581	NM_198253.2	-/1132			0.422241204237246	3	FACETS	0.849	0.797	0.902	0.849	0.797	0.902	INDETERMINATE	2	TRUE	1	0.761524181906649	3		345	412	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0041194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	170	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.0563257731929014	6	FACETS	1	0.975	1	0.744	0.689	0.799	INDETERMINATE	2	TRUE	3	0.761524181906649	6		288	505	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923045	44923048	+	frameshift_variant	Frame_Shift_Del	DEL	CTAT	CTAT	-	rs398122969	NA	P-0041196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	71	302	0	ENST00000377967.4:c.1909_1912del	p.Ser637ThrfsTer53	p.S637Tfs*53	ENST00000377967	NM_021140.2	636	CTATct/ct	16/29	1	1	FACETS	1	0.888	1	1	0.982	1	CLONAL	2	TRUE	0	0.16	1		302	403	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0041202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	295	548	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.826	0.781	0.871	1	0.995	1	CLONAL	2	FALSE	1	0.465635854541431	2		548	767	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0041202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	8	247	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.128	0.082	0.188	0.128	0.082	0.188	SUBCLONAL	1	FALSE	1	0.465635854541431	2		247	268	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177458	56177458	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs189290632	NA	P-0041202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	89	354	0	ENST00000399503.3:c.2431A>G	p.Met811Val	p.M811V	ENST00000399503	NM_005921.1	811	Atg/Gtg	14/20	1	2	FACETS	0.881	0.785	0.982	0.881	0.785	0.982	CLONAL	1	FALSE	1	0.465635854541431	2		354	434	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0041203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	47	662	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.979	0.823	1	0.979	0.823	1	CLONAL	1	TRUE	1	0.11	2		662	873	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578230	7578230	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	155	690	0	ENST00000269305.4:c.619del	p.Asp207MetfsTer40	p.D207Mfs*40	ENST00000269305	NM_001126112.2	207	Gat/at	6/11	0.3	3	FACETS	1	0.938	1	1	0.988	1	CLONAL	3	TRUE	1	0.11	3		690	962	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916947	178916947	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	87	394	0	ENST00000263967.3:c.334A>T	p.Ile112Phe	p.I112F	ENST00000263967	NM_006218.2	112	Atc/Ttc	2/21	0.118855125424058	4	FACETS	0.938	0.831	1	1	0.976	1	CLONAL	3	TRUE	2	0.11	4		394	624	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249457	153249457	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	34	500	0	ENST00000281708.4:c.1321C>G	p.Arg441Gly	p.R441G	ENST00000281708	NM_033632.3	441	Cgg/Ggg	9/12	1	2	FACETS	0.974	0.793	1	0.974	0.793	1	CLONAL	1	TRUE	1	0.11	2		500	635	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	108	345	0				ENST00000310581	NM_198253.2	-/1132			0.213559503593115	4	FACETS	0.878	0.791	0.969	0.878	0.791	0.969	CLONAL	2	TRUE	2	0.304669504908388	4		345	527	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	248	517	2	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	2	TRUE	NA	0.304669504908388	2		519	766	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771344	68771344	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	151	267	0	ENST00000261769.5:c.26C>A	p.Ser9Ter	p.S9*	ENST00000261769	NM_004360.3	9	tCg/tAg	1/16	0.304669504908388	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.304669504908388	2		267	401	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118350888	118350888	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0041220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	141	409	0	ENST00000534358.1:c.3570-1G>A		p.X1190_splice	ENST00000534358	NM_005933.3	1190			0.304669504908388	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	0	0.304669504908388	2		409	452	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955580	48955580	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587778857	NA	P-0041220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	110	337	0	ENST00000267163.4:c.1695+1G>A		p.X565_splice	ENST00000267163	NM_000321.2	565			NA	2	FACETS	0.989	0.898	1			1	INDETERMINATE	2	TRUE	NA	0.304669504908388	2		337	365	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993510	72993510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	235	606	0	ENST00000268489.5:c.535G>A	p.Gly179Ser	p.G179S	ENST00000268489	NM_006885.3	179	Ggc/Agc	2/10	0.304669504908388	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.304669504908388	2		606	687	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626805	14626805	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377706903	NA	P-0041220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	108	587	0	ENST00000254322.2:c.970G>A	p.Glu324Lys	p.E324K	ENST00000254322	NM_006145.1	324	Gaa/Aaa	3/3	0.213661145127701	3	FACETS	0.991	0.889	1	0.496	0.444	0.55	CLONAL	1	TRUE	1	0.304669504908388	3		587	824	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753271	42753271	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1330	247	707	0	ENST00000222329.4:c.993C>G	p.Phe331Leu	p.F331L	ENST00000222329	NM_006494.2	331	ttC/ttG	4/4	0.304669504908388	6	FACETS	0.827	0.771	0.886	0.552	0.514	0.591	CLONAL	2	TRUE	3	0.304669504908388	6		707	1577	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750667	39750667	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	124	269	0	ENST00000361337.2:c.2067G>C	p.Lys689Asn	p.K689N	ENST00000361337	NM_003286.2	689	aaG/aaC	20/21	0.300133473086385	4	FACETS	0.943	0.857	1	0.943	0.857	1	CLONAL	2	TRUE	2	0.304669504908388	4		269	563	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051582	30051582	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1064796632	NA	P-0041220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	131	275	0	ENST00000338641.4:c.517-1G>A		p.X173_splice	ENST00000338641	NM_000268.3	173			0.304669504908388	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	0	0.304669504908388	2		275	416	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931326	131931326	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	171	450	0	ENST00000265335.6:c.2031C>A	p.Asn677Lys	p.N677K	ENST00000265335		677	aaC/aaA	13/25	0.300133473086385	4	FACETS	0.935	0.862	1	0.935	0.862	1	CLONAL	2	TRUE	2	0.304669504908388	4		450	783	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298760	15298775	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGCGCATTCGTCCA	CTGGCGCATTCGTCCA	-	novel	NA	P-0041224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	95	713	0	ENST00000263388.2:c.1523_1538del	p.Val508AlafsTer86	p.V508Afs*86	ENST00000263388	NM_000435.2	508	gTGGACGAATGCGCCAGc/gc	10/33	1	2	FACETS	0.689	0.612	0.771	0.689	0.612	0.771	SUBCLONAL	1	TRUE	1	0.286375561795553	2		713	963	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443569	52443569	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0041224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	73	498	0	ENST00000460680.1:c.122+1G>T		p.X41_splice	ENST00000460680	NM_004656.3	41			1	2	FACETS	0.761	0.665	0.864	0.761	0.665	0.864	SUBCLONAL	1	TRUE	1	0.286375561795553	2		498	670	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970823	55970824	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	54	541	0	ENST00000263923.4:c.1973dup	p.Leu659AlafsTer44	p.L659Afs*44	ENST00000263923	NM_002253.2	658	cag/caAg	13/30	1	2	FACETS	0.614	0.524	0.713	0.614	0.524	0.713	SUBCLONAL	1	TRUE	1	0.286375561795553	2		541	614	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	89	345	0				ENST00000310581	NM_198253.2	-/1132			0.787560556320567	3	FACETS	1	0.968	1	0.596	0.537	0.658	CLONAL	1	TRUE	1	0.827184262025861	3		345	255	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630379	90630379	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	170	560	0	ENST00000330062.3:c.932A>G	p.Tyr311Cys	p.Y311C	ENST00000330062	NM_002168.2	311	tAt/tGt	7/11	0.827184262025861	3	FACETS	1	0.929	1	0.503	0.465	0.542	CLONAL	1	TRUE	1	0.827184262025861	3		560	578	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737024	162737024	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1210114531	NA	P-0041233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	118	458	0	ENST00000367921.3:c.1168A>G	p.Met390Val	p.M390V	ENST00000367921	NM_006182.2	390	Atg/Gtg	11/18	0.827184262025861	3	FACETS	1	0.939	1	0.52	0.473	0.568	CLONAL	1	TRUE	1	0.827184262025861	3		458	388	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	114	296	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.935	0.846	1	1	0.988	1	CLONAL	2	TRUE	1	0.24	2		297	508	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0041244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	116	491	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.854	0.768	0.946	0.854	0.768	0.946	CLONAL	1	TRUE	1	0.24	2		491	1132	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0041244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	52	672	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.24	2		672	383	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0041244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	125	596	3	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.889	0.802	0.98	0.889	0.802	0.98	CLONAL	1	TRUE	1	0.24	2		599	1172	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166284	7166284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747464322	NA	P-0041244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	118	764	0	ENST00000302850.5:c.1742G>A	p.Arg581Gln	p.R581Q	ENST00000302850	NM_000208.2	581	cGg/cAg	8/22	1	2	FACETS	0.881	0.793	0.975	0.881	0.793	0.975	CLONAL	1	TRUE	1	0.24	2		764	1116	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649012	86649012	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	22	177	0	ENST00000274376.6:c.1292T>C	p.Ile431Thr	p.I431T	ENST00000274376	NM_002890.2	431	aTt/aCt	9/25	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.24	2		177	143	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600475	43600475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756216318	NA	P-0041244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	139	701	3	ENST00000355710.3:c.701G>A	p.Arg234Gln	p.R234Q	ENST00000355710	NM_020975.4	234	cGg/cAg	4/20	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.24	2		704	1140	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0041244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	67	457	0	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	1	2	FACETS	0.879	0.764	1	0.879	0.764	1	CLONAL	1	TRUE	1	0.24	2		457	635	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0041244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	38	623	1	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	0.742	0.613	0.885	0.742	0.613	0.885	SUBCLONAL	1	TRUE	1	0.24	2		624	427	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	68	305	0	ENST00000256196.4:c.68G>T	p.Gly23Val	p.G23V	ENST00000256196		23	gGc/gTc	1/6	1	2	FACETS	0.87	0.757	0.993	0.87	0.757	0.993	CLONAL	1	TRUE	1	0.24	2		305	651	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0041244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	124	732	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.987	0.891	1	0.987	0.891	1	CLONAL	1	TRUE	1	0.24	2		735	1047	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692780	89692780	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1554898056	NA	P-0041244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	33	257	0	ENST00000371953.3:c.264T>A	p.Tyr88Ter	p.Y88*	ENST00000371953	NM_000314.4	88	taT/taA	5/9	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.24	2		257	203	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948755	71948755	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1565399032	NA	P-0041244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	120	800	0	ENST00000298229.2:c.3470del	p.Gly1157AspfsTer45	p.G1157Dfs*45	ENST00000298229	NM_001567.3	1156	cGg/cg	26/28	1	2	FACETS	0.95	0.856	1	0.95	0.856	1	CLONAL	1	TRUE	1	0.24	2		800	1053	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163822	47163823	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0041244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	22	308	0	ENST00000409792.3:c.2303_2304del	p.Val768GlyfsTer8	p.V768Gfs*8	ENST00000409792	NM_014159.6	768	gTG/g	3/21	1	2	FACETS	0.777	0.604	0.976	0.777	0.604	0.976	CLONAL	1	TRUE	1	0.24	2		308	236	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100388	27100389	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	TGCT	novel	NA	P-0041244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	50	534	0	ENST00000324856.7:c.4100_4101insTGCT	p.Gln1367HisfsTer79	p.Q1367Hfs*79	ENST00000324856	NM_006015.4	1367	cag/caTGCTg	17/20	1	2	FACETS	0.612	0.518	0.715	0.612	0.518	0.715	SUBCLONAL	1	TRUE	1	0.24	2		534	681	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639380	3639380	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs781663547	NA	P-0041244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	109	780	0	ENST00000294008.3:c.4259del	p.Pro1420GlnfsTer30	p.P1420Qfs*30	ENST00000294008	NM_032444.2	1420	cCa/ca	12/15	1	2	FACETS	0.833	0.747	0.926	0.833	0.747	0.926	CLONAL	1	TRUE	1	0.24	2		780	1090	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645350	67645350	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	68	474	0	ENST00000264010.4:c.615del	p.Thr207ProfsTer15	p.T207Pfs*15	ENST00000264010	NM_006565.3	205	aaG/aa	3/12	1	2	FACETS	0.97	0.845	1	0.97	0.845	1	CLONAL	1	TRUE	1	0.24	2		474	584	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533460	63533460	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs534983760	NA	P-0041244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	62	708	0	ENST00000307078.5:c.1694T>C	p.Met565Thr	p.M565T	ENST00000307078	NM_004655.3	565	aTg/aCg	6/11	1	2	FACETS	0.46	0.396	0.531	0.46	0.396	0.531	SUBCLONAL	1	TRUE	1	0.24	2		708	1123	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284990	15284990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	147	799	2	ENST00000263388.2:c.4625C>T	p.Ser1542Leu	p.S1542L	ENST00000263388	NM_000435.2	1542	tCg/tTg	25/33	1	2	FACETS	0.942	0.858	1	0.942	0.858	1	CLONAL	1	TRUE	1	0.24	2		801	1300	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212287	36212287	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	101	726	0	ENST00000222270.7:c.2038G>T	p.Glu680Ter	p.E680*	ENST00000222270	NM_014727.1	680	Gag/Tag	3/37	1	2	FACETS	0.767	0.684	0.856	0.767	0.684	0.856	SUBCLONAL	1	TRUE	1	0.24	2		726	1097	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693887	47693887	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	25	223	0	ENST00000233146.2:c.1601del	p.Arg534LeufsTer9	p.R534Lfs*9	ENST00000233146	NM_000251.2	534	cGt/ct	10/16	1	2	FACETS	0.934	0.74	1	0.934	0.74	1	CLONAL	1	TRUE	1	0.24	2		223	223	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279204	142279204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	39	305	0	ENST00000350721.4:c.1442G>A	p.Gly481Asp	p.G481D	ENST00000350721	NM_001184.3	481	gGc/gAc	6/47	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.24	2		305	273	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576774	67576799	+	frameshift_variant	Frame_Shift_Del	DEL	CTCATAAAAGTTATAGAAATTTTAAT	CTCATAAAAGTTATAGAAATTTTAAT	-	novel	NA	P-0041244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	20	207	0	ENST00000274335.5:c.860_885del	p.Ile287AsnfsTer2	p.I287Nfs*2	ENST00000274335		286	CTCATAAAAGTTATAGAAATTTTAATc/c	6/15	1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	1	0.24	2		207	144	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456852	149456853	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	106	723	0	ENST00000286301.3:c.875dup	p.Phe293LeufsTer14	p.F293Lfs*14	ENST00000286301	NM_005211.3	292	ttc/ttTc	6/22	1	2	FACETS	0.777	0.695	0.865	0.777	0.695	0.865	SUBCLONAL	1	TRUE	1	0.24	2		723	1137	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912168	29912168	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0041244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	20	182	0	ENST00000376809.5:c.889A>T	p.Arg297Ter	p.R297*	ENST00000376809	NM_002116.7	297	Aga/Tga	4/8	1	2	FACETS	0.838	0.643	1	0.838	0.643	1	CLONAL	1	TRUE	1	0.24	2		182	199	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0041254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	140	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.466429711504462	2		473	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0041254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	153	644	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.714	0.653	0.778	0.714	0.653	0.778	SUBCLONAL	1	TRUE	1	0.466429711504462	2		645	919	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0041254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	116	259	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.953	0.863	1	0.953	0.863	1	CLONAL	1	TRUE	1	0.466429711504462	2		259	522	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0041254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	143	683	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.466429711504462	2		683	468	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	33	301	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	0.704	0.578	0.843	0.704	0.578	0.843	SUBCLONAL	1	TRUE	1	0.466429711504462	2		301	201	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411246	63411246	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	283	521	0	ENST00000330258.3:c.1921C>T	p.Arg641Ter	p.R641*	ENST00000330258	NM_152424.3	641	Cga/Tga	2/2	1	1	FACETS	0.907	0.864	0.95	1	0.996	1	CLONAL	2	TRUE	0	0.466429711504462	1		521	513	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576891	7576891	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0041254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	253	582	0	ENST00000269305.4:c.955A>T	p.Lys319Ter	p.K319*	ENST00000269305	NM_001126112.2	319	Aag/Tag	9/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.466429711504462	2		582	894	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965231	81965231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	199	515	2	ENST00000359376.3:c.2711G>A	p.Arg904Gln	p.R904Q	ENST00000359376	NM_002661.3	904	cGa/cAa	25/33	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.466429711504462	2		517	745	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576887	7576887	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	244	577	0	ENST00000269305.4:c.959A>G	p.Lys320Arg	p.K320R	ENST00000269305	NM_001126112.2	320	aAg/aGg	9/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.466429711504462	2		577	879	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554484	63554492	+	inframe_deletion	In_Frame_Del	DEL	TAAGGAGTG	TAAGGAGTG	-	novel	NA	P-0041254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	238	617	0	ENST00000307078.5:c.247_255del	p.His83_Leu85del	p.H83_L85del	ENST00000307078	NM_004655.3	83	CACTCCTTA/-	2/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.466429711504462	2		617	903	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0041295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	146	472	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	0.847	0.776	0.92	0.847	0.776	0.92	CLONAL	1	TRUE	1	0.603959155622677	2		472	571	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074397	8074397	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	120	316	0	ENST00000377482.5:c.262C>T	p.Gln88Ter	p.Q88*	ENST00000377482	NM_018948.3	88	Caa/Taa	4/4	0.603959155622677	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.603959155622677	1		316	267	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023212	27023223	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGGGCCCTAG	CGCGGGCCCTAG	A	novel	NA	P-0041295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	46	107	0	ENST00000324856.7:c.318_329delinsA	p.Asn106LysfsTer7	p.N106Kfs*7	ENST00000324856	NM_006015.4	106	aaCGCGGGCCCTAGg/aaAg	1/20	0.603959155622677	1	FACETS	0.776	0.669	0.889	0.776	0.669	0.889	SUBCLONAL	1	TRUE	0	0.603959155622677	1		107	137	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0041298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	39	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.19	2		473	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0041298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	40	692	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	1	2	FACETS	0.936	0.778	1	0.936	0.778	1	CLONAL	1	TRUE	1	0.19	2		692	450	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500832	8500832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756198535	NA	P-0041298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	25	351	0	ENST00000356435.5:c.2050C>T	p.Arg684Trp	p.R684W	ENST00000356435		684	Cgg/Tgg	13/35	0.21833185911487	0	FACETS	0.594	0.468	0.739			1	SUBCLONAL	1	TRUE	0	0.19	0		351	359	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293154	212293154	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	21	269	0	ENST00000342788.4:c.2698C>T	p.Gln900Ter	p.Q900*	ENST00000342788	NM_005235.2	900	Cag/Tag	22/28	1	2	FACETS	0.709	0.546	0.898	0.709	0.546	0.898	SUBCLONAL	1	TRUE	1	0.19	2		269	312	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433885	78433885	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	21	244	0	ENST00000370768.2:c.214C>T	p.Gln72Ter	p.Q72*	ENST00000370768	NM_003902.3	72	Caa/Taa	3/20	1	2	FACETS	0.637	0.49	0.809	0.637	0.49	0.809	SUBCLONAL	1	TRUE	1	0.19	2		244	347	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970995	21971002	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCTCCT	CAGCTCCT	-	novel	NA	P-0041298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	24	435	0	ENST00000304494.5:c.356_363del	p.Glu119GlyfsTer20	p.E119Gfs*20	ENST00000304494	NM_000077.4	119	gAGGAGCTG/g	2/3	0.21833185911487	0	FACETS	0.526	0.412	0.658			1	SUBCLONAL	1	TRUE	0	0.19	0		435	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0041303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	306	723	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.394108178176983	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.4131835152514	2		723	731	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519893	NA	P-0041303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	152	742	0	ENST00000267101.3:c.310G>T	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ttg	3/28	0.407709887384421	3	FACETS	0.997	0.912	1	0.499	0.456	0.544	CLONAL	1	TRUE	1	0.4131835152514	3		742	890	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	368	515	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.254587457526993	5	FACETS	1	0.99	1			1	CLONAL	3	TRUE	NA	0.4131835152514	5		515	849	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909998	100910019	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACAAGCTGTTGGTTTAACAAAT	ACAAGCTGTTGGTTTAACAAAT	TCAAAC	novel	NA	P-0041303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	33	325	2	ENST00000325455.5:c.2647-17_2651delinsGTTTGA		p.X883_splice	ENST00000325455	NM_001202474.3	883		8/8	0.407709887384421	3	FACETS	0.531	0.433	0.641	0.265	0.216	0.321	SUBCLONAL	1	TRUE	1	0.4131835152514	3		327	363	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20153943	20153943	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	86	406	0	ENST00000379607.5:c.117C>G	p.Ile39Met	p.I39M	ENST00000379607	NM_001412.3	39	atC/atG	3/7	0.342978632849466	3	FACETS	1	0.923	1			1	CLONAL	1	TRUE	NA	0.4131835152514	3		406	478	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0041309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	63	393	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.893	1	1	0.98	1	CLONAL	2	FALSE	1	0.18795605458719	2		393	326	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs121913292	NA	P-0041309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	195	452	0	ENST00000371953.3:c.389del	p.Arg130GlnfsTer4	p.R130Qfs*4	ENST00000371953	NM_000314.4	130	cGa/ca	5/9	0.18795605458719	6	FACETS	0.939	0.876	1	1	0.991	1	CLONAL	6	FALSE	2	0.18795605458719	6		452	507	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696461	47696461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	96	409	0	ENST00000347630.2:c.362G>A	p.Arg121Gln	p.R121Q	ENST00000347630	NM_001007230.1	121	cGg/cAg	6/11	1	2	FACETS	1	0.971	1	1	0.989	1	CLONAL	2	FALSE	1	0.18795605458719	2		409	412	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609156	46609156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1462311206	NA	P-0041309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	264	719	1	ENST00000263734.3:c.2215C>T	p.Arg739Trp	p.R739W	ENST00000263734	NM_001430.4	739	Cgg/Tgg	14/16	0.18795605458719	5	FACETS	0.936	0.884	0.989	1	0.993	1	CLONAL	6	FALSE	1	0.18795605458719	5		720	641	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101552	27101552	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	206	716	0	ENST00000324856.7:c.4837del	p.Met1613CysfsTer13	p.M1613Cfs*13	ENST00000324856	NM_006015.4	1612	Aaa/aa	18/20	1	2	FACETS	1	0.978	1	1	0.995	1	CLONAL	3	FALSE	1	0.18795605458719	2		716	655	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398283	25398284	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCAGCT	novel	NA	P-0041309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	152	393	0	ENST00000311936.3:c.30_35dup	p.Ala11_Gly12dup	p.A11_G12dup	ENST00000311936	NM_004985.3	11	ggt/ggAGCTGGt	2/5	0.127212520375801	3	FACETS	1	0.958	1	1	0.992	1	CLONAL	4	FALSE	1	0.18795605458719	3		393	420	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273208	115273208	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	127	536	0	ENST00000438362.2:c.1250del	p.Arg417LeufsTer21	p.R417Lfs*21	ENST00000438362	NM_001242891.1	417	cGt/ct	11/20	1	2	FACETS	0.979	0.893	1	1	0.992	1	CLONAL	3	FALSE	1	0.18795605458719	2		536	460	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118907	115118907	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	34	358	0	ENST00000257566.3:c.434A>T	p.Lys145Ile	p.K145I	ENST00000257566	NM_016569.3	145	aAa/aTa	2/8	0.18795605458719	3	FACETS	1	0.897	1	0.382	0.313	0.46	CLONAL	1	FALSE	0	0.18795605458719	3		358	345	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218927	133218927	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	343	810	0	ENST00000320574.5:c.5009A>G	p.Asp1670Gly	p.D1670G	ENST00000320574	NM_006231.2	1670	gAc/gGc	38/49	0.18795605458719	3	FACETS	0.938	0.892	0.985	1	0.995	1	CLONAL	5	FALSE	0	0.18795605458719	3		810	851	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927436	49927436	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	225	712	0	ENST00000296474.3:c.3868C>T	p.His1290Tyr	p.H1290Y	ENST00000296474	NM_002447.2	1290	Cac/Tac	19/20	1	2	FACETS	1	0.979	1	1	0.996	1	CLONAL	3	FALSE	1	0.18795605458719	2		712	721	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0041317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	18	548	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.296	0.222	0.384	0.296	0.222	0.384	SUBCLONAL	1	TRUE	1	0.28	2		548	434	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0041317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	81	259	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.786	0.697	0.88	1	0.98	1	SUBCLONAL	2	TRUE	1	0.28	2		259	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0041317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	30	735	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.307	0.246	0.376	0.307	0.246	0.376	SUBCLONAL	1	TRUE	1	0.28	2		735	698	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0041317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	46	281	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.771	0.65	0.904	0.771	0.65	0.904	CLONAL	1	TRUE	1	0.28	2		281	426	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0041317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	147	553	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.989	0.908	1	1	0.991	1	CLONAL	2	TRUE	1	0.28	2		553	531	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0041317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	93	335	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.802	0.718	0.891	1	0.983	1	CLONAL	2	TRUE	1	0.28	2		335	414	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367288	50367288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775793261	NA	P-0041317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	71	328	0	ENST00000331340.3:c.95C>T	p.Pro32Leu	p.P32L	ENST00000331340	NM_006060.4	32	cCg/cTg	3/8	0.223647700608442	4	FACETS	1	0.963	1	0.427	0.373	0.485	CLONAL	1	TRUE	1	0.28	4		328	507	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353918	15353918	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	19	326	2	ENST00000263377.2:c.2962C>T	p.Gln988Ter	p.Q988*	ENST00000263377	NM_058243.2	988	Cag/Tag	14/20	1	2	FACETS	0.368	0.278	0.473	0.368	0.278	0.473	SUBCLONAL	1	TRUE	1	0.28	2		328	369	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445229	49445229	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371911838	NA	P-0041317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	70	727	1	ENST00000301067.7:c.2237G>A	p.Arg746Gln	p.R746Q	ENST00000301067	NM_003482.3	746	cGg/cAg	10/54	1	2	FACETS	0.691	0.601	0.787	0.691	0.601	0.787	SUBCLONAL	1	TRUE	1	0.28	2		728	724	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665762	29665762	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	48	239	0	ENST00000356175.3:c.6797G>C	p.Ser2266Thr	p.S2266T	ENST00000356175	NM_000267.3	2266	aGt/aCt	45/57	1	2	FACETS	0.741	0.627	0.866	0.741	0.627	0.866	SUBCLONAL	1	TRUE	1	0.28	2		239	463	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681045	117681045	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	39	362	0	ENST00000368508.3:c.3575A>C	p.Asp1192Ala	p.D1192A	ENST00000368508	NM_002944.2	1192	gAt/gCt	23/43	1	2	FACETS	0.541	0.448	0.645	0.541	0.448	0.645	SUBCLONAL	1	TRUE	1	0.28	2		362	515	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164920	123164920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	63	274	0	ENST00000218089.9:c.233G>A	p.Gly78Glu	p.G78E	ENST00000218089	NM_001042749.1	78	gGa/gAa	5/35	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.28	2		274	413	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916929	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519931	NA	P-0041319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	17	402	0	ENST00000263967.3:c.316G>C	p.Gly106Arg	p.G106R	ENST00000263967	NM_006218.2	106	Ggc/Cgc	2/21	1	2	FACETS	0.24	0.178	0.315	0.24	0.178	0.315	SUBCLONAL	1	TRUE	1	0.239036766899679	2		402	592	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141426	11141426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	153	588	0	ENST00000358026.2:c.3403C>T	p.Arg1135Trp	p.R1135W	ENST00000358026	NM_001128849.1	1135	Cgg/Tgg	25/36	0.2053611677497	3	FACETS	0.812	0.742	0.884	0.812	0.742	0.884	CLONAL	2	TRUE	1	0.239036766899679	3		588	883	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0041319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	60	277	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.239036766899679	3	FACETS	0.94	0.81	1	0.47	0.405	0.541	CLONAL	1	TRUE	1	0.239036766899679	3		277	598	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788618	3788618	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	19	398	0	ENST00000262367.5:c.4336C>A	p.Arg1446Ser	p.R1446S	ENST00000262367	NM_004380.2	1446	Cgc/Agc	26/31	1	2	FACETS	0.259	0.195	0.334	0.259	0.195	0.334	SUBCLONAL	1	TRUE	1	0.239036766899679	2		398	614	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147513	47147513	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	72	348	0	ENST00000409792.3:c.4813T>A	p.Tyr1605Asn	p.Y1605N	ENST00000409792	NM_014159.6	1605	Tat/Aat	6/21	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.239036766899679	2		348	559	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638582	176638582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	175	571	0	ENST00000439151.2:c.3182G>A	p.Ser1061Asn	p.S1061N	ENST00000439151	NM_022455.4	1061	aGt/aAt	5/23	0.2053611677497	3	FACETS	0.902	0.831	0.976	0.902	0.831	0.976	CLONAL	2	TRUE	1	0.239036766899679	3		571	909	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932277	39932278	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	150	839	0	ENST00000378444.4:c.2321dup	p.Leu775ValfsTer42	p.L775Vfs*42	ENST00000378444	NM_001123385.1	774	aag/aaAg	4/15	0.239036766899679	1	FACETS	0.99	0.903	1	0.99	0.903	1	CLONAL	1	TRUE	0	0.239036766899679	1		839	1116	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0041343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	106	583	0	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	1	2	FACETS	0.495	0.444	0.549	0.495	0.444	0.549	SUBCLONAL	1	TRUE	1	0.661886387995013	2		583	647	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425644	49425644	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057517992	NA	P-0041343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	114	607	0	ENST00000301067.7:c.12844C>T	p.Arg4282Ter	p.R4282*	ENST00000301067	NM_003482.3	4282	Cga/Tga	39/54	1	2	FACETS	0.516	0.465	0.569	0.516	0.465	0.569	SUBCLONAL	1	TRUE	1	0.661886387995013	2		607	668	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711979	89711980	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	96	256	1	ENST00000371953.3:c.600dup	p.Glu201Ter	p.E201*	ENST00000371953	NM_000314.4	199	-/T	6/9	0.316272555512219	2	FACETS	0.826	0.743	0.913	0.413	0.371	0.457	INDETERMINATE	1	TRUE	0	0.661886387995013	2		257	351	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205663	128205674	+	inframe_deletion	In_Frame_Del	DEL	GAGACGCGCGCC	GAGACGCGCGCC	-	novel	NA	P-0041343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	404	475	0	ENST00000341105.2:c.201_212del	p.Ala68_Ser71del	p.A68_S71del	ENST00000341105	NM_032638.4	67	cgGGCGCGCGTCTCc/cgc	2/6	0.601962895941555	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.661886387995013	3		475	803	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074473	39074473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	39	400	0	ENST00000357387.3:c.7G>A	p.Ala3Thr	p.A3T	ENST00000357387	NM_152756.3	3	Gcg/Acg	1/38	1	2	FACETS	0.246	0.203	0.293	0.246	0.203	0.293	SUBCLONAL	1	TRUE	1	0.661886387995013	2		400	480	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910805	29910805	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0041343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	90	444	0	ENST00000376809.5:c.343+2T>G		p.X115_splice	ENST00000376809	NM_002116.7	115			0.661886387995013	1	FACETS	0.527	0.472	0.585	0.527	0.472	0.585	SUBCLONAL	1	TRUE	0	0.661886387995013	1		444	345	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0041347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	201	732	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.981	1	1	0.994	1	CLONAL	2	FALSE	1	0.236616429337073	2		735	738	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0041347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	102	453	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.236616429337073	2		453	620	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0041347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	56	662	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.766	0.656	0.887	0.766	0.656	0.887	SUBCLONAL	1	FALSE	1	0.236616429337073	2		663	618	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	72	564	0	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	FALSE	1	0.236616429337073	2		564	598	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061169	38061169	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1489466891	NA	P-0041347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	67	260	1	ENST00000250448.2:c.820del	p.Ala274ProfsTer47	p.A274Pfs*47	ENST00000250448	NM_004496.3	274	Gcc/cc	2/2	1	2	FACETS	0.853	0.746	0.966	1	0.978	1	CLONAL	2	FALSE	1	0.236616429337073	2		261	332	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	105	624	0	ENST00000227507.2:c.859C>T	p.Pro287Ser	p.P287S	ENST00000227507	NM_053056.2	287	Ccc/Tcc	5/5	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	FALSE	1	0.236616429337073	2		624	870	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151825	108151825	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	26	327	1	ENST00000278616.4:c.3510del	p.Lys1170AsnfsTer11	p.K1170Nfs*11	ENST00000278616	NM_000051.3	1169	gAa/ga	24/63	1	2	FACETS	0.678	0.538	0.839	0.678	0.538	0.839	SUBCLONAL	1	FALSE	1	0.236616429337073	2		328	324	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0041347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	81	664	1	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	FALSE	1	0.236616429337073	2		665	627	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984559	72984559	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770062973	NA	P-0041347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	137	589	1	ENST00000268489.5:c.3025G>A	p.Val1009Met	p.V1009M	ENST00000268489	NM_006885.3	1009	Gtg/Atg	3/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.236616429337073	2		590	1017	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432208	121432208	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs137853240	NA	P-0041347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	63	429	0	ENST00000257555.6:c.955G>A	p.Gly319Ser	p.G319S	ENST00000257555		319	Ggt/Agt	4/10	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	FALSE	1	0.236616429337073	2		429	529	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829701	72829701	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	93	488	0	ENST00000268489.5:c.6880C>T	p.Arg2294Ter	p.R2294*	ENST00000268489	NM_006885.3	2294	Cga/Tga	9/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.236616429337073	2		488	657	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094289	27094290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0041347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	67	264	0	ENST00000324856.7:c.2999_3000dup	p.Ser1001LeufsTer39	p.S1001Lfs*39	ENST00000324856	NM_006015.4	999	-/TC	11/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.236616429337073	2		264	400	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699491	117699491	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	45	288	0	ENST00000369458.3:c.150G>T	p.Glu50Asp	p.E50D	ENST00000369458	NM_024626.3	50	gaG/gaT	3/6	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	FALSE	1	0.236616429337073	2		288	338	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685306	89685313	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	ATACAATC	ATACAATC	-	novel	NA	P-0041347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	21	166	0	ENST00000371953.3:c.201_208del	p.Tyr68LeufsTer3	p.Y68Lfs*3	ENST00000371953	NM_000314.4	67	atATACAATCtt/attt	3/9	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	FALSE	1	0.236616429337073	2		166	153	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316396	14316397	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0041347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	39	338	0	ENST00000256196.4:c.208_209delinsTT	p.Ala70Leu	p.A70L	ENST00000256196		70	GCa/TTa	3/6	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	FALSE	1	0.236616429337073	2		338	318	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343387	118343387	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782213033	NA	P-0041347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	59	338	1	ENST00000534358.1:c.1513G>A	p.Asp505Asn	p.D505N	ENST00000534358	NM_005933.3	505	Gat/Aat	3/36	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.236616429337073	2		339	338	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139045	50139045	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	120	621	0	ENST00000246792.3:c.518C>T	p.Ala173Val	p.A173V	ENST00000246792	NM_006270.3	173	gCc/gTc	5/6	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	FALSE	1	0.236616429337073	2		621	943	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795105	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0041347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	103	628	0	ENST00000334409.5:c.104_105del	p.Pro35HisfsTer70	p.P35Hfs*70	ENST00000334409	NM_005018.2	35	cCC/c	2/5	1	2	FACETS	0.992	0.886	1	0.992	0.886	1	CLONAL	1	FALSE	1	0.236616429337073	2		628	878	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294907	1294907	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	13	89	0	ENST00000310581.5:c.198del	p.Ala67ProfsTer11	p.A67Pfs*11	ENST00000310581	NM_198253.2	66	ccC/cc	1/16	1	2	FACETS	0.796	0.58	1	1	0.89	1	CLONAL	2	FALSE	1	0.236616429337073	2		89	69	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925514	131925514	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	22	213	0	ENST00000265335.6:c.1437G>T	p.Gln479His	p.Q479H	ENST00000265335		479	caG/caT	9/25	1	2	FACETS	0.802	0.623	1	0.802	0.623	1	CLONAL	1	FALSE	1	0.236616429337073	2		213	232	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778752	76778752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	32	331	0	ENST00000373344.5:c.6827C>T	p.Ala2276Val	p.A2276V	ENST00000373344	NM_000489.3	2276	gCt/gTt	31/35	1	2	FACETS	1	0.82	1	1	0.82	1	CLONAL	1	FALSE	1	0.236616429337073	2		331	269	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939984	76939984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	46	429	1	ENST00000373344.5:c.764C>T	p.Thr255Ile	p.T255I	ENST00000373344	NM_000489.3	255	aCa/aTa	9/35	1	2	FACETS	0.896	0.755	1	0.896	0.755	1	CLONAL	1	FALSE	1	0.236616429337073	2		430	434	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940035	76940035	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	74	369	0	ENST00000373344.5:c.713C>T	p.Ala238Val	p.A238V	ENST00000373344	NM_000489.3	238	gCt/gTt	9/35	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.236616429337073	2		369	457	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015010	37015010	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762649232	NA	P-0041348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	27	459	0	ENST00000358127.4:c.394G>A	p.Val132Ile	p.V132I	ENST00000358127	NM_001280556.1	132	Gtc/Atc	3/10	0.309739754405904	3	FACETS	0.745	0.596	0.913	0.372	0.298	0.457	CLONAL	1	TRUE	1	0.382206782624869	3		459	226	SUCCESS
APC	324	MSKCC	GRCh37	5	112175770	112175773	+	frameshift_variant	Frame_Shift_Del	DEL	GGAA	GGAA	-	novel	NA	P-0041348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	16	309	0	ENST00000257430.4:c.4479_4482del	p.Glu1494ValfsTer12	p.E1494Vfs*12	ENST00000257430	NM_000038.5	1493	acGGAA/ac	16/16	0.309739754405904	3	FACETS	1	0.896	1	0.712	0.539	0.907	CLONAL	1	TRUE	1	0.382206782624869	3		309	70	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691003	NA	P-0041348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	86	649	2	ENST00000269305.4:c.96+1G>T		p.X32_splice	ENST00000269305	NM_001126112.2	32			0.221251611066599	4	FACETS	1	0.947	1	0.802	0.726	0.878	INDETERMINATE	3	TRUE	0	0.382206782624869	4		651	194	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	178	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.954	0.888	1	0.954	0.888	1	CLONAL	1	TRUE	1	0.807730171974448	2		473	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567546196	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	176	838	1	ENST00000269305.4:c.949del	p.Gln317SerfsTer28	p.Q317Sfs*28	ENST00000269305	NM_001126112.2	317	Cag/ag	9/11	1	2	FACETS	0.535	0.494	0.579	0.535	0.494	0.579	SUBCLONAL	1	TRUE	1	0.807730171974448	2		839	814	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	24	468	1	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.122	0.095	0.153	0.122	0.095	0.153	SUBCLONAL	1	TRUE	1	0.807730171974448	2		469	487	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057209	30057209	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	64	598	0	ENST00000338641.4:c.691G>T	p.Glu231Ter	p.E231*	ENST00000338641	NM_000268.3	231	Gag/Tag	8/16	1	2	FACETS	0.301	0.26	0.344	0.301	0.26	0.344	SUBCLONAL	1	TRUE	1	0.807730171974448	2		598	527	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026115	14026116	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs769120755	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	58	280	0	ENST00000311895.7:c.1081dup	p.Met361AsnfsTer4	p.M361Nfs*4	ENST00000311895	NM_005236.2	359	gaa/gAaa	6/11	1	2	FACETS	0.445	0.384	0.51	0.445	0.384	0.51	SUBCLONAL	1	TRUE	1	0.807730171974448	2		280	323	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	30	227	0	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.184	0.148	0.225	0.184	0.148	0.225	SUBCLONAL	1	TRUE	1	0.807730171974448	2		227	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	282	841	1	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	1	2	FACETS	0.977	0.923	1	0.977	0.923	1	CLONAL	1	TRUE	1	0.807730171974448	2		842	715	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958479	90958480	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs780235686	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	129	402	0	ENST00000265433.3:c.1958dup	p.Leu654AlafsTer5	p.L654Afs*5	ENST00000265433	NM_002485.4	653	aag/aaAg	13/16	1	2	FACETS	0.87	0.798	0.944	0.87	0.798	0.944	CLONAL	1	TRUE	1	0.807730171974448	2		402	367	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736510	85736511	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs387906351	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	113	310	2	ENST00000370580.1:c.136dup	p.Ile46AsnfsTer4	p.I46Nfs*4	ENST00000370580	NM_003921.4	46	ata/aAta	2/3	1	2	FACETS	0.797	0.725	0.871	0.797	0.725	0.871	SUBCLONAL	1	TRUE	1	0.807730171974448	2		312	351	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637121	176637122	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1299932363	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	41	743	0	ENST00000439151.2:c.1727dup	p.Asn576LysfsTer8	p.N576Kfs*8	ENST00000439151	NM_022455.4	574	gga/ggAa	5/23	1	2	FACETS	0.153	0.127	0.182	0.153	0.127	0.182	SUBCLONAL	1	TRUE	1	0.807730171974448	2		743	663	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957464	175957465	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	120	594	0	ENST00000367669.3:c.1931dup	p.Asn644LysfsTer17	p.N644Kfs*17	ENST00000367669	NM_022457.5	644	aac/aaAc	17/20	0.807730171974448	1	FACETS	0.521	0.476	0.567	0.521	0.476	0.567	SUBCLONAL	1	TRUE	0	0.807730171974448	1		594	340	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694716	176694716	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	60	470	0	ENST00000439151.2:c.5300A>G	p.Tyr1767Cys	p.Y1767C	ENST00000439151	NM_022455.4	1767	tAc/tGc	15/23	1	2	FACETS	0.295	0.254	0.34	0.295	0.254	0.34	SUBCLONAL	1	TRUE	1	0.807730171974448	2		470	503	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628355	86628355	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	69	301	0	ENST00000274376.6:c.724G>A	p.Gly242Ser	p.G242S	ENST00000274376	NM_002890.2	242	Ggt/Agt	3/25	1	2	FACETS	0.724	0.639	0.813	0.724	0.639	0.813	SUBCLONAL	1	TRUE	1	0.807730171974448	2		301	236	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	86	650	3	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.266	0.235	0.3	0.266	0.235	0.3	SUBCLONAL	1	TRUE	1	0.807730171974448	2		653	800	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384726	17384726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368554117	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	331	850	1	ENST00000359435.4:c.358G>A	p.Ala120Thr	p.A120T	ENST00000359435	NM_001033549.1	120	Gcc/Acc	4/9	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.807730171974448	2		851	803	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99473480	99473480	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	130	411	0	ENST00000268035.6:c.2902G>T	p.Gly968Trp	p.G968W	ENST00000268035	NM_000875.3	968	Ggg/Tgg	15/21	1	2	FACETS	0.768	0.703	0.836	0.768	0.703	0.836	SUBCLONAL	1	TRUE	1	0.807730171974448	2		411	419	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441815	49441816	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs756471180	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	314	855	0	ENST00000301067.7:c.4168dup	p.Ala1390GlyfsTer42	p.A1390Gfs*42	ENST00000301067	NM_003482.3	1390	gca/gGca	14/54	1	2	FACETS	0.913	0.864	0.962	0.913	0.864	0.962	CLONAL	1	TRUE	1	0.807730171974448	2		855	852	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589609	67589610	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	89	232	0	ENST00000274335.5:c.1378dup	p.Ser460LysfsTer5	p.S460Kfs*5	ENST00000274335		458	gaa/gAaa	10/15	1	2	FACETS	0.954	0.861	1	0.954	0.861	1	CLONAL	1	TRUE	1	0.807730171974448	2		232	231	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508715	38508715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758973243	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	69	834	3	ENST00000254066.5:c.763G>A	p.Ala255Thr	p.A255T	ENST00000254066	NM_000964.3	255	Gcc/Acc	6/9	0.807730171974448	1	FACETS	0.219	0.191	0.249	0.219	0.191	0.249	SUBCLONAL	1	TRUE	0	0.807730171974448	1		837	465	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627721	14627722	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1239666815	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	336	880	4	ENST00000254322.2:c.348dup	p.Gly117TrpfsTer12	p.G117Wfs*12	ENST00000254322	NM_006145.1	116	-/T	2/3	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.807730171974448	2		884	829	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156139	106156139	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755979073	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	57	447	1	ENST00000380013.4:c.1040C>T	p.Ala347Val	p.A347V	ENST00000380013	NM_001127208.2	347	gCg/gTg	3/11	1	2	FACETS	0.356	0.306	0.409	0.356	0.306	0.409	SUBCLONAL	1	TRUE	1	0.807730171974448	2		448	397	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435030	56435030	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	295	885	1	ENST00000407977.2:c.2107C>T	p.Pro703Ser	p.P703S	ENST00000407977		703	Cct/Tct	9/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.807730171974448	2		886	717	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391198	89391198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	62	493	0	ENST00000336596.2:c.1264C>T	p.Pro422Ser	p.P422S	ENST00000336596	NM_005233.5	422	Cca/Tca	5/17	1	2	FACETS	0.296	0.255	0.339	0.296	0.255	0.339	SUBCLONAL	1	TRUE	1	0.807730171974448	2		493	519	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665110	182665110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1361986556	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	20	350	0	ENST00000292782.4:c.616C>T	p.Arg206Ter	p.R206*	ENST00000292782	NM_020640.2	206	Cga/Tga	6/7	1	2	FACETS	0.15	0.114	0.192	0.15	0.114	0.192	SUBCLONAL	1	TRUE	1	0.807730171974448	2		350	330	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435263	110435263	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	38	206	0	ENST00000375856.3:c.3138del	p.Ala1047ProfsTer59	p.A1047Pfs*59	ENST00000375856	NM_003749.2	1046	ccC/cc	1/2	1	2	FACETS	0.381	0.317	0.452	0.381	0.317	0.452	SUBCLONAL	1	TRUE	1	0.807730171974448	2		206	247	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690602	88690602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745856667	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	220	556	0	ENST00000360948.2:c.428C>T	p.Ser143Leu	p.S143L	ENST00000360948	NM_001012338.2	143	tCg/tTg	5/19	1	2	FACETS	0.98	0.919	1	0.98	0.919	1	CLONAL	1	TRUE	1	0.807730171974448	2		556	556	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212195	36212195	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1436747286	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	50	866	0	ENST00000222270.7:c.1946C>T	p.Ala649Val	p.A649V	ENST00000222270	NM_014727.1	649	gCc/gTc	3/37	1	2	FACETS	0.173	0.146	0.203	0.173	0.146	0.203	SUBCLONAL	1	TRUE	1	0.807730171974448	2		866	716	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240795	55240795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373336251	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	312	1177	1	ENST00000275493.2:c.2039G>A	p.Arg680Gln	p.R680Q	ENST00000275493	NM_005228.3	680	cGg/cAg	17/28	1	2	FACETS	0.805	0.761	0.85	0.805	0.761	0.85	CLONAL	1	TRUE	1	0.807730171974448	2		1178	960	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085885	16085885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs185639773	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	235	689	0	ENST00000281043.3:c.1061C>T	p.Ala354Val	p.A354V	ENST00000281043	NM_005378.4	354	gCg/gTg	3/3	1	2	FACETS	0.97	0.912	1	0.97	0.912	1	CLONAL	1	TRUE	1	0.807730171974448	2		689	600	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967945	93967945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745827385	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	196	615	1	ENST00000369303.4:c.1982C>T	p.Ala661Val	p.A661V	ENST00000369303	NM_004440.3	661	gCa/gTa	11/17	1	2	FACETS	0.99	0.926	1	0.99	0.926	1	CLONAL	1	TRUE	1	0.807730171974448	2		616	490	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811652	102811652	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	344	781	3	ENST00000307046.8:c.532C>T	p.Gln178Ter	p.Q178*	ENST00000307046	NM_001111285.1	178	Cag/Tag	4/4	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.807730171974448	2		784	810	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439673	51439673	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	26	470	0	ENST00000262662.1:c.238G>T	p.Ala80Ser	p.A80S	ENST00000262662		80	Gca/Tca	4/4	1	2	FACETS	0.142	0.112	0.177	0.142	0.112	0.177	SUBCLONAL	1	TRUE	1	0.807730171974448	2		470	453	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845434	156845434	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	356	1056	0	ENST00000524377.1:c.1477A>G	p.Asn493Asp	p.N493D	ENST00000524377	NM_002529.3	493	Aac/Gac	12/17	0.684861604488746	3	FACETS	0.933	0.884	0.984	0.467	0.442	0.492	CLONAL	1	TRUE	1	0.807730171974448	3		1056	1326	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615192	43615192	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	267	880	1	ENST00000355710.3:c.2606A>G	p.Lys869Arg	p.K869R	ENST00000355710	NM_020975.4	869	aAg/aGg	14/20	1	2	FACETS	0.884	0.833	0.936	0.884	0.833	0.936	CLONAL	1	TRUE	1	0.807730171974448	2		881	748	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450120	32450120	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1372808262	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	115	876	1	ENST00000332351.3:c.692C>T	p.Thr231Met	p.T231M	ENST00000332351	NM_024426.4	231	aCg/aTg	2/10	1	2	FACETS	0.275	0.247	0.304	0.275	0.247	0.304	SUBCLONAL	1	TRUE	1	0.807730171974448	2		877	1037	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307522	118307522	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1170856958	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	125	445	0	ENST00000534358.1:c.295G>T	p.Ala99Ser	p.A99S	ENST00000534358	NM_005933.3	99	Gcc/Tcc	1/36	0.807730171974448	1	FACETS	0.593	0.545	0.642	0.593	0.545	0.642	SUBCLONAL	1	TRUE	0	0.807730171974448	1		445	311	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944895	31944895	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	185	460	0	ENST00000340398.3:c.206G>T	p.Arg69Met	p.R69M	ENST00000340398	NM_001013699.2	69	aGg/aTg	1/1	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.807730171974448	2		460	411	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440540	49440540	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	389	1106	0	ENST00000301067.7:c.4270T>C	p.Cys1424Arg	p.C1424R	ENST00000301067	NM_003482.3	1424	Tgt/Cgt	15/54	1	2	FACETS	0.945	0.901	0.99	0.945	0.901	0.99	CLONAL	1	TRUE	1	0.807730171974448	2		1106	1019	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923260	26923260	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	129	388	1	ENST00000381527.3:c.256C>A	p.Leu86Met	p.L86M	ENST00000381527	NM_001260.1	86	Ctg/Atg	3/13	1	2	FACETS	0.878	0.805	0.952	0.878	0.805	0.952	CLONAL	1	TRUE	1	0.807730171974448	2		389	364	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609643	28609643	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	188	535	2	ENST00000241453.7:c.1586T>C	p.Leu529Ser	p.L529S	ENST00000241453	NM_004119.2	529	tTa/tCa	12/24	1	2	FACETS	0.95	0.886	1	0.95	0.886	1	CLONAL	1	TRUE	1	0.807730171974448	2		537	490	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396642	396642	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	270	803	0	ENST00000262320.3:c.384G>T	p.Glu128Asp	p.E128D	ENST00000262320	NM_003502.3	128	gaG/gaT	2/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.807730171974448	2		803	664	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2113048	2113048	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	305	898	0	ENST00000219476.3:c.1437C>A	p.Phe479Leu	p.F479L	ENST00000219476	NM_000548.3	479	ttC/ttA	14/42	1	2	FACETS	0.936	0.886	0.986	0.936	0.886	0.986	CLONAL	1	TRUE	1	0.807730171974448	2		898	807	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789628	3789629	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1555473668	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	263	686	0	ENST00000262367.5:c.4230dup	p.Gly1411TrpfsTer10	p.G1411Wfs*10	ENST00000262367	NM_004380.2	1410	-/T	25/31	1	2	FACETS	0.913	0.861	0.967	0.913	0.861	0.967	CLONAL	1	TRUE	1	0.807730171974448	2		686	713	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828179	72828179	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	259	822	0	ENST00000268489.5:c.8402G>T	p.Ser2801Ile	p.S2801I	ENST00000268489	NM_006885.3	2801	aGc/aTc	9/10	1	2	FACETS	0.929	0.876	0.984	0.929	0.876	0.984	CLONAL	1	TRUE	1	0.807730171974448	2		822	690	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351401	89351401	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	153	941	0	ENST00000301030.4:c.1549T>C	p.Ser517Pro	p.S517P	ENST00000301030	NM_001256183.1	517	Tcc/Ccc	9/13	1	2	FACETS	0.496	0.454	0.539	0.496	0.454	0.539	SUBCLONAL	1	TRUE	1	0.807730171974448	2		941	764	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216977	7216977	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	260	630	1	ENST00000380728.2:c.544G>T	p.Gly182Cys	p.G182C	ENST00000380728		182	Ggc/Tgc	7/11	1	2	FACETS	0.983	0.927	1	0.983	0.927	1	CLONAL	1	TRUE	1	0.807730171974448	2		631	655	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029394	16029394	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	105	360	0	ENST00000268712.3:c.1634+2T>C		p.X545_splice	ENST00000268712	NM_006311.3	545			1	2	FACETS	0.712	0.644	0.783	0.712	0.644	0.783	SUBCLONAL	1	TRUE	1	0.807730171974448	2		360	365	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40876328	40876328	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	157	731	0	ENST00000428826.2:c.361T>G	p.Phe121Val	p.F121V	ENST00000428826		121	Ttt/Gtt	5/21	1	2	FACETS	0.607	0.558	0.658	0.607	0.558	0.658	SUBCLONAL	1	TRUE	1	0.807730171974448	2		731	640	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245482	41245482	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	402	963	0	ENST00000357654.3:c.2066G>T	p.Ser689Ile	p.S689I	ENST00000357654	NM_007294.3	689	aGt/aTt	10/23	1	2	FACETS	0.936	0.892	0.98	0.936	0.892	0.98	CLONAL	1	TRUE	1	0.807730171974448	2		963	1064	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677855	47677855	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	137	741	2	ENST00000347630.2:c.1010G>A	p.Gly337Glu	p.G337E	ENST00000347630	NM_001007230.1	337	gGg/gAg	11/11	1	2	FACETS	0.551	0.502	0.601	0.551	0.502	0.601	SUBCLONAL	1	TRUE	1	0.807730171974448	2		743	616	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78519505	78519505	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	281	721	1	ENST00000306801.3:c.76C>A	p.Leu26Ile	p.L26I	ENST00000306801	NM_020761.2	26	Cta/Ata	1/34	1	2	FACETS	0.988	0.934	1	0.988	0.934	1	CLONAL	1	TRUE	1	0.807730171974448	2		722	704	SUCCESS
YES1	7525	MSKCC	GRCh37	18	739785	739785	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	49	589	0	ENST00000314574.4:c.1087G>T	p.Gly363Ter	p.G363*	ENST00000314574	NM_005433.3	363	Gga/Tga	9/12	1	2	FACETS	0.195	0.165	0.229	0.195	0.165	0.229	SUBCLONAL	1	TRUE	1	0.807730171974448	2		589	621	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394765	45394765	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	161	483	0	ENST00000262160.6:c.584A>T	p.Asp195Val	p.D195V	ENST00000262160	NM_005901.5	195	gAc/gTc	5/11	1	2	FACETS	0.89	0.824	0.957	0.89	0.824	0.957	CLONAL	1	TRUE	1	0.807730171974448	2		483	448	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218535	5218535	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	53	981	0	ENST00000357368.4:c.3944del	p.Lys1315ArgfsTer11	p.K1315Rfs*11	ENST00000357368	NM_002850.3	1315	aAg/ag	25/38	1	2	FACETS	0.141	0.12	0.165	0.141	0.12	0.165	SUBCLONAL	1	TRUE	1	0.807730171974448	2		981	928	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271711	15271711	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	435	1301	3	ENST00000263388.2:c.6728C>A	p.Pro2243His	p.P2243H	ENST00000263388	NM_000435.2	2243	cCt/cAt	33/33	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.807730171974448	2		1304	1028	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285125	15285125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	77	861	3	ENST00000263388.2:c.4490G>A	p.Gly1497Glu	p.G1497E	ENST00000263388	NM_000435.2	1497	gGg/gAg	25/33	1	2	FACETS	0.225	0.197	0.256	0.225	0.197	0.256	SUBCLONAL	1	TRUE	1	0.807730171974448	2		864	846	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257923	19257923	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	79	1192	0	ENST00000162023.5:c.463A>G	p.Ser155Gly	p.S155G	ENST00000162023		155	Agt/Ggt	9/13	1	2	FACETS	0.183	0.16	0.208	0.183	0.16	0.208	SUBCLONAL	1	TRUE	1	0.807730171974448	2		1192	1070	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791048	42791048	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	220	660	0	ENST00000575354.2:c.193C>A	p.Pro65Thr	p.P65T	ENST00000575354	NM_015125.3	65	Cca/Aca	2/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.807730171974448	2		660	532	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921116	50921116	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	276	829	0	ENST00000440232.2:c.3236T>C	p.Phe1079Ser	p.F1079S	ENST00000440232	NM_002691.3	1079	tTc/tCc	27/27	1	2	FACETS	0.982	0.928	1	0.982	0.928	1	CLONAL	1	TRUE	1	0.807730171974448	2		829	696	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594143	158594143	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	170	445	0	ENST00000263640.3:c.1430G>A	p.Cys477Tyr	p.C477Y	ENST00000263640	NM_001105.4	477	tGc/tAc	11/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.807730171974448	2		445	413	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198262717	198262717	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	140	437	1	ENST00000335508.6:c.3258G>T	p.Lys1086Asn	p.K1086N	ENST00000335508	NM_012433.2	1086	aaG/aaT	22/25	1	2	FACETS	0.764	0.701	0.828	0.764	0.701	0.828	SUBCLONAL	1	TRUE	1	0.807730171974448	2		438	454	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46277848	46277848	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	195	450	0	ENST00000371998.3:c.3646T>C	p.Ser1216Pro	p.S1216P	ENST00000371998		1216	Tcc/Ccc	19/23	1	2	FACETS	0.943	0.881	1	0.943	0.881	1	CLONAL	1	TRUE	1	0.807730171974448	2		450	512	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572250	41572250	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	49	676	0	ENST00000263253.7:c.4780-1G>T		p.X1594_splice	ENST00000263253	NM_001429.3	1594			1	2	FACETS	0.176	0.148	0.207	0.176	0.148	0.207	SUBCLONAL	1	TRUE	1	0.807730171974448	2		676	689	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626370	12626370	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	44	683	0	ENST00000251849.4:c.1779G>T	p.Lys593Asn	p.K593N	ENST00000251849	NM_002880.3	593	aaG/aaT	16/17	1	2	FACETS	0.172	0.144	0.204	0.172	0.144	0.204	SUBCLONAL	1	TRUE	1	0.807730171974448	2		683	632	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138375117	138375117	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	201	464	0	ENST00000289153.2:c.2943-1G>T		p.X981_splice	ENST00000289153	NM_006219.2	981			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.807730171974448	2		464	486	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502791	186502791	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	120	526	0	ENST00000323963.5:c.249G>T	p.Lys83Asn	p.K83N	ENST00000323963		83	aaG/aaT	4/11	1	2	FACETS	0.57	0.517	0.626	0.57	0.517	0.626	SUBCLONAL	1	TRUE	1	0.807730171974448	2		526	521	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509934	187509934	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	163	474	0	ENST00000441802.2:c.13579T>A	p.Phe4527Ile	p.F4527I	ENST00000441802	NM_005245.3	4527	Ttc/Atc	27/27	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.807730171974448	2		474	388	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945792	38945792	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	76	282	0	ENST00000357387.3:c.4434T>A	p.Asn1478Lys	p.N1478K	ENST00000357387	NM_152756.3	1478	aaT/aaA	34/38	1	2	FACETS	0.833	0.742	0.926	0.833	0.742	0.926	CLONAL	1	TRUE	1	0.807730171974448	2		282	226	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827863	170827864	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	25	386	0	ENST00000296930.5:c.608dup	p.Asn203LysfsTer34	p.N203Kfs*34	ENST00000296930	NM_002520.6	201	-/A	8/11	1	2	FACETS	0.155	0.122	0.194	0.155	0.122	0.194	SUBCLONAL	1	TRUE	1	0.807730171974448	2		386	399	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636766	176636766	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	208	585	0	ENST00000439151.2:c.1366C>T	p.Pro456Ser	p.P456S	ENST00000439151	NM_022455.4	456	Cca/Tca	5/23	1	2	FACETS	0.938	0.878	0.999	0.938	0.878	0.999	CLONAL	1	TRUE	1	0.807730171974448	2		585	549	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20483086	20483086	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	174	476	0	ENST00000346618.3:c.819A>C	p.Leu273Phe	p.L273F	ENST00000346618	NM_001949.4	273	ttA/ttC	4/7	1	2	FACETS	0.984	0.916	1	0.984	0.916	1	CLONAL	1	TRUE	1	0.807730171974448	2		476	438	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188279	32188279	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	357	1034	0	ENST00000375023.3:c.1062G>T	p.Glu354Asp	p.E354D	ENST00000375023	NM_004557.3	354	gaG/gaT	6/30	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.807730171974448	2		1034	883	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026600	6026600	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs878854039	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	535	1295	0	ENST00000265849.7:c.1796A>T	p.Asp599Val	p.D599V	ENST00000265849	NM_000535.5	599	gAc/gTc	11/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.807730171974448	2		1295	1316	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380034	116380034	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	157	630	0	ENST00000397752.3:c.1423C>A	p.Pro475Thr	p.P475T	ENST00000397752	NM_000245.2	475	Cct/Act	4/21	1	2	FACETS	0.613	0.564	0.665	0.613	0.564	0.665	SUBCLONAL	1	TRUE	1	0.807730171974448	2		630	634	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851580	128851580	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	269	937	1	ENST00000249373.3:c.1905G>T	p.Gln635His	p.Q635H	ENST00000249373	NM_005631.4	635	caG/caT	11/12	1	2	FACETS	0.885	0.834	0.936	0.885	0.834	0.936	CLONAL	1	TRUE	1	0.807730171974448	2		938	753	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117870637	117870637	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	162	443	0	ENST00000297338.2:c.435G>T	p.Met145Ile	p.M145I	ENST00000297338	NM_006265.2	145	atG/atT	5/14	1	2	FACETS	0.899	0.833	0.967	0.899	0.833	0.967	CLONAL	1	TRUE	1	0.807730171974448	2		443	446	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738026	145738026	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	69	1148	1	ENST00000428558.2:c.2884A>G	p.Arg962Gly	p.R962G	ENST00000428558	NM_004260.3	962	Agg/Ggg	17/22	1	2	FACETS	0.21	0.182	0.24	0.21	0.182	0.24	SUBCLONAL	1	TRUE	1	0.807730171974448	2		1149	814	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5081725	5081725	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	91	198	0	ENST00000381652.3:c.2435A>T	p.Asp812Val	p.D812V	ENST00000381652	NM_004972.3	812	gAt/gTt	19/25	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.807730171974448	2		198	199	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485794	8485794	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	25	352	0	ENST00000356435.5:c.3023G>T	p.Ser1008Ile	p.S1008I	ENST00000356435		1008	aGt/aTt	17/35	1	2	FACETS	0.164	0.129	0.205	0.164	0.129	0.205	SUBCLONAL	1	TRUE	1	0.807730171974448	2		352	377	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528734	8528734	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	37	494	0	ENST00000356435.5:c.398A>G	p.Gln133Arg	p.Q133R	ENST00000356435		133	cAg/cGg	4/35	1	2	FACETS	0.173	0.142	0.207	0.173	0.142	0.207	SUBCLONAL	1	TRUE	1	0.807730171974448	2		494	530	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635128	87635128	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	176	508	0	ENST00000277120.3:c.2180G>T	p.Gly727Val	p.G727V	ENST00000277120		727	gGc/gTc	18/19	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.807730171974448	2		508	433	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787837	135787837	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	78	372	0	ENST00000298552.3:c.745A>G	p.Arg249Gly	p.R249G	ENST00000298552	NM_001162426.1	249	Aga/Gga	9/23	1	2	FACETS	0.423	0.372	0.476	0.423	0.372	0.476	SUBCLONAL	1	TRUE	1	0.807730171974448	2		372	457	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617587	100617587	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	45	460	0	ENST00000308731.7:c.482del	p.Asn161MetfsTer15	p.N161Mfs*15	ENST00000308731	NM_000061.2	161	aAt/at	6/19	1	1	FACETS	0.163	0.137	0.192	0.163	0.137	0.192	SUBCLONAL	1	TRUE	0	0.807730171974448	1		460	408	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480539	123480539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	200	377	0	ENST00000371139.4:c.47G>A	p.Gly16Asp	p.G16D	ENST00000371139	NM_001114937.2	16	gGc/gAc	1/4	1	1	FACETS	0.881	0.834	0.928	0.881	0.834	0.928	CLONAL	1	TRUE	0	0.807730171974448	1		377	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0041463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	297	699	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.606172581670282	1	FACETS	0.888	0.841	0.936	0.888	0.841	0.936	CLONAL	1	TRUE	0	0.630668387209077	1		699	726	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0041463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	229	601	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.630668387209077	2		601	643	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187221	38187222	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	467	867	0	ENST00000317025.8:c.1255dup	p.Thr419AsnfsTer28	p.T419Nfs*28	ENST00000317025	NM_023034.1	419	acc/aAcc	6/24	0.630668387209077	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.630668387209077	1		867	951	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016634	12016634	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	137	420	0	ENST00000353533.5:c.770C>A	p.Ser257Tyr	p.S257Y	ENST00000353533	NM_003010.3	257	tCt/tAt	7/11	0.606172581670282	1	FACETS	0.918	0.848	0.989	0.918	0.848	0.989	CLONAL	1	TRUE	0	0.630668387209077	1		420	324	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591246	67591246	+	splice_acceptor_variant	Splice_Site	DEL	A	A	-	novel	NA	P-0041463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	246	485	0	ENST00000274335.5:c.1746-2del		p.X582_splice	ENST00000274335		582			0.434432318236766	2	FACETS	0.769	0.727	0.811	0.769	0.727	0.811	SUBCLONAL	2	TRUE	0	0.630668387209077	2		485	507	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397235	397235	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	88	471	0	ENST00000380956.4:c.620G>A	p.Gly207Asp	p.G207D	ENST00000380956	NM_001195286.1	207	gGc/gAc	5/9	0.584035302367161	1	FACETS	0.312	0.277	0.35	0.312	0.277	0.35	SUBCLONAL	1	TRUE	0	0.630668387209077	1		471	612	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608966	100608966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	217	541	0	ENST00000308731.7:c.1642G>A	p.Asp548Asn	p.D548N	ENST00000308731	NM_000061.2	548	Gat/Aat	17/19	0.59224580771295	1	FACETS	0.874	0.82	0.929	0.874	0.82	0.929	CLONAL	1	TRUE	0	0.630668387209077	1		541	539	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076958	41076958	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	34	646	0	ENST00000373198.4:c.1462G>T	p.Val488Phe	p.V488F	ENST00000373198	NM_133170.3	488	Gtt/Ttt	9/32	1	2	FACETS	0.179	0.146	0.217	0.179	0.146	0.217	SUBCLONAL	1	NA	1	0.649353948781032	2		646	584	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0041475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	84	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.432248515986713	1	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	0	0.432248515986713	1		288	303	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0041475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	215	792	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.432248515986713	1	FACETS	0.915	0.852	0.98	0.915	0.852	0.98	CLONAL	1	TRUE	0	0.432248515986713	1		793	852	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333863	70333863	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs750883311	NA	P-0041475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	121	367	0	ENST00000373644.4:c.1768C>T	p.Arg590Ter	p.R590*	ENST00000373644	NM_030625.2	590	Cga/Tga	2/12	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.432248515986713	2		367	554	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026184	71026184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	78	289	0	ENST00000318789.4:c.1438G>A	p.Glu480Lys	p.E480K	ENST00000318789	NM_032682.5	480	Gaa/Aaa	17/21	1	2	FACETS	0.833	0.736	0.938	0.833	0.736	0.938	CLONAL	1	TRUE	1	0.432248515986713	2		289	433	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844780	156844780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	134	597	0	ENST00000524377.1:c.1334G>A	p.Arg445Lys	p.R445K	ENST00000524377	NM_002529.3	445	aGa/aAa	11/17	1	2	FACETS	0.647	0.587	0.71	0.647	0.587	0.71	SUBCLONAL	1	TRUE	1	0.432248515986713	2		597	959	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431508	49431508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	222	634	0	ENST00000301067.7:c.9631G>A	p.Glu3211Lys	p.E3211K	ENST00000301067	NM_003482.3	3211	Gaa/Aaa	34/54	0.432248515986713	1	FACETS	0.95	0.886	1	0.95	0.886	1	CLONAL	1	TRUE	0	0.432248515986713	1		634	848	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435531	110435531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	168	425	0	ENST00000375856.3:c.2870C>T	p.Ser957Leu	p.S957L	ENST00000375856	NM_003749.2	957	tCg/tTg	1/2	1	2	FACETS	0.94	0.865	1	0.94	0.865	1	CLONAL	1	TRUE	1	0.432248515986713	2		425	827	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216151	36216151	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	223	581	0	ENST00000222270.7:c.3559A>C	p.Met1187Leu	p.M1187L	ENST00000222270	NM_014727.1	1187	Atg/Ctg	11/37	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.432248515986713	2		581	921	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537980	212537980	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	109	323	0	ENST00000342788.4:c.1625A>C	p.Glu542Ala	p.E542A	ENST00000342788	NM_005235.2	542	gAa/gCa	14/28	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.432248515986713	2		323	442	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217193	66217193	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	106	421	0	ENST00000273854.3:c.2422A>C	p.Ile808Leu	p.I808L	ENST00000273854	NM_004439.5	808	Atc/Ctc	14/18	1	2	FACETS	0.857	0.771	0.949	0.857	0.771	0.949	CLONAL	1	TRUE	1	0.432248515986713	2		421	572	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158504	26158504	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	172	435	0	ENST00000289316.2:c.107A>C	p.Glu36Ala	p.E36A	ENST00000289316	NM_138720.2	36	gAg/gCg	1/2	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.432248515986713	2		435	739	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050832	5050832	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0041475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	74	362	0	ENST00000381652.3:c.614+1G>T		p.X205_splice	ENST00000381652	NM_004972.3	205			0.432248515986713	1	FACETS	0.877	0.775	0.985	0.877	0.775	0.985	CLONAL	1	TRUE	0	0.432248515986713	1		362	306	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0041476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	104	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.389022527316026	4	FACETS	0.928	0.838	1	0.928	0.838	1	CLONAL	2	TRUE	2	0.389022527316026	4		473	400	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150496	157150496	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs17318151	NA	P-0041476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	144	529	0	ENST00000346085.5:c.1678A>G	p.Ile560Val	p.I560V	ENST00000346085	NM_020732.3	560	Att/Gtt	2/20	0.389022527316026	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	0	0.389022527316026	2		529	366	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs967461896	NA	P-0041476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	171	619	0	ENST00000269305.4:c.526T>A	p.Cys176Ser	p.C176S	ENST00000269305	NM_001126112.2	176	Tgc/Agc	5/11	0.389022527316026	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.389022527316026	2		619	417	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412030	116412048	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TACTTTTCCAGAAGGTATA	TACTTTTCCAGAAGGTATA	-	novel	NA	P-0041506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	80	908	0	ENST00000397752.3:c.3016_3028+6del		p.X1006_splice	ENST00000397752	NM_000245.2	1006		14/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		908	872	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	79	345	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.316935755631974	2		345	456	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183739	10183739	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs5030802	NA	P-0041511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	95	995	1	ENST00000256474.2:c.208G>T	p.Glu70Ter	p.E70*	ENST00000256474	NM_000551.3	70	Gag/Tag	1/3	0.316935755631974	1	FACETS	0.954	0.852	1	0.954	0.852	1	CLONAL	1	TRUE	0	0.316935755631974	1		996	529	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174383	11174383	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057524044	NA	P-0041511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	76	697	1	ENST00000361445.4:c.7292T>C	p.Leu2431Pro	p.L2431P	ENST00000361445	NM_004958.3	2431	cTg/cCg	53/58	0.316935755631974	0	FACETS	0.733	0.645	0.826			1	SUBCLONAL	1	TRUE	0	0.316935755631974	0		698	447	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866383	37866383	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776960538	NA	P-0041511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	124	919	1	ENST00000269571.5:c.688C>T	p.Pro230Ser	p.P230S	ENST00000269571		230	Cca/Tca	6/27	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.316935755631974	2		920	654	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584650	52584650	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	104	812	1	ENST00000394830.3:c.4363G>T	p.Gly1455Ter	p.G1455*	ENST00000394830	NM_018313.4	1455	Gga/Tga	29/30	0.316935755631974	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	0	0.316935755631974	1		813	545	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0041528-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	174	275	1	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	1	2	FACETS	0.909	0.839	0.981	0.909	0.839	0.981	CLONAL	1	TRUE	1	0.534696874756645	2		276	716	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346338	73346338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041528-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	106	494	0	ENST00000377767.4:c.1462G>A	p.Asp488Asn	p.D488N	ENST00000377767	NM_014953.3	488	Gat/Aat	10/21	1	2	FACETS	0.75	0.674	0.829	0.75	0.674	0.829	SUBCLONAL	1	TRUE	1	0.534696874756645	2		494	529	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468912	25468912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780672407	NA	P-0041528-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	157	511	1	ENST00000264709.3:c.1451G>A	p.Arg484Gln	p.R484Q	ENST00000264709	NM_175629.2	484	cGg/cAg	12/23	1	2	FACETS	0.875	0.804	0.949	0.875	0.804	0.949	CLONAL	1	TRUE	1	0.534696874756645	2		512	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577106	+	inframe_insertion	In_Frame_Ins	INS	-	-	GACAGGCACAAACACGCACCTCAAAGCTGTTCCGTCCCAGTAGATTACCAT	novel	NA	P-0041528-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	140	777	0	ENST00000269305.4:c.832_833insATGGTAATCTACTGGGACGGAACAGCTTTGAGGTGCGTGTTTGTGCCTGTC	p.Cys277_Pro278insHisGlyAsnLeuLeuGlyArgAsnSerPheGluValArgValCysAlaCys	p.C277_P278insHGNLLGRNSFEVRVCAC	ENST00000269305	NM_001126112.2	278	cct/cATGGTAATCTACTGGGACGGAACAGCTTTGAGGTGCGTGTTTGTGCCTGTCct	8/11	0.534696874756645	1	FACETS	0.426	0.388	0.467	0.426	0.388	0.467	SUBCLONAL	1	TRUE	0	0.534696874756645	1		777	900	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011106	12011106	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0041528-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	114	413	0	ENST00000353533.5:c.514-1G>A		p.X172_splice	ENST00000353533	NM_003010.3	172			0.534696874756645	1	FACETS	0.87	0.792	0.951	0.87	0.792	0.951	CLONAL	1	TRUE	0	0.534696874756645	1		413	359	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554451	63554452	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0041528-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	240	816	0	ENST00000307078.5:c.287_288delinsTT	p.Arg96Leu	p.R96L	ENST00000307078	NM_004655.3	96	cGA/cTT	2/11	1	2	FACETS	0.855	0.798	0.913	0.855	0.798	0.913	CLONAL	1	TRUE	1	0.534696874756645	2		816	1050	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31424568	31424569	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CG	novel	NA	P-0041528-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	212	518	0	ENST00000344624.3:c.3225_3226dup	p.Glu1076AlafsTer42	p.E1076Afs*42	ENST00000344624		1076	gaa/gCGaa	25/33	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.534696874756645	2		518	731	SUCCESS
APC	324	MSKCC	GRCh37	5	112174774	112174774	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041528-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	222	665	0	ENST00000257430.4:c.3484del	p.Tyr1162IlefsTer3	p.Y1162Ifs*3	ENST00000257430	NM_000038.5	1161	aaT/aa	16/16	1	2	FACETS	0.97	0.905	1	0.97	0.905	1	CLONAL	1	TRUE	1	0.534696874756645	2		665	856	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554452	63554452	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041528-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	240	811	0	ENST00000307078.5:c.287G>T	p.Arg96Leu	p.R96L	ENST00000307078	NM_004655.3	96	cGa/cTa	2/11	1	2	FACETS	0.855	0.798	0.913	0.855	0.798	0.913	CLONAL	1	TRUE	1	0.534696874756645	2		811	1050	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	493262	493262	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041528-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	41	601	0	ENST00000399788.2:c.301C>T	p.Gln101Ter	p.Q101*	ENST00000399788	NM_001042603.1	101	Caa/Taa	3/28	1	2	FACETS	0.202	0.167	0.241	0.202	0.167	0.241	SUBCLONAL	1	TRUE	1	0.534696874756645	2		601	759	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182641	38182641	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs387907272	NA	P-0041531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	19	900	0	ENST00000396334.3:c.794T>C	p.Leu265Pro	p.L265P	ENST00000396334	NM_002468.4	265	cTg/cCg	5/5	1	2	FACETS	0.471	0.355	0.607	0.471	0.355	0.607	SUBCLONAL	1	TRUE	1	0.12	2		900	673	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482340	56482341	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0041531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	29	624	0	ENST00000267101.3:c.888_889delinsTT	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	296	gtGGat/gtTTat	8/28	1	2	FACETS	0.448	0.358	0.552	0.448	0.358	0.552	SUBCLONAL	1	TRUE	1	0.12	2		624	1078	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115852	8115853	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs1085307641	NA	P-0041534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	196	380	0	ENST00000346208.3:c.1198_1199del	p.Met400ValfsTer106	p.M400Vfs*106	ENST00000346208		400	ATg/g	6/6	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.432390267651976	2		380	791	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0041540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	303	548	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.7	2		548	734	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538311	9538311	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	24	500	0	ENST00000353224.5:c.1687G>A	p.Gly563Arg	p.G563R	ENST00000353224	NM_177990.2	563	Gga/Aga	7/10	1	2	FACETS	0.146	0.114	0.183	0.146	0.114	0.183	SUBCLONAL	1	TRUE	1	0.7	2		500	469	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670400	88670400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	161	402	0	ENST00000360948.2:c.1286C>T	p.Thr429Ile	p.T429I	ENST00000360948	NM_001012338.2	429	aCt/aTt	11/19	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.7	2		402	410	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0041569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	18	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.499	0.374	0.647	0.499	0.374	0.647	SUBCLONAL	1	TRUE	1	0.16	2		336	451	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626883	14626883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	57	681	0	ENST00000254322.2:c.892C>T	p.Pro298Ser	p.P298S	ENST00000254322	NM_006145.1	298	Cct/Tct	3/3	1	2	FACETS	0.894	0.765	1	0.894	0.765	1	CLONAL	1	TRUE	1	0.16	2		681	797	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	177	662	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.40647536288303	2		663	688	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	23	625	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	1	2	FACETS	0.181	0.14	0.229	0.181	0.14	0.229	SUBCLONAL	1	TRUE	1	0.40647536288303	2		625	625	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645760	12645760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587777588	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	34	442	0	ENST00000251849.4:c.709G>A	p.Ala237Thr	p.A237T	ENST00000251849	NM_002880.3	237	Gcc/Acc	7/17	1	2	FACETS	0.349	0.285	0.422	0.349	0.285	0.422	SUBCLONAL	1	TRUE	1	0.40647536288303	2		442	479	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736166	204736166	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	85	371	0	ENST00000302823.3:c.529del	p.Tyr177IlefsTer10	p.Y177Ifs*10	ENST00000302823	NM_005214.4	175	Ttt/tt	3/4	1	2	FACETS	0.836	0.742	0.937	0.836	0.742	0.937	CLONAL	1	TRUE	1	0.40647536288303	2		371	500	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	109	571	4	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.933	0.84	1	0.933	0.84	1	CLONAL	1	TRUE	1	0.40647536288303	2		575	575	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170027	32170027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746443332	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	216	886	0	ENST00000375023.3:c.3581C>T	p.Pro1194Leu	p.P1194L	ENST00000375023	NM_004557.3	1194	cCg/cTg	21/30	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.40647536288303	2		886	912	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	141	700	5	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	0.404338615771772	3	FACETS	1	0.964	1	0.553	0.504	0.604	CLONAL	1	TRUE	1	0.40647536288303	3		705	755	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777838	3777838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863223334	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	231	1002	2	ENST00000262367.5:c.7210G>A	p.Glu2404Lys	p.E2404K	ENST00000262367	NM_004380.2	2404	Gaa/Aaa	31/31	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.40647536288303	2		1004	1012	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514495	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	193	809	0	ENST00000269305.4:c.542G>A	p.Arg181His	p.R181H	ENST00000269305	NM_001126112.2	181	cGc/cAc	5/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.40647536288303	2		809	741	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	78	282	1	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	1	2	FACETS	0.994	0.879	1	0.994	0.879	1	CLONAL	1	TRUE	1	0.40647536288303	2		283	386	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114817	108114817	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786204543	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	135	410	0	ENST00000278616.4:c.640del	p.Ser214ProfsTer16	p.S214Pfs*16	ENST00000278616	NM_000051.3	212	Ttt/tt	6/63	1	2	FACETS	0.944	0.859	1	0.944	0.859	1	CLONAL	1	TRUE	1	0.40647536288303	2		410	704	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	36	179	2	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.881	0.732	1	0.881	0.732	1	CLONAL	1	TRUE	1	0.40647536288303	2		181	201	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	175	609	1	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.40647536288303	2		610	730	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	163	863	3	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.956	0.878	1	0.956	0.878	1	CLONAL	1	TRUE	1	0.40647536288303	2		866	839	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204842	128204842	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs768767517	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	78	909	1	ENST00000341105.2:c.599del	p.Gly200ValfsTer18	p.G200Vfs*18	ENST00000341105	NM_032638.4	200	gGt/gt	3/6	0.40647536288303	1	FACETS	0.343	0.3	0.389	0.343	0.3	0.389	SUBCLONAL	1	TRUE	0	0.40647536288303	1		910	892	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831226	3831226	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398406959	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	98	351	0	ENST00000262367.5:c.1655C>T	p.Pro552Leu	p.P552L	ENST00000262367	NM_004380.2	552	cCg/cTg	7/31	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.40647536288303	2		351	455	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137710	64137710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1441850972	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	221	849	1	ENST00000334205.4:c.1811C>T	p.Ser604Leu	p.S604L	ENST00000334205	NM_003942.2	604	tCg/tTg	15/17	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.40647536288303	2		850	755	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380283	25380283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913528	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	253	424	0	ENST00000311936.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000311936	NM_004985.3	59	Gca/Aca	3/5	0.404338615771772	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.40647536288303	3		424	726	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	206	735	2	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.40647536288303	2		737	810	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437605	56437605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329721997	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	135	510	0	ENST00000407977.2:c.857G>A	p.Arg286Gln	p.R286Q	ENST00000407977		286	cGg/cAg	8/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.40647536288303	2		510	532	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554512	63554512	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	44	630	1	ENST00000307078.5:c.227C>T	p.Thr76Ile	p.T76I	ENST00000307078	NM_004655.3	76	aCc/aTc	2/11	1	2	FACETS	0.319	0.267	0.377	0.319	0.267	0.377	SUBCLONAL	1	TRUE	1	0.40647536288303	2		631	679	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	110	431	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.40647536288303	2		437	489	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492937	56492937	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	45	227	0	ENST00000407977.2:c.2T>C	p.Met1?	p.M1?	ENST00000407977		1	aTg/aCg	2/10	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.40647536288303	2		227	184	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905055	50905055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	160	503	2	ENST00000440232.2:c.342del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	113	Ggg/gg	4/27	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.40647536288303	2		505	594	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138915	64138915	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	105	300	3	ENST00000334205.4:c.2287del	p.Arg763AlafsTer21	p.R763Afs*21	ENST00000334205	NM_003942.2	761	gCc/gc	17/17	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.40647536288303	2		303	461	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044449	5044449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371826393	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	121	448	0	ENST00000381652.3:c.397C>T	p.Arg133Trp	p.R133W	ENST00000381652	NM_004972.3	133	Cgg/Tgg	5/25	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.40647536288303	2		448	527	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030416	49030416	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	115	396	1	ENST00000267163.4:c.1891C>T	p.Gln631Ter	p.Q631*	ENST00000267163	NM_000321.2	631	Caa/Taa	19/27	1	2	FACETS	0.953	0.861	1	0.953	0.861	1	CLONAL	1	TRUE	1	0.40647536288303	2		397	594	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136804	55136804	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	82	325	0	ENST00000257290.5:c.1126C>T	p.Arg376Ter	p.R376*	ENST00000257290	NM_006206.4	376	Cga/Tga	8/23	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.40647536288303	2		325	378	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106649	27106649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	176	670	0	ENST00000324856.7:c.6260G>A	p.Gly2087Glu	p.G2087E	ENST00000324856	NM_006015.4	2087	gGa/gAa	20/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.40647536288303	2		670	736	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119666143	119666143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769576748	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	71	396	0	ENST00000316626.5:c.338G>A	p.Arg113His	p.R113H	ENST00000316626		113	cGt/cAt	3/12	1	2	FACETS	0.785	0.688	0.89	0.785	0.688	0.89	SUBCLONAL	1	TRUE	1	0.40647536288303	2		396	445	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668729	52668729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759670972	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	148	413	0	ENST00000394830.3:c.1190G>A	p.Arg397Gln	p.R397Q	ENST00000394830	NM_018313.4	397	cGg/cAg	12/30	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.40647536288303	2		413	679	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512474	38512474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770732457	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	175	969	1	ENST00000254066.5:c.1385C>T	p.Pro462Leu	p.P462L	ENST00000254066	NM_000964.3	462	cCg/cTg	9/9	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.40647536288303	2		970	840	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	204	465	3	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.40647536288303	2		468	964	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542584	141542584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1238499211	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	157	638	0	ENST00000220592.5:c.2402C>T	p.Ala801Val	p.A801V	ENST00000220592	NM_012154.3	801	gCg/gTg	18/19	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.40647536288303	2		638	681	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	197	472	8	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	0.404338615771772	3	FACETS	1	0.991	1	0.741	0.688	0.796	CLONAL	1	TRUE	1	0.40647536288303	3		480	787	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240613	133240613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201115064	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	225	483	3	ENST00000320574.5:c.2683G>A	p.Ala895Thr	p.A895T	ENST00000320574	NM_006231.2	895	Gcc/Acc	23/49	0.404338615771772	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.40647536288303	3		486	565	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	168	715	1	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.905	0.832	0.982	0.905	0.832	0.982	CLONAL	1	TRUE	1	0.40647536288303	2		716	913	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438211	49438211	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	331	747	1	ENST00000301067.7:c.5058del	p.Lys1686AsnfsTer36	p.K1686Nfs*36	ENST00000301067	NM_003482.3	1686	aaA/aa	20/54	0.404338615771772	3	FACETS	0.984	0.932	1	0.984	0.932	1	CLONAL	2	TRUE	1	0.40647536288303	3		748	996	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470920	25470920	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773312511	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	155	710	0	ENST00000264709.3:c.841G>A	p.Glu281Lys	p.E281K	ENST00000264709	NM_175629.2	281	Gag/Aag	7/23	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.40647536288303	2		710	731	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748399150	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	213	875	2	ENST00000220592.5:c.1806del	p.Ala603ProfsTer92	p.A603Pfs*92	ENST00000220592	NM_012154.3	602	ccC/cc	14/19	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.40647536288303	2		877	964	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645975	215645975	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs587780033	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	34	427	1	ENST00000260947.4:c.623del	p.Lys208ArgfsTer4	p.K208Rfs*4	ENST00000260947	NM_000465.2	208	aAg/ag	4/11	1	2	FACETS	0.31	0.252	0.375	0.31	0.252	0.375	SUBCLONAL	1	TRUE	1	0.40647536288303	2		428	540	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453399	40453399	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs759027671	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	221	844	6	ENST00000345506.4:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000345506	NM_003152.3	366	Ccc/cc	10/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.40647536288303	2		850	868	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284919	15284919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	204	927	1	ENST00000263388.2:c.4696G>A	p.Glu1566Lys	p.E1566K	ENST00000263388	NM_000435.2	1566	Gaa/Aaa	25/33	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.40647536288303	2		928	900	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910774	29910774	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs9260139	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	160	397	1	ENST00000376809.5:c.314T>C	p.Leu105Pro	p.L105P	ENST00000376809	NM_002116.7	105	cTg/cCg	2/8	1	2	FACETS	0.997	0.925	1	1	0.993	1	CLONAL	2	TRUE	1	0.40647536288303	2		398	395	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885632	23885632	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	101	414	1	ENST00000374561.5:c.286del	p.His96ThrfsTer30	p.H96Tfs*30	ENST00000374561	NM_002167.4	96	Cac/ac	1/3	1	2	FACETS	0.925	0.83	1	0.925	0.83	1	CLONAL	1	TRUE	1	0.40647536288303	2		415	537	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966781	18966781	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	200	882	1	ENST00000262803.5:c.1592C>T	p.Thr531Met	p.T531M	ENST00000262803	NM_002911.3	531	aCg/aTg	12/24	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.40647536288303	2		883	941	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612776	228612776	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	181	666	0	ENST00000366696.1:c.251G>A	p.Arg84His	p.R84H	ENST00000366696	NM_003493.2	84	cGc/cAc	1/1	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.40647536288303	2		666	740	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607420	46607420	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137853036	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	229	854	1	ENST00000263734.3:c.1609G>A	p.Gly537Arg	p.G537R	ENST00000263734	NM_001430.4	537	Ggg/Agg	12/16	0.40647536288303	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.40647536288303	1		855	621	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570293	87570293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202111708	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	133	588	0	ENST00000277120.3:c.2033C>T	p.Ala678Val	p.A678V	ENST00000277120		678	gCg/gTg	17/19	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.40647536288303	2		588	587	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213990	36213990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543584446	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	191	947	1	ENST00000222270.7:c.2816C>T	p.Thr939Ile	p.T939I	ENST00000222270	NM_014727.1	939	aCa/aTa	6/37	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.40647536288303	2		948	893	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450715	70450715	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576727317	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	167	521	1	ENST00000373644.4:c.5555C>T	p.Pro1852Leu	p.P1852L	ENST00000373644	NM_030625.2	1852	cCg/cTg	12/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.40647536288303	2		522	588	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777936	3777936	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	210	1035	1	ENST00000262367.5:c.7112C>A	p.Pro2371His	p.P2371H	ENST00000262367	NM_004380.2	2371	cCt/cAt	31/31	1	2	FACETS	0.946	0.878	1	0.946	0.878	1	CLONAL	1	TRUE	1	0.40647536288303	2		1036	1092	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11194508	11194508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	121	539	0	ENST00000361445.4:c.5146C>T	p.His1716Tyr	p.H1716Y	ENST00000361445	NM_004958.3	1716	Cac/Tac	37/58	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.40647536288303	2		539	535	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743754	46743754	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs368105178	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	166	740	1	ENST00000371975.4:c.2044C>T	p.Arg682Ter	p.R682*	ENST00000371975	NM_003579.3	682	Cga/Tga	18/18	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.40647536288303	2		741	745	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710637	114710637	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	163	485	0	ENST00000543371.1:c.122T>C	p.Leu41Ser	p.L41S	ENST00000543371	NM_001198531.1	41	tTa/tCa	1/14	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.40647536288303	2		485	594	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022376	12022376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	230	866	0	ENST00000396373.4:c.486del	p.Arg163GlyfsTer46	p.R163Gfs*46	ENST00000396373	NM_001987.4	161	aCc/ac	5/8	0.40647536288303	3	FACETS	1	0.988	1	0.63	0.587	0.675	CLONAL	1	TRUE	1	0.40647536288303	3		866	1080	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245699	46245699	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	102	475	0	ENST00000334344.6:c.3793G>T	p.Val1265Phe	p.V1265F	ENST00000334344	NM_152641.2	1265	Gtc/Ttc	15/21	0.404338615771772	3	FACETS	0.998	0.895	1	0.499	0.447	0.554	CLONAL	1	TRUE	1	0.40647536288303	3		475	605	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434315	49434315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	244	997	0	ENST00000301067.7:c.7238C>T	p.Ala2413Val	p.A2413V	ENST00000301067	NM_003482.3	2413	gCc/gTc	31/54	0.404338615771772	3	FACETS	1	0.986	1	0.599	0.559	0.641	CLONAL	1	TRUE	1	0.40647536288303	3		997	1205	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254219	133254219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500862	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	310	526	0	ENST00000320574.5:c.665G>A	p.Arg222His	p.R222H	ENST00000320574	NM_006231.2	222	cGc/cAc	7/49	0.404338615771772	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.40647536288303	3		526	768	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435996	110435996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	217	912	0	ENST00000375856.3:c.2405G>A	p.Cys802Tyr	p.C802Y	ENST00000375856	NM_003749.2	802	tGc/tAc	1/2	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.40647536288303	2		912	899	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562612	95562612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	88	307	1	ENST00000393063.1:c.4645C>T	p.His1549Tyr	p.H1549Y	ENST00000393063	NM_030621.3	1549	Cac/Tac	24/28	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.40647536288303	2		308	375	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105237186	105237186	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	122	437	0	ENST00000349310.3:c.1261-2A>G		p.X421_splice	ENST00000349310	NM_001014432.1	421			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.40647536288303	2		437	506	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782311	56782311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573467287	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	225	635	1	ENST00000308159.5:c.152C>T	p.Thr51Met	p.T51M	ENST00000308159	NM_014669.4	51	aCg/aTg	2/22	1	2	FACETS	0.75	0.701	0.8	1	0.992	1	SUBCLONAL	2	TRUE	1	0.40647536288303	2		636	738	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965158	15965158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765553300	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	83	363	0	ENST00000268712.3:c.5438G>A	p.Arg1813His	p.R1813H	ENST00000268712	NM_006311.3	1813	cGt/cAt	37/46	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.40647536288303	2		363	374	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40460232	40460232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746268770	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	149	663	0	ENST00000345506.4:c.1943C>T	p.Thr648Met	p.T648M	ENST00000345506	NM_003152.3	648	aCg/aTg	17/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.40647536288303	2		663	694	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985740	60985740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	21	227	0	ENST00000333681.4:c.160G>A	p.Gly54Arg	p.G54R	ENST00000333681		54	Ggg/Agg	2/3	1	2	FACETS	0.438	0.338	0.554	0.438	0.338	0.554	SUBCLONAL	1	TRUE	1	0.40647536288303	2		227	236	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208030	5208030	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	181	612	0	ENST00000357368.4:c.5681G>A	p.Ser1894Asn	p.S1894N	ENST00000357368	NM_002850.3	1894	aGc/aAc	37/38	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.40647536288303	2		612	668	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220126	5220126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781134304	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	134	631	0	ENST00000357368.4:c.3589C>T	p.Arg1197Trp	p.R1197W	ENST00000357368	NM_002850.3	1197	Cgg/Tgg	22/38	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.40647536288303	2		631	502	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374344	15374344	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200659364	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	139	613	0	ENST00000263377.2:c.1228C>T	p.Arg410Cys	p.R410C	ENST00000263377	NM_058243.2	410	Cgt/Tgt	7/20	1	2	FACETS	0.987	0.9	1	0.987	0.9	1	CLONAL	1	TRUE	1	0.40647536288303	2		613	693	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637390	47637391	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs587779164	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	194	653	0	ENST00000233146.2:c.528_529del	p.Cys176Ter	p.C176*	ENST00000233146	NM_000251.2	175	cTG/c	3/16	0.40647536288303	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.40647536288303	1		653	618	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164595	36164595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	123	594	1	ENST00000300305.3:c.1280G>A	p.Arg427His	p.R427H	ENST00000300305		427	cGc/cAc	8/8	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.40647536288303	2		595	582	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035201	30035201	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	115	458	0	ENST00000338641.4:c.363G>T	p.Gln121His	p.Q121H	ENST00000338641	NM_000268.3	121	caG/caT	3/16	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.40647536288303	2		458	535	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807357	1807357	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	156	721	4	ENST00000260795.2:c.1610del	p.Asn537ThrfsTer89	p.N537Tfs*89	ENST00000260795		536	Aaa/aa	11/17	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.40647536288303	2		725	702	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531001	187531001	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754491592	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	154	501	3	ENST00000441802.2:c.10022C>T	p.Thr3341Met	p.T3341M	ENST00000441802	NM_005245.3	3341	aCg/aTg	15/27	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.40647536288303	2		504	681	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531085	187531085	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	115	425	0	ENST00000441802.2:c.9938C>A	p.Pro3313His	p.P3313H	ENST00000441802	NM_005245.3	3313	cCt/cAt	15/27	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.40647536288303	2		425	517	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540359	187540359	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	113	482	0	ENST00000441802.2:c.7381del	p.Tyr2461ThrfsTer20	p.Y2461Tfs*20	ENST00000441802	NM_005245.3	2461	Tac/ac	10/27	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.40647536288303	2		482	519	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20483037	20483037	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	34	353	0	ENST00000346618.3:c.770A>G	p.Gln257Arg	p.Q257R	ENST00000346618	NM_001949.4	257	cAa/cGa	4/7	1	2	FACETS	0.372	0.303	0.449	0.372	0.303	0.449	SUBCLONAL	1	TRUE	1	0.40647536288303	2		353	450	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858440	27858440	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	91	451	0	ENST00000359303.2:c.131del	p.Pro44GlnfsTer47	p.P44Qfs*47	ENST00000359303	NM_003535.2	44	cCa/ca	1/1	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.40647536288303	2		451	412	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912363	29912363	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773946546	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	67	601	0	ENST00000376809.5:c.982G>A	p.Ala328Thr	p.A328T	ENST00000376809	NM_002116.7	328	Gct/Act	5/8	1	2	FACETS	0.56	0.486	0.639	0.56	0.486	0.639	SUBCLONAL	1	TRUE	1	0.40647536288303	2		601	589	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288657	33288657	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1213838920	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	85	409	0	ENST00000374542.5:c.895C>T	p.Arg299Ter	p.R299*	ENST00000374542	NM_001141970.1	299	Cga/Tga	3/8	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.40647536288303	2		409	361	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14017073	14017073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	122	299	0	ENST00000405192.2:c.214C>T	p.Pro72Ser	p.P72S	ENST00000405192	NM_001163147.1	72	Cca/Tca	5/12	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.40647536288303	2		299	504	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520098	106520098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	22	189	0	ENST00000359195.3:c.2526G>A	p.Met842Ile	p.M842I	ENST00000359195	NM_002649.2	842	atG/atA	6/11	1	2	FACETS	0.36	0.279	0.453	0.36	0.279	0.453	SUBCLONAL	1	TRUE	1	0.40647536288303	2		189	301	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140508768	140508768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs770494089	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	109	436	1	ENST00000288602.6:c.532C>T	p.Arg178Ter	p.R178*	ENST00000288602	NM_004333.4	178	Cga/Tga	4/18	1	2	FACETS	0.968	0.872	1	0.968	0.872	1	CLONAL	1	TRUE	1	0.40647536288303	2		437	554	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342143	70342143	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	110	548	0	ENST00000374080.3:c.1195A>G	p.Ile399Val	p.I399V	ENST00000374080		399	Att/Gtt	8/45	0.389182615921472	1	FACETS	0.851	0.768	0.938	0.851	0.768	0.938	CLONAL	1	TRUE	0	0.40647536288303	1		548	507	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608911	100608911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057521814	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	150	484	0	ENST00000308731.7:c.1697C>T	p.Pro566Leu	p.P566L	ENST00000308731	NM_000061.2	566	cCg/cTg	17/19	0.389182615921472	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.40647536288303	1		484	569	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152853844	152853844	+	synonymous_variant	Silent	SNP	G	G	T	novel	NA	P-0041576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	16	216	1	ENST00000406277.2:c.720C>A	p.Thr240=	p.T240=	ENST00000406277	NM_152274.4	240	acC/acA	7/7	NA	2	FACETS	0.295	0.218	0.387			1	INDETERMINATE	1	TRUE	NA	0.40647536288303	2		217	267	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0041604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	115	763	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.326131485032194	1	FACETS	0.897	0.809	0.989	0.897	0.809	0.989	CLONAL	1	TRUE	0	0.326131485032194	1		763	658	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0041604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	65	307	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.722	0.627	0.826	0.722	0.627	0.826	SUBCLONAL	1	TRUE	1	0.326131485032194	2		307	552	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0041604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	35	305	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	0.326131485032194	1	FACETS	0.781	0.645	0.932	0.781	0.645	0.932	CLONAL	1	TRUE	0	0.326131485032194	1		305	230	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0041632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	724	644	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.897120155780201	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	FALSE	0	0.895224522443236	2		645	767	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946790	71946790	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	63	622	0	ENST00000298229.2:c.2731G>T	p.Glu911Ter	p.E911*	ENST00000298229	NM_001567.3	911	Gag/Tag	24/28	0.897120155780201	2	FACETS	0.187	0.161	0.215	0.094	0.08	0.108	SUBCLONAL	1	FALSE	0	0.895224522443236	2		622	752	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291611	15291611	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	204	750	0	ENST00000263388.2:c.3023C>G	p.Pro1008Arg	p.P1008R	ENST00000263388	NM_000435.2	1008	cCt/cGt	19/33	0.897120155780201	2	FACETS	0.518	0.481	0.557	0.259	0.24	0.279	SUBCLONAL	1	FALSE	0	0.895224522443236	2		750	879	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743931	41743931	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2074	381	759	0	ENST00000301178.4:c.866T>G	p.Val289Gly	p.V289G	ENST00000301178	NM_021913.4	289	gTg/gGg	7/20	0.895224522443236	6	FACETS	0.967	0.914	1			1	CLONAL	1	FALSE	NA	0.895224522443236	6		759	2455	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794625	42794625	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1790	309	729	0	ENST00000575354.2:c.1705G>T	p.Gly569Cys	p.G569C	ENST00000575354	NM_015125.3	569	Ggc/Tgc	10/20	0.897120155780201	6	FACETS	0.918	0.861	0.976	0.184	0.172	0.196	CLONAL	1	FALSE	1	0.895224522443236	6		729	2099	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527483	41527483	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	320	557	0	ENST00000263253.7:c.1374G>C	p.Gln458His	p.Q458H	ENST00000263253	NM_001429.3	458	caG/caC	6/31	0.731127681887618	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	FALSE	0	0.895224522443236	1		557	354	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801539	1801539	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1490	230	773	0	ENST00000260795.2:c.445G>C	p.Gly149Arg	p.G149R	ENST00000260795		149	Ggg/Cgg	3/17	0.897120155780201	4	FACETS	0.566	0.526	0.608			1	SUBCLONAL	1	FALSE	NA	0.895224522443236	4		773	1720	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541007	187541007	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	307	302	0	ENST00000441802.2:c.6733G>C	p.Glu2245Gln	p.E2245Q	ENST00000441802	NM_005245.3	2245	Gag/Cag	10/27	0.897120155780201	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	FALSE	0	0.895224522443236	2		302	324	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721930	176721930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1356	516	511	0	ENST00000439151.2:c.7561G>A	p.Ala2521Thr	p.A2521T	ENST00000439151	NM_022455.4	2521	Gcc/Acc	23/23	0.895224522443236	8	FACETS	1	0.991	1			1	CLONAL	2	FALSE	NA	0.895224522443236	8		511	1872	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396119	139396761	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGTACCCCAGCCTCGGGGCTTAGGGGAGAGAGGCAGGTGGGCCACGGGGCTAGGGAAGCCCTGGCTGCTGGCACCCTTACCAGGCCCGCGGACATTGACGTCCATGCAGTCGGCGTCAACCTCACCCTGGGGCGGTGTGGGGGCCATGGCAGACATGCGCAGGTCAGCGGCATCCAGGTGCTGCTGAGTCCACTGCCGGTGGTCTGTCTGGTCGTCCAGGTCAGGCAGAACCACGGGCTCCTCGAACTACATAGAGGGAGTGAGCAGAGCCTGTCAGGGCAGCCCGGCAGCAGGTGCCCGGGAGCCCAGGAGCCCGGGAGCCTCGCGACTCACCCGGAACTTCTTGGTCTCCAGGTCCTCGTCCCCCCACTCATTCTGGTTGTCGTCCATGAGGGCACCGTCTGAAGCGTTCTTCAGGGGCCTGGGGGGTGAGGGGTCGAGAAGTGAGGCTGAGCGAGCTCCCTAGGAAGCCCCCAGAGACCCCTGGCCCGGGCCTGGCGTGGGAGGTGGGCCCTGGGTCGGGAGGGGCAGACTCCCGGTGAGGATGCTCGGCCAGGTCCCACCTCCCACCGGGGACCCAGAAGCAGGGGCGGCGTCCGCTCACTTGAGGCCCACGGAGTCCTCGCCGAGGGGCTCCCGCCG	CTGTACCCCAGCCTCGGGGCTTAGGGGAGAGAGGCAGGTGGGCCACGGGGCTAGGGAAGCCCTGGCTGCTGGCACCCTTACCAGGCCCGCGGACATTGACGTCCATGCAGTCGGCGTCAACCTCACCCTGGGGCGGTGTGGGGGCCATGGCAGACATGCGCAGGTCAGCGGCATCCAGGTGCTGCTGAGTCCACTGCCGGTGGTCTGTCTGGTCGTCCAGGTCAGGCAGAACCACGGGCTCCTCGAACTACATAGAGGGAGTGAGCAGAGCCTGTCAGGGCAGCCCGGCAGCAGGTGCCCGGGAGCCCAGGAGCCCGGGAGCCTCGCGACTCACCCGGAACTTCTTGGTCTCCAGGTCCTCGTCCCCCCACTCATTCTGGTTGTCGTCCATGAGGGCACCGTCTGAAGCGTTCTTCAGGGGCCTGGGGGGTGAGGGGTCGAGAAGTGAGGCTGAGCGAGCTCCCTAGGAAGCCCCCAGAGACCCCTGGCCCGGGCCTGGCGTGGGAGGTGGGCCCTGGGTCGGGAGGGGCAGACTCCCGGTGAGGATGCTCGGCCAGGTCCCACCTCCCACCGGGGACCCAGAAGCAGGGGCGGCGTCCGCTCACTTGAGGCCCACGGAGTCCTCGCCGAGGGGCTCCCGCCG	-	novel	NA	P-0041632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	240	235	0	ENST00000277541.6:c.5347_5638+81del		p.X1783_splice	ENST00000277541	NM_017617.3	1783		28-30/34	0.897120155780201	3	FACETS	0.94	0.893	0.986	0.626	0.595	0.658	CLONAL	2	FALSE	0	0.895224522443236	3		235	413	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842339	151842339	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs151023183	NA	P-0041646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	167	282	0	ENST00000262189.6:c.14073C>A	p.Tyr4691Ter	p.Y4691*	ENST00000262189	NM_170606.2	4691	taC/taA	54/59	0.896223571739236	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	FALSE	0	0.896223571739236	1		282	175	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770823	59770823	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	76	328	0	ENST00000259008.2:c.2543G>C	p.Arg848Pro	p.R848P	ENST00000259008	NM_032043.2	848	cGc/cCc	18/20	1	2	FACETS	0.43	0.379	0.485	0.43	0.379	0.485	SUBCLONAL	1	FALSE	1	0.896223571739236	2		328	394	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390659	139390660	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	406	937	0	ENST00000277541.6:c.7531dup	p.Thr2511AsnfsTer5	p.T2511Nfs*5	ENST00000277541	NM_017617.3	2511	acc/aAcc	34/34	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.896223571739236	2		937	831	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76764072	76764075	+	frameshift_variant	Frame_Shift_Del	DEL	TCTG	TCTG	-	novel	NA	P-0041646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	119	513	0	ENST00000373344.5:c.7233_7236del	p.Asn2411LysfsTer15	p.N2411Kfs*15	ENST00000373344	NM_000489.3	2411	aaCAGA/aa	35/35	1	2	FACETS	0.482	0.436	0.53	0.482	0.436	0.53	SUBCLONAL	1	FALSE	1	0.896223571739236	2		513	551	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0041669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	235	548	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.407422475330375	2	FACETS	0.819	0.767	0.871	0.819	0.767	0.871	CLONAL	2	TRUE	0	0.409564377407401	2		548	701	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0041669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	175	662	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.409564377407401	2		663	793	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174386	11174386	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	188	618	0	ENST00000361445.4:c.7289G>T	p.Arg2430Met	p.R2430M	ENST00000361445	NM_004958.3	2430	aGg/aTg	53/58	0.409564377407401	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.409564377407401	1		618	687	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804981	43804981	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	35	493	0	ENST00000372470.3:c.431G>T	p.Gly144Val	p.G144V	ENST00000372470	NM_005373.2	144	gGg/gTg	4/12	0.409564377407401	1	FACETS	0.28	0.229	0.337	0.28	0.229	0.337	SUBCLONAL	1	TRUE	0	0.409564377407401	1		493	486	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248285	59248285	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	21	150	0	ENST00000371222.2:c.458del	p.Gly153AlafsTer29	p.G153Afs*29	ENST00000371222	NM_002228.3	153	gGc/gc	1/1	0.409564377407401	1	FACETS	0.748	0.585	0.931	0.748	0.585	0.931	CLONAL	1	TRUE	0	0.409564377407401	1		150	109	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850704	63850705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	71	363	0	ENST00000279873.7:c.1489dup	p.Ile497AsnfsTer31	p.I497Nfs*31	ENST00000279873	NM_032199.2	494	-/A	10/10	1	2	FACETS	0.772	0.676	0.875	0.772	0.676	0.875	SUBCLONAL	1	TRUE	1	0.409564377407401	2		363	449	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196885	108196885	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1064795166	NA	P-0041669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	78	324	0	ENST00000278616.4:c.6908A>G	p.Lys2303Arg	p.K2303R	ENST00000278616	NM_000051.3	2303	aAg/aGg	47/63	1	2	FACETS	0.947	0.837	1	0.947	0.837	1	CLONAL	1	TRUE	1	0.409564377407401	2		324	402	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643747	38643747	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	155	765	0	ENST00000299084.4:c.1219del	p.Leu407TrpfsTer2	p.L407Wfs*2	ENST00000299084	NM_152594.2	406	gCc/gc	7/7	1	2	FACETS	0.851	0.779	0.927	0.851	0.779	0.927	CLONAL	1	TRUE	1	0.409564377407401	2		765	889	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337295	89337295	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1250432793	NA	P-0041669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	167	723	1	ENST00000301030.4:c.7736G>A	p.Arg2579His	p.R2579H	ENST00000301030	NM_001256183.1	2579	cGc/cAc	12/13	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.409564377407401	2		724	796	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349019	89349019	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	179	886	0	ENST00000301030.4:c.3931C>T	p.Arg1311Ter	p.R1311*	ENST00000301030	NM_001256183.1	1311	Cga/Tga	9/13	1	2	FACETS	0.929	0.856	1	0.929	0.856	1	CLONAL	1	TRUE	1	0.409564377407401	2		886	941	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41199707	41199707	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	170	781	0	ENST00000357654.3:c.5420T>C	p.Ile1807Thr	p.I1807T	ENST00000357654	NM_007294.3	1807	aTt/aCt	22/23	1	2	FACETS	0.919	0.846	0.996	0.919	0.846	0.996	CLONAL	1	TRUE	1	0.409564377407401	2		781	903	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435168	56435168	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	137	816	0	ENST00000407977.2:c.1969del	p.Arg657GlyfsTer43	p.R657Gfs*43	ENST00000407977		657	Cgg/gg	9/10	1	2	FACETS	0.847	0.771	0.927	0.847	0.771	0.927	CLONAL	1	TRUE	1	0.409564377407401	2		816	790	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152184	11152184	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	186	728	0	ENST00000358026.2:c.4468C>A	p.Leu1490Ile	p.L1490I	ENST00000358026	NM_001128849.1	1490	Ctc/Atc	31/36	1	2	FACETS	0.999	0.923	1	0.999	0.923	1	CLONAL	1	TRUE	1	0.409564377407401	2		728	909	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	225	900	2	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.409564377407401	2		902	1088	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149917	202149917	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	130	671	0	ENST00000358485.4:c.1358C>G	p.Pro453Arg	p.P453R	ENST00000358485	NM_001080125.1	453	cCg/cGg	8/9	1	2	FACETS	0.857	0.778	0.939	0.857	0.778	0.939	CLONAL	1	TRUE	1	0.409564377407401	2		671	741	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199945	138199945	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	40	601	0	ENST00000237289.4:c.1368del	p.Pro457LeufsTer20	p.P457Lfs*20	ENST00000237289	NM_001270507.1	455	Ggg/gg	7/9	1	2	FACETS	0.344	0.285	0.41	0.344	0.285	0.41	SUBCLONAL	1	TRUE	1	0.409564377407401	2		601	568	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001395	150001395	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	95	529	0	ENST00000253339.5:c.2209C>T	p.Arg737Ter	p.R737*	ENST00000253339		737	Cga/Tga	4/7	1	2	FACETS	0.933	0.834	1	0.933	0.834	1	CLONAL	1	TRUE	1	0.409564377407401	2		529	497	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859709	151859709	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	87	367	0	ENST00000262189.6:c.10953G>C	p.Glu3651Asp	p.E3651D	ENST00000262189	NM_170606.2	3651	gaG/gaC	43/59	1	2	FACETS	0.983	0.875	1	0.983	0.875	1	CLONAL	1	TRUE	1	0.409564377407401	2		367	432	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	247	345	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.99	0.932	1	0.99	0.932	1	CLONAL	1	TRUE	1	0.797251855954849	2		345	626	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572237	64572237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471493357	NA	P-0041670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	357	909	0	ENST00000312049.6:c.1402G>A	p.Glu468Lys	p.E468K	ENST00000312049	NM_130799.2	468	Gag/Aag	10/10	1	2	FACETS	0.972	0.925	1	0.972	0.925	1	CLONAL	1	TRUE	1	0.797251855954849	2		909	921	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420360	49420360	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	346	845	0	ENST00000301067.7:c.15389C>T	p.Thr5130Ile	p.T5130I	ENST00000301067	NM_003482.3	5130	aCc/aTc	48/54	1	2	FACETS	0.934	0.887	0.982	0.934	0.887	0.982	CLONAL	1	TRUE	1	0.797251855954849	2		845	929	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778995	3778995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	321	752	1	ENST00000262367.5:c.6053C>T	p.Pro2018Leu	p.P2018L	ENST00000262367	NM_004380.2	2018	cCc/cTc	31/31	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.797251855954849	2		753	777	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352531	89352531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	345	841	0	ENST00000301030.4:c.808C>T	p.Pro270Ser	p.P270S	ENST00000301030	NM_001256183.1	270	Ccg/Tcg	8/13	1	2	FACETS	0.965	0.917	1	0.965	0.917	1	CLONAL	1	TRUE	1	0.797251855954849	2		841	897	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989508	7989508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1459425557	NA	P-0041670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	327	781	0	ENST00000319144.4:c.178G>A	p.Asp60Asn	p.D60N	ENST00000319144	NM_001139.2	60	Gac/Aac	2/15	1	2	FACETS	0.978	0.928	1	0.978	0.928	1	CLONAL	1	TRUE	1	0.797251855954849	2		781	839	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527461	29527461	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786203950	NA	P-0041670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	194	449	2	ENST00000356175.3:c.910C>T	p.Arg304Ter	p.R304*	ENST00000356175	NM_000267.3	304	Cga/Tga	9/57	1	2	FACETS	0.969	0.905	1	0.969	0.905	1	CLONAL	1	TRUE	1	0.797251855954849	2		451	502	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0041670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	148	302	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	1	2	FACETS	0.954	0.882	1	0.954	0.882	1	CLONAL	1	TRUE	1	0.797251855954849	2		302	389	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7163168	7163168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	349	889	0	ENST00000302850.5:c.1904C>T	p.Ser635Leu	p.S635L	ENST00000302850	NM_000208.2	635	tCa/tTa	9/22	1	2	FACETS	0.913	0.867	0.96	0.913	0.867	0.96	CLONAL	1	TRUE	1	0.797251855954849	2		889	959	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221504	36221504	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	446	1044	0	ENST00000222270.7:c.5263C>T	p.Pro1755Ser	p.P1755S	ENST00000222270	NM_014727.1	1755	Ccc/Tcc	25/37	1	2	FACETS	0.961	0.919	1	0.961	0.919	1	CLONAL	1	TRUE	1	0.797251855954849	2		1044	1164	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530114	212530114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	144	353	0	ENST00000342788.4:c.1805G>A	p.Ser602Asn	p.S602N	ENST00000342788	NM_005235.2	602	aGt/aAt	15/28	1	2	FACETS	0.917	0.846	0.99	0.917	0.846	0.99	CLONAL	1	TRUE	1	0.797251855954849	2		353	394	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710637	40710637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1161104430	NA	P-0041670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	257	650	1	ENST00000373198.4:c.4214G>A	p.Gly1405Glu	p.G1405E	ENST00000373198	NM_133170.3	1405	gGa/gAa	31/32	1	2	FACETS	0.88	0.827	0.933	0.88	0.827	0.933	CLONAL	1	TRUE	1	0.797251855954849	2		651	733	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733280	40733280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370508724	NA	P-0041670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	265	633	0	ENST00000373198.4:c.3526C>T	p.Arg1176Cys	p.R1176C	ENST00000373198	NM_133170.3	1176	Cgt/Tgt	26/32	1	2	FACETS	0.935	0.881	0.989	0.935	0.881	0.989	CLONAL	1	TRUE	1	0.797251855954849	2		633	711	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163892	47163892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	150	422	0	ENST00000409792.3:c.2234C>T	p.Pro745Leu	p.P745L	ENST00000409792	NM_014159.6	745	cCa/cTa	3/21	1	2	FACETS	0.833	0.767	0.899	0.833	0.767	0.899	CLONAL	1	TRUE	1	0.797251855954849	2		422	452	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628712	187628712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	326	714	0	ENST00000441802.2:c.2270C>T	p.Ser757Phe	p.S757F	ENST00000441802	NM_005245.3	757	tCt/tTt	2/27	1	2	FACETS	0.947	0.898	0.996	0.947	0.898	0.996	CLONAL	1	TRUE	1	0.797251855954849	2		714	864	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449784	149449784	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	384	890	0	ENST00000286301.3:c.1280C>T	p.Pro427Leu	p.P427L	ENST00000286301	NM_005211.3	427	cCc/cTc	9/22	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.797251855954849	2		890	945	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499120	149499120	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780199485	NA	P-0041670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	310	679	0	ENST00000261799.4:c.2708C>T	p.Pro903Leu	p.P903L	ENST00000261799	NM_002609.3	903	cCt/cTt	20/23	1	2	FACETS	0.908	0.86	0.958	0.908	0.86	0.958	CLONAL	1	TRUE	1	0.797251855954849	2		679	856	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523654	176523654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	489	1176	0	ENST00000292408.4:c.2065C>T	p.Pro689Ser	p.P689S	ENST00000292408	NM_213647.1	689	Ccg/Tcg	16/18	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.797251855954849	2		1176	1195	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647518	117647518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	194	471	0	ENST00000368508.3:c.5426G>A	p.Gly1809Glu	p.G1809E	ENST00000368508	NM_002944.2	1809	gGa/gAa	33/43	1	2	FACETS	0.868	0.808	0.928	0.868	0.808	0.928	CLONAL	1	TRUE	1	0.797251855954849	2		471	561	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058575	69058575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	229	560	0	ENST00000288368.4:c.4219C>T	p.Leu1407Phe	p.L1407F	ENST00000288368	NM_024870.2	1407	Ctt/Ttt	34/40	0.120480943730904	5	FACETS	1	0.939	1			1	INDETERMINATE	2	TRUE	NA	0.797251855954849	5		560	630	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742076	145742076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	456	946	1	ENST00000428558.2:c.427C>T	p.Pro143Ser	p.P143S	ENST00000428558	NM_004260.3	143	Cca/Tca	5/22	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.797251855954849	2		947	1042	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27204970	27204970	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	618	746	1	ENST00000380036.4:c.2271G>A	p.Met757Ile	p.M757I	ENST00000380036	NM_000459.3	757	atG/atA	14/23	0.797251855954849	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.797251855954849	2		747	746	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0041682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	141	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.366423768418556	3	FACETS	0.881	0.811	0.954			1	CLONAL	2	TRUE	NA	0.47619147410498	3		485	416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587782197	NA	P-0041682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	250	750	0	ENST00000269305.4:c.434T>A	p.Leu145Gln	p.L145Q	ENST00000269305	NM_001126112.2	145	cTg/cAg	5/11	0.46471537724523	1	FACETS	0.881	0.825	0.938	0.881	0.825	0.938	CLONAL	1	TRUE	0	0.47619147410498	1		750	908	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649544	206649544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370426628	NA	P-0041682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	144	487	0	ENST00000367120.3:c.379C>T	p.Arg127Trp	p.R127W	ENST00000367120	NM_014002.3	127	Cgg/Tgg	6/22	1	2	FACETS	0.951	0.87	1	0.951	0.87	1	CLONAL	1	TRUE	1	0.47619147410498	2		487	636	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419949	152419949	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	111	636	1	ENST00000206249.3:c.1636G>A	p.Ala546Thr	p.A546T	ENST00000206249	NM_000125.3	546	Gcc/Acc	8/8	1	2	FACETS	0.855	0.77	0.945	0.855	0.77	0.945	CLONAL	1	TRUE	1	0.392666606465734	2		637	661	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495647	72495647	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	66	311	0	ENST00000477973.2:c.425G>A	p.Arg142Lys	p.R142K	ENST00000477973	NM_012234.5	142	aGa/aAa	1/4	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.392666606465734	2		311	336	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754644	42754644	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	97	766	0	ENST00000222329.4:c.96T>G	p.Phe32Leu	p.F32L	ENST00000222329	NM_006494.2	32	ttT/ttG	2/4	1	2	FACETS	0.778	0.695	0.867	0.778	0.695	0.867	SUBCLONAL	1	TRUE	1	0.392666606465734	2		766	635	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578518	7578518	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934875	NA	P-0041699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	150	874	0	ENST00000269305.4:c.412G>C	p.Ala138Pro	p.A138P	ENST00000269305	NM_001126112.2	138	Gcc/Ccc	5/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.290705060802858	2		874	942	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601304	28601304	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	27	118	0	ENST00000241453.7:c.2128T>A	p.Phe710Ile	p.F710I	ENST00000241453	NM_004119.2	710	Ttt/Att	17/24	0.192399663605165	3	FACETS	0.484	0.384	0.597	0.242	0.192	0.299	SUBCLONAL	1	FALSE	1	0.290705060802858	3		118	440	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167720	185167720	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	48	208	0	ENST00000265026.3:c.1043C>A	p.Thr348Lys	p.T348K	ENST00000265026	NM_004721.4	348	aCa/aAa	6/14	0.0964936522824758	3	FACETS	0.685	0.579	0.802	0.343	0.289	0.401	INDETERMINATE	1	FALSE	1	0.290705060802858	3		208	552	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80168986	80168986	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	32	164	0	ENST00000265081.6:c.3182G>T	p.Arg1061Ile	p.R1061I	ENST00000265081	NM_002439.4	1061	aGa/aTa	23/24	0.192399663605165	3	FACETS	0.483	0.391	0.587	0.242	0.195	0.294	SUBCLONAL	1	FALSE	1	0.290705060802858	3		164	522	SUCCESS
APC	324	MSKCC	GRCh37	5	112174117	112174117	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	19	85	0	ENST00000257430.4:c.2827del	p.Ser943GlnfsTer12	p.S943Qfs*12	ENST00000257430	NM_000038.5	942	aaT/aa	16/16	0.192399663605165	3	FACETS	0.508	0.385	0.651	0.254	0.192	0.326	SUBCLONAL	1	FALSE	1	0.290705060802858	3		85	295	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0041717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	119	548	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.27205983612503	2		548	843	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	28	296	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.387	0.308	0.477	0.387	0.308	0.477	SUBCLONAL	1	TRUE	1	0.27205983612503	2		297	532	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0041717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	58	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.876	0.753	1	0.876	0.753	1	CLONAL	1	TRUE	1	0.27205983612503	2		336	487	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0041717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	53	368	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	0.742	0.633	0.862	0.742	0.633	0.862	SUBCLONAL	1	TRUE	1	0.27205983612503	2		368	525	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654642	67654642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	42	600	1	ENST00000264010.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000264010	NM_006565.3	377	Cgt/Tgt	6/12	0.27205983612503	1	FACETS	0.4	0.333	0.475	0.4	0.333	0.475	SUBCLONAL	1	TRUE	0	0.27205983612503	1		601	667	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307280	65307283	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0041717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	25	438	0	ENST00000342505.4:c.2405_2408del	p.Lys802ArgfsTer11	p.K802Rfs*11	ENST00000342505	NM_002227.2	802	aAAGAg/ag	18/25	1	2	FACETS	0.381	0.299	0.475	0.381	0.299	0.475	SUBCLONAL	1	TRUE	1	0.27205983612503	2		438	483	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100897	27100897	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0041717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	107	677	0	ENST00000324856.7:c.4179C>G	p.Tyr1393Ter	p.Y1393*	ENST00000324856	NM_006015.4	1393	taC/taG	18/20	1	2	FACETS	0.971	0.871	1	0.971	0.871	1	CLONAL	1	TRUE	1	0.27205983612503	2		677	810	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118914	70118915	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0041717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	144	961	0	ENST00000245479.2:c.487dup	p.Val163GlyfsTer89	p.V163Gfs*89	ENST00000245479	NM_000346.3	162	-/G	2/3	1	2	FACETS	0.904	0.823	0.99	0.904	0.823	0.99	CLONAL	1	TRUE	1	0.27205983612503	2		961	1171	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0041837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	307	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.508349114811528	4	FACETS	0.844	0.804	0.884	0.844	0.804	0.884	CLONAL	3	TRUE	1	0.689981647098343	4		473	594	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156740	20156740	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	155	215	0	ENST00000379607.5:c.17G>A	p.Gly6Asp	p.G6D	ENST00000379607	NM_001412.3	6	gGt/gAt	2/7	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.689981647098343	2		215	368	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340407	8340407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201651279	NA	P-0041837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	133	586	0	ENST00000356435.5:c.5189G>A	p.Arg1730Gln	p.R1730Q	ENST00000356435		1730	cGg/cAg	31/35	NA	2	FACETS	0.886	0.812	0.963			1	INDETERMINATE	1	TRUE	NA	0.689981647098343	2		586	435	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0041850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	64	346	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	0.968	0.84	1	0.968	0.84	1	CLONAL	1	TRUE	1	0.28943521043549	2		346	457	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717713	89717714	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	165	444	0	ENST00000371953.3:c.740dup	p.Leu247PhefsTer6	p.L247Ffs*6	ENST00000371953	NM_000314.4	246	-/T	7/9	0.257740841741961	2	FACETS	0.856	0.789	0.926	0.856	0.789	0.926	CLONAL	2	TRUE	0	0.28943521043549	2		444	666	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436599	49436599	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886041405	NA	P-0041850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	123	748	2	ENST00000301067.7:c.5707C>T	p.Arg1903Ter	p.R1903*	ENST00000301067	NM_003482.3	1903	Cga/Tga	26/54	1	2	FACETS	0.847	0.765	0.935	0.847	0.765	0.935	CLONAL	1	TRUE	1	0.28943521043549	2		750	1003	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553776	106553776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs941078758	NA	P-0041850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	59	366	0	ENST00000369096.4:c.1741G>A	p.Ala581Thr	p.A581T	ENST00000369096	NM_001198.3	581	Gcc/Acc	5/7	1	2	FACETS	0.651	0.56	0.751	0.651	0.56	0.751	SUBCLONAL	1	TRUE	1	0.28943521043549	2		366	626	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163896	152163896	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	63	502	0	ENST00000206249.3:c.617A>G	p.Lys206Arg	p.K206R	ENST00000206249	NM_000125.3	206	aAg/aGg	2/8	1	2	FACETS	0.729	0.631	0.836	0.729	0.631	0.836	SUBCLONAL	1	TRUE	1	0.28943521043549	2		502	597	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949057	44949063	+	frameshift_variant	Frame_Shift_Del	DEL	AGTGTAT	AGTGTAT	-	novel	NA	P-0041850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	51	461	0	ENST00000377967.4:c.3620_3626del	p.Val1207GlyfsTer12	p.V1207Gfs*12	ENST00000377967	NM_021140.2	1206	ccAGTGTAT/cc	25/29	1	2	FACETS	0.598	0.508	0.698	0.598	0.508	0.698	SUBCLONAL	1	TRUE	1	0.28943521043549	2		461	589	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0041887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	88	662	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.789	0.697	0.888	0.789	0.697	0.888	SUBCLONAL	1	TRUE	1	0.2	2		663	1115	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0041887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	72	325	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.2	2		325	606	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0041887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	91	251	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.2	2		251	667	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0041887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	29	395	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.411	0.329	0.506	0.411	0.329	0.506	SUBCLONAL	1	TRUE	1	0.2	2		395	705	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405953	157405954	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1554294674	NA	P-0041887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	44	658	1	ENST00000346085.5:c.2201dup	p.Ser736IlefsTer27	p.S736Ifs*27	ENST00000346085	NM_020732.3	732	ccg/ccGg	6/20	0.3	0	FACETS	0.406	0.339	0.48			1	SUBCLONAL	1	TRUE	0	0.2	0		659	868	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805488	1805488	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373496046	NA	P-0041887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1304	85	1116	3	ENST00000260795.2:c.1000G>A	p.Ala334Thr	p.A334T	ENST00000260795		334	Gcc/Acc	7/17	1	2	FACETS	0.612	0.539	0.691	0.612	0.539	0.691	SUBCLONAL	1	TRUE	1	0.2	2		1119	1389	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176338	24176338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041892-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	14	593	2	ENST00000263121.7:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000263121	NM_003073.3	377	Cgt/Tgt	9/9	0.356232614489552	1	FACETS	0.038	0.027	0.051	0.038	0.027	0.051	INDETERMINATE	1	TRUE	0	0.697761840131984	1		595	696	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421834	49421834	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs117904191	NA	P-0041892-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	46	688	2	ENST00000301067.7:c.14473C>T	p.Arg4825Trp	p.R4825W	ENST00000301067	NM_003482.3	4825	Cgg/Tgg	46/54	0.219951347096149	1	FACETS	0.099	0.082	0.117	0.099	0.082	0.117	INDETERMINATE	1	TRUE	0	0.697761840131984	1		690	869	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468391	89468391	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	21	261	0	ENST00000336596.2:c.1925T>G	p.Leu642Arg	p.L642R	ENST00000336596	NM_005233.5	642	cTt/cGt	11/17	1	2	FACETS	0.986	0.764	1	0.986	0.764	1	CLONAL	1	TRUE	1	0.230269723016135	2		261	185	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610695	52610695	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	29	526	0	ENST00000394830.3:c.3478C>T	p.Arg1160Ter	p.R1160*	ENST00000394830	NM_018313.4	1160	Cga/Tga	23/30	1	2	FACETS	0.916	0.738	1	0.916	0.738	1	CLONAL	1	TRUE	1	0.230269723016135	2		526	275	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0041905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	112	842	1	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.230269723016135	2		843	649	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260707	16260707	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	48	706	0	ENST00000375759.3:c.7972G>T	p.Val2658Leu	p.V2658L	ENST00000375759	NM_015001.2	2658	Gtg/Ttg	11/15	1	2	FACETS	0.835	0.706	0.977	0.835	0.706	0.977	CLONAL	1	TRUE	1	0.230269723016135	2		706	499	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660472	67660472	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	33	442	0	ENST00000264010.4:c.1372A>G	p.Lys458Glu	p.K458E	ENST00000264010	NM_006565.3	458	Aag/Gag	8/12	1	2	FACETS	0.831	0.678	1	0.831	0.678	1	CLONAL	1	TRUE	1	0.230269723016135	2		442	345	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56402502	56402502	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0041905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	23	270	0	ENST00000348428.3:c.1544T>A	p.Leu515Ter	p.L515*	ENST00000348428	NM_006785.3	515	tTa/tAa	13/17	1	2	FACETS	0.839	0.657	1	0.839	0.657	1	CLONAL	1	TRUE	1	0.230269723016135	2		270	238	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231825	36231825	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	53	711	0	ENST00000300305.3:c.559G>T	p.Ala187Ser	p.A187S	ENST00000300305		187	Gcc/Tcc	5/8	1	2	FACETS	0.835	0.712	0.97	0.835	0.712	0.97	CLONAL	1	TRUE	1	0.230269723016135	2		711	551	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280085	66280085	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	30	336	1	ENST00000273854.3:c.1604T>A	p.Val535Asp	p.V535D	ENST00000273854	NM_004439.5	535	gTt/gAt	7/18	0.175705114607172	1	FACETS	0.877	0.709	1	0.877	0.709	1	CLONAL	1	TRUE	0	0.230269723016135	1		337	263	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004267	150004267	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	16	380	0	ENST00000253339.5:c.1958C>G	p.Ser653Cys	p.S653C	ENST00000253339		653	tCt/tGt	3/7	1	2	FACETS	0.134	0.098	0.176	0.134	0.098	0.176	SUBCLONAL	1	TRUE	1	0.852780023632566	2		380	281	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0041948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	132	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.974	0.891	1	0.974	0.891	1	CLONAL	1	TRUE	1	0.591640810538648	2		336	458	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692792	89692792	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs779530981	NA	P-0041948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	277	315	0	ENST00000371953.3:c.276C>A	p.Asp92Glu	p.D92E	ENST00000371953	NM_000314.4	92	gaC/gaA	5/9	0.591640810538648	2	FACETS	0.927	0.882	0.971	0.927	0.882	0.971	CLONAL	2	TRUE	0	0.591640810538648	2		315	505	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40498610	40498610	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	202	385	0	ENST00000264657.5:c.250C>T	p.Arg84Ter	p.R84*	ENST00000264657	NM_139276.2	84	Cga/Tga	3/24	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.591640810538648	2		385	654	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339326	70339330	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTG	AGGTG	-	novel	NA	P-0041948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	187	417	0	ENST00000374080.3:c.204+1_204+5del		p.X68_splice	ENST00000374080		68		2/45	1	2	FACETS	0.976	0.905	1	0.976	0.905	1	CLONAL	1	TRUE	1	0.591640810538648	2		417	648	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937076	76937076	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	118	340	0	ENST00000373344.5:c.3672G>C	p.Gln1224His	p.Q1224H	ENST00000373344	NM_000489.3	1224	caG/caC	9/35	1	2	FACETS	0.819	0.743	0.898	0.819	0.743	0.898	CLONAL	1	TRUE	1	0.591640810538648	2		340	487	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	99	345	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.543670639764788	2		345	288	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0041987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	127	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.543670639764788	2		336	372	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0041987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	161	489	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.543670639764788	2		489	542	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577600	7577600	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	66	472	0	ENST00000269305.4:c.681del	p.Asp228ThrfsTer19	p.D228Tfs*19	ENST00000269305	NM_001126112.2	227	tcT/tc	7/11	1	2	FACETS	0.407	0.353	0.465	0.407	0.353	0.465	SUBCLONAL	1	TRUE	1	0.543670639764788	2		472	597	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891287	101891287	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757374917	NA	P-0041987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	101	407	0	ENST00000374994.4:c.248C>T	p.Pro83Leu	p.P83L	ENST00000374994	NM_004612.2	83	cCg/cTg	2/9	0.543670639764788	1	FACETS	0.634	0.57	0.7	0.634	0.57	0.7	SUBCLONAL	1	TRUE	0	0.543670639764788	1		407	427	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132438	11132438	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	133	722	2	ENST00000358026.2:c.2654G>T	p.Arg885Leu	p.R885L	ENST00000358026	NM_001128849.1	885	cGc/cTc	19/36	1	2	FACETS	0.597	0.542	0.655	0.597	0.542	0.655	SUBCLONAL	1	TRUE	1	0.543670639764788	2		724	819	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30954259	30954259	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0041987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	111	311	0	ENST00000375687.4:c.130A>T	p.Lys44Ter	p.K44*	ENST00000375687	NM_015338.5	44	Aag/Tag	2/13	1	2	FACETS	0.947	0.858	1	0.947	0.858	1	CLONAL	1	TRUE	1	0.543670639764788	2		311	431	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383280	31383280	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778547539	NA	P-0041987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	201	437	0	ENST00000328111.2:c.1192C>T	p.Arg398Cys	p.R398C	ENST00000328111	NM_006892.3	398	Cgc/Tgc	11/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.543670639764788	2		437	646	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922830	44922831	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0041987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	150	339	0	ENST00000377967.4:c.1692_1693dup	p.Gln565ArgfsTer29	p.Q565Rfs*29	ENST00000377967	NM_021140.2	564	ggg/ggGCg	16/29	0.438312969620767	1	FACETS	0.885	0.816	0.956	0.885	0.816	0.956	CLONAL	1	TRUE	0	0.543670639764788	1		339	454	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0042019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	178	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.136636668849954	5	FACETS	0.871	0.806	0.939	0.653	0.604	0.704	INDETERMINATE	3	FALSE	1	0.28636608512736	5		288	680	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0042019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	90	344	1				ENST00000310581	NM_198253.2	-/1132			0.235835351665926	0	FACETS	0.795	0.707	0.889			1	SUBCLONAL	1	FALSE	0	0.28636608512736	0		345	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587782272	NA	P-0042019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	147	637	0	ENST00000269305.4:c.994-1G>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.28636608512736	1	FACETS	0.885	0.807	0.967	0.885	0.807	0.967	CLONAL	1	FALSE	0	0.28636608512736	1		637	994	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213554	27213554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	88	521	0	ENST00000380036.4:c.2950G>A	p.Gly984Arg	p.G984R	ENST00000380036	NM_000459.3	984	Gga/Aga	18/23	0.28636608512736	0	FACETS	0.783	0.695	0.877			1	SUBCLONAL	1	FALSE	0	0.28636608512736	0		521	560	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11172948	11172949	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	99	528	0	ENST00000361445.4:c.7326_7327delinsTT	p.Arg2443Ter	p.R2443*	ENST00000361445	NM_004958.3	2442	tcCCga/tcTTga	54/58	1	2	FACETS	0.776	0.692	0.866	0.776	0.692	0.866	SUBCLONAL	1	FALSE	1	0.28636608512736	2		528	891	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914712	32914712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs34309943	NA	P-0042019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	86	443	0	ENST00000380152.3:c.6220C>T	p.His2074Tyr	p.H2074Y	ENST00000380152		2074	Cac/Tac	11/27	1	2	FACETS	0.928	0.822	1	0.928	0.822	1	CLONAL	1	FALSE	1	0.28636608512736	2		443	647	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941639	48941639	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	27	184	0	ENST00000267163.4:c.949C>T	p.Leu317Phe	p.L317F	ENST00000267163	NM_000321.2	317	Ctt/Ttt	10/27	1	2	FACETS	0.779	0.623	0.956	0.779	0.623	0.956	CLONAL	1	FALSE	1	0.28636608512736	2		184	242	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271513	15271513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1386	125	996	0	ENST00000263388.2:c.6926C>T	p.Pro2309Leu	p.P2309L	ENST00000263388	NM_000435.2	2309	cCc/cTc	33/33	1	2	FACETS	0.578	0.521	0.638	0.578	0.521	0.638	SUBCLONAL	1	FALSE	1	0.28636608512736	2		996	1511	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643606	52643606	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	50	483	0	ENST00000394830.3:c.2290G>T	p.Glu764Ter	p.E764*	ENST00000394830	NM_018313.4	764	Gag/Tag	17/30	1	2	FACETS	0.478	0.405	0.56	0.478	0.405	0.56	SUBCLONAL	1	FALSE	1	0.28636608512736	2		483	730	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455605	189455605	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	177	478	0	ENST00000264731.3:c.139A>T	p.Asn47Tyr	p.N47Y	ENST00000264731	NM_003722.4	47	Aat/Tat	2/14	0.103208335040297	3	FACETS	0.868	0.801	0.938	0.868	0.801	0.938	INDETERMINATE	2	FALSE	1	0.28636608512736	3		478	814	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0042054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	693	575	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.840588964928262	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.840588964928262	1		575	833	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0042054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	191	385	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.927	0.866	0.99	0.927	0.866	0.99	CLONAL	1	TRUE	1	0.840588964928262	2		385	490	SUCCESS
APC	324	MSKCC	GRCh37	5	112175162	112175162	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561588104	NA	P-0042054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	79	294	0	ENST00000257430.4:c.3871C>T	p.Gln1291Ter	p.Q1291*	ENST00000257430	NM_000038.5	1291	Cag/Tag	16/16	1	2	FACETS	0.847	0.758	0.938	0.847	0.758	0.938	CLONAL	1	TRUE	1	0.840588964928262	2		294	222	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61213503	61213503	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768954974	NA	P-0042054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	196	550	0	ENST00000301761.2:c.461G>A	p.Arg154His	p.R154H	ENST00000301761	NM_017841.2	154	cGt/cAt	4/4	0.558375011736588	2	FACETS	0.448	0.414	0.483	0.224	0.207	0.242	SUBCLONAL	1	TRUE	0	0.840588964928262	2		550	1041	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483946	88483946	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	54	770	0	ENST00000360948.2:c.1624del	p.Arg542GlufsTer30	p.R542Efs*30	ENST00000360948	NM_001012338.2	542	Cga/ga	14/19	0.418895770269066	2	FACETS	0.14	0.118	0.163	0.07	0.059	0.082	INDETERMINATE	1	TRUE	0	0.840588964928262	2		770	920	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157699	106157699	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs765107506	NA	P-0042054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	81	395	0	ENST00000380013.4:c.2600A>G	p.Tyr867Cys	p.Y867C	ENST00000380013	NM_001127208.2	867	tAt/tGt	3/11	0.394682539291021	3	FACETS	0.563	0.498	0.633	0.282	0.249	0.317	INDETERMINATE	1	TRUE	1	0.840588964928262	3		395	486	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878640	151878640	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	125	642	0	ENST00000262189.6:c.6305A>T	p.His2102Leu	p.H2102L	ENST00000262189	NM_170606.2	2102	cAt/cTt	36/59	0.185164781981378	5	FACETS	0.665	0.601	0.733	0.222	0.2	0.245	INDETERMINATE	1	TRUE	2	0.840588964928262	5		642	1011	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0042100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	141	437	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.482472007937164	2		437	480	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252966	36252967	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0042100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	112	255	0	ENST00000300305.3:c.395_396del	p.Val132AspfsTer5	p.V132Dfs*5	ENST00000300305		132	gTG/g	4/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.482472007937164	2		255	359	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917681	178917681	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	44	158	0	ENST00000263967.3:c.556G>C	p.Asp186His	p.D186H	ENST00000263967	NM_006218.2	186	Gat/Cat	3/21	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.482472007937164	2		158	168	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863224499	NA	P-0042108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	130	590	0	ENST00000269305.4:c.672+1G>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.2	2		590	934	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342918	225342918	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	28	246	0	ENST00000264414.4:c.2174A>T	p.Glu725Val	p.E725V	ENST00000264414	NM_003590.4	725	gAg/gTg	15/16	1	2	FACETS	0.57	0.455	0.702	0.57	0.455	0.702	SUBCLONAL	1	TRUE	1	0.2	2		246	491	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725208	49725208	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752708882	NA	P-0042108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	15	142	1	ENST00000449682.2:c.217C>T	p.Arg73Cys	p.R73C	ENST00000449682	NM_020998.3	73	Cgc/Tgc	2/18	1	2	FACETS	0.806	0.592	1	0.806	0.592	1	CLONAL	1	TRUE	1	0.2	2		143	186	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0042134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	710	775	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.322582830157076	2	FACETS	1	0.995	1	1	0.998	1	CLONAL	5	TRUE	0	0.322582830157076	2		775	848	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609813	117609813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761155034	NA	P-0042134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	313	593	0	ENST00000368508.3:c.6886G>A	p.Glu2296Lys	p.E2296K	ENST00000368508	NM_002944.2	2296	Gaa/Aaa	43/43	1	2	FACETS	0.937	0.891	0.984	1	0.997	1	CLONAL	3	TRUE	1	0.322582830157076	2		593	690	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0042134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	284	584	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.322582830157076	3	FACETS	0.908	0.863	0.953	1	0.996	1	CLONAL	4	TRUE	1	0.322582830157076	3		584	563	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0042134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	390	302	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.322582830157076	2	FACETS	1	0.991	1	1	0.998	1	CLONAL	5	TRUE	0	0.322582830157076	2		302	465	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388032	81388032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	196	427	1	ENST00000222390.5:c.343G>A	p.Glu115Lys	p.E115K	ENST00000222390	NM_000601.4	115	Gaa/Aaa	3/18	1	2	FACETS	1	0.987	1	1	0.994	1	CLONAL	2	TRUE	1	0.322582830157076	2		428	499	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024380	31024380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201302084	NA	P-0042134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	419	748	0	ENST00000375687.4:c.3865C>T	p.Arg1289Trp	p.R1289W	ENST00000375687	NM_015338.5	1289	Cgg/Tgg	13/13	1	2	FACETS	0.91	0.87	0.949	1	0.997	1	CLONAL	3	TRUE	1	0.322582830157076	2		748	952	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458512	120458512	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	328	671	2	ENST00000256646.2:c.6833C>T	p.Thr2278Ile	p.T2278I	ENST00000256646	NM_024408.3	2278	aCc/aTc	34/34	1	2	FACETS	0.848	0.806	0.891	1	0.997	1	CLONAL	3	TRUE	1	0.322582830157076	2		673	799	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0042134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	240	571	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.924	0.871	0.977	1	0.996	1	CLONAL	3	TRUE	1	0.322582830157076	2		571	537	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852247	63852247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	387	613	1	ENST00000279873.7:c.3025G>A	p.Ala1009Thr	p.A1009T	ENST00000279873	NM_032199.2	1009	Gcg/Acg	10/10	1	2	FACETS	0.968	0.926	1	1	0.997	1	CLONAL	3	TRUE	1	0.322582830157076	2		614	826	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609728	28609728	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1195767772	NA	P-0042134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	237	637	0	ENST00000241453.7:c.1501C>G	p.Leu501Val	p.L501V	ENST00000241453	NM_004119.2	501	Cta/Gta	12/24	0.322582830157076	1	FACETS	0.843	0.79	0.897	1	0.994	1	CLONAL	2	TRUE	0	0.322582830157076	1		637	731	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42053952	42053952	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	172	260	0	ENST00000219905.7:c.7414C>T	p.Gln2472Ter	p.Q2472*	ENST00000219905	NM_001164273.1	2472	Cag/Tag	21/24	1	2	FACETS	0.958	0.895	1	1	0.994	1	CLONAL	3	TRUE	1	0.322582830157076	2		260	371	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448294	56448294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	414	815	0	ENST00000407977.2:c.353C>T	p.Pro118Leu	p.P118L	ENST00000407977		118	cCc/cTc	3/10	1	2	FACETS	0.89	0.851	0.93	1	0.997	1	CLONAL	3	TRUE	1	0.322582830157076	2		815	961	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533934	63533934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349969629	NA	P-0042134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	283	530	1	ENST00000307078.5:c.1220C>T	p.Ser407Phe	p.S407F	ENST00000307078	NM_004655.3	407	tCc/tTc	6/11	1	2	FACETS	0.879	0.833	0.927	1	0.996	1	CLONAL	3	TRUE	1	0.322582830157076	2		531	665	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628414	86628414	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	37	248	0	ENST00000274376.6:c.783T>G	p.Cys261Trp	p.C261W	ENST00000274376	NM_002890.2	261	tgT/tgG	3/25	1	2	FACETS	0.805	0.667	0.958	0.805	0.667	0.958	CLONAL	1	TRUE	1	0.322582830157076	2		248	285	SUCCESS
APC	324	MSKCC	GRCh37	5	112178582	112178582	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	24	340	0	ENST00000257430.4:c.7291A>G	p.Arg2431Gly	p.R2431G	ENST00000257430	NM_000038.5	2431	Aga/Gga	16/16	1	2	FACETS	0.352	0.275	0.44	0.352	0.275	0.44	SUBCLONAL	1	TRUE	1	0.322582830157076	2		340	423	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131951716	131951716	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	103	204	0	ENST00000265335.6:c.3058G>A	p.Asp1020Asn	p.D1020N	ENST00000265335		1020	Gat/Aat	20/25	1	2	FACETS	1	0.965	1	1	0.989	1	CLONAL	2	TRUE	1	0.322582830157076	2		204	282	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056259	26056260	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	461	513	1	ENST00000343677.2:c.397_398delinsAA	p.Gly133Lys	p.G133K	ENST00000343677	NM_005319.3	133	GGg/AAg	1/1	0.27497415191789	5	FACETS	1	0.983	1	1	0.996	1	CLONAL	5	TRUE	1	0.322582830157076	5		514	819	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974361	93974361	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	248	458	0	ENST00000369303.4:c.1693G>A	p.Gly565Arg	p.G565R	ENST00000369303	NM_004440.3	565	Ggg/Agg	8/17	1	2	FACETS	0.899	0.848	0.95	1	0.996	1	CLONAL	3	TRUE	1	0.322582830157076	2		458	570	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386526	81386526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	211	375	0	ENST00000222390.5:c.461C>T	p.Ser154Phe	p.S154F	ENST00000222390	NM_000601.4	154	tCc/tTc	4/18	1	2	FACETS	1	0.989	1	1	0.995	1	CLONAL	2	TRUE	1	0.322582830157076	2		375	525	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0042141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	132	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.533585383711169	3	FACETS	0.879	0.799	0.963	0.44	0.399	0.482	CLONAL	1	TRUE	1	0.533585383711169	3		473	713	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732964	30732964	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	195	487	0	ENST00000295754.5:c.1577A>G	p.Glu526Gly	p.E526G	ENST00000295754	NM_003242.5	526	gAg/gGg	7/7	0.441113074290586	2	FACETS	0.827	0.774	0.88	0.827	0.774	0.88	CLONAL	2	TRUE	0	0.533585383711169	2		487	442	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643770	52643771	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0042141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	135	675	0	ENST00000394830.3:c.2125dup	p.Ile709AsnfsTer14	p.I709Nfs*14	ENST00000394830	NM_018313.4	709	att/aAtt	17/30	1	2	FACETS	0.702	0.639	0.768	0.702	0.639	0.768	SUBCLONAL	1	TRUE	1	0.533585383711169	2		675	721	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522720	176522720	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757092386	NA	P-0042147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	80	686	3	ENST00000292408.4:c.1817G>A	p.Arg606Gln	p.R606Q	ENST00000292408	NM_213647.1	606	cGg/cAg	13/18	0.286047994330767	1	FACETS	0.641	0.564	0.724	0.641	0.564	0.724	SUBCLONAL	1	TRUE	0	0.286047994330767	1		689	748	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265683	10265683	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	59	686	0	ENST00000340748.4:c.1494A>G	p.Ile498Met	p.I498M	ENST00000340748		498	atA/atG	19/40	1	2	FACETS	0.464	0.397	0.536	0.464	0.397	0.536	SUBCLONAL	1	TRUE	1	0.286047994330767	2		686	890	SUCCESS
ALK	238	MSKCC	GRCh37	2	29497974	29497974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	61	501	1	ENST00000389048.3:c.2032G>A	p.Asp678Asn	p.D678N	ENST00000389048	NM_004304.4	678	Gac/Aac	11/29	0.286047994330767	1	FACETS	0.504	0.434	0.581	0.504	0.434	0.581	SUBCLONAL	1	TRUE	0	0.286047994330767	1		502	725	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0042156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	516	711	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.929144146420285	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.929144146420285	1		711	594	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039248	49039248	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1131690882	NA	P-0042156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	607	510	0	ENST00000267163.4:c.2325+1G>A		p.X775_splice	ENST00000267163	NM_000321.2	775			0.918126663171828	2	FACETS	0.965	0.949	0.98	0.965	0.949	0.98	CLONAL	2	TRUE	0	0.929144146420285	2		510	677	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223182	36223182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	629	980	2	ENST00000222270.7:c.5732G>A	p.Arg1911Lys	p.R1911K	ENST00000222270	NM_014727.1	1911	aGa/aAa	28/37	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.929144146420285	2		982	1307	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609043	43609043	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	482	677	2	ENST00000355710.3:c.1799G>T	p.Arg600Leu	p.R600L	ENST00000355710	NM_020975.4	600	cGg/cTg	10/20	0.929144146420285	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.929144146420285	1		679	542	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235911	133235911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201744227	NA	P-0042156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	438	609	0	ENST00000320574.5:c.3245G>A	p.Arg1082His	p.R1082H	ENST00000320574	NM_006231.2	1082	cGc/cAc	26/49	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.929144146420285	2		609	892	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518985	103518985	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	337	498	0	ENST00000355739.4:c.2323C>A	p.Leu775Ile	p.L775I	ENST00000355739	NM_000123.3	775	Ctc/Atc	11/15	0.918126663171828	2	FACETS	1	0.995	1	0.657	0.63	0.684	CLONAL	1	TRUE	0	0.929144146420285	2		498	552	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437611	110437611	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	893	781	0	ENST00000375856.3:c.790G>T	p.Val264Phe	p.V264F	ENST00000375856	NM_003749.2	264	Gtc/Ttc	1/2	0.918126663171828	2	FACETS	0.99	0.978	1	0.99	0.978	1	CLONAL	2	TRUE	0	0.929144146420285	2		781	971	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627792	187627792	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0042156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	475	600	0	ENST00000441802.2:c.3190A>T	p.Arg1064Ter	p.R1064*	ENST00000441802	NM_005245.3	1064	Aga/Tga	2/27	0.929144146420285	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.929144146420285	1		600	527	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513200	106513200	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	270	343	2	ENST00000359195.3:c.2104G>A	p.Glu702Lys	p.E702K	ENST00000359195	NM_002649.2	702	Gag/Aag	4/11	0.124161910473158	3	FACETS	1	0.994	1	0.736	0.697	0.775	INDETERMINATE	1	TRUE	1	0.929144146420285	3		345	578	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738374	133738374	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	404	625	0	ENST00000318560.5:c.774G>T	p.Glu258Asp	p.E258D	ENST00000318560	NM_005157.4	258	gaG/gaT	4/11	0.503589337553494	1	FACETS	0.669	0.643	0.695	0.669	0.643	0.695	INDETERMINATE	1	TRUE	0	0.929144146420285	1		625	696	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0042207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	140	703	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.446305712125745	2	FACETS	0.909	0.84	0.98	0.909	0.84	0.98	CLONAL	2	TRUE	0	0.446305712125745	2		703	345	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46251044	46251044	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145438835	NA	P-0042207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	86	374	0	ENST00000371998.3:c.53G>A	p.Arg18His	p.R18H	ENST00000371998		18	cGc/cAc	3/23	0.446305712125745	4	FACETS	0.908	0.812	1	0.908	0.812	1	CLONAL	2	TRUE	2	0.446305712125745	4		374	307	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0042215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	89	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.338290218587574	1	FACETS	0.885	0.787	0.988	0.885	0.787	0.988	CLONAL	1	TRUE	0	0.338290218587574	1		473	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	301	1000	1	ENST00000269305.4:c.403del	p.Cys135AlafsTer35	p.C135Afs*35	ENST00000269305	NM_001126112.2	135	Tgc/gc	5/11	0.338290218587574	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.338290218587574	1		1001	1210	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929410	32929410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	81	426	0	ENST00000380152.3:c.7420G>A	p.Glu2474Lys	p.E2474K	ENST00000380152		2474	Gaa/Aaa	14/27	1	2	FACETS	0.766	0.675	0.863	0.766	0.675	0.863	SUBCLONAL	1	TRUE	1	0.338290218587574	2		426	625	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1650176	1650176	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	149	768	0	ENST00000344749.5:c.72G>A	p.Met24Ile	p.M24I	ENST00000344749	NM_001136139.2	24	atG/atA	2/19	0.338290218587574	1	FACETS	0.844	0.771	0.92	0.844	0.771	0.92	CLONAL	1	TRUE	0	0.338290218587574	1		768	867	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0042216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	249	662	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.860608190650565	3	FACETS	1	0.953	1			1	CLONAL	1	TRUE	NA	0.860608190650565	3		662	813	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0042216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	365	895	1	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.860608190650565	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.860608190650565	1		896	479	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288168	21288168	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	199	570	0	ENST00000354336.3:c.413A>G	p.Asp138Gly	p.D138G	ENST00000354336	NM_005207.3	138	gAt/gGt	2/3	0.853338058576073	3	FACETS	0.921	0.856	0.988	0.461	0.428	0.494	CLONAL	1	TRUE	1	0.860608190650565	3		570	718	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0042216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	236	290	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.860608190650565	7	FACETS	1	0.987	1	0.889	0.845	0.931	CLONAL	4	TRUE	2	0.860608190650565	7		290	389	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820290	139820290	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1265393184	NA	P-0042216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	96	776	0	ENST00000247668.2:c.1443G>T	p.Lys481Asn	p.K481N	ENST00000247668	NM_021138.3	481	aaG/aaT	11/11	0.797086692915821	4	FACETS	0.345	0.306	0.387	0.173	0.153	0.194	SUBCLONAL	1	TRUE	2	0.860608190650565	4		776	1203	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0042219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	121	241	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	0.540829108708734	2	FACETS	0.951	0.881	1	0.951	0.881	1	CLONAL	2	TRUE	0	0.555511769175738	2		241	229	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993128	72993128	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142256050	NA	P-0042219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	217	850	1	ENST00000268489.5:c.917G>A	p.Arg306Gln	p.R306Q	ENST00000268489	NM_006885.3	306	cGa/cAa	2/10	0.547765592277758	3	FACETS	1	0.976	1	0.553	0.515	0.593	CLONAL	1	TRUE	1	0.555511769175738	3		851	902	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1555525429	NA	P-0042219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	124	658	0	ENST00000269305.4:c.782+1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.486356477783663	1	FACETS	0.951	0.872	1	0.951	0.872	1	CLONAL	1	TRUE	0	0.555511769175738	1		658	339	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0042226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	110	307	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.154865087029652	3	FACETS	0.791	0.713	0.873	0.791	0.713	0.873	INDETERMINATE	2	TRUE	1	0.3	3		307	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	155	800	0	ENST00000269305.4:c.398T>G	p.Met133Arg	p.M133R	ENST00000269305	NM_001126112.2	133	aTg/aGg	5/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.3	2		800	925	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0042226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	51	556	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.3	1	FACETS	0.73	0.622	0.847	0.73	0.622	0.847	SUBCLONAL	1	TRUE	0	0.3	1		556	396	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401368	139401368	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773926521	NA	P-0042226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	120	961	1	ENST00000277541.6:c.3701G>A	p.Arg1234Gln	p.R1234Q	ENST00000277541	NM_017617.3	1234	cGg/cAg	23/34	1	2	FACETS	0.954	0.861	1	0.954	0.861	1	CLONAL	1	TRUE	1	0.3	2		962	839	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0042239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	184	775	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.27661060872425	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.27661060872425	1		775	950	SUCCESS
APC	324	MSKCC	GRCh37	5	112173451	112173451	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	65	341	0	ENST00000257430.4:c.2162del	p.Gly721GlufsTer6	p.G721Efs*6	ENST00000257430	NM_000038.5	720	atG/at	16/16	0.271137775267166	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.27661060872425	1		341	375	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117851	70117851	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	156	645	2	ENST00000245479.2:c.319C>T	p.Arg107Trp	p.R107W	ENST00000245479	NM_000346.3	107	Cgg/Tgg	1/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.27661060872425	2		647	835	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424740	49424740	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs917419349	NA	P-0042239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	174	819	2	ENST00000301067.7:c.13607G>A	p.Arg4536Gln	p.R4536Q	ENST00000301067	NM_003482.3	4536	cGa/cAa	40/54	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.27661060872425	2		821	1178	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488250	56488250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs865824076	NA	P-0042239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	181	732	1	ENST00000267101.3:c.1769C>T	p.Pro590Leu	p.P590L	ENST00000267101	NM_001982.3	590	cCc/cTc	15/28	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.27661060872425	2		733	1003	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876349	35876349	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	106	605	0	ENST00000303115.3:c.1141A>G	p.Ile381Val	p.I381V	ENST00000303115	NM_002185.3	381	Att/Gtt	8/8	1	2	FACETS	0.965	0.865	1	0.965	0.865	1	CLONAL	1	TRUE	1	0.27661060872425	2		605	794	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444282	50444282	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	74	399	0	ENST00000331340.3:c.212G>T	p.Cys71Phe	p.C71F	ENST00000331340	NM_006060.4	71	tGt/tTt	4/8	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.27661060872425	2		399	515	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	310	345	0				ENST00000310581	NM_198253.2	-/1132			0.353182920120464	9	FACETS	0.974	0.932	1	1	0.99	1	CLONAL	8	TRUE	2	0.353182920120464	9		345	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579316	7579317	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0042248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	300	447	0	ENST00000269305.4:c.370dup	p.Cys124LeufsTer25	p.C124Lfs*25	ENST00000269305	NM_001126112.2	124	tgc/tTgc	4/11	0.353255729136761	3	FACETS	1	0.973	1	1	0.995	1	CLONAL	4	TRUE	0	0.353182920120464	3		447	489	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310483	65310483	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs751933525	NA	P-0042248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	86	432	0	ENST00000342505.4:c.2205C>G	p.Ile735Met	p.I735M	ENST00000342505	NM_002227.2	735	atC/atG	16/25	0.353182920120464	4	FACETS	1	0.958	1	0.586	0.52	0.657	CLONAL	1	TRUE	2	0.353182920120464	4		432	562	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919236	48919236	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0042248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	11	83	0	ENST00000267163.4:c.401T>A	p.Leu134Ter	p.L134*	ENST00000267163	NM_000321.2	134	tTa/tAa	4/27	0.353255729136761	4	FACETS	0.659	0.457	0.905	0.22	0.152	0.302	SUBCLONAL	1	TRUE	1	0.353182920120464	4		83	128	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047674	180047674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	132	593	1	ENST00000261937.6:c.2341G>A	p.Gly781Ser	p.G781S	ENST00000261937	NM_182925.4	781	Ggt/Agt	16/30	0.353255729136761	3	FACETS	1	0.98	1	0.637	0.579	0.698	CLONAL	1	TRUE	1	0.353182920120464	3		594	690	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8527354	8527354	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0042248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	29	151	0	ENST00000356435.5:c.542-1G>A		p.X181_splice	ENST00000356435		181			0.353182920120464	5	FACETS	1	0.826	1	0.342	0.275	0.417	CLONAL	1	TRUE	2	0.353182920120464	5		151	245	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775657	9775657	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	215	491	0	ENST00000377346.4:c.200C>A	p.Ala67Asp	p.A67D	ENST00000377346	NM_005026.3	67	gCc/gAc	4/24	0.353182920120464	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.353182920120464	4		491	703	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097721	27097721	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	95	386	0	ENST00000324856.7:c.3310G>C	p.Glu1104Gln	p.E1104Q	ENST00000324856	NM_006015.4	1104	Gaa/Caa	12/20	0.353182920120464	4	FACETS	1	0.954	1	0.566	0.504	0.632	CLONAL	1	TRUE	2	0.353182920120464	4		386	643	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981551	201981569	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCAGGGCCCTTTGGTGAG	CCCAGGGCCCTTTGGTGAG	-	novel	NA	P-0042248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	64	612	0	ENST00000359651.3:c.465_478+5del		p.X155_splice	ENST00000359651		155		3/8	0.353182920120464	6	FACETS	0.614	0.53	0.706	0.154	0.132	0.177	SUBCLONAL	1	TRUE	2	0.353182920120464	6		612	1007	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348902	118348902	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	34	151	0	ENST00000534358.1:c.3555G>C	p.Lys1185Asn	p.K1185N	ENST00000534358	NM_005933.3	1185	aaG/aaC	5/36	0.353182920120464	4	FACETS	1	0.893	1	0.561	0.462	0.672	CLONAL	1	TRUE	2	0.353182920120464	4		151	232	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864774	57864774	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	112	594	0	ENST00000228682.2:c.2251C>G	p.Leu751Val	p.L751V	ENST00000228682	NM_005269.2	751	Ctg/Gtg	12/12	0.353182920120464	4	FACETS	1	0.973	1	0.615	0.553	0.68	CLONAL	1	TRUE	2	0.353182920120464	4		594	698	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941654	48941654	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	89	149	0	ENST00000267163.4:c.964del	p.Glu322LysfsTer10	p.E322Kfs*10	ENST00000267163	NM_000321.2	322	Gaa/aa	10/27	0.353255729136761	4	FACETS	0.958	0.873	1	1	0.979	1	CLONAL	4	TRUE	1	0.353182920120464	4		149	178	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785624	50785624	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	226	454	0	ENST00000398568.2:c.614T>C	p.Ile205Thr	p.I205T	ENST00000398568	NM_001042412.1	205	aTa/aCa	4/18	0.353255729136761	4	FACETS	0.887	0.831	0.944	1	0.991	1	CLONAL	3	TRUE	2	0.353182920120464	4		454	651	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41228615	41228615	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	66	282	0	ENST00000357654.3:c.4374G>C	p.Gln1458His	p.Q1458H	ENST00000357654	NM_007294.3	1458	caG/caC	13/23	0.353255729136761	3	FACETS	1	0.965	1	0.66	0.577	0.749	CLONAL	1	TRUE	1	0.353182920120464	3		282	333	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761287	59761287	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	85	405	0	ENST00000259008.2:c.3120G>C	p.Lys1040Asn	p.K1040N	ENST00000259008	NM_032043.2	1040	aaG/aaC	20/20	0.353255729136761	3	FACETS	1	0.92	1	0.524	0.464	0.588	CLONAL	1	TRUE	1	0.353182920120464	3		405	540	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519809	29519809	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	94	450	1	ENST00000389048.3:c.1762G>A	p.Glu588Lys	p.E588K	ENST00000389048	NM_004304.4	588	Gaa/Aaa	9/29	0.353255729136761	4	FACETS	1	0.969	1	0.415	0.369	0.463	CLONAL	1	TRUE	1	0.353182920120464	4		451	579	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39709872	39709872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	34	161	0	ENST00000361337.2:c.499G>A	p.Glu167Lys	p.E167K	ENST00000361337	NM_003286.2	167	Gaa/Aaa	7/21	0.353182920120464	5	FACETS	1	0.883	1			1	CLONAL	1	TRUE	NA	0.353182920120464	5		161	267	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514674	44514674	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0042248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	75	377	0	ENST00000291552.4:c.483-1G>C		p.X161_splice	ENST00000291552	NM_006758.2	161			0.353182920120464	6	FACETS	1	0.955	1	0.299	0.262	0.339	CLONAL	1	TRUE	2	0.353182920120464	6		377	605	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169953027	169953027	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	88	289	0	ENST00000295797.4:c.111G>A	p.Met37Ile	p.M37I	ENST00000295797	NM_002740.5	37	atG/atA	2/18	0.353182920120464	6	FACETS	0.782	0.694	0.875	0.391	0.347	0.438	SUBCLONAL	2	TRUE	2	0.353182920120464	6		289	544	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652243	36652250	+	frameshift_variant	Frame_Shift_Del	DEL	GCTCAGGG	GCTCAGGG	-	novel	NA	P-0042248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	110	481	0	ENST00000244741.5:c.366_373del	p.Ser123AlafsTer3	p.S123Afs*3	ENST00000244741	NM_000389.4	122	cGCTCAGGG/c	2/3	0.353255729136761	3	FACETS	1	0.979	1	0.669	0.603	0.738	CLONAL	1	TRUE	1	0.353182920120464	3		481	548	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004897	150004897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	75	303	0	ENST00000253339.5:c.1328C>T	p.Ser443Leu	p.S443L	ENST00000253339		443	tCa/tTa	3/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.353182920120464	2		303	288	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528159	157528159	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	33	432	0	ENST00000346085.5:c.5884G>T	p.Asp1962Tyr	p.D1962Y	ENST00000346085	NM_020732.3	1962	Gat/Tat	20/20	1	2	FACETS	0.539	0.439	0.65	0.539	0.439	0.65	SUBCLONAL	1	TRUE	1	0.353182920120464	2		432	347	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	127	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.507708591039075	3	FACETS	0.868	0.787	0.952	0.434	0.393	0.476	CLONAL	1	TRUE	1	0.530435620702245	3		485	698	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986928	36986928	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	222	552	0	ENST00000354822.5:c.761C>G	p.Ala254Gly	p.A254G	ENST00000354822	NM_001079668.2	254	gCg/gGg	3/3	0.51836113330886	2	FACETS	1	0.985	1	0.585	0.547	0.625	CLONAL	1	TRUE	0	0.530435620702245	2		552	715	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640454	3640454	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369435228	NA	P-0042269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	525	895	1	ENST00000294008.3:c.3185G>A	p.Arg1062His	p.R1062H	ENST00000294008	NM_032444.2	1062	cGt/cAt	12/15	0.530435620702245	3	FACETS	0.932	0.894	0.97	0.932	0.894	0.97	CLONAL	2	TRUE	1	0.530435620702245	3		896	1344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0042269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	448	515	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.513626240441003	2	FACETS	0.96	0.922	0.998	0.96	0.922	0.998	CLONAL	2	TRUE	0	0.530435620702245	2		515	880	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207065	1207066	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	rs1131690917	NA	P-0042269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	645	891	0	ENST00000326873.7:c.156_157del	p.Asp53ProfsTer109	p.D53Pfs*109	ENST00000326873	NM_000455.4	51	atGGgg/atgg	1/10	0.494236509059679	3	FACETS	0.856	0.829	0.884	0.856	0.829	0.884	CLONAL	3	TRUE	0	0.530435620702245	3		891	1198	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249013	55249014	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACCCCC	novel	NA	P-0042274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	235	770	0	ENST00000275493.2:c.2314_2319dup	p.Pro772_His773dup	p.P772_H773dup	ENST00000275493	NM_005228.3	772	aac/aACCCCCac	20/28	0.327263361301371	6	FACETS	1	0.975	1	0.546	0.509	0.585	CLONAL	2	TRUE	2	0.327263361301371	6		770	1087	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609600	81609600	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	97	607	0	ENST00000298171.2:c.1198C>A	p.Pro400Thr	p.P400T	ENST00000298171	NM_000369.2	400	Ccc/Acc	10/10	1	2	FACETS	0.947	0.846	1	0.947	0.846	1	CLONAL	1	TRUE	1	0.327263361301371	2		607	626	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142932	7142932	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs371294434	NA	P-0042274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	283	1012	1	ENST00000302850.5:c.2437C>T	p.Arg813Ter	p.R813*	ENST00000302850	NM_000208.2	813	Cga/Tga	12/22	0.30755304420538	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.327263361301371	3		1013	931	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050031	13050031	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	74	589	0	ENST00000316448.5:c.175G>T	p.Asp59Tyr	p.D59Y	ENST00000316448	NM_004343.3	59	Gac/Tac	2/9	0.30755304420538	3	FACETS	0.876	0.767	0.992	0.438	0.383	0.496	CLONAL	1	TRUE	1	0.327263361301371	3		589	601	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970990	55970990	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	88	628	1	ENST00000263923.4:c.1807T>A	p.Cys603Ser	p.C603S	ENST00000263923	NM_002253.2	603	Tgc/Agc	13/30	1	2	FACETS	0.852	0.756	0.955	0.852	0.756	0.955	CLONAL	1	TRUE	1	0.327263361301371	2		629	631	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855282	76855282	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	49	154	0	ENST00000373344.5:c.5705T>C	p.Phe1902Ser	p.F1902S	ENST00000373344	NM_000489.3	1902	tTt/tCt	24/35	1	2	FACETS	0.927	0.789	1	0.927	0.789	1	CLONAL	1	TRUE	1	0.327263361301371	2		154	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579545	7579545	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	301	768	0	ENST00000269305.4:c.142del	p.Asp48ThrfsTer75	p.D48Tfs*75	ENST00000269305	NM_001126112.2	48	Gac/ac	4/11	0.29992468665364	0	FACETS	0.751	0.713	0.789			1	SUBCLONAL	2	TRUE	0	0.38	0		768	654	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856433	111856433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1046057518	NA	P-0042276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	19	177	1	ENST00000341259.2:c.484G>A	p.Ala162Thr	p.A162T	ENST00000341259	NM_005475.2	162	Gcc/Acc	2/8	0.29992468665364	1	FACETS	0.379	0.288	0.484	0.379	0.288	0.484	SUBCLONAL	1	TRUE	0	0.38	1		178	214	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169139	119169139	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	43	491	0	ENST00000264033.4:c.2323G>A	p.Asp775Asn	p.D775N	ENST00000264033	NM_005188.3	775	Gat/Aat	15/16	1	2	FACETS	0.321	0.267	0.38	0.321	0.267	0.38	SUBCLONAL	1	TRUE	1	0.38	2		491	706	SUCCESS
APC	324	MSKCC	GRCh37	5	112174094	112174095	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs863225332	NA	P-0042316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	87	395	0	ENST00000257430.4:c.2804dup	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	tac/tAac	16/16	0.214214542062351	2	FACETS	1	0.977	1	0.706	0.628	0.788	CLONAL	1	TRUE	0	0.275182830747817	2		395	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519986	NA	P-0042316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	450	795	0	ENST00000269305.4:c.809T>G	p.Phe270Cys	p.F270C	ENST00000269305	NM_001126112.2	270	tTt/tGt	8/11	0.275182830747817	3	FACETS	0.991	0.947	1	0.991	0.947	1	CLONAL	3	TRUE	0	0.275182830747817	3		795	1251	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0042328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	347	699	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	NA	2	FACETS	1	0.978	1			1	INDETERMINATE	2	TRUE	NA	0.432088551986997	2		699	770	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478927	56478927	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	379	674	0	ENST00000267101.3:c.383G>T	p.Ser128Ile	p.S128I	ENST00000267101	NM_001982.3	128	aGc/aTc	3/28	0.420569979338045	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.432088551986997	2		674	874	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52661288	52661288	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0042328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	213	326	0	ENST00000394830.3:c.1541+1G>C		p.X514_splice	ENST00000394830	NM_018313.4	514			0.420569979338045	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.432088551986997	2		326	463	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0042347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	142	453	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.377743588688676	2		453	727	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	194	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.362708727800354	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.377743588688676	3		485	570	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0042347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	62	295	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	0.362708727800354	3	FACETS	0.94	0.815	1	0.47	0.407	0.538	CLONAL	1	TRUE	1	0.377743588688676	3		295	415	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720637	89720659	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTTTTTTTTTAGGACAAAATG	TTTTTTTTTTTTAGGACAAAATG	-	novel	NA	P-0042347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	159	111	0	ENST00000371953.3:c.802-11_813del		p.X268_splice	ENST00000371953	NM_000314.4	268		8/9	0.377743588688676	3	FACETS	0.956	0.89	1	0.956	0.89	1	CLONAL	3	TRUE	0	0.377743588688676	3		111	349	SUCCESS
ATR	545	MSKCC	GRCh37	3	142184012	142184012	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	218	171	0	ENST00000350721.4:c.6968T>G	p.Ile2323Ser	p.I2323S	ENST00000350721	NM_001184.3	2323	aTc/aGc	41/47	0.362708727800354	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.377743588688676	3		171	613	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251235	115251235	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs758669528	NA	P-0042373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	48	508	0	ENST00000369535.4:c.491G>T	p.Arg164Leu	p.R164L	ENST00000369535	NM_002524.4	164	cGc/cTc	5/7	1	2	FACETS	0.494	0.417	0.579	0.494	0.417	0.579	SUBCLONAL	1	TRUE	1	0.315787849439949	2		508	615	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163784	47163785	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0042373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	74	466	0	ENST00000409792.3:c.2341dup	p.Thr781AsnfsTer20	p.T781Nfs*20	ENST00000409792	NM_014159.6	781	acg/aAcg	3/21	0.315787849439949	1	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	0	0.315787849439949	1		466	388	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436854	52436857	+	frameshift_variant	Frame_Shift_Del	DEL	CAGC	CAGC	-	novel	NA	P-0042373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	108	608	0	ENST00000460680.1:c.1921_1924del	p.Ala641ArgfsTer13	p.A641Rfs*13	ENST00000460680	NM_004656.3	641	GCTGag/ag	15/17	0.315787849439949	1	FACETS	0.843	0.758	0.934	0.843	0.758	0.934	CLONAL	1	TRUE	0	0.315787849439949	1		608	683	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374438	81374438	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0042373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	78	369	0	ENST00000222390.5:c.626-2A>G		p.X209_splice	ENST00000222390	NM_000601.4	209			1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.315787849439949	2		369	419	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633599	69633599	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1430586811	NA	P-0042374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	12	115	0	ENST00000334134.2:c.103G>T	p.Val35Phe	p.V35F	ENST00000334134	NM_005247.2	35	Gtc/Ttc	1/3	0.209537436747242	1	FACETS	0.16	0.112	0.218	0.16	0.112	0.218	INDETERMINATE	1	TRUE	0	0.486393644939884	1		115	234	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847307	68847307	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	30	508	0	ENST00000261769.5:c.1229A>T	p.Glu410Val	p.E410V	ENST00000261769	NM_004360.3	410	gAg/gTg	9/16	0.486393644939884	1	FACETS	0.165	0.132	0.203	0.165	0.132	0.203	SUBCLONAL	1	TRUE	0	0.486393644939884	1		508	565	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524617	176524617	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	55	637	0	ENST00000292408.4:c.2349C>G	p.Ser783Arg	p.S783R	ENST00000292408	NM_213647.1	783	agC/agG	18/18	1	2	FACETS	0.224	0.191	0.261	0.224	0.191	0.261	SUBCLONAL	1	TRUE	1	0.486393644939884	2		637	1008	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357204	70357204	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	37	252	0	ENST00000374080.3:c.5719C>G	p.Gln1907Glu	p.Q1907E	ENST00000374080		1907	Caa/Gaa	39/45	1	1	FACETS	0.229	0.189	0.275	0.229	0.189	0.275	SUBCLONAL	1	TRUE	0	0.486393644939884	1		252	502	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0042377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	71	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.144890791808086	3	FACETS	1	0.93	1	0.543	0.477	0.613	INDETERMINATE	1	TRUE	1	0.445361129663564	3		473	359	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	148	800	0	ENST00000269305.4:c.398T>G	p.Met133Arg	p.M133R	ENST00000269305	NM_001126112.2	133	aTg/aGg	5/11	0.445361129663564	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.445361129663564	1		800	438	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0042377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	236	435	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.445361129663564	1	FACETS	0.981	0.93	1	1	0.995	1	CLONAL	2	TRUE	0	0.445361129663564	1		435	420	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	75	453	0	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	0.445361129663564	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.445361129663564	1		453	247	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0042396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	210	842	1	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.29820309915717	1	FACETS	0.973	0.903	1	0.973	0.903	1	CLONAL	1	TRUE	0	0.368811304991248	1		843	955	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183771	10183771	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	160	589	0	ENST00000256474.2:c.240T>G	p.Ser80Arg	p.S80R	ENST00000256474	NM_000551.3	80	agT/agG	1/3	0.368811304991248	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.368811304991248	1		589	611	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463287	25463287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761934754	NA	P-0042396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	114	597	0	ENST00000264709.3:c.2206C>T	p.Arg736Cys	p.R736C	ENST00000264709	NM_175629.2	736	Cgc/Tgc	19/23	1	2	FACETS	0.921	0.831	1	0.921	0.831	1	CLONAL	1	TRUE	1	0.368811304991248	2		597	671	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45800097	45800097	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	174	704	0	ENST00000450313.1:c.123del	p.Asn42ThrfsTer16	p.N42Tfs*16	ENST00000450313	NM_012222.2	41	aaG/aa	2/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.368811304991248	2		704	863	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584552	52584552	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	36	733	0	ENST00000394830.3:c.4461del	p.Phe1487LeufsTer2	p.F1487Lfs*2	ENST00000394830	NM_018313.4	1487	ttT/tt	29/30	0.368811304991248	1	FACETS	0.233	0.191	0.281	0.233	0.191	0.281	SUBCLONAL	1	TRUE	0	0.368811304991248	1		733	682	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0042416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	61	584	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	1	0.927	1	1	0.981	1	CLONAL	2	TRUE	1	0.2	2		584	278	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199469672	NA	P-0042431-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	314	650	0	ENST00000374080.3:c.131G>T	p.Gly44Val	p.G44V	ENST00000374080		44	gGt/gTt	2/45	1	2	FACETS	0.905	0.856	0.954	0.905	0.856	0.954	CLONAL	1	TRUE	1	0.763515269960476	2		650	909	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500476	149500476	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042431-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	375	824	0	ENST00000261799.4:c.2561A>G	p.Asp854Gly	p.D854G	ENST00000261799	NM_002609.3	854	gAc/gGc	18/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.763515269960476	2		824	952	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505053	149505058	+	inframe_deletion	In_Frame_Del	DEL	GCAGCT	GCAGCT	-	novel	NA	P-0042431-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	242	721	0	ENST00000261799.4:c.1757_1762del	p.Gln586_Leu587del	p.Q586_L587del	ENST00000261799	NM_002609.3	586	cAGCTGCcc/ccc	12/23	1	2	FACETS	0.849	0.796	0.902	0.849	0.796	0.902	CLONAL	1	TRUE	1	0.763515269960476	2		721	747	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204864	NA	P-0042476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	33	314	0	ENST00000371953.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000371953	NM_000314.4	171	Cag/Tag	6/9	0.680684161997616	1	FACETS	0.173	0.141	0.21	0.173	0.141	0.21	SUBCLONAL	1	TRUE	0	0.680684161997616	1		314	369	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266822	198266822	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	274	682	0	ENST00000335508.6:c.2110A>T	p.Ile704Phe	p.I704F	ENST00000335508	NM_012433.2	704	Atc/Ttc	15/25	1	2	FACETS	0.914	0.86	0.969	0.914	0.86	0.969	CLONAL	1	TRUE	1	0.680684161997616	2		682	881	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0042487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	17	434	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.515	0.383	0.673	0.515	0.383	0.673	SUBCLONAL	1	TRUE	1	0.13	2		434	508	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692848	89692848	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	13	200	0	ENST00000371953.3:c.332G>A	p.Trp111Ter	p.W111*	ENST00000371953	NM_000314.4	111	tGg/tAg	5/9	1	2	FACETS	0.922	0.658	1	0.922	0.658	1	CLONAL	1	TRUE	1	0.13	2		200	217	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579397	7579398	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0042487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	44	954	0	ENST00000269305.4:c.289dup	p.Val97GlyfsTer52	p.V97Gfs*52	ENST00000269305	NM_001126112.2	97	gtc/gGtc	4/11	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.13	2		954	603	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0042492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	152	584	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.189630756230218	5	FACETS	1	0.967	1	1	0.989	1	CLONAL	4	TRUE	2	0.227630660609207	5		584	413	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518190	103518190	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371246879	NA	P-0042492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	35	649	0	ENST00000355739.4:c.2128G>A	p.Val710Met	p.V710M	ENST00000355739	NM_000123.3	710	Gtg/Atg	9/15	0.148139973105975	4	FACETS	1	0.856	1	0.524	0.43	0.63	CLONAL	1	TRUE	2	0.227630660609207	4		649	360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0042500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	757	497	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.843852295693287	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.843852295693287	3		497	817	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577599	7577599	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	470	510	0	ENST00000269305.4:c.682G>C	p.Asp228His	p.D228H	ENST00000269305	NM_001126112.2	228	Gac/Cac	7/11	0.843852295693287	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.843852295693287	3		510	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579337	7579337	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs755238756	NA	P-0042500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	659	640	0	ENST00000269305.4:c.350G>C	p.Gly117Ala	p.G117A	ENST00000269305	NM_001126112.2	117	gGg/gCg	4/11	0.843852295693287	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.843852295693287	3		640	708	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916920	178916929	+	protein_altering_variant	In_Frame_Del	DEL	GAACCAGTAG	GAACCAGTAG	AAAA	novel	NA	P-0042509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	76	472	1	ENST00000263967.3:c.307_316delinsAAAA	p.Glu103_Gly106delinsLysSer	p.E103_G106delinsKS	ENST00000263967	NM_006218.2	103	GAACCAGTAGgc/AAAAgc	2/21	1	2	FACETS	0.932	0.817	1	0.932	0.817	1	CLONAL	1	TRUE	1	0.22	2		473	741	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0042542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	26	217	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.127611022430967	3	FACETS	1	0.891	1	0.603	0.479	0.746	CLONAL	1	FALSE	1	0.153077917101744	3		217	303	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0042542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	47	354	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	1	2	FACETS	0.751	0.635	0.878	1	0.961	1	SUBCLONAL	2	FALSE	1	0.153077917101744	2		354	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0042542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	70	701	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	0.757	0.66	0.862	1	0.974	1	SUBCLONAL	2	FALSE	1	0.153077917101744	2		701	604	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129620	2129620	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878854092	NA	P-0042542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	44	1060	2	ENST00000219476.3:c.3347C>T	p.Ala1116Val	p.A1116V	ENST00000219476	NM_000548.3	1116	gCt/gTt	29/42	0.153077917101744	1	FACETS	0.869	0.728	1	0.869	0.728	1	CLONAL	1	FALSE	0	0.153077917101744	1		1062	611	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129133	152129133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	44	921	0	ENST00000206249.3:c.86C>T	p.Pro29Leu	p.P29L	ENST00000206249	NM_000125.3	29	cCg/cTg	1/8	0.127611022430967	3	FACETS	0.883	0.739	1	0.441	0.369	0.522	CLONAL	1	FALSE	1	0.153077917101744	3		921	701	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023919	27023919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1438830885	NA	P-0042542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	11	69	0	ENST00000324856.7:c.1025C>T	p.Ala342Val	p.A342V	ENST00000324856	NM_006015.4	342	gCg/gTg	1/20	1	2	FACETS	1	0.829	1	1	0.829	1	CLONAL	1	FALSE	1	0.153077917101744	2		69	108	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633607	69633607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	10	109	0	ENST00000334134.2:c.95G>A	p.Arg32His	p.R32H	ENST00000334134	NM_005247.2	32	cGt/cAt	1/3	0.153077917101744	2	FACETS	1	0.808	1	0.647	0.442	0.9	CLONAL	1	FALSE	0	0.153077917101744	2		109	101	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0042584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	214	737	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.337901810204126	2	FACETS	0.772	0.72	0.824	0.772	0.72	0.824	SUBCLONAL	2	TRUE	0	0.397930879307612	2		737	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0042602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	712	456	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.737110814279799	2	FACETS	0.951	0.928	0.973	0.951	0.928	0.973	CLONAL	2	TRUE	0	0.766552772674623	2		456	977	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713285	30713285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773431795	NA	P-0042602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	140	429	0	ENST00000295754.5:c.610G>A	p.Gly204Ser	p.G204S	ENST00000295754	NM_003242.5	204	Ggc/Agc	4/7	0.741268371229586	2	FACETS	0.758	0.695	0.823	0.379	0.347	0.412	SUBCLONAL	1	TRUE	0	0.766552772674623	2		429	482	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876536	35876536	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0042602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	54	476	0	ENST00000303115.3:c.1328C>G	p.Ser443Ter	p.S443*	ENST00000303115	NM_002185.3	443	tCa/tGa	8/8	0.763209030367133	2	FACETS	0.223	0.19	0.259	0.111	0.095	0.13	SUBCLONAL	1	TRUE	0	0.766552772674623	2		476	633	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517370	157517370	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554234363	NA	P-0042602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	518	550	0	ENST00000346085.5:c.3934C>T	p.Gln1312Ter	p.Q1312*	ENST00000346085	NM_020732.3	1312	Caa/Taa	16/20	0.763209030367133	2	FACETS	0.967	0.94	0.992	0.967	0.94	0.992	CLONAL	2	TRUE	0	0.766552772674623	2		550	699	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0042603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	46	672	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.868	0.742	1	0.868	0.742	1	CLONAL	1	TRUE	1	0.576051636960854	2		672	184	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	55	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.576051636960854	2		485	162	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866689	37866689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149210045	NA	P-0042603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	325	845	0	ENST00000269571.5:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269571		286	Gag/Aag	7/27	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.576051636960854	2		845	1097	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266028	41266605	+	splice_donor_variant,splice_acceptor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	GAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACAT	GAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACAT	-	novel	NA	P-0042603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	20	288	0	ENST00000349496.5:c.26_403del		p.X9_splice	ENST00000349496	NM_001904.3	9	GAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACAT/-	3-4/15	1	2	FACETS	0.584	0.452	0.733	0.584	0.452	0.733	SUBCLONAL	1	TRUE	1	0.576051636960854	2		288	119	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592037	67592037	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	57	279	0	ENST00000274335.5:c.1853A>G	p.His618Arg	p.H618R	ENST00000274335		618	cAt/cGt	14/15	1	2	FACETS	0.933	0.812	1	0.933	0.812	1	CLONAL	1	TRUE	1	0.576051636960854	2		279	212	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0042604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	40	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.874	0.728	1	0.874	0.728	1	CLONAL	1	TRUE	1	0.2709188923981	2		473	338	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0042604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	101	799	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.147765134021036	1	FACETS	0.938	0.839	1	0.938	0.839	1	INDETERMINATE	1	TRUE	0	0.2709188923981	1		799	687	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584513	48584514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs377767334	NA	P-0042604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	25	477	0	ENST00000342988.3:c.692dup	p.Ser232GlnfsTer3	p.S232Qfs*3	ENST00000342988	NM_005359.5	229	ctg/ctGg	6/12	0.2709188923981	1	FACETS	0.457	0.36	0.569	0.457	0.36	0.569	SUBCLONAL	1	TRUE	0	0.2709188923981	1		477	349	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971170	21971170	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	40	492	0	ENST00000304494.5:c.188T>G	p.Leu63Arg	p.L63R	ENST00000304494	NM_000077.4	63	cTg/cGg	2/3	1	2	FACETS	0.8	0.666	0.949	0.8	0.666	0.949	CLONAL	1	TRUE	1	0.2709188923981	2		492	369	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0042625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	97	672	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.587	0.524	0.654	0.587	0.524	0.654	SUBCLONAL	1	TRUE	1	0.539739082804718	2		672	612	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0042625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	112	364	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.273853532744395	1	FACETS	0.771	0.699	0.845	0.771	0.699	0.845	INDETERMINATE	1	TRUE	0	0.539739082804718	1		364	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371524413	NA	P-0042625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	305	918	0	ENST00000269305.4:c.467G>A	p.Arg156His	p.R156H	ENST00000269305	NM_001126112.2	156	cGc/cAc	5/11	0.539739082804718	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.539739082804718	1		918	757	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0042625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	203	597	0	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	0.539739082804718	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.539739082804718	1		597	496	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911607	134911607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1384145752	NA	P-0042625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	100	511	0	ENST00000398015.3:c.2072G>A	p.Arg691Gln	p.R691Q	ENST00000398015	NM_004441.4	691	cGg/cAg	11/16	1	2	FACETS	0.698	0.625	0.774	0.698	0.625	0.774	SUBCLONAL	1	TRUE	1	0.539739082804718	2		511	531	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943988	71943988	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	53	749	2	ENST00000298229.2:c.1921C>T	p.Arg641Trp	p.R641W	ENST00000298229	NM_001567.3	641	Cgg/Tgg	16/28	0.273853532744395	1	FACETS	0.183	0.155	0.213	0.183	0.155	0.213	INDETERMINATE	1	TRUE	0	0.539739082804718	1		751	785	SUCCESS
APC	324	MSKCC	GRCh37	5	112175330	112175331	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCAGGCA	novel	NA	P-0042625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	36	242	0	ENST00000257430.4:c.4041_4047dup	p.Lys1350GlnfsTer6	p.K1350Qfs*6	ENST00000257430	NM_000038.5	1347	gcc/gCCAGGCAcc	16/16	0.273853532744395	1	FACETS	0.365	0.301	0.435	0.365	0.301	0.435	INDETERMINATE	1	TRUE	0	0.539739082804718	1		242	267	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750956	128750956	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	238	567	1	ENST00000377970.2:c.493G>A	p.Ala165Thr	p.A165T	ENST00000377970	NM_002467.4	165	Gcc/Acc	2/3	0.598164205767941	3	FACETS	0.977	0.922	1	0.977	0.922	1	CLONAL	2	TRUE	1	0.598164205767941	3		568	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0042661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	777	753	1	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.401181714862075	1	FACETS	1	0.998	1	1	0.998	1	INDETERMINATE	1	TRUE	0	0.718690500374061	1		754	1078	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638317	117638317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758446263	NA	P-0042661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	99	348	0	ENST00000368508.3:c.6124C>T	p.Arg2042Trp	p.R2042W	ENST00000368508	NM_002944.2	2042	Cgg/Tgg	38/43	0.718690500374061	1	FACETS	0.975	0.897	1	0.975	0.897	1	CLONAL	1	TRUE	0	0.718690500374061	1		348	181	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0042663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	297	627	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.374910318978904	0	FACETS	0.894	0.852	0.936			1	CLONAL	2	TRUE	0	0.374910318978904	0		628	554	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0042670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	90	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.524825137717823	1	FACETS	0.373	0.335	0.412	0.373	0.335	0.412	INDETERMINATE	1	TRUE	0	0.935000042714999	1		336	275	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0042670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	175	1042	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	0.488198874216612	1	FACETS	0.282	0.26	0.305	0.282	0.26	0.305	INDETERMINATE	1	TRUE	0	0.935000042714999	1		1042	707	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716095	243716095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	102	597	1	ENST00000263826.5:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000263826	NM_005465.4	367	Cga/Tga	10/13	0.624073026659991	3	FACETS	0.424	0.379	0.471			1	SUBCLONAL	1	TRUE	NA	0.935000042714999	3		598	756	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031893	10031893	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	143	717	1	ENST00000330684.3:c.930C>A	p.Phe310Leu	p.F310L	ENST00000330684	NM_001134407.1	310	ttC/ttA	3/13	0.459607169483434	3	FACETS	0.588	0.537	0.642	0.294	0.268	0.321	INDETERMINATE	1	TRUE	1	0.935000042714999	3		718	763	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462662	29462662	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762395127	NA	P-0042670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	364	928	0	ENST00000389048.3:c.2239G>A	p.Gly747Arg	p.G747R	ENST00000389048	NM_004304.4	747	Ggg/Agg	13/29	0.453472065791316	2	FACETS	0.984	0.939	1	0.492	0.469	0.515	INDETERMINATE	1	TRUE	0	0.935000042714999	2		928	791	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653792	89653792	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1564814427	NA	P-0042670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	249	332	0	ENST00000371953.3:c.92del	p.Asn31ThrfsTer23	p.N31Tfs*23	ENST00000371953	NM_000314.4	30	ccA/cc	2/9	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	2	TRUE	NA	0.935000042714999	2		332	266	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844229	68844229	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	212	648	1	ENST00000261769.5:c.817G>T	p.Glu273Ter	p.E273*	ENST00000261769	NM_004360.3	273	Gaa/Taa	6/16	0.935000042714999	1	FACETS	0.925	0.891	0.957	0.925	0.891	0.957	CLONAL	1	TRUE	0	0.935000042714999	1		649	261	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	107	345	0				ENST00000310581	NM_198253.2	-/1132			0.234038662622653	6	FACETS	1	0.969	1	0.796	0.716	0.88	CLONAL	2	TRUE	3	0.234038662622653	6		345	562	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42851169	42851169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775960588	NA	P-0042682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	40	424	1	ENST00000398585.3:c.724G>A	p.Gly242Arg	p.G242R	ENST00000398585	NM_001135099.1	242	Gga/Aga	7/14	1	2	FACETS	0.708	0.588	0.841	0.708	0.588	0.841	SUBCLONAL	1	TRUE	1	0.234038662622653	2		425	483	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145736889	145736949	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCAGAAGCGTCGGTCCTGCCCGTACACCTGGGCCGGGTAGCAGGGGCTTCCTACGGTGGAG	CCAGAAGCGTCGGTCCTGCCCGTACACCTGGGCCGGGTAGCAGGGGCTTCCTACGGTGGAG	-	novel	NA	P-0042682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	89	1087	0	ENST00000428558.2:c.3503-11_3552del		p.X1168_splice	ENST00000428558	NM_004260.3	1168		22/22	0.234038662622653	4	FACETS	0.849	0.75	0.954	0.283	0.25	0.318	CLONAL	1	TRUE	1	0.234038662622653	4		1087	1106	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717626	89717632	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCCAG	CTGCCAG	-	novel	NA	P-0042711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	67	490	1	ENST00000371953.3:c.653_659del	p.Cys218Ter	p.C218*	ENST00000371953	NM_000314.4	217	gtCTGCCAG/gt	7/9	0.645059729824595	1	FACETS	0.863	0.769	0.96	0.863	0.769	0.96	CLONAL	1	TRUE	0	0.645059729824595	1		491	163	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969860	81969860	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	40	758	0	ENST00000359376.3:c.2929T>C	p.Tyr977His	p.Y977H	ENST00000359376	NM_002661.3	977	Tac/Cac	27/33	0.645059729824595	1	FACETS	0.16	0.132	0.19	0.16	0.132	0.19	SUBCLONAL	1	TRUE	0	0.645059729824595	1		758	526	SUCCESS
AR	367	MSKCC	GRCh37	X	66931289	66931289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	53	272	0	ENST00000374690.3:c.1931G>A	p.Gly644Glu	p.G644E	ENST00000374690	NM_000044.3	644	gGa/gAa	4/8	1	1	FACETS	0.612	0.53	0.698	0.612	0.53	0.698	SUBCLONAL	1	TRUE	0	0.645059729824595	1		272	182	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0042743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	31	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.687	0.555	0.836	0.687	0.555	0.836	SUBCLONAL	1	TRUE	1	0.21	2		473	430	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441613	6441613	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	75	411	0	ENST00000356142.4:c.460A>C	p.Thr154Pro	p.T154P	ENST00000356142	NM_018890.3	154	Act/Cct	6/7	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.21	2		411	607	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101910068	101910068	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0042743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	26	185	0	ENST00000374994.4:c.1386+2T>G		p.X462_splice	ENST00000374994	NM_004612.2	462			1	2	FACETS	1	0.813	1	1	0.813	1	CLONAL	1	TRUE	1	0.21	2		185	242	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573997	7574013	+	frameshift_variant	Frame_Shift_Del	DEL	GCTCTCGGAACATCTCG	GCTCTCGGAACATCTCG	-	novel	NA	P-0042744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	197	645	0	ENST00000269305.4:c.1014_1030del	p.Met340Ter	p.M340*	ENST00000269305	NM_001126112.2	338	ttCGAGATGTTCCGAGAGCtg/tttg	10/11	0.573860310998669	1	FACETS	0.781	0.728	0.835	0.781	0.728	0.835	SUBCLONAL	1	TRUE	0	0.605635560978718	1		645	581	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905067	50905067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	168	541	0	ENST00000440232.2:c.349C>T	p.Pro117Ser	p.P117S	ENST00000440232	NM_002691.3	117	Cca/Tca	4/27	1	2	FACETS	0.791	0.729	0.856	0.791	0.729	0.856	SUBCLONAL	1	TRUE	1	0.605635560978718	2		541	701	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028657	12028657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	146	376	0	ENST00000353533.5:c.860G>A	p.Arg287His	p.R287H	ENST00000353533	NM_003010.3	287	cGc/cAc	8/11	0.50575999901909	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.505250588068825	1		376	375	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115972	8115973	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0042786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	106	289	0	ENST00000346208.3:c.1320dup	p.Ala441ArgfsTer66	p.A441Rfs*66	ENST00000346208		440	acc/aCcc	6/6	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.505250588068825	2		289	358	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0042810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	209	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.544196059218378	3	FACETS	0.954	0.894	1	0.954	0.894	1	CLONAL	2	TRUE	1	0.544196059218378	3		473	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0042810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	252	857	1	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.544196059218378	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.544196059218378	1		858	649	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640238	3640238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1433489753	NA	P-0042810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	315	1403	1	ENST00000294008.3:c.3401C>T	p.Ser1134Leu	p.S1134L	ENST00000294008	NM_032444.2	1134	tCg/tTg	12/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.544196059218378	2		1404	1121	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970993	21970993	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	235	898	0	ENST00000304494.5:c.365del	p.Gly122AlafsTer24	p.G122Afs*24	ENST00000304494	NM_000077.4	122	gGc/gc	2/3	0.544196059218378	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.544196059218378	1		898	623	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0042817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	201	394	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.565653968046274	2		394	633	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200419	138200419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778025601	NA	P-0042817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	67	700	0	ENST00000237289.4:c.1837G>A	p.Val613Met	p.V613M	ENST00000237289	NM_001270507.1	613	Gtg/Atg	7/9	0.228384085757804	0	FACETS	0.16	0.139	0.183			1	INDETERMINATE	1	TRUE	0	0.565653968046274	0		700	642	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870878	12870896	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGGACCACGAAGAGTTA	GGTGGACCACGAAGAGTTA	-	novel	NA	P-0042817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	41	303	0	ENST00000228872.4:c.105_123del	p.Val36ProfsTer29	p.V36Pfs*29	ENST00000228872	NM_004064.3	35	ccGGTGGACCACGAAGAGTTA/cc	1/3	0.146025837195345	5	FACETS	0.74	0.618	0.875	0.247	0.206	0.292	INDETERMINATE	1	TRUE	2	0.565653968046274	5		303	362	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063389	67063389	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0042817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	168	452	0	ENST00000412916.2:c.78+1G>T		p.X26_splice	ENST00000412916		26			0.565653968046274	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.565653968046274	1		452	372	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0042830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	155	661	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.525187443574984	2	FACETS	0.829	0.776	0.882	0.829	0.776	0.882	CLONAL	2	TRUE	0	0.669843175368351	2		661	279	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0042830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	65	311	0	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	0.525187443574984	2	FACETS	1	0.969	1	0.643	0.572	0.714	CLONAL	1	TRUE	0	0.669843175368351	2		311	151	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100117	157100119	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs797045268	NA	P-0042830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	11	38	0	ENST00000346085.5:c.1069_1071del	p.Gly357del	p.G357del	ENST00000346085	NM_020732.3	352	GGC/-	1/20	NA	2	FACETS	0.271	0.188	0.373			1	INDETERMINATE	1	TRUE	NA	0.669843175368351	2		38	121	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775638	9775638	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057524823	NA	P-0042830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	131	706	0	ENST00000377346.4:c.181A>G	p.Met61Val	p.M61V	ENST00000377346	NM_005026.3	61	Atg/Gtg	4/24	0.187351795171972	2	FACETS	0.985	0.903	1	0.493	0.451	0.535	INDETERMINATE	1	TRUE	0	0.669843175368351	2		706	397	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119595259	119595267	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CCTTAGTCC	CCTTAGTCC	G	novel	NA	P-0042830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	29	250	0	ENST00000316626.5:c.902_909+1delinsC		p.X301_splice	ENST00000316626		301		8/12	0.283794426258569	4	FACETS	0.769	0.634	0.914	0.769	0.634	0.914	INDETERMINATE	2	TRUE	2	0.669843175368351	4		250	94	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	155	345	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.842122435037281	2		345	332	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0042867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	130	562	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.855	0.785	0.927	0.855	0.785	0.927	CLONAL	1	TRUE	1	0.842122435037281	2		562	361	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794104	42794104	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0042867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	11	665	1	ENST00000575354.2:c.1464+1G>A		p.X488_splice	ENST00000575354	NM_015125.3	488			0.842122435037281	1	FACETS	0.072	0.049	0.1	0.072	0.049	0.1	SUBCLONAL	1	TRUE	0	0.842122435037281	1		666	210	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094361	27094361	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	241	800	0	ENST00000324856.7:c.3069G>A	p.Trp1023Ter	p.W1023*	ENST00000324856	NM_006015.4	1023	tgG/tgA	11/20	0.842122435037281	1	FACETS	0.941	0.9	0.981	0.941	0.9	0.981	CLONAL	1	TRUE	0	0.842122435037281	1		800	352	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78422351	78422351	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs869025239	NA	P-0042867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	203	506	1	ENST00000370768.2:c.1611G>A	p.Trp537Ter	p.W537*	ENST00000370768	NM_003902.3	537	tgG/tgA	17/20	0.842122435037281	1	FACETS	0.993	0.949	1	0.993	0.949	1	CLONAL	1	TRUE	0	0.842122435037281	1		507	281	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42790999	42791026	+	frameshift_variant	Frame_Shift_Del	DEL	GCCTGACCCCTCCGTGCAGCCGAGCGAG	GCCTGACCCCTCCGTGCAGCCGAGCGAG	-	novel	NA	P-0042867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	33	1035	0	ENST00000575354.2:c.147_174del	p.Asp50SerfsTer146	p.D50Sfs*146	ENST00000575354	NM_015125.3	48	caGCCTGACCCCTCCGTGCAGCCGAGCGAG/ca	2/20	0.842122435037281	1	FACETS	0.123	0.1	0.149	0.123	0.1	0.149	SUBCLONAL	1	TRUE	0	0.842122435037281	1		1035	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579409	7579409	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1567556114	NA	P-0042868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	381	1148	0	ENST00000269305.4:c.278del	p.Leu93ArgfsTer30	p.L93Rfs*30	ENST00000269305	NM_001126112.2	93	cTg/cg	4/11	0.644795473521781	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.644795473521781	1		1148	734	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939109	48939109	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0042868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	121	105	0	ENST00000267163.4:c.939+2T>A		p.X313_splice	ENST00000267163	NM_000321.2	313			0.621689639929281	1	FACETS	0.942	0.867	1	0.942	0.867	1	CLONAL	1	TRUE	0	0.644795473521781	1		105	270	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38506044	38506044	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	232	759	0	ENST00000254066.5:c.336C>G	p.Phe112Leu	p.F112L	ENST00000254066	NM_000964.3	112	ttC/ttG	4/9	0.644795473521781	1	FACETS	0.915	0.861	0.969	0.915	0.861	0.969	CLONAL	1	TRUE	0	0.644795473521781	1		759	533	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271826	15271826	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	348	1169	0	ENST00000263388.2:c.6613C>T	p.Gln2205Ter	p.Q2205*	ENST00000263388	NM_000435.2	2205	Cag/Tag	33/33	0.631532621144251	3	FACETS	0.966	0.913	1	0.483	0.456	0.51	CLONAL	1	TRUE	1	0.644795473521781	3		1169	1478	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281487	15281487	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	307	918	0	ENST00000263388.2:c.4886T>G	p.Val1629Gly	p.V1629G	ENST00000263388	NM_000435.2	1629	gTg/gGg	26/33	0.631532621144251	3	FACETS	0.982	0.925	1	0.491	0.462	0.521	CLONAL	1	TRUE	1	0.644795473521781	3		918	1282	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143398	30143398	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs78378278	NA	P-0042868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	189	779	0	ENST00000389048.3:c.128C>T	p.Pro43Leu	p.P43L	ENST00000389048	NM_004304.4	43	cCa/cTa	1/29	1	2	FACETS	0.842	0.781	0.905	0.842	0.781	0.905	CLONAL	1	TRUE	1	0.644795473521781	2		779	696	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503772	186503772	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	220	516	0	ENST00000323963.5:c.449C>T	p.Ala150Val	p.A150V	ENST00000323963		150	gCt/gTt	5/11	0.216164473826408	1	FACETS	0.693	0.648	0.739	0.693	0.648	0.739	INDETERMINATE	1	TRUE	0	0.644795473521781	1		516	667	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111737	56111737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs931213715	NA	P-0042868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	31	68	0	ENST00000399503.3:c.337C>T	p.Pro113Ser	p.P113S	ENST00000399503	NM_005921.1	113	Ccc/Tcc	1/20	0.644795473521781	1	FACETS	0.931	0.786	1	0.931	0.786	1	CLONAL	1	TRUE	0	0.644795473521781	1		68	70	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624621	93624621	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	179	638	1	ENST00000375746.1:c.712T>A	p.Trp238Arg	p.W238R	ENST00000375746	NM_001174167.1	238	Tgg/Agg	4/14	0.644795473521781	1	FACETS	0.982	0.919	1	0.982	0.919	1	CLONAL	1	TRUE	0	0.644795473521781	1		639	383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577576	7577578	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	novel	NA	P-0042873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	232	487	1	ENST00000269305.4:c.703_705del	p.Asn235del	p.N235del	ENST00000269305	NM_001126112.2	235	AAC/-	7/11	0.726688705656435	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.726688705656435	1		488	400	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487152	56487152	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	212	410	0	ENST00000267101.3:c.1298T>C	p.Met433Thr	p.M433T	ENST00000267101	NM_001982.3	433	aTg/aCg	12/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.726688705656435	2		410	544	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86642491	86642491	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	61	251	0	ENST00000274376.6:c.1052G>A	p.Trp351Ter	p.W351*	ENST00000274376	NM_002890.2	351	tGg/tAg	7/25	0.726688705656435	1	FACETS	0.656	0.578	0.736	0.656	0.578	0.736	SUBCLONAL	1	TRUE	0	0.726688705656435	1		251	163	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0042877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	93	385	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.883	0.789	0.982	1	0.985	1	CLONAL	2	FALSE	1	0.228021725759159	2		385	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0042877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	208	527	0	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	0.228021725759159	0	FACETS	1	0.946	1			1	CLONAL	2	FALSE	0	0.228021725759159	0		527	692	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs770248150	NA	P-0042877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	337	203	0	ENST00000311936.3:c.351A>C	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaC	4/5	1	2	FACETS	0.955	0.908	1	1	0.997	1	CLONAL	4	FALSE	1	0.228021725759159	2		203	774	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120460	2120460	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	170	600	1	ENST00000219476.3:c.1721del	p.Lys574SerfsTer124	p.K574Sfs*124	ENST00000219476	NM_000548.3	574	Aag/ag	17/42	0.228021725759159	0	FACETS	0.88	0.812	0.95			1	CLONAL	2	FALSE	0	0.228021725759159	0		601	654	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272843	142272843	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	91	129	0	ENST00000350721.4:c.2356C>A	p.Leu786Ile	p.L786I	ENST00000350721	NM_001184.3	786	Cta/Ata	11/47	1	2	FACETS	0.893	0.797	0.994	1	0.984	1	CLONAL	2	FALSE	1	0.228021725759159	2		129	447	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672006	30672006	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	244	764	0	ENST00000376406.3:c.4954C>A	p.Pro1652Thr	p.P1652T	ENST00000376406	NM_014641.2	1652	Cca/Aca	10/15	0.228021725759159	4	FACETS	0.961	0.896	1	0.641	0.597	0.686	CLONAL	2	FALSE	1	0.228021725759159	4		764	1367	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0042914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	151	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.565853976960919	2	FACETS	0.795	0.739	0.851	0.795	0.739	0.851	SUBCLONAL	2	TRUE	0	0.591728072701515	2		473	321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0042914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	405	331	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.567807864382136	2	FACETS	0.974	0.936	1	0.974	0.936	1	CLONAL	2	TRUE	0	0.591728072701515	2		331	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0042957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	72	575	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	1	2	FACETS	0.958	0.838	1	0.958	0.838	1	CLONAL	1	TRUE	1	0.284688983907385	2		575	528	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0042957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	77	357	0	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	1	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.284688983907385	1		357	321	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106898	27106898	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	59	635	0	ENST00000324856.7:c.6509T>G	p.Leu2170Arg	p.L2170R	ENST00000324856	NM_006015.4	2170	cTg/cGg	20/20	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.284688983907385	2		635	410	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551215	29551215	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs777414641	NA	P-0042957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	50	526	4	ENST00000389048.3:c.1414+1G>A		p.X472_splice	ENST00000389048	NM_004304.4	472			1	2	FACETS	0.96	0.817	1	0.96	0.817	1	CLONAL	1	TRUE	1	0.284688983907385	2		530	366	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0042969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	41	723	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.170469096274548	1	FACETS	0.948	0.797	1	1	0.968	1	CLONAL	2	FALSE	0	0.170469096274548	1		723	232	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510107	120510107	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	116	481	1	ENST00000256646.2:c.1402G>T	p.Asp468Tyr	p.D468Y	ENST00000256646	NM_024408.3	468	Gat/Tat	8/34	0.170469096274548	41	FACETS	0.993	0.893	1			1	CLONAL	5	FALSE	NA	0.170469096274548	41		482	1185	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510170	120510170	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	136	533	2	ENST00000256646.2:c.1339G>T	p.Gly447Cys	p.G447C	ENST00000256646	NM_024408.3	447	Ggt/Tgt	8/34	0.170469096274548	41	FACETS	1	0.953	1			1	CLONAL	5	FALSE	NA	0.170469096274548	41		535	1278	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510724	120510724	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	118	601	0	ENST00000256646.2:c.1240G>T	p.Glu414Ter	p.E414*	ENST00000256646	NM_024408.3	414	Gaa/Taa	7/34	0.170469096274548	41	FACETS	1	0.937	1			1	CLONAL	5	FALSE	NA	0.170469096274548	41		601	1135	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0042975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	227	514	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	0.357470050096893	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.365027353170377	3		514	716	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859638	57859638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777659251	NA	P-0042975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	102	576	0	ENST00000228682.2:c.692C>T	p.Ser231Phe	p.S231F	ENST00000228682	NM_005269.2	231	tCt/tTt	7/12	0.357470050096893	3	FACETS	0.904	0.809	1	0.452	0.404	0.503	CLONAL	1	TRUE	1	0.365027353170377	3		576	731	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881515	111881515	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	56	542	1	ENST00000393256.3:c.193G>A	p.Ala65Thr	p.A65T	ENST00000393256	NM_006538.4	65	Gcc/Acc	2/4	0.337820676480221	4	FACETS	0.515	0.44	0.598	0.258	0.22	0.299	SUBCLONAL	1	TRUE	2	0.365027353170377	4		543	813	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270593	98270595	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs756897237	NA	P-0042998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	10	33	0	ENST00000331920.6:c.49_51del	p.Gly17del	p.G17del	ENST00000331920	NM_000264.3	17	GGC/-	1/24	0.20373130390253	3	FACETS	0.362	0.246	0.506	0.121	0.082	0.169	INDETERMINATE	1	TRUE	0	0.584922108325414	3		33	122	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317070	11317070	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766996808	NA	P-0042998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	252	616	2	ENST00000361445.4:c.424G>A	p.Ala142Thr	p.A142T	ENST00000361445	NM_004958.3	142	Gct/Act	4/58	0.402357882993567	1	FACETS	0.777	0.729	0.825	0.777	0.729	0.825	SUBCLONAL	1	TRUE	0	0.584922108325414	1		618	785	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374890	45374890	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	411	620	0	ENST00000262160.6:c.953A>T	p.Asn318Ile	p.N318I	ENST00000262160	NM_005901.5	318	aAt/aTt	8/11	0.584922108325414	2	FACETS	0.934	0.897	0.971	0.934	0.897	0.971	CLONAL	2	TRUE	0	0.584922108325414	2		620	752	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874169	155874169	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	191	706	0	ENST00000368323.3:c.362T>C	p.Val121Ala	p.V121A	ENST00000368323	NM_006912.5	121	gTc/gCc	5/6	0.462826051116923	1	FACETS	0.525	0.486	0.566	0.525	0.486	0.566	SUBCLONAL	1	TRUE	0	0.584922108325414	1		706	880	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88651892	88651892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	125	462	0	ENST00000372037.3:c.239G>A	p.Gly80Glu	p.G80E	ENST00000372037	NM_004329.2	80	gGa/gAa	5/13	0.584922108325414	1	FACETS	0.905	0.83	0.982	0.905	0.83	0.982	CLONAL	1	TRUE	0	0.584922108325414	1		462	334	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895641	28895641	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1475572191	NA	P-0042998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	440	607	0	ENST00000282397.4:c.3133C>T	p.Arg1045Trp	p.R1045W	ENST00000282397	NM_002019.4	1045	Cgg/Tgg	23/30	0.584922108325414	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.584922108325414	2		607	731	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99472846	99472846	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778465734	NA	P-0042998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	196	600	0	ENST00000268035.6:c.2842G>A	p.Val948Met	p.V948M	ENST00000268035	NM_000875.3	948	Gtg/Atg	14/21	1	2	FACETS	0.808	0.75	0.869	0.808	0.75	0.869	CLONAL	1	TRUE	1	0.584922108325414	2		600	829	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577151	7577152	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0042998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	398	598	1	ENST00000269305.4:c.786dup	p.Asn263Ter	p.N263*	ENST00000269305	NM_001126112.2	262	-/T	8/11	0.584922108325414	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.584922108325414	1		599	768	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332874	152332874	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs755020320	NA	P-0042998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	144	441	0	ENST00000206249.3:c.1180C>A	p.Arg394Ser	p.R394S	ENST00000206249	NM_000125.3	394	Cgc/Agc	5/8	1	2	FACETS	0.884	0.81	0.96	0.884	0.81	0.96	CLONAL	1	TRUE	1	0.584922108325414	2		441	557	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431455	121431553	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCAGAAGAACCCTAGCAAGGAGGAGCGAGAGACGCTAGTGGAGGAGTGCAATAGGTACAACGGCGGGCGGGAAACAGTGCTGGTTTGGTCTGGGCTGC	GGCAGAAGAACCCTAGCAAGGAGGAGCGAGAGACGCTAGTGGAGGAGTGCAATAGGTACAACGGCGGGCGGGAAACAGTGCTGGTTTGGTCTGGGCTGC	-	novel	NA	P-0042998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	67	815	0	ENST00000257555.6:c.663_713+48del		p.X221_splice	ENST00000257555		221		3/10	1	2	FACETS	0.233	0.201	0.267	0.233	0.201	0.267	SUBCLONAL	1	TRUE	1	0.584922108325414	2		815	984	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0043021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	28	393	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		393	582	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711840	89711901	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCAATTTGGCTTCTCTTTTTTTTCTGTCCACCAGGGAGTAACTATTCCCAGTCAGAGGCGC	TTCAATTTGGCTTCTCTTTTTTTTCTGTCCACCAGGGAGTAACTATTCCCAGTCAGAGGCGC	-	novel	NA	P-0043021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	14	307	0	ENST00000371953.3:c.493-34_520del		p.X165_splice	ENST00000371953	NM_000314.4	165		6/9	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		307	252	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0043022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	378	627	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.293420684796283	2	FACETS	0.922	0.889	0.954	1	0.997	1	CLONAL	5	FALSE	0	0.293404887863788	2		628	559	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0043022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	73	562	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.943	1	1	0.985	1	CLONAL	2	FALSE	1	0.293404887863788	2		562	226	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589147	67589147	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	47	265	0	ENST00000274335.5:c.1135A>G	p.Lys379Glu	p.K379E	ENST00000274335		379	Aaa/Gaa	9/15	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	FALSE	1	0.293404887863788	2		265	265	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875997	76875997	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	93	81	0	ENST00000373344.5:c.5138C>G	p.Pro1713Arg	p.P1713R	ENST00000373344	NM_000489.3	1713	cCt/cGt	20/35	0.196245951327423	2	FACETS	0.968	0.902	1			1	CLONAL	5	FALSE	NA	0.293404887863788	2		81	131	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0043035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	75	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.12436649715482	4	FACETS	1	0.911	1	1	0.911	1	INDETERMINATE	2	FALSE	2	0.213532238897187	4		485	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0043035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	156	841	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.213532238897187	3	FACETS	0.963	0.882	1	0.963	0.882	1	CLONAL	2	FALSE	1	0.213532238897187	3		841	840	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888157	112888157	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs751437780	NA	P-0043035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	50	850	0	ENST00000351677.2:c.173A>G	p.Asn58Ser	p.N58S	ENST00000351677	NM_002834.3	58	aAc/aGc	3/16	0.12436649715482	4	FACETS	0.754	0.642	0.876	0.754	0.642	0.876	INDETERMINATE	2	FALSE	2	0.213532238897187	4		850	377	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959121	2959121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778152	NA	P-0043035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	101	856	0	ENST00000396946.4:c.2395G>A	p.Asp799Asn	p.D799N	ENST00000396946	NM_032415.4	799	Gat/Aat	18/25	0.20371298755932	3	FACETS	1	0.904	1	0.507	0.452	0.566	CLONAL	1	FALSE	1	0.213532238897187	3		856	1032	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11269446	11269446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	126	728	0	ENST00000361445.4:c.3724G>A	p.Gly1242Arg	p.G1242R	ENST00000361445	NM_004958.3	1242	Ggg/Agg	25/58	0.213532238897187	4	FACETS	1	0.964	1	0.749	0.68	0.822	CLONAL	2	FALSE	1	0.213532238897187	4		728	637	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170426	119170426	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1435757249	NA	P-0043035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	96	625	0	ENST00000264033.4:c.2656G>A	p.Glu886Lys	p.E886K	ENST00000264033	NM_005188.3	886	Gag/Aag	16/16	0.12436649715482	4	FACETS	0.902	0.805	1	0.902	0.805	1	INDETERMINATE	2	FALSE	2	0.213532238897187	4		625	605	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257618	16257618	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	106	714	0	ENST00000375759.3:c.4883A>T	p.Asp1628Val	p.D1628V	ENST00000375759	NM_015001.2	1628	gAt/gTt	11/15	0.213532238897187	4	FACETS	0.905	0.816	0.997	0.905	0.816	0.997	CLONAL	3	FALSE	1	0.213532238897187	4		714	444	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598321	28598321	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	115	971	0	ENST00000253063.3:c.293A>T	p.Tyr98Phe	p.Y98F	ENST00000253063	NM_031459.4	98	tAc/tTc	3/10	0.12436649715482	4	FACETS	1	0.944	1	0.538	0.483	0.597	INDETERMINATE	1	FALSE	2	0.213532238897187	4		971	1214	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595983	43595983	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	168	869	1	ENST00000355710.3:c.150G>T	p.Leu50Phe	p.L50F	ENST00000355710	NM_020975.4	50	ttG/ttT	2/20	0.213532238897187	7	FACETS	1	0.926	1	0.505	0.463	0.549	CLONAL	2	FALSE	3	0.213532238897187	7		870	1194	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619216	43619216	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	237	742	0	ENST00000355710.3:c.2899G>T	p.Gly967Cys	p.G967C	ENST00000355710	NM_020975.4	967	Ggc/Tgc	17/20	0.213532238897187	7	FACETS	1	0.983	1	0.866	0.809	0.925	CLONAL	3	FALSE	3	0.213532238897187	7		742	983	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332675	70332675	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	91	782	1	ENST00000373644.4:c.580C>T	p.Gln194Ter	p.Q194*	ENST00000373644	NM_030625.2	194	Caa/Taa	2/12	0.213532238897187	7	FACETS	0.964	0.856	1	0.482	0.428	0.54	CLONAL	2	FALSE	3	0.213532238897187	7		783	678	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256545	133256545	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	26	600	0	ENST00000320574.5:c.418G>T	p.Asp140Tyr	p.D140Y	ENST00000320574	NM_006231.2	140	Gac/Tac	5/49	0.12436649715482	4	FACETS	0.699	0.553	0.866	0.349	0.276	0.433	INDETERMINATE	1	FALSE	2	0.213532238897187	4		600	423	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543878	212543878	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0043035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	87	587	0	ENST00000342788.4:c.1521T>A	p.Cys507Ter	p.C507*	ENST00000342788	NM_005235.2	507	tgT/tgA	13/28	0.20371298755932	3	FACETS	0.834	0.74	0.933	0.834	0.74	0.933	CLONAL	2	FALSE	1	0.213532238897187	3		587	541	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259070	89259070	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	43	437	0	ENST00000336596.2:c.215del	p.Asn72MetfsTer11	p.N72Mfs*11	ENST00000336596	NM_005233.5	72	Aat/at	3/17	0.212317643236933	2	FACETS	1	0.958	1	0.746	0.628	0.874	CLONAL	1	FALSE	0	0.213532238897187	2		437	270	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521224	187521224	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	90	829	0	ENST00000441802.2:c.11931G>C	p.Met3977Ile	p.M3977I	ENST00000441802	NM_005245.3	3977	atG/atC	22/27	0.20371298755932	3	FACETS	1	0.973	1	0.665	0.59	0.745	CLONAL	1	FALSE	1	0.213532238897187	3		829	702	SUCCESS
APC	324	MSKCC	GRCh37	5	112179495	112179495	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	84	561	0	ENST00000257430.4:c.8204G>T	p.Gly2735Val	p.G2735V	ENST00000257430	NM_000038.5	2735	gGa/gTa	16/16	0.12436649715482	4	FACETS	1	0.938	1	1	0.938	1	INDETERMINATE	2	FALSE	2	0.213532238897187	4		561	440	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324073	31324073	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	100	184	2	ENST00000412585.2:c.490G>T	p.Ala164Ser	p.A164S	ENST00000412585	NM_005514.6	164	Gct/Tct	3/8	0.213532238897187	3	FACETS	0.989	0.898	1	1	0.988	1	CLONAL	4	FALSE	1	0.213532238897187	3		186	262	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517414	157517414	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	159	657	0	ENST00000346085.5:c.3979del	p.Gln1327SerfsTer121	p.Q1327Sfs*121	ENST00000346085	NM_020732.3	1326	cgC/cg	16/20	0.213532238897187	4	FACETS	1	0.981	1	0.823	0.756	0.893	CLONAL	2	FALSE	1	0.213532238897187	4		657	732	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968287	2968287	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	116	849	0	ENST00000396946.4:c.1699C>A	p.Pro567Thr	p.P567T	ENST00000396946	NM_032415.4	567	Ccc/Acc	13/25	0.20371298755932	3	FACETS	1	0.95	1	0.546	0.491	0.605	CLONAL	1	FALSE	1	0.213532238897187	3		849	1101	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729952	41729952	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	67	794	0	ENST00000242208.4:c.577G>T	p.Glu193Ter	p.E193*	ENST00000242208	NM_002192.2	193	Gag/Tag	3/3	0.20371298755932	3	FACETS	0.904	0.785	1	0.452	0.392	0.517	CLONAL	1	FALSE	1	0.213532238897187	3		794	768	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449833	8449833	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	91	569	0	ENST00000356435.5:c.3880A>T	p.Arg1294Trp	p.R1294W	ENST00000356435		1294	Agg/Tgg	23/35	0.212317643236933	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	FALSE	0	0.213532238897187	2		569	353	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486248	8486248	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768330226	NA	P-0043035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	66	508	0	ENST00000356435.5:c.2569C>A	p.Arg857Ser	p.R857S	ENST00000356435		857	Cgt/Agt	17/35	0.212317643236933	2	FACETS	0.954	0.834	1	0.954	0.834	1	CLONAL	2	FALSE	0	0.213532238897187	2		508	324	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814273	76814273	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	12	236	0	ENST00000373344.5:c.6371T>A	p.Ile2124Asn	p.I2124N	ENST00000373344	NM_000489.3	2124	aTt/aAt	29/35	0.145764376216855	2	FACETS	1	0.762	1			1	CLONAL	2	FALSE	NA	0.213532238897187	2		236	53	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0043042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	25	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.859	0.675	1	0.859	0.675	1	CLONAL	1	TRUE	1	0.11	2		473	529	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0043042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	20	358	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.574	0.437	0.736	0.574	0.437	0.736	SUBCLONAL	1	TRUE	1	0.11	2		359	633	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	192	345	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.88217402274328	2		345	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0043043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	747	792	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.88217402274328	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.88217402274328	2		793	832	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717769	89717770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	241	379	0	ENST00000371953.3:c.800dup	p.Asp268GlyfsTer30	p.D268Gfs*30	ENST00000371953	NM_000314.4	265	cta/ctAa	7/9	0.872907579043105	2	FACETS	0.92	0.888	0.949	0.92	0.888	0.949	CLONAL	2	TRUE	0	0.88217402274328	2		379	297	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829066	128829066	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs41304185	NA	P-0043043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	17	18	0	ENST00000249373.3:c.74A>G	p.Asp25Gly	p.D25G	ENST00000249373	NM_005631.4	25	gAc/gGc	1/12	0.863887173991287	3	FACETS	0.992	0.81	1	0.992	0.81	1	CLONAL	2	TRUE	1	0.88217402274328	3		18	28	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508998	106508998	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	217	627	0	ENST00000359195.3:c.992G>A	p.Gly331Glu	p.G331E	ENST00000359195	NM_002649.2	331	gGa/gAa	2/11	0.863887173991287	3	FACETS	0.953	0.889	1	0.476	0.444	0.509	CLONAL	1	TRUE	1	0.88217402274328	3		627	744	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982062	70982062	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	334	819	0	ENST00000276594.2:c.34C>G	p.Gln12Glu	p.Q12E	ENST00000276594	NM_024504.3	12	Cag/Gag	2/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.88217402274328	2		819	732	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0043048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	185	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.39895998018627	2		485	699	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0043048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	203	789	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	0.39895998018627	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.39895998018627	1		789	785	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247373	153247373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	67	306	1	ENST00000281708.4:c.1429G>A	p.Gly477Ser	p.G477S	ENST00000281708	NM_033632.3	477	Ggt/Agt	10/12	0.325613422586897	1	FACETS	0.617	0.538	0.702	0.617	0.538	0.702	SUBCLONAL	1	TRUE	0	0.39895998018627	1		307	436	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038893	12038893	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	153	362	0	ENST00000396373.4:c.1186A>G	p.Arg396Gly	p.R396G	ENST00000396373	NM_001987.4	396	Aga/Gga	7/8	0.328425044689061	3	FACETS	1	0.977	1	0.595	0.545	0.647	CLONAL	1	TRUE	1	0.39895998018627	3		362	773	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115269636	115269637	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0043048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	168	540	0	ENST00000438362.2:c.1569_1570delinsTT	p.Glu524Ter	p.E524*	ENST00000438362	NM_001242891.1	523	gtGGaa/gtTTaa	13/20	0.325613422586897	1	FACETS	0.791	0.728	0.858	0.791	0.728	0.858	SUBCLONAL	1	TRUE	0	0.39895998018627	1		540	852	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866356	37866356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	203	697	0	ENST00000269571.5:c.661G>A	p.Ala221Thr	p.A221T	ENST00000269571		221	Gcc/Acc	6/27	0.14262986369843	3	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.39895998018627	3		697	1073	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604837	48604837	+	stop_lost	Nonstop_Mutation	SNP	A	A	T	novel	NA	P-0043048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	108	315	1	ENST00000342988.3:c.1659A>T	p.Ter553CysextTer40	p.*553Cext*40	ENST00000342988	NM_005359.5	553	tgA/tgT	12/12	0.39895998018627	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.39895998018627	1		316	356	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752799	57752800	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	190	268	0	ENST00000274289.3:c.1128dup	p.Asp377ArgfsTer7	p.D377Rfs*7	ENST00000274289	NM_006622.3	376	-/A	8/14	0.375380819478185	2	FACETS	0.976	0.911	1	0.976	0.911	1	CLONAL	2	TRUE	0	0.39895998018627	2		268	488	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347919	128347919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	151	885	0	ENST00000265960.3:c.586G>A	p.Val196Met	p.V196M	ENST00000265960	NM_001006617.1	196	Gtg/Atg	5/12	0.325613422586897	1	FACETS	0.56	0.511	0.612	0.56	0.511	0.612	SUBCLONAL	1	TRUE	0	0.39895998018627	1		885	1082	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0043075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	176	711	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.495667348548699	1	FACETS	0.927	0.859	0.997	0.927	0.859	0.997	CLONAL	1	TRUE	0	0.495667348548699	1		711	576	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105673	27105673	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	173	496	0	ENST00000324856.7:c.5287del	p.Glu1763LysfsTer7	p.E1763Kfs*7	ENST00000324856	NM_006015.4	1762	Ggg/gg	20/20	0.264953426107099	3	FACETS	0.779	0.721	0.838	0.779	0.721	0.838	INDETERMINATE	2	TRUE	1	0.495667348548699	3		496	559	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392883	118392883	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	83	440	0	ENST00000534358.1:c.11915A>G	p.Asn3972Ser	p.N3972S	ENST00000534358	NM_005933.3	3972	aAc/aGc	36/36	1	2	FACETS	0.819	0.727	0.916	0.819	0.727	0.916	CLONAL	1	TRUE	1	0.495667348548699	2		440	409	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0043092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	165	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.181045478288589	1	FACETS	0.651	0.603	0.7	0.651	0.603	0.7	INDETERMINATE	1	TRUE	0	0.704478620180786	1		473	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0043092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	383	651	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.704478620180786	1	FACETS	0.969	0.928	1	0.969	0.928	1	CLONAL	1	TRUE	0	0.704478620180786	1		651	727	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0043092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	214	352	0	ENST00000304494.5:c.151-1G>A		p.X51_splice	ENST00000304494	NM_000077.4	51			0.704478620180786	1	FACETS	0.919	0.867	0.972	0.919	0.867	0.972	CLONAL	1	TRUE	0	0.704478620180786	1		352	428	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31472258	31472258	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	271	546	0	ENST00000344624.3:c.2153A>C	p.Glu718Ala	p.E718A	ENST00000344624		718	gAg/gCg	14/33	0.181045478288589	1	FACETS	0.606	0.571	0.643	0.606	0.571	0.643	INDETERMINATE	1	TRUE	0	0.704478620180786	1		546	822	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966783	44966783	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0043092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	233	520	0	ENST00000377967.4:c.4005+2T>G		p.X1335_splice	ENST00000377967	NM_021140.2	1335			0.704478620180786	1	FACETS	0.999	0.946	1	0.999	0.946	1	CLONAL	1	TRUE	0	0.704478620180786	1		520	429	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188271	10188272	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	137	615	0	ENST00000256474.2:c.415dup	p.Ser139PhefsTer5	p.S139Ffs*5	ENST00000256474	NM_000551.3	138	-/T	2/3	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.44	2		615	617	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139721	55139721	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	118	489	0	ENST00000257290.5:c.1382C>T	p.Ser461Phe	p.S461F	ENST00000257290	NM_006206.4	461	tCc/tTc	10/23	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.515575480428201	2		489	428	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0043094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	103	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.826	0.742	0.913	0.826	0.742	0.913	CLONAL	1	TRUE	1	0.515575480428201	2		288	484	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0043094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	64	571	0				ENST00000310581	NM_198253.2	-/1132			0.141153193917145	1	FACETS	0.635	0.555	0.721	0.635	0.555	0.721	INDETERMINATE	1	TRUE	0	0.515575480428201	1		571	290	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812260	212812260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751175543	NA	P-0043094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	110	317	0	ENST00000342788.4:c.316C>T	p.Arg106Cys	p.R106C	ENST00000342788	NM_005235.2	106	Cgt/Tgt	3/28	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.515575480428201	2		317	425	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980844	40980844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	125	599	0	ENST00000373198.4:c.1642G>A	p.Glu548Lys	p.E548K	ENST00000373198	NM_133170.3	548	Gaa/Aaa	10/32	1	2	FACETS	0.911	0.829	0.998	0.911	0.829	0.998	CLONAL	1	TRUE	1	0.515575480428201	2		599	532	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720803	89720804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs786204892	NA	P-0043094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	45	277	0	ENST00000371953.3:c.955dup	p.Thr319AsnfsTer6	p.T319Nfs*6	ENST00000371953	NM_000314.4	318	-/A	8/9	0.515575480428201	1	FACETS	0.758	0.647	0.876	0.758	0.647	0.876	SUBCLONAL	1	TRUE	0	0.515575480428201	1		277	171	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0043094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	329	773	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	0.515575480428201	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.515575480428201	3		773	779	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716366	18716366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs935135637	NA	P-0043094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	118	347	0	ENST00000266497.5:c.3713C>T	p.Ser1238Leu	p.S1238L	ENST00000266497		1238	tCa/tTa	26/31	1	2	FACETS	0.962	0.873	1	0.962	0.873	1	CLONAL	1	TRUE	1	0.515575480428201	2		347	476	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955149	93955149	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	118	445	1	ENST00000369303.4:c.2749C>T	p.Gln917Ter	p.Q917*	ENST00000369303	NM_004440.3	917	Caa/Taa	16/17	1	2	FACETS	0.938	0.851	1	0.938	0.851	1	CLONAL	1	TRUE	1	0.515575480428201	2		446	488	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93640037	93640037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	77	290	0	ENST00000375746.1:c.1366C>T	p.Leu456Phe	p.L456F	ENST00000375746	NM_001174167.1	456	Ctc/Ttc	10/14	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.515575480428201	2		290	288	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073655	8073656	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0043094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	63	426	0	ENST00000377482.5:c.1003_1004delinsTT	p.Pro335Phe	p.P335F	ENST00000377482	NM_018948.3	335	CCc/TTc	4/4	1	2	FACETS	0.696	0.606	0.794	0.696	0.606	0.794	SUBCLONAL	1	TRUE	1	0.515575480428201	2		426	351	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243102	105243102	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	127	623	1	ENST00000349310.3:c.181C>T	p.Gln61Ter	p.Q61*	ENST00000349310	NM_001014432.1	61	Cag/Tag	5/15	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.515575480428201	2		624	487	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99163051	99163051	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	88	323	1	ENST00000074304.5:c.1057C>T	p.Gln353Ter	p.Q353*	ENST00000074304	NM_001134224.1	353	Cag/Tag	13/26	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.515575480428201	2		324	300	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728857	190728857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	106	345	0	ENST00000441310.2:c.2245C>T	p.Pro749Ser	p.P749S	ENST00000441310	NM_000534.4	749	Cca/Tca	10/13	1	2	FACETS	0.939	0.847	1	0.939	0.847	1	CLONAL	1	TRUE	1	0.515575480428201	2		345	438	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520219	9520219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867360779	NA	P-0043094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	129	405	1	ENST00000353224.5:c.2050G>A	p.Glu684Lys	p.E684K	ENST00000353224	NM_177990.2	684	Gag/Aag	10/10	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.515575480428201	2		406	487	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566516	41566516	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	91	369	0	ENST00000263253.7:c.4393G>A	p.Glu1465Lys	p.E1465K	ENST00000263253	NM_001429.3	1465	Gaa/Aaa	27/31	1	2	FACETS	0.972	0.871	1	0.972	0.871	1	CLONAL	1	TRUE	1	0.515575480428201	2		369	363	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090558	71090558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369057936	NA	P-0043094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	110	347	0	ENST00000318789.4:c.790C>T	p.Pro264Ser	p.P264S	ENST00000318789	NM_032682.5	264	Cct/Tct	11/21	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.515575480428201	NA		347	424	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665387	117665387	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	134	281	0	ENST00000368508.3:c.4360C>G	p.Pro1454Ala	p.P1454A	ENST00000368508	NM_002944.2	1454	Cca/Gca	27/43	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.515575480428201	2		281	408	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709191	117709191	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	63	255	0	ENST00000368508.3:c.1766T>A	p.Ile589Asn	p.I589N	ENST00000368508	NM_002944.2	589	aTc/aAc	13/43	1	2	FACETS	0.882	0.77	1	0.882	0.77	1	CLONAL	1	TRUE	1	0.515575480428201	2		255	277	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005563	150005563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	97	292	0	ENST00000253339.5:c.662C>T	p.Ser221Leu	p.S221L	ENST00000253339		221	tCa/tTa	3/7	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.515575480428201	2		292	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577594	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0043098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	95	497	0	ENST00000269305.4:c.687T>A	p.Cys229Ter	p.C229*	ENST00000269305	NM_001126112.2	229	tgT/tgA	7/11	0.547182073819172	1	FACETS	0.709	0.636	0.784	0.709	0.636	0.784	SUBCLONAL	1	TRUE	0	0.547182073819172	1		497	356	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868140	45868140	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	227	1324	1	ENST00000391945.4:c.550G>T	p.Gly184Trp	p.G184W	ENST00000391945	NM_000400.3	184	Ggg/Tgg	7/23	1	2	FACETS	0.662	0.616	0.71	0.662	0.616	0.71	SUBCLONAL	1	TRUE	1	0.547182073819172	2		1325	1253	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007353	143007353	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	87	306	0	ENST00000262992.4:c.2431C>T	p.Gln811Ter	p.Q811*	ENST00000262992	NM_001101669.1	811	Caa/Taa	22/24	0.547182073819172	1	FACETS	0.816	0.732	0.904	0.816	0.732	0.904	CLONAL	1	TRUE	0	0.547182073819172	1		306	283	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699426	47699426	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0043098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	52	274	0	ENST00000347630.2:c.82A>T	p.Lys28Ter	p.K28*	ENST00000347630	NM_001007230.1	28	Aag/Tag	4/11	0.547182073819172	1	FACETS	0.69	0.596	0.791	0.69	0.596	0.791	SUBCLONAL	1	TRUE	0	0.547182073819172	1		274	200	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567643	226567643	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	101	495	0	ENST00000366794.5:c.1523A>G	p.Lys508Arg	p.K508R	ENST00000366794	NM_001618.3	508	aAg/aGg	10/23	1	2	FACETS	0.732	0.657	0.812	0.732	0.657	0.812	SUBCLONAL	1	TRUE	1	0.547182073819172	2		495	504	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690632	88690632	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	105	361	1	ENST00000360948.2:c.398A>T	p.Asn133Ile	p.N133I	ENST00000360948	NM_001012338.2	133	aAc/aTc	5/19	1	2	FACETS	0.638	0.572	0.706	0.638	0.572	0.706	SUBCLONAL	1	TRUE	1	0.547182073819172	2		362	602	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679950	30680001	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGCTGTTAGGGAGGTGCCCTCCTCTGCATCTGTTTCACAGTCCCCATGCA	GAGGCTGTTAGGGAGGTGCCCTCCTCTGCATCTGTTTCACAGTCCCCATGCA	-	novel	NA	P-0043098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	98	436	0	ENST00000376406.3:c.1718_1769del	p.Leu573GlnfsTer2	p.L573Qfs*2	ENST00000376406	NM_014641.2	573	cTGCATGGGGACTGTGAAACAGATGCAGAGGAGGGCACCTCCCTAACAGCCTCa/ca	5/15	1	2	FACETS	0.916	0.824	1	0.916	0.824	1	CLONAL	1	TRUE	1	0.547182073819172	2		436	391	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0043103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	137	434	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.885	0.812	0.96	0.885	0.812	0.96	CLONAL	1	TRUE	1	0.726960858242867	2		434	426	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413010	49413010	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519952	NA	P-0043103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	309	728	1	ENST00000418115.1:c.13C>T	p.Arg5Trp	p.R5W	ENST00000418115	NM_001664.2	5	Cgg/Tgg	2/5	1	2	FACETS	0.892	0.843	0.942	0.892	0.843	0.942	CLONAL	1	TRUE	1	0.726960858242867	2		729	953	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0043103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	344	861	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	1	2	FACETS	0.927	0.879	0.976	0.927	0.879	0.976	CLONAL	1	TRUE	1	0.726960858242867	2		861	1021	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867249	68867250	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	295	705	0	ENST00000261769.5:c.2499dup	p.Asp834Ter	p.D834*	ENST00000261769	NM_004360.3	832	-/T	16/16	0.726960858242867	1	FACETS	0.924	0.88	0.968	0.924	0.88	0.968	CLONAL	1	TRUE	0	0.726960858242867	1		705	559	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955426	48955426	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	181	342	0	ENST00000267163.4:c.1544del	p.Pro515HisfsTer4	p.P515Hfs*4	ENST00000267163	NM_000321.2	514	ttC/tt	17/27	0.675333419362552	1	FACETS	0.883	0.828	0.938	0.883	0.828	0.938	CLONAL	1	TRUE	0	0.726960858242867	1		342	359	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371742	45371742	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	172	454	0	ENST00000262160.6:c.1249A>C	p.Ser417Arg	p.S417R	ENST00000262160	NM_005901.5	417	Agt/Cgt	10/11	0.726960858242867	1	FACETS	0.918	0.861	0.975	0.918	0.861	0.975	CLONAL	1	TRUE	0	0.726960858242867	1		454	328	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206778	36206779	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGGCTGGGTGGTGT	novel	NA	P-0043103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	139	768	0	ENST00000300305.3:c.720_733dup	p.Pro245HisfsTer14	p.P245Hfs*14	ENST00000300305		245	ccc/cACACCACCCAGCCCcc	6/8	1	2	FACETS	0.505	0.46	0.552	0.505	0.46	0.552	SUBCLONAL	1	TRUE	1	0.726960858242867	2		768	758	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0043106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	343	672	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.65702185877175	2		672	908	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0043106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	128	302	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	1	2	FACETS	0.994	0.91	1	0.994	0.91	1	CLONAL	1	TRUE	1	0.65702185877175	2		302	392	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0043106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	184	579	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.65702185877175	1	FACETS	0.959	0.898	1	0.959	0.898	1	CLONAL	1	TRUE	0	0.65702185877175	1		579	392	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723067	52723067	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770861676	NA	P-0043106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	172	585	2	ENST00000322088.6:c.1252C>T	p.Arg418Trp	p.R418W	ENST00000322088	NM_014225.5	418	Cgg/Tgg	10/15	0.65702185877175	3	FACETS	0.894	0.824	0.967	0.447	0.412	0.484	CLONAL	1	TRUE	1	0.65702185877175	3		587	778	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361214	66361214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375878596	NA	P-0043106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	131	325	0	ENST00000273854.3:c.958G>A	p.Gly320Ser	p.G320S	ENST00000273854	NM_004439.5	320	Ggc/Agc	4/18	1	2	FACETS	0.932	0.853	1	0.932	0.853	1	CLONAL	1	TRUE	1	0.65702185877175	2		325	428	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147534	47147534	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	160	396	1	ENST00000409792.3:c.4792C>T	p.Arg1598Ter	p.R1598*	ENST00000409792	NM_014159.6	1598	Cga/Tga	6/21	1	2	FACETS	0.968	0.894	1	0.968	0.894	1	CLONAL	1	TRUE	1	0.65702185877175	2		397	503	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208051	5208051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1477222866	NA	P-0043106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	215	652	0	ENST00000357368.4:c.5660C>T	p.Thr1887Met	p.T1887M	ENST00000357368	NM_002850.3	1887	aCg/aTg	37/38	0.65702185877175	3	FACETS	1	0.979	1	0.56	0.521	0.599	CLONAL	1	TRUE	1	0.65702185877175	3		652	777	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120360	94120360	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs749418654	NA	P-0043106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	19	314	0	ENST00000369303.4:c.691C>T	p.Arg231Ter	p.R231*	ENST00000369303	NM_004440.3	231	Cga/Tga	3/17	1	2	FACETS	0.173	0.131	0.223	0.173	0.131	0.223	SUBCLONAL	1	TRUE	1	0.65702185877175	2		314	334	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545677	63545677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151247101	NA	P-0043106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	258	484	0	ENST00000307078.5:c.917C>T	p.Ala306Val	p.A306V	ENST00000307078	NM_004655.3	306	gCg/gTg	3/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.65702185877175	2		484	694	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220554	123220554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	215	290	0	ENST00000218089.9:c.3211C>T	p.Arg1071Trp	p.R1071W	ENST00000218089	NM_001042749.1	1071	Cgg/Tgg	30/35	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.65702185877175	1		290	339	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453468	40453468	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866679330	NA	P-0043106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	224	849	0	ENST00000345506.4:c.1165C>T	p.Arg389Cys	p.R389C	ENST00000345506	NM_003152.3	389	Cgc/Tgc	10/20	1	2	FACETS	0.851	0.795	0.909	0.851	0.795	0.909	CLONAL	1	TRUE	1	0.65702185877175	2		849	801	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942724	48942725	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0043106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	19	258	0	ENST00000267163.4:c.1117_1118dup	p.Pro374LeufsTer7	p.P374Lfs*7	ENST00000267163	NM_000321.2	371	cca/cCAca	11/27	0.582659715920089	1	FACETS	0.138	0.104	0.177	0.138	0.104	0.177	SUBCLONAL	1	TRUE	0	0.65702185877175	1		258	282	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595345	141595345	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777295689	NA	P-0043106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	337	823	1	ENST00000220592.5:c.88G>A	p.Asp30Asn	p.D30N	ENST00000220592	NM_012154.3	30	Gac/Aac	2/19	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.65702185877175	2		824	898	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577572	7577577	+	inframe_deletion	In_Frame_Del	DEL	TGTAGT	TGTAGT	-	rs794727846	NA	P-0043106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	219	635	0	ENST00000269305.4:c.704_709del	p.Asn235_Tyr236del	p.N235_Y236del	ENST00000269305	NM_001126112.2	235	aACTACAtg/atg	7/11	1	2	FACETS	0.928	0.867	0.991	0.928	0.867	0.991	CLONAL	1	TRUE	1	0.65702185877175	2		635	718	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891078	112891078	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs267606989	NA	P-0043106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	132	576	0	ENST00000351677.2:c.412C>T	p.Arg138Ter	p.R138*	ENST00000351677	NM_002834.3	138	Cga/Tga	4/16	1	2	FACETS	0.673	0.613	0.736	0.673	0.613	0.736	SUBCLONAL	1	TRUE	1	0.65702185877175	2		576	597	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383885	15383885	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	39	523	0	ENST00000263377.2:c.26C>T	p.Thr9Met	p.T9M	ENST00000263377	NM_058243.2	9	aCg/aTg	2/20	0.65702185877175	3	FACETS	0.213	0.175	0.254	0.106	0.087	0.127	SUBCLONAL	1	TRUE	1	0.65702185877175	3		523	742	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342401	118342401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	37	310	0	ENST00000534358.1:c.527G>A	p.Arg176His	p.R176H	ENST00000534358	NM_005933.3	176	cGt/cAt	3/36	1	2	FACETS	0.356	0.295	0.425	0.356	0.295	0.425	SUBCLONAL	1	TRUE	1	0.65702185877175	2		310	316	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039483	49039484	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	33	500	0	ENST00000267163.4:c.2473dup	p.Met825AsnfsTer13	p.M825Nfs*13	ENST00000267163	NM_000321.2	823	aca/acAa	23/27	0.582659715920089	1	FACETS	0.15	0.122	0.182	0.15	0.122	0.182	SUBCLONAL	1	TRUE	0	0.65702185877175	1		500	449	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514823	103514823	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	24	408	0	ENST00000355739.4:c.1324T>C	p.Phe442Leu	p.F442L	ENST00000355739	NM_000123.3	442	Ttt/Ctt	8/15	0.582659715920089	1	FACETS	0.158	0.124	0.198	0.158	0.124	0.198	SUBCLONAL	1	TRUE	0	0.65702185877175	1		408	310	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396844	396844	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747093980	NA	P-0043106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	45	832	0	ENST00000262320.3:c.182C>T	p.Pro61Leu	p.P61L	ENST00000262320	NM_003502.3	61	cCg/cTg	2/11	1	2	FACETS	0.156	0.13	0.184	0.156	0.13	0.184	SUBCLONAL	1	TRUE	1	0.65702185877175	2		832	880	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350045	89350045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	271	807	0	ENST00000301030.4:c.2905G>A	p.Glu969Lys	p.E969K	ENST00000301030	NM_001256183.1	969	Gag/Aag	9/13	1	2	FACETS	0.943	0.887	1	0.943	0.887	1	CLONAL	1	TRUE	1	0.65702185877175	2		807	875	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490245	29490248	+	frameshift_variant	Frame_Shift_Del	DEL	CAAA	CAAA	-	rs1135402787	NA	P-0043106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	159	398	0	ENST00000356175.3:c.332_335del	p.Lys111SerfsTer53	p.K111Sfs*53	ENST00000356175	NM_000267.3	110	gtCAAA/gt	4/57	1	2	FACETS	0.978	0.903	1	0.978	0.903	1	CLONAL	1	TRUE	1	0.65702185877175	2		398	495	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559741	29559741	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	120	247	0	ENST00000356175.3:c.3341del	p.Leu1114Ter	p.L1114*	ENST00000356175	NM_000267.3	1113	cTt/ct	26/57	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.65702185877175	2		247	301	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11019819	11019819	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	239	612	1	ENST00000327064.4:c.494A>T	p.Asp165Val	p.D165V	ENST00000327064	NM_199141.1	165	gAc/gTc	4/16	0.65702185877175	3	FACETS	0.967	0.903	1	0.483	0.451	0.516	CLONAL	1	TRUE	1	0.65702185877175	3		613	1000	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299887	15299887	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	245	992	0	ENST00000263388.2:c.1291G>A	p.Asp431Asn	p.D431N	ENST00000263388	NM_000435.2	431	Gat/Aat	8/33	0.65702185877175	3	FACETS	0.703	0.655	0.753	0.352	0.327	0.377	SUBCLONAL	1	TRUE	1	0.65702185877175	3		992	1409	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257952	19257952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	370	1037	0	ENST00000162023.5:c.434G>A	p.Gly145Glu	p.G145E	ENST00000162023		145	gGg/gAg	9/13	0.65702185877175	3	FACETS	1	0.976	1	0.526	0.498	0.554	CLONAL	1	TRUE	1	0.65702185877175	3		1037	1423	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30956891	30956891	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	227	530	0	ENST00000375687.4:c.217A>G	p.Lys73Glu	p.K73E	ENST00000375687	NM_015338.5	73	Aaa/Gaa	4/13	0.65702185877175	3	FACETS	1	0.958	1	0.517	0.483	0.553	CLONAL	1	TRUE	1	0.65702185877175	3		530	887	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281226	142281226	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	20	446	1	ENST00000350721.4:c.1018G>T	p.Asp340Tyr	p.D340Y	ENST00000350721	NM_001184.3	340	Gat/Tat	4/47	0.647595807258445	1	FACETS	0.118	0.09	0.152	0.118	0.09	0.152	SUBCLONAL	1	TRUE	0	0.65702185877175	1		447	345	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683388	182683388	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	107	418	0	ENST00000292782.4:c.157C>T	p.Arg53Ter	p.R53*	ENST00000292782	NM_020640.2	53	Cga/Tga	2/7	NA	2	FACETS	0.711	0.641	0.784			1	INDETERMINATE	1	TRUE	NA	0.65702185877175	2		418	458	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528463	157528463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	188	609	0	ENST00000346085.5:c.6188C>T	p.Ala2063Val	p.A2063V	ENST00000346085	NM_020732.3	2063	gCa/gTa	20/20	1	2	FACETS	0.82	0.76	0.881	0.82	0.76	0.881	CLONAL	1	TRUE	1	0.65702185877175	2		609	698	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964391	70964391	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	124	424	0	ENST00000276594.2:c.1637G>A	p.Cys546Tyr	p.C546Y	ENST00000276594	NM_024504.3	546	tGc/tAc	8/8	1	2	FACETS	0.813	0.741	0.889	0.813	0.741	0.889	CLONAL	1	TRUE	1	0.65702185877175	2		424	464	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778764	76778767	+	frameshift_variant	Frame_Shift_Del	DEL	TTTC	TTTC	-	novel	NA	P-0043106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	148	221	0	ENST00000373344.5:c.6812_6815del	p.Arg2271LysfsTer14	p.R2271Kfs*14	ENST00000373344	NM_000489.3	2271	aGAAAa/aa	31/35	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.65702185877175	1		221	250	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38632024	38632024	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	72	642	0	ENST00000299084.4:c.510C>A	p.Ser170Arg	p.S170R	ENST00000299084	NM_152594.2	170	agC/agA	5/7	0.845582544441247	1	FACETS	0.622	0.558	0.687	0.622	0.558	0.687	SUBCLONAL	1	TRUE	0	0.845582544441247	1		642	158	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578411	+	inframe_deletion	In_Frame_Del	DEL	TGGTGGGGGCAGCGCCTC	TGGTGGGGGCAGCGCCTC	-	novel	NA	P-0043108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	532	698	0	ENST00000269305.4:c.519_536del	p.Arg174_His179del	p.R174_H179del	ENST00000269305	NM_001126112.2	173	gtGAGGCGCTGCCCCCACCAt/gtt	5/11	0.845582544441247	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.845582544441247	1		698	699	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672704	30672704	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	592	944	1	ENST00000376406.3:c.4256C>A	p.Ser1419Tyr	p.S1419Y	ENST00000376406	NM_014641.2	1419	tCc/tAc	10/15	0.725913336747458	1	FACETS	0.867	0.841	0.893	0.867	0.841	0.893	CLONAL	1	TRUE	0	0.845582544441247	1		945	932	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851684	134851684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373293977	NA	P-0043113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	50	594	1	ENST00000398015.3:c.1090C>T	p.Arg364Trp	p.R364W	ENST00000398015	NM_004441.4	364	Cgg/Tgg	5/16	0.209562786260401	1	FACETS	0.829	0.704	0.967	0.829	0.704	0.967	CLONAL	1	TRUE	0	0.209562786260401	1		595	515	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140154	50140154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1374610832	NA	P-0043113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	93	720	0	ENST00000246792.3:c.271G>A	p.Gly91Arg	p.G91R	ENST00000246792	NM_006270.3	91	Ggg/Agg	3/6	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.209562786260401	2		720	804	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285837	39285837	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	65	549	0	ENST00000402219.2:c.322G>C	p.Glu108Gln	p.E108Q	ENST00000402219	NM_005633.3	108	Gaa/Caa	3/23	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.209562786260401	2		549	618	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057894	27057894	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	82	705	0	ENST00000324856.7:c.1605del	p.Ser536ProfsTer83	p.S536Pfs*83	ENST00000324856	NM_006015.4	534	taC/ta	3/20	0.209562786260401	1	FACETS	0.984	0.867	1	0.984	0.867	1	CLONAL	1	TRUE	0	0.209562786260401	1		705	712	SUCCESS
CBL	867	MSKCC	GRCh37	11	119158629	119158629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	68	581	0	ENST00000264033.4:c.2009C>T	p.Ala670Val	p.A670V	ENST00000264033	NM_005188.3	670	gCc/gTc	12/16	0.163299384651979	3	FACETS	1	0.938	1	0.567	0.493	0.647	CLONAL	1	TRUE	1	0.209562786260401	3		581	632	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643252	38643252	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	45	365	0	ENST00000299084.4:c.722A>G	p.Asp241Gly	p.D241G	ENST00000299084	NM_152594.2	241	gAt/gGt	7/7	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.209562786260401	2		365	394	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482863	67482863	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	96	544	0	ENST00000327367.4:c.1267A>G	p.Ser423Gly	p.S423G	ENST00000327367	NM_005902.3	423	Agt/Ggt	9/9	1	2	FACETS	0.766	0.684	0.853	1	0.981	1	SUBCLONAL	2	TRUE	1	0.209562786260401	2		544	598	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658840	3658840	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs767940346	NA	P-0043113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	77	689	0	ENST00000294008.3:c.126G>C	p.Gln42His	p.Q42H	ENST00000294008	NM_032444.2	42	caG/caC	2/15	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.209562786260401	2		689	727	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89806286	89806420	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGCTTATAAACTTACTTAGCAAGGAACCTCAAGGAGGGCTCGTTCTTAACCATTTGCAAGATGCCTCTGAAAAGAGCGGCCCTCCGCATTTGTGCCTCAGCAGCGTGTTTCTTACCACTCTCTGTCAACTGAAA	GAGCTTATAAACTTACTTAGCAAGGAACCTCAAGGAGGGCTCGTTCTTAACCATTTGCAAGATGCCTCTGAAAAGAGCGGCCCTCCGCATTTGTGCCTCAGCAGCGTGTTTCTTACCACTCTCTGTCAACTGAAA	-	novel	NA	P-0043113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	53	200	0	ENST00000389301.3:c.3916_3934+116del		p.X1306_splice	ENST00000389301	NM_000135.2	1306		39/43	0.209562786260401	2	FACETS	1	0.945	1	1	0.976	1	CLONAL	3	TRUE	0	0.209562786260401	2		200	145	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940530	131940530	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	34	384	0	ENST00000265335.6:c.2557A>T	p.Ile853Leu	p.I853L	ENST00000265335		853	Ata/Tta	16/25	1	2	FACETS	0.889	0.727	1	0.889	0.727	1	CLONAL	1	TRUE	1	0.209562786260401	2		384	365	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917699	151917699	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	38	303	0	ENST00000262189.6:c.3621G>T	p.Lys1207Asn	p.K1207N	ENST00000262189	NM_170606.2	1207	aaG/aaT	23/59	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.209562786260401	2		303	281	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0043147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	151	437	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.399671632384883	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	FALSE	2	0.546625762473665	4		437	406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0043147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	43	525	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.10740379941918	5	FACETS	0.791	0.664	0.931			1	INDETERMINATE	1	FALSE	NA	0.546625762473665	5		525	362	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782329	NA	P-0043147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	31	607	0	ENST00000269305.4:c.746G>A	p.Arg249Lys	p.R249K	ENST00000269305	NM_001126112.2	249	aGg/aAg	7/11	0.10740379941918	5	FACETS	0.564	0.456	0.686			1	INDETERMINATE	1	FALSE	NA	0.546625762473665	5		607	366	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847305	68847305	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	167	537	0	ENST00000261769.5:c.1227G>A	p.Trp409Ter	p.W409*	ENST00000261769	NM_004360.3	409	tgG/tgA	9/16	0.546625762473665	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	0	0.546625762473665	1		537	316	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515435	103515435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748923127	NA	P-0043147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	33	260	0	ENST00000355739.4:c.1936G>A	p.Glu646Lys	p.E646K	ENST00000355739	NM_000123.3	646	Gaa/Aaa	8/15	0.178952259708667	0	FACETS	0.355	0.293	0.423			1	INDETERMINATE	1	FALSE	0	0.546625762473665	0		260	154	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712533	43712533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	26	647	4	ENST00000382044.4:c.4651G>A	p.Ala1551Thr	p.A1551T	ENST00000382044	NM_001141980.1	1551	Gcc/Acc	21/28	0.317905206043093	4	FACETS	0.299	0.236	0.372	0.15	0.118	0.186	INDETERMINATE	1	FALSE	2	0.546625762473665	4		651	492	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132612	67132612	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0043147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	30	395	0	ENST00000412916.2:c.496-1G>A		p.X166_splice	ENST00000412916		166			0.546625762473665	1	FACETS	0.219	0.176	0.268	0.219	0.176	0.268	SUBCLONAL	1	FALSE	0	0.546625762473665	1		395	364	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741008	40741008	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	144	812	0	ENST00000392038.2:c.1310G>A	p.Arg437Lys	p.R437K	ENST00000392038	NM_001626.4	437	aGg/aAg	13/14	0.213202194568739	3	FACETS	0.775	0.713	0.838	0.775	0.713	0.838	INDETERMINATE	2	FALSE	1	0.546625762473665	3		812	433	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0043172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	13	295	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	1	2	FACETS	0.537	0.382	0.726	0.537	0.382	0.726	SUBCLONAL	1	TRUE	1	0.18	2		295	269	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	72	557	3	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.18	2		560	601	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282115	38282115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554562012	NA	P-0043172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	74	826	0	ENST00000425967.3:c.941C>T	p.Pro314Leu	p.P314L	ENST00000425967	NM_001174067.1	314	cCg/cTg	8/19	1	2	FACETS	0.896	0.782	1	0.896	0.782	1	CLONAL	1	TRUE	1	0.18	2		826	918	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259397	11259397	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	53	560	0	ENST00000361445.4:c.4171C>G	p.Arg1391Gly	p.R1391G	ENST00000361445	NM_004958.3	1391	Cga/Gga	28/58	1	2	FACETS	0.948	0.808	1	0.948	0.808	1	CLONAL	1	TRUE	1	0.18	2		560	621	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	31	355	0	ENST00000256196.4:c.68G>A	p.Gly23Asp	p.G23D	ENST00000256196		23	gGc/gAc	1/6	1	2	FACETS	0.746	0.602	0.908	0.746	0.602	0.908	CLONAL	1	TRUE	1	0.18	2		355	462	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188153	11188153	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	52	540	0	ENST00000361445.4:c.5941A>G	p.Lys1981Glu	p.K1981E	ENST00000361445	NM_004958.3	1981	Aag/Gag	43/58	1	2	FACETS	0.919	0.781	1	0.919	0.781	1	CLONAL	1	TRUE	1	0.18	2		540	629	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057973	27057973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	60	572	1	ENST00000324856.7:c.1681C>T	p.Gln561Ter	p.Q561*	ENST00000324856	NM_006015.4	561	Cag/Tag	3/20	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.18	2		573	667	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653790	89653790	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	55	350	0	ENST00000371953.3:c.89del	p.Pro30GlnfsTer24	p.P30Qfs*24	ENST00000371953	NM_000314.4	30	Cca/ca	2/9	0.193113403253516	2	FACETS	0.982	0.846	1	0.982	0.846	1	CLONAL	2	TRUE	0	0.18	2		350	311	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650715	67650715	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	69	614	0	ENST00000264010.4:c.1020T>A	p.His340Gln	p.H340Q	ENST00000264010	NM_006565.3	340	caT/caA	5/12	1	2	FACETS	0.832	0.723	0.951	0.832	0.723	0.951	CLONAL	1	TRUE	1	0.18	2		614	921	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80160711	80160711	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs777247211	NA	P-0043172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	81	672	0	ENST00000265081.6:c.3080A>G	p.Asn1027Ser	p.N1027S	ENST00000265081	NM_002439.4	1027	aAt/aGt	22/24	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.18	2		672	685	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0043173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	137	735	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.321905142833309	2		735	842	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913250	NA	P-0043173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	186	367	0	ENST00000369535.4:c.34G>A	p.Gly12Ser	p.G12S	ENST00000369535	NM_002524.4	12	Ggt/Agt	2/7	0.321905142833309	3	FACETS	0.995	0.923	1			1	CLONAL	2	TRUE	NA	0.321905142833309	3		367	674	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0043173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	108	453	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	1	2	FACETS	0.912	0.819	1	0.912	0.819	1	CLONAL	1	TRUE	1	0.321905142833309	2		453	736	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029445	16029446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	86	362	3	ENST00000268712.3:c.1584dup	p.Glu529ArgfsTer7	p.E529Rfs*7	ENST00000268712	NM_006311.3	528	-/A	15/46	1	2	FACETS	0.849	0.752	0.953	0.849	0.752	0.953	CLONAL	1	TRUE	1	0.321905142833309	2		365	629	SUCCESS
APC	324	MSKCC	GRCh37	5	112175015	112175015	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1460397656	NA	P-0043173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	37	174	0	ENST00000257430.4:c.3724C>T	p.Gln1242Ter	p.Q1242*	ENST00000257430	NM_000038.5	1242	Cag/Tag	16/16	1	2	FACETS	0.958	0.795	1	0.958	0.795	1	CLONAL	1	TRUE	1	0.321905142833309	2		174	240	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045705	26045705	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs745690555	NA	P-0043173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	56	279	0	ENST00000540144.1:c.67A>G	p.Thr23Ala	p.T23A	ENST00000540144	NM_003531.2	23	Act/Gct	1/1	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.321905142833309	2		279	346	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	227	345	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.890020546295697	2		345	450	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0043175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	161	562	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.890020546295697	2		562	360	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175857	24175859	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs875989800	NA	P-0043175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	225	505	0	ENST00000263121.7:c.1091_1093del	p.Lys364del	p.K364del	ENST00000263121	NM_003073.3	362	gAGAag/gag	8/9	1	2	FACETS	0.68	0.636	0.726	0.68	0.636	0.726	SUBCLONAL	1	TRUE	1	0.890020546295697	2		505	743	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444577	78444578	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0043175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	242	311	0	ENST00000370768.2:c.111_112del	p.Arg37SerfsTer11	p.R37Sfs*11	ENST00000370768	NM_003902.3	37	agAGcc/agcc	1/20	0.890020546295697	1	FACETS	0.999	0.964	1	0.999	0.964	1	CLONAL	1	TRUE	0	0.890020546295697	1		311	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs967461896	NA	P-0043175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	60	529	0	ENST00000269305.4:c.526T>G	p.Cys176Gly	p.C176G	ENST00000269305	NM_001126112.2	176	Tgc/Ggc	5/11	1	2	FACETS	0.159	0.136	0.184	0.159	0.136	0.184	SUBCLONAL	1	TRUE	1	0.890020546295697	2		529	848	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089618	27089619	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0043175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	48	536	0	ENST00000324856.7:c.2575_2576del	p.His860ArgfsTer11	p.H860Rfs*11	ENST00000324856	NM_006015.4	858	atGAgt/atgt	8/20	0.890020546295697	1	FACETS	0.136	0.115	0.16	0.136	0.115	0.16	SUBCLONAL	1	TRUE	0	0.890020546295697	1		536	439	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434213	12434213	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148195788	NA	P-0043175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	36	365	0	ENST00000287820.6:c.581G>A	p.Arg194Gln	p.R194Q	ENST00000287820	NM_015869.4	194	cGg/cAg	4/7	0.890020546295697	1	FACETS	0.135	0.111	0.162	0.135	0.111	0.162	SUBCLONAL	1	TRUE	0	0.890020546295697	1		365	332	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539542	187539542	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	19	305	0	ENST00000441802.2:c.8198T>C	p.Val2733Ala	p.V2733A	ENST00000441802	NM_005245.3	2733	gTt/gCt	10/27	1	2	FACETS	0.121	0.091	0.156	0.121	0.091	0.156	SUBCLONAL	1	TRUE	1	0.890020546295697	2		305	353	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0043223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	144	307	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.23034027937515	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	2	TRUE	0	0.29	2		307	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0043223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	130	519	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.235408742484451	2	FACETS	1	0.982	1	0.674	0.613	0.738	CLONAL	1	TRUE	0	0.29	2		519	665	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913386	NA	P-0043223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	139	372	0	ENST00000304494.5:c.341C>A	p.Pro114His	p.P114H	ENST00000304494	NM_000077.4	114	cCc/cAc	2/3	0.236256986367359	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.29	2		372	448	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30302732	30302732	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1012001581	NA	P-0043223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	44	341	0	ENST00000322652.5:c.823G>A	p.Asp275Asn	p.D275N	ENST00000322652	NM_015355.2	275	Gat/Aat	7/16	0.235408742484451	2	FACETS	1	0.86	1	0.511	0.43	0.599	CLONAL	1	TRUE	0	0.29	2		341	297	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0043230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	167	672	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.673842162935246	2	FACETS	0.681	0.627	0.737	0.341	0.313	0.369	SUBCLONAL	1	TRUE	0	0.674284697340651	2		672	727	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0043230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	133	601	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.670582600183719	2	FACETS	0.533	0.485	0.584	0.267	0.242	0.292	SUBCLONAL	1	TRUE	0	0.674284697340651	2		601	740	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0043230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	239	701	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.674284697340651	2	FACETS	0.711	0.664	0.759	0.356	0.332	0.38	SUBCLONAL	1	TRUE	0	0.674284697340651	2		701	997	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439853	51439853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1557609882	NA	P-0043230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	165	500	3	ENST00000262662.1:c.418G>A	p.Ala140Thr	p.A140T	ENST00000262662		140	Gcc/Acc	4/4	0.674284697340651	2	FACETS	0.674	0.62	0.73	0.337	0.31	0.365	SUBCLONAL	1	TRUE	0	0.674284697340651	2		503	726	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0043230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	333	482	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	0.670582600183719	2	FACETS	0.982	0.944	1	0.982	0.944	1	CLONAL	2	TRUE	0	0.674284697340651	2		482	503	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946468	71946468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	132	773	1	ENST00000298229.2:c.2632C>T	p.Arg878Cys	p.R878C	ENST00000298229	NM_001567.3	878	Cgc/Tgc	23/28	0.673842162935246	2	FACETS	0.539	0.49	0.591	0.27	0.245	0.296	SUBCLONAL	1	TRUE	0	0.674284697340651	2		774	726	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117799	108117799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202160435	NA	P-0043230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	59	373	0	ENST00000278616.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000278616	NM_000051.3	337	cGt/cAt	8/63	0.673842162935246	2	FACETS	0.459	0.397	0.527	0.23	0.198	0.264	SUBCLONAL	1	TRUE	0	0.674284697340651	2		373	381	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443502	49443502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751561975	NA	P-0043230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	263	534	0	ENST00000301067.7:c.3869G>A	p.Arg1290Gln	p.R1290Q	ENST00000301067	NM_003482.3	1290	cGg/cAg	11/54	0.611258275971116	3	FACETS	1	0.989	1	0.405	0.381	0.431	CLONAL	1	TRUE	0	0.674284697340651	3		534	858	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0043230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	40	295	3	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			0.668806340778692	2	FACETS	0.584	0.491	0.686	0.292	0.245	0.343	SUBCLONAL	1	TRUE	0	0.674284697340651	2		298	203	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0043230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	109	481	0	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	0.668806340778692	2	FACETS	0.576	0.519	0.637	0.288	0.259	0.319	SUBCLONAL	1	TRUE	0	0.674284697340651	2		481	561	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560493	65560493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	121	512	0	ENST00000358664.4:c.104G>A	p.Arg35His	p.R35H	ENST00000358664	NM_002382.4	35	cGt/cAt	3/5	0.673842162935246	2	FACETS	0.503	0.454	0.553	0.251	0.227	0.277	SUBCLONAL	1	TRUE	0	0.674284697340651	2		512	714	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712824	43712824	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1201648831	NA	P-0043230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	190	753	2	ENST00000382044.4:c.4360C>T	p.Arg1454Ter	p.R1454*	ENST00000382044	NM_001141980.1	1454	Cga/Tga	21/28	0.670582600183719	2	FACETS	0.642	0.594	0.692	0.321	0.297	0.346	SUBCLONAL	1	TRUE	0	0.674284697340651	2		755	878	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130289	2130289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368666554	NA	P-0043230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	488	804	1	ENST00000219476.3:c.3521G>A	p.Arg1174Gln	p.R1174Q	ENST00000219476	NM_000548.3	1174	cGg/cAg	30/42	0.532383881297018	4	FACETS	0.979	0.938	1	0.979	0.938	1	CLONAL	2	TRUE	2	0.674284697340651	4		805	1238	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134536	2134536	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45448791	NA	P-0043230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	575	764	0	ENST00000219476.3:c.4313G>A	p.Arg1438Gln	p.R1438Q	ENST00000219476	NM_000548.3	1438	cGg/cAg	34/42	0.532383881297018	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	2	0.674284697340651	4		764	1327	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856093	68856093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121964878	NA	P-0043230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	124	676	0	ENST00000261769.5:c.1901C>T	p.Ala634Val	p.A634V	ENST00000261769	NM_004360.3	634	gCg/gTg	12/16	0.532383881297018	4	FACETS	0.554	0.5	0.611	0.277	0.25	0.306	SUBCLONAL	1	TRUE	2	0.674284697340651	4		676	1112	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577070	7577070	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770374782	NA	P-0043230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	28	735	1	ENST00000269305.4:c.868C>T	p.Arg290Cys	p.R290C	ENST00000269305	NM_001126112.2	290	Cgc/Tgc	8/11	0.674284697340651	2	FACETS	0.08	0.063	0.1	0.04	0.031	0.05	SUBCLONAL	1	TRUE	0	0.674284697340651	2		736	1034	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0043230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	370	503	0	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	0.674284697340651	2	FACETS	1	0.995	1	0.672	0.642	0.703	CLONAL	1	TRUE	0	0.674284697340651	2		503	816	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0043230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	191	484	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.674284697340651	2	FACETS	0.675	0.625	0.727	0.338	0.312	0.364	SUBCLONAL	1	TRUE	0	0.674284697340651	2		484	839	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578470	7578470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852789	NA	P-0043230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	200	804	1	ENST00000269305.4:c.460G>A	p.Gly154Ser	p.G154S	ENST00000269305	NM_001126112.2	154	Ggc/Agc	5/11	0.674284697340651	2	FACETS	0.602	0.557	0.648	0.301	0.278	0.324	SUBCLONAL	1	TRUE	0	0.674284697340651	2		805	986	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29497003	29497003	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397514641	NA	P-0043230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	163	242	0	ENST00000356175.3:c.574C>T	p.Arg192Ter	p.R192*	ENST00000356175	NM_000267.3	192	Cga/Tga	5/57	0.674284697340651	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.674284697340651	2		242	232	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212230	5212230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367918810	NA	P-0043230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	330	741	1	ENST00000357368.4:c.4801G>A	p.Val1601Ile	p.V1601I	ENST00000357368	NM_002850.3	1601	Gtc/Atc	32/38	0.670582600183719	2	FACETS	1	0.995	1	0.702	0.669	0.736	CLONAL	1	TRUE	0	0.674284697340651	2		742	697	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231350	5231350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370338775	NA	P-0043230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	177	727	0	ENST00000357368.4:c.2126C>T	p.Ser709Leu	p.S709L	ENST00000357368	NM_002850.3	709	tCg/tTg	14/38	0.670582600183719	2	FACETS	0.772	0.714	0.832	0.386	0.357	0.416	SUBCLONAL	1	TRUE	0	0.674284697340651	2		727	680	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599937	10599937	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369083385	NA	P-0043230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	149	732	0	ENST00000171111.5:c.1639G>A	p.Val547Ile	p.V547I	ENST00000171111	NM_203500.1	547	Gta/Ata	5/6	0.670582600183719	2	FACETS	0.516	0.472	0.563	0.258	0.236	0.282	SUBCLONAL	1	TRUE	0	0.674284697340651	2		732	856	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374390	31374390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773207465	NA	P-0043230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	127	604	1	ENST00000328111.2:c.389G>A	p.Arg130His	p.R130H	ENST00000328111	NM_006892.3	130	cGc/cAc	5/23	0.656732668002725	2	FACETS	0.579	0.525	0.635	0.289	0.262	0.318	SUBCLONAL	1	TRUE	0	0.674284697340651	2		605	651	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165918	47165918	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs775039657	NA	P-0043230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	109	448	0	ENST00000409792.3:c.208C>T	p.Arg70Ter	p.R70*	ENST00000409792	NM_014159.6	70	Cga/Tga	3/21	0.673842162935246	2	FACETS	0.573	0.516	0.633	0.287	0.258	0.317	SUBCLONAL	1	TRUE	0	0.674284697340651	2		448	564	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177002	56177002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	53	340	0	ENST00000399503.3:c.2272C>T	p.Leu758Phe	p.L758F	ENST00000399503	NM_005921.1	758	Ctt/Ttt	13/20	0.602500645399873	4	FACETS	0.387	0.329	0.451	0.194	0.164	0.226	SUBCLONAL	1	TRUE	2	0.674284697340651	4		340	680	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441304	149441304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	407	693	0	ENST00000286301.3:c.1735C>T	p.Arg579Trp	p.R579W	ENST00000286301	NM_005211.3	579	Cgg/Tgg	12/22	0.602500645399873	4	FACETS	0.878	0.837	0.92	0.878	0.837	0.92	CLONAL	2	TRUE	2	0.674284697340651	4		693	1151	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481601	20481601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	265	316	1	ENST00000346618.3:c.670G>A	p.Val224Ile	p.V224I	ENST00000346618	NM_001949.4	224	Gtt/Att	3/7	0.674284697340651	2	FACETS	0.947	0.905	0.988	0.947	0.905	0.988	CLONAL	2	TRUE	0	0.674284697340651	2		317	415	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146045	38146045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200818177	NA	P-0043230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	199	755	1	ENST00000317025.8:c.3461G>A	p.Arg1154Gln	p.R1154Q	ENST00000317025	NM_023034.1	1154	cGg/cAg	19/24	0.673842162935246	2	FACETS	0.599	0.555	0.645	0.3	0.277	0.323	SUBCLONAL	1	TRUE	0	0.674284697340651	2		756	985	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396925	139396925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766358616	NA	P-0043230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	254	436	2	ENST00000277541.6:c.5183C>T	p.Pro1728Leu	p.P1728L	ENST00000277541	NM_017617.3	1728	cCg/cTg	28/34	0.532383881297018	4	FACETS	0.893	0.841	0.947	0.893	0.841	0.947	CLONAL	2	TRUE	2	0.674284697340651	4		438	706	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397775	139397775	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1261408162	NA	P-0043230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	180	677	0	ENST00000277541.6:c.5026G>A	p.Val1676Ile	p.V1676I	ENST00000277541	NM_017617.3	1676	Gtc/Atc	27/34	0.532383881297018	4	FACETS	0.823	0.758	0.891	0.412	0.379	0.446	CLONAL	1	TRUE	2	0.674284697340651	4		677	1086	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802618	139802618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	437	684	1	ENST00000247668.2:c.463G>A	p.Glu155Lys	p.E155K	ENST00000247668	NM_021138.3	155	Gag/Aag	5/11	0.532383881297018	4	FACETS	0.91	0.869	0.952	0.91	0.869	0.952	CLONAL	2	TRUE	2	0.674284697340651	4		685	1192	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226066	53226066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556837402	NA	P-0043230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	112	395	0	ENST00000375401.3:c.2783C>T	p.Ala928Val	p.A928V	ENST00000375401	NM_004187.3	928	gCg/gTg	19/26	0.661462558785429	2	FACETS	0.534	0.481	0.59			1	SUBCLONAL	1	TRUE	NA	0.674284697340651	2		395	622	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436414	52436414	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	175	655	1	ENST00000460680.1:c.2080C>T	p.Gln694Ter	p.Q694*	ENST00000460680	NM_004656.3	694	Cag/Tag	17/17	0.398314277628426	1	FACETS	0.859	0.792	0.929	0.859	0.792	0.929	CLONAL	1	TRUE	0	0.398314277628426	1		656	819	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188196	10188196	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs869025637	NA	P-0043232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	160	464	0	ENST00000256474.2:c.341-2A>G		p.X114_splice	ENST00000256474	NM_000551.3	114			0.398314277628426	1	FACETS	0.926	0.851	1	0.926	0.851	1	CLONAL	1	TRUE	0	0.398314277628426	1		464	695	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188043	151188043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	187	421	0	ENST00000262187.5:c.110C>T	p.Pro37Leu	p.P37L	ENST00000262187	NM_005614.3	37	cCa/cTa	2/8	0.398314277628426	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.398314277628426	3		421	532	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0043246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	189	548	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.386203505909637	2		548	807	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285231	212285231	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	128	468	0	ENST00000342788.4:c.3070G>T	p.Val1024Phe	p.V1024F	ENST00000342788	NM_005235.2	1024	Gtc/Ttc	25/28	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.386203505909637	2		468	591	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244148	153244148	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	142	428	0	ENST00000281708.4:c.2009G>T	p.Gly670Val	p.G670V	ENST00000281708	NM_033632.3	670	gGa/gTa	12/12	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.386203505909637	2		428	729	SUCCESS
APC	324	MSKCC	GRCh37	5	112175909	112175909	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	65	234	0	ENST00000257430.4:c.4618G>T	p.Glu1540Ter	p.E1540*	ENST00000257430	NM_000038.5	1540	Gag/Tag	16/16	0.386203505909637	1	FACETS	0.943	0.825	1	0.943	0.825	1	CLONAL	1	TRUE	0	0.386203505909637	1		234	288	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0043278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	689	484	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	2	TRUE	NA	0.706374334703861	2		484	970	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0043278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	172	383	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.928	0.86	0.997	0.928	0.86	0.997	CLONAL	1	TRUE	1	0.706374334703861	2		383	525	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0043323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	519	1026	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	2	TRUE	NA	0.672288299889677	2		1026	759	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061412	38061412	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1310740071	NA	P-0043323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	431	702	0	ENST00000250448.2:c.577C>G	p.Leu193Val	p.L193V	ENST00000250448	NM_004496.3	193	Ctg/Gtg	2/2	0.671111921022402	5	FACETS	1	0.985	1			1	CLONAL	2	TRUE	NA	0.672288299889677	5		702	1205	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021919	246021919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763591857	NA	P-0043323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	197	949	0	ENST00000388985.4:c.955C>T	p.Arg319Trp	p.R319W	ENST00000388985		319	Cgg/Tgg	10/12	0.455529748496438	3	FACETS	0.981	0.911	1	0.491	0.455	0.527	CLONAL	1	TRUE	1	0.672288299889677	3		949	798	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991666	72991666	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	290	604	1	ENST00000268489.5:c.2379del	p.Ser794ArgfsTer30	p.S794Rfs*30	ENST00000268489	NM_006885.3	793	ccC/cc	2/10	0.672288299889677	2	FACETS	0.952	0.912	0.992	0.952	0.912	0.992	CLONAL	2	TRUE	0	0.672288299889677	2		605	453	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673104	30673104	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	423	769	0	ENST00000376406.3:c.3856C>G	p.Pro1286Ala	p.P1286A	ENST00000376406	NM_014641.2	1286	Ccc/Gcc	10/15	0.648160036785902	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.672288299889677	4		769	1032	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273266	55273266	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1431	187	797	0	ENST00000275493.2:c.3589T>G	p.Tyr1197Asp	p.Y1197D	ENST00000275493	NM_005228.3	1197	Tac/Gac	28/28	0.672288299889677	7	FACETS	0.922	0.848	0.999	0.23	0.212	0.25	CLONAL	1	TRUE	3	0.672288299889677	7		797	1618	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982420	201982420	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0043351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	298	775	0	ENST00000359651.3:c.799A>T	p.Lys267Ter	p.K267*	ENST00000359651		267	Aag/Tag	6/8	0.655019787474507	3	FACETS	0.994	0.936	1	0.497	0.468	0.527	CLONAL	1	TRUE	1	0.732057325331545	3		775	1119	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619864	21619864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1235573411	NA	P-0043351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1229	91	494	1	ENST00000382592.4:c.302G>A	p.Arg101Gln	p.R101Q	ENST00000382592	NM_014572.2	101	cGg/cAg	2/8	0.732057325331545	7	FACETS	0.533	0.471	0.599			1	SUBCLONAL	1	TRUE	NA	0.732057325331545	7		495	1320	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662047	227662047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1301402217	NA	P-0043351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	223	676	0	ENST00000305123.5:c.1408G>A	p.Gly470Ser	p.G470S	ENST00000305123	NM_005544.2	470	Ggc/Agc	1/2	0.479455332726	4	FACETS	1	0.965	1	0.529	0.492	0.567	CLONAL	1	TRUE	2	0.732057325331545	4		676	998	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537145	41537145	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs973317775	NA	P-0043351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	561	506	0	ENST00000263253.7:c.1972C>G	p.Leu658Val	p.L658V	ENST00000263253	NM_001429.3	658	Cta/Gta	10/31	0.732057325331545	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.732057325331545	3		506	1034	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444528	187444528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1438511659	NA	P-0043351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	490	649	1	ENST00000232014.4:c.1699G>A	p.Val567Ile	p.V567I	ENST00000232014	NM_001130845.1	567	Gtc/Atc	7/10	0.644339503856186	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.732057325331545	4		650	1127	SUCCESS
APC	324	MSKCC	GRCh37	5	112176018	112176018	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	265	380	0	ENST00000257430.4:c.4728del	p.Glu1577AsnfsTer73	p.E1577Nfs*73	ENST00000257430	NM_000038.5	1576	gAa/ga	16/16	0.732057325331545	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.732057325331545	2		380	348	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	80	345	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.824	0.732	0.922	0.824	0.732	0.922	CLONAL	1	TRUE	1	0.58111413799983	2		345	334	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661663	227661664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761880048	NA	P-0043366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	241	610	1	ENST00000305123.5:c.1791dup	p.His598AlafsTer13	p.H598Afs*13	ENST00000305123	NM_005544.2	597	-/G	1/2	1	2	FACETS	0.96	0.899	1	0.96	0.899	1	CLONAL	1	TRUE	1	0.58111413799983	2		611	864	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431649	6431649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	226	550	0	ENST00000356142.4:c.202C>T	p.Arg68Cys	p.R68C	ENST00000356142	NM_018890.3	68	Cgc/Tgc	3/7	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.58111413799983	2		550	704	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658237	18658238	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	142	482	0	ENST00000266497.5:c.3047dup	p.Tyr1017LeufsTer17	p.Y1017Lfs*17	ENST00000266497		1014	-/T	22/31	0.58111413799983	3	FACETS	0.811	0.739	0.885	0.405	0.369	0.443	CLONAL	1	TRUE	1	0.58111413799983	3		482	778	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798824	135798824	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	116	360	0	ENST00000298552.3:c.419T>G	p.Leu140Arg	p.L140R	ENST00000298552	NM_001162426.1	140	cTa/cGa	6/23	0.58111413799983	1	FACETS	0.796	0.725	0.869	0.796	0.725	0.869	SUBCLONAL	1	TRUE	0	0.58111413799983	1		360	356	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	117	732	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.345	0.311	0.382	0.345	0.311	0.382	SUBCLONAL	1	TRUE	1	0.71	2		735	954	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	355	662	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.924	0.877	0.972	0.924	0.877	0.972	CLONAL	1	TRUE	1	0.71	2		663	1082	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	338	331	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.964	0.914	1	0.964	0.914	1	CLONAL	1	TRUE	1	0.71	2		331	988	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	346	484	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.941	0.892	0.99	0.941	0.892	0.99	CLONAL	1	TRUE	1	0.71	2		484	1036	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073868	8073868	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	192	484	0	ENST00000377482.5:c.791T>C	p.Ile264Thr	p.I264T	ENST00000377482	NM_018948.3	264	aTa/aCa	4/4	0.3	1	FACETS	0.632	0.589	0.676	0.632	0.589	0.676	INDETERMINATE	1	TRUE	0	0.71	1		484	552	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	311	822	0	ENST00000324856.7:c.4555del	p.Gln1519ArgfsTer8	p.Q1519Rfs*8	ENST00000324856	NM_006015.4	1517	gCc/gc	18/20	1	2	FACETS	0.933	0.882	0.985	0.933	0.882	0.985	CLONAL	1	TRUE	1	0.71	2		822	939	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39321378	39321378	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	134	466	0	ENST00000373001.3:c.641+2T>C		p.X214_splice	ENST00000373001	NM_022157.3	214			1	2	FACETS	0.983	0.903	1	0.983	0.903	1	CLONAL	1	TRUE	1	0.71	2		466	384	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330576	65330576	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	176	592	0	ENST00000342505.4:c.1070del	p.Asn357ThrfsTer20	p.N357Tfs*20	ENST00000342505	NM_002227.2	357	aAc/ac	8/25	1	2	FACETS	0.901	0.836	0.969	0.901	0.836	0.969	CLONAL	1	TRUE	1	0.71	2		592	550	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226576366	226576366	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	252	584	0	ENST00000366794.5:c.708del	p.Ala237ProfsTer2	p.A237Pfs*2	ENST00000366794	NM_001618.3	236	aaA/aa	5/23	1	2	FACETS	0.996	0.936	1	0.996	0.936	1	CLONAL	1	TRUE	1	0.71	2		584	713	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578195	226578195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202057244	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	305	647	0	ENST00000366794.5:c.533C>T	p.Ala178Val	p.A178V	ENST00000366794	NM_001618.3	178	gCg/gTg	4/23	1	2	FACETS	0.87	0.821	0.919	0.87	0.821	0.919	CLONAL	1	TRUE	1	0.71	2		647	988	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100728	8100728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs771019738	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	308	779	3	ENST00000346208.3:c.708del	p.Ser237AlafsTer28	p.S237Afs*28	ENST00000346208		234	ttC/tt	3/6	1	2	FACETS	0.862	0.813	0.911	0.862	0.813	0.911	CLONAL	1	TRUE	1	0.71	2		782	1007	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624254	89624256	+	inframe_deletion	In_Frame_Del	DEL	AGC	AGC	-	rs1114167649	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	141	303	0	ENST00000371953.3:c.30_32del	p.Ser10del	p.S10del	ENST00000371953	NM_000314.4	10	AGC/-	1/9	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.71	2		303	357	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	41	333	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	0.75	0.636	0.872	0.75	0.636	0.872	SUBCLONAL	1	TRUE	1	0.71	2		333	154	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	131	341	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	0.706	0.644	0.77	0.706	0.644	0.77	SUBCLONAL	1	TRUE	1	0.71	2		341	523	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981721	101981721	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555075353	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	117	252	0	ENST00000282441.5:c.147del	p.Ala50ProfsTer24	p.A50Pfs*24	ENST00000282441	NM_001130145.2	48	Ccc/cc	1/9	1	2	FACETS	0.936	0.854	1	0.936	0.854	1	CLONAL	1	TRUE	1	0.71	2		252	352	SUCCESS
ATM	472	MSKCC	GRCh37	11	108181042	108181042	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	47	300	0	ENST00000278616.4:c.5918G>T	p.Arg1973Ile	p.R1973I	ENST00000278616	NM_000051.3	1973	aGa/aTa	39/63	1	2	FACETS	0.988	0.854	1	0.988	0.854	1	CLONAL	1	TRUE	1	0.71	2		300	134	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481620	56481620	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	346	799	0	ENST00000267101.3:c.655T>G	p.Phe219Val	p.F219V	ENST00000267101	NM_001982.3	219	Ttt/Gtt	6/28	0.13109497596865	3	FACETS	1	0.991	1	0.603	0.571	0.635	INDETERMINATE	1	TRUE	1	0.71	3		799	1095	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112919929	112919929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1214510641	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	101	314	0	ENST00000351677.2:c.1144G>A	p.Val382Ile	p.V382I	ENST00000351677	NM_002834.3	382	Gtc/Atc	10/16	0.13109497596865	3	FACETS	1	0.977	1	0.634	0.574	0.696	INDETERMINATE	1	TRUE	1	0.71	3		314	304	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563207	21563207	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	301	780	0	ENST00000382592.4:c.712A>G	p.Ser238Gly	p.S238G	ENST00000382592	NM_014572.2	238	Agc/Ggc	4/8	1	2	FACETS	0.919	0.867	0.971	0.919	0.867	0.971	CLONAL	1	TRUE	1	0.71	2		780	923	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923236	26923236	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	122	405	0	ENST00000381527.3:c.232G>C	p.Val78Leu	p.V78L	ENST00000381527	NM_001260.1	78	Gtc/Ctc	3/13	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.71	2		405	337	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907421	32907421	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359306	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	85	367	2	ENST00000380152.3:c.1813del	p.Ile605TyrfsTer9	p.I605Yfs*9	ENST00000380152		602	ggA/gg	10/27	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.71	2		369	233	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527786	103527786	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1566474373	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	201	418	0	ENST00000355739.4:c.3094A>G	p.Ser1032Gly	p.S1032G	ENST00000355739	NM_000123.3	1032	Agc/Ggc	15/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.71	2		418	538	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436791	110436793	+	inframe_deletion	In_Frame_Del	DEL	CCG	CCG	-	rs769193882	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	235	754	4	ENST00000375856.3:c.1608_1610del	p.Gly537del	p.G537del	ENST00000375856	NM_003749.2	536	ggCGGt/ggt	1/2	1	2	FACETS	0.692	0.646	0.739	0.692	0.646	0.739	SUBCLONAL	1	TRUE	1	0.71	2		758	957	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569898	95569898	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	193	497	0	ENST00000393063.1:c.3835C>T	p.Gln1279Ter	p.Q1279*	ENST00000393063	NM_030621.3	1279	Cag/Tag	22/28	1	2	FACETS	0.858	0.797	0.919	0.858	0.797	0.919	CLONAL	1	TRUE	1	0.71	2		497	634	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705410	43705410	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764425387	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	460	859	1	ENST00000382044.4:c.5212G>A	p.Ala1738Thr	p.A1738T	ENST00000382044	NM_001141980.1	1738	Gca/Aca	24/28	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.71	2		860	1183	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396234	396234	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	52	674	0	ENST00000262320.3:c.792del	p.Gly265GlufsTer149	p.G265Efs*149	ENST00000262320	NM_003502.3	264	ccC/cc	2/11	0.13109497596865	3	FACETS	0.192	0.162	0.225	0.096	0.081	0.113	INDETERMINATE	1	TRUE	1	0.71	3		674	1034	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396425	396425	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	58	846	0	ENST00000262320.3:c.601T>G	p.Phe201Val	p.F201V	ENST00000262320	NM_003502.3	201	Ttc/Gtc	2/11	0.13109497596865	3	FACETS	0.217	0.185	0.251	0.108	0.092	0.126	INDETERMINATE	1	TRUE	1	0.71	3		846	1021	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843515	3843515	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	289	593	0	ENST00000262367.5:c.1088A>G	p.His363Arg	p.H363R	ENST00000262367	NM_004380.2	363	cAt/cGt	4/31	0.13109497596865	3	FACETS	1	0.988	1	0.591	0.556	0.625	INDETERMINATE	1	TRUE	1	0.71	3		593	934	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857958	9857958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140536516	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	337	705	0	ENST00000330684.3:c.3443C>T	p.Pro1148Leu	p.P1148L	ENST00000330684	NM_001134407.1	1148	cCg/cTg	13/13	0.13109497596865	3	FACETS	1	0.993	1	0.66	0.625	0.695	INDETERMINATE	1	TRUE	1	0.71	3		705	975	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9928079	9928079	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	143	352	0	ENST00000330684.3:c.1660A>G	p.Ser554Gly	p.S554G	ENST00000330684	NM_001134407.1	554	Agc/Ggc	8/13	0.13109497596865	3	FACETS	1	0.982	1	0.626	0.576	0.678	INDETERMINATE	1	TRUE	1	0.71	3		352	436	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845237	89845237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765036744	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	343	620	1	ENST00000389301.3:c.1798C>T	p.Arg600Cys	p.R600C	ENST00000389301	NM_000135.2	600	Cgt/Tgt	20/43	0.13109497596865	3	FACETS	1	0.993	1	0.659	0.625	0.694	INDETERMINATE	1	TRUE	1	0.71	3		621	993	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38506138	38506138	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	331	611	0	ENST00000254066.5:c.430C>T	p.Arg144Ter	p.R144*	ENST00000254066	NM_000964.3	144	Cga/Tga	4/9	1	2	FACETS	0.956	0.906	1	0.956	0.906	1	CLONAL	1	TRUE	1	0.71	2		611	975	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	383	718	3	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	1	2	FACETS	0.936	0.89	0.983	0.936	0.89	0.983	CLONAL	1	TRUE	1	0.71	2		721	1153	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119974	70120026	+	frameshift_variant	Frame_Shift_Del	DEL	GCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAGGCGCCGCC	GCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAGGCGCCGCC	-	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	47	262	0	ENST00000245479.2:c.984_1036del	p.Ser330AlafsTer230	p.S330Afs*230	ENST00000245479	NM_000346.3	326	GCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAGGCGCCGCCg/g	3/3	1	2	FACETS	0.42	0.356	0.49	0.42	0.356	0.49	SUBCLONAL	1	TRUE	1	0.71	2		262	315	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78914400	78914400	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	257	585	0	ENST00000306801.3:c.3024G>T	p.Lys1008Asn	p.K1008N	ENST00000306801	NM_020761.2	1008	aaG/aaT	25/34	1	2	FACETS	0.906	0.851	0.962	0.906	0.851	0.962	CLONAL	1	TRUE	1	0.71	2		585	799	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985400	60985400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	361	656	0	ENST00000333681.4:c.500C>T	p.Ser167Leu	p.S167L	ENST00000333681		167	tCg/tTg	2/3	1	2	FACETS	0.924	0.877	0.972	0.924	0.877	0.972	CLONAL	1	TRUE	1	0.71	2		656	1100	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215356	5215356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1420232605	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	327	734	0	ENST00000357368.4:c.4262G>A	p.Arg1421His	p.R1421H	ENST00000357368	NM_002850.3	1421	cGc/cAc	28/38	0.13109497596865	3	FACETS	1	0.992	1	0.63	0.597	0.665	INDETERMINATE	1	TRUE	1	0.71	3		734	990	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274303	5274304	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs777078756	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	342	706	0	ENST00000357368.4:c.143dup	p.Val49CysfsTer11	p.V49Cfs*11	ENST00000357368	NM_002850.3	48	ggt/ggGt	3/38	0.13109497596865	3	FACETS	1	0.987	1	0.564	0.533	0.595	INDETERMINATE	1	TRUE	1	0.71	3		706	1158	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031170	11031170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	429	485	0	ENST00000327064.4:c.1255C>T	p.Arg419Trp	p.R419W	ENST00000327064	NM_199141.1	419	Cgg/Tgg	11/16	0.13109497596865	3	FACETS	1	0.995	1	0.698	0.666	0.73	INDETERMINATE	1	TRUE	1	0.71	3		485	1173	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271804	15271804	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	381	885	0	ENST00000263388.2:c.6635T>C	p.Leu2212Pro	p.L2212P	ENST00000263388	NM_000435.2	2212	cTg/cCg	33/33	0.13109497596865	3	FACETS	1	0.994	1	0.666	0.633	0.699	INDETERMINATE	1	TRUE	1	0.71	3		885	1092	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353819	15353819	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	165	580	2	ENST00000263377.2:c.3061del	p.His1021IlefsTer47	p.H1021Ifs*47	ENST00000263377	NM_058243.2	1021	Cat/at	14/20	0.13109497596865	3	FACETS	0.864	0.795	0.935	0.432	0.397	0.468	INDETERMINATE	1	TRUE	1	0.71	3		582	729	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942593	17942593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	145	615	0	ENST00000458235.1:c.2695C>T	p.Arg899Trp	p.R899W	ENST00000458235	NM_000215.3	899	Cgg/Tgg	20/24	0.13109497596865	3	FACETS	0.552	0.503	0.604	0.276	0.251	0.302	INDETERMINATE	1	TRUE	1	0.71	3		615	1002	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277990	18277990	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	321	685	1	ENST00000222254.8:c.1610A>C	p.Glu537Ala	p.E537A	ENST00000222254	NM_005027.3	537	gAg/gCg	13/16	0.13109497596865	3	FACETS	1	0.99	1	0.596	0.563	0.629	INDETERMINATE	1	TRUE	1	0.71	3		686	1028	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313352	30313352	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	308	658	1	ENST00000262643.3:c.953-1G>T		p.X318_splice	ENST00000262643	NM_001238.2	318			0.13109497596865	3	FACETS	1	0.994	1	0.7	0.662	0.738	INDETERMINATE	1	TRUE	1	0.71	3		659	840	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796976	42796976	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	412	851	0	ENST00000575354.2:c.3437del	p.Pro1146GlnfsTer15	p.P1146Qfs*15	ENST00000575354	NM_015125.3	1145	aCc/ac	14/20	0.13109497596865	3	FACETS	1	0.994	1	0.654	0.623	0.685	INDETERMINATE	1	TRUE	1	0.71	3		851	1203	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731499	47731499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	23	31	0	ENST00000449228.1:c.293G>A	p.Arg98His	p.R98H	ENST00000449228	NM_001127240.2	98	cGc/cAc	2/4	0.13109497596865	3	FACETS	1	0.919	1	0.655	0.529	0.789	INDETERMINATE	1	TRUE	1	0.71	3		31	67	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085728	16085728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144939456	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	330	683	1	ENST00000281043.3:c.904C>T	p.Arg302Cys	p.R302C	ENST00000281043	NM_005378.4	302	Cgt/Tgt	3/3	1	2	FACETS	0.916	0.867	0.966	0.916	0.867	0.966	CLONAL	1	TRUE	1	0.71	2		684	1015	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463209	25463209	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	320	703	0	ENST00000264709.3:c.2284G>T	p.Gly762Cys	p.G762C	ENST00000264709	NM_175629.2	762	Ggc/Tgc	19/23	1	2	FACETS	0.954	0.903	1	0.954	0.903	1	CLONAL	1	TRUE	1	0.71	2		703	945	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523009	25523009	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	352	733	2	ENST00000264709.3:c.176del	p.Pro59ArgfsTer13	p.P59Rfs*13	ENST00000264709	NM_175629.2	59	cCg/cg	3/23	1	2	FACETS	0.917	0.87	0.965	0.917	0.87	0.965	CLONAL	1	TRUE	1	0.71	2		735	1081	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705493	47705493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750368	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	70	428	1	ENST00000233146.2:c.2293G>A	p.Ala765Thr	p.A765T	ENST00000233146	NM_000251.2	765	Gct/Act	14/16	0.242788254805127	1	FACETS	0.451	0.397	0.508	0.451	0.397	0.508	INDETERMINATE	1	TRUE	0	0.71	1		429	282	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026204	48026204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750440	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	185	445	0	ENST00000234420.5:c.1082G>A	p.Arg361His	p.R361H	ENST00000234420	NM_000179.2	361	cGc/cAc	4/10	0.242788254805127	1	FACETS	0.634	0.59	0.679	0.634	0.59	0.679	INDETERMINATE	1	TRUE	0	0.71	1		445	530	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150001	202150001	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	357	703	0	ENST00000358485.4:c.1442T>C	p.Ile481Thr	p.I481T	ENST00000358485	NM_001080125.1	481	aTc/aCc	8/9	1	2	FACETS	0.957	0.908	1	0.957	0.908	1	CLONAL	1	TRUE	1	0.71	2		703	1051	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306553	41306553	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	323	645	0	ENST00000373198.4:c.1106del	p.Gly369ValfsTer28	p.G369Vfs*28	ENST00000373198	NM_133170.3	369	gGt/gt	7/32	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.71	2		645	892	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46277765	46277765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774124954	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	223	430	0	ENST00000371998.3:c.3563G>A	p.Arg1188Gln	p.R1188Q	ENST00000371998		1188	cGa/cAa	19/23	1	2	FACETS	0.978	0.916	1	0.978	0.916	1	CLONAL	1	TRUE	1	0.71	2		430	642	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755416	39755416	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	284	665	0	ENST00000288319.7:c.1349A>C	p.Asn450Thr	p.N450T	ENST00000288319	NM_182918.3	450	aAc/aCc	10/10	1	2	FACETS	0.941	0.888	0.996	0.941	0.888	0.996	CLONAL	1	TRUE	1	0.71	2		665	850	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934952	49934952	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	349	719	0	ENST00000296474.3:c.2046+1G>A		p.X682_splice	ENST00000296474	NM_002447.2	682			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.71	2		719	956	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936695	49936695	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	308	585	0	ENST00000296474.3:c.1232C>A	p.Pro411His	p.P411H	ENST00000296474	NM_002447.2	411	cCt/cAt	2/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.71	2		585	822	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998128	169998128	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs753143066	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	189	716	3	ENST00000295797.4:c.826del	p.Thr276GlnfsTer7	p.T276Qfs*7	ENST00000295797	NM_002740.5	273	ttA/tt	9/18	1	2	FACETS	0.907	0.843	0.972	0.907	0.843	0.972	CLONAL	1	TRUE	1	0.71	2		719	587	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443346	187443346	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs752044631	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	215	489	1	ENST00000232014.4:c.1780C>T	p.Arg594Ter	p.R594*	ENST00000232014	NM_001130845.1	594	Cga/Tga	8/10	1	2	FACETS	0.792	0.738	0.847	0.792	0.738	0.847	SUBCLONAL	1	TRUE	1	0.71	2		490	765	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589576	67589576	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1289537429	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	16	300	0	ENST00000274335.5:c.1344del	p.Lys448AsnfsTer32	p.K448Nfs*32	ENST00000274335		447	Aaa/aa	10/15	1	2	FACETS	0.593	0.448	0.758	0.593	0.448	0.758	SUBCLONAL	1	TRUE	1	0.71	2		300	76	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs1057519842	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	88	313	0	ENST00000274335.5:c.1727_1729del	p.Thr576del	p.T576del	ENST00000274335		575	aaGACg/aag	12/15	1	2	FACETS	0.81	0.726	0.898	0.81	0.726	0.898	CLONAL	1	TRUE	1	0.71	2		313	306	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	265	581	7	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.917	0.877	0.956	1	0.996	1	CLONAL	2	TRUE	1	0.71	2		588	407	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519378	176519378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148292303	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	357	674	0	ENST00000292408.4:c.784G>A	p.Val262Met	p.V262M	ENST00000292408	NM_213647.1	262	Gtg/Atg	7/18	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.71	2		674	916	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323092	31323093	+	splice_donor_variant	Splice_Site	INS	-	-	C	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	281	870	0	ENST00000412585.2:c.895+1dup		p.X299_splice	ENST00000412585	NM_005514.6	299			1	2	FACETS	0.736	0.691	0.781	0.736	0.691	0.781	SUBCLONAL	1	TRUE	1	0.71	2		870	1076	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800223	32800223	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	216	432	0	ENST00000374899.4:c.1159del	p.Val387CysfsTer4	p.V387Cfs*4	ENST00000374899	NM_018833.2	387	Gtg/tg	7/12	1	2	FACETS	0.926	0.866	0.988	0.926	0.866	0.988	CLONAL	1	TRUE	1	0.71	2		432	657	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220319	55220319	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	368	738	1	ENST00000275493.2:c.709G>A	p.Ala237Thr	p.A237T	ENST00000275493	NM_005228.3	237	Gct/Act	6/28	1	2	FACETS	0.96	0.912	1	0.96	0.912	1	CLONAL	1	TRUE	1	0.71	2		739	1080	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501302	140501302	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs180177035	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	17	429	0	ENST00000288602.6:c.770A>G	p.Gln257Arg	p.Q257R	ENST00000288602	NM_004333.4	257	cAg/cGg	6/18	1	2	FACETS	0.165	0.122	0.215	0.165	0.122	0.215	SUBCLONAL	1	TRUE	1	0.71	2		429	291	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38137094	38137094	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1351115556	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	246	745	0	ENST00000317025.8:c.3724C>T	p.Arg1242Ter	p.R1242*	ENST00000317025	NM_023034.1	1242	Cga/Tga	21/24	1	2	FACETS	0.84	0.787	0.894	0.84	0.787	0.894	CLONAL	1	TRUE	1	0.71	2		745	825	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033246	69033246	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	242	603	0	ENST00000288368.4:c.3686T>C	p.Val1229Ala	p.V1229A	ENST00000288368	NM_024870.2	1229	gTc/gCc	30/40	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.71	2		603	669	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549445	5549445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141466336	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	384	785	0	ENST00000397747.3:c.472G>A	p.Val158Ile	p.V158I	ENST00000397747	NM_025239.3	158	Gtc/Atc	4/7	1	2	FACETS	0.904	0.859	0.949	0.904	0.859	0.949	CLONAL	1	TRUE	1	0.71	2		785	1197	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484349	8484349	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	180	464	0	ENST00000356435.5:c.3183A>C	p.Glu1061Asp	p.E1061D	ENST00000356435		1061	gaA/gaC	19/35	1	2	FACETS	0.971	0.903	1	0.971	0.903	1	CLONAL	1	TRUE	1	0.71	2		464	522	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633376	8633376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	230	598	0	ENST00000356435.5:c.293G>A	p.Cys98Tyr	p.C98Y	ENST00000356435		98	tGt/tAt	3/35	1	2	FACETS	0.964	0.904	1	0.964	0.904	1	CLONAL	1	TRUE	1	0.71	2		598	672	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970966	21970966	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1563888782	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	388	542	2	ENST00000304494.5:c.392G>A	p.Arg131His	p.R131H	ENST00000304494	NM_000077.4	131	cGc/cAc	2/3	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.71	2		544	918	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771795	135771795	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs118203753	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	325	780	2	ENST00000298552.3:c.3322G>A	p.Gly1108Ser	p.G1108S	ENST00000298552	NM_001162426.1	1108	Ggc/Agc	23/23	1	2	FACETS	0.866	0.819	0.914	0.866	0.819	0.914	CLONAL	1	TRUE	1	0.71	2		782	1057	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399434	139399434	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199860726	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	417	740	2	ENST00000277541.6:c.4709C>T	p.Ala1570Val	p.A1570V	ENST00000277541	NM_017617.3	1570	gCg/gTg	26/34	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.71	2		742	1165	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411707	63411707	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	182	438	0	ENST00000330258.3:c.1460del	p.Leu487ArgfsTer54	p.L487Rfs*54	ENST00000330258	NM_152424.3	487	cTg/cg	2/2	0.3	2	FACETS	0.903	0.838	0.969	0.451	0.419	0.485	INDETERMINATE	1	TRUE	0	0.71	2		438	568	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351422	70351422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	356	375	0	ENST00000374080.3:c.4070G>A	p.Arg1357His	p.R1357H	ENST00000374080		1357	cGc/cAc	29/45	0.3	2	FACETS	0.934	0.899	0.968	0.934	0.899	0.968	INDETERMINATE	2	TRUE	0	0.71	2		375	537	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0043404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	28	307	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.501	0.4	0.616	0.501	0.4	0.616	SUBCLONAL	1	FALSE	1	0.258845486561883	2		307	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579861	7579861	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs876658627	NA	P-0043404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	98	657	0	ENST00000269305.4:c.52del	p.Thr18HisfsTer26	p.T18Hfs*26	ENST00000269305	NM_001126112.2	18	Aca/ca	2/11	1	2	FACETS	0.792	0.705	0.885	0.792	0.705	0.885	SUBCLONAL	1	FALSE	1	0.258845486561883	2		657	956	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288969	212288969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148791072	NA	P-0043404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	38	454	0	ENST00000342788.4:c.2777C>T	p.Thr926Met	p.T926M	ENST00000342788	NM_005235.2	926	aCg/aTg	23/28	1	2	FACETS	0.932	0.773	1	0.932	0.773	1	CLONAL	1	FALSE	1	0.258845486561883	2		454	315	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133523	55133523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142492533	NA	P-0043404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	67	488	1	ENST00000257290.5:c.827C>T	p.Thr276Met	p.T276M	ENST00000257290	NM_006206.4	276	aCg/aTg	6/23	1	2	FACETS	0.66	0.573	0.755	0.66	0.573	0.755	SUBCLONAL	1	FALSE	1	0.258845486561883	2		489	784	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717777	89717777	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs786204873	NA	P-0043404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	28	252	0	ENST00000371953.3:c.801+1G>A		p.X267_splice	ENST00000371953	NM_000314.4	267			1	2	FACETS	0.52	0.415	0.64	0.52	0.415	0.64	SUBCLONAL	1	FALSE	1	0.258845486561883	2		252	416	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188964	11188964	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753081675	NA	P-0043404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	71	488	0	ENST00000361445.4:c.5759A>G	p.Asn1920Ser	p.N1920S	ENST00000361445	NM_004958.3	1920	aAt/aGt	41/58	0.258845486561883	1	FACETS	0.614	0.535	0.699	0.614	0.535	0.699	SUBCLONAL	1	FALSE	0	0.258845486561883	1		488	778	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0043410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	152	325	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.403534411253211	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.603403969176723	4		325	341	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631837	90631837	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	166	499	0	ENST00000330062.3:c.516G>T	p.Arg172Ser	p.R172S	ENST00000330062	NM_002168.2	172	agG/agT	4/11	0.581435754542661	3	FACETS	1	0.947	1	0.518	0.477	0.561	CLONAL	1	TRUE	1	0.603403969176723	3		499	691	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464434	120464434	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0043410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	71	301	0	ENST00000256646.2:c.5214-2A>G		p.X1738_splice	ENST00000256646	NM_024408.3	1738			0.598618247218734	3	FACETS	0.957	0.842	1	0.479	0.421	0.54	CLONAL	1	TRUE	1	0.603403969176723	3		301	320	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692833	89692833	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	31	196	0	ENST00000371953.3:c.317A>G	p.Glu106Gly	p.E106G	ENST00000371953	NM_000314.4	106	gAa/gGa	5/9	0.476865793583657	4	FACETS	1	0.889	1	0.56	0.46	0.671	CLONAL	1	TRUE	2	0.603403969176723	4		196	147	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610028	81610028	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	177	334	0	ENST00000298171.2:c.1626G>C	p.Met542Ile	p.M542I	ENST00000298171	NM_000369.2	542	atG/atC	10/10	0.598618247218734	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.603403969176723	3		334	347	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275742	41275742	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	140	475	0	ENST00000349496.5:c.1637A>G	p.Asp546Gly	p.D546G	ENST00000349496	NM_001904.3	546	gAt/gGt	10/15	0.603403969176723	4	FACETS	1	0.936	1	0.516	0.47	0.564	CLONAL	1	TRUE	2	0.603403969176723	4		475	721	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468294	50468294	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs971487743	NA	P-0043410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	120	551	1	ENST00000331340.3:c.1529C>T	p.Thr510Met	p.T510M	ENST00000331340	NM_006060.4	510	aCg/aTg	8/8	0.603403969176723	7	FACETS	0.811	0.73	0.897	0.135	0.121	0.15	CLONAL	1	TRUE	1	0.603403969176723	7		552	1230	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039350	47039351	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0043410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	350	692	0	ENST00000377604.3:c.974_975del	p.Val325AlafsTer55	p.V325Afs*55	ENST00000377604	NM_001204468.1	325	GTg/g	10/24	0.603403969176723	2	FACETS	0.986	0.946	1	0.986	0.946	1	CLONAL	2	TRUE	0	0.603403969176723	2		692	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0043425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	286	666	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.641394513516408	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.641394513516408	2		667	430	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458223	12458223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	76	441	0	ENST00000287820.6:c.840G>A	p.Met280Ile	p.M280I	ENST00000287820	NM_015869.4	280	atG/atA	6/7	0.587789454984298	3	FACETS	0.907	0.802	1	0.454	0.401	0.51	CLONAL	1	TRUE	1	0.641394513516408	3		441	345	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512359	120512359	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	81	395	0	ENST00000256646.2:c.883T>G	p.Cys295Gly	p.C295G	ENST00000256646	NM_024408.3	295	Tgc/Ggc	6/34	0.156151002259972	2	FACETS	0.856	0.763	0.954	0.428	0.381	0.477	INDETERMINATE	1	TRUE	0	0.641394513516408	2		395	295	SUCCESS
APC	324	MSKCC	GRCh37	5	112157616	112157617	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCTG	novel	NA	P-0043425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	18	365	0	ENST00000257430.4:c.1339_1342dup	p.Pro448LeufsTer13	p.P448Lfs*13	ENST00000257430	NM_000038.5	446	atc/aTCTGtc	11/16	0.627960641391503	2	FACETS	0.291	0.22	0.374	0.145	0.11	0.187	SUBCLONAL	1	TRUE	0	0.641394513516408	2		365	193	SUCCESS
APC	324	MSKCC	GRCh37	5	112176647	112176821	+	frameshift_variant	Frame_Shift_Del	DEL	AGGACACGTGTAAGAAAAAATGCAGACTCAAAAAATAATTTAAATGCTGAGAGAGTTTTCTCAGACAACAAAGATTCAAAGAAACAGAATTTGAAAAATAATTCCAAGGTCTTCAATGATAAGCTCCCAAATAATGAAGATAGAGTCAGAGGAAGTTTTGCTTTTGATTCACCTC	AGGACACGTGTAAGAAAAAATGCAGACTCAAAAAATAATTTAAATGCTGAGAGAGTTTTCTCAGACAACAAAGATTCAAAGAAACAGAATTTGAAAAATAATTCCAAGGTCTTCAATGATAAGCTCCCAAATAATGAAGATAGAGTCAGAGGAAGTTTTGCTTTTGATTCACCTC	-	novel	NA	P-0043425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	60	271	0	ENST00000257430.4:c.5357_5531del	p.Arg1786IlefsTer19	p.R1786Ifs*19	ENST00000257430	NM_000038.5	1786	AGGACACGTGTAAGAAAAAATGCAGACTCAAAAAATAATTTAAATGCTGAGAGAGTTTTCTCAGACAACAAAGATTCAAAGAAACAGAATTTGAAAAATAATTCCAAGGTCTTCAATGATAAGCTCCCAAATAATGAAGATAGAGTCAGAGGAAGTTTTGCTTTTGATTCACCTCat/at	16/16	0.627960641391503	2	FACETS	0.874	0.785	0.962	0.874	0.785	0.962	CLONAL	2	TRUE	0	0.641394513516408	2		271	107	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11181408	11181410	+	missense_variant	Missense_Mutation	TNP	GTC	GTC	ATA	novel	NA	P-0043425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	108	637	0	ENST00000361445.4:c.6826_6828delinsTAT	p.Asp2276Tyr	p.D2276Y	ENST00000361445	NM_004958.3	2276	GAC/TAT	49/58	0.156151002259972	2	FACETS	0.674	0.607	0.743	0.337	0.303	0.372	INDETERMINATE	1	TRUE	0	0.641394513516408	2		637	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0043472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	169	735	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.31643079007718	2	FACETS	0.863	0.797	0.931	0.863	0.797	0.931	CLONAL	2	TRUE	0	0.31643079007718	2		735	619	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245522	153245522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	90	351	0	ENST00000281708.4:c.1669G>A	p.Gly557Arg	p.G557R	ENST00000281708	NM_033632.3	557	Gga/Aga	11/12	0.31643079007718	3	FACETS	0.848	0.764	0.935	1	0.975	1	CLONAL	3	TRUE	1	0.31643079007718	3		351	259	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044510	47044510	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	103	624	0	ENST00000377604.3:c.2007C>G	p.Phe669Leu	p.F669L	ENST00000377604	NM_001204468.1	669	ttC/ttG	18/24	0.231531863181655	4	FACETS	1	0.937	1	0.356	0.318	0.396	CLONAL	1	TRUE	1	0.31643079007718	4		624	803	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442589	52442589	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	117	401	0	ENST00000460680.1:c.156G>A	p.Trp52Ter	p.W52*	ENST00000460680	NM_004656.3	52	tgG/tgA	4/17	0.44885017567297	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.44885017567297	1		401	403	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191473	10191474	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATACTCTGAAAGAGCGATGCCTC	novel	NA	P-0043488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	77	428	0	ENST00000256474.2:c.467_489dup	p.Gln164IlefsTer3	p.Q164Ifs*3	ENST00000256474	NM_000551.3	156	tat/tATACTCTGAAAGAGCGATGCCTCat	3/3	0.44885017567297	1	FACETS	0.672	0.593	0.756	0.672	0.593	0.756	SUBCLONAL	1	TRUE	0	0.44885017567297	1		428	396	SUCCESS
APC	324	MSKCC	GRCh37	5	112179791	112179791	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	160	262	0	ENST00000257430.4:c.8500C>G	p.His2834Asp	p.H2834D	ENST00000257430	NM_000038.5	2834	Cat/Gat	16/16	0.44885017567297	3	FACETS	0.994	0.921	1	0.994	0.921	1	CLONAL	2	TRUE	1	0.44885017567297	3		262	439	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0043512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	155	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.884	0.813	0.957	0.884	0.813	0.957	CLONAL	1	TRUE	1	0.608783590400143	2		485	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587782197	NA	P-0043512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	803	750	0	ENST00000269305.4:c.434T>A	p.Leu145Gln	p.L145Q	ENST00000269305	NM_001126112.2	145	cTg/cAg	5/11	0.580477413923409	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.608783590400143	2		750	1234	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107032	27107033	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0043512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	233	551	0	ENST00000324856.7:c.6644_6645del	p.Leu2215ProfsTer9	p.L2215Pfs*9	ENST00000324856	NM_006015.4	2215	CTc/c	20/20	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.608783590400143	2		551	763	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115558	108115558	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs886042866	NA	P-0043512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	143	405	0	ENST00000278616.4:c.706C>G	p.Leu236Val	p.L236V	ENST00000278616	NM_000051.3	236	Ctt/Gtt	7/63	1	2	FACETS	0.965	0.886	1	0.965	0.886	1	CLONAL	1	TRUE	1	0.608783590400143	2		405	487	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347829	347829	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs149536239	NA	P-0043512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	271	892	0	ENST00000262320.3:c.1677G>C	p.Gln559His	p.Q559H	ENST00000262320	NM_003502.3	559	caG/caC	6/11	0.39233436972791	1	FACETS	0.674	0.633	0.715	0.674	0.633	0.715	SUBCLONAL	1	TRUE	0	0.608783590400143	1		892	919	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992897	72992897	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	133	619	0	ENST00000268489.5:c.1148C>G	p.Ser383Cys	p.S383C	ENST00000268489	NM_006885.3	383	tCc/tGc	2/10	0.39233436972791	1	FACETS	0.419	0.38	0.459	0.419	0.38	0.459	SUBCLONAL	1	TRUE	0	0.608783590400143	1		619	726	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593559	48593559	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0043512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	100	195	0	ENST00000342988.3:c.1308+2T>G		p.X436_splice	ENST00000342988	NM_005359.5	436			0.608783590400143	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.608783590400143	1		195	225	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207050	1207050	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	393	789	0	ENST00000326873.7:c.138C>G	p.Ile46Met	p.I46M	ENST00000326873	NM_000455.4	46	atC/atG	1/10	0.608783590400143	0	FACETS	0.604	0.578	0.631			1	SUBCLONAL	1	TRUE	0	0.608783590400143	0		789	836	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118698	11118698	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	290	555	0	ENST00000358026.2:c.2122G>C	p.Glu708Gln	p.E708Q	ENST00000358026	NM_001128849.1	708	Gag/Cag	14/36	0.608783590400143	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.608783590400143	1		555	619	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155478	47155478	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	120	303	0	ENST00000409792.3:c.4603A>G	p.Asn1535Asp	p.N1535D	ENST00000409792	NM_014159.6	1535	Aat/Gat	5/21	1	2	FACETS	0.948	0.863	1	0.948	0.863	1	CLONAL	1	TRUE	1	0.608783590400143	2		303	416	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851228	151851228	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	96	275	0	ENST00000262189.6:c.12143C>T	p.Ser4048Leu	p.S4048L	ENST00000262189	NM_170606.2	4048	tCa/tTa	48/59	1	2	FACETS	0.805	0.722	0.891	0.805	0.722	0.891	CLONAL	1	TRUE	1	0.608783590400143	2		275	392	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118632	11118637	+	frameshift_variant	Frame_Shift_Del	DEL	GAGAAG	GAGAAG	AAAAA	novel	NA	P-0043512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	258	628	1	ENST00000358026.2:c.2056_2061delinsAAAAA	p.Glu686LysfsTer88	p.E686Kfs*88	ENST00000358026	NM_001128849.1	686	GAGAAG/AAAAA	14/36	0.608783590400143	1	FACETS	0.962	0.908	1	0.962	0.908	1	CLONAL	1	TRUE	0	0.608783590400143	1		629	613	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0043515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	211	275	1	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.525282055966368	2	FACETS	0.916	0.863	0.97	0.916	0.863	0.97	CLONAL	2	TRUE	0	0.531815120835004	2		276	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0043515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	298	740	0	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	0.531815120835004	2	FACETS	1	0.966	1	0.517	0.487	0.548	CLONAL	1	TRUE	0	0.531815120835004	2		740	1083	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984374	201984377	+	frameshift_variant	Frame_Shift_Del	DEL	GGCC	GGCC	-	novel	NA	P-0043515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	266	599	0	ENST00000359651.3:c.1042_1045del	p.Arg348AspfsTer98	p.R348Dfs*98	ENST00000359651		347	GGCCgg/gg	8/8	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.531815120835004	2		599	970	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77051695	77051695	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145870074	NA	P-0043515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	173	396	2	ENST00000356341.3:c.1112G>A	p.Arg371His	p.R371H	ENST00000356341	NM_002576.4	371	cGt/cAt	11/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.531815120835004	2		398	595	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	58	296	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.644	0.555	0.739	0.644	0.555	0.739	SUBCLONAL	1	TRUE	1	0.476709403647963	2		297	378	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	117	609	1	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.78	0.705	0.859	0.78	0.705	0.859	SUBCLONAL	1	TRUE	1	0.476709403647963	2		610	629	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339111	65339111	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	87	408	7	ENST00000342505.4:c.425del	p.Lys142ArgfsTer26	p.K142Rfs*26	ENST00000342505	NM_002227.2	142	aAg/ag	5/25	1	2	FACETS	0.759	0.674	0.849	0.759	0.674	0.849	SUBCLONAL	1	TRUE	1	0.476709403647963	2		415	481	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	110	377	2	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	0.839	0.756	0.926	0.839	0.756	0.926	CLONAL	1	TRUE	1	0.476709403647963	2		379	550	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612209	1612209	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs915880927	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	74	384	0	ENST00000344749.5:c.1810C>T	p.Arg604Ter	p.R604*	ENST00000344749	NM_001136139.2	604	Cga/Tga	18/19	1	2	FACETS	0.729	0.641	0.823	0.729	0.641	0.823	SUBCLONAL	1	TRUE	1	0.476709403647963	2		384	426	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245720	46245720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	94	381	0	ENST00000334344.6:c.3814C>T	p.Arg1272Ter	p.R1272*	ENST00000334344	NM_152641.2	1272	Cga/Tga	15/21	1	2	FACETS	0.802	0.716	0.892	0.802	0.716	0.892	CLONAL	1	TRUE	1	0.476709403647963	2		381	492	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508835	106508835	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	94	442	0	ENST00000359195.3:c.829C>T	p.Arg277Trp	p.R277W	ENST00000359195	NM_002649.2	277	Cgg/Tgg	2/11	1	2	FACETS	0.718	0.641	0.801	0.718	0.641	0.801	SUBCLONAL	1	TRUE	1	0.476709403647963	2		442	549	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991949	72991949	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs753977275	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	96	522	3	ENST00000268489.5:c.2096del	p.Gly699AlafsTer125	p.G699Afs*125	ENST00000268489	NM_006885.3	699	gGc/gc	2/10	1	2	FACETS	0.76	0.679	0.845	0.76	0.679	0.845	SUBCLONAL	1	TRUE	1	0.476709403647963	2		525	530	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749573	41749573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144824336	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	149	574	0	ENST00000301178.4:c.1498G>A	p.Val500Met	p.V500M	ENST00000301178	NM_021913.4	500	Gtg/Atg	12/20	1	2	FACETS	0.862	0.789	0.938	0.862	0.789	0.938	CLONAL	1	TRUE	1	0.476709403647963	2		574	725	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149982977	149982977	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	47	396	0	ENST00000253339.5:c.3281C>T	p.Pro1094Leu	p.P1094L	ENST00000253339		1094	cCg/cTg	7/7	1	2	FACETS	0.795	0.677	0.923	0.795	0.677	0.923	CLONAL	1	TRUE	1	0.476709403647963	2		396	248	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696688	47696688	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519971	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	91	423	0	ENST00000347630.2:c.260A>C	p.Tyr87Ser	p.Y87S	ENST00000347630	NM_001007230.1	87	tAc/tCc	5/11	1	2	FACETS	0.894	0.798	0.995	0.894	0.798	0.995	CLONAL	1	TRUE	1	0.476709403647963	2		423	427	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106333	27106333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201604768	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	147	509	0	ENST00000324856.7:c.5944G>A	p.Val1982Ile	p.V1982I	ENST00000324856	NM_006015.4	1982	Gtc/Atc	20/20	1	2	FACETS	0.988	0.906	1	0.988	0.906	1	CLONAL	1	TRUE	1	0.476709403647963	2		509	624	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449577	32449577	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1060501253	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	147	586	3	ENST00000332351.3:c.797del	p.Pro266ArgfsTer20	p.P266Rfs*20	ENST00000332351	NM_024426.4	266	cCg/cg	3/10	1	2	FACETS	0.947	0.868	1	0.947	0.868	1	CLONAL	1	TRUE	1	0.476709403647963	2		589	651	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630173	100630173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141488935	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	93	213	1	ENST00000308731.7:c.100G>A	p.Val34Met	p.V34M	ENST00000308731	NM_000061.2	34	Gtg/Atg	2/19	1	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.476709403647963	1		214	255	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78914339	78914339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147686617	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	152	564	0	ENST00000306801.3:c.2963G>A	p.Arg988Gln	p.R988Q	ENST00000306801	NM_020761.2	988	cGg/cAg	25/34	1	2	FACETS	0.819	0.75	0.891	0.819	0.75	0.891	CLONAL	1	TRUE	1	0.476709403647963	2		564	779	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655248	45655248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs533193731	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	137	565	0	ENST00000407780.3:c.604G>A	p.Val202Met	p.V202M	ENST00000407780	NM_001283052.1	202	Gtg/Atg	4/7	1	2	FACETS	0.879	0.802	0.96	0.879	0.802	0.96	CLONAL	1	TRUE	1	0.476709403647963	2		565	654	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572041	64572041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	153	583	0	ENST00000312049.6:c.1598G>A	p.Ser533Asn	p.S533N	ENST00000312049	NM_130799.2	533	aGc/aAc	10/10	1	2	FACETS	0.883	0.809	0.96	0.883	0.809	0.96	CLONAL	1	TRUE	1	0.476709403647963	2		583	727	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439750	49439750	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs200119692	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	119	473	0	ENST00000301067.7:c.4694C>T	p.Ala1565Val	p.A1565V	ENST00000301067	NM_003482.3	1565	gCg/gTg	18/54	1	2	FACETS	0.776	0.702	0.854	0.776	0.702	0.854	SUBCLONAL	1	TRUE	1	0.476709403647963	2		473	643	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101967	11101967	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779161503	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	145	576	1	ENST00000358026.2:c.1387G>A	p.Glu463Lys	p.E463K	ENST00000358026	NM_001128849.1	463	Gag/Aag	8/36	1	2	FACETS	0.798	0.729	0.871	0.798	0.729	0.871	SUBCLONAL	1	TRUE	1	0.476709403647963	2		577	762	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155594	106155594	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1560540913	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	84	322	0	ENST00000380013.4:c.499del	p.Ser167GlnfsTer16	p.S167Qfs*16	ENST00000380013	NM_001127208.2	165	agT/ag	3/11	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.476709403647963	2		322	347	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961007	79961007	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	82	426	0	ENST00000265081.6:c.408del	p.Lys136AsnfsTer2	p.K136Nfs*2	ENST00000265081	NM_002439.4	135	gAa/ga	3/24	0.42629599556069	1	FACETS	0.843	0.75	0.939	0.843	0.75	0.939	CLONAL	1	TRUE	0	0.476709403647963	1		426	311	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480411	89480411	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	87	271	0	ENST00000336596.2:c.2248C>T	p.Arg750Trp	p.R750W	ENST00000336596	NM_005233.5	750	Cgg/Tgg	13/17	1	2	FACETS	0.966	0.861	1	0.966	0.861	1	CLONAL	1	TRUE	1	0.476709403647963	2		271	378	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023445	31023445	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	88	426	0	ENST00000375687.4:c.2930A>C	p.Gln977Pro	p.Q977P	ENST00000375687	NM_015338.5	977	cAg/cCg	13/13	1	2	FACETS	0.686	0.609	0.768	0.686	0.609	0.768	SUBCLONAL	1	TRUE	1	0.476709403647963	2		426	538	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829787	76829787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057517948	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	40	234	0	ENST00000373344.5:c.6254G>A	p.Arg2085His	p.R2085H	ENST00000373344	NM_000489.3	2085	cGt/cAt	28/35	1	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.476709403647963	1		234	116	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88672089	88672089	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	64	218	0	ENST00000372037.3:c.623A>T	p.Asp208Val	p.D208V	ENST00000372037	NM_004329.2	208	gAc/gTc	8/13	0.440980316264388	2	FACETS	0.877	0.78	0.977	0.877	0.78	0.977	CLONAL	2	TRUE	0	0.476709403647963	2		218	153	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413587	32413587	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	82	355	0	ENST00000332351.3:c.1363del	p.Thr455LeufsTer12	p.T455Lfs*12	ENST00000332351	NM_024426.4	455	Act/ct	9/10	1	2	FACETS	0.738	0.653	0.829	0.738	0.653	0.829	SUBCLONAL	1	TRUE	1	0.476709403647963	2		355	466	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129428	64129428	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	128	564	0	ENST00000334205.4:c.860C>A	p.Ala287Glu	p.A287E	ENST00000334205	NM_003942.2	287	gCg/gAg	8/17	1	2	FACETS	0.745	0.676	0.817	0.745	0.676	0.817	SUBCLONAL	1	TRUE	1	0.476709403647963	2		564	721	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102098217	102098217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	94	370	0	ENST00000282441.5:c.1181G>A	p.Arg394Gln	p.R394Q	ENST00000282441	NM_001130145.2	394	cGa/cAa	8/9	1	2	FACETS	0.932	0.835	1	0.932	0.835	1	CLONAL	1	TRUE	1	0.476709403647963	2		370	423	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445949	49445949	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	193	818	1	ENST00000301067.7:c.1517del	p.Pro506HisfsTer424	p.P506Hfs*424	ENST00000301067	NM_003482.3	506	cCa/ca	10/54	1	2	FACETS	0.845	0.782	0.911	0.845	0.782	0.911	CLONAL	1	TRUE	1	0.476709403647963	2		819	958	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489093	56489093	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1200363001	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	42	441	0	ENST00000267101.3:c.1912G>A	p.Gly638Ser	p.G638S	ENST00000267101	NM_001982.3	638	Ggc/Agc	16/28	1	2	FACETS	0.382	0.319	0.452	0.382	0.319	0.452	SUBCLONAL	1	TRUE	1	0.476709403647963	2		441	461	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250262	133250262	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	117	507	1	ENST00000320574.5:c.1258G>T	p.Gly420Cys	p.G420C	ENST00000320574	NM_006231.2	420	Ggc/Tgc	13/49	1	2	FACETS	0.748	0.676	0.824	0.748	0.676	0.824	SUBCLONAL	1	TRUE	1	0.476709403647963	2		508	656	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121876	2121876	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876658578	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	130	588	1	ENST00000219476.3:c.2038C>T	p.Arg680Trp	p.R680W	ENST00000219476	NM_000548.3	680	Cgg/Tgg	19/42	1	2	FACETS	0.917	0.834	1	0.917	0.834	1	CLONAL	1	TRUE	1	0.476709403647963	2		589	595	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827670	72827670	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	123	491	0	ENST00000268489.5:c.8911C>G	p.Pro2971Ala	p.P2971A	ENST00000268489	NM_006885.3	2971	Ccc/Gcc	9/10	1	2	FACETS	0.963	0.875	1	0.963	0.875	1	CLONAL	1	TRUE	1	0.476709403647963	2		491	536	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244170	5244170	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	151	655	0	ENST00000357368.4:c.1312C>T	p.Leu438Phe	p.L438F	ENST00000357368	NM_002850.3	438	Ctc/Ttc	11/38	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.476709403647963	2		655	628	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10283821	10283821	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	100	414	0	ENST00000340748.4:c.665C>A	p.Pro222His	p.P222H	ENST00000340748		222	cCt/cAt	8/40	1	2	FACETS	0.802	0.719	0.89	0.802	0.719	0.89	CLONAL	1	TRUE	1	0.476709403647963	2		414	523	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258538	19258538	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	143	652	0	ENST00000162023.5:c.362del	p.Gly121ValfsTer102	p.G121Vfs*102	ENST00000162023		121	gGt/gt	8/13	1	2	FACETS	0.805	0.735	0.879	0.805	0.735	0.879	CLONAL	1	TRUE	1	0.476709403647963	2		652	745	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635617	47635617	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750970	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	99	438	0	ENST00000233146.2:c.289C>T	p.Gln97Ter	p.Q97*	ENST00000233146	NM_000251.2	97	Cag/Tag	2/16	0.476709403647963	1	FACETS	0.884	0.796	0.975	0.884	0.796	0.975	CLONAL	1	TRUE	0	0.476709403647963	1		438	358	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141668	202141668	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	60	354	1	ENST00000358485.4:c.956G>T	p.Arg319Met	p.R319M	ENST00000358485	NM_001080125.1	319	aGg/aTg	7/9	1	2	FACETS	0.717	0.621	0.82	0.717	0.621	0.82	SUBCLONAL	1	TRUE	1	0.476709403647963	2		355	351	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866343	42866343	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266959483	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	142	591	0	ENST00000398585.3:c.289G>A	p.Ala97Thr	p.A97T	ENST00000398585	NM_001135099.1	97	Gct/Act	3/14	1	2	FACETS	0.796	0.727	0.869	0.796	0.727	0.869	SUBCLONAL	1	TRUE	1	0.476709403647963	2		591	748	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967304	38967304	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	67	236	1	ENST00000357387.3:c.1177G>T	p.Ala393Ser	p.A393S	ENST00000357387	NM_152756.3	393	Gca/Tca	14/38	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.476709403647963	2		237	270	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720871	176720871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1260544167	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	96	438	0	ENST00000439151.2:c.6502G>A	p.Gly2168Arg	p.G2168R	ENST00000439151	NM_022455.4	2168	Ggg/Agg	23/23	1	2	FACETS	0.846	0.757	0.94	0.846	0.757	0.94	CLONAL	1	TRUE	1	0.476709403647963	2		438	476	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839783	27839783	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	118	448	0	ENST00000328488.2:c.311T>C	p.Leu104Pro	p.L104P	ENST00000328488	NM_003533.2	104	cTa/cCa	1/1	1	2	FACETS	0.831	0.752	0.914	0.831	0.752	0.914	CLONAL	1	TRUE	1	0.476709403647963	2		448	596	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930109	68930109	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	131	367	0	ENST00000288368.4:c.170C>T	p.Ala57Val	p.A57V	ENST00000288368	NM_024870.2	57	gCa/gTa	2/40	0.36491442897653	3	FACETS	0.818	0.749	0.889	0.818	0.749	0.889	CLONAL	2	TRUE	1	0.476709403647963	3		367	416	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248069	110248069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867964623	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	37	405	0	ENST00000374672.4:c.1403C>T	p.Ser468Leu	p.S468L	ENST00000374672	NM_004235.4	468	tCg/tTg	5/5	1	2	FACETS	0.256	0.21	0.308	0.256	0.21	0.308	SUBCLONAL	1	TRUE	1	0.476709403647963	2		405	606	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399469	139399469	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	175	617	0	ENST00000277541.6:c.4674del	p.Leu1559TrpfsTer21	p.L1559Wfs*21	ENST00000277541	NM_017617.3	1558	ggG/gg	26/34	1	2	FACETS	0.949	0.875	1	0.949	0.875	1	CLONAL	1	TRUE	1	0.476709403647963	2		617	774	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411846	63411846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	202	370	0	ENST00000330258.3:c.1321C>T	p.Pro441Ser	p.P441S	ENST00000330258	NM_152424.3	441	Cca/Tca	2/2	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.476709403647963	1		370	442	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344033	70344033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	123	307	0	ENST00000374080.3:c.1769G>A	p.Arg590Gln	p.R590Q	ENST00000374080		590	cGg/cAg	13/45	1	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.476709403647963	1		307	352	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76777854	76777854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782342279	NA	P-0043520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	63	216	2	ENST00000373344.5:c.6862C>T	p.Arg2288Cys	p.R2288C	ENST00000373344	NM_000489.3	2288	Cgt/Tgt	32/35	1	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.476709403647963	1		218	183	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0043564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	61	731	1	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.14	2		732	799	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574829	41574829	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs768061933	NA	P-0043583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	373	449	0	ENST00000263253.7:c.7114A>G	p.Met2372Val	p.M2372V	ENST00000263253	NM_001429.3	2372	Atg/Gtg	31/31	1	2	FACETS	0.904	0.859	0.948	1	0.997	1	CLONAL	4	TRUE	1	0.2	2		449	1032	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009261	69009261	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	185	96	0	ENST00000288368.4:c.2378A>G	p.Asp793Gly	p.D793G	ENST00000288368	NM_024870.2	793	gAc/gGc	22/40	1	2	FACETS	1	0.969	1	1	0.995	1	CLONAL	3	TRUE	1	0.2	2		96	572	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216554	7216567	+	frameshift_variant	Frame_Shift_Del	DEL	GGTTAGCATGTTCC	GGTTAGCATGTTCC	T	novel	NA	P-0043583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	273	355	0	ENST00000380728.2:c.768_781delinsA	p.Met256IlefsTer85	p.M256Ifs*85	ENST00000380728		256	atGGAACATGCTAACCag/atAag	9/11	0.0682292362649801	3	FACETS	0.989	0.941	1			1	INDETERMINATE	6	TRUE	NA	0.2	3		355	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0043588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	238	696	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.279906753264405	2	FACETS	0.994	0.931	1	0.994	0.931	1	CLONAL	2	TRUE	0	0.306635542599671	2		696	781	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0043588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	25	268	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.306635542599671	1	FACETS	0.673	0.534	0.832	0.673	0.534	0.832	SUBCLONAL	1	TRUE	0	0.306635542599671	1		268	205	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307188	65307188	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	86	585	1	ENST00000342505.4:c.2500C>T	p.Gln834Ter	p.Q834*	ENST00000342505	NM_002227.2	834	Cag/Tag	18/25	1	2	FACETS	0.888	0.786	0.996	0.888	0.786	0.996	CLONAL	1	TRUE	1	0.306635542599671	2		586	632	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029303	14029303	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	68	424	0	ENST00000311895.7:c.1515del	p.Glu506ArgfsTer13	p.E506Rfs*13	ENST00000311895	NM_005236.2	505	gAa/ga	8/11	0.294433247374193	3	FACETS	0.935	0.815	1	0.468	0.407	0.533	CLONAL	1	TRUE	1	0.306635542599671	3		424	547	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128246829	128246829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1389464216	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	58	687	0	ENST00000265960.3:c.1100C>T	p.Ser367Leu	p.S367L	ENST00000265960	NM_001006617.1	367	tCg/tTg	9/12	1	2	FACETS	0.373	0.319	0.432	0.373	0.319	0.432	SUBCLONAL	1	TRUE	1	0.34	2		687	915	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	92	672	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.956	0.852	1	0.956	0.852	1	CLONAL	1	TRUE	1	0.34	2		672	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	141	735	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.733	0.666	0.803	0.733	0.666	0.803	SUBCLONAL	1	TRUE	1	0.34	2		735	1132	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	55	792	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.268	0.228	0.313	0.268	0.228	0.313	SUBCLONAL	1	TRUE	1	0.34	2		793	1205	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514495	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	105	809	0	ENST00000269305.4:c.542G>A	p.Arg181His	p.R181H	ENST00000269305	NM_001126112.2	181	cGc/cAc	5/11	1	2	FACETS	0.649	0.58	0.722	0.649	0.58	0.722	SUBCLONAL	1	TRUE	1	0.34	2		809	952	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	98	806	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.545	0.485	0.61	0.545	0.485	0.61	SUBCLONAL	1	TRUE	1	0.34	2		806	1057	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	45	385	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.655	0.552	0.769	0.655	0.552	0.769	SUBCLONAL	1	TRUE	1	0.34	2		385	404	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	67	474	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.776	0.675	0.884	0.776	0.675	0.884	SUBCLONAL	1	TRUE	1	0.34	2		474	508	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317111	87317111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	47	467	0	ENST00000277120.3:c.250G>A	p.Glu84Lys	p.E84K	ENST00000277120		84	Gaa/Aaa	3/19	1	2	FACETS	0.531	0.448	0.622	0.531	0.448	0.622	SUBCLONAL	1	TRUE	1	0.34	2		467	521	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545585	106545585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376453517	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	25	387	0	ENST00000359195.3:c.3062G>A	p.Arg1021His	p.R1021H	ENST00000359195	NM_002649.2	1021	cGt/cAt	11/11	1	2	FACETS	0.377	0.297	0.47	0.377	0.297	0.47	SUBCLONAL	1	TRUE	1	0.34	2		387	390	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261434	16261434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	84	668	1	ENST00000375759.3:c.8699C>T	p.Ser2900Leu	p.S2900L	ENST00000375759	NM_015001.2	2900	tCg/tTg	11/15	1	2	FACETS	0.563	0.497	0.635	0.563	0.497	0.635	SUBCLONAL	1	TRUE	1	0.34	2		669	877	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102080254	102080254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193100333	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	98	350	0	ENST00000282441.5:c.991C>T	p.Arg331Trp	p.R331W	ENST00000282441	NM_001130145.2	331	Cgg/Tgg	6/9	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.34	2		350	408	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37058999	37058999	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs63751194	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	35	390	1	ENST00000231790.2:c.793C>T	p.Arg265Cys	p.R265C	ENST00000231790	NM_000249.3	265	Cgt/Tgt	10/19	1	2	FACETS	0.451	0.37	0.543	0.451	0.37	0.543	SUBCLONAL	1	TRUE	1	0.34	2		391	456	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692782	89692782	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	37	264	0	ENST00000371953.3:c.266C>A	p.Pro89His	p.P89H	ENST00000371953	NM_000314.4	89	cCt/cAt	5/9	1	2	FACETS	0.777	0.644	0.925	0.777	0.644	0.925	CLONAL	1	TRUE	1	0.34	2		264	280	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	38	388	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.837	0.696	0.993	0.837	0.696	0.993	CLONAL	1	TRUE	1	0.34	2		388	267	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	85	348	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	0.772	0.689	0.859	1	0.981	1	SUBCLONAL	2	TRUE	1	0.34	2		348	324	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342421	70342421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771266719	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	97	644	0	ENST00000374080.3:c.1312C>T	p.Arg438Cys	p.R438C	ENST00000374080		438	Cgc/Tgc	9/45	1	2	FACETS	0.597	0.532	0.668	0.597	0.532	0.668	SUBCLONAL	1	TRUE	1	0.34	2		644	955	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242457	55242457	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759256622	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	88	454	0	ENST00000275493.2:c.2227G>A	p.Ala743Thr	p.A743T	ENST00000275493	NM_005228.3	743	Gct/Act	19/28	1	2	FACETS	0.853	0.757	0.955	0.853	0.757	0.955	CLONAL	1	TRUE	1	0.34	2		454	607	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	10	555	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.131	0.088	0.185	0.131	0.088	0.185	SUBCLONAL	1	TRUE	1	0.34	2		555	450	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090381	77090381	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369339512	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	64	507	0	ENST00000356341.3:c.344C>T	p.Ser115Leu	p.S115L	ENST00000356341	NM_002576.4	115	tCg/tTg	4/15	1	2	FACETS	0.45	0.389	0.517	0.45	0.389	0.517	SUBCLONAL	1	TRUE	1	0.34	2		507	836	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681353	88681353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140592056	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	48	132	0	ENST00000372037.3:c.1243G>A	p.Glu415Lys	p.E415K	ENST00000372037	NM_004329.2	415	Gaa/Aaa	11/13	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.34	2		132	246	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612175	189612175	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1560311554	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	110	657	0	ENST00000264731.3:c.1927C>T	p.Arg643Ter	p.R643*	ENST00000264731	NM_003722.4	643	Cga/Tga	14/14	1	2	FACETS	0.685	0.615	0.76	0.685	0.615	0.76	SUBCLONAL	1	TRUE	1	0.34	2		657	944	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7168073	7168073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754537233	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	203	495	2	ENST00000302850.5:c.1516C>T	p.Arg506Trp	p.R506W	ENST00000302850	NM_000208.2	506	Cgg/Tgg	7/22	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.34	2		497	827	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546847	9546847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	69	627	0	ENST00000353224.5:c.1175C>T	p.Ser392Leu	p.S392L	ENST00000353224	NM_177990.2	392	tCg/tTg	5/10	1	2	FACETS	0.584	0.508	0.666	0.584	0.508	0.666	SUBCLONAL	1	TRUE	1	0.34	2		627	695	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706977	117706977	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764959275	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	105	607	0	ENST00000368508.3:c.2173G>A	p.Asp725Asn	p.D725N	ENST00000368508	NM_002944.2	725	Gac/Aac	15/43	1	2	FACETS	0.727	0.651	0.809	0.727	0.651	0.809	SUBCLONAL	1	TRUE	1	0.34	2		607	849	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267385	7267385	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1189720431	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	206	519	0	ENST00000302850.5:c.623G>A	p.Arg208Gln	p.R208Q	ENST00000302850	NM_000208.2	208	cGa/cAa	2/22	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.34	2		519	876	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518099	8518099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764400127	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	90	519	0	ENST00000356435.5:c.1292C>T	p.Ser431Leu	p.S431L	ENST00000356435		431	tCg/tTg	10/35	1	2	FACETS	0.796	0.707	0.891	0.796	0.707	0.891	SUBCLONAL	1	TRUE	1	0.34	2		519	665	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225939	133225939	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs754411056	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	103	886	0	ENST00000320574.5:c.3958C>T	p.Arg1320Ter	p.R1320*	ENST00000320574	NM_006231.2	1320	Cga/Tga	31/49	1	2	FACETS	0.556	0.496	0.62	0.556	0.496	0.62	SUBCLONAL	1	TRUE	1	0.34	2		886	1089	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285609	38285609	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs762665767	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	77	326	0	ENST00000425967.3:c.544G>A	p.Val182Ile	p.V182I	ENST00000425967	NM_001174067.1	182	Gta/Ata	6/19	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.34	2		326	432	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720870	89720870	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1554825652	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	87	199	0	ENST00000371953.3:c.1021T>G	p.Phe341Val	p.F341V	ENST00000371953	NM_000314.4	341	Ttt/Gtt	8/9	1	2	FACETS	0.792	0.708	0.88	1	0.982	1	SUBCLONAL	2	TRUE	1	0.34	2		199	323	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143551	108143551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201780199	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	26	308	0	ENST00000278616.4:c.3256C>T	p.Arg1086Cys	p.R1086C	ENST00000278616	NM_000051.3	1086	Cgc/Tgc	22/63	1	2	FACETS	0.397	0.314	0.492	0.397	0.314	0.492	SUBCLONAL	1	TRUE	1	0.34	2		308	385	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123025128	123025128	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	81	75	0	ENST00000355640.3:c.1018A>C	p.Asn340His	p.N340H	ENST00000355640		340	Aac/Cac	4/7	1	2	FACETS	0.869	0.776	0.967	1	0.983	1	CLONAL	2	TRUE	1	0.34	2		75	274	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132438	11132438	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794284	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	145	744	1	ENST00000358026.2:c.2654G>A	p.Arg885His	p.R885H	ENST00000358026	NM_001128849.1	885	cGc/cAc	19/36	1	2	FACETS	0.796	0.725	0.87	0.796	0.725	0.87	SUBCLONAL	1	TRUE	1	0.34	2		745	1072	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956220	55956220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190050670	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	120	493	0	ENST00000263923.4:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000263923	NM_002253.2	1032	cGa/cAa	23/30	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.34	2		493	639	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467646	66467646	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	66	299	0	ENST00000273854.3:c.623del	p.Lys208ArgfsTer60	p.K208Rfs*60	ENST00000273854	NM_004439.5	208	aAg/ag	3/18	1	2	FACETS	0.931	0.811	1	0.931	0.811	1	CLONAL	1	TRUE	1	0.34	2		299	417	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873660	35873660	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs201559094	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	44	311	0	ENST00000303115.3:c.616C>T	p.Arg206Ter	p.R206*	ENST00000303115	NM_002185.3	206	Cga/Tga	5/8	1	2	FACETS	0.63	0.529	0.741	0.63	0.529	0.741	SUBCLONAL	1	TRUE	1	0.34	2		311	411	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030613	48030613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779617676	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	162	542	1	ENST00000234420.5:c.3227G>A	p.Arg1076His	p.R1076H	ENST00000234420	NM_000179.2	1076	cGc/cAc	5/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.34	2		543	656	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636143	28636143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371663652	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	106	576	0	ENST00000241453.7:c.229G>A	p.Glu77Lys	p.E77K	ENST00000241453	NM_004119.2	77	Gaa/Aaa	3/24	1	2	FACETS	0.618	0.553	0.687	0.618	0.553	0.687	SUBCLONAL	1	TRUE	1	0.34	2		576	1009	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25498386	25498386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1274769751	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	42	588	0	ENST00000264709.3:c.475G>A	p.Glu159Lys	p.E159K	ENST00000264709	NM_175629.2	159	Gaa/Aaa	5/23	1	2	FACETS	0.338	0.282	0.402	0.338	0.282	0.402	SUBCLONAL	1	TRUE	1	0.34	2		588	730	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845086	128845086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761395599	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	206	788	1	ENST00000249373.3:c.580G>A	p.Glu194Lys	p.E194K	ENST00000249373	NM_005631.4	194	Gaa/Aaa	3/12	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.34	2		789	1187	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941657	48941657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1060503077	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	12	248	0	ENST00000267163.4:c.967G>T	p.Glu323Ter	p.E323*	ENST00000267163	NM_000321.2	323	Gaa/Taa	10/27	1	2	FACETS	0.48	0.339	0.653	0.48	0.339	0.653	SUBCLONAL	1	TRUE	1	0.34	2		248	147	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337650	73337650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	46	198	0	ENST00000377767.4:c.2066G>A	p.Arg689Gln	p.R689Q	ENST00000377767	NM_014953.3	689	cGa/cAa	16/21	1	2	FACETS	0.96	0.813	1	0.96	0.813	1	CLONAL	1	TRUE	1	0.34	2		198	282	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601972	43601972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774829203	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	157	841	2	ENST00000355710.3:c.1016C>T	p.Ser339Leu	p.S339L	ENST00000355710	NM_020975.4	339	tCg/tTg	5/20	1	2	FACETS	0.802	0.733	0.874	0.802	0.733	0.874	CLONAL	1	TRUE	1	0.34	2		843	1152	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395776	45395776	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	53	372	0	ENST00000262160.6:c.358C>T	p.Arg120Ter	p.R120*	ENST00000262160	NM_005901.5	120	Cga/Tga	4/11	1	2	FACETS	0.718	0.614	0.832	0.718	0.614	0.832	SUBCLONAL	1	TRUE	1	0.34	2		372	434	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100871	27100871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761500441	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	107	528	1	ENST00000324856.7:c.4153G>A	p.Glu1385Lys	p.E1385K	ENST00000324856	NM_006015.4	1385	Gaa/Aaa	18/20	1	2	FACETS	0.797	0.714	0.884	0.797	0.714	0.884	SUBCLONAL	1	TRUE	1	0.34	2		529	790	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520000	106520000	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs759433704	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	67	234	0	ENST00000359195.3:c.2428C>A	p.Pro810Thr	p.P810T	ENST00000359195	NM_002649.2	810	Cca/Aca	6/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.34	2		234	264	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890221	72890221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752101890	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	74	475	0	ENST00000325599.8:c.461G>A	p.Arg154Gln	p.R154Q	ENST00000325599	NM_018130.2	154	cGa/cAa	4/11	1	2	FACETS	0.673	0.589	0.763	0.673	0.589	0.763	SUBCLONAL	1	TRUE	1	0.34	2		475	647	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521103	187521103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs183364307	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	48	475	0	ENST00000441802.2:c.12052G>A	p.Ala4018Thr	p.A4018T	ENST00000441802	NM_005245.3	4018	Gcc/Acc	22/27	1	2	FACETS	0.387	0.326	0.455	0.387	0.326	0.455	SUBCLONAL	1	TRUE	1	0.34	2		475	729	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59886057	59886057	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759031349	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	54	486	0	ENST00000259008.2:c.689C>T	p.Ser230Leu	p.S230L	ENST00000259008	NM_032043.2	230	tCg/tTg	7/20	1	2	FACETS	0.581	0.496	0.674	0.581	0.496	0.674	SUBCLONAL	1	TRUE	1	0.34	2		486	547	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50481162	50481162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	92	448	0	ENST00000394963.4:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000394963	NM_003076.4	183	cGa/cAa	5/13	1	2	FACETS	0.831	0.739	0.929	0.831	0.739	0.929	CLONAL	1	TRUE	1	0.34	2		448	651	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172385	108172385	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764389018	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	70	296	0	ENST00000278616.4:c.5188C>T	p.Arg1730Ter	p.R1730*	ENST00000278616	NM_000051.3	1730	Cga/Tga	35/63	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.34	2		296	319	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919244	48919244	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913296	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	12	29	0	ENST00000267163.4:c.409G>T	p.Glu137Ter	p.E137*	ENST00000267163	NM_000321.2	137	Gaa/Taa	4/27	1	2	FACETS	0.767	0.546	1	0.767	0.546	1	CLONAL	1	TRUE	1	0.34	2		29	92	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990402	69990402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765051386	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	31	210	0	ENST00000394351.3:c.361G>A	p.Asp121Asn	p.D121N	ENST00000394351	NM_000248.3	121	Gat/Aat	4/9	1	2	FACETS	0.691	0.561	0.836	0.691	0.561	0.836	SUBCLONAL	1	TRUE	1	0.34	2		210	264	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442709	99442709	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1567185393	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	176	540	0	ENST00000268035.6:c.1106A>G	p.Asn369Ser	p.N369S	ENST00000268035	NM_000875.3	369	aAc/aGc	5/21	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.34	2		540	776	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351098	89351098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140370885	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	111	730	3	ENST00000301030.4:c.1852G>A	p.Ala618Thr	p.A618T	ENST00000301030	NM_001256183.1	618	Gct/Act	9/13	1	2	FACETS	0.686	0.616	0.761	0.686	0.616	0.761	SUBCLONAL	1	TRUE	1	0.34	2		733	952	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420308	88420308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367985043	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	74	552	0	ENST00000360948.2:c.2378G>A	p.Arg793Gln	p.R793Q	ENST00000360948	NM_001012338.2	793	cGa/cAa	19/19	1	2	FACETS	0.546	0.477	0.621	0.546	0.477	0.621	SUBCLONAL	1	TRUE	1	0.34	2		552	797	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523285	9523285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767541766	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	133	610	0	ENST00000353224.5:c.1952C>T	p.Ala651Val	p.A651V	ENST00000353224	NM_177990.2	651	gCg/gTg	9/10	1	2	FACETS	0.889	0.807	0.975	0.889	0.807	0.975	CLONAL	1	TRUE	1	0.34	2		610	880	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027998	48027998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757653982	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	30	333	0	ENST00000234420.5:c.2876G>A	p.Arg959His	p.R959H	ENST00000234420	NM_000179.2	959	cGc/cAc	4/10	1	2	FACETS	0.504	0.406	0.615	0.504	0.406	0.615	SUBCLONAL	1	TRUE	1	0.34	2		333	350	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652411	206652411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781909564	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	284	733	1	ENST00000367120.3:c.1118C>T	p.Thr373Met	p.T373M	ENST00000367120	NM_014002.3	373	aCg/aTg	10/22	1	2	FACETS	0.811	0.763	0.86	1	0.994	1	CLONAL	2	TRUE	1	0.34	2		734	1030	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535283	66535283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs547670481	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	83	655	2	ENST00000273854.3:c.178G>A	p.Glu60Lys	p.E60K	ENST00000273854	NM_004439.5	60	Gaa/Aaa	1/18	1	2	FACETS	0.604	0.532	0.681	0.604	0.532	0.681	SUBCLONAL	1	TRUE	1	0.34	2		657	808	SUCCESS
ALK	238	MSKCC	GRCh37	2	29450509	29450509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774004991	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	262	786	0	ENST00000389048.3:c.2845G>A	p.Glu949Lys	p.E949K	ENST00000389048	NM_004304.4	949	Gaa/Aaa	17/29	1	2	FACETS	0.774	0.726	0.824	1	0.993	1	SUBCLONAL	2	TRUE	1	0.34	2		786	995	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40497584	40497584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774724351	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	253	642	1	ENST00000264657.5:c.365C>T	p.Ala122Val	p.A122V	ENST00000264657	NM_139276.2	122	gCg/gTg	4/24	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.34	2		643	1063	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374881	45374881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	114	475	1	ENST00000262160.6:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000262160	NM_005901.5	321	cGa/cAa	8/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.34	2		476	524	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027751	48027751	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	35	279	0	ENST00000234420.5:c.2629G>T	p.Glu877Ter	p.E877*	ENST00000234420	NM_000179.2	877	Gaa/Taa	4/10	1	2	FACETS	0.615	0.505	0.737	0.615	0.505	0.737	SUBCLONAL	1	TRUE	1	0.34	2		279	335	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056376	180056376	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	92	742	0	ENST00000261937.6:c.868G>T	p.Glu290Ter	p.E290*	ENST00000261937	NM_182925.4	290	Gaa/Taa	7/30	1	2	FACETS	0.613	0.544	0.687	0.613	0.544	0.687	SUBCLONAL	1	TRUE	1	0.34	2		742	883	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915943	127915943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781486938	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	54	448	0	ENST00000373547.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000373547	NM_002721.4	180	Gaa/Aaa	6/7	1	2	FACETS	0.538	0.459	0.625	0.538	0.459	0.625	SUBCLONAL	1	TRUE	1	0.34	2		448	590	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	154	544	0	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.34	2		544	668	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218483	1218483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775595174	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	178	560	0	ENST00000326873.7:c.358G>A	p.Glu120Lys	p.E120K	ENST00000326873	NM_000455.4	120	Gaa/Aaa	2/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.34	2		560	718	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606304	93606304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	151	736	0	ENST00000375746.1:c.124C>T	p.Arg42Cys	p.R42C	ENST00000375746	NM_001174167.1	42	Cgc/Tgc	2/14	1	2	FACETS	0.939	0.858	1	0.939	0.858	1	CLONAL	1	TRUE	1	0.34	2		736	946	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123788	11123788	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1064795105	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	79	589	1	ENST00000358026.2:c.2438C>T	p.Ser813Leu	p.S813L	ENST00000358026	NM_001128849.1	813	tCa/tTa	16/36	1	2	FACETS	0.596	0.523	0.674	0.596	0.523	0.674	SUBCLONAL	1	TRUE	1	0.34	2		590	780	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11313967	11313967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	151	751	1	ENST00000361445.4:c.769C>T	p.Arg257Trp	p.R257W	ENST00000361445	NM_004958.3	257	Cgg/Tgg	6/58	1	2	FACETS	0.919	0.839	1	0.919	0.839	1	CLONAL	1	TRUE	1	0.34	2		752	967	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645069	67645069	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	73	646	0	ENST00000264010.4:c.334G>T	p.Glu112Ter	p.E112*	ENST00000264010	NM_006565.3	112	Gaa/Taa	3/12	1	2	FACETS	0.524	0.458	0.596	0.524	0.458	0.596	SUBCLONAL	1	TRUE	1	0.34	2		646	819	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677876	47677876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	135	577	1	ENST00000347630.2:c.989C>T	p.Ser330Leu	p.S330L	ENST00000347630	NM_001007230.1	330	tCg/tTg	11/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.34	2		578	711	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916843	48916843	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	15	149	0	ENST00000267163.4:c.373G>T	p.Glu125Ter	p.E125*	ENST00000267163	NM_000321.2	125	Gaa/Taa	3/27	1	2	FACETS	0.365	0.266	0.482	0.365	0.266	0.482	SUBCLONAL	1	TRUE	1	0.34	2		149	242	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188854	32188854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1183058401	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	108	829	2	ENST00000375023.3:c.700C>T	p.Arg234Trp	p.R234W	ENST00000375023	NM_004557.3	234	Cgg/Tgg	4/30	1	2	FACETS	0.81	0.727	0.899	0.81	0.727	0.899	CLONAL	1	TRUE	1	0.34	2		831	784	SUCCESS
APC	324	MSKCC	GRCh37	5	112176873	112176873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	30	277	0	ENST00000257430.4:c.5582C>A	p.Ser1861Tyr	p.S1861Y	ENST00000257430	NM_000038.5	1861	tCt/tAt	16/16	1	2	FACETS	0.543	0.438	0.661	0.543	0.438	0.661	SUBCLONAL	1	TRUE	1	0.34	2		277	325	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828772	3828772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	204	623	1	ENST00000262367.5:c.1870C>T	p.Arg624Cys	p.R624C	ENST00000262367	NM_004380.2	624	Cgc/Tgc	9/31	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.34	2		624	856	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170840	99170840	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1442257080	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	78	659	1	ENST00000074304.5:c.1469C>T	p.Ser490Leu	p.S490L	ENST00000074304	NM_001134224.1	490	tCg/tTg	16/26	1	2	FACETS	0.518	0.454	0.587	0.518	0.454	0.587	SUBCLONAL	1	TRUE	1	0.34	2		660	886	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843724	156843724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	152	931	0	ENST00000524377.1:c.1150G>A	p.Glu384Lys	p.E384K	ENST00000524377	NM_002529.3	384	Gag/Aag	8/17	1	2	FACETS	0.736	0.671	0.804	0.736	0.671	0.804	SUBCLONAL	1	TRUE	1	0.34	2		931	1215	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332853	153332853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751626529	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	101	519	1	ENST00000281708.4:c.103C>T	p.Arg35Cys	p.R35C	ENST00000281708	NM_033632.3	35	Cgt/Tgt	2/12	1	2	FACETS	0.792	0.708	0.882	0.792	0.708	0.882	SUBCLONAL	1	TRUE	1	0.34	2		520	750	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405958	70405958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370887665	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	47	585	0	ENST00000373644.4:c.3472C>T	p.Arg1158Trp	p.R1158W	ENST00000373644	NM_030625.2	1158	Cgg/Tgg	4/12	1	2	FACETS	0.462	0.389	0.542	0.462	0.389	0.542	SUBCLONAL	1	TRUE	1	0.34	2		585	599	SUCCESS
APC	324	MSKCC	GRCh37	5	112173495	112173495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147655929	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	36	334	0	ENST00000257430.4:c.2204C>T	p.Ala735Val	p.A735V	ENST00000257430	NM_000038.5	735	gCg/gTg	16/16	1	2	FACETS	0.588	0.484	0.704	0.588	0.484	0.704	SUBCLONAL	1	TRUE	1	0.34	2		334	360	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821931	59821931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764803896	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	26	257	0	ENST00000259008.2:c.2119C>T	p.Arg707Cys	p.R707C	ENST00000259008	NM_032043.2	707	Cgt/Tgt	15/20	1	2	FACETS	0.556	0.441	0.687	0.556	0.441	0.687	SUBCLONAL	1	TRUE	1	0.34	2		257	275	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310506	65310506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	105	646	0	ENST00000342505.4:c.2182G>A	p.Asp728Asn	p.D728N	ENST00000342505	NM_002227.2	728	Gac/Aac	16/25	1	2	FACETS	0.639	0.572	0.711	0.639	0.572	0.711	SUBCLONAL	1	TRUE	1	0.34	2		646	966	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228613019	228613019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773567566	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	98	430	0	ENST00000366696.1:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000366696	NM_003493.2	3	cGa/cAa	1/1	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.34	2		430	573	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213800	66213800	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	35	380	0	ENST00000273854.3:c.2630G>A	p.Arg877Lys	p.R877K	ENST00000273854	NM_004439.5	877	aGa/aAa	15/18	1	2	FACETS	0.528	0.433	0.634	0.528	0.433	0.634	SUBCLONAL	1	TRUE	1	0.34	2		380	390	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675571	30675571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772732783	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	138	860	0	ENST00000376406.3:c.2785G>A	p.Asp929Asn	p.D929N	ENST00000376406	NM_014641.2	929	Gat/Aat	8/15	1	2	FACETS	0.711	0.645	0.78	0.711	0.645	0.78	SUBCLONAL	1	TRUE	1	0.34	2		860	1142	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939351	76939351	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	22	434	1	ENST00000373344.5:c.1397G>T	p.Arg466Ile	p.R466I	ENST00000373344	NM_000489.3	466	aGa/aTa	9/35	1	2	FACETS	0.299	0.231	0.378	0.299	0.231	0.378	SUBCLONAL	1	TRUE	1	0.34	2		435	433	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306568	41306568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	127	662	0	ENST00000373198.4:c.1091G>A	p.Arg364Gln	p.R364Q	ENST00000373198	NM_133170.3	364	cGa/cAa	7/32	1	2	FACETS	0.873	0.79	0.96	0.873	0.79	0.96	CLONAL	1	TRUE	1	0.34	2		662	856	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103716	47103716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs981018402	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	75	533	0	ENST00000409792.3:c.6230G>A	p.Arg2077Gln	p.R2077Q	ENST00000409792	NM_014159.6	2077	cGa/cAa	14/21	1	2	FACETS	0.614	0.538	0.697	0.614	0.538	0.697	SUBCLONAL	1	TRUE	1	0.34	2		533	718	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915939	127915939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	52	458	1	ENST00000373547.4:c.542G>A	p.Arg181Gln	p.R181Q	ENST00000373547	NM_002721.4	181	cGg/cAg	6/7	1	2	FACETS	0.506	0.43	0.589	0.506	0.43	0.589	SUBCLONAL	1	TRUE	1	0.34	2		459	605	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740264	162740264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756149068	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	77	406	0	ENST00000367921.3:c.1466G>A	p.Arg489Gln	p.R489Q	ENST00000367921	NM_006182.2	489	cGa/cAa	12/18	1	2	FACETS	0.681	0.598	0.771	0.681	0.598	0.771	SUBCLONAL	1	TRUE	1	0.34	2		406	665	SUCCESS
FH	2271	MSKCC	GRCh37	1	241661199	241661199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201115573	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	83	577	0	ENST00000366560.3:c.1462G>A	p.Glu488Lys	p.E488K	ENST00000366560	NM_000143.3	488	Gaa/Aaa	10/10	1	2	FACETS	0.806	0.712	0.906	0.806	0.712	0.906	CLONAL	1	TRUE	1	0.34	2		577	606	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	14	381	0	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	0.175	0.126	0.236	0.175	0.126	0.236	SUBCLONAL	1	TRUE	1	0.34	2		381	470	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201816	66201816	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556854839	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	150	471	0	ENST00000273854.3:c.2686C>T	p.Arg896Cys	p.R896C	ENST00000273854	NM_004439.5	896	Cgt/Tgt	16/18	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.34	2		471	667	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751901	57751901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148954251	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	62	522	0	ENST00000274289.3:c.1336C>T	p.Arg446Trp	p.R446W	ENST00000274289	NM_006622.3	446	Cgg/Tgg	10/14	1	2	FACETS	0.469	0.404	0.539	0.469	0.404	0.539	SUBCLONAL	1	TRUE	1	0.34	2		522	778	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672842	86672842	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	58	234	0	ENST00000274376.6:c.2329G>T	p.Glu777Ter	p.E777*	ENST00000274376	NM_002890.2	777	Gaa/Taa	17/25	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.34	2		234	249	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32931937	32931937	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	21	212	0	ENST00000380152.3:c.7676C>A	p.Ser2559Tyr	p.S2559Y	ENST00000380152		2559	tCt/tAt	16/27	1	2	FACETS	0.481	0.371	0.608	0.481	0.371	0.608	SUBCLONAL	1	TRUE	1	0.34	2		212	257	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161405	185161405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	59	395	0	ENST00000265026.3:c.832C>T	p.Arg278Cys	p.R278C	ENST00000265026	NM_004721.4	278	Cgt/Tgt	4/14	1	2	FACETS	0.705	0.608	0.812	0.705	0.608	0.812	SUBCLONAL	1	TRUE	1	0.34	2		395	492	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230405	46230405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1391481708	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	30	230	0	ENST00000334344.6:c.739C>T	p.Arg247Cys	p.R247C	ENST00000334344	NM_152641.2	247	Cgt/Tgt	7/21	1	2	FACETS	0.489	0.394	0.596	0.489	0.394	0.596	SUBCLONAL	1	TRUE	1	0.34	2		230	361	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502609	149502609	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	68	420	0	ENST00000261799.4:c.2179C>T	p.Pro727Ser	p.P727S	ENST00000261799	NM_002609.3	727	Ccc/Tcc	15/23	1	2	FACETS	0.714	0.622	0.814	0.714	0.622	0.814	SUBCLONAL	1	TRUE	1	0.34	2		420	560	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413577	32413577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1037084691	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	107	480	0	ENST00000332351.3:c.1373G>A	p.Arg458Gln	p.R458Q	ENST00000332351	NM_024426.4	458	cGa/cAa	9/10	1	2	FACETS	0.938	0.842	1	0.938	0.842	1	CLONAL	1	TRUE	1	0.34	2		480	671	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562982	29562982	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1306237220	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	71	356	0	ENST00000356175.3:c.3917G>A	p.Arg1306Gln	p.R1306Q	ENST00000356175	NM_000267.3	1306	cGa/cAa	29/57	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.34	2		356	341	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686796	117686796	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759586931	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	57	415	0	ENST00000368508.3:c.2921C>T	p.Ala974Val	p.A974V	ENST00000368508	NM_002944.2	974	gCg/gTg	19/43	1	2	FACETS	0.73	0.628	0.842	0.73	0.628	0.842	SUBCLONAL	1	TRUE	1	0.34	2		415	459	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553011	106553011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs955184509	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	91	732	1	ENST00000369096.4:c.976C>T	p.Arg326Cys	p.R326C	ENST00000369096	NM_001198.3	326	Cgc/Tgc	5/7	1	2	FACETS	0.539	0.477	0.605	0.539	0.477	0.605	SUBCLONAL	1	TRUE	1	0.34	2		733	994	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653437	206653437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782340929	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	195	652	1	ENST00000367120.3:c.1321C>T	p.Arg441Trp	p.R441W	ENST00000367120	NM_014002.3	441	Cgg/Tgg	12/22	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.34	2		653	857	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232137	98232137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1382474804	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	71	424	0	ENST00000331920.6:c.1805G>A	p.Arg602Gln	p.R602Q	ENST00000331920	NM_000264.3	602	cGa/cAa	13/24	1	2	FACETS	0.639	0.557	0.727	0.639	0.557	0.727	SUBCLONAL	1	TRUE	1	0.34	2		424	654	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644754	67644754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779609208	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	96	546	0	ENST00000264010.4:c.19G>A	p.Glu7Lys	p.E7K	ENST00000264010	NM_006565.3	7	Gaa/Aaa	3/12	1	2	FACETS	0.741	0.66	0.827	0.741	0.66	0.827	SUBCLONAL	1	TRUE	1	0.34	2		546	762	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028618	12028618	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	45	353	1	ENST00000353533.5:c.821G>T	p.Arg274Ile	p.R274I	ENST00000353533	NM_003010.3	274	aGa/aTa	8/11	1	2	FACETS	0.554	0.465	0.651	0.554	0.465	0.651	SUBCLONAL	1	TRUE	1	0.34	2		354	478	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231773	36231773	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1569061762	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	43	697	1	ENST00000300305.3:c.611G>A	p.Arg204Gln	p.R204Q	ENST00000300305		204	cGa/cAa	5/8	1	2	FACETS	0.252	0.21	0.299	0.252	0.21	0.299	SUBCLONAL	1	TRUE	1	0.34	2		698	1003	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946225	81946225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1325870340	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	142	545	0	ENST00000359376.3:c.1958G>A	p.Arg653His	p.R653H	ENST00000359376	NM_002661.3	653	cGc/cAc	19/33	1	2	FACETS	0.979	0.893	1	0.979	0.893	1	CLONAL	1	TRUE	1	0.34	2		545	853	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965761	25965761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377352572	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	95	684	0	ENST00000435504.4:c.3445C>T	p.Arg1149Cys	p.R1149C	ENST00000435504		1149	Cgt/Tgt	13/13	1	2	FACETS	0.551	0.489	0.617	0.551	0.489	0.617	SUBCLONAL	1	TRUE	1	0.34	2		684	1015	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052632	42052632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779811318	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	65	541	0	ENST00000219905.7:c.7303C>T	p.Arg2435Trp	p.R2435W	ENST00000219905	NM_001164273.1	2435	Cgg/Tgg	20/24	1	2	FACETS	0.422	0.364	0.484	0.422	0.364	0.484	SUBCLONAL	1	TRUE	1	0.34	2		541	907	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839785	42839785	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773001010	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	75	535	2	ENST00000398585.3:c.1454C>T	p.Ser485Leu	p.S485L	ENST00000398585	NM_001135099.1	485	tCg/tTg	13/14	1	2	FACETS	0.64	0.561	0.726	0.64	0.561	0.726	SUBCLONAL	1	TRUE	1	0.34	2		537	689	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729984	41729984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	139	695	0	ENST00000242208.4:c.545C>T	p.Pro182Leu	p.P182L	ENST00000242208	NM_002192.2	182	cCg/cTg	3/3	1	2	FACETS	0.832	0.756	0.911	0.832	0.756	0.911	CLONAL	1	TRUE	1	0.34	2		695	983	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250046	53250046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1569282235	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	234	669	1	ENST00000375401.3:c.203G>A	p.Arg68Gln	p.R68Q	ENST00000375401	NM_004187.3	68	cGa/cAa	2/26	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.34	2		670	1049	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617551	100617551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	51	523	0	ENST00000308731.7:c.518G>A	p.Gly173Glu	p.G173E	ENST00000308731	NM_000061.2	173	gGa/gAa	6/19	1	2	FACETS	0.488	0.414	0.569	0.488	0.414	0.569	SUBCLONAL	1	TRUE	1	0.34	2		523	615	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674234	86674234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	69	337	1	ENST00000274376.6:c.2366G>A	p.Arg789Gln	p.R789Q	ENST00000274376	NM_002890.2	789	cGa/cAa	18/25	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.34	2		338	360	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410553	63410553	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	233	822	0	ENST00000330258.3:c.2614T>C	p.Tyr872His	p.Y872H	ENST00000330258	NM_152424.3	872	Tac/Cac	2/2	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.34	2		822	1026	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276723	15276723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1031506714	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	90	776	1	ENST00000263388.2:c.5542C>T	p.Arg1848Cys	p.R1848C	ENST00000263388	NM_000435.2	1848	Cgt/Tgt	30/33	1	2	FACETS	0.512	0.453	0.575	0.512	0.453	0.575	SUBCLONAL	1	TRUE	1	0.34	2		777	1035	SUCCESS
AR	367	MSKCC	GRCh37	X	66765025	66765025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1335991486	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	168	781	0	ENST00000374690.3:c.37C>T	p.Arg13Trp	p.R13W	ENST00000374690	NM_000044.3	13	Cgg/Tgg	1/8	1	2	FACETS	0.857	0.786	0.931	0.857	0.786	0.931	CLONAL	1	TRUE	1	0.34	2		781	1153	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829617	72829617	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	85	623	0	ENST00000268489.5:c.6964C>T	p.Arg2322Ter	p.R2322*	ENST00000268489	NM_006885.3	2322	Cga/Tga	9/10	1	2	FACETS	0.691	0.61	0.777	0.691	0.61	0.777	SUBCLONAL	1	TRUE	1	0.34	2		623	724	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989557	85989557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	36	356	1	ENST00000263360.6:c.1316G>A	p.Arg439Gln	p.R439Q	ENST00000263360	NM_003797.3	439	cGa/cAa	12/12	1	2	FACETS	0.442	0.363	0.531	0.442	0.363	0.531	SUBCLONAL	1	TRUE	1	0.34	2		357	479	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121669	108121669	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750280306	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	36	395	0	ENST00000278616.4:c.1477C>T	p.Arg493Cys	p.R493C	ENST00000278616	NM_000051.3	493	Cgt/Tgt	10/63	1	2	FACETS	0.488	0.401	0.585	0.488	0.401	0.585	SUBCLONAL	1	TRUE	1	0.34	2		395	434	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638912	176638912	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs111638717	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	106	662	0	ENST00000439151.2:c.3512G>A	p.Arg1171His	p.R1171H	ENST00000439151	NM_022455.4	1171	cGt/cAt	5/23	1	2	FACETS	0.658	0.589	0.731	0.658	0.589	0.731	SUBCLONAL	1	TRUE	1	0.34	2		662	948	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231134	98231134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1311707136	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	83	677	0	ENST00000331920.6:c.2149G>A	p.Asp717Asn	p.D717N	ENST00000331920	NM_000264.3	717	Gac/Aac	14/24	1	2	FACETS	0.541	0.477	0.611	0.541	0.477	0.611	SUBCLONAL	1	TRUE	1	0.34	2		677	902	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750454	57750454	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	35	382	0	ENST00000274289.3:c.2014C>T	p.Arg672Ter	p.R672*	ENST00000274289	NM_006622.3	672	Cga/Tga	14/14	1	2	FACETS	0.493	0.404	0.592	0.493	0.404	0.592	SUBCLONAL	1	TRUE	1	0.34	2		382	418	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563383	21563383	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	105	993	0	ENST00000382592.4:c.536C>T	p.Ser179Leu	p.S179L	ENST00000382592	NM_014572.2	179	tCg/tTg	4/8	1	2	FACETS	0.515	0.46	0.574	0.515	0.46	0.574	SUBCLONAL	1	TRUE	1	0.34	2		993	1200	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543637	29543637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	101	663	0	ENST00000389048.3:c.1526C>T	p.Ala509Val	p.A509V	ENST00000389048	NM_004304.4	509	gCc/gTc	7/29	1	2	FACETS	0.614	0.548	0.685	0.614	0.548	0.685	SUBCLONAL	1	TRUE	1	0.34	2		663	967	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067243	37067243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750430	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	152	478	0	ENST00000231790.2:c.1154G>A	p.Arg385His	p.R385H	ENST00000231790	NM_000249.3	385	cGt/cAt	12/19	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.34	2		478	659	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471050	8471050	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	45	315	0	ENST00000356435.5:c.3449C>A	p.Ser1150Tyr	p.S1150Y	ENST00000356435		1150	tCt/tAt	20/35	1	2	FACETS	0.635	0.534	0.746	0.635	0.534	0.746	SUBCLONAL	1	TRUE	1	0.34	2		315	417	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255694	16255694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376676096	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	37	507	0	ENST00000375759.3:c.2959C>T	p.Arg987Cys	p.R987C	ENST00000375759	NM_015001.2	987	Cgc/Tgc	11/15	1	2	FACETS	0.312	0.256	0.375	0.312	0.256	0.375	SUBCLONAL	1	TRUE	1	0.34	2		507	697	SUCCESS
YES1	7525	MSKCC	GRCh37	18	732915	732915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542568142	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	89	540	0	ENST00000314574.4:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000314574	NM_005433.3	448	Cgg/Tgg	11/12	1	2	FACETS	0.77	0.683	0.863	0.77	0.683	0.863	SUBCLONAL	1	TRUE	1	0.34	2		540	680	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622495	158622495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316254232	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	66	461	1	ENST00000263640.3:c.1004G>A	p.Arg335Gln	p.R335Q	ENST00000263640	NM_001105.4	335	cGa/cAa	8/11	1	2	FACETS	0.692	0.601	0.79	0.692	0.601	0.79	SUBCLONAL	1	TRUE	1	0.34	2		462	561	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003277	143003277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369778611	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	69	522	1	ENST00000262992.4:c.2549C>T	p.Ser850Leu	p.S850L	ENST00000262992	NM_001101669.1	850	tCg/tTg	23/24	1	2	FACETS	0.555	0.483	0.634	0.555	0.483	0.634	SUBCLONAL	1	TRUE	1	0.34	2		523	731	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302801	15302801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756520455	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	106	805	0	ENST00000263388.2:c.649G>A	p.Asp217Asn	p.D217N	ENST00000263388	NM_000435.2	217	Gac/Aac	4/33	1	2	FACETS	0.629	0.563	0.7	0.629	0.563	0.7	SUBCLONAL	1	TRUE	1	0.34	2		805	991	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227938	55227938	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	24	344	0	ENST00000275493.2:c.1405T>G	p.Leu469Val	p.L469V	ENST00000275493	NM_005228.3	469	Ttg/Gtg	12/28	1	2	FACETS	0.341	0.267	0.427	0.341	0.267	0.427	SUBCLONAL	1	TRUE	1	0.34	2		344	414	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119007	3119007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769503200	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	110	801	3	ENST00000078429.4:c.691G>A	p.Ala231Thr	p.A231T	ENST00000078429	NM_002067.2	231	Gcc/Acc	5/7	1	2	FACETS	0.658	0.59	0.73	0.658	0.59	0.73	SUBCLONAL	1	TRUE	1	0.34	2		804	984	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453531	138453531	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372119491	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	67	215	0	ENST00000289153.2:c.917G>A	p.Arg306Gln	p.R306Q	ENST00000289153	NM_006219.2	306	cGa/cAa	5/22	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.34	2		215	277	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349353	73349353	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1026175478	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	56	229	0	ENST00000377767.4:c.983G>A	p.Arg328Gln	p.R328Q	ENST00000377767	NM_014953.3	328	cGa/cAa	6/21	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.34	2		229	287	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832265	72832265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267604632	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	60	501	1	ENST00000268489.5:c.4316G>A	p.Arg1439Gln	p.R1439Q	ENST00000268489	NM_006885.3	1439	cGa/cAa	9/10	1	2	FACETS	0.546	0.47	0.629	0.546	0.47	0.629	SUBCLONAL	1	TRUE	1	0.34	2		502	646	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108548	8108548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	82	707	0	ENST00000585124.1:c.847C>T	p.Arg283Cys	p.R283C	ENST00000585124	NM_004217.3	283	Cgc/Tgc	8/9	1	2	FACETS	0.508	0.447	0.574	0.508	0.447	0.574	SUBCLONAL	1	TRUE	1	0.34	2		707	950	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650845	37650845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	110	651	0	ENST00000447079.4:c.2317C>T	p.Arg773Cys	p.R773C	ENST00000447079	NM_015083.1	773	Cgt/Tgt	5/14	1	2	FACETS	0.753	0.676	0.835	0.753	0.676	0.835	SUBCLONAL	1	TRUE	1	0.34	2		651	859	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740837	58740837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200809297	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	123	550	0	ENST00000305921.3:c.1742G>A	p.Arg581Gln	p.R581Q	ENST00000305921	NM_003620.3	581	cGa/cAa	6/6	1	2	FACETS	0.888	0.803	0.977	0.888	0.803	0.977	CLONAL	1	TRUE	1	0.34	2		550	815	SUCCESS
APC	324	MSKCC	GRCh37	5	112173303	112173303	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	17	172	0	ENST00000257430.4:c.2012C>A	p.Ser671Tyr	p.S671Y	ENST00000257430	NM_000038.5	671	tCt/tAt	16/16	1	2	FACETS	0.435	0.325	0.565	0.435	0.325	0.565	SUBCLONAL	1	TRUE	1	0.34	2		172	230	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160347	108160347	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	12	94	0	ENST00000278616.4:c.4255C>A	p.Leu1419Ile	p.L1419I	ENST00000278616	NM_000051.3	1419	Ctt/Att	29/63	1	2	FACETS	0.458	0.323	0.623	0.458	0.323	0.623	SUBCLONAL	1	TRUE	1	0.34	2		94	154	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622579	158622579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766547414	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	65	562	0	ENST00000263640.3:c.920G>A	p.Arg307Gln	p.R307Q	ENST00000263640	NM_001105.4	307	cGa/cAa	8/11	1	2	FACETS	0.551	0.477	0.631	0.551	0.477	0.631	SUBCLONAL	1	TRUE	1	0.34	2		562	694	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647532	117647532	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	73	301	0	ENST00000368508.3:c.5412G>T	p.Lys1804Asn	p.K1804N	ENST00000368508	NM_002944.2	1804	aaG/aaT	33/43	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.34	2		301	398	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736480	85736480	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	48	242	0	ENST00000370580.1:c.167C>A	p.Ser56Tyr	p.S56Y	ENST00000370580	NM_003921.4	56	tCt/tAt	2/3	1	2	FACETS	0.838	0.711	0.976	0.838	0.711	0.976	CLONAL	1	TRUE	1	0.34	2		242	337	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692978	89692978	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	143	388	0	ENST00000371953.3:c.462C>A	p.Phe154Leu	p.F154L	ENST00000371953	NM_000314.4	154	ttC/ttA	5/9	1	2	FACETS	1	0.962	1	1	0.992	1	CLONAL	2	TRUE	1	0.34	2		388	392	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026290	48026290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147737737	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	37	386	0	ENST00000234420.5:c.1168G>A	p.Asp390Asn	p.D390N	ENST00000234420	NM_000179.2	390	Gat/Aat	4/10	1	2	FACETS	0.524	0.432	0.627	0.524	0.432	0.627	SUBCLONAL	1	TRUE	1	0.34	2		386	415	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58701094	58701094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	84	518	0	ENST00000305921.3:c.685G>A	p.Glu229Lys	p.E229K	ENST00000305921	NM_003620.3	229	Gaa/Aaa	2/6	1	2	FACETS	0.691	0.61	0.778	0.691	0.61	0.778	SUBCLONAL	1	TRUE	1	0.34	2		518	715	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061825	38061825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1019690230	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	286	904	0	ENST00000250448.2:c.164C>T	p.Thr55Met	p.T55M	ENST00000250448	NM_004496.3	55	aCg/aTg	2/2	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.34	2		904	1171	SUCCESS
EED	8726	MSKCC	GRCh37	11	85979575	85979575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	53	288	0	ENST00000263360.6:c.938G>A	p.Arg313Gln	p.R313Q	ENST00000263360	NM_003797.3	313	cGa/cAa	9/12	1	2	FACETS	0.682	0.583	0.791	0.682	0.583	0.791	SUBCLONAL	1	TRUE	1	0.34	2		288	457	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905974	50905974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746087148	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	223	822	0	ENST00000440232.2:c.946G>A	p.Asp316Asn	p.D316N	ENST00000440232	NM_002691.3	316	Gat/Aat	8/27	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.34	2		822	910	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346713	225346713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	114	430	0	ENST00000264414.4:c.1925G>A	p.Arg642Gln	p.R642Q	ENST00000264414	NM_003590.4	642	cGg/cAg	14/16	1	2	FACETS	0.787	0.714	0.863	1	0.986	1	SUBCLONAL	2	TRUE	1	0.34	2		430	426	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572092	64572092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1565637104	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	139	711	2	ENST00000312049.6:c.1547G>A	p.Arg516Gln	p.R516Q	ENST00000312049	NM_130799.2	516	cGg/cAg	10/10	1	2	FACETS	0.814	0.74	0.891	0.814	0.74	0.891	CLONAL	1	TRUE	1	0.34	2		713	1005	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653842	89653842	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057518425	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	48	105	0	ENST00000371953.3:c.140G>A	p.Arg47Lys	p.R47K	ENST00000371953	NM_000314.4	47	aGg/aAg	2/9	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.34	2		105	231	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715350	117715350	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1466068877	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	47	201	0	ENST00000368508.3:c.1139G>T	p.Arg380Ile	p.R380I	ENST00000368508	NM_002944.2	380	aGa/aTa	10/43	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.34	2		201	220	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588241	69588241	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs533842802	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	37	477	0	ENST00000168712.1:c.457G>A	p.Asp153Asn	p.D153N	ENST00000168712	NM_002007.2	153	Gat/Aat	3/3	1	2	FACETS	0.327	0.268	0.392	0.327	0.268	0.392	SUBCLONAL	1	TRUE	1	0.34	2		477	666	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741604	17741604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866359886	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	61	279	0	ENST00000250003.3:c.275G>A	p.Arg92His	p.R92H	ENST00000250003	NM_002478.4	92	cGc/cAc	1/3	1	2	FACETS	0.783	0.677	0.898	0.783	0.677	0.898	SUBCLONAL	1	TRUE	1	0.34	2		279	458	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912349	97912349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs182879858	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	76	468	0	ENST00000289081.3:c.542C>T	p.Ala181Val	p.A181V	ENST00000289081	NM_000136.2	181	gCg/gTg	7/15	1	2	FACETS	0.677	0.594	0.767	0.677	0.594	0.767	SUBCLONAL	1	TRUE	1	0.34	2		468	660	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857515	57857515	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	125	826	0	ENST00000228682.2:c.41G>A	p.Gly14Asp	p.G14D	ENST00000228682	NM_005269.2	14	gGc/gAc	2/12	1	2	FACETS	0.654	0.591	0.721	0.654	0.591	0.721	SUBCLONAL	1	TRUE	1	0.34	2		826	1124	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321280	1321280	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763471203	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	104	468	2	ENST00000400841.2:c.475G>A	p.Glu159Lys	p.E159K	ENST00000400841		159	Gag/Aag	4/6	1	2	FACETS	0.919	0.823	1	0.919	0.823	1	CLONAL	1	TRUE	1	0.34	2		470	666	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023223	31023223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754790367	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	100	717	0	ENST00000375687.4:c.2708C>T	p.Ser903Leu	p.S903L	ENST00000375687	NM_015338.5	903	tCg/tTg	13/13	1	2	FACETS	0.617	0.55	0.688	0.617	0.55	0.688	SUBCLONAL	1	TRUE	1	0.34	2		717	954	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506251	120506251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781827529	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	109	402	0	ENST00000256646.2:c.1861C>T	p.Arg621Cys	p.R621C	ENST00000256646	NM_024408.3	621	Cgc/Tgc	11/34	1	2	FACETS	0.997	0.897	1	0.997	0.897	1	CLONAL	1	TRUE	1	0.34	2		402	643	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819695	81819695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs537204469	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	153	629	1	ENST00000359376.3:c.101G>A	p.Arg34His	p.R34H	ENST00000359376	NM_002661.3	34	cGc/cAc	2/33	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.34	2		630	849	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181431	185181431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377513650	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	57	503	0	ENST00000265026.3:c.1372C>T	p.Arg458Cys	p.R458C	ENST00000265026	NM_004721.4	458	Cgc/Tgc	8/14	1	2	FACETS	0.492	0.421	0.569	0.492	0.421	0.569	SUBCLONAL	1	TRUE	1	0.34	2		503	682	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029554	14029554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147105770	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	46	375	0	ENST00000311895.7:c.1765C>T	p.Arg589Trp	p.R589W	ENST00000311895	NM_005236.2	589	Cgg/Tgg	8/11	1	2	FACETS	0.502	0.422	0.59	0.502	0.422	0.59	SUBCLONAL	1	TRUE	1	0.34	2		375	539	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386401	31386401	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	88	697	0	ENST00000328111.2:c.1626G>T	p.Trp542Cys	p.W542C	ENST00000328111	NM_006892.3	542	tgG/tgT	15/23	1	2	FACETS	0.507	0.448	0.571	0.507	0.448	0.571	SUBCLONAL	1	TRUE	1	0.34	2		697	1020	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347446	91347446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757088548	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	68	336	0	ENST00000355112.3:c.3608C>T	p.Ala1203Val	p.A1203V	ENST00000355112	NM_000057.2	1203	gCg/gTg	19/22	1	2	FACETS	0.846	0.738	0.962	0.846	0.738	0.962	CLONAL	1	TRUE	1	0.34	2		336	473	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114233	73114233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201957466	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	35	322	0	ENST00000356692.5:c.869G>A	p.Arg290His	p.R290H	ENST00000356692		290	cGt/cAt	8/9	1	2	FACETS	0.41	0.336	0.494	0.41	0.336	0.494	SUBCLONAL	1	TRUE	1	0.34	2		322	502	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670598	134670598	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs563780078	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	119	749	0	ENST00000398015.3:c.509G>A	p.Arg170Gln	p.R170Q	ENST00000398015	NM_004441.4	170	cGg/cAg	3/16	1	2	FACETS	0.674	0.607	0.745	0.674	0.607	0.745	SUBCLONAL	1	TRUE	1	0.34	2		749	1038	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039404	47039404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556778215	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	159	769	0	ENST00000377604.3:c.1027C>T	p.Arg343Cys	p.R343C	ENST00000377604	NM_001204468.1	343	Cgc/Tgc	10/24	1	2	FACETS	0.932	0.853	1	0.932	0.853	1	CLONAL	1	TRUE	1	0.34	2		769	1004	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931862	68931862	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200600940	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	137	543	0	ENST00000288368.4:c.292G>A	p.Glu98Lys	p.E98K	ENST00000288368	NM_024870.2	98	Gaa/Aaa	3/40	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.34	2		543	656	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979561	55979561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	69	495	0	ENST00000263923.4:c.886G>A	p.Gly296Ser	p.G296S	ENST00000263923	NM_002253.2	296	Ggt/Agt	7/30	1	2	FACETS	0.67	0.583	0.763	0.67	0.583	0.763	SUBCLONAL	1	TRUE	1	0.34	2		495	606	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953115	81953115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1336595726	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	45	386	0	ENST00000359376.3:c.2081G>A	p.Arg694His	p.R694H	ENST00000359376	NM_002661.3	694	cGc/cAc	20/33	1	2	FACETS	0.493	0.414	0.58	0.493	0.414	0.58	SUBCLONAL	1	TRUE	1	0.34	2		386	537	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280137	142280137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs986166179	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	116	546	0	ENST00000350721.4:c.1297C>T	p.Arg433Cys	p.R433C	ENST00000350721	NM_001184.3	433	Cgt/Tgt	5/47	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.34	2		546	582	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114277	143114277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs76891221	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	53	344	0	ENST00000262992.4:c.1144C>T	p.Arg382Trp	p.R382W	ENST00000262992	NM_001101669.1	382	Cgg/Tgg	13/24	1	2	FACETS	0.768	0.657	0.889	0.768	0.657	0.889	SUBCLONAL	1	TRUE	1	0.34	2		344	406	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430353	47430353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773486607	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	93	822	0	ENST00000377045.4:c.1628G>A	p.Arg543Gln	p.R543Q	ENST00000377045	NM_001654.4	543	cGg/cAg	15/16	1	2	FACETS	0.51	0.452	0.572	0.51	0.452	0.572	SUBCLONAL	1	TRUE	1	0.34	2		822	1073	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11293466	11293466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	152	548	1	ENST00000361445.4:c.2410G>A	p.Glu804Lys	p.E804K	ENST00000361445	NM_004958.3	804	Gaa/Aaa	15/58	1	2	FACETS	0.801	0.737	0.868	1	0.99	1	CLONAL	2	TRUE	1	0.34	2		549	558	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984460	7984460	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	86	790	3	ENST00000319144.4:c.398G>T	p.Arg133Ile	p.R133I	ENST00000319144	NM_001139.2	133	aGa/aTa	3/15	1	2	FACETS	0.497	0.438	0.56	0.497	0.438	0.56	SUBCLONAL	1	TRUE	1	0.34	2		793	1018	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997499	149997499	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	33	303	0	ENST00000253339.5:c.2780A>G	p.Tyr927Cys	p.Y927C	ENST00000253339		927	tAc/tGc	6/7	1	2	FACETS	0.452	0.368	0.547	0.452	0.368	0.547	SUBCLONAL	1	TRUE	1	0.34	2		303	429	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199821	138199821	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	191	564	2	ENST00000237289.4:c.1239G>T	p.Lys413Asn	p.K413N	ENST00000237289	NM_001270507.1	413	aaG/aaT	7/9	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.34	2		566	761	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180441	94180441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139461096	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	93	645	0	ENST00000323929.3:c.1727G>A	p.Arg576Gln	p.R576Q	ENST00000323929	NM_005591.3	576	cGa/cAa	15/20	1	2	FACETS	0.555	0.493	0.623	0.555	0.493	0.623	SUBCLONAL	1	TRUE	1	0.34	2		645	985	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948079	178948079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	34	193	0	ENST00000263967.3:c.2851C>T	p.Arg951Cys	p.R951C	ENST00000263967	NM_006218.2	951	Cgt/Tgt	20/21	1	2	FACETS	0.769	0.632	0.922	0.769	0.632	0.922	CLONAL	1	TRUE	1	0.34	2		193	260	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332884	65332884	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	52	149	0	ENST00000342505.4:c.655C>T	p.Arg219Ter	p.R219*	ENST00000342505	NM_002227.2	219	Cga/Tga	7/25	1	2	FACETS	0.753	0.65	0.863	1	0.968	1	SUBCLONAL	2	TRUE	1	0.34	2		149	203	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63817051	63817051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	33	232	1	ENST00000279873.7:c.1022G>A	p.Arg341Gln	p.R341Q	ENST00000279873	NM_032199.2	341	cGa/cAa	6/10	1	2	FACETS	0.733	0.599	0.881	0.733	0.599	0.881	SUBCLONAL	1	TRUE	1	0.34	2		233	265	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550566	29550566	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	18	144	0	ENST00000356175.3:c.1826A>T	p.Lys609Ile	p.K609I	ENST00000356175	NM_000267.3	609	aAa/aTa	16/57	1	2	FACETS	0.56	0.423	0.72	0.56	0.423	0.72	SUBCLONAL	1	TRUE	1	0.34	2		144	189	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553610	29553610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1350468182	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	34	330	0	ENST00000356175.3:c.2159G>A	p.Arg720Gln	p.R720Q	ENST00000356175	NM_000267.3	720	cGg/cAg	18/57	1	2	FACETS	0.494	0.403	0.595	0.494	0.403	0.595	SUBCLONAL	1	TRUE	1	0.34	2		330	405	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303222	11303222	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747412972	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	227	648	1	ENST00000361445.4:c.1361G>A	p.Arg454His	p.R454H	ENST00000361445	NM_004958.3	454	cGc/cAc	9/58	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.34	2		649	969	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518921	187518921	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs748249672	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	80	506	0	ENST00000441802.2:c.12283G>T	p.Asp4095Tyr	p.D4095Y	ENST00000441802	NM_005245.3	4095	Gat/Tat	24/27	1	2	FACETS	0.662	0.582	0.747	0.662	0.582	0.747	SUBCLONAL	1	TRUE	1	0.34	2		506	711	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127414	55127414	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501504	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	128	594	0	ENST00000257290.5:c.202G>A	p.Asp68Asn	p.D68N	ENST00000257290	NM_006206.4	68	Gat/Aat	3/23	1	2	FACETS	0.76	0.688	0.836	0.76	0.688	0.836	SUBCLONAL	1	TRUE	1	0.34	2		594	991	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406163	70406163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773912826	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	59	579	0	ENST00000373644.4:c.3677C>T	p.Thr1226Met	p.T1226M	ENST00000373644	NM_030625.2	1226	aCg/aTg	4/12	1	2	FACETS	0.547	0.47	0.63	0.547	0.47	0.63	SUBCLONAL	1	TRUE	1	0.34	2		579	635	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341251	89341251	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	69	507	0	ENST00000301030.4:c.7684G>A	p.Glu2562Lys	p.E2562K	ENST00000301030	NM_001256183.1	2562	Gag/Aag	11/13	1	2	FACETS	0.645	0.562	0.735	0.645	0.562	0.735	SUBCLONAL	1	TRUE	1	0.34	2		507	629	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276929	123276929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200204947	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	59	420	1	ENST00000358487.5:c.988C>T	p.Arg330Trp	p.R330W	ENST00000358487	NM_000141.4	330	Cgg/Tgg	8/18	1	2	FACETS	0.717	0.618	0.825	0.717	0.618	0.825	SUBCLONAL	1	TRUE	1	0.34	2		421	484	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280032	66280032	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	17	276	0	ENST00000273854.3:c.1657C>T	p.Arg553Ter	p.R553*	ENST00000273854	NM_004439.5	553	Cga/Tga	7/18	1	2	FACETS	0.311	0.231	0.405	0.311	0.231	0.405	SUBCLONAL	1	TRUE	1	0.34	2		276	322	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532616	63532616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767111161	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	146	860	0	ENST00000307078.5:c.1963G>A	p.Glu655Lys	p.E655K	ENST00000307078	NM_004655.3	655	Gaa/Aaa	8/11	1	2	FACETS	0.658	0.598	0.72	0.658	0.598	0.72	SUBCLONAL	1	TRUE	1	0.34	2		860	1306	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964903	25964903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561088610	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	52	394	0	ENST00000435504.4:c.4303C>T	p.Arg1435Trp	p.R1435W	ENST00000435504		1435	Cgg/Tgg	13/13	1	2	FACETS	0.549	0.467	0.639	0.549	0.467	0.639	SUBCLONAL	1	TRUE	1	0.34	2		394	557	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876188	35876188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536561203	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	57	520	0	ENST00000303115.3:c.980C>T	p.Thr327Met	p.T327M	ENST00000303115	NM_002185.3	327	aCg/aTg	8/8	1	2	FACETS	0.522	0.447	0.604	0.522	0.447	0.604	SUBCLONAL	1	TRUE	1	0.34	2		520	642	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931826	68931826	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs759461290	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	77	426	0	ENST00000288368.4:c.256G>T	p.Glu86Ter	p.E86*	ENST00000288368	NM_024870.2	86	Gaa/Taa	3/40	1	2	FACETS	0.81	0.712	0.915	0.81	0.712	0.915	CLONAL	1	TRUE	1	0.34	2		426	559	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468149	31468149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	94	533	0	ENST00000344624.3:c.2263G>A	p.Asp755Asn	p.D755N	ENST00000344624		755	Gat/Aat	15/33	1	2	FACETS	0.708	0.63	0.792	0.708	0.63	0.792	SUBCLONAL	1	TRUE	1	0.34	2		533	781	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266570	115266570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	140	629	0	ENST00000438362.2:c.1945C>T	p.Arg649Cys	p.R649C	ENST00000438362	NM_001242891.1	649	Cgc/Tgc	16/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.34	2		629	686	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103525656	103525656	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	45	382	0	ENST00000355739.4:c.2927C>A	p.Ser976Tyr	p.S976Y	ENST00000355739	NM_000123.3	976	tCt/tAt	14/15	1	2	FACETS	0.537	0.451	0.632	0.537	0.451	0.632	SUBCLONAL	1	TRUE	1	0.34	2		382	493	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028639	12028639	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	50	434	0	ENST00000353533.5:c.842G>A	p.Arg281Gln	p.R281Q	ENST00000353533	NM_003010.3	281	cGa/cAa	8/11	1	2	FACETS	0.512	0.434	0.598	0.512	0.434	0.598	SUBCLONAL	1	TRUE	1	0.34	2		434	574	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191526	10191526	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	182	573	0	ENST00000256474.2:c.519G>T	p.Glu173Asp	p.E173D	ENST00000256474	NM_000551.3	173	gaG/gaT	3/3	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.34	2		573	775	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260151	149260151	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1307297959	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	57	503	1	ENST00000360632.3:c.742C>T	p.Arg248Ter	p.R248*	ENST00000360632	NM_015472.4	248	Cga/Tga	4/7	1	2	FACETS	0.452	0.387	0.524	0.452	0.387	0.524	SUBCLONAL	1	TRUE	1	0.34	2		504	741	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162945	38162945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs185811622	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	158	506	0	ENST00000317025.8:c.2261C>T	p.Ser754Leu	p.S754L	ENST00000317025	NM_023034.1	754	tCg/tTg	13/24	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.34	2		506	738	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352674	68352674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199981178	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	18	420	0	ENST00000487270.1:c.541C>T	p.Arg181Trp	p.R181W	ENST00000487270	NM_133509.3	181	Cgg/Tgg	6/11	1	2	FACETS	0.355	0.267	0.459	0.355	0.267	0.459	SUBCLONAL	1	TRUE	1	0.34	2		420	298	SUCCESS
APC	324	MSKCC	GRCh37	5	112175486	112175486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424719678	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	116	362	0	ENST00000257430.4:c.4195C>T	p.Arg1399Cys	p.R1399C	ENST00000257430	NM_000038.5	1399	Cgt/Tgt	16/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.34	2		362	516	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054649	5054649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373174105	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	23	244	2	ENST00000381652.3:c.701G>A	p.Arg234His	p.R234H	ENST00000381652	NM_004972.3	234	cGc/cAc	7/25	1	2	FACETS	0.535	0.418	0.669	0.535	0.418	0.669	SUBCLONAL	1	TRUE	1	0.34	2		246	253	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349904	89349904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141871215	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	198	869	2	ENST00000301030.4:c.3046G>A	p.Asp1016Asn	p.D1016N	ENST00000301030	NM_001256183.1	1016	Gat/Aat	9/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.34	2		871	1052	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242899	142242899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750252420	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	50	560	1	ENST00000350721.4:c.4088C>T	p.Ala1363Val	p.A1363V	ENST00000350721	NM_001184.3	1363	gCg/gTg	22/47	1	2	FACETS	0.43	0.364	0.503	0.43	0.364	0.503	SUBCLONAL	1	TRUE	1	0.34	2		561	684	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098638	2098638	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	76	590	2	ENST00000219476.3:c.22G>T	p.Asp8Tyr	p.D8Y	ENST00000219476	NM_000548.3	8	Gat/Tat	2/42	1	2	FACETS	0.511	0.447	0.58	0.511	0.447	0.58	SUBCLONAL	1	TRUE	1	0.34	2		592	875	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095873	29095873	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1555915433	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	231	616	0	ENST00000328354.6:c.961G>T	p.Glu321Ter	p.E321*	ENST00000328354	NM_007194.3	321	Gaa/Taa	9/15	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.34	2		616	983	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485254	8485254	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	59	411	0	ENST00000356435.5:c.3126G>T	p.Glu1042Asp	p.E1042D	ENST00000356435		1042	gaG/gaT	18/35	1	2	FACETS	0.693	0.597	0.797	0.693	0.597	0.797	SUBCLONAL	1	TRUE	1	0.34	2		411	501	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410598	63410598	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1394000391	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	97	860	1	ENST00000330258.3:c.2569C>T	p.Arg857Ter	p.R857*	ENST00000330258	NM_152424.3	857	Cga/Tga	2/2	1	2	FACETS	0.579	0.515	0.648	0.579	0.515	0.648	SUBCLONAL	1	TRUE	1	0.34	2		861	985	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438161	438161	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	164	427	0	ENST00000399788.2:c.1808G>A	p.Arg603Gln	p.R603Q	ENST00000399788	NM_001042603.1	603	cGa/cAa	14/28	0.3	2	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.34	2		427	646	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641221	3641221	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	191	930	0	ENST00000294008.3:c.2418G>T	p.Glu806Asp	p.E806D	ENST00000294008	NM_032444.2	806	gaG/gaT	12/15	1	2	FACETS	0.955	0.881	1	0.955	0.881	1	CLONAL	1	TRUE	1	0.34	2		930	1177	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210116	55210116	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778638117	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	40	398	0	ENST00000275493.2:c.226C>A	p.Leu76Ile	p.L76I	ENST00000275493	NM_005228.3	76	Ctt/Att	2/28	1	2	FACETS	0.468	0.388	0.556	0.468	0.388	0.556	SUBCLONAL	1	TRUE	1	0.34	2		398	503	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781403	135781403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759379027	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	101	638	0	ENST00000298552.3:c.1562C>T	p.Ser521Leu	p.S521L	ENST00000298552	NM_001162426.1	521	tCg/tTg	15/23	1	2	FACETS	0.65	0.58	0.725	0.65	0.58	0.725	SUBCLONAL	1	TRUE	1	0.34	2		638	914	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274310	5274310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	139	786	0	ENST00000357368.4:c.137C>T	p.Ser46Leu	p.S46L	ENST00000357368	NM_002850.3	46	tCg/tTg	3/38	1	2	FACETS	0.777	0.706	0.852	0.777	0.706	0.852	SUBCLONAL	1	TRUE	1	0.34	2		786	1052	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708603	43708603	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	60	448	2	ENST00000382044.4:c.4693G>T	p.Gly1565Ter	p.G1565*	ENST00000382044	NM_001141980.1	1565	Gga/Tga	22/28	1	2	FACETS	0.544	0.468	0.626	0.544	0.468	0.626	SUBCLONAL	1	TRUE	1	0.34	2		450	649	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37061814	37061814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752430684	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	72	493	0	ENST00000231790.2:c.898C>T	p.Pro300Ser	p.P300S	ENST00000231790	NM_000249.3	300	Ccc/Tcc	11/19	1	2	FACETS	0.69	0.603	0.784	0.69	0.603	0.784	SUBCLONAL	1	TRUE	1	0.34	2		493	614	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072541	5072541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368927897	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	40	337	0	ENST00000381652.3:c.1691G>A	p.Arg564Gln	p.R564Q	ENST00000381652	NM_004972.3	564	cGa/cAa	13/25	1	2	FACETS	0.682	0.568	0.808	0.682	0.568	0.808	SUBCLONAL	1	TRUE	1	0.34	2		337	345	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741473	145741473	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768850000	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	178	913	0	ENST00000428558.2:c.1030C>T	p.Arg344Trp	p.R344W	ENST00000428558	NM_004260.3	344	Cgg/Tgg	5/22	1	2	FACETS	0.893	0.821	0.967	0.893	0.821	0.967	CLONAL	1	TRUE	1	0.34	2		913	1173	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15821891	15821891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768039905	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	47	343	1	ENST00000307771.7:c.284C>T	p.Ala95Val	p.A95V	ENST00000307771	NM_005089.3	95	gCg/gTg	4/11	1	2	FACETS	0.556	0.469	0.652	0.556	0.469	0.652	SUBCLONAL	1	TRUE	1	0.34	2		344	497	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982057	38982057	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	44	465	0	ENST00000357387.3:c.665G>A	p.Arg222Gln	p.R222Q	ENST00000357387	NM_152756.3	222	cGa/cAa	8/38	1	2	FACETS	0.578	0.485	0.68	0.578	0.485	0.68	SUBCLONAL	1	TRUE	1	0.34	2		465	448	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252163	226252163	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	30	117	0	ENST00000366813.1:c.111G>T	p.Lys37Asn	p.K37N	ENST00000366813		37	aaG/aaT	1/3	1	2	FACETS	1	0.816	1	1	0.816	1	CLONAL	1	TRUE	1	0.34	2		117	176	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349892	15349892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1427595023	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	110	807	0	ENST00000263377.2:c.3760C>T	p.Arg1254Trp	p.R1254W	ENST00000263377	NM_058243.2	1254	Cgg/Tgg	18/20	1	2	FACETS	0.781	0.702	0.866	0.781	0.702	0.866	SUBCLONAL	1	TRUE	1	0.34	2		807	828	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210893	36210893	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	123	780	3	ENST00000222270.7:c.649del	p.Arg217GlyfsTer22	p.R217Gfs*22	ENST00000222270	NM_014727.1	215	aCc/ac	3/37	1	2	FACETS	0.77	0.695	0.849	0.77	0.695	0.849	SUBCLONAL	1	TRUE	1	0.34	2		783	940	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643705	38643705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1345810751	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	146	678	1	ENST00000299084.4:c.1175C>T	p.Ser392Leu	p.S392L	ENST00000299084	NM_152594.2	392	tCg/tTg	7/7	1	2	FACETS	0.841	0.767	0.919	0.841	0.767	0.919	CLONAL	1	TRUE	1	0.34	2		679	1021	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5073735	5073735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	36	210	0	ENST00000381652.3:c.1814C>T	p.Ser605Phe	p.S605F	ENST00000381652	NM_004972.3	605	tCt/tTt	14/25	1	2	FACETS	0.642	0.529	0.767	0.642	0.529	0.767	SUBCLONAL	1	TRUE	1	0.34	2		210	330	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291364	11291364	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1375320238	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	124	521	0	ENST00000361445.4:c.2642G>A	p.Arg881His	p.R881H	ENST00000361445	NM_004958.3	881	cGc/cAc	17/58	1	2	FACETS	0.934	0.845	1	0.934	0.845	1	CLONAL	1	TRUE	1	0.34	2		521	781	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109720	115109720	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	192	825	0	ENST00000257566.3:c.2158G>A	p.Glu720Lys	p.E720K	ENST00000257566	NM_016569.3	720	Gaa/Aaa	8/8	1	2	FACETS	0.929	0.857	1	0.929	0.857	1	CLONAL	1	TRUE	1	0.34	2		825	1216	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829497	72829497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761486040	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	265	567	0	ENST00000268489.5:c.7084G>A	p.Asp2362Asn	p.D2362N	ENST00000268489	NM_006885.3	2362	Gac/Aac	9/10	1	2	FACETS	1	0.967	1	1	0.995	1	CLONAL	2	TRUE	1	0.34	2		567	750	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211440	98211440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758411912	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	212	643	1	ENST00000331920.6:c.3715C>T	p.Arg1239Trp	p.R1239W	ENST00000331920	NM_000264.3	1239	Cgg/Tgg	22/24	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.34	2		644	881	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962543	100962544	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	233	564	0	ENST00000325455.5:c.1853dup	p.Asn618LysfsTer8	p.N618Kfs*8	ENST00000325455	NM_001202474.3	618	aac/aaAc	3/8	1	2	FACETS	0.812	0.759	0.866	1	0.993	1	CLONAL	2	TRUE	1	0.34	2		564	844	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905944	50905944	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755457889	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	149	873	2	ENST00000440232.2:c.916C>T	p.Arg306Cys	p.R306C	ENST00000440232	NM_002691.3	306	Cgc/Tgc	8/27	1	2	FACETS	0.878	0.802	0.959	0.878	0.802	0.959	CLONAL	1	TRUE	1	0.34	2		875	998	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916752	48916753	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	28	174	0	ENST00000267163.4:c.287dup	p.Glu97GlyfsTer13	p.E97Gfs*13	ENST00000267163	NM_000321.2	94	-/A	3/27	1	2	FACETS	0.608	0.487	0.744	0.608	0.487	0.744	SUBCLONAL	1	TRUE	1	0.34	2		174	271	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066712	77066712	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1482673833	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	45	317	0	ENST00000356341.3:c.772+1G>A		p.X258_splice	ENST00000356341	NM_002576.4	258			1	2	FACETS	0.774	0.653	0.907	0.774	0.653	0.907	CLONAL	1	TRUE	1	0.34	2		317	342	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517874	187517874	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs983524169	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	147	487	1	ENST00000441802.2:c.12820G>A	p.Glu4274Lys	p.E4274K	ENST00000441802	NM_005245.3	4274	Gaa/Aaa	25/27	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.34	2		488	672	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015053	27015053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151098324	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	119	503	0	ENST00000335756.4:c.155G>A	p.Arg52Gln	p.R52Q	ENST00000335756	NM_001809.3	52	cGa/cAa	2/5	1	2	FACETS	0.809	0.73	0.893	0.809	0.73	0.893	CLONAL	1	TRUE	1	0.34	2		503	865	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128432165	128432165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1371596131	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	41	114	0	ENST00000265960.3:c.281G>A	p.Arg94Gln	p.R94Q	ENST00000265960	NM_001006617.1	94	cGa/cAa	3/12	1	2	FACETS	0.89	0.746	1	0.89	0.746	1	CLONAL	1	TRUE	1	0.34	2		114	271	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020558	69020558	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753700	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	44	345	0	ENST00000288368.4:c.2930C>T	p.Ser977Leu	p.S977L	ENST00000288368	NM_024870.2	977	tCg/tTg	24/40	1	2	FACETS	0.616	0.517	0.725	0.616	0.517	0.725	SUBCLONAL	1	TRUE	1	0.34	2		345	420	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845355	89845355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778093769	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	101	786	0	ENST00000389301.3:c.1772G>A	p.Arg591Gln	p.R591Q	ENST00000389301	NM_000135.2	591	cGa/cAa	19/43	1	2	FACETS	0.511	0.455	0.571	0.511	0.455	0.571	SUBCLONAL	1	TRUE	1	0.34	2		786	1162	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222259	2222259	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371443260	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	264	837	2	ENST00000398665.3:c.3091G>A	p.Asp1031Asn	p.D1031N	ENST00000398665	NM_032482.2	1031	Gat/Aat	24/28	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.34	2		839	1078	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341701	8341701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766088715	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	56	433	1	ENST00000356435.5:c.4939G>A	p.Glu1647Lys	p.E1647K	ENST00000356435		1647	Gaa/Aaa	29/35	1	2	FACETS	0.626	0.537	0.724	0.626	0.537	0.724	SUBCLONAL	1	TRUE	1	0.34	2		434	526	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418986	116418986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199763277	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	108	317	0	ENST00000397752.3:c.3497G>A	p.Arg1166Gln	p.R1166Q	ENST00000397752	NM_000245.2	1166	cGa/cAa	17/21	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.34	2		317	448	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293719	1293719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1400139919	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	177	872	1	ENST00000310581.5:c.1282C>T	p.Arg428Trp	p.R428W	ENST00000310581	NM_198253.2	428	Cgg/Tgg	2/16	1	2	FACETS	0.995	0.916	1	0.995	0.916	1	CLONAL	1	TRUE	1	0.34	2		873	1046	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234270	39234270	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	41	287	0	ENST00000402219.2:c.2575C>A	p.Leu859Ile	p.L859I	ENST00000402219	NM_005633.3	859	Cta/Ata	16/23	1	2	FACETS	0.59	0.492	0.698	0.59	0.492	0.698	SUBCLONAL	1	TRUE	1	0.34	2		287	409	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682712	86682712	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	26	106	0	ENST00000274376.6:c.2917G>T	p.Glu973Ter	p.E973*	ENST00000274376	NM_002890.2	973	Gaa/Taa	23/25	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.34	2		106	136	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054631	5054631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760174050	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	19	222	0	ENST00000381652.3:c.683G>A	p.Arg228Gln	p.R228Q	ENST00000381652	NM_004972.3	228	cGa/cAa	7/25	1	2	FACETS	0.478	0.363	0.612	0.478	0.363	0.612	SUBCLONAL	1	TRUE	1	0.34	2		222	234	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060728	38060728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	184	1022	0	ENST00000250448.2:c.1261G>A	p.Glu421Lys	p.E421K	ENST00000250448	NM_004496.3	421	Gaa/Aaa	2/2	1	2	FACETS	0.855	0.787	0.926	0.855	0.787	0.926	CLONAL	1	TRUE	1	0.34	2		1022	1266	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614469	38614469	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	71	234	0	ENST00000299084.4:c.235G>T	p.Asp79Tyr	p.D79Y	ENST00000299084	NM_152594.2	79	Gac/Tac	3/7	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.34	2		234	335	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295255	15295255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752312396	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	103	861	0	ENST00000263388.2:c.2417G>A	p.Arg806Gln	p.R806Q	ENST00000263388	NM_000435.2	806	cGa/cAa	16/33	1	2	FACETS	0.55	0.491	0.613	0.55	0.491	0.613	SUBCLONAL	1	TRUE	1	0.34	2		861	1102	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508508	106508508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	94	314	0	ENST00000359195.3:c.502G>A	p.Val168Met	p.V168M	ENST00000359195	NM_002649.2	168	Gtg/Atg	2/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.34	2		314	383	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31451654	31451654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600599	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	36	309	0	ENST00000344624.3:c.2668C>T	p.Arg890Cys	p.R890C	ENST00000344624		890	Cgt/Tgt	18/33	1	2	FACETS	0.598	0.493	0.716	0.598	0.493	0.716	SUBCLONAL	1	TRUE	1	0.34	2		309	354	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230818	66230818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs910705978	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	77	269	0	ENST00000273854.3:c.2153G>A	p.Arg718His	p.R718H	ENST00000273854	NM_004439.5	718	cGc/cAc	12/18	1	2	FACETS	0.765	0.679	0.856	1	0.979	1	SUBCLONAL	2	TRUE	1	0.34	2		269	296	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738617	43738617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	94	467	0	ENST00000382044.4:c.3008C>T	p.Ala1003Val	p.A1003V	ENST00000382044	NM_001141980.1	1003	gCg/gTg	14/28	1	2	FACETS	0.772	0.687	0.863	0.772	0.687	0.863	SUBCLONAL	1	TRUE	1	0.34	2		467	716	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15952264	15952264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779213445	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	83	661	0	ENST00000268712.3:c.6431C>T	p.Ser2144Leu	p.S2144L	ENST00000268712	NM_006311.3	2144	tCg/tTg	41/46	1	2	FACETS	0.497	0.437	0.561	0.497	0.437	0.561	SUBCLONAL	1	TRUE	1	0.34	2		661	983	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170015161	170015161	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs866058843	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	79	477	2	ENST00000295797.4:c.1567C>T	p.Arg523Ter	p.R523*	ENST00000295797	NM_002740.5	523	Cga/Tga	16/18	1	2	FACETS	0.704	0.619	0.795	0.704	0.619	0.795	SUBCLONAL	1	TRUE	1	0.34	2		479	660	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525837	148525837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765147666	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	84	292	0	ENST00000320356.2:c.620G>A	p.Arg207Gln	p.R207Q	ENST00000320356	NM_004456.4	207	cGa/cAa	6/20	1	2	FACETS	0.751	0.669	0.837	1	0.98	1	SUBCLONAL	2	TRUE	1	0.34	2		292	329	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70967581	70967581	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	153	563	2	ENST00000276594.2:c.1442G>A	p.Arg481Gln	p.R481Q	ENST00000276594	NM_024504.3	481	cGa/cAa	7/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.34	2		565	678	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952164	76952164	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	18	115	0	ENST00000373344.5:c.271G>T	p.Glu91Ter	p.E91*	ENST00000373344	NM_000489.3	91	Gaa/Taa	5/35	1	2	FACETS	0.445	0.335	0.574	0.445	0.335	0.574	SUBCLONAL	1	TRUE	1	0.34	2		115	238	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656991	47656991	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	50	310	0	ENST00000233146.2:c.1187G>T	p.Arg396Ile	p.R396I	ENST00000233146	NM_000251.2	396	aGa/aTa	7/16	1	2	FACETS	0.593	0.503	0.691	0.593	0.503	0.691	SUBCLONAL	1	TRUE	1	0.34	2		310	496	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845479	128845479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	164	764	0	ENST00000249373.3:c.776C>T	p.Ser259Leu	p.S259L	ENST00000249373	NM_005631.4	259	tCg/tTg	4/12	1	2	FACETS	0.843	0.773	0.917	0.843	0.773	0.917	CLONAL	1	TRUE	1	0.34	2		764	1144	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222991	1222991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750366043	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	111	593	0	ENST00000326873.7:c.928C>T	p.Arg310Trp	p.R310W	ENST00000326873	NM_000455.4	310	Cgg/Tgg	8/10	1	2	FACETS	0.814	0.732	0.902	0.814	0.732	0.902	CLONAL	1	TRUE	1	0.34	2		593	802	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161392	55161392	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767697835	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	185	517	1	ENST00000257290.5:c.3223G>A	p.Asp1075Asn	p.D1075N	ENST00000257290	NM_006206.4	1075	Gac/Aac	23/23	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.34	2		518	755	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552212	29552212	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	33	412	0	ENST00000356175.3:c.1945G>T	p.Glu649Ter	p.E649*	ENST00000356175	NM_000267.3	649	Gaa/Taa	17/57	1	2	FACETS	0.447	0.364	0.541	0.447	0.364	0.541	SUBCLONAL	1	TRUE	1	0.34	2		412	434	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17941396	17941396	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	98	799	0	ENST00000458235.1:c.3012C>A	p.Phe1004Leu	p.F1004L	ENST00000458235	NM_000215.3	1004	ttC/ttA	22/24	1	2	FACETS	0.525	0.467	0.587	0.525	0.467	0.587	SUBCLONAL	1	TRUE	1	0.34	2		799	1098	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582911	95582911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143533680	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	65	324	0	ENST00000393063.1:c.1631G>A	p.Arg544Gln	p.R544Q	ENST00000393063	NM_030621.3	544	cGa/cAa	11/28	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.34	2		324	291	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391522	84391522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779497289	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	38	322	0	ENST00000321945.7:c.310C>T	p.Arg104Cys	p.R104C	ENST00000321945	NM_139076.2	104	Cgt/Tgt	5/9	1	2	FACETS	0.611	0.506	0.728	0.611	0.506	0.728	SUBCLONAL	1	TRUE	1	0.34	2		322	366	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967511	90967511	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	41	277	0	ENST00000265433.3:c.1397G>T	p.Arg466Met	p.R466M	ENST00000265433	NM_002485.4	466	aGg/aTg	10/16	1	2	FACETS	0.666	0.556	0.788	0.666	0.556	0.788	SUBCLONAL	1	TRUE	1	0.34	2		277	362	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120467977	120467977	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1131691315	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	99	689	3	ENST00000256646.2:c.4462G>A	p.Glu1488Lys	p.E1488K	ENST00000256646	NM_024408.3	1488	Gag/Aag	25/34	1	2	FACETS	0.545	0.485	0.609	0.545	0.485	0.609	SUBCLONAL	1	TRUE	1	0.34	2		692	1068	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724631	112724631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1333953583	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	41	483	0	ENST00000369452.4:c.515G>A	p.Arg172Gln	p.R172Q	ENST00000369452	NM_007373.3	172	cGg/cAg	2/9	1	2	FACETS	0.457	0.38	0.542	0.457	0.38	0.542	SUBCLONAL	1	TRUE	1	0.34	2		483	528	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813058	76813058	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	62	536	0	ENST00000373344.5:c.6563G>A	p.Arg2188Gln	p.R2188Q	ENST00000373344	NM_000489.3	2188	cGa/cAa	30/35	1	2	FACETS	0.746	0.645	0.855	0.746	0.645	0.855	SUBCLONAL	1	TRUE	1	0.34	2		536	489	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280292	1280292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201927653	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	339	847	0	ENST00000310581.5:c.1931C>T	p.Thr644Met	p.T644M	ENST00000310581	NM_198253.2	644	aCg/aTg	4/16	1	2	FACETS	0.798	0.754	0.842	1	0.995	1	SUBCLONAL	2	TRUE	1	0.34	2		847	1250	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967503	26967503	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	21	130	0	ENST00000381527.3:c.647-1G>T		p.X216_splice	ENST00000381527	NM_001260.1	216			1	2	FACETS	0.702	0.544	0.883	0.702	0.544	0.883	SUBCLONAL	1	TRUE	1	0.34	2		130	176	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093456	30093456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1008608681	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	20	150	0	ENST00000331968.5:c.1807C>T	p.Arg603Cys	p.R603C	ENST00000331968	NM_002742.2	603	Cgt/Tgt	13/18	1	2	FACETS	0.558	0.428	0.708	0.558	0.428	0.708	SUBCLONAL	1	TRUE	1	0.34	2		150	211	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47004894	47004894	+	intron_variant	Intron	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	194	927	0	ENST00000377604.3:c.-126+10G>A		p.*42*	ENST00000377604	NM_001204468.1	-/163			1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.34	2		927	768	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58700977	58700977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375732384	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	135	642	0	ENST00000305921.3:c.568G>A	p.Val190Ile	p.V190I	ENST00000305921	NM_003620.3	190	Gta/Ata	2/6	1	2	FACETS	0.821	0.746	0.901	0.821	0.746	0.901	CLONAL	1	TRUE	1	0.34	2		642	967	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093411	30093411	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs201154555	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	29	255	0	ENST00000331968.5:c.1852C>T	p.Arg618Ter	p.R618*	ENST00000331968	NM_002742.2	618	Cga/Tga	13/18	1	2	FACETS	0.461	0.37	0.565	0.461	0.37	0.565	SUBCLONAL	1	TRUE	1	0.34	2		255	370	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646149	215646149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881412	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	34	387	0	ENST00000260947.4:c.449G>A	p.Arg150Gln	p.R150Q	ENST00000260947	NM_000465.2	150	cGa/cAa	4/11	1	2	FACETS	0.48	0.392	0.578	0.48	0.392	0.578	SUBCLONAL	1	TRUE	1	0.34	2		387	417	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285186	15285186	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs975580649	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	172	862	2	ENST00000263388.2:c.4429G>A	p.Asp1477Asn	p.D1477N	ENST00000263388	NM_000435.2	1477	Gac/Aac	25/33	1	2	FACETS	0.79	0.725	0.858	0.79	0.725	0.858	SUBCLONAL	1	TRUE	1	0.34	2		864	1281	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784005	120784005	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	238	794	0	ENST00000257552.2:c.980C>T	p.Ser327Leu	p.S327L	ENST00000257552	NM_002442.3	327	tCg/tTg	13/15	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.34	2		794	1049	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10274006	10274006	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	113	506	0	ENST00000340748.4:c.874G>T	p.Asp292Tyr	p.D292Y	ENST00000340748		292	Gat/Tat	11/40	1	2	FACETS	0.836	0.752	0.925	0.836	0.752	0.925	CLONAL	1	TRUE	1	0.34	2		506	795	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568635	41568635	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1569118537	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	56	343	0	ENST00000263253.7:c.4585C>T	p.Arg1529Ter	p.R1529*	ENST00000263253	NM_001429.3	1529	Cga/Tga	28/31	1	2	FACETS	0.756	0.649	0.872	0.756	0.649	0.872	SUBCLONAL	1	TRUE	1	0.34	2		343	436	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515182	106515182	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	53	377	0	ENST00000359195.3:c.2325G>T	p.Gln775His	p.Q775H	ENST00000359195	NM_002649.2	775	caG/caT	5/11	1	2	FACETS	0.592	0.504	0.687	0.592	0.504	0.687	SUBCLONAL	1	TRUE	1	0.34	2		377	527	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464368	120464368	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1034013158	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	115	662	0	ENST00000256646.2:c.5278G>A	p.Asp1760Asn	p.D1760N	ENST00000256646	NM_024408.3	1760	Gat/Aat	29/34	1	2	FACETS	0.76	0.684	0.841	0.76	0.684	0.841	SUBCLONAL	1	TRUE	1	0.34	2		662	890	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539619	187539619	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	49	374	0	ENST00000441802.2:c.8121C>A	p.Phe2707Leu	p.F2707L	ENST00000441802	NM_005245.3	2707	ttC/ttA	10/27	1	2	FACETS	0.724	0.615	0.844	0.724	0.615	0.844	SUBCLONAL	1	TRUE	1	0.34	2		374	398	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024168	112024168	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	112	534	1	ENST00000368678.4:c.617G>A	p.Arg206His	p.R206H	ENST00000368678		206	cGc/cAc	7/13	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.34	2		535	547	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395775	45395775	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374809046	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	45	375	0	ENST00000262160.6:c.359G>A	p.Arg120Gln	p.R120Q	ENST00000262160	NM_005901.5	120	cGa/cAa	4/11	1	2	FACETS	0.603	0.507	0.709	0.603	0.507	0.709	SUBCLONAL	1	TRUE	1	0.34	2		375	439	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610328	81610328	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	51	430	0	ENST00000298171.2:c.1926C>A	p.Phe642Leu	p.F642L	ENST00000298171	NM_000369.2	642	ttC/ttA	10/10	1	2	FACETS	0.505	0.429	0.589	0.505	0.429	0.589	SUBCLONAL	1	TRUE	1	0.34	2		430	594	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508439	106508439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	66	344	0	ENST00000359195.3:c.433G>A	p.Glu145Lys	p.E145K	ENST00000359195	NM_002649.2	145	Gag/Aag	2/11	1	2	FACETS	0.995	0.868	1	0.995	0.868	1	CLONAL	1	TRUE	1	0.34	2		344	390	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517301	157517301	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	132	322	0	ENST00000346085.5:c.3865C>T	p.Pro1289Ser	p.P1289S	ENST00000346085	NM_020732.3	1289	Cct/Tct	16/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.34	2		322	523	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52722992	52722992	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1362406458	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	104	754	1	ENST00000322088.6:c.1177G>A	p.Glu393Lys	p.E393K	ENST00000322088	NM_014225.5	393	Gag/Aag	10/15	1	2	FACETS	0.591	0.528	0.658	0.591	0.528	0.658	SUBCLONAL	1	TRUE	1	0.34	2		755	1035	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851292	156851292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758359269	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	124	771	1	ENST00000524377.1:c.2249G>A	p.Arg750His	p.R750H	ENST00000524377	NM_002529.3	750	cGt/cAt	17/17	1	2	FACETS	0.795	0.718	0.875	0.795	0.718	0.875	SUBCLONAL	1	TRUE	1	0.34	2		772	918	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950343	15950343	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	142	575	0	ENST00000268712.3:c.6601A>G	p.Thr2201Ala	p.T2201A	ENST00000268712	NM_006311.3	2201	Aca/Gca	42/46	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.34	2		575	631	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519502	137519502	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	55	360	0	ENST00000367739.4:c.1136C>A	p.Ser379Tyr	p.S379Y	ENST00000367739	NM_000416.2	379	tCt/tAt	7/7	1	2	FACETS	0.815	0.699	0.94	0.815	0.699	0.94	CLONAL	1	TRUE	1	0.34	2		360	397	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444297	49444297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746163543	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	120	997	1	ENST00000301067.7:c.3074C>T	p.Ser1025Leu	p.S1025L	ENST00000301067	NM_003482.3	1025	tCg/tTg	11/54	1	2	FACETS	0.576	0.519	0.637	0.576	0.519	0.637	SUBCLONAL	1	TRUE	1	0.34	2		998	1225	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230572	46230572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1170640220	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	91	427	0	ENST00000334344.6:c.821G>A	p.Arg274Gln	p.R274Q	ENST00000334344	NM_152641.2	274	cGa/cAa	8/21	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.34	2		427	495	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319327	62319327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778782744	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	121	771	3	ENST00000360203.5:c.1519G>A	p.Asp507Asn	p.D507N	ENST00000360203	NM_001283009.1	507	Gac/Aac	18/35	1	2	FACETS	0.681	0.614	0.752	0.681	0.614	0.752	SUBCLONAL	1	TRUE	1	0.34	2		774	1045	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000305	42000305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1272090898	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	31	268	0	ENST00000219905.7:c.2324C>T	p.Ala775Val	p.A775V	ENST00000219905	NM_001164273.1	775	gCg/gTg	7/24	1	2	FACETS	0.546	0.442	0.663	0.546	0.442	0.663	SUBCLONAL	1	TRUE	1	0.34	2		268	334	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94910992	94910992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	208	557	0	ENST00000536441.1:c.1138C>T	p.Arg380Trp	p.R380W	ENST00000536441	NM_144665.3	380	Cgg/Tgg	8/10	1	2	FACETS	1	0.94	1	1	0.994	1	CLONAL	2	TRUE	1	0.34	2		557	608	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098936	47098936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	112	560	0	ENST00000409792.3:c.6338G>A	p.Arg2113His	p.R2113H	ENST00000409792	NM_014159.6	2113	cGc/cAc	15/21	1	2	FACETS	0.748	0.672	0.828	0.748	0.672	0.828	SUBCLONAL	1	TRUE	1	0.34	2		560	881	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133803	41133803	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768488321	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	41	373	0	ENST00000379561.5:c.1825C>T	p.Arg609Cys	p.R609C	ENST00000379561	NM_002015.3	609	Cgc/Tgc	2/3	1	2	FACETS	0.515	0.429	0.611	0.515	0.429	0.611	SUBCLONAL	1	TRUE	1	0.34	2		373	468	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448552	89448552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	77	589	0	ENST00000336596.2:c.1516G>A	p.Val506Ile	p.V506I	ENST00000336596	NM_005233.5	506	Gta/Ata	7/17	1	2	FACETS	0.55	0.482	0.623	0.55	0.482	0.623	SUBCLONAL	1	TRUE	1	0.34	2		589	824	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261326	16261326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760319148	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	69	658	0	ENST00000375759.3:c.8591C>T	p.Ser2864Leu	p.S2864L	ENST00000375759	NM_015001.2	2864	tCg/tTg	11/15	1	2	FACETS	0.5	0.434	0.571	0.5	0.434	0.571	SUBCLONAL	1	TRUE	1	0.34	2		658	812	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641447	47641447	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	94	254	0	ENST00000233146.2:c.832G>T	p.Glu278Ter	p.E278*	ENST00000233146	NM_000251.2	278	Gaa/Taa	5/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.34	2		254	451	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251853	8251853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748397251	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	90	671	0	ENST00000335790.3:c.224G>A	p.Arg75Gln	p.R75Q	ENST00000335790	NM_002315.2	75	cGa/cAa	2/4	1	2	FACETS	0.56	0.496	0.629	0.56	0.496	0.629	SUBCLONAL	1	TRUE	1	0.34	2		671	945	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512179	120512179	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781979575	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	48	533	0	ENST00000256646.2:c.1063G>A	p.Asp355Asn	p.D355N	ENST00000256646	NM_024408.3	355	Gac/Aac	6/34	1	2	FACETS	0.362	0.305	0.426	0.362	0.305	0.426	SUBCLONAL	1	TRUE	1	0.34	2		533	779	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828333	50828333	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	84	439	3	ENST00000398568.2:c.2671C>T	p.Arg891Trp	p.R891W	ENST00000398568	NM_001042412.1	891	Cgg/Tgg	17/18	1	2	FACETS	0.787	0.695	0.885	0.787	0.695	0.885	SUBCLONAL	1	TRUE	1	0.34	2		442	628	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434643	128434643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371524490	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	65	622	1	ENST00000265960.3:c.211G>A	p.Asp71Asn	p.D71N	ENST00000265960	NM_001006617.1	71	Gat/Aat	2/12	1	2	FACETS	0.527	0.456	0.604	0.527	0.456	0.604	SUBCLONAL	1	TRUE	1	0.34	2		623	725	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286951	33286951	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1453165364	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	90	744	0	ENST00000374542.5:c.1986G>T	p.Lys662Asn	p.K662N	ENST00000374542	NM_001141970.1	662	aaG/aaT	7/8	1	2	FACETS	0.574	0.508	0.645	0.574	0.508	0.645	SUBCLONAL	1	TRUE	1	0.34	2		744	922	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246297	46246297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770601353	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	64	372	0	ENST00000334344.6:c.4391G>A	p.Arg1464His	p.R1464H	ENST00000334344	NM_152641.2	1464	cGc/cAc	15/21	1	2	FACETS	0.773	0.671	0.884	0.773	0.671	0.884	SUBCLONAL	1	TRUE	1	0.34	2		372	487	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202176	138202176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763346708	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	173	523	0	ENST00000237289.4:c.2093C>T	p.Ser698Leu	p.S698L	ENST00000237289	NM_001270507.1	698	tCg/tTg	9/9	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.34	2		523	679	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670256	134670256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	91	524	1	ENST00000398015.3:c.167G>A	p.Arg56His	p.R56H	ENST00000398015	NM_004441.4	56	cGc/cAc	3/16	1	2	FACETS	0.709	0.629	0.794	0.709	0.629	0.794	SUBCLONAL	1	TRUE	1	0.34	2		525	755	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517885	187517885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1222913841	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	77	499	0	ENST00000441802.2:c.12809G>A	p.Arg4270Gln	p.R4270Q	ENST00000441802	NM_005245.3	4270	cGa/cAa	25/27	1	2	FACETS	0.655	0.574	0.741	0.655	0.574	0.741	SUBCLONAL	1	TRUE	1	0.34	2		499	692	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566300	141566300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	76	490	0	ENST00000220592.5:c.1112C>T	p.Ser371Leu	p.S371L	ENST00000220592	NM_012154.3	371	tCg/tTg	9/19	1	2	FACETS	0.566	0.496	0.642	0.566	0.496	0.642	SUBCLONAL	1	TRUE	1	0.34	2		490	790	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539012	187539012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753412687	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	91	586	0	ENST00000441802.2:c.8728G>A	p.Asp2910Asn	p.D2910N	ENST00000441802	NM_005245.3	2910	Gat/Aat	10/27	1	2	FACETS	0.65	0.576	0.728	0.65	0.576	0.728	SUBCLONAL	1	TRUE	1	0.34	2		586	824	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149886	202149886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	156	605	0	ENST00000358485.4:c.1327G>A	p.Asp443Asn	p.D443N	ENST00000358485	NM_001080125.1	443	Gat/Aat	8/9	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.34	2		605	746	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198263198	198263198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	47	282	0	ENST00000335508.6:c.3121C>T	p.Arg1041Cys	p.R1041C	ENST00000335508	NM_012433.2	1041	Cgt/Tgt	21/25	1	2	FACETS	0.757	0.641	0.885	0.757	0.641	0.885	SUBCLONAL	1	TRUE	1	0.34	2		282	365	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021103	31021103	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	76	560	0	ENST00000375687.4:c.1102G>T	p.Glu368Ter	p.E368*	ENST00000375687	NM_015338.5	368	Gaa/Taa	12/13	1	2	FACETS	0.514	0.45	0.584	0.514	0.45	0.584	SUBCLONAL	1	TRUE	1	0.34	2		560	869	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771166	161771166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1490851246	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	136	728	3	ENST00000366898.1:c.1363C>T	p.Arg455Cys	p.R455C	ENST00000366898	NM_004562.2	455	Cgc/Tgc	12/12	1	2	FACETS	0.725	0.657	0.795	0.725	0.657	0.795	SUBCLONAL	1	TRUE	1	0.34	2		731	1104	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273245	198273245	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	199	559	0	ENST00000335508.6:c.965C>A	p.Ser322Tyr	p.S322Y	ENST00000335508	NM_012433.2	322	tCt/tAt	8/25	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.34	2		559	843	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215617254	215617254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757281184	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	36	319	0	ENST00000260947.4:c.1594G>A	p.Asp532Asn	p.D532N	ENST00000260947	NM_000465.2	532	Gat/Aat	7/11	1	2	FACETS	0.592	0.487	0.708	0.592	0.487	0.708	SUBCLONAL	1	TRUE	1	0.34	2		319	358	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540917	187540917	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558300184	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	80	375	1	ENST00000441802.2:c.6823G>A	p.Asp2275Asn	p.D2275N	ENST00000441802	NM_005245.3	2275	Gac/Aac	10/27	1	2	FACETS	0.943	0.833	1	0.943	0.833	1	CLONAL	1	TRUE	1	0.34	2		376	499	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123080	5123080	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	35	448	0	ENST00000381652.3:c.3136G>T	p.Glu1046Ter	p.E1046*	ENST00000381652	NM_004972.3	1046	Gaa/Taa	23/25	1	2	FACETS	0.424	0.347	0.51	0.424	0.347	0.51	SUBCLONAL	1	TRUE	1	0.34	2		448	486	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934525	9934525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	57	477	0	ENST00000330684.3:c.1630G>A	p.Val544Ile	p.V544I	ENST00000330684	NM_001134407.1	544	Gtc/Atc	7/13	1	2	FACETS	0.589	0.505	0.681	0.589	0.505	0.681	SUBCLONAL	1	TRUE	1	0.34	2		477	569	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911561	134911561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757883750	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	144	672	1	ENST00000398015.3:c.2026G>A	p.Asp676Asn	p.D676N	ENST00000398015	NM_004441.4	676	Gac/Aac	11/16	1	2	FACETS	0.999	0.911	1	0.999	0.911	1	CLONAL	1	TRUE	1	0.34	2		673	848	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865314	57865314	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	115	810	0	ENST00000228682.2:c.2791C>A	p.Leu931Met	p.L931M	ENST00000228682	NM_005269.2	931	Ctg/Atg	12/12	1	2	FACETS	0.614	0.552	0.68	0.614	0.552	0.68	SUBCLONAL	1	TRUE	1	0.34	2		810	1102	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430201	181430201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	60	315	1	ENST00000325404.1:c.53C>T	p.Ser18Leu	p.S18L	ENST00000325404	NM_003106.3	18	tCg/tTg	1/1	1	2	FACETS	0.859	0.742	0.984	0.859	0.742	0.984	CLONAL	1	TRUE	1	0.34	2		316	411	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993674	72993674	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	97	768	0	ENST00000268489.5:c.371G>T	p.Ser124Ile	p.S124I	ENST00000268489	NM_006885.3	124	aGt/aTt	2/10	1	2	FACETS	0.64	0.57	0.716	0.64	0.57	0.716	SUBCLONAL	1	TRUE	1	0.34	2		768	891	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40469240	40469240	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs747667389	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	50	395	2	ENST00000264657.5:c.2104G>A	p.Ala702Thr	p.A702T	ENST00000264657	NM_139276.2	702	Gct/Act	22/24	1	2	FACETS	0.493	0.417	0.575	0.493	0.417	0.575	SUBCLONAL	1	TRUE	1	0.34	2		397	597	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224206	98224206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750373573	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	39	404	0	ENST00000331920.6:c.2635G>A	p.Asp879Asn	p.D879N	ENST00000331920	NM_000264.3	879	Gat/Aat	16/24	1	2	FACETS	0.361	0.298	0.431	0.361	0.298	0.431	SUBCLONAL	1	TRUE	1	0.34	2		404	636	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40856677	40856677	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs376492983	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	47	375	1	ENST00000428826.2:c.1960C>T	p.Arg654Ter	p.R654*	ENST00000428826		654	Cga/Tga	18/21	1	2	FACETS	0.54	0.455	0.633	0.54	0.455	0.633	SUBCLONAL	1	TRUE	1	0.34	2		376	512	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3645656	3645656	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	267	845	0	ENST00000294008.3:c.1963T>C	p.Phe655Leu	p.F655L	ENST00000294008	NM_032444.2	655	Ttt/Ctt	9/15	1	2	FACETS	0.759	0.712	0.807	1	0.993	1	SUBCLONAL	2	TRUE	1	0.34	2		845	1035	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891412	76891412	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	54	221	0	ENST00000373344.5:c.4693G>T	p.Val1565Leu	p.V1565L	ENST00000373344	NM_000489.3	1565	Gta/Tta	16/35	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.34	2		221	290	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434992	110434992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	93	820	0	ENST00000375856.3:c.3409C>T	p.Arg1137Cys	p.R1137C	ENST00000375856	NM_003749.2	1137	Cgc/Tgc	1/2	1	2	FACETS	0.563	0.5	0.632	0.563	0.5	0.632	SUBCLONAL	1	TRUE	1	0.34	2		820	971	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115267948	115267948	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	36	395	0	ENST00000438362.2:c.1785C>A	p.Phe595Leu	p.F595L	ENST00000438362	NM_001242891.1	595	ttC/ttA	15/20	1	2	FACETS	0.411	0.337	0.494	0.411	0.337	0.494	SUBCLONAL	1	TRUE	1	0.34	2		395	515	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169474	11169474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555795341	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	194	735	0	ENST00000358026.2:c.4640G>A	p.Arg1547His	p.R1547H	ENST00000358026	NM_001128849.1	1547	cGc/cAc	33/36	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.34	2		735	951	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856392	111856392	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868066223	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	46	115	0	ENST00000341259.2:c.443G>A	p.Arg148His	p.R148H	ENST00000341259	NM_005475.2	148	cGc/cAc	2/8	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.34	2		115	228	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583923	46583923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	217	474	0	ENST00000263734.3:c.430C>T	p.Arg144Cys	p.R144C	ENST00000263734	NM_001430.4	144	Cgt/Tgt	4/16	1	2	FACETS	0.99	0.925	1	1	0.994	1	CLONAL	2	TRUE	1	0.34	2		474	645	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903815	41903815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	126	680	0	ENST00000372991.4:c.742G>A	p.Glu248Lys	p.E248K	ENST00000372991	NM_001760.3	248	Gaa/Aaa	5/5	1	2	FACETS	0.907	0.822	0.997	0.907	0.822	0.997	CLONAL	1	TRUE	1	0.34	2		680	817	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828251	72828251	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	125	665	0	ENST00000268489.5:c.8330G>A	p.Ser2777Asn	p.S2777N	ENST00000268489	NM_006885.3	2777	aGt/aAt	9/10	1	2	FACETS	0.855	0.774	0.941	0.855	0.774	0.941	CLONAL	1	TRUE	1	0.34	2		665	860	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061636	38061636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	50	249	0	ENST00000250448.2:c.353C>T	p.Ala118Val	p.A118V	ENST00000250448	NM_004496.3	118	gCg/gTg	2/2	1	2	FACETS	0.943	0.804	1	0.943	0.804	1	CLONAL	1	TRUE	1	0.34	2		249	312	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628869	187628869	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200902471	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	63	600	1	ENST00000441802.2:c.2113G>A	p.Asp705Asn	p.D705N	ENST00000441802	NM_005245.3	705	Gat/Aat	2/27	1	2	FACETS	0.514	0.444	0.59	0.514	0.444	0.59	SUBCLONAL	1	TRUE	1	0.34	2		601	721	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227600	36227600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367682204	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	76	531	0	ENST00000222270.7:c.7169C>T	p.Ser2390Leu	p.S2390L	ENST00000222270	NM_014727.1	2390	tCg/tTg	31/37	1	2	FACETS	0.699	0.613	0.791	0.699	0.613	0.791	SUBCLONAL	1	TRUE	1	0.34	2		531	640	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390416	118390416	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520053	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	111	611	1	ENST00000534358.1:c.11230C>T	p.Arg3744Ter	p.R3744*	ENST00000534358	NM_005933.3	3744	Cga/Tga	32/36	1	2	FACETS	0.687	0.617	0.762	0.687	0.617	0.762	SUBCLONAL	1	TRUE	1	0.34	2		612	950	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727188	40727188	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	180	563	0	ENST00000373198.4:c.3776A>G	p.His1259Arg	p.H1259R	ENST00000373198	NM_133170.3	1259	cAc/cGc	28/32	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.34	2		563	803	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663590	117663590	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	61	265	0	ENST00000368508.3:c.4642G>T	p.Glu1548Ter	p.E1548*	ENST00000368508	NM_002944.2	1548	Gag/Tag	28/43	1	2	FACETS	0.983	0.852	1	0.983	0.852	1	CLONAL	1	TRUE	1	0.34	2		265	365	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949769	151949769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760928040	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	100	348	0	ENST00000262189.6:c.1331G>A	p.Arg444Gln	p.R444Q	ENST00000262189	NM_170606.2	444	cGg/cAg	10/59	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.34	2		348	494	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263350	123263350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	108	552	1	ENST00000358487.5:c.1393G>A	p.Glu465Lys	p.E465K	ENST00000358487	NM_000141.4	465	Gag/Aag	10/18	1	2	FACETS	0.844	0.757	0.935	0.844	0.757	0.935	CLONAL	1	TRUE	1	0.34	2		553	753	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860907	151860907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	38	297	0	ENST00000262189.6:c.9755G>A	p.Arg3252His	p.R3252H	ENST00000262189	NM_170606.2	3252	cGt/cAt	43/59	1	2	FACETS	0.688	0.57	0.818	0.688	0.57	0.818	SUBCLONAL	1	TRUE	1	0.34	2		297	325	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781281	9781281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	89	790	4	ENST00000377346.4:c.1786G>A	p.Ala596Thr	p.A596T	ENST00000377346	NM_005026.3	596	Gcc/Acc	14/24	1	2	FACETS	0.535	0.473	0.601	0.535	0.473	0.601	SUBCLONAL	1	TRUE	1	0.34	2		794	979	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187822	11187822	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	120	575	0	ENST00000361445.4:c.6075G>T	p.Glu2025Asp	p.E2025D	ENST00000361445	NM_004958.3	2025	gaG/gaT	44/58	1	2	FACETS	0.875	0.79	0.964	0.875	0.79	0.964	CLONAL	1	TRUE	1	0.34	2		575	807	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259424	11259424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	96	516	1	ENST00000361445.4:c.4144C>A	p.Leu1382Met	p.L1382M	ENST00000361445	NM_004958.3	1382	Ctg/Atg	28/58	1	2	FACETS	0.776	0.691	0.866	0.776	0.691	0.866	SUBCLONAL	1	TRUE	1	0.34	2		517	728	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259444	11259444	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	99	488	0	ENST00000361445.4:c.4124G>T	p.Arg1375Ile	p.R1375I	ENST00000361445	NM_004958.3	1375	aGa/aTa	28/58	1	2	FACETS	0.811	0.724	0.903	0.811	0.724	0.903	CLONAL	1	TRUE	1	0.34	2		488	718	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11313928	11313928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	233	702	0	ENST00000361445.4:c.808G>A	p.Glu270Lys	p.E270K	ENST00000361445	NM_004958.3	270	Gag/Aag	6/58	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.34	2		702	931	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16174584	16174584	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	47	392	0	ENST00000375759.3:c.22C>A	p.Leu8Ile	p.L8I	ENST00000375759	NM_015001.2	8	Ctc/Atc	1/15	1	2	FACETS	0.431	0.363	0.507	0.431	0.363	0.507	SUBCLONAL	1	TRUE	1	0.34	2		392	641	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16235925	16235925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	76	444	0	ENST00000375759.3:c.991C>T	p.Pro331Ser	p.P331S	ENST00000375759	NM_015001.2	331	Ccc/Tcc	4/15	1	2	FACETS	0.571	0.5	0.648	0.571	0.5	0.648	SUBCLONAL	1	TRUE	1	0.34	2		444	783	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242644	16242644	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	31	366	0	ENST00000375759.3:c.1265T>G	p.Phe422Cys	p.F422C	ENST00000375759	NM_015001.2	422	tTt/tGt	6/15	1	2	FACETS	0.397	0.321	0.484	0.397	0.321	0.484	SUBCLONAL	1	TRUE	1	0.34	2		366	459	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254858	16254858	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	83	595	0	ENST00000375759.3:c.2123G>T	p.Arg708Ile	p.R708I	ENST00000375759	NM_015001.2	708	aGa/aTa	11/15	1	2	FACETS	0.598	0.527	0.674	0.598	0.527	0.674	SUBCLONAL	1	TRUE	1	0.34	2		595	817	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256495	16256495	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	121	700	0	ENST00000375759.3:c.3760G>T	p.Asp1254Tyr	p.D1254Y	ENST00000375759	NM_015001.2	1254	Gat/Tat	11/15	1	2	FACETS	0.76	0.686	0.839	0.76	0.686	0.839	SUBCLONAL	1	TRUE	1	0.34	2		700	936	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262357	16262357	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200205688	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	60	349	0	ENST00000375759.3:c.9622G>A	p.Glu3208Lys	p.E3208K	ENST00000375759	NM_015001.2	3208	Gag/Aag	11/15	1	2	FACETS	0.832	0.719	0.955	0.832	0.719	0.955	CLONAL	1	TRUE	1	0.34	2		349	424	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22408288	22408288	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	21	211	0	ENST00000344548.3:c.178+1G>A		p.X60_splice	ENST00000344548	NM_001039802.1	60			1	2	FACETS	0.463	0.357	0.586	0.463	0.357	0.586	SUBCLONAL	1	TRUE	1	0.34	2		211	267	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28601444	28601444	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	97	711	1	ENST00000253063.3:c.1129A>G	p.Thr377Ala	p.T377A	ENST00000253063	NM_031459.4	377	Acc/Gcc	8/10	1	2	FACETS	0.589	0.524	0.659	0.589	0.524	0.659	SUBCLONAL	1	TRUE	1	0.34	2		712	968	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36826893	36826893	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201394626	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	105	689	1	ENST00000373129.3:c.41C>T	p.Ser14Leu	p.S14L	ENST00000373129	NM_032017.1	14	tCg/tTg	3/12	1	2	FACETS	0.612	0.547	0.681	0.612	0.547	0.681	SUBCLONAL	1	TRUE	1	0.34	2		690	1009	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39311661	39311661	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	39	274	0	ENST00000373001.3:c.998A>C	p.Lys333Thr	p.K333T	ENST00000373001	NM_022157.3	333	aAa/aCa	6/7	1	2	FACETS	0.511	0.423	0.608	0.511	0.423	0.608	SUBCLONAL	1	TRUE	1	0.34	2		274	449	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322572	39322572	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	51	508	0	ENST00000373001.3:c.420G>T	p.Leu140Phe	p.L140F	ENST00000373001	NM_022157.3	140	ttG/ttT	2/7	1	2	FACETS	0.613	0.522	0.714	0.613	0.522	0.714	SUBCLONAL	1	TRUE	1	0.34	2		508	489	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797942	45797942	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1553127779	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	51	836	0	ENST00000450313.1:c.829G>T	p.Asp277Tyr	p.D277Y	ENST00000450313	NM_012222.2	277	Gat/Tat	10/16	1	2	FACETS	0.299	0.252	0.349	0.299	0.252	0.349	SUBCLONAL	1	TRUE	1	0.34	2		836	1005	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726400	46726400	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	64	509	0	ENST00000371975.4:c.479G>T	p.Gly160Val	p.G160V	ENST00000371975	NM_003579.3	160	gGa/gTa	7/18	1	2	FACETS	0.621	0.538	0.712	0.621	0.538	0.712	SUBCLONAL	1	TRUE	1	0.34	2		509	606	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436072	51436072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748312116	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	69	434	0	ENST00000262662.1:c.32C>T	p.Ser11Phe	p.S11F	ENST00000262662		11	tCc/tTc	3/4	1	2	FACETS	0.595	0.518	0.679	0.595	0.518	0.679	SUBCLONAL	1	TRUE	1	0.34	2		434	682	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439634	51439634	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	73	405	0	ENST00000262662.1:c.199G>A	p.Asp67Asn	p.D67N	ENST00000262662		67	Gac/Aac	4/4	1	2	FACETS	0.702	0.614	0.796	0.702	0.614	0.796	SUBCLONAL	1	TRUE	1	0.34	2		405	612	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310556	65310556	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	174	494	0	ENST00000342505.4:c.2132T>C	p.Val711Ala	p.V711A	ENST00000342505	NM_002227.2	711	gTc/gCc	16/25	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.34	2		494	713	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344822	65344822	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	56	320	0	ENST00000342505.4:c.215C>A	p.Pro72His	p.P72H	ENST00000342505	NM_002227.2	72	cCt/cAt	4/25	1	2	FACETS	0.756	0.649	0.872	0.756	0.649	0.872	SUBCLONAL	1	TRUE	1	0.34	2		320	436	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076766	72076766	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	139	585	0	ENST00000357731.5:c.731G>T	p.Arg244Ile	p.R244I	ENST00000357731	NM_173808.2	244	aGa/aTa	5/7	1	2	FACETS	0.869	0.79	0.952	0.869	0.79	0.952	CLONAL	1	TRUE	1	0.34	2		585	941	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400791	72400791	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	30	311	0	ENST00000357731.5:c.380G>T	p.Arg127Ile	p.R127I	ENST00000357731	NM_173808.2	127	aGa/aTa	2/7	1	2	FACETS	0.538	0.434	0.656	0.538	0.434	0.656	SUBCLONAL	1	TRUE	1	0.34	2		311	328	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165572	118165572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1374365686	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	81	452	1	ENST00000369448.3:c.82G>A	p.Val28Ile	p.V28I	ENST00000369448	NM_017709.3	28	Gtc/Atc	2/2	1	2	FACETS	0.744	0.656	0.839	0.744	0.656	0.839	SUBCLONAL	1	TRUE	1	0.34	2		453	640	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458083	120458083	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	117	724	2	ENST00000256646.2:c.7262C>A	p.Ser2421Tyr	p.S2421Y	ENST00000256646	NM_024408.3	2421	tCt/tAt	34/34	1	2	FACETS	0.786	0.708	0.868	0.786	0.708	0.868	SUBCLONAL	1	TRUE	1	0.34	2		726	876	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724494	162724494	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1286548568	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	198	596	0	ENST00000367921.3:c.266T>C	p.Ile89Thr	p.I89T	ENST00000367921	NM_006182.2	89	aTt/aCt	5/18	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.34	2		596	838	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163310212	163310212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138752079	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	32	175	0	ENST00000271452.3:c.665G>A	p.Arg222His	p.R222H	ENST00000271452	NM_145697.2	222	cGt/cAt	9/14	1	2	FACETS	0.599	0.488	0.725	0.599	0.488	0.725	SUBCLONAL	1	TRUE	1	0.34	2		175	314	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957439	175957439	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	56	338	0	ENST00000367669.3:c.1957G>T	p.Asp653Tyr	p.D653Y	ENST00000367669	NM_022457.5	653	Gat/Tat	17/20	1	2	FACETS	0.729	0.626	0.841	0.729	0.626	0.841	SUBCLONAL	1	TRUE	1	0.34	2		338	452	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012322	176012322	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	69	316	0	ENST00000367669.3:c.1612G>T	p.Val538Leu	p.V538L	ENST00000367669	NM_022457.5	538	Gtg/Ttg	14/20	1	2	FACETS	0.886	0.774	1	0.886	0.774	1	CLONAL	1	TRUE	1	0.34	2		316	458	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176105672	176105672	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	22	168	0	ENST00000367669.3:c.843G>T	p.Gln281His	p.Q281H	ENST00000367669	NM_022457.5	281	caG/caT	7/20	1	2	FACETS	0.512	0.397	0.644	0.512	0.397	0.644	SUBCLONAL	1	TRUE	1	0.34	2		168	253	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226590039	226590039	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	240	638	0	ENST00000366794.5:c.162C>A	p.Phe54Leu	p.F54L	ENST00000366794	NM_001618.3	54	ttC/ttA	2/23	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.34	2		638	1035	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243777011	243777011	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	32	288	0	ENST00000263826.5:c.658C>A	p.Arg220Ser	p.R220S	ENST00000263826	NM_005465.4	220	Cgt/Agt	7/13	1	2	FACETS	0.462	0.375	0.561	0.462	0.375	0.561	SUBCLONAL	1	TRUE	1	0.34	2		288	407	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243778435	243778435	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	22	107	0	ENST00000263826.5:c.590G>T	p.Ser197Ile	p.S197I	ENST00000263826	NM_005465.4	197	aGc/aTc	6/13	1	2	FACETS	0.52	0.404	0.654	0.52	0.404	0.654	SUBCLONAL	1	TRUE	1	0.34	2		107	249	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246490640	246490640	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	40	219	0	ENST00000388985.4:c.395-1G>A		p.X132_splice	ENST00000388985		132			1	2	FACETS	0.888	0.742	1	0.888	0.742	1	CLONAL	1	TRUE	1	0.34	2		219	265	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670438	246670438	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	158	679	0	ENST00000388985.4:c.82G>T	p.Glu28Ter	p.E28*	ENST00000388985		28	Gag/Tag	1/12	1	2	FACETS	0.948	0.868	1	0.948	0.868	1	CLONAL	1	TRUE	1	0.34	2		679	980	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115851	8115851	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	130	704	0	ENST00000346208.3:c.1197C>A	p.His399Gln	p.H399Q	ENST00000346208		399	caC/caA	6/6	1	2	FACETS	0.745	0.675	0.82	0.745	0.675	0.82	SUBCLONAL	1	TRUE	1	0.34	2		704	1026	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615032	43615032	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	117	692	0	ENST00000355710.3:c.2446C>A	p.Leu816Ile	p.L816I	ENST00000355710	NM_020975.4	816	Ctc/Atc	14/20	1	2	FACETS	0.815	0.735	0.901	0.815	0.735	0.901	CLONAL	1	TRUE	1	0.34	2		692	844	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63810759	63810759	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	61	400	0	ENST00000279873.7:c.846G>T	p.Lys282Asn	p.K282N	ENST00000279873	NM_032199.2	282	aaG/aaT	5/10	1	2	FACETS	0.576	0.497	0.662	0.576	0.497	0.662	SUBCLONAL	1	TRUE	1	0.34	2		400	623	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724663	112724663	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	47	454	1	ENST00000369452.4:c.547G>T	p.Glu183Ter	p.E183*	ENST00000369452	NM_007373.3	183	Gaa/Taa	2/9	1	2	FACETS	0.519	0.437	0.608	0.519	0.437	0.608	SUBCLONAL	1	TRUE	1	0.34	2		455	533	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14300915	14300915	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	11	154	0	ENST00000256196.4:c.583G>T	p.Asp195Tyr	p.D195Y	ENST00000256196		195	Gac/Tac	6/6	1	2	FACETS	0.301	0.208	0.417	0.301	0.208	0.417	SUBCLONAL	1	TRUE	1	0.34	2		154	215	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64126759	64126759	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	132	639	0	ENST00000334205.4:c.52G>T	p.Glu18Ter	p.E18*	ENST00000334205	NM_003942.2	18	Gaa/Taa	1/17	1	2	FACETS	0.988	0.897	1	0.988	0.897	1	CLONAL	1	TRUE	1	0.34	2		639	786	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127670	64127670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	172	464	0	ENST00000334205.4:c.163G>A	p.Gly55Arg	p.G55R	ENST00000334205	NM_003942.2	55	Ggg/Agg	3/17	1	2	FACETS	0.979	0.9	1	0.979	0.9	1	CLONAL	1	TRUE	1	0.34	2		464	1033	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135964	64135964	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1451318965	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	98	793	2	ENST00000334205.4:c.1225G>A	p.Glu409Lys	p.E409K	ENST00000334205	NM_003942.2	409	Gag/Aag	11/17	1	2	FACETS	0.578	0.514	0.646	0.578	0.514	0.646	SUBCLONAL	1	TRUE	1	0.34	2		795	998	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514036	69514036	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	114	630	0	ENST00000294312.3:c.645G>T	p.Glu215Asp	p.E215D	ENST00000294312	NM_005117.2	215	gaG/gaT	3/3	1	2	FACETS	0.824	0.741	0.911	0.824	0.741	0.911	CLONAL	1	TRUE	1	0.34	2		630	814	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94211920	94211920	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	62	288	0	ENST00000323929.3:c.525G>T	p.Lys175Asn	p.K175N	ENST00000323929	NM_005591.3	175	aaG/aaT	6/20	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.34	2		288	361	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94224027	94224027	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	98	256	0	ENST00000323929.3:c.125A>C	p.Glu42Ala	p.E42A	ENST00000323929	NM_005591.3	42	gAa/gCa	3/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.34	2		256	429	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917655	94917655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746291519	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	33	388	0	ENST00000536441.1:c.866G>A	p.Arg289His	p.R289H	ENST00000536441	NM_144665.3	289	cGt/cAt	6/10	1	2	FACETS	0.441	0.359	0.534	0.441	0.359	0.534	SUBCLONAL	1	TRUE	1	0.34	2		388	440	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917698	94917698	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	51	394	0	ENST00000536441.1:c.823G>T	p.Glu275Ter	p.E275*	ENST00000536441	NM_144665.3	275	Gaa/Taa	6/10	1	2	FACETS	0.649	0.552	0.755	0.649	0.552	0.755	SUBCLONAL	1	TRUE	1	0.34	2		394	462	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94922974	94922974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1409733830	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	48	319	0	ENST00000536441.1:c.494G>A	p.Arg165Gln	p.R165Q	ENST00000536441	NM_144665.3	165	cGa/cAa	4/10	1	2	FACETS	0.69	0.585	0.806	0.69	0.585	0.806	SUBCLONAL	1	TRUE	1	0.34	2		319	409	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195500	102195500	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	41	432	0	ENST00000263464.3:c.260A>G	p.Lys87Arg	p.K87R	ENST00000263464	NM_001165.4	87	aAa/aGa	2/9	1	2	FACETS	0.452	0.376	0.536	0.452	0.376	0.536	SUBCLONAL	1	TRUE	1	0.34	2		432	534	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195814	102195814	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	62	400	0	ENST00000263464.3:c.574G>T	p.Ala192Ser	p.A192S	ENST00000263464	NM_001165.4	192	Gca/Tca	2/9	1	2	FACETS	0.661	0.571	0.758	0.661	0.571	0.758	SUBCLONAL	1	TRUE	1	0.34	2		400	552	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141852	108141852	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	93	261	0	ENST00000278616.4:c.2900T>G	p.Leu967Arg	p.L967R	ENST00000278616	NM_000051.3	967	cTt/cGt	19/63	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.34	2		261	372	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155074	108155074	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	62	325	0	ENST00000278616.4:c.3867G>T	p.Lys1289Asn	p.K1289N	ENST00000278616	NM_000051.3	1289	aaG/aaT	26/63	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.34	2		325	361	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164087	108164087	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	27	51	0	ENST00000278616.4:c.4659A>C	p.Glu1553Asp	p.E1553D	ENST00000278616	NM_000051.3	1553	gaA/gaC	31/63	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.34	2		51	122	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192142	108192142	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	64	445	1	ENST00000278616.4:c.6567C>A	p.Phe2189Leu	p.F2189L	ENST00000278616	NM_000051.3	2189	ttC/ttA	45/63	1	2	FACETS	0.595	0.515	0.682	0.595	0.515	0.682	SUBCLONAL	1	TRUE	1	0.34	2		446	633	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202620	108202620	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	58	212	0	ENST00000278616.4:c.7644T>G	p.Ile2548Met	p.I2548M	ENST00000278616	NM_000051.3	2548	atT/atG	52/63	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.34	2		212	241	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344222	118344222	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	131	618	0	ENST00000534358.1:c.2348C>A	p.Ser783Tyr	p.S783Y	ENST00000534358	NM_005933.3	783	tCt/tAt	3/36	1	2	FACETS	0.897	0.814	0.985	0.897	0.814	0.985	CLONAL	1	TRUE	1	0.34	2		618	859	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362546	118362546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782229111	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	72	456	1	ENST00000534358.1:c.4907G>A	p.Arg1636Gln	p.R1636Q	ENST00000534358	NM_005933.3	1636	cGa/cAa	15/36	1	2	FACETS	0.53	0.462	0.604	0.53	0.462	0.604	SUBCLONAL	1	TRUE	1	0.34	2		457	799	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371754	118371754	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	75	305	0	ENST00000534358.1:c.6211A>G	p.Thr2071Ala	p.T2071A	ENST00000534358	NM_005933.3	2071	Aca/Gca	25/36	1	2	FACETS	0.774	0.679	0.876	0.774	0.679	0.876	SUBCLONAL	1	TRUE	1	0.34	2		305	570	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392721	118392721	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	78	504	0	ENST00000534358.1:c.11753C>A	p.Ser3918Tyr	p.S3918Y	ENST00000534358	NM_005933.3	3918	tCt/tAt	36/36	1	2	FACETS	0.62	0.544	0.702	0.62	0.544	0.702	SUBCLONAL	1	TRUE	1	0.34	2		504	740	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142500	119142500	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	133	439	0	ENST00000264033.4:c.499G>T	p.Gly167Ter	p.G167*	ENST00000264033	NM_005188.3	167	Gga/Tga	3/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.34	2		439	575	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416120	416120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777946084	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	42	317	2	ENST00000399788.2:c.4066G>A	p.Asp1356Asn	p.D1356N	ENST00000399788	NM_001042603.1	1356	Gac/Aac	24/28	0.3	2	FACETS	0.513	0.428	0.607			1	SUBCLONAL	1	TRUE	NA	0.34	2		319	482	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244818	46244818	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	61	646	0	ENST00000334344.6:c.2912C>A	p.Ser971Tyr	p.S971Y	ENST00000334344	NM_152641.2	971	tCt/tAt	15/21	1	2	FACETS	0.417	0.358	0.481	0.417	0.358	0.481	SUBCLONAL	1	TRUE	1	0.34	2		646	861	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416438	49416438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	85	665	0	ENST00000301067.7:c.16273G>A	p.Glu5425Lys	p.E5425K	ENST00000301067	NM_003482.3	5425	Gag/Aag	51/54	1	2	FACETS	0.546	0.481	0.615	0.546	0.481	0.615	SUBCLONAL	1	TRUE	1	0.34	2		665	916	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418445	49418445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745599611	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	71	642	1	ENST00000301067.7:c.15968G>A	p.Arg5323His	p.R5323H	ENST00000301067	NM_003482.3	5323	cGc/cAc	50/54	1	2	FACETS	0.436	0.379	0.497	0.436	0.379	0.497	SUBCLONAL	1	TRUE	1	0.34	2		643	959	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420204	49420204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	240	754	1	ENST00000301067.7:c.15545G>A	p.Gly5182Asp	p.G5182D	ENST00000301067	NM_003482.3	5182	gGc/gAc	48/54	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.34	2		755	1043	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478842	56478842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	95	868	0	ENST00000267101.3:c.298C>T	p.Pro100Ser	p.P100S	ENST00000267101	NM_001982.3	100	Ccc/Tcc	3/28	1	2	FACETS	0.458	0.406	0.514	0.458	0.406	0.514	SUBCLONAL	1	TRUE	1	0.34	2		868	1220	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143279	58143279	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	133	353	0	ENST00000257904.6:c.641T>C	p.Phe214Ser	p.F214S	ENST00000257904	NM_000075.3	214	tTc/tCc	6/8	1	2	FACETS	0.792	0.724	0.863	1	0.988	1	SUBCLONAL	2	TRUE	1	0.34	2		353	494	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884566	111884566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776172124	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	155	479	0	ENST00000341259.2:c.742C>T	p.Pro248Ser	p.P248S	ENST00000341259	NM_005475.2	248	Ccc/Tcc	3/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.34	2		479	675	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888193	112888193	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	66	593	0	ENST00000351677.2:c.209A>C	p.Lys70Thr	p.K70T	ENST00000351677	NM_002834.3	70	aAa/aCa	3/16	1	2	FACETS	0.667	0.579	0.762	0.667	0.579	0.762	SUBCLONAL	1	TRUE	1	0.34	2		593	582	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924292	112924292	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	133	681	0	ENST00000351677.2:c.1238G>T	p.Arg413Ile	p.R413I	ENST00000351677	NM_002834.3	413	aGa/aTa	11/16	1	2	FACETS	0.823	0.746	0.903	0.823	0.746	0.903	CLONAL	1	TRUE	1	0.34	2		681	951	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112365	115112365	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751549922	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	50	411	0	ENST00000257566.3:c.1375C>T	p.Arg459Cys	p.R459C	ENST00000257566	NM_016569.3	459	Cgc/Tgc	7/8	1	2	FACETS	0.466	0.395	0.545	0.466	0.395	0.545	SUBCLONAL	1	TRUE	1	0.34	2		411	631	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434409	121434409	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	125	875	1	ENST00000257555.6:c.1173G>T	p.Gln391His	p.Q391H	ENST00000257555		391	caG/caT	6/10	1	2	FACETS	0.68	0.614	0.749	0.68	0.614	0.749	SUBCLONAL	1	TRUE	1	0.34	2		876	1082	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212572	133212572	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	154	568	0	ENST00000320574.5:c.5717C>T	p.Ser1906Phe	p.S1906F	ENST00000320574	NM_006231.2	1906	tCt/tTt	42/49	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.34	2		568	664	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219551	133219551	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1292909825	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	230	674	1	ENST00000320574.5:c.4583C>T	p.Ala1528Val	p.A1528V	ENST00000320574	NM_006231.2	1528	gCc/gTc	36/49	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.34	2		675	944	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923248	26923249	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	31	316	0	ENST00000381527.3:c.248dup	p.Val84GlyfsTer7	p.V84Gfs*7	ENST00000381527	NM_001260.1	82	caa/cAaa	3/13	1	2	FACETS	0.46	0.372	0.56	0.46	0.372	0.56	SUBCLONAL	1	TRUE	1	0.34	2		316	396	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601369	28601369	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	63	203	0	ENST00000241453.7:c.2063A>G	p.Tyr688Cys	p.Y688C	ENST00000241453	NM_004119.2	688	tAc/tGc	17/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.34	2		203	273	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609767	28609767	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	43	582	0	ENST00000241453.7:c.1462A>G	p.Asn488Asp	p.N488D	ENST00000241453	NM_004119.2	488	Aac/Gac	12/24	1	2	FACETS	0.36	0.301	0.427	0.36	0.301	0.427	SUBCLONAL	1	TRUE	1	0.34	2		582	702	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28971144	28971144	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	40	322	0	ENST00000282397.4:c.1613C>T	p.Ser538Phe	p.S538F	ENST00000282397	NM_002019.4	538	tCc/tTc	12/30	1	2	FACETS	0.614	0.511	0.729	0.614	0.511	0.729	SUBCLONAL	1	TRUE	1	0.34	2		322	383	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32899306	32899306	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	50	97	0	ENST00000380152.3:c.410C>A	p.Ser137Tyr	p.S137Y	ENST00000380152		137	tCt/tAt	4/27	1	2	FACETS	0.782	0.674	0.898	1	0.969	1	SUBCLONAL	2	TRUE	1	0.34	2		97	188	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912129	32912129	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1566228876	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	33	564	0	ENST00000380152.3:c.3637G>T	p.Glu1213Ter	p.E1213*	ENST00000380152		1213	Gaa/Taa	11/27	1	2	FACETS	0.356	0.289	0.431	0.356	0.289	0.431	SUBCLONAL	1	TRUE	1	0.34	2		564	546	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937518	32937518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	54	549	0	ENST00000380152.3:c.8179G>A	p.Ala2727Thr	p.A2727T	ENST00000380152		2727	Gct/Act	18/27	1	2	FACETS	0.516	0.44	0.599	0.516	0.44	0.599	SUBCLONAL	1	TRUE	1	0.34	2		549	616	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972672	32972672	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786202073	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	94	347	0	ENST00000380152.3:c.10022A>G	p.Asp3341Gly	p.D3341G	ENST00000380152		3341	gAc/gGc	27/27	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.34	2		347	445	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134682	41134682	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	50	406	0	ENST00000379561.5:c.946C>T	p.Arg316Ter	p.R316*	ENST00000379561	NM_002015.3	316	Cga/Tga	2/3	1	2	FACETS	0.604	0.513	0.704	0.604	0.513	0.704	SUBCLONAL	1	TRUE	1	0.34	2		406	487	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240201	41240201	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1003365110	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	18	87	1	ENST00000379561.5:c.149C>A	p.Ala50Asp	p.A50D	ENST00000379561	NM_002015.3	50	gCc/gAc	1/3	1	2	FACETS	0.89	0.678	1	0.89	0.678	1	CLONAL	1	TRUE	1	0.34	2		88	119	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337612	73337612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	21	188	0	ENST00000377767.4:c.2104C>T	p.Leu702Phe	p.L702F	ENST00000377767	NM_014953.3	702	Ctt/Ttt	16/21	1	2	FACETS	0.433	0.334	0.549	0.433	0.334	0.549	SUBCLONAL	1	TRUE	1	0.34	2		188	285	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73350214	73350214	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	46	137	0	ENST00000377767.4:c.671G>T	p.Gly224Val	p.G224V	ENST00000377767	NM_014953.3	224	gGa/gTa	5/21	1	2	FACETS	0.815	0.698	0.939	1	0.968	1	CLONAL	2	TRUE	1	0.34	2		137	166	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514637	103514637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1246763212	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	72	447	0	ENST00000355739.4:c.1138G>A	p.Glu380Lys	p.E380K	ENST00000355739	NM_000123.3	380	Gaa/Aaa	8/15	1	2	FACETS	0.641	0.56	0.728	0.641	0.56	0.728	SUBCLONAL	1	TRUE	1	0.34	2		447	661	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518109	103518109	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	60	378	0	ENST00000355739.4:c.2047G>T	p.Glu683Ter	p.E683*	ENST00000355739	NM_000123.3	683	Gag/Tag	9/15	1	2	FACETS	0.689	0.594	0.792	0.689	0.594	0.792	SUBCLONAL	1	TRUE	1	0.34	2		378	512	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528243	103528243	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	78	288	0	ENST00000355739.4:c.3551G>T	p.Arg1184Met	p.R1184M	ENST00000355739	NM_000123.3	1184	aGg/aTg	15/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.34	2		288	339	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435376	110435376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	130	575	1	ENST00000375856.3:c.3025G>A	p.Glu1009Lys	p.E1009K	ENST00000375856	NM_003749.2	1009	Gag/Aag	1/2	1	2	FACETS	0.911	0.827	1	0.911	0.827	1	CLONAL	1	TRUE	1	0.34	2		576	839	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436084	110436084	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	104	849	0	ENST00000375856.3:c.2317G>A	p.Asp773Asn	p.D773N	ENST00000375856	NM_003749.2	773	Gac/Aac	1/2	1	2	FACETS	0.521	0.465	0.581	0.521	0.465	0.581	SUBCLONAL	1	TRUE	1	0.34	2		849	1174	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436092	110436092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755626807	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	116	848	0	ENST00000375856.3:c.2309C>T	p.Ser770Phe	p.S770F	ENST00000375856	NM_003749.2	770	tCc/tTc	1/2	1	2	FACETS	0.58	0.521	0.642	0.58	0.521	0.642	SUBCLONAL	1	TRUE	1	0.34	2		848	1177	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68292193	68292193	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	82	312	0	ENST00000487270.1:c.97C>A	p.Leu33Ile	p.L33I	ENST00000487270	NM_133509.3	33	Ctt/Att	3/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.34	2		312	402	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609498	81609498	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	75	493	0	ENST00000298171.2:c.1096T>G	p.Phe366Val	p.F366V	ENST00000298171	NM_000369.2	366	Ttt/Gtt	10/10	1	2	FACETS	0.723	0.634	0.819	0.723	0.634	0.819	SUBCLONAL	1	TRUE	1	0.34	2		493	610	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582958	95582958	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	66	327	0	ENST00000393063.1:c.1584A>G	p.Ile528Met	p.I528M	ENST00000393063	NM_030621.3	528	atA/atG	11/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.34	2		327	269	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590950	95590950	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs779851333	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	40	275	0	ENST00000393063.1:c.959A>G	p.Lys320Arg	p.K320R	ENST00000393063	NM_030621.3	320	aAa/aGa	9/28	1	2	FACETS	0.715	0.596	0.847	0.715	0.596	0.847	SUBCLONAL	1	TRUE	1	0.34	2		275	329	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239351	105239351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1168658858	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	117	858	0	ENST00000349310.3:c.1036C>T	p.Arg346Cys	p.R346C	ENST00000349310	NM_001014432.1	346	Cgc/Tgc	12/15	1	2	FACETS	0.628	0.565	0.695	0.628	0.565	0.695	SUBCLONAL	1	TRUE	1	0.34	2		858	1096	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38617003	38617003	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	39	204	0	ENST00000299084.4:c.416A>C	p.Asp139Ala	p.D139A	ENST00000299084	NM_152594.2	139	gAc/gCc	4/7	1	2	FACETS	0.657	0.546	0.781	0.657	0.546	0.781	SUBCLONAL	1	TRUE	1	0.34	2		204	349	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643282	38643282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	40	371	0	ENST00000299084.4:c.752G>A	p.Arg251Gln	p.R251Q	ENST00000299084	NM_152594.2	251	cGa/cAa	7/7	1	2	FACETS	0.591	0.492	0.702	0.591	0.492	0.702	SUBCLONAL	1	TRUE	1	0.34	2		371	398	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40684192	40684192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199907924	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	62	472	1	ENST00000249776.8:c.790G>A	p.Glu264Lys	p.E264K	ENST00000249776	NM_033286.3	264	Gaa/Aaa	8/9	1	2	FACETS	0.586	0.506	0.674	0.586	0.506	0.674	SUBCLONAL	1	TRUE	1	0.34	2		473	622	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961573	41961573	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	54	541	1	ENST00000219905.7:c.481G>T	p.Glu161Ter	p.E161*	ENST00000219905	NM_001164273.1	161	Gaa/Taa	2/24	1	2	FACETS	0.585	0.5	0.678	0.585	0.5	0.678	SUBCLONAL	1	TRUE	1	0.34	2		542	543	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989088	41989088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs938158021	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	54	601	0	ENST00000219905.7:c.1880G>A	p.Arg627Gln	p.R627Q	ENST00000219905	NM_001164273.1	627	cGa/cAa	3/24	1	2	FACETS	0.49	0.418	0.569	0.49	0.418	0.569	SUBCLONAL	1	TRUE	1	0.34	2		601	648	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021423	42021423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	134	475	0	ENST00000219905.7:c.3719G>A	p.Arg1240Gln	p.R1240Q	ENST00000219905	NM_001164273.1	1240	cGa/cAa	11/24	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.34	2		475	547	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042723	42042723	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	56	403	0	ENST00000219905.7:c.6918A>C	p.Glu2306Asp	p.E2306D	ENST00000219905	NM_001164273.1	2306	gaA/gaC	17/24	1	2	FACETS	0.726	0.623	0.837	0.726	0.623	0.837	SUBCLONAL	1	TRUE	1	0.34	2		403	454	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058210	42058210	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	30	199	0	ENST00000219905.7:c.7930G>A	p.Asp2644Asn	p.D2644N	ENST00000219905	NM_001164273.1	2644	Gac/Aac	24/24	1	2	FACETS	0.874	0.709	1	0.874	0.709	1	CLONAL	1	TRUE	1	0.34	2		199	202	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701901	43701901	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	34	261	0	ENST00000382044.4:c.5344G>T	p.Glu1782Ter	p.E1782*	ENST00000382044	NM_001141980.1	1782	Gaa/Taa	25/28	1	2	FACETS	0.673	0.552	0.809	0.673	0.552	0.809	SUBCLONAL	1	TRUE	1	0.34	2		261	297	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762232	43762232	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	197	627	0	ENST00000382044.4:c.1213G>T	p.Glu405Ter	p.E405*	ENST00000382044	NM_001141980.1	405	Gaa/Taa	11/28	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.34	2		627	785	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43771617	43771617	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	81	523	0	ENST00000382044.4:c.766G>T	p.Glu256Ter	p.E256*	ENST00000382044	NM_001141980.1	256	Gag/Tag	7/28	1	2	FACETS	0.65	0.572	0.734	0.65	0.572	0.734	SUBCLONAL	1	TRUE	1	0.34	2		523	733	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423631	88423631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	116	457	0	ENST00000360948.2:c.2204G>A	p.Arg735His	p.R735H	ENST00000360948	NM_001012338.2	735	cGc/cAc	18/19	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.34	2		457	583	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472448	88472448	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	101	570	0	ENST00000360948.2:c.2107G>T	p.Asp703Tyr	p.D703Y	ENST00000360948	NM_001012338.2	703	Gat/Tat	16/19	1	2	FACETS	0.759	0.678	0.845	0.759	0.678	0.845	SUBCLONAL	1	TRUE	1	0.34	2		570	783	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483961	88483961	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	104	611	0	ENST00000360948.2:c.1609G>T	p.Asp537Tyr	p.D537Y	ENST00000360948	NM_001012338.2	537	Gac/Tac	14/19	1	2	FACETS	0.733	0.655	0.815	0.733	0.655	0.815	SUBCLONAL	1	TRUE	1	0.34	2		611	835	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669595	88669595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	45	464	0	ENST00000360948.2:c.1303G>A	p.Ala435Thr	p.A435T	ENST00000360948	NM_001012338.2	435	Gca/Aca	12/19	1	2	FACETS	0.467	0.392	0.55	0.467	0.392	0.55	SUBCLONAL	1	TRUE	1	0.34	2		464	567	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303988	91303988	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	64	480	0	ENST00000355112.3:c.1385C>A	p.Ser462Tyr	p.S462Y	ENST00000355112	NM_000057.2	462	tCt/tAt	7/22	1	2	FACETS	0.628	0.544	0.72	0.628	0.544	0.72	SUBCLONAL	1	TRUE	1	0.34	2		480	599	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99460077	99460077	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	146	503	0	ENST00000268035.6:c.2173T>G	p.Phe725Val	p.F725V	ENST00000268035	NM_000875.3	725	Ttc/Gtc	10/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.34	2		503	630	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347146	347146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	125	841	0	ENST00000262320.3:c.1865C>T	p.Ala622Val	p.A622V	ENST00000262320	NM_003502.3	622	gCc/gTc	7/11	1	2	FACETS	0.631	0.569	0.696	0.631	0.569	0.696	SUBCLONAL	1	TRUE	1	0.34	2		841	1166	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636765	2636765	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs535986266	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	273	711	0	ENST00000342085.4:c.1214C>A	p.Pro405His	p.P405H	ENST00000342085	NM_002613.4	405	cCc/cAc	11/14	1	2	FACETS	0.776	0.728	0.824	1	0.994	1	SUBCLONAL	2	TRUE	1	0.34	2		711	1035	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633383	3633383	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200178217	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	199	910	0	ENST00000294008.3:c.4868C>T	p.Ala1623Val	p.A1623V	ENST00000294008	NM_032444.2	1623	gCg/gTg	14/15	1	2	FACETS	0.991	0.917	1	0.991	0.917	1	CLONAL	1	TRUE	1	0.34	2		910	1181	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639913	3639913	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	182	767	0	ENST00000294008.3:c.3726G>T	p.Glu1242Asp	p.E1242D	ENST00000294008	NM_032444.2	1242	gaG/gaT	12/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.34	2		767	971	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641118	3641118	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	123	1012	0	ENST00000294008.3:c.2521G>T	p.Glu841Ter	p.E841*	ENST00000294008	NM_032444.2	841	Gaa/Taa	12/15	1	2	FACETS	0.579	0.522	0.64	0.579	0.522	0.64	SUBCLONAL	1	TRUE	1	0.34	2		1012	1249	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779335	3779335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	96	785	0	ENST00000262367.5:c.5713C>T	p.Pro1905Ser	p.P1905S	ENST00000262367	NM_004380.2	1905	Ccc/Tcc	31/31	1	2	FACETS	0.586	0.521	0.655	0.586	0.521	0.655	SUBCLONAL	1	TRUE	1	0.34	2		785	964	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828113	3828113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	47	557	0	ENST00000262367.5:c.2012C>T	p.Ser671Leu	p.S671L	ENST00000262367	NM_004380.2	671	tCg/tTg	10/31	1	2	FACETS	0.294	0.247	0.347	0.294	0.247	0.347	SUBCLONAL	1	TRUE	1	0.34	2		557	939	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857568	9857568	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	90	472	0	ENST00000330684.3:c.3833A>T	p.Gln1278Leu	p.Q1278L	ENST00000330684	NM_001134407.1	1278	cAa/cTa	13/13	1	2	FACETS	0.823	0.731	0.922	0.823	0.731	0.922	CLONAL	1	TRUE	1	0.34	2		472	643	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031922	10031922	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	190	677	0	ENST00000330684.3:c.901A>G	p.Thr301Ala	p.T301A	ENST00000330684	NM_001134407.1	301	Acc/Gcc	3/13	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.34	2		677	802	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024589	14024589	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	25	296	0	ENST00000311895.7:c.815C>A	p.Pro272His	p.P272H	ENST00000311895	NM_005236.2	272	cCt/cAt	5/11	1	2	FACETS	0.473	0.373	0.587	0.473	0.373	0.587	SUBCLONAL	1	TRUE	1	0.34	2		296	311	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646423	23646423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753470554	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	86	549	0	ENST00000261584.4:c.1444C>T	p.Leu482Phe	p.L482F	ENST00000261584	NM_024675.3	482	Ctc/Ttc	4/13	1	2	FACETS	0.616	0.544	0.693	0.616	0.544	0.693	SUBCLONAL	1	TRUE	1	0.34	2		549	821	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128549	30128549	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	178	710	0	ENST00000263025.4:c.833G>A	p.Arg278Gln	p.R278Q	ENST00000263025	NM_002746.2	278	cGa/cAa	6/9	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.34	2		710	906	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782163	56782163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	90	351	0	ENST00000308159.5:c.4G>A	p.Asp2Asn	p.D2N	ENST00000308159	NM_014669.4	2	Gat/Aat	2/22	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.34	2		351	461	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56855435	56855435	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	65	323	0	ENST00000308159.5:c.584A>C	p.Lys195Thr	p.K195T	ENST00000308159	NM_014669.4	195	aAa/aCa	7/22	1	2	FACETS	0.734	0.637	0.839	0.734	0.637	0.839	SUBCLONAL	1	TRUE	1	0.34	2		323	521	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063329	67063329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763073693	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	87	256	0	ENST00000412916.2:c.19G>A	p.Asp7Asn	p.D7N	ENST00000412916		7	Gac/Aac	1/6	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.34	2		256	423	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650716	67650716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780911615	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	103	663	1	ENST00000264010.4:c.1021C>T	p.Arg341Cys	p.R341C	ENST00000264010	NM_006565.3	341	Cgt/Tgt	5/12	1	2	FACETS	0.551	0.492	0.615	0.551	0.492	0.615	SUBCLONAL	1	TRUE	1	0.34	2		664	1099	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857486	68857486	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	134	516	0	ENST00000261769.5:c.2121T>G	p.Ile707Met	p.I707M	ENST00000261769	NM_004360.3	707	atT/atG	13/16	1	2	FACETS	0.944	0.858	1	0.944	0.858	1	CLONAL	1	TRUE	1	0.34	2		516	835	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867239	68867239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	137	665	0	ENST00000261769.5:c.2486C>T	p.Ser829Phe	p.S829F	ENST00000261769	NM_004360.3	829	tCt/tTt	16/16	1	2	FACETS	0.878	0.798	0.962	0.878	0.798	0.962	CLONAL	1	TRUE	1	0.34	2		665	918	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831993	72831993	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	197	630	0	ENST00000268489.5:c.4588G>T	p.Gly1530Cys	p.G1530C	ENST00000268489	NM_006885.3	1530	Ggt/Tgt	9/10	1	2	FACETS	0.761	0.707	0.818	1	0.991	1	SUBCLONAL	2	TRUE	1	0.34	2		630	761	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984615	72984615	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753727111	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	64	799	1	ENST00000268489.5:c.2969G>A	p.Arg990His	p.R990H	ENST00000268489	NM_006885.3	990	cGc/cAc	3/10	1	2	FACETS	0.314	0.271	0.361	0.314	0.271	0.361	SUBCLONAL	1	TRUE	1	0.34	2		800	1199	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81892729	81892729	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	28	218	0	ENST00000359376.3:c.440G>T	p.Arg147Ile	p.R147I	ENST00000359376	NM_002661.3	147	aGa/aTa	5/33	1	2	FACETS	0.56	0.449	0.687	0.56	0.449	0.687	SUBCLONAL	1	TRUE	1	0.34	2		218	294	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934244	81934244	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	83	641	0	ENST00000359376.3:c.1221G>T	p.Glu407Asp	p.E407D	ENST00000359376	NM_002661.3	407	gaG/gaT	14/33	1	2	FACETS	0.62	0.546	0.699	0.62	0.546	0.699	SUBCLONAL	1	TRUE	1	0.34	2		641	788	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972466	81972466	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	95	569	1	ENST00000359376.3:c.3259G>T	p.Val1087Leu	p.V1087L	ENST00000359376	NM_002661.3	1087	Gtg/Ttg	29/33	1	2	FACETS	0.683	0.608	0.764	0.683	0.608	0.764	SUBCLONAL	1	TRUE	1	0.34	2		570	818	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350552	89350552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	48	367	1	ENST00000301030.4:c.2398G>A	p.Glu800Lys	p.E800K	ENST00000301030	NM_001256183.1	800	Gaa/Aaa	9/13	1	2	FACETS	0.529	0.447	0.619	0.529	0.447	0.619	SUBCLONAL	1	TRUE	1	0.34	2		368	534	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813066	89813066	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	79	692	0	ENST00000389301.3:c.3439G>T	p.Asp1147Tyr	p.D1147Y	ENST00000389301	NM_000135.2	1147	Gac/Tac	35/43	1	2	FACETS	0.566	0.497	0.64	0.566	0.497	0.64	SUBCLONAL	1	TRUE	1	0.34	2		692	821	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816220	89816220	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376103033	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	121	742	0	ENST00000389301.3:c.3157C>T	p.Arg1053Cys	p.R1053C	ENST00000389301	NM_000135.2	1053	Cgc/Tgc	32/43	1	2	FACETS	0.748	0.675	0.826	0.748	0.675	0.826	SUBCLONAL	1	TRUE	1	0.34	2		742	951	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217618	7217618	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	31	435	0	ENST00000380728.2:c.309G>T	p.Lys103Asn	p.K103N	ENST00000380728		103	aaG/aaT	4/11	1	2	FACETS	0.307	0.247	0.375	0.307	0.247	0.375	SUBCLONAL	1	TRUE	1	0.34	2		435	594	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7978920	7978920	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	140	440	0	ENST00000319144.4:c.1647G>T	p.Glu549Asp	p.E549D	ENST00000319144	NM_001139.2	549	gaG/gaT	12/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.34	2		440	571	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971428	15971428	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	150	386	0	ENST00000268712.3:c.4521T>G	p.Ile1507Met	p.I1507M	ENST00000268712	NM_006311.3	1507	atT/atG	32/46	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.34	2		386	618	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15975504	15975504	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	44	461	0	ENST00000268712.3:c.3850T>C	p.Ser1284Pro	p.S1284P	ENST00000268712	NM_006311.3	1284	Tct/Cct	29/46	1	2	FACETS	0.545	0.457	0.642	0.545	0.457	0.642	SUBCLONAL	1	TRUE	1	0.34	2		461	475	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16001703	16001703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1176533842	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	35	424	0	ENST00000268712.3:c.2798G>A	p.Arg933Gln	p.R933Q	ENST00000268712	NM_006311.3	933	cGa/cAa	21/46	1	2	FACETS	0.349	0.285	0.421	0.349	0.285	0.421	SUBCLONAL	1	TRUE	1	0.34	2		424	590	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483092	29483092	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1351732760	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	31	241	0	ENST00000356175.3:c.152T>G	p.Phe51Cys	p.F51C	ENST00000356175	NM_000267.3	51	tTt/tGt	2/57	1	2	FACETS	0.482	0.39	0.587	0.482	0.39	0.587	SUBCLONAL	1	TRUE	1	0.34	2		241	378	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509525	29509525	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	31	269	0	ENST00000356175.3:c.731-1G>T		p.X244_splice	ENST00000356175	NM_000267.3	244			1	2	FACETS	0.594	0.481	0.721	0.594	0.481	0.721	SUBCLONAL	1	TRUE	1	0.34	2		269	307	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652860	29652860	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	13	197	0	ENST00000356175.3:c.4795G>T	p.Gly1599Cys	p.G1599C	ENST00000356175	NM_000267.3	1599	Ggt/Tgt	36/57	1	2	FACETS	0.348	0.248	0.469	0.348	0.248	0.469	SUBCLONAL	1	TRUE	1	0.34	2		197	220	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701099	29701099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778233452	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	110	532	0	ENST00000356175.3:c.8383G>A	p.Gly2795Arg	p.G2795R	ENST00000356175	NM_000267.3	2795	Gga/Aga	57/57	1	2	FACETS	0.804	0.722	0.891	0.804	0.722	0.891	CLONAL	1	TRUE	1	0.34	2		532	805	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30323877	30323877	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	25	124	0	ENST00000322652.5:c.1855C>A	p.Leu619Ile	p.L619I	ENST00000322652	NM_015355.2	619	Ctc/Atc	15/16	1	2	FACETS	0.621	0.491	0.768	0.621	0.491	0.768	SUBCLONAL	1	TRUE	1	0.34	2		124	237	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667820	37667820	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	131	540	0	ENST00000447079.4:c.2705G>A	p.Arg902Gln	p.R902Q	ENST00000447079	NM_015083.1	902	cGa/cAa	8/14	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.34	2		540	679	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38504581	38504582	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGC	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	92	683	0	ENST00000254066.5:c.198_200dup	p.Ser68dup	p.S68dup	ENST00000254066	NM_000964.3	68	-/AGC	3/9	1	2	FACETS	0.568	0.504	0.638	0.568	0.504	0.638	SUBCLONAL	1	TRUE	1	0.34	2		683	952	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243786	41243786	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	57	469	0	ENST00000357654.3:c.3762G>T	p.Lys1254Asn	p.K1254N	ENST00000357654	NM_007294.3	1254	aaG/aaT	10/23	1	2	FACETS	0.631	0.542	0.729	0.631	0.542	0.729	SUBCLONAL	1	TRUE	1	0.34	2		469	531	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47684725	47684725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	41	315	0	ENST00000347630.2:c.724G>A	p.Glu242Lys	p.E242K	ENST00000347630	NM_001007230.1	242	Gaa/Aaa	9/11	1	2	FACETS	0.553	0.461	0.656	0.553	0.461	0.656	SUBCLONAL	1	TRUE	1	0.34	2		315	436	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47700156	47700156	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	72	504	0	ENST00000347630.2:c.17G>T	p.Ser6Ile	p.S6I	ENST00000347630	NM_001007230.1	6	aGt/aTt	3/11	1	2	FACETS	0.54	0.471	0.614	0.54	0.471	0.614	SUBCLONAL	1	TRUE	1	0.34	2		504	785	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55339540	55339540	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1439557709	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	95	606	0	ENST00000284073.2:c.299G>A	p.Arg100Gln	p.R100Q	ENST00000284073	NM_138962.2	100	cGa/cAa	5/14	1	2	FACETS	0.728	0.648	0.813	0.728	0.648	0.813	SUBCLONAL	1	TRUE	1	0.34	2		606	768	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55478759	55478759	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	133	473	0	ENST00000284073.2:c.332A>C	p.Lys111Thr	p.K111T	ENST00000284073	NM_138962.2	111	aAa/aCa	6/14	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.34	2		473	633	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58701062	58701062	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	105	612	0	ENST00000305921.3:c.653A>C	p.Lys218Thr	p.K218T	ENST00000305921	NM_003620.3	218	aAg/aCg	2/6	1	2	FACETS	0.718	0.643	0.798	0.718	0.643	0.798	SUBCLONAL	1	TRUE	1	0.34	2		612	860	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740570	58740570	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	133	450	0	ENST00000305921.3:c.1475A>C	p.Asn492Thr	p.N492T	ENST00000305921	NM_003620.3	492	aAt/aCt	6/6	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.34	2		450	578	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761475	59761475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	76	280	0	ENST00000259008.2:c.2932G>A	p.Gly978Arg	p.G978R	ENST00000259008	NM_032043.2	978	Ggg/Agg	20/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.34	2		280	363	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770803	59770803	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146031731	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	57	226	0	ENST00000259008.2:c.2563C>T	p.Arg855Cys	p.R855C	ENST00000259008	NM_032043.2	855	Cgc/Tgc	18/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.34	2		226	257	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117691	70117691	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	163	773	0	ENST00000245479.2:c.159C>A	p.Phe53Leu	p.F53L	ENST00000245479	NM_000346.3	53	ttC/ttA	1/3	1	2	FACETS	0.926	0.849	1	0.926	0.849	1	CLONAL	1	TRUE	1	0.34	2		773	1035	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736813	736813	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	43	252	0	ENST00000314574.4:c.1286G>T	p.Arg429Ile	p.R429I	ENST00000314574	NM_005433.3	429	aGa/aTa	10/12	1	2	FACETS	0.719	0.603	0.846	0.719	0.603	0.846	SUBCLONAL	1	TRUE	1	0.34	2		252	352	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39620659	39620659	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	38	303	0	ENST00000262039.4:c.2057A>C	p.Gln686Pro	p.Q686P	ENST00000262039	NM_002647.2	686	cAg/cCg	19/25	1	2	FACETS	0.64	0.531	0.763	0.64	0.531	0.763	SUBCLONAL	1	TRUE	1	0.34	2		303	349	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637929	39637929	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	171	572	0	ENST00000262039.4:c.2346A>C	p.Glu782Asp	p.E782D	ENST00000262039	NM_002647.2	782	gaA/gaC	22/25	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.34	2		572	703	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394794	45394794	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	74	426	0	ENST00000262160.6:c.555G>T	p.Glu185Asp	p.E185D	ENST00000262160	NM_005901.5	185	gaG/gaT	5/11	1	2	FACETS	0.844	0.74	0.955	0.844	0.74	0.955	CLONAL	1	TRUE	1	0.34	2		426	516	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395628	45395628	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	47	265	0	ENST00000262160.6:c.506G>T	p.Arg169Ile	p.R169I	ENST00000262160	NM_005901.5	169	aGa/aTa	4/11	1	2	FACETS	0.739	0.625	0.864	0.739	0.625	0.864	SUBCLONAL	1	TRUE	1	0.34	2		265	374	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573565	48573565	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	64	189	0	ENST00000342988.3:c.149A>C	p.Lys50Thr	p.K50T	ENST00000342988	NM_005359.5	50	aAa/aCa	2/12	1	2	FACETS	0.848	0.745	0.956	1	0.978	1	CLONAL	2	TRUE	1	0.34	2		189	222	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56367713	56367713	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	42	249	0	ENST00000348428.3:c.539T>C	p.Val180Ala	p.V180A	ENST00000348428	NM_006785.3	180	gTg/gCg	4/17	1	2	FACETS	0.72	0.603	0.849	0.72	0.603	0.849	SUBCLONAL	1	TRUE	1	0.34	2		249	343	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118983	3118983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778948783	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	59	809	3	ENST00000078429.4:c.667G>A	p.Val223Met	p.V223M	ENST00000078429	NM_002067.2	223	Gtg/Atg	5/7	1	2	FACETS	0.338	0.289	0.391	0.338	0.289	0.391	SUBCLONAL	1	TRUE	1	0.34	2		812	1028	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244190	5244190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760369713	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	137	749	0	ENST00000357368.4:c.1292G>A	p.Arg431Gln	p.R431Q	ENST00000357368	NM_002850.3	431	cGg/cAg	11/38	1	2	FACETS	0.93	0.845	1	0.93	0.845	1	CLONAL	1	TRUE	1	0.34	2		749	867	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265061	5265061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1363057483	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	156	826	1	ENST00000357368.4:c.526G>A	p.Asp176Asn	p.D176N	ENST00000357368	NM_002850.3	176	Gat/Aat	5/38	1	2	FACETS	0.799	0.73	0.871	0.799	0.73	0.871	SUBCLONAL	1	TRUE	1	0.34	2		827	1149	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273516	5273516	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1015763824	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1184	80	814	0	ENST00000357368.4:c.316G>A	p.Glu106Lys	p.E106K	ENST00000357368	NM_002850.3	106	Gag/Aag	4/38	1	2	FACETS	0.372	0.326	0.422	0.372	0.326	0.422	SUBCLONAL	1	TRUE	1	0.34	2		814	1264	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251851	10251851	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	64	639	0	ENST00000340748.4:c.3276G>T	p.Lys1092Asn	p.K1092N	ENST00000340748		1092	aaG/aaT	30/40	1	2	FACETS	0.462	0.399	0.531	0.462	0.399	0.531	SUBCLONAL	1	TRUE	1	0.34	2		639	814	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10284576	10284576	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	70	351	0	ENST00000340748.4:c.606G>T	p.Glu202Asp	p.E202D	ENST00000340748		202	gaG/gaT	7/40	1	2	FACETS	0.853	0.745	0.968	0.853	0.745	0.968	CLONAL	1	TRUE	1	0.34	2		351	483	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032390	11032390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775185209	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	165	874	2	ENST00000327064.4:c.1784C>T	p.Ser595Leu	p.S595L	ENST00000327064	NM_199141.1	595	tCg/tTg	16/16	1	2	FACETS	0.895	0.821	0.973	0.895	0.821	0.973	CLONAL	1	TRUE	1	0.34	2		876	1084	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281295	15281295	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	130	772	0	ENST00000263388.2:c.4961T>C	p.Leu1654Pro	p.L1654P	ENST00000263388	NM_000435.2	1654	cTg/cCg	27/33	1	2	FACETS	0.775	0.702	0.852	0.775	0.702	0.852	SUBCLONAL	1	TRUE	1	0.34	2		772	987	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375262	15375262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1299618611	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	71	700	1	ENST00000263377.2:c.1165G>A	p.Asp389Asn	p.D389N	ENST00000263377	NM_058243.2	389	Gac/Aac	6/20	1	2	FACETS	0.443	0.386	0.506	0.443	0.386	0.506	SUBCLONAL	1	TRUE	1	0.34	2		701	942	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384795	17384795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376352234	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	64	826	0	ENST00000359435.4:c.427G>A	p.Glu143Lys	p.E143K	ENST00000359435	NM_001033549.1	143	Gag/Aag	4/9	1	2	FACETS	0.315	0.271	0.363	0.315	0.271	0.363	SUBCLONAL	1	TRUE	1	0.34	2		826	1195	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946747	17946747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756418657	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	272	743	3	ENST00000458235.1:c.1900G>A	p.Ala634Thr	p.A634T	ENST00000458235	NM_000215.3	634	Gcc/Acc	14/24	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.34	2		746	1113	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273116	18273116	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	92	734	0	ENST00000222254.8:c.1006T>C	p.Ser336Pro	p.S336P	ENST00000222254	NM_005027.3	336	Tca/Cca	8/16	1	2	FACETS	0.55	0.487	0.617	0.55	0.487	0.617	SUBCLONAL	1	TRUE	1	0.34	2		734	984	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277959	18277959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	109	586	3	ENST00000222254.8:c.1579C>T	p.Arg527Trp	p.R527W	ENST00000222254	NM_005027.3	527	Cgg/Tgg	13/16	1	2	FACETS	0.723	0.648	0.802	0.723	0.648	0.802	SUBCLONAL	1	TRUE	1	0.34	2		589	887	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214671	36214671	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226451581	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	134	678	0	ENST00000222270.7:c.3097G>A	p.Asp1033Asn	p.D1033N	ENST00000222270	NM_014727.1	1033	Gat/Aat	8/37	1	2	FACETS	0.886	0.804	0.971	0.886	0.804	0.971	CLONAL	1	TRUE	1	0.34	2		678	890	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40744853	40744853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780894376	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	85	757	0	ENST00000392038.2:c.667G>A	p.Asp223Asn	p.D223N	ENST00000392038	NM_001626.4	223	Gac/Aac	8/14	1	2	FACETS	0.473	0.416	0.533	0.473	0.416	0.533	SUBCLONAL	1	TRUE	1	0.34	2		757	1058	SUCCESS
AXL	558	MSKCC	GRCh37	19	41759575	41759575	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	118	693	1	ENST00000301178.4:c.1998G>T	p.Lys666Asn	p.K666N	ENST00000301178	NM_021913.4	666	aaG/aaT	17/20	1	2	FACETS	0.748	0.674	0.826	0.748	0.674	0.826	SUBCLONAL	1	TRUE	1	0.34	2		694	928	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763475	41763475	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	93	646	0	ENST00000301178.4:c.2274T>G	p.Ile758Met	p.I758M	ENST00000301178	NM_021913.4	758	atT/atG	19/20	1	2	FACETS	0.62	0.55	0.694	0.62	0.55	0.694	SUBCLONAL	1	TRUE	1	0.34	2		646	883	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797300	42797300	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	61	763	0	ENST00000575354.2:c.3662C>A	p.Ser1221Tyr	p.S1221Y	ENST00000575354	NM_015125.3	1221	tCt/tAt	15/20	1	2	FACETS	0.38	0.326	0.438	0.38	0.326	0.438	SUBCLONAL	1	TRUE	1	0.34	2		763	945	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867140	45867140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	73	786	2	ENST00000391945.4:c.979G>A	p.Glu327Lys	p.E327K	ENST00000391945	NM_000400.3	327	Gag/Aag	11/23	1	2	FACETS	0.422	0.368	0.481	0.422	0.368	0.481	SUBCLONAL	1	TRUE	1	0.34	2		788	1017	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52729040	52729040	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	186	551	0	ENST00000322088.6:c.1732T>G	p.Phe578Val	p.F578V	ENST00000322088	NM_014225.5	578	Ttt/Gtt	14/15	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.34	2		551	808	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029131	26029131	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	89	323	0	ENST00000435504.4:c.219G>T	p.Lys73Asn	p.K73N	ENST00000435504		73	aaG/aaT	4/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.34	2		323	394	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436878	29436878	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	132	702	0	ENST00000389048.3:c.3715T>C	p.Tyr1239His	p.Y1239H	ENST00000389048	NM_004304.4	1239	Tat/Cat	24/29	1	2	FACETS	0.876	0.795	0.962	0.876	0.795	0.962	CLONAL	1	TRUE	1	0.34	2		702	886	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213383	39213383	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	127	783	2	ENST00000402219.2:c.3584G>A	p.Arg1195Gln	p.R1195Q	ENST00000402219	NM_005633.3	1195	cGa/cAa	23/23	1	2	FACETS	0.786	0.712	0.865	0.786	0.712	0.865	SUBCLONAL	1	TRUE	1	0.34	2		785	950	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222288	39222288	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs199856844	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	65	512	0	ENST00000402219.2:c.3322G>C	p.Asp1108His	p.D1108H	ENST00000402219	NM_005633.3	1108	Gat/Cat	20/23	1	2	FACETS	0.525	0.455	0.602	0.525	0.455	0.602	SUBCLONAL	1	TRUE	1	0.34	2		512	728	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224088	39224088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	43	241	0	ENST00000402219.2:c.3056G>A	p.Arg1019Gln	p.R1019Q	ENST00000402219	NM_005633.3	1019	cGa/cAa	19/23	1	2	FACETS	0.572	0.479	0.675	0.572	0.479	0.675	SUBCLONAL	1	TRUE	1	0.34	2		241	442	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224453	39224453	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	33	356	0	ENST00000402219.2:c.2905G>T	p.Gly969Ter	p.G969*	ENST00000402219	NM_005633.3	969	Gga/Tga	18/23	1	2	FACETS	0.395	0.321	0.478	0.395	0.321	0.478	SUBCLONAL	1	TRUE	1	0.34	2		356	492	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693820	47693820	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	82	236	0	ENST00000233146.2:c.1534A>C	p.Lys512Gln	p.K512Q	ENST00000233146	NM_000251.2	512	Aaa/Caa	10/16	1	2	FACETS	0.807	0.719	0.898	1	0.981	1	CLONAL	2	TRUE	1	0.34	2		236	299	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47709928	47709928	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1284087975	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	52	151	0	ENST00000233146.2:c.2645A>C	p.Lys882Thr	p.K882T	ENST00000233146	NM_000251.2	882	aAa/aCa	16/16	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.34	2		151	257	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027770	48027770	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs764816440	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	75	294	0	ENST00000234420.5:c.2648A>C	p.Lys883Thr	p.K883T	ENST00000234420	NM_000179.2	883	aAg/aCg	4/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.34	2		294	366	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118896	61118896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	172	437	0	ENST00000295025.8:c.89G>A	p.Arg30Gln	p.R30Q	ENST00000295025	NM_002908.2	30	cGa/cAa	2/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.34	2		437	713	SUCCESS
REL	5966	MSKCC	GRCh37	2	61128189	61128189	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	48	89	0	ENST00000295025.8:c.365G>T	p.Arg122Ile	p.R122I	ENST00000295025	NM_002908.2	122	aGa/aTa	4/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.34	2		89	240	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715334	61715334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	53	496	0	ENST00000401558.2:c.2279C>A	p.Ser760Tyr	p.S760Y	ENST00000401558	NM_003400.3	760	tCt/tAt	19/25	1	2	FACETS	0.509	0.434	0.592	0.509	0.434	0.592	SUBCLONAL	1	TRUE	1	0.34	2		496	612	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719849	61719849	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	26	248	0	ENST00000401558.2:c.1419A>C	p.Glu473Asp	p.E473D	ENST00000401558	NM_003400.3	473	gaA/gaC	14/25	1	2	FACETS	0.495	0.392	0.612	0.495	0.392	0.612	SUBCLONAL	1	TRUE	1	0.34	2		248	309	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128018908	128018908	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	68	455	1	ENST00000285398.2:c.1960G>T	p.Glu654Ter	p.E654*	ENST00000285398	NM_000122.1	654	Gag/Tag	13/15	1	2	FACETS	0.641	0.558	0.731	0.641	0.558	0.731	SUBCLONAL	1	TRUE	1	0.34	2		456	624	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158595013	158595013	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	116	447	0	ENST00000263640.3:c.1334G>T	p.Arg445Met	p.R445M	ENST00000263640	NM_001105.4	445	aGg/aTg	10/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.34	2		447	640	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682865	190682865	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	28	157	0	ENST00000441310.2:c.541A>C	p.Ile181Leu	p.I181L	ENST00000441310	NM_000534.4	181	Atc/Ctc	5/13	1	2	FACETS	0.507	0.405	0.622	0.507	0.405	0.622	SUBCLONAL	1	TRUE	1	0.34	2		157	325	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719736	190719736	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	19	173	0	ENST00000441310.2:c.1738C>A	p.Leu580Ile	p.L580I	ENST00000441310	NM_000534.4	580	Ctt/Att	9/13	1	2	FACETS	0.501	0.381	0.641	0.501	0.381	0.641	SUBCLONAL	1	TRUE	1	0.34	2		173	223	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198261006	198261006	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	59	391	0	ENST00000335508.6:c.3313G>T	p.Glu1105Ter	p.E1105*	ENST00000335508	NM_012433.2	1105	Gaa/Taa	23/25	1	2	FACETS	0.74	0.638	0.851	0.74	0.638	0.851	SUBCLONAL	1	TRUE	1	0.34	2		391	469	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268406	198268406	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	46	369	0	ENST00000335508.6:c.1622C>A	p.Ser541Tyr	p.S541Y	ENST00000335508	NM_012433.2	541	tCt/tAt	12/25	1	2	FACETS	0.652	0.55	0.764	0.652	0.55	0.764	SUBCLONAL	1	TRUE	1	0.34	2		369	415	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273209	198273209	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	246	642	0	ENST00000335508.6:c.1001G>T	p.Arg334Ile	p.R334I	ENST00000335508	NM_012433.2	334	aGa/aTa	8/25	1	2	FACETS	0.762	0.713	0.812	1	0.993	1	SUBCLONAL	2	TRUE	1	0.34	2		642	950	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137409	202137409	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	66	410	0	ENST00000358485.4:c.637G>T	p.Glu213Ter	p.E213*	ENST00000358485	NM_001080125.1	213	Gaa/Taa	4/9	1	2	FACETS	0.763	0.663	0.87	0.763	0.663	0.87	SUBCLONAL	1	TRUE	1	0.34	2		410	509	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578355	212578355	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	76	311	0	ENST00000342788.4:c.902C>T	p.Ser301Phe	p.S301F	ENST00000342788	NM_005235.2	301	tCc/tTc	8/28	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.34	2		311	335	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546878	9546878	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs759137024	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	65	637	0	ENST00000353224.5:c.1144T>G	p.Leu382Val	p.L382V	ENST00000353224	NM_177990.2	382	Ttg/Gtg	5/10	1	2	FACETS	0.518	0.448	0.594	0.518	0.448	0.594	SUBCLONAL	1	TRUE	1	0.34	2		637	738	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253760	30253760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746342082	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	106	558	0	ENST00000307677.4:c.694C>T	p.Arg232Trp	p.R232W	ENST00000307677	NM_138578.1	232	Cgg/Tgg	3/3	1	2	FACETS	0.871	0.781	0.966	0.871	0.781	0.966	CLONAL	1	TRUE	1	0.34	2		558	716	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387976	31387976	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	72	344	2	ENST00000328111.2:c.1777G>T	p.Glu593Ter	p.E593*	ENST00000328111	NM_006892.3	593	Gag/Tag	17/23	1	2	FACETS	0.839	0.734	0.951	0.839	0.734	0.951	CLONAL	1	TRUE	1	0.34	2		346	505	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39746816	39746816	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	148	527	1	ENST00000361337.2:c.1830G>T	p.Glu610Asp	p.E610D	ENST00000361337	NM_003286.2	610	gaG/gaT	18/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.34	2		528	719	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730799	40730799	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	199	678	0	ENST00000373198.4:c.3736G>T	p.Glu1246Ter	p.E1246*	ENST00000373198	NM_133170.3	1246	Gaa/Taa	27/32	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.34	2		678	883	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514525	41514525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	70	595	0	ENST00000373198.4:c.136G>A	p.Ala46Thr	p.A46T	ENST00000373198	NM_133170.3	46	Gct/Act	2/32	1	2	FACETS	0.519	0.452	0.592	0.519	0.452	0.592	SUBCLONAL	1	TRUE	1	0.34	2		595	793	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62293223	62293223	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	255	731	0	ENST00000360203.5:c.322A>G	p.Lys108Glu	p.K108E	ENST00000360203	NM_001283009.1	108	Aag/Gag	4/35	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.34	2		731	1042	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321662	62321662	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	130	679	0	ENST00000360203.5:c.2281C>T	p.Pro761Ser	p.P761S	ENST00000360203	NM_001283009.1	761	Ccc/Tcc	26/35	1	2	FACETS	0.778	0.705	0.855	0.778	0.705	0.855	SUBCLONAL	1	TRUE	1	0.34	2		679	983	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36421159	36421159	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	185	438	0	ENST00000300305.3:c.38A>G	p.Tyr13Cys	p.Y13C	ENST00000300305		13	tAc/tGc	1/8	1	2	FACETS	0.941	0.875	1	1	0.993	1	CLONAL	2	TRUE	1	0.34	2		438	578	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656980	45656980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1399685576	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	239	718	2	ENST00000407780.3:c.176C>T	p.Ser59Leu	p.S59L	ENST00000407780	NM_001283052.1	59	tCg/tTg	3/7	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.34	2		720	1079	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45658337	45658337	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	226	671	0	ENST00000407780.3:c.49C>T	p.Arg17Ter	p.R17*	ENST00000407780	NM_001283052.1	17	Cga/Tga	2/7	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.34	2		671	940	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091826	29091826	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	45	361	1	ENST00000328354.6:c.1131G>T	p.Glu377Asp	p.E377D	ENST00000328354	NM_007194.3	377	gaG/gaT	11/15	1	2	FACETS	0.52	0.437	0.612	0.52	0.437	0.612	SUBCLONAL	1	TRUE	1	0.34	2		362	509	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533751	41533751	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs926253992	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	80	484	0	ENST00000263253.7:c.1717G>A	p.Glu573Lys	p.E573K	ENST00000263253	NM_001429.3	573	Gaa/Aaa	8/31	1	2	FACETS	0.685	0.603	0.773	0.685	0.603	0.773	SUBCLONAL	1	TRUE	1	0.34	2		484	687	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447433	12447433	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	244	607	1	ENST00000287820.6:c.672G>T	p.Glu224Asp	p.E224D	ENST00000287820	NM_015869.4	224	gaG/gaT	5/7	1	2	FACETS	0.751	0.702	0.801	1	0.993	1	SUBCLONAL	2	TRUE	1	0.34	2		608	956	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633275	12633275	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	210	574	0	ENST00000251849.4:c.1125G>T	p.Lys375Asn	p.K375N	ENST00000251849	NM_002880.3	375	aaG/aaT	11/17	1	2	FACETS	0.786	0.731	0.842	1	0.992	1	SUBCLONAL	2	TRUE	1	0.34	2		574	786	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050314	37050315	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs63751101	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	29	284	0	ENST00000231790.2:c.469dup	p.Tyr157LeufsTer15	p.Y157Lfs*15	ENST00000231790	NM_000249.3	155	ctt/cTtt	6/19	1	2	FACETS	0.395	0.316	0.484	0.395	0.316	0.484	SUBCLONAL	1	TRUE	1	0.34	2		284	432	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37092134	37092134	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	81	305	0	ENST00000231790.2:c.2261A>C	p.Glu754Ala	p.E754A	ENST00000231790	NM_000249.3	754	gAg/gCg	19/19	1	2	FACETS	0.781	0.695	0.871	1	0.98	1	SUBCLONAL	2	TRUE	1	0.34	2		305	305	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165772	47165772	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	71	467	0	ENST00000409792.3:c.354G>T	p.Met118Ile	p.M118I	ENST00000409792	NM_014159.6	118	atG/atT	3/21	1	2	FACETS	0.718	0.627	0.816	0.718	0.627	0.816	SUBCLONAL	1	TRUE	1	0.34	2		467	582	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927489	49927489	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	77	608	0	ENST00000296474.3:c.3815C>A	p.Ser1272Ter	p.S1272*	ENST00000296474	NM_002447.2	1272	tCa/tAa	19/20	1	2	FACETS	0.581	0.509	0.658	0.581	0.509	0.658	SUBCLONAL	1	TRUE	1	0.34	2		608	780	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008491	70008491	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	61	425	0	ENST00000394351.3:c.778G>T	p.Glu260Ter	p.E260*	ENST00000394351	NM_000248.3	260	Gaa/Taa	8/9	1	2	FACETS	0.481	0.414	0.554	0.481	0.414	0.554	SUBCLONAL	1	TRUE	1	0.34	2		425	746	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72881596	72881596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	62	380	0	ENST00000325599.8:c.523G>A	p.Asp175Asn	p.D175N	ENST00000325599	NM_018130.2	175	Gat/Aat	5/11	1	2	FACETS	0.552	0.476	0.634	0.552	0.476	0.634	SUBCLONAL	1	TRUE	1	0.34	2		380	661	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156959	89156959	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141456190	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	188	681	1	ENST00000336596.2:c.61G>A	p.Glu21Lys	p.E21K	ENST00000336596	NM_005233.5	21	Gaa/Aaa	1/17	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.34	2		682	790	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259116	89259116	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	52	400	0	ENST00000336596.2:c.260T>C	p.Val87Ala	p.V87A	ENST00000336596	NM_005233.5	87	gTc/gCc	3/17	1	2	FACETS	0.71	0.605	0.824	0.71	0.605	0.824	SUBCLONAL	1	TRUE	1	0.34	2		400	431	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448525	89448525	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	73	448	0	ENST00000336596.2:c.1489A>C	p.Ser497Arg	p.S497R	ENST00000336596	NM_005233.5	497	Agt/Cgt	7/17	1	2	FACETS	0.681	0.595	0.773	0.681	0.595	0.773	SUBCLONAL	1	TRUE	1	0.34	2		448	631	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462381	89462381	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	87	594	0	ENST00000336596.2:c.1853C>A	p.Ala618Asp	p.A618D	ENST00000336596	NM_005233.5	618	gCc/gAc	10/17	1	2	FACETS	0.986	0.876	1	0.986	0.876	1	CLONAL	1	TRUE	1	0.34	2		594	519	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200066	128200066	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	115	884	0	ENST00000341105.2:c.1239C>A	p.Cys413Ter	p.C413*	ENST00000341105	NM_032638.4	413	tgC/tgA	6/6	1	2	FACETS	0.554	0.497	0.614	0.554	0.497	0.614	SUBCLONAL	1	TRUE	1	0.34	2		884	1221	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670295	134670295	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	103	506	0	ENST00000398015.3:c.206A>C	p.Asn69Thr	p.N69T	ENST00000398015	NM_004441.4	69	aAc/aCc	3/16	1	2	FACETS	0.825	0.739	0.917	0.825	0.739	0.917	CLONAL	1	TRUE	1	0.34	2		506	734	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898765	134898765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777467287	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	36	452	0	ENST00000398015.3:c.1823G>A	p.Arg608Gln	p.R608Q	ENST00000398015	NM_004441.4	608	cGg/cAg	10/16	1	2	FACETS	0.358	0.293	0.43	0.358	0.293	0.43	SUBCLONAL	1	TRUE	1	0.34	2		452	592	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920428	134920428	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	120	688	0	ENST00000398015.3:c.2243G>T	p.Arg748Met	p.R748M	ENST00000398015	NM_004441.4	748	aGg/aTg	12/16	1	2	FACETS	0.785	0.708	0.866	0.785	0.708	0.866	SUBCLONAL	1	TRUE	1	0.34	2		688	899	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474682	138474682	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	51	457	1	ENST00000289153.2:c.311C>A	p.Pro104His	p.P104H	ENST00000289153	NM_006219.2	104	cCt/cAt	2/22	1	2	FACETS	0.628	0.534	0.73	0.628	0.534	0.73	SUBCLONAL	1	TRUE	1	0.34	2		458	478	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474703	138474703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1467994756	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	66	428	0	ENST00000289153.2:c.290G>A	p.Arg97Gln	p.R97Q	ENST00000289153	NM_006219.2	97	cGa/cAa	2/22	1	2	FACETS	0.835	0.727	0.952	0.835	0.727	0.952	CLONAL	1	TRUE	1	0.34	2		428	465	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188970	142188970	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	20	121	0	ENST00000350721.4:c.6277C>A	p.Leu2093Ile	p.L2093I	ENST00000350721	NM_001184.3	2093	Cta/Ata	37/47	1	2	FACETS	0.48	0.368	0.611	0.48	0.368	0.611	SUBCLONAL	1	TRUE	1	0.34	2		121	245	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268340	142268340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770645649	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	16	141	0	ENST00000350721.4:c.3152G>A	p.Arg1051His	p.R1051H	ENST00000350721	NM_001184.3	1051	cGt/cAt	15/47	1	2	FACETS	0.413	0.305	0.541	0.413	0.305	0.541	SUBCLONAL	1	TRUE	1	0.34	2		141	228	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169999725	169999725	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	50	305	0	ENST00000295797.4:c.1036C>T	p.Arg346Ter	p.R346*	ENST00000295797	NM_002740.5	346	Cga/Tga	11/18	1	2	FACETS	0.795	0.677	0.924	0.795	0.677	0.924	CLONAL	1	TRUE	1	0.34	2		305	370	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916719	178916719	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs777956032	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	43	292	0	ENST00000263967.3:c.106T>C	p.Cys36Arg	p.C36R	ENST00000263967	NM_006218.2	36	Tgc/Cgc	2/21	1	2	FACETS	0.746	0.626	0.878	0.746	0.626	0.878	SUBCLONAL	1	TRUE	1	0.34	2		292	339	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431079	181431079	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	113	672	0	ENST00000325404.1:c.931A>G	p.Thr311Ala	p.T311A	ENST00000325404	NM_003106.3	311	Aca/Gca	1/1	1	2	FACETS	0.722	0.649	0.799	0.722	0.649	0.799	SUBCLONAL	1	TRUE	1	0.34	2		672	921	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190867	185190867	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	104	768	1	ENST00000265026.3:c.1748G>T	p.Arg583Leu	p.R583L	ENST00000265026	NM_004721.4	583	cGa/cTa	11/14	1	2	FACETS	0.56	0.5	0.624	0.56	0.5	0.624	SUBCLONAL	1	TRUE	1	0.34	2		769	1093	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504989	186504989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	34	369	0	ENST00000323963.5:c.845C>T	p.Thr282Met	p.T282M	ENST00000323963		282	aCg/aTg	8/11	1	2	FACETS	0.353	0.288	0.427	0.353	0.288	0.427	SUBCLONAL	1	TRUE	1	0.34	2		369	566	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447188	187447188	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	135	722	0	ENST00000232014.4:c.1005G>T	p.Gln335His	p.Q335H	ENST00000232014	NM_001130845.1	335	caG/caT	5/10	1	2	FACETS	0.847	0.769	0.929	0.847	0.769	0.929	CLONAL	1	TRUE	1	0.34	2		722	938	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127368	55127368	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	74	584	0	ENST00000257290.5:c.156G>T	p.Glu52Asp	p.E52D	ENST00000257290	NM_006206.4	52	gaG/gaT	3/23	1	2	FACETS	0.545	0.477	0.62	0.545	0.477	0.62	SUBCLONAL	1	TRUE	1	0.34	2		584	798	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139736	55139736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	107	492	2	ENST00000257290.5:c.1397C>T	p.Ala466Val	p.A466V	ENST00000257290	NM_006206.4	466	gCc/gTc	10/23	1	2	FACETS	0.869	0.78	0.964	0.869	0.78	0.964	CLONAL	1	TRUE	1	0.34	2		494	724	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161404	55161404	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	74	534	1	ENST00000257290.5:c.3235G>T	p.Asp1079Tyr	p.D1079Y	ENST00000257290	NM_006206.4	1079	Gac/Tac	23/23	1	2	FACETS	0.565	0.493	0.641	0.565	0.493	0.641	SUBCLONAL	1	TRUE	1	0.34	2		535	771	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592196	55592196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	28	363	0	ENST00000288135.5:c.1520C>T	p.Ala507Val	p.A507V	ENST00000288135	NM_000222.2	507	gCa/gTa	9/21	1	2	FACETS	0.336	0.268	0.414	0.336	0.268	0.414	SUBCLONAL	1	TRUE	1	0.34	2		363	490	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946236	55946236	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	108	474	0	ENST00000263923.4:c.3943G>T	p.Asp1315Tyr	p.D1315Y	ENST00000263923	NM_002253.2	1315	Gac/Tac	30/30	1	2	FACETS	0.905	0.813	1	0.905	0.813	1	CLONAL	1	TRUE	1	0.34	2		474	702	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948169	55948169	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	51	415	0	ENST00000263923.4:c.3802G>A	p.Glu1268Lys	p.E1268K	ENST00000263923	NM_002253.2	1268	Gag/Aag	29/30	1	2	FACETS	0.609	0.517	0.708	0.609	0.517	0.708	SUBCLONAL	1	TRUE	1	0.34	2		415	493	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961000	55961002	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs1394396368	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	77	559	0	ENST00000263923.4:c.2938_2940del	p.Glu980del	p.E980del	ENST00000263923	NM_002253.2	980	GAG/-	21/30	1	2	FACETS	0.585	0.513	0.663	0.585	0.513	0.663	SUBCLONAL	1	TRUE	1	0.34	2		559	774	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286248	66286248	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	21	244	0	ENST00000273854.3:c.1438A>C	p.Ile480Leu	p.I480L	ENST00000273854	NM_004439.5	480	Att/Ctt	6/18	1	2	FACETS	0.38	0.292	0.482	0.38	0.292	0.482	SUBCLONAL	1	TRUE	1	0.34	2		244	325	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467460	66467460	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	49	361	0	ENST00000273854.3:c.809A>C	p.Glu270Ala	p.E270A	ENST00000273854	NM_004439.5	270	gAa/gCa	3/18	1	2	FACETS	0.575	0.487	0.672	0.575	0.487	0.672	SUBCLONAL	1	TRUE	1	0.34	2		361	501	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467882	66467882	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	45	365	0	ENST00000273854.3:c.387A>T	p.Glu129Asp	p.E129D	ENST00000273854	NM_004439.5	129	gaA/gaT	3/18	1	2	FACETS	0.65	0.547	0.764	0.65	0.547	0.764	SUBCLONAL	1	TRUE	1	0.34	2		365	407	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99802261	99802261	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	12	121	0	ENST00000280892.6:c.632C>T	p.Pro211Leu	p.P211L	ENST00000280892	NM_001130678.1	211	cCa/cTa	7/7	1	2	FACETS	0.408	0.287	0.556	0.408	0.287	0.556	SUBCLONAL	1	TRUE	1	0.34	2		121	173	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99806092	99806092	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	10	94	0	ENST00000280892.6:c.580G>T	p.Glu194Ter	p.E194*	ENST00000280892	NM_001130678.1	194	Gaa/Taa	6/7	1	2	FACETS	0.482	0.328	0.673	0.482	0.328	0.673	SUBCLONAL	1	TRUE	1	0.34	2		94	122	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003288	143003288	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	179	540	0	ENST00000262992.4:c.2538A>C	p.Lys846Asn	p.K846N	ENST00000262992	NM_001101669.1	846	aaA/aaC	23/24	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.34	2		540	754	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143033767	143033767	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	54	420	0	ENST00000262992.4:c.2204A>C	p.Glu735Ala	p.E735A	ENST00000262992	NM_001101669.1	735	gAa/gCa	20/24	1	2	FACETS	0.746	0.638	0.863	0.746	0.638	0.863	SUBCLONAL	1	TRUE	1	0.34	2		420	426	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114280	143114280	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	32	349	1	ENST00000262992.4:c.1141C>T	p.Leu381Phe	p.L381F	ENST00000262992	NM_001101669.1	381	Ctt/Ttt	13/24	1	2	FACETS	0.459	0.372	0.557	0.459	0.372	0.557	SUBCLONAL	1	TRUE	1	0.34	2		350	410	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352409	143352409	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	114	485	0	ENST00000262992.4:c.4G>T	p.Glu2Ter	p.E2*	ENST00000262992	NM_001101669.1	2	Gaa/Taa	2/24	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.34	2		485	585	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251927	153251927	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	139	395	0	ENST00000281708.4:c.1079G>T	p.Arg360Ile	p.R360I	ENST00000281708	NM_033632.3	360	aGa/aTa	7/12	1	2	FACETS	0.973	0.895	1	1	0.991	1	CLONAL	2	TRUE	1	0.34	2		395	420	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524982	187524982	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	121	626	0	ENST00000441802.2:c.10698G>T	p.Lys3566Asn	p.K3566N	ENST00000441802	NM_005245.3	3566	aaG/aaT	19/27	1	2	FACETS	0.839	0.758	0.925	0.839	0.758	0.925	CLONAL	1	TRUE	1	0.34	2		626	848	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532563	187532563	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	33	282	0	ENST00000441802.2:c.9830A>C	p.Lys3277Thr	p.K3277T	ENST00000441802	NM_005245.3	3277	aAa/aCa	14/27	1	2	FACETS	0.618	0.505	0.745	0.618	0.505	0.745	SUBCLONAL	1	TRUE	1	0.34	2		282	314	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539635	187539635	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	32	381	0	ENST00000441802.2:c.8105A>C	p.Lys2702Thr	p.K2702T	ENST00000441802	NM_005245.3	2702	aAa/aCa	10/27	1	2	FACETS	0.512	0.415	0.62	0.512	0.415	0.62	SUBCLONAL	1	TRUE	1	0.34	2		381	368	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540227	187540227	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770932444	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	66	465	0	ENST00000441802.2:c.7513G>A	p.Ala2505Thr	p.A2505T	ENST00000441802	NM_005245.3	2505	Gct/Act	10/27	1	2	FACETS	0.63	0.547	0.721	0.63	0.547	0.721	SUBCLONAL	1	TRUE	1	0.34	2		465	616	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542524	187542524	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	28	443	0	ENST00000441802.2:c.5216G>T	p.Gly1739Val	p.G1739V	ENST00000441802	NM_005245.3	1739	gGa/gTa	10/27	1	2	FACETS	0.337	0.268	0.415	0.337	0.268	0.415	SUBCLONAL	1	TRUE	1	0.34	2		443	489	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542552	187542552	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	61	444	0	ENST00000441802.2:c.5188T>G	p.Leu1730Val	p.L1730V	ENST00000441802	NM_005245.3	1730	Ttg/Gtg	10/27	1	2	FACETS	0.79	0.683	0.906	0.79	0.683	0.906	CLONAL	1	TRUE	1	0.34	2		444	454	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557332	187557332	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764891067	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	44	619	0	ENST00000441802.2:c.4030G>A	p.Glu1344Lys	p.E1344K	ENST00000441802	NM_005245.3	1344	Gaa/Aaa	6/27	1	2	FACETS	0.314	0.263	0.372	0.314	0.263	0.372	SUBCLONAL	1	TRUE	1	0.34	2		619	823	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628649	187628649	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	142	622	0	ENST00000441802.2:c.2333C>A	p.Ser778Tyr	p.S778Y	ENST00000441802	NM_005245.3	778	tCt/tAt	2/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.34	2		622	686	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282613	1282613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039438	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	105	767	3	ENST00000310581.5:c.1700C>T	p.Thr567Met	p.T567M	ENST00000310581	NM_198253.2	567	aCg/aTg	3/16	1	2	FACETS	0.515	0.46	0.574	0.515	0.46	0.574	SUBCLONAL	1	TRUE	1	0.34	2		770	1199	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294616	1294616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	96	473	0	ENST00000310581.5:c.385G>A	p.Asp129Asn	p.D129N	ENST00000310581	NM_198253.2	129	Gac/Aac	2/16	1	2	FACETS	0.792	0.706	0.884	0.792	0.706	0.884	SUBCLONAL	1	TRUE	1	0.34	2		473	713	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31401571	31401571	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	81	487	0	ENST00000344624.3:c.4093G>T	p.Glu1365Ter	p.E1365*	ENST00000344624		1365	Gag/Tag	33/33	1	2	FACETS	0.713	0.628	0.804	0.713	0.628	0.804	SUBCLONAL	1	TRUE	1	0.34	2		487	668	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950237	38950237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766110639	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	60	461	0	ENST00000357387.3:c.3713G>A	p.Arg1238Gln	p.R1238Q	ENST00000357387	NM_152756.3	1238	cGa/cAa	31/38	1	2	FACETS	0.712	0.614	0.818	0.712	0.614	0.818	SUBCLONAL	1	TRUE	1	0.34	2		461	496	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170881	56170881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	85	322	0	ENST00000399503.3:c.1709G>A	p.Gly570Asp	p.G570D	ENST00000399503	NM_005921.1	570	gGc/gAc	10/20	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.34	2		322	453	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180553	56180553	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	27	252	0	ENST00000399503.3:c.3882G>T	p.Glu1294Asp	p.E1294D	ENST00000399503	NM_005921.1	1294	gaG/gaT	16/20	1	2	FACETS	0.588	0.469	0.723	0.588	0.469	0.723	SUBCLONAL	1	TRUE	1	0.34	2		252	270	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961170	79961170	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1354731566	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	51	352	0	ENST00000265081.6:c.567A>C	p.Gln189His	p.Q189H	ENST00000265081	NM_002439.4	189	caA/caC	3/24	1	2	FACETS	0.775	0.661	0.9	0.775	0.661	0.9	SUBCLONAL	1	TRUE	1	0.34	2		352	387	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682686	86682686	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	12	147	0	ENST00000274376.6:c.2891A>T	p.Lys964Ile	p.K964I	ENST00000274376	NM_002890.2	964	aAa/aTa	23/25	1	2	FACETS	0.413	0.291	0.562	0.413	0.291	0.562	SUBCLONAL	1	TRUE	1	0.34	2		147	171	SUCCESS
APC	324	MSKCC	GRCh37	5	112163693	112163693	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1432714177	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	20	274	0	ENST00000257430.4:c.1616A>G	p.Asp539Gly	p.D539G	ENST00000257430	NM_000038.5	539	gAc/gGc	13/16	1	2	FACETS	0.348	0.266	0.445	0.348	0.266	0.445	SUBCLONAL	1	TRUE	1	0.34	2		274	338	SUCCESS
APC	324	MSKCC	GRCh37	5	112173445	112173445	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	30	327	0	ENST00000257430.4:c.2154T>G	p.Ile718Met	p.I718M	ENST00000257430	NM_000038.5	718	atT/atG	16/16	1	2	FACETS	0.518	0.417	0.631	0.518	0.417	0.631	SUBCLONAL	1	TRUE	1	0.34	2		327	341	SUCCESS
APC	324	MSKCC	GRCh37	5	112177390	112177390	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	50	256	0	ENST00000257430.4:c.6099C>A	p.Asp2033Glu	p.D2033E	ENST00000257430	NM_000038.5	2033	gaC/gaA	16/16	1	2	FACETS	0.958	0.818	1	0.958	0.818	1	CLONAL	1	TRUE	1	0.34	2		256	307	SUCCESS
APC	324	MSKCC	GRCh37	5	112178901	112178901	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	94	360	0	ENST00000257430.4:c.7610C>A	p.Ser2537Tyr	p.S2537Y	ENST00000257430	NM_000038.5	2537	tCt/tAt	16/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.34	2		360	444	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915730	131915730	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	30	124	0	ENST00000265335.6:c.728C>A	p.Ser243Tyr	p.S243Y	ENST00000265335		243	tCc/tAc	5/25	1	2	FACETS	0.679	0.549	0.824	0.679	0.549	0.824	SUBCLONAL	1	TRUE	1	0.34	2		124	260	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939681	131939681	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060501936	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	97	279	1	ENST00000265335.6:c.2467C>T	p.Arg823Ter	p.R823*	ENST00000265335		823	Cga/Tga	15/25	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.34	2		280	448	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131972851	131972851	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	100	296	0	ENST00000265335.6:c.3434A>C	p.Lys1145Thr	p.K1145T	ENST00000265335		1145	aAa/aCa	22/25	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.34	2		296	495	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977950	131977950	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	113	370	0	ENST00000265335.6:c.3833G>A	p.Gly1278Glu	p.G1278E	ENST00000265335		1278	gGa/gAa	25/25	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.34	2		370	458	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524540	176524540	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148143006	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	117	966	0	ENST00000292408.4:c.2272C>T	p.Arg758Cys	p.R758C	ENST00000292408	NM_213647.1	758	Cgc/Tgc	18/18	1	2	FACETS	0.602	0.541	0.666	0.602	0.541	0.666	SUBCLONAL	1	TRUE	1	0.34	2		966	1144	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639124	176639124	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	74	549	0	ENST00000439151.2:c.3724G>T	p.Ala1242Ser	p.A1242S	ENST00000439151	NM_022455.4	1242	Gcc/Tcc	5/23	1	2	FACETS	0.647	0.566	0.734	0.647	0.566	0.734	SUBCLONAL	1	TRUE	1	0.34	2		549	673	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176662922	176662922	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	35	312	0	ENST00000439151.2:c.3897G>T	p.Lys1299Asn	p.K1299N	ENST00000439151	NM_022455.4	1299	aaG/aaT	6/23	1	2	FACETS	0.658	0.541	0.788	0.658	0.541	0.788	SUBCLONAL	1	TRUE	1	0.34	2		312	313	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721900	176721900	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	79	571	0	ENST00000439151.2:c.7531G>A	p.Asp2511Asn	p.D2511N	ENST00000439151	NM_022455.4	2511	Gat/Aat	23/23	1	2	FACETS	0.578	0.508	0.654	0.578	0.508	0.654	SUBCLONAL	1	TRUE	1	0.34	2		571	804	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046717	180046717	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	135	848	3	ENST00000261937.6:c.2595C>A	p.Phe865Leu	p.F865L	ENST00000261937	NM_182925.4	865	ttC/ttA	18/30	1	2	FACETS	0.735	0.666	0.807	0.735	0.666	0.807	SUBCLONAL	1	TRUE	1	0.34	2		851	1081	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180049741	180049741	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	69	649	0	ENST00000261937.6:c.1647C>A	p.Phe549Leu	p.F549L	ENST00000261937	NM_182925.4	549	ttC/ttA	12/30	1	2	FACETS	0.48	0.417	0.548	0.48	0.417	0.548	SUBCLONAL	1	TRUE	1	0.34	2		649	846	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052971	180052971	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753074837	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	173	873	0	ENST00000261937.6:c.1319G>A	p.Arg440His	p.R440H	ENST00000261937	NM_182925.4	440	cGc/cAc	10/30	1	2	FACETS	0.94	0.864	1	0.94	0.864	1	CLONAL	1	TRUE	1	0.34	2		873	1083	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393180	393180	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1403333371	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	99	423	0	ENST00000380956.4:c.28G>A	p.Gly10Arg	p.G10R	ENST00000380956	NM_001195286.1	10	Gga/Aga	2/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.34	NA		423	682	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393295	393295	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	96	613	0	ENST00000380956.4:c.143G>T	p.Ser48Ile	p.S48I	ENST00000380956	NM_001195286.1	48	aGc/aTc	2/9	1	2	FACETS	0.664	0.59	0.742	0.664	0.59	0.742	SUBCLONAL	1	TRUE	1	0.34	2		613	851	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481495	20481495	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	48	407	0	ENST00000346618.3:c.564G>T	p.Lys188Asn	p.K188N	ENST00000346618	NM_001949.4	188	aaG/aaT	3/7	1	2	FACETS	0.53	0.448	0.62	0.53	0.448	0.62	SUBCLONAL	1	TRUE	1	0.34	2		407	533	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286963	33286963	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	134	699	0	ENST00000374542.5:c.1974G>T	p.Lys658Asn	p.K658N	ENST00000374542	NM_001141970.1	658	aaG/aaT	7/8	1	2	FACETS	0.926	0.841	1	0.926	0.841	1	CLONAL	1	TRUE	1	0.34	2		699	851	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652161	36652161	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	155	780	0	ENST00000244741.5:c.283C>T	p.Pro95Ser	p.P95S	ENST00000244741	NM_000389.4	95	Cct/Tct	2/3	1	2	FACETS	0.908	0.831	0.989	0.908	0.831	0.989	CLONAL	1	TRUE	1	0.34	2		780	1004	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955066	93955066	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	25	244	0	ENST00000369303.4:c.2832C>A	p.Phe944Leu	p.F944L	ENST00000369303	NM_004440.3	944	ttC/ttA	16/17	1	2	FACETS	0.563	0.445	0.698	0.563	0.445	0.698	SUBCLONAL	1	TRUE	1	0.34	2		244	261	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553523	106553523	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs768991091	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	78	490	0	ENST00000369096.4:c.1488C>A	p.Phe496Leu	p.F496L	ENST00000369096	NM_001198.3	496	ttC/ttA	5/7	1	2	FACETS	0.707	0.621	0.799	0.707	0.621	0.799	SUBCLONAL	1	TRUE	1	0.34	2		490	649	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681175	117681175	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	31	226	0	ENST00000368508.3:c.3446-1G>T		p.X1149_splice	ENST00000368508	NM_002944.2	1149			1	2	FACETS	0.881	0.718	1	0.881	0.718	1	CLONAL	1	TRUE	1	0.34	2		226	207	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708992	117708992	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	86	554	0	ENST00000368508.3:c.1965G>T	p.Lys655Asn	p.K655N	ENST00000368508	NM_002944.2	655	aaG/aaT	13/43	1	2	FACETS	0.627	0.554	0.705	0.627	0.554	0.705	SUBCLONAL	1	TRUE	1	0.34	2		554	807	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192443	138192443	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	45	345	0	ENST00000237289.4:c.79G>T	p.Glu27Ter	p.E27*	ENST00000237289	NM_001270507.1	27	Gaa/Taa	2/9	1	2	FACETS	0.617	0.519	0.725	0.617	0.519	0.725	SUBCLONAL	1	TRUE	1	0.34	2		345	429	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196921	138196921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	61	375	0	ENST00000237289.4:c.583C>T	p.His195Tyr	p.H195Y	ENST00000237289	NM_001270507.1	195	Cac/Tac	4/9	1	2	FACETS	0.737	0.637	0.845	0.737	0.637	0.845	SUBCLONAL	1	TRUE	1	0.34	2		375	487	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138197194	138197194	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	54	493	0	ENST00000237289.4:c.696T>G	p.Ile232Met	p.I232M	ENST00000237289	NM_001270507.1	232	atT/atG	5/9	1	2	FACETS	0.544	0.464	0.631	0.544	0.464	0.631	SUBCLONAL	1	TRUE	1	0.34	2		493	584	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199663	138199663	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751096907	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	126	526	0	ENST00000237289.4:c.1081G>A	p.Glu361Lys	p.E361K	ENST00000237289	NM_001270507.1	361	Gag/Aag	7/9	1	2	FACETS	0.904	0.818	0.994	0.904	0.818	0.994	CLONAL	1	TRUE	1	0.34	2		526	820	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983143	149983143	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	40	402	0	ENST00000253339.5:c.3115T>G	p.Phe1039Val	p.F1039V	ENST00000253339		1039	Ttt/Gtt	7/7	1	2	FACETS	0.6	0.499	0.712	0.6	0.499	0.712	SUBCLONAL	1	TRUE	1	0.34	2		402	392	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527985	157527985	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	117	681	1	ENST00000346085.5:c.5710C>A	p.Pro1904Thr	p.P1904T	ENST00000346085	NM_020732.3	1904	Ccc/Acc	20/20	1	2	FACETS	0.735	0.661	0.812	0.735	0.661	0.812	SUBCLONAL	1	TRUE	1	0.34	2		682	937	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6037000	6037000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	81	547	0	ENST00000265849.7:c.760G>T	p.Glu254Ter	p.E254*	ENST00000265849	NM_000535.5	254	Gag/Tag	7/15	1	2	FACETS	0.636	0.56	0.718	0.636	0.56	0.718	SUBCLONAL	1	TRUE	1	0.34	2		547	749	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426880	6426880	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	34	215	0	ENST00000356142.4:c.73A>G	p.Thr25Ala	p.T25A	ENST00000356142	NM_018890.3	25	Acc/Gcc	2/7	1	2	FACETS	0.44	0.359	0.531	0.44	0.359	0.531	SUBCLONAL	1	TRUE	1	0.34	2		215	455	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331924	81331924	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	13	227	0	ENST00000222390.5:c.2160T>G	p.Ile720Met	p.I720M	ENST00000222390	NM_000601.4	720	atT/atG	18/18	1	2	FACETS	0.357	0.255	0.482	0.357	0.255	0.482	SUBCLONAL	1	TRUE	1	0.34	2		227	214	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381456	81381456	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	66	333	0	ENST00000222390.5:c.605A>G	p.Asp202Gly	p.D202G	ENST00000222390	NM_000601.4	202	gAc/gGc	5/18	1	2	FACETS	0.831	0.723	0.948	0.831	0.723	0.948	CLONAL	1	TRUE	1	0.34	2		333	467	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545817	106545817	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	78	264	0	ENST00000359195.3:c.3294G>T	p.Glu1098Asp	p.E1098D	ENST00000359195	NM_002649.2	1098	gaG/gaT	11/11	1	2	FACETS	0.765	0.679	0.855	1	0.979	1	SUBCLONAL	2	TRUE	1	0.34	2		264	300	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395491	116395491	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	133	434	0	ENST00000397752.3:c.1784A>C	p.Lys595Thr	p.K595T	ENST00000397752	NM_000245.2	595	aAa/aCa	6/21	1	2	FACETS	0.764	0.698	0.833	1	0.987	1	SUBCLONAL	2	TRUE	1	0.34	2		434	512	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482826	140482826	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1249895723	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	52	439	1	ENST00000288602.6:c.1309C>T	p.Arg437Ter	p.R437*	ENST00000288602	NM_004333.4	437	Cga/Tga	10/18	1	2	FACETS	0.561	0.478	0.653	0.561	0.478	0.653	SUBCLONAL	1	TRUE	1	0.34	2		440	545	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140549911	140549911	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	44	150	0	ENST00000288602.6:c.240G>T	p.Glu80Asp	p.E80D	ENST00000288602	NM_004333.4	80	gaG/gaT	2/18	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.34	2		150	232	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512614	148512614	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	64	336	0	ENST00000320356.2:c.1530G>T	p.Lys510Asn	p.K510N	ENST00000320356	NM_004456.4	510	aaG/aaT	13/20	1	2	FACETS	0.678	0.588	0.776	0.678	0.588	0.776	SUBCLONAL	1	TRUE	1	0.34	2		336	555	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151168675	151168675	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	29	138	0	ENST00000262187.5:c.292G>T	p.Val98Phe	p.V98F	ENST00000262187	NM_005614.3	98	Gtt/Ttt	5/8	1	2	FACETS	0.547	0.44	0.668	0.547	0.44	0.668	SUBCLONAL	1	TRUE	1	0.34	2		138	312	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851523	151851523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564716850	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	55	271	0	ENST00000262189.6:c.11968G>A	p.Asp3990Asn	p.D3990N	ENST00000262189	NM_170606.2	3990	Gat/Aat	47/59	1	2	FACETS	0.77	0.661	0.89	0.77	0.661	0.89	SUBCLONAL	1	TRUE	1	0.34	2		271	420	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859545	151859545	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	143	494	0	ENST00000262189.6:c.11117A>C	p.Lys3706Thr	p.K3706T	ENST00000262189	NM_170606.2	3706	aAg/aCg	43/59	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.34	2		494	638	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859881	151859881	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	49	397	0	ENST00000262189.6:c.10781C>A	p.Ser3594Tyr	p.S3594Y	ENST00000262189	NM_170606.2	3594	tCt/tAt	43/59	1	2	FACETS	0.654	0.554	0.763	0.654	0.554	0.763	SUBCLONAL	1	TRUE	1	0.34	2		397	441	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878597	151878597	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	103	691	0	ENST00000262189.6:c.6348T>G	p.Phe2116Leu	p.F2116L	ENST00000262189	NM_170606.2	2116	ttT/ttG	36/59	1	2	FACETS	0.775	0.693	0.862	0.775	0.693	0.862	SUBCLONAL	1	TRUE	1	0.34	2		691	782	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879463	151879463	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	159	491	0	ENST00000262189.6:c.5482G>T	p.Glu1828Ter	p.E1828*	ENST00000262189	NM_170606.2	1828	Gaa/Taa	36/59	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.34	2		491	634	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902253	151902253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1230955155	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	47	284	0	ENST00000262189.6:c.3899G>T	p.Arg1300Ile	p.R1300I	ENST00000262189	NM_170606.2	1300	aGa/aTa	25/59	1	2	FACETS	0.83	0.704	0.969	0.83	0.704	0.969	CLONAL	1	TRUE	1	0.34	2		284	333	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345765	152345765	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	33	232	0	ENST00000359321.1:c.805T>G	p.Phe269Val	p.F269V	ENST00000359321	NM_005431.1	269	Ttt/Gtt	3/3	1	2	FACETS	0.583	0.476	0.703	0.583	0.476	0.703	SUBCLONAL	1	TRUE	1	0.34	2		232	333	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345941	152345941	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	112	479	0	ENST00000359321.1:c.629C>A	p.Ser210Tyr	p.S210Y	ENST00000359321	NM_005431.1	210	tCt/tAt	3/3	1	2	FACETS	0.821	0.739	0.909	0.821	0.739	0.909	CLONAL	1	TRUE	1	0.34	2		479	802	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162155	38162155	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	60	537	0	ENST00000317025.8:c.2561G>T	p.Ser854Ile	p.S854I	ENST00000317025	NM_023034.1	854	aGc/aTc	14/24	1	2	FACETS	0.551	0.474	0.634	0.551	0.474	0.634	SUBCLONAL	1	TRUE	1	0.34	2		537	641	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38184323	38184323	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	54	404	1	ENST00000317025.8:c.1633A>C	p.Ile545Leu	p.I545L	ENST00000317025	NM_023034.1	545	Att/Ctt	7/24	1	2	FACETS	0.53	0.452	0.616	0.53	0.452	0.616	SUBCLONAL	1	TRUE	1	0.34	2		405	599	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56860194	56860194	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	49	531	1	ENST00000519728.1:c.196G>T	p.Asp66Tyr	p.D66Y	ENST00000519728	NM_002350.3	66	Gac/Tac	4/13	1	2	FACETS	0.363	0.306	0.425	0.363	0.306	0.425	SUBCLONAL	1	TRUE	1	0.34	2		532	795	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005898	69005898	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	83	506	0	ENST00000288368.4:c.2309A>C	p.Lys770Thr	p.K770T	ENST00000288368	NM_024870.2	770	aAa/aCa	21/40	1	2	FACETS	0.901	0.797	1	0.901	0.797	1	CLONAL	1	TRUE	1	0.34	2		506	542	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90949283	90949283	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	52	97	0	ENST00000265433.3:c.2205A>C	p.Lys735Asn	p.K735N	ENST00000265433	NM_002485.4	735	aaA/aaC	15/16	1	2	FACETS	0.784	0.678	0.898	1	0.97	1	SUBCLONAL	2	TRUE	1	0.34	2		97	195	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90960115	90960115	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	22	92	0	ENST00000265433.3:c.1851A>C	p.Glu617Asp	p.E617D	ENST00000265433	NM_002485.4	617	gaA/gaC	12/16	1	2	FACETS	0.711	0.555	0.89	0.711	0.555	0.89	SUBCLONAL	1	TRUE	1	0.34	2		92	182	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976728	90976728	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	17	247	0	ENST00000265433.3:c.904C>A	p.Leu302Ile	p.L302I	ENST00000265433	NM_002485.4	302	Ctt/Att	8/16	1	2	FACETS	0.329	0.245	0.429	0.329	0.245	0.429	SUBCLONAL	1	TRUE	1	0.34	2		247	304	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054592	5054592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749863048	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	38	171	0	ENST00000381652.3:c.644G>A	p.Arg215Gln	p.R215Q	ENST00000381652	NM_004972.3	215	cGa/cAa	7/25	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.34	2		171	191	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054847	5054847	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	45	286	0	ENST00000381652.3:c.899G>T	p.Arg300Ile	p.R300I	ENST00000381652	NM_004972.3	300	aGa/aTa	7/25	1	2	FACETS	0.84	0.71	0.983	0.84	0.71	0.983	CLONAL	1	TRUE	1	0.34	2		286	315	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080241	5080241	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	20	173	0	ENST00000381652.3:c.2144G>T	p.Arg715Ile	p.R715I	ENST00000381652	NM_004972.3	715	aGa/aTa	17/25	1	2	FACETS	0.61	0.468	0.773	0.61	0.468	0.773	SUBCLONAL	1	TRUE	1	0.34	2		173	193	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090529	5090529	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	34	124	0	ENST00000381652.3:c.2845G>T	p.Asp949Tyr	p.D949Y	ENST00000381652	NM_004972.3	949	Gat/Tat	21/25	1	2	FACETS	0.82	0.674	0.982	0.82	0.674	0.982	CLONAL	1	TRUE	1	0.34	2		124	244	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389311	8389311	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs746067788	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	64	582	0	ENST00000356435.5:c.4307T>G	p.Phe1436Cys	p.F1436C	ENST00000356435		1436	tTt/tGt	26/35	1	2	FACETS	0.551	0.477	0.632	0.551	0.477	0.632	SUBCLONAL	1	TRUE	1	0.34	2		582	683	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636736	8636736	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	39	388	0	ENST00000356435.5:c.173A>G	p.Asn58Ser	p.N58S	ENST00000356435		58	aAc/aGc	2/35	1	2	FACETS	0.428	0.354	0.511	0.428	0.354	0.511	SUBCLONAL	1	TRUE	1	0.34	2		388	536	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27168553	27168553	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	74	324	0	ENST00000380036.4:c.425C>A	p.Ser142Tyr	p.S142Y	ENST00000380036	NM_000459.3	142	tCt/tAt	3/23	1	2	FACETS	0.953	0.837	1	0.953	0.837	1	CLONAL	1	TRUE	1	0.34	2		324	457	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27209157	27209157	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	51	489	0	ENST00000380036.4:c.2614G>A	p.Glu872Lys	p.E872K	ENST00000380036	NM_000459.3	872	Gaa/Aaa	16/23	1	2	FACETS	0.437	0.37	0.51	0.437	0.37	0.51	SUBCLONAL	1	TRUE	1	0.34	2		489	687	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27220118	27220118	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	141	643	0	ENST00000380036.4:c.3175A>G	p.Lys1059Glu	p.K1059E	ENST00000380036	NM_000459.3	1059	Aag/Gag	21/23	1	2	FACETS	0.822	0.748	0.9	0.822	0.748	0.9	CLONAL	1	TRUE	1	0.34	2		643	1009	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412450	80412450	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	121	324	0	ENST00000286548.4:c.591A>C	p.Gln197His	p.Q197H	ENST00000286548	NM_002072.3	197	caA/caC	4/7	1	2	FACETS	0.794	0.723	0.869	1	0.987	1	SUBCLONAL	2	TRUE	1	0.34	2		324	448	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641115	93641115	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	123	605	0	ENST00000375746.1:c.1461G>T	p.Glu487Asp	p.E487D	ENST00000375746	NM_001174167.1	487	gaG/gaT	11/14	1	2	FACETS	0.935	0.846	1	0.935	0.846	1	CLONAL	1	TRUE	1	0.34	2		605	774	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209563	98209563	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	194	677	0	ENST00000331920.6:c.3975T>G	p.Ile1325Met	p.I1325M	ENST00000331920	NM_000264.3	1325	atT/atG	23/24	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.34	2		677	849	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248084	110248084	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	139	527	0	ENST00000374672.4:c.1388G>A	p.Arg463Gln	p.R463Q	ENST00000374672	NM_004235.4	463	cGa/cAa	5/5	1	2	FACETS	0.922	0.839	1	0.922	0.839	1	CLONAL	1	TRUE	1	0.34	2		527	887	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249320	110249320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	176	932	0	ENST00000374672.4:c.1253G>A	p.Arg418Gln	p.R418Q	ENST00000374672	NM_004235.4	418	cGa/cAa	4/5	1	2	FACETS	0.766	0.703	0.831	0.766	0.703	0.831	SUBCLONAL	1	TRUE	1	0.34	2		932	1352	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915817	127915817	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	51	415	0	ENST00000373547.4:c.664A>C	p.Asn222His	p.N222H	ENST00000373547	NM_002721.4	222	Aat/Cat	6/7	1	2	FACETS	0.595	0.506	0.693	0.595	0.506	0.693	SUBCLONAL	1	TRUE	1	0.34	2		415	504	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127933444	127933444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758410873	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	87	437	0	ENST00000373547.4:c.91G>A	p.Val31Ile	p.V31I	ENST00000373547	NM_002721.4	31	Gtt/Att	2/7	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.34	2		437	481	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128420009	128420009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	56	649	0	ENST00000265960.3:c.419C>T	p.Ser140Leu	p.S140L	ENST00000265960	NM_001006617.1	140	tCg/tTg	4/12	1	2	FACETS	0.451	0.385	0.522	0.451	0.385	0.522	SUBCLONAL	1	TRUE	1	0.34	2		649	731	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135800979	135800979	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554820263	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	82	301	0	ENST00000298552.3:c.358C>A	p.Leu120Ile	p.L120I	ENST00000298552	NM_001162426.1	120	Ctc/Atc	5/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.34	2		301	360	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300872	137300872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	57	723	1	ENST00000481739.1:c.517G>A	p.Asp173Asn	p.D173N	ENST00000481739	NM_002957.4	173	Gac/Aac	4/10	1	2	FACETS	0.312	0.267	0.362	0.312	0.267	0.362	SUBCLONAL	1	TRUE	1	0.34	2		724	1074	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300927	137300927	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1564289265	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	141	763	1	ENST00000481739.1:c.572G>A	p.Arg191His	p.R191H	ENST00000481739	NM_002957.4	191	cGc/cAc	4/10	1	2	FACETS	0.828	0.753	0.906	0.828	0.753	0.906	CLONAL	1	TRUE	1	0.34	2		764	1002	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328320	137328320	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	80	628	0	ENST00000481739.1:c.1249A>G	p.Lys417Glu	p.K417E	ENST00000481739	NM_002957.4	417	Aag/Gag	10/10	1	2	FACETS	0.516	0.453	0.584	0.516	0.453	0.584	SUBCLONAL	1	TRUE	1	0.34	2		628	912	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317450	1317450	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	143	748	1	ENST00000400841.2:c.615G>T	p.Glu205Asp	p.E205D	ENST00000400841		205	gaG/gaT	5/6	1	2	FACETS	0.813	0.74	0.889	0.813	0.74	0.889	CLONAL	1	TRUE	1	0.34	2		749	1035	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317520	1317520	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	94	687	0	ENST00000400841.2:c.545C>A	p.Ser182Tyr	p.S182Y	ENST00000400841		182	tCt/tAt	5/6	1	2	FACETS	0.634	0.563	0.71	0.634	0.563	0.71	SUBCLONAL	1	TRUE	1	0.34	2		687	872	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931652	39931652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	243	669	1	ENST00000378444.4:c.2947G>A	p.Glu983Lys	p.E983K	ENST00000378444	NM_001123385.1	983	Gaa/Aaa	4/15	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.34	2		670	989	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933044	39933044	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	129	786	0	ENST00000378444.4:c.1555G>T	p.Glu519Ter	p.E519*	ENST00000378444	NM_001123385.1	519	Gag/Tag	4/15	1	2	FACETS	0.795	0.72	0.875	0.795	0.72	0.875	SUBCLONAL	1	TRUE	1	0.34	2		786	954	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39935760	39935760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745470688	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	132	194	0	ENST00000378444.4:c.112G>A	p.Ala38Thr	p.A38T	ENST00000378444	NM_001123385.1	38	Gct/Act	3/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.34	2		194	676	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941876	44941876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	29	127	0	ENST00000377967.4:c.3200C>T	p.Ser1067Leu	p.S1067L	ENST00000377967	NM_021140.2	1067	tCg/tTg	21/29	1	2	FACETS	0.599	0.482	0.731	0.599	0.482	0.731	SUBCLONAL	1	TRUE	1	0.34	2		127	285	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038892	47038892	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	201	712	0	ENST00000377604.3:c.899A>G	p.Asp300Gly	p.D300G	ENST00000377604	NM_001204468.1	300	gAc/gGc	9/24	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.34	2		712	863	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044481	47044481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	87	806	0	ENST00000377604.3:c.1978C>T	p.Arg660Cys	p.R660C	ENST00000377604	NM_001204468.1	660	Cgc/Tgc	18/24	1	2	FACETS	0.522	0.461	0.588	0.522	0.461	0.588	SUBCLONAL	1	TRUE	1	0.34	2		806	980	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225127	53225127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	103	701	0	ENST00000375401.3:c.3091G>A	p.Ala1031Thr	p.A1031T	ENST00000375401	NM_004187.3	1031	Gcc/Acc	20/26	1	2	FACETS	0.682	0.609	0.759	0.682	0.609	0.759	SUBCLONAL	1	TRUE	1	0.34	2		701	889	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53254069	53254069	+	start_lost	Translation_Start_Site	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	58	566	0	ENST00000375401.3:c.3G>T	p.Met1?	p.M1?	ENST00000375401	NM_004187.3	1	atG/atT	1/26	1	2	FACETS	0.527	0.452	0.609	0.527	0.452	0.609	SUBCLONAL	1	TRUE	1	0.34	2		566	647	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411619	63411619	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	98	825	0	ENST00000330258.3:c.1548G>T	p.Glu516Asp	p.E516D	ENST00000330258	NM_152424.3	516	gaG/gaT	2/2	1	2	FACETS	0.602	0.536	0.672	0.602	0.536	0.672	SUBCLONAL	1	TRUE	1	0.34	2		825	958	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411660	63411660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	133	825	0	ENST00000330258.3:c.1507G>A	p.Asp503Asn	p.D503N	ENST00000330258	NM_152424.3	503	Gat/Aat	2/2	1	2	FACETS	0.787	0.714	0.864	0.787	0.714	0.864	SUBCLONAL	1	TRUE	1	0.34	2		825	994	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411957	63411957	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	83	826	0	ENST00000330258.3:c.1210G>T	p.Asp404Tyr	p.D404Y	ENST00000330258	NM_152424.3	404	Gat/Tat	2/2	1	2	FACETS	0.597	0.526	0.673	0.597	0.526	0.673	SUBCLONAL	1	TRUE	1	0.34	2		826	818	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412398	63412398	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	104	866	0	ENST00000330258.3:c.769G>T	p.Asp257Tyr	p.D257Y	ENST00000330258	NM_152424.3	257	Gat/Tat	2/2	1	2	FACETS	0.584	0.522	0.651	0.584	0.522	0.651	SUBCLONAL	1	TRUE	1	0.34	2		866	1047	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412638	63412638	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	67	716	0	ENST00000330258.3:c.529C>A	p.Arg177Ser	p.R177S	ENST00000330258	NM_152424.3	177	Cgc/Agc	2/2	1	2	FACETS	0.489	0.424	0.56	0.489	0.424	0.56	SUBCLONAL	1	TRUE	1	0.34	2		716	806	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412669	63412669	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	80	691	0	ENST00000330258.3:c.498G>T	p.Lys166Asn	p.K166N	ENST00000330258	NM_152424.3	166	aaG/aaT	2/2	1	2	FACETS	0.597	0.525	0.675	0.597	0.525	0.675	SUBCLONAL	1	TRUE	1	0.34	2		691	788	SUCCESS
AR	367	MSKCC	GRCh37	X	66766581	66766581	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	126	782	0	ENST00000374690.3:c.1593C>A	p.Tyr531Ter	p.Y531*	ENST00000374690	NM_000044.3	531	taC/taA	1/8	1	2	FACETS	0.738	0.667	0.813	0.738	0.667	0.813	SUBCLONAL	1	TRUE	1	0.34	2		782	1004	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344631	70344631	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	145	606	0	ENST00000374080.3:c.1992A>C	p.Glu664Asp	p.E664D	ENST00000374080		664	gaA/gaC	14/45	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.34	2		606	655	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352768	70352768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868164882	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	246	781	1	ENST00000374080.3:c.4489G>A	p.Glu1497Lys	p.E1497K	ENST00000374080		1497	Gag/Aag	32/45	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.34	2		782	1072	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855041	76855041	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	72	285	0	ENST00000373344.5:c.5795A>C	p.Lys1932Thr	p.K1932T	ENST00000373344	NM_000489.3	1932	aAa/aCa	25/35	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.34	2		285	296	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889074	76889074	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	48	214	0	ENST00000373344.5:c.4936A>C	p.Lys1646Gln	p.K1646Q	ENST00000373344	NM_000489.3	1646	Aaa/Caa	18/35	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.34	2		214	243	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912132	76912132	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	35	197	0	ENST00000373344.5:c.4132G>T	p.Asp1378Tyr	p.D1378Y	ENST00000373344	NM_000489.3	1378	Gat/Tat	13/35	1	2	FACETS	0.789	0.65	0.943	0.789	0.65	0.943	CLONAL	1	TRUE	1	0.34	2		197	261	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937078	76937079	+	stop_gained	Nonsense_Mutation	DNP	GT	GT	AC	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	69	322	0	ENST00000373344.5:c.3669_3670inv	p.Gln1224Ter	p.Q1224*	ENST00000373344	NM_000489.3	1223	gaACag/gaGTag	9/35	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.34	2		322	294	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937269	76937269	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	14	198	0	ENST00000373344.5:c.3479A>C	p.Glu1160Ala	p.E1160A	ENST00000373344	NM_000489.3	1160	gAa/gCa	9/35	1	2	FACETS	0.36	0.26	0.48	0.36	0.26	0.48	SUBCLONAL	1	TRUE	1	0.34	2		198	229	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937880	76937880	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	93	291	0	ENST00000373344.5:c.2868A>C	p.Lys956Asn	p.K956N	ENST00000373344	NM_000489.3	956	aaA/aaC	9/35	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.34	2		291	382	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937936	76937936	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	50	399	0	ENST00000373344.5:c.2812A>C	p.Lys938Gln	p.K938Q	ENST00000373344	NM_000489.3	938	Aaa/Caa	9/35	1	2	FACETS	0.668	0.568	0.778	0.668	0.568	0.778	SUBCLONAL	1	TRUE	1	0.34	2		399	440	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938973	76938973	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	34	368	0	ENST00000373344.5:c.1775C>A	p.Pro592His	p.P592H	ENST00000373344	NM_000489.3	592	cCt/cAt	9/35	1	2	FACETS	0.498	0.407	0.6	0.498	0.407	0.6	SUBCLONAL	1	TRUE	1	0.34	2		368	402	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76954115	76954115	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	29	131	0	ENST00000373344.5:c.136A>G	p.Lys46Glu	p.K46E	ENST00000373344	NM_000489.3	46	Aaa/Gaa	3/35	1	2	FACETS	0.772	0.623	0.939	0.772	0.623	0.939	CLONAL	1	TRUE	1	0.34	2		131	221	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972719	76972719	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	50	267	0	ENST00000373344.5:c.22G>T	p.Glu8Ter	p.E8*	ENST00000373344	NM_000489.3	8	Gaa/Taa	2/35	1	2	FACETS	0.886	0.755	1	0.886	0.755	1	CLONAL	1	TRUE	1	0.34	2		267	332	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608930	100608930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	76	587	0	ENST00000308731.7:c.1678C>T	p.Pro560Ser	p.P560S	ENST00000308731	NM_000061.2	560	Cca/Tca	17/19	1	2	FACETS	0.598	0.524	0.678	0.598	0.524	0.678	SUBCLONAL	1	TRUE	1	0.34	2		587	747	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611221	100611221	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	79	539	0	ENST00000308731.7:c.1385G>A	p.Gly462Asp	p.G462D	ENST00000308731	NM_000061.2	462	gGc/gAc	15/19	1	2	FACETS	0.658	0.579	0.744	0.658	0.579	0.744	SUBCLONAL	1	TRUE	1	0.34	2		539	706	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123025136	123025136	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	26	74	0	ENST00000355640.3:c.1026T>G	p.Ile342Met	p.I342M	ENST00000355640		342	atT/atG	4/7	1	2	FACETS	0.582	0.462	0.718	0.582	0.462	0.718	SUBCLONAL	1	TRUE	1	0.34	2		74	263	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182883	123182883	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	28	83	0	ENST00000218089.9:c.848A>G	p.Asn283Ser	p.N283S	ENST00000218089	NM_001042749.1	283	aAt/aGt	10/35	1	2	FACETS	0.792	0.637	0.966	0.792	0.637	0.966	CLONAL	1	TRUE	1	0.34	2		83	208	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196773	123196773	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	66	338	0	ENST00000218089.9:c.1660A>G	p.Lys554Glu	p.K554E	ENST00000218089	NM_001042749.1	554	Aag/Gag	18/35	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.34	2		338	335	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197739	123197739	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	29	365	0	ENST00000218089.9:c.1863G>T	p.Glu621Asp	p.E621D	ENST00000218089	NM_001042749.1	621	gaG/gaT	20/35	1	2	FACETS	0.543	0.437	0.664	0.543	0.437	0.664	SUBCLONAL	1	TRUE	1	0.34	2		365	314	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197803	123197803	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	35	312	0	ENST00000218089.9:c.1927G>T	p.Glu643Ter	p.E643*	ENST00000218089	NM_001042749.1	643	Gag/Tag	20/35	1	2	FACETS	0.675	0.555	0.809	0.675	0.555	0.809	SUBCLONAL	1	TRUE	1	0.34	2		312	305	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210287	123210287	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	74	230	0	ENST00000218089.9:c.2639A>C	p.Asn880Thr	p.N880T	ENST00000218089	NM_001042749.1	880	aAt/aCt	26/35	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.34	2		230	317	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215253	123215253	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	35	189	0	ENST00000218089.9:c.2799A>T	p.Glu933Asp	p.E933D	ENST00000218089	NM_001042749.1	933	gaA/gaT	28/35	1	2	FACETS	0.783	0.645	0.936	0.783	0.645	0.936	CLONAL	1	TRUE	1	0.34	2		189	263	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504063	123504064	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	25	243	0	ENST00000371139.4:c.245dup	p.Asn82LysfsTer22	p.N82Kfs*22	ENST00000371139	NM_001114937.2	80	ata/atAa	3/4	1	2	FACETS	0.549	0.433	0.68	0.549	0.433	0.68	SUBCLONAL	1	TRUE	1	0.34	2		243	268	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123505209	123505209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	16	135	0	ENST00000371139.4:c.355G>A	p.Glu119Lys	p.E119K	ENST00000371139	NM_001114937.2	119	Gaa/Aaa	4/4	1	2	FACETS	0.395	0.292	0.518	0.395	0.292	0.518	SUBCLONAL	1	TRUE	1	0.34	2		135	238	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738769	145738769	+	coding_sequence_variant	Missense_Mutation	SNP	G	G	A	rs1563028079	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	254	867	1	ENST00000428558.2:c.2295+1C>T		p.*765*	ENST00000428558	NM_004260.3	-/1208			1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.34	2		868	1099	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030940	36030940	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs186207963	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	66	824	0	ENST00000358208.4:c.1219G>A	p.Asp407Asn	p.D407N	ENST00000358208		407	Gac/Aac	10/12	1	2	FACETS	0.37	0.32	0.425	0.37	0.32	0.425	SUBCLONAL	1	TRUE	1	0.34	2		824	1048	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508774	29508774	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	27	115	0	ENST00000356175.3:c.701T>C	p.Leu234Pro	p.L234P	ENST00000356175	NM_000267.3	234	cTg/cCg	7/57	1	2	FACETS	0.633	0.505	0.777	0.633	0.505	0.777	SUBCLONAL	1	TRUE	1	0.34	2		115	251	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868310	45868310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201294521	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	124	738	0	ENST00000391945.4:c.467G>A	p.Arg156Gln	p.R156Q	ENST00000391945	NM_000400.3	156	cGa/cAa	6/23	1	2	FACETS	0.757	0.684	0.835	0.757	0.684	0.835	SUBCLONAL	1	TRUE	1	0.34	2		738	963	SUCCESS
APC	324	MSKCC	GRCh37	5	112176558	112176558	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773178712	NA	P-0043596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	49	371	0	ENST00000257430.4:c.5267C>T	p.Ser1756Phe	p.S1756F	ENST00000257430	NM_000038.5	1756	tCt/tTt	16/16	1	2	FACETS	0.779	0.662	0.907	0.779	0.662	0.907	CLONAL	1	TRUE	1	0.34	2		371	370	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0043615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	175	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.263426557786652	2	FACETS	0.888	0.83	0.946	1	0.993	1	CLONAL	4	TRUE	0	0.263426557786652	2		473	374	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0043615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	118	460	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.263426557786652	1	FACETS	1	0.931	1	1	0.99	1	CLONAL	2	TRUE	0	0.263426557786652	1		460	379	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0043615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	61	240	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	0.919	0.802	1	1	0.978	1	CLONAL	2	TRUE	1	0.263426557786652	2		240	252	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117739	70117739	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	166	571	0	ENST00000245479.2:c.210del	p.Val71CysfsTer39	p.V71Cfs*39	ENST00000245479	NM_000346.3	69	ttC/tt	1/3	0.263426557786652	0	FACETS	1	0.983	1			1	CLONAL	1	TRUE	0	0.263426557786652	0		571	741	SUCCESS
ATM	472	MSKCC	GRCh37	11	108159759	108159759	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	35	198	0	ENST00000278616.4:c.4165A>G	p.Thr1389Ala	p.T1389A	ENST00000278616	NM_000051.3	1389	Aca/Gca	28/63	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.263426557786652	2		198	220	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577572	7577573	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTA	novel	NA	P-0043615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	211	512	0	ENST00000269305.4:c.706_708dup	p.Tyr236dup	p.Y236dup	ENST00000269305	NM_001126112.2	236	-/TAC	7/11	0.263426557786652	1	FACETS	1	0.974	1	1	0.994	1	CLONAL	2	TRUE	0	0.263426557786652	1		512	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs587781433	NA	P-0043623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	50	477	1	ENST00000269305.4:c.766A>C	p.Thr256Pro	p.T256P	ENST00000269305	NM_001126112.2	256	Aca/Cca	7/11	1	2	FACETS	0.855	0.726	0.998	0.855	0.726	0.998	CLONAL	1	TRUE	1	0.216109747944083	2		478	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577544	7577544	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587780074	NA	P-0043624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	722	454	1	ENST00000269305.4:c.737T>G	p.Met246Arg	p.M246R	ENST00000269305	NM_001126112.2	246	aTg/aGg	7/11	0.815992046407067	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	4	TRUE	0	0.815992046407067	4		455	790	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1036426	1036426	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	338	352	0	ENST00000358495.3:c.352G>C	p.Gly118Arg	p.G118R	ENST00000358495	NM_134424.2	118	Ggt/Cgt	6/12	0.815992046407067	5	FACETS	1	0.987	1			1	CLONAL	2	TRUE	NA	0.815992046407067	5		352	830	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919240	48919244	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	novel	NA	P-0043624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	179	85	0	ENST00000267163.4:c.408_412del	p.Lys136AsnfsTer2	p.K136Nfs*2	ENST00000267163	NM_000321.2	135	ctAAAAGaa/ctaa	4/27	0.815992046407067	5	FACETS	1	0.993	1	1	0.993	1	CLONAL	5	TRUE	0	0.815992046407067	5		85	186	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593639	215593639	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	21	244	0	ENST00000260947.4:c.2095G>T	p.Gly699Trp	p.G699W	ENST00000260947	NM_000465.2	699	Ggg/Tgg	11/11	0.815992046407067	2	FACETS	0.185	0.142	0.235	0.093	0.071	0.118	SUBCLONAL	1	TRUE	0	0.815992046407067	2		244	278	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469672	NA	P-0043636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	555	642	0	ENST00000374080.3:c.131G>A	p.Gly44Asp	p.G44D	ENST00000374080		44	gGt/gAt	2/45	NA	2	FACETS	0.985	0.964	1			1	INDETERMINATE	2	TRUE	NA	0.852486538891459	2		642	661	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576223	88576223	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs556136306	NA	P-0043636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	255	676	0	ENST00000360948.2:c.1450A>G	p.Ile484Val	p.I484V	ENST00000360948	NM_001012338.2	484	Atc/Gtc	13/19	0.852486538891459	4	FACETS	0.984	0.921	1	0.246	0.23	0.263	CLONAL	1	TRUE	0	0.852486538891459	4		676	1126	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0043642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	33	489	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.335	0.272	0.406	0.335	0.272	0.406	SUBCLONAL	1	TRUE	1	0.343251323488234	2		489	574	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444304	49444304	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	168	924	1	ENST00000301067.7:c.3067C>T	p.Gln1023Ter	p.Q1023*	ENST00000301067	NM_003482.3	1023	Cag/Tag	11/54	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.343251323488234	2		925	963	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018161	48018161	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1060502893	NA	P-0043642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	100	579	1	ENST00000234420.5:c.356T>G	p.Phe119Cys	p.F119C	ENST00000234420	NM_000179.2	119	tTc/tGc	2/10	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.343251323488234	NA		580	741	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239706	53239706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	121	686	1	ENST00000375401.3:c.1636G>A	p.Glu546Lys	p.E546K	ENST00000375401	NM_004187.3	546	Gaa/Aaa	12/26	0.170647849911051	3	FACETS	0.992	0.896	1			1	INDETERMINATE	1	TRUE	NA	0.343251323488234	3		687	833	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	178	345	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.987	0.92	1	0.987	0.92	1	CLONAL	1	TRUE	1	0.842811936170708	2		345	428	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0043645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	161	576	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.842811936170708	2		576	367	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909656	76909656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1557118764	NA	P-0043645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	21	407	1	ENST00000373344.5:c.4249C>T	p.Arg1417Trp	p.R1417W	ENST00000373344	NM_000489.3	1417	Cgg/Tgg	14/35	1	2	FACETS	0.245	0.19	0.31	0.245	0.19	0.31	SUBCLONAL	1	TRUE	1	0.842811936170708	2		408	203	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363246	40363250	+	frameshift_variant	Frame_Shift_Del	DEL	CGCAG	CGCAG	-	novel	NA	P-0043645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	188	810	0	ENST00000397332.2:c.979_983del	p.Leu327PhefsTer39	p.L327Ffs*39	ENST00000397332	NM_001033082.2	327	CTGCGt/t	3/3	1	2	FACETS	0.685	0.636	0.736	0.685	0.636	0.736	SUBCLONAL	1	TRUE	1	0.842811936170708	2		810	651	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0043660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	142	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.349380685092171	4	FACETS	0.901	0.83	0.974	0.901	0.83	0.974	CLONAL	3	TRUE	1	0.355086129825094	4		473	401	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299048	15299048	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs114207045	NA	P-0043660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	37	564	1	ENST00000263388.2:c.1490C>T	p.Ser497Leu	p.S497L	ENST00000263388	NM_000435.2	497	tCg/tTg	9/33	0.194818223546086	2	FACETS	0.526	0.434	0.629	0.263	0.217	0.315	INDETERMINATE	1	TRUE	0	0.355086129825094	2		565	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	246	704	0	ENST00000269305.4:c.659del	p.Tyr220LeufsTer27	p.Y220Lfs*27	ENST00000269305	NM_001126112.2	220	tAt/tt	6/11	0.355086129825094	3	FACETS	0.923	0.87	0.977			1	CLONAL	3	TRUE	NA	0.355086129825094	3		704	589	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971163	21971185	+	frameshift_variant	Frame_Shift_Del	DEL	GAGCAGCAGCAGCTCCGCCACTC	GAGCAGCAGCAGCTCCGCCACTC	-	novel	NA	P-0043660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	33	378	0	ENST00000304494.5:c.173_195del	p.Arg58ProfsTer54	p.R58Pfs*54	ENST00000304494	NM_000077.4	58	cGAGTGGCGGAGCTGCTGCTGCTC/c	2/3	1	2	FACETS	0.861	0.706	1	0.861	0.706	1	CLONAL	1	TRUE	1	0.355086129825094	2		378	216	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0043667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	25	548	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.494	0.388	0.617	0.494	0.388	0.617	SUBCLONAL	1	TRUE	1	0.14	2		548	723	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0043667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	45	453	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.3	2	FACETS	0.767	0.643	0.906			1	CLONAL	1	TRUE	NA	0.14	2		453	838	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0043667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	39	555	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.14	2		555	478	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467646	66467646	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	21	299	0	ENST00000273854.3:c.623del	p.Lys208ArgfsTer60	p.K208Rfs*60	ENST00000273854	NM_004439.5	208	aAg/ag	3/18	1	2	FACETS	0.885	0.681	1	0.885	0.681	1	CLONAL	1	TRUE	1	0.14	2		299	339	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936093	178936093	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913275	NA	P-0043667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	33	491	1	ENST00000263967.3:c.1635G>T	p.Glu545Asp	p.E545D	ENST00000263967	NM_006218.2	545	gaG/gaT	10/21	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.14	2		492	435	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0043667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	35	564	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	1	2	FACETS	0.822	0.673	0.991	0.822	0.673	0.991	CLONAL	1	TRUE	1	0.14	2		564	608	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089727	27089727	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	48	583	0	ENST00000324856.7:c.2683C>T	p.Gln895Ter	p.Q895*	ENST00000324856	NM_006015.4	895	Caa/Taa	8/20	1	2	FACETS	0.737	0.621	0.866	0.737	0.621	0.866	SUBCLONAL	1	TRUE	1	0.14	2		583	930	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845412	42845412	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	34	794	0	ENST00000398585.3:c.850A>C	p.Asn284His	p.N284H	ENST00000398585	NM_001135099.1	284	Aac/Cac	9/14	0.321599082744709	1	FACETS	0.418	0.342	0.505	0.418	0.342	0.505	SUBCLONAL	1	FALSE	0	0.321599082744709	1		794	424	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519927	66519927	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	44	338	0	ENST00000358598.2:c.410T>A	p.Leu137Gln	p.L137Q	ENST00000358598	NM_212471.2	137	cTg/cAg	4/11	1	2	FACETS	0.659	0.554	0.776	0.659	0.554	0.776	SUBCLONAL	1	FALSE	1	0.321599082744709	2		338	415	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061261	38061261	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	255	418	0	ENST00000250448.2:c.728A>G	p.Tyr243Cys	p.Y243C	ENST00000250448	NM_004496.3	243	tAc/tGc	2/2	0.343194603884745	1	FACETS	1	0.991	1	1	0.991	1	INDETERMINATE	1	TRUE	0	0.594537391521182	1		418	499	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644855	67644856	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCC	novel	NA	P-0043686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	119	334	0	ENST00000264010.4:c.122_124dup	p.Pro41dup	p.P41dup	ENST00000264010	NM_006565.3	41	-/CCC	3/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.594537391521182	2		334	345	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688642	47688642	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	84	160	0	ENST00000347630.2:c.658G>A	p.Ala220Thr	p.A220T	ENST00000347630	NM_001007230.1	220	Gct/Act	7/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.594537391521182	2		160	255	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	162	393	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.971	0.903	1	0.971	0.903	1	CLONAL	1	FALSE	1	0.88473299767153	2		393	377	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	126	302	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.88473299767153	7	FACETS	0.789	0.712	0.87			1	SUBCLONAL	1	FALSE	NA	0.88473299767153	7		302	1160	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295674	212295674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1362156940	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	118	282	0	ENST00000342788.4:c.2639G>A	p.Gly880Glu	p.G880E	ENST00000342788	NM_005235.2	880	gGa/gAa	21/28	NA	2	FACETS	0.992	0.911	1			1	INDETERMINATE	1	FALSE	NA	0.88473299767153	2		282	269	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804242	43804242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	135	394	0	ENST00000372470.3:c.242C>T	p.Ser81Phe	p.S81F	ENST00000372470	NM_005373.2	81	tCc/tTc	3/12	1	2	FACETS	0.951	0.877	1	0.951	0.877	1	CLONAL	1	FALSE	1	0.88473299767153	2		394	321	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488718	212488718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267599191	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	150	387	0	ENST00000342788.4:c.2131C>T	p.Arg711Cys	p.R711C	ENST00000342788	NM_005235.2	711	Cgt/Tgt	18/28	NA	2	FACETS	0.825	0.762	0.889			1	INDETERMINATE	1	FALSE	NA	0.88473299767153	2		387	411	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719882	18719882	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	79	210	0	ENST00000266497.5:c.3780-1G>A		p.X1260_splice	ENST00000266497		1260			NA	2	FACETS	0.921	0.827	1			1	INDETERMINATE	1	FALSE	NA	0.88473299767153	2		210	194	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164508	47164508	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs201756643	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	102	235	0	ENST00000409792.3:c.1618C>T	p.Arg540Ter	p.R540*	ENST00000409792	NM_014159.6	540	Cga/Tga	3/21	1	2	FACETS	0.901	0.82	0.983	0.901	0.82	0.983	CLONAL	1	FALSE	1	0.88473299767153	2		235	256	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295230	+	upstream_gene_variant	5'Flank	TNP	GGG	GGG	AGA	novel	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	140	349	0				ENST00000310581	NM_198253.2	-/1132			0.206472980715372	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.88473299767153	0		349	242	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068079	94068079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375147203	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	107	259	0	ENST00000369303.4:c.883C>T	p.Arg295Cys	p.R295C	ENST00000369303	NM_004440.3	295	Cgt/Tgt	4/17	0.88473299767153	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	0	0.88473299767153	1		259	125	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359593	40359593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	205	394	0	ENST00000293328.3:c.2060C>T	p.Pro687Leu	p.P687L	ENST00000293328	NM_012448.3	687	cCc/cTc	16/19	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.88473299767153	2		394	453	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779194	3779194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	164	452	0	ENST00000262367.5:c.5854C>T	p.Pro1952Ser	p.P1952S	ENST00000262367	NM_004380.2	1952	Cct/Tct	31/31	NA	2	FACETS	1	0.95	1			1	INDETERMINATE	1	FALSE	NA	0.88473299767153	2		452	362	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995601	68995601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	250	381	0	ENST00000288368.4:c.2005C>T	p.Leu669Phe	p.L669F	ENST00000288368	NM_024870.2	669	Ctt/Ttt	18/40	0.309156514166278	5	FACETS	1	0.973	1	0.703	0.662	0.744	INDETERMINATE	2	FALSE	2	0.88473299767153	5		381	624	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528682	157528682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	272	447	0	ENST00000346085.5:c.6407C>T	p.Ser2136Leu	p.S2136L	ENST00000346085	NM_020732.3	2136	tCg/tTg	20/20	0.590527813590524	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	0	0.88473299767153	1		447	329	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435523	18435523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	63	173	0	ENST00000266497.5:c.508G>A	p.Gly170Arg	p.G170R	ENST00000266497		170	Gga/Aga	1/31	NA	2	FACETS	0.879	0.778	0.983			1	INDETERMINATE	1	FALSE	NA	0.88473299767153	2		173	162	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247492	71247492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	34	472	1	ENST00000318789.4:c.41C>T	p.Ser14Leu	p.S14L	ENST00000318789	NM_032682.5	14	tCa/tTa	6/21	1	2	FACETS	0.203	0.165	0.245	0.203	0.165	0.245	SUBCLONAL	1	FALSE	1	0.88473299767153	2		473	379	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949069	151949069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776295921	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	202	367	0	ENST00000262189.6:c.1576C>T	p.Arg526Cys	p.R526C	ENST00000262189	NM_170606.2	526	Cgt/Tgt	11/59	0.807635517998518	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	0	0.88473299767153	1		367	246	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936395	49936395	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	217	562	0	ENST00000296474.3:c.1453T>C	p.Tyr485His	p.Y485H	ENST00000296474	NM_002447.2	485	Tat/Cat	3/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.88473299767153	2		562	474	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678458	88678458	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747624231	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	162	571	0	ENST00000360948.2:c.1078G>A	p.Glu360Lys	p.E360K	ENST00000360948	NM_001012338.2	360	Gag/Aag	9/19	NA	2	FACETS	0.904	0.84	0.97			1	INDETERMINATE	1	FALSE	NA	0.88473299767153	2		571	405	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414220	32414220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769499906	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	95	328	0	ENST00000332351.3:c.1331G>A	p.Arg444Lys	p.R444K	ENST00000332351	NM_024426.4	444	aGa/aAa	8/10	0.206472980715372	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.88473299767153	0		328	263	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857920	9857920	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	213	456	0	ENST00000330684.3:c.3481G>A	p.Gly1161Arg	p.G1161R	ENST00000330684	NM_001134407.1	1161	Ggg/Agg	13/13	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	FALSE	NA	0.88473299767153	2		456	413	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645276	67645276	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	220	561	2	ENST00000264010.4:c.541G>A	p.Gly181Arg	p.G181R	ENST00000264010	NM_006565.3	181	Ggg/Agg	3/12	1	2	FACETS	0.86	0.807	0.915	0.86	0.807	0.915	CLONAL	1	FALSE	1	0.88473299767153	2		563	578	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845507	72845507	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	180	505	1	ENST00000268489.5:c.3833C>A	p.Ala1278Glu	p.A1278E	ENST00000268489	NM_006885.3	1278	gCa/gAa	7/10	1	2	FACETS	0.923	0.86	0.986	0.923	0.86	0.986	CLONAL	1	FALSE	1	0.88473299767153	2		506	441	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89335025	89335025	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	71	148	0	ENST00000301030.4:c.7853C>T	p.Ala2618Val	p.A2618V	ENST00000301030	NM_001256183.1	2618	gCc/gTc	13/13	1	2	FACETS	0.928	0.829	1	0.928	0.829	1	CLONAL	1	FALSE	1	0.88473299767153	2		148	173	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50143244	50143244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	195	406	2	ENST00000246792.3:c.112G>A	p.Gly38Ser	p.G38S	ENST00000246792	NM_006270.3	38	Ggc/Agc	1/6	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.88473299767153	2		408	420	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439994	220439994	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	277	825	0	ENST00000243786.2:c.847C>T	p.Pro283Ser	p.P283S	ENST00000243786	NM_002191.3	283	Cct/Tct	2/2	NA	2	FACETS	0.997	0.944	1			1	INDETERMINATE	1	FALSE	NA	0.88473299767153	2		825	628	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156336	106156336	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	225	231	0	ENST00000380013.4:c.1237C>G	p.Pro413Ala	p.P413A	ENST00000380013	NM_001127208.2	413	Cca/Gca	3/11	0.88473299767153	3	FACETS	0.97	0.921	1	0.97	0.921	1	CLONAL	2	FALSE	1	0.88473299767153	3		231	378	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540457	187540457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	118	255	0	ENST00000441802.2:c.7283C>T	p.Ser2428Phe	p.S2428F	ENST00000441802	NM_005245.3	2428	tCc/tTc	10/27	0.88473299767153	3	FACETS	0.882	0.802	0.966	0.441	0.401	0.483	CLONAL	1	FALSE	1	0.88473299767153	3		255	436	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557191	187557191	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	155	339	0	ENST00000441802.2:c.4171T>C	p.Phe1391Leu	p.F1391L	ENST00000441802	NM_005245.3	1391	Ttt/Ctt	6/27	0.88473299767153	3	FACETS	0.929	0.855	1	0.465	0.427	0.503	CLONAL	1	FALSE	1	0.88473299767153	3		339	544	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293562	1293562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	204	791	0	ENST00000310581.5:c.1439C>T	p.Ser480Phe	p.S480F	ENST00000310581	NM_198253.2	480	tCc/tTc	2/16	0.206472980715372	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.88473299767153	0		791	572	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415027	116415027	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	238	409	1	ENST00000397752.3:c.3121G>A	p.Asp1041Asn	p.D1041N	ENST00000397752	NM_000245.2	1041	Gat/Aat	15/21	0.88473299767153	5	FACETS	0.907	0.845	0.972			1	CLONAL	1	FALSE	NA	0.88473299767153	5		410	1380	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851529	128851529	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1385995572	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1766	227	641	0	ENST00000249373.3:c.1854G>A	p.Trp618Ter	p.W618*	ENST00000249373	NM_005631.4	618	tgG/tgA	11/12	0.88473299767153	7	FACETS	0.827	0.767	0.89			1	CLONAL	1	FALSE	NA	0.88473299767153	7		641	1993	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104697	69104697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148366673	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	182	454	0	ENST00000288368.4:c.4541C>T	p.Ser1514Phe	p.S1514F	ENST00000288368	NM_024870.2	1514	tCc/tTc	37/40	0.309156514166278	5	FACETS	1	0.982	1	0.399	0.369	0.431	INDETERMINATE	1	FALSE	2	0.88473299767153	5		454	799	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937842	76937842	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	205	196	0	ENST00000373344.5:c.2906T>C	p.Leu969Pro	p.L969P	ENST00000373344	NM_000489.3	969	cTa/cCa	9/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	FALSE	0	0.88473299767153	1		196	223	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215968	36215970	+	frameshift_variant	Frame_Shift_Del	DEL	CGC	CGC	TG	novel	NA	P-0043691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	224	682	2	ENST00000222270.7:c.3508_3510delinsTG	p.Arg1170TrpfsTer12	p.R1170Wfs*12	ENST00000222270	NM_014727.1	1170	CGC/TG	10/37	1	2	FACETS	0.895	0.84	0.95	0.895	0.84	0.95	CLONAL	1	FALSE	1	0.88473299767153	2		684	566	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0043693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	40	331	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.734	0.611	0.87	0.734	0.611	0.87	SUBCLONAL	1	TRUE	1	0.292168629051644	2		331	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0043693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	130	892	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.292168629051644	2		892	611	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119485	193119485	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	49	269	0	ENST00000367435.3:c.880G>A	p.Asp294Asn	p.D294N	ENST00000367435	NM_024529.4	294	Gat/Aat	9/17	1	2	FACETS	0.814	0.691	0.949	0.814	0.691	0.949	CLONAL	1	TRUE	1	0.292168629051644	2		269	412	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981539	201981540	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0043693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	102	803	1	ENST00000359651.3:c.455_456dup	p.Ala153ArgfsTer3	p.A153Rfs*3	ENST00000359651		151	-/GA	3/8	1	2	FACETS	0.883	0.789	0.982	0.883	0.789	0.982	CLONAL	1	TRUE	1	0.292168629051644	2		804	791	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927426	245927426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138010213	NA	P-0043693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	65	458	1	ENST00000388985.4:c.1102G>A	p.Val368Ile	p.V368I	ENST00000388985		368	Gtc/Atc	11/12	1	2	FACETS	0.738	0.64	0.844	0.738	0.64	0.844	SUBCLONAL	1	TRUE	1	0.292168629051644	2		459	603	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038506	47038535	+	inframe_deletion	In_Frame_Del	DEL	GCGTCCAGAACTTCAAACGCCGAGAGAAGT	GCGTCCAGAACTTCAAACGCCGAGAGAAGT	-	novel	NA	P-0043693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	50	277	0	ENST00000377604.3:c.670_699del	p.Val224_Cys233del	p.V224_C233del	ENST00000377604	NM_001204468.1	223	gGCGTCCAGAACTTCAAACGCCGAGAGAAGTgc/ggc	8/24	1	1	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	0	0.292168629051644	1		277	292	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0043698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	190	484	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.384342754267512	1	FACETS	0.757	0.702	0.815	0.757	0.702	0.815	SUBCLONAL	1	TRUE	0	0.496459011286648	1		484	760	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0043698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	55	607	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.384342754267512	1	FACETS	0.199	0.17	0.232	0.199	0.17	0.232	SUBCLONAL	1	TRUE	0	0.496459011286648	1		607	835	SUCCESS
APC	324	MSKCC	GRCh37	5	112175399	112175400	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0043698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	92	202	0	ENST00000257430.4:c.4110_4111del	p.Pro1372ThrfsTer2	p.P1372Tfs*2	ENST00000257430	NM_000038.5	1370	AAa/a	16/16	0.384342754267512	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.496459011286648	1		202	258	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175212	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	22	151	0	ENST00000257430.4:c.3924del	p.Glu1309LysfsTer12	p.E1309Kfs*12	ENST00000257430	NM_000038.5	1307	atA/at	16/16	0.384342754267512	1	FACETS	0.327	0.254	0.41	0.327	0.254	0.41	SUBCLONAL	1	TRUE	0	0.496459011286648	1		151	204	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197785	66197785	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	31	292	0	ENST00000273854.3:c.2914G>T	p.Glu972Ter	p.E972*	ENST00000273854	NM_004439.5	972	Gaa/Taa	17/18	0.384342754267512	1	FACETS	0.241	0.194	0.293	0.241	0.194	0.293	SUBCLONAL	1	TRUE	0	0.496459011286648	1		292	390	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622285	162622285	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0043698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	62	238	0	ENST00000366898.1:c.413-1G>T		p.X138_splice	ENST00000366898	NM_004562.2	138			1	2	FACETS	0.776	0.675	0.884	0.776	0.675	0.884	SUBCLONAL	1	TRUE	1	0.496459011286648	2		238	322	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0043721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	16	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		485	379	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0043721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	22	270	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		270	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0043729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	224	519	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.440585909887586	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.440585909887586	1		519	783	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0043729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	767	366	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.440585909887586	5	FACETS	1	0.993	1			1	CLONAL	4	TRUE	NA	0.440585909887586	5		366	1352	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0043778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	214	701	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	NA	2	FACETS	1	0.962	1			1	INDETERMINATE	2	TRUE	NA	0.343970275408318	2		701	598	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188196	10188196	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs869025637	NA	P-0043779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	171	464	0	ENST00000256474.2:c.341-2A>G		p.X114_splice	ENST00000256474	NM_000551.3	114			0.290278365315622	2	FACETS	0.929	0.86	1	0.929	0.86	1	CLONAL	2	TRUE	0	0.325233117386821	2		464	566	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804954	43804954	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	139	400	0	ENST00000372470.3:c.404C>T	p.Pro135Leu	p.P135L	ENST00000372470	NM_005373.2	135	cCc/cTc	4/12	0.325233117386821	3	FACETS	0.883	0.807	0.961	0.883	0.807	0.961	CLONAL	2	TRUE	1	0.325233117386821	3		400	563	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645944	215645944	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	57	360	0	ENST00000260947.4:c.654G>C	p.Trp218Cys	p.W218C	ENST00000260947	NM_000465.2	218	tgG/tgC	4/11	0.297615833478076	4	FACETS	0.966	0.83	1	0.483	0.415	0.557	CLONAL	1	TRUE	2	0.325233117386821	4		360	481	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161753	47161753	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	82	313	0	ENST00000409792.3:c.4373del	p.Gln1458ArgfsTer25	p.Q1458Rfs*25	ENST00000409792	NM_014159.6	1458	cAg/cg	3/21	0.290278365315622	2	FACETS	1	0.973	1	0.671	0.595	0.75	CLONAL	1	TRUE	0	0.325233117386821	2		313	376	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584560	52584561	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0043779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	191	681	0	ENST00000394830.3:c.4452_4453del	p.Pro1485HisfsTer23	p.P1485Hfs*23	ENST00000394830	NM_018313.4	1484	acACcc/accc	29/30	0.290278365315622	2	FACETS	1	0.99	1	0.746	0.691	0.803	CLONAL	1	TRUE	0	0.325233117386821	2		681	787	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561910	55561911	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0043779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	46	260	0	ENST00000288135.5:c.302_303del	p.His101ArgfsTer11	p.H101Rfs*11	ENST00000288135	NM_000222.2	100	aaACac/aaac	2/21	1	2	FACETS	0.878	0.743	1	0.878	0.743	1	CLONAL	1	TRUE	1	0.325233117386821	2		260	322	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	137	345	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.884	0.811	0.958	0.884	0.811	0.958	CLONAL	1	TRUE	1	0.749099789409224	2		345	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs17849781	NA	P-0043785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	616	585	0	ENST00000269305.4:c.832C>G	p.Pro278Ala	p.P278A	ENST00000269305	NM_001126112.2	278	Cct/Gct	8/11	0.749099789409224	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.749099789409224	1		585	864	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636736	176636736	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	242	406	0	ENST00000439151.2:c.1336T>A	p.Ser446Thr	p.S446T	ENST00000439151	NM_022455.4	446	Tca/Aca	5/23	1	2	FACETS	0.98	0.921	1	0.98	0.921	1	CLONAL	1	TRUE	1	0.749099789409224	2		406	659	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0043804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	421	672	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.122827098792555	4	FACETS	1	0.988	1	1	0.996	1	INDETERMINATE	3	TRUE	2	0.381906694387247	4		672	934	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0043804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	92	571	0				ENST00000310581	NM_198253.2	-/1132			0.381906694387247	0	FACETS	0.683	0.619	0.748			1	SUBCLONAL	2	TRUE	0	0.381906694387247	0		571	218	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118859	115118859	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	161	377	0	ENST00000257566.3:c.482G>C	p.Cys161Ser	p.C161S	ENST00000257566	NM_016569.3	161	tGt/tCt	2/8	0.181167148798056	0	FACETS	0.636	0.59	0.682			1	INDETERMINATE	2	TRUE	0	0.381906694387247	0		377	410	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0043814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	44	395	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	TRUE	1	0.18	2		395	486	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106476	27106476	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	60	439	0	ENST00000324856.7:c.6088del	p.Thr2030LeufsTer12	p.T2030Lfs*12	ENST00000324856	NM_006015.4	2029	ctA/ct	20/20	1	2	FACETS	0.947	0.815	1	0.947	0.815	1	CLONAL	1	TRUE	1	0.18	2		439	704	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692988	89692989	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	35	314	0	ENST00000371953.3:c.473dup	p.Arg159LysfsTer21	p.R159Kfs*21	ENST00000371953	NM_000314.4	158	gta/gTta	5/9	1	2	FACETS	0.919	0.754	1	0.919	0.754	1	CLONAL	1	TRUE	1	0.18	2		314	423	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866551	117866554	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0043828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	23	371	0	ENST00000297338.2:c.1091_1094del	p.Lys364ArgfsTer5	p.K364Rfs*5	ENST00000297338	NM_006265.2	364	aAAGAg/ag	9/14	0.340556133283478	3	FACETS	0.682	0.535	0.851	0.341	0.267	0.426	SUBCLONAL	1	TRUE	1	0.395886284598264	3		371	204	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776169	135776226	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AACAGCTGCCTGTTCAAGAACTCCATCTGCTGCTGGACCGACTCACTGTTTGAGAGCT	AACAGCTGCCTGTTCAAGAACTCCATCTGCTGCTGGACCGACTCACTGTTTGAGAGCT	-	novel	NA	P-0043828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	51	419	0	ENST00000298552.3:c.2503-2_2558del		p.X835_splice	ENST00000298552	NM_001162426.1	835		20/23	0.395886284598264	1	FACETS	0.537	0.457	0.623	0.537	0.457	0.623	SUBCLONAL	1	TRUE	0	0.395886284598264	1		419	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577546	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	C	novel	NA	P-0043828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	117	522	0	ENST00000269305.4:c.735_736delinsG	p.Met246Ter	p.M246*	ENST00000269305	NM_001126112.2	245	ggCAtg/ggGtg	7/11	0.385571222280713	1	FACETS	0.797	0.72	0.877	0.797	0.72	0.877	SUBCLONAL	1	TRUE	0	0.395886284598264	1		522	595	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0043836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	30	460	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.460109427267876	1	FACETS	0.352	0.284	0.429	0.352	0.284	0.429	SUBCLONAL	1	FALSE	0	0.460109427267876	1		460	285	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865456	57865456	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	165	914	0	ENST00000228682.2:c.2933C>A	p.Ala978Glu	p.A978E	ENST00000228682	NM_005269.2	978	gCa/gAa	12/12	1	2	FACETS	0.865	0.795	0.938	0.865	0.795	0.938	CLONAL	1	FALSE	1	0.460109427267876	2		914	829	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438215	56438239	+	frameshift_variant	Frame_Shift_Del	DEL	GCCACTCACCCCGGGCCTGCCTGCA	GCCACTCACCCCGGGCCTGCCTGCA	-	novel	NA	P-0043836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	135	859	0	ENST00000407977.2:c.754_778del	p.Cys252GlnfsTer159	p.C252Qfs*159	ENST00000407977		252	TGCAGGCAGGCCCGGGGTGAGTGGCca/ca	7/10	0.125710826840492	0	FACETS	0.317	0.288	0.348			1	INDETERMINATE	1	FALSE	0	0.460109427267876	0		859	999	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201129	108201135	+	protein_altering_variant	In_Frame_Del	DEL	AAGTCAA	AAGTCAA	C	novel	NA	P-0043836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	40	384	0	ENST00000278616.4:c.7496_7502delinsC	p.Glu2499_Asn2501delinsAla	p.E2499_N2501delinsA	ENST00000278616	NM_000051.3	2499	gAAGTCAAt/gCt	50/63	0.460109427267876	1	FACETS	0.842	0.711	0.983	0.842	0.711	0.983	CLONAL	1	FALSE	0	0.460109427267876	1		384	159	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0043839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	215	701	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.157879239850873	2	FACETS	0.927	0.861	0.994	0.927	0.861	0.994	CLONAL	2	TRUE	0	0.234142083394193	2		701	991	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740554	145740554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	124	709	0	ENST00000428558.2:c.1463C>T	p.Ala488Val	p.A488V	ENST00000428558	NM_004260.3	488	gCa/gTa	8/22	0.234142083394193	3	FACETS	1	0.969	1	0.589	0.532	0.65	CLONAL	1	TRUE	1	0.234142083394193	3		709	1004	SUCCESS
ATR	545	MSKCC	GRCh37	3	142218544	142218544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	50	346	0	ENST00000350721.4:c.5305G>A	p.Glu1769Lys	p.E1769K	ENST00000350721	NM_001184.3	1769	Gaa/Aaa	31/47	0.212572657410567	3	FACETS	0.749	0.635	0.875	0.374	0.317	0.438	SUBCLONAL	1	TRUE	1	0.234142083394193	3		346	637	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77054963	77054963	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	75	389	0	ENST00000356341.3:c.899A>G	p.Gln300Arg	p.Q300R	ENST00000356341	NM_002576.4	300	cAg/cGg	10/15	0.181828691274717	4	FACETS	1	0.957	1	0.608	0.533	0.689	CLONAL	1	TRUE	2	0.234142083394193	4		389	650	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736152	204736152	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	76	323	0	ENST00000302823.3:c.509T>G	p.Val170Gly	p.V170G	ENST00000302823	NM_005214.4	170	gTt/gGt	3/4	0.234142083394193	5	FACETS	1	0.939	1	0.373	0.327	0.424	CLONAL	1	TRUE	2	0.234142083394193	5		323	783	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129837	55129837	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	62	420	0	ENST00000257290.5:c.371C>G	p.Pro124Arg	p.P124R	ENST00000257290	NM_006206.4	124	cCa/cGa	4/23	0.157879239850873	2	FACETS	0.904	0.781	1	0.452	0.39	0.519	CLONAL	1	TRUE	0	0.234142083394193	2		420	586	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38964900	38964900	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	26	167	0	ENST00000357387.3:c.1394del	p.Lys465ArgfsTer9	p.K465Rfs*9	ENST00000357387	NM_152756.3	465	aAg/ag	16/38	0.232236293459939	3	FACETS	0.909	0.722	1	0.454	0.361	0.561	CLONAL	1	TRUE	1	0.234142083394193	3		167	273	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287980	33287980	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	46	451	1	ENST00000374542.5:c.1273C>T	p.Gln425Ter	p.Q425*	ENST00000374542	NM_001141970.1	425	Cag/Tag	5/8	0.201585656854118	3	FACETS	0.753	0.633	0.885	0.251	0.211	0.295	SUBCLONAL	1	TRUE	0	0.234142083394193	3		452	583	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0043868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	137	385	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.158845833365648	4	FACETS	1	0.967	1	1	0.967	1	INDETERMINATE	2	TRUE	2	0.370849921603422	4		385	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0043868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	245	484	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.347858627444733	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.370849921603422	2		484	633	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0043868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	5485	584	59	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.370849921603422	36	FACETS	0.994	0.989	0.999			1	CLONAL	36	TRUE	NA	0.370849921603422	36		643	6038	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0043868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	59	450	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.370849921603422	3	FACETS	0.674	0.58	0.776	0.337	0.29	0.388	SUBCLONAL	1	TRUE	1	0.370849921603422	3		450	560	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144118	11144118	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	243	806	0	ENST00000358026.2:c.3699G>T	p.Met1233Ile	p.M1233I	ENST00000358026	NM_001128849.1	1233	atG/atT	26/36	0.370849921603422	3	FACETS	0.86	0.805	0.917	0.86	0.805	0.917	CLONAL	2	TRUE	1	0.370849921603422	3		806	903	SUCCESS
APC	324	MSKCC	GRCh37	5	112175531	112175532	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1554085654	NA	P-0043868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	122	326	0	ENST00000257430.4:c.4241dup	p.Ser1415LysfsTer8	p.S1415Kfs*8	ENST00000257430	NM_000038.5	1414	gta/gTta	16/16	0.158845833365648	4	FACETS	0.937	0.858	1	1	0.985	1	INDETERMINATE	3	TRUE	2	0.370849921603422	4		326	321	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874636	35874637	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1384901919	NA	P-0043868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	137	299	0	ENST00000303115.3:c.799dup	p.Arg267LysfsTer3	p.R267Kfs*3	ENST00000303115	NM_002185.3	264	-/A	6/8	0.158845833365648	4	FACETS	1	0.96	1	1	0.96	1	INDETERMINATE	2	TRUE	2	0.370849921603422	4		299	469	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711367	114711367	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0043868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	91	192	1	ENST00000543371.1:c.381+1G>C		p.X127_splice	ENST00000543371	NM_001198531.1	127			0.238754874225557	4	FACETS	0.89	0.803	0.979	1	0.978	1	CLONAL	3	TRUE	2	0.370849921603422	4		193	252	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139211	108139214	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	novel	NA	P-0043868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	139	599	0	ENST00000278616.4:c.2716_2719del	p.Leu906ValfsTer2	p.L906Vfs*2	ENST00000278616	NM_000051.3	905	TGTTtg/tg	18/63	0.317213419957509	3	FACETS	1	0.971	1	0.577	0.526	0.631	CLONAL	1	TRUE	1	0.370849921603422	3		599	770	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115111574	115112303	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAAGTCACTCAACATCTCTGGGCGTCTTCGCCTTCATCTGTAAAGTGGAGGTGATAATAGTACCCCTGAAGGGTTAGGTCAAATGAGTCAATACAGAGCAAGCACTTAGAAGAATGCCTGAAAGTAAGTGCTGTGTCCAGCTGTTATCTTTGTTACTACCTATCTACTCTGCTGGAAACAGCCTTTAACTTCGGAAAAATTTTAAAGATTTTTGGGGTGAATGGGGAGAATGAAGTCATAATAACTCCATGAGCTAAGCCTTGAACCCGGTAATGGCTCAGTAAAAATTATTACAGCTACTAGGCCAAAGGGATCGGGTGAGGGTCTGCTGGCAAAGGACAGGGAAACTGGACGAAAGGTGGAAAGACTGGTGGAGGCAGGAAGAAGGATCCATACCTGAGAGGCCAGGACGTGCTGCTGGAGGTGGAAGGGCAGGGTGGCCGCGGACGCCCCGGACAGTCCCTGCGCCGCAGCGGCAGAGGCCATGGCCGTGGAATCCAGGCCCGAGACACCGGTGGAGGCCCCAGAAACCGTGGCCAGGAGGGGACCCATGCCAGCGGCCGCCATGCTGGAGAAGGCGCCCCCCATGGCAAACTGGCTGGGGTGCAGGAAGAGCGGGTGCCCGTTGAAGAACTGTTGGCCCGCCAGGCCCGGGGCGAAGCCGAGGCCAGGCAGGGGGCCCTGGGCCAGGTGCGCGGCGGCCGCGTCCGTCTGCACCGTGAGCGGCGCG	CAAGTCACTCAACATCTCTGGGCGTCTTCGCCTTCATCTGTAAAGTGGAGGTGATAATAGTACCCCTGAAGGGTTAGGTCAAATGAGTCAATACAGAGCAAGCACTTAGAAGAATGCCTGAAAGTAAGTGCTGTGTCCAGCTGTTATCTTTGTTACTACCTATCTACTCTGCTGGAAACAGCCTTTAACTTCGGAAAAATTTTAAAGATTTTTGGGGTGAATGGGGAGAATGAAGTCATAATAACTCCATGAGCTAAGCCTTGAACCCGGTAATGGCTCAGTAAAAATTATTACAGCTACTAGGCCAAAGGGATCGGGTGAGGGTCTGCTGGCAAAGGACAGGGAAACTGGACGAAAGGTGGAAAGACTGGTGGAGGCAGGAAGAAGGATCCATACCTGAGAGGCCAGGACGTGCTGCTGGAGGTGGAAGGGCAGGGTGGCCGCGGACGCCCCGGACAGTCCCTGCGCCGCAGCGGCAGAGGCCATGGCCGTGGAATCCAGGCCCGAGACACCGGTGGAGGCCCCAGAAACCGTGGCCAGGAGGGGACCCATGCCAGCGGCCGCCATGCTGGAGAAGGCGCCCCCCATGGCAAACTGGCTGGGGTGCAGGAAGAGCGGGTGCCCGTTGAAGAACTGTTGGCCCGCCAGGCCCGGGGCGAAGCCGAGGCCAGGCAGGGGGCCCTGGGCCAGGTGCGCGGCGGCCGCGTCCGTCTGCACCGTGAGCGGCGCG	-	novel	NA	P-0043868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2	27	3	0	ENST00000257566.3:c.1437_1770+396del		p.X479_splice	ENST00000257566	NM_016569.3	479		7/8	0.370849921603422	3	FACETS	0.992	0.918	1	1	0.973	1	CLONAL	6	TRUE	1	0.370849921603422	3		3	29	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555725	21555725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778450722	NA	P-0043868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1447	79	711	0	ENST00000382592.4:c.2545C>T	p.Arg849Trp	p.R849W	ENST00000382592	NM_014572.2	849	Cgg/Tgg	6/8	0.370849921603422	9	FACETS	0.642	0.562	0.728			1	SUBCLONAL	1	TRUE	NA	0.370849921603422	9		711	1526	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986961	36986961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057524869	NA	P-0043868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	99	538	0	ENST00000354822.5:c.728G>A	p.Arg243His	p.R243H	ENST00000354822	NM_001079668.2	243	cGc/cAc	3/3	0.308828668861122	3	FACETS	1	0.952	1	0.556	0.498	0.618	CLONAL	1	TRUE	1	0.370849921603422	3		538	569	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67646018	67646018	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	62	428	2	ENST00000264010.4:c.946C>T	p.His316Tyr	p.H316Y	ENST00000264010	NM_006565.3	316	Cac/Tac	4/12	0.238754874225557	4	FACETS	0.698	0.602	0.802	0.349	0.301	0.401	SUBCLONAL	1	TRUE	2	0.370849921603422	4		430	657	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219050	36219050	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1459799356	NA	P-0043868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	95	786	2	ENST00000222270.7:c.4549C>T	p.Arg1517Ter	p.R1517*	ENST00000222270	NM_014727.1	1517	Cga/Tga	19/37	0.370849921603422	3	FACETS	0.742	0.66	0.829	0.371	0.33	0.415	SUBCLONAL	1	TRUE	1	0.370849921603422	3		788	819	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467950	66467950	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	144	290	2	ENST00000273854.3:c.319C>A	p.Gln107Lys	p.Q107K	ENST00000273854	NM_004439.5	107	Cag/Aag	3/18	0.370849921603422	2	FACETS	0.925	0.861	0.988	1	0.989	1	CLONAL	3	TRUE	0	0.370849921603422	2		292	280	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295245	1295247	+	upstream_gene_variant	5'Flank	DEL	CCC	CCC	-	novel	NA	P-0043868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	128	180	1				ENST00000310581	NM_198253.2	-/1132			0.158845833365648	4	FACETS	1	0.956	1	1	0.989	1	INDETERMINATE	3	TRUE	2	0.370849921603422	4		181	299	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876465	35876465	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	261	574	2	ENST00000303115.3:c.1257T>G	p.Phe419Leu	p.F419L	ENST00000303115	NM_002185.3	419	ttT/ttG	8/8	0.158845833365648	4	FACETS	0.956	0.901	1	1	0.993	1	INDETERMINATE	3	TRUE	2	0.370849921603422	4		576	673	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0043871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	122	584	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.7	2		584	285	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	28	662	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.17	0.135	0.21	0.17	0.135	0.21	SUBCLONAL	1	TRUE	1	0.481262152491855	2		662	685	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	24	296	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.217	0.169	0.272	0.217	0.169	0.272	SUBCLONAL	1	TRUE	1	0.481262152491855	2		297	460	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	143	732	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.868	0.793	0.946	0.868	0.793	0.946	CLONAL	1	TRUE	1	0.481262152491855	2		735	685	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	145	453	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.994	0.911	1	0.994	0.911	1	CLONAL	1	TRUE	1	0.481262152491855	2		453	606	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	13	325	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.106	0.075	0.144	0.106	0.075	0.144	SUBCLONAL	1	TRUE	1	0.481262152491855	2		325	509	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	44	481	1	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.294	0.245	0.347	0.294	0.245	0.347	SUBCLONAL	1	TRUE	1	0.481262152491855	2		482	623	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	10	198	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	1	2	FACETS	0.153	0.103	0.217	0.153	0.103	0.217	SUBCLONAL	1	TRUE	1	0.481262152491855	2		198	271	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968322	2968323	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762770988	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	107	774	0	ENST00000396946.4:c.1663dup	p.Arg555ProfsTer38	p.R555Pfs*38	ENST00000396946	NM_032415.4	555	cgg/cCgg	13/25	1	2	FACETS	0.657	0.59	0.728	0.657	0.59	0.728	SUBCLONAL	1	TRUE	1	0.481262152491855	2		774	677	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742463	17742463	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	34	483	0	ENST00000250003.3:c.650del	p.Pro217ArgfsTer33	p.P217Rfs*33	ENST00000250003	NM_002478.4	215	ggC/gg	2/3	1	2	FACETS	0.235	0.191	0.285	0.235	0.191	0.285	SUBCLONAL	1	TRUE	1	0.481262152491855	2		483	601	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973547	15973547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143125039	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	83	271	0	ENST00000268712.3:c.4445G>A	p.Arg1482Gln	p.R1482Q	ENST00000268712	NM_006311.3	1482	cGg/cAg	31/46	1	2	FACETS	0.726	0.643	0.815	0.726	0.643	0.815	SUBCLONAL	1	TRUE	1	0.481262152491855	2		271	475	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	73	330	2	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.729	0.641	0.824	0.729	0.641	0.824	SUBCLONAL	1	TRUE	1	0.481262152491855	2		332	416	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	43	255	0	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	1	2	FACETS	0.508	0.426	0.598	0.508	0.426	0.598	SUBCLONAL	1	TRUE	1	0.481262152491855	2		255	352	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412095	63412095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852217	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	213	662	1	ENST00000330258.3:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000330258	NM_152424.3	358	Cga/Tga	2/2	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.481262152491855	2		663	885	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692902	89692902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909218	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	97	398	0	ENST00000371953.3:c.386G>A	p.Gly129Glu	p.G129E	ENST00000371953	NM_000314.4	129	gGa/gAa	5/9	1	2	FACETS	0.933	0.837	1	0.933	0.837	1	CLONAL	1	TRUE	1	0.481262152491855	2		398	432	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099103	27099103	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	114	444	0	ENST00000324856.7:c.3524del	p.Pro1175HisfsTer5	p.P1175Hfs*5	ENST00000324856	NM_006015.4	1173	atC/at	13/20	1	2	FACETS	0.938	0.849	1	0.938	0.849	1	CLONAL	1	TRUE	1	0.481262152491855	2		444	505	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654553	29654553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876657714	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	68	237	0	ENST00000356175.3:c.5242C>T	p.Arg1748Ter	p.R1748*	ENST00000356175	NM_000267.3	1748	Cga/Tga	37/57	1	2	FACETS	0.638	0.557	0.725	0.638	0.557	0.725	SUBCLONAL	1	TRUE	1	0.481262152491855	2		237	443	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790819	89790819	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	95	459	6	ENST00000336032.3:c.211del	p.Gln71SerfsTer112	p.Q71Sfs*112	ENST00000336032	NM_006813.2	69	aCc/ac	1/2	1	2	FACETS	0.582	0.519	0.65	0.582	0.519	0.65	SUBCLONAL	1	TRUE	1	0.481262152491855	2		465	678	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40497609	40497609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs964892419	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	191	577	2	ENST00000264657.5:c.340C>T	p.Arg114Cys	p.R114C	ENST00000264657	NM_139276.2	114	Cgc/Tgc	4/24	1	2	FACETS	0.94	0.871	1	0.94	0.871	1	CLONAL	1	TRUE	1	0.481262152491855	2		579	844	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591085	67591085	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	100	211	0	ENST00000274335.5:c.1678G>C	p.Asp560His	p.D560H	ENST00000274335		560	Gac/Cac	12/15	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.481262152491855	2		211	393	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991722	72991722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	15	167	1	ENST00000268489.5:c.2323G>A	p.Ala775Thr	p.A775T	ENST00000268489	NM_006885.3	775	Gcg/Acg	2/10	1	2	FACETS	0.318	0.233	0.42	0.318	0.233	0.42	SUBCLONAL	1	TRUE	1	0.481262152491855	2		168	196	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273980	10273980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	130	672	2	ENST00000330684.3:c.289G>A	p.Gly97Ser	p.G97S	ENST00000330684	NM_001134407.1	97	Ggc/Agc	2/13	1	2	FACETS	0.685	0.621	0.751	0.685	0.621	0.751	SUBCLONAL	1	TRUE	1	0.481262152491855	2		674	789	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555271	226555271	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	76	438	0	ENST00000366794.5:c.2316G>T	p.Glu772Asp	p.E772D	ENST00000366794	NM_001618.3	772	gaG/gaT	17/23	0.481262152491855	3	FACETS	0.419	0.366	0.475	0.209	0.183	0.238	SUBCLONAL	1	TRUE	1	0.481262152491855	3		438	936	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670657	134670657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1441537601	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	158	517	1	ENST00000398015.3:c.568C>T	p.Arg190Cys	p.R190C	ENST00000398015	NM_004441.4	190	Cgt/Tgt	3/16	1	2	FACETS	0.941	0.864	1	0.941	0.864	1	CLONAL	1	TRUE	1	0.481262152491855	2		518	698	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939111	36939111	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	160	665	0	ENST00000361632.4:c.598G>T	p.Gly200Cys	p.G200C	ENST00000361632		200	Ggc/Tgc	5/16	1	2	FACETS	0.8	0.734	0.869	0.8	0.734	0.869	SUBCLONAL	1	TRUE	1	0.481262152491855	2		665	831	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321372	65321372	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	47	454	0	ENST00000342505.4:c.1468G>T	p.Gly490Cys	p.G490C	ENST00000342505	NM_002227.2	490	Ggt/Tgt	11/25	1	2	FACETS	0.292	0.246	0.343	0.292	0.246	0.343	SUBCLONAL	1	TRUE	1	0.481262152491855	2		454	669	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138086	64138086	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	30	537	1	ENST00000334205.4:c.2009G>A	p.Gly670Asp	p.G670D	ENST00000334205	NM_003942.2	670	gGc/gAc	16/17	1	2	FACETS	0.208	0.167	0.256	0.208	0.167	0.256	SUBCLONAL	1	TRUE	1	0.481262152491855	2		538	598	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466031	69466031	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	184	554	1	ENST00000227507.2:c.869T>A	p.Val290Glu	p.V290E	ENST00000227507	NM_053056.2	290	gTg/gAg	5/5	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.481262152491855	2		555	726	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822105	72822105	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	105	421	3	ENST00000268489.5:c.10070del	p.Pro3357GlnfsTer128	p.P3357Qfs*128	ENST00000268489	NM_006885.3	3357	cCa/ca	10/10	1	2	FACETS	0.852	0.767	0.942	0.852	0.767	0.942	CLONAL	1	TRUE	1	0.481262152491855	2		424	512	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799006	42799006	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs754160310	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	205	707	1	ENST00000575354.2:c.4490A>G	p.Tyr1497Cys	p.Y1497C	ENST00000575354	NM_015125.3	1497	tAt/tGt	20/20	1	2	FACETS	0.93	0.863	0.999	0.93	0.863	0.999	CLONAL	1	TRUE	1	0.481262152491855	2		708	916	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921112	50921112	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060501852	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	130	509	0	ENST00000440232.2:c.3232A>G	p.Ile1078Val	p.I1078V	ENST00000440232	NM_002691.3	1078	Atc/Gtc	27/27	1	2	FACETS	0.805	0.732	0.882	0.805	0.732	0.882	CLONAL	1	TRUE	1	0.481262152491855	2		509	671	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956166	55956166	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	149	416	1	ENST00000263923.4:c.3149C>T	p.Ala1050Val	p.A1050V	ENST00000263923	NM_002253.2	1050	gCc/gTc	23/30	1	2	FACETS	0.96	0.88	1	0.96	0.88	1	CLONAL	1	TRUE	1	0.481262152491855	2		417	645	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694571	176694571	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	77	237	0	ENST00000439151.2:c.5155C>A	p.Leu1719Ile	p.L1719I	ENST00000439151	NM_022455.4	1719	Ctt/Att	15/23	1	2	FACETS	0.739	0.652	0.832	0.739	0.652	0.832	SUBCLONAL	1	TRUE	1	0.481262152491855	2		237	433	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80343544	80343544	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs149046601	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	77	313	0	ENST00000286548.4:c.775A>G	p.Ile259Val	p.I259V	ENST00000286548	NM_002072.3	259	Atc/Gtc	6/7	1	2	FACETS	0.685	0.603	0.772	0.685	0.603	0.772	SUBCLONAL	1	TRUE	1	0.481262152491855	2		313	467	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422625	47422625	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	52	433	0	ENST00000377045.4:c.97G>A	p.Val33Met	p.V33M	ENST00000377045	NM_001654.4	33	Gtg/Atg	3/16	1	2	FACETS	0.39	0.332	0.454	0.39	0.332	0.454	SUBCLONAL	1	TRUE	1	0.481262152491855	2		433	554	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424464	49424469	+	frameshift_variant	Frame_Shift_Del	DEL	CATTGA	CATTGA	AG	novel	NA	P-0043941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	69	614	1	ENST00000301067.7:c.13754_13759delinsCT	p.Val4585AlafsTer6	p.V4585Afs*6	ENST00000301067	NM_003482.3	4585	gTCAATGgg/gCTgg	41/54	1	2	FACETS	0.821	0.716	0.936	0.821	0.716	0.936	CLONAL	1	TRUE	1	0.28	2		615	600	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0043949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	253	429	0	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	0.615092391396021	1	FACETS	0.855	0.811	0.899	0.855	0.811	0.899	CLONAL	1	TRUE	0	0.769595111817119	1		429	473	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982977	201982978	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0043949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	320	569	0	ENST00000359651.3:c.829dup	p.Glu277GlyfsTer24	p.E277Gfs*24	ENST00000359651		276	tgg/tGgg	7/8	1	2	FACETS	0.982	0.931	1	0.982	0.931	1	CLONAL	1	TRUE	1	0.769595111817119	2		569	847	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112029183	112029183	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs370983835	NA	P-0043949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	100	341	0	ENST00000368678.4:c.385G>C	p.Glu129Gln	p.E129Q	ENST00000368678		129	Gag/Cag	5/13	1	2	FACETS	0.454	0.407	0.505	0.454	0.407	0.505	SUBCLONAL	1	TRUE	1	0.769595111817119	2		341	572	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197793	123197794	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	205	203	0	ENST00000218089.9:c.1918dup	p.Cys640LeufsTer2	p.C640Lfs*2	ENST00000218089	NM_001042749.1	639	-/T	20/35	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.769595111817119	1		203	294	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085708	16085708	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	65	585	0	ENST00000281043.3:c.884C>A	p.Thr295Asn	p.T295N	ENST00000281043	NM_005378.4	295	aCc/aAc	3/3	0.120595303429577	0	FACETS	0.822	0.723	0.926			1	CLONAL	4	FALSE	0	0.151154756028385	0		585	222	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0043965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	32	217	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.22	2		217	222	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442040	52442040	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	73	572	1	ENST00000460680.1:c.309C>A	p.Cys103Ter	p.C103*	ENST00000460680	NM_004656.3	103	tgC/tgA	5/17	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.22	2		573	494	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71064705	71064706	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0043965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	38	331	0	ENST00000318789.4:c.968_969del	p.Phe323SerfsTer7	p.F323Sfs*7	ENST00000318789	NM_032682.5	323	tTT/t	12/21	1	2	FACETS	0.902	0.747	1	0.902	0.747	1	CLONAL	1	TRUE	1	0.22	2		331	383	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93629466	93629466	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	19	277	0	ENST00000375746.1:c.900G>T	p.Lys300Asn	p.K300N	ENST00000375746	NM_001174167.1	300	aaG/aaT	7/14	1	2	FACETS	0.523	0.397	0.672	0.523	0.397	0.672	SUBCLONAL	1	TRUE	1	0.22	2		277	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577544	7577544	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587780074	NA	P-0043992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	81	525	0	ENST00000269305.4:c.737T>C	p.Met246Thr	p.M246T	ENST00000269305	NM_001126112.2	246	aTg/aCg	7/11	1	2	FACETS	0.891	0.784	1	0.891	0.784	1	CLONAL	1	TRUE	1	0.22	2		525	826	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928226	178928226	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519872	NA	P-0043992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	41	293	0	ENST00000263967.3:c.1412C>T	p.Pro471Leu	p.P471L	ENST00000263967	NM_006218.2	471	cCa/cTa	9/21	1	2	FACETS	0.737	0.613	0.874	0.737	0.613	0.874	SUBCLONAL	1	TRUE	1	0.22	2		293	506	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0043992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	54	251	0	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	0.135630932528968	3	FACETS	1	0.957	1	0.669	0.573	0.774	CLONAL	1	TRUE	1	0.22	3		251	407	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871182	12871182	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs752620765	NA	P-0043992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	24	277	0	ENST00000228872.4:c.409C>G	p.Pro137Ala	p.P137A	ENST00000228872	NM_004064.3	137	Ccg/Gcg	1/3	0.132282916220192	3	FACETS	0.552	0.432	0.691			1	SUBCLONAL	1	TRUE	NA	0.22	3		277	439	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412365	139412365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	95	574	0	ENST00000277541.6:c.1280G>A	p.Gly427Asp	p.G427D	ENST00000277541	NM_017617.3	427	gGc/gAc	8/34	0.264637976576648	2	FACETS	0.67	0.595	0.75	0.335	0.297	0.375	SUBCLONAL	1	TRUE	0	0.264637976576648	2		574	1072	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640853	3640853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs117707719	NA	P-0044010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	148	656	0	ENST00000294008.3:c.2786C>T	p.Pro929Leu	p.P929L	ENST00000294008	NM_032444.2	929	cCg/cTg	12/15	1	2	FACETS	0.961	0.876	1	0.961	0.876	1	CLONAL	1	TRUE	1	0.264637976576648	2		656	1164	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781287	135781287	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746304922	NA	P-0044010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	162	480	0	ENST00000298552.3:c.1678G>A	p.Gly560Ser	p.G560S	ENST00000298552	NM_001162426.1	560	Ggc/Agc	15/23	0.264637976576648	2	FACETS	1	0.985	1	0.674	0.618	0.732	CLONAL	1	TRUE	0	0.264637976576648	2		480	908	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574032	7574034	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	TNP	ATC	ATC	GAT	novel	NA	P-0044010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	269	456	1	ENST00000269305.4:c.994-1_995inv		p.X332_splice	ENST00000269305	NM_001126112.2	332		10/11	0.264637976576648	3	FACETS	0.856	0.805	0.909	0.856	0.805	0.909	CLONAL	3	TRUE	0	0.264637976576648	3		457	896	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843727	151843728	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0044010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	48	308	0	ENST00000262189.6:c.13987_13988del	p.Leu4663ValfsTer19	p.L4663Vfs*19	ENST00000262189	NM_170606.2	4663	CTg/g	53/59	NA	2	FACETS	0.549	0.463	0.644			1	INDETERMINATE	1	TRUE	NA	0.264637976576648	2		308	661	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399769	139399769	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	176	527	0	ENST00000277541.6:c.4579C>T	p.Gln1527Ter	p.Q1527*	ENST00000277541	NM_017617.3	1527	Cag/Tag	25/34	0.264637976576648	2	FACETS	1	0.986	1	0.662	0.61	0.717	CLONAL	1	TRUE	0	0.264637976576648	2		527	1004	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417632	139417632	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1195	65	657	0	ENST00000277541.6:c.412T>A	p.Cys138Ser	p.C138S	ENST00000277541	NM_017617.3	138	Tgc/Agc	4/34	0.264637976576648	2	FACETS	0.39	0.336	0.448	0.195	0.168	0.224	SUBCLONAL	1	TRUE	0	0.264637976576648	2		657	1260	SUCCESS
AR	367	MSKCC	GRCh37	X	66941797	66941797	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	81	192	0	ENST00000374690.3:c.2441T>C	p.Phe814Ser	p.F814S	ENST00000374690	NM_000044.3	814	tTc/tCc	6/8	1	1	FACETS	0.807	0.717	0.902	1	0.981	1	CLONAL	2	TRUE	0	0.264637976576648	1		192	329	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950066	44950066	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs863224886	NA	P-0044024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	45	407	0	ENST00000377967.4:c.3835C>T	p.Arg1279Ter	p.R1279*	ENST00000377967	NM_021140.2	1279	Cga/Tga	26/29	1	2	FACETS	0.471	0.397	0.553	0.471	0.397	0.553	SUBCLONAL	1	TRUE	1	0.471536463089409	2		407	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576910	7576910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	302	612	0	ENST00000269305.4:c.936del	p.Ser313AlafsTer32	p.S313Afs*32	ENST00000269305	NM_001126112.2	312	acC/ac	9/11	0.471536463089409	2	FACETS	0.877	0.832	0.924	0.877	0.832	0.924	CLONAL	2	TRUE	0	0.471536463089409	2		612	730	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948631	71948631	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	72	769	0	ENST00000298229.2:c.3343A>C	p.Ser1115Arg	p.S1115R	ENST00000298229	NM_001567.3	1115	Agt/Cgt	26/28	0.393435548607003	1	FACETS	0.272	0.237	0.31	0.272	0.237	0.31	SUBCLONAL	1	TRUE	0	0.471536463089409	1		769	858	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28979996	28979996	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	33	374	0	ENST00000282397.4:c.1472T>A	p.Ile491Asn	p.I491N	ENST00000282397	NM_002019.4	491	aTc/aAc	11/30	0.471536463089409	1	FACETS	0.303	0.247	0.366	0.303	0.247	0.366	SUBCLONAL	1	TRUE	0	0.471536463089409	1		374	353	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835674	68835674	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	116	494	0	ENST00000261769.5:c.265C>G	p.Leu89Val	p.L89V	ENST00000261769	NM_004360.3	89	Cta/Gta	3/16	0.434653699776326	1	FACETS	0.558	0.503	0.615	0.558	0.503	0.615	SUBCLONAL	1	TRUE	0	0.471536463089409	1		494	674	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119634916	119634917	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0044024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	72	232	0	ENST00000316626.5:c.582_583delinsCT	p.Val195Leu	p.V195L	ENST00000316626		194	gcTGta/gcCTta	5/12	0.225493895977639	5	FACETS	0.931	0.822	1	0.621	0.548	0.697	INDETERMINATE	2	TRUE	2	0.471536463089409	5		232	280	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151919118	151919118	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	37	246	0	ENST00000262189.6:c.3467T>C	p.Val1156Ala	p.V1156A	ENST00000262189	NM_170606.2	1156	gTa/gCa	22/59	0.128638492461612	3	FACETS	0.626	0.517	0.746	0.313	0.258	0.373	INDETERMINATE	1	TRUE	1	0.471536463089409	3		246	310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0044048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	124	484	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.346732227949431	2		484	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578178	7578178	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	114	593	0	ENST00000269305.4:c.671del	p.Glu224GlyfsTer23	p.E224Gfs*23	ENST00000269305	NM_001126112.2	224	gAg/gg	6/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.346732227949431	2		593	590	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793172	33793172	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	26	115	0	ENST00000498907.2:c.149A>T	p.Glu50Val	p.E50V	ENST00000498907	NM_004364.3	50	gAg/gTg	1/1	0.130930980958599	3	FACETS	1	0.858	1			1	INDETERMINATE	1	TRUE	NA	0.346732227949431	3		115	161	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863224499	NA	P-0044049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	37	590	0	ENST00000269305.4:c.672+1G>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			1	2	FACETS	0.45	0.37	0.54	0.45	0.37	0.54	SUBCLONAL	1	TRUE	1	0.224064503501189	2		590	734	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0044049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	111	484	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.224064503501189	2		484	693	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535409	66535409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768337164	NA	P-0044049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	34	249	0	ENST00000273854.3:c.52G>A	p.Gly18Ser	p.G18S	ENST00000273854	NM_004439.5	18	Ggc/Agc	1/18	0.224064503501189	1	FACETS	0.959	0.787	1	0.959	0.787	1	CLONAL	1	TRUE	0	0.224064503501189	1		249	281	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101195	27101195	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	109	499	1	ENST00000324856.7:c.4477C>T	p.Gln1493Ter	p.Q1493*	ENST00000324856	NM_006015.4	1493	Cag/Tag	18/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.224064503501189	2		500	705	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267902	46267902	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs143016947	NA	P-0044049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	113	326	0	ENST00000371998.3:c.2663A>G	p.Asn888Ser	p.N888S	ENST00000371998		888	aAt/aGt	14/23	0.224064503501189	4	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	2	0.224064503501189	4		326	585	SUCCESS
ATR	545	MSKCC	GRCh37	3	142180908	142180909	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0044049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	14	68	0	ENST00000350721.4:c.7065_7066del	p.Arg2356Ter	p.R2356*	ENST00000350721	NM_001184.3	2355	tcTCgt/tcgt	42/47	0.224064503501189	3	FACETS	0.681	0.493	0.908			1	SUBCLONAL	1	TRUE	NA	0.224064503501189	3		68	204	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371885	55371885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	20	175	0	ENST00000297316.4:c.575C>T	p.Pro192Leu	p.P192L	ENST00000297316	NM_022454.3	192	cCg/cTg	2/2	0.143861978184273	4	FACETS	0.707	0.541	0.902	0.354	0.27	0.451	CLONAL	1	TRUE	2	0.224064503501189	4		175	309	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727483	66727483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504317	NA	P-0044058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	168	420	1	ENST00000307102.5:c.199G>A	p.Asp67Asn	p.D67N	ENST00000307102	NM_002755.3	67	Gac/Aac	2/11	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.54365425075643	2		421	617	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245115	46245116	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	142	424	0	ENST00000334344.6:c.3211dup	p.Ser1071PhefsTer6	p.S1071Ffs*6	ENST00000334344	NM_152641.2	1070	cct/ccTt	15/21	1	2	FACETS	0.918	0.841	0.999	0.918	0.841	0.999	CLONAL	1	TRUE	1	0.54365425075643	2		424	569	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754686	41754686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1338560133	NA	P-0044058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	78	608	0	ENST00000301178.4:c.1672G>A	p.Asp558Asn	p.D558N	ENST00000301178	NM_021913.4	558	Gac/Aac	14/20	1	2	FACETS	0.395	0.346	0.447	0.395	0.346	0.447	SUBCLONAL	1	TRUE	1	0.54365425075643	2		608	727	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926270	112926270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918457	NA	P-0044065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	83	335	0	ENST00000351677.2:c.1403C>T	p.Thr468Met	p.T468M	ENST00000351677	NM_002834.3	468	aCg/aTg	12/16	1	2	FACETS	0.535	0.473	0.6	0.535	0.473	0.6	SUBCLONAL	1	TRUE	1	0.618416565667451	2		335	502	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518783	176518783	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199935139	NA	P-0044065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	84	463	0	ENST00000292408.4:c.701G>A	p.Arg234His	p.R234H	ENST00000292408	NM_213647.1	234	cGc/cAc	6/18	0.249141627858116	3	FACETS	0.455	0.401	0.512	0.152	0.133	0.171	INDETERMINATE	1	TRUE	0	0.618416565667451	3		463	782	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577527	7577527	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555525470	NA	P-0044065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	316	530	3	ENST00000269305.4:c.754del	p.Leu252SerfsTer93	p.L252Sfs*93	ENST00000269305	NM_001126112.2	252	Ctc/tc	7/11	0.552879816261648	2	FACETS	0.856	0.816	0.895	0.856	0.816	0.895	CLONAL	2	TRUE	0	0.618416565667451	2		533	597	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022769	31022769	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	79	451	1	ENST00000375687.4:c.2254G>C	p.Ala752Pro	p.A752P	ENST00000375687	NM_015338.5	752	Gct/Cct	13/13	0.618416565667451	3	FACETS	0.434	0.381	0.491	0.217	0.19	0.246	SUBCLONAL	1	TRUE	1	0.618416565667451	3		452	770	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134266	11134266	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064796254	NA	P-0044078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	383	548	0	ENST00000358026.2:c.2932C>T	p.Arg978Ter	p.R978*	ENST00000358026	NM_001128849.1	978	Cga/Tga	20/36	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.94	2		548	797	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132620	11132621	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	419	561	0	ENST00000358026.2:c.2836_2837insA	p.Pro946HisfsTer13	p.P946Hfs*13	ENST00000358026	NM_001128849.1	946	ccc/cAcc	19/36	1	2	FACETS	0.995	0.953	1	0.995	0.953	1	CLONAL	1	TRUE	1	0.94	2		561	896	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0044098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	198	571	0				ENST00000310581	NM_198253.2	-/1132			0.28597768567424	4	FACETS	0.902	0.842	0.963	1	0.99	1	CLONAL	3	TRUE	2	0.364276067602162	4		571	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579585	7579585	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	204	567	0	ENST00000269305.4:c.102del	p.Leu35CysfsTer9	p.L35Cfs*9	ENST00000269305	NM_001126112.2	34	ccC/cc	4/11	0.351636373981464	2	FACETS	0.938	0.876	1	0.938	0.876	1	CLONAL	2	TRUE	0	0.364276067602162	2		567	597	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290180	15290180	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371437217	NA	P-0044098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	224	695	0	ENST00000263388.2:c.3455C>T	p.Thr1152Met	p.T1152M	ENST00000263388	NM_000435.2	1152	aCg/aTg	21/33	0.156409664674486	5	FACETS	1	0.975	1	0.727	0.678	0.778	INDETERMINATE	2	TRUE	2	0.364276067602162	5		695	872	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0044098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	300	767	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.364276067602162	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.364276067602162	2		767	806	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289922	15289922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	289	744	0	ENST00000263388.2:c.3632C>T	p.Ser1211Leu	p.S1211L	ENST00000263388	NM_000435.2	1211	tCa/tTa	22/33	0.156409664674486	5	FACETS	1	0.988	1	0.782	0.736	0.829	INDETERMINATE	2	TRUE	2	0.364276067602162	5		744	1046	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289995	15289995	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	309	768	0	ENST00000263388.2:c.3559G>T	p.Gly1187Cys	p.G1187C	ENST00000263388	NM_000435.2	1187	Ggt/Tgt	22/33	0.156409664674486	5	FACETS	1	0.985	1	0.753	0.709	0.797	INDETERMINATE	2	TRUE	2	0.364276067602162	5		768	1162	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290202	15290202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	241	748	1	ENST00000263388.2:c.3433C>T	p.Leu1145Phe	p.L1145F	ENST00000263388	NM_000435.2	1145	Ctc/Ttc	21/33	0.156409664674486	5	FACETS	1	0.971	1	0.711	0.665	0.759	INDETERMINATE	2	TRUE	2	0.364276067602162	5		749	959	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047811	128047811	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	109	462	0	ENST00000285398.2:c.510G>C	p.Leu170Phe	p.L170F	ENST00000285398	NM_000122.1	170	ttG/ttC	4/15	0.364276067602162	3	FACETS	0.938	0.843	1	0.469	0.421	0.52	CLONAL	1	TRUE	1	0.364276067602162	3		462	754	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067215	37067215	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	123	442	0	ENST00000231790.2:c.1126G>C	p.Asp376His	p.D376H	ENST00000231790	NM_000249.3	376	Gat/Cat	12/19	0.156409664674486	5	FACETS	1	0.984	1	0.479	0.434	0.528	INDETERMINATE	1	TRUE	2	0.364276067602162	5		442	726	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259791	142259791	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	171	519	0	ENST00000350721.4:c.3536G>C	p.Arg1179Thr	p.R1179T	ENST00000350721	NM_001184.3	1179	aGa/aCa	18/47	0.156409664674486	5	FACETS	0.969	0.893	1	0.646	0.595	0.699	INDETERMINATE	2	TRUE	2	0.364276067602162	5		519	749	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940423	13940423	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	176	335	0	ENST00000405192.2:c.1083G>T	p.Met361Ile	p.M361I	ENST00000405192	NM_001163147.1	361	atG/atT	11/12	0.302240501237801	4	FACETS	1	0.984	1	0.811	0.752	0.871	CLONAL	2	TRUE	1	0.364276067602162	4		335	542	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0044103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	536	738	2	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.56258929415755	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.56258929415755	1		740	1116	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0044103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	190	322	0	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	0.56258929415755	3	FACETS	1	0.932	1	0.504	0.466	0.543	CLONAL	1	TRUE	1	0.56258929415755	3		322	859	SUCCESS
APC	324	MSKCC	GRCh37	5	112173374	112173374	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	55	296	0	ENST00000257430.4:c.2083C>T	p.Gln695Ter	p.Q695*	ENST00000257430	NM_000038.5	695	Cag/Tag	16/16	1	2	FACETS	0.811	0.701	0.929	0.811	0.701	0.929	CLONAL	1	TRUE	1	0.56258929415755	2		296	241	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950665	79950665	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	291	287	0	ENST00000265081.6:c.119C>T	p.Ser40Phe	p.S40F	ENST00000265081	NM_002439.4	40	tCc/tTc	1/24	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.56258929415755	2		287	910	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	157	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.907557306418412	5	FACETS	1	0.986	1	0.828	0.771	0.885	CLONAL	2	FALSE	2	0.907557306418412	5		485	329	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337636	73337636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1376504733	NA	P-0044118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	55	236	0	ENST00000377767.4:c.2080C>T	p.Pro694Ser	p.P694S	ENST00000377767	NM_014953.3	694	Cca/Tca	16/21	0.521779914012553	6	FACETS	0.948	0.838	1	0.948	0.838	1	INDETERMINATE	3	FALSE	3	0.907557306418412	6		236	120	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42842599	42842599	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755712060	NA	P-0044118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	121	828	2	ENST00000398585.3:c.1258G>A	p.Gly420Arg	p.G420R	ENST00000398585	NM_001135099.1	420	Ggg/Agg	11/14	0.907557306418412	3	FACETS	0.706	0.64	0.775	0.353	0.32	0.388	SUBCLONAL	1	FALSE	1	0.907557306418412	3		830	549	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	213	345	0				ENST00000310581	NM_198253.2	-/1132			0.519511744734531	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.627729133075541	4		345	512	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0044121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	280	437	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.627729133075541	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.627729133075541	4		437	647	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210451	2210451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138206172	NA	P-0044121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	60	981	0	ENST00000398665.3:c.1058C>T	p.Ala353Val	p.A353V	ENST00000398665	NM_032482.2	353	gCg/gTg	13/28	0.255314935122949	4	FACETS	0.307	0.263	0.354	0.153	0.131	0.177	INDETERMINATE	1	TRUE	2	0.627729133075541	4		981	1015	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0044121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	90	772	4	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	0.288193055998983	3	FACETS	0.547	0.485	0.613	0.273	0.242	0.307	INDETERMINATE	1	TRUE	1	0.627729133075541	3		776	689	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206616	108206616	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1183442138	NA	P-0044121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	201	353	0	ENST00000278616.4:c.8196C>G	p.Phe2732Leu	p.F2732L	ENST00000278616	NM_000051.3	2732	ttC/ttG	56/63	0.627729133075541	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.627729133075541	2		353	303	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634318	23634318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	91	633	0	ENST00000261584.4:c.2968G>A	p.Glu990Lys	p.E990K	ENST00000261584	NM_024675.3	990	Gaa/Aaa	9/13	0.34309127106228	3	FACETS	0.618	0.55	0.692	0.206	0.183	0.231	INDETERMINATE	1	TRUE	0	0.627729133075541	3		633	616	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372093	55372093	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	269	522	1	ENST00000297316.4:c.788del	p.Pro263ArgfsTer124	p.P263Rfs*124	ENST00000297316	NM_022454.3	261	ggC/gg	2/2	0.342680637972039	5	FACETS	1	0.986	1	0.759	0.715	0.803	INDETERMINATE	2	TRUE	2	0.627729133075541	5		523	731	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526171	63526171	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	82	742	0	ENST00000307078.5:c.2455G>C	p.Glu819Gln	p.E819Q	ENST00000307078	NM_004655.3	819	Gag/Cag	11/11	0.43205307245314	5	FACETS	0.45	0.395	0.509	0.15	0.131	0.17	SUBCLONAL	1	TRUE	2	0.627729133075541	5		742	1128	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652057	36652058	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0044121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	396	1051	0	ENST00000244741.5:c.182dup	p.Asp62Ter	p.D62*	ENST00000244741	NM_000389.4	60	gag/gaGg	2/3	0.500746838996732	4	FACETS	0.752	0.714	0.79	0.501	0.476	0.527	SUBCLONAL	2	TRUE	1	0.627729133075541	4		1051	1366	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63700167	63700167	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	83	206	0	ENST00000279873.7:c.502G>C	p.Gly168Arg	p.G168R	ENST00000279873	NM_032199.2	168	Ggg/Cgg	3/10	0.321304003290211	4	FACETS	0.92	0.825	1	0.92	0.825	1	INDETERMINATE	2	TRUE	2	0.627729133075541	4		206	234	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909939	100909939	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	242	442	0	ENST00000325455.5:c.2710G>C	p.Glu904Gln	p.E904Q	ENST00000325455	NM_001202474.3	904	Gaa/Caa	8/8	0.627729133075541	5	FACETS	0.967	0.913	1	0.967	0.913	1	CLONAL	3	TRUE	2	0.627729133075541	5		442	516	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799384	88799384	+	start_lost	Translation_Start_Site	SNP	T	T	A	novel	NA	P-0044121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	185	334	0	ENST00000360948.2:c.1A>T	p.Met1?	p.M1?	ENST00000360948	NM_001012338.2	1	Atg/Ttg	2/19	0.309808089735024	4	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.627729133075541	4		334	385	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781420	3781421	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	368	707	2	ENST00000262367.5:c.4944_4945insT	p.Ile1649TyrfsTer11	p.I1649Yfs*11	ENST00000262367	NM_004380.2	1648	-/T	30/31	0.34309127106228	3	FACETS	1	0.993	1	0.78	0.748	0.813	INDETERMINATE	2	TRUE	0	0.627729133075541	3		709	658	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892240	9892240	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	66	539	0	ENST00000330684.3:c.2250C>G	p.Ile750Met	p.I750M	ENST00000330684	NM_001134407.1	750	atC/atG	11/13	0.34309127106228	3	FACETS	0.504	0.438	0.576	0.168	0.146	0.192	INDETERMINATE	1	TRUE	0	0.627729133075541	3		539	548	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827349	72827349	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	329	839	0	ENST00000268489.5:c.9232C>G	p.Gln3078Glu	p.Q3078E	ENST00000268489	NM_006885.3	3078	Caa/Gaa	9/10	0.573391642343592	4	FACETS	1	0.994	1	0.724	0.684	0.765	CLONAL	1	TRUE	2	0.627729133075541	4		839	1178	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829131	72829131	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	364	652	0	ENST00000268489.5:c.7450C>T	p.Pro2484Ser	p.P2484S	ENST00000268489	NM_006885.3	2484	Cct/Tct	9/10	0.573391642343592	4	FACETS	0.995	0.946	1	0.995	0.946	1	CLONAL	2	TRUE	2	0.627729133075541	4		652	949	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218529	5218529	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	331	857	0	ENST00000357368.4:c.3950C>A	p.Ser1317Ter	p.S1317*	ENST00000357368	NM_002850.3	1317	tCa/tAa	25/38	0.255314935122949	4	FACETS	0.828	0.783	0.873	0.828	0.783	0.873	INDETERMINATE	2	TRUE	2	0.627729133075541	4		857	1037	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858929	45858929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	100	821	0	ENST00000391945.4:c.1537G>A	p.Asp513Asn	p.D513N	ENST00000391945	NM_000400.3	513	Gat/Aat	16/23	0.245339174893637	5	FACETS	0.587	0.523	0.655	0.196	0.174	0.219	INDETERMINATE	1	TRUE	2	0.627729133075541	5		821	1054	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225365093	225365093	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs772779469	NA	P-0044121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	50	379	0	ENST00000264414.4:c.1597G>C	p.Glu533Gln	p.E533Q	ENST00000264414	NM_003590.4	533	Gag/Cag	11/16	0.10996574584725	3	FACETS	0.595	0.506	0.691	0.297	0.253	0.346	INDETERMINATE	1	TRUE	1	0.627729133075541	3		379	352	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256367	46256367	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs759276868	NA	P-0044121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	245	413	0	ENST00000371998.3:c.595A>G	p.Met199Val	p.M199V	ENST00000371998		199	Atg/Gtg	7/23	0.519511744734531	4	FACETS	0.993	0.934	1	0.993	0.934	1	CLONAL	2	TRUE	2	0.627729133075541	4		413	640	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537116	41537116	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	161	436	1	ENST00000263253.7:c.1943G>A	p.Arg648Gln	p.R648Q	ENST00000263253	NM_001429.3	648	cGa/cAa	10/31	0.411341344375303	4	FACETS	1	0.989	1	0.747	0.689	0.807	CLONAL	1	TRUE	2	0.627729133075541	4		437	559	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12393173	12393173	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	139	426	1	ENST00000287820.6:c.82G>A	p.Glu28Lys	p.E28K	ENST00000287820	NM_015869.4	28	Gaa/Aaa	1/7	0.627729133075541	3	FACETS	1	0.929	1	0.509	0.465	0.554	CLONAL	1	TRUE	1	0.627729133075541	3		427	572	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803599	1803610	+	inframe_deletion	In_Frame_Del	DEL	GCCGGCCAACCA	GCCGGCCAACCA	-	novel	NA	P-0044121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	107	682	0	ENST00000260795.2:c.778_789del	p.Pro260_Gln263del	p.P260_Q263del	ENST00000260795		259	ctGCCGGCCAACCAg/ctg	6/17	0.288193055998983	3	FACETS	0.587	0.526	0.651	0.294	0.263	0.326	INDETERMINATE	1	TRUE	1	0.627729133075541	3		682	763	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1905942	1905942	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0044121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	217	588	0	ENST00000382891.5:c.598-1G>C		p.X200_splice	ENST00000382891	NM_133335.3	200			0.288193055998983	3	FACETS	1	0.989	1	0.641	0.598	0.684	INDETERMINATE	1	TRUE	1	0.627729133075541	3		588	709	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361235	66361235	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	202	326	0	ENST00000273854.3:c.937T>A	p.Ser313Thr	p.S313T	ENST00000273854	NM_004439.5	313	Tca/Aca	4/18	0.342680637972039	5	FACETS	0.913	0.857	0.971	0.913	0.857	0.971	INDETERMINATE	3	TRUE	2	0.627729133075541	5		326	456	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564449	86564449	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	435	709	0	ENST00000274376.6:c.181C>G	p.Leu61Val	p.L61V	ENST00000274376	NM_002890.2	61	Ctg/Gtg	1/25	0.627729133075541	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.627729133075541	2		709	598	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346355	152346355	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	254	597	0	ENST00000359321.1:c.215G>T	p.Gly72Val	p.G72V	ENST00000359321	NM_005431.1	72	gGt/gTt	3/3	0.237617641144874	5	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.627729133075541	5		597	630	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396284	139396284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	554	955	0	ENST00000277541.6:c.5554G>A	p.Asp1852Asn	p.D1852N	ENST00000277541	NM_017617.3	1852	Gac/Aac	30/34	0.627729133075541	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.627729133075541	2		955	797	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44920639	44920640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0044121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	247	244	0	ENST00000377967.4:c.1403_1404dup	p.Leu469ValfsTer2	p.L469Vfs*2	ENST00000377967	NM_021140.2	467	tgg/tgGTg	14/29	0.545099887248854	2	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.627729133075541	2		244	341	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0044123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	436	892	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.563993105031705	2	FACETS	0.936	0.899	0.973	0.936	0.899	0.973	CLONAL	2	TRUE	0	0.564662033327755	2		892	825	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212179	98212179	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	195	451	0	ENST00000331920.6:c.3493C>G	p.Leu1165Val	p.L1165V	ENST00000331920	NM_000264.3	1165	Ctc/Gtc	21/24	0.564662033327755	3	FACETS	0.872	0.814	0.93	0.872	0.814	0.93	CLONAL	2	TRUE	1	0.564662033327755	3		451	508	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357429	70357429	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	347	904	0	ENST00000374080.3:c.5770C>G	p.Gln1924Glu	p.Q1924E	ENST00000374080		1924	Cag/Gag	40/45	0.310656145177925	5	FACETS	0.998	0.946	1	0.666	0.63	0.701	INDETERMINATE	2	TRUE	2	0.564662033327755	5		904	1137	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0044142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	97	465	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	1	2	FACETS	0.804	0.721	0.893	0.804	0.721	0.893	CLONAL	1	TRUE	1	0.519737589487192	2		465	464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0044169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	704	792	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.986	0.97	1	1	0.998	1	CLONAL	2	FALSE	1	0.900356313685167	2		793	793	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413565	32413565	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121907903	NA	P-0044169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	321	440	0	ENST00000332351.3:c.1385G>A	p.Arg462Gln	p.R462Q	ENST00000332351	NM_024426.4	462	cGg/cAg	9/10	0.68033805618872	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	FALSE	2	0.900356313685167	4		440	670	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390221	89390221	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs531563474	NA	P-0044169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	182	290	0	ENST00000336596.2:c.970C>G	p.Arg324Gly	p.R324G	ENST00000336596	NM_005233.5	324	Cga/Gga	4/17	0.885474171372524	4	FACETS	0.998	0.934	1	0.998	0.934	1	CLONAL	2	FALSE	2	0.900356313685167	4		290	385	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446165	49446166	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs398123715	NA	P-0044169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	159	765	2	ENST00000301067.7:c.1300dup	p.Leu434ProfsTer12	p.L434Pfs*12	ENST00000301067	NM_003482.3	434	cta/cCta	10/54	0.900356313685167	3	FACETS	0.608	0.557	0.66	0.304	0.278	0.33	SUBCLONAL	1	FALSE	1	0.900356313685167	3		767	843	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916842	48916854	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGAAATCAGGTAA	AGAAATCAGGTAA	-	novel	NA	P-0044169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	110	286	0	ENST00000267163.4:c.374_380+6del		p.X125_splice	ENST00000267163	NM_000321.2	125		3/27	0.866006548323368	2	FACETS	0.947	0.903	0.986	0.947	0.903	0.986	CLONAL	2	FALSE	0	0.900356313685167	2		286	129	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	19	345	0				ENST00000310581	NM_198253.2	-/1132			0.173950613307588	0	FACETS	1	0.816	1			1	CLONAL	4	TRUE	0	0.11	0		345	73	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0044194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	36	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.86	1	1	0.978	1	CLONAL	6	TRUE	1	0.11	2		288	107	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522485	157522485	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777745107	NA	P-0044194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	11	695	0	ENST00000346085.5:c.4757C>T	p.Thr1586Met	p.T1586M	ENST00000346085	NM_020732.3	1586	aCg/aTg	18/20	0.173950613307588	4	FACETS	1	0.733	1	0.534	0.369	0.739	CLONAL	1	TRUE	2	0.11	4		695	208	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170416	119170416	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	14	470	0	ENST00000264033.4:c.2646G>C	p.Gln882His	p.Q882H	ENST00000264033	NM_005188.3	882	caG/caC	16/16	1	2	FACETS	1	0.784	1	1	0.919	1	CLONAL	2	TRUE	1	0.11	2		470	117	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076646	102076646	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	38	371	0	ENST00000282441.5:c.825G>C	p.Gln275His	p.Q275H	ENST00000282441	NM_001130145.2	275	caG/caC	5/9	1	2	FACETS	0.929	0.785	1	1	0.979	1	CLONAL	6	TRUE	1	0.11	2		371	124	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346925	91346925	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1567062835	NA	P-0044194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	13	366	0	ENST00000355112.3:c.3535del	p.Thr1179LeufsTer3	p.T1179Lfs*3	ENST00000355112	NM_000057.2	1178	cAa/ca	18/22	1	2	FACETS	0.875	0.633	1	1	0.923	1	CLONAL	3	TRUE	1	0.11	2		366	90	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007560	62007560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	11	781	1	ENST00000392795.3:c.307G>A	p.Glu103Lys	p.E103K	ENST00000392795	NM_001039933.1	103	Gaa/Aaa	3/6	0.173950613307588	3	FACETS	1	0.783	1	0.589	0.408	0.814	CLONAL	1	TRUE	1	0.11	3		782	179	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432284	432284	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	117	557	0	ENST00000399788.2:c.2239A>G	p.Thr747Ala	p.T747A	ENST00000399788	NM_001042603.1	747	Aca/Gca	16/28	NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.34	2		557	636	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0044263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	213	331	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.841076963539086	2		331	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0044321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	37	525	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	1	2	FACETS	0.83	0.682	0.996	0.83	0.682	0.996	CLONAL	1	TRUE	1	0.12	2		525	743	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771344	68771344	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	25	307	0	ENST00000261769.5:c.26C>G	p.Ser9Trp	p.S9W	ENST00000261769	NM_004360.3	9	tCg/tGg	1/16	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.12	2		307	359	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687598	29687598	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	50	572	0	ENST00000356175.3:c.8191G>C	p.Glu2731Gln	p.E2731Q	ENST00000356175	NM_000267.3	2731	Gaa/Caa	56/57	1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	1	0.12	2		572	832	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978423	2978423	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	43	755	0	ENST00000396946.4:c.907G>A	p.Asp303Asn	p.D303N	ENST00000396946	NM_032415.4	303	Gac/Aac	7/25	1	2	FACETS	0.939	0.784	1	0.939	0.784	1	CLONAL	1	TRUE	1	0.12	2		755	763	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922731	44922731	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	35	231	0	ENST00000377967.4:c.1592C>A	p.Ser531Ter	p.S531*	ENST00000377967	NM_021140.2	531	tCa/tAa	16/29	0.3	2	FACETS	0.876	0.72	1	0.876	0.72	1	CLONAL	2	TRUE	0	0.12	2		231	333	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0044323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	91	732	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.14	2		735	943	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0044323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	66	662	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.973	0.842	1	0.973	0.842	1	CLONAL	1	TRUE	1	0.14	2		663	969	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	67	900	2	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.892	0.773	1	0.892	0.773	1	CLONAL	1	TRUE	1	0.14	2		902	1073	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	46	822	0	ENST00000324856.7:c.4555del	p.Gln1519ArgfsTer8	p.Q1519Rfs*8	ENST00000324856	NM_006015.4	1517	gCc/gc	18/20	1	2	FACETS	0.761	0.638	0.896	0.761	0.638	0.896	SUBCLONAL	1	TRUE	1	0.14	2		822	864	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855966	68855966	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35187787	NA	P-0044323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	52	773	1	ENST00000261769.5:c.1774G>A	p.Ala592Thr	p.A592T	ENST00000261769	NM_004360.3	592	Gcc/Acc	12/16	1	2	FACETS	0.802	0.681	0.936	0.802	0.681	0.936	CLONAL	1	TRUE	1	0.14	2		774	926	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0044323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	65	820	7	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.14	2		827	819	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371644	89371644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs949172972	NA	P-0044323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	61	888	0	ENST00000301030.4:c.196G>A	p.Ala66Thr	p.A66T	ENST00000301030	NM_001256183.1	66	Gcc/Acc	4/13	1	2	FACETS	0.802	0.69	0.926	0.802	0.69	0.926	CLONAL	1	TRUE	1	0.14	2		888	1086	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0044323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	36	180	1	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	0.732	0.6	0.88	0.732	0.6	0.88	SUBCLONAL	1	TRUE	1	0.14	2		181	703	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163554	32163554	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	54	773	3	ENST00000375023.3:c.5672del	p.Gly1891AlafsTer13	p.G1891Afs*13	ENST00000375023	NM_004557.3	1891	gGc/gc	30/30	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.14	2		776	662	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624296	89624296	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786201995	NA	P-0044323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	100	664	0	ENST00000371953.3:c.70G>T	p.Asp24Tyr	p.D24Y	ENST00000371953	NM_000314.4	24	Gac/Tac	1/9	1	2	FACETS	0.798	0.712	0.89	1	0.983	1	SUBCLONAL	2	TRUE	1	0.14	2		664	895	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585361	29585361	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0044323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	53	510	0	ENST00000356175.3:c.4111-1G>T		p.X1371_splice	ENST00000356175	NM_000267.3	1371			1	2	FACETS	0.946	0.805	1	0.946	0.805	1	CLONAL	1	TRUE	1	0.14	2		510	800	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748576	40748576	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	38	641	0	ENST00000373198.4:c.2940A>C	p.Gln980His	p.Q980H	ENST00000373198	NM_133170.3	980	caA/caC	21/32	1	2	FACETS	0.792	0.653	0.949	0.792	0.653	0.949	CLONAL	1	TRUE	1	0.14	2		641	685	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916855	178916855	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	59	229	0	ENST00000263967.3:c.242A>C	p.Glu81Ala	p.E81A	ENST00000263967	NM_006218.2	81	gAa/gCa	2/21	1	2	FACETS	0.839	0.72	0.971	0.839	0.72	0.971	CLONAL	1	TRUE	1	0.14	2		229	1004	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202912	16202912	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	55	712	0	ENST00000375759.3:c.620A>G	p.Glu207Gly	p.E207G	ENST00000375759	NM_015001.2	207	gAg/gGg	3/15	1	2	FACETS	0.927	0.791	1	0.927	0.791	1	CLONAL	1	TRUE	1	0.14	2		712	848	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654712	67654712	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	53	552	0	ENST00000264010.4:c.1199C>A	p.Thr400Asn	p.T400N	ENST00000264010	NM_006565.3	400	aCc/aAc	6/12	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.14	2		552	740	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145642	11145642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	61	985	2	ENST00000358026.2:c.4004C>T	p.Pro1335Leu	p.P1335L	ENST00000358026	NM_001128849.1	1335	cCg/cTg	29/36	1	2	FACETS	0.847	0.728	0.977	0.847	0.728	0.977	CLONAL	1	TRUE	1	0.14	2		987	1029	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626878	158626878	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0044323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	37	385	0	ENST00000263640.3:c.790+2T>C		p.X264_splice	ENST00000263640	NM_001105.4	264			1	2	FACETS	0.859	0.707	1	0.859	0.707	1	CLONAL	1	TRUE	1	0.14	2		385	615	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735602	204735602	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	36	596	0	ENST00000302823.3:c.403T>C	p.Tyr135His	p.Y135H	ENST00000302823	NM_005214.4	135	Tac/Cac	2/4	1	2	FACETS	0.806	0.661	0.969	0.806	0.661	0.969	CLONAL	1	TRUE	1	0.14	2		596	638	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180969	32180969	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	52	912	2	ENST00000375023.3:c.2381C>A	p.Ala794Asp	p.A794D	ENST00000375023	NM_004557.3	794	gCc/gAc	15/30	1	2	FACETS	0.773	0.656	0.902	0.773	0.656	0.902	CLONAL	1	TRUE	1	0.14	2		914	961	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852242	128852242	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	59	1008	0	ENST00000249373.3:c.2314C>A	p.Arg772Ser	p.R772S	ENST00000249373	NM_005631.4	772	Cgc/Agc	12/12	1	2	FACETS	0.847	0.726	0.979	0.847	0.726	0.979	CLONAL	1	TRUE	1	0.14	2		1008	995	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0044334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	529	484	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.908125171994431	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.910004531418529	1		484	622	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859843	151859847	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTT	TTCTT	-	novel	NA	P-0044334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	255	254	0	ENST00000262189.6:c.10815_10819del	p.Lys3605AsnfsTer8	p.K3605Nfs*8	ENST00000262189	NM_170606.2	3605	aaAAGAAca/aaca	43/59	0.4513332328045	1	FACETS	0.611	0.579	0.643	0.611	0.579	0.643	INDETERMINATE	1	TRUE	0	0.910004531418529	1		254	500	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255491	16255492	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0044334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	456	406	1	ENST00000375759.3:c.2760_2761del	p.Gln921AspfsTer7	p.Q921Dfs*7	ENST00000375759	NM_015001.2	919	gTC/g	11/15	0.908125171994431	1	FACETS	0.957	0.932	0.98	0.957	0.932	0.98	CLONAL	1	TRUE	0	0.910004531418529	1		407	571	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885844	23885844	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	426	265	2	ENST00000374561.5:c.74C>A	p.Ala25Asp	p.A25D	ENST00000374561	NM_002167.4	25	gCc/gAc	1/3	0.908125171994431	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.910004531418529	1		267	499	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942853	44942853	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	22	347	0	ENST00000377967.4:c.3433G>A	p.Gly1145Ser	p.G1145S	ENST00000377967	NM_021140.2	1145	Ggt/Agt	23/29	0.693885171654247	0	FACETS		NA	1			1	NA	1	TRUE	0	0.910004531418529	0		347	233	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1060501197	NA	P-0044353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	1098	602	2	ENST00000269305.4:c.716del	p.Asn239ThrfsTer8	p.N239Tfs*8	ENST00000269305	NM_001126112.2	239	aAc/ac	7/11	0.649613925269548	3	FACETS	0.962	0.947	0.976			1	CLONAL	3	TRUE	NA	0.81958297844724	3		604	1309	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059260	27059260	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	352	552	0	ENST00000324856.7:c.1897C>T	p.Gln633Ter	p.Q633*	ENST00000324856	NM_006015.4	633	Cag/Tag	4/20	0.81958297844724	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.81958297844724	1		552	483	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039340	49039340	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0044353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	314	597	0	ENST00000267163.4:c.2326-1del		p.X776_splice	ENST00000267163	NM_000321.2	776			0.806210630581874	1	FACETS	0.96	0.922	0.997	0.96	0.922	0.997	CLONAL	1	TRUE	0	0.81958297844724	1		597	471	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405959	70405959	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	351	602	0	ENST00000373644.4:c.3473G>C	p.Arg1158Pro	p.R1158P	ENST00000373644	NM_030625.2	1158	cGg/cCg	4/12	0.806210630581874	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.81958297844724	1		602	504	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552754	18552754	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	217	470	0	ENST00000266497.5:c.2165T>C	p.Leu722Ser	p.L722S	ENST00000266497		722	tTa/tCa	14/31	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.81958297844724	2		470	519	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431583	49431584	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	347	721	0	ENST00000301067.7:c.9555dup	p.Gly3186TrpfsTer29	p.G3186Wfs*29	ENST00000301067	NM_003482.3	3185	-/T	34/54	1	2	FACETS	0.914	0.869	0.961	0.914	0.869	0.961	CLONAL	1	TRUE	1	0.81958297844724	2		721	926	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915007	32915007	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0044353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	184	521	0	ENST00000380152.3:c.6515C>G	p.Ser2172Ter	p.S2172*	ENST00000380152		2172	tCa/tGa	11/27	0.806210630581874	1	FACETS	0.978	0.928	1	0.978	0.928	1	CLONAL	1	TRUE	0	0.81958297844724	1		521	271	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136242	2136242	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs397514905	NA	P-0044353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	373	756	0	ENST00000219476.3:c.4711T>C	p.Tyr1571His	p.Y1571H	ENST00000219476	NM_000548.3	1571	Tac/Cac	37/42	0.81962909969748	1	FACETS	0.931	0.896	0.965	0.931	0.896	0.965	CLONAL	1	TRUE	0	0.81958297844724	1		756	577	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743994	41743994	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	422	854	0	ENST00000301178.4:c.929C>A	p.Ala310Glu	p.A310E	ENST00000301178	NM_021913.4	310	gCa/gAa	7/20	1	2	FACETS	0.927	0.885	0.969	0.927	0.885	0.969	CLONAL	1	TRUE	1	0.81958297844724	2		854	1111	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017378	31017774	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCCATAGGTTCTAGTGCTGGGCTCTGCTGTGTGCCTTCCTCTTTGTCTCCCAGGGCAGTCGTGAGGATCCAACGGAGGATTTGATTATGCCAGTGCTTTGTAAAAGGTGTAGTGCTATACAAATAAAGATGGCAGTTTGGCACCTGTAAGGTGATATTTTAAAGCCAGACCATGAAGTGGTGGTTTCTCTCAGCCTAAGGCTGGGAGATGGAAGCATCCCAGTATTGCTGGCAGCATCTCAGGGAGAGCTGGGAGAAATGAGCTTGTCTGAGAGCCATGGGCGCGGCTTGGTGATACTTTTGACCAGTGGAATGCTGTGCCTTCAGGGTTCTCGGGCTGCCACGCCGATGGCGAGAGCGGCAGCCCGTCCAGCAGCAGCAGCGGCTCTCTGGCCCTG	GCCATAGGTTCTAGTGCTGGGCTCTGCTGTGTGCCTTCCTCTTTGTCTCCCAGGGCAGTCGTGAGGATCCAACGGAGGATTTGATTATGCCAGTGCTTTGTAAAAGGTGTAGTGCTATACAAATAAAGATGGCAGTTTGGCACCTGTAAGGTGATATTTTAAAGCCAGACCATGAAGTGGTGGTTTCTCTCAGCCTAAGGCTGGGAGATGGAAGCATCCCAGTATTGCTGGCAGCATCTCAGGGAGAGCTGGGAGAAATGAGCTTGTCTGAGAGCCATGGGCGCGGCTTGGTGATACTTTTGACCAGTGGAATGCTGTGCCTTCAGGGTTCTCGGGCTGCCACGCCGATGGCGAGAGCGGCAGCCCGTCCAGCAGCAGCAGCGGCTCTCTGGCCCTG	-	novel	NA	P-0044353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	22	60	0	ENST00000375687.4:c.565+145_637del		p.X189_splice	ENST00000375687	NM_015338.5	189		8/13	1	2	FACETS	0.577	0.457	0.71	0.577	0.457	0.71	SUBCLONAL	1	TRUE	1	0.81958297844724	2		60	93	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713425	40713438	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CCCGGTAGGCAGGC	CCCGGTAGGCAGGC	-	novel	NA	P-0044353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	403	829	0	ENST00000373198.4:c.4077_4090del	p.Trp1359Ter	p.W1359*	ENST00000373198	NM_133170.3	1359	tgGCCTGCCTACCGGGac/tgac	30/32	1	2	FACETS	0.934	0.891	0.978	0.934	0.891	0.978	CLONAL	1	TRUE	1	0.81958297844724	2		829	1053	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953877	55953877	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	276	425	0	ENST00000263923.4:c.3559G>A	p.Glu1187Lys	p.E1187K	ENST00000263923	NM_002253.2	1187	Gaa/Aaa	27/30	0.804937053564264	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.81958297844724	1		425	397	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41904279	41904301	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGCTACCCAGCACTCACCACTT	CAGCTACCCAGCACTCACCACTT	-	novel	NA	P-0044353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	138	377	0	ENST00000372991.4:c.707_711+18del		p.X236_splice	ENST00000372991	NM_001760.3	236		4/5	0.283939132184732	1	FACETS	0.437	0.4	0.474	0.437	0.4	0.474	INDETERMINATE	1	TRUE	0	0.81958297844724	1		377	455	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866592	117866592	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	214	516	0	ENST00000297338.2:c.1053G>C	p.Leu351Phe	p.L351F	ENST00000297338	NM_006265.2	351	ttG/ttC	9/14	1	2	FACETS	0.879	0.823	0.937	0.879	0.823	0.937	CLONAL	1	TRUE	1	0.81958297844724	2		516	594	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0044362-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	14	325	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.228	0.164	0.306	0.228	0.164	0.306	SUBCLONAL	1	TRUE	1	0.367879442774242	2		325	334	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520162	9520162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044362-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	40	667	0	ENST00000353224.5:c.2107G>A	p.Ala703Thr	p.A703T	ENST00000353224	NM_177990.2	703	Gca/Aca	10/10	1	2	FACETS	0.453	0.376	0.539	0.453	0.376	0.539	SUBCLONAL	1	TRUE	1	0.367879442774242	2		667	480	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040995	47040995	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044362-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	54	440	0	ENST00000377604.3:c.1525C>T	p.Gln509Ter	p.Q509*	ENST00000377604	NM_001204468.1	509	Caa/Taa	14/24	1	1	FACETS	0.823	0.708	0.947	0.823	0.708	0.947	CLONAL	1	TRUE	0	0.367879442774242	1		440	291	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962304	2962304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs895009948	NA	P-0044362-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	51	575	0	ENST00000396946.4:c.2233G>A	p.Gly745Ser	p.G745S	ENST00000396946	NM_032415.4	745	Ggc/Agc	17/25	1	2	FACETS	0.745	0.636	0.865	0.745	0.636	0.865	SUBCLONAL	1	TRUE	1	0.367879442774242	2		575	372	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658284	18658284	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044362-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	57	630	0	ENST00000266497.5:c.3089G>T	p.Gly1030Val	p.G1030V	ENST00000266497		1030	gGa/gTa	22/31	1	2	FACETS	0.62	0.532	0.715	0.62	0.532	0.715	SUBCLONAL	1	TRUE	1	0.367879442774242	2		630	500	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231201	46231201	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0044362-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	52	325	0	ENST00000334344.6:c.1120+1G>C		p.X374_splice	ENST00000334344	NM_152641.2	374			1	2	FACETS	0.664	0.566	0.77	0.664	0.566	0.77	SUBCLONAL	1	TRUE	1	0.367879442774242	2		325	426	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117761	115117761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780398425	NA	P-0044362-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	75	508	0	ENST00000257566.3:c.674G>A	p.Ser225Asn	p.S225N	ENST00000257566	NM_016569.3	225	aGt/aAt	3/8	1	2	FACETS	0.992	0.874	1	0.992	0.874	1	CLONAL	1	TRUE	1	0.367879442774242	2		508	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578408	7578408	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044362-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	23	890	0	ENST00000269305.4:c.522G>T	p.Arg174Ser	p.R174S	ENST00000269305	NM_001126112.2	174	agG/agT	5/11	1	2	FACETS	0.221	0.171	0.279	0.221	0.171	0.279	SUBCLONAL	1	TRUE	1	0.367879442774242	2		890	566	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593638	55593661	+	inframe_deletion	In_Frame_Del	DEL	TGTTTACATAGACCCAACACAACT	TGTTTACATAGACCCAACACAACT	-	novel	NA	P-0044370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	167	232	0	ENST00000288135.5:c.1705_1728del	p.Val569_Leu576del	p.V569_L576del	ENST00000288135	NM_000222.2	568	taTGTTTACATAGACCCAACACAACTt/tat	11/21	1	2	FACETS	0.863	0.801	0.927	0.863	0.801	0.927	CLONAL	1	TRUE	1	0.835556530181299	2		232	463	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3114941	3114941	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0044370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	50	500	2	ENST00000078429.4:c.477-1G>T		p.X159_splice	ENST00000078429	NM_002067.2	159			1	2	FACETS	0.147	0.124	0.172	0.147	0.124	0.172	SUBCLONAL	1	TRUE	1	0.835556530181299	2		502	814	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0044388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	42	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.944	0.79	1	0.944	0.79	1	CLONAL	1	TRUE	1	0.25	2		288	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578260	7578260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204041	NA	P-0044388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	90	532	0	ENST00000269305.4:c.589G>A	p.Val197Met	p.V197M	ENST00000269305	NM_001126112.2	197	Gtg/Atg	6/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.25	2		532	555	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962566	100962566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749564230	NA	P-0044388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	32	325	1	ENST00000325455.5:c.1831G>A	p.Val611Ile	p.V611I	ENST00000325455	NM_001202474.3	611	Gtt/Att	3/8	1	2	FACETS	0.58	0.471	0.705	0.58	0.471	0.705	SUBCLONAL	1	TRUE	1	0.25	2		326	441	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636367	21636367	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs376839517	NA	P-0044388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	50	366	2	ENST00000421138.2:c.643C>T	p.Arg215Ter	p.R215*	ENST00000421138		215	Cga/Tga	7/16	1	2	FACETS	0.917	0.78	1	0.917	0.78	1	CLONAL	1	TRUE	1	0.25	2		368	436	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368291	45368291	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	24	299	0	ENST00000262160.6:c.1311G>T	p.Trp437Cys	p.W437C	ENST00000262160	NM_005901.5	437	tgG/tgT	11/11	1	2	FACETS	0.535	0.419	0.668	0.535	0.419	0.668	SUBCLONAL	1	TRUE	1	0.25	2		299	359	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917804	29917804	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	43	619	0	ENST00000389048.3:c.864G>A	p.Trp288Ter	p.W288*	ENST00000389048	NM_004304.4	288	tgG/tgA	3/29	1	2	FACETS	0.457	0.381	0.541	0.457	0.381	0.541	SUBCLONAL	1	TRUE	1	0.25	2		619	753	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204864	NA	P-0044392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	160	314	0	ENST00000371953.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000371953	NM_000314.4	171	Cag/Tag	6/9	0.78801483352041	1	FACETS	0.618	0.574	0.664	0.618	0.574	0.664	SUBCLONAL	1	TRUE	0	0.78801483352041	1		314	398	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	267	311	0	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	0.78801483352041	1	FACETS	0.938	0.895	0.98	0.938	0.895	0.98	CLONAL	1	TRUE	0	0.78801483352041	1		311	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0044392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	1091	626	1	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.784829126028256	3	FACETS	1	0.994	1			1	CLONAL	3	TRUE	NA	0.78801483352041	3		627	1268	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717661	89717661	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0044392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	76	431	0	ENST00000371953.3:c.686C>G	p.Ser229Ter	p.S229*	ENST00000371953	NM_000314.4	229	tCa/tGa	7/9	0.78801483352041	1	FACETS	0.254	0.223	0.287	0.254	0.223	0.287	SUBCLONAL	1	TRUE	0	0.78801483352041	1		431	460	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336663	81336663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	160	244	0	ENST00000222390.5:c.1559G>A	p.Gly520Glu	p.G520E	ENST00000222390	NM_000601.4	520	gGa/gAa	14/18	1	2	FACETS	0.885	0.819	0.952	0.885	0.819	0.952	CLONAL	1	TRUE	1	0.78801483352041	2		244	459	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440208	49440208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0044392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	224	440	0	ENST00000301067.7:c.4419-1G>A		p.X1473_splice	ENST00000301067	NM_003482.3	1473			1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.78801483352041	2		440	563	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428594	49428594	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0044392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	254	530	0	ENST00000301067.7:c.10355+1G>T		p.X3452_splice	ENST00000301067	NM_003482.3	3452			1	2	FACETS	0.981	0.924	1	0.981	0.924	1	CLONAL	1	TRUE	1	0.78801483352041	2		530	657	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644813	67644813	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	230	484	0	ENST00000264010.4:c.78G>C	p.Gln26His	p.Q26H	ENST00000264010	NM_006565.3	26	caG/caC	3/12	0.78801483352041	1	FACETS	0.926	0.88	0.971	0.926	0.88	0.971	CLONAL	1	TRUE	0	0.78801483352041	1		484	382	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89818553	89818553	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs777061373	NA	P-0044392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	48	359	0	ENST00000389301.3:c.3059G>C	p.Arg1020Thr	p.R1020T	ENST00000389301	NM_000135.2	1020	aGa/aCa	31/43	0.78801483352041	1	FACETS	0.202	0.171	0.236	0.202	0.171	0.236	SUBCLONAL	1	TRUE	0	0.78801483352041	1		359	366	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111807	56111807	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	14	20	0	ENST00000399503.3:c.407C>G	p.Ser136Trp	p.S136W	ENST00000399503	NM_005921.1	136	tCg/tGg	1/20	1	2	FACETS	0.846	0.685	0.989	1	0.931	1	CLONAL	2	TRUE	1	0.78801483352041	2		20	21	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033260	69033260	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	218	315	0	ENST00000288368.4:c.3700C>G	p.Gln1234Glu	p.Q1234E	ENST00000288368	NM_024870.2	1234	Cag/Gag	30/40	0.78801483352041	3	FACETS	0.872	0.813	0.934	0.436	0.406	0.467	CLONAL	1	TRUE	1	0.78801483352041	3		315	884	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777856	27777856	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	40	244	0	ENST00000369163.2:c.5C>A	p.Ala2Glu	p.A2E	ENST00000369163	NM_003536.2	2	gCg/gAg	1/1	1	2	FACETS	0.654	0.551	0.765	0.654	0.551	0.765	SUBCLONAL	1	TRUE	1	0.695275229168652	2		244	176	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0044403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	168	651	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.167354990056214	3	FACETS	0.997	0.916	1	0.498	0.458	0.541	INDETERMINATE	1	TRUE	1	0.460121183862141	3		651	901	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339554	81339554	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs571102402	NA	P-0044403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	49	295	0	ENST00000222390.5:c.1450G>T	p.Val484Leu	p.V484L	ENST00000222390	NM_000601.4	484	Gta/Tta	13/18	0.419610571892492	3	FACETS	0.936	0.798	1	0.468	0.399	0.543	CLONAL	1	TRUE	1	0.460121183862141	3		295	280	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630136	100630136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555980871	NA	P-0044403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	93	339	1	ENST00000308731.7:c.137G>A	p.Arg46His	p.R46H	ENST00000308731	NM_000061.2	46	cGt/cAt	2/19	0.460121183862141	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.460121183862141	1		340	244	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139811005	139811005	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369480645	NA	P-0044403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	146	610	0	ENST00000247668.2:c.616G>A	p.Val206Ile	p.V206I	ENST00000247668	NM_021138.3	206	Gtc/Atc	7/11	0.162843750124337	5	FACETS	1	0.974	1	0.293	0.267	0.32	INDETERMINATE	1	TRUE	1	0.460121183862141	5		610	916	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439780	52439780	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0044403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	258	445	0	ENST00000460680.1:c.931+1G>T		p.X311_splice	ENST00000460680	NM_004656.3	311			0.318815482781484	3	FACETS	1	0.983	1	0.736	0.694	0.778	CLONAL	2	TRUE	0	0.460121183862141	3		445	625	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776535	9776535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	307	640	0	ENST00000377346.4:c.638C>T	p.Pro213Leu	p.P213L	ENST00000377346	NM_005026.3	213	cCg/cTg	6/24	0.387564194404286	2	FACETS	1	0.994	1	0.704	0.665	0.744	CLONAL	1	TRUE	0	0.460121183862141	2		640	948	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579409	7579410	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0044403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	144	604	0	ENST00000269305.4:c.277dup	p.Leu93ProfsTer56	p.L93Pfs*56	ENST00000269305	NM_001126112.2	93	ctg/cCtg	4/11	0.167354990056214	3	FACETS	0.958	0.874	1	0.479	0.437	0.523	INDETERMINATE	1	TRUE	1	0.460121183862141	3		604	804	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434187	49434187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754060706	NA	P-0044403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	223	840	0	ENST00000301067.7:c.7366C>T	p.Arg2456Cys	p.R2456C	ENST00000301067	NM_003482.3	2456	Cgc/Tgc	31/54	0.460121183862141	3	FACETS	0.869	0.807	0.933	0.435	0.403	0.467	CLONAL	1	TRUE	1	0.460121183862141	3		840	1372	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166470	118166470	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	158	384	0	ENST00000369448.3:c.980G>T	p.Arg327Met	p.R327M	ENST00000369448	NM_017709.3	327	aGg/aTg	2/2	0.318815482781484	3	FACETS	0.992	0.918	1	0.661	0.612	0.711	CLONAL	2	TRUE	0	0.460121183862141	3		384	426	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936757	78936757	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	353	670	0	ENST00000306801.3:c.3839A>G	p.Tyr1280Cys	p.Y1280C	ENST00000306801	NM_020761.2	1280	tAc/tGc	33/34	0.239648139888033	2	FACETS	1	0.994	1	0.694	0.658	0.73	INDETERMINATE	1	TRUE	0	0.460121183862141	2		670	1106	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207073	1207073	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	242	675	0	ENST00000326873.7:c.161T>A	p.Leu54Gln	p.L54Q	ENST00000326873	NM_000455.4	54	cTg/cAg	1/10	0.395200996965383	2	FACETS	1	0.975	1	0.543	0.507	0.579	CLONAL	1	TRUE	0	0.460121183862141	2		675	969	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169289	99169289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	101	542	0	ENST00000074304.5:c.1219G>A	p.Asp407Asn	p.D407N	ENST00000074304	NM_001134224.1	407	Gat/Aat	15/26	1	2	FACETS	0.851	0.763	0.943	0.851	0.763	0.943	CLONAL	1	TRUE	1	0.460121183862141	2		542	516	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273237	198273237	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	94	447	0	ENST00000335508.6:c.973G>A	p.Glu325Lys	p.E325K	ENST00000335508	NM_012433.2	325	Gaa/Aaa	8/25	1	2	FACETS	0.736	0.657	0.821	0.736	0.657	0.821	SUBCLONAL	1	TRUE	1	0.460121183862141	2		447	555	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587145	212587145	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	52	294	0	ENST00000342788.4:c.856G>C	p.Gly286Arg	p.G286R	ENST00000342788	NM_005235.2	286	Gga/Cga	7/28	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.460121183862141	2		294	217	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207078	1207079	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	44	704	0	ENST00000326873.7:c.166_167insT	p.Gly56ValfsTer107	p.G56Vfs*107	ENST00000326873	NM_000455.4	56	ggg/gTgg	1/10	0.395200996965383	2	FACETS	0.243	0.203	0.287	0.121	0.101	0.144	SUBCLONAL	1	TRUE	0	0.460121183862141	2		704	788	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0044409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	120	346	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.618039651587774	2		346	386	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724632	162724632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767283136	NA	P-0044409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	60	469	1	ENST00000367921.3:c.404G>A	p.Arg135His	p.R135H	ENST00000367921	NM_006182.2	135	cGt/cAt	5/18	0.34967545622805	3	FACETS	0.545	0.471	0.626	0.273	0.235	0.313	INDETERMINATE	1	TRUE	1	0.618039651587774	3		470	466	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959073	28959073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761475937	NA	P-0044409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	58	386	0	ENST00000282397.4:c.2065G>A	p.Glu689Lys	p.E689K	ENST00000282397	NM_002019.4	689	Gag/Aag	14/30	1	2	FACETS	0.429	0.37	0.494	0.429	0.37	0.494	SUBCLONAL	1	TRUE	1	0.618039651587774	2		386	437	SUCCESS
BLM	641	MSKCC	GRCh37	15	91306262	91306262	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	22	351	0	ENST00000355112.3:c.1949C>T	p.Pro650Leu	p.P650L	ENST00000355112	NM_000057.2	650	cCt/cTt	8/22	1	2	FACETS	0.167	0.129	0.212	0.167	0.129	0.212	SUBCLONAL	1	TRUE	1	0.618039651587774	2		351	426	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779755	3779755	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	71	707	0	ENST00000262367.5:c.5293del	p.Gln1765ArgfsTer6	p.Q1765Rfs*6	ENST00000262367	NM_004380.2	1765	Cag/ag	31/31	1	2	FACETS	0.416	0.363	0.473	0.416	0.363	0.473	SUBCLONAL	1	TRUE	1	0.618039651587774	2		707	552	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66520176	66520176	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	44	406	1	ENST00000358598.2:c.463del	p.Ser155ArgfsTer10	p.S155Rfs*10	ENST00000358598	NM_212471.2	154	Ttt/tt	5/11	1	2	FACETS	0.289	0.242	0.341	0.289	0.242	0.341	SUBCLONAL	1	TRUE	1	0.618039651587774	2		407	493	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62305359	62305359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200429535	NA	P-0044409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	82	794	0	ENST00000360203.5:c.832G>A	p.Val278Ile	p.V278I	ENST00000360203	NM_001283009.1	278	Gtc/Atc	10/35	1	2	FACETS	0.375	0.33	0.423	0.375	0.33	0.423	SUBCLONAL	1	TRUE	1	0.618039651587774	2		794	708	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539216	187539216	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	41	363	0	ENST00000441802.2:c.8524G>T	p.Gly2842Cys	p.G2842C	ENST00000441802	NM_005245.3	2842	Ggc/Tgc	10/27	1	2	FACETS	0.352	0.293	0.417	0.352	0.293	0.417	SUBCLONAL	1	TRUE	1	0.618039651587774	2		363	377	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659309	86659309	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	17	156	0	ENST00000274376.6:c.1598G>T	p.Ser533Ile	p.S533I	ENST00000274376	NM_002890.2	533	aGt/aTt	11/25	1	2	FACETS	0.243	0.182	0.316	0.243	0.182	0.316	SUBCLONAL	1	TRUE	1	0.618039651587774	2		156	226	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519397	176519397	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	86	725	0	ENST00000292408.4:c.803A>G	p.Glu268Gly	p.E268G	ENST00000292408	NM_213647.1	268	gAg/gGg	7/18	1	2	FACETS	0.419	0.371	0.471	0.419	0.371	0.471	SUBCLONAL	1	TRUE	1	0.618039651587774	2		725	664	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992721	68992721	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs764112302	NA	P-0044409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	91	439	1	ENST00000288368.4:c.1693del	p.Ser565ArgfsTer10	p.S565Rfs*10	ENST00000288368	NM_024870.2	562	cgT/cg	16/40	0.602852576191663	3	FACETS	0.508	0.451	0.569	0.254	0.225	0.285	SUBCLONAL	1	TRUE	1	0.618039651587774	3		440	759	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653794	89653797	+	frameshift_variant	Frame_Shift_Del	DEL	ACAT	ACAT	-	novel	NA	P-0044409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	150	301	0	ENST00000371953.3:c.92_95del	p.Asn31IlefsTer22	p.N31Ifs*22	ENST00000371953	NM_000314.4	31	aACATt/at	2/9	0.602852576191663	3	FACETS	0.784	0.725	0.845	0.784	0.725	0.845	SUBCLONAL	2	TRUE	1	0.618039651587774	3		301	405	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52649459	52649459	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	81	418	0	ENST00000394830.3:c.1832C>A	p.Ala611Glu	p.A611E	ENST00000394830	NM_018313.4	611	gCa/gAa	16/30	0.425638034403136	1	FACETS	0.858	0.762	0.96	0.858	0.762	0.96	CLONAL	1	TRUE	0	0.425638034403136	1		418	349	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784047	9784047	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	138	684	0	ENST00000377346.4:c.2615T>C	p.Ile872Thr	p.I872T	ENST00000377346	NM_005026.3	872	aTt/aCt	21/24	1	2	FACETS	0.769	0.7	0.842	0.769	0.7	0.842	SUBCLONAL	1	TRUE	1	0.425638034403136	2		684	843	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778111	135778111	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397514783	NA	P-0044442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	125	499	0	ENST00000298552.3:c.2272C>T	p.Gln758Ter	p.Q758*	ENST00000298552	NM_001162426.1	758	Caa/Taa	18/23	0.425638034403136	1	FACETS	0.891	0.81	0.975	0.891	0.81	0.975	CLONAL	1	TRUE	0	0.425638034403136	1		499	519	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	223	571	0				ENST00000310581	NM_198253.2	-/1132			0.229074244204074	3	FACETS	1	0.951	1			1	CLONAL	2	TRUE	NA	0.352530997456617	3		571	729	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851228	151851228	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	30	275	0	ENST00000262189.6:c.12143C>T	p.Ser4048Leu	p.S4048L	ENST00000262189	NM_170606.2	4048	tCa/tTa	48/59	1	2	FACETS	0.826	0.671	1	0.826	0.671	1	CLONAL	1	TRUE	1	0.352530997456617	2		275	206	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	225	553	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.26571376762201	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.352530997456617	2		553	596	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163297	32163297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1239036035	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	417	990	0	ENST00000375023.3:c.5929G>A	p.Glu1977Lys	p.E1977K	ENST00000375023	NM_004557.3	1977	Gag/Aag	30/30	0.18836574344149	3	FACETS	0.981	0.934	1	0.981	0.934	1	INDETERMINATE	2	TRUE	1	0.352530997456617	3		990	1418	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023037	33023037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	75	478	0	ENST00000300177.4:c.146C>T	p.Ser49Leu	p.S49L	ENST00000300177	NM_001191322.1	49	tCg/tTg	2/2	0.345114055484344	3	FACETS	1	0.911	1	0.522	0.459	0.59	CLONAL	1	TRUE	1	0.352530997456617	3		478	479	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339981	70339981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	180	221	0	ENST00000374080.3:c.514G>A	p.Glu172Lys	p.E172K	ENST00000374080		172	Gag/Aag	4/45	0.120314781403936	2	FACETS	0.871	0.814	0.927			1	INDETERMINATE	3	TRUE	NA	0.352530997456617	2		221	391	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	185	265	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	0.120314781403936	2	FACETS	0.881	0.825	0.938			1	INDETERMINATE	3	TRUE	NA	0.352530997456617	2		265	397	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843447	3843447	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783461	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	225	504	0	ENST00000262367.5:c.1156C>T	p.Arg386Ter	p.R386*	ENST00000262367	NM_004380.2	386	Cga/Tga	4/31	0.295783670762117	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.352530997456617	2		504	581	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193530	99193530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	297	677	0	ENST00000074304.5:c.2725G>A	p.Glu909Lys	p.E909K	ENST00000074304	NM_001134224.1	909	Gag/Aag	25/26	0.352530997456617	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.352530997456617	3		677	878	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793134	33793134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1452063514	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	208	394	0	ENST00000498907.2:c.187G>A	p.Asp63Asn	p.D63N	ENST00000498907	NM_004364.3	63	Gac/Aac	1/1	0.352530997456617	8	FACETS	1	0.978	1	0.56	0.521	0.599	CLONAL	3	TRUE	2	0.352530997456617	8		394	723	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870966	12870966	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	174	432	0	ENST00000228872.4:c.193C>T	p.Gln65Ter	p.Q65*	ENST00000228872	NM_004064.3	65	Cag/Tag	1/3	0.352530997456617	5	FACETS	1	0.977	1	0.763	0.705	0.823	CLONAL	2	TRUE	2	0.352530997456617	5		432	659	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618547	37618547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	340	597	0	ENST00000447079.4:c.223G>A	p.Asp75Asn	p.D75N	ENST00000447079	NM_015083.1	75	Gat/Aat	1/14	0.146458284902499	5	FACETS	0.949	0.899	0.999	0.949	0.899	0.999	INDETERMINATE	3	TRUE	2	0.352530997456617	5		597	1036	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619292	37619292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	279	515	0	ENST00000447079.4:c.968C>T	p.Ser323Leu	p.S323L	ENST00000447079	NM_015083.1	323	tCg/tTg	1/14	0.146458284902499	5	FACETS	0.926	0.872	0.981	0.926	0.872	0.981	INDETERMINATE	3	TRUE	2	0.352530997456617	5		515	871	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855787	45855787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	205	699	0	ENST00000391945.4:c.2023G>T	p.Gly675Cys	p.G675C	ENST00000391945	NM_000400.3	675	Ggc/Tgc	21/23	1	2	FACETS	0.783	0.728	0.839	1	0.992	1	SUBCLONAL	2	TRUE	1	0.352530997456617	2		699	743	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952304	17952304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	163	872	0	ENST00000458235.1:c.1036G>A	p.Asp346Asn	p.D346N	ENST00000458235	NM_000215.3	346	Gac/Aac	8/24	0.352530997456617	3	FACETS	1	0.952	1	0.527	0.483	0.573	CLONAL	1	TRUE	1	0.352530997456617	3		872	1032	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374909	149374909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	326	617	0	ENST00000360632.3:c.185C>T	p.Ser62Leu	p.S62L	ENST00000360632	NM_015472.4	62	tCg/tTg	2/7	0.345114055484344	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.352530997456617	3		617	998	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794999	242794999	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424422486	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	166	923	2	ENST00000334409.5:c.210G>A	p.Met70Ile	p.M70I	ENST00000334409	NM_005018.2	70	atG/atA	2/5	0.352530997456617	3	FACETS	0.997	0.915	1	0.499	0.457	0.542	CLONAL	1	TRUE	1	0.352530997456617	3		925	1111	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660138	227660138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1448309277	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	128	655	2	ENST00000305123.5:c.3317C>T	p.Ser1106Leu	p.S1106L	ENST00000305123	NM_005544.2	1106	tCa/tTa	1/2	0.352530997456617	3	FACETS	1	0.92	1	0.508	0.461	0.559	CLONAL	1	TRUE	1	0.352530997456617	3		657	840	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023943	27023943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	34	105	0	ENST00000324856.7:c.1049C>T	p.Ser350Leu	p.S350L	ENST00000324856	NM_006015.4	350	tCg/tTg	1/20	0.352530997456617	3	FACETS	1	0.871	1	0.535	0.441	0.639	CLONAL	1	TRUE	1	0.352530997456617	3		105	212	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247882	59247882	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	239	872	0	ENST00000371222.2:c.861G>C	p.Leu287Phe	p.L287F	ENST00000371222	NM_002228.3	287	ttG/ttC	1/1	0.345114055484344	3	FACETS	1	0.983	1	0.584	0.544	0.626	CLONAL	1	TRUE	1	0.352530997456617	3		872	1365	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78425916	78425916	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	207	406	0	ENST00000370768.2:c.1529G>A	p.Trp510Ter	p.W510*	ENST00000370768	NM_003902.3	510	tGg/tAg	16/20	0.345114055484344	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.352530997456617	3		406	626	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466576	120466576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	95	530	0	ENST00000256646.2:c.4543G>A	p.Asp1515Asn	p.D1515N	ENST00000256646	NM_024408.3	1515	Gac/Aac	26/34	0.345114055484344	3	FACETS	0.994	0.886	1	0.497	0.443	0.554	CLONAL	1	TRUE	1	0.352530997456617	3		530	638	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551376	150551376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1246	349	979	1	ENST00000369026.2:c.631G>A	p.Glu211Lys	p.E211K	ENST00000369026	NM_021960.4	211	Gag/Aag	1/3	0.345114055484344	3	FACETS	1	0.994	1	0.73	0.689	0.772	CLONAL	1	TRUE	1	0.352530997456617	3		980	1595	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119447	193119447	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	70	317	0	ENST00000367435.3:c.842G>C	p.Arg281Pro	p.R281P	ENST00000367435	NM_024529.4	281	cGc/cCc	9/17	0.345114055484344	3	FACETS	0.74	0.645	0.843	0.37	0.322	0.422	SUBCLONAL	1	TRUE	1	0.352530997456617	3		317	631	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575515	64575525	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCCTGGCAG	GGGCCTGGCAG	-	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	192	674	0	ENST00000312049.6:c.492_502del	p.Cys165GlyfsTer11	p.C165Gfs*11	ENST00000312049	NM_130799.2	164	gcCTGCCAGGCCCtg/gctg	3/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.352530997456617	2		674	816	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206918	102206918	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	70	321	0	ENST00000263464.3:c.1546G>A	p.Glu516Lys	p.E516K	ENST00000263464	NM_001165.4	516	Gaa/Aaa	7/9	0.203906263491429	3	FACETS	1	0.926	1	0.542	0.474	0.615	INDETERMINATE	1	TRUE	1	0.352530997456617	3		321	431	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214016	108214016	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs876660461	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	30	377	0	ENST00000278616.4:c.8336T>G	p.Phe2779Cys	p.F2779C	ENST00000278616	NM_000051.3	2779	tTt/tGt	57/63	0.203906263491429	3	FACETS	0.355	0.285	0.435	0.177	0.142	0.218	INDETERMINATE	1	TRUE	1	0.352530997456617	3		377	564	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352519	118352519	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	164	549	0	ENST00000534358.1:c.3724C>T	p.Gln1242Ter	p.Q1242*	ENST00000534358	NM_005933.3	1242	Cag/Tag	7/36	0.203906263491429	3	FACETS	1	0.984	1	0.645	0.592	0.699	INDETERMINATE	1	TRUE	1	0.352530997456617	3		549	849	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427885	49427885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	252	701	0	ENST00000301067.7:c.10705G>A	p.Glu3569Lys	p.E3569K	ENST00000301067	NM_003482.3	3569	Gag/Aag	38/54	0.352530997456617	5	FACETS	1	0.98	1	0.738	0.691	0.787	CLONAL	2	TRUE	2	0.352530997456617	5		701	987	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444499	49444499	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	151	740	0	ENST00000301067.7:c.2872G>C	p.Glu958Gln	p.E958Q	ENST00000301067	NM_003482.3	958	Gag/Cag	11/54	0.352530997456617	5	FACETS	1	0.948	1	0.351	0.32	0.384	CLONAL	1	TRUE	2	0.352530997456617	5		740	1242	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588597	28588597	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	41	384	0	ENST00000241453.7:c.2851G>C	p.Glu951Gln	p.E951Q	ENST00000241453	NM_004119.2	951	Gaa/Caa	23/24	0.352530997456617	3	FACETS	0.632	0.527	0.749	0.316	0.263	0.375	SUBCLONAL	1	TRUE	1	0.352530997456617	3		384	433	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527705	103527705	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746776649	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	82	312	0	ENST00000355739.4:c.3013G>A	p.Glu1005Lys	p.E1005K	ENST00000355739	NM_000123.3	1005	Gaa/Aaa	15/15	0.352530997456617	3	FACETS	1	0.962	1	0.605	0.536	0.679	CLONAL	1	TRUE	1	0.352530997456617	3		312	452	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023114	33023114	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	196	550	0	ENST00000300177.4:c.223G>A	p.Glu75Lys	p.E75K	ENST00000300177	NM_001191322.1	75	Gag/Aag	2/2	0.345114055484344	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.352530997456617	3		550	541	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591728	38591728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	78	451	0	ENST00000299084.4:c.187G>A	p.Glu63Lys	p.E63K	ENST00000299084	NM_152594.2	63	Gag/Aag	2/7	0.345114055484344	3	FACETS	0.81	0.711	0.915	0.405	0.355	0.458	CLONAL	1	TRUE	1	0.352530997456617	3		451	643	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041908	42041908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	91	543	0	ENST00000219905.7:c.6103G>A	p.Glu2035Lys	p.E2035K	ENST00000219905	NM_001164273.1	2035	Gaa/Aaa	17/24	0.345114055484344	3	FACETS	0.89	0.791	0.997	0.445	0.395	0.499	CLONAL	1	TRUE	1	0.352530997456617	3		543	682	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762144	43762144	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	172	743	2	ENST00000382044.4:c.1301C>T	p.Ser434Leu	p.S434L	ENST00000382044	NM_001141980.1	434	tCa/tTa	11/28	0.345114055484344	3	FACETS	0.983	0.903	1	0.491	0.451	0.534	CLONAL	1	TRUE	1	0.352530997456617	3		745	1168	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138583	2138583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778484981	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	44	730	0	ENST00000219476.3:c.5396C>T	p.Ser1799Leu	p.S1799L	ENST00000219476	NM_000548.3	1799	tCg/tTg	42/42	0.295783670762117	2	FACETS	0.33	0.276	0.391	0.165	0.138	0.196	SUBCLONAL	1	TRUE	0	0.352530997456617	2		730	756	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817781	3817781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886041006	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	291	597	0	ENST00000262367.5:c.3190G>A	p.Glu1064Lys	p.E1064K	ENST00000262367	NM_004380.2	1064	Gag/Aag	16/31	0.295783670762117	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.352530997456617	2		597	805	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14021937	14021937	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	156	466	0	ENST00000311895.7:c.637G>A	p.Glu213Lys	p.E213K	ENST00000311895	NM_005236.2	213	Gaa/Aaa	4/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.352530997456617	NA		466	485	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821848	72821848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1287091663	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	161	536	0	ENST00000268489.5:c.10327G>A	p.Glu3443Lys	p.E3443K	ENST00000268489	NM_006885.3	3443	Gaa/Aaa	10/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.352530997456617	2		536	686	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882287	89882287	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	47	453	0	ENST00000389301.3:c.187G>A	p.Glu63Lys	p.E63K	ENST00000389301	NM_000135.2	63	Gag/Aag	2/43	0.33940177355897	1	FACETS	0.447	0.377	0.524	0.447	0.377	0.524	SUBCLONAL	1	TRUE	0	0.352530997456617	1		453	491	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684350	29684350	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	158	468	0	ENST00000356175.3:c.7870G>T	p.Glu2624Ter	p.E2624*	ENST00000356175	NM_000267.3	2624	Gag/Tag	53/57	0.146458284902499	5	FACETS	1	0.939	1	0.684	0.628	0.741	INDETERMINATE	2	TRUE	2	0.352530997456617	5		468	668	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942499	17942499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	163	800	0	ENST00000458235.1:c.2789C>T	p.Ser930Phe	p.S930F	ENST00000458235	NM_000215.3	930	tCc/tTc	20/24	0.352530997456617	3	FACETS	1	0.969	1	0.558	0.512	0.607	CLONAL	1	TRUE	1	0.352530997456617	3		800	974	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18956873	18956873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758924331	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	125	681	0	ENST00000262803.5:c.316G>A	p.Glu106Lys	p.E106K	ENST00000262803	NM_002911.3	106	Gag/Aag	2/24	0.352530997456617	3	FACETS	0.983	0.889	1	0.491	0.444	0.541	CLONAL	1	TRUE	1	0.352530997456617	3		681	849	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18958573	18958573	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	299	600	1	ENST00000262803.5:c.392C>T	p.Pro131Leu	p.P131L	ENST00000262803	NM_002911.3	131	cCt/cTt	3/24	0.352530997456617	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.352530997456617	3		601	959	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211411	36211411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	1062	935	0	ENST00000222270.7:c.1162G>A	p.Glu388Lys	p.E388K	ENST00000222270	NM_014727.1	388	Gag/Aag	3/37	0.352530997456617	8	FACETS	1	0.991	1	1	0.991	1	CLONAL	6	TRUE	2	0.352530997456617	8		935	2001	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753786	42753786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765102149	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	377	1004	0	ENST00000222329.4:c.478C>T	p.Arg160Cys	p.R160C	ENST00000222329	NM_006494.2	160	Cgc/Tgc	4/4	1	2	FACETS	0.863	0.819	0.908	1	0.996	1	CLONAL	2	TRUE	1	0.352530997456617	2		1004	1239	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796483	42796483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751173226	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	316	852	0	ENST00000575354.2:c.3040G>A	p.Ala1014Thr	p.A1014T	ENST00000575354	NM_015125.3	1014	Gcg/Acg	13/20	1	2	FACETS	0.864	0.816	0.912	1	0.995	1	CLONAL	2	TRUE	1	0.352530997456617	2		852	1038	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967285	25967285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	53	474	0	ENST00000435504.4:c.1921C>T	p.Arg641Cys	p.R641C	ENST00000435504		641	Cgt/Tgt	13/13	0.352530997456617	3	FACETS	0.444	0.377	0.517	0.222	0.188	0.259	SUBCLONAL	1	TRUE	1	0.352530997456617	3		474	797	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967335	25967335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	204	423	0	ENST00000435504.4:c.1871C>T	p.Ser624Phe	p.S624F	ENST00000435504		624	tCc/tTc	13/13	0.352530997456617	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.352530997456617	3		423	648	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047360	128047360	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	171	473	0	ENST00000285398.2:c.562C>T	p.Leu188Phe	p.L188F	ENST00000285398	NM_000122.1	188	Ctt/Ttt	5/15	0.352530997456617	3	FACETS	0.834	0.77	0.901	0.834	0.77	0.901	CLONAL	2	TRUE	1	0.352530997456617	3		473	684	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989531	212989531	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1443958987	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	205	348	0	ENST00000342788.4:c.180G>A	p.Met60Ile	p.M60I	ENST00000342788	NM_005235.2	60	atG/atA	2/28	0.352530997456617	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.352530997456617	3		348	573	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659740	227659740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	183	461	0	ENST00000305123.5:c.3715G>A	p.Glu1239Lys	p.E1239K	ENST00000305123	NM_005544.2	1239	Gag/Aag	1/2	0.352530997456617	3	FACETS	0.972	0.902	1	0.972	0.902	1	CLONAL	2	TRUE	1	0.352530997456617	3		461	628	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661616	227661616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	126	692	0	ENST00000305123.5:c.1839G>A	p.Met613Ile	p.M613I	ENST00000305123	NM_005544.2	613	atG/atA	1/2	0.352530997456617	3	FACETS	1	0.908	1	0.502	0.454	0.552	CLONAL	1	TRUE	1	0.352530997456617	3		692	838	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309757	30309757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs996600059	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	245	636	0	ENST00000307677.4:c.265G>A	p.Ala89Thr	p.A89T	ENST00000307677	NM_138578.1	89	Gcg/Acg	2/3	0.18836574344149	3	FACETS	0.917	0.859	0.978	0.917	0.859	0.978	INDETERMINATE	2	TRUE	1	0.352530997456617	3		636	891	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385023	31385023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	222	597	1	ENST00000328111.2:c.1408G>A	p.Asp470Asn	p.D470N	ENST00000328111	NM_006892.3	470	Gat/Aat	14/23	0.18836574344149	3	FACETS	0.803	0.748	0.859	0.803	0.748	0.859	INDETERMINATE	2	TRUE	1	0.352530997456617	3		598	923	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280649	41280649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	281	635	0	ENST00000349496.5:c.2162C>T	p.Ser721Phe	p.S721F	ENST00000349496	NM_001904.3	721	tCt/tTt	15/15	0.352530997456617	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.352530997456617	3		635	860	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502882	186502882	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	177	403	0	ENST00000323963.5:c.340G>C	p.Ala114Pro	p.A114P	ENST00000323963		114	Gct/Cct	4/11	0.345114055484344	3	FACETS	0.871	0.805	0.939	0.871	0.805	0.939	CLONAL	2	TRUE	1	0.352530997456617	3		403	678	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806615	1806615	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761325047	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	141	877	0	ENST00000260795.2:c.1331C>T	p.Ser444Phe	p.S444F	ENST00000260795		444	tCc/tTc	9/17	1	2	FACETS	0.986	0.899	1	0.986	0.899	1	CLONAL	1	TRUE	1	0.352530997456617	2		877	811	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146626	55146626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	230	503	1	ENST00000257290.5:c.2300C>T	p.Ser767Leu	p.S767L	ENST00000257290	NM_006206.4	767	tCa/tTa	16/23	1	2	FACETS	0.86	0.804	0.916	1	0.994	1	CLONAL	2	TRUE	1	0.352530997456617	2		504	759	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029321	143029321	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	41	227	0	ENST00000262992.4:c.2299G>C	p.Glu767Gln	p.E767Q	ENST00000262992	NM_001101669.1	767	Gaa/Caa	21/24	1	2	FACETS	0.69	0.577	0.815	0.69	0.577	0.815	SUBCLONAL	1	TRUE	1	0.352530997456617	2		227	337	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519281	187519281	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	111	414	0	ENST00000441802.2:c.12104-2A>C		p.X4035_splice	ENST00000441802	NM_005245.3	4035			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.352530997456617	2		414	488	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542269	187542269	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	47	327	0	ENST00000441802.2:c.5471C>T	p.Ser1824Phe	p.S1824F	ENST00000441802	NM_005245.3	1824	tCt/tTt	10/27	1	2	FACETS	0.782	0.662	0.913	0.782	0.662	0.913	CLONAL	1	TRUE	1	0.352530997456617	2		327	341	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629169	187629169	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	90	548	0	ENST00000441802.2:c.1813C>T	p.Gln605Ter	p.Q605*	ENST00000441802	NM_005245.3	605	Cag/Tag	2/27	1	2	FACETS	0.868	0.772	0.971	0.868	0.772	0.971	CLONAL	1	TRUE	1	0.352530997456617	2		548	588	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630295	187630295	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	110	569	0	ENST00000441802.2:c.687G>A	p.Met229Ile	p.M229I	ENST00000441802	NM_005245.3	229	atG/atA	2/27	1	2	FACETS	0.922	0.829	1	0.922	0.829	1	CLONAL	1	TRUE	1	0.352530997456617	2		569	677	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915627	131915627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	135	304	2	ENST00000265335.6:c.625G>A	p.Glu209Lys	p.E209K	ENST00000265335		209	Gaa/Aaa	5/25	0.352530997456617	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	1	0.352530997456617	3		306	420	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158737	26158737	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	241	532	0	ENST00000289316.2:c.340G>C	p.Glu114Gln	p.E114Q	ENST00000289316	NM_138720.2	114	Gag/Cag	1/2	0.317456153024345	4	FACETS	0.967	0.904	1	0.967	0.904	1	CLONAL	2	TRUE	2	0.352530997456617	4		532	956	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181961	32181961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	299	745	0	ENST00000375023.3:c.2093C>T	p.Ala698Val	p.A698V	ENST00000375023	NM_004557.3	698	gCa/gTa	13/30	0.18836574344149	3	FACETS	0.916	0.863	0.97	0.916	0.863	0.97	INDETERMINATE	2	TRUE	1	0.352530997456617	3		745	1089	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821421	32821421	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	248	843	0	ENST00000354258.4:c.173G>A	p.Arg58Gln	p.R58Q	ENST00000354258	NM_000593.5	58	cGa/cAa	1/11	0.18836574344149	3	FACETS	1	0.992	1	0.74	0.692	0.79	INDETERMINATE	1	TRUE	1	0.352530997456617	3		843	1118	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864457	162864457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	175	488	0	ENST00000366898.1:c.56C>T	p.Ser19Phe	p.S19F	ENST00000366898	NM_004562.2	19	tCt/tTt	2/12	0.18836574344149	3	FACETS	0.789	0.728	0.852	0.789	0.728	0.852	INDETERMINATE	2	TRUE	1	0.352530997456617	3		488	740	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6037009	6037009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142434011	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	218	519	0	ENST00000265849.7:c.751G>A	p.Val251Met	p.V251M	ENST00000265849	NM_000535.5	251	Gtg/Atg	7/15	0.345114055484344	3	FACETS	0.863	0.804	0.923	0.863	0.804	0.923	CLONAL	2	TRUE	1	0.352530997456617	3		519	843	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859429	151859429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	80	502	1	ENST00000262189.6:c.11233G>A	p.Glu3745Lys	p.E3745K	ENST00000262189	NM_170606.2	3745	Gaa/Aaa	43/59	1	2	FACETS	0.873	0.77	0.982	0.873	0.77	0.982	CLONAL	1	TRUE	1	0.352530997456617	2		503	520	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56911053	56911053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	235	469	0	ENST00000519728.1:c.1199G>A	p.Arg400Lys	p.R400K	ENST00000519728	NM_002350.3	400	aGg/aAg	11/13	0.352530997456617	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.352530997456617	3		469	667	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021812	69021812	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	311	573	0	ENST00000288368.4:c.3100C>T	p.Gln1034Ter	p.Q1034*	ENST00000288368	NM_024870.2	1034	Cag/Tag	25/40	0.352530997456617	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.352530997456617	3		573	881	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76949351	76949351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	130	236	0	ENST00000373344.5:c.446G>A	p.Arg149Lys	p.R149K	ENST00000373344	NM_000489.3	149	aGa/aAa	6/35	0.120314781403936	2	FACETS	0.914	0.846	0.982			1	INDETERMINATE	3	TRUE	NA	0.352530997456617	2		236	269	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100349	8100349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	123	882	0	ENST00000346208.3:c.323C>A	p.Thr108Asn	p.T108N	ENST00000346208		108	aCc/aAc	3/6	0.711634613129771	3	FACETS	0.888	0.834	0.938	0.888	0.834	0.938	CLONAL	3	TRUE	0	0.711634613129771	3		882	176	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575479	64575480	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	rs1555165809	NA	P-0044471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	27	714	1	ENST00000312049.6:c.537_538delinsTT	p.Glu179_Asp180delinsAspTyr	p.E179_D180delinsDY	ENST00000312049	NM_130799.2	179	gaGGat/gaTTat	3/10	0.474781112176296	4	FACETS	0.991	0.801	1	0.496	0.4	0.601	CLONAL	1	TRUE	2	0.711634613129771	4		715	131	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679798	88679798	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs774739739	NA	P-0044471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	35	573	0	ENST00000360948.2:c.665G>T	p.Arg222Leu	p.R222L	ENST00000360948	NM_001012338.2	222	cGa/cTa	7/19	0.551244740598998	3	FACETS	0.959	0.8	1	0.48	0.4	0.566	CLONAL	1	TRUE	1	0.711634613129771	3		573	139	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857586	9857586	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	38	453	0	ENST00000330684.3:c.3815C>A	p.Ala1272Glu	p.A1272E	ENST00000330684	NM_001134407.1	1272	gCa/gAa	13/13	0.348493213623693	3	FACETS	0.823	0.706	0.943	0.548	0.47	0.629	INDETERMINATE	2	TRUE	0	0.711634613129771	3		453	88	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574000	7574000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	82	788	2	ENST00000269305.4:c.1027G>T	p.Glu343Ter	p.E343*	ENST00000269305	NM_001126112.2	343	Gag/Tag	10/11	0.627312018102341	2	FACETS	0.907	0.835	0.976	0.907	0.835	0.976	CLONAL	2	TRUE	0	0.711634613129771	2		790	127	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485770	40485771	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0044471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	60	496	0	ENST00000264657.5:c.969_970delinsTT	p.Glu324Ter	p.E324*	ENST00000264657	NM_139276.2	323	gtGGag/gtTTag	10/24	0.474781112176296	4	FACETS	0.789	0.692	0.889	0.789	0.692	0.889	SUBCLONAL	2	TRUE	2	0.711634613129771	4		496	183	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610198	10610198	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	67	888	0	ENST00000171111.5:c.512G>T	p.Cys171Phe	p.C171F	ENST00000171111	NM_203500.1	171	tGc/tTc	2/6	0.623924019896479	2	FACETS	0.785	0.709	0.859	0.785	0.709	0.859	SUBCLONAL	2	TRUE	0	0.711634613129771	2		888	120	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152019	11152019	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	73	572	0	ENST00000358026.2:c.4303G>T	p.Glu1435Ter	p.E1435*	ENST00000358026	NM_001128849.1	1435	Gag/Tag	31/36	0.623924019896479	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	0	0.711634613129771	2		572	101	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223713	36223713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	150	1008	1	ENST00000222270.7:c.6263C>T	p.Pro2088Leu	p.P2088L	ENST00000222270	NM_014727.1	2088	cCa/cTa	28/37	0.711634613129771	3	FACETS	0.899	0.85	0.945	0.899	0.85	0.945	CLONAL	3	TRUE	0	0.711634613129771	3		1009	212	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868193	45868193	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	82	996	0	ENST00000391945.4:c.497G>T	p.Arg166Leu	p.R166L	ENST00000391945	NM_000400.3	166	cGt/cTt	7/23	0.711634613129771	3	FACETS	0.835	0.754	0.918	0.557	0.503	0.612	CLONAL	2	TRUE	0	0.711634613129771	3		996	187	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215889	142215890	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0044471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	36	354	0	ENST00000350721.4:c.5703_5704delinsTT	p.Ala1902Ser	p.A1902S	ENST00000350721	NM_001184.3	1901	ctGGct/ctTTct	33/47	0.4951839421933	5	FACETS	1	0.897	1	0.719	0.609	0.833	CLONAL	2	TRUE	2	0.711634613129771	5		354	97	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500844	149500844	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	80	759	0	ENST00000261799.4:c.2386C>A	p.Pro796Thr	p.P796T	ENST00000261799	NM_002609.3	796	Cca/Aca	17/23	0.609560840685106	3	FACETS	0.847	0.78	0.91	0.847	0.78	0.91	CLONAL	3	TRUE	0	0.711634613129771	3		759	120	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056218	26056218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs527943061	NA	P-0044471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	38	500	0	ENST00000343677.2:c.439C>T	p.Pro147Ser	p.P147S	ENST00000343677	NM_005319.3	147	Ccg/Tcg	1/1	0.711634613129771	6	FACETS	1	0.923	1	0.24	0.2	0.284	CLONAL	1	TRUE	1	0.711634613129771	6		500	216	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945027	151945027	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	13	77	0	ENST00000262189.6:c.2492C>A	p.Thr831Asn	p.T831N	ENST00000262189	NM_170606.2	831	aCt/aAt	14/59	0.711634613129771	4	FACETS	1	0.848	1	0.625	0.461	0.811	CLONAL	1	TRUE	2	0.711634613129771	4		77	50	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273468	38273468	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	29	991	0	ENST00000425967.3:c.1867G>T	p.Glu623Ter	p.E623*	ENST00000425967	NM_001174067.1	623	Gag/Tag	14/19	0.348493213623693	3	FACETS	0.686	0.557	0.83	0.229	0.185	0.277	INDETERMINATE	1	TRUE	0	0.711634613129771	3		991	161	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485846	8485846	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs146684382	NA	P-0044471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	44	356	0	ENST00000356435.5:c.2971G>C	p.Asp991His	p.D991H	ENST00000356435		991	Gat/Cat	17/35	0.627312018102341	2	FACETS	0.824	0.729	0.917	0.824	0.729	0.917	CLONAL	2	TRUE	0	0.711634613129771	2		356	75	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518144	8518144	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	79	413	0	ENST00000356435.5:c.1247C>A	p.Ala416Glu	p.A416E	ENST00000356435		416	gCa/gAa	10/35	0.627312018102341	2	FACETS	0.903	0.829	0.973	0.903	0.829	0.973	CLONAL	2	TRUE	0	0.711634613129771	2		413	123	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	150	345	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.903	0.836	0.971			1	INDETERMINATE	2	TRUE	NA	0.44650368048531	2		345	372	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0044491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	166	489	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.187253550282542	2	FACETS	1	0.986	1	0.659	0.609	0.711	INDETERMINATE	1	TRUE	0	0.44650368048531	2		489	564	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	156	359	0	ENST00000335508.6:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000335508	NM_012433.2	902	Gaa/Aaa	18/25	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.44650368048531	2		359	494	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032138	26032138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	40	467	0	ENST00000244661.2:c.151G>A	p.Glu51Lys	p.E51K	ENST00000244661	NM_003537.3	51	Gag/Aag	1/1	1	2	FACETS	0.377	0.313	0.449	0.377	0.313	0.449	SUBCLONAL	1	TRUE	1	0.44650368048531	2		467	475	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057835	27057835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	145	855	1	ENST00000324856.7:c.1543C>T	p.Gln515Ter	p.Q515*	ENST00000324856	NM_006015.4	515	Cag/Tag	3/20	0.36021973101482	1	FACETS	0.554	0.505	0.605	0.554	0.505	0.605	SUBCLONAL	1	TRUE	0	0.44650368048531	1		856	911	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290207	15290207	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144559574	NA	P-0044491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	209	939	2	ENST00000263388.2:c.3428G>A	p.Arg1143His	p.R1143H	ENST00000263388	NM_000435.2	1143	cGc/cAc	21/33	1	2	FACETS	0.93	0.863	0.999	0.93	0.863	0.999	CLONAL	1	TRUE	1	0.44650368048531	2		941	1007	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849121	156849121	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	65	1030	0	ENST00000524377.1:c.2013G>C	p.Met671Ile	p.M671I	ENST00000524377	NM_002529.3	671	atG/atC	15/17	1	2	FACETS	0.26	0.225	0.299	0.26	0.225	0.299	SUBCLONAL	1	TRUE	1	0.44650368048531	2		1030	1118	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057775	27057775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	170	848	0	ENST00000324856.7:c.1483C>T	p.His495Tyr	p.H495Y	ENST00000324856	NM_006015.4	495	Cat/Tat	3/20	0.36021973101482	1	FACETS	0.598	0.549	0.649	0.598	0.549	0.649	SUBCLONAL	1	TRUE	0	0.44650368048531	1		848	989	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059213	27059213	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	78	515	0	ENST00000324856.7:c.1850C>A	p.Ser617Ter	p.S617*	ENST00000324856	NM_006015.4	617	tCa/tAa	4/20	0.36021973101482	1	FACETS	0.475	0.418	0.537	0.475	0.418	0.537	SUBCLONAL	1	TRUE	0	0.44650368048531	1		515	571	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274262	5274262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	91	881	1	ENST00000357368.4:c.185C>T	p.Pro62Leu	p.P62L	ENST00000357368	NM_002850.3	62	cCa/cTa	3/38	1	2	FACETS	0.39	0.346	0.439	0.39	0.346	0.439	SUBCLONAL	1	TRUE	1	0.44650368048531	2		882	1044	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288680	198288680	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	63	402	2	ENST00000335508.6:c.47G>T	p.Arg16Leu	p.R16L	ENST00000335508	NM_012433.2	16	cGa/cTa	2/25	NA	2	FACETS	0.523	0.452	0.599			1	INDETERMINATE	1	TRUE	NA	0.44650368048531	2		404	540	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546128	41546128	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377517076	NA	P-0044491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	145	493	0	ENST00000263253.7:c.2743C>T	p.Arg915Cys	p.R915C	ENST00000263253	NM_001429.3	915	Cgc/Tgc	14/31	0.36021973101482	1	FACETS	0.934	0.857	1	0.934	0.857	1	CLONAL	1	TRUE	0	0.44650368048531	1		493	540	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86676334	86676334	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	12	172	0	ENST00000274376.6:c.2612G>C	p.Arg871Thr	p.R871T	ENST00000274376	NM_002890.2	871	aGa/aCa	20/25	0.248365151093938	0	FACETS	0.207	0.145	0.281			1	INDETERMINATE	1	TRUE	0	0.44650368048531	0		172	144	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225786	26225786	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	28	450	0	ENST00000360408.1:c.404G>A	p.Arg135Lys	p.R135K	ENST00000360408	NM_003532.2	135	aGg/aAg	1/1	1	2	FACETS	0.23	0.183	0.283	0.23	0.183	0.283	SUBCLONAL	1	TRUE	1	0.44650368048531	2		450	546	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941877	44941878	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	107	172	0	ENST00000377967.4:c.3202dup	p.Ser1068PhefsTer3	p.S1068Ffs*3	ENST00000377967	NM_021140.2	1067	-/T	21/29	1	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.44650368048531	1		172	276	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264313	16264313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774985232	NA	P-0044503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	205	515	0	ENST00000375759.3:c.10516C>T	p.Pro3506Ser	p.P3506S	ENST00000375759	NM_015001.2	3506	Ccc/Tcc	13/15	0.351230900002832	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.351230900002832	4		515	669	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999282	100999282	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	350	943	0	ENST00000325455.5:c.520G>C	p.Asp174His	p.D174H	ENST00000325455	NM_001202474.3	174	Gac/Cac	1/8	0.351230900002832	5	FACETS	1	0.966	1			1	CLONAL	3	TRUE	NA	0.351230900002832	5		943	992	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284915	15284915	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	442	994	0	ENST00000263388.2:c.4700C>A	p.Pro1567His	p.P1567H	ENST00000263388	NM_000435.2	1567	cCc/cAc	25/33	0.351230900002832	4	FACETS	0.92	0.879	0.962	1	0.995	1	CLONAL	3	TRUE	2	0.351230900002832	4		994	1232	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907677	111907677	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	217	467	0	ENST00000393256.3:c.451G>T	p.Glu151Ter	p.E151*	ENST00000393256	NM_006538.4	151	Gag/Tag	3/4	0.351230900002832	5	FACETS	1	0.94	1	1	0.94	1	CLONAL	3	TRUE	2	0.351230900002832	5		467	626	SUCCESS
APC	324	MSKCC	GRCh37	5	112179266	112179266	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	135	305	1	ENST00000257430.4:c.7975G>A	p.Val2659Met	p.V2659M	ENST00000257430	NM_000038.5	2659	Gtg/Atg	16/16	0.293757062366748	5	FACETS	1	0.959	1	1	0.959	1	CLONAL	3	TRUE	2	0.351230900002832	5		306	367	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117629985	117629985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	145	366	0	ENST00000368508.3:c.6541G>C	p.Glu2181Gln	p.E2181Q	ENST00000368508	NM_002944.2	2181	Gag/Cag	41/43	0.351230900002832	3	FACETS	0.917	0.848	0.986	1	0.987	1	CLONAL	3	TRUE	1	0.351230900002832	3		366	353	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247079	53247079	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	47	637	0	ENST00000375401.3:c.421C>T	p.Leu141Phe	p.L141F	ENST00000375401	NM_004187.3	141	Ctc/Ttc	4/26	0.16172374459136	4	FACETS	0.457	0.384	0.537	0.228	0.192	0.269	INDETERMINATE	1	TRUE	2	0.351230900002832	4		637	792	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	17	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.173	0.128	0.227	0.173	0.128	0.227	SUBCLONAL	1	TRUE	1	0.391716787704943	2		485	501	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0044510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	24	366	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.186	0.145	0.234	0.186	0.145	0.234	SUBCLONAL	1	TRUE	1	0.391716787704943	2		366	658	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344032	70344032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	88	715	5	ENST00000374080.3:c.1768C>T	p.Arg590Trp	p.R590W	ENST00000374080		590	Cgg/Tgg	13/45	0.207810114934482	1	FACETS	0.409	0.361	0.46	0.409	0.361	0.46	INDETERMINATE	1	TRUE	0	0.391716787704943	1		720	884	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907719	76907719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	43	468	0	ENST00000373344.5:c.4442G>A	p.Arg1481Gln	p.R1481Q	ENST00000373344	NM_000489.3	1481	cGg/cAg	15/35	0.207810114934482	1	FACETS	0.294	0.245	0.348	0.294	0.245	0.348	INDETERMINATE	1	TRUE	0	0.391716787704943	1		468	601	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38955712	38955712	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	41	335	0	ENST00000357387.3:c.2594G>A	p.Arg865His	p.R865H	ENST00000357387	NM_152756.3	865	cGt/cAt	26/38	1	2	FACETS	0.469	0.391	0.556	0.469	0.391	0.556	SUBCLONAL	1	TRUE	1	0.391716787704943	2		335	446	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883158	37883158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	157	836	0	ENST00000269571.5:c.3061G>A	p.Glu1021Lys	p.E1021K	ENST00000269571		1021	Gag/Aag	25/27	1	2	FACETS	0.725	0.663	0.791	0.725	0.663	0.791	SUBCLONAL	1	TRUE	1	0.391716787704943	2		836	1105	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355326	81355326	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	25	230	0	ENST00000222390.5:c.1048C>T	p.Arg350Ter	p.R350*	ENST00000222390	NM_000601.4	350	Cga/Tga	9/18	1	2	FACETS	0.381	0.3	0.474	0.381	0.3	0.474	SUBCLONAL	1	TRUE	1	0.391716787704943	2		230	335	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231286	46231286	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	38	287	0	ENST00000334344.6:c.1126G>T	p.Glu376Ter	p.E376*	ENST00000334344	NM_152641.2	376	Gaa/Taa	10/21	1	2	FACETS	0.551	0.457	0.656	0.551	0.457	0.656	SUBCLONAL	1	TRUE	1	0.391716787704943	2		287	352	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246330	46246331	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0044510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	57	311	0	ENST00000334344.6:c.4424_4425del	p.Thr1475IlefsTer27	p.T1475Ifs*27	ENST00000334344	NM_152641.2	1475	aCC/a	15/21	1	2	FACETS	0.666	0.573	0.767	0.666	0.573	0.767	SUBCLONAL	1	TRUE	1	0.391716787704943	2		311	437	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514617	103514617	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	37	382	0	ENST00000355739.4:c.1118A>C	p.Asn373Thr	p.N373T	ENST00000355739	NM_000123.3	373	aAc/aCc	8/15	0.256503833499561	3	FACETS	0.417	0.343	0.5	0.208	0.171	0.25	SUBCLONAL	1	TRUE	1	0.391716787704943	3		382	542	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521871	157521872	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0044510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	76	392	0	ENST00000346085.5:c.4148dup	p.Ala1384SerfsTer75	p.A1384Sfs*75	ENST00000346085	NM_020732.3	1381	-/C	18/20	1	2	FACETS	0.582	0.51	0.659	0.582	0.51	0.659	SUBCLONAL	1	TRUE	1	0.391716787704943	2		392	667	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0044551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	70	571	0				ENST00000310581	NM_198253.2	-/1132			0.31258322654745	3	FACETS	0.996	0.9	1	1	0.985	1	CLONAL	4	TRUE	1	0.31258322654745	3		571	130	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789685	3789685	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	21	440	14	ENST00000262367.5:c.4174C>T	p.Arg1392Ter	p.R1392*	ENST00000262367	NM_004380.2	1392	Cga/Tga	25/31	0.31258322654745	2	FACETS	1	0.854	1	0.565	0.441	0.704	CLONAL	1	TRUE	0	0.31258322654745	2		454	119	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0044565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	37	732	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.237	0.195	0.285	0.237	0.195	0.285	SUBCLONAL	1	TRUE	1	0.424975763229001	2		735	734	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs1057519842	NA	P-0044565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	33	313	0	ENST00000274335.5:c.1727_1729del	p.Thr576del	p.T576del	ENST00000274335		575	aaGACg/aag	12/15	1	2	FACETS	0.547	0.447	0.659	0.547	0.447	0.659	SUBCLONAL	1	TRUE	1	0.424975763229001	2		313	284	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589586	67589591	+	inframe_deletion	In_Frame_Del	DEL	ATGAAT	ATGAAT	-	novel	NA	P-0044565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	13	269	0	ENST00000274335.5:c.1351_1356del	p.Glu451_Tyr452del	p.E451_Y452del	ENST00000274335		450	cATGAATat/cat	10/15	1	2	FACETS	0.312	0.223	0.421	0.312	0.223	0.421	SUBCLONAL	1	TRUE	1	0.424975763229001	2		269	196	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145645	11145645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	96	710	0	ENST00000358026.2:c.4007G>A	p.Arg1336His	p.R1336H	ENST00000358026	NM_001128849.1	1336	cGc/cAc	29/36	1	2	FACETS	0.473	0.42	0.529	0.473	0.42	0.529	SUBCLONAL	1	TRUE	1	0.424975763229001	2		710	956	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845573	72845574	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0044565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	111	681	1	ENST00000268489.5:c.3766dup	p.Leu1256ProfsTer25	p.L1256Pfs*25	ENST00000268489	NM_006885.3	1256	ctg/cCtg	7/10	1	2	FACETS	0.535	0.48	0.593	0.535	0.48	0.593	SUBCLONAL	1	TRUE	1	0.424975763229001	2		682	977	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506462	148506462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587783626	NA	P-0044565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	25	307	0	ENST00000320356.2:c.2050C>T	p.Arg684Cys	p.R684C	ENST00000320356	NM_004456.4	684	Cgc/Tgc	18/20	1	2	FACETS	0.341	0.269	0.424	0.341	0.269	0.424	SUBCLONAL	1	TRUE	1	0.424975763229001	2		307	345	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138431133	138431133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	16	324	1	ENST00000289153.2:c.1316C>T	p.Ala439Val	p.A439V	ENST00000289153	NM_006219.2	439	gCg/gTg	8/22	1	2	FACETS	0.277	0.204	0.363	0.277	0.204	0.363	SUBCLONAL	1	TRUE	1	0.424975763229001	2		325	272	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097721	27097721	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	148	558	0	ENST00000324856.7:c.3310G>T	p.Glu1104Ter	p.E1104*	ENST00000324856	NM_006015.4	1104	Gaa/Taa	12/20	1	2	FACETS	0.98	0.897	1	0.98	0.897	1	CLONAL	1	TRUE	1	0.424975763229001	2		558	711	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141569579	141569582	+	frameshift_variant	Frame_Shift_Del	DEL	ACAA	ACAA	-	novel	NA	P-0044565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	75	467	0	ENST00000220592.5:c.702_705del	p.Cys235LysfsTer15	p.C235Kfs*15	ENST00000220592	NM_012154.3	234	gtTTGT/gt	6/19	0.424975763229001	3	FACETS	0.599	0.524	0.679	0.299	0.262	0.34	SUBCLONAL	1	TRUE	1	0.424975763229001	3		467	715	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874543	155874543	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	69	562	0	ENST00000368323.3:c.216C>A	p.Asp72Glu	p.D72E	ENST00000368323	NM_006912.5	72	gaC/gaA	4/6	0.412728944019193	3	FACETS	0.65	0.566	0.74	0.325	0.283	0.37	SUBCLONAL	1	TRUE	1	0.424975763229001	3		562	606	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692915	89692915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	63	480	0	ENST00000371953.3:c.400del	p.Met134Ter	p.M134*	ENST00000371953	NM_000314.4	133	gtA/gt	5/9	1	2	FACETS	0.743	0.645	0.848	0.743	0.645	0.848	SUBCLONAL	1	TRUE	1	0.424975763229001	2		480	399	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717731	89717732	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0044565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	110	419	0	ENST00000371953.3:c.757_758insAA	p.Ile253LysfsTer4	p.I253Kfs*4	ENST00000371953	NM_000314.4	252	-/AA	7/9	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.424975763229001	2		419	473	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052645	42052645	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	57	529	1	ENST00000219905.7:c.7316T>A	p.Met2439Lys	p.M2439K	ENST00000219905	NM_001164273.1	2439	aTg/aAg	20/24	1	2	FACETS	0.328	0.28	0.38	0.328	0.28	0.38	SUBCLONAL	1	TRUE	1	0.424975763229001	2		530	819	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	364544	364544	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs143974067	NA	P-0044565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	59	661	0	ENST00000262320.3:c.1018G>A	p.Val340Met	p.V340M	ENST00000262320	NM_003502.3	340	Gtg/Atg	3/11	1	2	FACETS	0.295	0.253	0.341	0.295	0.253	0.341	SUBCLONAL	1	TRUE	1	0.424975763229001	2		661	942	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222982	1222982	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	rs727504172	NA	P-0044565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	147	542	0	ENST00000326873.7:c.921-2A>C		p.X307_splice	ENST00000326873	NM_000455.4	307			1	2	FACETS	0.994	0.91	1	0.994	0.91	1	CLONAL	1	TRUE	1	0.424975763229001	2		542	696	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793101	42793101	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	52	813	1	ENST00000575354.2:c.996del	p.Ser333AlafsTer36	p.S333Afs*36	ENST00000575354	NM_015125.3	331	ccG/cc	7/20	1	2	FACETS	0.243	0.206	0.284	0.243	0.206	0.284	SUBCLONAL	1	TRUE	1	0.424975763229001	2		814	1006	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62320932	62320932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	63	757	0	ENST00000360203.5:c.1956G>A	p.Met652Ile	p.M652I	ENST00000360203	NM_001283009.1	652	atG/atA	23/35	1	2	FACETS	0.303	0.261	0.349	0.303	0.261	0.349	SUBCLONAL	1	TRUE	1	0.424975763229001	2		757	977	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971206	21971207	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0044565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	152	353	0	ENST00000304494.5:c.151_152del	p.Val51HisfsTer68	p.V51Hfs*68	ENST00000304494	NM_000077.4	51	GTc/c	2/3	0.419266182978728	2	FACETS	0.888	0.821	0.956	0.888	0.821	0.956	CLONAL	2	TRUE	0	0.424975763229001	2		353	403	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345961	70345961	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	46	645	0	ENST00000374080.3:c.2498T>C	p.Phe833Ser	p.F833S	ENST00000374080		833	tTc/tCc	18/45	1	2	FACETS	0.263	0.221	0.311	0.263	0.221	0.311	SUBCLONAL	1	TRUE	1	0.424975763229001	2		645	822	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0044574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	353	792	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.649989621253641	1	FACETS	0.941	0.897	0.985	0.941	0.897	0.985	CLONAL	1	TRUE	0	0.649989621253641	1		793	779	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0044574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	116	236	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.808	0.733	0.885	0.808	0.733	0.885	CLONAL	1	TRUE	1	0.649989621253641	2		236	442	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258744	115258744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434596	NA	P-0044574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	182	325	0	ENST00000369535.4:c.38G>A	p.Gly13Asp	p.G13D	ENST00000369535	NM_002524.4	13	gGt/gAt	2/7	1	2	FACETS	0.959	0.89	1	0.959	0.89	1	CLONAL	1	TRUE	1	0.649989621253641	2		325	584	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981792	70981792	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	332	667	1	ENST00000276594.2:c.304T>C	p.Tyr102His	p.Y102H	ENST00000276594	NM_024504.3	102	Tac/Cac	2/8	1	2	FACETS	0.979	0.927	1	0.979	0.927	1	CLONAL	1	TRUE	1	0.649989621253641	2		668	1043	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228998	36228998	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	365	593	1	ENST00000222270.7:c.7778G>A	p.Arg2593His	p.R2593H	ENST00000222270	NM_014727.1	2593	cGc/cAc	36/37	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.649989621253641	2		594	1104	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920419	114920419	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs750925453	NA	P-0044574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	234	409	0	ENST00000543371.1:c.1360G>T	p.Asp454Tyr	p.D454Y	ENST00000543371	NM_001198531.1	454	Gac/Tac	13/14	1	2	FACETS	0.892	0.835	0.951	0.892	0.835	0.951	CLONAL	1	TRUE	1	0.649989621253641	2		409	807	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	124	345	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.95	0.861	1	0.95	0.861	1	CLONAL	1	TRUE	1	0.399880021484569	2		345	653	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0044579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	395	529	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.386021343621703	3	FACETS	0.925	0.885	0.966	0.925	0.885	0.966	CLONAL	3	TRUE	0	0.399880021484569	3		529	854	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0044579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	209	772	4	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	NA	2	FACETS	1	0.933	1			1	INDETERMINATE	1	TRUE	NA	0.399880021484569	2		776	1039	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082307	16082307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1191742873	NA	P-0044579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	252	1017	1	ENST00000281043.3:c.121G>A	p.Asp41Asn	p.D41N	ENST00000281043	NM_005378.4	41	Gac/Aac	2/3	1	2	FACETS	0.938	0.876	1	0.938	0.876	1	CLONAL	1	TRUE	1	0.399880021484569	2		1018	1344	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879279	151879279	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0044579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	141	559	0	ENST00000262189.6:c.5666C>G	p.Ser1889Ter	p.S1889*	ENST00000262189	NM_170606.2	1889	tCa/tGa	36/59	1	2	FACETS	0.781	0.711	0.854	0.781	0.711	0.854	SUBCLONAL	1	TRUE	1	0.399880021484569	2		559	903	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917721	151917721	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0044579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	23	235	0	ENST00000262189.6:c.3599C>G	p.Ser1200Ter	p.S1200*	ENST00000262189	NM_170606.2	1200	tCa/tGa	23/59	1	2	FACETS	0.39	0.304	0.489	0.39	0.304	0.489	SUBCLONAL	1	TRUE	1	0.399880021484569	2		235	295	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097818	8097818	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	209	771	0	ENST00000346208.3:c.200C>G	p.Ser67Trp	p.S67W	ENST00000346208		67	tCg/tGg	2/6	1	2	FACETS	0.932	0.864	1	0.932	0.864	1	CLONAL	1	TRUE	1	0.399880021484569	2		771	1122	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098935	178098935	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	113	444	1	ENST00000397062.3:c.110T>C	p.Phe37Ser	p.F37S	ENST00000397062	NM_006164.4	37	tTt/tCt	2/5	1	2	FACETS	0.768	0.691	0.849	0.768	0.691	0.849	SUBCLONAL	1	TRUE	1	0.399880021484569	2		445	736	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152044	11152044	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886054155	NA	P-0044579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	213	741	0	ENST00000358026.2:c.4328G>A	p.Arg1443Gln	p.R1443Q	ENST00000358026	NM_001128849.1	1443	cGg/cAg	31/36	1	2	FACETS	0.946	0.878	1	0.946	0.878	1	CLONAL	1	TRUE	1	0.399880021484569	2		741	1126	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420613	49420614	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0044579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	210	786	0	ENST00000301067.7:c.15135dup	p.Pro5046AlafsTer26	p.P5046Afs*26	ENST00000301067	NM_003482.3	5045	-/G	48/54	1	2	FACETS	0.824	0.764	0.887	0.824	0.764	0.887	CLONAL	1	TRUE	1	0.399880021484569	2		786	1274	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435710	49435711	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0044579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	233	801	0	ENST00000301067.7:c.6172dup	p.Ala2058GlyfsTer10	p.A2058Gfs*10	ENST00000301067	NM_003482.3	2058	gcc/gGcc	29/54	1	2	FACETS	0.87	0.809	0.932	0.87	0.809	0.932	CLONAL	1	TRUE	1	0.399880021484569	2		801	1340	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832925	3832925	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	105	499	0	ENST00000262367.5:c.1333A>G	p.Ile445Val	p.I445V	ENST00000262367	NM_004380.2	445	Atc/Gtc	6/31	1	2	FACETS	0.767	0.687	0.851	0.767	0.687	0.851	SUBCLONAL	1	TRUE	1	0.399880021484569	2		499	685	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568611	41568611	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	143	657	2	ENST00000263253.7:c.4561G>A	p.Glu1521Lys	p.E1521K	ENST00000263253	NM_001429.3	1521	Gaa/Aaa	28/31	0.397002113807946	1	FACETS	0.811	0.74	0.884	0.811	0.74	0.884	CLONAL	1	TRUE	0	0.399880021484569	1		659	706	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157495219	157495219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	111	622	1	ENST00000346085.5:c.3103G>A	p.Glu1035Lys	p.E1035K	ENST00000346085	NM_020732.3	1035	Gaa/Aaa	11/20	1	2	FACETS	0.684	0.614	0.757	0.684	0.614	0.757	SUBCLONAL	1	TRUE	1	0.399880021484569	2		623	812	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0044581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	70	489	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.308	0.267	0.352	0.308	0.267	0.352	SUBCLONAL	1	TRUE	1	0.455210973051142	2		489	1000	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910685	29910685	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs199474408	NA	P-0044581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1475	139	1038	0	ENST00000376809.5:c.225G>A	p.Trp75Ter	p.W75*	ENST00000376809	NM_002116.7	75	tgG/tgA	2/8	0.455210973051142	2	FACETS	0.378	0.343	0.416	0.189	0.171	0.208	SUBCLONAL	1	TRUE	0	0.455210973051142	2		1038	1614	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917639	178917639	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	68	400	0	ENST00000263967.3:c.514G>C	p.Glu172Gln	p.E172Q	ENST00000263967	NM_006218.2	172	Gaa/Caa	3/21	0.455210973051142	5	FACETS	0.462	0.4	0.529	0.154	0.133	0.177	SUBCLONAL	1	TRUE	2	0.455210973051142	5		400	1088	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624426	21624426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	315	688	1	ENST00000421138.2:c.1603C>T	p.Pro535Ser	p.P535S	ENST00000421138		535	Ccc/Tcc	14/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.455210973051142	2		689	1352	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226447	41226447	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs878853294	NA	P-0044581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1386	109	860	1	ENST00000357654.3:c.4576G>T	p.Glu1526Ter	p.E1526*	ENST00000357654	NM_007294.3	1526	Gag/Tag	14/23	1	2	FACETS	0.32	0.286	0.357	0.32	0.286	0.357	SUBCLONAL	1	TRUE	1	0.455210973051142	2		861	1495	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427743	49427743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	352	829	0	ENST00000301067.7:c.10745G>A	p.Arg3582Gln	p.R3582Q	ENST00000301067	NM_003482.3	3582	cGg/cAg	39/54	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.455210973051142	2		829	1487	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412685	63412685	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1212	93	765	1	ENST00000330258.3:c.482C>G	p.Ser161Cys	p.S161C	ENST00000330258	NM_152424.3	161	tCt/tGt	2/2	0.191807293063575	2	FACETS	0.313	0.277	0.352	0.157	0.138	0.176	INDETERMINATE	1	TRUE	0	0.455210973051142	2		766	1305	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425839	49425839	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	90	751	0	ENST00000301067.7:c.12649C>T	p.Gln4217Ter	p.Q4217*	ENST00000301067	NM_003482.3	4217	Cag/Tag	39/54	1	2	FACETS	0.305	0.269	0.343	0.305	0.269	0.343	SUBCLONAL	1	TRUE	1	0.455210973051142	2		751	1297	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527943	157527943	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	121	719	0	ENST00000346085.5:c.5668G>C	p.Glu1890Gln	p.E1890Q	ENST00000346085	NM_020732.3	1890	Gaa/Caa	20/20	1	2	FACETS	0.396	0.357	0.439	0.396	0.357	0.439	SUBCLONAL	1	TRUE	1	0.455210973051142	2		719	1341	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902413	1902413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	145	736	0	ENST00000382891.5:c.32C>T	p.Ser11Phe	p.S11F	ENST00000382891	NM_133335.3	11	tCt/tTt	2/22	1	2	FACETS	0.496	0.451	0.543	0.496	0.451	0.543	SUBCLONAL	1	TRUE	1	0.455210973051142	2		736	1285	SUCCESS
EED	8726	MSKCC	GRCh37	11	85966323	85966341	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGCTGATGTATCCTTTCCT	TGCTGATGTATCCTTTCCT	CC	novel	NA	P-0044581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	73	315	2	ENST00000263360.6:c.420_426+12delinsCC		p.X140_splice	ENST00000263360	NM_003797.3	140		4/12	0.455210973051142	1	FACETS	0.528	0.463	0.598	0.528	0.463	0.598	SUBCLONAL	1	TRUE	0	0.455210973051142	1		317	469	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830336	72830336	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	70	523	0	ENST00000268489.5:c.6245C>T	p.Ser2082Leu	p.S2082L	ENST00000268489	NM_006885.3	2082	tCa/tTa	9/10	1	2	FACETS	0.346	0.301	0.395	0.346	0.301	0.395	SUBCLONAL	1	TRUE	1	0.455210973051142	2		523	889	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226444	41226444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80357237	NA	P-0044581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1404	105	876	0	ENST00000357654.3:c.4579G>A	p.Glu1527Lys	p.E1527K	ENST00000357654	NM_007294.3	1527	Gag/Aag	14/23	1	2	FACETS	0.306	0.272	0.341	0.306	0.272	0.341	SUBCLONAL	1	TRUE	1	0.455210973051142	2		876	1509	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117188	7117188	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1534	107	783	1	ENST00000302850.5:c.4028G>T	p.Arg1343Leu	p.R1343L	ENST00000302850	NM_000208.2	1343	cGg/cTg	22/22	0.344066226490493	3	FACETS	0.352	0.314	0.392	0.176	0.157	0.196	SUBCLONAL	1	TRUE	1	0.455210973051142	3		784	1641	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728557	190728557	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	64	522	0	ENST00000441310.2:c.1945G>C	p.Asp649His	p.D649H	ENST00000441310	NM_000534.4	649	Gat/Cat	10/13	1	2	FACETS	0.251	0.216	0.289	0.251	0.216	0.289	SUBCLONAL	1	TRUE	1	0.455210973051142	2		522	1122	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502759	186502759	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1480206121	NA	P-0044581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1354	250	453	0	ENST00000323963.5:c.217G>A	p.Val73Met	p.V73M	ENST00000323963		73	Gtg/Atg	4/11	0.455210973051142	5	FACETS	1	0.982	1	0.384	0.358	0.411	CLONAL	1	TRUE	2	0.455210973051142	5		453	1604	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163848	32163848	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	197	673	2	ENST00000375023.3:c.5378G>T	p.Arg1793Leu	p.R1793L	ENST00000375023	NM_004557.3	1793	cGa/cTa	30/30	0.455210973051142	2	FACETS	0.763	0.705	0.822	0.381	0.352	0.411	SUBCLONAL	1	TRUE	0	0.455210973051142	2		675	1135	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528514	157528514	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1266	103	798	0	ENST00000346085.5:c.6239G>C	p.Arg2080Thr	p.R2080T	ENST00000346085	NM_020732.3	2080	aGa/aCa	20/20	1	2	FACETS	0.331	0.294	0.369	0.331	0.294	0.369	SUBCLONAL	1	TRUE	1	0.455210973051142	2		798	1369	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873585	151873585	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	93	622	0	ENST00000262189.6:c.8953C>T	p.Gln2985Ter	p.Q2985*	ENST00000262189	NM_170606.2	2985	Cag/Tag	38/59	0.455210973051142	1	FACETS	0.348	0.308	0.39	0.348	0.308	0.39	SUBCLONAL	1	TRUE	0	0.455210973051142	1		622	908	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389303	8389303	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1257	121	747	0	ENST00000356435.5:c.4315T>G	p.Phe1439Val	p.F1439V	ENST00000356435		1439	Ttt/Gtt	26/35	0.344066226490493	3	FACETS	0.474	0.426	0.524	0.237	0.213	0.262	SUBCLONAL	1	TRUE	1	0.455210973051142	3		747	1378	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500945	8500945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	76	553	0	ENST00000356435.5:c.1937C>G	p.Ser646Cys	p.S646C	ENST00000356435		646	tCc/tGc	13/35	0.344066226490493	3	FACETS	0.331	0.289	0.376	0.165	0.144	0.188	SUBCLONAL	1	TRUE	1	0.455210973051142	3		553	1239	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0044586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	124	437	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.694	0.631	0.761	0.694	0.631	0.761	SUBCLONAL	1	TRUE	1	0.644708706859986	2		437	554	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0044586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	27	206	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.145	0.114	0.179	0.145	0.114	0.179	SUBCLONAL	1	TRUE	1	0.644708706859986	2		206	579	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0044586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	36	530	2	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	1	2	FACETS	0.14	0.114	0.169	0.14	0.114	0.169	SUBCLONAL	1	TRUE	1	0.644708706859986	2		532	798	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	93	485	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	1	2	FACETS	0.28	0.248	0.315	0.28	0.248	0.315	SUBCLONAL	1	TRUE	1	0.644708706859986	2		485	1029	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911679	32911679	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876657678	NA	P-0044586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	26	609	0	ENST00000380152.3:c.3187C>T	p.Gln1063Ter	p.Q1063*	ENST00000380152		1063	Cag/Tag	11/27	1	2	FACETS	0.175	0.138	0.217	0.175	0.138	0.217	SUBCLONAL	1	TRUE	1	0.644708706859986	2		609	462	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755539	133755539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	54	628	0	ENST00000318560.5:c.1508C>T	p.Ser503Leu	p.S503L	ENST00000318560	NM_005157.4	503	tCa/tTa	9/11	1	2	FACETS	0.175	0.149	0.205	0.175	0.149	0.205	SUBCLONAL	1	TRUE	1	0.644708706859986	2		628	955	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982387	201982387	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1462	89	939	0	ENST00000359651.3:c.766G>A	p.Glu256Lys	p.E256K	ENST00000359651		256	Gag/Aag	6/8	1	2	FACETS	0.178	0.157	0.201	0.178	0.157	0.201	SUBCLONAL	1	TRUE	1	0.644708706859986	2		939	1551	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941696	48941697	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0044586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	50	323	0	ENST00000267163.4:c.1009_1010del	p.Leu337GlyfsTer3	p.L337Gfs*3	ENST00000267163	NM_000321.2	336	TTt/t	10/27	1	2	FACETS	0.533	0.455	0.617	0.533	0.455	0.617	SUBCLONAL	1	TRUE	1	0.644708706859986	2		323	291	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5206850	5206850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	57	749	0	ENST00000357368.4:c.5782G>A	p.Glu1928Lys	p.E1928K	ENST00000357368	NM_002850.3	1928	Gag/Aag	38/38	1	2	FACETS	0.168	0.143	0.195	0.168	0.143	0.195	SUBCLONAL	1	TRUE	1	0.644708706859986	2		749	1054	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225367698	225367698	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	29	523	1	ENST00000264414.4:c.1469A>C	p.His490Pro	p.H490P	ENST00000264414	NM_003590.4	490	cAt/cCt	10/16	1	2	FACETS	0.19	0.152	0.234	0.19	0.152	0.234	SUBCLONAL	1	TRUE	1	0.644708706859986	2		524	473	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937049	178937049	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	22	396	0	ENST00000263967.3:c.1730G>C	p.Arg577Thr	p.R577T	ENST00000263967	NM_006218.2	577	aGa/aCa	11/21	1	2	FACETS	0.175	0.135	0.222	0.175	0.135	0.222	SUBCLONAL	1	TRUE	1	0.644708706859986	2		396	389	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950583	38950583	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	83	544	1	ENST00000357387.3:c.3367G>A	p.Glu1123Lys	p.E1123K	ENST00000357387	NM_152756.3	1123	Gaa/Aaa	31/38	0.644708706859986	3	FACETS	0.423	0.373	0.478	0.212	0.186	0.239	SUBCLONAL	1	TRUE	1	0.644708706859986	3		545	804	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686291	117686291	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	46	396	0	ENST00000368508.3:c.3050C>G	p.Ser1017Cys	p.S1017C	ENST00000368508	NM_002944.2	1017	tCt/tGt	20/43	1	2	FACETS	0.355	0.299	0.416	0.355	0.299	0.416	SUBCLONAL	1	TRUE	1	0.644708706859986	2		396	402	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411726	139411726	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs377535397	NA	P-0044604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	98	488	1	ENST00000277541.6:c.1553C>T	p.Thr518Met	p.T518M	ENST00000277541	NM_017617.3	518	aCg/aTg	9/34	0.279219142829024	3	FACETS	1	0.925	1	0.516	0.464	0.569	INDETERMINATE	1	TRUE	1	0.751353133393544	3		489	348	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577290	64577290	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886039413	NA	P-0044604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	326	679	0	ENST00000312049.6:c.292C>T	p.Arg98Ter	p.R98*	ENST00000312049	NM_130799.2	98	Cga/Tga	2/10	0.703066786256046	2	FACETS	0.893	0.858	0.926	0.893	0.858	0.926	CLONAL	2	TRUE	0	0.751353133393544	2		679	486	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287316	33287325	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGATTGCT	TCTGATTGCT	-	novel	NA	P-0044604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	142	381	0	ENST00000374542.5:c.1772_1781del	p.Lys591ArgfsTer8	p.K591Rfs*8	ENST00000374542	NM_001141970.1	591	aAGCAATCAGAg/ag	6/8	0.675877907660198	2	FACETS	0.964	0.912	1	0.964	0.912	1	CLONAL	2	TRUE	0	0.751353133393544	2		381	196	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	30	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.806	0.649	0.985	0.806	0.649	0.985	CLONAL	1	TRUE	1	0.16	2		485	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0044608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	74	456	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.16	2		456	907	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0044608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	55	572	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.876	0.748	1	0.876	0.748	1	CLONAL	1	TRUE	1	0.16	2		572	785	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22412934	22412934	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	46	136	0	ENST00000344548.3:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000344548	NM_001039802.1	61	Caa/Aaa	5/7	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		136	176	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87338617	87338617	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	236	407	0	ENST00000277120.3:c.713A>G	p.Lys238Arg	p.K238R	ENST00000277120		238	aAa/aGa	7/19	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.82622751889551	2		407	567	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533763	63533763	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777283610	NA	P-0044780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	114	643	0	ENST00000307078.5:c.1391C>T	p.Ser464Phe	p.S464F	ENST00000307078	NM_004655.3	464	tCc/tTc	6/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.292088687299072	2		643	727	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937422	178937422	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	39	195	0	ENST00000263967.3:c.1810T>C	p.Cys604Arg	p.C604R	ENST00000263967	NM_006218.2	604	Tgt/Cgt	12/21	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.292088687299072	2		195	208	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492687	56492687	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	78	443	0	ENST00000267101.3:c.2837A>T	p.Lys946Met	p.K946M	ENST00000267101	NM_001982.3	946	aAg/aTg	23/28	1	2	FACETS	0.93	0.819	1	0.93	0.819	1	CLONAL	1	TRUE	1	0.292088687299072	2		443	574	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183756	10183757	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	122	613	0	ENST00000256474.2:c.227dup	p.Cys77LeufsTer55	p.C77Lfs*55	ENST00000256474	NM_000551.3	75	-/T	1/3	0.292088687299072	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.292088687299072	1		613	623	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702517	52702517	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0044780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	32	209	0	ENST00000394830.3:c.381T>G	p.Tyr127Ter	p.Y127*	ENST00000394830	NM_018313.4	127	taT/taG	4/30	0.292088687299072	1	FACETS	0.761	0.621	0.917	0.761	0.621	0.917	CLONAL	1	TRUE	0	0.292088687299072	1		209	246	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267482	198267483	+	missense_variant	Missense_Mutation	DNP	AC	AC	GA	novel	NA	P-0044787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	89	305	0	ENST00000335508.6:c.1874_1875delinsTC	p.Arg625Leu	p.R625L	ENST00000335508	NM_012433.2	625	cGT/cTC	14/25	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.568146076708772	2		305	270	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	69	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.946	0.827	1	0.946	0.827	1	CLONAL	1	TRUE	1	0.319162967134776	2		473	457	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717650	89717650	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs1057520900	NA	P-0044802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	90	439	0	ENST00000371953.3:c.675T>G	p.Tyr225Ter	p.Y225*	ENST00000371953	NM_000314.4	225	taT/taG	7/9	1	2	FACETS	0.834	0.741	0.934	0.834	0.741	0.934	CLONAL	1	TRUE	1	0.319162967134776	2		439	676	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690837	89690837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	29	267	0	ENST00000371953.3:c.245del	p.Asn82IlefsTer17	p.N82Ifs*17	ENST00000371953	NM_000314.4	82	Aat/at	4/9	1	2	FACETS	0.455	0.365	0.558	0.455	0.365	0.558	SUBCLONAL	1	TRUE	1	0.319162967134776	2		267	399	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	97	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.996	0.891	1	0.996	0.891	1	CLONAL	1	TRUE	1	0.36	2		288	541	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	66	662	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.509	0.441	0.582	0.509	0.441	0.582	SUBCLONAL	1	TRUE	1	0.36	2		663	721	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	47	482	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.483	0.407	0.566	0.483	0.407	0.566	SUBCLONAL	1	TRUE	1	0.36	2		484	541	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437565	56437566	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	142	520	0	ENST00000407977.2:c.896_897del	p.Val299GlyfsTer143	p.V299Gfs*143	ENST00000407977		299	gTG/g	8/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.36	2		520	716	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480582	120480582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368918146	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	99	452	0	ENST00000256646.2:c.3235G>A	p.Val1079Ile	p.V1079I	ENST00000256646	NM_024408.3	1079	Gtt/Att	20/34	1	2	FACETS	0.975	0.873	1	0.975	0.873	1	CLONAL	1	TRUE	1	0.36	2		452	564	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965666	90965666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	85	315	1	ENST00000265433.3:c.1651del	p.Arg551GlyfsTer8	p.R551Gfs*8	ENST00000265433	NM_002485.4	551	Agg/gg	11/16	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.36	2		316	435	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	74	327	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.941	0.827	1	0.941	0.827	1	CLONAL	1	TRUE	1	0.36	2		328	437	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	121	632	4	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.36	2		636	638	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	65	299	0	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	1	2	FACETS	0.926	0.806	1	0.926	0.806	1	CLONAL	1	TRUE	1	0.36	2		299	390	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169362	11169362	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	99	404	0	ENST00000361445.4:c.7513C>T	p.Arg2505Ter	p.R2505*	ENST00000361445	NM_004958.3	2505	Cga/Tga	56/58	1	2	FACETS	0.972	0.87	1	0.972	0.87	1	CLONAL	1	TRUE	1	0.36	2		404	566	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574678	41574679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs754418509	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	172	728	0	ENST00000263253.7:c.6970dup	p.His2324ProfsTer55	p.H2324Pfs*55	ENST00000263253	NM_001429.3	2321	-/C	31/31	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.36	2		728	757	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138645	55138645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1031763557	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	119	414	0	ENST00000257290.5:c.1322C>T	p.Pro441Leu	p.P441L	ENST00000257290	NM_006206.4	441	cCg/cTg	9/23	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.36	2		414	586	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201671	66201671	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773217274	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	93	369	0	ENST00000273854.3:c.2831C>T	p.Thr944Met	p.T944M	ENST00000273854	NM_004439.5	944	aCg/aTg	16/18	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.36	2		369	448	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911443	32911443	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359365	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	70	339	0	ENST00000380152.3:c.2957del	p.Asn986IlefsTer5	p.N986Ifs*5	ENST00000380152		984	gAa/ga	11/27	1	2	FACETS	0.992	0.869	1	0.992	0.869	1	CLONAL	1	TRUE	1	0.36	2		339	392	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	143	485	6	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.36	2		491	543	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740623	58740624	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs763475304	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	107	562	0	ENST00000305921.3:c.1535dup	p.Asn512LysfsTer16	p.N512Kfs*16	ENST00000305921	NM_003620.3	510	caa/cAaa	6/6	1	2	FACETS	0.879	0.79	0.974	0.879	0.79	0.974	CLONAL	1	TRUE	1	0.36	2		562	676	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	136	711	0	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	0.976	0.888	1	0.976	0.888	1	CLONAL	1	TRUE	1	0.36	2		711	774	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120115	70120115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	17	139	0	ENST00000245479.2:c.1121del	p.Pro374ArgfsTer9	p.P374Rfs*9	ENST00000245479	NM_000346.3	373	Ccc/cc	3/3	1	2	FACETS	0.787	0.594	1	0.787	0.594	1	CLONAL	1	TRUE	1	0.36	2		139	120	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513282	44513287	+	inframe_deletion	In_Frame_Del	DEL	CCACCG	CCACCG	-	rs745888281	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	97	591	1	ENST00000291552.4:c.648_653del	p.Gly222_Gly223del	p.G222_G223del	ENST00000291552	NM_006758.2	216	ggCGGTGGt/ggt	8/8	0.103469305284551	3	FACETS	0.975	0.871	1	0.488	0.435	0.544	INDETERMINATE	1	TRUE	1	0.36	3		592	652	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214592	5214592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369295620	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	157	780	0	ENST00000357368.4:c.4474C>T	p.Arg1492Trp	p.R1492W	ENST00000357368	NM_002850.3	1492	Cgg/Tgg	29/38	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.36	2		780	688	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845640	72845640	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148354034	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	141	554	0	ENST00000268489.5:c.3700G>A	p.Asp1234Asn	p.D1234N	ENST00000268489	NM_006885.3	1234	Gat/Aat	7/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.36	2		554	734	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337603	73337603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	47	172	0	ENST00000377767.4:c.2113G>A	p.Ala705Thr	p.A705T	ENST00000377767	NM_014953.3	705	Gca/Aca	16/21	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.36	2		172	255	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151290	202151290	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	27	306	0	ENST00000358485.4:c.1596del	p.Lys532AsnfsTer73	p.K532Nfs*73	ENST00000358485	NM_001080125.1	530	agA/ag	9/9	1	2	FACETS	0.289	0.229	0.358	0.289	0.229	0.358	SUBCLONAL	1	TRUE	1	0.36	2		306	519	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955112	17955112	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755706305	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	162	721	5	ENST00000458235.1:c.115del	p.Gln39SerfsTer108	p.Q39Sfs*108	ENST00000458235	NM_000215.3	39	Cag/ag	2/24	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.36	2		726	787	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439919	56439919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	176	509	1	ENST00000407977.2:c.673del	p.Arg225AlafsTer194	p.R225Afs*194	ENST00000407977		225	Cgc/gc	6/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.36	2		510	759	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259480	16259480	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	100	317	0	ENST00000375759.3:c.6750del	p.Ala2251GlnfsTer102	p.A2251Qfs*102	ENST00000375759	NM_015001.2	2249	Ccc/cc	11/15	1	2	FACETS	0.999	0.895	1	0.999	0.895	1	CLONAL	1	TRUE	1	0.36	2		317	556	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138135	2138135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201206500	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	145	790	1	ENST00000219476.3:c.5155G>A	p.Ala1719Thr	p.A1719T	ENST00000219476	NM_000548.3	1719	Gca/Aca	40/42	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.36	2		791	716	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119909	70119910	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	62	514	1	ENST00000245479.2:c.916dup	p.Val306GlyfsTer272	p.V306Gfs*272	ENST00000245479	NM_000346.3	304	ccg/ccGg	3/3	1	2	FACETS	0.523	0.452	0.602	0.523	0.452	0.602	SUBCLONAL	1	TRUE	1	0.36	2		515	658	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741349	17741349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	136	663	0	ENST00000250003.3:c.20C>T	p.Pro7Leu	p.P7L	ENST00000250003	NM_002478.4	7	cCg/cTg	1/3	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.36	2		663	703	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	124	409	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.36	2		409	502	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457719	149457719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149911279	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	164	591	0	ENST00000286301.3:c.685G>A	p.Val229Ile	p.V229I	ENST00000286301	NM_005211.3	229	Gtt/Att	5/22	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.36	2		591	755	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158026	27158026	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	42	504	0	ENST00000380036.4:c.255del	p.Val86LeufsTer31	p.V86Lfs*31	ENST00000380036	NM_000459.3	84	Aaa/aa	2/23	1	2	FACETS	0.309	0.257	0.368	0.309	0.257	0.368	SUBCLONAL	1	TRUE	1	0.36	2		504	754	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339110	65339111	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	101	460	2	ENST00000342505.4:c.425dup	p.Ile143AspfsTer9	p.I143Dfs*9	ENST00000342505	NM_002227.2	142	aag/aaAg	5/25	1	2	FACETS	0.926	0.829	1	0.926	0.829	1	CLONAL	1	TRUE	1	0.36	2		462	606	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099427	157099432	+	inframe_deletion	In_Frame_Del	DEL	CAGCAG	CAGCAG	-	rs587779744	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	26	336	0	ENST00000346085.5:c.381_386del	p.Gln130_Gln131del	p.Q130_Q131del	ENST00000346085	NM_020732.3	122	CAGCAG/-	1/20	1	2	FACETS	0.486	0.386	0.601	0.486	0.386	0.601	SUBCLONAL	1	TRUE	1	0.36	2		336	297	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207672	2207672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	126	548	0	ENST00000398665.3:c.956G>A	p.Arg319His	p.R319H	ENST00000398665	NM_032482.2	319	cGc/cAc	11/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.36	2		548	570	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495050	56495050	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758743468	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	179	589	0	ENST00000267101.3:c.3407G>A	p.Arg1136His	p.R1136H	ENST00000267101	NM_001982.3	1136	cGc/cAc	27/28	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.36	2		589	703	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271295	18271295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754343201	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	141	593	0	ENST00000222254.8:c.337G>A	p.Asp113Asn	p.D113N	ENST00000222254	NM_005027.3	113	Gac/Aac	3/16	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.36	2		593	735	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941988	44941988	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	94	326	0	ENST00000377967.4:c.3241del	p.Thr1081ProfsTer2	p.T1081Pfs*2	ENST00000377967	NM_021140.2	1080	Aaa/aa	22/29	1	2	FACETS	0.841	0.749	0.938	0.841	0.749	0.938	CLONAL	1	TRUE	1	0.36	2		326	621	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460475	149460476	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs753211296	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	118	623	0	ENST00000286301.3:c.161dup	p.Ser55IlefsTer9	p.S55Ifs*9	ENST00000286301	NM_005211.3	54	cca/ccCa	3/22	1	2	FACETS	0.961	0.868	1	0.961	0.868	1	CLONAL	1	TRUE	1	0.36	2		623	682	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168677	56168678	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	112	366	0	ENST00000399503.3:c.1535dup	p.Ser513PhefsTer28	p.S513Ffs*28	ENST00000399503	NM_005921.1	511	tcc/tCcc	9/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.36	2		366	533	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161310419	161310419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778582853	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	34	379	0	ENST00000367975.2:c.215G>A	p.Arg72His	p.R72H	ENST00000367975	NM_003001.3	72	cGt/cAt	4/6	1	2	FACETS	0.293	0.238	0.354	0.293	0.238	0.354	SUBCLONAL	1	TRUE	1	0.36	2		379	645	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209276	133209276	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	52	733	0	ENST00000320574.5:c.6110C>A	p.Ala2037Asp	p.A2037D	ENST00000320574	NM_006231.2	2037	gCc/gAc	44/49	1	2	FACETS	0.395	0.335	0.46	0.395	0.335	0.46	SUBCLONAL	1	TRUE	1	0.36	2		733	732	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032349	10032349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	105	390	0	ENST00000330684.3:c.474G>A	p.Met158Ile	p.M158I	ENST00000330684	NM_001134407.1	158	atG/atA	3/13	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.36	2		390	481	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024380	16024380	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148932674	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	67	294	0	ENST00000268712.3:c.1838C>T	p.Pro613Leu	p.P613L	ENST00000268712	NM_006311.3	613	cCg/cTg	16/46	1	2	FACETS	0.862	0.751	0.98	0.862	0.751	0.98	CLONAL	1	TRUE	1	0.36	2		294	432	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094973	11094973	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	176	814	1	ENST00000358026.2:c.146C>A	p.Pro49Gln	p.P49Q	ENST00000358026	NM_001128849.1	49	cCg/cAg	2/36	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.36	2		815	752	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50138859	50138859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369588682	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	161	803	0	ENST00000246792.3:c.631G>A	p.Gly211Arg	p.G211R	ENST00000246792	NM_006270.3	211	Ggg/Agg	6/6	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.36	2		803	886	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028096	48028096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774755404	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	51	310	0	ENST00000234420.5:c.2974G>A	p.Glu992Lys	p.E992K	ENST00000234420	NM_000179.2	992	Gaa/Aaa	4/10	1	2	FACETS	0.781	0.666	0.905	0.781	0.666	0.905	CLONAL	1	TRUE	1	0.36	2		310	363	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29120999	29120999	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	130	410	0	ENST00000328354.6:c.558T>G	p.Asn186Lys	p.N186K	ENST00000328354	NM_007194.3	186	aaT/aaG	4/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.36	2		410	590	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648422	30648422	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	144	605	0	ENST00000295754.5:c.47T>C	p.Leu16Pro	p.L16P	ENST00000295754	NM_003242.5	16	cTg/cCg	1/7	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.36	2		605	614	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119634972	119634972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	63	278	0	ENST00000316626.5:c.527G>A	p.Gly176Glu	p.G176E	ENST00000316626		176	gGa/gAa	5/12	1	2	FACETS	0.895	0.778	1	0.895	0.778	1	CLONAL	1	TRUE	1	0.36	2		278	391	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156216	106156217	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1392160935	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	69	307	0	ENST00000380013.4:c.1121dup	p.Asn374LysfsTer2	p.N374Kfs*2	ENST00000380013	NM_001127208.2	373	caa/cAaa	3/11	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.36	2		307	377	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753129	57753129	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	95	311	0	ENST00000274289.3:c.887G>T	p.Arg296Met	p.R296M	ENST00000274289	NM_006622.3	296	aGg/aTg	7/14	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.36	2		311	438	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517963	176517963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201257476	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	124	625	0	ENST00000292408.4:c.461G>A	p.Arg154His	p.R154H	ENST00000292408	NM_213647.1	154	cGc/cAc	5/18	1	2	FACETS	0.966	0.875	1	0.966	0.875	1	CLONAL	1	TRUE	1	0.36	2		625	713	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163432	32163432	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	169	671	0	ENST00000375023.3:c.5794G>A	p.Gly1932Arg	p.G1932R	ENST00000375023	NM_004557.3	1932	Gga/Aga	30/30	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.36	2		671	745	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272341	38272341	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	130	555	0	ENST00000425967.3:c.2026G>A	p.Ala676Thr	p.A676T	ENST00000425967	NM_001174067.1	676	Gca/Aca	15/19	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.36	2		555	623	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90995030	90995030	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876658553	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	124	395	0	ENST00000265433.3:c.91T>C	p.Cys31Arg	p.C31R	ENST00000265433	NM_002485.4	31	Tgt/Cgt	2/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.36	2		395	627	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400110	139400110	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371068504	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	186	793	0	ENST00000277541.6:c.4238G>A	p.Arg1413His	p.R1413H	ENST00000277541	NM_017617.3	1413	cGt/cAt	25/34	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.36	2		793	853	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409111	139409111	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	134	752	0	ENST00000277541.6:c.2058del	p.Cys687AlafsTer85	p.C687Afs*85	ENST00000277541	NM_017617.3	686	ccC/cc	13/34	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.36	2		752	738	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285056	15285056	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774386192	NA	P-0044805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	138	736	0	ENST00000263388.2:c.4559C>T	p.Pro1520Leu	p.P1520L	ENST00000263388	NM_000435.2	1520	cCg/cTg	25/33	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.36	2		736	762	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0044817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	464	955	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.720733514886276	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.720733514886276	1		955	776	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674233	86674233	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1463885690	NA	P-0044817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	124	301	0	ENST00000274376.6:c.2365C>T	p.Arg789Ter	p.R789*	ENST00000274376	NM_002890.2	789	Cga/Tga	18/25	1	2	FACETS	0.885	0.808	0.963	0.885	0.808	0.963	CLONAL	1	TRUE	1	0.720733514886276	2		301	389	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435294	121435294	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	292	848	0	ENST00000257555.6:c.1327G>T	p.Ala443Ser	p.A443S	ENST00000257555		443	Gca/Tca	7/10	1	2	FACETS	0.97	0.916	1	0.97	0.916	1	CLONAL	1	TRUE	1	0.720733514886276	2		848	835	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016264	150016264	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	184	579	1	ENST00000253339.5:c.442C>T	p.Arg148Ter	p.R148*	ENST00000253339		148	Cga/Tga	2/7	0.720733514886276	1	FACETS	0.871	0.817	0.925	0.871	0.817	0.925	CLONAL	1	TRUE	0	0.720733514886276	1		580	375	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120879	115120879	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs978439271	NA	P-0044817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	223	651	0	ENST00000257566.3:c.127G>A	p.Ala43Thr	p.A43T	ENST00000257566	NM_016569.3	43	Gcg/Acg	1/8	1	2	FACETS	0.97	0.908	1	0.97	0.908	1	CLONAL	1	TRUE	1	0.720733514886276	2		651	638	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061291	38061291	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	332	779	0	ENST00000250448.2:c.698G>C	p.Arg233Pro	p.R233P	ENST00000250448	NM_004496.3	233	cGc/cCc	2/2	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.720733514886276	2		779	871	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975502	13975502	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	143	306	0	ENST00000405192.2:c.385C>A	p.Gln129Lys	p.Q129K	ENST00000405192	NM_001163147.1	129	Caa/Aaa	7/12	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.720733514886276	2		306	359	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0044831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	725	692	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.65003157643163	2	FACETS	0.982	0.956	1	0.982	0.956	1	CLONAL	2	TRUE	0	0.662330147571048	2		692	1115	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203666	94203666	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	92	233	0	ENST00000323929.3:c.988C>A	p.Gln330Lys	p.Q330K	ENST00000323929	NM_005591.3	330	Caa/Aaa	9/20	0.652886014483427	2	FACETS	0.855	0.767	0.946	0.427	0.383	0.473	CLONAL	1	TRUE	0	0.662330147571048	2		233	325	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435981	110435981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	451	760	1	ENST00000375856.3:c.2420C>T	p.Pro807Leu	p.P807L	ENST00000375856	NM_003749.2	807	cCc/cTc	1/2	1	2	FACETS	0.997	0.952	1	0.997	0.952	1	CLONAL	1	TRUE	1	0.662330147571048	2		761	1366	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	278	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.612140016254417	2	FACETS	0.934	0.891	0.978	0.934	0.891	0.978	CLONAL	2	TRUE	0	0.612140016254417	2		473	486	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0044851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	256	349	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.612140016254417	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.612140016254417	1		349	455	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395560	116395560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753407699	NA	P-0044851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	182	439	1	ENST00000397752.3:c.1853C>T	p.Thr618Met	p.T618M	ENST00000397752	NM_000245.2	618	aCg/aTg	6/21	0.612140016254417	3	FACETS	1	0.96	1	0.529	0.489	0.57	CLONAL	1	TRUE	1	0.612140016254417	3		440	734	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820605	3820605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147083140	NA	P-0044851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	429	864	0	ENST00000262367.5:c.2846C>T	p.Pro949Leu	p.P949L	ENST00000262367	NM_004380.2	949	cCg/cTg	14/31	0.23165915152676	3	FACETS	1	0.996	1	0.724	0.69	0.758	INDETERMINATE	1	TRUE	1	0.612140016254417	3		864	1265	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970971	21970971	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0044851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	428	804	0	ENST00000304494.5:c.387C>G	p.Tyr129Ter	p.Y129*	ENST00000304494	NM_000077.4	129	taC/taG	2/3	0.612140016254417	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.612140016254417	1		804	790	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020604	14020604	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	157	394	0	ENST00000311895.7:c.575T>A	p.Leu192Gln	p.L192Q	ENST00000311895	NM_005236.2	192	cTg/cAg	3/11	0.23165915152676	3	FACETS	1	0.988	1	0.71	0.655	0.765	INDETERMINATE	1	TRUE	1	0.612140016254417	3		394	472	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247165	153247165	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	147	310	0	ENST00000281708.4:c.1637C>A	p.Ser546Ter	p.S546*	ENST00000281708	NM_033632.3	546	tCa/tAa	10/12	0.207414881957878	2	FACETS	1	0.986	1	0.654	0.605	0.704	INDETERMINATE	1	TRUE	0	0.612140016254417	2		310	367	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403180	116403180	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	228	588	0	ENST00000397752.3:c.2441C>G	p.Pro814Arg	p.P814R	ENST00000397752	NM_000245.2	814	cCc/cGc	11/21	0.612140016254417	3	FACETS	1	0.95	1	0.512	0.477	0.547	CLONAL	1	TRUE	1	0.612140016254417	3		588	951	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410112	139410112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1409484433	NA	P-0044851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	493	1085	0	ENST00000277541.6:c.1726C>T	p.His576Tyr	p.H576Y	ENST00000277541	NM_017617.3	576	Cac/Tac	11/34	0.574934140064553	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.612140016254417	1		1085	952	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0044857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	159	251	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.539385269432532	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.554256023844311	2		251	274	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0044857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	107	349	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.86	0.776	0.948	0.86	0.776	0.948	CLONAL	1	TRUE	1	0.554256023844311	2		349	449	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023811	27023811	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1470097993	NA	P-0044857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	127	300	0	ENST00000324856.7:c.920del	p.Gly307AlafsTer56	p.G307Afs*56	ENST00000324856	NM_006015.4	306	cGg/cg	1/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.554256023844311	2		300	424	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338671	70338671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	181	513	1	ENST00000374080.3:c.67G>T	p.Asp23Tyr	p.D23Y	ENST00000374080		23	Gat/Tat	1/45	1	2	FACETS	0.955	0.884	1	0.955	0.884	1	CLONAL	1	TRUE	1	0.554256023844311	2		514	684	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589625	67589627	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	novel	NA	P-0044857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	38	171	0	ENST00000274335.5:c.1390_1392del	p.Asp464del	p.D464del	ENST00000274335		463	tATGat/tat	10/15	1	2	FACETS	0.766	0.641	0.902	0.766	0.641	0.902	CLONAL	1	TRUE	1	0.554256023844311	2		171	179	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242741	66242741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777294375	NA	P-0044857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	126	272	2	ENST00000273854.3:c.1831G>A	p.Ala611Thr	p.A611T	ENST00000273854	NM_004439.5	611	Gct/Act	9/18	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.554256023844311	2		274	390	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987130	69987130	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1328440915	NA	P-0044857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	196	411	0	ENST00000394351.3:c.191C>A	p.Pro64Gln	p.P64Q	ENST00000394351	NM_000248.3	64	cCg/cAg	2/9	1	2	FACETS	0.992	0.921	1	0.992	0.921	1	CLONAL	1	TRUE	1	0.554256023844311	2		411	713	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	100	345	0				ENST00000310581	NM_198253.2	-/1132			0.175590416935142	0	FACETS	0.373	0.338	0.409			1	INDETERMINATE	1	TRUE	0	0.665996354359175	0		345	269	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0044861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	341	685	0	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	0.665996354359175	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.665996354359175	1		685	674	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925523	114925523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780741000	NA	P-0044862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	319	659	1	ENST00000543371.1:c.1601C>T	p.Pro534Leu	p.P534L	ENST00000543371	NM_001198531.1	534	cCg/cTg	14/14	0.23096039280393	5	FACETS	0.847	0.806	0.889	0.847	0.806	0.889	INDETERMINATE	3	FALSE	2	0.808050494461792	5		660	687	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615546	43615546	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	234	600	0	ENST00000355710.3:c.2625G>C	p.Leu875Phe	p.L875F	ENST00000355710	NM_020975.4	875	ttG/ttC	15/20	0.23096039280393	5	FACETS	1	0.977	1	0.719	0.676	0.763	INDETERMINATE	2	FALSE	2	0.808050494461792	5		600	594	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348506	89348506	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs973573531	NA	P-0044862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	478	765	0	ENST00000301030.4:c.4444G>A	p.Asp1482Asn	p.D1482N	ENST00000301030	NM_001256183.1	1482	Gat/Aat	9/13	0.780389146515539	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	FALSE	2	0.808050494461792	4		765	1068	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713367	40713367	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	813	761	0	ENST00000373198.4:c.4148A>G	p.Gln1383Arg	p.Q1383R	ENST00000373198	NM_133170.3	1383	cAg/cGg	30/32	0.808050494461792	6	FACETS	1	0.98	1	1	0.98	1	CLONAL	4	FALSE	2	0.808050494461792	6		761	1307	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565832	55565832	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	106	532	0	ENST00000288135.5:c.656C>A	p.Ala219Glu	p.A219E	ENST00000288135	NM_000222.2	219	gCa/gAa	4/21	0.780389146515539	4	FACETS	0.735	0.66	0.815	0.368	0.33	0.408	SUBCLONAL	1	FALSE	2	0.808050494461792	4		532	645	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476794	140476794	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	217	462	0	ENST00000288602.6:c.1612T>G	p.Tyr538Asp	p.Y538D	ENST00000288602	NM_004333.4	538	Tat/Gat	13/18	0.765320808296924	4	FACETS	0.948	0.891	1	0.948	0.891	1	CLONAL	2	FALSE	2	0.808050494461792	4		462	512	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436956	49436957	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	T	novel	NA	P-0044862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	406	716	0	ENST00000301067.7:c.5546_5547delinsA	p.Gly1849GlufsTer3	p.G1849Efs*3	ENST00000301067	NM_003482.3	1849	gGG/gA	25/54	0.808050494461792	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	FALSE	0	0.808050494461792	2		716	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578393	7578393	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876660821	NA	P-0044883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	445	561	1	ENST00000269305.4:c.537T>G	p.His179Gln	p.H179Q	ENST00000269305	NM_001126112.2	179	caT/caG	5/11	0.452405703863319	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.452405703863319	2		562	884	SUCCESS
APC	324	MSKCC	GRCh37	5	112174502	112174502	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876659539	NA	P-0044883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	50	281	0	ENST00000257430.4:c.3211C>T	p.Gln1071Ter	p.Q1071*	ENST00000257430	NM_000038.5	1071	Caa/Taa	16/16	NA	2	FACETS	0.754	0.644	0.874			1	INDETERMINATE	1	TRUE	NA	0.452405703863319	2		281	293	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0044883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	35	168	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	NA	2	FACETS	0.723	0.597	0.861			1	INDETERMINATE	1	TRUE	NA	0.452405703863319	2		168	214	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513527	149513527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	169	569	1	ENST00000261799.4:c.676C>T	p.Arg226Cys	p.R226C	ENST00000261799	NM_002609.3	226	Cgc/Tgc	5/23	0.452405703863319	3	FACETS	0.881	0.809	0.956	0.44	0.404	0.478	CLONAL	1	TRUE	1	0.452405703863319	3		570	1040	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956781	68956781	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1320143244	NA	P-0044883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	194	604	0	ENST00000288368.4:c.899T>C	p.Ile300Thr	p.I300T	ENST00000288368	NM_024870.2	300	aTc/aCc	8/40	0.452405703863319	4	FACETS	0.953	0.88	1	0.318	0.293	0.343	CLONAL	1	TRUE	1	0.452405703863319	4		604	1307	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410621	63410621	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	126	653	0	ENST00000330258.3:c.2546A>C	p.His849Pro	p.H849P	ENST00000330258	NM_152424.3	849	cAt/cCt	2/2	0.17393945959886	4	FACETS	0.735	0.664	0.811	0.368	0.332	0.406	INDETERMINATE	1	TRUE	2	0.452405703863319	4		653	1100	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0044901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	86	311	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.337488178733373	3	FACETS	0.779	0.689	0.875	0.389	0.344	0.438	SUBCLONAL	1	TRUE	1	0.34913428178816	3		311	743	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936103	178936103	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	94	674	0	ENST00000263967.3:c.1645G>C	p.Asp549His	p.D549H	ENST00000263967	NM_006218.2	549	Gat/Cat	10/21	0.316581569118298	5	FACETS	0.897	0.797	1	0.224	0.199	0.251	CLONAL	1	TRUE	1	0.34913428178816	5		674	915	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946375	2946375	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	143	924	0	ENST00000396946.4:c.3362A>G	p.Glu1121Gly	p.E1121G	ENST00000396946	NM_032415.4	1121	gAa/gGa	25/25	0.274699283060285	4	FACETS	0.886	0.805	0.97	0.443	0.402	0.485	CLONAL	1	TRUE	2	0.34913428178816	4		924	1248	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348991	70348991	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	118	726	0	ENST00000374080.3:c.3503G>A	p.Gly1168Glu	p.G1168E	ENST00000374080		1168	gGg/gAg	25/45	0.25365824547367	2	FACETS	0.765	0.689	0.844	0.382	0.344	0.422	SUBCLONAL	1	TRUE	0	0.34913428178816	2		726	884	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966764	44966778	+	frameshift_variant	Frame_Shift_Del	DEL	TACTGTAGCATTTGT	TACTGTAGCATTTGT	C	novel	NA	P-0044901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	32	550	0	ENST00000377967.4:c.3988_4002delinsC	p.Tyr1330ArgfsTer6	p.Y1330Rfs*6	ENST00000377967	NM_021140.2	1330	TACTGTAGCATTTGT/C	27/29	0.25365824547367	2	FACETS	0.316	0.256	0.385	0.158	0.128	0.193	SUBCLONAL	1	TRUE	0	0.34913428178816	2		550	580	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	protein_altering_variant	In_Frame_Ins	INS	G	G	AAAAGATTCA	novel	NA	P-0044901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	175	453	0	ENST00000263967.3:c.1357delinsAAAAGATTCA	p.Glu453delinsLysArgPheLys	p.E453delinsKRFK	ENST00000263967	NM_006218.2	453	Gaa/AAAAGATTCAaa	8/21	0.316581569118298	5	FACETS	1	0.977	1	0.572	0.528	0.617	CLONAL	2	TRUE	1	0.34913428178816	5		453	668	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0044920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	66	307	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.328886862629231	1	FACETS	0.873	0.762	0.993	0.873	0.762	0.993	CLONAL	1	TRUE	0	0.328886862629231	1		307	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578444	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0044920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	168	711	0	ENST00000269305.4:c.486dup	p.Tyr163LeufsTer18	p.Y163Lfs*18	ENST00000269305	NM_001126112.2	162	-/C	5/11	0.328886862629231	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.328886862629231	1		711	731	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	130	529	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.463449461826186	4	FACETS	1	0.983	1	0.438	0.401	0.478	INDETERMINATE	1	TRUE	1	0.80919694990603	4		529	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	278	699	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.784299223205441	2	FACETS	0.976	0.943	1	0.976	0.943	1	CLONAL	2	TRUE	0	0.80919694990603	2		699	352	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	381	489	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.74300552639125	4	FACETS	0.878	0.843	0.912	0.878	0.843	0.912	CLONAL	3	TRUE	1	0.80919694990603	4		489	647	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	170	571	0				ENST00000310581	NM_198253.2	-/1132			0.12715641236862	5	FACETS	1	0.984	1	0.795	0.741	0.85	INDETERMINATE	2	TRUE	2	0.80919694990603	5		571	390	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057835	27057835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	315	855	1	ENST00000324856.7:c.1543C>T	p.Gln515Ter	p.Q515*	ENST00000324856	NM_006015.4	515	Cag/Tag	3/20	0.463449461826186	4	FACETS	1	0.991	1	0.771	0.735	0.807	INDETERMINATE	2	TRUE	1	0.80919694990603	4		856	609	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913381	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	311	509	0	ENST00000304494.5:c.322G>A	p.Asp108Asn	p.D108N	ENST00000304494	NM_000077.4	108	Gat/Aat	2/3	0.75629009962838	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.80919694990603	2		509	378	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930393	39930393	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	192	350	1	ENST00000378444.4:c.3071C>T	p.Ser1024Leu	p.S1024L	ENST00000378444	NM_001123385.1	1024	tCa/tTa	6/15	0.784299223205441	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.80919694990603	2		351	224	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242475	55242475	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057520037	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	157	398	0	ENST00000275493.2:c.2245G>C	p.Glu749Gln	p.E749Q	ENST00000275493	NM_005228.3	749	Gaa/Caa	19/28	0.763134281570426	3	FACETS	0.987	0.926	1	0.987	0.926	1	CLONAL	2	TRUE	1	0.80919694990603	3		398	276	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100915	41100915	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	173	593	0	ENST00000373198.4:c.1441G>A	p.Glu481Lys	p.E481K	ENST00000373198	NM_133170.3	481	Gag/Aag	8/32	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.80919694990603	2		593	332	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845922	156845922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	312	893	0	ENST00000524377.1:c.1552G>A	p.Glu518Lys	p.E518K	ENST00000524377	NM_002529.3	518	Gag/Aag	13/17	0.656292204200021	4	FACETS	0.924	0.877	0.972	0.924	0.877	0.972	CLONAL	2	TRUE	2	0.80919694990603	4		893	755	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41999952	41999952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	83	529	0	ENST00000219905.7:c.2215C>T	p.Pro739Ser	p.P739S	ENST00000219905	NM_001164273.1	739	Cca/Tca	6/24	1	2	FACETS	0.834	0.747	0.924	0.834	0.747	0.924	CLONAL	1	TRUE	1	0.80919694990603	2		529	246	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938567	44938567	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	200	448	0	ENST00000377967.4:c.3115C>T	p.Gln1039Ter	p.Q1039*	ENST00000377967	NM_021140.2	1039	Cag/Tag	20/29	0.784299223205441	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.80919694990603	2		448	241	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557373	187557373	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs874111	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	108	470	0	ENST00000441802.2:c.3989A>G	p.Asn1330Ser	p.N1330S	ENST00000441802	NM_005245.3	1330	aAt/aGt	6/27	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.80919694990603	2		470	252	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748601	40748601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200545231	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	67	421	0	ENST00000373198.4:c.2915G>A	p.Arg972Gln	p.R972Q	ENST00000373198	NM_133170.3	972	cGa/cAa	21/32	NA	2	FACETS	0.611	0.537	0.69			1	INDETERMINATE	1	TRUE	NA	0.80919694990603	2		421	271	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971003	21971003	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1563888963	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	413	594	0	ENST00000304494.5:c.355G>A	p.Glu119Lys	p.E119K	ENST00000304494	NM_000077.4	119	Gag/Aag	2/3	0.75629009962838	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.80919694990603	2		594	483	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242416	55242416	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	146	335	0	ENST00000275493.2:c.2186G>A	p.Gly729Glu	p.G729E	ENST00000275493	NM_005228.3	729	gGa/gAa	19/28	0.763134281570426	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.80919694990603	3		335	238	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123892056	123892056	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	263	428	0	ENST00000330479.4:c.865G>C	p.Glu289Gln	p.E289Q	ENST00000330479	NM_020382.3	289	Gag/Cag	8/9	0.690468813467861	4	FACETS	0.958	0.916	1	0.958	0.916	1	CLONAL	3	TRUE	1	0.80919694990603	4		428	409	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912933	32912933	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	79	531	0	ENST00000380152.3:c.4441G>C	p.Glu1481Gln	p.E1481Q	ENST00000380152		1481	Gag/Cag	11/27	1	2	FACETS	0.775	0.691	0.862	0.775	0.691	0.862	SUBCLONAL	1	TRUE	1	0.80919694990603	2		531	252	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914835	32914835	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	76	499	0	ENST00000380152.3:c.6343G>C	p.Glu2115Gln	p.E2115Q	ENST00000380152		2115	Gag/Cag	11/27	1	2	FACETS	0.831	0.741	0.925	0.831	0.741	0.925	CLONAL	1	TRUE	1	0.80919694990603	2		499	226	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915032	32915032	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs398122560	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	97	599	0	ENST00000380152.3:c.6540G>C	p.Leu2180Phe	p.L2180F	ENST00000380152		2180	ttG/ttC	11/27	1	2	FACETS	0.835	0.755	0.918	0.835	0.755	0.918	CLONAL	1	TRUE	1	0.80919694990603	2		599	287	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281598	49281598	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	122	763	0	ENST00000282018.3:c.645C>G	p.Phe215Leu	p.F215L	ENST00000282018	NM_020377.2	215	ttC/ttG	1/1	0.558605902345831	1	FACETS	0.549	0.503	0.596	0.549	0.503	0.596	SUBCLONAL	1	TRUE	0	0.80919694990603	1		763	327	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136365	2136365	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886051795	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	215	695	0	ENST00000219476.3:c.4834G>A	p.Asp1612Asn	p.D1612N	ENST00000219476	NM_000548.3	1612	Gat/Aat	37/42	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.80919694990603	2		695	439	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828391	72828391	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	166	554	0	ENST00000268489.5:c.8190C>G	p.Ile2730Met	p.I2730M	ENST00000268489	NM_006885.3	2730	atC/atG	9/10	0.631209241905602	3	FACETS	0.884	0.827	0.941	0.884	0.827	0.941	CLONAL	2	TRUE	1	0.80919694990603	3		554	326	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830235	72830235	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	129	416	0	ENST00000268489.5:c.6346C>T	p.Pro2116Ser	p.P2116S	ENST00000268489	NM_006885.3	2116	Ccg/Tcg	9/10	0.631209241905602	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.80919694990603	3		416	212	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16046958	16046958	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	183	416	0	ENST00000268712.3:c.1135G>C	p.Glu379Gln	p.E379Q	ENST00000268712	NM_006311.3	379	Gag/Cag	11/46	0.784299223205441	2	FACETS	0.95	0.909	0.989	0.95	0.909	0.989	CLONAL	2	TRUE	0	0.80919694990603	2		416	238	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369246	40369246	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	182	556	0	ENST00000293328.3:c.1312G>T	p.Glu438Ter	p.E438*	ENST00000293328	NM_012448.3	438	Gaa/Taa	11/19	0.763134281570426	3	FACETS	1	0.99	1	0.696	0.649	0.744	CLONAL	1	TRUE	1	0.80919694990603	3		556	454	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724549	724549	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	102	247	0	ENST00000314574.4:c.1507G>T	p.Glu503Ter	p.E503*	ENST00000314574	NM_005433.3	503	Gaa/Taa	12/12	0.656292204200021	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.80919694990603	4		247	183	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264644	46264644	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	60	286	0	ENST00000371998.3:c.1514C>G	p.Ser505Cys	p.S505C	ENST00000371998		505	tCt/tGt	12/23	0.763134281570426	3	FACETS	1	0.952	1	0.588	0.517	0.663	CLONAL	1	TRUE	1	0.80919694990603	3		286	177	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169988314	169988314	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	43	327	0	ENST00000295797.4:c.556G>C	p.Val186Leu	p.V186L	ENST00000295797	NM_002740.5	186	Gtc/Ctc	6/18	0.463449461826186	4	FACETS	0.757	0.638	0.887	0.252	0.212	0.296	INDETERMINATE	1	TRUE	1	0.80919694990603	4		327	254	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803208	1803209	+	missense_variant	Missense_Mutation	DNP	CC	CC	GT	novel	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	619	819	3	ENST00000260795.2:c.560_561delinsGT	p.Ser187Cys	p.S187C	ENST00000260795		187	tCC/tGT	4/17	0.74300552639125	4	FACETS	0.955	0.927	0.982	0.955	0.927	0.982	CLONAL	3	TRUE	1	0.80919694990603	4		822	966	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750526	57750526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs954831050	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	162	443	0	ENST00000274289.3:c.1942G>A	p.Glu648Lys	p.E648K	ENST00000274289	NM_006622.3	648	Gag/Aag	14/14	0.748721743222977	4	FACETS	0.982	0.913	1	0.982	0.913	1	CLONAL	2	TRUE	2	0.80919694990603	4		443	369	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911595	131911595	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	148	309	0	ENST00000265335.6:c.340C>G	p.Leu114Val	p.L114V	ENST00000265335		114	Ctg/Gtg	3/25	0.748721743222977	4	FACETS	0.899	0.832	0.967	0.899	0.832	0.967	CLONAL	2	TRUE	2	0.80919694990603	4		309	368	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931753	39931753	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	316	648	1	ENST00000378444.4:c.2846C>G	p.Ser949Ter	p.S949*	ENST00000378444	NM_001123385.1	949	tCa/tGa	4/15	0.784299223205441	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.80919694990603	2		649	384	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038856	47038856	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	379	770	0	ENST00000377604.3:c.863C>G	p.Ser288Ter	p.S288*	ENST00000377604	NM_001204468.1	288	tCa/tGa	9/24	0.784299223205441	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.80919694990603	2		770	464	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939463	76939463	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1478989105	NA	P-0044932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	121	689	0	ENST00000373344.5:c.1285A>G	p.Thr429Ala	p.T429A	ENST00000373344	NM_000489.3	429	Acc/Gcc	9/35	0.784299223205441	2	FACETS	1	0.973	1	0.564	0.519	0.609	CLONAL	1	TRUE	0	0.80919694990603	2		689	265	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	36	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.663	0.547	0.792	0.663	0.547	0.792	SUBCLONAL	1	TRUE	1	0.36176189550191	2		473	300	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0044967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	50	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.36176189550191	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.36176189550191	1		336	166	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0044967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	33	555	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.742	0.607	0.891	0.742	0.607	0.891	SUBCLONAL	1	TRUE	1	0.36176189550191	2		555	246	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729892	41729892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762543780	NA	P-0044967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	52	550	0	ENST00000242208.4:c.637G>A	p.Ala213Thr	p.A213T	ENST00000242208	NM_002192.2	213	Gct/Act	3/3	1	2	FACETS	0.636	0.542	0.739	0.636	0.542	0.739	SUBCLONAL	1	TRUE	1	0.36176189550191	2		550	452	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094413	27094413	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	82	546	0	ENST00000324856.7:c.3121del	p.Leu1041CysfsTer18	p.L1041Cfs*18	ENST00000324856	NM_006015.4	1041	Ctg/tg	11/20	1	2	FACETS	0.873	0.772	0.982	0.873	0.772	0.982	CLONAL	1	TRUE	1	0.36176189550191	2		546	519	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692913	89692914	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	36	471	0	ENST00000371953.3:c.398dup	p.Met134AsnfsTer46	p.M134Nfs*46	ENST00000371953	NM_000314.4	133	gta/gTta	5/9	1	2	FACETS	0.78	0.645	0.93	0.78	0.645	0.93	CLONAL	1	TRUE	1	0.36176189550191	2		471	255	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197282	94197282	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	28	321	0	ENST00000323929.3:c.1222del	p.Thr408GlnfsTer20	p.T408Qfs*20	ENST00000323929	NM_005591.3	408	Aca/ca	11/20	1	2	FACETS	0.967	0.782	1	0.967	0.782	1	CLONAL	1	TRUE	1	0.36176189550191	2		321	160	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713265	43713265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs969434400	NA	P-0044967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	48	905	2	ENST00000382044.4:c.4208G>A	p.Arg1403His	p.R1403H	ENST00000382044	NM_001141980.1	1403	cGt/cAt	20/28	1	2	FACETS	0.293	0.247	0.345	0.293	0.247	0.345	SUBCLONAL	1	TRUE	1	0.36176189550191	2		907	905	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655414	67655414	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	33	518	0	ENST00000264010.4:c.1280del	p.Leu427TyrfsTer20	p.L427Yfs*20	ENST00000264010	NM_006565.3	426	aTt/at	7/12	1	2	FACETS	0.55	0.448	0.663	0.55	0.448	0.663	SUBCLONAL	1	TRUE	1	0.36176189550191	2		518	332	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287623	33287623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	38	473	1	ENST00000374542.5:c.1474G>A	p.Gly492Arg	p.G492R	ENST00000374542	NM_001141970.1	492	Gga/Aga	6/8	1	2	FACETS	0.646	0.536	0.769	0.646	0.536	0.769	SUBCLONAL	1	TRUE	1	0.36176189550191	2		474	325	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0044993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	128	306	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.856304634418034	2		306	292	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588751	29588751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760703505	NA	P-0044993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	114	224	2	ENST00000356175.3:c.4537C>T	p.Arg1513Ter	p.R1513*	ENST00000356175	NM_000267.3	1513	Cga/Tga	34/57	0.856304634418034	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.856304634418034	1		226	151	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599266	55599266	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	155	270	0	ENST00000288135.5:c.2392A>G	p.Ile798Val	p.I798V	ENST00000288135	NM_000222.2	798	Atc/Gtc	17/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.856304634418034	2		270	331	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656263	18656263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762092026	NA	P-0044993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	124	365	0	ENST00000266497.5:c.2942G>A	p.Arg981His	p.R981H	ENST00000266497		981	cGc/cAc	21/31	1	2	FACETS	0.798	0.73	0.868	0.798	0.73	0.868	SUBCLONAL	1	TRUE	1	0.856304634418034	2		365	363	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163309266	163309266	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs144627000	NA	P-0044993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	85	223	0	ENST00000271452.3:c.605C>T	p.Thr202Met	p.T202M	ENST00000271452	NM_145697.2	202	aCg/aTg	8/14	0.856304634418034	3	FACETS	0.939	0.839	1	0.469	0.419	0.522	CLONAL	1	TRUE	1	0.856304634418034	3		223	302	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740794	58740794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1487712457	NA	P-0044993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	288	503	0	ENST00000305921.3:c.1699C>T	p.Pro567Ser	p.P567S	ENST00000305921	NM_003620.3	567	Ccc/Tcc	6/6	0.856304634418034	3	FACETS	0.99	0.933	1	0.495	0.466	0.525	CLONAL	1	TRUE	1	0.856304634418034	3		503	970	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0045004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	117	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.358775165670851	5	FACETS	0.878	0.799	0.959	0.878	0.799	0.959	CLONAL	3	TRUE	2	0.358775165670851	5		473	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577035	7577047	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGGGCAGCTCG	TGGGGGCAGCTCG	-	novel	NA	P-0045004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	208	714	0	ENST00000269305.4:c.891_903del	p.His297GlnfsTer44	p.H297Qfs*44	ENST00000269305	NM_001126112.2	297	caCGAGCTGCCCCCA/ca	8/11	0.265241033727063	3	FACETS	1	0.969	1	0.709	0.661	0.758	CLONAL	2	TRUE	0	0.358775165670851	3		714	643	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742933	17742933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	19	690	0	ENST00000250003.3:c.841C>T	p.Arg281Cys	p.R281C	ENST00000250003	NM_002478.4	281	Cgc/Tgc	3/3	0.331557057352472	3	FACETS	0.415	0.315	0.533	0.207	0.157	0.267	SUBCLONAL	1	TRUE	1	0.331557057352472	3		690	322	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929334	32929334	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	30	328	0	ENST00000380152.3:c.7344G>C	p.Lys2448Asn	p.K2448N	ENST00000380152		2448	aaG/aaC	14/27	0.331557057352472	3	FACETS	0.611	0.493	0.745	0.306	0.246	0.373	SUBCLONAL	1	TRUE	1	0.331557057352472	3		328	345	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350549	89350552	+	frameshift_variant	Frame_Shift_Del	DEL	TTTC	TTTC	-	rs797045027	NA	P-0045010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	90	531	0	ENST00000301030.4:c.2398_2401del	p.Glu800AsnfsTer62	p.E800Nfs*62	ENST00000301030	NM_001256183.1	800	GAAAaa/aa	9/13	0.198806924037664	3	FACETS	0.939	0.841	1	0.939	0.841	1	INDETERMINATE	2	TRUE	1	0.331557057352472	3		531	337	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442599	52442604	+	inframe_deletion	In_Frame_Del	DEL	AGGAAG	AGGAAG	-	novel	NA	P-0045010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	92	281	0	ENST00000460680.1:c.141_146del	p.Ile47_Leu49delinsMet	p.I47_L49delinsM	ENST00000460680	NM_004656.3	47	atCTTCCTg/atg	4/17	0.331557057352472	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.331557057352472	2		281	245	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138729528	NA	P-0045237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	103	618	0	ENST00000269305.4:c.523C>G	p.Arg175Gly	p.R175G	ENST00000269305	NM_001126112.2	175	Cgc/Ggc	5/11	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.24	2		618	799	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	114	296	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.754	0.691	0.818	1	0.987	1	SUBCLONAL	2	TRUE	1	0.56	2		297	270	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	70	732	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.364	0.317	0.415	0.364	0.317	0.415	SUBCLONAL	1	TRUE	1	0.56	2		735	687	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	82	393	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.996	0.888	1	0.996	0.888	1	CLONAL	1	TRUE	1	0.56	2		393	294	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	71	227	0	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.56	2		227	245	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	135	700	5	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.72	0.655	0.787	0.72	0.655	0.787	SUBCLONAL	1	TRUE	1	0.56	2		705	670	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905055	50905055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	114	503	2	ENST00000440232.2:c.342del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	113	Ggg/gg	4/27	1	2	FACETS	0.709	0.641	0.782	0.709	0.641	0.782	SUBCLONAL	1	TRUE	1	0.56	2		505	574	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	50	900	2	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.2	0.169	0.235	0.2	0.169	0.235	SUBCLONAL	1	TRUE	1	0.56	2		902	891	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	71	251	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.56	2		251	245	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	38	268	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.754	0.631	0.887	0.754	0.631	0.887	SUBCLONAL	1	TRUE	1	0.56	2		268	180	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	80	330	2	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.898	0.798	1	0.898	0.798	1	CLONAL	1	TRUE	1	0.56	2		332	318	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259480	16259480	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	17	317	0	ENST00000375759.3:c.6750del	p.Ala2251GlnfsTer102	p.A2251Qfs*102	ENST00000375759	NM_015001.2	2249	Ccc/cc	11/15	1	2	FACETS	0.189	0.14	0.246	0.189	0.14	0.246	SUBCLONAL	1	TRUE	1	0.56	2		317	322	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161907	47161907	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	80	257	0	ENST00000409792.3:c.4219del	p.Arg1407GlyfsTer5	p.R1407Gfs*5	ENST00000409792	NM_014159.6	1407	Agg/gg	3/21	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.56	2		257	274	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	17	432	0	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	1	2	FACETS	0.166	0.124	0.217	0.166	0.124	0.217	SUBCLONAL	1	TRUE	1	0.56	2		432	365	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375544	15375544	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1405614933	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	141	750	0	ENST00000263377.2:c.883A>C	p.Thr295Pro	p.T295P	ENST00000263377	NM_058243.2	295	Acc/Ccc	6/20	1	2	FACETS	0.682	0.622	0.745	0.682	0.622	0.745	SUBCLONAL	1	TRUE	1	0.56	2		750	738	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	91	373	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.934	0.837	1	0.934	0.837	1	CLONAL	1	TRUE	1	0.56	2		373	348	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12647737	12647737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773051648	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	59	223	0	ENST00000251849.4:c.643C>T	p.Arg215Cys	p.R215C	ENST00000251849	NM_002880.3	215	Cgt/Tgt	6/17	1	2	FACETS	0.912	0.795	1	0.912	0.795	1	CLONAL	1	TRUE	1	0.56	2		223	231	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	55	307	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	1	2	FACETS	0.987	0.857	1	0.987	0.857	1	CLONAL	1	TRUE	1	0.56	2		307	199	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	135	539	2	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.992	0.908	1	0.992	0.908	1	CLONAL	1	TRUE	1	0.56	2		541	486	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620470	52620470	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	25	360	0	ENST00000394830.3:c.3283C>T	p.Arg1095Ter	p.R1095*	ENST00000394830	NM_018313.4	1095	Cga/Tga	21/30	1	2	FACETS	0.218	0.172	0.272	0.218	0.172	0.272	SUBCLONAL	1	TRUE	1	0.56	2		360	409	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922301	178922301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	43	268	0	ENST00000263967.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000263967	NM_006218.2	357	cGa/cAa	6/21	1	2	FACETS	0.978	0.833	1	0.978	0.833	1	CLONAL	1	TRUE	1	0.56	2		268	157	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716335	52716335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	166	535	1	ENST00000322088.6:c.779G>A	p.Arg260His	p.R260H	ENST00000322088	NM_014225.5	260	cGc/cAc	6/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.56	2		536	557	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088659	27088659	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	128	573	0	ENST00000324856.7:c.2272del	p.Gln758ArgfsTer75	p.Q758Rfs*75	ENST00000324856	NM_006015.4	756	aaC/aa	7/20	1	2	FACETS	0.821	0.747	0.898	0.821	0.747	0.898	CLONAL	1	TRUE	1	0.56	2		573	557	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240271	5240271	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	141	774	0	ENST00000357368.4:c.1643del	p.Pro548ArgfsTer37	p.P548Rfs*37	ENST00000357368	NM_002850.3	548	cCg/cg	12/38	1	2	FACETS	0.684	0.624	0.747	0.684	0.624	0.747	SUBCLONAL	1	TRUE	1	0.56	2		774	736	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653833	89653833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1085308042	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	58	293	0	ENST00000371953.3:c.131G>A	p.Gly44Asp	p.G44D	ENST00000371953	NM_000314.4	44	gGc/gAc	2/9	1	2	FACETS	0.825	0.717	0.941	0.825	0.717	0.941	CLONAL	1	TRUE	1	0.56	2		293	251	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400299	139400299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150343794	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	159	741	1	ENST00000277541.6:c.4049G>A	p.Arg1350His	p.R1350H	ENST00000277541	NM_017617.3	1350	cGt/cAt	25/34	1	2	FACETS	0.974	0.897	1	0.974	0.897	1	CLONAL	1	TRUE	1	0.56	2		742	583	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058576	42058577	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	43	181	0	ENST00000219905.7:c.8301_8302del	p.Arg2767SerfsTer10	p.R2767Sfs*10	ENST00000219905	NM_001164273.1	2766	GAg/g	24/24	1	2	FACETS	0.883	0.75	1	0.883	0.75	1	CLONAL	1	TRUE	1	0.56	2		181	174	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101081	26101081	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	111	455	1	ENST00000435504.4:c.11del	p.Lys4ArgfsTer18	p.K4Rfs*18	ENST00000435504		4	aAg/ag	1/13	1	2	FACETS	0.819	0.74	0.902	0.819	0.74	0.902	CLONAL	1	TRUE	1	0.56	2		456	484	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411384	63411384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149055969	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	161	686	1	ENST00000330258.3:c.1783G>A	p.Ala595Thr	p.A595T	ENST00000330258	NM_152424.3	595	Gcc/Acc	2/2	0.138729873164562	1	FACETS	0.739	0.682	0.799	0.739	0.682	0.799	INDETERMINATE	1	TRUE	0	0.56	1		687	560	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607663	46607663	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1259062822	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	200	627	0	ENST00000263734.3:c.1852C>T	p.Pro618Ser	p.P618S	ENST00000263734	NM_001430.4	618	Cca/Tca	12/16	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.56	2		627	648	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074250	8074250	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	107	352	2	ENST00000377482.5:c.409C>A	p.Pro137Thr	p.P137T	ENST00000377482	NM_018948.3	137	Cct/Act	4/4	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.56	2		354	381	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2105492	2105492	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	111	403	1	ENST00000219476.3:c.571C>A	p.Leu191Ile	p.L191I	ENST00000219476	NM_000548.3	191	Ctc/Atc	6/42	1	2	FACETS	0.899	0.813	0.988	0.899	0.813	0.988	CLONAL	1	TRUE	1	0.56	2		404	441	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647460	3647460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776394340	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	191	505	0	ENST00000294008.3:c.1603G>A	p.Ala535Thr	p.A535T	ENST00000294008	NM_032444.2	535	Gca/Aca	7/15	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.56	2		505	675	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619266	37619268	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	99	387	1	ENST00000447079.4:c.945_947del	p.Arg315del	p.R315del	ENST00000447079	NM_015083.1	314	gaAAGa/gaa	1/14	1	2	FACETS	0.864	0.777	0.956	0.864	0.777	0.956	CLONAL	1	TRUE	1	0.56	2		388	409	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265032	10265032	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	136	410	0	ENST00000340748.4:c.1908T>G	p.Ile636Met	p.I636M	ENST00000340748		636	atT/atG	21/40	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.56	2		410	473	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965826	18965826	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	108	554	0	ENST00000262803.5:c.1407del	p.Asp470ThrfsTer10	p.D470Tfs*10	ENST00000262803	NM_002911.3	468	ctC/ct	10/24	1	2	FACETS	0.739	0.666	0.816	0.739	0.666	0.816	SUBCLONAL	1	TRUE	1	0.56	2		554	522	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693911	47693911	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1553366630	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	46	302	0	ENST00000233146.2:c.1625T>C	p.Val542Ala	p.V542A	ENST00000233146	NM_000251.2	542	gTa/gCa	10/16	1	2	FACETS	0.809	0.69	0.938	0.809	0.69	0.938	CLONAL	1	TRUE	1	0.56	2		302	203	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437350	220437350	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	140	702	3	ENST00000243786.2:c.257del	p.Phe86SerfsTer41	p.F86Sfs*41	ENST00000243786	NM_002191.3	85	cTt/ct	1/2	1	2	FACETS	0.718	0.655	0.784	0.718	0.655	0.784	SUBCLONAL	1	TRUE	1	0.56	2		705	696	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661392	227661392	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	134	461	0	ENST00000305123.5:c.2063C>T	p.Ala688Val	p.A688V	ENST00000305123	NM_005544.2	688	gCc/gTc	1/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.56	2		461	416	SUCCESS
ATR	545	MSKCC	GRCh37	3	142211979	142211980	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	52	268	0	ENST00000350721.4:c.6072dup	p.Tyr2025IlefsTer2	p.Y2025Ifs*2	ENST00000350721	NM_001184.3	2024	-/A	35/47	1	2	FACETS	0.929	0.802	1	0.929	0.802	1	CLONAL	1	TRUE	1	0.56	2		268	200	SUCCESS
ATR	545	MSKCC	GRCh37	3	142241587	142241587	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	56	267	0	ENST00000350721.4:c.4249G>A	p.Ala1417Thr	p.A1417T	ENST00000350721	NM_001184.3	1417	Gct/Act	23/47	1	2	FACETS	0.862	0.747	0.984	0.862	0.747	0.984	CLONAL	1	TRUE	1	0.56	2		267	232	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430951	181430951	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	43	764	2	ENST00000325404.1:c.803G>A	p.Gly268Glu	p.G268E	ENST00000325404	NM_003106.3	268	gGg/gAg	1/1	1	2	FACETS	0.199	0.166	0.237	0.199	0.166	0.237	SUBCLONAL	1	TRUE	1	0.56	2		766	770	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675181	176675181	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	47	139	1	ENST00000439151.2:c.4498-1G>T		p.X1500_splice	ENST00000439151	NM_022455.4	1500			1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.56	2		140	165	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948454	31948454	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	83	313	0	ENST00000375333.2:c.937G>A	p.Val313Ile	p.V313I	ENST00000375333	NM_032454.1	313	Gtc/Atc	7/8	1	2	FACETS	0.995	0.888	1	0.995	0.888	1	CLONAL	1	TRUE	1	0.56	2		313	298	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805755	32805755	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	61	633	0	ENST00000374899.4:c.256del	p.Ala86ProfsTer34	p.A86Pfs*34	ENST00000374899	NM_018833.2	86	Gcc/cc	2/12	1	2	FACETS	0.336	0.29	0.387	0.336	0.29	0.387	SUBCLONAL	1	TRUE	1	0.56	2		633	648	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198230	138198230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	47	183	0	ENST00000237289.4:c.823C>T	p.Leu275Phe	p.L275F	ENST00000237289	NM_001270507.1	275	Ctt/Ttt	6/9	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.56	2		183	138	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232200	98232202	+	inframe_deletion	In_Frame_Del	DEL	ACT	ACT	-	novel	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	69	217	0	ENST00000331920.6:c.1740_1742del	p.Val582del	p.V582del	ENST00000331920	NM_000264.3	580	gtAGTg/gtg	13/24	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.56	2		217	241	SUCCESS
BTK	695	MSKCC	GRCh37	X	100629616	100629616	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	71	298	1	ENST00000308731.7:c.148G>T	p.Gly50Cys	p.G50C	ENST00000308731	NM_000061.2	50	Ggc/Tgc	3/19	0.138729873164562	1	FACETS	0.841	0.746	0.94	0.841	0.746	0.94	INDETERMINATE	1	TRUE	0	0.56	1		299	217	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123022525	123022525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	119	466	2	ENST00000355640.3:c.934C>T	p.Pro312Ser	p.P312S	ENST00000355640		312	Ccc/Tcc	3/7	0.138729873164562	1	FACETS	0.743	0.676	0.812	0.743	0.676	0.812	INDETERMINATE	1	TRUE	0	0.56	1		468	412	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217339	123217339	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	47	429	0	ENST00000218089.9:c.2993C>T	p.Ala998Val	p.A998V	ENST00000218089	NM_001042749.1	998	gCa/gTa	29/35	0.138729873164562	1	FACETS	0.392	0.333	0.458	0.392	0.333	0.458	INDETERMINATE	1	TRUE	0	0.56	1		429	308	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0045950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	156	644	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.267307881108938	2	FACETS	0.759	0.697	0.823	0.759	0.697	0.823	SUBCLONAL	2	FALSE	0	0.300976127050524	2		645	683	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0045950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	159	511	1	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.300976127050524	5	FACETS	1	0.976	1	0.769	0.707	0.833	CLONAL	2	FALSE	2	0.300976127050524	5		512	665	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193530	99193530	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	95	702	0	ENST00000074304.5:c.2725G>C	p.Glu909Gln	p.E909Q	ENST00000074304	NM_001134224.1	909	Gag/Cag	25/26	1	2	FACETS	0.713	0.634	0.798	0.713	0.634	0.798	SUBCLONAL	1	FALSE	1	0.300976127050524	2		702	885	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877837	151877837	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	34	221	0	ENST00000262189.6:c.7108A>G	p.Thr2370Ala	p.T2370A	ENST00000262189	NM_170606.2	2370	Act/Gct	36/59	0.286590541079255	3	FACETS	0.769	0.63	0.925	0.385	0.315	0.463	CLONAL	1	FALSE	1	0.300976127050524	3		221	338	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81892729	81892729	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	16	218	0	ENST00000359376.3:c.440G>T	p.Arg147Ile	p.R147I	ENST00000359376	NM_002661.3	147	aGa/aTa	5/33	0.149474806855948	3	FACETS	0.499	0.369	0.656	0.25	0.184	0.328	SUBCLONAL	1	TRUE	1	0.24	3		218	299	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0045960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	157	365	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	1	2	FACETS	1	0.971	1	1	0.994	1	CLONAL	3	TRUE	1	0.24	2		365	398	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424062	49424062	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs886041779	NA	P-0045960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	40	607	0	ENST00000301067.7:c.13999+1G>A		p.X4667_splice	ENST00000301067	NM_003482.3	4667			1	2	FACETS	0.442	0.366	0.527	0.442	0.366	0.527	SUBCLONAL	1	TRUE	1	0.24	2		607	755	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	101	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.624361308830704	2		473	303	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748512	162748512	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	97	277	0	ENST00000367921.3:c.2426G>A	p.Gly809Glu	p.G809E	ENST00000367921	NM_006182.2	809	gGg/gAg	17/18	0.544201137491935	3	FACETS	1	0.956	1	0.557	0.501	0.616	CLONAL	1	TRUE	1	0.624361308830704	3		277	366	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435300	110435302	+	inframe_deletion	In_Frame_Del	DEL	GGT	GGT	-	rs765493638	NA	P-0046024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	12	225	2	ENST00000375856.3:c.3099_3101del	p.Pro1036del	p.P1036del	ENST00000375856	NM_003749.2	1033	ccACCg/ccg	1/2	0.162336293279836	4	FACETS	0.405	0.286	0.551	0.203	0.143	0.276	INDETERMINATE	1	TRUE	2	0.624361308830704	4		227	154	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0046024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	87	308	1	ENST00000288602.6:c.1397G>T	p.Gly466Val	p.G466V	ENST00000288602	NM_004333.4	466	gGa/gTa	11/18	0.212532160312484	3	FACETS	0.785	0.707	0.865	0.785	0.707	0.865	INDETERMINATE	2	TRUE	1	0.624361308830704	3		309	233	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952086	178952086	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	56	311	0	ENST00000263967.3:c.3141T>A	p.His1047Gln	p.H1047Q	ENST00000263967	NM_006218.2	1047	caT/caA	21/21	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.624361308830704	2		311	178	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622179	162622179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781608005	NA	P-0046024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	81	265	0	ENST00000366898.1:c.518C>T	p.Thr173Met	p.T173M	ENST00000366898	NM_004562.2	173	aCg/aTg	4/12	0.212532160312484	3	FACETS	1	0.953	1	0.566	0.503	0.631	INDETERMINATE	1	TRUE	1	0.624361308830704	3		265	301	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598110	52598110	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	102	388	0	ENST00000394830.3:c.3756T>G	p.Phe1252Leu	p.F1252L	ENST00000394830	NM_018313.4	1252	ttT/ttG	24/30	1	2	FACETS	0.978	0.885	1	0.978	0.885	1	CLONAL	1	TRUE	1	0.624361308830704	2		388	334	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778785	76778787	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1557042392	NA	P-0046215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	144	247	0	ENST00000373344.5:c.6792_6794del	p.Glu2265del	p.E2265del	ENST00000373344	NM_000489.3	2264	gaAGAg/gag	31/35	0.219044788591074	2	FACETS	0.976	0.898	1			1	CLONAL	3	TRUE	NA	0.219044788591074	2		247	449	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	69	345	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.948	0.84	1	0.948	0.84	1	CLONAL	1	TRUE	1	0.700207887943874	2		345	208	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0046531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	116	562	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.700207887943874	2		562	330	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528572	89528572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762601076	NA	P-0046531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	31	242	0	ENST00000336596.2:c.2872G>A	p.Val958Met	p.V958M	ENST00000336596	NM_005233.5	958	Gtg/Atg	17/17	1	2	FACETS	0.229	0.185	0.279	0.229	0.185	0.279	SUBCLONAL	1	TRUE	1	0.700207887943874	2		242	387	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795828	42795853	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGCCACTGCCACTGGTGAGCCCGC	CCAGCCACTGCCACTGGTGAGCCCGC	-	novel	NA	P-0046531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	285	672	0	ENST00000575354.2:c.2819_2844del	p.Gln940LeufsTer202	p.Q940Lfs*202	ENST00000575354	NM_015125.3	939	ggCCAGCCACTGCCACTGGTGAGCCCGCcc/ggcc	11/20	0.700207887943874	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.700207887943874	1		672	489	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010495	48010498	+	frameshift_variant	Frame_Shift_Del	DEL	TCCT	TCCT	-	novel	NA	P-0046531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	73	330	0	ENST00000234420.5:c.126_129del	p.Ser43GlnfsTer37	p.S43Qfs*37	ENST00000234420	NM_000179.2	41	tcTCCT/tc	1/10	1	2	FACETS	0.596	0.524	0.671	0.596	0.524	0.671	SUBCLONAL	1	TRUE	1	0.700207887943874	2		330	350	SUCCESS
APC	324	MSKCC	GRCh37	5	112179072	112179073	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	125	239	0	ENST00000257430.4:c.7782dup	p.Ile2595TyrfsTer8	p.I2595Yfs*8	ENST00000257430	NM_000038.5	2594	tct/tcTt	16/16	1	2	FACETS	0.97	0.888	1	0.97	0.888	1	CLONAL	1	TRUE	1	0.700207887943874	2		239	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0046723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	310	644	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.968	0.916	1	0.968	0.916	1	CLONAL	1	TRUE	1	0.742956814655116	2		645	862	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0046723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	100	562	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.951	0.862	1	0.951	0.862	1	CLONAL	1	TRUE	1	0.742956814655116	2		562	283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520008	NA	P-0046723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	255	622	0	ENST00000269305.4:c.613T>C	p.Tyr205His	p.Y205H	ENST00000269305	NM_001126112.2	205	Tat/Cat	6/11	1	2	FACETS	0.93	0.875	0.987	0.93	0.875	0.987	CLONAL	1	TRUE	1	0.742956814655116	2		622	738	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889181	76889181	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	152	122	0	ENST00000373344.5:c.4829C>G	p.Thr1610Arg	p.T1610R	ENST00000373344	NM_000489.3	1610	aCa/aGa	18/35	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.742956814655116	1		122	207	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	276	345	0				ENST00000310581	NM_198253.2	-/1132			0.949765812638684	2	FACETS	0.953	0.93	0.972	0.953	0.93	0.972	CLONAL	2	TRUE	0	0.953151507137208	2		345	304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	436	497	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.89681312118437	3	FACETS	0.947	0.913	0.981	0.947	0.913	0.981	CLONAL	2	TRUE	1	0.953151507137208	3		497	713	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	241	474	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	0.953151507137208	5	FACETS	0.984	0.917	1	0.328	0.305	0.351	CLONAL	1	TRUE	2	0.953151507137208	5		474	1249	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303223	11303223	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1012774947	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1386	77	594	1	ENST00000361445.4:c.1360C>T	p.Arg454Cys	p.R454C	ENST00000361445	NM_004958.3	454	Cgc/Tgc	9/58	0.953151507137208	5	FACETS	0.268	0.234	0.305	0.089	0.078	0.102	SUBCLONAL	1	TRUE	2	0.953151507137208	5		595	1463	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518437	204518437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201947927	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	237	695	0	ENST00000367182.3:c.1100C>T	p.Ser367Leu	p.S367L	ENST00000367182	NM_001278516.1	367	tCg/tTg	11/11	0.929083323316847	2	FACETS	0.589	0.55	0.628	0.294	0.275	0.314	SUBCLONAL	1	TRUE	0	0.953151507137208	2		695	845	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495772	56495772	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	266	512	0	ENST00000267101.3:c.3962C>G	p.Ser1321Cys	p.S1321C	ENST00000267101	NM_001982.3	1321	tCt/tGt	28/28	0.82004325992755	5	FACETS	0.964	0.902	1			1	CLONAL	1	TRUE	NA	0.953151507137208	5		512	1407	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241911	133241911	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	126	513	0	ENST00000320574.5:c.2445C>A	p.Phe815Leu	p.F815L	ENST00000320574	NM_006231.2	815	ttC/ttA	21/49	1	2	FACETS	0.525	0.477	0.574	0.525	0.477	0.574	SUBCLONAL	1	TRUE	1	0.953151507137208	2		513	504	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549092	21549092	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	318	564	0	ENST00000382592.4:c.3184G>C	p.Glu1062Gln	p.E1062Q	ENST00000382592	NM_014572.2	1062	Gaa/Caa	8/8	0.916704469423145	4	FACETS	0.97	0.914	1	0.485	0.457	0.514	CLONAL	1	TRUE	2	0.953151507137208	4		564	1344	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609656	28609656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	320	503	0	ENST00000241453.7:c.1573G>A	p.Glu525Lys	p.E525K	ENST00000241453	NM_004119.2	525	Gag/Aag	12/24	0.916704469423145	4	FACETS	1	0.945	1	0.501	0.473	0.531	CLONAL	1	TRUE	2	0.953151507137208	4		503	1308	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953964	32953964	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	190	461	0	ENST00000380152.3:c.9031C>G	p.Leu3011Val	p.L3011V	ENST00000380152		3011	Ctt/Gtt	23/27	0.916704469423145	4	FACETS	0.87	0.805	0.938	0.435	0.402	0.469	CLONAL	1	TRUE	2	0.953151507137208	4		461	895	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954022	32954023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs397507419	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	269	491	4	ENST00000380152.3:c.9097dup	p.Thr3033AsnfsTer11	p.T3033Nfs*11	ENST00000380152		3030	aca/acAa	23/27	0.916704469423145	4	FACETS	1	0.964	1	0.52	0.487	0.553	CLONAL	1	TRUE	2	0.953151507137208	4		495	1061	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878061	48878062	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1131690852	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	513	607	0	ENST00000267163.4:c.19dup	p.Arg7ProfsTer24	p.R7Pfs*24	ENST00000267163	NM_000321.2	5	acc/aCcc	1/27	0.916704469423145	4	FACETS	0.766	0.734	0.798	0.766	0.734	0.798	SUBCLONAL	2	TRUE	2	0.953151507137208	4		607	1372	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953729	48953729	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	119	234	0	ENST00000267163.4:c.1333-1G>C		p.X445_splice	ENST00000267163	NM_000321.2	445			0.916704469423145	4	FACETS	0.949	0.874	1	0.949	0.874	1	CLONAL	2	TRUE	2	0.953151507137208	4		234	257	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570407	95570407	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	278	487	0	ENST00000393063.1:c.3326C>T	p.Ser1109Leu	p.S1109L	ENST00000393063	NM_030621.3	1109	tCa/tTa	22/28	0.89681312118437	3	FACETS	0.992	0.935	1	0.496	0.467	0.526	CLONAL	1	TRUE	1	0.953151507137208	3		487	868	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42053967	42053967	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	146	400	0	ENST00000219905.7:c.7429C>T	p.Gln2477Ter	p.Q2477*	ENST00000219905	NM_001164273.1	2477	Cag/Tag	21/24	0.502085656912359	4	FACETS	1	0.949	1	0.349	0.32	0.38	INDETERMINATE	1	TRUE	1	0.953151507137208	4		400	571	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51503112	51503112	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	84	530	0	ENST00000260433.2:c.1405G>C	p.Glu469Gln	p.E469Q	ENST00000260433		469	Gag/Cag	10/10	0.502085656912359	4	FACETS	0.336	0.295	0.379	0.112	0.098	0.127	INDETERMINATE	1	TRUE	1	0.953151507137208	4		530	1026	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640791	3640791	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	186	642	0	ENST00000294008.3:c.2848G>C	p.Glu950Gln	p.E950Q	ENST00000294008	NM_032444.2	950	Gag/Cag	12/15	0.953151507137208	4	FACETS	0.552	0.508	0.597	0.276	0.254	0.299	SUBCLONAL	1	TRUE	2	0.953151507137208	4		642	1382	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858327	9858327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	396	615	0	ENST00000330684.3:c.3074C>T	p.Ser1025Leu	p.S1025L	ENST00000330684	NM_001134407.1	1025	tCa/tTa	13/13	0.953151507137208	4	FACETS	1	0.977	1	0.525	0.498	0.552	CLONAL	1	TRUE	2	0.953151507137208	4		615	1546	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856113	68856113	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	286	501	0	ENST00000261769.5:c.1921C>A	p.Gln641Lys	p.Q641K	ENST00000261769	NM_004360.3	641	Cag/Aag	12/16	0.667157365176055	4	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.953151507137208	4		501	1092	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89383388	89383388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	287	627	0	ENST00000301030.4:c.40G>A	p.Glu14Lys	p.E14K	ENST00000301030	NM_001256183.1	14	Gag/Aag	3/13	0.953151507137208	4	FACETS	1	0.979	1	0.544	0.512	0.577	CLONAL	1	TRUE	2	0.953151507137208	4		627	1081	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579536	7579536	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567556930	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	356	678	0	ENST00000269305.4:c.151G>T	p.Glu51Ter	p.E51*	ENST00000269305	NM_001126112.2	51	Gaa/Taa	4/11	0.89681312118437	3	FACETS	1	0.987	1	0.557	0.528	0.585	CLONAL	1	TRUE	1	0.953151507137208	3		678	991	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509525	29509525	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2641	190	399	0	ENST00000356175.3:c.731-1G>C		p.X244_splice	ENST00000356175	NM_000267.3	244			0.953151507137208	14	FACETS	0.946	0.87	1			1	CLONAL	1	TRUE	NA	0.953151507137208	14		399	2831	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78599554	78599554	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	253	508	0	ENST00000306801.3:c.226G>C	p.Val76Leu	p.V76L	ENST00000306801	NM_020761.2	76	Gtg/Ctg	2/34	0.953151507137208	5	FACETS	1	0.978	1	0.367	0.343	0.392	CLONAL	1	TRUE	2	0.953151507137208	5		508	1171	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050003	13050003	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	211	494	0	ENST00000316448.5:c.147C>G	p.Phe49Leu	p.F49L	ENST00000316448	NM_004343.3	49	ttC/ttG	2/9	0.953151507137208	3	FACETS	1	0.95	1	0.51	0.476	0.545	CLONAL	1	TRUE	1	0.953151507137208	3		494	641	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445253	29445253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	282	586	0	ENST00000389048.3:c.3472G>A	p.Glu1158Lys	p.E1158K	ENST00000389048	NM_004304.4	1158	Gaa/Aaa	22/29	0.953151507137208	4	FACETS	1	0.95	1	0.506	0.475	0.538	CLONAL	1	TRUE	2	0.953151507137208	4		586	1142	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030588	48030588	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63749843	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	624	662	0	ENST00000234420.5:c.3202C>T	p.Arg1068Ter	p.R1068*	ENST00000234420	NM_000179.2	1068	Cga/Tga	5/10	0.953151507137208	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.953151507137208	4		662	1252	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225367736	225367736	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	178	408	0	ENST00000264414.4:c.1431G>C	p.Met477Ile	p.M477I	ENST00000264414	NM_003590.4	477	atG/atC	10/16	0.502085656912359	4	FACETS	1	0.988	1	0.445	0.412	0.478	INDETERMINATE	1	TRUE	1	0.953151507137208	4		408	547	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022583	31022583	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	190	687	0	ENST00000375687.4:c.2068G>C	p.Asp690His	p.D690H	ENST00000375687	NM_015338.5	690	Gat/Cat	13/13	0.953151507137208	4	FACETS	0.639	0.59	0.691	0.213	0.196	0.231	SUBCLONAL	1	TRUE	1	0.953151507137208	4		687	1218	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713171	30713171	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	282	512	0	ENST00000295754.5:c.496C>G	p.Gln166Glu	p.Q166E	ENST00000295754	NM_003242.5	166	Caa/Gaa	4/7	0.953151507137208	5	FACETS	0.983	0.922	1	0.328	0.307	0.349	CLONAL	1	TRUE	2	0.953151507137208	5		512	1462	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84406214	84406214	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	281	464	0	ENST00000321945.7:c.12G>C	p.Glu4Asp	p.E4D	ENST00000321945	NM_139076.2	4	gaG/gaC	1/9	0.502085656912359	4	FACETS	1	0.994	1	0.485	0.457	0.513	INDETERMINATE	1	TRUE	1	0.953151507137208	4		464	792	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1296322	1296322	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	59	481	0				ENST00000310581	NM_198253.2	-/1132			0.949765812638684	2	FACETS	0.202	0.173	0.233	0.101	0.086	0.117	SUBCLONAL	1	TRUE	0	0.953151507137208	2		481	613	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944564	38944564	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	131	375	0	ENST00000357387.3:c.4897G>A	p.Glu1633Lys	p.E1633K	ENST00000357387	NM_152756.3	1633	Gag/Aag	36/38	0.949765812638684	2	FACETS	0.537	0.49	0.586	0.268	0.245	0.293	SUBCLONAL	1	TRUE	0	0.953151507137208	2		375	512	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514377	149514377	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	384	658	0	ENST00000261799.4:c.567C>G	p.Ile189Met	p.I189M	ENST00000261799	NM_002609.3	189	atC/atG	4/23	0.949765812638684	2	FACETS	0.965	0.922	1	0.482	0.461	0.504	CLONAL	1	TRUE	0	0.953151507137208	2		658	835	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38135859	38135859	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	206	428	0	ENST00000317025.8:c.3832G>C	p.Asp1278His	p.D1278H	ENST00000317025	NM_023034.1	1278	Gat/Cat	22/24	0.953151507137208	3	FACETS	0.94	0.876	1	0.47	0.438	0.503	CLONAL	1	TRUE	1	0.953151507137208	3		428	679	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753927	133753927	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs749303459	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	187	462	1	ENST00000318560.5:c.1396G>C	p.Glu466Gln	p.E466Q	ENST00000318560	NM_005157.4	466	Gag/Cag	8/11	0.832630119513419	4	FACETS	0.986	0.913	1	0.329	0.304	0.354	CLONAL	1	TRUE	1	0.953151507137208	4		463	777	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933212	39933212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	35	313	0	ENST00000378444.4:c.1387C>T	p.Pro463Ser	p.P463S	ENST00000378444	NM_001123385.1	463	Ccc/Tcc	4/15	1	1	FACETS	0.098	0.08	0.118	0.098	0.08	0.118	SUBCLONAL	1	TRUE	0	0.953151507137208	1		313	393	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220428	123220428	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046726-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	32	207	0	ENST00000218089.9:c.3085C>T	p.Gln1029Ter	p.Q1029*	ENST00000218089	NM_001042749.1	1029	Cag/Tag	30/35	0.946635264056508	2	FACETS	0.123	0.099	0.15			1	SUBCLONAL	1	TRUE	NA	0.953151507137208	2		207	545	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835613	68835613	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	224	658	1	ENST00000261769.5:c.208del	p.Ser70ProfsTer13	p.S70Pfs*13	ENST00000261769	NM_004360.3	68	taT/ta	3/16	0.580144897969777	1	FACETS	0.999	0.938	1	0.999	0.938	1	CLONAL	1	TRUE	0	0.580144897969777	1		659	549	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347223	70347223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	44	732	1	ENST00000374080.3:c.2887G>A	p.Asp963Asn	p.D963N	ENST00000374080		963	Gat/Aat	21/45	1	2	FACETS	0.199	0.166	0.236	0.199	0.166	0.236	SUBCLONAL	1	TRUE	1	0.580144897969777	2		733	762	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243859019	243859019	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0046999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	195	215	0	ENST00000263826.5:c.47-1G>C		p.X16_splice	ENST00000263826	NM_005465.4	16			0.36287185984638	5	FACETS	0.897	0.84	0.956	0.897	0.84	0.956	CLONAL	3	TRUE	2	0.580144897969777	5		215	467	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907380	32907380	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	128	251	0	ENST00000380152.3:c.1766del	p.Lys589SerfsTer25	p.K589Sfs*25	ENST00000380152		589	Aag/ag	10/27	0.491787647293591	1	FACETS	0.964	0.886	1	0.964	0.886	1	CLONAL	1	TRUE	0	0.580144897969777	1		251	325	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028649	12028660	+	inframe_deletion	In_Frame_Del	DEL	TGATGTCCGCTC	TGATGTCCGCTC	-	novel	NA	P-0046999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	134	396	0	ENST00000353533.5:c.859_870del	p.Arg287_Val290del	p.R287_V290del	ENST00000353533	NM_003010.3	284	taTGATGTCCGCTCt/tat	8/11	0.580144897969777	1	FACETS	0.894	0.822	0.967	0.894	0.822	0.967	CLONAL	1	TRUE	0	0.580144897969777	1		396	367	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430824	181430824	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	410	1255	0	ENST00000325404.1:c.676T>G	p.Ser226Ala	p.S226A	ENST00000325404	NM_003106.3	226	Tcc/Gcc	1/1	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.580144897969777	2		1255	1371	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0047235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	65	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.127999052956606	3	FACETS	1	0.936	1	0.74	0.649	0.837	INDETERMINATE	2	FALSE	0	0.250432976640836	3		288	263	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0047235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	34	571	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.7	0.572	0.843	0.7	0.572	0.843	SUBCLONAL	1	FALSE	1	0.250432976640836	2		571	388	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519742	NA	P-0047235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	51	787	0	ENST00000078429.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000078429	NM_002067.2	209	cAg/cCg	5/7	1	2	FACETS	0.545	0.462	0.636	0.545	0.462	0.636	SUBCLONAL	1	FALSE	1	0.250432976640836	2		787	748	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257642	16257642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	31	384	1	ENST00000375759.3:c.4907C>T	p.Ser1636Phe	p.S1636F	ENST00000375759	NM_015001.2	1636	tCc/tTc	11/15	1	2	FACETS	0.539	0.436	0.657	0.539	0.436	0.657	SUBCLONAL	1	FALSE	1	0.250432976640836	2		385	459	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970916	55970916	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	21	397	0	ENST00000263923.4:c.1881G>A	p.Met627Ile	p.M627I	ENST00000263923	NM_002253.2	627	atG/atA	13/30	1	2	FACETS	0.428	0.329	0.544	0.428	0.329	0.544	SUBCLONAL	1	FALSE	1	0.250432976640836	2		397	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0047611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	171	331	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.454703632641776	3	FACETS	1	0.983	1	0.775	0.725	0.826	CLONAL	2	FALSE	0	0.528299233483976	3		331	352	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0047611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	74	366	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.528299233483976	2		366	187	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0047611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	20	236	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.174087364492953	4	FACETS	1	0.905	1	0.673	0.526	0.836	INDETERMINATE	1	FALSE	2	0.528299233483976	4		236	86	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944943	31944943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	50	449	0	ENST00000340398.3:c.158G>A	p.Arg53His	p.R53H	ENST00000340398	NM_001013699.2	53	cGt/cAt	1/1	1	2	FACETS	0.932	0.802	1	0.932	0.802	1	CLONAL	1	FALSE	1	0.528299233483976	2		449	203	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711034	114711034	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0047611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	153	213	0	ENST00000543371.1:c.256+2T>A		p.X86_splice	ENST00000543371	NM_001198531.1	86			0.454703632641776	3	FACETS	1	0.941	1	1	0.941	1	CLONAL	3	FALSE	0	0.528299233483976	3		213	244	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	64	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.32609601627029	4	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	FALSE	2	0.381915325377538	4		485	217	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395738	45395738	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	36	312	0	ENST00000262160.6:c.396G>A	p.Trp132Ter	p.W132*	ENST00000262160	NM_005901.5	132	tgG/tgA	4/11	1	2	FACETS	0.972	0.807	1	0.972	0.807	1	CLONAL	1	FALSE	1	0.381915325377538	2		312	194	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278106	41278106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	20	367	0	ENST00000349496.5:c.1982G>A	p.Arg661Gln	p.R661Q	ENST00000349496	NM_001904.3	661	cGa/cAa	13/15	1	2	FACETS	0.663	0.511	0.838	0.663	0.511	0.838	SUBCLONAL	1	FALSE	1	0.381915325377538	2		367	158	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038929	12038929	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	94	220	0	ENST00000396373.4:c.1222A>T	p.Arg408Trp	p.R408W	ENST00000396373	NM_001987.4	408	Agg/Tgg	7/8	0.381915325377538	6	FACETS	1	0.92	1	0.767	0.692	0.845	CLONAL	3	FALSE	2	0.381915325377538	6		220	283	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323096	31323096	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs41551113	NA	P-0047736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	20	917	1	ENST00000412585.2:c.893G>A	p.Trp298Ter	p.W298*	ENST00000412585	NM_005514.6	298	tGg/tAg	4/8	1	2	FACETS	0.29	0.221	0.371	0.29	0.221	0.371	SUBCLONAL	1	FALSE	1	0.381915325377538	2		918	361	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374349	118374349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	15	324	0	ENST00000534358.1:c.7742C>A	p.Thr2581Asn	p.T2581N	ENST00000534358	NM_005933.3	2581	aCc/aAc	27/36	1	2	FACETS	0.586	0.432	0.768	0.586	0.432	0.768	SUBCLONAL	1	FALSE	1	0.381915325377538	2		324	134	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477191	67477191	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	96	500	0	ENST00000327367.4:c.998A>T	p.Lys333Met	p.K333M	ENST00000327367	NM_005902.3	333	aAg/aTg	7/9	0.381915325377538	2	FACETS	0.766	0.69	0.846	0.766	0.69	0.846	SUBCLONAL	2	FALSE	0	0.381915325377538	2		500	328	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374903	45374903	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	42	435	0	ENST00000262160.6:c.940G>C	p.Gly314Arg	p.G314R	ENST00000262160	NM_005901.5	314	Ggt/Cgt	8/11	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	FALSE	1	0.381915325377538	2		435	199	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786863	135786863	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs118203483	NA	P-0047736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	36	433	0	ENST00000298552.3:c.1006C>T	p.Arg336Trp	p.R336W	ENST00000298552	NM_001162426.1	336	Cgg/Tgg	10/23	0.132531324109879	0	FACETS	0.422	0.348	0.504			1	INDETERMINATE	1	FALSE	0	0.381915325377538	0		433	276	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	89	449	1	ENST00000394830.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000394830	NM_018313.4	710	Cga/Tga	17/30	0.420293361846783	1	FACETS	0.964	0.862	1	0.964	0.862	1	CLONAL	1	TRUE	0	0.420293361846783	1		450	347	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183771	10183771	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	192	832	0	ENST00000256474.2:c.240T>A	p.Ser80Arg	p.S80R	ENST00000256474	NM_000551.3	80	agT/agA	1/3	0.420293361846783	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.420293361846783	1		832	713	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0049743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	150	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.879	0.811	0.948	0.879	0.811	0.948	CLONAL	1	TRUE	1	0.797524779363635	2		485	428	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0049743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	254	364	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.797524779363635	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.797524779363635	2		364	313	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0049743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	81	389	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.631	0.561	0.704	0.631	0.561	0.704	SUBCLONAL	1	TRUE	1	0.797524779363635	2		389	322	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0049743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	15	412	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.345	0.255	0.451	0.345	0.255	0.451	SUBCLONAL	1	TRUE	1	0.797524779363635	2		412	109	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625218	69625218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168737490	NA	P-0049743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	379	791	0	ENST00000334134.2:c.575G>A	p.Arg192Gln	p.R192Q	ENST00000334134	NM_005247.2	192	cGg/cAg	3/3	1	2	FACETS	0.967	0.921	1	0.967	0.921	1	CLONAL	1	TRUE	1	0.797524779363635	2		791	983	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946901	71946901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748853590	NA	P-0049743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	331	774	1	ENST00000298229.2:c.2750G>A	p.Arg917His	p.R917H	ENST00000298229	NM_001567.3	917	cGc/cAc	25/28	1	2	FACETS	0.899	0.853	0.947	0.899	0.853	0.947	CLONAL	1	TRUE	1	0.797524779363635	2		775	923	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	103	672	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.948	0.852	1	0.948	0.852	1	CLONAL	1	TRUE	1	0.439117520769068	2		672	495	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	379	662	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.971	0.926	1	1	0.997	1	CLONAL	2	TRUE	1	0.439117520769068	2		663	889	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	133	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.439117520769068	2		336	595	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380283	25380283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913528	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	127	424	0	ENST00000311936.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000311936	NM_004985.3	59	Gca/Aca	3/5	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.439117520769068	2		424	538	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138915	64138915	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	93	300	3	ENST00000334205.4:c.2287del	p.Arg763AlafsTer21	p.R763Afs*21	ENST00000334205	NM_003942.2	761	gCc/gc	17/17	1	2	FACETS	0.992	0.887	1	0.992	0.887	1	CLONAL	1	TRUE	1	0.439117520769068	2		303	427	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	121	472	8	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.893	0.809	0.981	0.893	0.809	0.981	CLONAL	1	TRUE	1	0.439117520769068	2		480	617	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	139	715	1	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.744	0.677	0.814	0.744	0.677	0.814	SUBCLONAL	1	TRUE	1	0.439117520769068	2		716	851	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610695	52610695	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	95	526	0	ENST00000394830.3:c.3478C>T	p.Arg1160Ter	p.R1160*	ENST00000394830	NM_018313.4	1160	Cga/Tga	23/30	0.439117520769068	2	FACETS	0.798	0.713	0.889	0.399	0.356	0.445	SUBCLONAL	1	TRUE	0	0.439117520769068	2		526	542	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352674	68352674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199981178	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	121	420	0	ENST00000487270.1:c.541C>T	p.Arg181Trp	p.R181W	ENST00000487270	NM_133509.3	181	Cgg/Tgg	6/11	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.439117520769068	2		420	542	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	112	409	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	0.835	0.753	0.921	0.835	0.753	0.921	CLONAL	1	TRUE	1	0.439117520769068	2		409	611	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1685060	1685060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761321804	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	113	439	0	ENST00000378625.1:c.1565C>T	p.Thr522Ile	p.T522I	ENST00000378625	NM_001198994.1	522	aCa/aTa	13/14	1	2	FACETS	0.811	0.731	0.894	0.811	0.731	0.894	CLONAL	1	TRUE	1	0.439117520769068	2		439	635	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073538	8073538	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	158	547	0	ENST00000377482.5:c.1121G>A	p.Ser374Asn	p.S374N	ENST00000377482	NM_018948.3	374	aGt/aAt	4/4	1	2	FACETS	0.991	0.91	1	0.991	0.91	1	CLONAL	1	TRUE	1	0.439117520769068	2		547	726	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199600	16199600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	166	538	0	ENST00000375759.3:c.373C>T	p.Arg125Ter	p.R125*	ENST00000375759	NM_015001.2	125	Cga/Tga	2/15	1	2	FACETS	0.974	0.896	1	0.974	0.896	1	CLONAL	1	TRUE	1	0.439117520769068	2		538	776	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106593	27106593	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	189	1006	1	ENST00000324856.7:c.6207del	p.Gln2070SerfsTer65	p.Q2070Sfs*65	ENST00000324856	NM_006015.4	2068	tcG/tc	20/20	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.439117520769068	2		1007	859	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	150	546	1	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	0.989	0.906	1	0.989	0.906	1	CLONAL	1	TRUE	1	0.439117520769068	2		547	691	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400779	72400779	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	97	383	0	ENST00000357731.5:c.392T>C	p.Val131Ala	p.V131A	ENST00000357731	NM_173808.2	131	gTg/gCg	2/7	1	2	FACETS	0.95	0.851	1	0.95	0.851	1	CLONAL	1	TRUE	1	0.439117520769068	2		383	465	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166472	118166472	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	195	632	0	ENST00000369448.3:c.982C>T	p.Gln328Ter	p.Q328*	ENST00000369448	NM_017709.3	328	Cag/Tag	2/2	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.439117520769068	2		632	783	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578178	226578178	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	196	542	0	ENST00000366794.5:c.550T>G	p.Phe184Val	p.F184V	ENST00000366794	NM_001618.3	184	Ttc/Gtc	4/23	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.439117520769068	2		542	855	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578205	226578205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765820369	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	183	525	0	ENST00000366794.5:c.523G>A	p.Glu175Lys	p.E175K	ENST00000366794	NM_001618.3	175	Gag/Aag	4/23	1	2	FACETS	0.998	0.922	1	0.998	0.922	1	CLONAL	1	TRUE	1	0.439117520769068	2		525	835	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610033	43610033	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	155	659	0	ENST00000355710.3:c.1985A>C	p.Lys662Thr	p.K662T	ENST00000355710	NM_020975.4	662	aAg/aCg	11/20	1	2	FACETS	0.863	0.791	0.939	0.863	0.791	0.939	CLONAL	1	TRUE	1	0.439117520769068	2		659	818	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623628	43623628	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	127	583	0	ENST00000355710.3:c.3256G>T	p.Gly1086Trp	p.G1086W	ENST00000355710	NM_020975.4	1086	Ggg/Tgg	20/20	1	2	FACETS	0.76	0.689	0.835	0.76	0.689	0.835	SUBCLONAL	1	TRUE	1	0.439117520769068	2		583	761	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239441	123239442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	154	630	0	ENST00000358487.5:c.2395dup	p.Ser799PhefsTer22	p.S799Ffs*22	ENST00000358487	NM_000141.4	799	tct/tTct	18/18	1	2	FACETS	0.913	0.837	0.993	0.913	0.837	0.993	CLONAL	1	TRUE	1	0.439117520769068	2		630	768	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10795710	10795710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	123	534	0	ENST00000361367.2:c.2879G>A	p.Arg960Lys	p.R960K	ENST00000361367	NM_014633.3	960	aGg/aAg	22/25	1	2	FACETS	0.937	0.85	1	0.937	0.85	1	CLONAL	1	TRUE	1	0.439117520769068	2		534	598	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47599467	47599467	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751630870	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	167	534	0	ENST00000430070.2:c.133C>T	p.Arg45Cys	p.R45C	ENST00000430070	NM_018095.4	45	Cgt/Tgt	2/4	1	2	FACETS	0.899	0.827	0.974	0.899	0.827	0.974	CLONAL	1	TRUE	1	0.439117520769068	2		534	846	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625453	69625453	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147952743	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	143	525	0	ENST00000334134.2:c.340G>A	p.Glu114Lys	p.E114K	ENST00000334134	NM_005247.2	114	Gag/Aag	3/3	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.439117520769068	2		525	651	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942228	71942228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746333764	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	149	527	1	ENST00000298229.2:c.1492C>T	p.Arg498Cys	p.R498C	ENST00000298229	NM_001567.3	498	Cgc/Tgc	12/28	1	2	FACETS	0.901	0.825	0.981	0.901	0.825	0.981	CLONAL	1	TRUE	1	0.439117520769068	2		528	753	SUCCESS
EED	8726	MSKCC	GRCh37	11	85961344	85961344	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138343311	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	110	380	0	ENST00000263360.6:c.121G>A	p.Ala41Thr	p.A41T	ENST00000263360	NM_003797.3	41	Gct/Act	2/12	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.439117520769068	2		380	497	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	81	443	7	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.772	0.682	0.867	0.772	0.682	0.867	SUBCLONAL	1	TRUE	1	0.439117520769068	2		450	478	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394767	394767	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	149	516	0	ENST00000399788.2:c.4928T>C	p.Val1643Ala	p.V1643A	ENST00000399788	NM_001042603.1	1643	gTa/gCa	28/28	1	2	FACETS	0.961	0.88	1	0.961	0.88	1	CLONAL	1	TRUE	1	0.439117520769068	2		516	706	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641389	18641389	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1229278001	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	80	421	0	ENST00000266497.5:c.2393del	p.Asn798MetfsTer16	p.N798Mfs*16	ENST00000266497		796	ctA/ct	17/31	1	2	FACETS	0.794	0.701	0.892	0.794	0.701	0.892	SUBCLONAL	1	TRUE	1	0.439117520769068	2		421	459	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432029	49432030	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	191	675	0	ENST00000301067.7:c.9109dup	p.His3037ProfsTer4	p.H3037Pfs*4	ENST00000301067	NM_003482.3	3037	cac/cCac	34/54	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.439117520769068	2		675	849	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484321	50484321	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	172	401	0	ENST00000394963.4:c.1081C>A	p.Leu361Ile	p.L361I	ENST00000394963	NM_003076.4	361	Ctc/Atc	9/13	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.439117520769068	2		401	684	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488225	56488225	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	159	509	0	ENST00000267101.3:c.1744G>T	p.Gly582Trp	p.G582W	ENST00000267101	NM_001982.3	582	Ggg/Tgg	15/28	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.439117520769068	2		509	723	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144753	58144753	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	235	717	0	ENST00000257904.6:c.475T>G	p.Phe159Val	p.F159V	ENST00000257904	NM_000075.3	159	Ttt/Gtt	4/8	1	2	FACETS	0.965	0.9	1	0.965	0.9	1	CLONAL	1	TRUE	1	0.439117520769068	2		717	1109	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120806670	120806670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	226	857	0	ENST00000257552.2:c.66G>A	p.Met22Ile	p.M22I	ENST00000257552	NM_002442.3	22	atG/atA	2/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.439117520769068	2		857	974	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133242014	133242014	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500855	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	182	552	1	ENST00000320574.5:c.2342C>T	p.Ala781Val	p.A781V	ENST00000320574	NM_006231.2	781	gCg/gTg	21/49	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.439117520769068	2		553	775	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32905159	32905159	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876659434	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	33	320	0	ENST00000380152.3:c.785C>T	p.Ala262Val	p.A262V	ENST00000380152		262	gCa/gTa	9/27	1	2	FACETS	0.282	0.229	0.342	0.282	0.229	0.342	SUBCLONAL	1	TRUE	1	0.439117520769068	2		320	533	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134889	41134889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs977061170	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	148	500	0	ENST00000379561.5:c.739G>A	p.Gly247Arg	p.G247R	ENST00000379561	NM_002015.3	247	Ggg/Agg	2/3	1	2	FACETS	0.922	0.844	1	0.922	0.844	1	CLONAL	1	TRUE	1	0.439117520769068	2		500	731	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346972	73346972	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	119	364	0	ENST00000377767.4:c.1245C>A	p.His415Gln	p.H415Q	ENST00000377767	NM_014953.3	415	caC/caA	9/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.439117520769068	2		364	477	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781375	3781375	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	142	517	0	ENST00000262367.5:c.4990C>T	p.Arg1664Cys	p.R1664C	ENST00000262367	NM_004380.2	1664	Cgc/Tgc	30/31	1	2	FACETS	0.895	0.817	0.976	0.895	0.817	0.976	CLONAL	1	TRUE	1	0.439117520769068	2		517	723	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828863	72828863	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	168	627	0	ENST00000268489.5:c.7718C>T	p.Pro2573Leu	p.P2573L	ENST00000268489	NM_006885.3	2573	cCt/cTt	9/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.439117520769068	2		627	639	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944306	81944306	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	37	451	0	ENST00000359376.3:c.1915A>T	p.Asn639Tyr	p.N639Y	ENST00000359376	NM_002661.3	639	Aac/Tac	18/33	1	2	FACETS	0.25	0.205	0.3	0.25	0.205	0.3	SUBCLONAL	1	TRUE	1	0.439117520769068	2		451	674	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7218293	7218293	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	110	453	0	ENST00000380728.2:c.79G>T	p.Glu27Ter	p.E27*	ENST00000380728		27	Gag/Tag	2/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.439117520769068	2		453	443	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576097	29576098	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	145	474	0	ENST00000356175.3:c.4076dup	p.Gln1360SerfsTer14	p.Q1360Sfs*14	ENST00000356175	NM_000267.3	1357	ttc/ttCc	30/57	1	2	FACETS	0.949	0.868	1	0.949	0.868	1	CLONAL	1	TRUE	1	0.439117520769068	2		474	696	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33434020	33434020	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	177	566	0	ENST00000345365.6:c.467A>G	p.Asp156Gly	p.D156G	ENST00000345365	NM_002878.3	156	gAt/gGt	5/10	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.439117520769068	2		566	798	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686901	37686901	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	148	436	4	ENST00000447079.4:c.3810del	p.Gly1271AspfsTer23	p.G1271Dfs*23	ENST00000447079	NM_015083.1	1269	Ccc/cc	14/14	1	2	FACETS	0.983	0.9	1	0.983	0.9	1	CLONAL	1	TRUE	1	0.439117520769068	2		440	686	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099318	4099318	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	91	568	0	ENST00000262948.5:c.800T>C	p.Ile267Thr	p.I267T	ENST00000262948	NM_030662.3	267	aTc/aCc	7/11	1	2	FACETS	0.601	0.533	0.672	0.601	0.533	0.672	SUBCLONAL	1	TRUE	1	0.439117520769068	2		568	690	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982521	10982521	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	213	660	1	ENST00000327064.4:c.143A>G	p.Gln48Arg	p.Q48R	ENST00000327064	NM_199141.1	48	cAg/cGg	1/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.439117520769068	2		661	867	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296068	15296068	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	136	519	0	ENST00000263388.2:c.2296G>T	p.Gly766Ter	p.G766*	ENST00000263388	NM_000435.2	766	Gga/Tga	14/33	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.439117520769068	2		519	610	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297733	15297733	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	138	492	0	ENST00000263388.2:c.1907A>G	p.Asp636Gly	p.D636G	ENST00000263388	NM_000435.2	636	gAt/gGt	12/33	1	2	FACETS	0.957	0.873	1	0.957	0.873	1	CLONAL	1	TRUE	1	0.439117520769068	2		492	657	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955111	17955112	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755706305	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	87	507	1	ENST00000458235.1:c.115dup	p.Gln39ProfsTer13	p.Q39Pfs*13	ENST00000458235	NM_000215.3	39	cag/cCag	2/24	1	2	FACETS	0.631	0.559	0.708	0.631	0.559	0.708	SUBCLONAL	1	TRUE	1	0.439117520769068	2		508	628	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752695	42752695	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1366176199	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	130	519	3	ENST00000222329.4:c.1569del	p.Leu525SerfsTer6	p.L525Sfs*6	ENST00000222329	NM_006494.2	523	ggG/gg	4/4	1	2	FACETS	0.896	0.814	0.981	0.896	0.814	0.981	CLONAL	1	TRUE	1	0.439117520769068	2		522	661	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424841	47424841	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	187	634	1	ENST00000404338.3:c.2914del	p.Arg972GlyfsTer55	p.R972Gfs*55	ENST00000404338	NM_004491.4	970	tCc/tc	1/6	1	2	FACETS	0.942	0.871	1	0.942	0.871	1	CLONAL	1	TRUE	1	0.439117520769068	2		635	904	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921184	50921184	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	118	411	0	ENST00000440232.2:c.3304C>A	p.Pro1102Thr	p.P1102T	ENST00000440232	NM_002691.3	1102	Cct/Act	27/27	1	2	FACETS	0.906	0.82	0.997	0.906	0.82	0.997	CLONAL	1	TRUE	1	0.439117520769068	2		411	593	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715964	52715964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	80	580	0	ENST00000322088.6:c.529G>A	p.Asp177Asn	p.D177N	ENST00000322088	NM_014225.5	177	Gac/Aac	5/15	1	2	FACETS	0.544	0.479	0.614	0.544	0.479	0.614	SUBCLONAL	1	TRUE	1	0.439117520769068	2		580	670	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61720184	61720184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1265247519	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	98	379	0	ENST00000401558.2:c.1250G>A	p.Arg417His	p.R417H	ENST00000401558	NM_003400.3	417	cGt/cAt	13/25	1	2	FACETS	0.913	0.818	1	0.913	0.818	1	CLONAL	1	TRUE	1	0.439117520769068	2		379	489	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137404	202137404	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	179	487	0	ENST00000358485.4:c.632T>C	p.Leu211Pro	p.L211P	ENST00000358485	NM_001080125.1	211	cTg/cCg	4/9	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.439117520769068	2		487	703	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149679	202149679	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	169	612	0	ENST00000358485.4:c.1120C>A	p.Leu374Ile	p.L374I	ENST00000358485	NM_001080125.1	374	Ctc/Atc	8/9	1	2	FACETS	0.981	0.903	1	0.981	0.903	1	CLONAL	1	TRUE	1	0.439117520769068	2		612	785	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108234	209108234	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	121	459	0	ENST00000345146.2:c.615G>A	p.Trp205Ter	p.W205*	ENST00000345146	NM_005896.2	205	tgG/tgA	6/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.439117520769068	2		459	510	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215595163	215595163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377227840	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	105	402	1	ENST00000260947.4:c.1973G>A	p.Arg658His	p.R658H	ENST00000260947	NM_000465.2	658	cGc/cAc	10/11	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.439117520769068	2		403	473	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022443	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	rs750318549	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	175	517	0	ENST00000375687.4:c.1933_1934del	p.Gly645TrpfsTer12	p.G645Wfs*12	ENST00000375687	NM_015338.5	643	GGg/g	13/13	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.439117520769068	2		517	756	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29445680	29445680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	141	550	1	ENST00000544604.2:c.1511G>A	p.Ser504Asn	p.S504N	ENST00000544604	NM_001206998.1	504	aGt/aAt	8/9	1	2	FACETS	0.99	0.904	1	0.99	0.904	1	CLONAL	1	TRUE	1	0.439117520769068	2		551	649	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691872	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs79375991	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	296	638	18	ENST00000295754.5:c.383del	p.Lys128SerfsTer35	p.K128Sfs*35	ENST00000295754	NM_003242.5	125	gAa/ga	3/7	0.439117520769068	2	FACETS	0.913	0.865	0.963	0.913	0.865	0.963	CLONAL	2	TRUE	0	0.439117520769068	2		656	738	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405906	49405906	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	156	458	0	ENST00000418115.1:c.232G>A	p.Asp78Asn	p.D78N	ENST00000418115	NM_001664.2	78	Gat/Aat	3/5	0.439117520769068	2	FACETS	0.934	0.856	1	0.467	0.428	0.507	CLONAL	1	TRUE	0	0.439117520769068	2		458	761	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442542	52442542	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1194652468	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	168	523	0	ENST00000460680.1:c.203A>G	p.Asp68Gly	p.D68G	ENST00000460680	NM_004656.3	68	gAt/gGt	4/17	0.439117520769068	2	FACETS	0.896	0.824	0.971	0.448	0.412	0.486	CLONAL	1	TRUE	0	0.439117520769068	2		523	854	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682400	52682400	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	131	418	0	ENST00000394830.3:c.773del	p.Asn258MetfsTer25	p.N258Mfs*25	ENST00000394830	NM_018313.4	258	aAt/at	8/30	0.439117520769068	2	FACETS	1	0.922	1	0.506	0.461	0.554	CLONAL	1	TRUE	0	0.439117520769068	2		418	589	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799851	72799851	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	158	518	0	ENST00000325599.8:c.1318C>T	p.His440Tyr	p.H440Y	ENST00000325599	NM_018130.2	440	Cat/Tat	11/11	1	2	FACETS	0.919	0.843	0.998	0.919	0.843	0.998	CLONAL	1	TRUE	1	0.439117520769068	2		518	783	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178158	142178158	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	100	360	0	ENST00000350721.4:c.7260del	p.Lys2420AsnfsTer22	p.K2420Nfs*22	ENST00000350721	NM_001184.3	2420	aaA/aa	43/47	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.439117520769068	2		360	442	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs753143066	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	230	444	3	ENST00000295797.4:c.826dup	p.Thr276AsnfsTer16	p.T276Nfs*16	ENST00000295797	NM_002740.5	273	tta/ttAa	9/18	1	2	FACETS	0.925	0.87	0.982	1	0.994	1	CLONAL	2	TRUE	1	0.439117520769068	2		447	566	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504339	186504339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1560085211	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	83	274	1	ENST00000323963.5:c.681del	p.Lys227AsnfsTer3	p.K227Nfs*3	ENST00000323963		226	Aaa/aa	7/11	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.439117520769068	2		275	362	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143191850	143191850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779307499	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	123	406	0	ENST00000262992.4:c.581C>T	p.Ala194Val	p.A194V	ENST00000262992	NM_001101669.1	194	gCc/gTc	8/24	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.439117520769068	2		406	547	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268186	153268186	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	141	561	0	ENST00000281708.4:c.622A>G	p.Thr208Ala	p.T208A	ENST00000281708	NM_033632.3	208	Act/Gct	4/12	1	2	FACETS	0.915	0.835	0.998	0.915	0.835	0.998	CLONAL	1	TRUE	1	0.439117520769068	2		561	702	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293800	1293800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370887827	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	172	586	0	ENST00000310581.5:c.1201G>A	p.Ala401Thr	p.A401T	ENST00000310581	NM_198253.2	401	Gcg/Acg	2/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.439117520769068	2		586	734	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752807	57752807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	134	387	0	ENST00000274289.3:c.1121G>A	p.Gly374Asp	p.G374D	ENST00000274289	NM_006622.3	374	gGc/gAc	8/14	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.439117520769068	2		387	553	SUCCESS
APC	324	MSKCC	GRCh37	5	112174270	112174271	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	134	567	0	ENST00000257430.4:c.2983dup	p.Cys995LeufsTer13	p.C995Lfs*13	ENST00000257430	NM_000038.5	993	-/T	16/16	1	2	FACETS	0.966	0.88	1	0.966	0.88	1	CLONAL	1	TRUE	1	0.439117520769068	2		567	632	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	160	629	1	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.823	0.755	0.895	0.823	0.755	0.895	CLONAL	1	TRUE	1	0.439117520769068	2		630	885	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927018	131927018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753680691	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	94	478	1	ENST00000265335.6:c.1555C>T	p.Arg519Cys	p.R519C	ENST00000265335		519	Cgt/Tgt	10/25	1	2	FACETS	0.971	0.869	1	0.971	0.869	1	CLONAL	1	TRUE	1	0.439117520769068	2		479	441	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636997	176636997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	38	639	0	ENST00000439151.2:c.1597C>T	p.Leu533Phe	p.L533F	ENST00000439151	NM_022455.4	533	Ctt/Ttt	5/23	1	2	FACETS	0.235	0.193	0.281	0.235	0.193	0.281	SUBCLONAL	1	TRUE	1	0.439117520769068	2		639	738	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675194	176675194	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	148	523	0	ENST00000439151.2:c.4510C>T	p.Pro1504Ser	p.P1504S	ENST00000439151	NM_022455.4	1504	Cct/Tct	11/23	1	2	FACETS	0.904	0.827	0.984	0.904	0.827	0.984	CLONAL	1	TRUE	1	0.439117520769068	2		523	746	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323360	31323361	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	141	385	0	ENST00000412585.2:c.628_629del	p.Lys210AspfsTer10	p.K210Dfs*10	ENST00000412585	NM_005514.6	210	AAg/g	4/8	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.439117520769068	2		385	581	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200266	138200266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	99	684	0	ENST00000237289.4:c.1684C>T	p.Arg562Cys	p.R562C	ENST00000237289	NM_001270507.1	562	Cgt/Tgt	7/9	1	2	FACETS	0.545	0.486	0.607	0.545	0.486	0.607	SUBCLONAL	1	TRUE	1	0.439117520769068	2		684	828	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951838	2951838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199916182	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	152	479	0	ENST00000396946.4:c.3112G>A	p.Ala1038Thr	p.A1038T	ENST00000396946	NM_032415.4	1038	Gcc/Acc	23/25	1	2	FACETS	0.983	0.901	1	0.983	0.901	1	CLONAL	1	TRUE	1	0.439117520769068	2		479	704	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009347	69009347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs190776975	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	118	417	0	ENST00000288368.4:c.2464G>A	p.Val822Met	p.V822M	ENST00000288368	NM_024870.2	822	Gtg/Atg	22/40	1	2	FACETS	0.993	0.9	1	0.993	0.9	1	CLONAL	1	TRUE	1	0.439117520769068	2		417	541	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141567270	141567270	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	167	534	0	ENST00000220592.5:c.944G>T	p.Arg315Met	p.R315M	ENST00000220592	NM_012154.3	315	aGg/aTg	8/19	1	2	FACETS	0.992	0.913	1	0.992	0.913	1	CLONAL	1	TRUE	1	0.439117520769068	2		534	767	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739092	145739092	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	181	587	0	ENST00000428558.2:c.2063T>G	p.Leu688Arg	p.L688R	ENST00000428558	NM_004260.3	688	cTg/cGg	13/22	1	2	FACETS	0.872	0.805	0.943	0.872	0.805	0.943	CLONAL	1	TRUE	1	0.439117520769068	2		587	945	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2056829	2056829	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	173	471	0	ENST00000349721.2:c.1331G>A	p.Arg444His	p.R444H	ENST00000349721	NM_003070.3	444	cGc/cAc	7/34	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.439117520769068	2		471	769	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798867	135798867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514843	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	136	439	0	ENST00000298552.3:c.376G>A	p.Val126Ile	p.V126I	ENST00000298552	NM_001162426.1	126	Gtc/Atc	6/23	1	2	FACETS	0.956	0.872	1	0.956	0.872	1	CLONAL	1	TRUE	1	0.439117520769068	2		439	648	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933593	39933594	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0050932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	161	290	0	ENST00000378444.4:c.1005dup	p.Ser336LeufsTer45	p.S336Lfs*45	ENST00000378444	NM_001123385.1	335	-/C	4/15	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.439117520769068	1		290	426	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0051041-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	160	662	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.916	0.841	0.995	0.916	0.841	0.995	CLONAL	1	TRUE	1	0.41989197334035	2		662	832	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519985	NA	P-0051041-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	215	793	0	ENST00000269305.4:c.857A>G	p.Glu286Gly	p.E286G	ENST00000269305	NM_001126112.2	286	gAa/gGa	8/11	0.41989197334035	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.41989197334035	1		793	686	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0051041-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	256	419	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	0.396995784097282	3	FACETS	1	0.989	1	0.791	0.746	0.836	CLONAL	2	TRUE	0	0.41989197334035	3		419	622	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31238074	31238075	+	missense_variant	Missense_Mutation	DNP	CT	CT	AC	novel	NA	P-0051041-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	10	26	0	ENST00000376228.5:c.807_808delinsGT	p.Ala270Ser	p.A270S	ENST00000376228	NM_002117.5	269	gcAGct/gcGTct	4/8	1	2	FACETS	0.547	0.375	0.759	0.547	0.375	0.759	SUBCLONAL	1	TRUE	1	0.41989197334035	2		26	87	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434664	110434664	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051041-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	72	794	0	ENST00000375856.3:c.3737del	p.Gly1246AlafsTer13	p.G1246Afs*13	ENST00000375856	NM_003749.2	1246	gGc/gc	1/2	0.41989197334035	1	FACETS	0.522	0.457	0.592	0.522	0.457	0.592	SUBCLONAL	1	TRUE	0	0.41989197334035	1		794	519	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644668	134644668	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	33	543	0	ENST00000398015.3:c.69G>T	p.Met23Ile	p.M23I	ENST00000398015	NM_004441.4	23	atG/atT	2/16	1	2	FACETS	0.962	0.786	1	0.962	0.786	1	CLONAL	1	FALSE	1	0.233322655888866	2		543	294	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846083	68846083	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	79	699	0	ENST00000261769.5:c.1054G>C	p.Gly352Arg	p.G352R	ENST00000261769	NM_004360.3	352	Ggt/Cgt	8/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.233322655888866	2		699	549	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058708	47058714	+	frameshift_variant	Frame_Shift_Del	DEL	AGTACTT	AGTACTT	-	novel	NA	P-0051781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	39	512	0	ENST00000409792.3:c.7564_7570del	p.Lys2522ValfsTer13	p.K2522Vfs*13	ENST00000409792	NM_014159.6	2522	AAGTACTgt/gt	21/21	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	FALSE	1	0.233322655888866	2		512	275	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155465	47155465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	20	333	1	ENST00000409792.3:c.4616G>A	p.Cys1539Tyr	p.C1539Y	ENST00000409792	NM_014159.6	1539	tGt/tAt	5/21	1	2	FACETS	0.963	0.741	1	0.963	0.741	1	CLONAL	1	FALSE	1	0.233322655888866	2		334	178	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111995830	111995830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	27	369	0	ENST00000368678.4:c.1268C>T	p.Ala423Val	p.A423V	ENST00000368678		423	gCa/gTa	12/13	0.188530128709616	3	FACETS	0.916	0.731	1	0.458	0.365	0.564	CLONAL	1	FALSE	1	0.233322655888866	3		369	282	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445512	49445512	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301516107	NA	P-0051864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	90	523	0	ENST00000301067.7:c.1954C>T	p.Arg652Cys	p.R652C	ENST00000301067	NM_003482.3	652	Cgc/Tgc	10/54	0.286882033847863	3	FACETS	0.989	0.878	1	0.495	0.439	0.555	CLONAL	1	FALSE	1	0.293384429780422	3		523	711	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912125	114912125	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	67	411	0	ENST00000543371.1:c.1195T>C	p.Tyr399His	p.Y399H	ENST00000543371	NM_001198531.1	399	Tac/Cac	11/14	0.286882033847863	3	FACETS	0.846	0.735	0.966	0.423	0.367	0.483	CLONAL	1	FALSE	1	0.293384429780422	3		411	619	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518134	187518136	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	rs750605265	NA	P-0051864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	82	450	0	ENST00000441802.2:c.12558_12560del	p.Val4187del	p.V4187del	ENST00000441802	NM_005245.3	4186	gtTGTg/gtg	25/27	0.286882033847863	3	FACETS	0.929	0.819	1	0.464	0.409	0.524	CLONAL	1	FALSE	1	0.293384429780422	3		450	690	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	397	345	0				ENST00000310581	NM_198253.2	-/1132			0.728994021867362	5	FACETS	1	0.99	1	1	0.99	1	CLONAL	4	TRUE	1	0.728994021867362	5		345	539	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	145	485	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	0.728994021867362	3	FACETS	0.954	0.874	1	0.477	0.437	0.518	CLONAL	1	TRUE	1	0.728994021867362	3		485	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	203	656	1	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.728994021867362	3	FACETS	1	0.951	1	0.514	0.478	0.551	CLONAL	1	TRUE	1	0.728994021867362	3		657	739	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	446	695	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.728994021867362	3	FACETS	0.997	0.959	1	0.997	0.959	1	CLONAL	2	TRUE	1	0.728994021867362	3		695	837	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817754	3817754	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	362	483	0	ENST00000262367.5:c.3217C>T	p.Gln1073Ter	p.Q1073*	ENST00000262367	NM_004380.2	1073	Cag/Tag	16/31	0.724950152181071	3	FACETS	1	0.993	1	0.768	0.738	0.798	CLONAL	2	TRUE	0	0.728994021867362	3		483	588	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402595	20402595	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	118	319	1	ENST00000346618.3:c.132C>A	p.Phe44Leu	p.F44L	ENST00000346618	NM_001949.4	44	ttC/ttA	1/7	0.347051211551304	5	FACETS	0.76	0.69	0.832	0.507	0.46	0.555	INDETERMINATE	2	TRUE	2	0.728994021867362	5		320	446	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742108	145742108	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	153	599	0	ENST00000428558.2:c.395G>C	p.Arg132Thr	p.R132T	ENST00000428558	NM_004260.3	132	aGa/aCa	5/22	0.347051211551304	5	FACETS	1	0.987	1	0.476	0.437	0.517	INDETERMINATE	1	TRUE	2	0.728994021867362	5		599	615	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122397	17122397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	160	607	0	ENST00000285071.4:c.998C>T	p.Ser333Leu	p.S333L	ENST00000285071	NM_144997.5	333	tCa/tTa	9/14	0.728994021867362	3	FACETS	0.988	0.91	1	0.494	0.455	0.535	CLONAL	1	TRUE	1	0.728994021867362	3		607	606	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923119	48923119	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	204	236	0	ENST00000267163.4:c.568del	p.Val190CysfsTer2	p.V190Cfs*2	ENST00000267163	NM_000321.2	189	ttG/tt	6/27	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	2	TRUE	NA	0.728994021867362	2		236	269	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663734	29663734	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	168	561	1	ENST00000356175.3:c.6166G>A	p.Asp2056Asn	p.D2056N	ENST00000356175	NM_000267.3	2056	Gat/Aat	41/57	0.728994021867362	3	FACETS	0.957	0.883	1	0.479	0.441	0.517	CLONAL	1	TRUE	1	0.728994021867362	3		562	657	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533950	63533950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	97	307	0	ENST00000307078.5:c.1204G>A	p.Glu402Lys	p.E402K	ENST00000307078	NM_004655.3	402	Gaa/Aaa	6/11	0.728994021867362	5	FACETS	0.961	0.858	1	0.32	0.286	0.357	CLONAL	1	TRUE	2	0.728994021867362	5		307	580	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371641	225371641	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	115	490	0	ENST00000264414.4:c.963G>C	p.Leu321Phe	p.L321F	ENST00000264414	NM_003590.4	321	ttG/ttC	7/16	1	2	FACETS	0.864	0.787	0.945	0.864	0.787	0.945	CLONAL	1	TRUE	1	0.728994021867362	2		490	365	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120460379	120460379	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	286	383	0	ENST00000256646.2:c.5936C>G	p.Ser1979Cys	p.S1979C	ENST00000256646	NM_024408.3	1979	tCt/tGt	33/34	0.608011788327213	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.728994021867362	3		383	510	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733140	74733140	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	146	559	0	ENST00000359995.5:c.103G>C	p.Glu35Gln	p.E35Q	ENST00000359995	NM_001195427.1	35	Gag/Cag	1/3	0.728994021867362	5	FACETS	0.9	0.821	0.983	0.3	0.273	0.328	CLONAL	1	TRUE	2	0.728994021867362	5		559	932	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972753	25972753	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs369128452	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	264	431	0	ENST00000435504.4:c.1672C>G	p.Leu558Val	p.L558V	ENST00000435504		558	Ctt/Gtt	12/13	0.728994021867362	3	FACETS	0.986	0.937	1	0.658	0.624	0.691	CLONAL	2	TRUE	0	0.728994021867362	3		431	501	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663366	29663366	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	138	422	0	ENST00000356175.3:c.5959G>C	p.Asp1987His	p.D1987H	ENST00000356175	NM_000267.3	1987	Gat/Cat	40/57	0.728994021867362	3	FACETS	1	0.935	1	0.513	0.469	0.558	CLONAL	1	TRUE	1	0.728994021867362	3		422	504	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476785	140476785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	130	519	0	ENST00000288602.6:c.1621C>T	p.Leu541Phe	p.L541F	ENST00000288602	NM_004333.4	541	Ctc/Ttc	13/18	0.728994021867362	3	FACETS	0.916	0.835	1	0.458	0.417	0.501	CLONAL	1	TRUE	1	0.728994021867362	3		519	531	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055755	152055755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1403418496	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	84	369	1	ENST00000262189.6:c.167G>A	p.Arg56Gln	p.R56Q	ENST00000262189	NM_170606.2	56	cGa/cAa	2/59	0.728994021867362	3	FACETS	0.891	0.793	0.994	0.445	0.396	0.497	CLONAL	1	TRUE	1	0.728994021867362	3		370	353	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868298	37868298	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs532077147	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	167	472	0	ENST00000269571.5:c.1019G>A	p.Arg340Gln	p.R340Q	ENST00000269571		340	cGa/cAa	8/27	0.728994021867362	3	FACETS	1	0.979	1	0.582	0.538	0.627	CLONAL	1	TRUE	1	0.728994021867362	3		472	537	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564566	41564566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	201	538	2	ENST00000263253.7:c.3988G>A	p.Asp1330Asn	p.D1330N	ENST00000263253	NM_001429.3	1330	Gac/Aac	24/31	0.723105715125081	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.728994021867362	1		540	283	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	204	643	0	ENST00000267101.3:c.273G>C	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atC	3/28	0.728994021867362	3	FACETS	0.963	0.895	1	0.482	0.447	0.517	CLONAL	1	TRUE	1	0.728994021867362	3		643	793	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201074	108201074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	99	390	0	ENST00000278616.4:c.7441G>A	p.Asp2481Asn	p.D2481N	ENST00000278616	NM_000051.3	2481	Gat/Aat	50/63	0.63273653105481	3	FACETS	0.88	0.791	0.974	0.293	0.263	0.325	CLONAL	1	TRUE	0	0.728994021867362	3		390	421	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775007	73775007	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	63	288	0	ENST00000254810.4:c.166C>T	p.Gln56Ter	p.Q56*	ENST00000254810	NM_005324.3	56	Cag/Tag	3/4	0.728994021867362	5	FACETS	0.828	0.718	0.946	0.276	0.239	0.316	CLONAL	1	TRUE	2	0.728994021867362	5		288	437	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105238746	105238746	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749544983	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	207	641	0	ENST00000349310.3:c.1216C>T	p.Arg406Cys	p.R406C	ENST00000349310	NM_001014432.1	406	Cgc/Tgc	13/15	0.728994021867362	3	FACETS	1	0.961	1	0.524	0.487	0.561	CLONAL	1	TRUE	1	0.728994021867362	3		641	740	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11308144	11308144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751686958	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	155	413	0	ENST00000361445.4:c.848G>A	p.Arg283Lys	p.R283K	ENST00000361445	NM_004958.3	283	aGa/aAa	7/58	0.728994021867362	3	FACETS	1	0.977	1	0.579	0.534	0.626	CLONAL	1	TRUE	1	0.728994021867362	3		413	501	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510724	120510724	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	173	575	1	ENST00000256646.2:c.1240G>A	p.Glu414Lys	p.E414K	ENST00000256646	NM_024408.3	414	Gaa/Aaa	7/34	0.608011788327213	3	FACETS	0.937	0.865	1	0.469	0.432	0.506	CLONAL	1	TRUE	1	0.728994021867362	3		576	691	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226574074	226574074	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	156	495	0	ENST00000366794.5:c.787G>C	p.Glu263Gln	p.E263Q	ENST00000366794	NM_001618.3	263	Gag/Cag	6/23	0.728994021867362	3	FACETS	0.942	0.866	1	0.471	0.433	0.511	CLONAL	1	TRUE	1	0.728994021867362	3		495	620	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402005	402005	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	160	373	0	ENST00000399788.2:c.4786G>C	p.Asp1596His	p.D1596H	ENST00000399788	NM_001042603.1	1596	Gac/Cac	27/28	0.608534531675363	4	FACETS	1	0.924	1	0.503	0.462	0.546	CLONAL	1	TRUE	2	0.728994021867362	4		373	754	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402286	402286	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1285922080	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	70	547	0	ENST00000399788.2:c.4505C>T	p.Ser1502Leu	p.S1502L	ENST00000399788	NM_001042603.1	1502	tCa/tTa	27/28	0.608534531675363	4	FACETS	0.331	0.288	0.379	0.166	0.144	0.19	SUBCLONAL	1	TRUE	2	0.728994021867362	4		547	1002	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231349	46231349	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	80	409	0	ENST00000334344.6:c.1189C>T	p.Gln397Ter	p.Q397*	ENST00000334344	NM_152641.2	397	Cag/Tag	10/21	0.728994021867362	3	FACETS	0.78	0.691	0.874	0.39	0.345	0.437	SUBCLONAL	1	TRUE	1	0.728994021867362	3		409	384	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222689	69222689	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	251	479	0	ENST00000462284.1:c.662C>G	p.Ser221Cys	p.S221C	ENST00000462284	NM_002392.5	221	tCt/tGt	8/11	0.728994021867362	3	FACETS	0.845	0.798	0.892	0.845	0.798	0.892	CLONAL	2	TRUE	1	0.728994021867362	3		479	556	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597565	28597565	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	204	556	0	ENST00000241453.7:c.2340G>C	p.Leu780Phe	p.L780F	ENST00000241453	NM_004119.2	780	ttG/ttC	19/24	0.728994021867362	5	FACETS	1	0.94	1	0.339	0.314	0.365	CLONAL	1	TRUE	2	0.728994021867362	5		556	1152	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915148	32915148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	134	472	0	ENST00000380152.3:c.6656C>T	p.Ser2219Leu	p.S2219L	ENST00000380152		2219	tCa/tTa	11/27	0.728994021867362	5	FACETS	0.955	0.868	1	0.318	0.289	0.349	CLONAL	1	TRUE	2	0.728994021867362	5		472	806	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337651	73337651	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	73	276	0	ENST00000377767.4:c.2065C>G	p.Arg689Gly	p.R689G	ENST00000377767	NM_014953.3	689	Cga/Gga	16/21	0.728994021867362	5	FACETS	0.926	0.812	1	0.309	0.27	0.349	CLONAL	1	TRUE	2	0.728994021867362	5		276	453	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023294	33023294	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1354011335	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	198	660	0	ENST00000300177.4:c.403G>A	p.Glu135Lys	p.E135K	ENST00000300177	NM_001191322.1	135	Gaa/Aaa	2/2	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.728994021867362	2		660	527	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423587	88423587	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	180	664	0	ENST00000360948.2:c.2248G>C	p.Glu750Gln	p.E750Q	ENST00000360948	NM_001012338.2	750	Gag/Cag	18/19	1	2	FACETS	0.974	0.906	1	0.974	0.906	1	CLONAL	1	TRUE	1	0.728994021867362	2		664	507	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799337	88799337	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	157	450	0	ENST00000360948.2:c.48C>G	p.Phe16Leu	p.F16L	ENST00000360948	NM_001012338.2	16	ttC/ttG	2/19	0.728994021867362	3	FACETS	1	0.989	1	0.72	0.667	0.774	CLONAL	1	TRUE	1	0.728994021867362	3		450	408	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646305	23646305	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	99	668	0	ENST00000261584.4:c.1562C>G	p.Thr521Ser	p.T521S	ENST00000261584	NM_024675.3	521	aCc/aGc	4/13	0.724950152181071	3	FACETS	0.53	0.473	0.591	0.177	0.157	0.197	SUBCLONAL	1	TRUE	0	0.728994021867362	3		668	699	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663861	29663861	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	152	500	0	ENST00000356175.3:c.6293G>C	p.Arg2098Thr	p.R2098T	ENST00000356175	NM_000267.3	2098	aGa/aCa	41/57	0.728994021867362	3	FACETS	0.948	0.871	1	0.474	0.435	0.514	CLONAL	1	TRUE	1	0.728994021867362	3		500	600	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664388	29664388	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	128	336	0	ENST00000356175.3:c.6367G>C	p.Glu2123Gln	p.E2123Q	ENST00000356175	NM_000267.3	2123	Gag/Cag	42/57	0.728994021867362	3	FACETS	1	0.94	1	0.519	0.473	0.566	CLONAL	1	TRUE	1	0.728994021867362	3		336	462	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325985	30325985	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	97	327	0	ENST00000322652.5:c.2183C>G	p.Ser728Ter	p.S728*	ENST00000322652	NM_015355.2	728	tCa/tGa	16/16	0.728994021867362	3	FACETS	0.958	0.861	1	0.479	0.43	0.53	CLONAL	1	TRUE	1	0.728994021867362	3		327	379	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775215	73775215	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	165	554	0	ENST00000254810.4:c.41G>T	p.Gly14Val	p.G14V	ENST00000254810	NM_005324.3	14	gGg/gTg	2/4	0.728994021867362	5	FACETS	1	0.938	1	0.342	0.314	0.371	CLONAL	1	TRUE	2	0.728994021867362	5		554	924	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394784	45394784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	103	400	0	ENST00000262160.6:c.565G>A	p.Glu189Lys	p.E189K	ENST00000262160	NM_005901.5	189	Gaa/Aaa	5/11	0.728994021867362	4	FACETS	0.839	0.753	0.931	0.28	0.251	0.311	CLONAL	1	TRUE	1	0.728994021867362	4		400	582	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229672	5229672	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs960841066	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	19	20	0	ENST00000357368.4:c.2179G>A	p.Val727Met	p.V727M	ENST00000357368	NM_002850.3	727	Gtg/Atg	15/38	0.728994021867362	3	FACETS	0.773	0.617	0.936	0.773	0.617	0.936	CLONAL	2	TRUE	1	0.728994021867362	3		20	46	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943694	17943694	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs201241352	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	165	603	0	ENST00000458235.1:c.2395C>G	p.Arg799Gly	p.R799G	ENST00000458235	NM_000215.3	799	Cgt/Ggt	18/24	0.728994021867362	3	FACETS	0.967	0.891	1	0.483	0.445	0.523	CLONAL	1	TRUE	1	0.728994021867362	3		603	639	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630400	47630400	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	149	583	0	ENST00000233146.2:c.70C>A	p.Gln24Lys	p.Q24K	ENST00000233146	NM_000251.2	24	Cag/Aag	1/16	0.728994021867362	3	FACETS	0.942	0.865	1	0.314	0.288	0.341	CLONAL	1	TRUE	0	0.728994021867362	3		583	592	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371586	225371586	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	79	414	0	ENST00000264414.4:c.1018G>C	p.Asp340His	p.D340H	ENST00000264414	NM_003590.4	340	Gac/Cac	7/16	1	2	FACETS	0.803	0.715	0.895	0.803	0.715	0.895	CLONAL	1	TRUE	1	0.728994021867362	2		414	270	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852507	42852507	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	151	549	0	ENST00000398585.3:c.579C>A	p.Phe193Leu	p.F193L	ENST00000398585	NM_001135099.1	193	ttC/ttA	6/14	0.728994021867362	6	FACETS	0.879	0.802	0.96	0.22	0.2	0.24	CLONAL	1	TRUE	2	0.728994021867362	6		549	1159	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165816	47165816	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs539506462	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	168	518	0	ENST00000409792.3:c.310C>A	p.Pro104Thr	p.P104T	ENST00000409792	NM_014159.6	104	Cca/Aca	3/21	0.726005898509938	3	FACETS	1	0.933	1	0.506	0.466	0.546	CLONAL	1	TRUE	1	0.728994021867362	3		518	622	SUCCESS
ATR	545	MSKCC	GRCh37	3	142254021	142254021	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	92	356	0	ENST00000350721.4:c.3846G>C	p.Gln1282His	p.Q1282H	ENST00000350721	NM_001184.3	1282	caG/caC	21/47	0.589548076349862	4	FACETS	0.927	0.827	1	0.463	0.413	0.516	CLONAL	1	TRUE	2	0.728994021867362	4		356	471	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149245641	149245641	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	440	646	0	ENST00000360632.3:c.887C>T	p.Ser296Leu	p.S296L	ENST00000360632	NM_015472.4	296	tCa/tTa	5/7	0.589548076349862	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.728994021867362	4		646	1011	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280088	66280088	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	98	320	0	ENST00000273854.3:c.1601C>T	p.Ser534Leu	p.S534L	ENST00000273854	NM_004439.5	534	tCa/tTa	7/18	1	2	FACETS	0.838	0.756	0.923	0.838	0.756	0.923	CLONAL	1	TRUE	1	0.728994021867362	2		320	321	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158129	106158129	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	95	319	0	ENST00000380013.4:c.3030G>C	p.Glu1010Asp	p.E1010D	ENST00000380013	NM_001127208.2	1010	gaG/gaC	3/11	1	2	FACETS	0.958	0.866	1	0.958	0.866	1	CLONAL	1	TRUE	1	0.728994021867362	2		319	272	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233625	233625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760542965	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	72	374	1	ENST00000264932.6:c.929G>A	p.Gly310Glu	p.G310E	ENST00000264932	NM_004168.2	310	gGa/gAa	8/15	0.728994021867362	5	FACETS	0.727	0.636	0.825	0.182	0.159	0.207	SUBCLONAL	1	TRUE	1	0.728994021867362	5		375	569	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38991158	38991158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	101	389	0	ENST00000357387.3:c.476C>T	p.Ser159Phe	p.S159F	ENST00000357387	NM_152756.3	159	tCc/tTc	7/38	0.728994021867362	5	FACETS	0.783	0.7	0.871			1	SUBCLONAL	1	TRUE	NA	0.728994021867362	5		389	741	SUCCESS
APC	324	MSKCC	GRCh37	5	112173556	112173556	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	111	294	0	ENST00000257430.4:c.2265G>C	p.Arg755Ser	p.R755S	ENST00000257430	NM_000038.5	755	agG/agC	16/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.728994021867362	2		294	266	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927011	131927011	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	59	268	0	ENST00000265335.6:c.1548G>C	p.Arg516Ser	p.R516S	ENST00000265335		516	agG/agC	10/25	1	2	FACETS	0.894	0.784	1	0.894	0.784	1	CLONAL	1	TRUE	1	0.728994021867362	2		268	181	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680137	30680137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	188	623	0	ENST00000376406.3:c.1582G>A	p.Glu528Lys	p.E528K	ENST00000376406	NM_014641.2	528	Gaa/Aaa	5/15	0.347051211551304	5	FACETS	1	0.983	1	0.407	0.376	0.439	INDETERMINATE	1	TRUE	2	0.728994021867362	5		623	884	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137540382	137540382	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	100	496	0	ENST00000367739.4:c.83C>T	p.Ser28Leu	p.S28L	ENST00000367739	NM_000416.2	28	tCa/tTa	1/7	0.347051211551304	5	FACETS	1	0.921	1	0.344	0.308	0.383	INDETERMINATE	1	TRUE	2	0.728994021867362	5		496	556	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527386	157527386	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	143	385	0	ENST00000346085.5:c.5111G>T	p.Gly1704Val	p.G1704V	ENST00000346085	NM_020732.3	1704	gGa/gTa	20/20	0.347051211551304	5	FACETS	1	0.984	1	0.445	0.407	0.485	INDETERMINATE	1	TRUE	2	0.728994021867362	5		385	615	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527871	157527871	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	131	465	0	ENST00000346085.5:c.5596G>C	p.Glu1866Gln	p.E1866Q	ENST00000346085	NM_020732.3	1866	Gaa/Caa	20/20	0.347051211551304	5	FACETS	1	0.963	1	0.371	0.337	0.407	INDETERMINATE	1	TRUE	2	0.728994021867362	5		465	676	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92354990	92354990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	110	324	0	ENST00000265734.4:c.487G>A	p.Asp163Asn	p.D163N	ENST00000265734	NM_001259.6	163	Gac/Aac	4/8	0.728994021867362	3	FACETS	0.919	0.831	1	0.46	0.415	0.506	CLONAL	1	TRUE	1	0.728994021867362	3		324	448	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506471	148506471	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	104	282	0	ENST00000320356.2:c.2041G>C	p.Asp681His	p.D681H	ENST00000320356	NM_004456.4	681	Gat/Cat	18/20	0.728994021867362	3	FACETS	1	0.956	1	0.55	0.497	0.605	CLONAL	1	TRUE	1	0.728994021867362	3		282	354	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860534	151860534	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	192	567	0	ENST00000262189.6:c.10128G>C	p.Gln3376His	p.Q3376H	ENST00000262189	NM_170606.2	3376	caG/caC	43/59	0.728994021867362	3	FACETS	1	0.931	1	0.502	0.466	0.539	CLONAL	1	TRUE	1	0.728994021867362	3		567	716	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878254	151878254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	188	571	0	ENST00000262189.6:c.6691G>A	p.Glu2231Lys	p.E2231K	ENST00000262189	NM_170606.2	2231	Gag/Aag	36/59	0.728994021867362	3	FACETS	1	0.964	1	0.531	0.492	0.57	CLONAL	1	TRUE	1	0.728994021867362	3		571	663	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486257	8486257	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs778093636	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	80	314	0	ENST00000356435.5:c.2560C>G	p.Gln854Glu	p.Q854E	ENST00000356435		854	Cag/Gag	17/35	0.704064372252512	3	FACETS	0.837	0.742	0.937	0.418	0.371	0.469	CLONAL	1	TRUE	1	0.728994021867362	3		314	358	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507412	8507412	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	69	256	0	ENST00000356435.5:c.1566C>G	p.Phe522Leu	p.F522L	ENST00000356435		522	ttC/ttG	11/35	0.704064372252512	3	FACETS	0.85	0.746	0.959	0.425	0.373	0.48	CLONAL	1	TRUE	1	0.728994021867362	3		256	304	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342644	70342644	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	155	331	0	ENST00000374080.3:c.1405G>C	p.Glu469Gln	p.E469Q	ENST00000374080		469	Gaa/Caa	10/45	0.728994021867362	2	FACETS	0.702	0.645	0.76			1	SUBCLONAL	1	TRUE	NA	0.728994021867362	2		331	606	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651513	52651513	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053509-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	125	477	0	ENST00000394830.3:c.1583A>T	p.Asn528Ile	p.N528I	ENST00000394830	NM_018313.4	528	aAt/aTt	15/30	0.430464105525603	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.430464105525603	1		477	445	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864331	151864331	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775712660	NA	P-0053509-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	141	460	0	ENST00000262189.6:c.9650G>A	p.Arg3217His	p.R3217H	ENST00000262189	NM_170606.2	3217	cGt/cAt	42/59	1	2	FACETS	0.976	0.892	1	0.976	0.892	1	CLONAL	1	TRUE	1	0.430464105525603	2		460	671	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900698	3900698	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053509-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	184	696	0	ENST00000262367.5:c.398T>C	p.Leu133Pro	p.L133P	ENST00000262367	NM_004380.2	133	cTg/cCg	2/31	1	2	FACETS	0.955	0.882	1	0.955	0.882	1	CLONAL	1	TRUE	1	0.430464105525603	2		696	895	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188303	10188303	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053509-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	144	546	0	ENST00000256474.2:c.446C>A	p.Ala149Asp	p.A149D	ENST00000256474	NM_000551.3	149	gCc/gAc	2/3	0.430464105525603	1	FACETS	0.998	0.916	1	0.998	0.916	1	CLONAL	1	TRUE	0	0.430464105525603	1		546	526	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231085	53231085	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1556842070	NA	P-0053509-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	166	339	0	ENST00000375401.3:c.1817A>T	p.Asn606Ile	p.N606I	ENST00000375401	NM_004187.3	606	aAc/aTc	13/26	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.430464105525603	1		339	407	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696688	47696688	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519971	NA	P-0053565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	96	441	0	ENST00000347630.2:c.260A>G	p.Tyr87Cys	p.Y87C	ENST00000347630	NM_001007230.1	87	tAc/tGc	5/11	0.2688137774007	3	FACETS	1	0.975	1	0.656	0.586	0.73	CLONAL	1	TRUE	1	0.316793068373278	3		441	535	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	39	301	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	0.971	0.817	1	0.971	0.817	1	CLONAL	1	TRUE	1	0.480967339183687	2		301	167	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	100	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.480967339183687	2		336	380	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114817	108114817	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786204543	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	127	410	0	ENST00000278616.4:c.640del	p.Ser214ProfsTer16	p.S214Pfs*16	ENST00000278616	NM_000051.3	212	Ttt/tt	6/63	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.480967339183687	2		410	508	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512474	38512474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770732457	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1447	213	969	1	ENST00000254066.5:c.1385C>T	p.Pro462Leu	p.P462L	ENST00000254066	NM_000964.3	462	cCg/cTg	9/9	1	2	FACETS	0.534	0.494	0.575	0.534	0.494	0.575	SUBCLONAL	1	TRUE	1	0.480967339183687	2		970	1660	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	175	472	8	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	0.308306351384233	3	FACETS	1	0.958	1	0.53	0.488	0.573	CLONAL	1	TRUE	1	0.480967339183687	3		480	852	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992721	68992721	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs764112302	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	48	439	1	ENST00000288368.4:c.1693del	p.Ser565ArgfsTer10	p.S565Rfs*10	ENST00000288368	NM_024870.2	562	cgT/cg	16/40	1	2	FACETS	0.409	0.346	0.479	0.409	0.346	0.479	SUBCLONAL	1	TRUE	1	0.480967339183687	2		440	488	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238958	5238958	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	244	551	0	ENST00000357368.4:c.1821del	p.Val608TrpfsTer30	p.V608Wfs*30	ENST00000357368	NM_002850.3	607	ccC/cc	13/38	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.480967339183687	2		551	990	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519896	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	142	275	0	ENST00000281708.4:c.1514G>A	p.Arg505His	p.R505H	ENST00000281708	NM_033632.3	505	cGc/cAc	10/12	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.480967339183687	2		275	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	522	529	1	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	0.480967339183687	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.480967339183687	2		530	979	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	211	718	3	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.95	0.883	1	0.95	0.883	1	CLONAL	1	TRUE	1	0.480967339183687	2		721	924	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	187	374	0	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	0.949	0.878	1	0.949	0.878	1	CLONAL	1	TRUE	1	0.480967339183687	2		374	819	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817489	39817489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763409220	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	98	492	0	ENST00000288319.7:c.74C>T	p.Thr25Met	p.T25M	ENST00000288319	NM_182918.3	25	aCg/aTg	2/10	0.403497433635693	1	FACETS	0.4	0.356	0.446	0.4	0.356	0.446	SUBCLONAL	1	TRUE	0	0.480967339183687	1		492	774	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	146	421	0	ENST00000311936.3:c.180_181delinsAA	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggAAaa	3/5	0.467299985003116	3	FACETS	0.953	0.871	1			1	CLONAL	1	TRUE	NA	0.480967339183687	3		421	790	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393659	139393659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773137647	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1216	475	1009	0	ENST00000277541.6:c.5987C>T	p.Thr1996Met	p.T1996M	ENST00000277541	NM_017617.3	1996	aCg/aTg	32/34	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.480967339183687	2		1009	1691	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602746	10602746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1197	364	977	3	ENST00000171111.5:c.832C>T	p.Pro278Ser	p.P278S	ENST00000171111	NM_203500.1	278	Ccg/Tcg	3/6	1	2	FACETS	0.97	0.917	1	0.97	0.917	1	CLONAL	1	TRUE	1	0.480967339183687	2		980	1561	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468080	50468080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	167	547	0	ENST00000331340.3:c.1315C>T	p.Arg439Cys	p.R439C	ENST00000331340	NM_006060.4	439	Cgc/Tgc	8/8	0.480967339183687	3	FACETS	0.786	0.721	0.854	0.393	0.36	0.427	SUBCLONAL	1	TRUE	1	0.480967339183687	3		547	1096	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160574	56160574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	27	182	0	ENST00000399503.3:c.848G>A	p.Arg283Lys	p.R283K	ENST00000399503	NM_005921.1	283	aGa/aAa	4/20	1	2	FACETS	0.316	0.251	0.39	0.316	0.251	0.39	SUBCLONAL	1	TRUE	1	0.480967339183687	2		182	355	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829075	128829075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1247591045	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	25	30	0	ENST00000249373.3:c.88del	p.Ala30ArgfsTer25	p.A30Rfs*25	ENST00000249373	NM_005631.4	28	cGg/cg	1/12	0.480967339183687	3	FACETS	0.759	0.614	0.914	0.759	0.614	0.914	CLONAL	2	TRUE	1	0.480967339183687	3		30	85	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161456	2161456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs970922682	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	332	678	0	ENST00000434045.2:c.71G>A	p.Arg24His	p.R24H	ENST00000434045	NM_001127598.1	24	cGc/cAc	2/5	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.480967339183687	2		678	1281	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897046	28897047	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	170	426	0	ENST00000282397.4:c.2833dup	p.Met945AsnfsTer15	p.M945Nfs*15	ENST00000282397	NM_002019.4	945	atg/aAtg	21/30	0.480967339183687	3	FACETS	0.967	0.889	1	0.483	0.444	0.524	CLONAL	1	TRUE	1	0.480967339183687	3		426	907	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229256	36229256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	309	713	0	ENST00000222270.7:c.7946G>A	p.Arg2649His	p.R2649H	ENST00000222270	NM_014727.1	2649	cGc/cAc	37/37	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.480967339183687	2		713	1203	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381559	81381559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777026877	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	86	218	1	ENST00000222390.5:c.502C>T	p.Arg168Trp	p.R168W	ENST00000222390	NM_000601.4	168	Cgg/Tgg	5/18	0.480967339183687	3	FACETS	1	0.938	1	0.54	0.48	0.603	CLONAL	1	TRUE	1	0.480967339183687	3		219	411	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259533	55259533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	217	522	0	ENST00000275493.2:c.2591C>T	p.Ala864Val	p.A864V	ENST00000275493	NM_005228.3	864	gCg/gTg	21/28	0.480967339183687	3	FACETS	0.953	0.885	1	0.476	0.442	0.512	CLONAL	1	TRUE	1	0.480967339183687	3		522	1175	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7152776	7152776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	310	650	2	ENST00000302850.5:c.2192C>T	p.Thr731Met	p.T731M	ENST00000302850	NM_000208.2	731	aCg/aTg	10/22	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.480967339183687	2		652	1186	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958587	38958587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs532413623	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	22	141	0	ENST00000357387.3:c.2378C>T	p.Ala793Val	p.A793V	ENST00000357387	NM_152756.3	793	gCg/gTg	24/38	1	2	FACETS	0.438	0.341	0.549	0.438	0.341	0.549	SUBCLONAL	1	TRUE	1	0.480967339183687	2		141	209	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864391	57864391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753413155	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	351	811	2	ENST00000228682.2:c.1868G>A	p.Arg623Gln	p.R623Q	ENST00000228682	NM_005269.2	623	cGa/cAa	12/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.480967339183687	2		813	1347	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247767	10247767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781301028	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	348	827	0	ENST00000340748.4:c.4435G>A	p.Val1479Met	p.V1479M	ENST00000340748		1479	Gtg/Atg	36/40	1	2	FACETS	0.989	0.935	1	0.989	0.935	1	CLONAL	1	TRUE	1	0.480967339183687	2		827	1463	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267003	41267003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144087793	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	159	384	0	ENST00000349496.5:c.674G>A	p.Arg225His	p.R225H	ENST00000349496	NM_001904.3	225	cGt/cAt	5/15	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.480967339183687	2		384	649	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058545	72058545	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	160	412	0	ENST00000357731.5:c.895G>T	p.Ala299Ser	p.A299S	ENST00000357731	NM_173808.2	299	Gct/Tct	6/7	1	2	FACETS	0.99	0.911	1	0.99	0.911	1	CLONAL	1	TRUE	1	0.480967339183687	2		412	672	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88676895	88676895	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	37	493	0	ENST00000372037.3:c.680A>G	p.Gln227Arg	p.Q227R	ENST00000372037	NM_004329.2	227	cAg/cGg	9/13	0.480967339183687	1	FACETS	0.183	0.15	0.22	0.183	0.15	0.22	SUBCLONAL	1	TRUE	0	0.480967339183687	1		493	639	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681405	88681405	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	153	286	1	ENST00000372037.3:c.1295G>T	p.Ser432Ile	p.S432I	ENST00000372037	NM_004329.2	432	aGc/aTc	11/13	0.480967339183687	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.480967339183687	1		287	403	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18576963	18576963	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	241	341	0	ENST00000266497.5:c.2371C>A	p.Arg791Ser	p.R791S	ENST00000266497		791	Cgt/Agt	16/31	0.308306351384233	3	FACETS	0.949	0.892	1	0.949	0.892	1	CLONAL	2	TRUE	1	0.480967339183687	3		341	655	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81968079	81968079	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	183	348	0	ENST00000359376.3:c.2785G>A	p.Glu929Lys	p.E929K	ENST00000359376	NM_002661.3	929	Gag/Aag	26/33	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.480967339183687	2		348	752	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350571	89350571	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	198	445	0	ENST00000301030.4:c.2379G>T	p.Lys793Asn	p.K793N	ENST00000301030	NM_001256183.1	793	aaG/aaT	9/13	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.480967339183687	2		445	713	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250867	10250867	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	336	745	0	ENST00000340748.4:c.3613A>G	p.Asn1205Asp	p.N1205D	ENST00000340748		1205	Aac/Gac	32/40	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.480967339183687	2		745	1327	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214683	36214683	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	328	766	0	ENST00000222270.7:c.3109G>T	p.Glu1037Ter	p.E1037*	ENST00000222270	NM_014727.1	1037	Gag/Tag	8/37	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.480967339183687	2		766	1179	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551328	29551329	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	236	547	0	ENST00000389048.3:c.1301dup	p.Met435AspfsTer22	p.M435Dfs*22	ENST00000389048	NM_004304.4	434	aag/aaAg	6/29	1	2	FACETS	0.996	0.93	1	0.996	0.93	1	CLONAL	1	TRUE	1	0.480967339183687	2		547	985	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205736	128205736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553771139	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	349	706	0	ENST00000341105.2:c.139G>A	p.Val47Ile	p.V47I	ENST00000341105	NM_032638.4	47	Gtc/Atc	2/6	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.480967339183687	2		706	1364	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821372	32821372	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	66	1015	1	ENST00000354258.4:c.222C>A	p.Cys74Ter	p.C74*	ENST00000354258	NM_000593.5	74	tgC/tgA	1/11	0.480967339183687	1	FACETS	0.176	0.151	0.202	0.176	0.151	0.202	SUBCLONAL	1	TRUE	0	0.480967339183687	1		1016	1187	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528189	157528189	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	383	507	1	ENST00000346085.5:c.5914G>A	p.Val1972Met	p.V1972M	ENST00000346085	NM_020732.3	1972	Gtg/Atg	20/20	0.339965003167012	3	FACETS	0.973	0.927	1	0.973	0.927	1	CLONAL	2	TRUE	1	0.480967339183687	3		508	1015	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649661	48649662	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	434	896	0	ENST00000376670.3:c.149dup	p.Ser51GlufsTer17	p.S51Efs*17	ENST00000376670	NM_002049.3	49	gcc/gCcc	2/6	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.480967339183687	2		896	1500	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411417	63411417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370276785	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	323	779	0	ENST00000330258.3:c.1750C>T	p.Arg584Cys	p.R584C	ENST00000330258	NM_152424.3	584	Cgt/Tgt	2/2	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.480967339183687	2		779	1307	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413062	63413062	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	471	849	0	ENST00000330258.3:c.105G>T	p.Glu35Asp	p.E35D	ENST00000330258	NM_152424.3	35	gaG/gaT	2/2	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.480967339183687	2		849	1526	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0056813-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	23	529	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.825	0.645	1	0.825	0.645	1	CLONAL	1	TRUE	1	0.216128636566579	2		529	258	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0056813-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	192	571	0				ENST00000310581	NM_198253.2	-/1132			0.216128636566579	6	FACETS	0.983	0.914	1	0.983	0.914	1	CLONAL	4	TRUE	2	0.216128636566579	6		571	647	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0056813-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	117	857	1	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.216128636566579	2		858	868	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160227	22160227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056813-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	34	680	0	ENST00000215832.6:c.404G>A	p.Arg135Lys	p.R135K	ENST00000215832	NM_002745.4	135	aGa/aAa	3/9	1	2	FACETS	0.547	0.446	0.661	0.547	0.446	0.661	SUBCLONAL	1	TRUE	1	0.216128636566579	2		680	575	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828782	72828782	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0056813-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	46	794	0	ENST00000268489.5:c.7799C>G	p.Ser2600Ter	p.S2600*	ENST00000268489	NM_006885.3	2600	tCa/tGa	9/10	1	2	FACETS	0.492	0.413	0.58	0.492	0.413	0.58	SUBCLONAL	1	TRUE	1	0.216128636566579	2		794	865	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0056813-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	64	625	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	1	2	FACETS	0.914	0.791	1	0.914	0.791	1	CLONAL	1	TRUE	1	0.216128636566579	2		625	648	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0056813-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	43	575	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	0.978	0.819	1	0.978	0.819	1	CLONAL	1	TRUE	1	0.216128636566579	2		575	407	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786767	3786767	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587783495	NA	P-0056813-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	41	665	0	ENST00000262367.5:c.4444T>G	p.Tyr1482Asp	p.Y1482D	ENST00000262367	NM_004380.2	1482	Tac/Gac	27/31	1	2	FACETS	0.569	0.473	0.676	0.569	0.473	0.676	SUBCLONAL	1	TRUE	1	0.216128636566579	2		665	667	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112311	115112311	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056813-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	40	849	0	ENST00000257566.3:c.1429G>A	p.Glu477Lys	p.E477K	ENST00000257566	NM_016569.3	477	Gag/Aag	7/8	1	2	FACETS	0.516	0.428	0.615	0.516	0.428	0.615	SUBCLONAL	1	TRUE	1	0.216128636566579	2		849	717	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100403	8100403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056813-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	112	1046	0	ENST00000346208.3:c.377C>T	p.Ser126Phe	p.S126F	ENST00000346208		126	tCc/tTc	3/6	1	2	FACETS	0.947	0.85	1	0.947	0.85	1	CLONAL	1	TRUE	1	0.216128636566579	2		1046	1094	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513574	41513574	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056813-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	60	864	0	ENST00000263253.7:c.478C>T	p.Gln160Ter	p.Q160*	ENST00000263253	NM_001429.3	160	Cag/Tag	2/31	1	2	FACETS	0.727	0.625	0.838	0.727	0.625	0.838	SUBCLONAL	1	TRUE	1	0.216128636566579	2		864	764	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041576	47041576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056813-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	63	412	0	ENST00000377604.3:c.1801C>T	p.Gln601Ter	p.Q601*	ENST00000377604	NM_001204468.1	601	Cag/Tag	17/24	1	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.216128636566579	1		412	437	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427764	72427764	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056813-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	115	682	0	ENST00000477973.2:c.726G>C	p.Arg242Ser	p.R242S	ENST00000477973	NM_012234.5	242	agG/agC	4/4	1	2	FACETS	0.952	0.855	1	0.952	0.855	1	CLONAL	1	TRUE	1	0.216128636566579	2		682	1118	SUCCESS
CBL	867	MSKCC	GRCh37	11	119158623	119158623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056813-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	92	534	0	ENST00000264033.4:c.2003C>T	p.Ser668Leu	p.S668L	ENST00000264033	NM_005188.3	668	tCa/tTa	12/16	0.162118081397344	2	FACETS	1	0.979	1	0.73	0.65	0.815	CLONAL	1	TRUE	0	0.216128636566579	2		534	583	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517446	157517446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761133847	NA	P-0056813-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	26	0	0	ENST00000346085.5:c.4010G>A	p.Arg1337Gln	p.R1337Q	ENST00000346085	NM_020732.3	1337	cGa/cAa	16/20	1	2	FACETS	0.459	0.363	0.57	0.459	0.363	0.57	SUBCLONAL	1	TRUE	1	0.216128636566579	2		0	524	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097818	8097818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290396136	NA	P-0056813-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	81	852	0	ENST00000346208.3:c.200C>T	p.Ser67Leu	p.S67L	ENST00000346208		67	tCg/tTg	2/6	1	2	FACETS	0.851	0.748	0.961	0.851	0.748	0.961	CLONAL	1	TRUE	1	0.216128636566579	2		852	881	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003132	42003132	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1363709175	NA	P-0056813-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	53	669	0	ENST00000219905.7:c.2669C>G	p.Ser890Cys	p.S890C	ENST00000219905	NM_001164273.1	890	tCt/tGt	8/24	0.216128636566579	1	FACETS	0.797	0.679	0.925	0.797	0.679	0.925	CLONAL	1	TRUE	0	0.216128636566579	1		669	549	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347768	347768	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056813-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	74	723	0	ENST00000262320.3:c.1738G>C	p.Glu580Gln	p.E580Q	ENST00000262320	NM_003502.3	580	Gag/Cag	6/11	1	2	FACETS	0.896	0.784	1	0.896	0.784	1	CLONAL	1	TRUE	1	0.216128636566579	2		723	764	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639171	3639171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1378182049	NA	P-0056813-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	81	916	0	ENST00000294008.3:c.4468G>A	p.Glu1490Lys	p.E1490K	ENST00000294008	NM_032444.2	1490	Gag/Aag	12/15	1	2	FACETS	0.827	0.727	0.935	0.827	0.727	0.935	CLONAL	1	TRUE	1	0.216128636566579	2		916	906	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37672051	37672051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056813-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	29	451	0	ENST00000447079.4:c.2836G>A	p.Glu946Lys	p.E946K	ENST00000447079	NM_015083.1	946	Gaa/Aaa	9/14	1	2	FACETS	0.495	0.396	0.608	0.495	0.396	0.608	SUBCLONAL	1	TRUE	1	0.216128636566579	2		451	542	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865298	40865298	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056813-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	107	622	0	ENST00000428826.2:c.1133C>T	p.Ser378Phe	p.S378F	ENST00000428826		378	tCt/tTt	11/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.216128636566579	2		622	851	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220291	5220291	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056813-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	50	781	0	ENST00000357368.4:c.3529G>A	p.Glu1177Lys	p.E1177K	ENST00000357368	NM_002850.3	1177	Gag/Aag	21/38	1	2	FACETS	0.698	0.591	0.816	0.698	0.591	0.816	SUBCLONAL	1	TRUE	1	0.216128636566579	2		781	663	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10244895	10244895	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0056813-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	36	630	0	ENST00000340748.4:c.4814C>G	p.Ser1605Ter	p.S1605*	ENST00000340748		1605	tCa/tGa	39/40	1	2	FACETS	0.514	0.421	0.619	0.514	0.421	0.619	SUBCLONAL	1	TRUE	1	0.216128636566579	2		630	648	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218684	36218684	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056813-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	220	947	0	ENST00000222270.7:c.4388C>T	p.Ser1463Phe	p.S1463F	ENST00000222270	NM_014727.1	1463	tCt/tTt	17/37	0.216128636566579	3	FACETS	1	0.962	1	0.701	0.652	0.752	CLONAL	2	TRUE	0	0.216128636566579	3		947	1073	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940037	49940037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146988970	NA	P-0056813-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	56	970	0	ENST00000296474.3:c.1006G>A	p.Glu336Lys	p.E336K	ENST00000296474	NM_002447.2	336	Gag/Aag	1/20	1	2	FACETS	0.558	0.476	0.647	0.558	0.476	0.647	SUBCLONAL	1	TRUE	1	0.216128636566579	2		970	929	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969386	44969387	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CATTGCCAAGATTGTGCACGAAAAACAAGCGG	novel	NA	P-0056813-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	19	317	0	ENST00000377967.4:c.4069_4100dup	p.Asn1368IlefsTer19	p.N1368Ifs*19	ENST00000377967	NM_021140.2	1356	-/CATTGCCAAGATTGTGCACGAAAAACAAGCGG	28/29	1	1	FACETS	0.659	0.501	0.844	0.659	0.501	0.844	SUBCLONAL	1	TRUE	0	0.216128636566579	1		317	238	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21643295	21643295	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056813-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	23	339	0	ENST00000421138.2:c.232A>G	p.Lys78Glu	p.K78E	ENST00000421138		78	Aaa/Gaa	5/16	1	2	FACETS	0.724	0.565	0.907	0.724	0.565	0.907	CLONAL	1	TRUE	1	0.216128636566579	2		339	294	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	624	345	0				ENST00000310581	NM_198253.2	-/1132			0.704789591387229	5	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	2	0.704789591387229	5		345	1209	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0058637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	337	699	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.704789591387229	2		699	871	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514495	NA	P-0058637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	388	809	0	ENST00000269305.4:c.542G>A	p.Arg181His	p.R181H	ENST00000269305	NM_001126112.2	181	cGc/cAc	5/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.704789591387229	2		809	1071	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105551	27105551	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	513	663	0	ENST00000324856.7:c.5162G>C	p.Arg1721Pro	p.R1721P	ENST00000324856	NM_006015.4	1721	cGa/cCa	20/20	0.430575544211358	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.704789591387229	1		663	751	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150936725	150936725	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	391	767	0	ENST00000271640.5:c.3761G>A	p.Arg1254Lys	p.R1254K	ENST00000271640	NM_001145415.1	1254	aGa/aAa	22/22	0.358043100664319	3	FACETS	1	0.994	1	0.669	0.636	0.702	INDETERMINATE	1	TRUE	1	0.704789591387229	3		767	1122	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243859016	243859016	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs397514606	NA	P-0058637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	9	447	0	ENST00000263826.5:c.49G>A	p.Glu17Lys	p.E17K	ENST00000263826	NM_005465.4	17	Gaa/Aaa	2/13	0.358043100664319	3	FACETS	0.096	0.063	0.139	0.048	0.031	0.07	INDETERMINATE	1	TRUE	1	0.704789591387229	3		447	358	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111437	8111437	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	287	607	0	ENST00000346208.3:c.923C>T	p.Ser308Phe	p.S308F	ENST00000346208		308	tCt/tTt	5/6	0.383868336526251	1	FACETS	0.835	0.791	0.878	0.835	0.791	0.878	INDETERMINATE	1	TRUE	0	0.704789591387229	1		607	632	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63816885	63816885	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	242	501	0	ENST00000279873.7:c.856G>C	p.Glu286Gln	p.E286Q	ENST00000279873	NM_032199.2	286	Gag/Cag	6/10	0.383868336526251	1	FACETS	0.751	0.707	0.796	0.751	0.707	0.796	INDETERMINATE	1	TRUE	0	0.704789591387229	1		501	592	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32932056	32932056	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	250	635	0	ENST00000380152.3:c.7795G>C	p.Glu2599Gln	p.E2599Q	ENST00000380152		2599	Gaa/Caa	16/27	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.704789591387229	2		635	686	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951120	48951120	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	148	434	0	ENST00000267163.4:c.1282G>T	p.Glu428Ter	p.E428*	ENST00000267163	NM_000321.2	428	Gag/Tag	13/27	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.704789591387229	2		434	388	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955394	48955394	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886043247	NA	P-0058637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	88	409	0	ENST00000267163.4:c.1510C>T	p.Gln504Ter	p.Q504*	ENST00000267163	NM_000321.2	504	Cag/Tag	17/27	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.704789591387229	2		409	235	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988856	41988856	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	160	639	0	ENST00000219905.7:c.1648C>G	p.Gln550Glu	p.Q550E	ENST00000219905	NM_001164273.1	550	Cag/Gag	3/24	0.445648092967794	1	FACETS	0.51	0.469	0.551	0.51	0.469	0.551	SUBCLONAL	1	TRUE	0	0.704789591387229	1		639	577	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456507	189456507	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	293	586	0	ENST00000264731.3:c.268G>C	p.Glu90Gln	p.E90Q	ENST00000264731	NM_003722.4	90	Gag/Cag	3/14	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.704789591387229	2		586	778	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057000	180057000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762995809	NA	P-0058637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	315	679	0	ENST00000261937.6:c.619G>A	p.Glu207Lys	p.E207K	ENST00000261937	NM_182925.4	207	Gag/Aag	5/30	0.445648092967794	1	FACETS	0.859	0.817	0.901	0.859	0.817	0.901	CLONAL	1	TRUE	0	0.704789591387229	1		679	674	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845722	151845722	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058637-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	273	649	0	ENST00000262189.6:c.13290G>C	p.Leu4430Phe	p.L4430F	ENST00000262189	NM_170606.2	4430	ttG/ttC	52/59	0.323579087347622	1	FACETS	0.562	0.528	0.596	0.562	0.528	0.596	INDETERMINATE	1	TRUE	0	0.704789591387229	1		649	893	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1690591	1690592	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGAG	novel	NA	P-0060468-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	73	670	0	ENST00000378625.1:c.519_523dup	p.Gly175AlafsTer7	p.G175Afs*7	ENST00000378625	NM_001198994.1	175	ggc/gCTCTGgc	5/14	0.489858363305995	3	FACETS	0.511	0.446	0.581	0.255	0.223	0.291	SUBCLONAL	1	TRUE	1	0.503926042511502	3		670	710	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498477	89498477	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs753130827	NA	P-0060468-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	39	680	0	ENST00000336596.2:c.2449G>T	p.Val817Leu	p.V817L	ENST00000336596	NM_005233.5	817	Gtg/Ttg	14/17	1	2	FACETS	0.27	0.223	0.323	0.27	0.223	0.323	SUBCLONAL	1	TRUE	1	0.503926042511502	2		680	573	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0060489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	7834	734	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.383778040870649	46	FACETS	1	0.997	1			1	CLONAL	46	TRUE	NA	0.383778040870649	46		734	8371	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36945090	36945090	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	108	650	0	ENST00000361632.4:c.8G>T	p.Arg3Met	p.R3M	ENST00000361632		3	aGg/aTg	2/16	1	2	FACETS	0.972	0.875	1	0.972	0.875	1	CLONAL	1	TRUE	1	0.383778040870649	2		650	579	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911721	26911721	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	11	33	0	ENST00000381527.3:c.146A>G	p.Tyr49Cys	p.Y49C	ENST00000381527	NM_001260.1	49	tAt/tGt	2/13	0.383778040870649	6	FACETS	0.779	0.549	1	0.52	0.366	0.702	CLONAL	2	TRUE	3	0.383778040870649	6		33	65	SUCCESS
APC	324	MSKCC	GRCh37	5	112128171	112128171	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs863225371	NA	P-0060489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	38	181	0	ENST00000257430.4:c.677del	p.Lys226ArgfsTer67	p.K226Rfs*67	ENST00000257430	NM_000038.5	225	gAa/ga	7/16	0.350157968259218	2	FACETS	0.839	0.711	0.975	0.839	0.711	0.975	CLONAL	2	TRUE	0	0.383778040870649	2		181	118	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0060557-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	29	529	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.817	1	1	0.959	1	CLONAL	2	TRUE	1	0.220955997248665	2		529	131	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0060557-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	75	403	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.756	0.665	0.853	1	0.976	1	SUBCLONAL	2	TRUE	1	0.220955997248665	2		403	449	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057988	27057988	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060557-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	87	489	0	ENST00000324856.7:c.1696C>T	p.Gln566Ter	p.Q566*	ENST00000324856	NM_006015.4	566	Cag/Tag	3/20	1	2	FACETS	0.879	0.782	0.982	1	0.983	1	CLONAL	2	TRUE	1	0.220955997248665	2		489	448	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102098	27102098	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060557-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	86	482	0	ENST00000324856.7:c.5026del	p.Leu1676SerfsTer13	p.L1676Sfs*13	ENST00000324856	NM_006015.4	1675	tCc/tc	19/20	1	2	FACETS	0.936	0.832	1	1	0.984	1	CLONAL	2	TRUE	1	0.220955997248665	2		482	416	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799563	72799563	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060557-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	75	390	1	ENST00000325599.8:c.1606G>A	p.Gly536Arg	p.G536R	ENST00000325599	NM_018130.2	536	Ggg/Agg	11/11	1	2	FACETS	0.9	0.794	1	1	0.981	1	CLONAL	2	TRUE	1	0.220955997248665	2		391	377	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317085	87317085	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060557-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	42	375	0	ENST00000277120.3:c.224A>T	p.Asn75Ile	p.N75I	ENST00000277120		75	aAc/aTc	3/19	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.220955997248665	2		375	345	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0060791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	26	437	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.251693232971187	4	FACETS	0.754	0.61	0.912	0.754	0.61	0.912	INDETERMINATE	2	FALSE	2	0.482039010689163	4		437	106	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859595	151859595	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	54	717	0	ENST00000262189.6:c.11067C>G	p.Phe3689Leu	p.F3689L	ENST00000262189	NM_170606.2	3689	ttC/ttG	43/59	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	FALSE	1	0.482039010689163	2		717	223	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992577	72992578	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0060791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	69	739	1	ENST00000268489.5:c.1467_1468delinsTT	p.Glu489_Gly490delinsAspCys	p.E489_G490delinsDC	ENST00000268489	NM_006885.3	489	gaGGgt/gaTTgt	2/10	0.482039010689163	1	FACETS	0.988	0.874	1	0.988	0.874	1	CLONAL	1	FALSE	0	0.482039010689163	1		740	220	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272097	18272097	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	63	847	0	ENST00000222254.8:c.607G>C	p.Gly203Arg	p.G203R	ENST00000222254	NM_005027.3	203	Ggg/Cgg	6/16	1	2	FACETS	0.602	0.522	0.688	0.602	0.522	0.688	SUBCLONAL	1	FALSE	1	0.482039010689163	2		847	434	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793432	42793437	+	inframe_deletion	In_Frame_Del	DEL	GCCACT	GCCACT	-	novel	NA	P-0060791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	60	647	0	ENST00000575354.2:c.1235_1240del	p.Ala412_Thr413del	p.A412_T413del	ENST00000575354	NM_015125.3	412	GCCACT/-	8/20	0.351609855749086	4	FACETS	0.944	0.816	1	0.472	0.408	0.541	CLONAL	1	FALSE	2	0.482039010689163	4		647	391	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252884	36252884	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	166	459	0	ENST00000300305.3:c.478G>C	p.Asp160His	p.D160H	ENST00000300305		160	Gac/Cac	4/8	0.265566982939271	3	FACETS	0.766	0.708	0.826	0.766	0.708	0.826	INDETERMINATE	2	FALSE	1	0.482039010689163	3		459	558	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249744	110249744	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	56	596	0	ENST00000374672.4:c.931C>G	p.Leu311Val	p.L311V	ENST00000374672	NM_004235.4	311	Ctc/Gtc	3/5	1	2	FACETS	0.662	0.57	0.762	0.662	0.57	0.762	SUBCLONAL	1	FALSE	1	0.482039010689163	2		596	351	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060879-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	248	345	0				ENST00000310581	NM_198253.2	-/1132			0.673851129230301	3	FACETS	0.956	0.904	1	0.956	0.904	1	CLONAL	2	TRUE	1	0.675369515881295	3		345	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0060879-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	320	699	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.673851129230301	3	FACETS	0.98	0.933	1	0.98	0.933	1	CLONAL	2	TRUE	1	0.675369515881295	3		699	647	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0060879-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	219	608	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.673851129230301	3	FACETS	1	0.981	1	0.566	0.528	0.605	CLONAL	1	TRUE	1	0.675369515881295	3		608	767	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0060879-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	338	867	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	0.673851129230301	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.675369515881295	3		867	669	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38968131	38968131	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs143280630	NA	P-0060879-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	100	273	0	ENST00000357387.3:c.974G>A	p.Arg325Gln	p.R325Q	ENST00000357387	NM_152756.3	325	cGa/cAa	12/38	0.675369515881295	6	FACETS	0.699	0.623	0.78			1	SUBCLONAL	1	TRUE	NA	0.675369515881295	6		273	996	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160485	108160485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060879-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	167	405	0	ENST00000278616.4:c.4393C>T	p.Leu1465Phe	p.L1465F	ENST00000278616	NM_000051.3	1465	Ctt/Ttt	29/63	0.673851129230301	3	FACETS	1	0.965	1	0.539	0.497	0.582	CLONAL	1	TRUE	1	0.675369515881295	3		405	614	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503192	125503192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060879-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	219	478	1	ENST00000428830.2:c.559G>A	p.Glu187Lys	p.E187K	ENST00000428830	NM_001114121.2	187	Gaa/Aaa	6/14	0.673851129230301	3	FACETS	1	0.985	1	0.591	0.552	0.631	CLONAL	1	TRUE	1	0.675369515881295	3		479	734	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630800	90630800	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0060879-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	260	640	0	ENST00000330062.3:c.686C>G	p.Ser229Ter	p.S229*	ENST00000330062	NM_002168.2	229	tCa/tGa	6/11	0.249963587603839	5	FACETS	1	0.977	1	0.717	0.675	0.759	INDETERMINATE	2	TRUE	2	0.675369515881295	5		640	721	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041884	14041884	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060879-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	236	598	0	ENST00000311895.7:c.2431G>A	p.Glu811Lys	p.E811K	ENST00000311895	NM_005236.2	811	Gag/Aag	11/11	0.673851129230301	3	FACETS	1	0.981	1	0.56	0.523	0.597	CLONAL	1	TRUE	1	0.675369515881295	3		598	835	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721190	61721190	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060879-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	1612	409	0	ENST00000401558.2:c.1084G>C	p.Glu362Gln	p.E362Q	ENST00000401558	NM_003400.3	362	Gaa/Caa	12/25	0.675369515881295	12	FACETS	0.995	0.983	1			1	CLONAL	11	TRUE	NA	0.675369515881295	12		409	1909	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137320992	137321003	+	inframe_deletion	In_Frame_Del	DEL	TCCATCGCCGTG	TCCATCGCCGTG	-	novel	NA	P-0060879-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	356	643	0	ENST00000481739.1:c.949_960del	p.Ser317_Val320del	p.S317_V320del	ENST00000481739	NM_002957.4	317	TCCATCGCCGTG/-	7/10	0.673851129230301	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.675369515881295	2		643	462	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941963	44941963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060879-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	366	242	0	ENST00000377967.4:c.3213del	p.Arg1073GlyfsTer10	p.R1073Gfs*10	ENST00000377967	NM_021140.2	1071	tcT/tc	22/29	0.673851129230301	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.675369515881295	2		242	464	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1688072	1688072	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060879-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	57	559	0	ENST00000378625.1:c.804G>C	p.Met268Ile	p.M268I	ENST00000378625	NM_001198994.1	268	atG/atC	7/14	0.673851129230301	3	FACETS	0.323	0.276	0.374	0.162	0.138	0.187	SUBCLONAL	1	TRUE	1	0.675369515881295	3		559	699	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150913892	150913892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060879-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	43	400	0	ENST00000271640.5:c.535G>A	p.Asp179Asn	p.D179N	ENST00000271640	NM_001145415.1	179	Gat/Aat	5/22	0.673851129230301	3	FACETS	0.3	0.25	0.355	0.15	0.125	0.178	SUBCLONAL	1	TRUE	1	0.675369515881295	3		400	568	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170204	119170204	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0060879-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	160	469	0	ENST00000264033.4:c.2435-1G>C		p.X812_splice	ENST00000264033	NM_005188.3	812			0.673851129230301	3	FACETS	1	0.93	1	0.505	0.465	0.547	CLONAL	1	TRUE	1	0.675369515881295	3		469	627	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488300	56488300	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772678619	NA	P-0060879-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	63	527	0	ENST00000267101.3:c.1819C>T	p.Gln607Ter	p.Q607*	ENST00000267101	NM_001982.3	607	Cag/Tag	15/28	0.673851129230301	3	FACETS	0.347	0.299	0.398	0.173	0.149	0.199	SUBCLONAL	1	TRUE	1	0.675369515881295	3		527	720	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40678688	40678688	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060879-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	45	511	0	ENST00000249776.8:c.430G>C	p.Glu144Gln	p.E144Q	ENST00000249776	NM_033286.3	144	Gag/Cag	3/9	0.249963587603839	5	FACETS	0.384	0.322	0.454	0.128	0.107	0.152	INDETERMINATE	1	TRUE	2	0.675369515881295	5		511	698	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646669	23646669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060879-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	37	500	0	ENST00000261584.4:c.1198G>A	p.Glu400Lys	p.E400K	ENST00000261584	NM_024675.3	400	Gaa/Aaa	4/13	0.673851129230301	3	FACETS	0.236	0.194	0.283	0.118	0.097	0.142	SUBCLONAL	1	TRUE	1	0.675369515881295	3		500	621	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056437	26056437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781281855	NA	P-0060879-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	34	588	0	ENST00000343677.2:c.220G>A	p.Glu74Lys	p.E74K	ENST00000343677	NM_005319.3	74	Gag/Aag	1/1	0.673851129230301	3	FACETS	0.202	0.164	0.244	0.101	0.082	0.122	SUBCLONAL	1	TRUE	1	0.675369515881295	3		588	668	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740416	145740493	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTGCCGGCACCTGTAGGCAGCACCAGCAGCGTGGAGATGCCTGGATGGGGCGGGAGTCAGCAGCAGGGTTCTGCAGC	CTTGCCGGCACCTGTAGGCAGCACCAGCAGCGTGGAGATGCCTGGATGGGGCGGGAGTCAGCAGCAGGGTTCTGCAGC	-	novel	NA	P-0060879-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	55	740	0	ENST00000428558.2:c.1484-37_1524del		p.X495_splice	ENST00000428558	NM_004260.3	495		9/22	0.673851129230301	4	FACETS	0.278	0.236	0.323	0.093	0.078	0.108	SUBCLONAL	1	TRUE	1	0.675369515881295	4		740	983	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0061346-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	133	437	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.596789620257222	4	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	2	0.685530852766004	4		437	317	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0061346-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	427	311	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.685530852766004	3	FACETS	0.961	0.932	0.989	0.961	0.932	0.989	CLONAL	3	TRUE	0	0.685530852766004	3		311	580	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0061346-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	299	510	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	0.596789620257222	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.685530852766004	4		510	670	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153609	55153609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501520	NA	P-0061346-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	138	541	0	ENST00000257290.5:c.2575G>A	p.Val859Met	p.V859M	ENST00000257290	NM_006206.4	859	Gtg/Atg	19/23	1	2	FACETS	0.841	0.77	0.913	0.841	0.77	0.913	CLONAL	1	TRUE	1	0.685530852766004	2		541	479	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248394	59248394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329490786	NA	P-0061346-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	235	944	0	ENST00000371222.2:c.349G>A	p.Ala117Thr	p.A117T	ENST00000371222	NM_002228.3	117	Gcc/Acc	1/1	0.603931994717464	2	FACETS	0.974	0.913	1	0.487	0.456	0.518	CLONAL	1	TRUE	0	0.685530852766004	2		944	704	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604521	43604532	+	inframe_deletion	In_Frame_Del	DEL	CCATGCAGCTGG	CCATGCAGCTGG	-	novel	NA	P-0061346-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	148	846	0	ENST00000355710.3:c.1107_1118del	p.Met370_Ala373del	p.M370_A373del	ENST00000355710	NM_020975.4	369	aCCATGCAGCTGGcg/acg	6/20	0.208814661762562	3	FACETS	0.993	0.911	1	0.331	0.303	0.36	INDETERMINATE	1	TRUE	0	0.685530852766004	3		846	584	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	465627	465627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1490638667	NA	P-0061346-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	63	413	0	ENST00000399788.2:c.749G>A	p.Gly250Asp	p.G250D	ENST00000399788	NM_001042603.1	250	gGc/gAc	6/28	0.149435881870258	4	FACETS	0.639	0.553	0.731			1	INDETERMINATE	1	TRUE	NA	0.685530852766004	4		413	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578511	7578528	+	inframe_deletion	In_Frame_Del	DEL	GTCTTGGCCAGTTGGCAA	GTCTTGGCCAGTTGGCAA	-	novel	NA	P-0061346-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	382	859	0	ENST00000269305.4:c.402_419del	p.Gln136_Cys141del	p.Q136_C141del	ENST00000269305	NM_001126112.2	134	ttTTGCCAACTGGCCAAGACc/ttc	5/11	0.603931994717464	2	FACETS	0.949	0.915	0.983	0.949	0.915	0.983	CLONAL	2	TRUE	0	0.685530852766004	2		859	587	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0061632-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	164	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.35759289306975	2	FACETS	0.892	0.825	0.961	0.892	0.825	0.961	CLONAL	2	TRUE	0	0.366279100737461	2		473	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0061632-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	176	735	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.366279100737461	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.366279100737461	1		735	758	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359447	118359462	+	frameshift_variant	Frame_Shift_Del	DEL	TTTGTGGAAGGCAACA	TTTGTGGAAGGCAACA	-	novel	NA	P-0061632-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	134	599	0	ENST00000534358.1:c.4452_4467del	p.Cys1485ArgfsTer96	p.C1485Rfs*96	ENST00000534358	NM_005933.3	1484	gTTTGTGGAAGGCAACAt/gt	11/36	1	2	FACETS	0.931	0.846	1	0.931	0.846	1	CLONAL	1	TRUE	1	0.366279100737461	2		599	786	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884754	111884754	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061632-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	173	729	0	ENST00000341259.2:c.843C>A	p.Asp281Glu	p.D281E	ENST00000341259	NM_005475.2	281	gaC/gaA	4/8	0.366279100737461	1	FACETS	0.912	0.84	0.987	0.912	0.84	0.987	CLONAL	1	TRUE	0	0.366279100737461	1		729	846	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623592	28623592	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061632-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	146	531	0	ENST00000241453.7:c.965G>C	p.Arg322Thr	p.R322T	ENST00000241453	NM_004119.2	322	aGa/aCa	8/24	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.366279100737461	2		531	726	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335933	73335933	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061632-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	154	504	0	ENST00000377767.4:c.2362C>G	p.His788Asp	p.H788D	ENST00000377767	NM_014953.3	788	Cat/Gat	18/21	1	2	FACETS	0.961	0.88	1	0.961	0.88	1	CLONAL	1	TRUE	1	0.366279100737461	2		504	875	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790552	3790552	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0061632-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	108	493	0	ENST00000262367.5:c.3983-2A>T		p.X1328_splice	ENST00000262367	NM_004380.2	1328			1	2	FACETS	0.894	0.803	0.989	0.894	0.803	0.989	CLONAL	1	TRUE	1	0.366279100737461	2		493	660	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659755	227659755	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061632-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	163	524	0	ENST00000305123.5:c.3700T>G	p.Phe1234Val	p.F1234V	ENST00000305123	NM_005544.2	1234	Ttc/Gtc	1/2	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.366279100737461	2		524	814	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540560	187540560	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs955550584	NA	P-0061632-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	43	701	0	ENST00000441802.2:c.7180A>G	p.Ile2394Val	p.I2394V	ENST00000441802	NM_005245.3	2394	Att/Gtt	10/27	0.366279100737461	1	FACETS	0.238	0.198	0.282	0.238	0.198	0.282	SUBCLONAL	1	TRUE	0	0.366279100737461	1		701	807	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798777	135798777	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061632-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	137	491	0	ENST00000298552.3:c.466G>A	p.Asp156Asn	p.D156N	ENST00000298552	NM_001162426.1	156	Gac/Aac	6/23	0.366279100737461	1	FACETS	0.933	0.851	1	0.933	0.851	1	CLONAL	1	TRUE	0	0.366279100737461	1		491	655	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513316	149513316	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061634-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	33	760	1	ENST00000261799.4:c.767G>T	p.Arg256Leu	p.R256L	ENST00000261799	NM_002609.3	256	cGg/cTg	6/23	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	1	0.290371850122226	2		761	152	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602580	10602580	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061634-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	10	795	1	ENST00000171111.5:c.998G>T	p.Gly333Val	p.G333V	ENST00000171111	NM_203500.1	333	gGc/gTc	3/6	0.285069894824982	0	FACETS	0.73	0.503	1			1	CLONAL	1	FALSE	0	0.290371850122226	0		796	67	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220691	1220691	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs878853247	NA	P-0061634-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	13	718	0	ENST00000326873.7:c.709G>T	p.Asp237Tyr	p.D237Y	ENST00000326873	NM_000455.4	237	Gac/Tac	5/10	0.285069894824982	0	FACETS	1	0.79	1			1	CLONAL	1	FALSE	0	0.290371850122226	0		718	58	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73633489	73633489	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061634-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	30	542	0	ENST00000377687.4:c.24G>T	p.Met8Ile	p.M8I	ENST00000377687	NM_001730.3	8	atG/atT	1/4	0.290371850122226	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	0	0.290371850122226	1		542	118	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569817	95569817	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061634-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	26	607	0	ENST00000393063.1:c.3916G>T	p.Ala1306Ser	p.A1306S	ENST00000393063	NM_030621.3	1306	Gct/Tct	22/28	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	FALSE	1	0.290371850122226	2		607	148	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220087	36220087	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061634-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	11	819	0	ENST00000222270.7:c.4807C>T	p.Gln1603Ter	p.Q1603*	ENST00000222270	NM_014727.1	1603	Cag/Tag	22/37	1	2	FACETS	0.565	0.392	0.778	0.565	0.392	0.778	SUBCLONAL	1	FALSE	1	0.290371850122226	2		819	134	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511254	157511254	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061634-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	30	700	0	ENST00000346085.5:c.3772G>T	p.Ala1258Ser	p.A1258S	ENST00000346085	NM_020732.3	1258	Gcc/Tcc	15/20	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	FALSE	1	0.290371850122226	2		700	179	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401802	139401802	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061634-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	15	805	0	ENST00000277541.6:c.3598G>T	p.Asp1200Tyr	p.D1200Y	ENST00000277541	NM_017617.3	1200	Gac/Tac	22/34	1	2	FACETS	1	0.79	1	1	0.79	1	CLONAL	1	FALSE	1	0.290371850122226	2		805	96	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139562786	139562786	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061634-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	19	802	0	ENST00000308874.7:c.52G>T	p.Gly18Cys	p.G18C	ENST00000308874		18	Ggc/Tgc	3/10	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	FALSE	1	0.290371850122226	2		802	104	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0061638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	32	325	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.383	0.31	0.464	0.383	0.31	0.464	SUBCLONAL	1	TRUE	1	0.43	2		325	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0061638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	46	538	0	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	1	2	FACETS	0.317	0.266	0.373	0.317	0.266	0.373	SUBCLONAL	1	TRUE	1	0.43	2		538	675	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0061638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	22	648	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	1	2	FACETS	0.158	0.121	0.2	0.158	0.121	0.2	SUBCLONAL	1	TRUE	1	0.43	2		648	648	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876393	35876393	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	92	785	0	ENST00000303115.3:c.1185G>T	p.Lys395Asn	p.K395N	ENST00000303115	NM_002185.3	395	aaG/aaT	8/8	1	2	FACETS	0.478	0.424	0.536	0.478	0.424	0.536	SUBCLONAL	1	TRUE	1	0.43	2		785	895	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476309	88476309	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	70	550	0	ENST00000360948.2:c.1823del	p.Gly608AlafsTer13	p.G608Afs*13	ENST00000360948	NM_001012338.2	608	gGc/gc	15/19	1	2	FACETS	0.501	0.436	0.571	0.501	0.436	0.571	SUBCLONAL	1	TRUE	1	0.43	2		550	650	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274029	10274029	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	119	867	0	ENST00000330684.3:c.240G>T	p.Lys80Asn	p.K80N	ENST00000330684	NM_001134407.1	80	aaG/aaT	2/13	1	2	FACETS	0.545	0.491	0.603	0.545	0.491	0.603	SUBCLONAL	1	TRUE	1	0.43	2		867	1015	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026059	14026059	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs753728949	NA	P-0061638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	63	438	0	ENST00000311895.7:c.1019G>C	p.Arg340Pro	p.R340P	ENST00000311895	NM_005236.2	340	cGa/cCa	6/11	1	2	FACETS	0.522	0.452	0.599	0.522	0.452	0.599	SUBCLONAL	1	TRUE	1	0.43	2		438	561	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241096	39241096	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	64	369	0	ENST00000402219.2:c.1975G>C	p.Asp659His	p.D659H	ENST00000402219	NM_005633.3	659	Gat/Cat	12/23	1	2	FACETS	0.633	0.55	0.724	0.633	0.55	0.724	SUBCLONAL	1	TRUE	1	0.43	2		369	470	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751221	57751221	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	65	557	0	ENST00000274289.3:c.1646A>T	p.Glu549Val	p.E549V	ENST00000274289	NM_006622.3	549	gAg/gTg	12/14	1	2	FACETS	0.406	0.352	0.466	0.406	0.352	0.466	SUBCLONAL	1	TRUE	1	0.43	2		557	744	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407576	407576	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs756602021	NA	P-0061638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	28	490	0	ENST00000380956.4:c.1334G>T	p.Arg445Leu	p.R445L	ENST00000380956	NM_001195286.1	445	cGc/cTc	9/9	NA	2	FACETS	0.242	0.192	0.298			1	INDETERMINATE	1	TRUE	NA	0.43	2		490	539	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288978	33288978	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061638-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	94	836	0	ENST00000374542.5:c.574G>T	p.Glu192Ter	p.E192*	ENST00000374542	NM_001141970.1	192	Gag/Tag	3/8	1	2	FACETS	0.429	0.381	0.481	0.429	0.381	0.481	SUBCLONAL	1	TRUE	1	0.43	2		836	1018	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0061677-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	124	555	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.302304689892706	1	FACETS	0.861	0.781	0.945	0.861	0.781	0.945	CLONAL	1	TRUE	0	0.373937219793125	1		555	626	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453124	140453136	+	protein_altering_variant	In_Frame_Del	DEL	CATCGAGATTTCA	CATCGAGATTTCA	T	novel	NA	P-0061677-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	78	413	0	ENST00000288602.6:c.1799_1811delinsA	p.Val600_Trp604delinsGlu	p.V600_W604delinsE	ENST00000288602	NM_004333.4	600	gTGAAATCTCGATGg/gAg	15/18	1	2	FACETS	0.711	0.625	0.802	0.711	0.625	0.802	SUBCLONAL	1	TRUE	1	0.373937219793125	2		413	587	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295803	212295803	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061677-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	88	461	0	ENST00000342788.4:c.2510G>C	p.Arg837Thr	p.R837T	ENST00000342788	NM_005235.2	837	aGa/aCa	21/28	0.247498604702495	1	FACETS	0.668	0.593	0.748	0.668	0.593	0.748	SUBCLONAL	1	TRUE	0	0.373937219793125	1		461	573	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0061781-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	252	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.452967021880014	4	FACETS	0.91	0.859	0.962	0.91	0.859	0.962	CLONAL	3	TRUE	1	0.452967021880014	4		473	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0061781-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	187	736	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	0.452967021880014	1	FACETS	0.901	0.835	0.969	0.901	0.835	0.969	CLONAL	1	TRUE	0	0.452967021880014	1		736	709	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001366	29001366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779189056	NA	P-0061781-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	120	572	2	ENST00000282397.4:c.1366G>A	p.Ala456Thr	p.A456T	ENST00000282397	NM_002019.4	456	Gca/Aca	10/30	1	2	FACETS	0.771	0.697	0.849	0.771	0.697	0.849	SUBCLONAL	1	TRUE	1	0.452967021880014	2		574	687	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17116985	17116985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763604691	NA	P-0061782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	40	736	0	ENST00000285071.4:c.1724C>T	p.Ser575Leu	p.S575L	ENST00000285071	NM_144997.5	575	tCg/tTg	14/14	0.686166962157627	2	FACETS	1	0.939	1	0.597	0.512	0.685	CLONAL	1	TRUE	0	0.670135367563985	2		736	100	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0061782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	38	760	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.686166962157627	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	0	0.670135367563985	2		760	52	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2161878	2161878	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764576819	NA	P-0061782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	63	565	0	ENST00000349721.2:c.4174G>A	p.Asp1392Asn	p.D1392N	ENST00000349721	NM_003070.3	1392	Gat/Aat	28/34	0.336647992443809	5	FACETS	0.885	0.777	0.998			1	INDETERMINATE	2	TRUE	NA	0.670135367563985	5		565	213	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86545139	86545139	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1597291829	NA	P-0061782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	22	688	0	ENST00000262426.4:c.964C>G	p.Pro322Ala	p.P322A	ENST00000262426	NM_001451.2	322	Cca/Gca	1/2	0.549525504974212	3	FACETS	0.707	0.555	0.878	0.353	0.277	0.439	SUBCLONAL	1	TRUE	1	0.670135367563985	3		688	124	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260193	149260194	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAG	novel	NA	P-0061782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	30	543	0	ENST00000360632.3:c.699_700insCTT	p.Gln233_Lys234insLeu	p.Q233_K234insL	ENST00000360632	NM_015472.4	233	-/CTT	4/7	0.619590035755744	5	FACETS	0.809	0.656	0.98	0.27	0.218	0.327	CLONAL	1	TRUE	2	0.670135367563985	5		543	222	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149290701	149290701	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	36	523	0	ENST00000360632.3:c.518G>T	p.Ser173Ile	p.S173I	ENST00000360632	NM_015472.4	173	aGt/aTt	3/7	0.619590035755744	5	FACETS	1	0.921	1	0.399	0.332	0.472	CLONAL	1	TRUE	2	0.670135367563985	5		523	180	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038466	180038466	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	67	682	0	ENST00000261937.6:c.3551T>C	p.Val1184Ala	p.V1184A	ENST00000261937	NM_182925.4	1184	gTc/gCc	27/30	0.686166962157627	2	FACETS	0.752	0.675	0.828	0.752	0.675	0.828	SUBCLONAL	2	TRUE	0	0.670135367563985	2		682	133	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625218	69625218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168737490	NA	P-0061783-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	365	791	0	ENST00000334134.2:c.575G>A	p.Arg192Gln	p.R192Q	ENST00000334134	NM_005247.2	192	cGg/cAg	3/3	0.317116359048308	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	4	TRUE	0	0.317264559394434	4		791	698	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587781525	NA	P-0061783-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	204	688	0	ENST00000269305.4:c.842A>G	p.Asp281Gly	p.D281G	ENST00000269305	NM_001126112.2	281	gAc/gGc	8/11	0.317116359048308	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.317264559394434	2		688	582	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303669	30303669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061783-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	143	743	0	ENST00000262643.3:c.97G>T	p.Ala33Ser	p.A33S	ENST00000262643	NM_001238.2	33	Gca/Tca	3/12	0.305750860795917	4	FACETS	0.825	0.753	0.899	0.825	0.753	0.899	CLONAL	2	TRUE	2	0.317264559394434	4		743	720	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790161	40790161	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061783-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	66	660	0	ENST00000373198.4:c.2570T>A	p.Leu857His	p.L857H	ENST00000373198	NM_133170.3	857	cTt/cAt	18/32	0.26012431910631	3	FACETS	0.75	0.65	0.857	0.375	0.325	0.429	SUBCLONAL	1	TRUE	1	0.317264559394434	3		660	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0061784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	458	806	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.738626528933134	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.738276293532433	2		806	579	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458525	120458525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369659944	NA	P-0061784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	208	927	0	ENST00000256646.2:c.6820C>T	p.Pro2274Ser	p.P2274S	ENST00000256646	NM_024408.3	2274	Cca/Tca	34/34	0.651993460927259	4	FACETS	0.941	0.873	1	0.47	0.436	0.506	CLONAL	1	TRUE	2	0.738276293532433	4		927	1041	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410657	32410657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	361	644	1	ENST00000332351.3:c.1501C>T	p.Arg501Cys	p.R501C	ENST00000332351	NM_024426.4	501	Cgc/Tgc	10/10	0.548688395305083	4	FACETS	0.956	0.91	1	0.956	0.91	1	CLONAL	2	TRUE	2	0.738276293532433	4		645	889	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77991770	77991770	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	110	713	0	ENST00000361507.4:c.253G>T	p.Val85Leu	p.V85L	ENST00000361507	NM_080491.2	85	Gtg/Ttg	2/10	0.548688395305083	4	FACETS	0.576	0.517	0.639	0.288	0.258	0.32	SUBCLONAL	1	TRUE	2	0.738276293532433	4		713	899	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602315	28602315	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	48	447	0	ENST00000241453.7:c.2053G>T	p.Gly685Ter	p.G685*	ENST00000241453	NM_004119.2	685	Gga/Tga	16/24	0.738626528933134	2	FACETS	0.339	0.287	0.395	0.169	0.143	0.198	SUBCLONAL	1	TRUE	0	0.738276293532433	2		447	384	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799271	88799315	+	inframe_deletion	In_Frame_Del	DEL	GCAGACACAATTTGCAGGGCAAGCCAGCACGGAGCCCACATAGTC	GCAGACACAATTTGCAGGGCAAGCCAGCACGGAGCCCACATAGTC	-	novel	NA	P-0061784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	110	601	0	ENST00000360948.2:c.70_114del	p.Asp24_Cys38del	p.D24_C38del	ENST00000360948	NM_001012338.2	24	GACTATGTGGGCTCCGTGCTGGCTTGCCCTGCAAATTGTGTCTGC/-	2/19	0.738626528933134	3	FACETS	0.569	0.511	0.63			1	SUBCLONAL	1	TRUE	NA	0.738276293532433	3		601	717	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786190	3786240	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGTTTGAAAATATCCTGAGTGGGCAAAGCACAACAGTGAGATGAGGGCCA	TTGTTTGAAAATATCCTGAGTGGGCAAAGCACAACAGTGAGATGAGGGCCA	-	novel	NA	P-0061784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	36	602	0	ENST00000262367.5:c.4561-36_4575del		p.X1521_splice	ENST00000262367	NM_004380.2	1521		28/31	0.738626528933134	1	FACETS	0.229	0.189	0.273	0.229	0.189	0.273	SUBCLONAL	1	TRUE	0	0.738276293532433	1		602	269	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029093	14029093	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	49	668	0	ENST00000311895.7:c.1304T>A	p.Leu435His	p.L435H	ENST00000311895	NM_005236.2	435	cTc/cAc	8/11	1	2	FACETS	0.232	0.196	0.271	0.232	0.196	0.271	SUBCLONAL	1	TRUE	1	0.738276293532433	2		668	573	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821621	72821638	+	inframe_deletion	In_Frame_Del	DEL	GCCGCCGCCGCCGCCACT	GCCGCCGCCGCCGCCACT	-	rs775843921	NA	P-0061784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	93	766	0	ENST00000268489.5:c.10537_10554del	p.Ser3513_Gly3518del	p.S3513_G3518del	ENST00000268489	NM_006885.3	3513	AGTGGCGGCGGCGGCGGC/-	10/10	0.738626528933134	1	FACETS	0.6	0.541	0.66	0.6	0.541	0.66	SUBCLONAL	1	TRUE	0	0.738276293532433	1		766	265	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021226	31021226	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	60	736	0	ENST00000375687.4:c.1225A>G	p.Lys409Glu	p.K409E	ENST00000375687	NM_015338.5	409	Aag/Gag	12/13	0.234183515006853	5	FACETS	0.387	0.332	0.446	0.129	0.11	0.149	INDETERMINATE	1	TRUE	2	0.738276293532433	5		736	886	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039819	47039819	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	50	518	0	ENST00000377604.3:c.1162G>T	p.Asp388Tyr	p.D388Y	ENST00000377604	NM_001204468.1	388	Gac/Tac	12/24	0.738626528933134	4	FACETS	0.32	0.271	0.374			1	SUBCLONAL	1	TRUE	NA	0.738276293532433	4		518	736	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256952	41256956	+	frameshift_variant	Frame_Shift_Del	DEL	TCTCG	TCTCG	C	novel	NA	P-0061784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	289	444	0	ENST00000357654.3:c.230_234delinsG	p.Thr77SerfsTer10	p.T77Sfs*10	ENST00000357654	NM_007294.3	77	aCGAGA/aG	5/23	0.738626528933134	2	FACETS	0.994	0.957	1	0.994	0.957	1	CLONAL	2	TRUE	0	0.738276293532433	2		444	394	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061785-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	157	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.689956830004347	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.709613861919319	2		485	215	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074242	8074246	+	frameshift_variant	Frame_Shift_Del	DEL	AAGGG	AAGGG	-	novel	NA	P-0061785-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	216	652	0	ENST00000377482.5:c.413_417del	p.Ser138PhefsTer8	p.S138Ffs*8	ENST00000377482	NM_018948.3	138	tCCCTT/t	4/4	0.697609256294924	1	FACETS	0.997	0.943	1	0.997	0.943	1	CLONAL	1	TRUE	0	0.709613861919319	1		652	394	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244270	98244270	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061785-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	117	494	0	ENST00000331920.6:c.707G>A	p.Trp236Ter	p.W236*	ENST00000331920	NM_000264.3	236	tGg/tAg	5/24	1	2	FACETS	0.981	0.896	1	0.981	0.896	1	CLONAL	1	TRUE	1	0.709613861919319	2		494	336	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262275	115262275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061785-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	15	424	0	ENST00000438362.2:c.2279G>A	p.Gly760Glu	p.G760E	ENST00000438362	NM_001242891.1	760	gGa/gAa	18/20	0.709613861919319	1	FACETS	0.096	0.069	0.127	0.096	0.069	0.127	SUBCLONAL	1	TRUE	0	0.709613861919319	1		424	285	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206676	108206676	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555128574	NA	P-0061785-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	11	348	0	ENST00000278616.4:c.8256C>G	p.Ile2752Met	p.I2752M	ENST00000278616	NM_000051.3	2752	atC/atG	56/63	0.709613861919319	1	FACETS	0.115	0.079	0.159	0.115	0.079	0.159	SUBCLONAL	1	TRUE	0	0.709613861919319	1		348	174	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675610	30675610	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061785-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	143	594	0	ENST00000376406.3:c.2746G>C	p.Glu916Gln	p.E916Q	ENST00000376406	NM_014641.2	916	Gag/Cag	8/15	1	2	FACETS	0.824	0.757	0.894	0.824	0.757	0.894	CLONAL	1	TRUE	1	0.709613861919319	2		594	489	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0061786-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	429	723	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.461806010129691	3	FACETS	0.966	0.928	1	0.966	0.928	1	CLONAL	3	TRUE	0	0.468612416117864	3		723	780	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434170	121434170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757068809	NA	P-0061786-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	194	788	0	ENST00000257555.6:c.1061C>T	p.Thr354Met	p.T354M	ENST00000257555		354	aCg/aTg	5/10	0.470297110977448	3	FACETS	1	0.981	1	0.589	0.545	0.634	CLONAL	1	TRUE	1	0.468612416117864	3		788	868	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913237	NA	P-0061786-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	138	438	0	ENST00000369535.4:c.35G>C	p.Gly12Ala	p.G12A	ENST00000369535	NM_002524.4	12	gGt/gCt	2/7	0.470297110977448	2	FACETS	1	0.972	1	0.571	0.522	0.621	CLONAL	1	TRUE	0	0.468612416117864	2		438	516	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0061786-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	113	201	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.895	0.808	0.985	0.895	0.808	0.985	CLONAL	1	TRUE	1	0.468612416117864	2		201	539	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912188	114912188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061786-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	212	411	0	ENST00000543371.1:c.1258C>T	p.Arg420Trp	p.R420W	ENST00000543371	NM_001198531.1	420	Cgg/Tgg	11/14	0.442052813661624	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.468612416117864	3		411	500	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100999	41100999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1371429276	NA	P-0061786-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	214	648	0	ENST00000373198.4:c.1357C>T	p.Arg453Cys	p.R453C	ENST00000373198	NM_133170.3	453	Cgc/Tgc	8/32	0.293303466394551	5	FACETS	0.851	0.791	0.912			1	CLONAL	2	TRUE	NA	0.468612416117864	5		648	914	SUCCESS
APC	324	MSKCC	GRCh37	5	112116577	112116577	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854583	NA	P-0061786-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	91	457	0	ENST00000257430.4:c.622C>T	p.Gln208Ter	p.Q208*	ENST00000257430	NM_000038.5	208	Cag/Tag	6/16	1	2	FACETS	0.907	0.81	1	0.907	0.81	1	CLONAL	1	TRUE	1	0.468612416117864	2		457	428	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431404	121431404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780357	NA	P-0061786-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	148	663	0	ENST00000257555.6:c.608G>A	p.Arg203His	p.R203H	ENST00000257555		203	cGt/cAt	3/10	0.470297110977448	3	FACETS	0.955	0.873	1	0.478	0.436	0.521	CLONAL	1	TRUE	1	0.468612416117864	3		663	816	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620387	43620387	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061786-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	141	600	0	ENST00000355710.3:c.2996C>G	p.Ala999Gly	p.A999G	ENST00000355710	NM_020975.4	999	gCg/gGg	18/20	0.470297110977448	3	FACETS	1	0.974	1	0.584	0.533	0.637	CLONAL	1	TRUE	1	0.468612416117864	3		600	636	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358545	67358545	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061786-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	148	708	0	ENST00000327367.4:c.53G>A	p.Trp18Ter	p.W18*	ENST00000327367	NM_005902.3	18	tGg/tAg	1/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.468612416117864	NA		708	838	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576104	88576104	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061786-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	36	633	0	ENST00000360948.2:c.1569C>A	p.Cys523Ter	p.C523*	ENST00000360948	NM_001012338.2	523	tgC/tgA	13/19	0.470297110977448	3	FACETS	0.342	0.281	0.412	0.171	0.14	0.206	SUBCLONAL	1	TRUE	1	0.468612416117864	3		633	554	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391832	139391832	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061786-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	225	732	0	ENST00000277541.6:c.6359G>T	p.Arg2120Leu	p.R2120L	ENST00000277541	NM_017617.3	2120	cGc/cTc	34/34	0.249530257921553	4	FACETS	0.84	0.784	0.898	0.84	0.784	0.898	INDETERMINATE	2	TRUE	2	0.468612416117864	4		732	839	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	112	277	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.968	0.879	1	0.968	0.879	1	CLONAL	1	TRUE	1	0.617026280460814	2		277	375	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	137	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.921	0.844	1	0.921	0.844	1	CLONAL	1	TRUE	1	0.617026280460814	2		336	482	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	133	700	5	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.896	0.819	0.976	0.896	0.819	0.976	CLONAL	1	TRUE	1	0.617026280460814	2		705	481	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	151	609	1	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.617026280460814	2		610	479	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513282	44513287	+	inframe_deletion	In_Frame_Del	DEL	CCACCG	CCACCG	-	rs745888281	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	164	591	1	ENST00000291552.4:c.648_653del	p.Gly222_Gly223del	p.G222_G223del	ENST00000291552	NM_006758.2	216	ggCGGTGGt/ggt	8/8	1	2	FACETS	0.871	0.804	0.942	0.871	0.804	0.942	CLONAL	1	TRUE	1	0.617026280460814	2		592	610	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691872	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs79375991	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	317	638	18	ENST00000295754.5:c.383del	p.Lys128SerfsTer35	p.K128Sfs*35	ENST00000295754	NM_003242.5	125	gAa/ga	3/7	0.617026280460814	2	FACETS	0.812	0.773	0.85	0.812	0.773	0.85	CLONAL	2	TRUE	0	0.617026280460814	2		656	633	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738411	145738416	+	inframe_deletion	In_Frame_Del	DEL	GGTGCA	GGTGCA	-	rs548804317	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	138	771	0	ENST00000428558.2:c.2569_2574del	p.Cys857_Thr858del	p.C857_T858del	ENST00000428558	NM_004260.3	857	TGCACC/-	16/22	1	2	FACETS	0.818	0.748	0.89	0.818	0.748	0.89	CLONAL	1	TRUE	1	0.617026280460814	2		771	547	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1232964733	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	150	729	0	ENST00000324856.7:c.1015del	p.Ala339LeufsTer24	p.A339Lfs*24	ENST00000324856	NM_006015.4	337	tGg/tg	1/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.617026280460814	2		729	445	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030314	180030314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777755208	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	193	809	2	ENST00000261937.6:c.3970C>T	p.Arg1324Trp	p.R1324W	ENST00000261937	NM_182925.4	1324	Cgg/Tgg	30/30	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.617026280460814	2		811	605	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	323	682	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	1	0.983	1	1	0.997	1	CLONAL	2	TRUE	1	0.617026280460814	2		682	502	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101090	26101090	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	138	446	0	ENST00000435504.4:c.2T>C	p.Met1?	p.M1?	ENST00000435504		1	aTg/aCg	1/13	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.617026280460814	2		446	363	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413049	139413049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064795070	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	144	576	0	ENST00000277541.6:c.1093C>T	p.Arg365Cys	p.R365C	ENST00000277541	NM_017617.3	365	Cgc/Tgc	6/34	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.617026280460814	2		576	459	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931452	131931452	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507178	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	165	508	17	ENST00000265335.6:c.2165del	p.Lys722ArgfsTer14	p.K722Rfs*14	ENST00000265335		719	ctA/ct	13/25	1	2	FACETS	0.99	0.915	1	0.99	0.915	1	CLONAL	1	TRUE	1	0.617026280460814	2		525	540	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896587	78896587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144632265	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	150	666	0	ENST00000306801.3:c.2584G>A	p.Ala862Thr	p.A862T	ENST00000306801	NM_020761.2	862	Gcc/Acc	22/34	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.617026280460814	2		666	472	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	207	760	13	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.617026280460814	2		773	669	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847400	68847400	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	14	558	0	ENST00000261769.5:c.1320+2T>G		p.X440_splice	ENST00000261769	NM_004360.3	440			1	2	FACETS	0.078	0.055	0.105	0.078	0.055	0.105	SUBCLONAL	1	TRUE	1	0.617026280460814	2		558	584	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	159	588	3	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	0.949	0.875	1	0.949	0.875	1	CLONAL	1	TRUE	1	0.617026280460814	2		591	543	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721164	176721165	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1562308992	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	192	671	1	ENST00000439151.2:c.6801dup	p.Ala2268SerfsTer13	p.A2268Sfs*13	ENST00000439151	NM_022455.4	2265	-/A	23/23	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.617026280460814	2		672	577	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117594	70117594	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	197	737	0	ENST00000245479.2:c.66del	p.Ser23AlafsTer38	p.S23Afs*38	ENST00000245479	NM_000346.3	21	gCc/gc	1/3	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.617026280460814	2		737	553	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993676	90993676	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	121	367	0	ENST00000265433.3:c.247del	p.Met83CysfsTer9	p.M83Cfs*9	ENST00000265433	NM_002485.4	83	Atg/tg	3/16	1	2	FACETS	0.895	0.815	0.979	0.895	0.815	0.979	CLONAL	1	TRUE	1	0.617026280460814	2		367	438	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835781	68835781	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060501215	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	240	692	0	ENST00000261769.5:c.377del	p.Pro126ArgfsTer89	p.P126Rfs*89	ENST00000261769	NM_004360.3	124	cgC/cg	3/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.617026280460814	2		692	688	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022999	27022999	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1436957504	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	122	565	0	ENST00000324856.7:c.110del	p.Gly37AlafsTer14	p.G37Afs*14	ENST00000324856	NM_006015.4	35	gcG/gc	1/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.617026280460814	2		565	343	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806171	1806171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542210035	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	192	762	0	ENST00000260795.2:c.1190G>A	p.Arg397His	p.R397H	ENST00000260795		397	cGc/cAc	8/17	0.499050943641106	3	FACETS	1	0.965	1	0.534	0.495	0.574	CLONAL	1	TRUE	1	0.617026280460814	3		762	763	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962530	100962530	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752817186	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	167	484	0	ENST00000325455.5:c.1867C>T	p.Arg623Cys	p.R623C	ENST00000325455	NM_001202474.3	623	Cgc/Tgc	3/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.617026280460814	2		484	476	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119910	70119910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1297203260	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	299	714	0	ENST00000245479.2:c.916del	p.Val306CysfsTer77	p.V306Cfs*77	ENST00000245479	NM_000346.3	304	ccG/cc	3/3	1	2	FACETS	1	0.988	1	1	0.997	1	CLONAL	2	TRUE	1	0.617026280460814	2		714	451	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099468	157099470	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	rs1429292576	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	168	775	0	ENST00000346085.5:c.413_415del	p.Asn138del	p.N138del	ENST00000346085	NM_020732.3	135	tcCAAc/tcc	1/20	1	2	FACETS	0.903	0.834	0.974	0.903	0.834	0.974	CLONAL	1	TRUE	1	0.617026280460814	2		775	603	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412940	63412940	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	169	732	0	ENST00000330258.3:c.227del	p.Gly76AspfsTer24	p.G76Dfs*24	ENST00000330258	NM_152424.3	76	gGa/ga	2/2	1	2	FACETS	0.985	0.911	1	0.985	0.911	1	CLONAL	1	TRUE	1	0.617026280460814	2		732	556	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692892	89692892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554898129	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	110	365	0	ENST00000371953.3:c.376G>A	p.Ala126Thr	p.A126T	ENST00000371953	NM_000314.4	126	Gct/Act	5/9	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.617026280460814	2		365	315	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681120	117681120	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs748436511	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	154	567	1	ENST00000368508.3:c.3500del	p.Leu1167Ter	p.L1167*	ENST00000368508	NM_002944.2	1167	tTa/ta	23/43	1	2	FACETS	0.944	0.869	1	0.944	0.869	1	CLONAL	1	TRUE	1	0.617026280460814	2		568	529	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349640	89349641	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs772267579	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	140	570	8	ENST00000301030.4:c.3309dup	p.Asp1104ArgfsTer2	p.D1104Rfs*2	ENST00000301030	NM_001256183.1	1103	-/A	9/13	1	2	FACETS	0.864	0.792	0.94	0.864	0.792	0.94	CLONAL	1	TRUE	1	0.617026280460814	2		578	525	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	149	737	5	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.923	0.849	1	0.923	0.849	1	CLONAL	1	TRUE	1	0.617026280460814	2		742	523	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522693	67522693	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	206	583	0	ENST00000274335.5:c.193del	p.Glu65LysfsTer10	p.E65Kfs*10	ENST00000274335		64	Ggg/gg	1/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.617026280460814	2		583	634	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395001	395001	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1300046652	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	149	672	1	ENST00000380956.4:c.402del	p.Gly135GlufsTer14	p.G135Efs*14	ENST00000380956	NM_001195286.1	133	Aaa/aa	3/9	1	2	FACETS	0.953	0.876	1	0.953	0.876	1	CLONAL	1	TRUE	1	0.617026280460814	2		673	507	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625143	69625143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	82	660	0	ENST00000334134.2:c.650C>T	p.Pro217Leu	p.P217L	ENST00000334134	NM_005247.2	217	cCg/cTg	3/3	1	2	FACETS	0.703	0.624	0.787	0.703	0.624	0.787	SUBCLONAL	1	TRUE	1	0.617026280460814	2		660	378	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719526	61719526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	190	571	0	ENST00000401558.2:c.1657C>T	p.Arg553Cys	p.R553C	ENST00000401558	NM_003400.3	553	Cgt/Tgt	15/25	1	2	FACETS	0.961	0.892	1	0.961	0.892	1	CLONAL	1	TRUE	1	0.617026280460814	2		571	641	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717719	89717720	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs780264945	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	110	390	0	ENST00000371953.3:c.750_751del	p.Cys250TrpfsTer2	p.C250Wfs*2	ENST00000371953	NM_000314.4	248	ccTGtg/cctg	7/9	1	2	FACETS	0.885	0.801	0.972	0.885	0.801	0.972	CLONAL	1	TRUE	1	0.617026280460814	2		390	403	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481659	56481659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140656187	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	241	750	0	ENST00000267101.3:c.694G>A	p.Ala232Thr	p.A232T	ENST00000267101	NM_001982.3	232	Gcc/Acc	6/28	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.617026280460814	2		750	672	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	119	837	0	ENST00000222270.7:c.520_521dup	p.Lys175GlnfsTer20	p.K175Qfs*20	ENST00000222270	NM_014727.1	172	acc/aCCcc	3/37	1	2	FACETS	0.634	0.574	0.698	0.634	0.574	0.698	SUBCLONAL	1	TRUE	1	0.617026280460814	2		837	608	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457951	69457951	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	142	669	0	ENST00000227507.2:c.355del	p.Leu119Ter	p.L119*	ENST00000227507	NM_053056.2	117	atC/at	2/5	1	2	FACETS	0.965	0.886	1	0.965	0.886	1	CLONAL	1	TRUE	1	0.617026280460814	2		669	477	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226345	2226345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	189	820	0	ENST00000326181.6:c.1958G>A	p.Arg653Gln	p.R653Q	ENST00000326181	NM_032271.2	653	cGg/cAg	20/21	1	2	FACETS	0.947	0.879	1	0.947	0.879	1	CLONAL	1	TRUE	1	0.617026280460814	2		820	647	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466773	25466773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1431156021	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	147	618	0	ENST00000264709.3:c.1930G>A	p.Ala644Thr	p.A644T	ENST00000264709	NM_175629.2	644	Gct/Act	16/23	1	2	FACETS	0.929	0.853	1	0.929	0.853	1	CLONAL	1	TRUE	1	0.617026280460814	2		618	513	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553111	106553111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	206	798	0	ENST00000369096.4:c.1076C>T	p.Thr359Met	p.T359M	ENST00000369096	NM_001198.3	359	aCg/aTg	5/7	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.617026280460814	2		798	628	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492686	56492686	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	167	521	0	ENST00000407977.2:c.252+1G>A		p.X84_splice	ENST00000407977		84			1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.617026280460814	2		521	531	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652243	36652243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs558863376	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	180	624	2	ENST00000244741.5:c.365G>A	p.Arg122His	p.R122H	ENST00000244741	NM_000389.4	122	cGc/cAc	2/3	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.617026280460814	2		626	487	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44515559	44515559	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	165	586	0	ENST00000291552.4:c.337G>A	p.Val113Met	p.V113M	ENST00000291552	NM_006758.2	113	Gtg/Atg	5/8	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.617026280460814	2		586	524	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196745	106196745	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	29	646	0	ENST00000380013.4:c.5078A>G	p.Tyr1693Cys	p.Y1693C	ENST00000380013	NM_001127208.2	1693	tAc/tGc	11/11	1	2	FACETS	0.186	0.148	0.228	0.186	0.148	0.228	SUBCLONAL	1	TRUE	1	0.617026280460814	2		646	506	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132781	152132781	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	146	536	0	ENST00000262189.6:c.91G>A	p.Ala31Thr	p.A31T	ENST00000262189	NM_170606.2	31	Gcc/Acc	1/59	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.617026280460814	2		536	383	SUCCESS
AR	367	MSKCC	GRCh37	X	66941758	66941758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	89	526	3	ENST00000374690.3:c.2407del	p.Gln803ArgfsTer6	p.Q803Rfs*6	ENST00000374690	NM_000044.3	801	aCc/ac	6/8	0.617026280460814	1	FACETS	0.529	0.472	0.589	0.529	0.472	0.589	SUBCLONAL	1	TRUE	0	0.617026280460814	1		529	377	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779608	3779608	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	205	878	0	ENST00000262367.5:c.5440G>A	p.Gly1814Arg	p.G1814R	ENST00000262367	NM_004380.2	1814	Ggg/Agg	31/31	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.617026280460814	2		878	656	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103189	119103189	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757898729	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	187	612	0	ENST00000264033.4:c.227C>T	p.Ala76Val	p.A76V	ENST00000264033	NM_005188.3	76	gCg/gTg	2/16	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.617026280460814	2		612	587	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919785	50919785	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs780926432	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	179	813	1	ENST00000440232.2:c.2953C>T	p.Arg985Trp	p.R985W	ENST00000440232	NM_002691.3	985	Cgg/Tgg	23/27	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.617026280460814	2		814	535	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796750	57796750	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1199978831	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	174	685	1	ENST00000309042.7:c.1732del	p.Ser578ValfsTer7	p.S578Vfs*7	ENST00000309042	NM_005612.4	576	Aaa/aa	4/4	1	2	FACETS	0.887	0.82	0.956	0.887	0.82	0.956	CLONAL	1	TRUE	1	0.617026280460814	2		686	636	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29279846	29279846	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	39	212	0	ENST00000544604.2:c.92del	p.Leu31ArgfsTer91	p.L31Rfs*91	ENST00000544604	NM_001206998.1	31	cTg/cg	1/9	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.617026280460814	2		212	117	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22413187	22413187	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	93	371	0	ENST00000344548.3:c.314G>A	p.Cys105Tyr	p.C105Y	ENST00000344548	NM_001039802.1	105	tGt/tAt	6/7	1	2	FACETS	0.881	0.791	0.976	0.881	0.791	0.976	CLONAL	1	TRUE	1	0.617026280460814	2		371	342	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003835	57003835	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	G	G	A	rs532639542	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	150	788	0	ENST00000257254.3:c.644C>T	p.Thr215Ile	p.T215I	ENST00000257254		215	aCc/aTc	1/2	1	2	FACETS	0.905	0.832	0.981	0.905	0.832	0.981	CLONAL	1	TRUE	1	0.617026280460814	2		788	537	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373227	118373227	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782109378	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	191	644	0	ENST00000534358.1:c.6620G>A	p.Arg2207Gln	p.R2207Q	ENST00000534358	NM_005933.3	2207	cGg/cAg	27/36	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.617026280460814	2		644	592	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376371	118376371	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	197	778	0	ENST00000534358.1:c.9764T>C	p.Met3255Thr	p.M3255T	ENST00000534358	NM_005933.3	3255	aTg/aCg	27/36	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.617026280460814	2		778	595	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888141	81888141	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	172	618	0	ENST00000359376.3:c.286T>G	p.Phe96Val	p.F96V	ENST00000359376	NM_002661.3	96	Ttc/Gtc	3/33	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.617026280460814	2		618	543	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960830	15960831	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	156	461	0	ENST00000268712.3:c.6389dup	p.Ser2131LysfsTer2	p.S2131Kfs*2	ENST00000268712	NM_006311.3	2130	gga/ggGa	40/46	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.617026280460814	2		461	487	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701094	29701094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	218	555	0	ENST00000356175.3:c.8378G>A	p.Arg2793His	p.R2793H	ENST00000356175	NM_000267.3	2793	cGc/cAc	57/57	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.617026280460814	2		555	646	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492775	56492776	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	214	631	0	ENST00000407977.2:c.163dup	p.Met55AsnfsTer20	p.M55Nfs*20	ENST00000407977		55	atg/aAtg	2/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.617026280460814	2		631	644	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29439321	29439321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	155	602	0	ENST00000544604.2:c.536C>T	p.Pro179Leu	p.P179L	ENST00000544604	NM_001206998.1	179	cCg/cTg	4/9	1	2	FACETS	0.9	0.829	0.974	0.9	0.829	0.974	CLONAL	1	TRUE	1	0.617026280460814	2		602	558	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446652	29446652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs557631529	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	164	755	4	ENST00000544604.2:c.2483G>A	p.Arg828His	p.R828H	ENST00000544604	NM_001206998.1	828	cGc/cAc	8/9	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.617026280460814	2		759	494	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513526	149513526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	193	689	0	ENST00000261799.4:c.677G>A	p.Arg226His	p.R226H	ENST00000261799	NM_002609.3	226	cGc/cAc	5/23	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.617026280460814	2		689	601	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562163	176562163	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	35	660	0	ENST00000439151.2:c.59T>C	p.Val20Ala	p.V20A	ENST00000439151	NM_022455.4	20	gTg/gCg	2/23	1	2	FACETS	0.176	0.144	0.213	0.176	0.144	0.213	SUBCLONAL	1	TRUE	1	0.617026280460814	2		660	643	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983274	149983274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	175	624	0	ENST00000253339.5:c.2984G>A	p.Arg995His	p.R995H	ENST00000253339		995	cGc/cAc	7/7	1	2	FACETS	0.95	0.88	1	0.95	0.88	1	CLONAL	1	TRUE	1	0.617026280460814	2		624	597	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157470004	157470004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	148	743	1	ENST00000346085.5:c.2798C>T	p.Pro933Leu	p.P933L	ENST00000346085	NM_020732.3	933	cCg/cTg	9/20	1	2	FACETS	0.858	0.788	0.931	0.858	0.788	0.931	CLONAL	1	TRUE	1	0.617026280460814	2		744	559	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524613	106524613	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	139	446	0	ENST00000359195.3:c.2774T>C	p.Val925Ala	p.V925A	ENST00000359195	NM_002649.2	925	gTg/gCg	9/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.617026280460814	2		446	421	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781044	135781050	+	frameshift_variant	Frame_Shift_Del	DEL	GCACACC	GCACACC	-	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	168	587	0	ENST00000298552.3:c.1915_1921del	p.Gly639ProfsTer12	p.G639Pfs*12	ENST00000298552	NM_001162426.1	639	GGTGTGCcc/cc	15/23	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.617026280460814	2		587	531	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918300	44918300	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	91	389	0	ENST00000377967.4:c.925C>T	p.Gln309Ter	p.Q309*	ENST00000377967	NM_021140.2	309	Cag/Tag	11/29	1	2	FACETS	0.822	0.736	0.912	0.822	0.736	0.912	CLONAL	1	TRUE	1	0.617026280460814	2		389	359	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0061789-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	101	648	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		648	433	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274897	41274897	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061789-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	106	593	0	ENST00000349496.5:c.1147T>C	p.Trp383Arg	p.W383R	ENST00000349496	NM_001904.3	383	Tgg/Cgg	8/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		593	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0061790-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	1146	484	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.372431687419339	2	FACETS	0.966	0.955	0.977			1	CLONAL	5	TRUE	0	0.372431687419339	2		484	1274	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913499	NA	P-0061790-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	316	593	0	ENST00000345146.2:c.394C>A	p.Arg132Ser	p.R132S	ENST00000345146	NM_005896.2	132	Cgt/Agt	4/10	1	2	FACETS	1	0.992	1	1	0.996	1	CLONAL	2	TRUE	1	0.372431687419339	2		593	694	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119004	3119004	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1309810840	NA	P-0061790-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	918	738	0	ENST00000078429.4:c.688G>A	p.Val230Ile	p.V230I	ENST00000078429	NM_002067.2	230	Gtc/Atc	5/7	0.372431687419339	4	FACETS	0.911	0.888	0.933	1	0.998	1	CLONAL	5	TRUE	1	0.372431687419339	4		738	1486	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937183	76937183	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061790-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	129	600	1	ENST00000373344.5:c.3565del	p.Leu1189Ter	p.L1189*	ENST00000373344	NM_000489.3	1189	Cta/ta	9/35	0.372431687419339	0	FACETS	0.898	0.834	0.962			1	CLONAL	2	TRUE	0	0.372431687419339	0		601	242	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346338	73346338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	40	494	0	ENST00000377767.4:c.1462G>A	p.Asp488Asn	p.D488N	ENST00000377767	NM_014953.3	488	Gat/Aat	10/21	1	2	FACETS	0.874	0.728	1	0.874	0.728	1	CLONAL	1	TRUE	1	0.248115573660658	2		494	369	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220691	1220691	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs878853247	NA	P-0061791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	83	718	0	ENST00000326873.7:c.709G>T	p.Asp237Tyr	p.D237Y	ENST00000326873	NM_000455.4	237	Gac/Tac	5/10	0.248115573660658	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.248115573660658	1		718	482	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602341	10602341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1178941219	NA	P-0061791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	96	842	0	ENST00000171111.5:c.1237C>T	p.Arg413Cys	p.R413C	ENST00000171111	NM_203500.1	413	Cgt/Tgt	3/6	0.248115573660658	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.248115573660658	1		842	609	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76777866	76777866	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	51	305	0	ENST00000373344.5:c.6850G>T	p.Gly2284Ter	p.G2284*	ENST00000373344	NM_000489.3	2284	Gga/Tga	32/35	1	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.248115573660658	1		305	297	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637248	47637248	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs145649774	NA	P-0061791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	58	490	0	ENST00000233146.2:c.382C>G	p.Leu128Val	p.L128V	ENST00000233146	NM_000251.2	128	Ctc/Gtc	3/16	1	2	FACETS	0.911	0.784	1	0.911	0.784	1	CLONAL	1	TRUE	1	0.248115573660658	2		490	513	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215341	123215341	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	44	199	0	ENST00000218089.9:c.2887C>T	p.Gln963Ter	p.Q963*	ENST00000218089	NM_001042749.1	963	Cag/Tag	28/35	1	1	FACETS	0.809	0.687	0.94	1	0.966	1	CLONAL	2	TRUE	0	0.248115573660658	1		199	192	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690426	33690426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376084054	NA	P-0061791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	90	612	0	ENST00000308377.4:c.401G>A	p.Arg134His	p.R134H	ENST00000308377	NM_152270.3	134	cGt/cAt	2/5	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.248115573660658	2		612	646	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923308	78923308	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	132	588	0	ENST00000306801.3:c.3331G>T	p.Ala1111Ser	p.A1111S	ENST00000306801	NM_020761.2	1111	Gcg/Tcg	28/34	0.248115573660658	3	FACETS	0.963	0.877	1	0.963	0.877	1	CLONAL	2	TRUE	1	0.248115573660658	3		588	621	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707957	47707957	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750291	NA	P-0061791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	53	485	0	ENST00000233146.2:c.2581C>T	p.Gln861Ter	p.Q861*	ENST00000233146	NM_000251.2	861	Caa/Taa	15/16	1	2	FACETS	0.905	0.773	1	0.905	0.773	1	CLONAL	1	TRUE	1	0.248115573660658	2		485	472	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632380	215632380	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0061791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	64	418	0	ENST00000260947.4:c.1396-2A>T		p.X466_splice	ENST00000260947	NM_000465.2	466			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.248115573660658	2		418	409	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971107	55971107	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	71	525	0	ENST00000263923.4:c.1690C>T	p.Gln564Ter	p.Q564*	ENST00000263923	NM_002253.2	564	Cag/Tag	13/30	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.248115573660658	2		525	482	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910666	29910666	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	222	1261	0	ENST00000376809.5:c.206T>G	p.Met69Arg	p.M69R	ENST00000376809	NM_002116.7	69	aTg/aGg	2/8	0.248115573660658	2	FACETS	0.854	0.794	0.915	0.854	0.794	0.915	CLONAL	2	TRUE	0	0.248115573660658	2		1261	1048	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169268	32169268	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0061791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	142	635	0	ENST00000375023.3:c.3765T>G	p.Tyr1255Ter	p.Y1255*	ENST00000375023	NM_004557.3	1255	taT/taG	22/30	0.248115573660658	2	FACETS	0.98	0.897	1	0.98	0.897	1	CLONAL	2	TRUE	0	0.248115573660658	2		635	584	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523558	148523558	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0061791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	52	445	0	ENST00000320356.2:c.895A>T	p.Lys299Ter	p.K299*	ENST00000320356	NM_004456.4	299	Aag/Tag	8/20	1	2	FACETS	0.884	0.754	1	0.884	0.754	1	CLONAL	1	TRUE	1	0.248115573660658	2		445	474	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117875489	117875489	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	62	541	0	ENST00000297338.2:c.154G>T	p.Ala52Ser	p.A52S	ENST00000297338	NM_006265.2	52	Gca/Tca	3/14	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.248115573660658	2		541	492	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	156	345	0				ENST00000310581	NM_198253.2	-/1132			0.389815556055081	3	FACETS	0.836	0.771	0.903	0.836	0.771	0.903	CLONAL	2	TRUE	1	0.464509705969448	3		345	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0061792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	345	763	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.438130683178349	2	FACETS	0.962	0.916	1	0.962	0.916	1	CLONAL	2	TRUE	0	0.464509705969448	2		763	772	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951087	48951088	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs1131690889	NA	P-0061792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	130	335	0	ENST00000267163.4:c.1251_1252del	p.Arg418SerfsTer9	p.R418Sfs*9	ENST00000267163	NM_000321.2	417	AAa/a	13/27	0.464509705969448	2	FACETS	0.912	0.84	0.984	0.912	0.84	0.984	CLONAL	2	TRUE	0	0.464509705969448	2		335	307	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156048	106156048	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1434577007	NA	P-0061792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	135	750	0	ENST00000380013.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000380013	NM_001127208.2	317	Cag/Tag	3/11	0.30692628882314	3	FACETS	0.855	0.777	0.937	0.427	0.388	0.469	CLONAL	1	TRUE	1	0.464509705969448	3		750	838	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750872	128750872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	247	665	0	ENST00000377970.2:c.409G>A	p.Glu137Lys	p.E137K	ENST00000377970	NM_002467.4	137	Gag/Aag	2/3	0.192785760548613	6	FACETS	1	0.973	1	0.716	0.67	0.763	INDETERMINATE	2	TRUE	3	0.464509705969448	6		665	955	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325140	39325140	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	127	668	0	ENST00000373001.3:c.179C>G	p.Ser60Cys	p.S60C	ENST00000373001	NM_022157.3	60	tCc/tGc	1/7	0.389815556055081	3	FACETS	0.837	0.758	0.92	0.419	0.379	0.46	CLONAL	1	TRUE	1	0.464509705969448	3		668	805	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873144	71873144	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	91	485	0	ENST00000357731.5:c.1050T>A	p.Asn350Lys	p.N350K	ENST00000357731	NM_173808.2	350	aaT/aaA	7/7	0.389815556055081	3	FACETS	0.838	0.746	0.937	0.419	0.373	0.469	CLONAL	1	TRUE	1	0.464509705969448	3		485	576	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150935088	150935088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587677129	NA	P-0061792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	134	529	0	ENST00000271640.5:c.3184G>A	p.Gly1062Ser	p.G1062S	ENST00000271640	NM_001145415.1	1062	Ggt/Agt	18/22	0.464509705969448	7	FACETS	0.949	0.86	1	0.19	0.172	0.209	CLONAL	1	TRUE	2	0.464509705969448	7		529	1314	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175942	176175942	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	105	603	0	ENST00000367669.3:c.173C>A	p.Ser58Ter	p.S58*	ENST00000367669	NM_022457.5	58	tCg/tAg	1/20	0.393913728222996	3	FACETS	0.91	0.817	1	0.455	0.408	0.505	CLONAL	1	TRUE	1	0.464509705969448	3		603	612	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176176062	176176062	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	251	663	0	ENST00000367669.3:c.53C>A	p.Ser18Tyr	p.S18Y	ENST00000367669	NM_022457.5	18	tCc/tAc	1/20	0.393913728222996	3	FACETS	0.935	0.879	0.992	0.935	0.879	0.992	CLONAL	2	TRUE	1	0.464509705969448	3		663	712	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119491	193119491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	120	540	0	ENST00000367435.3:c.886G>A	p.Glu296Lys	p.E296K	ENST00000367435	NM_024529.4	296	Gaa/Aaa	9/17	0.393913728222996	3	FACETS	0.929	0.841	1	0.465	0.42	0.512	CLONAL	1	TRUE	1	0.464509705969448	3		540	685	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784009	120784009	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	175	826	1	ENST00000257552.2:c.976G>A	p.Asp326Asn	p.D326N	ENST00000257552	NM_002442.3	326	Gac/Aac	13/15	0.464509705969448	2	FACETS	0.938	0.865	1	0.469	0.432	0.507	CLONAL	1	TRUE	0	0.464509705969448	2		827	803	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042166	42042166	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	157	625	0	ENST00000219905.7:c.6361G>C	p.Asp2121His	p.D2121H	ENST00000219905	NM_001164273.1	2121	Gac/Cac	17/24	1	2	FACETS	0.967	0.888	1	0.967	0.888	1	CLONAL	1	TRUE	1	0.464509705969448	2		625	699	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042323	42042323	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	135	706	0	ENST00000219905.7:c.6518G>C	p.Arg2173Thr	p.R2173T	ENST00000219905	NM_001164273.1	2173	aGa/aCa	17/24	1	2	FACETS	0.803	0.731	0.878	0.803	0.731	0.878	CLONAL	1	TRUE	1	0.464509705969448	2		706	724	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89176391	89176391	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	46	442	0	ENST00000336596.2:c.121G>C	p.Glu41Gln	p.E41Q	ENST00000336596	NM_005233.5	41	Gag/Cag	2/17	0.316959475803573	4	FACETS	0.786	0.664	0.92	0.393	0.332	0.46	CLONAL	1	TRUE	2	0.464509705969448	4		442	369	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	893159	893159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	85	477	0	ENST00000166345.3:c.46G>A	p.Ala16Thr	p.A16T	ENST00000166345	NM_004237.3	16	Gcc/Acc	1/13	0.389815556055081	3	FACETS	0.726	0.642	0.816	0.363	0.321	0.408	SUBCLONAL	1	TRUE	1	0.464509705969448	3		477	621	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1296399	1296399	+	upstream_gene_variant	5'Flank	SNP	G	G	C	novel	NA	P-0061792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	62	362	0				ENST00000310581	NM_198253.2	-/1132			0.389815556055081	3	FACETS	0.746	0.646	0.854	0.373	0.323	0.427	SUBCLONAL	1	TRUE	1	0.464509705969448	3		362	441	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526394	31526394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	323	762	0	ENST00000344624.3:c.646C>T	p.Pro216Ser	p.P216S	ENST00000344624		216	Ccc/Tcc	2/33	0.389815556055081	3	FACETS	0.904	0.856	0.953	0.904	0.856	0.953	CLONAL	2	TRUE	1	0.464509705969448	3		762	948	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374383	81374383	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180926109	NA	P-0061792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	134	441	0	ENST00000222390.5:c.679G>A	p.Glu227Lys	p.E227K	ENST00000222390	NM_000601.4	227	Gaa/Aaa	6/18	0.393913728222996	3	FACETS	0.834	0.765	0.906	0.834	0.765	0.906	CLONAL	2	TRUE	1	0.464509705969448	3		441	426	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630152	100630152	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	88	231	0	ENST00000308731.7:c.121G>C	p.Glu41Gln	p.E41Q	ENST00000308731	NM_000061.2	41	Gag/Cag	2/19	0.386784673174532	2	FACETS	0.989	0.883	1			1	CLONAL	1	TRUE	NA	0.464509705969448	2		231	383	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229283	123229283	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0061792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	108	209	0	ENST00000218089.9:c.3767C>G	p.Ser1256Ter	p.S1256*	ENST00000218089	NM_001042749.1	1256	tCa/tGa	34/35	0.386784673174532	2	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.464509705969448	2		209	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0061794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	151	453	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	0.281049932661993	2	FACETS	0.993	0.913	1	0.993	0.913	1	CLONAL	2	TRUE	0	0.281049932661993	2		453	541	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0061794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	118	389	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.281049932661993	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.281049932661993	4		389	468	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023423	27023424	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	204	666	0	ENST00000324856.7:c.532dup	p.Ser178LysfsTer222	p.S178Kfs*222	ENST00000324856	NM_006015.4	177	caa/cAaa	1/20	0.24934723619048	4	FACETS	1	0.951	1	1	0.951	1	CLONAL	3	TRUE	1	0.281049932661993	4		666	606	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804183	46804183	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	171	598	0	ENST00000290295.7:c.824T>C	p.Leu275Pro	p.L275P	ENST00000290295	NM_006361.5	275	cTc/cCc	2/2	0.281049932661993	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.281049932661993	2		598	496	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247303	153247303	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	179	457	0	ENST00000281708.4:c.1499del	p.His500LeufsTer24	p.H500Lfs*24	ENST00000281708	NM_033632.3	500	cAt/ct	10/12	0.276067772990364	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.281049932661993	3		457	638	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933406	39933406	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	212	765	0	ENST00000378444.4:c.1193A>G	p.Glu398Gly	p.E398G	ENST00000378444	NM_001123385.1	398	gAa/gGa	4/15	0.269991122817214	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.281049932661993	4		765	907	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842633	68842633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061796-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	141	623	0	ENST00000261769.5:c.569A>G	p.Tyr190Cys	p.Y190C	ENST00000261769	NM_004360.3	190	tAc/tGc	5/16	0.151119274092166	2	FACETS	1	0.975	1	0.599	0.545	0.655	INDETERMINATE	1	TRUE	0	0.27	2		623	872	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728676	190728678	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs777263508	NA	P-0061796-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	38	492	0	ENST00000441310.2:c.2067_2069del	p.Arg690del	p.R690del	ENST00000441310	NM_000534.4	688	aaAAGa/aaa	10/13	1	2	FACETS	0.484	0.4	0.58	0.484	0.4	0.58	SUBCLONAL	1	TRUE	1	0.27	2		492	581	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680747	88680747	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061796-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	53	537	0	ENST00000360948.2:c.510G>T	p.Trp170Cys	p.W170C	ENST00000360948	NM_001012338.2	170	tgG/tgT	6/19	0.3	1	FACETS	0.484	0.412	0.564	0.484	0.412	0.564	SUBCLONAL	1	TRUE	0	0.27	1		537	701	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099379	27099394	+	frameshift_variant	Frame_Shift_Del	DEL	ACTCCAAACCCTGGGT	ACTCCAAACCCTGGGT	-	novel	NA	P-0061796-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	143	664	0	ENST00000324856.7:c.3617_3632del	p.Thr1206IlefsTer5	p.T1206Ifs*5	ENST00000324856	NM_006015.4	1206	ACTCCAAACCCTGGGTat/at	14/20	0.171874872378809	2	FACETS	1	0.976	1	0.598	0.545	0.654	CLONAL	1	TRUE	0	0.27	2		664	885	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1555525367	NA	P-0061797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	300	535	0	ENST00000269305.4:c.783-1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.391781039302288	3	FACETS	1	0.989	1			1	INDETERMINATE	3	TRUE	NA	0.760004225342814	3		535	351	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020560	69020560	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	164	406	0	ENST00000288368.4:c.2932G>T	p.Glu978Ter	p.E978*	ENST00000288368	NM_024870.2	978	Gag/Tag	24/40	0.689776901147625	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.760004225342814	3		406	279	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198986	67198986	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	93	546	0	ENST00000312629.5:c.457G>T	p.Gly153Cys	p.G153C	ENST00000312629	NM_003952.2	153	Ggt/Tgt	5/15	0.613706662596414	3	FACETS	0.91	0.816	1	0.455	0.408	0.505	CLONAL	1	TRUE	1	0.760004225342814	3		546	371	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983615	7983615	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	18	513	0	ENST00000319144.4:c.692A>T	p.His231Leu	p.H231L	ENST00000319144	NM_001139.2	231	cAt/cTt	6/15	0.391781039302288	3	FACETS	0.183	0.137	0.237			1	INDETERMINATE	1	TRUE	NA	0.760004225342814	3		513	357	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854865	76854878	+	splice_donor_variant,intron_variant	Splice_Site	DEL	ATTCATTAGACTCA	ATTCATTAGACTCA	-	novel	NA	P-0061797-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	76	377	0	ENST00000373344.5:c.5956+2_5956+15del		p.X1986_splice	ENST00000373344	NM_000489.3	1986			0.760004225342814	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.760004225342814	1		377	102	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0061798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	1582	571	0				ENST00000310581	NM_198253.2	-/1132			0.64374545569781	7	FACETS	1	0.996	1			1	CLONAL	6	TRUE	NA	0.64374545569781	7		571	2072	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174873	11174873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	142	308	0	ENST00000361445.4:c.7161G>A	p.Met2387Ile	p.M2387I	ENST00000361445	NM_004958.3	2387	atG/atA	52/58	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.64374545569781	2		308	408	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28601347	28601347	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	232	663	0	ENST00000253063.3:c.1032G>A	p.Trp344Ter	p.W344*	ENST00000253063	NM_031459.4	344	tgG/tgA	8/10	1	2	FACETS	0.919	0.86	0.98	0.919	0.86	0.98	CLONAL	1	TRUE	1	0.64374545569781	2		663	784	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740309	46740309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	254	570	0	ENST00000371975.4:c.1789C>T	p.Pro597Ser	p.P597S	ENST00000371975	NM_003579.3	597	Cca/Tca	16/18	1	2	FACETS	0.924	0.867	0.982	0.924	0.867	0.982	CLONAL	1	TRUE	1	0.64374545569781	2		570	854	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850793	63850793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537465187	NA	P-0061798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	277	731	0	ENST00000279873.7:c.1571C>T	p.Ser524Phe	p.S524F	ENST00000279873	NM_032199.2	524	tCc/tTc	10/10	1	2	FACETS	0.958	0.902	1	0.958	0.902	1	CLONAL	1	TRUE	1	0.64374545569781	2		731	898	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248646	8248646	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	278	745	0	ENST00000335790.3:c.241C>T	p.Leu81Phe	p.L81F	ENST00000335790	NM_002315.2	81	Ctc/Ttc	3/4	1	2	FACETS	0.94	0.885	0.996	0.94	0.885	0.996	CLONAL	1	TRUE	1	0.64374545569781	2		745	919	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205316	46205316	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	187	368	0	ENST00000334344.6:c.400C>T	p.Gln134Ter	p.Q134*	ENST00000334344	NM_152641.2	134	Cag/Tag	4/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.64374545569781	2		368	534	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249251	133249251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1385107035	NA	P-0061798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	267	672	0	ENST00000320574.5:c.1648G>A	p.Gly550Arg	p.G550R	ENST00000320574	NM_006231.2	550	Ggg/Agg	15/49	0.64374545569781	3	FACETS	1	0.967	1	0.523	0.49	0.556	CLONAL	1	TRUE	1	0.64374545569781	3		672	1049	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993735	72993735	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	311	971	0	ENST00000268489.5:c.310C>T	p.Pro104Ser	p.P104S	ENST00000268489	NM_006885.3	104	Ccc/Tcc	2/10	1	2	FACETS	0.901	0.851	0.953	0.901	0.851	0.953	CLONAL	1	TRUE	1	0.64374545569781	2		971	1072	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474133	29474133	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	231	652	0	ENST00000389048.3:c.2042T>C	p.Val681Ala	p.V681A	ENST00000389048	NM_004304.4	681	gTt/gCt	12/29	0.64374545569781	3	FACETS	0.972	0.907	1	0.486	0.453	0.52	CLONAL	1	TRUE	1	0.64374545569781	3		652	976	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095694	178095694	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	216	480	0	ENST00000397062.3:c.1637A>T	p.Asn546Ile	p.N546I	ENST00000397062	NM_006164.4	546	aAt/aTt	5/5	0.64374545569781	3	FACETS	0.972	0.904	1	0.486	0.452	0.521	CLONAL	1	TRUE	1	0.64374545569781	3		480	913	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525123	9525123	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	170	470	0	ENST00000353224.5:c.1762G>A	p.Gly588Ser	p.G588S	ENST00000353224	NM_177990.2	588	Ggt/Agt	8/10	1	2	FACETS	0.989	0.916	1	0.989	0.916	1	CLONAL	1	TRUE	1	0.64374545569781	2		470	534	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790003	40790003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	209	578	0	ENST00000373198.4:c.2728G>A	p.Glu910Lys	p.E910K	ENST00000373198	NM_133170.3	910	Gag/Aag	18/32	1	2	FACETS	0.899	0.838	0.962	0.899	0.838	0.962	CLONAL	1	TRUE	1	0.64374545569781	2		578	722	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458248	12458248	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	200	534	0	ENST00000287820.6:c.865A>G	p.Lys289Glu	p.K289E	ENST00000287820	NM_015869.4	289	Aaa/Gaa	6/7	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.64374545569781	2		534	601	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747967	41747967	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758728895	NA	P-0061798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	244	671	1	ENST00000226382.2:c.802G>A	p.Gly268Ser	p.G268S	ENST00000226382	NM_003924.3	268	Ggc/Agc	3/3	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.64374545569781	2		672	757	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976666	55976666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	217	476	0	ENST00000263923.4:c.1159G>A	p.Glu387Lys	p.E387K	ENST00000263923	NM_002253.2	387	Gaa/Aaa	9/30	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.64374545569781	2		476	664	SUCCESS
ALB	213	MSKCC	GRCh37	4	74277741	74277741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1259433502	NA	P-0061798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	176	402	0	ENST00000295897.4:c.742C>T	p.Pro248Ser	p.P248S	ENST00000295897	NM_000477.5	248	Ccc/Tcc	7/15	1	2	FACETS	0.978	0.907	1	0.978	0.907	1	CLONAL	1	TRUE	1	0.64374545569781	2		402	559	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	231057	231057	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746145822	NA	P-0061798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	179	346	0	ENST00000264932.6:c.837G>A	p.Met279Ile	p.M279I	ENST00000264932	NM_004168.2	279	atG/atA	7/15	0.612983939842705	3	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.64374545569781	3		346	642	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	901535	901535	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1476	168	500	0	ENST00000166345.3:c.524T>G	p.Val175Gly	p.V175G	ENST00000166345	NM_004237.3	175	gTg/gGg	5/13	0.64374545569781	7	FACETS	0.828	0.758	0.902			1	CLONAL	1	TRUE	NA	0.64374545569781	7		500	1644	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294891	1294891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs943289163	NA	P-0061798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2333	322	974	0	ENST00000310581.5:c.214C>T	p.Arg72Cys	p.R72C	ENST00000310581	NM_198253.2	72	Cgc/Tgc	1/16	0.64374545569781	7	FACETS	0.983	0.923	1			1	CLONAL	1	TRUE	NA	0.64374545569781	7		974	2655	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295375	1295375	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0061798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2750	370	962	0				ENST00000310581	NM_198253.2	-/1132			0.64374545569781	7	FACETS	0.961	0.907	1			1	CLONAL	1	TRUE	NA	0.64374545569781	7		962	3120	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1296460	1296460	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0061798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	110	163	0				ENST00000310581	NM_198253.2	-/1132			0.64374545569781	7	FACETS	0.982	0.888	1			1	CLONAL	2	TRUE	NA	0.64374545569781	7		163	454	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874636	35874636	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	352	423	0	ENST00000303115.3:c.792G>A	p.Trp264Ter	p.W264*	ENST00000303115	NM_002185.3	264	tgG/tgA	6/8	0.64374545569781	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.64374545569781	3		423	704	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876265	35876265	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770274946	NA	P-0061798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	200	630	0	ENST00000303115.3:c.1057G>A	p.Asp353Asn	p.D353N	ENST00000303115	NM_002185.3	353	Gat/Aat	8/8	0.64374545569781	3	FACETS	0.85	0.788	0.915	0.425	0.394	0.458	CLONAL	1	TRUE	1	0.64374545569781	3		630	966	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589618	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519838	NA	P-0061798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	79	294	0	ENST00000274335.5:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000274335		461	Cga/Tga	10/15	0.64374545569781	3	FACETS	0.983	0.872	1	0.492	0.436	0.55	CLONAL	1	TRUE	1	0.64374545569781	3		294	330	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80109514	80109514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763008024	NA	P-0061798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	222	527	0	ENST00000265081.6:c.2767C>T	p.Pro923Ser	p.P923S	ENST00000265081	NM_002439.4	923	Cct/Tct	20/24	0.64374545569781	3	FACETS	1	0.972	1	0.539	0.503	0.577	CLONAL	1	TRUE	1	0.64374545569781	3		527	845	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520483	176520484	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0061798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	271	850	0	ENST00000292408.4:c.1328_1329delinsTT	p.Pro443Leu	p.P443L	ENST00000292408	NM_213647.1	443	cCC/cTT	10/18	0.64374545569781	3	FACETS	0.899	0.843	0.957	0.449	0.421	0.479	CLONAL	1	TRUE	1	0.64374545569781	3		850	1238	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057572	180057572	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	482	718	0	ENST00000261937.6:c.383C>T	p.Ser128Phe	p.S128F	ENST00000261937	NM_182925.4	128	tCc/tTc	3/30	0.64374545569781	3	FACETS	0.957	0.919	0.995	0.957	0.919	0.995	CLONAL	2	TRUE	1	0.64374545569781	3		718	1034	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519694	137519694	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	223	487	0	ENST00000367739.4:c.944C>T	p.Ser315Phe	p.S315F	ENST00000367739	NM_000416.2	315	tCc/tTc	7/7	0.64374545569781	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.64374545569781	1		487	470	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2104143	2104143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1457066061	NA	P-0061798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	165	440	0	ENST00000349721.2:c.3266G>A	p.Arg1089Gln	p.R1089Q	ENST00000349721	NM_003070.3	1089	cGg/cAg	23/34	1	2	FACETS	0.904	0.835	0.975	0.904	0.835	0.975	CLONAL	1	TRUE	1	0.64374545569781	2		440	567	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8339047	8339047	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	153	441	0	ENST00000356435.5:c.5254G>A	p.Glu1752Lys	p.E1752K	ENST00000356435		1752	Gag/Aag	32/35	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.64374545569781	2		441	431	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974778	21974798	+	inframe_deletion	In_Frame_Del	DEL	CCAGCCAGTCAGCCGAAGGCT	CCAGCCAGTCAGCCGAAGGCT	-	novel	NA	P-0061798-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	352	854	0	ENST00000304494.5:c.29_49del	p.Glu10_Leu16del	p.E10_L16del	ENST00000304494	NM_000077.4	10	gAGCCTTCGGCTGACTGGCTGGcc/gcc	1/3	0.64374545569781	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.64374545569781	1		854	701	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0061799-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	251	515	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.185311003334976	3	FACETS	1	0.988	1			1	INDETERMINATE	3	TRUE	NA	0.488074415380161	3		515	388	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0061800-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	40	307	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.287861536819849	3	FACETS	0.917	0.762	1			1	CLONAL	1	TRUE	NA	0.21	3		307	459	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0061800-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	52	241	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	0.287861536819849	3	FACETS	0.944	0.809	1			1	CLONAL	2	TRUE	NA	0.21	3		241	290	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859015	57859015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776846382	NA	P-0061800-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	65	640	0	ENST00000228682.2:c.511C>T	p.Arg171Trp	p.R171W	ENST00000228682	NM_005269.2	171	Cgg/Tgg	5/12	0.119667313164361	4	FACETS	1	0.96	1	0.648	0.562	0.741	INDETERMINATE	1	TRUE	2	0.21	4		640	578	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46240721	46240722	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0061800-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	104	311	0	ENST00000334344.6:c.1580+2dup		p.X527_splice	ENST00000334344	NM_152641.2	527			0.119667313164361	4	FACETS	1	0.968	1	1	0.987	1	INDETERMINATE	3	TRUE	2	0.21	4		311	343	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993287	72993287	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061800-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	55	839	0	ENST00000268489.5:c.758G>T	p.Ser253Ile	p.S253I	ENST00000268489	NM_006885.3	253	aGc/aTc	2/10	0.258634252846009	1	FACETS	0.81	0.692	0.938	0.81	0.692	0.938	CLONAL	1	TRUE	0	0.21	1		839	579	SUCCESS
APC	324	MSKCC	GRCh37	5	112174529	112174530	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	rs1060503327	NA	P-0061800-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	135	533	0	ENST00000257430.4:c.3241_3242del	p.Ser1081HisfsTer2	p.S1081Hfs*2	ENST00000257430	NM_000038.5	1080	GAg/g	16/16	1	2	FACETS	0.961	0.88	1	1	0.992	1	CLONAL	3	TRUE	1	0.21	2		533	446	SUCCESS
APC	324	MSKCC	GRCh37	5	112175148	112175149	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0061800-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	126	519	0	ENST00000257430.4:c.3858_3859del	p.Glu1286AspfsTer4	p.E1286Dfs*4	ENST00000257430	NM_000038.5	1286	gAA/g	16/16	1	2	FACETS	0.903	0.824	0.985	1	0.992	1	CLONAL	3	TRUE	1	0.21	2		519	443	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777966	27777966	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061800-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	311	1122	0	ENST00000369163.2:c.118del	p.His40IlefsTer23	p.H40Ifs*23	ENST00000369163	NM_003536.2	39	Ccc/cc	1/1	1	2	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	TRUE	1	0.21	2		1122	1188	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0061801-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	451	749	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	0.981	0.94	1	1	0.997	1	CLONAL	2	TRUE	1	0.458423576292137	2		749	1003	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420408	49420408	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061801-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	482	853	0	ENST00000301067.7:c.15341A>T	p.His5114Leu	p.H5114L	ENST00000301067	NM_003482.3	5114	cAt/cTt	48/54	1	2	FACETS	0.968	0.929	1	1	0.997	1	CLONAL	2	TRUE	1	0.458423576292137	2		853	1086	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448138	49448139	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061801-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	475	821	0	ENST00000301067.7:c.461_462insT	p.Glu156ArgfsTer64	p.E156Rfs*64	ENST00000301067	NM_003482.3	154	ggc/ggTc	4/54	1	2	FACETS	0.978	0.939	1	1	0.997	1	CLONAL	2	TRUE	1	0.458423576292137	2		821	1059	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902914	1902914	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1325306850	NA	P-0061801-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	366	552	0	ENST00000382891.5:c.533T>C	p.Leu178Ser	p.L178S	ENST00000382891	NM_133335.3	178	tTg/tCg	2/22	1	2	FACETS	0.989	0.944	1	1	0.997	1	CLONAL	2	TRUE	1	0.458423576292137	2		552	807	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878638	151878657	+	frameshift_variant	Frame_Shift_Del	DEL	GATGTGGGGTAAGGGGAGGC	GATGTGGGGTAAGGGGAGGC	-	novel	NA	P-0061801-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	431	660	0	ENST00000262189.6:c.6288_6307del	p.Gln2096HisfsTer5	p.Q2096Hfs*5	ENST00000262189	NM_170606.2	2096	caGCCTCCCCTTACCCCACATCca/caca	36/59	0.214341615838264	3	FACETS	0.851	0.816	0.887	1	0.995	1	INDETERMINATE	3	TRUE	1	0.458423576292137	3		660	905	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542531	141542557	+	inframe_deletion	In_Frame_Del	DEL	CCACCAGGTGGTACCTGGCCCGGAAGG	CCACCAGGTGGTACCTGGCCCGGAAGG	-	novel	NA	P-0061801-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	330	737	0	ENST00000220592.5:c.2429_2455del	p.Ala810_Val818del	p.A810_V818del	ENST00000220592	NM_012154.3	810	gCCTTCCGGGCCAGGTACCACCTGGTGGat/gat	18/19	1	2	FACETS	0.836	0.793	0.879	1	0.995	1	CLONAL	2	TRUE	1	0.458423576292137	2		737	861	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061802-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	182	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.459401577723976	5	FACETS	1	0.958	1			1	CLONAL	4	TRUE	NA	0.553369515071025	5		485	296	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057057	180057057	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372854098	NA	P-0061802-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	81	871	1	ENST00000261937.6:c.562C>T	p.Arg188Trp	p.R188W	ENST00000261937	NM_182925.4	188	Cgg/Tgg	5/30	1	2	FACETS	0.986	0.878	1	0.986	0.878	1	CLONAL	1	TRUE	1	0.553369515071025	2		872	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0061802-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	87	751	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	0.553369515071025	1	FACETS	0.985	0.887	1	0.985	0.887	1	CLONAL	1	TRUE	0	0.553369515071025	1		751	231	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0061802-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	103	960	0	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	0.553369515071025	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.553369515071025	1		960	266	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670393	246670393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061802-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	69	700	0	ENST00000388985.4:c.127G>A	p.Gly43Arg	p.G43R	ENST00000388985		43	Ggg/Agg	1/12	0.553369515071025	3	FACETS	0.959	0.841	1	0.479	0.42	0.542	CLONAL	1	TRUE	1	0.553369515071025	3		700	332	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348058	89348058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886568838	NA	P-0061802-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	85	795	0	ENST00000301030.4:c.4892G>A	p.Arg1631Gln	p.R1631Q	ENST00000301030	NM_001256183.1	1631	cGg/cAg	9/13	0.553369515071025	3	FACETS	1	0.949	1	0.557	0.496	0.621	CLONAL	1	TRUE	1	0.553369515071025	3		795	352	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798758	135798758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061802-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	71	428	0	ENST00000298552.3:c.485C>T	p.Ser162Leu	p.S162L	ENST00000298552	NM_001162426.1	162	tCa/tTa	6/23	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.553369515071025	2		428	202	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0061803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	83	442	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.214647604156845	5	FACETS	1	0.962	1	0.8	0.709	0.896	CLONAL	2	TRUE	2	0.214647604156845	5		442	426	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376149	225376149	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	38	372	0	ENST00000264414.4:c.805A>G	p.Ile269Val	p.I269V	ENST00000264414	NM_003590.4	269	Att/Gtt	6/16	1	2	FACETS	1	0.829	1	1	0.829	1	CLONAL	1	TRUE	1	0.214647604156845	2		372	354	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970899	21970899	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0061804-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	166	735	0	ENST00000304494.5:c.457+2T>G		p.X153_splice	ENST00000304494	NM_000077.4	153			0.670867872785308	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.670867872785308	1		735	306	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346916	73346916	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0061804-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	110	450	0	ENST00000377767.4:c.1301T>G	p.Leu434Ter	p.L434*	ENST00000377767	NM_014953.3	434	tTa/tGa	9/21	0.670867872785308	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.670867872785308	1		450	176	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0061815-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	400	792	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.604389681907584	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.642991719240696	2		793	616	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0061815-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	207	325	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.622294814158005	2	FACETS	0.979	0.929	1	0.979	0.929	1	CLONAL	2	TRUE	0	0.642991719240696	2		325	329	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923137	48923137	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061815-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	71	232	2	ENST00000267163.4:c.585G>A	p.Trp195Ter	p.W195*	ENST00000267163	NM_000321.2	195	tgG/tgA	6/27	0.622294814158005	2	FACETS	0.977	0.892	1	0.977	0.892	1	CLONAL	2	TRUE	0	0.642991719240696	2		234	113	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600447	10600447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061815-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	460	594	6	ENST00000171111.5:c.1408C>T	p.Arg470Cys	p.R470C	ENST00000171111	NM_203500.1	470	Cgt/Tgt	4/6	0.622294814158005	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.642991719240696	2		600	684	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781440	135781440	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203542	NA	P-0061815-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	400	440	6	ENST00000298552.3:c.1525C>T	p.Arg509Ter	p.R509*	ENST00000298552	NM_001162426.1	509	Cga/Tga	15/23	0.622294814158005	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.642991719240696	2		446	615	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715666	18715666	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061815-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	294	382	6	ENST00000266497.5:c.3497C>A	p.Pro1166His	p.P1166H	ENST00000266497		1166	cCt/cAt	25/31	0.622294814158005	2	FACETS	0.981	0.939	1	0.981	0.939	1	CLONAL	2	TRUE	0	0.642991719240696	2		388	466	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29440816	29440816	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs746065687	NA	P-0061815-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	336	399	14	ENST00000544604.2:c.682G>T	p.Val228Leu	p.V228L	ENST00000544604	NM_001206998.1	228	Gtg/Ttg	5/9	0.622294814158005	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.642991719240696	2		413	510	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965350	68965350	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061815-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	176	382	2	ENST00000288368.4:c.962G>C	p.Gly321Ala	p.G321A	ENST00000288368	NM_024870.2	321	gGa/gCa	9/40	0.583162572657035	4	FACETS	0.825	0.765	0.887	0.825	0.765	0.887	CLONAL	2	TRUE	2	0.642991719240696	4		384	545	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061860-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	177	345	0				ENST00000310581	NM_198253.2	-/1132			0.495447197314301	4	FACETS	0.93	0.863	0.998	0.93	0.863	0.998	CLONAL	2	TRUE	2	0.574229715877363	4		345	522	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0061860-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	258	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.254747029978689	5	FACETS	0.87	0.82	0.92	0.87	0.82	0.92	INDETERMINATE	3	TRUE	2	0.574229715877363	5		336	641	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061860-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	182	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.495447197314301	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	2	0.574229715877363	4		485	471	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380444	31380444	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061860-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	175	797	2	ENST00000328111.2:c.934C>T	p.Arg312Ter	p.R312*	ENST00000328111	NM_006892.3	312	Cga/Tga	9/23	0.439956042796078	4	FACETS	1	0.948	1	0.519	0.477	0.562	CLONAL	1	TRUE	2	0.574229715877363	4		799	925	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66518939	66518939	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061860-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	282	592	0	ENST00000358598.2:c.220C>G	p.Arg74Gly	p.R74G	ENST00000358598	NM_212471.2	74	Cgt/Ggt	3/11	0.329089115686306	6	FACETS	1	0.988	1	0.586	0.551	0.62	INDETERMINATE	2	TRUE	2	0.574229715877363	6		592	901	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0061861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	24	571	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.378126612373846	2		571	110	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30668382	30668382	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1210657939	NA	P-0061861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	29	560	0	ENST00000376406.3:c.6130C>T	p.Gln2044Ter	p.Q2044*	ENST00000376406	NM_014641.2	2044	Cag/Tag	15/15	0.378126612373846	10	FACETS	0.913	0.733	1			1	CLONAL	1	TRUE	NA	0.378126612373846	10		560	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577510	7577511	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGTGTGATGA	novel	NA	P-0061861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	73	562	0	ENST00000269305.4:c.761_770dup	p.Glu258HisfsTer9	p.E258Hfs*9	ENST00000269305	NM_001126112.2	257	ctg/ctTCATCACACTg	7/11	0.378126612373846	4	FACETS	0.978	0.865	1	0.652	0.577	0.731	CLONAL	2	TRUE	1	0.378126612373846	4		562	272	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631714	67631714	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	20	466	0	ENST00000272342.5:c.1900G>C	p.Glu634Gln	p.E634Q	ENST00000272342	NM_019002.3	634	Gaa/Caa	5/6	0.306477103536787	4	FACETS	0.524	0.401	0.668	0.262	0.2	0.334	SUBCLONAL	1	TRUE	2	0.378126612373846	4		466	278	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747898	41747899	+	missense_variant	Missense_Mutation	DNP	AG	AG	GT	novel	NA	P-0061861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	29	605	1	ENST00000226382.2:c.870_871delinsAC	p.Phe291Leu	p.F291L	ENST00000226382	NM_003924.3	290	ccCTtc/ccACtc	3/3	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.378126612373846	2		606	109	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509984	187509984	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	29	698	0	ENST00000441802.2:c.13529del	p.Ser4510IlefsTer51	p.S4510Ifs*51	ENST00000441802	NM_005245.3	4510	aGt/at	27/27	1	2	FACETS	0.862	0.698	1	0.862	0.698	1	CLONAL	1	TRUE	1	0.378126612373846	2		698	178	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115773	8115852	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGGCCGCCCTCTCCAGACACA	AAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGGCCGCCCTCTCCAGACACA	GGAGGACATGTGTCTGGAGAGGGCGGC	novel	NA	P-0061864-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	209	604	3	ENST00000346208.3:c.1119_1198delinsGGAGGACATGTGTCTGGAGAGGGCGGC	p.Lys374GlufsTer115	p.K374Efs*115	ENST00000346208		373	aaAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGGCCGCCCTCTCCAGACACAtg/aaGGAGGACATGTGTCTGGAGAGGGCGGCtg	6/6	1	2	FACETS	0.821	0.764	0.879	0.821	0.764	0.879	CLONAL	1	TRUE	1	0.679814763815018	2		607	749	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954202	48954205	+	frameshift_variant	Frame_Shift_Del	DEL	TATC	TATC	-	novel	NA	P-0061864-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	48	137	0	ENST00000267163.4:c.1403_1406del	p.Leu468SerfsTer9	p.L468Sfs*9	ENST00000267163	NM_000321.2	468	tTATCc/tc	15/27	0.679814763815018	1	FACETS	0.652	0.563	0.744	0.652	0.563	0.744	SUBCLONAL	1	TRUE	0	0.679814763815018	1		137	143	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447220	187447220	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749366850	NA	P-0061864-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	352	653	0	ENST00000232014.4:c.973C>T	p.Arg325Trp	p.R325W	ENST00000232014	NM_001130845.1	325	Cgg/Tgg	5/10	0.679814763815018	3	FACETS	1	0.988	1	0.57	0.54	0.601	CLONAL	1	TRUE	1	0.679814763815018	3		653	1217	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55524200	55524200	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1285711357	NA	P-0061864-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	209	458	1	ENST00000288135.5:c.19G>A	p.Ala7Thr	p.A7T	ENST00000288135	NM_000222.2	7	Gcc/Acc	1/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.679814763815018	2		459	553	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178459	56178460	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061864-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	197	429	0	ENST00000399503.3:c.3433dup	p.Thr1145AsnfsTer6	p.T1145Nfs*6	ENST00000399503	NM_005921.1	1144	-/A	14/20	1	2	FACETS	0.974	0.908	1	0.974	0.908	1	CLONAL	1	TRUE	1	0.679814763815018	2		429	595	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419921	152419922	+	missense_variant	Missense_Mutation	DNP	CT	CT	AA	novel	NA	P-0061864-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	261	528	0	ENST00000206249.3:c.1608_1609delinsAA	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	536	ctCTat/ctAAat	8/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.679814763815018	2		528	737	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509660	106509660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757849968	NA	P-0061864-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	282	542	0	ENST00000359195.3:c.1654C>T	p.Arg552Cys	p.R552C	ENST00000359195	NM_002649.2	552	Cgc/Tgc	2/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.679814763815018	2		542	792	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0061865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	226	277	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.526867804859452	2		277	669	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106648	27106648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553153748	NA	P-0061865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	41	850	0	ENST00000324856.7:c.6259G>A	p.Gly2087Arg	p.G2087R	ENST00000324856	NM_006015.4	2087	Gga/Aga	20/20	1	2	FACETS	0.132	0.109	0.158	0.132	0.109	0.158	SUBCLONAL	1	TRUE	1	0.526867804859452	2		850	1179	SUCCESS
APC	324	MSKCC	GRCh37	5	112174758	112174761	+	frameshift_variant	Frame_Shift_Del	DEL	AAGA	AAGA	-	rs1554085029	NA	P-0061865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	213	550	0	ENST00000257430.4:c.3467_3470del	p.Glu1156GlyfsTer8	p.E1156Gfs*8	ENST00000257430	NM_000038.5	1156	gAAGAg/gg	16/16	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.526867804859452	2		550	736	SUCCESS
APC	324	MSKCC	GRCh37	5	112175766	112175766	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	254	667	0	ENST00000257430.4:c.4476del	p.Thr1493ArgfsTer14	p.T1493Rfs*14	ENST00000257430	NM_000038.5	1492	gCc/gc	16/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.526867804859452	2		667	931	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578463	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371524413	NA	P-0061865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	178	826	0	ENST00000269305.4:c.467G>C	p.Arg156Pro	p.R156P	ENST00000269305	NM_001126112.2	156	cGc/cCc	5/11	1	2	FACETS	0.594	0.547	0.644	0.594	0.547	0.644	SUBCLONAL	1	TRUE	1	0.526867804859452	2		826	1137	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356251	70356251	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	121	684	0	ENST00000374080.3:c.5146C>T	p.Arg1716Ter	p.R1716*	ENST00000374080		1716	Cga/Tga	37/45	1	2	FACETS	0.42	0.379	0.464	0.42	0.379	0.464	SUBCLONAL	1	TRUE	1	0.526867804859452	2		684	1093	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519895	NA	P-0061865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	199	479	0	ENST00000281708.4:c.1394G>T	p.Arg465Leu	p.R465L	ENST00000281708	NM_033632.3	465	cGt/cTt	9/12	1	2	FACETS	0.962	0.894	1	0.962	0.894	1	CLONAL	1	TRUE	1	0.526867804859452	2		479	785	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31239627	31239627	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs281860326	NA	P-0061865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	161	212	0	ENST00000376228.5:c.92A>G	p.Tyr31Cys	p.Y31C	ENST00000376228	NM_002117.5	31	tAt/tGt	2/8	1	2	FACETS	0.967	0.904	1	1	0.993	1	CLONAL	2	TRUE	1	0.526867804859452	2		212	316	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740379	145740379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555407951	NA	P-0061865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	125	762	0	ENST00000428558.2:c.1561C>T	p.Arg521Trp	p.R521W	ENST00000428558	NM_004260.3	521	Cgg/Tgg	9/22	1	2	FACETS	0.401	0.362	0.442	0.401	0.362	0.442	SUBCLONAL	1	TRUE	1	0.526867804859452	2		762	1184	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227114	2227114	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	126	614	0	ENST00000398665.3:c.4594G>A	p.Gly1532Ser	p.G1532S	ENST00000398665	NM_032482.2	1532	Ggc/Agc	27/28	1	2	FACETS	0.516	0.467	0.568	0.516	0.467	0.568	SUBCLONAL	1	TRUE	1	0.526867804859452	2		614	927	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0061866-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	227	662	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.138111674000231	4	FACETS	0.949	0.893	1	0.949	0.893	1	INDETERMINATE	2	TRUE	2	0.827729864777506	4		662	528	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0061866-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	52	277	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.849	0.739	0.963	0.849	0.739	0.963	CLONAL	1	TRUE	1	0.827729864777506	2		277	148	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0061866-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	215	792	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.827729864777506	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.827729864777506	1		793	300	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451352	70451352	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061866-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	14	533	1	ENST00000373644.4:c.6192C>G	p.Asn2064Lys	p.N2064K	ENST00000373644	NM_030625.2	2064	aaC/aaG	12/12	1	2	FACETS	0.129	0.092	0.172	0.129	0.092	0.172	SUBCLONAL	1	TRUE	1	0.827729864777506	2		534	263	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748479	40748479	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061866-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	173	637	0	ENST00000392038.2:c.403G>T	p.Glu135Ter	p.E135*	ENST00000392038	NM_001626.4	135	Gag/Tag	5/14	0.138111674000231	4	FACETS	1	0.989	1	0.713	0.66	0.766	INDETERMINATE	1	TRUE	2	0.827729864777506	4		637	536	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0061867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	89	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.885	0.79	0.985	0.885	0.79	0.985	CLONAL	1	TRUE	1	0.52505543087586	2		473	383	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597401	10597401	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	176	620	0	ENST00000171111.5:c.1802G>T	p.Arg601Leu	p.R601L	ENST00000171111	NM_203500.1	601	cGg/cTg	6/6	0.52505543087586	1	FACETS	0.997	0.926	1	0.997	0.926	1	CLONAL	1	TRUE	0	0.52505543087586	1		620	496	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207198	1207198	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0061867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	107	576	0	ENST00000326873.7:c.286A>T	p.Lys96Ter	p.K96*	ENST00000326873	NM_000455.4	96	Aag/Tag	1/10	0.52505543087586	1	FACETS	0.828	0.75	0.909	0.828	0.75	0.909	CLONAL	1	TRUE	0	0.52505543087586	1		576	363	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61310688	61310688	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	124	442	0	ENST00000341074.5:c.124C>A	p.Leu42Ile	p.L42I	ENST00000341074	NM_002974.2	42	Ctc/Atc	2/8	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.52505543087586	2		442	425	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	65	485	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.987	0.858	1	0.987	0.858	1	CLONAL	1	TRUE	1	0.29	2		485	454	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099403	157099429	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAGCAACAG	CAGCAGCAGCAGCAGCAGCAGCAACAG	-	rs910569810	NA	P-0061867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	42	951	0	ENST00000346085.5:c.360_386del	p.Gln123_Gln131del	p.Q123_Q131del	ENST00000346085	NM_020732.3	114	CAGCAGCAGCAGCAGCAGCAGCAACAG/-	1/20	1	2	FACETS	0.394	0.328	0.468	0.394	0.328	0.468	SUBCLONAL	1	TRUE	1	0.29	2		951	735	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593495	48593495	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	104	463	1	ENST00000342988.3:c.1246A>G	p.Arg416Gly	p.R416G	ENST00000342988	NM_005359.5	416	Aga/Gga	10/12	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.29	2		464	641	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306741	41306741	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	86	652	0	ENST00000373198.4:c.918G>A	p.Trp306Ter	p.W306*	ENST00000373198	NM_133170.3	306	tgG/tgA	7/32	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.29	2		652	545	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987023	36987023	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	64	526	0	ENST00000354822.5:c.666G>T	p.Glu222Asp	p.E222D	ENST00000354822	NM_001079668.2	222	gaG/gaT	3/3	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.29	2		526	372	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551748	150551748	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1460845581	NA	P-0061867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	77	732	0	ENST00000369026.2:c.259C>T	p.Pro87Ser	p.P87S	ENST00000369026	NM_021960.4	87	Ccc/Tcc	1/3	0.298160168489255	3	FACETS	1	0.936	1	0.55	0.483	0.621	CLONAL	1	TRUE	1	0.29	3		732	553	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50782700	50782700	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	35	583	0	ENST00000307179.4:c.2212C>G	p.Pro738Ala	p.P738A	ENST00000307179		738	Cca/Gca	14/20	1	2	FACETS	0.372	0.304	0.449	0.372	0.304	0.449	SUBCLONAL	1	TRUE	1	0.29	2		583	649	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599885	10599885	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	122	615	0	ENST00000171111.5:c.1691G>T	p.Gly564Val	p.G564V	ENST00000171111	NM_203500.1	564	gGg/gTg	5/6	0.298160168489255	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.29	1		615	575	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662129	227662129	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	104	830	0	ENST00000305123.5:c.1326C>A	p.Phe442Leu	p.F442L	ENST00000305123	NM_005544.2	442	ttC/ttA	1/2	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.29	2		830	700	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	896841	896841	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	119	575	0	ENST00000166345.3:c.320C>G	p.Pro107Arg	p.P107R	ENST00000166345	NM_004237.3	107	cCc/cGc	3/13	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.29	2		575	683	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356306	70356306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	94	752	0	ENST00000374080.3:c.5201C>T	p.Pro1734Leu	p.P1734L	ENST00000374080		1734	cCc/cTc	37/45	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.29	2		752	570	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776295	76776295	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	24	440	0	ENST00000373344.5:c.7171del	p.Tyr2391ThrfsTer5	p.Y2391Tfs*5	ENST00000373344	NM_000489.3	2391	Tac/ac	34/35	1	2	FACETS	0.358	0.28	0.449	0.358	0.28	0.449	SUBCLONAL	1	TRUE	1	0.29	2		440	462	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504165	123504165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1212771107	NA	P-0061867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	51	349	0	ENST00000371139.4:c.341C>T	p.Thr114Ile	p.T114I	ENST00000371139	NM_001114937.2	114	aCt/aTt	3/4	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.29	2		349	345	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0061870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	47	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.23	2		473	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0061870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	114	644	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.151514205025431	2	FACETS	0.814	0.735	0.897	0.814	0.735	0.897	CLONAL	2	TRUE	0	0.23	2		645	609	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0061870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	151	435	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.151514205025431	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.23	2		435	584	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024001	27024002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0061870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	52	290	0	ENST00000324856.7:c.1113dup	p.Gln372AlafsTer28	p.Q372Afs*28	ENST00000324856	NM_006015.4	369	-/G	1/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.23	2		290	321	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604702	48604730	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGGGACCGGATTACCCAAGACAGAGCA	CTGGGGACCGGATTACCCAAGACAGAGCA	-	novel	NA	P-0061870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	72	462	0	ENST00000342988.3:c.1524_1552del	p.Trp509GlnfsTer8	p.W509Qfs*8	ENST00000342988	NM_005359.5	508	ggCTGGGGACCGGATTACCCAAGACAGAGCAtc/ggtc	12/12	0.234371165880728	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.23	1		462	503	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22123515	22123515	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	77	295	0	ENST00000215832.6:c.1061T>A	p.Phe354Tyr	p.F354Y	ENST00000215832	NM_002745.4	354	tTc/tAc	8/9	0.151514205025431	3	FACETS	1	0.974	1	0.718	0.632	0.81	CLONAL	1	TRUE	1	0.23	3		295	520	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0061873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	135	366	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.368164649808953	3	FACETS	0.935	0.857	1	0.935	0.857	1	CLONAL	2	TRUE	1	0.384028355795094	3		366	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs530941076	NA	P-0061873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	261	439	0	ENST00000269305.4:c.658T>C	p.Tyr220His	p.Y220H	ENST00000269305	NM_001126112.2	220	Tat/Cat	6/11	0.314219651098644	3	FACETS	0.871	0.823	0.92	0.871	0.823	0.92	CLONAL	3	TRUE	0	0.384028355795094	3		439	620	SUCCESS
APC	324	MSKCC	GRCh37	5	112155043	112155043	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1114167579	NA	P-0061873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	182	340	0	ENST00000257430.4:c.1312+2T>C		p.X438_splice	ENST00000257430	NM_000038.5	438			0.333539677748582	3	FACETS	1	0.986	1	0.824	0.768	0.881	CLONAL	2	TRUE	0	0.384028355795094	3		340	457	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026415	6026415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778531080	NA	P-0061873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	33	131	0	ENST00000265849.7:c.1981G>A	p.Glu661Lys	p.E661K	ENST00000265849	NM_000535.5	661	Gaa/Aaa	11/15	0.244722592340755	4	FACETS	0.772	0.638	0.919	0.772	0.638	0.919	CLONAL	2	TRUE	2	0.384028355795094	4		131	154	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252096	226252096	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	12	75	0	ENST00000366813.1:c.44A>C	p.Lys15Thr	p.K15T	ENST00000366813		15	aAa/aCa	1/3	0.384028355795094	5	FACETS	0.807	0.571	1	0.202	0.142	0.274	CLONAL	1	TRUE	1	0.384028355795094	5		75	122	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711243	114711262	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GGCCAAGAGGCAAGATGGAG	GGCCAAGAGGCAAGATGGAG	-	novel	NA	P-0061873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	54	255	0	ENST00000543371.1:c.261_280del	p.Lys88LeufsTer2	p.K88Lfs*2	ENST00000543371	NM_001198531.1	86	gcGGCCAAGAGGCAAGATGGAGgg/gcgg	3/14	0.365825625693965	3	FACETS	0.911	0.781	1	0.455	0.39	0.526	CLONAL	1	TRUE	1	0.384028355795094	3		255	368	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0061874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	20	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.248	0.189	0.317	0.248	0.189	0.317	SUBCLONAL	1	FALSE	1	0.363846584309189	2		473	444	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061875-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	94	355	0	ENST00000425967.3:c.1731C>G	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaG	13/19	0.222859383231239	3	FACETS	0.991	0.886	1	0.661	0.59	0.735	CLONAL	2	TRUE	0	0.222859383231239	3		355	473	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740623	58740624	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs763475304	NA	P-0061876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	37	562	0	ENST00000305921.3:c.1535dup	p.Asn512LysfsTer16	p.N512Kfs*16	ENST00000305921	NM_003620.3	510	caa/cAaa	6/6	1	2	FACETS	0.267	0.219	0.32	0.267	0.219	0.32	SUBCLONAL	1	FALSE	1	0.45503009108622	2		562	610	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604787	48604787	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519741	NA	P-0061876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	65	480	0	ENST00000342988.3:c.1609G>T	p.Asp537Tyr	p.D537Y	ENST00000342988	NM_005359.5	537	Gac/Tac	12/12	1	2	FACETS	0.474	0.411	0.542	0.474	0.411	0.542	SUBCLONAL	1	FALSE	1	0.45503009108622	2		480	603	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0061876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	34	280	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.408	0.334	0.492	0.408	0.334	0.492	SUBCLONAL	1	FALSE	1	0.45503009108622	2		280	366	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221252	1221252	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	36	524	0	ENST00000326873.7:c.776del	p.Asn259ThrfsTer28	p.N259Tfs*28	ENST00000326873	NM_000455.4	259	Aac/ac	6/10	1	2	FACETS	0.315	0.259	0.379	0.315	0.259	0.379	SUBCLONAL	1	FALSE	1	0.45503009108622	2		524	502	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123711	11123711	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	37	464	0	ENST00000358026.2:c.2361C>G	p.Ile787Met	p.I787M	ENST00000358026	NM_001128849.1	787	atC/atG	16/36	0.45503009108622	3	FACETS	0.31	0.255	0.373	0.155	0.127	0.187	SUBCLONAL	1	FALSE	1	0.45503009108622	3		464	643	SUCCESS
AR	367	MSKCC	GRCh37	X	66765725	66765725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	55	699	0	ENST00000374690.3:c.737C>T	p.Ser246Phe	p.S246F	ENST00000374690	NM_000044.3	246	tCc/tTc	1/8	1	2	FACETS	0.346	0.296	0.402	0.346	0.296	0.402	SUBCLONAL	1	FALSE	1	0.45503009108622	2		699	698	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0061877-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	76	482	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.354	0.31	0.402	0.354	0.31	0.402	SUBCLONAL	1	TRUE	1	0.599960870248169	2		484	715	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs775623976	NA	P-0061877-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	99	425	0	ENST00000335508.6:c.1873C>G	p.Arg625Gly	p.R625G	ENST00000335508	NM_012433.2	625	Cgt/Ggt	14/25	0.296831550878308	2	FACETS	0.529	0.473	0.588	0.264	0.236	0.294	INDETERMINATE	1	TRUE	0	0.599960870248169	2		425	624	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714412	40714412	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061877-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	173	389	0	ENST00000373198.4:c.3985G>A	p.Glu1329Lys	p.E1329K	ENST00000373198	NM_133170.3	1329	Gag/Aag	29/32	1	2	FACETS	0.969	0.897	1	0.969	0.897	1	CLONAL	1	TRUE	1	0.599960870248169	2		389	595	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351403	89351403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762766366	NA	P-0061877-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	91	422	0	ENST00000301030.4:c.1547G>T	p.Ser516Ile	p.S516I	ENST00000301030	NM_001256183.1	516	aGc/aTc	9/13	0.599960870248169	1	FACETS	0.507	0.452	0.564	0.507	0.452	0.564	SUBCLONAL	1	TRUE	0	0.599960870248169	1		422	419	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385233	41385233	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061877-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	165	371	0	ENST00000373198.4:c.728T>G	p.Val243Gly	p.V243G	ENST00000373198	NM_133170.3	243	gTc/gGc	6/32	0.599960870248169	3	FACETS	1	0.967	1	0.545	0.502	0.589	CLONAL	1	TRUE	1	0.599960870248169	3		371	656	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521158	187521162	+	frameshift_variant	Frame_Shift_Del	DEL	GATGT	GATGT	-	novel	NA	P-0061878-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	59	546	0	ENST00000441802.2:c.11993_11997del	p.His3998ArgfsTer51	p.H3998Rfs*51	ENST00000441802	NM_005245.3	3998	cACATC/c	22/27	1	2	FACETS	0.925	0.796	1	0.925	0.796	1	CLONAL	1	TRUE	1	0.238943078262891	2		546	534	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778143	27778143	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061878-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	73	798	0	ENST00000369163.2:c.292G>C	p.Glu98Gln	p.E98Q	ENST00000369163	NM_003536.2	98	Gag/Cag	1/1	1	2	FACETS	0.732	0.639	0.832	0.732	0.639	0.832	SUBCLONAL	1	TRUE	1	0.238943078262891	2		798	835	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862796	9862796	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs749678183	NA	P-0061879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	40	438	0	ENST00000330684.3:c.2507T>C	p.Ile836Thr	p.I836T	ENST00000330684	NM_001134407.1	836	aTc/aCc	12/13	1	2	FACETS	0.276	0.229	0.329	0.276	0.229	0.329	SUBCLONAL	1	TRUE	1	0.599061570449376	2		438	483	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625120	69625120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782246758	NA	P-0061880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	94	394	0	ENST00000334134.2:c.673G>A	p.Val225Ile	p.V225I	ENST00000334134	NM_005247.2	225	Gtt/Att	3/3	1	2	FACETS	0.898	0.803	0.999	0.898	0.803	0.999	CLONAL	1	TRUE	1	0.44431657470889	2		394	471	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22412956	22412956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553196096	NA	P-0061880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	60	181	0	ENST00000344548.3:c.203G>A	p.Arg68Gln	p.R68Q	ENST00000344548	NM_001039802.1	68	cGa/cAa	5/7	1	2	FACETS	0.9	0.782	1	0.9	0.782	1	CLONAL	1	TRUE	1	0.44431657470889	2		181	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0061880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	182	587	0	ENST00000269305.4:c.560-2A>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.44431657470889	1	FACETS	0.953	0.882	1	0.953	0.882	1	CLONAL	1	TRUE	0	0.44431657470889	1		587	669	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849873	151849873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141718495	NA	P-0061880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	112	408	0	ENST00000262189.6:c.12443C>T	p.Pro4148Leu	p.P4148L	ENST00000262189	NM_170606.2	4148	cCg/cTg	49/59	1	2	FACETS	0.807	0.727	0.891	0.807	0.727	0.891	CLONAL	1	TRUE	1	0.44431657470889	2		408	625	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984847	11984847	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	79	313	0	ENST00000353533.5:c.393A>T	p.Lys131Asn	p.K131N	ENST00000353533	NM_003010.3	131	aaA/aaT	3/11	0.44431657470889	1	FACETS	0.806	0.715	0.903	0.806	0.715	0.903	CLONAL	1	TRUE	0	0.44431657470889	1		313	343	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46727055	46727055	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	48	437	0	ENST00000371975.4:c.889G>A	p.Glu297Lys	p.E297K	ENST00000371975	NM_003579.3	297	Gag/Aag	8/18	0.310426315059736	1	FACETS	0.185	0.156	0.217	0.185	0.156	0.217	INDETERMINATE	1	TRUE	0	0.629971918037122	1		437	565	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120496312	120496312	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0061881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	179	345	0	ENST00000256646.2:c.2220-1G>A		p.X740_splice	ENST00000256646	NM_024408.3	740			0.297003022303527	1	FACETS	0.903	0.842	0.965	0.903	0.842	0.965	INDETERMINATE	1	TRUE	0	0.629971918037122	1		345	431	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844722	156844722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs986498490	NA	P-0061881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1248	152	662	1	ENST00000524377.1:c.1276G>A	p.Val426Ile	p.V426I	ENST00000524377	NM_002529.3	426	Gtc/Atc	11/17	0.511856452548678	4	FACETS	0.562	0.512	0.614	0.187	0.17	0.205	SUBCLONAL	1	TRUE	1	0.629971918037122	4		663	1400	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620407	43620407	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	272	426	0	ENST00000355710.3:c.3016G>A	p.Glu1006Lys	p.E1006K	ENST00000355710	NM_020975.4	1006	Gag/Aag	18/20	0.407667944032227	3	FACETS	0.795	0.75	0.841	0.795	0.75	0.841	SUBCLONAL	2	TRUE	1	0.629971918037122	3		426	714	SUCCESS
ATM	472	MSKCC	GRCh37	11	108168072	108168072	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	21	284	0	ENST00000278616.4:c.4968G>C	p.Lys1656Asn	p.K1656N	ENST00000278616	NM_000051.3	1656	aaG/aaC	33/63	0.597384899616378	2	FACETS	0.197	0.151	0.251	0.099	0.075	0.126	SUBCLONAL	1	TRUE	0	0.629971918037122	2		284	338	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440431	49440431	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1240601136	NA	P-0061881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	310	469	0	ENST00000301067.7:c.4379del	p.Pro1460HisfsTer46	p.P1460Hfs*46	ENST00000301067	NM_003482.3	1460	cCa/ca	15/54	0.206831541599626	5	FACETS	0.993	0.938	1	0.662	0.625	0.699	INDETERMINATE	2	TRUE	2	0.629971918037122	5		469	964	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445021	49445169	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGTGCGGCTCCTCAGTCTGGGGGGACAGGTGCAATTCCTCAGGCTGAGGGGACAGATGTGGTCCCTCAGCCTGGGGGGACAAGTGTGGCTCCTCAGGCACAGCGCATAGGCATGGCTCCTCAGGCTGGGGGGACAGGTGTGGCTCCT	CAGGTGCGGCTCCTCAGTCTGGGGGGACAGGTGCAATTCCTCAGGCTGAGGGGACAGATGTGGTCCCTCAGCCTGGGGGGACAAGTGTGGCTCCTCAGGCACAGCGCATAGGCATGGCTCCTCAGGCTGGGGGGACAGGTGTGGCTCCT	-	novel	NA	P-0061881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	227	594	0	ENST00000301067.7:c.2297_2445del	p.Glu766ValfsTer5	p.E766Vfs*5	ENST00000301067	NM_003482.3	766	gAGGAGCCACACCTGTCCCCCCAGCCTGAGGAGCCATGCCTATGCGCTGTGCCTGAGGAGCCACACTTGTCCCCCCAGGCTGAGGGACCACATCTGTCCCCTCAGCCTGAGGAATTGCACCTGTCCCCCCAGACTGAGGAGCCGCACCTG/g	10/54	0.206831541599626	5	FACETS	0.781	0.729	0.835	0.521	0.486	0.557	INDETERMINATE	2	TRUE	2	0.629971918037122	5		594	897	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820684	3820684	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	369	541	0	ENST00000262367.5:c.2767C>T	p.Gln923Ter	p.Q923*	ENST00000262367	NM_004380.2	923	Cag/Tag	14/31	0.592295088226451	2	FACETS	0.911	0.874	0.948	0.911	0.874	0.948	CLONAL	2	TRUE	0	0.629971918037122	2		541	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0061881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	210	372	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.629971918037122	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.629971918037122	1		372	406	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618598	37618598	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	48	481	0	ENST00000447079.4:c.274G>A	p.Asp92Asn	p.D92N	ENST00000447079	NM_015083.1	92	Gac/Aac	1/14	0.407667944032227	3	FACETS	0.21	0.176	0.247	0.105	0.088	0.124	SUBCLONAL	1	TRUE	1	0.629971918037122	3		481	956	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160330	22160330	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0061881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	35	327	0	ENST00000215832.6:c.303-2A>G		p.X101_splice	ENST00000215832	NM_002745.4	101			0.29401176819845	2	FACETS	0.217	0.177	0.261	0.108	0.088	0.131	INDETERMINATE	1	TRUE	0	0.629971918037122	2		327	513	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163004	47163004	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	202	353	0	ENST00000409792.3:c.3122C>A	p.Ser1041Tyr	p.S1041Y	ENST00000409792	NM_014159.6	1041	tCt/tAt	3/21	0.203791999733361	3	FACETS	1	0.991	1	0.705	0.658	0.754	INDETERMINATE	1	TRUE	1	0.629971918037122	3		353	598	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279184	142279184	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2065	139	301	0	ENST00000350721.4:c.1462G>C	p.Glu488Gln	p.E488Q	ENST00000350721	NM_001184.3	488	Gag/Cag	6/47	0.629971918037122	15	FACETS	1	0.922	1			1	CLONAL	1	TRUE	NA	0.629971918037122	15		301	2204	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790641	89790641	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	97	432	0	ENST00000336032.3:c.28G>A	p.Glu10Lys	p.E10K	ENST00000336032	NM_006813.2	10	Gag/Aag	1/2	0.297003022303527	1	FACETS	0.398	0.356	0.443	0.398	0.356	0.443	INDETERMINATE	1	TRUE	0	0.629971918037122	1		432	530	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431616	6431616	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	80	170	0	ENST00000356142.4:c.169G>T	p.Asp57Tyr	p.D57Y	ENST00000356142	NM_018890.3	57	Gat/Tat	3/7	0.286695954464877	3	FACETS	1	0.945	1	0.551	0.49	0.615	INDETERMINATE	1	TRUE	1	0.629971918037122	3		170	303	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124532325	124532325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	76	257	0	ENST00000357628.3:c.119G>A	p.Gly40Glu	p.G40E	ENST00000357628	NM_015450.2	40	gGa/gAa	6/19	0.574190403825852	3	FACETS	0.876	0.774	0.985	0.438	0.387	0.493	CLONAL	1	TRUE	1	0.629971918037122	3		257	362	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0061884-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	244	491	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.462069795989703	2		491	719	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0061884-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	19	735	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.462069795989703	1	FACETS	0.13	0.098	0.168	0.13	0.098	0.168	SUBCLONAL	1	TRUE	0	0.462069795989703	1		735	486	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305278	39305311	+	frameshift_variant	Frame_Shift_Del	DEL	CACTAGTCTGGTGACCACAGCTCCTGTGAGAAGT	CACTAGTCTGGTGACCACAGCTCCTGTGAGAAGT	-	novel	NA	P-0061884-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	58	410	0	ENST00000373001.3:c.1114_1147del	p.Thr372ProfsTer4	p.T372Pfs*4	ENST00000373001	NM_022157.3	372	ACTTCTCACAGGAGCTGTGGTCACCAGACTAGTGcc/cc	7/7	0.187912905442353	5	FACETS	0.488	0.418	0.565			1	INDETERMINATE	1	TRUE	NA	0.462069795989703	5		410	871	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560514	65560514	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061884-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	226	473	0	ENST00000358664.4:c.83A>G	p.His28Arg	p.H28R	ENST00000358664	NM_002382.4	28	cAt/cGt	3/5	0.462069795989703	1	FACETS	0.821	0.775	0.867	1	0.994	1	CLONAL	2	TRUE	0	0.462069795989703	1		473	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057520005	NA	P-0061884-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	189	465	0	ENST00000269305.4:c.820G>C	p.Val274Leu	p.V274L	ENST00000269305	NM_001126112.2	274	Gtt/Ctt	8/11	0.462069795989703	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.462069795989703	1		465	486	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249510	153249510	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1157879635	NA	P-0061884-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	162	350	0	ENST00000281708.4:c.1268G>T	p.Gly423Val	p.G423V	ENST00000281708	NM_033632.3	423	gGa/gTa	9/12	0.23126096431079	1	FACETS	1	0.929	1	1	0.929	1	INDETERMINATE	1	TRUE	0	0.462069795989703	1		350	536	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187537	32187537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061884-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	281	544	0	ENST00000375023.3:c.1342C>T	p.His448Tyr	p.H448Y	ENST00000375023	NM_004557.3	448	Cat/Tat	8/30	1	2	FACETS	0.772	0.728	0.816	1	0.994	1	SUBCLONAL	2	TRUE	1	0.462069795989703	2		544	788	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912326	97912326	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs377620735	NA	P-0061884-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	30	373	0	ENST00000289081.3:c.565C>G	p.Pro189Ala	p.P189A	ENST00000289081	NM_000136.2	189	Cca/Gca	7/15	1	2	FACETS	0.225	0.181	0.276	0.225	0.181	0.276	SUBCLONAL	1	TRUE	1	0.462069795989703	2		373	576	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0061885-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	139	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.222468949809582	1	FACETS	1	0.964	1	1	0.992	1	CLONAL	2	TRUE	0	0.222468949809582	1		336	506	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0061885-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	143	346	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	0.222468949809582	1	FACETS	0.947	0.867	1	1	0.991	1	CLONAL	2	TRUE	0	0.222468949809582	1		346	603	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267489	198267489	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1039242157	NA	P-0061885-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	132	409	0	ENST00000335508.6:c.1868A>G	p.Tyr623Cys	p.Y623C	ENST00000335508	NM_012433.2	623	tAt/tGt	14/25	1	2	FACETS	1	0.913	1	1	0.99	1	CLONAL	2	TRUE	1	0.222468949809582	2		409	592	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51520078	51520078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765243938	NA	P-0061885-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	109	302	0	ENST00000260433.2:c.349G>A	p.Gly117Ser	p.G117S	ENST00000260433		117	Ggc/Agc	4/10	0.222468949809582	1	FACETS	0.923	0.833	1	1	0.988	1	CLONAL	2	TRUE	0	0.222468949809582	1		302	472	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636731	2636731	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1272187031	NA	P-0061885-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	151	531	1	ENST00000342085.4:c.1180T>C	p.Ser394Pro	p.S394P	ENST00000342085	NM_002613.4	394	Tca/Cca	11/14	1	2	FACETS	1	0.951	1	1	0.992	1	CLONAL	2	TRUE	1	0.222468949809582	2		532	646	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47492845	47492845	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061885-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	87	367	0	ENST00000404338.3:c.3949G>A	p.Val1317Met	p.V1317M	ENST00000404338	NM_004491.4	1317	Gtg/Atg	4/6	0.222468949809582	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.222468949809582	1		367	466	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288678	198288681	+	frameshift_variant	Frame_Shift_Del	DEL	CTCG	CTCG	-	novel	NA	P-0061885-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	52	284	0	ENST00000335508.6:c.46_49del	p.Arg16LysfsTer39	p.R16Kfs*39	ENST00000335508	NM_012433.2	16	CGAGaa/aa	2/25	1	2	FACETS	0.917	0.781	1	0.917	0.781	1	CLONAL	1	TRUE	1	0.222468949809582	2		284	510	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023329	27023366	+	frameshift_variant	Frame_Shift_Del	DEL	CCCAGCCTACGGCTTCGGGCAACCCTACGGCCGGAGCC	CCCAGCCTACGGCTTCGGGCAACCCTACGGCCGGAGCC	G	novel	NA	P-0061885-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	70	348	0	ENST00000324856.7:c.435_472delinsG	p.Pro146ArgfsTer74	p.P146Rfs*74	ENST00000324856	NM_006015.4	145	ccCCCAGCCTACGGCTTCGGGCAACCCTACGGCCGGAGCCcg/ccGcg	1/20	0.222468949809582	1	FACETS	0.932	0.82	1	1	0.981	1	CLONAL	2	TRUE	0	0.222468949809582	1		348	300	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031170	11031170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061888-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	37	485	0	ENST00000327064.4:c.1255C>T	p.Arg419Trp	p.R419W	ENST00000327064	NM_199141.1	419	Cgg/Tgg	11/16	0.621555989877172	3	FACETS	0.247	0.203	0.297	0.082	0.067	0.099	SUBCLONAL	1	TRUE	0	0.617869482334429	3		485	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934576	NA	P-0061888-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	413	457	0	ENST00000269305.4:c.818G>C	p.Arg273Pro	p.R273P	ENST00000269305	NM_001126112.2	273	cGt/cCt	8/11	0.621555989877172	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.617869482334429	3		457	571	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235324	235324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061888-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	153	328	1	ENST00000264932.6:c.1130C>T	p.Ala377Val	p.A377V	ENST00000264932	NM_004168.2	377	gCc/gTc	9/15	0.621555989877172	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.617869482334429	1		329	264	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319456	11319456	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061888-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	282	426	0	ENST00000361445.4:c.11C>T	p.Thr4Ile	p.T4I	ENST00000361445	NM_004958.3	4	aCc/aTc	2/58	0.621555989877172	1	FACETS	0.771	0.74	0.801	1	0.996	1	SUBCLONAL	2	TRUE	0	0.617869482334429	1		426	409	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724541	162724541	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061888-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	183	505	0	ENST00000367921.3:c.313C>A	p.Arg105Ser	p.R105S	ENST00000367921	NM_006182.2	105	Cgc/Agc	5/18	0.621555989877172	3	FACETS	0.922	0.852	0.995	0.461	0.426	0.498	CLONAL	1	TRUE	1	0.617869482334429	3		505	841	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256583	133256583	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061888-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	41	429	0	ENST00000320574.5:c.380A>G	p.Lys127Arg	p.K127R	ENST00000320574	NM_006231.2	127	aAa/aGa	5/49	NA	2	FACETS	0.287	0.239	0.341			1	INDETERMINATE	1	TRUE	NA	0.617869482334429	2		429	462	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690304	33690304	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs778159998	NA	P-0061888-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	54	534	0	ENST00000308377.4:c.523C>G	p.Gln175Glu	p.Q175E	ENST00000308377	NM_152270.3	175	Caa/Gaa	2/5	0.621555989877172	2	FACETS	0.369	0.315	0.427	0.184	0.157	0.214	SUBCLONAL	1	TRUE	0	0.617869482334429	2		534	474	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38793763	38793763	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061888-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	64	425	0	ENST00000348513.6:c.218A>T	p.Tyr73Phe	p.Y73F	ENST00000348513	NM_003079.4	73	tAc/tTc	5/11	0.621555989877172	2	FACETS	0.398	0.345	0.456	0.199	0.172	0.228	SUBCLONAL	1	TRUE	0	0.617869482334429	2		425	520	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804337	46804337	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061888-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	246	391	0	ENST00000290295.7:c.670A>C	p.Ser224Arg	p.S224R	ENST00000290295	NM_006361.5	224	Agc/Cgc	2/2	0.621555989877172	3	FACETS	0.942	0.889	0.996	0.628	0.593	0.664	CLONAL	2	TRUE	0	0.617869482334429	3		391	553	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4123321	4123844	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCAGGGACCTCCCCTCACTCAACCTCGCTGCTCAGGGACCCCTGTCCCCATCCTCTCCTCTTAGAGACATCCTTCACCCCAACTTCACTACTCAGAGACTCCCGTTATCCCAATTCCACTCTTCAGGAACCCCACACCCCATCTTTTCCACCACAAGGACCTCCCCTCGCCCAATCTCACTGCTCAAAGACCCCCCTGCCCCGTGCACCCTTCGCCCCGTCCTCCGAGGGCCCCCTGCCCCGTCCTCCCCCGAGGGCCCCCTGCCCCGTCCTCCCCCGAGGGTCCCCTGCCCTGTCCTCCCCTCGAGAACCCCCTGCCCCGTGCACCACTCACCCCGTCCTCCCCCGTGACCCCCCTGCCTCGTGCACTCCTCGCGAACCCCCGTCCCCTCGCCCCGTCCTTCCCCGAGGGCTCCCTGCCCCGTGCACCCCAAGCCTCCGGCTGACCCCTGCCCACTCACTCGGAGGCGCCCTCGCTGGTAGGGGATGGGCCCTCGGCGATGGTAGGGTTGATGGTGAGCGCCG	GCAGGGACCTCCCCTCACTCAACCTCGCTGCTCAGGGACCCCTGTCCCCATCCTCTCCTCTTAGAGACATCCTTCACCCCAACTTCACTACTCAGAGACTCCCGTTATCCCAATTCCACTCTTCAGGAACCCCACACCCCATCTTTTCCACCACAAGGACCTCCCCTCGCCCAATCTCACTGCTCAAAGACCCCCCTGCCCCGTGCACCCTTCGCCCCGTCCTCCGAGGGCCCCCTGCCCCGTCCTCCCCCGAGGGCCCCCTGCCCCGTCCTCCCCCGAGGGTCCCCTGCCCTGTCCTCCCCTCGAGAACCCCCTGCCCCGTGCACCACTCACCCCGTCCTCCCCCGTGACCCCCCTGCCTCGTGCACTCCTCGCGAACCCCCGTCCCCTCGCCCCGTCCTTCCCCGAGGGCTCCCTGCCCCGTGCACCCCAAGCCTCCGGCTGACCCCTGCCCACTCACTCGGAGGCGCCCTCGCTGGTAGGGGATGGGCCCTCGGCGATGGTAGGGTTGATGGTGAGCGCCG	-	novel	NA	P-0061888-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2	34	2	0	ENST00000262948.5:c.29_92+460del		p.X10_splice	ENST00000262948	NM_030662.3	10		1/11	0.621555989877172	2	FACETS	1	0.953	1	1	0.977	1	CLONAL	3	TRUE	0	0.617869482334429	2		2	36	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026927	48026927	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs730881816	NA	P-0061888-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	303	437	0	ENST00000234420.5:c.1805C>G	p.Ser602Ter	p.S602*	ENST00000234420	NM_000179.2	602	tCa/tGa	4/10	0.621555989877172	3	FACETS	1	0.992	1	0.784	0.748	0.819	CLONAL	2	TRUE	0	0.617869482334429	3		437	546	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543775	212543775	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0061888-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	25	378	0	ENST00000342788.4:c.1622+2T>C		p.X541_splice	ENST00000342788	NM_005235.2	541			0.19105061055952	2	FACETS	0.17	0.134	0.213	0.085	0.067	0.107	INDETERMINATE	1	TRUE	0	0.617869482334429	2		378	475	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356173	66356173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061888-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	56	513	0	ENST00000273854.3:c.1324G>A	p.Glu442Lys	p.E442K	ENST00000273854	NM_004439.5	442	Gag/Aag	5/18	0.282992959395146	3	FACETS	0.357	0.305	0.414	0.179	0.152	0.207	INDETERMINATE	1	TRUE	1	0.617869482334429	3		513	664	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771197	161771197	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061888-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	31	374	0	ENST00000366898.1:c.1332G>T	p.Glu444Asp	p.E444D	ENST00000366898	NM_004562.2	444	gaG/gaT	12/12	0.230473790434247	5	FACETS	0.357	0.288	0.436			1	INDETERMINATE	1	TRUE	NA	0.617869482334429	5		374	541	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437311	220437311	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061889-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	247	512	1	ENST00000243786.2:c.215C>T	p.Ser72Phe	p.S72F	ENST00000243786	NM_002191.3	72	tCt/tTt	1/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.52488110157929	2		513	835	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0061889-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	400	302	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.447576609696985	4	FACETS	0.908	0.869	0.948	0.908	0.869	0.948	CLONAL	3	TRUE	1	0.52488110157929	4		302	853	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0061889-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	251	571	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.52488110157929	2		571	753	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0061889-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	340	329	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.447576609696985	4	FACETS	1	0.991	1	0.794	0.755	0.834	CLONAL	2	TRUE	1	0.52488110157929	4		329	829	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748479	43748479	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45533131	NA	P-0061889-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	209	405	0	ENST00000523873.1:c.433C>T	p.Arg145Ter	p.R145*	ENST00000523873		145	Cga/Tga	6/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.52488110157929	2		405	710	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862815	9862815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061889-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	181	490	0	ENST00000330684.3:c.2488C>T	p.Leu830Phe	p.L830F	ENST00000330684	NM_001134407.1	830	Ctt/Ttt	12/13	1	2	FACETS	0.886	0.819	0.956	0.886	0.819	0.956	CLONAL	1	TRUE	1	0.52488110157929	2		490	778	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857869	9857869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061889-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	256	578	0	ENST00000330684.3:c.3532C>T	p.Leu1178Phe	p.L1178F	ENST00000330684	NM_001134407.1	1178	Ctt/Ttt	13/13	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.52488110157929	2		578	964	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967867	93967867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061889-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	184	450	0	ENST00000369303.4:c.2060G>A	p.Gly687Glu	p.G687E	ENST00000369303	NM_004440.3	687	gGg/gAg	11/17	0.52488110157929	1	FACETS	0.945	0.879	1	0.945	0.879	1	CLONAL	1	TRUE	0	0.52488110157929	1		450	547	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170444	119170444	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061889-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	104	468	0	ENST00000264033.4:c.2674C>A	p.Leu892Ile	p.L892I	ENST00000264033	NM_005188.3	892	Ctc/Atc	16/16	0.288841692855677	1	FACETS	0.405	0.362	0.45	0.405	0.362	0.45	INDETERMINATE	1	TRUE	0	0.52488110157929	1		468	722	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100838	27100838	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061889-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	212	396	0	ENST00000324856.7:c.4120G>A	p.Asp1374Asn	p.D1374N	ENST00000324856	NM_006015.4	1374	Gat/Aat	18/20	0.288841692855677	1	FACETS	0.83	0.774	0.887	0.83	0.774	0.887	INDETERMINATE	1	TRUE	0	0.52488110157929	1		396	718	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811782	102811782	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0061889-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	193	513	0	ENST00000307046.8:c.403-1G>A		p.X135_splice	ENST00000307046	NM_001111285.1	135			0.20616562270163	1	FACETS	0.668	0.619	0.719	0.668	0.619	0.719	INDETERMINATE	1	TRUE	0	0.52488110157929	1		513	812	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924405	112924405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061889-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	165	429	0	ENST00000351677.2:c.1351G>A	p.Asp451Asn	p.D451N	ENST00000351677	NM_002834.3	451	Gat/Aat	11/16	0.20616562270163	1	FACETS	0.627	0.576	0.679	0.627	0.576	0.679	INDETERMINATE	1	TRUE	0	0.52488110157929	1		429	740	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609121	46609121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061889-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	171	405	1	ENST00000263734.3:c.2180C>T	p.Pro727Leu	p.P727L	ENST00000263734	NM_001430.4	727	cCa/cTa	14/16	1	2	FACETS	0.992	0.916	1	0.992	0.916	1	CLONAL	1	TRUE	1	0.52488110157929	2		406	657	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527820	157527842	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTTAAGCTCCGCAGGTAGAAA	CCCTTAAGCTCCGCAGGTAGAAA	-	novel	NA	P-0061889-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	262	606	0	ENST00000346085.5:c.5545_5567del	p.Pro1849GlufsTer10	p.P1849Efs*10	ENST00000346085	NM_020732.3	1849	CCCTTAAGCTCCGCAGGTAGAAAg/g	20/20	0.52488110157929	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.52488110157929	1		606	710	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958202	2958202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061889-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	531	436	0	ENST00000396946.4:c.2530G>A	p.Val844Met	p.V844M	ENST00000396946	NM_032415.4	844	Gtg/Atg	19/25	0.447576609696985	4	FACETS	0.992	0.956	1	0.992	0.956	1	CLONAL	3	TRUE	1	0.52488110157929	4		436	1037	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443675	29443675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1034835558	NA	P-0061890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	97	676	0	ENST00000389048.3:c.3542G>A	p.Arg1181His	p.R1181H	ENST00000389048	NM_004304.4	1181	cGc/cAc	23/29	0.185702307194781	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	FALSE	1	0.175075792002943	3		676	530	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523501	106523501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373006568	NA	P-0061890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	37	411	3	ENST00000359195.3:c.2653G>A	p.Ala885Thr	p.A885T	ENST00000359195	NM_002649.2	885	Gcc/Acc	8/11	0.287588543669091	3	FACETS	0.905	0.745	1	0.452	0.372	0.542	CLONAL	1	FALSE	1	0.175075792002943	3		414	508	SUCCESS
APC	324	MSKCC	GRCh37	5	112162807	112162807	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	73	343	1	ENST00000257430.4:c.1411G>T	p.Gly471Ter	p.G471*	ENST00000257430	NM_000038.5	471	Gga/Tga	12/16	0.172437301943262	3	FACETS	0.916	0.808	1	0.916	0.808	1	CLONAL	3	FALSE	0	0.175075792002943	3		344	330	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162722916	162722916	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	46	508	1	ENST00000367921.3:c.114del	p.Gly39AlafsTer45	p.G39Afs*45	ENST00000367921	NM_006182.2	38	ggA/gg	4/18	0.185702307194781	3	FACETS	1	0.895	1	0.542	0.456	0.637	CLONAL	1	FALSE	1	0.175075792002943	3		509	527	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910802	114910802	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	49	545	0	ENST00000543371.1:c.923del	p.Gly308AlafsTer7	p.G308Afs*7	ENST00000543371	NM_001198531.1	307	acG/ac	9/14	0.185702307194781	3	FACETS	0.937	0.792	1	0.468	0.396	0.548	CLONAL	1	FALSE	1	0.175075792002943	3		545	650	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952139	178952139	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1560150596	NA	P-0061891-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	53	345	0	ENST00000263967.3:c.3194A>T	p.His1065Leu	p.H1065L	ENST00000263967	NM_006218.2	1065	cAt/cTt	21/21	0.249860118002842	1	FACETS	0.409	0.349	0.473	0.409	0.349	0.473	INDETERMINATE	1	TRUE	0	0.518185635864695	1		345	371	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624415	140624415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1273585752	NA	P-0061891-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	175	296	1	ENST00000288602.6:c.89G>A	p.Gly30Asp	p.G30D	ENST00000288602	NM_004333.4	30	gGc/gAc	1/18	0.518185635864695	3	FACETS	1	0.988	1	0.458	0.423	0.493	CLONAL	1	TRUE	0	0.518185635864695	3		297	619	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124511004	124511004	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061891-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	144	284	4	ENST00000357628.3:c.216T>G	p.Ile72Met	p.I72M	ENST00000357628	NM_015450.2	72	atT/atG	7/19	0.518185635864695	3	FACETS	0.854	0.796	0.912	0.854	0.796	0.912	CLONAL	3	TRUE	0	0.518185635864695	3		288	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0061892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	405	484	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.45188423540014	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.453593436861754	2		484	788	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127670	64127670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	263	464	0	ENST00000334205.4:c.163G>A	p.Gly55Arg	p.G55R	ENST00000334205	NM_003942.2	55	Ggg/Agg	3/17	0.453593436861754	2	FACETS	0.947	0.895	1	0.947	0.895	1	CLONAL	2	TRUE	0	0.453593436861754	2		464	612	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273240	18273240	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	245	555	0	ENST00000222254.8:c.1033C>T	p.Arg345Trp	p.R345W	ENST00000222254	NM_005027.3	345	Cgg/Tgg	9/16	0.374647222063632	2	FACETS	0.772	0.725	0.819	0.772	0.725	0.819	SUBCLONAL	2	TRUE	0	0.453593436861754	2		555	700	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936995	48936995	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778842	NA	P-0061892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	157	420	0	ENST00000267163.4:c.763C>T	p.Arg255Ter	p.R255*	ENST00000267163	NM_000321.2	255	Cga/Tga	8/27	0.45188423540014	2	FACETS	0.828	0.767	0.891	0.828	0.767	0.891	CLONAL	2	TRUE	0	0.453593436861754	2		420	418	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471712	120471712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs75423398	NA	P-0061892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	239	510	0	ENST00000256646.2:c.3779G>A	p.Arg1260His	p.R1260H	ENST00000256646	NM_024408.3	1260	cGt/cAt	23/34	0.453593436861754	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.453593436861754	1		510	702	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024494	16024494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	124	452	1	ENST00000268712.3:c.1724C>T	p.Ala575Val	p.A575V	ENST00000268712	NM_006311.3	575	gCc/gTc	16/46	0.45188423540014	2	FACETS	0.672	0.608	0.739	0.336	0.304	0.37	SUBCLONAL	1	TRUE	0	0.453593436861754	2		453	814	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748229	41748229	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs865798137	NA	P-0061892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	91	409	0	ENST00000226382.2:c.540G>T	p.Arg180Ser	p.R180S	ENST00000226382	NM_003924.3	180	agG/agT	3/3	0.45188423540014	2	FACETS	0.649	0.577	0.726	0.325	0.288	0.363	SUBCLONAL	1	TRUE	0	0.453593436861754	2		409	618	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432609	78432609	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1233786882	NA	P-0061892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	53	431	0	ENST00000370768.2:c.374G>A	p.Arg125His	p.R125H	ENST00000370768	NM_003902.3	125	cGc/cAc	6/20	0.453593436861754	1	FACETS	0.759	0.654	0.871	0.759	0.654	0.871	SUBCLONAL	1	TRUE	0	0.453593436861754	1		431	238	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748545	40748545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1054914884	NA	P-0061892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	52	410	0	ENST00000392038.2:c.337C>T	p.Arg113Trp	p.R113W	ENST00000392038	NM_001626.4	113	Cgg/Tgg	5/14	0.110008707231523	4	FACETS	0.452	0.383	0.527	0.226	0.191	0.264	INDETERMINATE	1	TRUE	2	0.453593436861754	4		410	738	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155650	56155650	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	351	430	0	ENST00000399503.3:c.742C>T	p.Arg248Ter	p.R248*	ENST00000399503	NM_005921.1	248	Cga/Tga	3/20	0.45188423540014	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.453593436861754	2		430	710	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778500	3778500	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779996604	NA	P-0061892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	99	562	0	ENST00000262367.5:c.6548C>T	p.Ala2183Val	p.A2183V	ENST00000262367	NM_004380.2	2183	gCg/gTg	31/31	0.360121283027771	3	FACETS	0.694	0.619	0.773	0.231	0.206	0.258	SUBCLONAL	1	TRUE	0	0.453593436861754	3		562	772	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450363	50450363	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1441542459	NA	P-0061892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	128	448	0	ENST00000331340.3:c.547C>T	p.Arg183Cys	p.R183C	ENST00000331340	NM_006060.4	183	Cgc/Tgc	5/8	1	2	FACETS	0.789	0.716	0.866	0.789	0.716	0.866	SUBCLONAL	1	TRUE	1	0.453593436861754	2		448	715	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573318	41573318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781609478	NA	P-0061892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	405	645	1	ENST00000263253.7:c.5603C>T	p.Thr1868Met	p.T1868M	ENST00000263253	NM_001429.3	1868	aCg/aTg	31/31	0.453593436861754	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.453593436861754	2		646	864	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727934	41727934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748904765	NA	P-0061892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	171	410	0	ENST00000301178.4:c.559G>A	p.Gly187Ser	p.G187S	ENST00000301178	NM_021913.4	187	Ggc/Agc	4/20	0.110008707231523	4	FACETS	1	0.989	1	0.749	0.69	0.809	INDETERMINATE	1	TRUE	2	0.453593436861754	4		410	732	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46738397	46738397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137873579	NA	P-0061892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	560	548	2	ENST00000371975.4:c.1298C>T	p.Pro433Leu	p.P433L	ENST00000371975	NM_003579.3	433	cCg/cTg	12/18	0.450732968103189	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	0	0.453593436861754	3		550	1007	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231488466	231488466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	72	464	0	ENST00000295050.7:c.829G>A	p.Ala277Thr	p.A277T	ENST00000295050	NM_032018.5	277	Gcc/Acc	5/5	0.42973752886633	3	FACETS	0.825	0.723	0.935	0.275	0.241	0.312	CLONAL	1	TRUE	0	0.453593436861754	3		464	472	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77937768	77937768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs116286425	NA	P-0061892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	105	491	1	ENST00000361507.4:c.950C>T	p.Pro317Leu	p.P317L	ENST00000361507	NM_080491.2	317	cCg/cTg	4/10	0.453593436861754	2	FACETS	0.503	0.45	0.559	0.251	0.225	0.28	SUBCLONAL	1	TRUE	0	0.453593436861754	2		492	921	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549148	21549148	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1372551447	NA	P-0061892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	414	532	0	ENST00000382592.4:c.3128G>A	p.Arg1043Gln	p.R1043Q	ENST00000382592	NM_014572.2	1043	cGa/cAa	8/8	0.45188423540014	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.453593436861754	2		532	870	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43771658	43771658	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	75	410	0	ENST00000382044.4:c.725C>A	p.Pro242His	p.P242H	ENST00000382044	NM_001141980.1	242	cCt/cAt	7/28	0.374647222063632	2	FACETS	0.53	0.464	0.601	0.265	0.232	0.301	SUBCLONAL	1	TRUE	0	0.453593436861754	2		410	624	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2137871	2137871	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	324	462	0	ENST00000219476.3:c.4997T>C	p.Phe1666Ser	p.F1666S	ENST00000219476	NM_000548.3	1666	tTc/tCc	39/42	0.360121283027771	3	FACETS	0.853	0.812	0.894	0.853	0.812	0.894	CLONAL	3	TRUE	0	0.453593436861754	3		462	685	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353881	15353881	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	72	333	0	ENST00000263377.2:c.2999A>G	p.Gln1000Arg	p.Q1000R	ENST00000263377	NM_058243.2	1000	cAg/cGg	14/20	0.374647222063632	2	FACETS	0.707	0.62	0.8	0.354	0.31	0.4	SUBCLONAL	1	TRUE	0	0.453593436861754	2		333	449	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082694	16082694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1323722357	NA	P-0061892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	25	192	0	ENST00000281043.3:c.508C>T	p.Arg170Cys	p.R170C	ENST00000281043	NM_005378.4	170	Cgc/Tgc	2/3	0.386668678201514	3	FACETS	0.495	0.391	0.614	0.165	0.13	0.205	SUBCLONAL	1	TRUE	0	0.453593436861754	3		192	273	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267799	46267799	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778972158	NA	P-0061892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	229	396	0	ENST00000371998.3:c.2560C>T	p.Arg854Ter	p.R854*	ENST00000371998		854	Cga/Tga	14/23	0.360121283027771	3	FACETS	1	0.982	1	0.739	0.694	0.784	CLONAL	2	TRUE	0	0.453593436861754	3		396	559	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130492	29130492	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	81	458	0	ENST00000328354.6:c.218C>G	p.Ser73Cys	p.S73C	ENST00000328354	NM_007194.3	73	tCt/tGt	2/15	0.453593436861754	2	FACETS	0.496	0.437	0.56	0.248	0.218	0.28	SUBCLONAL	1	TRUE	0	0.453593436861754	2		458	720	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551055	41551055	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776310672	NA	P-0061892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	310	408	0	ENST00000263253.7:c.3199C>T	p.Arg1067Cys	p.R1067C	ENST00000263253	NM_001429.3	1067	Cgt/Tgt	17/31	0.453593436861754	2	FACETS	0.965	0.917	1	0.965	0.917	1	CLONAL	2	TRUE	0	0.453593436861754	2		408	708	SUCCESS
ATR	545	MSKCC	GRCh37	3	142253968	142253968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757622477	NA	P-0061892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	163	317	0	ENST00000350721.4:c.3899G>A	p.Arg1300His	p.R1300H	ENST00000350721	NM_001184.3	1300	cGt/cAt	21/47	0.42973752886633	3	FACETS	0.924	0.864	0.984	0.924	0.864	0.984	CLONAL	3	TRUE	0	0.453593436861754	3		317	318	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456295	189456543	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCTAGAGTTTCTAACTCCAAGAAACCAATGAGCCTTGCTGACTTTGAAGCAGAAAATGCTTGTTGTTAACAACAGCATGAGTATATTTTAGTCCCTTTCCATGCCTAACTCACTTTTTTCTTTCCTATGTGTTAGGCCTATATGTTCAGTTCAGCCCATTGACTTGAACTTTGTGGATGAACCATCAGAAGATGGTGCGACAAACAAGATTGAGATTAGCATGGACTGTATCCGCATGCAGGACTCGG	ACCTAGAGTTTCTAACTCCAAGAAACCAATGAGCCTTGCTGACTTTGAAGCAGAAAATGCTTGTTGTTAACAACAGCATGAGTATATTTTAGTCCCTTTCCATGCCTAACTCACTTTTTTCTTTCCTATGTGTTAGGCCTATATGTTCAGTTCAGCCCATTGACTTGAACTTTGTGGATGAACCATCAGAAGATGGTGCGACAAACAAGATTGAGATTAGCATGGACTGTATCCGCATGCAGGACTCGG	-	novel	NA	P-0061892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	48	69	0	ENST00000264731.3:c.192-132_308del		p.X64_splice	ENST00000264731	NM_003722.4	64		3/14	0.42973752886633	3	FACETS	1	0.958	1	0.832	0.729	0.937	CLONAL	2	TRUE	0	0.453593436861754	3		69	104	SUCCESS
REST	5978	MSKCC	GRCh37	4	57797986	57797986	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	85	450	0	ENST00000309042.7:c.2962A>G	p.Thr988Ala	p.T988A	ENST00000309042	NM_005612.4	988	Act/Gct	4/4	0.45188423540014	2	FACETS	0.621	0.549	0.697	0.31	0.274	0.349	SUBCLONAL	1	TRUE	0	0.453593436861754	2		450	604	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876386	35876386	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	118	515	0	ENST00000303115.3:c.1178G>T	p.Ser393Ile	p.S393I	ENST00000303115	NM_002185.3	393	aGt/aTt	8/8	0.45188423540014	2	FACETS	0.758	0.685	0.836	0.379	0.342	0.418	SUBCLONAL	1	TRUE	0	0.453593436861754	2		515	686	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100607	157100607	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0061892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	73	320	0	ENST00000346085.5:c.1542+2T>C		p.X514_splice	ENST00000346085	NM_020732.3	514			0.450732968103189	3	FACETS	0.804	0.705	0.911	0.268	0.235	0.304	CLONAL	1	TRUE	0	0.453593436861754	3		320	491	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124532326	124532326	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	39	295	0	ENST00000357628.3:c.118G>T	p.Gly40Ter	p.G40*	ENST00000357628	NM_015450.2	40	Gga/Tga	6/19	1	2	FACETS	0.616	0.513	0.73	0.616	0.513	0.73	SUBCLONAL	1	TRUE	1	0.453593436861754	2		295	279	SUCCESS
MTAP	4507	MSKCC	GRCh37	9	21854751	21854751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200708704	NA	P-0061892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	431	441	0	ENST00000380172.4:c.572C>T	p.Ala191Val	p.A191V	ENST00000380172	NM_002451.3	191	gCg/gTg	6/8	0.428571713869712	3	FACETS	0.944	0.907	0.982	0.944	0.907	0.982	CLONAL	3	TRUE	0	0.453593436861754	3		441	823	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0061893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	291	571	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		571	547	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781504	NA	P-0061894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	460	388	0	ENST00000269305.4:c.314G>T	p.Gly105Val	p.G105V	ENST00000269305	NM_001126112.2	105	gGc/gTc	4/11	0.54563861718618	2	FACETS	0.979	0.943	1	0.979	0.943	1	CLONAL	2	TRUE	0	0.570777231888562	2		388	823	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954675	48955566	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGCCAAAGGAGTATTCAAGAGTGGCCTCTACTGATATGGAAGCACTGCTGTAACCTCCATGGTTATGAAACTAAAGATTGAAGCTAGAATCCACTGGATAAACAGAACAAAGGCCAATTACAATGTTTTTAAAAACATAAATGTATATCACTTTGCAAATTATGTTGCAAATGTTAAAAGAAAGTTTTGCTTGCAGAAACAAAAGGAACATTTGTATAAGGATGCAAAACACAGAAAAAGAGGAACTTTTAGTTTCCTTATTAGTAAACAGATAAGGAAAACTGTGAATCCTCATTTATAACCAAGAAATGCATATTTTAATGAGATACCATTTTGTAACTAATGAAATTAGCAGAATCTTGAAGAATCTGTCTATCCTCTTACCAAGGATTAATGAGAATTAAAATAGATATGCCAATGGCTGATAAGATACTAAACCTGTTCCTGATATAAGTTTAGGGTATTTAAATCTTTGAAAATTTGAGATCAGCTATAAGTCCTTTCTCTAGGAAAAACACAGATTTGCTTACACTCAAAATTGGAAGGCTATTTCCTATGAGTCCGTAGACTCCAAAATAAAAAATTCTGCTCTAAATAAAAATGGTTTAACCTTTCTACTGTTTTCTTTGTCTGATAATAACTTCCAAAAAAATACCTAGCTCAAGGGTTAATATTTCATAAATAGTTACTTTTTTTTTTCATTTTTAGGAAGTACATCTCAGAATCTTGATTCTGGAACAGATTTGTCTTTCCCATGGATTCTGAATGTGCTTAATTTAAAAGCCTTTGATTTTTACAAAGTGATCGAAAGTTTTATCAAAGCAGAAGGCAACTTGACAAGAGAAATGATAAAACATTTAGAACGATGTGAACATCGAATCATGGAATCCCT	TGCCAAAGGAGTATTCAAGAGTGGCCTCTACTGATATGGAAGCACTGCTGTAACCTCCATGGTTATGAAACTAAAGATTGAAGCTAGAATCCACTGGATAAACAGAACAAAGGCCAATTACAATGTTTTTAAAAACATAAATGTATATCACTTTGCAAATTATGTTGCAAATGTTAAAAGAAAGTTTTGCTTGCAGAAACAAAAGGAACATTTGTATAAGGATGCAAAACACAGAAAAAGAGGAACTTTTAGTTTCCTTATTAGTAAACAGATAAGGAAAACTGTGAATCCTCATTTATAACCAAGAAATGCATATTTTAATGAGATACCATTTTGTAACTAATGAAATTAGCAGAATCTTGAAGAATCTGTCTATCCTCTTACCAAGGATTAATGAGAATTAAAATAGATATGCCAATGGCTGATAAGATACTAAACCTGTTCCTGATATAAGTTTAGGGTATTTAAATCTTTGAAAATTTGAGATCAGCTATAAGTCCTTTCTCTAGGAAAAACACAGATTTGCTTACACTCAAAATTGGAAGGCTATTTCCTATGAGTCCGTAGACTCCAAAATAAAAAATTCTGCTCTAAATAAAAATGGTTTAACCTTTCTACTGTTTTCTTTGTCTGATAATAACTTCCAAAAAAATACCTAGCTCAAGGGTTAATATTTCATAAATAGTTACTTTTTTTTTTCATTTTTAGGAAGTACATCTCAGAATCTTGATTCTGGAACAGATTTGTCTTTCCCATGGATTCTGAATGTGCTTAATTTAAAAGCCTTTGATTTTTACAAAGTGATCGAAAGTTTTATCAAAGCAGAAGGCAACTTGACAAGAGAAATGATAAAACATTTAGAACGATGTGAACATCGAATCATGGAATCCCT	-	novel	NA	P-0061894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	75	13	0	ENST00000267163.4:c.1498+301_1685del		p.X500_splice	ENST00000267163	NM_000321.2	500		17/27	0.536315797863471	2	FACETS	1	0.983	1	1	0.989	1	CLONAL	3	TRUE	0	0.570777231888562	2		13	81	SUCCESS
APC	324	MSKCC	GRCh37	5	112173690	112173690	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	325	334	0	ENST00000257430.4:c.2403del	p.Phe801LeufsTer19	p.F801Lfs*19	ENST00000257430	NM_000038.5	800	gTt/gt	16/16	0.54563861718618	2	FACETS	0.947	0.905	0.99	0.947	0.905	0.99	CLONAL	2	TRUE	0	0.570777231888562	2		334	601	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563488	87563488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	352	307	0	ENST00000277120.3:c.1876G>A	p.Gly626Ser	p.G626S	ENST00000277120		626	Ggc/Agc	16/19	0.536315797863471	2	FACETS	0.853	0.814	0.892	0.853	0.814	0.892	CLONAL	2	TRUE	0	0.570777231888562	2		307	723	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432146	121432146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772765008	NA	P-0061895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	41	456	0	ENST00000257555.6:c.893C>T	p.Ala298Val	p.A298V	ENST00000257555		298	gCg/gTg	4/10	0.884187903641886	1	FACETS	0.104	0.086	0.124	0.104	0.086	0.124	SUBCLONAL	1	TRUE	0	0.884187903641886	1		456	497	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394400	162394400	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	382	410	0	ENST00000366898.1:c.668C>A	p.Ser223Ter	p.S223*	ENST00000366898	NM_004562.2	223	tCa/tAa	6/12	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.884187903641886	2		410	861	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575362	64575362	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs794728622	NA	P-0061897-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	484	868	0	ENST00000312049.6:c.654+1G>A		p.X218_splice	ENST00000312049	NM_130799.2	218			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		868	621	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222704	69222704	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	65	621	0	ENST00000462284.1:c.677C>A	p.Ser226Ter	p.S226*	ENST00000462284	NM_002392.5	226	tCg/tAg	8/11	1	2	FACETS	0.917	0.812	1	0.917	0.812	1	CLONAL	1	TRUE	1	0.809878580188591	2		621	175	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519988	NA	P-0061898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	243	762	0	ENST00000269305.4:c.808T>C	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	Ttt/Ctt	8/11	0.834430227099813	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.809878580188591	1		762	300	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406042	70406042	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	66	763	0	ENST00000373644.4:c.3556A>G	p.Ile1186Val	p.I1186V	ENST00000373644	NM_030625.2	1186	Ata/Gta	4/12	0.158913491010794	3	FACETS	1	0.969	1	0.647	0.573	0.723	INDETERMINATE	1	TRUE	1	0.809878580188591	3		763	177	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222620	69222620	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	80	742	0	ENST00000462284.1:c.593C>A	p.Ser198Tyr	p.S198Y	ENST00000462284	NM_002392.5	198	tCc/tAc	8/11	1	2	FACETS	0.95	0.853	1	0.95	0.853	1	CLONAL	1	TRUE	1	0.809878580188591	2		742	208	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101161	41101161	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0061898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	242	764	0	ENST00000373198.4:c.1195A>T	p.Arg399Ter	p.R399*	ENST00000373198	NM_133170.3	399	Aga/Tga	8/32	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.809878580188591	2		764	517	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061899-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	46	345	0				ENST00000310581	NM_198253.2	-/1132			NA	4	FACETS	1	0.934	1	0.608	0.512	0.713	INDETERMINATE	1	TRUE	2	0.19390530874045	4		345	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0061899-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	148	607	1	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	0.152395141822873	3	FACETS	1	0.98	1	0.822	0.753	0.894	CLONAL	2	TRUE	0	0.19390530874045	3		608	679	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714426	40714426	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061899-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	79	753	0	ENST00000373198.4:c.3971C>A	p.Ser1324Tyr	p.S1324Y	ENST00000373198	NM_133170.3	1324	tCc/tAc	29/32	NA	4	FACETS	1	0.952	1	0.585	0.514	0.662	INDETERMINATE	1	TRUE	2	0.19390530874045	4		753	831	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441300	52441300	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061899-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	147	913	0	ENST00000460680.1:c.470A>G	p.Asn157Ser	p.N157S	ENST00000460680	NM_004656.3	157	aAt/aGt	7/17	0.101758147938503	5	FACETS	1	0.957	1	0.539	0.492	0.589	INDETERMINATE	2	TRUE	1	0.19390530874045	5		913	907	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0061900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	362	806	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.484443359019733	2	FACETS	0.879	0.845	0.912	1	0.995	1	CLONAL	3	TRUE	0	0.479139019159082	2		806	573	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459342	99459343	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0061900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	73	646	0	ENST00000268035.6:c.1980_1981del	p.His660GlnfsTer21	p.H660Qfs*21	ENST00000268035	NM_000875.3	660	CAc/c	9/21	0.454682009560389	1	FACETS	0.645	0.568	0.728	0.645	0.568	0.728	SUBCLONAL	1	TRUE	0	0.479139019159082	1		646	359	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474489	40474489	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1466712110	NA	P-0061900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	216	811	0	ENST00000264657.5:c.1912G>A	p.Glu638Lys	p.E638K	ENST00000264657	NM_139276.2	638	Gaa/Aaa	21/24	0.479139019159082	5	FACETS	0.76	0.707	0.816	0.38	0.353	0.408	SUBCLONAL	2	TRUE	1	0.479139019159082	5		811	1019	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78831617	78831617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199793733	NA	P-0061900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	135	755	0	ENST00000306801.3:c.1426G>A	p.Val476Met	p.V476M	ENST00000306801	NM_020761.2	476	Gtg/Atg	13/34	0.484443359019733	4	FACETS	1	0.985	1	0.477	0.435	0.52	CLONAL	1	TRUE	1	0.479139019159082	4		755	583	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022346	31022346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372418554	NA	P-0061900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	354	952	0	ENST00000375687.4:c.1831G>A	p.Ala611Thr	p.A611T	ENST00000375687	NM_015338.5	611	Gcc/Acc	13/13	0.479139019159082	5	FACETS	0.978	0.93	1	0.978	0.93	1	CLONAL	3	TRUE	2	0.479139019159082	5		952	866	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201765	66201765	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs878919973	NA	P-0061900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	189	818	0	ENST00000273854.3:c.2737G>T	p.Asp913Tyr	p.D913Y	ENST00000273854	NM_004439.5	913	Gat/Tat	16/18	0.344100692828781	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.479139019159082	1		818	525	SUCCESS
APC	324	MSKCC	GRCh37	5	112170652	112170652	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	92	474	0	ENST00000257430.4:c.1748C>A	p.Ser583Ter	p.S583*	ENST00000257430	NM_000038.5	583	tCa/tAa	15/16	0.144853642096317	3	FACETS	1	0.97	1	0.413	0.37	0.459	INDETERMINATE	1	TRUE	0	0.479139019159082	3		474	384	SUCCESS
APC	324	MSKCC	GRCh37	5	112175411	112175411	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	201	816	0	ENST00000257430.4:c.4120G>T	p.Glu1374Ter	p.E1374*	ENST00000257430	NM_000038.5	1374	Gaa/Taa	16/16	0.144853642096317	3	FACETS	1	0.978	1	0.73	0.684	0.777	INDETERMINATE	2	TRUE	0	0.479139019159082	3		816	475	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056604	26056604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs2230653	NA	P-0061900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	192	782	0	ENST00000343677.2:c.53C>T	p.Ala18Val	p.A18V	ENST00000343677	NM_005319.3	18	gCc/gTc	1/1	0.479139019159082	5	FACETS	0.837	0.775	0.901	0.558	0.517	0.601	CLONAL	2	TRUE	2	0.479139019159082	5		782	823	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0061901-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	105	683	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.914	0.819	1	1	0.986	1	CLONAL	2	TRUE	1	0.165843025288724	2		683	693	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411246	63411246	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061901-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	144	521	0	ENST00000330258.3:c.1921C>T	p.Arg641Ter	p.R641*	ENST00000330258	NM_152424.3	641	Cga/Tga	2/2	1	1	FACETS	1	0.929	1	1	0.994	1	CLONAL	4	TRUE	0	0.165843025288724	1		521	395	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0061901-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	87	277	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.9	1	1	0.985	1	CLONAL	2	TRUE	1	0.165843025288724	2		277	517	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0061901-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	126	388	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	1	0.928	1	1	0.99	1	CLONAL	2	TRUE	1	0.165843025288724	2		388	739	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577595	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0061901-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	81	712	1	ENST00000269305.4:c.686_687del	p.Cys229TyrfsTer10	p.C229Yfs*10	ENST00000269305	NM_001126112.2	229	tGT/t	7/11	0.165843025288724	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.165843025288724	1		713	615	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120103	70120103	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061901-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	201	775	0	ENST00000245479.2:c.1105C>T	p.Gln369Ter	p.Q369*	ENST00000245479	NM_000346.3	369	Cag/Tag	3/3	0.165843025288724	2	FACETS	1	0.982	1	1	0.993	1	CLONAL	3	TRUE	0	0.165843025288724	2		775	694	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975440	26975440	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061901-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	65	634	0	ENST00000381527.3:c.1066C>T	p.Arg356Ter	p.R356*	ENST00000381527	NM_001260.1	356	Cga/Tga	11/13	1	2	FACETS	0.896	0.775	1	0.896	0.775	1	CLONAL	1	TRUE	1	0.165843025288724	2		634	875	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0061901-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	136	786	1	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	0.963	0.875	1	1	0.99	1	CLONAL	2	TRUE	1	0.165843025288724	2		787	852	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106853	27106853	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061901-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	172	884	0	ENST00000324856.7:c.6464T>G	p.Leu2155Arg	p.L2155R	ENST00000324856	NM_006015.4	2155	cTc/cGc	20/20	1	2	FACETS	1	0.98	1	1	0.993	1	CLONAL	2	TRUE	1	0.165843025288724	2		884	868	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667551	29667551	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061901-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	92	674	0	ENST00000356175.3:c.6887G>A	p.Trp2296Ter	p.W2296*	ENST00000356175	NM_000267.3	2296	tGg/tAg	46/57	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.165843025288724	2		674	751	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715751	61715751	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061901-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	34	599	0	ENST00000401558.2:c.2178A>T	p.Glu726Asp	p.E726D	ENST00000401558	NM_003400.3	726	gaA/gaT	18/25	1	2	FACETS	0.631	0.514	0.763	0.631	0.514	0.763	SUBCLONAL	1	TRUE	1	0.165843025288724	2		599	650	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426671	212426671	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1264168721	NA	P-0061901-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	45	756	0	ENST00000342788.4:c.2444T>C	p.Ile815Thr	p.I815T	ENST00000342788	NM_005235.2	815	aTt/aCt	20/28	0.142859279176648	0	FACETS	0.579	0.485	0.683			1	SUBCLONAL	1	TRUE	0	0.165843025288724	0		756	782	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102858	71102858	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061901-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	80	803	0	ENST00000318789.4:c.349C>A	p.Gln117Lys	p.Q117K	ENST00000318789	NM_032682.5	117	Cag/Aag	8/21	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.165843025288724	2		803	801	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144134	55144134	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1279735973	NA	P-0061901-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	128	722	0	ENST00000257290.5:c.1963T>G	p.Leu655Val	p.L655V	ENST00000257290	NM_006206.4	655	Ttg/Gtg	14/23	1	2	FACETS	1	0.968	1	1	0.991	1	CLONAL	2	TRUE	1	0.165843025288724	2		722	675	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876284	35876284	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061901-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	71	739	0	ENST00000303115.3:c.1078del	p.Ser360AlafsTer29	p.S360Afs*29	ENST00000303115	NM_002185.3	359	gAa/ga	8/8	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.165843025288724	2		739	726	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659185	86659185	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061901-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	29	334	0	ENST00000274376.6:c.1474A>G	p.Asn492Asp	p.N492D	ENST00000274376	NM_002890.2	492	Aat/Gat	11/25	1	2	FACETS	0.793	0.636	0.972	0.793	0.636	0.972	CLONAL	1	TRUE	1	0.165843025288724	2		334	441	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202857	27202857	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs960097042	NA	P-0061901-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	52	674	0	ENST00000380036.4:c.1949T>C	p.Ile650Thr	p.I650T	ENST00000380036	NM_000459.3	650	aTt/aCt	13/23	1	2	FACETS	0.737	0.626	0.86	0.737	0.626	0.86	SUBCLONAL	1	TRUE	1	0.165843025288724	2		674	851	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780071	NA	P-0061902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	100	985	0	ENST00000269305.4:c.580C>T	p.Leu194Phe	p.L194F	ENST00000269305	NM_001126112.2	194	Ctt/Ttt	6/11	0.248345669492957	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.248345669492957	1		985	598	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426752	212426752	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	81	770	0	ENST00000342788.4:c.2363T>G	p.Leu788Arg	p.L788R	ENST00000342788	NM_005235.2	788	cTg/cGg	20/28	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.248345669492957	2		770	589	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683975	117683975	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	40	675	0	ENST00000368508.3:c.3172T>G	p.Cys1058Gly	p.C1058G	ENST00000368508	NM_002944.2	1058	Tgc/Ggc	21/43	0.208299610448685	1	FACETS	0.57	0.473	0.678	0.57	0.473	0.678	SUBCLONAL	1	TRUE	0	0.248345669492957	1		675	495	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	160	662	1	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.921	0.846	1	0.921	0.846	1	CLONAL	1	TRUE	1	0.440934887601187	2		663	788	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	152	465	3	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.440934887601187	2		468	687	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	101	715	1	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.659	0.589	0.733	0.659	0.589	0.733	SUBCLONAL	1	TRUE	1	0.440934887601187	2		716	695	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	97	331	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.868	0.777	0.964	0.868	0.777	0.964	CLONAL	1	TRUE	1	0.440934887601187	2		331	507	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	68	383	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.791	0.691	0.897	0.791	0.691	0.897	SUBCLONAL	1	TRUE	1	0.440934887601187	2		383	390	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	55	388	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.625	0.536	0.722	0.625	0.536	0.722	SUBCLONAL	1	TRUE	1	0.440934887601187	2		388	399	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	63	236	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.828	0.721	0.944	0.828	0.721	0.944	CLONAL	1	TRUE	1	0.440934887601187	2		236	345	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647460	3647460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776394340	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	227	505	0	ENST00000294008.3:c.1603G>A	p.Ala535Thr	p.A535T	ENST00000294008	NM_032444.2	535	Gca/Aca	7/15	0.327978448484708	3	FACETS	0.874	0.818	0.931	0.874	0.818	0.931	CLONAL	2	TRUE	1	0.440934887601187	3		505	719	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675438	30675438	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780670990	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	102	519	0	ENST00000376406.3:c.2918C>T	p.Ala973Val	p.A973V	ENST00000376406	NM_014641.2	973	gCg/gTg	8/15	1	2	FACETS	0.727	0.651	0.808	0.727	0.651	0.808	SUBCLONAL	1	TRUE	1	0.440934887601187	2		519	636	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979987	7979987	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746723399	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	120	472	1	ENST00000319144.4:c.1350del	p.Leu451SerfsTer16	p.L451Sfs*16	ENST00000319144	NM_001139.2	450	ggG/gg	10/15	1	2	FACETS	0.891	0.807	0.979	0.891	0.807	0.979	CLONAL	1	TRUE	1	0.440934887601187	2		473	611	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288978	212288978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	21	354	0	ENST00000342788.4:c.2768G>A	p.Gly923Glu	p.G923E	ENST00000342788	NM_005235.2	923	gGa/gAa	23/28	1	2	FACETS	0.266	0.204	0.338	0.266	0.204	0.338	SUBCLONAL	1	TRUE	1	0.440934887601187	2		354	358	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161221	56161221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781300314	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	55	344	1	ENST00000399503.3:c.1090C>T	p.Arg364Trp	p.R364W	ENST00000399503	NM_005921.1	364	Cgg/Tgg	5/20	1	2	FACETS	0.707	0.607	0.814	0.707	0.607	0.814	SUBCLONAL	1	TRUE	1	0.440934887601187	2		345	353	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788618	3788618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398124146	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	167	338	0	ENST00000262367.5:c.4336C>T	p.Arg1446Cys	p.R1446C	ENST00000262367	NM_004380.2	1446	Cgc/Tgc	26/31	0.327978448484708	3	FACETS	0.923	0.854	0.993	0.923	0.854	0.993	CLONAL	2	TRUE	1	0.440934887601187	3		338	501	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	58	420	0	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.462	0.396	0.533	0.462	0.396	0.533	SUBCLONAL	1	TRUE	1	0.440934887601187	2		420	570	SUCCESS
ATR	545	MSKCC	GRCh37	3	142255005	142255005	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	18	242	1	ENST00000350721.4:c.3764del	p.Leu1255TyrfsTer7	p.L1255Yfs*7	ENST00000350721	NM_001184.3	1255	tTa/ta	20/47	1	2	FACETS	0.729	0.556	0.927	0.729	0.556	0.927	CLONAL	1	TRUE	1	0.440934887601187	2		243	112	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051645	13051645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375135016	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	161	436	0	ENST00000316448.5:c.904G>A	p.Asp302Asn	p.D302N	ENST00000316448	NM_004343.3	302	Gat/Aat	7/9	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.440934887601187	2		436	646	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	119	470	4	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	0.871	0.788	0.958	0.871	0.788	0.958	CLONAL	1	TRUE	1	0.440934887601187	2		474	620	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	100	355	3	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	0.436683967322441	1	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	0	0.440934887601187	1		358	353	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953229	81953229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	99	381	1	ENST00000359376.3:c.2195G>A	p.Arg732His	p.R732H	ENST00000359376	NM_002661.3	732	cGc/cAc	20/33	0.436683967322441	1	FACETS	0.763	0.684	0.845	0.763	0.684	0.845	SUBCLONAL	1	TRUE	0	0.440934887601187	1		382	459	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482926	140482927	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs777474487	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	97	527	1	ENST00000288602.6:c.1208dup	p.Ala404CysfsTer9	p.A404Cfs*9	ENST00000288602	NM_004333.4	403	cct/ccCt	10/18	1	2	FACETS	0.675	0.602	0.752	0.675	0.602	0.752	SUBCLONAL	1	TRUE	1	0.440934887601187	2		528	652	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487588	38487588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs576185106	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	146	453	0	ENST00000254066.5:c.118G>A	p.Ala40Thr	p.A40T	ENST00000254066	NM_000964.3	40	Gct/Act	2/9	1	2	FACETS	0.96	0.878	1	0.96	0.878	1	CLONAL	1	TRUE	1	0.440934887601187	2		453	690	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998923	11998923	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	23	311	0	ENST00000353533.5:c.429del	p.Lys143AsnfsTer9	p.K143Nfs*9	ENST00000353533	NM_003010.3	142	cAa/ca	4/11	0.436683967322441	1	FACETS	0.363	0.284	0.454	0.363	0.284	0.454	SUBCLONAL	1	TRUE	0	0.440934887601187	1		311	224	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795061	242795061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1203794937	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	94	463	1	ENST00000334409.5:c.148G>A	p.Ala50Thr	p.A50T	ENST00000334409	NM_005018.2	50	Gcc/Acc	2/5	1	2	FACETS	0.707	0.63	0.789	0.707	0.63	0.789	SUBCLONAL	1	TRUE	1	0.440934887601187	2		464	603	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316397	14316397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782457908	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	58	573	1	ENST00000256196.4:c.208G>A	p.Ala70Thr	p.A70T	ENST00000256196		70	Gca/Aca	3/6	1	2	FACETS	0.721	0.622	0.827	0.721	0.622	0.827	SUBCLONAL	1	TRUE	1	0.440934887601187	2		574	365	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046674	42046674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780027483	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	80	369	0	ENST00000219905.7:c.7048G>A	p.Val2350Met	p.V2350M	ENST00000219905	NM_001164273.1	2350	Gtg/Atg	18/24	1	2	FACETS	0.965	0.855	1	0.965	0.855	1	CLONAL	1	TRUE	1	0.440934887601187	2		369	376	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519504	137519505	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	104	401	2	ENST00000367739.4:c.1132_1133dup	p.Ser378ArgfsTer6	p.S378Rfs*6	ENST00000367739	NM_000416.2	378	agt/agAGt	7/7	1	2	FACETS	0.789	0.708	0.874	0.789	0.708	0.874	SUBCLONAL	1	TRUE	1	0.440934887601187	2		403	598	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971088	21971089	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	105	399	0	ENST00000304494.5:c.269dup	p.Leu91ProfsTer29	p.L91Pfs*29	ENST00000304494	NM_000077.4	90	ttc/ttTc	2/3	0.436683967322441	1	FACETS	0.855	0.771	0.943	0.855	0.771	0.943	CLONAL	1	TRUE	0	0.440934887601187	1		399	434	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954180	32954180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45580035	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	65	377	0	ENST00000380152.3:c.9154C>T	p.Arg3052Trp	p.R3052W	ENST00000380152		3052	Cgg/Tgg	24/27	1	2	FACETS	0.81	0.706	0.921	0.81	0.706	0.921	CLONAL	1	TRUE	1	0.440934887601187	2		377	364	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316114	11316114	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746557535	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	107	432	0	ENST00000361445.4:c.640C>T	p.Arg214Cys	p.R214C	ENST00000361445	NM_004958.3	214	Cgt/Tgt	5/58	1	2	FACETS	0.87	0.783	0.962	0.87	0.783	0.962	CLONAL	1	TRUE	1	0.440934887601187	2		432	558	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328378	137328380	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs763369916	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	100	415	0	ENST00000481739.1:c.1315_1317del	p.Phe439del	p.F439del	ENST00000481739	NM_002957.4	436	cTCTtc/ctc	10/10	1	2	FACETS	0.886	0.794	0.982	0.886	0.794	0.982	CLONAL	1	TRUE	1	0.440934887601187	2		415	512	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022687	12022687	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1047383225	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	167	571	0	ENST00000396373.4:c.793G>A	p.Val265Met	p.V265M	ENST00000396373	NM_001987.4	265	Gtg/Atg	5/8	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.440934887601187	2		571	752	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409158	4409158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1199912313	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	103	420	1	ENST00000261254.3:c.853C>T	p.Arg285Trp	p.R285W	ENST00000261254	NM_001759.3	285	Cgg/Tgg	5/5	1	2	FACETS	0.848	0.761	0.939	0.848	0.761	0.939	CLONAL	1	TRUE	1	0.440934887601187	2		421	551	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47596650	47596651	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	89	273	0	ENST00000263735.4:c.11dup	p.Gln5AlafsTer26	p.Q5Afs*26	ENST00000263735	NM_002354.2	2	-/C	1/9	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.440934887601187	2		273	376	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933744	36933744	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	156	592	0	ENST00000361632.4:c.1655del	p.Pro552LeufsTer27	p.P552Lfs*27	ENST00000361632		552	cCt/ct	12/16	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.440934887601187	2		592	692	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425854	49425854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760279999	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	116	454	0	ENST00000301067.7:c.12634C>T	p.Arg4212Trp	p.R4212W	ENST00000301067	NM_003482.3	4212	Cgg/Tgg	39/54	1	2	FACETS	0.87	0.786	0.958	0.87	0.786	0.958	CLONAL	1	TRUE	1	0.440934887601187	2		454	605	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992895	72992895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs553932870	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	102	448	1	ENST00000268489.5:c.1150G>A	p.Ala384Thr	p.A384T	ENST00000268489	NM_006885.3	384	Gcc/Acc	2/10	0.436683967322441	1	FACETS	0.861	0.775	0.95	0.861	0.775	0.95	CLONAL	1	TRUE	0	0.440934887601187	1		449	419	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031657	36031657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1197051295	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	135	465	0	ENST00000358208.4:c.1486G>A	p.Asp496Asn	p.D496N	ENST00000358208		496	Gac/Aac	12/12	1	2	FACETS	0.914	0.833	0.999	0.914	0.833	0.999	CLONAL	1	TRUE	1	0.440934887601187	2		465	670	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121252	29121252	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	82	388	0	ENST00000328354.6:c.423G>T	p.Lys141Asn	p.K141N	ENST00000328354	NM_007194.3	141	aaG/aaT	3/15	0.440934887601187	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.440934887601187	1		388	275	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1749278	1749279	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	77	277	0	ENST00000378609.4:c.93_94del	p.Gln32AspfsTer46	p.Q32Dfs*46	ENST00000378609	NM_002074.3	31	tcTCag/tcag	4/12	1	2	FACETS	0.88	0.777	0.989	0.88	0.777	0.989	CLONAL	1	TRUE	1	0.440934887601187	2		277	397	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984392	201984393	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	333	475	0	ENST00000359651.3:c.1057_1058del	p.Lys353ValfsTer117	p.K353Vfs*117	ENST00000359651		353	AAg/g	8/8	0.440934887601187	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.440934887601187	2		475	684	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805768	43805768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	107	396	0	ENST00000372470.3:c.824C>T	p.Pro275Leu	p.P275L	ENST00000372470	NM_005373.2	275	cCt/cTt	5/12	1	2	FACETS	0.932	0.839	1	0.932	0.839	1	CLONAL	1	TRUE	1	0.440934887601187	2		396	521	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999780	100999780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	87	412	0	ENST00000325455.5:c.22G>A	p.Gly8Ser	p.G8S	ENST00000325455	NM_001202474.3	8	Ggt/Agt	1/8	1	2	FACETS	0.805	0.715	0.901	0.805	0.715	0.901	CLONAL	1	TRUE	1	0.440934887601187	2		412	490	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879761	123879761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368237921	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	42	152	0	ENST00000330479.4:c.457G>A	p.Ala153Thr	p.A153T	ENST00000330479	NM_020382.3	153	Gcc/Acc	4/9	1	2	FACETS	0.992	0.839	1	0.992	0.839	1	CLONAL	1	TRUE	1	0.440934887601187	2		152	192	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249856	133249856	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1403299291	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	66	364	0	ENST00000320574.5:c.1367C>T	p.Ala456Val	p.A456V	ENST00000320574	NM_006231.2	456	gCc/gTc	14/49	1	2	FACETS	0.572	0.497	0.653	0.572	0.497	0.653	SUBCLONAL	1	TRUE	1	0.440934887601187	2		364	523	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524575	103524575	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	27	343	0	ENST00000355739.4:c.2706T>A	p.Asn902Lys	p.N902K	ENST00000355739	NM_000123.3	902	aaT/aaA	13/15	0.436683967322441	1	FACETS	0.33	0.263	0.407	0.33	0.263	0.407	SUBCLONAL	1	TRUE	0	0.440934887601187	1		343	289	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994853	73994853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760181010	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	14	65	0	ENST00000318443.5:c.337C>T	p.Arg113Cys	p.R113C	ENST00000318443	NM_001024736.1	113	Cgt/Tgt	3/10	1	2	FACETS	0.794	0.584	1	0.794	0.584	1	CLONAL	1	TRUE	1	0.440934887601187	2		65	80	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799141	88799141	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	55	382	0	ENST00000360948.2:c.244T>C	p.Ser82Pro	p.S82P	ENST00000360948	NM_001012338.2	82	Tcc/Ccc	2/19	NA	2	FACETS	0.535	0.458	0.619			1	INDETERMINATE	1	TRUE	NA	0.440934887601187	2		382	466	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8111103	8111103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758885283	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	145	475	0	ENST00000585124.1:c.104C>T	p.Thr35Ile	p.T35I	ENST00000585124	NM_004217.3	35	aCc/aTc	3/9	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.440934887601187	2		475	627	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821908	59821908	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1567781516	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	29	330	0	ENST00000259008.2:c.2142G>A	p.Trp714Ter	p.W714*	ENST00000259008	NM_032043.2	714	tgG/tgA	15/20	1	2	FACETS	0.427	0.343	0.522	0.427	0.343	0.522	SUBCLONAL	1	TRUE	1	0.440934887601187	2		330	308	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210494	5210494	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	134	485	0	ENST00000357368.4:c.5473G>A	p.Val1825Ile	p.V1825I	ENST00000357368	NM_002850.3	1825	Gtc/Atc	35/38	1	2	FACETS	0.922	0.84	1	0.922	0.84	1	CLONAL	1	TRUE	1	0.440934887601187	2		485	659	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132617	11132617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1445478818	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	133	488	0	ENST00000358026.2:c.2833G>A	p.Ala945Thr	p.A945T	ENST00000358026	NM_001128849.1	945	Gca/Aca	19/36	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.440934887601187	2		488	581	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296082	15296082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150866973	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	112	480	1	ENST00000263388.2:c.2282C>T	p.Pro761Leu	p.P761L	ENST00000263388	NM_000435.2	761	cCg/cTg	14/33	1	2	FACETS	0.885	0.798	0.976	0.885	0.798	0.976	CLONAL	1	TRUE	1	0.440934887601187	2		481	574	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792031	42792031	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	133	482	0	ENST00000575354.2:c.835T>G	p.Ser279Ala	p.S279A	ENST00000575354	NM_015125.3	279	Tca/Gca	6/20	1	2	FACETS	0.845	0.768	0.925	0.845	0.768	0.925	CLONAL	1	TRUE	1	0.440934887601187	2		482	714	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033420	48033420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779285	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	23	366	0	ENST00000234420.5:c.3724C>T	p.Arg1242Cys	p.R1242C	ENST00000234420	NM_000179.2	1242	Cgt/Tgt	8/10	1	2	FACETS	0.284	0.221	0.357	0.284	0.221	0.357	SUBCLONAL	1	TRUE	1	0.440934887601187	2		366	367	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919673	96919673	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1231066976	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	149	406	0	ENST00000258439.3:c.590G>A	p.Arg197His	p.R197H	ENST00000258439	NM_001193304.2	197	cGc/cAc	4/4	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.440934887601187	2		406	661	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30956868	30956870	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	47	405	0	ENST00000375687.4:c.200_202del	p.Gly67del	p.G67del	ENST00000375687	NM_015338.5	65	aGAGga/aga	4/13	1	2	FACETS	0.439	0.37	0.514	0.439	0.37	0.514	SUBCLONAL	1	TRUE	1	0.440934887601187	2		405	486	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21351028	21351028	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141161152	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	168	501	0	ENST00000215739.8:c.2263C>T	p.Arg755Trp	p.R755W	ENST00000215739	NM_006767.3	755	Cgg/Tgg	19/21	0.440934887601187	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.440934887601187	1		501	540	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089986	37090013	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGTCCTTTTTCCTGCAAGCAGGAAGGG	TTGTCCTTTTTCCTGCAAGCAGGAAGGG	-	novel	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	79	344	0	ENST00000231790.2:c.1897-22_1902del		p.X633_splice	ENST00000231790	NM_000249.3	633		17/19	1	2	FACETS	0.861	0.761	0.968	0.861	0.761	0.968	CLONAL	1	TRUE	1	0.440934887601187	2		344	416	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394836	394836	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	34	398	0	ENST00000380956.4:c.232A>G	p.Lys78Glu	p.K78E	ENST00000380956	NM_001195286.1	78	Aaa/Gaa	3/9	NA	2	FACETS	0.295	0.24	0.356			1	INDETERMINATE	1	TRUE	NA	0.440934887601187	2		398	523	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023193	150023193	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	114	348	0	ENST00000253339.5:c.70A>G	p.Thr24Ala	p.T24A	ENST00000253339		24	Act/Gct	1/7	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.440934887601187	2		348	503	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874664	151874664	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	63	529	0	ENST00000262189.6:c.7874T>G	p.Leu2625Trp	p.L2625W	ENST00000262189	NM_170606.2	2625	tTg/tGg	38/59	1	2	FACETS	0.397	0.343	0.457	0.397	0.343	0.457	SUBCLONAL	1	TRUE	1	0.440934887601187	2		529	719	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542162	141542162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756991172	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	235	372	1	ENST00000220592.5:c.2561G>A	p.Arg854His	p.R854H	ENST00000220592	NM_012154.3	854	cGc/cAc	19/19	0.435654141257913	3	FACETS	0.908	0.851	0.967	0.908	0.851	0.967	CLONAL	2	TRUE	1	0.440934887601187	3		373	716	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044473	5044473	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	54	279	0	ENST00000381652.3:c.421G>T	p.Glu141Ter	p.E141*	ENST00000381652	NM_004972.3	141	Gaa/Taa	5/25	0.436683967322441	1	FACETS	0.812	0.702	0.931	0.812	0.702	0.931	CLONAL	1	TRUE	0	0.440934887601187	1		279	235	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624609	93624609	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	40	374	0	ENST00000375746.1:c.700T>A	p.Phe234Ile	p.F234I	ENST00000375746	NM_001174167.1	234	Ttc/Atc	4/14	1	2	FACETS	0.357	0.296	0.425	0.357	0.296	0.425	SUBCLONAL	1	TRUE	1	0.440934887601187	2		374	508	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127933459	127933459	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs551727025	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	41	264	0	ENST00000373547.4:c.76C>T	p.Arg26Trp	p.R26W	ENST00000373547	NM_002721.4	26	Cgg/Tgg	2/7	1	2	FACETS	0.729	0.612	0.858	0.729	0.612	0.858	SUBCLONAL	1	TRUE	1	0.440934887601187	2		264	255	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391160	139391160	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	118	573	0	ENST00000277541.6:c.7031A>G	p.His2344Arg	p.H2344R	ENST00000277541	NM_017617.3	2344	cAt/cGt	34/34	1	2	FACETS	0.859	0.777	0.946	0.859	0.777	0.946	CLONAL	1	TRUE	1	0.440934887601187	2		573	623	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918490	44918490	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	75	165	0	ENST00000377967.4:c.975-2A>G		p.X325_splice	ENST00000377967	NM_021140.2	325			1	1	FACETS	0.753	0.676	0.832	1	0.98	1	SUBCLONAL	2	TRUE	0	0.440934887601187	1		165	176	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360682	70360682	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	143	257	0	ENST00000374080.3:c.6242A>G	p.Gln2081Arg	p.Q2081R	ENST00000374080		2081	cAg/cGg	42/45	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.440934887601187	1		257	363	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0061906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	64	562	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		562	299	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	37	623	1	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	0.341142739584897	4	FACETS	0.345	0.283	0.414	0.172	0.141	0.207	SUBCLONAL	1	TRUE	2	0.426794735650243	4		624	718	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	40	179	2	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	0.334998995576246	3	FACETS	1	0.937	1	0.414	0.348	0.486	CLONAL	1	TRUE	0	0.426794735650243	3		181	183	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	68	503	0	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	0.341142739584897	4	FACETS	0.785	0.684	0.895	0.393	0.342	0.448	SUBCLONAL	1	TRUE	2	0.426794735650243	4		503	579	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	103	581	7	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.291614684078688	4	FACETS	1	0.982	1	0.744	0.669	0.822	CLONAL	1	TRUE	2	0.426794735650243	4		588	463	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39935760	39935760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745470688	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	69	194	0	ENST00000378444.4:c.112G>A	p.Ala38Thr	p.A38T	ENST00000378444	NM_001123385.1	38	Gct/Act	3/15	0.40398788785601	2	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.426794735650243	2		194	232	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	38	481	1	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	0.341142739584897	4	FACETS	0.478	0.394	0.571	0.239	0.197	0.286	SUBCLONAL	1	TRUE	2	0.426794735650243	4		482	532	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	31	443	7	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	0.341142739584897	4	FACETS	0.381	0.307	0.465	0.191	0.153	0.233	SUBCLONAL	1	TRUE	2	0.426794735650243	4		450	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	79	593	0	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	0.341142739584897	4	FACETS	0.744	0.654	0.841	0.372	0.327	0.421	SUBCLONAL	1	TRUE	2	0.426794735650243	4		593	710	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053023	180053023	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	117	635	0	ENST00000261937.6:c.1267del	p.Gln423ArgfsTer70	p.Q423Rfs*70	ENST00000261937	NM_182925.4	423	Cag/ag	10/30	0.291614684078688	4	FACETS	1	0.983	1	0.715	0.647	0.786	CLONAL	1	TRUE	2	0.426794735650243	4		635	547	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574006	7574006	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	45	459	0	ENST00000269305.4:c.1021T>G	p.Phe341Val	p.F341V	ENST00000269305	NM_001126112.2	341	Ttc/Gtc	10/11	0.341142739584897	4	FACETS	0.59	0.496	0.694	0.295	0.248	0.347	SUBCLONAL	1	TRUE	2	0.426794735650243	4		459	510	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813396	102813396	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316717107	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	62	521	0	ENST00000307046.8:c.293G>A	p.Arg98Gln	p.R98Q	ENST00000307046	NM_001111285.1	98	cGg/cAg	3/4	0.341142739584897	4	FACETS	0.785	0.679	0.9	0.393	0.339	0.45	SUBCLONAL	1	TRUE	2	0.426794735650243	4		521	528	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428494	72428496	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	124	442	0	ENST00000477973.2:c.506_508del	p.Lys170del	p.K170del	ENST00000477973	NM_012234.5	170	AAG/-	2/4	0.334998995576246	3	FACETS	1	0.983	1	0.46	0.418	0.504	CLONAL	1	TRUE	0	0.426794735650243	3		442	511	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158637067	158637068	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	rs141073095	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	159	579	4	ENST00000263640.3:c.111_112dup	p.Glu38ValfsTer21	p.E38Vfs*21	ENST00000263640	NM_001105.4	38	gaa/gTGaa	4/11	0.426794735650243	2	FACETS	0.775	0.716	0.835	0.775	0.716	0.835	SUBCLONAL	2	TRUE	0	0.426794735650243	2		583	481	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157790	106157790	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	77	526	0	ENST00000380013.4:c.2691G>T	p.Gln897His	p.Q897H	ENST00000380013	NM_001127208.2	897	caG/caT	3/11	0.291614684078688	4	FACETS	0.803	0.705	0.908	0.402	0.352	0.454	CLONAL	1	TRUE	2	0.426794735650243	4		526	641	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885299	111885299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200936167	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	90	656	0	ENST00000341259.2:c.1187C>T	p.Thr396Met	p.T396M	ENST00000341259	NM_005475.2	396	aCg/aTg	6/8	0.341142739584897	4	FACETS	1	0.941	1	0.544	0.484	0.608	CLONAL	1	TRUE	2	0.426794735650243	4		656	553	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45423102	45423102	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749758342	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	53	500	0	ENST00000262160.6:c.26C>T	p.Pro9Leu	p.P9L	ENST00000262160	NM_005901.5	9	cCg/cTg	2/11	0.291614684078688	4	FACETS	0.554	0.471	0.644	0.277	0.235	0.322	SUBCLONAL	1	TRUE	2	0.426794735650243	4		500	640	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128230293	128230293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772438885	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	119	540	0	ENST00000265960.3:c.1303G>A	p.Asp435Asn	p.D435N	ENST00000265960	NM_001006617.1	435	Gac/Aac	10/12	0.341142739584897	4	FACETS	1	0.974	1	0.61	0.552	0.672	CLONAL	1	TRUE	2	0.426794735650243	4		540	652	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150915378	150915378	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	34	520	0	ENST00000271640.5:c.724C>G	p.Leu242Val	p.L242V	ENST00000271640	NM_001145415.1	242	Ctg/Gtg	7/22	0.291614684078688	4	FACETS	0.394	0.321	0.476	0.197	0.16	0.238	SUBCLONAL	1	TRUE	2	0.426794735650243	4		520	577	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197308	94197308	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	41	357	0	ENST00000323929.3:c.1196del	p.Phe399SerfsTer29	p.F399Sfs*29	ENST00000323929	NM_005591.3	399	tTc/tc	11/20	0.341142739584897	4	FACETS	0.643	0.536	0.762	0.322	0.268	0.381	SUBCLONAL	1	TRUE	2	0.426794735650243	4		357	426	SUCCESS
CBL	867	MSKCC	GRCh37	11	119167707	119167707	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	105	456	0	ENST00000264033.4:c.2116A>G	p.Arg706Gly	p.R706G	ENST00000264033	NM_005188.3	706	Agg/Ggg	13/16	0.341142739584897	4	FACETS	1	0.971	1	0.613	0.55	0.678	CLONAL	1	TRUE	2	0.426794735650243	4		456	573	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857514	57857514	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	120	584	0	ENST00000228682.2:c.40G>T	p.Gly14Cys	p.G14C	ENST00000228682	NM_005269.2	14	Ggc/Tgc	2/12	0.341142739584897	4	FACETS	1	0.981	1	0.677	0.613	0.743	CLONAL	1	TRUE	2	0.426794735650243	4		584	593	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856014	111856014	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	92	519	0	ENST00000341259.2:c.68del	p.Pro23ArgfsTer13	p.P23Rfs*13	ENST00000341259	NM_005475.2	22	gCc/gc	2/8	0.341142739584897	4	FACETS	1	0.949	1	0.556	0.495	0.621	CLONAL	1	TRUE	2	0.426794735650243	4		519	553	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562409	21562409	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	42	495	0	ENST00000382592.4:c.1510del	p.Val504TrpfsTer155	p.V504Wfs*155	ENST00000382592	NM_014572.2	504	Gtg/tg	4/8	0.426794735650243	2	FACETS	0.532	0.445	0.628	0.266	0.222	0.314	SUBCLONAL	1	TRUE	0	0.426794735650243	2		495	370	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609634	81609634	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	132	654	0	ENST00000298171.2:c.1232T>C	p.Ile411Thr	p.I411T	ENST00000298171	NM_000369.2	411	aTa/aCa	10/10	0.368385637717195	5	FACETS	1	0.976	1	0.406	0.368	0.446	CLONAL	1	TRUE	2	0.426794735650243	5		654	833	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246434	105246436	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	92	538	0	ENST00000349310.3:c.164_166del	p.Phe55del	p.F55del	ENST00000349310	NM_001014432.1	55	tTCTct/tct	4/15	0.368385637717195	5	FACETS	1	0.951	1	0.375	0.333	0.419	CLONAL	1	TRUE	2	0.426794735650243	5		538	629	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99472850	99472850	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	92	494	0	ENST00000268035.6:c.2846G>A	p.Gly949Glu	p.G949E	ENST00000268035	NM_000875.3	949	gGa/gAa	14/21	0.341142739584897	4	FACETS	0.97	0.863	1	0.485	0.431	0.542	CLONAL	1	TRUE	2	0.426794735650243	4		494	634	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652842	29652842	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	26	352	0	ENST00000356175.3:c.4780del	p.Thr1594LeufsTer9	p.T1594Lfs*9	ENST00000356175	NM_000267.3	1593	Aaa/aa	36/57	0.341142739584897	4	FACETS	0.401	0.317	0.497	0.2	0.158	0.249	SUBCLONAL	1	TRUE	2	0.426794735650243	4		352	434	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56363702	56363702	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	25	282	0	ENST00000348428.3:c.481T>C	p.Phe161Leu	p.F161L	ENST00000348428	NM_006785.3	161	Ttc/Ctc	3/17	0.291614684078688	4	FACETS	0.381	0.299	0.475	0.19	0.149	0.238	SUBCLONAL	1	TRUE	2	0.426794735650243	4		282	439	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096124	178096124	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	63	576	0	ENST00000397062.3:c.1207A>G	p.Met403Val	p.M403V	ENST00000397062	NM_006164.4	403	Atg/Gtg	5/5	0.426794735650243	2	FACETS	0.616	0.534	0.705	0.308	0.267	0.353	SUBCLONAL	1	TRUE	0	0.426794735650243	2		576	479	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326232	62326232	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	99	540	0	ENST00000360203.5:c.3248T>C	p.Leu1083Pro	p.L1083P	ENST00000360203	NM_001283009.1	1083	cTg/cCg	32/35	0.189415087469188	6	FACETS	0.824	0.738	0.914	0.549	0.492	0.61	INDETERMINATE	2	TRUE	3	0.426794735650243	6		540	522	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074314	30074314	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	133	450	0	ENST00000338641.4:c.1574+2T>C		p.X525_splice	ENST00000338641	NM_000268.3	525			0.347915528219418	2	FACETS	1	0.987	1	0.738	0.677	0.802	CLONAL	1	TRUE	0	0.426794735650243	2		450	422	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200718	128200718	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	46	454	0	ENST00000341105.2:c.1087A>G	p.Asn363Asp	p.N363D	ENST00000341105	NM_032638.4	363	Aac/Gac	5/6	0.426794735650243	2	FACETS	0.607	0.513	0.711	0.304	0.256	0.356	SUBCLONAL	1	TRUE	0	0.426794735650243	2		454	355	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796411	57796412	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	97	502	0	ENST00000309042.7:c.1390_1391dup	p.Val466ProfsTer21	p.V466Pfs*21	ENST00000309042	NM_005612.4	463	gaa/gAAaa	4/4	0.291614684078688	4	FACETS	0.94	0.839	1	0.47	0.419	0.524	CLONAL	1	TRUE	2	0.426794735650243	4		502	690	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797844	32797844	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	122	480	0	ENST00000374899.4:c.1658C>A	p.Pro553His	p.P553H	ENST00000374899	NM_018833.2	553	cCt/cAt	10/12	0.426794735650243	2	FACETS	1	0.982	1	0.668	0.608	0.73	CLONAL	1	TRUE	0	0.426794735650243	2		480	428	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979516	2979516	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1247305409	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	95	463	0	ENST00000396946.4:c.731A>G	p.Lys244Arg	p.K244R	ENST00000396946	NM_032415.4	244	aAg/aGg	6/25	0.291614684078688	4	FACETS	1	0.971	1	0.63	0.563	0.701	CLONAL	1	TRUE	2	0.426794735650243	4		463	504	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92244539	92244539	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	84	466	0	ENST00000265734.4:c.896A>G	p.Tyr299Cys	p.Y299C	ENST00000265734	NM_001259.6	299	tAc/tGc	8/8	0.426794735650243	3	FACETS	0.88	0.779	0.987	0.44	0.389	0.494	CLONAL	1	TRUE	1	0.426794735650243	3		466	543	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124481102	124481102	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs758341603	NA	P-0061907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	104	391	0	ENST00000357628.3:c.1294C>T	p.Arg432Ter	p.R432*	ENST00000357628	NM_015450.2	432	Cga/Tga	14/19	0.426794735650243	3	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	1	0.426794735650243	3		391	289	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256566	115256566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746572499	NA	P-0061908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	19	317	0	ENST00000369535.4:c.145G>A	p.Glu49Lys	p.E49K	ENST00000369535	NM_002524.4	49	Gaa/Aaa	3/7	1	2	FACETS	0.939	0.715	1	0.939	0.715	1	CLONAL	1	TRUE	1	0.19	2		317	213	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017824	31017824	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576523117	NA	P-0061908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	18	330	0	ENST00000375687.4:c.686C>T	p.Pro229Leu	p.P229L	ENST00000375687	NM_015338.5	229	cCg/cTg	8/13	1	2	FACETS	0.694	0.523	0.896	0.694	0.523	0.896	SUBCLONAL	1	TRUE	1	0.19	2		330	273	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634437	23634437	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659160	NA	P-0061908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	14	359	0	ENST00000261584.4:c.2849C>T	p.Ser950Phe	p.S950F	ENST00000261584	NM_024675.3	950	tCc/tTc	9/13	1	2	FACETS	0.682	0.494	0.91	0.682	0.494	0.91	SUBCLONAL	1	TRUE	1	0.19	2		359	216	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687391	37687391	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs770201826	NA	P-0061908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	34	498	0	ENST00000447079.4:c.4295A>G	p.His1432Arg	p.H1432R	ENST00000447079	NM_015083.1	1432	cAt/cGt	14/14	1	2	FACETS	0.785	0.641	0.947	0.785	0.641	0.947	CLONAL	1	TRUE	1	0.19	2		498	456	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635220	87635220	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1368656393	NA	P-0061908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	32	418	0	ENST00000277120.3:c.2272G>A	p.Val758Met	p.V758M	ENST00000277120		758	Gtg/Atg	18/19	1	2	FACETS	0.875	0.711	1	0.875	0.711	1	CLONAL	1	TRUE	1	0.19	2		418	385	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	253	345	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.965803717052412	2		345	494	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0061909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	590	489	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.995	1	1	0.998	1	CLONAL	2	TRUE	1	0.965803717052412	2		489	607	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952006	178952006	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	15	366	0	ENST00000263967.3:c.3061T>C	p.Tyr1021His	p.Y1021H	ENST00000263967	NM_006218.2	1021	Tac/Cac	21/21	1	2	FACETS	0.048	0.034	0.064	0.048	0.034	0.064	SUBCLONAL	1	TRUE	1	0.965803717052412	2		366	648	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024721	14024721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1340754747	NA	P-0061909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	282	307	0	ENST00000311895.7:c.947C>T	p.Thr316Met	p.T316M	ENST00000311895	NM_005236.2	316	aCg/aTg	5/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.965803717052412	2		307	575	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0061909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	297	468	1	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	1	2	FACETS	0.751	0.71	0.793	0.751	0.71	0.793	SUBCLONAL	1	TRUE	1	0.965803717052412	2		469	819	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658568	3658568	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373586019	NA	P-0061909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	243	411	1	ENST00000294008.3:c.398C>T	p.Pro133Leu	p.P133L	ENST00000294008	NM_032444.2	133	cCg/cTg	2/15	0.368312447986395	1	FACETS	0.379	0.355	0.402	0.379	0.355	0.402	INDETERMINATE	1	TRUE	0	0.965803717052412	1		412	687	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3794910	3794910	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0061909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	224	329	0	ENST00000262367.5:c.3967A>T	p.Lys1323Ter	p.K1323*	ENST00000262367	NM_004380.2	1323	Aaa/Taa	23/31	0.368312447986395	1	FACETS	0.478	0.449	0.506	0.478	0.449	0.506	INDETERMINATE	1	TRUE	0	0.965803717052412	1		329	502	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883123	37883123	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	107	417	0	ENST00000269571.5:c.3026T>C	p.Leu1009Pro	p.L1009P	ENST00000269571		1009	cTg/cCg	25/27	1	2	FACETS	0.348	0.312	0.385	0.348	0.312	0.385	SUBCLONAL	1	TRUE	1	0.965803717052412	2		417	637	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120022	70120022	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	32	363	0	ENST00000245479.2:c.1024C>G	p.Pro342Ala	p.P342A	ENST00000245479	NM_000346.3	342	Ccg/Gcg	3/3	1	2	FACETS	0.124	0.1	0.151	0.124	0.1	0.151	SUBCLONAL	1	TRUE	1	0.965803717052412	2		363	536	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619173	1619173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375753059	NA	P-0061909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	71	562	0	ENST00000344749.5:c.1387G>A	p.Ala463Thr	p.A463T	ENST00000344749	NM_001136139.2	463	Gcg/Acg	16/19	1	2	FACETS	0.172	0.149	0.196	0.172	0.149	0.196	SUBCLONAL	1	TRUE	1	0.965803717052412	2		562	856	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31238916	31238917	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0061909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	11	73	0	ENST00000376228.5:c.552_553delinsTT	p.Glu185Ter	p.E185*	ENST00000376228	NM_002117.5	184	ctGGag/ctTTag	3/8	1	2	FACETS	0.177	0.122	0.243	0.177	0.122	0.243	SUBCLONAL	1	TRUE	1	0.965803717052412	2		73	129	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44919303	44919312	+	frameshift_variant	Frame_Shift_Del	DEL	AATAAAACTA	AATAAAACTA	-	novel	NA	P-0061909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	111	155	0	ENST00000377967.4:c.1234_1243del	p.Lys412TyrfsTer24	p.K412Yfs*24	ENST00000377967	NM_021140.2	411	AATAAAACTAaa/aa	13/29	1	2	FACETS	0.931	0.853	1	0.931	0.853	1	CLONAL	1	TRUE	1	0.965803717052412	2		155	247	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922996	44922997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	334	439	0	ENST00000377967.4:c.1859dup	p.Asn620LysfsTer19	p.N620Kfs*19	ENST00000377967	NM_021140.2	619	-/A	16/29	1	2	FACETS	0.862	0.82	0.906	0.862	0.82	0.906	CLONAL	1	TRUE	1	0.965803717052412	2		439	802	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0061910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	97	434	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.72998788549335	5	FACETS	0.839	0.768	0.911	0.839	0.768	0.911	CLONAL	3	FALSE	2	0.98205195008203	5		434	194	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0061910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	280	394	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			0.861058624723058	4	FACETS	0.931	0.883	0.98	0.931	0.883	0.98	CLONAL	2	FALSE	2	0.98205195008203	4		394	607	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063718	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0061910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	298	348	0	ENST00000412916.2:c.165+2dup		p.X55_splice	ENST00000412916		55			0.98205195008203	3	FACETS	0.963	0.922	1	0.963	0.922	1	CLONAL	2	FALSE	1	0.98205195008203	3		348	470	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098533	108098533	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs55861249	NA	P-0061911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	191	442	0	ENST00000278616.4:c.103C>T	p.Arg35Ter	p.R35*	ENST00000278616	NM_000051.3	35	Cga/Tga	3/63	0.693513653934641	1	FACETS	0.88	0.825	0.935	0.88	0.825	0.935	CLONAL	1	TRUE	0	0.693513653934641	1		442	409	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692917	89692917	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	216	486	0	ENST00000371953.3:c.401T>A	p.Met134Lys	p.M134K	ENST00000371953	NM_000314.4	134	aTg/aAg	5/9	0.693513653934641	1	FACETS	0.881	0.829	0.933	0.881	0.829	0.933	CLONAL	1	TRUE	0	0.693513653934641	1		486	462	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47594733	47594733	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	49	457	0	ENST00000430070.2:c.1354G>T	p.Ala452Ser	p.A452S	ENST00000430070	NM_018095.4	452	Gct/Tct	4/4	0.218350275393421	3	FACETS	0.99	0.846	1	0.99	0.846	1	CLONAL	2	TRUE	1	0.220690008303216	3		457	249	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026794	48026794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	45	461	0	ENST00000234420.5:c.1672G>A	p.Val558Met	p.V558M	ENST00000234420	NM_000179.2	558	Gtg/Atg	4/10	0.194809884279744	1	FACETS	0.86	0.731	0.999	1	0.968	1	CLONAL	2	TRUE	0	0.220690008303216	1		461	211	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0061914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	457	641	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.582224489612306	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.582224489612306	2		641	763	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924415	112924415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1566185599	NA	P-0061914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	257	405	0	ENST00000351677.2:c.1361C>T	p.Pro454Leu	p.P454L	ENST00000351677	NM_002834.3	454	cCg/cTg	11/16	0.132884200768098	6	FACETS	1	0.981	1			1	INDETERMINATE	3	TRUE	NA	0.582224489612306	6		405	588	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717661	89717661	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0061915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	259	431	0	ENST00000371953.3:c.686C>G	p.Ser229Ter	p.S229*	ENST00000371953	NM_000314.4	229	tCa/tGa	7/9	0.556847667887589	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.555532689448097	2		431	420	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0061915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	215	440	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.556847667887589	5	FACETS	0.913	0.851	0.977	0.609	0.567	0.651	CLONAL	2	TRUE	2	0.555532689448097	5		440	777	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913079	32913080	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs397507731	NA	P-0061915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	270	454	0	ENST00000380152.3:c.4593dup	p.Val1532SerfsTer2	p.V1532Sfs*2	ENST00000380152		1529	-/A	11/27	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	2	TRUE	NA	0.555532689448097	2		454	477	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77934458	77934458	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	198	465	0	ENST00000361507.4:c.1567G>C	p.Ala523Pro	p.A523P	ENST00000361507	NM_080491.2	523	Gca/Cca	6/10	0.556847667887589	3	FACETS	0.876	0.818	0.934	0.876	0.818	0.934	CLONAL	2	TRUE	1	0.555532689448097	3		465	520	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434148	121434164	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCTCCACCAAGTGTC	CCCCTCCACCAAGTGTC	-	novel	NA	P-0061915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	275	589	0	ENST00000257555.6:c.1043_1059del	p.Leu348HisfsTer65	p.L348Hfs*65	ENST00000257555		347	CCCCTCCACCAAGTGTCc/c	5/10	0.551555815115945	3	FACETS	0.933	0.882	0.985	0.933	0.882	0.985	CLONAL	2	TRUE	1	0.555532689448097	3		589	678	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129431	2129431	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0061915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	127	497	0	ENST00000219476.3:c.3284+2T>A		p.X1095_splice	ENST00000219476	NM_000548.3	1095			0.556847667887589	4	FACETS	0.973	0.882	1	0.324	0.294	0.356	CLONAL	1	TRUE	1	0.555532689448097	4		497	731	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375417	40375417	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	152	585	0	ENST00000293328.3:c.533A>G	p.Glu178Gly	p.E178G	ENST00000293328	NM_012448.3	178	gAg/gGg	5/19	0.556847667887589	4	FACETS	1	0.918	1	0.502	0.459	0.547	CLONAL	1	TRUE	2	0.555532689448097	4		585	848	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424436	47424436	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	153	509	0	ENST00000404338.3:c.2504T>G	p.Leu835Arg	p.L835R	ENST00000404338	NM_004491.4	835	cTg/cGg	1/6	0.531573322658164	3	FACETS	1	0.962	1			1	CLONAL	1	TRUE	NA	0.555532689448097	3		509	651	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690210	47690210	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	177	350	0	ENST00000233146.2:c.1427C>A	p.Pro476His	p.P476H	ENST00000233146	NM_000251.2	476	cCt/cAt	9/16	0.531991793163428	4	FACETS	0.895	0.83	0.961	0.895	0.83	0.961	CLONAL	2	TRUE	2	0.555532689448097	4		350	554	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57470684	57470684	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	211	409	1	ENST00000371085.3:c.157A>G	p.Lys53Glu	p.K53E	ENST00000371085	NM_000516.4	53	Aaa/Gaa	2/13	0.555532689448097	6	FACETS	0.991	0.923	1	0.496	0.461	0.531	CLONAL	2	TRUE	2	0.555532689448097	6		410	809	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73108193	73108223	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTTACTATTCAGCGACTATGTGAATTGTT	CTTTTACTATTCAGCGACTATGTGAATTGTT	-	novel	NA	P-0061915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	83	186	0	ENST00000356692.5:c.293_323del	p.Pro98GlnfsTer18	p.P98Qfs*18	ENST00000356692		98	cCTTTTACTATTCAGCGACTATGTGAATTGTTa/ca	4/9	0.531573322658164	3	FACETS	0.984	0.888	1			1	CLONAL	2	TRUE	NA	0.555532689448097	3		186	194	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180875	106180880	+	inframe_deletion	In_Frame_Del	DEL	CAGAAG	CAGAAG	-	novel	NA	P-0061915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	195	375	0	ENST00000380013.4:c.3905_3910del	p.Arg1302_Ser1303del	p.R1302_S1303del	ENST00000380013	NM_001127208.2	1301	gcCAGAAGc/gcc	7/11	0.556847667887589	2	FACETS	0.972	0.916	1	0.972	0.916	1	CLONAL	2	TRUE	0	0.555532689448097	2		375	361	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508834	31508834	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	117	391	0	ENST00000344624.3:c.1481C>A	p.Ser494Tyr	p.S494Y	ENST00000344624		494	tCt/tAt	7/33	0.555532689448097	8	FACETS	0.975	0.877	1	0.139	0.125	0.155	CLONAL	1	TRUE	1	0.555532689448097	8		391	1152	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0061925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	73	662	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.248174751640148	2		662	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579410	7579411	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0061925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	216	693	0	ENST00000269305.4:c.276_277del	p.Leu93ValfsTer55	p.L93Vfs*55	ENST00000269305	NM_001126112.2	92	ccCCtg/cctg	4/11	0.24121449265524	3	FACETS	0.932	0.87	0.995	0.932	0.87	0.995	CLONAL	3	TRUE	0	0.248174751640148	3		693	700	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981582	101981582	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0061925-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	44	558	0	ENST00000282441.5:c.3G>A	p.Met1?	p.M1?	ENST00000282441	NM_001130145.2	1	atG/atA	1/9	0.197679967738524	4	FACETS	0.968	0.813	1	0.484	0.406	0.571	CLONAL	1	TRUE	2	0.248174751640148	4		558	457	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0061926-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	124	346	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	0.616	0.559	0.677	0.616	0.559	0.677	SUBCLONAL	1	TRUE	1	0.62	2		346	649	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0061926-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	73	251	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.835	0.738	0.937	0.835	0.738	0.937	CLONAL	1	TRUE	1	0.62	2		251	282	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0061926-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	51	290	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.814	0.702	0.935	0.814	0.702	0.935	CLONAL	1	TRUE	1	0.62	2		290	202	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100664	8100664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1477514775	NA	P-0061926-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	240	463	0	ENST00000346208.3:c.638C>T	p.Ser213Leu	p.S213L	ENST00000346208		213	tCg/tTg	3/6	1	2	FACETS	0.99	0.928	1	0.99	0.928	1	CLONAL	1	TRUE	1	0.62	2		463	782	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692889	89692889	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061926-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	85	201	0	ENST00000371953.3:c.373A>G	p.Lys125Glu	p.K125E	ENST00000371953	NM_000314.4	125	Aaa/Gaa	5/9	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.62	2		201	223	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102199	27102199	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0061926-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	155	364	0	ENST00000324856.7:c.5124+1G>T		p.X1708_splice	ENST00000324856	NM_006015.4	1708			1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.62	2		364	500	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155663	56155672	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCTGGCAA	CTCCTGGCAA	-	novel	NA	P-0061926-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	173	336	0	ENST00000399503.3:c.759_768del	p.Gly254HisfsTer6	p.G254Hfs*6	ENST00000399503	NM_005921.1	252	tCTCCTGGCAAc/tc	3/20	1	2	FACETS	0.843	0.779	0.909	0.843	0.779	0.909	CLONAL	1	TRUE	1	0.62	2		336	662	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061927-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	57	515	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.129673640380486	3	FACETS	1	0.931	1	0.572	0.491	0.662	CLONAL	1	TRUE	1	0.18	3		515	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574030	7574030	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061927-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	33	372	0	ENST00000269305.4:c.997del	p.Arg333ValfsTer12	p.R333Vfs*12	ENST00000269305	NM_001126112.2	333	Cgt/gt	10/11	1	2	FACETS	0.794	0.646	0.96	0.794	0.646	0.96	CLONAL	1	TRUE	1	0.18	2		372	462	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202809	128202809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061927-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	115	638	0	ENST00000341105.2:c.911C>T	p.Pro304Leu	p.P304L	ENST00000341105	NM_032638.4	304	cCt/cTt	4/6	0.129673640380486	3	FACETS	0.95	0.856	1	0.95	0.856	1	CLONAL	2	TRUE	1	0.18	3		638	733	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	163	345	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.713348114105111	2		345	335	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0061929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	79	529	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.263134576330538	3	FACETS	0.868	0.784	0.954	0.868	0.784	0.954	INDETERMINATE	2	TRUE	1	0.713348114105111	3		529	173	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0061929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	42	473	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.566	0.478	0.662	0.566	0.478	0.662	SUBCLONAL	1	TRUE	1	0.713348114105111	2		473	208	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0061929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	430	497	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.713348114105111	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.713348114105111	2		497	582	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47004894	47004894	+	intron_variant	Intron	SNP	G	G	A	novel	NA	P-0061929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	130	927	0	ENST00000377604.3:c.-126+10G>A		p.*42*	ENST00000377604	NM_001204468.1	-/163			0.263134576330538	3	FACETS	0.49	0.444	0.539	0.245	0.222	0.27	INDETERMINATE	1	TRUE	1	0.713348114105111	3		927	1009	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62009584	62009584	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	163	539	0	ENST00000392795.3:c.38G>A	p.Trp13Ter	p.W13*	ENST00000392795	NM_001039933.1	13	tGg/tAg	1/6	0.266162430832416	2	FACETS	0.755	0.696	0.816	0.378	0.348	0.408	INDETERMINATE	1	TRUE	0	0.713348114105111	2		539	605	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032795	30032795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368773485	NA	P-0061929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	95	536	0	ENST00000338641.4:c.170G>A	p.Arg57Gln	p.R57Q	ENST00000338641	NM_000268.3	57	cGa/cAa	2/16	1	2	FACETS	0.384	0.342	0.429	0.384	0.342	0.429	SUBCLONAL	1	TRUE	1	0.713348114105111	2		536	693	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420268	49420268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757664799	NA	P-0061929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	213	639	0	ENST00000301067.7:c.15481G>A	p.Glu5161Lys	p.E5161K	ENST00000301067	NM_003482.3	5161	Gag/Aag	48/54	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.713348114105111	2		639	546	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448147	49448147	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	221	625	0	ENST00000301067.7:c.453del	p.Gln152ArgfsTer56	p.Q152Rfs*56	ENST00000301067	NM_003482.3	151	ggG/gg	4/54	1	2	FACETS	0.949	0.888	1	0.949	0.888	1	CLONAL	1	TRUE	1	0.713348114105111	2		625	653	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795752	42795752	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	181	673	0	ENST00000575354.2:c.2741C>T	p.Ser914Leu	p.S914L	ENST00000575354	NM_015125.3	914	tCa/tTa	11/20	0.287292387056891	3	FACETS	1	0.978	1	0.568	0.527	0.611	INDETERMINATE	1	TRUE	1	0.713348114105111	3		673	606	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465621	8465621	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	157	423	0	ENST00000356435.5:c.3559G>A	p.Glu1187Lys	p.E1187K	ENST00000356435		1187	Gaa/Aaa	21/35	0.263134576330538	3	FACETS	0.836	0.777	0.896	0.836	0.777	0.896	INDETERMINATE	2	TRUE	1	0.713348114105111	3		423	357	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426667	49426667	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	258	849	0	ENST00000301067.7:c.11821C>T	p.Gln3941Ter	p.Q3941*	ENST00000301067	NM_003482.3	3941	Caa/Taa	39/54	1	2	FACETS	0.946	0.889	1	0.946	0.889	1	CLONAL	1	TRUE	1	0.713348114105111	2		849	765	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043963	180043963	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	174	477	0	ENST00000261937.6:c.3033G>T	p.Met1011Ile	p.M1011I	ENST00000261937	NM_182925.4	1011	atG/atT	22/30	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.713348114105111	2		477	462	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47598965	47598965	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs371150449	NA	P-0061929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	63	583	0	ENST00000430070.2:c.635C>T	p.Ser212Leu	p.S212L	ENST00000430070	NM_018095.4	212	tCg/tTg	2/4	1	2	FACETS	0.323	0.279	0.37	0.323	0.279	0.37	SUBCLONAL	1	TRUE	1	0.713348114105111	2		583	547	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015337	176015337	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	67	291	0	ENST00000367669.3:c.1401G>A	p.Met467Ile	p.M467I	ENST00000367669	NM_022457.5	467	atG/atA	12/20	1	2	FACETS	0.944	0.835	1	0.944	0.835	1	CLONAL	1	TRUE	1	0.713348114105111	2		291	199	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955382	48955382	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1485450031	NA	P-0061929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	51	253	0	ENST00000267163.4:c.1499-1G>T		p.X500_splice	ENST00000267163	NM_000321.2	500			0.713348114105111	1	FACETS	0.868	0.765	0.971	0.868	0.765	0.971	CLONAL	1	TRUE	0	0.713348114105111	1		253	106	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515129	103515129	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	60	561	0	ENST00000355739.4:c.1630G>C	p.Glu544Gln	p.E544Q	ENST00000355739	NM_000123.3	544	Gag/Cag	8/15	1	2	FACETS	0.327	0.282	0.376	0.327	0.282	0.376	SUBCLONAL	1	TRUE	1	0.713348114105111	2		561	514	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279830	46279831	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	TT	novel	NA	P-0061929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	129	658	3	ENST00000371998.3:c.3756_3757delinsTT	p.Gln1252_Gln1253delinsHisTer	p.Q1252_Q1253delinsH*	ENST00000371998		1252	caGCag/caTTag	20/23	0.287292387056891	3	FACETS	0.573	0.519	0.63	0.287	0.259	0.315	INDETERMINATE	1	TRUE	1	0.713348114105111	3		661	856	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084142	47084142	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	63	542	0	ENST00000409792.3:c.7147C>A	p.Pro2383Thr	p.P2383T	ENST00000409792	NM_014159.6	2383	Cct/Act	17/21	0.263134576330538	3	FACETS	0.383	0.331	0.44	0.192	0.165	0.22	INDETERMINATE	1	TRUE	1	0.713348114105111	3		542	625	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664655	138664655	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	151	488	0	ENST00000330315.3:c.910G>T	p.Ala304Ser	p.A304S	ENST00000330315	NM_023067.3	304	Gca/Tca	1/1	0.263134576330538	3	FACETS	1	0.973	1	0.566	0.521	0.613	INDETERMINATE	1	TRUE	1	0.713348114105111	3		488	507	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036981	180036981	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1230678706	NA	P-0061929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	127	547	1	ENST00000261937.6:c.3731C>T	p.Ala1244Val	p.A1244V	ENST00000261937	NM_182925.4	1244	gCt/gTt	28/30	1	2	FACETS	0.636	0.578	0.696	0.636	0.578	0.696	SUBCLONAL	1	TRUE	1	0.713348114105111	2		548	560	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913175	39913175	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	127	530	0	ENST00000378444.4:c.4940T>C	p.Leu1647Ser	p.L1647S	ENST00000378444	NM_001123385.1	1647	tTa/tCa	14/15	0.263134576330538	3	FACETS	0.735	0.667	0.806	0.368	0.333	0.403	INDETERMINATE	1	TRUE	1	0.713348114105111	3		530	657	SUCCESS
AR	367	MSKCC	GRCh37	X	66931532	66931532	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0061929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	162	441	0	ENST00000374690.3:c.2173+1G>A		p.X725_splice	ENST00000374690	NM_000044.3	725			0.263134576330538	3	FACETS	1	0.986	1	0.645	0.596	0.694	INDETERMINATE	1	TRUE	1	0.713348114105111	3		441	478	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436149	56436149	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	108	502	0	ENST00000407977.2:c.988C>T	p.Arg330Ter	p.R330*	ENST00000407977		330	Cga/Tga	9/10	0.767634371699645	1	FACETS	0.958	0.888	1	0.958	0.888	1	CLONAL	1	TRUE	0	0.767634371699645	1		502	181	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236086	108236086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782292	NA	P-0061930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	34	498	0	ENST00000278616.4:c.9022C>T	p.Arg3008Cys	p.R3008C	ENST00000278616	NM_000051.3	3008	Cgt/Tgt	63/63	1	2	FACETS	0.251	0.205	0.302	0.251	0.205	0.302	SUBCLONAL	1	TRUE	1	0.767634371699645	2		498	353	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687514	37687514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs562860050	NA	P-0061930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	135	507	1	ENST00000447079.4:c.4418G>A	p.Arg1473Gln	p.R1473Q	ENST00000447079	NM_015083.1	1473	cGg/cAg	14/14	1	2	FACETS	0.999	0.92	1	0.999	0.92	1	CLONAL	1	TRUE	1	0.767634371699645	2		508	352	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TC	novel	NA	P-0061930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	90	378	0	ENST00000311936.3:c.180_181inv	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggGAaa	3/5	1	2	FACETS	0.834	0.75	0.922	0.834	0.75	0.922	CLONAL	1	TRUE	1	0.767634371699645	2		378	281	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81979861	81979861	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	154	456	0	ENST00000359376.3:c.3563C>G	p.Pro1188Arg	p.P1188R	ENST00000359376	NM_002661.3	1188	cCa/cGa	31/33	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.767634371699645	2		456	360	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124503409	124503409	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	78	335	0	ENST00000357628.3:c.541C>G	p.Leu181Val	p.L181V	ENST00000357628	NM_015450.2	181	Cta/Gta	8/19	1	2	FACETS	0.915	0.818	1	0.915	0.818	1	CLONAL	1	TRUE	1	0.767634371699645	2		335	222	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048214	180048214	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs139399208	NA	P-0061932-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	178	520	0	ENST00000261937.6:c.2059C>G	p.Leu687Val	p.L687V	ENST00000261937	NM_182925.4	687	Ctc/Gtc	14/30	0.809710843984487	4	FACETS	1	0.963	1	0.356	0.329	0.384	CLONAL	1	TRUE	1	0.809710843984487	4		520	745	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691022	NA	P-0061933-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	248	401	0	ENST00000269305.4:c.1024del	p.Arg342GlufsTer3	p.R342Efs*3	ENST00000269305	NM_001126112.2	342	Cga/ga	10/11	0.879051268831481	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.879051268831481	2		401	277	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0061934-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	8	336	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.2	0.129	0.292	0.2	0.129	0.292	SUBCLONAL	1	TRUE	1	0.570622446092852	2		336	140	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157488190	157488190	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34786733	NA	P-0061934-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	8	445	0	ENST00000346085.5:c.2896G>A	p.Gly966Ser	p.G966S	ENST00000346085	NM_020732.3	966	Ggc/Agc	10/20	1	2	FACETS	0.093	0.059	0.137	0.093	0.059	0.137	SUBCLONAL	1	TRUE	1	0.570622446092852	2		445	302	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696742	47696742	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061934-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	25	318	1	ENST00000347630.2:c.206T>C	p.Leu69Ser	p.L69S	ENST00000347630	NM_001007230.1	69	tTg/tCg	5/11	0.253569289788078	1	FACETS	0.423	0.337	0.519	0.423	0.337	0.519	INDETERMINATE	1	TRUE	0	0.570622446092852	1		319	148	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304160	65304160	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061934-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	26	323	0	ENST00000342505.4:c.2955del	p.Gln986ArgfsTer32	p.Q986Rfs*32	ENST00000342505	NM_002227.2	985	gtT/gt	21/25	1	2	FACETS	0.885	0.716	1	0.885	0.716	1	CLONAL	1	TRUE	1	0.570622446092852	2		323	103	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719427	190719427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061934-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	13	467	0	ENST00000441310.2:c.1429G>A	p.Glu477Lys	p.E477K	ENST00000441310	NM_000534.4	477	Gag/Aag	9/13	1	2	FACETS	0.294	0.21	0.395	0.294	0.21	0.395	SUBCLONAL	1	TRUE	1	0.570622446092852	2		467	155	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743837	40743837	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0061935-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	127	256	0	ENST00000373198.4:c.3156+2T>C		p.X1052_splice	ENST00000373198	NM_133170.3	1052			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		256	497	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0061936-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	164	365	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.590675909350822	2		365	525	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435395	18435395	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061936-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	52	436	0	ENST00000266497.5:c.380G>T	p.Gly127Val	p.G127V	ENST00000266497		127	gGa/gTa	1/31	1	2	FACETS	0.335	0.285	0.39	0.335	0.285	0.39	SUBCLONAL	1	TRUE	1	0.590675909350822	2		436	525	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061937-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	90	345	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.838	0.749	0.932	0.838	0.749	0.932	CLONAL	1	TRUE	1	0.549123200899789	2		345	391	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0061937-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	132	393	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.549123200899789	1	FACETS	0.915	0.84	0.993	0.915	0.84	0.993	CLONAL	1	TRUE	0	0.549123200899789	1		393	381	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0061937-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	146	302	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.549123200899789	2	FACETS	0.977	0.912	1	0.977	0.912	1	CLONAL	2	TRUE	0	0.549123200899789	2		302	272	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226859	2226879	+	inframe_deletion	In_Frame_Del	DEL	GCGGCGTCCTCCGCAGGCGGC	GCGGCGTCCTCCGCAGGCGGC	-	rs748637415	NA	P-0061937-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	125	644	0	ENST00000398665.3:c.4353_4373del	p.Gly1452_Ala1458del	p.G1452_A1458del	ENST00000398665	NM_032482.2	1447	GCGGCGTCCTCCGCAGGCGGC/-	27/28	1	2	FACETS	0.708	0.642	0.777	0.708	0.642	0.777	SUBCLONAL	1	TRUE	1	0.549123200899789	2		644	643	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42759139	42759139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061937-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	102	308	0	ENST00000222329.4:c.13G>A	p.Ala5Thr	p.A5T	ENST00000222329	NM_006494.2	5	Gcg/Acg	1/4	1	2	FACETS	0.862	0.776	0.952	0.862	0.776	0.952	CLONAL	1	TRUE	1	0.549123200899789	2		308	431	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050741	69050741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771859071	NA	P-0061937-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	28	207	0	ENST00000288368.4:c.4076C>T	p.Pro1359Leu	p.P1359L	ENST00000288368	NM_024870.2	1359	cCt/cTt	33/40	1	2	FACETS	0.68	0.55	0.824	0.68	0.55	0.824	SUBCLONAL	1	TRUE	1	0.549123200899789	2		207	150	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321341	1321341	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061937-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	193	437	0	ENST00000400841.2:c.414T>G	p.Cys138Trp	p.C138W	ENST00000400841		138	tgT/tgG	4/6	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.549123200899789	2		437	613	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061134	38061193	+	inframe_deletion	In_Frame_Del	DEL	GCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAA	GCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAA	-	novel	NA	P-0061938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	47	496	0	ENST00000250448.2:c.796_855del	p.Phe266_Ser285del	p.F266_S285del	ENST00000250448	NM_004496.3	266	TTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGC/-	2/2	1	2	FACETS	0.33	0.277	0.388	0.33	0.277	0.388	SUBCLONAL	1	TRUE	1	0.369116111163836	2		496	772	SUCCESS
AR	367	MSKCC	GRCh37	X	66943552	66943552	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137852578	NA	P-0062005-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	319	202	0	ENST00000374690.3:c.2632A>G	p.Thr878Ala	p.T878A	ENST00000374690	NM_000044.3	878	Act/Gct	8/8	0.783023695705391	2	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.861740003306093	2		202	681	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0062005-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	373	467	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.861740003306093	2		467	789	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508082	106508082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0062005-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	869	452	1	ENST00000359195.3:c.76C>T	p.Arg26Cys	p.R26C	ENST00000359195	NM_002649.2	26	Cgc/Tgc	2/11	0.861740003306093	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	1	0.861740003306093	4		453	1242	SUCCESS
APC	324	MSKCC	GRCh37	5	112173301	112173313	+	frameshift_variant	Frame_Shift_Del	DEL	ATCTCATAGTTTG	ATCTCATAGTTTG	-	novel	NA	P-0062005-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	289	347	0	ENST00000257430.4:c.2011_2023del	p.Ser671GlnfsTer2	p.S671Qfs*2	ENST00000257430	NM_000038.5	670	aaATCTCATAGTTTG/aa	16/16	0.861740003306093	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.861740003306093	1		347	366	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000066-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	18	439	0	ENST00000206249.3:c.1610A>G	p.Tyr537Cys	p.Y537C	ENST00000206249	NM_000125.3	537	tAt/tGt	8/8	0.269561553016772	3	FACETS	0.332	0.25	0.43	0.111	0.083	0.144	SUBCLONAL	1	FALSE	0	0.375030523144688	3		439	343	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510606	38510606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000066-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	270	579	2	ENST00000254066.5:c.860C>T	p.Ser287Leu	p.S287L	ENST00000254066	NM_000964.3	287	tCg/tTg	7/9	0.316565047601725	4	FACETS	1	0.991	1	0.687	0.642	0.732	CLONAL	1	FALSE	2	0.375030523144688	4		581	1442	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864343	151864343	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0000066-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	111	546	0	ENST00000262189.6:c.9638C>G	p.Ser3213Ter	p.S3213*	ENST00000262189	NM_170606.2	3213	tCa/tGa	42/59	NA	2	FACETS	0.943	0.849	1			1	INDETERMINATE	1	FALSE	NA	0.375030523144688	2		546	628	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349880	15349880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000066-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	101	228	0	ENST00000263377.2:c.3772G>A	p.Glu1258Lys	p.E1258K	ENST00000263377	NM_058243.2	1258	Gag/Aag	18/20	0.316565047601725	4	FACETS	0.919	0.827	1	0.919	0.827	1	CLONAL	2	FALSE	2	0.375030523144688	4		228	403	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0000606-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	123	667	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.300071804593079	3	FACETS	1	0.985	1	0.716	0.652	0.782	CLONAL	1	TRUE	1	0.480951460090327	3		667	443	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266709	198266709	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000606-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	343	351	0	ENST00000335508.6:c.2223G>C	p.Lys741Asn	p.K741N	ENST00000335508	NM_012433.2	741	aaG/aaC	15/25	0.300071804593079	3	FACETS	1	0.994	1	0.702	0.663	0.741	CLONAL	1	TRUE	1	0.480951460090327	3		351	1261	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878676	151878676	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0000606-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	168	206	0	ENST00000262189.6:c.6269C>G	p.Ser2090Ter	p.S2090*	ENST00000262189	NM_170606.2	2090	tCa/tGa	36/59	0.300071804593079	3	FACETS	1	0.981	1	0.602	0.554	0.651	CLONAL	1	TRUE	1	0.480951460090327	3		206	720	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273402	38273402	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000606-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	93	392	0	ENST00000425967.3:c.1933C>G	p.Leu645Val	p.L645V	ENST00000425967	NM_001174067.1	645	Ctg/Gtg	14/19	0.300071804593079	3	FACETS	0.403	0.357	0.452	0.201	0.178	0.226	SUBCLONAL	1	TRUE	1	0.480951460090327	3		392	1191	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0000606-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	341	437	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	0.480951460090327	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.480951460090327	1		437	816	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244280	5244280	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000606-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	269	456	0	ENST00000357368.4:c.1202G>A	p.Trp401Ter	p.W401*	ENST00000357368	NM_002850.3	401	tGg/tAg	11/38	0.480951460090327	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.480951460090327	1		456	759	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794044	42794044	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000606-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	290	312	0	ENST00000575354.2:c.1405G>C	p.Glu469Gln	p.E469Q	ENST00000575354	NM_015125.3	469	Gag/Cag	9/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.480951460090327	2		312	1066	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609948	43609948	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs75076352	NA	P-0000662-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	529	428	0	ENST00000355710.3:c.1900T>C	p.Cys634Arg	p.C634R	ENST00000355710	NM_020975.4	634	Tgc/Cgc	11/20	0.627338749935645	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.627338749935645	3		428	1054	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001396-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	93	308	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.380721201773375	4	FACETS	1	0.89	1	0.5	0.445	0.559	CLONAL	1	TRUE	2	0.402755504027751	4		308	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577524	7577524	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001396-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	104	773	0	ENST00000269305.4:c.757A>C	p.Thr253Pro	p.T253P	ENST00000269305	NM_001126112.2	253	Acc/Ccc	7/11	0.402755504027751	2	FACETS	0.953	0.867	1	0.953	0.867	1	CLONAL	2	TRUE	0	0.402755504027751	2		773	271	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687586	29687586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001396-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1228	169	629	1	ENST00000356175.3:c.8179G>A	p.Glu2727Lys	p.E2727K	ENST00000356175	NM_000267.3	2727	Gaa/Aaa	56/57	0.402755504027751	6	FACETS	1	0.962	1	0.271	0.248	0.295	CLONAL	1	TRUE	2	0.402755504027751	6		630	1397	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691950	30691950	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001396-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	51	401	0	ENST00000295754.5:c.453del	p.Glu152AsnfsTer11	p.E152Nfs*11	ENST00000295754	NM_003242.5	151	gAa/ga	3/7	0.331558809674916	4	FACETS	0.976	0.833	1			1	CLONAL	1	TRUE	NA	0.402755504027751	4		401	364	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001396-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	109	308	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.6147793370753	3	FACETS	0.873	0.787	0.963	0.437	0.393	0.482	CLONAL	1	TRUE	1	0.6147793370753	3		308	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577524	7577524	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001396-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	455	773	0	ENST00000269305.4:c.757A>C	p.Thr253Pro	p.T253P	ENST00000269305	NM_001126112.2	253	Acc/Ccc	7/11	0.6147793370753	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.6147793370753	2		773	736	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687586	29687586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001396-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	153	629	1	ENST00000356175.3:c.8179G>A	p.Glu2727Lys	p.E2727K	ENST00000356175	NM_000267.3	2727	Gaa/Aaa	56/57	0.6147793370753	5	FACETS	0.828	0.756	0.903	0.207	0.189	0.226	CLONAL	1	TRUE	1	0.6147793370753	5		630	1156	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691950	30691950	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001396-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	89	401	0	ENST00000295754.5:c.453del	p.Glu152AsnfsTer11	p.E152Nfs*11	ENST00000295754	NM_003242.5	151	gAa/ga	3/7	1	2	FACETS	0.888	0.795	0.985	0.888	0.795	0.985	CLONAL	1	TRUE	1	0.6147793370753	2		401	326	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40478169	40478169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1288968449	NA	P-0001396-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	196	659	0	ENST00000264657.5:c.1330G>A	p.Glu444Lys	p.E444K	ENST00000264657	NM_139276.2	444	Gag/Aag	15/24	0.6147793370753	3	FACETS	0.92	0.852	0.99	0.46	0.426	0.495	CLONAL	1	TRUE	1	0.6147793370753	3		659	906	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436042	49436042	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1164333482	NA	P-0001396-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	203	716	0	ENST00000301067.7:c.5939C>T	p.Thr1980Met	p.T1980M	ENST00000301067	NM_003482.3	1980	aCg/aTg	28/54	0.6147793370753	3	FACETS	1	0.975	1	0.552	0.513	0.592	CLONAL	1	TRUE	1	0.6147793370753	3		716	782	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0001817-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	165	704	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.224402339262767	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.224402339262767	1		704	999	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0001817-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1426	2477	653	2	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.224402339262767	24	FACETS	0.981	0.966	0.995			1	CLONAL	20	TRUE	NA	0.224402339262767	24		655	3903	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0001817-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	1762	385	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.224402339262767	24	FACETS	0.98	0.962	0.998			1	CLONAL	19	TRUE	NA	0.224402339262767	24		385	2925	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166184	118166184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371434677	NA	P-0001817-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	80	307	1	ENST00000369448.3:c.694G>A	p.Ala232Thr	p.A232T	ENST00000369448	NM_017709.3	232	Gcc/Acc	2/2	1	2	FACETS	0.72	0.632	0.815	0.72	0.632	0.815	SUBCLONAL	1	TRUE	1	0.224402339262767	2		308	990	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675502	30675502	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001817-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1371	146	587	2	ENST00000376406.3:c.2854G>C	p.Glu952Gln	p.E952Q	ENST00000376406	NM_014641.2	952	Gag/Cag	8/15	0.157397672512745	3	FACETS	0.954	0.868	1	0.477	0.434	0.523	CLONAL	1	TRUE	1	0.224402339262767	3		589	1517	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915792	112915792	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001817-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	67	325	0	ENST00000351677.2:c.1065G>A	p.Met355Ile	p.M355I	ENST00000351677	NM_002834.3	355	atG/atA	9/16	0.157397672512745	3	FACETS	0.703	0.609	0.805	0.351	0.304	0.403	SUBCLONAL	1	TRUE	1	0.224402339262767	3		325	945	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781200	3781200	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001817-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	76	279	0	ENST00000262367.5:c.5165T>A	p.Val1722Glu	p.V1722E	ENST00000262367	NM_004380.2	1722	gTg/gAg	30/31	0.202168259998758	4	FACETS	0.9	0.788	1	0.45	0.394	0.511	CLONAL	1	TRUE	2	0.224402339262767	4		279	921	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	223624	223624	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs142441643	NA	P-0002594-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	117	363	0	ENST00000264932.6:c.91C>T	p.Arg31Ter	p.R31*	ENST00000264932	NM_004168.2	31	Cga/Tga	2/15	0.121696452288583	1	FACETS	1	0.969	1	1	0.969	1	INDETERMINATE	1	TRUE	0	0.5	1		363	311	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	223624	223624	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs142441643	NA	P-0002594-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	406	363	0	ENST00000264932.6:c.91C>T	p.Arg31Ter	p.R31*	ENST00000264932	NM_004168.2	31	Cga/Tga	2/15	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		363	1017	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946178	55946178	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002594-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	141	551	0	ENST00000263923.4:c.4001T>A	p.Val1334Glu	p.V1334E	ENST00000263923	NM_002253.2	1334	gTg/gAg	30/30	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		551	1258	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	114	667	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.360576806308949	2		667	434	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	51	348	1				ENST00000310581	NM_198253.2	-/1132			0.317969711225383	1	FACETS	0.549	0.468	0.639	0.549	0.468	0.639	SUBCLONAL	1	TRUE	0	0.360576806308949	1		349	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	145	645	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.360576806308949	1	FACETS	0.978	0.895	1	0.978	0.895	1	CLONAL	1	TRUE	0	0.360576806308949	1		645	674	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338683	70338683	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	112	264	0	ENST00000374080.3:c.79C>G	p.Gln27Glu	p.Q27E	ENST00000374080		27	Cag/Gag	1/45	1	1	FACETS	0.756	0.687	0.826	1	0.985	1	SUBCLONAL	2	TRUE	0	0.360576806308949	1		264	337	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938203	36938203	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	176	728	0	ENST00000361632.4:c.758G>A	p.Trp253Ter	p.W253*	ENST00000361632		253	tGg/tAg	6/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.360576806308949	2		728	838	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149808	202149808	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	55	586	0	ENST00000358485.4:c.1249C>G	p.Gln417Glu	p.Q417E	ENST00000358485	NM_001080125.1	417	Cag/Gag	8/9	0.317969711225383	1	FACETS	0.422	0.361	0.49	0.422	0.361	0.49	SUBCLONAL	1	TRUE	0	0.360576806308949	1		586	592	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662805	227662805	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	140	633	0	ENST00000305123.5:c.650C>A	p.Ser217Ter	p.S217*	ENST00000305123	NM_005544.2	217	tCg/tAg	1/2	0.317969711225383	1	FACETS	0.897	0.818	0.979	0.897	0.818	0.979	CLONAL	1	TRUE	0	0.360576806308949	1		633	710	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294370	1294370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	94	610	1	ENST00000310581.5:c.631G>A	p.Gly211Arg	p.G211R	ENST00000310581	NM_198253.2	211	Ggg/Agg	2/16	0.317969711225383	1	FACETS	0.581	0.517	0.65	0.581	0.517	0.65	SUBCLONAL	1	TRUE	0	0.360576806308949	1		611	735	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742824	145742824	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	95	455	0	ENST00000428558.2:c.187G>T	p.Glu63Ter	p.E63*	ENST00000428558	NM_004260.3	63	Gag/Tag	3/22	0.202379557828693	3	FACETS	1	0.947	1	0.549	0.49	0.612	INDETERMINATE	1	TRUE	1	0.360576806308949	3		455	566	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853288	68853288	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	68	494	0	ENST00000261769.5:c.1671G>C	p.Lys557Asn	p.K557N	ENST00000261769	NM_004360.3	557	aaG/aaC	11/16	0.317969711225383	1	FACETS	0.506	0.44	0.577	0.506	0.44	0.577	SUBCLONAL	1	TRUE	0	0.360576806308949	1		494	611	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272338	15272338	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751050359	NA	P-0003279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	184	794	0	ENST00000263388.2:c.6101C>T	p.Pro2034Leu	p.P2034L	ENST00000263388	NM_000435.2	2034	cCc/cTc	33/33	0.250129608412816	1	FACETS	0.976	0.902	1	0.976	0.902	1	CLONAL	1	TRUE	0	0.360576806308949	1		794	857	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164851	36164852	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0003279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	125	798	0	ENST00000300305.3:c.1023dup	p.Ile342HisfsTer258	p.I342Hfs*258	ENST00000300305		341	-/C	8/8	0.250129608412816	1	FACETS	0.618	0.559	0.681	0.618	0.559	0.681	SUBCLONAL	1	TRUE	0	0.360576806308949	1		798	919	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440302	52440310	+	inframe_deletion	In_Frame_Del	DEL	CACCTTCAG	CACCTTCAG	-	novel	NA	P-0003279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	135	580	0	ENST00000460680.1:c.742_750del	p.Leu248_Val250del	p.L248_V250del	ENST00000460680	NM_004656.3	248	CTGAAGGTG/-	9/17	0.360576806308949	1	FACETS	0.974	0.888	1	0.974	0.888	1	CLONAL	1	TRUE	0	0.360576806308949	1		580	630	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881414	37881414	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1131692237	NA	P-0003279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	56	628	0	ENST00000269571.5:c.2606T>G	p.Leu869Arg	p.L869R	ENST00000269571		869	cTg/cGg	21/27	1	2	FACETS	0.321	0.274	0.373	0.321	0.274	0.373	SUBCLONAL	1	TRUE	1	0.360576806308949	2		628	967	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40876429	40876429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	118	527	0	ENST00000428826.2:c.260G>A	p.Ser87Asn	p.S87N	ENST00000428826		87	aGc/aAc	5/21	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.360576806308949	2		527	599	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495458	149495459	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0003279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	103	806	1	ENST00000261799.4:c.3188_3189delinsAA	p.Pro1063Gln	p.P1063Q	ENST00000261799	NM_002609.3	1063	cCC/cAA	23/23	0.317969711225383	1	FACETS	0.505	0.451	0.563	0.505	0.451	0.563	SUBCLONAL	1	TRUE	0	0.360576806308949	1		807	927	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802599	135802599	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	38	353	0	ENST00000298552.3:c.199C>A	p.Pro67Thr	p.P67T	ENST00000298552	NM_001162426.1	67	Cca/Aca	4/23	1	2	FACETS	0.456	0.377	0.545	0.456	0.377	0.545	SUBCLONAL	1	TRUE	1	0.360576806308949	2		353	462	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94129019	94129019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	52	753	0	ENST00000369303.4:c.41G>A	p.Cys14Tyr	p.C14Y	ENST00000369303	NM_004440.3	14	tGc/tAc	1/17	0.290375719282245	1	FACETS	0.366	0.31	0.427	0.366	0.31	0.427	SUBCLONAL	1	TRUE	0	0.290375719282245	1		753	837	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951092	17951092	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	103	552	0	ENST00000458235.1:c.1201C>G	p.Leu401Val	p.L401V	ENST00000458235	NM_000215.3	401	Ctc/Gtc	9/24	1	2	FACETS	0.931	0.833	1	0.931	0.833	1	CLONAL	1	TRUE	1	0.290375719282245	2		552	762	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685242	89685284	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTTTTTGTTTGTTTGTTTTGTTTTAAGGTTTTTGGATTCAAA	GCTTTTTGTTTGTTTGTTTTGTTTTAAGGTTTTTGGATTCAAA	-	novel	NA	P-0004735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	11	144	0	ENST00000371953.3:c.165-26_181del		p.X55_splice	ENST00000371953	NM_000314.4	55		3/9	1	2	FACETS	0.387	0.267	0.535	0.387	0.267	0.535	SUBCLONAL	1	TRUE	1	0.290375719282245	2		144	196	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910422	32910422	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507616	NA	P-0004735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	95	709	0	ENST00000380152.3:c.1933del	p.Arg645GlufsTer15	p.R645Efs*15	ENST00000380152		644	Aaa/aa	11/27	1	2	FACETS	0.619	0.55	0.693	0.619	0.55	0.693	SUBCLONAL	1	TRUE	1	0.290375719282245	2		709	1057	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576848	7576851	+	splice_donor_variant,intron_variant	Splice_Site	DEL	AGTA	AGTA	-	novel	NA	P-0004735-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	41	488	0	ENST00000269305.4:c.993+2_993+5del		p.X331_splice	ENST00000269305	NM_001126112.2	331			1	2	FACETS	0.536	0.446	0.636	0.536	0.446	0.636	SUBCLONAL	1	TRUE	1	0.290375719282245	2		488	527	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578206	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs886039484	NA	P-0004735-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	35	680	3	ENST00000269305.4:c.643A>G	p.Ser215Gly	p.S215G	ENST00000269305	NM_001126112.2	215	Agt/Ggt	6/11	0.787552822573947	1	FACETS	0.069	0.056	0.084	0.069	0.056	0.084	SUBCLONAL	1	TRUE	0	0.787552822573947	1		683	780	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94129019	94129019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004735-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	216	753	0	ENST00000369303.4:c.41G>A	p.Cys14Tyr	p.C14Y	ENST00000369303	NM_004440.3	14	tGc/tAc	1/17	0.785116168166074	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.787552822573947	1		753	326	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951092	17951092	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004735-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	524	552	0	ENST00000458235.1:c.1201C>G	p.Leu401Val	p.L401V	ENST00000458235	NM_000215.3	401	Ctc/Gtc	9/24	0.360852922614719	2	FACETS	1	0.997	1	0.688	0.664	0.712	INDETERMINATE	1	TRUE	0	0.787552822573947	2		552	967	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685242	89685284	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTTTTTGTTTGTTTGTTTTGTTTTAAGGTTTTTGGATTCAAA	GCTTTTTGTTTGTTTGTTTTGTTTTAAGGTTTTTGGATTCAAA	-	novel	NA	P-0004735-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	50	144	0	ENST00000371953.3:c.165-26_181del		p.X55_splice	ENST00000371953	NM_000314.4	55		3/9	0.787552822573947	1	FACETS	0.885	0.787	0.98	0.885	0.787	0.98	CLONAL	1	TRUE	0	0.787552822573947	1		144	87	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910422	32910422	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507616	NA	P-0004735-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	99	709	0	ENST00000380152.3:c.1933del	p.Arg645GlufsTer15	p.R645Efs*15	ENST00000380152		644	Aaa/aa	11/27	0.331807401019963	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.787552822573947	0		709	316	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576848	7576851	+	splice_donor_variant,intron_variant	Splice_Site	DEL	AGTA	AGTA	-	novel	NA	P-0004735-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	418	488	0	ENST00000269305.4:c.993+2_993+5del		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.787552822573947	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.787552822573947	1		488	598	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102033213	102034119	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGACCCCAGGAAGGCCATGCTGTCCCAGATGAACGTCACAGCCCCCACCAGTCCACCAGTGCAGCAGAATATGATGAACTCGGCTTCAGGTGAGTGAGACACTGTAATTACAGCACATGGAGTAATGCTTACGCATTGGTAAAAGTTGATGTGGAAAATAGTCATTACTCGTTTACAGAAACTGGGACATGGTGATGTTTATTGTCTCTCCAGTTTCATACAGAAGACATAGTCTATTTTAAAATAACGTAAGCTATATTATTGCCTTGTATAGTTGTTAACGCATAAGGGGGCCGATAACTGAAAGCCAGTGGTTCTTTAAGATTTGGTTCTGAAGCGGGTATCTCAAATTTGTAGTTCTGTTAATTTTGACGTATTTGGTTTTATTCTGCTGCTTTCTTGTGTCTCAGGTATTTGAGTTGAATTTACCCTCTTCCCTTTGTGGTTTGGATGGAAAGCCAAGCTATAGTGTTCTTATTTTTTATTATTATTATTTTTTTTTTCATTTTTTTTTTTTGCTATGGTGTTCTTAACCCAACTTTTAATGTGGTGTTATTCATTCTACTCTGAAAATATCTGGAAGGCAGTAACTTTTGTAAACCCAAAAGAATATTTCTTATTCCCAGGGCAAGCATGGATTATTAAACGCATCTTCACCTTTTTTACTAGAAGATAAACCTGAGTATAAATCTTTTTCTACCTCTTATTTGGCAATTTACTTGAATATGCAGTTTTTCTCATCTACATAATGGGGAGTAACAGTGCCCCTTATGATAGAAGGGAAGATATGAAAGGAAATAATACAATTTATATGAAGCCTCTAGTAATTACAGAGTAGGTACTAAGTGAAAGTTTAGCCCCTTCATCTTCCTTATCACATACTGTCTGGCGTCTTTCTCCTTTGTT	AGGACCCCAGGAAGGCCATGCTGTCCCAGATGAACGTCACAGCCCCCACCAGTCCACCAGTGCAGCAGAATATGATGAACTCGGCTTCAGGTGAGTGAGACACTGTAATTACAGCACATGGAGTAATGCTTACGCATTGGTAAAAGTTGATGTGGAAAATAGTCATTACTCGTTTACAGAAACTGGGACATGGTGATGTTTATTGTCTCTCCAGTTTCATACAGAAGACATAGTCTATTTTAAAATAACGTAAGCTATATTATTGCCTTGTATAGTTGTTAACGCATAAGGGGGCCGATAACTGAAAGCCAGTGGTTCTTTAAGATTTGGTTCTGAAGCGGGTATCTCAAATTTGTAGTTCTGTTAATTTTGACGTATTTGGTTTTATTCTGCTGCTTTCTTGTGTCTCAGGTATTTGAGTTGAATTTACCCTCTTCCCTTTGTGGTTTGGATGGAAAGCCAAGCTATAGTGTTCTTATTTTTTATTATTATTATTTTTTTTTTCATTTTTTTTTTTTGCTATGGTGTTCTTAACCCAACTTTTAATGTGGTGTTATTCATTCTACTCTGAAAATATCTGGAAGGCAGTAACTTTTGTAAACCCAAAAGAATATTTCTTATTCCCAGGGCAAGCATGGATTATTAAACGCATCTTCACCTTTTTTACTAGAAGATAAACCTGAGTATAAATCTTTTTCTACCTCTTATTTGGCAATTTACTTGAATATGCAGTTTTTCTCATCTACATAATGGGGAGTAACAGTGCCCCTTATGATAGAAGGGAAGATATGAAAGGAAATAATACAATTTATATGAAGCCTCTAGTAATTACAGAGTAGGTACTAAGTGAAAGTTTAGCCCCTTCATCTTCCTTATCACATACTGTCTGGCGTCTTTCTCCTTTGTT	-	novel	NA	P-0004735-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1270	76	578	0	ENST00000282441.5:c.602_688+820del		p.X201_splice	ENST00000282441	NM_001130145.2	201		3/9	0.787552822573947	4	FACETS	0.256	0.224	0.292	0.085	0.074	0.098	SUBCLONAL	1	TRUE	1	0.787552822573947	4		578	1346	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806623	1806623	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004735-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	470	898	0	ENST00000260795.2:c.1339G>C	p.Glu447Gln	p.E447Q	ENST00000260795		447	Gag/Cag	9/17	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.787552822573947	2		898	1169	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914438	32914440	+	missense_variant	Missense_Mutation	TNP	TGG	TGG	GGA	novel	NA	P-0004735-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	102	669	7	ENST00000380152.3:c.5946_5948delinsGGA	p.Ser1982_Gly1983delinsArgGlu	p.S1982_G1983delinsRE	ENST00000380152		1982	agTGGa/agGGAa	11/27	0.331807401019963	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.787552822573947	0		676	307	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916929	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519931	NA	P-0004841-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	93	426	0	ENST00000263967.3:c.316G>C	p.Gly106Arg	p.G106R	ENST00000263967	NM_006218.2	106	Ggc/Cgc	2/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.369342795539552	2		426	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876659675	NA	P-0004841-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	51	654	0	ENST00000269305.4:c.764T>G	p.Ile255Ser	p.I255S	ENST00000269305	NM_001126112.2	255	aTc/aGc	7/11	0.284647993379761	1	FACETS	0.801	0.686	0.926	0.801	0.686	0.926	CLONAL	1	TRUE	0	0.369342795539552	1		654	281	SUCCESS
AR	367	MSKCC	GRCh37	X	66905873	66905874	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAG	novel	NA	P-0004841-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	36	659	0	ENST00000374690.3:c.1794_1796dup	p.Ser598dup	p.S598dup	ENST00000374690	NM_000044.3	598	gcc/gcCAGc	3/8	0.197431545095359	0	FACETS	0.397	0.327	0.474			1	INDETERMINATE	1	TRUE	0	0.369342795539552	0		659	310	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916929	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519931	NA	P-0004841-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	87	426	0	ENST00000263967.3:c.316G>C	p.Gly106Arg	p.G106R	ENST00000263967	NM_006218.2	106	Ggc/Cgc	2/21	0.289584214902661	5	FACETS	1	0.945	1	0.733	0.653	0.817	CLONAL	2	FALSE	2	0.289584214902661	5		426	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876659675	NA	P-0004841-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	273	654	0	ENST00000269305.4:c.764T>G	p.Ile255Ser	p.I255S	ENST00000269305	NM_001126112.2	255	aTc/aGc	7/11	0.289584214902661	3	FACETS	0.971	0.912	1	0.971	0.912	1	CLONAL	2	FALSE	1	0.289584214902661	3		654	1111	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325634	87325634	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004841-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	65	435	0	ENST00000277120.3:c.511A>C	p.Thr171Pro	p.T171P	ENST00000277120		171	Act/Cct	6/19	0.175240412812137	3	FACETS	1	0.894	1	0.517	0.449	0.591	CLONAL	1	FALSE	1	0.289584214902661	3		435	497	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846398	128846398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879255280	NA	P-0005008-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	258	277	0	ENST00000249373.3:c.1234C>T	p.Leu412Phe	p.L412F	ENST00000249373	NM_005631.4	412	Ctc/Ttc	6/12	0.696642241665724	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.696642241665724	3		277	478	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0005242-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	1084	667	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.682206995243534	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.682206995243534	3		667	1407	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0005242-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	742	374	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.682206995243534	3	FACETS	0.956	0.934	0.978	0.956	0.934	0.978	CLONAL	3	TRUE	0	0.682206995243534	3		374	1017	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005242-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	375	652	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.682206995243534	2		652	1047	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255790	16255790	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005242-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	282	447	0	ENST00000375759.3:c.3055C>T	p.Gln1019Ter	p.Q1019*	ENST00000375759	NM_015001.2	1019	Cag/Tag	11/15	0.628779149199978	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.682206995243534	1		447	519	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105727	27105727	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772578230	NA	P-0005242-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	172	286	0	ENST00000324856.7:c.5338G>A	p.Glu1780Lys	p.E1780K	ENST00000324856	NM_006015.4	1780	Gaa/Aaa	20/20	1	2	FACETS	0.964	0.894	1	0.964	0.894	1	CLONAL	1	TRUE	1	0.682206995243534	2		286	523	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936379	49936379	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005242-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	742	734	0	ENST00000296474.3:c.1469C>A	p.Ser490Ter	p.S490*	ENST00000296474	NM_002447.2	490	tCa/tAa	3/20	0.682206995243534	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.682206995243534	2		734	1053	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178143	56178143	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005242-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	242	423	0	ENST00000399503.3:c.3116C>A	p.Ser1039Ter	p.S1039*	ENST00000399503	NM_005921.1	1039	tCa/tAa	14/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.682206995243534	2		423	686	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202720	133202720	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005242-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	200	580	0	ENST00000320574.5:c.6514G>C	p.Asp2172His	p.D2172H	ENST00000320574	NM_006231.2	2172	Gac/Cac	46/49	1	2	FACETS	0.802	0.746	0.86	0.802	0.746	0.86	CLONAL	1	TRUE	1	0.682206995243534	2		580	731	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237716	133237716	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005242-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	298	579	0	ENST00000320574.5:c.2899G>C	p.Glu967Gln	p.E967Q	ENST00000320574	NM_006231.2	967	Gag/Cag	25/49	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.682206995243534	2		579	871	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28901682	28901682	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005242-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	242	389	0	ENST00000282397.4:c.2713C>G	p.Leu905Val	p.L905V	ENST00000282397	NM_002019.4	905	Ctg/Gtg	20/30	1	2	FACETS	0.937	0.879	0.997	0.937	0.879	0.997	CLONAL	1	TRUE	1	0.682206995243534	2		389	757	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023895	27023895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005242-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	80	176	1	ENST00000324856.7:c.1001C>T	p.Ser334Leu	p.S334L	ENST00000324856	NM_006015.4	334	tCg/tTg	1/20	1	2	FACETS	0.8	0.712	0.893	0.8	0.712	0.893	SUBCLONAL	1	TRUE	1	0.682206995243534	2		177	293	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857532	68857532	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	C	novel	NA	P-0005242-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	204	434	0	ENST00000261769.5:c.2164+3A>C		p.X722_splice	ENST00000261769	NM_004360.3	722			0.682206995243534	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.682206995243534	1		434	375	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752931	42752931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005242-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	449	901	1	ENST00000222329.4:c.1333G>A	p.Asp445Asn	p.D445N	ENST00000222329	NM_006494.2	445	Gat/Aat	4/4	1	2	FACETS	0.926	0.883	0.969	0.926	0.883	0.969	CLONAL	1	TRUE	1	0.682206995243534	2		902	1422	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874386	151874386	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005242-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	463	394	0	ENST00000262189.6:c.8152G>A	p.Glu2718Lys	p.E2718K	ENST00000262189	NM_170606.2	2718	Gaa/Aaa	38/59	0.638591658714326	3	FACETS	0.95	0.912	0.988	0.95	0.912	0.988	CLONAL	2	TRUE	1	0.682206995243534	3		394	958	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0006795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	129	334	1	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.237780091370839	3	FACETS	0.811	0.74	0.886	0.811	0.74	0.886	CLONAL	2	TRUE	1	0.361708449492795	3		335	519	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215386	5215386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	51	1059	2	ENST00000357368.4:c.4232C>T	p.Ser1411Phe	p.S1411F	ENST00000357368	NM_002850.3	1411	tCc/tTc	28/38	1	2	FACETS	0.539	0.458	0.628	0.539	0.458	0.628	SUBCLONAL	1	TRUE	1	0.361708449492795	2		1061	523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578219	7578220	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	147	1182	0	ENST00000269305.4:c.629dup	p.Asn210LysfsTer6	p.N210Kfs*6	ENST00000269305	NM_001126112.2	210	aac/aaAc	6/11	0.348755204524852	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.361708449492795	1		1182	625	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	55	348	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.745671428174745	2		349	142	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0006947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	99	263	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.786	0.709	0.866	0.786	0.709	0.866	SUBCLONAL	1	TRUE	1	0.745671428174745	2		263	338	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791718	42791718	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1344635105	NA	P-0006947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	40	376	1	ENST00000575354.2:c.604C>T	p.Arg202Trp	p.R202W	ENST00000575354	NM_015125.3	202	Cgg/Tgg	5/20	0.745671428174745	1	FACETS	0.265	0.221	0.313	0.265	0.221	0.313	SUBCLONAL	1	TRUE	0	0.745671428174745	1		377	254	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791826	42791826	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	63	338	0	ENST00000575354.2:c.712T>A	p.Trp238Arg	p.W238R	ENST00000575354	NM_015125.3	238	Tgg/Agg	5/20	0.745671428174745	1	FACETS	0.351	0.306	0.399	0.351	0.306	0.399	SUBCLONAL	1	TRUE	0	0.745671428174745	1		338	302	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414939	78414967	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCTGACCACCTGGAGGAGCCCCAGTCG	TGGCTGACCACCTGGAGGAGCCCCAGTCG	-	novel	NA	P-0006947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	122	432	1	ENST00000370768.2:c.1799_1827del	p.Pro600ArgfsTer3	p.P600Rfs*3	ENST00000370768	NM_003902.3	600	cCGACTGGGGCTCCTCCAGGTGGTCAGCCA/c	19/20	0.745671428174745	1	FACETS	0.866	0.801	0.931	0.866	0.801	0.931	CLONAL	1	TRUE	0	0.745671428174745	1		433	237	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795608	42795609	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1555770200	NA	P-0006947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	40	502	1	ENST00000575354.2:c.2694dup	p.Lys899GlnfsTer32	p.K899Qfs*32	ENST00000575354	NM_015125.3	896	-/C	10/20	0.745671428174745	1	FACETS	0.265	0.221	0.313	0.265	0.221	0.313	SUBCLONAL	1	TRUE	0	0.745671428174745	1		503	254	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589619	67589621	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0006947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	82	317	0	ENST00000274335.5:c.1382_1384del	p.Arg461_Glu462delinsGln	p.R461_E462delinsQ	ENST00000274335		461	cGAGaa/caa	10/15	1	2	FACETS	0.797	0.711	0.886	0.797	0.711	0.886	SUBCLONAL	1	TRUE	1	0.745671428174745	2		317	276	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007791-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	49	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		539	949	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439652	51439653	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCAT	novel	NA	P-0008085-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	34	346	0	ENST00000262662.1:c.222_225dup	p.Asp76SerfsTer2	p.D76Sfs*2	ENST00000262662		73	gtc/gTCATtc	4/4	0.706739236847786	1	FACETS	0.13	0.106	0.158	0.13	0.106	0.158	SUBCLONAL	1	TRUE	0	0.706739236847786	1		346	477	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	676	602	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.726291472290201	4	FACETS	1	0.987	1			1	CLONAL	2	TRUE	NA	0.741313065814196	4		602	1523	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056026	26056026	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs928708568	NA	P-0008574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	290	433	0	ENST00000343677.2:c.631A>C	p.Lys211Gln	p.K211Q	ENST00000343677	NM_005319.3	211	Aag/Cag	1/1	0.729757585779221	2	FACETS	0.912	0.875	0.948	0.912	0.875	0.948	CLONAL	2	TRUE	0	0.741313065814196	2		433	429	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609685	81609685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	310	746	0	ENST00000298171.2:c.1283C>T	p.Ala428Val	p.A428V	ENST00000298171	NM_000369.2	428	gCt/gTt	10/10	1	2	FACETS	0.949	0.898	1	0.949	0.898	1	CLONAL	1	TRUE	1	0.741313065814196	2		746	881	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664915	138664915	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	67	413	0	ENST00000330315.3:c.650C>A	p.Ser217Tyr	p.S217Y	ENST00000330315	NM_023067.3	217	tCc/tAc	1/1	1	2	FACETS	0.35	0.305	0.4	0.35	0.305	0.4	SUBCLONAL	1	TRUE	1	0.741313065814196	2		413	516	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0010169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	55	544	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.801	0.682	0.931	0.801	0.682	0.931	CLONAL	1	TRUE	1	0.13	2		544	1057	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167817	56167817	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	52	434	0	ENST00000399503.3:c.1382A>G	p.Asp461Gly	p.D461G	ENST00000399503	NM_005921.1	461	gAc/gGc	7/20	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.13	2		434	739	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339551	81339551	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	60	468	0	ENST00000222390.5:c.1453A>T	p.Ile485Leu	p.I485L	ENST00000222390	NM_000601.4	485	Ata/Tta	13/18	1	2	FACETS	0.859	0.738	0.993	0.859	0.738	0.993	CLONAL	1	TRUE	1	0.13	2		468	1074	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986861	36986877	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCGGGCACCCGGTGC	CTGCGGGCACCCGGTGC	-	novel	NA	P-0010169-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	33	67	0	ENST00000354822.5:c.812_828del	p.Gly271AlafsTer162	p.G271Afs*162	ENST00000354822	NM_001079668.2	271	gGCACCGGGTGCCCGCAG/g	3/3	1	2	FACETS	1	0.898	1	1	0.972	1	CLONAL	3	TRUE	1	0.13	2		67	150	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0010169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	95	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.259171568598144	1	FACETS	0.891	0.801	0.986	1	0.986	1	CLONAL	2	TRUE	0	0.259171568598144	1		311	358	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141615	202141616	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	48	266	0	ENST00000358485.4:c.903_904insT	p.Asn302Ter	p.N302*	ENST00000358485	NM_001080125.1	301	-/T	7/9	1	2	FACETS	0.703	0.594	0.823	0.703	0.594	0.823	SUBCLONAL	1	TRUE	1	0.259171568598144	2		266	527	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141623	202141623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	45	275	0	ENST00000358485.4:c.911C>T	p.Ala304Val	p.A304V	ENST00000358485	NM_001080125.1	304	gCa/gTa	7/9	1	2	FACETS	0.663	0.557	0.78	0.663	0.557	0.78	SUBCLONAL	1	TRUE	1	0.259171568598144	2		275	524	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818753	32818753	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1425932292	NA	P-0010169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	112	523	0	ENST00000354258.4:c.1198C>T	p.Leu400Phe	p.L400F	ENST00000354258	NM_000593.5	400	Ctt/Ttt	4/11	1	2	FACETS	0.924	0.83	1	0.924	0.83	1	CLONAL	1	TRUE	1	0.259171568598144	2		523	935	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0010640-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	283	600	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.388095379471074	2	FACETS	0.9	0.85	0.95	0.9	0.85	0.95	CLONAL	2	TRUE	0	0.417754737260643	2		601	753	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0010640-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	293	653	2	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.417754737260643	6	FACETS	1	0.95	1	0.674	0.634	0.716	CLONAL	2	TRUE	3	0.417754737260643	6		655	1273	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242486	+	inframe_deletion	In_Frame_Del	DEL	TTAAGAGAAGCAACATCT	TTAAGAGAAGCAACATCT	-	rs121913440	NA	P-0010640-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	275	575	0	ENST00000275493.2:c.2239_2256del	p.Leu747_Ser752del	p.L747_S752del	ENST00000275493	NM_005228.3	747	TTAAGAGAAGCAACATCT/-	19/28	0.417754737260643	6	FACETS	1	0.975	1	0.714	0.67	0.759	CLONAL	2	TRUE	3	0.417754737260643	6		575	1128	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984952	101984952	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1384754271	NA	P-0010640-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	137	330	0	ENST00000282441.5:c.399G>T	p.Gln133His	p.Q133H	ENST00000282441	NM_001130145.2	133	caG/caT	2/9	0.417754737260643	5	FACETS	0.966	0.883	1	0.644	0.589	0.702	CLONAL	2	TRUE	2	0.417754737260643	5		330	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0011252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	319	766	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.70586797913758	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.727662538647264	1		767	529	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0011252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	479	530	2	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.727662538647264	2		532	1207	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021817	71021817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs797045586	NA	P-0011252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	359	308	0	ENST00000318789.4:c.1541G>A	p.Arg514His	p.R514H	ENST00000318789	NM_032682.5	514	cGt/cAt	18/21	0.727662538647264	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.727662538647264	1		308	624	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953760	48953760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913302	NA	P-0011252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	299	252	0	ENST00000267163.4:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000267163	NM_000321.2	455	Cga/Tga	14/27	0.713723449297806	1	FACETS	0.994	0.949	1	0.994	0.949	1	CLONAL	1	TRUE	0	0.727662538647264	1		252	526	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451406	187451406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779268890	NA	P-0011252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	418	409	4	ENST00000232014.4:c.76C>T	p.Arg26Trp	p.R26W	ENST00000232014	NM_001130845.1	26	Cgg/Tgg	3/10	0.727662538647264	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.727662538647264	1		413	712	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940000	76940000	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1311466929	NA	P-0011252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	567	520	1	ENST00000373344.5:c.748C>T	p.Arg250Ter	p.R250*	ENST00000373344	NM_000489.3	250	Cga/Tga	9/35	0.70586797913758	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.727662538647264	1		521	922	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987067	36987067	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	134	336	0	ENST00000354822.5:c.622C>T	p.Arg208Ter	p.R208*	ENST00000354822	NM_001079668.2	208	Cga/Tga	3/3	0.624400865733631	1	FACETS	0.528	0.483	0.574	0.528	0.483	0.574	SUBCLONAL	1	TRUE	0	0.727662538647264	1		336	444	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89335023	89335023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	151	153	0	ENST00000301030.4:c.7855G>A	p.Val2619Met	p.V2619M	ENST00000301030	NM_001256183.1	2619	Gtg/Atg	13/13	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.727662538647264	2		153	409	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796880	45796880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1441591597	NA	P-0011252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	153	335	0	ENST00000450313.1:c.1450G>A	p.Ala484Thr	p.A484T	ENST00000450313	NM_012222.2	484	Gca/Aca	14/16	NA	2	FACETS	0.509	0.466	0.554			1	INDETERMINATE	1	TRUE	NA	0.727662538647264	2		335	826	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054978	176054978	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	471	482	0	ENST00000367669.3:c.1075C>T	p.Arg359Ter	p.R359*	ENST00000367669	NM_022457.5	359	Cga/Tga	10/20	1	2	FACETS	0.918	0.877	0.96	0.918	0.877	0.96	CLONAL	1	TRUE	1	0.727662538647264	2		482	1410	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643617	52643617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199976998	NA	P-0011252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	343	321	0	ENST00000394830.3:c.2279G>A	p.Arg760His	p.R760H	ENST00000394830	NM_018313.4	760	cGc/cAc	17/30	1	2	FACETS	0.94	0.891	0.989	0.94	0.891	0.989	CLONAL	1	TRUE	1	0.727662538647264	2		321	1003	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518087	187518087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767899323	NA	P-0011252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	247	561	2	ENST00000441802.2:c.12607C>T	p.Arg4203Cys	p.R4203C	ENST00000441802	NM_005245.3	4203	Cgt/Tgt	25/27	0.727662538647264	1	FACETS	0.701	0.66	0.743	0.701	0.66	0.743	SUBCLONAL	1	TRUE	0	0.727662538647264	1		563	616	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549395	187549395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768661863	NA	P-0011252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	296	525	0	ENST00000441802.2:c.4723G>A	p.Ala1575Thr	p.A1575T	ENST00000441802	NM_005245.3	1575	Gca/Aca	9/27	0.727662538647264	1	FACETS	0.825	0.784	0.867	0.825	0.784	0.867	CLONAL	1	TRUE	0	0.727662538647264	1		525	627	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293754	1293754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	114	509	0	ENST00000310581.5:c.1247G>A	p.Arg416Gln	p.R416Q	ENST00000310581	NM_198253.2	416	cGa/cAa	2/16	1	2	FACETS	0.335	0.301	0.371	0.335	0.301	0.371	SUBCLONAL	1	TRUE	1	0.727662538647264	2		509	936	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659299	86659299	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771416114	NA	P-0011252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	186	392	0	ENST00000274376.6:c.1588G>A	p.Val530Ile	p.V530I	ENST00000274376	NM_002890.2	530	Gtt/Att	11/25	0.624400865733631	1	FACETS	0.435	0.402	0.468	0.435	0.402	0.468	SUBCLONAL	1	TRUE	0	0.727662538647264	1		392	748	SUCCESS
APC	324	MSKCC	GRCh37	5	112164604	112164604	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	317	210	0	ENST00000257430.4:c.1678A>G	p.Lys560Glu	p.K560E	ENST00000257430	NM_000038.5	560	Aaa/Gaa	14/16	NA	2	FACETS	1	0.952	1			1	INDETERMINATE	1	TRUE	NA	0.727662538647264	2		210	867	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481461	20481461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	322	295	0	ENST00000346618.3:c.530C>T	p.Thr177Met	p.T177M	ENST00000346618	NM_001949.4	177	aCg/aTg	3/7	0.727662538647264	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.727662538647264	1		295	561	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912306	29912306	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761593088	NA	P-0011252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	242	432	0	ENST00000376809.5:c.925G>A	p.Val309Met	p.V309M	ENST00000376809	NM_002116.7	309	Gtg/Atg	5/8	0.727662538647264	1	FACETS	0.573	0.538	0.61	0.573	0.538	0.61	SUBCLONAL	1	TRUE	0	0.727662538647264	1		432	738	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987215	2987215	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	259	322	0	ENST00000396946.4:c.214C>T	p.Arg72Ter	p.R72*	ENST00000396946	NM_032415.4	72	Cga/Tga	3/25	0.70586797913758	1	FACETS	0.943	0.896	0.991	0.943	0.896	0.991	CLONAL	1	TRUE	0	0.727662538647264	1		322	480	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238417	98238417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137903539	NA	P-0011252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	323	369	0	ENST00000331920.6:c.1627C>T	p.Arg543Cys	p.R543C	ENST00000331920	NM_000264.3	543	Cgc/Tgc	12/24	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.727662538647264	2		369	722	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760865	133760865	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	206	545	0	ENST00000318560.5:c.3188T>A	p.Leu1063His	p.L1063H	ENST00000318560	NM_005157.4	1063	cTc/cAc	11/11	NA	2	FACETS	0.439	0.406	0.473			1	INDETERMINATE	1	TRUE	NA	0.727662538647264	2		545	1290	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61213503	61213503	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768954974	NA	P-0011252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	171	302	0	ENST00000301761.2:c.461G>A	p.Arg154His	p.R154H	ENST00000301761	NM_017841.2	154	cGt/cAt	4/4	1	2	FACETS	0.472	0.434	0.512	0.472	0.434	0.512	SUBCLONAL	1	TRUE	1	0.727662538647264	2		302	995	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427360	49427360	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757243984	NA	P-0011252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	258	394	1	ENST00000301067.7:c.11128G>A	p.Gly3710Arg	p.G3710R	ENST00000301067	NM_003482.3	3710	Gga/Aga	39/54	1	2	FACETS	0.883	0.83	0.937	0.883	0.83	0.937	CLONAL	1	TRUE	1	0.727662538647264	2		395	803	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88671959	88671959	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767919095	NA	P-0011252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	424	284	0	ENST00000360948.2:c.1211C>T	p.Thr404Met	p.T404M	ENST00000360948	NM_001012338.2	404	aCg/aTg	10/19	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	1	TRUE	NA	0.727662538647264	2		284	835	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343506	343506	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141807086	NA	P-0011252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	415	537	1	ENST00000262320.3:c.2168G>A	p.Arg723Gln	p.R723Q	ENST00000262320	NM_003502.3	723	cGa/cAa	8/11	NA	2	FACETS	0.982	0.936	1			1	INDETERMINATE	1	TRUE	NA	0.727662538647264	2		538	1162	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029441	16029441	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1237	297	482	0	ENST00000268712.3:c.1589A>T	p.Glu530Val	p.E530V	ENST00000268712	NM_006311.3	530	gAa/gTa	15/46	1	2	FACETS	0.532	0.5	0.566	0.532	0.5	0.566	SUBCLONAL	1	TRUE	1	0.727662538647264	2		482	1534	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554707	63554707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776778201	NA	P-0011252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	144	253	1	ENST00000307078.5:c.32C>T	p.Pro11Leu	p.P11L	ENST00000307078	NM_004655.3	11	cCg/cTg	2/11	1	2	FACETS	0.426	0.388	0.466	0.426	0.388	0.466	SUBCLONAL	1	TRUE	1	0.727662538647264	2		254	929	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119842	70119842	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	470	472	1	ENST00000245479.2:c.844G>A	p.Val282Ile	p.V282I	ENST00000245479	NM_000346.3	282	Gtc/Atc	3/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.727662538647264	2		473	1241	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78931495	78931495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	210	468	0	ENST00000306801.3:c.3442C>T	p.Arg1148Trp	p.R1148W	ENST00000306801	NM_020761.2	1148	Cgg/Tgg	29/34	1	2	FACETS	0.516	0.478	0.555	0.516	0.478	0.555	SUBCLONAL	1	TRUE	1	0.727662538647264	2		468	1119	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52725413	52725413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758740333	NA	P-0011252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	463	459	1	ENST00000322088.6:c.1580G>A	p.Arg527His	p.R527H	ENST00000322088	NM_014225.5	527	cGc/cAc	13/15	0.414512297972446	1	FACETS	0.789	0.757	0.822	0.789	0.757	0.822	INDETERMINATE	1	TRUE	0	0.727662538647264	1		460	1026	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513268	44513268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761081553	NA	P-0011252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	200	450	0	ENST00000291552.4:c.667G>A	p.Gly223Arg	p.G223R	ENST00000291552	NM_006758.2	223	Gga/Aga	8/8	0.337372509936181	1	FACETS	0.349	0.323	0.376	0.349	0.323	0.376	INDETERMINATE	1	TRUE	0	0.727662538647264	1		450	1003	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551951	150551952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs750805885	NA	P-0011252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	163	424	0	ENST00000369026.2:c.55dup	p.Ala19GlyfsTer91	p.A19Gfs*91	ENST00000369026	NM_021960.4	19	gcc/gGcc	1/3	1	2	FACETS	0.357	0.327	0.389	0.357	0.327	0.389	SUBCLONAL	1	TRUE	1	0.727662538647264	2		424	1255	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0011252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	338	766	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.426346415216563	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.431092653845691	2		767	772	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643348	52643348	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	80	330	0	ENST00000394830.3:c.2548C>T	p.Arg850Ter	p.R850*	ENST00000394830	NM_018313.4	850	Cga/Tga	17/30	0.431092653845691	2	FACETS	0.987	0.889	1	0.987	0.889	1	CLONAL	2	TRUE	0	0.431092653845691	2		330	188	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0011252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	44	209	1	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	0.425023371236215	2	FACETS	1	0.959	1	0.704	0.602	0.811	CLONAL	1	TRUE	0	0.431092653845691	2		210	145	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023060	27023060	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	114	103	0	ENST00000324856.7:c.166C>T	p.Gln56Ter	p.Q56*	ENST00000324856	NM_006015.4	56	Cag/Tag	1/20	0.351532115070173	3	FACETS	1	0.925	1	1	0.925	1	CLONAL	3	TRUE	0	0.431092653845691	3		103	214	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0011252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	62	321	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.425023371236215	2	FACETS	0.831	0.733	0.933	0.831	0.733	0.933	CLONAL	2	TRUE	0	0.431092653845691	2		321	173	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646866	37646866	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141353560	NA	P-0011252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	159	509	1	ENST00000447079.4:c.1988G>A	p.Arg663His	p.R663H	ENST00000447079	NM_015083.1	663	cGt/cAt	3/14	0.426346415216563	2	FACETS	0.878	0.814	0.944	0.878	0.814	0.944	CLONAL	2	TRUE	0	0.431092653845691	2		510	420	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654856	29654856	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1049849034	NA	P-0011252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	82	220	0	ENST00000356175.3:c.5545C>T	p.Arg1849Trp	p.R1849W	ENST00000356175	NM_000267.3	1849	Cgg/Tgg	37/57	0.426346415216563	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	0	0.431092653845691	2		220	181	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219839	133219839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766511597	NA	P-0011252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	256	713	1	ENST00000320574.5:c.4522C>T	p.Arg1508Cys	p.R1508C	ENST00000320574	NM_006231.2	1508	Cgc/Tgc	35/49	0.426346415216563	2	FACETS	0.949	0.895	1	0.949	0.895	1	CLONAL	2	TRUE	0	0.431092653845691	2		714	626	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427369	49427369	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1565779294	NA	P-0011252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	254	810	0	ENST00000301067.7:c.11119C>T	p.Arg3707Ter	p.R3707*	ENST00000301067	NM_003482.3	3707	Cga/Tga	39/54	0.426346415216563	2	FACETS	0.938	0.885	0.993	0.938	0.885	0.993	CLONAL	2	TRUE	0	0.431092653845691	2		810	628	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783697	50783697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs912795080	NA	P-0011252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	93	494	3	ENST00000398568.2:c.88G>A	p.Val30Ile	p.V30I	ENST00000398568	NM_001042412.1	30	Gtt/Att	3/18	0.153915419989237	5	FACETS	0.927	0.831	1	0.618	0.554	0.686	INDETERMINATE	2	TRUE	2	0.431092653845691	5		497	383	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805298	89805298	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145148206	NA	P-0011252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	57	564	0	ENST00000389301.3:c.4252G>A	p.Val1418Met	p.V1418M	ENST00000389301	NM_000135.2	1418	Gtg/Atg	42/43	0.153915419989237	5	FACETS	0.579	0.496	0.67	0.193	0.165	0.224	INDETERMINATE	1	TRUE	2	0.431092653845691	5		564	752	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280136	142280136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369434236	NA	P-0011252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	118	443	0	ENST00000350721.4:c.1298G>A	p.Arg433His	p.R433H	ENST00000350721	NM_001184.3	433	cGt/cAt	5/47	0.431092653845691	2	FACETS	0.999	0.917	1	0.999	0.917	1	CLONAL	2	TRUE	0	0.431092653845691	2		443	274	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900081	151900081	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0011252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	86	327	0	ENST00000262189.6:c.4030del	p.Ile1344Ter	p.I1344*	ENST00000262189	NM_170606.2	1344	Ata/ta	26/59	0.34646625190577	4	FACETS	0.878	0.785	0.977	0.878	0.785	0.977	CLONAL	2	TRUE	2	0.431092653845691	4		327	325	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164466	36164466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	23	455	0	ENST00000300305.3:c.1409C>T	p.Ala470Val	p.A470V	ENST00000300305		470	gCg/gTg	8/8	0.431092653845691	2	FACETS	0.244	0.189	0.307	0.122	0.094	0.154	SUBCLONAL	1	TRUE	0	0.431092653845691	2		455	438	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028600	42028600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	171	585	0	ENST00000219905.7:c.4138C>T	p.Arg1380Ter	p.R1380*	ENST00000219905	NM_001164273.1	1380	Cga/Tga	13/24	0.425023371236215	2	FACETS	0.855	0.794	0.917	0.855	0.794	0.917	CLONAL	2	TRUE	0	0.431092653845691	2		585	464	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639657	3639657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1394177026	NA	P-0011252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	318	931	2	ENST00000294008.3:c.3982G>A	p.Val1328Ile	p.V1328I	ENST00000294008	NM_032444.2	1328	Gtc/Atc	12/15	0.153915419989237	5	FACETS	1	0.982	1	0.73	0.689	0.771	INDETERMINATE	2	TRUE	2	0.431092653845691	5		933	1110	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550541	29550541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782592	NA	P-0011252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	53	227	0	ENST00000356175.3:c.1801C>T	p.Arg601Trp	p.R601W	ENST00000356175	NM_000267.3	601	Cgg/Tgg	16/57	0.426346415216563	2	FACETS	1	0.966	1	0.703	0.61	0.8	CLONAL	1	TRUE	0	0.431092653845691	2		227	175	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543576	148543576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141583753	NA	P-0011252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	95	365	0	ENST00000320356.2:c.232C>T	p.Arg78Cys	p.R78C	ENST00000320356	NM_004456.4	78	Cgc/Tgc	3/20	0.34646625190577	4	FACETS	0.859	0.772	0.951	0.859	0.772	0.951	CLONAL	2	TRUE	2	0.431092653845691	4		365	367	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663346	67663346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771793540	NA	P-0011252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	76	337	0	ENST00000264010.4:c.1747G>A	p.Val583Ile	p.V583I	ENST00000264010	NM_006565.3	583	Gta/Ata	10/12	0.153915419989237	5	FACETS	0.762	0.672	0.857	0.508	0.448	0.572	INDETERMINATE	2	TRUE	2	0.431092653845691	5		337	381	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396962	396962	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1238203898	NA	P-0011252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	262	832	1	ENST00000262320.3:c.64C>T	p.Arg22Ter	p.R22*	ENST00000262320	NM_003502.3	22	Cga/Tga	2/11	0.153915419989237	5	FACETS	0.98	0.919	1	0.653	0.613	0.695	INDETERMINATE	2	TRUE	2	0.431092653845691	5		833	1021	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015317	176015317	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	36	221	0	ENST00000367669.3:c.1421G>T	p.Ser474Ile	p.S474I	ENST00000367669	NM_022457.5	474	aGc/aTc	12/20	0.431092653845691	2	FACETS	1	0.92	1	0.588	0.492	0.692	CLONAL	1	TRUE	0	0.431092653845691	2		221	142	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347927	347963	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCGTCCAGCTTCGCCCCTGACTTGGGTACGTGCTT	CCGCGTCCAGCTTCGCCCCTGACTTGGGTACGTGCTT	-	novel	NA	P-0011252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	264	1107	0	ENST00000262320.3:c.1543_1579del	p.Lys515ProfsTer178	p.K515Pfs*178	ENST00000262320	NM_003502.3	515	AAGCACGTACCCAAGTCAGGGGCGAAGCTGGACGCGGcc/cc	6/11	0.153915419989237	5	FACETS	0.923	0.866	0.983	0.616	0.577	0.656	INDETERMINATE	2	TRUE	2	0.431092653845691	5		1107	1092	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821286	72821286	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	138	545	0	ENST00000268489.5:c.10889del	p.Pro3630LeufsTer64	p.P3630Lfs*64	ENST00000268489	NM_006885.3	3630	cCt/ct	10/10	0.153915419989237	5	FACETS	0.837	0.764	0.913	0.558	0.509	0.609	INDETERMINATE	2	TRUE	2	0.431092653845691	5		545	630	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832064	72832064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201514050	NA	P-0011252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	144	561	1	ENST00000268489.5:c.4517C>T	p.Thr1506Met	p.T1506M	ENST00000268489	NM_006885.3	1506	aCg/aTg	9/10	0.153915419989237	5	FACETS	0.891	0.816	0.97	0.594	0.544	0.647	INDETERMINATE	2	TRUE	2	0.431092653845691	5		562	617	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490474	20490474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	211	572	0	ENST00000346618.3:c.1211C>T	p.Ala404Val	p.A404V	ENST00000346618	NM_001949.4	404	gCc/gTc	7/7	0.431092653845691	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.431092653845691	2		572	474	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27228230	27228230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536255448	NA	P-0011252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	139	466	0	ENST00000380036.4:c.3227G>A	p.Arg1076Gln	p.R1076Q	ENST00000380036	NM_000459.3	1076	cGg/cAg	22/23	0.425023371236215	2	FACETS	0.888	0.819	0.959	0.888	0.819	0.959	CLONAL	2	TRUE	0	0.431092653845691	2		466	363	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396208	139396208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772843787	NA	P-0011252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	306	856	3	ENST00000277541.6:c.5630G>A	p.Arg1877His	p.R1877H	ENST00000277541	NM_017617.3	1877	cGc/cAc	30/34	0.425023371236215	2	FACETS	0.927	0.878	0.976	0.927	0.878	0.976	CLONAL	2	TRUE	0	0.431092653845691	2		859	766	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	197	637	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.549801674267565	2		638	657	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	45	607	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.279	0.234	0.329	0.279	0.234	0.329	SUBCLONAL	1	TRUE	1	0.549801674267565	2		607	586	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	149	368	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.549801674267565	2		371	433	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	144	554	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.549801674267565	2		554	436	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	165	542	5	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.549801674267565	2		547	523	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	133	640	3	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.549801674267565	2		643	481	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	157	456	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.549801674267565	2		461	480	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	148	693	4	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.877	0.804	0.953	0.877	0.804	0.953	CLONAL	1	TRUE	1	0.549801674267565	2		697	614	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1684348	1684353	+	inframe_deletion	In_Frame_Del	DEL	CCTCCT	CCTCCT	-	rs71578334	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	127	700	2	ENST00000378625.1:c.1766_1771del	p.Glu589_Glu590del	p.E589_E590del	ENST00000378625	NM_001198994.1	589	gAGGAGGgc/ggc	14/14	1	2	FACETS	0.78	0.709	0.855	0.78	0.709	0.855	SUBCLONAL	1	TRUE	1	0.549801674267565	2		702	592	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106805	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	138	727	0	ENST00000324856.7:c.6415_6416insA	p.Pro2139HisfsTer11	p.P2139Hfs*11	ENST00000324856	NM_006015.4	2139	ccc/cAcc	20/20	1	2	FACETS	0.804	0.734	0.878	0.804	0.734	0.878	CLONAL	1	TRUE	1	0.549801674267565	2		727	624	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599271	28599271	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs770146088	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	219	686	2	ENST00000253063.3:c.722del	p.Pro241GlnfsTer6	p.P241Qfs*6	ENST00000253063	NM_031459.4	239	agC/ag	5/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.549801674267565	2		688	637	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809765	36809765	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	205	601	0	ENST00000373129.3:c.840G>T	p.Gln280His	p.Q280H	ENST00000373129	NM_032017.1	280	caG/caT	9/12	1	2	FACETS	0.797	0.747	0.847	1	0.993	1	SUBCLONAL	2	TRUE	1	0.549801674267565	2		601	468	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736511	85736511	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs387906351	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	172	465	5	ENST00000370580.1:c.136del	p.Ile46TyrfsTer24	p.I46Yfs*24	ENST00000370580	NM_003921.4	46	Ata/ta	2/3	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.549801674267565	2		470	480	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458869	120458869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755184344	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	196	723	0	ENST00000256646.2:c.6476C>T	p.Thr2159Met	p.T2159M	ENST00000256646	NM_024408.3	2159	aCg/aTg	34/34	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.549801674267565	2		723	569	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874250	155874250	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	188	572	0	ENST00000368323.3:c.281A>T	p.Glu94Val	p.E94V	ENST00000368323	NM_006912.5	94	gAa/gTa	5/6	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.549801674267565	2		572	604	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375060	104375060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137880855	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	205	529	0	ENST00000369902.3:c.1058C>T	p.Thr353Met	p.T353M	ENST00000369902	NM_016169.3	353	aCg/aTg	9/12	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.549801674267565	2		529	540	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741663	17741663	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	207	677	0	ENST00000250003.3:c.334A>G	p.Lys112Glu	p.K112E	ENST00000250003	NM_002478.4	112	Aag/Gag	1/3	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.549801674267565	2		677	574	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141982	108141982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	148	368	0	ENST00000278616.4:c.2926G>A	p.Val976Met	p.V976M	ENST00000278616	NM_000051.3	976	Gtg/Atg	20/63	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.549801674267565	2		368	394	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	227	782	2	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.549801674267565	2		784	682	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	265	803	1	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.785	0.742	0.828	1	0.994	1	SUBCLONAL	2	TRUE	1	0.549801674267565	2		804	614	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434525	49434525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764884530	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	143	775	0	ENST00000301067.7:c.7028C>T	p.Pro2343Leu	p.P2343L	ENST00000301067	NM_003482.3	2343	cCg/cTg	31/54	1	2	FACETS	0.876	0.802	0.953	0.876	0.802	0.953	CLONAL	1	TRUE	1	0.549801674267565	2		775	594	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437701	49437701	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555194045	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	240	739	0	ENST00000301067.7:c.5269C>T	p.Arg1757Ter	p.R1757*	ENST00000301067	NM_003482.3	1757	Cga/Tga	22/54	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.549801674267565	2		739	671	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444809	49444809	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	210	802	0	ENST00000301067.7:c.2657del	p.Pro886LeufsTer44	p.P886Lfs*44	ENST00000301067	NM_003482.3	886	cCt/ct	10/54	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.549801674267565	2		802	688	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445511	49445511	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776778856	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	184	651	0	ENST00000301067.7:c.1955G>A	p.Arg652His	p.R652H	ENST00000301067	NM_003482.3	652	cGc/cAc	10/54	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.549801674267565	2		651	595	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495375	56495377	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs780883720	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	193	658	0	ENST00000267101.3:c.3573_3575del	p.Glu1191del	p.E1191del	ENST00000267101	NM_001982.3	1189	GAA/-	28/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.549801674267565	2		658	650	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244124	133244124	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794759	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	185	545	0	ENST00000320574.5:c.2284C>T	p.Arg762Trp	p.R762W	ENST00000320574	NM_006231.2	762	Cgg/Tgg	20/49	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.549801674267565	2		545	541	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066937	30066937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771413120	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	38	409	0	ENST00000331968.5:c.2194C>T	p.Arg732Trp	p.R732W	ENST00000331968	NM_002742.2	732	Cgg/Tgg	16/18	1	2	FACETS	0.308	0.254	0.368	0.308	0.254	0.368	SUBCLONAL	1	TRUE	1	0.549801674267565	2		409	449	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059393	42059393	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747023024	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	285	643	0	ENST00000219905.7:c.9113G>A	p.Arg3038Gln	p.R3038Q	ENST00000219905	NM_001164273.1	3038	cGg/cAg	24/24	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.549801674267565	2		643	755	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112532	2112532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202187148	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	34	651	0	ENST00000219476.3:c.1292C>T	p.Ala431Val	p.A431V	ENST00000219476	NM_000548.3	431	gCg/gTg	13/42	1	2	FACETS	0.232	0.189	0.28	0.232	0.189	0.28	SUBCLONAL	1	TRUE	1	0.549801674267565	2		651	534	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124201	2124201	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs767252128	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	34	623	0	ENST00000219476.3:c.2356C>T	p.Arg786Cys	p.R786C	ENST00000219476	NM_000548.3	786	Cgc/Tgc	22/42	1	2	FACETS	0.219	0.178	0.265	0.219	0.178	0.265	SUBCLONAL	1	TRUE	1	0.549801674267565	2		623	565	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640611	3640611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868176090	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	186	757	0	ENST00000294008.3:c.3028G>A	p.Ala1010Thr	p.A1010T	ENST00000294008	NM_032444.2	1010	Gct/Act	12/15	1	2	FACETS	0.924	0.856	0.995	0.924	0.856	0.995	CLONAL	1	TRUE	1	0.549801674267565	2		757	732	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650719	67650719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1131691283	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	239	537	0	ENST00000264010.4:c.1024C>T	p.Arg342Cys	p.R342C	ENST00000264010	NM_006565.3	342	Cgt/Tgt	5/12	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.549801674267565	2		537	648	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822058	72822058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1445731408	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	262	789	0	ENST00000268489.5:c.10117G>A	p.Glu3373Lys	p.E3373K	ENST00000268489	NM_006885.3	3373	Gag/Aag	10/10	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.549801674267565	2		789	644	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16056703	16056704	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	90	188	0	ENST00000268712.3:c.738dup	p.Ala247SerfsTer6	p.A247Sfs*6	ENST00000268712	NM_006311.3	246	-/A	7/46	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.549801674267565	2		188	259	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322710	30322710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761306912	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	140	394	1	ENST00000322652.5:c.1723C>T	p.Arg575Cys	p.R575C	ENST00000322652	NM_015355.2	575	Cgt/Tgt	14/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.549801674267565	2		395	401	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883774	37883774	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	249	746	2	ENST00000269571.5:c.3391del	p.Leu1131Ter	p.L1131*	ENST00000269571		1129	gCc/gc	26/27	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.549801674267565	2		748	688	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865371	40865371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1017280875	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	182	547	0	ENST00000428826.2:c.1060C>T	p.Arg354Cys	p.R354C	ENST00000428826		354	Cgc/Tgc	11/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.549801674267565	2		547	584	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740357	58740357	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	129	402	0	ENST00000305921.3:c.1262C>A	p.Ser421Ter	p.S421*	ENST00000305921	NM_003620.3	421	tCa/tAa	6/6	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.549801674267565	2		402	418	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532603	63532603	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881400	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	255	748	0	ENST00000307078.5:c.1976G>A	p.Arg659Gln	p.R659Q	ENST00000307078	NM_004655.3	659	cGg/cAg	8/11	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.549801674267565	2		748	715	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223061	1223061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782267	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	202	682	1	ENST00000326873.7:c.998G>A	p.Arg333His	p.R333H	ENST00000326873	NM_000455.4	333	cGc/cAc	8/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.549801674267565	2		683	699	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191045	2191045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781606489	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	33	607	1	ENST00000398665.3:c.299C>T	p.Thr100Met	p.T100M	ENST00000398665	NM_032482.2	100	aCg/aTg	5/28	1	2	FACETS	0.207	0.168	0.252	0.207	0.168	0.252	SUBCLONAL	1	TRUE	1	0.549801674267565	2		608	579	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244239	5244239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	231	585	0	ENST00000357368.4:c.1243G>A	p.Glu415Lys	p.E415K	ENST00000357368	NM_002850.3	415	Gag/Aag	11/38	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.549801674267565	2		585	630	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6213976	6213976	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs772076449	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	140	562	6	ENST00000252674.7:c.1381del	p.Gln461ArgfsTer46	p.Q461Rfs*46	ENST00000252674	NM_005934.3	461	Cag/ag	9/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.549801674267565	2		568	424	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11022957	11022957	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	212	637	0	ENST00000327064.4:c.656C>T	p.Ala219Val	p.A219V	ENST00000327064	NM_199141.1	219	gCc/gTc	5/16	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.549801674267565	2		637	577	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141493	11141493	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	195	642	0	ENST00000358026.2:c.3470G>A	p.Arg1157Gln	p.R1157Q	ENST00000358026	NM_001128849.1	1157	cGg/cAg	25/36	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.549801674267565	2		642	593	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288438	15288438	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	46	597	0	ENST00000263388.2:c.4301G>A	p.Trp1434Ter	p.W1434*	ENST00000263388	NM_000435.2	1434	tGg/tAg	24/33	1	2	FACETS	0.329	0.277	0.387	0.329	0.277	0.387	SUBCLONAL	1	TRUE	1	0.549801674267565	2		597	508	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292447	15292447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	229	683	0	ENST00000263388.2:c.2732C>T	p.Thr911Ile	p.T911I	ENST00000263388	NM_000435.2	911	aCc/aTc	17/33	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.549801674267565	2		683	635	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796882	42796883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761345552	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	265	885	5	ENST00000575354.2:c.3347dup	p.Ser1117LysfsTer34	p.S1117Kfs*34	ENST00000575354	NM_015125.3	1114	gcc/gCcc	14/20	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.549801674267565	2		890	717	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672695	47672695	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63751693	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	112	294	0	ENST00000233146.2:c.1285C>T	p.Gln429Ter	p.Q429*	ENST00000233146	NM_000251.2	429	Cag/Tag	8/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.549801674267565	2		294	306	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150022	202150022	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	225	640	0	ENST00000358485.4:c.1463T>C	p.Leu488Pro	p.L488P	ENST00000358485	NM_001080125.1	488	cTg/cCg	8/9	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.549801674267565	2		640	639	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288967	212288967	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs537458255	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	142	446	0	ENST00000342788.4:c.2779C>T	p.Arg927Ter	p.R927*	ENST00000342788	NM_005235.2	927	Cga/Tga	23/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.549801674267565	2		446	402	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657119	215657119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780241203	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	27	493	1	ENST00000260947.4:c.266C>T	p.Pro89Leu	p.P89L	ENST00000260947	NM_000465.2	89	cCg/cTg	3/11	1	2	FACETS	0.229	0.182	0.284	0.229	0.182	0.284	SUBCLONAL	1	TRUE	1	0.549801674267565	2		494	428	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324330	62324331	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	211	666	0	ENST00000360203.5:c.2829dup	p.Lys944GlnfsTer18	p.K944Qfs*18	ENST00000360203	NM_001283009.1	942	gac/gaCc	29/35	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.549801674267565	2		666	583	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691872	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs79375991	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	463	510	18	ENST00000295754.5:c.383del	p.Lys128SerfsTer35	p.K128Sfs*35	ENST00000295754	NM_003242.5	125	gAa/ga	3/7	0.549801674267565	3	FACETS	1	0.991	1	1	0.997	1	CLONAL	3	TRUE	1	0.549801674267565	3		528	672	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575630	55575630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	87	347	0	ENST00000288135.5:c.1156G>A	p.Glu386Lys	p.E386K	ENST00000288135	NM_000222.2	386	Gaa/Aaa	7/21	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.549801674267565	2		347	286	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293976	1293976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773366454	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	219	1035	0	ENST00000310581.5:c.1025G>A	p.Arg342Gln	p.R342Q	ENST00000310581	NM_198253.2	342	cGg/cAg	2/16	1	2	FACETS	0.918	0.855	0.982	0.918	0.855	0.982	CLONAL	1	TRUE	1	0.549801674267565	2		1035	868	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519378	176519378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148292303	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	232	630	0	ENST00000292408.4:c.784G>A	p.Val262Met	p.V262M	ENST00000292408	NM_213647.1	262	Gtg/Atg	7/18	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.549801674267565	2		630	567	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686265	117686266	+	frameshift_variant	Frame_Shift_Ins	INS	TT	TT	GTC	novel	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	119	454	1	ENST00000368508.3:c.3075_3076delinsGAC	p.Lys1026ThrfsTer13	p.K1026Tfs*13	ENST00000368508	NM_002944.2	1025	ggAAag/ggGACag	20/43	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.549801674267565	2		455	363	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686266	117686267	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	119	450	0	ENST00000368508.3:c.3074dup	p.Lys1029GlnfsTer10	p.K1029Qfs*10	ENST00000368508	NM_002944.2	1025	gga/ggGa	20/43	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.549801674267565	2		450	363	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415658	152415658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	212	589	0	ENST00000206249.3:c.1508G>A	p.Arg503Gln	p.R503Q	ENST00000206249	NM_000125.3	503	cGg/cAg	7/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.549801674267565	2		589	613	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508092	106508092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	180	620	0	ENST00000359195.3:c.86C>T	p.Ala29Val	p.A29V	ENST00000359195	NM_002649.2	29	gCg/gTg	2/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.549801674267565	2		620	509	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508788	148508788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587783625	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	160	426	0	ENST00000320356.2:c.1876G>A	p.Val626Met	p.V626M	ENST00000320356	NM_004456.4	626	Gtg/Atg	16/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.549801674267565	2		426	457	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	338	456	17	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	1	2	FACETS	1	0.995	1	1	0.997	1	CLONAL	2	TRUE	1	0.549801674267565	2		473	501	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399320	139399320	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs76371972	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	193	681	0	ENST00000277541.6:c.4823G>A	p.Arg1608His	p.R1608H	ENST00000277541	NM_017617.3	1608	cGt/cAt	26/34	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.549801674267565	2		681	578	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156720	20156720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	137	344	0	ENST00000379607.5:c.37C>T	p.Arg13Cys	p.R13C	ENST00000379607	NM_001412.3	13	Cgc/Tgc	2/7	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.549801674267565	2		344	378	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932357	39932357	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774225795	NA	P-0011252-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	233	707	1	ENST00000378444.4:c.2242C>T	p.Arg748Trp	p.R748W	ENST00000378444	NM_001123385.1	748	Cgg/Tgg	4/15	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.549801674267565	2		708	686	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	202	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.375519211220655	1	FACETS	0.802	0.749	0.855	1	0.993	1	CLONAL	2	TRUE	0	0.375519211220655	1		311	545	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0012900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	88	189	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.375519211220655	1	FACETS	0.626	0.555	0.702	0.626	0.555	0.702	SUBCLONAL	1	TRUE	0	0.375519211220655	1		189	608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572929	7572929	+	stop_lost	Nonstop_Mutation	SNP	A	A	T	novel	NA	P-0012900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	588	1067	0	ENST00000269305.4:c.1180T>A	p.Ter394ArgextTer9	p.*394Rext*9	ENST00000269305	NM_001126112.2	394	Tga/Aga	11/11	0.375519211220655	2	FACETS	0.92	0.894	0.945	1	0.998	1	CLONAL	4	TRUE	0	0.375519211220655	2		1067	851	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692792	89692792	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs779530981	NA	P-0013339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	43	370	1	ENST00000371953.3:c.276C>A	p.Asp92Glu	p.D92E	ENST00000371953	NM_000314.4	92	gaC/gaA	5/9	0.352670026701068	1	FACETS	0.572	0.48	0.674	0.572	0.48	0.674	SUBCLONAL	1	TRUE	0	0.352670026701068	1		371	351	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061102	38061132	+	frameshift_variant	Frame_Shift_Del	DEL	TCCTTGCGGCTCTCAGGGCCGCCCTTGGCGC	TCCTTGCGGCTCTCAGGGCCGCCCTTGGCGC	-	novel	NA	P-0013339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	29	94	0	ENST00000250448.2:c.857_887del	p.Gly286AlafsTer25	p.G286Afs*25	ENST00000250448	NM_004496.3	286	gGCGCCAAGGGCGGCCCTGAGAGCCGCAAGGAc/gc	2/2	1	2	FACETS	0.962	0.78	1	0.962	0.78	1	CLONAL	1	TRUE	1	0.352670026701068	2		94	171	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830389	72830413	+	frameshift_variant	Frame_Shift_Del	DEL	GATGGCTGGTGTGGACGCCGGCTGA	GATGGCTGGTGTGGACGCCGGCTGA	-	novel	NA	P-0013339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	168	786	0	ENST00000268489.5:c.6168_6192del	p.Gln2057ProfsTer36	p.Q2057Pfs*36	ENST00000268489	NM_006885.3	2056	ccTCAGCCGGCGTCCACACCAGCCATC/cc	9/10	0.352670026701068	1	FACETS	0.899	0.827	0.974	0.899	0.827	0.974	CLONAL	1	TRUE	0	0.352670026701068	1		786	873	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289944	15289944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	299	1313	1	ENST00000263388.2:c.3610G>A	p.Ala1204Thr	p.A1204T	ENST00000263388	NM_000435.2	1204	Gca/Aca	22/33	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.645261863699784	2		1314	846	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003183	143003183	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0013339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	216	450	0	ENST00000262992.4:c.2642+1G>T		p.X881_splice	ENST00000262992	NM_001101669.1	881			0.643275480387193	4	FACETS	1	0.984	1			1	CLONAL	2	TRUE	NA	0.645261863699784	4		450	484	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	525	308	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.802174880065216	2	FACETS	0.983	0.958	1	0.983	0.958	1	CLONAL	2	TRUE	0	0.802174880065216	2		308	666	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	94	566	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.768107762044396	2	FACETS	0.389	0.347	0.435	0.195	0.173	0.218	SUBCLONAL	1	TRUE	0	0.802174880065216	2		566	602	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733279	40733279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201275244	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	86	516	0	ENST00000373198.4:c.3527G>A	p.Arg1176His	p.R1176H	ENST00000373198	NM_133170.3	1176	cGt/cAt	26/32	0.739546874187334	3	FACETS	0.271	0.238	0.305	0.135	0.119	0.153	SUBCLONAL	1	TRUE	1	0.802174880065216	3		516	1110	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168975	11168975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329240441	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	63	685	3	ENST00000358026.2:c.4565C>T	p.Ser1522Leu	p.S1522L	ENST00000358026	NM_001128849.1	1522	tCg/tTg	32/36	1	2	FACETS	0.164	0.141	0.19	0.164	0.141	0.19	SUBCLONAL	1	TRUE	1	0.802174880065216	2		688	955	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528478	157528478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	219	556	0	ENST00000346085.5:c.6203C>T	p.Pro2068Leu	p.P2068L	ENST00000346085	NM_020732.3	2068	cCa/cTa	20/20	1	2	FACETS	0.642	0.598	0.687	0.642	0.598	0.687	SUBCLONAL	1	TRUE	1	0.802174880065216	2		556	851	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9786991	9786991	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	49	559	0	ENST00000377346.4:c.3022G>A	p.Glu1008Lys	p.E1008K	ENST00000377346	NM_005026.3	1008	Gag/Aag	24/24	0.802174880065216	1	FACETS	0.138	0.116	0.162	0.138	0.116	0.162	SUBCLONAL	1	TRUE	0	0.802174880065216	1		559	530	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100564	8100564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1178153797	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1171	106	736	2	ENST00000346208.3:c.538G>A	p.Glu180Lys	p.E180K	ENST00000346208		180	Gag/Aag	3/6	1	2	FACETS	0.207	0.185	0.231	0.207	0.185	0.231	SUBCLONAL	1	TRUE	1	0.802174880065216	2		738	1277	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451437	70451437	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	59	710	1	ENST00000373644.4:c.6277G>T	p.Glu2093Ter	p.E2093*	ENST00000373644	NM_030625.2	2093	Gaa/Taa	12/12	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.802174880065216	NA		711	1041	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893363	32893363	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	353	620	0	ENST00000380152.3:c.217C>G	p.Gln73Glu	p.Q73E	ENST00000380152		73	Cag/Gag	3/27	0.802174880065216	1	FACETS	0.953	0.916	0.989	0.953	0.916	0.989	CLONAL	1	TRUE	0	0.802174880065216	1		620	553	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30098278	30098278	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370925513	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	142	550	0	ENST00000331968.5:c.1694C>T	p.Ser565Leu	p.S565L	ENST00000331968	NM_002742.2	565	tCa/tTa	11/18	0.260161041483405	1	FACETS	0.232	0.211	0.254	0.232	0.211	0.254	INDETERMINATE	1	TRUE	0	0.802174880065216	1		550	915	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061575	38061575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	69	303	0	ENST00000250448.2:c.414G>A	p.Met138Ile	p.M138I	ENST00000250448	NM_004496.3	138	atG/atA	2/2	0.260161041483405	1	FACETS	0.207	0.18	0.236	0.207	0.18	0.236	INDETERMINATE	1	TRUE	0	0.802174880065216	1		303	498	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95596436	95596436	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	133	520	1	ENST00000393063.1:c.532C>T	p.His178Tyr	p.H178Y	ENST00000393063	NM_030621.3	178	Cat/Tat	6/28	0.260161041483405	1	FACETS	0.24	0.218	0.264	0.24	0.218	0.264	INDETERMINATE	1	TRUE	0	0.802174880065216	1		521	827	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124366	2124366	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs549612492	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	439	845	1	ENST00000219476.3:c.2521G>A	p.Val841Ile	p.V841I	ENST00000219476	NM_000548.3	841	Gtc/Atc	22/42	0.19364627249273	3	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.802174880065216	3		846	1444	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855945	68855946	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTCTGATGTGAA	novel	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	279	587	0	ENST00000261769.5:c.1756_1768dup	p.Asp590ValfsTer2	p.D590Vfs*2	ENST00000261769	NM_004360.3	585	ctg/cTGTCTGATGTGAAtg	12/16	0.802174880065216	1	FACETS	0.723	0.686	0.76	0.723	0.686	0.76	SUBCLONAL	1	TRUE	0	0.802174880065216	1		587	576	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341600	89341600	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	76	496	0	ENST00000301030.4:c.7471-1G>C		p.X2491_splice	ENST00000301030	NM_001256183.1	2491			0.802174880065216	1	FACETS	0.335	0.296	0.376	0.335	0.296	0.376	SUBCLONAL	1	TRUE	0	0.802174880065216	1		496	339	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348883	89348883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	444	870	1	ENST00000301030.4:c.4067C>T	p.Ser1356Leu	p.S1356L	ENST00000301030	NM_001256183.1	1356	tCa/tTa	9/13	0.802174880065216	1	FACETS	0.968	0.935	1	0.968	0.935	1	CLONAL	1	TRUE	0	0.802174880065216	1		871	685	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349712	89349712	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	400	739	0	ENST00000301030.4:c.3238C>G	p.Leu1080Val	p.L1080V	ENST00000301030	NM_001256183.1	1080	Ctc/Gtc	9/13	0.802174880065216	1	FACETS	0.989	0.954	1	0.989	0.954	1	CLONAL	1	TRUE	0	0.802174880065216	1		739	604	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029478	16029478	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	38	414	0	ENST00000268712.3:c.1552G>C	p.Glu518Gln	p.E518Q	ENST00000268712	NM_006311.3	518	Gaa/Caa	15/46	0.768107762044396	2	FACETS	0.187	0.154	0.224	0.093	0.077	0.112	SUBCLONAL	1	TRUE	0	0.802174880065216	2		414	507	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678170	58678170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1414	204	899	0	ENST00000305921.3:c.395C>T	p.Ser132Leu	p.S132L	ENST00000305921	NM_003620.3	132	tCg/tTg	1/6	0.80166079352527	2	FACETS	0.314	0.29	0.34	0.157	0.145	0.17	SUBCLONAL	1	TRUE	0	0.802174880065216	2		899	1618	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792752	33792752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555742114	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	118	123	0	ENST00000498907.2:c.569C>T	p.Ser190Leu	p.S190L	ENST00000498907	NM_004364.3	190	tCg/tTg	1/1	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.802174880065216	2		123	242	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140083	50140083	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	132	634	0	ENST00000246792.3:c.342G>C	p.Gln114His	p.Q114H	ENST00000246792	NM_006270.3	114	caG/caC	3/6	1	2	FACETS	0.341	0.309	0.375	0.341	0.309	0.375	SUBCLONAL	1	TRUE	1	0.802174880065216	2		634	964	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622696	158622696	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	50	402	0	ENST00000263640.3:c.803C>G	p.Ser268Ter	p.S268*	ENST00000263640	NM_001105.4	268	tCa/tGa	8/11	0.175752910704598	3	FACETS	0.259	0.219	0.303	0.13	0.109	0.152	INDETERMINATE	1	TRUE	1	0.802174880065216	3		402	674	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267518	198267518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	79	359	0	ENST00000335508.6:c.1839G>A	p.Met613Ile	p.M613I	ENST00000335508	NM_012433.2	613	atG/atA	14/25	0.175752910704598	3	FACETS	0.411	0.361	0.464	0.205	0.18	0.232	INDETERMINATE	1	TRUE	1	0.802174880065216	3		359	672	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137492	202137492	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	337	627	0	ENST00000358485.4:c.720C>G	p.Phe240Leu	p.F240L	ENST00000358485	NM_001080125.1	240	ttC/ttG	4/9	0.175752910704598	3	FACETS	1	0.988	1	0.573	0.543	0.604	INDETERMINATE	1	TRUE	1	0.802174880065216	3		627	1027	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417883	138417883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	163	571	0	ENST00000289153.2:c.1636C>T	p.Pro546Ser	p.P546S	ENST00000289153	NM_006219.2	546	Ccc/Tcc	11/22	0.802174880065216	1	FACETS	0.408	0.376	0.441	0.408	0.376	0.441	SUBCLONAL	1	TRUE	0	0.802174880065216	1		571	597	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665015	138665015	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	27	272	1	ENST00000330315.3:c.550G>A	p.Asp184Asn	p.D184N	ENST00000330315	NM_023067.3	184	Gac/Aac	1/1	0.802174880065216	1	FACETS	0.141	0.112	0.174	0.141	0.112	0.174	SUBCLONAL	1	TRUE	0	0.802174880065216	1		273	286	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612200	189612200	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	380	527	0	ENST00000264731.3:c.1952C>G	p.Ser651Cys	p.S651C	ENST00000264731	NM_003722.4	651	tCt/tGt	14/14	0.802174880065216	2	FACETS	1	0.986	1	0.542	0.517	0.567	CLONAL	1	TRUE	0	0.802174880065216	2		527	874	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955040	55955040	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1300072747	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	44	469	0	ENST00000263923.4:c.3505C>T	p.Gln1169Ter	p.Q1169*	ENST00000263923	NM_002253.2	1169	Cag/Tag	26/30	1	2	FACETS	0.137	0.114	0.162	0.137	0.114	0.162	SUBCLONAL	1	TRUE	1	0.802174880065216	2		469	802	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197187	26197187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	258	413	0	ENST00000356476.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000356476		98	Gag/Aag	1/1	0.175752910704598	3	FACETS	1	0.991	1	0.638	0.601	0.676	INDETERMINATE	1	TRUE	1	0.802174880065216	3		413	706	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543581	148543581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	42	471	0	ENST00000320356.2:c.227C>T	p.Ser76Leu	p.S76L	ENST00000320356	NM_004456.4	76	tCa/tTa	3/20	1	2	FACETS	0.126	0.104	0.15	0.126	0.104	0.15	SUBCLONAL	1	TRUE	1	0.802174880065216	2		471	833	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835952	151835952	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	326	529	0	ENST00000262189.6:c.14572G>T	p.Glu4858Ter	p.E4858*	ENST00000262189	NM_170606.2	4858	Gaa/Taa	58/59	1	2	FACETS	0.923	0.875	0.971	0.923	0.875	0.971	CLONAL	1	TRUE	1	0.802174880065216	2		529	881	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151893033	151893033	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	97	401	2	ENST00000262189.6:c.4337G>A	p.Gly1446Glu	p.G1446E	ENST00000262189	NM_170606.2	1446	gGa/gAa	28/59	1	2	FACETS	0.355	0.316	0.396	0.355	0.316	0.396	SUBCLONAL	1	TRUE	1	0.802174880065216	2		403	682	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132763	152132763	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	507	685	1	ENST00000262189.6:c.109C>T	p.Arg37Trp	p.R37W	ENST00000262189	NM_170606.2	37	Cgg/Tgg	1/59	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.802174880065216	2		686	1118	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371698	55371698	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1269	82	771	1	ENST00000297316.4:c.388C>T	p.Gln130Ter	p.Q130*	ENST00000297316	NM_022454.3	130	Cag/Tag	2/2	1	2	FACETS	0.151	0.133	0.172	0.151	0.133	0.172	SUBCLONAL	1	TRUE	1	0.802174880065216	2		772	1351	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5462858	5462858	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747598352	NA	P-0014260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	20	249	0	ENST00000381577.3:c.419G>C	p.Arg140Thr	p.R140T	ENST00000381577	NM_014143.3	140	aGa/aCa	4/7	1	2	FACETS	0.144	0.109	0.184	0.144	0.109	0.184	SUBCLONAL	1	TRUE	1	0.802174880065216	2		249	347	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	87	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.769	0.679	0.865	0.769	0.679	0.865	SUBCLONAL	1	TRUE	1	0.22	2		539	1029	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0015298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	72	380	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.861	0.752	0.98	0.861	0.752	0.98	CLONAL	1	TRUE	1	0.22	2		380	760	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391168	89391168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772463834	NA	P-0015298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	79	673	0	ENST00000336596.2:c.1234G>A	p.Val412Ile	p.V412I	ENST00000336596	NM_005233.5	412	Gtt/Att	5/17	1	2	FACETS	0.802	0.704	0.907	0.802	0.704	0.907	CLONAL	1	TRUE	1	0.22	2		673	896	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790512	3790512	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	124	781	1	ENST00000262367.5:c.4021C>T	p.Arg1341Ter	p.R1341*	ENST00000262367	NM_004380.2	1341	Cga/Tga	24/31	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.22	2		782	1125	SUCCESS
APC	324	MSKCC	GRCh37	5	112175789	112175789	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	65	455	0	ENST00000257430.4:c.4501del	p.Ser1501LeufsTer6	p.S1501Lfs*6	ENST00000257430	NM_000038.5	1500	Ttt/tt	16/16	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.22	2		455	539	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501350	140501350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906660	NA	P-0015298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	59	521	0	ENST00000288602.6:c.722C>T	p.Thr241Met	p.T241M	ENST00000288602	NM_004333.4	241	aCg/aTg	6/18	1	2	FACETS	0.716	0.615	0.827	0.716	0.615	0.827	SUBCLONAL	1	TRUE	1	0.22	2		521	749	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196143	108196143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564652222	NA	P-0015298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	119	815	1	ENST00000278616.4:c.6679C>T	p.Arg2227Cys	p.R2227C	ENST00000278616	NM_000051.3	2227	Cgc/Tgc	46/63	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.22	2		816	1019	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238978	5238978	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	67	586	0	ENST00000357368.4:c.1801G>T	p.Gly601Cys	p.G601C	ENST00000357368	NM_002850.3	601	Ggc/Tgc	13/38	1	2	FACETS	0.946	0.822	1	0.946	0.822	1	CLONAL	1	TRUE	1	0.22	2		586	644	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051469	13051469	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	62	622	0	ENST00000316448.5:c.816+1G>A		p.X272_splice	ENST00000316448	NM_004343.3	272			1	2	FACETS	0.749	0.645	0.861	0.749	0.645	0.861	SUBCLONAL	1	TRUE	1	0.22	2		622	753	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508425	106508425	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754761135	NA	P-0015298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	26	270	1	ENST00000359195.3:c.419G>A	p.Arg140Gln	p.R140Q	ENST00000359195	NM_002649.2	140	cGg/cAg	2/11	1	2	FACETS	0.736	0.584	0.911	0.736	0.584	0.911	CLONAL	1	TRUE	1	0.22	2		271	321	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0015598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	238	308	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.581672452242817	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.581672452242817	1		308	565	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11210212	11210212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1403372273	NA	P-0015598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	96	397	0	ENST00000361445.4:c.4541G>A	p.Arg1514Gln	p.R1514Q	ENST00000361445	NM_004958.3	1514	cGg/cAg	31/58	1	2	FACETS	0.345	0.306	0.386	0.345	0.306	0.386	SUBCLONAL	1	TRUE	1	0.581672452242817	2		397	957	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274851	38274851	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519898	NA	P-0015598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	5937	376	0	ENST00000425967.3:c.1729A>G	p.Asn577Asp	p.N577D	ENST00000425967	NM_001174067.1	577	Aac/Gac	13/19	0.581672452242817	20	FACETS	1	0.999	1			1	CLONAL	19	TRUE	NA	0.581672452242817	20		376	6540	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509822	187509822	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs770217697	NA	P-0015598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	107	176	0	ENST00000441802.2:c.13691A>G	p.Tyr4564Cys	p.Y4564C	ENST00000441802	NM_005245.3	4564	tAt/tGt	27/27	0.581672452242817	3	FACETS	0.875	0.787	0.967	0.437	0.393	0.484	CLONAL	1	TRUE	1	0.581672452242817	3		176	543	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435297	56435297	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	40	577	2	ENST00000407977.2:c.1840C>A	p.Gln614Lys	p.Q614K	ENST00000407977		614	Cag/Aag	9/10	0.33836755210296	2	FACETS	0.278	0.231	0.331	0.139	0.115	0.166	SUBCLONAL	1	TRUE	0	0.533332838828746	2		579	539	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737524	204737524	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015814-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	43	425	0	ENST00000302823.3:c.661C>G	p.Pro221Ala	p.P221A	ENST00000302823	NM_005214.4	221	Ccc/Gcc	4/4	0.443909825024991	3	FACETS	0.375	0.313	0.443	0.187	0.156	0.222	SUBCLONAL	1	TRUE	1	0.443909825024991	3		425	632	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0016864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	95	766	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.799	0.712	0.891	1	0.982	1	SUBCLONAL	2	TRUE	1	0.182147049185197	2		767	653	SUCCESS
APC	324	MSKCC	GRCh37	5	112175411	112175411	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	51	230	0	ENST00000257430.4:c.4120G>T	p.Glu1374Ter	p.E1374*	ENST00000257430	NM_000038.5	1374	Gaa/Taa	16/16	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.182147049185197	2		230	545	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730876	40730876	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372862828	NA	P-0016864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	335	424	0	ENST00000373198.4:c.3659G>A	p.Arg1220Gln	p.R1220Q	ENST00000373198	NM_133170.3	1220	cGg/cAg	27/32	0.182147049185197	4	FACETS	0.894	0.845	0.944	1	0.99	1	CLONAL	4	TRUE	1	0.182147049185197	4		424	1216	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498422	89498422	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	74	283	1	ENST00000336596.2:c.2394C>A	p.Tyr798Ter	p.Y798*	ENST00000336596	NM_005233.5	798	taC/taA	14/17	1	2	FACETS	0.796	0.7	0.899	0.796	0.7	0.899	SUBCLONAL	1	FALSE	1	0.436257528352006	2		284	426	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACAACCCTC	novel	NA	P-0016886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	127	478	0	ENST00000275493.2:c.2315_2316insTCACAACCC	p.Asn771_His773dup	p.N771_H773dup	ENST00000275493	NM_005228.3	771	gac/gACAACCCTCac	20/28	1	2	FACETS	0.709	0.642	0.78	0.709	0.642	0.78	SUBCLONAL	1	FALSE	1	0.436257528352006	2		478	821	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923065	39923065	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0016886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	222	587	0	ENST00000378444.4:c.3643A>T	p.Arg1215Ter	p.R1215*	ENST00000378444	NM_001123385.1	1215	Aga/Tga	8/15	0.177811127392654	3	FACETS	1	0.984	1	0.597	0.556	0.64	INDETERMINATE	1	FALSE	1	0.436257528352006	3		587	1038	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53254033	53254085	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	CTCCGGTGGCGGTAGGAAATCGTCGGACCCCGGCTCCATGGTGGGCCCGAGGT	CTCCGGTGGCGGTAGGAAATCGTCGGACCCCGGCTCCATGGTGGGCCCGAGGT	-	novel	NA	P-0016886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	102	497	0	ENST00000375401.3:c.-14_39del		p.*5*	ENST00000375401	NM_004187.3	?-13/1560		1/26	0.177811127392654	3	FACETS	0.673	0.602	0.75	0.337	0.301	0.375	INDETERMINATE	1	FALSE	1	0.436257528352006	3		497	846	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0016886-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	26	653	2	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		655	629	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0016886-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	68	477	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		477	590	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0016886-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	12	383	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		383	328	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959424	26959424	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016886-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	42	624	0	ENST00000381527.3:c.591C>G	p.Phe197Leu	p.F197L	ENST00000381527	NM_001260.1	197	ttC/ttG	6/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		624	528	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0017272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	211	443	9	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.952	0.885	1	0.952	0.885	1	CLONAL	1	TRUE	1	0.486096956565672	2		452	912	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0017272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	123	513	0				ENST00000310581	NM_198253.2	-/1132			0.486096956565672	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.486096956565672	1		513	377	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435619	18435619	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1164190418	NA	P-0017272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	95	339	0	ENST00000266497.5:c.604G>A	p.Glu202Lys	p.E202K	ENST00000266497		202	Gaa/Aaa	1/31	1	2	FACETS	0.603	0.537	0.673	0.603	0.537	0.673	SUBCLONAL	1	TRUE	1	0.486096956565672	2		339	648	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36931969	36931969	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	166	452	0	ENST00000361632.4:c.2500G>A	p.Gly834Arg	p.G834R	ENST00000361632		834	Ggg/Agg	16/16	1	2	FACETS	0.939	0.865	1	0.939	0.865	1	CLONAL	1	TRUE	1	0.486096956565672	2		452	727	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423638	88423639	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0017272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	66	291	1	ENST00000360948.2:c.2196_2197delinsTT	p.Pro733Ser	p.P733S	ENST00000360948	NM_001012338.2	732	ctCCcc/ctTTcc	18/19	0.357397445333281	3	FACETS	0.386	0.334	0.443	0.193	0.167	0.222	SUBCLONAL	1	TRUE	1	0.486096956565672	3		292	874	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267511	7267511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267605760	NA	P-0017272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	167	443	0	ENST00000302850.5:c.497C>T	p.Ser166Phe	p.S166F	ENST00000302850	NM_000208.2	166	tCc/tTc	2/22	1	2	FACETS	0.852	0.784	0.924	0.852	0.784	0.924	CLONAL	1	TRUE	1	0.486096956565672	2		443	806	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537972	212537972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	175	382	0	ENST00000342788.4:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000342788	NM_005235.2	545	Gag/Aag	14/28	1	2	FACETS	0.896	0.826	0.968	0.896	0.826	0.968	CLONAL	1	TRUE	1	0.486096956565672	2		382	804	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961556	54961556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	156	346	1	ENST00000312783.6:c.76C>T	p.Leu26Phe	p.L26F	ENST00000312783	NM_198436.1	26	Ctc/Ttc	4/10	1	2	FACETS	0.909	0.835	0.987	0.909	0.835	0.987	CLONAL	1	TRUE	1	0.486096956565672	2		347	706	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713924	30713924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	125	292	0	ENST00000295754.5:c.1249G>A	p.Gly417Arg	p.G417R	ENST00000295754	NM_003242.5	417	Ggg/Agg	4/7	0.482487102450958	1	FACETS	0.978	0.894	1	0.978	0.894	1	CLONAL	1	TRUE	0	0.486096956565672	1		292	398	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217305	123217306	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0017272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	211	509	0	ENST00000218089.9:c.2959_2960delinsTT	p.Pro987Leu	p.P987L	ENST00000218089	NM_001042749.1	987	CCg/TTg	29/35	1	2	FACETS	0.873	0.81	0.937	0.873	0.81	0.937	CLONAL	1	TRUE	1	0.486096956565672	2		509	995	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468393	89468393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	93	248	0	ENST00000336596.2:c.1927C>T	p.Pro643Ser	p.P643S	ENST00000336596	NM_005233.5	643	Cct/Tct	11/17	0.482487102450958	1	FACETS	0.741	0.663	0.822	0.741	0.663	0.822	SUBCLONAL	1	TRUE	0	0.486096956565672	1		248	391	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665752	29665755	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1555535032	NA	P-0017291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	449	565	1	ENST00000356175.3:c.6789_6792del	p.Tyr2264ThrfsTer5	p.Y2264Tfs*5	ENST00000356175	NM_000267.3	2263	ACTTac/ac	45/57	0.610580969954718	1	FACETS	0.945	0.905	0.986	0.945	0.905	0.986	CLONAL	1	TRUE	0	0.610580969954718	1		566	1081	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0017291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	412	518	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.610580969954718	1	FACETS	0.946	0.904	0.989	0.946	0.904	0.989	CLONAL	1	TRUE	0	0.610580969954718	1		518	991	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916850	48916850	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	319	350	0	ENST00000267163.4:c.380+1del		p.S127fs	ENST00000267163	NM_000321.2	127	aGt/at	3/27	0.610580969954718	1	FACETS	0.977	0.928	1	0.977	0.928	1	CLONAL	1	TRUE	0	0.610580969954718	1		350	743	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0017479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	5516	470	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.230615859740859	46	FACETS	0.992	0.986	0.998			1	CLONAL	46	TRUE	NA	0.230615859740859	46		470	6368	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161293415	161293415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767802663	NA	P-0017479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	55	395	0	ENST00000367975.2:c.32G>A	p.Arg11His	p.R11H	ENST00000367975	NM_003001.3	11	cGt/cAt	2/6	0.163663859799554	2	FACETS	0.47	0.401	0.547	0.235	0.2	0.274	SUBCLONAL	1	TRUE	0	0.230615859740859	2		395	1014	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426660	49426662	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	rs1413843050	NA	P-0017479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	111	125	0	ENST00000301067.7:c.11826_11828del	p.Gln3947del	p.Q3947del	ENST00000301067	NM_003482.3	3942	caACAg/cag	39/54	0.230615859740859	7	FACETS	0.88	0.797	0.967	0.503	0.455	0.553	CLONAL	4	TRUE	0	0.230615859740859	7		125	431	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940508	31940508	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1339	235	381	0	ENST00000375333.2:c.541G>C	p.Asp181His	p.D181H	ENST00000375333	NM_032454.1	181	Gac/Cac	3/8	0.220529956768162	4	FACETS	0.797	0.741	0.855	0.797	0.741	0.855	SUBCLONAL	2	TRUE	2	0.230615859740859	4		381	1574	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0017589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	193	378	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.480415818519076	3	FACETS	1	0.965	1	0.536	0.496	0.577	CLONAL	1	TRUE	1	0.480415818519076	3		378	930	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0017589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	695	621	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.480415818519076	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.480415818519076	2		622	1353	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0017589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	199	469	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.480415818519076	3	FACETS	0.988	0.915	1	0.494	0.457	0.532	CLONAL	1	TRUE	1	0.480415818519076	3		470	1040	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0017589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	212	238	0				ENST00000310581	NM_198253.2	-/1132			0.480415818519076	3	FACETS	0.967	0.905	1	0.967	0.905	1	CLONAL	2	TRUE	1	0.480415818519076	3		238	566	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782378	9782378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200226248	NA	P-0017589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	248	594	1	ENST00000377346.4:c.2311G>A	p.Gly771Ser	p.G771S	ENST00000377346	NM_005026.3	771	Ggc/Agc	18/24	0.480415818519076	3	FACETS	1	0.953	1	0.513	0.478	0.548	CLONAL	1	TRUE	1	0.480415818519076	3		595	1249	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528572	89528572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762601076	NA	P-0017589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	306	377	0	ENST00000336596.2:c.2872G>A	p.Val958Met	p.V958M	ENST00000336596	NM_005233.5	958	Gtg/Atg	17/17	0.480415818519076	3	FACETS	0.989	0.936	1	0.989	0.936	1	CLONAL	2	TRUE	1	0.480415818519076	3		377	799	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008432	70008432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1195515853	NA	P-0017589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	121	344	0	ENST00000394351.3:c.719G>A	p.Arg240His	p.R240H	ENST00000394351	NM_000248.3	240	cGc/cAc	8/9	0.480415818519076	3	FACETS	0.935	0.846	1	0.468	0.423	0.515	CLONAL	1	TRUE	1	0.480415818519076	3		344	668	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099957	27099958	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	318	587	0	ENST00000324856.7:c.3837dup	p.Pro1280SerfsTer7	p.P1280Sfs*7	ENST00000324856	NM_006015.4	1279	tat/taTt	15/20	0.480415818519076	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.480415818519076	1		587	845	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035164	42035164	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1345	455	1145	0	ENST00000219905.7:c.5006C>G	p.Pro1669Arg	p.P1669R	ENST00000219905	NM_001164273.1	1669	cCt/cGt	15/24	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.480415818519076	2		1145	1800	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794891	242794891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	292	599	0	ENST00000334409.5:c.318C>A	p.Phe106Leu	p.F106L	ENST00000334409	NM_005018.2	106	ttC/ttA	2/5	0.480415818519076	3	FACETS	1	0.981	1	0.552	0.519	0.587	CLONAL	1	TRUE	1	0.480415818519076	3		599	1365	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0018415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	92	498	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	1	2	FACETS	0.976	0.87	1	0.976	0.87	1	CLONAL	1	TRUE	1	0.342111129218171	2		498	551	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879237	151879237	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	99	482	0	ENST00000262189.6:c.5708G>C	p.Gly1903Ala	p.G1903A	ENST00000262189	NM_170606.2	1903	gGt/gCt	36/59	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.342111129218171	2		482	509	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0018669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	306	399	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.66338960029672	3	FACETS	0.977	0.929	1	0.977	0.929	1	CLONAL	2	TRUE	1	0.66338960029672	3		399	629	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0018669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	373	460	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	1	2	FACETS	1	0.987	1	1	0.997	1	CLONAL	2	TRUE	1	0.66338960029672	2		460	538	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845101	128845101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201246258	NA	P-0018669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	330	734	2	ENST00000249373.3:c.595C>T	p.Arg199Trp	p.R199W	ENST00000249373	NM_005631.4	199	Cgg/Tgg	3/12	0.66338960029672	3	FACETS	0.99	0.935	1	0.495	0.467	0.524	CLONAL	1	TRUE	1	0.66338960029672	3		736	1338	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038526	47038526	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	278	719	1	ENST00000377604.3:c.688C>T	p.Arg230Ter	p.R230*	ENST00000377604	NM_001204468.1	230	Cga/Tga	8/24	0.66338960029672	2	FACETS	0.994	0.937	1	0.497	0.468	0.527	CLONAL	1	TRUE	0	0.66338960029672	2		720	843	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176329	24176329	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1568963596	NA	P-0018669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	570	692	0	ENST00000263121.7:c.1120C>T	p.Arg374Trp	p.R374W	ENST00000263121	NM_003073.3	374	Cgg/Tgg	9/9	0.66338960029672	2	FACETS	0.986	0.957	1	0.986	0.957	1	CLONAL	2	TRUE	0	0.66338960029672	2		692	871	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920446	114920446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	378	414	0	ENST00000543371.1:c.1387del	p.Cys463AlafsTer28	p.C463Afs*28	ENST00000543371	NM_001198531.1	463	Tgc/gc	13/14	0.66338960029672	3	FACETS	0.965	0.923	1	0.965	0.923	1	CLONAL	2	TRUE	1	0.66338960029672	3		414	786	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217572	142217572	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	397	550	0	ENST00000350721.4:c.5425T>G	p.Leu1809Val	p.L1809V	ENST00000350721	NM_001184.3	1809	Tta/Gta	32/47	0.554598569966614	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.66338960029672	4		550	940	SUCCESS
APC	324	MSKCC	GRCh37	5	112116518	112116519	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATTGGAAT	novel	NA	P-0018669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	108	439	0	ENST00000257430.4:c.566_573dup	p.Glu192TrpfsTer16	p.E192Wfs*16	ENST00000257430	NM_000038.5	188	caa/caATTGGAATa	6/16	0.66338960029672	3	FACETS	0.791	0.713	0.874	0.396	0.356	0.437	SUBCLONAL	1	TRUE	1	0.66338960029672	3		439	548	SUCCESS
APC	324	MSKCC	GRCh37	5	112137083	112137083	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	T	novel	NA	P-0018669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	236	315	0	ENST00000257430.4:c.834+3A>T		p.X278_splice	ENST00000257430	NM_000038.5	278			0.66338960029672	3	FACETS	0.993	0.939	1	0.993	0.939	1	CLONAL	2	TRUE	1	0.66338960029672	3		315	477	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457698	149457698	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	249	669	0	ENST00000286301.3:c.706T>G	p.Phe236Val	p.F236V	ENST00000286301	NM_005211.3	236	Ttc/Gtc	5/22	0.66338960029672	3	FACETS	0.834	0.779	0.891	0.417	0.389	0.446	CLONAL	1	TRUE	1	0.66338960029672	3		669	1199	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500945	8500945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	186	497	0	ENST00000356435.5:c.1937C>T	p.Ser646Phe	p.S646F	ENST00000356435		646	tCc/tTc	13/35	0.66338960029672	2	FACETS	1	0.959	1	0.522	0.486	0.559	CLONAL	1	TRUE	0	0.66338960029672	2		497	537	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	250	652	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.925	0.869	0.982	0.925	0.869	0.982	CLONAL	1	TRUE	1	0.739314787238705	2		652	731	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115872	8115874	+	frameshift_variant	Frame_Shift_Del	DEL	CTC	CTC	T	novel	NA	P-0019537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	255	668	0	ENST00000346208.3:c.1218_1220delinsT	p.Ser407AlafsTer99	p.S407Afs*99	ENST00000346208		406	atCTCg/atTg	6/6	0.2296855318913	5	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.739314787238705	5		668	1142	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40444011	40444012	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	199	684	0	ENST00000345506.4:c.308dup	p.Glu104GlyfsTer13	p.E104Gfs*13	ENST00000345506	NM_003152.3	103	ctg/cTtg	5/20	0.392737289335994	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.392737289335994	1		684	678	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631269	117631269	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1158125322	NA	P-0019577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	144	564	0	ENST00000368508.3:c.6409A>C	p.Ile2137Leu	p.I2137L	ENST00000368508	NM_002944.2	2137	Atc/Ctc	40/43	0.392737289335994	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.392737289335994	1		564	562	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	742	617	1	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.612590770907833	3	FACETS	0.907	0.884	0.928	0.907	0.884	0.928	CLONAL	3	TRUE	0	0.692227679414271	3		618	1061	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0019902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	282	364	2	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.593918769442886	2	FACETS	0.865	0.826	0.904	0.865	0.826	0.904	CLONAL	2	TRUE	0	0.692227679414271	2		366	471	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115928	8115929	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	186	314	0	ENST00000346208.3:c.1275dup	p.Ser426IlefsTer81	p.S426Ifs*81	ENST00000346208		425	cca/ccAa	6/6	0.401296043909178	4	FACETS	1	0.991	1	0.743	0.69	0.798	INDETERMINATE	1	TRUE	2	0.692227679414271	4		314	612	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984672	11984672	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0019902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	319	331	0	ENST00000353533.5:c.219-1G>A		p.X73_splice	ENST00000353533	NM_003010.3	73			0.612590770907833	3	FACETS	0.878	0.844	0.911	0.878	0.844	0.911	CLONAL	3	TRUE	0	0.692227679414271	3		331	471	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793509	89793509	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs772546197	NA	P-0019902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	331	295	0	ENST00000336032.3:c.578C>A	p.Ala193Asp	p.A193D	ENST00000336032	NM_006813.2	193	gCc/gAc	2/2	0.578533527880276	5	FACETS	0.857	0.815	0.899	0.857	0.815	0.899	CLONAL	3	TRUE	2	0.692227679414271	5		295	758	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467865	66467865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs939351025	NA	P-0020106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	54	295	0	ENST00000273854.3:c.404G>A	p.Arg135Gln	p.R135Q	ENST00000273854	NM_004439.5	135	cGg/cAg	3/18	1	2	FACETS	0.76	0.652	0.877	0.76	0.652	0.877	SUBCLONAL	1	TRUE	1	0.395943401587294	2		295	359	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057947	27057948	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	48	567	1	ENST00000324856.7:c.1656dup	p.Gln553ThrfsTer70	p.Q553Tfs*70	ENST00000324856	NM_006015.4	552	tca/tcAa	3/20	0.286115234601696	4	FACETS	0.641	0.542	0.75			1	SUBCLONAL	1	TRUE	NA	0.395943401587294	4		568	528	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857335	68857335	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	94	450	0	ENST00000261769.5:c.1971del	p.Leu658Ter	p.L658*	ENST00000261769	NM_004360.3	657	gCc/gc	13/16	0.32479235903501	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.395943401587294	1		450	315	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097706	27097707	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	123	563	0	ENST00000324856.7:c.3296dup	p.Cys1099TrpfsTer6	p.C1099Wfs*6	ENST00000324856	NM_006015.4	1099	tgt/tGgt	12/20	0.286115234601696	4	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.395943401587294	4		563	644	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0020342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	257	891	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.753091651964642	3	FACETS	1	0.947	1	0.505	0.473	0.538	CLONAL	1	TRUE	1	0.753091651964642	3		892	930	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117321	115117321	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	329	548	0	ENST00000257566.3:c.853C>G	p.Gln285Glu	p.Q285E	ENST00000257566	NM_016569.3	285	Cag/Gag	4/8	0.753091651964642	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.753091651964642	2		548	417	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161703	47161703	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs774624204	NA	P-0020342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	97	362	0	ENST00000409792.3:c.4423C>G	p.Leu1475Val	p.L1475V	ENST00000409792	NM_014159.6	1475	Ctt/Gtt	3/21	0.663591609169738	4	FACETS	0.887	0.794	0.986	0.444	0.397	0.493	CLONAL	1	TRUE	2	0.753091651964642	4		362	509	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721420	176721420	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	193	714	0	ENST00000439151.2:c.7051G>A	p.Glu2351Lys	p.E2351K	ENST00000439151	NM_022455.4	2351	Gaa/Aaa	23/23	0.663591609169738	4	FACETS	1	0.968	1	0.539	0.499	0.581	CLONAL	1	TRUE	2	0.753091651964642	4		714	833	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0020380-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	160	334	1	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.0502961203247816	4	FACETS	0.923	0.859	0.988	1	0.993	1	INDETERMINATE	5	FALSE	2	0.237590004431514	4		335	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0020380-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	494	789	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	0.899	0.862	0.935	1	0.998	1	CLONAL	4	FALSE	1	0.237590004431514	2		789	1157	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020380-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	531	1294	0	ENST00000269305.4:c.461del	p.Gly154AlafsTer16	p.G154Afs*16	ENST00000269305	NM_001126112.2	154	gGc/gc	5/11	1	2	FACETS	0.91	0.875	0.946	1	0.998	1	CLONAL	4	FALSE	1	0.237590004431514	2		1294	1228	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938538	76938540	+	frameshift_variant	Frame_Shift_Del	DEL	ATT	ATT	TA	novel	NA	P-0020380-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	246	422	1	ENST00000373344.5:c.2208_2210delinsTA	p.Ile737ThrfsTer5	p.I737Tfs*5	ENST00000373344	NM_000489.3	736	gcAATc/gcTAc	9/35	0.123543150105772	2	FACETS	0.993	0.96	1			1	INDETERMINATE	7	FALSE	NA	0.237590004431514	2		423	298	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851321	156851321	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	104	1090	0	ENST00000524377.1:c.2278A>C	p.Met760Leu	p.M760L	ENST00000524377	NM_002529.3	760	Atg/Ctg	17/17	1	2	FACETS	0.956	0.855	1	0.956	0.855	1	CLONAL	1	TRUE	1	0.246156016691641	2		1090	884	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660409	227660409	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	34	704	0	ENST00000305123.5:c.3046C>G	p.Arg1016Gly	p.R1016G	ENST00000305123	NM_005544.2	1016	Cga/Gga	1/2	1	2	FACETS	0.432	0.352	0.522	0.432	0.352	0.522	SUBCLONAL	1	TRUE	1	0.246156016691641	2		704	640	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0020972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	89	334	1	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.22236057222238	1	FACETS	0.974	0.871	1	0.974	0.871	1	INDETERMINATE	1	TRUE	0	0.41206434781687	1		335	352	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735436	204735436	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	58	492	1	ENST00000302823.3:c.237C>A	p.Ser79Arg	p.S79R	ENST00000302823	NM_005214.4	79	agC/agA	2/4	0.22236057222238	1	FACETS	0.474	0.407	0.545	0.474	0.407	0.545	INDETERMINATE	1	TRUE	0	0.41206434781687	1		493	472	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138423323	138423323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747790462	NA	P-0020972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	143	653	1	ENST00000289153.2:c.1543G>A	p.Ala515Thr	p.A515T	ENST00000289153	NM_006219.2	515	Gca/Aca	10/22	0.41206434781687	1	FACETS	0.945	0.865	1	0.945	0.865	1	CLONAL	1	TRUE	0	0.41206434781687	1		654	583	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	243	602	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.789889049739472	3	FACETS	1	0.971	1			1	CLONAL	1	TRUE	NA	0.787894883035261	3		602	809	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0021149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	564	679	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.789889049739472	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.787894883035261	3		679	617	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0021149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	318	209	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.789889049739472	3	FACETS	0.979	0.951	1	0.979	0.951	1	CLONAL	3	TRUE	0	0.787894883035261	3		209	383	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637689	52637689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	288	614	0	ENST00000394830.3:c.2627G>A	p.Arg876His	p.R876H	ENST00000394830	NM_018313.4	876	cGt/cAt	18/30	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.787894883035261	2		614	663	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273849	18273851	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0021149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	443	745	0	ENST00000222254.8:c.1184_1186del	p.Phe395del	p.F395del	ENST00000222254	NM_005027.3	394	acCTTc/acc	10/16	0.625433581049856	3	FACETS	0.921	0.885	0.957			1	CLONAL	2	TRUE	NA	0.787894883035261	3		745	851	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021299	31021299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	204	535	0	ENST00000375687.4:c.1298C>T	p.Ala433Val	p.A433V	ENST00000375687	NM_015338.5	433	gCa/gTa	12/13	0.789889049739472	3	FACETS	1	0.967	1	0.354	0.33	0.38	CLONAL	1	TRUE	0	0.787894883035261	3		535	679	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375973	8375973	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	103	384	0	ENST00000356435.5:c.4624A>C	p.Asn1542His	p.N1542H	ENST00000356435		1542	Aac/Cac	28/35	0.313463448390523	3	FACETS	1	0.928	1	0.344	0.311	0.379	INDETERMINATE	1	TRUE	0	0.787894883035261	3		384	353	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935523	13935523	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	44	396	0	ENST00000405192.2:c.1333C>G	p.Pro445Ala	p.P445A	ENST00000405192	NM_001163147.1	445	Ccc/Gcc	12/12	0.580671562834338	4	FACETS	0.334	0.28	0.395	0.167	0.14	0.198	SUBCLONAL	1	TRUE	2	0.787894883035261	4		396	597	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0021318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	767	513	0				ENST00000310581	NM_198253.2	-/1132			0.436507624627657	5	FACETS	0.979	0.954	1	0.979	0.954	1	CLONAL	5	TRUE	0	0.436507624627657	5		513	1188	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881002	37881003	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCTCCCCA	rs397516982	NA	P-0021318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	468	946	0	ENST00000269571.5:c.2332_2340dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	-/GGCTCCCCA	20/27	0.436507624627657	3	FACETS	0.87	0.831	0.91	0.87	0.831	0.91	CLONAL	2	TRUE	1	0.436507624627657	3		946	1501	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438143	56438143	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0021318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	296	1027	0	ENST00000407977.2:c.849+1G>T		p.X283_splice	ENST00000407977		283			0.436507624627657	3	FACETS	1	0.986	1	0.581	0.546	0.618	CLONAL	1	TRUE	1	0.436507624627657	3		1027	1421	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484331	120484331	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	53	509	0	ENST00000256646.2:c.2799C>G	p.Phe933Leu	p.F933L	ENST00000256646	NM_024408.3	933	ttC/ttG	18/34	1	2	FACETS	0.399	0.34	0.464	0.399	0.34	0.464	SUBCLONAL	1	TRUE	1	0.436507624627657	2		509	608	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482806	67482806	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	226	790	0	ENST00000327367.4:c.1210T>G	p.Leu404Val	p.L404V	ENST00000327367	NM_005902.3	404	Ttg/Gtg	9/9	0.41336583467149	1	FACETS	0.964	0.9	1	0.964	0.9	1	CLONAL	1	TRUE	0	0.436507624627657	1		790	840	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992390	72992390	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs754146286	NA	P-0021318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	141	1143	0	ENST00000268489.5:c.1655C>G	p.Ser552Cys	p.S552C	ENST00000268489	NM_006885.3	552	tCt/tGt	2/10	1	2	FACETS	0.551	0.501	0.604	0.551	0.501	0.604	SUBCLONAL	1	TRUE	1	0.436507624627657	2		1143	1172	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22153321	22153321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	71	750	1	ENST00000215832.6:c.589G>A	p.Glu197Lys	p.E197K	ENST00000215832	NM_002745.4	197	Gaa/Aaa	4/9	1	2	FACETS	0.39	0.34	0.445	0.39	0.34	0.445	SUBCLONAL	1	TRUE	1	0.436507624627657	2		751	834	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	152	348	1				ENST00000310581	NM_198253.2	-/1132			0.614822412839894	3	FACETS	0.931	0.854	1	0.466	0.427	0.506	CLONAL	1	TRUE	1	0.614822412839894	3		349	694	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929487	44929487	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	148	837	2	ENST00000377967.4:c.2587C>T	p.Gln863Ter	p.Q863*	ENST00000377967	NM_021140.2	863	Cag/Tag	17/29	0.614822412839894	3	FACETS	0.987	0.904	1	0.493	0.452	0.536	CLONAL	1	TRUE	1	0.614822412839894	3		839	638	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582020	189582020	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0021532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	80	571	0	ENST00000264731.3:c.580-1G>A		p.X194_splice	ENST00000264731	NM_003722.4	194			0.614822412839894	3	FACETS	0.592	0.521	0.667	0.296	0.26	0.334	SUBCLONAL	1	TRUE	1	0.614822412839894	3		571	575	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599255	28599255	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	241	925	0	ENST00000253063.3:c.701C>G	p.Pro234Arg	p.P234R	ENST00000253063	NM_031459.4	234	cCt/cGt	5/10	0.614822412839894	3	FACETS	1	0.955	1	0.514	0.48	0.549	CLONAL	1	TRUE	1	0.614822412839894	3		925	997	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740204	162740204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749040833	NA	P-0021532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	376	840	0	ENST00000367921.3:c.1406C>T	p.Ser469Leu	p.S469L	ENST00000367921	NM_006182.2	469	tCg/tTg	12/18	0.520735142413233	4	FACETS	0.968	0.921	1	0.968	0.921	1	CLONAL	2	TRUE	2	0.614822412839894	4		840	1020	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138140	64138140	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	224	856	0	ENST00000334205.4:c.2063C>G	p.Pro688Arg	p.P688R	ENST00000334205	NM_003942.2	688	cCc/cGc	16/17	0.0667778950924043	4	FACETS	0.767	0.716	0.819	0.767	0.716	0.819	INDETERMINATE	2	TRUE	2	0.614822412839894	4		856	767	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372495	118372495	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0021532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	175	894	0	ENST00000534358.1:c.6428C>G	p.Ser2143Ter	p.S2143*	ENST00000534358	NM_005933.3	2143	tCa/tGa	26/36	0.178955115519637	3	FACETS	1	0.974	1	0.559	0.516	0.603	INDETERMINATE	1	TRUE	1	0.614822412839894	3		894	666	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427350	49427350	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0021532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	981	802	0	ENST00000301067.7:c.11138C>G	p.Ser3713Ter	p.S3713*	ENST00000301067	NM_003482.3	3713	tCa/tGa	39/54	0.614822412839894	7	FACETS	0.936	0.916	0.957			1	CLONAL	6	TRUE	NA	0.614822412839894	7		802	1441	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864217	57864217	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	141	722	0	ENST00000228682.2:c.1694T>C	p.Phe565Ser	p.F565S	ENST00000228682	NM_005269.2	565	tTc/tCc	12/12	0.614822412839894	4	FACETS	0.847	0.772	0.927			1	CLONAL	1	TRUE	NA	0.614822412839894	4		722	874	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133290	30133290	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs746736375	NA	P-0021532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	280	852	1	ENST00000263025.4:c.208A>G	p.Ile70Val	p.I70V	ENST00000263025	NM_002746.2	70	Atc/Gtc	2/9	0.614822412839894	3	FACETS	1	0.983	1	0.56	0.526	0.595	CLONAL	1	TRUE	1	0.614822412839894	3		853	1063	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577019	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0021532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	458	853	2	ENST00000269305.4:c.919_919+1delinsTT		p.X307_splice	ENST00000269305	NM_001126112.2	307		8/11	0.61388218916463	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.614822412839894	2		855	731	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761480	59761480	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	57	656	0	ENST00000259008.2:c.2927A>T	p.Glu976Val	p.E976V	ENST00000259008	NM_032043.2	976	gAa/gTa	20/20	0.614822412839894	3	FACETS	0.695	0.599	0.798	0.347	0.299	0.399	SUBCLONAL	1	TRUE	1	0.614822412839894	3		656	349	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727073	41727073	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	225	1004	0	ENST00000301178.4:c.331G>C	p.Asp111His	p.D111H	ENST00000301178	NM_021913.4	111	Gac/Cac	3/20	0.614822412839894	3	FACETS	0.917	0.853	0.982	0.458	0.426	0.491	CLONAL	1	TRUE	1	0.614822412839894	3		1004	1044	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217460	142217460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	145	602	1	ENST00000350721.4:c.5537G>A	p.Arg1846Gln	p.R1846Q	ENST00000350721	NM_001184.3	1846	cGa/cAa	32/47	0.595256186123049	4	FACETS	0.846	0.779	0.916	0.846	0.779	0.916	CLONAL	2	TRUE	2	0.614822412839894	4		603	450	SUCCESS
ATR	545	MSKCC	GRCh37	3	142297528	142297541	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGGCCATGTTCC	CCAGGCCATGTTCC	-	novel	NA	P-0021532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	252	759	0	ENST00000350721.4:c.6_19del	p.Glu3AlafsTer20	p.E3Afs*20	ENST00000350721	NM_001184.3	2	ggGGAACATGGCCTGGag/ggag	1/47	0.595256186123049	4	FACETS	1	0.993	1	0.734	0.688	0.781	CLONAL	1	TRUE	2	0.614822412839894	4		759	902	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950075	38950075	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	150	660	0	ENST00000357387.3:c.3875C>G	p.Ser1292Cys	p.S1292C	ENST00000357387	NM_152756.3	1292	tCt/tGt	31/38	0.614822412839894	3	FACETS	1	0.968	1	0.555	0.509	0.602	CLONAL	1	TRUE	1	0.614822412839894	3		660	575	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778211	27778211	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	355	870	0	ENST00000369163.2:c.360C>G	p.Ile120Met	p.I120M	ENST00000369163	NM_003536.2	120	atC/atG	1/1	0.52652014706268	3	FACETS	0.887	0.844	0.93			1	CLONAL	2	TRUE	NA	0.614822412839894	3		870	851	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437655	49437655	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1850	265	1033	2	ENST00000301067.7:c.5315T>C	p.Leu1772Ser	p.L1772S	ENST00000301067	NM_003482.3	1772	tTg/tCg	22/54	0.614822412839894	7	FACETS	1	0.957	1			1	CLONAL	1	TRUE	NA	0.614822412839894	7		1035	2115	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117377	115117378	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0021792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	51	522	0	ENST00000257566.3:c.795_796dup	p.Ser266IlefsTer17	p.S266Ifs*17	ENST00000257566	NM_016569.3	266	agt/aTAgt	4/8	1	2	FACETS	0.212	0.179	0.247	0.212	0.179	0.247	SUBCLONAL	1	TRUE	1	0.676761499789161	2		522	712	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0022504-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	17	540	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.157	0.116	0.205	0.157	0.116	0.205	SUBCLONAL	1	TRUE	1	0.31	2		540	700	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0022504-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	15	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.204	0.148	0.272	0.204	0.148	0.272	SUBCLONAL	1	TRUE	1	0.31	2		539	474	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921546	178921546	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022504-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	54	380	0	ENST00000263967.3:c.1028A>T	p.Tyr343Phe	p.Y343F	ENST00000263967	NM_006218.2	343	tAc/tTc	5/21	0.266997915422424	3	FACETS	0.786	0.672	0.911	0.393	0.336	0.456	CLONAL	1	TRUE	1	0.31	3		380	512	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099579	157099579	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1562376341	NA	P-0022998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	10	138	0	ENST00000346085.5:c.521del	p.Pro174ArgfsTer6	p.P174Rfs*6	ENST00000346085	NM_020732.3	172	gaC/ga	1/20	1	2	FACETS	0.359	0.243	0.505	0.359	0.243	0.505	SUBCLONAL	1	TRUE	1	0.310927279811792	2		138	179	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0023616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	138	766	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.39064966325231	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.39064966325231	1		767	474	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0023616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	32	636	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.39064966325231	1	FACETS	0.385	0.313	0.467	0.385	0.313	0.467	SUBCLONAL	1	TRUE	0	0.39064966325231	1		636	342	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0023616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	70	622	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.898	0.787	1	0.898	0.787	1	CLONAL	1	TRUE	1	0.39064966325231	2		622	399	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0023616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	41	451	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	1	2	FACETS	0.726	0.608	0.856	0.726	0.608	0.856	SUBCLONAL	1	TRUE	1	0.39064966325231	2		451	289	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730831	40730831	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372700928	NA	P-0023616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	199	1032	2	ENST00000373198.4:c.3704G>A	p.Arg1235His	p.R1235H	ENST00000373198	NM_133170.3	1235	cGc/cAc	27/32	0.39064966325231	3	FACETS	0.768	0.713	0.825			1	SUBCLONAL	2	TRUE	NA	0.39064966325231	3		1034	793	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591955	48591972	+	inframe_deletion	In_Frame_Del	DEL	CAGAAGCCATTGAGAGAG	CAGAAGCCATTGAGAGAG	-	novel	NA	P-0023616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	23	529	2	ENST00000342988.3:c.1120_1137del	p.Glu374_Ala379del	p.E374_A379del	ENST00000342988	NM_005359.5	373	aCAGAAGCCATTGAGAGAGca/aca	9/12	0.39064966325231	1	FACETS	0.343	0.268	0.43	0.343	0.268	0.43	SUBCLONAL	1	TRUE	0	0.39064966325231	1		531	276	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72881616	72881616	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	93	665	0	ENST00000325599.8:c.503T>G	p.Val168Gly	p.V168G	ENST00000325599	NM_018130.2	168	gTt/gGt	5/11	1	2	FACETS	0.939	0.838	1	0.939	0.838	1	CLONAL	1	TRUE	1	0.39064966325231	2		665	507	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0024150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	232	443	9	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.314891171012526	3	FACETS	0.806	0.752	0.862	0.806	0.752	0.862	CLONAL	2	TRUE	1	0.348759731178977	3		452	969	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0024150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	69	399	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.721	0.628	0.82	0.721	0.628	0.82	SUBCLONAL	1	TRUE	1	0.348759731178977	2		399	549	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0024150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	157	770	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.932	0.853	1	0.932	0.853	1	CLONAL	1	TRUE	1	0.348759731178977	2		770	966	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0024150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	131	622	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.348759731178977	2		622	739	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0024150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	429	911	1	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.34494577837278	2	FACETS	0.986	0.94	1	0.986	0.94	1	CLONAL	2	TRUE	0	0.348759731178977	2		912	1248	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40864888	40864888	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	45	710	0	ENST00000373198.4:c.2380T>C	p.Tyr794His	p.Y794H	ENST00000373198	NM_133170.3	794	Tat/Cat	16/32	0.348759731178977	1	FACETS	0.264	0.221	0.312	0.264	0.221	0.312	SUBCLONAL	1	TRUE	0	0.348759731178977	1		710	806	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0024425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	18	586	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.14	0.105	0.182	0.14	0.105	0.182	SUBCLONAL	1	TRUE	1	0.509741387067769	2		586	505	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0024425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	40	308	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.447	0.372	0.53	0.447	0.372	0.53	SUBCLONAL	1	TRUE	1	0.509741387067769	2		308	351	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0024425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	160	482	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.476896445027064	3	FACETS	0.75	0.692	0.81	0.75	0.692	0.81	SUBCLONAL	2	TRUE	1	0.509741387067769	3		482	525	SUCCESS
APC	324	MSKCC	GRCh37	5	112176027	112176030	+	frameshift_variant	Frame_Shift_Del	DEL	TTAT	TTAT	-	novel	NA	P-0024425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	66	310	0	ENST00000257430.4:c.4738_4741del	p.Ile1580LeufsTer69	p.I1580Lfs*69	ENST00000257430	NM_000038.5	1579	aTTATt/at	16/16	1	2	FACETS	0.766	0.669	0.869	0.766	0.669	0.869	SUBCLONAL	1	TRUE	1	0.509741387067769	2		310	338	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120085	70120085	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	24	32	1	ENST00000245479.2:c.1087C>T	p.Gln363Ter	p.Q363*	ENST00000245479	NM_000346.3	363	Cag/Tag	3/3	0.313938261574907	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	2	TRUE	0	0.509741387067769	2		33	43	SUCCESS
APC	324	MSKCC	GRCh37	5	112174262	112174262	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs786202995	NA	P-0024425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	51	346	0	ENST00000257430.4:c.2971G>T	p.Glu991Ter	p.E991*	ENST00000257430	NM_000038.5	991	Gaa/Taa	16/16	1	2	FACETS	0.71	0.607	0.82	0.71	0.607	0.82	SUBCLONAL	1	TRUE	1	0.509741387067769	2		346	282	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250906	153250906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	66	330	1	ENST00000281708.4:c.1154C>T	p.Thr385Ile	p.T385I	ENST00000281708	NM_033632.3	385	aCa/aTa	8/12	1	2	FACETS	0.789	0.69	0.895	0.789	0.69	0.895	SUBCLONAL	1	TRUE	1	0.509741387067769	2		331	328	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332465	153332468	+	frameshift_variant	Frame_Shift_Del	DEL	TTTG	TTTG	-	novel	NA	P-0024425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	61	287	0	ENST00000281708.4:c.488_491del	p.Thr163LysfsTer5	p.T163Kfs*5	ENST00000281708	NM_033632.3	163	aCAAAa/aa	2/12	1	2	FACETS	0.736	0.639	0.84	0.736	0.639	0.84	SUBCLONAL	1	TRUE	1	0.509741387067769	2		287	325	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0024634-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	151	674	1	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.483811021940742	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	0	0.483811021940742	1		675	435	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821283	72821283	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024634-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	132	589	0	ENST00000268489.5:c.10892C>A	p.Ser3631Tyr	p.S3631Y	ENST00000268489	NM_006885.3	3631	tCt/tAt	10/10	NA	2	FACETS	0.974	0.888	1			1	INDETERMINATE	1	FALSE	NA	0.483811021940742	2		589	560	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0024979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	95	308	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.30642157511618	2		308	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0025070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	440	623	1	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.409488198975582	2	FACETS	0.999	0.955	1	0.999	0.955	1	CLONAL	2	TRUE	0	0.409488198975582	2		624	1076	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653795	89653817	+	frameshift_variant	Frame_Shift_Del	DEL	CATTATTGCTATGGGATTTCCTG	CATTATTGCTATGGGATTTCCTG	-	novel	NA	P-0025070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	54	419	0	ENST00000371953.3:c.95_117del	p.Ile32ArgfsTer4	p.I32Rfs*4	ENST00000371953	NM_000314.4	31	aaCATTATTGCTATGGGATTTCCTGca/aaca	2/9	0.409488198975582	1	FACETS	0.801	0.69	0.919	0.801	0.69	0.919	CLONAL	1	TRUE	0	0.409488198975582	1		419	262	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48877685	48878056	+	coding_sequence_variant,5_prime_UTR_variant	In_Frame_Del	DEL	CACGTCCGGGCCGCGCCGGATGCCTCCTGGAAGGCGCCTGGACCCACGCCAGGTTTCCCAGTTTAATTCCTCATGACTTAGCGTCCCAGCCCGCGCACCGACCAGCGCCCCAGTTCCCCACAGACGCCGGCGGGCCCGGGAGCCTCGCGGACGTGACGCCGCGGGCGGAAGTGACGTTTTCCCGCGGTTGGACGCGGCGCTCAGTTGCCGGGCGGGGGAGGGCGCGTCCGGTTTTTCTCAGGGGACGTTGAAATTATTTTTGTAACGGGAGTCGGGAGAGGACGGGGCGTGCCCCGACGTGCGCGCGCGTCGTCCTCCCCGGCGCTCCTCCACAGCTCGCTGGCTCCCGCCGCGGAAAGGCGTCATGCCGCC	CACGTCCGGGCCGCGCCGGATGCCTCCTGGAAGGCGCCTGGACCCACGCCAGGTTTCCCAGTTTAATTCCTCATGACTTAGCGTCCCAGCCCGCGCACCGACCAGCGCCCCAGTTCCCCACAGACGCCGGCGGGCCCGGGAGCCTCGCGGACGTGACGCCGCGGGCGGAAGTGACGTTTTCCCGCGGTTGGACGCGGCGCTCAGTTGCCGGGCGGGGGAGGGCGCGTCCGGTTTTTCTCAGGGGACGTTGAAATTATTTTTGTAACGGGAGTCGGGAGAGGACGGGGCGTGCCCCGACGTGCGCGCGCGTCGTCCTCCCCGGCGCTCCTCCACAGCTCGCTGGCTCCCGCCGCGGAAAGGCGTCATGCCGCC	-	novel	NA	P-0025070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	2	159	0				ENST00000267163	NM_000321.2	?-3/928		1/27	0.409488198975582	2	FACETS	1	0.532	1	0.698	0.292	1	CLONAL	1	TRUE	0	0.409488198975582	2		159	7	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878115	48878120	+	inframe_deletion	In_Frame_Del	DEL	CCGCCG	CCGCCG	-	novel	NA	P-0025070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	251	171	0	ENST00000267163.4:c.75_80del	p.Pro28_Pro29del	p.P28_P29del	ENST00000267163	NM_000321.2	23	CCGCCG/-	1/27	0.409488198975582	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.409488198975582	2		171	505	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944419	40944419	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs770482461	NA	P-0025070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	167	658	0	ENST00000373198.4:c.2083C>G	p.Leu695Val	p.L695V	ENST00000373198	NM_133170.3	695	Ctc/Gtc	12/32	1	2	FACETS	0.825	0.757	0.895	0.825	0.757	0.895	CLONAL	1	TRUE	1	0.409488198975582	2		658	989	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119634894	119634895	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	68	302	0	ENST00000316626.5:c.604_605insT	p.Gly202ValfsTer22	p.G202Vfs*22	ENST00000316626		202	gga/gTga	5/12	1	2	FACETS	0.795	0.694	0.902	0.795	0.694	0.902	CLONAL	1	TRUE	1	0.409488198975582	2		302	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0025070-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	325	623	1	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.473893347079772	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	FALSE	0	0.473893347079772	2		624	646	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653795	89653817	+	frameshift_variant	Frame_Shift_Del	DEL	CATTATTGCTATGGGATTTCCTG	CATTATTGCTATGGGATTTCCTG	-	novel	NA	P-0025070-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	131	419	0	ENST00000371953.3:c.95_117del	p.Ile32ArgfsTer4	p.I32Rfs*4	ENST00000371953	NM_000314.4	31	aaCATTATTGCTATGGGATTTCCTGca/aaca	2/9	NA	2	FACETS	0.925	0.853	0.997			1	INDETERMINATE	2	FALSE	NA	0.473893347079772	2		419	299	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48877685	48878056	+	coding_sequence_variant,5_prime_UTR_variant	In_Frame_Del	DEL	CACGTCCGGGCCGCGCCGGATGCCTCCTGGAAGGCGCCTGGACCCACGCCAGGTTTCCCAGTTTAATTCCTCATGACTTAGCGTCCCAGCCCGCGCACCGACCAGCGCCCCAGTTCCCCACAGACGCCGGCGGGCCCGGGAGCCTCGCGGACGTGACGCCGCGGGCGGAAGTGACGTTTTCCCGCGGTTGGACGCGGCGCTCAGTTGCCGGGCGGGGGAGGGCGCGTCCGGTTTTTCTCAGGGGACGTTGAAATTATTTTTGTAACGGGAGTCGGGAGAGGACGGGGCGTGCCCCGACGTGCGCGCGCGTCGTCCTCCCCGGCGCTCCTCCACAGCTCGCTGGCTCCCGCCGCGGAAAGGCGTCATGCCGCC	CACGTCCGGGCCGCGCCGGATGCCTCCTGGAAGGCGCCTGGACCCACGCCAGGTTTCCCAGTTTAATTCCTCATGACTTAGCGTCCCAGCCCGCGCACCGACCAGCGCCCCAGTTCCCCACAGACGCCGGCGGGCCCGGGAGCCTCGCGGACGTGACGCCGCGGGCGGAAGTGACGTTTTCCCGCGGTTGGACGCGGCGCTCAGTTGCCGGGCGGGGGAGGGCGCGTCCGGTTTTTCTCAGGGGACGTTGAAATTATTTTTGTAACGGGAGTCGGGAGAGGACGGGGCGTGCCCCGACGTGCGCGCGCGTCGTCCTCCCCGGCGCTCCTCCACAGCTCGCTGGCTCCCGCCGCGGAAAGGCGTCATGCCGCC	-	novel	NA	P-0025070-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3	207	159	0				ENST00000267163	NM_000321.2	?-3/928		1/27	0.473893347079772	3	FACETS	1	0.995	1	1	0.996	1	CLONAL	5	FALSE	0	0.473893347079772	3		159	210	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878115	48878120	+	inframe_deletion	In_Frame_Del	DEL	CCGCCG	CCGCCG	-	novel	NA	P-0025070-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	289	171	0	ENST00000267163.4:c.75_80del	p.Pro28_Pro29del	p.P28_P29del	ENST00000267163	NM_000321.2	23	CCGCCG/-	1/27	0.473893347079772	3	FACETS	1	0.982	1	1	0.996	1	CLONAL	4	FALSE	0	0.473893347079772	3		171	368	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944419	40944419	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs770482461	NA	P-0025070-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	228	658	0	ENST00000373198.4:c.2083C>G	p.Leu695Val	p.L695V	ENST00000373198	NM_133170.3	695	Ctc/Gtc	12/32	0.239275827641591	5	FACETS	0.944	0.881	1	0.629	0.587	0.673	INDETERMINATE	2	FALSE	2	0.473893347079772	5		658	872	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119634895	119634895	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025070-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	108	249	0	ENST00000316626.5:c.604G>T	p.Gly202Ter	p.G202*	ENST00000316626		202	Gga/Tga	5/12	0.448662987515539	4	FACETS	0.827	0.748	0.91	0.827	0.748	0.91	CLONAL	2	FALSE	2	0.473893347079772	4		249	406	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119634894	119634895	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025070-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	104	302	0	ENST00000316626.5:c.604_605insT	p.Gly202ValfsTer22	p.G202Vfs*22	ENST00000316626		202	gga/gTga	5/12	0.448662987515539	4	FACETS	0.797	0.719	0.878	0.797	0.719	0.878	SUBCLONAL	2	FALSE	2	0.473893347079772	4		302	406	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866353	42866355	+	frameshift_variant	Frame_Shift_Del	DEL	GAC	GAC	AA	novel	NA	P-0025070-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	138	622	2	ENST00000398585.3:c.277_279delinsTT	p.Val93PhefsTer2	p.V93Ffs*2	ENST00000398585	NM_001135099.1	93	GTC/TT	3/14	0.473893347079772	4	FACETS	0.94	0.855	1	0.235	0.213	0.258	CLONAL	1	FALSE	0	0.473893347079772	4		624	913	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025396-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	151	931	1	ENST00000418115.1:c.50G>T	p.Gly17Val	p.G17V	ENST00000418115	NM_001664.2	17	gGa/gTa	2/5	1	2	FACETS	0.573	0.525	0.624	0.573	0.525	0.624	SUBCLONAL	1	TRUE	1	0.677994452064609	2		932	777	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370965	55370965	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025396-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	130	1005	2	ENST00000297316.4:c.267G>T	p.Gln89His	p.Q89H	ENST00000297316	NM_022454.3	89	caG/caT	1/2	0.639181375443839	2	FACETS	0.485	0.44	0.533	0.243	0.22	0.267	SUBCLONAL	1	TRUE	0	0.677994452064609	2		1007	790	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608277	100608277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025396-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	108	1075	1	ENST00000308731.7:c.1813G>A	p.Glu605Lys	p.E605K	ENST00000308731	NM_000061.2	605	Gag/Aag	18/19	0.443073641419106	1	FACETS	0.31	0.278	0.344	0.31	0.278	0.344	SUBCLONAL	1	TRUE	0	0.677994452064609	1		1076	679	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021124	31021124	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748644253	NA	P-0025396-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1301	102	738	3	ENST00000375687.4:c.1123G>A	p.Val375Met	p.V375M	ENST00000375687	NM_015338.5	375	Gtg/Atg	12/13	0.677994452064609	6	FACETS	0.505	0.45	0.564	0.101	0.09	0.113	SUBCLONAL	1	TRUE	1	0.677994452064609	6		741	1403	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530381	187530381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753202486	NA	P-0025396-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	54	421	0	ENST00000441802.2:c.10162G>A	p.Val3388Ile	p.V3388I	ENST00000441802	NM_005245.3	3388	Gtc/Atc	16/27	1	2	FACETS	0.495	0.425	0.57	0.495	0.425	0.57	SUBCLONAL	1	TRUE	1	0.677994452064609	2		421	322	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849484	68849484	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025396-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	244	906	0	ENST00000261769.5:c.1387G>C	p.Glu463Gln	p.E463Q	ENST00000261769	NM_004360.3	463	Gag/Cag	10/16	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.677994452064609	2		906	572	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780830	9780830	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1185305370	NA	P-0025396-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	141	1037	0	ENST00000377346.4:c.1552C>T	p.Arg518Trp	p.R518W	ENST00000377346	NM_005026.3	518	Cgg/Tgg	13/24	1	2	FACETS	0.518	0.472	0.566	0.518	0.472	0.566	SUBCLONAL	1	TRUE	1	0.677994452064609	2		1037	803	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305329	39305329	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025396-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	141	817	1	ENST00000373001.3:c.1096G>T	p.Val366Phe	p.V366F	ENST00000373001	NM_022157.3	366	Gtt/Ttt	7/7	0.382567947391049	3	FACETS	0.62	0.564	0.678	0.31	0.282	0.339	INDETERMINATE	1	TRUE	1	0.677994452064609	3		818	899	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464379	464379	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025396-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	66	753	1	ENST00000399788.2:c.815C>T	p.Ser272Leu	p.S272L	ENST00000399788	NM_001042603.1	272	tCa/tTa	7/28	1	2	FACETS	0.429	0.373	0.489	0.429	0.373	0.489	SUBCLONAL	1	TRUE	1	0.677994452064609	2		754	454	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428259	49428259	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025396-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	72	987	0	ENST00000301067.7:c.10441G>A	p.Glu3481Lys	p.E3481K	ENST00000301067	NM_003482.3	3481	Gag/Aag	37/54	0.164824640898455	3	FACETS	0.337	0.294	0.384			1	INDETERMINATE	1	TRUE	NA	0.677994452064609	3		987	844	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292893	91292893	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775197136	NA	P-0025396-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	55	709	0	ENST00000355112.3:c.395G>A	p.Arg132Gln	p.R132Q	ENST00000355112	NM_000057.2	132	cGg/cAg	3/22	0.289926602819406	1	FACETS	0.276	0.236	0.318	0.276	0.236	0.318	INDETERMINATE	1	TRUE	0	0.677994452064609	1		709	389	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244808	41244808	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs80357419	NA	P-0025396-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	38	828	1	ENST00000357654.3:c.2740G>C	p.Glu914Gln	p.E914Q	ENST00000357654	NM_007294.3	914	Gag/Cag	10/23	0.457188963170309	1	FACETS	0.24	0.199	0.285	0.24	0.199	0.285	SUBCLONAL	1	TRUE	0	0.677994452064609	1		829	309	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216640	36216640	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025396-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	76	961	0	ENST00000222270.7:c.3806A>G	p.Glu1269Gly	p.E1269G	ENST00000222270	NM_014727.1	1269	gAg/gGg	13/37	0.677994452064609	3	FACETS	0.297	0.259	0.337	0.148	0.129	0.169	SUBCLONAL	1	TRUE	1	0.677994452064609	3		961	1012	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443680	29443680	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025396-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	103	809	0	ENST00000389048.3:c.3537T>G	p.Ile1179Met	p.I1179M	ENST00000389048	NM_004304.4	1179	atT/atG	23/29	1	2	FACETS	0.481	0.431	0.534	0.481	0.431	0.534	SUBCLONAL	1	TRUE	1	0.677994452064609	2		809	632	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497253	149497253	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025396-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	115	1028	0	ENST00000261799.4:c.3065T>G	p.Ile1022Ser	p.I1022S	ENST00000261799	NM_002609.3	1022	aTc/aGc	22/23	NA	2	FACETS	0.388	0.349	0.429			1	INDETERMINATE	1	TRUE	NA	0.677994452064609	2		1028	874	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027956	48027956	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025396-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	16	400	0	ENST00000234420.5:c.2834G>A	p.Arg945Lys	p.R945K	ENST00000234420	NM_000179.2	945	aGa/aAa	4/10	0.315520778109572	2	FACETS	0.179	0.132	0.236	0.09	0.066	0.118	INDETERMINATE	1	TRUE	0	0.677994452064609	2		400	263	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152437	56152437	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025396-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	39	277	0	ENST00000399503.3:c.493G>T	p.Glu165Ter	p.E165*	ENST00000399503	NM_005921.1	165	Gag/Tag	2/20	0.59344162851768	4	FACETS	0.956	0.8	1			1	CLONAL	1	TRUE	NA	0.677994452064609	4		277	202	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518092	8518092	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025396-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	45	550	0	ENST00000356435.5:c.1299del	p.Ile434PhefsTer34	p.I434Ffs*34	ENST00000356435		433	acC/ac	10/35	0.306590251172257	2	FACETS	0.368	0.31	0.431	0.184	0.155	0.216	INDETERMINATE	1	TRUE	0	0.677994452064609	2		550	361	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350039	70350039	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746705248	NA	P-0025396-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	89	684	0	ENST00000374080.3:c.4022G>A	p.Arg1341Gln	p.R1341Q	ENST00000374080		1341	cGg/cAg	28/45	0.544805883115503	1	FACETS	0.396	0.353	0.442	0.396	0.353	0.442	SUBCLONAL	1	TRUE	0	0.677994452064609	1		684	438	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925358	114925358	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	64	543	0	ENST00000543371.1:c.1436G>C	p.Cys479Ser	p.C479S	ENST00000543371	NM_001198531.1	479	tGc/tCc	14/14	0.530766141123413	1	FACETS	0.309	0.267	0.354	0.309	0.267	0.354	SUBCLONAL	1	TRUE	0	0.530766141123413	1		543	574	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944765	71944765	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	312	679	2	ENST00000298229.2:c.2190del	p.Ser731ProfsTer27	p.S731Pfs*27	ENST00000298229	NM_001567.3	730	aCc/ac	19/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.530766141123413	2		681	1114	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133923	41133923	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	26	328	0	ENST00000379561.5:c.1705C>T	p.Pro569Ser	p.P569S	ENST00000379561	NM_002015.3	569	Ccc/Tcc	2/3	0.530766141123413	1	FACETS	0.184	0.145	0.228	0.184	0.145	0.228	SUBCLONAL	1	TRUE	0	0.530766141123413	1		328	391	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462667	40462667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	285	446	2	ENST00000345506.4:c.2365G>A	p.Ala789Thr	p.A789T	ENST00000345506	NM_003152.3	789	Gcc/Acc	20/20	0.530766141123413	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.530766141123413	1		448	572	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41219624	41219624	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs80358053	NA	P-0025479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	297	458	1	ENST00000357654.3:c.5074+1G>A		p.X1692_splice	ENST00000357654	NM_007294.3	1692			0.530766141123413	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.530766141123413	1		459	637	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223192	41223193	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	81	585	0	ENST00000357654.3:c.4738dup	p.Ser1580PhefsTer2	p.S1580Ffs*2	ENST00000357654	NM_007294.3	1580	tct/tTct	15/23	0.530766141123413	1	FACETS	0.326	0.287	0.368	0.326	0.287	0.368	SUBCLONAL	1	TRUE	0	0.530766141123413	1		585	687	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418870	116418870	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	168	399	0	ENST00000397752.3:c.3381G>T	p.Glu1127Asp	p.E1127D	ENST00000397752	NM_000245.2	1127	gaG/gaT	17/21	NA	2	FACETS	0.959	0.885	1			1	INDETERMINATE	1	TRUE	NA	0.530766141123413	2		399	660	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0026918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	201	521	1	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	1	2	FACETS	0.925	0.86	0.992	0.925	0.86	0.992	CLONAL	1	TRUE	1	0.591405154328332	2		522	735	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0027064-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	53	221	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	1	2	FACETS	0.932	0.806	1	0.932	0.806	1	CLONAL	1	TRUE	1	0.549475853891133	2		221	207	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0027064-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	515	455	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.549475853891133	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.549475853891133	3		455	1149	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447561	12447561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027064-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	191	415	0	ENST00000287820.6:c.800G>A	p.Gly267Glu	p.G267E	ENST00000287820	NM_015869.4	267	gGa/gAa	5/7	1	2	FACETS	0.922	0.855	0.991	0.922	0.855	0.991	CLONAL	1	TRUE	1	0.549475853891133	2		415	754	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247355	153247357	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0027064-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	98	196	0	ENST00000281708.4:c.1445_1447del	p.Thr482_Leu483delinsIle	p.T482_L483delinsI	ENST00000281708	NM_033632.3	482	aCTCtt/att	10/12	1	2	FACETS	0.905	0.814	1	0.905	0.814	1	CLONAL	1	TRUE	1	0.549475853891133	2		196	394	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117629997	117629997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027064-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	98	330	0	ENST00000368508.3:c.6529G>A	p.Gly2177Arg	p.G2177R	ENST00000368508	NM_002944.2	2177	Gga/Aga	41/43	1	2	FACETS	0.809	0.726	0.896	0.809	0.726	0.896	CLONAL	1	TRUE	1	0.549475853891133	2		330	441	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205490	38205490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776197580	NA	P-0027064-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	261	650	0	ENST00000317025.8:c.200C>T	p.Pro67Leu	p.P67L	ENST00000317025	NM_023034.1	67	cCt/cTt	2/24	1	2	FACETS	0.921	0.863	0.98	0.921	0.863	0.98	CLONAL	1	TRUE	1	0.549475853891133	2		650	1032	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851537	63851537	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027064-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	208	413	0	ENST00000279873.7:c.2315T>C	p.Ile772Thr	p.I772T	ENST00000279873	NM_032199.2	772	aTc/aCc	10/10	NA	2	FACETS	1	0.945	1			1	INDETERMINATE	1	TRUE	NA	0.549475853891133	2		413	745	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95596436	95596436	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027064-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	31	314	0	ENST00000393063.1:c.532C>G	p.His178Asp	p.H178D	ENST00000393063	NM_030621.3	178	Cat/Gat	6/28	1	2	FACETS	0.362	0.293	0.439	0.362	0.293	0.439	SUBCLONAL	1	TRUE	1	0.549475853891133	2		314	312	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354072	15354072	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027064-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	222	471	0	ENST00000263377.2:c.2808G>C	p.Gln936His	p.Q936H	ENST00000263377	NM_058243.2	936	caG/caC	14/20	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.549475853891133	2		471	807	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180602	56180743	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGAGCCACGTGTGAGAAGAGCAATTACAATCTCTTCATTGAATGGATGGCAGGTATGTTAATGTTTTAAATTACAAAATAGTAGTACGTGGATTTAACTTTCTGCAATTTAGGAAAAACCAGTTTAATTAAAATTTATTTCT	GGAGCCACGTGTGAGAAGAGCAATTACAATCTCTTCATTGAATGGATGGCAGGTATGTTAATGTTTTAAATTACAAAATAGTAGTACGTGGATTTAACTTTCTGCAATTTAGGAAAAACCAGTTTAATTAAAATTTATTTCT	-	novel	NA	P-0027064-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	26	272	0	ENST00000399503.3:c.3931_3982+90del		p.X1311_splice	ENST00000399503	NM_005921.1	1311		16/20	1	2	FACETS	0.299	0.236	0.37	0.299	0.236	0.37	SUBCLONAL	1	TRUE	1	0.549475853891133	2		272	317	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046317	69046317	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027064-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	128	361	0	ENST00000288368.4:c.3790G>A	p.Asp1264Asn	p.D1264N	ENST00000288368	NM_024870.2	1264	Gac/Aac	32/40	1	2	FACETS	0.801	0.728	0.876	0.801	0.728	0.876	CLONAL	1	TRUE	1	0.549475853891133	2		361	582	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0027130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	212	600	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.286049103976813	2		601	1063	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0027130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	177	646	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.172564474167402	3	FACETS	1	0.986	1	0.441	0.405	0.478	CLONAL	1	TRUE	0	0.286049103976813	3		647	1070	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467637	50467637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1262982300	NA	P-0027130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	72	406	1	ENST00000331340.3:c.872C>T	p.Thr291Met	p.T291M	ENST00000331340	NM_006060.4	291	aCg/aTg	8/8	0.2270564804435	3	FACETS	0.737	0.643	0.839	0.368	0.321	0.42	SUBCLONAL	1	TRUE	1	0.286049103976813	3		407	781	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245494	153245494	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	184	547	1	ENST00000281708.4:c.1697G>T	p.Trp566Leu	p.W566L	ENST00000281708	NM_033632.3	566	tGg/tTg	11/12	0.275339542401002	2	FACETS	0.832	0.77	0.897	0.832	0.77	0.897	CLONAL	2	TRUE	0	0.286049103976813	2		548	773	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037510	12037510	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	121	307	0	ENST00000396373.4:c.1141G>A	p.Gly381Arg	p.G381R	ENST00000396373	NM_001987.4	381	Gga/Aga	6/8	1	2	FACETS	0.789	0.716	0.866	1	0.986	1	SUBCLONAL	2	TRUE	1	0.286049103976813	2		307	536	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611752	1611752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1019768299	NA	P-0027130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	66	780	0	ENST00000344749.5:c.1910C>T	p.Pro637Leu	p.P637L	ENST00000344749	NM_001136139.2	637	cCc/cTc	19/19	1	2	FACETS	0.397	0.343	0.456	0.397	0.343	0.456	SUBCLONAL	1	TRUE	1	0.286049103976813	2		780	1162	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31521255	31521255	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	156	619	0	ENST00000344624.3:c.922A>G	p.Lys308Glu	p.K308E	ENST00000344624		308	Aaa/Gaa	3/33	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.286049103976813	2		619	881	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0027467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	65	263	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.745	0.651	0.846	0.745	0.651	0.846	SUBCLONAL	1	TRUE	1	0.552006916418683	2		263	316	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937769	76937770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	197	288	0	ENST00000373344.5:c.2978dup	p.Lys994GlufsTer6	p.K994Efs*6	ENST00000373344	NM_000489.3	993	aag/aaAg	9/35	1	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.552006916418683	1		288	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0027467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	580	940	1	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.501421641491918	2	FACETS	0.963	0.93	0.996	0.963	0.93	0.996	CLONAL	2	TRUE	0	0.552006916418683	2		941	1091	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394628	394629	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0027467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	103	586	1	ENST00000399788.2:c.5066_5067delinsAA	p.Thr1689Lys	p.T1689K	ENST00000399788	NM_001042603.1	1689	aCC/aAA	28/28	0.552006916418683	3	FACETS	0.67	0.6	0.744			1	SUBCLONAL	1	TRUE	NA	0.552006916418683	3		587	711	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56409180	56409180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs930567184	NA	P-0027467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	159	598	0	ENST00000348428.3:c.1687C>T	p.Pro563Ser	p.P563S	ENST00000348428	NM_006785.3	563	Cca/Tca	14/17	1	2	FACETS	0.843	0.775	0.914	0.843	0.775	0.914	CLONAL	1	TRUE	1	0.552006916418683	2		598	683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0027793-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	623	795	2	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.846364799632905	3	FACETS	0.998	0.981	1	0.998	0.981	1	CLONAL	3	TRUE	0	0.846364799632905	3		797	700	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679547	86679547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027793-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	76	318	0	ENST00000274376.6:c.2708G>A	p.Arg903Gln	p.R903Q	ENST00000274376	NM_002890.2	903	cGa/cAa	21/25	1	2	FACETS	0.859	0.768	0.954	0.859	0.768	0.954	CLONAL	1	TRUE	1	0.846364799632905	2		318	209	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883163	37883163	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027793-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6479	6755	829	5	ENST00000269571.5:c.3066G>T	p.Glu1022Asp	p.E1022D	ENST00000269571		1022	gaG/gaT	25/27	0.846364799632905	33	FACETS	1	0.991	1			1	CLONAL	17	TRUE	NA	0.846364799632905	33		834	13234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0028066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	177	621	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.251656989612844	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	FALSE	0	0.251656989612844	2		622	623	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426812	121426812	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377110124	NA	P-0028066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	106	558	1	ENST00000257555.6:c.503G>A	p.Arg168His	p.R168H	ENST00000257555		168	cGc/cAc	2/10	0.204944902438176	4	FACETS	1	0.982	1			1	CLONAL	1	FALSE	NA	0.251656989612844	4		559	704	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546704	9546704	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	32	254	0	ENST00000353224.5:c.1318G>T	p.Val440Phe	p.V440F	ENST00000353224	NM_177990.2	440	Gtc/Ttc	5/10	0.251656989612844	5	FACETS	1	0.834	1	0.342	0.278	0.415	CLONAL	1	FALSE	2	0.251656989612844	5		254	341	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528635	89528635	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	60	267	0	ENST00000336596.2:c.2935G>C	p.Gly979Arg	p.G979R	ENST00000336596	NM_005233.5	979	Ggc/Cgc	17/17	0.213261551869341	3	FACETS	1	0.957	1	0.644	0.556	0.738	CLONAL	1	FALSE	1	0.251656989612844	3		267	417	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101099	27101099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	251	768	1	ENST00000324856.7:c.4381C>T	p.Arg1461Ter	p.R1461*	ENST00000324856	NM_006015.4	1461	Cga/Tga	18/20	1	2	FACETS	1	0.957	1	1	0.995	1	CLONAL	2	TRUE	1	0.271042986239638	2		769	902	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779172	135779172	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203631	NA	P-0028079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	151	494	1	ENST00000298552.3:c.2074C>T	p.Arg692Ter	p.R692*	ENST00000298552	NM_001162426.1	692	Cga/Tga	17/23	0.233044462487831	2	FACETS	0.964	0.885	1	0.964	0.885	1	CLONAL	2	TRUE	0	0.271042986239638	2		495	578	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440346	52440346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1559589762	NA	P-0028079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	152	592	1	ENST00000460680.1:c.706G>A	p.Asp236Asn	p.D236N	ENST00000460680	NM_004656.3	236	Gac/Aac	9/17	NA	2	FACETS	0.876	0.804	0.951			1	INDETERMINATE	2	TRUE	NA	0.271042986239638	2		593	640	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52663032	52663032	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	85	239	1	ENST00000394830.3:c.1321G>T	p.Glu441Ter	p.E441*	ENST00000394830	NM_018313.4	441	Gaa/Taa	13/30	NA	2	FACETS	0.925	0.825	1			1	INDETERMINATE	2	TRUE	NA	0.271042986239638	2		240	339	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225060	NA	P-0028283-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	210	527	1	ENST00000263967.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000263967	NM_006218.2	104	cCa/cTa	2/21	0.525322049851823	4	FACETS	0.884	0.83	0.937	0.884	0.83	0.937	CLONAL	3	TRUE	1	0.525322049851823	4		528	460	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738607	43738608	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0028283-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	134	496	0	ENST00000382044.4:c.3017_3018del	p.Glu1006ValfsTer13	p.E1006Vfs*13	ENST00000382044	NM_001141980.1	1006	gAG/g	14/28	0.494470399099768	2	FACETS	0.8	0.738	0.862	0.8	0.738	0.862	SUBCLONAL	2	TRUE	0	0.525322049851823	2		496	319	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933281	39933281	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028283-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	127	668	0	ENST00000378444.4:c.1318C>G	p.Pro440Ala	p.P440A	ENST00000378444	NM_001123385.1	440	Cca/Gca	4/15	0.213528699140621	5	FACETS	1	0.968	1	0.384	0.348	0.422	INDETERMINATE	1	TRUE	2	0.525322049851823	5		668	750	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	281	681	1	ENST00000269305.4:c.859G>T	p.Glu287Ter	p.E287*	ENST00000269305	NM_001126112.2	287	Gag/Tag	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		682	402	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522568	106522568	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs754441790	NA	P-0028328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	146	431	0	ENST00000359195.3:c.2545C>T	p.Arg849Ter	p.R849*	ENST00000359195	NM_002649.2	849	Cga/Tga	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		431	340	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199867	128199867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	131	385	1	ENST00000341105.2:c.1438G>A	p.Gly480Ser	p.G480S	ENST00000341105	NM_032638.4	480	Ggc/Agc	6/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		386	322	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625330	69625330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143483033	NA	P-0028785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	41	616	1	ENST00000334134.2:c.463G>A	p.Val155Met	p.V155M	ENST00000334134	NM_005247.2	155	Gtg/Atg	3/3	1	2	FACETS	0.798	0.663	0.95	0.798	0.663	0.95	CLONAL	1	TRUE	1	0.13	2		617	790	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844181	68844181	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	72	709	0	ENST00000261769.5:c.769G>A	p.Asp257Asn	p.D257N	ENST00000261769	NM_004360.3	257	Gac/Aac	6/16	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.13	2		709	1007	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397639	139397639	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	354	693	0	ENST00000277541.6:c.5162T>G	p.Val1721Gly	p.V1721G	ENST00000277541	NM_017617.3	1721	gTg/gGg	27/34	1	2	FACETS	0.797	0.756	0.838	0.797	0.756	0.838	SUBCLONAL	1	TRUE	1	0.835266222858464	2		693	1064	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390793	139390793	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	135	881	0	ENST00000277541.6:c.7398del	p.Ser2467ArgfsTer10	p.S2467Rfs*10	ENST00000277541	NM_017617.3	2466	acG/ac	34/34	1	2	FACETS	0.262	0.237	0.288	0.262	0.237	0.288	SUBCLONAL	1	TRUE	1	0.835266222858464	2		881	1233	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390904	139390908	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGT	CAGGT	ACTG	novel	NA	P-0029293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	377	755	1	ENST00000277541.6:c.7283_7287delinsCAGT	p.His2428ProfsTer7	p.H2428Pfs*7	ENST00000277541	NM_017617.3	2428	cACCTG/cCAGT	34/34	1	2	FACETS	0.78	0.741	0.82	0.78	0.741	0.82	SUBCLONAL	1	TRUE	1	0.835266222858464	2		756	1157	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923604	39923604	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0029293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	124	294	0	ENST00000378444.4:c.3487del	p.Arg1163AspfsTer13	p.R1163Dfs*13	ENST00000378444	NM_001123385.1	1163	Cga/ga	7/15	1	1	FACETS	0.331	0.3	0.362	0.331	0.3	0.362	SUBCLONAL	1	TRUE	0	0.835266222858464	1		294	523	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0029480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	187	308	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.907	0.84	0.976	0.907	0.84	0.976	CLONAL	1	TRUE	1	0.557399288260534	2		308	740	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032460	12032460	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	192	410	0	ENST00000353533.5:c.896A>T	p.Glu299Val	p.E299V	ENST00000353533	NM_003010.3	299	gAg/gTg	9/11	0.557399288260534	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.557399288260534	1		410	452	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637008	93637008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201479078	NA	P-0029480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	242	518	0	ENST00000375746.1:c.1058C>T	p.Ala353Val	p.A353V	ENST00000375746	NM_001174167.1	353	gCg/gTg	9/14	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.557399288260534	2		518	779	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116156	67116157	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0029480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	196	519	0	ENST00000412916.2:c.443_444dup	p.Arg149GlufsTer31	p.R149Efs*31	ENST00000412916		147	cgg/cgGAg	5/6	0.557399288260534	1	FACETS	0.861	0.802	0.922	0.861	0.802	0.922	CLONAL	1	TRUE	0	0.557399288260534	1		519	589	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754268	57754268	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	468	511	0	ENST00000274289.3:c.583T>C	p.Tyr195His	p.Y195H	ENST00000274289	NM_006622.3	195	Tac/Cac	4/14	0.557399288260534	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.557399288260534	3		511	1010	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15976840	15976843	+	frameshift_variant	Frame_Shift_Ins	INS	AGCT	AGCT	GACTCCTAGTCCTA	novel	NA	P-0029480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	154	505	0	ENST00000268712.3:c.3711_3714delinsTAGGACTAGGAGTC	p.Ala1238ArgfsTer6	p.A1238Rfs*6	ENST00000268712	NM_006311.3	1237	acAGCT/acTAGGACTAGGAGTC	28/46	0.557399288260534	1	FACETS	0.775	0.714	0.838	0.775	0.714	0.838	SUBCLONAL	1	TRUE	0	0.557399288260534	1		505	514	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0030198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	51	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.161356370636021	3	FACETS	0.794	0.677	0.923	0.794	0.677	0.923	CLONAL	2	TRUE	1	0.173110055714356	3		311	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0030198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	127	766	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.173110055714356	1	FACETS	0.819	0.742	0.9	1	0.987	1	CLONAL	2	TRUE	0	0.173110055714356	1		767	818	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839699	27839699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	32	383	0	ENST00000328488.2:c.395G>A	p.Arg132Gln	p.R132Q	ENST00000328488	NM_003533.2	132	cGa/cAa	1/1	1	2	FACETS	0.587	0.475	0.714	0.587	0.475	0.714	SUBCLONAL	1	TRUE	1	0.173110055714356	2		383	630	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993912	72993912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1187392987	NA	P-0030198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	72	469	1	ENST00000268489.5:c.133G>A	p.Glu45Lys	p.E45K	ENST00000268489	NM_006885.3	45	Gag/Aag	2/10	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.173110055714356	2		470	797	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121912651	NA	P-0030380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	483	572	0	ENST00000269305.4:c.742C>G	p.Arg248Gly	p.R248G	ENST00000269305	NM_001126112.2	248	Cgg/Ggg	7/11	0.937586299289769	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.95101292973534	1		572	515	SUCCESS
ATR	545	MSKCC	GRCh37	3	142285074	142285077	+	frameshift_variant	Frame_Shift_Del	DEL	AGTC	AGTC	-	novel	NA	P-0030380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	355	404	0	ENST00000350721.4:c.178_181del	p.Asp60LeufsTer6	p.D60Lfs*6	ENST00000350721	NM_001184.3	60	GACTct/ct	3/47	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.95101292973534	2		404	714	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271519	26271519	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	138	294	0	ENST00000305910.3:c.94G>T	p.Ala32Ser	p.A32S	ENST00000305910	NM_003534.2	32	Gcc/Tcc	1/1	0.489914836744952	1	FACETS	0.384	0.353	0.416	0.384	0.353	0.416	INDETERMINATE	1	TRUE	0	0.95101292973534	1		294	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0030998-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	94	448	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.477654698457244	1	FACETS	0.954	0.859	1	0.954	0.859	1	CLONAL	1	TRUE	0	0.477654698457244	1		448	314	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0030998-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	561	477	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.477654698457244	8	FACETS	0.998	0.966	1	0.998	0.966	1	CLONAL	6	TRUE	2	0.477654698457244	8		477	954	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909214	41909214	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030998-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	113	504	0	ENST00000372991.4:c.174G>C	p.Lys58Asn	p.K58N	ENST00000372991	NM_001760.3	58	aaG/aaC	1/5	0.477654698457244	7	FACETS	0.895	0.803	0.993			1	CLONAL	1	TRUE	NA	0.477654698457244	7		504	1160	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909235	41909235	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030998-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	98	495	0	ENST00000372991.4:c.153G>C	p.Glu51Asp	p.E51D	ENST00000372991	NM_001760.3	51	gaG/gaC	1/5	0.477654698457244	7	FACETS	0.816	0.726	0.912			1	CLONAL	1	TRUE	NA	0.477654698457244	7		495	1104	SUCCESS
BTK	695	MSKCC	GRCh37	X	100604886	100604886	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030998-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	21	347	0	ENST00000308731.7:c.1967A>T	p.Asp656Val	p.D656V	ENST00000308731	NM_000061.2	656	gAt/gTt	19/19	0.47340500516547	2	FACETS	0.423	0.327	0.534	0.211	0.163	0.267	SUBCLONAL	1	TRUE	0	0.477654698457244	2		347	208	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909320	41909320	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030998-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	122	450	0	ENST00000372991.4:c.68G>C	p.Gly23Ala	p.G23A	ENST00000372991	NM_001760.3	23	gGg/gCg	1/5	0.477654698457244	7	FACETS	1	0.908	1			1	CLONAL	1	TRUE	NA	0.477654698457244	7		450	1113	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505377	125505377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030998-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	16	322	0	ENST00000428830.2:c.667G>A	p.Glu223Lys	p.E223K	ENST00000428830	NM_001114121.2	223	Gaa/Aaa	7/14	0.477654698457244	4	FACETS	0.421	0.311	0.552	0.105	0.077	0.138	SUBCLONAL	1	TRUE	0	0.477654698457244	4		322	235	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031131-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	2	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.2	0.076	0.413	0.2	0.076	0.413	SUBCLONAL	1	TRUE	1	0.14	2		311	143	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0031131-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	18	585	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			1	2	FACETS	0.501	0.376	0.651	0.501	0.376	0.651	SUBCLONAL	1	TRUE	1	0.14	2		585	513	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047205	77047205	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031131-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	26	548	0	ENST00000356341.3:c.1339A>G	p.Ile447Val	p.I447V	ENST00000356341	NM_002576.4	447	Atc/Gtc	13/15	1	2	FACETS	0.904	0.715	1	0.904	0.715	1	CLONAL	1	TRUE	1	0.14	2		548	411	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0031213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	22	444	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.62	0.479	0.786	0.62	0.479	0.786	SUBCLONAL	1	TRUE	1	0.12	2		444	591	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691929	30691929	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	32	492	0	ENST00000295754.5:c.431A>G	p.Asn144Ser	p.N144S	ENST00000295754	NM_003242.5	144	aAt/aGt	3/7	1	2	FACETS	0.963	0.78	1	0.963	0.78	1	CLONAL	1	TRUE	1	0.12	2		492	554	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405962	49405962	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	44	587	0	ENST00000418115.1:c.176A>G	p.Asp59Gly	p.D59G	ENST00000418115	NM_001664.2	59	gAc/gGc	3/5	1	2	FACETS	0.875	0.732	1	0.875	0.732	1	CLONAL	1	TRUE	1	0.12	2		587	838	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	185	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.876	0.81	0.945	0.876	0.81	0.945	CLONAL	1	TRUE	1	0.50680353346973	2		539	833	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126342	5126342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746602942	NA	P-0031231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	115	361	0	ENST00000381652.3:c.3187C>T	p.Arg1063Cys	p.R1063C	ENST00000381652	NM_004972.3	1063	Cgt/Tgt	24/25	1	2	FACETS	0.984	0.892	1	0.984	0.892	1	CLONAL	1	TRUE	1	0.50680353346973	2		361	461	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852095	63852095	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0031231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	231	702	0	ENST00000279873.7:c.2873C>G	p.Ser958Ter	p.S958*	ENST00000279873	NM_032199.2	958	tCa/tGa	10/10	0.50680353346973	1	FACETS	0.823	0.769	0.878	0.823	0.769	0.878	CLONAL	1	TRUE	0	0.50680353346973	1		702	827	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912525	32912525	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	637	521	1	ENST00000380152.3:c.4033del	p.Asp1345IlefsTer29	p.D1345Ifs*29	ENST00000380152		1345	Gat/at	11/27	0.50680353346973	3	FACETS	0.964	0.934	0.993	0.964	0.934	0.993	CLONAL	3	TRUE	0	0.50680353346973	3		522	1090	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343642	343642	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	379	890	2	ENST00000262320.3:c.2032C>A	p.Gln678Lys	p.Q678K	ENST00000262320	NM_003502.3	678	Cag/Aag	8/11	NA	2	FACETS	0.998	0.946	1			1	INDETERMINATE	1	TRUE	NA	0.50680353346973	2		892	1499	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14028066	14028066	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	168	441	0	ENST00000311895.7:c.1120G>C	p.Val374Leu	p.V374L	ENST00000311895	NM_005236.2	374	Gtc/Ctc	7/11	0.449811890525472	3	FACETS	0.919	0.845	0.997			1	CLONAL	1	TRUE	NA	0.50680353346973	3		441	904	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753123	42753123	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	286	622	0	ENST00000222329.4:c.1141C>G	p.Pro381Ala	p.P381A	ENST00000222329	NM_006494.2	381	Ccg/Gcg	4/4	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.50680353346973	2		622	1067	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38996937	38996937	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	267	591	0	ENST00000357387.3:c.440T>G	p.Leu147Arg	p.L147R	ENST00000357387	NM_152756.3	147	cTt/cGt	6/38	1	2	FACETS	0.991	0.93	1	0.991	0.93	1	CLONAL	1	TRUE	1	0.50680353346973	2		591	1063	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578179	7578179	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	602	662	0	ENST00000269305.4:c.670G>T	p.Glu224Ter	p.E224*	ENST00000269305	NM_001126112.2	224	Gag/Tag	6/11	0.413597848082348	4	FACETS	1	0.994	1			1	CLONAL	3	TRUE	NA	0.401869560743631	4		662	1248	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115967	8115968	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	112	327	0	ENST00000346208.3:c.1315dup	p.Val439GlyfsTer68	p.V439Gfs*68	ENST00000346208		438	atg/atGg	6/6	0.265192938229432	4	FACETS	0.775	0.7	0.853	0.775	0.7	0.853	SUBCLONAL	2	TRUE	2	0.401869560743631	4		327	504	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519308	137519308	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	211	528	0	ENST00000367739.4:c.1330G>T	p.Glu444Ter	p.E444*	ENST00000367739	NM_000416.2	444	Gag/Tag	7/7	0.170071106313289	4	FACETS	1	0.947	1			1	INDETERMINATE	2	TRUE	NA	0.401869560743631	4		528	723	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321067	137321067	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	100	580	0	ENST00000481739.1:c.1024G>A	p.Val342Met	p.V342M	ENST00000481739	NM_002957.4	342	Gtg/Atg	7/10	0.389371137195204	4	FACETS	0.995	0.89	1	0.332	0.296	0.37	CLONAL	1	TRUE	1	0.401869560743631	4		580	701	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	12	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.282842774464332	5	FACETS	0.889	0.657	1	1	0.831	1	CLONAL	4	FALSE	2	0.282842774464332	5		539	34	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578281	7578281	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660254	NA	P-0031582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	19	606	0	ENST00000269305.4:c.568C>A	p.Pro190Thr	p.P190T	ENST00000269305	NM_001126112.2	190	Cct/Act	6/11	0.282842774464332	1	FACETS	1	0.84	1	1	0.956	1	CLONAL	3	FALSE	0	0.282842774464332	1		606	37	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45649954	45649954	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs186459476	NA	P-0031582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	35	551	1	ENST00000407780.3:c.881C>T	p.Pro294Leu	p.P294L	ENST00000407780	NM_001283052.1	294	cCg/cTg	6/7	0.282842774464332	6	FACETS	0.897	0.741	1	0.598	0.494	0.713	CLONAL	2	FALSE	3	0.282842774464332	6		552	216	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925570	114925570	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	228	654	0	ENST00000543371.1:c.1648C>G	p.Leu550Val	p.L550V	ENST00000543371	NM_001198531.1	550	Ctc/Gtc	14/14	0.282842774464332	2	FACETS	0.93	0.873	0.987	1	0.992	1	CLONAL	3	FALSE	0	0.282842774464332	2		654	578	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661797	227661798	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0031582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	19	695	0	ENST00000305123.5:c.1657dup	p.Glu553GlyfsTer58	p.E553Gfs*58	ENST00000305123	NM_005544.2	553	gag/gGag	1/2	0.282842774464332	4	FACETS	0.833	0.634	1	0.278	0.211	0.355	CLONAL	1	FALSE	1	0.282842774464332	4		695	207	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974768	21974788	+	protein_altering_variant	In_Frame_Del	DEL	GCGGCCGTGGCCAGCCAGTCA	GCGGCCGTGGCCAGCCAGTCA	CCG	novel	NA	P-0031582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	106	258	2	ENST00000304494.5:c.39_59delinsCGG	p.Asp14_Ala20delinsGly	p.D14_A20delinsG	ENST00000304494	NM_000077.4	13	gcTGACTGGCTGGCCACGGCCGCg/gcCGGg	1/3	0.282842774464332	31	FACETS	1	0.922	1			1	CLONAL	11	FALSE	NA	0.282842774464332	31		260	341	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0031811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	70	309	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.265042615836746	3	FACETS	0.852	0.748	0.963	0.852	0.748	0.963	CLONAL	2	TRUE	1	0.265042615836746	3		309	351	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0031811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	60	586	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.814	0.702	0.937	0.814	0.702	0.937	CLONAL	1	TRUE	1	0.265042615836746	2		586	556	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440757	56440757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774211426	NA	P-0031811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	178	608	0	ENST00000407977.2:c.461C>T	p.Pro154Leu	p.P154L	ENST00000407977		154	cCg/cTg	5/10	0.265042615836746	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.265042615836746	2		608	616	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385120	41385120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	94	787	1	ENST00000373198.4:c.841G>A	p.Ala281Thr	p.A281T	ENST00000373198	NM_133170.3	281	Gcg/Acg	6/32	1	2	FACETS	0.996	0.887	1	0.996	0.887	1	CLONAL	1	TRUE	1	0.265042615836746	2		788	712	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0032117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	391	496	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.349436721132565	3	FACETS	0.975	0.944	1	1	0.997	1	CLONAL	5	FALSE	0	0.349436721132565	3		496	539	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0032117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	90	399	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.753	0.674	0.836	1	0.981	1	SUBCLONAL	2	FALSE	1	0.349436721132565	2		399	342	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950754	38950754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	18	353	0	ENST00000357387.3:c.3196G>A	p.Glu1066Lys	p.E1066K	ENST00000357387	NM_152756.3	1066	Gaa/Aaa	31/38	0.320192518687733	3	FACETS	1	0.809	1	0.535	0.408	0.681	CLONAL	1	FALSE	1	0.349436721132565	3		353	113	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261448	16261448	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1456771008	NA	P-0032117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	168	576	1	ENST00000375759.3:c.8713G>A	p.Asp2905Asn	p.D2905N	ENST00000375759	NM_015001.2	2905	Gat/Aat	11/15	0.320192518687733	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	FALSE	1	0.349436721132565	3		577	482	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653782	89653783	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	35	340	1	ENST00000371953.3:c.81dup	p.Ile28TyrfsTer16	p.I28Yfs*16	ENST00000371953	NM_000314.4	27	tat/taTt	2/9	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.349436721132565	2		341	148	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273096	198273096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	45	533	0	ENST00000335508.6:c.1114C>G	p.Pro372Ala	p.P372A	ENST00000335508	NM_012433.2	372	Cca/Gca	8/25	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	FALSE	1	0.349436721132565	2		533	249	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942800	68942800	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	102	560	0	ENST00000288368.4:c.612G>T	p.Met204Ile	p.M204I	ENST00000288368	NM_024870.2	204	atG/atT	6/40	0.349436721132565	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	FALSE	1	0.349436721132565	3		560	293	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443697	29443697	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs281864719	NA	P-0032149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	157	465	0	ENST00000389048.3:c.3520T>A	p.Phe1174Ile	p.F1174I	ENST00000389048	NM_004304.4	1174	Ttc/Atc	23/29	0.801512017428998	3	FACETS	0.948	0.873	1	0.474	0.436	0.513	CLONAL	1	TRUE	1	0.801512017428998	3		465	579	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999161	100999161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1050185598	NA	P-0032250-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	519	598	0	ENST00000325455.5:c.641C>T	p.Pro214Leu	p.P214L	ENST00000325455	NM_001202474.3	214	cCg/cTg	1/8	0.913585861675045	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.920593740747598	3		598	788	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061143	38061202	+	inframe_deletion	In_Frame_Del	DEL	GCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTG	GCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTG	-	novel	NA	P-0032250-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	240	558	0	ENST00000250448.2:c.787_846del	p.Gln263_Ser282del	p.Q263_S282del	ENST00000250448	NM_004496.3	263	CAGAAGCGCTTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGC/-	2/2	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.920593740747598	2		558	499	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879525	151879526	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0032250-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	566	560	0	ENST00000262189.6:c.5419_5420del	p.Gln1807GlufsTer20	p.Q1807Efs*20	ENST00000262189	NM_170606.2	1807	CAg/g	36/59	0.877403834813014	3	FACETS	0.947	0.917	0.977	0.947	0.917	0.977	CLONAL	2	TRUE	1	0.920593740747598	3		560	948	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061210	38061213	+	missense_variant	Missense_Mutation	ONP	AAGT	AAGT	GAGA	novel	NA	P-0032250-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	241	549	0	ENST00000250448.2:c.776_779delinsTCTC	p.Tyr259_Leu260delinsPheSer	p.Y259_L260delinsFS	ENST00000250448	NM_004496.3	259	tACTTg/tTCTCg	2/2	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.920593740747598	2		549	493	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226672	2226727	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCGGCAAGGAGGCAGGGGAGGGCGGCCTACCGCTGTGCGGGCCCACGGACAAGA	CCGCGGCAAGGAGGCAGGGGAGGGCGGCCTACCGCTGTGCGGGCCCACGGACAAGA	-	novel	NA	P-0032250-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	292	744	0	ENST00000398665.3:c.4154_4209del	p.Arg1385ProfsTer134	p.R1385Pfs*134	ENST00000398665	NM_032482.2	1384	agCCGCGGCAAGGAGGCAGGGGAGGGCGGCCTACCGCTGTGCGGGCCCACGGACAAGAcc/agcc	27/28	0.920593740747598	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.920593740747598	1		744	333	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	76	348	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.958	0.851	1	0.958	0.851	1	CLONAL	1	TRUE	1	0.596347727218444	2		349	266	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012386	152012386	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	48	358	0	ENST00000262189.6:c.427del	p.Ser143ValfsTer3	p.S143Vfs*3	ENST00000262189	NM_170606.2	143	Agt/gt	4/59	0.559919138399684	3	FACETS	0.733	0.624	0.852	0.367	0.312	0.426	SUBCLONAL	1	TRUE	1	0.596347727218444	3		358	285	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470573	25470573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553414070	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	216	611	0	ENST00000264709.3:c.901C>T	p.Arg301Trp	p.R301W	ENST00000264709	NM_175629.2	301	Cgg/Tgg	8/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.596347727218444	2		611	664	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579529	7579529	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658483	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	158	651	2	ENST00000269305.4:c.158G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tGg/tAg	4/11	0.596347727218444	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.596347727218444	1		653	341	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	16	693	4	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	0.559919138399684	3	FACETS	0.566	0.423	0.734	0.283	0.211	0.367	SUBCLONAL	1	TRUE	1	0.596347727218444	3		697	123	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276755	15276755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138265894	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	35	662	2	ENST00000263388.2:c.5510G>A	p.Arg1837His	p.R1837H	ENST00000263388	NM_000435.2	1837	cGt/cAt	30/33	1	2	FACETS	0.19	0.155	0.229	0.19	0.155	0.229	SUBCLONAL	1	TRUE	1	0.596347727218444	2		664	618	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226361	133226361	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs745750549	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	44	685	0	ENST00000320574.5:c.3697C>T	p.Arg1233Ter	p.R1233*	ENST00000320574	NM_006231.2	1233	Cga/Tga	30/49	1	2	FACETS	0.239	0.2	0.282	0.239	0.2	0.282	SUBCLONAL	1	TRUE	1	0.596347727218444	2		685	618	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652833	212652833	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs370840578	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	68	394	0	ENST00000342788.4:c.473C>A	p.Ala158Glu	p.A158E	ENST00000342788	NM_005235.2	158	gCa/gAa	4/28	1	2	FACETS	0.975	0.86	1	0.975	0.86	1	CLONAL	1	TRUE	1	0.596347727218444	2		394	234	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188297	32188297	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs753855314	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	28	612	4	ENST00000375023.3:c.1044del	p.Gly349AlafsTer49	p.G349Afs*49	ENST00000375023	NM_004557.3	348	ggC/gg	6/30	1	2	FACETS	0.184	0.146	0.227	0.184	0.146	0.227	SUBCLONAL	1	TRUE	1	0.596347727218444	2		616	511	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89809344	89809344	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1250230818	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	17	333	0	ENST00000389301.3:c.3629T>C	p.Phe1210Ser	p.F1210S	ENST00000389301	NM_000135.2	1210	tTc/tCc	37/43	1	2	FACETS	0.193	0.144	0.252	0.193	0.144	0.252	SUBCLONAL	1	TRUE	1	0.596347727218444	2		333	295	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424178	49424178	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs886040960	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	37	339	1	ENST00000301067.7:c.13884del	p.Thr4629ProfsTer11	p.T4629Pfs*11	ENST00000301067	NM_003482.3	4628	ccC/cc	42/54	1	2	FACETS	0.387	0.319	0.461	0.387	0.319	0.461	SUBCLONAL	1	TRUE	1	0.596347727218444	2		340	321	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300076	137300076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373515948	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	179	686	0	ENST00000481739.1:c.361G>A	p.Ala121Thr	p.A121T	ENST00000481739	NM_002957.4	121	Gcc/Acc	3/10	1	2	FACETS	0.888	0.822	0.957	0.888	0.822	0.957	CLONAL	1	TRUE	1	0.596347727218444	2		686	676	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609930	81609930	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	62	297	0	ENST00000298171.2:c.1528T>C	p.Tyr510His	p.Y510H	ENST00000298171	NM_000369.2	510	Tat/Cat	10/10	0.559919138399684	3	FACETS	0.931	0.811	1	0.465	0.405	0.53	CLONAL	1	TRUE	1	0.596347727218444	3		297	290	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056187	27056187	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1484601889	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	100	347	0	ENST00000324856.7:c.1183T>C	p.Tyr395His	p.Y395H	ENST00000324856	NM_006015.4	395	Tat/Cat	2/20	0.186573787924988	3	FACETS	1	0.966	1	0.389	0.35	0.43	INDETERMINATE	1	TRUE	0	0.596347727218444	3		347	373	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246078875	246078875	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	86	544	0	ENST00000388985.4:c.770A>G	p.Tyr257Cys	p.Y257C	ENST00000388985		257	tAc/tGc	8/12	0.186573787924988	3	FACETS	0.639	0.566	0.717	0.213	0.188	0.239	INDETERMINATE	1	TRUE	0	0.596347727218444	3		544	586	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203663	94203663	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	30	290	0	ENST00000323929.3:c.991G>T	p.Ala331Ser	p.A331S	ENST00000323929	NM_005591.3	331	Gcc/Tcc	9/20	1	2	FACETS	0.521	0.423	0.63	0.521	0.423	0.63	SUBCLONAL	1	TRUE	1	0.596347727218444	2		290	193	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924582	94924582	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	17	408	0	ENST00000536441.1:c.328T>C	p.Tyr110His	p.Y110H	ENST00000536441	NM_144665.3	110	Tat/Cat	3/10	1	2	FACETS	0.322	0.241	0.417	0.322	0.241	0.417	SUBCLONAL	1	TRUE	1	0.596347727218444	2		408	177	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144699	119144700	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	18	427	0	ENST00000264033.4:c.717dup	p.Glu240Ter	p.E240*	ENST00000264033	NM_005188.3	238	gtt/gTtt	4/16	1	2	FACETS	0.175	0.132	0.227	0.175	0.132	0.227	SUBCLONAL	1	TRUE	1	0.596347727218444	2		427	344	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245976	46245976	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	10	278	0	ENST00000334344.6:c.4070T>C	p.Leu1357Pro	p.L1357P	ENST00000334344	NM_152641.2	1357	cTa/cCa	15/21	1	2	FACETS	0.206	0.139	0.289	0.206	0.139	0.289	SUBCLONAL	1	TRUE	1	0.596347727218444	2		278	163	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865583	57865584	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	80	706	0	ENST00000228682.2:c.3065dup	p.Pro1023SerfsTer13	p.P1023Sfs*13	ENST00000228682	NM_005269.2	1020	-/G	12/12	1	2	FACETS	0.647	0.572	0.726	0.647	0.572	0.726	SUBCLONAL	1	TRUE	1	0.596347727218444	2		706	415	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953607	32953607	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	114	342	0	ENST00000380152.3:c.8908T>C	p.Trp2970Arg	p.W2970R	ENST00000380152		2970	Tgg/Cgg	22/27	0.57241371976242	3	FACETS	1	0.953	1	0.701	0.645	0.757	CLONAL	2	TRUE	0	0.596347727218444	3		342	236	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955457	48955457	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	247	355	0	ENST00000267163.4:c.1573del	p.Ala525ProfsTer7	p.A525Pfs*7	ENST00000267163	NM_000321.2	525	Gcc/cc	17/27	0.57241371976242	3	FACETS	0.907	0.865	0.949	0.907	0.865	0.949	CLONAL	3	TRUE	0	0.596347727218444	3		355	395	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061793	38061793	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	91	629	0	ENST00000250448.2:c.196A>T	p.Met66Leu	p.M66L	ENST00000250448	NM_004496.3	66	Atg/Ttg	2/2	0.559919138399684	3	FACETS	0.618	0.549	0.691	0.309	0.274	0.346	SUBCLONAL	1	TRUE	1	0.596347727218444	3		629	641	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094791	2094791	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	41	662	0	ENST00000219066.1:c.389A>G	p.Tyr130Cys	p.Y130C	ENST00000219066	NM_002528.5	130	tAc/tGc	3/6	1	2	FACETS	0.231	0.192	0.275	0.231	0.192	0.275	SUBCLONAL	1	TRUE	1	0.596347727218444	2		662	594	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644477	3644477	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs760126773	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	204	618	0	ENST00000294008.3:c.2137C>T	p.Arg713Ter	p.R713*	ENST00000294008	NM_032444.2	713	Cga/Tga	10/15	1	2	FACETS	0.946	0.881	1	0.946	0.881	1	CLONAL	1	TRUE	1	0.596347727218444	2		618	723	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761163	59761163	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	19	578	0	ENST00000259008.2:c.3244A>G	p.Thr1082Ala	p.T1082A	ENST00000259008	NM_032043.2	1082	Acc/Gcc	20/20	1	2	FACETS	0.186	0.141	0.24	0.186	0.141	0.24	SUBCLONAL	1	TRUE	1	0.596347727218444	2		578	342	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63553997	63553997	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs758769942	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	183	404	0	ENST00000307078.5:c.742G>T	p.Val248Phe	p.V248F	ENST00000307078	NM_004655.3	248	Gtt/Ttt	2/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.596347727218444	2		404	496	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78931470	78931470	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	161	531	0	ENST00000306801.3:c.3417G>C	p.Met1139Ile	p.M1139I	ENST00000306801	NM_020761.2	1139	atG/atC	29/34	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.596347727218444	2		531	529	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390415	56390415	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	22	360	0	ENST00000348428.3:c.1154A>G	p.Asp385Gly	p.D385G	ENST00000348428	NM_006785.3	385	gAt/gGt	10/17	1	2	FACETS	0.34	0.264	0.427	0.34	0.264	0.427	SUBCLONAL	1	TRUE	1	0.596347727218444	2		360	217	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621047	1621047	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	198	761	0	ENST00000344749.5:c.1015-2A>G		p.X339_splice	ENST00000344749	NM_001136139.2	339			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.596347727218444	2		761	647	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245973	5245973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	165	677	0	ENST00000357368.4:c.802G>A	p.Ala268Thr	p.A268T	ENST00000357368	NM_002850.3	268	Gcc/Acc	10/38	1	2	FACETS	0.946	0.873	1	0.946	0.873	1	CLONAL	1	TRUE	1	0.596347727218444	2		677	585	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140124	50140124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1311348311	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	80	577	0	ENST00000246792.3:c.301G>A	p.Gly101Ser	p.G101S	ENST00000246792	NM_006270.3	101	Ggc/Agc	3/6	1	2	FACETS	0.504	0.445	0.568	0.504	0.445	0.568	SUBCLONAL	1	TRUE	1	0.596347727218444	2		577	532	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158595001	158595001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	43	391	0	ENST00000263640.3:c.1346G>A	p.Cys449Tyr	p.C449Y	ENST00000263640	NM_001105.4	449	tGt/tAt	10/11	1	2	FACETS	0.353	0.296	0.417	0.353	0.296	0.417	SUBCLONAL	1	TRUE	1	0.596347727218444	2		391	408	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198272769	198272769	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	15	593	0	ENST00000335508.6:c.1192C>A	p.Pro398Thr	p.P398T	ENST00000335508	NM_012433.2	398	Cca/Aca	9/25	1	2	FACETS	0.185	0.135	0.245	0.185	0.135	0.245	SUBCLONAL	1	TRUE	1	0.596347727218444	2		593	272	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645646	215645646	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs565582076	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	70	521	1	ENST00000260947.4:c.952A>G	p.Asn318Asp	p.N318D	ENST00000260947	NM_000465.2	318	Aat/Gat	4/11	1	2	FACETS	0.943	0.833	1	0.943	0.833	1	CLONAL	1	TRUE	1	0.596347727218444	2		522	249	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370686	225370686	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	11	309	0	ENST00000264414.4:c.1193A>G	p.Lys398Arg	p.K398R	ENST00000264414	NM_003590.4	398	aAg/aGg	8/16	1	2	FACETS	0.198	0.137	0.275	0.198	0.137	0.275	SUBCLONAL	1	TRUE	1	0.596347727218444	2		309	186	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561200	9561200	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	79	406	0	ENST00000353224.5:c.582A>T	p.Arg194Ser	p.R194S	ENST00000353224	NM_177990.2	194	agA/agT	4/10	0.559919138399684	3	FACETS	1	0.894	1	0.504	0.447	0.565	CLONAL	1	TRUE	1	0.596347727218444	3		406	341	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121020	29121020	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	220	669	0	ENST00000328354.6:c.537A>T	p.Lys179Asn	p.K179N	ENST00000328354	NM_007194.3	179	aaA/aaT	4/15	0.55222837616823	2	FACETS	0.898	0.848	0.946	0.898	0.848	0.946	CLONAL	2	TRUE	0	0.596347727218444	2		669	411	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513422	41513422	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	22	502	0	ENST00000263253.7:c.326A>G	p.Gln109Arg	p.Q109R	ENST00000263253	NM_001429.3	109	cAa/cGa	2/31	0.55222837616823	2	FACETS	0.197	0.152	0.249	0.098	0.076	0.125	SUBCLONAL	1	TRUE	0	0.596347727218444	2		502	375	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254605	1254605	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	119	436	0	ENST00000310581.5:c.3173C>G	p.Ala1058Gly	p.A1058G	ENST00000310581	NM_198253.2	1058	gCc/gGc	15/16	1	2	FACETS	0.84	0.763	0.921	0.84	0.763	0.921	CLONAL	1	TRUE	1	0.596347727218444	2		436	475	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659203	86659203	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	16	170	1	ENST00000274376.6:c.1492G>T	p.Glu498Ter	p.E498*	ENST00000274376	NM_002890.2	498	Gag/Tag	11/25	0.578039361169646	1	FACETS	0.414	0.311	0.532	0.414	0.311	0.532	SUBCLONAL	1	TRUE	0	0.596347727218444	1		171	91	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525012	157525012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1022849043	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	30	337	1	ENST00000346085.5:c.4907C>T	p.Ala1636Val	p.A1636V	ENST00000346085	NM_020732.3	1636	gCg/gTg	19/20	1	2	FACETS	0.367	0.297	0.447	0.367	0.297	0.447	SUBCLONAL	1	TRUE	1	0.596347727218444	2		338	274	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841814	151841814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	19	295	0	ENST00000262189.6:c.14327C>T	p.Ala4776Val	p.A4776V	ENST00000262189	NM_170606.2	4776	gCa/gTa	55/59	0.559919138399684	3	FACETS	0.282	0.214	0.363	0.141	0.107	0.182	SUBCLONAL	1	TRUE	1	0.596347727218444	3		295	293	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205098	38205098	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	23	591	0	ENST00000317025.8:c.592A>G	p.Lys198Glu	p.K198E	ENST00000317025	NM_023034.1	198	Aaa/Gaa	2/24	0.596347727218444	1	FACETS	0.138	0.107	0.174	0.138	0.107	0.174	SUBCLONAL	1	TRUE	0	0.596347727218444	1		591	393	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069166	5069166	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	102	390	0	ENST00000381652.3:c.1471A>T	p.Ile491Leu	p.I491L	ENST00000381652	NM_004972.3	491	Ata/Tta	11/25	1	2	FACETS	0.92	0.83	1	0.92	0.83	1	CLONAL	1	TRUE	1	0.596347727218444	2		390	372	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407551	139407551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	111	677	0	ENST00000277541.6:c.2389T>C	p.Ser797Pro	p.S797P	ENST00000277541	NM_017617.3	797	Tcc/Ccc	15/34	1	2	FACETS	0.461	0.414	0.511	0.461	0.414	0.511	SUBCLONAL	1	TRUE	1	0.596347727218444	2		677	807	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139563015	139563015	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	56	633	0	ENST00000308874.7:c.87G>T	p.Arg29Ser	p.R29S	ENST00000308874		29	agG/agT	4/10	1	2	FACETS	0.285	0.244	0.33	0.285	0.244	0.33	SUBCLONAL	1	TRUE	1	0.596347727218444	2		633	659	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931625	39931625	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	21	235	0	ENST00000378444.4:c.2974A>G	p.Ser992Gly	p.S992G	ENST00000378444	NM_001123385.1	992	Agc/Ggc	4/15	0.245149402500129	2	FACETS	0.345	0.267	0.436			1	INDETERMINATE	1	TRUE	NA	0.596347727218444	2		235	204	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs760043106	NA	P-0032294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	269	560	0	ENST00000269305.4:c.584T>G	p.Ile195Ser	p.I195S	ENST00000269305	NM_001126112.2	195	aTc/aGc	6/11	0.728019245766883	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.728019245766883	1		560	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0032316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	487	940	1	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.459262520978759	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	1	0.459132534609621	3		941	1060	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881440	37881440	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	2117	517	0	ENST00000269571.5:c.2632C>T	p.His878Tyr	p.H878Y	ENST00000269571		878	Cat/Tat	21/27	0.722740644299086	10	FACETS	1	0.998	1			1	CLONAL	8	TRUE	NA	0.722740644299086	10		517	2707	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62323163	62323165	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs1555812473	NA	P-0032333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	99	345	0	ENST00000360203.5:c.2630_2632del	p.Lys877del	p.K877del	ENST00000360203	NM_001283009.1	875	agGAAg/agg	28/35	0.188260804463411	6	FACETS	0.776	0.692	0.866			1	INDETERMINATE	1	TRUE	NA	0.722740644299086	6		345	863	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060709	38060709	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	215	721	1	ENST00000250448.2:c.1280C>T	p.Ser427Leu	p.S427L	ENST00000250448	NM_004496.3	427	tCg/tTg	2/2	0.40991789635865	1	FACETS	0.39	0.362	0.419	0.39	0.362	0.419	INDETERMINATE	1	TRUE	0	0.722740644299086	1		722	974	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670416	134670421	+	inframe_deletion	In_Frame_Del	DEL	CTTCAA	CTTCAA	-	novel	NA	P-0032333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	149	454	0	ENST00000398015.3:c.330_335del	p.Phe110_Asn111del	p.F110_N111del	ENST00000398015	NM_004441.4	109	acCTTCAAc/acc	3/16	0.290346460667895	3	FACETS	0.752	0.688	0.819	0.251	0.229	0.273	INDETERMINATE	1	TRUE	0	0.722740644299086	3		454	746	SUCCESS
ATR	545	MSKCC	GRCh37	3	142180783	142180783	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	275	273	0	ENST00000350721.4:c.7191G>T	p.Lys2397Asn	p.K2397N	ENST00000350721	NM_001184.3	2397	aaG/aaT	42/47	0.290346460667895	3	FACETS	1	0.99	1	0.761	0.726	0.795	INDETERMINATE	2	TRUE	0	0.722740644299086	3		273	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934573	NA	P-0032335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	269	491	1	ENST00000269305.4:c.722C>A	p.Ser241Tyr	p.S241Y	ENST00000269305	NM_001126112.2	241	tCc/tAc	7/11	0.53476880626557	1	FACETS	0.801	0.755	0.848	0.801	0.755	0.848	CLONAL	1	FALSE	0	0.627082787551671	1		492	735	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937034	48937035	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	167	269	0	ENST00000267163.4:c.806dup	p.Asn269LysfsTer2	p.N269Kfs*2	ENST00000267163	NM_000321.2	268	gaa/gAaa	8/27	0.627082787551671	1	FACETS	0.901	0.838	0.964	0.901	0.838	0.964	CLONAL	1	FALSE	0	0.627082787551671	1		269	406	SUCCESS
APC	324	MSKCC	GRCh37	5	112173624	112173625	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1554084079	NA	P-0034036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	22	177	0	ENST00000257430.4:c.2336dup	p.Leu779PhefsTer9	p.L779Ffs*9	ENST00000257430	NM_000038.5	778	aat/aaTt	16/16	1	2	FACETS	0.797	0.617	1	0.797	0.617	1	CLONAL	1	TRUE	1	0.15	2		177	368	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911133	32911133	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	24	178	0	ENST00000380152.3:c.2641G>C	p.Glu881Gln	p.E881Q	ENST00000380152		881	Gaa/Caa	11/27	1	2	FACETS	0.844	0.662	1	0.844	0.662	1	CLONAL	1	TRUE	1	0.15	2		178	379	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0034036-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	28	124	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.337954101694402	2	FACETS	0.499	0.402	0.608	0.25	0.201	0.304	SUBCLONAL	1	TRUE	0	0.558239208945387	2		124	201	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0034036-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	96	189	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.337954101694402	2	FACETS	1	0.984	1	0.744	0.676	0.814	CLONAL	1	TRUE	0	0.558239208945387	2		189	231	SUCCESS
APC	324	MSKCC	GRCh37	5	112173624	112173625	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1554084079	NA	P-0034036-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	86	177	0	ENST00000257430.4:c.2336dup	p.Leu779PhefsTer9	p.L779Ffs*9	ENST00000257430	NM_000038.5	778	aat/aaTt	16/16	0.337954101694402	2	FACETS	1	0.979	1	0.685	0.617	0.754	CLONAL	1	TRUE	0	0.558239208945387	2		177	225	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911133	32911133	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034036-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	50	178	0	ENST00000380152.3:c.2641G>C	p.Glu881Gln	p.E881Q	ENST00000380152		881	Gaa/Caa	11/27	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.558239208945387	2		178	175	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508535	106508535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034036-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	106	269	0	ENST00000359195.3:c.529C>T	p.Arg177Cys	p.R177C	ENST00000359195	NM_002649.2	177	Cgc/Tgc	2/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.558239208945387	2		269	351	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293800	1293800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370887827	NA	P-0034036-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	95	764	0	ENST00000310581.5:c.1201G>A	p.Ala401Thr	p.A401T	ENST00000310581	NM_198253.2	401	Gcg/Acg	2/16	1	2	FACETS	0.401	0.357	0.449	0.401	0.357	0.449	SUBCLONAL	1	TRUE	1	0.558239208945387	2		764	848	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394807	45394807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034036-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	59	164	0	ENST00000262160.6:c.542C>T	p.Pro181Leu	p.P181L	ENST00000262160	NM_005901.5	181	cCc/cTc	5/11	0.558239208945387	1	FACETS	0.632	0.55	0.719	0.632	0.55	0.719	SUBCLONAL	1	TRUE	0	0.558239208945387	1		164	241	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031681	69031681	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034036-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	21	236	0	ENST00000288368.4:c.3436T>A	p.Leu1146Ile	p.L1146I	ENST00000288368	NM_024870.2	1146	Tta/Ata	28/40	0.558239208945387	3	FACETS	0.267	0.205	0.34	0.134	0.102	0.17	SUBCLONAL	1	TRUE	1	0.558239208945387	3		236	360	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534885	5534885	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034036-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	95	304	0	ENST00000397747.3:c.196A>C	p.Thr66Pro	p.T66P	ENST00000397747	NM_025239.3	66	Aca/Cca	3/7	1	2	FACETS	0.689	0.616	0.766	0.689	0.616	0.766	SUBCLONAL	1	TRUE	1	0.558239208945387	2		304	494	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207162	1207162	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs137853076	NA	P-0037134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	319	892	0	ENST00000326873.7:c.250A>T	p.Lys84Ter	p.K84*	ENST00000326873	NM_000455.4	84	Aag/Tag	1/10	0.746054538273984	1	FACETS	0.952	0.91	0.994	0.952	0.91	0.994	CLONAL	1	TRUE	0	0.746054538273984	1		892	563	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610247	10610247	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	285	838	0	ENST00000171111.5:c.463G>T	p.Val155Phe	p.V155F	ENST00000171111	NM_203500.1	155	Gtc/Ttc	2/6	0.746054538273984	1	FACETS	0.945	0.901	0.989	0.945	0.901	0.989	CLONAL	1	TRUE	0	0.746054538273984	1		838	507	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0037135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	250	352	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.6081450489004	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.6081450489004	2		352	399	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0037135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	351	565	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.447666989591153	5	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.6081450489004	5		565	983	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0037135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	101	370	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	0.85	0.765	0.938	0.85	0.765	0.938	CLONAL	1	TRUE	1	0.6081450489004	2		370	391	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120173	70120173	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	926	415	1	ENST00000245479.2:c.1177del	p.Gln393SerfsTer10	p.Q393Sfs*10	ENST00000245479	NM_000346.3	392	tCc/tc	3/3	0.6081450489004	4	FACETS	1	0.997	1			1	CLONAL	4	TRUE	NA	0.6081450489004	4		416	1116	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0037135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	300	309	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.6081450489004	3	FACETS	0.954	0.906	1	0.954	0.906	1	CLONAL	2	TRUE	1	0.6081450489004	3		309	674	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876658468	NA	P-0037135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	453	690	0	ENST00000269305.4:c.577C>G	p.His193Asp	p.H193D	ENST00000269305	NM_001126112.2	193	Cat/Gat	6/11	0.6081450489004	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.6081450489004	2		690	687	SUCCESS
APC	324	MSKCC	GRCh37	5	112175952	112175952	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587783031	NA	P-0037135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	79	239	0	ENST00000257430.4:c.4666del	p.Thr1556LeufsTer9	p.T1556Lfs*9	ENST00000257430	NM_000038.5	1554	gAa/ga	16/16	1	2	FACETS	0.863	0.767	0.964	0.863	0.767	0.964	CLONAL	1	TRUE	1	0.6081450489004	2		239	301	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389107	31389107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749860839	NA	P-0037135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	471	537	0	ENST00000328111.2:c.2020G>A	p.Glu674Lys	p.E674K	ENST00000328111	NM_006892.3	674	Gaa/Aaa	19/23	0.500451060567578	5	FACETS	0.929	0.891	0.967	0.929	0.891	0.967	CLONAL	3	TRUE	2	0.6081450489004	5		537	1063	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044533	12044533	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	160	618	0	ENST00000353533.5:c.1156G>T	p.Asp386Tyr	p.D386Y	ENST00000353533	NM_003010.3	386	Gat/Tat	11/11	0.6081450489004	2	FACETS	0.821	0.755	0.889	0.41	0.377	0.445	CLONAL	1	TRUE	0	0.6081450489004	2		618	641	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619340	37619350	+	frameshift_variant	Frame_Shift_Del	DEL	AGCGGTCTCTG	AGCGGTCTCTG	-	novel	NA	P-0037135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	207	413	0	ENST00000447079.4:c.1018_1028del	p.Arg340SerfsTer7	p.R340Sfs*7	ENST00000447079	NM_015083.1	339	aAGCGGTCTCTG/a	1/14	0.447666989591153	5	FACETS	0.979	0.913	1			1	CLONAL	2	TRUE	NA	0.6081450489004	5		413	665	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210574	5210574	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771577284	NA	P-0037135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	254	624	0	ENST00000357368.4:c.5393G>A	p.Arg1798His	p.R1798H	ENST00000357368	NM_002850.3	1798	cGc/cAc	35/38	0.278428112462059	4	FACETS	1	0.992	1	0.712	0.667	0.758	INDETERMINATE	1	TRUE	2	0.6081450489004	4		624	943	SUCCESS
APC	324	MSKCC	GRCh37	5	112154780	112154780	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	201	596	0	ENST00000257430.4:c.1051G>T	p.Gly351Ter	p.G351*	ENST00000257430	NM_000038.5	351	Gga/Tga	10/16	1	2	FACETS	0.987	0.918	1	0.987	0.918	1	CLONAL	1	TRUE	1	0.6081450489004	2		596	670	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	127	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.186820984072803	5	FACETS	0.936	0.849	1	0.624	0.566	0.685	CLONAL	2	FALSE	2	0.286054697160047	5		311	678	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0037148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	182	481	3	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.233058948868109	2	FACETS	0.762	0.704	0.822	0.762	0.704	0.822	SUBCLONAL	2	FALSE	0	0.286054697160047	2		484	835	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267361	198267361	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754688962	NA	P-0037148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	97	386	0	ENST00000335508.6:c.1996A>G	p.Lys666Glu	p.K666E	ENST00000335508	NM_012433.2	666	Aag/Gag	14/25	1	2	FACETS	0.872	0.777	0.973	0.872	0.777	0.973	CLONAL	1	FALSE	1	0.286054697160047	2		386	778	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871626	35871626	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	34	323	0	ENST00000216797.5:c.880G>C	p.Glu294Gln	p.E294Q	ENST00000216797	NM_020529.2	294	Gag/Cag	5/6	1	2	FACETS	0.455	0.371	0.55	0.455	0.371	0.55	SUBCLONAL	1	FALSE	1	0.286054697160047	2		323	522	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445381	29445381	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0037148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	233	660	0	ENST00000389048.3:c.3450+2T>C		p.X1150_splice	ENST00000389048	NM_004304.4	1150			0.286054697160047	3	FACETS	0.9	0.839	0.962			1	CLONAL	2	FALSE	NA	0.286054697160047	3		660	1035	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323325	31323325	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	25	170	0	ENST00000412585.2:c.664G>C	p.Glu222Gln	p.E222Q	ENST00000412585	NM_005514.6	222	Gag/Cag	4/8	0.230569737443185	2	FACETS	0.809	0.641	1	0.405	0.32	0.5	CLONAL	1	FALSE	0	0.286054697160047	2		170	216	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789628	3789628	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	224	313	0	ENST00000262367.5:c.4231G>T	p.Gly1411Ter	p.G1411*	ENST00000262367	NM_004380.2	1411	Gga/Tga	25/31	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.880822159023411	2		313	499	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217370	123217371	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0037173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	238	259	0	ENST00000218089.9:c.3027dup	p.Leu1010ThrfsTer44	p.L1010Tfs*44	ENST00000218089	NM_001042749.1	1008	-/A	29/35	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.880822159023411	1		259	282	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696644	47696644	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519964	NA	P-0037176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	21	487	0	ENST00000347630.2:c.304T>G	p.Phe102Val	p.F102V	ENST00000347630	NM_001007230.1	102	Ttc/Gtc	5/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		487	388	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0037245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	104	309	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.803	0.722	0.887	0.803	0.722	0.887	CLONAL	1	TRUE	1	0.524640215964707	2		309	494	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0037245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	14	891	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.081	0.058	0.109	0.081	0.058	0.109	SUBCLONAL	1	TRUE	1	0.524640215964707	2		892	661	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0037245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	71	388	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.524640215964707	1	FACETS	0.765	0.676	0.859	0.765	0.676	0.859	SUBCLONAL	1	TRUE	0	0.524640215964707	1		388	261	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915455	112915455	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121918463	NA	P-0037245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	135	514	1	ENST00000351677.2:c.854T>C	p.Phe285Ser	p.F285S	ENST00000351677	NM_002834.3	285	tTt/tCt	8/16	1	2	FACETS	0.863	0.788	0.943	0.863	0.788	0.943	CLONAL	1	TRUE	1	0.524640215964707	2		515	596	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952993	2952993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369115970	NA	P-0037245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	118	609	1	ENST00000396946.4:c.2947G>A	p.Val983Met	p.V983M	ENST00000396946	NM_032415.4	983	Gtg/Atg	22/25	1	2	FACETS	0.579	0.522	0.639	0.579	0.522	0.639	SUBCLONAL	1	TRUE	1	0.524640215964707	2		610	777	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287229	46287229	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	116	388	0	ENST00000334344.6:c.5174C>A	p.Ser1725Ter	p.S1725*	ENST00000334344	NM_152641.2	1725	tCa/tAa	19/21	1	2	FACETS	0.877	0.795	0.964	0.877	0.795	0.964	CLONAL	1	TRUE	1	0.524640215964707	2		388	504	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493442	56493442	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	96	401	0	ENST00000267101.3:c.2850T>G	p.Ile950Met	p.I950M	ENST00000267101	NM_001982.3	950	atT/atG	24/28	1	2	FACETS	0.697	0.623	0.775	0.697	0.623	0.775	SUBCLONAL	1	TRUE	1	0.524640215964707	2		401	525	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141447	11141447	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	116	525	0	ENST00000358026.2:c.3424T>G	p.Phe1142Val	p.F1142V	ENST00000358026	NM_001128849.1	1142	Ttc/Gtc	25/36	1	2	FACETS	0.598	0.539	0.66	0.598	0.539	0.66	SUBCLONAL	1	TRUE	1	0.524640215964707	2		525	740	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530088	212530088	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149498255	NA	P-0037245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	92	346	0	ENST00000342788.4:c.1831G>A	p.Asp611Asn	p.D611N	ENST00000342788	NM_005235.2	611	Gat/Aat	15/28	1	2	FACETS	0.767	0.685	0.854	0.767	0.685	0.854	SUBCLONAL	1	TRUE	1	0.524640215964707	2		346	457	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38954932	38954932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	31	357	0	ENST00000357387.3:c.2641C>T	p.His881Tyr	p.H881Y	ENST00000357387	NM_152756.3	881	Cac/Tac	27/38	1	2	FACETS	0.49	0.399	0.593	0.49	0.399	0.593	SUBCLONAL	1	TRUE	1	0.524640215964707	2		357	241	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0037278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	68	435	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	1	2	FACETS	0.932	0.818	1	0.932	0.818	1	CLONAL	1	TRUE	1	0.494537046204599	2		435	295	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0037278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	114	586	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.494537046204599	2		586	449	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049691	16049691	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	116	588	0	ENST00000268712.3:c.1081C>T	p.Arg361Ter	p.R361*	ENST00000268712	NM_006311.3	361	Cga/Tga	10/46	1	2	FACETS	0.838	0.758	0.922	0.838	0.758	0.922	CLONAL	1	TRUE	1	0.494537046204599	2		588	560	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362446	40362447	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1202978138	NA	P-0037278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	28	702	0	ENST00000293328.3:c.1749dup	p.His584ThrfsTer8	p.H584Tfs*8	ENST00000293328	NM_012448.3	583	-/A	14/19	1	2	FACETS	0.206	0.164	0.255	0.206	0.164	0.255	SUBCLONAL	1	TRUE	1	0.494537046204599	2		702	549	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433620	49433620	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555191740	NA	P-0037278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	104	991	2	ENST00000301067.7:c.7933C>T	p.Arg2645Ter	p.R2645*	ENST00000301067	NM_003482.3	2645	Cga/Tga	31/54	1	2	FACETS	0.783	0.704	0.867	0.783	0.704	0.867	SUBCLONAL	1	TRUE	1	0.494537046204599	2		993	537	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959432	26959432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	217	585	1	ENST00000381527.3:c.599G>A	p.Arg200Gln	p.R200Q	ENST00000381527	NM_001260.1	200	cGa/cAa	6/13	0.446151312068777	2	FACETS	0.912	0.858	0.967	0.912	0.858	0.967	CLONAL	2	TRUE	0	0.494537046204599	2		586	481	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190824	11190824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868040471	NA	P-0037278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	66	467	0	ENST00000361445.4:c.5375C>T	p.Ala1792Val	p.A1792V	ENST00000361445	NM_004958.3	1792	gCg/gTg	39/58	0.386508469042663	1	FACETS	0.632	0.552	0.716	0.632	0.552	0.716	SUBCLONAL	1	TRUE	0	0.494537046204599	1		467	318	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023170	27023186	+	frameshift_variant	Frame_Shift_Del	DEL	CGGGCCCGGCGCGGAGC	CGGGCCCGGCGCGGAGC	-	novel	NA	P-0037278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	18	31	0	ENST00000324856.7:c.279_295del	p.Gly95GlufsTer10	p.G95Efs*10	ENST00000324856	NM_006015.4	92	ggCGGGCCCGGCGCGGAGCcg/ggcg	1/20	1	2	FACETS	0.91	0.726	1	1	0.939	1	CLONAL	2	TRUE	1	0.494537046204599	2		31	40	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136068	64136068	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	71	554	0	ENST00000334205.4:c.1329T>G	p.Ser443Arg	p.S443R	ENST00000334205	NM_003942.2	443	agT/agG	11/17	1	2	FACETS	0.929	0.818	1	0.929	0.818	1	CLONAL	1	TRUE	1	0.494537046204599	2		554	309	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026605	48026605	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779212	NA	P-0037278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	162	521	1	ENST00000234420.5:c.1483C>T	p.Arg495Ter	p.R495*	ENST00000234420	NM_000179.2	495	Cga/Tga	4/10	1	2	FACETS	0.89	0.828	0.953	1	0.992	1	CLONAL	2	TRUE	1	0.494537046204599	2		522	368	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37059048	37059048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63749950	NA	P-0037278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	81	502	1	ENST00000231790.2:c.842C>T	p.Ala281Val	p.A281V	ENST00000231790	NM_000249.3	281	gCa/gTa	10/19	1	2	FACETS	0.734	0.65	0.825	0.734	0.65	0.825	SUBCLONAL	1	TRUE	1	0.494537046204599	2		503	446	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750467	41750467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	73	501	0	ENST00000226382.2:c.161C>T	p.Thr54Met	p.T54M	ENST00000226382	NM_003924.3	54	aCg/aTg	1/3	NA	2	FACETS	0.931	0.821	1			1	INDETERMINATE	1	TRUE	NA	0.494537046204599	2		501	317	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845933	151845933	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	99	792	0	ENST00000262189.6:c.13079G>T	p.Trp4360Leu	p.W4360L	ENST00000262189	NM_170606.2	4360	tGg/tTg	52/59	1	2	FACETS	0.898	0.806	0.994	0.898	0.806	0.994	CLONAL	1	TRUE	1	0.494537046204599	2		792	446	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36846857	36846857	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	68	422	2	ENST00000358127.4:c.1082C>A	p.Pro361His	p.P361H	ENST00000358127	NM_001280556.1	361	cCc/cAc	9/10	1	2	FACETS	0.968	0.851	1	0.968	0.851	1	CLONAL	1	TRUE	1	0.494537046204599	2		424	284	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665752	29665755	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1555535032	NA	P-0037310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	25	565	1	ENST00000356175.3:c.6789_6792del	p.Tyr2264ThrfsTer5	p.Y2264Tfs*5	ENST00000356175	NM_000267.3	2263	ACTTac/ac	45/57	0.679934813704703	2	FACETS	0.675	0.542	0.821	0.337	0.271	0.411	SUBCLONAL	1	TRUE	0	0.679934813704703	2		566	109	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433387	49433387	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	239	585	0	ENST00000301067.7:c.8060G>C	p.Arg2687Pro	p.R2687P	ENST00000301067	NM_003482.3	2687	cGa/cCa	32/54	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.679934813704703	NA		585	892	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433617	49433617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	497	772	1	ENST00000301067.7:c.7936G>A	p.Glu2646Lys	p.E2646K	ENST00000301067	NM_003482.3	2646	Gaa/Aaa	31/54	0.621117095603321	4	FACETS	0.889	0.851	0.927			1	CLONAL	2	TRUE	NA	0.679934813704703	4		773	1382	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433781	49433781	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	496	730	2	ENST00000301067.7:c.7772G>A	p.Gly2591Asp	p.G2591D	ENST00000301067	NM_003482.3	2591	gGc/gAc	31/54	0.621117095603321	4	FACETS	0.998	0.957	1			1	CLONAL	2	TRUE	NA	0.679934813704703	4		732	1228	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435135	49435135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	249	316	0	ENST00000301067.7:c.6418G>A	p.Asp2140Asn	p.D2140N	ENST00000301067	NM_003482.3	2140	Gac/Aac	31/54	0.621117095603321	4	FACETS	0.969	0.912	1			1	CLONAL	2	TRUE	NA	0.679934813704703	4		316	635	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508813	106508813	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	190	403	0	ENST00000359195.3:c.807T>A	p.Asp269Glu	p.D269E	ENST00000359195	NM_002649.2	269	gaT/gaA	2/11	0.326198022781199	5	FACETS	0.893	0.83	0.958	0.595	0.553	0.639	INDETERMINATE	2	TRUE	2	0.679934813704703	5		403	632	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988166	85988166	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	69	380	0	ENST00000263360.6:c.1111G>T	p.Asp371Tyr	p.D371Y	ENST00000263360	NM_003797.3	371	Gat/Tat	10/12	1	2	FACETS	0.841	0.735	0.955	0.841	0.735	0.955	CLONAL	1	TRUE	1	0.376208522447127	2		380	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691022	NA	P-0037343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	648	758	0	ENST00000269305.4:c.1024del	p.Arg342GlufsTer3	p.R342Efs*3	ENST00000269305	NM_001126112.2	342	Cga/ga	10/11	0.527068232563279	3	FACETS	0.993	0.965	1			1	CLONAL	3	TRUE	NA	0.559465959616137	3		758	995	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039179	49039179	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	33	436	2	ENST00000267163.4:c.2257del	p.Ile753Ter	p.I753*	ENST00000267163	NM_000321.2	753	Ata/ta	22/27	0.558293826086323	1	FACETS	0.273	0.223	0.33	0.273	0.223	0.33	SUBCLONAL	1	TRUE	0	0.559465959616137	1		438	311	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361799	70361799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	330	770	1	ENST00000374080.3:c.6475C>A	p.Gln2159Lys	p.Q2159K	ENST00000374080		2159	Caa/Aaa	44/45	0.293209197748657	4	FACETS	0.906	0.858	0.955	0.906	0.858	0.955	INDETERMINATE	2	TRUE	2	0.559465959616137	4		771	1015	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577569	7577569	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519981	NA	P-0037353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	421	750	0	ENST00000269305.4:c.712T>C	p.Cys238Arg	p.C238R	ENST00000269305	NM_001126112.2	238	Tgt/Cgt	7/11	0.617740306951156	2	FACETS	0.993	0.959	1	0.993	0.959	1	CLONAL	2	TRUE	0	0.664472643391869	2		750	638	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	146	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.408161137938687	3	FACETS	0.925	0.851	1	0.925	0.851	1	CLONAL	2	TRUE	1	0.424286127250832	3		311	451	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0037381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	103	388	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.408161137938687	3	FACETS	0.897	0.812	0.985	0.897	0.812	0.985	CLONAL	2	TRUE	1	0.424286127250832	3		388	328	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0037381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	177	667	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.407622390513559	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.424286127250832	3		667	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578214	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs864309495	NA	P-0037381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	279	537	0	ENST00000269305.4:c.635_636del	p.Phe212SerfsTer3	p.F212Sfs*3	ENST00000269305	NM_001126112.2	212	tTT/t	6/11	0.424286127250832	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.424286127250832	2		537	606	SUCCESS
APC	324	MSKCC	GRCh37	5	112173582	112173582	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0037381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	71	258	0	ENST00000257430.4:c.2291T>A	p.Leu764Ter	p.L764*	ENST00000257430	NM_000038.5	764	tTa/tAa	16/16	0.408161137938687	3	FACETS	1	0.923	1	0.535	0.47	0.605	CLONAL	1	TRUE	1	0.424286127250832	3		258	379	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929426	81929426	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1364308657	NA	P-0037381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	181	376	0	ENST00000359376.3:c.1087G>A	p.Gly363Arg	p.G363R	ENST00000359376	NM_002661.3	363	Ggg/Agg	13/33	0.318913392332561	4	FACETS	0.971	0.9	1	0.971	0.9	1	CLONAL	2	TRUE	2	0.424286127250832	4		376	626	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813903	50813903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1363261645	NA	P-0037381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	207	407	1	ENST00000398568.2:c.1457G>A	p.Arg486His	p.R486H	ENST00000398568	NM_001042412.1	486	cGt/cAt	8/18	0.318913392332561	4	FACETS	0.957	0.891	1	0.957	0.891	1	CLONAL	2	TRUE	2	0.424286127250832	4		408	726	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62322275	62322275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758245234	NA	P-0037381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	267	734	2	ENST00000360203.5:c.2531G>A	p.Arg844Gln	p.R844Q	ENST00000360203	NM_001283009.1	844	cGg/cAg	27/35	0.424286127250832	5	FACETS	0.828	0.776	0.883	0.414	0.388	0.442	CLONAL	2	TRUE	1	0.424286127250832	5		736	1243	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267361	198267361	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754688962	NA	P-0037382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	178	386	0	ENST00000335508.6:c.1996A>G	p.Lys666Glu	p.K666E	ENST00000335508	NM_012433.2	666	Aag/Gag	14/25	1	2	FACETS	0.907	0.842	0.973	0.907	0.842	0.973	CLONAL	1	TRUE	1	0.733962961377596	2		386	535	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0037382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	93	222	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.733962961377596	2		222	240	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246445	105246445	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	214	433	0	ENST00000349310.3:c.155T>A	p.Leu52His	p.L52H	ENST00000349310	NM_001014432.1	52	cTc/cAc	4/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.733962961377596	2		433	564	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224698	36224698	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	260	588	1	ENST00000222270.7:c.7085del	p.Pro2362ArgfsTer77	p.P2362Rfs*77	ENST00000222270	NM_014727.1	2362	Ccg/cg	30/37	1	2	FACETS	0.99	0.932	1	0.99	0.932	1	CLONAL	1	TRUE	1	0.733962961377596	2		589	716	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0037388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	248	451	0	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	0.504216364198743	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.504216364198743	2		451	489	SUCCESS
APC	324	MSKCC	GRCh37	5	112157646	112157647	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0037388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	137	410	0	ENST00000257430.4:c.1369dup	p.Ser457PhefsTer3	p.S457Ffs*3	ENST00000257430	NM_000038.5	456	ctt/cTtt	11/16	0.129363318014825	6	FACETS	1	0.979	1	0.805	0.738	0.874	INDETERMINATE	2	TRUE	3	0.504216364198743	6		410	452	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161420	2161420	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1176659285	NA	P-0037388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	270	441	0	ENST00000434045.2:c.107G>T	p.Trp36Leu	p.W36L	ENST00000434045	NM_001127598.1	36	tGg/tTg	2/5	0.402380255602667	3	FACETS	1	0.987	1	0.599	0.561	0.637	CLONAL	1	TRUE	1	0.504216364198743	3		441	1120	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976939	18976946	+	frameshift_variant	Frame_Shift_Del	DEL	GCATGGCG	GCATGGCG	-	novel	NA	P-0037388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	47	352	0	ENST00000262803.5:c.3325_3332del	p.His1109GlyfsTer32	p.H1109Gfs*32	ENST00000262803	NM_002911.3	1108	caGCATGGCGgg/cagg	23/24	0.129363318014825	6	FACETS	0.561	0.473	0.66	0.187	0.157	0.22	INDETERMINATE	1	TRUE	3	0.504216364198743	6		352	667	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599320	55599320	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913506	NA	P-0037402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	106	390	1	ENST00000288135.5:c.2446G>T	p.Asp816Tyr	p.D816Y	ENST00000288135	NM_000222.2	816	Gac/Tac	17/21	0.716116996953885	3	FACETS	0.882	0.795	0.973	0.441	0.397	0.487	CLONAL	1	FALSE	1	0.716116996953885	3		391	456	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288969	212288969	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	92	423	0	ENST00000342788.4:c.2777C>A	p.Thr926Lys	p.T926K	ENST00000342788	NM_005235.2	926	aCg/aAg	23/28	0.59375229649317	4	FACETS	0.959	0.856	1	0.479	0.428	0.534	CLONAL	1	FALSE	2	0.716116996953885	4		423	460	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540055	187540055	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	80	370	0	ENST00000441802.2:c.7685A>C	p.Lys2562Thr	p.K2562T	ENST00000441802	NM_005245.3	2562	aAa/aCa	10/27	0.716116996953885	2	FACETS	0.963	0.862	1	0.482	0.431	0.534	CLONAL	1	FALSE	0	0.716116996953885	2		370	232	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0037442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	244	616	1	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	1	2	FACETS	0.976	0.913	1	1	0.996	1	CLONAL	3	TRUE	1	0.18	2		617	926	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0037442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	60	600	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.823	0.708	0.949	0.823	0.708	0.949	CLONAL	1	TRUE	1	0.18	2		601	810	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346592	81346592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764869064	NA	P-0037442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	33	373	0	ENST00000222390.5:c.1361C>T	p.Thr454Met	p.T454M	ENST00000222390	NM_000601.4	454	aCg/aTg	11/18	1	2	FACETS	0.7	0.569	0.848	0.7	0.569	0.848	SUBCLONAL	1	TRUE	1	0.18	2		373	524	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981475	201981496	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGCTCTTCTGATGAGCTCAG	CCAGCTCTTCTGATGAGCTCAG	-	novel	NA	P-0037442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	62	597	0	ENST00000359651.3:c.389_410del	p.Ser130PhefsTer18	p.S130Ffs*18	ENST00000359651		130	tCCAGCTCTTCTGATGAGCTCAGt/tt	3/8	1	2	FACETS	0.831	0.716	0.956	0.831	0.716	0.956	CLONAL	1	TRUE	1	0.18	2		597	829	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428659	49428659	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	50	682	0	ENST00000301067.7:c.10291G>T	p.Ala3431Ser	p.A3431S	ENST00000301067	NM_003482.3	3431	Gct/Tct	35/54	1	2	FACETS	0.57	0.482	0.668	0.57	0.482	0.668	SUBCLONAL	1	TRUE	1	0.18	2		682	974	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38184284	38184284	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2861	212	509	0	ENST00000317025.8:c.1672A>T	p.Ser558Cys	p.S558C	ENST00000317025	NM_023034.1	558	Agt/Tgt	7/24	0.906354059641818	10	FACETS	0.704	0.65	0.761			1	SUBCLONAL	1	TRUE	NA	0.906354059641818	10		509	3073	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	325	817	0	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.754811508202143	2		817	847	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764146326	NA	P-0037483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	492	777	0	ENST00000269305.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000269305	NM_001126112.2	281	Gac/Aac	8/11	0.754811508202143	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.754811508202143	1		777	715	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205050	128205050	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	296	803	0	ENST00000341105.2:c.391G>A	p.Ala131Thr	p.A131T	ENST00000341105	NM_032638.4	131	Gct/Act	3/6	0.454331892467076	1	FACETS	0.749	0.711	0.787	0.749	0.711	0.787	SUBCLONAL	1	TRUE	0	0.754811508202143	1		803	652	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226806	2226806	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	164	362	0	ENST00000398665.3:c.4286C>G	p.Ser1429Cys	p.S1429C	ENST00000398665	NM_032482.2	1429	tCt/tGt	27/28	0.212121173624173	1	FACETS	0.638	0.592	0.685	0.638	0.592	0.685	INDETERMINATE	1	TRUE	0	0.754811508202143	1		362	424	SUCCESS
APC	324	MSKCC	GRCh37	5	112175230	112175233	+	frameshift_variant	Frame_Shift_Del	DEL	TAGG	TAGG	-	novel	NA	P-0037483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	159	350	0	ENST00000257430.4:c.3940_3943del	p.Arg1314GlnfsTer6	p.R1314Qfs*6	ENST00000257430	NM_000038.5	1313	acTAGG/ac	16/16	0.741395572554602	2	FACETS	0.896	0.847	0.943	0.896	0.847	0.943	CLONAL	2	TRUE	0	0.754811508202143	2		350	235	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0037490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	134	352	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.192373300419839	4	FACETS	0.941	0.859	1	0.941	0.859	1	INDETERMINATE	2	FALSE	2	0.323726764844595	4		352	582	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	216	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.269462834735299	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	FALSE	2	0.323726764844595	4		311	759	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0037490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	286	690	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.323834451778008	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	FALSE	0	0.323726764844595	2		692	723	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0037490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	7767	378	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.323726764844595	61	FACETS	1	0.998	1			1	CLONAL	60	FALSE	NA	0.323726764844595	61		378	8394	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0037490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	176	348	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.323726764844595	4	FACETS	0.995	0.919	1	0.995	0.919	1	CLONAL	2	FALSE	2	0.323726764844595	4		348	723	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0037490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	163	319	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.323726764844595	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	FALSE	2	0.323726764844595	4		319	539	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245456	153245456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	281	551	0	ENST00000281708.4:c.1735G>A	p.Gly579Arg	p.G579R	ENST00000281708	NM_033632.3	579	Ggg/Agg	11/12	0.192373300419839	4	FACETS	1	0.99	1	1	0.99	1	INDETERMINATE	2	FALSE	2	0.323726764844595	4		551	932	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607759	46607759	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	118	641	0	ENST00000263734.3:c.1948del	p.Thr650GlnfsTer46	p.T650Qfs*46	ENST00000263734	NM_001430.4	650	Aca/ca	12/16	0.323726764844595	4	FACETS	0.896	0.807	0.991	0.448	0.403	0.496	CLONAL	1	FALSE	2	0.323726764844595	4		641	1077	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385164	41385164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	250	591	0	ENST00000373198.4:c.797G>A	p.Arg266His	p.R266H	ENST00000373198	NM_133170.3	266	cGc/cAc	6/32	0.323726764844595	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	FALSE	2	0.323726764844595	4		591	912	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523100	176523101	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGGACAATGT	novel	NA	P-0037490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	260	655	0	ENST00000292408.4:c.1865_1874dup	p.Met626GlyfsTer8	p.M626Gfs*8	ENST00000292408	NM_213647.1	622	gag/gAGGACAATGTag	14/18	0.323726764844595	4	FACETS	0.958	0.897	1	0.958	0.897	1	CLONAL	2	FALSE	2	0.323726764844595	4		655	1110	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374372	81374372	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	218	453	0	ENST00000222390.5:c.690G>T	p.Lys230Asn	p.K230N	ENST00000222390	NM_000601.4	230	aaG/aaT	6/18	0.323726764844595	5	FACETS	1	0.97	1	0.717	0.667	0.768	CLONAL	2	FALSE	2	0.323726764844595	5		453	930	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405240	139405240	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1420968156	NA	P-0037490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	118	623	1	ENST00000277541.6:c.2605G>A	p.Asp869Asn	p.D869N	ENST00000277541	NM_017617.3	869	Gac/Aac	17/34	0.323834451778008	3	FACETS	1	0.947	1	0.537	0.484	0.592	CLONAL	1	FALSE	1	0.323726764844595	3		624	789	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0037535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	182	660	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.524339980330303	1	FACETS	0.883	0.82	0.948	0.883	0.82	0.948	CLONAL	1	TRUE	0	0.524339980330303	1		660	580	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519886	NA	P-0037535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	28	369	0	ENST00000349496.5:c.97T>G	p.Ser33Ala	p.S33A	ENST00000349496	NM_001904.3	33	Tct/Gct	3/15	0.294697920445109	1	FACETS	0.177	0.141	0.218	0.177	0.141	0.218	INDETERMINATE	1	TRUE	0	0.524339980330303	1		369	445	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222868	5222868	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1028304582	NA	P-0037535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	75	600	0	ENST00000357368.4:c.2935C>T	p.Arg979Ter	p.R979*	ENST00000357368	NM_002850.3	979	Cga/Tga	18/38	0.524339980330303	1	FACETS	0.42	0.369	0.475	0.42	0.369	0.475	SUBCLONAL	1	TRUE	0	0.524339980330303	1		600	502	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992054	72992054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	203	675	1	ENST00000268489.5:c.1991C>T	p.Ser664Phe	p.S664F	ENST00000268489	NM_006885.3	664	tCt/tTt	2/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.524339980330303	2		676	709	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775583	39775583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369318352	NA	P-0037535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	178	536	1	ENST00000288319.7:c.437C>T	p.Ala146Val	p.A146V	ENST00000288319	NM_182918.3	146	gCg/gTg	4/10	0.238254938601141	2	FACETS	1	0.985	1	0.615	0.57	0.661	INDETERMINATE	1	TRUE	0	0.524339980330303	2		537	552	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069562	69069562	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	94	388	0	ENST00000288368.4:c.4237G>C	p.Glu1413Gln	p.E1413Q	ENST00000288368	NM_024870.2	1413	Gag/Cag	35/40	1	2	FACETS	0.806	0.721	0.895	0.806	0.721	0.895	CLONAL	1	TRUE	1	0.524339980330303	2		388	445	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245849	46245849	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	71	430	0	ENST00000334344.6:c.3943G>A	p.Glu1315Lys	p.E1315K	ENST00000334344	NM_152641.2	1315	Gag/Aag	15/21	0.261629960153074	3	FACETS	0.572	0.499	0.65	0.191	0.166	0.217	INDETERMINATE	1	TRUE	0	0.524339980330303	3		430	598	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727493	88727493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	199	643	0	ENST00000360948.2:c.286G>T	p.Ala96Ser	p.A96S	ENST00000360948	NM_001012338.2	96	Gcc/Tcc	3/19	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.524339980330303	2		643	723	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038252	30038252	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	133	519	0	ENST00000338641.4:c.425C>G	p.Ala142Gly	p.A142G	ENST00000338641	NM_000268.3	142	gCt/gGt	4/16	0.495031562191745	3	FACETS	0.835	0.759	0.915	0.278	0.253	0.305	CLONAL	1	TRUE	0	0.524339980330303	3		519	767	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389360	8389360	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	73	576	0	ENST00000356435.5:c.4258A>G	p.Arg1420Gly	p.R1420G	ENST00000356435		1420	Agg/Ggg	26/35	0.439157532548814	3	FACETS	0.411	0.359	0.468	0.206	0.179	0.234	SUBCLONAL	1	TRUE	1	0.524339980330303	3		576	855	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220703	1220703	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	23	576	0	ENST00000326873.7:c.721G>C	p.Ala241Pro	p.A241P	ENST00000326873	NM_000455.4	241	Gct/Cct	5/10	1	2	FACETS	0.592	0.463	0.742	0.592	0.463	0.742	SUBCLONAL	1	TRUE	1	0.282387931219177	2		576	275	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982653	90982653	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	24	447	0	ENST00000265433.3:c.835C>T	p.Gln279Ter	p.Q279*	ENST00000265433	NM_002485.4	279	Cag/Tag	7/16	0.167344377327519	3	FACETS	0.595	0.467	0.743	0.298	0.233	0.372	INDETERMINATE	1	TRUE	1	0.282387931219177	3		447	326	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920413	114920413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767830105	NA	P-0037541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	127	578	0	ENST00000543371.1:c.1354G>A	p.Gly452Arg	p.G452R	ENST00000543371	NM_001198531.1	452	Ggg/Agg	13/14	1	2	FACETS	0.666	0.603	0.731	0.666	0.603	0.731	SUBCLONAL	1	TRUE	1	0.494240306216207	2		578	772	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577544	7577544	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587780074	NA	P-0037541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	100	677	1	ENST00000269305.4:c.737T>G	p.Met246Arg	p.M246R	ENST00000269305	NM_001126112.2	246	aTg/aGg	7/11	0.439521407560168	1	FACETS	0.438	0.392	0.488	0.438	0.392	0.488	SUBCLONAL	1	TRUE	0	0.494240306216207	1		678	695	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579722	7579722	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0037541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	94	554	0	ENST00000269305.4:c.75-1G>A		p.X25_splice	ENST00000269305	NM_001126112.2	25			0.439521407560168	1	FACETS	0.609	0.544	0.678	0.609	0.544	0.678	SUBCLONAL	1	TRUE	0	0.494240306216207	1		554	470	SUCCESS
APC	324	MSKCC	GRCh37	5	112174291	112174291	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1114167586	NA	P-0037541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	125	347	0	ENST00000257430.4:c.3002del	p.Pro1001GlnfsTer4	p.P1001Qfs*4	ENST00000257430	NM_000038.5	1000	taC/ta	16/16	0.494240306216207	1	FACETS	0.974	0.89	1	0.974	0.89	1	CLONAL	1	TRUE	0	0.494240306216207	1		347	391	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	65	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.723	0.629	0.824	0.723	0.629	0.824	SUBCLONAL	1	TRUE	1	0.42816611253358	2		311	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577029	7577029	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	208	776	0	ENST00000269305.4:c.909del	p.Ser303ArgfsTer42	p.S303Rfs*42	ENST00000269305	NM_001126112.2	303	agC/ag	8/11	0.42816611253358	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.42816611253358	1		776	680	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593446	48593447	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0037544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	134	484	0	ENST00000342988.3:c.1198_1199insAA	p.Arg400LysfsTer16	p.R400Kfs*16	ENST00000342988	NM_005359.5	399	-/AA	10/12	0.42816611253358	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.42816611253358	1		484	447	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068422	26068426	+	frameshift_variant	Frame_Shift_Del	DEL	TTTTC	TTTTC	-	novel	NA	P-0037544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	64	468	0	ENST00000435504.4:c.64_68del	p.Glu22IlefsTer9	p.E22Ifs*9	ENST00000435504		22	GAAAAa/a	2/13	1	2	FACETS	0.909	0.792	1	0.909	0.792	1	CLONAL	1	TRUE	1	0.42816611253358	2		468	329	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913385	NA	P-0037544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	146	565	0	ENST00000304494.5:c.247C>G	p.His83Asp	p.H83D	ENST00000304494	NM_000077.4	83	Cac/Gac	2/3	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.42816611253358	2		565	651	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974744	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAGCAGCGCCCGCA	CCTCCAGCAGCGCCCGCA	-	novel	NA	P-0037544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	81	348	0	ENST00000304494.5:c.83_100del	p.Val28_Glu33del	p.V28_E33del	ENST00000304494	NM_000077.4	28	gTGCGGGCGCTGCTGGAGGcg/gcg	1/3	1	2	FACETS	0.894	0.792	1	0.894	0.792	1	CLONAL	1	TRUE	1	0.42816611253358	2		348	423	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50816372	50816372	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	113	329	0	ENST00000398568.2:c.1812A>T	p.Leu604Phe	p.L604F	ENST00000398568	NM_001042412.1	604	ttA/ttT	10/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		329	353	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80160741	80160741	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1454115884	NA	P-0037610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	181	569	0	ENST00000265081.6:c.3110A>G	p.Asp1037Gly	p.D1037G	ENST00000265081	NM_002439.4	1037	gAt/gGt	22/24	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		569	486	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223188	5223188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374591804	NA	P-0037750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	10	1016	0	ENST00000357368.4:c.2615G>A	p.Arg872His	p.R872H	ENST00000357368	NM_002850.3	872	cGt/cAt	18/38	1	2	FACETS	0.409	0.278	0.572	0.409	0.278	0.572	SUBCLONAL	1	TRUE	1	0.35965843819377	2		1016	136	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0037760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	152	600	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.354166114939156	1	FACETS	0.821	0.751	0.895	0.821	0.751	0.895	CLONAL	1	TRUE	0	0.354166114939156	1		601	860	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0037760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	98	308	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.354166114939156	2		308	523	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014298	70014298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142372494	NA	P-0037760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	151	547	1	ENST00000394351.3:c.1159G>A	p.Gly387Ser	p.G387S	ENST00000394351	NM_000248.3	387	Ggt/Agt	9/9	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.354166114939156	2		548	842	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184137	56184137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	92	377	0	ENST00000399503.3:c.4342C>T	p.Pro1448Ser	p.P1448S	ENST00000399503	NM_005921.1	1448	Cca/Tca	19/20	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.354166114939156	2		377	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0037763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	34	704	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.474	0.385	0.575	0.474	0.385	0.575	SUBCLONAL	1	TRUE	1	0.13	2		704	1103	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106861	27106861	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	54	700	1	ENST00000324856.7:c.6472C>T	p.Arg2158Ter	p.R2158*	ENST00000324856	NM_006015.4	2158	Cga/Tga	20/20	1	2	FACETS	0.83	0.706	0.966	0.83	0.706	0.966	CLONAL	1	TRUE	1	0.13	2		701	1001	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	4	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.055	0.028	0.094	0.055	0.028	0.094	SUBCLONAL	1	TRUE	1	0.57	2		311	256	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59878748	59878748	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1214800958	NA	P-0037868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	70	316	0	ENST00000259008.2:c.1006G>T	p.Asp336Tyr	p.D336Y	ENST00000259008	NM_032043.2	336	Gat/Tat	8/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	FALSE	1	0.449420220442176	2		316	274	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884563	151884563	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0037868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	60	292	0	ENST00000262189.6:c.4794-2A>T		p.X1598_splice	ENST00000262189	NM_170606.2	1598			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.449420220442176	2		292	213	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0037874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	104	660	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.492484865189124	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.492484865189124	1		660	219	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916734	48916736	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GGG	GGG	-	novel	NA	P-0037874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	27	226	0	ENST00000267163.4:c.265-1_266del		p.X89_splice	ENST00000267163	NM_000321.2	89		3/27	0.483605899648297	2	FACETS	1	0.909	1	0.602	0.492	0.721	CLONAL	1	TRUE	0	0.492484865189124	2		226	91	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110711	2110711	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	26	594	0	ENST00000219476.3:c.1016T>C	p.Val339Ala	p.V339A	ENST00000219476	NM_000548.3	339	gTc/gCc	11/42	0.218833079597377	4	FACETS	0.369	0.292	0.458	0.185	0.146	0.229	INDETERMINATE	1	TRUE	2	0.492484865189124	4		594	427	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508486	29508486	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	72	290	0	ENST00000356175.3:c.633del	p.Val212LeufsTer2	p.V212Lfs*2	ENST00000356175	NM_000267.3	211	gcA/gc	6/57	0.492484865189124	1	FACETS	0.755	0.68	0.83	1	0.981	1	SUBCLONAL	2	TRUE	0	0.492484865189124	1		290	146	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0037876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	122	435	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.444880499023083	1	FACETS	0.937	0.853	1	0.937	0.853	1	CLONAL	1	TRUE	0	0.444880499023083	1		435	455	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0037876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	146	476	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	0.444880499023083	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.444880499023083	1		476	428	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380320	25380320	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs904755552	NA	P-0037876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	84	281	0	ENST00000311936.3:c.138T>G	p.Ile46Met	p.I46M	ENST00000311936	NM_004985.3	46	atT/atG	3/5	0.444880499023083	1	FACETS	0.944	0.843	1	0.944	0.843	1	CLONAL	1	TRUE	0	0.444880499023083	1		281	311	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653833	89653844	+	inframe_deletion	In_Frame_Del	DEL	GCGTATACAGGA	GCGTATACAGGA	-	novel	NA	P-0037876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	48	288	0	ENST00000371953.3:c.131_142del	p.Gly44_Asn48delinsAsp	p.G44_N48delinsD	ENST00000371953	NM_000314.4	44	gGCGTATACAGGAac/gac	2/9	0.444880499023083	1	FACETS	0.653	0.556	0.757	0.653	0.556	0.757	SUBCLONAL	1	TRUE	0	0.444880499023083	1		288	257	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926888	112926888	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507546	NA	P-0121467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	154	666	0	ENST00000351677.2:c.1508G>T	p.Gly503Val	p.G503V	ENST00000351677	NM_002834.3	503	gGg/gTg	13/16	0.843576389694412	3	FACETS	0.76	0.697	0.825	0.38	0.348	0.413	SUBCLONAL	1	NA	1	0.843576389694412	3		666	683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0037893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	208	766	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.229753139131291	3	FACETS	0.888	0.829	0.949	0.888	0.829	0.949	CLONAL	3	TRUE	0	0.276256697339875	3		767	643	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412643	63412643	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	39	443	0	ENST00000330258.3:c.524G>C	p.Ser175Thr	p.S175T	ENST00000330258	NM_152424.3	175	aGt/aCt	2/2	0.219639499170477	3	FACETS	0.61	0.505	0.727	0.305	0.252	0.364	SUBCLONAL	1	TRUE	1	0.276256697339875	3		443	527	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0037896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	30	444	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.206598547927141	3	FACETS	0.825	0.671	0.995	0.825	0.671	0.995	CLONAL	2	TRUE	1	0.224762661398249	3		444	180	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0037896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	39	366	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.211875623318501	4	FACETS	0.908	0.765	1	0.908	0.765	1	CLONAL	3	TRUE	1	0.224762661398249	4		366	156	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577043	7577044	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	rs761885916	NA	P-0037896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	69	605	0	ENST00000269305.4:c.893_894dup	p.Leu299SerfsTer47	p.L299Sfs*47	ENST00000269305	NM_001126112.2	298	-/AG	8/11	0.201409706091906	2	FACETS	0.867	0.76	0.981	0.867	0.76	0.981	CLONAL	2	TRUE	0	0.224762661398249	2		605	354	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0037907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	47	308	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.25191991726746	1	FACETS	0.451	0.383	0.525	0.451	0.383	0.525	INDETERMINATE	1	TRUE	0	0.528710061568689	1		308	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0037907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	194	540	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.528710061568689	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.528710061568689	1		540	522	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239462	123239462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	164	491	0	ENST00000358487.5:c.2375C>T	p.Ser792Leu	p.S792L	ENST00000358487	NM_000141.4	792	tCa/tTa	18/18	0.528710061568689	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.528710061568689	1		491	452	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233228	69233228	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	49	211	0	ENST00000462284.1:c.1093G>A	p.Val365Ile	p.V365I	ENST00000462284	NM_002392.5	365	Gtt/Att	11/11	1	2	FACETS	0.763	0.652	0.882	0.763	0.652	0.882	SUBCLONAL	1	TRUE	1	0.528710061568689	2		211	243	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209247	98209247	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	226	539	0	ENST00000331920.6:c.4291G>C	p.Glu1431Gln	p.E1431Q	ENST00000331920	NM_000264.3	1431	Gag/Cag	23/24	0.28022312096299	6	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.528710061568689	6		539	1311	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0037915-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	17	621	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.343	0.256	0.444	0.343	0.256	0.444	SUBCLONAL	1	TRUE	1	0.514052593366771	2		621	193	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0037944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	23	334	1	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.619	0.483	0.777	0.619	0.483	0.777	SUBCLONAL	1	TRUE	1	0.228594461181526	2		335	325	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101040	27101056	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCTACTGAGCGCCGA	CTGCTACTGAGCGCCGA	-	novel	NA	P-0037944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	49	628	0	ENST00000324856.7:c.4323_4339del	p.Ala1442SerfsTer43	p.A1442Sfs*43	ENST00000324856	NM_006015.4	1441	gCTGCTACTGAGCGCCGA/g	18/20	1	2	FACETS	0.552	0.466	0.647	0.552	0.466	0.647	SUBCLONAL	1	TRUE	1	0.228594461181526	2		628	777	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820971	36820971	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766507697	NA	P-0037948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	131	728	0	ENST00000373129.3:c.406C>T	p.Arg136Cys	p.R136C	ENST00000373129	NM_032017.1	136	Cgc/Tgc	6/12	0.570855514400833	3	FACETS	0.566	0.513	0.623	0.283	0.256	0.312	SUBCLONAL	1	TRUE	1	0.570855514400833	3		728	1042	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0037948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	505	951	2	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.570855514400833	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.570855514400833	2		953	855	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218760	66218760	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	65	222	0	ENST00000273854.3:c.2298G>T	p.Lys766Asn	p.K766N	ENST00000273854	NM_004439.5	766	aaG/aaT	13/18	0.34228066854178	3	FACETS	0.915	0.799	1	0.457	0.399	0.519	INDETERMINATE	1	TRUE	1	0.570855514400833	3		222	320	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638533	176638533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377148087	NA	P-0037948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	129	715	0	ENST00000439151.2:c.3133C>T	p.Arg1045Cys	p.R1045C	ENST00000439151	NM_022455.4	1045	Cgt/Tgt	5/23	0.570855514400833	1	FACETS	0.528	0.48	0.578	0.528	0.48	0.578	SUBCLONAL	1	TRUE	0	0.570855514400833	1		715	612	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874178	151874178	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	55	319	0	ENST00000262189.6:c.8360A>G	p.Asn2787Ser	p.N2787S	ENST00000262189	NM_170606.2	2787	aAt/aGt	38/59	0.436073407891541	5	FACETS	0.408	0.348	0.475			1	SUBCLONAL	1	TRUE	NA	0.570855514400833	5		319	876	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304160	65304178	+	frameshift_variant	Frame_Shift_Del	DEL	AACGGCATATTTTAGCTGC	AACGGCATATTTTAGCTGC	-	novel	NA	P-0037953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	137	573	0	ENST00000342505.4:c.2937_2955del	p.Gln979HisfsTer33	p.Q979Hfs*33	ENST00000342505	NM_002227.2	979	caGCAGCTAAAATATGCCGTT/ca	21/25	0.692441549210705	1	FACETS	0.756	0.698	0.816	0.756	0.698	0.816	SUBCLONAL	1	TRUE	0	0.692441549210705	1		573	342	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599048	28599048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781675235	NA	P-0037953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	322	520	0	ENST00000241453.7:c.2240C>T	p.Pro747Leu	p.P747L	ENST00000241453	NM_004119.2	747	cCg/cTg	18/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.692441549210705	2		520	903	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs869025608	NA	P-0037953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	27	728	0	ENST00000307102.5:c.171G>T	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaT	2/11	0.692441549210705	1	FACETS	0.107	0.085	0.133	0.107	0.085	0.133	SUBCLONAL	1	TRUE	0	0.692441549210705	1		728	476	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950436	17950436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1274345651	NA	P-0037953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	91	899	0	ENST00000458235.1:c.1291C>T	p.Arg431Trp	p.R431W	ENST00000458235	NM_000215.3	431	Cgg/Tgg	10/24	0.692441549210705	1	FACETS	0.334	0.297	0.373	0.334	0.297	0.373	SUBCLONAL	1	TRUE	0	0.692441549210705	1		899	515	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526145	189526145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	301	856	0	ENST00000264731.3:c.409G>A	p.Asp137Asn	p.D137N	ENST00000264731	NM_003722.4	137	Gac/Aac	4/14	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.692441549210705	2		856	772	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	253	602	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	0.942	0.885	1	0.942	0.885	1	CLONAL	1	TRUE	1	0.692441549210705	2		602	776	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53254060	53254060	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	210	730	0	ENST00000375401.3:c.12del	p.Ser5ProfsTer68	p.S5Pfs*68	ENST00000375401	NM_004187.3	4	ggG/gg	1/26	1	2	FACETS	0.937	0.875	1	0.937	0.875	1	CLONAL	1	TRUE	1	0.692441549210705	2		730	647	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0037968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	258	443	9	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.453933168271991	2		452	898	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0037968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	386	713	1	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.404103930669346	2	FACETS	0.823	0.784	0.863	0.823	0.784	0.863	CLONAL	2	TRUE	0	0.453933168271991	2		714	1033	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052626	42052626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	154	582	4	ENST00000219905.7:c.7297C>T	p.Arg2433Trp	p.R2433W	ENST00000219905	NM_001164273.1	2433	Cgg/Tgg	20/24	0.152809737182059	4	FACETS	0.884	0.808	0.964	0.221	0.202	0.241	INDETERMINATE	1	TRUE	0	0.453933168271991	4		586	1116	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948737	55948737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150847930	NA	P-0037968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	91	675	0	ENST00000263923.4:c.3728C>T	p.Pro1243Leu	p.P1243L	ENST00000263923	NM_002253.2	1243	cCg/cTg	28/30	NA	2	FACETS	0.324	0.286	0.364			1	INDETERMINATE	1	TRUE	NA	0.453933168271991	2		675	1238	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132959	176132959	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	166	486	0	ENST00000367669.3:c.634A>C	p.Ser212Arg	p.S212R	ENST00000367669	NM_022457.5	212	Agt/Cgt	4/20	1	2	FACETS	0.878	0.807	0.952	0.878	0.807	0.952	CLONAL	1	TRUE	1	0.453933168271991	2		486	833	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969817	81969817	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	81	618	0	ENST00000359376.3:c.2886G>C	p.Lys962Asn	p.K962N	ENST00000359376	NM_002661.3	962	aaG/aaC	27/33	0.106178672118729	4	FACETS	0.468	0.411	0.53	0.234	0.205	0.265	INDETERMINATE	1	TRUE	2	0.453933168271991	4		618	1109	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836417	89836417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242381795	NA	P-0037968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	271	613	0	ENST00000389301.3:c.2332G>A	p.Ala778Thr	p.A778T	ENST00000389301	NM_000135.2	778	Gcc/Acc	26/43	0.106178672118729	4	FACETS	0.836	0.785	0.889	0.836	0.785	0.889	INDETERMINATE	2	TRUE	2	0.453933168271991	4		613	1038	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097131	11097131	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748298484	NA	P-0037968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	372	851	0	ENST00000358026.2:c.622C>T	p.Arg208Trp	p.R208W	ENST00000358026	NM_001128849.1	208	Cgg/Tgg	4/36	0.195140820068121	2	FACETS	1	0.995	1	0.717	0.681	0.754	INDETERMINATE	1	TRUE	0	0.453933168271991	2		851	1143	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663651	117663651	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	55	488	0	ENST00000368508.3:c.4581G>C	p.Met1527Ile	p.M1527I	ENST00000368508	NM_002944.2	1527	atG/atC	28/43	0.420334536785755	1	FACETS	0.219	0.186	0.254	0.219	0.186	0.254	SUBCLONAL	1	TRUE	0	0.453933168271991	1		488	857	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987388	2987388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1192456063	NA	P-0037968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	252	600	0	ENST00000396946.4:c.41C>T	p.Thr14Met	p.T14M	ENST00000396946	NM_032415.4	14	aCg/aTg	3/25	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.453933168271991	2		600	953	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0037974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	550	689	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.644824416512176	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.668876570950042	2		689	818	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995282	15995282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	113	575	0	ENST00000268712.3:c.2911G>A	p.Ala971Thr	p.A971T	ENST00000268712	NM_006311.3	971	Gca/Aca	22/46	0.644824416512176	2	FACETS	0.507	0.456	0.56	0.253	0.228	0.28	SUBCLONAL	1	TRUE	0	0.668876570950042	2		575	667	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0038051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	358	621	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA	2	FACETS	0.933	0.888	0.978			1	INDETERMINATE	2	TRUE	NA	0.448447739744463	2		622	856	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473779	67473779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906850	NA	P-0038051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	93	552	0	ENST00000327367.4:c.859C>T	p.Arg287Trp	p.R287W	ENST00000327367	NM_005902.3	287	Cgg/Tgg	6/9	0.380108509758778	4	FACETS	0.76	0.676	0.851	0.253	0.225	0.284	SUBCLONAL	1	TRUE	1	0.448447739744463	4		552	790	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735503	40735503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763584414	NA	P-0038051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	148	621	0	ENST00000373198.4:c.3370G>A	p.Glu1124Lys	p.E1124K	ENST00000373198	NM_133170.3	1124	Gag/Aag	25/32	0.111558245395293	3	FACETS	1	0.96	1	0.361	0.33	0.394	INDETERMINATE	1	TRUE	0	0.448447739744463	3		621	746	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs770248150	NA	P-0038051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	157	518	1	ENST00000311936.3:c.351A>T	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaT	4/5	0.0778424209765231	6	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.448447739744463	6		519	534	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983146	201983146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	121	550	0	ENST00000359651.3:c.995C>T	p.Ala332Val	p.A332V	ENST00000359651		332	gCc/gTc	7/8	1	2	FACETS	0.904	0.819	0.993	0.904	0.819	0.993	CLONAL	1	TRUE	1	0.448447739744463	2		550	597	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477097	67477115	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGTCTTCGCAGAGTGCC	GAGGTCTTCGCAGAGTGCC	CA	novel	NA	P-0038051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	358	662	2	ENST00000327367.4:c.904_922delinsCA	p.Glu302HisfsTer3	p.E302Hfs*3	ENST00000327367	NM_005902.3	302	GAGGTCTTCGCAGAGTGCCtc/CAtc	7/9	0.380108509758778	4	FACETS	1	0.993	1	0.831	0.79	0.872	CLONAL	2	TRUE	1	0.448447739744463	4		664	928	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156029	99156029	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	115	558	1	ENST00000074304.5:c.709A>T	p.Thr237Ser	p.T237S	ENST00000074304	NM_001134224.1	237	Acc/Tcc	10/26	1	2	FACETS	0.929	0.84	1	0.929	0.84	1	CLONAL	1	TRUE	1	0.448447739744463	2		559	552	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141611	202141611	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	108	468	0	ENST00000358485.4:c.899A>C	p.Asn300Thr	p.N300T	ENST00000358485	NM_001080125.1	300	aAt/aCt	7/9	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.448447739744463	2		468	463	SUCCESS
APC	324	MSKCC	GRCh37	5	112175558	112175561	+	frameshift_variant	Frame_Shift_Del	DEL	CTTC	CTTC	-	novel	NA	P-0038051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	134	370	0	ENST00000257430.4:c.4268_4271del	p.Leu1423GlnfsTer49	p.L1423Qfs*49	ENST00000257430	NM_000038.5	1423	CTTCca/ca	16/16	0.430932575781975	2	FACETS	0.864	0.795	0.933	0.864	0.795	0.933	CLONAL	2	TRUE	0	0.448447739744463	2		370	346	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115681	108115681	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs876660933	NA	P-0038071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	74	270	0	ENST00000278616.4:c.829G>T	p.Glu277Ter	p.E277*	ENST00000278616	NM_000051.3	277	Gaa/Taa	7/63	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.422932024322268	2		270	307	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235838	108235838	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1060501650	NA	P-0038071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	79	311	0	ENST00000278616.4:c.8880G>A	p.Trp2960Ter	p.W2960*	ENST00000278616	NM_000051.3	2960	tgG/tgA	62/63	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.422932024322268	2		311	366	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982414	25982414	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	62	256	0	ENST00000435504.4:c.876T>G	p.Phe292Leu	p.F292L	ENST00000435504		292	ttT/ttG	9/13	1	2	FACETS	0.961	0.837	1	0.961	0.837	1	CLONAL	1	TRUE	1	0.422932024322268	2		256	305	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225343024	225343024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	92	367	0	ENST00000264414.4:c.2068G>A	p.Glu690Lys	p.E690K	ENST00000264414	NM_003590.4	690	Gaa/Aaa	15/16	1	2	FACETS	0.892	0.795	0.993	0.892	0.795	0.993	CLONAL	1	TRUE	1	0.422932024322268	2		367	488	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164331	47164331	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	69	255	0	ENST00000409792.3:c.1795G>T	p.Glu599Ter	p.E599*	ENST00000409792	NM_014159.6	599	Gaa/Taa	3/21	0.422932024322268	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	0	0.422932024322268	1		255	250	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52685805	52685806	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCATAATAATCTGGATATTGCTGGAAGAC	novel	NA	P-0038071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	50	332	0	ENST00000394830.3:c.646-9_666dup	p.Ala222_Ile223insValPheGlnGlnTyrProAspTyrTyrAla	p.A222_I223insVFQQYPDYYA	ENST00000394830	NM_018313.4	222	-/GTCTTCCAGCAATATCCAGATTATTATGCA	7/30	0.422932024322268	1	FACETS	0.613	0.523	0.711	0.613	0.523	0.711	SUBCLONAL	1	TRUE	0	0.422932024322268	1		332	304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578502	7578502	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	249	906	0	ENST00000269305.4:c.428T>C	p.Val143Ala	p.V143A	ENST00000269305	NM_001126112.2	143	gTg/gCg	5/11	0.564111770628811	2	FACETS	0.802	0.758	0.845	0.802	0.758	0.845	CLONAL	2	TRUE	0	0.612696345841198	2		906	507	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641462	18641462	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	50	437	1	ENST00000266497.5:c.2461G>T	p.Gly821Cys	p.G821C	ENST00000266497		821	Ggt/Tgt	17/31	0.612696345841198	3	FACETS	0.658	0.561	0.763	0.329	0.28	0.382	SUBCLONAL	1	TRUE	1	0.612696345841198	3		438	324	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428238	47428238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754803899	NA	P-0038146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	194	800	0	ENST00000377045.4:c.1198C>T	p.Arg400Cys	p.R400C	ENST00000377045	NM_001654.4	400	Cgc/Tgc	11/16	0.343866372173558	4	FACETS	1	0.99	1	0.714	0.663	0.767	INDETERMINATE	1	TRUE	2	0.612696345841198	4		800	715	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs775623976	NA	P-0038421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	208	528	0	ENST00000335508.6:c.1873C>G	p.Arg625Gly	p.R625G	ENST00000335508	NM_012433.2	625	Cgt/Ggt	14/25	1	2	FACETS	0.963	0.903	1	0.963	0.903	1	CLONAL	1	TRUE	1	0.88166962526714	2		528	490	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591119	67591124	+	inframe_deletion	In_Frame_Del	DEL	TCCAGC	TCCAGC	-	novel	NA	P-0038421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	40	389	0	ENST00000274335.5:c.1713_1718del	p.Ile571_Leu573delinsMet	p.I571_L573delinsM	ENST00000274335		571	aTCCAGCtg/atg	12/15	1	2	FACETS	0.292	0.243	0.345	0.292	0.243	0.345	SUBCLONAL	1	TRUE	1	0.88166962526714	2		389	311	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0038498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	307	830	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.420123925118174	2	FACETS	0.881	0.834	0.929	0.881	0.834	0.929	CLONAL	2	TRUE	0	0.420123925118174	2		830	829	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0038498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	204	398	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.420123925118174	2	FACETS	0.797	0.744	0.852	0.797	0.744	0.852	SUBCLONAL	2	TRUE	0	0.420123925118174	2		398	609	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17349179	17349179	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782604	NA	P-0038498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	83	687	0	ENST00000375499.3:c.689G>A	p.Arg230His	p.R230H	ENST00000375499	NM_003000.2	230	cGc/cAc	7/8	0.260032945166884	2	FACETS	0.407	0.358	0.46	0.204	0.179	0.23	SUBCLONAL	1	TRUE	0	0.420123925118174	2		687	970	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266493	41266501	+	inframe_deletion	In_Frame_Del	DEL	CTATGTTCC	CTATGTTCC	-	novel	NA	P-0038498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	118	582	0	ENST00000349496.5:c.292_300del	p.Met98_Pro100del	p.M98_P100del	ENST00000349496	NM_001904.3	97	gCTATGTTCCct/gct	4/15	0.389647192390779	3	FACETS	0.777	0.7	0.858	0.388	0.35	0.429	SUBCLONAL	1	TRUE	1	0.420123925118174	3		582	875	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0038498-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	425	830	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.0602689706821646	3	FACETS	0.886	0.852	0.921			1	INDETERMINATE	3	TRUE	NA	0.5231422764709	3		830	771	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0038498-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	88	398	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.97	0.866	1	0.97	0.866	1	CLONAL	1	TRUE	1	0.5231422764709	2		398	347	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17349179	17349179	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782604	NA	P-0038498-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	199	687	0	ENST00000375499.3:c.689G>A	p.Arg230His	p.R230H	ENST00000375499	NM_003000.2	230	cGc/cAc	7/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.5231422764709	2		687	704	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266493	41266501	+	inframe_deletion	In_Frame_Del	DEL	CTATGTTCC	CTATGTTCC	-	novel	NA	P-0038498-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	133	582	0	ENST00000349496.5:c.292_300del	p.Met98_Pro100del	p.M98_P100del	ENST00000349496	NM_001904.3	97	gCTATGTTCCct/gct	4/15	0.314057918554041	3	FACETS	1	0.923	1	0.507	0.462	0.555	CLONAL	1	TRUE	1	0.5231422764709	3		582	632	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569784	67569784	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs767073354	NA	P-0038498-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	42	391	0	ENST00000274335.5:c.445C>G	p.Leu149Val	p.L149V	ENST00000274335		149	Cta/Gta	3/15	1	2	FACETS	0.37	0.309	0.438	0.37	0.309	0.438	SUBCLONAL	1	TRUE	1	0.5231422764709	2		391	434	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	167	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.933	0.865	1	0.933	0.865	1	CLONAL	1	TRUE	1	0.770175952813018	2		311	465	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0038761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	290	803	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	0.957	0.904	1	0.957	0.904	1	CLONAL	1	TRUE	1	0.770175952813018	2		803	787	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0038761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	147	478	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.878	0.809	0.948	0.878	0.809	0.948	CLONAL	1	TRUE	1	0.770175952813018	2		478	435	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0038761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	171	378	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.98	0.911	1	0.98	0.911	1	CLONAL	1	TRUE	1	0.770175952813018	2		378	453	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921555	178921555	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	124	431	0	ENST00000263967.3:c.1037T>A	p.Val346Glu	p.V346E	ENST00000263967	NM_006218.2	346	gTa/gAa	5/21	1	2	FACETS	0.956	0.876	1	0.956	0.876	1	CLONAL	1	TRUE	1	0.770175952813018	2		431	337	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023539	27023539	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0038761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	357	415	0	ENST00000324856.7:c.645C>G	p.Tyr215Ter	p.Y215*	ENST00000324856	NM_006015.4	215	taC/taG	1/20	0.734574741436345	2	FACETS	0.968	0.936	0.998	0.968	0.936	0.998	CLONAL	2	TRUE	0	0.770175952813018	2		415	479	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633207	12633207	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs730880382	NA	P-0038761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	223	577	0	ENST00000251849.4:c.1193G>T	p.Arg398Leu	p.R398L	ENST00000251849	NM_002880.3	398	cGc/cTc	11/17	1	2	FACETS	0.939	0.879	0.999	0.939	0.879	0.999	CLONAL	1	TRUE	1	0.770175952813018	2		577	617	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653843	89653843	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	143	521	0	ENST00000371953.3:c.141G>T	p.Arg47Ser	p.R47S	ENST00000371953	NM_000314.4	47	agG/agT	2/9	1	2	FACETS	0.87	0.8	0.941	0.87	0.8	0.941	CLONAL	1	TRUE	1	0.770175952813018	2		521	427	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	461475	461475	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs998253161	NA	P-0038761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	186	535	0	ENST00000399788.2:c.1045C>G	p.Arg349Gly	p.R349G	ENST00000399788	NM_001042603.1	349	Cga/Gga	9/28	NA	2	FACETS	0.932	0.868	0.998			1	INDETERMINATE	1	TRUE	NA	0.770175952813018	2		535	518	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90970987	90970987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765403660	NA	P-0038761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	198	450	1	ENST00000265433.3:c.1090G>A	p.Val364Ile	p.V364I	ENST00000265433	NM_002485.4	364	Gta/Ata	9/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.770175952813018	2		451	496	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665752	29665755	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1555535032	NA	P-0038884-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	161	565	1	ENST00000356175.3:c.6789_6792del	p.Tyr2264ThrfsTer5	p.Y2264Tfs*5	ENST00000356175	NM_000267.3	2263	ACTTac/ac	45/57	1	2	FACETS	0.84	0.777	0.905	0.84	0.777	0.905	CLONAL	1	TRUE	1	0.796585768287214	2		566	481	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0038884-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	308	766	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.967	0.916	1	0.967	0.916	1	CLONAL	1	TRUE	1	0.796585768287214	2		767	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0038884-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	343	540	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.956	0.908	1	0.956	0.908	1	CLONAL	1	TRUE	1	0.796585768287214	2		541	901	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557331	29557332	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0038884-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	168	308	0	ENST00000356175.3:c.3047_3048del	p.Cys1016SerfsTer4	p.C1016Sfs*4	ENST00000356175	NM_000267.3	1015	cTG/c	23/57	1	2	FACETS	0.929	0.862	0.997	0.929	0.862	0.997	CLONAL	1	TRUE	1	0.796585768287214	2		308	454	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938089	76938092	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	novel	NA	P-0038884-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	292	596	0	ENST00000373344.5:c.2656_2659del	p.Glu886LeufsTer18	p.E886Lfs*18	ENST00000373344	NM_000489.3	886	GAGAct/ct	9/35	1	2	FACETS	0.938	0.886	0.989	0.938	0.886	0.989	CLONAL	1	TRUE	1	0.796585768287214	2		596	782	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252155	226252155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553260624	NA	P-0038884-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	67	96	0	ENST00000366813.1:c.103G>A	p.Gly35Arg	p.G35R	ENST00000366813		35	Ggg/Agg	1/3	0.796585768287214	3	FACETS	0.96	0.845	1	0.48	0.422	0.541	CLONAL	1	TRUE	1	0.796585768287214	3		96	245	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922084	39922085	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0038884-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	333	668	0	ENST00000378444.4:c.4087_4088del	p.Cys1363GlnfsTer45	p.C1363Qfs*45	ENST00000378444	NM_001123385.1	1363	TGc/c	9/15	1	2	FACETS	0.898	0.851	0.945	0.898	0.851	0.945	CLONAL	1	TRUE	1	0.796585768287214	2		668	931	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196783	123196783	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0038884-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	225	468	0	ENST00000218089.9:c.1670T>A	p.Leu557Ter	p.L557*	ENST00000218089	NM_001042749.1	557	tTg/tAg	18/35	1	2	FACETS	0.913	0.856	0.971	0.913	0.856	0.971	CLONAL	1	TRUE	1	0.796585768287214	2		468	619	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	38	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.110517451343071	4	FACETS	1	0.941	1	0.679	0.561	0.809	CLONAL	1	TRUE	2	0.16	4		311	406	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	18	348	1				ENST00000310581	NM_198253.2	-/1132			0.117731577484553	0	FACETS	1	0.805	1			1	CLONAL	1	TRUE	0	0.16	0		349	176	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs397517201	NA	P-0039115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	48	563	2	ENST00000263967.3:c.1637A>T	p.Gln546Leu	p.Q546L	ENST00000263967	NM_006218.2	546	cAg/cTg	10/21	0.3	3	FACETS	1	0.939	1	0.618	0.523	0.724	CLONAL	1	TRUE	1	0.16	3		565	524	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044518	5044518	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	26	337	0	ENST00000381652.3:c.466C>G	p.Gln156Glu	p.Q156E	ENST00000381652	NM_004972.3	156	Cag/Gag	5/25	1	2	FACETS	1	0.823	1	1	0.823	1	CLONAL	1	TRUE	1	0.16	2		337	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519980	NA	P-0039254-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	155	815	0	ENST00000269305.4:c.528C>G	p.Cys176Trp	p.C176W	ENST00000269305	NM_001126112.2	176	tgC/tgG	5/11	0.22358827370042	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.22358827370042	2		815	651	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447613	187447613	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039254-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	132	695	0	ENST00000232014.4:c.580T>G	p.Ser194Ala	p.S194A	ENST00000232014	NM_001130845.1	194	Tct/Gct	5/10	0.220229842548389	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.22358827370042	2		695	562	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0039618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	133	308	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.24645497042817	3	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	1	0.24645497042817	3		308	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0039618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	99	766	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.24645497042817	1	FACETS	0.974	0.87	1	0.974	0.87	1	CLONAL	1	TRUE	0	0.24645497042817	1		767	723	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534285	534285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894226	NA	P-0039618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	77	754	0	ENST00000451590.1:c.38G>A	p.Gly13Asp	p.G13D	ENST00000451590	NM_001130442.1	13	gGt/gAt	2/5	NA	2	FACETS	0.812	0.712	0.919			1	INDETERMINATE	1	TRUE	NA	0.24645497042817	2		754	770	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305323	65305323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	84	529	0	ENST00000342505.4:c.2805G>T	p.Glu935Asp	p.E935D	ENST00000342505	NM_002227.2	935	gaG/gaT	20/25	1	2	FACETS	0.986	0.871	1	0.986	0.871	1	CLONAL	1	TRUE	1	0.24645497042817	2		529	691	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212178	5212178	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1393306881	NA	P-0039618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	127	943	1	ENST00000357368.4:c.4853A>G	p.Tyr1618Cys	p.Y1618C	ENST00000357368	NM_002850.3	1618	tAt/tGt	32/38	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.24645497042817	2		944	925	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0039619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	818	600	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.491294664708101	3	FACETS	0.993	0.966	1	0.993	0.966	1	CLONAL	3	TRUE	0	0.491294664708101	3		601	1392	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413105	63413105	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374303948	NA	P-0039619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	240	1022	4	ENST00000330258.3:c.62G>A	p.Arg21His	p.R21H	ENST00000330258	NM_152424.3	21	cGt/cAt	2/2	0.314800281613715	3	FACETS	0.904	0.843	0.968	0.452	0.421	0.484	CLONAL	1	TRUE	1	0.491294664708101	3		1026	1346	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209685	98209685	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1216794003	NA	P-0039619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	247	952	1	ENST00000331920.6:c.3853C>A	p.Gln1285Lys	p.Q1285K	ENST00000331920	NM_000264.3	1285	Cag/Aag	23/24	0.436682266659262	3	FACETS	1	0.944	1	0.506	0.472	0.541	CLONAL	1	TRUE	1	0.491294664708101	3		953	1237	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	433	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.610937618351481	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	0	0.610937618351481	3		539	608	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936093	178936093	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913275	NA	P-0039633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	237	674	3	ENST00000263967.3:c.1635G>T	p.Glu545Asp	p.E545D	ENST00000263967	NM_006218.2	545	gaG/gaT	10/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.610937618351481	2		677	674	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907621	76907621	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	189	477	0	ENST00000373344.5:c.4540C>T	p.Arg1514Ter	p.R1514*	ENST00000373344	NM_000489.3	1514	Cga/Tga	15/35	0.610937618351481	3	FACETS	0.922	0.853	0.994	0.461	0.426	0.497	CLONAL	1	TRUE	1	0.610937618351481	3		477	876	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182910	123182910	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	116	325	0	ENST00000218089.9:c.875T>C	p.Val292Ala	p.V292A	ENST00000218089	NM_001042749.1	292	gTg/gCg	10/35	0.610937618351481	3	FACETS	0.864	0.781	0.951	0.432	0.39	0.476	CLONAL	1	TRUE	1	0.610937618351481	3		325	574	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732946	30732946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	123	410	0	ENST00000295754.5:c.1559G>A	p.Cys520Tyr	p.C520Y	ENST00000295754	NM_003242.5	520	tGc/tAc	7/7	0.610937618351481	2	FACETS	1	0.934	1	0.514	0.469	0.56	CLONAL	1	TRUE	0	0.610937618351481	2		410	392	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064770	80064770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1261908217	NA	P-0039633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	311	497	1	ENST00000265081.6:c.2201G>A	p.Arg734Gln	p.R734Q	ENST00000265081	NM_002439.4	734	cGa/cAa	15/24	0.610937618351481	3	FACETS	0.962	0.914	1	0.962	0.914	1	CLONAL	2	TRUE	1	0.610937618351481	3		498	691	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169109	119169109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373587039	NA	P-0039633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	190	532	1	ENST00000264033.4:c.2293G>A	p.Glu765Lys	p.E765K	ENST00000264033	NM_005188.3	765	Gag/Aag	15/16	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.610937618351481	2		533	562	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117835	70117836	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0039633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	185	650	0	ENST00000245479.2:c.304_305dup	p.Pro103SerfsTer8	p.P103Sfs*8	ENST00000245479	NM_000346.3	101	-/AA	1/3	1	2	FACETS	0.942	0.874	1	0.942	0.874	1	CLONAL	1	TRUE	1	0.610937618351481	2		650	643	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208247	5208247	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0039633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	148	680	1	ENST00000357368.4:c.5642+1G>A		p.X1881_splice	ENST00000357368	NM_002850.3	1881			1	2	FACETS	0.731	0.669	0.795	0.731	0.669	0.795	SUBCLONAL	1	TRUE	1	0.610937618351481	2		681	663	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564520	41564521	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0039633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	234	547	0	ENST00000263253.7:c.3942_3943del	p.Asn1314LysfsTer3	p.N1314Kfs*3	ENST00000263253	NM_001429.3	1314	aaTCac/aaac	24/31	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.610937618351481	2		547	721	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715720	30715720	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	143	329	2	ENST00000295754.5:c.1378C>G	p.Arg460Gly	p.R460G	ENST00000295754	NM_003242.5	460	Cgc/Ggc	5/7	0.610937618351481	2	FACETS	1	0.968	1	0.549	0.505	0.595	CLONAL	1	TRUE	0	0.610937618351481	2		331	426	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265774	41266180	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACC	TCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACC	-	novel	NA	P-0039633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	183	42	0	ENST00000349496.5:c.13+204_179del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.610937618351481	2	FACETS	0.938	0.905	0.967	1	0.994	1	CLONAL	3	TRUE	0	0.610937618351481	2		42	213	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981474	55981474	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	165	435	0	ENST00000263923.4:c.463del	p.Ser155GlnfsTer37	p.S155Qfs*37	ENST00000263923	NM_002253.2	155	Tca/ca	4/30	1	2	FACETS	0.953	0.88	1	0.953	0.88	1	CLONAL	1	TRUE	1	0.610937618351481	2		435	567	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196375	106196375	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1311791804	NA	P-0039633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	136	336	0	ENST00000380013.4:c.4708A>G	p.Met1570Val	p.M1570V	ENST00000380013	NM_001127208.2	1570	Atg/Gtg	11/11	1	2	FACETS	0.972	0.891	1	0.972	0.891	1	CLONAL	1	TRUE	1	0.610937618351481	2		336	458	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057248	180057248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775547530	NA	P-0039633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	471	821	2	ENST00000261937.6:c.490G>A	p.Gly164Ser	p.G164S	ENST00000261937	NM_182925.4	164	Ggc/Agc	4/30	0.610937618351481	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.610937618351481	3		823	927	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662614	117662614	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs751986538	NA	P-0039633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	144	437	2	ENST00000368508.3:c.4851G>T	p.Arg1617Ser	p.R1617S	ENST00000368508	NM_002944.2	1617	agG/agT	29/43	1	2	FACETS	0.879	0.807	0.955	0.879	0.807	0.955	CLONAL	1	TRUE	1	0.610937618351481	2		439	536	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708157	117708157	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	112	437	1	ENST00000368508.3:c.2020G>T	p.Glu674Ter	p.E674*	ENST00000368508	NM_002944.2	674	Gaa/Taa	14/43	1	2	FACETS	0.79	0.715	0.869	0.79	0.715	0.869	SUBCLONAL	1	TRUE	1	0.610937618351481	2		438	464	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151947938	151947938	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	134	480	0	ENST00000262189.6:c.1735G>T	p.Ala579Ser	p.A579S	ENST00000262189	NM_170606.2	579	Gcg/Tcg	12/59	1	2	FACETS	0.818	0.747	0.892	0.818	0.747	0.892	CLONAL	1	TRUE	1	0.610937618351481	2		480	536	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938212	76938212	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	197	600	0	ENST00000373344.5:c.2536G>T	p.Asp846Tyr	p.D846Y	ENST00000373344	NM_000489.3	846	Gat/Tat	9/35	0.610937618351481	3	FACETS	0.86	0.796	0.926	0.43	0.398	0.463	CLONAL	1	TRUE	1	0.610937618351481	3		600	979	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0039658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	67	951	2	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.224140906827354	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.224140906827354	1		953	498	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	42	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.892	0.746	1	0.892	0.746	1	CLONAL	1	TRUE	1	0.224140906827354	2		539	420	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044539	47044548	+	frameshift_variant	Frame_Shift_Del	DEL	TGCGAGATGA	TGCGAGATGA	-	novel	NA	P-0039658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	101	592	0	ENST00000377604.3:c.2036_2045del	p.Leu679ProfsTer22	p.L679Pfs*22	ENST00000377604	NM_001204468.1	679	cTGCGAGATGAc/cc	18/24	1	2	FACETS	0.778	0.697	0.864	1	0.983	1	SUBCLONAL	2	TRUE	1	0.224140906827354	2		592	579	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579321	7579322	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs587780067	NA	P-0039683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	37	724	0	ENST00000269305.4:c.365_366del	p.Val122AspfsTer26	p.V122Dfs*26	ENST00000269305	NM_001126112.2	122	gTG/g	4/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		724	693	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858279	27858279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	41	582	2	ENST00000359303.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000359303	NM_003535.2	98	Gag/Aag	1/1	0.104431566805251	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		584	689	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0039693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	236	372	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.911	0.852	0.971	0.911	0.852	0.971	CLONAL	1	TRUE	1	0.632698768800851	2		372	819	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0039693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	251	654	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.632698768800851	1	FACETS	0.972	0.918	1	0.972	0.918	1	CLONAL	1	TRUE	0	0.632698768800851	1		654	558	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0039693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	104	370	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	0.632698768800851	1	FACETS	0.644	0.582	0.708	0.644	0.582	0.708	SUBCLONAL	1	TRUE	0	0.632698768800851	1		370	349	SUCCESS
APC	324	MSKCC	GRCh37	5	112173374	112173374	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	167	363	1	ENST00000257430.4:c.2083C>T	p.Gln695Ter	p.Q695*	ENST00000257430	NM_000038.5	695	Cag/Tag	16/16	0.188241867111722	3	FACETS	0.821	0.763	0.881	0.548	0.509	0.587	INDETERMINATE	2	TRUE	0	0.632698768800851	3		364	423	SUCCESS
APC	324	MSKCC	GRCh37	5	112175630	112175630	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	67	378	0	ENST00000257430.4:c.4339del	p.Gln1447LysfsTer26	p.Q1447Kfs*26	ENST00000257430	NM_000038.5	1447	Caa/aa	16/16	0.188241867111722	3	FACETS	0.522	0.454	0.595	0.174	0.151	0.199	INDETERMINATE	1	TRUE	0	0.632698768800851	3		378	534	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100594	157100594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	137	310	0	ENST00000346085.5:c.1531G>A	p.Gly511Ser	p.G511S	ENST00000346085	NM_020732.3	511	Ggc/Agc	1/20	1	2	FACETS	0.98	0.899	1	0.98	0.899	1	CLONAL	1	TRUE	1	0.632698768800851	2		310	442	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741739	145741740	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGGCTGGGGGCTCCCCACACGGATGCTGACTT	novel	NA	P-0039693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	124	556	0	ENST00000428558.2:c.731_763dup	p.Pro254_Ser255insLysValSerIleArgValGlySerProGlnPro	p.P254_S255insKVSIRVGSPQP	ENST00000428558	NM_004260.3	255	agc/aAAGTCAGCATCCGTGTGGGGAGCCCCCAGCCCAgc	5/22	1	2	FACETS	0.564	0.511	0.62	0.564	0.511	0.62	SUBCLONAL	1	TRUE	1	0.632698768800851	2		556	695	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	193	348	1				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		349	471	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	179	429	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	0.313217799206617	3	FACETS	0.845	0.788	0.903	0.845	0.788	0.903	INDETERMINATE	2	TRUE	1	0.634045166734929	3		429	440	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555526101	NA	P-0039735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	302	806	0	ENST00000269305.4:c.497C>G	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tGa	5/11	0.634045166734929	1	FACETS	0.981	0.932	1	0.981	0.932	1	CLONAL	1	TRUE	0	0.634045166734929	1		806	663	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164619	36164628	+	frameshift_variant	Frame_Shift_Del	DEL	ACCATGGAGA	ACCATGGAGA	-	novel	NA	P-0039735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	220	638	0	ENST00000300305.3:c.1247_1256del	p.Phe416TrpfsTer175	p.F416Wfs*175	ENST00000300305		416	tTCTCCATGGTg/tg	8/8	1	2	FACETS	0.93	0.869	0.994	0.93	0.869	0.994	CLONAL	1	TRUE	1	0.634045166734929	2		638	746	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566472	41566472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	61	297	0	ENST00000263253.7:c.4349G>A	p.Cys1450Tyr	p.C1450Y	ENST00000263253	NM_001429.3	1450	tGc/tAc	27/31	0.199457233482514	5	FACETS	0.685	0.591	0.787			1	INDETERMINATE	1	TRUE	NA	0.634045166734929	5		297	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0039749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	268	542	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.606331702030765	2	FACETS	0.921	0.878	0.964	0.921	0.878	0.964	CLONAL	2	TRUE	0	0.642233648758129	2		542	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0039814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	136	810	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.271889190272506	3	FACETS	0.897	0.829	0.966	0.897	0.829	0.966	CLONAL	3	TRUE	0	0.382219031067736	3		810	315	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658296	18658296	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371412006	NA	P-0039814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	79	614	1	ENST00000266497.5:c.3101G>A	p.Arg1034His	p.R1034H	ENST00000266497		1034	cGt/cAt	22/31	0.382219031067736	3	FACETS	0.892	0.794	0.994	0.892	0.794	0.994	CLONAL	2	TRUE	1	0.382219031067736	3		615	276	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18473932	18473932	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	88	363	0	ENST00000266497.5:c.1174C>A	p.Leu392Ile	p.L392I	ENST00000266497		392	Ctt/Att	6/31	0.382219031067736	3	FACETS	0.93	0.833	1	0.93	0.833	1	CLONAL	2	TRUE	1	0.382219031067736	3		363	295	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41209108	41209108	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	108	808	0	ENST00000357654.3:c.5238C>A	p.His1746Gln	p.H1746Q	ENST00000357654	NM_007294.3	1746	caC/caA	19/23	0.382219031067736	3	FACETS	0.865	0.783	0.951	0.577	0.522	0.634	CLONAL	2	TRUE	0	0.382219031067736	3		808	389	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422530	225422530	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	59	418	0	ENST00000264414.4:c.110T>C	p.Leu37Pro	p.L37P	ENST00000264414	NM_003590.4	37	cTg/cCg	2/16	0.245386406235451	4	FACETS	0.86	0.748	0.979	0.86	0.748	0.979	CLONAL	2	TRUE	2	0.382219031067736	4		418	248	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572589	141572589	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	42	810	0	ENST00000220592.5:c.481G>T	p.Ala161Ser	p.A161S	ENST00000220592	NM_012154.3	161	Gcc/Tcc	4/19	0.245386406235451	4	FACETS	0.996	0.835	1	0.498	0.417	0.586	CLONAL	1	TRUE	2	0.382219031067736	4		810	305	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0039862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	75	443	9	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		452	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs17849781	NA	P-0039865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	362	986	0	ENST00000269305.4:c.832C>A	p.Pro278Thr	p.P278T	ENST00000269305	NM_001126112.2	278	Cct/Act	8/11	1	2	FACETS	0.783	0.741	0.826	0.783	0.741	0.826	SUBCLONAL	1	TRUE	1	0.604008141870809	2		986	1531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782082	NA	P-0039865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	434	894	0	ENST00000269305.4:c.745A>T	p.Arg249Trp	p.R249W	ENST00000269305	NM_001126112.2	249	Agg/Tgg	7/11	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.604008141870809	2		894	1199	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100556	8100556	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528856735	NA	P-0039865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	940	846	2	ENST00000346208.3:c.530G>A	p.Arg177Gln	p.R177Q	ENST00000346208		177	cGg/cAg	3/6	0.604008141870809	4	FACETS	1	0.997	1	0.804	0.78	0.827	CLONAL	2	TRUE	1	0.604008141870809	4		848	2071	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731445	47731445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	11	54	0	ENST00000449228.1:c.347C>T	p.Pro116Leu	p.P116L	ENST00000449228	NM_001127240.2	116	cCg/cTg	2/4	0.185482392860697	2	FACETS	0.675	0.478	0.904	0.337	0.239	0.452	INDETERMINATE	1	TRUE	0	0.604008141870809	2		54	54	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0039868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	343	766	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.637035050399299	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.637035050399299	1		767	729	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	178	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.637035050399299	2		539	553	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0039868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	206	637	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.829	0.771	0.889	0.829	0.771	0.889	CLONAL	1	TRUE	1	0.637035050399299	2		638	780	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022913	27022938	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGCCGCCGCCAGCAGCCTGGGCAA	CCCGCCGCCGCCAGCAGCCTGGGCAA	-	rs797045262	NA	P-0039868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	27	69	0	ENST00000324856.7:c.31_56del	p.Ser11AlafsTer91	p.S11Afs*91	ENST00000324856	NM_006015.4	7	CCCGCCGCCGCCAGCAGCCTGGGCAAc/c	1/20	0.635085885247955	2	FACETS	0.831	0.701	0.959	0.831	0.701	0.959	CLONAL	2	TRUE	0	0.637035050399299	2		69	51	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624279	89624280	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	416	554	0	ENST00000371953.3:c.55dup	p.Asp19GlyfsTer25	p.D19Gfs*25	ENST00000371953	NM_000314.4	18	gag/gaGg	1/9	0.635085885247955	2	FACETS	0.979	0.944	1	0.979	0.944	1	CLONAL	2	TRUE	0	0.637035050399299	2		554	667	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699372	47699372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	124	484	1	ENST00000347630.2:c.136G>A	p.Glu46Lys	p.E46K	ENST00000347630	NM_001007230.1	46	Gag/Aag	4/11	0.637035050399299	1	FACETS	0.881	0.81	0.954	0.881	0.81	0.954	CLONAL	1	TRUE	0	0.637035050399299	1		485	301	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602870	10602870	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	470	1243	0	ENST00000171111.5:c.708C>G	p.Asp236Glu	p.D236E	ENST00000171111	NM_203500.1	236	gaC/gaG	3/6	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.637035050399299	2		1243	1447	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591142	67591142	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	117	372	0	ENST00000274335.5:c.1735C>T	p.Gln579Ter	p.Q579*	ENST00000274335		579	Caa/Taa	12/15	1	2	FACETS	0.87	0.791	0.953	0.87	0.791	0.953	CLONAL	1	TRUE	1	0.637035050399299	2		372	422	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128018812	128018813	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	177	544	0	ENST00000285398.2:c.2055dup	p.Ser686Ter	p.S686*	ENST00000285398	NM_000122.1	685	-/T	13/15	1	2	FACETS	0.926	0.858	0.996	0.926	0.858	0.996	CLONAL	1	TRUE	1	0.637035050399299	2		544	600	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719260	190719260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	105	360	0	ENST00000441310.2:c.1262G>A	p.Cys421Tyr	p.C421Y	ENST00000441310	NM_000534.4	421	tGt/tAt	9/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.637035050399299	2		360	303	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361164	66361164	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0039868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	128	413	0	ENST00000273854.3:c.1008T>A	p.Cys336Ter	p.C336*	ENST00000273854	NM_004439.5	336	tgT/tgA	4/18	1	2	FACETS	0.837	0.764	0.914	0.837	0.764	0.914	CLONAL	1	TRUE	1	0.637035050399299	2		413	480	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593292	67593298	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTTTG	GGCTTTG	-	novel	NA	P-0039868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	131	355	0	ENST00000274335.5:c.2038_2044del	p.Gly680ProfsTer10	p.G680Pfs*10	ENST00000274335		680	GGCTTTGcc/cc	15/15	1	2	FACETS	0.864	0.789	0.942	0.864	0.789	0.942	CLONAL	1	TRUE	1	0.637035050399299	2		355	476	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469780	157469780	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	296	903	0	ENST00000346085.5:c.2574del	p.Tyr859IlefsTer55	p.Y859Ifs*55	ENST00000346085	NM_020732.3	858	gcG/gc	9/20	1	2	FACETS	0.916	0.863	0.969	0.916	0.863	0.969	CLONAL	1	TRUE	1	0.637035050399299	2		903	1015	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555526101	NA	P-0039930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	145	806	0	ENST00000269305.4:c.497C>G	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tGa	5/11	0.446304365433226	2	FACETS	0.949	0.868	1	0.474	0.434	0.517	CLONAL	1	TRUE	0	0.446304365433226	2		806	685	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118941	115118941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	125	276	1	ENST00000257566.3:c.400C>T	p.Pro134Ser	p.P134S	ENST00000257566	NM_016569.3	134	Cct/Tct	2/8	0.346790775227154	3	FACETS	0.928	0.859	0.997	0.928	0.859	0.997	CLONAL	3	TRUE	0	0.446304365433226	3		277	246	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692847	89692847	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123321	NA	P-0039930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	68	192	2	ENST00000371953.3:c.331T>C	p.Trp111Arg	p.W111R	ENST00000371953	NM_000314.4	111	Tgg/Cgg	5/9	0.367558349460503	3	FACETS	1	0.962	1	0.791	0.707	0.877	CLONAL	2	TRUE	0	0.446304365433226	3		194	157	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944188	71944188	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	120	682	0	ENST00000298229.2:c.2021A>C	p.His674Pro	p.H674P	ENST00000298229	NM_001567.3	674	cAc/cCc	17/28	0.446304365433226	2	FACETS	1	0.932	1	0.516	0.468	0.566	CLONAL	1	TRUE	0	0.446304365433226	2		682	521	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945399	71945400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1370512716	NA	P-0039930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	95	863	0	ENST00000298229.2:c.2289dup	p.Lys764GlnfsTer19	p.K764Qfs*19	ENST00000298229	NM_001567.3	763	acc/aCcc	20/28	0.446304365433226	2	FACETS	0.637	0.568	0.711	0.319	0.284	0.356	SUBCLONAL	1	TRUE	0	0.446304365433226	2		863	668	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220640	1220640	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690940	NA	P-0039942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	178	918	0	ENST00000326873.7:c.658C>T	p.Gln220Ter	p.Q220*	ENST00000326873	NM_000455.4	220	Cag/Tag	5/10	0.326710820512778	1	FACETS	0.712	0.654	0.772	0.712	0.654	0.772	SUBCLONAL	1	TRUE	0	0.326710820512778	1		918	1281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579316	7579317	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	136	707	0	ENST00000269305.4:c.370dup	p.Cys124LeufsTer25	p.C124Lfs*25	ENST00000269305	NM_001126112.2	124	tgc/tTgc	4/11	0.326710820512778	1	FACETS	0.805	0.732	0.882	0.805	0.732	0.882	CLONAL	1	TRUE	0	0.326710820512778	1		707	865	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26974675	26974676	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0039942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	116	581	0	ENST00000381527.3:c.1019_1020del	p.Leu340ProfsTer25	p.L340Pfs*25	ENST00000381527	NM_001260.1	340	cTT/c	10/13	0.326710820512778	1	FACETS	0.765	0.689	0.844	0.765	0.689	0.844	SUBCLONAL	1	TRUE	0	0.326710820512778	1		581	777	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857527	68857530	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TAAG	TAAG	-	rs1415253676	NA	P-0039942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	172	471	0	ENST00000261769.5:c.2164+3_2164+6del		p.X722_splice	ENST00000261769	NM_004360.3	722		13/16	0.273340787784379	2	FACETS	1	0.988	1	0.711	0.656	0.769	CLONAL	1	TRUE	0	0.326710820512778	2		471	740	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0039962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	318	585	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.341007697122163	3	FACETS	1	0.965	1	0.682	0.646	0.718	CLONAL	2	TRUE	0	0.443162531079311	3		585	857	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70442723	70442723	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	39	339	0	ENST00000373644.4:c.5045G>T	p.Ser1682Ile	p.S1682I	ENST00000373644	NM_030625.2	1682	aGc/aTc	10/12	0.16521505114439	3	FACETS	0.56	0.465	0.666	0.187	0.155	0.222	INDETERMINATE	1	TRUE	0	0.443162531079311	3		339	384	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27190655	27190655	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334811	NA	P-0039962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	64	378	1	ENST00000380036.4:c.1456G>A	p.Val486Ile	p.V486I	ENST00000380036	NM_000459.3	486	Gtt/Att	10/23	0.318288534097363	2	FACETS	0.515	0.446	0.59	0.257	0.223	0.295	SUBCLONAL	1	TRUE	0	0.443162531079311	2		379	561	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TC	novel	NA	P-0039962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	286	313	0	ENST00000311936.3:c.180_181inv	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggGAaa	3/5	0.367524181026739	4	FACETS	0.919	0.87	0.968			1	CLONAL	3	TRUE	NA	0.443162531079311	4		313	676	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125499290	125499290	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	148	239	0	ENST00000428830.2:c.359A>T	p.Tyr120Phe	p.Y120F	ENST00000428830	NM_001114121.2	120	tAt/tTt	5/14	0.422378970774727	4	FACETS	1	0.986	1	0.701	0.641	0.762	CLONAL	1	TRUE	2	0.443162531079311	4		239	688	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0039964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	109	308	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.345842123998241	2		308	478	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46277762	46277762	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	68	317	0	ENST00000371998.3:c.3560G>C	p.Ser1187Thr	p.S1187T	ENST00000371998		1187	aGc/aCc	19/23	1	2	FACETS	0.973	0.851	1	0.973	0.851	1	CLONAL	1	TRUE	1	0.345842123998241	2		317	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	141	690	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.79	0.72	0.864	1	0.988	1	SUBCLONAL	2	TRUE	1	0.22	2		692	811	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	56	443	9	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.786	0.677	0.903	1	0.97	1	CLONAL	2	TRUE	1	0.22	2		452	324	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	28	607	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.695	0.556	0.854	0.695	0.556	0.854	SUBCLONAL	1	TRUE	1	0.22	2		607	366	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	26	399	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.22	2		399	165	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	168	644	1	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	1	2	FACETS	0.989	0.911	1	1	0.992	1	CLONAL	2	TRUE	1	0.22	2		645	772	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129329	152129329	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	58	755	1	ENST00000206249.3:c.287del	p.Gly96ValfsTer13	p.G96Vfs*13	ENST00000206249	NM_000125.3	94	ctG/ct	1/8	1	2	FACETS	0.96	0.826	1	0.96	0.826	1	CLONAL	1	TRUE	1	0.22	2		756	549	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	99	516	3	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.815	0.73	0.906	1	0.984	1	CLONAL	2	TRUE	1	0.22	2		519	552	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912580	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	56	302	0	ENST00000342988.3:c.1157G>A	p.Gly386Asp	p.G386D	ENST00000342988	NM_005359.5	386	gGt/gAt	10/12	0.171057808818103	1	FACETS	0.921	0.797	1	1	0.976	1	CLONAL	2	TRUE	0	0.22	1		302	246	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	111	745	7	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.86	0.775	0.949	1	0.986	1	CLONAL	2	TRUE	1	0.22	2		752	587	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161324	55161324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514550	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	43	355	0	ENST00000257290.5:c.3155C>T	p.Thr1052Met	p.T1052M	ENST00000257290	NM_006206.4	1052	aCg/aTg	23/23	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.22	2		355	329	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	64	587	6	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.895	0.781	1	1	0.978	1	CLONAL	2	TRUE	1	0.22	2		593	325	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981861	101981863	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	164	721	1	ENST00000282441.5:c.286_288del	p.Phe96del	p.F96del	ENST00000282441	NM_001130145.2	94	tcCTTc/tcc	1/9	1	2	FACETS	0.84	0.772	0.912	1	0.99	1	CLONAL	2	TRUE	1	0.22	2		722	887	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729601	41729601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	92	465	0	ENST00000242208.4:c.928C>T	p.Arg310Trp	p.R310W	ENST00000242208	NM_002192.2	310	Cgg/Tgg	3/3	1	2	FACETS	0.825	0.735	0.92	1	0.983	1	CLONAL	2	TRUE	1	0.22	2		465	507	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674234	86674234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	41	244	0	ENST00000274376.6:c.2366G>A	p.Arg789Gln	p.R789Q	ENST00000274376	NM_002890.2	789	cGa/cAa	18/25	1	2	FACETS	0.923	0.777	1	1	0.968	1	CLONAL	2	TRUE	1	0.22	2		244	202	SUCCESS
APC	324	MSKCC	GRCh37	5	112170660	112170660	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554083100	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	31	285	0	ENST00000257430.4:c.1759del	p.Ser587AlafsTer3	p.S587Afs*3	ENST00000257430	NM_000038.5	586	Aaa/aa	15/16	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.22	2		285	223	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054540	42054541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	64	308	1	ENST00000219905.7:c.7731dup	p.Asp2578ArgfsTer45	p.D2578Rfs*45	ENST00000219905	NM_001164273.1	2575	aga/agAa	22/24	1	2	FACETS	0.996	0.87	1	1	0.98	1	CLONAL	2	TRUE	1	0.22	2		309	292	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097781	8097781	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763176056	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	163	702	0	ENST00000346208.3:c.163G>A	p.Gly55Ser	p.G55S	ENST00000346208		55	Ggt/Agt	2/6	1	2	FACETS	0.949	0.872	1	1	0.992	1	CLONAL	2	TRUE	1	0.22	2		702	781	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937603	76937603	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	30	243	0	ENST00000373344.5:c.3145del	p.Ile1049Ter	p.I1049*	ENST00000373344	NM_000489.3	1049	Ata/ta	9/35	0.171057808818103	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.22	1		243	197	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	89	368	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.814	0.724	0.909	1	0.982	1	CLONAL	2	TRUE	1	0.22	2		371	497	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711903	89711903	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs864622341	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	62	392	0	ENST00000371953.3:c.521A>G	p.Tyr174Cys	p.Y174C	ENST00000371953	NM_000314.4	174	tAt/tGt	6/9	1	2	FACETS	0.798	0.693	0.911	1	0.974	1	CLONAL	2	TRUE	1	0.22	2		392	353	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391361	139391361	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	167	720	2	ENST00000277541.6:c.6830C>A	p.Pro2277His	p.P2277H	ENST00000277541	NM_017617.3	2277	cCt/cAt	34/34	1	2	FACETS	0.904	0.831	0.979	1	0.991	1	CLONAL	2	TRUE	1	0.22	2		722	840	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182677	38182678	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	118	401	0	ENST00000396334.3:c.834dup	p.Ser279GlnfsTer153	p.S279Qfs*153	ENST00000396334	NM_002468.4	277	ttc/ttCc	5/5	1	2	FACETS	1	0.966	1	1	0.99	1	CLONAL	2	TRUE	1	0.22	2		401	471	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166763	32166763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761314959	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	152	739	0	ENST00000375023.3:c.4475G>A	p.Arg1492Gln	p.R1492Q	ENST00000375023	NM_004557.3	1492	cGg/cAg	24/30	1	2	FACETS	0.775	0.708	0.844	1	0.988	1	SUBCLONAL	2	TRUE	1	0.22	2		739	892	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434325	49434325	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	198	805	0	ENST00000301067.7:c.7228C>T	p.Arg2410Ter	p.R2410*	ENST00000301067	NM_003482.3	2410	Cga/Tga	31/54	1	2	FACETS	0.968	0.897	1	1	0.993	1	CLONAL	2	TRUE	1	0.22	2		805	930	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268792	98268793	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	109	467	0	ENST00000331920.6:c.290dup	p.Asn97LysfsTer43	p.N97Kfs*43	ENST00000331920	NM_000264.3	97	aac/aaAc	2/24	1	2	FACETS	0.824	0.742	0.911	1	0.985	1	CLONAL	2	TRUE	1	0.22	2		467	601	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665377	176665377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	80	340	0	ENST00000439151.2:c.4061G>A	p.Gly1354Asp	p.G1354D	ENST00000439151	NM_022455.4	1354	gGc/gAc	7/23	1	2	FACETS	0.852	0.753	0.956	1	0.981	1	CLONAL	2	TRUE	1	0.22	2		340	427	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809860	36809860	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	105	524	2	ENST00000373129.3:c.745C>T	p.Pro249Ser	p.P249S	ENST00000373129	NM_032017.1	249	Ccg/Tcg	9/12	1	2	FACETS	0.754	0.677	0.836	1	0.982	1	SUBCLONAL	2	TRUE	1	0.22	2		526	633	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31493321	31493322	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1330233722	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	48	301	0	ENST00000344624.3:c.1834dup	p.Leu612ProfsTer8	p.L612Pfs*8	ENST00000344624		612	ctg/cCtg	10/33	1	2	FACETS	0.842	0.718	0.977	1	0.969	1	CLONAL	2	TRUE	1	0.22	2		301	259	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533536	533536	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369106578	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	158	698	2	ENST00000451590.1:c.367C>T	p.Arg123Cys	p.R123C	ENST00000451590	NM_001130442.1	123	Cgc/Tgc	4/5	1	2	FACETS	0.884	0.811	0.961	1	0.991	1	CLONAL	2	TRUE	1	0.22	2		700	812	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946996	71946996	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs754591389	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	199	818	1	ENST00000298229.2:c.2845C>T	p.Arg949Ter	p.R949*	ENST00000298229	NM_001567.3	949	Cga/Tga	25/28	1	2	FACETS	0.966	0.896	1	1	0.993	1	CLONAL	2	TRUE	1	0.22	2		819	936	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394891	394891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	52	459	0	ENST00000380956.4:c.287G>A	p.Arg96His	p.R96H	ENST00000380956	NM_001195286.1	96	cGc/cAc	3/9	0.3	2	FACETS	0.784	0.667	0.913			1	CLONAL	1	TRUE	NA	0.22	2		459	603	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023993	27023993	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs932715321	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	17	97	0	ENST00000324856.7:c.1099A>G	p.Ser367Gly	p.S367G	ENST00000324856	NM_006015.4	367	Agc/Ggc	1/20	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.22	2		97	111	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138881	64138881	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	104	563	0	ENST00000334205.4:c.2248A>G	p.Asn750Asp	p.N750D	ENST00000334205	NM_003942.2	750	Aac/Gac	17/17	1	2	FACETS	0.811	0.728	0.898	1	0.984	1	CLONAL	2	TRUE	1	0.22	2		563	583	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94209522	94209523	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	40	292	0	ENST00000323929.3:c.591dup	p.Val198SerfsTer10	p.V198Sfs*10	ENST00000323929	NM_005591.3	197	-/A	7/20	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.22	2		292	272	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999273	100999273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767280663	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	126	756	1	ENST00000325455.5:c.529G>A	p.Gly177Arg	p.G177R	ENST00000325455	NM_001202474.3	177	Ggg/Agg	1/8	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.22	2		757	797	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201943	102201943	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	29	218	0	ENST00000263464.3:c.1295G>T	p.Arg432Ile	p.R432I	ENST00000263464	NM_001165.4	432	aGa/aTa	6/9	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.22	2		218	181	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427572	427572	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	63	389	0	ENST00000399788.2:c.2597A>G	p.Asp866Gly	p.D866G	ENST00000399788	NM_001042603.1	866	gAt/gGt	19/28	0.3	2	FACETS	0.832	0.724	0.948			1	CLONAL	2	TRUE	NA	0.22	2		389	344	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491370	18491372	+	inframe_deletion	In_Frame_Del	DEL	ATA	ATA	-	rs1565612941	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	54	170	0	ENST00000266497.5:c.1286_1288del	p.Asn429del	p.N429del	ENST00000266497		428	tATAat/tat	8/31	1	2	FACETS	1	0.943	1	1	0.98	1	CLONAL	2	TRUE	1	0.22	2		170	209	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125084	46125084	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	38	176	0	ENST00000334344.6:c.271C>T	p.Gln91Ter	p.Q91*	ENST00000334344	NM_152641.2	91	Cag/Tag	3/21	1	2	FACETS	1	0.864	1	1	0.969	1	CLONAL	2	TRUE	1	0.22	2		176	167	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554314	81554314	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	67	346	0	ENST00000298171.2:c.334A>T	p.Arg112Trp	p.R112W	ENST00000298171	NM_000369.2	112	Agg/Tgg	4/10	1	2	FACETS	1	0.912	1	1	0.982	1	CLONAL	2	TRUE	1	0.22	2		346	290	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992904	72992904	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778464341	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	158	656	0	ENST00000268489.5:c.1141G>T	p.Ala381Ser	p.A381S	ENST00000268489	NM_006885.3	381	Gcg/Tcg	2/10	1	2	FACETS	0.945	0.867	1	1	0.991	1	CLONAL	2	TRUE	1	0.22	2		656	760	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884014	37884014	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	168	678	0	ENST00000269571.5:c.3485C>T	p.Pro1162Leu	p.P1162L	ENST00000269571		1162	cCt/cTt	27/27	1	2	FACETS	0.967	0.89	1	1	0.992	1	CLONAL	2	TRUE	1	0.22	2		678	790	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533066	63533066	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	112	572	0	ENST00000307078.5:c.1828del	p.Arg610GlyfsTer79	p.R610Gfs*79	ENST00000307078	NM_004655.3	610	Cgg/gg	7/11	1	2	FACETS	0.859	0.774	0.947	1	0.987	1	CLONAL	2	TRUE	1	0.22	2		572	593	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218786	36218786	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	136	641	0	ENST00000222270.7:c.4397G>T	p.Ser1466Ile	p.S1466I	ENST00000222270	NM_014727.1	1466	aGc/aTc	18/37	1	2	FACETS	0.927	0.845	1	1	0.99	1	CLONAL	2	TRUE	1	0.22	2		641	667	SUCCESS
REL	5966	MSKCC	GRCh37	2	61121668	61121668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373752427	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	36	299	0	ENST00000295025.8:c.290G>A	p.Arg97His	p.R97H	ENST00000295025	NM_002908.2	97	cGc/cAc	3/11	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.22	2		299	234	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266493	41266493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	73	340	0	ENST00000349496.5:c.290C>A	p.Ala97Asp	p.A97D	ENST00000349496	NM_001904.3	97	gCt/gAt	4/15	1	2	FACETS	1	0.917	1	1	0.984	1	CLONAL	2	TRUE	1	0.22	2		340	316	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125290	47125290	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	32	356	1	ENST00000409792.3:c.5980del	p.Arg1994GlyfsTer12	p.R1994Gfs*12	ENST00000409792	NM_014159.6	1994	Agg/gg	12/21	1	2	FACETS	0.918	0.747	1	0.918	0.747	1	CLONAL	1	TRUE	1	0.22	2		357	317	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015104	71015104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757539300	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	69	313	0	ENST00000318789.4:c.1826C>T	p.Ala609Val	p.A609V	ENST00000318789	NM_032682.5	609	gCa/gTa	20/21	1	2	FACETS	0.879	0.77	0.994	1	0.979	1	CLONAL	2	TRUE	1	0.22	2		313	357	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149440513	149440515	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1554101963	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	113	608	0	ENST00000286301.3:c.1879_1881del	p.Lys627del	p.K627del	ENST00000286301	NM_005211.3	627	AAG/-	14/22	1	2	FACETS	0.796	0.718	0.879	1	0.985	1	SUBCLONAL	2	TRUE	1	0.22	2		608	645	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675522	30675523	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	122	666	0	ENST00000376406.3:c.2833_2834del	p.Asp945TyrfsTer70	p.D945Yfs*70	ENST00000376406	NM_014641.2	945	GAt/t	8/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.22	2		666	747	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111995801	111995802	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	26	404	0	ENST00000368678.4:c.1296dup	p.Glu433ArgfsTer13	p.E433Rfs*13	ENST00000368678		432	-/C	12/13	1	2	FACETS	0.457	0.361	0.568	0.457	0.361	0.568	SUBCLONAL	1	TRUE	1	0.22	2		404	517	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419998	152419998	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	83	573	0	ENST00000206249.3:c.1685A>C	p.Glu562Ala	p.E562A	ENST00000206249	NM_000125.3	562	gAg/gCg	8/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.22	2		573	536	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394441	162394442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	44	286	0	ENST00000366898.1:c.626dup	p.Phe210LeufsTer2	p.F210Lfs*2	ENST00000366898	NM_004562.2	209	ttc/ttTc	6/12	1	2	FACETS	0.772	0.652	0.903	1	0.962	1	CLONAL	2	TRUE	1	0.22	2		286	259	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772594	135772594	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	67	464	0	ENST00000298552.3:c.2952A>C	p.Glu984Asp	p.E984D	ENST00000298552	NM_001162426.1	984	gaA/gaC	22/23	1	2	FACETS	0.819	0.715	0.929	1	0.977	1	CLONAL	2	TRUE	1	0.22	2		464	372	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339930	70339930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866469400	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	51	463	1	ENST00000374080.3:c.463C>T	p.Arg155Trp	p.R155W	ENST00000374080		155	Cgg/Tgg	4/45	0.171057808818103	1	FACETS	0.921	0.784	1	0.921	0.784	1	CLONAL	1	TRUE	0	0.22	1		464	448	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342401	70342401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	71	542	1	ENST00000374080.3:c.1292G>A	p.Arg431Gln	p.R431Q	ENST00000374080		431	cGg/cAg	9/45	0.171057808818103	1	FACETS	0.899	0.785	1	0.899	0.785	1	CLONAL	1	TRUE	0	0.22	1		543	639	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0040040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	149	308	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.352320539829683	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.352320539829683	3		308	443	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437606	56437606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886926322	NA	P-0040040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	86	521	1	ENST00000407977.2:c.856C>T	p.Arg286Trp	p.R286W	ENST00000407977		286	Cgg/Tgg	8/10	0.347069650678337	4	FACETS	1	0.933	1	0.359	0.318	0.403	CLONAL	1	TRUE	1	0.352320539829683	4		522	613	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16247440	16247440	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	37	253	0	ENST00000375759.3:c.1711G>C	p.Glu571Gln	p.E571Q	ENST00000375759	NM_015001.2	571	Gag/Cag	9/15	0.287253456296982	1	FACETS	0.684	0.567	0.813	0.684	0.567	0.813	SUBCLONAL	1	TRUE	0	0.352320539829683	1		253	253	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148931	119148931	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	11	384	0	ENST00000264033.4:c.1151G>C	p.Cys384Ser	p.C384S	ENST00000264033	NM_005188.3	384	tGt/tCt	8/16	0.352320539829683	1	FACETS	0.156	0.107	0.218	0.156	0.107	0.218	SUBCLONAL	1	TRUE	0	0.352320539829683	1		384	329	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134378	41134378	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	64	502	0	ENST00000379561.5:c.1250C>A	p.Pro417His	p.P417H	ENST00000379561	NM_002015.3	417	cCc/cAc	2/3	1	2	FACETS	0.737	0.639	0.843	0.737	0.639	0.843	SUBCLONAL	1	TRUE	1	0.352320539829683	2		502	493	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43699623	43699623	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	44	520	0	ENST00000382044.4:c.5892C>G	p.Phe1964Leu	p.F1964L	ENST00000382044	NM_001141980.1	1964	ttC/ttG	28/28	1	2	FACETS	0.51	0.427	0.601	0.51	0.427	0.601	SUBCLONAL	1	TRUE	1	0.352320539829683	2		520	490	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46602843	46602843	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	65	686	0	ENST00000263734.3:c.901C>T	p.Gln301Ter	p.Q301*	ENST00000263734	NM_001430.4	301	Cag/Tag	8/16	1	2	FACETS	0.582	0.504	0.666	0.582	0.504	0.666	SUBCLONAL	1	TRUE	1	0.352320539829683	2		686	634	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872563	136872563	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	26	317	0	ENST00000241393.3:c.935C>G	p.Ser312Cys	p.S312C	ENST00000241393	NM_003467.2	312	tCt/tGt	2/2	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.352320539829683	NA		317	328	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660493	227660493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	59	581	0	ENST00000305123.5:c.2962G>A	p.Asp988Asn	p.D988N	ENST00000305123	NM_005544.2	988	Gac/Aac	1/2	1	2	FACETS	0.594	0.511	0.684	0.594	0.511	0.684	SUBCLONAL	1	TRUE	1	0.352320539829683	2		581	564	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702579	52702579	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	14	452	0	ENST00000394830.3:c.319G>T	p.Asp107Tyr	p.D107Y	ENST00000394830	NM_018313.4	107	Gat/Tat	4/30	0.352320539829683	1	FACETS	0.244	0.176	0.327	0.244	0.176	0.327	SUBCLONAL	1	TRUE	0	0.352320539829683	1		452	268	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	50	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.824	0.7	0.961	0.824	0.7	0.961	CLONAL	1	TRUE	1	0.248580517769373	2		311	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0040064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	135	704	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.248580517769373	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.248580517769373	1		704	786	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593532	48593532	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555686620	NA	P-0040064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	37	180	0	ENST00000342988.3:c.1283A>C	p.Lys428Thr	p.K428T	ENST00000342988	NM_005359.5	428	aAg/aCg	10/12	0.248580517769373	1	FACETS	0.951	0.788	1	0.951	0.788	1	CLONAL	1	TRUE	0	0.248580517769373	1		180	274	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0040064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	72	380	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.248580517769373	2		380	529	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459759	149459759	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374166176	NA	P-0040064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	120	618	1	ENST00000286301.3:c.448C>T	p.Arg150Cys	p.R150C	ENST00000286301	NM_005211.3	150	Cgc/Tgc	4/22	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.248580517769373	2		619	891	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927989	49927989	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374259168	NA	P-0040064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	122	554	0	ENST00000296474.3:c.3739G>A	p.Ala1247Thr	p.A1247T	ENST00000296474	NM_002447.2	1247	Gct/Act	18/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.248580517769373	2		554	862	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554476	63554476	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1186148018	NA	P-0040064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	94	476	0	ENST00000307078.5:c.263A>G	p.Asp88Gly	p.D88G	ENST00000307078	NM_004655.3	88	gAt/gGt	2/11	1	2	FACETS	0.978	0.87	1	0.978	0.87	1	CLONAL	1	TRUE	1	0.248580517769373	2		476	773	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622174	1622174	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756170287	NA	P-0040064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	113	604	0	ENST00000344749.5:c.701C>T	p.Ala234Val	p.A234V	ENST00000344749	NM_001136139.2	234	gCg/gTg	10/19	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.248580517769373	2		604	870	SUCCESS
APC	324	MSKCC	GRCh37	5	112175974	112175974	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	40	180	0	ENST00000257430.4:c.4684del	p.Asp1562ThrfsTer3	p.D1562Tfs*3	ENST00000257430	NM_000038.5	1561	aaG/aa	16/16	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.248580517769373	2		180	293	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371718	55371718	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	100	504	0	ENST00000297316.4:c.408del	p.Lys136AsnfsTer10	p.K136Nfs*10	ENST00000297316	NM_022454.3	136	aaG/aa	2/2	0.240279484470333	2	FACETS	1	0.939	1	0.537	0.48	0.598	CLONAL	1	TRUE	0	0.248580517769373	2		504	749	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566342	141566342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	67	319	0	ENST00000220592.5:c.1070C>T	p.Thr357Met	p.T357M	ENST00000220592	NM_012154.3	357	aCg/aTg	9/19	0.240279484470333	2	FACETS	1	0.888	1	0.511	0.445	0.583	CLONAL	1	TRUE	0	0.248580517769373	2		319	527	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412987	63412987	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	117	716	0	ENST00000330258.3:c.180del	p.Phe60LeufsTer40	p.F60Lfs*40	ENST00000330258	NM_152424.3	60	ttT/tt	2/2	1	2	FACETS	0.851	0.766	0.942	0.851	0.766	0.942	CLONAL	1	TRUE	1	0.248580517769373	2		716	1106	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0040087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	139	554	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.887	0.81	0.968	0.887	0.81	0.968	CLONAL	1	TRUE	1	0.483726129119018	2		554	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578266	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	456	567	0	ENST00000269305.4:c.583dup	p.Ile195AsnfsTer14	p.I195Nfs*14	ENST00000269305	NM_001126112.2	195	atc/aAtc	6/11	0.470025976900697	2	FACETS	0.895	0.858	0.933	0.895	0.858	0.933	CLONAL	2	TRUE	0	0.483726129119018	2		567	1053	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954321	48954321	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	91	223	0	ENST00000267163.4:c.1446del	p.His483IlefsTer12	p.H483Ifs*12	ENST00000267163	NM_000321.2	481	aTt/at	16/27	0.483726129119018	3	FACETS	0.826	0.735	0.922	0.413	0.367	0.461	CLONAL	1	TRUE	1	0.483726129119018	3		223	566	SUCCESS
APC	324	MSKCC	GRCh37	5	112176018	112176018	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	103	223	0	ENST00000257430.4:c.4728del	p.Glu1577AsnfsTer73	p.E1577Nfs*73	ENST00000257430	NM_000038.5	1576	gAa/ga	16/16	0.410056999247628	1	FACETS	0.904	0.817	0.995	0.904	0.817	0.995	CLONAL	1	TRUE	0	0.483726129119018	1		223	357	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549031	21549031	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	73	208	0	ENST00000382592.4:c.3245G>T	p.Gly1082Val	p.G1082V	ENST00000382592	NM_014572.2	1082	gGc/gTc	8/8	0.483726129119018	3	FACETS	0.742	0.65	0.841	0.371	0.325	0.421	SUBCLONAL	1	TRUE	1	0.483726129119018	3		208	505	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292418	15292418	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1258	264	719	0	ENST00000263388.2:c.2761T>G	p.Cys921Gly	p.C921G	ENST00000263388	NM_000435.2	921	Tgc/Ggc	17/33	0.483726129119018	3	FACETS	0.891	0.832	0.951	0.445	0.416	0.476	CLONAL	1	TRUE	1	0.483726129119018	3		719	1522	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171922	32171922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	291	352	0	ENST00000375023.3:c.3110G>A	p.Gly1037Glu	p.G1037E	ENST00000375023	NM_004557.3	1037	gGa/gAa	19/30	0.483726129119018	3	FACETS	0.949	0.897	1	0.949	0.897	1	CLONAL	2	TRUE	1	0.483726129119018	3		352	787	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741892	17741892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	11	77	0	ENST00000250003.3:c.563G>A	p.Arg188His	p.R188H	ENST00000250003	NM_002478.4	188	cGc/cAc	1/3	0.0983641182634012	0	FACETS	1	0.781	1			1	INDETERMINATE	1	TRUE	0	0.18	0		77	87	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421029	49421029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs189256695	NA	P-0040106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	47	439	0	ENST00000301067.7:c.14720C>T	p.Ser4907Leu	p.S4907L	ENST00000301067	NM_003482.3	4907	tCg/tTg	48/54	0.0983641182634012	3	FACETS	1	0.928	1	0.59	0.498	0.692	INDETERMINATE	1	TRUE	1	0.18	3		439	482	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386332	31386339	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGCCCT	GGAGCCCT	-	novel	NA	P-0040106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	53	562	0	ENST00000328111.2:c.1562_1569del	p.Pro521LeufsTer30	p.P521Lfs*30	ENST00000328111	NM_006892.3	519	caGGAGCCCTgg/cagg	15/23	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.18	2		562	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0040110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	147	766	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.653442774328535	2	FACETS	0.937	0.88	0.994	0.937	0.88	0.994	CLONAL	2	TRUE	0	0.653442774328535	2		767	240	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0040110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	145	385	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	0.573987575110029	4	FACETS	0.934	0.861	1	0.934	0.861	1	CLONAL	2	TRUE	2	0.653442774328535	4		385	393	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	103	756	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.653442774328535	3	FACETS	1	0.96	1	0.562	0.507	0.619	CLONAL	1	TRUE	1	0.653442774328535	3		756	372	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134335	2134335	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	91	716	5	ENST00000219476.3:c.4112C>T	p.Ser1371Phe	p.S1371F	ENST00000219476	NM_000548.3	1371	tCt/tTt	34/42	0.17067598965099	4	FACETS	1	0.967	1	0.404	0.361	0.449	INDETERMINATE	1	TRUE	1	0.653442774328535	4		721	380	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106251	27106251	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	144	517	8	ENST00000324856.7:c.5863del	p.Leu1955Ter	p.L1955*	ENST00000324856	NM_006015.4	1954	atC/at	20/20	0.63777152791054	4	FACETS	0.987	0.912	1	0.987	0.912	1	CLONAL	2	TRUE	2	0.653442774328535	4		525	369	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256095	123256095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	79	461	2	ENST00000358487.5:c.1814C>T	p.Ser605Leu	p.S605L	ENST00000358487	NM_000141.4	605	tCa/tTa	13/18	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.653442774328535	2		463	217	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672315	86672315	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	150	295	1	ENST00000274376.6:c.2117T>A	p.Leu706Gln	p.L706Q	ENST00000274376	NM_002890.2	706	cTg/cAg	16/25	0.42421419133621	6	FACETS	0.905	0.837	0.975	0.905	0.837	0.975	CLONAL	3	TRUE	3	0.653442774328535	6		296	390	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350032	70350032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	33	438	5	ENST00000374080.3:c.4015C>T	p.Pro1339Ser	p.P1339S	ENST00000374080		1339	Ccc/Tcc	28/45	0.327777590213641	2	FACETS	0.537	0.442	0.642	0.269	0.221	0.321	INDETERMINATE	1	TRUE	0	0.653442774328535	2		443	188	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56401549	56401549	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	183	327	0	ENST00000348428.3:c.1411G>A	p.Asp471Asn	p.D471N	ENST00000348428	NM_006785.3	471	Gat/Aat	12/17	NA	2	FACETS	1	0.938	1			1	INDETERMINATE	1	TRUE	NA	0.805379136550094	2		327	452	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	51	478	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.108522394732312	4	FACETS	0.984	0.853	1	1	0.98	1	CLONAL	5	FALSE	2	0.148807049337802	4		478	160	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022913	27022938	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGCCGCCGCCAGCAGCCTGGGCAA	CCCGCCGCCGCCAGCAGCCTGGGCAA	-	rs797045262	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	16	69	0	ENST00000324856.7:c.31_56del	p.Ser11AlafsTer91	p.S11Afs*91	ENST00000324856	NM_006015.4	7	CCCGCCGCCGCCAGCAGCCTGGGCAAc/c	1/20	1	2	FACETS	1	0.82	1	1	0.931	1	CLONAL	2	FALSE	1	0.148807049337802	2		69	96	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	78	368	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.966	0.864	1	1	0.989	1	CLONAL	5	FALSE	1	0.148807049337802	2		371	217	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	116	428	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	0.108522394732312	4	FACETS	1	0.917	1	1	0.989	1	CLONAL	4	FALSE	2	0.148807049337802	4		428	443	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374292	138374292	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	90	448	0	ENST00000289153.2:c.3152A>G	p.Glu1051Gly	p.E1051G	ENST00000289153	NM_006219.2	1051	gAa/gGa	22/22	1	2	FACETS	0.96	0.861	1	1	0.99	1	CLONAL	4	FALSE	1	0.148807049337802	2		448	315	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177584	56177584	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368201444	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	85	365	0	ENST00000399503.3:c.2557C>T	p.Arg853Cys	p.R853C	ENST00000399503	NM_005921.1	853	Cgt/Tgt	14/20	1	2	FACETS	1	0.95	1	1	0.989	1	CLONAL	3	FALSE	1	0.148807049337802	2		365	342	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	37	124	0	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.987	0.831	1	1	0.977	1	CLONAL	4	FALSE	1	0.148807049337802	2		124	126	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	317	1003	1	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	1	2	FACETS	1	0.946	1	1	0.997	1	CLONAL	4	FALSE	1	0.148807049337802	2		1004	1064	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	245	697	1	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	0.108522394732312	4	FACETS	0.916	0.858	0.975	1	0.995	1	CLONAL	5	FALSE	2	0.148807049337802	4		698	826	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	220	459	2	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	0.108522394732312	4	FACETS	0.992	0.927	1	1	0.995	1	CLONAL	5	FALSE	2	0.148807049337802	4		461	685	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	69	279	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	0.148807049337802	4	FACETS	0.907	0.801	1	1	0.984	1	CLONAL	5	FALSE	2	0.148807049337802	4		279	235	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512402	38512402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	158	506	2	ENST00000254066.5:c.1319del	p.Pro440ArgfsTer203	p.P440Rfs*203	ENST00000254066	NM_000964.3	438	gCc/gc	9/9	1	2	FACETS	0.976	0.9	1	1	0.994	1	CLONAL	4	FALSE	1	0.148807049337802	2		508	544	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957464	175957465	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	37	362	0	ENST00000367669.3:c.1931dup	p.Asn644LysfsTer17	p.N644Kfs*17	ENST00000367669	NM_022457.5	644	aac/aaAc	17/20	0.148807049337802	6	FACETS	0.948	0.787	1	0.569	0.472	0.674	CLONAL	3	FALSE	1	0.148807049337802	6		362	227	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655428	45655428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372772395	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	221	497	2	ENST00000407780.3:c.424G>A	p.Val142Ile	p.V142I	ENST00000407780	NM_001283052.1	142	Gtc/Atc	4/7	1	2	FACETS	0.916	0.854	0.979	1	0.996	1	CLONAL	4	FALSE	1	0.148807049337802	2		499	811	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448408	49448408	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs797045661	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	215	504	2	ENST00000301067.7:c.303del	p.Ser102AlafsTer28	p.S102Afs*28	ENST00000301067	NM_003482.3	101	ggG/gg	3/54	0.108522394732312	4	FACETS	0.974	0.909	1	1	0.995	1	CLONAL	5	FALSE	2	0.148807049337802	4		506	682	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225609	26225609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	33	393	0	ENST00000360408.1:c.227C>T	p.Ala76Val	p.A76V	ENST00000360408	NM_003532.2	76	gCt/gTt	1/1	0.148807049337802	4	FACETS	1	0.824	1	0.506	0.412	0.614	CLONAL	1	FALSE	2	0.148807049337802	4		393	503	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67462920	67462920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202094530	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	119	422	0	ENST00000327367.4:c.636G>A	p.Met212Ile	p.M212I	ENST00000327367	NM_005902.3	212	atG/atA	5/9	0.108574230323829	1	FACETS	1	0.951	1	1	0.992	1	CLONAL	3	FALSE	0	0.148807049337802	1		422	461	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753139	128753139	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	95	291	0	ENST00000377970.2:c.1300T>G	p.Leu434Val	p.L434V	ENST00000377970	NM_002467.4	434	Ttg/Gtg	3/3	1	2	FACETS	1	0.958	1	1	0.991	1	CLONAL	4	FALSE	1	0.148807049337802	2		291	286	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784098	120784098	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	257	579	0	ENST00000257552.2:c.887del	p.Pro296LeufsTer57	p.P296Lfs*57	ENST00000257552	NM_002442.3	296	cCt/ct	13/15	0.108522394732312	4	FACETS	1	0.971	1	1	0.995	1	CLONAL	4	FALSE	2	0.148807049337802	4		579	936	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436050	51436050	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	106	285	1	ENST00000262662.1:c.10C>T	p.Pro4Ser	p.P4S	ENST00000262662		4	Cct/Tct	3/4	1	2	FACETS	1	0.962	1	1	0.991	1	CLONAL	3	FALSE	1	0.148807049337802	2		286	419	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717697	89717698	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	51	377	0	ENST00000371953.3:c.723_724insCT	p.Glu242LeufsTer15	p.E242Lfs*15	ENST00000371953	NM_000314.4	241	ttt/ttTCt	7/9	0.108522394732312	4	FACETS	1	0.906	1	1	0.978	1	CLONAL	4	FALSE	2	0.148807049337802	4		377	185	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325025	123325025	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	152	460	0	ENST00000358487.5:c.303C>A	p.Asp101Glu	p.D101E	ENST00000358487	NM_000141.4	101	gaC/gaA	3/18	0.108522394732312	4	FACETS	1	0.971	1	1	0.992	1	CLONAL	4	FALSE	2	0.148807049337802	4		460	525	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742468	17742468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	203	521	1	ENST00000250003.3:c.650C>T	p.Pro217Leu	p.P217L	ENST00000250003	NM_002478.4	217	cCg/cTg	2/3	1	2	FACETS	1	0.963	1	1	0.995	1	CLONAL	4	FALSE	1	0.148807049337802	2		522	650	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742822	17742822	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1245243056	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	250	606	0	ENST00000250003.3:c.730G>A	p.Ala244Thr	p.A244T	ENST00000250003	NM_002478.4	244	Gcg/Acg	3/3	1	2	FACETS	1	0.979	1	1	0.996	1	CLONAL	4	FALSE	1	0.148807049337802	2		606	770	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1039247	1039247	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	143	435	0	ENST00000358495.3:c.250T>C	p.Trp84Arg	p.W84R	ENST00000358495	NM_134424.2	84	Tgg/Cgg	4/12	0.108522394732312	4	FACETS	1	0.942	1	1	0.993	1	CLONAL	5	FALSE	2	0.148807049337802	4		435	429	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378595	25378595	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	35	327	0	ENST00000311936.3:c.403A>G	p.Arg135Gly	p.R135G	ENST00000311936	NM_004985.3	135	Aga/Gga	4/5	0.108522394732312	4	FACETS	1	0.89	1	1	0.958	1	CLONAL	3	FALSE	2	0.148807049337802	4		327	164	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060844	38060845	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	206	583	0	ENST00000250448.2:c.1144dup	p.His382ProfsTer33	p.H382Pfs*33	ENST00000250448	NM_004496.3	382	cac/cCac	2/2	1	2	FACETS	1	0.98	1	1	0.995	1	CLONAL	3	FALSE	1	0.148807049337802	2		583	811	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872802	37872802	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	230	527	0	ENST00000269571.5:c.1681T>G	p.Leu561Val	p.L561V	ENST00000269571		561	Ttg/Gtg	14/27	1	2	FACETS	1	0.972	1	1	0.996	1	CLONAL	4	FALSE	1	0.148807049337802	2		527	723	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530037	63530037	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	83	374	0	ENST00000307078.5:c.2398A>T	p.Asn800Tyr	p.N800Y	ENST00000307078	NM_004655.3	800	Aat/Tat	10/11	1	2	FACETS	1	0.958	1	1	0.989	1	CLONAL	3	FALSE	1	0.148807049337802	2		374	321	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216681	36216681	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs750707578	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	209	499	0	ENST00000222270.7:c.3847A>G	p.Ser1283Gly	p.S1283G	ENST00000222270	NM_014727.1	1283	Agc/Ggc	13/37	0.148807049337802	4	FACETS	1	0.978	1	1	0.994	1	CLONAL	4	FALSE	2	0.148807049337802	4		499	724	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40739834	40739834	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	297	549	1	ENST00000392038.2:c.1391T>C	p.Leu464Pro	p.L464P	ENST00000392038	NM_001626.4	464	cTg/cCg	14/14	0.148807049337802	4	FACETS	0.941	0.89	0.993	1	0.996	1	CLONAL	6	FALSE	2	0.148807049337802	4		550	812	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096610	178096610	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	11	252	0	ENST00000397062.3:c.721A>G	p.Asn241Asp	p.N241D	ENST00000397062	NM_006164.4	241	Aac/Gac	5/5	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	FALSE	1	0.148807049337802	2		252	101	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62293846	62293846	+	intron_variant	Intron	SNP	C	C	A	novel	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	177	480	0	ENST00000360203.5:c.396-53C>A		p.*132*	ENST00000360203	NM_001283009.1	139/1243			1	2	FACETS	1	0.979	1	1	0.994	1	CLONAL	3	FALSE	1	0.148807049337802	2		480	682	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672324	86672324	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	45	329	0	ENST00000274376.6:c.2126G>C	p.Arg709Pro	p.R709P	ENST00000274376	NM_002890.2	709	cGa/cCa	16/25	1	2	FACETS	0.933	0.798	1	1	0.98	1	CLONAL	4	FALSE	1	0.148807049337802	2		329	162	SUCCESS
APC	324	MSKCC	GRCh37	5	112179489	112179489	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	41	318	0	ENST00000257430.4:c.8202del	p.Gly2735GlufsTer4	p.G2735Efs*4	ENST00000257430	NM_000038.5	2733	cAa/ca	16/16	1	2	FACETS	1	0.925	1	1	0.978	1	CLONAL	3	FALSE	1	0.148807049337802	2		318	158	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849900	151849900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773458258	NA	P-0040149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	116	345	0	ENST00000262189.6:c.12416G>A	p.Arg4139Gln	p.R4139Q	ENST00000262189	NM_170606.2	4139	cGa/cAa	49/59	0.108522394732312	4	FACETS	0.945	0.856	1	1	0.989	1	CLONAL	4	FALSE	2	0.148807049337802	4		345	474	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0040194-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	111	603	3	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	0.533662878639222	1	FACETS	0.799	0.726	0.874	0.799	0.726	0.874	SUBCLONAL	1	TRUE	0	0.574065790906739	1		606	345	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0040199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	215	600	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.27274289912164	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.32256883043458	1		601	859	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412252	139412252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057523819	NA	P-0040199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	237	697	0	ENST00000277541.6:c.1393G>A	p.Ala465Thr	p.A465T	ENST00000277541	NM_017617.3	465	Gcc/Acc	8/34	0.32256883043458	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.32256883043458	1		697	862	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936978	48936978	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	54	478	0	ENST00000267163.4:c.746C>A	p.Ser249Ter	p.S249*	ENST00000267163	NM_000321.2	249	tCa/tAa	8/27	0.32256883043458	1	FACETS	0.843	0.724	0.972	0.843	0.724	0.972	CLONAL	1	TRUE	0	0.32256883043458	1		478	333	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228334	228334	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs756877901	NA	P-0040199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	35	420	1	ENST00000264932.6:c.656A>G	p.Tyr219Cys	p.Y219C	ENST00000264932	NM_004168.2	219	tAt/tGt	6/15	0.289641276834978	4	FACETS	0.624	0.511	0.751	0.312	0.255	0.376	SUBCLONAL	1	TRUE	2	0.32256883043458	4		421	460	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0040263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	230	309	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.648916625867546	3	FACETS	0.842	0.792	0.892	0.842	0.792	0.892	CLONAL	2	TRUE	1	0.664365823144062	3		309	548	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0040263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	79	146	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.678	0.6	0.759	0.678	0.6	0.759	SUBCLONAL	1	TRUE	1	0.664365823144062	2		146	351	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0040263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	95	301	1	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	1	2	FACETS	0.929	0.837	1	0.929	0.837	1	CLONAL	1	TRUE	1	0.664365823144062	2		302	308	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266611	198266611	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs755415626	NA	P-0040263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	91	302	0	ENST00000335508.6:c.2225G>A	p.Gly742Asp	p.G742D	ENST00000335508	NM_012433.2	742	gGt/gAt	16/25	1	2	FACETS	0.763	0.683	0.847	0.763	0.683	0.847	SUBCLONAL	1	TRUE	1	0.664365823144062	2		302	359	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568574	41568574	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	168	462	0	ENST00000263253.7:c.4524C>G	p.Phe1508Leu	p.F1508L	ENST00000263253	NM_001429.3	1508	ttC/ttG	28/31	1	2	FACETS	0.83	0.767	0.896	0.83	0.767	0.896	CLONAL	1	TRUE	1	0.664365823144062	2		462	609	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163863	32163863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	205	606	0	ENST00000375023.3:c.5363G>A	p.Gly1788Glu	p.G1788E	ENST00000375023	NM_004557.3	1788	gGg/gAg	30/30	1	2	FACETS	0.941	0.877	1	0.941	0.877	1	CLONAL	1	TRUE	1	0.664365823144062	2		606	656	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0040297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	208	900	0	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	0.237243417607643	2	FACETS	0.859	0.798	0.923	0.859	0.798	0.923	CLONAL	2	TRUE	0	0.254869929913371	2		900	950	SUCCESS
AR	367	MSKCC	GRCh37	X	66766238	66766238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1327366080	NA	P-0040297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	37	203	0	ENST00000374690.3:c.1250C>T	p.Ala417Val	p.A417V	ENST00000374690	NM_000044.3	417	gCg/gTg	1/8	1	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.254869929913371	1		203	190	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604769	48604769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766833269	NA	P-0040297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	57	473	2	ENST00000342988.3:c.1591C>T	p.Arg531Trp	p.R531W	ENST00000342988	NM_005359.5	531	Cgg/Tgg	12/12	1	2	FACETS	0.92	0.791	1	0.92	0.791	1	CLONAL	1	TRUE	1	0.254869929913371	2		475	486	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643348	52643348	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	128	330	0	ENST00000394830.3:c.2548C>T	p.Arg850Ter	p.R850*	ENST00000394830	NM_018313.4	850	Cga/Tga	17/30	0.211457034104422	3	FACETS	1	0.962	1	0.734	0.669	0.802	CLONAL	2	TRUE	0	0.254869929913371	3		330	514	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975372	13975372	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761565850	NA	P-0040297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	112	537	0	ENST00000405192.2:c.515C>T	p.Ser172Leu	p.S172L	ENST00000405192	NM_001163147.1	172	tCg/tTg	7/12	0.254869929913371	3	FACETS	1	0.98	1	0.693	0.624	0.766	CLONAL	1	TRUE	1	0.254869929913371	3		537	715	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150549903	150549908	+	inframe_deletion	In_Frame_Del	DEL	GCCAGC	GCCAGC	-	novel	NA	P-0040297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	42	342	0	ENST00000369026.2:c.996_1001del	p.Leu333_Ala334del	p.L333_A334del	ENST00000369026	NM_021960.4	332	ctGCTGGCt/ctt	3/3	0.22478881159679	4	FACETS	0.731	0.609	0.866	0.244	0.203	0.289	SUBCLONAL	1	TRUE	1	0.254869929913371	4		342	566	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944564	71944564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1164813504	NA	P-0040297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	71	714	0	ENST00000298229.2:c.2120A>G	p.Tyr707Cys	p.Y707C	ENST00000298229	NM_001567.3	707	tAt/tGt	18/28	0.254869929913371	3	FACETS	0.728	0.634	0.83	0.364	0.317	0.415	SUBCLONAL	1	TRUE	1	0.254869929913371	3		714	863	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015688	112015688	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	63	511	0	ENST00000368678.4:c.1154A>G	p.His385Arg	p.H385R	ENST00000368678		385	cAt/cGt	11/13	0.215821255983866	3	FACETS	0.868	0.751	0.996	0.434	0.375	0.498	CLONAL	1	TRUE	1	0.254869929913371	3		511	642	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	181	756	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.333920566455209	2		756	846	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519896	NA	P-0040330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	14	352	0	ENST00000281708.4:c.1514G>T	p.Arg505Leu	p.R505L	ENST00000281708	NM_033632.3	505	cGc/cTc	10/12	0.278247909624614	3	FACETS	0.239	0.172	0.32	0.119	0.086	0.16	SUBCLONAL	1	TRUE	1	0.333920566455209	3		352	410	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455575	189455575	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs147340040	NA	P-0040330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	62	346	2	ENST00000264731.3:c.109C>T	p.Arg37Ter	p.R37*	ENST00000264731	NM_003722.4	37	Cga/Tga	2/14	0.278247909624614	3	FACETS	0.775	0.67	0.889	0.388	0.335	0.445	SUBCLONAL	1	TRUE	1	0.333920566455209	3		348	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578452	7578453	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCGC	novel	NA	P-0040330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	178	784	0	ENST00000269305.4:c.473_477dup	p.Met160AlafsTer12	p.M160Afs*12	ENST00000269305	NM_001126112.2	159	-/GCGCC	5/11	0.254442862232001	2	FACETS	1	0.985	1	0.645	0.595	0.696	CLONAL	1	TRUE	0	0.333920566455209	2		784	827	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	356	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.276265824352897	5	FACETS	1	0.989	1	0.874	0.837	0.911	CLONAL	4	TRUE	0	0.401497420414632	5		311	650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0040342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	179	445	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.401497420414632	2	FACETS	0.935	0.87	1	0.935	0.87	1	CLONAL	2	TRUE	0	0.401497420414632	2		445	477	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141427	11141427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	153	409	0	ENST00000358026.2:c.3404G>A	p.Arg1135Gln	p.R1135Q	ENST00000358026	NM_001128849.1	1135	cGg/cAg	25/36	0.220980817870719	2	FACETS	0.858	0.792	0.926	0.858	0.792	0.926	INDETERMINATE	2	TRUE	0	0.401497420414632	2		409	444	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932813	39932813	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	179	222	0	ENST00000378444.4:c.1786C>T	p.Gln596Ter	p.Q596*	ENST00000378444	NM_001123385.1	596	Cag/Tag	4/15	0.373863102350967	2	FACETS	0.898	0.844	0.952			1	CLONAL	3	TRUE	NA	0.401497420414632	2		222	331	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821970	72821970	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	68	381	0	ENST00000268489.5:c.10205C>A	p.Pro3402Gln	p.P3402Q	ENST00000268489	NM_006885.3	3402	cCa/cAa	10/10	0.401497420414632	2	FACETS	0.843	0.736	0.957	0.421	0.368	0.479	CLONAL	1	TRUE	0	0.401497420414632	2		381	402	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981731	70981731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	83	570	2	ENST00000276594.2:c.365C>T	p.Ala122Val	p.A122V	ENST00000276594	NM_024504.3	122	gCg/gTg	2/8	NA	2	FACETS	0.669	0.591	0.753			1	INDETERMINATE	1	TRUE	NA	0.401497420414632	2		572	618	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937486	76937486	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	95	131	0	ENST00000373344.5:c.3262G>C	p.Gly1088Arg	p.G1088R	ENST00000373344	NM_000489.3	1088	Ggt/Cgt	9/35	1	1	FACETS	0.871	0.793	0.951	1	0.987	1	CLONAL	2	TRUE	0	0.401497420414632	1		131	217	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0040380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	319	481	3	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.353162908353309	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.353162908353309	2		484	745	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807914	3807914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	67	344	0	ENST00000262367.5:c.3505C>T	p.Arg1169Cys	p.R1169C	ENST00000262367	NM_004380.2	1169	Cgc/Tgc	18/31	0.353162908353309	5	FACETS	0.854	0.741	0.975	0.213	0.185	0.244	CLONAL	1	TRUE	1	0.353162908353309	5		344	680	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041265	47041265	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1556779896	NA	P-0040380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	72	454	0	ENST00000377604.3:c.1693C>T	p.Pro565Ser	p.P565S	ENST00000377604	NM_001204468.1	565	Cct/Tct	15/24	0.238192938329674	5	FACETS	0.729	0.635	0.83	0.243	0.211	0.277	SUBCLONAL	1	TRUE	2	0.353162908353309	5		454	856	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004246	150004246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	30	174	0	ENST00000253339.5:c.1979G>A	p.Arg660His	p.R660H	ENST00000253339		660	cGt/cAt	3/7	0.347877965511627	3	FACETS	0.84	0.68	1	0.42	0.34	0.51	CLONAL	1	TRUE	1	0.353162908353309	3		174	238	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828860	26828860	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	62	303	0	ENST00000381527.3:c.82G>A	p.Gly28Ser	p.G28S	ENST00000381527	NM_001260.1	28	Ggc/Agc	1/13	0.353162908353309	6	FACETS	0.985	0.851	1	0.246	0.212	0.283	CLONAL	1	TRUE	2	0.353162908353309	6		303	608	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912606	32912606	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	116	288	0	ENST00000380152.3:c.4114T>C	p.Phe1372Leu	p.F1372L	ENST00000380152		1372	Ttt/Ctt	11/27	0.353162908353309	6	FACETS	1	0.974	1	0.604	0.548	0.663	CLONAL	2	TRUE	2	0.353162908353309	6		288	464	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478832	57478832	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	43	260	0	ENST00000371085.3:c.418T>G	p.Phe140Val	p.F140V	ENST00000371085	NM_000516.4	140	Ttt/Gtt	5/13	0.353162908353309	5	FACETS	0.625	0.522	0.739	0.208	0.174	0.247	SUBCLONAL	1	TRUE	2	0.353162908353309	5		260	596	SUCCESS
APC	324	MSKCC	GRCh37	5	112174517	112174517	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	61	186	0	ENST00000257430.4:c.3227del	p.Pro1076LeufsTer50	p.P1076Lfs*50	ENST00000257430	NM_000038.5	1076	Cct/ct	16/16	0.353162908353309	2	FACETS	0.864	0.757	0.975	0.864	0.757	0.975	CLONAL	2	TRUE	0	0.353162908353309	2		186	200	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0040385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	596	496	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	NA	2	FACETS	0.994	0.97	1			1	INDETERMINATE	2	TRUE	NA	0.771514463536572	2		496	777	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	330	520	0	ENST00000206249.3:c.1607T>C	p.Leu536Pro	p.L536P	ENST00000206249	NM_000125.3	536	cTc/cCc	8/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.771514463536572	2		520	834	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168749	56168749	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	219	484	0	ENST00000399503.3:c.1603C>T	p.Gln535Ter	p.Q535*	ENST00000399503	NM_005921.1	535	Caa/Taa	9/20	1	2	FACETS	0.891	0.834	0.95	0.891	0.834	0.95	CLONAL	1	TRUE	1	0.771514463536572	2		484	637	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177812	56177812	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	203	369	0	ENST00000399503.3:c.2785G>T	p.Glu929Ter	p.E929*	ENST00000399503	NM_005921.1	929	Gag/Tag	14/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.771514463536572	2		369	519	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0040445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	82	492	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.31268928604459	3	FACETS	0.883	0.779	0.995	0.442	0.389	0.498	CLONAL	1	TRUE	1	0.317944849524114	3		492	677	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370871	55370871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	128	450	0	ENST00000297316.4:c.173C>T	p.Ala58Val	p.A58V	ENST00000297316	NM_022454.3	58	gCc/gTc	1/2	0.303247284450641	4	FACETS	0.896	0.815	0.981	0.896	0.815	0.981	CLONAL	2	TRUE	2	0.317944849524114	4		450	592	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0040492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	174	348	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.700930377418651	2		348	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0040492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	169	704	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.700930377418651	1	FACETS	0.432	0.398	0.467	0.432	0.398	0.467	SUBCLONAL	1	TRUE	0	0.700930377418651	1		704	725	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0040492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	305	540	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.700930377418651	1	FACETS	0.767	0.727	0.807	0.767	0.727	0.807	SUBCLONAL	1	TRUE	0	0.700930377418651	1		540	737	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0040492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	201	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.700930377418651	2		539	570	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519896	NA	P-0040492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	179	352	0	ENST00000281708.4:c.1514G>T	p.Arg505Leu	p.R505L	ENST00000281708	NM_033632.3	505	cGc/cTc	10/12	0.700930377418651	1	FACETS	0.999	0.939	1	0.999	0.939	1	CLONAL	1	TRUE	0	0.700930377418651	1		352	332	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120115	70120115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	112	153	0	ENST00000245479.2:c.1121del	p.Pro374ArgfsTer9	p.P374Rfs*9	ENST00000245479	NM_000346.3	373	Ccc/cc	3/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.700930377418651	2		153	253	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206908	162206908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1233588284	NA	P-0040492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	60	439	0	ENST00000366898.1:c.767G>A	p.Arg256His	p.R256H	ENST00000366898	NM_004562.2	256	cGc/cAc	7/12	0.21250902185576	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.700930377418651	0		439	447	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209250	133209250	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1462887616	NA	P-0040492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	332	759	2	ENST00000320574.5:c.6136G>A	p.Gly2046Arg	p.G2046R	ENST00000320574	NM_006231.2	2046	Gga/Aga	44/49	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.700930377418651	2		761	918	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042476	42042477	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	73	550	0	ENST00000219905.7:c.6672dup	p.Leu2225ThrfsTer8	p.L2225Tfs*8	ENST00000219905	NM_001164273.1	2224	tta/ttAa	17/24	1	2	FACETS	0.239	0.208	0.272	0.239	0.208	0.272	SUBCLONAL	1	TRUE	1	0.700930377418651	2		550	871	SUCCESS
APC	324	MSKCC	GRCh37	5	112175336	112175337	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACAAAGCTGTTGA	novel	NA	P-0040492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	79	235	0	ENST00000257430.4:c.4047_4059dup	p.Phe1354GlnfsTer4	p.F1354Qfs*4	ENST00000257430	NM_000038.5	1349	cac/cACAAAGCTGTTGAac	16/16	1	2	FACETS	0.657	0.582	0.736	0.657	0.582	0.736	SUBCLONAL	1	TRUE	1	0.700930377418651	2		235	343	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739487	145739487	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	209	848	2	ENST00000428558.2:c.1883T>C	p.Leu628Pro	p.L628P	ENST00000428558	NM_004260.3	628	cTt/cCt	12/22	1	2	FACETS	0.529	0.49	0.569	0.529	0.49	0.569	SUBCLONAL	1	TRUE	1	0.700930377418651	2		850	1128	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0040494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	273	600	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.450727941456798	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.450727941456798	1		601	872	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0040494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	116	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.968	0.876	1	0.968	0.876	1	CLONAL	1	TRUE	1	0.450727941456798	2		539	532	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738280	145738280	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372205013	NA	P-0040494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	306	958	0	ENST00000428558.2:c.2705G>A	p.Arg902Gln	p.R902Q	ENST00000428558	NM_004260.3	902	cGg/cAg	16/22	0.128780177673803	3	FACETS	1	0.99	1	0.62	0.584	0.658	INDETERMINATE	1	TRUE	1	0.450727941456798	3		958	1341	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430809	47430809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	182	809	3	ENST00000377045.4:c.1774G>A	p.Asp592Asn	p.D592N	ENST00000377045	NM_001654.4	592	Gat/Aat	16/16	1	2	FACETS	0.744	0.686	0.805	0.744	0.686	0.805	SUBCLONAL	1	TRUE	1	0.450727941456798	2		812	1085	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440658	56440661	+	frameshift_variant	Frame_Shift_Del	DEL	TCAA	TCAA	-	novel	NA	P-0040494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	225	734	0	ENST00000407977.2:c.557_560del	p.Ile186SerfsTer2	p.I186Sfs*2	ENST00000407977		186	aTTGAg/ag	5/10	0.450727941456798	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.450727941456798	1		734	749	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	154	348	1				ENST00000310581	NM_198253.2	-/1132			0.273382344799896	3	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	1	0.358146892975203	3		349	504	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064418	30064418	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	209	515	0	ENST00000338641.4:c.982G>T	p.Glu328Ter	p.E328*	ENST00000338641	NM_000268.3	328	Gag/Tag	10/16	0.358146892975203	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.358146892975203	2		515	567	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182002	38182002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772678256	NA	P-0040532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	94	625	1	ENST00000396334.3:c.626G>A	p.Arg209His	p.R209H	ENST00000396334	NM_002468.4	209	cGc/cAc	3/5	1	2	FACETS	0.879	0.784	0.981	0.879	0.784	0.981	CLONAL	1	TRUE	1	0.358146892975203	2		626	597	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105715	27105715	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	141	456	0	ENST00000324856.7:c.5326G>T	p.Glu1776Ter	p.E1776*	ENST00000324856	NM_006015.4	1776	Gaa/Taa	20/20	0.346895535759914	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.358146892975203	2		456	361	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280107	66280107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs77407591	NA	P-0040532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	49	349	0	ENST00000273854.3:c.1582G>A	p.Glu528Lys	p.E528K	ENST00000273854	NM_004439.5	528	Gag/Aag	7/18	1	2	FACETS	0.681	0.578	0.793	0.681	0.578	0.793	SUBCLONAL	1	TRUE	1	0.358146892975203	2		349	402	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89833608	89833608	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs753223258	NA	P-0040532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	83	427	0	ENST00000389301.3:c.2542T>C	p.Phe848Leu	p.F848L	ENST00000389301	NM_000135.2	848	Ttt/Ctt	27/43	0.358146892975203	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.358146892975203	1		427	325	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89833619	89833619	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	71	390	0	ENST00000389301.3:c.2531C>T	p.Ser844Phe	p.S844F	ENST00000389301	NM_000135.2	844	tCt/tTt	27/43	0.358146892975203	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.358146892975203	1		390	285	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372155	55372155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1219111000	NA	P-0040532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1184	125	799	0	ENST00000297316.4:c.845C>T	p.Ser282Leu	p.S282L	ENST00000297316	NM_022454.3	282	tCg/tTg	2/2	0.358146892975203	7	FACETS	1	0.911	1	0.202	0.182	0.223	CLONAL	1	TRUE	2	0.358146892975203	7		799	1309	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344240	70344240	+	splice_donor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0040532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	15	181	0	ENST00000374080.3:c.1974+2del		p.X658_splice	ENST00000374080		658			1	1	FACETS	0.573	0.423	0.749	0.573	0.423	0.749	SUBCLONAL	1	TRUE	0	0.358146892975203	1		181	120	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	58	348	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.677	0.583	0.78	0.677	0.583	0.78	SUBCLONAL	1	TRUE	1	0.37892971744518	2		349	452	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398917	398917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356308443	NA	P-0040533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	48	521	0	ENST00000380956.4:c.727G>A	p.Glu243Lys	p.E243K	ENST00000380956	NM_001195286.1	243	Gaa/Aaa	6/9	0.188641621762022	2	FACETS	0.454	0.383	0.532	0.227	0.191	0.266	INDETERMINATE	1	TRUE	0	0.37892971744518	2		521	558	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682991	241682991	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1226883651	NA	P-0040533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	86	627	0	ENST00000366560.3:c.32C>G	p.Ser11Trp	p.S11W	ENST00000366560	NM_000143.3	11	tCg/tGg	1/10	1	2	FACETS	0.707	0.626	0.794	0.707	0.626	0.794	SUBCLONAL	1	TRUE	1	0.37892971744518	2		627	642	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224531	108224531	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	97	445	0	ENST00000278616.4:c.8710G>C	p.Glu2904Gln	p.E2904Q	ENST00000278616	NM_000051.3	2904	Gag/Cag	60/63	0.2836983062765	2	FACETS	1	0.956	1	0.564	0.505	0.626	CLONAL	1	TRUE	0	0.37892971744518	2		445	454	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511637	46511637	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	109	592	0	ENST00000262741.5:c.1140C>G	p.Phe380Leu	p.F380L	ENST00000262741	NM_003629.3	380	ttC/ttG	9/10	1	2	FACETS	0.839	0.754	0.928	0.839	0.754	0.928	CLONAL	1	TRUE	1	0.37892971744518	2		592	686	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106271	27106302	+	frameshift_variant	Frame_Shift_Del	DEL	GTAAGGATGAGACCCCACTGTGTACCCTTCTG	GTAAGGATGAGACCCCACTGTGTACCCTTCTG	-	novel	NA	P-0040533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	156	707	0	ENST00000324856.7:c.5883_5914del	p.Ser1961ArgfsTer27	p.S1961Rfs*27	ENST00000324856	NM_006015.4	1961	aGTAAGGATGAGACCCCACTGTGTACCCTTCTG/a	20/20	0.37892971744518	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.37892971744518	1		707	647	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983018	201983019	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	226	995	0	ENST00000359651.3:c.868dup	p.Glu290GlyfsTer11	p.E290Gfs*11	ENST00000359651		289	-/G	7/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.37892971744518	2		995	1103	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432341	432341	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	74	440	0	ENST00000399788.2:c.2182C>G	p.Leu728Val	p.L728V	ENST00000399788	NM_001042603.1	728	Ctg/Gtg	16/28	NA	2	FACETS	0.721	0.632	0.816			1	INDETERMINATE	1	TRUE	NA	0.37892971744518	2		440	542	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864474	57864474	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	134	828	0	ENST00000228682.2:c.1951C>G	p.Pro651Ala	p.P651A	ENST00000228682	NM_005269.2	651	Cca/Gca	12/12	1	2	FACETS	0.883	0.803	0.967	0.883	0.803	0.967	CLONAL	1	TRUE	1	0.37892971744518	2		828	801	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355171	15355171	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	141	1050	0	ENST00000263377.2:c.2452G>C	p.Asp818His	p.D818H	ENST00000263377	NM_058243.2	818	Gac/Cac	13/20	0.364988637138461	1	FACETS	0.628	0.571	0.687	0.628	0.571	0.687	SUBCLONAL	1	TRUE	0	0.37892971744518	1		1050	961	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582062	189582062	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	134	466	0	ENST00000264731.3:c.621G>C	p.Lys207Asn	p.K207N	ENST00000264731	NM_003722.4	207	aaG/aaC	5/14	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.37892971744518	2		466	671	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280127	66280127	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	187	342	0	ENST00000273854.3:c.1562A>C	p.Lys521Thr	p.K521T	ENST00000273854	NM_004439.5	521	aAa/aCa	7/18	0.378511196178309	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.37892971744518	2		342	476	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29913230	29913230	+	stop_lost,splice_region_variant	Nonstop_Mutation	SNP	T	T	G	novel	NA	P-0040533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	165	552	0	ENST00000376809.5:c.1096T>G	p.Ter366GlyextTer8	p.*366Gext*8	ENST00000376809	NM_002116.7	366	Tga/Gga	8/8	0.188641621762022	2	FACETS	1	0.982	1	0.616	0.567	0.667	INDETERMINATE	1	TRUE	0	0.37892971744518	2		552	707	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	89	348	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.745	0.663	0.831	0.745	0.663	0.831	SUBCLONAL	1	TRUE	1	0.509468652698734	2		349	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0040535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	320	853	1	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.509468652698734	2		854	1043	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266457	55266457	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775695605	NA	P-0040535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	116	779	0	ENST00000275493.2:c.2749G>A	p.Gly917Arg	p.G917R	ENST00000275493	NM_005228.3	917	Gga/Aga	23/28	0.295970903768537	3	FACETS	0.684	0.616	0.756	0.342	0.308	0.378	INDETERMINATE	1	TRUE	1	0.509468652698734	3		779	835	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0040550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	99	398	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.871	0.783	0.964	1	0.985	1	CLONAL	2	TRUE	1	0.27	2		398	421	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0040550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	103	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.963	0.869	1	1	0.988	1	CLONAL	2	TRUE	1	0.27	2		539	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0040550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	86	957	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	1	2	FACETS	0.974	0.862	1	0.974	0.862	1	CLONAL	1	TRUE	1	0.27	2		957	654	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0040550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	19	415	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.238	0.179	0.307	0.238	0.179	0.307	SUBCLONAL	1	TRUE	1	0.27	2		415	592	SUCCESS
APC	324	MSKCC	GRCh37	5	112175925	112175925	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs863225356	NA	P-0040550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	36	178	0	ENST00000257430.4:c.4634C>G	p.Ser1545Ter	p.S1545*	ENST00000257430	NM_000038.5	1545	tCa/tGa	16/16	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.27	2		178	193	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982378	201982379	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0040550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	256	755	0	ENST00000359651.3:c.758_759insTT	p.Ser254Ter	p.S254*	ENST00000359651		253	ctg/cTTtg	6/8	1	2	FACETS	1	0.949	1	1	0.995	1	CLONAL	2	TRUE	1	0.27	2		755	936	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487911	56487911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762488062	NA	P-0040550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	51	580	0	ENST00000267101.3:c.1642G>A	p.Glu548Lys	p.E548K	ENST00000267101	NM_001982.3	548	Gaa/Aaa	14/28	1	2	FACETS	0.646	0.548	0.753	0.646	0.548	0.753	SUBCLONAL	1	TRUE	1	0.27	2		580	585	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645155	67645155	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	80	550	0	ENST00000264010.4:c.420T>G	p.Asn140Lys	p.N140K	ENST00000264010	NM_006565.3	140	aaT/aaG	3/12	1	2	FACETS	0.847	0.745	0.956	0.847	0.745	0.956	CLONAL	1	TRUE	1	0.27	2		550	700	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051059	180051059	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs747401546	NA	P-0040550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	65	521	0	ENST00000261937.6:c.1424G>A	p.Arg475Gln	p.R475Q	ENST00000261937	NM_182925.4	475	cGg/cAg	11/30	1	2	FACETS	0.963	0.836	1	0.963	0.836	1	CLONAL	1	TRUE	1	0.27	2		521	500	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	76	348	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.46395088796524	2		349	312	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682400	52682400	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	63	292	0	ENST00000394830.3:c.773del	p.Asn258MetfsTer25	p.N258Mfs*25	ENST00000394830	NM_018313.4	258	aAt/at	8/30	0.46395088796524	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.46395088796524	1		292	192	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936201	71936201	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	95	475	0	ENST00000298229.2:c.173T>C	p.Leu58Pro	p.L58P	ENST00000298229	NM_001567.3	58	cTc/cCc	1/28	0.196060309462359	1	FACETS	0.965	0.868	1	0.965	0.868	1	INDETERMINATE	1	TRUE	0	0.46395088796524	1		475	326	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970971	21970971	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0040583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	68	656	0	ENST00000304494.5:c.387C>G	p.Tyr129Ter	p.Y129*	ENST00000304494	NM_000077.4	129	taC/taG	2/3	0.130635223361624	0	FACETS	0.218	0.189	0.249			1	INDETERMINATE	1	TRUE	0	0.46395088796524	0		656	722	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1646407	1646408	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0040583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	135	670	0	ENST00000344749.5:c.91_92insAA	p.Thr31LysfsTer91	p.T31Kfs*91	ENST00000344749	NM_001136139.2	31	acc/aAAcc	3/19	1	2	FACETS	0.981	0.895	1	0.981	0.895	1	CLONAL	1	TRUE	1	0.46395088796524	2		670	593	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573275	55573275	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	42	339	0	ENST00000288135.5:c.937A>G	p.Ile313Val	p.I313V	ENST00000288135	NM_000222.2	313	Att/Gtt	6/21	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.46395088796524	2		339	156	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272496	11272496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	184	447	0	ENST00000361445.4:c.3434C>T	p.Ser1145Phe	p.S1145F	ENST00000361445	NM_004958.3	1145	tCc/tTc	23/58	0.511148414466477	5	FACETS	0.814	0.753	0.877	0.542	0.502	0.585	CLONAL	2	TRUE	2	0.54260942648441	5		447	756	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257320	16257320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	218	504	0	ENST00000375759.3:c.4585C>T	p.Arg1529Cys	p.R1529C	ENST00000375759	NM_015001.2	1529	Cgt/Tgt	11/15	0.511148414466477	5	FACETS	1	0.971	1	0.713	0.667	0.761	CLONAL	2	TRUE	2	0.54260942648441	5		504	681	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106178	27106178	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	168	527	0	ENST00000324856.7:c.5789C>G	p.Ser1930Ter	p.S1930*	ENST00000324856	NM_006015.4	1930	tCa/tGa	20/20	0.511148414466477	5	FACETS	0.783	0.722	0.847	0.522	0.481	0.565	SUBCLONAL	2	TRUE	2	0.54260942648441	5		527	717	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28605694	28605694	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	110	577	0	ENST00000253063.3:c.1298A>G	p.Glu433Gly	p.E433G	ENST00000253063	NM_031459.4	433	gAg/gGg	9/10	0.511148414466477	5	FACETS	0.854	0.767	0.947	0.285	0.255	0.316	CLONAL	1	TRUE	2	0.54260942648441	5		577	861	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932368	36932368	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1474949172	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	356	549	0	ENST00000361632.4:c.2101G>A	p.Glu701Lys	p.E701K	ENST00000361632		701	Gag/Aag	16/16	0.511148414466477	5	FACETS	1	0.967	1	1	0.967	1	CLONAL	3	TRUE	2	0.54260942648441	5		549	780	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458438	120458438	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	82	490	0	ENST00000256646.2:c.6907C>T	p.Pro2303Ser	p.P2303S	ENST00000256646	NM_024408.3	2303	Ccc/Tcc	34/34	0.206436264682583	5	FACETS	1	0.917	1	0.349	0.308	0.392	INDETERMINATE	1	TRUE	2	0.54260942648441	5		490	524	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459209	120459209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	239	484	0	ENST00000256646.2:c.6136C>T	p.Pro2046Ser	p.P2046S	ENST00000256646	NM_024408.3	2046	Ccc/Tcc	34/34	0.206436264682583	5	FACETS	1	0.989	1	0.823	0.773	0.874	INDETERMINATE	2	TRUE	2	0.54260942648441	5		484	647	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838389	156838389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1357016517	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	102	627	0	ENST00000524377.1:c.667G>A	p.Glu223Lys	p.E223K	ENST00000524377	NM_002529.3	223	Gag/Aag	6/17	0.206436264682583	5	FACETS	0.991	0.887	1	0.33	0.295	0.368	INDETERMINATE	1	TRUE	2	0.54260942648441	5		627	688	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176104194	176104194	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	63	323	0	ENST00000367669.3:c.920G>A	p.Ser307Asn	p.S307N	ENST00000367669	NM_022457.5	307	aGt/aAt	8/20	0.206436264682583	5	FACETS	1	0.958	1	0.419	0.365	0.478	INDETERMINATE	1	TRUE	2	0.54260942648441	5		323	335	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596098	43596098	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	93	547	0	ENST00000355710.3:c.265C>T	p.Gln89Ter	p.Q89*	ENST00000355710	NM_020975.4	89	Cag/Tag	2/20	0.441601166481596	3	FACETS	0.941	0.841	1	0.471	0.42	0.524	CLONAL	1	TRUE	1	0.54260942648441	3		547	463	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405991	70405991	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	69	525	1	ENST00000373644.4:c.3505C>T	p.Gln1169Ter	p.Q1169*	ENST00000373644	NM_030625.2	1169	Caa/Taa	4/12	0.441601166481596	3	FACETS	0.704	0.615	0.8	0.352	0.307	0.4	SUBCLONAL	1	TRUE	1	0.54260942648441	3		526	459	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942059	71942059	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	300	655	0	ENST00000298229.2:c.1323C>G	p.Asn441Lys	p.N441K	ENST00000298229	NM_001567.3	441	aaC/aaG	12/28	0.379090778138913	5	FACETS	0.865	0.819	0.912	0.865	0.819	0.912	CLONAL	3	TRUE	2	0.54260942648441	5		655	773	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103520	77103520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	63	298	0	ENST00000356341.3:c.46C>T	p.Pro16Ser	p.P16S	ENST00000356341	NM_002576.4	16	Ccg/Tcg	2/15	0.379090778138913	5	FACETS	0.81	0.701	0.928	0.27	0.233	0.31	CLONAL	1	TRUE	2	0.54260942648441	5		298	520	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998389	100998403	+	inframe_deletion	In_Frame_Del	DEL	CTGGGGCGGCGCGCC	CTGGGGCGGCGCGCC	-	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	77	144	0	ENST00000325455.5:c.1399_1413del	p.Gly467_Gln471del	p.G467_Q471del	ENST00000325455	NM_001202474.3	467	GGCGCGCCGCCCCAG/-	1/8	0.379090778138913	5	FACETS	1	0.934	1	1	0.934	1	CLONAL	3	TRUE	2	0.54260942648441	5		144	164	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344819	118344819	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	97	307	0	ENST00000534358.1:c.2945C>T	p.Ser982Phe	p.S982F	ENST00000534358	NM_005933.3	982	tCc/tTc	3/36	0.44034013684352	3	FACETS	0.76	0.686	0.836			1	SUBCLONAL	2	TRUE	NA	0.54260942648441	3		307	299	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118353184	118353184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	40	256	0	ENST00000534358.1:c.4060C>T	p.Pro1354Ser	p.P1354S	ENST00000534358	NM_005933.3	1354	Cct/Tct	8/36	0.44034013684352	3	FACETS	0.66	0.551	0.78			1	SUBCLONAL	1	TRUE	NA	0.54260942648441	3		256	284	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	441059	441059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	152	408	0	ENST00000399788.2:c.1699C>T	p.Pro567Ser	p.P567S	ENST00000399788	NM_001042603.1	567	Cct/Tct	13/28	0.302229159786734	5	FACETS	0.857	0.787	0.929	0.571	0.525	0.62	INDETERMINATE	2	TRUE	2	0.54260942648441	5		408	593	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4387932	4387932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	55	433	0	ENST00000261254.3:c.418G>A	p.Glu140Lys	p.E140K	ENST00000261254	NM_001759.3	140	Gaa/Aaa	3/5	0.302229159786734	5	FACETS	0.769	0.659	0.89	0.256	0.219	0.297	INDETERMINATE	1	TRUE	2	0.54260942648441	5		433	478	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022646	12022646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	69	419	0	ENST00000396373.4:c.752C>T	p.Ser251Phe	p.S251F	ENST00000396373	NM_001987.4	251	tCc/tTc	5/8	0.302229159786734	5	FACETS	0.957	0.836	1	0.319	0.278	0.363	INDETERMINATE	1	TRUE	2	0.54260942648441	5		419	482	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022772	12022772	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	113	414	0	ENST00000396373.4:c.878C>T	p.Ser293Phe	p.S293F	ENST00000396373	NM_001987.4	293	tCc/tTc	5/8	0.302229159786734	5	FACETS	0.991	0.901	1	0.661	0.6	0.724	INDETERMINATE	2	TRUE	2	0.54260942648441	5		414	381	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435455	18435455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	30	236	0	ENST00000266497.5:c.440C>T	p.Ser147Leu	p.S147L	ENST00000266497		147	tCa/tTa	1/31	0.302229159786734	5	FACETS	0.924	0.75	1	0.308	0.25	0.373	INDETERMINATE	1	TRUE	2	0.54260942648441	5		236	217	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466994	18466994	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773615749	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	93	299	0	ENST00000266497.5:c.1133G>A	p.Arg378Gln	p.R378Q	ENST00000266497		378	cGa/cAa	5/31	0.302229159786734	5	FACETS	0.868	0.779	0.962	0.579	0.519	0.642	INDETERMINATE	2	TRUE	2	0.54260942648441	5		299	358	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573894	18573894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759658584	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	30	336	0	ENST00000266497.5:c.2212C>T	p.Arg738Cys	p.R738C	ENST00000266497		738	Cgt/Tgt	15/31	0.302229159786734	5	FACETS	0.666	0.538	0.811	0.222	0.179	0.271	INDETERMINATE	1	TRUE	2	0.54260942648441	5		336	301	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244256	46244256	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	70	369	0	ENST00000334344.6:c.2350C>T	p.Pro784Ser	p.P784S	ENST00000334344	NM_152641.2	784	Cct/Tct	15/21	0.302229159786734	5	FACETS	0.848	0.747	0.954	0.565	0.498	0.636	INDETERMINATE	2	TRUE	2	0.54260942648441	5		369	276	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425511	49425511	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	436	709	0	ENST00000301067.7:c.12977C>T	p.Pro4326Leu	p.P4326L	ENST00000301067	NM_003482.3	4326	cCc/cTc	39/54	0.54260942648441	6	FACETS	0.906	0.868	0.943			1	CLONAL	4	TRUE	NA	0.54260942648441	6		709	925	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857527	57857527	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	97	578	0	ENST00000228682.2:c.53G>T	p.Cys18Phe	p.C18F	ENST00000228682	NM_005269.2	18	tGt/tTt	2/12	1	2	FACETS	0.777	0.696	0.862	0.777	0.696	0.862	SUBCLONAL	1	TRUE	1	0.54260942648441	2		578	460	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858925	57858925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	88	605	0	ENST00000228682.2:c.421C>T	p.His141Tyr	p.H141Y	ENST00000228682	NM_005269.2	141	Cac/Tac	5/12	1	2	FACETS	0.714	0.636	0.798	0.714	0.636	0.798	SUBCLONAL	1	TRUE	1	0.54260942648441	2		605	454	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859664	57859664	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	76	475	0	ENST00000228682.2:c.718G>A	p.Asp240Asn	p.D240N	ENST00000228682	NM_005269.2	240	Gat/Aat	7/12	1	2	FACETS	0.761	0.672	0.856	0.761	0.672	0.856	SUBCLONAL	1	TRUE	1	0.54260942648441	2		475	368	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144849	58144849	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	75	433	0	ENST00000257904.6:c.379G>A	p.Gly127Ser	p.G127S	ENST00000257904	NM_000075.3	127	Ggc/Agc	4/8	1	2	FACETS	0.747	0.659	0.841	0.747	0.659	0.841	SUBCLONAL	1	TRUE	1	0.54260942648441	2		433	370	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112062	115112062	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1219837774	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	101	601	0	ENST00000257566.3:c.1678G>A	p.Ala560Thr	p.A560T	ENST00000257566	NM_016569.3	560	Gcc/Acc	7/8	1	2	FACETS	0.824	0.74	0.911	0.824	0.74	0.911	CLONAL	1	TRUE	1	0.54260942648441	2		601	452	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967641	26967641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	50	297	0	ENST00000381527.3:c.784C>T	p.Pro262Ser	p.P262S	ENST00000381527	NM_001260.1	262	Cct/Tct	7/13	0.356306156135118	3	FACETS	0.831	0.71	0.962	0.415	0.355	0.481	CLONAL	1	TRUE	1	0.54260942648441	3		297	282	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578234	28578234	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	88	491	0	ENST00000241453.7:c.2937G>A	p.Met979Ile	p.M979I	ENST00000241453	NM_004119.2	979	atG/atA	24/24	0.356306156135118	3	FACETS	0.772	0.686	0.864	0.386	0.343	0.432	SUBCLONAL	1	TRUE	1	0.54260942648441	3		491	534	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908251	28908251	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	122	400	0	ENST00000282397.4:c.2504G>A	p.Arg835Lys	p.R835K	ENST00000282397	NM_002019.4	835	aGa/aAa	18/30	0.356306156135118	3	FACETS	1	0.986	1	0.729	0.665	0.795	CLONAL	1	TRUE	1	0.54260942648441	3		400	392	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	335	638	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	0.339179058197132	3	FACETS	0.893	0.855	0.931	1	0.995	1	CLONAL	3	TRUE	1	0.54260942648441	3		638	586	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675118	40675118	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	111	648	0	ENST00000249776.8:c.82C>T	p.Pro28Ser	p.P28S	ENST00000249776	NM_033286.3	28	Ccg/Tcg	1/9	0.339179058197132	3	FACETS	0.861	0.776	0.951	0.431	0.388	0.476	CLONAL	1	TRUE	1	0.54260942648441	3		648	604	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42002918	42002918	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	50	323	0	ENST00000219905.7:c.2455C>T	p.Arg819Cys	p.R819C	ENST00000219905	NM_001164273.1	819	Cgt/Tgt	8/24	0.339179058197132	3	FACETS	1	0.866	1	0.505	0.433	0.582	CLONAL	1	TRUE	1	0.54260942648441	3		323	232	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74001997	74001997	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	98	595	0	ENST00000318443.5:c.1513G>C	p.Asp505His	p.D505H	ENST00000318443	NM_001024736.1	505	Gac/Cac	8/10	0.339179058197132	3	FACETS	0.955	0.856	1	0.477	0.428	0.53	CLONAL	1	TRUE	1	0.54260942648441	3		595	481	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631934	90631934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913502	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	223	768	0	ENST00000330062.3:c.419G>A	p.Arg140Gln	p.R140Q	ENST00000330062	NM_002168.2	140	cGg/cAg	4/11	0.339179058197132	3	FACETS	0.901	0.845	0.957	0.901	0.845	0.957	CLONAL	2	TRUE	1	0.54260942648441	3		768	580	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778674	3778691	+	inframe_deletion	In_Frame_Del	DEL	GGCTGGGACTGGAGGCCA	GGCTGGGACTGGAGGCCA	-	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	136	656	0	ENST00000262367.5:c.6357_6374del	p.Leu2121_Gly2126del	p.L2121_G2126del	ENST00000262367	NM_004380.2	2119	ccTGGCCTCCAGTCCCAGCCc/ccc	31/31	0.356306156135118	3	FACETS	0.805	0.739	0.872	0.805	0.739	0.872	CLONAL	2	TRUE	1	0.54260942648441	3		656	396	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857172	9857172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555481986	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	66	430	0	ENST00000330684.3:c.4229C>T	p.Ser1410Leu	p.S1410L	ENST00000330684	NM_001134407.1	1410	tCg/tTg	13/13	0.356306156135118	3	FACETS	0.787	0.686	0.895	0.393	0.343	0.448	SUBCLONAL	1	TRUE	1	0.54260942648441	3		430	393	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273929	10273929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	95	657	1	ENST00000330684.3:c.340G>A	p.Asp114Asn	p.D114N	ENST00000330684	NM_001134407.1	114	Gat/Aat	2/13	0.356306156135118	3	FACETS	0.851	0.76	0.947	0.426	0.38	0.474	CLONAL	1	TRUE	1	0.54260942648441	3		658	523	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813746	50813746	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	98	589	0	ENST00000398568.2:c.1300C>T	p.Pro434Ser	p.P434S	ENST00000398568	NM_001042412.1	434	Cca/Tca	8/18	0.356306156135118	3	FACETS	0.741	0.662	0.824	0.37	0.331	0.412	SUBCLONAL	1	TRUE	1	0.54260942648441	3		589	620	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350753	89350753	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886041791	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	72	702	0	ENST00000301030.4:c.2197C>T	p.Arg733Ter	p.R733*	ENST00000301030	NM_001256183.1	733	Cga/Tga	9/13	0.356306156135118	3	FACETS	0.594	0.519	0.674	0.297	0.259	0.337	SUBCLONAL	1	TRUE	1	0.54260942648441	3		702	568	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813063	89813063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	73	558	0	ENST00000389301.3:c.3442C>T	p.Pro1148Ser	p.P1148S	ENST00000389301	NM_000135.2	1148	Ccc/Tcc	35/43	0.356306156135118	3	FACETS	0.765	0.672	0.865	0.383	0.336	0.433	SUBCLONAL	1	TRUE	1	0.54260942648441	3		558	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577540	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	rs1555525498	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	315	595	1	ENST00000269305.4:c.741_742delinsTT	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	247	aaCCgg/aaTTgg	7/11	0.54260942648441	3	FACETS	0.909	0.87	0.949	0.909	0.87	0.949	CLONAL	3	TRUE	0	0.54260942648441	3		596	541	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979560	7979560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	73	573	0	ENST00000319144.4:c.1465G>A	p.Gly489Arg	p.G489R	ENST00000319144	NM_001139.2	489	Ggg/Agg	11/15	0.54260942648441	3	FACETS	0.613	0.537	0.695	0.204	0.179	0.232	SUBCLONAL	1	TRUE	0	0.54260942648441	3		573	558	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553491	29553492	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	304	450	0	ENST00000356175.3:c.2040_2041delinsTT	p.Arg681Ter	p.R681*	ENST00000356175	NM_000267.3	680	tgCCga/tgTTga	18/57	0.54260942648441	3	FACETS	1	0.992	1	0.801	0.762	0.839	CLONAL	2	TRUE	0	0.54260942648441	3		450	593	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325777	30325777	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	45	237	0	ENST00000322652.5:c.1975C>T	p.His659Tyr	p.H659Y	ENST00000322652	NM_015355.2	659	Cat/Tat	16/16	0.54260942648441	3	FACETS	0.882	0.748	1	0.294	0.249	0.343	CLONAL	1	TRUE	0	0.54260942648441	3		237	239	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375537	40375537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567662106	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	139	530	0	ENST00000293328.3:c.413C>T	p.Ser138Phe	p.S138F	ENST00000293328	NM_012448.3	138	tCc/tTc	5/19	0.54260942648441	3	FACETS	1	0.977	1	0.398	0.364	0.433	CLONAL	1	TRUE	0	0.54260942648441	3		530	546	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441907	40441907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	107	754	0	ENST00000345506.4:c.152C>T	p.Pro51Leu	p.P51L	ENST00000345506	NM_003152.3	51	cCc/cTc	4/20	0.54260942648441	3	FACETS	0.69	0.619	0.765	0.23	0.206	0.255	SUBCLONAL	1	TRUE	0	0.54260942648441	3		754	727	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40856677	40856677	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs376492983	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	62	377	0	ENST00000428826.2:c.1960C>T	p.Arg654Ter	p.R654*	ENST00000428826		654	Cga/Tga	18/21	0.54260942648441	3	FACETS	0.755	0.655	0.862	0.252	0.218	0.288	SUBCLONAL	1	TRUE	0	0.54260942648441	3		377	385	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780673	56780673	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751528808	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	87	380	0	ENST00000337432.4:c.688C>T	p.Leu230Phe	p.L230F	ENST00000337432	NM_058216.2	230	Ctt/Ttt	4/9	0.54260942648441	3	FACETS	1	0.97	1	0.417	0.372	0.463	CLONAL	1	TRUE	0	0.54260942648441	3		380	326	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526135	66526135	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	46	299	0	ENST00000358598.2:c.966T>A	p.Asp322Glu	p.D322E	ENST00000358598	NM_212471.2	322	gaT/gaA	10/11	0.54260942648441	3	FACETS	0.496	0.418	0.581	0.165	0.139	0.194	SUBCLONAL	1	TRUE	0	0.54260942648441	3		299	435	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222472	2222472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	75	566	0	ENST00000398665.3:c.3304G>A	p.Gly1102Ser	p.G1102S	ENST00000398665	NM_032482.2	1102	Ggc/Agc	24/28	0.356306156135118	3	FACETS	0.795	0.699	0.897	0.398	0.349	0.449	SUBCLONAL	1	TRUE	1	0.54260942648441	3		566	442	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267775	7267775	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	84	536	0	ENST00000302850.5:c.233T>C	p.Phe78Ser	p.F78S	ENST00000302850	NM_000208.2	78	tTc/tCc	2/22	0.356306156135118	3	FACETS	0.761	0.674	0.854	0.381	0.337	0.427	SUBCLONAL	1	TRUE	1	0.54260942648441	3		536	517	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290058	15290058	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770044132	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	74	644	0	ENST00000263388.2:c.3496C>T	p.Pro1166Ser	p.P1166S	ENST00000263388	NM_000435.2	1166	Cca/Tca	22/33	0.356306156135118	3	FACETS	0.741	0.651	0.838	0.37	0.325	0.419	SUBCLONAL	1	TRUE	1	0.54260942648441	3		644	468	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279700	18279700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	53	416	1	ENST00000222254.8:c.1973C>T	p.Ser658Phe	p.S658F	ENST00000222254	NM_005027.3	658	tCc/tTc	15/16	0.356306156135118	3	FACETS	0.73	0.626	0.844	0.365	0.313	0.422	SUBCLONAL	1	TRUE	1	0.54260942648441	3		417	340	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976432	18976432	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	83	694	0	ENST00000262803.5:c.3082C>T	p.Pro1028Ser	p.P1028S	ENST00000262803	NM_002911.3	1028	Cct/Tct	22/24	0.356306156135118	3	FACETS	0.734	0.649	0.824	0.367	0.324	0.412	SUBCLONAL	1	TRUE	1	0.54260942648441	3		694	530	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792646	33792647	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	13	65	0	ENST00000498907.2:c.674_675delinsTT	p.Pro225Leu	p.P225L	ENST00000498907	NM_004364.3	225	cCC/cTT	1/1	0.356306156135118	3	FACETS	0.491	0.353	0.657	0.246	0.176	0.329	SUBCLONAL	1	TRUE	1	0.54260942648441	3		65	124	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215923	36215923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	111	563	0	ENST00000222270.7:c.3463C>T	p.Pro1155Ser	p.P1155S	ENST00000222270	NM_014727.1	1155	Ccc/Tcc	10/37	0.356306156135118	3	FACETS	0.913	0.823	1	0.456	0.411	0.504	CLONAL	1	TRUE	1	0.54260942648441	3		563	570	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223989	36223990	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	194	727	2	ENST00000222270.7:c.6539_6540delinsTT	p.Ala2180Val	p.A2180V	ENST00000222270	NM_014727.1	2180	gCC/gTT	28/37	0.356306156135118	3	FACETS	0.826	0.77	0.884	0.826	0.77	0.884	CLONAL	2	TRUE	1	0.54260942648441	3		729	550	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918082	50918082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	68	564	0	ENST00000440232.2:c.2399C>T	p.Pro800Leu	p.P800L	ENST00000440232	NM_002691.3	800	cCa/cTa	20/27	0.356306156135118	3	FACETS	0.85	0.743	0.964	0.425	0.371	0.482	CLONAL	1	TRUE	1	0.54260942648441	3		564	375	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976476	25976476	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	93	334	0	ENST00000435504.4:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000435504		357	Cga/Tga	11/13	0.54260942648441	4	FACETS	0.769	0.69	0.851	0.512	0.46	0.567	SUBCLONAL	2	TRUE	1	0.54260942648441	4		334	344	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61717801	61717801	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	58	443	0	ENST00000401558.2:c.1998T>A	p.Asp666Glu	p.D666E	ENST00000401558	NM_003400.3	666	gaT/gaA	17/25	0.54260942648441	4	FACETS	0.718	0.618	0.827	0.239	0.206	0.276	SUBCLONAL	1	TRUE	1	0.54260942648441	4		443	459	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248617	212248617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765120252	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	86	465	0	ENST00000342788.4:c.3650G>A	p.Gly1217Glu	p.G1217E	ENST00000342788	NM_005235.2	1217	gGa/gAa	28/28	0.441601166481596	3	FACETS	0.814	0.723	0.911	0.407	0.361	0.456	CLONAL	1	TRUE	1	0.54260942648441	3		465	495	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660866	227660867	+	missense_variant	Missense_Mutation	DNP	CA	CA	AT	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	119	530	0	ENST00000305123.5:c.2588_2589delinsAT	p.Leu863His	p.L863H	ENST00000305123	NM_005544.2	863	cTG/cAT	1/2	0.441601166481596	3	FACETS	0.754	0.687	0.822	0.754	0.687	0.822	SUBCLONAL	2	TRUE	1	0.54260942648441	3		530	370	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543565	9543565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	71	424	0	ENST00000353224.5:c.1589C>T	p.Ala530Val	p.A530V	ENST00000353224	NM_177990.2	530	gCc/gTc	6/10	0.441601166481596	3	FACETS	0.613	0.535	0.696	0.306	0.267	0.348	SUBCLONAL	1	TRUE	1	0.54260942648441	3		424	543	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546575	9546576	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	120	430	0	ENST00000353224.5:c.1446_1447delinsTT	p.Arg483Trp	p.R483W	ENST00000353224	NM_177990.2	482	ctCCgg/ctTTgg	5/10	0.441601166481596	3	FACETS	1	0.93	1	0.515	0.467	0.565	CLONAL	1	TRUE	1	0.54260942648441	3		430	546	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561309	9561309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760330867	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	58	373	0	ENST00000353224.5:c.473C>T	p.Pro158Leu	p.P158L	ENST00000353224	NM_177990.2	158	cCg/cTg	4/10	0.441601166481596	3	FACETS	0.739	0.637	0.848	0.369	0.318	0.424	SUBCLONAL	1	TRUE	1	0.54260942648441	3		373	368	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024366	31024366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	93	544	0	ENST00000375687.4:c.3851C>T	p.Pro1284Leu	p.P1284L	ENST00000375687	NM_015338.5	1284	cCa/cTa	13/13	0.441601166481596	3	FACETS	0.716	0.637	0.799	0.358	0.318	0.4	SUBCLONAL	1	TRUE	1	0.54260942648441	3		544	609	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012615	36012615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	71	279	0	ENST00000358208.4:c.59C>T	p.Pro20Leu	p.P20L	ENST00000358208		20	cCc/cTc	2/12	0.441601166481596	3	FACETS	0.794	0.696	0.899	0.397	0.348	0.45	SUBCLONAL	1	TRUE	1	0.54260942648441	3		279	419	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980798	40980798	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	86	556	0	ENST00000373198.4:c.1688C>T	p.Ser563Phe	p.S563F	ENST00000373198	NM_133170.3	563	tCc/tTc	10/32	0.441601166481596	3	FACETS	0.687	0.608	0.77	0.343	0.304	0.385	SUBCLONAL	1	TRUE	1	0.54260942648441	3		556	587	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420005	41420005	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	80	465	0	ENST00000373198.4:c.316C>T	p.His106Tyr	p.H106Y	ENST00000373198	NM_133170.3	106	Cat/Tat	3/32	0.441601166481596	3	FACETS	0.692	0.61	0.779	0.346	0.305	0.39	SUBCLONAL	1	TRUE	1	0.54260942648441	3		465	542	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945284	54945284	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	123	306	0	ENST00000312783.6:c.1142C>A	p.Pro381His	p.P381H	ENST00000312783	NM_198436.1	381	cCc/cAc	10/10	0.441601166481596	3	FACETS	0.783	0.716	0.852	0.783	0.716	0.852	SUBCLONAL	2	TRUE	1	0.54260942648441	3		306	368	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660132	12660132	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1179404518	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	84	410	0	ENST00000251849.4:c.89C>A	p.Pro30His	p.P30H	ENST00000251849	NM_002880.3	30	cCt/cAt	2/17	0.441601166481596	3	FACETS	0.802	0.71	0.899	0.401	0.355	0.45	CLONAL	1	TRUE	1	0.54260942648441	3		410	491	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164327	47164327	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	51	276	0	ENST00000409792.3:c.1799T>C	p.Leu600Ser	p.L600S	ENST00000409792	NM_014159.6	600	tTa/tCa	3/21	0.441601166481596	3	FACETS	1	0.962	1	0.683	0.59	0.78	CLONAL	1	TRUE	1	0.54260942648441	3		276	175	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164573	47164573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	24	272	0	ENST00000409792.3:c.1553C>T	p.Ser518Phe	p.S518F	ENST00000409792	NM_014159.6	518	tCt/tTt	3/21	0.441601166481596	3	FACETS	0.491	0.386	0.611	0.246	0.193	0.306	SUBCLONAL	1	TRUE	1	0.54260942648441	3		272	229	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405915	49405915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866298036	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	112	585	0	ENST00000418115.1:c.223C>T	p.Pro75Ser	p.P75S	ENST00000418115	NM_001664.2	75	Cca/Tca	3/5	0.441601166481596	3	FACETS	0.914	0.825	1	0.457	0.412	0.504	CLONAL	1	TRUE	1	0.54260942648441	3		585	574	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935637	49935637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	69	498	2	ENST00000296474.3:c.1727C>T	p.Pro576Leu	p.P576L	ENST00000296474	NM_002447.2	576	cCc/cTc	5/20	0.441601166481596	3	FACETS	0.665	0.581	0.756	0.333	0.29	0.378	SUBCLONAL	1	TRUE	1	0.54260942648441	3		500	486	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588752	52588752	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	77	532	0	ENST00000394830.3:c.4276A>T	p.Ile1426Phe	p.I1426F	ENST00000394830	NM_018313.4	1426	Atc/Ttc	27/30	0.441601166481596	3	FACETS	0.783	0.689	0.882	0.391	0.344	0.441	SUBCLONAL	1	TRUE	1	0.54260942648441	3		532	461	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637690	52637690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239654517	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	98	380	0	ENST00000394830.3:c.2626C>T	p.Arg876Cys	p.R876C	ENST00000394830	NM_018313.4	876	Cgt/Tgt	18/30	0.441601166481596	3	FACETS	0.838	0.759	0.919	0.838	0.759	0.919	CLONAL	2	TRUE	1	0.54260942648441	3		380	274	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72897449	72897449	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	45	396	0	ENST00000325599.8:c.43C>G	p.Leu15Val	p.L15V	ENST00000325599	NM_018130.2	15	Ctg/Gtg	1/11	0.441601166481596	3	FACETS	0.496	0.417	0.583	0.248	0.208	0.292	SUBCLONAL	1	TRUE	1	0.54260942648441	3		396	425	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443345	187443345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	83	396	1	ENST00000232014.4:c.1781G>A	p.Arg594Gln	p.R594Q	ENST00000232014	NM_001130845.1	594	cGa/cAa	8/10	0.441601166481596	3	FACETS	0.857	0.759	0.96	0.428	0.379	0.48	CLONAL	1	TRUE	1	0.54260942648441	3		397	454	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526096	189526096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	156	520	0	ENST00000264731.3:c.360G>A	p.Met120Ile	p.M120I	ENST00000264731	NM_003722.4	120	atG/atA	4/14	0.441601166481596	3	FACETS	1	0.986	1	0.663	0.611	0.718	CLONAL	1	TRUE	1	0.54260942648441	3		520	551	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1941432	1941433	+	missense_variant	Missense_Mutation	DNP	CT	CT	TA	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	82	543	0	ENST00000382891.5:c.1808_1809delinsTA	p.Ala603Val	p.A603V	ENST00000382891	NM_133335.3	603	gCT/gTA	9/22	0.356306156135118	3	FACETS	0.733	0.648	0.824	0.367	0.324	0.412	SUBCLONAL	1	TRUE	1	0.54260942648441	3		543	524	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1959680	1959680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868806171	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	39	272	1	ENST00000382891.5:c.2902C>T	p.Arg968Cys	p.R968C	ENST00000382891	NM_133335.3	968	Cgt/Tgt	16/22	0.356306156135118	3	FACETS	0.603	0.502	0.715	0.302	0.251	0.358	SUBCLONAL	1	TRUE	1	0.54260942648441	3		273	303	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139714	55139714	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600186	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	53	385	0	ENST00000257290.5:c.1375G>A	p.Glu459Lys	p.E459K	ENST00000257290	NM_006206.4	459	Gaa/Aaa	10/23	0.356306156135118	3	FACETS	0.696	0.596	0.804	0.348	0.298	0.402	SUBCLONAL	1	TRUE	1	0.54260942648441	3		385	357	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984930	55984930	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	75	409	0	ENST00000263923.4:c.199C>T	p.Gln67Ter	p.Q67*	ENST00000263923	NM_002253.2	67	Cag/Tag	3/30	0.356306156135118	3	FACETS	1	0.918	1	0.525	0.463	0.59	CLONAL	1	TRUE	1	0.54260942648441	3		409	335	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280068	66280068	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	45	271	2	ENST00000273854.3:c.1621C>T	p.Arg541Ter	p.R541*	ENST00000273854	NM_004439.5	541	Cga/Tga	7/18	0.356306156135118	3	FACETS	0.698	0.59	0.817	0.349	0.295	0.409	SUBCLONAL	1	TRUE	1	0.54260942648441	3		273	302	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	119	366	0				ENST00000310581	NM_198253.2	-/1132			0.302229159786734	5	FACETS	1	0.979	1	0.824	0.753	0.895	INDETERMINATE	2	TRUE	2	0.54260942648441	5		366	322	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056973	180056974	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	347	705	2	ENST00000261937.6:c.645_646delinsTT	p.Leu216Phe	p.L216F	ENST00000261937	NM_182925.4	215	ttCCtt/ttTTtt	5/30	0.287909634066849	5	FACETS	1	0.986	1			1	INDETERMINATE	4	TRUE	NA	0.54260942648441	5		707	550	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187470	32187470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	78	663	2	ENST00000375023.3:c.1409C>T	p.Ser470Phe	p.S470F	ENST00000375023	NM_004557.3	470	tCc/tTc	8/30	0.54260942648441	4	FACETS	0.661	0.581	0.747	0.22	0.193	0.249	SUBCLONAL	1	TRUE	1	0.54260942648441	4		665	671	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187546	32187546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	87	583	0	ENST00000375023.3:c.1333C>T	p.Pro445Ser	p.P445S	ENST00000375023	NM_004557.3	445	Ccc/Tcc	8/30	0.54260942648441	4	FACETS	0.758	0.671	0.85	0.253	0.223	0.284	SUBCLONAL	1	TRUE	1	0.54260942648441	4		583	653	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821169	32821169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1439343261	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	114	683	1	ENST00000354258.4:c.425C>T	p.Ser142Phe	p.S142F	ENST00000354258	NM_000593.5	142	tCc/tTc	1/11	0.54260942648441	4	FACETS	0.91	0.82	1	0.303	0.273	0.335	CLONAL	1	TRUE	1	0.54260942648441	4		684	712	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109311890	109311890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	74	512	0	ENST00000436639.2:c.1382G>A	p.Arg461Lys	p.R461K	ENST00000436639	NM_014454.2	461	aGa/aAa	8/10	0.441601166481596	3	FACETS	0.808	0.711	0.913	0.404	0.355	0.457	CLONAL	1	TRUE	1	0.54260942648441	3		512	429	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522149	157522149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	128	517	1	ENST00000346085.5:c.4421C>T	p.Pro1474Leu	p.P1474L	ENST00000346085	NM_020732.3	1474	cCc/cTc	18/20	0.441601166481596	3	FACETS	0.833	0.764	0.904	0.833	0.764	0.904	CLONAL	2	TRUE	1	0.54260942648441	3		518	360	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729388	41729388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	102	534	1	ENST00000242208.4:c.1141C>T	p.His381Tyr	p.H381Y	ENST00000242208	NM_002192.2	381	Cat/Tat	3/3	0.206436264682583	5	FACETS	1	0.925	1	0.347	0.31	0.386	INDETERMINATE	1	TRUE	2	0.54260942648441	5		535	655	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221807	55221807	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	203	600	0	ENST00000275493.2:c.851A>C	p.Lys284Thr	p.K284T	ENST00000275493	NM_005228.3	284	aAa/aCa	7/28	0.206436264682583	5	FACETS	0.925	0.86	0.991	0.616	0.573	0.661	INDETERMINATE	2	TRUE	2	0.54260942648441	5		600	734	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359060	81359060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	49	368	0	ENST00000222390.5:c.901G>A	p.Glu301Lys	p.E301K	ENST00000222390	NM_000601.4	301	Gaa/Aaa	8/18	0.206436264682583	5	FACETS	0.778	0.66	0.907	0.259	0.22	0.303	INDETERMINATE	1	TRUE	2	0.54260942648441	5		368	421	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381466	81381466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	119	346	0	ENST00000222390.5:c.595G>A	p.Glu199Lys	p.E199K	ENST00000222390	NM_000601.4	199	Gaa/Aaa	5/18	0.206436264682583	5	FACETS	0.859	0.78	0.941	0.573	0.52	0.628	INDETERMINATE	2	TRUE	2	0.54260942648441	5		346	463	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434503	140434503	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758134174	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	140	323	0	ENST00000288602.6:c.2195C>T	p.Ser732Phe	p.S732F	ENST00000288602	NM_004333.4	732	tCc/tTc	18/18	0.206436264682583	5	FACETS	0.919	0.842	0.999	0.613	0.561	0.666	INDETERMINATE	2	TRUE	2	0.54260942648441	5		323	509	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129878	69129878	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	115	298	0	ENST00000288368.4:c.4632A>C	p.Gln1544His	p.Q1544H	ENST00000288368	NM_024870.2	1544	caA/caC	38/40	0.339179058197132	3	FACETS	1	0.984	1	0.711	0.646	0.778	CLONAL	1	TRUE	1	0.54260942648441	3		298	379	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317926	8317926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	59	349	0	ENST00000356435.5:c.5687C>T	p.Ser1896Phe	p.S1896F	ENST00000356435		1896	tCc/tTc	35/35	0.464294943990363	2	FACETS	0.695	0.602	0.795	0.347	0.301	0.398	SUBCLONAL	1	TRUE	0	0.54260942648441	2		349	313	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499693	8499693	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	84	428	0	ENST00000356435.5:c.2276C>T	p.Pro759Leu	p.P759L	ENST00000356435		759	cCc/cTc	14/35	0.464294943990363	2	FACETS	0.722	0.641	0.808	0.361	0.32	0.404	SUBCLONAL	1	TRUE	0	0.54260942648441	2		428	429	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528644	8528644	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	67	350	0	ENST00000356435.5:c.488T>G	p.Phe163Cys	p.F163C	ENST00000356435		163	tTc/tGc	4/35	0.464294943990363	2	FACETS	0.976	0.859	1	0.488	0.429	0.55	CLONAL	1	TRUE	0	0.54260942648441	2		350	253	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915838	127915838	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	71	427	0	ENST00000373547.4:c.643C>T	p.Leu215Phe	p.L215F	ENST00000373547	NM_002721.4	215	Ctt/Ttt	6/7	0.464294943990363	2	FACETS	0.743	0.653	0.84	0.372	0.326	0.42	SUBCLONAL	1	TRUE	0	0.54260942648441	2		427	352	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615124	100615124	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	109	223	0	ENST00000308731.7:c.791T>C	p.Ile264Thr	p.I264T	ENST00000308731	NM_000061.2	264	aTt/aCt	9/19	0.287909634066849	2	FACETS	1	0.943	1			1	INDETERMINATE	2	TRUE	NA	0.54260942648441	2		223	196	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123499651	123499651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	61	232	0	ENST00000371139.4:c.178G>A	p.Glu60Lys	p.E60K	ENST00000371139	NM_001114937.2	60	Gaa/Aaa	2/4	0.287909634066849	2	FACETS	1	0.926	1			1	INDETERMINATE	1	TRUE	NA	0.54260942648441	2		232	208	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152859948	152860038	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGAACAGAGACCATGGCTTGAGCCTCTCCAAACAGGCACCAGTTCCCCAGTATGTACCTTGTGTGGATGCTGGAAGGAGACCTGGAAGCGC	AGAACAGAGACCATGGCTTGAGCCTCTCCAAACAGGCACCAGTTCCCCAGTATGTACCTTGTGTGGATGCTGGAAGGAGACCTGGAAGCGC	-	novel	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	85	98	0	ENST00000406277.2:c.390_423+57del		p.X130_splice	ENST00000406277	NM_152274.4	130		5/7	0.287909634066849		FACETS		0.926	1				INDETERMINATE	3	TRUE	NA	0.54260942648441	2		98	106	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223989	36223989	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868077834	NA	P-0040623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	194	725	1	ENST00000222270.7:c.6539C>T	p.Ala2180Val	p.A2180V	ENST00000222270	NM_014727.1	2180	gCc/gTc	28/37	0.356306156135118	3	FACETS	0.826	0.77	0.884	0.826	0.77	0.884	CLONAL	2	TRUE	1	0.54260942648441	3		726	550	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412612	63412613	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTGACCTTGCTCTTCCGGTGACGGCG	novel	NA	P-0040657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	166	275	0	ENST00000330258.3:c.529_554dup	p.Gly186AlafsTer32	p.G186Afs*32	ENST00000330258	NM_152424.3	185	act/acCGCCGTCACCGGAAGAGCAAGGTCACt	2/2	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.519947349431401	1		275	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0040675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	131	744	2	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.277028986470662	1	FACETS	0.979	0.889	1	0.979	0.889	1	CLONAL	1	TRUE	0	0.277028986470662	1		746	832	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057713	27057713	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	162	960	0	ENST00000324856.7:c.1423del	p.Ser475ValfsTer144	p.S475Vfs*144	ENST00000324856	NM_006015.4	474	cAa/ca	3/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.277028986470662	2		960	1007	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262393	39262393	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	75	738	0	ENST00000402219.2:c.1034C>A	p.Ala345Asp	p.A345D	ENST00000402219	NM_005633.3	345	gCc/gAc	8/23	1	2	FACETS	0.952	0.835	1	0.952	0.835	1	CLONAL	1	TRUE	1	0.277028986470662	2		738	569	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44910953	44910953	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0040675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	31	161	0	ENST00000377967.4:c.655-1G>C		p.X219_splice	ENST00000377967	NM_021140.2	219			0.0454597001159476	2	FACETS	0.973	0.804	1			1	INDETERMINATE	2	TRUE	NA	0.277028986470662	2		161	115	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44911004	44911004	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	42	217	0	ENST00000377967.4:c.705G>C	p.Glu235Asp	p.E235D	ENST00000377967	NM_021140.2	235	gaG/gaC	9/29	0.0454597001159476	2	FACETS	0.887	0.751	1			1	INDETERMINATE	2	TRUE	NA	0.277028986470662	2		217	171	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0040677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	37	60	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	0.128096088584759	0	FACETS	0.907	0.777	1			1	INDETERMINATE	2	FALSE	0	0.326774127985497	0		60	84	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0040677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	55	82	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	0.183007033266127	1	FACETS	1	0.946	1	1	0.982	1	INDETERMINATE	2	FALSE	0	0.326774127985497	1		82	124	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0040686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	206	704	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.367181458754095	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.367181458754095	1		704	897	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0040686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	98	385	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.367181458754095	2		385	486	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922694	44922694	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397514628	NA	P-0040686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	93	355	0	ENST00000377967.4:c.1555C>T	p.Arg519Ter	p.R519*	ENST00000377967	NM_021140.2	519	Cga/Tga	16/29	0.367181458754095	1	FACETS	0.856	0.764	0.953	0.856	0.764	0.953	CLONAL	1	TRUE	0	0.367181458754095	1		355	483	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223523	36223523	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368364777	NA	P-0040686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	175	748	0	ENST00000222270.7:c.6073G>A	p.Glu2025Lys	p.E2025K	ENST00000222270	NM_014727.1	2025	Gag/Aag	28/37	0.189923465698122	3	FACETS	1	0.966	1	0.546	0.502	0.591	INDETERMINATE	1	TRUE	1	0.367181458754095	3		748	1034	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0040687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	44	444	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.982	0.823	1	0.982	0.823	1	CLONAL	1	TRUE	1	0.18	2		444	498	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044970	47044970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	68	801	1	ENST00000377604.3:c.2296C>T	p.Arg766Cys	p.R766C	ENST00000377604	NM_001204468.1	766	Cgc/Tgc	20/24	0.181780865654854	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	0	0.18	1		802	649	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102199656	102199661	+	inframe_deletion	In_Frame_Del	DEL	ATGAAA	ATGAAA	-	novel	NA	P-0040687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	21	336	0	ENST00000263464.3:c.1064_1069del	p.Glu355_Asn356del	p.E355_N356del	ENST00000263464	NM_001165.4	354	gATGAAAat/gat	5/9	1	2	FACETS	0.636	0.489	0.807	0.636	0.489	0.807	SUBCLONAL	1	TRUE	1	0.18	2		336	367	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912532	32912533	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	rs886037800	NA	P-0040687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	40	411	1	ENST00000380152.3:c.4041_4042del	p.Cys1348TyrfsTer3	p.C1348Yfs*3	ENST00000380152		1347	gTT/g	11/27	1	2	FACETS	0.871	0.724	1	0.871	0.724	1	CLONAL	1	TRUE	1	0.18	2		412	510	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787833	135787833	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs118203447	NA	P-0040687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	45	389	1	ENST00000298552.3:c.749T>C	p.Leu250Ser	p.L250S	ENST00000298552	NM_001162426.1	250	tTa/tCa	9/23	1	2	FACETS	0.99	0.832	1	0.99	0.832	1	CLONAL	1	TRUE	1	0.18	2		390	505	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416114	49416114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	86	545	0	ENST00000301067.7:c.16361G>A	p.Arg5454Gln	p.R5454Q	ENST00000301067	NM_003482.3	5454	cGa/cAa	52/54	0.458894877416576	3	FACETS	0.599	0.531	0.672	0.3	0.265	0.336	SUBCLONAL	1	TRUE	1	0.686119040650957	3		545	562	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620140	21620140	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767021401	NA	P-0040697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	105	597	0	ENST00000382592.4:c.26C>T	p.Thr9Met	p.T9M	ENST00000382592	NM_014572.2	9	aCg/aTg	2/8	0.458248563537386	4	FACETS	0.531	0.475	0.591	0.177	0.158	0.197	SUBCLONAL	1	TRUE	1	0.686119040650957	4		597	972	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3645656	3645656	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	40	853	1	ENST00000294008.3:c.1963T>C	p.Phe655Leu	p.F655L	ENST00000294008	NM_032444.2	655	Ttt/Ctt	9/15	0.370547791835104	2	FACETS	0.161	0.133	0.193	0.081	0.066	0.097	INDETERMINATE	1	TRUE	0	0.686119040650957	2		854	722	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867293	68867293	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	424	638	0	ENST00000261769.5:c.2542del	p.Leu848Ter	p.L848*	ENST00000261769	NM_004360.3	847	tCc/tc	16/16	0.68229743975454	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.686119040650957	3		638	829	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576918	7576924	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TGGGCAG	TGGGCAG	-	novel	NA	P-0040697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	288	746	0	ENST00000269305.4:c.922_928del	p.Leu308ThrfsTer35	p.L308Tfs*35	ENST00000269305	NM_001126112.2	308	CTGCCCAac/ac	9/11	0.684502069748046	1	FACETS	0.973	0.925	1	0.973	0.925	1	CLONAL	1	TRUE	0	0.686119040650957	1		746	567	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556101	29556101	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	28	243	0	ENST00000356175.3:c.2468G>C	p.Gly823Ala	p.G823A	ENST00000356175	NM_000267.3	823	gGa/gCa	21/57	0.148621202171747	5	FACETS	0.531	0.425	0.651	0.177	0.141	0.217	INDETERMINATE	1	TRUE	2	0.686119040650957	5		243	312	SUCCESS
APC	324	MSKCC	GRCh37	5	112175352	112175359	+	frameshift_variant	Frame_Shift_Del	DEL	TTTCTTCA	TTTCTTCA	-	novel	NA	P-0040697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	40	286	0	ENST00000257430.4:c.4061_4068del	p.Phe1354TrpfsTer18	p.F1354Wfs*18	ENST00000257430	NM_000038.5	1354	tTTTCTTCA/t	16/16	0.261316195187531	2	FACETS	0.447	0.373	0.527	0.223	0.186	0.264	INDETERMINATE	1	TRUE	0	0.686119040650957	2		286	261	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87366972	87366972	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	50	673	0	ENST00000277120.3:c.1368G>C	p.Leu456Phe	p.L456F	ENST00000277120		456	ttG/ttC	12/19	0.355197914694165	1	FACETS	0.152	0.128	0.178	0.152	0.128	0.178	INDETERMINATE	1	TRUE	0	0.686119040650957	1		673	630	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0040727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	283	678	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	0.38872319785218	2	FACETS	0.769	0.726	0.814	0.769	0.726	0.814	SUBCLONAL	2	TRUE	0	0.448550510459578	2		678	820	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678532	88678532	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	43	331	0	ENST00000360948.2:c.1004G>A	p.Trp335Ter	p.W335*	ENST00000360948	NM_001012338.2	335	tGg/tAg	9/19	0.290209992511926	5	FACETS	0.47	0.392	0.556			1	SUBCLONAL	1	TRUE	NA	0.448550510459578	5		331	683	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126172	2126172	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs45517262	NA	P-0040727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	153	463	0	ENST00000219476.3:c.2742+1G>T		p.X914_splice	ENST00000219476	NM_000548.3	914			0.137343207867837	4	FACETS	1	0.986	1	0.699	0.641	0.759	INDETERMINATE	1	TRUE	2	0.448550510459578	4		463	707	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164286	47164286	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	78	244	0	ENST00000409792.3:c.1840T>G	p.Ser614Ala	p.S614A	ENST00000409792	NM_014159.6	614	Tct/Gct	3/21	0.448550510459578	3	FACETS	1	0.94	1	0.55	0.486	0.618	CLONAL	1	TRUE	1	0.448550510459578	3		244	387	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	126	348	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.732821128609195	2		349	236	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0040728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	112	260	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	0.732821128609195	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.732821128609195	1		260	154	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95592924	95592924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755944755	NA	P-0040728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	129	284	0	ENST00000393063.1:c.896C>T	p.Ser299Leu	p.S299L	ENST00000393063	NM_030621.3	299	tCg/tTg	8/28	1	2	FACETS	0.967	0.887	1	0.967	0.887	1	CLONAL	1	TRUE	1	0.732821128609195	2		284	364	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395479	116395479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775965879	NA	P-0040728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	142	400	1	ENST00000397752.3:c.1772G>A	p.Arg591Gln	p.R591Q	ENST00000397752	NM_000245.2	591	cGg/cAg	6/21	0.622068461406617	4	FACETS	1	0.982	1	0.425	0.389	0.462	CLONAL	1	TRUE	1	0.732821128609195	4		401	527	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196472	67196472	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	215	518	0	ENST00000312629.5:c.98A>C	p.Glu33Ala	p.E33A	ENST00000312629	NM_003952.2	33	gAg/gCg	2/15	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.732821128609195	2		518	578	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024730	11024730	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	85	252	0	ENST00000327064.4:c.847G>A	p.Gly283Arg	p.G283R	ENST00000327064	NM_199141.1	283	Gga/Aga	6/16	0.69300657260414	2	FACETS	0.879	0.788	0.973	0.439	0.394	0.487	CLONAL	1	TRUE	0	0.732821128609195	2		252	264	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0040743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	99	496	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.27192932571673	2		496	575	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0040743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	99	399	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.751	0.673	0.832	1	0.982	1	SUBCLONAL	2	TRUE	1	0.27192932571673	2		399	485	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0040761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	100	308	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.884	0.795	0.977	0.884	0.795	0.977	CLONAL	1	TRUE	1	0.541285163339646	2		308	418	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0040761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	106	397	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.842	0.759	0.929	0.842	0.759	0.929	CLONAL	1	TRUE	1	0.541285163339646	2		397	465	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0040761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	197	716	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.541285163339646	2		716	713	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	132	560	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.907	0.827	0.989	0.907	0.827	0.989	CLONAL	1	TRUE	1	0.541285163339646	2		560	538	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717699	89717699	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554825210	NA	P-0040761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	150	520	0	ENST00000371953.3:c.724G>T	p.Glu242Ter	p.E242*	ENST00000371953	NM_000314.4	242	Gag/Tag	7/9	1	2	FACETS	0.924	0.848	1	0.924	0.848	1	CLONAL	1	TRUE	1	0.541285163339646	2		520	600	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857217	9857217	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199696775	NA	P-0040761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	171	609	3	ENST00000330684.3:c.4184C>T	p.Ala1395Val	p.A1395V	ENST00000330684	NM_001134407.1	1395	gCg/gTg	13/13	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.541285163339646	2		612	609	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717696	89717698	+	frameshift_variant	Frame_Shift_Del	DEL	TTT	TTT	G	novel	NA	P-0040761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	155	514	0	ENST00000371953.3:c.721_723delinsG	p.Phe241GlyfsTer11	p.F241Gfs*11	ENST00000371953	NM_000314.4	241	TTT/G	7/9	1	2	FACETS	0.948	0.872	1	0.948	0.872	1	CLONAL	1	TRUE	1	0.541285163339646	2		514	604	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117410	115117410	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	146	387	0	ENST00000257566.3:c.764T>A	p.Val255Glu	p.V255E	ENST00000257566	NM_016569.3	255	gTa/gAa	4/8	1	2	FACETS	0.88	0.81	0.952	0.88	0.81	0.952	CLONAL	1	TRUE	1	0.734124326770661	2		387	452	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181855	56181855	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	119	345	0	ENST00000399503.3:c.4079T>A	p.Leu1360His	p.L1360H	ENST00000399503	NM_005921.1	1360	cTc/cAc	17/20	1	2	FACETS	0.732	0.665	0.801	0.732	0.665	0.801	SUBCLONAL	1	TRUE	1	0.734124326770661	2		345	443	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183241	56183241	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	179	475	0	ENST00000399503.3:c.4151T>G	p.Leu1384Arg	p.L1384R	ENST00000399503	NM_005921.1	1384	cTa/cGa	18/20	1	2	FACETS	0.73	0.675	0.786	0.73	0.675	0.786	SUBCLONAL	1	TRUE	1	0.734124326770661	2		475	668	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0040784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	379	621	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.859462748652838	1	FACETS	0.538	0.512	0.564	0.538	0.512	0.564	SUBCLONAL	1	TRUE	0	0.859462748652838	1		622	935	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040101	180040101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909652	NA	P-0040784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	270	304	1	ENST00000261937.6:c.3341C>T	p.Pro1114Leu	p.P1114L	ENST00000261937	NM_182925.4	1114	cCg/cTg	25/30	1	2	FACETS	0.709	0.667	0.752	0.709	0.667	0.752	SUBCLONAL	1	TRUE	1	0.859462748652838	2		305	886	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552641	18552641	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	90	290	0	ENST00000266497.5:c.2052C>A	p.Cys684Ter	p.C684*	ENST00000266497		684	tgC/tgA	14/31	1	2	FACETS	0.472	0.42	0.526	0.472	0.42	0.526	SUBCLONAL	1	TRUE	1	0.859462748652838	2		290	444	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459018	120459018	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	246	673	0	ENST00000256646.2:c.6327G>C	p.Lys2109Asn	p.K2109N	ENST00000256646	NM_024408.3	2109	aaG/aaC	34/34	0.56991493909986	6	FACETS	1	0.973	1	0.532	0.499	0.566	CLONAL	2	TRUE	2	0.710983949664276	6		673	787	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456753	32456753	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1212035248	NA	P-0040794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	82	626	0	ENST00000332351.3:c.139G>A	p.Glu47Lys	p.E47K	ENST00000332351	NM_024426.4	47	Gag/Aag	1/10	0.296782331747693	5	FACETS	0.801	0.707	0.902	0.267	0.235	0.301	INDETERMINATE	1	TRUE	2	0.710983949664276	5		626	595	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173601	108173601	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	19	354	0	ENST00000278616.4:c.5341G>C	p.Asp1781His	p.D1781H	ENST00000278616	NM_000051.3	1781	Gac/Cac	36/63	0.296782331747693	5	FACETS	0.324	0.245	0.416	0.108	0.081	0.139	INDETERMINATE	1	TRUE	2	0.710983949664276	5		354	341	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21643138	21643138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	67	482	0	ENST00000421138.2:c.389C>T	p.Ser130Leu	p.S130L	ENST00000421138		130	tCa/tTa	5/16	0.710983949664276	3	FACETS	0.525	0.457	0.598	0.262	0.228	0.299	SUBCLONAL	1	TRUE	1	0.710983949664276	3		482	487	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245398	46245398	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs373042061	NA	P-0040794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	46	456	0	ENST00000334344.6:c.3492C>G	p.Phe1164Leu	p.F1164L	ENST00000334344	NM_152641.2	1164	ttC/ttG	15/21	0.710983949664276	6	FACETS	0.551	0.463	0.648	0.138	0.115	0.162	SUBCLONAL	1	TRUE	2	0.710983949664276	6		456	569	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425224	49425224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	189	787	1	ENST00000301067.7:c.13264G>A	p.Glu4422Lys	p.E4422K	ENST00000301067	NM_003482.3	4422	Gag/Aag	39/54	0.710983949664276	6	FACETS	1	0.986	1	0.326	0.301	0.352	CLONAL	1	TRUE	2	0.710983949664276	6		788	988	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121804	2121804	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	207	783	0	ENST00000219476.3:c.1966G>C	p.Glu656Gln	p.E656Q	ENST00000219476	NM_000548.3	656	Gag/Cag	19/42	0.706398721269393	2	FACETS	0.961	0.915	1	0.961	0.915	1	CLONAL	2	TRUE	0	0.710983949664276	2		783	303	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779191	3779191	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	112	516	0	ENST00000262367.5:c.5857C>A	p.Pro1953Thr	p.P1953T	ENST00000262367	NM_004380.2	1953	Cct/Act	31/31	0.706398721269393	2	FACETS	0.966	0.904	1	0.966	0.904	1	CLONAL	2	TRUE	0	0.710983949664276	2		516	163	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779295	3779295	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	184	544	0	ENST00000262367.5:c.5753C>G	p.Pro1918Arg	p.P1918R	ENST00000262367	NM_004380.2	1918	cCa/cGa	31/31	0.706398721269393	2	FACETS	0.977	0.928	1	0.977	0.928	1	CLONAL	2	TRUE	0	0.710983949664276	2		544	265	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024633	14024633	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	34	315	0	ENST00000311895.7:c.859G>C	p.Asp287His	p.D287H	ENST00000311895	NM_005236.2	287	Gat/Cat	5/11	0.326391724375788	4	FACETS	0.458	0.375	0.552	0.229	0.187	0.276	INDETERMINATE	1	TRUE	2	0.710983949664276	4		315	357	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350233	89350233	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763544660	NA	P-0040794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	65	779	1	ENST00000301030.4:c.2717G>A	p.Arg906Gln	p.R906Q	ENST00000301030	NM_001256183.1	906	cGa/cAa	9/13	0.326391724375788	4	FACETS	0.446	0.386	0.511	0.223	0.193	0.256	INDETERMINATE	1	TRUE	2	0.710983949664276	4		780	701	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587782289	NA	P-0040794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	424	643	0	ENST00000269305.4:c.706T>A	p.Tyr236Asn	p.Y236N	ENST00000269305	NM_001126112.2	236	Tac/Aac	7/11	0.710983949664276	3	FACETS	1	0.983	1			1	CLONAL	3	TRUE	NA	0.710983949664276	3		643	532	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369257	40369257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1449203089	NA	P-0040794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	292	582	0	ENST00000293328.3:c.1301C>T	p.Ser434Leu	p.S434L	ENST00000293328	NM_012448.3	434	tCg/tTg	11/19	0.710983949664276	2	FACETS	0.901	0.863	0.938	0.901	0.863	0.938	CLONAL	2	TRUE	0	0.710983949664276	2		582	456	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550374	39550374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	58	343	0	ENST00000262039.4:c.485G>A	p.Arg162Lys	p.R162K	ENST00000262039	NM_002647.2	162	aGa/aAa	4/25	0.296389267141713	6	FACETS	0.966	0.833	1	0.322	0.277	0.37	INDETERMINATE	1	TRUE	3	0.710983949664276	6		343	409	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098380	11098380	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	114	707	0	ENST00000358026.2:c.898C>G	p.Gln300Glu	p.Q300E	ENST00000358026	NM_001128849.1	300	Cag/Gag	6/36	0.68285782490828	2	FACETS	0.908	0.827	0.993	0.454	0.413	0.497	CLONAL	1	TRUE	0	0.710983949664276	2		707	353	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383740	15383740	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	308	615	0	ENST00000263377.2:c.171G>T	p.Lys57Asn	p.K57N	ENST00000263377	NM_058243.2	57	aaG/aaT	2/20	0.415537857717698	5	FACETS	0.993	0.946	1			1	INDETERMINATE	3	TRUE	NA	0.710983949664276	5		615	601	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743942	41743942	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	133	867	0	ENST00000301178.4:c.877C>T	p.Gln293Ter	p.Q293*	ENST00000301178	NM_021913.4	293	Cag/Tag	7/20	NA	2	FACETS	0.701	0.639	0.764			1	INDETERMINATE	1	TRUE	NA	0.710983949664276	2		867	534	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0040794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	14	344	1	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.663547019114547	2	FACETS	0.165	0.119	0.221	0.083	0.059	0.111	SUBCLONAL	1	TRUE	0	0.710983949664276	2		345	238	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436649	52436649	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	185	633	0	ENST00000460680.1:c.2025C>G	p.Ile675Met	p.I675M	ENST00000460680	NM_004656.3	675	atC/atG	16/17	0.663547019114547	2	FACETS	0.798	0.752	0.844	0.798	0.752	0.844	SUBCLONAL	2	TRUE	0	0.710983949664276	2		633	326	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436679	52436679	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	167	620	0	ENST00000460680.1:c.1995G>C	p.Gln665His	p.Q665H	ENST00000460680	NM_004656.3	665	caG/caC	16/17	0.663547019114547	2	FACETS	0.794	0.745	0.841	0.794	0.745	0.841	SUBCLONAL	2	TRUE	0	0.710983949664276	2		620	296	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437587	52437587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	262	710	0	ENST00000460680.1:c.1574C>T	p.Ser525Phe	p.S525F	ENST00000460680	NM_004656.3	525	tCc/tTc	13/17	0.663547019114547	2	FACETS	0.95	0.909	0.989	0.95	0.909	0.989	CLONAL	2	TRUE	0	0.710983949664276	2		710	388	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437774	52437774	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	152	619	0	ENST00000460680.1:c.1387C>A	p.Leu463Met	p.L463M	ENST00000460680	NM_004656.3	463	Ctg/Atg	13/17	0.663547019114547	2	FACETS	0.795	0.744	0.845	0.795	0.744	0.845	SUBCLONAL	2	TRUE	0	0.710983949664276	2		619	269	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437782	52437782	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0040794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	148	644	0	ENST00000460680.1:c.1379C>G	p.Ser460Ter	p.S460*	ENST00000460680	NM_004656.3	460	tCa/tGa	13/17	0.663547019114547	2	FACETS	0.807	0.755	0.858	0.807	0.755	0.858	CLONAL	2	TRUE	0	0.710983949664276	2		644	258	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437826	52437826	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	211	715	0	ENST00000460680.1:c.1335C>G	p.Ile445Met	p.I445M	ENST00000460680	NM_004656.3	445	atC/atG	13/17	0.663547019114547	2	FACETS	0.919	0.874	0.962	0.919	0.874	0.962	CLONAL	2	TRUE	0	0.710983949664276	2		715	323	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437866	52437866	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	244	726	0	ENST00000460680.1:c.1295C>A	p.Ser432Tyr	p.S432Y	ENST00000460680	NM_004656.3	432	tCt/tAt	13/17	0.663547019114547	2	FACETS	0.956	0.914	0.997	0.956	0.914	0.997	CLONAL	2	TRUE	0	0.710983949664276	2		726	359	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438478	52438478	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	182	511	0	ENST00000460680.1:c.1241C>G	p.Ser414Cys	p.S414C	ENST00000460680	NM_004656.3	414	tCt/tGt	12/17	0.663547019114547	2	FACETS	0.895	0.847	0.942	0.895	0.847	0.942	CLONAL	2	TRUE	0	0.710983949664276	2		511	286	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442557	52442557	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747311942	NA	P-0040794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	212	465	0	ENST00000460680.1:c.188C>G	p.Ser63Cys	p.S63C	ENST00000460680	NM_004656.3	63	tCt/tGt	4/17	0.663547019114547	2	FACETS	0.885	0.84	0.928	0.885	0.84	0.928	CLONAL	2	TRUE	0	0.710983949664276	2		465	337	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536271	106536271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	56	405	0	ENST00000369096.4:c.238G>A	p.Glu80Lys	p.E80K	ENST00000369096	NM_001198.3	80	Gag/Aag	2/7	0.296782331747693	5	FACETS	0.806	0.692	0.929	0.269	0.23	0.31	INDETERMINATE	1	TRUE	2	0.710983949664276	5		405	404	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129338	152129338	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	122	600	3	ENST00000206249.3:c.291C>A	p.Phe97Leu	p.F97L	ENST00000206249	NM_000125.3	97	ttC/ttA	1/8	0.296782331747693	5	FACETS	1	0.971	1	0.391	0.355	0.43	INDETERMINATE	1	TRUE	2	0.710983949664276	5		603	604	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415066	116415066	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	94	561	1	ENST00000397752.3:c.3160G>T	p.Asp1054Tyr	p.D1054Y	ENST00000397752	NM_000245.2	1054	Gac/Tac	15/21	1	2	FACETS	0.958	0.865	1	0.958	0.865	1	CLONAL	1	TRUE	1	0.710983949664276	2		562	276	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866562	117866562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	64	452	0	ENST00000297338.2:c.1083G>A	p.Met361Ile	p.M361I	ENST00000297338	NM_006265.2	361	atG/atA	9/14	0.249995841454639	4	FACETS	0.997	0.87	1	0.498	0.435	0.566	INDETERMINATE	1	TRUE	2	0.710983949664276	4		452	309	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317908	8317908	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	132	413	0	ENST00000356435.5:c.5705A>G	p.Glu1902Gly	p.E1902G	ENST00000356435		1902	gAg/gGg	35/35	0.249995841454639	4	FACETS	0.868	0.797	0.94	0.868	0.797	0.94	INDETERMINATE	2	TRUE	2	0.710983949664276	4		413	366	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0040831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	21	309	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.362	0.278	0.46	0.362	0.278	0.46	SUBCLONAL	1	TRUE	1	0.272538694525513	2		309	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0040831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	49	481	3	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.392	0.33	0.46	0.392	0.33	0.46	SUBCLONAL	1	TRUE	1	0.272538694525513	2		484	918	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0040831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	17	554	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.297	0.221	0.388	0.297	0.221	0.388	SUBCLONAL	1	TRUE	1	0.272538694525513	2		554	420	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88677066	88677066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	32	591	0	ENST00000372037.3:c.851G>A	p.Arg284His	p.R284H	ENST00000372037	NM_004329.2	284	cGc/cAc	9/13	1	2	FACETS	0.444	0.359	0.54	0.444	0.359	0.54	SUBCLONAL	1	TRUE	1	0.272538694525513	2		591	529	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0040831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	14	261	0	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	1	2	FACETS	0.441	0.319	0.589	0.441	0.319	0.589	SUBCLONAL	1	TRUE	1	0.272538694525513	2		261	233	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913250	NA	P-0040846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	880	372	0	ENST00000369535.4:c.34G>T	p.Gly12Cys	p.G12C	ENST00000369535	NM_002524.4	12	Ggt/Tgt	2/7	0.620133942143118	8	FACETS	0.965	0.941	0.989	0.965	0.941	0.989	CLONAL	6	TRUE	2	0.620133942143118	8		372	1402	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291029	11291029	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	155	486	0	ENST00000361445.4:c.2732A>T	p.Asp911Val	p.D911V	ENST00000361445	NM_004958.3	911	gAt/gTt	18/58	0.620133942143118	3	FACETS	1	0.939	1	0.513	0.471	0.557	CLONAL	1	TRUE	1	0.620133942143118	3		486	638	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587481	29587481	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622348	NA	P-0040846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	50	513	1	ENST00000356175.3:c.4462C>T	p.Arg1488Cys	p.R1488C	ENST00000356175	NM_000267.3	1488	Cgt/Tgt	33/57	0.608977766706059	4	FACETS	0.302	0.255	0.354	0.151	0.127	0.177	SUBCLONAL	1	TRUE	2	0.620133942143118	4		514	864	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0040853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	193	766	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.359638142885424	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.359638142885424	1		767	854	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670777	134670777	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	61	576	0	ENST00000398015.3:c.688G>A	p.Glu230Lys	p.E230K	ENST00000398015	NM_004441.4	230	Gag/Aag	3/16	1	2	FACETS	0.426	0.366	0.491	0.426	0.366	0.491	SUBCLONAL	1	TRUE	1	0.359638142885424	2		576	797	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	44	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.180538474363467	2		311	398	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	23	348	1				ENST00000310581	NM_198253.2	-/1132			0.180538474363467	1	FACETS	1	0.834	1	1	0.834	1	CLONAL	1	TRUE	0	0.180538474363467	1		349	215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	127	886	0	ENST00000269305.4:c.398T>A	p.Met133Lys	p.M133K	ENST00000269305	NM_001126112.2	133	aTg/aAg	5/11	1	2	FACETS	0.827	0.749	0.909	1	0.987	1	CLONAL	2	TRUE	1	0.180538474363467	2		886	851	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2972186	2972186	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748468563	NA	P-0040856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	64	592	0	ENST00000396946.4:c.1553G>A	p.Arg518Gln	p.R518Q	ENST00000396946	NM_032415.4	518	cGa/cAa	11/25	0.180538474363467	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.180538474363467	1		592	577	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175212	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	10	213	0	ENST00000257430.4:c.3924del	p.Glu1309LysfsTer12	p.E1309Kfs*12	ENST00000257430	NM_000038.5	1307	atA/at	16/16	0.180538474363467	2	FACETS	0.688	0.467	0.965	0.344	0.233	0.483	SUBCLONAL	1	TRUE	0	0.180538474363467	2		213	161	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101420	27101420	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	77	578	0	ENST00000324856.7:c.4702C>G	p.Pro1568Ala	p.P1568A	ENST00000324856	NM_006015.4	1568	Cct/Gct	18/20	0.180538474363467	2	FACETS	0.766	0.673	0.865	0.766	0.673	0.865	SUBCLONAL	2	TRUE	0	0.180538474363467	2		578	557	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828846	72828846	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	46	589	0	ENST00000268489.5:c.7735C>G	p.Pro2579Ala	p.P2579A	ENST00000268489	NM_006885.3	2579	Ccc/Gcc	9/10	1	2	FACETS	0.856	0.72	1	0.856	0.72	1	CLONAL	1	TRUE	1	0.180538474363467	2		589	595	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902679	50902679	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	84	1029	0	ENST00000440232.2:c.254C>A	p.Pro85Gln	p.P85Q	ENST00000440232	NM_002691.3	85	cCa/cAa	3/27	0.142175756987227	0	FACETS	1	0.911	1			1	CLONAL	1	TRUE	0	0.180538474363467	0		1029	735	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857020	9857020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555481892	NA	P-0040882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	22	194	0	ENST00000330684.3:c.4381G>A	p.Glu1461Lys	p.E1461K	ENST00000330684	NM_001134407.1	1461	Gaa/Aaa	13/13	1	2	FACETS	0.274	0.212	0.345	0.274	0.212	0.345	SUBCLONAL	1	TRUE	1	0.658715317378648	2		194	244	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	51	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.864	0.735	1	0.864	0.735	1	CLONAL	1	TRUE	1	0.2534412642459	2		311	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0040895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	52	448	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	1	2	FACETS	0.709	0.603	0.825	0.709	0.603	0.825	SUBCLONAL	1	TRUE	1	0.2534412642459	2		448	579	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050956	13050957	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	31	397	0	ENST00000316448.5:c.488dup	p.Cys163TrpfsTer4	p.C163Wfs*4	ENST00000316448	NM_004343.3	163	tgc/tGgc	4/9	0.2534412642459	1	FACETS	0.413	0.333	0.504	0.413	0.333	0.504	SUBCLONAL	1	TRUE	0	0.2534412642459	1		397	517	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	104	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.232475001944978	3	FACETS	0.92	0.826	1	0.92	0.826	1	CLONAL	2	TRUE	1	0.232475001944978	3		311	543	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0040917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	63	398	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.232475001944978	2		398	489	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598910	28598910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758133085	NA	P-0040917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	76	689	0	ENST00000253063.3:c.470G>A	p.Arg157His	p.R157H	ENST00000253063	NM_031459.4	157	cGc/cAc	4/10	0.232475001944978	0	FACETS	0.963	0.847	1			1	CLONAL	1	TRUE	0	0.232475001944978	0		689	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782329	NA	P-0040917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	168	626	1	ENST00000269305.4:c.746G>A	p.Arg249Lys	p.R249K	ENST00000269305	NM_001126112.2	249	aGg/aAg	7/11	0.232475001944978	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.232475001944978	2		627	632	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372153	45372153	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	42	432	0	ENST00000262160.6:c.1016A>T	p.Tyr339Phe	p.Y339F	ENST00000262160	NM_005901.5	339	tAc/tTc	9/11	1	2	FACETS	0.78	0.652	0.923	0.78	0.652	0.923	CLONAL	1	TRUE	1	0.232475001944978	2		432	463	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010496	48010496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs34014629	NA	P-0040917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	52	559	0	ENST00000234420.5:c.124C>T	p.Pro42Ser	p.P42S	ENST00000234420	NM_000179.2	42	Cct/Tct	1/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.232475001944978	2		559	335	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749443	41749443	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	62	507	0	ENST00000226382.2:c.352G>A	p.Ala118Thr	p.A118T	ENST00000226382	NM_003924.3	118	Gcg/Acg	2/3	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.232475001944978	2		507	440	SUCCESS
APC	324	MSKCC	GRCh37	5	112174461	112174461	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	32	304	0	ENST00000257430.4:c.3171del	p.Asp1058MetfsTer3	p.D1058Mfs*3	ENST00000257430	NM_000038.5	1057	gAa/ga	16/16	1	2	FACETS	1	0.819	1	1	0.819	1	CLONAL	1	TRUE	1	0.232475001944978	2		304	274	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527925	157527925	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	67	541	0	ENST00000346085.5:c.5650del	p.Arg1884GlyfsTer90	p.R1884Gfs*90	ENST00000346085	NM_020732.3	1884	Cgg/gg	20/20	0.232475001944978	3	FACETS	1	0.925	1	0.547	0.475	0.625	CLONAL	1	TRUE	1	0.232475001944978	3		541	588	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199469669	NA	P-0040917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	88	327	0	ENST00000374080.3:c.130G>T	p.Gly44Cys	p.G44C	ENST00000374080		44	Ggt/Tgt	2/45	1	1	FACETS	0.981	0.877	1	1	0.986	1	CLONAL	2	TRUE	0	0.232475001944978	1		327	341	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0040951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	78	544	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.263179921227365	1	FACETS	0.66	0.579	0.747	0.66	0.579	0.747	SUBCLONAL	1	TRUE	0	0.263179921227365	1		544	780	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577075	7577075	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	128	1050	0	ENST00000269305.4:c.863del	p.Asn288IlefsTer57	p.N288Ifs*57	ENST00000269305	NM_001126112.2	288	aAt/at	8/11	0.263179921227365	1	FACETS	0.719	0.65	0.792	0.719	0.65	0.792	SUBCLONAL	1	TRUE	0	0.263179921227365	1		1050	1175	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089064	37089064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173853120	NA	P-0040951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	90	514	0	ENST00000231790.2:c.1786G>A	p.Gly596Ser	p.G596S	ENST00000231790	NM_000249.3	596	Ggc/Agc	16/19	1	2	FACETS	0.966	0.857	1	0.966	0.857	1	CLONAL	1	TRUE	1	0.263179921227365	2		514	708	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38981986	38981986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	62	517	0	ENST00000357387.3:c.736G>A	p.Ala246Thr	p.A246T	ENST00000357387	NM_152756.3	246	Gct/Act	8/38	1	2	FACETS	0.774	0.668	0.888	0.774	0.668	0.888	SUBCLONAL	1	TRUE	1	0.263179921227365	2		517	609	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456995	149456995	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs41338945	NA	P-0040986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	176	263	0	ENST00000286301.3:c.733G>T	p.Ala245Ser	p.A245S	ENST00000286301	NM_005211.3	245	Gca/Tca	6/22	0.132972343702896	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.896165203479179	0		263	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576667	7576955	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATATATTATGGTATAAGTTGGTGTTCTGAAGTTAGTTAGCTACAACCAGGAGCCATTGTCTTTGAGGCATCACTGCCCCCTGATGGCAAATGCCCCAATTGCAGGTAAAACAGTCAAGAAGAAAACGGCATTTTGAGTGTTAGACTGGAAACTTTCCACTTGATAAGAGGTCCCAAGACTTAGTACCTGAAGGGTGAAATATTCTCCATCCAGTGGTTTCTTCTTTGGCTGGGGAGAGGAGCTGGTGTTGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAA	ATATATTATGGTATAAGTTGGTGTTCTGAAGTTAGTTAGCTACAACCAGGAGCCATTGTCTTTGAGGCATCACTGCCCCCTGATGGCAAATGCCCCAATTGCAGGTAAAACAGTCAAGAAGAAAACGGCATTTTGAGTGTTAGACTGGAAACTTTCCACTTGATAAGAGGTCCCAAGACTTAGTACCTGAAGGGTGAAATATTCTCCATCCAGTGGTTTCTTCTTTGGCTGGGGAGAGGAGCTGGTGTTGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAA	-	novel	NA	P-0040986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	289	357	0	ENST00000269305.4:c.920-29_993+186del		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.896165203479179	2		357	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578188	7578189	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATAGGGCACCACCACACT	novel	NA	P-0040986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	337	692	0	ENST00000269305.4:c.643_660dup	p.Ser215_Tyr220dup	p.S215_Y220dup	ENST00000269305	NM_001126112.2	215	-/AGTGTGGTGGTGCCCTAT	6/11	1	2	FACETS	0.698	0.661	0.736	0.698	0.661	0.736	SUBCLONAL	1	TRUE	1	0.896165203479179	2		692	1077	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907675	111907676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0040986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	267	367	0	ENST00000393256.3:c.452_453dup	p.Leu152SerfsTer19	p.L152Sfs*19	ENST00000393256	NM_006538.4	150	caa/caAGa	3/4	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.896165203479179	2		367	595	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	114	443	9	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.893	0.809	0.981	0.893	0.809	0.981	CLONAL	1	TRUE	1	0.55	2		452	464	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	275	368	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.55	2		371	912	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	212	459	2	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.55	2		461	768	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777114	9777114	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs754116182	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	291	868	2	ENST00000377346.4:c.883del	p.Gln295ArgfsTer39	p.Q295Rfs*39	ENST00000377346	NM_005026.3	293	gCc/gc	7/24	1	2	FACETS	0.976	0.919	1	0.976	0.919	1	CLONAL	1	TRUE	1	0.55	2		870	1084	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780884	9780884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	183	886	0	ENST00000377346.4:c.1606C>T	p.His536Tyr	p.H536Y	ENST00000377346	NM_005026.3	536	Cat/Tat	13/24	1	2	FACETS	0.669	0.617	0.724	0.669	0.617	0.724	SUBCLONAL	1	TRUE	1	0.55	2		886	994	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187758	11187758	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	209	651	0	ENST00000361445.4:c.6139A>G	p.Met2047Val	p.M2047V	ENST00000361445	NM_004958.3	2047	Atg/Gtg	44/58	1	2	FACETS	0.873	0.811	0.936	0.873	0.811	0.936	CLONAL	1	TRUE	1	0.55	2		651	871	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099089	27099089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	148	473	0	ENST00000324856.7:c.3505C>T	p.Pro1169Ser	p.P1169S	ENST00000324856	NM_006015.4	1169	Cca/Tca	13/20	1	2	FACETS	0.911	0.835	0.989	0.911	0.835	0.989	CLONAL	1	TRUE	1	0.55	2		473	591	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797213	45797213	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	198	739	0	ENST00000450313.1:c.1202T>C	p.Leu401Pro	p.L401P	ENST00000450313	NM_012222.2	401	cTg/cCg	13/16	1	2	FACETS	0.905	0.84	0.972	0.905	0.84	0.972	CLONAL	1	TRUE	1	0.55	2		739	796	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726564	46726564	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	140	555	0	ENST00000371975.4:c.643G>A	p.Val215Met	p.V215M	ENST00000371975	NM_003579.3	215	Gtg/Atg	7/18	1	2	FACETS	0.775	0.707	0.845	0.775	0.707	0.845	SUBCLONAL	1	TRUE	1	0.55	2		555	657	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414949	78414949	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	147	446	0	ENST00000370768.2:c.1817G>A	p.Gly606Asp	p.G606D	ENST00000370768	NM_003902.3	606	gGt/gAt	19/20	1	2	FACETS	0.92	0.844	0.999	0.92	0.844	0.999	CLONAL	1	TRUE	1	0.55	2		446	581	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275287	115275287	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs746569183	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	193	613	0	ENST00000438362.2:c.1126C>T	p.Arg376Ter	p.R376*	ENST00000438362	NM_001242891.1	376	Cga/Tga	10/20	1	2	FACETS	0.879	0.815	0.946	0.879	0.815	0.946	CLONAL	1	TRUE	1	0.55	2		613	798	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107231	193107231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	51	247	0	ENST00000367435.3:c.440G>A	p.Arg147His	p.R147H	ENST00000367435	NM_024529.4	147	cGc/cAc	6/17	1	2	FACETS	0.724	0.621	0.836	0.724	0.621	0.836	SUBCLONAL	1	TRUE	1	0.55	2		247	256	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246091265	246091265	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs777672375	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	203	538	0	ENST00000388985.4:c.670C>T	p.Arg224Ter	p.R224*	ENST00000388985		224	Cga/Tga	7/12	1	2	FACETS	0.969	0.901	1	0.969	0.901	1	CLONAL	1	TRUE	1	0.55	2		538	762	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70412322	70412322	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	100	317	0	ENST00000373644.4:c.4432A>G	p.Ser1478Gly	p.S1478G	ENST00000373644	NM_030625.2	1478	Agc/Ggc	6/12	1	2	FACETS	0.852	0.766	0.942	0.852	0.766	0.942	CLONAL	1	TRUE	1	0.55	2		317	427	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426854	70426854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1288019869	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	140	370	0	ENST00000373644.4:c.4514G>A	p.Arg1505His	p.R1505H	ENST00000373644	NM_030625.2	1505	cGt/cAt	7/12	1	2	FACETS	0.924	0.846	1	0.924	0.846	1	CLONAL	1	TRUE	1	0.55	2		370	551	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88651979	88651979	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	82	337	0	ENST00000372037.3:c.326A>G	p.Gln109Arg	p.Q109R	ENST00000372037	NM_004329.2	109	cAg/cGg	5/13	1	2	FACETS	0.804	0.714	0.899	0.804	0.714	0.899	CLONAL	1	TRUE	1	0.55	2		337	371	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683228	88683228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876658515	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	165	501	0	ENST00000372037.3:c.1438C>T	p.Arg480Trp	p.R480W	ENST00000372037	NM_004329.2	480	Cgg/Tgg	12/13	1	2	FACETS	0.995	0.918	1	0.995	0.918	1	CLONAL	1	TRUE	1	0.55	2		501	603	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720712	89720712	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	41	123	0	ENST00000371953.3:c.867del	p.Val290Ter	p.V290*	ENST00000371953	NM_000314.4	288	gAa/ga	8/9	1	2	FACETS	0.734	0.618	0.86	0.734	0.618	0.86	SUBCLONAL	1	TRUE	1	0.55	2		123	203	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	90	323	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.783	0.699	0.872	0.783	0.699	0.872	SUBCLONAL	1	TRUE	1	0.55	2		323	418	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263395	123263395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536181987	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	157	430	1	ENST00000358487.5:c.1348C>T	p.Arg450Cys	p.R450C	ENST00000358487	NM_000141.4	450	Cgc/Tgc	10/18	1	2	FACETS	0.947	0.871	1	0.947	0.871	1	CLONAL	1	TRUE	1	0.55	2		431	603	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742951	17742951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1332082680	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	227	793	0	ENST00000250003.3:c.859G>A	p.Ala287Thr	p.A287T	ENST00000250003	NM_002478.4	287	Gcc/Acc	3/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.55	2		793	771	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518449	69518449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs912723093	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	127	302	0	ENST00000294312.3:c.196G>A	p.Gly66Ser	p.G66S	ENST00000294312	NM_005117.2	66	Ggc/Agc	1/3	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.55	2		302	431	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941273	71941273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753375974	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	268	833	0	ENST00000298229.2:c.1048C>T	p.Arg350Trp	p.R350W	ENST00000298229	NM_001567.3	350	Cgg/Tgg	9/28	1	2	FACETS	0.92	0.863	0.979	0.92	0.863	0.979	CLONAL	1	TRUE	1	0.55	2		833	1059	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946486	71946486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	174	633	1	ENST00000298229.2:c.2650C>T	p.Arg884Trp	p.R884W	ENST00000298229	NM_001567.3	884	Cgg/Tgg	23/28	1	2	FACETS	0.796	0.734	0.86	0.796	0.734	0.86	SUBCLONAL	1	TRUE	1	0.55	2		634	795	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948208	71948209	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs749079348	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	273	657	4	ENST00000298229.2:c.2927dup	p.Pro977ThrfsTer7	p.P977Tfs*7	ENST00000298229	NM_001567.3	974	gcc/gCcc	26/28	1	2	FACETS	0.815	0.764	0.867	0.815	0.764	0.867	CLONAL	1	TRUE	1	0.55	2		661	1218	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420215	420215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs994813080	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	99	357	0	ENST00000399788.2:c.3052G>A	p.Ala1018Thr	p.A1018T	ENST00000399788	NM_001042603.1	1018	Gct/Act	21/28	0.3	2	FACETS	0.732	0.656	0.812			1	INDETERMINATE	1	TRUE	NA	0.55	2		357	492	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491390	18491390	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1377942847	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	94	272	0	ENST00000266497.5:c.1309del	p.Ile437TyrfsTer5	p.I437Yfs*5	ENST00000266497		435	Aaa/aa	8/31	1	2	FACETS	0.844	0.756	0.936	0.844	0.756	0.936	CLONAL	1	TRUE	1	0.55	2		272	405	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	105	471	2	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.598	0.536	0.663	0.598	0.536	0.663	SUBCLONAL	1	TRUE	1	0.55	2		473	639	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446755	49446755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564617479	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	190	624	1	ENST00000301067.7:c.1055C>T	p.Ala352Val	p.A352V	ENST00000301067	NM_003482.3	352	gCc/gTc	8/54	1	2	FACETS	0.92	0.853	0.989	0.92	0.853	0.989	CLONAL	1	TRUE	1	0.55	2		625	751	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447841	49447841	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748834953	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	220	668	0	ENST00000301067.7:c.593C>T	p.Ala198Val	p.A198V	ENST00000301067	NM_003482.3	198	gCg/gTg	5/54	1	2	FACETS	0.912	0.85	0.976	0.912	0.85	0.976	CLONAL	1	TRUE	1	0.55	2		668	877	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50482355	50482355	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	197	492	1	ENST00000394963.4:c.711del	p.Phe237LeufsTer5	p.F237Lfs*5	ENST00000394963	NM_003076.4	236	Ttt/tt	6/13	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.55	2		493	711	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233624	69233624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	12	188	0	ENST00000462284.1:c.1489C>T	p.Pro497Ser	p.P497S	ENST00000462284	NM_002392.5	497	Ccc/Tcc	11/11	1	2	FACETS	0.19	0.133	0.26	0.19	0.133	0.26	SUBCLONAL	1	TRUE	1	0.55	2		188	230	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885145	111885145	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs892433462	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	214	621	0	ENST00000341259.2:c.1038del	p.Leu347CysfsTer26	p.L347Cfs*26	ENST00000341259	NM_005475.2	345	Ggg/gg	6/8	1	2	FACETS	0.988	0.92	1	0.988	0.92	1	CLONAL	1	TRUE	1	0.55	2		621	788	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238261	133238261	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs935816567	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	116	428	0	ENST00000320574.5:c.2716A>G	p.Thr906Ala	p.T906A	ENST00000320574	NM_006231.2	906	Acc/Gcc	24/49	1	2	FACETS	0.827	0.749	0.909	0.827	0.749	0.909	CLONAL	1	TRUE	1	0.55	2		428	510	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975423	26975423	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	143	404	0	ENST00000381527.3:c.1049A>G	p.Gln350Arg	p.Q350R	ENST00000381527	NM_001260.1	350	cAa/cGa	11/13	1	2	FACETS	0.92	0.843	1	0.92	0.843	1	CLONAL	1	TRUE	1	0.55	2		404	565	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907420	32907421	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359306	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	75	261	2	ENST00000380152.3:c.1813dup	p.Ile605AsnfsTer11	p.I605Nfs*11	ENST00000380152		602	gga/ggAa	10/27	1	2	FACETS	0.819	0.723	0.92	0.819	0.723	0.92	CLONAL	1	TRUE	1	0.55	2		263	333	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519045	103519045	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751772171	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	175	462	0	ENST00000355739.4:c.2383G>A	p.Ala795Thr	p.A795T	ENST00000355739	NM_000123.3	795	Gcc/Acc	11/15	1	2	FACETS	0.932	0.861	1	0.932	0.861	1	CLONAL	1	TRUE	1	0.55	2		462	683	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81534643	81534645	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	118	377	1	ENST00000298171.2:c.290_292del	p.Phe97del	p.F97del	ENST00000298171	NM_000369.2	96	tcCTTc/tcc	3/10	1	2	FACETS	0.915	0.83	1	0.915	0.83	1	CLONAL	1	TRUE	1	0.55	2		378	469	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566220	95566220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767112987	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	177	538	1	ENST00000393063.1:c.4103G>A	p.Arg1368His	p.R1368H	ENST00000393063	NM_030621.3	1368	cGc/cAc	23/28	1	2	FACETS	0.834	0.77	0.9	0.834	0.77	0.9	CLONAL	1	TRUE	1	0.55	2		539	772	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643438	38643438	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	180	537	0	ENST00000299084.4:c.908G>T	p.Ser303Ile	p.S303I	ENST00000299084	NM_152594.2	303	aGt/aTt	7/7	1	2	FACETS	0.936	0.866	1	0.936	0.866	1	CLONAL	1	TRUE	1	0.55	2		537	699	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347139	347139	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	287	924	1	ENST00000262320.3:c.1872G>T	p.Glu624Asp	p.E624D	ENST00000262320	NM_003502.3	624	gaG/gaT	7/11	1	2	FACETS	0.93	0.875	0.987	0.93	0.875	0.987	CLONAL	1	TRUE	1	0.55	2		925	1122	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106687	2106687	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	258	839	0	ENST00000219476.3:c.691C>A	p.Leu231Met	p.L231M	ENST00000219476	NM_000548.3	231	Ctg/Atg	8/42	1	2	FACETS	0.916	0.858	0.976	0.916	0.858	0.976	CLONAL	1	TRUE	1	0.55	2		839	1024	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126130	2126130	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs796053512	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	259	742	0	ENST00000219476.3:c.2701C>T	p.Arg901Cys	p.R901C	ENST00000219476	NM_000548.3	901	Cgc/Tgc	24/42	1	2	FACETS	0.95	0.891	1	0.95	0.891	1	CLONAL	1	TRUE	1	0.55	2		742	991	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222500	2222500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766165474	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	284	941	0	ENST00000326181.6:c.694C>T	p.Arg232Trp	p.R232W	ENST00000326181	NM_032271.2	232	Cgg/Tgg	9/21	1	2	FACETS	0.958	0.901	1	0.958	0.901	1	CLONAL	1	TRUE	1	0.55	2		941	1078	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647028	23647028	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1555461597	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	210	731	1	ENST00000261584.4:c.839del	p.Asn280ThrfsTer8	p.N280Tfs*8	ENST00000261584	NM_024675.3	280	aAc/ac	4/13	1	2	FACETS	0.919	0.855	0.985	0.919	0.855	0.985	CLONAL	1	TRUE	1	0.55	2		732	831	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	142	543	1	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.743	0.678	0.81	0.743	0.678	0.81	SUBCLONAL	1	TRUE	1	0.55	2		544	695	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821707	72821707	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	100	349	0	ENST00000268489.5:c.10468T>G	p.Phe3490Val	p.F3490V	ENST00000268489	NM_006885.3	3490	Ttc/Gtc	10/10	1	2	FACETS	0.67	0.6	0.743	0.67	0.6	0.743	SUBCLONAL	1	TRUE	1	0.55	2		349	543	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357120	89357120	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	235	704	0	ENST00000301030.4:c.514C>A	p.Leu172Met	p.L172M	ENST00000301030	NM_001256183.1	172	Ctg/Atg	6/13	1	2	FACETS	0.913	0.853	0.975	0.913	0.853	0.975	CLONAL	1	TRUE	1	0.55	2		704	936	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831344	89831345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	167	594	0	ENST00000389301.3:c.2730_2731dup	p.Trp911SerfsTer11	p.W911Sfs*11	ENST00000389301	NM_000135.2	911	tgg/tCTgg	28/43	1	2	FACETS	0.79	0.727	0.855	0.79	0.727	0.855	SUBCLONAL	1	TRUE	1	0.55	2		594	769	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990757	7990757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs925216708	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	154	430	0	ENST00000319144.4:c.4G>A	p.Ala2Thr	p.A2T	ENST00000319144	NM_001139.2	2	Gcc/Acc	1/15	1	2	FACETS	0.991	0.912	1	0.991	0.912	1	CLONAL	1	TRUE	1	0.55	2		430	565	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961810	15961810	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	131	431	0	ENST00000268712.3:c.5985G>T	p.Glu1995Asp	p.E1995D	ENST00000268712	NM_006311.3	1995	gaG/gaT	38/46	1	2	FACETS	0.785	0.714	0.858	0.785	0.714	0.858	SUBCLONAL	1	TRUE	1	0.55	2		431	607	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619372	37619372	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	98	353	0	ENST00000447079.4:c.1046+2T>C		p.X349_splice	ENST00000447079	NM_015083.1	349			1	2	FACETS	0.893	0.803	0.988	0.893	0.803	0.988	CLONAL	1	TRUE	1	0.55	2		353	399	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	194	772	10	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	0.719	0.665	0.775	0.719	0.665	0.775	SUBCLONAL	1	TRUE	1	0.55	2		782	981	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	418	721	8	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.883	0.846	0.92	1	0.997	1	CLONAL	2	TRUE	1	0.55	2		729	861	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437608	56437608	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	178	512	0	ENST00000407977.2:c.854T>C	p.Leu285Pro	p.L285P	ENST00000407977		285	cTa/cCa	8/10	1	2	FACETS	0.982	0.909	1	0.982	0.909	1	CLONAL	1	TRUE	1	0.55	2		512	659	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740836	58740836	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs747668756	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	203	487	0	ENST00000305921.3:c.1741C>T	p.Arg581Ter	p.R581*	ENST00000305921	NM_003620.3	581	Cga/Tga	6/6	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.55	2		487	698	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372069	45372069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	182	502	0	ENST00000262160.6:c.1100G>A	p.Gly367Asp	p.G367D	ENST00000262160	NM_005901.5	367	gGc/gAc	9/11	0.3	3	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.55	3		502	672	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575057	48575057	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	86	274	0	ENST00000342988.3:c.251T>C	p.Val84Ala	p.V84A	ENST00000342988	NM_005359.5	84	gTg/gCg	3/12	0.3	3	FACETS	1	0.957	1			1	INDETERMINATE	1	TRUE	NA	0.55	3		274	348	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222730	5222731	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs756013055	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	175	758	1	ENST00000357368.4:c.3072dup	p.Val1025ArgfsTer34	p.V1025Rfs*34	ENST00000357368	NM_002850.3	1024	-/C	18/38	1	2	FACETS	0.683	0.629	0.739	0.683	0.629	0.739	SUBCLONAL	1	TRUE	1	0.55	2		759	932	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274304	5274304	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	219	753	0	ENST00000357368.4:c.143del	p.Gly48ValfsTer17	p.G48Vfs*17	ENST00000357368	NM_002850.3	48	gGt/gt	3/38	1	2	FACETS	0.781	0.726	0.837	0.781	0.726	0.837	SUBCLONAL	1	TRUE	1	0.55	2		753	1020	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291083	10291084	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755889652	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	226	755	6	ENST00000340748.4:c.387dup	p.Lys130GlnfsTer19	p.K130Qfs*19	ENST00000340748		129	-/C	4/40	1	2	FACETS	0.845	0.787	0.904	0.845	0.787	0.904	CLONAL	1	TRUE	1	0.55	2		761	973	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266930	18266930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755171275	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	212	505	1	ENST00000222254.8:c.241G>A	p.Val81Met	p.V81M	ENST00000222254	NM_005027.3	81	Gtg/Atg	2/16	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.55	2		506	627	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	253	840	2	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	0.942	0.882	1	0.942	0.882	1	CLONAL	1	TRUE	1	0.55	2		842	977	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917060	50917060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139235742	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	303	878	1	ENST00000440232.2:c.2312C>T	p.Ala771Val	p.A771V	ENST00000440232	NM_002691.3	771	gCg/gTg	19/27	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.55	2		879	1059	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919743	50919743	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs897259743	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	254	860	2	ENST00000440232.2:c.2911G>A	p.Glu971Lys	p.E971K	ENST00000440232	NM_002691.3	971	Gag/Aag	23/27	1	2	FACETS	0.877	0.821	0.935	0.877	0.821	0.935	CLONAL	1	TRUE	1	0.55	2		862	1053	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966872	25966873	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	40	562	4	ENST00000435504.4:c.2333dup	p.Val779SerfsTer25	p.V779Sfs*25	ENST00000435504		778	cca/ccCa	13/13	1	2	FACETS	0.227	0.187	0.27	0.227	0.187	0.27	SUBCLONAL	1	TRUE	1	0.55	2		566	642	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	126	709	11	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.73	0.662	0.8	0.73	0.662	0.8	SUBCLONAL	1	TRUE	1	0.55	2		720	628	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033789	48033789	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs773763465	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	82	268	0	ENST00000234420.5:c.4000C>T	p.Arg1334Trp	p.R1334W	ENST00000234420	NM_000179.2	1334	Cgg/Tgg	9/10	1	2	FACETS	0.828	0.736	0.926	0.828	0.736	0.926	CLONAL	1	TRUE	1	0.55	2		268	360	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131211	202131211	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	101	349	0	ENST00000358485.4:c.179T>C	p.Met60Thr	p.M60T	ENST00000358485	NM_001080125.1	60	aTg/aCg	2/9	1	2	FACETS	0.854	0.768	0.944	0.854	0.768	0.944	CLONAL	1	TRUE	1	0.55	2		349	430	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794881	242794881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs190602950	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	277	783	0	ENST00000334409.5:c.328G>A	p.Val110Met	p.V110M	ENST00000334409	NM_005018.2	110	Gtg/Atg	2/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.55	2		783	939	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384650	31384651	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs756395138	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	225	653	2	ENST00000328111.2:c.1359dup	p.Leu454AlafsTer11	p.L454Afs*11	ENST00000328111	NM_006892.3	451	gag/gaGg	13/23	1	2	FACETS	0.939	0.876	1	0.939	0.876	1	CLONAL	1	TRUE	1	0.55	2		655	871	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	121	514	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.853	0.774	0.935	0.853	0.774	0.935	CLONAL	1	TRUE	1	0.55	2		515	516	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139521	47139521	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	130	335	0	ENST00000409792.3:c.5066T>C	p.Leu1689Pro	p.L1689P	ENST00000409792	NM_014159.6	1689	cTg/cCg	9/21	1	2	FACETS	0.807	0.734	0.882	0.807	0.734	0.882	CLONAL	1	TRUE	1	0.55	2		335	586	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163933	47163933	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	97	286	0	ENST00000409792.3:c.2193C>A	p.Asp731Glu	p.D731E	ENST00000409792	NM_014159.6	731	gaC/gaA	3/21	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.55	2		286	336	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436395	52436395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	244	758	0	ENST00000460680.1:c.2099G>A	p.Arg700Gln	p.R700Q	ENST00000460680	NM_004656.3	700	cGg/cAg	17/17	1	2	FACETS	0.979	0.917	1	0.979	0.917	1	CLONAL	1	TRUE	1	0.55	2		758	906	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090656	71090656	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs202064883	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	85	256	0	ENST00000318789.4:c.692T>C	p.Leu231Pro	p.L231P	ENST00000318789	NM_032682.5	231	cTc/cCc	11/21	1	2	FACETS	0.957	0.854	1	0.957	0.854	1	CLONAL	1	TRUE	1	0.55	2		256	323	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138400844	138400844	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	146	511	0	ENST00000289153.2:c.2469G>T	p.Met823Ile	p.M823I	ENST00000289153	NM_006219.2	823	atG/atT	17/22	1	2	FACETS	0.903	0.828	0.981	0.903	0.828	0.981	CLONAL	1	TRUE	1	0.55	2		511	588	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664546	138664546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757937453	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	131	239	0	ENST00000330315.3:c.1019C>T	p.Ala340Val	p.A340V	ENST00000330315	NM_023067.3	340	gCg/gTg	1/1	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.55	2		239	419	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149375074	149375074	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	210	910	0	ENST00000360632.3:c.20C>G	p.Pro7Arg	p.P7R	ENST00000360632	NM_015472.4	7	cCc/cGc	2/7	1	2	FACETS	0.574	0.532	0.618	0.574	0.532	0.618	SUBCLONAL	1	TRUE	1	0.55	2		910	1330	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	62	298	0	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	0.711	0.619	0.81	0.711	0.619	0.81	SUBCLONAL	1	TRUE	1	0.55	2		298	317	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155367	185155367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs902931460	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	149	450	1	ENST00000265026.3:c.608C>T	p.Thr203Met	p.T203M	ENST00000265026	NM_004721.4	203	aCg/aTg	3/14	1	2	FACETS	0.936	0.859	1	0.936	0.859	1	CLONAL	1	TRUE	1	0.55	2		451	579	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217231	66217231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	112	389	2	ENST00000273854.3:c.2384G>A	p.Gly795Asp	p.G795D	ENST00000273854	NM_004439.5	795	gGc/gAc	14/18	1	2	FACETS	0.838	0.758	0.922	0.838	0.758	0.922	CLONAL	1	TRUE	1	0.55	2		391	486	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397112	397112	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	104	320	0	ENST00000380956.4:c.497T>C	p.Val166Ala	p.V166A	ENST00000380956	NM_001195286.1	166	gTt/gCt	5/9	1	2	FACETS	0.938	0.847	1	0.938	0.847	1	CLONAL	1	TRUE	1	0.55	2		320	403	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324157	31324157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137854720	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	184	317	0	ENST00000412585.2:c.406G>A	p.Gly136Arg	p.G136R	ENST00000412585	NM_005514.6	136	Ggg/Agg	3/8	1	2	FACETS	0.826	0.773	0.88	1	0.993	1	CLONAL	2	TRUE	1	0.55	2		317	405	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188832	32188832	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	230	760	1	ENST00000375023.3:c.722G>T	p.Arg241Met	p.R241M	ENST00000375023	NM_004557.3	241	aGg/aTg	4/30	1	2	FACETS	0.997	0.931	1	0.997	0.931	1	CLONAL	1	TRUE	1	0.55	2		761	839	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815865	32815865	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	167	637	0	ENST00000354258.4:c.1751T>C	p.Leu584Pro	p.L584P	ENST00000354258	NM_000593.5	584	cTg/cCg	8/11	1	2	FACETS	0.843	0.777	0.913	0.843	0.777	0.913	CLONAL	1	TRUE	1	0.55	2		637	720	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818296	32818296	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	148	535	0	ENST00000354258.4:c.1231-2A>G		p.X411_splice	ENST00000354258	NM_000593.5	411			1	2	FACETS	0.759	0.695	0.826	0.759	0.695	0.826	SUBCLONAL	1	TRUE	1	0.55	2		535	709	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139051	37139051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	202	625	0	ENST00000373509.5:c.391G>A	p.Asp131Asn	p.D131N	ENST00000373509	NM_002648.3	131	Gac/Aac	4/6	1	2	FACETS	0.905	0.84	0.971	0.905	0.84	0.971	CLONAL	1	TRUE	1	0.55	2		625	812	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41905033	41905033	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	159	508	0	ENST00000372991.4:c.514C>A	p.Arg172Ser	p.R172S	ENST00000372991	NM_001760.3	172	Cgt/Agt	3/5	1	2	FACETS	0.844	0.776	0.915	0.844	0.776	0.915	CLONAL	1	TRUE	1	0.55	2		508	685	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979309	93979309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	103	381	0	ENST00000369303.4:c.1519C>T	p.Pro507Ser	p.P507S	ENST00000369303	NM_004440.3	507	Cca/Tca	7/17	1	2	FACETS	0.925	0.834	1	0.925	0.834	1	CLONAL	1	TRUE	1	0.55	2		381	405	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519505	137519506	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs780346130	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	86	315	2	ENST00000367739.4:c.1132_1133del	p.Ser378PhefsTer6	p.S378Ffs*6	ENST00000367739	NM_000416.2	378	AGt/t	7/7	1	2	FACETS	0.794	0.707	0.886	0.794	0.707	0.886	SUBCLONAL	1	TRUE	1	0.55	2		317	394	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137522040	137522041	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	75	175	0	ENST00000367739.4:c.838dup	p.Ser280LysfsTer22	p.S280Kfs*22	ENST00000367739	NM_000416.2	280	agc/aAgc	6/7	1	2	FACETS	0.921	0.816	1	0.921	0.816	1	CLONAL	1	TRUE	1	0.55	2		175	296	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528284	157528284	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs749055122	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	245	735	0	ENST00000346085.5:c.6013del	p.Val2005TrpfsTer16	p.V2005Wfs*16	ENST00000346085	NM_020732.3	2003	aaG/aa	20/20	1	2	FACETS	0.972	0.909	1	0.972	0.909	1	CLONAL	1	TRUE	1	0.55	2		735	917	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968322	2968323	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762770988	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	197	753	1	ENST00000396946.4:c.1663dup	p.Arg555ProfsTer38	p.R555Pfs*38	ENST00000396946	NM_032415.4	555	cgg/cCgg	13/25	1	2	FACETS	0.794	0.736	0.855	0.794	0.736	0.855	SUBCLONAL	1	TRUE	1	0.55	2		754	902	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026929	6026929	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	15	17	0	ENST00000265849.7:c.1467G>T	p.Glu489Asp	p.E489D	ENST00000265849	NM_000535.5	489	gaG/gaT	11/15	1	2	FACETS	0.758	0.587	0.936	1	0.911	1	CLONAL	2	TRUE	1	0.55	2		17	36	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441515	6441515	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769283316	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	94	267	0	ENST00000356142.4:c.362G>A	p.Arg121Gln	p.R121Q	ENST00000356142	NM_018890.3	121	cGg/cAg	6/7	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.55	2		267	335	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345759	152345760	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs730882049	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	77	255	0	ENST00000359321.1:c.810dup	p.Ile271TyrfsTer8	p.I271Yfs*8	ENST00000359321	NM_005431.1	270	-/T	3/3	1	2	FACETS	0.851	0.753	0.954	0.851	0.753	0.954	CLONAL	1	TRUE	1	0.55	2		255	329	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372066	55372066	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs748768438	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	214	622	0	ENST00000297316.4:c.756C>A	p.Ser252Arg	p.S252R	ENST00000297316	NM_022454.3	252	agC/agA	2/2	1	2	FACETS	0.983	0.915	1	0.983	0.915	1	CLONAL	1	TRUE	1	0.55	2		622	792	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978495	70978495	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	29	411	0	ENST00000276594.2:c.1158del	p.Lys387SerfsTer90	p.K387Sfs*90	ENST00000276594	NM_024504.3	386	ggG/gg	5/8	1	2	FACETS	0.22	0.176	0.27	0.22	0.176	0.27	SUBCLONAL	1	TRUE	1	0.55	2		411	479	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958479	90958480	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs780235686	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	50	337	1	ENST00000265433.3:c.1958dup	p.Leu654AlafsTer5	p.L654Afs*5	ENST00000265433	NM_002485.4	653	aag/aaAg	13/16	1	2	FACETS	0.413	0.351	0.481	0.413	0.351	0.481	SUBCLONAL	1	TRUE	1	0.55	2		338	440	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400023	139400023	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	278	842	0	ENST00000277541.6:c.4325del	p.Pro1442ArgfsTer3	p.P1442Rfs*3	ENST00000277541	NM_017617.3	1442	cCg/cg	25/34	1	2	FACETS	0.981	0.923	1	0.981	0.923	1	CLONAL	1	TRUE	1	0.55	2		842	1030	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139794916	139794916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267602174	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	181	557	0	ENST00000247668.2:c.310C>T	p.Pro104Ser	p.P104S	ENST00000247668	NM_021138.3	104	Ccg/Tcg	4/11	1	2	FACETS	0.889	0.822	0.959	0.889	0.822	0.959	CLONAL	1	TRUE	1	0.55	2		557	740	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941830	44941831	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	116	288	0	ENST00000377967.4:c.3160dup	p.Arg1054LysfsTer5	p.R1054Kfs*5	ENST00000377967	NM_021140.2	1052	gaa/gAaa	21/29	1	2	FACETS	0.888	0.805	0.975	0.888	0.805	0.975	CLONAL	1	TRUE	1	0.55	2		288	475	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222366	53222366	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	236	919	0	ENST00000375401.3:c.4466C>T	p.Ala1489Val	p.A1489V	ENST00000375401	NM_004187.3	1489	gCt/gTt	26/26	1	2	FACETS	0.885	0.826	0.945	0.885	0.826	0.945	CLONAL	1	TRUE	1	0.55	2		919	970	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223419	53223419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370060257	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	304	864	0	ENST00000375401.3:c.3940C>T	p.Arg1314Trp	p.R1314W	ENST00000375401	NM_004187.3	1314	Cgg/Tgg	23/26	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.55	2		864	1032	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	141	672	0	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	1	2	FACETS	0.809	0.739	0.881	0.809	0.739	0.881	CLONAL	1	TRUE	1	0.55	2		672	634	SUCCESS
AR	367	MSKCC	GRCh37	X	66766496	66766496	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	223	676	1	ENST00000374690.3:c.1508G>T	p.Trp503Leu	p.W503L	ENST00000374690	NM_000044.3	503	tGg/tTg	1/8	1	2	FACETS	0.883	0.823	0.945	0.883	0.823	0.945	CLONAL	1	TRUE	1	0.55	2		677	918	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341463	70341463	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	218	671	0	ENST00000374080.3:c.898T>G	p.Phe300Val	p.F300V	ENST00000374080		300	Ttc/Gtc	7/45	1	2	FACETS	0.915	0.853	0.98	0.915	0.853	0.98	CLONAL	1	TRUE	1	0.55	2		671	866	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993830	72993831	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0041005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	116	542	1	ENST00000268489.5:c.214_215insG	p.Ser72CysfsTer47	p.S72Cfs*47	ENST00000268489	NM_006885.3	72	tcc/tGcc	2/10	1	2	FACETS	0.774	0.7	0.851	0.774	0.7	0.851	SUBCLONAL	1	TRUE	1	0.55	2		543	545	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041024-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	90	348	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.511908170264218	2		349	345	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0041024-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	216	405	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.511908170264218	2		405	669	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911514	131911514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143802516	NA	P-0041024-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	94	113	0	ENST00000265335.6:c.259C>T	p.Arg87Cys	p.R87C	ENST00000265335		87	Cgt/Tgt	3/25	1	2	FACETS	0.783	0.7	0.871	0.783	0.7	0.871	SUBCLONAL	1	TRUE	1	0.511908170264218	2		113	469	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453145	140453146	+	missense_variant	Missense_Mutation	DNP	AG	AG	GA	rs121913368	NA	P-0041024-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	628	266	0	ENST00000288602.6:c.1789_1790delinsTC	p.Leu597Ser	p.L597S	ENST00000288602	NM_004333.4	597	CTa/TCa	15/18	0.511908170264218	6	FACETS	0.955	0.93	0.978	0.955	0.93	0.978	CLONAL	6	TRUE	0	0.511908170264218	6		266	867	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456528	189456528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121908848	NA	P-0041024-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	154	468	0	ENST00000264731.3:c.289C>T	p.Arg97Cys	p.R97C	ENST00000264731	NM_003722.4	97	Cgc/Tgc	3/14	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.511908170264218	2		468	553	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217326	123217326	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041024-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	109	563	0	ENST00000218089.9:c.2980C>T	p.Pro994Ser	p.P994S	ENST00000218089	NM_001042749.1	994	Cct/Tct	29/35	1	2	FACETS	0.75	0.675	0.828	0.75	0.675	0.828	SUBCLONAL	1	TRUE	1	0.511908170264218	2		563	568	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223220	2223220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041024-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	185	855	1	ENST00000326181.6:c.832C>T	p.His278Tyr	p.H278Y	ENST00000326181	NM_032271.2	278	Cac/Tac	10/21	1	2	FACETS	0.801	0.74	0.865	0.801	0.74	0.865	CLONAL	1	TRUE	1	0.511908170264218	2		856	902	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932584	39932584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041024-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	204	900	0	ENST00000378444.4:c.2015C>T	p.Ser672Phe	p.S672F	ENST00000378444	NM_001123385.1	672	tCc/tTc	4/15	1	2	FACETS	0.877	0.814	0.942	0.877	0.814	0.942	CLONAL	1	TRUE	1	0.511908170264218	2		900	909	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800150	32800150	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041024-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	101	371	0	ENST00000374899.4:c.1232C>T	p.Ser411Phe	p.S411F	ENST00000374899	NM_018833.2	411	tCc/tTc	7/12	1	2	FACETS	0.899	0.808	0.994	0.899	0.808	0.994	CLONAL	1	TRUE	1	0.511908170264218	2		371	439	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68999972	68999972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041024-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	122	519	0	ENST00000288368.4:c.2041C>T	p.Pro681Ser	p.P681S	ENST00000288368	NM_024870.2	681	Cca/Tca	19/40	1	2	FACETS	0.748	0.678	0.822	0.748	0.678	0.822	SUBCLONAL	1	TRUE	1	0.511908170264218	2		519	637	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782314	56782314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041024-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	205	660	0	ENST00000308159.5:c.155C>T	p.Ser52Phe	p.S52F	ENST00000308159	NM_014669.4	52	tCc/tTc	2/22	1	2	FACETS	0.957	0.889	1	0.957	0.889	1	CLONAL	1	TRUE	1	0.511908170264218	2		660	837	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005437	150005437	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778494156	NA	P-0041024-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	129	503	0	ENST00000253339.5:c.788C>T	p.Pro263Leu	p.P263L	ENST00000253339		263	cCa/cTa	3/7	1	2	FACETS	0.939	0.855	1	0.939	0.855	1	CLONAL	1	TRUE	1	0.511908170264218	2		503	537	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607595	43607595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041024-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	196	934	1	ENST00000355710.3:c.1571G>A	p.Arg524Lys	p.R524K	ENST00000355710	NM_020975.4	524	aGa/aAa	8/20	1	2	FACETS	0.905	0.839	0.974	0.905	0.839	0.974	CLONAL	1	TRUE	1	0.511908170264218	2		935	846	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122704	108122704	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587780614	NA	P-0041024-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	80	399	0	ENST00000278616.4:c.1748A>G	p.Tyr583Cys	p.Y583C	ENST00000278616	NM_000051.3	583	tAt/tGt	11/63	1	2	FACETS	0.706	0.624	0.793	0.706	0.624	0.793	SUBCLONAL	1	TRUE	1	0.511908170264218	2		399	443	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472233	472233	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041024-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	80	365	0	ENST00000399788.2:c.568G>A	p.Glu190Lys	p.E190K	ENST00000399788	NM_001042603.1	190	Gaa/Aaa	5/28	1	2	FACETS	0.732	0.647	0.822	0.732	0.647	0.822	SUBCLONAL	1	TRUE	1	0.511908170264218	2		365	427	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905417	11905417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041024-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	91	389	0	ENST00000396373.4:c.67C>T	p.Pro23Ser	p.P23S	ENST00000396373	NM_001987.4	23	Cca/Tca	2/8	1	2	FACETS	0.684	0.609	0.763	0.684	0.609	0.763	SUBCLONAL	1	TRUE	1	0.511908170264218	2		389	520	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862709	9862709	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041024-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	109	459	0	ENST00000330684.3:c.2594G>A	p.Arg865Lys	p.R865K	ENST00000330684	NM_001134407.1	865	aGg/aAg	12/13	1	2	FACETS	0.862	0.778	0.95	0.862	0.778	0.95	CLONAL	1	TRUE	1	0.511908170264218	2		459	494	SUCCESS
APC	324	MSKCC	GRCh37	5	112179402	112179402	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041024-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	48	465	0	ENST00000257430.4:c.8114del	p.Asn2705MetfsTer18	p.N2705Mfs*18	ENST00000257430	NM_000038.5	2704	cAa/ca	16/16	1	2	FACETS	0.34	0.287	0.398	0.34	0.287	0.398	SUBCLONAL	1	TRUE	1	0.511908170264218	2		465	552	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683782	162683782	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1435195836	NA	P-0041024-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	88	361	0	ENST00000366898.1:c.187C>T	p.Gln63Ter	p.Q63*	ENST00000366898	NM_004562.2	63	Cag/Tag	3/12	1	2	FACETS	0.776	0.691	0.866	0.776	0.691	0.866	SUBCLONAL	1	TRUE	1	0.511908170264218	2		361	443	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412587	63412588	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0041024-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	127	559	0	ENST00000330258.3:c.579_580delinsAT	p.Ala194Ser	p.A194S	ENST00000330258	NM_152424.3	193	ggGGcc/ggATcc	2/2	1	2	FACETS	0.917	0.835	1	0.917	0.835	1	CLONAL	1	TRUE	1	0.511908170264218	2		559	541	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0041027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	258	667	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.847372988127749	2		667	568	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008300	29008300	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	172	237	0	ENST00000282397.4:c.571G>T	p.Gly191Cys	p.G191C	ENST00000282397	NM_002019.4	191	Ggc/Tgc	5/30	1	2	FACETS	0.946	0.881	1	0.946	0.881	1	CLONAL	1	TRUE	1	0.847372988127749	2		237	429	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436002	56436002	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1366537134	NA	P-0041027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	693	379	0	ENST00000407977.2:c.1135C>T	p.Gln379Ter	p.Q379*	ENST00000407977		379	Cag/Tag	9/10	0.847372988127749	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.847372988127749	3		379	770	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438494	52438494	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756443059	NA	P-0041027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	329	500	2	ENST00000460680.1:c.1225G>A	p.Val409Met	p.V409M	ENST00000460680	NM_004656.3	409	Gtg/Atg	12/17	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.847372988127749	2		502	738	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259996	16260007	+	frameshift_variant	Frame_Shift_Del	DEL	ACTCCAACCAAA	ACTCCAACCAAA	GG	novel	NA	P-0041027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	299	564	1	ENST00000375759.3:c.7261_7272delinsGG	p.Thr2421GlyfsTer36	p.T2421Gfs*36	ENST00000375759	NM_015001.2	2421	ACTCCAACCAAA/GG	11/15	1	2	FACETS	0.922	0.873	0.972	0.922	0.873	0.972	CLONAL	1	TRUE	1	0.847372988127749	2		565	765	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867496	45867496	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	417	711	0	ENST00000391945.4:c.812T>C	p.Leu271Pro	p.L271P	ENST00000391945	NM_000400.3	271	cTc/cCc	9/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.847372988127749	2		711	981	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860692	151860692	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs772605130	NA	P-0041027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	251	369	0	ENST00000262189.6:c.9970A>G	p.Thr3324Ala	p.T3324A	ENST00000262189	NM_170606.2	3324	Act/Gct	43/59	1	2	FACETS	0.97	0.914	1	0.97	0.914	1	CLONAL	1	TRUE	1	0.847372988127749	2		369	611	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	120	348	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.924	0.847	1	0.924	0.847	1	CLONAL	1	TRUE	1	0.848796331551526	2		349	306	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272308	38272308	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs869320694	NA	P-0041058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	196	525	0	ENST00000425967.3:c.2059A>G	p.Lys687Glu	p.K687E	ENST00000425967	NM_001174067.1	687	Aag/Gag	15/19	1	2	FACETS	0.962	0.9	1	0.962	0.9	1	CLONAL	1	TRUE	1	0.848796331551526	2		525	480	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550577	29550577	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	94	177	0	ENST00000356175.3:c.1841del	p.Asn614IlefsTer17	p.N614Ifs*17	ENST00000356175	NM_000267.3	613	Aaa/aa	16/57	1	2	FACETS	0.971	0.881	1	0.971	0.881	1	CLONAL	1	TRUE	1	0.848796331551526	2		177	228	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667610	29667612	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0041058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	239	475	0	ENST00000356175.3:c.6949_6951del	p.Leu2317del	p.L2317del	ENST00000356175	NM_000267.3	2316	CTT/-	46/57	1	2	FACETS	0.973	0.916	1	0.973	0.916	1	CLONAL	1	TRUE	1	0.848796331551526	2		475	579	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791820	42791820	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	211	638	3	ENST00000575354.2:c.706G>A	p.Glu236Lys	p.E236K	ENST00000575354	NM_015125.3	236	Gag/Aag	5/20	1	2	FACETS	0.872	0.816	0.929	0.872	0.816	0.929	CLONAL	1	TRUE	1	0.848796331551526	2		641	570	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339241	70339261	+	inframe_deletion	In_Frame_Del	DEL	AATGTAAAACAAGGTTTCAAT	AATGTAAAACAAGGTTTCAAT	-	novel	NA	P-0041058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	166	522	0	ENST00000374080.3:c.120_140del	p.Val41_Asn47del	p.V41_N47del	ENST00000374080		40	AATGTAAAACAAGGTTTCAAT/-	2/45	1	2	FACETS	0.856	0.794	0.919	0.856	0.794	0.919	CLONAL	1	TRUE	1	0.848796331551526	2		522	457	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0041145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	118	308	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.564501572420366	3	FACETS	0.903	0.819	0.991	0.452	0.409	0.496	CLONAL	1	TRUE	1	0.694380513009841	3		308	507	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888189	112888189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507511	NA	P-0041145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	420	608	0	ENST00000351677.2:c.205G>A	p.Glu69Lys	p.E69K	ENST00000351677	NM_002834.3	69	Gag/Aag	3/16	0.680495505433412	3	FACETS	0.943	0.904	0.982	0.943	0.904	0.982	CLONAL	2	TRUE	1	0.694380513009841	3		608	864	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557890	29557890	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555614635	NA	P-0041145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	123	179	0	ENST00000356175.3:c.3144G>A	p.Trp1048Ter	p.W1048*	ENST00000356175	NM_000267.3	1048	tgG/tgA	24/57	0.694380513009841	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.694380513009841	2		179	170	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631934	90631934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913502	NA	P-0041148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	225	768	0	ENST00000330062.3:c.419G>A	p.Arg140Gln	p.R140Q	ENST00000330062	NM_002168.2	140	cGg/cAg	4/11	1	2	FACETS	0.911	0.849	0.975	0.911	0.849	0.975	CLONAL	1	TRUE	1	0.513631101986145	2		768	962	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842419	68842420	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	193	631	0	ENST00000261769.5:c.481dup	p.Ile161AsnfsTer7	p.I161Nfs*7	ENST00000261769	NM_004360.3	160	-/A	4/16	0.513631101986145	1	FACETS	0.923	0.859	0.989	0.923	0.859	0.989	CLONAL	1	TRUE	0	0.513631101986145	1		631	605	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0041151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	212	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.594170795365616	3	FACETS	0.897	0.841	0.953	0.897	0.841	0.953	CLONAL	2	TRUE	1	0.594170795365616	3		311	516	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0041151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	92	388	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.9	0.807	0.997	0.9	0.807	0.997	CLONAL	1	TRUE	1	0.594170795365616	2		388	344	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0041151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	89	146	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.927	0.831	1	0.927	0.831	1	CLONAL	1	TRUE	1	0.594170795365616	2		146	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0041151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	329	1060	0	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.594170795365616	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.594170795365616	1		1060	749	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411246	63411246	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	498	742	0	ENST00000330258.3:c.1921C>T	p.Arg641Ter	p.R641*	ENST00000330258	NM_152424.3	641	Cga/Tga	2/2	0.594170795365616	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.594170795365616	3		742	1011	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0041164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	49	763	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	FALSE	1	0.180864412833228	2		763	462	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468463	89468463	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	10	357	0	ENST00000336596.2:c.1997A>G	p.Asp666Gly	p.D666G	ENST00000336596	NM_005233.5	666	gAc/gGc	11/17	1	2	FACETS	0.595	0.403	0.835	0.595	0.403	0.835	SUBCLONAL	1	FALSE	1	0.180864412833228	2		357	186	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921555	178921555	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	27	298	0	ENST00000263967.3:c.1037T>G	p.Val346Gly	p.V346G	ENST00000263967	NM_006218.2	346	gTa/gGa	5/21	1	2	FACETS	0.816	0.655	0.997	1	0.943	1	CLONAL	2	FALSE	1	0.180864412833228	2		298	183	SUCCESS
APC	324	MSKCC	GRCh37	5	112173340	112173340	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	18	301	0	ENST00000257430.4:c.2051del	p.Leu684CysfsTer34	p.L684Cfs*34	ENST00000257430	NM_000038.5	683	acT/ac	16/16	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	FALSE	1	0.180864412833228	2		301	145	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413033	63413033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1190709308	NA	P-0041164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	24	930	0	ENST00000330258.3:c.134C>T	p.Ser45Phe	p.S45F	ENST00000330258	NM_152424.3	45	tCc/tTc	2/2	1	2	FACETS	0.638	0.499	0.798	0.638	0.499	0.798	SUBCLONAL	1	FALSE	1	0.180864412833228	2		930	416	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0041167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	18	667	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.376	0.281	0.489	0.376	0.281	0.489	SUBCLONAL	1	TRUE	1	0.12	2		667	798	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0041167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	104	704	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	2	TRUE	NA	0.12	2		704	741	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842471	68842479	+	splice_donor_variant,intron_variant	Splice_Site	DEL	GTAGAGAAA	GTAGAGAAA	-	novel	NA	P-0041167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	116	536	0	ENST00000261769.5:c.531+2_531+10del		p.X177_splice	ENST00000261769	NM_004360.3	177			0.216221172264991	2	FACETS	1	0.947	1	1	0.986	1	CLONAL	3	TRUE	0	0.12	2		536	602	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115903	8115904	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0041171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	112	514	0	ENST00000346208.3:c.1251dup	p.Thr418HisfsTer89	p.T418Hfs*89	ENST00000346208		417	acc/aCcc	6/6	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.372906586028854	2		514	515	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257131	16257131	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	100	569	1	ENST00000375759.3:c.4396G>T	p.Asp1466Tyr	p.D1466Y	ENST00000375759	NM_015001.2	1466	Gat/Tat	11/15	0.372906586028854	1	FACETS	0.94	0.844	1	0.94	0.844	1	CLONAL	1	TRUE	0	0.372906586028854	1		570	464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0041183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	112	689	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.3	1	FACETS	0.829	0.747	0.916	1	0.986	1	CLONAL	2	TRUE	0	0.18	1		689	683	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0041183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	54	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.18	2		539	414	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0041183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	32	554	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.785	0.637	0.953	0.785	0.637	0.953	CLONAL	1	TRUE	1	0.18	2		554	453	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0041183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	22	180	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	1	2	FACETS	0.796	0.617	1	0.796	0.617	1	CLONAL	1	TRUE	1	0.18	2		180	307	SUCCESS
APC	324	MSKCC	GRCh37	5	112174466	112174466	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	51	289	0	ENST00000257430.4:c.3175G>T	p.Glu1059Ter	p.E1059*	ENST00000257430	NM_000038.5	1059	Gaa/Taa	16/16	1	2	FACETS	1	0.914	1	1	0.977	1	CLONAL	2	TRUE	1	0.18	2		289	259	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119114	70119114	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0041183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	68	385	0	ENST00000245479.2:c.685+1G>A		p.X229_splice	ENST00000245479	NM_000346.3	229			0.20635314958397	2	FACETS	0.95	0.836	1	1	0.973	1	CLONAL	3	TRUE	0	0.18	2		385	265	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713411	30713412	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	83	550	1	ENST00000295754.5:c.737dup	p.Asp247GlyfsTer11	p.D247Gfs*11	ENST00000295754	NM_003242.5	246	ctg/cTtg	4/7	0.178064107568114	2	FACETS	0.915	0.81	1	0.915	0.81	1	CLONAL	2	TRUE	0	0.18	2		551	504	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098615	47098615	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	307	557	0	ENST00000409792.3:c.6659del	p.Pro2220LeufsTer28	p.P2220Lfs*28	ENST00000409792	NM_014159.6	2220	cCt/ct	15/21	1	2	FACETS	0.986	0.935	1	0.986	0.935	1	CLONAL	1	TRUE	1	0.844885925515931	2		557	737	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131976480	131976481	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0041191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	263	456	0	ENST00000265335.6:c.3736dup	p.Ala1246GlyfsTer6	p.A1246Gfs*6	ENST00000265335		1245	-/G	24/25	1	2	FACETS	0.974	0.92	1	0.974	0.92	1	CLONAL	1	TRUE	1	0.844885925515931	2		456	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0041198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	254	853	1	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.617910201936618	1	FACETS	0.976	0.922	1	0.976	0.922	1	CLONAL	1	TRUE	0	0.617910201936618	1		854	582	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711879	89711879	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1554900515	NA	P-0041198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	134	422	0	ENST00000371953.3:c.497T>A	p.Val166Glu	p.V166E	ENST00000371953	NM_000314.4	166	gTa/gAa	6/9	0.617910201936618	2	FACETS	1	0.966	1	0.55	0.505	0.597	CLONAL	1	TRUE	0	0.617910201936618	2		422	394	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347911	73347911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146500302	NA	P-0041198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	218	335	0	ENST00000377767.4:c.1150C>T	p.Arg384Cys	p.R384C	ENST00000377767	NM_014953.3	384	Cgc/Tgc	8/21	0.617910201936618	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.617910201936618	2		335	352	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097641	27097642	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	211	632	0	ENST00000324856.7:c.3232dup	p.Thr1078AsnfsTer27	p.T1078Nfs*27	ENST00000324856	NM_006015.4	1077	gca/gcAa	12/20	1	2	FACETS	0.889	0.828	0.952	0.889	0.828	0.952	CLONAL	1	TRUE	1	0.617910201936618	2		632	768	SUCCESS
APC	324	MSKCC	GRCh37	5	112174223	112174223	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	121	441	0	ENST00000257430.4:c.2932C>T	p.Gln978Ter	p.Q978*	ENST00000257430	NM_000038.5	978	Caa/Taa	16/16	1	2	FACETS	0.965	0.879	1	0.965	0.879	1	CLONAL	1	TRUE	1	0.617910201936618	2		441	406	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656682	3656682	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201769293	NA	P-0041198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	336	891	0	ENST00000294008.3:c.553G>A	p.Asp185Asn	p.D185N	ENST00000294008	NM_032444.2	185	Gac/Aac	3/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.617910201936618	2		891	1034	SUCCESS
APC	324	MSKCC	GRCh37	5	112174664	112174664	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	121	438	0	ENST00000257430.4:c.3373del	p.Val1125Ter	p.V1125*	ENST00000257430	NM_000038.5	1125	Gta/ta	16/16	1	2	FACETS	0.902	0.821	0.986	0.902	0.821	0.986	CLONAL	1	TRUE	1	0.617910201936618	2		438	434	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	65	348	1				ENST00000310581	NM_198253.2	-/1132			0.319634404743685	3	FACETS	0.828	0.727	0.935	0.828	0.727	0.935	CLONAL	2	TRUE	1	0.38514466108191	3		349	243	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	230	510	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	NA	2	FACETS	0.894	0.838	0.951			1	INDETERMINATE	2	TRUE	NA	0.38514466108191	2		510	668	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771344	68771344	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	106	264	0	ENST00000261769.5:c.26C>A	p.Ser9Ter	p.S9*	ENST00000261769	NM_004360.3	9	tCg/tAg	1/16	0.32714956796429	2	FACETS	0.927	0.842	1	0.927	0.842	1	CLONAL	2	TRUE	0	0.38514466108191	2		264	297	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118350888	118350888	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0041220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	105	332	0	ENST00000534358.1:c.3570-1G>A		p.X1190_splice	ENST00000534358	NM_005933.3	1190			0.347697164966995	2	FACETS	0.915	0.831	1	0.915	0.831	1	CLONAL	2	TRUE	0	0.38514466108191	2		332	298	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955580	48955580	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587778857	NA	P-0041220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	86	269	0	ENST00000267163.4:c.1695+1G>A		p.X565_splice	ENST00000267163	NM_000321.2	565			0.148403382142382	1	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	1	TRUE	0	0.38514466108191	1		269	261	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993510	72993510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	289	807	0	ENST00000268489.5:c.535G>A	p.Gly179Ser	p.G179S	ENST00000268489	NM_006885.3	179	Ggc/Agc	2/10	0.32714956796429	2	FACETS	0.978	0.925	1	0.978	0.925	1	CLONAL	2	TRUE	0	0.38514466108191	2		807	767	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626805	14626805	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377706903	NA	P-0041220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	136	617	1	ENST00000254322.2:c.970G>A	p.Glu324Lys	p.E324K	ENST00000254322	NM_006145.1	324	Gaa/Aaa	3/3	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.38514466108191	2		618	690	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753271	42753271	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	186	918	0	ENST00000222329.4:c.993C>G	p.Phe331Leu	p.F331L	ENST00000222329	NM_006494.2	331	ttC/ttG	4/4	0.28749319222052	5	FACETS	1	0.974	1	0.377	0.347	0.408	CLONAL	1	TRUE	2	0.38514466108191	5		918	1349	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750667	39750667	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	79	281	0	ENST00000361337.2:c.2067G>C	p.Lys689Asn	p.K689N	ENST00000361337	NM_003286.2	689	aaG/aaC	20/21	0.243474730607729	3	FACETS	1	0.975	1	0.699	0.619	0.783	CLONAL	1	TRUE	1	0.38514466108191	3		281	350	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051582	30051582	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1064796632	NA	P-0041220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	99	296	0	ENST00000338641.4:c.517-1G>A		p.X173_splice	ENST00000338641	NM_000268.3	173			0.32714956796429	2	FACETS	0.851	0.77	0.936	0.851	0.77	0.936	CLONAL	2	TRUE	0	0.38514466108191	2		296	302	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931326	131931326	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	146	467	0	ENST00000265335.6:c.2031C>A	p.Asn677Lys	p.N677K	ENST00000265335		677	aaC/aaA	13/25	0.319634404743685	3	FACETS	1	0.988	1	0.745	0.682	0.81	CLONAL	1	TRUE	1	0.38514466108191	3		467	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0041234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	450	600	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.654698773623462	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.654698773623462	2		601	676	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121800	108121800	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0041234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	81	292	0	ENST00000278616.4:c.1607+1G>A		p.X536_splice	ENST00000278616	NM_000051.3	536			0.654698773623462	3	FACETS	0.773	0.684	0.867	0.258	0.228	0.289	SUBCLONAL	1	TRUE	0	0.654698773623462	3		292	425	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733268	40733268	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs779305073	NA	P-0041234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	183	541	1	ENST00000373198.4:c.3538T>A	p.Tyr1180Asn	p.Y1180N	ENST00000373198	NM_133170.3	1180	Tac/Aac	26/32	0.344392315014904	5	FACETS	1	0.952	1	0.348	0.321	0.377	INDETERMINATE	1	TRUE	2	0.654698773623462	5		542	1060	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385216	4385216	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	90	570	1	ENST00000261254.3:c.241A>C	p.Met81Leu	p.M81L	ENST00000261254	NM_001759.3	81	Atg/Ctg	2/5	0.300190253372587	6	FACETS	1	0.931	1	0.266	0.236	0.298	INDETERMINATE	1	TRUE	2	0.561169759124254	6		571	639	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437349	220437349	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	101	805	0	ENST00000243786.2:c.253C>G	p.Leu85Val	p.L85V	ENST00000243786	NM_002191.3	85	Ctt/Gtt	1/2	0.316390231565082	4	FACETS	0.898	0.804	0.997	0.449	0.402	0.499	INDETERMINATE	1	TRUE	2	0.561169759124254	4		805	626	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043401	180043401	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	117	734	0	ENST00000261937.6:c.3185T>G	p.Ile1062Ser	p.I1062S	ENST00000261937	NM_182925.4	1062	aTc/aGc	23/30	0.507117968375632	2	FACETS	0.925	0.839	1	0.462	0.419	0.507	CLONAL	1	TRUE	0	0.561169759124254	2		734	451	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242514	55242514	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs397517104	NA	P-0041279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	54	397	0	ENST00000275493.2:c.2283+1G>A		p.X761_splice	ENST00000275493	NM_005228.3	761			0.497736547588296	1	FACETS	0.558	0.481	0.641	0.558	0.481	0.641	SUBCLONAL	1	TRUE	0	0.561169759124254	1		397	248	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0041292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	112	1003	1	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.212597594222769	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.212597594222769	1		1004	727	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	82	245	0	ENST00000257430.4:c.4199del	p.Ser1400Ter	p.S1400*	ENST00000257430	NM_000038.5	1400	tCg/tg	16/16	0.212597594222769	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.212597594222769	2		245	348	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118924	70118926	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0041292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	37	684	0	ENST00000245479.2:c.499_501del	p.Lys167del	p.K167del	ENST00000245479	NM_000346.3	166	AAG/-	2/3	1	2	FACETS	0.572	0.471	0.687	0.572	0.471	0.687	SUBCLONAL	1	TRUE	1	0.212597594222769	2		684	608	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217680	7217681	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0041292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	52	367	0	ENST00000380728.2:c.246_247del	p.Lys83AlafsTer13	p.K83Afs*13	ENST00000380728		82	gaGAag/gaag	4/11	0.212597594222769	1	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	0	0.212597594222769	1		367	431	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603138	48603138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	47	374	0	ENST00000342988.3:c.1439C>T	p.Pro480Leu	p.P480L	ENST00000342988	NM_005359.5	480	cCa/cTa	11/12	0.212597594222769	1	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	0	0.212597594222769	1		374	373	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625632	1625657	+	frameshift_variant	Frame_Shift_Del	DEL	GGGAGGTCCCCTTCATGCCCGAAGGG	GGGAGGTCCCCTTCATGCCCGAAGGG	-	novel	NA	P-0041292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	55	797	0	ENST00000344749.5:c.417_442del	p.Pro140ValfsTer43	p.P140Vfs*43	ENST00000344749	NM_001136139.2	139	tcCCCTTCGGGCATGAAGGGGACCTCCCag/tcag	7/19	1	2	FACETS	0.767	0.655	0.889	0.767	0.655	0.889	SUBCLONAL	1	TRUE	1	0.212597594222769	2		797	675	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611135	100611135	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	41	507	0	ENST00000308731.7:c.1471C>A	p.His491Asn	p.H491N	ENST00000308731	NM_000061.2	491	Cac/Aac	15/19	1	2	FACETS	0.805	0.671	0.955	0.805	0.671	0.955	CLONAL	1	TRUE	1	0.212597594222769	2		507	479	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	375	756	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.131009098307346	5	FACETS	0.929	0.894	0.963			1	INDETERMINATE	4	FALSE	NA	0.71059144876151	5		756	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0041303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	433	957	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.502008516988576	3	FACETS	0.994	0.966	1			1	CLONAL	3	FALSE	NA	0.71059144876151	3		957	554	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519893	NA	P-0041303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	239	996	2	ENST00000267101.3:c.310G>T	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ttg	3/28	0.30425417907405	6	FACETS	0.828	0.773	0.884			1	INDETERMINATE	2	FALSE	NA	0.71059144876151	6		998	984	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909998	100910019	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACAAGCTGTTGGTTTAACAAAT	ACAAGCTGTTGGTTTAACAAAT	TCAAAC	novel	NA	P-0041303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	78	163	1	ENST00000325455.5:c.2647-17_2651delinsGTTTGA		p.X883_splice	ENST00000325455	NM_001202474.3	883		8/8	0.648506842355352	3	FACETS	0.904	0.801	1	0.452	0.4	0.507	CLONAL	1	FALSE	1	0.71059144876151	3		164	329	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440018	99440018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs969092160	NA	P-0041303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	26	364	0	ENST00000268035.6:c.986C>T	p.Pro329Leu	p.P329L	ENST00000268035	NM_000875.3	329	cCg/cTg	4/21	0.320133468125357	3	FACETS	0.264	0.209	0.327	0.088	0.069	0.109	INDETERMINATE	1	FALSE	0	0.71059144876151	3		364	376	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510059	187510059	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs376173860	NA	P-0041303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	52	528	0	ENST00000441802.2:c.13454A>G	p.Asn4485Ser	p.N4485S	ENST00000441802	NM_005245.3	4485	aAc/aGc	27/27	0.428027887441681	1	FACETS	0.421	0.363	0.484	0.421	0.363	0.484	SUBCLONAL	1	FALSE	0	0.71059144876151	1		528	224	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0041323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	43	482	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.599	0.506	0.7	0.599	0.506	0.7	SUBCLONAL	1	TRUE	1	0.638054010295958	2		482	225	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0041323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	57	646	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.264	0.225	0.305	0.264	0.225	0.305	SUBCLONAL	1	TRUE	1	0.638054010295958	2		647	678	SUCCESS
APC	324	MSKCC	GRCh37	5	112174112	112174112	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	81	227	0	ENST00000257430.4:c.2821G>T	p.Glu941Ter	p.E941*	ENST00000257430	NM_000038.5	941	Gaa/Taa	16/16	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.638054010295958	2		227	245	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610695	52610695	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	77	286	0	ENST00000394830.3:c.3478C>T	p.Arg1160Ter	p.R1160*	ENST00000394830	NM_018313.4	1160	Cga/Tga	23/30	1	2	FACETS	0.832	0.739	0.931	0.832	0.739	0.931	CLONAL	1	TRUE	1	0.638054010295958	2		286	290	SUCCESS
APC	324	MSKCC	GRCh37	5	112175720	112175720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	95	267	0	ENST00000257430.4:c.4429C>T	p.Gln1477Ter	p.Q1477*	ENST00000257430	NM_000038.5	1477	Cag/Tag	16/16	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.638054010295958	2		267	293	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222435	39222435	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	276	561	0	ENST00000402219.2:c.3175G>A	p.Glu1059Lys	p.E1059K	ENST00000402219	NM_005633.3	1059	Gag/Aag	20/23	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.638054010295958	2		561	755	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590401	67590402	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	57	114	0	ENST00000274335.5:c.1464dup	p.Glu489Ter	p.E489*	ENST00000274335		488	aat/aaTt	11/15	0.638054010295958	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.638054010295958	1		114	117	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821346	32821346	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	280	709	0	ENST00000354258.4:c.248T>A	p.Leu83Gln	p.L83Q	ENST00000354258	NM_000593.5	83	cTg/cAg	1/11	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.638054010295958	2		709	672	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559090	29559090	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1223905930	NA	P-0041326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	44	60	0	ENST00000356175.3:c.3198-1G>A		p.X1066_splice	ENST00000356175	NM_000267.3	1066			0.293174206764396	1	FACETS	1	0.951	1	1	0.951	1	INDETERMINATE	1	TRUE	0	0.498429196091322	1		60	107	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226664	2226664	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	83	549	0	ENST00000398665.3:c.4144G>A	p.Glu1382Lys	p.E1382K	ENST00000398665	NM_032482.2	1382	Gag/Aag	27/28	0.498429196091322	1	FACETS	0.468	0.414	0.526	0.468	0.414	0.526	SUBCLONAL	1	TRUE	0	0.498429196091322	1		549	534	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442579	52442599	+	inframe_deletion	In_Frame_Del	DEL	GCTCTTCGATCCATTTGAACA	GCTCTTCGATCCATTTGAACA	-	novel	NA	P-0041326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	83	292	0	ENST00000460680.1:c.146_166del	p.Leu49_Glu55del	p.L49_E55del	ENST00000460680	NM_004656.3	49	cTGTTCAAATGGATCGAAGAGCgc/cgc	4/17	0.498429196091322	1	FACETS	0.731	0.651	0.816	0.731	0.651	0.816	SUBCLONAL	1	TRUE	0	0.498429196091322	1		292	342	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855029	76855029	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1557085898	NA	P-0041328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	9	341	0	ENST00000373344.5:c.5807A>G	p.Lys1936Arg	p.K1936R	ENST00000373344	NM_000489.3	1936	aAg/aGg	25/35	1	2	FACETS	0.139	0.091	0.2	0.139	0.091	0.2	SUBCLONAL	1	TRUE	1	0.31	2		341	418	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651289	52651289	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	75	372	1	ENST00000394830.3:c.1807G>T	p.Glu603Ter	p.E603*	ENST00000394830	NM_018313.4	603	Gag/Tag	15/30	0.297767976390814	1	FACETS	0.94	0.827	1	0.94	0.827	1	CLONAL	1	TRUE	0	0.31	1		373	435	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175507	108175507	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	50	362	0	ENST00000278616.4:c.5602G>T	p.Gly1868Ter	p.G1868*	ENST00000278616	NM_000051.3	1868	Gga/Tga	37/63	0.297767976390814	1	FACETS	0.569	0.483	0.663	0.569	0.483	0.663	SUBCLONAL	1	TRUE	0	0.31	1		362	479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579396	7579397	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	205	730	0	ENST00000269305.4:c.290dup	p.Ser99PhefsTer50	p.S99Ffs*50	ENST00000269305	NM_001126112.2	97	gtc/gtTc	4/11	0.297767976390814	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.31	1		730	980	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17125859	17125867	+	inframe_deletion	In_Frame_Del	DEL	TGTCAGCGA	TGTCAGCGA	-	rs1209487287	NA	P-0041328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	134	626	0	ENST00000285071.4:c.727_735del	p.Leu244_Ser246del	p.L244_S246del	ENST00000285071	NM_144997.5	243	TCGCTGACA/-	7/14	0.297767976390814	1	FACETS	0.835	0.758	0.915	0.835	0.758	0.915	CLONAL	1	TRUE	0	0.31	1		626	875	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771285	68771331	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	GGCGCCTGCCCTCGCTCGGCGTCCCCGGCCAGCCATGGGCCCTTGGA	GGCGCCTGCCCTCGCTCGGCGTCCCCGGCCAGCCATGGGCCCTTGGA	-	novel	NA	P-0041389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	58	302	0	ENST00000261769.5:c.-33_14del		p.*11*	ENST00000261769	NM_004360.3	?-5/882		1/16	0.454236181445276	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.454236181445276	1		302	175	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210790	36210790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	161	1004	0	ENST00000222270.7:c.541C>T	p.Arg181Trp	p.R181W	ENST00000222270	NM_014727.1	181	Cgg/Tgg	3/37	1	2	FACETS	0.97	0.891	1	0.97	0.891	1	CLONAL	1	TRUE	1	0.454236181445276	2		1004	731	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748092	41748092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	23	82	0	ENST00000226382.2:c.677C>T	p.Ala226Val	p.A226V	ENST00000226382	NM_003924.3	226	gCg/gTg	3/3	1	2	FACETS	0.904	0.738	1	1	0.95	1	CLONAL	2	TRUE	1	0.454236181445276	2		82	56	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589619	67589766	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGAATATGATAGATTATATGAAGAATATACCCGCACATCCCAGGTGAGTTTTCTATGAAAATCAGATTAAAAAATAAGAGTTCTAAACTTTTAAAGACTAACATGGAAAAAAGAATTTAAAAGGTTGAGTTTTTACGAATGAGGTGG	GAGAATATGATAGATTATATGAAGAATATACCCGCACATCCCAGGTGAGTTTTCTATGAAAATCAGATTAAAAAATAAGAGTTCTAAACTTTTAAAGACTAACATGGAAAAAAGAATTTAAAAGGTTGAGTTTTTACGAATGAGGTGG	-	novel	NA	P-0041389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	26	278	0	ENST00000274335.5:c.1383_1425+105del		p.X461_splice	ENST00000274335		461		10/15	0.454236181445276	3	FACETS	0.312	0.247	0.388	0.156	0.123	0.194	SUBCLONAL	1	TRUE	1	0.454236181445276	3		278	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0041414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	234	674	1	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.555623341377554	1	FACETS	0.981	0.922	1	0.981	0.922	1	CLONAL	1	TRUE	0	0.555623341377554	1		675	620	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224106	36224106	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	81	810	0	ENST00000222270.7:c.6656C>G	p.Pro2219Arg	p.P2219R	ENST00000222270	NM_014727.1	2219	cCt/cGt	28/37	1	2	FACETS	0.261	0.229	0.295	0.261	0.229	0.295	SUBCLONAL	1	TRUE	1	0.555623341377554	2		810	1118	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693006	89693009	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	AAGG	AAGG	-	novel	NA	P-0041432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	131	339	0	ENST00000371953.3:c.490_492+1del		p.X164_splice	ENST00000371953	NM_000314.4	164		5/9	NA	2	FACETS	0.967	0.9	1			1	INDETERMINATE	2	TRUE	NA	0.574176376881574	2		339	236	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001416	29001416	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	750	374	1	ENST00000282397.4:c.1316C>A	p.Pro439Gln	p.P439Q	ENST00000282397	NM_002019.4	439	cCa/cAa	10/30	0.574176376881574	8	FACETS	0.998	0.98	1	1	0.998	1	CLONAL	8	TRUE	1	0.574176376881574	8		375	891	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061129	38061130	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0041432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	216	319	0	ENST00000250448.2:c.859_860del	p.Ala287GlnfsTer5	p.A287Qfs*5	ENST00000250448	NM_004496.3	287	GCc/c	2/2	0.574176376881574	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.574176376881574	4		319	526	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498066	29498066	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	225	652	0	ENST00000389048.3:c.1940A>G	p.Asn647Ser	p.N647S	ENST00000389048	NM_004304.4	647	aAt/aGt	11/29	0.25222190972548	5	FACETS	0.937	0.876	1	0.625	0.584	0.667	INDETERMINATE	2	TRUE	2	0.574176376881574	5		652	778	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38975650	38975650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1333272721	NA	P-0041432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	431	544	0	ENST00000357387.3:c.878G>A	p.Arg293Gln	p.R293Q	ENST00000357387	NM_152756.3	293	cGa/cAa	10/38	0.574176376881574	6	FACETS	1	0.977	1	1	0.977	1	CLONAL	4	TRUE	2	0.574176376881574	6		544	789	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	163	348	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.475862416338679	2		349	542	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381466	81381466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	84	346	0	ENST00000222390.5:c.595G>A	p.Glu199Lys	p.E199K	ENST00000222390	NM_000601.4	199	Gaa/Aaa	5/18	1	2	FACETS	0.954	0.849	1	0.954	0.849	1	CLONAL	1	TRUE	1	0.475862416338679	2		346	370	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980744	40980744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199751250	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	126	545	0	ENST00000373198.4:c.1742G>A	p.Arg581Gln	p.R581Q	ENST00000373198	NM_133170.3	581	cGg/cAg	10/32	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.475862416338679	2		545	524	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956220	55956220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190050670	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	120	529	0	ENST00000263923.4:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000263923	NM_002253.2	1032	cGa/cAa	23/30	0.352451102766052	1	FACETS	0.86	0.782	0.941	0.86	0.782	0.941	CLONAL	1	TRUE	0	0.475862416338679	1		529	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	219	645	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.475862416338679	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.475862416338679	1		645	574	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106364	27106364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	218	671	0	ENST00000324856.7:c.5975C>T	p.Ser1992Leu	p.S1992L	ENST00000324856	NM_006015.4	1992	tCa/tTa	20/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.475862416338679	2		671	798	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528070	29528070	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	41	172	0	ENST00000356175.3:c.1078C>T	p.Pro360Ser	p.P360S	ENST00000356175	NM_000267.3	360	Cca/Tca	10/57	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.475862416338679	2		172	152	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424707	47424707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371247311	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	222	445	1	ENST00000377045.4:c.515C>T	p.Ser172Leu	p.S172L	ENST00000377045	NM_001654.4	172	tCg/tTg	6/16	1	1	FACETS	0.837	0.79	0.883	1	0.994	1	CLONAL	2	TRUE	0	0.475862416338679	1		446	425	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	117	365	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.475862416338679	2		365	427	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321372	1321372	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1319865856	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	168	634	2	ENST00000400841.2:c.383C>T	p.Ser128Leu	p.S128L	ENST00000400841		128	tCg/tTg	4/6	1	1	FACETS	0.857	0.791	0.925	0.857	0.791	0.925	CLONAL	1	TRUE	0	0.475862416338679	1		636	628	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862887	9862887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868222927	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	319	718	1	ENST00000330684.3:c.2416G>A	p.Glu806Lys	p.E806K	ENST00000330684	NM_001134407.1	806	Gag/Aag	12/13	1	2	FACETS	1	0.974	1	1	0.996	1	CLONAL	2	TRUE	1	0.475862416338679	2		719	648	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586470	189586470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147148566	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	123	507	0	ENST00000264731.3:c.1094C>T	p.Ser365Leu	p.S365L	ENST00000264731	NM_003722.4	365	tCg/tTg	8/14	1	2	FACETS	0.987	0.896	1	0.987	0.896	1	CLONAL	1	TRUE	1	0.475862416338679	2		507	524	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781201	161781201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55830907	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	158	599	0	ENST00000366898.1:c.1204C>T	p.Arg402Cys	p.R402C	ENST00000366898	NM_004562.2	402	Cgt/Tgt	11/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.475862416338679	2		599	601	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504401	8504401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757922864	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	63	485	0	ENST00000356435.5:c.1682G>A	p.Arg561Gln	p.R561Q	ENST00000356435		561	cGa/cAa	12/35	0.221001478014439	1	FACETS	0.508	0.441	0.58	0.508	0.441	0.58	INDETERMINATE	1	TRUE	0	0.475862416338679	1		485	397	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911144	40911144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776134993	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	82	468	0	ENST00000373198.4:c.2161C>T	p.Arg721Cys	p.R721C	ENST00000373198	NM_133170.3	721	Cgt/Tgt	13/32	1	2	FACETS	0.893	0.792	0.999	0.893	0.792	0.999	CLONAL	1	TRUE	1	0.475862416338679	2		468	386	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041739	29041739	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	67	413	0	ENST00000282397.4:c.80C>T	p.Ser27Leu	p.S27L	ENST00000282397	NM_002019.4	27	tCa/tTa	2/30	1	2	FACETS	0.763	0.667	0.866	0.763	0.667	0.866	SUBCLONAL	1	TRUE	1	0.475862416338679	2		413	369	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245843	46245843	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	110	407	0	ENST00000334344.6:c.3937C>T	p.Gln1313Ter	p.Q1313*	ENST00000334344	NM_152641.2	1313	Caa/Taa	15/21	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.475862416338679	2		407	455	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250922	99250922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	179	694	0	ENST00000268035.6:c.226C>T	p.Pro76Ser	p.P76S	ENST00000268035	NM_000875.3	76	Ccc/Tcc	2/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.475862416338679	2		694	710	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888286	112888286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	102	440	0	ENST00000351677.2:c.302C>T	p.Pro101Leu	p.P101L	ENST00000351677	NM_002834.3	101	cCt/cTt	3/16	1	2	FACETS	0.884	0.794	0.978	0.884	0.794	0.978	CLONAL	1	TRUE	1	0.475862416338679	2		440	485	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498004	29498004	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1208550472	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	180	696	0	ENST00000389048.3:c.2002G>A	p.Glu668Lys	p.E668K	ENST00000389048	NM_004304.4	668	Gaa/Aaa	11/29	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.475862416338679	2		696	662	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857784	9857784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145861983	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	157	542	0	ENST00000330684.3:c.3617G>A	p.Arg1206Gln	p.R1206Q	ENST00000330684	NM_001134407.1	1206	cGa/cAa	13/13	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.475862416338679	2		542	626	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030485	49030485	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs483352690	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	54	296	0	ENST00000267163.4:c.1960G>A	p.Val654Met	p.V654M	ENST00000267163	NM_000321.2	654	Gtg/Atg	19/27	1	2	FACETS	0.88	0.758	1	0.88	0.758	1	CLONAL	1	TRUE	1	0.475862416338679	2		296	258	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087961	27087961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	173	558	1	ENST00000324856.7:c.2248C>T	p.Arg750Ter	p.R750*	ENST00000324856	NM_006015.4	750	Cga/Tga	6/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.475862416338679	2		559	608	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781225	161781225	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1801334	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	111	569	1	ENST00000366898.1:c.1180G>A	p.Asp394Asn	p.D394N	ENST00000366898	NM_004562.2	394	Gat/Aat	11/12	1	2	FACETS	0.862	0.778	0.951	0.862	0.778	0.951	CLONAL	1	TRUE	1	0.475862416338679	2		570	541	SUCCESS
AXL	558	MSKCC	GRCh37	19	41736901	41736901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201799923	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	199	900	1	ENST00000301178.4:c.616G>A	p.Glu206Lys	p.E206K	ENST00000301178	NM_021913.4	206	Gaa/Aaa	5/20	0.475862416338679	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.475862416338679	1		901	626	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156738	2156738	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	198	758	0	ENST00000434045.2:c.184G>A	p.Gly62Arg	p.G62R	ENST00000434045	NM_001127598.1	62	Ggg/Agg	3/5	0.475862416338679	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.475862416338679	1		758	597	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286913	33286913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	224	787	0	ENST00000374542.5:c.2024C>T	p.Ser675Phe	p.S675F	ENST00000374542	NM_001141970.1	675	tCc/tTc	7/8	0.450129080760029	3	FACETS	1	0.96	1	0.522	0.486	0.56	CLONAL	1	TRUE	1	0.475862416338679	3		787	1116	SUCCESS
REL	5966	MSKCC	GRCh37	2	61128146	61128146	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	57	288	0	ENST00000295025.8:c.322C>T	p.Arg108Ter	p.R108*	ENST00000295025	NM_002908.2	108	Cga/Tga	4/11	1	2	FACETS	0.715	0.617	0.821	0.715	0.617	0.821	SUBCLONAL	1	TRUE	1	0.475862416338679	2		288	335	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	256524	256524	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	93	476	0	ENST00000264932.6:c.1984C>T	p.Arg662Cys	p.R662C	ENST00000264932	NM_004168.2	662	Cgc/Tgc	15/15	1	2	FACETS	0.809	0.722	0.901	0.809	0.722	0.901	CLONAL	1	TRUE	1	0.475862416338679	2		476	483	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68301905	68301905	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	174	578	2	ENST00000487270.1:c.307C>T	p.Leu103Phe	p.L103F	ENST00000487270	NM_133509.3	103	Ctc/Ttc	4/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.475862416338679	2		580	599	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965706	93965706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	71	361	0	ENST00000369303.4:c.2222G>A	p.Gly741Glu	p.G741E	ENST00000369303	NM_004440.3	741	gGa/gAa	13/17	1	2	FACETS	0.843	0.74	0.952	0.843	0.74	0.952	CLONAL	1	TRUE	1	0.475862416338679	2		361	354	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509768	187509768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766893768	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	29	323	0	ENST00000441802.2:c.13745C>T	p.Ser4582Phe	p.S4582F	ENST00000441802	NM_005245.3	4582	tCc/tTc	27/27	0.352451102766052	1	FACETS	0.402	0.324	0.49	0.402	0.324	0.49	SUBCLONAL	1	TRUE	0	0.475862416338679	1		323	231	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244706	46244706	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	152	607	1	ENST00000334344.6:c.2800C>T	p.Gln934Ter	p.Q934*	ENST00000334344	NM_152641.2	934	Caa/Taa	15/21	1	2	FACETS	0.929	0.851	1	0.929	0.851	1	CLONAL	1	TRUE	1	0.475862416338679	2		608	688	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713536	30713536	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	143	589	0	ENST00000295754.5:c.861G>A	p.Trp287Ter	p.W287*	ENST00000295754	NM_003242.5	287	tgG/tgA	4/7	1	2	FACETS	0.957	0.875	1	0.957	0.875	1	CLONAL	1	TRUE	1	0.475862416338679	2		589	628	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435061	18435061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603400	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	83	371	0	ENST00000266497.5:c.46G>A	p.Glu16Lys	p.E16K	ENST00000266497		16	Gaa/Aaa	1/31	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.475862416338679	2		371	307	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460515	149460515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777239066	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	151	853	0	ENST00000286301.3:c.122G>A	p.Arg41Gln	p.R41Q	ENST00000286301	NM_005211.3	41	cGa/cAa	3/22	1	2	FACETS	0.835	0.764	0.909	0.835	0.764	0.909	CLONAL	1	TRUE	1	0.475862416338679	2		853	760	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969912	161969912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1460011098	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	154	617	1	ENST00000366898.1:c.1057G>A	p.Glu353Lys	p.E353K	ENST00000366898	NM_004562.2	353	Gaa/Aaa	9/12	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.475862416338679	2		618	615	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518111	8518111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	130	485	0	ENST00000356435.5:c.1280G>A	p.Arg427Gln	p.R427Q	ENST00000356435		427	cGa/cAa	10/35	0.221001478014439	1	FACETS	0.86	0.785	0.938	0.86	0.785	0.938	INDETERMINATE	1	TRUE	0	0.475862416338679	1		485	484	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968610	55968610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374980446	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	150	756	0	ENST00000263923.4:c.2053G>A	p.Glu685Lys	p.E685K	ENST00000263923	NM_002253.2	685	Gaa/Aaa	14/30	0.352451102766052	1	FACETS	0.812	0.745	0.881	0.812	0.745	0.881	CLONAL	1	TRUE	0	0.475862416338679	1		756	592	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499354	89499354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	101	415	0	ENST00000336596.2:c.2524C>T	p.Arg842Ter	p.R842*	ENST00000336596	NM_005233.5	842	Cga/Tga	15/17	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.475862416338679	2		415	397	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288600	33288600	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs779014832	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	288	496	0	ENST00000374542.5:c.952C>T	p.Arg318Ter	p.R318*	ENST00000374542	NM_001141970.1	318	Cga/Tga	3/8	0.450129080760029	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.475862416338679	3		496	672	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570054	212570054	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368876919	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	83	444	0	ENST00000342788.4:c.1187G>A	p.Arg396Lys	p.R396K	ENST00000342788	NM_005235.2	396	aGa/aAa	10/28	1	2	FACETS	0.935	0.831	1	0.935	0.831	1	CLONAL	1	TRUE	1	0.475862416338679	2		444	373	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829272	128829272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs924171569	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	212	764	0	ENST00000249373.3:c.280G>A	p.Gly94Arg	p.G94R	ENST00000249373	NM_005631.4	94	Gga/Aga	1/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.475862416338679	2		764	792	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459737	149459737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148673905	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	219	807	1	ENST00000286301.3:c.470C>T	p.Ser157Leu	p.S157L	ENST00000286301	NM_005211.3	157	tCg/tTg	4/22	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.475862416338679	2		808	851	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256144	16256144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138355680	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	159	612	0	ENST00000375759.3:c.3409C>T	p.Arg1137Cys	p.R1137C	ENST00000375759	NM_015001.2	1137	Cgt/Tgt	11/15	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.475862416338679	2		612	668	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455312	29455312	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	101	516	0	ENST00000389048.3:c.2490G>A	p.Met830Ile	p.M830I	ENST00000389048	NM_004304.4	830	atG/atA	15/29	1	2	FACETS	0.812	0.728	0.9	0.812	0.728	0.9	CLONAL	1	TRUE	1	0.475862416338679	2		516	523	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317921	8317921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150063446	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	50	453	0	ENST00000356435.5:c.5692C>T	p.Arg1898Cys	p.R1898C	ENST00000356435		1898	Cgt/Tgt	35/35	0.221001478014439	1	FACETS	0.396	0.337	0.461	0.396	0.337	0.461	INDETERMINATE	1	TRUE	0	0.475862416338679	1		453	404	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341941	8341941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	46	367	0	ENST00000356435.5:c.4699G>A	p.Asp1567Asn	p.D1567N	ENST00000356435		1567	Gat/Aat	29/35	0.221001478014439	1	FACETS	0.453	0.383	0.53	0.453	0.383	0.53	INDETERMINATE	1	TRUE	0	0.475862416338679	1		367	325	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499483	89499483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1426641543	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	115	513	0	ENST00000336596.2:c.2653C>T	p.Pro885Ser	p.P885S	ENST00000336596	NM_005233.5	885	Ccc/Tcc	15/17	1	2	FACETS	0.905	0.819	0.996	0.905	0.819	0.996	CLONAL	1	TRUE	1	0.475862416338679	2		513	534	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2114301	2114301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45517176	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	201	804	1	ENST00000219476.3:c.1472C>T	p.Ser491Leu	p.S491L	ENST00000219476	NM_000548.3	491	tCg/tTg	15/42	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.475862416338679	2		805	758	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560883	9560883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	114	537	0	ENST00000353224.5:c.899G>A	p.Gly300Glu	p.G300E	ENST00000353224	NM_177990.2	300	gGa/gAa	4/10	1	2	FACETS	0.874	0.79	0.963	0.874	0.79	0.963	CLONAL	1	TRUE	1	0.475862416338679	2		537	548	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893668	28893668	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs374452662	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	107	461	0	ENST00000282397.4:c.3178C>T	p.Arg1060Ter	p.R1060*	ENST00000282397	NM_002019.4	1060	Cga/Tga	24/30	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.475862416338679	2		461	388	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230405	46230405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1391481708	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	106	414	0	ENST00000334344.6:c.739C>T	p.Arg247Cys	p.R247C	ENST00000334344	NM_152641.2	247	Cgt/Tgt	7/21	1	2	FACETS	0.956	0.862	1	0.956	0.862	1	CLONAL	1	TRUE	1	0.475862416338679	2		414	466	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629367	187629367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754114613	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	59	842	0	ENST00000441802.2:c.1615C>T	p.Arg539Cys	p.R539C	ENST00000441802	NM_005245.3	539	Cgt/Tgt	2/27	0.352451102766052	1	FACETS	0.307	0.264	0.354	0.307	0.264	0.354	SUBCLONAL	1	TRUE	0	0.475862416338679	1		842	616	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244913	123244913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1224606327	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	154	909	2	ENST00000358487.5:c.2191G>A	p.Glu731Lys	p.E731K	ENST00000358487	NM_000141.4	731	Gaa/Aaa	16/18	1	2	FACETS	0.753	0.689	0.819	0.753	0.689	0.819	SUBCLONAL	1	TRUE	1	0.475862416338679	2		911	860	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972424	81972424	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	131	535	0	ENST00000359376.3:c.3217C>T	p.Leu1073Phe	p.L1073F	ENST00000359376	NM_002661.3	1073	Ctc/Ttc	29/33	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.475862416338679	2		535	503	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130427	29130427	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587781269	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	173	722	0	ENST00000328354.6:c.283C>T	p.Arg95Ter	p.R95*	ENST00000328354	NM_007194.3	95	Cga/Tga	2/15	1	2	FACETS	0.977	0.902	1	0.977	0.902	1	CLONAL	1	TRUE	1	0.475862416338679	2		722	744	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400190	41400190	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	101	557	0	ENST00000373198.4:c.569G>A	p.Arg190Lys	p.R190K	ENST00000373198	NM_133170.3	190	aGa/aAa	5/32	1	2	FACETS	0.899	0.808	0.996	0.899	0.808	0.996	CLONAL	1	TRUE	1	0.475862416338679	2		557	472	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961460	54961460	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	156	634	0	ENST00000312783.6:c.172C>T	p.Pro58Ser	p.P58S	ENST00000312783	NM_198436.1	58	Cct/Tct	4/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.475862416338679	2		634	597	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202299	138202299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	172	625	0	ENST00000237289.4:c.2216C>T	p.Pro739Leu	p.P739L	ENST00000237289	NM_001270507.1	739	cCc/cTc	9/9	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.475862416338679	2		625	688	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858642	9858642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	128	556	0	ENST00000330684.3:c.2759G>A	p.Arg920Lys	p.R920K	ENST00000330684	NM_001134407.1	920	aGa/aAa	13/13	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.475862416338679	2		556	509	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989551	212989551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	98	410	0	ENST00000342788.4:c.160G>A	p.Glu54Lys	p.E54K	ENST00000342788	NM_005235.2	54	Gaa/Aaa	2/28	1	2	FACETS	0.967	0.868	1	0.967	0.868	1	CLONAL	1	TRUE	1	0.475862416338679	2		410	426	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743942	40743942	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868489194	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	113	550	1	ENST00000373198.4:c.3053G>A	p.Arg1018Gln	p.R1018Q	ENST00000373198	NM_133170.3	1018	cGa/cAa	23/32	1	2	FACETS	0.95	0.859	1	0.95	0.859	1	CLONAL	1	TRUE	1	0.475862416338679	2		551	500	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719980	18719980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs889775181	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	67	330	0	ENST00000266497.5:c.3877G>A	p.Glu1293Lys	p.E1293K	ENST00000266497		1293	Gaa/Aaa	27/31	1	2	FACETS	0.9	0.788	1	0.9	0.788	1	CLONAL	1	TRUE	1	0.475862416338679	2		330	313	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391527	139391527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	195	1098	3	ENST00000277541.6:c.6664C>T	p.Pro2222Ser	p.P2222S	ENST00000277541	NM_017617.3	2222	Ccg/Tcg	34/34	1	2	FACETS	0.819	0.757	0.882	0.819	0.757	0.882	CLONAL	1	TRUE	1	0.475862416338679	2		1101	1001	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432102	121432102	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1215273865	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	210	883	1	ENST00000257555.6:c.849G>A	p.Met283Ile	p.M283I	ENST00000257555		283	atG/atA	4/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.475862416338679	2		884	847	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189349321	189349321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	46	343	0	ENST00000264731.3:c.17C>T	p.Ser6Leu	p.S6L	ENST00000264731	NM_003722.4	6	tCa/tTa	1/14	1	2	FACETS	0.589	0.498	0.689	0.589	0.498	0.689	SUBCLONAL	1	TRUE	1	0.475862416338679	2		343	328	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970884	55970884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	36	562	0	ENST00000263923.4:c.1913G>A	p.Gly638Glu	p.G638E	ENST00000263923	NM_002253.2	638	gGa/gAa	13/30	0.352451102766052	1	FACETS	0.253	0.207	0.304	0.253	0.207	0.304	SUBCLONAL	1	TRUE	0	0.475862416338679	1		562	456	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157539	106157539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs192553789	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	60	342	0	ENST00000380013.4:c.2440C>T	p.Arg814Cys	p.R814C	ENST00000380013	NM_001127208.2	814	Cgt/Tgt	3/11	0.352451102766052	1	FACETS	0.717	0.624	0.817	0.717	0.624	0.817	SUBCLONAL	1	TRUE	0	0.475862416338679	1		342	268	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670597	134670597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1330628001	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	217	913	1	ENST00000398015.3:c.508C>T	p.Arg170Trp	p.R170W	ENST00000398015	NM_004441.4	170	Cgg/Tgg	3/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.475862416338679	2		914	824	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683508	182683508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	56	470	1	ENST00000292782.4:c.37C>T	p.Arg13Cys	p.R13C	ENST00000292782	NM_020640.2	13	Cgt/Tgt	2/7	1	2	FACETS	0.57	0.489	0.657	0.57	0.489	0.657	SUBCLONAL	1	TRUE	1	0.475862416338679	2		471	413	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294403	1294403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1322987070	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	152	842	1	ENST00000310581.5:c.598G>A	p.Glu200Lys	p.E200K	ENST00000310581	NM_198253.2	200	Gaa/Aaa	2/16	1	2	FACETS	0.81	0.741	0.881	0.81	0.741	0.881	CLONAL	1	TRUE	1	0.475862416338679	2		843	789	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249824	110249824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	238	936	1	ENST00000374672.4:c.851C>T	p.Ser284Leu	p.S284L	ENST00000374672	NM_004235.4	284	tCg/tTg	3/5	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.475862416338679	2		937	869	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225525	133225525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762090058	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	178	660	0	ENST00000320574.5:c.4139C>T	p.Ser1380Leu	p.S1380L	ENST00000320574	NM_006231.2	1380	tCg/tTg	32/49	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.475862416338679	2		660	723	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650845	37650845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	149	753	0	ENST00000447079.4:c.2317C>T	p.Arg773Cys	p.R773C	ENST00000447079	NM_015083.1	773	Cgt/Tgt	5/14	1	2	FACETS	0.909	0.832	0.989	0.909	0.832	0.989	CLONAL	1	TRUE	1	0.475862416338679	2		753	689	SUCCESS
BTK	695	MSKCC	GRCh37	X	100609658	100609658	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782740486	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	137	253	1	ENST00000308731.7:c.1591G>A	p.Asp531Asn	p.D531N	ENST00000308731	NM_000061.2	531	Gat/Aat	16/19	1	1	FACETS	0.854	0.794	0.913	1	0.991	1	CLONAL	2	TRUE	0	0.475862416338679	1		254	257	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508337	106508337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760070255	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	128	409	0	ENST00000359195.3:c.331G>A	p.Asp111Asn	p.D111N	ENST00000359195	NM_002649.2	111	Gac/Aac	2/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.475862416338679	2		409	447	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358478	91358478	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1022266595	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	139	607	0	ENST00000355112.3:c.4223C>T	p.Pro1408Leu	p.P1408L	ENST00000355112	NM_000057.2	1408	cCg/cTg	22/22	1	2	FACETS	0.91	0.831	0.993	0.91	0.831	0.993	CLONAL	1	TRUE	1	0.475862416338679	2		607	642	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257107	16257107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1476670608	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	147	666	2	ENST00000375759.3:c.4372C>T	p.Arg1458Cys	p.R1458C	ENST00000375759	NM_015001.2	1458	Cgt/Tgt	11/15	1	2	FACETS	0.987	0.904	1	0.987	0.904	1	CLONAL	1	TRUE	1	0.475862416338679	2		668	626	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466031	69466031	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	593	911	0	ENST00000227507.2:c.869T>G	p.Val290Gly	p.V290G	ENST00000227507	NM_053056.2	290	gTg/gGg	5/5	0.322332778573616	4	FACETS	0.931	0.897	0.965			1	CLONAL	3	TRUE	NA	0.475862416338679	4		911	1317	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70411686	70411686	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	95	448	0	ENST00000373644.4:c.4360G>A	p.Glu1454Lys	p.E1454K	ENST00000373644	NM_030625.2	1454	Gag/Aag	5/12	1	2	FACETS	0.924	0.828	1	0.924	0.828	1	CLONAL	1	TRUE	1	0.475862416338679	2		448	432	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097228	11097228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201600949	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	347	878	0	ENST00000358026.2:c.719C>T	p.Pro240Leu	p.P240L	ENST00000358026	NM_001128849.1	240	cCg/cTg	4/36	0.289948253133191	3	FACETS	0.932	0.884	0.98	0.932	0.884	0.98	CLONAL	2	TRUE	1	0.475862416338679	3		878	969	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416895	416895	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	150	472	0	ENST00000399788.2:c.3655C>T	p.Arg1219Ter	p.R1219*	ENST00000399788	NM_001042603.1	1219	Cga/Tga	23/28	0.264328275859396	3	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.475862416338679	3		472	555	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561325	9561325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	113	458	0	ENST00000353224.5:c.457G>A	p.Gly153Arg	p.G153R	ENST00000353224	NM_177990.2	153	Gga/Aga	4/10	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.475862416338679	2		458	455	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976761	2976761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	200	954	0	ENST00000396946.4:c.1251G>A	p.Met417Ile	p.M417I	ENST00000396946	NM_032415.4	417	atG/atA	9/25	1	2	FACETS	0.963	0.893	1	0.963	0.893	1	CLONAL	1	TRUE	1	0.475862416338679	2		954	873	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40789994	40789994	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs746391800	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	109	583	0	ENST00000373198.4:c.2737G>A	p.Glu913Lys	p.E913K	ENST00000373198	NM_133170.3	913	Gag/Aag	18/32	1	2	FACETS	0.914	0.825	1	0.914	0.825	1	CLONAL	1	TRUE	1	0.475862416338679	2		583	501	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756700	756700	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765855267	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	155	625	0	ENST00000314574.4:c.128C>T	p.Pro43Leu	p.P43L	ENST00000314574	NM_005433.3	43	cCg/cTg	2/12	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.475862416338679	2		625	626	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376991	118376991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1350317713	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	136	425	0	ENST00000534358.1:c.10384C>T	p.Leu3462Phe	p.L3462F	ENST00000534358	NM_005933.3	3462	Ctt/Ttt	27/36	0.475862416338679	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.475862416338679	1		425	405	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470516	25470516	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs778270132	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	277	886	0	ENST00000264709.3:c.958C>T	p.Arg320Ter	p.R320*	ENST00000264709	NM_175629.2	320	Cga/Tga	8/23	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.475862416338679	2		886	878	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965644	93965644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	99	452	0	ENST00000369303.4:c.2284C>T	p.Arg762Cys	p.R762C	ENST00000369303	NM_004440.3	762	Cgc/Tgc	13/17	1	2	FACETS	0.863	0.774	0.957	0.863	0.774	0.957	CLONAL	1	TRUE	1	0.475862416338679	2		452	482	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156520	106156520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202152392	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	37	413	0	ENST00000380013.4:c.1421C>T	p.Pro474Leu	p.P474L	ENST00000380013	NM_001127208.2	474	cCg/cTg	3/11	0.352451102766052	1	FACETS	0.302	0.249	0.362	0.302	0.249	0.362	SUBCLONAL	1	TRUE	0	0.475862416338679	1		413	392	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619163	43619163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	161	738	1	ENST00000355710.3:c.2846G>A	p.Gly949Glu	p.G949E	ENST00000355710	NM_020975.4	949	gGa/gAa	17/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.475862416338679	2		739	654	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188525	11188525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs922525420	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	149	521	0	ENST00000361445.4:c.5896C>T	p.Arg1966Trp	p.R1966W	ENST00000361445	NM_004958.3	1966	Cgg/Tgg	42/58	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.475862416338679	2		521	564	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852443	42852443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139092674	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	157	688	0	ENST00000398585.3:c.643G>A	p.Glu215Lys	p.E215K	ENST00000398585	NM_001135099.1	215	Gag/Aag	6/14	0.100526401341054	0	FACETS	0.541	0.497	0.587			1	INDETERMINATE	1	TRUE	0	0.475862416338679	0		688	639	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162945	38162945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs185811622	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	106	540	3	ENST00000317025.8:c.2261C>T	p.Ser754Leu	p.S754L	ENST00000317025	NM_023034.1	754	tCg/tTg	13/24	1	2	FACETS	0.754	0.677	0.834	0.754	0.677	0.834	SUBCLONAL	1	TRUE	1	0.475862416338679	2		543	591	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857250	9857250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866228360	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	165	613	0	ENST00000330684.3:c.4151C>T	p.Ser1384Leu	p.S1384L	ENST00000330684	NM_001134407.1	1384	tCg/tTg	13/13	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.475862416338679	2		613	648	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876497	35876497	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	160	606	0	ENST00000303115.3:c.1289C>T	p.Pro430Leu	p.P430L	ENST00000303115	NM_002185.3	430	cCa/cTa	8/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.475862416338679	2		606	575	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188273	10188273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780732	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	201	729	0	ENST00000256474.2:c.416C>T	p.Ser139Phe	p.S139F	ENST00000256474	NM_000551.3	139	tCt/tTt	2/3	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.475862416338679	2		729	779	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166364	118166364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	102	428	0	ENST00000369448.3:c.874C>T	p.Leu292Phe	p.L292F	ENST00000369448	NM_017709.3	292	Ctt/Ttt	2/2	1	2	FACETS	0.934	0.84	1	0.934	0.84	1	CLONAL	1	TRUE	1	0.475862416338679	2		428	459	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992766	72992766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	190	772	0	ENST00000268489.5:c.1279C>T	p.Pro427Ser	p.P427S	ENST00000268489	NM_006885.3	427	Cct/Tct	2/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.475862416338679	2		772	694	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56859043	56859043	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	86	480	0	ENST00000519728.1:c.169C>T	p.Gln57Ter	p.Q57*	ENST00000519728	NM_002350.3	57	Caa/Taa	3/13	1	2	FACETS	0.759	0.674	0.85	0.759	0.674	0.85	SUBCLONAL	1	TRUE	1	0.475862416338679	2		480	476	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224714	36224714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768250201	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	277	1104	0	ENST00000222270.7:c.7100C>T	p.Pro2367Leu	p.P2367L	ENST00000222270	NM_014727.1	2367	cCc/cTc	30/37	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.475862416338679	2		1104	1047	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31504673	31504673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	93	583	0	ENST00000344624.3:c.1657C>T	p.Pro553Ser	p.P553S	ENST00000344624		553	Cct/Tct	8/33	1	2	FACETS	0.842	0.752	0.937	0.842	0.752	0.937	CLONAL	1	TRUE	1	0.475862416338679	2		583	464	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058515	69058515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	127	619	0	ENST00000288368.4:c.4159C>T	p.His1387Tyr	p.H1387Y	ENST00000288368	NM_024870.2	1387	Cat/Tat	34/40	1	2	FACETS	0.972	0.885	1	0.972	0.885	1	CLONAL	1	TRUE	1	0.475862416338679	2		619	549	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117027	193117027	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	80	391	0	ENST00000367435.3:c.760C>T	p.Gln254Ter	p.Q254*	ENST00000367435	NM_024529.4	254	Caa/Taa	8/17	1	2	FACETS	0.834	0.738	0.936	0.834	0.738	0.936	CLONAL	1	TRUE	1	0.475862416338679	2		391	403	SUCCESS
AR	367	MSKCC	GRCh37	X	66765304	66765304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	214	439	0	ENST00000374690.3:c.316G>A	p.Gly106Ser	p.G106S	ENST00000374690	NM_000044.3	106	Ggc/Agc	1/8	1	1	FACETS	0.853	0.805	0.9	1	0.994	1	CLONAL	2	TRUE	0	0.475862416338679	1		439	402	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224713	36224713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1280550594	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	277	1084	0	ENST00000222270.7:c.7099C>T	p.Pro2367Ser	p.P2367S	ENST00000222270	NM_014727.1	2367	Ccc/Tcc	30/37	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.475862416338679	2		1084	1047	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528593	8528593	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	90	405	0	ENST00000356435.5:c.539C>T	p.Ser180Leu	p.S180L	ENST00000356435		180	tCa/tTa	4/35	0.221001478014439	1	FACETS	0.884	0.792	0.98	0.884	0.792	0.98	INDETERMINATE	1	TRUE	0	0.475862416338679	1		405	326	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750452	41750452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	148	676	0	ENST00000226382.2:c.176C>T	p.Ser59Phe	p.S59F	ENST00000226382	NM_003924.3	59	tCc/tTc	1/3	NA	2	FACETS	0.934	0.855	1			1	INDETERMINATE	1	TRUE	NA	0.475862416338679	2		676	666	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683984	117683984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	72	515	0	ENST00000368508.3:c.3163G>A	p.Gly1055Arg	p.G1055R	ENST00000368508	NM_002944.2	1055	Gga/Aga	21/43	1	2	FACETS	0.724	0.635	0.819	0.724	0.635	0.819	SUBCLONAL	1	TRUE	1	0.475862416338679	2		515	418	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570468	39570468	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs267605182	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	40	230	1	ENST00000262039.4:c.664C>T	p.Arg222Ter	p.R222*	ENST00000262039	NM_002647.2	222	Cga/Tga	6/25	1	2	FACETS	0.754	0.632	0.887	0.754	0.632	0.887	SUBCLONAL	1	TRUE	1	0.475862416338679	2		231	223	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37863284	37863284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	191	823	0	ENST00000269571.5:c.115C>T	p.Pro39Ser	p.P39S	ENST00000269571		39	Ccc/Tcc	2/27	1	2	FACETS	0.95	0.88	1	0.95	0.88	1	CLONAL	1	TRUE	1	0.475862416338679	2		823	845	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857769	9857769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	144	541	0	ENST00000330684.3:c.3632C>T	p.Ser1211Phe	p.S1211F	ENST00000330684	NM_001134407.1	1211	tCc/tTc	13/13	1	2	FACETS	0.997	0.913	1	0.997	0.913	1	CLONAL	1	TRUE	1	0.475862416338679	2		541	607	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39542579	39542579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200002230	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	130	507	1	ENST00000262039.4:c.383C>T	p.Ser128Leu	p.S128L	ENST00000262039	NM_002647.2	128	tCg/tTg	3/25	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.475862416338679	2		508	546	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959181	2959181	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	205	889	2	ENST00000396946.4:c.2335C>T	p.Arg779Trp	p.R779W	ENST00000396946	NM_032415.4	779	Cgg/Tgg	18/25	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.475862416338679	2		891	842	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939072	76939072	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060499760	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	140	268	0	ENST00000373344.5:c.1676C>T	p.Ser559Leu	p.S559L	ENST00000373344	NM_000489.3	559	tCa/tTa	9/35	1	1	FACETS	0.752	0.698	0.807	1	0.989	1	SUBCLONAL	2	TRUE	0	0.475862416338679	1		268	298	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032099	10032099	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	188	730	0	ENST00000330684.3:c.724G>A	p.Glu242Lys	p.E242K	ENST00000330684	NM_001134407.1	242	Gag/Aag	3/13	1	2	FACETS	0.97	0.897	1	0.97	0.897	1	CLONAL	1	TRUE	1	0.475862416338679	2		730	815	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094880	11094880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502087	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	415	1008	1	ENST00000358026.2:c.53C>T	p.Pro18Leu	p.P18L	ENST00000358026	NM_001128849.1	18	cCg/cTg	2/36	0.289948253133191	3	FACETS	0.936	0.893	0.98	0.936	0.893	0.98	CLONAL	2	TRUE	1	0.475862416338679	3		1009	1153	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614583	38614583	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434312	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	110	556	0	ENST00000299084.4:c.349C>T	p.Arg117Ter	p.R117*	ENST00000299084	NM_152594.2	117	Cga/Tga	3/7	1	2	FACETS	0.923	0.833	1	0.923	0.833	1	CLONAL	1	TRUE	1	0.475862416338679	2		556	501	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893590	28893590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752645756	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	66	512	0	ENST00000282397.4:c.3256G>A	p.Gly1086Arg	p.G1086R	ENST00000282397	NM_002019.4	1086	Gga/Aga	24/30	1	2	FACETS	0.63	0.549	0.718	0.63	0.549	0.718	SUBCLONAL	1	TRUE	1	0.475862416338679	2		512	440	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466982	18466982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	63	396	0	ENST00000266497.5:c.1121G>A	p.Gly374Glu	p.G374E	ENST00000266497		374	gGa/gAa	5/31	1	2	FACETS	0.746	0.649	0.85	0.746	0.649	0.85	SUBCLONAL	1	TRUE	1	0.475862416338679	2		396	355	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956528	93956528	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	48	362	0	ENST00000369303.4:c.2708C>T	p.Pro903Leu	p.P903L	ENST00000369303	NM_004440.3	903	cCc/cTc	15/17	1	2	FACETS	0.6	0.51	0.699	0.6	0.51	0.699	SUBCLONAL	1	TRUE	1	0.475862416338679	2		362	336	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433072	49433072	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	244	1032	1	ENST00000301067.7:c.8299C>T	p.Pro2767Ser	p.P2767S	ENST00000301067	NM_003482.3	2767	Cct/Tct	33/54	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.475862416338679	2		1033	923	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233129	55233129	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	135	588	0	ENST00000275493.2:c.1879G>T	p.Gly627Ter	p.G627*	ENST00000275493	NM_005228.3	627	Gga/Tga	15/28	1	2	FACETS	0.884	0.805	0.966	0.884	0.805	0.966	CLONAL	1	TRUE	1	0.475862416338679	2		588	642	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747109	40747109	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	161	664	1	ENST00000373198.4:c.2973G>A	p.Trp991Ter	p.W991*	ENST00000373198	NM_133170.3	991	tgG/tgA	22/32	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.475862416338679	2		665	667	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979375	93979375	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	49	311	1	ENST00000369303.4:c.1453C>T	p.Gln485Ter	p.Q485*	ENST00000369303	NM_004440.3	485	Caa/Taa	7/17	1	2	FACETS	0.865	0.74	1	0.865	0.74	1	CLONAL	1	TRUE	1	0.475862416338679	2		312	238	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647536	117647536	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	94	570	0	ENST00000368508.3:c.5408G>A	p.Trp1803Ter	p.W1803*	ENST00000368508	NM_002944.2	1803	tGg/tAg	33/43	NA	2	FACETS	0.705	0.629	0.786			1	INDETERMINATE	1	TRUE	NA	0.475862416338679	2		570	560	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11168269	11168269	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	190	583	0	ENST00000361445.4:c.7603C>T	p.His2535Tyr	p.H2535Y	ENST00000361445	NM_004958.3	2535	Cat/Tat	57/58	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.475862416338679	2		583	753	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11270948	11270948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	82	404	0	ENST00000361445.4:c.3577C>T	p.Pro1193Ser	p.P1193S	ENST00000361445	NM_004958.3	1193	Cca/Tca	24/58	1	2	FACETS	0.787	0.697	0.882	0.787	0.697	0.882	SUBCLONAL	1	TRUE	1	0.475862416338679	2		404	438	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11293483	11293483	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	125	675	0	ENST00000361445.4:c.2393T>G	p.Val798Gly	p.V798G	ENST00000361445	NM_004958.3	798	gTc/gGc	15/58	1	2	FACETS	0.884	0.803	0.97	0.884	0.803	0.97	CLONAL	1	TRUE	1	0.475862416338679	2		675	594	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17380498	17380498	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	266	888	0	ENST00000375499.3:c.17C>A	p.Ala6Asp	p.A6D	ENST00000375499	NM_003000.2	6	gCc/gAc	1/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.475862416338679	2		888	1035	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935442	36935442	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	226	804	0	ENST00000361632.4:c.1286-1G>A		p.X429_splice	ENST00000361632		429			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.475862416338679	2		804	855	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511684	46511684	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs762065227	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	129	615	0	ENST00000262741.5:c.1093C>T	p.Arg365Ter	p.R365*	ENST00000262741	NM_003629.3	365	Cga/Tga	9/10	1	2	FACETS	0.972	0.885	1	0.972	0.885	1	CLONAL	1	TRUE	1	0.475862416338679	2		615	558	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739033	46739033	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	132	500	1	ENST00000371975.4:c.1382C>T	p.Ala461Val	p.A461V	ENST00000371975	NM_003579.3	461	gCt/gTt	13/18	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.475862416338679	2		501	546	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834198	156834198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs2274496	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	279	1055	1	ENST00000524377.1:c.265G>A	p.Gly89Ser	p.G89S	ENST00000524377	NM_002529.3	89	Ggc/Agc	2/17	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.475862416338679	2		1056	1051	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843751	156843751	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	289	1011	1	ENST00000524377.1:c.1177G>A	p.Val393Ile	p.V393I	ENST00000524377	NM_002529.3	393	Gtc/Atc	8/17	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.475862416338679	2		1012	1029	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651600	206651600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	291	1054	1	ENST00000367120.3:c.910G>A	p.Asp304Asn	p.D304N	ENST00000367120	NM_014002.3	304	Gac/Aac	9/22	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.475862416338679	2		1055	1041	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651669	206651669	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868950433	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	239	983	0	ENST00000367120.3:c.979C>T	p.His327Tyr	p.H327Y	ENST00000367120	NM_014002.3	327	Cat/Tat	9/22	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.475862416338679	2		983	960	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653791	206653791	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	158	723	0	ENST00000367120.3:c.1342G>A	p.Glu448Lys	p.E448K	ENST00000367120	NM_014002.3	448	Gag/Aag	13/22	1	2	FACETS	0.896	0.823	0.973	0.896	0.823	0.973	CLONAL	1	TRUE	1	0.475862416338679	2		723	741	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666435	206666435	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	165	678	1	ENST00000367120.3:c.1915C>T	p.Gln639Ter	p.Q639*	ENST00000367120	NM_014002.3	639	Cag/Tag	19/22	1	2	FACETS	0.947	0.872	1	0.947	0.872	1	CLONAL	1	TRUE	1	0.475862416338679	2		679	732	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612876	228612876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	200	785	0	ENST00000366696.1:c.151G>A	p.Glu51Lys	p.E51K	ENST00000366696	NM_003493.2	51	Gag/Aag	1/1	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.475862416338679	2		785	814	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675323	241675323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	102	504	0	ENST00000366560.3:c.499G>A	p.Gly167Ser	p.G167S	ENST00000366560	NM_000143.3	167	Ggt/Agt	4/10	1	2	FACETS	0.988	0.889	1	0.988	0.889	1	CLONAL	1	TRUE	1	0.475862416338679	2		504	434	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246027149	246027149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	167	671	1	ENST00000388985.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000388985		285	Gaa/Aaa	9/12	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.475862416338679	2		672	682	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612093	43612093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1564497340	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	169	726	3	ENST00000355710.3:c.2198G>A	p.Gly733Asp	p.G733D	ENST00000355710	NM_020975.4	733	gGc/gAc	12/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.475862416338679	2		729	615	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615010	43615010	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	244	742	0	ENST00000355710.3:c.2424A>T	p.Lys808Asn	p.K808N	ENST00000355710	NM_020975.4	808	aaA/aaT	14/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.475862416338679	2		742	802	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63661945	63661945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	118	458	0	ENST00000279873.7:c.49G>A	p.Gly17Arg	p.G17R	ENST00000279873	NM_032199.2	17	Gga/Aga	2/10	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.475862416338679	2		458	490	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925616	114925616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776874056	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	165	815	0	ENST00000543371.1:c.1694C>T	p.Pro565Leu	p.P565L	ENST00000543371	NM_001198531.1	565	cCt/cTt	14/14	1	2	FACETS	0.873	0.803	0.947	0.873	0.803	0.947	CLONAL	1	TRUE	1	0.475862416338679	2		815	794	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276872	123276872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	83	451	0	ENST00000358487.5:c.1045G>A	p.Gly349Arg	p.G349R	ENST00000358487	NM_000141.4	349	Ggg/Agg	8/18	1	2	FACETS	0.839	0.744	0.939	0.839	0.744	0.939	CLONAL	1	TRUE	1	0.475862416338679	2		451	416	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435082	18435082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	89	413	0	ENST00000266497.5:c.67G>A	p.Glu23Lys	p.E23K	ENST00000266497		23	Gaa/Aaa	1/31	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.475862416338679	2		413	342	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435184	18435184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1251272146	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	72	375	1	ENST00000266497.5:c.169G>A	p.Glu57Lys	p.E57K	ENST00000266497		57	Gaa/Aaa	1/31	1	2	FACETS	0.822	0.723	0.928	0.822	0.723	0.928	CLONAL	1	TRUE	1	0.475862416338679	2		376	368	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435395	18435395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1344663732	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	96	351	1	ENST00000266497.5:c.380G>A	p.Gly127Glu	p.G127E	ENST00000266497		127	gGa/gAa	1/31	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.475862416338679	2		352	361	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524140	18524140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	71	436	0	ENST00000266497.5:c.1652C>T	p.Ser551Leu	p.S551L	ENST00000266497		551	tCa/tTa	11/31	1	2	FACETS	0.933	0.821	1	0.933	0.821	1	CLONAL	1	TRUE	1	0.475862416338679	2		436	320	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691118	18691118	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	68	446	0	ENST00000266497.5:c.3229G>A	p.Glu1077Lys	p.E1077K	ENST00000266497		1077	Gag/Aag	23/31	1	2	FACETS	0.785	0.687	0.89	0.785	0.687	0.89	SUBCLONAL	1	TRUE	1	0.475862416338679	2		446	364	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46240677	46240677	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	77	398	0	ENST00000334344.6:c.1537C>T	p.Pro513Ser	p.P513S	ENST00000334344	NM_152641.2	513	Cca/Tca	12/21	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.475862416338679	2		398	319	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244719	46244719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	183	609	0	ENST00000334344.6:c.2813C>T	p.Thr938Ile	p.T938I	ENST00000334344	NM_152641.2	938	aCt/aTt	15/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.475862416338679	2		609	656	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432618	49432618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	263	1035	1	ENST00000301067.7:c.8521C>T	p.Pro2841Ser	p.P2841S	ENST00000301067	NM_003482.3	2841	Cct/Tct	34/54	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.475862416338679	2		1036	1016	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434729	49434729	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761636357	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	239	945	0	ENST00000301067.7:c.6824C>T	p.Pro2275Leu	p.P2275L	ENST00000301067	NM_003482.3	2275	cCc/cTc	31/54	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.475862416338679	2		945	995	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434906	49434906	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1466593517	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	251	905	0	ENST00000301067.7:c.6647C>T	p.Ser2216Phe	p.S2216F	ENST00000301067	NM_003482.3	2216	tCt/tTt	31/54	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.475862416338679	2		905	882	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437199	49437199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483821975	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	191	719	0	ENST00000301067.7:c.5480C>T	p.Pro1827Leu	p.P1827L	ENST00000301067	NM_003482.3	1827	cCa/cTa	24/54	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.475862416338679	2		719	768	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486551	56486551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1034050608	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	160	708	0	ENST00000267101.3:c.1130C>T	p.Pro377Leu	p.P377L	ENST00000267101	NM_001982.3	377	cCt/cTt	10/28	1	2	FACETS	0.86	0.79	0.933	0.86	0.79	0.933	CLONAL	1	TRUE	1	0.475862416338679	2		708	782	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233625	69233625	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	65	268	0	ENST00000462284.1:c.1490C>T	p.Pro497Leu	p.P497L	ENST00000462284	NM_002392.5	497	cCc/cTc	11/11	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.475862416338679	2		268	268	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245274	133245274	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	244	890	0	ENST00000320574.5:c.1973A>G	p.Lys658Arg	p.K658R	ENST00000320574	NM_006231.2	658	aAg/aGg	18/49	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.475862416338679	2		890	911	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557555	21557555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1331631745	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	169	724	1	ENST00000382592.4:c.2290C>T	p.Pro764Ser	p.P764S	ENST00000382592	NM_014572.2	764	Cct/Tct	5/8	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.475862416338679	2		725	702	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28624342	28624342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	65	444	0	ENST00000241453.7:c.632C>T	p.Pro211Leu	p.P211L	ENST00000241453	NM_004119.2	211	cCa/cTa	6/24	1	2	FACETS	0.753	0.656	0.856	0.753	0.656	0.856	SUBCLONAL	1	TRUE	1	0.475862416338679	2		444	363	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910477	32910477	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	62	357	0	ENST00000380152.3:c.1985C>T	p.Ser662Phe	p.S662F	ENST00000380152		662	tCt/tTt	11/27	1	2	FACETS	0.852	0.741	0.969	0.852	0.741	0.969	CLONAL	1	TRUE	1	0.475862416338679	2		357	306	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913867	32913867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	76	492	0	ENST00000380152.3:c.5375C>T	p.Ser1792Phe	p.S1792F	ENST00000380152		1792	tCc/tTc	11/27	1	2	FACETS	0.724	0.638	0.817	0.724	0.638	0.817	SUBCLONAL	1	TRUE	1	0.475862416338679	2		492	441	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134471	41134471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	121	635	0	ENST00000379561.5:c.1157C>T	p.Ser386Leu	p.S386L	ENST00000379561	NM_002015.3	386	tCa/tTa	2/3	1	2	FACETS	0.918	0.833	1	0.918	0.833	1	CLONAL	1	TRUE	1	0.475862416338679	2		635	554	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643795	38643795	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	200	728	0	ENST00000299084.4:c.1265C>T	p.Pro422Leu	p.P422L	ENST00000299084	NM_152594.2	422	cCt/cTt	7/7	1	2	FACETS	0.95	0.881	1	0.95	0.881	1	CLONAL	1	TRUE	1	0.475862416338679	2		728	885	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354479	91354479	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773830810	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	91	522	1	ENST00000355112.3:c.3919C>T	p.Pro1307Ser	p.P1307S	ENST00000355112	NM_000057.2	1307	Ccc/Tcc	21/22	1	2	FACETS	0.792	0.706	0.883	0.792	0.706	0.883	SUBCLONAL	1	TRUE	1	0.475862416338679	2		523	483	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343575	343575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765360584	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	235	932	2	ENST00000262320.3:c.2099C>T	p.Ala700Val	p.A700V	ENST00000262320	NM_003502.3	700	gCt/gTt	8/11	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.475862416338679	2		934	859	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129662	2129662	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1163066622	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	194	935	0	ENST00000219476.3:c.3389C>T	p.Ser1130Phe	p.S1130F	ENST00000219476	NM_000548.3	1130	tCc/tTc	29/42	NA	2	FACETS	0.936	0.867	1			1	INDETERMINATE	1	TRUE	NA	0.475862416338679	2		935	871	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778060	3778060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064796531	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	273	1109	1	ENST00000262367.5:c.6988C>T	p.Leu2330Phe	p.L2330F	ENST00000262367	NM_004380.2	2330	Ctc/Ttc	31/31	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.475862416338679	2		1110	1029	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857205	9857205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	137	607	0	ENST00000330684.3:c.4196G>A	p.Ser1399Asn	p.S1399N	ENST00000330684	NM_001134407.1	1399	aGc/aAc	13/13	1	2	FACETS	0.998	0.912	1	0.998	0.912	1	CLONAL	1	TRUE	1	0.475862416338679	2		607	577	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916227	9916227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	135	640	0	ENST00000330684.3:c.2062G>A	p.Gly688Arg	p.G688R	ENST00000330684	NM_001134407.1	688	Gga/Aga	10/13	1	2	FACETS	0.992	0.905	1	0.992	0.905	1	CLONAL	1	TRUE	1	0.475862416338679	2		640	572	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9927967	9927967	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867195830	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	98	443	0	ENST00000330684.3:c.1772G>A	p.Gly591Glu	p.G591E	ENST00000330684	NM_001134407.1	591	gGg/gAg	8/13	1	2	FACETS	0.962	0.864	1	0.962	0.864	1	CLONAL	1	TRUE	1	0.475862416338679	2		443	428	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50810116	50810116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	75	613	0	ENST00000398568.2:c.940C>T	p.Pro314Ser	p.P314S	ENST00000398568	NM_001042412.1	314	Ccc/Tcc	6/18	1	2	FACETS	0.728	0.64	0.821	0.728	0.64	0.821	SUBCLONAL	1	TRUE	1	0.475862416338679	2		613	433	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655387	67655387	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	105	649	0	ENST00000264010.4:c.1250C>T	p.Thr417Ile	p.T417I	ENST00000264010	NM_006565.3	417	aCc/aTc	7/12	1	2	FACETS	0.744	0.668	0.824	0.744	0.668	0.824	SUBCLONAL	1	TRUE	1	0.475862416338679	2		649	593	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81979794	81979794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374517633	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	112	514	0	ENST00000359376.3:c.3496C>T	p.Pro1166Ser	p.P1166S	ENST00000359376	NM_002661.3	1166	Cct/Tct	31/33	1	2	FACETS	0.873	0.788	0.962	0.873	0.788	0.962	CLONAL	1	TRUE	1	0.475862416338679	2		514	539	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346430	89346430	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	220	840	0	ENST00000301030.4:c.6520A>T	p.Ile2174Leu	p.I2174L	ENST00000301030	NM_001256183.1	2174	Ata/Tta	9/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.475862416338679	2		840	796	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654799	29654799	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267604793	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	110	396	0	ENST00000356175.3:c.5488C>T	p.Pro1830Ser	p.P1830S	ENST00000356175	NM_000267.3	1830	Cct/Tct	37/57	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.475862416338679	2		396	380	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667784	37667784	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	67	452	1	ENST00000447079.4:c.2669G>T	p.Arg890Leu	p.R890L	ENST00000447079	NM_015083.1	890	cGc/cTc	8/14	1	2	FACETS	0.677	0.59	0.77	0.677	0.59	0.77	SUBCLONAL	1	TRUE	1	0.475862416338679	2		453	416	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686955	37686955	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	128	572	0	ENST00000447079.4:c.3859T>C	p.Ser1287Pro	p.S1287P	ENST00000447079	NM_015083.1	1287	Tcc/Ccc	14/14	1	2	FACETS	0.851	0.773	0.933	0.851	0.773	0.933	CLONAL	1	TRUE	1	0.475862416338679	2		572	632	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508728	38508728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	220	694	0	ENST00000254066.5:c.776C>T	p.Thr259Ile	p.T259I	ENST00000254066	NM_000964.3	259	aCc/aTc	6/9	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.475862416338679	2		694	739	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40491339	40491339	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	159	544	0	ENST00000264657.5:c.461G>A	p.Arg154Lys	p.R154K	ENST00000264657	NM_139276.2	154	aGa/aAa	5/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.475862416338679	2		544	609	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761450	59761450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	88	514	0	ENST00000259008.2:c.2957C>T	p.Ser986Phe	p.S986F	ENST00000259008	NM_032043.2	986	tCc/tTc	20/20	1	2	FACETS	0.792	0.705	0.885	0.792	0.705	0.885	SUBCLONAL	1	TRUE	1	0.475862416338679	2		514	467	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727927	78727927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	131	645	0	ENST00000306801.3:c.772C>T	p.Leu258Phe	p.L258F	ENST00000306801	NM_020761.2	258	Ctc/Ttc	6/34	1	2	FACETS	0.932	0.848	1	0.932	0.848	1	CLONAL	1	TRUE	1	0.475862416338679	2		645	591	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78921078	78921079	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	226	751	0	ENST00000306801.3:c.3192_3193delinsTT	p.Pro1065Ser	p.P1065S	ENST00000306801	NM_020761.2	1064	aaCCct/aaTTct	27/34	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.475862416338679	2		751	788	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78921079	78921079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	226	751	0	ENST00000306801.3:c.3193C>T	p.Pro1065Ser	p.P1065S	ENST00000306801	NM_020761.2	1065	Cct/Tct	27/34	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.475862416338679	2		751	788	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637903	39637903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	146	560	0	ENST00000262039.4:c.2320C>T	p.Pro774Ser	p.P774S	ENST00000262039	NM_002647.2	774	Cct/Tct	22/25	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.475862416338679	2		560	561	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191143	2191143	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	247	997	0	ENST00000398665.3:c.397C>T	p.Pro133Ser	p.P133S	ENST00000398665	NM_032482.2	133	Ccc/Tcc	5/28	0.364292075787084	3	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.475862416338679	3		997	1116	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4095405	4095405	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	196	1049	0	ENST00000262948.5:c.1027C>T	p.Gln343Ter	p.Q343*	ENST00000262948	NM_030662.3	343	Cag/Tag	9/11	1	2	FACETS	0.819	0.758	0.882	0.819	0.758	0.882	CLONAL	1	TRUE	1	0.475862416338679	2		1049	1006	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240272	5240272	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	269	982	0	ENST00000357368.4:c.1642C>T	p.Pro548Ser	p.P548S	ENST00000357368	NM_002850.3	548	Ccg/Tcg	12/38	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.475862416338679	2		982	883	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7126627	7126627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	194	772	0	ENST00000302850.5:c.2981C>T	p.Ser994Phe	p.S994F	ENST00000302850	NM_000208.2	994	tCt/tTt	16/22	0.289948253133191	3	FACETS	1	0.975	1	0.558	0.516	0.601	CLONAL	1	TRUE	1	0.475862416338679	3		772	905	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143051	7143051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	187	764	0	ENST00000302850.5:c.2318C>T	p.Ala773Val	p.A773V	ENST00000302850	NM_000208.2	773	gCc/gTc	12/22	0.289948253133191	3	FACETS	1	0.948	1	0.516	0.477	0.557	CLONAL	1	TRUE	1	0.475862416338679	3		764	942	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284901	15284901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	248	958	0	ENST00000263388.2:c.4714G>A	p.Glu1572Lys	p.E1572K	ENST00000263388	NM_000435.2	1572	Gag/Aag	25/33	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.475862416338679	2		958	968	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288757	15288757	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	56	185	0	ENST00000263388.2:c.3982C>T	p.Pro1328Ser	p.P1328S	ENST00000263388	NM_000435.2	1328	Ccg/Tcg	24/33	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.475862416338679	2		185	170	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955175	17955175	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	295	982	0	ENST00000458235.1:c.52C>T	p.Leu18Phe	p.L18F	ENST00000458235	NM_000215.3	18	Ctc/Ttc	2/24	0.264328275859396	3	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.475862416338679	3		982	1186	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212077	36212077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs911830364	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	223	1054	0	ENST00000222270.7:c.1828C>T	p.Arg610Cys	p.R610C	ENST00000222270	NM_014727.1	610	Cgc/Tgc	3/37	NA	2	FACETS	0.99	0.922	1			1	INDETERMINATE	1	TRUE	NA	0.475862416338679	2		1054	947	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224713	36224714	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	277	1104	0	ENST00000222270.7:c.7099_7100delinsTT	p.Pro2367Phe	p.P2367F	ENST00000222270	NM_014727.1	2367	CCc/TTc	30/37	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.475862416338679	2		1104	1047	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40743904	40743904	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757245351	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	339	835	2	ENST00000392038.2:c.803C>T	p.Ser268Leu	p.S268L	ENST00000392038	NM_001626.4	268	tCg/tTg	9/14	0.264328275859396	3	FACETS	0.894	0.847	0.941			1	INDETERMINATE	2	TRUE	NA	0.475862416338679	3		837	987	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796244	42796244	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	173	746	1	ENST00000575354.2:c.2893C>T	p.Gln965Ter	p.Q965*	ENST00000575354	NM_015125.3	965	Cag/Tag	12/20	NA	2	FACETS	0.912	0.841	0.986			1	INDETERMINATE	1	TRUE	NA	0.475862416338679	2		747	797	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463287	25463292	+	protein_altering_variant	In_Frame_Del	DEL	GGTAGA	GGTAGA	AGT	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	112	614	1	ENST00000264709.3:c.2201_2206delinsACT	p.Phe734_Arg736delinsTyrCys	p.F734_R736delinsYC	ENST00000264709	NM_175629.2	734	tTCTACCgc/tACTgc	19/23	1	2	FACETS	0.85	0.767	0.937	0.85	0.767	0.937	CLONAL	1	TRUE	1	0.475862416338679	2		615	554	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470994	25470995	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	223	828	0	ENST00000264709.3:c.766_767delinsTT	p.Pro256Phe	p.P256F	ENST00000264709	NM_175629.2	256	CCc/TTc	7/23	1	2	FACETS	0.995	0.927	1	0.995	0.927	1	CLONAL	1	TRUE	1	0.475862416338679	2		828	942	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719177	61719177	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	81	303	0	ENST00000401558.2:c.1880C>T	p.Pro627Leu	p.P627L	ENST00000401558	NM_003400.3	627	cCt/cTt	16/25	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.475862416338679	2		303	316	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881615	111881615	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866570504	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	216	795	0	ENST00000393256.3:c.293C>T	p.Ser98Phe	p.S98F	ENST00000393256	NM_006538.4	98	tCt/tTt	2/4	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.475862416338679	2		795	816	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634777	158634777	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	93	415	0	ENST00000263640.3:c.409C>T	p.Leu137Phe	p.L137F	ENST00000263640	NM_001105.4	137	Ctt/Ttt	5/11	1	2	FACETS	0.918	0.821	1	0.918	0.821	1	CLONAL	1	TRUE	1	0.475862416338679	2		415	426	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483922	212483922	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780689946	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	91	573	0	ENST00000342788.4:c.2281G>A	p.Ala761Thr	p.A761T	ENST00000342788	NM_005235.2	761	Gca/Aca	19/28	1	2	FACETS	0.889	0.794	0.99	0.889	0.794	0.99	CLONAL	1	TRUE	1	0.475862416338679	2		573	430	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568841	212568841	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1182226451	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	80	580	0	ENST00000342788.4:c.1277G>A	p.Arg426Lys	p.R426K	ENST00000342788	NM_005235.2	426	aGa/aAa	11/28	1	2	FACETS	0.725	0.64	0.815	0.725	0.64	0.815	SUBCLONAL	1	TRUE	1	0.475862416338679	2		580	464	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645408	215645408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	151	665	0	ENST00000260947.4:c.1190C>T	p.Ser397Phe	p.S397F	ENST00000260947	NM_000465.2	397	tCt/tTt	4/11	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.475862416338679	2		665	623	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660282	227660282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	197	751	0	ENST00000305123.5:c.3173C>T	p.Ser1058Phe	p.S1058F	ENST00000305123	NM_005544.2	1058	tCc/tTc	1/2	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.475862416338679	2		751	766	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561409	9561409	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	125	561	0	ENST00000353224.5:c.373T>C	p.Phe125Leu	p.F125L	ENST00000353224	NM_177990.2	125	Ttc/Ctc	4/10	1	2	FACETS	0.935	0.849	1	0.935	0.849	1	CLONAL	1	TRUE	1	0.475862416338679	2		561	562	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877456	40877456	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	141	573	0	ENST00000373198.4:c.2240C>T	p.Ser747Phe	p.S747F	ENST00000373198	NM_133170.3	747	tCc/tTc	15/32	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.475862416338679	2		573	509	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385186	41385187	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	152	792	1	ENST00000373198.4:c.774_775delinsTT	p.Gln259Ter	p.Q259*	ENST00000373198	NM_133170.3	258	gcCCag/gcTTag	6/32	1	2	FACETS	0.829	0.759	0.901	0.829	0.759	0.901	CLONAL	1	TRUE	1	0.475862416338679	2		793	771	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845345	42845345	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	222	875	0	ENST00000398585.3:c.917G>A	p.Trp306Ter	p.W306*	ENST00000398585	NM_001135099.1	306	tGg/tAg	9/14	0.100526401341054	0	FACETS	0.598	0.558	0.639			1	INDETERMINATE	1	TRUE	0	0.475862416338679	0		875	818	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091145	29091145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	128	659	0	ENST00000328354.6:c.1345C>T	p.Pro449Ser	p.P449S	ENST00000328354	NM_007194.3	449	Cct/Tct	12/15	1	2	FACETS	0.993	0.904	1	0.993	0.904	1	CLONAL	1	TRUE	1	0.475862416338679	2		659	542	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458404	12458404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	210	795	1	ENST00000287820.6:c.1021G>A	p.Asp341Asn	p.D341N	ENST00000287820	NM_015869.4	341	Gac/Aac	6/7	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.475862416338679	2		796	829	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458434	12458434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	215	763	2	ENST00000287820.6:c.1051C>T	p.His351Tyr	p.H351Y	ENST00000287820	NM_015869.4	351	Cac/Tac	6/7	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.475862416338679	2		765	831	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933740	49933740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	277	928	0	ENST00000296474.3:c.2537G>A	p.Gly846Glu	p.G846E	ENST00000296474	NM_002447.2	846	gGg/gAg	10/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.475862416338679	2		928	949	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73096348	73096348	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	21	64	0	ENST00000356692.5:c.128C>T	p.Ser43Phe	p.S43F	ENST00000356692		43	tCc/tTc	3/9	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.475862416338679	2		64	77	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499490	89499490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	110	483	0	ENST00000336596.2:c.2660G>A	p.Ser887Asn	p.S887N	ENST00000336596	NM_005233.5	887	aGc/aAc	15/17	1	2	FACETS	0.919	0.83	1	0.919	0.83	1	CLONAL	1	TRUE	1	0.475862416338679	2		483	503	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528570	89528570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	69	262	0	ENST00000336596.2:c.2870C>T	p.Thr957Ile	p.T957I	ENST00000336596	NM_005233.5	957	aCc/aTc	17/17	1	2	FACETS	0.915	0.803	1	0.915	0.803	1	CLONAL	1	TRUE	1	0.475862416338679	2		262	317	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670768	134670768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	173	584	2	ENST00000398015.3:c.679C>T	p.Pro227Ser	p.P227S	ENST00000398015	NM_004441.4	227	Ccc/Tcc	3/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.475862416338679	2		586	602	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825302	134825302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	120	369	0	ENST00000398015.3:c.818G>A	p.Gly273Glu	p.G273E	ENST00000398015	NM_004441.4	273	gGg/gAg	4/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.475862416338679	2		369	421	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259836	142259836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	107	525	0	ENST00000350721.4:c.3491C>T	p.Pro1164Leu	p.P1164L	ENST00000350721	NM_001184.3	1164	cCc/cTc	18/47	1	2	FACETS	0.882	0.794	0.974	0.882	0.794	0.974	CLONAL	1	TRUE	1	0.475862416338679	2		525	510	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169953053	169953054	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	108	574	1	ENST00000295797.4:c.137_138delinsTT	p.Ser46Phe	p.S46F	ENST00000295797	NM_002740.5	46	tCC/tTT	2/18	1	2	FACETS	0.811	0.73	0.896	0.811	0.73	0.896	CLONAL	1	TRUE	1	0.475862416338679	2		575	560	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146596	185146596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	153	701	1	ENST00000265026.3:c.227C>T	p.Ser76Phe	p.S76F	ENST00000265026	NM_004721.4	76	tCc/tTc	2/14	1	2	FACETS	0.954	0.875	1	0.954	0.875	1	CLONAL	1	TRUE	1	0.475862416338679	2		702	674	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198124	185198124	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	135	569	0	ENST00000265026.3:c.2606G>A	p.Ser869Asn	p.S869N	ENST00000265026	NM_004721.4	869	aGt/aAt	13/14	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.475862416338679	2		569	540	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1959686	1959686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772239992	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	82	361	0	ENST00000382891.5:c.2908C>T	p.Arg970Cys	p.R970C	ENST00000382891	NM_133335.3	970	Cgt/Tgt	16/22	NA	2	FACETS	1	0.896	1			1	INDETERMINATE	1	TRUE	NA	0.475862416338679	2		361	342	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133898	55133898	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	76	358	0	ENST00000257290.5:c.1111C>T	p.Gln371Ter	p.Q371*	ENST00000257290	NM_006206.4	371	Cag/Tag	7/23	0.352451102766052	1	FACETS	0.817	0.724	0.915	0.817	0.724	0.915	CLONAL	1	TRUE	0	0.475862416338679	1		358	298	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584575	187584575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	41	482	2	ENST00000441802.2:c.3458C>T	p.Pro1153Leu	p.P1153L	ENST00000441802	NM_005245.3	1153	cCt/cTt	3/27	0.352451102766052	1	FACETS	0.282	0.235	0.335	0.282	0.235	0.335	SUBCLONAL	1	TRUE	0	0.475862416338679	1		484	465	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295240	1295240	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1481772358	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	114	593	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.871	0.787	0.959	0.871	0.787	0.959	CLONAL	1	TRUE	1	0.475862416338679	2		594	550	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867421	35867421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1354581284	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	54	442	0	ENST00000303115.3:c.235G>A	p.Glu79Lys	p.E79K	ENST00000303115	NM_002185.3	79	Gag/Aag	3/8	1	2	FACETS	0.694	0.596	0.8	0.694	0.596	0.8	SUBCLONAL	1	TRUE	1	0.475862416338679	2		442	327	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876418	35876418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761882064	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	139	691	0	ENST00000303115.3:c.1210C>T	p.Leu404Phe	p.L404F	ENST00000303115	NM_002185.3	404	Ctc/Ttc	8/8	1	2	FACETS	0.844	0.77	0.922	0.844	0.77	0.922	CLONAL	1	TRUE	1	0.475862416338679	2		691	692	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751234	57751234	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226697571	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	64	356	1	ENST00000274289.3:c.1633C>T	p.His545Tyr	p.H545Y	ENST00000274289	NM_006622.3	545	Cac/Tac	12/14	1	2	FACETS	0.727	0.633	0.828	0.727	0.633	0.828	SUBCLONAL	1	TRUE	1	0.475862416338679	2		357	370	SUCCESS
APC	324	MSKCC	GRCh37	5	112174278	112174278	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	66	344	0	ENST00000257430.4:c.2987G>T	p.Ser996Ile	p.S996I	ENST00000257430	NM_000038.5	996	aGt/aTt	16/16	1	2	FACETS	0.856	0.749	0.971	0.856	0.749	0.971	CLONAL	1	TRUE	1	0.475862416338679	2		344	324	SUCCESS
APC	324	MSKCC	GRCh37	5	112178465	112178466	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	104	441	0	ENST00000257430.4:c.7174_7175delinsTT	p.Pro2392Leu	p.P2392L	ENST00000257430	NM_000038.5	2392	CCa/TTa	16/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.475862416338679	2		441	390	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510223	149510223	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	136	689	2	ENST00000261799.4:c.1246C>A	p.Pro416Thr	p.P416T	ENST00000261799	NM_002609.3	416	Cct/Act	9/23	1	2	FACETS	0.895	0.816	0.977	0.895	0.816	0.977	CLONAL	1	TRUE	1	0.475862416338679	2		691	639	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696769	176696769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	97	395	0	ENST00000439151.2:c.5470G>A	p.Asp1824Asn	p.D1824N	ENST00000439151	NM_022455.4	1824	Gat/Aat	16/23	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.475862416338679	2		395	391	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721237	176721237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767645475	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	82	469	0	ENST00000439151.2:c.6868C>T	p.Pro2290Ser	p.P2290S	ENST00000439151	NM_022455.4	2290	Ccc/Tcc	23/23	1	2	FACETS	0.727	0.643	0.816	0.727	0.643	0.816	SUBCLONAL	1	TRUE	1	0.475862416338679	2		469	474	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045793	180045793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	235	915	0	ENST00000261937.6:c.2978G>A	p.Arg993Lys	p.R993K	ENST00000261937	NM_182925.4	993	aGg/aAg	21/30	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.475862416338679	2		915	774	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225407	26225407	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	110	300	0	ENST00000360408.1:c.25C>T	p.Arg9Cys	p.R9C	ENST00000360408	NM_003532.2	9	Cgt/Tgt	1/1	0.450129080760029	3	FACETS	1	0.978	1	0.649	0.587	0.714	CLONAL	1	TRUE	1	0.475862416338679	3		300	441	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680529	30680529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	243	614	0	ENST00000376406.3:c.1190C>T	p.Ser397Phe	p.S397F	ENST00000376406	NM_014641.2	397	tCc/tTc	5/15	0.450129080760029	3	FACETS	0.83	0.778	0.882	0.83	0.778	0.882	CLONAL	2	TRUE	1	0.475862416338679	3		614	762	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168737	32168737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	534	859	0	ENST00000375023.3:c.4186C>T	p.His1396Tyr	p.H1396Y	ENST00000375023	NM_004557.3	1396	Cac/Tac	23/30	0.475862416338679	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.475862416338679	3		859	1257	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169887	32169887	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	467	925	2	ENST00000375023.3:c.3721G>A	p.Asp1241Asn	p.D1241N	ENST00000375023	NM_004557.3	1241	Gat/Aat	21/30	0.475862416338679	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.475862416338679	3		927	1195	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184930	32184930	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	174	629	0	ENST00000375023.3:c.1738G>A	p.Gly580Ser	p.G580S	ENST00000375023	NM_004557.3	580	Ggc/Agc	10/30	0.475862416338679	3	FACETS	1	0.94	1	0.512	0.471	0.554	CLONAL	1	TRUE	1	0.475862416338679	3		629	884	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94128966	94128966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	91	382	1	ENST00000369303.4:c.94G>A	p.Glu32Lys	p.E32K	ENST00000369303	NM_004440.3	32	Gaa/Aaa	1/17	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.475862416338679	2		383	366	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547420	106547420	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	86	337	0	ENST00000369096.4:c.657G>A	p.Met219Ile	p.M219I	ENST00000369096	NM_001198.3	219	atG/atA	4/7	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.475862416338679	2		337	320	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553044	106553044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	205	754	1	ENST00000369096.4:c.1009C>T	p.Pro337Ser	p.P337S	ENST00000369096	NM_001198.3	337	Ccc/Tcc	5/7	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.475862416338679	2		755	754	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109311867	109311867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	92	611	0	ENST00000436639.2:c.1405C>T	p.His469Tyr	p.H469Y	ENST00000436639	NM_014454.2	469	Cac/Tac	8/10	1	2	FACETS	0.715	0.637	0.797	0.715	0.637	0.797	SUBCLONAL	1	TRUE	1	0.475862416338679	2		611	541	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686838	117686838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868806134	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	108	483	0	ENST00000368508.3:c.2879G>A	p.Gly960Glu	p.G960E	ENST00000368508	NM_002944.2	960	gGa/gAa	19/43	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.475862416338679	2		483	423	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332892	152332892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	126	477	1	ENST00000206249.3:c.1198G>A	p.Gly400Arg	p.G400R	ENST00000206249	NM_000125.3	400	Ggg/Agg	5/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.475862416338679	2		478	459	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222567	157222567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	198	678	0	ENST00000346085.5:c.1834C>T	p.Pro612Ser	p.P612S	ENST00000346085	NM_020732.3	612	Cca/Tca	4/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.475862416338679	2		678	682	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622282	162622282	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1321208493	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	84	381	0	ENST00000366898.1:c.415G>A	p.Gly139Ser	p.G139S	ENST00000366898	NM_004562.2	139	Ggt/Agt	4/12	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.475862416338679	2		381	315	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683729	162683729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	138	634	0	ENST00000366898.1:c.240G>A	p.Met80Ile	p.M80I	ENST00000366898	NM_004562.2	80	atG/atA	3/12	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.475862416338679	2		634	561	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729451	41729451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	162	681	0	ENST00000242208.4:c.1078G>A	p.Gly360Ser	p.G360S	ENST00000242208	NM_002192.2	360	Ggc/Agc	3/3	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.475862416338679	2		681	662	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729652	41729652	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	165	595	0	ENST00000242208.4:c.877C>T	p.Leu293Phe	p.L293F	ENST00000242208	NM_002192.2	293	Ctc/Ttc	3/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.475862416338679	2		595	619	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730006	41730006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	162	709	0	ENST00000242208.4:c.523C>T	p.Leu175Phe	p.L175F	ENST00000242208	NM_002192.2	175	Ctc/Ttc	3/3	1	2	FACETS	0.977	0.899	1	0.977	0.899	1	CLONAL	1	TRUE	1	0.475862416338679	2		709	697	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227896	55227896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	51	463	0	ENST00000275493.2:c.1363G>A	p.Glu455Lys	p.E455K	ENST00000275493	NM_005228.3	455	Gag/Aag	12/28	1	2	FACETS	0.552	0.471	0.641	0.552	0.471	0.641	SUBCLONAL	1	TRUE	1	0.475862416338679	2		463	388	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509620	106509621	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	167	634	2	ENST00000359195.3:c.1614_1615delinsAA	p.Glu539Lys	p.E539K	ENST00000359195	NM_002649.2	538	ccGGaa/ccAAaa	2/11	1	2	FACETS	0.967	0.89	1	0.967	0.89	1	CLONAL	1	TRUE	1	0.475862416338679	2		636	726	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339553	116339553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	129	319	0	ENST00000397752.3:c.415G>A	p.Gly139Arg	p.G139R	ENST00000397752	NM_000245.2	139	Ggg/Agg	2/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.475862416338679	2		319	411	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194773	29194773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	230	987	1	ENST00000240100.2:c.955C>T	p.Pro319Ser	p.P319S	ENST00000240100	NM_001394.6	319	Ccc/Tcc	4/4	1	2	FACETS	0.962	0.897	1	0.962	0.897	1	CLONAL	1	TRUE	1	0.475862416338679	2		988	1005	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205280	38205280	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	218	1095	0	ENST00000317025.8:c.410C>T	p.Pro137Leu	p.P137L	ENST00000317025	NM_023034.1	137	cCt/cTt	2/24	1	2	FACETS	0.891	0.829	0.956	0.891	0.829	0.956	CLONAL	1	TRUE	1	0.475862416338679	2		1095	1028	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56910933	56910933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201895605	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	188	655	1	ENST00000519728.1:c.1079G>A	p.Arg360Gln	p.R360Q	ENST00000519728	NM_002350.3	360	cGg/cAg	11/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.475862416338679	2		656	710	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981636	70981636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1441295182	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	297	1133	0	ENST00000276594.2:c.460C>T	p.Pro154Ser	p.P154S	ENST00000276594	NM_024504.3	154	Cct/Tct	2/8	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.475862416338679	2		1133	1161	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517958	8517958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1425203347	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	91	442	0	ENST00000356435.5:c.1433C>T	p.Thr478Ile	p.T478I	ENST00000356435		478	aCt/aTt	10/35	0.221001478014439	1	FACETS	0.727	0.65	0.808	0.727	0.65	0.808	INDETERMINATE	1	TRUE	0	0.475862416338679	1		442	401	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197556	27197556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	70	655	1	ENST00000380036.4:c.1868G>A	p.Gly623Glu	p.G623E	ENST00000380036	NM_000459.3	623	gGg/gAg	12/23	0.221001478014439	1	FACETS	0.418	0.364	0.475	0.418	0.364	0.475	INDETERMINATE	1	TRUE	0	0.475862416338679	1		656	537	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212725	27212725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	111	909	0	ENST00000380036.4:c.2707G>A	p.Glu903Lys	p.E903K	ENST00000380036	NM_000459.3	903	Gag/Aag	17/23	0.221001478014439	1	FACETS	0.451	0.405	0.5	0.451	0.405	0.5	INDETERMINATE	1	TRUE	0	0.475862416338679	1		909	788	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212810	27212810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	122	820	1	ENST00000380036.4:c.2792G>A	p.Ser931Asn	p.S931N	ENST00000380036	NM_000459.3	931	aGc/aAc	17/23	0.221001478014439	1	FACETS	0.485	0.438	0.534	0.485	0.438	0.534	INDETERMINATE	1	TRUE	0	0.475862416338679	1		821	806	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97933383	97933383	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	86	452	0	ENST00000289081.3:c.499A>G	p.Asn167Asp	p.N167D	ENST00000289081	NM_000136.2	167	Aat/Gat	6/15	1	2	FACETS	0.835	0.742	0.933	0.835	0.742	0.933	CLONAL	1	TRUE	1	0.475862416338679	2		452	433	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912095	127912095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	62	335	0	ENST00000373547.4:c.775C>T	p.Pro259Ser	p.P259S	ENST00000373547	NM_002721.4	259	Cct/Tct	7/7	1	2	FACETS	0.749	0.65	0.854	0.749	0.65	0.854	SUBCLONAL	1	TRUE	1	0.475862416338679	2		335	348	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347961	128347961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751738081	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	207	890	1	ENST00000265960.3:c.544C>T	p.Pro182Ser	p.P182S	ENST00000265960	NM_001006617.1	182	Cct/Tct	5/12	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.475862416338679	2		891	789	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776208	135776208	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1564475110	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	113	493	0	ENST00000298552.3:c.2519C>T	p.Ser840Leu	p.S840L	ENST00000298552	NM_001162426.1	840	tCg/tTg	20/23	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.475862416338679	2		493	474	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391746	139391746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	231	941	0	ENST00000277541.6:c.6445C>T	p.Leu2149Phe	p.L2149F	ENST00000277541	NM_017617.3	2149	Ctc/Ttc	34/34	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.475862416338679	2		941	822	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44935995	44935995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	95	338	0	ENST00000377967.4:c.2756C>T	p.Pro919Leu	p.P919L	ENST00000377967	NM_021140.2	919	cCa/cTa	18/29	1	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.475862416338679	1		338	236	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409801	63409802	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	105	289	0	ENST00000330258.3:c.3365_3366delinsTT	p.Thr1122Ile	p.T1122I	ENST00000330258	NM_152424.3	1122	aCC/aTT	2/2	1	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.475862416338679	1		289	265	SUCCESS
BTK	695	MSKCC	GRCh37	X	100625048	100625048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	135	315	0	ENST00000308731.7:c.329C>T	p.Pro110Leu	p.P110L	ENST00000308731	NM_000061.2	110	cCt/cTt	5/19	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.475862416338679	1		315	292	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164875	123164875	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	89	200	0	ENST00000218089.9:c.188C>T	p.Pro63Leu	p.P63L	ENST00000218089	NM_001042749.1	63	cCt/cTt	5/35	1	1	FACETS	0.908	0.832	0.982	1	0.988	1	CLONAL	2	TRUE	0	0.475862416338679	1		200	157	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463287	25463289	+	inframe_deletion	In_Frame_Del	DEL	GGT	GGT	-	novel	NA	P-0041437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	108	607	0	ENST00000264709.3:c.2204_2206del	p.Tyr735_Arg736delinsCys	p.Y735_R736delinsC	ENST00000264709	NM_175629.2	735	tACCgc/tgc	19/23	1	2	FACETS	0.827	0.745	0.913	0.827	0.745	0.913	CLONAL	1	TRUE	1	0.475862416338679	2		607	549	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0041455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	62	366	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.202140302148448	3	FACETS	1	0.874	1	0.505	0.437	0.578	CLONAL	1	TRUE	1	0.322727469944533	3		366	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0041455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	83	575	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.322727469944533	1	FACETS	0.802	0.709	0.901	0.802	0.709	0.901	CLONAL	1	TRUE	0	0.322727469944533	1		575	538	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711892	89711892	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	89	337	0	ENST00000371953.3:c.510T>G	p.Ser170Arg	p.S170R	ENST00000371953	NM_000314.4	170	agT/agG	6/9	0.283891362389742	2	FACETS	0.779	0.696	0.866	0.779	0.696	0.866	SUBCLONAL	2	TRUE	0	0.322727469944533	2		337	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578502	7578502	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555526241	NA	P-0041466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	89	719	0	ENST00000269305.4:c.428T>G	p.Val143Gly	p.V143G	ENST00000269305	NM_001126112.2	143	gTg/gGg	5/11	0.164354038413068	2	FACETS	1	0.954	1	0.577	0.51	0.649	CLONAL	1	TRUE	0	0.15	2		719	1028	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953855	55953855	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	38	443	0	ENST00000263923.4:c.3581T>C	p.Leu1194Pro	p.L1194P	ENST00000263923	NM_002253.2	1194	cTg/cCg	27/30	1	2	FACETS	0.926	0.765	1	0.926	0.765	1	CLONAL	1	TRUE	1	0.15	2		443	547	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410930	63410935	+	inframe_deletion	In_Frame_Del	DEL	GGGTAG	GGGTAG	-	novel	NA	P-0041466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	47	633	0	ENST00000330258.3:c.2232_2237del	p.Tyr745_Pro746del	p.Y745_P746del	ENST00000330258	NM_152424.3	744	gcCTACCCt/gct	2/2	1	2	FACETS	0.803	0.676	0.945	0.803	0.676	0.945	CLONAL	1	TRUE	1	0.15	2		633	780	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0041476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	88	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.342815319372987	2		311	402	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150496	157150496	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs17318151	NA	P-0041476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	95	638	0	ENST00000346085.5:c.1678A>G	p.Ile560Val	p.I560V	ENST00000346085	NM_020732.3	560	Att/Gtt	2/20	0.342815319372987	1	FACETS	0.928	0.829	1	0.928	0.829	1	CLONAL	1	TRUE	0	0.342815319372987	1		638	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs967461896	NA	P-0041476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	118	733	0	ENST00000269305.4:c.526T>A	p.Cys176Ser	p.C176S	ENST00000269305	NM_001126112.2	176	Tgc/Agc	5/11	0.342815319372987	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.342815319372987	1		733	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	522	910	0	ENST00000269305.4:c.1045del	p.Glu349AsnfsTer21	p.E349Nfs*21	ENST00000269305	NM_001126112.2	349	Gaa/aa	10/11	0.858835913036512	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.858835913036512	1		910	665	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266985	41266985	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	270	498	0	ENST00000349496.5:c.656A>G	p.His219Arg	p.H219R	ENST00000349496	NM_001904.3	219	cAt/cGt	5/15	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.858835913036512	2		498	569	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714376	40714376	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	306	557	0	ENST00000373198.4:c.4021A>G	p.Met1341Val	p.M1341V	ENST00000373198	NM_133170.3	1341	Atg/Gtg	29/32	1	2	FACETS	0.99	0.939	1	0.99	0.939	1	CLONAL	1	TRUE	1	0.858835913036512	2		557	720	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730078	41730078	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	171	630	0	ENST00000242208.4:c.451G>C	p.Glu151Gln	p.E151Q	ENST00000242208	NM_002192.2	151	Gag/Cag	3/3	0.481512536115077	1	FACETS	0.366	0.338	0.395	0.366	0.338	0.395	INDETERMINATE	1	TRUE	0	0.858835913036512	1		630	621	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0041547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	15	667	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.231	0.168	0.308	0.231	0.168	0.308	SUBCLONAL	1	TRUE	1	0.24	2		667	540	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0041547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	42	476	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.3	2	FACETS	0.497	0.414	0.59			1	SUBCLONAL	1	TRUE	NA	0.24	2		476	704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0041547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	60	652	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	1	2	FACETS	0.572	0.491	0.66	0.572	0.491	0.66	SUBCLONAL	1	TRUE	1	0.24	2		652	874	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466366	120466366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	87	494	0	ENST00000256646.2:c.4753G>T	p.Gly1585Trp	p.G1585W	ENST00000256646	NM_024408.3	1585	Ggg/Tgg	26/34	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.24	2		494	675	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0041553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	113	446	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		446	811	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0041584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	16	397	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.137	0.101	0.181	0.137	0.101	0.181	SUBCLONAL	1	TRUE	1	0.53185311194573	2		397	438	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950726	38950726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370517295	NA	P-0041584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	39	219	0	ENST00000357387.3:c.3224G>A	p.Arg1075Gln	p.R1075Q	ENST00000357387	NM_152756.3	1075	cGa/cAa	31/38	0.359068513915444	3	FACETS	0.532	0.442	0.632	0.177	0.147	0.211	SUBCLONAL	1	TRUE	0	0.53185311194573	3		219	349	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636999	158636999	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772534199	NA	P-0041584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	308	451	0	ENST00000263640.3:c.181G>A	p.Asp61Asn	p.D61N	ENST00000263640	NM_001105.4	61	Gat/Aat	4/11	0.261520390447056	1	FACETS	1	0.994	1	1	0.994	1	INDETERMINATE	1	TRUE	0	0.53185311194573	1		451	626	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456254	32456254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756414084	NA	P-0041584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	373	505	1	ENST00000332351.3:c.638G>A	p.Arg213His	p.R213H	ENST00000332351	NM_024426.4	213	cGc/cAc	1/10	1	2	FACETS	0.757	0.721	0.793	1	0.995	1	SUBCLONAL	2	TRUE	1	0.53185311194573	2		506	927	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0041584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	438	602	1	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	NA	2	FACETS	0.814	0.779	0.849			1	INDETERMINATE	2	TRUE	NA	0.53185311194573	2		603	1012	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42843797	42843798	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0041584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	295	417	0	ENST00000398585.3:c.1121_1122del	p.Tyr374Ter	p.Y374*	ENST00000398585	NM_001135099.1	374	tAT/t	10/14	NA	2	FACETS	0.777	0.736	0.818			1	INDETERMINATE	2	TRUE	NA	0.53185311194573	2		417	714	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021727	71021727	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	172	292	0	ENST00000318789.4:c.1631G>T	p.Arg544Leu	p.R544L	ENST00000318789	NM_032682.5	544	cGa/cTa	18/21	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.53185311194573	2		292	499	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0041585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	74	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.858	0.753	0.97	0.858	0.753	0.97	CLONAL	1	TRUE	1	0.35	2		311	493	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0041585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	61	405	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.701	0.606	0.805	0.701	0.606	0.805	SUBCLONAL	1	TRUE	1	0.35	2		405	497	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715678	30715678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039551	NA	P-0041585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	48	255	0	ENST00000295754.5:c.1336G>A	p.Asp446Asn	p.D446N	ENST00000295754	NM_003242.5	446	Gat/Aat	5/7	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.35	2		255	271	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751553	57751553	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463906111	NA	P-0041585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	71	249	0	ENST00000274289.3:c.1438C>T	p.Arg480Trp	p.R480W	ENST00000274289	NM_006622.3	480	Cgg/Tgg	11/14	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.35	2		249	347	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003749	45003749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368160918	NA	P-0041607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	162	458	0	ENST00000558401.1:c.5C>T	p.Ser2Phe	p.S2F	ENST00000558401	NM_004048.2	2	tCt/tTt	1/4	1	2	FACETS	0.872	0.804	0.941	1	0.991	1	CLONAL	2	TRUE	1	0.332487908582446	2		458	559	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573524	41573524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	82	852	0	ENST00000263253.7:c.5809G>A	p.Glu1937Lys	p.E1937K	ENST00000263253	NM_001429.3	1937	Gag/Aag	31/31	1	2	FACETS	0.752	0.663	0.847	0.752	0.663	0.847	SUBCLONAL	1	TRUE	1	0.332487908582446	2		852	656	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587782272	NA	P-0041607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	163	676	0	ENST00000269305.4:c.994-1G>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.332487908582446	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.332487908582446	1		676	662	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953930	131953930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	23	342	1	ENST00000265335.6:c.3333G>A	p.Met1111Ile	p.M1111I	ENST00000265335		1111	atG/atA	21/25	0.329055234561648	2	FACETS	0.579	0.453	0.724	0.289	0.226	0.362	SUBCLONAL	1	TRUE	0	0.332487908582446	2		343	239	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486587	56486587	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	416	571	0	ENST00000267101.3:c.1166C>T	p.Thr389Ile	p.T389I	ENST00000267101	NM_001982.3	389	aCa/aTa	10/28	0.298925364678145	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.332487908582446	3		571	857	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121523	193121523	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	61	275	0	ENST00000367435.3:c.921C>G	p.Phe307Leu	p.F307L	ENST00000367435	NM_024529.4	307	ttC/ttG	10/17	0.307075549200176	4	FACETS	1	0.952	1	0.791	0.693	0.894	CLONAL	2	TRUE	1	0.332487908582446	4		275	206	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911905	94911905	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	108	607	0	ENST00000536441.1:c.1025G>A	p.Gly342Glu	p.G342E	ENST00000536441	NM_144665.3	342	gGa/gAa	7/10	0.274333126714429	3	FACETS	1	0.976	1	0.648	0.583	0.716	CLONAL	1	TRUE	1	0.332487908582446	3		607	585	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252829	10252829	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs548883904	NA	P-0041607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	91	768	1	ENST00000340748.4:c.3136G>A	p.Asp1046Asn	p.D1046N	ENST00000340748		1046	Gac/Aac	29/40	0.332487908582446	6	FACETS	0.794	0.703	0.892	0.132	0.117	0.149	SUBCLONAL	1	TRUE	0	0.332487908582446	6		769	1148	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033958	48033958	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	28	309	0	ENST00000234420.5:c.4042G>A	p.Glu1348Lys	p.E1348K	ENST00000234420	NM_000179.2	1348	Gaa/Aaa	10/10	1	2	FACETS	0.626	0.502	0.767	0.626	0.502	0.767	SUBCLONAL	1	TRUE	1	0.332487908582446	2		309	269	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573708	41573708	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	78	841	1	ENST00000263253.7:c.5993G>T	p.Gly1998Val	p.G1998V	ENST00000263253	NM_001429.3	1998	gGa/gTa	31/31	1	2	FACETS	0.618	0.543	0.7	0.618	0.543	0.7	SUBCLONAL	1	TRUE	1	0.332487908582446	2		842	759	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948532	31948532	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	24	170	0	ENST00000375333.2:c.1015C>G	p.Leu339Val	p.L339V	ENST00000375333	NM_032454.1	339	Ctc/Gtc	7/8	0.329055234561648	2	FACETS	0.825	0.652	1	0.412	0.326	0.511	CLONAL	1	TRUE	0	0.332487908582446	2		170	175	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128849207	128849207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	105	633	0	ENST00000249373.3:c.1435G>A	p.Glu479Lys	p.E479K	ENST00000249373	NM_005631.4	479	Gag/Aag	8/12	0.274333126714429	3	FACETS	0.963	0.863	1	0.481	0.431	0.535	CLONAL	1	TRUE	1	0.332487908582446	3		633	765	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978321	2978321	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs138920531	NA	P-0041618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	113	655	0	ENST00000396946.4:c.1009C>T	p.Arg337Ter	p.R337*	ENST00000396946	NM_032415.4	337	Cga/Tga	7/25	0.22576362241894	3	FACETS	1	0.918	1	0.339	0.306	0.373	INDETERMINATE	1	TRUE	0	0.550629708024969	3		655	515	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390740	118390740	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1285242662	NA	P-0041618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	207	420	0	ENST00000534358.1:c.11390A>G	p.Asn3797Ser	p.N3797S	ENST00000534358	NM_005933.3	3797	aAt/aGt	33/36	0.536911566767818	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.550629708024969	3		420	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579362	+	frameshift_variant	Frame_Shift_Del	DEL	AGACGGAA	AGACGGAA	-	novel	NA	P-0041618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	406	821	0	ENST00000269305.4:c.325_332del	p.Phe109GlyfsTer37	p.F109Gfs*37	ENST00000269305	NM_001126112.2	109	TTCCGTCTg/g	4/11	0.508027205168543	3	FACETS	0.948	0.913	0.983			1	CLONAL	3	TRUE	NA	0.550629708024969	3		821	661	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945731	17945731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	305	765	0	ENST00000458235.1:c.2129G>A	p.Gly710Asp	p.G710D	ENST00000458235	NM_000215.3	710	gGc/gAc	16/24	0.285852338313531	5	FACETS	1	0.98	1	0.718	0.678	0.759	INDETERMINATE	2	TRUE	2	0.550629708024969	5		765	939	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278905	1278905	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	91	593	0	ENST00000310581.5:c.2137G>T	p.Val713Leu	p.V713L	ENST00000310581	NM_198253.2	713	Gtg/Ttg	6/16	0.550629708024969	3	FACETS	0.722	0.642	0.807	0.361	0.321	0.404	SUBCLONAL	1	TRUE	1	0.550629708024969	3		593	584	SUCCESS
APC	324	MSKCC	GRCh37	5	112177264	112177279	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCCCTGACTCACAG	GCCCCCTGACTCACAG	-	novel	NA	P-0041618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	47	334	0	ENST00000257430.4:c.5974_5989del	p.Pro1992GlufsTer47	p.P1992Efs*47	ENST00000257430	NM_000038.5	1991	gaGCCCCCTGACTCACAG/ga	16/16	0.550629708024969	2	FACETS	0.762	0.65	0.883	0.381	0.325	0.442	SUBCLONAL	1	TRUE	0	0.550629708024969	2		334	224	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231012	98231031	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CCTTAAGTTGTGGCAGATTA	CCTTAAGTTGTGGCAGATTA	-	novel	NA	P-0041618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	99	471	0	ENST00000331920.6:c.2250+2_2250+21del		p.X750_splice	ENST00000331920	NM_000264.3	750			0.285852338313531	5	FACETS	1	0.982	1	0.497	0.446	0.551	INDETERMINATE	1	TRUE	2	0.550629708024969	5		471	440	SUCCESS
APC	324	MSKCC	GRCh37	5	112174786	112174787	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0041620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	59	233	0	ENST00000257430.4:c.3498_3499del	p.Tyr1166Ter	p.Y1166*	ENST00000257430	NM_000038.5	1165	aaATat/aaat	16/16	1	2	FACETS	0.83	0.726	0.938	0.83	0.726	0.938	CLONAL	1	TRUE	1	0.740702584496049	2		233	192	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579344	7579345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0041620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	539	738	0	ENST00000269305.4:c.342dup	p.His115AlafsTer34	p.H115Afs*34	ENST00000269305	NM_001126112.2	114	-/G	4/11	0.72805188700526	2	FACETS	0.925	0.898	0.951	0.925	0.898	0.951	CLONAL	2	TRUE	0	0.740702584496049	2		738	787	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117878	70117888	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCAGGCGGC	GCGCAGGCGGC	-	novel	NA	P-0041620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	82	493	0	ENST00000245479.2:c.353_363del	p.Ala118GlufsTer130	p.A118Efs*130	ENST00000245479	NM_000346.3	116	GCGCAGGCGGCg/g	1/3	0.740702584496049	3	FACETS	0.467	0.412	0.526	0.233	0.206	0.263	SUBCLONAL	1	TRUE	1	0.740702584496049	3		493	650	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344220	70344220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	118	309	0	ENST00000374080.3:c.1956C>A	p.Ser652Arg	p.S652R	ENST00000374080		652	agC/agA	13/45	0.740702584496049	3	FACETS	1	0.954	1	0.539	0.49	0.59	CLONAL	1	TRUE	1	0.740702584496049	3		309	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578505	7578505	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	421	937	0	ENST00000269305.4:c.425del	p.Pro142LeufsTer28	p.P142Lfs*28	ENST00000269305	NM_001126112.2	142	cCt/ct	5/11	0.589247168125055	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.771756733944958	1		937	654	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872120	76872120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	82	322	0	ENST00000373344.5:c.5527C>T	p.Gln1843Ter	p.Q1843*	ENST00000373344	NM_000489.3	1843	Cag/Tag	22/35	0.738029148900227	2	FACETS	0.9	0.833	0.963	0.9	0.833	0.963	CLONAL	2	TRUE	0	0.771756733944958	2		322	118	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	94	309	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.912	0.815	1	0.912	0.815	1	CLONAL	1	FALSE	1	0.409765452337261	2		309	503	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129329	152129329	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	174	755	1	ENST00000206249.3:c.287del	p.Gly96ValfsTer13	p.G96Vfs*13	ENST00000206249	NM_000125.3	94	ctG/ct	1/8	1	2	FACETS	0.885	0.814	0.958	0.885	0.814	0.958	CLONAL	1	FALSE	1	0.409765452337261	2		756	960	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	115	516	3	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.818	0.738	0.903	0.818	0.738	0.903	CLONAL	1	FALSE	1	0.409765452337261	2		519	686	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	106	368	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.250945406669204	3	FACETS	0.999	0.897	1	0.499	0.448	0.553	CLONAL	1	FALSE	1	0.409765452337261	3		371	624	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	58	124	0	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.86	0.744	0.986	0.86	0.744	0.986	CLONAL	1	FALSE	1	0.409765452337261	2		124	329	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	197	721	8	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.925	0.856	0.997	0.925	0.856	0.997	CLONAL	1	FALSE	1	0.409765452337261	2		729	1039	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	223	845	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.985	0.916	1	0.985	0.916	1	CLONAL	1	FALSE	1	0.409765452337261	2		845	1105	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	120	456	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	FALSE	1	0.409765452337261	2		461	573	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	227	852	2	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	1	0.409765452337261	2		854	1088	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876449	35876449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2229232	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	181	620	0	ENST00000303115.3:c.1241C>T	p.Thr414Met	p.T414M	ENST00000303115	NM_002185.3	414	aCg/aTg	8/8	1	2	FACETS	0.987	0.911	1	0.987	0.911	1	CLONAL	1	FALSE	1	0.409765452337261	2		620	895	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537184	41537184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	128	557	0	ENST00000263253.7:c.2011C>T	p.Pro671Ser	p.P671S	ENST00000263253	NM_001429.3	671	Cca/Tca	10/31	1	2	FACETS	0.863	0.783	0.947	0.863	0.783	0.947	CLONAL	1	FALSE	1	0.409765452337261	2		557	724	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606150	81606150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373712078	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	94	485	1	ENST00000298171.2:c.820C>T	p.Arg274Trp	p.R274W	ENST00000298171	NM_000369.2	274	Cgg/Tgg	9/10	1	2	FACETS	0.831	0.741	0.926	0.831	0.741	0.926	CLONAL	1	FALSE	1	0.409765452337261	2		486	552	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	112	503	1	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	0.838	0.755	0.926	0.838	0.755	0.926	CLONAL	1	FALSE	1	0.409765452337261	2		504	652	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372022	55372022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	180	645	3	ENST00000297316.4:c.712G>A	p.Ala238Thr	p.A238T	ENST00000297316	NM_022454.3	238	Gcc/Acc	2/2	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.409765452337261	2		648	838	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053022	180053023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750808726	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	205	975	0	ENST00000261937.6:c.1267dup	p.Gln423ProfsTer4	p.Q423Pfs*4	ENST00000261937	NM_182925.4	423	cag/cCag	10/30	1	2	FACETS	0.889	0.824	0.957	0.889	0.824	0.957	CLONAL	1	FALSE	1	0.409765452337261	2		975	1125	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	77	805	6	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	1	2	FACETS	0.335	0.293	0.381	0.335	0.293	0.381	SUBCLONAL	1	FALSE	1	0.409765452337261	2		811	1122	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80343580	80343580	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	68	114	0	ENST00000286548.4:c.739C>T	p.Arg247Ter	p.R247*	ENST00000286548	NM_002072.3	247	Cga/Tga	6/7	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	FALSE	1	0.409765452337261	2		114	326	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	230	784	6	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.409765452337261	2		790	1046	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243045	105243045	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	238	933	0	ENST00000349310.3:c.238T>C	p.Trp80Arg	p.W80R	ENST00000349310	NM_001014432.1	80	Tgg/Cgg	5/15	1	2	FACETS	0.931	0.868	0.996	0.931	0.868	0.996	CLONAL	1	FALSE	1	0.409765452337261	2		933	1248	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534801	18534801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759595930	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	103	417	0	ENST00000266497.5:c.1859C>T	p.Pro620Leu	p.P620L	ENST00000266497		620	cCg/cTg	12/31	1	2	FACETS	0.898	0.806	0.995	0.898	0.806	0.995	CLONAL	1	FALSE	1	0.409765452337261	2		417	560	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193849	106193850	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs777908833	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	82	296	0	ENST00000380013.4:c.4317dup	p.Arg1440ThrfsTer38	p.R1440Tfs*38	ENST00000380013	NM_001127208.2	1437	-/A	10/11	1	2	FACETS	0.951	0.843	1	0.951	0.843	1	CLONAL	1	FALSE	1	0.409765452337261	2		296	421	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900984	114900984	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778855667	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	172	614	0	ENST00000543371.1:c.598del	p.Leu200SerfsTer25	p.L200Sfs*25	ENST00000543371	NM_001198531.1	198	caC/ca	6/14	1	2	FACETS	0.996	0.917	1	0.996	0.917	1	CLONAL	1	FALSE	1	0.409765452337261	2		614	843	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444659	78444659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs908264837	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	140	465	0	ENST00000370768.2:c.30del	p.Ser11LeufsTer43	p.S11Lfs*43	ENST00000370768	NM_003902.3	10	ccC/cc	1/20	1	2	FACETS	0.993	0.906	1	0.993	0.906	1	CLONAL	1	FALSE	1	0.409765452337261	2		465	688	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257770	16257770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779103344	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	52	497	1	ENST00000375759.3:c.5035G>A	p.Val1679Ile	p.V1679I	ENST00000375759	NM_015001.2	1679	Gtc/Atc	11/15	1	2	FACETS	0.373	0.317	0.435	0.373	0.317	0.435	SUBCLONAL	1	FALSE	1	0.409765452337261	2		498	680	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540634	187540634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201741692	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	87	338	0	ENST00000441802.2:c.7106C>T	p.Thr2369Met	p.T2369M	ENST00000441802	NM_005245.3	2369	aCg/aTg	10/27	1	2	FACETS	0.876	0.778	0.979	0.876	0.778	0.979	CLONAL	1	FALSE	1	0.409765452337261	2		338	485	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435777	56435777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1055597951	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	167	595	0	ENST00000407977.2:c.1360C>T	p.Arg454Cys	p.R454C	ENST00000407977		454	Cgc/Tgc	9/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.409765452337261	2		595	774	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574664	41574664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	250	971	1	ENST00000263253.7:c.6949C>T	p.Arg2317Trp	p.R2317W	ENST00000263253	NM_001429.3	2317	Cgg/Tgg	31/31	1	2	FACETS	0.971	0.907	1	0.971	0.907	1	CLONAL	1	FALSE	1	0.409765452337261	2		972	1257	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	136	407	1	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	0.871	0.793	0.953	0.871	0.793	0.953	CLONAL	1	FALSE	1	0.409765452337261	2		408	762	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795609	42795609	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	265	927	1	ENST00000575354.2:c.2694del	p.Ala900ProfsTer24	p.A900Pfs*24	ENST00000575354	NM_015125.3	897	Ccc/cc	10/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.409765452337261	2		928	1241	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981721	101981721	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555075353	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	37	358	0	ENST00000282441.5:c.147del	p.Ala50ProfsTer24	p.A50Pfs*24	ENST00000282441	NM_001130145.2	48	Ccc/cc	1/9	1	2	FACETS	0.355	0.292	0.425	0.355	0.292	0.425	SUBCLONAL	1	FALSE	1	0.409765452337261	2		358	509	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368196	31368196	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367766007	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	228	866	0	ENST00000328111.2:c.67G>A	p.Val23Ile	p.V23I	ENST00000328111	NM_006892.3	23	Gtc/Atc	2/23	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	FALSE	1	0.409765452337261	2		866	1099	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641388	23641388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780820	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	168	723	0	ENST00000261584.4:c.2087C>T	p.Thr696Met	p.T696M	ENST00000261584	NM_024675.3	696	aCg/aTg	5/13	1	2	FACETS	0.857	0.787	0.93	0.857	0.787	0.93	CLONAL	1	FALSE	1	0.409765452337261	2		723	957	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225360560	225360561	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	26	83	0	ENST00000264414.4:c.1830dup	p.Tyr611IlefsTer4	p.Y611Ifs*4	ENST00000264414	NM_003590.4	610	-/A	13/16	1	2	FACETS	0.887	0.712	1	0.887	0.712	1	CLONAL	1	FALSE	1	0.409765452337261	2		83	143	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128201212	128201212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374025668	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	73	689	0	ENST00000265960.3:c.1523G>A	p.Arg508His	p.R508H	ENST00000265960	NM_001006617.1	508	cGt/cAt	12/12	1	2	FACETS	0.384	0.335	0.438	0.384	0.335	0.438	SUBCLONAL	1	FALSE	1	0.409765452337261	2		689	927	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135297	2135297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1332979299	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	233	813	1	ENST00000219476.3:c.4636G>A	p.Ala1546Thr	p.A1546T	ENST00000219476	NM_000548.3	1546	Gcc/Acc	36/42	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.409765452337261	2		814	1081	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	211	808	7	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	1	0.409765452337261	2		815	1007	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630711	90630711	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1339259178	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	189	599	2	ENST00000330062.3:c.775G>A	p.Asp259Asn	p.D259N	ENST00000330062	NM_002168.2	259	Gat/Aat	6/11	1	2	FACETS	0.995	0.92	1	0.995	0.92	1	CLONAL	1	FALSE	1	0.409765452337261	2		601	927	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806153	1806153	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28931615	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1244	33	1046	1	ENST00000260795.2:c.1172C>T	p.Ala391Val	p.A391V	ENST00000260795		391	gCg/gTg	8/17	1	2	FACETS	0.126	0.102	0.154	0.126	0.102	0.154	SUBCLONAL	1	FALSE	1	0.409765452337261	2		1047	1277	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384726	17384726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368554117	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	205	750	1	ENST00000359435.4:c.358G>A	p.Ala120Thr	p.A120T	ENST00000359435	NM_001033549.1	120	Gcc/Acc	4/9	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	1	0.409765452337261	2		751	985	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350059	89350059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	206	830	3	ENST00000301030.4:c.2891G>A	p.Gly964Asp	p.G964D	ENST00000301030	NM_001256183.1	964	gGc/gAc	9/13	1	2	FACETS	0.903	0.837	0.972	0.903	0.837	0.972	CLONAL	1	FALSE	1	0.409765452337261	2		833	1113	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959240	2959240	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148354898	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	161	674	0	ENST00000396946.4:c.2276G>A	p.Arg759Gln	p.R759Q	ENST00000396946	NM_032415.4	759	cGg/cAg	18/25	1	2	FACETS	0.995	0.914	1	0.995	0.914	1	CLONAL	1	FALSE	1	0.409765452337261	2		674	790	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11027404	11027404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868638712	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	283	1027	3	ENST00000327064.4:c.971C>T	p.Ser324Leu	p.S324L	ENST00000327064	NM_199141.1	324	tCg/tTg	8/16	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.409765452337261	2		1030	1205	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166275	32166275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs967436228	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	226	781	1	ENST00000375023.3:c.4679C>T	p.Ala1560Val	p.A1560V	ENST00000375023	NM_004557.3	1560	gCg/gTg	26/30	1	2	FACETS	0.986	0.918	1	0.986	0.918	1	CLONAL	1	FALSE	1	0.409765452337261	2		782	1119	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425823	49425824	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs754290613	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	142	747	0	ENST00000301067.7:c.12662_12664dup	p.Gln4221dup	p.Q4221dup	ENST00000301067	NM_003482.3	4221	cta/cAGCta	39/54	1	2	FACETS	0.793	0.723	0.867	0.793	0.723	0.867	SUBCLONAL	1	FALSE	1	0.409765452337261	2		747	874	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426973	49426973	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1565778024	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	184	747	3	ENST00000301067.7:c.11515del	p.Gln3839SerfsTer42	p.Q3839Sfs*42	ENST00000301067	NM_003482.3	3839	Cag/ag	39/54	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.409765452337261	2		750	853	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470968	25470968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1483397095	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	239	945	1	ENST00000264709.3:c.793G>A	p.Val265Met	p.V265M	ENST00000264709	NM_175629.2	265	Gtg/Atg	7/23	0.409765452337261	2	FACETS	1	0.974	1	0.543	0.507	0.581	CLONAL	1	FALSE	0	0.409765452337261	2		946	1074	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794899	242794899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	246	913	1	ENST00000334409.5:c.310C>T	p.Arg104Cys	p.R104C	ENST00000334409	NM_005018.2	104	Cgt/Tgt	2/5	0.292734592004619	1	FACETS	0.834	0.779	0.891	0.834	0.779	0.891	CLONAL	1	FALSE	0	0.409765452337261	1		914	1145	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722238	49722238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369252300	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	160	623	0	ENST00000449682.2:c.1702C>T	p.Arg568Trp	p.R568W	ENST00000449682	NM_020998.3	568	Cgg/Tgg	15/18	1	2	FACETS	0.982	0.902	1	0.982	0.902	1	CLONAL	1	FALSE	1	0.409765452337261	2		623	795	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919939	50919939	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757190258	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	235	916	1	ENST00000440232.2:c.3026G>A	p.Arg1009His	p.R1009H	ENST00000440232	NM_002691.3	1009	cGc/cAc	24/27	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	1	0.409765452337261	2		917	1124	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25536804	25536804	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1299885148	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	271	955	5	ENST00000264709.3:c.50C>T	p.Ala17Val	p.A17V	ENST00000264709	NM_175629.2	17	gCg/gTg	2/23	0.409765452337261	2	FACETS	1	0.977	1	0.544	0.51	0.579	CLONAL	1	FALSE	0	0.409765452337261	2		960	1216	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524600	187524600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150034185	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	46	576	1	ENST00000441802.2:c.11080G>A	p.Val3694Ile	p.V3694I	ENST00000441802	NM_005245.3	3694	Gtc/Atc	19/27	1	2	FACETS	0.289	0.243	0.341	0.289	0.243	0.341	SUBCLONAL	1	FALSE	1	0.409765452337261	2		577	776	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512297	38512297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762998209	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	249	980	4	ENST00000254066.5:c.1208C>T	p.Pro403Leu	p.P403L	ENST00000254066	NM_000964.3	403	cCg/cTg	9/9	1	2	FACETS	0.985	0.92	1	0.985	0.92	1	CLONAL	1	FALSE	1	0.409765452337261	2		984	1234	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821644	72821644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762700822	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	34	127	0	ENST00000268489.5:c.10531G>A	p.Gly3511Ser	p.G3511S	ENST00000268489	NM_006885.3	3511	Ggt/Agt	10/10	1	2	FACETS	0.927	0.766	1	0.927	0.766	1	CLONAL	1	FALSE	1	0.409765452337261	2		127	179	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468108	50468108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750934235	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	50	512	1	ENST00000331340.3:c.1343C>T	p.Ala448Val	p.A448V	ENST00000331340	NM_006060.4	448	gCg/gTg	8/8	1	2	FACETS	0.382	0.323	0.446	0.382	0.323	0.446	SUBCLONAL	1	FALSE	1	0.409765452337261	2		513	639	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391521	84391521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542570943	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	79	170	0	ENST00000321945.7:c.311G>A	p.Arg104His	p.R104H	ENST00000321945	NM_139076.2	104	cGt/cAt	5/9	1	2	FACETS	0.905	0.8	1	0.905	0.8	1	CLONAL	1	FALSE	1	0.409765452337261	2		170	426	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187710	11187710	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	41	609	1	ENST00000361445.4:c.6187del	p.Gln2063ArgfsTer3	p.Q2063Rfs*3	ENST00000361445	NM_004958.3	2063	Cag/ag	44/58	1	2	FACETS	0.252	0.209	0.301	0.252	0.209	0.301	SUBCLONAL	1	FALSE	1	0.409765452337261	2		610	793	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076758	72076758	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	39	582	0	ENST00000357731.5:c.739G>T	p.Gly247Cys	p.G247C	ENST00000357731	NM_173808.2	247	Ggt/Tgt	5/7	1	2	FACETS	0.28	0.231	0.335	0.28	0.231	0.335	SUBCLONAL	1	FALSE	1	0.409765452337261	2		582	680	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512155	120512155	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	43	440	0	ENST00000256646.2:c.1087A>G	p.Met363Val	p.M363V	ENST00000256646	NM_024408.3	363	Atg/Gtg	6/34	1	2	FACETS	0.356	0.297	0.421	0.356	0.297	0.421	SUBCLONAL	1	FALSE	1	0.409765452337261	2		440	590	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253376	226253376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	63	208	0	ENST00000366813.1:c.148C>T	p.Arg50Cys	p.R50C	ENST00000366813		50	Cgt/Tgt	2/3	1	2	FACETS	0.937	0.816	1	0.937	0.816	1	CLONAL	1	FALSE	1	0.409765452337261	2		208	328	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263922	104263922	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs948353979	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	30	110	0	ENST00000369902.3:c.13C>T	p.Arg5Trp	p.R5W	ENST00000369902	NM_016169.3	5	Cgg/Tgg	1/12	1	2	FACETS	0.866	0.706	1	0.866	0.706	1	CLONAL	1	FALSE	1	0.409765452337261	2		110	169	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625177	69625177	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs281860305	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	84	907	0	ENST00000334134.2:c.616del	p.Val206SerfsTer?	p.V206Sfs*?	ENST00000334134	NM_005247.2	206	Gtc/tc	3/3	1	2	FACETS	0.392	0.345	0.443	0.392	0.345	0.443	SUBCLONAL	1	FALSE	1	0.409765452337261	2		907	1045	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447013	49447013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	118	394	0	ENST00000301067.7:c.931C>T	p.Pro311Ser	p.P311S	ENST00000301067	NM_003482.3	311	Cct/Tct	7/54	1	2	FACETS	0.986	0.893	1	0.986	0.893	1	CLONAL	1	FALSE	1	0.409765452337261	2		394	584	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861960	57861960	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	119	608	0	ENST00000228682.2:c.1261G>T	p.Gly421Cys	p.G421C	ENST00000228682	NM_005269.2	421	Ggt/Tgt	10/12	1	2	FACETS	0.801	0.724	0.883	0.801	0.724	0.883	CLONAL	1	FALSE	1	0.409765452337261	2		608	725	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241948	133241948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565962323	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	206	791	0	ENST00000320574.5:c.2408C>T	p.Ser803Leu	p.S803L	ENST00000320574	NM_006231.2	803	tCg/tTg	21/49	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	1	0.409765452337261	2		791	982	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562867	21562867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	254	954	1	ENST00000382592.4:c.1052C>T	p.Ser351Leu	p.S351L	ENST00000382592	NM_014572.2	351	tCg/tTg	4/8	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.409765452337261	2		955	1201	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954332	48954332	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	72	105	0	ENST00000267163.4:c.1453T>C	p.Ser485Pro	p.S485P	ENST00000267163	NM_000321.2	485	Tct/Cct	16/27	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.409765452337261	2		105	300	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42050011	42050012	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	33	97	0	ENST00000219905.7:c.7170dup	p.Ala2391SerfsTer3	p.A2391Sfs*3	ENST00000219905	NM_001164273.1	2389	gaa/gAaa	19/24	1	2	FACETS	0.544	0.444	0.656	0.544	0.444	0.656	SUBCLONAL	1	FALSE	1	0.409765452337261	2		97	296	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727458	88727459	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	171	617	0	ENST00000360948.2:c.320dup	p.Leu108AlafsTer30	p.L108Afs*30	ENST00000360948	NM_001012338.2	107	aag/aaAg	3/19	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	FALSE	1	0.409765452337261	2		617	813	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778834	3778834	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1346068669	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	226	928	1	ENST00000262367.5:c.6214C>T	p.Arg2072Trp	p.R2072W	ENST00000262367	NM_004380.2	2072	Cgg/Tgg	31/31	1	2	FACETS	0.995	0.926	1	0.995	0.926	1	CLONAL	1	FALSE	1	0.409765452337261	2		929	1109	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647475	23647475	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	124	414	0	ENST00000261584.4:c.392G>T	p.Arg131Met	p.R131M	ENST00000261584	NM_024675.3	131	aGg/aTg	4/13	1	2	FACETS	0.97	0.88	1	0.97	0.88	1	CLONAL	1	FALSE	1	0.409765452337261	2		414	624	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50811799	50811799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	33	84	0	ENST00000398568.2:c.1076C>A	p.Ser359Tyr	p.S359Y	ENST00000398568	NM_001042412.1	359	tCt/tAt	7/18	1	2	FACETS	0.532	0.434	0.641	0.532	0.434	0.641	SUBCLONAL	1	FALSE	1	0.409765452337261	2		84	303	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865836	56865836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747390049	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	117	357	2	ENST00000308159.5:c.1168G>A	p.Val390Met	p.V390M	ENST00000308159	NM_014669.4	390	Gtg/Atg	11/22	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	1	0.409765452337261	2		359	538	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772272	68772272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786202465	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	268	1027	0	ENST00000261769.5:c.121G>A	p.Val41Met	p.V41M	ENST00000261769	NM_004360.3	41	Gtg/Atg	2/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.409765452337261	2		1027	1230	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346113	89346114	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs1555525296	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	48	231	0	ENST00000301030.4:c.6836_6837del	p.Val2279GlyfsTer16	p.V2279Gfs*16	ENST00000301030	NM_001256183.1	2279	gTG/g	9/13	1	2	FACETS	0.884	0.753	1	0.884	0.753	1	CLONAL	1	FALSE	1	0.409765452337261	2		231	265	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701085	29701085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	148	401	0	ENST00000356175.3:c.8369G>A	p.Gly2790Glu	p.G2790E	ENST00000356175	NM_000267.3	2790	gGa/gAa	57/57	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.409765452337261	2		401	606	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649063	37649063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	122	353	0	ENST00000447079.4:c.2168G>A	p.Cys723Tyr	p.C723Y	ENST00000447079	NM_015083.1	723	tGt/tAt	4/14	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	1	0.409765452337261	2		353	564	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650861	37650861	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	161	401	0	ENST00000447079.4:c.2333T>C	p.Leu778Pro	p.L778P	ENST00000447079	NM_015083.1	778	cTt/cCt	5/14	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	FALSE	1	0.409765452337261	2		401	771	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883558	37883558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1198735577	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	215	784	0	ENST00000269571.5:c.3170G>A	p.Gly1057Glu	p.G1057E	ENST00000269571		1057	gGg/gAg	26/27	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.409765452337261	2		784	977	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858844	78858844	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199928822	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	218	856	0	ENST00000306801.3:c.1879G>A	p.Val627Met	p.V627M	ENST00000306801	NM_020761.2	627	Gtg/Atg	17/34	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	FALSE	1	0.409765452337261	2		856	1058	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216398	2216398	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749779365	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	242	898	1	ENST00000398665.3:c.2042G>A	p.Arg681His	p.R681H	ENST00000398665	NM_032482.2	681	cGc/cAc	20/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.409765452337261	2		899	1067	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210578	5210578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1420539666	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	205	718	0	ENST00000357368.4:c.5389G>A	p.Glu1797Lys	p.E1797K	ENST00000357368	NM_002850.3	1797	Gag/Aag	35/38	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.409765452337261	2		718	970	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267524	7267524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	191	670	1	ENST00000302850.5:c.484C>T	p.Arg162Cys	p.R162C	ENST00000302850	NM_000208.2	162	Cgt/Tgt	2/22	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.409765452337261	2		671	888	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251522	10251522	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	57	787	0	ENST00000340748.4:c.3410C>A	p.Pro1137His	p.P1137H	ENST00000340748		1137	cCc/cAc	31/40	1	2	FACETS	0.284	0.243	0.33	0.284	0.243	0.33	SUBCLONAL	1	FALSE	1	0.409765452337261	2		787	978	SUCCESS
CALR	811	MSKCC	GRCh37	19	13049581	13049581	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1199946705	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	182	783	0	ENST00000316448.5:c.88G>A	p.Gly30Arg	p.G30R	ENST00000316448	NM_004343.3	30	Gga/Aga	1/9	1	2	FACETS	0.944	0.871	1	0.944	0.871	1	CLONAL	1	FALSE	1	0.409765452337261	2		783	941	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271945	15271945	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	244	970	0	ENST00000263388.2:c.6494C>A	p.Pro2165His	p.P2165H	ENST00000263388	NM_000435.2	2165	cCt/cAt	33/33	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.409765452337261	2		970	1167	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753419	42753419	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	252	946	0	ENST00000222329.4:c.845C>T	p.Thr282Met	p.T282M	ENST00000222329	NM_006494.2	282	aCg/aTg	4/4	1	2	FACETS	0.977	0.913	1	0.977	0.913	1	CLONAL	1	FALSE	1	0.409765452337261	2		946	1259	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905630	50905630	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1366413924	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	259	968	1	ENST00000440232.2:c.758G>A	p.Arg253Gln	p.R253Q	ENST00000440232	NM_002691.3	253	cGg/cAg	6/27	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.409765452337261	2		969	1224	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030588	48030588	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63749843	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	73	364	0	ENST00000234420.5:c.3202C>T	p.Arg1068Ter	p.R1068*	ENST00000234420	NM_000179.2	1068	Cga/Tga	5/10	0.115088803594596	6	FACETS	1	0.972	1			1	INDETERMINATE	1	FALSE	NA	0.409765452337261	6		364	456	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215609821	215609821	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	30	126	0	ENST00000260947.4:c.1873C>G	p.Leu625Val	p.L625V	ENST00000260947	NM_000465.2	625	Ctc/Gtc	9/11	1	2	FACETS	0.396	0.319	0.483	0.396	0.319	0.483	SUBCLONAL	1	FALSE	1	0.409765452337261	2		126	370	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660771	227660771	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs778801905	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	170	629	1	ENST00000305123.5:c.2684A>G	p.Glu895Gly	p.E895G	ENST00000305123	NM_005544.2	895	gAa/gGa	1/2	1	2	FACETS	0.925	0.851	1	0.925	0.851	1	CLONAL	1	FALSE	1	0.409765452337261	2		630	897	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30733030	30733030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755070814	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	111	466	2	ENST00000295754.5:c.1643C>T	p.Ser548Leu	p.S548L	ENST00000295754	NM_003242.5	548	tCg/tTg	7/7	1	2	FACETS	0.925	0.833	1	0.925	0.833	1	CLONAL	1	FALSE	1	0.409765452337261	2		468	586	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721516	49721516	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	191	719	0	ENST00000449682.2:c.2123T>C	p.Phe708Ser	p.F708S	ENST00000449682	NM_020998.3	708	tTc/tCc	18/18	1	2	FACETS	0.945	0.874	1	0.945	0.874	1	CLONAL	1	FALSE	1	0.409765452337261	2		719	986	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673821	30673821	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	99	444	0	ENST00000376406.3:c.3139G>C	p.Ala1047Pro	p.A1047P	ENST00000376406	NM_014641.2	1047	Gcc/Ccc	10/15	1	2	FACETS	0.905	0.81	1	0.905	0.81	1	CLONAL	1	FALSE	1	0.409765452337261	2		444	534	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209409	98209409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745337014	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	195	780	0	ENST00000331920.6:c.4129G>A	p.Val1377Met	p.V1377M	ENST00000331920	NM_000264.3	1377	Gtg/Atg	23/24	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	FALSE	1	0.409765452337261	2		780	951	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344102	70344102	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	231	392	0	ENST00000374080.3:c.1838T>C	p.Met613Thr	p.M613T	ENST00000374080		613	aTg/aCg	13/45	1	1	FACETS	0.829	0.78	0.878	1	0.994	1	CLONAL	2	FALSE	0	0.409765452337261	1		392	541	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	160	721	8	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.31616195689019	2	FACETS	1	0.973	1	0.571	0.524	0.621	CLONAL	1	FALSE	0	0.31616195689019	2		729	886	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	95	410	0	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	0.154594863454015	4	FACETS	1	0.976	1	0.676	0.603	0.753	INDETERMINATE	1	FALSE	2	0.31616195689019	4		410	585	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	119	524	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.31616195689019	2		525	696	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129087	30129087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	109	644	1	ENST00000263025.4:c.679G>A	p.Asp227Asn	p.D227N	ENST00000263025	NM_002746.2	227	Gac/Aac	5/9	1	2	FACETS	0.817	0.733	0.906	0.817	0.733	0.906	CLONAL	1	FALSE	1	0.31616195689019	2		645	844	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	92	456	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	FALSE	1	0.31616195689019	2		461	556	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	198	1123	2	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.31616195689019	2		1125	1168	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	117	808	7	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	1	2	FACETS	0.841	0.758	0.929	0.841	0.758	0.929	CLONAL	1	FALSE	1	0.31616195689019	2		815	880	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041169	112041169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766059845	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	137	537	2	ENST00000368678.4:c.86G>A	p.Arg29His	p.R29H	ENST00000368678		29	cGc/cAc	3/13	0.100174974210749	4	FACETS	0.75	0.683	0.821	0.75	0.683	0.821	INDETERMINATE	2	FALSE	2	0.31616195689019	4		539	760	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166784	32166784	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	164	812	0	ENST00000375023.3:c.4454del	p.Pro1485LeufsTer20	p.P1485Lfs*20	ENST00000375023	NM_004557.3	1485	cCt/ct	24/30	1	2	FACETS	0.94	0.861	1	0.94	0.861	1	CLONAL	1	FALSE	1	0.31616195689019	2		812	1104	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294665	1294665	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	89	669	4	ENST00000310581.5:c.336del	p.Glu113ArgfsTer15	p.E113Rfs*15	ENST00000310581	NM_198253.2	112	ccC/cc	2/16	1	2	FACETS	0.789	0.699	0.884	0.789	0.699	0.884	SUBCLONAL	1	FALSE	1	0.31616195689019	2		673	714	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641389	18641389	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1229278001	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	47	226	0	ENST00000266497.5:c.2393del	p.Asn798MetfsTer16	p.N798Mfs*16	ENST00000266497		796	ctA/ct	17/31	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.31616195689019	2		226	215	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519710	176519710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150737523	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	185	799	0	ENST00000292408.4:c.982G>A	p.Ala328Thr	p.A328T	ENST00000292408	NM_213647.1	328	Gca/Aca	8/18	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.31616195689019	2		799	974	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	33	194	1	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.659	0.538	0.794	0.659	0.538	0.794	SUBCLONAL	1	FALSE	1	0.31616195689019	2		195	317	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211514	98211514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200029534	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	121	663	0	ENST00000331920.6:c.3641C>T	p.Thr1214Met	p.T1214M	ENST00000331920	NM_000264.3	1214	aCg/aTg	22/24	1	2	FACETS	0.994	0.899	1	0.994	0.899	1	CLONAL	1	FALSE	1	0.31616195689019	2		663	770	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852118	63852118	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	111	549	3	ENST00000279873.7:c.2901del	p.Lys967AsnfsTer15	p.K967Nfs*15	ENST00000279873	NM_032199.2	966	Aaa/aa	10/10	1	2	FACETS	0.969	0.871	1	0.969	0.871	1	CLONAL	1	FALSE	1	0.31616195689019	2		552	725	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411072	63411072	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1464385859	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	109	335	0	ENST00000330258.3:c.2095C>T	p.Arg699Cys	p.R699C	ENST00000330258	NM_152424.3	699	Cgt/Tgt	2/2	1	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	0	0.31616195689019	1		335	409	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257144	19257144	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	116	810	0	ENST00000162023.5:c.819del	p.Thr274ProfsTer?	p.T274Pfs*?	ENST00000162023		273	ccC/cc	12/13	1	2	FACETS	0.868	0.782	0.96	0.868	0.782	0.96	CLONAL	1	FALSE	1	0.31616195689019	2		810	845	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5225777	5225777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751437578	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	142	714	1	ENST00000357368.4:c.2455G>A	p.Ala819Thr	p.A819T	ENST00000357368	NM_002850.3	819	Gct/Act	17/38	1	2	FACETS	0.924	0.841	1	0.924	0.841	1	CLONAL	1	FALSE	1	0.31616195689019	2		715	972	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795187	42795187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377759151	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	140	1006	2	ENST00000575354.2:c.2267C>T	p.Ala756Val	p.A756V	ENST00000575354	NM_015125.3	756	gCg/gTg	10/20	0.31616195689019	3	FACETS	0.935	0.85	1	0.467	0.425	0.513	CLONAL	1	FALSE	1	0.31616195689019	3		1008	1097	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771987	135771988	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs2234980	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	70	518	0	ENST00000298552.3:c.3127_3129dup	p.Ser1043dup	p.S1043dup	ENST00000298552	NM_001162426.1	1043	-/AGC	23/23	1	2	FACETS	0.727	0.634	0.828	0.727	0.634	0.828	SUBCLONAL	1	FALSE	1	0.31616195689019	2		518	609	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120031	70120031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	28	104	0	ENST00000245479.2:c.1037del	p.Pro346ArgfsTer37	p.P346Rfs*37	ENST00000245479	NM_000346.3	345	Ccc/cc	3/3	0.31616195689019	2	FACETS	1	0.881	1	0.564	0.456	0.684	CLONAL	1	FALSE	0	0.31616195689019	2		104	157	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019464	31019464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	101	458	0	ENST00000375687.4:c.961C>T	p.Arg321Trp	p.R321W	ENST00000375687	NM_015338.5	321	Cgg/Tgg	10/13	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	FALSE	1	0.31616195689019	2		458	630	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100260	157100260	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1554248082	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	33	157	0	ENST00000346085.5:c.1202del	p.Gly401AlafsTer29	p.G401Afs*29	ENST00000346085	NM_020732.3	399	gcG/gc	1/20	0.270030028030981	1	FACETS	0.999	0.823	1	0.999	0.823	1	CLONAL	1	FALSE	0	0.31616195689019	1		157	176	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857238	78857238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866939416	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	141	617	1	ENST00000306801.3:c.1604C>T	p.Thr535Met	p.T535M	ENST00000306801	NM_020761.2	535	aCg/aTg	15/34	0.31616195689019	2	FACETS	0.992	0.904	1	0.496	0.452	0.543	CLONAL	1	FALSE	0	0.31616195689019	2		618	899	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371683	55371683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753693798	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	133	755	3	ENST00000297316.4:c.373C>T	p.Arg125Cys	p.R125C	ENST00000297316	NM_022454.3	125	Cgc/Tgc	2/2	1	2	FACETS	0.959	0.871	1	0.959	0.871	1	CLONAL	1	FALSE	1	0.31616195689019	2		758	877	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453127	140453127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372569965	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	67	402	0	ENST00000288602.6:c.1808G>A	p.Arg603Gln	p.R603Q	ENST00000288602	NM_004333.4	603	cGa/cAa	15/18	1	2	FACETS	0.942	0.821	1	0.942	0.821	1	CLONAL	1	FALSE	1	0.31616195689019	2		402	450	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448297	56448298	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1567880599	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	291	689	0	ENST00000407977.2:c.349dup	p.Arg117ProfsTer8	p.R117Pfs*8	ENST00000407977		117	cgc/cCgc	3/10	0.31616195689019	2	FACETS	0.947	0.892	1	0.947	0.892	1	CLONAL	2	FALSE	0	0.31616195689019	2		689	972	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224336	55224336	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	75	501	0	ENST00000275493.2:c.1117C>T	p.Pro373Ser	p.P373S	ENST00000275493	NM_005228.3	373	Ccg/Tcg	9/28	1	2	FACETS	0.893	0.784	1	0.893	0.784	1	CLONAL	1	FALSE	1	0.31616195689019	2		501	531	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847319	68847319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755571454	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	100	545	0	ENST00000261769.5:c.1241C>T	p.Thr414Ile	p.T414I	ENST00000261769	NM_004360.3	414	aCc/aTc	9/16	1	2	FACETS	0.91	0.814	1	0.91	0.814	1	CLONAL	1	FALSE	1	0.31616195689019	2		545	695	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465448	99465448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773205989	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	103	458	0	ENST00000268035.6:c.2273C>T	p.Thr758Met	p.T758M	ENST00000268035	NM_000875.3	758	aCg/aTg	11/21	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	1	0.31616195689019	2		458	603	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	260	738	0	ENST00000322088.6:c.548G>T	p.Arg183Leu	p.R183L	ENST00000322088	NM_014225.5	183	cGg/cTg	5/15	0.31616195689019	3	FACETS	0.969	0.908	1	0.969	0.908	1	CLONAL	2	FALSE	1	0.31616195689019	3		738	983	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570819	226570820	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	155	669	0	ENST00000366794.5:c.1076dup	p.Glu360ArgfsTer29	p.E360Rfs*29	ENST00000366794	NM_001618.3	359	cca/ccCa	8/23	1	2	FACETS	0.98	0.896	1	0.98	0.896	1	CLONAL	1	FALSE	1	0.31616195689019	2		669	1001	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	155	874	4	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	1	2	FACETS	0.851	0.778	0.928	0.851	0.778	0.928	CLONAL	1	FALSE	1	0.31616195689019	2		878	1152	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128420047	128420047	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	94	624	3	ENST00000265960.3:c.381del	p.Lys127AsnfsTer20	p.K127Nfs*20	ENST00000265960	NM_001006617.1	127	aaA/aa	4/12	1	2	FACETS	0.858	0.764	0.958	0.858	0.764	0.958	CLONAL	1	FALSE	1	0.31616195689019	2		627	693	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100324	27100324	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	147	682	1	ENST00000324856.7:c.4036C>T	p.Gln1346Ter	p.Q1346*	ENST00000324856	NM_006015.4	1346	Caa/Taa	17/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.31616195689019	2		683	866	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556250	29556250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199474739	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	54	513	0	ENST00000356175.3:c.2617C>T	p.Arg873Cys	p.R873C	ENST00000356175	NM_000267.3	873	Cgt/Tgt	21/57	1	2	FACETS	0.609	0.52	0.706	0.609	0.52	0.706	SUBCLONAL	1	FALSE	1	0.31616195689019	2		513	561	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158026	27158026	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	136	566	0	ENST00000380036.4:c.255del	p.Val86LeufsTer31	p.V86Lfs*31	ENST00000380036	NM_000459.3	84	Aaa/aa	2/23	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.31616195689019	2		566	724	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640449	3640449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142079276	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	187	898	1	ENST00000294008.3:c.3190G>A	p.Gly1064Arg	p.G1064R	ENST00000294008	NM_032444.2	1064	Gga/Aga	12/15	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	1	0.31616195689019	2		899	1159	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024476	16024476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	107	473	0	ENST00000268712.3:c.1742G>A	p.Arg581His	p.R581H	ENST00000268712	NM_006311.3	581	cGt/cAt	16/46	1	2	FACETS	0.952	0.855	1	0.952	0.855	1	CLONAL	1	FALSE	1	0.31616195689019	2		473	711	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436851	29436851	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs145028315	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	91	547	0	ENST00000389048.3:c.3742C>T	p.Arg1248Ter	p.R1248*	ENST00000389048	NM_004304.4	1248	Cga/Tga	24/29	0.31616195689019	2	FACETS	0.867	0.77	0.97	0.433	0.385	0.485	CLONAL	1	FALSE	0	0.31616195689019	2		547	664	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609957	81609957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756016910	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	80	383	0	ENST00000298171.2:c.1555C>T	p.Arg519Cys	p.R519C	ENST00000298171	NM_000369.2	519	Cgc/Tgc	10/10	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	FALSE	1	0.31616195689019	2		383	494	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323315	31323315	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	42	179	0	ENST00000412585.2:c.674T>C	p.Leu225Pro	p.L225P	ENST00000412585	NM_005514.6	225	cTg/cCg	4/8	0.31616195689019	3	FACETS	1	0.951	1	0.684	0.576	0.801	CLONAL	1	FALSE	1	0.31616195689019	3		179	225	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755916	133755916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766145624	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	118	588	1	ENST00000318560.5:c.1543G>A	p.Val515Ile	p.V515I	ENST00000318560	NM_005157.4	515	Gtc/Atc	10/11	1	2	FACETS	0.829	0.748	0.916	0.829	0.748	0.916	CLONAL	1	FALSE	1	0.31616195689019	2		589	900	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217286	7217286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	124	638	0	ENST00000380728.2:c.419G>A	p.Arg140His	p.R140H	ENST00000380728		140	cGc/cAc	6/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.31616195689019	2		638	742	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968279	15968279	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	46	330	0	ENST00000268712.3:c.5006del	p.Gly1669GlufsTer93	p.G1669Efs*93	ENST00000268712	NM_006311.3	1669	gGa/ga	34/46	1	2	FACETS	0.858	0.726	1	0.858	0.726	1	CLONAL	1	FALSE	1	0.31616195689019	2		330	339	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632769	23632770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	67	441	0	ENST00000261584.4:c.3026dup	p.Glu1010Ter	p.E1010*	ENST00000261584	NM_024675.3	1009	cct/ccCt	10/13	1	2	FACETS	0.773	0.673	0.882	0.773	0.673	0.882	SUBCLONAL	1	FALSE	1	0.31616195689019	2		441	548	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914013	32914013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	49	472	0	ENST00000380152.3:c.5521C>T	p.Pro1841Ser	p.P1841S	ENST00000380152		1841	Cca/Tca	11/27	0.154594863454015	4	FACETS	0.942	0.799	1	0.471	0.399	0.55	INDETERMINATE	1	FALSE	2	0.31616195689019	4		472	433	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612269	189612269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34713855	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	73	393	1	ENST00000264731.3:c.2021G>A	p.Arg674His	p.R674H	ENST00000264731	NM_003722.4	674	cGc/cAc	14/14	0.31616195689019	3	FACETS	0.903	0.791	1	0.452	0.395	0.513	CLONAL	1	FALSE	1	0.31616195689019	3		394	592	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003382	42003383	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAG	rs565548940	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	68	486	0	ENST00000219905.7:c.2931_2933dup	p.Gln981dup	p.Q981dup	ENST00000219905	NM_001164273.1	981	-/CAG	8/24	1	2	FACETS	0.637	0.554	0.728	0.637	0.554	0.728	SUBCLONAL	1	FALSE	1	0.31616195689019	2		486	675	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919674	96919674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140860906	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	80	564	0	ENST00000258439.3:c.589C>T	p.Arg197Cys	p.R197C	ENST00000258439	NM_001193304.2	197	Cgc/Tgc	4/4	1	2	FACETS	0.838	0.738	0.945	0.838	0.738	0.945	CLONAL	1	FALSE	1	0.31616195689019	2		564	604	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398831	398831	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	86	508	0	ENST00000380956.4:c.641G>A	p.Cys214Tyr	p.C214Y	ENST00000380956	NM_001195286.1	214	tGc/tAc	6/9	0.270030028030981	1	FACETS	0.712	0.63	0.8	0.712	0.63	0.8	SUBCLONAL	1	FALSE	0	0.31616195689019	1		508	643	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444467	50444467	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1271291854	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	79	287	0	ENST00000331340.3:c.397A>G	p.Met133Val	p.M133V	ENST00000331340	NM_006060.4	133	Atg/Gtg	4/8	1	2	FACETS	0.97	0.856	1	0.97	0.856	1	CLONAL	1	FALSE	1	0.31616195689019	2		287	515	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78797016	78797016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771235157	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	121	508	0	ENST00000306801.3:c.1129G>A	p.Ala377Thr	p.A377T	ENST00000306801	NM_020761.2	377	Gcc/Acc	9/34	0.31616195689019	2	FACETS	1	0.954	1	0.546	0.494	0.601	CLONAL	1	FALSE	0	0.31616195689019	2		508	701	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89828358	89828358	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs755546887	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	69	398	0	ENST00000389301.3:c.2851C>T	p.Arg951Trp	p.R951W	ENST00000389301	NM_000135.2	951	Cgg/Tgg	29/43	1	2	FACETS	0.755	0.658	0.86	0.755	0.658	0.86	SUBCLONAL	1	FALSE	1	0.31616195689019	2		398	578	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794079	42794080	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	102	602	0	ENST00000575354.2:c.1444dup	p.Glu482GlyfsTer32	p.E482Gfs*32	ENST00000575354	NM_015125.3	480	-/G	9/20	0.31616195689019	3	FACETS	0.907	0.81	1	0.453	0.405	0.505	CLONAL	1	FALSE	1	0.31616195689019	3		602	824	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097672	11097672	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	70	872	0	ENST00000358026.2:c.852G>A	p.Trp284Ter	p.W284*	ENST00000358026	NM_001128849.1	284	tgG/tgA	5/36	1	2	FACETS	0.423	0.367	0.483	0.423	0.367	0.483	SUBCLONAL	1	FALSE	1	0.31616195689019	2		872	1047	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348221	89348221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1488507469	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	156	659	2	ENST00000301030.4:c.4729G>A	p.Asp1577Asn	p.D1577N	ENST00000301030	NM_001256183.1	1577	Gac/Aac	9/13	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.31616195689019	2		661	884	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76777854	76777854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782342279	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	77	212	0	ENST00000373344.5:c.6862C>T	p.Arg2288Cys	p.R2288C	ENST00000373344	NM_000489.3	2288	Cgt/Tgt	32/35	0.31616195689019	2	FACETS	0.959	0.853	1			1	CLONAL	2	FALSE	NA	0.31616195689019	2		212	254	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647656	3647657	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs774532876	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	92	825	1	ENST00000294008.3:c.1406dup	p.Leu470IlefsTer8	p.L470Ifs*8	ENST00000294008	NM_032444.2	469	cca/ccCa	7/15	1	2	FACETS	0.58	0.514	0.65	0.58	0.514	0.65	SUBCLONAL	1	FALSE	1	0.31616195689019	2		826	1004	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176505	142176505	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	57	405	0	ENST00000350721.4:c.7596del	p.Arg2533GlufsTer8	p.R2533Efs*8	ENST00000350721	NM_001184.3	2532	ttT/tt	45/47	NA	2	FACETS	0.915	0.788	1			1	INDETERMINATE	1	FALSE	NA	0.31616195689019	2		405	394	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168996	32168996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs8192573	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	156	851	1	ENST00000375023.3:c.4037G>A	p.Arg1346Gln	p.R1346Q	ENST00000375023	NM_004557.3	1346	cGg/cAg	22/30	1	2	FACETS	0.996	0.911	1	0.996	0.911	1	CLONAL	1	FALSE	1	0.31616195689019	2		852	991	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268904	115268904	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	72	475	0	ENST00000438362.2:c.1706T>C	p.Val569Ala	p.V569A	ENST00000438362	NM_001242891.1	569	gTg/gCg	14/20	1	2	FACETS	0.818	0.715	0.928	0.818	0.715	0.928	CLONAL	1	FALSE	1	0.31616195689019	2		475	557	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135944	64135944	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1221790001	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	189	867	0	ENST00000334205.4:c.1205C>T	p.Ser402Leu	p.S402L	ENST00000334205	NM_003942.2	402	tCg/tTg	11/17	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.31616195689019	2		867	1088	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203730	94203731	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587781828	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	33	288	0	ENST00000323929.3:c.923dup	p.Met309HisfsTer8	p.M309Hfs*8	ENST00000323929	NM_005591.3	308	ttc/ttTc	9/20	1	2	FACETS	0.708	0.578	0.852	0.708	0.578	0.852	SUBCLONAL	1	FALSE	1	0.31616195689019	2		288	295	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109852	115109852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1013102657	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	174	708	0	ENST00000257566.3:c.2026G>A	p.Ala676Thr	p.A676T	ENST00000257566	NM_016569.3	676	Gcc/Acc	8/8	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.31616195689019	2		708	820	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107996	30107996	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1165306493	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	95	578	1	ENST00000331968.5:c.811C>T	p.His271Tyr	p.H271Y	ENST00000331968	NM_002742.2	271	Cac/Tac	5/18	1	2	FACETS	0.789	0.702	0.881	0.789	0.702	0.881	SUBCLONAL	1	FALSE	1	0.31616195689019	2		579	762	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250912	99250912	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	119	548	0	ENST00000268035.6:c.216C>A	p.Ser72Arg	p.S72R	ENST00000268035	NM_000875.3	72	agC/agA	2/21	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.31616195689019	2		548	685	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041801	14041801	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs375263578	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	94	508	0	ENST00000311895.7:c.2348A>G	p.Asp783Gly	p.D783G	ENST00000311895	NM_005236.2	783	gAc/gGc	11/11	1	2	FACETS	0.936	0.834	1	0.936	0.834	1	CLONAL	1	FALSE	1	0.31616195689019	2		508	635	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827451	72827451	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	113	608	0	ENST00000268489.5:c.9130T>G	p.Phe3044Val	p.F3044V	ENST00000268489	NM_006885.3	3044	Ttt/Gtt	9/10	1	2	FACETS	0.87	0.782	0.962	0.87	0.782	0.962	CLONAL	1	FALSE	1	0.31616195689019	2		608	822	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8111125	8111125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	115	715	1	ENST00000585124.1:c.82G>A	p.Val28Ile	p.V28I	ENST00000585124	NM_004217.3	28	Gtc/Atc	3/9	1	2	FACETS	0.871	0.784	0.963	0.871	0.784	0.963	CLONAL	1	FALSE	1	0.31616195689019	2		716	835	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118335	17118335	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	137	788	1	ENST00000285071.4:c.1502A>G	p.Asp501Gly	p.D501G	ENST00000285071	NM_144997.5	501	gAc/gGc	13/14	1	2	FACETS	0.832	0.755	0.912	0.832	0.755	0.912	CLONAL	1	FALSE	1	0.31616195689019	2		789	1042	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487496	38487496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762408148	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	86	473	1	ENST00000254066.5:c.26C>T	p.Pro9Leu	p.P9L	ENST00000254066	NM_000964.3	9	cCg/cTg	2/9	1	2	FACETS	0.961	0.852	1	0.961	0.852	1	CLONAL	1	FALSE	1	0.31616195689019	2		474	566	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007631	62007631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	119	675	0	ENST00000392795.3:c.236G>A	p.Trp79Ter	p.W79*	ENST00000392795	NM_001039933.1	79	tGg/tAg	3/6	0.31616195689019	2	FACETS	0.906	0.817	0.999	0.453	0.408	0.5	CLONAL	1	FALSE	0	0.31616195689019	2		675	831	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4090682	4090682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	131	824	0	ENST00000262948.5:c.1117G>A	p.Glu373Lys	p.E373K	ENST00000262948	NM_030662.3	373	Gag/Aag	11/11	1	2	FACETS	0.821	0.744	0.903	0.821	0.744	0.903	CLONAL	1	FALSE	1	0.31616195689019	2		824	1009	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244109	5244109	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	147	843	0	ENST00000357368.4:c.1373G>A	p.Arg458His	p.R458H	ENST00000357368	NM_002850.3	458	cGc/cAc	11/38	1	2	FACETS	0.912	0.831	0.996	0.912	0.831	0.996	CLONAL	1	FALSE	1	0.31616195689019	2		843	1020	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297721	15297721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377689004	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	137	747	0	ENST00000263388.2:c.1919G>A	p.Arg640His	p.R640H	ENST00000263388	NM_000435.2	640	cGc/cAc	12/33	1	2	FACETS	0.938	0.853	1	0.938	0.853	1	CLONAL	1	FALSE	1	0.31616195689019	2		747	924	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182613	99182613	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	73	456	0	ENST00000074304.5:c.2416C>T	p.Gln806Ter	p.Q806*	ENST00000074304	NM_001134224.1	806	Cag/Tag	22/26	1	2	FACETS	0.881	0.772	0.998	0.881	0.772	0.998	CLONAL	1	FALSE	1	0.31616195689019	2		456	524	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661381	227661381	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs367626263	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	83	616	0	ENST00000305123.5:c.2074G>T	p.Gly692Trp	p.G692W	ENST00000305123	NM_005544.2	692	Ggg/Tgg	1/2	1	2	FACETS	0.747	0.659	0.841	0.747	0.659	0.841	SUBCLONAL	1	FALSE	1	0.31616195689019	2		616	703	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30946591	30946592	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGA	rs752094508	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	29	269	0	ENST00000375687.4:c.25_27dup	p.Lys9dup	p.K9dup	ENST00000375687	NM_015338.5	9	cag/cAGAag	1/13	1	2	FACETS	0.466	0.373	0.57	0.466	0.373	0.57	SUBCLONAL	1	FALSE	1	0.31616195689019	2		269	394	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395666	31395666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908946	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	134	654	0	ENST00000328111.2:c.2519G>A	p.Arg840Gln	p.R840Q	ENST00000328111	NM_006892.3	840	cGa/cAa	23/23	1	2	FACETS	0.925	0.84	1	0.925	0.84	1	CLONAL	1	FALSE	1	0.31616195689019	2		654	916	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164805	36164805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745561479	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	163	915	3	ENST00000300305.3:c.1070C>T	p.Pro357Leu	p.P357L	ENST00000300305		357	cCg/cTg	8/8	1	2	FACETS	0.959	0.879	1	0.959	0.879	1	CLONAL	1	FALSE	1	0.31616195689019	2		918	1075	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556645	41556645	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	84	398	0	ENST00000263253.7:c.3591-1G>T		p.X1197_splice	ENST00000263253	NM_001429.3	1197			1	2	FACETS	0.921	0.815	1	0.921	0.815	1	CLONAL	1	FALSE	1	0.31616195689019	2		398	577	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014017	70014017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774249941	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	76	382	0	ENST00000394351.3:c.878G>A	p.Arg293Gln	p.R293Q	ENST00000394351	NM_000248.3	293	cGa/cAa	9/9	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	FALSE	1	0.31616195689019	2		382	446	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670669	134670669	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	100	660	0	ENST00000398015.3:c.584del	p.Lys195SerfsTer16	p.K195Sfs*16	ENST00000398015	NM_004441.4	194	Aaa/aa	3/16	NA	2	FACETS	0.795	0.709	0.885			1	INDETERMINATE	1	FALSE	NA	0.31616195689019	2		660	796	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748179	41748179	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	99	581	0	ENST00000226382.2:c.590del	p.Gly197AlafsTer112	p.G197Afs*112	ENST00000226382	NM_003924.3	197	gGc/gc	3/3	1	2	FACETS	0.869	0.776	0.967	0.869	0.776	0.967	CLONAL	1	FALSE	1	0.31616195689019	2		581	721	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976674	55976674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201708587	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	83	560	0	ENST00000263923.4:c.1151C>T	p.Thr384Met	p.T384M	ENST00000263923	NM_002253.2	384	aCg/aTg	9/30	1	2	FACETS	0.953	0.843	1	0.953	0.843	1	CLONAL	1	FALSE	1	0.31616195689019	2		560	551	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517952	187517952	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	91	470	0	ENST00000441802.2:c.12742del	p.Gln4248ArgfsTer101	p.Q4248Rfs*101	ENST00000441802	NM_005245.3	4248	Cag/ag	25/27	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	FALSE	1	0.31616195689019	2		470	568	SUCCESS
APC	324	MSKCC	GRCh37	5	112178880	112178880	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778043	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	59	311	0	ENST00000257430.4:c.7589G>A	p.Arg2530Gln	p.R2530Q	ENST00000257430	NM_000038.5	2530	cGg/cAg	16/16	0.31616195689019	3	FACETS	1	0.924	1	0.553	0.477	0.634	CLONAL	1	FALSE	1	0.31616195689019	3		311	391	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679999	30679999	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	114	576	1	ENST00000376406.3:c.1720C>T	p.His574Tyr	p.H574Y	ENST00000376406	NM_014641.2	574	Cat/Tat	5/15	0.31616195689019	3	FACETS	1	0.969	1	0.595	0.536	0.657	CLONAL	1	FALSE	1	0.31616195689019	3		577	702	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190863	32190863	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	157	787	0	ENST00000375023.3:c.74G>T	p.Gly25Val	p.G25V	ENST00000375023	NM_004557.3	25	gGg/gTg	2/30	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	FALSE	1	0.31616195689019	2		787	970	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133301	38133301	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	121	540	1	ENST00000317025.8:c.4172del	p.Lys1391ArgfsTer32	p.K1391Rfs*32	ENST00000317025	NM_023034.1	1391	aAg/ag	24/24	1	2	FACETS	0.988	0.893	1	0.988	0.893	1	CLONAL	1	FALSE	1	0.31616195689019	2		541	775	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133761021	133761021	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	125	765	1	ENST00000318560.5:c.3344G>A	p.Ser1115Asn	p.S1115N	ENST00000318560	NM_005157.4	1115	aGc/aAc	11/11	1	2	FACETS	0.872	0.788	0.96	0.872	0.788	0.96	CLONAL	1	FALSE	1	0.31616195689019	2		766	907	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578179	7578197	+	protein_altering_variant,splice_region_variant	In_Frame_Del	DEL	CAGGCGGCTCATAGGGCAC	CAGGCGGCTCATAGGGCAC	G	novel	NA	P-0041719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	193	715	0	ENST00000269305.4:c.652_670delinsC	p.Val218_Glu224delinsGln	p.V218_E224delinsQ	ENST00000269305	NM_001126112.2	218	GTGCCCTATGAGCCGCCTGag/Cag	6/11	0.325174517818484	2	FACETS	0.881	0.819	0.944	0.881	0.819	0.944	CLONAL	2	TRUE	0	0.350507543806553	2		715	625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0041721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	85	660	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.736500818757408	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.736500818757408	1		660	130	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0041721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	105	372	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.736500818757408	2		372	227	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346328	152346328	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs878854772	NA	P-0041721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	30	523	0	ENST00000359321.1:c.242T>C	p.Ile81Thr	p.I81T	ENST00000359321	NM_005431.1	81	aTt/aCt	3/3	1	2	FACETS	0.876	0.726	1	0.876	0.726	1	CLONAL	1	TRUE	1	0.736500818757408	2		523	93	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	100	348	1				ENST00000310581	NM_198253.2	-/1132			0.27782764197395	6	FACETS	1	0.972	1	0.619	0.556	0.686	CLONAL	2	TRUE	2	0.27782764197395	6		349	452	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936978	48936978	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	128	478	0	ENST00000267163.4:c.746C>A	p.Ser249Ter	p.S249*	ENST00000267163	NM_000321.2	249	tCa/tAa	8/27	0.27782764197395	2	FACETS	0.912	0.831	0.996	0.912	0.831	0.996	CLONAL	2	TRUE	0	0.27782764197395	2		478	505	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042524	42042524	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	68	646	0	ENST00000219905.7:c.6719A>C	p.Glu2240Ala	p.E2240A	ENST00000219905	NM_001164273.1	2240	gAa/gCa	17/24	0.27782764197395	2	FACETS	0.86	0.749	0.98	0.43	0.374	0.49	CLONAL	1	TRUE	0	0.27782764197395	2		646	569	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137522140	137522140	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766163240	NA	P-0041831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	60	240	0	ENST00000367739.4:c.739C>T	p.Leu247Phe	p.L247F	ENST00000367739	NM_000416.2	247	Ctt/Ttt	6/7	0.182997194545596	3	FACETS	0.996	0.868	1			1	CLONAL	2	TRUE	NA	0.27782764197395	3		240	247	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524726	137524734	+	inframe_deletion	In_Frame_Del	DEL	CACAGTACT	CACAGTACT	-	novel	NA	P-0041831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	54	608	0	ENST00000367739.4:c.635_643del	p.Gln212_Val215delinsLeu	p.Q212_V215delinsL	ENST00000367739	NM_000416.2	212	cAGTACTGTGtt/ctt	5/7	0.182997194545596	3	FACETS	0.837	0.715	0.97			1	CLONAL	1	TRUE	NA	0.27782764197395	3		608	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577094	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCG	CGCCG	T	novel	NA	P-0041831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	279	880	0	ENST00000269305.4:c.844_848delinsA	p.Arg282ThrfsTer62	p.R282Tfs*62	ENST00000269305	NM_001126112.2	282	CGGCGc/Ac	8/11	0.27782764197395	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.27782764197395	2		880	981	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0041834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	16	891	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.387702588070063	9	FACETS	0.49	0.361	0.645			1	SUBCLONAL	1	TRUE	NA	0.387702588070063	9		892	397	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249012	55249013	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGTTT	novel	NA	P-0041834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	53	790	0	ENST00000275493.2:c.2310_2311insGGGTTT	p.Asp770_Asn771insGlyPhe	p.D770_N771insGF	ENST00000275493	NM_005228.3	770	-/GGGTTT	20/28	0.393090877059365	1	FACETS	0.918	0.808	1	1	0.978	1	CLONAL	2	TRUE	0	0.387702588070063	1		790	120	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981211	201981212	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0041834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	283	1132	0	ENST00000359651.3:c.292dup	p.Asp98GlyfsTer11	p.D98Gfs*11	ENST00000359651		97	atg/atGg	2/8	0.387702588070063	5	FACETS	0.92	0.877	0.963	1	0.995	1	CLONAL	5	TRUE	2	0.387702588070063	5		1132	502	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873690	37873690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	58	1043	2	ENST00000269571.5:c.1855G>A	p.Glu619Lys	p.E619K	ENST00000269571		619	Gag/Aag	15/27	0.387702588070063	9	FACETS	0.789	0.679	0.908			1	CLONAL	2	TRUE	NA	0.387702588070063	9		1045	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0041836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	199	789	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.236958357188278	2	FACETS	1	0.99	1	0.723	0.671	0.778	CLONAL	1	TRUE	0	0.317381942248167	2		789	867	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099855	27099855	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1198502333	NA	P-0041836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	123	608	0	ENST00000324856.7:c.3734T>C	p.Phe1245Ser	p.F1245S	ENST00000324856	NM_006015.4	1245	tTc/tCc	15/20	0.195864061174163	2	FACETS	1	0.983	1	0.695	0.63	0.762	CLONAL	1	TRUE	0	0.317381942248167	2		608	558	SUCCESS
REL	5966	MSKCC	GRCh37	2	61121634	61121634	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	109	501	0	ENST00000295025.8:c.256G>C	p.Asp86His	p.D86H	ENST00000295025	NM_002908.2	86	Gac/Cac	3/11	0.066099552360974	4	FACETS	1	0.982	1	0.718	0.646	0.794	INDETERMINATE	1	TRUE	2	0.317381942248167	4		501	630	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608295	100608295	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	83	916	0	ENST00000308731.7:c.1795G>T	p.Glu599Ter	p.E599*	ENST00000308731	NM_000061.2	599	Gag/Tag	18/19	0.317381942248167	1	FACETS	0.71	0.627	0.798	0.71	0.627	0.798	SUBCLONAL	1	TRUE	0	0.317381942248167	1		916	620	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0041848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	564	692	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.55572759502309	4	FACETS	0.919	0.893	0.944	0.919	0.893	0.944	CLONAL	4	TRUE	0	0.617719958895445	4		692	804	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	81	448	0	ENST00000263967.3:c.3012G>A	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atA	21/21	0.585503377074775	3	FACETS	0.894	0.805	0.984	0.894	0.805	0.984	CLONAL	2	TRUE	1	0.617719958895445	3		448	192	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252865	36252865	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	187	331	0	ENST00000300305.3:c.497G>T	p.Arg166Leu	p.R166L	ENST00000300305		166	cGa/cTa	4/8	0.531399292736852	3	FACETS	0.855	0.808	0.901	0.855	0.808	0.901	CLONAL	3	TRUE	0	0.617719958895445	3		331	309	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262581	39262581	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs397517180	NA	P-0041848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	154	509	0	ENST00000402219.2:c.925G>T	p.Asp309Tyr	p.D309Y	ENST00000402219	NM_005633.3	309	Gat/Tat	7/23	0.617719958895445	4	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	2	0.617719958895445	4		509	391	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115955	8115956	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0041848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	1627	415	0	ENST00000346208.3:c.1304_1305dup	p.Ser436ProfsTer40	p.S436Pfs*40	ENST00000346208		434	cac/caCCc	6/6	0.617719958895445	17	FACETS	1	0.995	1			1	CLONAL	12	TRUE	NA	0.617719958895445	17		415	2388	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913196	44913196	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	83	286	0	ENST00000377967.4:c.871G>T	p.Gly291Ter	p.G291*	ENST00000377967	NM_021140.2	291	Gga/Tga	10/29	0.300952749778069	2	FACETS	0.981	0.9	1			1	INDETERMINATE	2	TRUE	NA	0.617719958895445	2		286	137	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312916	30312916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146040933	NA	P-0041848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	198	586	0	ENST00000262643.3:c.719G>A	p.Arg240His	p.R240H	ENST00000262643	NM_001238.2	240	cGt/cAt	9/12	0.527440567047861	4	FACETS	0.923	0.861	0.986	0.923	0.861	0.986	CLONAL	2	TRUE	2	0.617719958895445	4		586	562	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654554	29654554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555533559	NA	P-0041848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	217	311	0	ENST00000356175.3:c.5243G>A	p.Arg1748Gln	p.R1748Q	ENST00000356175	NM_000267.3	1748	cGa/cAa	37/57	0.617719958895445	6	FACETS	0.888	0.837	0.939			1	CLONAL	4	TRUE	NA	0.617719958895445	6		311	442	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10244895	10244895	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	206	798	0	ENST00000340748.4:c.4814C>T	p.Ser1605Leu	p.S1605L	ENST00000340748		1605	tCa/tTa	39/40	0.527440567047861	4	FACETS	0.89	0.824	0.958	0.445	0.412	0.479	CLONAL	1	TRUE	2	0.617719958895445	4		798	1213	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549319	187549319	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	143	550	0	ENST00000441802.2:c.4799C>G	p.Ser1600Trp	p.S1600W	ENST00000441802	NM_005245.3	1600	tCg/tGg	9/27	1	2	FACETS	0.967	0.888	1	0.967	0.888	1	CLONAL	1	TRUE	1	0.617719958895445	2		550	479	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950524	38950533	+	frameshift_variant	Frame_Shift_Del	DEL	ATTAAAATCA	ATTAAAATCA	-	novel	NA	P-0041848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	85	474	0	ENST00000357387.3:c.3417_3426del	p.Asp1140IlefsTer17	p.D1140Ifs*17	ENST00000357387	NM_152756.3	1139	gtTGATTTTAAT/gt	31/38	0.357454198704525	5	FACETS	0.968	0.867	1	0.645	0.578	0.715	INDETERMINATE	2	TRUE	2	0.617719958895445	5		474	274	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0041849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	35	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.297	0.243	0.359	0.297	0.243	0.359	SUBCLONAL	1	TRUE	1	0.415952184054142	2		311	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579838	7579839	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0041849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	59	725	0	ENST00000269305.4:c.74_74+1insTT	p.Leu26TyrfsTer19	p.L26Yfs*19	ENST00000269305	NM_001126112.2	25	cta/ctTTa		1	2	FACETS	0.39	0.334	0.45	0.39	0.334	0.45	SUBCLONAL	1	TRUE	1	0.415952184054142	2		725	728	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144678	55144678	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375434317	NA	P-0041849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	38	373	0	ENST00000257290.5:c.2152C>T	p.Arg718Trp	p.R718W	ENST00000257290	NM_006206.4	718	Cgg/Tgg	15/23	1	2	FACETS	0.417	0.345	0.498	0.417	0.345	0.498	SUBCLONAL	1	TRUE	1	0.415952184054142	2		373	438	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858570	27858570	+	start_lost	Translation_Start_Site	SNP	T	T	C	rs766949103	NA	P-0041891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	56	337	0	ENST00000359303.2:c.1A>G	p.Met1?	p.M1?	ENST00000359303	NM_003535.2	1	Atg/Gtg	1/1	0.0918352859814668	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		337	297	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409107	4409107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3217921	NA	P-0041891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	110	573	0	ENST00000261254.3:c.802G>A	p.Gly268Arg	p.G268R	ENST00000261254	NM_001759.3	268	Gga/Aga	5/5	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		573	535	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240695	55240695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764359156	NA	P-0041902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	60	965	1	ENST00000275493.2:c.1939G>A	p.Ala647Thr	p.A647T	ENST00000275493	NM_005228.3	647	Gcc/Acc	17/28	0.27740870751273	1	FACETS	0.905	0.796	1	1	0.979	1	CLONAL	2	TRUE	0	0.333011858039741	1		966	166	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115943	8115982	+	frameshift_variant	Frame_Shift_Del	DEL	TTGGACCACACCACCCCTCCAGCATGGTCACCGCCATGGG	TTGGACCACACCACCCCTCCAGCATGGTCACCGCCATGGG	-	novel	NA	P-0041902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	179	498	0	ENST00000346208.3:c.1291_1330del	p.Gly431ArgfsTer31	p.G431Rfs*31	ENST00000346208		430	tTTGGACCACACCACCCCTCCAGCATGGTCACCGCCATGGGt/tt	6/6	0.333011858039741	5	FACETS	0.948	0.903	0.99	1	0.995	1	CLONAL	7	TRUE	2	0.333011858039741	5		498	243	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435978	116435978	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778444	NA	P-0041902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	78	704	0	ENST00000397752.3:c.3973G>A	p.Glu1325Lys	p.E1325K	ENST00000397752	NM_000245.2	1325	Gaa/Aaa	21/21	0.333011858039741	4	FACETS	0.86	0.767	0.957	0.86	0.767	0.957	CLONAL	3	TRUE	1	0.333011858039741	4		704	242	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0041903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	19	586	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.414	0.313	0.535	0.414	0.313	0.535	SUBCLONAL	1	TRUE	1	0.14	2		586	655	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0041903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	32	667	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.702	0.568	0.854	0.702	0.568	0.854	SUBCLONAL	1	TRUE	1	0.14	2		667	651	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0041903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	26	443	9	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.613	0.484	0.762	0.613	0.484	0.762	SUBCLONAL	1	TRUE	1	0.14	2		452	606	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746002	162746002	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1056323839	NA	P-0041903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	28	433	1	ENST00000367921.3:c.2125C>T	p.Arg709Ter	p.R709*	ENST00000367921	NM_006182.2	709	Cga/Tga	16/18	1	2	FACETS	0.759	0.605	0.935	0.759	0.605	0.935	CLONAL	1	TRUE	1	0.14	2		434	527	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0041903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	29	410	0	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	1	2	FACETS	0.766	0.613	0.94	0.766	0.613	0.94	CLONAL	1	TRUE	1	0.14	2		410	541	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46727002	46727002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1363172157	NA	P-0041903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	41	581	2	ENST00000371975.4:c.836G>A	p.Arg279His	p.R279H	ENST00000371975	NM_003579.3	279	cGc/cAc	8/18	1	2	FACETS	0.743	0.617	0.884	0.743	0.617	0.884	SUBCLONAL	1	TRUE	1	0.14	2		583	788	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191480	10191480	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913346	NA	P-0041936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	43	310	0	ENST00000256474.2:c.473T>C	p.Leu158Pro	p.L158P	ENST00000256474	NM_000551.3	158	cTg/cCg	3/3	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.15	2		310	440	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0041936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	23	47	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.761	0.592	0.956	0.761	0.592	0.956	CLONAL	1	TRUE	1	0.15	2		47	403	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023072	27023084	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCCCGCCGTGG	GGCCCCGCCGTGG	CA	novel	NA	P-0041936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	12	55	1	ENST00000324856.7:c.178_190delinsCA	p.Gly60GlnfsTer47	p.G60Qfs*47	ENST00000324856	NM_006015.4	60	GGCCCCGCCGTGGgg/CAgg	1/20	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.15	2		56	112	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0041958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	79	621	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.441427156693234	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.441427156693234	1		622	208	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818424	43818424	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	36	508	0	ENST00000372470.3:c.1889G>C	p.Ser630Thr	p.S630T	ENST00000372470	NM_005373.2	630	aGc/aCc	12/12	0.32818181666697	2	FACETS	0.773	0.641	0.918	0.387	0.32	0.459	CLONAL	1	TRUE	0	0.441427156693234	2		508	211	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89811465	89811465	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	29	611	0	ENST00000389301.3:c.3528C>G	p.Ser1176Arg	p.S1176R	ENST00000389301	NM_000135.2	1176	agC/agG	36/43	1	2	FACETS	0.587	0.473	0.714	0.587	0.473	0.714	SUBCLONAL	1	TRUE	1	0.441427156693234	2		611	224	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15838416	15838416	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	19	364	0	ENST00000307771.7:c.914C>G	p.Thr305Ser	p.T305S	ENST00000307771	NM_005089.3	305	aCc/aGc	10/11	0.441427156693234	1	FACETS	0.404	0.309	0.515	0.404	0.309	0.515	SUBCLONAL	1	TRUE	0	0.441427156693234	1		364	166	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0041966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	175	462	0	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	0.321855791653359	1	FACETS	0.815	0.758	0.873	0.815	0.758	0.873	INDETERMINATE	1	TRUE	0	0.637650582584932	1		462	459	SUCCESS
APC	324	MSKCC	GRCh37	5	112175437	112175438	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	134	255	0	ENST00000257430.4:c.4147dup	p.Met1383AsnfsTer3	p.M1383Nfs*3	ENST00000257430	NM_000038.5	1382	-/A	16/16	0.566751949742213	2	FACETS	0.764	0.708	0.82	0.764	0.708	0.82	SUBCLONAL	2	TRUE	0	0.637650582584932	2		255	275	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578278	7578293	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGGGGCCAGACCTAA	GAGGGGCCAGACCTAA	-	novel	NA	P-0041966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	185	642	0	ENST00000269305.4:c.560-4_571del		p.X187_splice	ENST00000269305	NM_001126112.2	187		6/11	0.637650582584932	1	FACETS	0.873	0.814	0.931	0.873	0.814	0.931	CLONAL	1	TRUE	0	0.637650582584932	1		642	453	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578283	212578283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1162491783	NA	P-0041966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	93	413	0	ENST00000342788.4:c.974C>T	p.Pro325Leu	p.P325L	ENST00000342788	NM_005235.2	325	cCt/cTt	8/28	0.380357844179862	1	FACETS	0.387	0.345	0.432	0.387	0.345	0.432	INDETERMINATE	1	TRUE	0	0.637650582584932	1		413	513	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036903	180036903	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0041966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	71	599	0	ENST00000261937.6:c.3807+2T>C		p.X1269_splice	ENST00000261937	NM_182925.4	1269			0.594266529944682	1	FACETS	0.346	0.303	0.393	0.346	0.303	0.393	SUBCLONAL	1	TRUE	0	0.637650582584932	1		599	438	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274794	123274794	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913478	NA	P-0041971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	145	506	0	ENST00000358487.5:c.1124A>G	p.Tyr375Cys	p.Y375C	ENST00000358487	NM_000141.4	375	tAc/tGc	9/18	1	2	FACETS	0.821	0.752	0.893	0.821	0.752	0.893	CLONAL	1	TRUE	1	0.575071838063999	2		506	614	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274786	123274786	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	157	509	0	ENST00000358487.5:c.1132A>G	p.Ile378Val	p.I378V	ENST00000358487	NM_000141.4	378	Ata/Gta	9/18	1	2	FACETS	0.849	0.781	0.92	0.849	0.781	0.92	CLONAL	1	TRUE	1	0.575071838063999	2		509	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0041972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	122	481	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.3	1	FACETS	0.942	0.853	1	1	0.989	1	CLONAL	2	TRUE	0	0.17	1		481	697	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131411	202131411	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs777784105	NA	P-0041972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	57	489	0	ENST00000358485.4:c.379C>T	p.Arg127Ter	p.R127*	ENST00000358485	NM_001080125.1	127	Cga/Tga	2/9	0.3	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.17	1		489	538	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138445	2138445	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0041972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	79	632	1	ENST00000219476.3:c.5260-2A>G		p.X1754_splice	ENST00000219476	NM_000548.3	1754			1	2	FACETS	0.978	0.859	1	0.978	0.859	1	CLONAL	1	TRUE	1	0.17	2		633	950	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271273	153271274	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CATC	novel	NA	P-0041972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	29	141	0	ENST00000281708.4:c.502-1_504dup	p.Lys169AspfsTer10	p.K169Dfs*10	ENST00000281708	NM_033632.3	168	-/GATG	3/12	0.3	1	FACETS	0.8	0.648	0.971	1	0.946	1	CLONAL	2	TRUE	0	0.17	1		141	195	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138201244	138201244	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543704449	NA	P-0041972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	57	383	0	ENST00000237289.4:c.1943C>T	p.Ala648Val	p.A648V	ENST00000237289	NM_001270507.1	648	gCg/gTg	8/9	0.3	1	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	0	0.17	1		383	581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0042001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	476	660	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.601089743602161	2		660	748	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0042001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	142	380	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.956	0.878	1	0.956	0.878	1	CLONAL	1	TRUE	1	0.601089743602161	2		380	494	SUCCESS
APC	324	MSKCC	GRCh37	5	112175766	112175766	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	105	321	0	ENST00000257430.4:c.4476del	p.Thr1493ArgfsTer14	p.T1493Rfs*14	ENST00000257430	NM_000038.5	1492	gCc/gc	16/16	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.601089743602161	2		321	345	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591902	48591902	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519740	NA	P-0042001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	143	486	0	ENST00000342988.3:c.1065C>A	p.Asp355Glu	p.D355E	ENST00000342988	NM_005359.5	355	gaC/gaA	9/12	0.601089743602161	1	FACETS	0.927	0.856	0.999	0.927	0.856	0.999	CLONAL	1	TRUE	0	0.601089743602161	1		486	359	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920402	114920402	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	227	470	0	ENST00000543371.1:c.1345del	p.Ala449HisfsTer42	p.A449Hfs*42	ENST00000543371	NM_001198531.1	448	cGg/cg	13/14	1	2	FACETS	0.892	0.832	0.953	0.892	0.832	0.953	CLONAL	1	TRUE	1	0.601089743602161	2		470	847	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0042011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	41	444	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.233	0.193	0.278	0.233	0.193	0.278	SUBCLONAL	1	TRUE	1	0.48	2		444	733	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640478	3640478	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373091194	NA	P-0042011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	110	835	0	ENST00000294008.3:c.3161C>T	p.Ser1054Leu	p.S1054L	ENST00000294008	NM_032444.2	1054	tCg/tTg	12/15	1	2	FACETS	0.408	0.366	0.454	0.408	0.366	0.454	SUBCLONAL	1	TRUE	1	0.48	2		835	1122	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577520	+	inframe_deletion	In_Frame_Del	DEL	TGATGA	TGATGA	-	novel	NA	P-0042011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	86	668	0	ENST00000269305.4:c.761_766del	p.Ile254_Ile255del	p.I254_I255del	ENST00000269305	NM_001126112.2	254	aTCATCAca/aca	7/11	0.159455530503547	1	FACETS	0.281	0.248	0.317	0.281	0.248	0.317	INDETERMINATE	1	TRUE	0	0.48	1		668	969	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806234	1806234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781361431	NA	P-0042011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	67	694	1	ENST00000260795.2:c.1253C>T	p.Pro418Leu	p.P418L	ENST00000260795		418	cCg/cTg	8/17	1	2	FACETS	0.308	0.266	0.353	0.308	0.266	0.353	SUBCLONAL	1	TRUE	1	0.48	2		695	907	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459448	50459448	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs761227924	NA	P-0042011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	71	302	0	ENST00000331340.3:c.737A>G	p.His246Arg	p.H246R	ENST00000331340	NM_006060.4	246	cAc/cGc	7/8	1	2	FACETS	0.62	0.543	0.703	0.62	0.543	0.703	SUBCLONAL	1	TRUE	1	0.48	2		302	477	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191763	123191763	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	36	476	0	ENST00000218089.9:c.1352G>T	p.Arg451Ile	p.R451I	ENST00000218089	NM_001042749.1	451	aGa/aTa	15/35	1	2	FACETS	0.225	0.184	0.271	0.225	0.184	0.271	SUBCLONAL	1	TRUE	1	0.48	2		476	667	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0042035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	66	445	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.390343886364126	3	FACETS	0.515	0.446	0.589			1	SUBCLONAL	1	TRUE	NA	0.411113156508209	3		445	752	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0042035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	385	217	0	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	0.411113156508209	4	FACETS	0.997	0.957	1			1	CLONAL	4	TRUE	NA	0.411113156508209	4		217	663	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792820	33792820	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	34	247	0	ENST00000498907.2:c.501G>C	p.Glu167Asp	p.E167D	ENST00000498907	NM_004364.3	167	gaG/gaC	1/1	0.112924804557729	3	FACETS	0.482	0.393	0.581	0.241	0.196	0.291	INDETERMINATE	1	TRUE	1	0.411113156508209	3		247	414	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845382	42845382	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs770521585	NA	P-0042035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	118	804	0	ENST00000398585.3:c.880G>C	p.Val294Leu	p.V294L	ENST00000398585	NM_001135099.1	294	Gtg/Ctg	9/14	0.112924804557729	3	FACETS	0.627	0.565	0.694	0.314	0.282	0.347	INDETERMINATE	1	TRUE	1	0.411113156508209	3		804	1103	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060962	38060979	+	frameshift_variant	Frame_Shift_Del	DEL	TCGCCGTCGCCCCACTGT	TCGCCGTCGCCCCACTGT	GGCCA	novel	NA	P-0042035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	70	545	2	ENST00000250448.2:c.1010_1027delinsTGGCC	p.His337LeufsTer9	p.H337Lfs*9	ENST00000250448	NM_004496.3	337	cACAGTGGGGCGACGGCGAca/cTGGCCca	2/2	1	2	FACETS	0.438	0.381	0.5	0.438	0.381	0.5	SUBCLONAL	1	TRUE	1	0.411113156508209	2		547	777	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630275	187630275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	41	802	0	ENST00000441802.2:c.707G>A	p.Gly236Asp	p.G236D	ENST00000441802	NM_005245.3	236	gGc/gAc	2/27	1	2	FACETS	0.856	0.711	1	0.856	0.711	1	CLONAL	1	TRUE	1	0.13	2		802	737	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073473	8073473	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	40	682	0	ENST00000377482.5:c.1186C>A	p.Leu396Ile	p.L396I	ENST00000377482	NM_018948.3	396	Cta/Ata	4/4	1	2	FACETS	0.916	0.759	1	0.916	0.759	1	CLONAL	1	TRUE	1	0.13	2		682	672	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161516	2161516	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	32	714	0	ENST00000434045.2:c.11C>G	p.Pro4Arg	p.P4R	ENST00000434045	NM_001127598.1	4	cCa/cGa	2/5	1	2	FACETS	0.871	0.706	1	0.871	0.706	1	CLONAL	1	TRUE	1	0.13	2		714	565	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325680	30325680	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	15	206	0	ENST00000322652.5:c.1878T>A	p.Phe626Leu	p.F626L	ENST00000322652	NM_015355.2	626	ttT/ttA	16/16	1	2	FACETS	1	0.787	1	1	0.787	1	CLONAL	1	TRUE	1	0.13	2		206	212	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405037	405037	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	35	648	0	ENST00000380956.4:c.1119C>A	p.His373Gln	p.H373Q	ENST00000380956	NM_001195286.1	373	caC/caA	8/9	1	2	FACETS	0.983	0.804	1	0.983	0.804	1	CLONAL	1	TRUE	1	0.13	2		648	548	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230921	53230921	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	50	506	0	ENST00000375401.3:c.1872del	p.Ala625LeufsTer34	p.A625Lfs*34	ENST00000375401	NM_004187.3	624	ccT/cc	14/26	1	1	FACETS	0.871	0.74	1	1	0.97	1	CLONAL	2	TRUE	0	0.13	1		506	413	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658850	3658850	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1205588827	NA	P-0042063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	39	888	0	ENST00000294008.3:c.116A>C	p.Lys39Thr	p.K39T	ENST00000294008	NM_032444.2	39	aAa/aCa	2/15	0.203874871968861	5	FACETS	0.352	0.291	0.42	0.07	0.058	0.084	INDETERMINATE	1	TRUE	0	0.7149715299219	5		888	643	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144099	11144099	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	127	1081	0	ENST00000358026.2:c.3680A>C	p.Lys1227Thr	p.K1227T	ENST00000358026	NM_001128849.1	1227	aAg/aCg	26/36	0.611088095875392	1	FACETS	0.734	0.675	0.794	0.734	0.675	0.794	SUBCLONAL	1	TRUE	0	0.7149715299219	1		1081	311	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753403	57753403	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	81	620	0	ENST00000274289.3:c.721T>C	p.Cys241Arg	p.C241R	ENST00000274289	NM_006622.3	241	Tgt/Cgt	6/14	0.625320917300958	5	FACETS	0.707	0.623	0.797	0.236	0.207	0.266	SUBCLONAL	1	TRUE	2	0.7149715299219	5		620	664	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456854	149456854	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	208	1028	0	ENST00000286301.3:c.874T>G	p.Phe292Val	p.F292V	ENST00000286301	NM_005211.3	292	Ttc/Gtc	6/22	0.438650514867199	4	FACETS	0.86	0.804	0.917	0.86	0.804	0.917	CLONAL	2	TRUE	2	0.7149715299219	4		1028	580	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0042064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	200	309	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.470666893054604	3	FACETS	0.903	0.843	0.966	0.903	0.843	0.966	CLONAL	2	TRUE	1	0.470666893054604	3		309	581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0042064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	569	481	3	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.439265816587787	3	FACETS	0.919	0.888	0.951	0.919	0.888	0.951	CLONAL	3	TRUE	0	0.470666893054604	3		484	1083	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680751	88680751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201252722	NA	P-0042064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	214	815	0	ENST00000360948.2:c.506G>A	p.Arg169His	p.R169H	ENST00000360948	NM_001012338.2	169	cGc/cAc	6/19	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.470666893054604	2		815	893	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439887	51439887	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	39	426	0	ENST00000262662.1:c.452A>C	p.Glu151Ala	p.E151A	ENST00000262662		151	gAg/gCg	4/4	1	2	FACETS	0.317	0.262	0.378	0.317	0.262	0.378	SUBCLONAL	1	TRUE	1	0.470666893054604	2		426	523	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729345	41729345	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs771243659	NA	P-0042064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	64	702	0	ENST00000242208.4:c.1184A>G	p.Lys395Arg	p.K395R	ENST00000242208	NM_002192.2	395	aAg/aGg	3/3	0.429324035744591	4	FACETS	0.337	0.29	0.388	0.168	0.145	0.194	SUBCLONAL	1	TRUE	2	0.470666893054604	4		702	1188	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753200	128753200	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	33	423	0	ENST00000377970.2:c.1361C>G	p.Ala454Gly	p.A454G	ENST00000377970	NM_002467.4	454	gCg/gGg	3/3	0.464131996929785	3	FACETS	0.286	0.232	0.347	0.143	0.116	0.174	SUBCLONAL	1	TRUE	1	0.470666893054604	3		423	605	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0042065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	83	865	1	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.210272753549377	1	FACETS	0.853	0.752	0.962	0.853	0.752	0.962	CLONAL	1	TRUE	0	0.22	1		866	787	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576097	29576098	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0042065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	80	621	0	ENST00000356175.3:c.4076dup	p.Gln1360SerfsTer14	p.Q1360Sfs*14	ENST00000356175	NM_000267.3	1357	ttc/ttCc	30/57	0.210272753549377	1	FACETS	0.933	0.821	1	0.933	0.821	1	CLONAL	1	TRUE	0	0.22	1		621	694	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891277	101891277	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	71	734	0	ENST00000374994.4:c.238C>T	p.Arg80Ter	p.R80*	ENST00000374994	NM_004612.2	80	Cga/Tga	2/9	0.3	1	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	0	0.22	1		734	564	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645163	86645163	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	42	394	0	ENST00000274376.6:c.1235G>C	p.Gly412Ala	p.G412A	ENST00000274376	NM_002890.2	412	gGa/gCa	8/25	0.210272753549377	1	FACETS	0.805	0.673	0.952	0.805	0.673	0.952	CLONAL	1	TRUE	0	0.22	1		394	422	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976405	18976405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	76	972	1	ENST00000262803.5:c.3055G>A	p.Gly1019Arg	p.G1019R	ENST00000262803	NM_002911.3	1019	Gga/Aga	22/24	1	2	FACETS	0.841	0.736	0.953	0.841	0.736	0.953	CLONAL	1	TRUE	1	0.22	2		973	822	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884800	151884800	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	55	416	0	ENST00000262189.6:c.4793G>A	p.Arg1598Lys	p.R1598K	ENST00000262189	NM_170606.2	1598	aGg/aAg	32/59	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.22	2		416	489	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0042079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	163	766	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.162012486033174	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	FALSE	0	0.162012486033174	2		767	975	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0042079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	88	380	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.162012486033174	2	FACETS	0.792	0.702	0.888	0.792	0.702	0.888	SUBCLONAL	2	FALSE	0	0.162012486033174	2		380	686	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	126	348	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.305062027010899	2		349	666	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971029	21971029	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519852	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	129	551	0	ENST00000304494.5:c.329G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tGg/tAg	2/3	0.305062027010899	1	FACETS	0.966	0.877	1	0.966	0.877	1	CLONAL	1	TRUE	0	0.305062027010899	1		551	742	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665101	138665101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	81	354	0	ENST00000330315.3:c.464C>T	p.Pro155Leu	p.P155L	ENST00000330315	NM_023067.3	155	cCg/cTg	1/1	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.305062027010899	2		354	528	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536625	120536625	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs202018032	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	139	728	0	ENST00000229340.5:c.467A>G	p.Asn156Ser	p.N156S	ENST00000229340	NM_006861.6	156	aAc/aGc	5/6	1	2	FACETS	0.923	0.84	1	0.923	0.84	1	CLONAL	1	TRUE	1	0.305062027010899	2		728	987	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851837	63851837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755029955	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	186	590	0	ENST00000279873.7:c.2615C>T	p.Ser872Phe	p.S872F	ENST00000279873	NM_032199.2	872	tCc/tTc	10/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.305062027010899	2		590	1082	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908197	28908197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	134	558	0	ENST00000282397.4:c.2558C>T	p.Pro853Leu	p.P853L	ENST00000282397	NM_002019.4	853	cCt/cTt	18/30	1	2	FACETS	0.963	0.875	1	0.963	0.875	1	CLONAL	1	TRUE	1	0.305062027010899	2		558	912	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	198	585	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.305062027010899	2		585	1189	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856216	111856217	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	61	268	2	ENST00000341259.2:c.267_268delinsTT	p.Arg90Trp	p.R90W	ENST00000341259	NM_005475.2	89	taCCgg/taTTgg	2/8	1	2	FACETS	0.948	0.82	1	0.948	0.82	1	CLONAL	1	TRUE	1	0.305062027010899	2		270	422	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995347	15995347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	102	417	0	ENST00000268712.3:c.2846C>T	p.Pro949Leu	p.P949L	ENST00000268712	NM_006311.3	949	cCa/cTa	22/46	1	2	FACETS	0.915	0.818	1	0.915	0.818	1	CLONAL	1	TRUE	1	0.305062027010899	2		417	731	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950458	68950458	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	129	516	0	ENST00000288368.4:c.770C>T	p.Ser257Phe	p.S257F	ENST00000288368	NM_024870.2	257	tCt/tTt	7/40	1	2	FACETS	0.988	0.896	1	0.988	0.896	1	CLONAL	1	TRUE	1	0.305062027010899	2		516	856	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490506	20490506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	156	609	2	ENST00000346618.3:c.1243C>T	p.Pro415Ser	p.P415S	ENST00000346618	NM_001949.4	415	Cct/Tct	7/7	1	2	FACETS	0.981	0.897	1	0.981	0.897	1	CLONAL	1	TRUE	1	0.305062027010899	2		611	1043	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780287	9780287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	138	609	0	ENST00000377346.4:c.1457C>T	p.Pro486Leu	p.P486L	ENST00000377346	NM_005026.3	486	cCc/cTc	11/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.305062027010899	2		609	796	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782664	9782665	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	152	738	3	ENST00000377346.4:c.2426_2426+1delinsAA		p.X809_splice	ENST00000377346	NM_005026.3	809		19/24	1	2	FACETS	0.932	0.851	1	0.932	0.851	1	CLONAL	1	TRUE	1	0.305062027010899	2		741	1069	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276724	115276724	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	102	355	0	ENST00000438362.2:c.735T>G	p.Phe245Leu	p.F245L	ENST00000438362	NM_001242891.1	245	ttT/ttG	8/20	1	2	FACETS	0.969	0.867	1	0.969	0.867	1	CLONAL	1	TRUE	1	0.305062027010899	2		355	690	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551679	150551679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	131	558	0	ENST00000369026.2:c.328G>A	p.Glu110Lys	p.E110K	ENST00000369026	NM_021960.4	110	Gag/Aag	1/3	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.305062027010899	2		558	744	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170387	119170387	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	112	537	0	ENST00000264033.4:c.2617G>A	p.Asp873Asn	p.D873N	ENST00000264033	NM_005188.3	873	Gac/Aac	16/16	1	2	FACETS	0.954	0.858	1	0.954	0.858	1	CLONAL	1	TRUE	1	0.305062027010899	2		537	770	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1036350	1036350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	84	693	0	ENST00000358495.3:c.428G>A	p.Arg143Lys	p.R143K	ENST00000358495	NM_134424.2	143	aGg/aAg	6/12	1	2	FACETS	0.52	0.457	0.586	0.52	0.457	0.586	SUBCLONAL	1	TRUE	1	0.305062027010899	2		693	1060	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435151	18435151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs183245589	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	105	419	0	ENST00000266497.5:c.136G>A	p.Glu46Lys	p.E46K	ENST00000266497		46	Gag/Aag	1/31	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.305062027010899	2		419	673	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431087	49431087	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	170	682	0	ENST00000301067.7:c.10052C>T	p.Ser3351Phe	p.S3351F	ENST00000301067	NM_003482.3	3351	tCc/tTc	34/54	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.305062027010899	2		682	1027	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858986	57858987	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	177	734	0	ENST00000228682.2:c.482_483delinsAA	p.Arg161Gln	p.R161Q	ENST00000228682	NM_005269.2	161	cGG/cAA	5/12	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.305062027010899	2		734	1126	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820989	3820989	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	123	504	1	ENST00000262367.5:c.2464-2A>T		p.X822_splice	ENST00000262367	NM_004380.2	822			1	2	FACETS	0.963	0.871	1	0.963	0.871	1	CLONAL	1	TRUE	1	0.305062027010899	2		505	837	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031909	10031909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	157	681	0	ENST00000330684.3:c.914C>T	p.Ser305Phe	p.S305F	ENST00000330684	NM_001134407.1	305	tCt/tTt	3/13	1	2	FACETS	0.999	0.914	1	0.999	0.914	1	CLONAL	1	TRUE	1	0.305062027010899	2		681	1030	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349233	89349233	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1233	235	944	1	ENST00000301030.4:c.3717del	p.Glu1240ArgfsTer78	p.E1240Rfs*78	ENST00000301030	NM_001256183.1	1239	ccC/cc	9/13	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.305062027010899	2		945	1468	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475292	40475293	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	91	615	3	ENST00000264657.5:c.1733_1734delinsTT	p.Ala578Val	p.A578V	ENST00000264657	NM_139276.2	578	gCC/gTT	19/24	1	2	FACETS	0.631	0.559	0.708	0.631	0.559	0.708	SUBCLONAL	1	TRUE	1	0.305062027010899	2		618	945	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533008	63533008	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	160	663	0	ENST00000307078.5:c.1886A>C	p.Gln629Pro	p.Q629P	ENST00000307078	NM_004655.3	629	cAg/cCg	7/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.305062027010899	2		663	987	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303203	15303203	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	162	819	0	ENST00000263388.2:c.325C>T	p.Pro109Ser	p.P109S	ENST00000263388	NM_000435.2	109	Ccc/Tcc	3/33	1	2	FACETS	0.919	0.841	1	0.919	0.841	1	CLONAL	1	TRUE	1	0.305062027010899	2		819	1156	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279324	18279324	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	120	601	0	ENST00000222254.8:c.1776C>G	p.Asn592Lys	p.N592K	ENST00000222254	NM_005027.3	592	aaC/aaG	14/16	1	2	FACETS	0.83	0.748	0.916	0.83	0.748	0.916	CLONAL	1	TRUE	1	0.305062027010899	2		601	948	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635599	47635599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	126	443	0	ENST00000233146.2:c.271G>A	p.Asp91Asn	p.D91N	ENST00000233146	NM_000251.2	91	Gat/Aat	2/16	1	2	FACETS	0.902	0.816	0.993	0.902	0.816	0.993	CLONAL	1	TRUE	1	0.305062027010899	2		443	916	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721067	61721067	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	130	597	0	ENST00000401558.2:c.1207C>T	p.Pro403Ser	p.P403S	ENST00000401558	NM_003400.3	403	Cct/Tct	12/25	1	2	FACETS	0.89	0.806	0.978	0.89	0.806	0.978	CLONAL	1	TRUE	1	0.305062027010899	2		597	958	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578332	212578333	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	97	463	1	ENST00000342788.4:c.924_925delinsTT	p.Pro309Ser	p.P309S	ENST00000342788	NM_005235.2	308	tgCCct/tgTTct	8/28	1	2	FACETS	0.864	0.77	0.964	0.864	0.77	0.964	CLONAL	1	TRUE	1	0.305062027010899	2		464	736	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566439	41566439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	251	386	0	ENST00000263253.7:c.4316C>T	p.Pro1439Leu	p.P1439L	ENST00000263253	NM_001429.3	1439	cCa/cTa	27/31	0.195594890240273	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.305062027010899	2		386	745	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626450	12626450	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs778476881	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	124	588	0	ENST00000251849.4:c.1699T>A	p.Ser567Thr	p.S567T	ENST00000251849	NM_002880.3	567	Tcc/Acc	16/17	NA	2	FACETS	0.993	0.898	1			1	INDETERMINATE	1	TRUE	NA	0.305062027010899	2		588	819	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259340	89259340	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	122	453	0	ENST00000336596.2:c.484C>A	p.Leu162Met	p.L162M	ENST00000336596	NM_005233.5	162	Ctg/Atg	3/17	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.305062027010899	2		453	762	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361155	66361155	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	91	378	0	ENST00000273854.3:c.1017A>T	p.Glu339Asp	p.E339D	ENST00000273854	NM_004439.5	339	gaA/gaT	4/18	1	2	FACETS	0.983	0.874	1	0.983	0.874	1	CLONAL	1	TRUE	1	0.305062027010899	2		378	607	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245431	153245431	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	166	659	0	ENST00000281708.4:c.1760T>G	p.Met587Arg	p.M587R	ENST00000281708	NM_033632.3	587	aTg/aGg	11/12	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.305062027010899	2		659	1046	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542407	187542407	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	75	456	0	ENST00000441802.2:c.5333C>T	p.Ala1778Val	p.A1778V	ENST00000441802	NM_005245.3	1778	gCc/gTc	10/27	1	2	FACETS	0.759	0.665	0.86	0.759	0.665	0.86	SUBCLONAL	1	TRUE	1	0.305062027010899	2		456	648	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526760	31526760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1478024603	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	77	651	0	ENST00000344624.3:c.280C>T	p.Pro94Ser	p.P94S	ENST00000344624		94	Ccc/Tcc	2/33	1	2	FACETS	0.542	0.474	0.614	0.542	0.474	0.614	SUBCLONAL	1	TRUE	1	0.305062027010899	2		651	932	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497371	149497371	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	170	602	0	ENST00000261799.4:c.2947C>T	p.Pro983Ser	p.P983S	ENST00000261799	NM_002609.3	983	Cca/Tca	22/23	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.305062027010899	2		602	978	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609747	117609747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768332561	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	141	560	0	ENST00000368508.3:c.6952G>A	p.Glu2318Lys	p.E2318K	ENST00000368508	NM_002944.2	2318	Gaa/Aaa	43/43	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.305062027010899	2		560	918	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265609	152265610	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	130	499	3	ENST00000206249.3:c.1062_1063delinsAA	p.Val355Ile	p.V355I	ENST00000206249	NM_000125.3	354	ctGGtt/ctAAtt	4/8	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.305062027010899	2		502	833	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099473	157099473	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	86	358	0	ENST00000346085.5:c.410A>C	p.Asn137Thr	p.N137T	ENST00000346085	NM_020732.3	137	aAc/aCc	1/20	1	2	FACETS	0.967	0.857	1	0.967	0.857	1	CLONAL	1	TRUE	1	0.305062027010899	2		358	583	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162876	38162876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	167	666	1	ENST00000317025.8:c.2330C>T	p.Ala777Val	p.A777V	ENST00000317025	NM_023034.1	777	gCc/gTc	13/24	1	2	FACETS	0.949	0.87	1	0.949	0.87	1	CLONAL	1	TRUE	1	0.305062027010899	2		667	1154	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737109	145737110	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	159	835	1	ENST00000428558.2:c.3456_3457delinsAA	p.Glu1153Lys	p.E1153K	ENST00000428558	NM_004260.3	1152	gaGGag/gaAAag	21/22	1	2	FACETS	0.906	0.829	0.987	0.906	0.829	0.987	CLONAL	1	TRUE	1	0.305062027010899	2		836	1151	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0042107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	748	830	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.966623063402592	2		830	1547	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934152	48934152	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0042107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	118	238	0	ENST00000267163.4:c.608-1G>A		p.X203_splice	ENST00000267163	NM_000321.2	203			0.966623063402592	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.966623063402592	1		238	124	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814303	76814306	+	frameshift_variant	Frame_Shift_Del	DEL	ATAA	ATAA	-	novel	NA	P-0042107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	164	136	0	ENST00000373344.5:c.6338_6341del	p.Phe2113SerfsTer9	p.F2113Sfs*9	ENST00000373344	NM_000489.3	2113	tTTATc/tc	29/35	1	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.966623063402592	1		136	175	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093441	30093441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	173	388	0	ENST00000331968.5:c.1822G>A	p.Asp608Asn	p.D608N	ENST00000331968	NM_002742.2	608	Gat/Aat	13/18	1	2	FACETS	0.846	0.788	0.905	0.846	0.788	0.905	CLONAL	1	TRUE	1	0.966623063402592	2		388	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579508	7579508	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	199	927	0	ENST00000269305.4:c.179del	p.Pro60GlnfsTer63	p.P60Qfs*63	ENST00000269305	NM_001126112.2	60	cCa/ca	4/11	0.295696505689828	2	FACETS	0.953	0.886	1	0.953	0.886	1	CLONAL	2	TRUE	0	0.295696505689828	2		927	706	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871746	37871746	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	209	864	0	ENST00000269571.5:c.1270G>T	p.Val424Phe	p.V424F	ENST00000269571		424	Gtc/Ttc	11/27	0.295696505689828	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.295696505689828	2		864	650	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467173	99467193	+	inframe_deletion	In_Frame_Del	DEL	TGGCCGGAACCTGAGAATCCC	TGGCCGGAACCTGAGAATCCC	-	novel	NA	P-0042111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	47	495	0	ENST00000268035.6:c.2554_2574del	p.Trp852_Pro858del	p.W852_P858del	ENST00000268035	NM_000875.3	852	TGGCCGGAACCTGAGAATCCC/-	12/21	0.295696505689828	2	FACETS	0.644	0.543	0.754	0.322	0.271	0.377	SUBCLONAL	1	TRUE	0	0.295696505689828	2		495	494	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905289	50905289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750144413	NA	P-0042111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	248	1096	0	ENST00000440232.2:c.497G>A	p.Arg166Gln	p.R166Q	ENST00000440232	NM_002691.3	166	cGg/cAg	5/27	0.169613414715162	4	FACETS	1	0.956	1	1	0.956	1	INDETERMINATE	2	TRUE	2	0.295696505689828	4		1096	1057	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0042138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	15	621	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.2	0.145	0.266	0.2	0.145	0.266	SUBCLONAL	1	TRUE	1	0.291010679164253	2		621	516	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	63	348	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.291010679164253	2		349	374	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916774	48916775	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs587778825	NA	P-0042138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	54	430	0	ENST00000267163.4:c.305_306del	p.Cys102TyrfsTer7	p.C102Yfs*7	ENST00000267163	NM_000321.2	102	TGt/t	3/27	0.291010679164253	1	FACETS	0.862	0.739	0.995	0.862	0.739	0.995	CLONAL	1	TRUE	0	0.291010679164253	1		430	368	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29497003	29497003	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397514641	NA	P-0042138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	45	267	0	ENST00000356175.3:c.574C>T	p.Arg192Ter	p.R192*	ENST00000356175	NM_000267.3	192	Cga/Tga	5/57	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.291010679164253	2		267	265	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0042149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	368	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.491732854441639	3	FACETS	0.876	0.833	0.92	0.876	0.833	0.92	CLONAL	2	TRUE	1	0.504762222548957	3		311	1042	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0042149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	198	405	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.856	0.794	0.922	0.856	0.794	0.922	CLONAL	1	TRUE	1	0.504762222548957	2		405	916	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0042149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	185	381	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.504762222548957	2		381	507	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604764	48604765	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs377767376	NA	P-0042149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	216	558	1	ENST00000342988.3:c.1587dup	p.His530ThrfsTer47	p.H530Tfs*47	ENST00000342988	NM_005359.5	529	tta/ttAa	12/12	0.504762222548957	1	FACETS	0.994	0.929	1	0.994	0.929	1	CLONAL	1	TRUE	0	0.504762222548957	1		559	644	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577501	7577501	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	rs1427471466	NA	P-0042160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	93	692	0	ENST00000269305.4:c.780del	p.Ser261ValfsTer84	p.S261Vfs*84	ENST00000269305	NM_001126112.2	260	tcC/tc	7/11	0.156093589116435	2	FACETS	1	0.978	1	0.72	0.64	0.807	CLONAL	1	TRUE	0	0.156093589116435	2		692	827	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0042166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	172	785	23	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.361581853145347	1	FACETS	0.852	0.784	0.923	0.852	0.784	0.923	CLONAL	1	TRUE	0	0.361581853145347	1		808	915	SUCCESS
APC	324	MSKCC	GRCh37	5	112175466	112175466	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786204170	NA	P-0042166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	87	423	1	ENST00000257430.4:c.4175C>A	p.Ser1392Ter	p.S1392*	ENST00000257430	NM_000038.5	1392	tCa/tAa	16/16	1	2	FACETS	0.824	0.731	0.923	0.824	0.731	0.923	CLONAL	1	TRUE	1	0.361581853145347	2		424	584	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969884	81969884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199840870	NA	P-0042166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	186	749	0	ENST00000359376.3:c.2953G>A	p.Val985Ile	p.V985I	ENST00000359376	NM_002661.3	985	Gtc/Atc	27/33	1	2	FACETS	0.94	0.867	1	0.94	0.867	1	CLONAL	1	TRUE	1	0.361581853145347	2		749	1095	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581171	48581171	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0042166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	130	392	0	ENST00000342988.3:c.475A>T	p.Lys159Ter	p.K159*	ENST00000342988	NM_005359.5	159	Aag/Tag	5/12	0.361581853145347	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.361581853145347	1		392	566	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194800	30194800	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	141	707	0	ENST00000331968.5:c.345G>T	p.Gln115His	p.Q115H	ENST00000331968	NM_002742.2	115	caG/caT	2/18	1	2	FACETS	0.797	0.726	0.873	0.797	0.726	0.873	SUBCLONAL	1	TRUE	1	0.361581853145347	2		707	978	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350554	15350554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199839337	NA	P-0042166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	195	884	0	ENST00000263377.2:c.3361C>T	p.Arg1121Cys	p.R1121C	ENST00000263377	NM_058243.2	1121	Cgc/Tgc	16/20	1	2	FACETS	0.857	0.791	0.925	0.857	0.791	0.925	CLONAL	1	TRUE	1	0.361581853145347	2		884	1259	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468095	50468095	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	127	613	0	ENST00000331340.3:c.1330A>T	p.Asn444Tyr	p.N444Y	ENST00000331340	NM_006060.4	444	Aac/Tac	8/8	0.332753246210781	3	FACETS	0.9	0.814	0.99	0.45	0.407	0.495	CLONAL	1	TRUE	1	0.361581853145347	3		613	922	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542702	141542702	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1271	109	683	0	ENST00000220592.5:c.2284C>T	p.Pro762Ser	p.P762S	ENST00000220592	NM_012154.3	762	Cct/Tct	18/19	0.361581853145347	3	FACETS	0.516	0.461	0.574	0.258	0.23	0.287	SUBCLONAL	1	TRUE	1	0.361581853145347	3		683	1380	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	70	348	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.187417222249062	2		349	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0042176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	100	1003	1	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	1	2	FACETS	0.865	0.771	0.967	0.865	0.771	0.967	CLONAL	1	TRUE	1	0.187417222249062	2		1004	1233	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298776	15298776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755398328	NA	P-0042176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	114	889	3	ENST00000263388.2:c.1522G>A	p.Val508Met	p.V508M	ENST00000263388	NM_000435.2	508	Gtg/Atg	10/33	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.187417222249062	2		892	1165	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578530	7578530	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs267605077	NA	P-0042176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1274	129	1037	0	ENST00000269305.4:c.400T>C	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	Ttt/Ctt	5/11	1	2	FACETS	0.981	0.887	1	0.981	0.887	1	CLONAL	1	TRUE	1	0.187417222249062	2		1037	1403	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953897	17953897	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	91	835	0	ENST00000458235.1:c.505G>T	p.Asp169Tyr	p.D169Y	ENST00000458235	NM_000215.3	169	Gac/Tac	5/24	1	2	FACETS	0.851	0.753	0.956	0.851	0.753	0.956	CLONAL	1	TRUE	1	0.187417222249062	2		835	1141	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162224	47162224	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	79	578	0	ENST00000409792.3:c.3902A>T	p.Gln1301Leu	p.Q1301L	ENST00000409792	NM_014159.6	1301	cAa/cTa	3/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.187417222249062	2		578	676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0042201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	233	763	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.399591708863161	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.399591708863161	1		763	873	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069931	5069931	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0042201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	30	196	0	ENST00000381652.3:c.1520C>G	p.Ser507Ter	p.S507*	ENST00000381652	NM_004972.3	507	tCa/tGa	12/25	0.399591708863161	1	FACETS	0.586	0.476	0.709	0.586	0.476	0.709	SUBCLONAL	1	TRUE	0	0.399591708863161	1		196	205	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55143626	55143626	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	40	335	0	ENST00000257290.5:c.1858C>A	p.Pro620Thr	p.P620T	ENST00000257290	NM_006206.4	620	Cct/Act	13/23	1	2	FACETS	0.358	0.296	0.426	0.358	0.296	0.426	SUBCLONAL	1	TRUE	1	0.399591708863161	2		335	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574026	7574026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1286563734	NA	P-0042201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	71	643	0	ENST00000269305.4:c.1001G>A	p.Gly334Glu	p.G334E	ENST00000269305	NM_001126112.2	334	gGg/gAg	10/11	0.399591708863161	1	FACETS	0.359	0.313	0.41	0.359	0.313	0.41	SUBCLONAL	1	TRUE	0	0.399591708863161	1		643	791	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981559	201981559	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	81	906	0	ENST00000359651.3:c.473C>G	p.Pro158Arg	p.P158R	ENST00000359651		158	cCc/cGc	3/8	0.399591708863161	1	FACETS	0.389	0.342	0.44	0.389	0.342	0.44	SUBCLONAL	1	TRUE	0	0.399591708863161	1		906	833	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440392	49440393	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0042201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	54	714	1	ENST00000301067.7:c.4417_4418delinsCT	p.Trp1473Leu	p.W1473L	ENST00000301067	NM_003482.3	1473	TGg/CTg	15/54	0.346381497146438	2	FACETS	0.313	0.266	0.365	0.157	0.133	0.183	SUBCLONAL	1	TRUE	0	0.399591708863161	2		715	863	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448103	49448103	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0042201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	50	529	0	ENST00000301067.7:c.497C>G	p.Ser166Ter	p.S166*	ENST00000301067	NM_003482.3	166	tCa/tGa	4/54	0.346381497146438	2	FACETS	0.406	0.344	0.475	0.203	0.172	0.238	SUBCLONAL	1	TRUE	0	0.399591708863161	2		529	616	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118779	115118779	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs989654838	NA	P-0042201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	85	541	1	ENST00000257566.3:c.562C>T	p.Pro188Ser	p.P188S	ENST00000257566	NM_016569.3	188	Ccg/Tcg	2/8	0.346381497146438	2	FACETS	0.544	0.48	0.612	0.272	0.24	0.306	SUBCLONAL	1	TRUE	0	0.399591708863161	2		542	782	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975485	26975485	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0042201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	26	313	0	ENST00000381527.3:c.1110+1G>C		p.X370_splice	ENST00000381527	NM_001260.1	370			0.399591708863161	1	FACETS	0.279	0.221	0.346	0.279	0.221	0.346	SUBCLONAL	1	TRUE	0	0.399591708863161	1		313	373	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508438	29508438	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs1057518360	NA	P-0042201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	90	168	2	ENST00000356175.3:c.587-2A>T		p.X196_splice	ENST00000356175	NM_000267.3	196			0.399591708863161	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.399591708863161	1		170	285	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561154	9561154	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	31	416	0	ENST00000353224.5:c.628A>G	p.Ser210Gly	p.S210G	ENST00000353224	NM_177990.2	210	Agt/Ggt	4/10	1	2	FACETS	0.318	0.256	0.388	0.318	0.256	0.388	SUBCLONAL	1	TRUE	1	0.399591708863161	2		416	488	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827957	40827957	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	58	545	0	ENST00000373198.4:c.2471A>T	p.Asp824Val	p.D824V	ENST00000373198	NM_133170.3	824	gAc/gTc	17/32	1	2	FACETS	0.344	0.295	0.399	0.344	0.295	0.399	SUBCLONAL	1	TRUE	1	0.399591708863161	2		545	843	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143181692	143181692	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	45	368	0	ENST00000262992.4:c.641C>A	p.Ala214Asp	p.A214D	ENST00000262992	NM_001101669.1	214	gCc/gAc	9/24	1	2	FACETS	0.326	0.273	0.385	0.326	0.273	0.385	SUBCLONAL	1	TRUE	1	0.399591708863161	2		368	690	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180954	32180954	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	52	704	0	ENST00000375023.3:c.2396G>C	p.Gly799Ala	p.G799A	ENST00000375023	NM_004557.3	799	gGc/gCc	15/30	0.36937382255122	3	FACETS	0.311	0.263	0.363	0.104	0.087	0.121	SUBCLONAL	1	TRUE	0	0.399591708863161	3		704	1005	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877164	151877164	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	197	389	1	ENST00000262189.6:c.7197G>T	p.Lys2399Asn	p.K2399N	ENST00000262189	NM_170606.2	2399	aaG/aaT	37/59	0.10631322473471	6	FACETS	1	0.968	1	0.719	0.666	0.772	INDETERMINATE	2	TRUE	3	0.399591708863161	6		390	823	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845345	76845345	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	22	212	0	ENST00000373344.5:c.6176G>T	p.Arg2059Met	p.R2059M	ENST00000373344	NM_000489.3	2059	aGg/aTg	27/35	0.399591708863161	1	FACETS	0.233	0.18	0.295	0.233	0.18	0.295	SUBCLONAL	1	TRUE	0	0.399591708863161	1		212	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0042206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	828	704	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.905740157964434	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.905740157964434	3		704	864	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	323	348	1				ENST00000310581	NM_198253.2	-/1132			0.856258650029227	4	FACETS	0.935	0.889	0.981	0.935	0.889	0.981	CLONAL	2	TRUE	2	0.905740157964434	4		349	727	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947596	48947596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1566196458	NA	P-0042206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	81	284	0	ENST00000267163.4:c.1183C>T	p.Gln395Ter	p.Q395*	ENST00000267163	NM_000321.2	395	Caa/Taa	12/27	0.905740157964434	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.905740157964434	1		284	91	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792545	33792545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746895795	NA	P-0042206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	106	198	1	ENST00000498907.2:c.776C>T	p.Ala259Val	p.A259V	ENST00000498907	NM_004364.3	259	gCg/gTg	1/1	0.893801818960593	3	FACETS	1	0.981	1	0.651	0.594	0.71	CLONAL	1	TRUE	1	0.905740157964434	3		199	261	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16090003	16090003	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0042206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	283	188	0	ENST00000268712.3:c.109-2A>G		p.X37_splice	ENST00000268712	NM_006311.3	37			0.905740157964434	3	FACETS	0.992	0.972	1	1	0.997	1	CLONAL	3	TRUE	1	0.905740157964434	3		188	305	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711932	89711945	+	frameshift_variant	Frame_Shift_Del	DEL	AATCATCTGGATTA	AATCATCTGGATTA	-	novel	NA	P-0042206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	109	395	0	ENST00000371953.3:c.550_563del	p.Asn184Ter	p.N184*	ENST00000371953	NM_000314.4	184	AATCATCTGGATTAt/t	6/9	0.905740157964434	2	FACETS	0.86	0.812	0.904	0.86	0.812	0.904	CLONAL	2	TRUE	0	0.905740157964434	2		395	140	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371667	225371667	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	267	453	0	ENST00000264414.4:c.937A>G	p.Met313Val	p.M313V	ENST00000264414	NM_003590.4	313	Atg/Gtg	7/16	0.905740157964434	2	FACETS	0.993	0.968	1	0.993	0.968	1	CLONAL	2	TRUE	0	0.905740157964434	2		453	297	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288533	33288533	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	168	388	0	ENST00000374542.5:c.1019T>C	p.Leu340Pro	p.L340P	ENST00000374542	NM_001141970.1	340	cTc/cCc	3/8	0.905740157964434	3	FACETS	0.934	0.863	1	0.467	0.431	0.504	CLONAL	1	TRUE	1	0.905740157964434	3		388	577	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975515	13975846	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATAGGCACTACCCAGGGGACAAAAGAAGAGAGAACATTTCTTTCTTTGGAGCAATTTTTTAAAAAAGTTTCTAATCCAAAGGAAGAAAAGATATTTTAGACTTAAGTCAAATGGAAATGAAAACTTTGTTGTTGCTATTGTTGTTTAAATCCAGAACAGATAAACTTCAAAATCACAACACCCTTAAACAGAAAATAGGATGATTAATGCAAAACCTTGTAACAGAACAAATATTAAATGTGTATTTTTAATGCATATACAAACAACTTAGTACAGGGAAAATTACGTCCAAAAAAGCAGTGGTATTTTTTCCATCTATTCTTGATATATCT	ATAGGCACTACCCAGGGGACAAAAGAAGAGAGAACATTTCTTTCTTTGGAGCAATTTTTTAAAAAAGTTTCTAATCCAAAGGAAGAAAAGATATTTTAGACTTAAGTCAAATGGAAATGAAAACTTTGTTGTTGCTATTGTTGTTTAAATCCAGAACAGATAAACTTCAAAATCACAACACCCTTAAACAGAAAATAGGATGATTAATGCAAAACCTTGTAACAGAACAAATATTAAATGTGTATTTTTAATGCATATACAAACAACTTAGTACAGGGAAAATTACGTCCAAAAAAGCAGTGGTATTTTTTCCATCTATTCTTGATATATCT	-	novel	NA	P-0042206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	272	259	1	ENST00000405192.2:c.366-325_372del		p.X122_splice	ENST00000405192	NM_001163147.1	122		7/12	0.905740157964434	6	FACETS	1	0.984	1	0.813	0.773	0.854	CLONAL	3	TRUE	2	0.905740157964434	6		260	519	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955548	90955548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	145	328	0	ENST00000265433.3:c.2117C>T	p.Ser706Leu	p.S706L	ENST00000265433	NM_002485.4	706	tCa/tTa	14/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.905740157964434	2		328	298	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855594	45855597	+	missense_variant	Missense_Mutation	ONP	TCCC	TCCC	ACCA	novel	NA	P-0042206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	284	727	1	ENST00000391945.4:c.2060_2063delinsTGGT	p.Gly687_Asp688delinsValVal	p.G687_D688delinsVV	ENST00000391945	NM_000400.3	687	gGGGAc/gTGGTc	22/23	0.893801818960593	3	FACETS	1	0.944	1	0.501	0.472	0.531	CLONAL	1	TRUE	1	0.905740157964434	3		728	909	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0042223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	75	443	9	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.855	0.751	0.968	0.855	0.751	0.968	CLONAL	1	TRUE	1	0.32	2		452	548	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0042223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	42	399	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.3	1	FACETS	0.98	0.826	1	0.98	0.826	1	CLONAL	1	TRUE	0	0.32	1		399	225	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356134	66356134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756357402	NA	P-0042223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	80	510	1	ENST00000273854.3:c.1363C>T	p.Arg455Trp	p.R455W	ENST00000273854	NM_004439.5	455	Cgg/Tgg	5/18	1	2	FACETS	0.859	0.757	0.968	0.859	0.757	0.968	CLONAL	1	TRUE	1	0.32	2		511	582	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953041	2953041	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149857605	NA	P-0042223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	154	886	0	ENST00000396946.4:c.2899C>T	p.Arg967Cys	p.R967C	ENST00000396946	NM_032415.4	967	Cgc/Tgc	22/25	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.32	2		886	954	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720803	89720804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0042223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	36	281	0	ENST00000371953.3:c.955_956dup	p.Thr321Ter	p.T321*	ENST00000371953	NM_000314.4	318	-/AC	8/9	1	2	FACETS	0.753	0.621	0.899	0.753	0.621	0.899	SUBCLONAL	1	TRUE	1	0.32	2		281	299	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584817	48584826	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GGACATTACT	GGACATTACT	-	novel	NA	P-0042223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	66	347	0	ENST00000342988.3:c.896_904+1del		p.GHYW299fs	ENST00000342988	NM_005359.5	299	GGACATTACTgg/gg	7/12	0.3	1	FACETS	0.888	0.775	1	0.888	0.775	1	CLONAL	1	TRUE	0	0.32	1		347	390	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204878	128204878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	155	971	2	ENST00000341105.2:c.563C>T	p.Thr188Met	p.T188M	ENST00000341105	NM_032638.4	188	aCg/aTg	3/6	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.32	2		973	962	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965706	93965706	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	58	369	0	ENST00000369303.4:c.2222G>T	p.Gly741Val	p.G741V	ENST00000369303	NM_004440.3	741	gGa/gTa	13/17	1	2	FACETS	0.884	0.762	1	0.884	0.762	1	CLONAL	1	TRUE	1	0.32	2		369	410	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759865	133759865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	107	846	0	ENST00000318560.5:c.2188G>A	p.Glu730Lys	p.E730K	ENST00000318560	NM_005157.4	730	Gag/Aag	11/11	1	2	FACETS	0.874	0.784	0.97	0.874	0.784	0.97	CLONAL	1	TRUE	1	0.32	2		846	765	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0042227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	309	554	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.948	0.901	0.996	0.948	0.901	0.996	CLONAL	1	TRUE	1	0.95	2		554	686	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0042227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	313	515	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.876	0.831	0.922	0.876	0.831	0.922	CLONAL	1	TRUE	1	0.95	2		515	752	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473722	67473722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs794727798	NA	P-0042227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	384	708	0	ENST00000327367.4:c.802C>T	p.Arg268Cys	p.R268C	ENST00000327367	NM_005902.3	268	Cgc/Tgc	6/9	1	2	FACETS	0.953	0.911	0.996	0.953	0.911	0.996	CLONAL	1	TRUE	1	0.95	2		708	848	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129169	64129169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746466314	NA	P-0042227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	551	993	5	ENST00000334205.4:c.707C>T	p.Ser236Leu	p.S236L	ENST00000334205	NM_003942.2	236	tCg/tTg	7/17	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.95	2		998	1088	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443617	49443617	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs727503987	NA	P-0042227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	429	787	1	ENST00000301067.7:c.3754C>T	p.Arg1252Ter	p.R1252*	ENST00000301067	NM_003482.3	1252	Cga/Tga	11/54	1	2	FACETS	0.951	0.91	0.991	0.951	0.91	0.991	CLONAL	1	TRUE	1	0.95	2		788	950	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426976	49426979	+	frameshift_variant	Frame_Shift_Del	DEL	GGGA	GGGA	-	novel	NA	P-0042227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	382	769	0	ENST00000301067.7:c.11509_11512del	p.Ser3837ProfsTer43	p.S3837Pfs*43	ENST00000301067	NM_003482.3	3837	TCCCcc/cc	39/54	1	2	FACETS	0.907	0.865	0.949	0.907	0.865	0.949	CLONAL	1	TRUE	1	0.95	2		769	887	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861656	59861656	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	230	431	0	ENST00000259008.2:c.1603G>C	p.Asp535His	p.D535H	ENST00000259008	NM_032043.2	535	Gac/Cac	11/20	1	2	FACETS	0.944	0.889	0.999	0.944	0.889	0.999	CLONAL	1	TRUE	1	0.95	2		431	513	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223167	36223168	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0042227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	679	1121	0	ENST00000222270.7:c.5720dup	p.Ala1908SerfsTer64	p.A1908Sfs*64	ENST00000222270	NM_014727.1	1906	ttc/ttCc	28/37	1	2	FACETS	0.952	0.92	0.985	0.952	0.92	0.985	CLONAL	1	TRUE	1	0.95	2		1121	1501	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961583	54961583	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	224	425	0	ENST00000312783.6:c.49G>T	p.Ala17Ser	p.A17S	ENST00000312783	NM_198436.1	17	Gct/Tct	4/10	1	2	FACETS	0.934	0.879	0.989	0.934	0.879	0.989	CLONAL	1	TRUE	1	0.95	2		425	505	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836279	151836279	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	363	553	0	ENST00000262189.6:c.14526del	p.Ala4844GlnfsTer17	p.A4844Qfs*17	ENST00000262189	NM_170606.2	4842	ggG/gg	57/59	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.95	2		553	748	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845541	151845541	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	414	691	0	ENST00000262189.6:c.13471G>C	p.Ala4491Pro	p.A4491P	ENST00000262189	NM_170606.2	4491	Gca/Cca	52/59	1	2	FACETS	0.976	0.934	1	0.976	0.934	1	CLONAL	1	TRUE	1	0.95	2		691	893	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0042237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	251	308	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.800715649644874	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.80127809600975	2		308	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579321	7579322	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs587780067	NA	P-0042237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	312	724	0	ENST00000269305.4:c.365_366del	p.Val122AspfsTer26	p.V122Dfs*26	ENST00000269305	NM_001126112.2	122	gTG/g	4/11	0.80127809600975	2	FACETS	0.918	0.886	0.95	0.918	0.886	0.95	CLONAL	2	TRUE	0	0.80127809600975	2		724	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0042247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	201	649	2	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.700404981566044	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.700404981566044	1		651	370	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575232	48575232	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0042247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	97	152	0	ENST00000342988.3:c.424+2T>A		p.X142_splice	ENST00000342988	NM_005359.5	142			0.649964295927936	2	FACETS	0.923	0.856	0.988	0.923	0.856	0.988	CLONAL	2	TRUE	0	0.700404981566044	2		152	150	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719818	52719818	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	174	377	0	ENST00000322088.6:c.1030G>T	p.Ala344Ser	p.A344S	ENST00000322088	NM_014225.5	344	Gcc/Tcc	9/15	1	2	FACETS	0.9	0.834	0.968	0.9	0.834	0.968	CLONAL	1	TRUE	1	0.700404981566044	2		377	552	SUCCESS
APC	324	MSKCC	GRCh37	5	112175191	112175193	+	frameshift_variant	Frame_Shift_Del	DEL	TAC	TAC	AG	novel	NA	P-0042247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	43	83	0	ENST00000257430.4:c.3900_3902delinsAG	p.Asn1300LysfsTer5	p.N1300Kfs*5	ENST00000257430	NM_000038.5	1300	aaTACc/aaAGc	16/16	0.700404981566044	1	FACETS	0.877	0.763	0.992	0.877	0.763	0.992	CLONAL	1	TRUE	0	0.700404981566044	1		83	91	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	52	227	0	ENST00000288602.6:c.1742A>T	p.Asn581Ile	p.N581I	ENST00000288602	NM_004333.4	581	aAt/aTt	15/18	0.543300669219923	3	FACETS	1	0.881	1	0.514	0.442	0.591	CLONAL	1	TRUE	1	0.543300669219923	3		227	237	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378639	25378639	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	52	372	0	ENST00000311936.3:c.359T>C	p.Leu120Ser	p.L120S	ENST00000311936	NM_004985.3	120	tTg/tCg	4/5	1	2	FACETS	0.832	0.716	0.956	0.832	0.716	0.956	CLONAL	1	TRUE	1	0.543300669219923	2		372	230	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518271	187518272	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0042262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	56	282	0	ENST00000441802.2:c.12422_12423insAT	p.Cys4142SerfsTer65	p.C4142Sfs*65	ENST00000441802	NM_005245.3	4141	ctc/ctATc	25/27	1	2	FACETS	0.924	0.802	1	0.924	0.802	1	CLONAL	1	TRUE	1	0.543300669219923	2		282	223	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916947	178916947	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	52	337	0	ENST00000263967.3:c.334A>T	p.Ile112Phe	p.I112F	ENST00000263967	NM_006218.2	112	Atc/Ttc	2/21	1	2	FACETS	0.566	0.481	0.659	0.566	0.481	0.659	SUBCLONAL	1	TRUE	1	0.320779859054778	2		337	573	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846040	68846040	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	76	534	0	ENST00000261769.5:c.1013del	p.Phe338SerfsTer18	p.F338Sfs*18	ENST00000261769	NM_004360.3	337	agT/ag	8/16	1	2	FACETS	0.731	0.641	0.828	0.731	0.641	0.828	SUBCLONAL	1	TRUE	1	0.320779859054778	2		534	648	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164805	36164833	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGAGTAGGTGAAGGCGCCTGGATAGTG	GGGGAGTAGGTGAAGGCGCCTGGATAGTG	T	novel	NA	P-0042272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	93	747	0	ENST00000300305.3:c.1042_1070delinsA	p.His348ArgfsTer237	p.H348Rfs*237	ENST00000300305		348	CACTATCCAGGCGCCTTCACCTACTCCCCg/Ag	8/8	1	2	FACETS	0.63	0.559	0.705	0.63	0.559	0.705	SUBCLONAL	1	TRUE	1	0.320779859054778	2		747	921	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0042338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	159	308	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.820429569751492	2		308	381	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572234	64572234	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	354	537	5	ENST00000312049.6:c.1405G>T	p.Glu469Ter	p.E469*	ENST00000312049	NM_130799.2	469	Gag/Tag	10/10	0.820429569751492	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.820429569751492	1		542	473	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630260	187630260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	253	499	8	ENST00000441802.2:c.722C>T	p.Ala241Val	p.A241V	ENST00000441802	NM_005245.3	241	gCc/gTc	2/27	1	2	FACETS	0.914	0.86	0.968	0.914	0.86	0.968	CLONAL	1	TRUE	1	0.820429569751492	2		507	675	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	176	348	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.967	0.899	1	0.967	0.899	1	CLONAL	1	TRUE	1	0.76	2		349	479	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0042376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	272	515	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.76	2		515	693	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415856	49415858	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	rs587783704	NA	P-0042376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	172	368	1	ENST00000301067.7:c.16489_16491del	p.Ile5497del	p.I5497del	ENST00000301067	NM_003482.3	5497	ATC/-	53/54	1	2	FACETS	0.848	0.785	0.912	0.848	0.785	0.912	CLONAL	1	TRUE	1	0.76	2		369	534	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422612	49422612	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	268	0	0	ENST00000301067.7:c.14381A>G	p.Lys4794Arg	p.K4794R	ENST00000301067	NM_003482.3	4794	aAg/aGg	45/54	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.76	2		0	688	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156618	2156618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	267	0	0	ENST00000434045.2:c.304G>A	p.Gly102Arg	p.G102R	ENST00000434045	NM_001127598.1	102	Ggg/Agg	3/5	1	2	FACETS	0.995	0.939	1	0.995	0.939	1	CLONAL	1	TRUE	1	0.76	2		0	706	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008995	152008996	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0042376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	179	0	0	ENST00000262189.6:c.626dup	p.Ser210LysfsTer10	p.S210Kfs*10	ENST00000262189	NM_170606.2	209	gta/gtTa	5/59	1	2	FACETS	0.844	0.783	0.907	0.844	0.783	0.907	CLONAL	1	TRUE	1	0.76	2		0	558	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200023	123200023	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0042376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	86	0	0	ENST00000218089.9:c.2097-2A>T		p.X699_splice	ENST00000218089	NM_001042749.1	699			1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.76	2		0	221	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183748	10183748	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs869025619	NA	P-0042376-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	85	653	3	ENST00000256474.2:c.217C>T	p.Gln73Ter	p.Q73*	ENST00000256474	NM_000551.3	73	Cag/Tag	1/3	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.23	2		656	516	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682383	52682383	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042376-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	52	382	0	ENST00000394830.3:c.790G>T	p.Glu264Ter	p.E264*	ENST00000394830	NM_018313.4	264	Gag/Tag	8/30	0.260488905403451	1	FACETS	0.839	0.715	0.975	0.839	0.715	0.975	CLONAL	1	TRUE	0	0.23	1		382	477	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845229	151845229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	80	474	0	ENST00000262189.6:c.13783C>T	p.Arg4595Cys	p.R4595C	ENST00000262189	NM_170606.2	4595	Cgc/Tgc	52/59	0.129897358009709	4	FACETS	1	0.91	1	1	0.91	1	CLONAL	2	FALSE	2	0.166442949190736	4		474	540	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828850	72828884	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGAGCATGAAAGGCATATCCAGGGACCTGTCCA	AAAGAGCATGAAAGGCATATCCAGGGACCTGTCCA	-	novel	NA	P-0042378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	31	572	0	ENST00000268489.5:c.7697_7731del	p.Leu2566Ter	p.L2566*	ENST00000268489	NM_006885.3	2566	tTGGACAGGTCCCTGGATATGCCTTTCATGCTCTTT/t	9/10	1	2	FACETS	0.828	0.669	1	0.828	0.669	1	CLONAL	1	FALSE	1	0.166442949190736	2		572	450	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732957	30732957	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs727504421	NA	P-0042378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	82	418	0	ENST00000295754.5:c.1570G>T	p.Asp524Tyr	p.D524Y	ENST00000295754	NM_003242.5	524	Gac/Tac	7/7	1	2	FACETS	0.94	0.831	1	1	0.983	1	CLONAL	2	FALSE	1	0.166442949190736	2		418	524	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	64	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	FALSE	1	0.206269982969722	2		539	561	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164375	47164378	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	novel	NA	P-0042388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	45	304	0	ENST00000409792.3:c.1748_1751del	p.Lys583SerfsTer17	p.K583Sfs*17	ENST00000409792	NM_014159.6	583	aAACAg/ag	3/21	1	2	FACETS	0.98	0.825	1	0.98	0.825	1	CLONAL	1	FALSE	1	0.206269982969722	2		304	445	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604673	48604673	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060500738	NA	P-0042388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	56	387	0	ENST00000342988.3:c.1495T>C	p.Cys499Arg	p.C499R	ENST00000342988	NM_005359.5	499	Tgc/Cgc	12/12	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	1	0.206269982969722	2		387	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520008	NA	P-0042388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	86	650	0	ENST00000269305.4:c.613T>G	p.Tyr205Asp	p.Y205D	ENST00000269305	NM_001126112.2	205	Tat/Gat	6/11	0.206269982969722	1	FACETS	0.928	0.82	1	0.928	0.82	1	CLONAL	1	FALSE	0	0.206269982969722	1		650	806	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119762	70119763	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGGGC	novel	NA	P-0042388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	55	656	0	ENST00000245479.2:c.766_770dup	p.Pro258GlyfsTer23	p.P258Gfs*23	ENST00000245479	NM_000346.3	255	gag/gaGGGGCg	3/3	1	2	FACETS	0.706	0.603	0.82	0.706	0.603	0.82	SUBCLONAL	1	FALSE	1	0.206269982969722	2		656	755	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	79	348	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.888	0.795	0.985	0.888	0.795	0.985	CLONAL	1	TRUE	1	0.804655904259701	2		349	221	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409147	4409147	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587777622	NA	P-0042393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	187	610	0	ENST00000261254.3:c.842C>G	p.Pro281Arg	p.P281R	ENST00000261254	NM_001759.3	281	cCt/cGt	5/5	1	2	FACETS	0.723	0.671	0.776	0.723	0.671	0.776	SUBCLONAL	1	TRUE	1	0.804655904259701	2		610	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0042394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	363	621	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.906110661269006	1	FACETS	0.878	0.849	0.907	0.878	0.849	0.907	CLONAL	1	TRUE	0	0.906110661269006	1		622	499	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156076	119156076	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	378	712	0	ENST00000264033.4:c.1741G>C	p.Val581Leu	p.V581L	ENST00000264033	NM_005188.3	581	Gtc/Ctc	11/16	1	2	FACETS	0.928	0.885	0.972	0.928	0.885	0.972	CLONAL	1	TRUE	1	0.906110661269006	2		712	899	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43699735	43699735	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137879443	NA	P-0042475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	358	504	1	ENST00000382044.4:c.5780C>T	p.Thr1927Met	p.T1927M	ENST00000382044	NM_001141980.1	1927	aCg/aTg	28/28	0.865323010846678	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.865323010846678	1		505	467	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858944	57858944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	559	819	3	ENST00000228682.2:c.440C>T	p.Pro147Leu	p.P147L	ENST00000228682	NM_005269.2	147	cCt/cTt	5/12	1	2	FACETS	0.984	0.947	1	0.984	0.947	1	CLONAL	1	TRUE	1	0.865323010846678	2		822	1313	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0042488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	141	616	1	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	1	2	FACETS	0.964	0.892	1	1	0.994	1	CLONAL	8	FALSE	1	0.114301659076002	2		617	320	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0042488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	165	721	8	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.114301605188608	0	FACETS	0.961	0.895	1			1	CLONAL	7	FALSE	0	0.114301659076002	0		729	380	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100069	27100069	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0042488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	182	813	0	ENST00000324856.7:c.3867-2A>G		p.X1289_splice	ENST00000324856	NM_006015.4	1289			0.114301605188608	0	FACETS	0.941	0.879	1			1	CLONAL	7	FALSE	0	0.114301659076002	0		813	428	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106592	27106592	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	36	822	0	ENST00000324856.7:c.6203C>T	p.Ser2068Leu	p.S2068L	ENST00000324856	NM_006015.4	2068	tCg/tTg	20/20	0.114301605188608	0	FACETS	1	0.873	1			1	CLONAL	1	FALSE	0	0.114301659076002	0		822	517	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106727	27106727	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	192	747	2	ENST00000324856.7:c.6341del	p.Pro2114ArgfsTer21	p.P2114Rfs*21	ENST00000324856	NM_006015.4	2113	tCc/tc	20/20	0.114301605188608	0	FACETS	0.973	0.911	1			1	CLONAL	7	FALSE	0	0.114301659076002	0		749	437	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	184	609	1	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	0.114301605188608	0	FACETS	0.897	0.837	0.958			1	CLONAL	7	FALSE	0	0.114301659076002	0		610	454	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838362	156838362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372041586	NA	P-0042488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	67	1093	0	ENST00000524377.1:c.640C>T	p.Arg214Trp	p.R214W	ENST00000524377	NM_002529.3	214	Cgg/Tgg	6/17	0.114301659076002	14	FACETS	1	0.868	1	0.143	0.124	0.164	CLONAL	2	FALSE	0	0.114301659076002	14		1093	987	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692793	89692793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	50	411	0	ENST00000371953.3:c.277C>T	p.His93Tyr	p.H93Y	ENST00000371953	NM_000314.4	93	Cat/Tat	5/9	1	2	FACETS	0.999	0.867	1	1	0.984	1	CLONAL	6	FALSE	1	0.114301659076002	2		411	146	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0042488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	120	680	1	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	1	0.952	1	1	0.993	1	CLONAL	6	FALSE	1	0.114301659076002	2		681	330	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0042488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	109	459	1	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	1	0.926	1	1	0.993	1	CLONAL	8	FALSE	1	0.114301659076002	2		460	236	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195343	102195343	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	138	448	0	ENST00000263464.3:c.103A>G	p.Thr35Ala	p.T35A	ENST00000263464	NM_001165.4	35	Acg/Gcg	2/9	1	2	FACETS	1	0.953	1	1	0.994	1	CLONAL	8	FALSE	1	0.114301659076002	2		448	291	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195362	102195362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	131	432	1	ENST00000263464.3:c.122C>T	p.Ala41Val	p.A41V	ENST00000263464	NM_001165.4	41	gCt/gTt	2/9	1	2	FACETS	1	0.935	1	1	0.994	1	CLONAL	8	FALSE	1	0.114301659076002	2		433	283	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68301797	68301797	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	87	375	0	ENST00000487270.1:c.199G>A	p.Ala67Thr	p.A67T	ENST00000487270	NM_133509.3	67	Gct/Act	4/11	1	2	FACETS	0.956	0.869	1	1	0.991	1	CLONAL	9	FALSE	1	0.114301659076002	2		375	177	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900873	3900873	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	23	698	1	ENST00000262367.5:c.223C>T	p.Arg75Ter	p.R75*	ENST00000262367	NM_004380.2	75	Cga/Tga	2/31	1	2	FACETS	0.929	0.723	1	0.929	0.723	1	CLONAL	1	FALSE	1	0.114301659076002	2		699	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578369	7578369	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0042488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	122	747	0	ENST00000269305.4:c.559+2T>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.114301605188608	0	FACETS	0.888	0.815	0.963			1	CLONAL	7	FALSE	0	0.114301659076002	0		747	304	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661949	29661950	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs863224835	NA	P-0042488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	90	519	0	ENST00000356175.3:c.5844_5845del	p.Arg1949SerfsTer6	p.R1949Sfs*6	ENST00000356175	NM_000267.3	1948	cAA/c	39/57	0.114301605188608	0	FACETS	0.953	0.864	1			1	CLONAL	7	FALSE	0	0.114301659076002	0		519	209	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29662024	29662025	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0042488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	61	443	0	ENST00000356175.3:c.5923dup	p.Ile1975AsnfsTer13	p.I1975Nfs*13	ENST00000356175	NM_000267.3	1973	gca/gcAa	39/57	0.114301605188608	0	FACETS	0.997	0.881	1			1	CLONAL	6	FALSE	0	0.114301659076002	0		443	158	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120092	70120092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1201663893	NA	P-0042488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	12	59	0	ENST00000245479.2:c.1094C>T	p.Ala365Val	p.A365V	ENST00000245479	NM_000346.3	365	gCg/gTg	3/3	0.114301605188608	0	FACETS	0.969	0.739	1			1	CLONAL	8	FALSE	0	0.114301659076002	0		59	24	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599949	10599950	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0042488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	288	902	0	ENST00000171111.5:c.1626_1627del	p.Glu542AspfsTer31	p.E542Dfs*31	ENST00000171111	NM_203500.1	542	gaGAcg/gacg	5/6	1	2	FACETS	0.94	0.891	0.99	1	0.997	1	CLONAL	8	FALSE	1	0.114301659076002	2		902	670	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627722	14627722	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	39	721	2	ENST00000254322.2:c.348del	p.Phe116LeufsTer29	p.F116Lfs*29	ENST00000254322	NM_006145.1	116	ttT/tt	2/3	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	1	0.114301659076002	2		723	495	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617584	158617584	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	101	505	0	ENST00000263640.3:c.1072G>A	p.Ala358Thr	p.A358T	ENST00000263640	NM_001105.4	358	Gca/Aca	9/11	1	2	FACETS	1	0.928	1	1	0.992	1	CLONAL	7	FALSE	1	0.114301659076002	2		505	247	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098804	178098804	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	201	693	2	ENST00000397062.3:c.241G>T	p.Gly81Cys	p.G81C	ENST00000397062	NM_006164.4	81	Ggt/Tgt	2/5	1	2	FACETS	0.988	0.927	1	1	0.996	1	CLONAL	8	FALSE	1	0.114301659076002	2		695	445	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520218	9520218	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	140	571	0	ENST00000353224.5:c.2051A>G	p.Glu684Gly	p.E684G	ENST00000353224	NM_177990.2	684	gAg/gGg	10/10	0.114301605188608	0	FACETS	0.898	0.83	0.968			1	CLONAL	7	FALSE	0	0.114301659076002	0		571	345	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523280	9523280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769363113	NA	P-0042488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	167	665	1	ENST00000353224.5:c.1957C>T	p.Arg653Trp	p.R653W	ENST00000353224	NM_177990.2	653	Cgg/Tgg	9/10	0.114301605188608	0	FACETS	0.953	0.887	1			1	CLONAL	7	FALSE	0	0.114301659076002	0		666	388	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0042488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	46	357	8	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	0.114301605188608	0	FACETS	0.886	0.768	1			1	CLONAL	7	FALSE	0	0.114301659076002	0		365	115	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650398	12650398	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	77	531	1	ENST00000251849.4:c.448G>A	p.Ala150Thr	p.A150T	ENST00000251849	NM_002880.3	150	Gcc/Acc	5/17	1	2	FACETS	0.948	0.849	1	1	0.99	1	CLONAL	7	FALSE	1	0.114301659076002	2		532	203	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259335	89259335	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750779844	NA	P-0042488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	88	527	0	ENST00000336596.2:c.479G>A	p.Arg160His	p.R160H	ENST00000336596	NM_005233.5	160	cGt/cAt	3/17	1	2	FACETS	0.95	0.865	1	1	0.991	1	CLONAL	9	FALSE	1	0.114301659076002	2		527	180	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916726	178916726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772110575	NA	P-0042488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	50	398	0	ENST00000263967.3:c.113G>A	p.Arg38His	p.R38H	ENST00000263967	NM_006218.2	38	cGt/cAt	2/21	1	2	FACETS	0.954	0.831	1	1	0.984	1	CLONAL	7	FALSE	1	0.114301659076002	2		398	131	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0042488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	61	542	5	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.988	0.878	1	1	0.987	1	CLONAL	8	FALSE	1	0.114301659076002	2		547	135	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739873	41739873	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1261664857	NA	P-0042488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	133	517	0	ENST00000242208.4:c.100G>A	p.Asp34Asn	p.D34N	ENST00000242208	NM_002192.2	34	Gac/Aac	2/3	1	2	FACETS	0.973	0.899	1	1	0.994	1	CLONAL	8	FALSE	1	0.114301659076002	2		517	299	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238442	98238442	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0042488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	115	423	1	ENST00000331920.6:c.1603-1G>T		p.X535_splice	ENST00000331920	NM_000264.3	535			0.114301605188608	0	FACETS	0.884	0.812	0.956			1	CLONAL	8	FALSE	0	0.114301659076002	0		424	252	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22408273	22408273	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	148	278	0	ENST00000344548.3:c.164T>A	p.Leu55His	p.L55H	ENST00000344548	NM_001039802.1	55	cTt/cAt	4/7	0.251838086655759	3	FACETS	1	0.984	1	0.653	0.599	0.708	INDETERMINATE	1	TRUE	1	0.534065633049818	3		278	538	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28601414	28601414	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	242	693	0	ENST00000253063.3:c.1099T>A	p.Phe367Ile	p.F367I	ENST00000253063	NM_031459.4	367	Ttc/Atc	8/10	0.251838086655759	3	FACETS	1	0.984	1	0.579	0.541	0.618	INDETERMINATE	1	TRUE	1	0.534065633049818	3		693	992	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941187	36941187	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	275	801	0	ENST00000361632.4:c.152A>C	p.Asn51Thr	p.N51T	ENST00000361632		51	aAc/aCc	3/16	0.251838086655759	3	FACETS	1	0.99	1	0.626	0.587	0.665	INDETERMINATE	1	TRUE	1	0.534065633049818	3		801	1043	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165873	118165873	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs761490678	NA	P-0042507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	156	341	0	ENST00000369448.3:c.383A>G	p.Lys128Arg	p.K128R	ENST00000369448	NM_017709.3	128	aAa/aGa	2/2	0.251838086655759	3	FACETS	1	0.986	1	0.674	0.621	0.729	INDETERMINATE	1	TRUE	1	0.534065633049818	3		341	549	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743353	162743353	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	112	296	0	ENST00000367921.3:c.1823A>T	p.Lys608Ile	p.K608I	ENST00000367921	NM_006182.2	608	aAa/aTa	14/18	0.534065633049818	4	FACETS	0.905	0.815	1	0.302	0.271	0.334	CLONAL	1	TRUE	1	0.534065633049818	4		296	711	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012890	176012890	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	138	383	0	ENST00000367669.3:c.1486A>T	p.Ile496Phe	p.I496F	ENST00000367669	NM_022457.5	496	Att/Ttt	13/20	0.534065633049818	3	FACETS	0.879	0.801	0.961	0.439	0.4	0.481	CLONAL	1	TRUE	1	0.534065633049818	3		383	745	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056848	102056848	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	261	433	0	ENST00000282441.5:c.788T>C	p.Leu263Pro	p.L263P	ENST00000282441	NM_001130145.2	263	cTt/cCt	4/9	0.519108521938927	2	FACETS	0.882	0.835	0.929	0.882	0.835	0.929	CLONAL	2	TRUE	0	0.534065633049818	2		433	554	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344309	118344309	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	199	314	0	ENST00000534358.1:c.2435A>G	p.Lys812Arg	p.K812R	ENST00000534358	NM_005933.3	812	aAa/aGa	3/36	0.519108521938927	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.534065633049818	2		314	369	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658271	18658271	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	301	444	0	ENST00000266497.5:c.3076A>T	p.Thr1026Ser	p.T1026S	ENST00000266497		1026	Aca/Tca	22/31	0.320544127328619	5	FACETS	1	0.988	1	0.777	0.734	0.82	CLONAL	2	TRUE	2	0.534065633049818	5		444	871	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037966	49037966	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	366	296	0	ENST00000267163.4:c.2206C>T	p.Gln736Ter	p.Q736*	ENST00000267163	NM_000321.2	736	Cag/Tag	21/27	0.534065633049818	4	FACETS	0.878	0.843	0.911			1	CLONAL	4	TRUE	NA	0.534065633049818	4		296	599	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039240	49039240	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267603841	NA	P-0042507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	588	426	0	ENST00000267163.4:c.2318C>T	p.Ser773Phe	p.S773F	ENST00000267163	NM_000321.2	773	tCc/tTc	22/27	0.534065633049818	4	FACETS	0.945	0.917	0.972			1	CLONAL	4	TRUE	NA	0.534065633049818	4		426	894	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99452040	99452040	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	42	365	0	ENST00000268035.6:c.1374A>T	p.Glu458Asp	p.E458D	ENST00000268035	NM_000875.3	458	gaA/gaT	6/21	0.312467868180945	1	FACETS	0.267	0.223	0.317	0.267	0.223	0.317	INDETERMINATE	1	TRUE	0	0.534065633049818	1		365	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574009	7574009	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1131691005	NA	P-0042507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	459	699	0	ENST00000269305.4:c.1018del	p.Met340CysfsTer5	p.M340Cfs*5	ENST00000269305	NM_001126112.2	340	Atg/tg	10/11	0.392532506353569	2	FACETS	0.931	0.894	0.968	0.931	0.894	0.968	CLONAL	2	TRUE	0	0.534065633049818	2		699	923	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676182	29676182	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	67	318	0	ENST00000356175.3:c.7171A>G	p.Ile2391Val	p.I2391V	ENST00000356175	NM_000267.3	2391	Att/Gtt	48/57	0.369294471185392	3	FACETS	0.687	0.598	0.782	0.343	0.299	0.391	SUBCLONAL	1	TRUE	1	0.534065633049818	3		318	463	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41209145	41209145	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397509237	NA	P-0042507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	130	531	0	ENST00000357654.3:c.5201T>C	p.Phe1734Ser	p.F1734S	ENST00000357654	NM_007294.3	1734	tTt/tCt	19/23	1	2	FACETS	0.692	0.628	0.758	0.692	0.628	0.758	SUBCLONAL	1	TRUE	1	0.534065633049818	2		531	704	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600477	10600477	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	281	707	0	ENST00000171111.5:c.1378A>G	p.Arg460Gly	p.R460G	ENST00000171111	NM_203500.1	460	Agg/Ggg	4/6	0.534065633049818	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.534065633049818	1		707	689	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198269828	198269828	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	214	381	1	ENST00000335508.6:c.1511T>A	p.Ile504Asn	p.I504N	ENST00000335508	NM_012433.2	504	aTt/aAt	11/25	0.372111328032789	4	FACETS	0.81	0.755	0.866			1	CLONAL	2	TRUE	NA	0.534065633049818	4		382	759	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54959379	54959379	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	rs1022155570	NA	P-0042507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	130	269	0	ENST00000312783.6:c.321A>T	p.Glu107Asp	p.E107D	ENST00000312783	NM_198436.1	107	gaA/gaT	5/10	0.276088045452003	3	FACETS	0.897	0.824	0.971	0.598	0.549	0.647	INDETERMINATE	2	TRUE	0	0.534065633049818	3		269	344	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091839	29091839	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	179	407	1	ENST00000328354.6:c.1118A>T	p.Lys373Met	p.K373M	ENST00000328354	NM_007194.3	373	aAg/aTg	11/15	0.188450084582022	3	FACETS	0.781	0.725	0.838	0.781	0.725	0.838	INDETERMINATE	2	TRUE	1	0.534065633049818	3		408	544	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092923	29092923	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	142	442	0	ENST00000328354.6:c.1061del	p.Leu354TyrfsTer11	p.L354Yfs*11	ENST00000328354	NM_007194.3	354	tTa/ta	10/15	0.188450084582022	3	FACETS	1	0.955	1	0.534	0.488	0.582	INDETERMINATE	1	TRUE	1	0.534065633049818	3		442	631	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138409963	138409976	+	frameshift_variant	Frame_Shift_Del	DEL	GATATTGAGAAAGT	GATATTGAGAAAGT	-	novel	NA	P-0042507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	56	361	0	ENST00000289153.2:c.1902_1915del	p.Glu634AspfsTer11	p.E634Dfs*11	ENST00000289153	NM_006219.2	634	gaACTTTCTCAATATCtt/gatt	13/22	0.534065633049818	3	FACETS	0.558	0.479	0.645	0.279	0.239	0.323	SUBCLONAL	1	TRUE	1	0.534065633049818	3		361	476	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461542	138461542	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	287	444	0	ENST00000289153.2:c.479T>C	p.Ile160Thr	p.I160T	ENST00000289153	NM_006219.2	160	aTc/aCc	3/22	0.534065633049818	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	1	0.534065633049818	3		444	671	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204033	142204033	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	309	514	0	ENST00000350721.4:c.6170A>C	p.Lys2057Thr	p.K2057T	ENST00000350721	NM_001184.3	2057	aAa/aCa	36/47	0.534065633049818	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.534065633049818	3		514	706	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259767	142259767	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs762440684	NA	P-0042507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	74	355	0	ENST00000350721.4:c.3560A>G	p.Asp1187Gly	p.D1187G	ENST00000350721	NM_001184.3	1187	gAt/gGt	18/47	0.534065633049818	3	FACETS	0.577	0.506	0.655	0.289	0.253	0.328	SUBCLONAL	1	TRUE	1	0.534065633049818	3		355	608	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275272	142275272	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	281	451	0	ENST00000350721.4:c.2031C>G	p.Ile677Met	p.I677M	ENST00000350721	NM_001184.3	677	atC/atG	9/47	0.534065633049818	3	FACETS	0.938	0.886	0.99	0.938	0.886	0.99	CLONAL	2	TRUE	1	0.534065633049818	3		451	711	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612119	189612119	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	403	656	0	ENST00000264731.3:c.1871C>T	p.Ser624Phe	p.S624F	ENST00000264731	NM_003722.4	624	tCt/tTt	14/14	0.534065633049818	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.534065633049818	3		656	912	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629027	187629027	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1027080321	NA	P-0042507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	159	529	0	ENST00000441802.2:c.1955A>G	p.Asn652Ser	p.N652S	ENST00000441802	NM_005245.3	652	aAt/aGt	2/27	0.312467868180945	1	FACETS	0.861	0.795	0.929	0.861	0.795	0.929	INDETERMINATE	1	TRUE	0	0.534065633049818	1		529	507	SUCCESS
APC	324	MSKCC	GRCh37	5	112177914	112177914	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	147	328	0	ENST00000257430.4:c.6625del	p.Ile2209PhefsTer5	p.I2209Ffs*5	ENST00000257430	NM_000038.5	2208	gAa/ga	16/16	0.451178204270135	2	FACETS	1	0.989	1	0.728	0.673	0.784	CLONAL	1	TRUE	0	0.534065633049818	2		328	378	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681076	30681076	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs774373309	NA	P-0042507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	112	434	0	ENST00000376406.3:c.643A>G	p.Asn215Asp	p.N215D	ENST00000376406	NM_014641.2	215	Aat/Gat	5/15	0.534065633049818	3	FACETS	0.82	0.739	0.906	0.41	0.369	0.453	CLONAL	1	TRUE	1	0.534065633049818	3		434	648	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527318	157527318	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	81	255	0	ENST00000346085.5:c.5043A>T	p.Glu1681Asp	p.E1681D	ENST00000346085	NM_020732.3	1681	gaA/gaT	20/20	0.230424127609377	1	FACETS	0.625	0.554	0.699	0.625	0.554	0.699	INDETERMINATE	1	TRUE	0	0.534065633049818	1		255	356	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50358678	50358678	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	30	236	0	ENST00000331340.3:c.21A>C	p.Gln7His	p.Q7H	ENST00000331340	NM_006060.4	7	caA/caC	2/8	0.246525029341845	4	FACETS	0.473	0.382	0.578	0.118	0.095	0.145	INDETERMINATE	1	TRUE	0	0.534065633049818	4		236	364	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879089	151879089	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	213	571	0	ENST00000262189.6:c.5856A>T	p.Leu1952Phe	p.L1952F	ENST00000262189	NM_170606.2	1952	ttA/ttT	36/59	0.230424127609377	1	FACETS	0.957	0.895	1	0.957	0.895	1	INDETERMINATE	1	TRUE	0	0.534065633049818	1		571	611	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127933416	127933416	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	368	460	0	ENST00000373547.4:c.119A>G	p.Asn40Ser	p.N40S	ENST00000373547	NM_002721.4	40	aAt/aGt	2/7	0.483516656236418	2	FACETS	0.943	0.901	0.984	0.943	0.901	0.984	CLONAL	2	TRUE	0	0.534065633049818	2		460	731	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0042522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	41	308	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.644	0.539	0.759	0.644	0.539	0.759	SUBCLONAL	1	TRUE	1	0.439137891507962	2		308	290	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	25	607	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.307	0.241	0.382	0.307	0.241	0.382	SUBCLONAL	1	TRUE	1	0.439137891507962	2		607	371	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0042522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	88	368	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.682	0.605	0.763	0.682	0.605	0.763	SUBCLONAL	1	TRUE	1	0.439137891507962	2		371	588	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	49	594	2	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.388	0.328	0.454	0.388	0.328	0.454	SUBCLONAL	1	TRUE	1	0.439137891507962	2		596	575	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0042522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	163	403	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.439137891507962	2	FACETS	0.985	0.916	1	0.985	0.916	1	CLONAL	2	TRUE	0	0.439137891507962	2		403	377	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375193	31375194	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0042522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	144	763	0	ENST00000328111.2:c.596dup	p.Met200HisfsTer89	p.M200Hfs*89	ENST00000328111	NM_006892.3	197	cag/caGg	6/23	1	2	FACETS	0.921	0.842	1	0.921	0.842	1	CLONAL	1	TRUE	1	0.439137891507962	2		763	712	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672318	86672318	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	87	388	1	ENST00000274376.6:c.2120G>A	p.Arg707His	p.R707H	ENST00000274376	NM_002890.2	707	cGt/cAt	16/25	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.439137891507962	2		389	359	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466040	69466040	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	147	798	0	ENST00000227507.2:c.878T>G	p.Val293Gly	p.V293G	ENST00000227507	NM_053056.2	293	gTg/gGg	5/5	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.439137891507962	2		798	653	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916644	178916644	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	58	247	0	ENST00000263967.3:c.31T>C	p.Trp11Arg	p.W11R	ENST00000263967	NM_006218.2	11	Tgg/Cgg	2/21	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.439137891507962	2		247	246	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	123	532	0	ENST00000378444.4:c.4376A>C	p.Asn1459Thr	p.N1459T	ENST00000378444	NM_001123385.1	1459	aAt/aCt	10/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.439137891507962	2		532	503	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395000	395001	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0042522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	91	393	0	ENST00000380956.4:c.402dup	p.Gly135ArgfsTer77	p.G135Rfs*77	ENST00000380956	NM_001195286.1	132	-/A	3/9	1	2	FACETS	0.948	0.847	1	0.948	0.847	1	CLONAL	1	TRUE	1	0.439137891507962	2		393	437	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0042522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	85	621	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.439137891507962	2		621	365	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210704	5210704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766174955	NA	P-0042522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	117	669	1	ENST00000357368.4:c.5347C>T	p.Arg1783Trp	p.R1783W	ENST00000357368	NM_002850.3	1783	Cgg/Tgg	34/38	1	2	FACETS	0.924	0.835	1	0.924	0.835	1	CLONAL	1	TRUE	1	0.439137891507962	2		670	577	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089591	27089595	+	frameshift_variant	Frame_Shift_Del	DEL	TTATG	TTATG	-	novel	NA	P-0042522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	118	724	0	ENST00000324856.7:c.2547_2551del	p.Tyr850HisfsTer20	p.Y850Hfs*20	ENST00000324856	NM_006015.4	849	ccTTATGgc/ccgc	8/20	1	2	FACETS	0.97	0.879	1	0.97	0.879	1	CLONAL	1	TRUE	1	0.439137891507962	2		724	554	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100666	67100666	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	73	502	0	ENST00000412916.2:c.364A>C	p.Met122Leu	p.M122L	ENST00000412916		122	Atg/Ctg	4/6	1	2	FACETS	0.574	0.502	0.651	0.574	0.502	0.651	SUBCLONAL	1	TRUE	1	0.439137891507962	2		502	579	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830685	72830695	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGCTTGTTC	TCTGCTTGTTC	-	novel	NA	P-0042522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	93	566	1	ENST00000268489.5:c.5886_5896del	p.Asn1963GlyfsTer9	p.N1963Gfs*9	ENST00000268489	NM_006885.3	1962	gaGAACAAGCAGAag/gaag	9/10	1	2	FACETS	0.783	0.698	0.873	0.783	0.698	0.873	SUBCLONAL	1	TRUE	1	0.439137891507962	2		567	541	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923737	72923738	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0042522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	155	643	0	ENST00000268489.5:c.3340_3341del	p.Arg1114LysfsTer40	p.R1114Kfs*40	ENST00000268489	NM_006885.3	1114	CGa/a	4/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.439137891507962	2		643	600	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976463	25976463	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	26	391	0	ENST00000435504.4:c.1082A>G	p.Glu361Gly	p.E361G	ENST00000435504		361	gAg/gGg	11/13	0.27609816189698	3	FACETS	0.366	0.289	0.453	0.183	0.144	0.227	SUBCLONAL	1	TRUE	1	0.439137891507962	3		391	395	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447328	187447328	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	105	567	0	ENST00000232014.4:c.865C>T	p.Arg289Ter	p.R289*	ENST00000232014	NM_001130845.1	289	Cga/Tga	5/10	1	2	FACETS	0.857	0.77	0.949	0.857	0.77	0.949	CLONAL	1	TRUE	1	0.439137891507962	2		567	558	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157256645	157256646	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0042522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	25	302	0	ENST00000346085.5:c.1977dup	p.Gly660ArgfsTer4	p.G660Rfs*4	ENST00000346085	NM_020732.3	658	gcc/gCcc	5/20	1	2	FACETS	0.295	0.232	0.367	0.295	0.232	0.367	SUBCLONAL	1	TRUE	1	0.439137891507962	2		302	386	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162475161	162475161	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	69	428	0	ENST00000366898.1:c.580G>A	p.Gly194Ser	p.G194S	ENST00000366898	NM_004562.2	194	Ggt/Agt	5/12	1	2	FACETS	0.883	0.774	0.999	0.883	0.774	0.999	CLONAL	1	TRUE	1	0.439137891507962	2		428	356	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755991	133755991	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	98	663	0	ENST00000318560.5:c.1618G>A	p.Glu540Lys	p.E540K	ENST00000318560	NM_005157.4	540	Gag/Aag	10/11	1	2	FACETS	0.746	0.667	0.83	0.746	0.667	0.83	SUBCLONAL	1	TRUE	1	0.439137891507962	2		663	598	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	45	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.0928350170224654	3	FACETS	1	0.946	1	0.661	0.556	0.778	CLONAL	1	TRUE	1	0.14	3		539	520	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748822	43748822	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	47	817	2	ENST00000382044.4:c.1984G>T	p.Glu662Ter	p.E662*	ENST00000382044	NM_001141980.1	662	Gag/Tag	12/28	1	2	FACETS	0.811	0.682	0.954	0.811	0.682	0.954	CLONAL	1	TRUE	1	0.14	2		819	828	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579405	7579405	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	44	775	0	ENST00000269305.4:c.282del	p.Ser95LeufsTer28	p.S95Lfs*28	ENST00000269305	NM_001126112.2	94	tcA/tc	4/11	1	2	FACETS	0.878	0.734	1	0.878	0.734	1	CLONAL	1	TRUE	1	0.14	2		775	716	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	22	348	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.605	0.47	0.761	0.605	0.47	0.761	SUBCLONAL	1	TRUE	1	0.289634077970102	2		349	251	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0042531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	32	196	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	1	2	FACETS	0.809	0.66	0.977	0.809	0.66	0.977	CLONAL	1	TRUE	1	0.289634077970102	2		196	273	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0042531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	65	374	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.909	0.789	1	0.909	0.789	1	CLONAL	1	TRUE	1	0.289634077970102	2		374	494	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	52	286	0	ENST00000335508.6:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000335508	NM_012433.2	902	Gaa/Aaa	18/25	1	2	FACETS	0.766	0.653	0.889	0.766	0.653	0.889	SUBCLONAL	1	TRUE	1	0.289634077970102	2		286	469	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202753	108202753	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs781215442	NA	P-0042531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	59	243	0	ENST00000278616.4:c.7777C>T	p.Gln2593Ter	p.Q2593*	ENST00000278616	NM_000051.3	2593	Cag/Tag	52/63	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.289634077970102	2		243	373	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475550	12475550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479145908	NA	P-0042531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	94	437	0	ENST00000287820.6:c.1424C>T	p.Thr475Met	p.T475M	ENST00000287820	NM_015869.4	475	aCg/aTg	7/7	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.289634077970102	2		437	622	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222259	2222259	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371443260	NA	P-0042531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	79	742	3	ENST00000398665.3:c.3091G>A	p.Asp1031Asn	p.D1031N	ENST00000398665	NM_032482.2	1031	Gat/Aat	24/28	1	2	FACETS	0.848	0.746	0.958	0.848	0.746	0.958	CLONAL	1	TRUE	1	0.289634077970102	2		745	643	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908816	101908816	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	52	313	0	ENST00000374994.4:c.1180G>T	p.Glu394Ter	p.E394*	ENST00000374994	NM_004612.2	394	Gaa/Taa	7/9	0.289634077970102	1	FACETS	0.714	0.609	0.829	0.714	0.609	0.829	SUBCLONAL	1	TRUE	0	0.289634077970102	1		313	430	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938442	44938442	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	86	184	0	ENST00000377967.4:c.2990del	p.Met997ArgfsTer2	p.M997Rfs*2	ENST00000377967	NM_021140.2	997	aTg/ag	20/29	1	1	FACETS	0.816	0.73	0.907	1	0.983	1	CLONAL	2	TRUE	0	0.289634077970102	1		184	311	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0042532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	66	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.268925118918889	5	FACETS	0.885	0.772	1	0.59	0.515	0.671	CLONAL	2	TRUE	2	0.268925118918889	5		311	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0042532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	131	789	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.207160525509853	2	FACETS	1	0.981	1	0.657	0.596	0.72	CLONAL	1	TRUE	0	0.268925118918889	2		789	742	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0042532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	21	261	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.181639500648103	3	FACETS	0.591	0.455	0.749	0.295	0.227	0.375	SUBCLONAL	1	TRUE	1	0.268925118918889	3		261	300	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581234	48581234	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767332	NA	P-0042532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	90	531	0	ENST00000342988.3:c.538C>T	p.Gln180Ter	p.Q180*	ENST00000342988	NM_005359.5	180	Caa/Taa	5/12	0.207160525509853	2	FACETS	0.766	0.683	0.853	0.766	0.683	0.853	SUBCLONAL	2	TRUE	0	0.268925118918889	2		531	437	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549692	226549692	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	32	403	0	ENST00000366794.5:c.2941G>C	p.Asp981His	p.D981H	ENST00000366794	NM_001618.3	981	Gac/Cac	22/23	0.191932028748572	3	FACETS	0.657	0.533	0.797	0.328	0.266	0.399	SUBCLONAL	1	TRUE	1	0.268925118918889	3		403	411	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0042545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	226	443	9	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.564749476086719	6	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	3	0.564749476086719	6		452	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0042545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	205	448	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.449922101913281	2	FACETS	0.95	0.896	1	0.95	0.896	1	CLONAL	2	TRUE	0	0.564749476086719	2		448	382	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0042545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	117	47	0				ENST00000310581	NM_198253.2	-/1132			0.393693196947411	5	FACETS	0.921	0.845	0.998	0.921	0.845	0.998	CLONAL	3	TRUE	2	0.564749476086719	5		47	277	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439722	220439722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	283	860	1	ENST00000243786.2:c.575C>T	p.Pro192Leu	p.P192L	ENST00000243786	NM_002191.3	192	cCc/cTc	2/2	0.442321655916306	4	FACETS	0.909	0.863	0.955	0.909	0.863	0.955	CLONAL	3	TRUE	1	0.564749476086719	4		861	575	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100603	102100603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	151	488	0	ENST00000282441.5:c.1447C>T	p.Leu483Phe	p.L483F	ENST00000282441	NM_001130145.2	483	Ctt/Ttt	9/9	0.501923245300215	3	FACETS	0.939	0.871	1	0.939	0.871	1	CLONAL	2	TRUE	1	0.564749476086719	3		488	365	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500505	99500505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	205	684	0	ENST00000268035.6:c.3938C>T	p.Ser1313Phe	p.S1313F	ENST00000268035	NM_000875.3	1313	tCc/tTc	21/21	0.393693196947411	5	FACETS	0.925	0.868	0.984	0.925	0.868	0.984	CLONAL	3	TRUE	2	0.564749476086719	5		684	483	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59871065	59871065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1379791142	NA	P-0042545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	58	230	0	ENST00000259008.2:c.1366C>T	p.Leu456Phe	p.L456F	ENST00000259008	NM_032043.2	456	Ctt/Ttt	10/20	0.138636667921483	6	FACETS	1	0.941	1	0.759	0.663	0.86	INDETERMINATE	2	TRUE	3	0.564749476086719	6		230	192	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265574	198265575	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	69	437	0	ENST00000335508.6:c.2582_2583delinsTT	p.Ala861Val	p.A861V	ENST00000335508	NM_012433.2	861	gCC/gTT	18/25	0.442321655916306	4	FACETS	1	0.883	1	0.336	0.294	0.381	CLONAL	1	TRUE	1	0.564749476086719	4		437	379	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851825	134851825	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	220	667	1	ENST00000398015.3:c.1231G>A	p.Gly411Arg	p.G411R	ENST00000398015	NM_004441.4	411	Gga/Aga	5/16	0.478360807229739	4	FACETS	0.977	0.915	1	0.977	0.915	1	CLONAL	2	TRUE	2	0.564749476086719	4		668	624	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524619	106524619	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	122	253	0	ENST00000359195.3:c.2780G>A	p.Arg927Lys	p.R927K	ENST00000359195	NM_002649.2	927	aGa/aAa	9/11	0.564749476086719	6	FACETS	0.915	0.838	0.995	0.915	0.838	0.995	CLONAL	3	TRUE	3	0.564749476086719	6		253	335	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	102	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.233932165450486	3	FACETS	0.885	0.794	0.982	0.885	0.794	0.982	CLONAL	2	TRUE	1	0.233932165450486	3		539	550	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0042547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	65	180	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	0.209901539208329	3	FACETS	1	0.903	1	1	0.903	1	CLONAL	2	TRUE	1	0.233932165450486	3		180	299	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394849	394849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1377317453	NA	P-0042547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	59	416	0	ENST00000380956.4:c.245G>A	p.Arg82Gln	p.R82Q	ENST00000380956	NM_001195286.1	82	cGa/cAa	3/9	0.233932165450486	4	FACETS	0.979	0.842	1	0.489	0.421	0.564	CLONAL	1	TRUE	2	0.233932165450486	4		416	636	SUCCESS
APC	324	MSKCC	GRCh37	5	112174893	112174893	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs730881247	NA	P-0042547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	19	223	0	ENST00000257430.4:c.3602C>A	p.Ser1201Ter	p.S1201*	ENST00000257430	NM_000038.5	1201	tCa/tAa	16/16	0.209901539208329	3	FACETS	0.709	0.539	0.908	0.354	0.269	0.454	CLONAL	1	TRUE	1	0.233932165450486	3		223	256	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549381	21549381	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3091	637	531	0	ENST00000382592.4:c.2895T>A	p.Asp965Glu	p.D965E	ENST00000382592	NM_014572.2	965	gaT/gaA	8/8	0.233932165450486	37	FACETS	1	0.986	1	0.219	0.209	0.229	CLONAL	7	TRUE	3	0.233932165450486	37		531	3728	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577150	7577151	+	inframe_insertion	In_Frame_Ins	INS	-	-	TACCAC	novel	NA	P-0042547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	164	558	0	ENST00000269305.4:c.783-1_787dup	p.Ser261_Gly262dup	p.S261_G262dup	ENST00000269305	NM_001126112.2	261	aat/aGTGGTAat	8/11	1	2	FACETS	0.933	0.859	1	1	0.992	1	CLONAL	2	TRUE	1	0.233932165450486	2		558	751	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0042555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	44	443	9	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		452	255	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522551	176522551	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774571806	NA	P-0042571-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	232	779	0	ENST00000292408.4:c.1648G>A	p.Val550Met	p.V550M	ENST00000292408	NM_213647.1	550	Gtg/Atg	13/18	0.52099549452103	3	FACETS	0.943	0.879	1	0.471	0.439	0.504	CLONAL	1	TRUE	1	0.641592566979192	3		779	1013	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419025	419025	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042571-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	216	678	0	ENST00000399788.2:c.3322G>T	p.Glu1108Ter	p.E1108*	ENST00000399788	NM_001042603.1	1108	Gag/Tag	22/28	NA	2	FACETS	0.733	0.682	0.786			1	INDETERMINATE	1	TRUE	NA	0.641592566979192	2		678	918	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	264	724	0	ENST00000269305.4:c.470T>G	p.Val157Gly	p.V157G	ENST00000269305	NM_001126112.2	157	gTc/gGc	5/11	0.302952352643016	2	FACETS	0.86	0.81	0.911	0.86	0.81	0.911	CLONAL	2	TRUE	0	0.412551514901859	2		724	744	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433722	49433722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572359740	NA	P-0042577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	40	827	1	ENST00000301067.7:c.7831C>T	p.Arg2611Cys	p.R2611C	ENST00000301067	NM_003482.3	2611	Cgc/Tgc	31/54	1	2	FACETS	0.291	0.241	0.347	0.291	0.241	0.347	SUBCLONAL	1	TRUE	1	0.412551514901859	2		828	667	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883114	37883114	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749454186	NA	P-0042577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	202	821	1	ENST00000269571.5:c.3017G>A	p.Arg1006His	p.R1006H	ENST00000269571		1006	cGc/cAc	25/27	0.329795883431806	3	FACETS	0.835	0.777	0.895	0.557	0.518	0.597	CLONAL	2	TRUE	0	0.412551514901859	3		822	707	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988163	85988163	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs759299377	NA	P-0042577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	85	457	0	ENST00000263360.6:c.1108A>G	p.Met370Val	p.M370V	ENST00000263360	NM_003797.3	370	Atg/Gtg	10/12	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.412551514901859	2		457	401	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072612	5072613	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0042577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	28	430	0	ENST00000381652.3:c.1763_1764del	p.Arg588LysfsTer8	p.R588Kfs*8	ENST00000381652	NM_004972.3	588	AGa/a	13/25	0.412551514901859	3	FACETS	0.361	0.288	0.444	0.18	0.144	0.222	SUBCLONAL	1	TRUE	1	0.412551514901859	3		430	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0042601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	137	588	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			1	2	FACETS	0.882	0.804	0.964	1	0.992	1	CLONAL	3	TRUE	1	0.15	2		588	690	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942124	81942124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781434235	NA	P-0042601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	45	645	1	ENST00000359376.3:c.1661C>T	p.Thr554Met	p.T554M	ENST00000359376	NM_002661.3	554	aCg/aTg	17/33	1	2	FACETS	0.982	0.824	1	0.982	0.824	1	CLONAL	1	TRUE	1	0.15	2		646	611	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218353	69218353	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	36	458	0	ENST00000462284.1:c.445C>A	p.Gln149Lys	p.Q149K	ENST00000462284	NM_002392.5	149	Cag/Aag	7/11	0.233305050995784	3	FACETS	0.808	0.662	0.971	0.404	0.331	0.486	CLONAL	1	TRUE	1	0.15	3		458	639	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266079	41266629	+	splice_donor_variant,splice_acceptor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	CAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTAT	CAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTAT	-	novel	NA	P-0042601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	44	292	0	ENST00000349496.5:c.78_428del		p.X26_splice	ENST00000349496	NM_001904.3	26	CAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTAT/-	3-4/15	1	2	FACETS	0.838	0.705	0.984	1	0.965	1	CLONAL	2	TRUE	1	0.15	2		292	350	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0042614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	44	667	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.242370652711135	2		667	290	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0042614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	71	410	0	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	0.184620073513466	3	FACETS	1	0.958	1	0.619	0.541	0.702	CLONAL	1	TRUE	1	0.242370652711135	3		410	531	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225560	26225560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375842011	NA	P-0042614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	88	533	0	ENST00000360408.1:c.178G>A	p.Glu60Lys	p.E60K	ENST00000360408	NM_003532.2	60	Gag/Aag	1/1	0.206366895844896	4	FACETS	0.789	0.7	0.883	0.789	0.7	0.883	SUBCLONAL	2	TRUE	2	0.242370652711135	4		533	572	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27104491	27105513	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CAGAGGTTGCAGTGAGCTGAGATCGTGCCACTGCACTCCAGCCTGGGCAACAGAGCGGGACTCTGTCTCAAAAAAAAAAAAAAAAAAATACACACACACACACTCTCACACACTAGCCCGATGTGGTGGCAGGCGCCTGTAATCCCAGCTACTTGGGAGGCTAAGGCAGGAGAAAAATCGCTTGAACCCAGGAGGCGGAGGCTGCAGCCAACTGAGATCACACCACTGTACTCCAGCCTGGATGACAGAGTGAGACTTCATCTCAAAAAAAAAAAAAAGTGTTGGGATTACAGGTGTGAGCCACTGCTTCCAGCCCCTAGATCTAATTCGAAAGCCCTTATTTTTTTTTCCATCTGCTCTACTGTTCAGCCAAAGATTGTGACTGGAGAGGAGTGTTTTCTTCTAGAGGTAAATAAATGGCCTATATATTATCCAAGGTGGAATTTGGGTCTCTGTAGCACCAGCTTGGACCAGTGTTTGGAGAGCTGAAGCCTCGTCCCACTCCTTATGCTGCAAGATCCATGGAGTTCCAGCCCCCTGGACTTGTGGGGAGCTTGGAGAAGAGAGCCATGAACATCTGCCCACATGGCATTCTCTTCTCTTAGCTTAAGTCACCATGCCTAAGCTTGGGTTCCACTTGGCAGTGAGATGGAGAGAGTGTCCTAAAAGAGATAATGGCAATGACCACCAGGTTGAAAACTGGCCTGGTGAAGAAAAGCAGAAGATTAATTGGGAAAAGAGAAGGCTAAGAGATGATTGGCCCTGGTGGGTGAGGTGCAAAGCTGTTGGCTAGTGTTCCTGGAGATAGGCTTACGTGAAGGTAGGTTGGGCAGAAGAAAGAACTTTGTGTTGGGCATAGAAGAGATTAAGATGAACAATTTGCTCTGTGGAGAACCTTTGGGAAAGGAGCAACTCTGCCTCTCCCAACTGATACAGAAGACTTGGGGAGGTCTCTCAAGTCAATAATTCTGTTCTTAGGCCACTTTTCTCCCTTAATTTATTTCCTGTTCTTTCTCTTTTTAG	CAGAGGTTGCAGTGAGCTGAGATCGTGCCACTGCACTCCAGCCTGGGCAACAGAGCGGGACTCTGTCTCAAAAAAAAAAAAAAAAAAATACACACACACACACTCTCACACACTAGCCCGATGTGGTGGCAGGCGCCTGTAATCCCAGCTACTTGGGAGGCTAAGGCAGGAGAAAAATCGCTTGAACCCAGGAGGCGGAGGCTGCAGCCAACTGAGATCACACCACTGTACTCCAGCCTGGATGACAGAGTGAGACTTCATCTCAAAAAAAAAAAAAAGTGTTGGGATTACAGGTGTGAGCCACTGCTTCCAGCCCCTAGATCTAATTCGAAAGCCCTTATTTTTTTTTCCATCTGCTCTACTGTTCAGCCAAAGATTGTGACTGGAGAGGAGTGTTTTCTTCTAGAGGTAAATAAATGGCCTATATATTATCCAAGGTGGAATTTGGGTCTCTGTAGCACCAGCTTGGACCAGTGTTTGGAGAGCTGAAGCCTCGTCCCACTCCTTATGCTGCAAGATCCATGGAGTTCCAGCCCCCTGGACTTGTGGGGAGCTTGGAGAAGAGAGCCATGAACATCTGCCCACATGGCATTCTCTTCTCTTAGCTTAAGTCACCATGCCTAAGCTTGGGTTCCACTTGGCAGTGAGATGGAGAGAGTGTCCTAAAAGAGATAATGGCAATGACCACCAGGTTGAAAACTGGCCTGGTGAAGAAAAGCAGAAGATTAATTGGGAAAAGAGAAGGCTAAGAGATGATTGGCCCTGGTGGGTGAGGTGCAAAGCTGTTGGCTAGTGTTCCTGGAGATAGGCTTACGTGAAGGTAGGTTGGGCAGAAGAAAGAACTTTGTGTTGGGCATAGAAGAGATTAAGATGAACAATTTGCTCTGTGGAGAACCTTTGGGAAAGGAGCAACTCTGCCTCTCCCAACTGATACAGAAGACTTGGGGAGGTCTCTCAAGTCAATAATTCTGTTCTTAGGCCACTTTTCTCCCTTAATTTATTTCCTGTTCTTTCTCTTTTTAG	-	novel	NA	P-0042614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	72	0	0	ENST00000324856.7:c.5125-1022_5125del		p.X1709_splice	ENST00000324856	NM_006015.4	1709			0.242370652711135	2	FACETS	1	0.939	1	0.562	0.491	0.637	CLONAL	1	TRUE	0	0.242370652711135	2		0	529	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980415	201980415	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	98	900	0	ENST00000359651.3:c.152del	p.Leu51TrpfsTer104	p.L51Wfs*104	ENST00000359651		51	Ttg/tg	1/8	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.242370652711135	2		900	793	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348757	11348769	+	frameshift_variant	Frame_Shift_Del	DEL	GCGAGCCAGGTTC	GCGAGCCAGGTTC	-	novel	NA	P-0042614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	60	741	0	ENST00000332029.2:c.567_579del	p.Asn190SerfsTer11	p.N190Sfs*11	ENST00000332029	NM_003745.1	189	gaGAACCTGGCTCGC/ga	2/2	1	2	FACETS	0.857	0.738	0.986	0.857	0.738	0.986	CLONAL	1	TRUE	1	0.242370652711135	2		741	578	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480422	89480422	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	59	428	0	ENST00000336596.2:c.2259G>C	p.Leu753Phe	p.L753F	ENST00000336596	NM_005233.5	753	ttG/ttC	13/17	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.242370652711135	2		428	429	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223905	53223905	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	114	1093	2	ENST00000375401.3:c.3454G>T	p.Glu1152Ter	p.E1152*	ENST00000375401	NM_004187.3	1152	Gag/Tag	23/26	0.214793101112234	1	FACETS	0.916	0.823	1	0.916	0.823	1	CLONAL	1	TRUE	0	0.242370652711135	1		1095	903	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0042623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	410	763	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	NA	2	FACETS	0.951	0.908	0.993			1	INDETERMINATE	2	TRUE	NA	0.440102593969025	2		763	980	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976509	7976509	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	410	674	1	ENST00000319144.4:c.1883C>T	p.Thr628Met	p.T628M	ENST00000319144	NM_001139.2	628	aCg/aTg	14/15	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	2	TRUE	NA	0.440102593969025	2		675	892	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288240	33288240	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573854582	NA	P-0042623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	247	553	0	ENST00000374542.5:c.1168G>A	p.Glu390Lys	p.E390K	ENST00000374542	NM_001141970.1	390	Gag/Aag	4/8	0.202527756758914	5	FACETS	0.925	0.865	0.987	0.617	0.577	0.658	INDETERMINATE	2	TRUE	2	0.440102593969025	5		553	1007	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435346	18435346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	170	345	0	ENST00000266497.5:c.331C>T	p.Pro111Ser	p.P111S	ENST00000266497		111	Cct/Tct	1/31	0.217108865930099	4	FACETS	0.993	0.919	1			1	INDETERMINATE	2	TRUE	NA	0.440102593969025	4		345	560	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183719	10183720	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAA	novel	NA	P-0042623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	519	933	0	ENST00000256474.2:c.189_190insAAG	p.Leu63_Arg64insLys	p.L63_R64insK	ENST00000256474	NM_000551.3	63	ctg/ctGAAg	1/3	0.440102593969025	2	FACETS	0.943	0.906	0.981	0.943	0.906	0.981	CLONAL	2	TRUE	0	0.440102593969025	2		933	1250	SUCCESS
APC	324	MSKCC	GRCh37	5	112173618	112173651	+	frameshift_variant	Frame_Shift_Del	DEL	TAGACAATTTAAGTCCCAAGGCATCTCATCGTAG	TAGACAATTTAAGTCCCAAGGCATCTCATCGTAG	-	novel	NA	P-0042623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	134	293	0	ENST00000257430.4:c.2329_2362del	p.Asp777SerfsTer32	p.D777Sfs*32	ENST00000257430	NM_000038.5	776	aTAGACAATTTAAGTCCCAAGGCATCTCATCGTAGt/at	16/16	0.440102593969025	2	FACETS	0.853	0.785	0.923	0.853	0.785	0.923	CLONAL	2	TRUE	0	0.440102593969025	2		293	357	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939270	76939270	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	282	694	0	ENST00000373344.5:c.1478A>C	p.His493Pro	p.H493P	ENST00000373344	NM_000489.3	493	cAt/cCt	9/35	0.329088947378466	4	FACETS	0.915	0.861	0.971	0.915	0.861	0.971	CLONAL	2	TRUE	2	0.440102593969025	4		694	1008	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779748	3779748	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0121463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	272	729	0	ENST00000262367.5:c.5300C>A	p.Ser1767Ter	p.S1767*	ENST00000262367	NM_004380.2	1767	tCa/tAa	31/31	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	NA	1	0.735772705180383	2		729	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0042641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	169	621	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		622	799	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0042641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	77	368	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		368	328	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169985727	169985727	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369872734	NA	P-0042641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	123	455	0	ENST00000295797.4:c.389G>A	p.Arg130His	p.R130H	ENST00000295797	NM_002740.5	130	cGc/cAc	5/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		455	714	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714543	52714543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	144	675	0	ENST00000322088.6:c.301G>A	p.Glu101Lys	p.E101K	ENST00000322088	NM_014225.5	101	Gag/Aag	4/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		675	760	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692839	89692839	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1064793243	NA	P-0042645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	28	224	0	ENST00000371953.3:c.323T>C	p.Leu108Pro	p.L108P	ENST00000371953	NM_000314.4	108	cTt/cCt	5/9	0.895465090257027	1	FACETS	0.175	0.141	0.214	0.175	0.141	0.214	SUBCLONAL	1	TRUE	0	0.895465090257027	1		224	197	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0042646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	33	438	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	0.651	0.533	0.782	0.651	0.533	0.782	SUBCLONAL	1	TRUE	1	0.399392812927297	2		438	254	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0042653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	100	308	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.230058381889782	1	FACETS	0.742	0.668	0.818	0.742	0.668	0.818	INDETERMINATE	1	TRUE	0	0.540587153481724	1		308	364	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161803	56161807	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTT	AGGTT	-	novel	NA	P-0042653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	41	347	0	ENST00000399503.3:c.1301+1_1301+5del		p.X434_splice	ENST00000399503	NM_005921.1	434		6/20	0.230058381889782	1	FACETS	0.299	0.249	0.354	0.299	0.249	0.354	INDETERMINATE	1	TRUE	0	0.540587153481724	1		347	370	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178442	56178443	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0042653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	89	317	0	ENST00000399503.3:c.3416dup	p.Met1140TyrfsTer5	p.M1140Yfs*5	ENST00000399503	NM_005921.1	1139	tct/tCct	14/20	0.230058381889782	1	FACETS	0.893	0.803	0.986	0.893	0.803	0.986	INDETERMINATE	1	TRUE	0	0.540587153481724	1		317	269	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936070	178936070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042670-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	13	382	0	ENST00000263967.3:c.1612G>A	p.Asp538Asn	p.D538N	ENST00000263967	NM_006218.2	538	Gat/Aat	10/21	0.191660628454636	2	FACETS	0.566	0.406	0.759	0.283	0.203	0.38	INDETERMINATE	1	FALSE	0	0.323299682039202	2		382	142	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462662	29462662	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762395127	NA	P-0042670-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	105	772	1	ENST00000389048.3:c.2239G>A	p.Gly747Arg	p.G747R	ENST00000389048	NM_004304.4	747	Ggg/Agg	13/29	0.323299682039202	3	FACETS	0.851	0.761	0.946	0.425	0.38	0.473	CLONAL	1	FALSE	1	0.323299682039202	3		773	887	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653792	89653792	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1564814427	NA	P-0042670-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	30	305	0	ENST00000371953.3:c.92del	p.Asn31ThrfsTer23	p.N31Tfs*23	ENST00000371953	NM_000314.4	30	ccA/cc	2/9	0.269844220853697	4	FACETS	0.91	0.755	1	1	0.94	1	CLONAL	3	FALSE	2	0.323299682039202	4		305	90	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844229	68844229	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042670-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	86	541	0	ENST00000261769.5:c.817G>T	p.Glu273Ter	p.E273*	ENST00000261769	NM_004360.3	273	Gaa/Taa	6/16	0.323299682039202	1	FACETS	0.957	0.862	1	1	0.986	1	CLONAL	2	FALSE	0	0.323299682039202	1		541	233	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0042675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	118	667	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.918	0.837	1	0.918	0.837	1	CLONAL	1	TRUE	1	0.730466785230935	2		667	352	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0042675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	358	478	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.730466785230935	3	FACETS	0.984	0.941	1	0.984	0.941	1	CLONAL	2	TRUE	1	0.730466785230935	3		478	680	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058052	27058052	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	251	617	0	ENST00000324856.7:c.1762del	p.Gln588SerfsTer31	p.Q588Sfs*31	ENST00000324856	NM_006015.4	587	tCc/tc	3/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.730466785230935	2		617	637	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448310	56448310	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567880628	NA	P-0042675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	795	1013	1	ENST00000407977.2:c.337C>T	p.Arg113Ter	p.R113*	ENST00000407977		113	Cga/Tga	3/10	0.730466785230935	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.730466785230935	2		1014	1031	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268138	153268138	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1406877044	NA	P-0042675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	134	479	0	ENST00000281708.4:c.670C>T	p.Arg224Ter	p.R224*	ENST00000281708	NM_033632.3	224	Cga/Tga	4/12	1	2	FACETS	0.704	0.643	0.768	0.704	0.643	0.768	SUBCLONAL	1	TRUE	1	0.730466785230935	2		479	521	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9770535	9770535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	88	1037	2	ENST00000377346.4:c.22C>T	p.Pro8Ser	p.P8S	ENST00000377346	NM_005026.3	8	Ccc/Tcc	3/24	1	2	FACETS	0.264	0.233	0.297	0.264	0.233	0.297	SUBCLONAL	1	TRUE	1	0.730466785230935	2		1039	913	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692769	89692769	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0042675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	128	400	0	ENST00000371953.3:c.254-1G>T		p.X85_splice	ENST00000371953	NM_000314.4	85			0.730466785230935	3	FACETS	0.974	0.888	1	0.487	0.444	0.532	CLONAL	1	TRUE	1	0.730466785230935	3		400	491	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559209	29559209	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0042675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	107	456	0	ENST00000356175.3:c.3314+2T>C		p.X1105_splice	ENST00000356175	NM_000267.3	1105			1	2	FACETS	0.651	0.587	0.718	0.651	0.587	0.718	SUBCLONAL	1	TRUE	1	0.730466785230935	2		456	450	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0042675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	241	529	0	ENST00000324856.7:c.666C>G	p.Tyr222Ter	p.Y222*	ENST00000324856	NM_006015.4	222	taC/taG	1/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.730466785230935	2		529	613	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662312	67662312	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	254	613	0	ENST00000264010.4:c.1558G>T	p.Glu520Ter	p.E520*	ENST00000264010	NM_006565.3	520	Gag/Tag	9/12	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.730466785230935	2		613	616	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0042705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	127	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.147757514232855	3	FACETS	1	0.97	1	0.758	0.693	0.825	INDETERMINATE	2	TRUE	0	0.320833215187127	3		311	404	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023266	27023278	+	frameshift_variant	Frame_Shift_Del	DEL	CGGTGGCGGCAGC	CGGTGGCGGCAGC	-	novel	NA	P-0042705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	37	112	0	ENST00000324856.7:c.372_384del	p.Gly125AlafsTer103	p.G125Afs*103	ENST00000324856	NM_006015.4	124	ggCGGTGGCGGCAGC/gg	1/20	1	2	FACETS	1	0.881	1	1	0.97	1	CLONAL	2	TRUE	1	0.320833215187127	2		112	110	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003335	42003357	+	frameshift_variant	Frame_Shift_Del	DEL	ACTTTGGATGAAAATATATTTCC	ACTTTGGATGAAAATATATTTCC	-	novel	NA	P-0042705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	108	485	0	ENST00000219905.7:c.2873_2895del	p.Thr958LysfsTer4	p.T958Kfs*4	ENST00000219905	NM_001164273.1	958	ACTTTGGATGAAAATATATTTCCa/a	8/24	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.320833215187127	2		485	595	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577098	7577109	+	inframe_deletion	In_Frame_Del	DEL	TCTCCCAGGACA	TCTCCCAGGACA	-	novel	NA	P-0042705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	155	699	0	ENST00000269305.4:c.829_840del	p.Cys277_Arg280del	p.C277_R280del	ENST00000269305	NM_001126112.2	277	TGTCCTGGGAGA/-	8/11	0.320833215187127	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.320833215187127	1		699	657	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047366	128047366	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	77	503	1	ENST00000285398.2:c.556C>A	p.Gln186Lys	p.Q186K	ENST00000285398	NM_000122.1	186	Cag/Aag	5/15	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.320833215187127	2		504	427	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0042746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	79	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.178265736882842	3	FACETS	0.977	0.864	1	0.977	0.864	1	CLONAL	2	TRUE	1	0.23	3		311	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0042757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	262	679	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.485652616228173	2	FACETS	1	0.994	1	0.727	0.688	0.767	CLONAL	1	TRUE	0	0.617736509407684	2		679	583	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41267796	41267796	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0042757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	190	464	0	ENST00000357654.3:c.81T>A	p.Cys27Ter	p.C27*	ENST00000357654	NM_007294.3	27	tgT/tgA	3/23	0.485652616228173	2	FACETS	1	0.991	1	0.696	0.651	0.741	CLONAL	1	TRUE	0	0.617736509407684	2		464	442	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007481	62007481	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	124	540	0	ENST00000392795.3:c.386A>G	p.Asn129Ser	p.N129S	ENST00000392795	NM_001039933.1	129	aAc/aGc	3/6	0.485652616228173	2	FACETS	0.725	0.658	0.794	0.362	0.329	0.397	SUBCLONAL	1	TRUE	0	0.617736509407684	2		540	554	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285435	38285441	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTACCTT	GTACCTT	-	novel	NA	P-0042757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	257	574	0	ENST00000425967.3:c.712_714+4del		p.X238_splice	ENST00000425967	NM_001174067.1	238		6/19	0.452235262442843	4	FACETS	0.767	0.719	0.815	0.767	0.719	0.815	SUBCLONAL	2	TRUE	2	0.617736509407684	4		574	878	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0042758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	265	443	9	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.407036512172157	3	FACETS	0.97	0.913	1	0.97	0.913	1	CLONAL	2	TRUE	1	0.455245884441808	3		452	737	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0042758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	54	47	0				ENST00000310581	NM_198253.2	-/1132			0.252113846273037	1	FACETS	0.406	0.347	0.47	0.406	0.347	0.47	INDETERMINATE	1	TRUE	0	0.455245884441808	1		47	451	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490506	20490506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	90	609	2	ENST00000346618.3:c.1243C>T	p.Pro415Ser	p.P415S	ENST00000346618	NM_001949.4	415	Cct/Tct	7/7	0.252113846273037	1	FACETS	0.456	0.405	0.511	0.456	0.405	0.511	INDETERMINATE	1	TRUE	0	0.455245884441808	1		611	669	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274248	10274248	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555491563	NA	P-0042758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	149	434	0	ENST00000330684.3:c.21G>A	p.Trp7Ter	p.W7*	ENST00000330684	NM_001134407.1	7	tgG/tgA	2/13	0.240558040260755	2	FACETS	0.812	0.75	0.875	0.812	0.75	0.875	INDETERMINATE	2	TRUE	0	0.455245884441808	2		434	403	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0042758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	28	385	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.313082729249023	2	FACETS	0.255	0.203	0.314	0.127	0.101	0.157	SUBCLONAL	1	TRUE	0	0.455245884441808	2		385	483	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	338190	338190	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs370661416	NA	P-0042758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	327	730	1	ENST00000262320.3:c.2521C>T	p.Arg841Ter	p.R841*	ENST00000262320	NM_003502.3	841	Cga/Tga	11/11	0.240558040260755	2	FACETS	0.778	0.737	0.82	0.778	0.737	0.82	INDETERMINATE	2	TRUE	0	0.455245884441808	2		731	923	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971121	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	83	522	1	ENST00000304494.5:c.237_238delinsTT	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	79	acCCga/acTTga	2/3	0.455245884441808	1	FACETS	0.667	0.592	0.747	0.667	0.592	0.747	SUBCLONAL	1	TRUE	0	0.455245884441808	1		523	422	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915925	127915925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	257	532	0	ENST00000373547.4:c.556C>T	p.Pro186Ser	p.P186S	ENST00000373547	NM_002721.4	186	Cct/Tct	6/7	0.313082729249023	2	FACETS	0.839	0.79	0.888	0.839	0.79	0.888	CLONAL	2	TRUE	0	0.455245884441808	2		532	673	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274803	123274803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	159	528	0	ENST00000358487.5:c.1115C>T	p.Ser372Phe	p.S372F	ENST00000358487	NM_000141.4	372	tCc/tTc	9/18	0.455245884441808	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.455245884441808	1		528	496	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275779	38275779	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	175	678	0	ENST00000425967.3:c.1490C>T	p.Pro497Leu	p.P497L	ENST00000425967	NM_001174067.1	497	cCc/cTc	11/19	0.407036512172157	3	FACETS	0.922	0.848	0.998	0.461	0.424	0.499	CLONAL	1	TRUE	1	0.455245884441808	3		678	1024	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302837	15302837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	205	813	0	ENST00000263388.2:c.613C>T	p.Pro205Ser	p.P205S	ENST00000263388	NM_000435.2	205	Cca/Tca	4/33	0.252113846273037	1	FACETS	0.927	0.863	0.994	0.927	0.863	0.994	INDETERMINATE	1	TRUE	0	0.455245884441808	1		813	750	SUCCESS
CBL	867	MSKCC	GRCh37	11	119168192	119168192	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0042758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	61	379	0	ENST00000264033.4:c.2251+1G>C		p.X751_splice	ENST00000264033	NM_005188.3	751			0.252113846273037	1	FACETS	0.469	0.406	0.538	0.469	0.406	0.538	INDETERMINATE	1	TRUE	0	0.455245884441808	1		379	441	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434752	49434752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	94	816	0	ENST00000301067.7:c.6801del	p.Ala2268LeufsTer18	p.A2268Lfs*18	ENST00000301067	NM_003482.3	2267	aaA/aa	31/54	0.252113846273037	1	FACETS	0.415	0.369	0.464	0.415	0.369	0.464	INDETERMINATE	1	TRUE	0	0.455245884441808	1		816	769	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927992	49927992	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1235783876	NA	P-0042758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	211	641	0	ENST00000296474.3:c.3736C>T	p.His1246Tyr	p.H1246Y	ENST00000296474	NM_002447.2	1246	Cac/Tac	18/20	0.252113846273037	1	FACETS	0.971	0.905	1	0.971	0.905	1	INDETERMINATE	1	TRUE	0	0.455245884441808	1		641	737	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447763	187447763	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398495055	NA	P-0042758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	173	503	0	ENST00000232014.4:c.430C>T	p.Leu144Phe	p.L144F	ENST00000232014	NM_001130845.1	144	Ctc/Ttc	5/10	0.252113846273037	1	FACETS	0.932	0.861	1	0.932	0.861	1	INDETERMINATE	1	TRUE	0	0.455245884441808	1		503	630	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956128	55956128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	127	447	0	ENST00000263923.4:c.3187G>A	p.Gly1063Arg	p.G1063R	ENST00000263923	NM_002253.2	1063	Gga/Aga	23/30	0.252113846273037	1	FACETS	0.801	0.729	0.876	0.801	0.729	0.876	INDETERMINATE	1	TRUE	0	0.455245884441808	1		447	538	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562790	21562790	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1327443204	NA	P-0042785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	173	514	0	ENST00000382592.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000382592	NM_014572.2	377	Cgc/Tgc	4/8	0.434145959118306	1	FACETS	0.873	0.805	0.942	0.873	0.805	0.942	CLONAL	1	TRUE	0	0.434145959118306	1		514	715	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579447	7579447	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	333	639	0	ENST00000269305.4:c.240del	p.Thr81HisfsTer42	p.T81Hfs*42	ENST00000269305	NM_001126112.2	80	ccT/cc	4/11	0.434145959118306	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.434145959118306	1		639	998	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226568862	226568862	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765392279	NA	P-0042802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	263	985	0	ENST00000366794.5:c.1207C>T	p.Arg403Trp	p.R403W	ENST00000366794	NM_001618.3	403	Cgg/Tgg	9/23	0.676229627036116	4	FACETS	0.78	0.733	0.828	0.78	0.733	0.828	SUBCLONAL	2	TRUE	2	0.676229627036116	4		985	836	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0042802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	181	311	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.676229627036116	3	FACETS	0.847	0.791	0.904	0.847	0.791	0.904	CLONAL	2	TRUE	1	0.676229627036116	3		311	423	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858093	9858093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064796904	NA	P-0042802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	253	824	0	ENST00000330684.3:c.3308G>A	p.Arg1103His	p.R1103H	ENST00000330684	NM_001134407.1	1103	cGc/cAc	13/13	0.676229627036116	4	FACETS	0.875	0.823	0.928	0.875	0.823	0.928	CLONAL	2	TRUE	2	0.676229627036116	4		824	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs967461896	NA	P-0042802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	185	1156	0	ENST00000269305.4:c.526T>C	p.Cys176Arg	p.C176R	ENST00000269305	NM_001126112.2	176	Tgc/Cgc	5/11	0.344685069437133	5	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.676229627036116	5		1156	880	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604750	48604750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	190	661	0	ENST00000342988.3:c.1572G>T	p.Trp524Cys	p.W524C	ENST00000342988	NM_005359.5	524	tgG/tgT	12/12	0.456801296592882	3	FACETS	1	0.984	1	0.75	0.708	0.793	CLONAL	2	TRUE	0	0.676229627036116	3		661	334	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128028932	128028932	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1427747564	NA	P-0042802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	244	920	0	ENST00000285398.2:c.1925G>A	p.Arg642Gln	p.R642Q	ENST00000285398	NM_000122.1	642	cGg/cAg	12/15	0.676229627036116	3	FACETS	0.773	0.727	0.819	0.773	0.727	0.819	SUBCLONAL	2	TRUE	1	0.676229627036116	3		920	625	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249510	153249510	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1157879635	NA	P-0042802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	107	558	0	ENST00000281708.4:c.1268G>T	p.Gly423Val	p.G423V	ENST00000281708	NM_033632.3	423	gGa/gTa	9/12	1	2	FACETS	0.86	0.779	0.944	0.86	0.779	0.944	CLONAL	1	TRUE	1	0.676229627036116	2		558	368	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0042802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	110	221	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	0.676229627036116	3	FACETS	1	0.983	1	0.467	0.425	0.51	CLONAL	1	TRUE	0	0.676229627036116	3		221	311	SUCCESS
APC	324	MSKCC	GRCh37	5	112173249	112173249	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs863225321	NA	P-0042802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	145	125	0	ENST00000257430.4:c.1959-1G>A		p.X653_splice	ENST00000257430	NM_000038.5	653			0.676229627036116	3	FACETS	0.981	0.93	1	0.981	0.93	1	CLONAL	3	TRUE	0	0.676229627036116	3		125	195	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508083	106508083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339698935	NA	P-0042802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	133	405	0	ENST00000359195.3:c.77G>A	p.Arg26His	p.R26H	ENST00000359195	NM_002649.2	26	cGc/cAc	2/11	0.676229627036116	3	FACETS	0.763	0.702	0.825	0.763	0.702	0.825	SUBCLONAL	2	TRUE	1	0.676229627036116	3		405	345	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0042821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	395	789	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.570494789849674	2	FACETS	0.885	0.851	0.918	0.885	0.851	0.918	CLONAL	2	TRUE	0	0.682722782133198	2		789	654	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94906431	94906431	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	107	448	0	ENST00000536441.1:c.1467del	p.His490IlefsTer2	p.H490Ifs*2	ENST00000536441	NM_144665.3	489	cgG/cg	10/10	1	2	FACETS	0.648	0.584	0.715	0.648	0.584	0.715	SUBCLONAL	1	TRUE	1	0.682722782133198	2		448	484	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0042850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	102	334	1	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.783	0.708	0.861	1	0.985	1	SUBCLONAL	2	TRUE	1	0.390967958305854	2		335	333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0042850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	688	621	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.390967958305854	2	FACETS	0.983	0.961	1	1	0.998	1	CLONAL	4	TRUE	0	0.390967958305854	2		622	895	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10257046	10257046	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	49	806	0	ENST00000340748.4:c.2827C>T	p.Pro943Ser	p.P943S	ENST00000340748		943	Cct/Tct	27/40	0.376283225858927	4	FACETS	0.367	0.309	0.43	0.122	0.103	0.144	SUBCLONAL	1	TRUE	1	0.390967958305854	4		806	951	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937622	76937622	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	190	152	0	ENST00000373344.5:c.3126del	p.Glu1043LysfsTer7	p.E1043Kfs*7	ENST00000373344	NM_000489.3	1042	ggA/gg	9/35	1	1	FACETS	1	0.981	1	1	0.995	1	CLONAL	3	TRUE	0	0.390967958305854	1		152	249	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343258	118343258	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs781991683	NA	P-0042851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	24	365	1	ENST00000534358.1:c.1384T>A	p.Ser462Thr	p.S462T	ENST00000534358	NM_005933.3	462	Tca/Aca	3/36	1	2	FACETS	0.982	0.77	1	0.982	0.77	1	CLONAL	1	TRUE	1	0.15	2		366	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577577	7577577	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	45	680	0	ENST00000269305.4:c.704del	p.Asn235ThrfsTer12	p.N235Tfs*12	ENST00000269305	NM_001126112.2	235	aAc/ac	7/11	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.15	2		680	553	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162885	38162885	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs780272184	NA	P-0042851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	57	787	0	ENST00000317025.8:c.2321A>T	p.Tyr774Phe	p.Y774F	ENST00000317025	NM_023034.1	774	tAt/tTt	13/24	1	2	FACETS	0.784	0.671	0.909	0.784	0.671	0.909	CLONAL	1	TRUE	1	0.15	2		787	969	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0042862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	206	308	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.0812362138847701	5	FACETS	0.88	0.823	0.938	0.88	0.823	0.938	INDETERMINATE	3	TRUE	2	0.503856848540425	5		308	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0042862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	469	704	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.429737648150067	3	FACETS	0.86	0.827	0.893	0.86	0.827	0.893	CLONAL	3	TRUE	0	0.503856848540425	3		704	903	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106434	27106434	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	175	750	0	ENST00000324856.7:c.6046del	p.Leu2016CysfsTer14	p.L2016Cfs*14	ENST00000324856	NM_006015.4	2015	atC/at	20/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.503856848540425	2		750	676	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173731	108173731	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1565479465	NA	P-0042862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	164	430	0	ENST00000278616.4:c.5471T>C	p.Leu1824Pro	p.L1824P	ENST00000278616	NM_000051.3	1824	cTt/cCt	36/63	0.503856848540425	2	FACETS	0.925	0.862	0.987	0.925	0.862	0.987	CLONAL	2	TRUE	0	0.503856848540425	2		430	352	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410076	63410076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	60	966	0	ENST00000330258.3:c.3091G>A	p.Gly1031Ser	p.G1031S	ENST00000330258	NM_152424.3	1031	Ggc/Agc	2/2	0.0812362138847701	5	FACETS	0.463	0.397	0.534	0.154	0.132	0.178	INDETERMINATE	1	TRUE	2	0.503856848540425	5		966	904	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	111	348	1				ENST00000310581	NM_198253.2	-/1132			0.172817780910415	3	FACETS	0.934	0.851	1	1	0.99	1	CLONAL	5	FALSE	1	0.172817780910415	3		349	299	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099380	27099380	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	56	407	0	ENST00000324856.7:c.3617del	p.Thr1206IlefsTer10	p.T1206Ifs*10	ENST00000324856	NM_006015.4	1206	aCt/at	14/20	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	FALSE	1	0.172817780910415	2		407	593	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982963	201982963	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs549132954	NA	P-0042907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	49	569	1	ENST00000359651.3:c.812G>C	p.Arg271Thr	p.R271T	ENST00000359651		271	aGa/aCa	7/8	1	2	FACETS	0.822	0.695	0.962	0.822	0.695	0.962	CLONAL	1	FALSE	1	0.172817780910415	2		570	690	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428450	49428450	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0042907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	38	433	0	ENST00000301067.7:c.10356-1G>A		p.X3452_splice	ENST00000301067	NM_003482.3	3452			1	2	FACETS	0.719	0.593	0.86	0.719	0.593	0.86	SUBCLONAL	1	FALSE	1	0.172817780910415	2		433	612	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028411	42028411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	18	254	2	ENST00000219905.7:c.3949G>A	p.Glu1317Lys	p.E1317K	ENST00000219905	NM_001164273.1	1317	Gaa/Aaa	13/24	1	2	FACETS	0.674	0.507	0.872	0.674	0.507	0.872	SUBCLONAL	1	FALSE	1	0.172817780910415	2		256	309	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832863	3832863	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	27	366	0	ENST00000262367.5:c.1395G>C	p.Gln465His	p.Q465H	ENST00000262367	NM_004380.2	465	caG/caC	6/31	0.172817780910415	1	FACETS	0.618	0.491	0.764	0.618	0.491	0.764	SUBCLONAL	1	FALSE	0	0.172817780910415	1		366	462	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041758	14041758	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	50	362	0	ENST00000311895.7:c.2305C>G	p.Leu769Val	p.L769V	ENST00000311895	NM_005236.2	769	Ctc/Gtc	11/11	0.172817780910415	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	FALSE	0	0.172817780910415	1		362	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0042907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	142	700	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	1	2	FACETS	0.892	0.813	0.976	1	0.989	1	CLONAL	2	FALSE	1	0.172817780910415	2		700	921	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856009	45856009	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	125	538	0	ENST00000391945.4:c.1897C>G	p.Leu633Val	p.L633V	ENST00000391945	NM_000400.3	633	Ctc/Gtc	20/23	0.172817780910415	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	FALSE	0	0.172817780910415	2		538	665	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388063	31388063	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs758473556	NA	P-0042907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	25	244	0	ENST00000328111.2:c.1864A>G	p.Ile622Val	p.I622V	ENST00000328111	NM_006892.3	622	Atc/Gtc	17/23	1	2	FACETS	0.793	0.625	0.986	0.793	0.625	0.986	CLONAL	1	FALSE	1	0.172817780910415	2		244	365	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240795	55240796	+	missense_variant	Missense_Mutation	DNP	GG	GG	AC	novel	NA	P-0042907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	50	681	0	ENST00000275493.2:c.2039_2040delinsAC	p.Arg680His	p.R680H	ENST00000275493	NM_005228.3	680	cGG/cAC	17/28	0.146958660969255	3	FACETS	0.675	0.57	0.79	0.337	0.285	0.395	SUBCLONAL	1	FALSE	1	0.172817780910415	3		681	932	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349434	73349434	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	142	355	0	ENST00000377767.4:c.902A>C	p.Gln301Pro	p.Q301P	ENST00000377767	NM_014953.3	301	cAg/cCg	6/21	NA	2	FACETS	0.861	0.789	0.936			1	INDETERMINATE	1	TRUE	NA	0.601877028595403	2		355	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578448	7578467	+	frameshift_variant	Frame_Shift_Del	DEL	GCCATGGCGCGGACGCGGGT	GCCATGGCGCGGACGCGGGT	-	novel	NA	P-0042933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	724	707	0	ENST00000269305.4:c.463_482del	p.Thr155HisfsTer19	p.T155Hfs*19	ENST00000269305	NM_001126112.2	155	ACCCGCGTCCGCGCCATGGCc/c	5/11	0.56430363887898	3	FACETS	0.93	0.905	0.954	0.93	0.905	0.954	CLONAL	3	TRUE	0	0.601877028595403	3		707	1122	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266546	41266546	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	105	390	0	ENST00000349496.5:c.343G>C	p.Asp115His	p.D115H	ENST00000349496	NM_001904.3	115	Gat/Cat	4/15	0.601877028595403	3	FACETS	0.737	0.661	0.817	0.246	0.22	0.273	SUBCLONAL	1	TRUE	0	0.601877028595403	3		390	616	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391220	89391220	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs750191873	NA	P-0042933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	147	319	0	ENST00000336596.2:c.1286G>T	p.Ser429Ile	p.S429I	ENST00000336596	NM_005233.5	429	aGc/aTc	5/17	0.559207210089297	2	FACETS	1	0.97	1	0.555	0.511	0.6	CLONAL	1	TRUE	0	0.601877028595403	2		319	440	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38178652	38178657	+	inframe_deletion	In_Frame_Del	DEL	TTCTAA	TTCTAA	-	novel	NA	P-0042933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	78	261	0	ENST00000317025.8:c.1742_1747del	p.Ile581_Arg582del	p.I581_R582del	ENST00000317025	NM_023034.1	581	aTTAGAAct/act	8/24	0.559207210089297	2	FACETS	0.611	0.54	0.688	0.306	0.27	0.344	SUBCLONAL	1	TRUE	0	0.601877028595403	2		261	424	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	23	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.784	0.611	0.984	0.784	0.611	0.984	CLONAL	1	TRUE	1	0.18	2		311	326	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	103	697	1	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.18	2		698	1143	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	11	323	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.736	0.51	1	0.736	0.51	1	CLONAL	1	TRUE	1	0.18	2		323	166	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	59	721	8	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.699	0.599	0.808	0.699	0.599	0.808	SUBCLONAL	1	TRUE	1	0.18	2		729	938	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131411	202131411	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs777784105	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	58	489	0	ENST00000358485.4:c.379C>T	p.Arg127Ter	p.R127*	ENST00000358485	NM_001080125.1	127	Cga/Tga	2/9	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.18	2		489	586	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	63	524	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.872	0.752	1	0.872	0.752	1	CLONAL	1	TRUE	1	0.18	2		525	803	SUCCESS
FH	2271	MSKCC	GRCh37	1	241661238	241661238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	39	600	0	ENST00000366560.3:c.1423G>A	p.Ala475Thr	p.A475T	ENST00000366560	NM_000143.3	475	Gca/Aca	10/10	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.18	2		600	412	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735470	40735470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761910971	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	49	785	2	ENST00000373198.4:c.3403G>A	p.Val1135Met	p.V1135M	ENST00000373198	NM_133170.3	1135	Gtg/Atg	25/32	1	2	FACETS	0.643	0.543	0.754	0.643	0.543	0.754	SUBCLONAL	1	TRUE	1	0.18	2		787	847	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440943	56440943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786205215	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	67	703	0	ENST00000407977.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000407977		132	Cga/Tga	4/10	1	2	FACETS	0.83	0.719	0.95	0.83	0.719	0.95	CLONAL	1	TRUE	1	0.18	2		703	897	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	62	888	1	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.664	0.571	0.765	0.664	0.571	0.765	SUBCLONAL	1	TRUE	1	0.18	2		889	1038	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	70	834	0	ENST00000227507.2:c.859C>T	p.Pro287Ser	p.P287S	ENST00000227507	NM_053056.2	287	Ccc/Tcc	5/5	1	2	FACETS	0.753	0.654	0.86	0.753	0.654	0.86	SUBCLONAL	1	TRUE	1	0.18	2		834	1033	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851558	134851558	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs770155473	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	31	486	0	ENST00000398015.3:c.964G>A	p.Val322Ile	p.V322I	ENST00000398015	NM_004441.4	322	Gtc/Atc	5/16	1	2	FACETS	0.562	0.453	0.686	0.562	0.453	0.686	SUBCLONAL	1	TRUE	1	0.18	2		486	613	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430775	78430775	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	40	620	0	ENST00000370768.2:c.614del	p.Gly205GlufsTer17	p.G205Efs*17	ENST00000370768	NM_003902.3	205	gGa/ga	8/20	1	2	FACETS	0.825	0.684	0.981	0.825	0.684	0.981	CLONAL	1	TRUE	1	0.18	2		620	539	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	85	811	4	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	0.953	0.84	1	0.953	0.84	1	CLONAL	1	TRUE	1	0.18	2		815	991	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434991	110434991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	75	759	1	ENST00000375856.3:c.3410G>A	p.Arg1137His	p.R1137H	ENST00000375856	NM_003749.2	1137	cGc/cAc	1/2	1	2	FACETS	0.807	0.706	0.918	0.807	0.706	0.918	CLONAL	1	TRUE	1	0.18	2		760	1032	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058747	180058748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755445139	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	49	661	2	ENST00000261937.6:c.89dup	p.Thr31AspfsTer15	p.T31Dfs*15	ENST00000261937	NM_182925.4	30	ccg/ccCg	2/30	1	2	FACETS	0.655	0.553	0.768	0.655	0.553	0.768	SUBCLONAL	1	TRUE	1	0.18	2		663	831	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405954	157405954	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	64	636	0	ENST00000346085.5:c.2201del	p.Gly734AlafsTer11	p.G734Afs*11	ENST00000346085	NM_020732.3	732	ccG/cc	6/20	0.155417085820447	3	FACETS	0.928	0.802	1	0.464	0.401	0.533	CLONAL	1	TRUE	1	0.18	3		636	835	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2492096	2492097	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs772088410	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	58	736	1	ENST00000355716.4:c.500dup	p.Thr169AspfsTer65	p.T169Dfs*65	ENST00000355716	NM_003820.2	165	tgc/tgCc	5/8	1	2	FACETS	0.683	0.585	0.791	0.683	0.585	0.791	SUBCLONAL	1	TRUE	1	0.18	2		737	943	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991757	72991758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760959844	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	26	350	1	ENST00000268489.5:c.2287dup	p.Glu763GlyfsTer26	p.E763Gfs*26	ENST00000268489	NM_006885.3	763	gag/gGag	2/10	1	2	FACETS	0.646	0.511	0.802	0.646	0.511	0.802	SUBCLONAL	1	TRUE	1	0.18	2		351	447	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	38	621	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	0.155417085820447	3	FACETS	0.882	0.728	1	0.441	0.364	0.527	CLONAL	1	TRUE	1	0.18	3		621	522	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519927	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	33	546	0	ENST00000263967.3:c.1625A>G	p.Glu542Gly	p.E542G	ENST00000263967	NM_006218.2	542	gAa/gGa	10/21	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.18	2		546	334	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223649	36223649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533229757	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	66	829	1	ENST00000222270.7:c.6199G>A	p.Gly2067Ser	p.G2067S	ENST00000222270	NM_014727.1	2067	Ggc/Agc	28/37	1	2	FACETS	0.739	0.639	0.847	0.739	0.639	0.847	SUBCLONAL	1	TRUE	1	0.18	2		830	993	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720666	89720666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	11	198	0	ENST00000371953.3:c.820del	p.Trp274GlyfsTer2	p.W274Gfs*2	ENST00000371953	NM_000314.4	273	Ttt/tt	8/9	1	2	FACETS	0.879	0.61	1	0.879	0.61	1	CLONAL	1	TRUE	1	0.18	2		198	139	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863054	56863054	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1266824391	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	36	621	2	ENST00000519728.1:c.327del	p.Glu110LysfsTer15	p.E110Kfs*15	ENST00000519728	NM_002350.3	107	acA/ac	5/13	1	2	FACETS	0.988	0.813	1	0.988	0.813	1	CLONAL	1	TRUE	1	0.18	2		623	405	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377186	118377186	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1376377461	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	48	527	2	ENST00000534358.1:c.10579C>T	p.Arg3527Trp	p.R3527W	ENST00000534358	NM_005933.3	3527	Cgg/Tgg	27/36	1	2	FACETS	0.818	0.69	0.959	0.818	0.69	0.959	CLONAL	1	TRUE	1	0.18	2		529	652	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864118	57864118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200306754	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	66	617	0	ENST00000228682.2:c.1595G>A	p.Arg532His	p.R532H	ENST00000228682	NM_005269.2	532	cGc/cAc	12/12	1	2	FACETS	0.846	0.733	0.969	0.846	0.733	0.969	CLONAL	1	TRUE	1	0.18	2		617	867	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223996	36223997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs747928028	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	71	862	1	ENST00000222270.7:c.6552dup	p.Lys2185GlnfsTer25	p.K2185Qfs*25	ENST00000222270	NM_014727.1	2182	-/C	28/37	1	2	FACETS	0.731	0.636	0.835	0.731	0.636	0.835	SUBCLONAL	1	TRUE	1	0.18	2		863	1079	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867026	45867026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751177434	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	63	593	1	ENST00000391945.4:c.1093G>A	p.Val365Met	p.V365M	ENST00000391945	NM_000400.3	365	Gtg/Atg	11/23	1	2	FACETS	0.919	0.793	1	0.919	0.793	1	CLONAL	1	TRUE	1	0.18	2		594	762	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803901	43803901	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs780738649	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	58	546	0	ENST00000372470.3:c.211C>T	p.Arg71Trp	p.R71W	ENST00000372470	NM_005373.2	71	Cgg/Tgg	2/12	1	2	FACETS	0.93	0.798	1	0.93	0.798	1	CLONAL	1	TRUE	1	0.18	2		546	693	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755570	39755570	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	43	545	0	ENST00000288319.7:c.1195C>A	p.Leu399Ile	p.L399I	ENST00000288319	NM_182918.3	399	Ctc/Atc	10/10	1	2	FACETS	0.658	0.549	0.779	0.658	0.549	0.779	SUBCLONAL	1	TRUE	1	0.18	2		545	726	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980744	40980744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199751250	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	48	545	0	ENST00000373198.4:c.1742G>A	p.Arg581Gln	p.R581Q	ENST00000373198	NM_133170.3	581	cGg/cAg	10/32	1	2	FACETS	0.89	0.752	1	0.89	0.752	1	CLONAL	1	TRUE	1	0.18	2		545	599	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716236	52716236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs945817997	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	81	706	2	ENST00000322088.6:c.680C>T	p.Ala227Val	p.A227V	ENST00000322088	NM_014225.5	227	gCg/gTg	6/15	1	2	FACETS	0.958	0.843	1	0.958	0.843	1	CLONAL	1	TRUE	1	0.18	2		708	939	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073679	8073679	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776817307	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	76	464	0	ENST00000377482.5:c.980C>T	p.Pro327Leu	p.P327L	ENST00000377482	NM_018948.3	327	cCg/cTg	4/4	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.18	2		464	706	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202717	16202717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756131351	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	45	457	0	ENST00000375759.3:c.425G>A	p.Arg142His	p.R142H	ENST00000375759	NM_015001.2	142	cGt/cAt	3/15	1	2	FACETS	0.88	0.739	1	0.88	0.739	1	CLONAL	1	TRUE	1	0.18	2		457	568	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099874	27099874	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	48	601	0	ENST00000324856.7:c.3756del	p.Asn1253ThrfsTer16	p.N1253Tfs*16	ENST00000324856	NM_006015.4	1251	ggC/gg	15/20	1	2	FACETS	0.666	0.561	0.782	0.666	0.561	0.782	SUBCLONAL	1	TRUE	1	0.18	2		601	801	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106154	27106154	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	62	606	0	ENST00000324856.7:c.5765T>C	p.Leu1922Ser	p.L1922S	ENST00000324856	NM_006015.4	1922	tTg/tCg	20/20	1	2	FACETS	0.919	0.792	1	0.919	0.792	1	CLONAL	1	TRUE	1	0.18	2		606	750	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94926668	94926668	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1407767283	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	17	503	0	ENST00000536441.1:c.97T>C	p.Ser33Pro	p.S33P	ENST00000536441	NM_144665.3	33	Tct/Cct	2/10	1	2	FACETS	0.594	0.443	0.774	0.594	0.443	0.774	SUBCLONAL	1	TRUE	1	0.18	2		503	318	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415906	49415909	+	frameshift_variant	Frame_Shift_Del	DEL	AGTT	AGTT	-	rs587783703	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	50	529	0	ENST00000301067.7:c.16438_16441del	p.Asn5480ValfsTer6	p.N5480Vfs*6	ENST00000301067	NM_003482.3	5480	AACTgt/gt	53/54	1	2	FACETS	0.889	0.753	1	0.889	0.753	1	CLONAL	1	TRUE	1	0.18	2		529	625	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821725	72821725	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	55	450	0	ENST00000268489.5:c.10450C>A	p.Leu3484Met	p.L3484M	ENST00000268489	NM_006885.3	3484	Ctg/Atg	10/10	1	2	FACETS	0.86	0.734	0.997	0.86	0.734	0.997	CLONAL	1	TRUE	1	0.18	2		450	711	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845389	89845389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769158149	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	85	733	0	ENST00000389301.3:c.1738G>A	p.Val580Met	p.V580M	ENST00000389301	NM_000135.2	580	Gtg/Atg	19/43	1	2	FACETS	0.992	0.875	1	0.992	0.875	1	CLONAL	1	TRUE	1	0.18	2		733	952	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302606	15302606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555729405	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	86	858	0	ENST00000263388.2:c.752G>A	p.Cys251Tyr	p.C251Y	ENST00000263388	NM_000435.2	251	tGc/tAc	5/33	1	2	FACETS	0.936	0.826	1	0.936	0.826	1	CLONAL	1	TRUE	1	0.18	2		858	1021	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795574	42795574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	95	936	1	ENST00000575354.2:c.2654G>A	p.Gly885Asp	p.G885D	ENST00000575354	NM_015125.3	885	gGc/gAc	10/20	1	2	FACETS	0.966	0.858	1	0.966	0.858	1	CLONAL	1	TRUE	1	0.18	2		937	1093	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703652	47703652	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779139	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	38	547	0	ENST00000233146.2:c.2152C>T	p.Gln718Ter	p.Q718*	ENST00000233146	NM_000251.2	718	Caa/Taa	13/16	1	2	FACETS	0.683	0.564	0.817	0.683	0.564	0.817	SUBCLONAL	1	TRUE	1	0.18	2		547	618	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149800	202149800	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	69	650	0	ENST00000358485.4:c.1241T>C	p.Phe414Ser	p.F414S	ENST00000358485	NM_001080125.1	414	tTt/tCt	8/9	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.18	2		650	664	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721214	39721214	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	31	525	2	ENST00000361337.2:c.717G>T	p.Lys239Asn	p.K239N	ENST00000361337	NM_003286.2	239	aaG/aaT	9/21	1	2	FACETS	0.944	0.764	1	0.944	0.764	1	CLONAL	1	TRUE	1	0.18	2		527	365	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928496	69928496	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	80	743	0	ENST00000352241.4:c.316C>A	p.Leu106Ile	p.L106I	ENST00000352241	NM_198159.2	106	Ctt/Att	2/10	1	2	FACETS	0.889	0.78	1	0.889	0.78	1	CLONAL	1	TRUE	1	0.18	2		743	1000	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445013	89445013	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	44	541	0	ENST00000336596.2:c.1333A>G	p.Lys445Glu	p.K445E	ENST00000336596	NM_005233.5	445	Aaa/Gaa	6/17	1	2	FACETS	0.844	0.707	0.996	0.844	0.707	0.996	CLONAL	1	TRUE	1	0.18	2		541	579	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517945	176517945	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	58	630	0	ENST00000292408.4:c.443A>G	p.Tyr148Cys	p.Y148C	ENST00000292408	NM_213647.1	148	tAc/tGc	5/18	1	2	FACETS	0.944	0.81	1	0.944	0.81	1	CLONAL	1	TRUE	1	0.18	2		630	683	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911082	29911082	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1449230893	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	64	940	0	ENST00000376809.5:c.384del	p.Ser129ArgfsTer22	p.S129Rfs*22	ENST00000376809	NM_002116.7	127	gtG/gt	3/8	0.155417085820447	3	FACETS	0.62	0.534	0.713	0.31	0.267	0.357	SUBCLONAL	1	TRUE	1	0.18	3		940	1251	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859666	151859666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	39	492	0	ENST00000262189.6:c.10996C>T	p.Pro3666Ser	p.P3666S	ENST00000262189	NM_170606.2	3666	Cca/Tca	43/59	1	2	FACETS	0.764	0.632	0.912	0.764	0.632	0.912	CLONAL	1	TRUE	1	0.18	2		492	567	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874093	151874093	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	32	630	0	ENST00000262189.6:c.8445del	p.Lys2815AsnfsTer8	p.K2815Nfs*8	ENST00000262189	NM_170606.2	2815	aaA/aa	38/59	1	2	FACETS	0.887	0.72	1	0.887	0.72	1	CLONAL	1	TRUE	1	0.18	2		630	401	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912295	97912295	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs143213659	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	68	567	0	ENST00000289081.3:c.596T>C	p.Leu199Pro	p.L199P	ENST00000289081	NM_000136.2	199	cTg/cCg	7/15	1	2	FACETS	0.993	0.863	1	0.993	0.863	1	CLONAL	1	TRUE	1	0.18	2		567	761	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249857	110249857	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	60	808	0	ENST00000374672.4:c.818del	p.Thr273SerfsTer53	p.T273Sfs*53	ENST00000374672	NM_004235.4	273	aCg/ag	3/5	1	2	FACETS	0.712	0.612	0.822	0.712	0.612	0.822	SUBCLONAL	1	TRUE	1	0.18	2		808	936	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419996	41419996	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	55	812	0	ENST00000373198.4:c.325T>G	p.Phe109Val	p.F109V	ENST00000373198	NM_133170.3	109	Ttc/Gtc	3/32	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.12	2		812	909	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	126	745	7	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	0.151881016389823	3	FACETS	1	0.982	1	0.663	0.604	0.724	INDETERMINATE	1	TRUE	1	0.5	3		752	475	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	47	587	6	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.79	0.673	0.917	0.79	0.673	0.917	CLONAL	1	TRUE	1	0.5	2		593	238	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	66	554	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.767	0.67	0.871	0.767	0.67	0.871	SUBCLONAL	1	TRUE	1	0.5	2		554	344	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	240	1123	2	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	0.151881016389823	3	FACETS	0.799	0.749	0.85	0.799	0.749	0.85	INDETERMINATE	2	TRUE	1	0.5	3		1125	751	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438316	110438317	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	rs532810290	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	39	196	1	ENST00000375856.3:c.82_84dup	p.Asn28dup	p.N28dup	ENST00000375856	NM_003749.2	28	-/AAC	1/2	0.216928284323884	4	FACETS	0.707	0.588	0.839	0.353	0.294	0.42	INDETERMINATE	1	TRUE	2	0.5	4		197	331	SUCCESS
APC	324	MSKCC	GRCh37	5	112178804	112178804	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	45	477	0	ENST00000257430.4:c.7513C>T	p.Arg2505Ter	p.R2505*	ENST00000257430	NM_000038.5	2505	Cga/Tga	16/16	1	2	FACETS	0.793	0.673	0.923	0.793	0.673	0.923	CLONAL	1	TRUE	1	0.5	2		477	227	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	126	621	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	0.151881016389823	3	FACETS	0.963	0.884	1	0.963	0.884	1	INDETERMINATE	2	TRUE	1	0.5	3		621	327	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489535	56489535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1403278713	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	124	710	0	ENST00000267101.3:c.2000G>A	p.Arg667His	p.R667H	ENST00000267101	NM_001982.3	667	cGt/cAt	17/28	0.216928284323884	4	FACETS	1	0.972	1	0.594	0.539	0.652	INDETERMINATE	1	TRUE	2	0.5	4		710	626	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916957	178916957	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200018596	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	26	409	0	ENST00000263967.3:c.344G>T	p.Arg115Leu	p.R115L	ENST00000263967	NM_006218.2	115	cGa/cTa	2/21	0.216928284323884	3	FACETS	0.537	0.427	0.662	0.269	0.213	0.331	INDETERMINATE	1	TRUE	1	0.5	3		409	242	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223917	53223917	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782205045	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	107	993	0	ENST00000375401.3:c.3442G>A	p.Val1148Met	p.V1148M	ENST00000375401	NM_004187.3	1148	Gtg/Atg	23/26	1	2	FACETS	0.872	0.786	0.962	0.872	0.786	0.962	CLONAL	1	TRUE	1	0.5	2		993	491	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	105	454	5	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	0.151881016389823	3	FACETS	0.717	0.643	0.796	0.359	0.321	0.398	INDETERMINATE	1	TRUE	1	0.5	3		459	732	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154241	2154242	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755455183	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	147	1000	5	ENST00000434045.2:c.686dup	p.Glu230ArgfsTer50	p.E230Rfs*50	ENST00000434045	NM_001127598.1	229	cca/ccCa	5/5	0.151881016389823	3	FACETS	1	0.971	1	0.568	0.52	0.618	INDETERMINATE	1	TRUE	1	0.5	3		1005	647	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416659	29416659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	86	606	1	ENST00000389048.3:c.4294C>T	p.Arg1432Trp	p.R1432W	ENST00000389048	NM_004304.4	1432	Cgg/Tgg	29/29	1	2	FACETS	0.986	0.879	1	0.986	0.879	1	CLONAL	1	TRUE	1	0.5	2		607	349	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806177	1806177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761896295	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	233	986	0	ENST00000260795.2:c.1196G>A	p.Arg399His	p.R399H	ENST00000260795		399	cGc/cAc	8/17	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.5	2		986	733	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	201	1102	7	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	0.151881016389823	3	FACETS	1	0.985	1	0.617	0.572	0.662	INDETERMINATE	1	TRUE	1	0.5	3		1109	815	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026194	71026194	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	43	371	0	ENST00000318789.4:c.1429-1G>T		p.X477_splice	ENST00000318789	NM_032682.5	477			0.216928284323884	3	FACETS	0.76	0.639	0.891	0.38	0.319	0.446	INDETERMINATE	1	TRUE	1	0.5	3		371	283	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752695	42752695	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1366176199	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	204	897	5	ENST00000222329.4:c.1569del	p.Leu525SerfsTer6	p.L525Sfs*6	ENST00000222329	NM_006494.2	523	ggG/gg	4/4	0.151881016389823	3	FACETS	1	0.988	1	0.652	0.606	0.7	INDETERMINATE	1	TRUE	1	0.5	3		902	782	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599970	10599970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749651891	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	242	997	0	ENST00000171111.5:c.1606C>T	p.Arg536Cys	p.R536C	ENST00000171111	NM_203500.1	536	Cgc/Tgc	5/6	0.151881016389823	3	FACETS	1	0.99	1	0.658	0.615	0.701	INDETERMINATE	1	TRUE	1	0.5	3		997	920	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231345	5231345	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765642813	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	148	842	1	ENST00000357368.4:c.2131G>A	p.Val711Met	p.V711M	ENST00000357368	NM_002850.3	711	Gtg/Atg	14/38	0.151881016389823	3	FACETS	1	0.981	1	0.624	0.572	0.678	INDETERMINATE	1	TRUE	1	0.5	3		843	593	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992720	68992721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs764112302	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	90	767	7	ENST00000288368.4:c.1693dup	p.Ser565PhefsTer3	p.S565Ffs*3	ENST00000288368	NM_024870.2	562	cgt/cgTt	16/40	0.151881016389823	3	FACETS	1	0.919	1	0.518	0.462	0.578	INDETERMINATE	1	TRUE	1	0.5	3		774	434	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937422	178937422	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	39	280	0	ENST00000263967.3:c.1810T>C	p.Cys604Arg	p.C604R	ENST00000263967	NM_006218.2	604	Tgt/Cgt	12/21	0.216928284323884	3	FACETS	0.951	0.797	1	0.476	0.398	0.56	INDETERMINATE	1	TRUE	1	0.5	3		280	205	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256265	16256265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	82	668	0	ENST00000375759.3:c.3530G>A	p.Arg1177His	p.R1177H	ENST00000375759	NM_015001.2	1177	cGt/cAt	11/15	0.151881016389823	3	FACETS	0.96	0.851	1	0.48	0.425	0.538	INDETERMINATE	1	TRUE	1	0.5	3		668	427	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741906	40741906	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568518786	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	237	909	0	ENST00000392038.2:c.1066G>A	p.Glu356Lys	p.E356K	ENST00000392038	NM_001626.4	356	Gag/Aag	11/14	0.151881016389823	3	FACETS	1	0.992	1	0.735	0.688	0.783	INDETERMINATE	1	TRUE	1	0.5	3		909	806	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220899	36220899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555731828	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	53	363	0	ENST00000222270.7:c.4949C>T	p.Thr1650Met	p.T1650M	ENST00000222270	NM_014727.1	1650	aCg/aTg	23/37	0.151881016389823	3	FACETS	0.927	0.81	1	0.927	0.81	1	INDETERMINATE	2	TRUE	1	0.5	3		363	143	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89444996	89444996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	39	480	0	ENST00000336596.2:c.1316C>T	p.Pro439Leu	p.P439L	ENST00000336596	NM_005233.5	439	cCt/cTt	6/17	0.216928284323884	3	FACETS	0.717	0.597	0.848	0.358	0.298	0.424	INDETERMINATE	1	TRUE	1	0.5	3		480	272	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420625	49420625	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	134	814	0	ENST00000301067.7:c.15124del	p.Ala5042ProfsTer9	p.A5042Pfs*9	ENST00000301067	NM_003482.3	5042	Gcc/cc	48/54	0.216928284323884	4	FACETS	1	0.97	1	0.576	0.524	0.63	INDETERMINATE	1	TRUE	2	0.5	4		814	698	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257653	16257653	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1269904215	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	96	604	0	ENST00000375759.3:c.4918C>T	p.Pro1640Ser	p.P1640S	ENST00000375759	NM_015001.2	1640	Cca/Tca	11/15	0.151881016389823	3	FACETS	1	0.935	1	0.53	0.474	0.588	INDETERMINATE	1	TRUE	1	0.5	3		604	453	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023751	27023752	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	121	421	0	ENST00000324856.7:c.858_859del	p.Gln288AlafsTer111	p.Q288Afs*111	ENST00000324856	NM_006015.4	286	aCT/a	1/20	0.151881016389823	3	FACETS	0.962	0.871	1	0.481	0.435	0.529	INDETERMINATE	1	TRUE	1	0.5	3		421	629	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089697	27089697	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	123	706	2	ENST00000324856.7:c.2657del	p.Pro886HisfsTer5	p.P886Hfs*5	ENST00000324856	NM_006015.4	885	Ccc/cc	8/20	0.151881016389823	3	FACETS	1	0.936	1	0.52	0.472	0.571	INDETERMINATE	1	TRUE	1	0.5	3		708	591	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102070	27102070	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	138	675	0	ENST00000324856.7:c.4996A>G	p.Thr1666Ala	p.T1666A	ENST00000324856	NM_006015.4	1666	Acc/Gcc	19/20	0.151881016389823	3	FACETS	1	0.972	1	0.576	0.526	0.628	INDETERMINATE	1	TRUE	1	0.5	3		675	599	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981135	201981136	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	202	853	0	ENST00000359651.3:c.216dup	p.Leu73SerfsTer19	p.L73Sfs*19	ENST00000359651		72	gtt/gTtt	2/8	0.151881016389823	3	FACETS	1	0.988	1	0.653	0.607	0.701	INDETERMINATE	1	TRUE	1	0.5	3		853	773	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917624	94917624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	58	580	0	ENST00000536441.1:c.897del	p.Phe299LeufsTer20	p.F299Lfs*20	ENST00000536441	NM_144665.3	299	ttT/tt	6/10	0.151881016389823	3	FACETS	0.702	0.605	0.807	0.351	0.302	0.404	INDETERMINATE	1	TRUE	1	0.5	3		580	413	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236119	108236119	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	99	661	0	ENST00000278616.4:c.9055G>T	p.Gly3019Ter	p.G3019*	ENST00000278616	NM_000051.3	3019	Gga/Tga	63/63	0.151881016389823	3	FACETS	1	0.978	1	0.667	0.601	0.737	INDETERMINATE	1	TRUE	1	0.5	3		661	371	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906952	32906952	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	44	520	0	ENST00000380152.3:c.1337T>C	p.Leu446Ser	p.L446S	ENST00000380152		446	tTg/tCg	10/27	0.216928284323884	4	FACETS	1	0.95	1	0.66	0.56	0.768	INDETERMINATE	1	TRUE	2	0.5	4		520	200	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640588	3640588	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	255	1057	1	ENST00000294008.3:c.3051G>T	p.Glu1017Asp	p.E1017D	ENST00000294008	NM_032444.2	1017	gaG/gaT	12/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.5	2		1058	914	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347402	89347402	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	174	952	0	ENST00000301030.4:c.5548T>C	p.Tyr1850His	p.Y1850H	ENST00000301030	NM_001256183.1	1850	Tac/Cac	9/13	1	2	FACETS	0.982	0.906	1	0.982	0.906	1	CLONAL	1	TRUE	1	0.5	2		952	709	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362202	40362202	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	78	538	0	ENST00000293328.3:c.1893G>T	p.Trp631Cys	p.W631C	ENST00000293328	NM_012448.3	631	tgG/tgT	15/19	0.151881016389823	3	FACETS	0.99	0.875	1	0.495	0.437	0.556	INDETERMINATE	1	TRUE	1	0.5	3		538	394	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805751	46805751	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	108	836	0	ENST00000290295.7:c.205del	p.Val69CysfsTer29	p.V69Cfs*29	ENST00000290295	NM_006361.5	69	Gtg/tg	1/2	0.151881016389823	3	FACETS	1	0.972	1	0.603	0.544	0.664	INDETERMINATE	1	TRUE	1	0.5	3		836	448	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985768	60985768	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	18	334	0	ENST00000333681.4:c.132del	p.Ala45HisfsTer51	p.A45Hfs*51	ENST00000333681		44	ccC/cc	2/3	0.151881016389823	3	FACETS	0.279	0.209	0.361	0.139	0.104	0.181	INDETERMINATE	1	TRUE	1	0.5	3		334	323	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097631	11097631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769414440	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	211	1082	1	ENST00000358026.2:c.811G>A	p.Gly271Arg	p.G271R	ENST00000358026	NM_001128849.1	271	Ggg/Agg	5/36	0.151881016389823	3	FACETS	1	0.982	1	0.582	0.54	0.624	INDETERMINATE	1	TRUE	1	0.5	3		1083	907	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965994	18965994	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773934024	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	57	804	0	ENST00000262803.5:c.1487C>T	p.Thr496Met	p.T496M	ENST00000262803	NM_002911.3	496	aCg/aTg	11/24	0.151881016389823	3	FACETS	0.383	0.327	0.443	0.191	0.163	0.222	INDETERMINATE	1	TRUE	1	0.5	3		804	745	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214900	36214900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768950486	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	183	961	0	ENST00000222270.7:c.3326G>A	p.Arg1109Gln	p.R1109Q	ENST00000222270	NM_014727.1	1109	cGa/cAa	8/37	0.151881016389823	3	FACETS	1	0.975	1	0.562	0.519	0.606	INDETERMINATE	1	TRUE	1	0.5	3		961	814	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909458	50909458	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	236	989	0	ENST00000440232.2:c.1262T>C	p.Leu421Pro	p.L421P	ENST00000440232	NM_002691.3	421	cTg/cCg	11/27	0.151881016389823	3	FACETS	0.775	0.726	0.826	0.775	0.726	0.826	INDETERMINATE	2	TRUE	1	0.5	3		989	761	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690264	47690264	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	51	456	0	ENST00000233146.2:c.1481C>A	p.Ser494Ter	p.S494*	ENST00000233146	NM_000251.2	494	tCa/tAa	9/16	1	2	FACETS	0.788	0.675	0.909	0.788	0.675	0.909	CLONAL	1	TRUE	1	0.5	2		456	259	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873203	136873203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755899324	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	85	487	0	ENST00000241393.3:c.295G>A	p.Val99Met	p.V99M	ENST00000241393	NM_003467.2	99	Gtg/Atg	2/2	1	2	FACETS	0.983	0.876	1	0.983	0.876	1	CLONAL	1	TRUE	1	0.5	2		487	346	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546027	41546027	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	120	948	0	ENST00000263253.7:c.2642C>A	p.Pro881His	p.P881H	ENST00000263253	NM_001429.3	881	cCt/cAt	14/31	1	2	FACETS	0.598	0.54	0.659	0.598	0.54	0.659	SUBCLONAL	1	TRUE	1	0.5	2		948	803	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940886	49940886	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	229	1006	1	ENST00000296474.3:c.157G>T	p.Gly53Cys	p.G53C	ENST00000296474	NM_002447.2	53	Ggc/Tgc	1/20	0.216928284323884	3	FACETS	1	0.992	1	0.725	0.677	0.773	INDETERMINATE	1	TRUE	1	0.5	3		1007	790	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851807	134851807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1406552743	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	128	801	0	ENST00000398015.3:c.1213G>A	p.Asp405Asn	p.D405N	ENST00000398015	NM_004441.4	405	Gac/Aac	5/16	0.216928284323884	3	FACETS	1	0.977	1	0.611	0.556	0.668	INDETERMINATE	1	TRUE	1	0.5	3		801	524	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541130	187541130	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750302176	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	66	433	0	ENST00000441802.2:c.6610G>A	p.Val2204Met	p.V2204M	ENST00000441802	NM_005245.3	2204	Gtg/Atg	10/27	1	2	FACETS	0.868	0.76	0.984	0.868	0.76	0.984	CLONAL	1	TRUE	1	0.5	2		433	304	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797269	32797269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs972577711	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	192	1014	1	ENST00000374899.4:c.1840C>T	p.Arg614Cys	p.R614C	ENST00000374899	NM_018833.2	614	Cgt/Tgt	11/12	0.292454285034035	4	FACETS	1	0.976	1	0.566	0.523	0.611	INDETERMINATE	1	TRUE	2	0.5	4		1015	1017	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137323818	137323818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043033-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	177	992	1	ENST00000481739.1:c.1111C>T	p.Arg371Cys	p.R371C	ENST00000481739	NM_002957.4	371	Cgc/Tgc	8/10	1	2	FACETS	0.897	0.828	0.969	0.897	0.828	0.969	CLONAL	1	TRUE	1	0.5	2		993	789	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519922	NA	P-0043041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	63	521	0	ENST00000397062.3:c.235G>A	p.Glu79Lys	p.E79K	ENST00000397062	NM_006164.4	79	Gag/Aag	2/5	1	2	FACETS	0.863	0.746	0.992	0.863	0.746	0.992	CLONAL	1	TRUE	1	0.19	2		521	768	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682896	241682896	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs200496951	NA	P-0043041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	34	333	0	ENST00000366560.3:c.127C>G	p.Arg43Gly	p.R43G	ENST00000366560	NM_000143.3	43	Cga/Gga	1/10	1	2	FACETS	0.733	0.599	0.885	0.733	0.599	0.885	SUBCLONAL	1	TRUE	1	0.19	2		333	488	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783617	50783617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	31	358	1	ENST00000398568.2:c.8C>T	p.Ser3Leu	p.S3L	ENST00000398568	NM_001042412.1	3	tCa/tTa	3/18	1	2	FACETS	0.743	0.601	0.905	0.743	0.601	0.905	CLONAL	1	TRUE	1	0.19	2		359	439	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226934	2226934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	26	362	0	ENST00000398665.3:c.4414C>T	p.Pro1472Ser	p.P1472S	ENST00000398665	NM_032482.2	1472	Ccg/Tcg	27/28	1	2	FACETS	0.551	0.435	0.684	0.551	0.435	0.684	SUBCLONAL	1	TRUE	1	0.19	2		362	497	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522456	187522456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	98	501	0	ENST00000441802.2:c.11607G>A	p.Met3869Ile	p.M3869I	ENST00000441802	NM_005245.3	3869	atG/atA	21/27	0.156430951494309	3	FACETS	0.807	0.72	0.899	0.807	0.72	0.899	CLONAL	2	TRUE	1	0.19	3		501	700	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931775	39931775	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	75	620	0	ENST00000378444.4:c.2824G>C	p.Asp942His	p.D942H	ENST00000378444	NM_001123385.1	942	Gat/Cat	4/15	1	2	FACETS	0.886	0.775	1	0.886	0.775	1	CLONAL	1	TRUE	1	0.19	2		620	891	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	204	348	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.851867278738679	2		349	421	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427046	49427047	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	rs1371040047	NA	P-0043047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	177	572	0	ENST00000301067.7:c.11439_11441dup	p.Gln3813dup	p.Q3813dup	ENST00000301067	NM_003482.3	3813	cac/caGCAc	39/54	1	2	FACETS	0.774	0.718	0.831	0.774	0.718	0.831	SUBCLONAL	1	TRUE	1	0.851867278738679	2		572	537	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212018	36212018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781774179	NA	P-0043047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	467	1007	1	ENST00000222270.7:c.1769C>T	p.Pro590Leu	p.P590L	ENST00000222270	NM_014727.1	590	cCa/cTa	3/37	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.851867278738679	2		1008	1084	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139742	55139742	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7607	4882	534	0	ENST00000257290.5:c.1403A>G	p.Asn468Ser	p.N468S	ENST00000257290	NM_006206.4	468	aAt/aGt	10/23	0.851867278738679	37	FACETS	0.973	0.96	0.987			1	CLONAL	15	TRUE	NA	0.851867278738679	37		534	12489	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043047-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	78	348	1				ENST00000310581	NM_198253.2	-/1132			0.256523675456514	1	FACETS	0.556	0.495	0.62	0.556	0.495	0.62	INDETERMINATE	1	FALSE	0	0.697203101269699	1		349	262	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427046	49427047	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	rs1371040047	NA	P-0043047-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	187	572	0	ENST00000301067.7:c.11439_11441dup	p.Gln3813dup	p.Q3813dup	ENST00000301067	NM_003482.3	3813	cac/caGCAc	39/54	0.519085442890812	3	FACETS	1	0.972	1			1	CLONAL	1	FALSE	NA	0.697203101269699	3		572	662	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212018	36212018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781774179	NA	P-0043047-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	418	1007	1	ENST00000222270.7:c.1769C>T	p.Pro590Leu	p.P590L	ENST00000222270	NM_014727.1	590	cCa/cTa	3/37	0.163050577295047	3	FACETS	1	0.995	1	0.667	0.636	0.699	INDETERMINATE	1	FALSE	1	0.697203101269699	3		1008	1212	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133833	55133833	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043047-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7996	2561	484	0	ENST00000257290.5:c.1046G>T	p.Trp349Leu	p.W349L	ENST00000257290	NM_006206.4	349	tGg/tTg	7/23	0.697203101269699	47	FACETS	0.968	0.948	0.988			1	CLONAL	12	FALSE	NA	0.697203101269699	47		484	10557	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	45	398	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.902	0.761	1	0.902	0.761	1	CLONAL	1	TRUE	1	0.31	2		398	322	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	86	368	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.933	0.826	1	0.933	0.826	1	CLONAL	1	TRUE	1	0.31	2		371	595	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	117	709	11	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.31	2		720	560	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131411	202131411	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs777784105	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	109	489	0	ENST00000358485.4:c.379C>T	p.Arg127Ter	p.R127*	ENST00000358485	NM_001080125.1	127	Cga/Tga	2/9	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.31	2		489	573	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682399	52682400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	32	296	0	ENST00000394830.3:c.773dup	p.Asn258LysfsTer6	p.N258Kfs*6	ENST00000394830	NM_018313.4	258	aat/aaAt	8/30	0.300402526190358	1	FACETS	0.746	0.609	0.898	0.746	0.609	0.898	SUBCLONAL	1	TRUE	0	0.31	1		296	234	SUCCESS
APC	324	MSKCC	GRCh37	5	112175675	112175676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	36	368	0	ENST00000257430.4:c.4393_4394dup	p.Ser1465ArgfsTer9	p.S1465Rfs*9	ENST00000257430	NM_000038.5	1462	aag/aAGag	16/16	1	2	FACETS	0.647	0.533	0.774	0.647	0.533	0.774	SUBCLONAL	1	TRUE	1	0.31	2		368	359	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	95	845	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.754	0.671	0.843	0.754	0.671	0.843	SUBCLONAL	1	TRUE	1	0.31	2		845	813	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521487	8521487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758577045	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	108	478	0	ENST00000356435.5:c.751G>A	p.Gly251Arg	p.G251R	ENST00000356435		251	Gga/Aga	9/35	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.31	2		478	694	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	71	429	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	0.757	0.661	0.861	0.757	0.661	0.861	SUBCLONAL	1	TRUE	1	0.31	2		429	605	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935633	13935633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756650303	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	91	402	0	ENST00000405192.2:c.1223G>A	p.Arg408His	p.R408H	ENST00000405192	NM_001163147.1	408	cGt/cAt	12/12	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.31	2		402	561	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	60	432	1	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	1	2	FACETS	0.641	0.552	0.738	0.641	0.552	0.738	SUBCLONAL	1	TRUE	1	0.31	2		433	604	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424734	47424734	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	111	577	3	ENST00000377045.4:c.547del	p.Gln183ArgfsTer109	p.Q183Rfs*109	ENST00000377045	NM_001654.4	181	aCc/ac	6/16	1	2	FACETS	0.969	0.872	1	0.969	0.872	1	CLONAL	1	TRUE	1	0.31	2		580	739	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219908	133219908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs969429633	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	214	604	0	ENST00000320574.5:c.4453C>T	p.Arg1485Cys	p.R1485C	ENST00000320574	NM_006231.2	1485	Cgc/Tgc	35/49	0.300402526190358	3	FACETS	0.923	0.859	0.989	0.923	0.859	0.989	CLONAL	2	TRUE	1	0.31	3		604	864	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	28	103	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.31	2		103	170	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043355	6043355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188006077	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	41	196	1	ENST00000265849.7:c.319C>T	p.Arg107Trp	p.R107W	ENST00000265849	NM_000535.5	107	Cgg/Tgg	4/15	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.31	2		197	194	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907421	32907421	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359306	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	34	273	3	ENST00000380152.3:c.1813del	p.Ile605TyrfsTer9	p.I605Yfs*9	ENST00000380152		602	ggA/gg	10/27	1	2	FACETS	0.91	0.748	1	0.91	0.748	1	CLONAL	1	TRUE	1	0.31	2		276	241	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178635	32178635	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs761063325	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	134	768	4	ENST00000375023.3:c.2759del	p.Pro920LeufsTer12	p.P920Lfs*12	ENST00000375023	NM_004557.3	920	cCt/ct	18/30	1	2	FACETS	0.968	0.879	1	0.968	0.879	1	CLONAL	1	TRUE	1	0.31	2		772	893	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204869	128204869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767059760	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	184	871	0	ENST00000341105.2:c.572C>T	p.Ala191Val	p.A191V	ENST00000341105	NM_032638.4	191	gCg/gTg	3/6	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.31	2		871	953	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042300	42042301	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs866465268	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	78	483	0	ENST00000219905.7:c.6499_6500del	p.Leu2167GlyfsTer27	p.L2167Gfs*27	ENST00000219905	NM_001164273.1	2165	gaCTct/gact	17/24	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.31	2		483	496	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542357	187542357	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs769432838	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	64	322	0	ENST00000441802.2:c.5383C>T	p.Arg1795Ter	p.R1795*	ENST00000441802	NM_005245.3	1795	Cga/Tga	10/27	0.300402526190358	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.31	1		322	251	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196879	108196880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs773570504	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	56	321	0	ENST00000278616.4:c.6908dup	p.Glu2304GlyfsTer69	p.E2304Gfs*69	ENST00000278616	NM_000051.3	2301	gca/gcAa	47/63	0.300402526190358	2	FACETS	0.961	0.827	1	0.48	0.413	0.553	CLONAL	1	TRUE	0	0.31	2		321	376	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270726	10270726	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	98	487	0	ENST00000340748.4:c.1009del	p.Met337TrpfsTer8	p.M337Wfs*8	ENST00000340748		337	Atg/tg	14/40	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.31	2		487	613	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273944	10273944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	146	886	3	ENST00000330684.3:c.325G>A	p.Val109Ile	p.V109I	ENST00000330684	NM_001134407.1	109	Gta/Ata	2/13	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.31	2		889	884	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524967	8524967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	58	316	0	ENST00000356435.5:c.637G>A	p.Ala213Thr	p.A213T	ENST00000356435		213	Gcg/Acg	7/35	1	2	FACETS	0.9	0.775	1	0.9	0.775	1	CLONAL	1	TRUE	1	0.31	2		316	416	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919734	50919734	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878854545	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	114	751	0	ENST00000440232.2:c.2902C>T	p.Arg968Cys	p.R968C	ENST00000440232	NM_002691.3	968	Cgc/Tgc	23/27	1	2	FACETS	0.751	0.675	0.832	0.751	0.675	0.832	SUBCLONAL	1	TRUE	1	0.31	2		751	979	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs753143066	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	110	625	7	ENST00000295797.4:c.826dup	p.Thr276AsnfsTer16	p.T276Nfs*16	ENST00000295797	NM_002740.5	273	tta/ttAa	9/18	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.31	2		632	702	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200946	108200946	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147604227	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	42	268	0	ENST00000278616.4:c.7313C>T	p.Thr2438Ile	p.T2438I	ENST00000278616	NM_000051.3	2438	aCa/aTa	50/63	0.300402526190358	2	FACETS	1	0.884	1	0.531	0.447	0.624	CLONAL	1	TRUE	0	0.31	2		268	255	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953214	81953214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369516453	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	65	373	1	ENST00000359376.3:c.2180G>A	p.Arg727Gln	p.R727Q	ENST00000359376	NM_002661.3	727	cGa/cAa	20/33	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.31	2		374	403	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897444	78897444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746953724	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	136	771	1	ENST00000306801.3:c.2779C>T	p.Arg927Trp	p.R927W	ENST00000306801	NM_020761.2	927	Cgg/Tgg	23/34	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.31	2		772	857	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265516	152265517	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	101	523	1	ENST00000206249.3:c.974dup	p.Ile326AspfsTer7	p.I326Dfs*7	ENST00000206249	NM_000125.3	323	-/C	4/8	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.31	2		524	564	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778452	3778452	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs765821935	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	117	799	3	ENST00000262367.5:c.6596A>T	p.Gln2199Leu	p.Q2199L	ENST00000262367	NM_004380.2	2199	cAg/cTg	31/31	1	2	FACETS	0.898	0.809	0.991	0.898	0.809	0.991	CLONAL	1	TRUE	1	0.31	2		802	841	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874092	151874093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	66	522	0	ENST00000262189.6:c.8445dup	p.Ser2816IlefsTer6	p.S2816Ifs*6	ENST00000262189	NM_170606.2	2815	-/A	38/59	1	2	FACETS	0.961	0.837	1	0.961	0.837	1	CLONAL	1	TRUE	1	0.31	2		522	443	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324886	31324887	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760037174	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	51	525	0	ENST00000412585.2:c.49_50insG	p.Leu17ArgfsTer82	p.L17Rfs*82	ENST00000412585	NM_005514.6	17	ctg/cGtg	1/8	1	2	FACETS	0.559	0.474	0.651	0.559	0.474	0.651	SUBCLONAL	1	TRUE	1	0.31	2		525	589	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933438	49933438	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	131	693	1	ENST00000296474.3:c.2752del	p.Leu918CysfsTer18	p.L918Cfs*18	ENST00000296474	NM_002447.2	918	Ctg/tg	11/20	0.300402526190358	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.31	1		694	637	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948747	71948748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760925109	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	136	757	9	ENST00000298229.2:c.3466dup	p.Arg1156ProfsTer59	p.R1156Pfs*59	ENST00000298229	NM_001567.3	1153	-/C	26/28	0.300402526190358	2	FACETS	1	0.956	1	0.542	0.492	0.593	CLONAL	1	TRUE	0	0.31	2		766	810	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520202	176520202	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763979974	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	137	858	1	ENST00000292408.4:c.1121C>T	p.Ala374Val	p.A374V	ENST00000292408	NM_213647.1	374	gCg/gTg	9/18	1	2	FACETS	0.936	0.851	1	0.936	0.851	1	CLONAL	1	TRUE	1	0.31	2		859	944	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929161	32929162	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs397507899	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	50	499	0	ENST00000380152.3:c.7177dup	p.Met2393AsnfsTer19	p.M2393Nfs*19	ENST00000380152		2391	gaa/gAaa	14/27	1	2	FACETS	0.932	0.794	1	0.932	0.794	1	CLONAL	1	TRUE	1	0.31	2		499	346	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097143	11097143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886937766	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	141	779	1	ENST00000358026.2:c.634G>A	p.Gly212Arg	p.G212R	ENST00000358026	NM_001128849.1	212	Ggg/Agg	4/36	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.31	2		780	793	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525977	41525977	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	49	458	0	ENST00000263253.7:c.1256del	p.Asn419MetfsTer12	p.N419Mfs*12	ENST00000263253	NM_001429.3	418	Aaa/aa	5/31	1	2	FACETS	0.83	0.705	0.966	0.83	0.705	0.966	CLONAL	1	TRUE	1	0.31	2		458	381	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161392	55161392	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767697835	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	102	472	0	ENST00000257290.5:c.3223G>A	p.Asp1075Asn	p.D1075N	ENST00000257290	NM_006206.4	1075	Gac/Aac	23/23	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.31	2		472	610	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355204	15355204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147958185	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	127	821	1	ENST00000263377.2:c.2419G>A	p.Val807Ile	p.V807I	ENST00000263377	NM_058243.2	807	Gtc/Atc	13/20	1	2	FACETS	0.954	0.864	1	0.954	0.864	1	CLONAL	1	TRUE	1	0.31	2		822	859	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961526	54961526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1211313151	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	78	497	0	ENST00000312783.6:c.106C>T	p.Pro36Ser	p.P36S	ENST00000312783	NM_198436.1	36	Cca/Tca	4/10	1	2	FACETS	0.866	0.762	0.978	0.866	0.762	0.978	CLONAL	1	TRUE	1	0.31	2		497	581	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226712	2226712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780009010	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	118	734	1	ENST00000398665.3:c.4192G>A	p.Gly1398Arg	p.G1398R	ENST00000398665	NM_032482.2	1398	Ggg/Agg	27/28	1	2	FACETS	0.985	0.889	1	0.985	0.889	1	CLONAL	1	TRUE	1	0.31	2		735	773	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239981	98239981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142791675	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	51	405	0	ENST00000331920.6:c.1351G>A	p.Ala451Thr	p.A451T	ENST00000331920	NM_000264.3	451	Gcc/Acc	10/24	1	2	FACETS	0.791	0.674	0.919	0.791	0.674	0.919	CLONAL	1	TRUE	1	0.31	2		405	416	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350878	89350878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1336431815	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	115	763	1	ENST00000301030.4:c.2072G>A	p.Arg691His	p.R691H	ENST00000301030	NM_001256183.1	691	cGc/cAc	9/13	1	2	FACETS	0.987	0.889	1	0.987	0.889	1	CLONAL	1	TRUE	1	0.31	2		764	752	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244200	153244200	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	72	431	0	ENST00000281708.4:c.1957del	p.Thr653ArgfsTer8	p.T653Rfs*8	ENST00000281708	NM_033632.3	653	Acg/cg	12/12	1	2	FACETS	0.828	0.724	0.94	0.828	0.724	0.94	CLONAL	1	TRUE	1	0.31	2		431	561	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118367048	118367048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782094920	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	70	454	1	ENST00000534358.1:c.5630C>T	p.Ala1877Val	p.A1877V	ENST00000534358	NM_005933.3	1877	gCg/gTg	20/36	0.300402526190358	2	FACETS	0.995	0.87	1	0.497	0.435	0.564	CLONAL	1	TRUE	0	0.31	2		455	454	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096334	2096334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139165943	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	155	657	1	ENST00000219066.1:c.173C>T	p.Pro58Leu	p.P58L	ENST00000219066	NM_002528.5	58	cCg/cTg	2/6	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.31	2		658	947	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11276210	11276210	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	45	412	0	ENST00000361445.4:c.3112A>G	p.Met1038Val	p.M1038V	ENST00000361445	NM_004958.3	1038	Atg/Gtg	20/58	1	2	FACETS	0.655	0.551	0.77	0.655	0.551	0.77	SUBCLONAL	1	TRUE	1	0.31	2		412	443	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257616	16257616	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	73	487	0	ENST00000375759.3:c.4881A>C	p.Lys1627Asn	p.K1627N	ENST00000375759	NM_015001.2	1627	aaA/aaC	11/15	1	2	FACETS	0.953	0.836	1	0.953	0.836	1	CLONAL	1	TRUE	1	0.31	2		487	494	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748173	72748173	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	63	279	0	ENST00000357731.5:c.5A>G	p.Asp2Gly	p.D2G	ENST00000357731	NM_173808.2	2	gAc/gGc	1/7	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.31	2		279	399	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85741977	85741977	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	86	518	0	ENST00000370580.1:c.57+2T>C		p.X19_splice	ENST00000370580	NM_003921.4	19			1	2	FACETS	0.81	0.717	0.91	0.81	0.717	0.91	CLONAL	1	TRUE	1	0.31	2		518	685	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651526	206651526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553385960	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	86	499	0	ENST00000367120.3:c.836C>T	p.Pro279Leu	p.P279L	ENST00000367120	NM_014002.3	279	cCc/cTc	9/22	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.31	2		499	515	SUCCESS
FH	2271	MSKCC	GRCh37	1	241661163	241661163	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	51	439	0	ENST00000366560.3:c.1498T>C	p.Trp500Arg	p.W500R	ENST00000366560	NM_000143.3	500	Tgg/Cgg	10/10	1	2	FACETS	0.78	0.664	0.906	0.78	0.664	0.906	CLONAL	1	TRUE	1	0.31	2		439	422	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944498	71944498	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	117	678	0	ENST00000298229.2:c.2054T>C	p.Val685Ala	p.V685A	ENST00000298229	NM_001567.3	685	gTg/gCg	18/28	0.300402526190358	2	FACETS	0.997	0.9	1	0.499	0.45	0.55	CLONAL	1	TRUE	0	0.31	2		678	757	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444209	49444210	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	177	911	0	ENST00000301067.7:c.3161dup	p.Leu1055ValfsTer13	p.L1055Vfs*13	ENST00000301067	NM_003482.3	1054	ccg/ccCg	11/54	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.31	2		911	1049	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143011	58143011	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	87	752	1	ENST00000257904.6:c.773A>G	p.Gln258Arg	p.Q258R	ENST00000257904	NM_000075.3	258	cAg/cGg	7/8	1	2	FACETS	0.575	0.507	0.647	0.575	0.507	0.647	SUBCLONAL	1	TRUE	1	0.31	2		753	977	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194833	30194833	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	81	579	0	ENST00000331968.5:c.312del	p.Arg105AlafsTer13	p.R105Afs*13	ENST00000331968	NM_002742.2	104	ttT/tt	2/18	1	2	FACETS	0.962	0.85	1	0.962	0.85	1	CLONAL	1	TRUE	1	0.31	2		579	543	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042736	42042736	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	51	406	0	ENST00000219905.7:c.6934del	p.Thr2312LeufsTer23	p.T2312Lfs*23	ENST00000219905	NM_001164273.1	2311	Aaa/aa	17/24	1	2	FACETS	0.846	0.721	0.982	0.846	0.721	0.982	CLONAL	1	TRUE	1	0.31	2		406	389	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251015	99251015	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	95	591	0	ENST00000268035.6:c.319C>A	p.Arg107Ser	p.R107S	ENST00000268035	NM_000875.3	107	Cgc/Agc	2/21	1	2	FACETS	0.94	0.838	1	0.94	0.838	1	CLONAL	1	TRUE	1	0.31	2		591	652	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2132439	2132439	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	118	807	0	ENST00000219476.3:c.3817G>A	p.Ala1273Thr	p.A1273T	ENST00000219476	NM_000548.3	1273	Gcc/Acc	32/42	1	2	FACETS	0.932	0.841	1	0.932	0.841	1	CLONAL	1	TRUE	1	0.31	2		807	817	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650714	67650714	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	123	597	0	ENST00000264010.4:c.1019A>G	p.His340Arg	p.H340R	ENST00000264010	NM_006565.3	340	cAt/cGt	5/12	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.31	2		597	783	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89862428	89862428	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs976556567	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	77	527	0	ENST00000389301.3:c.894-2A>G		p.X298_splice	ENST00000389301	NM_000135.2	298			1	2	FACETS	0.745	0.654	0.843	0.745	0.654	0.843	SUBCLONAL	1	TRUE	1	0.31	2		527	667	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546108	29546108	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	89	417	0	ENST00000356175.3:c.1613T>C	p.Met538Thr	p.M538T	ENST00000356175	NM_000267.3	538	aTg/aCg	14/57	1	2	FACETS	0.975	0.866	1	0.975	0.866	1	CLONAL	1	TRUE	1	0.31	2		417	589	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664859	29664859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369803831	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	30	310	0	ENST00000356175.3:c.6602C>T	p.Thr2201Met	p.T2201M	ENST00000356175	NM_000267.3	2201	aCg/aTg	43/57	1	2	FACETS	0.842	0.682	1	0.842	0.682	1	CLONAL	1	TRUE	1	0.31	2		310	230	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533931	63533931	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	49	460	0	ENST00000307078.5:c.1223A>G	p.Glu408Gly	p.E408G	ENST00000307078	NM_004655.3	408	gAg/gGg	6/11	1	2	FACETS	0.703	0.596	0.82	0.703	0.596	0.82	SUBCLONAL	1	TRUE	1	0.31	2		460	450	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250383	10250383	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	99	463	0	ENST00000340748.4:c.3869T>C	p.Met1290Thr	p.M1290T	ENST00000340748		1290	aTg/aCg	33/40	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.31	2		463	581	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303319	15303319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1174452738	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	186	823	0	ENST00000263388.2:c.209G>A	p.Gly70Asp	p.G70D	ENST00000263388	NM_000435.2	70	gGc/gAc	3/33	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.31	2		823	925	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223547	36223547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762187488	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	151	904	0	ENST00000222270.7:c.6097C>T	p.Arg2033Cys	p.R2033C	ENST00000222270	NM_014727.1	2033	Cgc/Tgc	28/37	1	2	FACETS	0.998	0.912	1	0.998	0.912	1	CLONAL	1	TRUE	1	0.31	2		904	976	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40740981	40740981	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	142	797	0	ENST00000392038.2:c.1337A>G	p.Gln446Arg	p.Q446R	ENST00000392038	NM_001626.4	446	cAg/cGg	13/14	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.31	2		797	888	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796881	42796881	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	132	773	0	ENST00000575354.2:c.3340del	p.Ala1114ProfsTer47	p.A1114Pfs*47	ENST00000575354	NM_015125.3	1113	caG/ca	14/20	1	2	FACETS	0.901	0.817	0.99	0.901	0.817	0.99	CLONAL	1	TRUE	1	0.31	2		773	945	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61713016	61713016	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	60	401	0	ENST00000401558.2:c.2395G>C	p.Glu799Gln	p.E799Q	ENST00000401558	NM_003400.3	799	Gaa/Caa	20/25	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.31	2		401	376	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99179972	99179972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1231469932	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	124	689	1	ENST00000074304.5:c.1915G>A	p.Asp639Asn	p.D639N	ENST00000074304	NM_001134224.1	639	Gac/Aac	19/26	1	2	FACETS	0.94	0.85	1	0.94	0.85	1	CLONAL	1	TRUE	1	0.31	2		690	851	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030854	36030854	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	90	400	0	ENST00000358208.4:c.1133C>T	p.Ala378Val	p.A378V	ENST00000358208		378	gCg/gTg	10/12	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.31	2		400	504	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121096	29121096	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	87	529	1	ENST00000328354.6:c.461del	p.Asn154ThrfsTer7	p.N154Tfs*7	ENST00000328354	NM_007194.3	154	aAc/ac	4/15	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.31	2		530	518	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430566	181430566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	108	627	0	ENST00000325404.1:c.418G>A	p.Ala140Thr	p.A140T	ENST00000325404	NM_003106.3	140	Gcg/Acg	1/1	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.31	2		627	595	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446923	187446923	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	114	742	0	ENST00000232014.4:c.1270G>T	p.Asp424Tyr	p.D424Y	ENST00000232014	NM_001130845.1	424	Gac/Tac	5/10	1	2	FACETS	0.913	0.821	1	0.913	0.821	1	CLONAL	1	TRUE	1	0.31	2		742	806	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807315	1807315	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	122	755	0	ENST00000260795.2:c.1564C>A	p.Leu522Met	p.L522M	ENST00000260795		522	Ctg/Atg	11/17	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.31	2		755	724	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561780	55561780	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	74	322	0	ENST00000288135.5:c.170T>C	p.Leu57Ser	p.L57S	ENST00000288135	NM_000222.2	57	tTa/tCa	2/21	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.31	2		322	458	SUCCESS
APC	324	MSKCC	GRCh37	5	112178973	112178973	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	42	309	0	ENST00000257430.4:c.7682T>C	p.Val2561Ala	p.V2561A	ENST00000257430	NM_000038.5	2561	gTa/gCa	16/16	1	2	FACETS	0.847	0.71	0.997	0.847	0.71	0.997	CLONAL	1	TRUE	1	0.31	2		309	320	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910618	29910618	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	148	843	0	ENST00000376809.5:c.158A>T	p.Asp53Val	p.D53V	ENST00000376809	NM_002116.7	53	gAc/gTc	2/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.31	2		843	810	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323270	31323273	+	frameshift_variant	Frame_Shift_Del	DEL	GTCA	GTCA	-	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	66	385	0	ENST00000412585.2:c.716_719del	p.Leu239ProfsTer57	p.L239Pfs*57	ENST00000412585	NM_005514.6	239	cTGACc/cc	4/8	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.31	2		385	425	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104712	69104712	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	79	488	0	ENST00000288368.4:c.4556A>G	p.Asn1519Ser	p.N1519S	ENST00000288368	NM_024870.2	1519	aAc/aGc	37/40	1	2	FACETS	0.815	0.718	0.92	0.815	0.718	0.92	CLONAL	1	TRUE	1	0.31	2		488	625	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937186	76937186	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	51	516	0	ENST00000373344.5:c.3562T>C	p.Ser1188Pro	p.S1188P	ENST00000373344	NM_000489.3	1188	Tcc/Ccc	9/35	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.31	2		516	320	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0043097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	267	47	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.840816322751739	2		47	538	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919331	48919331	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1131690874	NA	P-0043097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	98	165	0	ENST00000267163.4:c.496G>T	p.Glu166Ter	p.E166*	ENST00000267163	NM_000321.2	166	Gaa/Taa	4/27	0.840816322751739	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.840816322751739	1		165	124	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653808	89653808	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs786204854	NA	P-0043097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	127	312	0	ENST00000371953.3:c.106G>C	p.Gly36Arg	p.G36R	ENST00000371953	NM_000314.4	36	Gga/Cga	2/9	0.840816322751739	1	FACETS	0.85	0.794	0.905	0.85	0.794	0.905	CLONAL	1	TRUE	0	0.840816322751739	1		312	206	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984904	9984904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	230	400	0	ENST00000330684.3:c.1061G>T	p.Gly354Val	p.G354V	ENST00000330684	NM_001134407.1	354	gGc/gTc	4/13	1	2	FACETS	0.916	0.861	0.973	0.916	0.861	0.973	CLONAL	1	TRUE	1	0.840816322751739	2		400	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0043133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	160	713	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.257501541181699	3	FACETS	1	0.95	1	0.688	0.637	0.741	CLONAL	2	FALSE	0	0.425091999584591	3		713	442	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0043249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	144	443	9	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.263593372373162	4	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	FALSE	2	0.289753470423404	4		452	612	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0043249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	244	678	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	2	FALSE	NA	0.289753470423404	2		678	752	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0043249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	95	359	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	0.256272465575297	3	FACETS	0.883	0.791	0.98	0.883	0.791	0.98	CLONAL	2	FALSE	1	0.289753470423404	3		359	425	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345913	70345913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749801457	NA	P-0043249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	135	598	0	ENST00000374080.3:c.2450G>A	p.Arg817His	p.R817H	ENST00000374080		817	cGc/cAc	18/45	0.289753470423404	3	FACETS	1	0.976	1	0.612	0.556	0.671	CLONAL	1	FALSE	1	0.289753470423404	3		598	871	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681320	88681320	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	76	431	0	ENST00000372037.3:c.1210del	p.Thr404ProfsTer14	p.T404Pfs*14	ENST00000372037	NM_004329.2	404	Acc/cc	11/13	0.256272465575297	3	FACETS	1	0.884	1	0.504	0.442	0.57	CLONAL	1	FALSE	1	0.289753470423404	3		431	596	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257953	19257953	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1179358806	NA	P-0043249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	287	961	1	ENST00000162023.5:c.433G>A	p.Gly145Arg	p.G145R	ENST00000162023		145	Ggg/Agg	9/13	0.106489698856033	4	FACETS	0.955	0.897	1	0.955	0.897	1	INDETERMINATE	2	FALSE	2	0.289753470423404	4		962	1337	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0043253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	61	398	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.339984456028748	2		398	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0043253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	148	649	2	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.339984456028748	1	FACETS	0.845	0.772	0.922	0.845	0.772	0.922	CLONAL	1	TRUE	0	0.339984456028748	1		651	855	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0043253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	39	124	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.956	0.798	1	0.956	0.798	1	CLONAL	1	TRUE	1	0.339984456028748	2		124	240	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741849	17741849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750173588	NA	P-0043253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	36	117	1	ENST00000250003.3:c.520G>A	p.Ala174Thr	p.A174T	ENST00000250003	NM_002478.4	174	Gcc/Acc	1/3	0.302736901569111	1	FACETS	0.732	0.606	0.872	0.732	0.606	0.872	SUBCLONAL	1	TRUE	0	0.339984456028748	1		118	240	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350983	89350983	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	110	776	0	ENST00000301030.4:c.1967G>A	p.Ser656Asn	p.S656N	ENST00000301030	NM_001256183.1	656	aGt/aAt	9/13	1	2	FACETS	0.74	0.665	0.821	0.74	0.665	0.821	SUBCLONAL	1	TRUE	1	0.339984456028748	2		776	874	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775146	73775146	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	100	580	0	ENST00000254810.4:c.110A>T	p.Lys37Met	p.K37M	ENST00000254810	NM_005324.3	37	aAg/aTg	2/4	0.21300442109287	2	FACETS	0.611	0.545	0.682	0.305	0.272	0.341	SUBCLONAL	1	TRUE	0	0.339984456028748	2		580	963	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710882	117710886	+	frameshift_variant	Frame_Shift_Del	DEL	CTTGT	CTTGT	-	novel	NA	P-0043253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	68	424	0	ENST00000368508.3:c.1386_1390del	p.Lys465AsnfsTer6	p.K465Nfs*6	ENST00000368508	NM_002944.2	462	ccACAAGcc/cccc	12/43	1	2	FACETS	0.667	0.58	0.76	0.667	0.58	0.76	SUBCLONAL	1	TRUE	1	0.339984456028748	2		424	600	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739872	41739872	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	63	412	0	ENST00000242208.4:c.101A>G	p.Asp34Gly	p.D34G	ENST00000242208	NM_002192.2	34	gAc/gGc	2/3	0.107054184242038	3	FACETS	0.611	0.527	0.701	0.305	0.263	0.351	INDETERMINATE	1	TRUE	1	0.339984456028748	3		412	710	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859509	151859509	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	90	521	1	ENST00000262189.6:c.11153T>A	p.Ile3718Lys	p.I3718K	ENST00000262189	NM_170606.2	3718	aTa/aAa	43/59	0.107054184242038	3	FACETS	0.761	0.674	0.854	0.38	0.337	0.427	INDETERMINATE	1	TRUE	1	0.339984456028748	3		522	814	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0043290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	267	372	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.672835439249354	2		372	572	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156742	20156742	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0043290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	85	195	0	ENST00000379607.5:c.17-2A>T		p.X6_splice	ENST00000379607	NM_001412.3	6			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.672835439249354	2		195	235	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0043330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	411	646	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.600002035009043	2	FACETS	0.841	0.811	0.87	0.841	0.811	0.87	CLONAL	2	TRUE	0	0.768403273577537	2		647	636	SUCCESS
APC	324	MSKCC	GRCh37	5	112175897	112175897	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	57	314	0	ENST00000257430.4:c.4606G>T	p.Glu1536Ter	p.E1536*	ENST00000257430	NM_000038.5	1536	Gaa/Taa	16/16	0.768403273577537	3	FACETS	0.964	0.839	1	0.482	0.419	0.549	CLONAL	1	TRUE	1	0.768403273577537	3		314	213	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412110	63412110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852216	NA	P-0043330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	310	490	1	ENST00000330258.3:c.1057C>T	p.Arg353Ter	p.R353*	ENST00000330258	NM_152424.3	353	Cga/Tga	2/2	0.718663587399889	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.768403273577537	2		491	351	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943692	9943692	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749504561	NA	P-0043330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	159	782	1	ENST00000330684.3:c.1249G>A	p.Val417Ile	p.V417I	ENST00000330684	NM_001134407.1	417	Gtc/Atc	5/13	0.768403273577537	6	FACETS	0.791	0.723	0.862	0.198	0.18	0.216	SUBCLONAL	1	TRUE	2	0.768403273577537	6		783	1328	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158554	26158554	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	558	599	0	ENST00000289316.2:c.157A>G	p.Thr53Ala	p.T53A	ENST00000289316	NM_138720.2	53	Acc/Gcc	1/2	0.768403273577537	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	TRUE	1	0.768403273577537	4		599	856	SUCCESS
APC	324	MSKCC	GRCh37	5	112170705	112170705	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	165	557	1	ENST00000257430.4:c.1801G>T	p.Glu601Ter	p.E601*	ENST00000257430	NM_000038.5	601	Gag/Tag	15/16	0.768403273577537	3	FACETS	0.912	0.853	0.971	0.912	0.853	0.971	CLONAL	2	TRUE	1	0.768403273577537	3		558	326	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322565	39322565	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1442884461	NA	P-0043330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	250	552	1	ENST00000373001.3:c.427G>A	p.Val143Ile	p.V143I	ENST00000373001	NM_022157.3	143	Gtc/Atc	2/7	0.600002035009043	2	FACETS	0.771	0.734	0.808	0.771	0.734	0.808	SUBCLONAL	2	TRUE	0	0.768403273577537	2		553	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579369	7579370	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTGCC	novel	NA	P-0043330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	475	825	0	ENST00000269305.4:c.313_317dup	p.Ser106ArgfsTer19	p.S106Rfs*19	ENST00000269305	NM_001126112.2	106	agc/agGGCAGc	4/11	NA	2	FACETS	0.833	0.805	0.86			1	INDETERMINATE	2	TRUE	NA	0.768403273577537	2		825	742	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984928	55984928	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	86	570	0	ENST00000263923.4:c.201G>T	p.Gln67His	p.Q67H	ENST00000263923	NM_002253.2	67	caG/caT	3/30	0.57087715500084	1	FACETS	0.332	0.295	0.371	0.332	0.295	0.371	SUBCLONAL	1	TRUE	0	0.768403273577537	1		570	415	SUCCESS
APC	324	MSKCC	GRCh37	5	112174389	112174389	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	49	339	0	ENST00000257430.4:c.3098A>T	p.Asp1033Val	p.D1033V	ENST00000257430	NM_000038.5	1033	gAt/gTt	16/16	0.768403273577537	3	FACETS	0.87	0.746	1	0.435	0.373	0.501	CLONAL	1	TRUE	1	0.768403273577537	3		339	203	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981194	201981195	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	436	830	0	ENST00000359651.3:c.275dup	p.Ser93LeufsTer4	p.S93Lfs*4	ENST00000359651		91	-/T	2/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.643710408065482	2		830	1275	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832829	3832829	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	282	582	0	ENST00000262367.5:c.1429G>C	p.Asp477His	p.D477H	ENST00000262367	NM_004380.2	477	Gac/Cac	6/31	1	2	FACETS	0.97	0.914	1	0.97	0.914	1	CLONAL	1	TRUE	1	0.643710408065482	2		582	903	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033248	69033248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143386950	NA	P-0043332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	99	576	0	ENST00000288368.4:c.3688C>T	p.Arg1230Trp	p.R1230W	ENST00000288368	NM_024870.2	1230	Cgg/Tgg	30/40	1	2	FACETS	0.399	0.356	0.445	0.399	0.356	0.445	SUBCLONAL	1	TRUE	1	0.643710408065482	2		576	771	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949149	44949149	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	250	257	0	ENST00000377967.4:c.3710T>G	p.Ile1237Ser	p.I1237S	ENST00000377967	NM_021140.2	1237	aTt/aGt	25/29	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.643710408065482	1		257	379	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981194	201981195	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	287	830	0	ENST00000359651.3:c.275dup	p.Ser93LeufsTer4	p.S93Lfs*4	ENST00000359651		91	-/T	2/8	0.184984511446511	2	FACETS	0.865	0.816	0.915	0.865	0.816	0.915	INDETERMINATE	2	TRUE	0	0.384824500364631	2		830	862	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832829	3832829	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	79	582	0	ENST00000262367.5:c.1429G>C	p.Asp477His	p.D477H	ENST00000262367	NM_004380.2	477	Gac/Cac	6/31	0.251116537378929	1	FACETS	0.603	0.531	0.68	0.603	0.531	0.68	SUBCLONAL	1	TRUE	0	0.384824500364631	1		582	550	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949149	44949149	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	124	257	0	ENST00000377967.4:c.3710T>G	p.Ile1237Ser	p.I1237S	ENST00000377967	NM_021140.2	1237	aTt/aGt	25/29	1	1	FACETS	0.873	0.803	0.945	1	0.99	1	CLONAL	2	TRUE	0	0.384824500364631	1		257	298	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0043347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	46	555	1	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	0.202537025042704	1	FACETS	0.631	0.53	0.742	0.631	0.53	0.742	SUBCLONAL	1	TRUE	0	0.222034096090126	1		556	584	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817741	3817741	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770693450	NA	P-0043347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	48	617	0	ENST00000262367.5:c.3230C>T	p.Pro1077Leu	p.P1077L	ENST00000262367	NM_004380.2	1077	cCt/cTt	16/31	1	2	FACETS	0.769	0.65	0.901	0.769	0.65	0.901	CLONAL	1	TRUE	1	0.222034096090126	2		617	562	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188195	10188196	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	novel	NA	P-0043347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	54	569	0	ENST00000256474.2:c.341-2dup		p.X114_splice	ENST00000256474	NM_000551.3	114			0.202537025042704	1	FACETS	0.87	0.744	1	0.87	0.744	1	CLONAL	1	TRUE	0	0.222034096090126	1		569	497	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103791	47103792	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0043347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	65	644	0	ENST00000409792.3:c.6154_6155insTA	p.Pro2052LeufsTer96	p.P2052Lfs*96	ENST00000409792	NM_014159.6	2052	cct/cTAct	14/21	0.202537025042704	1	FACETS	0.875	0.759	1	0.875	0.759	1	CLONAL	1	TRUE	0	0.222034096090126	1		644	595	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651368	52651369	+	missense_variant	Missense_Mutation	DNP	GC	GC	TG	novel	NA	P-0043347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	38	574	0	ENST00000394830.3:c.1727_1728delinsCA	p.Arg576Pro	p.R576P	ENST00000394830	NM_018313.4	576	cGC/cCA	15/30	0.202537025042704	1	FACETS	0.753	0.623	0.898	0.753	0.623	0.898	SUBCLONAL	1	TRUE	0	0.222034096090126	1		574	404	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928527	69928527	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	77	765	0	ENST00000352241.4:c.347T>A	p.Val116Asp	p.V116D	ENST00000352241	NM_198159.2	116	gTc/gAc	2/10	0.202537025042704	1	FACETS	0.971	0.853	1	0.971	0.853	1	CLONAL	1	TRUE	0	0.222034096090126	1		765	635	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111489	8111490	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0043360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	268	588	0	ENST00000346208.3:c.978_979del	p.Trp328GlufsTer23	p.W328Efs*23	ENST00000346208		325	acCAca/acca	5/6	0.321498879413189	4	FACETS	0.957	0.898	1	0.638	0.598	0.679	CLONAL	2	TRUE	1	0.333267306646656	4		588	1120	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315380	30315380	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	187	533	0	ENST00000322652.5:c.1065G>C	p.Leu355Phe	p.L355F	ENST00000322652	NM_015355.2	355	ttG/ttC	10/16	0.271354061242989	5	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.333267306646656	5		533	1270	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315407	30315407	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	200	564	0	ENST00000322652.5:c.1092G>C	p.Glu364Asp	p.E364D	ENST00000322652	NM_015355.2	364	gaG/gaC	10/16	0.271354061242989	5	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.333267306646656	5		564	1325	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0043368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	484	554	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.949368249315337	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.956810604512178	2		554	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0043368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	737	795	2	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.95011062190847	2	FACETS	0.995	0.985	1	0.995	0.985	1	CLONAL	2	TRUE	0	0.956810604512178	2		797	774	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913283	NA	P-0043368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	186	461	0	ENST00000263967.3:c.3129G>T	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atT	21/21	1	2	FACETS	0.906	0.847	0.966	0.906	0.847	0.966	CLONAL	1	TRUE	1	0.956810604512178	2		461	429	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941686	48941686	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	339	233	1	ENST00000267163.4:c.996del	p.Asp332GlufsTer17	p.D332Efs*17	ENST00000267163	NM_000321.2	332	gaT/ga	10/27	0.956810604512178	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.956810604512178	3		234	345	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085759	16085759	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200236475	NA	P-0043368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	203	689	0	ENST00000281043.3:c.935G>A	p.Arg312Lys	p.R312K	ENST00000281043	NM_005378.4	312	aGg/aAg	3/3	0.510106260917368	4	FACETS	0.853	0.791	0.918	0.284	0.263	0.306	INDETERMINATE	1	TRUE	1	0.956810604512178	4		689	973	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140165	50140165	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043376-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	217	514	0	ENST00000246792.3:c.260A>T	p.Gln87Leu	p.Q87L	ENST00000246792	NM_006270.3	87	cAg/cTg	3/6	0.489111516731677	3	FACETS	1	0.984	1	0.592	0.551	0.634	CLONAL	1	TRUE	1	0.489111516731677	3		514	933	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581285	48581286	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0043376-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	43	341	0	ENST00000342988.3:c.593dup	p.Ala199SerfsTer7	p.A199Sfs*7	ENST00000342988	NM_005359.5	197	acc/aCcc	5/12	0.489111516731677	2	FACETS	0.36	0.301	0.426	0.18	0.15	0.213	SUBCLONAL	1	TRUE	0	0.489111516731677	2		341	488	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186767	108186767	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1565499657	NA	P-0043376-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	192	349	0	ENST00000278616.4:c.6125G>T	p.Trp2042Leu	p.W2042L	ENST00000278616	NM_000051.3	2042	tGg/tTg	42/63	0.489111516731677	2	FACETS	0.896	0.839	0.954	0.896	0.839	0.954	CLONAL	2	TRUE	0	0.489111516731677	2		349	438	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774154	56774154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043376-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	218	402	0	ENST00000337432.4:c.505G>A	p.Val169Met	p.V169M	ENST00000337432	NM_058216.2	169	Gtg/Atg	3/9	0.225247709504816	5	FACETS	1	0.979	1	0.741	0.692	0.791	INDETERMINATE	2	TRUE	2	0.489111516731677	5		402	695	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792013	42792013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043376-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	390	577	0	ENST00000575354.2:c.817G>A	p.Asp273Asn	p.D273N	ENST00000575354	NM_015125.3	273	Gac/Aac	6/20	0.489111516731677	3	FACETS	0.94	0.895	0.985	0.94	0.895	0.985	CLONAL	2	TRUE	1	0.489111516731677	3		577	1056	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513442	41513442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1320689399	NA	P-0043376-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	164	449	1	ENST00000263253.7:c.346G>A	p.Gly116Ser	p.G116S	ENST00000263253	NM_001429.3	116	Ggt/Agt	2/31	0.274585312997559	4	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.489111516731677	4		450	868	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696275	52696275	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0043376-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	123	313	0	ENST00000394830.3:c.402T>G	p.Tyr134Ter	p.Y134*	ENST00000394830	NM_018313.4	134	taT/taG	5/30	0.24492588401152	2	FACETS	1	0.973	1	0.588	0.535	0.642	INDETERMINATE	1	TRUE	0	0.489111516731677	2		313	428	SUCCESS
APC	324	MSKCC	GRCh37	5	112178469	112178469	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043376-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	73	279	0	ENST00000257430.4:c.7178G>T	p.Arg2393Ile	p.R2393I	ENST00000257430	NM_000038.5	2393	aGa/aTa	16/16	1	2	FACETS	0.913	0.805	1	0.913	0.805	1	CLONAL	1	TRUE	1	0.489111516731677	2		279	327	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37006500	37006500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043376-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	102	286	0	ENST00000358127.4:c.445C>T	p.Gln149Ter	p.Q149*	ENST00000358127	NM_001280556.1	149	Caa/Taa	4/10	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.489111516731677	2		286	386	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	177	366	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.194411316097334	4	FACETS	1	0.96	1	1	0.96	1	INDETERMINATE	2	TRUE	2	0.438152723049578	4		366	552	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	40	348	1				ENST00000310581	NM_198253.2	-/1132			0.370383619742542	0	FACETS	0.666	0.563	0.777			1	SUBCLONAL	1	TRUE	0	0.438152723049578	0		349	154	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	187	629	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	1	2	FACETS	0.931	0.86	1	0.931	0.86	1	CLONAL	1	TRUE	1	0.438152723049578	2		629	917	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956220	55956220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190050670	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	99	529	0	ENST00000263923.4:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000263923	NM_002253.2	1032	cGa/cAa	23/30	1	2	FACETS	0.853	0.764	0.947	0.853	0.764	0.947	CLONAL	1	TRUE	1	0.438152723049578	2		529	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578537	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs879254214	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	206	810	0	ENST00000269305.4:c.393_395del	p.Asn131del	p.N131del	ENST00000269305	NM_001126112.2	131	aaCAAg/aag	5/11	1	2	FACETS	0.885	0.82	0.951	0.885	0.82	0.951	CLONAL	1	TRUE	1	0.438152723049578	2		810	1063	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858202	9858202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	68	449	0	ENST00000330684.3:c.3199C>T	p.Arg1067Trp	p.R1067W	ENST00000330684	NM_001134407.1	1067	Cgg/Tgg	13/13	1	2	FACETS	0.86	0.752	0.974	0.86	0.752	0.974	CLONAL	1	TRUE	1	0.438152723049578	2		449	361	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931862	68931862	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200600940	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	86	553	1	ENST00000288368.4:c.292G>A	p.Glu98Lys	p.E98K	ENST00000288368	NM_024870.2	98	Gaa/Aaa	3/40	1	2	FACETS	0.791	0.702	0.886	0.791	0.702	0.886	SUBCLONAL	1	TRUE	1	0.438152723049578	2		554	496	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575023	64575023	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs794728652	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	97	344	0	ENST00000312049.6:c.783+1G>A		p.X261_splice	ENST00000312049	NM_130799.2	261			1	2	FACETS	0.829	0.742	0.922	0.829	0.742	0.922	CLONAL	1	TRUE	1	0.438152723049578	2		344	534	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302469	15302469	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	100	625	0	ENST00000263388.2:c.803-1G>A		p.X268_splice	ENST00000263388	NM_000435.2	268			1	2	FACETS	0.906	0.812	1	0.906	0.812	1	CLONAL	1	TRUE	1	0.438152723049578	2		625	504	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849128	156849128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	159	759	1	ENST00000524377.1:c.2020G>A	p.Asp674Asn	p.D674N	ENST00000524377	NM_002529.3	674	Gat/Aat	15/17	1	2	FACETS	0.93	0.854	1	0.93	0.854	1	CLONAL	1	TRUE	1	0.438152723049578	2		760	780	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979995	7979995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	149	601	0	ENST00000319144.4:c.1342G>A	p.Glu448Lys	p.E448K	ENST00000319144	NM_001139.2	448	Gag/Aag	10/15	1	2	FACETS	0.857	0.783	0.933	0.857	0.783	0.933	CLONAL	1	TRUE	1	0.438152723049578	2		601	794	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230679	46230679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	61	404	0	ENST00000334344.6:c.928C>T	p.Arg310Cys	p.R310C	ENST00000334344	NM_152641.2	310	Cgt/Tgt	8/21	0.165190264412998	3	FACETS	0.842	0.729	0.964	0.421	0.364	0.482	INDETERMINATE	1	TRUE	1	0.438152723049578	3		404	403	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391869	139391869	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780963597	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	132	662	1	ENST00000277541.6:c.6322G>A	p.Asp2108Asn	p.D2108N	ENST00000277541	NM_017617.3	2108	Gac/Aac	34/34	1	2	FACETS	0.941	0.857	1	0.941	0.857	1	CLONAL	1	TRUE	1	0.438152723049578	2		663	640	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273033	115273033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1230709037	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	87	424	0	ENST00000438362.2:c.1340C>T	p.Ser447Phe	p.S447F	ENST00000438362	NM_001242891.1	447	tCt/tTt	12/20	1	2	FACETS	0.907	0.807	1	0.907	0.807	1	CLONAL	1	TRUE	1	0.438152723049578	2		424	438	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120478095	120478095	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	83	400	0	ENST00000256646.2:c.3655G>A	p.Gly1219Ser	p.G1219S	ENST00000256646	NM_024408.3	1219	Ggc/Agc	22/34	1	2	FACETS	0.778	0.689	0.873	0.778	0.689	0.873	SUBCLONAL	1	TRUE	1	0.438152723049578	2		400	487	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680601	241680601	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	77	333	0	ENST00000366560.3:c.148T>A	p.Phe50Ile	p.F50I	ENST00000366560	NM_000143.3	50	Ttc/Atc	2/10	1	2	FACETS	0.911	0.804	1	0.911	0.804	1	CLONAL	1	TRUE	1	0.438152723049578	2		333	386	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415834	49415834	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	82	282	0	ENST00000301067.7:c.16513G>A	p.Gly5505Arg	p.G5505R	ENST00000301067	NM_003482.3	5505	Gga/Aga	53/54	0.165190264412998	3	FACETS	0.963	0.852	1	0.481	0.426	0.54	INDETERMINATE	1	TRUE	1	0.438152723049578	3		282	474	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924333	112924333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	155	560	0	ENST00000351677.2:c.1279G>A	p.Gly427Ser	p.G427S	ENST00000351677	NM_002834.3	427	Ggc/Agc	11/16	0.438152723049578	1	FACETS	0.817	0.75	0.887	0.817	0.75	0.887	CLONAL	1	TRUE	0	0.438152723049578	1		560	676	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636077	28636077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs988701709	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	84	482	0	ENST00000241453.7:c.295G>A	p.Gly99Arg	p.G99R	ENST00000241453	NM_004119.2	99	Ggg/Agg	3/24	0.34239592113661	0	FACETS	0.375	0.332	0.422			1	SUBCLONAL	1	TRUE	0	0.438152723049578	0		482	574	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514776	103514776	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	79	331	0	ENST00000355739.4:c.1277A>C	p.Glu426Ala	p.E426A	ENST00000355739	NM_000123.3	426	gAg/gCg	8/15	1	2	FACETS	0.703	0.62	0.792	0.703	0.62	0.792	SUBCLONAL	1	TRUE	1	0.438152723049578	2		331	513	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40855776	40855776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	101	467	0	ENST00000428826.2:c.2080C>T	p.Pro694Ser	p.P694S	ENST00000428826		694	Ccc/Tcc	19/21	0.438152723049578	1	FACETS	0.714	0.641	0.792	0.714	0.641	0.792	SUBCLONAL	1	TRUE	0	0.438152723049578	1		467	504	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688708	47688708	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs985933794	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	119	387	1	ENST00000347630.2:c.592C>T	p.Arg198Trp	p.R198W	ENST00000347630	NM_001007230.1	198	Cgg/Tgg	7/11	0.438152723049578	1	FACETS	0.92	0.836	1	0.92	0.836	1	CLONAL	1	TRUE	0	0.438152723049578	1		388	461	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796033	78796033	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	136	598	0	ENST00000306801.3:c.923C>T	p.Pro308Leu	p.P308L	ENST00000306801	NM_020761.2	308	cCc/cTc	8/34	1	2	FACETS	0.815	0.741	0.891	0.815	0.741	0.891	CLONAL	1	TRUE	1	0.438152723049578	2		598	762	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098477	11098477	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1013942482	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	69	298	0	ENST00000358026.2:c.995C>T	p.Ser332Phe	p.S332F	ENST00000358026	NM_001128849.1	332	tCc/tTc	6/36	0.0641915408969114	3	FACETS	1	0.886	1			1	INDETERMINATE	1	TRUE	NA	0.438152723049578	3		298	379	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375537	15375537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	208	816	1	ENST00000263377.2:c.890C>T	p.Pro297Leu	p.P297L	ENST00000263377	NM_058243.2	297	cCc/cTc	6/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.438152723049578	2		817	817	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763517	41763518	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	168	383	1	ENST00000301178.4:c.2316_2317delinsAA	p.Asp773Asn	p.D773N	ENST00000301178	NM_021913.4	772	gcGGac/gcAAac	19/20	0.438152723049578	3	FACETS	0.807	0.746	0.87	0.807	0.746	0.87	CLONAL	2	TRUE	1	0.438152723049578	3		384	579	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726995	61726995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	76	389	0	ENST00000401558.2:c.443C>T	p.Thr148Ile	p.T148I	ENST00000401558	NM_003400.3	148	aCt/aTt	7/25	1	2	FACETS	0.82	0.723	0.924	0.82	0.723	0.924	CLONAL	1	TRUE	1	0.438152723049578	2		389	423	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022453	31022454	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	45	249	0	ENST00000375687.4:c.1938_1939delinsTT	p.Pro647Ser	p.P647S	ENST00000375687	NM_015338.5	646	ggCCcg/ggTTcg	13/13	1	2	FACETS	0.882	0.748	1	0.882	0.748	1	CLONAL	1	TRUE	1	0.438152723049578	2		249	233	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574379	41574381	+	inframe_deletion	In_Frame_Del	DEL	CAG	CAG	-	rs761639659	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	118	581	3	ENST00000263253.7:c.6674_6676del	p.Gln2225del	p.Q2225del	ENST00000263253	NM_001429.3	2222	CAG/-	31/31	0.438152723049578	1	FACETS	0.83	0.752	0.911	0.83	0.752	0.911	CLONAL	1	TRUE	0	0.438152723049578	1		584	507	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274834	41274835	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	42	297	0	ENST00000349496.5:c.1084_1085delinsAA	p.Gly362Lys	p.G362K	ENST00000349496	NM_001904.3	362	GGa/AAa	8/15	1	2	FACETS	0.663	0.557	0.78	0.663	0.557	0.78	SUBCLONAL	1	TRUE	1	0.438152723049578	2		297	289	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170002373	170002373	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	83	218	0	ENST00000295797.4:c.1192G>T	p.Gly398Cys	p.G398C	ENST00000295797	NM_002740.5	398	Ggc/Tgc	12/18	0.194411316097334	4	FACETS	1	0.958	1	1	0.958	1	INDETERMINATE	2	TRUE	2	0.438152723049578	4		218	240	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557939	187557939	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	110	394	0	ENST00000441802.2:c.3772del	p.Glu1258LysfsTer18	p.E1258Kfs*18	ENST00000441802	NM_005245.3	1258	Gaa/aa	5/27	0.438152723049578	1	FACETS	0.927	0.839	1	0.927	0.839	1	CLONAL	1	TRUE	0	0.438152723049578	1		394	423	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958818	38958818	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	32	254	0	ENST00000357387.3:c.2294C>G	p.Thr765Arg	p.T765R	ENST00000357387	NM_152756.3	765	aCg/aGg	23/38	1	2	FACETS	0.543	0.442	0.655	0.543	0.442	0.655	SUBCLONAL	1	TRUE	1	0.438152723049578	2		254	269	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168666	56168666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	65	338	0	ENST00000399503.3:c.1520G>A	p.Ser507Asn	p.S507N	ENST00000399503	NM_005921.1	507	aGt/aAt	9/20	1	2	FACETS	0.616	0.535	0.703	0.616	0.535	0.703	SUBCLONAL	1	TRUE	1	0.438152723049578	2		338	482	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803038	32803038	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	339	565	0	ENST00000374899.4:c.838G>A	p.Gly280Arg	p.G280R	ENST00000374899	NM_018833.2	280	Ggg/Agg	5/12	0.400968513680931	3	FACETS	0.85	0.804	0.896	0.85	0.804	0.896	CLONAL	2	TRUE	1	0.438152723049578	3		565	1110	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818185	32818185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772241365	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	181	541	0	ENST00000354258.4:c.1340C>T	p.Ala447Val	p.A447V	ENST00000354258	NM_000593.5	447	gCc/gTc	5/11	0.400968513680931	3	FACETS	0.854	0.786	0.924	0.427	0.393	0.462	CLONAL	1	TRUE	1	0.438152723049578	3		541	1180	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729963	41729964	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	106	551	1	ENST00000242208.4:c.565_566delinsAA	p.Gly189Lys	p.G189K	ENST00000242208	NM_002192.2	189	GGg/AAg	3/3	1	2	FACETS	0.728	0.653	0.807	0.728	0.653	0.807	SUBCLONAL	1	TRUE	1	0.438152723049578	2		552	665	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730102	41730102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	96	368	0	ENST00000242208.4:c.427G>A	p.Glu143Lys	p.E143K	ENST00000242208	NM_002192.2	143	Gaa/Aaa	3/3	1	2	FACETS	0.976	0.874	1	0.976	0.874	1	CLONAL	1	TRUE	1	0.438152723049578	2		368	449	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279452	38279452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	88	460	0	ENST00000425967.3:c.1037G>A	p.Gly346Glu	p.G346E	ENST00000425967	NM_001174067.1	346	gGa/gAa	9/19	1	2	FACETS	0.828	0.736	0.925	0.828	0.736	0.925	CLONAL	1	TRUE	1	0.438152723049578	2		460	485	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974675	21974675	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	123	403	0	ENST00000304494.5:c.150+2T>A		p.X50_splice	ENST00000304494	NM_000077.4	50			0.438152723049578	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.438152723049578	1		403	404	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239870	98239870	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1131690999	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	109	535	0	ENST00000331920.6:c.1462T>C	p.Cys488Arg	p.C488R	ENST00000331920	NM_000264.3	488	Tgc/Cgc	10/24	1	2	FACETS	0.896	0.808	0.99	0.896	0.808	0.99	CLONAL	1	TRUE	1	0.438152723049578	2		535	555	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418173	139418173	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	135	649	0	ENST00000277541.6:c.399G>A	p.Trp133Ter	p.W133*	ENST00000277541	NM_017617.3	133	tgG/tgA	3/34	1	2	FACETS	0.921	0.839	1	0.921	0.839	1	CLONAL	1	TRUE	1	0.438152723049578	2		649	669	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221726	22221726	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	10	27	0	ENST00000215832.6:c.5C>T	p.Ala2Val	p.A2V	ENST00000215832	NM_002745.4	2	gCg/gTg	1/9	0.38126561960737	1	FACETS	0.091	0.062	0.128	0.091	0.062	0.128	INDETERMINATE	1	TRUE	0	0.840306960468359	1		27	151	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0043475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	272	460	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	1	2	FACETS	0.996	0.943	1	0.996	0.943	1	CLONAL	1	TRUE	1	0.876453662787448	2		460	623	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268715	98268715	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	299	441	0	ENST00000331920.6:c.368C>G	p.Thr123Ser	p.T123S	ENST00000331920	NM_000264.3	123	aCc/aGc	2/24	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.876453662787448	2		441	612	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845607	72845607	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	398	648	0	ENST00000268489.5:c.3733C>T	p.Gln1245Ter	p.Q1245*	ENST00000268489	NM_006885.3	1245	Cag/Tag	7/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.876453662787448	2		648	856	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659743	227659743	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	218	476	0	ENST00000305123.5:c.3712C>G	p.Pro1238Ala	p.P1238A	ENST00000305123	NM_005544.2	1238	Cca/Gca	1/2	1	2	FACETS	0.923	0.866	0.981	0.923	0.866	0.981	CLONAL	1	TRUE	1	0.876453662787448	2		476	539	SUCCESS
APC	324	MSKCC	GRCh37	5	112163695	112163696	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0043475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	65	244	0	ENST00000257430.4:c.1618_1619del	p.Leu540ThrfsTer19	p.L540Tfs*19	ENST00000257430	NM_000038.5	540	TTa/a	13/16	0.876453662787448	1	FACETS	0.842	0.768	0.912	0.842	0.768	0.912	CLONAL	1	TRUE	0	0.876453662787448	1		244	99	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0043476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	74	766	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	0.92	0.806	1			1	INDETERMINATE	1	TRUE	NA	0.24	2		767	670	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683677	162683677	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	59	493	0	ENST00000366898.1:c.292G>T	p.Glu98Ter	p.E98*	ENST00000366898	NM_004562.2	98	Gag/Tag	3/12	1	2	FACETS	0.762	0.655	0.879	0.762	0.655	0.879	SUBCLONAL	1	TRUE	1	0.24	2		493	645	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0043491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	760	704	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.450011491941329	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.450011491941329	3		704	1266	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	328	348	1				ENST00000310581	NM_198253.2	-/1132			0.450011491941329	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	1	0.450011491941329	4		349	634	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101050	41101050	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs192944843	NA	P-0043491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	362	677	0	ENST00000373198.4:c.1306G>A	p.Glu436Lys	p.E436K	ENST00000373198	NM_133170.3	436	Gag/Aag	8/32	0.246110270715157	5	FACETS	1	0.988	1	0.757	0.718	0.797	INDETERMINATE	2	TRUE	2	0.450011491941329	5		677	1186	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247367	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	129	282	0	ENST00000281708.4:c.1435C>T	p.Arg479Ter	p.R479*	ENST00000281708	NM_033632.3	479	Cga/Tga	10/12	0.442368078331351	2	FACETS	0.769	0.704	0.834	0.769	0.704	0.834	SUBCLONAL	2	TRUE	0	0.450011491941329	2		282	373	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472561	88472561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	274	597	0	ENST00000360948.2:c.1994C>T	p.Ser665Leu	p.S665L	ENST00000360948	NM_001012338.2	665	tCg/tTg	16/19	0.450011491941329	2	FACETS	0.937	0.886	0.988	0.937	0.886	0.988	CLONAL	2	TRUE	0	0.450011491941329	2		597	650	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526441	66526441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	233	399	1	ENST00000358598.2:c.997C>T	p.Arg333Cys	p.R333C	ENST00000358598	NM_212471.2	333	Cgt/Tgt	11/11	0.292220433413747	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	2	0.450011491941329	4		400	732	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058542	69058542	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	68	660	4	ENST00000288368.4:c.4190del	p.Asn1397MetfsTer16	p.N1397Mfs*16	ENST00000288368	NM_024870.2	1396	Aaa/aa	34/40	0.450011491941329	2	FACETS	0.735	0.642	0.835	0.368	0.321	0.418	SUBCLONAL	1	TRUE	0	0.450011491941329	2		664	411	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316135	11316135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	357	677	0	ENST00000361445.4:c.619G>A	p.Glu207Lys	p.E207K	ENST00000361445	NM_004958.3	207	Gag/Aag	5/58	0.448681120780815	3	FACETS	0.95	0.902	0.999	0.95	0.902	0.999	CLONAL	2	TRUE	1	0.450011491941329	3		677	1023	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481905	56481905	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	229	701	0	ENST00000267101.3:c.833C>G	p.Thr278Ser	p.T278S	ENST00000267101	NM_001982.3	278	aCc/aGc	7/28	0.383848000853628	3	FACETS	1	0.978	1	0.558	0.52	0.598	CLONAL	1	TRUE	1	0.450011491941329	3		701	1117	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774689	73774689	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	44	87	0	ENST00000254810.4:c.398G>C	p.Gly133Ala	p.G133A	ENST00000254810	NM_005324.3	133	gGa/gCa	4/4	0.292220433413747	4	FACETS	0.903	0.771	1	0.903	0.771	1	CLONAL	2	TRUE	2	0.450011491941329	4		87	157	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202123044	202123044	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	222	468	0	ENST00000358485.4:c.90C>G	p.His30Gln	p.H30Q	ENST00000358485	NM_001080125.1	30	caC/caG	1/9	0.142314687336134	5	FACETS	0.947	0.882	1			1	INDETERMINATE	2	TRUE	NA	0.450011491941329	5		468	873	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225362543	225362543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	134	432	0	ENST00000264414.4:c.1634G>A	p.Gly545Asp	p.G545D	ENST00000264414	NM_003590.4	545	gGt/gAt	12/16	0.450011491941329	2	FACETS	0.856	0.788	0.925	0.856	0.788	0.925	CLONAL	2	TRUE	0	0.450011491941329	2		432	348	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101041	41101041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	369	673	1	ENST00000373198.4:c.1315G>A	p.Glu439Lys	p.E439K	ENST00000373198	NM_133170.3	439	Gag/Aag	8/32	0.246110270715157	5	FACETS	1	0.989	1	0.762	0.723	0.802	INDETERMINATE	2	TRUE	2	0.450011491941329	5		674	1201	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374757	149374757	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	127	432	1	ENST00000360632.3:c.337C>T	p.Leu113Phe	p.L113F	ENST00000360632	NM_015472.4	113	Ctc/Ttc	2/7	0.450011491941329	3	FACETS	0.947	0.859	1	0.474	0.429	0.52	CLONAL	1	TRUE	1	0.450011491941329	3		433	730	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31423045	31423045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	75	470	0	ENST00000344624.3:c.3268G>A	p.Glu1090Lys	p.E1090K	ENST00000344624		1090	Gag/Aag	26/33	0.450011491941329	4	FACETS	0.726	0.636	0.823	0.242	0.212	0.275	SUBCLONAL	1	TRUE	1	0.450011491941329	4		470	666	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38946569	38946569	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0043491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	41	325	2	ENST00000357387.3:c.4399+1G>A		p.X1467_splice	ENST00000357387	NM_152756.3	1467			0.450011491941329	4	FACETS	0.917	0.768	1	0.306	0.256	0.361	CLONAL	1	TRUE	1	0.450011491941329	4		327	288	SUCCESS
APC	324	MSKCC	GRCh37	5	112175952	112175952	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587783031	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	19	239	0	ENST00000257430.4:c.4666del	p.Thr1556LeufsTer9	p.T1556Lfs*9	ENST00000257430	NM_000038.5	1554	gAa/ga	16/16	1	2	FACETS	0.411	0.312	0.527	0.411	0.312	0.527	SUBCLONAL	1	TRUE	1	0.318017325848273	2		239	291	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	184	721	8	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.318017325848273	2		729	931	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	18	374	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.264	0.198	0.342	0.264	0.198	0.342	SUBCLONAL	1	TRUE	1	0.318017325848273	2		374	429	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	123	524	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.939	0.849	1	0.939	0.849	1	CLONAL	1	TRUE	1	0.318017325848273	2		525	824	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087393	27087393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	138	624	0	ENST00000324856.7:c.1967C>T	p.Ala656Val	p.A656V	ENST00000324856	NM_006015.4	656	gCt/gTt	5/20	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.318017325848273	2		624	864	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599288	28599288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769937470	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	153	732	0	ENST00000253063.3:c.734C>T	p.Pro245Leu	p.P245L	ENST00000253063	NM_031459.4	245	cCg/cTg	5/10	1	2	FACETS	0.94	0.859	1	0.94	0.859	1	CLONAL	1	TRUE	1	0.318017325848273	2		732	1024	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546323	46546324	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	23	319	0	ENST00000262741.5:c.205dup	p.Asp69GlyfsTer9	p.D69Gfs*9	ENST00000262741	NM_003629.3	69	gat/gGat	2/10	1	2	FACETS	0.377	0.293	0.474	0.377	0.293	0.474	SUBCLONAL	1	TRUE	1	0.318017325848273	2		319	384	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115844	8115844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	128	615	0	ENST00000346208.3:c.1190C>T	p.Ser397Phe	p.S397F	ENST00000346208		397	tCc/tTc	6/6	1	2	FACETS	0.887	0.803	0.975	0.887	0.803	0.975	CLONAL	1	TRUE	1	0.318017325848273	2		615	908	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251881	8251881	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	132	649	0	ENST00000335790.3:c.196T>G	p.Tyr66Asp	p.Y66D	ENST00000335790	NM_002315.2	66	Tac/Gac	2/4	1	2	FACETS	0.913	0.829	1	0.913	0.829	1	CLONAL	1	TRUE	1	0.318017325848273	2		649	909	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572600	64572600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	150	748	1	ENST00000312049.6:c.1256G>A	p.Gly419Asp	p.G419D	ENST00000312049	NM_130799.2	419	gGc/gAc	9/10	1	2	FACETS	0.848	0.773	0.926	0.848	0.773	0.926	CLONAL	1	TRUE	1	0.318017325848273	2		749	1113	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942053	71942053	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	127	732	1	ENST00000298229.2:c.1322del	p.Asn441ThrfsTer2	p.N441Tfs*2	ENST00000298229	NM_001567.3	439	ccA/cc	12/28	1	2	FACETS	0.873	0.79	0.96	0.873	0.79	0.96	CLONAL	1	TRUE	1	0.318017325848273	2		733	915	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	163	723	2	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	0.0764223394519061	3	FACETS	1	0.98	1	0.607	0.556	0.66	INDETERMINATE	1	TRUE	1	0.318017325848273	3		725	979	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489534	56489534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775164134	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	115	540	0	ENST00000267101.3:c.1999C>T	p.Arg667Cys	p.R667C	ENST00000267101	NM_001982.3	667	Cgt/Tgt	17/28	0.0764223394519061	3	FACETS	1	0.923	1	0.514	0.463	0.569	INDETERMINATE	1	TRUE	1	0.318017325848273	3		540	815	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860074	57860075	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs759448855	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	141	795	1	ENST00000228682.2:c.821dup	p.Cys275LeufsTer32	p.C275Lfs*32	ENST00000228682	NM_005269.2	272	tgg/tGgg	8/12	0.0764223394519061	3	FACETS	0.918	0.834	1	0.459	0.417	0.503	INDETERMINATE	1	TRUE	1	0.318017325848273	3		796	1120	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233090	69233090	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746910913	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	62	326	0	ENST00000462284.1:c.961del	p.Leu321PhefsTer52	p.L321Ffs*52	ENST00000462284	NM_002392.5	319	Ccc/cc	11/11	1	2	FACETS	0.94	0.814	1	0.94	0.814	1	CLONAL	1	TRUE	1	0.318017325848273	2		326	415	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237692	133237692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753759783	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	116	610	1	ENST00000320574.5:c.2923C>T	p.Arg975Cys	p.R975C	ENST00000320574	NM_006231.2	975	Cgc/Tgc	25/49	1	2	FACETS	0.792	0.713	0.876	0.792	0.713	0.876	SUBCLONAL	1	TRUE	1	0.318017325848273	2		611	921	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636193	28636193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777905087	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	97	459	0	ENST00000241453.7:c.179C>T	p.Pro60Leu	p.P60L	ENST00000241453	NM_004119.2	60	cCg/cTg	3/24	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.318017325848273	2		459	570	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434889	110434889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1021457672	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	160	752	0	ENST00000375856.3:c.3512G>A	p.Arg1171His	p.R1171H	ENST00000375856	NM_003749.2	1171	cGc/cAc	1/2	1	2	FACETS	0.856	0.784	0.933	0.856	0.784	0.933	CLONAL	1	TRUE	1	0.318017325848273	2		752	1175	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435192	110435192	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	116	505	1	ENST00000375856.3:c.3209G>A	p.Gly1070Asp	p.G1070D	ENST00000375856	NM_003749.2	1070	gGt/gAt	1/2	1	2	FACETS	0.845	0.761	0.934	0.845	0.761	0.934	CLONAL	1	TRUE	1	0.318017325848273	2		506	863	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543301	65543301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779789251	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	125	565	2	ENST00000358664.4:c.376G>A	p.Ala126Thr	p.A126T	ENST00000358664	NM_002382.4	126	Gcc/Acc	5/5	1	2	FACETS	0.906	0.819	0.997	0.906	0.819	0.997	CLONAL	1	TRUE	1	0.318017325848273	2		567	868	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828057	3828057	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	95	559	0	ENST00000262367.5:c.2068del	p.Ala690LeufsTer5	p.A690Lfs*5	ENST00000262367	NM_004380.2	690	Gct/ct	10/31	1	2	FACETS	0.7	0.623	0.783	0.7	0.623	0.783	SUBCLONAL	1	TRUE	1	0.318017325848273	2		559	853	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134428	30134428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	143	597	0	ENST00000263025.4:c.103C>T	p.Pro35Ser	p.P35S	ENST00000263025	NM_002746.2	35	Ccg/Tcg	1/9	1	2	FACETS	0.83	0.756	0.909	0.83	0.756	0.909	CLONAL	1	TRUE	1	0.318017325848273	2		597	1083	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993174	72993174	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	52	716	0	ENST00000268489.5:c.871T>G	p.Phe291Val	p.F291V	ENST00000268489	NM_006885.3	291	Ttt/Gtt	2/10	1	2	FACETS	0.32	0.271	0.374	0.32	0.271	0.374	SUBCLONAL	1	TRUE	1	0.318017325848273	2		716	1022	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81971428	81971428	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	112	550	0	ENST00000359376.3:c.3118C>T	p.Pro1040Ser	p.P1040S	ENST00000359376	NM_002661.3	1040	Cct/Tct	28/33	1	2	FACETS	0.938	0.844	1	0.938	0.844	1	CLONAL	1	TRUE	1	0.318017325848273	2		550	751	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805557	89805557	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	141	632	0	ENST00000389301.3:c.4151T>C	p.Leu1384Pro	p.L1384P	ENST00000389301	NM_000135.2	1384	cTg/cCg	41/43	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.318017325848273	2		632	870	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131277	17131277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778275358	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	162	800	1	ENST00000285071.4:c.175C>T	p.Arg59Cys	p.R59C	ENST00000285071	NM_144997.5	59	Cgt/Tgt	4/14	1	2	FACETS	0.954	0.874	1	0.954	0.874	1	CLONAL	1	TRUE	1	0.318017325848273	2		801	1068	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985805	60985805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	84	361	0	ENST00000333681.4:c.95C>T	p.Ala32Val	p.A32V	ENST00000333681		32	gCg/gTg	2/3	1	2	FACETS	0.859	0.759	0.965	0.859	0.759	0.965	CLONAL	1	TRUE	1	0.318017325848273	2		361	615	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054650	13054658	+	inframe_deletion	In_Frame_Del	DEL	GAGGATGAG	GAGGATGAG	-	rs550353351	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	73	505	1	ENST00000316448.5:c.1191_1199del	p.Glu398_Asp400del	p.E398_D400del	ENST00000316448	NM_004343.3	393	GAGGATGAG/-	9/9	1	2	FACETS	0.628	0.549	0.714	0.628	0.549	0.714	SUBCLONAL	1	TRUE	1	0.318017325848273	2		506	731	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955112	17955112	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755706305	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	163	738	3	ENST00000458235.1:c.115del	p.Gln39SerfsTer108	p.Q39Sfs*108	ENST00000458235	NM_000215.3	39	Cag/ag	2/24	1	2	FACETS	0.917	0.84	0.997	0.917	0.84	0.997	CLONAL	1	TRUE	1	0.318017325848273	2		741	1118	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18276986	18276986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748211099	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	83	409	0	ENST00000222254.8:c.1433G>A	p.Arg478His	p.R478H	ENST00000222254	NM_005027.3	478	cGt/cAt	12/16	1	2	FACETS	0.745	0.657	0.839	0.745	0.657	0.839	SUBCLONAL	1	TRUE	1	0.318017325848273	2		409	701	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910593	50910593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372429157	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	152	817	0	ENST00000440232.2:c.1696G>A	p.Glu566Lys	p.E566K	ENST00000440232	NM_002691.3	566	Gag/Aag	14/27	1	2	FACETS	0.879	0.802	0.959	0.879	0.802	0.959	CLONAL	1	TRUE	1	0.318017325848273	2		817	1088	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027634	48027634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	44	304	0	ENST00000234420.5:c.2512C>T	p.Pro838Ser	p.P838S	ENST00000234420	NM_000179.2	838	Cca/Tca	4/10	1	2	FACETS	0.876	0.738	1	0.876	0.738	1	CLONAL	1	TRUE	1	0.318017325848273	2		304	316	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281634	198281634	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs542810619	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	68	394	0	ENST00000335508.6:c.497G>A	p.Arg166Gln	p.R166Q	ENST00000335508	NM_012433.2	166	cGa/cAa	6/25	1	2	FACETS	0.875	0.763	0.995	0.875	0.763	0.995	CLONAL	1	TRUE	1	0.318017325848273	2		394	489	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	22	325	0	ENST00000375687.4:c.1933_1934dup	p.Gly646ValfsTer58	p.G646Vfs*58	ENST00000375687	NM_015338.5	642	-/GG	13/13	1	2	FACETS	0.391	0.302	0.494	0.391	0.302	0.494	SUBCLONAL	1	TRUE	1	0.318017325848273	2		325	354	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543913	41543913	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	136	649	0	ENST00000263253.7:c.2204A>G	p.His735Arg	p.H735R	ENST00000263253	NM_001429.3	735	cAc/cGc	12/31	1	2	FACETS	0.85	0.772	0.933	0.85	0.772	0.933	CLONAL	1	TRUE	1	0.318017325848273	2		649	1006	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125722	47125722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376063996	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	91	441	0	ENST00000409792.3:c.5548C>T	p.Arg1850Cys	p.R1850C	ENST00000409792	NM_014159.6	1850	Cgt/Tgt	12/21	1	2	FACETS	0.926	0.823	1	0.926	0.823	1	CLONAL	1	TRUE	1	0.318017325848273	2		441	618	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665383	138665383	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	168	638	0	ENST00000330315.3:c.182C>T	p.Ala61Val	p.A61V	ENST00000330315	NM_023067.3	61	gCg/gTg	1/1	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.318017325848273	2		638	997	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	36	289	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.854	0.706	1	0.854	0.706	1	CLONAL	1	TRUE	1	0.318017325848273	2		289	265	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803180	1803180	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	165	777	0	ENST00000260795.2:c.532G>A	p.Ala178Thr	p.A178T	ENST00000260795		178	Gcc/Acc	4/17	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.318017325848273	2		777	996	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081701	143081701	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	54	313	0	ENST00000262992.4:c.1373T>C	p.Val458Ala	p.V458A	ENST00000262992	NM_001101669.1	458	gTa/gCa	15/24	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.318017325848273	2		313	333	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945141	38945141	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	30	284	0	ENST00000357387.3:c.4663T>C	p.Cys1555Arg	p.C1555R	ENST00000357387	NM_152756.3	1555	Tgt/Cgt	35/38	1	2	FACETS	0.538	0.433	0.655	0.538	0.433	0.655	SUBCLONAL	1	TRUE	1	0.318017325848273	2		284	351	SUCCESS
APC	324	MSKCC	GRCh37	5	112178079	112178079	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	27	397	0	ENST00000257430.4:c.6788A>G	p.Glu2263Gly	p.E2263G	ENST00000257430	NM_000038.5	2263	gAa/gGa	16/16	1	2	FACETS	0.37	0.294	0.457	0.37	0.294	0.457	SUBCLONAL	1	TRUE	1	0.318017325848273	2		397	459	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513319	149513319	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	111	530	0	ENST00000261799.4:c.764G>T	p.Gly255Val	p.G255V	ENST00000261799	NM_002609.3	255	gGg/gTg	6/23	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.318017325848273	2		530	605	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520178	176520178	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	169	820	0	ENST00000292408.4:c.1097G>T	p.Arg366Met	p.R366M	ENST00000292408	NM_213647.1	366	aGg/aTg	9/18	1	2	FACETS	0.989	0.908	1	0.989	0.908	1	CLONAL	1	TRUE	1	0.318017325848273	2		820	1075	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393342	393342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	82	410	0	ENST00000380956.4:c.190C>T	p.Arg64Cys	p.R64C	ENST00000380956	NM_001195286.1	64	Cgc/Tgc	2/9	1	2	FACETS	0.79	0.697	0.89	0.79	0.697	0.89	SUBCLONAL	1	TRUE	1	0.318017325848273	2		410	653	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398860	398860	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1561714266	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	72	519	0	ENST00000380956.4:c.670G>A	p.Ala224Thr	p.A224T	ENST00000380956	NM_001195286.1	224	Gcc/Acc	6/9	1	2	FACETS	0.637	0.556	0.724	0.637	0.556	0.724	SUBCLONAL	1	TRUE	1	0.318017325848273	2		519	711	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708097	117708097	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	64	443	0	ENST00000368508.3:c.2080T>G	p.Phe694Val	p.F694V	ENST00000368508	NM_002944.2	694	Ttt/Gtt	14/43	0.134979243940076	0	FACETS	0.668	0.58	0.762			1	INDETERMINATE	1	TRUE	0	0.318017325848273	0		443	411	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715491	117715491	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	53	315	0	ENST00000368508.3:c.998A>G	p.His333Arg	p.H333R	ENST00000368508	NM_002944.2	333	cAc/cGc	10/43	0.134979243940076	0	FACETS	0.743	0.637	0.857			1	INDETERMINATE	1	TRUE	0	0.318017325848273	0		315	306	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729727	41729727	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	45	471	0	ENST00000242208.4:c.802del	p.Glu268LysfsTer91	p.E268Kfs*91	ENST00000242208	NM_002192.2	268	Gaa/aa	3/3	1	2	FACETS	0.473	0.397	0.558	0.473	0.397	0.558	SUBCLONAL	1	TRUE	1	0.318017325848273	2		471	598	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187222	38187222	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	165	719	3	ENST00000317025.8:c.1255del	p.Thr419ProfsTer8	p.T419Pfs*8	ENST00000317025	NM_023034.1	419	Acc/cc	6/24	0.287158950042398	3	FACETS	0.976	0.894	1	0.488	0.447	0.531	CLONAL	1	TRUE	1	0.318017325848273	3		722	1232	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	99	594	2	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.878	0.784	0.978	0.878	0.784	0.978	CLONAL	1	TRUE	1	0.318017325848273	2		596	709	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912079	127912079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	61	299	0	ENST00000373547.4:c.791G>A	p.Arg264His	p.R264H	ENST00000373547	NM_002721.4	264	cGt/cAt	7/7	1	2	FACETS	0.918	0.794	1	0.918	0.794	1	CLONAL	1	TRUE	1	0.318017325848273	2		299	418	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940469	76940471	+	inframe_deletion	In_Frame_Del	DEL	ATC	ATC	-	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	71	232	0	ENST00000373344.5:c.622_624del	p.Asp208del	p.D208del	ENST00000373344	NM_000489.3	208	GAT/-	8/35	1	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.318017325848273	1		232	259	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349946	70349946	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	124	368	0	ENST00000374080.3:c.3929C>A	p.Pro1310Gln	p.P1310Q	ENST00000374080		1310	cCa/cAa	28/45	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.318017325848273	1		368	500	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438316	110438317	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	rs532810290	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	40	196	1	ENST00000375856.3:c.82_84dup	p.Asn28dup	p.N28dup	ENST00000375856	NM_003749.2	28	-/AAC	1/2	1	2	FACETS	0.648	0.54	0.769	0.648	0.54	0.769	SUBCLONAL	1	TRUE	1	0.318017325848273	2		197	388	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910371	29910372	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	65	642	0	ENST00000376809.5:c.46dup	p.Ala16GlyfsTer83	p.A16Gfs*83	ENST00000376809	NM_002116.7	14	tcg/tcGg	1/8	1	2	FACETS	0.467	0.403	0.536	0.467	0.403	0.536	SUBCLONAL	1	TRUE	1	0.318017325848273	2		642	876	SUCCESS
AR	367	MSKCC	GRCh37	X	66931262	66931262	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	14	238	0	ENST00000374690.3:c.1904T>G	p.Leu635Arg	p.L635R	ENST00000374690	NM_000044.3	635	cTt/cGt	4/8	1	1	FACETS	0.295	0.213	0.394	0.295	0.213	0.394	SUBCLONAL	1	TRUE	0	0.318017325848273	1		238	251	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176700745	176700745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745582394	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	37	380	0	ENST00000439151.2:c.5582G>A	p.Arg1861Gln	p.R1861Q	ENST00000439151	NM_022455.4	1861	cGa/cAa	17/23	1	2	FACETS	0.412	0.339	0.494	0.412	0.339	0.494	SUBCLONAL	1	TRUE	1	0.318017325848273	2		380	565	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88679165	88679165	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	16	129	0	ENST00000372037.3:c.1105C>A	p.Leu369Ile	p.L369I	ENST00000372037	NM_004329.2	369	Ctc/Atc	10/13	1	2	FACETS	0.751	0.56	0.975	0.751	0.56	0.975	CLONAL	1	TRUE	1	0.318017325848273	2		129	134	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112152	115112152	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1444457719	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	56	613	3	ENST00000257566.3:c.1588G>A	p.Ala530Thr	p.A530T	ENST00000257566	NM_016569.3	530	Gcc/Acc	7/8	1	2	FACETS	0.412	0.352	0.478	0.412	0.352	0.478	SUBCLONAL	1	TRUE	1	0.318017325848273	2		616	855	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120044	70120044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	11	16	0	ENST00000245479.2:c.1046C>T	p.Pro349Leu	p.P349L	ENST00000245479	NM_000346.3	349	cCc/cTc	3/3	1	2	FACETS	1	0.81	1	1	0.81	1	CLONAL	1	TRUE	1	0.318017325848273	2		16	57	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228593	36228594	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1198	96	789	0	ENST00000222270.7:c.7612dup	p.Ala2538GlyfsTer4	p.A2538Gfs*4	ENST00000222270	NM_014727.1	2536	gag/gaGg	34/37	1	2	FACETS	0.467	0.414	0.523	0.467	0.414	0.523	SUBCLONAL	1	TRUE	1	0.318017325848273	2		789	1294	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923853	39923853	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0043518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	21	289	0	ENST00000378444.4:c.3239-1G>T		p.X1080_splice	ENST00000378444	NM_001123385.1	1080			1	1	FACETS	0.307	0.236	0.39	0.307	0.236	0.39	SUBCLONAL	1	TRUE	0	0.318017325848273	1		289	362	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	196	745	7	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.457372054980763	2		752	725	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	310	721	8	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.76	0.719	0.802	1	0.994	1	SUBCLONAL	2	TRUE	1	0.457372054980763	2		729	892	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	79	542	5	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.457372054980763	2		547	331	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	65	374	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.601	0.522	0.686	0.601	0.522	0.686	SUBCLONAL	1	TRUE	1	0.457372054980763	2		374	473	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	151	524	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.457372054980763	2		525	649	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087393	27087393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	181	624	0	ENST00000324856.7:c.1967C>T	p.Ala656Val	p.A656V	ENST00000324856	NM_006015.4	656	gCt/gTt	5/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.457372054980763	2		624	769	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599288	28599288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769937470	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	319	732	0	ENST00000253063.3:c.734C>T	p.Pro245Leu	p.P245L	ENST00000253063	NM_031459.4	245	cCg/cTg	5/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.457372054980763	2		732	1197	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546323	46546324	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	22	319	0	ENST00000262741.5:c.205dup	p.Asp69GlyfsTer9	p.D69Gfs*9	ENST00000262741	NM_003629.3	69	gat/gGat	2/10	1	2	FACETS	0.376	0.292	0.473	0.376	0.292	0.473	SUBCLONAL	1	TRUE	1	0.457372054980763	2		319	256	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115844	8115844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	222	615	0	ENST00000346208.3:c.1190C>T	p.Ser397Phe	p.S397F	ENST00000346208		397	tCc/tTc	6/6	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.457372054980763	2		615	964	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251881	8251881	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	261	649	0	ENST00000335790.3:c.196T>G	p.Tyr66Asp	p.Y66D	ENST00000335790	NM_002315.2	66	Tac/Gac	2/4	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.457372054980763	2		649	1047	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572600	64572600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	269	748	1	ENST00000312049.6:c.1256G>A	p.Gly419Asp	p.G419D	ENST00000312049	NM_130799.2	419	gGc/gAc	9/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.457372054980763	2		749	1021	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942053	71942053	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	265	732	1	ENST00000298229.2:c.1322del	p.Asn441ThrfsTer2	p.N441Tfs*2	ENST00000298229	NM_001567.3	439	ccA/cc	12/28	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.457372054980763	2		733	1002	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	216	723	2	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.457372054980763	2		725	893	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489534	56489534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775164134	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	166	540	0	ENST00000267101.3:c.1999C>T	p.Arg667Cys	p.R667C	ENST00000267101	NM_001982.3	667	Cgt/Tgt	17/28	1	2	FACETS	0.892	0.82	0.966	0.892	0.82	0.966	CLONAL	1	TRUE	1	0.457372054980763	2		540	814	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860074	57860075	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs759448855	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	280	795	1	ENST00000228682.2:c.821dup	p.Cys275LeufsTer32	p.C275Lfs*32	ENST00000228682	NM_005269.2	272	tgg/tGgg	8/12	1	2	FACETS	0.991	0.93	1	0.991	0.93	1	CLONAL	1	TRUE	1	0.457372054980763	2		796	1235	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233090	69233090	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746910913	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	66	326	0	ENST00000462284.1:c.961del	p.Leu321PhefsTer52	p.L321Ffs*52	ENST00000462284	NM_002392.5	319	Ccc/cc	11/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.457372054980763	2		326	242	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237692	133237692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753759783	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	187	610	1	ENST00000320574.5:c.2923C>T	p.Arg975Cys	p.R975C	ENST00000320574	NM_006231.2	975	Cgc/Tgc	25/49	1	2	FACETS	0.84	0.775	0.906	0.84	0.775	0.906	CLONAL	1	TRUE	1	0.457372054980763	2		611	974	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636193	28636193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777905087	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	166	459	0	ENST00000241453.7:c.179C>T	p.Pro60Leu	p.P60L	ENST00000241453	NM_004119.2	60	cCg/cTg	3/24	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.457372054980763	2		459	678	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434889	110434889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1021457672	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	373	752	0	ENST00000375856.3:c.3512G>A	p.Arg1171His	p.R1171H	ENST00000375856	NM_003749.2	1171	cGc/cAc	1/2	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.457372054980763	2		752	1442	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435192	110435192	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	250	505	1	ENST00000375856.3:c.3209G>A	p.Gly1070Asp	p.G1070D	ENST00000375856	NM_003749.2	1070	gGt/gAt	1/2	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.457372054980763	2		506	1037	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543301	65543301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779789251	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	200	565	2	ENST00000358664.4:c.376G>A	p.Ala126Thr	p.A126T	ENST00000358664	NM_002382.4	126	Gcc/Acc	5/5	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.457372054980763	2		567	827	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127688	2127688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779832805	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	70	578	1	ENST00000219476.3:c.2927G>A	p.Arg976Gln	p.R976Q	ENST00000219476	NM_000548.3	976	cGg/cAg	26/42	0.170980509087956	3	FACETS	0.422	0.367	0.482	0.211	0.183	0.241	INDETERMINATE	1	TRUE	1	0.457372054980763	3		579	891	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808863	3808863	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866498372	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	66	426	3	ENST00000262367.5:c.3361G>A	p.Gly1121Arg	p.G1121R	ENST00000262367	NM_004380.2	1121	Gga/Aga	17/31	0.170980509087956	3	FACETS	0.535	0.464	0.612	0.267	0.232	0.306	INDETERMINATE	1	TRUE	1	0.457372054980763	3		429	663	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828057	3828057	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	225	559	0	ENST00000262367.5:c.2068del	p.Ala690LeufsTer5	p.A690Lfs*5	ENST00000262367	NM_004380.2	690	Gct/ct	10/31	0.170980509087956	3	FACETS	1	0.988	1	0.641	0.597	0.686	INDETERMINATE	1	TRUE	1	0.457372054980763	3		559	943	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134428	30134428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	242	597	0	ENST00000263025.4:c.103C>T	p.Pro35Ser	p.P35S	ENST00000263025	NM_002746.2	35	Ccg/Tcg	1/9	0.170980509087956	3	FACETS	1	0.99	1	0.649	0.606	0.693	INDETERMINATE	1	TRUE	1	0.457372054980763	3		597	1002	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993174	72993174	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	176	716	0	ENST00000268489.5:c.871T>G	p.Phe291Val	p.F291V	ENST00000268489	NM_006885.3	291	Ttt/Gtt	2/10	0.170980509087956	3	FACETS	0.774	0.712	0.84	0.387	0.356	0.42	INDETERMINATE	1	TRUE	1	0.457372054980763	3		716	1221	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81971428	81971428	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	166	550	0	ENST00000359376.3:c.3118C>T	p.Pro1040Ser	p.P1040S	ENST00000359376	NM_002661.3	1040	Cct/Tct	28/33	0.170980509087956	3	FACETS	1	0.982	1	0.619	0.569	0.67	INDETERMINATE	1	TRUE	1	0.457372054980763	3		550	721	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805557	89805557	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	171	632	0	ENST00000389301.3:c.4151T>C	p.Leu1384Pro	p.L1384P	ENST00000389301	NM_000135.2	1384	cTg/cCg	41/43	0.170980509087956	3	FACETS	1	0.972	1	0.559	0.514	0.605	INDETERMINATE	1	TRUE	1	0.457372054980763	3		632	822	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004825	16004825	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	95	624	0	ENST00000268712.3:c.2429T>G	p.Val810Gly	p.V810G	ENST00000268712	NM_006311.3	810	gTt/gGt	20/46	1	2	FACETS	0.472	0.42	0.528	0.472	0.42	0.528	SUBCLONAL	1	TRUE	1	0.457372054980763	2		624	880	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131277	17131277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778275358	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	306	800	1	ENST00000285071.4:c.175C>T	p.Arg59Cys	p.R59C	ENST00000285071	NM_144997.5	59	Cgt/Tgt	4/14	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.457372054980763	2		801	1238	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553478	29553478	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781807	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	286	760	3	ENST00000356175.3:c.2033del	p.Pro678ArgfsTer10	p.P678Rfs*10	ENST00000356175	NM_000267.3	676	aCc/ac	18/57	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.457372054980763	2		763	1134	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512401	38512402	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs745553450	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	142	782	0	ENST00000254066.5:c.1319dup	p.Pro441AlafsTer5	p.P441Afs*5	ENST00000254066	NM_000964.3	438	gcc/gCcc	9/9	1	2	FACETS	0.732	0.667	0.8	0.732	0.667	0.8	SUBCLONAL	1	TRUE	1	0.457372054980763	2		782	848	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985805	60985805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	133	361	0	ENST00000333681.4:c.95C>T	p.Ala32Val	p.A32V	ENST00000333681		32	gCg/gTg	2/3	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.457372054980763	2		361	572	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054650	13054658	+	inframe_deletion	In_Frame_Del	DEL	GAGGATGAG	GAGGATGAG	-	rs550353351	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	111	505	1	ENST00000316448.5:c.1191_1199del	p.Glu398_Asp400del	p.E398_D400del	ENST00000316448	NM_004343.3	393	GAGGATGAG/-	9/9	1	2	FACETS	0.766	0.689	0.846	0.766	0.689	0.846	SUBCLONAL	1	TRUE	1	0.457372054980763	2		506	634	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955112	17955112	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755706305	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	304	738	3	ENST00000458235.1:c.115del	p.Gln39SerfsTer108	p.Q39Sfs*108	ENST00000458235	NM_000215.3	39	Cag/ag	2/24	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.457372054980763	2		741	1149	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18276986	18276986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748211099	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	100	409	0	ENST00000222254.8:c.1433G>A	p.Arg478His	p.R478H	ENST00000222254	NM_005027.3	478	cGt/cAt	12/16	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.457372054980763	2		409	434	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910593	50910593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372429157	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	275	817	0	ENST00000440232.2:c.1696G>A	p.Glu566Lys	p.E566K	ENST00000440232	NM_002691.3	566	Gag/Aag	14/27	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.457372054980763	2		817	1138	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143212	30143212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772569032	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	92	697	0	ENST00000389048.3:c.314C>T	p.Ala105Val	p.A105V	ENST00000389048	NM_004304.4	105	gCg/gTg	1/29	1	2	FACETS	0.541	0.481	0.606	0.541	0.481	0.606	SUBCLONAL	1	TRUE	1	0.457372054980763	2		697	743	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027634	48027634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	47	304	0	ENST00000234420.5:c.2512C>T	p.Pro838Ser	p.P838S	ENST00000234420	NM_000179.2	838	Cca/Tca	4/10	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.457372054980763	2		304	191	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281634	198281634	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs542810619	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	85	394	0	ENST00000335508.6:c.497G>A	p.Arg166Gln	p.R166Q	ENST00000335508	NM_012433.2	166	cGa/cAa	6/25	1	2	FACETS	0.845	0.75	0.945	0.845	0.75	0.945	CLONAL	1	TRUE	1	0.457372054980763	2		394	440	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	32	325	0	ENST00000375687.4:c.1933_1934dup	p.Gly646ValfsTer58	p.G646Vfs*58	ENST00000375687	NM_015338.5	642	-/GG	13/13	1	2	FACETS	0.516	0.421	0.623	0.516	0.421	0.623	SUBCLONAL	1	TRUE	1	0.457372054980763	2		325	271	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543913	41543913	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	249	649	0	ENST00000263253.7:c.2204A>G	p.His735Arg	p.H735R	ENST00000263253	NM_001429.3	735	cAc/cGc	12/31	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.457372054980763	2		649	1073	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125722	47125722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376063996	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	95	441	0	ENST00000409792.3:c.5548C>T	p.Arg1850Cys	p.R1850C	ENST00000409792	NM_014159.6	1850	Cgt/Tgt	12/21	1	2	FACETS	0.785	0.701	0.874	0.785	0.701	0.874	SUBCLONAL	1	TRUE	1	0.457372054980763	2		441	529	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665383	138665383	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	323	638	0	ENST00000330315.3:c.182C>T	p.Ala61Val	p.A61V	ENST00000330315	NM_023067.3	61	gCg/gTg	1/1	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.457372054980763	2		638	1146	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	45	289	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.457372054980763	2		289	154	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803180	1803180	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	274	777	0	ENST00000260795.2:c.532G>A	p.Ala178Thr	p.A178T	ENST00000260795		178	Gcc/Acc	4/17	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.457372054980763	2		777	1145	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081701	143081701	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	78	313	0	ENST00000262992.4:c.1373T>C	p.Val458Ala	p.V458A	ENST00000262992	NM_001101669.1	458	gTa/gCa	15/24	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.457372054980763	2		313	300	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278901	1278901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772441504	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	139	630	1	ENST00000310581.5:c.2141C>T	p.Thr714Met	p.T714M	ENST00000310581	NM_198253.2	714	aCg/aTg	6/16	1	2	FACETS	0.688	0.626	0.754	0.688	0.626	0.754	SUBCLONAL	1	TRUE	1	0.457372054980763	2		631	883	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945141	38945141	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	16	284	0	ENST00000357387.3:c.4663T>C	p.Cys1555Arg	p.C1555R	ENST00000357387	NM_152756.3	1555	Tgt/Cgt	35/38	1	2	FACETS	0.259	0.191	0.34	0.259	0.191	0.34	SUBCLONAL	1	TRUE	1	0.457372054980763	2		284	270	SUCCESS
APC	324	MSKCC	GRCh37	5	112178079	112178079	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	80	397	0	ENST00000257430.4:c.6788A>G	p.Glu2263Gly	p.E2263G	ENST00000257430	NM_000038.5	2263	gAa/gGa	16/16	1	2	FACETS	0.772	0.682	0.868	0.772	0.682	0.868	SUBCLONAL	1	TRUE	1	0.457372054980763	2		397	453	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513319	149513319	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	149	530	0	ENST00000261799.4:c.764G>T	p.Gly255Val	p.G255V	ENST00000261799	NM_002609.3	255	gGg/gTg	6/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.457372054980763	2		530	573	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520178	176520178	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	323	820	0	ENST00000292408.4:c.1097G>T	p.Arg366Met	p.R366M	ENST00000292408	NM_213647.1	366	aGg/aTg	9/18	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.457372054980763	2		820	1282	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393342	393342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	179	410	0	ENST00000380956.4:c.190C>T	p.Arg64Cys	p.R64C	ENST00000380956	NM_001195286.1	64	Cgc/Tgc	2/9	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.457372054980763	2		410	712	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398860	398860	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1561714266	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	149	519	0	ENST00000380956.4:c.670G>A	p.Ala224Thr	p.A224T	ENST00000380956	NM_001195286.1	224	Gcc/Acc	6/9	1	2	FACETS	0.932	0.854	1	0.932	0.854	1	CLONAL	1	TRUE	1	0.457372054980763	2		519	699	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708097	117708097	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	66	443	0	ENST00000368508.3:c.2080T>G	p.Phe694Val	p.F694V	ENST00000368508	NM_002944.2	694	Ttt/Gtt	14/43	1	2	FACETS	0.972	0.851	1	0.972	0.851	1	CLONAL	1	TRUE	1	0.457372054980763	2		443	297	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715491	117715491	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	55	315	0	ENST00000368508.3:c.998A>G	p.His333Arg	p.H333R	ENST00000368508	NM_002944.2	333	cAc/cGc	10/43	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.457372054980763	2		315	236	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729727	41729727	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	35	471	0	ENST00000242208.4:c.802del	p.Glu268LysfsTer91	p.E268Kfs*91	ENST00000242208	NM_002192.2	268	Gaa/aa	3/3	1	2	FACETS	0.241	0.197	0.291	0.241	0.197	0.291	SUBCLONAL	1	TRUE	1	0.457372054980763	2		471	634	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187222	38187222	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	212	719	3	ENST00000317025.8:c.1255del	p.Thr419ProfsTer8	p.T419Pfs*8	ENST00000317025	NM_023034.1	419	Acc/cc	6/24	0.457372054980763	3	FACETS	0.849	0.787	0.913	0.424	0.393	0.457	CLONAL	1	TRUE	1	0.457372054980763	3		722	1342	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	188	594	2	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.968	0.896	1	0.968	0.896	1	CLONAL	1	TRUE	1	0.457372054980763	2		596	849	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220354	98220354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	41	470	1	ENST00000331920.6:c.3109G>A	p.Ala1037Thr	p.A1037T	ENST00000331920	NM_000264.3	1037	Gcc/Acc	18/24	1	2	FACETS	0.26	0.216	0.31	0.26	0.216	0.31	SUBCLONAL	1	TRUE	1	0.457372054980763	2		471	689	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912079	127912079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	53	299	0	ENST00000373547.4:c.791G>A	p.Arg264His	p.R264H	ENST00000373547	NM_002721.4	264	cGt/cAt	7/7	1	2	FACETS	0.865	0.744	0.995	0.865	0.744	0.995	CLONAL	1	TRUE	1	0.457372054980763	2		299	268	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940469	76940471	+	inframe_deletion	In_Frame_Del	DEL	ATC	ATC	-	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	48	232	0	ENST00000373344.5:c.622_624del	p.Asp208del	p.D208del	ENST00000373344	NM_000489.3	208	GAT/-	8/35	1	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.457372054980763	1		232	146	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349946	70349946	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	242	368	0	ENST00000374080.3:c.3929C>A	p.Pro1310Gln	p.P1310Q	ENST00000374080		1310	cCa/cAa	28/45	1	1	FACETS	0.836	0.791	0.882	1	0.995	1	CLONAL	2	TRUE	0	0.457372054980763	1		368	488	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438316	110438317	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	rs532810290	NA	P-0043518-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	39	196	1	ENST00000375856.3:c.82_84dup	p.Asn28dup	p.N28dup	ENST00000375856	NM_003749.2	28	-/AAC	1/2	1	2	FACETS	0.452	0.375	0.538	0.452	0.375	0.538	SUBCLONAL	1	TRUE	1	0.457372054980763	2		197	377	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	133	348	1				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.952	0.878	1			1	INDETERMINATE	1	TRUE	NA	0.86767001971399	2		349	322	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0043525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	64	308	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.911	0.807	1	0.911	0.807	1	CLONAL	1	TRUE	1	0.86767001971399	2		308	162	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362499	40362499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	122	437	0	ENST00000293328.3:c.1697G>A	p.Arg566Gln	p.R566Q	ENST00000293328	NM_012448.3	566	cGg/cAg	14/19	1	2	FACETS	0.873	0.8	0.948	0.873	0.8	0.948	CLONAL	1	TRUE	1	0.86767001971399	2		437	322	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0043527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	67	415	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.995	0.867	1	1	0.981	1	CLONAL	2	TRUE	1	0.15	2		415	449	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106648	27106648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553153748	NA	P-0043527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	46	491	2	ENST00000324856.7:c.6259G>A	p.Gly2087Arg	p.G2087R	ENST00000324856	NM_006015.4	2087	Gga/Aga	20/20	1	2	FACETS	0.89	0.748	1	0.89	0.748	1	CLONAL	1	TRUE	1	0.15	2		493	689	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602530	10602530	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777308626	NA	P-0043527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	49	471	1	ENST00000171111.5:c.1048G>A	p.Gly350Ser	p.G350S	ENST00000171111	NM_203500.1	350	Ggc/Agc	3/6	1	2	FACETS	0.966	0.817	1	0.966	0.817	1	CLONAL	1	TRUE	1	0.15	2		472	676	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928074	178928074	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	30	391	0	ENST00000263967.3:c.1352G>T	p.Gly451Val	p.G451V	ENST00000263967	NM_006218.2	451	gGa/gTa	8/21	1	2	FACETS	0.893	0.719	1	0.893	0.719	1	CLONAL	1	TRUE	1	0.15	2		391	448	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325157	123325174	+	inframe_deletion	In_Frame_Del	DEL	CGACTCCCCTGGCGCAGC	CGACTCCCCTGGCGCAGC	-	novel	NA	P-0043527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	105	428	0	ENST00000358487.5:c.154_171del	p.Ala52_Ser57del	p.A52_S57del	ENST00000358487	NM_000141.4	52	GCTGCGCCAGGGGAGTCG/-	3/18	1	2	FACETS	0.97	0.869	1	1	0.987	1	CLONAL	2	TRUE	1	0.15	2		428	722	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197365	94197365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781646	NA	P-0043527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	42	374	0	ENST00000323929.3:c.1139G>A	p.Arg380His	p.R380H	ENST00000323929	NM_005591.3	380	cGc/cAc	11/20	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.15	2		374	498	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435072	49435072	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	58	675	0	ENST00000301067.7:c.6481del	p.Leu2161SerfsTer103	p.L2161Sfs*103	ENST00000301067	NM_003482.3	2161	Ctc/tc	31/54	0.135563557690173	3	FACETS	1	0.948	1	0.616	0.529	0.711	CLONAL	1	TRUE	1	0.17	3		675	601	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573228	64573228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1114167474	NA	P-0043557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	65	549	0	ENST00000312049.6:c.1064G>A	p.Arg355Gln	p.R355Q	ENST00000312049	NM_130799.2	355	cGg/cAg	8/10	0.135563557690173	1	FACETS	0.965	0.836	1	0.965	0.836	1	CLONAL	1	TRUE	0	0.17	1		549	725	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66520090	66520167	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGCTTAATGTTTGAAATTCACGGAAGAGACATGTGAAATGTAACACGAGGCCTTCTCTCTTTTGCAGTGATATTTTTG	AGCTTAATGTTTGAAATTCACGGAAGAGACATGTGAAATGTAACACGAGGCCTTCTCTCTTTTGCAGTGATATTTTTG	-	novel	NA	P-0043557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	17	309	0	ENST00000358598.2:c.441-66_452del		p.X147_splice	ENST00000358598	NM_212471.2	147		5/11	1	2	FACETS	0.816	0.61	1	0.816	0.61	1	CLONAL	1	TRUE	1	0.17	2		309	245	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639010	176639010	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	49	620	0	ENST00000439151.2:c.3610C>G	p.Pro1204Ala	p.P1204A	ENST00000439151	NM_022455.4	1204	Cca/Gca	5/23	1	2	FACETS	0.891	0.754	1	0.891	0.754	1	CLONAL	1	TRUE	1	0.17	2		620	647	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692900	89692900	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	152	339	0	ENST00000371953.3:c.384G>T	p.Lys128Asn	p.K128N	ENST00000371953	NM_000314.4	128	aaG/aaT	5/9	0.715685229152701	1	FACETS	0.958	0.897	1	0.958	0.897	1	CLONAL	1	TRUE	0	0.745345713045909	1		339	267	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911475	39911475	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	193	258	1	ENST00000378444.4:c.5155G>C	p.Glu1719Gln	p.E1719Q	ENST00000378444	NM_001123385.1	1719	Gaa/Caa	15/15	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.745345713045909	1		259	270	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953267	17953267	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	203	618	1	ENST00000458235.1:c.719T>A	p.Met240Lys	p.M240K	ENST00000458235	NM_000215.3	240	aTg/aAg	6/24	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.745345713045909	2		619	543	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930587	131930587	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	55	267	0	ENST00000265335.6:c.1820A>G	p.Asn607Ser	p.N607S	ENST00000265335		607	aAt/aGt	12/25	1	2	FACETS	0.445	0.382	0.512	0.445	0.382	0.512	SUBCLONAL	1	TRUE	1	0.745345713045909	2		267	332	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41740034	41740669	+	splice_acceptor_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	CGCGCAGGTTTTTTTGTGTGTGTGGATTTTTTTATTTTTTTTTTTGGTGTTTTTTTTTTCCTTCTCCTCTTCAGCAAATTCTCTGGAACAAGAACAAAAAGTTTTCTGTGAAGTTTTGTTTGCAGGTTCCTCTCTGAATGCAGTCAGTGCTGTAGGTTTGTGGCTGTCAGGGAGGAGAGTTCTGACTGTCTCCGAGTAAGAGAGAAGGAAGGAGGGAGGGAGGGAGGGAGACAGGGAGGGAGGGAGAGACAGGGTGGCGGGGAGACAGACAGAGACAGAGAGAGAGGATGGGAGGGAGACAGAGACAGAGAGAGAGGAGAGAGGGGGAGAGAAGAGAGAGGGAAAGAAGGGGGAGAGAGAGGGAGAGAGGGAGGGAAGGGAGGGGGAGAGGGAGAGAGGGAAAGGAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAAGGATTGGCCCTAAGTAAGTGAGTGAATGGAGAGGGAGGGAGTTTGCTGTGAGTAGGGCTGTGATTAGGGAGGGAGGGACAGCCCGTTTTCTGACAGGCTGCTCTCCTTCTGCTCTTAGCTTCCTCACAGACACCTCTCTTCAAATATCACCATTTTCGGGGGTTCTACTTTCTCTTCTAAAATAAATTATC	CGCGCAGGTTTTTTTGTGTGTGTGGATTTTTTTATTTTTTTTTTTGGTGTTTTTTTTTTCCTTCTCCTCTTCAGCAAATTCTCTGGAACAAGAACAAAAAGTTTTCTGTGAAGTTTTGTTTGCAGGTTCCTCTCTGAATGCAGTCAGTGCTGTAGGTTTGTGGCTGTCAGGGAGGAGAGTTCTGACTGTCTCCGAGTAAGAGAGAAGGAAGGAGGGAGGGAGGGAGGGAGACAGGGAGGGAGGGAGAGACAGGGTGGCGGGGAGACAGACAGAGACAGAGAGAGAGGATGGGAGGGAGACAGAGACAGAGAGAGAGGAGAGAGGGGGAGAGAAGAGAGAGGGAAAGAAGGGGGAGAGAGAGGGAGAGAGGGAGGGAAGGGAGGGGGAGAGGGAGAGAGGGAAAGGAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAAGGATTGGCCCTAAGTAAGTGAGTGAATGGAGAGGGAGGGAGTTTGCTGTGAGTAGGGCTGTGATTAGGGAGGGAGGGACAGCCCGTTTTCTGACAGGCTGCTCTCCTTCTGCTCTTAGCTTCCTCACAGACACCTCTCTTCAAATATCACCATTTTCGGGGGTTCTACTTTCTCTTCTAAAATAAATTATC	-	novel	NA	P-0043565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	82	193	0	ENST00000242208.4:c.-143-554_-62del		p.X48_splice	ENST00000242208	NM_002192.2	48		2/3	0.745345713045909	3	FACETS	1	0.935	1			1	CLONAL	1	TRUE	NA	0.745345713045909	3		193	283	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	165	520	0	ENST00000206249.3:c.1607T>C	p.Leu536Pro	p.L536P	ENST00000206249	NM_000125.3	536	cTc/cCc	8/8	1	2	FACETS	0.957	0.884	1	0.957	0.884	1	CLONAL	1	TRUE	1	0.628070874355437	2		520	549	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207090	1207091	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs876661012	NA	P-0043566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	221	671	0	ENST00000326873.7:c.179dup	p.Tyr60Ter	p.Y60*	ENST00000326873	NM_000455.4	60	tac/tAac	1/10	0.628070874355437	1	FACETS	0.969	0.912	1	0.969	0.912	1	CLONAL	1	TRUE	0	0.628070874355437	1		671	498	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940970	49940970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	145	480	0	ENST00000296474.3:c.73G>A	p.Glu25Lys	p.E25K	ENST00000296474	NM_002447.2	25	Gag/Aag	1/20	1	2	FACETS	0.991	0.911	1	0.991	0.911	1	CLONAL	1	TRUE	1	0.628070874355437	2		480	466	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0043568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	91	469	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.442201226036075	2		470	296	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	55	347	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.442201226036075	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	0	0.442201226036075	1		347	183	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918694	44918694	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	11	238	0	ENST00000377967.4:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000377967	NM_021140.2	393	Cga/Tga	12/29	1	1	FACETS	0.242	0.167	0.334	0.242	0.167	0.334	SUBCLONAL	1	TRUE	0	0.442201226036075	1		238	160	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488228	56488228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	96	586	0	ENST00000267101.3:c.1747C>T	p.Pro583Ser	p.P583S	ENST00000267101	NM_001982.3	583	Ccc/Tcc	15/28	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.442201226036075	2		586	363	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372065	45372065	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	59	487	0	ENST00000262160.6:c.1104G>A	p.Trp368Ter	p.W368*	ENST00000262160	NM_005901.5	368	tgG/tgA	9/11	0.442201226036075	1	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	0	0.442201226036075	1		487	205	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101185	27101198	+	frameshift_variant	Frame_Shift_Del	DEL	TGAGGTTGCTCAGC	TGAGGTTGCTCAGC	G	novel	NA	P-0043568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	96	776	1	ENST00000324856.7:c.4467_4480delinsG	p.Glu1490LysfsTer11	p.E1490Kfs*11	ENST00000324856	NM_006015.4	1489	gcTGAGGTTGCTCAGCaa/gcGaa	18/20	0.442201226036075	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.442201226036075	1		777	271	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577606	7577618	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AACCTAGGAGATA	AACCTAGGAGATA	-	novel	NA	P-0043571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	186	548	0	ENST00000269305.4:c.673-10_675del		p.X225_splice	ENST00000269305	NM_001126112.2	225		7/11	0.781000322915388	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.781000322915388	1		548	254	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133748402	133748402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	176	500	0	ENST00000318560.5:c.1063G>A	p.Glu355Lys	p.E355K	ENST00000318560	NM_005157.4	355	Gag/Aag	6/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.781000322915388	2		500	428	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307242	118307242	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0043602-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	19	233	0	ENST00000534358.1:c.15T>A	p.Cys5Ter	p.C5*	ENST00000534358	NM_005933.3	5	tgT/tgA	1/36	1	2	FACETS	0.373	0.283	0.479	0.373	0.283	0.479	SUBCLONAL	1	TRUE	1	0.352241813767442	2		233	289	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579554	7579555	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0043634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	193	792	0	ENST00000269305.4:c.132dup	p.Leu45AlafsTer7	p.L45Afs*7	ENST00000269305	NM_001126112.2	44	-/G	4/11	0.335523637987208	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	2	0.335523637987208	4		792	729	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143236	30143236	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs765290844	NA	P-0043634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	22	597	0	ENST00000389048.3:c.290C>G	p.Pro97Arg	p.P97R	ENST00000389048	NM_004304.4	97	cCg/cGg	1/29	0.246258797151673	3	FACETS	0.396	0.306	0.5	0.198	0.153	0.25	SUBCLONAL	1	TRUE	1	0.335523637987208	3		597	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0043638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	183	763	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.740400595579833	1	FACETS	0.98	0.928	1	0.98	0.928	1	CLONAL	1	TRUE	0	0.789883330569539	1		763	286	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948451	71948451	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	102	1164	1	ENST00000298229.2:c.3163C>G	p.Pro1055Ala	p.P1055A	ENST00000298229	NM_001567.3	1055	Cct/Gct	26/28	0.515417009659914	4	FACETS	0.609	0.545	0.678	0.203	0.181	0.226	SUBCLONAL	1	TRUE	1	0.789883330569539	4		1165	759	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349660	89349660	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	394	820	0	ENST00000301030.4:c.3290A>C	p.Glu1097Ala	p.E1097A	ENST00000301030	NM_001256183.1	1097	gAa/gCa	9/13	0.789883330569539	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.789883330569539	3		820	627	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227021	2227021	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	126	690	1	ENST00000398665.3:c.4501G>T	p.Val1501Leu	p.V1501L	ENST00000398665	NM_032482.2	1501	Gtg/Ttg	27/28	0.789883330569539	3	FACETS	0.674	0.612	0.74	0.225	0.204	0.247	SUBCLONAL	1	TRUE	0	0.789883330569539	3		691	660	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0043647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	118	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.883	0.799	0.971	0.883	0.799	0.971	CLONAL	1	TRUE	1	0.438938523769789	2		539	609	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579575	7579575	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	256	791	0	ENST00000269305.4:c.112C>T	p.Gln38Ter	p.Q38*	ENST00000269305	NM_001126112.2	38	Caa/Taa	4/11	0.438938523769789	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.438938523769789	1		791	864	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591800	48591800	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	141	384	0	ENST00000342988.3:c.963del	p.Glu321AspfsTer15	p.E321Dfs*15	ENST00000342988	NM_005359.5	321	gaG/ga	9/12	0.438938523769789	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.438938523769789	1		384	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0043653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	389	766	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.451492173372225	2	FACETS	0.962	0.919	1	0.962	0.919	1	CLONAL	2	TRUE	0	0.477505620882007	2		767	847	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0043653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	190	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.333443161042382	4	FACETS	0.927	0.861	0.995	0.927	0.861	0.995	CLONAL	2	TRUE	2	0.477505620882007	4		539	634	SUCCESS
APC	324	MSKCC	GRCh37	5	112175772	112175772	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	112	259	0	ENST00000257430.4:c.4483del	p.Ser1495ValfsTer12	p.S1495Vfs*12	ENST00000257430	NM_000038.5	1494	gAa/ga	16/16	0.451492173372225	2	FACETS	0.872	0.798	0.947	0.872	0.798	0.947	CLONAL	2	TRUE	0	0.477505620882007	2		259	269	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400922	72400922	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	80	315	0	ENST00000357731.5:c.249T>A	p.Asp83Glu	p.D83E	ENST00000357731	NM_173808.2	83	gaT/gaA	2/7	0.558202481431559	3	FACETS	0.906	0.802	1	0.453	0.401	0.509	CLONAL	1	TRUE	1	0.5717559649493	3		315	397	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624281	89624281	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	99	449	0	ENST00000371953.3:c.55G>C	p.Asp19His	p.D19H	ENST00000371953	NM_000314.4	19	Gat/Cat	1/9	0.573804546637207	3	FACETS	0.887	0.795	0.984			1	CLONAL	1	TRUE	NA	0.5717559649493	3		449	502	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813255	89813255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	124	718	1	ENST00000389301.3:c.3392C>T	p.Thr1131Ile	p.T1131I	ENST00000389301	NM_000135.2	1131	aCt/aTt	34/43	0.573804546637207	5	FACETS	0.903	0.817	0.995	0.181	0.163	0.199	CLONAL	1	TRUE	0	0.5717559649493	5		719	892	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905747	50906522	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTGGAGCTCCCAGCTGGGAAATACGCCCTGAGGCTGAAGGAGAAGGTGCAGGGCTTCCCAGGGCAGGGCTGGGTGGGGAGCTGGTACCCTGCTGCCACCGCTGACCCACCCATGCCCACAGGCTACGCAGTGCCAGCTGGAGGCGGACGTGCTGTGGTCTGACGTGGTCAGTCACCCACCGGAAGGGCCATGGCAGCGCATTGCGCCCTTGCGCGTGCTCAGCTTCGATATCGAGTGCGCCGGCCGCAAAGGTCTGTCCCCGGGCCCGGGCTCCTGCCCGCCTCATTGATGTGCCAAGTCGGGGGTCGGAAAGGCAGGTCCGGTGGAGGGAATGGCAAGCATGAAGGTGCCGGGGCAGGAGCACCCCAGCCCATGTGGCCAGATGGAGTGAGCACAGAGGGTGTGGAGATGGCCTGGAGGTGAGAGCAGAGCAGGAGCCAGGGTGAGCCACGTAGGGCCGGCAGGCAGCGGGGACAGCCCCGGGGAGATGGCAGGTGCAGCCTCCCTGCTGTGTTGGGAGTGAGGGGCAGGAGTCAGGCCCCTGCATCCTCCTGCCTCGCAGGCATCTTCCCTGAGCCTGAGCGGGACCCTGTCATCCAGATCTGCTCGCTGGGCCTGCGCTGGGGGGAGCCGGAGCCCTTCCTACGCCTGGCGCTCACCCTGCGGCCCTGTGCCCCCATCCTGGGTGCCAAGGTGCAGAGCTACGAGAAGGAGGAGGACCTGCTGCAGGTAGCTCTCGCTCCACGCCCCACACCATTTCCCGGGGTCCCCGCCA	GCTGGAGCTCCCAGCTGGGAAATACGCCCTGAGGCTGAAGGAGAAGGTGCAGGGCTTCCCAGGGCAGGGCTGGGTGGGGAGCTGGTACCCTGCTGCCACCGCTGACCCACCCATGCCCACAGGCTACGCAGTGCCAGCTGGAGGCGGACGTGCTGTGGTCTGACGTGGTCAGTCACCCACCGGAAGGGCCATGGCAGCGCATTGCGCCCTTGCGCGTGCTCAGCTTCGATATCGAGTGCGCCGGCCGCAAAGGTCTGTCCCCGGGCCCGGGCTCCTGCCCGCCTCATTGATGTGCCAAGTCGGGGGTCGGAAAGGCAGGTCCGGTGGAGGGAATGGCAAGCATGAAGGTGCCGGGGCAGGAGCACCCCAGCCCATGTGGCCAGATGGAGTGAGCACAGAGGGTGTGGAGATGGCCTGGAGGTGAGAGCAGAGCAGGAGCCAGGGTGAGCCACGTAGGGCCGGCAGGCAGCGGGGACAGCCCCGGGGAGATGGCAGGTGCAGCCTCCCTGCTGTGTTGGGAGTGAGGGGCAGGAGTCAGGCCCCTGCATCCTCCTGCCTCGCAGGCATCTTCCCTGAGCCTGAGCGGGACCCTGTCATCCAGATCTGCTCGCTGGGCCTGCGCTGGGGGGAGCCGGAGCCCTTCCTACGCCTGGCGCTCACCCTGCGGCCCTGTGCCCCCATCCTGGGTGCCAAGGTGCAGAGCTACGAGAAGGAGGAGGACCTGCTGCAGGTAGCTCTCGCTCCACGCCCCACACCATTTCCCGGGGTCCCCGCCA	-	novel	NA	P-0043662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	91	1018	0	ENST00000440232.2:c.797_1137+48del		p.X266_splice	ENST00000440232	NM_002691.3	266		7-9/27	0.212093311267421	4	FACETS	0.682	0.605	0.763	0.227	0.201	0.255	INDETERMINATE	1	TRUE	1	0.5717559649493	4		1018	734	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022878	31022878	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	107	590	0	ENST00000375687.4:c.2363A>C	p.Glu788Ala	p.E788A	ENST00000375687	NM_015338.5	788	gAa/gCa	13/13	0.265023269268365	4	FACETS	1	0.964	1	0.287	0.258	0.318	INDETERMINATE	1	TRUE	0	0.5717559649493	4		590	512	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961451	1961451	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1162500705	NA	P-0043662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	204	533	0	ENST00000382891.5:c.3239A>G	p.Lys1080Arg	p.K1080R	ENST00000382891	NM_133335.3	1080	aAg/aGg	17/22	0.491732462546273	5	FACETS	0.944	0.879	1			1	CLONAL	2	TRUE	NA	0.5717559649493	5		533	702	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271241	38271241	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	131	901	0	ENST00000425967.3:c.2467G>C	p.Glu823Gln	p.E823Q	ENST00000425967	NM_001174067.1	823	Gag/Cag	19/19	0.374824137948279	4	FACETS	0.94	0.854	1	0.47	0.427	0.516	CLONAL	1	TRUE	2	0.5717559649493	4		901	766	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559274	141559274	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1306	155	853	0	ENST00000220592.5:c.1527G>C	p.Lys509Asn	p.K509N	ENST00000220592	NM_012154.3	509	aaG/aaC	12/19	0.5717559649493	7	FACETS	0.902	0.823	0.985			1	CLONAL	1	TRUE	NA	0.5717559649493	7		853	1461	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47088063	47088065	+	frameshift_variant	Frame_Shift_Del	DEL	TGA	TGA	GG	novel	NA	P-0043662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	134	513	0	ENST00000409792.3:c.7010_7012delinsCC	p.Phe2337SerfsTer16	p.F2337Sfs*16	ENST00000409792	NM_014159.6	2337	tTCAca/tCCca	16/21	0.573804546637207	3	FACETS	0.905	0.824	0.99			1	CLONAL	1	TRUE	NA	0.5717559649493	3		513	666	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0043722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	109	309	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.0974944296708002	3	FACETS	1	0.976	1	0.625	0.566	0.686	INDETERMINATE	1	TRUE	1	0.6	3		309	378	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0043722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	55	146	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.0754761264191683	4	FACETS	1	0.966	1	0.709	0.615	0.808	INDETERMINATE	1	TRUE	2	0.6	4		146	207	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0043722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	247	496	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	2	TRUE	NA	0.6	2		496	393	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268144	153268144	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs920052554	NA	P-0043722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	215	265	0	ENST00000281708.4:c.664C>T	p.Arg222Ter	p.R222*	ENST00000281708	NM_033632.3	222	Cga/Tga	4/12	0.3	2	FACETS	1	0.957	1	1	0.957	1	INDETERMINATE	2	TRUE	0	0.6	2		265	355	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133574	55133574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373948582	NA	P-0043722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	132	396	0	ENST00000257290.5:c.878G>A	p.Arg293His	p.R293H	ENST00000257290	NM_006206.4	293	cGc/cAc	6/23	NA	2	FACETS	1	0.936	1			1	INDETERMINATE	1	TRUE	NA	0.6	2		396	429	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245712	46245712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752984515	NA	P-0043722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	90	356	0	ENST00000334344.6:c.3806C>T	p.Pro1269Leu	p.P1269L	ENST00000334344	NM_152641.2	1269	cCg/cTg	15/21	0.0974944296708002	3	FACETS	1	0.975	1	0.65	0.583	0.719	INDETERMINATE	1	TRUE	1	0.6	3		356	300	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871000	12871000	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121917832	NA	P-0043722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	42	343	0	ENST00000228872.4:c.227G>A	p.Trp76Ter	p.W76*	ENST00000228872	NM_004064.3	76	tGg/tAg	1/3	0.225429657827239	4	FACETS	0.742	0.622	0.873	0.371	0.311	0.437	INDETERMINATE	1	TRUE	2	0.6	4		343	302	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094422	27094422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	93	467	0	ENST00000324856.7:c.3130G>A	p.Val1044Met	p.V1044M	ENST00000324856	NM_006015.4	1044	Gtg/Atg	11/20	1	2	FACETS	0.771	0.69	0.856	0.771	0.69	0.856	SUBCLONAL	1	TRUE	1	0.6	2		467	402	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025618	1025618	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1410408833	NA	P-0043722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	106	566	0	ENST00000358495.3:c.757G>A	p.Ala253Thr	p.A253T	ENST00000358495	NM_134424.2	253	Gcc/Acc	9/12	1	2	FACETS	0.851	0.769	0.938	0.851	0.769	0.938	CLONAL	1	TRUE	1	0.6	2		566	415	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265666	10265666	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	90	422	0	ENST00000340748.4:c.1511A>G	p.Glu504Gly	p.E504G	ENST00000340748		504	gAg/gGg	19/40	0.3	1	FACETS	0.569	0.509	0.632	0.569	0.509	0.632	INDETERMINATE	1	TRUE	0	0.6	1		422	369	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067309	37067309	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	82	329	0	ENST00000231790.2:c.1220A>G	p.Gln407Arg	p.Q407R	ENST00000231790	NM_000249.3	407	cAg/cGg	12/19	1	2	FACETS	0.852	0.758	0.95	0.852	0.758	0.95	CLONAL	1	TRUE	1	0.6	2		329	321	SUCCESS
APC	324	MSKCC	GRCh37	5	112175643	112175644	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	G	novel	NA	P-0043722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	73	236	0	ENST00000257430.4:c.4352_4353delinsG	p.Glu1451GlyfsTer22	p.E1451Gfs*22	ENST00000257430	NM_000038.5	1451	gAA/gG	16/16	0.0754761264191683	4	FACETS	0.752	0.666	0.842	0.752	0.666	0.842	INDETERMINATE	2	TRUE	2	0.6	4		236	259	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0043782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	98	279	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.978	0.88	1	0.978	0.88	1	CLONAL	1	TRUE	1	0.54025239661723	2		279	371	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851645	134851645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395878132	NA	P-0043782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	221	442	0	ENST00000398015.3:c.1051C>T	p.Arg351Trp	p.R351W	ENST00000398015	NM_004441.4	351	Cgg/Tgg	5/16	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.54025239661723	2		442	661	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56477595	56477595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759044259	NA	P-0043782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	290	552	0	ENST00000267101.3:c.143C>T	p.Thr48Ile	p.T48I	ENST00000267101	NM_001982.3	48	aCa/aTa	2/28	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.54025239661723	2		552	838	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094394	27094394	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	359	478	0	ENST00000324856.7:c.3103del	p.Ala1035ProfsTer4	p.A1035Pfs*4	ENST00000324856	NM_006015.4	1034	aaG/aa	11/20	0.184530407646502	2	FACETS	0.819	0.781	0.858	0.819	0.781	0.858	INDETERMINATE	2	TRUE	0	0.54025239661723	2		478	811	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102153	27102153	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	154	451	1	ENST00000324856.7:c.5080del	p.Leu1694CysfsTer9	p.L1694Cfs*9	ENST00000324856	NM_006015.4	1693	atC/at	19/20	0.184530407646502	2	FACETS	0.909	0.835	0.986	0.455	0.417	0.493	INDETERMINATE	1	TRUE	0	0.54025239661723	2		452	627	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717735	89717735	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	137	370	0	ENST00000371953.3:c.760A>C	p.Lys254Gln	p.K254Q	ENST00000371953	NM_000314.4	254	Aaa/Caa	7/9	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.54025239661723	2		370	436	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717741	89717745	+	frameshift_variant	Frame_Shift_Del	DEL	GAGTT	GAGTT	-	novel	NA	P-0043782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	126	341	0	ENST00000371953.3:c.766_770del	p.Glu256LeufsTer40	p.E256Lfs*40	ENST00000371953	NM_000314.4	256	GAGTTc/c	7/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.54025239661723	2		341	411	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439845	49439848	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CACC	CACC	-	novel	NA	P-0043782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	259	531	1	ENST00000301067.7:c.4693_4693+3del		p.X1565_splice	ENST00000301067	NM_003482.3	1565		17/54	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.54025239661723	2		532	732	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485752	40485752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	267	479	0	ENST00000264657.5:c.988C>T	p.Pro330Ser	p.P330S	ENST00000264657	NM_139276.2	330	Ccc/Tcc	10/24	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.54025239661723	2		479	719	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589203	67589214	+	inframe_deletion	In_Frame_Del	DEL	CTTCAGTTCTGT	CTTCAGTTCTGT	-	novel	NA	P-0043782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	45	298	0	ENST00000274335.5:c.1191_1202del	p.Phe398_Val401del	p.F398_V401del	ENST00000274335		397	acCTTCAGTTCTGTg/acg	9/15	1	2	FACETS	0.643	0.544	0.751	0.643	0.544	0.751	SUBCLONAL	1	TRUE	1	0.54025239661723	2		298	259	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589606	67589607	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAG	novel	NA	P-0043782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	16	215	0	ENST00000274335.5:c.1372_1374dup	p.Glu458dup	p.E458dup	ENST00000274335		458	caa/cAAGaa	10/15	1	2	FACETS	0.282	0.209	0.369	0.282	0.209	0.369	SUBCLONAL	1	TRUE	1	0.54025239661723	2		215	210	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469824	157469825	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0043782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	172	580	0	ENST00000346085.5:c.2620_2621dup	p.Met874IlefsTer41	p.M874Ifs*41	ENST00000346085	NM_020732.3	873	ggt/ggTAt	9/20	1	2	FACETS	0.777	0.716	0.841	0.777	0.716	0.841	SUBCLONAL	1	TRUE	1	0.54025239661723	2		580	819	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0043795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	141	667	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.432462181321413	3	FACETS	0.874	0.796	0.956	0.437	0.398	0.478	CLONAL	1	TRUE	1	0.461823037813842	3		667	860	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0043795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	130	311	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.88	0.8	0.963	0.88	0.8	0.963	CLONAL	1	TRUE	1	0.461823037813842	2		311	640	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797482	45797482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778538	NA	P-0043795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1240	216	777	0	ENST00000450313.1:c.1037C>T	p.Ser346Leu	p.S346L	ENST00000450313	NM_012222.2	346	tCg/tTg	12/16	0.461823037813842	3	FACETS	0.791	0.733	0.851	0.395	0.366	0.426	SUBCLONAL	1	TRUE	1	0.461823037813842	3		777	1456	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133234554	133234554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	131	379	0	ENST00000320574.5:c.3278C>T	p.Ala1093Val	p.A1093V	ENST00000320574	NM_006231.2	1093	gCc/gTc	27/49	1	2	FACETS	0.994	0.905	1	0.994	0.905	1	CLONAL	1	TRUE	1	0.461823037813842	2		379	571	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22153309	22153309	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	114	383	0	ENST00000215832.6:c.601A>G	p.Asn201Asp	p.N201D	ENST00000215832	NM_002745.4	201	Aat/Gat	4/9	1	2	FACETS	0.838	0.757	0.924	0.838	0.757	0.924	CLONAL	1	TRUE	1	0.461823037813842	2		383	589	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776393	76776406	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CACTAAAAGAAAAA	CACTAAAAGAAAAA	-	novel	NA	P-0043795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	83	377	0	ENST00000373344.5:c.7072-12_7073del		p.X2358_splice	ENST00000373344	NM_000489.3	2358		34/35	1	2	FACETS	0.901	0.8	1	0.901	0.8	1	CLONAL	1	TRUE	1	0.461823037813842	2		377	399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs786203436	NA	P-0043825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	411	644	0	ENST00000269305.4:c.487T>A	p.Tyr163Asn	p.Y163N	ENST00000269305	NM_001126112.2	163	Tac/Aac	5/11	0.447283479254286	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.454283174636808	2		644	846	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015094	37015094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	313	511	0	ENST00000358127.4:c.310C>T	p.Arg104Cys	p.R104C	ENST00000358127	NM_001280556.1	104	Cgc/Tgc	3/10	0.454283174636808	2	FACETS	0.895	0.849	0.941	0.895	0.849	0.941	CLONAL	2	TRUE	0	0.454283174636808	2		511	770	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588880	69588880	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	65	457	0	ENST00000168712.1:c.356C>T	p.Ser119Leu	p.S119L	ENST00000168712	NM_002007.2	119	tCg/tTg	2/3	0.312586349349401	3	FACETS	0.528	0.457	0.605	0.176	0.152	0.202	SUBCLONAL	1	TRUE	0	0.454283174636808	3		457	665	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980575	70980575	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1301	169	506	0	ENST00000276594.2:c.802G>T	p.Val268Leu	p.V268L	ENST00000276594	NM_024504.3	268	Gtg/Ttg	4/8	0.454283174636808	7	FACETS	1	0.961	1	0.18	0.165	0.196	CLONAL	1	TRUE	1	0.454283174636808	7		506	1470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0043838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	417	1079	1	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.383627816148917	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.383627816148917	2		1080	1003	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729929	39729929	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	128	680	0	ENST00000361337.2:c.1244C>A	p.Ser415Tyr	p.S415Y	ENST00000361337	NM_003286.2	415	tCc/tAc	13/21	0.383627816148917	5	FACETS	1	0.974	1	0.404	0.366	0.445	CLONAL	1	TRUE	2	0.383627816148917	5		680	867	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0043857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	73	47	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.394934400222068	2		47	357	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911514	131911514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143802516	NA	P-0043857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	92	113	0	ENST00000265335.6:c.259C>T	p.Arg87Cys	p.R87C	ENST00000265335		87	Cgt/Tgt	3/25	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.394934400222068	2		113	442	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830853	156830853	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	129	94	0	ENST00000524377.1:c.127C>T	p.His43Tyr	p.H43Y	ENST00000524377	NM_002529.3	43	Cac/Tac	1/17	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.394934400222068	2		94	598	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71947024	71947024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768989262	NA	P-0043857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	178	199	0	ENST00000298229.2:c.2873C>T	p.Thr958Ile	p.T958I	ENST00000298229	NM_001567.3	958	aCc/aTc	25/28	1	2	FACETS	0.984	0.907	1	0.984	0.907	1	CLONAL	1	TRUE	1	0.394934400222068	2		199	916	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	459924	459924	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	106	111	0	ENST00000399788.2:c.1171G>A	p.Glu391Lys	p.E391K	ENST00000399788	NM_001042603.1	391	Gaa/Aaa	10/28	1	2	FACETS	0.718	0.643	0.796	0.718	0.643	0.796	SUBCLONAL	1	TRUE	1	0.394934400222068	2		111	748	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287305	46287315	+	frameshift_variant	Frame_Shift_Del	DEL	CCTTGTCTTTC	CCTTGTCTTTC	-	novel	NA	P-0043857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	114	132	0	ENST00000334344.6:c.5250_5260del	p.Asn1750LysfsTer6	p.N1750Kfs*6	ENST00000334344	NM_152641.2	1750	aaCCTTGTCTTTCga/aaga	19/21	0.394934400222068	1	FACETS	0.855	0.773	0.941	0.855	0.773	0.941	CLONAL	1	TRUE	0	0.394934400222068	1		132	542	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857925	9857925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs534440095	NA	P-0043857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	142	120	0	ENST00000330684.3:c.3476G>A	p.Arg1159His	p.R1159H	ENST00000330684	NM_001134407.1	1159	cGc/cAc	13/13	1	2	FACETS	0.905	0.825	0.988	0.905	0.825	0.988	CLONAL	1	TRUE	1	0.394934400222068	2		120	795	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032006	10032006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	131	157	0	ENST00000330684.3:c.817C>T	p.Pro273Ser	p.P273S	ENST00000330684	NM_001134407.1	273	Cca/Tca	3/13	1	2	FACETS	0.83	0.754	0.911	0.83	0.754	0.911	CLONAL	1	TRUE	1	0.394934400222068	2		157	799	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244595	41244595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555588649	NA	P-0043857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	136	146	0	ENST00000357654.3:c.2953C>T	p.Pro985Ser	p.P985S	ENST00000357654	NM_007294.3	985	Ccc/Tcc	10/23	1	2	FACETS	0.955	0.87	1	0.955	0.87	1	CLONAL	1	TRUE	1	0.394934400222068	2		146	721	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55693334	55693334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	153	147	0	ENST00000284073.2:c.541G>A	p.Glu181Lys	p.E181K	ENST00000284073	NM_138962.2	181	Gaa/Aaa	9/14	1	2	FACETS	0.892	0.816	0.971	0.892	0.816	0.971	CLONAL	1	TRUE	1	0.394934400222068	2		147	869	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858325	59858325	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	88	110	0	ENST00000259008.2:c.1670C>G	p.Ser557Cys	p.S557C	ENST00000259008	NM_032043.2	557	tCc/tGc	12/20	1	2	FACETS	0.877	0.78	0.981	0.877	0.78	0.981	CLONAL	1	TRUE	1	0.394934400222068	2		110	508	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276800	15276800	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	172	143	0	ENST00000263388.2:c.5465C>T	p.Ser1822Phe	p.S1822F	ENST00000263388	NM_000435.2	1822	tCc/tTc	30/33	1	2	FACETS	0.989	0.91	1	0.989	0.91	1	CLONAL	1	TRUE	1	0.394934400222068	2		143	881	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302292	15302292	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767905805	NA	P-0043857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	145	164	1	ENST00000263388.2:c.979G>A	p.Ala327Thr	p.A327T	ENST00000263388	NM_000435.2	327	Gcc/Acc	6/33	1	2	FACETS	0.822	0.75	0.898	0.822	0.75	0.898	CLONAL	1	TRUE	1	0.394934400222068	2		165	893	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212390	36212390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1475030129	NA	P-0043857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	193	167	1	ENST00000222270.7:c.2141C>T	p.Pro714Leu	p.P714L	ENST00000222270	NM_014727.1	714	cCt/cTt	3/37	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.394934400222068	2		168	960	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660327	227660327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	113	138	0	ENST00000305123.5:c.3128C>T	p.Ser1043Phe	p.S1043F	ENST00000305123	NM_005544.2	1043	tCc/tTc	1/2	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.394934400222068	2		138	534	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713407	40713407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768298187	NA	P-0043857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	170	145	0	ENST00000373198.4:c.4108C>T	p.Arg1370Cys	p.R1370C	ENST00000373198	NM_133170.3	1370	Cgc/Tgc	30/32	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.394934400222068	2		145	854	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499419	89499419	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	136	99	0	ENST00000336596.2:c.2589A>T	p.Lys863Asn	p.K863N	ENST00000336596	NM_005233.5	863	aaA/aaT	15/17	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.394934400222068	2		99	629	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542078	187542078	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	101	93	0	ENST00000441802.2:c.5662C>T	p.Leu1888Phe	p.L1888F	ENST00000441802	NM_005245.3	1888	Ctt/Ttt	10/27	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.394934400222068	2		93	470	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176715849	176715849	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	154	111	0	ENST00000439151.2:c.6181G>A	p.Glu2061Lys	p.E2061K	ENST00000439151	NM_022455.4	2061	Gaa/Aaa	21/23	1	2	FACETS	0.933	0.854	1	0.933	0.854	1	CLONAL	1	TRUE	1	0.394934400222068	2		111	836	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0043857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	19	113	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	1	2	FACETS	0.147	0.111	0.19	0.147	0.111	0.19	SUBCLONAL	1	TRUE	1	0.394934400222068	2		113	654	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444323	50444323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	120	97	0	ENST00000331340.3:c.253C>T	p.Leu85Phe	p.L85F	ENST00000331340	NM_006060.4	85	Ctt/Ttt	4/8	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.394934400222068	2		97	602	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439724	140439724	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	248	87	0	ENST00000288602.6:c.2015G>A	p.Gly672Glu	p.G672E	ENST00000288602	NM_004333.4	672	gGa/gAa	17/18	0.394934400222068	3	FACETS	1	0.972	1			1	CLONAL	2	TRUE	NA	0.394934400222068	3		87	711	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0043857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	177	86	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.394934400222068	3	FACETS	0.866	0.801	0.932			1	CLONAL	2	TRUE	NA	0.394934400222068	3		86	620	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046476	69046476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	121	137	0	ENST00000288368.4:c.3949C>T	p.Leu1317Phe	p.L1317F	ENST00000288368	NM_024870.2	1317	Ctt/Ttt	32/40	1	2	FACETS	0.837	0.757	0.922	0.837	0.757	0.922	CLONAL	1	TRUE	1	0.394934400222068	2		137	732	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970955	70970955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	151	161	0	ENST00000276594.2:c.1306C>T	p.Leu436Phe	p.L436F	ENST00000276594	NM_024504.3	436	Ctc/Ttc	6/8	1	2	FACETS	0.85	0.777	0.926	0.85	0.777	0.926	CLONAL	1	TRUE	1	0.394934400222068	2		161	900	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486248	8486248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768330226	NA	P-0043857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	86	90	0	ENST00000356435.5:c.2569C>T	p.Arg857Cys	p.R857C	ENST00000356435		857	Cgt/Tgt	17/35	0.394934400222068	1	FACETS	0.772	0.686	0.863	0.772	0.686	0.863	SUBCLONAL	1	TRUE	0	0.394934400222068	1		90	453	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8501045	8501045	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	72	76	0	ENST00000356435.5:c.1837C>T	p.Pro613Ser	p.P613S	ENST00000356435		613	Cct/Tct	13/35	0.394934400222068	1	FACETS	0.884	0.778	0.996	0.884	0.778	0.996	CLONAL	1	TRUE	0	0.394934400222068	1		76	331	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797282	135797282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	90	67	0	ENST00000298552.3:c.587C>T	p.Pro196Leu	p.P196L	ENST00000298552	NM_001162426.1	196	cCt/cTt	7/23	0.394934400222068	1	FACETS	0.912	0.815	1	0.912	0.815	1	CLONAL	1	TRUE	0	0.394934400222068	1		67	401	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	357	617	1	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.333442778722804	2	FACETS	0.904	0.856	0.952	0.904	0.856	0.952	CLONAL	2	TRUE	0	0.333442778722804	2		618	1185	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579362	7579362	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057523496	NA	P-0043870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	63	804	0	ENST00000269305.4:c.325T>G	p.Phe109Val	p.F109V	ENST00000269305	NM_001126112.2	109	Ttc/Gtc	4/11	0.333442778722804	2	FACETS	0.417	0.359	0.479	0.208	0.179	0.24	SUBCLONAL	1	TRUE	0	0.333442778722804	2		804	907	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978321	2978321	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs138920531	NA	P-0043870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	60	655	0	ENST00000396946.4:c.1009C>T	p.Arg337Ter	p.R337*	ENST00000396946	NM_032415.4	337	Cga/Tga	7/25	0.238819638834251	4	FACETS	0.576	0.495	0.665	0.288	0.247	0.333	SUBCLONAL	1	TRUE	2	0.333442778722804	4		655	833	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0043873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	92	660	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.196978294212912	2		660	851	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912580	NA	P-0043873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	79	302	0	ENST00000342988.3:c.1157G>A	p.Gly386Asp	p.G386D	ENST00000342988	NM_005359.5	386	gGt/gAt	10/12	1	2	FACETS	0.785	0.692	0.884	1	0.978	1	SUBCLONAL	2	TRUE	1	0.196978294212912	2		302	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576865	7576865	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	rs879254077	NA	P-0043873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	113	600	0	ENST00000269305.4:c.981T>G	p.Tyr327Ter	p.Y327*	ENST00000269305	NM_001126112.2	327	taT/taG	9/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.196978294212912	2		600	789	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098495	47098495	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759979231	NA	P-0043873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	84	430	0	ENST00000409792.3:c.6779C>T	p.Pro2260Leu	p.P2260L	ENST00000409792	NM_014159.6	2260	cCg/cTg	15/21	1	2	FACETS	0.831	0.736	0.932	1	0.981	1	CLONAL	2	TRUE	1	0.196978294212912	2		430	513	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044299	128044299	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	67	532	0	ENST00000285398.2:c.1322A>T	p.Asp441Val	p.D441V	ENST00000285398	NM_000122.1	441	gAt/gTt	8/15	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.196978294212912	2		532	622	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	102	348	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.986	0.9	1	0.986	0.9	1	CLONAL	1	TRUE	1	0.884155819134876	2		349	234	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131161	55131161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	6301	535	1	ENST00000257290.5:c.704G>A	p.Cys235Tyr	p.C235Y	ENST00000257290	NM_006206.4	235	tGt/tAt	5/23	0.884155819134876	38	FACETS	0.992	0.986	0.998			1	CLONAL	34	TRUE	NA	0.884155819134876	38		536	7148	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692775	89692775	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554898053	NA	P-0043906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	91	368	0	ENST00000371953.3:c.259C>T	p.Gln87Ter	p.Q87*	ENST00000371953	NM_000314.4	87	Caa/Taa	5/9	0.884155819134876	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.884155819134876	1		368	114	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439605	51439605	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	153	367	0	ENST00000262662.1:c.170T>G	p.Leu57Arg	p.L57R	ENST00000262662		57	cTa/cGa	4/4	0.710734010293788	3	FACETS	0.904	0.867	0.938	1	0.993	1	CLONAL	3	TRUE	1	0.884155819134876	3		367	184	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0043933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	197	652	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.718613242519425	1	FACETS	0.925	0.873	0.976	0.925	0.873	0.976	CLONAL	1	TRUE	0	0.759219972261334	1		652	348	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625090	69625090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554980287	NA	P-0043933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	172	481	0	ENST00000334134.2:c.703G>A	p.Glu235Lys	p.E235K	ENST00000334134	NM_005247.2	235	Gag/Aag	3/3	0.191856911220433	5	FACETS	1	0.98	1	0.758	0.706	0.812	INDETERMINATE	2	TRUE	2	0.759219972261334	5		481	426	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141568614	141568614	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs755874332	NA	P-0043933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1240	172	578	0	ENST00000220592.5:c.848A>G	p.Asn283Ser	p.N283S	ENST00000220592	NM_012154.3	283	aAt/aGt	7/19	0.683603174931874	6	FACETS	0.808	0.741	0.878	0.269	0.247	0.293	CLONAL	1	TRUE	3	0.759219972261334	6		578	1412	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249802	133249802	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	196	454	0	ENST00000320574.5:c.1421T>G	p.Val474Gly	p.V474G	ENST00000320574	NM_006231.2	474	gTc/gGc	14/49	0.641334903175265	3	FACETS	0.808	0.757	0.859	0.808	0.757	0.859	CLONAL	2	TRUE	1	0.759219972261334	3		454	441	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28886237	28886237	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0043933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	93	337	0	ENST00000282397.4:c.3387-2A>G		p.X1129_splice	ENST00000282397	NM_002019.4	1129			0.750022804556091	2	FACETS	0.935	0.844	1	0.468	0.422	0.514	CLONAL	1	TRUE	0	0.759219972261334	2		337	262	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867279	68867279	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	120	430	0	ENST00000261769.5:c.2526del	p.Ala843LeufsTer3	p.A843Lfs*3	ENST00000261769	NM_004360.3	842	gcT/gc	16/16	0.740878847236315	1	FACETS	0.766	0.706	0.827	0.766	0.706	0.827	SUBCLONAL	1	TRUE	0	0.759219972261334	1		430	256	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700251	117700251	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	148	347	0	ENST00000368508.3:c.2568C>G	p.His856Gln	p.H856Q	ENST00000368508	NM_002944.2	856	caC/caG	17/43	0.64271380973497	4	FACETS	0.832	0.768	0.898			1	CLONAL	2	TRUE	NA	0.759219972261334	4		347	412	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98011441	98011441	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	246	413	0	ENST00000289081.3:c.133C>A	p.Leu45Ile	p.L45I	ENST00000289081	NM_000136.2	45	Cta/Ata	2/15	0.639806498626379	4	FACETS	0.966	0.911	1	0.966	0.911	1	CLONAL	2	TRUE	2	0.759219972261334	4		413	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	202	666	2	ENST00000269305.4:c.833del	p.Pro278LeufsTer67	p.P278Lfs*67	ENST00000269305	NM_001126112.2	278	cCt/ct	8/11	0.311754823015638	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.311754823015638	1		668	839	SUCCESS
APC	324	MSKCC	GRCh37	5	112175240	112175240	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	53	238	0	ENST00000257430.4:c.3949G>T	p.Glu1317Ter	p.E1317*	ENST00000257430	NM_000038.5	1317	Gaa/Taa	16/16	0.20587084725293	2	FACETS	1	0.913	1	0.545	0.467	0.629	CLONAL	1	TRUE	0	0.311754823015638	2		238	312	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661945	29661945	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854552	NA	P-0043936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	114	372	0	ENST00000356175.3:c.5839C>T	p.Arg1947Ter	p.R1947*	ENST00000356175	NM_000267.3	1947	Cga/Tga	39/57	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.311754823015638	2		372	524	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481403	140481403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913357	NA	P-0043936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	127	325	0	ENST00000288602.6:c.1405G>A	p.Gly469Arg	p.G469R	ENST00000288602	NM_004333.4	469	Gga/Aga	11/18	0.266172271050771	3	FACETS	0.965	0.879	1	0.965	0.879	1	CLONAL	2	TRUE	1	0.311754823015638	3		325	488	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738156	133738156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756003964	NA	P-0043936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	124	405	0	ENST00000318560.5:c.556G>A	p.Val186Ile	p.V186I	ENST00000318560	NM_005157.4	186	Gtc/Atc	4/11	0.311754823015638	2	FACETS	1	0.982	1	0.676	0.614	0.742	CLONAL	1	TRUE	0	0.311754823015638	2		405	588	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851748	134851748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	65	572	0	ENST00000398015.3:c.1154G>A	p.Gly385Asp	p.G385D	ENST00000398015	NM_004441.4	385	gGc/gAc	5/16	1	2	FACETS	0.547	0.474	0.627	0.547	0.474	0.627	SUBCLONAL	1	TRUE	1	0.311754823015638	2		572	762	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591062	67591070	+	inframe_deletion	In_Frame_Del	DEL	AGGCAGCTG	AGGCAGCTG	-	novel	NA	P-0043936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	64	217	0	ENST00000274335.5:c.1657_1665del	p.Ala553_Glu555del	p.A553_E555del	ENST00000274335		552	cAGGCAGCTGag/cag	12/15	0.20587084725293	2	FACETS	1	0.924	1	0.545	0.474	0.621	CLONAL	1	TRUE	0	0.311754823015638	2		217	377	SUCCESS
APC	324	MSKCC	GRCh37	5	112175512	112175512	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	24	312	0	ENST00000257430.4:c.4221del	p.Ser1407ArgfsTer8	p.S1407Rfs*8	ENST00000257430	NM_000038.5	1407	agT/ag	16/16	0.20587084725293	2	FACETS	0.341	0.267	0.428	0.171	0.133	0.214	SUBCLONAL	1	TRUE	0	0.311754823015638	2		312	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691003	NA	P-0043953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	301	457	0	ENST00000269305.4:c.96+1G>T		p.X32_splice	ENST00000269305	NM_001126112.2	32			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		457	385	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111495	8111496	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGGA	novel	NA	P-0044040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	180	689	0	ENST00000346208.3:c.982_985dup	p.Arg329MetfsTer24	p.R329Mfs*24	ENST00000346208		327	-/TGGA	5/6	0.32223883357177	1	FACETS	0.613	0.566	0.663	0.613	0.566	0.663	SUBCLONAL	1	TRUE	0	0.496763271249136	1		689	888	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137474	202137474	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	139	573	0	ENST00000358485.4:c.702del	p.Asn235ThrfsTer30	p.N235Tfs*30	ENST00000358485	NM_001080125.1	234	atC/at	4/9	1	2	FACETS	0.768	0.7	0.839	0.768	0.7	0.839	SUBCLONAL	1	TRUE	1	0.496763271249136	2		573	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0044041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	418	1102	1	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	NA	2	FACETS	0.856	0.819	0.893			1	INDETERMINATE	2	TRUE	NA	0.531809819729239	2		1103	918	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519704	176519704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143108014	NA	P-0044041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	430	915	3	ENST00000292408.4:c.976G>A	p.Glu326Lys	p.E326K	ENST00000292408	NM_213647.1	326	Gag/Aag	8/18	0.531809819729239	3	FACETS	0.862	0.828	0.895	0.862	0.828	0.895	CLONAL	3	TRUE	0	0.531809819729239	3		918	792	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562837	95562837	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	134	400	0	ENST00000393063.1:c.4420A>G	p.Thr1474Ala	p.T1474A	ENST00000393063	NM_030621.3	1474	Acc/Gcc	24/28	0.531809819729239	3	FACETS	0.958	0.883	1	0.639	0.588	0.69	CLONAL	2	TRUE	0	0.531809819729239	3		400	333	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514229	69514229	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	138	835	0	ENST00000294312.3:c.452G>C	p.Arg151Pro	p.R151P	ENST00000294312	NM_005117.2	151	cGg/cCg	3/3	0.531809819729239	6	FACETS	0.924	0.839	1	0.154	0.139	0.169	CLONAL	1	TRUE	0	0.531809819729239	6		835	1159	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348892	118348912	+	inframe_deletion	In_Frame_Del	DEL	GCAATATAAAGAAGCAGTGCT	GCAATATAAAGAAGCAGTGCT	-	novel	NA	P-0044041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	37	218	0	ENST00000534358.1:c.3549_3569del	p.Asn1183_Cys1189del	p.N1183_C1189del	ENST00000534358	NM_005933.3	1182	cGCAATATAAAGAAGCAGTGCTgc/cgc	5/36	0.434192457052743	3	FACETS	0.79	0.656	0.936	0.263	0.218	0.312	CLONAL	1	TRUE	0	0.531809819729239	3		218	223	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21626574	21626574	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	34	417	1	ENST00000421138.2:c.1358G>C	p.Cys453Ser	p.C453S	ENST00000421138		453	tGt/tCt	13/16	0.349746484515059	6	FACETS	0.859	0.704	1	0.286	0.234	0.345	CLONAL	1	TRUE	3	0.531809819729239	6		418	307	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858909	57858913	+	frameshift_variant	Frame_Shift_Del	DEL	CCCAG	CCCAG	-	novel	NA	P-0044041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	128	895	0	ENST00000228682.2:c.410_414del	p.Ala137AspfsTer20	p.A137Dfs*20	ENST00000228682	NM_005269.2	135	ttCCCAGcc/ttcc	5/12	0.531809819729239	3	FACETS	0.754	0.684	0.829	0.377	0.342	0.415	SUBCLONAL	1	TRUE	1	0.531809819729239	3		895	808	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107939	30107939	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	85	687	1	ENST00000331968.5:c.868C>A	p.Leu290Ile	p.L290I	ENST00000331968	NM_002742.2	290	Ctt/Att	5/18	0.531809819729239	7	FACETS	0.868	0.766	0.977			1	CLONAL	1	TRUE	NA	0.531809819729239	7		688	858	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220661	2220661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202208831	NA	P-0044041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	105	869	1	ENST00000326181.6:c.278G>A	p.Arg93His	p.R93H	ENST00000326181	NM_032271.2	93	cGc/cAc	5/21	0.289843766093296	5	FACETS	0.779	0.697	0.867	0.26	0.232	0.289	INDETERMINATE	1	TRUE	2	0.531809819729239	5		870	911	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557896	29557896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555614639	NA	P-0044041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	13	178	0	ENST00000356175.3:c.3150G>A	p.Met1050Ile	p.M1050I	ENST00000356175	NM_000267.3	1050	atG/atA	24/57	0.531809819729239	6	FACETS	0.855	0.615	1			1	CLONAL	1	TRUE	NA	0.531809819729239	6		178	118	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277948	18277948	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	138	598	0	ENST00000222254.8:c.1568T>A	p.Leu523Gln	p.L523Q	ENST00000222254	NM_005027.3	523	cTg/cAg	13/16	0.531809819729239	4	FACETS	0.941	0.856	1	0.314	0.285	0.344	CLONAL	1	TRUE	1	0.531809819729239	4		598	845	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912056	50912056	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	197	1108	0	ENST00000440232.2:c.1790C>G	p.Pro597Arg	p.P597R	ENST00000440232	NM_002691.3	597	cCc/cGc	15/27	0.379707360039803	4	FACETS	0.942	0.871	1			1	CLONAL	1	TRUE	NA	0.531809819729239	4		1108	1205	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873042	134873042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	129	682	0	ENST00000398015.3:c.1346G>A	p.Ser449Asn	p.S449N	ENST00000398015	NM_004441.4	449	aGc/aAc	6/16	NA	2	FACETS	0.76	0.691	0.833			1	INDETERMINATE	1	TRUE	NA	0.531809819729239	2		682	638	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911589	134911589	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	84	596	0	ENST00000398015.3:c.2054G>C	p.Gly685Ala	p.G685A	ENST00000398015	NM_004441.4	685	gGt/gCt	11/16	NA	2	FACETS	0.674	0.597	0.755			1	INDETERMINATE	1	TRUE	NA	0.531809819729239	2		596	469	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401640	401640	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	98	692	0	ENST00000380956.4:c.962C>G	p.Pro321Arg	p.P321R	ENST00000380956	NM_001195286.1	321	cCc/cGc	7/9	0.438563079590242	4	FACETS	1	0.971	1	0.62	0.556	0.688	CLONAL	1	TRUE	2	0.531809819729239	4		692	455	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163807	32163807	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs751250725	NA	P-0044041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	147	762	0	ENST00000375023.3:c.5419G>C	p.Ala1807Pro	p.A1807P	ENST00000375023	NM_004557.3	1807	Gct/Cct	30/30	0.531809819729239	3	FACETS	0.991	0.907	1	0.496	0.453	0.54	CLONAL	1	TRUE	1	0.531809819729239	3		762	706	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6029454	6029454	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	179	471	1	ENST00000265849.7:c.1121A>T	p.Gln374Leu	p.Q374L	ENST00000265849	NM_000535.5	374	cAg/cTg	10/15	NA	2	FACETS	0.883	0.827	0.941			1	INDETERMINATE	2	TRUE	NA	0.531809819729239	2		472	381	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499694	8499694	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	36	606	2	ENST00000356435.5:c.2275C>A	p.Pro759Thr	p.P759T	ENST00000356435		759	Ccc/Acc	14/35	0.531809819729239	1	FACETS	0.339	0.28	0.405	0.339	0.28	0.405	SUBCLONAL	1	TRUE	0	0.531809819729239	1		608	293	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748124	72748142	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCAGCCACTGGTTCGAG	CGCCAGCCACTGGTTCGAG	AC	novel	NA	P-0044041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	68	582	2	ENST00000357731.5:c.36_54delinsGT	p.Cys12TrpfsTer42	p.C12Wfs*42	ENST00000357731	NM_173808.2	12	tgCTCGAACCAGTGGCTGGCG/tgGT	1/7	0.531809819729239	3	FACETS	0.479	0.416	0.547	0.239	0.208	0.274	SUBCLONAL	1	TRUE	1	0.531809819729239	3		584	676	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717650	89717650	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs1057520900	NA	P-0044061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	259	395	0	ENST00000371953.3:c.675T>G	p.Tyr225Ter	p.Y225*	ENST00000371953	NM_000314.4	225	taT/taG	7/9	0.688158042065399	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.688158042065399	1		395	481	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979219	93979219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1009626356	NA	P-0044061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	369	287	0	ENST00000369303.4:c.1609G>A	p.Glu537Lys	p.E537K	ENST00000369303	NM_004440.3	537	Gaa/Aaa	7/17	1	2	FACETS	0.802	0.768	0.835	1	0.996	1	CLONAL	2	TRUE	1	0.688158042065399	2		287	669	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627950	187627950	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1285798739	NA	P-0044061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	309	564	0	ENST00000441802.2:c.3032C>G	p.Ser1011Cys	p.S1011C	ENST00000441802	NM_005245.3	1011	tCt/tGt	2/27	0.688158042065399	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.688158042065399	1		564	571	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012355	176012355	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0044061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	231	374	0	ENST00000367669.3:c.1579A>T	p.Lys527Ter	p.K527*	ENST00000367669	NM_022457.5	527	Aaa/Taa	14/20	0.688158042065399	2	FACETS	0.995	0.932	1	0.497	0.466	0.529	CLONAL	1	TRUE	0	0.688158042065399	2		374	675	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944568	71944568	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0044061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	275	506	0	ENST00000298229.2:c.2122+2T>G		p.X708_splice	ENST00000298229	NM_001567.3	708			0.688158042065399	1	FACETS	0.948	0.9	0.996	0.948	0.9	0.996	CLONAL	1	TRUE	0	0.688158042065399	1		506	553	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622425	28622425	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	162	413	0	ENST00000241453.7:c.1192G>C	p.Asp398His	p.D398H	ENST00000241453	NM_004119.2	398	Gat/Cat	9/24	0.262944851626596	1	FACETS	0.55	0.507	0.594	0.55	0.507	0.594	INDETERMINATE	1	TRUE	0	0.688158042065399	1		413	562	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912895	32912895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	117	228	0	ENST00000380152.3:c.4403C>T	p.Ser1468Phe	p.S1468F	ENST00000380152		1468	tCt/tTt	11/27	0.262944851626596	1	FACETS	0.453	0.411	0.498	0.453	0.411	0.498	INDETERMINATE	1	TRUE	0	0.688158042065399	1		228	492	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044491	12044491	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	141	295	0	ENST00000353533.5:c.1114G>T	p.Glu372Ter	p.E372*	ENST00000353533	NM_003010.3	372	Gaa/Taa	11/11	0.688158042065399	1	FACETS	0.94	0.873	1	0.94	0.873	1	CLONAL	1	TRUE	0	0.688158042065399	1		295	286	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131945064	131945064	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	152	107	0	ENST00000265335.6:c.3012G>A	p.Met1004Ile	p.M1004I	ENST00000265335		1004	atG/atA	19/25	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.688158042065399	2		107	430	SUCCESS
AR	367	MSKCC	GRCh37	X	66766134	66766134	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	229	527	0	ENST00000374690.3:c.1146T>A	p.His382Gln	p.H382Q	ENST00000374690	NM_000044.3	382	caT/caA	1/8	1	2	FACETS	0.88	0.823	0.939	0.88	0.823	0.939	CLONAL	1	TRUE	1	0.688158042065399	2		527	756	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578495	7578507	+	stop_gained	Nonsense_Mutation	DEL	CAGCTGCACAGGG	CAGCTGCACAGGG	T	novel	NA	P-0044061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	378	684	0	ENST00000269305.4:c.423_435delinsA	p.Cys141_Leu145delinsTer	p.C141_L145delins*	ENST00000269305	NM_001126112.2	141	tgCCCTGTGCAGCTG/tgA	5/11	0.688158042065399	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.688158042065399	1		684	709	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0044063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	289	481	3	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.646630705985671	2		484	816	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579419	7579420	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs587783062	NA	P-0044063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	224	597	0	ENST00000269305.4:c.267dup	p.Ser90LeufsTer59	p.S90Lfs*59	ENST00000269305	NM_001126112.2	89	-/C	4/11	NA	2	FACETS	0.97	0.907	1			1	INDETERMINATE	1	TRUE	NA	0.646630705985671	2		597	714	SUCCESS
APC	324	MSKCC	GRCh37	5	112175246	112175246	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1057517558	NA	P-0044063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	144	207	0	ENST00000257430.4:c.3956del	p.Pro1319LeufsTer2	p.P1319Lfs*2	ENST00000257430	NM_000038.5	1319	Cct/ct	16/16	0.646630705985671	2	FACETS	0.898	0.84	0.955	0.898	0.84	0.955	CLONAL	2	TRUE	0	0.646630705985671	2		207	248	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548881	29548881	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	71	540	0	ENST00000356175.3:c.1655T>C	p.Leu552Pro	p.L552P	ENST00000356175	NM_000267.3	552	cTt/cCt	15/57	0.146379614476937	2	FACETS	1	0.953	1	0.6	0.524	0.683	CLONAL	1	TRUE	0	0.180903730954723	2		540	654	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0044144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	84	377	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.486663297948542	1	FACETS	0.768	0.684	0.856	0.768	0.684	0.856	SUBCLONAL	1	TRUE	0	0.486663297948542	1		377	340	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138773	64138773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568464055	NA	P-0044144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	225	825	1	ENST00000334205.4:c.2140C>T	p.Arg714Trp	p.R714W	ENST00000334205	NM_003942.2	714	Cgg/Tgg	17/17	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.486663297948542	2		826	881	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120346	70120347	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0044144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	576	1272	0	ENST00000245479.2:c.1350dup	p.Tyr451LeufsTer127	p.Y451Lfs*127	ENST00000245479	NM_000346.3	450	tcc/tCcc	3/3	0.486663297948542	2	FACETS	0.985	0.95	1	0.985	0.95	1	CLONAL	2	TRUE	0	0.486663297948542	2		1272	1201	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263950	104263950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	11	160	0	ENST00000369902.3:c.41C>T	p.Ala14Val	p.A14V	ENST00000369902	NM_016169.3	14	gCg/gTg	1/12	1	2	FACETS	0.716	0.495	0.989	0.716	0.495	0.989	CLONAL	1	FALSE	1	0.174614487747843	2		160	176	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	36	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.758	0.622	0.91	0.758	0.622	0.91	CLONAL	1	TRUE	1	0.17	2		539	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0044210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	89	575	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.17	2		575	1041	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202806	16202806	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1235481729	NA	P-0044210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	43	483	0	ENST00000375759.3:c.514G>C	p.Asp172His	p.D172H	ENST00000375759	NM_015001.2	172	Gat/Cat	3/15	1	2	FACETS	0.594	0.496	0.705	0.594	0.496	0.705	SUBCLONAL	1	TRUE	1	0.17	2		483	851	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091332	193091332	+	start_lost	Translation_Start_Site	SNP	T	T	C	rs1553277483	NA	P-0044210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	42	242	0	ENST00000367435.3:c.2T>C	p.Met1?	p.M1?	ENST00000367435	NM_024529.4	1	aTg/aCg	1/17	1	2	FACETS	0.91	0.759	1	0.91	0.759	1	CLONAL	1	TRUE	1	0.17	2		242	543	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383700	42383700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	71	617	0	ENST00000221972.3:c.475C>T	p.Pro159Ser	p.P159S	ENST00000221972	NM_021601.3	159	Cct/Tct	3/5	1	2	FACETS	0.737	0.641	0.842	0.737	0.641	0.842	SUBCLONAL	1	TRUE	1	0.17	2		617	1133	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	92	348	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.36	2		349	385	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561124	9561124	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	73	364	0	ENST00000353224.5:c.658C>T	p.Gln220Ter	p.Q220*	ENST00000353224	NM_177990.2	220	Cag/Tag	4/10	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.36	2		364	373	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0044212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	81	319	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.36	2		319	372	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017824	31017824	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576523117	NA	P-0044212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	141	800	0	ENST00000375687.4:c.686C>T	p.Pro229Leu	p.P229L	ENST00000375687	NM_015338.5	229	cCg/cTg	8/13	1	2	FACETS	0.846	0.77	0.926	0.846	0.77	0.926	CLONAL	1	TRUE	1	0.36	2		800	926	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946136	55946136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771593658	NA	P-0044212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	43	294	0	ENST00000263923.4:c.4043G>A	p.Gly1348Glu	p.G1348E	ENST00000263923	NM_002253.2	1348	gGg/gAg	30/30	1	2	FACETS	0.573	0.48	0.676	0.573	0.48	0.676	SUBCLONAL	1	TRUE	1	0.36	2		294	417	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486104	8486104	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	101	460	0	ENST00000356435.5:c.2713G>T	p.Glu905Ter	p.E905*	ENST00000356435		905	Gag/Tag	17/35	0.3	1	FACETS	0.776	0.695	0.862	0.776	0.695	0.862	SUBCLONAL	1	TRUE	0	0.36	1		460	593	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190726	11190727	+	missense_variant	Missense_Mutation	DNP	TG	TG	CT	novel	NA	P-0044212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	83	751	2	ENST00000361445.4:c.5472_5473delinsAG	p.Asn1824_Ile1825delinsLysVal	p.N1824_I1825delinsKV	ENST00000361445	NM_004958.3	1824	aaCAtc/aaAGtc	39/58	0.3	1	FACETS	0.462	0.407	0.521	0.462	0.407	0.521	SUBCLONAL	1	TRUE	0	0.36	1		753	819	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100393	8100393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564398686	NA	P-0044212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	78	823	0	ENST00000346208.3:c.367C>T	p.His123Tyr	p.H123Y	ENST00000346208		123	Cac/Tac	3/6	1	2	FACETS	0.509	0.446	0.576	0.509	0.446	0.576	SUBCLONAL	1	TRUE	1	0.36	2		823	852	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571982	64571982	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	93	901	0	ENST00000312049.6:c.1657T>C	p.Phe553Leu	p.F553L	ENST00000312049	NM_130799.2	553	Ttc/Ctc	10/10	1	2	FACETS	0.491	0.435	0.55	0.491	0.435	0.55	SUBCLONAL	1	TRUE	1	0.36	2		901	1053	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699278	18699278	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381086997	NA	P-0044212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	19	259	0	ENST00000266497.5:c.3379G>A	p.Glu1127Lys	p.E1127K	ENST00000266497		1127	Gag/Aag	24/31	1	2	FACETS	0.335	0.254	0.431	0.335	0.254	0.431	SUBCLONAL	1	TRUE	1	0.36	2		259	315	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624031	21624031	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs3207640	NA	P-0044212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	31	213	0	ENST00000421138.2:c.1669G>A	p.Glu557Lys	p.E557K	ENST00000421138		557	Gaa/Aaa	15/16	1	2	FACETS	0.783	0.637	0.945	0.783	0.637	0.945	CLONAL	1	TRUE	1	0.36	2		213	220	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43769934	43769934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	79	327	0	ENST00000382044.4:c.812C>T	p.Pro271Leu	p.P271L	ENST00000382044	NM_001141980.1	271	cCc/cTc	8/28	1	2	FACETS	0.946	0.835	1	0.946	0.835	1	CLONAL	1	TRUE	1	0.36	2		327	464	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556430	29556430	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	104	457	0	ENST00000356175.3:c.2797del	p.Leu933TyrfsTer5	p.L933Yfs*5	ENST00000356175	NM_000267.3	933	Cta/ta	21/57	0.3	1	FACETS	0.791	0.71	0.877	0.791	0.71	0.877	SUBCLONAL	1	TRUE	0	0.36	1		457	599	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5239044	5239044	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	156	818	0	ENST00000357368.4:c.1735T>C	p.Tyr579His	p.Y579H	ENST00000357368	NM_002850.3	579	Tac/Cac	13/38	0.3	1	FACETS	0.778	0.712	0.846	0.778	0.712	0.846	SUBCLONAL	1	TRUE	0	0.36	1		818	914	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215939	36215939	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	77	825	0	ENST00000222270.7:c.3479G>A	p.Gly1160Glu	p.G1160E	ENST00000222270	NM_014727.1	1160	gGa/gAa	10/37	0.3	1	FACETS	0.342	0.299	0.388	0.342	0.299	0.388	SUBCLONAL	1	TRUE	0	0.36	1		825	1026	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626963	158626963	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	60	411	0	ENST00000263640.3:c.707T>C	p.Ile236Thr	p.I236T	ENST00000263640	NM_001105.4	236	aTc/aCc	7/11	1	2	FACETS	0.601	0.518	0.691	0.601	0.518	0.691	SUBCLONAL	1	TRUE	1	0.36	2		411	555	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794135	242794135	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	72	749	0	ENST00000334409.5:c.593G>A	p.Gly198Glu	p.G198E	ENST00000334409	NM_005018.2	198	gGg/gAg	4/5	1	2	FACETS	0.473	0.413	0.539	0.473	0.413	0.539	SUBCLONAL	1	TRUE	1	0.36	2		749	845	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939935	49939935	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	182	863	0	ENST00000296474.3:c.1108C>T	p.Pro370Ser	p.P370S	ENST00000296474	NM_002447.2	370	Ccc/Tcc	1/20	1	2	FACETS	0.934	0.86	1	0.934	0.86	1	CLONAL	1	TRUE	1	0.36	2		863	1083	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488474	20488474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	59	355	0	ENST00000346618.3:c.1130C>T	p.Ser377Phe	p.S377F	ENST00000346618	NM_001949.4	377	tCc/tTc	6/7	1	2	FACETS	0.702	0.605	0.807	0.702	0.605	0.807	SUBCLONAL	1	TRUE	1	0.36	2		355	467	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222624	157222624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	103	512	0	ENST00000346085.5:c.1891C>T	p.Pro631Ser	p.P631S	ENST00000346085	NM_020732.3	631	Ccg/Tcg	4/20	1	2	FACETS	0.789	0.707	0.877	0.789	0.707	0.877	SUBCLONAL	1	TRUE	1	0.36	2		512	725	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850271	128850271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1018551272	NA	P-0044212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	136	784	2	ENST00000249373.3:c.1534C>T	p.Arg512Cys	p.R512C	ENST00000249373	NM_005631.4	512	Cgc/Tgc	9/12	1	2	FACETS	0.785	0.713	0.86	0.785	0.713	0.86	SUBCLONAL	1	TRUE	1	0.36	2		786	963	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	44	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.178051778021421	2		539	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579369	7579369	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555526581	NA	P-0044222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	86	893	0	ENST00000269305.4:c.318C>G	p.Ser106Arg	p.S106R	ENST00000269305	NM_001126112.2	106	agC/agG	4/11	0.178051778021421	1	FACETS	0.842	0.743	0.949	0.842	0.743	0.949	CLONAL	1	TRUE	0	0.178051778021421	1		893	1045	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575089	48575089	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	36	420	0	ENST00000342988.3:c.283T>C	p.Tyr95His	p.Y95H	ENST00000342988	NM_005359.5	95	Tat/Cat	3/12	1	2	FACETS	0.919	0.756	1	0.919	0.756	1	CLONAL	1	TRUE	1	0.178051778021421	2		420	440	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105809	27105810	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	51	495	0	ENST00000324856.7:c.5421dup	p.Lys1808Ter	p.K1808*	ENST00000324856	NM_006015.4	1807	agt/agTt	20/20	1	2	FACETS	0.814	0.69	0.95	0.814	0.69	0.95	CLONAL	1	TRUE	1	0.178051778021421	2		495	704	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955417	48955417	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs748352319	NA	P-0044222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	46	275	0	ENST00000267163.4:c.1535del	p.Leu512CysfsTer7	p.L512Cfs*7	ENST00000267163	NM_000321.2	511	gaT/ga	17/27	0.178051778021421	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.178051778021421	1		275	379	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	143	348	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.936	0.859	1	0.936	0.859	1	CLONAL	1	TRUE	1	0.580651569143616	2		349	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579329	7579329	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912658	NA	P-0044223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	321	819	0	ENST00000269305.4:c.358A>G	p.Lys120Glu	p.K120E	ENST00000269305	NM_001126112.2	120	Aag/Gag	4/11	0.257627804175207	1	FACETS	0.784	0.741	0.827	0.784	0.741	0.827	INDETERMINATE	1	TRUE	0	0.580651569143616	1		819	1001	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398032	4398032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	259	579	0	ENST00000261254.3:c.596C>T	p.Pro199Leu	p.P199L	ENST00000261254	NM_001759.3	199	cCg/cTg	4/5	1	2	FACETS	0.972	0.912	1	0.972	0.912	1	CLONAL	1	TRUE	1	0.580651569143616	2		579	918	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94923059	94923059	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	163	532	0	ENST00000536441.1:c.409G>T	p.Gly137Cys	p.G137C	ENST00000536441	NM_144665.3	137	Ggt/Tgt	4/10	1	2	FACETS	0.985	0.909	1	0.985	0.909	1	CLONAL	1	TRUE	1	0.580651569143616	2		532	570	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999779	100999779	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	64	847	0	ENST00000325455.5:c.23G>A	p.Gly8Asp	p.G8D	ENST00000325455	NM_001202474.3	8	gGt/gAt	1/8	1	2	FACETS	0.201	0.173	0.232	0.201	0.173	0.232	SUBCLONAL	1	TRUE	1	0.580651569143616	2		847	1096	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884011	37884011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150680317	NA	P-0044228-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	28	1244	1	ENST00000269571.5:c.3482G>A	p.Arg1161Gln	p.R1161Q	ENST00000269571		1161	cGa/cAa	27/27	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		1245	380	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0044296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	237	544	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.418727629221143	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.469629690675881	4		544	670	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974695	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691187	NA	P-0044296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	207	341	0	ENST00000304494.5:c.132del	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	taC/ta	1/3	0.469789885508532	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.469629690675881	1		341	491	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039708	47039708	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	277	664	1	ENST00000377604.3:c.1160G>A	p.Arg387Lys	p.R387K	ENST00000377604	NM_001204468.1	387	aGg/aAg	11/24	0.469789885508532	2	FACETS	0.887	0.839	0.936	0.887	0.839	0.936	CLONAL	2	TRUE	0	0.469629690675881	2		665	665	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63531823	63531823	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	231	433	0	ENST00000307078.5:c.2158C>G	p.Gln720Glu	p.Q720E	ENST00000307078	NM_004655.3	720	Cag/Gag	9/11	0.418727629221143	4	FACETS	0.868	0.811	0.926	0.868	0.811	0.926	CLONAL	2	TRUE	2	0.469629690675881	4		433	833	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170015161	170015161	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	99	405	0	ENST00000295797.4:c.1567C>G	p.Arg523Gly	p.R523G	ENST00000295797	NM_002740.5	523	Cga/Gga	16/18	0.381954611583819	3	FACETS	0.888	0.795	0.987	0.444	0.397	0.494	CLONAL	1	TRUE	1	0.469629690675881	3		405	586	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0044319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	225	385	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	0.359908667571202	4	FACETS	0.942	0.88	1	0.942	0.88	1	CLONAL	2	TRUE	2	0.485577421453498	4		385	731	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941669	48941670	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0044319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	12	107	0	ENST00000267163.4:c.982_983del	p.Asn328Ter	p.N328*	ENST00000267163	NM_000321.2	327	AAa/a	10/27	0.485577421453498	1	FACETS	0.186	0.131	0.254	0.186	0.131	0.254	SUBCLONAL	1	TRUE	0	0.485577421453498	1		107	201	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039464	49039464	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	114	440	0	ENST00000267163.4:c.2449G>T	p.Glu817Ter	p.E817*	ENST00000267163	NM_000321.2	817	Gaa/Taa	23/27	0.485577421453498	1	FACETS	0.735	0.665	0.807	0.735	0.665	0.807	SUBCLONAL	1	TRUE	0	0.485577421453498	1		440	484	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117710	115117727	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAGCCTACCTGAGTACCA	TAGCCTACCTGAGTACCA	-	novel	NA	P-0044319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	52	341	0	ENST00000257566.3:c.708_717+8del		p.X236_splice	ENST00000257566	NM_016569.3	236		3/8	1	2	FACETS	0.498	0.425	0.578	0.498	0.425	0.578	SUBCLONAL	1	TRUE	1	0.485577421453498	2		341	430	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857376	68857396	+	inframe_deletion	In_Frame_Del	DEL	GATAACCAGAATAAAGACCAA	GATAACCAGAATAAAGACCAA	-	novel	NA	P-0044319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	289	524	0	ENST00000261769.5:c.2012_2032del	p.Asp671_Gln677del	p.D671_Q677del	ENST00000261769	NM_004360.3	671	GATAACCAGAATAAAGACCAA/-	13/16	0.485577421453498	2	FACETS	0.939	0.89	0.987	0.939	0.89	0.987	CLONAL	2	TRUE	0	0.485577421453498	2		524	634	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306778	41306778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	89	383	0	ENST00000373198.4:c.881C>T	p.Pro294Leu	p.P294L	ENST00000373198	NM_133170.3	294	cCc/cTc	7/32	0.485577421453498	3	FACETS	0.874	0.778	0.977	0.437	0.389	0.489	CLONAL	1	TRUE	1	0.485577421453498	3		383	521	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	294	348	1				ENST00000310581	NM_198253.2	-/1132			0.385645987762875	6	FACETS	1	0.986	1	0.824	0.783	0.865	INDETERMINATE	3	TRUE	2	0.719492986001158	6		349	605	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0044324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	26	515	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.144	0.113	0.179	0.144	0.113	0.179	SUBCLONAL	1	TRUE	1	0.719492986001158	2		515	503	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941858	44941858	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0044324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	87	220	0	ENST00000377967.4:c.3182C>G	p.Ser1061Ter	p.S1061*	ENST00000377967	NM_021140.2	1061	tCa/tGa	21/29	0.143744529302833	2	FACETS	1	0.964	1			1	INDETERMINATE	2	TRUE	NA	0.719492986001158	2		220	115	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974898	15974898	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1219026707	NA	P-0044324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	121	451	1	ENST00000268712.3:c.3977G>A	p.Arg1326Gln	p.R1326Q	ENST00000268712	NM_006311.3	1326	cGa/cAa	30/46	0.719492986001158	3	FACETS	0.961	0.873	1	0.48	0.436	0.526	CLONAL	1	TRUE	1	0.719492986001158	3		452	476	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724427	112724427	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	323	622	0	ENST00000369452.4:c.311G>C	p.Arg104Pro	p.R104P	ENST00000369452	NM_007373.3	104	cGt/cCt	2/9	0.405023885494411	1	FACETS	1	0.996	1	1	0.996	1	INDETERMINATE	1	TRUE	0	0.719492986001158	1		622	427	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988251	36988251	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	335	563	0	ENST00000354822.5:c.402G>A	p.Met134Ile	p.M134I	ENST00000354822	NM_001079668.2	134	atG/atA	2/3	0.566610811259501	4	FACETS	0.89	0.844	0.936			1	CLONAL	2	TRUE	NA	0.719492986001158	4		563	900	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966344	25966352	+	inframe_deletion	In_Frame_Del	DEL	AGTCACTAA	AGTCACTAA	-	novel	NA	P-0044324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	296	719	0	ENST00000435504.4:c.2854_2862del	p.Leu952_Thr954del	p.L952_T954del	ENST00000435504		952	TTAGTGACT/-	13/13	0.719492986001158	4	FACETS	1	0.992	1	0.444	0.418	0.471	CLONAL	1	TRUE	1	0.719492986001158	4		719	1062	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268433	198268433	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	25	507	0	ENST00000335508.6:c.1595T>G	p.Phe532Cys	p.F532C	ENST00000335508	NM_012433.2	532	tTt/tGt	12/25	0.719492986001158	3	FACETS	0.21	0.165	0.262	0.07	0.055	0.088	SUBCLONAL	1	TRUE	0	0.719492986001158	3		507	450	SUCCESS
APC	324	MSKCC	GRCh37	5	112162840	112162840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554081666	NA	P-0044324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	129	453	0	ENST00000257430.4:c.1444G>A	p.Asp482Asn	p.D482N	ENST00000257430	NM_000038.5	482	Gac/Aac	12/16	0.175319988619172	5	FACETS	1	0.946	1	0.767	0.712	0.822	INDETERMINATE	3	TRUE	1	0.719492986001158	5		453	243	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0044336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	150	621	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.403427515337406	2	FACETS	0.968	0.896	1	0.968	0.896	1	CLONAL	2	TRUE	0	0.403427515337406	2		622	384	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0044336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	111	459	2	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	0.403427515337406	2	FACETS	0.777	0.706	0.851	0.777	0.706	0.851	SUBCLONAL	2	TRUE	0	0.403427515337406	2		461	354	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948208	71948209	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs749079348	NA	P-0044336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	26	657	4	ENST00000298229.2:c.2927dup	p.Pro977ThrfsTer7	p.P977Tfs*7	ENST00000298229	NM_001567.3	974	gcc/gCcc	26/28	0.403427515337406	2	FACETS	0.252	0.199	0.314	0.126	0.099	0.157	SUBCLONAL	1	TRUE	0	0.403427515337406	2		661	511	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867546	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs11466445	NA	P-0044336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	12	5	0	ENST00000374994.4:c.70_78del	p.Ala24_Ala26del	p.A24_A26del	ENST00000374994	NM_004612.2	17	ctGGCGGCGGCg/ctg	1/9	0.403427515337406	2	FACETS	1	0.726	1	0.504	0.363	0.668	CLONAL	1	TRUE	0	0.403427515337406	2		5	59	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637699	52637700	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	30	354	0	ENST00000394830.3:c.2616dup	p.Ile873TyrfsTer2	p.I873Yfs*2	ENST00000394830	NM_018313.4	872	-/T	18/30	0.403427515337406	2	FACETS	0.978	0.818	1	0.978	0.818	1	CLONAL	2	TRUE	0	0.403427515337406	2		354	76	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115111984	115111984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	142	543	1	ENST00000257566.3:c.1756G>A	p.Val586Ile	p.V586I	ENST00000257566	NM_016569.3	586	Gtc/Atc	7/8	0.403427515337406	2	FACETS	0.898	0.827	0.97	0.898	0.827	0.97	CLONAL	2	TRUE	0	0.403427515337406	2		544	392	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829039	128829040	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs570242755	NA	P-0044336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	19	26	0	ENST00000249373.3:c.67_69dup	p.Leu23dup	p.L23dup	ENST00000249373	NM_005631.4	23	ggg/ggGCTg	1/12	0.403427515337406	2	FACETS	1	0.912	1	0.703	0.55	0.871	CLONAL	1	TRUE	0	0.403427515337406	2		26	67	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86668007	86668007	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	40	205	0	ENST00000274376.6:c.1771C>T	p.Arg591Cys	p.R591C	ENST00000274376	NM_002890.2	591	Cgt/Tgt	13/25	0.403427515337406	2	FACETS	0.931	0.815	1	1	0.965	1	CLONAL	3	TRUE	0	0.403427515337406	2		205	71	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656567	3656567	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762475814	NA	P-0044336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	188	593	0	ENST00000294008.3:c.668G>A	p.Arg223His	p.R223H	ENST00000294008	NM_032444.2	223	cGt/cAt	3/15	0.403427515337406	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.403427515337406	2		593	436	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620578	52620578	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	74	412	0	ENST00000394830.3:c.3175A>G	p.Arg1059Gly	p.R1059G	ENST00000394830	NM_018313.4	1059	Agg/Ggg	21/30	0.403427515337406	2	FACETS	1	0.973	1	0.684	0.606	0.766	CLONAL	1	TRUE	0	0.403427515337406	2		412	268	SUCCESS
APC	324	MSKCC	GRCh37	5	112128220	112128220	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	12	303	0	ENST00000257430.4:c.723A>C	p.Glu241Asp	p.E241D	ENST00000257430	NM_000038.5	241	gaA/gaC	7/16	0.403427515337406	2	FACETS	0.826	0.591	1	0.413	0.295	0.552	CLONAL	1	TRUE	0	0.403427515337406	2		303	72	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0044346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	175	674	1	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.162388142231462	3	FACETS	1	0.935	1			1	CLONAL	3	TRUE	NA	0.162388142231462	3		675	766	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027248	49027248	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0044346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	67	325	0	ENST00000267163.4:c.1814+1G>A		p.X605_splice	ENST00000267163	NM_000321.2	605			0.162388142231462	3	FACETS	1	0.914	1	1	0.914	1	CLONAL	2	TRUE	1	0.162388142231462	3		325	420	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851573	134851573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1281577436	NA	P-0044346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	45	507	0	ENST00000398015.3:c.979C>T	p.Arg327Cys	p.R327C	ENST00000398015	NM_004441.4	327	Cgc/Tgc	5/16	0.162388142231462	2	FACETS	1	0.848	1	0.505	0.424	0.594	CLONAL	1	TRUE	0	0.162388142231462	2		507	549	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778167	27778167	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	44	756	0	ENST00000369163.2:c.316G>C	p.Glu106Gln	p.E106Q	ENST00000369163	NM_003536.2	106	Gag/Cag	1/1	1	2	FACETS	0.799	0.669	0.944	0.799	0.669	0.944	CLONAL	1	TRUE	1	0.162388142231462	2		756	678	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913503	NA	P-0044352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	74	612	0	ENST00000330062.3:c.515G>T	p.Arg172Met	p.R172M	ENST00000330062	NM_002168.2	172	aGg/aTg	4/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		612	665	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0044367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	216	600	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.440415822827027	1	FACETS	0.912	0.849	0.976	0.912	0.849	0.976	CLONAL	1	TRUE	0	0.440415822827027	1		601	839	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913355	NA	P-0044367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	113	325	0	ENST00000288602.6:c.1406G>T	p.Gly469Val	p.G469V	ENST00000288602	NM_004333.4	469	gGa/gTa	11/18	1	2	FACETS	0.921	0.832	1	0.921	0.832	1	CLONAL	1	TRUE	1	0.440415822827027	2		325	557	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120178	70120178	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057518216	NA	P-0044367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	249	337	0	ENST00000245479.2:c.1180C>T	p.Arg394Ter	p.R394*	ENST00000245479	NM_000346.3	394	Cga/Tga	3/3	0.440415822827027	2	FACETS	0.976	0.921	1	0.976	0.921	1	CLONAL	2	TRUE	0	0.440415822827027	2		337	579	SUCCESS
APC	324	MSKCC	GRCh37	5	112175215	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0044367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	116	201	0	ENST00000257430.4:c.3925_3926del	p.Glu1309LysfsTer5	p.E1309Kfs*5	ENST00000257430	NM_000038.5	1308	aaAGaa/aaaa	16/16	0.405936364545034	2	FACETS	0.855	0.782	0.93	0.855	0.782	0.93	CLONAL	2	TRUE	0	0.440415822827027	2		201	308	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910752	114910770	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTAGGTTCCCTCCCCATA	TCTAGGTTCCCTCCCCATA	-	novel	NA	P-0044367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	130	411	0	ENST00000543371.1:c.876-4_890del		p.X292_splice	ENST00000543371	NM_001198531.1	292		9/14	1	2	FACETS	0.771	0.7	0.846	0.771	0.7	0.846	SUBCLONAL	1	TRUE	1	0.440415822827027	2		411	766	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573628	48573628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	109	313	0	ENST00000342988.3:c.212G>A	p.Cys71Tyr	p.C71Y	ENST00000342988	NM_005359.5	71	tGt/tAt	2/12	0.440415822827027	1	FACETS	0.98	0.887	1	0.98	0.887	1	CLONAL	1	TRUE	0	0.440415822827027	1		313	394	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0044368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	461	366	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.373491332009331	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	4	TRUE	0	0.373491332009331	4		366	840	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	171	348	1				ENST00000310581	NM_198253.2	-/1132			0.373491332009331	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.373491332009331	3		349	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0044368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	228	629	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.354929672655819	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.373491332009331	1		629	792	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252994	36252995	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0044368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	133	372	0	ENST00000300305.3:c.367dup	p.Asp123GlyfsTer15	p.D123Gfs*15	ENST00000300305		123	gat/gGat	4/8	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.373491332009331	2		372	664	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059260	27059260	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	140	473	0	ENST00000324856.7:c.1897C>T	p.Gln633Ter	p.Q633*	ENST00000324856	NM_006015.4	633	Cag/Tag	4/20	1	2	FACETS	0.929	0.846	1	0.929	0.846	1	CLONAL	1	TRUE	1	0.373491332009331	2		473	807	SUCCESS
REL	5966	MSKCC	GRCh37	2	61128201	61128201	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	43	197	0	ENST00000295025.8:c.377G>C	p.Gly126Ala	p.G126A	ENST00000295025	NM_002908.2	126	gGa/gCa	4/11	1	2	FACETS	0.726	0.61	0.854	0.726	0.61	0.854	SUBCLONAL	1	TRUE	1	0.373491332009331	2		197	317	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6038788	6038788	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	155	593	0	ENST00000265849.7:c.656G>T	p.Gly219Val	p.G219V	ENST00000265849	NM_000535.5	219	gGa/gTa	6/15	1	2	FACETS	0.93	0.852	1	0.93	0.852	1	CLONAL	1	TRUE	1	0.373491332009331	2		593	892	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863331	56863331	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	115	432	0	ENST00000519728.1:c.475G>A	p.Glu159Lys	p.E159K	ENST00000519728	NM_002350.3	159	Gaa/Aaa	6/13	1	2	FACETS	0.976	0.881	1	0.976	0.881	1	CLONAL	1	TRUE	1	0.373491332009331	2		432	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	231	766	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.24221475682933	4	FACETS	0.96	0.895	1	0.96	0.895	1	CLONAL	2	FALSE	2	0.330561680111192	4		767	969	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	60	348	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.871	0.752	0.998	0.871	0.752	0.998	CLONAL	1	FALSE	1	0.330561680111192	2		349	417	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568563	41568563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555911574	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	169	525	0	ENST00000263253.7:c.4513G>A	p.Glu1505Lys	p.E1505K	ENST00000263253	NM_001429.3	1505	Gag/Aag	28/31	0.281850827146878	3	FACETS	0.905	0.835	0.978	0.604	0.557	0.652	CLONAL	2	FALSE	0	0.330561680111192	3		525	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	251	808	1	ENST00000269305.4:c.166G>T	p.Glu56Ter	p.E56*	ENST00000269305	NM_001126112.2	56	Gaa/Taa	4/11	0.24221475682933	4	FACETS	0.93	0.87	0.992	0.93	0.87	0.992	CLONAL	2	FALSE	2	0.330561680111192	4		809	1086	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163720	32163720	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	153	558	0	ENST00000375023.3:c.5506G>C	p.Glu1836Gln	p.E1836Q	ENST00000375023	NM_004557.3	1836	Gag/Cag	30/30	0.310151624899991	3	FACETS	0.86	0.79	0.933	0.86	0.79	0.933	CLONAL	2	FALSE	1	0.330561680111192	3		558	627	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30061031	30061031	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	216	416	0	ENST00000338641.4:c.863C>G	p.Ser288Ter	p.S288*	ENST00000338641	NM_000268.3	288	tCa/tGa	9/16	0.281850827146878	3	FACETS	1	0.988	1	0.829	0.776	0.884	CLONAL	2	FALSE	0	0.330561680111192	3		416	612	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914890	32914890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	53	321	0	ENST00000380152.3:c.6398C>T	p.Ser2133Leu	p.S2133L	ENST00000380152		2133	tCa/tTa	11/27	0.309453345513054	3	FACETS	0.842	0.719	0.975	0.421	0.359	0.488	CLONAL	1	FALSE	1	0.330561680111192	3		321	444	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651879	36651879	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	126	565	0	ENST00000244741.5:c.1A>G	p.Met1?	p.M1?	ENST00000244741	NM_000389.4	1	Atg/Gtg	2/3	0.310151624899991	3	FACETS	1	0.975	1	0.608	0.551	0.668	CLONAL	1	FALSE	1	0.330561680111192	3		565	731	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652225	36652226	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	204	618	0	ENST00000244741.5:c.349dup	p.Cys117LeufsTer12	p.C117Lfs*12	ENST00000244741	NM_000389.4	116	tct/tcTt	2/3	0.310151624899991	3	FACETS	0.817	0.759	0.878	0.817	0.759	0.878	CLONAL	2	FALSE	1	0.330561680111192	3		618	880	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394757	45394757	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	119	367	0	ENST00000262160.6:c.592C>G	p.His198Asp	p.H198D	ENST00000262160	NM_005901.5	198	Cac/Gac	5/11	0.217900383119288	4	FACETS	0.832	0.753	0.914	0.832	0.753	0.914	CLONAL	2	FALSE	2	0.330561680111192	4		367	576	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856067	111856067	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1001185161	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	118	531	1	ENST00000341259.2:c.118G>A	p.Glu40Lys	p.E40K	ENST00000341259	NM_005475.2	40	Gag/Aag	2/8	0.260594639044481	3	FACETS	1	0.957	1	0.554	0.5	0.611	CLONAL	1	FALSE	1	0.330561680111192	3		532	751	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790830	89790830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	133	746	0	ENST00000336032.3:c.217C>T	p.Arg73Cys	p.R73C	ENST00000336032	NM_006813.2	73	Cgc/Tgc	1/2	0.310151624899991	3	FACETS	0.964	0.874	1	0.482	0.437	0.529	CLONAL	1	FALSE	1	0.330561680111192	3		746	973	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839802	27839802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	85	548	0	ENST00000328488.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000328488	NM_003533.2	98	Gag/Aag	1/1	0.310151624899991	3	FACETS	0.775	0.685	0.872	0.388	0.342	0.436	SUBCLONAL	1	FALSE	1	0.330561680111192	3		548	773	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790788	89790788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1375885569	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	138	822	1	ENST00000336032.3:c.175C>T	p.His59Tyr	p.H59Y	ENST00000336032	NM_006813.2	59	Cat/Tat	1/2	0.310151624899991	3	FACETS	0.908	0.825	0.996	0.454	0.412	0.498	CLONAL	1	FALSE	1	0.330561680111192	3		823	1071	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437052	110437052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	43	115	0	ENST00000375856.3:c.1349C>T	p.Ser450Phe	p.S450F	ENST00000375856	NM_003749.2	450	tCc/tTc	1/2	0.310151624899991	3	FACETS	1	0.954	1	0.695	0.588	0.812	CLONAL	1	FALSE	1	0.330561680111192	3		115	218	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568626	41568626	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	151	432	0	ENST00000263253.7:c.4576G>C	p.Glu1526Gln	p.E1526Q	ENST00000263253	NM_001429.3	1526	Gag/Cag	28/31	0.281850827146878	3	FACETS	0.995	0.915	1	0.663	0.61	0.718	CLONAL	2	FALSE	0	0.330561680111192	3		432	535	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562134	21562134	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1337	184	1025	0	ENST00000382592.4:c.1785G>C	p.Lys595Asn	p.K595N	ENST00000382592	NM_014572.2	595	aaG/aaC	4/8	0.309453345513054	3	FACETS	0.853	0.785	0.924	0.426	0.392	0.462	CLONAL	1	FALSE	1	0.330561680111192	3		1025	1521	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551355	141551355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1386824799	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	161	889	1	ENST00000220592.5:c.1942G>A	p.Glu648Lys	p.E648K	ENST00000220592	NM_012154.3	648	Gag/Aag	15/19	0.260594639044481	3	FACETS	0.955	0.875	1	0.478	0.437	0.52	CLONAL	1	FALSE	1	0.330561680111192	3		890	1188	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057916	27057916	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	786	677	0	ENST00000324856.7:c.1624C>T	p.Gln542Ter	p.Q542*	ENST00000324856	NM_006015.4	542	Cag/Tag	3/20	0.330561680111192	8	FACETS	0.983	0.955	1			1	CLONAL	7	FALSE	NA	0.330561680111192	8		677	1377	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984450	201984450	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	185	592	0	ENST00000359651.3:c.1115G>C	p.Ter372SerextTer43	p.*372Sext*43	ENST00000359651		372	tGa/tCa	8/8	0.24221475682933	4	FACETS	0.838	0.774	0.904	0.838	0.774	0.904	CLONAL	2	FALSE	2	0.330561680111192	4		592	889	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670452	246670452	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	248	660	0	ENST00000388985.4:c.68C>A	p.Pro23Gln	p.P23Q	ENST00000388985		23	cCg/cAg	1/12	NA	2	FACETS	0.959	0.9	1			1	INDETERMINATE	2	FALSE	NA	0.330561680111192	2		660	782	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609084	43609084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769971379	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	200	850	1	ENST00000355710.3:c.1840G>A	p.Glu614Lys	p.E614K	ENST00000355710	NM_020975.4	614	Gag/Aag	10/20	0.217900383119288	4	FACETS	0.821	0.76	0.883	0.821	0.76	0.883	CLONAL	2	FALSE	2	0.330561680111192	4		851	981	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155165	108155165	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	71	436	0	ENST00000278616.4:c.3958G>C	p.Asp1320His	p.D1320H	ENST00000278616	NM_000051.3	1320	Gat/Cat	26/63	0.260594639044481	3	FACETS	0.961	0.84	1	0.48	0.42	0.546	CLONAL	1	FALSE	1	0.330561680111192	3		436	521	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406210	406210	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	47	276	0	ENST00000399788.2:c.4231C>G	p.Gln1411Glu	p.Q1411E	ENST00000399788	NM_001042603.1	1411	Caa/Gaa	25/28	0.310151624899991	3	FACETS	0.78	0.659	0.912	0.39	0.329	0.456	CLONAL	1	FALSE	1	0.330561680111192	3		276	425	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406233	406233	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	56	338	0	ENST00000399788.2:c.4208C>G	p.Ser1403Cys	p.S1403C	ENST00000399788	NM_001042603.1	1403	tCt/tGt	25/28	0.310151624899991	3	FACETS	0.706	0.605	0.817	0.353	0.302	0.409	SUBCLONAL	1	FALSE	1	0.330561680111192	3		338	559	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443931	18443931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	39	247	0	ENST00000266497.5:c.904C>T	p.His302Tyr	p.H302Y	ENST00000266497		302	Cat/Tat	3/31	0.310151624899991	3	FACETS	0.777	0.645	0.922	0.388	0.322	0.461	CLONAL	1	FALSE	1	0.330561680111192	3		247	354	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50481174	50481174	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	77	402	0	ENST00000394963.4:c.560C>G	p.Ser187Cys	p.S187C	ENST00000394963	NM_003076.4	187	tCt/tGt	5/13	0.260594639044481	3	FACETS	0.84	0.738	0.951	0.42	0.369	0.476	CLONAL	1	FALSE	1	0.330561680111192	3		402	646	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005308	29005308	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	43	423	0	ENST00000282397.4:c.953C>T	p.Ser318Leu	p.S318L	ENST00000282397	NM_002019.4	318	tCa/tTa	7/30	0.309453345513054	3	FACETS	0.663	0.555	0.783	0.332	0.277	0.392	SUBCLONAL	1	FALSE	1	0.330561680111192	3		423	457	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058651	42058651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	117	241	0	ENST00000219905.7:c.8371G>A	p.Glu2791Lys	p.E2791K	ENST00000219905	NM_001164273.1	2791	Gaa/Aaa	24/24	0.330561680111192	7	FACETS	1	0.97	1	0.59	0.534	0.649	CLONAL	2	FALSE	3	0.330561680111192	7		241	548	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457371	67457371	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	598	750	0	ENST00000327367.4:c.345G>A	p.Met115Ile	p.M115I	ENST00000327367	NM_005902.3	115	atG/atA	2/9	0.330561680111192	7	FACETS	0.953	0.918	0.988	1	0.995	1	CLONAL	5	FALSE	3	0.330561680111192	7		750	1387	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303873	91303873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	124	446	0	ENST00000355112.3:c.1270C>T	p.Leu424Phe	p.L424F	ENST00000355112	NM_000057.2	424	Ctt/Ttt	7/22	0.330561680111192	7	FACETS	0.787	0.711	0.866	0.393	0.355	0.433	SUBCLONAL	2	FALSE	3	0.330561680111192	7		446	871	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640979	3640979	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1162	136	922	0	ENST00000294008.3:c.2660C>G	p.Ser887Cys	p.S887C	ENST00000294008	NM_032444.2	887	tCt/tGt	12/15	0.24221475682933	4	FACETS	0.843	0.765	0.927	0.422	0.382	0.464	CLONAL	1	FALSE	2	0.330561680111192	4		922	1298	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900978	3900978	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	179	537	0	ENST00000262367.5:c.118C>G	p.Leu40Val	p.L40V	ENST00000262367	NM_004380.2	40	Ctt/Gtt	2/31	0.24221475682933	4	FACETS	0.852	0.786	0.92	0.852	0.786	0.92	CLONAL	2	FALSE	2	0.330561680111192	4		537	846	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116185	67116185	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	190	475	0	ENST00000412916.2:c.469G>C	p.Asp157His	p.D157H	ENST00000412916		157	Gac/Cac	5/6	0.281850827146878	3	FACETS	0.847	0.784	0.911	0.565	0.523	0.608	CLONAL	2	FALSE	0	0.330561680111192	3		475	791	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576872	7576873	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	75	567	1	ENST00000269305.4:c.973_974delinsAA	p.Gly325Lys	p.G325K	ENST00000269305	NM_001126112.2	325	GGa/AAa	9/11	0.24221475682933	4	FACETS	0.639	0.558	0.726	0.319	0.279	0.363	SUBCLONAL	1	FALSE	2	0.330561680111192	4		568	945	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664421	29664421	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	82	431	0	ENST00000356175.3:c.6400G>C	p.Glu2134Gln	p.E2134Q	ENST00000356175	NM_000267.3	2134	Gag/Cag	42/57	0.309453345513054	3	FACETS	0.921	0.812	1	0.46	0.406	0.518	CLONAL	1	FALSE	1	0.330561680111192	3		431	628	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760950	59760950	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	295	423	0	ENST00000259008.2:c.3457G>C	p.Asp1153His	p.D1153H	ENST00000259008	NM_032043.2	1153	Gat/Cat	20/20	0.330561680111192	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	FALSE	1	0.330561680111192	4		423	767	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56401570	56401570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	77	371	0	ENST00000348428.3:c.1432G>A	p.Asp478Asn	p.D478N	ENST00000348428	NM_006785.3	478	Gat/Aat	12/17	0.217900383119288	4	FACETS	1	0.903	1	0.516	0.453	0.583	CLONAL	1	FALSE	2	0.330561680111192	4		371	601	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215939	36215939	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	118	899	0	ENST00000222270.7:c.3479G>C	p.Gly1160Ala	p.G1160A	ENST00000222270	NM_014727.1	1160	gGa/gCa	10/37	0.330561680111192	4	FACETS	0.763	0.686	0.845	0.254	0.228	0.282	SUBCLONAL	1	FALSE	1	0.330561680111192	4		899	1245	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752982	42752982	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	113	799	0	ENST00000222329.4:c.1282G>C	p.Glu428Gln	p.E428Q	ENST00000222329	NM_006494.2	428	Gag/Cag	4/4	0.330561680111192	4	FACETS	0.752	0.675	0.835	0.251	0.225	0.279	SUBCLONAL	1	FALSE	1	0.330561680111192	4		799	1209	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023026	31023026	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	288	602	0	ENST00000375687.4:c.2511G>A	p.Met837Ile	p.M837I	ENST00000375687	NM_015338.5	837	atG/atA	13/13	0.330561680111192	5	FACETS	0.896	0.844	0.949			1	CLONAL	3	FALSE	NA	0.330561680111192	5		602	970	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944470	40944470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	172	546	1	ENST00000373198.4:c.2032C>T	p.Pro678Ser	p.P678S	ENST00000373198	NM_133170.3	678	Cca/Tca	12/32	0.330561680111192	3	FACETS	0.766	0.705	0.828	0.51	0.47	0.552	SUBCLONAL	2	FALSE	0	0.330561680111192	3		547	792	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920511	134920511	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	56	485	0	ENST00000398015.3:c.2326C>G	p.Pro776Ala	p.P776A	ENST00000398015	NM_004441.4	776	Ccc/Gcc	12/16	0.330561680111192	5	FACETS	0.522	0.446	0.606	0.174	0.148	0.202	SUBCLONAL	1	FALSE	2	0.330561680111192	5		485	971	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259775	142259775	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	170	379	0	ENST00000350721.4:c.3552C>G	p.Phe1184Leu	p.F1184L	ENST00000350721	NM_001184.3	1184	ttC/ttG	18/47	0.330561680111192	6	FACETS	1	0.982	1	0.809	0.746	0.874	CLONAL	2	FALSE	3	0.330561680111192	6		379	704	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504428	186504428	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	67	425	0	ENST00000323963.5:c.765G>C	p.Glu255Asp	p.E255D	ENST00000323963		255	gaG/gaC	7/11	0.330561680111192	6	FACETS	0.702	0.608	0.804	0.234	0.202	0.268	SUBCLONAL	1	FALSE	3	0.330561680111192	6		425	959	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38960523	38960523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	37	219	0	ENST00000357387.3:c.1828G>A	p.Glu610Lys	p.E610K	ENST00000357387	NM_152756.3	610	Gaa/Aaa	20/38	1	2	FACETS	0.67	0.554	0.8	0.67	0.554	0.8	SUBCLONAL	1	FALSE	1	0.330561680111192	2		219	334	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591096	67591096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	120	307	0	ENST00000274335.5:c.1689G>C	p.Met563Ile	p.M563I	ENST00000274335		563	atG/atC	12/15	0.24221475682933	4	FACETS	0.966	0.877	1	0.966	0.877	1	CLONAL	2	FALSE	2	0.330561680111192	4		307	500	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679918	30679918	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	115	442	0	ENST00000376406.3:c.1801C>T	p.Pro601Ser	p.P601S	ENST00000376406	NM_014641.2	601	Cca/Tca	5/15	0.310151624899991	3	FACETS	1	0.982	1	0.7	0.633	0.771	CLONAL	1	FALSE	1	0.330561680111192	3		442	579	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415138	109415138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761108393	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	138	787	0	ENST00000436639.2:c.139C>T	p.His47Tyr	p.H47Y	ENST00000436639	NM_014454.2	47	Cat/Tat	1/10	0.310151624899991	3	FACETS	0.848	0.769	0.93	0.424	0.384	0.465	CLONAL	1	FALSE	1	0.330561680111192	3		787	1148	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502191	157502191	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	56	498	0	ENST00000346085.5:c.3224G>C	p.Arg1075Pro	p.R1075P	ENST00000346085	NM_020732.3	1075	cGa/cCa	12/20	1	2	FACETS	0.52	0.445	0.602	0.52	0.445	0.602	SUBCLONAL	1	FALSE	1	0.330561680111192	2		498	652	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441652	6441652	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	291	915	0	ENST00000356142.4:c.499G>C	p.Glu167Gln	p.E167Q	ENST00000356142	NM_018890.3	167	Gag/Cag	6/7	0.24221475682933	4	FACETS	0.881	0.828	0.936	0.881	0.828	0.936	CLONAL	2	FALSE	2	0.330561680111192	4		915	1329	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564704	139564704	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	136	937	0	ENST00000308874.7:c.493G>C	p.Glu165Gln	p.E165Q	ENST00000308874		165	Gag/Cag	7/10	NA	2	FACETS	0.77	0.699	0.846			1	INDETERMINATE	1	FALSE	NA	0.330561680111192	2		937	1068	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	47	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.2	2		311	462	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647685	2647685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	58	602	1	ENST00000342085.4:c.1588G>A	p.Gly530Arg	p.G530R	ENST00000342085	NM_002613.4	530	Ggg/Agg	14/14	1	2	FACETS	0.757	0.649	0.875	0.757	0.649	0.875	SUBCLONAL	1	TRUE	1	0.2	2		603	766	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270531	98270531	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143494325	NA	P-0044391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	22	316	1	ENST00000331920.6:c.113G>A	p.Gly38Glu	p.G38E	ENST00000331920	NM_000264.3	38	gGg/gAg	1/24	1	2	FACETS	0.609	0.472	0.769	0.609	0.472	0.769	SUBCLONAL	1	TRUE	1	0.2	2		317	361	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936093	178936096	+	missense_variant	Missense_Mutation	ONP	GCAG	GCAG	TCAC	novel	NA	P-0044391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	135	542	1	ENST00000263967.3:c.1635_1638delinsTCAC	p.Glu545_Gln546delinsAspHis	p.E545_Q546delinsDH	ENST00000263967	NM_006218.2	545	gaGCAG/gaTCAC	10/21	1	2	FACETS	0.881	0.802	0.965	1	0.989	1	CLONAL	2	TRUE	1	0.2	2		543	766	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0044393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	91	476	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.170458742633416	0	FACETS	0.711	0.633	0.794			1	INDETERMINATE	1	FALSE	0	0.313332883943439	0		476	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	221	886	0	ENST00000269305.4:c.398T>A	p.Met133Lys	p.M133K	ENST00000269305	NM_001126112.2	133	aTg/aAg	5/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.313332883943439	2		886	1265	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577595	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0044393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	114	445	0	ENST00000269305.4:c.686_687del	p.Cys229TyrfsTer10	p.C229Yfs*10	ENST00000269305	NM_001126112.2	229	tGT/t	7/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.313332883943439	2		445	643	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30047493	30047493	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	68	302	0	ENST00000331968.5:c.2508C>A	p.His836Gln	p.H836Q	ENST00000331968	NM_002742.2	836	caC/caA	17/18	1	2	FACETS	0.792	0.69	0.902	0.792	0.69	0.902	CLONAL	1	FALSE	1	0.313332883943439	2		302	548	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0044407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	191	180	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	0.6299073355266	2	FACETS	0.876	0.826	0.926	0.876	0.826	0.926	CLONAL	2	TRUE	0	0.642864456127976	2		180	339	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0044407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	101	311	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.606379578260809	1	FACETS	0.704	0.637	0.773	0.704	0.637	0.773	SUBCLONAL	1	TRUE	0	0.642864456127976	1		311	303	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0044407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	10	308	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.085	0.057	0.121	0.085	0.057	0.121	SUBCLONAL	1	TRUE	1	0.642864456127976	2		308	366	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863224683	NA	P-0044407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	648	788	0	ENST00000269305.4:c.388C>G	p.Leu130Val	p.L130V	ENST00000269305	NM_001126112.2	130	Ctc/Gtc	5/11	0.616126820014503	2	FACETS	0.971	0.943	0.999	0.971	0.943	0.999	CLONAL	2	TRUE	0	0.642864456127976	2		788	1038	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248030	98248030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772368023	NA	P-0044407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	196	460	0	ENST00000331920.6:c.521C>T	p.Ala174Val	p.A174V	ENST00000331920	NM_000264.3	174	gCg/gTg	3/24	1	2	FACETS	0.962	0.895	1	0.962	0.895	1	CLONAL	1	TRUE	1	0.642864456127976	2		460	634	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0044407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	49	509	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.216	0.182	0.254	0.216	0.182	0.254	SUBCLONAL	1	TRUE	1	0.642864456127976	2		509	705	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564477	55564477	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	160	417	0	ENST00000288135.5:c.365G>A	p.Arg122His	p.R122H	ENST00000288135	NM_000222.2	122	cGc/cAc	3/21	0.642864456127976	1	FACETS	0.968	0.901	1	0.968	0.901	1	CLONAL	1	TRUE	0	0.642864456127976	1		417	349	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793877	89793877	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	124	295	0	ENST00000336032.3:c.946G>A	p.Ala316Thr	p.A316T	ENST00000336032	NM_006813.2	316	Gca/Aca	2/2	1	2	FACETS	0.908	0.828	0.99	0.908	0.828	0.99	CLONAL	1	TRUE	1	0.642864456127976	2		295	425	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654616	67654616	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1259610303	NA	P-0044407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	142	362	1	ENST00000264010.4:c.1103G>A	p.Arg368His	p.R368H	ENST00000264010	NM_006565.3	368	cGt/cAt	6/12	1	2	FACETS	0.851	0.78	0.925	0.851	0.78	0.925	CLONAL	1	TRUE	1	0.642864456127976	2		363	519	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996195	73996195	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs765178509	NA	P-0044407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	209	599	1	ENST00000318443.5:c.929G>T	p.Arg310Leu	p.R310L	ENST00000318443	NM_001024736.1	310	cGc/cTc	5/10	1	2	FACETS	0.916	0.854	0.98	0.916	0.854	0.98	CLONAL	1	TRUE	1	0.642864456127976	2		600	710	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36024600	36024600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755567292	NA	P-0044407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	538	727	0	ENST00000358208.4:c.589G>A	p.Ala197Thr	p.A197T	ENST00000358208		197	Gcc/Acc	6/12	0.629299245008998	4	FACETS	0.956	0.917	0.995	0.637	0.611	0.664	CLONAL	2	TRUE	1	0.642864456127976	4		727	1438	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	64	311	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.81	0.702	0.926	1	0.974	1	CLONAL	2	TRUE	1	0.16	2		311	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0044416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	93	766	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.16	2		767	848	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	50	609	1	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.813	0.688	0.951	0.813	0.688	0.951	CLONAL	1	TRUE	1	0.16	2		610	769	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991757	72991758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760959844	NA	P-0044416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	31	350	1	ENST00000268489.5:c.2287dup	p.Glu763GlyfsTer26	p.E763Gfs*26	ENST00000268489	NM_006885.3	763	gag/gGag	2/10	1	2	FACETS	1	0.824	1	1	0.824	1	CLONAL	1	TRUE	1	0.16	2		351	380	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0044416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	103	716	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.883	0.79	0.981	1	0.985	1	CLONAL	2	TRUE	1	0.16	2		716	729	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0044416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	192	770	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.222823367941518	2	FACETS	1	0.965	1	1	0.991	1	CLONAL	3	TRUE	0	0.16	2		770	751	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	31	640	3	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.976	0.79	1	0.976	0.79	1	CLONAL	1	TRUE	1	0.16	2		643	397	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	77	560	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.76	0.668	0.86	1	0.976	1	SUBCLONAL	2	TRUE	1	0.16	2		560	633	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913253	39913253	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	82	481	6	ENST00000378444.4:c.4862del	p.Pro1621GlnfsTer53	p.P1621Qfs*53	ENST00000378444	NM_001123385.1	1621	cCa/ca	14/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.16	2		487	802	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199945	138199945	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	68	479	0	ENST00000237289.4:c.1368del	p.Pro457LeufsTer20	p.P457Lfs*20	ENST00000237289	NM_001270507.1	455	Ggg/gg	7/9	1	2	FACETS	0.825	0.719	0.94	1	0.976	1	CLONAL	2	TRUE	1	0.16	2		479	515	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041630	14041630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368096448	NA	P-0044416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	73	330	0	ENST00000311895.7:c.2177G>A	p.Arg726His	p.R726H	ENST00000311895	NM_005236.2	726	cGc/cAc	11/11	1	2	FACETS	0.831	0.728	0.942	1	0.978	1	CLONAL	2	TRUE	1	0.16	2		330	549	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041037	112041037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761032788	NA	P-0044416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	33	440	0	ENST00000368678.4:c.218C>T	p.Thr73Met	p.T73M	ENST00000368678		73	aCg/aTg	3/13	1	2	FACETS	0.645	0.523	0.782	0.645	0.523	0.782	SUBCLONAL	1	TRUE	1	0.16	2		440	640	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2093651	2093651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	55	841	1	ENST00000219066.1:c.626C>T	p.Ala209Val	p.A209V	ENST00000219066	NM_002528.5	209	gCc/gTc	4/6	1	2	FACETS	0.674	0.574	0.784	0.674	0.574	0.784	SUBCLONAL	1	TRUE	1	0.16	2		842	1020	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120469214	120469214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587688280	NA	P-0044416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	75	455	0	ENST00000256646.2:c.3913G>A	p.Val1305Ile	p.V1305I	ENST00000256646	NM_024408.3	1305	Gtc/Atc	24/34	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.16	2		455	787	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450715	70450715	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576727317	NA	P-0044416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	89	536	0	ENST00000373644.4:c.5555C>T	p.Pro1852Leu	p.P1852L	ENST00000373644	NM_030625.2	1852	cCg/cTg	12/12	1	2	FACETS	0.798	0.708	0.895	1	0.981	1	SUBCLONAL	2	TRUE	1	0.16	2		536	697	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992291	72992291	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	136	790	2	ENST00000268489.5:c.1754G>A	p.Gly585Asp	p.G585D	ENST00000268489	NM_006885.3	585	gGc/gAc	2/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.16	2		792	1211	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716325	52716325	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	98	613	0	ENST00000322088.6:c.769T>G	p.Trp257Gly	p.W257G	ENST00000322088	NM_014225.5	257	Tgg/Ggg	6/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.16	2		613	900	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164017	106164017	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	55	285	0	ENST00000380013.4:c.3527G>T	p.Arg1176Met	p.R1176M	ENST00000380013	NM_001127208.2	1176	aGg/aTg	5/11	1	2	FACETS	0.83	0.712	0.959	1	0.971	1	CLONAL	2	TRUE	1	0.16	2		285	414	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750951	128750953	+	inframe_deletion	In_Frame_Del	DEL	AGC	AGC	-	novel	NA	P-0044416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	51	528	0	ENST00000377970.2:c.488_490del	p.Lys163_Leu164delinsMet	p.K163_L164delinsM	ENST00000377970	NM_002467.4	163	aAGCtg/atg	2/3	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.16	2		528	532	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760750	133760750	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764616226	NA	P-0044416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	49	791	0	ENST00000318560.5:c.3073G>A	p.Gly1025Ser	p.G1025S	ENST00000318560	NM_005157.4	1025	Ggc/Agc	11/11	1	2	FACETS	0.652	0.55	0.764	0.652	0.55	0.764	SUBCLONAL	1	TRUE	1	0.16	2		791	940	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815613	139815613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374009362	NA	P-0044416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	51	595	1	ENST00000247668.2:c.1084G>A	p.Ala362Thr	p.A362T	ENST00000247668	NM_021138.3	362	Gcc/Acc	9/11	1	2	FACETS	0.728	0.617	0.851	0.728	0.617	0.851	SUBCLONAL	1	TRUE	1	0.16	2		596	876	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0044438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	199	444	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.294235586663785	3	FACETS	0.844	0.787	0.902	0.844	0.787	0.902	CLONAL	3	TRUE	0	0.315322424607809	3		444	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0044438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	1112	795	2	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.315322424607809	7	FACETS	0.982	0.96	1			1	CLONAL	7	TRUE	NA	0.315322424607809	7		797	1835	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575209	48575209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767326	NA	P-0044438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	39	237	0	ENST00000342988.3:c.403C>T	p.Arg135Ter	p.R135*	ENST00000342988	NM_005359.5	135	Cga/Tga	3/12	0.315322424607809	1	FACETS	0.755	0.629	0.894	0.755	0.629	0.894	SUBCLONAL	1	TRUE	0	0.315322424607809	1		237	276	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56878417	56878417	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs190188561	NA	P-0044438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	83	393	0	ENST00000308159.5:c.2356C>T	p.Arg786Ter	p.R786*	ENST00000308159	NM_014669.4	786	Cga/Tga	22/22	1	2	FACETS	0.962	0.851	1	0.962	0.851	1	CLONAL	1	TRUE	1	0.315322424607809	2		393	547	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37083797	37083797	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	65	350	0	ENST00000231790.2:c.1706C>A	p.Ala569Asp	p.A569D	ENST00000231790	NM_000249.3	569	gCc/gAc	15/19	1	2	FACETS	0.892	0.776	1	0.892	0.776	1	CLONAL	1	TRUE	1	0.315322424607809	2		350	462	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84403340	84403340	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	86	376	0	ENST00000321945.7:c.145C>T	p.Gln49Ter	p.Q49*	ENST00000321945	NM_139076.2	49	Caa/Taa	2/9	1	2	FACETS	0.971	0.86	1	0.971	0.86	1	CLONAL	1	TRUE	1	0.315322424607809	2		376	562	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0044439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	112	260	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	0.59939194845837	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.59939194845837	1		260	261	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0044439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	242	624	0	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	0.59939194845837	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.59939194845837	1		624	511	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672258	86672261	+	frameshift_variant	Frame_Shift_Del	DEL	ATGA	ATGA	-	novel	NA	P-0044439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	178	357	0	ENST00000274376.6:c.2063_2066del	p.Glu688GlyfsTer10	p.E688Gfs*10	ENST00000274376	NM_002890.2	687	gATGAa/ga	16/25	0.59939194845837	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.59939194845837	1		357	367	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974783	21974786	+	frameshift_variant	Frame_Shift_Del	DEL	CAGT	CAGT	-	novel	NA	P-0044439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	39	134	0	ENST00000304494.5:c.41_44del	p.Asp14GlyfsTer11	p.D14Gfs*11	ENST00000304494	NM_000077.4	14	gACTGg/gg	1/3	0.59939194845837	1	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	0	0.59939194845837	1		134	87	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390906	139390906	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	271	828	0	ENST00000277541.6:c.7285C>G	p.Leu2429Val	p.L2429V	ENST00000277541	NM_017617.3	2429	Ctg/Gtg	34/34	0.332973851320477	1	FACETS	0.961	0.908	1	0.961	0.908	1	INDETERMINATE	1	TRUE	0	0.59939194845837	1		828	659	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057813	27057814	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs370698486	NA	P-0044439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	190	758	0	ENST00000324856.7:c.1523dup	p.Pro509ThrfsTer114	p.P509Tfs*114	ENST00000324856	NM_006015.4	507	-/C	3/20	1	2	FACETS	0.897	0.832	0.964	0.897	0.832	0.964	CLONAL	1	TRUE	1	0.59939194845837	2		758	707	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999785	100999785	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	48	671	0	ENST00000325455.5:c.17C>G	p.Ala6Gly	p.A6G	ENST00000325455	NM_001202474.3	6	gCa/gGa	1/8	1	2	FACETS	0.3	0.254	0.352	0.3	0.254	0.352	SUBCLONAL	1	TRUE	1	0.59939194845837	2		671	533	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3645634	3645634	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	49	686	0	ENST00000294008.3:c.1985A>C	p.Lys662Thr	p.K662T	ENST00000294008	NM_032444.2	662	aAg/aCg	9/15	0.255746790576631	1	FACETS	0.17	0.143	0.2	0.17	0.143	0.2	INDETERMINATE	1	TRUE	0	0.59939194845837	1		686	673	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956122	55956123	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	ATCT	novel	NA	P-0044439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	153	359	0	ENST00000263923.4:c.3189_3192dup	p.Ala1065ArgfsTer16	p.A1065Rfs*16	ENST00000263923	NM_002253.2	1064	-/AGAT		1	2	FACETS	0.987	0.909	1	0.987	0.909	1	CLONAL	1	TRUE	1	0.59939194845837	2		359	517	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911816	32911816	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1555283170	NA	P-0044464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	81	252	0	ENST00000380152.3:c.3324G>T	p.Lys1108Asn	p.K1108N	ENST00000380152		1108	aaG/aaT	11/27	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.404259747797413	2		252	399	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128018924	128018924	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0044464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	100	396	0	ENST00000285398.2:c.1946-2A>T		p.X649_splice	ENST00000285398	NM_000122.1	649			1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.404259747797413	2		396	480	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443868	52443884	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCAGCTCCAGCCAGC	CTCCAGCTCCAGCCAGC	-	novel	NA	P-0044464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	139	799	0	ENST00000460680.1:c.11_27del	p.Gly4GlufsTer59	p.G4Efs*59	ENST00000460680	NM_004656.3	4	gGCTGGCTGGAGCTGGAG/g	1/17	0.404259747797413	1	FACETS	0.71	0.647	0.776	0.71	0.647	0.776	SUBCLONAL	1	TRUE	0	0.404259747797413	1		799	773	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121438901	121438901	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0044476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	40	892	0	ENST00000257555.6:c.1802C>G	p.Ser601Ter	p.S601*	ENST00000257555		601	tCa/tGa	10/10	0.0781665421686925	0	FACETS	0.747	0.619	0.89			1	SUBCLONAL	1	TRUE	0	0.13	0		892	717	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805601	46805601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	64	1062	0	ENST00000290295.7:c.355G>A	p.Glu119Lys	p.E119K	ENST00000290295	NM_006361.5	119	Gag/Aag	1/2	1	2	FACETS	0.983	0.848	1	0.983	0.848	1	CLONAL	1	TRUE	1	0.13	2		1062	1002	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235896	133235896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	31	585	0	ENST00000320574.5:c.3260C>T	p.Ser1087Phe	p.S1087F	ENST00000320574	NM_006231.2	1087	tCc/tTc	26/49	0.0781665421686925	0	FACETS	0.859	0.694	1			1	CLONAL	1	TRUE	0	0.13	0		585	483	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514428	103514428	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	13	242	0	ENST00000355739.4:c.929C>T	p.Ser310Phe	p.S310F	ENST00000355739	NM_000123.3	310	tCt/tTt	8/15	1	2	FACETS	0.769	0.548	1	0.769	0.548	1	CLONAL	1	TRUE	1	0.13	2		242	260	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660829	227660829	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765919941	NA	P-0044476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	25	695	0	ENST00000305123.5:c.2626G>A	p.Glu876Lys	p.E876K	ENST00000305123	NM_005544.2	876	Gag/Aag	1/2	1	2	FACETS	0.825	0.649	1	0.825	0.649	1	CLONAL	1	TRUE	1	0.13	2		695	466	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928850	49928850	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	56	957	0	ENST00000296474.3:c.3516C>G	p.Phe1172Leu	p.F1172L	ENST00000296474	NM_002447.2	1172	ttC/ttG	16/20	0.118657753058572	3	FACETS	1	0.893	1	0.527	0.45	0.612	CLONAL	1	TRUE	1	0.13	3		957	870	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242849	142242849	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	29	374	0	ENST00000350721.4:c.4138G>A	p.Asp1380Asn	p.D1380N	ENST00000350721	NM_001184.3	1380	Gat/Aat	22/47	0.118657753058572	3	FACETS	0.878	0.703	1	0.439	0.351	0.539	CLONAL	1	TRUE	1	0.13	3		374	541	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554274	106554274	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	24	441	1	ENST00000369096.4:c.1802G>A	p.Arg601Gln	p.R601Q	ENST00000369096	NM_001198.3	601	cGg/cAg	6/7	1	2	FACETS	0.779	0.609	0.975	0.779	0.609	0.975	CLONAL	1	TRUE	1	0.13	2		442	474	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0044477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	192	352	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.410677409265351	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.412774532331744	2		352	454	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0044477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	77	124	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.410677409265351	2	FACETS	0.794	0.708	0.883	0.794	0.708	0.883	SUBCLONAL	2	TRUE	0	0.412774532331744	2		124	235	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0044477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	166	703	0	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.412774532331744	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.412774532331744	1		703	607	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130435	29130435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779269031	NA	P-0044477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	209	711	0	ENST00000328354.6:c.275C>T	p.Pro92Leu	p.P92L	ENST00000328354	NM_007194.3	92	cCc/cTc	2/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.412774532331744	2		711	887	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106730	27106730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773818181	NA	P-0044477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	152	612	0	ENST00000324856.7:c.6341C>T	p.Pro2114Leu	p.P2114L	ENST00000324856	NM_006015.4	2114	cCg/cTg	20/20	1	2	FACETS	0.932	0.854	1	0.932	0.854	1	CLONAL	1	TRUE	1	0.412774532331744	2		612	790	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0044490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	74	314	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.494075115888746	6	FACETS	1	0.931	1	1	0.931	1	CLONAL	3	FALSE	3	0.769116989745272	6		314	156	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31423030	31423030	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	27	493	0	ENST00000344624.3:c.3283del	p.Arg1095AspfsTer22	p.R1095Dfs*22	ENST00000344624		1095	Cga/ga	26/33	1	2	FACETS	0.78	0.638	0.933	0.78	0.638	0.933	CLONAL	1	FALSE	1	0.769116989745272	2		493	90	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682461	37682461	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs186741659	NA	P-0044494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	4574	356	0	ENST00000447079.4:c.3652A>G	p.Met1218Val	p.M1218V	ENST00000447079	NM_015083.1	1218	Atg/Gtg	13/14	0.537698177890311	59	FACETS	1	0.999	1			1	CLONAL	58	TRUE	NA	0.537698177890311	59		356	4752	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577607	7577608	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0044494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	268	585	0	ENST00000269305.4:c.673_674del	p.Val225TrpfsTer3	p.V225Wfs*3	ENST00000269305	NM_001126112.2	225	GTt/t	7/11	0.387629604119563	3	FACETS	0.958	0.914	1	0.958	0.914	1	CLONAL	3	TRUE	0	0.537698177890311	3		585	440	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372025	55372025	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	62	451	2	ENST00000297316.4:c.715G>A	p.Ala239Thr	p.A239T	ENST00000297316	NM_022454.3	239	Gcc/Acc	2/2	0.281037227810505	5	FACETS	0.467	0.401	0.538	0.156	0.133	0.18	SUBCLONAL	1	TRUE	2	0.394575615743578	5		453	1072	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587781702	NA	P-0044499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	368	589	0	ENST00000269305.4:c.920-1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.380946498197139	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.394575615743578	2		589	774	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323261	31323261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576012253	NA	P-0044499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	68	343	0	ENST00000412585.2:c.728G>A	p.Arg243Gln	p.R243Q	ENST00000412585	NM_005514.6	243	cGg/cAg	4/8	0.193473710464313	5	FACETS	0.775	0.674	0.885	0.258	0.224	0.295	INDETERMINATE	1	TRUE	2	0.394575615743578	5		343	708	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432290	49432290	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	251	842	1	ENST00000301067.7:c.8849C>T	p.Pro2950Leu	p.P2950L	ENST00000301067	NM_003482.3	2950	cCc/cTc	34/54	0.394575615743578	3	FACETS	1	0.967	1	0.529	0.493	0.565	CLONAL	1	TRUE	1	0.394575615743578	3		843	1441	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332645	70332645	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0044499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	66	525	0	ENST00000373644.4:c.550A>T	p.Lys184Ter	p.K184*	ENST00000373644	NM_030625.2	184	Aag/Tag	2/12	0.204271061258001	3	FACETS	0.463	0.401	0.531	0.232	0.2	0.266	INDETERMINATE	1	TRUE	1	0.394575615743578	3		525	865	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195318	102195318	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs375640711	NA	P-0044499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	267	335	0	ENST00000263464.3:c.78G>T	p.Leu26Phe	p.L26F	ENST00000263464	NM_001165.4	26	ttG/ttT	2/9	0.366244836077787	4	FACETS	0.849	0.8	0.899	1	0.991	1	CLONAL	3	TRUE	2	0.394575615743578	4		335	741	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771148	161771148	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1305965991	NA	P-0044499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	97	611	0	ENST00000366898.1:c.1381C>T	p.His461Tyr	p.H461Y	ENST00000366898	NM_004562.2	461	Cac/Tac	12/12	0.204271061258001	3	FACETS	0.643	0.573	0.719	0.322	0.286	0.36	INDETERMINATE	1	TRUE	1	0.394575615743578	3		611	915	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006243	22006243	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	143	575	0	ENST00000276925.6:c.160A>G	p.Met54Val	p.M54V	ENST00000276925	NM_004936.3	54	Atg/Gtg	2/2	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.394575615743578	2		575	719	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0044502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	47	309	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.584	0.492	0.685	0.584	0.492	0.685	SUBCLONAL	1	TRUE	1	0.28	2		309	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0044502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	42	690	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.296718350897746	1	FACETS	0.275	0.229	0.328	0.275	0.229	0.328	SUBCLONAL	1	TRUE	0	0.28	1		692	937	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0044502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	116	772	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.296718350897746	1	FACETS	0.752	0.676	0.831	0.752	0.676	0.831	SUBCLONAL	1	TRUE	0	0.28	1		772	948	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867333	45867333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765839639	NA	P-0044502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	73	866	0	ENST00000391945.4:c.860G>A	p.Arg287His	p.R287H	ENST00000391945	NM_000400.3	287	cGt/cAt	10/23	1	2	FACETS	0.477	0.415	0.543	0.477	0.415	0.543	SUBCLONAL	1	TRUE	1	0.28	2		866	1094	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27228298	27228298	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	45	459	0	ENST00000380036.4:c.3295C>T	p.Arg1099Ter	p.R1099*	ENST00000380036	NM_000459.3	1099	Cga/Tga	22/23	0.233120479042062	1	FACETS	0.452	0.379	0.533	0.452	0.379	0.533	SUBCLONAL	1	TRUE	0	0.28	1		459	611	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467761	99467761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1047436404	NA	P-0044502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	23	283	0	ENST00000268035.6:c.2630G>A	p.Arg877Gln	p.R877Q	ENST00000268035	NM_000875.3	877	cGa/cAa	13/21	0.233120479042062	1	FACETS	0.37	0.288	0.465	0.37	0.288	0.465	SUBCLONAL	1	TRUE	0	0.28	1		283	382	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156301	106156301	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	25	309	0	ENST00000380013.4:c.1202C>A	p.Pro401Gln	p.P401Q	ENST00000380013	NM_001127208.2	401	cCa/cAa	3/11	0.296718350897746	1	FACETS	0.431	0.34	0.537	0.431	0.34	0.537	SUBCLONAL	1	TRUE	0	0.28	1		309	356	SUCCESS
APC	324	MSKCC	GRCh37	5	112164636	112164642	+	frameshift_variant	Frame_Shift_Del	DEL	AGCATTG	AGCATTG	-	novel	NA	P-0044502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	37	295	0	ENST00000257430.4:c.1711_1717del	p.Ala571TrpfsTer5	p.A571Wfs*5	ENST00000257430	NM_000038.5	570	aaAGCATTG/aa	14/16	0.296718350897746	1	FACETS	0.653	0.54	0.78	0.653	0.54	0.78	SUBCLONAL	1	TRUE	0	0.28	1		295	348	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	140	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.265917184540279	6	FACETS	1	0.917	1	0.503	0.459	0.55	CLONAL	2	TRUE	2	0.265917184540279	6		539	801	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882019	NA	P-0044512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	200	866	0	ENST00000269305.4:c.455dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	ccg/ccCg	5/11	0.265917184540279	3	FACETS	0.844	0.781	0.908	0.844	0.781	0.908	CLONAL	2	TRUE	1	0.265917184540279	3		866	1010	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216504	36216504	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	68	848	1	ENST00000222270.7:c.3767G>T	p.Gly1256Val	p.G1256V	ENST00000222270	NM_014727.1	1256	gGa/gTa	12/37	0.265917184540279	5	FACETS	0.685	0.594	0.784	0.228	0.198	0.262	SUBCLONAL	1	TRUE	2	0.265917184540279	5		849	1045	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069476	30069476	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0044547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	254	451	2	ENST00000338641.4:c.1340+1G>T		p.X447_splice	ENST00000338641	NM_000268.3	447			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		453	418	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464917	120464917	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1195210396	NA	P-0044555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	236	356	0	ENST00000256646.2:c.5155C>T	p.Arg1719Ter	p.R1719*	ENST00000256646	NM_024408.3	1719	Cga/Tga	28/34	1	2	FACETS	0.694	0.648	0.74	0.694	0.648	0.74	SUBCLONAL	1	TRUE	1	0.78407644624155	2		356	868	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	189	429	0	ENST00000269305.4:c.991del	p.Gln331ArgfsTer14	p.Q331Rfs*14	ENST00000269305	NM_001126112.2	331	Cag/ag	9/11	0.78407644624155	1	FACETS	0.98	0.928	1	0.98	0.928	1	CLONAL	1	TRUE	0	0.78407644624155	1		429	299	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414998	56414998	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	22	381	0	ENST00000348428.3:c.2399G>A	p.Arg800Lys	p.R800K	ENST00000348428	NM_006785.3	800	aGa/aAa	17/17	NA	2	FACETS	0.131	0.101	0.166			1	INDETERMINATE	1	TRUE	NA	0.78407644624155	2		381	429	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268044	55268044	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs17337451	NA	P-0044555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	45	484	0	ENST00000275493.2:c.2884C>G	p.Arg962Gly	p.R962G	ENST00000275493	NM_005228.3	962	Cgt/Ggt	24/28	1	2	FACETS	0.139	0.116	0.164	0.139	0.116	0.164	SUBCLONAL	1	TRUE	1	0.78407644624155	2		484	828	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955489	90955489	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	107	295	0	ENST00000265433.3:c.2176G>C	p.Glu726Gln	p.E726Q	ENST00000265433	NM_002485.4	726	Gaa/Caa	14/16	0.622689133151742	4	FACETS	0.763	0.686	0.845	0.382	0.343	0.423	SUBCLONAL	1	TRUE	2	0.78407644624155	4		295	638	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923655	39923655	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	671	494	0	ENST00000378444.4:c.3436G>T	p.Glu1146Ter	p.E1146*	ENST00000378444	NM_001123385.1	1146	Gag/Tag	7/15	0.615382529867476	3	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.78407644624155	3		494	1110	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0044567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	34	766	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		767	649	SUCCESS
APC	324	MSKCC	GRCh37	5	112175360	112175360	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	14	243	0	ENST00000257430.4:c.4069G>T	p.Gly1357Ter	p.G1357*	ENST00000257430	NM_000038.5	1357	Gga/Tga	16/16	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		243	251	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	231	348	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.72859956918579	2		349	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0044580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	94	789	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.72859956918579	1	FACETS	0.249	0.221	0.278	0.249	0.221	0.278	SUBCLONAL	1	TRUE	0	0.72859956918579	1		789	659	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0044580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	3556	822	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	0.72859956918579	10	FACETS	0.986	0.977	0.994			1	CLONAL	9	TRUE	NA	0.72859956918579	10		822	4307	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231497	5231497	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200771602	NA	P-0044580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	104	750	1	ENST00000357368.4:c.1979C>T	p.Pro660Leu	p.P660L	ENST00000357368	NM_002850.3	660	cCg/cTg	14/38	1	2	FACETS	0.344	0.308	0.383	0.344	0.308	0.383	SUBCLONAL	1	TRUE	1	0.72859956918579	2		751	829	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190691	108190691	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	172	464	0	ENST00000278616.4:c.6358G>T	p.Glu2120Ter	p.E2120*	ENST00000278616	NM_000051.3	2120	Gaa/Taa	44/63	1	2	FACETS	0.96	0.89	1	0.96	0.89	1	CLONAL	1	TRUE	1	0.72859956918579	2		464	492	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26971318	26971318	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	94	358	0	ENST00000381527.3:c.889A>G	p.Met297Val	p.M297V	ENST00000381527	NM_001260.1	297	Atg/Gtg	9/13	1	2	FACETS	0.899	0.811	0.991	0.899	0.811	0.991	CLONAL	1	TRUE	1	0.72859956918579	2		358	287	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30323833	30323833	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	257	313	0	ENST00000322652.5:c.1811C>A	p.Ser604Tyr	p.S604Y	ENST00000322652	NM_015355.2	604	tCt/tAt	15/16	0.72859956918579	3	FACETS	0.905	0.856	0.953	0.905	0.856	0.953	CLONAL	2	TRUE	1	0.72859956918579	3		313	532	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930727	131930727	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	192	390	0	ENST00000265335.6:c.1960A>G	p.Lys654Glu	p.K654E	ENST00000265335		654	Aaa/Gaa	12/25	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.72859956918579	2		390	509	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782190	135782193	+	frameshift_variant	Frame_Shift_Del	DEL	GAGT	GAGT	-	novel	NA	P-0044580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	177	532	0	ENST00000298552.3:c.1363_1366del	p.Thr455Ter	p.T455*	ENST00000298552	NM_001162426.1	455	ACTCta/ta	14/23	0.72859956918579	1	FACETS	0.959	0.902	1	0.959	0.902	1	CLONAL	1	TRUE	0	0.72859956918579	1		532	322	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955145	17955145	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	122	981	0	ENST00000458235.1:c.82G>T	p.Val28Leu	p.V28L	ENST00000458235	NM_000215.3	28	Gtg/Ttg	2/24	0.198432726171607	3	FACETS	1	0.979	1	0.626	0.571	0.682	INDETERMINATE	1	TRUE	1	0.668718178701494	3		981	389	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95556899	95556899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	74	436	0	ENST00000393063.1:c.5705C>T	p.Ser1902Phe	p.S1902F	ENST00000393063	NM_030621.3	1902	tCt/tTt	28/28	0.196966876795661	5	FACETS	0.981	0.872	1	0.654	0.581	0.729	INDETERMINATE	2	TRUE	2	0.668718178701494	5		436	226	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961999	41961999	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	110	654	2	ENST00000219905.7:c.907C>G	p.Gln303Glu	p.Q303E	ENST00000219905	NM_001164273.1	303	Caa/Gaa	2/24	0.176842813913175	2	FACETS	1	0.966	1	0.561	0.512	0.612	INDETERMINATE	1	TRUE	0	0.668718178701494	2		656	293	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684042	29684042	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	195	674	2	ENST00000356175.3:c.7742del	p.Asn2581MetfsTer22	p.N2581Mfs*22	ENST00000356175	NM_000267.3	2580	tcA/tc	52/57	0.609729330623465	3	FACETS	0.894	0.85	0.937	0.894	0.85	0.937	CLONAL	3	TRUE	0	0.668718178701494	3		676	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0044602-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	151	789	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.169396050807756	0	FACETS	0.891	0.833	0.949			1	CLONAL	6	FALSE	0	0.169396050807756	0		789	277	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0044602-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	17	263	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.956	0.762	1	1	0.955	1	CLONAL	6	FALSE	1	0.169396050807756	2		263	35	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579310	7579310	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1555526469	NA	P-0044602-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	132	479	0	ENST00000269305.4:c.375+2T>C		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.169396050807756	0	FACETS	0.981	0.909	1			1	CLONAL	5	FALSE	0	0.169396050807756	0		479	264	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447395	12447395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044602-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	74	469	4	ENST00000287820.6:c.634C>T	p.Arg212Trp	p.R212W	ENST00000287820	NM_015869.4	212	Cgg/Tgg	5/7	1	2	FACETS	1	0.888	1	1	0.987	1	CLONAL	3	FALSE	1	0.169396050807756	2		473	290	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918978	76918981	+	frameshift_variant	Frame_Shift_Del	DEL	TGTC	TGTC	-	novel	NA	P-0044602-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	24	335	0	ENST00000373344.5:c.4010_4013del	p.Arg1337IlefsTer8	p.R1337Ifs*8	ENST00000373344	NM_000489.3	1337	aGACAt/at	12/35	0.169396050807756	1	FACETS	0.943	0.776	1	1	0.967	1	CLONAL	5	FALSE	0	0.169396050807756	1		335	55	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932396	39932396	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044602-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	22	681	0	ENST00000378444.4:c.2203A>C	p.Ile735Leu	p.I735L	ENST00000378444	NM_001123385.1	735	Ata/Cta	4/15	0.169396050807756	1	FACETS	0.837	0.65	1	0.837	0.65	1	CLONAL	1	FALSE	0	0.169396050807756	1		681	284	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289112	33289112	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	70	606	0	ENST00000374542.5:c.440del	p.Pro147LeufsTer82	p.P147Lfs*82	ENST00000374542	NM_001141970.1	147	cCt/ct	3/8	1	2	FACETS	0.277	0.241	0.317	0.277	0.241	0.317	SUBCLONAL	1	TRUE	1	0.68	2		606	742	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0044611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	138	444	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.501436923009849	4	FACETS	1	0.945	1	0.69	0.634	0.747	CLONAL	2	TRUE	1	0.505856485236602	4		444	397	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	261	368	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.844	0.793	0.896	1	0.994	1	CLONAL	2	TRUE	1	0.37	2		371	836	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	255	721	8	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.943	0.887	1	1	0.995	1	CLONAL	2	TRUE	1	0.37	2		729	731	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411246	63411246	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	117	742	0	ENST00000330258.3:c.1921C>T	p.Arg641Ter	p.R641*	ENST00000330258	NM_152424.3	641	Cga/Tga	2/2	1	2	FACETS	0.852	0.769	0.94	0.852	0.769	0.94	CLONAL	1	TRUE	1	0.37	2		742	742	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	132	845	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.883	0.802	0.968	0.883	0.802	0.968	CLONAL	1	TRUE	1	0.37	2		845	808	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	52	429	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	0.603	0.514	0.701	0.603	0.514	0.701	SUBCLONAL	1	TRUE	1	0.37	2		429	466	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	185	456	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.937	1	1	0.993	1	CLONAL	2	TRUE	1	0.37	2		461	497	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182104	11182104	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs181023452	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	129	694	0	ENST00000361445.4:c.6742G>A	p.Ala2248Thr	p.A2248T	ENST00000361445	NM_004958.3	2248	Gcc/Acc	48/58	1	2	FACETS	0.915	0.83	1	0.915	0.83	1	CLONAL	1	TRUE	1	0.37	2		694	762	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11270918	11270918	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	102	476	0	ENST00000361445.4:c.3607C>T	p.Arg1203Ter	p.R1203*	ENST00000361445	NM_004958.3	1203	Cga/Tga	24/58	1	2	FACETS	0.837	0.749	0.929	0.837	0.749	0.929	CLONAL	1	TRUE	1	0.37	2		476	659	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22412996	22412996	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	39	160	0	ENST00000344548.3:c.247del	p.Ser83GlnfsTer11	p.S83Qfs*11	ENST00000344548	NM_001039802.1	81	tgT/tg	5/7	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.37	2		160	183	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28607287	28607287	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778863205	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	127	575	0	ENST00000253063.3:c.1417C>T	p.Arg473Cys	p.R473C	ENST00000253063	NM_031459.4	473	Cgt/Tgt	10/10	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.37	2		575	661	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938213	36938213	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	130	877	0	ENST00000361632.4:c.748C>T	p.Gln250Ter	p.Q250*	ENST00000361632		250	Cag/Tag	6/16	1	2	FACETS	0.876	0.795	0.962	0.876	0.795	0.962	CLONAL	1	TRUE	1	0.37	2		877	802	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78426155	78426155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	56	363	0	ENST00000370768.2:c.1370C>A	p.Pro457His	p.P457H	ENST00000370768	NM_003902.3	457	cCt/cAt	15/20	1	2	FACETS	0.888	0.765	1	0.888	0.765	1	CLONAL	1	TRUE	1	0.37	2		363	341	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838326	156838326	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553261428	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	143	943	0	ENST00000524377.1:c.604A>G	p.Asn202Asp	p.N202D	ENST00000524377	NM_002529.3	202	Aat/Gat	6/17	1	2	FACETS	0.893	0.814	0.975	0.893	0.814	0.975	CLONAL	1	TRUE	1	0.37	2		943	866	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843449	156843449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764645590	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	104	666	0	ENST00000524377.1:c.875C>T	p.Thr292Met	p.T292M	ENST00000524377	NM_002529.3	292	aCg/aTg	8/17	1	2	FACETS	0.889	0.798	0.986	0.889	0.798	0.986	CLONAL	1	TRUE	1	0.37	2		666	632	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176085808	176085810	+	inframe_deletion	In_Frame_Del	DEL	AAT	AAT	-	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	70	386	0	ENST00000367669.3:c.976_978del	p.Ile326del	p.I326del	ENST00000367669	NM_022457.5	326	ATT/-	9/20	1	2	FACETS	0.805	0.704	0.914	0.805	0.704	0.914	CLONAL	1	TRUE	1	0.37	2		386	470	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218980	193218980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465509067	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	51	276	0	ENST00000367435.3:c.1538G>A	p.Arg513Gln	p.R513Q	ENST00000367435	NM_024529.4	513	cGg/cAg	16/17	1	2	FACETS	0.938	0.802	1	0.938	0.802	1	CLONAL	1	TRUE	1	0.37	2		276	294	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680543	241680543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	70	458	0	ENST00000366560.3:c.206G>A	p.Gly69Asp	p.G69D	ENST00000366560	NM_000143.3	69	gGc/gAc	2/10	1	2	FACETS	0.575	0.501	0.655	0.575	0.501	0.655	SUBCLONAL	1	TRUE	1	0.37	2		458	658	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601893	43601893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057521089	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	138	778	1	ENST00000355710.3:c.937C>T	p.Arg313Trp	p.R313W	ENST00000355710	NM_020975.4	313	Cgg/Tgg	5/20	1	2	FACETS	0.924	0.842	1	0.924	0.842	1	CLONAL	1	TRUE	1	0.37	2		779	807	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692884	89692884	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121909222	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	69	373	0	ENST00000371953.3:c.368A>G	p.His123Arg	p.H123R	ENST00000371953	NM_000314.4	123	cAc/cGc	5/9	1	2	FACETS	0.949	0.831	1	0.949	0.831	1	CLONAL	1	TRUE	1	0.37	2		373	393	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	69	433	1	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	0.79	0.69	0.898	0.79	0.69	0.898	SUBCLONAL	1	TRUE	1	0.37	2		434	472	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309777	104309777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745958724	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	139	633	1	ENST00000369902.3:c.368G>A	p.Arg123His	p.R123H	ENST00000369902	NM_016169.3	123	cGt/cAt	3/12	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.37	2		634	738	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247593	123247593	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	75	485	2	ENST00000358487.5:c.1898del	p.Leu633TrpfsTer2	p.L633Wfs*2	ENST00000358487	NM_000141.4	633	tTg/tg	14/18	1	2	FACETS	0.616	0.54	0.698	0.616	0.54	0.698	SUBCLONAL	1	TRUE	1	0.37	2		487	658	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129325	64129325	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs376604355	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	97	746	1	ENST00000334205.4:c.757C>T	p.Arg253Trp	p.R253W	ENST00000334205	NM_003942.2	253	Cgg/Tgg	8/17	1	2	FACETS	0.827	0.738	0.921	0.827	0.738	0.921	CLONAL	1	TRUE	1	0.37	2		747	634	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588869	69588869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766381502	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	91	756	1	ENST00000168712.1:c.367C>T	p.Arg123Trp	p.R123W	ENST00000168712	NM_002007.2	123	Cgg/Tgg	2/3	1	2	FACETS	0.816	0.725	0.912	0.816	0.725	0.912	CLONAL	1	TRUE	1	0.37	2		757	603	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514026	125514026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775909758	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	83	500	1	ENST00000428830.2:c.964C>T	p.Arg322Cys	p.R322C	ENST00000428830	NM_001114121.2	322	Cgc/Tgc	10/14	1	2	FACETS	0.813	0.719	0.913	0.813	0.719	0.913	CLONAL	1	TRUE	1	0.37	2		501	552	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	459885	459885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	124	755	0	ENST00000399788.2:c.1210G>A	p.Asp404Asn	p.D404N	ENST00000399788	NM_001042603.1	404	Gat/Aat	10/28	1	2	FACETS	0.843	0.763	0.928	0.843	0.763	0.928	CLONAL	1	TRUE	1	0.37	2		755	795	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21626494	21626494	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	72	484	0	ENST00000421138.2:c.1438A>G	p.Lys480Glu	p.K480E	ENST00000421138		480	Aaa/Gaa	13/16	1	2	FACETS	0.76	0.665	0.862	0.76	0.665	0.862	SUBCLONAL	1	TRUE	1	0.37	2		484	512	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628716	21628716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755679996	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	68	417	0	ENST00000421138.2:c.992C>T	p.Thr331Met	p.T331M	ENST00000421138		331	aCg/aTg	10/16	1	2	FACETS	0.746	0.65	0.849	0.746	0.65	0.849	SUBCLONAL	1	TRUE	1	0.37	2		417	493	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944842	31944842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	145	819	0	ENST00000340398.3:c.259G>A	p.Ala87Thr	p.A87T	ENST00000340398	NM_001013699.2	87	Gca/Aca	1/1	1	2	FACETS	0.813	0.741	0.889	0.813	0.741	0.889	CLONAL	1	TRUE	1	0.37	2		819	964	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245470	46245470	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	61	376	0	ENST00000334344.6:c.3564T>G	p.Ser1188Arg	p.S1188R	ENST00000334344	NM_152641.2	1188	agT/agG	15/21	1	2	FACETS	0.818	0.708	0.937	0.818	0.708	0.937	CLONAL	1	TRUE	1	0.37	2		376	403	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434959	49434959	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555192751	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	91	698	0	ENST00000301067.7:c.6594del	p.Tyr2199IlefsTer65	p.Y2199Ifs*65	ENST00000301067	NM_003482.3	2198	ccC/cc	31/54	1	2	FACETS	0.872	0.776	0.974	0.872	0.776	0.974	CLONAL	1	TRUE	1	0.37	2		698	564	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445203	49445203	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	125	961	4	ENST00000301067.7:c.2263del	p.Arg755GlyfsTer175	p.R755Gfs*175	ENST00000301067	NM_003482.3	755	Cgg/gg	10/54	1	2	FACETS	0.754	0.682	0.83	0.754	0.682	0.83	SUBCLONAL	1	TRUE	1	0.37	2		965	896	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432040	121432040	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771108132	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	155	947	3	ENST00000257555.6:c.787C>T	p.Arg263Cys	p.R263C	ENST00000257555		263	Cgt/Tgt	4/10	1	2	FACETS	0.929	0.85	1	0.929	0.85	1	CLONAL	1	TRUE	1	0.37	2		950	902	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	114	769	3	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.861	0.776	0.951	0.861	0.776	0.951	CLONAL	1	TRUE	1	0.37	2		772	716	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712700	43712700	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1282655302	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	161	893	0	ENST00000382044.4:c.4484G>A	p.Arg1495His	p.R1495H	ENST00000382044	NM_001141980.1	1495	cGt/cAt	21/28	1	2	FACETS	0.968	0.888	1	0.968	0.888	1	CLONAL	1	TRUE	1	0.37	2		893	899	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423579	88423579	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	89	657	0	ENST00000360948.2:c.2256T>G	p.Asp752Glu	p.D752E	ENST00000360948	NM_001012338.2	752	gaT/gaG	18/19	1	2	FACETS	0.754	0.669	0.845	0.754	0.669	0.845	SUBCLONAL	1	TRUE	1	0.37	2		657	638	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	166	828	2	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.37	2		830	856	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434635	99434635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148823172	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	140	681	0	ENST00000268035.6:c.722C>T	p.Ala241Val	p.A241V	ENST00000268035	NM_000875.3	241	gCg/gTg	3/21	1	2	FACETS	0.968	0.882	1	0.968	0.882	1	CLONAL	1	TRUE	1	0.37	2		681	782	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465555	99465555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753047347	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	94	580	1	ENST00000268035.6:c.2380C>T	p.Arg794Trp	p.R794W	ENST00000268035	NM_000875.3	794	Cgg/Tgg	11/21	1	2	FACETS	0.864	0.77	0.964	0.864	0.77	0.964	CLONAL	1	TRUE	1	0.37	2		581	588	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121909	2121909	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760489473	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	154	931	2	ENST00000219476.3:c.2071C>T	p.Arg691Cys	p.R691C	ENST00000219476	NM_000548.3	691	Cgc/Tgc	19/42	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.37	2		933	825	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222371	2222371	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1419349453	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	100	849	0	ENST00000326181.6:c.655C>T	p.Arg219Trp	p.R219W	ENST00000326181	NM_032271.2	219	Cgg/Tgg	8/21	1	2	FACETS	0.849	0.759	0.943	0.849	0.759	0.943	CLONAL	1	TRUE	1	0.37	2		849	637	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779560	3779560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	134	1090	0	ENST00000262367.5:c.5488G>A	p.Ala1830Thr	p.A1830T	ENST00000262367	NM_004380.2	1830	Gcc/Acc	31/31	1	2	FACETS	0.703	0.637	0.771	0.703	0.637	0.771	SUBCLONAL	1	TRUE	1	0.37	2		1090	1031	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832927	3832927	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	20	372	0	ENST00000262367.5:c.1331C>T	p.Thr444Ile	p.T444I	ENST00000262367	NM_004380.2	444	aCc/aTc	6/31	1	2	FACETS	0.306	0.234	0.391	0.306	0.234	0.391	SUBCLONAL	1	TRUE	1	0.37	2		372	353	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50811827	50811827	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	69	422	0	ENST00000398568.2:c.1109del	p.Asn370IlefsTer35	p.N370Ifs*35	ENST00000398568	NM_001042412.1	368	tcA/tc	7/18	1	2	FACETS	0.723	0.631	0.822	0.723	0.631	0.822	SUBCLONAL	1	TRUE	1	0.37	2		422	516	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875638	56875638	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239777742	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	27	463	0	ENST00000308159.5:c.2242G>A	p.Val748Met	p.V748M	ENST00000308159	NM_014669.4	748	Gtg/Atg	21/22	1	2	FACETS	0.272	0.215	0.337	0.272	0.215	0.337	SUBCLONAL	1	TRUE	1	0.37	2		463	537	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821906	72821908	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs767338198	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	66	390	0	ENST00000268489.5:c.10267_10269del	p.Glu3423del	p.E3423del	ENST00000268489	NM_006885.3	3423	GAA/-	10/10	1	2	FACETS	0.864	0.753	0.983	0.864	0.753	0.983	CLONAL	1	TRUE	1	0.37	2		390	413	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829368	72829368	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201280219	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	111	704	0	ENST00000268489.5:c.7213G>A	p.Ala2405Thr	p.A2405T	ENST00000268489	NM_006885.3	2405	Gct/Act	9/10	1	2	FACETS	0.932	0.839	1	0.932	0.839	1	CLONAL	1	TRUE	1	0.37	2		704	644	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944126	81944126	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1324356186	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	80	540	0	ENST00000359376.3:c.1735C>T	p.Arg579Trp	p.R579W	ENST00000359376	NM_002661.3	579	Cgg/Tgg	18/33	1	2	FACETS	0.84	0.741	0.945	0.84	0.741	0.945	CLONAL	1	TRUE	1	0.37	2		540	515	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960943	15960943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs575750270	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	71	382	0	ENST00000268712.3:c.6277G>A	p.Val2093Met	p.V2093M	ENST00000268712	NM_006311.3	2093	Gtg/Atg	40/46	1	2	FACETS	0.822	0.719	0.932	0.822	0.719	0.932	CLONAL	1	TRUE	1	0.37	2		382	467	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462635	40462635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762056710	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	134	627	2	ENST00000345506.4:c.2333G>A	p.Arg778His	p.R778H	ENST00000345506	NM_003152.3	778	cGc/cAc	20/20	1	2	FACETS	0.981	0.893	1	0.981	0.893	1	CLONAL	1	TRUE	1	0.37	2		629	738	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439919	56439919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	170	683	2	ENST00000407977.2:c.673del	p.Arg225AlafsTer194	p.R225Afs*194	ENST00000407977		225	Cgc/gc	6/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.37	2		685	796	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439936	56439936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377765604	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	178	757	0	ENST00000407977.2:c.656G>A	p.Arg219His	p.R219H	ENST00000407977		219	cGc/cAc	6/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.37	2		757	907	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	93	593	0	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	0.907	0.809	1	0.907	0.809	1	CLONAL	1	TRUE	1	0.37	2		593	554	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533905	63533905	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	173	501	1	ENST00000307078.5:c.1249del	p.Ala417ArgfsTer41	p.A417Rfs*41	ENST00000307078	NM_004655.3	417	Gcg/cg	6/11	1	2	FACETS	0.915	0.849	0.983	1	0.992	1	CLONAL	2	TRUE	1	0.37	2		502	511	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533939	63533940	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs771001164	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	61	435	1	ENST00000307078.5:c.1214_1215del	p.Glu405GlyfsTer56	p.E405Gfs*56	ENST00000307078	NM_004655.3	405	gAG/g	6/11	1	2	FACETS	0.717	0.62	0.822	0.717	0.62	0.822	SUBCLONAL	1	TRUE	1	0.37	2		436	460	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626843	14626843	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377564300	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	130	782	0	ENST00000254322.2:c.932G>A	p.Arg311His	p.R311H	ENST00000254322	NM_006145.1	311	cGt/cAt	3/3	1	2	FACETS	0.876	0.795	0.962	0.876	0.795	0.962	CLONAL	1	TRUE	1	0.37	2		782	802	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295797	15295797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1166093165	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	190	930	0	ENST00000263388.2:c.2330C>T	p.Pro777Leu	p.P777L	ENST00000263388	NM_000435.2	777	cCg/cTg	15/33	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.37	2		930	917	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302604	15302604	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115836330	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	143	899	1	ENST00000263388.2:c.754G>A	p.Val252Met	p.V252M	ENST00000263388	NM_000435.2	252	Gtg/Atg	5/33	1	2	FACETS	0.873	0.796	0.955	0.873	0.796	0.955	CLONAL	1	TRUE	1	0.37	2		900	885	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350333	15350333	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	26	595	0	ENST00000263377.2:c.3446G>T	p.Arg1149Leu	p.R1149L	ENST00000263377	NM_058243.2	1149	cGg/cTg	17/20	1	2	FACETS	0.318	0.251	0.395	0.318	0.251	0.395	SUBCLONAL	1	TRUE	1	0.37	2		595	442	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384941	17384941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	177	884	0	ENST00000359435.4:c.491G>A	p.Arg164His	p.R164H	ENST00000359435	NM_001033549.1	164	cGc/cAc	5/9	1	2	FACETS	0.989	0.911	1	0.989	0.911	1	CLONAL	1	TRUE	1	0.37	2		884	967	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951140	17951140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	116	662	0	ENST00000458235.1:c.1153G>A	p.Ala385Thr	p.A385T	ENST00000458235	NM_000215.3	385	Gcc/Acc	9/24	1	2	FACETS	0.876	0.79	0.966	0.876	0.79	0.966	CLONAL	1	TRUE	1	0.37	2		662	716	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968288	18968288	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776533487	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	129	897	0	ENST00000262803.5:c.2128G>A	p.Ala710Thr	p.A710T	ENST00000262803	NM_002911.3	710	Gcc/Acc	15/24	1	2	FACETS	0.917	0.833	1	0.917	0.833	1	CLONAL	1	TRUE	1	0.37	2		897	760	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314561	30314561	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	121	578	0	ENST00000262643.3:c.1111-1G>A		p.X371_splice	ENST00000262643	NM_001238.2	371			1	2	FACETS	0.947	0.856	1	0.947	0.856	1	CLONAL	1	TRUE	1	0.37	2		578	691	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228998	36228998	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	157	800	1	ENST00000222270.7:c.7778G>A	p.Arg2593His	p.R2593H	ENST00000222270	NM_014727.1	2593	cGc/cAc	36/37	1	2	FACETS	0.926	0.849	1	0.926	0.849	1	CLONAL	1	TRUE	1	0.37	2		801	916	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383182	42383182	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782657641	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	145	766	4	ENST00000221972.3:c.202C>T	p.Arg68Cys	p.R68C	ENST00000221972	NM_021601.3	68	Cgc/Tgc	2/5	1	2	FACETS	0.981	0.896	1	0.981	0.896	1	CLONAL	1	TRUE	1	0.37	2		770	799	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009132	27009132	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1319855787	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	30	137	0	ENST00000335756.4:c.72del	p.Gly25AlafsTer9	p.G25Afs*9	ENST00000335756	NM_001809.3	23	aCc/ac	1/5	1	2	FACETS	0.927	0.754	1	0.927	0.754	1	CLONAL	1	TRUE	1	0.37	2		137	175	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213243	39213243	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	172	881	6	ENST00000402219.2:c.3724del	p.Ser1242ValfsTer37	p.S1242Vfs*37	ENST00000402219	NM_005633.3	1242	Agt/gt	23/23	1	2	FACETS	0.961	0.884	1	0.961	0.884	1	CLONAL	1	TRUE	1	0.37	2		887	967	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630498	47630498	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	123	772	0	ENST00000233146.2:c.169del	p.Val57CysfsTer7	p.V57Cfs*7	ENST00000233146	NM_000251.2	56	gaG/ga	1/16	1	2	FACETS	0.879	0.796	0.968	0.879	0.796	0.968	CLONAL	1	TRUE	1	0.37	2		772	756	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594104	158594104	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554387941	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	75	382	0	ENST00000263640.3:c.1469G>A	p.Arg490His	p.R490H	ENST00000263640	NM_001105.4	490	cGt/cAt	11/11	1	2	FACETS	0.798	0.701	0.902	0.798	0.701	0.902	CLONAL	1	TRUE	1	0.37	2		382	508	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483981	212483981	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	24	429	0	ENST00000342788.4:c.2222del	p.Gly741GlufsTer4	p.G741Efs*4	ENST00000342788	NM_005235.2	741	gGa/ga	19/28	1	2	FACETS	0.305	0.239	0.382	0.305	0.239	0.382	SUBCLONAL	1	TRUE	1	0.37	2		429	425	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375133	31375133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	117	862	0	ENST00000328111.2:c.530C>T	p.Thr177Ile	p.T177I	ENST00000328111	NM_006892.3	177	aCa/aTa	6/23	0.08133666572316	0	FACETS	0.506	0.456	0.558			1	INDETERMINATE	1	TRUE	0	0.37	0		862	788	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031202	36031202	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202242810	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	144	755	0	ENST00000358208.4:c.1321C>T	p.Arg441Cys	p.R441C	ENST00000358208		441	Cgc/Tgc	11/12	0.08133666572316	0	FACETS	0.61	0.556	0.666			1	INDETERMINATE	1	TRUE	0	0.37	0		755	804	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980756	40980756	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	98	512	1	ENST00000373198.4:c.1730del	p.Pro577LeufsTer24	p.P577Lfs*24	ENST00000373198	NM_133170.3	577	cCt/ct	10/32	0.08133666572316	0	FACETS	0.575	0.514	0.64			1	INDETERMINATE	1	TRUE	0	0.37	0		513	580	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306584	41306584	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	100	747	1	ENST00000373198.4:c.1075C>T	p.Arg359Ter	p.R359*	ENST00000373198	NM_133170.3	359	Cga/Tga	7/32	0.08133666572316	0	FACETS	0.507	0.453	0.564			1	INDETERMINATE	1	TRUE	0	0.37	0		748	672	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713246	30713246	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56105708	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	42	382	0	ENST00000295754.5:c.571G>A	p.Val191Ile	p.V191I	ENST00000295754	NM_003242.5	191	Gtt/Att	4/7	1	2	FACETS	0.55	0.459	0.65	0.55	0.459	0.65	SUBCLONAL	1	TRUE	1	0.37	2		382	413	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125763	47125763	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144171734	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	77	337	0	ENST00000409792.3:c.5507C>T	p.Pro1836Leu	p.P1836L	ENST00000409792	NM_014159.6	1836	cCg/cTg	12/21	1	2	FACETS	0.919	0.81	1	0.919	0.81	1	CLONAL	1	TRUE	1	0.37	2		337	453	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430546	181430546	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	93	589	0	ENST00000325404.1:c.402del	p.Gly135AlafsTer19	p.G135Afs*19	ENST00000325404	NM_003106.3	133	gCc/gc	1/1	1	2	FACETS	0.934	0.833	1	0.934	0.833	1	CLONAL	1	TRUE	1	0.37	2		589	538	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1976716	1976717	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	70	687	0	ENST00000382891.5:c.3501_3502del	p.Cys1167Ter	p.C1167*	ENST00000382891	NM_133335.3	1167	TGt/t	19/22	1	2	FACETS	0.493	0.429	0.563	0.493	0.429	0.563	SUBCLONAL	1	TRUE	1	0.37	2		687	767	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971073	55971073	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs754856383	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	63	499	0	ENST00000263923.4:c.1724G>T	p.Arg575Ile	p.R575I	ENST00000263923	NM_002253.2	575	aGa/aTa	13/30	1	2	FACETS	0.572	0.495	0.656	0.572	0.495	0.656	SUBCLONAL	1	TRUE	1	0.37	2		499	595	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244091	153244091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	111	483	0	ENST00000281708.4:c.2066G>A	p.Arg689Gln	p.R689Q	ENST00000281708	NM_033632.3	689	cGg/cAg	12/12	1	2	FACETS	0.972	0.876	1	0.972	0.876	1	CLONAL	1	TRUE	1	0.37	2		483	617	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538244	187538244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746286358	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	107	575	0	ENST00000441802.2:c.8990C>T	p.Thr2997Met	p.T2997M	ENST00000441802	NM_005245.3	2997	aCg/aTg	11/27	1	2	FACETS	0.883	0.793	0.978	0.883	0.793	0.978	CLONAL	1	TRUE	1	0.37	2		575	655	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627747	187627747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143694311	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	89	412	0	ENST00000441802.2:c.3235G>A	p.Val1079Ile	p.V1079I	ENST00000441802	NM_005245.3	1079	Gtt/Att	2/27	1	2	FACETS	0.873	0.776	0.976	0.873	0.776	0.976	CLONAL	1	TRUE	1	0.37	2		412	551	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1255456	1255456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374968697	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	129	712	0	ENST00000310581.5:c.3103G>A	p.Val1035Ile	p.V1035I	ENST00000310581	NM_198253.2	1035	Gtc/Atc	14/16	1	2	FACETS	0.97	0.88	1	0.97	0.88	1	CLONAL	1	TRUE	1	0.37	2		712	719	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168713	56168713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483289809	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	83	386	0	ENST00000399503.3:c.1567G>A	p.Val523Ile	p.V523I	ENST00000399503	NM_005921.1	523	Gta/Ata	9/20	1	2	FACETS	0.835	0.739	0.938	0.835	0.739	0.938	CLONAL	1	TRUE	1	0.37	2		386	537	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629102	86629102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	63	288	0	ENST00000274376.6:c.847C>T	p.Arg283Cys	p.R283C	ENST00000274376	NM_002890.2	283	Cgt/Tgt	4/25	1	2	FACETS	0.918	0.798	1	0.918	0.798	1	CLONAL	1	TRUE	1	0.37	2		288	371	SUCCESS
APC	324	MSKCC	GRCh37	5	112178804	112178804	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	69	477	0	ENST00000257430.4:c.7513C>T	p.Arg2505Ter	p.R2505*	ENST00000257430	NM_000038.5	2505	Cga/Tga	16/16	1	2	FACETS	0.923	0.808	1	0.923	0.808	1	CLONAL	1	TRUE	1	0.37	2		477	404	SUCCESS
APC	324	MSKCC	GRCh37	5	112179789	112179789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587779810	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	42	298	0	ENST00000257430.4:c.8498G>A	p.Arg2833His	p.R2833H	ENST00000257430	NM_000038.5	2833	cGc/cAc	16/16	1	2	FACETS	0.666	0.558	0.785	0.666	0.558	0.785	SUBCLONAL	1	TRUE	1	0.37	2		298	341	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519731	176519731	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1348650129	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	123	834	1	ENST00000292408.4:c.1003G>A	p.Ala335Thr	p.A335T	ENST00000292408	NM_213647.1	335	Gca/Aca	8/18	1	2	FACETS	0.988	0.895	1	0.988	0.895	1	CLONAL	1	TRUE	1	0.37	2		835	673	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638884	176638884	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765811504	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	129	662	0	ENST00000439151.2:c.3484C>T	p.Arg1162Cys	p.R1162C	ENST00000439151	NM_022455.4	1162	Cgt/Tgt	5/23	1	2	FACETS	0.891	0.808	0.978	0.891	0.808	0.978	CLONAL	1	TRUE	1	0.37	2		662	783	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045918	180045920	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CTC	CTC	-	rs746341092	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	48	475	0	ENST00000261937.6:c.2851_2853del	p.Glu951del	p.E951del	ENST00000261937	NM_182925.4	951	GAG/-	21/30	1	2	FACETS	0.652	0.552	0.761	0.652	0.552	0.761	SUBCLONAL	1	TRUE	1	0.37	2		475	398	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047959	180047959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs933223149	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	131	880	1	ENST00000261937.6:c.2216G>A	p.Arg739His	p.R739H	ENST00000261937	NM_182925.4	739	cGc/cAc	15/30	1	2	FACETS	0.876	0.795	0.961	0.876	0.795	0.961	CLONAL	1	TRUE	1	0.37	2		881	808	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798105	32798105	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1562326716	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	80	810	0	ENST00000374899.4:c.1574del	p.Gly525AspfsTer36	p.G525Dfs*36	ENST00000374899	NM_018833.2	525	gGa/ga	9/12	1	2	FACETS	0.516	0.453	0.584	0.516	0.453	0.584	SUBCLONAL	1	TRUE	1	0.37	2		810	838	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	112	816	7	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	0.714	0.642	0.791	0.714	0.642	0.791	SUBCLONAL	1	TRUE	1	0.37	2		823	848	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32806009	32806009	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1397817921	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	106	708	0	ENST00000374899.4:c.2T>C	p.Met1?	p.M1?	ENST00000374899	NM_018833.2	1	aTg/aCg	2/12	1	2	FACETS	0.834	0.748	0.925	0.834	0.748	0.925	CLONAL	1	TRUE	1	0.37	2		708	687	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651936	36651936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748554042	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	135	708	1	ENST00000244741.5:c.58C>T	p.Arg20Cys	p.R20C	ENST00000244741	NM_000389.4	20	Cgc/Tgc	2/3	1	2	FACETS	0.949	0.863	1	0.949	0.863	1	CLONAL	1	TRUE	1	0.37	2		709	769	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983028	111983028	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	144	731	0	ENST00000368678.4:c.1519C>T	p.Arg507Cys	p.R507C	ENST00000368678		507	Cgc/Tgc	13/13	1	2	FACETS	0.931	0.849	1	0.931	0.849	1	CLONAL	1	TRUE	1	0.37	2		731	836	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041169	112041169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766059845	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	103	537	2	ENST00000368678.4:c.86G>A	p.Arg29His	p.R29H	ENST00000368678		29	cGc/cAc	3/13	1	2	FACETS	0.95	0.852	1	0.95	0.852	1	CLONAL	1	TRUE	1	0.37	2		539	586	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150022919	150022919	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	74	333	0	ENST00000253339.5:c.344A>G	p.Asp115Gly	p.D115G	ENST00000253339		115	gAt/gGt	1/7	1	2	FACETS	0.889	0.781	1	0.889	0.781	1	CLONAL	1	TRUE	1	0.37	2		333	450	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962298	2962298	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769577430	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	191	786	2	ENST00000396946.4:c.2239G>A	p.Val747Ile	p.V747I	ENST00000396946	NM_032415.4	747	Gtc/Atc	17/25	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.37	2		788	839	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6027156	6027157	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs267608159	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	14	13	0	ENST00000265849.7:c.1239dup	p.Asp414ArgfsTer44	p.D414Rfs*44	ENST00000265849	NM_000535.5	413	-/A	11/15	1	2	FACETS	0.772	0.578	0.988	1	0.899	1	CLONAL	2	TRUE	1	0.37	2		13	49	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431665	6431665	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	142	774	0	ENST00000356142.4:c.218C>T	p.Pro73Leu	p.P73L	ENST00000356142	NM_018890.3	73	cCg/cTg	3/7	1	2	FACETS	0.768	0.699	0.841	0.768	0.699	0.841	SUBCLONAL	1	TRUE	1	0.37	2		774	999	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468251	50468251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548117828	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	108	686	0	ENST00000331340.3:c.1486G>A	p.Gly496Ser	p.G496S	ENST00000331340	NM_006060.4	496	Ggc/Agc	8/8	1	2	FACETS	0.948	0.852	1	0.948	0.852	1	CLONAL	1	TRUE	1	0.37	2		686	616	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221719	55221719	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs776490661	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	81	480	1	ENST00000275493.2:c.763C>T	p.Arg255Ter	p.R255*	ENST00000275493	NM_005228.3	255	Cga/Tga	7/28	1	2	FACETS	0.96	0.849	1	0.96	0.849	1	CLONAL	1	TRUE	1	0.37	2		481	456	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55272981	55272981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	113	600	0	ENST00000275493.2:c.3304G>A	p.Ala1102Thr	p.A1102T	ENST00000275493	NM_005228.3	1102	Gct/Act	28/28	1	2	FACETS	0.883	0.795	0.975	0.883	0.795	0.975	CLONAL	1	TRUE	1	0.37	2		600	692	SUCCESS
MET	4233	MSKCC	GRCh37	7	116409799	116409799	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199502137	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	51	293	0	ENST00000397752.3:c.2684C>T	p.Thr895Met	p.T895M	ENST00000397752	NM_000245.2	895	aCg/aTg	12/21	1	2	FACETS	0.851	0.727	0.985	0.851	0.727	0.985	CLONAL	1	TRUE	1	0.37	2		293	324	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151181886	151181886	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	72	286	0	ENST00000262187.5:c.129del	p.Phe43LeufsTer4	p.F43Lfs*4	ENST00000262187	NM_005614.3	43	ttT/tt	3/8	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.37	2		286	374	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38283643	38283643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs186746130	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	74	458	0	ENST00000425967.3:c.835G>A	p.Val279Met	p.V279M	ENST00000425967	NM_001174067.1	279	Gtg/Atg	7/19	1	2	FACETS	0.794	0.696	0.898	0.794	0.696	0.898	SUBCLONAL	1	TRUE	1	0.37	2		458	504	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521481	8521481	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760428875	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	153	577	0	ENST00000356435.5:c.757G>A	p.Val253Ile	p.V253I	ENST00000356435		253	Gtt/Att	9/35	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.37	2		577	805	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570404	87570404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	130	776	0	ENST00000277120.3:c.2144G>A	p.Arg715Gln	p.R715Q	ENST00000277120		715	cGg/cAg	17/19	1	2	FACETS	0.826	0.749	0.907	0.826	0.749	0.907	CLONAL	1	TRUE	1	0.37	2		776	851	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624511	93624511	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	25	410	0	ENST00000375746.1:c.602G>A	p.Gly201Asp	p.G201D	ENST00000375746	NM_001174167.1	201	gGc/gAc	4/14	1	2	FACETS	0.337	0.265	0.42	0.337	0.265	0.42	SUBCLONAL	1	TRUE	1	0.37	2		410	401	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314918	1314920	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	74	508	0	ENST00000400841.2:c.741_743del	p.Leu249del	p.L249del	ENST00000400841		247	ctCCTt/ctt	6/6	1	2	FACETS	0.755	0.662	0.854	0.755	0.662	0.854	SUBCLONAL	1	TRUE	1	0.37	2		508	530	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918695	44918695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746746824	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	80	397	1	ENST00000377967.4:c.1178G>A	p.Arg393Gln	p.R393Q	ENST00000377967	NM_021140.2	393	cGa/cAa	12/29	1	2	FACETS	0.801	0.706	0.902	0.801	0.706	0.902	CLONAL	1	TRUE	1	0.37	2		398	540	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44921908	44921908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778421870	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	95	398	0	ENST00000377967.4:c.1442G>A	p.Arg481His	p.R481H	ENST00000377967	NM_021140.2	481	cGc/cAc	15/29	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.37	2		398	483	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351422	70351422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	127	656	0	ENST00000374080.3:c.4070G>A	p.Arg1357His	p.R1357H	ENST00000374080		1357	cGc/cAc	29/45	1	2	FACETS	0.913	0.828	1	0.913	0.828	1	CLONAL	1	TRUE	1	0.37	2		656	752	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937602	76937603	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	42	363	0	ENST00000373344.5:c.3145dup	p.Ile1049AsnfsTer4	p.I1049Nfs*4	ENST00000373344	NM_000489.3	1049	ata/aAta	9/35	1	2	FACETS	0.676	0.566	0.797	0.676	0.566	0.797	SUBCLONAL	1	TRUE	1	0.37	2		363	336	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191783	123191783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	72	432	0	ENST00000218089.9:c.1372G>A	p.Ala458Thr	p.A458T	ENST00000218089	NM_001042749.1	458	Gcc/Acc	15/35	1	2	FACETS	0.732	0.64	0.83	0.732	0.64	0.83	SUBCLONAL	1	TRUE	1	0.37	2		432	532	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0044646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	175	667	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.263728710910687	3	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	1	0.322781291880069	3		667	615	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752965	128752965	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	72	439	0	ENST00000377970.2:c.1126G>C	p.Val376Leu	p.V376L	ENST00000377970	NM_002467.4	376	Gtc/Ctc	3/3	1	2	FACETS	0.694	0.606	0.788	0.694	0.606	0.788	SUBCLONAL	1	TRUE	1	0.322781291880069	2		439	643	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481442	40481442	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1290480970	NA	P-0044646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	102	502	1	ENST00000264657.5:c.1267C>T	p.Arg423Ter	p.R423*	ENST00000264657	NM_139276.2	423	Cga/Tga	14/24	0.23404196710582	3	FACETS	1	0.907	1	0.508	0.454	0.565	CLONAL	1	TRUE	1	0.322781291880069	3		503	723	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437901	52437901	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	121	821	0	ENST00000460680.1:c.1260del	p.Lys421ArgfsTer9	p.K421Rfs*9	ENST00000460680	NM_004656.3	420	ggG/gg	13/17	0.322781291880069	2	FACETS	0.918	0.829	1	0.459	0.414	0.506	CLONAL	1	TRUE	0	0.322781291880069	2		821	817	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106584	27106586	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	novel	NA	P-0044646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	118	720	0	ENST00000324856.7:c.6197_6199del	p.Asn2066del	p.N2066del	ENST00000324856	NM_006015.4	2065	gcCAAc/gcc	20/20	1	2	FACETS	0.861	0.777	0.951	0.861	0.777	0.951	CLONAL	1	TRUE	1	0.322781291880069	2		720	849	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	111	348	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.360907638820787	2		349	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	207	510	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.211132033580566	2	FACETS	1	0.989	1	0.684	0.636	0.734	INDETERMINATE	1	TRUE	0	0.360907638820787	2		510	838	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81954830	81954830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758623675	NA	P-0044694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	97	451	0	ENST00000359376.3:c.2263G>A	p.Val755Ile	p.V755I	ENST00000359376	NM_002661.3	755	Gtc/Atc	21/33	0.230967990398186	1	FACETS	0.643	0.574	0.717	0.643	0.574	0.717	SUBCLONAL	1	TRUE	0	0.360907638820787	1		451	685	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923045	44923048	+	frameshift_variant	Frame_Shift_Del	DEL	CTAT	CTAT	-	rs398122969	NA	P-0044694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	100	417	0	ENST00000377967.4:c.1909_1912del	p.Ser637ThrfsTer53	p.S637Tfs*53	ENST00000377967	NM_021140.2	636	CTATct/ct	16/29	0.360907638820787	1	FACETS	0.608	0.543	0.677	0.608	0.543	0.677	SUBCLONAL	1	TRUE	0	0.360907638820787	1		417	747	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981764	201981768	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCAGA	CCAGA	-	novel	NA	P-0044694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	126	557	0	ENST00000359651.3:c.479_483del		p.X160_splice	ENST00000359651		160		4/8	1	2	FACETS	0.718	0.649	0.79	0.718	0.649	0.79	SUBCLONAL	1	TRUE	1	0.360907638820787	2		557	973	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984373	201984374	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCC	novel	NA	P-0044694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	181	533	0	ENST00000359651.3:c.1042_1045dup	p.Arg349ProfsTer123	p.R349Pfs*123	ENST00000359651		346	-/GGCC	8/8	1	2	FACETS	0.992	0.915	1	0.992	0.915	1	CLONAL	1	TRUE	1	0.360907638820787	2		533	1011	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732609	190732610	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GATCCTCGTCTTACAGCGAATG	novel	NA	P-0044694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	48	286	0	ENST00000441310.2:c.2429_2450dup	p.Phe818SerfsTer20	p.F818Sfs*20	ENST00000441310	NM_000534.4	809	-/GATCCTCGTCTTACAGCGAATG	11/13	1	2	FACETS	0.47	0.397	0.551	0.47	0.397	0.551	SUBCLONAL	1	TRUE	1	0.360907638820787	2		286	566	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735464	40735464	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	59	536	0	ENST00000373198.4:c.3409G>C	p.Glu1137Gln	p.E1137Q	ENST00000373198	NM_133170.3	1137	Gag/Cag	25/32	0.211132033580566	2	FACETS	0.375	0.322	0.434	0.188	0.161	0.217	INDETERMINATE	1	TRUE	0	0.360907638820787	2		536	871	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911182	29911182	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765672807	NA	P-0044694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	35	203	2	ENST00000376809.5:c.481G>A	p.Asp161Asn	p.D161N	ENST00000376809	NM_002116.7	161	Gac/Aac	3/8	1	2	FACETS	0.655	0.539	0.785	0.655	0.539	0.785	SUBCLONAL	1	TRUE	1	0.360907638820787	2		205	296	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802682	135802682	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	62	203	0	ENST00000298552.3:c.116del	p.Pro39LeufsTer4	p.P39Lfs*4	ENST00000298552	NM_001162426.1	39	cCt/ct	4/23	0.360907638820787	1	FACETS	0.751	0.652	0.858	0.751	0.652	0.858	SUBCLONAL	1	TRUE	0	0.360907638820787	1		203	375	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528170	157528170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1466725801	NA	P-0044698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	106	459	2	ENST00000346085.5:c.5895G>A	p.Met1965Ile	p.M1965I	ENST00000346085	NM_020732.3	1965	atG/atA	20/20	0.323911608751994	3	FACETS	0.924	0.831	1	0.462	0.415	0.511	INDETERMINATE	1	TRUE	1	0.548710293720439	3		461	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0044737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	492	621	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.553737700806759	3	FACETS	1	0.995	1	0.812	0.784	0.84	CLONAL	2	TRUE	0	0.639365572378461	3		622	834	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0044737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	232	332	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	0.639365572378461	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	2	0.639365572378461	4		332	572	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830958	72830958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393698686	NA	P-0044737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	243	531	0	ENST00000268489.5:c.5623G>A	p.Glu1875Lys	p.E1875K	ENST00000268489	NM_006885.3	1875	Gaa/Aaa	9/10	0.639365572378461	3	FACETS	0.886	0.835	0.937	0.886	0.835	0.937	CLONAL	2	TRUE	1	0.639365572378461	3		531	566	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363442	40363442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775579460	NA	P-0044737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	161	685	0	ENST00000397332.2:c.787C>T	p.Pro263Ser	p.P263S	ENST00000397332	NM_001033082.2	263	Ccc/Tcc	3/3	0.426848893963896	4	FACETS	0.89	0.816	0.967	0.297	0.272	0.323	CLONAL	1	TRUE	1	0.639365572378461	4		685	928	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7168097	7168097	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1215683348	NA	P-0044737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	37	410	1	ENST00000302850.5:c.1492G>T	p.Glu498Ter	p.E498*	ENST00000302850	NM_000208.2	498	Gag/Tag	7/22	0.639365572378461	3	FACETS	0.252	0.207	0.303	0.126	0.103	0.152	SUBCLONAL	1	TRUE	1	0.639365572378461	3		411	606	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141564	11141564	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	400	692	0	ENST00000358026.2:c.3541C>T	p.His1181Tyr	p.H1181Y	ENST00000358026	NM_001128849.1	1181	Cac/Tac	25/36	0.639365572378461	3	FACETS	0.882	0.842	0.922	0.882	0.842	0.922	CLONAL	2	TRUE	1	0.639365572378461	3		692	936	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056200	26056200	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1334949972	NA	P-0044737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	251	468	0	ENST00000343677.2:c.457A>G	p.Lys153Glu	p.K153E	ENST00000343677	NM_005319.3	153	Aaa/Gaa	1/1	0.639365572378461	6	FACETS	0.802	0.749	0.855	0.401	0.374	0.428	CLONAL	2	TRUE	2	0.639365572378461	6		468	1116	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183060	32183060	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1234	267	904	0	ENST00000375023.3:c.1964G>T	p.Ser655Ile	p.S655I	ENST00000375023	NM_004557.3	655	aGc/aTc	12/30	0.639365572378461	6	FACETS	1	0.989	1	0.317	0.296	0.339	CLONAL	1	TRUE	2	0.639365572378461	6		904	1501	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0044755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	58	490	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	0.835	0.717	0.965	0.835	0.717	0.965	CLONAL	1	TRUE	1	0.202138498546338	2		490	687	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581178	48581179	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0044755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	50	294	0	ENST00000342988.3:c.485_486dup	p.Val163MetfsTer40	p.V163Mfs*40	ENST00000342988	NM_005359.5	161	gaa/gaATa	5/12	0.202138498546338	1	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	0	0.202138498546338	1		294	412	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0044762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	12	667	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.243017605808503	6	FACETS	1	0.779	1	0.282	0.199	0.383	CLONAL	1	FALSE	2	0.243017605808503	6		667	130	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566718	212566718	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	14	233	0	ENST00000342788.4:c.1463G>T	p.Arg488Leu	p.R488L	ENST00000342788	NM_005235.2	488	cGg/cTg	12/28	0.198356515789184	3	FACETS	0.867	0.63	1	0.434	0.315	0.576	CLONAL	1	FALSE	1	0.243017605808503	3		233	149	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1131691035	NA	P-0044762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	82	714	0	ENST00000269305.4:c.592del	p.Glu198LysfsTer49	p.E198Kfs*49	ENST00000269305	NM_001126112.2	198	Gaa/aa	6/11	0.198356515789184	3	FACETS	1	0.95	1	0.573	0.506	0.646	CLONAL	1	FALSE	1	0.243017605808503	3		714	660	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0044762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	84	513	0	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	0.211744566882886	4	FACETS	0.817	0.723	0.917	0.817	0.723	0.917	CLONAL	2	FALSE	2	0.243017605808503	4		513	526	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267359	198267359	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs377023736	NA	P-0044762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	46	428	0	ENST00000335508.6:c.1998G>T	p.Lys666Asn	p.K666N	ENST00000335508	NM_012433.2	666	aaG/aaT	14/25	0.198356515789184	3	FACETS	1	0.854	1	0.507	0.427	0.594	CLONAL	1	FALSE	1	0.243017605808503	3		428	419	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687259	117687259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	19	252	0	ENST00000368508.3:c.2792C>T	p.Thr931Ile	p.T931I	ENST00000368508	NM_002944.2	931	aCa/aTa	18/43	0.243017605808503	1	FACETS	0.904	0.692	1	0.904	0.692	1	CLONAL	1	FALSE	0	0.243017605808503	1		252	152	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112892398	112892398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143433437	NA	P-0044762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	32	456	0	ENST00000351677.2:c.556C>T	p.Arg186Trp	p.R186W	ENST00000351677	NM_002834.3	186	Cgg/Tgg	5/16	0.211744566882886	4	FACETS	1	0.866	1	0.54	0.44	0.653	CLONAL	1	FALSE	2	0.243017605808503	4		456	303	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602367	10602367	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	136	1001	2	ENST00000171111.5:c.1211C>A	p.Ser404Ter	p.S404*	ENST00000171111	NM_203500.1	404	tCg/tAg	3/6	0.158640829486815	2	FACETS	1	0.978	1	0.62	0.564	0.68	CLONAL	1	FALSE	0	0.243017605808503	2		1003	902	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294685	1294685	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	36	508	0	ENST00000310581.5:c.316G>T	p.Gly106Trp	p.G106W	ENST00000310581	NM_198253.2	106	Ggg/Tgg	2/16	1	2	FACETS	0.433	0.355	0.521	0.433	0.355	0.521	SUBCLONAL	1	FALSE	1	0.243017605808503	2		508	684	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741828	162741828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	68	365	0	ENST00000367921.3:c.1519G>A	p.Val507Met	p.V507M	ENST00000367921	NM_006182.2	507	Gtg/Atg	13/18	0.169771039920461	4	FACETS	1	0.956	1			1	CLONAL	1	FALSE	NA	0.243017605808503	4		365	563	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81534626	81534626	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	21	358	2	ENST00000298171.2:c.271C>A	p.Gln91Lys	p.Q91K	ENST00000298171	NM_000369.2	91	Cag/Aag	3/10	0.177931227303662	4	FACETS	1	0.899	1	0.663	0.515	0.833	CLONAL	1	FALSE	2	0.243017605808503	4		360	162	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326556	62326556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	116	880	0	ENST00000360203.5:c.3481C>T	p.His1161Tyr	p.H1161Y	ENST00000360203	NM_001283009.1	1161	Cac/Tac	33/35	0.211744566882886	4	FACETS	1	0.97	1	0.599	0.539	0.663	CLONAL	1	FALSE	2	0.243017605808503	4		880	991	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955908	55955908	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs761483205	NA	P-0044762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	39	414	0	ENST00000263923.4:c.3254A>G	p.Gln1085Arg	p.Q1085R	ENST00000263923	NM_002253.2	1085	cAg/cGg	24/30	0.243017605808503	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	FALSE	0	0.243017605808503	1		414	240	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984794	55984794	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	38	487	0	ENST00000263923.4:c.335C>A	p.Ser112Ter	p.S112*	ENST00000263923	NM_002253.2	112	tCg/tAg	3/30	0.243017605808503	1	FACETS	0.964	0.801	1	0.964	0.801	1	CLONAL	1	FALSE	0	0.243017605808503	1		487	285	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629182	187629182	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	50	564	0	ENST00000441802.2:c.1800G>T	p.Gln600His	p.Q600H	ENST00000441802	NM_005245.3	600	caG/caT	2/27	0.198356515789184	3	FACETS	1	0.943	1	0.617	0.525	0.717	CLONAL	1	FALSE	1	0.243017605808503	3		564	374	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509583	106509583	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs749714535	NA	P-0044762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	68	528	0	ENST00000359195.3:c.1577C>G	p.Pro526Arg	p.P526R	ENST00000359195	NM_002649.2	526	cCg/cGg	2/11	0.198356515789184	3	FACETS	0.952	0.828	1	0.476	0.414	0.544	CLONAL	1	FALSE	1	0.243017605808503	3		528	659	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413217	139413217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	135	935	1	ENST00000277541.6:c.925G>A	p.Gly309Ser	p.G309S	ENST00000277541	NM_017617.3	309	Ggc/Agc	6/34	0.243017605808503	4	FACETS	1	0.982	1	0.447	0.405	0.49	CLONAL	1	FALSE	1	0.243017605808503	4		936	1031	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0044765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	322	766	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.355132817759517	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.355132817759517	2		767	865	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0044765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	177	444	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.334043181217413	3	FACETS	0.964	0.9	1	0.964	0.9	1	CLONAL	3	TRUE	0	0.355132817759517	3		444	406	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440713	56440713	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	247	555	0	ENST00000407977.2:c.505G>C	p.Ala169Pro	p.A169P	ENST00000407977		169	Gct/Cct	5/10	0.355132817759517	2	FACETS	0.988	0.928	1	0.988	0.928	1	CLONAL	2	TRUE	0	0.355132817759517	2		555	704	SUCCESS
ATR	545	MSKCC	GRCh37	3	142172076	142172076	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0044765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	26	302	0	ENST00000350721.4:c.7656-1G>A		p.X2552_splice	ENST00000350721	NM_001184.3	2552			0.355132817759517	3	FACETS	0.435	0.344	0.54	0.218	0.172	0.27	SUBCLONAL	1	TRUE	1	0.355132817759517	3		302	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0044792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	1230	600	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.839769909143338	6	FACETS	0.976	0.967	0.984	0.976	0.967	0.984	CLONAL	6	TRUE	0	0.910435415917049	6		601	1302	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0044792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	255	697	1	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	0.641513339214188	4	FACETS	1	0.988	1	0.405	0.38	0.431	CLONAL	1	TRUE	1	0.910435415917049	4		698	880	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056238	27056238	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	575	590	0	ENST00000324856.7:c.1234C>T	p.Gln412Ter	p.Q412*	ENST00000324856	NM_006015.4	412	Cag/Tag	2/20	0.810868827060488	4	FACETS	0.934	0.918	0.949	0.934	0.918	0.949	CLONAL	4	TRUE	0	0.910435415917049	4		590	646	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165579	185165580	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TTAAAGTG	novel	NA	P-0044792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	28	237	0	ENST00000265026.3:c.856_857insAAAGTGTT	p.Leu286Ter	p.L286*	ENST00000265026	NM_004721.4	285	gtt/gtTTAAAGTGt	5/14	0.910435415917049	7	FACETS	0.659	0.527	0.808	0.132	0.105	0.162	SUBCLONAL	1	TRUE	2	0.910435415917049	7		237	306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578252	7578270	+	frameshift_variant	Frame_Shift_Del	DEL	TCCTTCCACTCGGATAAGA	TCCTTCCACTCGGATAAGA	-	novel	NA	P-0044843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	357	829	0	ENST00000269305.4:c.579_597del	p.His193GlnfsTer48	p.H193Qfs*48	ENST00000269305	NM_001126112.2	193	caTCTTATCCGAGTGGAAGGA/ca	6/11	0.604529674240378	3	FACETS	0.924	0.889	0.957	0.924	0.889	0.957	CLONAL	3	TRUE	0	0.626808403862759	3		829	540	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942091	17942091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745535201	NA	P-0044843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	142	960	1	ENST00000458235.1:c.2924C>T	p.Pro975Leu	p.P975L	ENST00000458235	NM_000215.3	975	cCg/cTg	21/24	0.626808403862759	5	FACETS	0.853	0.777	0.934	0.284	0.259	0.312	CLONAL	1	TRUE	2	0.626808403862759	5		961	1030	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0044850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	93	365	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	0.57	0.508	0.636	0.57	0.508	0.636	SUBCLONAL	1	TRUE	1	0.607583902505537	2		365	537	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0044850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	64	468	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.398	0.345	0.456	0.398	0.345	0.456	SUBCLONAL	1	TRUE	1	0.607583902505537	2		468	529	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690805	89690805	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1554897856	NA	P-0044850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	30	293	2	ENST00000371953.3:c.212G>T	p.Cys71Phe	p.C71F	ENST00000371953	NM_000314.4	71	tGt/tTt	4/9	1	2	FACETS	0.276	0.222	0.337	0.276	0.222	0.337	SUBCLONAL	1	TRUE	1	0.607583902505537	2		295	358	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371799	55371820	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCCGCGCTGGGCCCCGAG	GGCGGCCGCGCTGGGCCCCGAG	-	novel	NA	P-0044850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	107	223	0	ENST00000297316.4:c.499_520del	p.Leu167TrpfsTer213	p.L167Wfs*213	ENST00000297316	NM_022454.3	163	caGGCGGCCGCGCTGGGCCCCGAG/ca	2/2	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.607583902505537	2		223	325	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720682	89720728	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTCATACCAGGACCAGAGGAAACCTCAGAAAAAGTAGAAAATGGA	TCTTCATACCAGGACCAGAGGAAACCTCAGAAAAAGTAGAAAATGGA	-	novel	NA	P-0044850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	25	280	0	ENST00000371953.3:c.833_879del	p.Phe278Ter	p.F278*	ENST00000371953	NM_000314.4	278	tTCTTCATACCAGGACCAGAGGAAACCTCAGAAAAAGTAGAAAATGGA/t	8/9	1	2	FACETS	0.218	0.172	0.272	0.218	0.172	0.272	SUBCLONAL	1	TRUE	1	0.607583902505537	2		280	377	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591053	67591054	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAAGAAGCA	novel	NA	P-0044850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	38	247	0	ENST00000274335.5:c.1648_1656dup	p.Lys550_Gln552dup	p.K550_Q552dup	ENST00000274335		550	ttg/ttGAAGAAGCAg	12/15	1	2	FACETS	0.333	0.275	0.397	0.333	0.275	0.397	SUBCLONAL	1	TRUE	1	0.607583902505537	2		247	376	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593379	67593380	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0044850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	75	318	0	ENST00000274335.5:c.2127_2128dup	p.Leu710ProfsTer6	p.L710Pfs*6	ENST00000274335		709	tcc/tCCcc	15/15	1	2	FACETS	0.52	0.457	0.587	0.52	0.457	0.587	SUBCLONAL	1	TRUE	1	0.607583902505537	2		318	475	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0044881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	605	621	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.770478684851519	2	FACETS	0.929	0.906	0.952	0.929	0.906	0.952	CLONAL	2	TRUE	0	0.79378491171453	2		622	820	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0044881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	60	180	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	0.459509865309581	1	FACETS	0.317	0.275	0.361	0.317	0.275	0.361	INDETERMINATE	1	TRUE	0	0.79378491171453	1		180	288	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0044881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	142	189	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.459509865309581	1	FACETS	0.642	0.594	0.691	0.642	0.594	0.691	INDETERMINATE	1	TRUE	0	0.79378491171453	1		189	336	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920401	114920401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1422891742	NA	P-0044881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	153	456	2	ENST00000543371.1:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000543371	NM_001198531.1	448	Cgg/Tgg	13/14	0.459509865309581	1	FACETS	0.348	0.319	0.378	0.348	0.319	0.378	INDETERMINATE	1	TRUE	0	0.79378491171453	1		458	669	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677912	117677912	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	166	371	0	ENST00000368508.3:c.4021G>C	p.Ala1341Pro	p.A1341P	ENST00000368508	NM_002944.2	1341	Gct/Cct	25/43	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.79378491171453	2		371	416	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	98	348	1				ENST00000310581	NM_198253.2	-/1132			0.293680257438023	3	FACETS	0.759	0.682	0.841	0.759	0.682	0.841	SUBCLONAL	2	TRUE	1	0.36	3		349	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	206	645	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.300223615147488	2	FACETS	0.868	0.81	0.929	0.868	0.81	0.929	CLONAL	2	TRUE	0	0.36	2		645	659	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212149	5212149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1377011238	NA	P-0044934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	137	680	0	ENST00000357368.4:c.4882C>T	p.Arg1628Cys	p.R1628C	ENST00000357368	NM_002850.3	1628	Cgc/Tgc	32/38	0.293680257438023	3	FACETS	0.919	0.835	1	0.46	0.417	0.504	CLONAL	1	TRUE	1	0.36	3		680	977	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106364	27106364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	117	671	0	ENST00000324856.7:c.5975C>T	p.Ser1992Leu	p.S1992L	ENST00000324856	NM_006015.4	1992	tCa/tTa	20/20	1	2	FACETS	0.998	0.902	1	0.998	0.902	1	CLONAL	1	TRUE	1	0.36	2		671	651	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164664	36164665	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0044934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	112	665	0	ENST00000300305.3:c.1210dup	p.His404ProfsTer196	p.H404Pfs*196	ENST00000300305		404	cac/cCac	8/8	0.293680257438023	3	FACETS	0.853	0.766	0.944	0.426	0.383	0.472	CLONAL	1	TRUE	1	0.36	3		665	861	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488226	56488226	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	122	477	0	ENST00000267101.3:c.1745G>A	p.Gly582Glu	p.G582E	ENST00000267101	NM_001982.3	582	gGg/gAg	15/28	0.288457956879145	3	FACETS	1	0.966	1	0.574	0.519	0.631	CLONAL	1	TRUE	1	0.36	3		477	697	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138583	2138583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778484981	NA	P-0044934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	69	559	2	ENST00000219476.3:c.5396C>T	p.Ser1799Leu	p.S1799L	ENST00000219476	NM_000548.3	1799	tCg/tTg	42/42	0.293680257438023	3	FACETS	0.496	0.431	0.567	0.248	0.215	0.284	SUBCLONAL	1	TRUE	1	0.36	3		561	912	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057520007	NA	P-0044968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	49	635	0	ENST00000269305.4:c.614A>C	p.Tyr205Ser	p.Y205S	ENST00000269305	NM_001126112.2	205	tAt/tCt	6/11	1	2	FACETS	0.697	0.588	0.818	0.697	0.588	0.818	SUBCLONAL	1	TRUE	1	0.14	2		635	1004	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057641	27057641	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0044968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	50	429	0	ENST00000324856.7:c.1351-2A>G		p.X451_splice	ENST00000324856	NM_006015.4	451			0.3	2	FACETS	0.963	0.815	1			1	CLONAL	1	TRUE	NA	0.14	2		429	742	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346849	91346849	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1416261851	NA	P-0044968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	37	381	0	ENST00000355112.3:c.3458del	p.Lys1153ArgfsTer19	p.K1153Rfs*19	ENST00000355112	NM_000057.2	1153	Aag/ag	18/22	1	2	FACETS	0.879	0.724	1	0.879	0.724	1	CLONAL	1	TRUE	1	0.14	2		381	601	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0044989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	42	180	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	0.589507726552896	3	FACETS	0.783	0.66	0.917	0.392	0.33	0.459	CLONAL	1	TRUE	1	0.640842823584476	3		180	221	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579336	7579336	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	417	606	0	ENST00000269305.4:c.351del	p.Thr118GlnfsTer5	p.T118Qfs*5	ENST00000269305	NM_001126112.2	117	ggG/gg	4/11	0.611407717583505	2	FACETS	0.879	0.845	0.913	0.879	0.845	0.913	CLONAL	2	TRUE	0	0.640842823584476	2		606	740	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202926	27202926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772637203	NA	P-0044989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	117	298	0	ENST00000380036.4:c.2018G>A	p.Arg673His	p.R673H	ENST00000380036	NM_000459.3	673	cGt/cAt	13/23	0.348399463743892	3	FACETS	0.893	0.808	0.981	0.446	0.404	0.491	INDETERMINATE	1	TRUE	1	0.640842823584476	3		298	540	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29107979	29107979	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	89	259	0	ENST00000328354.6:c.710C>G	p.Ala237Gly	p.A237G	ENST00000328354	NM_007194.3	237	gCt/gGt	6/15	1	2	FACETS	0.7	0.624	0.779	0.7	0.624	0.779	SUBCLONAL	1	TRUE	1	0.640842823584476	2		259	397	SUCCESS
APC	324	MSKCC	GRCh37	5	112163683	112163683	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs138098808	NA	P-0044989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	114	130	0	ENST00000257430.4:c.1606G>T	p.Glu536Ter	p.E536*	ENST00000257430	NM_000038.5	536	Gaa/Taa	13/16	0.589507726552896	3	FACETS	0.94	0.863	1	0.94	0.863	1	CLONAL	2	TRUE	1	0.640842823584476	3		130	250	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0045000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	190	704	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.738656442019865	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.754713409430216	1		704	297	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0045000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	91	424	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.19361870605022	2	FACETS	1	0.977	1	0.625	0.568	0.681	INDETERMINATE	1	TRUE	0	0.754713409430216	2		424	193	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	26	212	3	ENST00000257430.4:c.3919dup	p.Ile1307AsnfsTer8	p.I1307Nfs*8	ENST00000257430	NM_000038.5	1306	gaa/gAaa	16/16	0.366702444079384	1	FACETS	0.604	0.496	0.718	0.604	0.496	0.718	INDETERMINATE	1	TRUE	0	0.754713409430216	1		215	71	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347320	89347320	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	262	937	0	ENST00000301030.4:c.5630C>G	p.Pro1877Arg	p.P1877R	ENST00000301030	NM_001256183.1	1877	cCg/cGg	9/13	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.754713409430216	2		937	662	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259146	89259146	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	23	379	0	ENST00000336596.2:c.290T>C	p.Val97Ala	p.V97A	ENST00000336596	NM_005233.5	97	gTg/gCg	3/17	0.50658437540488	1	FACETS	0.299	0.236	0.369	0.299	0.236	0.369	SUBCLONAL	1	TRUE	0	0.754713409430216	1		379	127	SUCCESS
APC	324	MSKCC	GRCh37	5	112174605	112174606	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	T	novel	NA	P-0045000-T01-IM6	NA	A	A	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	35	388	1	ENST00000257430.4:c.3314_3315delinsT	p.Arg1105LeufsTer21	p.R1105Lfs*21	ENST00000257430	NM_000038.5	1105	cGG/cT	16/16	0.366702444079384	1	FACETS	0.328	0.272	0.39	0.328	0.272	0.39	INDETERMINATE	1	TRUE	0	0.754713409430216	1		389	176	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	123	745	7	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.934	0.849	1	1	0.989	1	CLONAL	2	TRUE	1	0.27	2		752	488	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	66	380	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.27	2		380	371	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	43	709	11	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.576	0.481	0.681	0.576	0.481	0.681	SUBCLONAL	1	TRUE	1	0.27	2		720	553	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	82	456	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.27	2		461	451	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	65	348	3	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.27	2		351	378	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	34	347	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.884	0.725	1	0.884	0.725	1	CLONAL	1	TRUE	1	0.27	2		347	285	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101099	27101099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	51	768	1	ENST00000324856.7:c.4381C>T	p.Arg1461Ter	p.R1461*	ENST00000324856	NM_006015.4	1461	Cga/Tga	18/20	1	2	FACETS	0.533	0.452	0.622	0.533	0.452	0.622	SUBCLONAL	1	TRUE	1	0.27	2		769	709	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	44	831	3	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.475	0.397	0.562	0.475	0.397	0.562	SUBCLONAL	1	TRUE	1	0.27	2		834	686	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	30	419	1	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	0.476	0.383	0.582	0.476	0.383	0.582	SUBCLONAL	1	TRUE	1	0.27	2		420	467	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	43	209	1	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	1	2	FACETS	0.942	0.791	1	0.942	0.791	1	CLONAL	1	TRUE	1	0.27	2		210	338	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370841	55370841	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759612481	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	42	632	0	ENST00000297316.4:c.143C>T	p.Ala48Val	p.A48V	ENST00000297316	NM_022454.3	48	gCg/gTg	1/2	1	2	FACETS	0.588	0.491	0.697	0.588	0.491	0.697	SUBCLONAL	1	TRUE	1	0.27	2		632	529	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222934	5222934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768350891	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	94	762	0	ENST00000357368.4:c.2869G>A	p.Glu957Lys	p.E957K	ENST00000357368	NM_002850.3	957	Gag/Aag	18/38	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.27	2		762	553	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339744	116339746	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs764811491	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	57	368	0	ENST00000397752.3:c.611_613del	p.Ser204del	p.S204del	ENST00000397752	NM_000245.2	202	aaTTCt/aat	2/21	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.27	2		368	391	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646085	215646085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	54	568	1	ENST00000260947.4:c.513del	p.Asp172MetfsTer40	p.D172Mfs*40	ENST00000260947	NM_000465.2	171	aaA/aa	4/11	1	2	FACETS	0.621	0.53	0.721	0.621	0.53	0.721	SUBCLONAL	1	TRUE	1	0.27	2		569	644	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276860	15276861	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs753725730	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	46	692	3	ENST00000263388.2:c.5404dup	p.Ala1802GlyfsTer8	p.A1802Gfs*8	ENST00000263388	NM_000435.2	1802	gct/gGct	30/33	1	2	FACETS	0.514	0.432	0.605	0.514	0.432	0.605	SUBCLONAL	1	TRUE	1	0.27	2		695	663	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319959	8319959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745582718	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	18	220	0	ENST00000356435.5:c.5542G>A	p.Val1848Ile	p.V1848I	ENST00000356435		1848	Gtt/Att	34/35	1	2	FACETS	0.533	0.402	0.688	0.533	0.402	0.688	SUBCLONAL	1	TRUE	1	0.27	2		220	250	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55130043	55130043	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774431464	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	101	646	2	ENST00000257290.5:c.577G>A	p.Val193Ile	p.V193I	ENST00000257290	NM_006206.4	193	Gtc/Atc	4/23	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.27	2		648	633	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119910	70119910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1297203260	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	31	580	0	ENST00000245479.2:c.916del	p.Val306CysfsTer77	p.V306Cfs*77	ENST00000245479	NM_000346.3	304	ccG/cc	3/3	1	2	FACETS	0.432	0.349	0.527	0.432	0.349	0.527	SUBCLONAL	1	TRUE	1	0.27	2		580	531	SUCCESS
APC	324	MSKCC	GRCh37	5	112164664	112164664	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1060503259	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	44	238	0	ENST00000257430.4:c.1742del	p.Lys581ArgfsTer9	p.K581Rfs*9	ENST00000257430	NM_000038.5	580	Aaa/aa	14/16	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.27	2		238	276	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573977	41573977	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201569846	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	49	666	2	ENST00000263253.7:c.6262C>T	p.Arg2088Trp	p.R2088W	ENST00000263253	NM_001429.3	2088	Cgg/Tgg	31/31	1	2	FACETS	0.693	0.587	0.809	0.693	0.587	0.809	SUBCLONAL	1	TRUE	1	0.27	2		668	524	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	61	861	5	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	1	2	FACETS	0.553	0.476	0.637	0.553	0.476	0.637	SUBCLONAL	1	TRUE	1	0.27	2		866	817	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922974	44922974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs973676174	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	41	642	0	ENST00000377967.4:c.1835G>A	p.Arg612Gln	p.R612Q	ENST00000377967	NM_021140.2	612	cGa/cAa	16/29	1	2	FACETS	0.422	0.351	0.503	0.422	0.351	0.503	SUBCLONAL	1	TRUE	1	0.27	2		642	719	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752786	42752786	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762382429	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	54	969	1	ENST00000222329.4:c.1478G>A	p.Arg493His	p.R493H	ENST00000222329	NM_006494.2	493	cGc/cAc	4/4	1	2	FACETS	0.564	0.481	0.656	0.564	0.481	0.656	SUBCLONAL	1	TRUE	1	0.27	2		970	709	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163855	32163855	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	93	559	0	ENST00000375023.3:c.5371del	p.Ala1791GlnfsTer11	p.A1791Qfs*11	ENST00000375023	NM_004557.3	1791	Gca/ca	30/30	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.27	2		559	508	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132515	11132515	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	105	828	0	ENST00000358026.2:c.2731G>A	p.Gly911Ser	p.G911S	ENST00000358026	NM_001128849.1	911	Ggc/Agc	19/36	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.27	2		828	776	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383885	15383885	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	31	496	0	ENST00000263377.2:c.26C>T	p.Thr9Met	p.T9M	ENST00000263377	NM_058243.2	9	aCg/aTg	2/20	1	2	FACETS	0.493	0.398	0.6	0.493	0.398	0.6	SUBCLONAL	1	TRUE	1	0.27	2		496	466	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667607	29667607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781428	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	41	565	1	ENST00000356175.3:c.6943G>A	p.Ala2315Thr	p.A2315T	ENST00000356175	NM_000267.3	2315	Gca/Aca	46/57	1	2	FACETS	0.419	0.348	0.498	0.419	0.348	0.498	SUBCLONAL	1	TRUE	1	0.27	2		566	725	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322556	39322556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761415462	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	47	430	0	ENST00000373001.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000373001	NM_022157.3	146	Gca/Aca	2/7	1	2	FACETS	0.721	0.608	0.845	0.721	0.608	0.845	SUBCLONAL	1	TRUE	1	0.27	2		430	483	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973765	15973765	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	52	458	0	ENST00000268712.3:c.4227del	p.Pro1410LeufsTer18	p.P1410Lfs*18	ENST00000268712	NM_006311.3	1409	ggG/gg	31/46	1	2	FACETS	0.673	0.573	0.784	0.673	0.573	0.784	SUBCLONAL	1	TRUE	1	0.27	2		458	572	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102199631	102199631	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	25	275	0	ENST00000263464.3:c.1036C>A	p.Leu346Ile	p.L346I	ENST00000263464	NM_001165.4	346	Cta/Ata	5/9	1	2	FACETS	0.52	0.41	0.647	0.52	0.41	0.647	SUBCLONAL	1	TRUE	1	0.27	2		275	356	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs112445441	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	10	398	0	ENST00000311936.3:c.38G>C	p.Gly13Ala	p.G13A	ENST00000311936	NM_004985.3	13	gGc/gCc	2/5	1	2	FACETS	0.151	0.101	0.214	0.151	0.101	0.214	SUBCLONAL	1	TRUE	1	0.27	2		398	490	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112302	115112302	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	12	214	1	ENST00000257566.3:c.1438G>A	p.Ala480Thr	p.A480T	ENST00000257566	NM_016569.3	480	Gcg/Acg	7/8	1	2	FACETS	0.458	0.322	0.625	0.458	0.322	0.625	SUBCLONAL	1	TRUE	1	0.27	2		215	194	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348051	89348051	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	63	1030	1	ENST00000301030.4:c.4899G>T	p.Lys1633Asn	p.K1633N	ENST00000301030	NM_001256183.1	1633	aaG/aaT	9/13	1	2	FACETS	0.492	0.424	0.566	0.492	0.424	0.566	SUBCLONAL	1	TRUE	1	0.27	2		1031	949	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805913	89805913	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	44	727	1	ENST00000389301.3:c.3983C>A	p.Thr1328Asn	p.T1328N	ENST00000389301	NM_000135.2	1328	aCc/aAc	40/43	1	2	FACETS	0.491	0.411	0.58	0.491	0.411	0.58	SUBCLONAL	1	TRUE	1	0.27	2		728	664	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051678	13051678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1026947469	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	75	562	0	ENST00000316448.5:c.937G>A	p.Val313Met	p.V313M	ENST00000316448	NM_004343.3	313	Gtg/Atg	7/9	1	2	FACETS	0.906	0.795	1	0.906	0.795	1	CLONAL	1	TRUE	1	0.27	2		562	613	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313353	30313353	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	33	597	0	ENST00000262643.3:c.953G>T	p.Gly318Val	p.G318V	ENST00000262643	NM_001238.2	318	gGg/gTg	11/12	1	2	FACETS	0.401	0.325	0.486	0.401	0.325	0.486	SUBCLONAL	1	TRUE	1	0.27	2		597	610	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715991	52715991	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	98	688	1	ENST00000322088.6:c.556G>T	p.Ala186Ser	p.A186S	ENST00000322088	NM_014225.5	186	Gcc/Tcc	5/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.27	2		689	641	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542843	187542843	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	27	416	0	ENST00000441802.2:c.4897T>C	p.Tyr1633His	p.Y1633H	ENST00000441802	NM_005245.3	1633	Tat/Cat	10/27	1	2	FACETS	0.437	0.347	0.54	0.437	0.347	0.54	SUBCLONAL	1	TRUE	1	0.27	2		416	458	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970922	79970922	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs71539687	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	119	645	0	ENST00000265081.6:c.1148A>G	p.Lys383Arg	p.K383R	ENST00000265081	NM_002439.4	383	aAg/aGg	7/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.27	2		645	753	SUCCESS
APC	324	MSKCC	GRCh37	5	112174965	112174965	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	30	214	1	ENST00000257430.4:c.3674C>T	p.Ala1225Val	p.A1225V	ENST00000257430	NM_000038.5	1225	gCc/gTc	16/16	1	2	FACETS	1	0.829	1	1	0.829	1	CLONAL	1	TRUE	1	0.27	2		215	217	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415033	109415033	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	35	522	0	ENST00000436639.2:c.244A>T	p.Arg82Ter	p.R82*	ENST00000436639	NM_014454.2	82	Aga/Tga	1/10	1	2	FACETS	0.449	0.367	0.542	0.449	0.367	0.542	SUBCLONAL	1	TRUE	1	0.27	2		522	577	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509841	106509841	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	84	713	0	ENST00000359195.3:c.1835C>T	p.Ala612Val	p.A612V	ENST00000359195	NM_002649.2	612	gCc/gTc	2/11	1	2	FACETS	0.949	0.838	1	0.949	0.838	1	CLONAL	1	TRUE	1	0.27	2		713	656	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38153335	38153338	+	frameshift_variant	Frame_Shift_Del	DEL	CAAA	CAAA	-	novel	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	33	570	0	ENST00000317025.8:c.2891_2894del	p.Val964GlyfsTer22	p.V964Gfs*22	ENST00000317025	NM_023034.1	964	gTTTGg/gg	16/24	1	2	FACETS	0.416	0.338	0.505	0.416	0.338	0.505	SUBCLONAL	1	TRUE	1	0.27	2		570	587	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566347	141566347	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	26	404	0	ENST00000220592.5:c.1065del	p.Lys355AsnfsTer2	p.K355Nfs*2	ENST00000220592	NM_012154.3	355	aaA/aa	9/19	1	2	FACETS	0.378	0.298	0.469	0.378	0.298	0.469	SUBCLONAL	1	TRUE	1	0.27	2		404	510	SUCCESS
APC	324	MSKCC	GRCh37	5	112164566	112164566	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1554082091	NA	P-0045009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	18	223	0	ENST00000257430.4:c.1643del	p.Leu548Ter	p.L548*	ENST00000257430	NM_000038.5	547	gTt/gt	14/16	1	2	FACETS	0.45	0.339	0.582	0.45	0.339	0.582	SUBCLONAL	1	TRUE	1	0.27	2		223	296	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	25	690	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.117	0.092	0.147	0.117	0.092	0.147	SUBCLONAL	1	TRUE	1	0.55	2		692	774	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	127	478	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.55	2		478	449	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	99	378	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.986	0.888	1	0.986	0.888	1	CLONAL	1	TRUE	1	0.55	2		378	365	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073413	8073413	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	40	390	0	ENST00000377482.5:c.1246G>T	p.Glu416Ter	p.E416*	ENST00000377482	NM_018948.3	416	Gaa/Taa	4/4	1	2	FACETS	0.243	0.201	0.289	0.243	0.201	0.289	SUBCLONAL	1	TRUE	1	0.55	2		390	599	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780235	9780235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1397404017	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	64	717	0	ENST00000377346.4:c.1405G>A	p.Ala469Thr	p.A469T	ENST00000377346	NM_005026.3	469	Gct/Act	11/24	1	2	FACETS	0.318	0.275	0.365	0.318	0.275	0.365	SUBCLONAL	1	TRUE	1	0.55	2		717	732	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587777894	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	96	559	0	ENST00000361445.4:c.6644C>A	p.Ser2215Tyr	p.S2215Y	ENST00000361445	NM_004958.3	2215	tCt/tAt	47/58	1	2	FACETS	0.576	0.514	0.642	0.576	0.514	0.642	SUBCLONAL	1	TRUE	1	0.55	2		559	606	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11269484	11269484	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	38	509	1	ENST00000361445.4:c.3686C>A	p.Pro1229His	p.P1229H	ENST00000361445	NM_004958.3	1229	cCt/cAt	25/58	1	2	FACETS	0.309	0.255	0.369	0.309	0.255	0.369	SUBCLONAL	1	TRUE	1	0.55	2		510	447	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237703	16237703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	184	494	0	ENST00000375759.3:c.1150C>T	p.Arg384Trp	p.R384W	ENST00000375759	NM_015001.2	384	Cgg/Tgg	5/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.55	2		494	614	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16248759	16248759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775761539	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	91	336	0	ENST00000375759.3:c.1765C>T	p.Arg589Trp	p.R589W	ENST00000375759	NM_015001.2	589	Cgg/Tgg	10/15	1	2	FACETS	0.976	0.875	1	0.976	0.875	1	CLONAL	1	TRUE	1	0.55	2		336	339	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264311	16264311	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	21	491	0	ENST00000375759.3:c.10514A>G	p.Tyr3505Cys	p.Y3505C	ENST00000375759	NM_015001.2	3505	tAc/tGc	13/15	1	2	FACETS	0.188	0.144	0.239	0.188	0.144	0.239	SUBCLONAL	1	TRUE	1	0.55	2		491	406	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	170	515	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.55	2		515	577	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45800164	45800164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780081	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	53	590	0	ENST00000450313.1:c.56G>A	p.Arg19Gln	p.R19Q	ENST00000450313	NM_012222.2	19	cGa/cAa	2/16	1	2	FACETS	0.274	0.233	0.319	0.274	0.233	0.319	SUBCLONAL	1	TRUE	1	0.55	2		590	704	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46527716	46527716	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	82	272	0	ENST00000262741.5:c.649G>T	p.Glu217Ter	p.E217*	ENST00000262741	NM_003629.3	217	Gaa/Taa	6/10	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.55	2		272	286	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301869	65301869	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	65	222	0	ENST00000342505.4:c.3170A>C	p.Lys1057Thr	p.K1057T	ENST00000342505	NM_002227.2	1057	aAa/aCa	23/25	1	2	FACETS	0.931	0.816	1	0.931	0.816	1	CLONAL	1	TRUE	1	0.55	2		222	254	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65349159	65349159	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	98	358	0	ENST00000342505.4:c.7-1G>A		p.X3_splice	ENST00000342505	NM_002227.2	3			1	2	FACETS	0.865	0.777	0.957	0.865	0.777	0.957	CLONAL	1	TRUE	1	0.55	2		358	412	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241878	72241878	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	93	319	0	ENST00000357731.5:c.512C>A	p.Ser171Tyr	p.S171Y	ENST00000357731	NM_173808.2	171	tCt/tAt	3/7	1	2	FACETS	0.85	0.761	0.943	0.85	0.761	0.943	CLONAL	1	TRUE	1	0.55	2		319	398	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428511	78428511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408536007	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	95	432	0	ENST00000370768.2:c.1288C>T	p.Arg430Cys	p.R430C	ENST00000370768	NM_003902.3	430	Cgt/Tgt	14/20	1	2	FACETS	0.802	0.718	0.89	0.802	0.718	0.89	CLONAL	1	TRUE	1	0.55	2		432	431	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430402	78430402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372081866	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	122	400	2	ENST00000370768.2:c.766C>T	p.Arg256Cys	p.R256C	ENST00000370768	NM_003902.3	256	Cgt/Tgt	10/20	1	2	FACETS	0.995	0.906	1	0.995	0.906	1	CLONAL	1	TRUE	1	0.55	2		402	446	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736388	85736388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs949558985	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	44	297	0	ENST00000370580.1:c.259C>T	p.Arg87Trp	p.R87W	ENST00000370580	NM_003921.4	87	Cgg/Tgg	2/3	1	2	FACETS	0.338	0.283	0.398	0.338	0.283	0.398	SUBCLONAL	1	TRUE	1	0.55	2		297	474	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099338	193099338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	17	332	1	ENST00000367435.3:c.272G>A	p.Arg91Gln	p.R91Q	ENST00000367435	NM_024529.4	91	cGa/cAa	3/17	1	2	FACETS	0.19	0.141	0.248	0.19	0.141	0.248	SUBCLONAL	1	TRUE	1	0.55	2		333	326	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552729	226552729	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746139482	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	154	420	0	ENST00000366794.5:c.2632C>T	p.Arg878Trp	p.R878W	ENST00000366794	NM_001618.3	878	Cgg/Tgg	19/23	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.55	2		420	524	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106036	8106036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	140	515	0	ENST00000346208.3:c.856G>A	p.Ala286Thr	p.A286T	ENST00000346208		286	Gcc/Acc	4/6	1	2	FACETS	0.987	0.904	1	0.987	0.904	1	CLONAL	1	TRUE	1	0.55	2		515	516	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111467	8111467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759044265	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	49	565	1	ENST00000346208.3:c.953C>T	p.Ala318Val	p.A318V	ENST00000346208		318	gCg/gTg	5/6	1	2	FACETS	0.281	0.237	0.329	0.281	0.237	0.329	SUBCLONAL	1	TRUE	1	0.55	2		566	634	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601827	43601827	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	140	483	0	ENST00000355710.3:c.871A>G	p.Thr291Ala	p.T291A	ENST00000355710	NM_020975.4	291	Acc/Gcc	5/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.55	2		483	441	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845484	63845484	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	63	236	0	ENST00000279873.7:c.1223T>G	p.Phe408Cys	p.F408C	ENST00000279873	NM_032199.2	408	tTt/tGt	9/10	1	2	FACETS	0.793	0.692	0.9	0.793	0.692	0.9	SUBCLONAL	1	TRUE	1	0.55	2		236	289	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850777	63850777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374377066	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	99	423	0	ENST00000279873.7:c.1555G>A	p.Glu519Lys	p.E519K	ENST00000279873	NM_032199.2	519	Gaa/Aaa	10/10	1	2	FACETS	0.759	0.681	0.842	0.759	0.681	0.842	SUBCLONAL	1	TRUE	1	0.55	2		423	474	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404513	70404513	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	142	418	0	ENST00000373644.4:c.2027G>T	p.Arg676Ile	p.R676I	ENST00000373644	NM_030625.2	676	aGa/aTa	4/12	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.55	2		418	475	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88677066	88677066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	34	591	0	ENST00000372037.3:c.851G>A	p.Arg284His	p.R284H	ENST00000372037	NM_004329.2	284	cGc/cAc	9/13	1	2	FACETS	0.186	0.151	0.225	0.186	0.151	0.225	SUBCLONAL	1	TRUE	1	0.55	2		591	666	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624255	89624255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	40	244	0	ENST00000371953.3:c.29G>A	p.Ser10Asn	p.S10N	ENST00000371953	NM_000314.4	10	aGc/aAc	1/9	1	2	FACETS	0.58	0.485	0.683	0.58	0.485	0.683	SUBCLONAL	1	TRUE	1	0.55	2		244	251	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624270	89624270	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs398123324	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	28	326	0	ENST00000371953.3:c.44G>T	p.Arg15Ile	p.R15I	ENST00000371953	NM_000314.4	15	aGa/aTa	1/9	1	2	FACETS	0.264	0.21	0.325	0.264	0.21	0.325	SUBCLONAL	1	TRUE	1	0.55	2		326	386	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717673	89717673	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770025422	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	162	495	1	ENST00000371953.3:c.698G>A	p.Arg233Gln	p.R233Q	ENST00000371953	NM_000314.4	233	cGa/cAa	7/9	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.55	2		496	556	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925655	114925655	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	215	697	0	ENST00000543371.1:c.1733C>A	p.Ser578Tyr	p.S578Y	ENST00000543371	NM_001198531.1	578	tCt/tAt	14/14	1	2	FACETS	0.969	0.903	1	0.969	0.903	1	CLONAL	1	TRUE	1	0.55	2		697	807	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14303198	14303198	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	108	508	0	ENST00000256196.4:c.477G>T	p.Lys159Asn	p.K159N	ENST00000256196		159	aaG/aaT	5/6	1	2	FACETS	0.727	0.655	0.803	0.727	0.655	0.803	SUBCLONAL	1	TRUE	1	0.55	2		508	540	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421519	32421519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	180	496	0	ENST00000332351.3:c.1073C>T	p.Thr358Met	p.T358M	ENST00000332351	NM_024426.4	358	aCg/aTg	6/10	1	2	FACETS	0.974	0.902	1	0.974	0.902	1	CLONAL	1	TRUE	1	0.55	2		496	672	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137785	64137785	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779751342	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	61	857	1	ENST00000334205.4:c.1886G>A	p.Arg629His	p.R629H	ENST00000334205	NM_003942.2	629	cGc/cAc	15/17	1	2	FACETS	0.245	0.21	0.283	0.245	0.21	0.283	SUBCLONAL	1	TRUE	1	0.55	2		858	906	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625107	69625107	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs782554596	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	128	573	0	ENST00000334134.2:c.686G>T	p.Arg229Ile	p.R229I	ENST00000334134	NM_005247.2	229	aGa/aTa	3/3	1	2	FACETS	0.782	0.711	0.856	0.782	0.711	0.856	SUBCLONAL	1	TRUE	1	0.55	2		573	595	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633578	69633578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	87	167	0	ENST00000334134.2:c.124G>A	p.Ala42Thr	p.A42T	ENST00000334134	NM_005247.2	42	Gcg/Acg	1/3	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.55	2		167	262	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939260	71939260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	181	605	1	ENST00000298229.2:c.209G>A	p.Arg70His	p.R70H	ENST00000298229	NM_001567.3	70	cGc/cAc	2/28	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.55	2		606	646	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77064624	77064624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1392857529	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	104	377	0	ENST00000356341.3:c.793G>A	p.Asp265Asn	p.D265N	ENST00000356341	NM_002576.4	265	Gat/Aat	8/15	1	2	FACETS	0.842	0.759	0.93	0.842	0.759	0.93	CLONAL	1	TRUE	1	0.55	2		377	449	SUCCESS
EED	8726	MSKCC	GRCh37	11	85975288	85975288	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	83	263	0	ENST00000263360.6:c.709G>T	p.Asp237Tyr	p.D237Y	ENST00000263360	NM_003797.3	237	Gat/Tat	7/12	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.55	2		263	301	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195920	102195920	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	19	314	1	ENST00000263464.3:c.680G>T	p.Arg227Ile	p.R227I	ENST00000263464	NM_001165.4	227	aGa/aTa	2/9	1	2	FACETS	0.218	0.165	0.28	0.218	0.165	0.28	SUBCLONAL	1	TRUE	1	0.55	2		315	317	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115600	108115600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772821016	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	86	377	0	ENST00000278616.4:c.748C>T	p.Arg250Ter	p.R250*	ENST00000278616	NM_000051.3	250	Cga/Tga	7/63	1	2	FACETS	0.836	0.745	0.932	0.836	0.745	0.932	CLONAL	1	TRUE	1	0.55	2		377	374	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175528	108175528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs376603775	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	144	358	0	ENST00000278616.4:c.5623C>T	p.Arg1875Ter	p.R1875*	ENST00000278616	NM_000051.3	1875	Cga/Tga	37/63	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.55	2		358	498	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224541	108224541	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs56887719	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	33	306	0	ENST00000278616.4:c.8720C>A	p.Pro2907His	p.P2907H	ENST00000278616	NM_000051.3	2907	cCt/cAt	60/63	1	2	FACETS	0.314	0.256	0.38	0.314	0.256	0.38	SUBCLONAL	1	TRUE	1	0.55	2		306	382	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342931	118342931	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	52	304	1	ENST00000534358.1:c.1057C>T	p.Arg353Ter	p.R353*	ENST00000534358	NM_005933.3	353	Cga/Tga	3/36	1	2	FACETS	0.537	0.459	0.622	0.537	0.459	0.622	SUBCLONAL	1	TRUE	1	0.55	2		305	352	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149251	119149251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267606708	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	39	570	1	ENST00000264033.4:c.1259G>A	p.Arg420Gln	p.R420Q	ENST00000264033	NM_005188.3	420	cGa/cAa	9/16	1	2	FACETS	0.237	0.196	0.283	0.237	0.196	0.283	SUBCLONAL	1	TRUE	1	0.55	2		571	599	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404911	404911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	147	429	0	ENST00000399788.2:c.4283G>A	p.Arg1428Gln	p.R1428Q	ENST00000399788	NM_001042603.1	1428	cGa/cAa	26/28	0.3	2	FACETS	0.981	0.9	1			1	INDETERMINATE	1	TRUE	NA	0.55	2		429	545	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	493228	493228	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	98	393	0	ENST00000399788.2:c.335G>T	p.Arg112Ile	p.R112I	ENST00000399788	NM_001042603.1	112	aGa/aTa	3/28	0.3	2	FACETS	0.848	0.762	0.939			1	INDETERMINATE	1	TRUE	NA	0.55	2		393	420	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446936	18446936	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs377755015	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	47	247	0	ENST00000266497.5:c.1021G>T	p.Glu341Ter	p.E341*	ENST00000266497		341	Gaa/Taa	4/31	1	2	FACETS	0.89	0.761	1	0.89	0.761	1	CLONAL	1	TRUE	1	0.55	2		247	192	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18576934	18576934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765821860	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	163	472	0	ENST00000266497.5:c.2342G>A	p.Arg781His	p.R781H	ENST00000266497		781	cGc/cAc	16/31	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.55	2		472	580	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650565	18650565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	83	345	0	ENST00000266497.5:c.2776C>T	p.Leu926Phe	p.L926F	ENST00000266497		926	Ctt/Ttt	20/31	1	2	FACETS	0.87	0.774	0.971	0.87	0.774	0.971	CLONAL	1	TRUE	1	0.55	2		345	347	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945093	31945093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	133	567	1	ENST00000340398.3:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000340398	NM_001013699.2	3	cGa/cAa	1/1	1	2	FACETS	0.809	0.737	0.884	0.809	0.737	0.884	CLONAL	1	TRUE	1	0.55	2		568	598	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246416	46246416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140500006	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	95	309	0	ENST00000334344.6:c.4510C>T	p.Arg1504Trp	p.R1504W	ENST00000334344	NM_152641.2	1504	Cgg/Tgg	15/21	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.55	2		309	299	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435035	49435035	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765654409	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	167	660	0	ENST00000301067.7:c.6518C>T	p.Ser2173Leu	p.S2173L	ENST00000301067	NM_003482.3	2173	tCg/tTg	31/54	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.55	2		660	562	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50482339	50482339	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	34	444	0	ENST00000394963.4:c.690G>T	p.Lys230Asn	p.K230N	ENST00000394963	NM_003076.4	230	aaG/aaT	6/13	1	2	FACETS	0.253	0.206	0.306	0.253	0.206	0.306	SUBCLONAL	1	TRUE	1	0.55	2		444	488	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482393	56482393	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	142	627	0	ENST00000267101.3:c.941A>C	p.Lys314Thr	p.K314T	ENST00000267101	NM_001982.3	314	aAa/aCa	8/28	1	2	FACETS	0.92	0.843	1	0.92	0.843	1	CLONAL	1	TRUE	1	0.55	2		627	561	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864391	57864391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753413155	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	131	680	1	ENST00000228682.2:c.1868G>A	p.Arg623Gln	p.R623Q	ENST00000228682	NM_005269.2	623	cGa/cAa	12/12	1	2	FACETS	0.783	0.713	0.857	0.783	0.713	0.857	SUBCLONAL	1	TRUE	1	0.55	2		681	608	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865439	57865439	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	200	880	0	ENST00000228682.2:c.2916A>C	p.Glu972Asp	p.E972D	ENST00000228682	NM_005269.2	972	gaA/gaC	12/12	1	2	FACETS	0.987	0.917	1	0.987	0.917	1	CLONAL	1	TRUE	1	0.55	2		880	737	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865647	57865647	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	224	861	0	ENST00000228682.2:c.3124C>A	p.Leu1042Ile	p.L1042I	ENST00000228682	NM_005269.2	1042	Ctt/Att	12/12	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.55	2		861	814	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813334	102813334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1430553116	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	153	540	1	ENST00000307046.8:c.355C>T	p.Arg119Cys	p.R119C	ENST00000307046	NM_001111285.1	119	Cgc/Tgc	3/4	1	2	FACETS	0.986	0.907	1	0.986	0.907	1	CLONAL	1	TRUE	1	0.55	2		541	564	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115397	115115397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866796237	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	137	486	1	ENST00000257566.3:c.929G>A	p.Arg310Gln	p.R310Q	ENST00000257566	NM_016569.3	310	cGa/cAa	5/8	1	2	FACETS	0.768	0.7	0.838	0.768	0.7	0.838	SUBCLONAL	1	TRUE	1	0.55	2		487	649	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431398	121431398	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	160	589	0	ENST00000257555.6:c.602G>T	p.Arg201Met	p.R201M	ENST00000257555		201	aGg/aTg	3/10	1	2	FACETS	0.986	0.909	1	0.986	0.909	1	CLONAL	1	TRUE	1	0.55	2		589	590	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212497	133212497	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879254232	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	105	420	0	ENST00000320574.5:c.5792C>T	p.Ser1931Phe	p.S1931F	ENST00000320574	NM_006231.2	1931	tCt/tTt	42/49	1	2	FACETS	0.916	0.826	1	0.916	0.826	1	CLONAL	1	TRUE	1	0.55	2		420	417	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	112	435	0	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	1	2	FACETS	0.961	0.87	1	0.961	0.87	1	CLONAL	1	TRUE	1	0.55	2		435	424	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549404	21549404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753026198	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	131	514	0	ENST00000382592.4:c.2872C>T	p.Arg958Cys	p.R958C	ENST00000382592	NM_014572.2	958	Cgc/Tgc	8/8	1	2	FACETS	0.97	0.886	1	0.97	0.886	1	CLONAL	1	TRUE	1	0.55	2		514	491	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623562	28623562	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	134	389	0	ENST00000241453.7:c.995C>A	p.Ser332Tyr	p.S332Y	ENST00000241453	NM_004119.2	332	tCt/tAt	8/24	1	2	FACETS	0.992	0.907	1	0.992	0.907	1	CLONAL	1	TRUE	1	0.55	2		389	491	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636143	28636143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371663652	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	191	532	0	ENST00000241453.7:c.229G>A	p.Glu77Lys	p.E77K	ENST00000241453	NM_004119.2	77	Gaa/Aaa	3/24	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.55	2		532	637	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28971097	28971097	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	56	307	0	ENST00000282397.4:c.1660G>T	p.Asp554Tyr	p.D554Y	ENST00000282397	NM_002019.4	554	Gat/Tat	12/30	1	2	FACETS	0.594	0.511	0.683	0.594	0.511	0.683	SUBCLONAL	1	TRUE	1	0.55	2		307	343	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907121	32907121	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	72	411	0	ENST00000380152.3:c.1506A>C	p.Lys502Asn	p.K502N	ENST00000380152		502	aaA/aaC	10/27	1	2	FACETS	0.932	0.823	1	0.932	0.823	1	CLONAL	1	TRUE	1	0.55	2		411	281	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945129	32945129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80359104	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	65	282	0	ENST00000380152.3:c.8524C>T	p.Arg2842Cys	p.R2842C	ENST00000380152		2842	Cgc/Tgc	20/27	1	2	FACETS	0.821	0.718	0.93	0.821	0.718	0.93	CLONAL	1	TRUE	1	0.55	2		282	288	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968981	32968981	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	35	317	0	ENST00000380152.3:c.9412T>G	p.Leu3138Val	p.L3138V	ENST00000380152		3138	Tta/Gta	25/27	1	2	FACETS	0.321	0.263	0.386	0.321	0.263	0.386	SUBCLONAL	1	TRUE	1	0.55	2		317	396	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972575	32972575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80359251	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	129	443	0	ENST00000380152.3:c.9925G>A	p.Glu3309Lys	p.E3309K	ENST00000380152		3309	Gaa/Aaa	27/27	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.55	2		443	457	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941657	48941657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1060503077	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	16	204	0	ENST00000267163.4:c.967G>T	p.Glu323Ter	p.E323*	ENST00000267163	NM_000321.2	323	Gaa/Taa	10/27	1	2	FACETS	0.444	0.331	0.577	0.444	0.331	0.577	SUBCLONAL	1	TRUE	1	0.55	2		204	131	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955550	48955550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913304	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	60	321	1	ENST00000267163.4:c.1666C>T	p.Arg556Ter	p.R556*	ENST00000267163	NM_000321.2	556	Cga/Tga	17/27	1	2	FACETS	0.74	0.642	0.844	0.74	0.642	0.844	SUBCLONAL	1	TRUE	1	0.55	2		322	295	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515045	103515045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	74	282	0	ENST00000355739.4:c.1546C>T	p.Leu516Phe	p.L516F	ENST00000355739	NM_000123.3	516	Ctc/Ttc	8/15	1	2	FACETS	0.934	0.827	1	0.934	0.827	1	CLONAL	1	TRUE	1	0.55	2		282	288	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30103628	30103628	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763394987	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	128	491	1	ENST00000331968.5:c.1310C>T	p.Thr437Met	p.T437M	ENST00000331968	NM_002742.2	437	aCg/aTg	8/18	1	2	FACETS	0.798	0.726	0.874	0.798	0.726	0.874	SUBCLONAL	1	TRUE	1	0.55	2		492	583	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610257	81610257	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	9	418	0	ENST00000298171.2:c.1855G>T	p.Asp619Tyr	p.D619Y	ENST00000298171	NM_000369.2	619	Gat/Tat	10/10	1	2	FACETS	0.075	0.049	0.108	0.075	0.049	0.108	SUBCLONAL	1	TRUE	1	0.55	2		418	437	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95593064	95593064	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	120	372	0	ENST00000393063.1:c.756G>T	p.Glu252Asp	p.E252D	ENST00000393063	NM_030621.3	252	gaG/gaT	8/28	1	2	FACETS	0.957	0.87	1	0.957	0.87	1	CLONAL	1	TRUE	1	0.55	2		372	456	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041074	42041074	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	55	575	0	ENST00000219905.7:c.5452C>T	p.Arg1818Ter	p.R1818*	ENST00000219905	NM_001164273.1	1818	Cga/Tga	16/24	1	2	FACETS	0.296	0.253	0.344	0.296	0.253	0.344	SUBCLONAL	1	TRUE	1	0.55	2		575	675	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003799	45003799	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	88	487	1	ENST00000558401.1:c.55G>T	p.Glu19Ter	p.E19*	ENST00000558401	NM_004048.2	19	Gag/Tag	1/4	1	2	FACETS	0.703	0.626	0.785	0.703	0.626	0.785	SUBCLONAL	1	TRUE	1	0.55	2		488	455	SUCCESS
B2M	567	MSKCC	GRCh37	15	45008529	45008529	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	75	204	0	ENST00000558401.1:c.349C>T	p.Arg117Ter	p.R117*	ENST00000558401	NM_004048.2	117	Cga/Tga	3/4	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.55	2		204	234	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292990	91292990	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	36	440	0	ENST00000355112.3:c.492G>T	p.Glu164Asp	p.E164D	ENST00000355112	NM_000057.2	164	gaG/gaT	3/22	1	2	FACETS	0.274	0.225	0.329	0.274	0.225	0.329	SUBCLONAL	1	TRUE	1	0.55	2		440	478	SUCCESS
BLM	641	MSKCC	GRCh37	15	91308568	91308568	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	109	486	0	ENST00000355112.3:c.2117C>A	p.Ser706Tyr	p.S706Y	ENST00000355112	NM_000057.2	706	tCt/tAt	9/22	1	2	FACETS	0.67	0.603	0.74	0.67	0.603	0.74	SUBCLONAL	1	TRUE	1	0.55	2		486	592	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310233	91310233	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs896043726	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	45	231	0	ENST00000355112.3:c.2287C>A	p.Leu763Ile	p.L763I	ENST00000355112	NM_000057.2	763	Cta/Ata	10/22	1	2	FACETS	0.802	0.682	0.931	0.802	0.682	0.931	CLONAL	1	TRUE	1	0.55	2		231	204	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358367	91358367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779891	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	94	505	0	ENST00000355112.3:c.4112C>T	p.Thr1371Met	p.T1371M	ENST00000355112	NM_000057.2	1371	aCg/aTg	22/22	1	2	FACETS	0.594	0.53	0.663	0.594	0.53	0.663	SUBCLONAL	1	TRUE	1	0.55	2		505	575	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779869	3779869	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	214	675	0	ENST00000262367.5:c.5179G>A	p.Asp1727Asn	p.D1727N	ENST00000262367	NM_004380.2	1727	Gac/Aac	31/31	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.55	2		675	693	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828135	3828135	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	96	482	0	ENST00000262367.5:c.1990G>T	p.Glu664Ter	p.E664*	ENST00000262367	NM_004380.2	664	Gaa/Taa	10/31	1	2	FACETS	0.599	0.534	0.667	0.599	0.534	0.667	SUBCLONAL	1	TRUE	1	0.55	2		482	583	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632757	23632757	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	46	468	0	ENST00000261584.4:c.3039A>G	p.Ile1013Met	p.I1013M	ENST00000261584	NM_024675.3	1013	atA/atG	10/13	1	2	FACETS	0.309	0.259	0.363	0.309	0.259	0.363	SUBCLONAL	1	TRUE	1	0.55	2		468	542	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129087	30129087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	139	644	1	ENST00000263025.4:c.679G>A	p.Asp227Asn	p.D227N	ENST00000263025	NM_002746.2	227	Gac/Aac	5/9	1	2	FACETS	0.731	0.667	0.799	0.731	0.667	0.799	SUBCLONAL	1	TRUE	1	0.55	2		645	691	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864582	56864582	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	88	401	0	ENST00000308159.5:c.1070A>G	p.Asn357Ser	p.N357S	ENST00000308159	NM_014669.4	357	aAc/aGc	10/22	1	2	FACETS	0.679	0.604	0.759	0.679	0.604	0.759	SUBCLONAL	1	TRUE	1	0.55	2		401	471	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821299	72821299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1348379505	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	149	497	0	ENST00000268489.5:c.10876G>A	p.Ala3626Thr	p.A3626T	ENST00000268489	NM_006885.3	3626	Gca/Aca	10/10	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.55	2		497	530	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822461	72822461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs772483176	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	214	895	0	ENST00000268489.5:c.9714G>T	p.Glu3238Asp	p.E3238D	ENST00000268489	NM_006885.3	3238	gaG/gaT	10/10	1	2	FACETS	0.893	0.831	0.957	0.893	0.831	0.957	CLONAL	1	TRUE	1	0.55	2		895	871	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828014	72828014	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs781233918	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	264	701	0	ENST00000268489.5:c.8567A>G	p.Asp2856Gly	p.D2856G	ENST00000268489	NM_006885.3	2856	gAc/gGc	9/10	1	2	FACETS	0.969	0.909	1	0.969	0.909	1	CLONAL	1	TRUE	1	0.55	2		701	991	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830833	72830833	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	167	665	0	ENST00000268489.5:c.5748A>C	p.Lys1916Asn	p.K1916N	ENST00000268489	NM_006885.3	1916	aaA/aaC	9/10	1	2	FACETS	0.887	0.817	0.958	0.887	0.817	0.958	CLONAL	1	TRUE	1	0.55	2		665	685	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845838	72845838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762268017	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	35	573	2	ENST00000268489.5:c.3629G>A	p.Arg1210Gln	p.R1210Q	ENST00000268489	NM_006885.3	1210	cGa/cAa	6/10	1	2	FACETS	0.191	0.155	0.23	0.191	0.155	0.23	SUBCLONAL	1	TRUE	1	0.55	2		575	668	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993348	72993348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759852645	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	251	716	0	ENST00000268489.5:c.697G>A	p.Val233Met	p.V233M	ENST00000268489	NM_006885.3	233	Gtg/Atg	2/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.55	2		716	885	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341536	89341536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	160	546	0	ENST00000301030.4:c.7534C>T	p.Arg2512Trp	p.R2512W	ENST00000301030	NM_001256183.1	2512	Cgg/Tgg	10/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.55	2		546	552	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349127	89349127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771350366	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	320	949	0	ENST00000301030.4:c.3823G>A	p.Asp1275Asn	p.D1275N	ENST00000301030	NM_001256183.1	1275	Gac/Aac	9/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.55	2		949	1105	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579707	7579707	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	193	662	0	ENST00000269305.4:c.89A>G	p.Asn30Ser	p.N30S	ENST00000269305	NM_001126112.2	30	aAc/aGc	3/11	1	2	FACETS	0.942	0.874	1	0.942	0.874	1	CLONAL	1	TRUE	1	0.55	2		662	745	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984773	11984773	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	117	341	0	ENST00000353533.5:c.319G>T	p.Glu107Ter	p.E107*	ENST00000353533	NM_003010.3	107	Gaa/Taa	3/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.55	2		341	404	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974830	15974830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	111	397	0	ENST00000268712.3:c.4045C>T	p.Arg1349Cys	p.R1349C	ENST00000268712	NM_006311.3	1349	Cgt/Tgt	30/46	1	2	FACETS	0.868	0.785	0.955	0.868	0.785	0.955	CLONAL	1	TRUE	1	0.55	2		397	465	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490319	29490319	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500244	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	129	369	0	ENST00000356175.3:c.404G>A	p.Arg135Gln	p.R135Q	ENST00000356175	NM_000267.3	135	cGg/cAg	4/57	1	2	FACETS	0.933	0.85	1	0.933	0.85	1	CLONAL	1	TRUE	1	0.55	2		369	503	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528070	29528070	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	49	172	0	ENST00000356175.3:c.1078C>T	p.Pro360Ser	p.P360S	ENST00000356175	NM_000267.3	360	Cca/Tca	10/57	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.55	2		172	156	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	185	306	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.995	0.937	1	1	0.994	1	CLONAL	2	TRUE	1	0.55	2		306	338	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325752	30325752	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	49	262	0	ENST00000322652.5:c.1950G>T	p.Lys650Asn	p.K650N	ENST00000322652	NM_015355.2	650	aaG/aaT	16/16	1	2	FACETS	0.958	0.824	1	0.958	0.824	1	CLONAL	1	TRUE	1	0.55	2		262	186	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33433424	33433424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780491769	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	184	652	0	ENST00000345365.6:c.557G>A	p.Arg186Gln	p.R186Q	ENST00000345365	NM_002878.3	186	cGa/cAa	6/10	1	2	FACETS	0.96	0.889	1	0.96	0.889	1	CLONAL	1	TRUE	1	0.55	2		652	697	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804367	46804367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1187061907	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	167	492	1	ENST00000290295.7:c.640C>T	p.Arg214Cys	p.R214C	ENST00000290295	NM_006361.5	214	Cgt/Tgt	2/2	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.55	2		493	563	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435153	56435153	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768648593	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	172	720	1	ENST00000407977.2:c.1984G>A	p.Glu662Lys	p.E662K	ENST00000407977		662	Gag/Aag	9/10	1	2	FACETS	0.928	0.857	1	0.928	0.857	1	CLONAL	1	TRUE	1	0.55	2		721	674	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533916	63533916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1399215718	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	113	425	0	ENST00000307078.5:c.1238C>T	p.Ser413Leu	p.S413L	ENST00000307078	NM_004655.3	413	tCg/tTg	6/11	1	2	FACETS	0.909	0.823	0.999	0.909	0.823	0.999	CLONAL	1	TRUE	1	0.55	2		425	452	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570469	39570469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1380208670	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	11	207	0	ENST00000262039.4:c.665G>A	p.Arg222Gln	p.R222Q	ENST00000262039	NM_002647.2	222	cGa/cAa	6/25	1	2	FACETS	0.204	0.141	0.283	0.204	0.141	0.283	SUBCLONAL	1	TRUE	1	0.55	2		207	196	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10292746	10292746	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	28	335	0	ENST00000340748.4:c.88G>T	p.Asp30Tyr	p.D30Y	ENST00000340748		30	Gat/Tat	2/40	1	2	FACETS	0.284	0.226	0.349	0.284	0.226	0.349	SUBCLONAL	1	TRUE	1	0.55	2		335	359	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100016	11100016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749059769	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	55	553	0	ENST00000358026.2:c.1142G>A	p.Arg381Gln	p.R381Q	ENST00000358026	NM_001128849.1	381	cGa/cAa	7/36	1	2	FACETS	0.272	0.232	0.317	0.272	0.232	0.317	SUBCLONAL	1	TRUE	1	0.55	2		553	734	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291941	15291941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	193	745	0	ENST00000263388.2:c.2825G>A	p.Gly942Asp	p.G942D	ENST00000263388	NM_000435.2	942	gGc/gAc	18/33	1	2	FACETS	0.903	0.837	0.971	0.903	0.837	0.971	CLONAL	1	TRUE	1	0.55	2		745	777	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946809	17946809	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257320432	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	189	688	0	ENST00000458235.1:c.1838G>A	p.Arg613Gln	p.R613Q	ENST00000458235	NM_000215.3	613	cGa/cAa	14/24	1	2	FACETS	0.956	0.886	1	0.956	0.886	1	CLONAL	1	TRUE	1	0.55	2		688	719	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257899	19257899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374422850	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	165	849	1	ENST00000162023.5:c.487G>A	p.Ala163Thr	p.A163T	ENST00000162023		163	Gcc/Acc	9/13	1	2	FACETS	0.686	0.63	0.744	0.686	0.63	0.744	SUBCLONAL	1	TRUE	1	0.55	2		850	875	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210688	36210688	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	43	542	2	ENST00000222270.7:c.439C>T	p.Arg147Ter	p.R147*	ENST00000222270	NM_014727.1	147	Cga/Tga	3/37	1	2	FACETS	0.238	0.199	0.282	0.238	0.199	0.282	SUBCLONAL	1	TRUE	1	0.55	2		544	656	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40739784	40739784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1044344132	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	79	761	0	ENST00000392038.2:c.1441G>A	p.Glu481Lys	p.E481K	ENST00000392038	NM_001626.4	481	Gag/Aag	14/14	1	2	FACETS	0.34	0.298	0.385	0.34	0.298	0.385	SUBCLONAL	1	TRUE	1	0.55	2		761	845	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765513	41765513	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1004955	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	190	628	1	ENST00000301178.4:c.2389A>G	p.Thr797Ala	p.T797A	ENST00000301178	NM_021913.4	797	Aca/Gca	20/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.55	2		629	663	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383220	42383220	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs926961615	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	199	650	0	ENST00000221972.3:c.240C>A	p.Phe80Leu	p.F80L	ENST00000221972	NM_021601.3	80	ttC/ttA	2/5	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.55	2		650	675	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753438	42753438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	214	822	1	ENST00000222329.4:c.826G>A	p.Ala276Thr	p.A276T	ENST00000222329	NM_006494.2	276	Gcc/Acc	4/4	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.55	2		823	762	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085797	16085797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	126	539	0	ENST00000281043.3:c.973C>T	p.Pro325Ser	p.P325S	ENST00000281043	NM_005378.4	325	Ccc/Tcc	3/3	1	2	FACETS	0.957	0.872	1	0.957	0.872	1	CLONAL	1	TRUE	1	0.55	2		539	479	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241093	39241093	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	133	446	0	ENST00000402219.2:c.1978C>T	p.Arg660Cys	p.R660C	ENST00000402219	NM_005633.3	660	Cgc/Tgc	12/23	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.55	2		446	458	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47601183	47601183	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	164	472	0	ENST00000263735.4:c.421A>G	p.Thr141Ala	p.T141A	ENST00000263735	NM_002354.2	141	Acc/Gcc	3/9	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.55	2		472	508	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47602407	47602407	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	25	300	0	ENST00000263735.4:c.460G>T	p.Glu154Ter	p.E154*	ENST00000263735	NM_002354.2	154	Gaa/Taa	4/9	1	2	FACETS	0.26	0.204	0.323	0.26	0.204	0.323	SUBCLONAL	1	TRUE	1	0.55	2		300	350	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606097	47606097	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	53	242	0	ENST00000263735.4:c.561G>T	p.Glu187Asp	p.E187D	ENST00000263735	NM_002354.2	187	gaG/gaT	6/9	1	2	FACETS	0.936	0.809	1	0.936	0.809	1	CLONAL	1	TRUE	1	0.55	2		242	206	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672741	47672741	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs557339938	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	29	497	0	ENST00000233146.2:c.1331G>A	p.Arg444His	p.R444H	ENST00000233146	NM_000251.2	444	cGt/cAt	8/16	1	2	FACETS	0.233	0.186	0.286	0.233	0.186	0.286	SUBCLONAL	1	TRUE	1	0.55	2		497	453	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690230	47690230	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63749947	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	105	387	0	ENST00000233146.2:c.1447G>T	p.Glu483Ter	p.E483*	ENST00000233146	NM_000251.2	483	Gaa/Taa	9/16	1	2	FACETS	0.972	0.878	1	0.972	0.878	1	CLONAL	1	TRUE	1	0.55	2		387	393	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027998	48027998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757653982	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	80	259	0	ENST00000234420.5:c.2876G>A	p.Arg959His	p.R959H	ENST00000234420	NM_000179.2	959	cGc/cAc	4/10	1	2	FACETS	0.941	0.837	1	0.941	0.837	1	CLONAL	1	TRUE	1	0.55	2		259	309	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149254	61149254	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	24	310	0	ENST00000295025.8:c.1444T>G	p.Leu482Val	p.L482V	ENST00000295025	NM_002908.2	482	Tta/Gta	11/11	1	2	FACETS	0.341	0.268	0.425	0.341	0.268	0.425	SUBCLONAL	1	TRUE	1	0.55	2		310	256	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	30	527	0	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	0.183	0.147	0.224	0.183	0.147	0.224	SUBCLONAL	1	TRUE	1	0.55	2		527	596	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128016895	128016895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	162	541	0	ENST00000285398.2:c.2194G>A	p.Glu732Lys	p.E732K	ENST00000285398	NM_000122.1	732	Gaa/Aaa	14/15	1	2	FACETS	0.947	0.873	1	0.947	0.873	1	CLONAL	1	TRUE	1	0.55	2		541	622	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265573	198265573	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	119	417	1	ENST00000335508.6:c.2584G>A	p.Glu862Lys	p.E862K	ENST00000335508	NM_012433.2	862	Gaa/Aaa	18/25	1	2	FACETS	0.9	0.817	0.986	0.9	0.817	0.986	CLONAL	1	TRUE	1	0.55	2		418	481	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131412	202131412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339962485	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	124	468	0	ENST00000358485.4:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000358485	NM_001080125.1	127	cGa/cAa	2/9	1	2	FACETS	0.963	0.877	1	0.963	0.877	1	CLONAL	1	TRUE	1	0.55	2		468	468	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248609	212248609	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	88	463	0	ENST00000342788.4:c.3658G>T	p.Glu1220Ter	p.E1220*	ENST00000342788	NM_005235.2	1220	Gag/Tag	28/28	1	2	FACETS	0.645	0.573	0.721	0.645	0.573	0.721	SUBCLONAL	1	TRUE	1	0.55	2		463	496	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488718	212488718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267599191	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	15	486	1	ENST00000342788.4:c.2131C>T	p.Arg711Cys	p.R711C	ENST00000342788	NM_005235.2	711	Cgt/Tgt	18/28	1	2	FACETS	0.09	0.065	0.121	0.09	0.065	0.121	SUBCLONAL	1	TRUE	1	0.55	2		487	603	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225343003	225343003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	151	461	0	ENST00000264414.4:c.2089G>A	p.Asp697Asn	p.D697N	ENST00000264414	NM_003590.4	697	Gac/Aac	15/16	1	2	FACETS	0.945	0.868	1	0.945	0.868	1	CLONAL	1	TRUE	1	0.55	2		461	581	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346699	225346699	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	142	381	0	ENST00000264414.4:c.1939G>T	p.Glu647Ter	p.E647*	ENST00000264414	NM_003590.4	647	Gaa/Taa	14/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.55	2		381	430	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546847	9546847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	28	487	0	ENST00000353224.5:c.1175C>T	p.Ser392Leu	p.S392L	ENST00000353224	NM_177990.2	392	tCg/tTg	5/10	1	2	FACETS	0.213	0.169	0.262	0.213	0.169	0.262	SUBCLONAL	1	TRUE	1	0.55	2		487	479	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024421	31024421	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	40	654	0	ENST00000375687.4:c.3906G>T	p.Lys1302Asn	p.K1302N	ENST00000375687	NM_015338.5	1302	aaG/aaT	13/13	1	2	FACETS	0.208	0.172	0.249	0.208	0.172	0.249	SUBCLONAL	1	TRUE	1	0.55	2		654	698	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374312	31374312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs551752168	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	28	455	0	ENST00000328111.2:c.311G>A	p.Arg104Gln	p.R104Q	ENST00000328111	NM_006892.3	104	cGa/cAa	5/23	1	2	FACETS	0.221	0.176	0.273	0.221	0.176	0.273	SUBCLONAL	1	TRUE	1	0.55	2		455	460	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395645	31395645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781183120	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	55	646	1	ENST00000328111.2:c.2498C>T	p.Ser833Phe	p.S833F	ENST00000328111	NM_006892.3	833	tCc/tTc	23/23	1	2	FACETS	0.309	0.263	0.358	0.309	0.263	0.358	SUBCLONAL	1	TRUE	1	0.55	2		647	648	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39709836	39709836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	87	179	0	ENST00000361337.2:c.463G>A	p.Glu155Lys	p.E155K	ENST00000361337	NM_003286.2	155	Gaa/Aaa	7/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.55	2		179	234	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713470	40713470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318044562	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	47	610	0	ENST00000373198.4:c.4045C>T	p.Arg1349Cys	p.R1349C	ENST00000373198	NM_133170.3	1349	Cgt/Tgt	30/32	1	2	FACETS	0.273	0.229	0.32	0.273	0.229	0.32	SUBCLONAL	1	TRUE	1	0.55	2		610	627	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877376	40877376	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	93	452	0	ENST00000373198.4:c.2320C>A	p.Leu774Ile	p.L774I	ENST00000373198	NM_133170.3	774	Ctc/Atc	15/32	1	2	FACETS	0.642	0.572	0.715	0.642	0.572	0.715	SUBCLONAL	1	TRUE	1	0.55	2		452	527	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264951	46264951	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	125	390	0	ENST00000371998.3:c.1821G>T	p.Glu607Asp	p.E607D	ENST00000371998		607	gaG/gaT	12/23	1	2	FACETS	0.947	0.862	1	0.947	0.862	1	CLONAL	1	TRUE	1	0.55	2		390	480	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62323162	62323162	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	35	458	1	ENST00000360203.5:c.2624G>T	p.Arg875Met	p.R875M	ENST00000360203	NM_001283009.1	875	aGg/aTg	28/35	1	2	FACETS	0.236	0.193	0.284	0.236	0.193	0.284	SUBCLONAL	1	TRUE	1	0.55	2		459	540	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29107902	29107902	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	36	422	0	ENST00000328354.6:c.787G>T	p.Glu263Ter	p.E263*	ENST00000328354	NM_007194.3	263	Gag/Tag	6/15	1	2	FACETS	0.28	0.23	0.337	0.28	0.23	0.337	SUBCLONAL	1	TRUE	1	0.55	2		422	467	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513353	41513353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147121738	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	164	561	0	ENST00000263253.7:c.257G>A	p.Arg86Gln	p.R86Q	ENST00000263253	NM_001429.3	86	cGa/cAa	2/31	1	2	FACETS	0.987	0.911	1	0.987	0.911	1	CLONAL	1	TRUE	1	0.55	2		561	604	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513616	41513616	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	92	580	0	ENST00000263253.7:c.520A>C	p.Asn174His	p.N174H	ENST00000263253	NM_001429.3	174	Aat/Cat	2/31	1	2	FACETS	0.637	0.568	0.711	0.637	0.568	0.711	SUBCLONAL	1	TRUE	1	0.55	2		580	525	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536166	41536166	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	174	442	1	ENST00000263253.7:c.1783C>T	p.Pro595Ser	p.P595S	ENST00000263253	NM_001429.3	595	Ccg/Tcg	9/31	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.55	2		443	575	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536262	41536262	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	34	428	0	ENST00000263253.7:c.1878+1G>A		p.X626_splice	ENST00000263253	NM_001429.3	626			1	2	FACETS	0.241	0.196	0.291	0.241	0.196	0.291	SUBCLONAL	1	TRUE	1	0.55	2		428	513	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12653551	12653551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140884322	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	140	413	0	ENST00000251849.4:c.218G>A	p.Arg73Gln	p.R73Q	ENST00000251849	NM_002880.3	73	cGa/cAa	3/17	1	2	FACETS	0.948	0.868	1	0.948	0.868	1	CLONAL	1	TRUE	1	0.55	2		413	537	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913409	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	29	311	0	ENST00000349496.5:c.134C>A	p.Ser45Tyr	p.S45Y	ENST00000349496	NM_001904.3	45	tCt/tAt	3/15	1	2	FACETS	0.269	0.216	0.33	0.269	0.216	0.33	SUBCLONAL	1	TRUE	1	0.55	2		311	392	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127805	47127805	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	126	373	0	ENST00000409792.3:c.5278-1G>T		p.X1760_splice	ENST00000409792	NM_014159.6	1760			1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.55	2		373	445	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155366	47155366	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs750924110	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	102	283	0	ENST00000409792.3:c.4715C>T	p.Ser1572Leu	p.S1572L	ENST00000409792	NM_014159.6	1572	tCg/tTg	5/21	1	2	FACETS	0.966	0.871	1	0.966	0.871	1	CLONAL	1	TRUE	1	0.55	2		283	384	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164397	47164397	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	58	269	0	ENST00000409792.3:c.1729G>T	p.Glu577Ter	p.E577*	ENST00000409792	NM_014159.6	577	Gaa/Taa	3/21	1	2	FACETS	0.959	0.835	1	0.959	0.835	1	CLONAL	1	TRUE	1	0.55	2		269	220	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436810	52436810	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	169	560	0	ENST00000460680.1:c.1968G>T	p.Lys656Asn	p.K656N	ENST00000460680	NM_004656.3	656	aaG/aaT	15/17	1	2	FACETS	0.962	0.888	1	0.962	0.888	1	CLONAL	1	TRUE	1	0.55	2		560	639	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613124	52613124	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	169	456	0	ENST00000394830.3:c.3404T>C	p.Val1135Ala	p.V1135A	ENST00000394830	NM_018313.4	1135	gTt/gCt	22/30	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.55	2		456	592	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52692235	52692236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	97	301	0	ENST00000394830.3:c.624dup	p.Gln209SerfsTer6	p.Q209Sfs*6	ENST00000394830	NM_018313.4	208	-/T	6/30	1	2	FACETS	0.909	0.817	1	0.909	0.817	1	CLONAL	1	TRUE	1	0.55	2		301	388	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456487	89456487	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	105	337	0	ENST00000336596.2:c.1663C>A	p.Leu555Ile	p.L555I	ENST00000336596	NM_005233.5	555	Ctc/Atc	8/17	1	2	FACETS	0.992	0.896	1	0.992	0.896	1	CLONAL	1	TRUE	1	0.55	2		337	385	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670777	134670777	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	143	486	1	ENST00000398015.3:c.688G>T	p.Glu230Ter	p.E230*	ENST00000398015	NM_004441.4	230	Gag/Tag	3/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.55	2		487	492	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960122	134960122	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528389234	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	158	564	0	ENST00000398015.3:c.2479G>A	p.Asp827Asn	p.D827N	ENST00000398015	NM_004441.4	827	Gat/Aat	13/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.55	2		564	538	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138409924	138409924	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	72	392	1	ENST00000289153.2:c.1954C>A	p.Leu652Ile	p.L652I	ENST00000289153	NM_006219.2	652	Ctt/Att	13/22	1	2	FACETS	0.653	0.573	0.738	0.653	0.573	0.738	SUBCLONAL	1	TRUE	1	0.55	2		393	401	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138452281	138452281	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	61	274	0	ENST00000289153.2:c.973-1G>A		p.X325_splice	ENST00000289153	NM_006219.2	325			1	2	FACETS	0.831	0.724	0.945	0.831	0.724	0.945	CLONAL	1	TRUE	1	0.55	2		274	267	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177859	142177859	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	92	354	0	ENST00000350721.4:c.7444C>A	p.Leu2482Ile	p.L2482I	ENST00000350721	NM_001184.3	2482	Ctc/Atc	44/47	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.55	2		354	325	SUCCESS
ATR	545	MSKCC	GRCh37	3	142185171	142185171	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	21	333	0	ENST00000350721.4:c.6892G>T	p.Asp2298Tyr	p.D2298Y	ENST00000350721	NM_001184.3	2298	Gat/Tat	40/47	1	2	FACETS	0.243	0.187	0.309	0.243	0.187	0.309	SUBCLONAL	1	TRUE	1	0.55	2		333	314	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260151	149260151	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1307297959	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	126	448	0	ENST00000360632.3:c.742C>T	p.Arg248Ter	p.R248*	ENST00000360632	NM_015472.4	248	Cga/Tga	4/7	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.55	2		448	444	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169953079	169953079	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs755677529	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	159	443	0	ENST00000295797.4:c.163C>T	p.Arg55Ter	p.R55*	ENST00000295797	NM_002740.5	55	Cga/Tga	2/18	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.55	2		443	577	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170002262	170002262	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	12	133	0	ENST00000295797.4:c.1081G>T	p.Glu361Ter	p.E361*	ENST00000295797	NM_002740.5	361	Gaa/Taa	12/18	1	2	FACETS	0.424	0.3	0.572	0.424	0.3	0.572	SUBCLONAL	1	TRUE	1	0.55	2		133	103	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013719	170013719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388201066	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	34	318	0	ENST00000295797.4:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000295797	NM_002740.5	480	Cgc/Tgc	15/18	1	2	FACETS	0.275	0.225	0.332	0.275	0.225	0.332	SUBCLONAL	1	TRUE	1	0.55	2		318	449	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	29	356	0	ENST00000263967.3:c.333G>T	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaT	2/21	1	2	FACETS	0.279	0.224	0.342	0.279	0.224	0.342	SUBCLONAL	1	TRUE	1	0.55	2		356	378	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917681	178917681	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	44	196	0	ENST00000263967.3:c.556G>T	p.Asp186Tyr	p.D186Y	ENST00000263967	NM_006218.2	186	Gat/Tat	3/21	1	2	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	1	0.55	2		196	160	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947871	178947871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	63	322	0	ENST00000263967.3:c.2746C>T	p.Arg916Cys	p.R916C	ENST00000263967	NM_006218.2	916	Cgt/Tgt	19/21	1	2	FACETS	0.812	0.709	0.922	0.812	0.709	0.922	CLONAL	1	TRUE	1	0.55	2		322	282	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181425	185181425	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1435276633	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	140	397	1	ENST00000265026.3:c.1366C>T	p.Arg456Ter	p.R456*	ENST00000265026	NM_004721.4	456	Cga/Tga	8/14	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.55	2		398	461	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184698	185184698	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	36	386	0	ENST00000265026.3:c.1590G>T	p.Glu530Asp	p.E530D	ENST00000265026	NM_004721.4	530	gaG/gaT	10/14	1	2	FACETS	0.248	0.204	0.299	0.248	0.204	0.299	SUBCLONAL	1	TRUE	1	0.55	2		386	527	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447406	187447406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1460631604	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	56	576	0	ENST00000232014.4:c.787G>A	p.Glu263Lys	p.E263K	ENST00000232014	NM_001130845.1	263	Gaa/Aaa	5/10	1	2	FACETS	0.288	0.246	0.334	0.288	0.246	0.334	SUBCLONAL	1	TRUE	1	0.55	2		576	707	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607164	189607164	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	116	678	0	ENST00000264731.3:c.1543G>T	p.Asp515Tyr	p.D515Y	ENST00000264731	NM_003722.4	515	Gac/Tac	12/14	1	2	FACETS	0.659	0.595	0.726	0.659	0.595	0.726	SUBCLONAL	1	TRUE	1	0.55	2		678	640	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806243	1806243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778355	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	164	603	0	ENST00000260795.2:c.1262G>A	p.Arg421Gln	p.R421Q	ENST00000260795		421	cGa/cAa	8/17	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.55	2		603	595	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1952853	1952853	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	56	588	1	ENST00000382891.5:c.1936G>A	p.Glu646Lys	p.E646K	ENST00000382891	NM_133335.3	646	Gaa/Aaa	10/22	1	2	FACETS	0.31	0.265	0.36	0.31	0.265	0.36	SUBCLONAL	1	TRUE	1	0.55	2		589	656	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955180	1955180	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	44	539	0	ENST00000382891.5:c.2267G>A	p.Gly756Asp	p.G756D	ENST00000382891	NM_133335.3	756	gGt/gAt	12/22	1	2	FACETS	0.25	0.209	0.295	0.25	0.209	0.295	SUBCLONAL	1	TRUE	1	0.55	2		539	641	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131211	55131211	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	21	322	0	ENST00000257290.5:c.754G>T	p.Glu252Ter	p.E252*	ENST00000257290	NM_006206.4	252	Gaa/Taa	5/23	1	2	FACETS	0.194	0.149	0.247	0.194	0.149	0.247	SUBCLONAL	1	TRUE	1	0.55	2		322	394	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136805	55136805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41279521	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	67	337	0	ENST00000257290.5:c.1127G>A	p.Arg376Gln	p.R376Q	ENST00000257290	NM_006206.4	376	cGa/cAa	8/23	1	2	FACETS	0.909	0.799	1	0.909	0.799	1	CLONAL	1	TRUE	1	0.55	2		337	268	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136887	55136887	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	77	365	1	ENST00000257290.5:c.1209G>T	p.Lys403Asn	p.K403N	ENST00000257290	NM_006206.4	403	aaG/aaT	8/23	1	2	FACETS	0.872	0.773	0.977	0.872	0.773	0.977	CLONAL	1	TRUE	1	0.55	2		366	321	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602902	55602902	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	57	304	0	ENST00000288135.5:c.2612C>A	p.Pro871His	p.P871H	ENST00000288135	NM_000222.2	871	cCt/cAt	19/21	1	2	FACETS	0.573	0.493	0.658	0.573	0.493	0.658	SUBCLONAL	1	TRUE	1	0.55	2		304	362	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976613	55976613	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	85	432	0	ENST00000263923.4:c.1212T>G	p.Ile404Met	p.I404M	ENST00000263923	NM_002253.2	404	atT/atG	9/30	1	2	FACETS	0.594	0.527	0.666	0.594	0.527	0.666	SUBCLONAL	1	TRUE	1	0.55	2		432	520	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201816	66201816	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556854839	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	131	400	0	ENST00000273854.3:c.2686C>T	p.Arg896Cys	p.R896C	ENST00000273854	NM_004439.5	896	Cgt/Tgt	16/18	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.55	2		400	472	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217240	66217240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	113	361	0	ENST00000273854.3:c.2375C>T	p.Ser792Phe	p.S792F	ENST00000273854	NM_004439.5	792	tCt/tTt	14/18	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.55	2		361	352	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356329	66356329	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs755793306	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	124	394	0	ENST00000273854.3:c.1168T>C	p.Ser390Pro	p.S390P	ENST00000273854	NM_004439.5	390	Tca/Cca	5/18	1	2	FACETS	0.941	0.857	1	0.941	0.857	1	CLONAL	1	TRUE	1	0.55	2		394	479	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003277	143003277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369778611	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	187	496	0	ENST00000262992.4:c.2549C>T	p.Ser850Leu	p.S850L	ENST00000262992	NM_001101669.1	850	tCg/tTg	23/24	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.55	2		496	624	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143350363	143350363	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	36	203	0	ENST00000262992.4:c.99G>T	p.Gln33His	p.Q33H	ENST00000262992	NM_001101669.1	33	caG/caT	3/24	1	2	FACETS	0.856	0.714	1	0.856	0.714	1	CLONAL	1	TRUE	1	0.55	2		203	153	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630651	187630651	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	151	515	0	ENST00000441802.2:c.331G>T	p.Glu111Ter	p.E111*	ENST00000441802	NM_005245.3	111	Gaa/Taa	2/27	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.55	2		515	538	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294339	1294339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	160	656	0	ENST00000310581.5:c.662C>T	p.Ala221Val	p.A221V	ENST00000310581	NM_198253.2	221	gCg/gTg	2/16	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.55	2		656	582	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38968099	38968099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	82	329	0	ENST00000357387.3:c.1006C>T	p.Arg336Cys	p.R336C	ENST00000357387	NM_152756.3	336	Cgt/Tgt	12/38	1	2	FACETS	0.828	0.736	0.926	0.828	0.736	0.926	CLONAL	1	TRUE	1	0.55	2		329	360	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982000	38982000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1259225174	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	101	422	0	ENST00000357387.3:c.722G>A	p.Arg241Gln	p.R241Q	ENST00000357387	NM_152756.3	241	cGa/cAa	8/38	1	2	FACETS	0.86	0.774	0.951	0.86	0.774	0.951	CLONAL	1	TRUE	1	0.55	2		422	427	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152566	56152566	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	31	320	0	ENST00000399503.3:c.622C>T	p.Arg208Ter	p.R208*	ENST00000399503	NM_005921.1	208	Cga/Tga	2/20	1	2	FACETS	0.317	0.256	0.385	0.317	0.256	0.385	SUBCLONAL	1	TRUE	1	0.55	2		320	356	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753118	57753118	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	82	315	2	ENST00000274289.3:c.898C>T	p.Pro300Ser	p.P300S	ENST00000274289	NM_006622.3	300	Ccg/Tcg	7/14	1	2	FACETS	0.953	0.848	1	0.953	0.848	1	CLONAL	1	TRUE	1	0.55	2		317	313	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589618	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519838	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	100	218	0	ENST00000274335.5:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000274335		461	Cga/Tga	10/15	1	2	FACETS	0.999	0.919	1	1	0.99	1	CLONAL	2	TRUE	1	0.55	2		218	182	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86637139	86637139	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	47	181	0	ENST00000274376.6:c.1049+1G>T		p.X350_splice	ENST00000274376	NM_002890.2	350			1	2	FACETS	0.795	0.678	0.92	0.795	0.678	0.92	CLONAL	1	TRUE	1	0.55	2		181	215	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665697	86665697	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	68	275	0	ENST00000274376.6:c.1678G>T	p.Glu560Ter	p.E560*	ENST00000274376	NM_002890.2	560	Gaa/Taa	12/25	1	2	FACETS	0.977	0.861	1	0.977	0.861	1	CLONAL	1	TRUE	1	0.55	2		275	253	SUCCESS
APC	324	MSKCC	GRCh37	5	112173303	112173303	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	57	196	0	ENST00000257430.4:c.2012C>A	p.Ser671Tyr	p.S671Y	ENST00000257430	NM_000038.5	671	tCt/tAt	16/16	1	2	FACETS	0.978	0.851	1	0.978	0.851	1	CLONAL	1	TRUE	1	0.55	2		196	212	SUCCESS
APC	324	MSKCC	GRCh37	5	112176278	112176278	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758987855	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	22	381	0	ENST00000257430.4:c.4987G>A	p.Glu1663Lys	p.E1663K	ENST00000257430	NM_000038.5	1663	Gaa/Aaa	16/16	1	2	FACETS	0.194	0.149	0.245	0.194	0.149	0.245	SUBCLONAL	1	TRUE	1	0.55	2		381	413	SUCCESS
APC	324	MSKCC	GRCh37	5	112177368	112177368	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	80	261	0	ENST00000257430.4:c.6077C>A	p.Ser2026Tyr	p.S2026Y	ENST00000257430	NM_000038.5	2026	tCt/tAt	16/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.55	2		261	250	SUCCESS
APC	324	MSKCC	GRCh37	5	112177565	112177565	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	26	294	0	ENST00000257430.4:c.6274C>A	p.Leu2092Ile	p.L2092I	ENST00000257430	NM_000038.5	2092	Cta/Ata	16/16	1	2	FACETS	0.351	0.279	0.434	0.351	0.279	0.434	SUBCLONAL	1	TRUE	1	0.55	2		294	269	SUCCESS
APC	324	MSKCC	GRCh37	5	112177740	112177740	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	69	299	0	ENST00000257430.4:c.6449T>G	p.Leu2150Arg	p.L2150R	ENST00000257430	NM_000038.5	2150	cTt/cGt	16/16	1	2	FACETS	0.899	0.791	1	0.899	0.791	1	CLONAL	1	TRUE	1	0.55	2		299	279	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911610	131911610	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1554097579	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	72	273	1	ENST00000265335.6:c.355A>G	p.Thr119Ala	p.T119A	ENST00000265335		119	Act/Gct	3/25	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.55	2		274	251	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501461	149501461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751904503	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	49	730	1	ENST00000261799.4:c.2326G>A	p.Asp776Asn	p.D776N	ENST00000261799	NM_002609.3	776	Gat/Aat	16/23	1	2	FACETS	0.25	0.211	0.293	0.25	0.211	0.293	SUBCLONAL	1	TRUE	1	0.55	2		731	713	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694607	176694607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	43	412	1	ENST00000439151.2:c.5191C>T	p.Arg1731Cys	p.R1731C	ENST00000439151	NM_022455.4	1731	Cgt/Tgt	15/23	1	2	FACETS	0.351	0.293	0.414	0.351	0.293	0.414	SUBCLONAL	1	TRUE	1	0.55	2		413	446	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176710868	176710868	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	156	390	0	ENST00000439151.2:c.6090G>T	p.Gln2030His	p.Q2030H	ENST00000439151	NM_022455.4	2030	caG/caT	20/23	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.55	2		390	550	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839799	27839799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	137	575	1	ENST00000328488.2:c.295G>A	p.Ala99Thr	p.A99T	ENST00000328488	NM_003533.2	99	Gcc/Acc	1/1	1	2	FACETS	0.944	0.863	1	0.944	0.863	1	CLONAL	1	TRUE	1	0.55	2		576	528	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673310	30673310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140843115	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	266	807	1	ENST00000376406.3:c.3650G>A	p.Arg1217Gln	p.R1217Q	ENST00000376406	NM_014641.2	1217	cGa/cAa	10/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.55	2		808	873	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797185	32797185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765581144	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	154	617	0	ENST00000374899.4:c.1924G>A	p.Glu642Lys	p.E642K	ENST00000374899	NM_018833.2	642	Gag/Aag	11/12	1	2	FACETS	0.932	0.856	1	0.932	0.856	1	CLONAL	1	TRUE	1	0.55	2		617	601	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815416	32815416	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	62	563	0	ENST00000354258.4:c.1957A>G	p.Arg653Gly	p.R653G	ENST00000354258	NM_000593.5	653	Aga/Gga	9/11	1	2	FACETS	0.331	0.285	0.38	0.331	0.285	0.38	SUBCLONAL	1	TRUE	1	0.55	2		563	682	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609898	117609898	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	120	467	0	ENST00000368508.3:c.6801G>T	p.Lys2267Asn	p.K2267N	ENST00000368508	NM_002944.2	2267	aaG/aaT	43/43	1	2	FACETS	0.951	0.864	1	0.951	0.864	1	CLONAL	1	TRUE	1	0.55	2		467	459	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004616	150004616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150904756	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	185	515	2	ENST00000253339.5:c.1609G>A	p.Ala537Thr	p.A537T	ENST00000253339		537	Gct/Act	3/7	1	2	FACETS	0.991	0.918	1	0.991	0.918	1	CLONAL	1	TRUE	1	0.55	2		517	679	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099758	157099758	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	24	264	0	ENST00000346085.5:c.695A>C	p.Asn232Thr	p.N232T	ENST00000346085	NM_020732.3	232	aAt/aCt	1/20	1	2	FACETS	0.393	0.309	0.489	0.393	0.309	0.489	SUBCLONAL	1	TRUE	1	0.55	2		264	222	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525044	157525044	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	74	314	0	ENST00000346085.5:c.4939C>A	p.Leu1647Ile	p.L1647I	ENST00000346085	NM_020732.3	1647	Ctt/Att	19/20	1	2	FACETS	0.714	0.628	0.804	0.714	0.628	0.804	SUBCLONAL	1	TRUE	1	0.55	2		314	377	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394441	162394441	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	113	317	0	ENST00000366898.1:c.627C>A	p.Phe209Leu	p.F209L	ENST00000366898	NM_004562.2	209	ttC/ttA	6/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.55	2		317	357	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979533	2979533	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	112	449	0	ENST00000396946.4:c.714G>T	p.Lys238Asn	p.K238N	ENST00000396946	NM_032415.4	238	aaG/aaT	6/25	1	2	FACETS	0.905	0.819	0.995	0.905	0.819	0.995	CLONAL	1	TRUE	1	0.55	2		449	450	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6438299	6438299	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	32	459	0	ENST00000356142.4:c.232G>T	p.Glu78Ter	p.E78*	ENST00000356142	NM_018890.3	78	Gaa/Taa	4/7	1	2	FACETS	0.192	0.155	0.234	0.192	0.155	0.234	SUBCLONAL	1	TRUE	1	0.55	2		459	605	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946195	13946195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1433178930	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	108	496	1	ENST00000405192.2:c.901C>T	p.Arg301Trp	p.R301W	ENST00000405192	NM_001163147.1	301	Cgg/Tgg	10/12	1	2	FACETS	0.776	0.7	0.856	0.776	0.7	0.856	SUBCLONAL	1	TRUE	1	0.55	2		497	506	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467700	50467700	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	123	606	0	ENST00000331340.3:c.935A>G	p.Asp312Gly	p.D312G	ENST00000331340	NM_006060.4	312	gAc/gGc	8/8	1	2	FACETS	0.83	0.754	0.909	0.83	0.754	0.909	CLONAL	1	TRUE	1	0.55	2		606	539	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266502	55266502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223694747	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	161	517	0	ENST00000275493.2:c.2794C>T	p.Arg932Cys	p.R932C	ENST00000275493	NM_005228.3	932	Cgc/Tgc	23/28	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.55	2		517	575	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509539	106509539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	156	567	0	ENST00000359195.3:c.1533G>T	p.Glu511Asp	p.E511D	ENST00000359195	NM_002649.2	511	gaG/gaT	2/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.55	2		567	510	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523529	106523529	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	99	273	0	ENST00000359195.3:c.2681G>T	p.Ser894Ile	p.S894I	ENST00000359195	NM_002649.2	894	aGc/aTc	8/11	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.55	2		273	349	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418830	116418830	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	26	202	0	ENST00000397752.3:c.3341G>A	p.Arg1114Lys	p.R1114K	ENST00000397752	NM_000245.2	1114	aGa/aAa	17/21	1	2	FACETS	0.43	0.342	0.529	0.43	0.342	0.529	SUBCLONAL	1	TRUE	1	0.55	2		202	220	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418997	116418997	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200754673	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	104	225	0	ENST00000397752.3:c.3508C>T	p.Arg1170Ter	p.R1170*	ENST00000397752	NM_000245.2	1170	Cga/Tga	17/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.55	2		225	299	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856004	151856004	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201674711	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	159	459	1	ENST00000262189.6:c.11614G>A	p.Glu3872Lys	p.E3872K	ENST00000262189	NM_170606.2	3872	Gaa/Aaa	44/59	1	2	FACETS	0.94	0.865	1	0.94	0.865	1	CLONAL	1	TRUE	1	0.55	2		460	615	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873278	151873278	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs201164931	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	81	223	0	ENST00000262189.6:c.9260T>C	p.Ile3087Thr	p.I3087T	ENST00000262189	NM_170606.2	3087	aTt/aCt	38/59	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.55	2		223	262	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133173	38133173	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	37	465	0	ENST00000317025.8:c.4300G>T	p.Glu1434Ter	p.E1434*	ENST00000317025	NM_023034.1	1434	Gaa/Taa	24/24	1	2	FACETS	0.271	0.223	0.325	0.271	0.223	0.325	SUBCLONAL	1	TRUE	1	0.55	2		465	497	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005885	69005885	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	28	453	0	ENST00000288368.4:c.2296G>T	p.Glu766Ter	p.E766*	ENST00000288368	NM_024870.2	766	Gaa/Taa	21/40	1	2	FACETS	0.214	0.17	0.264	0.214	0.17	0.264	SUBCLONAL	1	TRUE	1	0.55	2		453	476	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033209	69033209	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	174	454	0	ENST00000288368.4:c.3649C>A	p.His1217Asn	p.H1217N	ENST00000288368	NM_024870.2	1217	Cat/Aat	30/40	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.55	2		454	580	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955537	90955537	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	62	386	0	ENST00000265433.3:c.2128G>T	p.Ala710Ser	p.A710S	ENST00000265433	NM_002485.4	710	Gct/Tct	14/16	1	2	FACETS	0.596	0.517	0.681	0.596	0.517	0.681	SUBCLONAL	1	TRUE	1	0.55	2		386	378	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141557641	141557641	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	255	801	1	ENST00000220592.5:c.1674G>T	p.Gln558His	p.Q558H	ENST00000220592	NM_012154.3	558	caG/caT	13/19	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.55	2		802	900	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090497	5090497	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1346944271	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	58	288	0	ENST00000381652.3:c.2813G>A	p.Arg938Gln	p.R938Q	ENST00000381652	NM_004972.3	938	cGa/cAa	21/25	1	2	FACETS	0.972	0.847	1	0.972	0.847	1	CLONAL	1	TRUE	1	0.55	2		288	217	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341976	8341976	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs377463668	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	13	295	0	ENST00000356435.5:c.4664C>T	p.Ala1555Val	p.A1555V	ENST00000356435		1555	gCg/gTg	29/35	1	2	FACETS	0.196	0.139	0.265	0.196	0.139	0.265	SUBCLONAL	1	TRUE	1	0.55	2		295	241	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239124	98239124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745669155	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	28	362	1	ENST00000331920.6:c.1519G>A	p.Ala507Thr	p.A507T	ENST00000331920	NM_000264.3	507	Gct/Act	11/24	1	2	FACETS	0.224	0.178	0.276	0.224	0.178	0.276	SUBCLONAL	1	TRUE	1	0.55	2		363	455	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250277	110250277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	72	736	1	ENST00000374672.4:c.398C>T	p.Ser133Leu	p.S133L	ENST00000374672	NM_004235.4	133	tCg/tTg	3/5	1	2	FACETS	0.351	0.306	0.4	0.351	0.306	0.4	SUBCLONAL	1	TRUE	1	0.55	2		737	745	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787719	135787719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424366444	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	165	433	0	ENST00000298552.3:c.863G>A	p.Arg288His	p.R288H	ENST00000298552	NM_001162426.1	288	cGt/cAt	9/23	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.55	2		433	595	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796753	135796753	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755859330	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	44	209	0	ENST00000298552.3:c.734G>A	p.Arg245Gln	p.R245Q	ENST00000298552	NM_001162426.1	245	cGa/cAa	8/23	1	2	FACETS	0.523	0.44	0.613	0.523	0.44	0.613	SUBCLONAL	1	TRUE	1	0.55	2		209	306	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300905	137300905	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	190	685	0	ENST00000481739.1:c.550C>T	p.Arg184Trp	p.R184W	ENST00000481739	NM_002957.4	184	Cgg/Tgg	4/10	1	2	FACETS	0.95	0.881	1	0.95	0.881	1	CLONAL	1	TRUE	1	0.55	2		685	727	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139565433	139565433	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	184	746	2	ENST00000308874.7:c.603G>T	p.Gln201His	p.Q201H	ENST00000308874		201	caG/caT	8/10	1	2	FACETS	0.842	0.778	0.907	0.842	0.778	0.907	CLONAL	1	TRUE	1	0.55	2		748	795	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841322	15841322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	43	608	0	ENST00000307771.7:c.1406C>T	p.Ser469Leu	p.S469L	ENST00000307771	NM_005089.3	469	tCg/tTg	11/11	1	2	FACETS	0.224	0.187	0.266	0.224	0.187	0.266	SUBCLONAL	1	TRUE	1	0.55	2		608	697	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424707	47424707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371247311	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	199	445	1	ENST00000377045.4:c.515C>T	p.Ser172Leu	p.S172L	ENST00000377045	NM_001654.4	172	tCg/tTg	6/16	1	2	FACETS	0.906	0.841	0.973	0.906	0.841	0.973	CLONAL	1	TRUE	1	0.55	2		446	799	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426063	47426063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	61	762	0	ENST00000377045.4:c.583G>A	p.Glu195Lys	p.E195K	ENST00000377045	NM_001654.4	195	Gag/Aag	7/16	1	2	FACETS	0.268	0.23	0.309	0.268	0.23	0.309	SUBCLONAL	1	TRUE	1	0.55	2		762	829	SUCCESS
AR	367	MSKCC	GRCh37	X	66765877	66765877	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749006575	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	218	839	3	ENST00000374690.3:c.889G>A	p.Asp297Asn	p.D297N	ENST00000374690	NM_000044.3	297	Gac/Aac	1/8	1	2	FACETS	0.934	0.87	0.999	0.934	0.87	0.999	CLONAL	1	TRUE	1	0.55	2		842	849	SUCCESS
AR	367	MSKCC	GRCh37	X	66942740	66942740	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852577	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	135	507	0	ENST00000374690.3:c.2521C>T	p.Arg841Cys	p.R841C	ENST00000374690	NM_000044.3	841	Cgt/Tgt	7/8	1	2	FACETS	0.833	0.76	0.91	0.833	0.76	0.91	CLONAL	1	TRUE	1	0.55	2		507	589	SUCCESS
AR	367	MSKCC	GRCh37	X	66942756	66942756	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	83	532	0	ENST00000374690.3:c.2537A>C	p.Lys846Thr	p.K846T	ENST00000374690	NM_000044.3	846	aAa/aCa	7/8	1	2	FACETS	0.501	0.442	0.563	0.501	0.442	0.563	SUBCLONAL	1	TRUE	1	0.55	2		532	603	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347795	70347795	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	147	523	0	ENST00000374080.3:c.3034G>A	p.Glu1012Lys	p.E1012K	ENST00000374080		1012	Gaa/Aaa	22/45	1	2	FACETS	0.918	0.842	0.997	0.918	0.842	0.997	CLONAL	1	TRUE	1	0.55	2		523	582	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350002	70350002	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	145	552	1	ENST00000374080.3:c.3985C>T	p.Arg1329Ter	p.R1329*	ENST00000374080		1329	Cga/Tga	28/45	1	2	FACETS	0.876	0.802	0.952	0.876	0.802	0.952	CLONAL	1	TRUE	1	0.55	2		553	602	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888769	76888769	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	121	484	1	ENST00000373344.5:c.5060G>T	p.Arg1687Ile	p.R1687I	ENST00000373344	NM_000489.3	1687	aGa/aTa	19/35	1	2	FACETS	0.946	0.86	1	0.946	0.86	1	CLONAL	1	TRUE	1	0.55	2		485	465	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938397	76938397	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	40	587	0	ENST00000373344.5:c.2351C>A	p.Ser784Tyr	p.S784Y	ENST00000373344	NM_000489.3	784	tCt/tAt	9/35	1	2	FACETS	0.286	0.237	0.341	0.286	0.237	0.341	SUBCLONAL	1	TRUE	1	0.55	2		587	508	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938406	76938406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	157	590	0	ENST00000373344.5:c.2342G>A	p.Arg781Gln	p.R781Q	ENST00000373344	NM_000489.3	781	cGa/cAa	9/35	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.55	2		590	493	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613311	100613311	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	42	431	0	ENST00000308731.7:c.1089G>T	p.Gln363His	p.Q363H	ENST00000308731	NM_000061.2	363	caG/caT	12/19	1	2	FACETS	0.277	0.231	0.329	0.277	0.231	0.329	SUBCLONAL	1	TRUE	1	0.55	2		431	551	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190012	123190013	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	140	416	0	ENST00000218089.9:c.1235dup	p.Asn412LysfsTer29	p.N412Kfs*29	ENST00000218089	NM_001042749.1	411	gaa/gAaa	14/35	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.55	2		416	504	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210235	123210235	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	127	489	0	ENST00000218089.9:c.2587A>C	p.Asn863His	p.N863H	ENST00000218089	NM_001042749.1	863	Aat/Cat	26/35	1	2	FACETS	0.972	0.887	1	0.972	0.887	1	CLONAL	1	TRUE	1	0.55	2		489	475	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220621	123220621	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	29	345	0	ENST00000218089.9:c.3277+1G>A		p.X1093_splice	ENST00000218089	NM_001042749.1	1093			1	2	FACETS	0.27	0.217	0.331	0.27	0.217	0.331	SUBCLONAL	1	TRUE	1	0.55	2		345	390	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8246180	8246180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1277982924	NA	P-0045015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	119	429	2	ENST00000335790.3:c.454G>A	p.Glu152Lys	p.E152K	ENST00000335790	NM_002315.2	152	Gaa/Aaa	4/4	1	2	FACETS	0.854	0.774	0.936	0.854	0.774	0.936	CLONAL	1	TRUE	1	0.55	2		431	507	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0045274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	80	377	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.208462646901812	1	FACETS	0.928	0.822	1	0.928	0.822	1	INDETERMINATE	1	TRUE	0	0.358257689001658	1		377	395	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480028	50480028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs759976916	NA	P-0045274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	91	719	3	ENST00000394963.4:c.262C>T	p.Arg88Ter	p.R88*	ENST00000394963	NM_003076.4	88	Cga/Tga	2/13	0.208462646901812	1	FACETS	0.557	0.494	0.624	0.557	0.494	0.624	INDETERMINATE	1	TRUE	0	0.358257689001658	1		722	749	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509847	187509847	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	42	375	0	ENST00000441802.2:c.13666G>T	p.Glu4556Ter	p.E4556*	ENST00000441802	NM_005245.3	4556	Gag/Tag	27/27	0.264486392709381	1	FACETS	0.607	0.509	0.715	0.607	0.509	0.715	SUBCLONAL	1	TRUE	0	0.358257689001658	1		375	317	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622229	162622229	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	88	369	0	ENST00000366898.1:c.468A>T	p.Arg156Ser	p.R156S	ENST00000366898	NM_004562.2	156	agA/agT	4/12	1	2	FACETS	0.992	0.882	1	0.992	0.882	1	CLONAL	1	TRUE	1	0.358257689001658	2		369	495	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0045864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	104	47	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.779947589654811	2		47	241	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519975	NA	P-0045864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	629	529	0	ENST00000269305.4:c.403T>C	p.Cys135Arg	p.C135R	ENST00000269305	NM_001126112.2	135	Tgc/Cgc	5/11	0.779775147378487	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.779947589654811	2		529	785	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888210	112888210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121918464	NA	P-0045864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	160	371	0	ENST00000351677.2:c.226G>A	p.Glu76Lys	p.E76K	ENST00000351677	NM_002834.3	76	Gag/Aag	3/16	1	2	FACETS	0.831	0.767	0.895	0.831	0.767	0.895	CLONAL	1	TRUE	1	0.779947589654811	2		371	494	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562657	29562660	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs1064794276	NA	P-0045864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	304	267	0	ENST00000356175.3:c.3739_3742del	p.Phe1247IlefsTer18	p.F1247Ifs*18	ENST00000356175	NM_000267.3	1246	cTGTTt/ct	28/57	1	2	FACETS	0.939	0.905	0.972	1	0.997	1	CLONAL	2	TRUE	1	0.779947589654811	2		267	415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0046465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	609	540	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.901143931709234	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	FALSE	0	0.901143931709234	3		540	650	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0046741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	49	273	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	1	2	FACETS	0.991	0.847	1	0.991	0.847	1	CLONAL	1	TRUE	1	0.398635493322278	2		273	248	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126756	5126756	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	63	329	1	ENST00000381652.3:c.3364C>T	p.Arg1122Ter	p.R1122*	ENST00000381652	NM_004972.3	1122	Cga/Tga	25/25	1	2	FACETS	0.903	0.786	1	0.903	0.786	1	CLONAL	1	TRUE	1	0.398635493322278	2		330	350	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069964	5069964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	45	219	0	ENST00000381652.3:c.1553C>T	p.Ser518Phe	p.S518F	ENST00000381652	NM_004972.3	518	tCt/tTt	12/25	1	2	FACETS	0.889	0.753	1	0.889	0.753	1	CLONAL	1	TRUE	1	0.398635493322278	2		219	254	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057727	27057727	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	168	635	2	ENST00000324856.7:c.1435C>T	p.Gln479Ter	p.Q479*	ENST00000324856	NM_006015.4	479	Cag/Tag	3/20	1	2	FACETS	0.957	0.88	1	0.957	0.88	1	CLONAL	1	TRUE	1	0.398635493322278	2		637	881	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006042	22006042	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746854404	NA	P-0046741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	165	798	1	ENST00000276925.6:c.361G>A	p.Glu121Lys	p.E121K	ENST00000276925	NM_004936.3	121	Gag/Aag	2/2	1	2	FACETS	0.784	0.719	0.852	0.784	0.719	0.852	SUBCLONAL	1	TRUE	1	0.398635493322278	2		799	1056	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717676	89717676	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	76	353	0	ENST00000371953.3:c.703del	p.Glu235LysfsTer21	p.E235Kfs*21	ENST00000371953	NM_000314.4	234	cGg/cg	7/9	0.33315812508102	1	FACETS	0.785	0.692	0.883	0.785	0.692	0.883	SUBCLONAL	1	TRUE	0	0.398635493322278	1		353	389	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630190	100630190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs128620185	NA	P-0046741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	89	372	0	ENST00000308731.7:c.83G>A	p.Arg28His	p.R28H	ENST00000308731	NM_000061.2	28	cGc/cAc	2/19	1	2	FACETS	0.832	0.739	0.93	0.832	0.739	0.93	CLONAL	1	TRUE	1	0.398635493322278	2		372	537	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14317322	14317322	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782597266	NA	P-0046741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	54	328	0	ENST00000256196.4:c.188G>A	p.Arg63Gln	p.R63Q	ENST00000256196		63	cGg/cAg	2/6	1	2	FACETS	0.65	0.556	0.751	0.65	0.556	0.751	SUBCLONAL	1	TRUE	1	0.398635493322278	2		328	417	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259004	16259004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	106	416	0	ENST00000375759.3:c.6269C>T	p.Ser2090Phe	p.S2090F	ENST00000375759	NM_015001.2	2090	tCt/tTt	11/15	1	2	FACETS	0.895	0.805	0.991	0.895	0.805	0.991	CLONAL	1	TRUE	1	0.398635493322278	2		416	594	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243776993	243776993	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	90	399	0	ENST00000263826.5:c.676G>C	p.Glu226Gln	p.E226Q	ENST00000263826	NM_005465.4	226	Gaa/Caa	7/13	0.398635493322278	3	FACETS	0.942	0.837	1	0.471	0.418	0.527	CLONAL	1	TRUE	1	0.398635493322278	3		399	575	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114917819	114917819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	85	363	2	ENST00000543371.1:c.1309G>A	p.Glu437Lys	p.E437K	ENST00000543371	NM_001198531.1	437	Gag/Aag	12/14	1	2	FACETS	0.771	0.683	0.865	0.771	0.683	0.865	SUBCLONAL	1	TRUE	1	0.398635493322278	2		365	553	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939887	71939887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1292522547	NA	P-0046741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	215	777	1	ENST00000298229.2:c.514G>A	p.Glu172Lys	p.E172K	ENST00000298229	NM_001567.3	172	Gag/Aag	4/28	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.398635493322278	2		778	1024	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211602	46211602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766610841	NA	P-0046741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	36	209	1	ENST00000334344.6:c.568G>A	p.Val190Ile	p.V190I	ENST00000334344	NM_152641.2	190	Gtc/Atc	5/21	1	2	FACETS	0.86	0.713	1	0.86	0.713	1	CLONAL	1	TRUE	1	0.398635493322278	2		210	210	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972431	32972431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	107	423	0	ENST00000380152.3:c.9781G>A	p.Asp3261Asn	p.D3261N	ENST00000380152		3261	Gac/Aac	27/27	1	2	FACETS	0.978	0.88	1	0.978	0.88	1	CLONAL	1	TRUE	1	0.398635493322278	2		423	549	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992468	72992468	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0046741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	168	644	0	ENST00000268489.5:c.1577C>G	p.Ser526Ter	p.S526*	ENST00000268489	NM_006885.3	526	tCa/tGa	2/10	0.371660224053773	1	FACETS	0.923	0.851	0.999	0.923	0.851	0.999	CLONAL	1	TRUE	0	0.398635493322278	1		644	731	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265715	10265715	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	107	329	0	ENST00000340748.4:c.1462C>G	p.Leu488Val	p.L488V	ENST00000340748		488	Ctg/Gtg	19/40	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.398635493322278	2		329	518	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212284	36212284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	165	686	1	ENST00000222270.7:c.2035C>T	p.Pro679Ser	p.P679S	ENST00000222270	NM_014727.1	679	Cca/Tca	3/37	1	2	FACETS	0.942	0.865	1	0.942	0.865	1	CLONAL	1	TRUE	1	0.398635493322278	2		687	879	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224142	36224142	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	158	670	0	ENST00000222270.7:c.6692C>A	p.Ser2231Tyr	p.S2231Y	ENST00000222270	NM_014727.1	2231	tCc/tAc	28/37	1	2	FACETS	0.969	0.889	1	0.969	0.889	1	CLONAL	1	TRUE	1	0.398635493322278	2		670	818	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758297	41758297	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	171	538	0	ENST00000301178.4:c.1753G>A	p.Glu585Lys	p.E585K	ENST00000301178	NM_021913.4	585	Gaa/Aaa	15/20	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.398635493322278	2		538	858	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47701340	47702202	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGCATGTGATACTGATGAGGAAAGAAAGCCAAACTGTCTTACGGTCAGTTCGTACAATATACCAGGCCTTGATGGTCACATTTCAACTTGCTACCTTTTTGCTTACATTTTTCTTATGGTGATTTTGAGGTGTCATTCTGGTTTCTCAGATACTTAAAATATAGGAAAAGGTGTGTCTTAAAATTGAGAGAATGTCTTGGATAAGCAGCTGTGTAGTTTTATATTTTGCTGATAAGGGAAGGTACTCTATTTTTGTTTTTTGTGTGTTTTTGTTTGTTTGTTTTTGAGACAGAATTGCCCAGGCTGGAGTGCTGTGGCGCAATCTCAGCTTACTGCAACTTCCACCTTCTGGGTTCATGCAATTCTGGTGCCTCAGCCTCCCAAGTATCTGGGTTTACAGACATGCACCACCATACCTGGCTAATTTTTGTATTTTTGGTAGAGATGGGGTTTCGCCGTGTTACCAGGCTGGTCTTGAATTCCTGGCCCCATGTGATCCCCCGGCCTCATGCGATCTGCCCGCCTCAGCCTCCCTAAGTGCTGGGATTATAGGCGTGAGCCACCCAACCCAGCCAGTACTCTGTTTTTGATAGCTATTCACAATGGGAAAGGATGTAGCAACACATTTTAACCCTATGTTGAGTTTTAGGTGGGTTCCTTTGAAATTTTGTTAAGGCTAACTTTTGTTAATTTTTTTAAAAAAGTGTAAATTAGGAAATGGGTTTTGAATTCCCAAATGGGGGGATTAAATGTATTTTTACGGCTTATATCTGTTTATTATTCAGTATTCCTGTGTACATTTTCTGTTTTTATTTTTATACAGGCTATGTAGAACCAATGCAGACACTCAATGATGTGTTAG	CTGCATGTGATACTGATGAGGAAAGAAAGCCAAACTGTCTTACGGTCAGTTCGTACAATATACCAGGCCTTGATGGTCACATTTCAACTTGCTACCTTTTTGCTTACATTTTTCTTATGGTGATTTTGAGGTGTCATTCTGGTTTCTCAGATACTTAAAATATAGGAAAAGGTGTGTCTTAAAATTGAGAGAATGTCTTGGATAAGCAGCTGTGTAGTTTTATATTTTGCTGATAAGGGAAGGTACTCTATTTTTGTTTTTTGTGTGTTTTTGTTTGTTTGTTTTTGAGACAGAATTGCCCAGGCTGGAGTGCTGTGGCGCAATCTCAGCTTACTGCAACTTCCACCTTCTGGGTTCATGCAATTCTGGTGCCTCAGCCTCCCAAGTATCTGGGTTTACAGACATGCACCACCATACCTGGCTAATTTTTGTATTTTTGGTAGAGATGGGGTTTCGCCGTGTTACCAGGCTGGTCTTGAATTCCTGGCCCCATGTGATCCCCCGGCCTCATGCGATCTGCCCGCCTCAGCCTCCCTAAGTGCTGGGATTATAGGCGTGAGCCACCCAACCCAGCCAGTACTCTGTTTTTGATAGCTATTCACAATGGGAAAGGATGTAGCAACACATTTTAACCCTATGTTGAGTTTTAGGTGGGTTCCTTTGAAATTTTGTTAAGGCTAACTTTTGTTAATTTTTTTAAAAAAGTGTAAATTAGGAAATGGGTTTTGAATTCCCAAATGGGGGGATTAAATGTATTTTTACGGCTTATATCTGTTTATTATTCAGTATTCCTGTGTACATTTTCTGTTTTTATTTTTATACAGGCTATGTAGAACCAATGCAGACACTCAATGATGTGTTAG	-	novel	NA	P-0046741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1	20	0	0	ENST00000233146.2:c.1760-822_1800del		p.X587_splice	ENST00000233146	NM_000251.2	587		12/16	0.360154411854686	1	FACETS	0.956	0.881	0.993	1	0.965	1	CLONAL	4	TRUE	0	0.398635493322278	1		0	21	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42843808	42843808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772196502	NA	P-0046741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	70	353	1	ENST00000398585.3:c.1111C>T	p.His371Tyr	p.H371Y	ENST00000398585	NM_001135099.1	371	Cat/Tat	10/14	1	2	FACETS	0.656	0.573	0.746	0.656	0.573	0.746	SUBCLONAL	1	TRUE	1	0.398635493322278	2		354	535	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0047316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	919	255	0	ENST00000374690.3:c.2105T>A	p.Leu702His	p.L702H	ENST00000374690	NM_000044.3	702	cTc/cAc	4/8	0.692214383895089	16	FACETS	1	0.991	1			1	CLONAL	14	TRUE	NA	0.692214383895089	16		255	1095	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181812	56181812	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs937257820	NA	P-0047316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	35	489	0	ENST00000399503.3:c.4036G>A	p.Val1346Ile	p.V1346I	ENST00000399503	NM_005921.1	1346	Gtt/Att	17/20	0.598721431373791	4	FACETS	0.761	0.628	0.907	0.38	0.314	0.454	CLONAL	1	TRUE	2	0.692214383895089	4		489	225	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856004	151856004	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201674711	NA	P-0047730-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	196	459	1	ENST00000262189.6:c.11614G>A	p.Glu3872Lys	p.E3872K	ENST00000262189	NM_170606.2	3872	Gaa/Aaa	44/59	0.318951982591326	4	FACETS	0.83	0.769	0.892	0.83	0.769	0.892	CLONAL	2	TRUE	2	0.395226217828112	4		460	834	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339175	65339175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180823763	NA	P-0047730-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	212	417	1	ENST00000342505.4:c.361G>A	p.Asp121Asn	p.D121N	ENST00000342505	NM_002227.2	121	Gac/Aac	5/25	0.395226217828112	6	FACETS	0.839	0.778	0.902			1	CLONAL	2	TRUE	NA	0.395226217828112	6		418	1145	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231183	46231183	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs772564527	NA	P-0047730-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	18	89	0	ENST00000334344.6:c.1103G>C	p.Arg368Thr	p.R368T	ENST00000334344	NM_152641.2	368	aGa/aCa	9/21	0.253155077440736	3	FACETS	0.808	0.614	1	0.404	0.307	0.516	CLONAL	1	TRUE	1	0.395226217828112	3		89	135	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0047730-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	306	546	0	ENST00000269305.4:c.375+1G>C		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.345286551435277	2	FACETS	0.773	0.73	0.818	0.773	0.73	0.818	SUBCLONAL	2	TRUE	0	0.395226217828112	2		546	1001	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545165	41545165	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1474261122	NA	P-0047730-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	407	354	0	ENST00000263253.7:c.2365G>A	p.Ala789Thr	p.A789T	ENST00000263253	NM_001429.3	789	Gct/Act	13/31	0.395226217828112	5	FACETS	1	0.992	1			1	CLONAL	3	TRUE	NA	0.395226217828112	5		354	942	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717741	89717780	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGTTCTTCCACAAACAGAACAAGATGCTAAAAAAGGTTT	GAGTTCTTCCACAAACAGAACAAGATGCTAAAAAAGGTTT	-	novel	NA	P-0047730-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	64	287	0	ENST00000371953.3:c.767_801+5del		p.X256_splice	ENST00000371953	NM_000314.4	256		7/9	0.345286551435277	2	FACETS	1	0.936	1	0.558	0.488	0.634	CLONAL	1	TRUE	0	0.395226217828112	2		287	290	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21304110	21304110	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047730-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	136	446	1	ENST00000354336.3:c.889C>A	p.Gln297Lys	p.Q297K	ENST00000354336	NM_005207.3	297	Caa/Aaa	3/3	0.253155077440736	3	FACETS	1	0.935	1	0.517	0.47	0.566	CLONAL	1	TRUE	1	0.395226217828112	3		447	797	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894230	NA	P-0048372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	39	360	0	ENST00000451590.1:c.35G>A	p.Gly12Asp	p.G12D	ENST00000451590	NM_001130442.1	12	gGc/gAc	2/5	1	2	FACETS	0.707	0.585	0.843	0.707	0.585	0.843	SUBCLONAL	1	TRUE	1	0.19	2		360	581	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0048372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	8	365	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	1	2	FACETS	0.228	0.146	0.335	0.228	0.146	0.335	SUBCLONAL	1	TRUE	1	0.19	2		365	370	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0048495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	450	851	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	0.939	0.898	0.98	0.939	0.898	0.98	CLONAL	1	TRUE	1	0.837122108779278	2		851	1145	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437210	52437210	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0048495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	873	729	0	ENST00000460680.1:c.1834A>T	p.Lys612Ter	p.K612*	ENST00000460680	NM_004656.3	612	Aag/Tag	14/17	0.837122108779278	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.837122108779278	2		729	1042	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0048585-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	139	47	0				ENST00000310581	NM_198253.2	-/1132			0.374027669336537	3	FACETS	0.929	0.852	1	0.929	0.852	1	CLONAL	2	TRUE	1	0.374027669336537	3		47	475	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0048585-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	345	518	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.374027669336537	2		518	818	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0048585-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	371	548	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.374027669336537	6	FACETS	0.973	0.927	1	0.973	0.927	1	CLONAL	4	TRUE	2	0.374027669336537	6		548	891	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873660	35873660	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs201559094	NA	P-0048585-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	89	349	0	ENST00000303115.3:c.616C>T	p.Arg206Ter	p.R206*	ENST00000303115	NM_002185.3	206	Cga/Tga	5/8	0.374027669336537	3	FACETS	1	0.965	1	0.604	0.537	0.674	CLONAL	1	TRUE	1	0.374027669336537	3		349	468	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227873	55227873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048585-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	123	382	0	ENST00000275493.2:c.1340C>T	p.Ser447Phe	p.S447F	ENST00000275493	NM_005228.3	447	tCc/tTc	12/28	0.374027669336537	3	FACETS	0.867	0.79	0.948	0.867	0.79	0.948	CLONAL	2	TRUE	1	0.374027669336537	3		382	450	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321372	1321372	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1319865856	NA	P-0048585-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	148	634	2	ENST00000400841.2:c.383C>T	p.Ser128Leu	p.S128L	ENST00000400841		128	tCg/tTg	4/6	1	1	FACETS	0.896	0.82	0.975	0.896	0.82	0.975	CLONAL	1	TRUE	0	0.374027669336537	1		636	718	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662618	117662618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048585-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	171	478	0	ENST00000368508.3:c.4847G>A	p.Gly1616Glu	p.G1616E	ENST00000368508	NM_002944.2	1616	gGa/gAa	29/43	0.359881098783516	2	FACETS	0.952	0.884	1	0.952	0.884	1	CLONAL	2	TRUE	0	0.374027669336537	2		478	480	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770630	40770630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048585-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	185	369	0	ENST00000373198.4:c.2752G>A	p.Gly918Arg	p.G918R	ENST00000373198	NM_133170.3	918	Ggg/Agg	19/32	0.309052510525787	4	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	2	0.374027669336537	4		369	659	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862887	9862887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868222927	NA	P-0048585-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	156	718	1	ENST00000330684.3:c.2416G>A	p.Glu806Lys	p.E806K	ENST00000330684	NM_001134407.1	806	Gag/Aag	12/13	1	2	FACETS	0.967	0.885	1	0.967	0.885	1	CLONAL	1	TRUE	1	0.374027669336537	2		719	863	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996237	73996237	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048585-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	153	243	0	ENST00000318443.5:c.971C>T	p.Ser324Phe	p.S324F	ENST00000318443	NM_001024736.1	324	tCc/tTc	5/10	0.359881098783516	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.374027669336537	2		243	342	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526594	31526594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048585-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	213	437	0	ENST00000344624.3:c.446C>T	p.Pro149Leu	p.P149L	ENST00000344624		149	cCc/cTc	2/33	0.374027669336537	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	1	0.374027669336537	3		437	664	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510155	187510155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048585-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	80	513	0	ENST00000441802.2:c.13358C>T	p.Pro4453Leu	p.P4453L	ENST00000441802	NM_005245.3	4453	cCc/cTc	27/27	1	2	FACETS	0.767	0.676	0.864	0.767	0.676	0.864	SUBCLONAL	1	TRUE	1	0.374027669336537	2		513	558	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2218123	2218123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747417102	NA	P-0048585-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	255	830	0	ENST00000326181.6:c.185C>T	p.Ser62Phe	p.S62F	ENST00000326181	NM_032271.2	62	tCc/tTc	4/21	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.374027669336537	2		830	1092	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486301	8486301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048585-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	133	318	0	ENST00000356435.5:c.2516C>T	p.Ala839Val	p.A839V	ENST00000356435		839	gCt/gTt	17/35	0.374027669336537	2	FACETS	0.961	0.883	1	0.961	0.883	1	CLONAL	2	TRUE	0	0.374027669336537	2		318	370	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193219826	193219826	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767254478	NA	P-0048585-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	66	321	0	ENST00000367435.3:c.1580C>T	p.Ser527Leu	p.S527L	ENST00000367435	NM_024529.4	527	tCg/tTg	17/17	0.371154244762427	3	FACETS	1	0.884	1	0.668	0.589	0.75	CLONAL	2	TRUE	0	0.374027669336537	3		321	209	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279524	123279524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048585-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	344	594	0	ENST00000358487.5:c.908C>T	p.Pro303Leu	p.P303L	ENST00000358487	NM_000141.4	303	cCc/cTc	7/18	0.374027669336537	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.374027669336537	2		594	808	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811733	102811733	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218506999	NA	P-0048585-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	173	671	0	ENST00000307046.8:c.451G>A	p.Gly151Ser	p.G151S	ENST00000307046	NM_001111285.1	151	Ggt/Agt	4/4	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.374027669336537	2		671	837	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238143	133238143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048585-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	105	453	0	ENST00000320574.5:c.2834C>T	p.Ser945Phe	p.S945F	ENST00000320574	NM_006231.2	945	tCc/tTc	24/49	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.374027669336537	2		453	529	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007683	45007689	+	frameshift_variant	Frame_Shift_Del	DEL	AATTGCT	AATTGCT	-	novel	NA	P-0048585-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	140	360	0	ENST00000558401.1:c.131_137del	p.Asn44MetfsTer15	p.N44Mfs*15	ENST00000558401	NM_004048.2	44	AATTGCTat/at	2/4	0.359881098783516	2	FACETS	0.965	0.888	1	0.965	0.888	1	CLONAL	2	TRUE	0	0.374027669336537	2		360	388	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647875	3647875	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569588858	NA	P-0048585-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	280	807	0	ENST00000294008.3:c.1289C>T	p.Ser430Leu	p.S430L	ENST00000294008	NM_032444.2	430	tCg/tTg	6/15	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.374027669336537	2		807	1213	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820750	3820750	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148286133	NA	P-0048585-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	332	893	1	ENST00000262367.5:c.2701C>T	p.Pro901Ser	p.P901S	ENST00000262367	NM_004380.2	901	Ccg/Tcg	14/31	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.374027669336537	2		894	1292	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541586	29541586	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048585-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	66	289	0	ENST00000356175.3:c.1510C>T	p.Pro504Ser	p.P504S	ENST00000356175	NM_000267.3	504	Cca/Tca	13/57	0.335270077572339	2	FACETS	1	0.974	1	0.735	0.646	0.829	CLONAL	1	TRUE	0	0.374027669336537	2		289	240	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896556	78896557	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0048585-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	722	856	1	ENST00000306801.3:c.2553_2554delinsAA	p.Asp852Asn	p.D852N	ENST00000306801	NM_020761.2	851	ctGGac/ctAAac	22/34	0.374027669336537	3	FACETS	0.882	0.856	0.908	1	0.996	1	CLONAL	4	TRUE	0	0.374027669336537	3		857	1299	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976138	18976139	+	missense_variant	Missense_Mutation	DNP	TG	TG	AT	novel	NA	P-0048585-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	387	906	0	ENST00000262803.5:c.2898_2899delinsAT	p.Gly967Cys	p.G967C	ENST00000262803	NM_002911.3	966	atTGgc/atATgc	21/24	0.374027669336537	3	FACETS	0.95	0.902	0.998	0.95	0.902	0.998	CLONAL	2	TRUE	1	0.374027669336537	3		906	1293	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431076	181431076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048585-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	347	615	0	ENST00000325404.1:c.928G>A	p.Gly310Ser	p.G310S	ENST00000325404	NM_003106.3	310	Ggc/Agc	1/1	0.335270077572339	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.374027669336537	2		615	872	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169002	32169002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048585-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	444	817	0	ENST00000375023.3:c.4031G>A	p.Gly1344Glu	p.G1344E	ENST00000375023	NM_004557.3	1344	gGg/gAg	22/30	0.309052510525787	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.374027669336537	4		817	1509	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945662	151945662	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs371433674	NA	P-0048585-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	117	705	0	ENST00000262189.6:c.1857T>G	p.Ile619Met	p.I619M	ENST00000262189	NM_170606.2	619	atT/atG	14/59	0.374027669336537	3	FACETS	0.939	0.847	1	0.469	0.423	0.518	CLONAL	1	TRUE	1	0.374027669336537	3		705	791	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69012034	69012034	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048585-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	102	552	0	ENST00000288368.4:c.2671G>A	p.Glu891Lys	p.E891K	ENST00000288368	NM_024870.2	891	Gaa/Aaa	23/40	0.374027669336537	3	FACETS	0.985	0.882	1	0.493	0.441	0.548	CLONAL	1	TRUE	1	0.374027669336537	3		552	657	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0048606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	223	951	2	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	1	0.292447540282723	2		953	625	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591892	48591892	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	121	767	0	ENST00000342988.3:c.1055G>T	p.Gly352Val	p.G352V	ENST00000342988	NM_005359.5	352	gGa/gTa	9/12	0.252324618465325	2	FACETS	0.797	0.724	0.874	0.797	0.724	0.874	SUBCLONAL	2	TRUE	0	0.292447540282723	2		767	519	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428327	33428327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781813	NA	P-0048606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	173	717	0	ENST00000345365.6:c.796C>T	p.Arg266Cys	p.R266C	ENST00000345365	NM_002878.3	266	Cgc/Tgc	9/10	0.225994848201297	4	FACETS	0.97	0.895	1	0.97	0.895	1	CLONAL	2	TRUE	2	0.292447540282723	4		717	788	SUCCESS
APC	324	MSKCC	GRCh37	5	112151191	112151191	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0048606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	65	495	0	ENST00000257430.4:c.835-1G>A		p.X279_splice	ENST00000257430	NM_000038.5	279			0.128243640406939	3	FACETS	1	0.97	1	0.476	0.415	0.541	INDETERMINATE	1	TRUE	0	0.292447540282723	3		495	357	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827429	72827429	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	147	843	0	ENST00000268489.5:c.9152A>C	p.Lys3051Thr	p.K3051T	ENST00000268489	NM_006885.3	3051	aAa/aCa	9/10	0.0747111578396262	3	FACETS	0.999	0.916	1	0.999	0.916	1	INDETERMINATE	2	TRUE	1	0.292447540282723	3		843	577	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662914	52662914	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1348721028	NA	P-0048606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	251	550	0	ENST00000394830.3:c.1439T>C	p.Met480Thr	p.M480T	ENST00000394830	NM_018313.4	480	aTg/aCg	13/30	0.262175580870766	4	FACETS	1	0.984	1	0.843	0.794	0.893	CLONAL	3	TRUE	0	0.292447540282723	4		550	658	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026096	71026096	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	75	474	0	ENST00000318789.4:c.1526G>C	p.Trp509Ser	p.W509S	ENST00000318789	NM_032682.5	509	tGg/tCg	17/21	0.262175580870766	4	FACETS	1	0.899	1	0.257	0.225	0.292	CLONAL	1	TRUE	0	0.292447540282723	4		474	644	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540508	187540508	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	116	614	0	ENST00000441802.2:c.7232G>T	p.Cys2411Phe	p.C2411F	ENST00000441802	NM_005245.3	2411	tGt/tTt	10/27	1	2	FACETS	0.853	0.773	0.936	1	0.987	1	CLONAL	2	TRUE	1	0.292447540282723	2		614	465	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741671	145741671	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749625708	NA	P-0048606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	845	1002	2	ENST00000428558.2:c.832G>A	p.Glu278Lys	p.E278K	ENST00000428558	NM_004260.3	278	Gag/Aag	5/22	0.292447540282723	10	FACETS	0.958	0.932	0.984	1	0.994	1	CLONAL	9	TRUE	2	0.292447540282723	10		1004	1454	SUCCESS
APC	324	MSKCC	GRCh37	5	112157613	112157613	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658802	NA	P-0048723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	57	563	0	ENST00000257430.4:c.1333C>T	p.Gln445Ter	p.Q445*	ENST00000257430	NM_000038.5	445	Cag/Tag	11/16	1	2	FACETS	0.786	0.677	0.903	0.786	0.677	0.903	CLONAL	1	TRUE	1	0.411038736104474	2		563	353	SUCCESS
APC	324	MSKCC	GRCh37	5	112176027	112176030	+	frameshift_variant	Frame_Shift_Del	DEL	TTAT	TTAT	-	novel	NA	P-0048723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	54	310	0	ENST00000257430.4:c.4738_4741del	p.Ile1580LeufsTer69	p.I1580Lfs*69	ENST00000257430	NM_000038.5	1579	aTTATt/at	16/16	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.411038736104474	2		310	262	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491282	2491282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1357340259	NA	P-0048723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	172	831	2	ENST00000355716.4:c.325C>T	p.Arg109Trp	p.R109W	ENST00000355716	NM_003820.2	109	Cgg/Tgg	4/8	1	2	FACETS	0.945	0.87	1	0.945	0.87	1	CLONAL	1	TRUE	1	0.411038736104474	2		833	886	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577021	7577022	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCTTA	novel	NA	P-0048723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	311	673	0	ENST00000269305.4:c.912_916dup	p.Arg306LeufsTer41	p.R306Lfs*41	ENST00000269305	NM_001126112.2	306	cga/cTAAGCga	8/11	0.411038736104474	2	FACETS	0.968	0.917	1	0.968	0.917	1	CLONAL	2	TRUE	0	0.411038736104474	2		673	782	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964948	25964948	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	104	535	1	ENST00000435504.4:c.4258G>T	p.Asp1420Tyr	p.D1420Y	ENST00000435504		1420	Gat/Tat	13/13	0.385571021742052	3	FACETS	0.946	0.848	1	0.473	0.424	0.525	CLONAL	1	TRUE	1	0.411038736104474	3		536	645	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	10	308	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.056	0.037	0.079	0.056	0.037	0.079	SUBCLONAL	1	TRUE	1	0.828270714287574	2		308	433	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	98	348	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.828270714287574	2		349	229	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412252	139412252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057523819	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	38	697	0	ENST00000277541.6:c.1393G>A	p.Ala465Thr	p.A465T	ENST00000277541	NM_017617.3	465	Gcc/Acc	8/34	1	2	FACETS	0.125	0.102	0.15	0.125	0.102	0.15	SUBCLONAL	1	TRUE	1	0.828270714287574	2		697	737	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096334	2096334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139165943	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	31	657	1	ENST00000219066.1:c.173C>T	p.Pro58Leu	p.P58L	ENST00000219066	NM_002528.5	58	cCg/cTg	2/6	1	2	FACETS	0.123	0.098	0.15	0.123	0.098	0.15	SUBCLONAL	1	TRUE	1	0.828270714287574	2		658	611	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	116	263	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.904	0.826	0.983	0.904	0.826	0.983	CLONAL	1	TRUE	1	0.828270714287574	2		263	310	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174889	11174889	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	31	470	0	ENST00000361445.4:c.7145T>C	p.Met2382Thr	p.M2382T	ENST00000361445	NM_004958.3	2382	aTg/aCg	52/58	0.828270714287574	1	FACETS	0.143	0.115	0.174	0.143	0.115	0.174	SUBCLONAL	1	TRUE	0	0.828270714287574	1		470	307	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089494	27089494	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	21	588	0	ENST00000324856.7:c.2450C>T	p.Ala817Val	p.A817V	ENST00000324856	NM_006015.4	817	gCc/gTc	8/20	0.828270714287574	1	FACETS	0.097	0.074	0.123	0.097	0.074	0.123	SUBCLONAL	1	TRUE	0	0.828270714287574	1		588	307	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509418	46509418	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	21	538	0	ENST00000262741.5:c.1313T>C	p.Val438Ala	p.V438A	ENST00000262741	NM_003629.3	438	gTt/gCt	10/10	0.828270714287574	1	FACETS	0.097	0.074	0.123	0.097	0.074	0.123	SUBCLONAL	1	TRUE	0	0.828270714287574	1		538	307	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439698	51439698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	140	387	0	ENST00000262662.1:c.263C>T	p.Thr88Ile	p.T88I	ENST00000262662		88	aCt/aTt	4/4	0.828270714287574	1	FACETS	0.865	0.81	0.918	0.865	0.81	0.918	CLONAL	1	TRUE	0	0.828270714287574	1		387	229	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163298661	163298661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1172182551	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	204	481	0	ENST00000271452.3:c.301G>A	p.Val101Met	p.V101M	ENST00000271452	NM_145697.2	101	Gtg/Atg	5/14	1	2	FACETS	0.849	0.793	0.907	0.849	0.793	0.907	CLONAL	1	TRUE	1	0.828270714287574	2		481	580	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957426	175957426	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	32	293	0	ENST00000367669.3:c.1970G>A	p.Cys657Tyr	p.C657Y	ENST00000367669	NM_022457.5	657	tGt/tAt	17/20	1	2	FACETS	0.198	0.161	0.241	0.198	0.161	0.241	SUBCLONAL	1	TRUE	1	0.828270714287574	2		293	390	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567722	226567722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879911445	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	195	557	0	ENST00000366794.5:c.1444G>A	p.Gly482Arg	p.G482R	ENST00000366794	NM_001618.3	482	Ggg/Agg	10/23	1	2	FACETS	0.927	0.866	0.989	0.927	0.866	0.989	CLONAL	1	TRUE	1	0.828270714287574	2		557	508	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669369	241669369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	197	412	0	ENST00000366560.3:c.838G>A	p.Gly280Ser	p.G280S	ENST00000366560	NM_000143.3	280	Ggt/Agt	6/10	1	2	FACETS	0.837	0.781	0.895	0.837	0.781	0.895	CLONAL	1	TRUE	1	0.828270714287574	2		412	568	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100678	8100678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	205	668	0	ENST00000346208.3:c.652C>T	p.Pro218Ser	p.P218S	ENST00000346208		218	Ccc/Tcc	3/6	1	2	FACETS	0.868	0.811	0.927	0.868	0.811	0.927	CLONAL	1	TRUE	1	0.828270714287574	2		668	570	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595972	43595972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529018971	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	49	646	0	ENST00000355710.3:c.139G>A	p.Gly47Ser	p.G47S	ENST00000355710	NM_020975.4	47	Ggc/Agc	2/20	1	2	FACETS	0.187	0.158	0.219	0.187	0.158	0.219	SUBCLONAL	1	TRUE	1	0.828270714287574	2		646	632	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601969	43601969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377767433	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	219	757	0	ENST00000355710.3:c.1013C>T	p.Thr338Ile	p.T338I	ENST00000355710	NM_020975.4	338	aCc/aTc	5/20	1	2	FACETS	0.901	0.844	0.959	0.901	0.844	0.959	CLONAL	1	TRUE	1	0.828270714287574	2		757	587	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649921	88649921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	165	355	0	ENST00000372037.3:c.170C>T	p.Pro57Leu	p.P57L	ENST00000372037	NM_004329.2	57	cCt/cTt	4/13	1	2	FACETS	0.903	0.838	0.97	0.903	0.838	0.97	CLONAL	1	TRUE	1	0.828270714287574	2		355	441	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692802	89692802	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123320	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	119	256	0	ENST00000371953.3:c.286C>T	p.Pro96Ser	p.P96S	ENST00000371953	NM_000314.4	96	Cca/Tca	5/9	1	2	FACETS	0.785	0.716	0.856	0.785	0.716	0.856	SUBCLONAL	1	TRUE	1	0.828270714287574	2		256	366	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711960	89711960	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1554900620	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	26	359	0	ENST00000371953.3:c.578T>C	p.Leu193Pro	p.L193P	ENST00000371953	NM_000314.4	193	cTg/cCg	6/9	1	2	FACETS	0.146	0.115	0.181	0.146	0.115	0.181	SUBCLONAL	1	TRUE	1	0.828270714287574	2		359	430	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207523	102207523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	166	322	0	ENST00000263464.3:c.1612G>A	p.Asp538Asn	p.D538N	ENST00000263464	NM_001165.4	538	Gat/Aat	8/9	1	2	FACETS	0.815	0.754	0.877	0.815	0.754	0.877	CLONAL	1	TRUE	1	0.828270714287574	2		322	492	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207736	102207736	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	169	340	0	ENST00000263464.3:c.1718G>A	p.Gly573Asp	p.G573D	ENST00000263464	NM_001165.4	573	gGt/gAt	9/9	1	2	FACETS	0.895	0.831	0.96	0.895	0.831	0.96	CLONAL	1	TRUE	1	0.828270714287574	2		340	456	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376035	118376035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	151	495	0	ENST00000534358.1:c.9428C>T	p.Pro3143Leu	p.P3143L	ENST00000534358	NM_005933.3	3143	cCa/cTa	27/36	1	2	FACETS	0.86	0.794	0.927	0.86	0.794	0.927	CLONAL	1	TRUE	1	0.828270714287574	2		495	424	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380704	118380704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	148	369	0	ENST00000534358.1:c.10942C>T	p.Pro3648Ser	p.P3648S	ENST00000534358	NM_005933.3	3648	Cca/Tca	30/36	1	2	FACETS	0.847	0.781	0.914	0.847	0.781	0.914	CLONAL	1	TRUE	1	0.828270714287574	2		369	422	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	493265	493265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	167	388	0	ENST00000399788.2:c.298C>T	p.Leu100Phe	p.L100F	ENST00000399788	NM_001042603.1	100	Ctt/Ttt	3/28	NA	2	FACETS	0.823	0.762	0.885			1	INDETERMINATE	1	TRUE	NA	0.828270714287574	2		388	490	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418630	49418630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	182	533	0	ENST00000301067.7:c.15884G>A	p.Gly5295Glu	p.G5295E	ENST00000301067	NM_003482.3	5295	gGg/gAg	49/54	1	2	FACETS	0.84	0.781	0.901	0.84	0.781	0.901	CLONAL	1	TRUE	1	0.828270714287574	2		533	523	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426993	49426993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	199	622	0	ENST00000301067.7:c.11495C>T	p.Ser3832Phe	p.S3832F	ENST00000301067	NM_003482.3	3832	tCc/tTc	39/54	1	2	FACETS	0.882	0.823	0.941	0.882	0.823	0.941	CLONAL	1	TRUE	1	0.828270714287574	2		622	545	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856250	111856250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1246649893	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	25	118	1	ENST00000341259.2:c.301G>A	p.Glu101Lys	p.E101K	ENST00000341259	NM_005475.2	101	Gag/Aag	2/8	1	2	FACETS	0.549	0.44	0.668	0.549	0.44	0.668	SUBCLONAL	1	TRUE	1	0.828270714287574	2		119	110	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562384	21562384	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	219	566	0	ENST00000382592.4:c.1535G>A	p.Arg512Lys	p.R512K	ENST00000382592	NM_014572.2	512	aGg/aAg	4/8	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.828270714287574	2		566	527	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26927898	26927898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	156	267	0	ENST00000381527.3:c.337G>A	p.Ala113Thr	p.A113T	ENST00000381527	NM_001260.1	113	Gct/Act	4/13	1	2	FACETS	0.942	0.873	1	0.942	0.873	1	CLONAL	1	TRUE	1	0.828270714287574	2		267	400	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623565	28623565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752394054	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	154	393	0	ENST00000241453.7:c.992C>T	p.Ser331Phe	p.S331F	ENST00000241453	NM_004119.2	331	tCc/tTc	8/24	1	2	FACETS	0.843	0.779	0.909	0.843	0.779	0.909	CLONAL	1	TRUE	1	0.828270714287574	2		393	441	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911308	32911308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	217	417	0	ENST00000380152.3:c.2816C>T	p.Thr939Ile	p.T939I	ENST00000380152		939	aCc/aTc	11/27	1	2	FACETS	0.866	0.811	0.923	0.866	0.811	0.923	CLONAL	1	TRUE	1	0.828270714287574	2		417	605	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050972	49050972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1460190600	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	119	249	0	ENST00000267163.4:c.2656G>A	p.Asp886Asn	p.D886N	ENST00000267163	NM_000321.2	886	Gat/Aat	25/27	1	2	FACETS	0.89	0.814	0.967	0.89	0.814	0.967	CLONAL	1	TRUE	1	0.828270714287574	2		249	323	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582881	95582881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	164	282	0	ENST00000393063.1:c.1661G>A	p.Arg554Lys	p.R554K	ENST00000393063	NM_030621.3	554	aGg/aAg	11/28	1	2	FACETS	0.988	0.918	1	0.988	0.918	1	CLONAL	1	TRUE	1	0.828270714287574	2		282	401	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003236	42003236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	227	451	0	ENST00000219905.7:c.2773C>T	p.Pro925Ser	p.P925S	ENST00000219905	NM_001164273.1	925	Cca/Tca	8/24	1	2	FACETS	0.95	0.892	1	0.95	0.892	1	CLONAL	1	TRUE	1	0.828270714287574	2		451	577	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712548	43712548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	273	618	1	ENST00000382044.4:c.4636G>A	p.Asp1546Asn	p.D1546N	ENST00000382044	NM_001141980.1	1546	Gac/Aac	21/28	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.828270714287574	2		619	652	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720356	43720358	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs755965497	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	183	465	0	ENST00000382044.4:c.3684_3686del	p.Glu1229del	p.E1229del	ENST00000382044	NM_001141980.1	1228	gaAGAg/gag	18/28	1	2	FACETS	0.775	0.72	0.832	0.775	0.72	0.832	SUBCLONAL	1	TRUE	1	0.828270714287574	2		465	570	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729231	66729231	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	199	431	0	ENST00000307102.5:c.438+1G>A		p.X146_splice	ENST00000307102	NM_002755.3	146			1	2	FACETS	0.991	0.927	1	0.991	0.927	1	CLONAL	1	TRUE	1	0.828270714287574	2		431	485	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2107181	2107181	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	29	686	0	ENST00000219476.3:c.848+2T>C		p.X283_splice	ENST00000219476	NM_000548.3	283			1	2	FACETS	0.126	0.101	0.155	0.126	0.101	0.155	SUBCLONAL	1	TRUE	1	0.828270714287574	2		686	555	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134271	2134271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	218	754	0	ENST00000219476.3:c.4048G>A	p.Glu1350Lys	p.E1350K	ENST00000219476	NM_000548.3	1350	Gag/Aag	34/42	1	2	FACETS	0.87	0.815	0.927	0.87	0.815	0.927	CLONAL	1	TRUE	1	0.828270714287574	2		754	605	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2645846	2645846	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753410336	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	20	438	0	ENST00000342085.4:c.1396C>T	p.Arg466Trp	p.R466W	ENST00000342085	NM_002613.4	466	Cgg/Tgg	12/14	1	2	FACETS	0.121	0.092	0.156	0.121	0.092	0.156	SUBCLONAL	1	TRUE	1	0.828270714287574	2		438	398	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656481	3656481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	210	572	0	ENST00000294008.3:c.754G>A	p.Gly252Arg	p.G252R	ENST00000294008	NM_032444.2	252	Ggg/Agg	3/15	1	2	FACETS	0.876	0.819	0.934	0.876	0.819	0.934	CLONAL	1	TRUE	1	0.828270714287574	2		572	579	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777883	3777883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	208	769	0	ENST00000262367.5:c.7165G>A	p.Val2389Ile	p.V2389I	ENST00000262367	NM_004380.2	2389	Gtc/Atc	31/31	1	2	FACETS	0.844	0.789	0.901	0.844	0.789	0.901	CLONAL	1	TRUE	1	0.828270714287574	2		769	595	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934639	9934639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368188808	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	126	358	0	ENST00000330684.3:c.1516G>A	p.Val506Ile	p.V506I	ENST00000330684	NM_001134407.1	506	Gtc/Atc	7/13	1	2	FACETS	0.89	0.816	0.965	0.89	0.816	0.965	CLONAL	1	TRUE	1	0.828270714287574	2		358	342	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014128	14014128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	195	595	0	ENST00000311895.7:c.106G>A	p.Ala36Thr	p.A36T	ENST00000311895	NM_005236.2	36	Gcc/Acc	1/11	1	2	FACETS	0.899	0.839	0.96	0.899	0.839	0.96	CLONAL	1	TRUE	1	0.828270714287574	2		595	524	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132631	67132631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	152	448	0	ENST00000412916.2:c.514C>T	p.Pro172Ser	p.P172S	ENST00000412916		172	Cct/Tct	6/6	1	2	FACETS	0.722	0.665	0.782	0.722	0.665	0.782	SUBCLONAL	1	TRUE	1	0.828270714287574	2		448	508	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662414	67662414	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	242	602	0	ENST00000264010.4:c.1660G>A	p.Ala554Thr	p.A554T	ENST00000264010	NM_006565.3	554	Gct/Act	9/12	1	2	FACETS	0.936	0.881	0.993	0.936	0.881	0.993	CLONAL	1	TRUE	1	0.828270714287574	2		602	624	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991846	72991846	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	32	528	0	ENST00000268489.5:c.2199C>A	p.Tyr733Ter	p.Y733*	ENST00000268489	NM_006885.3	733	taC/taA	2/10	1	2	FACETS	0.138	0.111	0.168	0.138	0.111	0.168	SUBCLONAL	1	TRUE	1	0.828270714287574	2		528	560	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991953	72991953	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375392183	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	206	523	0	ENST00000268489.5:c.2092G>A	p.Gly698Arg	p.G698R	ENST00000268489	NM_006885.3	698	Ggg/Agg	2/10	1	2	FACETS	0.953	0.892	1	0.953	0.892	1	CLONAL	1	TRUE	1	0.828270714287574	2		523	522	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341586	89341586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	153	538	0	ENST00000301030.4:c.7484C>T	p.Pro2495Leu	p.P2495L	ENST00000301030	NM_001256183.1	2495	cCc/cTc	10/13	1	2	FACETS	0.98	0.908	1	0.98	0.908	1	CLONAL	1	TRUE	1	0.828270714287574	2		538	377	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349940	89349940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	203	666	0	ENST00000301030.4:c.3010C>T	p.His1004Tyr	p.H1004Y	ENST00000301030	NM_001256183.1	1004	Cac/Tac	9/13	1	2	FACETS	0.82	0.765	0.876	0.82	0.765	0.876	CLONAL	1	TRUE	1	0.828270714287574	2		666	598	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845385	89845385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	223	601	2	ENST00000389301.3:c.1742C>T	p.Ser581Phe	p.S581F	ENST00000389301	NM_000135.2	581	tCc/tTc	19/43	1	2	FACETS	0.94	0.882	0.999	0.94	0.882	0.999	CLONAL	1	TRUE	1	0.828270714287574	2		603	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578412	7578412	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519747	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	20	645	0	ENST00000269305.4:c.518T>A	p.Val173Glu	p.V173E	ENST00000269305	NM_001126112.2	173	gTg/gAg	5/11	1	2	FACETS	0.08	0.06	0.103	0.08	0.06	0.103	SUBCLONAL	1	TRUE	1	0.828270714287574	2		645	606	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108696	8108696	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	117	455	0	ENST00000585124.1:c.699G>A	p.Met233Ile	p.M233I	ENST00000585124	NM_004217.3	233	atG/atA	8/9	1	2	FACETS	0.728	0.663	0.796	0.728	0.663	0.796	SUBCLONAL	1	TRUE	1	0.828270714287574	2		455	388	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011158	12011158	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	143	327	0	ENST00000353533.5:c.565T>C	p.Tyr189His	p.Y189H	ENST00000353533	NM_003010.3	189	Tac/Cac	5/11	1	2	FACETS	0.727	0.668	0.788	0.727	0.668	0.788	SUBCLONAL	1	TRUE	1	0.828270714287574	2		327	475	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973754	15973754	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	27	450	0	ENST00000268712.3:c.4238T>C	p.Leu1413Pro	p.L1413P	ENST00000268712	NM_006311.3	1413	cTa/cCa	31/46	1	2	FACETS	0.142	0.112	0.176	0.142	0.112	0.176	SUBCLONAL	1	TRUE	1	0.828270714287574	2		450	459	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16046997	16046997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	135	284	0	ENST00000268712.3:c.1096G>A	p.Gly366Arg	p.G366R	ENST00000268712	NM_006311.3	366	Gga/Aga	11/46	1	2	FACETS	0.807	0.741	0.875	0.807	0.741	0.875	CLONAL	1	TRUE	1	0.828270714287574	2		284	404	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17120409	17120409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779913370	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	24	456	1	ENST00000285071.4:c.1150G>A	p.Val384Ile	p.V384I	ENST00000285071	NM_144997.5	384	Gtc/Atc	10/14	1	2	FACETS	0.126	0.098	0.158	0.126	0.098	0.158	SUBCLONAL	1	TRUE	1	0.828270714287574	2		457	461	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17124922	17124922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	173	574	0	ENST00000285071.4:c.800G>A	p.Ser267Asn	p.S267N	ENST00000285071	NM_144997.5	267	aGc/aAc	8/14	1	2	FACETS	0.776	0.719	0.835	0.776	0.719	0.835	SUBCLONAL	1	TRUE	1	0.828270714287574	2		574	538	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548913	29548913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	83	317	0	ENST00000356175.3:c.1687C>T	p.Pro563Ser	p.P563S	ENST00000356175	NM_000267.3	563	Cct/Tct	15/57	1	2	FACETS	0.579	0.515	0.647	0.579	0.515	0.647	SUBCLONAL	1	TRUE	1	0.828270714287574	2		317	346	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37865703	37865703	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	125	406	0	ENST00000269571.5:c.572C>T	p.Ala191Val	p.A191V	ENST00000269571		191	gCc/gTc	4/27	1	2	FACETS	0.843	0.772	0.916	0.843	0.772	0.916	CLONAL	1	TRUE	1	0.828270714287574	2		406	358	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40879700	40879700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	195	418	0	ENST00000428826.2:c.199C>T	p.Pro67Ser	p.P67S	ENST00000428826		67	Cct/Tct	4/21	1	2	FACETS	0.867	0.809	0.927	0.867	0.809	0.927	CLONAL	1	TRUE	1	0.828270714287574	2		418	543	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40880884	40880884	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	244	512	0	ENST00000428826.2:c.76C>T	p.Leu26Phe	p.L26F	ENST00000428826		26	Ctt/Ttt	3/21	1	2	FACETS	0.89	0.837	0.944	0.89	0.837	0.944	CLONAL	1	TRUE	1	0.828270714287574	2		512	662	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243967	41243967	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357290	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	167	468	0	ENST00000357654.3:c.3581C>T	p.Thr1194Ile	p.T1194I	ENST00000357654	NM_007294.3	1194	aCc/aTc	10/23	1	2	FACETS	0.845	0.784	0.909	0.845	0.784	0.909	CLONAL	1	TRUE	1	0.828270714287574	2		468	477	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804402	46804402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	176	484	0	ENST00000290295.7:c.605C>T	p.Ser202Phe	p.S202F	ENST00000290295	NM_006361.5	202	tCc/tTc	2/2	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.828270714287574	2		484	416	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47679312	47679312	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371674237	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	158	449	1	ENST00000347630.2:c.895G>A	p.Val299Met	p.V299M	ENST00000347630	NM_001007230.1	299	Gtg/Atg	10/11	1	2	FACETS	0.788	0.728	0.85	0.788	0.728	0.85	SUBCLONAL	1	TRUE	1	0.828270714287574	2		450	484	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534422	63534422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	258	671	0	ENST00000307078.5:c.1099C>T	p.Pro367Ser	p.P367S	ENST00000307078	NM_004655.3	367	Ccc/Tcc	5/11	1	2	FACETS	0.93	0.876	0.984	0.93	0.876	0.984	CLONAL	1	TRUE	1	0.828270714287574	2		671	670	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554720	63554720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878854723	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	164	462	0	ENST00000307078.5:c.19G>A	p.Val7Met	p.V7M	ENST00000307078	NM_004655.3	7	Gtg/Atg	2/11	1	2	FACETS	0.99	0.92	1	0.99	0.92	1	CLONAL	1	TRUE	1	0.828270714287574	2		462	400	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66521968	66521968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	132	280	0	ENST00000358598.2:c.623G>A	p.Gly208Glu	p.G208E	ENST00000358598	NM_212471.2	208	gGa/gAa	7/11	1	2	FACETS	0.871	0.8	0.944	0.871	0.8	0.944	CLONAL	1	TRUE	1	0.828270714287574	2		280	366	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867596	78867596	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	37	660	0	ENST00000306801.3:c.2332A>G	p.Ile778Val	p.I778V	ENST00000306801	NM_020761.2	778	Atc/Gtc	20/34	1	2	FACETS	0.154	0.126	0.185	0.154	0.126	0.185	SUBCLONAL	1	TRUE	1	0.828270714287574	2		660	581	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56378151	56378151	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	24	295	0	ENST00000348428.3:c.926-2A>G		p.X309_splice	ENST00000348428	NM_006785.3	309			1	2	FACETS	0.134	0.104	0.168	0.134	0.104	0.168	SUBCLONAL	1	TRUE	1	0.828270714287574	2		295	434	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60795956	60795956	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	168	465	0	ENST00000333681.4:c.622C>T	p.Pro208Ser	p.P208S	ENST00000333681		208	Cct/Tct	3/3	1	2	FACETS	0.815	0.755	0.876	0.815	0.755	0.876	CLONAL	1	TRUE	1	0.828270714287574	2		465	498	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612236	1612236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	196	577	0	ENST00000344749.5:c.1783G>A	p.Val595Ile	p.V595I	ENST00000344749	NM_001136139.2	595	Gtc/Atc	18/19	1	2	FACETS	0.968	0.905	1	0.968	0.905	1	CLONAL	1	TRUE	1	0.828270714287574	2		577	489	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244098	5244098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs73545312	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	125	723	1	ENST00000357368.4:c.1384G>A	p.Val462Ile	p.V462I	ENST00000357368	NM_002850.3	462	Gtc/Atc	11/38	1	2	FACETS	0.443	0.402	0.487	0.443	0.402	0.487	SUBCLONAL	1	TRUE	1	0.828270714287574	2		724	681	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244370	5244370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	277	666	0	ENST00000357368.4:c.1112G>A	p.Ser371Asn	p.S371N	ENST00000357368	NM_002850.3	371	aGc/aAc	11/38	1	2	FACETS	0.972	0.919	1	0.972	0.919	1	CLONAL	1	TRUE	1	0.828270714287574	2		666	688	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353726	15353726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	248	597	1	ENST00000263377.2:c.3154G>A	p.Asp1052Asn	p.D1052N	ENST00000263377	NM_058243.2	1052	Gac/Aac	14/20	1	2	FACETS	0.892	0.839	0.946	0.892	0.839	0.946	CLONAL	1	TRUE	1	0.828270714287574	2		598	671	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15365022	15365022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	205	579	1	ENST00000263377.2:c.2099C>T	p.Ser700Phe	p.S700F	ENST00000263377	NM_058243.2	700	tCc/tTc	11/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.828270714287574	2		580	479	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216627	36216627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	178	671	1	ENST00000222270.7:c.3793C>T	p.Leu1265Phe	p.L1265F	ENST00000222270	NM_014727.1	1265	Ctc/Ttc	13/37	0.828270714287574	1	FACETS	0.815	0.767	0.862	0.815	0.767	0.862	CLONAL	1	TRUE	0	0.828270714287574	1		672	309	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224211	36224211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764595621	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	145	514	2	ENST00000222270.7:c.6761C>T	p.Pro2254Leu	p.P2254L	ENST00000222270	NM_014727.1	2254	cCc/cTc	28/37	0.828270714287574	1	FACETS	0.904	0.849	0.956	0.904	0.849	0.956	CLONAL	1	TRUE	0	0.828270714287574	1		516	227	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752723	42752723	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1410725157	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	33	695	0	ENST00000222329.4:c.1541G>A	p.Arg514His	p.R514H	ENST00000222329	NM_006494.2	514	cGt/cAt	4/4	0.828270714287574	1	FACETS	0.148	0.12	0.179	0.148	0.12	0.179	SUBCLONAL	1	TRUE	0	0.828270714287574	1		695	316	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795243	42795243	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	171	742	0	ENST00000575354.2:c.2327del	p.Pro776LeufsTer148	p.P776Lfs*148	ENST00000575354	NM_015125.3	775	Ccc/cc	10/20	0.828270714287574	1	FACETS	0.703	0.658	0.749	0.703	0.658	0.749	SUBCLONAL	1	TRUE	0	0.828270714287574	1		742	344	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797386	42797386	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	20	759	0	ENST00000575354.2:c.3752del	p.Pro1251HisfsTer51	p.P1251Hfs*51	ENST00000575354	NM_015125.3	1250	Ccc/cc	15/20	0.828270714287574	1	FACETS	0.088	0.067	0.112	0.088	0.067	0.112	SUBCLONAL	1	TRUE	0	0.828270714287574	1		759	323	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920463	50920463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1005672452	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	34	745	0	ENST00000440232.2:c.3155C>T	p.Ser1052Leu	p.S1052L	ENST00000440232	NM_002691.3	1052	tCg/tTg	26/27	0.828270714287574	1	FACETS	0.13	0.106	0.157	0.13	0.106	0.157	SUBCLONAL	1	TRUE	0	0.828270714287574	1		745	369	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029096	26029096	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	22	284	0	ENST00000435504.4:c.252+2T>C		p.X84_splice	ENST00000435504		84			1	2	FACETS	0.16	0.124	0.203	0.16	0.124	0.203	SUBCLONAL	1	TRUE	1	0.828270714287574	2		284	331	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241937	39241937	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	133	312	0	ENST00000402219.2:c.1909C>T	p.Pro637Ser	p.P637S	ENST00000402219	NM_005633.3	637	Cct/Tct	11/23	1	2	FACETS	0.847	0.778	0.918	0.847	0.778	0.918	CLONAL	1	TRUE	1	0.828270714287574	2		312	379	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635695	47635695	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs267607924	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	149	272	0	ENST00000233146.2:c.366+1G>A		p.X122_splice	ENST00000233146	NM_000251.2	122			1	2	FACETS	0.843	0.777	0.909	0.843	0.777	0.909	CLONAL	1	TRUE	1	0.828270714287574	2		272	427	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095902	178095902	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	162	390	0	ENST00000397062.3:c.1429C>T	p.Pro477Ser	p.P477S	ENST00000397062	NM_006164.4	477	Cct/Tct	5/5	1	2	FACETS	0.916	0.85	0.984	0.916	0.85	0.984	CLONAL	1	TRUE	1	0.828270714287574	2		390	427	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267335	198267337	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	157	432	0	ENST00000335508.6:c.2020_2022del	p.Leu674del	p.L674del	ENST00000335508	NM_012433.2	674	CTT/-	14/25	1	2	FACETS	0.733	0.676	0.792	0.733	0.676	0.792	SUBCLONAL	1	TRUE	1	0.828270714287574	2		432	517	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202123063	202123063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	130	333	0	ENST00000358485.4:c.109G>A	p.Gly37Arg	p.G37R	ENST00000358485	NM_001080125.1	37	Ggg/Agg	1/9	1	2	FACETS	0.897	0.824	0.972	0.897	0.824	0.972	CLONAL	1	TRUE	1	0.828270714287574	2		333	350	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587207	212587207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	199	411	2	ENST00000342788.4:c.794C>T	p.Thr265Ile	p.T265I	ENST00000342788	NM_005235.2	265	aCc/aTc	7/28	1	2	FACETS	0.91	0.85	0.971	0.91	0.85	0.971	CLONAL	1	TRUE	1	0.828270714287574	2		413	528	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661501	227661501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780995783	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	29	683	1	ENST00000305123.5:c.1954C>T	p.Arg652Cys	p.R652C	ENST00000305123	NM_005544.2	652	Cgc/Tgc	1/2	1	2	FACETS	0.134	0.107	0.165	0.134	0.107	0.165	SUBCLONAL	1	TRUE	1	0.828270714287574	2		684	522	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741500	39741500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	158	357	0	ENST00000361337.2:c.1387G>A	p.Glu463Lys	p.E463K	ENST00000361337	NM_003286.2	463	Gaa/Aaa	14/21	1	2	FACETS	0.865	0.8	0.931	0.865	0.8	0.931	CLONAL	1	TRUE	1	0.828270714287574	2		357	441	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231783	36231783	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057519748	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	13	517	1	ENST00000300305.3:c.601C>T	p.Arg201Ter	p.R201*	ENST00000300305		201	Cga/Tga	5/8	1	2	FACETS	0.057	0.04	0.078	0.057	0.04	0.078	SUBCLONAL	1	TRUE	1	0.828270714287574	2		518	552	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655382	45655382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749547790	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	56	668	1	ENST00000407780.3:c.470C>T	p.Thr157Met	p.T157M	ENST00000407780	NM_001283052.1	157	aCg/aTg	4/7	1	2	FACETS	0.216	0.185	0.25	0.216	0.185	0.25	SUBCLONAL	1	TRUE	1	0.828270714287574	2		669	626	SUCCESS
NF2	4771	MSKCC	GRCh37	22	29999991	29999991	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	78	292	0	ENST00000338641.4:c.4G>A	p.Ala2Thr	p.A2T	ENST00000338641	NM_000268.3	2	Gcc/Acc	1/16	1	2	FACETS	0.942	0.845	1	0.942	0.845	1	CLONAL	1	TRUE	1	0.828270714287574	2		292	200	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421214	12421214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1010142067	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	167	434	0	ENST00000287820.6:c.94G>A	p.Val32Ile	p.V32I	ENST00000287820	NM_015869.4	32	Gtt/Att	2/7	1	2	FACETS	0.877	0.813	0.941	0.877	0.813	0.941	CLONAL	1	TRUE	1	0.828270714287574	2		434	460	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650412	12650412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762448032	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	100	325	0	ENST00000251849.4:c.434C>T	p.Thr145Met	p.T145M	ENST00000251849	NM_002880.3	145	aCg/aTg	5/17	1	2	FACETS	0.624	0.562	0.689	0.624	0.562	0.689	SUBCLONAL	1	TRUE	1	0.828270714287574	2		325	387	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278085	41278085	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	24	379	0	ENST00000349496.5:c.1961A>G	p.Tyr654Cys	p.Y654C	ENST00000349496	NM_001904.3	654	tAt/tGt	13/15	1	2	FACETS	0.159	0.124	0.199	0.159	0.124	0.199	SUBCLONAL	1	TRUE	1	0.828270714287574	2		379	364	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098809	47098810	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	185	579	0	ENST00000409792.3:c.6464_6465del	p.Leu2155ArgfsTer3	p.L2155Rfs*3	ENST00000409792	NM_014159.6	2155	cTT/c	15/21	1	2	FACETS	0.809	0.752	0.868	0.809	0.752	0.868	CLONAL	1	TRUE	1	0.828270714287574	2		579	552	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125401	47125401	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	184	376	0	ENST00000409792.3:c.5869del	p.Asp1957ThrfsTer4	p.D1957Tfs*4	ENST00000409792	NM_014159.6	1957	Gac/ac	12/21	1	2	FACETS	0.981	0.915	1	0.981	0.915	1	CLONAL	1	TRUE	1	0.828270714287574	2		376	453	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165642	47165642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1375690681	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	178	468	1	ENST00000409792.3:c.484G>A	p.Ala162Thr	p.A162T	ENST00000409792	NM_014159.6	162	Gca/Aca	3/21	1	2	FACETS	0.867	0.805	0.929	0.867	0.805	0.929	CLONAL	1	TRUE	1	0.828270714287574	2		469	496	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934016	49934016	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	28	681	0	ENST00000296474.3:c.2396T>C	p.Leu799Ser	p.L799S	ENST00000296474	NM_002447.2	799	tTa/tCa	9/20	1	2	FACETS	0.122	0.097	0.15	0.122	0.097	0.15	SUBCLONAL	1	TRUE	1	0.828270714287574	2		681	556	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149243908	149243908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	180	375	1	ENST00000360632.3:c.910C>T	p.Pro304Ser	p.P304S	ENST00000360632	NM_015472.4	304	Cca/Tca	6/7	1	2	FACETS	0.925	0.861	0.99	0.925	0.861	0.99	CLONAL	1	TRUE	1	0.828270714287574	2		376	470	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921488	178921488	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	30	363	0	ENST00000263967.3:c.970A>G	p.Thr324Ala	p.T324A	ENST00000263967	NM_006218.2	324	Aca/Gca	5/21	1	2	FACETS	0.143	0.115	0.175	0.143	0.115	0.175	SUBCLONAL	1	TRUE	1	0.828270714287574	2		363	506	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948088	178948088	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	24	256	0	ENST00000263967.3:c.2860T>C	p.Phe954Leu	p.F954L	ENST00000263967	NM_006218.2	954	Ttt/Ctt	20/21	1	2	FACETS	0.138	0.107	0.173	0.138	0.107	0.173	SUBCLONAL	1	TRUE	1	0.828270714287574	2		256	421	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447294	187447294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	197	563	1	ENST00000232014.4:c.899G>A	p.Ser300Asn	p.S300N	ENST00000232014	NM_001130845.1	300	aGc/aAc	5/10	1	2	FACETS	0.899	0.84	0.96	0.899	0.84	0.96	CLONAL	1	TRUE	1	0.828270714287574	2		564	529	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604263	189604263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	172	481	0	ENST00000264731.3:c.1430C>T	p.Ser477Phe	p.S477F	ENST00000264731	NM_003722.4	477	tCt/tTt	11/14	1	2	FACETS	0.842	0.782	0.905	0.842	0.782	0.905	CLONAL	1	TRUE	1	0.828270714287574	2		481	493	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920106	1920106	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	233	571	0	ENST00000382891.5:c.1166C>T	p.Ser389Phe	p.S389F	ENST00000382891	NM_133335.3	389	tCt/tTt	5/22	1	2	FACETS	0.942	0.886	1	0.942	0.886	1	CLONAL	1	TRUE	1	0.828270714287574	2		571	597	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972098	55972098	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	22	325	0	ENST00000263923.4:c.1546A>G	p.Thr516Ala	p.T516A	ENST00000263923	NM_002253.2	516	Acc/Gcc	12/30	1	2	FACETS	0.15	0.116	0.19	0.15	0.116	0.19	SUBCLONAL	1	TRUE	1	0.828270714287574	2		325	354	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522556	187522556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	162	339	0	ENST00000441802.2:c.11507G>A	p.Gly3836Glu	p.G3836E	ENST00000441802	NM_005245.3	3836	gGa/gAa	21/27	1	2	FACETS	0.875	0.811	0.941	0.875	0.811	0.941	CLONAL	1	TRUE	1	0.828270714287574	2		339	447	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233630	233630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	79	153	0	ENST00000264932.6:c.934C>T	p.Arg312Cys	p.R312C	ENST00000264932	NM_004168.2	312	Cgt/Tgt	8/15	1	2	FACETS	0.983	0.884	1	0.983	0.884	1	CLONAL	1	TRUE	1	0.828270714287574	2		153	194	SUCCESS
APC	324	MSKCC	GRCh37	5	112177554	112177554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	148	319	0	ENST00000257430.4:c.6263C>T	p.Ser2088Leu	p.S2088L	ENST00000257430	NM_000038.5	2088	tCa/tTa	16/16	1	2	FACETS	0.987	0.914	1	0.987	0.914	1	CLONAL	1	TRUE	1	0.828270714287574	2		319	362	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495406	149495406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554107047	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	262	722	0	ENST00000261799.4:c.3241G>A	p.Glu1081Lys	p.E1081K	ENST00000261799	NM_002609.3	1081	Gag/Aag	23/23	1	2	FACETS	0.982	0.927	1	0.982	0.927	1	CLONAL	1	TRUE	1	0.828270714287574	2		722	644	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524370	176524370	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	30	720	0	ENST00000292408.4:c.2231A>G	p.Asp744Gly	p.D744G	ENST00000292408	NM_213647.1	744	gAc/gGc	17/18	1	2	FACETS	0.126	0.101	0.155	0.126	0.101	0.155	SUBCLONAL	1	TRUE	1	0.828270714287574	2		720	575	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176662830	176662830	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	22	351	1	ENST00000439151.2:c.3805T>C	p.Ser1269Pro	p.S1269P	ENST00000439151	NM_022455.4	1269	Tca/Cca	6/23	1	2	FACETS	0.123	0.094	0.156	0.123	0.094	0.156	SUBCLONAL	1	TRUE	1	0.828270714287574	2		352	433	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393187	393187	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	23	418	0	ENST00000380956.4:c.35T>C	p.Phe12Ser	p.F12S	ENST00000380956	NM_001195286.1	12	tTc/tCc	2/9	1	2	FACETS	0.132	0.103	0.167	0.132	0.103	0.167	SUBCLONAL	1	TRUE	1	0.828270714287574	2		418	420	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815325	32815325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	213	653	0	ENST00000354258.4:c.2048G>A	p.Ser683Asn	p.S683N	ENST00000354258	NM_000593.5	683	aGt/aAt	9/11	1	2	FACETS	0.856	0.8	0.912	0.856	0.8	0.912	CLONAL	1	TRUE	1	0.828270714287574	2		653	601	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117717368	117717368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	107	322	0	ENST00000368508.3:c.839C>T	p.Thr280Ile	p.T280I	ENST00000368508	NM_002944.2	280	aCc/aTc	8/43	1	2	FACETS	0.776	0.704	0.85	0.776	0.704	0.85	SUBCLONAL	1	TRUE	1	0.828270714287574	2		322	333	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196861	138196861	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	17	271	0	ENST00000237289.4:c.523G>C	p.Ala175Pro	p.A175P	ENST00000237289	NM_001270507.1	175	Gct/Cct	4/9	1	2	FACETS	0.127	0.094	0.166	0.127	0.094	0.166	SUBCLONAL	1	TRUE	1	0.828270714287574	2		271	323	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265613	152265613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	147	414	0	ENST00000206249.3:c.1066C>T	p.His356Tyr	p.H356Y	ENST00000206249	NM_000125.3	356	Cac/Tac	4/8	1	2	FACETS	0.901	0.832	0.971	0.901	0.832	0.971	CLONAL	1	TRUE	1	0.828270714287574	2		414	394	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55231503	55231503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	167	494	0	ENST00000275493.2:c.1709C>T	p.Thr570Ile	p.T570I	ENST00000275493	NM_005228.3	570	aCc/aTc	14/28	0.771236763870503	3	FACETS	0.858	0.791	0.927	0.429	0.395	0.464	CLONAL	1	TRUE	1	0.828270714287574	3		494	665	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843264	128843264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1389568034	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	255	752	1	ENST00000249373.3:c.371C>T	p.Pro124Leu	p.P124L	ENST00000249373	NM_005631.4	124	cCc/cTc	2/12	0.771236763870503	3	FACETS	0.909	0.852	0.968	0.454	0.426	0.484	CLONAL	1	TRUE	1	0.828270714287574	3		753	958	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852027	128852027	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	209	746	2	ENST00000249373.3:c.2099C>T	p.Thr700Ile	p.T700I	ENST00000249373	NM_005631.4	700	aCc/aTc	12/12	0.771236763870503	3	FACETS	0.918	0.855	0.984	0.459	0.427	0.492	CLONAL	1	TRUE	1	0.828270714287574	3		748	777	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434495	140434495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	65	381	1	ENST00000288602.6:c.2203C>T	p.Arg735Trp	p.R735W	ENST00000288602	NM_004333.4	735	Cgg/Tgg	18/18	0.771236763870503	3	FACETS	0.439	0.381	0.501	0.219	0.19	0.251	SUBCLONAL	1	TRUE	1	0.828270714287574	3		382	506	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874226	151874226	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	137	351	0	ENST00000262189.6:c.8312del	p.Ser2771ThrfsTer7	p.S2771Tfs*7	ENST00000262189	NM_170606.2	2771	aGc/ac	38/59	0.771236763870503	3	FACETS	0.831	0.759	0.906	0.415	0.379	0.453	CLONAL	1	TRUE	1	0.828270714287574	3		351	563	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738520	145738520	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	163	613	0	ENST00000428558.2:c.2465G>A	p.Gly822Asp	p.G822D	ENST00000428558	NM_004260.3	822	gGc/gAc	16/22	1	2	FACETS	0.784	0.725	0.845	0.784	0.725	0.845	SUBCLONAL	1	TRUE	1	0.828270714287574	2		613	502	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340431	8340431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	168	400	0	ENST00000356435.5:c.5165C>T	p.Ala1722Val	p.A1722V	ENST00000356435		1722	gCa/gTa	31/35	1	2	FACETS	0.89	0.826	0.955	0.89	0.826	0.955	CLONAL	1	TRUE	1	0.828270714287574	2		400	456	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22008901	22008901	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	49	561	1	ENST00000276925.6:c.52C>A	p.Leu18Met	p.L18M	ENST00000276925	NM_004936.3	18	Ctg/Atg	1/2	1	2	FACETS	0.207	0.175	0.242	0.207	0.175	0.242	SUBCLONAL	1	TRUE	1	0.828270714287574	2		562	572	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636213	87636213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs988042143	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	118	485	0	ENST00000277120.3:c.2378C>T	p.Thr793Met	p.T793M	ENST00000277120		793	aCg/aTg	19/19	1	2	FACETS	0.732	0.667	0.8	0.732	0.667	0.8	SUBCLONAL	1	TRUE	1	0.828270714287574	2		485	389	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231217	98231217	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766812549	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	233	659	0	ENST00000331920.6:c.2066C>T	p.Pro689Leu	p.P689L	ENST00000331920	NM_000264.3	689	cCc/cTc	14/24	1	2	FACETS	0.867	0.813	0.921	0.867	0.813	0.921	CLONAL	1	TRUE	1	0.828270714287574	2		659	649	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98241300	98241300	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	221	489	0	ENST00000331920.6:c.1197G>A	p.Trp399Ter	p.W399*	ENST00000331920	NM_000264.3	399	tgG/tgA	8/24	1	2	FACETS	0.95	0.891	1	0.95	0.891	1	CLONAL	1	TRUE	1	0.828270714287574	2		489	562	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270447	98270447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1025299062	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	156	387	0	ENST00000331920.6:c.197C>T	p.Ser66Phe	p.S66F	ENST00000331920	NM_000264.3	66	tCc/tTc	1/24	1	2	FACETS	0.821	0.758	0.885	0.821	0.758	0.885	CLONAL	1	TRUE	1	0.828270714287574	2		387	459	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779816	135779816	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768189353	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	164	382	0	ENST00000298552.3:c.2023G>A	p.Asp675Asn	p.D675N	ENST00000298552	NM_001162426.1	675	Gac/Aac	16/23	1	2	FACETS	0.886	0.821	0.952	0.886	0.821	0.952	CLONAL	1	TRUE	1	0.828270714287574	2		382	447	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390926	139390926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	247	839	1	ENST00000277541.6:c.7265G>A	p.Ser2422Asn	p.S2422N	ENST00000277541	NM_017617.3	2422	aGc/aAc	34/34	1	2	FACETS	0.845	0.794	0.897	0.845	0.794	0.897	CLONAL	1	TRUE	1	0.828270714287574	2		840	706	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923844	39923845	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	TA	TA	-	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	190	301	0	ENST00000378444.4:c.3246_3247del	p.Tyr1082Ter	p.Y1082*	ENST00000378444	NM_001123385.1	1082	taTAgt/tagt	7/15	1	1	FACETS	0.985	0.937	1	0.985	0.937	1	CLONAL	1	TRUE	0	0.828270714287574	1		301	273	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918958	76918958	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	25	192	0	ENST00000373344.5:c.4033T>A	p.Leu1345Met	p.L1345M	ENST00000373344	NM_000489.3	1345	Ttg/Atg	12/35	1	1	FACETS	0.107	0.084	0.133	0.107	0.084	0.133	SUBCLONAL	1	TRUE	0	0.828270714287574	1		192	331	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	30	308	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.358	0.288	0.438	0.358	0.288	0.438	SUBCLONAL	1	TRUE	1	0.33	2		308	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	169	766	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.33	2		767	996	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	152	721	8	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.928	0.848	1	0.928	0.848	1	CLONAL	1	TRUE	1	0.33	2		729	993	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312916	30312916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146040933	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	105	586	0	ENST00000262643.3:c.719G>A	p.Arg240His	p.R240H	ENST00000262643	NM_001238.2	240	cGt/cAt	9/12	1	2	FACETS	0.936	0.839	1	0.936	0.839	1	CLONAL	1	TRUE	1	0.33	2		586	680	SUCCESS
APC	324	MSKCC	GRCh37	5	112175675	112175676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	50	368	0	ENST00000257430.4:c.4393_4394dup	p.Ser1465ArgfsTer9	p.S1465Rfs*9	ENST00000257430	NM_000038.5	1462	aag/aAGag	16/16	1	2	FACETS	0.604	0.512	0.704	0.604	0.512	0.704	SUBCLONAL	1	TRUE	1	0.33	2		368	502	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775731	9775731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	60	970	4	ENST00000377346.4:c.274G>A	p.Val92Met	p.V92M	ENST00000377346	NM_005026.3	92	Gtg/Atg	4/24	1	2	FACETS	0.335	0.287	0.387	0.335	0.287	0.387	SUBCLONAL	1	TRUE	1	0.33	2		974	1086	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255883	16255883	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	96	497	0	ENST00000375759.3:c.3154del	p.Ile1052SerfsTer40	p.I1052Sfs*40	ENST00000375759	NM_015001.2	1050	Aaa/aa	11/15	1	2	FACETS	0.921	0.821	1	0.921	0.821	1	CLONAL	1	TRUE	1	0.33	2		497	632	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444588	78444588	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	78	563	0	ENST00000370768.2:c.101C>T	p.Ala34Val	p.A34V	ENST00000370768	NM_003902.3	34	gCa/gTa	1/20	1	2	FACETS	0.645	0.566	0.73	0.645	0.566	0.73	SUBCLONAL	1	TRUE	1	0.33	2		563	733	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	195	456	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.941	0.875	1	1	0.993	1	CLONAL	2	TRUE	1	0.33	2		461	628	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206727	102206727	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	73	461	0	ENST00000263464.3:c.1355T>C	p.Met452Thr	p.M452T	ENST00000263464	NM_001165.4	452	aTg/aCg	7/9	1	2	FACETS	0.873	0.765	0.988	0.873	0.765	0.988	CLONAL	1	TRUE	1	0.33	2		461	507	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424087	49424087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs558561472	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	141	726	1	ENST00000301067.7:c.13975C>T	p.Arg4659Trp	p.R4659W	ENST00000301067	NM_003482.3	4659	Cgg/Tgg	42/54	1	2	FACETS	0.979	0.892	1	0.979	0.892	1	CLONAL	1	TRUE	1	0.33	2		727	873	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964203	28964203	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144651121	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	70	371	1	ENST00000282397.4:c.1699C>T	p.Pro567Ser	p.P567S	ENST00000282397	NM_002019.4	567	Ccg/Tcg	13/30	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.33	2		372	413	SUCCESS
BLM	641	MSKCC	GRCh37	15	91352484	91352484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1031421025	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	57	355	0	ENST00000355112.3:c.3869C>T	p.Ser1290Leu	p.S1290L	ENST00000355112	NM_000057.2	1290	tCg/tTg	20/22	1	2	FACETS	0.783	0.674	0.903	0.783	0.674	0.903	CLONAL	1	TRUE	1	0.33	2		355	441	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486193	99486193	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374121578	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	44	690	1	ENST00000268035.6:c.3499C>T	p.Arg1167Trp	p.R1167W	ENST00000268035	NM_000875.3	1167	Cgg/Tgg	19/21	1	2	FACETS	0.337	0.281	0.398	0.337	0.281	0.398	SUBCLONAL	1	TRUE	1	0.33	2		691	792	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781194	3781194	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	109	847	0	ENST00000262367.5:c.5171A>G	p.Glu1724Gly	p.E1724G	ENST00000262367	NM_004380.2	1724	gAg/gGg	30/31	1	2	FACETS	0.743	0.666	0.824	0.743	0.666	0.824	SUBCLONAL	1	TRUE	1	0.33	2		847	889	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350068	89350068	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750887042	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	154	859	0	ENST00000301030.4:c.2882G>A	p.Arg961His	p.R961H	ENST00000301030	NM_001256183.1	961	cGc/cAc	9/13	1	2	FACETS	0.987	0.902	1	0.987	0.902	1	CLONAL	1	TRUE	1	0.33	2		859	946	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577563	7577563	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	36	644	0	ENST00000269305.4:c.718A>C	p.Ser240Arg	p.S240R	ENST00000269305	NM_001126112.2	240	Agt/Cgt	7/11	1	2	FACETS	0.254	0.207	0.306	0.254	0.207	0.306	SUBCLONAL	1	TRUE	1	0.33	2		644	860	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578397	7578397	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	29	767	0	ENST00000269305.4:c.533A>G	p.His178Arg	p.H178R	ENST00000269305	NM_001126112.2	178	cAc/cGc	5/11	1	2	FACETS	0.18	0.143	0.221	0.18	0.143	0.221	SUBCLONAL	1	TRUE	1	0.33	2		767	979	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490288	29490288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876659418	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	84	497	0	ENST00000356175.3:c.373C>T	p.Arg125Cys	p.R125C	ENST00000356175	NM_000267.3	125	Cgt/Tgt	4/57	1	2	FACETS	0.835	0.738	0.938	0.835	0.738	0.938	CLONAL	1	TRUE	1	0.33	2		497	610	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881103	37881103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775752713	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	165	845	0	ENST00000269571.5:c.2432G>A	p.Arg811Gln	p.R811Q	ENST00000269571		811	cGg/cAg	20/27	1	2	FACETS	0.966	0.886	1	0.966	0.886	1	CLONAL	1	TRUE	1	0.33	2		845	1035	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	176	852	2	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.33	2		854	975	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18963836	18963836	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	69	540	0	ENST00000262803.5:c.1013A>G	p.Asn338Ser	p.N338S	ENST00000262803	NM_002911.3	338	aAc/aGc	7/24	1	2	FACETS	0.571	0.497	0.652	0.571	0.497	0.652	SUBCLONAL	1	TRUE	1	0.33	2		540	732	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211047	36211047	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	184	952	1	ENST00000222270.7:c.798G>A	p.Trp266Ter	p.W266*	ENST00000222270	NM_014727.1	266	tgG/tgA	3/37	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.33	2		953	1114	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868404	45868404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372425466	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	58	858	2	ENST00000391945.4:c.373C>T	p.Arg125Cys	p.R125C	ENST00000391945	NM_000400.3	125	Cgc/Tgc	6/23	1	2	FACETS	0.342	0.292	0.396	0.342	0.292	0.396	SUBCLONAL	1	TRUE	1	0.33	2		860	1029	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446229	29446229	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199987354	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	86	646	0	ENST00000389048.3:c.3338G>A	p.Arg1113Gln	p.R1113Q	ENST00000389048	NM_004304.4	1113	cGg/cAg	20/29	1	2	FACETS	0.76	0.672	0.854	0.76	0.672	0.854	SUBCLONAL	1	TRUE	1	0.33	2		646	686	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570075	212570075	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	81	439	1	ENST00000342788.4:c.1166T>C	p.Leu389Pro	p.L389P	ENST00000342788	NM_005235.2	389	cTg/cCg	10/28	1	2	FACETS	0.909	0.803	1	0.909	0.803	1	CLONAL	1	TRUE	1	0.33	2		440	540	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439701	220439701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	108	1051	0	ENST00000243786.2:c.554C>T	p.Ala185Val	p.A185V	ENST00000243786	NM_002191.3	185	gCt/gTt	2/2	1	2	FACETS	0.638	0.571	0.709	0.638	0.571	0.709	SUBCLONAL	1	TRUE	1	0.33	2		1051	1026	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024287	31024287	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	92	535	0	ENST00000375687.4:c.3772G>A	p.Ala1258Thr	p.A1258T	ENST00000375687	NM_015338.5	1258	Gct/Act	13/13	1	2	FACETS	0.913	0.812	1	0.913	0.812	1	CLONAL	1	TRUE	1	0.33	2		535	611	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100934	41100934	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	36	635	0	ENST00000373198.4:c.1422G>T	p.Glu474Asp	p.E474D	ENST00000373198	NM_133170.3	474	gaG/gaT	8/32	1	2	FACETS	0.316	0.259	0.38	0.316	0.259	0.38	SUBCLONAL	1	TRUE	1	0.33	2		635	691	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167512	24167512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1362758319	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	56	779	1	ENST00000263121.7:c.896C>T	p.Ser299Leu	p.S299L	ENST00000263121	NM_003073.3	299	tCg/tTg	7/9	1	2	FACETS	0.345	0.295	0.401	0.345	0.295	0.401	SUBCLONAL	1	TRUE	1	0.33	2		780	983	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998128	169998128	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs753143066	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	92	620	0	ENST00000295797.4:c.826del	p.Thr276GlnfsTer7	p.T276Qfs*7	ENST00000295797	NM_002740.5	273	ttA/tt	9/18	1	2	FACETS	0.74	0.658	0.829	0.74	0.658	0.829	SUBCLONAL	1	TRUE	1	0.33	2		620	753	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1940200	1940200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	46	273	0	ENST00000382891.5:c.1697C>T	p.Thr566Met	p.T566M	ENST00000382891	NM_133335.3	566	aCg/aTg	8/22	1	2	FACETS	0.704	0.594	0.825	0.704	0.594	0.825	SUBCLONAL	1	TRUE	1	0.33	2		273	396	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183324	56183324	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	111	523	0	ENST00000399503.3:c.4234A>G	p.Thr1412Ala	p.T1412A	ENST00000399503	NM_005921.1	1412	Aca/Gca	18/20	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.33	2		523	668	SUCCESS
APC	324	MSKCC	GRCh37	5	112151245	112151246	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs1114167567	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	59	405	0	ENST00000257430.4:c.893_894del	p.His298LeufsTer28	p.H298Lfs*28	ENST00000257430	NM_000038.5	296	agCAca/agca	9/16	1	2	FACETS	0.692	0.596	0.796	0.692	0.596	0.796	SUBCLONAL	1	TRUE	1	0.33	2		405	517	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131951812	131951812	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	53	281	3	ENST00000265335.6:c.3154C>T	p.Gln1052Ter	p.Q1052*	ENST00000265335		1052	Caa/Taa	20/25	1	2	FACETS	0.885	0.758	1	0.885	0.758	1	CLONAL	1	TRUE	1	0.33	2		284	363	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163553	32163554	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs777647776	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	167	821	3	ENST00000375023.3:c.5672dup	p.Gly1892ArgfsTer24	p.G1892Rfs*24	ENST00000375023	NM_004557.3	1891	ggc/ggGc	30/30	1	2	FACETS	0.954	0.875	1	0.954	0.875	1	CLONAL	1	TRUE	1	0.33	2		824	1061	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163864	32163864	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	118	732	0	ENST00000375023.3:c.5362G>T	p.Gly1788Trp	p.G1788W	ENST00000375023	NM_004557.3	1788	Ggg/Tgg	30/30	1	2	FACETS	0.787	0.709	0.869	0.787	0.709	0.869	SUBCLONAL	1	TRUE	1	0.33	2		732	909	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	47	348	3	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	1	2	FACETS	0.57	0.481	0.668	0.57	0.481	0.668	SUBCLONAL	1	TRUE	1	0.33	2		351	500	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381528	81381528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776090604	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	59	360	1	ENST00000222390.5:c.533G>A	p.Arg178Gln	p.R178Q	ENST00000222390	NM_000601.4	178	cGa/cAa	5/18	1	2	FACETS	0.845	0.729	0.971	0.845	0.729	0.971	CLONAL	1	TRUE	1	0.33	2		361	423	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151855967	151855967	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140246095	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	75	498	0	ENST00000262189.6:c.11651C>T	p.Thr3884Met	p.T3884M	ENST00000262189	NM_170606.2	3884	aCg/aTg	44/59	1	2	FACETS	0.727	0.637	0.824	0.727	0.637	0.824	SUBCLONAL	1	TRUE	1	0.33	2		498	625	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209648	98209648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs386833412	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	121	844	0	ENST00000331920.6:c.3890G>A	p.Arg1297Gln	p.R1297Q	ENST00000331920	NM_000264.3	1297	cGg/cAg	23/24	1	2	FACETS	0.818	0.738	0.902	0.818	0.738	0.902	CLONAL	1	TRUE	1	0.33	2		844	897	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405201	139405201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767886377	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	180	1007	2	ENST00000277541.6:c.2644G>A	p.Ala882Thr	p.A882T	ENST00000277541	NM_017617.3	882	Gca/Aca	17/34	1	2	FACETS	0.946	0.871	1	0.946	0.871	1	CLONAL	1	TRUE	1	0.33	2		1009	1153	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802657	139802657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	162	771	1	ENST00000247668.2:c.502G>A	p.Ala168Thr	p.A168T	ENST00000247668	NM_021138.3	168	Gca/Aca	5/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.33	2		772	879	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247031	53247031	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	139	739	0	ENST00000375401.3:c.469T>C	p.Tyr157His	p.Y157H	ENST00000375401	NM_004187.3	157	Tac/Cac	4/26	1	2	FACETS	0.975	0.888	1	0.975	0.888	1	CLONAL	1	TRUE	1	0.33	2		739	864	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793217	42793217	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	12	589	0	ENST00000575354.2:c.1109G>C	p.Ser370Thr	p.S370T	ENST00000575354	NM_015125.3	370	aGt/aCt	7/20	0.0928424719907388	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		589	178	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220467	123220484	+	frameshift_variant	Frame_Shift_Del	DEL	ATGTCTTACCGAAATTCT	ATGTCTTACCGAAATTCT	TGTGGCTTCCACTG	novel	NA	P-0052670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	45	90	0	ENST00000218089.9:c.3124_3141delinsTGTGGCTTCCACTG	p.Met1042CysfsTer7	p.M1042Cfs*7	ENST00000218089	NM_001042749.1	1042	ATGTCTTACCGAAATTCT/TGTGGCTTCCACTG	30/35	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	0	NA	2		90	198	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651513	52651513	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	79	581	0	ENST00000394830.3:c.1583A>T	p.Asn528Ile	p.N528I	ENST00000394830	NM_018313.4	528	aAt/aTt	15/30	0.410489080711188	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.410489080711188	1		581	286	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864331	151864331	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775712660	NA	P-0053509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	96	567	0	ENST00000262189.6:c.9650G>A	p.Arg3217His	p.R3217H	ENST00000262189	NM_170606.2	3217	cGt/cAt	42/59	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.410489080711188	2		567	427	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900698	3900698	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	165	809	0	ENST00000262367.5:c.398T>C	p.Leu133Pro	p.L133P	ENST00000262367	NM_004380.2	133	cTg/cCg	2/31	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.410489080711188	2		809	702	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188303	10188303	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	125	507	0	ENST00000256474.2:c.446C>A	p.Ala149Asp	p.A149D	ENST00000256474	NM_000551.3	149	gCc/gAc	2/3	0.410489080711188	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.410489080711188	1		507	369	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231085	53231085	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1556842070	NA	P-0053509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	183	347	0	ENST00000375401.3:c.1817A>T	p.Asn606Ile	p.N606I	ENST00000375401	NM_004187.3	606	aAc/aTc	13/26	0.211295624371273	2	FACETS	1	0.984	1			1	INDETERMINATE	2	TRUE	NA	0.410489080711188	2		347	385	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651513	52651513	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053509-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	46	581	0	ENST00000394830.3:c.1583A>T	p.Asn528Ile	p.N528I	ENST00000394830	NM_018313.4	528	aAt/aTt	15/30	0.430856371438786	1	FACETS	0.701	0.596	0.815	0.701	0.596	0.815	SUBCLONAL	1	FALSE	0	0.430856371438786	1		581	239	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864331	151864331	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775712660	NA	P-0053509-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	70	567	0	ENST00000262189.6:c.9650G>A	p.Arg3217His	p.R3217H	ENST00000262189	NM_170606.2	3217	cGt/cAt	42/59	1	2	FACETS	0.973	0.854	1	0.973	0.854	1	CLONAL	1	FALSE	1	0.430856371438786	2		567	334	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900698	3900698	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053509-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	171	809	0	ENST00000262367.5:c.398T>C	p.Leu133Pro	p.L133P	ENST00000262367	NM_004380.2	133	cTg/cCg	2/31	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.430856371438786	2		809	759	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188303	10188303	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053509-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	63	507	0	ENST00000256474.2:c.446C>A	p.Ala149Asp	p.A149D	ENST00000256474	NM_000551.3	149	gCc/gAc	2/3	0.430856371438786	1	FACETS	0.886	0.775	1	0.886	0.775	1	CLONAL	1	FALSE	0	0.430856371438786	1		507	259	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231085	53231085	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1556842070	NA	P-0053509-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	183	347	0	ENST00000375401.3:c.1817A>T	p.Asn606Ile	p.N606I	ENST00000375401	NM_004187.3	606	aAc/aTc	13/26	0.250898863459169	2	FACETS	0.957	0.893	1			1	INDETERMINATE	2	FALSE	NA	0.430856371438786	2		347	444	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	37	539	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.29	2		539	217	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	21	399	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.947	0.736	1	0.947	0.736	1	CLONAL	1	TRUE	1	0.29	2		399	153	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	99	368	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.957	1	1	0.989	1	CLONAL	2	TRUE	1	0.29	2		371	309	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	35	380	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.29	2		380	189	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	38	514	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	0.3	2	FACETS	1	0.867	1	0.524	0.436	0.621	CLONAL	1	TRUE	0	0.29	2		515	250	SUCCESS
APC	324	MSKCC	GRCh37	5	112175720	112175720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	32	267	0	ENST00000257430.4:c.4429C>T	p.Gln1477Ter	p.Q1477*	ENST00000257430	NM_000038.5	1477	Cag/Tag	16/16	1	2	FACETS	1	0.831	1	1	0.831	1	CLONAL	1	TRUE	1	0.29	2		267	217	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	74	621	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	0.773	0.682	0.87	1	0.977	1	SUBCLONAL	2	TRUE	1	0.29	2		621	330	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	93	456	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.97	1	1	0.989	1	CLONAL	2	TRUE	1	0.29	2		461	268	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161689	56161689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1490957244	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	37	448	1	ENST00000399503.3:c.1186C>T	p.Arg396Cys	p.R396C	ENST00000399503	NM_005921.1	396	Cgt/Tgt	6/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.29	2		449	199	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	34	488	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.29	2		488	219	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	58	488	1	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.29	2		489	297	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119781	70119781	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1274036689	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	66	731	0	ENST00000245479.2:c.788del	p.Gly263AlafsTer16	p.G263Afs*16	ENST00000245479	NM_000346.3	261	gaG/ga	3/3	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.29	2		731	319	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274854	142274854	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769252606	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	42	468	0	ENST00000350721.4:c.2206G>A	p.Gly736Arg	p.G736R	ENST00000350721	NM_001184.3	736	Gga/Aga	10/47	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.29	2		468	264	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	72	711	1	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.29	2		712	406	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882050	36882050	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs780753361	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	94	1092	6	ENST00000358127.4:c.963del	p.Ala322LeufsTer11	p.A322Lfs*11	ENST00000358127	NM_001280556.1	321	ccC/cc	8/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.29	2		1098	460	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835781	68835781	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060501215	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	73	618	1	ENST00000261769.5:c.377del	p.Pro126ArgfsTer89	p.P126Rfs*89	ENST00000261769	NM_004360.3	124	cgC/cg	3/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.29	2		619	383	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458420	120458420	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	67	716	0	ENST00000256646.2:c.6925C>T	p.Leu2309Phe	p.L2309F	ENST00000256646	NM_024408.3	2309	Ctc/Ttc	34/34	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.29	2		716	366	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916463	39916463	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	91	430	1	ENST00000378444.4:c.4540C>T	p.Arg1514Ter	p.R1514*	ENST00000378444	NM_001123385.1	1514	Cga/Tga	11/15	1	1	FACETS	0.86	0.78	0.94	1	0.989	1	CLONAL	3	TRUE	0	0.29	1		431	208	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092965	27092965	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	36	373	0	ENST00000324856.7:c.2896G>T	p.Glu966Ter	p.E966*	ENST00000324856	NM_006015.4	966	Gag/Tag	10/20	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.29	2		373	211	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172340	7172340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs181150880	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	77	502	1	ENST00000302850.5:c.1229G>A	p.Arg410Gln	p.R410Q	ENST00000302850	NM_000208.2	410	cGg/cAg	5/22	1	2	FACETS	0.817	0.723	0.916	1	0.98	1	CLONAL	2	TRUE	1	0.29	2		503	325	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755585	39755585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	49	626	0	ENST00000288319.7:c.1180G>A	p.Gly394Arg	p.G394R	ENST00000288319	NM_182918.3	394	Ggg/Agg	10/10	1	2	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	1	0.29	2		626	337	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561289	9561289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985722631	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	49	466	0	ENST00000353224.5:c.493G>A	p.Ala165Thr	p.A165T	ENST00000353224	NM_177990.2	165	Gca/Aca	4/10	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.29	2		466	269	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	140	1123	2	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	1	0.969	1	1	0.992	1	CLONAL	2	TRUE	1	0.29	2		1125	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs878854073	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	63	541	1	ENST00000269305.4:c.673-1G>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.29	2		542	331	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866595	78866595	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	80	735	0	ENST00000306801.3:c.2168A>G	p.Tyr723Cys	p.Y723C	ENST00000306801	NM_020761.2	723	tAt/tGt	19/34	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.29	2		735	413	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012386	152012386	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	38	358	0	ENST00000262189.6:c.427del	p.Ser143ValfsTer3	p.S143Vfs*3	ENST00000262189	NM_170606.2	143	Agt/gt	4/59	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.29	2		358	196	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989591	212989592	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1553563398	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	34	312	0	ENST00000342788.4:c.119_120del	p.Ser40Ter	p.S40*	ENST00000342788	NM_005235.2	40	tCT/t	2/28	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.29	2		312	209	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646980	23646981	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	66	698	0	ENST00000261584.4:c.886dup	p.Met296AsnfsTer7	p.M296Nfs*7	ENST00000261584	NM_024675.3	296	atg/aAtg	4/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.29	2		698	326	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782079	9782079	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	85	1033	0	ENST00000377346.4:c.2102T>G	p.Leu701Arg	p.L701R	ENST00000377346	NM_005026.3	701	cTg/cGg	17/24	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.29	2		1033	391	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230807	66230807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	16	361	0	ENST00000273854.3:c.2164C>A	p.Leu722Ile	p.L722I	ENST00000273854	NM_004439.5	722	Cta/Ata	12/18	1	2	FACETS	0.869	0.648	1	0.869	0.648	1	CLONAL	1	TRUE	1	0.29	2		361	127	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347765	89347765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368667754	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	62	845	0	ENST00000301030.4:c.5185G>A	p.Ala1729Thr	p.A1729T	ENST00000301030	NM_001256183.1	1729	Gcc/Acc	9/13	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.29	2		845	392	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946233	71946233	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	77	833	0	ENST00000298229.2:c.2489G>A	p.Gly830Asp	p.G830D	ENST00000298229	NM_001567.3	830	gGc/gAc	22/28	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.29	2		833	429	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281324	49281324	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	74	832	1	ENST00000282018.3:c.371G>A	p.Ser124Asn	p.S124N	ENST00000282018	NM_020377.2	124	aGc/aAc	1/1	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.29	2		833	381	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034772	42034773	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	55	514	0	ENST00000219905.7:c.4618_4619del	p.Gln1540ValfsTer5	p.Q1540Vfs*5	ENST00000219905	NM_001164273.1	1538	ttCAca/ttca	15/24	0.223267293525542	3	FACETS	1	0.941	1	0.595	0.511	0.686	CLONAL	1	TRUE	1	0.29	3		514	365	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358503	67358503	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	12	304	0	ENST00000327367.4:c.11T>C	p.Ile4Thr	p.I4T	ENST00000327367	NM_005902.3	4	aTc/aCc	1/9	0.223267293525542	3	FACETS	0.46	0.323	0.628	0.23	0.161	0.314	SUBCLONAL	1	TRUE	1	0.29	3		304	206	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805049	89805049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	91	979	0	ENST00000389301.3:c.4328C>T	p.Ala1443Val	p.A1443V	ENST00000389301	NM_000135.2	1443	gCc/gTc	43/43	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.29	2		979	443	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119890	70119890	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	57	875	0	ENST00000245479.2:c.892C>A	p.Leu298Met	p.L298M	ENST00000245479	NM_000346.3	298	Ctg/Atg	3/3	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.29	2		875	345	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221227	5221227	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771119355	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	81	839	0	ENST00000357368.4:c.3239G>A	p.Arg1080His	p.R1080H	ENST00000357368	NM_002850.3	1080	cGt/cAt	20/38	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.29	2		839	388	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99180026	99180026	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs774985949	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	77	829	0	ENST00000074304.5:c.1969A>G	p.Met657Val	p.M657V	ENST00000074304	NM_001134224.1	657	Atg/Gtg	19/26	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.29	2		829	366	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578268	212578269	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	35	421	0	ENST00000342788.4:c.988dup	p.Cys330LeufsTer6	p.C330Lfs*6	ENST00000342788	NM_005235.2	330	tgc/tTgc	8/28	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.29	2		421	210	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610565	215610565	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	40	403	0	ENST00000260947.4:c.1691A>T	p.Gln564Leu	p.Q564L	ENST00000260947	NM_000465.2	564	cAg/cTg	8/11	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.29	2		403	228	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326103	62326103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	83	988	0	ENST00000360203.5:c.3119G>A	p.Gly1040Asp	p.G1040D	ENST00000360203	NM_001283009.1	1040	gGc/gAc	32/35	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.29	2		988	385	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035054	37035066	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGTTATTCGGC	GGGGTTATTCGGC	-	novel	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	133	506	0	ENST00000231790.2:c.18_30del	p.Val7TrpfsTer6	p.V7Wfs*6	ENST00000231790	NM_000249.3	6	GGGGTTATTCGGCgg/gg	1/19	0.3	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.29	2		506	394	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089061	37089061	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	46	383	0	ENST00000231790.2:c.1783A>G	p.Ser595Gly	p.S595G	ENST00000231790	NM_000249.3	595	Agt/Ggt	16/19	0.3	2	FACETS	1	0.918	1	0.567	0.48	0.661	CLONAL	1	TRUE	0	0.29	2		383	280	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665309	138665309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	72	1074	2	ENST00000330315.3:c.256G>A	p.Ala86Thr	p.A86T	ENST00000330315	NM_023067.3	86	Gcg/Acg	1/1	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.29	2		1076	365	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280140	142280140	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757006178	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	49	527	1	ENST00000350721.4:c.1294C>T	p.Arg432Cys	p.R432C	ENST00000350721	NM_001184.3	432	Cgt/Tgt	5/47	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.29	2		528	268	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911281	29911281	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	51	748	0	ENST00000376809.5:c.580A>G	p.Arg194Gly	p.R194G	ENST00000376809	NM_002116.7	194	Aga/Gga	3/8	0.223267293525542	3	FACETS	1	0.955	1	0.665	0.568	0.769	CLONAL	1	TRUE	1	0.29	3		748	303	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29913041	29913042	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	81	640	0	ENST00000376809.5:c.1077_1078del	p.Leu360HisfsTer4	p.L360Hfs*4	ENST00000376809	NM_002116.7	359	tCC/t	7/8	0.223267293525542	3	FACETS	0.822	0.729	0.921	0.822	0.729	0.921	CLONAL	2	TRUE	1	0.29	3		640	389	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323294	31323296	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	novel	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	10	233	0	ENST00000412585.2:c.693_695del	p.Phe232del	p.F232del	ENST00000412585	NM_005514.6	231	ggTTTc/ggc	4/8	1	2	FACETS	0.535	0.364	0.747	0.535	0.364	0.747	SUBCLONAL	1	TRUE	1	0.29	2		233	129	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213552	27213552	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	58	503	0	ENST00000380036.4:c.2948T>C	p.Phe983Ser	p.F983S	ENST00000380036	NM_000459.3	983	tTt/tCt	18/23	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.29	2		503	302	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	186	378	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.104309688970002	3	FACETS	0.809	0.754	0.866	0.809	0.754	0.866	INDETERMINATE	2	TRUE	1	0.57	3		378	518	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	38	348	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.104309688970002	3	FACETS	1	0.927	1	0.595	0.501	0.696	INDETERMINATE	1	TRUE	1	0.57	3		348	144	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	9	429	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.17	0.112	0.243	0.17	0.112	0.243	SUBCLONAL	1	TRUE	1	0.57	2		429	186	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	44	124	0	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.826	0.702	0.959	0.826	0.702	0.959	CLONAL	1	TRUE	1	0.57	2		124	187	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	51	514	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.619	0.53	0.716	0.619	0.53	0.716	SUBCLONAL	1	TRUE	1	0.57	2		515	289	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255883	16255883	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	41	497	0	ENST00000375759.3:c.3154del	p.Ile1052SerfsTer40	p.I1052Sfs*40	ENST00000375759	NM_015001.2	1050	Aaa/aa	11/15	1	2	FACETS	0.575	0.483	0.677	0.575	0.483	0.677	SUBCLONAL	1	TRUE	1	0.57	2		497	250	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	121	456	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.942	1	1	0.991	1	CLONAL	2	TRUE	1	0.57	2		461	209	SUCCESS
APC	324	MSKCC	GRCh37	5	112151245	112151246	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs1114167567	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	48	405	0	ENST00000257430.4:c.893_894del	p.His298LeufsTer28	p.H298Lfs*28	ENST00000257430	NM_000038.5	296	agCAca/agca	9/16	0.104309688970002	3	FACETS	1	0.879	1	0.515	0.441	0.595	INDETERMINATE	1	TRUE	1	0.57	3		405	210	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	86	495	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	0.811	0.723	0.904	0.811	0.723	0.904	CLONAL	1	TRUE	1	0.57	2		495	372	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	33	347	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.871	0.722	1	0.871	0.722	1	CLONAL	1	TRUE	1	0.57	2		347	133	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638325	117638325	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3752566	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	28	477	0	ENST00000368508.3:c.6116G>A	p.Arg2039His	p.R2039H	ENST00000368508	NM_002944.2	2039	cGt/cAt	38/43	1	2	FACETS	0.692	0.561	0.837	0.692	0.561	0.837	SUBCLONAL	1	TRUE	1	0.57	2		477	142	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434170	121434170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757068809	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	124	668	0	ENST00000257555.6:c.1061C>T	p.Thr354Met	p.T354M	ENST00000257555		354	aCg/aTg	5/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.57	2		668	373	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636729	8636729	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	100	421	0	ENST00000356435.5:c.180del	p.Gly61GlufsTer11	p.G61Efs*11	ENST00000356435		60	aaA/aa	2/35	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.57	2		421	294	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	164	764	1	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	0.979	0.903	1	0.979	0.903	1	CLONAL	1	TRUE	1	0.57	2		765	588	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245445	46245445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1390936994	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	82	628	1	ENST00000334344.6:c.3539C>T	p.Thr1180Met	p.T1180M	ENST00000334344	NM_152641.2	1180	aCg/aTg	15/21	0.368431938634587	4	FACETS	0.889	0.795	0.987	0.889	0.795	0.987	CLONAL	2	TRUE	2	0.57	4		629	254	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482926	140482927	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs777474487	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	45	634	1	ENST00000288602.6:c.1208dup	p.Ala404CysfsTer9	p.A404Cfs*9	ENST00000288602	NM_004333.4	403	cct/ccCt	10/18	1	2	FACETS	0.497	0.419	0.581	0.497	0.419	0.581	SUBCLONAL	1	TRUE	1	0.57	2		635	318	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399389	139399389	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	15	608	0	ENST00000277541.6:c.4754T>C	p.Leu1585Pro	p.L1585P	ENST00000277541	NM_017617.3	1585	cTg/cCg	26/34	0.626478307212397	4	FACETS	0.203	0.148	0.27	0.102	0.074	0.135	SUBCLONAL	1	TRUE	2	0.57	4		608	407	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285832	198285832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775351918	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	43	408	0	ENST00000335508.6:c.221C>T	p.Thr74Met	p.T74M	ENST00000335508	NM_012433.2	74	aCg/aTg	3/25	1	2	FACETS	0.725	0.614	0.846	0.725	0.614	0.846	SUBCLONAL	1	TRUE	1	0.57	2		408	208	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966873	25966873	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1271466699	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	71	660	2	ENST00000435504.4:c.2333del	p.Pro778GlnfsTer21	p.P778Qfs*21	ENST00000435504		778	cCa/ca	13/13	1	2	FACETS	0.706	0.62	0.797	0.706	0.62	0.797	SUBCLONAL	1	TRUE	1	0.57	2		662	353	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188893	32188893	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144962111	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	34	695	0	ENST00000375023.3:c.661C>T	p.Leu221Phe	p.L221F	ENST00000375023	NM_004557.3	221	Ctc/Ttc	4/30	0.272557268003749	3	FACETS	0.611	0.502	0.732	0.305	0.251	0.366	INDETERMINATE	1	TRUE	1	0.57	3		695	251	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582192	189582192	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	104	494	0	ENST00000264731.3:c.751C>T	p.Arg251Cys	p.R251C	ENST00000264731	NM_003722.4	251	Cgt/Tgt	5/14	1	2	FACETS	0.958	0.865	1	0.958	0.865	1	CLONAL	1	TRUE	1	0.57	2		494	381	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36940987	36940987	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs928090621	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	56	541	0	ENST00000361632.4:c.352C>T	p.Arg118Cys	p.R118C	ENST00000361632		118	Cgc/Tgc	3/16	1	2	FACETS	0.675	0.583	0.775	0.675	0.583	0.775	SUBCLONAL	1	TRUE	1	0.57	2		541	291	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524568	103524568	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	16	437	1	ENST00000355739.4:c.2705del	p.Asn902IlefsTer4	p.N902Ifs*4	ENST00000355739	NM_000123.3	900	cAa/ca	13/15	1	2	FACETS	0.326	0.242	0.426	0.326	0.242	0.426	SUBCLONAL	1	TRUE	1	0.57	2		438	172	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112323	115112324	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	rs1381943852	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	89	596	0	ENST00000257566.3:c.1416_1417del	p.Leu473ProfsTer218	p.L473Pfs*218	ENST00000257566	NM_016569.3	472	gcGCtc/gctc	7/8	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.57	2		596	272	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561324	9561324	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	69	514	0	ENST00000353224.5:c.458G>T	p.Gly153Val	p.G153V	ENST00000353224	NM_177990.2	153	gGa/gTa	4/10	0.104309688970002	0	FACETS	0.43	0.379	0.483			1	INDETERMINATE	1	TRUE	0	0.57	0		514	242	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562160	21562160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	21	720	0	ENST00000382592.4:c.1759G>A	p.Glu587Lys	p.E587K	ENST00000382592	NM_014572.2	587	Gaa/Aaa	4/8	1	2	FACETS	0.204	0.156	0.259	0.204	0.156	0.259	SUBCLONAL	1	TRUE	1	0.57	2		720	362	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61213502	61213502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778585796	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	91	474	1	ENST00000301761.2:c.460C>T	p.Arg154Cys	p.R154C	ENST00000301761	NM_017841.2	154	Cgt/Tgt	4/4	0.3	5	FACETS	0.971	0.872	1			1	INDETERMINATE	2	TRUE	NA	0.57	5		475	305	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821875	72821875	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	68	683	5	ENST00000268489.5:c.10300del	p.Leu3434SerfsTer51	p.L3434Sfs*51	ENST00000268489	NM_006885.3	3434	Ctc/tc	10/10	0.104309688970002	3	FACETS	0.958	0.84	1	0.479	0.42	0.542	INDETERMINATE	1	TRUE	1	0.57	3		688	320	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753838	133753838	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	67	477	0	ENST00000318560.5:c.1307G>A	p.Gly436Asp	p.G436D	ENST00000318560	NM_005157.4	436	gGc/gAc	8/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.57	2		477	211	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948386	71948386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760694548	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	77	703	0	ENST00000298229.2:c.3098G>A	p.Arg1033His	p.R1033H	ENST00000298229	NM_001567.3	1033	cGt/cAt	26/28	1	2	FACETS	0.928	0.824	1	0.928	0.824	1	CLONAL	1	TRUE	1	0.57	2		703	291	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139920	50139920	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757080959	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	42	527	0	ENST00000246792.3:c.409G>A	p.Val137Ile	p.V137I	ENST00000246792	NM_006270.3	137	Gtt/Att	4/6	0.104309688970002	3	FACETS	0.486	0.406	0.574	0.243	0.203	0.287	INDETERMINATE	1	TRUE	1	0.57	3		527	390	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973917	55973917	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1404646083	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	18	586	0	ENST00000263923.4:c.1399G>A	p.Ala467Thr	p.A467T	ENST00000263923	NM_002253.2	467	Gcc/Acc	10/30	1	2	FACETS	0.242	0.182	0.313	0.242	0.182	0.313	SUBCLONAL	1	TRUE	1	0.57	2		586	261	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711924	89711924	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	45	301	0	ENST00000371953.3:c.542T>C	p.Leu181Pro	p.L181P	ENST00000371953	NM_000314.4	181	cTg/cCg	6/9	1	2	FACETS	0.951	0.813	1	0.951	0.813	1	CLONAL	1	TRUE	1	0.57	2		301	166	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912440	50912440	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	58	510	0	ENST00000440232.2:c.1954C>T	p.Arg652Trp	p.R652W	ENST00000440232	NM_002691.3	652	Cgg/Tgg	16/27	0.104309688970002	3	FACETS	1	0.969	1	0.703	0.615	0.796	INDETERMINATE	1	TRUE	1	0.57	3		510	186	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775713	9775713	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	83	609	0	ENST00000377346.4:c.256C>T	p.Gln86Ter	p.Q86*	ENST00000377346	NM_005026.3	86	Caa/Taa	4/24	1	2	FACETS	0.987	0.881	1	0.987	0.881	1	CLONAL	1	TRUE	1	0.57	2		609	295	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345912	70345912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863223702	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	57	240	0	ENST00000374080.3:c.2449C>T	p.Arg817Cys	p.R817C	ENST00000374080		817	Cgc/Tgc	18/45	1	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.57	1		240	134	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440137	49440137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1190664201	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	105	666	0	ENST00000301067.7:c.4489C>T	p.His1497Tyr	p.H1497Y	ENST00000301067	NM_003482.3	1497	Cac/Tac	16/54	0.368431938634587	4	FACETS	0.81	0.733	0.89	0.81	0.733	0.89	CLONAL	2	TRUE	2	0.57	4		666	357	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1684395	1684395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774421787	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	139	605	1	ENST00000378625.1:c.1724G>A	p.Arg575Gln	p.R575Q	ENST00000378625	NM_001198994.1	575	cGg/cAg	14/14	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.57	2		606	431	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101627	27101627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1023142691	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	27	681	0	ENST00000324856.7:c.4909C>T	p.Arg1637Trp	p.R1637W	ENST00000324856	NM_006015.4	1637	Cgg/Tgg	18/20	1	2	FACETS	0.192	0.152	0.238	0.192	0.152	0.238	SUBCLONAL	1	TRUE	1	0.57	2		681	493	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521596	46521596	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	45	365	0	ENST00000262741.5:c.812A>G	p.His271Arg	p.H271R	ENST00000262741	NM_003629.3	271	cAt/cGt	7/10	1	2	FACETS	0.818	0.697	0.949	0.818	0.697	0.949	CLONAL	1	TRUE	1	0.57	2		365	193	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206669478	206669478	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	60	434	0	ENST00000367120.3:c.2151A>G	p.Ter717TrpextTer6	p.*717Wext*6	ENST00000367120	NM_014002.3	717	tgA/tgG	22/22	1	2	FACETS	0.97	0.848	1	0.97	0.848	1	CLONAL	1	TRUE	1	0.57	2		434	217	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88676927	88676927	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747728399	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	27	171	0	ENST00000372037.3:c.712C>T	p.Arg238Trp	p.R238W	ENST00000372037	NM_004329.2	238	Cgg/Tgg	9/13	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.57	2		171	87	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631171	69631171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782315409	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	12	560	0	ENST00000334134.2:c.241G>A	p.Val81Met	p.V81M	ENST00000334134	NM_005247.2	81	Gtg/Atg	2/3	1	2	FACETS	0.183	0.128	0.251	0.183	0.128	0.251	SUBCLONAL	1	TRUE	1	0.57	2		560	230	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042686	42042686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	18	621	0	ENST00000219905.7:c.6881C>T	p.Ala2294Val	p.A2294V	ENST00000219905	NM_001164273.1	2294	gCt/gTt	17/24	1	2	FACETS	0.238	0.179	0.308	0.238	0.179	0.308	SUBCLONAL	1	TRUE	1	0.57	2		621	265	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007871	45007871	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	94	492	0	ENST00000558401.1:c.320del	p.Leu107CysfsTer6	p.L107Cfs*6	ENST00000558401	NM_004048.2	106	acT/ac	2/4	1	2	FACETS	0.976	0.877	1	0.976	0.877	1	CLONAL	1	TRUE	1	0.57	2		492	338	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371785	45371785	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	25	519	0	ENST00000262160.6:c.1206del	p.Phe402LeufsTer7	p.F402Lfs*7	ENST00000262160	NM_005901.5	402	ttT/tt	10/11	1	2	FACETS	0.428	0.339	0.529	0.428	0.339	0.529	SUBCLONAL	1	TRUE	1	0.57	2		519	205	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985485	60985485	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	117	690	0	ENST00000333681.4:c.415A>G	p.Arg139Gly	p.R139G	ENST00000333681		139	Agg/Ggg	2/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.57	2		690	353	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145758	11145758	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1447890611	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	116	539	0	ENST00000358026.2:c.4120C>T	p.Arg1374Cys	p.R1374C	ENST00000358026	NM_001128849.1	1374	Cgc/Tgc	29/36	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.57	2		539	346	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955090	17955090	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	111	603	0	ENST00000458235.1:c.137G>T	p.Gly46Val	p.G46V	ENST00000458235	NM_000215.3	46	gGg/gTg	2/24	0.3	7	FACETS	0.856	0.777	0.937			1	INDETERMINATE	3	TRUE	NA	0.57	7		603	368	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223027	36223027	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	105	847	0	ENST00000222270.7:c.5656C>T	p.Pro1886Ser	p.P1886S	ENST00000222270	NM_014727.1	1886	Ccc/Tcc	27/37	0.104309688970002	3	FACETS	1	0.971	1	0.599	0.541	0.66	INDETERMINATE	1	TRUE	1	0.57	3		847	395	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860625	45860625	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	26	739	0	ENST00000391945.4:c.1382T>C	p.Leu461Pro	p.L461P	ENST00000391945	NM_000400.3	461	cTg/cCg	15/23	0.104309688970002	3	FACETS	0.327	0.259	0.406	0.164	0.129	0.203	INDETERMINATE	1	TRUE	1	0.57	3		739	358	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867755	45867755	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	92	712	0	ENST00000391945.4:c.645del	p.Lys216ArgfsTer32	p.K216Rfs*32	ENST00000391945	NM_000400.3	215	ccC/cc	8/23	0.104309688970002	3	FACETS	0.763	0.687	0.84	0.763	0.687	0.84	INDETERMINATE	2	TRUE	1	0.57	3		712	272	SUCCESS
ALK	238	MSKCC	GRCh37	2	29450496	29450496	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	18	714	0	ENST00000389048.3:c.2858A>G	p.Glu953Gly	p.E953G	ENST00000389048	NM_004304.4	953	gAa/gGa	17/29	1	2	FACETS	0.269	0.202	0.347	0.269	0.202	0.347	SUBCLONAL	1	TRUE	1	0.57	2		714	235	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010478	48010478	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	30	594	0	ENST00000234420.5:c.106G>A	p.Ala36Thr	p.A36T	ENST00000234420	NM_000179.2	36	Gct/Act	1/10	1	2	FACETS	0.446	0.361	0.541	0.446	0.361	0.541	SUBCLONAL	1	TRUE	1	0.57	2		594	236	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286803	212286803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	35	457	0	ENST00000342788.4:c.2893C>T	p.Pro965Ser	p.P965S	ENST00000342788	NM_005235.2	965	Cct/Tct	24/28	1	2	FACETS	0.722	0.6	0.856	0.722	0.6	0.856	SUBCLONAL	1	TRUE	1	0.57	2		457	170	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713283	30713283	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	140	609	0	ENST00000295754.5:c.608C>T	p.Thr203Ile	p.T203I	ENST00000295754	NM_003242.5	203	aCc/aTc	4/7	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.57	2		609	487	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69988262	69988262	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	40	426	0	ENST00000394351.3:c.275T>C	p.Phe92Ser	p.F92S	ENST00000394351	NM_000248.3	92	tTt/tCt	3/9	1	2	FACETS	0.659	0.553	0.775	0.659	0.553	0.775	SUBCLONAL	1	TRUE	1	0.57	2		426	213	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244147	153244148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	79	657	0	ENST00000281708.4:c.2009dup	p.Val671SerfsTer23	p.V671Sfs*23	ENST00000281708	NM_033632.3	670	gga/ggGa	12/12	1	2	FACETS	0.607	0.535	0.682	0.607	0.535	0.682	SUBCLONAL	1	TRUE	1	0.57	2		657	457	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046068	180046068	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	41	467	0	ENST00000261937.6:c.2803C>A	p.Leu935Ile	p.L935I	ENST00000261937	NM_182925.4	935	Ctc/Atc	20/30	0.272557268003749	0	FACETS	0.326	0.274	0.381			1	INDETERMINATE	1	TRUE	0	0.57	0		467	190	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673632	30673632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs539990635	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	23	624	0	ENST00000376406.3:c.3328C>T	p.Arg1110Trp	p.R1110W	ENST00000376406	NM_014641.2	1110	Cgg/Tgg	10/15	0.272557268003749	3	FACETS	0.243	0.189	0.306	0.121	0.094	0.153	INDETERMINATE	1	TRUE	1	0.57	3		624	427	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2058346	2058346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	41	431	0	ENST00000349721.2:c.1403C>T	p.Ser468Phe	p.S468F	ENST00000349721	NM_003070.3	468	tCt/tTt	8/34	1	2	FACETS	0.79	0.667	0.924	0.79	0.667	0.924	CLONAL	1	TRUE	1	0.57	2		431	182	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522552	176522552	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519793	NA	P-0059859-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	112	996	0	ENST00000292408.4:c.1649T>A	p.Val550Glu	p.V550E	ENST00000292408	NM_213647.1	550	gTg/gAg	13/18	0.40705150170845	1	FACETS	0.465	0.42	0.512	0.465	0.42	0.512	SUBCLONAL	1	TRUE	0	0.650042525943784	1		996	500	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056119	26056119	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059859-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	116	866	0	ENST00000343677.2:c.538G>C	p.Ala180Pro	p.A180P	ENST00000343677	NM_005319.3	180	Gcg/Ccg	1/1	0.436653649547226	3	FACETS	0.665	0.6	0.734	0.333	0.3	0.367	SUBCLONAL	1	TRUE	1	0.650042525943784	3		866	711	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0060720-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	206	515	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.937	0.877	0.997	1	0.995	1	CLONAL	4	FALSE	1	0.21599923790072	2		515	509	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179050	123179050	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060720-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	86	224	0	ENST00000218089.9:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000218089	NM_001042749.1	167	Cag/Tag	8/35	1	1	FACETS	1	0.967	1	1	0.991	1	CLONAL	6	FALSE	0	0.21599923790072	1		224	112	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30323847	30323847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060720-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	12	436	0	ENST00000322652.5:c.1825G>A	p.Gly609Arg	p.G609R	ENST00000322652	NM_015355.2	609	Gga/Aga	15/16	1	2	FACETS	0.567	0.399	0.773	0.567	0.399	0.773	SUBCLONAL	1	FALSE	1	0.21599923790072	2		436	196	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440519	49440519	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060720-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	271	741	0	ENST00000301067.7:c.4291G>T	p.Glu1431Ter	p.E1431*	ENST00000301067	NM_003482.3	1431	Gag/Tag	15/54	1	2	FACETS	1	0.969	1	1	0.996	1	CLONAL	4	FALSE	1	0.21599923790072	2		741	607	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363611	40363611	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060720-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	241	700	0	ENST00000397332.2:c.618G>C	p.Glu206Asp	p.E206D	ENST00000397332	NM_001033082.2	206	gaG/gaC	3/3	1	2	FACETS	1	0.969	1	1	0.996	1	CLONAL	4	FALSE	1	0.21599923790072	2		700	536	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426763	49426763	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060720-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	275	917	0	ENST00000301067.7:c.11725C>T	p.Gln3909Ter	p.Q3909*	ENST00000301067	NM_003482.3	3909	Caa/Taa	39/54	1	2	FACETS	1	0.954	1	1	0.997	1	CLONAL	4	FALSE	1	0.21599923790072	2		917	631	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117778	115117778	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0060720-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	37	502	0	ENST00000257566.3:c.658-1G>C		p.X220_splice	ENST00000257566	NM_016569.3	220			1	2	FACETS	0.784	0.646	0.938	0.784	0.646	0.938	CLONAL	1	FALSE	1	0.21599923790072	2		502	437	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781776	3781776	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0060720-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	32	688	0	ENST00000262367.5:c.4890+1G>A		p.X1630_splice	ENST00000262367	NM_004380.2	1630			1	2	FACETS	0.597	0.484	0.726	0.597	0.484	0.726	SUBCLONAL	1	FALSE	1	0.21599923790072	2		688	496	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393379	139393379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060720-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	30	764	0	ENST00000277541.6:c.6152G>A	p.Gly2051Glu	p.G2051E	ENST00000277541	NM_017617.3	2051	gGg/gAg	33/34	1	2	FACETS	0.5	0.401	0.611	0.5	0.401	0.611	SUBCLONAL	1	FALSE	1	0.21599923790072	2		764	556	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0060936-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	51	443	9	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.540889406230882	3	FACETS	0.929	0.811	1	0.929	0.811	1	CLONAL	2	TRUE	1	0.540889406230882	3		452	129	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0060936-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	64	709	11	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	0.524656171019766	4	FACETS	0.866	0.753	0.988	0.289	0.251	0.33	CLONAL	1	TRUE	1	0.540889406230882	4		720	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0060936-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	259	785	23	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.529012302810754	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.540889406230882	2		808	439	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060936-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	193	579	11	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	0.538271253800012	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.540889406230882	2		590	354	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042242	6042242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs114090343	NA	P-0060936-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	111	515	1	ENST00000265849.7:c.379G>A	p.Ala127Thr	p.A127T	ENST00000265849	NM_000535.5	127	Gca/Aca	5/15	0.540889406230882	3	FACETS	1	0.961	1	0.562	0.508	0.618	CLONAL	1	TRUE	1	0.540889406230882	3		516	464	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871997	37871997	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756345214	NA	P-0060936-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	103	708	5	ENST00000269571.5:c.1318G>A	p.Ala440Thr	p.A440T	ENST00000269571		440	Gcc/Acc	12/27	0.530045052671748	3	FACETS	0.898	0.806	0.994	0.449	0.403	0.497	CLONAL	1	TRUE	1	0.540889406230882	3		713	539	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336639	81336639	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060936-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	21	438	0	ENST00000222390.5:c.1583G>T	p.Trp528Leu	p.W528L	ENST00000222390	NM_000601.4	528	tGg/tTg	14/18	0.540889406230882	3	FACETS	1	0.885	1	0.602	0.475	0.741	CLONAL	1	TRUE	1	0.540889406230882	3		438	82	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37038192	37038192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750206	NA	P-0060936-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	56	479	7	ENST00000231790.2:c.199G>A	p.Gly67Arg	p.G67R	ENST00000231790	NM_000249.3	67	Ggg/Agg	2/19	0.540889406230882	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.540889406230882	1		486	117	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921774	111921774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150291943	NA	P-0060936-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	103	505	1	ENST00000393256.3:c.563G>A	p.Arg188His	p.R188H	ENST00000393256	NM_006538.4	188	cGt/cAt	4/4	0.530045052671748	3	FACETS	1	0.961	1	0.567	0.51	0.626	CLONAL	1	TRUE	1	0.540889406230882	3		506	427	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053156	180053156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1333005497	NA	P-0060936-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	104	794	9	ENST00000261937.6:c.1213G>A	p.Ala405Thr	p.A405T	ENST00000261937	NM_182925.4	405	Gct/Act	9/30	1	2	FACETS	0.918	0.828	1	0.918	0.828	1	CLONAL	1	TRUE	1	0.540889406230882	2		803	419	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681438	88681438	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659155	NA	P-0060936-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	43	383	1	ENST00000372037.3:c.1328G>A	p.Arg443His	p.R443H	ENST00000372037	NM_004329.2	443	cGt/cAt	11/13	0.482689152293144	0	FACETS	0.545	0.466	0.628			1	SUBCLONAL	1	TRUE	0	0.540889406230882	0		384	134	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663335	67663335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060936-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	53	546	18	ENST00000264010.4:c.1736G>A	p.Gly579Asp	p.G579D	ENST00000264010	NM_006565.3	579	gGc/gAc	10/12	1	2	FACETS	0.929	0.803	1	0.929	0.803	1	CLONAL	1	TRUE	1	0.540889406230882	2		564	211	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592353	29592353	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500316	NA	P-0060936-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	38	311	9	ENST00000356175.3:c.4768C>T	p.Arg1590Trp	p.R1590W	ENST00000356175	NM_000267.3	1590	Cgg/Tgg	35/57	0.540889406230882	3	FACETS	0.875	0.763	0.985	1	0.958	1	CLONAL	3	TRUE	1	0.540889406230882	3		320	68	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107184	11107186	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs1484395538	NA	P-0060936-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	113	558	5	ENST00000358026.2:c.1778_1780del	p.Glu593del	p.E593del	ENST00000358026	NM_001128849.1	592	gcAGAa/gca	11/36	0.538271253800012	2	FACETS	1	0.941	1	0.525	0.476	0.575	CLONAL	1	TRUE	0	0.540889406230882	2		563	398	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546551	9546551	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060936-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	77	522	0	ENST00000353224.5:c.1471C>A	p.Leu491Ile	p.L491I	ENST00000353224	NM_177990.2	491	Ctt/Att	5/10	0.533117622743202	2	FACETS	1	0.976	1	0.681	0.609	0.755	CLONAL	1	TRUE	0	0.540889406230882	2		522	209	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800230	32800230	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060936-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	98	612	10	ENST00000374899.4:c.1152C>A	p.His384Gln	p.H384Q	ENST00000374899	NM_018833.2	384	caC/caA	7/12	0.540889406230882	3	FACETS	0.961	0.861	1	0.481	0.43	0.533	CLONAL	1	TRUE	1	0.540889406230882	3		622	479	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864369	162864369	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060936-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	87	531	13	ENST00000366898.1:c.144G>T	p.Lys48Asn	p.K48N	ENST00000366898	NM_004562.2	48	aaG/aaT	2/12	0.530045052671748	3	FACETS	0.846	0.752	0.946	0.423	0.376	0.473	CLONAL	1	TRUE	1	0.540889406230882	3		544	483	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485884	8485884	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060936-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	75	616	2	ENST00000356435.5:c.2933C>T	p.Thr978Ile	p.T978I	ENST00000356435		978	aCt/aTt	17/35	0.530045052671748	3	FACETS	1	0.963	1	0.61	0.54	0.683	CLONAL	1	TRUE	1	0.540889406230882	3		618	289	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344964	70344964	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750304793	NA	P-0061297-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	28	570	2	ENST00000374080.3:c.2194G>A	p.Val732Met	p.V732M	ENST00000374080		732	Gtg/Atg	15/45	1	2	FACETS	0.556	0.444	0.685	0.556	0.444	0.685	SUBCLONAL	1	TRUE	1	0.223196994066078	2		572	451	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710860	117710860	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747288191	NA	P-0061297-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	35	566	0	ENST00000368508.3:c.1412A>G	p.Asn471Ser	p.N471S	ENST00000368508	NM_002944.2	471	aAt/aGt	12/43	0.223196994066078	3	FACETS	0.67	0.549	0.807	0.335	0.274	0.404	SUBCLONAL	1	TRUE	1	0.223196994066078	3		566	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0061422-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	245	481	3	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.734370326679802	2	FACETS	0.956	0.918	0.993	0.956	0.918	0.993	CLONAL	2	TRUE	0	0.762399408628931	2		484	336	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0061422-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	163	255	0	ENST00000374690.3:c.2105T>A	p.Leu702His	p.L702H	ENST00000374690	NM_000044.3	702	cTc/cAc	4/8	0.661251796287624	3	FACETS	0.82	0.764	0.877			1	CLONAL	2	TRUE	NA	0.762399408628931	3		255	360	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136153	11136153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061422-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	70	429	0	ENST00000358026.2:c.3137G>A	p.Cys1046Tyr	p.C1046Y	ENST00000358026	NM_001128849.1	1046	tGc/tAc	22/36	1	2	FACETS	0.827	0.732	0.926	0.827	0.732	0.926	CLONAL	1	TRUE	1	0.762399408628931	2		429	222	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981316	68981316	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061422-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	200	245	0	ENST00000288368.4:c.1388G>T	p.Arg463Leu	p.R463L	ENST00000288368	NM_024870.2	463	cGc/cTc	12/40	0.762399408628931	6	FACETS	0.925	0.86	0.992	0.463	0.43	0.496	CLONAL	2	TRUE	2	0.762399408628931	6		245	716	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009270	69009270	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061422-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	118	353	0	ENST00000288368.4:c.2387A>T	p.Asn796Ile	p.N796I	ENST00000288368	NM_024870.2	796	aAc/aTc	22/40	0.762399408628931	6	FACETS	0.873	0.787	0.964	0.218	0.196	0.241	CLONAL	1	TRUE	2	0.762399408628931	6		353	895	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	73	348	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.448370918399316	2		349	291	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402695	139402695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778118508	NA	P-0061668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	100	620	1	ENST00000277541.6:c.3314C>T	p.Ala1105Val	p.A1105V	ENST00000277541	NM_017617.3	1105	gCg/gTg	20/34	1	2	FACETS	0.972	0.873	1	0.972	0.873	1	CLONAL	1	TRUE	1	0.448370918399316	2		621	459	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39321411	39321411	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	35	437	0	ENST00000373001.3:c.610G>A	p.Ala204Thr	p.A204T	ENST00000373001	NM_022157.3	204	Gca/Aca	3/7	0.204547526459614	1	FACETS	0.471	0.388	0.563	0.471	0.388	0.563	INDETERMINATE	1	TRUE	0	0.448370918399316	1		437	257	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68878221	68878221	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	71	558	0	ENST00000487270.1:c.934T>C	p.Tyr312His	p.Y312H	ENST00000487270	NM_133509.3	312	Tac/Cac	9/11	0.196644094349085	3	FACETS	0.992	0.87	1	0.496	0.435	0.561	INDETERMINATE	1	TRUE	1	0.448370918399316	3		558	391	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565582	41565582	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	62	362	0	ENST00000263253.7:c.4248A>C	p.Glu1416Asp	p.E1416D	ENST00000263253	NM_001429.3	1416	gaA/gaC	26/31	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.448370918399316	2		362	241	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178942594	178942594	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	46	392	0	ENST00000263967.3:c.2401T>G	p.Phe801Val	p.F801V	ENST00000263967	NM_006218.2	801	Ttt/Gtt	16/21	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.448370918399316	2		392	194	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339925	116339925	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	77	504	0	ENST00000397752.3:c.787A>G	p.Thr263Ala	p.T263A	ENST00000397752	NM_000245.2	263	Acg/Gcg	2/21	1	2	FACETS	0.998	0.883	1	0.998	0.883	1	CLONAL	1	TRUE	1	0.448370918399316	2		504	344	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517848	8517848	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	33	392	0	ENST00000356435.5:c.1543G>A	p.Val515Ile	p.V515I	ENST00000356435		515	Gta/Ata	10/35	1	2	FACETS	0.543	0.444	0.654	0.543	0.444	0.654	SUBCLONAL	1	TRUE	1	0.448370918399316	2		392	271	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0061697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	19	448	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	1	2	FACETS	0.561	0.426	0.72	0.561	0.426	0.72	SUBCLONAL	1	TRUE	1	0.24	2		448	282	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0061697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	18	515	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.962	0.729	1	0.962	0.729	1	CLONAL	1	TRUE	1	0.24	2		515	156	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092809	27092809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	32	586	0	ENST00000324856.7:c.2830C>T	p.Gln944Ter	p.Q944*	ENST00000324856	NM_006015.4	944	Cag/Tag	9/20	1	2	FACETS	0.813	0.661	0.984	0.813	0.661	0.984	CLONAL	1	TRUE	1	0.24	2		586	328	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875645	35875645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201449880	NA	P-0061697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	19	431	0	ENST00000303115.3:c.832G>A	p.Asp278Asn	p.D278N	ENST00000303115	NM_002185.3	278	Gat/Aat	7/8	1	2	FACETS	0.43	0.326	0.553	0.43	0.326	0.553	SUBCLONAL	1	TRUE	1	0.24	2		431	368	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099981	27099981	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	37	705	0	ENST00000324856.7:c.3860G>C	p.Arg1287Thr	p.R1287T	ENST00000324856	NM_006015.4	1287	aGa/aCa	15/20	1	2	FACETS	0.739	0.61	0.884	0.739	0.61	0.884	SUBCLONAL	1	TRUE	1	0.24	2		705	417	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732409	74732409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326283685	NA	P-0061697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	79	701	0	ENST00000359995.5:c.500G>A	p.Arg167Gln	p.R167Q	ENST00000359995	NM_001195427.1	167	cGa/cAa	2/3	1	2	FACETS	0.733	0.643	0.83	0.733	0.643	0.83	SUBCLONAL	1	TRUE	1	0.24	2		701	898	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923035	44923035	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	41	294	0	ENST00000377967.4:c.1896G>A	p.Trp632Ter	p.W632*	ENST00000377967	NM_021140.2	632	tgG/tgA	16/29	1	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.24	1		294	247	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041348	47041348	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0061697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	40	386	0	ENST00000377604.3:c.1694-2A>G		p.X565_splice	ENST00000377604	NM_001204468.1	565			1	1	FACETS	0.784	0.66	0.919	1	0.96	1	CLONAL	2	TRUE	0	0.24	1		386	187	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092852	27092852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	31	573	0	ENST00000324856.7:c.2873C>T	p.Ser958Phe	p.S958F	ENST00000324856	NM_006015.4	958	tCt/tTt	9/20	1	2	FACETS	0.788	0.638	0.956	0.788	0.638	0.956	CLONAL	1	TRUE	1	0.24	2		573	328	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972491	32972491	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	33	564	0	ENST00000380152.3:c.9841C>G	p.Pro3281Ala	p.P3281A	ENST00000380152		3281	Cca/Gca	27/27	0.110633767137784	3	FACETS	0.683	0.556	0.826	0.341	0.278	0.413	INDETERMINATE	1	TRUE	1	0.24	3		564	451	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295446	1295446	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0061697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	11	743	0				ENST00000310581	NM_198253.2	-/1132			0.367329366316228	0	FACETS	0.718	0.501	0.982			1	CLONAL	1	TRUE	0	0.24	0		743	97	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64288834	64288834	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	25	328	0	ENST00000370651.3:c.230C>G	p.Ser77Cys	p.S77C	ENST00000370651	NM_003463.4	77	tCc/tGc	4/6	1	2	FACETS	0.52	0.409	0.647	0.52	0.409	0.647	SUBCLONAL	1	TRUE	1	0.24	2		328	401	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779041	135779041	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	23	514	0	ENST00000298552.3:c.2205del	p.Met736Ter	p.M736*	ENST00000298552	NM_001162426.1	735	gcC/gc	17/23	0.198633236575116	1	FACETS	0.753	0.589	0.941	0.753	0.589	0.941	CLONAL	1	TRUE	0	0.24	1		514	224	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0061760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	119	469	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.923	0.839	1	0.923	0.839	1	CLONAL	1	TRUE	1	0.599758791477897	2		470	430	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934578	NA	P-0061760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	253	780	0	ENST00000269305.4:c.524G>T	p.Arg175Leu	p.R175L	ENST00000269305	NM_001126112.2	175	cGc/cTc	5/11	0.599758791477897	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.599758791477897	1		780	548	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533844	63533844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	161	735	0	ENST00000307078.5:c.1310C>T	p.Thr437Met	p.T437M	ENST00000307078	NM_004655.3	437	aCg/aTg	6/11	0.599758791477897	3	FACETS	0.857	0.787	0.931	0.429	0.393	0.466	CLONAL	1	TRUE	1	0.599758791477897	3		735	814	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030221	180030221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143739828	NA	P-0061760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	212	767	0	ENST00000261937.6:c.4063G>A	p.Val1355Met	p.V1355M	ENST00000261937	NM_182925.4	1355	Gtg/Atg	30/30	0.599758791477897	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.599758791477897	1		767	460	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888819	76888819	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	163	628	0	ENST00000373344.5:c.5010G>T	p.Gln1670His	p.Q1670H	ENST00000373344	NM_000489.3	1670	caG/caT	19/35	1	2	FACETS	0.954	0.88	1	0.954	0.88	1	CLONAL	1	TRUE	1	0.599758791477897	2		628	570	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439577	51439577	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	182	528	0	ENST00000262662.1:c.142G>T	p.Gly48Ter	p.G48*	ENST00000262662		48	Gga/Tga	4/4	0.599758791477897	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.599758791477897	1		528	366	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233243	46233243	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	198	582	0	ENST00000334344.6:c.1462C>T	p.Gln488Ter	p.Q488*	ENST00000334344	NM_152641.2	488	Caa/Taa	11/21	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.599758791477897	2		582	655	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729907	41729907	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	196	636	0	ENST00000242208.4:c.622G>T	p.Glu208Ter	p.E208*	ENST00000242208	NM_002192.2	208	Gaa/Taa	3/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.599758791477897	2		636	603	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	244006427	244006428	+	stop_gained,splice_region_variant	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0061760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	277	453	0	ENST00000263826.5:c.45_46delinsTT	p.Arg15_Gly16delinsSerTer	p.R15_G16delinsS*	ENST00000263826	NM_005465.4	15	agGGga/agTTga	1/13	0.599758791477897	2	FACETS	0.972	0.927	1	0.972	0.927	1	CLONAL	2	TRUE	0	0.599758791477897	2		453	475	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427914	49427914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463174814	NA	P-0061760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	178	717	0	ENST00000301067.7:c.10676C>T	p.Ala3559Val	p.A3559V	ENST00000301067	NM_003482.3	3559	gCt/gTt	38/54	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.599758791477897	2		717	591	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911502	32911502	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	207	564	0	ENST00000380152.3:c.3010A>T	p.Ser1004Cys	p.S1004C	ENST00000380152		1004	Agt/Tgt	11/27	0.599758791477897	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.599758791477897	1		564	428	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562951	95562951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	170	631	0	ENST00000393063.1:c.4306G>A	p.Ala1436Thr	p.A1436T	ENST00000393063	NM_030621.3	1436	Gct/Act	24/28	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.599758791477897	2		631	556	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028458	42028459	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	195	695	0	ENST00000219905.7:c.3997dup	p.Thr1333AsnfsTer5	p.T1333Nfs*5	ENST00000219905	NM_001164273.1	1332	-/A	13/24	0.599758791477897	1	FACETS	0.941	0.879	1	0.941	0.879	1	CLONAL	1	TRUE	0	0.599758791477897	1		695	484	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476301	88476301	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	317	588	0	ENST00000360948.2:c.1831G>C	p.Asp611His	p.D611H	ENST00000360948	NM_001012338.2	611	Gac/Cac	15/19	0.596454571978257	2	FACETS	0.977	0.935	1	0.977	0.935	1	CLONAL	2	TRUE	0	0.599758791477897	2		588	541	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459916	99459916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	337	586	0	ENST00000268035.6:c.2012G>A	p.Arg671Lys	p.R671K	ENST00000268035	NM_000875.3	671	aGg/aAg	10/21	0.596454571978257	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.599758791477897	2		586	548	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226264	2226264	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0061760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	255	836	0	ENST00000326181.6:c.1879-2A>T		p.X627_splice	ENST00000326181	NM_032271.2	627			1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.599758791477897	2		836	696	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274134	10274134	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1432737328	NA	P-0061760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	176	705	0	ENST00000330684.3:c.135C>A	p.Asp45Glu	p.D45E	ENST00000330684	NM_001134407.1	45	gaC/gaA	2/13	1	2	FACETS	0.903	0.835	0.973	0.903	0.835	0.973	CLONAL	1	TRUE	1	0.599758791477897	2		705	650	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581226	48581226	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	202	596	0	ENST00000342988.3:c.530A>G	p.His177Arg	p.H177R	ENST00000342988	NM_005359.5	177	cAt/cGt	5/12	0.599758791477897	1	FACETS	0.953	0.892	1	0.953	0.892	1	CLONAL	1	TRUE	0	0.599758791477897	1		596	495	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748605	40748605	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	110	418	0	ENST00000373198.4:c.2911C>A	p.His971Asn	p.H971N	ENST00000373198	NM_133170.3	971	Cat/Aat	21/32	NA	2	FACETS	0.943	0.855	1			1	INDETERMINATE	1	TRUE	NA	0.599758791477897	2		418	389	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880992	134880992	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	356	661	0	ENST00000398015.3:c.1555G>T	p.Gly519Cys	p.G519C	ENST00000398015	NM_004441.4	519	Ggc/Tgc	7/16	0.568592702816614	3	FACETS	0.948	0.903	0.993	0.948	0.903	0.993	CLONAL	2	TRUE	1	0.599758791477897	3		661	814	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447633	187447633	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	261	941	0	ENST00000232014.4:c.560G>T	p.Gly187Val	p.G187V	ENST00000232014	NM_001130845.1	187	gGc/gTc	5/10	0.568592702816614	3	FACETS	1	0.938	1	0.501	0.469	0.534	CLONAL	1	TRUE	1	0.599758791477897	3		941	1130	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467389	66467389	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	206	714	0	ENST00000273854.3:c.880G>T	p.Gly294Ter	p.G294*	ENST00000273854	NM_004439.5	294	Gga/Tga	3/18	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.599758791477897	2		714	666	SUCCESS
ALB	213	MSKCC	GRCh37	4	74270054	74270054	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	182	528	0	ENST00000295897.4:c.10G>C	p.Val4Leu	p.V4L	ENST00000295897	NM_000477.5	4	Gta/Cta	1/15	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.599758791477897	2		528	590	SUCCESS
ALB	213	MSKCC	GRCh37	4	74283978	74283978	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	162	523	0	ENST00000295897.4:c.1602T>G	p.His534Gln	p.H534Q	ENST00000295897	NM_000477.5	534	caT/caG	12/15	1	2	FACETS	0.96	0.885	1	0.96	0.885	1	CLONAL	1	TRUE	1	0.599758791477897	2		523	563	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226155	226155	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	359	581	0	ENST00000264932.6:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000264932	NM_004168.2	205	tAt/tGt	5/15	0.114289298693497	6	FACETS	1	0.991	1			1	INDETERMINATE	3	TRUE	NA	0.599758791477897	6		581	769	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388088	81388088	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	115	329	0	ENST00000222390.5:c.287G>T	p.Cys96Phe	p.C96F	ENST00000222390	NM_000601.4	96	tGc/tTc	3/18	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.599758791477897	2		329	369	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894979	101894979	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0061760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	343	576	0	ENST00000374994.4:c.532A>T	p.Lys178Ter	p.K178*	ENST00000374994	NM_004612.2	178	Aaa/Taa	3/9	0.596454571978257	2	FACETS	0.995	0.954	1	0.995	0.954	1	CLONAL	2	TRUE	0	0.599758791477897	2		576	575	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922899	44922899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs962190659	NA	P-0061760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	180	709	0	ENST00000377967.4:c.1760G>A	p.Ser587Asn	p.S587N	ENST00000377967	NM_021140.2	587	aGt/aAt	16/29	1	2	FACETS	0.893	0.827	0.962	0.893	0.827	0.962	CLONAL	1	TRUE	1	0.599758791477897	2		709	672	SUCCESS
AR	367	MSKCC	GRCh37	X	66765035	66765035	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	206	699	0	ENST00000374690.3:c.47C>A	p.Ser16Tyr	p.S16Y	ENST00000374690	NM_000044.3	16	tCc/tAc	1/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.599758791477897	2		699	660	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0061766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	259	334	1	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.717027551501169	2		335	662	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0061766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	468	646	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	NA	2	FACETS	0.844	0.815	0.874			1	INDETERMINATE	2	FALSE	NA	0.717027551501169	2		647	773	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0061766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	155	47	0				ENST00000310581	NM_198253.2	-/1132			0.185007581794583	1	FACETS	0.639	0.591	0.688	0.639	0.591	0.688	INDETERMINATE	1	FALSE	0	0.717027551501169	1		47	434	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946283	2946283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147422861	NA	P-0061766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	240	576	0	ENST00000396946.4:c.3454G>A	p.Asp1152Asn	p.D1152N	ENST00000396946	NM_032415.4	1152	Gac/Aac	25/25	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.717027551501169	2		576	656	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120845	94120845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465346253	NA	P-0061766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	246	574	0	ENST00000369303.4:c.206G>A	p.Arg69Gln	p.R69Q	ENST00000369303	NM_004440.3	69	cGa/cAa	3/17	1	2	FACETS	0.971	0.912	1	0.971	0.912	1	CLONAL	1	FALSE	1	0.717027551501169	2		574	707	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858735	9858735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	245	604	0	ENST00000330684.3:c.2666G>A	p.Gly889Glu	p.G889E	ENST00000330684	NM_001134407.1	889	gGa/gAa	13/13	1	2	FACETS	0.944	0.886	1	0.944	0.886	1	CLONAL	1	FALSE	1	0.717027551501169	2		604	724	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40709551	40709551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568484928	NA	P-0061766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	194	469	0	ENST00000373198.4:c.4351G>A	p.Glu1451Lys	p.E1451K	ENST00000373198	NM_133170.3	1451	Gag/Aag	32/32	1	2	FACETS	0.944	0.88	1	0.944	0.88	1	CLONAL	1	FALSE	1	0.717027551501169	2		469	573	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857311	9857311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1245573153	NA	P-0061766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	249	693	0	ENST00000330684.3:c.4090G>A	p.Asp1364Asn	p.D1364N	ENST00000330684	NM_001134407.1	1364	Gat/Aat	13/13	1	2	FACETS	0.944	0.886	1	0.944	0.886	1	CLONAL	1	FALSE	1	0.717027551501169	2		693	736	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383360	4383360	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	270	713	0	ENST00000261254.3:c.154C>T	p.Gln52Ter	p.Q52*	ENST00000261254	NM_001759.3	52	Caa/Taa	1/5	1	2	FACETS	0.977	0.92	1	0.977	0.92	1	CLONAL	1	FALSE	1	0.717027551501169	2		713	771	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31369198	31369198	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752329190	NA	P-0061766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	291	574	0	ENST00000328111.2:c.182C>T	p.Ser61Phe	p.S61F	ENST00000328111	NM_006892.3	61	tCc/tTc	3/23	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.717027551501169	2		574	787	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019410	42019410	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs528009988	NA	P-0061766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	222	540	0	ENST00000219905.7:c.3463C>T	p.Arg1155Ter	p.R1155*	ENST00000219905	NM_001164273.1	1155	Cga/Tga	10/24	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.717027551501169	2		540	592	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867528	78867528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759154872	NA	P-0061766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	149	672	0	ENST00000306801.3:c.2264C>T	p.Ser755Phe	p.S755F	ENST00000306801	NM_020761.2	755	tCc/tTc	20/34	0.380849298968936	1	FACETS	0.385	0.353	0.419	0.385	0.353	0.419	INDETERMINATE	1	FALSE	0	0.717027551501169	1		672	692	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518124	8518124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	299	545	0	ENST00000356435.5:c.1267G>A	p.Asp423Asn	p.D423N	ENST00000356435		423	Gat/Aat	10/35	0.717027551501169	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	0	0.717027551501169	1		545	479	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604206	189604206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	264	631	0	ENST00000264731.3:c.1373C>T	p.Ser458Leu	p.S458L	ENST00000264731	NM_003722.4	458	tCa/tTa	11/14	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.717027551501169	2		631	667	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933280	100933280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	221	580	0	ENST00000325455.5:c.2110G>A	p.Asp704Asn	p.D704N	ENST00000325455	NM_001202474.3	704	Gac/Aac	4/8	1	2	FACETS	0.959	0.897	1	0.959	0.897	1	CLONAL	1	FALSE	1	0.717027551501169	2		580	643	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144359588	144359588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779671407	NA	P-0061766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	156	721	0	ENST00000262995.4:c.1030C>T	p.Arg344Trp	p.R344W	ENST00000262995	NM_207123.2	344	Cgg/Tgg	4/11	0.380849298968936	1	FACETS	0.373	0.342	0.405	0.373	0.342	0.405	INDETERMINATE	1	FALSE	0	0.717027551501169	1		721	749	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332853	70332853	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	130	647	0	ENST00000373644.4:c.758C>T	p.Pro253Leu	p.P253L	ENST00000373644	NM_030625.2	253	cCc/cTc	2/12	0.380849298968936	1	FACETS	0.396	0.36	0.433	0.396	0.36	0.433	INDETERMINATE	1	FALSE	0	0.717027551501169	1		647	588	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447287	49447287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779328648	NA	P-0061766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	186	641	0	ENST00000301067.7:c.811C>T	p.Pro271Ser	p.P271S	ENST00000301067	NM_003482.3	271	Cct/Tct	6/54	NA	2	FACETS	0.692	0.64	0.745			1	INDETERMINATE	1	FALSE	NA	0.717027551501169	2		641	750	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986788	36986788	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	202	456	0	ENST00000354822.5:c.901C>T	p.Gln301Ter	p.Q301*	ENST00000354822	NM_001079668.2	301	Cag/Tag	3/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.717027551501169	2		456	501	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943669	9943670	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0061766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	261	606	0	ENST00000330684.3:c.1271_1272delinsTT	p.Pro424Leu	p.P424L	ENST00000330684	NM_001134407.1	424	cCC/cTT	5/13	1	2	FACETS	0.936	0.88	0.992	0.936	0.88	0.992	CLONAL	1	FALSE	1	0.717027551501169	2		606	778	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670643	67670643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761615218	NA	P-0061766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	147	537	0	ENST00000264010.4:c.1888G>A	p.Val630Ile	p.V630I	ENST00000264010	NM_006565.3	630	Gta/Ata	11/12	0.380849298968936	1	FACETS	0.393	0.359	0.427	0.393	0.359	0.427	INDETERMINATE	1	FALSE	0	0.717027551501169	1		537	670	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630380	67630380	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	84	330	0	ENST00000272342.5:c.566A>G	p.Glu189Gly	p.E189G	ENST00000272342	NM_019002.3	189	gAa/gGa	5/6	1	2	FACETS	0.956	0.858	1	0.956	0.858	1	CLONAL	1	FALSE	1	0.717027551501169	2		330	245	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770600	40770601	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0061766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	246	592	1	ENST00000373198.4:c.2781_2782delinsAA	p.Glu928Lys	p.E928K	ENST00000373198	NM_133170.3	927	aaGGag/aaAAag	19/32	1	2	FACETS	0.877	0.823	0.933	0.877	0.823	0.933	CLONAL	1	FALSE	1	0.717027551501169	2		593	782	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21343965	21343966	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0061766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	212	556	0	ENST00000215739.8:c.645_646delinsAA	p.Trp215_Glu216delinsTer	p.W215_E216delins*	ENST00000215739	NM_006767.3	215	tgGGag/tgAAag	7/21	1	2	FACETS	0.924	0.863	0.986	0.924	0.863	0.986	CLONAL	1	FALSE	1	0.717027551501169	2		556	640	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21350034	21350034	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1189015572	NA	P-0061766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	278	613	0	ENST00000215739.8:c.1943-1G>A		p.X648_splice	ENST00000215739	NM_006767.3	648			1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	1	0.717027551501169	2		613	767	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397803	49397803	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775207141	NA	P-0061766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	243	501	0	ENST00000418115.1:c.421C>T	p.Pro141Ser	p.P141S	ENST00000418115	NM_001664.2	141	Cct/Tct	5/5	1	2	FACETS	0.899	0.843	0.956	0.899	0.843	0.956	CLONAL	1	FALSE	1	0.717027551501169	2		501	754	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745382	43745382	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	293	664	0	ENST00000523873.1:c.295G>T	p.Glu99Ter	p.E99*	ENST00000523873		99	Gag/Tag	3/8	0.717027551501169	3	FACETS	0.983	0.925	1	0.491	0.462	0.521	CLONAL	1	FALSE	1	0.717027551501169	3		664	1130	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411948	116411948	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060503540	NA	P-0061766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	333	786	0	ENST00000397752.3:c.2933C>T	p.Pro978Leu	p.P978L	ENST00000397752	NM_000245.2	978	cCt/cTt	14/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.717027551501169	2		786	906	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944355	76944355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	125	260	0	ENST00000373344.5:c.550G>A	p.Asp184Asn	p.D184N	ENST00000373344	NM_000489.3	184	Gat/Aat	7/35	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	0	0.717027551501169	1		260	174	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	169	737	0	ENST00000269305.4:c.497C>A	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tAa	5/11	0.299046620804717	1	FACETS	0.969	0.898	1	1	0.993	1	CLONAL	2	TRUE	0	0.29	1		737	514	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948133	178948133	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	51	485	0	ENST00000263967.3:c.2905C>A	p.Gln969Lys	p.Q969K	ENST00000263967	NM_006218.2	969	Caa/Aaa	20/21	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.29	2		485	306	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257630	19257630	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	32	871	0	ENST00000162023.5:c.596del	p.Pro199HisfsTer24	p.P199Hfs*24	ENST00000162023		199	cCa/ca	10/13	0.124795193736147	3	FACETS	0.396	0.32	0.482	0.132	0.106	0.161	INDETERMINATE	1	TRUE	0	0.29	3		871	638	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936775	32936775	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs886038177	NA	P-0061767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	27	538	0	ENST00000380152.3:c.7921G>T	p.Glu2641Ter	p.E2641*	ENST00000380152		2641	Gaa/Taa	17/27	0.299046620804717	1	FACETS	0.534	0.426	0.658	0.534	0.426	0.658	SUBCLONAL	1	TRUE	0	0.29	1		538	298	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50733649	50733649	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs932067821	NA	P-0061767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	13	402	0	ENST00000307179.4:c.208T>C	p.Tyr70His	p.Y70H	ENST00000307179		70	Tat/Cat	3/20	0.299046620804717	1	FACETS	0.417	0.298	0.561	0.417	0.298	0.561	SUBCLONAL	1	TRUE	0	0.29	1		402	184	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0061768-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	92	469	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.909	0.81	1	0.909	0.81	1	CLONAL	1	TRUE	1	0.374991775039196	2		470	540	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556079	29556079	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886041347	NA	P-0061768-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	22	477	0	ENST00000356175.3:c.2446C>T	p.Arg816Ter	p.R816*	ENST00000356175	NM_000267.3	816	Cga/Tga	21/57	1	2	FACETS	0.271	0.209	0.343	0.271	0.209	0.343	SUBCLONAL	1	TRUE	1	0.374991775039196	2		477	433	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106447	27106447	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0061768-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	97	876	0	ENST00000324856.7:c.6058A>T	p.Lys2020Ter	p.K2020*	ENST00000324856	NM_006015.4	2020	Aag/Tag	20/20	1	2	FACETS	0.742	0.662	0.828	0.742	0.662	0.828	SUBCLONAL	1	TRUE	1	0.374991775039196	2		876	697	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230459254	230459254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148414368	NA	P-0061768-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	71	824	2	ENST00000391860.1:c.1147G>A	p.Val383Met	p.V383M	ENST00000391860	NM_001258311.1	383	Gtg/Atg	7/7	0.374991775039196	3	FACETS	0.623	0.543	0.709	0.311	0.271	0.355	SUBCLONAL	1	TRUE	1	0.374991775039196	3		826	722	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647460	23647460	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061768-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	139	583	0	ENST00000261584.4:c.407G>T	p.Ser136Ile	p.S136I	ENST00000261584	NM_024675.3	136	aGt/aTt	4/13	0.304290392671235	3	FACETS	1	0.986	1	0.729	0.666	0.794	CLONAL	1	TRUE	1	0.374991775039196	3		583	604	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619200	1619200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061768-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	76	990	0	ENST00000344749.5:c.1360G>T	p.Gly454Cys	p.G454C	ENST00000344749	NM_001136139.2	454	Ggc/Tgc	16/19	1	2	FACETS	0.733	0.644	0.829	0.733	0.644	0.829	SUBCLONAL	1	TRUE	1	0.374991775039196	2		990	553	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226912	142226912	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061768-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	101	631	0	ENST00000350721.4:c.4892G>T	p.Arg1631Leu	p.R1631L	ENST00000350721	NM_001184.3	1631	cGt/cTt	28/47	0.374991775039196	1	FACETS	0.772	0.692	0.857	0.772	0.692	0.857	SUBCLONAL	1	TRUE	0	0.374991775039196	1		631	567	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984903	55984903	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061768-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	82	610	0	ENST00000263923.4:c.226G>T	p.Val76Leu	p.V76L	ENST00000263923	NM_002253.2	76	Gtg/Ttg	3/30	1	2	FACETS	0.813	0.718	0.914	0.813	0.718	0.914	CLONAL	1	TRUE	1	0.374991775039196	2		610	538	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673344	30673344	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061768-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	146	1177	0	ENST00000376406.3:c.3616G>C	p.Ala1206Pro	p.A1206P	ENST00000376406	NM_014641.2	1206	Gcc/Ccc	10/15	1	2	FACETS	0.809	0.738	0.884	0.809	0.738	0.884	CLONAL	1	TRUE	1	0.374991775039196	2		1177	962	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0000196-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	404	621	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.309040692981104	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	4	TRUE	0	0.309674828467452	4		621	851	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0000196-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	260	664	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.309674828467452	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.309674828467452	2		665	823	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161222	56161222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000196-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	137	513	1	ENST00000399503.3:c.1091G>A	p.Arg364Gln	p.R364Q	ENST00000399503	NM_005921.1	364	cGg/cAg	5/20	0.176467213323739	5	FACETS	0.94	0.857	1	0.627	0.571	0.685	INDETERMINATE	2	TRUE	2	0.309674828467452	5		514	689	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161259	56161259	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000196-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	144	417	0	ENST00000399503.3:c.1128G>A	p.Trp376Ter	p.W376*	ENST00000399503	NM_005921.1	376	tgG/tgA	5/20	0.176467213323739	5	FACETS	1	0.972	1	0.763	0.699	0.83	INDETERMINATE	2	TRUE	2	0.309674828467452	5		417	595	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619282	37619283	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0000196-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	209	497	0	ENST00000447079.4:c.959dup	p.Ser320ArgfsTer31	p.S320Rfs*31	ENST00000447079	NM_015083.1	320	agc/aGgc	1/14	0.309674828467452	2	FACETS	0.936	0.872	1	0.936	0.872	1	CLONAL	2	TRUE	0	0.309674828467452	2		497	721	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252988	36252988	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000196-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	166	467	2	ENST00000300305.3:c.374del	p.Pro125GlnfsTer8	p.P125Qfs*8	ENST00000300305		125	cCa/ca	4/8	0.172971938637126	2	FACETS	0.866	0.799	0.935	0.866	0.799	0.935	INDETERMINATE	2	TRUE	0	0.309674828467452	2		469	619	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000514-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	190	418	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.632157474326638	2		418	593	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0000514-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	308	719	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.632157474326638	2		719	964	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0000514-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	281	665	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.96	0.904	1	0.96	0.904	1	CLONAL	1	TRUE	1	0.632157474326638	2		665	926	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104264000	104264000	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000514-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	183	435	0	ENST00000369902.3:c.91C>A	p.Pro31Thr	p.P31T	ENST00000369902	NM_016169.3	31	Ccc/Acc	1/12	1	2	FACETS	0.844	0.782	0.908	0.844	0.782	0.908	CLONAL	1	TRUE	1	0.632157474326638	2		435	686	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771321	68771321	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs878854691	NA	P-0000514-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	194	364	0	ENST00000261769.5:c.3G>A	p.Met1?	p.M1?	ENST00000261769	NM_004360.3	1	atG/atA	1/16	0.632157474326638	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.632157474326638	1		364	380	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745987	162745987	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs374326234	NA	P-0000514-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	179	476	0	ENST00000367921.3:c.2110C>G	p.Leu704Val	p.L704V	ENST00000367921	NM_006182.2	704	Ctt/Gtt	16/18	0.632157474326638	4	FACETS	0.936	0.862	1	0.312	0.287	0.338	CLONAL	1	TRUE	1	0.632157474326638	4		476	988	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099397	27099397	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000514-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	256	686	1	ENST00000324856.7:c.3634C>T	p.Gln1212Ter	p.Q1212*	ENST00000324856	NM_006015.4	1212	Cag/Tag	14/20	0.632157474326638	1	FACETS	0.945	0.893	0.998	0.945	0.893	0.998	CLONAL	1	TRUE	0	0.632157474326638	1		687	586	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443551	49443551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759073506	NA	P-0000514-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	289	662	0	ENST00000301067.7:c.3820G>A	p.Asp1274Asn	p.D1274N	ENST00000301067	NM_003482.3	1274	Gat/Aat	11/54	1	2	FACETS	0.955	0.9	1	0.955	0.9	1	CLONAL	1	TRUE	1	0.632157474326638	2		662	957	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640191	3640191	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000514-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	361	964	0	ENST00000294008.3:c.3448G>C	p.Glu1150Gln	p.E1150Q	ENST00000294008	NM_032444.2	1150	Gag/Cag	12/15	0.56781244082029	3	FACETS	0.977	0.925	1	0.489	0.462	0.516	CLONAL	1	TRUE	1	0.632157474326638	3		964	1538	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212137	98212137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000514-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	161	425	1	ENST00000331920.6:c.3535G>A	p.Gly1179Arg	p.G1179R	ENST00000331920	NM_000264.3	1179	Gga/Aga	21/24	1	2	FACETS	0.919	0.848	0.993	0.919	0.848	0.993	CLONAL	1	TRUE	1	0.632157474326638	2		426	554	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10277280	10277280	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001048-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	29	551	0	ENST00000340748.4:c.837C>G	p.Asp279Glu	p.D279E	ENST00000340748		279	gaC/gaG	10/40	1	2	FACETS	0.249	0.199	0.306	0.249	0.199	0.306	SUBCLONAL	1	TRUE	1	0.433519723678392	2		551	537	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419932	152419932	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	86	932	0	ENST00000206249.3:c.1619T>A	p.Leu540Gln	p.L540Q	ENST00000206249	NM_000125.3	540	cTg/cAg	8/8	0.582482311336812	1	FACETS	0.374	0.332	0.42	0.374	0.332	0.42	SUBCLONAL	1	TRUE	0	0.582482311336812	1		932	559	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196056	67196056	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334740541	NA	P-0001504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1213	102	1008	2	ENST00000312629.5:c.40G>A	p.Gly14Ser	p.G14S	ENST00000312629	NM_003952.2	14	Ggc/Agc	1/15	0.582482311336812	4	FACETS	0.421	0.375	0.471	0.14	0.125	0.157	SUBCLONAL	1	TRUE	1	0.582482311336812	4		1010	1315	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62303924	62303924	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	77	770	0	ENST00000360203.5:c.715A>T	p.Asn239Tyr	p.N239Y	ENST00000360203	NM_001283009.1	239	Aac/Tac	9/35	0.152027244385742	4	FACETS	0.394	0.345	0.448	0.131	0.115	0.15	INDETERMINATE	1	TRUE	1	0.582482311336812	4		770	1061	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514511	44515490	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTGGAAGGGGGAGGGTTGTGAGGGGAGAAAGAAGCCACTGAGCTTAACAACGGGCACAGGAATACTCACTTCTTGCGACGGCGGCCATACAGCTCCCGCCGCAGCTCTCTGGAAATGGGCTTCAAATGCATGAAGTTGCAGAAGCCGCCTCGTGTGCATTCTCTGTGGGTGGGTTGGAAGGAGACATTTACTACCTCGTGTGCACACGGCCCCGAACTGTGCTCAGTCACGTCACTGGCCACTCCTCACTCACCCCATCTCATACTGACGGCAGCAGGCTTCTCTGAAGTCCGTCACGGGTGACAGCTCGGCGTGGATCGGCTGTCCATTAAACCAACGGTTATTCAAGTCAATCACAGCCTTTTCCGCATCTTCCTCACGGCGAAACTGAAAAGACAAAAACAGAAGTGCTTGCCATCCACGCTTTAATAAGACTTTCTCAATTACCAATCCAAGTATATCAGAGAGAGATATACACACTCAGGTATAGTAAGGTGGAATAGTATTACAGGATAATTGAAAAATCCTTTATTTTCAATGAGATTAACTTCAAGATAGTCCAAGATTTTGCCAAATGTTGCCTTCATTTTTCAAATTCAACTGGTTAAAGGAGCAAATATGGCTGTGTAGGCAAATAAAGTTTTATTCACTAAAAAAGAAAAAAGAAACCAAACATGTGAGTAAACCTAACTTTTCCTTAGTCCACACAGCTTCTAAACCAACAGGTACTAAATATTCTACACTGAAATAACGATGGCTGTGGTGTACGGTCCGTCCTTCAGTTCTGCTGGCTGGGCGCACGTGTGGGCTGGCCACCGCCACATATGACGCAGCTGGTAGGCGCCGAGCCAGTGCACCTGAGCCCTGCTGTGCGCCTGAGCATCCAGGATCTCAAGGTGCATGGCGACAGGCACCCCATCCTCTGTCGGCCTTGGCCCCGGCACACTAAGCGGCTGCACCACTGTCTCGCTTTCGCCTG	TTTGGAAGGGGGAGGGTTGTGAGGGGAGAAAGAAGCCACTGAGCTTAACAACGGGCACAGGAATACTCACTTCTTGCGACGGCGGCCATACAGCTCCCGCCGCAGCTCTCTGGAAATGGGCTTCAAATGCATGAAGTTGCAGAAGCCGCCTCGTGTGCATTCTCTGTGGGTGGGTTGGAAGGAGACATTTACTACCTCGTGTGCACACGGCCCCGAACTGTGCTCAGTCACGTCACTGGCCACTCCTCACTCACCCCATCTCATACTGACGGCAGCAGGCTTCTCTGAAGTCCGTCACGGGTGACAGCTCGGCGTGGATCGGCTGTCCATTAAACCAACGGTTATTCAAGTCAATCACAGCCTTTTCCGCATCTTCCTCACGGCGAAACTGAAAAGACAAAAACAGAAGTGCTTGCCATCCACGCTTTAATAAGACTTTCTCAATTACCAATCCAAGTATATCAGAGAGAGATATACACACTCAGGTATAGTAAGGTGGAATAGTATTACAGGATAATTGAAAAATCCTTTATTTTCAATGAGATTAACTTCAAGATAGTCCAAGATTTTGCCAAATGTTGCCTTCATTTTTCAAATTCAACTGGTTAAAGGAGCAAATATGGCTGTGTAGGCAAATAAAGTTTTATTCACTAAAAAAGAAAAAAGAAACCAAACATGTGAGTAAACCTAACTTTTCCTTAGTCCACACAGCTTCTAAACCAACAGGTACTAAATATTCTACACTGAAATAACGATGGCTGTGGTGTACGGTCCGTCCTTCAGTTCTGCTGGCTGGGCGCACGTGTGGGCTGGCCACCGCCACATATGACGCAGCTGGTAGGCGCCGAGCCAGTGCACCTGAGCCCTGCTGTGCGCCTGAGCATCCAGGATCTCAAGGTGCATGGCGACAGGCACCCCATCCTCTGTCGGCCTTGGCCCCGGCACACTAAGCGGCTGCACCACTGTCTCGCTTTCGCCTG	-	novel	NA	P-0001504-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	13	284	0	ENST00000291552.4:c.348+58_575+70del		p.X116_splice	ENST00000291552	NM_006758.2	116		6-7/8	1	2	FACETS	0.194	0.138	0.262	0.194	0.138	0.262	SUBCLONAL	1	TRUE	1	0.582482311336812	2		284	230	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	18	541	0				ENST00000310581	NM_198253.2	-/1132			0.185496068382025	1	FACETS	0.766	0.584	0.974	1	0.911	1	CLONAL	2	TRUE	0	0.185496068382025	1		541	115	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500499	99500499	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771642071	NA	P-0002392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	98	285	1	ENST00000268035.6:c.3932C>T	p.Ser1311Leu	p.S1311L	ENST00000268035	NM_000875.3	1311	tCg/tTg	21/21	0.185496068382025	3	FACETS	0.941	0.845	1			1	CLONAL	3	TRUE	NA	0.185496068382025	3		286	409	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7978952	7978952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139689690	NA	P-0002392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	125	426	0	ENST00000319144.4:c.1615G>A	p.Glu539Lys	p.E539K	ENST00000319144	NM_001139.2	539	Gaa/Aaa	12/15	0.185496068382025	1	FACETS	1	0.947	1	1	0.99	1	CLONAL	2	TRUE	0	0.185496068382025	1		426	576	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934152	48934152	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	176	327	0	ENST00000267163.4:c.608-1G>A		p.X203_splice	ENST00000267163	NM_000321.2	203			0.185496068382025	5	FACETS	1	0.935	1	1	0.935	1	CLONAL	3	TRUE	2	0.185496068382025	5		327	797	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911144	40911144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776134993	NA	P-0002392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	181	561	0	ENST00000373198.4:c.2161C>T	p.Arg721Cys	p.R721C	ENST00000373198	NM_133170.3	721	Cgt/Tgt	13/32	0.185496068382025	1	FACETS	0.949	0.875	1	1	0.992	1	CLONAL	2	TRUE	0	0.185496068382025	1		561	933	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726986	46726986	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	183	610	0	ENST00000371975.4:c.820T>A	p.Ser274Thr	p.S274T	ENST00000371975	NM_003579.3	274	Tcc/Acc	8/18	0.185496068382025	5	FACETS	1	0.977	1	0.768	0.708	0.831	CLONAL	2	TRUE	2	0.185496068382025	5		610	1094	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439832	51439832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	156	169	0	ENST00000262662.1:c.397C>T	p.Arg133Trp	p.R133W	ENST00000262662		133	Cgg/Tgg	4/4	0.185496068382025	5	FACETS	1	0.961	1	1	0.988	1	CLONAL	4	TRUE	2	0.185496068382025	5		169	503	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117753456	117753456	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	86	411	0	ENST00000369458.3:c.22C>T	p.Leu8Phe	p.L8F	ENST00000369458	NM_024626.3	8	Ctc/Ttc	1/6	0.185496068382025	5	FACETS	0.938	0.83	1	0.625	0.553	0.702	CLONAL	2	TRUE	2	0.185496068382025	5		411	632	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443591	29443591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747643140	NA	P-0002392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	73	238	0	ENST00000389048.3:c.3626G>A	p.Arg1209Gln	p.R1209Q	ENST00000389048	NM_004304.4	1209	cGa/cAa	23/29	NA	2	FACETS	1	0.941	1			1	INDETERMINATE	2	TRUE	NA	0.185496068382025	2		238	353	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660070	12660070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	97	428	0	ENST00000251849.4:c.151C>T	p.Pro51Ser	p.P51S	ENST00000251849	NM_002880.3	51	Cct/Tct	2/17	NA	2	FACETS	0.811	0.724	0.903			1	INDETERMINATE	2	TRUE	NA	0.185496068382025	2		428	645	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391084	89391084	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	112	479	0	ENST00000336596.2:c.1150C>T	p.Pro384Ser	p.P384S	ENST00000336596	NM_005233.5	384	Cct/Tct	5/17	1	2	FACETS	0.826	0.743	0.913	1	0.986	1	CLONAL	2	TRUE	1	0.185496068382025	2		479	731	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670708	134670708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	74	410	1	ENST00000398015.3:c.619C>T	p.Pro207Ser	p.P207S	ENST00000398015	NM_004441.4	207	Cca/Tca	3/16	0.185496068382025	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.185496068382025	1		411	493	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513482	149513482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	158	424	0	ENST00000261799.4:c.721G>A	p.Glu241Lys	p.E241K	ENST00000261799	NM_002609.3	241	Gag/Aag	5/23	0.1520713900955	3	FACETS	1	0.979	1			1	CLONAL	2	TRUE	NA	0.185496068382025	3		424	777	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140829	37140829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	95	362	0	ENST00000373509.5:c.665C>T	p.Ser222Leu	p.S222L	ENST00000373509	NM_002648.3	222	tCg/tTg	5/6	0.185496068382025	5	FACETS	0.793	0.705	0.886	0.528	0.47	0.591	SUBCLONAL	2	TRUE	2	0.185496068382025	5		362	826	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553119	106553119	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	93	345	0	ENST00000369096.4:c.1084C>T	p.Pro362Ser	p.P362S	ENST00000369096	NM_001198.3	362	Cct/Tct	5/7	0.185496068382025	9	FACETS	1	0.941	1			1	CLONAL	2	TRUE	NA	0.185496068382025	9		345	759	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545584	106545584	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142182764	NA	P-0002392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	280	434	0	ENST00000359195.3:c.3061C>T	p.Arg1021Cys	p.R1021C	ENST00000359195	NM_002649.2	1021	Cgt/Tgt	11/11	0.185496068382025	8	FACETS	0.969	0.912	1			1	CLONAL	5	TRUE	NA	0.185496068382025	8		434	970	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859377	151859377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	210	432	0	ENST00000262189.6:c.11285C>T	p.Ser3762Phe	p.S3762F	ENST00000262189	NM_170606.2	3762	tCt/tTt	43/59	0.185496068382025	4	FACETS	1	0.98	1	1	0.993	1	CLONAL	3	TRUE	2	0.185496068382025	4		432	788	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172506	108172506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	173	415	0	ENST00000278616.4:c.5309C>T	p.Ser1770Leu	p.S1770L	ENST00000278616	NM_000051.3	1770	tCa/tTa	35/63	0.185496068382025	3	FACETS	0.862	0.795	0.932	1	0.985	1	CLONAL	3	TRUE	1	0.185496068382025	3		415	788	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342653	118342653	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1376699515	NA	P-0002392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	40	378	0	ENST00000534358.1:c.779C>T	p.Pro260Leu	p.P260L	ENST00000534358	NM_005933.3	260	cCt/cTt	3/36	NA	2	FACETS	0.624	0.517	0.744			1	INDETERMINATE	1	TRUE	NA	0.185496068382025	2		378	691	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426949	49426949	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	128	288	0	ENST00000301067.7:c.11539C>T	p.Leu3847Phe	p.L3847F	ENST00000301067	NM_003482.3	3847	Ctt/Ttt	39/54	0.185496068382025	6	FACETS	0.977	0.891	1			1	CLONAL	4	TRUE	NA	0.185496068382025	6		288	484	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109863	115109863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	26	81	2	ENST00000257566.3:c.2015G>A	p.Gly672Asp	p.G672D	ENST00000257566	NM_016569.3	672	gGc/gAc	8/8	NA	2	FACETS	1	0.933	1			1	INDETERMINATE	1	TRUE	NA	0.185496068382025	2		83	188	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923314	26923314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	80	414	0	ENST00000381527.3:c.310C>T	p.Leu104Phe	p.L104F	ENST00000381527	NM_001260.1	104	Ctc/Ttc	3/13	0.185496068382025	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.185496068382025	1		414	573	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459232	99459232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	223	617	0	ENST00000268035.6:c.1868C>T	p.Ser623Phe	p.S623F	ENST00000268035	NM_000875.3	623	tCc/tTc	9/21	0.185496068382025	3	FACETS	0.897	0.836	0.961			1	CLONAL	3	TRUE	NA	0.185496068382025	3		617	976	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892299	9892299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs796052549	NA	P-0002392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	62	265	0	ENST00000330684.3:c.2191G>A	p.Asp731Asn	p.D731N	ENST00000330684	NM_001134407.1	731	Gat/Aat	11/13	0.185496068382025	1	FACETS	0.811	0.704	0.926	1	0.974	1	CLONAL	2	TRUE	0	0.185496068382025	1		265	374	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533324	29533324	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	214	420	1	ENST00000356175.3:c.1327T>C	p.Phe443Leu	p.F443L	ENST00000356175	NM_000267.3	443	Ttt/Ctt	12/57	0.185496068382025	4	FACETS	0.956	0.889	1	1	0.991	1	CLONAL	3	TRUE	2	0.185496068382025	4		421	954	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550586	29550586	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1567845945	NA	P-0002392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	175	318	0	ENST00000356175.3:c.1845+1G>A		p.X615_splice	ENST00000356175	NM_000267.3	615			0.185496068382025	4	FACETS	0.884	0.815	0.956	1	0.986	1	CLONAL	3	TRUE	2	0.185496068382025	4		318	843	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619057	37619057	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	156	423	0	ENST00000447079.4:c.733G>A	p.Asp245Asn	p.D245N	ENST00000447079	NM_015083.1	245	Gat/Aat	1/14	0.185496068382025	4	FACETS	0.839	0.769	0.912	1	0.982	1	CLONAL	3	TRUE	2	0.185496068382025	4		423	792	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561564	9561564	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867333778	NA	P-0002392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	89	272	0	ENST00000353224.5:c.218G>A	p.Gly73Glu	p.G73E	ENST00000353224	NM_177990.2	73	gGa/gAa	4/10	0.185496068382025	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.185496068382025	3		272	438	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817387	39817387	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	134	406	0	ENST00000288319.7:c.176A>C	p.Gln59Pro	p.Q59P	ENST00000288319	NM_182918.3	59	cAa/cCa	2/10	0.185496068382025	5	FACETS	1	0.975	1	0.801	0.728	0.877	CLONAL	2	TRUE	2	0.185496068382025	5		406	769	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077427	30077427	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	82	177	0	ENST00000338641.4:c.1575-1G>A		p.X525_splice	ENST00000338641	NM_000268.3	525			0.185496068382025	1	FACETS	1	0.91	1	1	0.988	1	CLONAL	3	TRUE	0	0.185496068382025	1		177	262	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247935	59247936	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0002392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	164	526	2	ENST00000371222.2:c.807_808delinsTT	p.Arg270Ter	p.R270*	ENST00000371222	NM_002228.3	269	tgCCga/tgTTga	1/1	0.185496068382025	5	FACETS	1	0.933	1	0.681	0.624	0.74	CLONAL	2	TRUE	2	0.185496068382025	5		528	1107	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667522	29667523	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0002392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	185	432	0	ENST00000356175.3:c.6859-1_6859delinsAA		p.X2287_splice	ENST00000356175	NM_000267.3	2287		46/57	0.185496068382025	4	FACETS	0.879	0.812	0.948	1	0.987	1	CLONAL	3	TRUE	2	0.185496068382025	4		432	897	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0002773-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	14	418	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		418	564	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	20	360	1	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.611	0.468	0.776	0.611	0.468	0.776	SUBCLONAL	1	TRUE	1	0.28	2		361	234	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0004255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	22	418	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.322	0.249	0.408	0.322	0.249	0.408	SUBCLONAL	1	TRUE	1	0.28	2		418	488	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0004255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	55	528	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.925	1	1	0.98	1	CLONAL	2	TRUE	1	0.28	2		528	180	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0004255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	27	714	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.248	0.196	0.308	0.248	0.196	0.308	SUBCLONAL	1	TRUE	1	0.28	2		714	777	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0004255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	66	634	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.20834499655558	0	FACETS	1	0.953	1			1	CLONAL	1	TRUE	0	0.28	0		634	285	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087503	27087503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	44	519	0	ENST00000324856.7:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000324856	NM_006015.4	693	Cga/Tga	5/20	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.28	2		519	274	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098804	178098804	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	85	633	0	ENST00000397062.3:c.241G>C	p.Gly81Arg	p.G81R	ENST00000397062	NM_006164.4	81	Ggt/Cgt	2/5	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.28	2		633	526	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231158	142231158	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs749750765	NA	P-0004255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	77	655	0	ENST00000350721.4:c.4796T>C	p.Leu1599Pro	p.L1599P	ENST00000350721	NM_001184.3	1599	cTg/cCg	27/47	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.28	2		655	514	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187560904	187560904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758878500	NA	P-0004255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	44	480	0	ENST00000441802.2:c.3614G>A	p.Arg1205Gln	p.R1205Q	ENST00000441802	NM_005245.3	1205	cGa/cAa	4/27	1	2	FACETS	0.703	0.59	0.828	0.703	0.59	0.828	SUBCLONAL	1	TRUE	1	0.28	2		480	447	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271265	1271265	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	25	459	0	ENST00000310581.5:c.2437A>G	p.Met813Val	p.M813V	ENST00000310581	NM_198253.2	813	Atg/Gtg	8/16	0.3	2	FACETS	0.801	0.634	0.99			1	CLONAL	1	TRUE	NA	0.28	2		459	223	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045847	26045847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	56	1041	0	ENST00000540144.1:c.209G>A	p.Arg70His	p.R70H	ENST00000540144	NM_003531.2	70	cGc/cAc	1/1	0.149164421089512	3	FACETS	0.613	0.524	0.71	0.306	0.262	0.355	INDETERMINATE	1	TRUE	1	0.28	3		1041	744	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170328	32170328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	29	311	0	ENST00000375023.3:c.3280C>T	p.His1094Tyr	p.H1094Y	ENST00000375023	NM_004557.3	1094	Cat/Tat	21/30	0.149164421089512	3	FACETS	1	0.937	1	0.72	0.584	0.87	INDETERMINATE	1	TRUE	1	0.28	3		311	164	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199883	138199883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144728856	NA	P-0004255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	12	277	0	ENST00000237289.4:c.1301C>T	p.Ala434Val	p.A434V	ENST00000237289	NM_001270507.1	434	gCg/gTg	7/9	1	2	FACETS	0.471	0.331	0.642	0.471	0.331	0.642	SUBCLONAL	1	TRUE	1	0.28	2		277	182	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522211	157522211	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	19	394	0	ENST00000346085.5:c.4483C>T	p.Arg1495Cys	p.R1495C	ENST00000346085	NM_020732.3	1495	Cgc/Tgc	18/20	1	2	FACETS	0.465	0.353	0.597	0.465	0.353	0.597	SUBCLONAL	1	TRUE	1	0.28	2		394	292	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63829475	63829475	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	30	358	0	ENST00000279873.7:c.1118A>G	p.Gln373Arg	p.Q373R	ENST00000279873	NM_032199.2	373	cAg/cGg	8/10	0.3	4	FACETS	0.638	0.514	0.779			1	SUBCLONAL	1	TRUE	NA	0.28	4		358	430	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715711	18715711	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1278385426	NA	P-0004255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	44	561	0	ENST00000266497.5:c.3542C>T	p.Ala1181Val	p.A1181V	ENST00000266497		1181	gCc/gTc	25/31	1	2	FACETS	0.582	0.488	0.687	0.582	0.488	0.687	SUBCLONAL	1	TRUE	1	0.28	2		561	540	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99460005	99460005	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201631492	NA	P-0004255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	46	415	0	ENST00000268035.6:c.2101G>A	p.Ala701Thr	p.A701T	ENST00000268035	NM_000875.3	701	Gcc/Acc	10/21	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.28	2		415	279	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974943	15974943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	33	497	0	ENST00000268712.3:c.3932G>A	p.Gly1311Asp	p.G1311D	ENST00000268712	NM_006311.3	1311	gGc/gAc	30/46	1	2	FACETS	0.622	0.507	0.751	0.622	0.507	0.751	SUBCLONAL	1	TRUE	1	0.28	2		497	379	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122496	17122496	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	37	708	0	ENST00000285071.4:c.899A>G	p.Asp300Gly	p.D300G	ENST00000285071	NM_144997.5	300	gAc/gGc	9/14	1	2	FACETS	0.709	0.585	0.846	0.709	0.585	0.846	SUBCLONAL	1	TRUE	1	0.28	2		708	373	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872647	37872647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140980495	NA	P-0004255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	24	459	0	ENST00000269571.5:c.1607G>A	p.Arg536Gln	p.R536Q	ENST00000269571		536	cGg/cAg	13/27	1	2	FACETS	0.635	0.499	0.791	0.635	0.499	0.791	SUBCLONAL	1	TRUE	1	0.28	2		459	270	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59793357	59793357	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	55	636	0	ENST00000259008.2:c.2447G>T	p.Trp816Leu	p.W816L	ENST00000259008	NM_032043.2	816	tGg/tTg	17/20	1	2	FACETS	0.822	0.704	0.95	0.822	0.704	0.95	CLONAL	1	TRUE	1	0.28	2		636	478	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300155	15300155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768208563	NA	P-0004255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	19	656	0	ENST00000263388.2:c.1121G>A	p.Arg374Gln	p.R374Q	ENST00000263388	NM_000435.2	374	cGg/cAg	7/33	0.108919776096248	0	FACETS	0.324	0.245	0.416			1	INDETERMINATE	1	TRUE	0	0.28	0		656	302	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693003	89693003	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs786204900	NA	P-0004255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	31	166	0	ENST00000371953.3:c.491del	p.Lys164ArgfsTer3	p.K164Rfs*3	ENST00000371953	NM_000314.4	163	Aaa/aa	5/9	1	2	FACETS	0.954	0.777	1	0.954	0.777	1	CLONAL	1	TRUE	1	0.28	2		166	232	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593375	67593376	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0004255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	21	492	0	ENST00000274335.5:c.2121_2122insTT	p.Asp708LeufsTer8	p.D708Lfs*8	ENST00000274335		707	-/TT	15/15	1	2	FACETS	0.384	0.295	0.488	0.384	0.295	0.488	SUBCLONAL	1	TRUE	1	0.28	2		492	391	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742547	145742547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1426829329	NA	P-0004255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	23	330	0	ENST00000428558.2:c.241del	p.His81IlefsTer2	p.H81Ifs*2	ENST00000428558	NM_004260.3	81	Cat/at	4/22	1	2	FACETS	1	0.82	1	1	0.82	1	CLONAL	1	TRUE	1	0.28	2		330	157	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936354	78936354	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	18	430	0	ENST00000306801.3:c.3790del	p.Gln1264ArgfsTer4	p.Q1264Rfs*4	ENST00000306801	NM_020761.2	1262	caC/ca	32/34	1	2	FACETS	0.612	0.462	0.788	0.612	0.462	0.788	SUBCLONAL	1	TRUE	1	0.28	2		430	210	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830603	72830604	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	81	1020	0	ENST00000268489.5:c.5977dup	p.Ser1993PhefsTer36	p.S1993Ffs*36	ENST00000268489	NM_006885.3	1993	tcc/tTcc	9/10	0.149164421089512	0	FACETS	0.866	0.766	0.973			1	INDETERMINATE	1	TRUE	0	0.28	0		1020	481	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923036	44923036	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004255-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	50	603	0	ENST00000377967.4:c.1901del	p.Asn634ThrfsTer57	p.N634Tfs*57	ENST00000377967	NM_021140.2	633	Aaa/aa	16/29	0.20834499655558	0	FACETS	0.565	0.48	0.658			1	SUBCLONAL	1	TRUE	0	0.28	0		603	455	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0004313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	311	326	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.83718015148502	2		326	707	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0004313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	587	714	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.83718015148502	2		714	1304	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0004313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	70	521	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.876	0.779	0.975	0.876	0.779	0.975	CLONAL	1	TRUE	1	0.83718015148502	2		521	191	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797278	42797278	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs968289754	NA	P-0004313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	173	363	0	ENST00000575354.2:c.3640C>T	p.Arg1214Ter	p.R1214*	ENST00000575354	NM_015125.3	1214	Cga/Tga	15/20	0.83718015148502	1	FACETS	0.993	0.944	1	0.993	0.944	1	CLONAL	1	TRUE	0	0.83718015148502	1		363	242	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136105	11136105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004313-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	278	475	0	ENST00000358026.2:c.3089G>A	p.Gly1030Asp	p.G1030D	ENST00000358026	NM_001128849.1	1030	gGc/gAc	22/36	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.83718015148502	2		475	659	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638605	176638605	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004814-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	87	464	0	ENST00000439151.2:c.3205C>G	p.Gln1069Glu	p.Q1069E	ENST00000439151	NM_022455.4	1069	Cag/Gag	5/23	1	2	FACETS	0.738	0.651	0.832	0.738	0.651	0.832	SUBCLONAL	1	TRUE	1	0.19342155527431	2		464	1219	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163486	108163486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770590652	NA	P-0004814-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	53	386	0	ENST00000278616.4:c.4577C>T	p.Pro1526Leu	p.P1526L	ENST00000278616	NM_000051.3	1526	cCc/cTc	30/63	0.19342155527431	1	FACETS	0.936	0.798	1	0.936	0.798	1	CLONAL	1	TRUE	0	0.19342155527431	1		386	529	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250874	153251572	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAACTATTCGGTTACCACAAAACTGTAAGCATGTGATCACATGATCATCATGTCCTTTCAGCACCTATAAGAAAGATGTGCAGATTAGAAATATGTTAATTAAATTATGTTCTTTAAAATACTGGTGAAGAGAAAAATGAAGGCATAAACAGGAACAGTAATTTGTAGTCTATCTCTAGAATTTAAATTTATATAAAGCATTATTTTTCCTGGCTGACGAATCCAGAATTAAACATTTTATTGTTTCCATAGTCTATTATTTATACTCAAAACATCAACTATTAAAGTTTTACTGCATCAAGACCTCATAAAGATGGTTCAAACACCAATGTATTTGACAATAATCTATTCCATCTGTTCAAACCAGAAGAATATGCCTCTAATTTTTACAACTTTGACACACAAGAACAAAATAAGCATCTATTAACCACAAAGAGTAACAATTATTAGCATTCTTAAAACAAAAAAAATCATAATATATACATATTAGTATAACAATGTCTCCCCAAATTGGTTTTTTCCAGTTGTAAAAATACGCCCAATAATTTCAAGTGTTTTTACCATTCTTTATGTATTTGAAATGTTATTAGACAGAAAACCAGAATTATGCTTCAATTTGTAAAAATAAGACACACAAAAGTCACCAAATCCAAAACACAGACACTCCTCAAAAAATCATGTTTGGAGTATGTGATCAGA	TAACTATTCGGTTACCACAAAACTGTAAGCATGTGATCACATGATCATCATGTCCTTTCAGCACCTATAAGAAAGATGTGCAGATTAGAAATATGTTAATTAAATTATGTTCTTTAAAATACTGGTGAAGAGAAAAATGAAGGCATAAACAGGAACAGTAATTTGTAGTCTATCTCTAGAATTTAAATTTATATAAAGCATTATTTTTCCTGGCTGACGAATCCAGAATTAAACATTTTATTGTTTCCATAGTCTATTATTTATACTCAAAACATCAACTATTAAAGTTTTACTGCATCAAGACCTCATAAAGATGGTTCAAACACCAATGTATTTGACAATAATCTATTCCATCTGTTCAAACCAGAAGAATATGCCTCTAATTTTTACAACTTTGACACACAAGAACAAAATAAGCATCTATTAACCACAAAGAGTAACAATTATTAGCATTCTTAAAACAAAAAAAATCATAATATATACATATTAGTATAACAATGTCTCCCCAAATTGGTTTTTTCCAGTTGTAAAAATACGCCCAATAATTTCAAGTGTTTTTACCATTCTTTATGTATTTGAAATGTTATTAGACAGAAAACCAGAATTATGCTTCAATTTGTAAAAATAAGACACACAAAAGTCACCAAATCCAAAACACAGACACTCCTCAAAAAATCATGTTTGGAGTATGTGATCAGA	-	novel	NA	P-0004814-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	59	354	0	ENST00000281708.4:c.1122+312_1186del		p.X374_splice	ENST00000281708	NM_033632.3	374		8/12	0.19342155527431	1	FACETS	0.898	0.772	1	0.898	0.772	1	CLONAL	1	TRUE	0	0.19342155527431	1		354	614	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054144	30054235	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTCCAATGACAGTGTCTTCCGTTCTCCCCACAGGGATGAAGCTGAAATGGAATATCTGAAGATAGCTCAGGACCTGGAGATGTACGGTGTG	GCTCCAATGACAGTGTCTTCCGTTCTCCCCACAGGGATGAAGCTGAAATGGAATATCTGAAGATAGCTCAGGACCTGGAGATGTACGGTGTG	-	novel	NA	P-0004814-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	53	212	0	ENST00000338641.4:c.600-34_657del		p.X200_splice	ENST00000338641	NM_000268.3	200		7/16	0.19342155527431	1	FACETS	0.922	0.786	1	0.922	0.786	1	CLONAL	1	TRUE	0	0.19342155527431	1		212	537	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440346	187440346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	122	486	1	ENST00000232014.4:c.2021G>A	p.Arg674Gln	p.R674Q	ENST00000232014	NM_001130845.1	674	cGa/cAa	10/10	1	2	FACETS	0.886	0.804	0.973	0.886	0.804	0.973	CLONAL	1	TRUE	1	0.483729922994839	2		487	569	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114816	108114816	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	90	492	1	ENST00000278616.4:c.633C>A	p.Asp211Glu	p.D211E	ENST00000278616	NM_000051.3	211	gaC/gaA	6/63	1	2	FACETS	0.716	0.637	0.799	0.716	0.637	0.799	SUBCLONAL	1	TRUE	1	0.483729922994839	2		493	520	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056465	26056466	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0005428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	94	272	0	ENST00000343677.2:c.191_192del	p.Lys64SerfsTer8	p.K64Sfs*8	ENST00000343677	NM_005319.3	64	aAA/a	1/1	0.318980118333444	4	FACETS	1	0.976	1	0.671	0.6	0.745	CLONAL	1	TRUE	2	0.483729922994839	4		272	430	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579310	7579310	+	splice_donor_variant	Splice_Site	SNP	A	A	T	rs1555526469	NA	P-0005428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	156	478	0	ENST00000269305.4:c.375+2T>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.483729922994839	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.483729922994839	1		478	375	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747964	41747964	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	67	175	0	ENST00000226382.2:c.805C>A	p.Pro269Thr	p.P269T	ENST00000226382	NM_003924.3	269	Cct/Act	3/3	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.483729922994839	2		175	210	SUCCESS
AR	367	MSKCC	GRCh37	X	66764996	66764996	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	474	335	0	ENST00000374690.3:c.8T>A	p.Val3Glu	p.V3E	ENST00000374690	NM_000044.3	3	gTg/gAg	1/8	0.483729922994839	4	FACETS	0.92	0.894	0.945			1	CLONAL	5	TRUE	NA	0.483729922994839	4		335	632	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0006352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1234	162	540	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.875	0.8	0.953	0.875	0.8	0.953	CLONAL	1	TRUE	1	0.265331647930417	2		540	1396	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115697	108115698	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0006352-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	159	326	0	ENST00000278616.4:c.846_847del	p.Leu282PhefsTer22	p.L282Ffs*22	ENST00000278616	NM_000051.3	282	tTA/t	7/63	0.250320346877144	1	FACETS	0.99	0.906	1	0.99	0.906	1	CLONAL	1	TRUE	0	0.265331647930417	1		326	1050	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574002	7574002	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs375338359	NA	P-0006532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	239	857	0	ENST00000269305.4:c.1025G>C	p.Arg342Pro	p.R342P	ENST00000269305	NM_001126112.2	342	cGa/cCa	10/11	0.340440672145944	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.340440672145944	1		857	926	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653818	89653818	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	32	484	0	ENST00000371953.3:c.116C>A	p.Ala39Glu	p.A39E	ENST00000371953	NM_000314.4	39	gCa/gAa	2/9	0.340440672145944	1	FACETS	0.262	0.212	0.319	0.262	0.212	0.319	SUBCLONAL	1	TRUE	0	0.340440672145944	1		484	596	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947571	48947583	+	frameshift_variant	Frame_Shift_Del	DEL	GATGATTTTAAAT	GATGATTTTAAAT	-	novel	NA	P-0006532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	94	358	0	ENST00000267163.4:c.1158_1170del	p.Met386IlefsTer11	p.M386Ifs*11	ENST00000267163	NM_000321.2	386	atGATGATTTTAAAT/at	12/27	0.217166754402735	2	FACETS	0.997	0.889	1	0.498	0.444	0.556	CLONAL	1	TRUE	0	0.340440672145944	2		358	554	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0006687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	302	455	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.440251245907932	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.440251245907932	1		455	1033	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836642	89836642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747723074	NA	P-0006687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	315	461	0	ENST00000389301.3:c.2248G>A	p.Val750Met	p.V750M	ENST00000389301	NM_000135.2	750	Gtg/Atg	25/43	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.440251245907932	2		461	1362	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619037	37619037	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3941	1695	385	0	ENST00000447079.4:c.713C>A	p.Ser238Ter	p.S238*	ENST00000447079	NM_015083.1	238	tCg/tAg	1/14	0.440251245907932	15	FACETS	1	0.994	1			1	CLONAL	5	TRUE	NA	0.440251245907932	15		385	5636	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266016	41266403	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	In_Frame_Del	DEL	GCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAAT	GCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAAT	-	novel	NA	P-0006687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	250	335	0	ENST00000349496.5:c.18_242-37del		p.A5_D81del	ENST00000349496	NM_001904.3	5		3/15	0.345118074251813	2	FACETS	1	0.99	1	0.642	0.601	0.683	CLONAL	1	TRUE	0	0.440251245907932	2		335	885	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106592	27106592	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	104	565	0	ENST00000324856.7:c.6203C>A	p.Ser2068Ter	p.S2068*	ENST00000324856	NM_006015.4	2068	tCg/tAg	20/20	1	2	FACETS	0.324	0.289	0.362	0.324	0.289	0.362	SUBCLONAL	1	TRUE	1	0.559507351914089	2		565	1146	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009001-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	152	540	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.305989983978011	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	1	0.305989983978011	3		540	550	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578525	7578525	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519976	NA	P-0009001-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	234	1122	0	ENST00000269305.4:c.405C>G	p.Cys135Trp	p.C135W	ENST00000269305	NM_001126112.2	135	tgC/tgG	5/11	0.2874370949757	2	FACETS	1	0.992	1	0.73	0.681	0.781	CLONAL	1	TRUE	0	0.305989983978011	2		1122	1047	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928075	178928095	+	inframe_deletion	In_Frame_Del	DEL	ATTAGAAGATTTGCTGAACCC	ATTAGAAGATTTGCTGAACCC	-	novel	NA	P-0009001-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	117	479	0	ENST00000263967.3:c.1353_1373del	p.Leu452_Pro458del	p.L452_P458del	ENST00000263967	NM_006218.2	451	ggATTAGAAGATTTGCTGAACCCt/ggt	8/21	0.305989983978011	4	FACETS	1	0.932	1	0.689	0.625	0.756	CLONAL	2	TRUE	1	0.305989983978011	4		479	483	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206756	36206757	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0009001-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	149	385	0	ENST00000300305.3:c.754_755dup	p.Leu253ProfsTer2	p.L253Pfs*2	ENST00000300305		252	tcc/tcTCc	6/8	0.201182008367343	3	FACETS	1	0.986	1	0.702	0.642	0.765	CLONAL	1	TRUE	1	0.305989983978011	3		385	800	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	85	388	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.402055745700543	5	FACETS	0.848	0.749	0.955	0.212	0.187	0.239	CLONAL	1	TRUE	1	0.402055745700543	5		388	799	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	432	418	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.402055745700543	5	FACETS	0.962	0.923	1	0.962	0.923	1	CLONAL	4	TRUE	1	0.402055745700543	5		418	895	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252994	36252995	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	188	546	0	ENST00000300305.3:c.367dup	p.Asp123GlyfsTer15	p.D123Gfs*15	ENST00000300305		123	gat/gGat	4/8	1	2	FACETS	0.994	0.918	1	0.994	0.918	1	CLONAL	1	TRUE	1	0.402055745700543	2		546	941	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226421	133226421	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	181	597	0	ENST00000320574.5:c.3637G>C	p.Glu1213Gln	p.E1213Q	ENST00000320574	NM_006231.2	1213	Gag/Cag	30/49	NA	2	FACETS	0.865	0.797	0.936			1	INDETERMINATE	1	TRUE	NA	0.402055745700543	2		597	1041	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163720	32163720	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	166	410	0	ENST00000375023.3:c.5506G>C	p.Glu1836Gln	p.E1836Q	ENST00000375023	NM_004557.3	1836	Gag/Cag	30/30	0.406397883576556	3	FACETS	1	0.95	1	0.524	0.481	0.569	CLONAL	1	TRUE	1	0.402055745700543	3		410	947	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911266	29911266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41562120	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	122	358	0	ENST00000376809.5:c.565G>A	p.Val189Met	p.V189M	ENST00000376809	NM_002116.7	189	Gtg/Atg	3/8	0.406397883576556	3	FACETS	1	0.974	1	0.602	0.546	0.662	CLONAL	1	TRUE	1	0.402055745700543	3		358	605	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259513	16259513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	139	498	1	ENST00000375759.3:c.6778G>T	p.Glu2260Ter	p.E2260*	ENST00000375759	NM_015001.2	2260	Gag/Tag	11/15	0.383166679281623	2	FACETS	1	0.936	1	0.515	0.47	0.563	CLONAL	1	TRUE	0	0.402055745700543	2		499	671	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262648	16262648	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	134	472	0	ENST00000375759.3:c.9913G>C	p.Glu3305Gln	p.E3305Q	ENST00000375759	NM_015001.2	3305	Gag/Cag	11/15	0.383166679281623	2	FACETS	0.923	0.84	1	0.462	0.42	0.505	CLONAL	1	TRUE	0	0.402055745700543	2		472	722	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010522	48010522	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659674	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	137	298	0	ENST00000234420.5:c.150G>C	p.Trp50Cys	p.W50C	ENST00000234420	NM_000179.2	50	tgG/tgC	1/10	0.406397883576556	3	FACETS	1	0.966	1	0.561	0.51	0.613	CLONAL	1	TRUE	1	0.402055745700543	3		298	730	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970945	21970945	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	180	605	0	ENST00000304494.5:c.413G>C	p.Arg138Thr	p.R138T	ENST00000304494	NM_000077.4	138	aGa/aCa	2/3	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.402055745700543	2		605	892	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172469	108172469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	104	522	0	ENST00000278616.4:c.5272G>A	p.Asp1758Asn	p.D1758N	ENST00000278616	NM_000051.3	1758	Gat/Aat	35/63	0.402055745700543	2	FACETS	0.949	0.853	1	0.475	0.426	0.526	CLONAL	1	TRUE	0	0.402055745700543	2		522	545	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518199	103518199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	87	341	1	ENST00000355739.4:c.2137G>A	p.Glu713Lys	p.E713K	ENST00000355739	NM_000123.3	713	Gag/Aag	9/15	1	2	FACETS	0.941	0.837	1	0.941	0.837	1	CLONAL	1	TRUE	1	0.402055745700543	2		342	460	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961991	41961991	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	191	623	0	ENST00000219905.7:c.899C>G	p.Ser300Ter	p.S300*	ENST00000219905	NM_001164273.1	300	tCa/tGa	2/24	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.402055745700543	2		623	861	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579709	7579710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	348	602	0	ENST00000269305.4:c.86dup	p.Asn29LysfsTer14	p.N29Kfs*14	ENST00000269305	NM_001126112.2	29	aac/aaAc	3/11	0.383166679281623	2	FACETS	0.93	0.883	0.977	0.93	0.883	0.977	CLONAL	2	TRUE	0	0.402055745700543	2		602	931	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031889	26031889	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	113	316	0	ENST00000244661.2:c.400G>C	p.Glu134Gln	p.E134Q	ENST00000244661	NM_003537.3	134	Gaa/Caa	1/1	0.396235134901808	5	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.402055745700543	5		316	658	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209263	36209263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	198	461	0	ENST00000222270.7:c.343G>A	p.Asp115Asn	p.D115N	ENST00000222270	NM_014727.1	115	Gac/Aac	1/37	0.402055745700543	5	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.402055745700543	5		461	1365	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547190	106547190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	1427	290	0	ENST00000369096.4:c.427G>A	p.Glu143Lys	p.E143K	ENST00000369096	NM_001198.3	143	Gag/Aag	4/7	0.402055745700543	21	FACETS	0.982	0.966	0.998			1	CLONAL	18	TRUE	NA	0.402055745700543	21		290	1935	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739876	46739876	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	146	556	0	ENST00000371975.4:c.1677C>A	p.Phe559Leu	p.F559L	ENST00000371975	NM_003579.3	559	ttC/ttA	15/18	0.383166679281623	2	FACETS	1	0.942	1	0.519	0.474	0.565	CLONAL	1	TRUE	0	0.402055745700543	2		556	700	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206571	108206571	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1398616877	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	84	334	0	ENST00000278616.4:c.8152-1G>A		p.X2718_splice	ENST00000278616	NM_000051.3	2718			0.402055745700543	2	FACETS	0.826	0.731	0.926	0.413	0.365	0.463	CLONAL	1	TRUE	0	0.402055745700543	2		334	506	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954253	32954253	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	127	655	0	ENST00000380152.3:c.9227G>C	p.Gly3076Ala	p.G3076A	ENST00000380152		3076	gGa/gCa	24/27	0.406397883576556	3	FACETS	0.699	0.632	0.77	0.349	0.316	0.385	SUBCLONAL	1	TRUE	1	0.402055745700543	3		655	1086	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986748	36986748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745510380	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	56	106	0	ENST00000354822.5:c.941G>A	p.Gly314Asp	p.G314D	ENST00000354822	NM_001079668.2	314	gGc/gAc	3/3	0.307627522295368	3	FACETS	0.876	0.763	0.995			1	CLONAL	2	TRUE	NA	0.402055745700543	3		106	191	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226378	2226378	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1291	177	702	0	ENST00000326181.6:c.1991C>G	p.Thr664Ser	p.T664S	ENST00000326181	NM_032271.2	664	aCt/aGt	20/21	0.333907826822762	4	FACETS	0.841	0.772	0.913			1	CLONAL	1	TRUE	NA	0.402055745700543	4		702	1468	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861728	59861728	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	169	705	0	ENST00000259008.2:c.1531G>C	p.Glu511Gln	p.E511Q	ENST00000259008	NM_032043.2	511	Gag/Cag	11/20	0.406397883576556	3	FACETS	0.946	0.869	1	0.473	0.434	0.514	CLONAL	1	TRUE	1	0.402055745700543	3		705	1067	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611758	1611758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	235	792	0	ENST00000344749.5:c.1904C>T	p.Ser635Leu	p.S635L	ENST00000344749	NM_001136139.2	635	tCa/tTa	19/19	0.239486176554196	1	FACETS	0.847	0.79	0.906	0.847	0.79	0.906	INDETERMINATE	1	TRUE	0	0.402055745700543	1		792	1103	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213859	2213859	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	163	759	0	ENST00000398665.3:c.1671G>T	p.Lys557Asn	p.K557N	ENST00000398665	NM_032482.2	557	aaG/aaT	18/28	NA	2	FACETS	0.709	0.649	0.771			1	INDETERMINATE	1	TRUE	NA	0.402055745700543	2		759	1144	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798127	42798127	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	227	722	0	ENST00000575354.2:c.4081G>A	p.Glu1361Lys	p.E1361K	ENST00000575354	NM_015125.3	1361	Gag/Aag	17/20	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.402055745700543	2		722	1069	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026737	48026737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553412999	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	117	467	1	ENST00000234420.5:c.1615C>T	p.Leu539Phe	p.L539F	ENST00000234420	NM_000179.2	539	Ctt/Ttt	4/10	0.406397883576556	3	FACETS	0.897	0.809	0.99	0.449	0.404	0.495	CLONAL	1	TRUE	1	0.402055745700543	3		468	779	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022714	31022714	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1261	136	707	0	ENST00000375687.4:c.2199G>C	p.Gln733His	p.Q733H	ENST00000375687	NM_015338.5	733	caG/caC	13/13	0.406397883576556	5	FACETS	0.776	0.703	0.853	0.259	0.234	0.285	SUBCLONAL	1	TRUE	2	0.402055745700543	5		707	1397	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024623	31024623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	141	636	0	ENST00000375687.4:c.4108G>A	p.Glu1370Lys	p.E1370K	ENST00000375687	NM_015338.5	1370	Gag/Aag	13/13	0.406397883576556	5	FACETS	0.865	0.786	0.949	0.288	0.262	0.317	CLONAL	1	TRUE	2	0.402055745700543	5		636	1300	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936558	49936558	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	206	811	0	ENST00000296474.3:c.1369G>C	p.Asp457His	p.D457H	ENST00000296474	NM_002447.2	457	Gac/Cac	2/20	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.402055745700543	2		811	1021	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591070	67591070	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	109	358	0	ENST00000274335.5:c.1663G>C	p.Glu555Gln	p.E555Q	ENST00000274335		555	Gag/Cag	12/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.402055745700543	2		358	490	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637618	176637618	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	168	665	0	ENST00000439151.2:c.2218C>A	p.His740Asn	p.H740N	ENST00000439151	NM_022455.4	740	Cac/Aac	5/23	NA	2	FACETS	0.913	0.839	0.99			1	INDETERMINATE	1	TRUE	NA	0.402055745700543	2		665	915	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638173	176638173	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	216	760	0	ENST00000439151.2:c.2773C>T	p.Gln925Ter	p.Q925*	ENST00000439151	NM_022455.4	925	Cag/Tag	5/23	NA	2	FACETS	1	0.94	1			1	INDETERMINATE	1	TRUE	NA	0.402055745700543	2		760	1061	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031927	26031927	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	152	454	0	ENST00000244661.2:c.362T>G	p.Met121Arg	p.M121R	ENST00000244661	NM_003537.3	121	aTg/aGg	1/1	0.396235134901808	5	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.402055745700543	5		454	922	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673866	30673866	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	131	410	0	ENST00000376406.3:c.3094G>A	p.Glu1032Lys	p.E1032K	ENST00000376406	NM_014641.2	1032	Gaa/Aaa	10/15	0.406397883576556	3	FACETS	1	0.969	1	0.575	0.522	0.629	CLONAL	1	TRUE	1	0.402055745700543	3		410	681	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675571	30675571	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1385	278	1020	0	ENST00000376406.3:c.2785G>C	p.Asp929His	p.D929H	ENST00000376406	NM_014641.2	929	Gat/Cat	8/15	0.406397883576556	3	FACETS	0.999	0.935	1	0.499	0.467	0.533	CLONAL	1	TRUE	1	0.402055745700543	3		1020	1663	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545704	106545704	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	130	756	0	ENST00000359195.3:c.3181G>C	p.Glu1061Gln	p.E1061Q	ENST00000359195	NM_002649.2	1061	Gag/Cag	11/11	1	2	FACETS	0.756	0.686	0.831	0.756	0.686	0.831	SUBCLONAL	1	TRUE	1	0.402055745700543	2		756	855	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740824	145740824	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1048010208	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	284	795	0	ENST00000428558.2:c.1276G>A	p.Asp426Asn	p.D426N	ENST00000428558	NM_004260.3	426	Gat/Aat	7/22	0.369035859212717	3	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.402055745700543	3		795	1411	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328367	+	frameshift_variant	Frame_Shift_Del	DEL	CCATCGGGCTCAAATGC	CCATCGGGCTCAAATGC	-	novel	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1392	293	911	0	ENST00000481739.1:c.1281_1297del	p.Ile428GlyfsTer15	p.I428Gfs*15	ENST00000481739	NM_002957.4	427	tCCATCGGGCTCAAATGC/t	10/10	0.369035859212717	3	FACETS	1	0.964	1			1	CLONAL	1	TRUE	NA	0.402055745700543	3		911	1685	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44921917	44921917	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	103	639	0	ENST00000377967.4:c.1451G>C	p.Arg484Thr	p.R484T	ENST00000377967	NM_021140.2	484	aGa/aCa	15/29	0.38669746239345	2	FACETS	0.789	0.707	0.876	0.395	0.353	0.438	SUBCLONAL	1	TRUE	0	0.402055745700543	2		639	649	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032536	47032536	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	138	601	0	ENST00000377604.3:c.442C>G	p.Gln148Glu	p.Q148E	ENST00000377604	NM_001204468.1	148	Cag/Gag	5/24	0.38669746239345	2	FACETS	0.856	0.779	0.936	0.428	0.389	0.468	CLONAL	1	TRUE	0	0.402055745700543	2		601	802	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0010043-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	151	418	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.981	0.899	1	0.981	0.899	1	CLONAL	1	TRUE	1	0.437176712140605	2		418	704	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010043-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	131	340	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.437176712140605	2		340	599	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0010043-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	77	183	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.437176712140605	2		183	329	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276310	15276310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369768722	NA	P-0010043-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	127	383	0	ENST00000263388.2:c.5684G>A	p.Arg1895His	p.R1895H	ENST00000263388	NM_000435.2	1895	cGc/cAc	31/33	1	2	FACETS	0.899	0.817	0.986	0.899	0.817	0.986	CLONAL	1	TRUE	1	0.437176712140605	2		383	646	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010427-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	249	721	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.726457270387041	2		721	673	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114276	115114276	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0010427-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	200	543	0	ENST00000257566.3:c.942-1G>C		p.X314_splice	ENST00000257566	NM_016569.3	314			0.578038769841641	3	FACETS	1	0.954	1	0.517	0.48	0.555	CLONAL	1	TRUE	1	0.726457270387041	3		543	726	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117632191	117632191	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010427-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	202	668	2	ENST00000368508.3:c.6225C>A	p.Phe2075Leu	p.F2075L	ENST00000368508	NM_002944.2	2075	ttC/ttA	39/43	0.726457270387041	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.726457270387041	1		670	319	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246347	53246347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010427-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	206	762	1	ENST00000375401.3:c.635G>A	p.Arg212Gln	p.R212Q	ENST00000375401	NM_004187.3	212	cGg/cAg	5/26	0.726457270387041	2	FACETS	0.985	0.92	1	0.492	0.46	0.525	CLONAL	1	TRUE	0	0.726457270387041	2		763	576	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0012444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	147	326	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.312462443392235	2		326	836	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796603	42796603	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012444-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	19	277	0	ENST00000575354.2:c.3160C>T	p.Gln1054Ter	p.Q1054*	ENST00000575354	NM_015125.3	1054	Cag/Tag	13/20	0.312462443392235	0	FACETS	0.333	0.253	0.427			1	SUBCLONAL	1	TRUE	0	0.312462443392235	0		277	251	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0014026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	88	371	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.50064190677801	4	FACETS	0.801	0.711	0.897	0.267	0.237	0.299	CLONAL	1	TRUE	1	0.590413670043391	4		371	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0014026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	402	656	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.294598246598508	2	FACETS	0.794	0.76	0.829	0.794	0.76	0.829	INDETERMINATE	2	TRUE	0	0.590413670043391	2		656	857	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263394	123263394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773245022	NA	P-0014026-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	332	341	0	ENST00000358487.5:c.1349G>A	p.Arg450His	p.R450H	ENST00000358487	NM_000141.4	450	cGc/cAc	10/18	0.590413670043391	3	FACETS	0.996	0.948	1	0.996	0.948	1	CLONAL	2	TRUE	1	0.590413670043391	3		341	731	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650699	67650699	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014178-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	164	312	0	ENST00000264010.4:c.1004G>T	p.Gly335Val	p.G335V	ENST00000264010	NM_006565.3	335	gGa/gTa	5/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.49276896918413	2		312	609	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0014232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	144	812	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.204994303151548	2		812	1175	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578525	7578525	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519976	NA	P-0014232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1360	183	1122	0	ENST00000269305.4:c.405C>G	p.Cys135Trp	p.C135W	ENST00000269305	NM_001126112.2	135	tgC/tgG	5/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.204994303151548	2		1122	1543	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212484000	212484000	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1369649105	NA	P-0014232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	31	526	1	ENST00000342788.4:c.2203G>T	p.Gly735Cys	p.G735C	ENST00000342788	NM_005235.2	735	Ggt/Tgt	19/28	1	2	FACETS	0.49	0.395	0.598	0.49	0.395	0.598	SUBCLONAL	1	TRUE	1	0.204994303151548	2		527	617	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677762	47677762	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	93	489	0	ENST00000347630.2:c.1103G>T	p.Arg368Leu	p.R368L	ENST00000347630	NM_001007230.1	368	cGc/cTc	11/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.204994303151548	2		489	767	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610641	52610641	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	140	664	0	ENST00000394830.3:c.3532G>T	p.Glu1178Ter	p.E1178*	ENST00000394830	NM_018313.4	1178	Gag/Tag	23/30	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.204994303151548	2		664	985	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149452957	149452957	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	117	779	0	ENST00000286301.3:c.989G>C	p.Gly330Ala	p.G330A	ENST00000286301	NM_005211.3	330	gGc/gCc	7/22	1	2	FACETS	0.988	0.889	1	0.988	0.889	1	CLONAL	1	TRUE	1	0.204994303151548	2		779	1155	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961055	55961055	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1229432573	NA	P-0014232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1201	85	946	4	ENST00000263923.4:c.2885G>A	p.Arg962His	p.R962H	ENST00000263923	NM_002253.2	962	cGc/cAc	21/30	0.168538473295165	2	FACETS	0.645	0.568	0.728	0.322	0.284	0.364	SUBCLONAL	1	TRUE	0	0.204994303151548	2		950	1286	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0014940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	159	500	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.996	0.919	1	0.996	0.919	1	CLONAL	1	TRUE	1	0.59803017453792	2		500	534	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0014940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	179	442	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.996	0.923	1	0.996	0.923	1	CLONAL	1	TRUE	1	0.59803017453792	2		442	601	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576135	29576135	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs868573462	NA	P-0014940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	24	499	0	ENST00000356175.3:c.4108C>T	p.Gln1370Ter	p.Q1370*	ENST00000356175	NM_000267.3	1370	Cag/Tag	30/57	0.59803017453792	1	FACETS	0.121	0.094	0.152	0.121	0.094	0.152	SUBCLONAL	1	TRUE	0	0.59803017453792	1		499	466	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853329	68853330	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0014940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	274	575	0	ENST00000261769.5:c.1711+2dup		p.X571_splice	ENST00000261769	NM_004360.3	571			0.59803017453792	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.59803017453792	1		575	589	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0017479-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	209	544	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.167644379186918	3	FACETS	0.784	0.729	0.841	0.523	0.486	0.561	INDETERMINATE	2	TRUE	0	0.362179875386825	3		544	869	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958409	90958409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881856	NA	P-0017479-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	41	350	0	ENST00000265433.3:c.2029G>A	p.Asp677Asn	p.D677N	ENST00000265433	NM_002485.4	677	Gat/Aat	13/16	0.362179875386825	4	FACETS	0.412	0.342	0.491	0.103	0.085	0.123	SUBCLONAL	1	TRUE	0	0.362179875386825	4		350	748	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940508	31940508	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017479-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	85	608	0	ENST00000375333.2:c.541G>C	p.Asp181His	p.D181H	ENST00000375333	NM_032454.1	181	Gac/Cac	3/8	0.167644379186918	3	FACETS	0.546	0.481	0.616	0.182	0.16	0.206	INDETERMINATE	1	TRUE	0	0.362179875386825	3		608	1015	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420191	88420191	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017479-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	94	513	0	ENST00000360948.2:c.2495C>A	p.Pro832Gln	p.P832Q	ENST00000360948	NM_001012338.2	832	cCa/cAa	19/19	1	2	FACETS	0.703	0.626	0.786	0.703	0.626	0.786	SUBCLONAL	1	TRUE	1	0.362179875386825	2		513	738	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038203	128038203	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017479-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	63	506	0	ENST00000285398.2:c.1347G>C	p.Lys449Asn	p.K449N	ENST00000285398	NM_000122.1	449	aaG/aaC	9/15	0.199863131903565	3	FACETS	0.54	0.466	0.62	0.27	0.233	0.31	INDETERMINATE	1	TRUE	1	0.362179875386825	3		506	761	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325116	39325116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017479-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	943	582	0	ENST00000373001.3:c.203G>A	p.Gly68Glu	p.G68E	ENST00000373001	NM_022157.3	68	gGa/gAa	1/7	0.362179875386825	11	FACETS	0.947	0.922	0.973			1	CLONAL	8	TRUE	NA	0.362179875386825	11		582	1807	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188788	32188788	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017479-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	173	642	0	ENST00000375023.3:c.766G>C	p.Asp256His	p.D256H	ENST00000375023	NM_004557.3	256	Gac/Cac	4/30	0.167644379186918	3	FACETS	1	0.924	1	0.335	0.308	0.364	INDETERMINATE	1	TRUE	0	0.362179875386825	3		642	1122	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210433	2210433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017515-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	26	800	0	ENST00000398665.3:c.1040G>A	p.Arg347His	p.R347H	ENST00000398665	NM_032482.2	347	cGc/cAc	13/28	0.258925557436431	1	FACETS	0.403	0.318	0.5	0.403	0.318	0.5	SUBCLONAL	1	TRUE	0	0.258925557436431	1		800	434	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928517	69928517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017515-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	65	585	1	ENST00000352241.4:c.337C>T	p.Pro113Ser	p.P113S	ENST00000352241	NM_198159.2	113	Ccg/Tcg	2/10	1	2	FACETS	0.721	0.625	0.826	0.721	0.625	0.826	SUBCLONAL	1	TRUE	1	0.258925557436431	2		586	696	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677890	117677890	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017515-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	43	304	0	ENST00000368508.3:c.4043A>G	p.Glu1348Gly	p.E1348G	ENST00000368508	NM_002944.2	1348	gAg/gGg	25/43	0.142380680766196	3	FACETS	1	0.885	1	0.534	0.448	0.629	INDETERMINATE	1	TRUE	1	0.258925557436431	3		304	351	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798773	42798773	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269420975	NA	P-0018206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	203	476	0	ENST00000575354.2:c.4345G>A	p.Val1449Met	p.V1449M	ENST00000575354	NM_015125.3	1449	Gtg/Atg	19/20	0.722049614444468	4	FACETS	0.836	0.775	0.9	0.418	0.387	0.45	CLONAL	1	TRUE	2	0.808125065473087	4		476	1086	SUCCESS
ATR	545	MSKCC	GRCh37	3	142183992	142183992	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	110	610	0	ENST00000350721.4:c.6988G>A	p.Asp2330Asn	p.D2330N	ENST00000350721	NM_001184.3	2330	Gat/Aat	41/47	0.808125065473087	5	FACETS	0.6	0.538	0.666	0.2	0.179	0.222	SUBCLONAL	1	TRUE	2	0.808125065473087	5		610	1003	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324917	31324917	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	594	497	0	ENST00000412585.2:c.19C>G	p.Arg7Gly	p.R7G	ENST00000412585	NM_005514.6	7	Cga/Gga	1/8	0.541033575071999	4	FACETS	0.97	0.942	0.998	1	0.997	1	CLONAL	3	TRUE	2	0.808125065473087	4		497	913	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0018415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	308	438	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	1	2	FACETS	0.92	0.872	0.968	0.92	0.872	0.968	CLONAL	1	TRUE	1	0.871143888592799	2		438	769	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226125	53226125	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	48	412	0	ENST00000375401.3:c.2724del	p.Arg909GlyfsTer26	p.R909Gfs*26	ENST00000375401	NM_004187.3	908	ggG/gg	19/26	1	1	FACETS	1	0.932	1	1	0.977	1	CLONAL	2	TRUE	0	0.17	1		412	222	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578468	7578468	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	64	1061	0	ENST00000269305.4:c.462del	p.Thr155ProfsTer15	p.T155Pfs*15	ENST00000269305	NM_001126112.2	154	ggC/gg	5/11	1	2	FACETS	0.898	0.776	1	0.898	0.776	1	CLONAL	1	TRUE	1	0.17	2		1061	838	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245357	153245357	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	36	758	0	ENST00000281708.4:c.1834C>T	p.Gln612Ter	p.Q612*	ENST00000281708	NM_033632.3	612	Cag/Tag	11/12	1	2	FACETS	0.795	0.652	0.955	0.795	0.652	0.955	CLONAL	1	TRUE	1	0.17	2		758	533	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0020216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	186	326	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.976	1	1	0.994	1	CLONAL	2	FALSE	1	0.38201778921748	2		326	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0020216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	1096	1103	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.38201778921748	2	FACETS	1	0.998	1	1	0.999	1	CLONAL	4	FALSE	0	0.38201778921748	2		1103	1297	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870930	12870930	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	229	425	0	ENST00000228872.4:c.157G>T	p.Glu53Ter	p.E53*	ENST00000228872	NM_004064.3	53	Gaa/Taa	1/3	0.341077565757299	1	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	FALSE	0	0.38201778921748	1		425	431	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983598	7983598	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	125	824	0	ENST00000319144.4:c.709A>C	p.Lys237Gln	p.K237Q	ENST00000319144	NM_001139.2	237	Aag/Cag	6/15	0.38201778921748	2	FACETS	0.592	0.534	0.653	0.296	0.267	0.327	SUBCLONAL	1	FALSE	0	0.38201778921748	2		824	1106	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937449	76937450	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0020216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	243	822	0	ENST00000373344.5:c.3298_3299del	p.Ser1100PhefsTer11	p.S1100Ffs*11	ENST00000373344	NM_000489.3	1100	AGt/t	9/35	0.296903337997193	1	FACETS	0.772	0.725	0.819	1	0.993	1	SUBCLONAL	2	FALSE	0	0.38201778921748	1		822	667	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938136	76938136	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0020216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	92	1034	0	ENST00000373344.5:c.2612C>G	p.Ser871Ter	p.S871*	ENST00000373344	NM_000489.3	871	tCa/tGa	9/35	0.296903337997193	1	FACETS	0.397	0.352	0.446	0.397	0.352	0.446	SUBCLONAL	1	FALSE	0	0.38201778921748	1		1034	981	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578266	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs942158624	NA	P-0020593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	126	304	0	ENST00000269305.4:c.583A>T	p.Ile195Phe	p.I195F	ENST00000269305	NM_001126112.2	195	Atc/Ttc	6/11	0.254001281829187	3	FACETS	1	0.959	1	0.723	0.66	0.788	CLONAL	2	TRUE	0	0.32030112789577	3		304	421	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509676	106509676	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139426517	NA	P-0020593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	158	249	0	ENST00000359195.3:c.1670C>T	p.Ala557Val	p.A557V	ENST00000359195	NM_002649.2	557	gCg/gTg	2/11	0.32030112789577	4	FACETS	0.843	0.778	0.91	1	0.984	1	CLONAL	3	TRUE	2	0.32030112789577	4		249	515	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426544	49426544	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555188379	NA	P-0020593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	138	386	1	ENST00000301067.7:c.11944C>T	p.Arg3982Ter	p.R3982*	ENST00000301067	NM_003482.3	3982	Cga/Tga	39/54	0.181152081292667	5	FACETS	0.933	0.85	1	0.622	0.567	0.679	INDETERMINATE	2	TRUE	2	0.32030112789577	5		387	684	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115386	115115386	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	236	241	0	ENST00000257566.3:c.940del	p.Arg314GlufsTer9	p.R314Efs*9	ENST00000257566	NM_016569.3	314	Aga/ga	5/8	0.32030112789577	7	FACETS	1	0.975	1	0.856	0.804	0.909	CLONAL	4	TRUE	2	0.32030112789577	7		241	620	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0020733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	348	664	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.833181116880731	1	FACETS	0.989	0.954	1	0.989	0.954	1	CLONAL	1	TRUE	0	0.833181116880731	1		665	493	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569702	95569702	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	168	333	0	ENST00000393063.1:c.4031C>T	p.Ser1344Leu	p.S1344L	ENST00000393063	NM_030621.3	1344	tCa/tTa	22/28	0.796309177667548	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.833181116880731	2		333	196	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0020733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	505	1326	2	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	0.833181116880731	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.833181116880731	1		1328	704	SUCCESS
APC	324	MSKCC	GRCh37	5	112175351	112175351	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	290	447	0	ENST00000257430.4:c.4063del	p.Ser1355LeufsTer60	p.S1355Lfs*60	ENST00000257430	NM_000038.5	1354	Ttt/tt	16/16	0.827884067425678	2	FACETS	0.959	0.928	0.988	0.959	0.928	0.988	CLONAL	2	TRUE	0	0.833181116880731	2		447	363	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266649	41266649	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	351	777	1	ENST00000349496.5:c.446C>A	p.Ala149Asp	p.A149D	ENST00000349496	NM_001904.3	149	gCc/gAc	4/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.833181116880731	2		778	821	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680736	30680736	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	132	828	0	ENST00000376406.3:c.983A>T	p.Asp328Val	p.D328V	ENST00000376406	NM_014641.2	328	gAc/gTc	5/15	1	2	FACETS	0.497	0.453	0.544	0.497	0.453	0.544	SUBCLONAL	1	TRUE	1	0.833181116880731	2		828	637	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	373	1141	3	ENST00000346208.3:c.1220_1221insA	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcAg	6/6	1	2	FACETS	0.998	0.949	1	1	0.996	1	CLONAL	2	FALSE	1	0.367491536720772	2		1144	1017	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969933	81969933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752209691	NA	P-0021182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	283	900	0	ENST00000359376.3:c.3002G>A	p.Arg1001His	p.R1001H	ENST00000359376	NM_002661.3	1001	cGc/cAc	27/33	1	2	FACETS	1	0.96	1	1	0.996	1	CLONAL	2	FALSE	1	0.367491536720772	2		900	755	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107135	27107136	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	374	944	0	ENST00000324856.7:c.6747dup	p.Glu2250ArgfsTer28	p.E2250Rfs*28	ENST00000324856	NM_006015.4	2249	tca/tcAa	20/20	0.280161754523643	3	FACETS	0.855	0.815	0.896	1	0.994	1	CLONAL	3	FALSE	1	0.367491536720772	3		944	939	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436952	49436952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748653082	NA	P-0021182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	349	1238	0	ENST00000301067.7:c.5551G>A	p.Val1851Met	p.V1851M	ENST00000301067	NM_003482.3	1851	Gtg/Atg	25/54	1	2	FACETS	0.952	0.903	1	1	0.996	1	CLONAL	2	FALSE	1	0.367491536720772	2		1238	998	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998987	11998988	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	186	673	0	ENST00000353533.5:c.493dup	p.Tyr165LeufsTer9	p.Y165Lfs*9	ENST00000353533	NM_003010.3	163	-/T	4/11	0.345243591332003	0	FACETS	0.863	0.81	0.916			1	CLONAL	2	FALSE	0	0.367491536720772	0		673	371	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	71	418	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.164357390006183	4	FACETS	1	0.92	1	1	0.92	1	INDETERMINATE	2	FALSE	2	0.3	4		418	291	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0021268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	177	971	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.287278617804726	2	FACETS	0.958	0.887	1	0.958	0.887	1	CLONAL	2	FALSE	0	0.3	2		972	616	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0021268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	90	521	0				ENST00000310581	NM_198253.2	-/1132			0.183954628009037	3	FACETS	0.876	0.782	0.974	0.876	0.782	0.974	CLONAL	2	FALSE	1	0.3	3		521	394	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484355	8484355	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	80	666	0	ENST00000356435.5:c.3177G>T	p.Met1059Ile	p.M1059I	ENST00000356435		1059	atG/atT	19/35	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	FALSE	NA	0.3	2		666	365	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179197	123179197	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	69	336	0	ENST00000218089.9:c.646C>T	p.Arg216Ter	p.R216*	ENST00000218089	NM_001042749.1	216	Cga/Tga	8/35	0.189571591160739	2	FACETS	0.861	0.767	0.959			1	CLONAL	3	FALSE	NA	0.3	2		336	178	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795022	45795022	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	75	850	0	ENST00000450313.1:c.1606C>G	p.His536Asp	p.H536D	ENST00000450313	NM_012222.2	536	Cac/Gac	16/16	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.3	NA		850	606	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196240	108196240	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786202094	NA	P-0021268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	65	601	0	ENST00000278616.4:c.6776C>G	p.Ser2259Cys	p.S2259C	ENST00000278616	NM_000051.3	2259	tCt/tGt	46/63	0.183954628009037	3	FACETS	0.767	0.669	0.87	0.767	0.669	0.87	SUBCLONAL	2	FALSE	1	0.3	3		601	325	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325723	30325723	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	54	441	0	ENST00000322652.5:c.1921G>C	p.Glu641Gln	p.E641Q	ENST00000322652	NM_015355.2	641	Gaa/Caa	16/16	0.164357390006183	4	FACETS	0.815	0.702	0.938	0.815	0.702	0.938	INDETERMINATE	2	FALSE	2	0.3	4		441	287	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903769	41903769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	61	885	0	ENST00000372991.4:c.788C>T	p.Ser263Phe	p.S263F	ENST00000372991	NM_001760.3	263	tCc/tTc	5/5	1	2	FACETS	0.785	0.678	0.901	0.785	0.678	0.901	CLONAL	1	FALSE	1	0.3	2		885	518	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93953233	93953233	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	59	754	0	ENST00000369303.4:c.2908C>A	p.Leu970Met	p.L970M	ENST00000369303	NM_004440.3	970	Ctg/Atg	17/17	0.183954628009037	3	FACETS	1	0.91	1	0.536	0.462	0.616	CLONAL	1	FALSE	1	0.3	3		754	422	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551324	141551324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1442254850	NA	P-0021268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	115	1223	1	ENST00000220592.5:c.1973G>A	p.Arg658His	p.R658H	ENST00000220592	NM_012154.3	658	cGc/cAc	15/19	0.127454292048347	4	FACETS	0.892	0.802	0.988	0.446	0.401	0.494	INDETERMINATE	1	FALSE	2	0.3	4		1224	1117	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692900	89692900	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	10	524	0	ENST00000371953.3:c.384G>T	p.Lys128Asn	p.K128N	ENST00000371953	NM_000314.4	128	aaG/aaT	5/9	0.300320480257154	1	FACETS	0.225	0.152	0.317	0.225	0.152	0.317	SUBCLONAL	1	TRUE	0	0.33	1		524	225	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544107	18544107	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	26	551	0	ENST00000266497.5:c.1924A>T	p.Asn642Tyr	p.N642Y	ENST00000266497		642	Aat/Tat	13/31	1	2	FACETS	0.646	0.513	0.796	0.646	0.513	0.796	SUBCLONAL	1	TRUE	1	0.33	2		551	244	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445628	49445628	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	59	1077	1	ENST00000301067.7:c.1838A>T	p.Glu613Val	p.E613V	ENST00000301067	NM_003482.3	613	gAg/gTg	10/54	0.104357798267177	4	FACETS	0.854	0.735	0.983	0.427	0.367	0.492	INDETERMINATE	1	TRUE	2	0.33	4		1078	557	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431413	121431413	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	8	691	1	ENST00000257555.6:c.617G>T	p.Trp206Leu	p.W206L	ENST00000257555		206	tGg/tTg	3/10	1	2	FACETS	0.131	0.083	0.192	0.131	0.083	0.192	SUBCLONAL	1	TRUE	1	0.33	2		692	371	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729163	66729163	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs397516792	NA	P-0021714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	11	779	0	ENST00000307102.5:c.371C>A	p.Pro124Gln	p.P124Q	ENST00000307102	NM_002755.3	124	cCg/cAg	3/11	0.255246580286293	1	FACETS	0.125	0.085	0.174	0.125	0.085	0.174	SUBCLONAL	1	TRUE	0	0.33	1		779	447	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788618	3788618	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	9	553	0	ENST00000262367.5:c.4336C>A	p.Arg1446Ser	p.R1446S	ENST00000262367	NM_004380.2	1446	Cgc/Agc	26/31	1	2	FACETS	0.136	0.089	0.197	0.136	0.089	0.197	SUBCLONAL	1	TRUE	1	0.33	2		553	400	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577552	7577552	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	11	770	0	ENST00000269305.4:c.729G>T	p.Met243Ile	p.M243I	ENST00000269305	NM_001126112.2	243	atG/atT	7/11	1	2	FACETS	0.131	0.09	0.184	0.131	0.09	0.184	SUBCLONAL	1	TRUE	1	0.33	2		770	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578464	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	10	841	0	ENST00000269305.4:c.466C>A	p.Arg156Ser	p.R156S	ENST00000269305	NM_001126112.2	156	Cgc/Agc	5/11	1	2	FACETS	0.133	0.089	0.189	0.133	0.089	0.189	SUBCLONAL	1	TRUE	1	0.33	2		841	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	10	858	2	ENST00000269305.4:c.455C>A	p.Pro152Gln	p.P152Q	ENST00000269305	NM_001126112.2	152	cCg/cAg	5/11	1	2	FACETS	0.129	0.086	0.182	0.129	0.086	0.182	SUBCLONAL	1	TRUE	1	0.33	2		860	471	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696430	47696430	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519970	NA	P-0021714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	10	614	0	ENST00000347630.2:c.393G>T	p.Trp131Cys	p.W131C	ENST00000347630	NM_001007230.1	131	tgG/tgT	6/11	1	2	FACETS	0.122	0.082	0.173	0.122	0.082	0.173	SUBCLONAL	1	TRUE	1	0.33	2		614	498	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45377662	45377662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	14	439	1	ENST00000262160.6:c.767C>A	p.Pro256His	p.P256H	ENST00000262160	NM_005901.5	256	cCt/cAt	7/11	1	2	FACETS	0.375	0.271	0.501	0.375	0.271	0.501	SUBCLONAL	1	TRUE	1	0.33	2		440	226	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221318	1221318	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs377208033	NA	P-0021714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	8	664	0	ENST00000326873.7:c.841C>A	p.Pro281Thr	p.P281T	ENST00000326873	NM_000455.4	281	Ccg/Acg	6/10	0.300320480257154	1	FACETS	0.124	0.079	0.183	0.124	0.079	0.183	SUBCLONAL	1	TRUE	0	0.33	1		664	326	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982484	10982484	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	10	206	0	ENST00000327064.4:c.106C>A	p.Arg36Ser	p.R36S	ENST00000327064	NM_199141.1	36	Cgc/Agc	1/16	0.255246580286293	1	FACETS	0.293	0.198	0.411	0.293	0.198	0.411	SUBCLONAL	1	TRUE	0	0.33	1		206	173	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945969	17945969	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs758959409	NA	P-0021714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	12	877	1	ENST00000458235.1:c.1970G>T	p.Arg657Leu	p.R657L	ENST00000458235	NM_000215.3	657	cGg/cTg	15/24	0.255246580286293	1	FACETS	0.142	0.099	0.195	0.142	0.099	0.195	SUBCLONAL	1	TRUE	0	0.33	1		878	428	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793280	33793280	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1007915253	NA	P-0021714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	13	363	1	ENST00000498907.2:c.41C>A	p.Pro14Gln	p.P14Q	ENST00000498907	NM_004364.3	14	cCg/cAg	1/1	0.255246580286293	1	FACETS	0.261	0.186	0.353	0.261	0.186	0.353	SUBCLONAL	1	TRUE	0	0.33	1		364	252	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731496	47731496	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	10	129	0	ENST00000449228.1:c.296C>A	p.Pro99His	p.P99H	ENST00000449228	NM_001127240.2	99	cCc/cAc	2/4	0.255246580286293	1	FACETS	0.452	0.308	0.63	0.452	0.308	0.63	SUBCLONAL	1	TRUE	0	0.33	1		129	112	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082316	16082316	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	11	894	2	ENST00000281043.3:c.130C>A	p.Pro44Thr	p.P44T	ENST00000281043	NM_005378.4	44	Ccc/Acc	2/3	0.164478305181705	3	FACETS	0.153	0.105	0.214	0.051	0.035	0.072	INDETERMINATE	1	TRUE	0	0.33	3		896	507	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116178	209116178	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	9	551	0	ENST00000345146.2:c.98C>A	p.Pro33His	p.P33H	ENST00000345146	NM_005896.2	33	cCc/cAc	3/10	1	2	FACETS	0.134	0.088	0.193	0.134	0.088	0.193	SUBCLONAL	1	TRUE	1	0.33	2		551	408	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748153	41748153	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	13	446	3	ENST00000226382.2:c.616C>A	p.Pro206Thr	p.P206T	ENST00000226382	NM_003924.3	206	Ccc/Acc	3/3	1	2	FACETS	0.331	0.236	0.447	0.331	0.236	0.447	SUBCLONAL	1	TRUE	1	0.33	2		449	238	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236676	236676	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	9	429	0	ENST00000264932.6:c.1394G>T	p.Arg465Leu	p.R465L	ENST00000264932	NM_004168.2	465	cGg/cTg	10/15	0.225151668962516	4	FACETS	0.173	0.114	0.25	0.058	0.038	0.084	SUBCLONAL	1	TRUE	1	0.33	4		429	419	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803074	32803074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	42	734	0	ENST00000374899.4:c.802G>A	p.Ala268Thr	p.A268T	ENST00000374899	NM_018833.2	268	Gcc/Acc	5/12	1	2	FACETS	0.499	0.416	0.591	0.499	0.416	0.591	SUBCLONAL	1	TRUE	1	0.33	2		734	510	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56911014	56911014	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	50	775	0	ENST00000519728.1:c.1160G>A	p.Gly387Asp	p.G387D	ENST00000519728	NM_002350.3	387	gGc/gAc	11/13	0.297671420729398	1	FACETS	0.549	0.466	0.64	0.549	0.466	0.64	SUBCLONAL	1	TRUE	0	0.33	1		775	461	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738365	133738365	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	10	582	1	ENST00000318560.5:c.765G>T	p.Glu255Asp	p.E255D	ENST00000318560	NM_005157.4	255	gaG/gaT	4/11	0.297671420729398	1	FACETS	0.132	0.089	0.188	0.132	0.089	0.188	SUBCLONAL	1	TRUE	0	0.33	1		583	382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0021977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	227	708	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.729733657009618	2		708	608	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0021977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	91	288	0	ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	4/10	1	2	FACETS	0.891	0.802	0.983	0.891	0.802	0.983	CLONAL	1	TRUE	1	0.729733657009618	2		288	280	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939666	76939669	+	frameshift_variant	Frame_Shift_Del	DEL	TCAA	TCAA	-	novel	NA	P-0021977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	182	712	0	ENST00000373344.5:c.1079_1082del	p.Ile360ArgfsTer6	p.I360Rfs*6	ENST00000373344	NM_000489.3	360	aTTGAg/ag	9/35	0.170542385988743	1	FACETS	0.68	0.633	0.727	0.68	0.633	0.727	INDETERMINATE	1	TRUE	0	0.729733657009618	1		712	466	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398278	25398278	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	10	595	0	ENST00000311936.3:c.41T>C	p.Val14Ala	p.V14A	ENST00000311936	NM_004985.3	14	gTa/gCa	2/5	0.245396051238351	1	FACETS	0.039	0.026	0.056	0.039	0.026	0.056	INDETERMINATE	1	TRUE	0	0.729733657009618	1		595	445	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880818	28880818	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	156	546	0	ENST00000282397.4:c.3812T>C	p.Ile1271Thr	p.I1271T	ENST00000282397	NM_002019.4	1271	aTt/aCt	29/30	1	2	FACETS	0.906	0.836	0.977	0.906	0.836	0.977	CLONAL	1	TRUE	1	0.729733657009618	2		546	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578210	7578212	+	missense_variant	Missense_Mutation	TNP	TCG	TCG	CCA	novel	NA	P-0021977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	228	624	0	ENST00000269305.4:c.637_639delinsTGG	p.Arg213Trp	p.R213W	ENST00000269305	NM_001126112.2	213	CGA/TGG	6/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.729733657009618	2		624	595	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0022132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	31	368	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.191637297153302	3	FACETS	1	0.845	1	0.526	0.425	0.64	CLONAL	1	TRUE	1	0.16	3		368	398	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0022132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	37	665	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.16	2		665	386	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0022132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	46	727	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.16	2		727	538	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0022132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	37	543	1	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.16	2		544	332	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0022132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	47	835	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.16	2		835	455	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038902	12038902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159945	NA	P-0022132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	67	595	0	ENST00000396373.4:c.1195C>T	p.Arg399Cys	p.R399C	ENST00000396373	NM_001987.4	399	Cgc/Tgc	7/8	1	2	FACETS	0.763	0.663	0.87	1	0.973	1	SUBCLONAL	2	TRUE	1	0.16	2		595	549	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	49	679	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.16	2		679	535	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	64	531	0	ENST00000342988.3:c.1610A>C	p.Asp537Ala	p.D537A	ENST00000342988	NM_005359.5	537	gAc/gCc	12/12	1	2	FACETS	0.915	0.795	1	1	0.978	1	CLONAL	2	TRUE	1	0.16	2		531	437	SUCCESS
APC	324	MSKCC	GRCh37	5	112175952	112175952	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587783031	NA	P-0022132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	22	323	0	ENST00000257430.4:c.4666del	p.Thr1556LeufsTer9	p.T1556Lfs*9	ENST00000257430	NM_000038.5	1554	gAa/ga	16/16	1	2	FACETS	1	0.832	1	1	0.832	1	CLONAL	1	TRUE	1	0.16	2		323	253	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969845	81969845	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369090249	NA	P-0022132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	71	738	2	ENST00000359376.3:c.2914G>A	p.Val972Ile	p.V972I	ENST00000359376	NM_002661.3	972	Gtc/Atc	27/33	1	2	FACETS	0.828	0.724	0.94	1	0.977	1	CLONAL	2	TRUE	1	0.16	2		740	536	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667846	37667846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	35	688	1	ENST00000447079.4:c.2731G>A	p.Glu911Lys	p.E911K	ENST00000447079	NM_015083.1	911	Gaa/Aaa	8/14	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.16	2		689	407	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814171	76814171	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	28	483	0	ENST00000373344.5:c.6473A>G	p.Lys2158Arg	p.K2158R	ENST00000373344	NM_000489.3	2158	aAg/aGg	29/35	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.16	2		483	324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578394	+	protein_altering_variant	In_Frame_Del	DEL	CGCTCAT	CGCTCAT	A	novel	NA	P-0022132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	44	689	0	ENST00000269305.4:c.536_542delinsT	p.His179_Arg181delinsLeu	p.H179_R181delinsL	ENST00000269305	NM_001126112.2	179	cATGAGCGc/cTc	5/11	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.16	2		689	498	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0022311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	96	364	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.984	0.882	1	0.984	0.882	1	CLONAL	1	TRUE	1	0.445576810522381	2		364	438	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0022311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	35	350	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.20643889433161	2	FACETS	0.444	0.364	0.533	0.222	0.182	0.267	INDETERMINATE	1	TRUE	0	0.445576810522381	2		350	354	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690847	89690847	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587776667	NA	P-0022311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	156	499	0	ENST00000371953.3:c.253+1G>T		p.X85_splice	ENST00000371953	NM_000314.4	85			0.20643889433161	2	FACETS	1	0.986	1	0.663	0.611	0.717	INDETERMINATE	1	TRUE	0	0.445576810522381	2		499	528	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624263	89624263	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	48	433	0	ENST00000371953.3:c.37A>G	p.Lys13Glu	p.K13E	ENST00000371953	NM_000314.4	13	Aaa/Gaa	1/9	0.20643889433161	2	FACETS	0.41	0.346	0.48	0.205	0.173	0.24	INDETERMINATE	1	TRUE	0	0.445576810522381	2		433	526	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0024043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	228	621	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.674337551937591	2		621	668	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022913	27022938	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGCCGCCGCCAGCAGCCTGGGCAA	CCCGCCGCCGCCAGCAGCCTGGGCAA	-	rs797045262	NA	P-0024043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	17	68	0	ENST00000324856.7:c.31_56del	p.Ser11AlafsTer91	p.S11Afs*91	ENST00000324856	NM_006015.4	7	CCCGCCGCCGCCAGCAGCCTGGGCAAc/c	1/20	1	2	FACETS	0.672	0.514	0.851	0.672	0.514	0.851	SUBCLONAL	1	TRUE	1	0.674337551937591	2		68	75	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106536	27106536	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	326	1022	0	ENST00000324856.7:c.6147G>A	p.Trp2049Ter	p.W2049*	ENST00000324856	NM_006015.4	2049	tgG/tgA	20/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.674337551937591	2		1022	917	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577157	64577160	+	frameshift_variant	Frame_Shift_Del	DEL	GACT	GACT	-	novel	NA	P-0024043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	300	887	0	ENST00000312049.6:c.422_425del	p.Gln141ProfsTer43	p.Q141Pfs*43	ENST00000312049	NM_130799.2	141	cAGTCc/cc	2/10	0.659466321936001	1	FACETS	0.959	0.912	1	0.959	0.912	1	CLONAL	1	TRUE	0	0.674337551937591	1		887	615	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610591	10610591	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	310	805	1	ENST00000171111.5:c.119C>A	p.Ala40Glu	p.A40E	ENST00000171111	NM_203500.1	40	gCg/gAg	2/6	1	2	FACETS	0.96	0.907	1	0.96	0.907	1	CLONAL	1	TRUE	1	0.674337551937591	2		806	958	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015053	27015053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151098324	NA	P-0024043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	201	567	0	ENST00000335756.4:c.155G>A	p.Arg52Gln	p.R52Q	ENST00000335756	NM_001809.3	52	cGa/cAa	2/5	1	2	FACETS	0.923	0.86	0.988	0.923	0.86	0.988	CLONAL	1	TRUE	1	0.674337551937591	2		567	646	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513455	41513458	+	frameshift_variant	Frame_Shift_Del	DEL	GCAT	GCAT	-	novel	NA	P-0024043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	190	685	0	ENST00000263253.7:c.360_363del	p.Ser120ArgfsTer6	p.S120Rfs*6	ENST00000263253	NM_001429.3	120	aGCATg/ag	2/31	1	2	FACETS	0.787	0.73	0.846	0.787	0.73	0.846	SUBCLONAL	1	TRUE	1	0.674337551937591	2		685	716	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0024513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	44	415	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.384776944656829	3	FACETS	0.551	0.462	0.65	0.275	0.231	0.325	SUBCLONAL	1	TRUE	1	0.384776944656829	3		415	495	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0024513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	63	534	1	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.695	0.603	0.795	0.695	0.603	0.795	SUBCLONAL	1	TRUE	1	0.384776944656829	2		535	471	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711876	89711876	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	34	412	0	ENST00000371953.3:c.494G>A	p.Gly165Glu	p.G165E	ENST00000371953	NM_000314.4	165	gGa/gAa	6/9	1	2	FACETS	0.612	0.501	0.734	0.612	0.501	0.734	SUBCLONAL	1	TRUE	1	0.384776944656829	2		412	289	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058039	27058039	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	113	520	1	ENST00000324856.7:c.1747C>T	p.Gln583Ter	p.Q583*	ENST00000324856	NM_006015.4	583	Cag/Tag	3/20	1	2	FACETS	0.946	0.853	1	0.946	0.853	1	CLONAL	1	TRUE	1	0.384776944656829	2		521	621	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026176	48026176	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881787	NA	P-0024513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	17	368	0	ENST00000234420.5:c.1054G>A	p.Val352Ile	p.V352I	ENST00000234420	NM_000179.2	352	Gtt/Att	4/10	1	2	FACETS	0.281	0.209	0.366	0.281	0.209	0.366	SUBCLONAL	1	TRUE	1	0.384776944656829	2		368	315	SUCCESS
APC	324	MSKCC	GRCh37	5	112170746	112170746	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	63	542	0	ENST00000257430.4:c.1842del	p.Leu616TrpfsTer14	p.L616Wfs*14	ENST00000257430	NM_000038.5	614	gcA/gc	15/16	1	2	FACETS	0.835	0.726	0.953	0.835	0.726	0.953	CLONAL	1	TRUE	1	0.384776944656829	2		542	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0024634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	199	568	0	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.563375276234242	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.563375276234242	1		568	460	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821283	72821283	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	127	438	2	ENST00000268489.5:c.10892C>A	p.Ser3631Tyr	p.S3631Y	ENST00000268489	NM_006885.3	3631	tCt/tAt	10/10	1	2	FACETS	0.9	0.82	0.983	0.9	0.82	0.983	CLONAL	1	TRUE	1	0.563375276234242	2		440	501	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720795	89720796	+	stop_gained	Nonsense_Mutation	DNP	CT	CT	TA	novel	NA	P-0024922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	11	282	0	ENST00000371953.3:c.946_947delinsTA	p.Leu316Ter	p.L316*	ENST00000371953	NM_000314.4	316	CTa/TAa	8/9	0.340899374207653	1	FACETS	0.335	0.231	0.462	0.335	0.231	0.462	SUBCLONAL	1	TRUE	0	0.340899374207653	1		282	160	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051594	30051595	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	72	463	0	ENST00000338641.4:c.529dup	p.Tyr177LeufsTer26	p.Y177Lfs*26	ENST00000338641	NM_000268.3	176	-/T	6/16	0.340899374207653	1	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	0	0.340899374207653	1		463	349	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183812	10183817	+	inframe_deletion	In_Frame_Del	DEL	AGCCGC	AGCCGC	-	novel	NA	P-0024922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	81	821	0	ENST00000256474.2:c.285_290del	p.Gln96_Pro97del	p.Q96_P97del	ENST00000256474	NM_000551.3	94	gAGCCGCag/gag	1/3	0.340899374207653	1	FACETS	0.62	0.546	0.699	0.62	0.546	0.699	SUBCLONAL	1	TRUE	0	0.340899374207653	1		821	636	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125592	47125593	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	53	450	0	ENST00000409792.3:c.5677dup	p.Ile1893AsnfsTer3	p.I1893Nfs*3	ENST00000409792	NM_014159.6	1893	atc/aAtc	12/21	0.340899374207653	1	FACETS	0.857	0.736	0.988	0.857	0.736	0.988	CLONAL	1	TRUE	0	0.340899374207653	1		450	301	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588782	52588783	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0024922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	72	720	0	ENST00000394830.3:c.4245dup	p.Leu1416SerfsTer93	p.L1416Sfs*93	ENST00000394830	NM_018313.4	1415	-/T	27/30	0.340899374207653	1	FACETS	0.775	0.68	0.878	0.775	0.68	0.878	SUBCLONAL	1	TRUE	0	0.340899374207653	1		720	452	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738116	145738116	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	107	1061	0	ENST00000428558.2:c.2794C>G	p.His932Asp	p.H932D	ENST00000428558	NM_004260.3	932	Cac/Gac	17/22	1	2	FACETS	0.766	0.686	0.85	0.766	0.686	0.85	SUBCLONAL	1	TRUE	1	0.340899374207653	2		1061	820	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0024926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	204	506	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		506	426	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0025657-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	278	361	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.379008224244662	3	FACETS	0.916	0.874	0.958	1	0.992	1	CLONAL	4	TRUE	0	0.379008224244662	3		361	476	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861055	35861055	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025657-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	58	331	0	ENST00000303115.3:c.184C>A	p.Pro62Thr	p.P62T	ENST00000303115	NM_002185.3	62	Cca/Aca	2/8	0.320531626172195	3	FACETS	0.992	0.856	1	0.496	0.428	0.57	CLONAL	1	TRUE	1	0.379008224244662	3		331	367	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180397	94180397	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025657-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	80	446	0	ENST00000323929.3:c.1771C>G	p.Gln591Glu	p.Q591E	ENST00000323929	NM_005591.3	591	Caa/Gaa	15/20	0.344903774267092	5	FACETS	1	0.953	1			1	CLONAL	1	TRUE	NA	0.379008224244662	5		446	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578209	7578209	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025657-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	308	658	0	ENST00000269305.4:c.640C>G	p.His214Asp	p.H214D	ENST00000269305	NM_001126112.2	214	Cat/Gat	6/11	0.379008224244662	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	3	TRUE	0	0.379008224244662	3		658	639	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411879	116411900	+	splice_region_variant,intron_variant	Splice_Region	DEL	CTCTTTCTTTCTCTCTGTTTTA	CTCTTTCTTTCTCTCTGTTTTA	-	novel	NA	P-0025657-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	1643	824	0	ENST00000397752.3:c.2888-24_2888-3del		p.X963_splice	ENST00000397752	NM_000245.2	963			0.379008224244662	14	FACETS	0.99	0.979	1			1	CLONAL	15	TRUE	NA	0.379008224244662	14		824	1911	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667344	241667344	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025657-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	48	426	0	ENST00000366560.3:c.1106C>G	p.Pro369Arg	p.P369R	ENST00000366560	NM_000143.3	369	cCa/cGa	7/10	0.362535527775736	3	FACETS	1	0.886	1	0.525	0.446	0.61	CLONAL	1	TRUE	1	0.379008224244662	3		426	287	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778239	27778239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025657-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	121	545	0	ENST00000369163.2:c.388C>T	p.Arg130Cys	p.R130C	ENST00000369163	NM_003536.2	130	Cgt/Tgt	1/1	0.272854644314453	4	FACETS	1	0.971	1	0.398	0.359	0.438	CLONAL	1	TRUE	1	0.379008224244662	4		545	738	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045760	26045760	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025657-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	86	434	0	ENST00000540144.1:c.122G>A	p.Arg41His	p.R41H	ENST00000540144	NM_003531.2	41	cGc/cAc	1/1	0.272854644314453	4	FACETS	1	0.955	1	0.385	0.341	0.432	CLONAL	1	TRUE	1	0.379008224244662	4		434	542	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0026453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	122	587	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	0.828	0.75	0.911	0.828	0.75	0.911	CLONAL	1	FALSE	1	0.426966489758579	2		587	690	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577599	7577600	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1567550002	NA	P-0026453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	389	686	4	ENST00000269305.4:c.681dup	p.Asp228Ter	p.D228*	ENST00000269305	NM_001126112.2	227	-/T	7/11	0.426966489758579	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	FALSE	0	0.426966489758579	2		690	911	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0027025-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	723	763	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	0.82375418597944	3	FACETS	0.988	0.971	1	0.988	0.971	1	CLONAL	3	TRUE	0	0.82375418597944	3		763	836	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251635	212251635	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1211840752	NA	P-0027025-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	129	436	2	ENST00000342788.4:c.3424C>T	p.Arg1142Ter	p.R1142*	ENST00000342788	NM_005235.2	1142	Cga/Tga	27/28	0.771450166994372	3	FACETS	0.85	0.775	0.929	0.283	0.258	0.31	CLONAL	1	TRUE	0	0.82375418597944	3		438	520	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971039	21971040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0027025-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	306	352	0	ENST00000304494.5:c.318dup	p.Arg107AlafsTer13	p.R107Afs*13	ENST00000304494	NM_000077.4	106	-/G	2/3	0.756081456824087	3	FACETS	0.843	0.812	0.871	0.843	0.812	0.871	CLONAL	3	TRUE	0	0.82375418597944	3		352	415	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027025-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	289	404	1	ENST00000324856.7:c.666C>A	p.Tyr222Ter	p.Y222*	ENST00000324856	NM_006015.4	222	taC/taA	1/20	0.82375418597944	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.82375418597944	3		405	492	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929084	32929099	+	frameshift_variant	Frame_Shift_Del	DEL	ATCTGACTTTGGAAAA	ATCTGACTTTGGAAAA	-	novel	NA	P-0027025-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	111	497	0	ENST00000380152.3:c.7098_7113del	p.Thr2367GlnfsTer4	p.T2367Qfs*4	ENST00000380152		2365	cATCTGACTTTGGAAAAa/ca	14/27	0.767418652337659	2	FACETS	0.832	0.757	0.909	0.416	0.378	0.455	CLONAL	1	TRUE	0	0.82375418597944	2		497	324	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435669	110435669	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910525456	NA	P-0027025-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	339	418	0	ENST00000375856.3:c.2732C>T	p.Pro911Leu	p.P911L	ENST00000375856	NM_003749.2	911	cCg/cTg	1/2	0.767418652337659	2	FACETS	0.978	0.949	1	0.978	0.949	1	CLONAL	2	TRUE	0	0.82375418597944	2		418	421	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95597861	95597861	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027025-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	132	405	0	ENST00000393063.1:c.423G>C	p.Glu141Asp	p.E141D	ENST00000393063	NM_030621.3	141	gaG/gaC	5/28	1	2	FACETS	0.954	0.878	1	0.954	0.878	1	CLONAL	1	TRUE	1	0.82375418597944	2		405	336	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113810	11113810	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027025-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	462	611	0	ENST00000358026.2:c.1918G>T	p.Glu640Ter	p.E640*	ENST00000358026	NM_001128849.1	640	Gag/Tag	12/36	0.82375418597944	4	FACETS	0.957	0.917	0.997	0.478	0.458	0.499	CLONAL	2	TRUE	0	0.82375418597944	4		611	1069	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55225370	55225370	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027025-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	529	477	1	ENST00000275493.2:c.1222C>T	p.Gln408Ter	p.Q408*	ENST00000275493	NM_005228.3	408	Cag/Tag	11/28	0.82375418597944	5	FACETS	1	0.995	1	0.598	0.575	0.622	CLONAL	2	TRUE	1	0.82375418597944	5		478	1200	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28882982	28882982	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027025-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	151	503	0	ENST00000282397.4:c.3718G>C	p.Asp1240His	p.D1240H	ENST00000282397	NM_002019.4	1240	Gat/Cat	28/30	0.767418652337659	2	FACETS	0.873	0.806	0.941	0.436	0.403	0.471	CLONAL	1	TRUE	0	0.82375418597944	2		503	420	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339548	116339548	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027025-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	75	307	0	ENST00000397752.3:c.410A>T	p.Asn137Ile	p.N137I	ENST00000397752	NM_000245.2	137	aAc/aTc	2/21	0.82223141327901	4	FACETS	0.9	0.794	1	0.3	0.264	0.338	CLONAL	1	TRUE	1	0.82375418597944	4		307	369	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0027706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	62	144	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.25153919545119	3	FACETS	0.957	0.838	1	0.638	0.559	0.722	CLONAL	2	TRUE	0	0.338176763941402	3		144	224	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0027706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	307	664	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.338176763941402	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.338176763941402	3		665	653	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0027958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	490	389	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.758658261860166	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	TRUE	1	0.758658261860166	4		389	757	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913400	NA	P-0027958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	147	376	1	ENST00000349496.5:c.98C>A	p.Ser33Tyr	p.S33Y	ENST00000349496	NM_001904.3	33	tCt/tAt	3/15	1	2	FACETS	0.981	0.906	1	0.981	0.906	1	CLONAL	1	TRUE	1	0.758658261860166	2		377	395	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198306	185198306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528512189	NA	P-0027958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	239	545	0	ENST00000265026.3:c.2788C>T	p.Arg930Cys	p.R930C	ENST00000265026	NM_004721.4	930	Cgt/Tgt	13/14	0.758658261860166	4	FACETS	0.914	0.852	0.978	0.305	0.284	0.326	CLONAL	1	TRUE	1	0.758658261860166	4		545	1212	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059176	27059176	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	201	447	0	ENST00000324856.7:c.1813C>T	p.Gln605Ter	p.Q605*	ENST00000324856	NM_006015.4	605	Caa/Taa	4/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.758658261860166	2		447	490	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27093027	27093028	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0027958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	214	512	0	ENST00000324856.7:c.2961dup	p.Thr988AspfsTer19	p.T988Dfs*19	ENST00000324856	NM_006015.4	986	-/G	10/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.758658261860166	2		512	530	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696718	47696718	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	381	443	0	ENST00000347630.2:c.230A>T	p.Asp77Val	p.D77V	ENST00000347630	NM_001007230.1	77	gAt/gTt	5/11	0.758658261860166	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.758658261860166	3		443	684	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793270	33793270	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1245499278	NA	P-0027958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	89	176	0	ENST00000498907.2:c.51C>A	p.Ser17Arg	p.S17R	ENST00000498907	NM_004364.3	17	agC/agA	1/1	1	2	FACETS	0.844	0.758	0.933	0.844	0.758	0.933	CLONAL	1	TRUE	1	0.758658261860166	2		176	278	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0028660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	40	326	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	1	2	FACETS	0.827	0.691	0.978	0.827	0.691	0.978	CLONAL	1	TRUE	1	0.33	2		326	293	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0028660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	38	144	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.3	2	FACETS	0.773	0.65	0.905	0.773	0.65	0.905	CLONAL	2	TRUE	0	0.33	2		144	149	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0028660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	48	327	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.238536118507714	1	FACETS	0.996	0.849	1	0.996	0.849	1	CLONAL	1	TRUE	0	0.33	1		327	244	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0028660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	21	273	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.123625594630073	0	FACETS	0.329	0.254	0.417			1	INDETERMINATE	1	TRUE	0	0.33	0		273	259	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912188	114912188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	60	334	0	ENST00000543371.1:c.1258C>T	p.Arg420Trp	p.R420W	ENST00000543371	NM_001198531.1	420	Cgg/Tgg	11/14	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.33	2		334	331	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172028	32172028	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761216718	NA	P-0028660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	31	328	0	ENST00000375023.3:c.3004C>T	p.Arg1002Cys	p.R1002C	ENST00000375023	NM_004557.3	1002	Cgc/Tgc	19/30	0.3	1	FACETS	0.754	0.615	0.91	0.754	0.615	0.91	CLONAL	1	TRUE	0	0.33	1		328	208	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0028660-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	62	326	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.208814909901961	3	FACETS	0.815	0.705	0.934	0.408	0.352	0.467	INDETERMINATE	1	TRUE	1	0.36654322201701	3		326	491	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0028660-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	43	144	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.208814909901961	3	FACETS	0.89	0.758	1	0.89	0.758	1	INDETERMINATE	2	TRUE	1	0.36654322201701	3		144	156	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0028660-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	70	327	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.36654322201701	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.36654322201701	1		327	244	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0028660-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	56	273	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.758	0.652	0.874	0.758	0.652	0.874	SUBCLONAL	1	TRUE	1	0.36654322201701	2		273	403	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912188	114912188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028660-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	55	334	0	ENST00000543371.1:c.1258C>T	p.Arg420Trp	p.R420W	ENST00000543371	NM_001198531.1	420	Cgg/Tgg	11/14	1	2	FACETS	0.968	0.834	1	0.968	0.834	1	CLONAL	1	TRUE	1	0.36654322201701	2		334	310	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172028	32172028	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761216718	NA	P-0028660-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	45	328	0	ENST00000375023.3:c.3004C>T	p.Arg1002Cys	p.R1002C	ENST00000375023	NM_004557.3	1002	Cgc/Tgc	19/30	0.289071118685889	1	FACETS	0.79	0.669	0.921	0.79	0.669	0.921	CLONAL	1	TRUE	0	0.36654322201701	1		328	254	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0029115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	53	368	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.832	0.708	0.968	0.832	0.708	0.968	CLONAL	1	FALSE	1	0.187905621463377	2		368	678	SUCCESS
AR	367	MSKCC	GRCh37	X	66765047	66765047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1297947716	NA	P-0029115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	74	646	1	ENST00000374690.3:c.59G>A	p.Arg20Gln	p.R20Q	ENST00000374690	NM_000044.3	20	cGa/cAa	1/8	1	2	FACETS	0.708	0.618	0.806	0.708	0.618	0.806	SUBCLONAL	1	FALSE	1	0.187905621463377	2		647	1112	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163588	47163589	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0029115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	44	286	0	ENST00000409792.3:c.2537_2538del	p.Lys846IlefsTer4	p.K846Ifs*4	ENST00000409792	NM_014159.6	846	aAA/a	3/21	1	2	FACETS	0.844	0.707	0.995	0.844	0.707	0.995	CLONAL	1	FALSE	1	0.187905621463377	2		286	555	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134555	41134555	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	71	352	0	ENST00000379561.5:c.1073C>G	p.Thr358Ser	p.T358S	ENST00000379561	NM_002015.3	358	aCt/aGt	2/3	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	FALSE	1	0.187905621463377	2		352	701	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162406	47162413	+	frameshift_variant	Frame_Shift_Del	DEL	AGAGGAAG	AGAGGAAG	-	novel	NA	P-0029115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	56	322	0	ENST00000409792.3:c.3713_3720del	p.Ser1238LeufsTer2	p.S1238Lfs*2	ENST00000409792	NM_014159.6	1238	tCTTCCTCT/t	3/21	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	FALSE	1	0.187905621463377	2		322	562	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205156	123205156	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	50	305	1	ENST00000218089.9:c.2516A>G	p.Asp839Gly	p.D839G	ENST00000218089	NM_001042749.1	839	gAt/gGt	25/35	1	2	FACETS	0.954	0.809	1	0.954	0.809	1	CLONAL	1	FALSE	1	0.187905621463377	2		306	558	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	90	541	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.325343558270555	2		541	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0029130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	104	513	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	1	2	FACETS	0.848	0.759	0.942	0.848	0.759	0.942	CLONAL	1	TRUE	1	0.325343558270555	2		513	754	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0029130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	105	469	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	1	2	FACETS	0.868	0.777	0.963	0.868	0.777	0.963	CLONAL	1	TRUE	1	0.325343558270555	2		469	744	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030368	49030368	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	62	306	2	ENST00000267163.4:c.1848del	p.Gly617ValfsTer6	p.G617Vfs*6	ENST00000267163	NM_000321.2	615	Aaa/aa	19/27	0.325343558270555	1	FACETS	0.808	0.701	0.923	0.808	0.701	0.923	CLONAL	1	TRUE	0	0.325343558270555	1		308	395	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916728	178916728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	55	326	0	ENST00000263967.3:c.115G>A	p.Glu39Lys	p.E39K	ENST00000263967	NM_006218.2	39	Gag/Aag	2/21	1	2	FACETS	0.755	0.647	0.872	0.755	0.647	0.872	SUBCLONAL	1	TRUE	1	0.325343558270555	2		326	448	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934606	9934606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	70	394	0	ENST00000330684.3:c.1549G>A	p.Glu517Lys	p.E517K	ENST00000330684	NM_001134407.1	517	Gaa/Aaa	7/13	0.325343558270555	1	FACETS	0.602	0.525	0.685	0.602	0.525	0.685	SUBCLONAL	1	TRUE	0	0.325343558270555	1		394	599	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599207	28599207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	166	639	0	ENST00000253063.3:c.653C>T	p.Pro218Leu	p.P218L	ENST00000253063	NM_031459.4	218	cCt/cTt	5/10	0.309994833573194	1	FACETS	0.975	0.896	1	0.975	0.896	1	CLONAL	1	TRUE	0	0.325343558270555	1		639	876	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745460	162745460	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	129	293	0	ENST00000367921.3:c.1875G>T	p.Glu625Asp	p.E625D	ENST00000367921	NM_006182.2	625	gaG/gaT	15/18	0.325343558270555	4	FACETS	0.935	0.851	1	0.935	0.851	1	CLONAL	2	TRUE	2	0.325343558270555	4		293	562	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121515	193121515	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	51	238	0	ENST00000367435.3:c.913G>A	p.Glu305Lys	p.E305K	ENST00000367435	NM_024529.4	305	Gaa/Aaa	10/17	0.310887796583326	2	FACETS	1	0.965	1	0.726	0.624	0.834	CLONAL	1	TRUE	0	0.325343558270555	2		238	216	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406072	70406072	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	116	541	0	ENST00000373644.4:c.3586C>T	p.Gln1196Ter	p.Q1196*	ENST00000373644	NM_030625.2	1196	Caa/Taa	4/12	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.325343558270555	2		541	684	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198915	67198915	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	84	431	0	ENST00000312629.5:c.386C>T	p.Pro129Leu	p.P129L	ENST00000312629	NM_003952.2	129	cCc/cTc	5/15	1	2	FACETS	0.724	0.639	0.815	0.724	0.639	0.815	SUBCLONAL	1	TRUE	1	0.325343558270555	2		431	713	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917644	94917644	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	55	467	0	ENST00000536441.1:c.877G>C	p.Glu293Gln	p.E293Q	ENST00000536441	NM_144665.3	293	Gag/Cag	6/10	1	2	FACETS	0.721	0.618	0.834	0.721	0.618	0.834	SUBCLONAL	1	TRUE	1	0.325343558270555	2		467	469	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610129	28610129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	103	410	0	ENST00000241453.7:c.1361C>T	p.Ser454Leu	p.S454L	ENST00000241453	NM_004119.2	454	tCg/tTg	11/24	1	2	FACETS	0.912	0.817	1	0.912	0.817	1	CLONAL	1	TRUE	1	0.325343558270555	2		410	694	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40681733	40681733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	70	384	1	ENST00000249776.8:c.512C>T	p.Ser171Leu	p.S171L	ENST00000249776	NM_033286.3	171	tCa/tTa	5/9	1	2	FACETS	0.742	0.647	0.844	0.742	0.647	0.844	SUBCLONAL	1	TRUE	1	0.325343558270555	2		385	580	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55704590	55704590	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	111	535	0	ENST00000284073.2:c.653G>T	p.Gly218Val	p.G218V	ENST00000284073	NM_138962.2	218	gGa/gTa	10/14	1	2	FACETS	0.761	0.683	0.843	0.761	0.683	0.843	SUBCLONAL	1	TRUE	1	0.325343558270555	2		535	897	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909455	50909455	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	99	545	0	ENST00000440232.2:c.1259T>G	p.Phe420Cys	p.F420C	ENST00000440232	NM_002691.3	420	tTc/tGc	11/27	1	2	FACETS	0.686	0.612	0.766	0.686	0.612	0.766	SUBCLONAL	1	TRUE	1	0.325343558270555	2		545	887	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539741	187539741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1423289460	NA	P-0029130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	63	317	0	ENST00000441802.2:c.7999G>A	p.Glu2667Lys	p.E2667K	ENST00000441802	NM_005245.3	2667	Gaa/Aaa	10/27	1	2	FACETS	0.79	0.685	0.905	0.79	0.685	0.905	CLONAL	1	TRUE	1	0.325343558270555	2		317	490	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967840	93967840	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	102	381	0	ENST00000369303.4:c.2087A>G	p.His696Arg	p.H696R	ENST00000369303	NM_004440.3	696	cAt/cGt	11/17	0.325343558270555	1	FACETS	0.881	0.79	0.978	0.881	0.79	0.978	CLONAL	1	TRUE	0	0.325343558270555	1		381	596	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715354	117715354	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	52	241	0	ENST00000368508.3:c.1135C>G	p.Gln379Glu	p.Q379E	ENST00000368508	NM_002944.2	379	Caa/Gaa	10/43	0.325343558270555	1	FACETS	0.977	0.838	1	0.977	0.838	1	CLONAL	1	TRUE	0	0.325343558270555	1		241	274	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129225	152129225	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1180943277	NA	P-0029130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	181	559	0	ENST00000206249.3:c.178T>C	p.Tyr60His	p.Y60H	ENST00000206249	NM_000125.3	60	Tac/Cac	1/8	0.325343558270555	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.325343558270555	1		559	925	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935676	13935676	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	80	407	0	ENST00000405192.2:c.1180G>C	p.Asp394His	p.D394H	ENST00000405192	NM_001163147.1	394	Gat/Cat	12/12	1	2	FACETS	0.731	0.643	0.825	0.731	0.643	0.825	SUBCLONAL	1	TRUE	1	0.325343558270555	2		407	673	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729909	41729909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	117	456	0	ENST00000242208.4:c.620C>T	p.Ser207Phe	p.S207F	ENST00000242208	NM_002192.2	207	tCt/tTt	3/3	1	2	FACETS	0.928	0.837	1	0.928	0.837	1	CLONAL	1	TRUE	1	0.325343558270555	2		456	775	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80343451	80343451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	66	268	0	ENST00000286548.4:c.868G>A	p.Asp290Asn	p.D290N	ENST00000286548	NM_002072.3	290	Gac/Aac	6/7	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.325343558270555	2		268	388	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399171	139399171	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	129	553	0	ENST00000277541.6:c.4972G>T	p.Glu1658Ter	p.E1658*	ENST00000277541	NM_017617.3	1658	Gag/Tag	26/34	1	2	FACETS	0.949	0.86	1	0.949	0.86	1	CLONAL	1	TRUE	1	0.325343558270555	2		553	836	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411996	63411996	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	183	280	0	ENST00000330258.3:c.1171G>C	p.Glu391Gln	p.E391Q	ENST00000330258	NM_152424.3	391	Gag/Cag	2/2	1	1	FACETS	0.923	0.859	0.989	1	0.993	1	CLONAL	2	TRUE	0	0.325343558270555	1		280	510	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105436	27105584	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGAGGTCTCTCAAGTCAATAATTCTGTTCTTAGGCCACTTTTCTCCCTTAATTTATTTCCTGTTCTTTCTCTTTTTAGCTCCCAGGGTTGCTAGAGCTCCTTGTAGAATATTTCCGACGATGCCTGATTGAGATCTTTGGCATTTTAAA	GGAGGTCTCTCAAGTCAATAATTCTGTTCTTAGGCCACTTTTCTCCCTTAATTTATTTCCTGTTCTTTCTCTTTTTAGCTCCCAGGGTTGCTAGAGCTCCTTGTAGAATATTTCCGACGATGCCTGATTGAGATCTTTGGCATTTTAAA	-	novel	NA	P-0029336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	21	90	0	ENST00000324856.7:c.5125-74_5199del		p.X1709_splice	ENST00000324856	NM_006015.4	1709		20/20	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	FALSE	1	0.281901201154684	2		90	116	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874250	155874250	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	67	508	0	ENST00000368323.3:c.281A>T	p.Glu94Val	p.E94V	ENST00000368323	NM_006912.5	94	gAa/gTa	5/6	1	2	FACETS	0.679	0.589	0.776	0.679	0.589	0.776	SUBCLONAL	1	FALSE	1	0.281901201154684	2		508	700	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533818	63533818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	180	439	0	ENST00000307078.5:c.1336G>A	p.Val446Ile	p.V446I	ENST00000307078	NM_004655.3	446	Gtc/Atc	6/11	1	2	FACETS	0.882	0.816	0.951	1	0.992	1	CLONAL	2	FALSE	1	0.281901201154684	2		439	724	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860354	151860354	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	106	425	0	ENST00000262189.6:c.10308G>C	p.Met3436Ile	p.M3436I	ENST00000262189	NM_170606.2	3436	atG/atC	43/59	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.281901201154684	2		425	506	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760456	133760456	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	91	539	0	ENST00000318560.5:c.2779G>C	p.Val927Leu	p.V927L	ENST00000318560	NM_005157.4	927	Gtc/Ctc	11/11	1	2	FACETS	0.784	0.696	0.879	0.784	0.696	0.879	SUBCLONAL	1	FALSE	1	0.281901201154684	2		539	823	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938455	44938456	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0029336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	20	260	0	ENST00000377967.4:c.3007_3008dup	p.Gln1003HisfsTer46	p.Q1003Hfs*46	ENST00000377967	NM_021140.2	1001	-/AC	20/29	1	1	FACETS	0.368	0.281	0.47	0.368	0.281	0.47	SUBCLONAL	1	FALSE	0	0.281901201154684	1		260	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576889	7576890	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	106	596	0	ENST00000269305.4:c.956dup	p.Lys320GlufsTer17	p.K320Efs*17	ENST00000269305	NM_001126112.2	319	aag/aaAg	9/11	1	2	FACETS	0.793	0.71	0.881	0.793	0.71	0.881	SUBCLONAL	1	TRUE	1	0.288719487637126	2		596	926	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006799	62006799	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	79	549	0	ENST00000392795.3:c.589T>G	p.Tyr197Asp	p.Y197D	ENST00000392795	NM_001039933.1	197	Tac/Gac	5/6	0.217724418679637	2	FACETS	0.66	0.58	0.747	0.33	0.29	0.374	SUBCLONAL	1	TRUE	0	0.288719487637126	2		549	829	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8252006	8252006	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	54	647	1	ENST00000335790.3:c.71G>T	p.Cys24Phe	p.C24F	ENST00000335790	NM_002315.2	24	tGt/tTt	2/4	1	2	FACETS	0.423	0.36	0.493	0.423	0.36	0.493	SUBCLONAL	1	TRUE	1	0.288719487637126	2		648	884	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951123	48951123	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0029585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	23	357	0	ENST00000267163.4:c.1285A>T	p.Lys429Ter	p.K429*	ENST00000267163	NM_000321.2	429	Aaa/Taa	13/27	1	2	FACETS	0.378	0.294	0.476	0.378	0.294	0.476	SUBCLONAL	1	TRUE	1	0.288719487637126	2		357	421	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514688	103514688	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	77	357	0	ENST00000355739.4:c.1189G>T	p.Asp397Tyr	p.D397Y	ENST00000355739	NM_000123.3	397	Gat/Tat	8/15	1	2	FACETS	0.872	0.766	0.985	0.872	0.766	0.985	CLONAL	1	TRUE	1	0.288719487637126	2		357	612	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138407752	138407752	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	37	444	0	ENST00000289153.2:c.2101G>A	p.Gly701Arg	p.G701R	ENST00000289153	NM_006219.2	701	Gga/Aga	14/22	1	2	FACETS	0.379	0.311	0.455	0.379	0.311	0.455	SUBCLONAL	1	TRUE	1	0.288719487637126	2		444	676	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876400	35876400	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	88	553	0	ENST00000303115.3:c.1192C>A	p.Pro398Thr	p.P398T	ENST00000303115	NM_002185.3	398	Cct/Act	8/8	1	2	FACETS	0.663	0.586	0.745	0.663	0.586	0.745	SUBCLONAL	1	TRUE	1	0.288719487637126	2		553	920	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046041	180046041	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	38	196	0	ENST00000261937.6:c.2830del	p.Asp944ThrfsTer63	p.D944Tfs*63	ENST00000261937	NM_182925.4	944	Gac/ac	20/30	1	2	FACETS	0.572	0.473	0.683	0.572	0.473	0.683	SUBCLONAL	1	TRUE	1	0.288719487637126	2		196	460	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047945	180047946	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AT	novel	NA	P-0029585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	152	664	1	ENST00000261937.6:c.2229_2230delinsAT	p.Gly744Ter	p.G744*	ENST00000261937	NM_182925.4	743	gcGGga/gcATga	15/30	1	2	FACETS	0.957	0.874	1	0.957	0.874	1	CLONAL	1	TRUE	1	0.288719487637126	2		665	1100	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163886	152163886	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0029585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	38	447	0	ENST00000206249.3:c.607G>T	p.Glu203Ter	p.E203*	ENST00000206249	NM_000125.3	203	Gag/Tag	2/8	1	2	FACETS	0.404	0.333	0.483	0.404	0.333	0.483	SUBCLONAL	1	TRUE	1	0.288719487637126	2		447	652	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374333	81374333	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	46	334	1	ENST00000222390.5:c.729C>A	p.His243Gln	p.H243Q	ENST00000222390	NM_000601.4	243	caC/caA	6/18	1	2	FACETS	0.691	0.582	0.811	0.691	0.582	0.811	SUBCLONAL	1	TRUE	1	0.288719487637126	2		335	461	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140508791	140508791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1409723450	NA	P-0029585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	41	373	0	ENST00000288602.6:c.509C>T	p.Pro170Leu	p.P170L	ENST00000288602	NM_004333.4	170	cCt/cTt	4/18	1	2	FACETS	0.612	0.51	0.726	0.612	0.51	0.726	SUBCLONAL	1	TRUE	1	0.288719487637126	2		373	464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0029982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	202	708	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.363933244950668	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.433952590782859	1		708	711	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	472	415	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.413666928400153	5	FACETS	0.988	0.95	1	0.988	0.95	1	CLONAL	4	TRUE	1	0.433952590782859	5		415	909	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134992	2134992	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774441486	NA	P-0029982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	228	692	1	ENST00000219476.3:c.4534G>A	p.Asp1512Asn	p.D1512N	ENST00000219476	NM_000548.3	1512	Gac/Aac	35/42	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.433952590782859	2		693	976	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129645	11129691	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGGCGTACGAGTTTGACAAGTGGGCCCCCTCCGTGGTGAAGGTGT	CTGGGCGTACGAGTTTGACAAGTGGGCCCCCTCCGTGGTGAAGGTGT	-	novel	NA	P-0029982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	61	575	0	ENST00000358026.2:c.2453_2499del	p.Trp818LeufsTer111	p.W818Lfs*111	ENST00000358026	NM_001128849.1	817	aaCTGGGCGTACGAGTTTGACAAGTGGGCCCCCTCCGTGGTGAAGGTGTct/aact	17/36	0.433952590782859	1	FACETS	0.399	0.344	0.458	0.399	0.344	0.458	SUBCLONAL	1	TRUE	0	0.433952590782859	1		575	552	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527514	41527514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	222	624	0	ENST00000263253.7:c.1405G>A	p.Ala469Thr	p.A469T	ENST00000263253	NM_001429.3	469	Gca/Aca	6/31	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.433952590782859	2		624	834	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971198	21971199	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0029982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	113	369	0	ENST00000304494.5:c.158_159dup	p.Met54Ter	p.M54*	ENST00000304494	NM_000077.4	53	-/TG	2/3	0.433952590782859	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.433952590782859	1		369	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0030882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	148	642	1	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.288174882713554	1	FACETS	0.778	0.711	0.848	0.778	0.711	0.848	SUBCLONAL	1	TRUE	0	0.38	1		643	811	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029257	14029257	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1367489461	NA	P-0030882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	98	393	0	ENST00000311895.7:c.1468C>T	p.Arg490Trp	p.R490W	ENST00000311895	NM_005236.2	490	Cgg/Tgg	8/11	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.38	2		393	504	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857250	9857250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866228360	NA	P-0030882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	77	504	0	ENST00000330684.3:c.4151C>T	p.Ser1384Leu	p.S1384L	ENST00000330684	NM_001134407.1	1384	tCg/tTg	13/13	1	2	FACETS	0.637	0.559	0.721	0.637	0.559	0.721	SUBCLONAL	1	TRUE	1	0.38	2		504	636	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823901	3823901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	125	606	0	ENST00000262367.5:c.2314C>T	p.Pro772Ser	p.P772S	ENST00000262367	NM_004380.2	772	Cct/Tct	13/31	1	2	FACETS	0.912	0.827	1	0.912	0.827	1	CLONAL	1	TRUE	1	0.38	2		606	721	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421502	32421502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1319143060	NA	P-0030882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	119	409	1	ENST00000332351.3:c.1090G>A	p.Gly364Ser	p.G364S	ENST00000332351	NM_024426.4	364	Ggc/Agc	6/10	1	2	FACETS	0.993	0.898	1	0.993	0.898	1	CLONAL	1	TRUE	1	0.38	2		410	631	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228985	36228989	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTT	CTGTT	-	novel	NA	P-0030882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	91	597	0	ENST00000222270.7:c.7769_7773del	p.Phe2590Ter	p.F2590*	ENST00000222270	NM_014727.1	2589	CTGTTc/c	36/37	1	2	FACETS	0.685	0.608	0.767	0.685	0.608	0.767	SUBCLONAL	1	TRUE	1	0.38	2		597	699	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0031103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	50	206	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.398549074582449	3	FACETS	0.831	0.708	0.965	0.415	0.354	0.483	CLONAL	1	TRUE	1	0.418159832531221	3		206	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0031103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	334	584	0	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	0.418159832531221	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.418159832531221	2		584	787	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0031103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	158	307	1	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.398549074582449	3	FACETS	0.95	0.877	1	0.95	0.877	1	CLONAL	2	TRUE	1	0.418159832531221	3		308	481	SUCCESS
CALR	811	MSKCC	GRCh37	19	13049996	13049996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	83	431	0	ENST00000316448.5:c.140G>A	p.Gly47Asp	p.G47D	ENST00000316448	NM_004343.3	47	gGc/gAc	2/9	0.413807511191234	3	FACETS	0.669	0.59	0.754	0.335	0.295	0.377	SUBCLONAL	1	TRUE	1	0.418159832531221	3		431	717	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691842	30691842	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	114	343	1	ENST00000295754.5:c.344A>T	p.Asp115Val	p.D115V	ENST00000295754	NM_003242.5	115	gAt/gTt	3/7	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.418159832531221	2		344	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0031174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	357	836	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.231824030663694	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.288498400979419	2		836	1201	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0031174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	252	356	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	0.288498400979419	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	0	0.288498400979419	3		356	615	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921551	178921551	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	99	525	0	ENST00000263967.3:c.1033A>T	p.Asn345Tyr	p.N345Y	ENST00000263967	NM_006218.2	345	Aat/Tat	5/21	0.231824030663694	2	FACETS	0.903	0.806	1	0.452	0.403	0.503	CLONAL	1	TRUE	0	0.288498400979419	2		525	760	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120502050	120502050	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	128	678	0	ENST00000256646.2:c.1991A>C	p.Asn664Thr	p.N664T	ENST00000256646	NM_024408.3	664	aAt/aCt	12/34	0.282879765725706	3	FACETS	1	0.906	1	0.501	0.453	0.551	CLONAL	1	TRUE	1	0.288498400979419	3		678	1014	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18473931	18473931	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	118	619	0	ENST00000266497.5:c.1173A>C	p.Gln391His	p.Q391H	ENST00000266497		391	caA/caC	6/31	0.219500373175102	3	FACETS	0.956	0.861	1			1	CLONAL	1	TRUE	NA	0.288498400979419	3		619	979	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923469	9923469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs775819322	NA	P-0031174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	257	703	0	ENST00000330684.3:c.1818G>T	p.Trp606Cys	p.W606C	ENST00000330684	NM_001134407.1	606	tgG/tgT	9/13	0.282879765725706	3	FACETS	0.945	0.885	1	0.945	0.885	1	CLONAL	2	TRUE	1	0.288498400979419	3		703	1079	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448604	89448604	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	275	706	0	ENST00000336596.2:c.1568A>G	p.Lys523Arg	p.K523R	ENST00000336596	NM_005233.5	523	aAg/aGg	7/17	NA	2	FACETS	0.794	0.745	0.845			1	INDETERMINATE	2	TRUE	NA	0.288498400979419	2		706	1200	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979523	2979523	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	103	695	0	ENST00000396946.4:c.724del	p.Glu242AsnfsTer10	p.E242Nfs*10	ENST00000396946	NM_032415.4	242	Gaa/aa	6/25	NA	2	FACETS	0.726	0.648	0.808			1	INDETERMINATE	1	TRUE	NA	0.288498400979419	2		695	984	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986652	36986653	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	31	138	0	ENST00000354822.5:c.1036dup	p.His346ProfsTer93	p.H346Pfs*93	ENST00000354822	NM_001079668.2	346	cac/cCac	3/3	0.269613797611799	1	FACETS	0.98	0.799	1	0.98	0.799	1	CLONAL	1	TRUE	0	0.269613797611799	1		138	203	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828780	72828780	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	131	577	0	ENST00000268489.5:c.7801G>C	p.Ala2601Pro	p.A2601P	ENST00000268489	NM_006885.3	2601	Gcc/Ccc	9/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.269613797611799	2		577	825	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937644	44937644	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1471773267	NA	P-0031229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	52	222	0	ENST00000377967.4:c.2833-1G>T		p.X945_splice	ENST00000377967	NM_021140.2	945			1	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.269613797611799	1		222	236	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	74	540	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.266909328978707	1	FACETS	0.971	0.852	1	0.971	0.852	1	CLONAL	1	TRUE	0	0.266909328978707	1		540	495	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0031530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	122	341	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.221518978477879	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.266909328978707	2		341	414	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797271	135797271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs118203410	NA	P-0031530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	50	353	1	ENST00000298552.3:c.598G>A	p.Val200Ile	p.V200I	ENST00000298552	NM_001162426.1	200	Gtc/Atc	7/23	1	2	FACETS	0.877	0.746	1	0.877	0.746	1	CLONAL	1	TRUE	1	0.266909328978707	2		354	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0031530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	119	644	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.266909328978707	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.266909328978707	1		644	615	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938558	44938559	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CACAT	novel	NA	P-0031530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	81	538	0	ENST00000377967.4:c.3110_3111insTCACA	p.Gln1037HisfsTer13	p.Q1037Hfs*13	ENST00000377967	NM_021140.2	1036	gca/gCACATca	20/29	0.266909328978707	1	FACETS	0.992	0.876	1	0.992	0.876	1	CLONAL	1	TRUE	0	0.266909328978707	1		538	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0031812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	128	807	0	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	1	2	FACETS	0.77	0.712	0.829	1	0.989	1	SUBCLONAL	2	TRUE	1	0.617940224187896	2		807	269	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56477621	56477621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	77	703	0	ENST00000267101.3:c.169G>A	p.Glu57Lys	p.E57K	ENST00000267101	NM_001982.3	57	Gag/Aag	2/28	1	2	FACETS	0.644	0.563	0.731	0.644	0.563	0.731	SUBCLONAL	1	TRUE	1	0.220274833889013	2		703	1086	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060628	38060628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1311	209	1028	2	ENST00000250448.2:c.1361C>T	p.Ala454Val	p.A454V	ENST00000250448	NM_004496.3	454	gCc/gTc	2/2	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.220274833889013	2		1030	1520	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343595	343596	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0031817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1296	73	987	0	ENST00000262320.3:c.2078_2079del	p.Pro693HisfsTer88	p.P693Hfs*88	ENST00000262320	NM_003502.3	693	cCC/c	8/11	1	2	FACETS	0.484	0.421	0.552	0.484	0.421	0.552	SUBCLONAL	1	TRUE	1	0.220274833889013	2		987	1369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0032092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	58	660	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	1	2	FACETS	0.917	0.788	1	0.917	0.788	1	CLONAL	1	TRUE	1	0.203326540774789	2		660	622	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0032094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	103	513	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.307200753402745	0	FACETS	0.762	0.684	0.844			1	SUBCLONAL	1	TRUE	0	0.337714292199442	0		513	530	SUCCESS
APC	324	MSKCC	GRCh37	5	112175198	112175198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	41	242	0	ENST00000257430.4:c.3907C>T	p.Gln1303Ter	p.Q1303*	ENST00000257430	NM_000038.5	1303	Caa/Taa	16/16	0.337714292199442	1	FACETS	0.844	0.709	0.992	0.844	0.709	0.992	CLONAL	1	TRUE	0	0.337714292199442	1		242	239	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249510	153249510	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1157879635	NA	P-0032094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	101	601	0	ENST00000281708.4:c.1268G>T	p.Gly423Val	p.G423V	ENST00000281708	NM_033632.3	423	gGa/gTa	9/12	1	2	FACETS	0.949	0.85	1	0.949	0.85	1	CLONAL	1	TRUE	1	0.337714292199442	2		601	630	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459531	50459531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	27	329	0	ENST00000331340.3:c.820C>T	p.Arg274Cys	p.R274C	ENST00000331340	NM_006060.4	274	Cgt/Tgt	7/8	1	2	FACETS	0.393	0.312	0.485	0.393	0.312	0.485	SUBCLONAL	1	TRUE	1	0.337714292199442	2		329	407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0032094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	210	790	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.170309794057428	2	FACETS	1	0.984	1	0.601	0.558	0.646	INDETERMINATE	1	TRUE	0	0.337714292199442	2		790	1035	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248711	212248711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	59	522	1	ENST00000342788.4:c.3556C>T	p.Pro1186Ser	p.P1186S	ENST00000342788	NM_005235.2	1186	Ccc/Tcc	28/28	1	2	FACETS	0.634	0.546	0.73	0.634	0.546	0.73	SUBCLONAL	1	TRUE	1	0.337714292199442	2		523	551	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911462	134911462	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs775938790	NA	P-0032094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	35	549	0	ENST00000398015.3:c.1927A>G	p.Lys643Glu	p.K643E	ENST00000398015	NM_004441.4	643	Aag/Gag	11/16	1	2	FACETS	0.311	0.254	0.376	0.311	0.254	0.376	SUBCLONAL	1	TRUE	1	0.337714292199442	2		549	666	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355326	81355326	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	27	375	0	ENST00000222390.5:c.1048C>T	p.Arg350Ter	p.R350*	ENST00000222390	NM_000601.4	350	Cga/Tga	9/18	1	2	FACETS	0.43	0.342	0.53	0.43	0.342	0.53	SUBCLONAL	1	TRUE	1	0.337714292199442	2		375	372	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	316	541	0				ENST00000310581	NM_198253.2	-/1132			0.710656378924172	4	FACETS	0.834	0.798	0.87	1	0.994	1	CLONAL	3	TRUE	2	0.890515172857056	4		541	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0032097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	471	719	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.890515172857056	3	FACETS	1	0.991	1	0.568	0.543	0.593	CLONAL	1	TRUE	1	0.890515172857056	3		719	1346	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149982897	149982897	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	155	505	0	ENST00000253339.5:c.3361G>A	p.Glu1121Lys	p.E1121K	ENST00000253339		1121	Gag/Aag	7/7	0.471195286561995	2	FACETS	0.534	0.49	0.579	0.267	0.245	0.29	INDETERMINATE	1	TRUE	0	0.890515172857056	2		505	652	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944872	31944872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	323	474	1	ENST00000340398.3:c.229G>A	p.Asp77Asn	p.D77N	ENST00000340398	NM_001013699.2	77	Gat/Aat	1/1	0.466986576836003	3	FACETS	1	0.992	1	0.622	0.59	0.655	INDETERMINATE	1	TRUE	1	0.890515172857056	3		475	843	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95592977	95592977	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	478	472	2	ENST00000393063.1:c.843C>G	p.Ile281Met	p.I281M	ENST00000393063	NM_030621.3	281	atC/atG	8/28	0.618411012982556	5	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.890515172857056	5		474	1133	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858621	9858621	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs752992319	NA	P-0032097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	142	535	0	ENST00000330684.3:c.2780G>C	p.Arg927Thr	p.R927T	ENST00000330684	NM_001134407.1	927	aGa/aCa	13/13	0.471195286561995	2	FACETS	0.492	0.45	0.537	0.246	0.225	0.269	INDETERMINATE	1	TRUE	0	0.890515172857056	2		535	648	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108203	8108203	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs267605101	NA	P-0032097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	154	538	0	ENST00000585124.1:c.1021C>T	p.Gln341Ter	p.Q341*	ENST00000585124	NM_004217.3	341	Caa/Taa	9/9	0.890515172857056	3	FACETS	0.521	0.476	0.568	0.261	0.238	0.284	SUBCLONAL	1	TRUE	1	0.890515172857056	3		538	959	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117755	70117755	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	158	549	1	ENST00000245479.2:c.223G>C	p.Glu75Gln	p.E75Q	ENST00000245479	NM_000346.3	75	Gag/Cag	1/3	0.458868445178253	3	FACETS	0.547	0.501	0.596	0.274	0.25	0.298	INDETERMINATE	1	TRUE	1	0.890515172857056	3		550	937	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252766	10252766	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	163	581	0	ENST00000340748.4:c.3199G>T	p.Asp1067Tyr	p.D1067Y	ENST00000340748		1067	Gac/Tac	29/40	0.628523336332149	4	FACETS	0.52	0.476	0.567	0.173	0.158	0.189	SUBCLONAL	1	TRUE	1	0.890515172857056	4		581	1330	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105636	11105636	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	144	534	0	ENST00000358026.2:c.1552G>C	p.Glu518Gln	p.E518Q	ENST00000358026	NM_001128849.1	518	Gag/Cag	9/36	0.628523336332149	4	FACETS	0.51	0.463	0.558	0.17	0.154	0.186	SUBCLONAL	1	TRUE	1	0.890515172857056	4		534	1200	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319512	62319512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs909417142	NA	P-0032097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	246	810	0	ENST00000360203.5:c.1616C>T	p.Ser539Phe	p.S539F	ENST00000360203	NM_001283009.1	539	tCc/tTc	19/35	0.466986576836003	3	FACETS	0.595	0.554	0.636	0.297	0.277	0.318	INDETERMINATE	1	TRUE	1	0.890515172857056	3		810	1343	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037213	71037213	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	136	387	0	ENST00000318789.4:c.1078G>C	p.Glu360Gln	p.E360Q	ENST00000318789	NM_032682.5	360	Gaa/Caa	14/21	0.516962346654373	1	FACETS	0.417	0.383	0.453	0.417	0.383	0.453	INDETERMINATE	1	TRUE	0	0.890515172857056	1		387	406	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202937	27202937	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	131	503	0	ENST00000380036.4:c.2029C>T	p.Gln677Ter	p.Q677*	ENST00000380036	NM_000459.3	677	Caa/Taa	13/23	0.466986576836003	3	FACETS	0.572	0.519	0.627	0.286	0.259	0.314	INDETERMINATE	1	TRUE	1	0.890515172857056	3		503	744	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578459	+	missense_variant	Missense_Mutation	TNP	CGG	CGG	GGA	novel	NA	P-0032097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	801	717	2	ENST00000269305.4:c.471_473delinsTCC	p.Arg158Pro	p.R158P	ENST00000269305	NM_001126112.2	157	gtCCGc/gtTCCc	5/11	0.890515172857056	3	FACETS	0.966	0.94	0.992	0.966	0.94	0.992	CLONAL	2	TRUE	1	0.890515172857056	3		719	1346	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252155	226252155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	12	96	0	ENST00000366813.1:c.103G>T	p.Gly35Trp	p.G35W	ENST00000366813		35	Ggg/Tgg	1/3	1	2	FACETS	0.635	0.449	0.86	0.635	0.449	0.86	SUBCLONAL	1	TRUE	1	0.290890811883499	2		96	130	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371667	89371667	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	66	577	0	ENST00000301030.4:c.173G>A	p.Arg58Gln	p.R58Q	ENST00000301030	NM_001256183.1	58	cGg/cAg	4/13	1	2	FACETS	0.577	0.499	0.66	0.577	0.499	0.66	SUBCLONAL	1	TRUE	1	0.290890811883499	2		577	787	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866543	56866543	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	74	671	0	ENST00000519728.1:c.790G>C	p.Gly264Arg	p.G264R	ENST00000519728	NM_002350.3	264	Ggt/Cgt	8/13	1	2	FACETS	0.523	0.457	0.596	0.523	0.457	0.596	SUBCLONAL	1	TRUE	1	0.290890811883499	2		671	972	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0032285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	163	373	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.436794192129285	2		373	539	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518301	204518301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1405649744	NA	P-0032285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	101	477	1	ENST00000367182.3:c.964C>T	p.Arg322Cys	p.R322C	ENST00000367182	NM_001278516.1	322	Cgt/Tgt	11/11	0.436794192129285	3	FACETS	0.684	0.611	0.762	0.342	0.305	0.381	SUBCLONAL	1	TRUE	1	0.436794192129285	3		478	824	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876660825	NA	P-0032285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	265	551	0	ENST00000269305.4:c.569C>G	p.Pro190Arg	p.P190R	ENST00000269305	NM_001126112.2	190	cCt/cGt	6/11	NA	2	FACETS	0.931	0.878	0.983			1	INDETERMINATE	2	TRUE	NA	0.436794192129285	2		551	652	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348163	348163	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1436071949	NA	P-0032285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	127	632	1	ENST00000262320.3:c.1343C>T	p.Pro448Leu	p.P448L	ENST00000262320	NM_003502.3	448	cCg/cTg	6/11	0.151324914876619	5	FACETS	0.872	0.788	0.96	0.291	0.262	0.32	INDETERMINATE	1	TRUE	2	0.436794192129285	5		633	1104	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324219	62324221	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0032285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	370	730	0	ENST00000360203.5:c.2716_2718del	p.Glu906del	p.E906del	ENST00000360203	NM_001283009.1	905	cAGGag/cag	29/35	0.151324914876619	5	FACETS	1	0.978	1	0.704	0.667	0.741	INDETERMINATE	2	TRUE	2	0.436794192129285	5		730	1328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863224499	NA	P-0032336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	552	513	0	ENST00000269305.4:c.672+1G>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.549336276859828	3	FACETS	0.988	0.957	1	0.988	0.957	1	CLONAL	3	TRUE	0	0.549091241269179	3		513	865	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281281	15281281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776163983	NA	P-0032336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	365	533	0	ENST00000263388.2:c.4975G>A	p.Val1659Ile	p.V1659I	ENST00000263388	NM_000435.2	1659	Gtc/Atc	27/33	0.529562200523457	3	FACETS	0.947	0.901	0.992	0.947	0.901	0.992	CLONAL	2	TRUE	1	0.549091241269179	3		533	895	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226539	1226539	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	235	523	1	ENST00000326873.7:c.1195C>T	p.Gln399Ter	p.Q399*	ENST00000326873	NM_000455.4	399	Cag/Tag	9/10	0.541026152215837	3	FACETS	0.86	0.801	0.921	0.43	0.4	0.461	CLONAL	1	TRUE	1	0.549091241269179	3		524	1269	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289324	33289324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	74	340	2	ENST00000374542.5:c.228G>A	p.Met76Ile	p.M76I	ENST00000374542	NM_001141970.1	76	atG/atA	3/8	1	2	FACETS	0.667	0.587	0.753	0.667	0.587	0.753	SUBCLONAL	1	TRUE	1	0.549091241269179	2		342	404	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455054	50455054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	225	286	0	ENST00000331340.3:c.601C>T	p.His201Tyr	p.H201Y	ENST00000331340	NM_006060.4	201	Cac/Tac	6/8	0.405300280505526	5	FACETS	0.874	0.821	0.928	0.874	0.821	0.928	CLONAL	3	TRUE	2	0.549091241269179	5		286	570	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933376	39933376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	44	284	0	ENST00000378444.4:c.1223G>A	p.Gly408Glu	p.G408E	ENST00000378444	NM_001123385.1	408	gGg/gAg	4/15	0.431713731495253	2	FACETS	0.225	0.188	0.266			1	SUBCLONAL	1	TRUE	NA	0.549091241269179	2		284	713	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913351	NA	P-0032342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	68	341	0	ENST00000288602.6:c.1397G>A	p.Gly466Glu	p.G466E	ENST00000288602	NM_004333.4	466	gGa/gAa	11/18	1	2	FACETS	0.275	0.239	0.314	0.275	0.239	0.314	SUBCLONAL	1	TRUE	1	0.86906711021485	2		341	569	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228998	36228998	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	219	601	1	ENST00000222270.7:c.7778G>A	p.Arg2593His	p.R2593H	ENST00000222270	NM_014727.1	2593	cGc/cAc	36/37	1	2	FACETS	0.746	0.697	0.795	0.746	0.697	0.795	SUBCLONAL	1	TRUE	1	0.86906711021485	2		602	676	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0032343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	176	540	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.52	2		540	676	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971115	21971133	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTCGGGTGAGAGTGGCG	GGGTCGGGTGAGAGTGGCG	-	rs730881674	NA	P-0032343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	34	364	0	ENST00000304494.5:c.225_243del	p.Ala76CysfsTer64	p.A76Cfs*64	ENST00000304494	NM_000077.4	75	ccCGCCACTCTCACCCGACCC/cc	2/3	1	2	FACETS	0.242	0.197	0.293	0.242	0.197	0.293	SUBCLONAL	1	TRUE	1	0.52	2		364	540	SUCCESS
APC	324	MSKCC	GRCh37	5	112175530	112175530	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	122	293	0	ENST00000257430.4:c.4240del	p.Val1414Ter	p.V1414*	ENST00000257430	NM_000038.5	1413	atG/at	16/16	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.52	2		293	469	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604665	48604665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660045	NA	P-0032343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	60	330	0	ENST00000342988.3:c.1487G>A	p.Arg496His	p.R496H	ENST00000342988	NM_005359.5	496	cGt/cAt	12/12	1	2	FACETS	0.476	0.41	0.547	0.476	0.41	0.547	SUBCLONAL	1	TRUE	1	0.52	2		330	485	SUCCESS
APC	324	MSKCC	GRCh37	5	112164585	112164585	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123116	NA	P-0032343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	115	262	0	ENST00000257430.4:c.1659G>A	p.Trp553Ter	p.W553*	ENST00000257430	NM_000038.5	553	tgG/tgA	14/16	1	2	FACETS	0.903	0.817	0.992	0.903	0.817	0.992	CLONAL	1	TRUE	1	0.52	2		262	490	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350062	81350062	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs759145490	NA	P-0032343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	42	283	0	ENST00000222390.5:c.1270C>T	p.Arg424Cys	p.R424C	ENST00000222390	NM_000601.4	424	Cgt/Tgt	10/18	NA	2	FACETS	0.375	0.313	0.443			1	INDETERMINATE	1	TRUE	NA	0.52	2		283	431	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569301	67569301	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	83	331	0	ENST00000274335.5:c.418G>T	p.Glu140Ter	p.E140*	ENST00000274335		140	Gaa/Taa	2/15	1	2	FACETS	0.579	0.512	0.651	0.579	0.512	0.651	SUBCLONAL	1	TRUE	1	0.52	2		331	551	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631153	69631153	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	124	432	0	ENST00000334134.2:c.259G>T	p.Ala87Ser	p.A87S	ENST00000334134	NM_005247.2	87	Gcc/Tcc	2/3	1	2	FACETS	0.566	0.512	0.624	0.566	0.512	0.624	SUBCLONAL	1	TRUE	1	0.52	2		432	842	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119669	108119669	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	28	122	0	ENST00000278616.4:c.1075G>T	p.Glu359Ter	p.E359*	ENST00000278616	NM_000051.3	359	Gaa/Taa	9/63	1	2	FACETS	0.479	0.384	0.585	0.479	0.384	0.585	SUBCLONAL	1	TRUE	1	0.52	2		122	225	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175490	108175490	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	188	341	0	ENST00000278616.4:c.5585T>C	p.Leu1862Pro	p.L1862P	ENST00000278616	NM_000051.3	1862	cTt/cCt	37/63	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.52	2		341	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576663	7577000	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAATATATATTATGGTATAAGTTGGTGTTCTGAAGTTAGTTAGCTACAACCAGGAGCCATTGTCTTTGAGGCATCACTGCCCCCTGATGGCAAATGCCCCAATTGCAGGTAAAACAGTCAAGAAGAAAACGGCATTTTGAGTGTTAGACTGGAAACTTTCCACTTGATAAGAGGTCCCAAGACTTAGTACCTGAAGGGTGAAATATTCTCCATCCAGTGGTTTCTTCTTTGGCTGGGGAGAGGAGCTGGTGTTGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAAGTGAATCTGAGGCATAACTGCACCCTTGGTCTCCTCCACCGCTT	AAATATATATTATGGTATAAGTTGGTGTTCTGAAGTTAGTTAGCTACAACCAGGAGCCATTGTCTTTGAGGCATCACTGCCCCCTGATGGCAAATGCCCCAATTGCAGGTAAAACAGTCAAGAAGAAAACGGCATTTTGAGTGTTAGACTGGAAACTTTCCACTTGATAAGAGGTCCCAAGACTTAGTACCTGAAGGGTGAAATATTCTCCATCCAGTGGTTTCTTCTTTGGCTGGGGAGAGGAGCTGGTGTTGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAAGTGAATCTGAGGCATAACTGCACCCTTGGTCTCCTCCACCGCTT	-	novel	NA	P-0032343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	122	385	0	ENST00000269305.4:c.919+19_993+190del		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	0.175968083968733	2	FACETS	0.69	0.625	0.759	0.345	0.312	0.38	INDETERMINATE	1	TRUE	0	0.52	2		385	680	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665336	117665336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1404057865	NA	P-0032343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	169	402	0	ENST00000368508.3:c.4411G>A	p.Ala1471Thr	p.A1471T	ENST00000368508	NM_002944.2	1471	Gcc/Acc	27/43	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.52	2		402	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0032425-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	413	760	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.683595270057346	2		760	558	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0032425-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	142	565	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.98	0.901	1	0.98	0.901	1	CLONAL	1	TRUE	1	0.683595270057346	2		565	424	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440126	99440126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1180612681	NA	P-0032425-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	513	367	0	ENST00000268035.6:c.1094G>A	p.Arg365Gln	p.R365Q	ENST00000268035	NM_000875.3	365	cGa/cAa	4/21	0.686456097896551	4	FACETS	1	0.992	1			1	CLONAL	4	TRUE	NA	0.683595270057346	4		367	613	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845371	89845371	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201212806	NA	P-0032425-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	225	569	0	ENST00000389301.3:c.1756G>A	p.Ala586Thr	p.A586T	ENST00000389301	NM_000135.2	586	Gcc/Acc	19/43	0.687265976415065	3	FACETS	1	0.974	1	0.542	0.506	0.579	CLONAL	1	TRUE	1	0.683595270057346	3		569	815	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160394	108160409	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGCACAGAATTCTT	GAAGCACAGAATTCTT	-	novel	NA	P-0032425-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	117	411	0	ENST00000278616.4:c.4302_4317del	p.His1436TyrfsTer10	p.H1436Yfs*10	ENST00000278616	NM_000051.3	1434	aaGAAGCACAGAATTCTT/aa	29/63	0.687265976415065	3	FACETS	0.953	0.864	1	0.476	0.432	0.523	CLONAL	1	TRUE	1	0.683595270057346	3		411	482	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120693	115120693	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032425-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	171	698	0	ENST00000257566.3:c.313G>T	p.Val105Leu	p.V105L	ENST00000257566	NM_016569.3	105	Gtg/Ttg	1/8	0.687265976415065	3	FACETS	0.939	0.866	1	0.469	0.433	0.507	CLONAL	1	TRUE	1	0.683595270057346	3		698	715	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640824	3640824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1478383926	NA	P-0032425-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	209	668	1	ENST00000294008.3:c.2815C>T	p.Arg939Trp	p.R939W	ENST00000294008	NM_032444.2	939	Cgg/Tgg	12/15	0.687265976415065	4	FACETS	1	0.952	1	0.258	0.239	0.278	CLONAL	1	TRUE	0	0.683595270057346	4		669	997	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264659	46264659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149192951	NA	P-0032425-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	106	326	2	ENST00000371998.3:c.1529C>T	p.Ser510Phe	p.S510F	ENST00000371998		510	tCt/tTt	12/23	0.683595270057346	8	FACETS	1	0.913	1			1	CLONAL	1	TRUE	NA	0.683595270057346	8		328	925	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092936	29092936	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032425-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	171	585	1	ENST00000328354.6:c.1048C>A	p.Pro350Thr	p.P350T	ENST00000328354	NM_007194.3	350	Cca/Aca	10/15	0.287483139510878	6	FACETS	1	0.988	1	0.472	0.434	0.511	INDETERMINATE	1	TRUE	3	0.683595270057346	6		586	837	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519990	NA	P-0032436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	282	453	0	ENST00000269305.4:c.796G>C	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Cga	8/11	0.542449996339753	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.542449996339753	2		453	488	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618428	37618458	+	frameshift_variant	Frame_Shift_Del	DEL	GTCACCGCTTGGTATCGAAGCACAAGCGGCA	GTCACCGCTTGGTATCGAAGCACAAGCGGCA	-	novel	NA	P-0032474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	320	417	0	ENST00000447079.4:c.104_134del	p.Arg35LeufsTer12	p.R35Lfs*12	ENST00000447079	NM_015083.1	35	cGTCACCGCTTGGTATCGAAGCACAAGCGGCAt/ct	1/14	0.834331442067695	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.834331442067695	1		417	436	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342389	70342389	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	441	373	0	ENST00000374080.3:c.1280del	p.Gln427ArgfsTer99	p.Q427Rfs*99	ENST00000374080		427	cAg/cg	9/45	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.834331442067695	1		373	550	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0032477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	93	344	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.160872288600208	3	FACETS	1	0.9	1	0.506	0.45	0.566	INDETERMINATE	1	TRUE	1	0.308390761821014	3		344	688	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0032477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	153	660	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.29447974647625	1	FACETS	0.925	0.846	1	0.925	0.846	1	CLONAL	1	TRUE	0	0.308390761821014	1		660	907	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918987	76918987	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	53	525	0	ENST00000373344.5:c.4004G>C	p.Arg1335Thr	p.R1335T	ENST00000373344	NM_000489.3	1335	aGa/aCa	12/35	1	2	FACETS	0.429	0.364	0.499	0.429	0.364	0.499	SUBCLONAL	1	TRUE	1	0.308390761821014	2		525	802	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0032613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	791	471	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.303664454443829	2	FACETS	1	0.998	1	1	0.998	1	INDETERMINATE	2	TRUE	0	0.73	2		471	901	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0032613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	99	326	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.296531116313405	1	FACETS	0.532	0.48	0.585	0.532	0.48	0.585	INDETERMINATE	1	TRUE	0	0.73	1		326	324	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814303	76814306	+	frameshift_variant	Frame_Shift_Del	DEL	ATAA	ATAA	-	novel	NA	P-0032613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	191	154	0	ENST00000373344.5:c.6338_6341del	p.Phe2113SerfsTer9	p.F2113Sfs*9	ENST00000373344	NM_000489.3	2113	tTTATc/tc	29/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.73	1		154	236	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354013	15354013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	96	262	0	ENST00000263377.2:c.2867C>T	p.Pro956Leu	p.P956L	ENST00000263377	NM_058243.2	956	cCc/cTc	14/20	1	2	FACETS	0.993	0.898	1	0.993	0.898	1	CLONAL	1	TRUE	1	0.73	2		262	265	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913351	NA	P-0032829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	26	341	0	ENST00000288602.6:c.1397G>A	p.Gly466Glu	p.G466E	ENST00000288602	NM_004333.4	466	gGa/gAa	11/18	1	2	FACETS	0.518	0.409	0.643	0.518	0.409	0.643	SUBCLONAL	1	TRUE	1	0.18	2		341	558	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274911	41274911	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs868651538	NA	P-0032829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	69	390	0	ENST00000349496.5:c.1161T>A	p.Asn387Lys	p.N387K	ENST00000349496	NM_001904.3	387	aaT/aaA	8/15	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.18	2		390	628	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105581	27105582	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	68	483	0	ENST00000324856.7:c.5195dup	p.Glu1733GlyfsTer3	p.E1733Gfs*3	ENST00000324856	NM_006015.4	1731	tta/ttAa	20/20	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.18	2		483	681	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971099	21971103	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCA	GGGCA	-	novel	NA	P-0032829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	27	270	0	ENST00000304494.5:c.255_259del	p.Ala86GlyfsTer32	p.A86Gfs*32	ENST00000304494	NM_000077.4	85	gcTGCCCgg/gcgg	2/3	1	2	FACETS	0.857	0.682	1	0.857	0.682	1	CLONAL	1	TRUE	1	0.18	2		270	350	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117757	115117757	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	25	290	0	ENST00000257566.3:c.678T>A	p.Asp226Glu	p.D226E	ENST00000257566	NM_016569.3	226	gaT/gaA	3/8	1	2	FACETS	0.624	0.491	0.778	0.624	0.491	0.778	SUBCLONAL	1	TRUE	1	0.18	2		290	445	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728798	190728798	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs201205478	NA	P-0032966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	108	322	0	ENST00000441310.2:c.2186A>G	p.Asn729Ser	p.N729S	ENST00000441310	NM_000534.4	729	aAt/aGt	10/13	1	2	FACETS	0.864	0.781	0.95	0.864	0.781	0.95	CLONAL	1	TRUE	1	0.617354248853302	2		322	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0033000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	144	660	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.211003821199427	2	FACETS	1	0.986	1	0.708	0.649	0.77	INDETERMINATE	1	TRUE	0	0.358647783891076	2		660	567	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0033000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	38	418	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.358647783891076	2		418	157	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099187	157099195	+	inframe_deletion	In_Frame_Del	DEL	GCGGCGGCA	GCGGCGGCA	-	rs769480864	NA	P-0033000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	54	284	0	ENST00000346085.5:c.133_141del	p.Ala45_Ala47del	p.A45_A47del	ENST00000346085	NM_020732.3	42	GCGGCGGCA/-	1/20	0.258277175510502	4	FACETS	1	0.917	1	0.551	0.473	0.637	CLONAL	1	TRUE	2	0.358647783891076	4		284	371	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845757	68845757	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587780784	NA	P-0033000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	71	293	0	ENST00000261769.5:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000261769	NM_004360.3	335	Cga/Tga	7/16	0.313496085644851	3	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	1	0.358647783891076	3		293	213	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32905152	32905152	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	26	295	0	ENST00000380152.3:c.778G>C	p.Glu260Gln	p.E260Q	ENST00000380152		260	Gaa/Caa	9/27	1	2	FACETS	0.767	0.612	0.942	0.767	0.612	0.942	CLONAL	1	TRUE	1	0.358647783891076	2		295	189	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819225	3819225	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	86	444	0	ENST00000262367.5:c.3010G>C	p.Glu1004Gln	p.E1004Q	ENST00000262367	NM_004380.2	1004	Gag/Cag	15/31	0.313496085644851	3	FACETS	0.957	0.848	1	0.478	0.424	0.537	CLONAL	1	TRUE	1	0.358647783891076	3		444	591	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861892	57861892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376293205	NA	P-0033000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	36	475	0	ENST00000228682.2:c.1193G>A	p.Arg398His	p.R398H	ENST00000228682	NM_005269.2	398	cGt/cAt	10/12	0.358647783891076	5	FACETS	0.651	0.535	0.782	0.217	0.178	0.261	SUBCLONAL	1	TRUE	2	0.358647783891076	5		475	474	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117313	115117315	+	inframe_deletion	In_Frame_Del	DEL	ATC	ATC	-	novel	NA	P-0033000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	26	243	0	ENST00000257566.3:c.859_861del	p.Asp287del	p.D287del	ENST00000257566	NM_016569.3	287	GAT/-	4/8	1	2	FACETS	0.642	0.511	0.79	0.642	0.511	0.79	SUBCLONAL	1	TRUE	1	0.358647783891076	2		243	226	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812305	212812305	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	10	234	0	ENST00000342788.4:c.271C>G	p.Leu91Val	p.L91V	ENST00000342788	NM_005235.2	91	Ctt/Gtt	3/28	0.211003821199427	2	FACETS	0.379	0.257	0.531	0.19	0.128	0.266	INDETERMINATE	1	TRUE	0	0.358647783891076	2		234	147	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561469	9561469	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	104	417	0	ENST00000353224.5:c.313C>G	p.Pro105Ala	p.P105A	ENST00000353224	NM_177990.2	105	Cca/Gca	4/10	0.216447795224768	4	FACETS	0.897	0.809	0.99	0.897	0.809	0.99	CLONAL	2	TRUE	2	0.358647783891076	4		417	439	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951863	2951863	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	30	605	0	ENST00000396946.4:c.3087G>C	p.Lys1029Asn	p.K1029N	ENST00000396946	NM_032415.4	1029	aaG/aaC	23/25	0.258277175510502	4	FACETS	0.402	0.323	0.492	0.201	0.161	0.246	SUBCLONAL	1	TRUE	2	0.358647783891076	4		605	566	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918872	76918875	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CTTT	CTTT	-	novel	NA	P-0033710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	119	591	0	ENST00000373344.5:c.4116_4119del	p.Lys1373Ter	p.K1373*	ENST00000373344	NM_000489.3	1372	agAAAG/ag	12/35	0.696749802998307	1	FACETS	0.863	0.794	0.932	0.863	0.794	0.932	CLONAL	1	TRUE	0	0.696749802998307	1		591	258	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968233	134968233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753895808	NA	P-0033924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	127	566	0	ENST00000398015.3:c.2746G>A	p.Val916Met	p.V916M	ENST00000398015	NM_004441.4	916	Gtg/Atg	15/16	1	2	FACETS	0.89	0.805	0.978	0.89	0.805	0.978	CLONAL	1	TRUE	1	0.32119291725109	2		566	889	SUCCESS
APC	324	MSKCC	GRCh37	5	112174253	112174253	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	103	423	1	ENST00000257430.4:c.2962G>T	p.Glu988Ter	p.E988*	ENST00000257430	NM_000038.5	988	Gaa/Taa	16/16	0.286253962086199	1	FACETS	0.94	0.843	1	0.94	0.843	1	CLONAL	1	TRUE	0	0.32119291725109	1		424	573	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608544	28608544	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs763688464	NA	P-0033924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	307	507	0	ENST00000241453.7:c.1598G>A	p.Gly533Asp	p.G533D	ENST00000241453	NM_004119.2	533	gGc/gAc	13/24	0.32119291725109	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.32119291725109	3		507	1033	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	189	656	0	ENST00000269305.4:c.659del	p.Tyr220LeufsTer27	p.Y220Lfs*27	ENST00000269305	NM_001126112.2	220	tAt/tt	6/11	0.312417231748384	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.32119291725109	1		656	903	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723144	49723148	+	frameshift_variant	Frame_Shift_Del	DEL	CGGTT	CGGTT	-	novel	NA	P-0033924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	146	578	0	ENST00000449682.2:c.1268_1272del	p.Glu423AlafsTer16	p.E423Afs*16	ENST00000449682	NM_020998.3	423	gAACCG/g	11/18	1	2	FACETS	0.988	0.901	1	0.988	0.901	1	CLONAL	1	TRUE	1	0.32119291725109	2		578	920	SUCCESS
APC	324	MSKCC	GRCh37	5	112176427	112176427	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	67	304	0	ENST00000257430.4:c.5136A>C	p.Glu1712Asp	p.E1712D	ENST00000257430	NM_000038.5	1712	gaA/gaC	16/16	0.286253962086199	1	FACETS	0.744	0.648	0.847	0.744	0.648	0.847	SUBCLONAL	1	TRUE	0	0.32119291725109	1		304	471	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741986	145741986	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	149	610	0	ENST00000428558.2:c.517C>G	p.Gln173Glu	p.Q173E	ENST00000428558	NM_004260.3	173	Cag/Gag	5/22	0.32119291725109	4	FACETS	0.916	0.835	1	0.305	0.278	0.334	CLONAL	1	TRUE	1	0.32119291725109	4		610	1338	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544748	65544748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	8	529	0	ENST00000358664.4:c.178C>T	p.Arg60Trp	p.R60W	ENST00000358664	NM_002382.4	60	Cgg/Tgg	4/5	0.181886641025588	4	FACETS	0.129	0.082	0.19	0.065	0.041	0.095	INDETERMINATE	1	TRUE	2	0.524304077596478	4		529	360	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976149	7976149	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	110	693	0	ENST00000319144.4:c.2046C>A	p.Cys682Ter	p.C682*	ENST00000319144	NM_001139.2	682	tgC/tgA	15/15	0.273044539454239	4	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.524304077596478	4		693	468	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127933435	127933435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	100	450	0	ENST00000373547.4:c.100C>T	p.Leu34Phe	p.L34F	ENST00000373547	NM_002721.4	34	Ctc/Ttc	2/7	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.524304077596478	2		450	343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0034184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	359	760	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.696396941397629	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.696396941397629	1		760	639	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0034184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	199	303	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	0.696396941397629	1	FACETS	0.929	0.873	0.984	0.929	0.873	0.984	CLONAL	1	TRUE	0	0.696396941397629	1		303	401	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930730	32930730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs74047012	NA	P-0034184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	49	596	0	ENST00000380152.3:c.7601C>T	p.Ala2534Val	p.A2534V	ENST00000380152		2534	gCg/gTg	15/27	0.696396941397629	1	FACETS	0.173	0.146	0.202	0.173	0.146	0.202	SUBCLONAL	1	TRUE	0	0.696396941397629	1		596	531	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785514	50785514	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0034184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	319	501	0	ENST00000398568.2:c.505-1G>A		p.X169_splice	ENST00000398568	NM_001042412.1	169			NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.696396941397629	2		501	753	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772310	68772310	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	314	732	0	ENST00000261769.5:c.159del	p.Arg54GlufsTer2	p.R54Efs*2	ENST00000261769	NM_004360.3	53	ggC/gg	2/16	0.696396941397629	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.696396941397629	1		732	576	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878863	151878863	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1563288201	NA	P-0034190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	279	629	0	ENST00000262189.6:c.6082C>T	p.Arg2028Ter	p.R2028*	ENST00000262189	NM_170606.2	2028	Cga/Tga	36/59	0.404151882897983	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.404151882897983	3		629	697	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427837	49427895	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGCTTTCCCCCACCTGATCCAGTTGTTTCTGGATCTTGCTCTGCTGCTCTGTAACCAGC	TGCTTTCCCCCACCTGATCCAGTTGTTTCTGGATCTTGCTCTGCTGCTCTGTAACCAGC	-	novel	NA	P-0034190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	98	703	0	ENST00000301067.7:c.10695_10740+13del		p.X3565_splice	ENST00000301067	NM_003482.3	3565		38/54	0.275838878947383	3	FACETS	0.756	0.674	0.843	0.378	0.337	0.422	SUBCLONAL	1	TRUE	1	0.404151882897983	3		703	771	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023181	33023181	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	68	606	0	ENST00000300177.4:c.290A>G	p.Gln97Arg	p.Q97R	ENST00000300177	NM_001191322.1	97	cAg/cGg	2/2	0.404151882897983	3	FACETS	0.657	0.571	0.749	0.219	0.19	0.25	SUBCLONAL	1	TRUE	0	0.404151882897983	3		606	616	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957901	1957901	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	66	371	0	ENST00000382891.5:c.2867G>C	p.Arg956Thr	p.R956T	ENST00000382891	NM_133335.3	956	aGa/aCa	15/22	0.404151882897983	3	FACETS	0.818	0.712	0.933	0.409	0.356	0.467	CLONAL	1	TRUE	1	0.404151882897983	3		371	480	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045670	26045670	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	58	330	0	ENST00000540144.1:c.32C>G	p.Ser11Cys	p.S11C	ENST00000540144	NM_003531.2	11	tCt/tGt	1/1	1	2	FACETS	0.511	0.442	0.587	0.511	0.442	0.587	SUBCLONAL	1	TRUE	1	0.644274715838423	2		330	352	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373791	118373791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	135	369	0	ENST00000534358.1:c.7184C>T	p.Ser2395Phe	p.S2395F	ENST00000534358	NM_005933.3	2395	tCt/tTt	27/36	1	2	FACETS	0.998	0.915	1	0.998	0.915	1	CLONAL	1	TRUE	1	0.644274715838423	2		369	420	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39713178	39713178	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs957960003	NA	P-0034327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	112	303	1	ENST00000361337.2:c.584C>T	p.Pro195Leu	p.P195L	ENST00000361337	NM_003286.2	195	cCg/cTg	8/21	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.644274715838423	2		304	340	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696240	52696240	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757924256	NA	P-0034327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	193	812	1	ENST00000394830.3:c.437G>A	p.Arg146Gln	p.R146Q	ENST00000394830	NM_018313.4	146	cGa/cAa	5/30	1	2	FACETS	0.579	0.536	0.625	0.579	0.536	0.625	SUBCLONAL	1	TRUE	1	0.644274715838423	2		813	1034	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0034500-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	268	665	1	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.48375016456335	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.48375016456335	2		666	497	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0034500-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	190	371	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.48375016456335	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	3	TRUE	0	0.48375016456335	3		371	322	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168695	32168695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143103753	NA	P-0034500-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	105	806	0	ENST00000375023.3:c.4228C>T	p.Arg1410Cys	p.R1410C	ENST00000375023	NM_004557.3	1410	Cgc/Tgc	23/30	0.328091792927876	4	FACETS	0.849	0.76	0.942	0.424	0.38	0.471	CLONAL	1	TRUE	2	0.48375016456335	4		806	759	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026137	71026138	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034500-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	188	395	0	ENST00000318789.4:c.1484dup	p.Thr496HisfsTer21	p.T496Hfs*21	ENST00000318789	NM_032682.5	495	ttc/ttTc	17/21	0.412995957537263	3	FACETS	0.973	0.907	1	0.973	0.907	1	CLONAL	2	TRUE	1	0.48375016456335	3		395	496	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672294	30672294	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034500-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	127	822	0	ENST00000376406.3:c.4666A>G	p.Thr1556Ala	p.T1556A	ENST00000376406	NM_014641.2	1556	Act/Gct	10/15	0.328091792927876	4	FACETS	0.931	0.843	1	0.465	0.421	0.512	CLONAL	1	TRUE	2	0.48375016456335	4		822	837	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772893	135772894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0034500-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	232	631	0	ENST00000298552.3:c.2728_2729dup	p.Leu910PhefsTer22	p.L910Ffs*22	ENST00000298552	NM_001162426.1	910	ttg/ttTTg	21/23	0.48375016456335	2	FACETS	0.933	0.879	0.987	0.933	0.879	0.987	CLONAL	2	TRUE	0	0.48375016456335	2		631	514	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	53	388	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.276855110098508	2		388	350	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	84	495	1	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.276855110098508	1	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	0	0.276855110098508	1		496	517	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986928	36986928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	88	392	2	ENST00000354822.5:c.761C>T	p.Ala254Val	p.A254V	ENST00000354822	NM_001079668.2	254	gCg/gTg	3/3	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.276855110098508	2		394	507	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061202	38061203	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCGGCGCAAGTA	novel	NA	P-0034539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	23	299	0	ENST00000250448.2:c.775_786dup	p.Tyr259_Arg262dup	p.Y259_R262dup	ENST00000250448	NM_004496.3	259	-/TACTTGCGCCGC	2/2	1	2	FACETS	0.385	0.299	0.484	0.385	0.299	0.484	SUBCLONAL	1	TRUE	1	0.276855110098508	2		299	432	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148875	119148875	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs397517076	NA	P-0034638-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	36	250	0	ENST00000264033.4:c.1096-1G>T		p.X366_splice	ENST00000264033	NM_005188.3	366			1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.23	2		250	250	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484597	57484597	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs137854533	NA	P-0034638-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	41	467	0	ENST00000371085.3:c.681G>T	p.Gln227His	p.Q227H	ENST00000371085	NM_000516.4	227	caG/caT	9/13	1	2	FACETS	0.657	0.546	0.779	0.657	0.546	0.779	SUBCLONAL	1	TRUE	1	0.23	2		467	543	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038783	47038783	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0034638-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	69	710	1	ENST00000377604.3:c.790G>T	p.Glu264Ter	p.E264*	ENST00000377604	NM_001204468.1	264	Gag/Tag	9/24	1	2	FACETS	0.927	0.808	1	0.927	0.808	1	CLONAL	1	TRUE	1	0.23	2		711	647	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730831	40730831	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs372700928	NA	P-0034638-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	92	673	0	ENST00000373198.4:c.3704G>T	p.Arg1235Leu	p.R1235L	ENST00000373198	NM_133170.3	1235	cGc/cTc	27/32	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.23	2		673	746	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200993	108200993	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1565529541	NA	P-0034638-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	48	344	0	ENST00000278616.4:c.7360G>C	p.Ala2454Pro	p.A2454P	ENST00000278616	NM_000051.3	2454	Gca/Cca	50/63	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.23	2		344	402	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031876	10031876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1452471642	NA	P-0034638-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	62	582	0	ENST00000330684.3:c.947C>T	p.Ala316Val	p.A316V	ENST00000330684	NM_001134407.1	316	gCc/gTc	3/13	1	2	FACETS	0.897	0.775	1	0.897	0.775	1	CLONAL	1	TRUE	1	0.23	2		582	601	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0034638-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	79	635	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	1	2	FACETS	0.938	0.825	1	0.938	0.825	1	CLONAL	1	TRUE	1	0.25	2		635	674	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0034638-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	60	604	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	1	2	FACETS	0.779	0.671	0.897	0.779	0.671	0.897	SUBCLONAL	1	TRUE	1	0.25	2		604	616	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745555	162745555	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034638-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	46	518	0	ENST00000367921.3:c.1970T>A	p.Met657Lys	p.M657K	ENST00000367921	NM_006182.2	657	aTg/aAg	15/18	0.301183101996238	3	FACETS	0.775	0.653	0.911	0.388	0.326	0.456	CLONAL	1	TRUE	1	0.25	3		518	534	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857428	68857428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034638-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	84	551	1	ENST00000261769.5:c.2063G>A	p.Cys688Tyr	p.C688Y	ENST00000261769	NM_004360.3	688	tGt/tAt	13/16	1	2	FACETS	0.942	0.832	1	0.942	0.832	1	CLONAL	1	TRUE	1	0.25	2		552	713	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333323	70333324	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0034638-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	88	837	2	ENST00000373644.4:c.1228_1229delinsTT	p.Gly410Phe	p.G410F	ENST00000373644	NM_030625.2	410	GGt/TTt	2/12	1	2	FACETS	0.899	0.796	1	0.899	0.796	1	CLONAL	1	TRUE	1	0.25	2		839	783	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337681	73337681	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034638-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	30	229	0	ENST00000377767.4:c.2035C>T	p.His679Tyr	p.H679Y	ENST00000377767	NM_014953.3	679	Cat/Tat	16/21	1	2	FACETS	0.825	0.666	1	0.825	0.666	1	CLONAL	1	TRUE	1	0.25	2		229	291	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218453	36218453	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034638-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	78	751	0	ENST00000222270.7:c.4232G>T	p.Gly1411Val	p.G1411V	ENST00000222270	NM_014727.1	1411	gGg/gTg	16/37	1	2	FACETS	0.918	0.806	1	0.918	0.806	1	CLONAL	1	TRUE	1	0.25	2		751	680	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416469	29416469	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034638-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	98	941	0	ENST00000389048.3:c.4484C>A	p.Ser1495Tyr	p.S1495Y	ENST00000389048	NM_004304.4	1495	tCc/tAc	29/29	1	2	FACETS	0.873	0.778	0.975	0.873	0.778	0.975	CLONAL	1	TRUE	1	0.25	2		941	898	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023704	31023704	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034638-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	92	757	0	ENST00000375687.4:c.3189G>T	p.Gln1063His	p.Q1063H	ENST00000375687	NM_015338.5	1063	caG/caT	13/13	1	2	FACETS	0.925	0.821	1	0.925	0.821	1	CLONAL	1	TRUE	1	0.25	2		757	796	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827952	40827952	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034638-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	38	581	0	ENST00000373198.4:c.2476C>A	p.Pro826Thr	p.P826T	ENST00000373198	NM_133170.3	826	Ccc/Acc	17/32	1	2	FACETS	0.525	0.433	0.628	0.525	0.433	0.628	SUBCLONAL	1	TRUE	1	0.25	2		581	579	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521616	89521616	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034638-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	36	411	0	ENST00000336596.2:c.2693C>T	p.Pro898Leu	p.P898L	ENST00000336596	NM_005233.5	898	cCa/cTa	16/17	0.251745692394276	1	FACETS	0.627	0.516	0.751	0.627	0.516	0.751	SUBCLONAL	1	TRUE	0	0.25	1		411	402	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151919153	151919153	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	rs1470642402	NA	P-0034638-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	23	276	0	ENST00000262189.6:c.3434-2A>T		p.X1145_splice	ENST00000262189	NM_170606.2	1145			1	2	FACETS	0.626	0.488	0.784	0.626	0.488	0.784	SUBCLONAL	1	TRUE	1	0.25	2		276	294	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499759	8499759	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1297546114	NA	P-0034638-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	65	525	0	ENST00000356435.5:c.2210C>T	p.Pro737Leu	p.P737L	ENST00000356435		737	cCc/cTc	14/35	0.256454231798065	1	FACETS	0.775	0.672	0.887	0.775	0.672	0.887	SUBCLONAL	1	TRUE	0	0.25	1		525	587	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343005	70343005	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034638-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	73	725	1	ENST00000374080.3:c.1546C>G	p.Arg516Gly	p.R516G	ENST00000374080		516	Cgt/Ggt	11/45	1	2	FACETS	0.752	0.656	0.855	0.752	0.656	0.855	SUBCLONAL	1	TRUE	1	0.25	2		726	777	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349640	70349640	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034638-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	51	775	0	ENST00000374080.3:c.3802A>T	p.Ile1268Phe	p.I1268F	ENST00000374080		1268	Atc/Ttc	27/45	1	2	FACETS	0.544	0.461	0.635	0.544	0.461	0.635	SUBCLONAL	1	TRUE	1	0.25	2		775	750	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827936	40827936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	91	565	0	ENST00000373198.4:c.2492G>A	p.Ser831Asn	p.S831N	ENST00000373198	NM_133170.3	831	aGc/aAc	17/32	1	2	FACETS	0.982	0.873	1	0.982	0.873	1	CLONAL	1	TRUE	1	0.316855761188903	2		565	585	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183733	10183733	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	112	698	0	ENST00000256474.2:c.202del	p.Ser68ArgfsTer91	p.S68Rfs*91	ENST00000256474	NM_000551.3	68	Tcg/cg	1/3	0.316855761188903	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.316855761188903	1		698	451	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597499	52597499	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	63	353	0	ENST00000394830.3:c.3811del	p.Val1271PhefsTer17	p.V1271Ffs*17	ENST00000394830	NM_018313.4	1271	Gtt/tt	25/30	0.316855761188903	1	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	0	0.316855761188903	1		353	314	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231773	36231773	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1569061762	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	165	471	0	ENST00000300305.3:c.611G>A	p.Arg204Gln	p.R204Q	ENST00000300305		204	cGa/cAa	5/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.547446432058758	2		471	524	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	21	528	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.189	0.145	0.241	0.189	0.145	0.241	SUBCLONAL	1	TRUE	1	0.547446432058758	2		528	405	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	110	373	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.547446432058758	2		373	398	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	267	360	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.547446432058758	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.547446432058758	2		360	391	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	119	342	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.547446432058758	2		342	362	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	19	335	1	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.196	0.148	0.252	0.196	0.148	0.252	SUBCLONAL	1	TRUE	1	0.547446432058758	2		336	355	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699360	47699360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	100	323	0	ENST00000347630.2:c.148G>A	p.Glu50Lys	p.E50K	ENST00000347630	NM_001007230.1	50	Gaa/Aaa	4/11	1	2	FACETS	0.998	0.9	1	0.998	0.9	1	CLONAL	1	TRUE	1	0.547446432058758	2		323	366	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	107	366	1	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	0.783	0.706	0.865	0.783	0.706	0.865	SUBCLONAL	1	TRUE	1	0.547446432058758	2		367	499	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589610	67589612	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	novel	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	73	176	0	ENST00000274335.5:c.1376_1378del	p.Lys459del	p.K459del	ENST00000274335		458	gAAAaa/gaa	10/15	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.547446432058758	2		176	261	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	78	332	1	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.547446432058758	2		333	258	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	177	399	0	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.547446432058758	2		399	535	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755554	39755554	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	110	338	0	ENST00000288319.7:c.1211del	p.Pro404ArgfsTer25	p.P404Rfs*25	ENST00000288319	NM_182918.3	404	cCg/cg	10/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.547446432058758	2		338	307	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046289	128046289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746827111	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	121	363	1	ENST00000285398.2:c.974G>A	p.Arg325Gln	p.R325Q	ENST00000285398	NM_000122.1	325	cGa/cAa	7/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.547446432058758	2		364	392	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099103	27099103	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	70	325	1	ENST00000324856.7:c.3524del	p.Pro1175HisfsTer5	p.P1175Hfs*5	ENST00000324856	NM_006015.4	1173	atC/at	13/20	1	2	FACETS	0.991	0.875	1	0.991	0.875	1	CLONAL	1	TRUE	1	0.547446432058758	2		326	258	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663356	67663356	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	105	277	1	ENST00000264010.4:c.1760del	p.Asn587MetfsTer44	p.N587Mfs*44	ENST00000264010	NM_006565.3	586	gAa/ga	10/12	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.547446432058758	2		278	347	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448297	56448298	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1567880599	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	127	497	0	ENST00000407977.2:c.349dup	p.Arg117ProfsTer8	p.R117Pfs*8	ENST00000407977		117	cgc/cCgc	3/10	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.547446432058758	2		497	443	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272237	15272238	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	94	495	0	ENST00000263388.2:c.6201dup	p.Gly2068ArgfsTer27	p.G2068Rfs*27	ENST00000263388	NM_000435.2	2067	-/C	33/33	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.547446432058758	2		495	313	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683557	29683558	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1060500295	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	72	197	0	ENST00000356175.3:c.7638dup	p.Lys2547GlnfsTer9	p.K2547Qfs*9	ENST00000356175	NM_000267.3	2544	-/C	51/57	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.547446432058758	2		197	231	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268792	98268793	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	146	377	0	ENST00000331920.6:c.290dup	p.Asn97LysfsTer43	p.N97Kfs*43	ENST00000331920	NM_000264.3	97	aac/aaAc	2/24	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.547446432058758	2		377	426	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211862	36211862	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	147	543	0	ENST00000222270.7:c.1613G>A	p.Arg538His	p.R538H	ENST00000222270	NM_014727.1	538	cGt/cAt	3/37	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.547446432058758	2		543	463	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489228	2489228	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	135	497	0	ENST00000355716.4:c.133G>A	p.Asp45Asn	p.D45N	ENST00000355716	NM_003820.2	45	Gac/Aac	2/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.547446432058758	2		497	368	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101255	27101255	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	95	424	0	ENST00000324856.7:c.4537del	p.Ser1513AlafsTer14	p.S1513Afs*14	ENST00000324856	NM_006015.4	1513	Agc/gc	18/20	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.547446432058758	2		424	328	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205520	61205520	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	133	443	0	ENST00000301761.2:c.305T>C	p.Leu102Pro	p.L102P	ENST00000301761	NM_017841.2	102	cTg/cCg	3/4	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.547446432058758	2		443	410	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514460	103514460	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756778477	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	52	211	0	ENST00000355739.4:c.961G>A	p.Val321Met	p.V321M	ENST00000355739	NM_000123.3	321	Gtg/Atg	8/15	1	2	FACETS	0.989	0.855	1	0.989	0.855	1	CLONAL	1	TRUE	1	0.547446432058758	2		211	192	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354517	91354517	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	105	268	0	ENST00000355112.3:c.3957A>G	p.Ile1319Met	p.I1319M	ENST00000355112	NM_000057.2	1319	atA/atG	21/22	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.547446432058758	2		268	318	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831054	72831054	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	116	379	1	ENST00000268489.5:c.5527C>T	p.Gln1843Ter	p.Q1843*	ENST00000268489	NM_006885.3	1843	Cag/Tag	9/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.547446432058758	2		380	344	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097116	11097116	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	76	507	0	ENST00000358026.2:c.607G>A	p.Ala203Thr	p.A203T	ENST00000358026	NM_001128849.1	203	Gcg/Acg	4/36	1	2	FACETS	0.819	0.724	0.92	0.819	0.724	0.92	CLONAL	1	TRUE	1	0.547446432058758	2		507	339	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754705	42754705	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381524812	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	13	173	1	ENST00000222329.4:c.35C>T	p.Pro12Leu	p.P12L	ENST00000222329	NM_006494.2	12	cCg/cTg	2/4	1	2	FACETS	0.413	0.297	0.552	0.413	0.297	0.552	SUBCLONAL	1	TRUE	1	0.547446432058758	2		174	115	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010573	48010574	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	96	427	0	ENST00000234420.5:c.203dup	p.Ala69GlyfsTer21	p.A69Gfs*21	ENST00000234420	NM_000179.2	67	-/A	1/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.547446432058758	2		427	321	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182126	99182126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	69	281	0	ENST00000074304.5:c.2191G>A	p.Asp731Asn	p.D731N	ENST00000074304	NM_001134224.1	731	Gac/Aac	21/26	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.547446432058758	2		281	246	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591082	67591096	+	inframe_deletion	In_Frame_Del	DEL	ATTGACAAACGTATG	ATTGACAAACGTATG	-	novel	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	81	208	0	ENST00000274335.5:c.1676_1690del	p.Ile559_Met563del	p.I559_M563del	ENST00000274335		559	ATTGACAAACGTATG/-	12/15	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.547446432058758	2		208	263	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80109499	80109500	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	130	419	0	ENST00000265081.6:c.2754dup	p.Gly919TrpfsTer29	p.G919Wfs*29	ENST00000265081	NM_002439.4	918	att/aTtt	20/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.547446432058758	2		419	418	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805626	32805626	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	125	567	1	ENST00000374899.4:c.385C>T	p.Gln129Ter	p.Q129*	ENST00000374899	NM_018833.2	129	Cag/Tag	2/12	1	2	FACETS	0.957	0.872	1	0.957	0.872	1	CLONAL	1	TRUE	1	0.547446432058758	2		568	477	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679074	117679074	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770388201	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	122	390	0	ENST00000368508.3:c.3747G>A	p.Met1249Ile	p.M1249I	ENST00000368508	NM_002944.2	1249	atG/atA	24/43	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.547446432058758	2		390	400	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524706	106524709	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	novel	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	52	252	0	ENST00000359195.3:c.2869_2872del	p.Thr957GlufsTer30	p.T957Efs*30	ENST00000359195	NM_002649.2	956	gAGACa/ga	9/11	1	2	FACETS	0.826	0.711	0.949	0.826	0.711	0.949	CLONAL	1	TRUE	1	0.547446432058758	2		252	230	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370972	55370972	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	145	461	0	ENST00000297316.4:c.274G>T	p.Asp92Tyr	p.D92Y	ENST00000297316	NM_022454.3	92	Gac/Tac	1/2	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.547446432058758	2		461	456	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0034881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	203	326	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.928	0.869	0.988	1	0.994	1	CLONAL	2	TRUE	1	0.44015781335401	2		326	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0034881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	756	750	1	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	0.44015781335401	2	FACETS	0.971	0.955	0.987	1	0.998	1	CLONAL	4	TRUE	0	0.44015781335401	2		751	884	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560463	95560463	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555366979	NA	P-0034881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	179	484	0	ENST00000393063.1:c.5126A>G	p.Asp1709Gly	p.D1709G	ENST00000393063	NM_030621.3	1709	gAt/gGt	25/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.44015781335401	2		484	732	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46240714	46240720	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GTCAGTG	GTCAGTG	-	novel	NA	P-0034881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	76	409	0	ENST00000334344.6:c.1576_1580+2del		p.CQW525fs	ENST00000334344	NM_152641.2	525	tGTCAGTGg/tg	12/21	1	2	FACETS	0.539	0.472	0.61	0.539	0.472	0.61	SUBCLONAL	1	TRUE	1	0.44015781335401	2		409	641	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961011	15961011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142717545	NA	P-0035162-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	34	428	0	ENST00000268712.3:c.6209C>T	p.Ser2070Leu	p.S2070L	ENST00000268712	NM_006311.3	2070	tCg/tTg	40/46	1	2	FACETS	0.923	0.771	1	0.923	0.771	1	CLONAL	1	TRUE	1	0.624566277496287	2		428	118	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120363	94120363	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035162-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	41	551	0	ENST00000369303.4:c.688G>T	p.Val230Phe	p.V230F	ENST00000369303	NM_004440.3	230	Gtt/Ttt	3/17	0.572363458696334	3	FACETS	0.809	0.68	0.948	0.404	0.34	0.474	CLONAL	1	TRUE	1	0.624566277496287	3		551	213	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411856	116411880	+	intron_variant	Intron	DEL	CCATGATAGCCGTCTTTAACAAGCT	CCATGATAGCCGTCTTTAACAAGCT	-	novel	NA	P-0035162-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	648	719	0	ENST00000397752.3:c.2888-46_2888-22del		p.*963*	ENST00000397752	NM_000245.2	-/1390			0.624566277496287	13	FACETS	1	0.992	1	1	0.992	1	CLONAL	13	TRUE	0	0.624566277496287	13		719	702	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422702	49422702	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035162-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	21	539	0	ENST00000301067.7:c.14291A>G	p.Glu4764Gly	p.E4764G	ENST00000301067	NM_003482.3	4764	gAg/gGg	45/54	0.572363458696334	3	FACETS	0.849	0.665	1	0.424	0.332	0.527	CLONAL	1	TRUE	1	0.624566277496287	3		539	104	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936268	78936268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035162-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	29	407	0	ENST00000306801.3:c.3700G>A	p.Gly1234Arg	p.G1234R	ENST00000306801	NM_020761.2	1234	Gga/Aga	32/34	0.558061228247712	5	FACETS	0.81	0.654	0.985	0.27	0.218	0.329	CLONAL	1	TRUE	2	0.624566277496287	5		407	222	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960105	134960105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035162-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	15	518	0	ENST00000398015.3:c.2462G>A	p.Gly821Glu	p.G821E	ENST00000398015	NM_004441.4	821	gGa/gAa	13/16	0.559490102953112	4	FACETS	0.406	0.298	0.536	0.203	0.149	0.268	SUBCLONAL	1	TRUE	2	0.624566277496287	4		518	192	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374341	138374341	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035162-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	31	400	1	ENST00000289153.2:c.3103G>A	p.Glu1035Lys	p.E1035K	ENST00000289153	NM_006219.2	1035	Gaa/Aaa	22/22	0.559490102953112	4	FACETS	0.943	0.771	1	0.472	0.385	0.567	CLONAL	1	TRUE	2	0.624566277496287	4		401	171	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423413	116423413	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035162-T08-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	22	409	0	ENST00000397752.3:c.3688T>A	p.Tyr1230Asn	p.Y1230N	ENST00000397752	NM_000245.2	1230	Tat/Aat	19/21	0.624566277496287	13	FACETS	1	0.855	1	0.088	0.068	0.111	CLONAL	1	TRUE	0	0.624566277496287	13		409	274	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491645	56491645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	76	559	2	ENST00000267101.3:c.2537G>T	p.Ser846Ile	p.S846I	ENST00000267101	NM_001982.3	846	aGt/aTt	21/28	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.16	2		561	843	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070573	67070573	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	36	270	0	ENST00000412916.2:c.197T>A	p.Leu66His	p.L66H	ENST00000412916		66	cTc/cAc	3/6	1	2	FACETS	0.976	0.802	1	0.976	0.802	1	CLONAL	1	TRUE	1	0.16	2		270	461	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772217	68772217	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs865838543	NA	P-0035199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	77	931	0	ENST00000261769.5:c.66C>A	p.Cys22Ter	p.C22*	ENST00000261769	NM_004360.3	22	tgC/tgA	2/16	1	2	FACETS	0.965	0.845	1	0.965	0.845	1	CLONAL	1	TRUE	1	0.16	2		931	997	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105848	27105849	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCTCT	novel	NA	P-0035613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	272	626	0	ENST00000324856.7:c.5460_5461insCTCTT	p.Asp1821LeufsTer64	p.D1821Lfs*64	ENST00000324856	NM_006015.4	1820	aat/aaTCTCTt	20/20	1	2	FACETS	0.96	0.906	1	1	0.995	1	CLONAL	2	FALSE	1	0.400075678633795	2		626	708	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431006	49431006	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0035613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	325	709	0	ENST00000301067.7:c.10133C>G	p.Ser3378Ter	p.S3378*	ENST00000301067	NM_003482.3	3378	tCa/tGa	34/54	1	2	FACETS	1	0.974	1	1	0.996	1	CLONAL	2	FALSE	1	0.400075678633795	2		709	781	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434939	49434940	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0035613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	230	538	0	ENST00000301067.7:c.6613dup	p.Ala2205GlyfsTer38	p.A2205Gfs*38	ENST00000301067	NM_003482.3	2205	gcc/gGcc	31/54	1	2	FACETS	0.902	0.847	0.959	1	0.994	1	CLONAL	2	FALSE	1	0.400075678633795	2		538	637	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788617	3788617	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	242	403	0	ENST00000262367.5:c.4337del	p.Arg1446ProfsTer13	p.R1446Pfs*13	ENST00000262367	NM_004380.2	1446	cGc/cc	26/31	1	2	FACETS	0.982	0.924	1	1	0.995	1	CLONAL	2	FALSE	1	0.400075678633795	2		403	616	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0035613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	327	665	1	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.400075678633795	0	FACETS		NA	1			1	NA	3	FALSE	0	0.400075678633795	0		666	415	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246462	41246462	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	86	855	0	ENST00000357654.3:c.1086G>C	p.Glu362Asp	p.E362D	ENST00000357654	NM_007294.3	362	gaG/gaC	10/23	0.400075678633795	1	FACETS	0.371	0.327	0.418	0.371	0.327	0.418	SUBCLONAL	1	FALSE	0	0.400075678633795	1		855	928	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395710	45395710	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	252	450	0	ENST00000262160.6:c.424G>T	p.Glu142Ter	p.E142*	ENST00000262160	NM_005901.5	142	Gaa/Taa	4/11	1	2	FACETS	1	0.963	1	1	0.995	1	CLONAL	2	FALSE	1	0.400075678633795	2		450	613	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	54	285	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	1	2	FACETS	0.511	0.437	0.593	0.511	0.437	0.593	SUBCLONAL	1	FALSE	1	0.400075678633795	2		285	528	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098959	178098959	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519921	NA	P-0035613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	157	326	0	ENST00000397062.3:c.86A>G	p.Asp29Gly	p.D29G	ENST00000397062	NM_006164.4	29	gAt/gGt	2/5	1	2	FACETS	0.866	0.801	0.933	1	0.991	1	CLONAL	2	FALSE	1	0.400075678633795	2		326	453	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266611	198266611	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs755415626	NA	P-0035613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	209	477	0	ENST00000335508.6:c.2225G>A	p.Gly742Asp	p.G742D	ENST00000335508	NM_012433.2	742	gGt/gAt	16/25	1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	FALSE	1	0.400075678633795	2		477	441	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021697	31021697	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	255	538	0	ENST00000375687.4:c.1696G>T	p.Glu566Ter	p.E566*	ENST00000375687	NM_015338.5	566	Gag/Tag	12/13	1	2	FACETS	0.933	0.879	0.989	1	0.995	1	CLONAL	2	FALSE	1	0.400075678633795	2		538	683	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0035613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	322	500	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.112684054011405	4	FACETS	0.998	0.948	1	1	0.995	1	INDETERMINATE	3	FALSE	2	0.400075678633795	4		500	753	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0035613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	175	810	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.979	0.911	1	1	0.993	1	CLONAL	2	FALSE	1	0.400075678633795	2		810	447	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806582	1806582	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	378	695	0	ENST00000260795.2:c.1298C>G	p.Ser433Cys	p.S433C	ENST00000260795		433	tCc/tGc	9/17	1	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	2	FALSE	1	0.400075678633795	2		695	853	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247192	153247192	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	235	424	0	ENST00000281708.4:c.1610T>C	p.Leu537Ser	p.L537S	ENST00000281708	NM_033632.3	537	tTg/tCg	10/12	1	2	FACETS	1	0.979	1	1	0.995	1	CLONAL	2	FALSE	1	0.400075678633795	2		424	542	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0035613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	285	267	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	FALSE	1	0.400075678633795	2		267	599	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350071	81350071	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	244	443	0	ENST00000222390.5:c.1261G>C	p.Asp421His	p.D421H	ENST00000222390	NM_000601.4	421	Gac/Cac	10/18	1	2	FACETS	1	0.976	1	1	0.995	1	CLONAL	2	FALSE	1	0.400075678633795	2		443	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0035633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	324	708	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.598768692399577	2	FACETS	0.932	0.891	0.972	0.932	0.891	0.972	CLONAL	2	TRUE	0	0.602607809910814	2		708	577	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350692	89350692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143279397	NA	P-0035633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	231	859	2	ENST00000301030.4:c.2258C>T	p.Pro753Leu	p.P753L	ENST00000301030	NM_001256183.1	753	cCg/cTg	9/13	0.598768692399577	2	FACETS	0.974	0.911	1	0.487	0.455	0.52	CLONAL	1	TRUE	0	0.602607809910814	2		861	787	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005470	150005470	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	129	414	0	ENST00000253339.5:c.755G>C	p.Arg252Thr	p.R252T	ENST00000253339		252	aGa/aCa	3/7	0.320089962934272	5	FACETS	1	0.962	1	0.372	0.337	0.408	INDETERMINATE	1	TRUE	2	0.602607809910814	5		414	731	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576858	7576858	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	192	487	0	ENST00000269305.4:c.988del	p.Leu330PhefsTer15	p.L330Ffs*15	ENST00000269305	NM_001126112.2	330	Ctt/tt	9/11	0.372936339223643	1	FACETS	0.936	0.869	1	0.936	0.869	1	CLONAL	1	TRUE	0	0.486196023998724	1		487	639	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620674	52620674	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	94	313	0	ENST00000394830.3:c.3079C>T	p.Arg1027Ter	p.R1027*	ENST00000394830	NM_018313.4	1027	Cga/Tga	21/30	0.486074801863979	1	FACETS	0.815	0.732	0.903	0.815	0.732	0.903	CLONAL	1	TRUE	0	0.486196023998724	1		313	359	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942107	17942107	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	229	761	0	ENST00000458235.1:c.2908C>G	p.Leu970Val	p.L970V	ENST00000458235	NM_000215.3	970	Cta/Gta	21/24	0.486196023998724	3	FACETS	0.973	0.906	1	0.487	0.453	0.522	CLONAL	1	TRUE	1	0.486196023998724	3		761	1203	SUCCESS
APC	324	MSKCC	GRCh37	5	112164564	112164565	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTTTTGAGGAATTTGTCTTG	novel	NA	P-0035691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	45	226	0	ENST00000257430.4:c.1640_1659dup	p.Arg554PhefsTer2	p.R554Ffs*2	ENST00000257430	NM_000038.5	546	-/GTTTTGAGGAATTTGTCTTG	14/16	0.432405664424053	1	FACETS	0.527	0.446	0.615	0.527	0.446	0.615	SUBCLONAL	1	TRUE	0	0.486196023998724	1		226	266	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138780	37138780	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	129	420	1	ENST00000373509.5:c.213G>T	p.Lys71Asn	p.K71N	ENST00000373509	NM_002648.3	71	aaG/aaT	3/6	1	2	FACETS	0.954	0.869	1	0.954	0.869	1	CLONAL	1	TRUE	1	0.486196023998724	2		421	556	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0035895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	80	418	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.621828593904338	3	FACETS	0.873	0.773	0.978	0.436	0.386	0.489	CLONAL	1	TRUE	1	0.620811420864585	3		418	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0035895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	248	688	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.538512932434951	2	FACETS	0.799	0.756	0.842	0.799	0.756	0.842	SUBCLONAL	2	TRUE	0	0.620811420864585	2		688	500	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827475	72827475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567512921	NA	P-0035895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	151	850	1	ENST00000268489.5:c.9106C>T	p.Arg3036Trp	p.R3036W	ENST00000268489	NM_006885.3	3036	Cgg/Tgg	9/10	0.553954731881542	3	FACETS	0.919	0.842	0.998	0.459	0.421	0.499	CLONAL	1	TRUE	1	0.620811420864585	3		851	694	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692889	89692889	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	252	473	0	ENST00000371953.3:c.373A>G	p.Lys125Glu	p.K125E	ENST00000371953	NM_000314.4	125	Aaa/Gaa	5/9	0.620811420864585	2	FACETS	0.908	0.863	0.953	0.908	0.863	0.953	CLONAL	2	TRUE	0	0.620811420864585	2		473	447	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554159	63554159	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	217	877	0	ENST00000307078.5:c.580G>C	p.Asp194His	p.D194H	ENST00000307078	NM_004655.3	194	Gat/Cat	2/11	0.538512932434951	2	FACETS	1	0.992	1	0.713	0.67	0.757	CLONAL	1	TRUE	0	0.620811420864585	2		877	490	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526700	106526700	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	166	507	0	ENST00000359195.3:c.2993C>G	p.Ser998Cys	p.S998C	ENST00000359195	NM_002649.2	998	tCt/tGt	10/11	0.548562741828665	2	FACETS	1	0.991	1	0.737	0.687	0.787	CLONAL	1	TRUE	0	0.620811420864585	2		507	363	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0035993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	108	640	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	0.392678956993759	1	FACETS	0.858	0.774	0.947	0.858	0.774	0.947	CLONAL	1	TRUE	0	0.392678956993759	1		640	515	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0035999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	69	466	2	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	0.986	0.858	1	0.986	0.858	1	CLONAL	1	TRUE	1	0.2	2		468	700	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156719	20156719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	73	507	0	ENST00000379607.5:c.38G>A	p.Arg13His	p.R13H	ENST00000379607	NM_001412.3	13	cGc/cAc	2/7	1	1	FACETS	0.764	0.671	0.864	1	0.976	1	SUBCLONAL	2	TRUE	0	0.2	1		507	430	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171431	123171431	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	36	295	0	ENST00000218089.9:c.343C>G	p.Leu115Val	p.L115V	ENST00000218089	NM_001042749.1	115	Ctt/Gtt	6/35	1	1	FACETS	0.736	0.605	0.883	0.736	0.605	0.883	SUBCLONAL	1	TRUE	0	0.2	1		295	440	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0035999-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	83	466	2	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	0.379833040315324	6	FACETS	1	0.963	1	0.844	0.766	0.922	INDETERMINATE	3	FALSE	2	0.715939711709435	6		468	167	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156719	20156719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035999-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	174	507	0	ENST00000379607.5:c.38G>A	p.Arg13His	p.R13H	ENST00000379607	NM_001412.3	13	cGc/cAc	2/7	0.577969129294847	3	FACETS	0.898	0.853	0.941			1	CLONAL	3	FALSE	NA	0.715939711709435	3		507	245	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604715	55604715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373152714	NA	P-0035999-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	35	371	1	ENST00000288135.5:c.2923G>A	p.Asp975Asn	p.D975N	ENST00000288135	NM_000222.2	975	Gat/Aat	21/21	0.379833040315324	6	FACETS	0.904	0.745	1	0.226	0.186	0.271	INDETERMINATE	1	FALSE	2	0.715939711709435	6		372	263	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118501	17118501	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs748878853	NA	P-0035999-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	10	503	0	ENST00000285071.4:c.1430G>A	p.Arg477Gln	p.R477Q	ENST00000285071	NM_144997.5	477	cGa/cAa	12/14	0.512818913282407	3	FACETS	0.214	0.145	0.301	0.107	0.072	0.151	SUBCLONAL	1	FALSE	1	0.715939711709435	3		503	177	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0036226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	91	326	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.893	0.805	0.984	0.893	0.805	0.984	CLONAL	1	TRUE	1	0.780622956413961	2		326	261	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	97	541	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.780622956413961	2		541	225	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796905	42796906	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0036226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	324	776	0	ENST00000575354.2:c.3365_3366del	p.Val1122GlyfsTer28	p.V1122Gfs*28	ENST00000575354	NM_015125.3	1121	acTGtg/actg	14/20	0.780622956413961	1	FACETS	0.865	0.827	0.903	0.865	0.827	0.903	CLONAL	1	TRUE	0	0.780622956413961	1		776	585	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429951	78430973	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAATGCGAACACCAGCATCATTTTGTATTTTTTTGATCATCTCTCCATTTCTTCCTATTACAATGCCAACAGCAAATCTTGGAATGGGGACCTTATGTAAAAAAGACTAAGTATTAAGAAAGCTAGCTTCTCAGGGTTTAAAGTAAAAAAAAGTATTTTAAAAAAGCGCCATTTCCTGAAAATCTGCCTCAAATCATAAAAGTACATATAATTCTATATTTATAGTAAATAGGGTAACAAGATATATAGAATTCTGTATTCTAAAGTATAAAGGTGAAATAAAAGGATAACAATGTTAGAGCTACTTAACACAAAACAGAAAACACTATTATATTTATGAATTAGCATACAACCATTTCTGAATGGGTATTTTTACTTACATCTATCCCTTCATTTCCTCCTATTCTTGACCCATACTCATTCCGAACTTCTCTGAAACCGCCTTGATCACGAATTAACTCTAACACCATTTCCTTGGCTTGCTAAAGCAGAAAAAGTTAGCTAATTTAGAAAGCATGTCTCAAAACATTTTAATTATTCATGCATATTTTGCCCAACCCCATTCAACCCACTCTTTCTTTATAAAGTATAAAGTTAAGTTTACTTGAACTTTATATGGGTCTCCTGTAATCCTAAGAGGTTTGTCAGCACCAGTGTTCTGCGGCCCGTCTTGAATCATAACCATTTTAACTCCAGCCCGTTCCTGTTACAATCATAGAAATAATATATATTAACAAAAGAAGTGGACAAAAATGGGCATCAAAACAGATCAAAAGTAGCCATTTCACAAAAATAACAATACCTGAAGCTGTTTAATAGTTTCTCCCCCTTTTCCAATGACTAATCCTGCCTTGCTAGCTGGAATCATGATTTCTTGAACTGCATTTCCCGGTCCATCGCCATGATGGAAGCCAGGAGCTGGTCTTCCTTTTTCAACAATCTGGTCCAGTAACCGTTTTGCTGACCTGTTAACAAATTAATATTTAAATAGTAAGCTGTAGCATACCCAAGCTTATTCAAATA	GAATGCGAACACCAGCATCATTTTGTATTTTTTTGATCATCTCTCCATTTCTTCCTATTACAATGCCAACAGCAAATCTTGGAATGGGGACCTTATGTAAAAAAGACTAAGTATTAAGAAAGCTAGCTTCTCAGGGTTTAAAGTAAAAAAAAGTATTTTAAAAAAGCGCCATTTCCTGAAAATCTGCCTCAAATCATAAAAGTACATATAATTCTATATTTATAGTAAATAGGGTAACAAGATATATAGAATTCTGTATTCTAAAGTATAAAGGTGAAATAAAAGGATAACAATGTTAGAGCTACTTAACACAAAACAGAAAACACTATTATATTTATGAATTAGCATACAACCATTTCTGAATGGGTATTTTTACTTACATCTATCCCTTCATTTCCTCCTATTCTTGACCCATACTCATTCCGAACTTCTCTGAAACCGCCTTGATCACGAATTAACTCTAACACCATTTCCTTGGCTTGCTAAAGCAGAAAAAGTTAGCTAATTTAGAAAGCATGTCTCAAAACATTTTAATTATTCATGCATATTTTGCCCAACCCCATTCAACCCACTCTTTCTTTATAAAGTATAAAGTTAAGTTTACTTGAACTTTATATGGGTCTCCTGTAATCCTAAGAGGTTTGTCAGCACCAGTGTTCTGCGGCCCGTCTTGAATCATAACCATTTTAACTCCAGCCCGTTCCTGTTACAATCATAGAAATAATATATATTAACAAAAGAAGTGGACAAAAATGGGCATCAAAACAGATCAAAAGTAGCCATTTCACAAAAATAACAATACCTGAAGCTGTTTAATAGTTTCTCCCCCTTTTCCAATGACTAATCCTGCCTTGCTAGCTGGAATCATGATTTCTTGAACTGCATTTCCCGGTCCATCGCCATGATGGAAGCCAGGAGCTGGTCTTCCTTTTTCAACAATCTGGTCCAGTAACCGTTTTGCTGACCTGTTAACAAATTAATATTTAAATAGTAAGCTGTAGCATACCCAAGCTTATTCAAATA	-	novel	NA	P-0036226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	43	531	0	ENST00000370768.2:c.474-58_928del		p.X158_splice	ENST00000370768	NM_003902.3	158		8-11/20	0.780622956413961	1	FACETS	0.422	0.359	0.49	0.422	0.359	0.49	SUBCLONAL	1	TRUE	0	0.780622956413961	1		531	159	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114749	108114749	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	271	567	0	ENST00000278616.4:c.566G>T	p.Arg189Ile	p.R189I	ENST00000278616	NM_000051.3	189	aGa/aTa	6/63	0.780622956413961	2	FACETS	0.933	0.897	0.968	0.933	0.897	0.968	CLONAL	2	TRUE	0	0.780622956413961	2		567	372	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141426	11141426	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	256	645	0	ENST00000358026.2:c.3403C>G	p.Arg1135Gly	p.R1135G	ENST00000358026	NM_001128849.1	1135	Cgg/Ggg	25/36	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.780622956413961	2		645	645	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79965847	79965929	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTCCGTCTCTGGGAACTTATTATTGTGGTTAATATTTTTAAAACTTTATACATCTTTTGGTTGCCAGGACACAACACTTTT	TTTTCCGTCTCTGGGAACTTATTATTGTGGTTAATATTTTTAAAACTTTATACATCTTTTGGTTGCCAGGACACAACACTTTT	-	novel	NA	P-0036226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	87	198	0	ENST00000265081.6:c.580-68_594del		p.X194_splice	ENST00000265081	NM_002439.4	194		4/24	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.780622956413961	2		198	164	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0036358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	21	660	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	1	2	FACETS	0.223	0.17	0.284	0.223	0.17	0.284	SUBCLONAL	1	TRUE	1	0.23	2		660	820	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0036358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	36	593	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.491	0.402	0.59	0.491	0.402	0.59	SUBCLONAL	1	TRUE	1	0.23	2		595	638	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819735	170819735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	30	88	0	ENST00000296930.5:c.374C>T	p.Ser125Leu	p.S125L	ENST00000296930	NM_002520.6	125	tCa/tTa	5/11	0.183186463359814	3	FACETS	1	0.94	1	0.735	0.597	0.888	CLONAL	1	TRUE	1	0.23	3		88	198	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720828	89720828	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0036358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	61	309	0	ENST00000371953.3:c.979A>T	p.Lys327Ter	p.K327*	ENST00000371953	NM_000314.4	327	Aaa/Taa	8/9	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.23	2		309	450	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271780	15271780	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	60	722	0	ENST00000263388.2:c.6659A>G	p.Glu2220Gly	p.E2220G	ENST00000263388	NM_000435.2	2220	gAg/gGg	33/33	1	2	FACETS	0.935	0.806	1	0.935	0.806	1	CLONAL	1	TRUE	1	0.23	2		722	558	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0036418-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	124	456	2	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.998	0.904	1	0.998	0.904	1	CLONAL	1	TRUE	1	0.345114450331387	2		458	720	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0036418-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	108	329	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.345114450331387	2		329	579	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466027	69466035	+	inframe_deletion	In_Frame_Del	DEL	GACGTGCGG	GACGTGCGG	-	novel	NA	P-0036418-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	136	680	1	ENST00000227507.2:c.871_879del	p.Arg291_Val293del	p.R291_V293del	ENST00000227507	NM_053056.2	289	GACGTGCGG/-	5/5	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.345114450331387	2		681	787	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589585	67589586	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATGAAT	novel	NA	P-0036418-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	70	278	0	ENST00000274335.5:c.1351_1356dup	p.Glu451_Tyr452dup	p.E451_Y452dup	ENST00000274335		451	cat/cATGAATat	10/15	1	2	FACETS	0.826	0.722	0.938	0.826	0.722	0.938	CLONAL	1	TRUE	1	0.345114450331387	2		278	491	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685314	89685314	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036418-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	91	246	2	ENST00000371953.3:c.209T>G	p.Leu70Arg	p.L70R	ENST00000371953	NM_000314.4	70	cTt/cGt	3/9	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.345114450331387	2		248	470	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038881	12038881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036418-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	102	359	0	ENST00000396373.4:c.1174G>A	p.Glu392Lys	p.E392K	ENST00000396373	NM_001987.4	392	Gag/Aag	7/8	0.100915066936565	4	FACETS	1	0.975	1	0.651	0.583	0.722	INDETERMINATE	1	TRUE	2	0.345114450331387	4		359	611	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023379	27023391	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCCGCCGCGGC	CCGCCGCCGCGGC	-	novel	NA	P-0036418-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	112	309	0	ENST00000324856.7:c.486_498del	p.Ala163ProfsTer65	p.A163Pfs*65	ENST00000324856	NM_006015.4	162	gCCGCCGCCGCGGCc/gc	1/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.345114450331387	2		309	450	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100835	27100853	+	frameshift_variant	Frame_Shift_Del	DEL	ATGGATGGCACATATGGCC	ATGGATGGCACATATGGCC	-	novel	NA	P-0036418-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	82	458	0	ENST00000324856.7:c.4117_4135del	p.Met1373LeufsTer102	p.M1373Lfs*102	ENST00000324856	NM_006015.4	1373	ATGGATGGCACATATGGCCct/ct	18/20	1	2	FACETS	0.736	0.649	0.829	0.736	0.649	0.829	SUBCLONAL	1	TRUE	1	0.345114450331387	2		458	646	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859418	57859418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036418-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	134	611	0	ENST00000228682.2:c.563G>A	p.Gly188Asp	p.G188D	ENST00000228682	NM_005269.2	188	gGc/gAc	6/12	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.345114450331387	2		611	766	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141504	11141504	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036418-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	141	667	1	ENST00000358026.2:c.3481C>T	p.Leu1161Phe	p.L1161F	ENST00000358026	NM_001128849.1	1161	Ctc/Ttc	25/36	1	2	FACETS	0.976	0.89	1	0.976	0.89	1	CLONAL	1	TRUE	1	0.345114450331387	2		668	837	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032748	30032748	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	114	421	0	ENST00000338641.4:c.123G>A	p.Trp41Ter	p.W41*	ENST00000338641	NM_000268.3	41	tgG/tgA	2/16	0.491294388292054	1	FACETS	0.997	0.908	1	0.997	0.908	1	CLONAL	1	TRUE	0	0.491294388292054	1		421	351	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517537	176517537	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772536234	NA	P-0036721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	44	935	0	ENST00000292408.4:c.238C>T	p.Arg80Trp	p.R80W	ENST00000292408	NM_213647.1	80	Cgg/Tgg	3/18	0.474473066798334	1	FACETS	0.168	0.14	0.199	0.168	0.14	0.199	SUBCLONAL	1	TRUE	0	0.491294388292054	1		935	805	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231773	36231773	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1569061762	NA	P-0036731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	826	471	0	ENST00000300305.3:c.611G>A	p.Arg204Gln	p.R204Q	ENST00000300305		204	cGa/cAa	5/8	0.882086344925873	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.881644376467779	3		471	895	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857311	68857312	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0036731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	158	324	0	ENST00000261769.5:c.1947_1948insTT	p.Ile650LeufsTer4	p.I650Lfs*4	ENST00000261769	NM_004360.3	649	tct/tcTTt	13/16	0.881644376467779	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.881644376467779	1		324	200	SUCCESS
APC	324	MSKCC	GRCh37	5	112174734	112174734	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	137	268	0	ENST00000257430.4:c.3443C>G	p.Ser1148Cys	p.S1148C	ENST00000257430	NM_000038.5	1148	tCt/tGt	16/16	1	2	FACETS	0.928	0.856	1	0.928	0.856	1	CLONAL	1	TRUE	1	0.881644376467779	2		268	335	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0036916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	147	500	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.74306194402691	2		500	387	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0036916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	172	326	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	1	2	FACETS	0.935	0.868	1	0.935	0.868	1	CLONAL	1	TRUE	1	0.74306194402691	2		326	495	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0036916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	129	144	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.709365364458023	2	FACETS	0.986	0.932	1	0.986	0.932	1	CLONAL	2	TRUE	0	0.74306194402691	2		144	176	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604756	48604756	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	94	279	0	ENST00000342988.3:c.1578A>C	p.Glu526Asp	p.E526D	ENST00000342988	NM_005359.5	526	gaA/gaC	12/12	0.74306194402691	1	FACETS	0.795	0.725	0.866	0.795	0.725	0.866	SUBCLONAL	1	TRUE	0	0.74306194402691	1		279	200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0036916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	99	391	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	0.670114560436047	1	FACETS	0.896	0.822	0.968	0.896	0.822	0.968	CLONAL	1	TRUE	0	0.74306194402691	1		391	187	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938932	178938932	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	54	251	0	ENST00000263967.3:c.2174A>G	p.Asp725Gly	p.D725G	ENST00000263967	NM_006218.2	725	gAt/gGt	14/21	1	2	FACETS	0.491	0.422	0.565	0.491	0.422	0.565	SUBCLONAL	1	TRUE	1	0.74306194402691	2		251	296	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247224	153247224	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	102	235	0	ENST00000281708.4:c.1578G>T	p.Trp526Cys	p.W526C	ENST00000281708	NM_033632.3	526	tgG/tgT	10/12	1	2	FACETS	0.921	0.835	1	0.921	0.835	1	CLONAL	1	TRUE	1	0.74306194402691	2		235	298	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718145	117718145	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	172	418	0	ENST00000368508.3:c.712A>C	p.Lys238Gln	p.K238Q	ENST00000368508	NM_002944.2	238	Aaa/Caa	7/43	1	2	FACETS	0.985	0.915	1	0.985	0.915	1	CLONAL	1	TRUE	1	0.74306194402691	2		418	470	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151830	108151854	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGCTTTGTTTGCCCTGTGTAAAT	CAGGCTTTGTTTGCCCTGTGTAAAT	-	novel	NA	P-0036972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	55	459	0	ENST00000278616.4:c.3512_3536del	p.Gln1171LeufsTer2	p.Q1171Lfs*2	ENST00000278616	NM_000051.3	1171	CAGGCTTTGTTTGCCCTGTGTAAATct/ct	24/63	0.303115137085822	1	FACETS	0.631	0.54	0.73	0.631	0.54	0.73	SUBCLONAL	1	TRUE	0	0.303115137085822	1		459	488	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37665979	37665979	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	55	529	0	ENST00000447079.4:c.2631T>G	p.Asp877Glu	p.D877E	ENST00000447079	NM_015083.1	877	gaT/gaG	7/14	0.362990918433114	3	FACETS	0.785	0.68	0.898	0.785	0.68	0.898	SUBCLONAL	2	TRUE	1	0.362990918433114	3		529	228	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646955	37646956	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CACCT	novel	NA	P-0037023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	34	585	0	ENST00000447079.4:c.2080_2084dup	p.Gln695HisfsTer60	p.Q695Hfs*60	ENST00000447079	NM_015083.1	693	cca/cCACCTca	3/14	0.362990918433114	3	FACETS	0.868	0.713	1	0.434	0.356	0.52	CLONAL	1	TRUE	1	0.362990918433114	3		585	255	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0037024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	47	669	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	1	2	FACETS	0.793	0.668	0.932	0.793	0.668	0.932	CLONAL	1	TRUE	1	0.17	2		669	697	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0037024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	36	347	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	1	2	FACETS	0.705	0.578	0.847	0.705	0.578	0.847	SUBCLONAL	1	TRUE	1	0.17	2		347	601	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs199469669	NA	P-0037024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	29	675	1	ENST00000374080.3:c.130G>C	p.Gly44Arg	p.G44R	ENST00000374080		44	Ggt/Cgt	2/45	1	2	FACETS	0.421	0.336	0.518	0.421	0.336	0.518	SUBCLONAL	1	TRUE	1	0.17	2		676	811	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896539	78896539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	72	747	1	ENST00000306801.3:c.2536C>T	p.Arg846Trp	p.R846W	ENST00000306801	NM_020761.2	846	Cgg/Tgg	22/34	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.17	2		748	838	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0037026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	607	886	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.636082347875186	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.636082347875186	2		886	863	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0037026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	115	442	4	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.636082347875186	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.636082347875186	1		446	239	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575068	48575068	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0037026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	131	445	0	ENST00000342988.3:c.262A>T	p.Lys88Ter	p.K88*	ENST00000342988	NM_005359.5	88	Aaa/Taa	3/12	0.636082347875186	1	FACETS	0.909	0.838	0.981	0.909	0.838	0.981	CLONAL	1	TRUE	0	0.636082347875186	1		445	309	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717777	89717777	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0037026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	94	366	0	ENST00000371953.3:c.801+1G>C		p.X267_splice	ENST00000371953	NM_000314.4	267			0.624633378693762	1	FACETS	0.896	0.813	0.98	0.896	0.813	0.98	CLONAL	1	TRUE	0	0.636082347875186	1		366	225	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710544	114710545	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0037026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	171	390	0	ENST00000543371.1:c.30dup	p.Asp11Ter	p.D11*	ENST00000543371	NM_001198531.1	10	gat/gaTt	1/14	1	2	FACETS	0.992	0.919	1	0.992	0.919	1	CLONAL	1	TRUE	1	0.636082347875186	2		390	542	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022687	12022687	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1047383225	NA	P-0037026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	223	487	0	ENST00000396373.4:c.793G>A	p.Val265Met	p.V265M	ENST00000396373	NM_001987.4	265	Gtg/Atg	5/8	0.188862935518163	4	FACETS	0.94	0.881	1	0.94	0.881	1	INDETERMINATE	2	TRUE	2	0.636082347875186	4		487	610	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482425	56482425	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	112	621	0	ENST00000267101.3:c.973G>C	p.Gly325Arg	p.G325R	ENST00000267101	NM_001982.3	325	Gga/Cga	8/28	0.449903658154811	1	FACETS	0.541	0.489	0.594	0.541	0.489	0.594	SUBCLONAL	1	TRUE	0	0.636082347875186	1		621	444	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061176	38061176	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	166	250	0	ENST00000250448.2:c.813G>T	p.Gln271His	p.Q271H	ENST00000250448	NM_004496.3	271	caG/caT	2/2	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.636082347875186	2		250	388	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252956	36252964	+	inframe_deletion	In_Frame_Del	DEL	TGCCAGCCA	TGCCAGCCA	-	novel	NA	P-0037026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	43	421	0	ENST00000300305.3:c.398_406del	p.Met133_Gly135del	p.M133_G135del	ENST00000300305		133	aTGGCTGGCAat/aat	4/8	0.636082347875186	1	FACETS	0.212	0.178	0.251	0.212	0.178	0.251	SUBCLONAL	1	TRUE	0	0.636082347875186	1		421	434	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209101835	209101838	+	missense_variant	Missense_Mutation	ONP	AGTT	AGTT	CGTG	novel	NA	P-0037026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	72	637	0	ENST00000345146.2:c.1210_1213delinsCACG	p.Asn404_Leu405delinsHisVal	p.N404_L405delinsHV	ENST00000345146	NM_005896.2	404	AACTtg/CACGtg	10/10	0.350636293980878	1	FACETS	0.307	0.268	0.348	0.307	0.268	0.348	INDETERMINATE	1	TRUE	0	0.636082347875186	1		637	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0037030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	188	664	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.234756976957275	2	FACETS	0.927	0.859	0.998	0.927	0.859	0.998	CLONAL	2	TRUE	0	0.26093531927109	2		665	777	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0037030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	63	384	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.26093531927109	2		384	451	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0037030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	169	640	1	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.232451097088395	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.26093531927109	2		641	617	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730876	40730876	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372862828	NA	P-0037030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	296	656	1	ENST00000373198.4:c.3659G>A	p.Arg1220Gln	p.R1220Q	ENST00000373198	NM_133170.3	1220	cGg/cAg	27/32	0.26093531927109	5	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	2	0.26093531927109	5		657	940	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710672	114710672	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs184454375	NA	P-0037030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	69	398	0	ENST00000543371.1:c.157G>A	p.Glu53Lys	p.E53K	ENST00000543371	NM_001198531.1	53	Gaa/Aaa	1/14	0.105026675377768	5	FACETS	1	0.971	1	0.477	0.416	0.543	INDETERMINATE	1	TRUE	2	0.26093531927109	5		398	514	SUCCESS
AR	367	MSKCC	GRCh37	X	66863125	66863125	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139524801	NA	P-0037030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	130	692	2	ENST00000374690.3:c.1644G>T	p.Leu548Phe	p.L548F	ENST00000374690	NM_000044.3	548	ttG/ttT	2/8	0.240599317655972	3	FACETS	1	0.983	1	0.69	0.626	0.758	CLONAL	1	TRUE	1	0.26093531927109	3		694	816	SUCCESS
APC	324	MSKCC	GRCh37	5	112174010	112174010	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	29	399	0	ENST00000257430.4:c.2721del	p.Ser908LeufsTer8	p.S908Lfs*8	ENST00000257430	NM_000038.5	907	Ggg/gg	16/16	1	2	FACETS	0.552	0.442	0.676	0.552	0.442	0.676	SUBCLONAL	1	TRUE	1	0.26093531927109	2		399	403	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984671	11984672	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	novel	NA	P-0037030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	54	288	0	ENST00000353533.5:c.224_225del		p.X75_splice	ENST00000353533	NM_003010.3	75			0.234756976957275	2	FACETS	1	0.961	1	0.688	0.591	0.792	CLONAL	1	TRUE	0	0.26093531927109	2		288	301	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636888	176636888	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	62	554	2	ENST00000439151.2:c.1488A>T	p.Lys496Asn	p.K496N	ENST00000439151	NM_022455.4	496	aaA/aaT	5/23	1	2	FACETS	0.783	0.676	0.899	0.783	0.676	0.899	SUBCLONAL	1	TRUE	1	0.26093531927109	2		556	607	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350431	89350431	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	544	1003	0	ENST00000301030.4:c.2519G>T	p.Arg840Leu	p.R840L	ENST00000301030	NM_001256183.1	840	cGg/cTg	9/13	0.834761617785721	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.834761617785721	1		1003	727	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156741	20156741	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1449534841	NA	P-0037043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	287	462	0	ENST00000379607.5:c.17-1G>A		p.X6_splice	ENST00000379607	NM_001412.3	6			1	2	FACETS	0.982	0.93	1	0.982	0.93	1	CLONAL	1	TRUE	1	0.834761617785721	2		462	700	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0037044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	378	665	1	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.345076533982138	3	FACETS	1	0.956	1			1	CLONAL	3	TRUE	NA	0.345076533982138	3		666	855	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579340	7579340	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	120	640	0	ENST00000269305.4:c.347C>T	p.Ser116Phe	p.S116F	ENST00000269305	NM_001126112.2	116	tCt/tTt	4/11	0.345076533982138	3	FACETS	0.992	0.896	1			1	CLONAL	1	TRUE	NA	0.345076533982138	3		640	822	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633551	69633551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1886	100	226	0	ENST00000334134.2:c.151G>A	p.Ala51Thr	p.A51T	ENST00000334134	NM_005247.2	51	Gcc/Acc	1/3	0.345076533982138	35	FACETS	0.977	0.868	1			1	CLONAL	2	TRUE	NA	0.345076533982138	35		226	1986	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376430	118376430	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	106	597	0	ENST00000534358.1:c.9823G>T	p.Gly3275Trp	p.G3275W	ENST00000534358	NM_005933.3	3275	Ggg/Tgg	27/36	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.345076533982138	2		597	610	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911675	32911675	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	95	675	1	ENST00000380152.3:c.3183G>T	p.Lys1061Asn	p.K1061N	ENST00000380152		1061	aaG/aaT	11/27	0.345076533982138	2	FACETS	1	0.94	1	0.539	0.481	0.6	CLONAL	1	TRUE	0	0.345076533982138	2		676	511	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36846865	36846865	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	79	456	0	ENST00000358127.4:c.1074G>C	p.Trp358Cys	p.W358C	ENST00000358127	NM_001280556.1	358	tgG/tgC	9/10	0.345076533982138	2	FACETS	1	0.904	1	0.513	0.453	0.577	CLONAL	1	TRUE	0	0.345076533982138	2		456	446	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0037066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	71	388	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.224240271504065	3	FACETS	1	0.914	1	0.529	0.462	0.601	CLONAL	1	TRUE	1	0.29	3		388	530	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0037066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	31	261	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.30193943535152	4	FACETS	0.663	0.536	0.807	0.221	0.178	0.269	SUBCLONAL	1	TRUE	1	0.29	4		261	416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0037066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	283	607	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.30193943535152	2	FACETS	1	0.967	1	1	0.995	1	CLONAL	3	TRUE	0	0.29	2		607	633	SUCCESS
APC	324	MSKCC	GRCh37	5	112175221	112175221	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	101	263	0	ENST00000257430.4:c.3930del	p.Ile1311LeufsTer10	p.I1311Lfs*10	ENST00000257430	NM_000038.5	1310	aaG/aa	16/16	0.30193943535152	4	FACETS	0.995	0.901	1	0.995	0.901	1	CLONAL	3	TRUE	1	0.29	4		263	301	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427531	49427531	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780464972	NA	P-0037066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	67	563	2	ENST00000301067.7:c.10957G>A	p.Gly3653Arg	p.G3653R	ENST00000301067	NM_003482.3	3653	Gga/Aga	39/54	0.30193943535152	3	FACETS	1	0.94	1	0.57	0.497	0.649	CLONAL	1	TRUE	1	0.29	3		565	464	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912183	114912183	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	182	518	0	ENST00000543371.1:c.1253C>G	p.Ser418Cys	p.S418C	ENST00000543371	NM_001198531.1	418	tCc/tGc	11/14	0.131429434089162	5	FACETS	0.858	0.794	0.924	0.858	0.794	0.924	INDETERMINATE	3	TRUE	2	0.29	5		518	700	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148507475	148507475	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	81	457	0	ENST00000320356.2:c.1979G>T	p.Gly660Val	p.G660V	ENST00000320356	NM_004456.4	660	gGg/gTg	17/20	0.30193943535152	5	FACETS	1	0.934	1	0.273	0.24	0.308	CLONAL	1	TRUE	1	0.29	5		457	734	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841899	151841899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773125481	NA	P-0037066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	71	423	1	ENST00000262189.6:c.14242G>A	p.Ala4748Thr	p.A4748T	ENST00000262189	NM_170606.2	4748	Gca/Aca	55/59	0.30193943535152	5	FACETS	1	0.922	1	0.269	0.235	0.307	CLONAL	1	TRUE	1	0.29	5		424	652	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0037077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	313	812	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.392329383965099	3	FACETS	0.89	0.843	0.938	0.89	0.843	0.938	CLONAL	2	TRUE	1	0.504387186656331	3		812	873	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0037077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	141	371	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.504387186656331	2		371	497	SUCCESS
APC	324	MSKCC	GRCh37	5	112175891	112175891	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	95	290	0	ENST00000257430.4:c.4602del	p.Asn1535MetfsTer30	p.N1535Mfs*30	ENST00000257430	NM_000038.5	1534	Ggg/gg	16/16	1	2	FACETS	0.971	0.871	1	0.971	0.871	1	CLONAL	1	TRUE	1	0.504387186656331	2		290	388	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368213	45368213	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	292	416	0	ENST00000262160.6:c.1389C>A	p.Cys463Ter	p.C463*	ENST00000262160	NM_005901.5	463	tgC/tgA	11/11	0.502419978282455	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.504387186656331	2		416	570	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358656	67358657	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0037077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	251	486	0	ENST00000327367.4:c.164_165delinsAT	p.Ile55Asn	p.I55N	ENST00000327367	NM_005902.3	55	aTC/aAT	1/9	0.502419978282455	2	FACETS	0.97	0.918	1	0.97	0.918	1	CLONAL	2	TRUE	0	0.504387186656331	2		486	513	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022697	31022697	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	181	614	1	ENST00000375687.4:c.2182G>T	p.Glu728Ter	p.E728*	ENST00000375687	NM_015338.5	728	Gaa/Taa	13/13	1	2	FACETS	0.987	0.913	1	0.987	0.913	1	CLONAL	1	TRUE	1	0.504387186656331	2		615	727	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259232	89259232	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	151	535	0	ENST00000336596.2:c.376G>T	p.Glu126Ter	p.E126*	ENST00000336596	NM_005233.5	126	Gag/Tag	3/17	1	2	FACETS	0.966	0.886	1	0.966	0.886	1	CLONAL	1	TRUE	1	0.504387186656331	2		535	620	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133710843	133710843	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	90	243	0	ENST00000318560.5:c.10A>G	p.Ile4Val	p.I4V	ENST00000318560	NM_005157.4	4	Atc/Gtc	1/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.504387186656331	2		243	310	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692964	89692964	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs786204934	NA	P-0037140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	100	560	0	ENST00000371953.3:c.448G>T	p.Glu150Ter	p.E150*	ENST00000371953	NM_000314.4	150	Gag/Tag	5/9	1	2	FACETS	0.72	0.645	0.799	0.72	0.645	0.799	SUBCLONAL	1	TRUE	1	0.51	2		560	545	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243701	41243701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555586946	NA	P-0037140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	83	507	0	ENST00000357654.3:c.3847C>T	p.His1283Tyr	p.H1283Y	ENST00000357654	NM_007294.3	1283	Cat/Tat	10/23	0.3	1	FACETS	0.503	0.445	0.565	0.503	0.445	0.565	INDETERMINATE	1	TRUE	0	0.51	1		507	482	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919879	50919879	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866317622	NA	P-0037140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	56	488	0	ENST00000440232.2:c.2966C>T	p.Thr989Met	p.T989M	ENST00000440232	NM_002691.3	989	aCg/aTg	24/27	0.180198842934933	0	FACETS	0.236	0.202	0.273			1	INDETERMINATE	1	TRUE	0	0.51	0		488	456	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25990461	25990462	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0037140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	148	343	0	ENST00000435504.4:c.765_766del	p.Arg255SerfsTer10	p.R255Sfs*10	ENST00000435504		255	agACtc/agtc	8/13	0.3	1	FACETS	1	0.98	1	1	0.98	1	INDETERMINATE	1	TRUE	0	0.51	1		343	369	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606457	93606458	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0037140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	128	509	0	ENST00000375746.1:c.280dup	p.Gln94ProfsTer4	p.Q94Pfs*4	ENST00000375746	NM_001174167.1	93	tcc/tCcc	2/14	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.51	2		509	499	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226580010	226580010	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1558241049	NA	P-0037142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	81	384	0	ENST00000366794.5:c.292G>A	p.Gly98Ser	p.G98S	ENST00000366794	NM_001618.3	98	Ggc/Agc	3/23	0.299143716675065	4	FACETS	0.853	0.751	0.962	0.284	0.25	0.321	CLONAL	1	TRUE	1	0.34224526184536	4		384	745	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1919974	1919974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1422010407	NA	P-0037142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	137	475	0	ENST00000382891.5:c.1034C>T	p.Thr345Ile	p.T345I	ENST00000382891	NM_133335.3	345	aCc/aTc	5/22	0.307643395687408	2	FACETS	1	0.952	1	0.534	0.486	0.584	CLONAL	1	TRUE	0	0.34224526184536	2		475	750	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220400	1220400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	244	608	1	ENST00000326873.7:c.493G>A	p.Glu165Lys	p.E165K	ENST00000326873	NM_000455.4	165	Gag/Aag	4/10	0.431062081950605	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.431062081950605	1		609	761	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579533	7579533	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	255	663	0	ENST00000269305.4:c.154C>T	p.Gln52Ter	p.Q52*	ENST00000269305	NM_001126112.2	52	Caa/Taa	4/11	0.431062081950605	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.431062081950605	1		663	803	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845395	89845395	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	214	446	0	ENST00000389301.3:c.1732T>C	p.Tyr578His	p.Y578H	ENST00000389301	NM_000135.2	578	Tac/Cac	19/43	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.431062081950605	2		446	738	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845397	89845398	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCTCCTGAATAT	novel	NA	P-0037146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	156	431	0	ENST00000389301.3:c.1717_1729dup	p.Pro577HisfsTer26	p.P577Hfs*26	ENST00000389301	NM_000135.2	577	cct/cATATTCAGGAGGCct	19/43	1	2	FACETS	0.972	0.891	1	0.972	0.891	1	CLONAL	1	TRUE	1	0.431062081950605	2		431	745	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772535	56772535	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	403	374	0	ENST00000337432.4:c.389G>C	p.Gly130Ala	p.G130A	ENST00000337432	NM_058216.2	130	gGa/gCa	2/9	0.431062081950605	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	0	0.431062081950605	3		374	742	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282623	1282641	+	frameshift_variant	Frame_Shift_Del	DEL	TGACATAAAAGAAAGACCT	TGACATAAAAGAAAGACCT	-	novel	NA	P-0037146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	179	547	0	ENST00000310581.5:c.1672_1690del	p.Ser559ArgfsTer29	p.S559Rfs*29	ENST00000310581	NM_198253.2	558	AGGTCTTTCTTTTATGTCAcg/cg	3/16	1	2	FACETS	0.966	0.891	1	0.966	0.891	1	CLONAL	1	TRUE	1	0.431062081950605	2		547	860	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652095	36652103	+	inframe_deletion	In_Frame_Del	DEL	CTGCCCAAG	CTGCCCAAG	-	novel	NA	P-0037146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	113	538	0	ENST00000244741.5:c.219_227del	p.Pro74_Leu76del	p.P74_L76del	ENST00000244741	NM_000389.4	73	CTGCCCAAG/-	2/3	0.188844579953852	3	FACETS	0.65	0.584	0.721	0.325	0.292	0.361	INDETERMINATE	1	TRUE	1	0.431062081950605	3		538	980	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717753	89717753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	247	350	0	ENST00000371953.3:c.780del	p.Lys260AsnfsTer6	p.K260Nfs*6	ENST00000371953	NM_000314.4	260	Aaa/aa	7/9	0.774936437570834	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.774936437570834	1		350	346	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124204	2124204	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs45517231	NA	P-0037158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	305	537	0	ENST00000219476.3:c.2359G>T	p.Glu787Ter	p.E787*	ENST00000219476	NM_000548.3	787	Gag/Tag	22/42	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.774936437570834	2		537	720	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129123	2129163	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGGAGCTCACGGAAACCTGTCTGGACATGATGGCTCGAT	CCTGGAGCTCACGGAAACCTGTCTGGACATGATGGCTCGAT	-	novel	NA	P-0037158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	246	619	0	ENST00000219476.3:c.3057_3097del	p.His1019GlnfsTer135	p.H1019Qfs*135	ENST00000219476	NM_000548.3	1019	caCCTGGAGCTCACGGAAACCTGTCTGGACATGATGGCTCGATac/caac	27/42	1	2	FACETS	0.792	0.742	0.842	0.792	0.742	0.842	SUBCLONAL	1	TRUE	1	0.774936437570834	2		619	802	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0037163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	122	388	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.929	0.847	1	0.929	0.847	1	CLONAL	1	TRUE	1	0.668464266173652	2		388	393	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878749	151878749	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1211949081	NA	P-0037163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	96	406	0	ENST00000262189.6:c.6196C>T	p.Arg2066Ter	p.R2066*	ENST00000262189	NM_170606.2	2066	Cga/Tga	36/59	0.113356135404577	4	FACETS	0.874	0.791	0.961	0.874	0.791	0.961	INDETERMINATE	2	TRUE	2	0.668464266173652	4		406	274	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445176	49445176	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	341	756	0	ENST00000301067.7:c.2290C>T	p.Gln764Ter	p.Q764*	ENST00000301067	NM_003482.3	764	Cag/Tag	10/54	0.510782327484634	4	FACETS	1	0.993	1	0.822	0.785	0.86	CLONAL	2	TRUE	1	0.668464266173652	4		756	690	SUCCESS
ATR	545	MSKCC	GRCh37	3	142222253	142222253	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	86	334	0	ENST00000350721.4:c.5239G>C	p.Gly1747Arg	p.G1747R	ENST00000350721	NM_001184.3	1747	Ggt/Cgt	30/47	1	2	FACETS	0.897	0.803	0.994	0.897	0.803	0.994	CLONAL	1	TRUE	1	0.668464266173652	2		334	287	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	49	540	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.693	0.586	0.812	0.693	0.586	0.812	SUBCLONAL	1	TRUE	1	0.2	2		540	707	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0037192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	56	594	1	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	1	2	FACETS	0.946	0.81	1	0.946	0.81	1	CLONAL	1	TRUE	1	0.2	2		595	592	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584605	48584606	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0037192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	31	430	0	ENST00000342988.3:c.779dup	p.Tyr260Ter	p.Y260*	ENST00000342988	NM_005359.5	260	tac/tAac	6/12	1	2	FACETS	0.629	0.508	0.766	0.629	0.508	0.766	SUBCLONAL	1	TRUE	1	0.2	2		430	493	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860276	151860276	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	41	570	0	ENST00000262189.6:c.10386del	p.Phe3462LeufsTer5	p.F3462Lfs*5	ENST00000262189	NM_170606.2	3462	ttT/tt	43/59	1	2	FACETS	0.702	0.584	0.834	0.702	0.584	0.834	SUBCLONAL	1	TRUE	1	0.2	2		570	584	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0037193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	185	456	2	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.479166717926754	2		458	588	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0037193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	160	329	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.479166717926754	2		329	490	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0037193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	102	388	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.748	0.671	0.83	0.748	0.671	0.83	SUBCLONAL	1	TRUE	1	0.479166717926754	2		388	569	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717615	89717615	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909227	NA	P-0037193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	190	473	0	ENST00000371953.3:c.640C>T	p.Gln214Ter	p.Q214*	ENST00000371953	NM_000314.4	214	Cag/Tag	7/9	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.479166717926754	2		473	628	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0037193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	277	565	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.479166717926754	2		565	829	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916836	178916836	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	242	600	0	ENST00000263967.3:c.223C>G	p.Gln75Glu	p.Q75E	ENST00000263967	NM_006218.2	75	Caa/Gaa	2/21	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.479166717926754	2		600	782	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231782	36231782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs74315450	NA	P-0037193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	33	639	1	ENST00000300305.3:c.602G>A	p.Arg201Gln	p.R201Q	ENST00000300305		201	cGa/cAa	5/8	1	2	FACETS	0.162	0.131	0.198	0.162	0.131	0.198	SUBCLONAL	1	TRUE	1	0.479166717926754	2		640	848	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191199	2191199	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	257	685	0	ENST00000398665.3:c.453C>G	p.Ile151Met	p.I151M	ENST00000398665	NM_032482.2	151	atC/atG	5/28	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.479166717926754	2		685	830	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056147	27056154	+	frameshift_variant	Frame_Shift_Del	DEL	CAGTCCAA	CAGTCCAA	GAC	novel	NA	P-0037193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	186	471	1	ENST00000324856.7:c.1143_1150delinsGAC	p.Ser382ThrfsTer16	p.S382Tfs*16	ENST00000324856	NM_006015.4	381	tcCAGTCCAAtg/tcGACtg	2/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.479166717926754	2		472	579	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097781	27097781	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0037193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	194	461	0	ENST00000324856.7:c.3370A>T	p.Lys1124Ter	p.K1124*	ENST00000324856	NM_006015.4	1124	Aag/Tag	12/20	1	2	FACETS	0.758	0.707	0.81	1	0.992	1	SUBCLONAL	2	TRUE	1	0.479166717926754	2		461	534	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176176011	176176011	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	152	329	0	ENST00000367669.3:c.104C>G	p.Pro35Arg	p.P35R	ENST00000367669	NM_022457.5	35	cCg/cGg	1/20	0.327252809785003	4	FACETS	0.885	0.815	0.958	0.59	0.543	0.639	CLONAL	2	TRUE	1	0.479166717926754	4		329	530	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204944	128204944	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs777283796	NA	P-0037193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	248	786	0	ENST00000341105.2:c.497C>G	p.Ser166Cys	p.S166C	ENST00000341105	NM_032638.4	166	tCt/tGt	3/6	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.479166717926754	2		786	826	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948169	55948169	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	252	555	0	ENST00000263923.4:c.3802G>C	p.Glu1268Gln	p.E1268Q	ENST00000263923	NM_002253.2	1268	Gag/Cag	29/30	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.479166717926754	2		555	794	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370827	55370828	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0037193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	182	493	0	ENST00000297316.4:c.131_132dup	p.Lys45Ter	p.K45*	ENST00000297316	NM_022454.3	43	-/GT	1/2	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.479166717926754	2		493	544	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517974	8517974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	182	564	1	ENST00000356435.5:c.1417G>A	p.Asp473Asn	p.D473N	ENST00000356435		473	Gac/Aac	10/35	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.479166717926754	2		565	667	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27203085	27203085	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	85	588	0	ENST00000380036.4:c.2177C>G	p.Ser726Cys	p.S726C	ENST00000380036	NM_000459.3	726	tCt/tGt	13/23	1	2	FACETS	0.492	0.435	0.554	0.492	0.435	0.554	SUBCLONAL	1	TRUE	1	0.479166717926754	2		588	721	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123199729	123199729	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	140	403	0	ENST00000218089.9:c.2029G>A	p.Glu677Lys	p.E677K	ENST00000218089	NM_001042749.1	677	Gaa/Aaa	21/35	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.479166717926754	2		403	491	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0037199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	19	621	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.739	0.563	0.945	0.739	0.563	0.945	CLONAL	1	TRUE	1	0.23695800142845	2		621	217	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55228032	55229054	+	splice_donor_variant,intron_variant	Splice_Site	DEL	GTAAGTCACCGCTTTCTGTTTAGTTTATGGAGTTGGTTCTAATGGGTCCTTTATTTGTATTTAGAATATTGAAGGGCTATTCCCATTTAAATTACTTTTTTCAGTTCCTTAAGAAGCAAATTAAAATCTTAAGATTCCTAACTGTGAAATTACCATGTGAATTCCATTAAAACTTTTTCCAGATCATTACCATTCAATGGGATGAATTTACCCTGAGGTTTAGGCTACCAATTATTTGTAATGTAAGTAACTAAATTTAGTATTAGTTATATTACCTTTTAGTTGTAGGTCACTCTCTGCTCATTTCAGCCTGTAAAGACTACAGCTACACACATACACACACAGAGGAATGGAATGAGCACTTTACATCAACACTTCCTGTTCTGGCTCTAGAGCCTCAGCTTTTGAAGCTGGTGAGAGCCTGGCCTGTGCTGGGCCTTGGCCACGGGCAGCGTCAGCTTTGAGTCAAGTGCTGGTCTGGCCTCCCTAGCTTTGAGCCTCTGTCAATTCCCTTAATCTGTTTAGGCTTTGGCTTCCTCATCCATAGAATGGAGATATGAATGATTCCTACGCCGTAGTGCTTTGAGAGAATTCAGTGAAATTCCTGTGTGTAAAACCCTTCCATGGTGCCTAGCACACAGCACACAGCCAATGGCCCAATGGCTCCTATCAGCTGTGGGATTTGTCATCAGAACACCACCAGCTCTGCTCCAGGCTGCCCTGGGTACCATCAAAACACACCCTGTGCCCAGCAGCACCTGCTCCTCTGCACACCTGGTTCCTTCAGCAGGGGCAGTGGCCGTGGGAGCACAGAAAACATGGAGTCCCATCTGGTTTAATTGATGCCATTGCCAAAGGGGAGGACTCACGGCACCCCCTCTCGGGTGCCAGGGTGCCTGGCTCCCACCAGGAGGAAGACCTGTCCTCCACTGTCAGGCACATTTCAGTCTTCCCAGCAGCCAGCACAACTACTTTGTCCTTCCAGTCACGGTCGGCCTCTGGGAAGCCCAGTCTGTGTCCTCC	GTAAGTCACCGCTTTCTGTTTAGTTTATGGAGTTGGTTCTAATGGGTCCTTTATTTGTATTTAGAATATTGAAGGGCTATTCCCATTTAAATTACTTTTTTCAGTTCCTTAAGAAGCAAATTAAAATCTTAAGATTCCTAACTGTGAAATTACCATGTGAATTCCATTAAAACTTTTTCCAGATCATTACCATTCAATGGGATGAATTTACCCTGAGGTTTAGGCTACCAATTATTTGTAATGTAAGTAACTAAATTTAGTATTAGTTATATTACCTTTTAGTTGTAGGTCACTCTCTGCTCATTTCAGCCTGTAAAGACTACAGCTACACACATACACACACAGAGGAATGGAATGAGCACTTTACATCAACACTTCCTGTTCTGGCTCTAGAGCCTCAGCTTTTGAAGCTGGTGAGAGCCTGGCCTGTGCTGGGCCTTGGCCACGGGCAGCGTCAGCTTTGAGTCAAGTGCTGGTCTGGCCTCCCTAGCTTTGAGCCTCTGTCAATTCCCTTAATCTGTTTAGGCTTTGGCTTCCTCATCCATAGAATGGAGATATGAATGATTCCTACGCCGTAGTGCTTTGAGAGAATTCAGTGAAATTCCTGTGTGTAAAACCCTTCCATGGTGCCTAGCACACAGCACACAGCCAATGGCCCAATGGCTCCTATCAGCTGTGGGATTTGTCATCAGAACACCACCAGCTCTGCTCCAGGCTGCCCTGGGTACCATCAAAACACACCCTGTGCCCAGCAGCACCTGCTCCTCTGCACACCTGGTTCCTTCAGCAGGGGCAGTGGCCGTGGGAGCACAGAAAACATGGAGTCCCATCTGGTTTAATTGATGCCATTGCCAAAGGGGAGGACTCACGGCACCCCCTCTCGGGTGCCAGGGTGCCTGGCTCCCACCAGGAGGAAGACCTGTCCTCCACTGTCAGGCACATTTCAGTCTTCCCAGCAGCCAGCACAACTACTTTGTCCTTCCAGTCACGGTCGGCCTCTGGGAAGCCCAGTCTGTGTCCTCC	-	novel	NA	P-0037199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	10	229	0	ENST00000275493.2:c.1498+1_1499-138del		p.X500_splice	ENST00000275493	NM_005228.3	500			0.23695800142845	1	FACETS	0.503	0.341	0.704	0.503	0.341	0.704	SUBCLONAL	1	TRUE	0	0.23695800142845	1		229	148	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199469672	NA	P-0037237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	17	228	0	ENST00000374080.3:c.131G>T	p.Gly44Val	p.G44V	ENST00000374080		44	gGt/gTt	2/45	1	1	FACETS	0.391	0.291	0.51	0.391	0.291	0.51	SUBCLONAL	1	TRUE	0	0.222711150132213	1		228	347	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442051	52442054	+	frameshift_variant	Frame_Shift_Del	DEL	GCAC	GCAC	-	novel	NA	P-0037237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	75	453	0	ENST00000460680.1:c.295_298del	p.Val99SerfsTer2	p.V99Sfs*2	ENST00000460680	NM_004656.3	99	GTGCtc/tc	5/17	0.205632702542991	1	FACETS	0.911	0.798	1	0.911	0.798	1	CLONAL	1	TRUE	0	0.222711150132213	1		453	657	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026115	71026115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1553667322	NA	P-0037237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	65	348	0	ENST00000318789.4:c.1507del	p.Arg503AspfsTer24	p.R503Dfs*24	ENST00000318789	NM_032682.5	503	Cga/ga	17/21	0.205632702542991	1	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	0	0.222711150132213	1		348	518	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156719	20156719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	101	507	0	ENST00000379607.5:c.38G>A	p.Arg13His	p.R13H	ENST00000379607	NM_001412.3	13	cGc/cAc	2/7	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.33457434458856	2		507	553	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	74	368	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.33457434458856	2		368	407	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	90	360	1	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.33457434458856	2		361	519	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	74	528	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.33457434458856	2		528	422	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	83	610	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	1	2	FACETS	0.94	0.831	1	0.94	0.831	1	CLONAL	1	TRUE	1	0.33457434458856	2		610	528	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	197	459	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	1	0.982	1	1	0.994	1	CLONAL	2	TRUE	1	0.33457434458856	2		460	514	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511575	38511575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866375031	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	100	637	0	ENST00000254066.5:c.1073C>T	p.Ala358Val	p.A358V	ENST00000254066	NM_000964.3	358	gCg/gTg	8/9	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.33457434458856	2		637	582	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	90	707	7	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.33457434458856	2		714	422	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932085	39932085	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	138	914	1	ENST00000378444.4:c.2514del	p.Lys839SerfsTer17	p.K839Sfs*17	ENST00000378444	NM_001123385.1	838	ccC/cc	4/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.33457434458856	2		915	743	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346158	89346158	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs878855327	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	25	313	1	ENST00000301030.4:c.6792del	p.Ala2265ProfsTer72	p.A2265Pfs*72	ENST00000301030	NM_001256183.1	2264	ccC/cc	9/13	1	2	FACETS	0.725	0.575	0.896	0.725	0.575	0.896	SUBCLONAL	1	TRUE	1	0.33457434458856	2		314	206	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25368433	25368434	+	intron_variant	Intron	INS	-	-	T	novel	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	72	436	0	ENST00000311936.3:c.451-5589dup		p.*151*	ENST00000311936	NM_004985.3	171/189			0.33457434458856	1	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	0	0.33457434458856	1		436	349	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36989307	36989307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	91	553	0	ENST00000354822.5:c.28C>T	p.Arg10Trp	p.R10W	ENST00000354822	NM_001079668.2	10	Cgg/Tgg	1/3	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.33457434458856	2		553	445	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2189768	2189768	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479024523	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	124	772	0	ENST00000398665.3:c.238C>T	p.Arg80Cys	p.R80C	ENST00000398665	NM_032482.2	80	Cgt/Tgt	4/28	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.33457434458856	2		772	665	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992720	68992720	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs182978151	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	195	644	0	ENST00000288368.4:c.1685G>A	p.Arg562His	p.R562H	ENST00000288368	NM_024870.2	562	cGt/cAt	16/40	0.33457434458856	3	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	1	0.33457434458856	3		644	674	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200877	67200877	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	82	755	1	ENST00000312629.5:c.870del	p.Tyr291ThrfsTer14	p.Y291Tfs*14	ENST00000312629	NM_003952.2	289	Ccc/cc	10/15	1	2	FACETS	0.777	0.685	0.875	0.777	0.685	0.875	SUBCLONAL	1	TRUE	1	0.33457434458856	2		756	631	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874013	151874013	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1248944002	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	61	669	1	ENST00000262189.6:c.8525del	p.Asn2842MetfsTer21	p.N2842Mfs*21	ENST00000262189	NM_170606.2	2842	aAt/at	38/59	1	2	FACETS	0.563	0.485	0.647	0.563	0.485	0.647	SUBCLONAL	1	TRUE	1	0.33457434458856	2		670	648	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041391	47041391	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	104	762	0	ENST00000377604.3:c.1735G>A	p.Gly579Ser	p.G579S	ENST00000377604	NM_001204468.1	579	Ggc/Agc	16/24	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.33457434458856	2		762	599	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467922	50467922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	77	515	0	ENST00000331340.3:c.1157G>A	p.Arg386His	p.R386H	ENST00000331340	NM_006060.4	386	cGc/cAc	8/8	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.33457434458856	2		515	367	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256497	115256497	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	137	648	0	ENST00000369535.4:c.214A>G	p.Met72Val	p.M72V	ENST00000369535	NM_002524.4	72	Atg/Gtg	3/7	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.33457434458856	2		648	688	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711887	89711888	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	92	426	2	ENST00000371953.3:c.506_507del	p.Pro169GlnfsTer10	p.P169Qfs*10	ENST00000371953	NM_000314.4	169	CCc/c	6/9	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.33457434458856	2		428	504	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937431	32937431	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80359052	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	104	570	0	ENST00000380152.3:c.8092G>A	p.Ala2698Thr	p.A2698T	ENST00000380152		2698	Gca/Aca	18/27	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.33457434458856	2		570	534	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007845	45007846	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	88	571	0	ENST00000558401.1:c.293_294del	p.Tyr98CysfsTer16	p.Y98Cfs*16	ENST00000558401	NM_004048.2	98	TAt/t	2/4	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.33457434458856	2		571	505	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822355	72822355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	139	944	0	ENST00000268489.5:c.9820G>A	p.Ala3274Thr	p.A3274T	ENST00000268489	NM_006885.3	3274	Gcc/Acc	10/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.33457434458856	2		944	756	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351436	89351436	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	66	676	0	ENST00000301030.4:c.1514C>T	p.Ser505Phe	p.S505F	ENST00000301030	NM_001256183.1	505	tCc/tTc	9/13	1	2	FACETS	0.716	0.622	0.818	0.716	0.622	0.818	SUBCLONAL	1	TRUE	1	0.33457434458856	2		676	551	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40483531	40483532	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	72	456	0	ENST00000264657.5:c.1067_1068del	p.Pro356ArgfsTer7	p.P356Rfs*7	ENST00000264657	NM_139276.2	356	cCT/c	11/24	1	2	FACETS	0.918	0.804	1	0.918	0.804	1	CLONAL	1	TRUE	1	0.33457434458856	2		456	469	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584320	39584320	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	43	212	1	ENST00000262039.4:c.985G>A	p.Ala329Thr	p.A329T	ENST00000262039	NM_002647.2	329	Gcc/Acc	10/25	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.33457434458856	2		213	240	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639587	47639588	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs63749897	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	57	312	0	ENST00000233146.2:c.687dup	p.Ala230SerfsTer2	p.A230Sfs*2	ENST00000233146	NM_000251.2	227	aga/agAa	4/16	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.33457434458856	2		312	340	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044416	128044416	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	147	773	2	ENST00000285398.2:c.1205G>A	p.Gly402Asp	p.G402D	ENST00000285398	NM_000122.1	402	gGc/gAc	8/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.33457434458856	2		775	673	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790046	40790046	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	129	646	0	ENST00000373198.4:c.2685G>T	p.Gln895His	p.Q895H	ENST00000373198	NM_133170.3	895	caG/caT	18/32	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.33457434458856	2		646	587	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480498	57480498	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137854532	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	114	409	1	ENST00000371085.3:c.493C>T	p.Arg165Cys	p.R165C	ENST00000371085	NM_000516.4	165	Cgc/Tgc	6/13	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.33457434458856	2		410	504	SUCCESS
APC	324	MSKCC	GRCh37	5	112177785	112177785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	33	314	0	ENST00000257430.4:c.6494C>T	p.Pro2165Leu	p.P2165L	ENST00000257430	NM_000038.5	2165	cCa/cTa	16/16	1	2	FACETS	0.687	0.562	0.828	0.687	0.562	0.828	SUBCLONAL	1	TRUE	1	0.33457434458856	2		314	287	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56859023	56859023	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	96	448	0	ENST00000519728.1:c.149T>C	p.Leu50Pro	p.L50P	ENST00000519728	NM_002350.3	50	cTt/cCt	3/13	0.33457434458856	3	FACETS	0.954	0.851	1	0.477	0.425	0.533	CLONAL	1	TRUE	1	0.33457434458856	3		448	702	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104585	69104585	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	132	770	0	ENST00000288368.4:c.4429A>G	p.Asn1477Asp	p.N1477D	ENST00000288368	NM_024870.2	1477	Aac/Gac	37/40	0.33457434458856	3	FACETS	1	0.945	1	0.529	0.48	0.58	CLONAL	1	TRUE	1	0.33457434458856	3		770	871	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482341	87482341	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	102	615	0	ENST00000277120.3:c.1628A>G	p.Asp543Gly	p.D543G	ENST00000277120		543	gAc/gGc	14/19	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.33457434458856	2		615	522	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942717	44942717	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	74	475	1	ENST00000377967.4:c.3297G>T	p.Gln1099His	p.Q1099H	ENST00000377967	NM_021140.2	1099	caG/caT	23/29	1	2	FACETS	0.793	0.695	0.898	0.793	0.695	0.898	SUBCLONAL	1	TRUE	1	0.33457434458856	2		476	558	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410721	63410721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765543269	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	115	779	2	ENST00000330258.3:c.2446C>T	p.Arg816Trp	p.R816W	ENST00000330258	NM_152424.3	816	Cgg/Tgg	2/2	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.33457434458856	2		781	655	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412395	63412395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	77	938	0	ENST00000330258.3:c.772C>T	p.Pro258Ser	p.P258S	ENST00000330258	NM_152424.3	258	Cca/Tca	2/2	1	2	FACETS	0.658	0.577	0.744	0.658	0.577	0.744	SUBCLONAL	1	TRUE	1	0.33457434458856	2		938	700	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354619	70354619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	145	703	1	ENST00000374080.3:c.4784C>T	p.Ala1595Val	p.A1595V	ENST00000374080		1595	gCt/gTt	35/45	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.33457434458856	2		704	687	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123026585	123026585	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	79	411	2	ENST00000355640.3:c.1061G>T	p.Arg354Ile	p.R354I	ENST00000355640		354	aGa/aTa	5/7	1	2	FACETS	0.87	0.766	0.98	0.87	0.766	0.98	CLONAL	1	TRUE	1	0.33457434458856	2		413	543	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0037270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	126	418	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.954	0.867	1	0.954	0.867	1	CLONAL	1	TRUE	1	0.463609360498354	2		418	570	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0037270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	121	433	1	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.941	0.853	1	0.941	0.853	1	CLONAL	1	TRUE	1	0.463609360498354	2		434	555	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061239	38061241	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0037270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	168	444	0	ENST00000250448.2:c.748_750del	p.Ser250del	p.S250del	ENST00000250448	NM_004496.3	250	TCC/-	2/2	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.463609360498354	2		444	684	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433884	149433884	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0037270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	194	543	0	ENST00000286301.3:c.2763+1del		p.X921_splice	ENST00000286301	NM_005211.3	921			1	2	FACETS	0.947	0.877	1	0.947	0.877	1	CLONAL	1	TRUE	1	0.463609360498354	2		543	884	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155105	108155107	+	missense_variant	Missense_Mutation	TNP	TAT	TAT	CAG	novel	NA	P-0037270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	135	459	0	ENST00000278616.4:c.3898_3900delinsCAG	p.Tyr1300Gln	p.Y1300Q	ENST00000278616	NM_000051.3	1300	TAT/CAG	26/63	1	2	FACETS	0.809	0.736	0.885	0.809	0.736	0.885	CLONAL	1	TRUE	1	0.463609360498354	2		459	720	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591085	67591085	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519839	NA	P-0037274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	62	262	0	ENST00000274335.5:c.1678G>T	p.Asp560Tyr	p.D560Y	ENST00000274335		560	Gac/Tac	12/15	1	2	FACETS	0.997	0.862	1	0.997	0.862	1	CLONAL	1	FALSE	1	0.217810521912753	2		262	571	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577526	7577526	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121912653	NA	P-0037274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	84	557	0	ENST00000269305.4:c.755T>C	p.Leu252Pro	p.L252P	ENST00000269305	NM_001126112.2	252	cTc/cCc	7/11	0.217810521912753	1	FACETS	0.752	0.663	0.848	0.752	0.663	0.848	SUBCLONAL	1	FALSE	0	0.217810521912753	1		557	914	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928225	178928225	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	76	410	0	ENST00000263967.3:c.1411C>G	p.Pro471Ala	p.P471A	ENST00000263967	NM_006218.2	471	Cca/Gca	9/21	1	2	FACETS	0.856	0.75	0.971	0.856	0.75	0.971	CLONAL	1	FALSE	1	0.217810521912753	2		410	815	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692818	89692818	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1339631701	NA	P-0037274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	45	215	0	ENST00000371953.3:c.302T>C	p.Ile101Thr	p.I101T	ENST00000371953	NM_000314.4	101	aTc/aCc	5/9	1	2	FACETS	0.896	0.754	1	0.896	0.754	1	CLONAL	1	FALSE	1	0.217810521912753	2		215	461	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720858	89720858	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1564568660	NA	P-0037274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	48	193	0	ENST00000371953.3:c.1012del	p.Ser338LeufsTer6	p.S338Lfs*6	ENST00000371953	NM_000314.4	337	Ttt/tt	8/9	1	2	FACETS	0.844	0.714	0.988	0.844	0.714	0.988	CLONAL	1	FALSE	1	0.217810521912753	2		193	522	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591032	67591042	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGAAGATTG	GAAGAAGATTG	-	novel	NA	P-0037274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	36	210	0	ENST00000274335.5:c.1633_1643del	p.Asp548AlafsTer4	p.D548Afs*4	ENST00000274335		542	aGAAGAAGATTG/a	12/15	1	2	FACETS	0.682	0.56	0.818	0.682	0.56	0.818	SUBCLONAL	1	FALSE	1	0.217810521912753	2		210	485	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023475	31023475	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	74	423	1	ENST00000375687.4:c.2960G>A	p.Gly987Glu	p.G987E	ENST00000375687	NM_015338.5	987	gGa/gAa	13/13	0.217810521912753	1	FACETS	0.855	0.748	0.971	0.855	0.748	0.971	CLONAL	1	FALSE	0	0.217810521912753	1		424	708	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056478	26056478	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	41	252	0	ENST00000343677.2:c.179C>A	p.Ala60Asp	p.A60D	ENST00000343677	NM_005319.3	60	gCt/gAt	1/1	1	2	FACETS	0.837	0.697	0.991	0.837	0.697	0.991	CLONAL	1	FALSE	1	0.217810521912753	2		252	450	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192600	138192600	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	39	371	0	ENST00000237289.4:c.236G>C	p.Ser79Thr	p.S79T	ENST00000237289	NM_001270507.1	79	aGc/aCc	2/9	0.217810521912753	1	FACETS	0.451	0.372	0.539	0.451	0.372	0.539	SUBCLONAL	1	FALSE	0	0.217810521912753	1		371	708	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519985	NA	P-0037303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	30	831	0	ENST00000269305.4:c.857A>T	p.Glu286Val	p.E286V	ENST00000269305	NM_001126112.2	286	gAa/gTa	8/11	0.313616203862246	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	FALSE	0	0.313616203862246	1		831	117	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259331	36259331	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	28	275	0	ENST00000300305.3:c.160G>A	p.Glu54Lys	p.E54K	ENST00000300305		54	Gag/Aag	3/8	0.102488276399734	4	FACETS	0.961	0.772	1	0.481	0.386	0.588	INDETERMINATE	1	FALSE	2	0.313616203862246	4		275	244	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248007	59248007	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	23	588	0	ENST00000371222.2:c.736G>A	p.Asp246Asn	p.D246N	ENST00000371222	NM_002228.3	246	Gac/Aac	1/1	0.313616203862246	2	FACETS	0.959	0.755	1	0.479	0.377	0.595	CLONAL	1	FALSE	0	0.313616203862246	2		588	153	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457279	67457279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	14	679	0	ENST00000327367.4:c.253C>T	p.His85Tyr	p.H85Y	ENST00000327367	NM_005902.3	85	Cat/Tat	2/9	1	2	FACETS	0.703	0.512	0.93	0.703	0.512	0.93	CLONAL	1	FALSE	1	0.313616203862246	2		679	127	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245383	46245383	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1326784750	NA	P-0037303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	10	485	0	ENST00000334344.6:c.3477C>A	p.Ser1159Arg	p.S1159R	ENST00000334344	NM_152641.2	1159	agC/agA	15/21	0.313616203862246	3	FACETS	1	0.785	1	0.595	0.411	0.816	CLONAL	1	FALSE	1	0.313616203862246	3		485	62	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562747	21562748	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCG	novel	NA	P-0037303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	13	249	0	ENST00000382592.4:c.1169_1171dup	p.Pro390dup	p.P390dup	ENST00000382592	NM_014572.2	390	cgc/cCGCgc	4/8	1	2	FACETS	0.846	0.624	1	1	0.901	1	CLONAL	2	FALSE	1	0.313616203862246	2		249	49	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637534	176637570	+	frameshift_variant	Frame_Shift_Del	DEL	TTAATGGGTTGTACTAAGAGTGCAGAGCCTGGAACCG	TTAATGGGTTGTACTAAGAGTGCAGAGCCTGGAACCG	-	novel	NA	P-0037303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	24	610	0	ENST00000439151.2:c.2134_2170del	p.Leu712ArgfsTer10	p.L712Rfs*10	ENST00000439151	NM_022455.4	712	TTAATGGGTTGTACTAAGAGTGCAGAGCCTGGAACCGag/ag	5/23	0.261008286188485	5	FACETS	1	0.874	1	1	0.874	1	CLONAL	3	FALSE	2	0.313616203862246	5		610	68	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671748	30671748	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	17	765	0	ENST00000376406.3:c.5212G>C	p.Asp1738His	p.D1738H	ENST00000376406	NM_014641.2	1738	Gac/Cac	10/15	0.261008286188485	5	FACETS	1	0.878	1	0.436	0.328	0.56	CLONAL	1	FALSE	2	0.313616203862246	5		765	122	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953087	2953087	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	19	807	0	ENST00000396946.4:c.2853G>C	p.Glu951Asp	p.E951D	ENST00000396946	NM_032415.4	951	gaG/gaC	22/25	1	2	FACETS	1	0.794	1	1	0.794	1	CLONAL	1	FALSE	1	0.313616203862246	2		807	117	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851528	128851528	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	10	792	0	ENST00000249373.3:c.1853G>T	p.Trp618Leu	p.W618L	ENST00000249373	NM_005631.4	618	tGg/tTg	11/12	1	2	FACETS	0.911	0.627	1	0.911	0.627	1	CLONAL	1	FALSE	1	0.313616203862246	2		792	70	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931784	39931784	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	10	799	0	ENST00000378444.4:c.2815T>A	p.Tyr939Asn	p.Y939N	ENST00000378444	NM_001123385.1	939	Tat/Aat	4/15	1	2	FACETS	0.807	0.554	1	0.807	0.554	1	CLONAL	1	FALSE	1	0.313616203862246	2		799	79	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231782	36231782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs74315450	NA	P-0037304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	10	639	1	ENST00000300305.3:c.602G>A	p.Arg201Gln	p.R201Q	ENST00000300305		201	cGa/cAa	5/8	1	2	FACETS	0.169	0.114	0.24	0.169	0.114	0.24	SUBCLONAL	1	FALSE	1	0.239865008214398	2		640	493	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0037304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	16	204	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.239452310142871	4	FACETS	0.889	0.668	1	0.889	0.668	1	CLONAL	2	FALSE	2	0.239865008214398	4		204	93	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0037304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	9	588	1	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	0.159231662489375	4	FACETS	0.318	0.209	0.456	0.159	0.104	0.228	SUBCLONAL	1	FALSE	2	0.239865008214398	4		589	293	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928924	44928924	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	63	228	0	ENST00000377967.4:c.2024G>T	p.Gly675Val	p.G675V	ENST00000377967	NM_021140.2	675	gGt/gTt	17/29	0.239865008214398	2	FACETS	1	0.934	1			1	CLONAL	3	FALSE	NA	0.239865008214398	2		228	162	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278406	39278406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775052125	NA	P-0121476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	156	517	1	ENST00000402219.2:c.743G>A	p.Arg248His	p.R248H	ENST00000402219	NM_005633.3	248	cGc/cAc	6/23	0.6121599283469	4	FACETS	0.694	0.635	0.756	0.231	0.211	0.252	SUBCLONAL	1	NA	1	0.843464694049136	4		518	982	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72864500	72864500	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0121476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	68	401	0	ENST00000325599.8:c.936+1G>T		p.X312_splice	ENST00000325599	NM_018130.2	312			1	2	FACETS	0.351	0.306	0.4	0.351	0.306	0.4	SUBCLONAL	1	NA	1	0.843464694049136	2		401	459	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	113	541	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.941	0.861	1	0.941	0.861	1	CLONAL	1	TRUE	1	0.870066380957237	2		541	276	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197716	123197716	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	220	205	0	ENST00000218089.9:c.1840C>T	p.Arg614Ter	p.R614*	ENST00000218089	NM_001042749.1	614	Cga/Tga	20/35	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.870066380957237	1		205	241	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0037395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	207	703	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.374233430496098	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.381915640682954	2		703	517	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59820438	59820438	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	76	417	0	ENST00000259008.2:c.2315C>T	p.Ser772Leu	p.S772L	ENST00000259008	NM_032043.2	772	tCa/tTa	16/20	0.381915640682954	4	FACETS	1	0.973	1	0.348	0.307	0.392	CLONAL	1	TRUE	0	0.381915640682954	4		417	395	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031606	36031606	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	137	533	0	ENST00000358208.4:c.1435G>C	p.Glu479Gln	p.E479Q	ENST00000358208		479	Gag/Cag	12/12	0.381915640682954	2	FACETS	0.906	0.833	0.981	0.906	0.833	0.981	CLONAL	2	TRUE	0	0.381915640682954	2		533	396	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	302	540	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.258960717118081	4	FACETS	0.985	0.934	1			1	CLONAL	4	TRUE	NA	0.258960717118081	4		540	745	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782664	NA	P-0037398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	231	447	0	ENST00000269305.4:c.711G>C	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atC	7/11	0.258960717118081	1	FACETS	0.93	0.869	0.993	1	0.994	1	CLONAL	2	TRUE	0	0.258960717118081	1		447	835	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827927	40827927	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536150112	NA	P-0037398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	219	624	1	ENST00000373198.4:c.2501G>A	p.Arg834His	p.R834H	ENST00000373198	NM_133170.3	834	cGc/cAc	17/32	1	2	FACETS	0.824	0.767	0.884	1	0.993	1	CLONAL	2	TRUE	1	0.258960717118081	2		625	1026	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971114	21971115	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGGTCGGGTGAGAGTGGCG	novel	NA	P-0037398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	120	225	0	ENST00000304494.5:c.225_243dup	p.Val82ArgfsTer44	p.V82Rfs*44	ENST00000304494	NM_000077.4	81	-/CGCCACTCTCACCCGACCC	2/3	0.258960717118081	2	FACETS	1	0.983	1	0.705	0.638	0.776	CLONAL	1	TRUE	0	0.258960717118081	2		225	657	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603146	48603146	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	164	375	0	ENST00000342988.3:c.1447del	p.Ser483ValfsTer21	p.S483Vfs*21	ENST00000342988	NM_005359.5	483	Agt/gt	11/12	0.258960717118081	1	FACETS	0.936	0.864	1	1	0.992	1	CLONAL	2	TRUE	0	0.258960717118081	1		375	589	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164984	47164984	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0037426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	80	316	0	ENST00000409792.3:c.1142C>G	p.Ser381Ter	p.S381*	ENST00000409792	NM_014159.6	381	tCa/tGa	3/21	0.466663895244879	1	FACETS	0.851	0.756	0.95	0.851	0.756	0.95	CLONAL	1	TRUE	0	0.466663895244879	1		316	309	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16248826	16248826	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	121	428	0	ENST00000375759.3:c.1834del	p.Met612CysfsTer2	p.M612Cfs*2	ENST00000375759	NM_015001.2	611	gAa/ga	10/15	0.43849091404538	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.466663895244879	1		428	394	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051655	30051656	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0037426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	102	332	0	ENST00000338641.4:c.589_590del	p.Gly197ProfsTer5	p.G197Pfs*5	ENST00000338641	NM_000268.3	197	GGc/c	6/16	0.466663895244879	1	FACETS	0.971	0.878	1	0.971	0.878	1	CLONAL	1	TRUE	0	0.466663895244879	1		332	345	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0037457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	91	415	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.245941748589891	0	FACETS	0.758	0.676	0.845			1	SUBCLONAL	1	TRUE	0	0.344415895956579	0		415	457	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0037457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	67	329	1	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.781	0.687	0.88	1	0.976	1	SUBCLONAL	2	TRUE	1	0.344415895956579	2		330	249	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903772	114903772	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	24	429	0	ENST00000543371.1:c.776G>A	p.Trp259Ter	p.W259*	ENST00000543371	NM_001198531.1	259	tGg/tAg	7/14	1	2	FACETS	0.312	0.244	0.391	0.312	0.244	0.391	SUBCLONAL	1	TRUE	1	0.344415895956579	2		429	446	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435201	18435202	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1565550462	NA	P-0037457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	14	306	0	ENST00000266497.5:c.192dup	p.Val65CysfsTer16	p.V65Cfs*16	ENST00000266497		62	-/T	1/31	0.245941748589891	0	FACETS	0.194	0.14	0.26			1	SUBCLONAL	1	TRUE	0	0.344415895956579	0		306	275	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119841	70119842	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0037457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	72	616	0	ENST00000245479.2:c.844dup	p.Val282GlyfsTer14	p.V282Gfs*14	ENST00000245479	NM_000346.3	281	-/G	3/3	1	2	FACETS	0.71	0.621	0.806	0.71	0.621	0.806	SUBCLONAL	1	TRUE	1	0.344415895956579	2		616	589	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374944	45374944	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	81	500	0	ENST00000262160.6:c.899A>T	p.Asp300Val	p.D300V	ENST00000262160	NM_005901.5	300	gAt/gTt	8/11	0.344415895956579	2	FACETS	0.891	0.787	1	0.445	0.393	0.501	CLONAL	1	TRUE	0	0.344415895956579	2		500	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764146326	NA	P-0037524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	185	637	0	ENST00000269305.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000269305	NM_001126112.2	281	Gac/Aac	8/11	0.570330920256829	3	FACETS	0.86	0.793	0.928	0.43	0.396	0.464	CLONAL	1	TRUE	1	0.570330920256829	3		637	970	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0037524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	334	718	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.570330920256829	3	FACETS	0.858	0.814	0.902	0.858	0.814	0.902	CLONAL	2	TRUE	1	0.570330920256829	3		718	877	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0037524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	160	299	0	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	0.444812189822816	3	FACETS	0.982	0.914	1	0.982	0.914	1	CLONAL	2	TRUE	1	0.570330920256829	3		299	367	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925316	114925317	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs745872748	NA	P-0037524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	219	421	17	ENST00000543371.1:c.1403dup	p.Cys469ValfsTer8	p.C469Vfs*8	ENST00000543371	NM_001198531.1	465	aga/agAa	14/14	0.515529489099054	2	FACETS	0.824	0.776	0.872	0.824	0.776	0.872	CLONAL	2	TRUE	0	0.570330920256829	2		438	466	SUCCESS
APC	324	MSKCC	GRCh37	5	112174043	112174044	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0037524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	89	330	0	ENST00000257430.4:c.2756_2757del	p.Arg919LysfsTer4	p.R919Kfs*4	ENST00000257430	NM_000038.5	918	GAg/g	16/16	0.444812189822816	3	FACETS	0.773	0.687	0.864	0.386	0.343	0.432	SUBCLONAL	1	TRUE	1	0.570330920256829	3		330	519	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264568	1264568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761308654	NA	P-0037524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	141	455	0	ENST00000310581.5:c.2794G>A	p.Gly932Ser	p.G932S	ENST00000310581	NM_198253.2	932	Ggc/Agc	11/16	0.570330920256829	3	FACETS	1	0.917	1	0.502	0.458	0.547	CLONAL	1	TRUE	1	0.570330920256829	3		455	633	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	205	541	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	FALSE	1	0.903795997464946	2		541	452	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917496	178917496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	171	444	0	ENST00000263967.3:c.371C>T	p.Pro124Leu	p.P124L	ENST00000263967	NM_006218.2	124	cCa/cTa	3/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.903795997464946	2		444	344	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0037527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	115	147	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.785170122617258	1	FACETS	0.551	0.503	0.6	0.551	0.503	0.6	SUBCLONAL	1	TRUE	0	0.785170122617258	1		147	323	SUCCESS
RET	5979	MSKCC	GRCh37	10	43613906	43613906	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs75030001	NA	P-0037527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	60	511	0	ENST00000355710.3:c.2370G>T	p.Leu790Phe	p.L790F	ENST00000355710	NM_020975.4	790	ttG/ttT	13/20	0.785170122617258	1	FACETS	0.166	0.142	0.191	0.166	0.142	0.191	SUBCLONAL	1	TRUE	0	0.785170122617258	1		511	560	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572227	64572227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060499991	NA	P-0037527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	340	512	0	ENST00000312049.6:c.1412G>A	p.Trp471Ter	p.W471*	ENST00000312049	NM_130799.2	471	tGg/tAg	10/10	0.785170122617258	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.785170122617258	1		512	507	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987059	36987059	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	159	502	0	ENST00000354822.5:c.630C>G	p.Phe210Leu	p.F210L	ENST00000354822	NM_001079668.2	210	ttC/ttG	3/3	1	2	FACETS	0.443	0.405	0.482	0.443	0.405	0.482	SUBCLONAL	1	TRUE	1	0.785170122617258	2		502	915	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288002	33288002	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0037527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	263	398	0	ENST00000374542.5:c.1252-1G>A		p.X418_splice	ENST00000374542	NM_001141970.1	418			0.785170122617258	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.785170122617258	1		398	385	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	33	541	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.18	2		541	268	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434958	49434958	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs398123753	NA	P-0037546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	36	503	0	ENST00000301067.7:c.6595del	p.Tyr2199IlefsTer65	p.Y2199Ifs*65	ENST00000301067	NM_003482.3	2199	Tat/at	31/54	1	2	FACETS	0.966	0.795	1	0.966	0.795	1	CLONAL	1	TRUE	1	0.18	2		503	414	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435072	49435072	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	34	565	0	ENST00000301067.7:c.6481del	p.Leu2161SerfsTer103	p.L2161Sfs*103	ENST00000301067	NM_003482.3	2161	Ctc/tc	31/54	1	2	FACETS	0.855	0.698	1	0.855	0.698	1	CLONAL	1	TRUE	1	0.18	2		565	442	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120785312	120785312	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	32	593	0	ENST00000257552.2:c.796C>T	p.Pro266Ser	p.P266S	ENST00000257552	NM_002442.3	266	Cct/Tct	12/15	1	2	FACETS	0.65	0.526	0.79	0.65	0.526	0.79	SUBCLONAL	1	TRUE	1	0.18	2		593	547	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26970436	26970436	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	18	161	0	ENST00000381527.3:c.805G>C	p.Asp269His	p.D269H	ENST00000381527	NM_001260.1	269	Gat/Cat	8/13	1	2	FACETS	1	0.795	1	1	0.795	1	CLONAL	1	TRUE	1	0.18	2		161	189	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43783886	43783886	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	78	703	4	ENST00000382044.4:c.352C>A	p.Gln118Lys	p.Q118K	ENST00000382044	NM_001141980.1	118	Cag/Aag	4/28	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.18	2		707	828	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	53	795	1	ENST00000269305.4:c.166G>T	p.Glu56Ter	p.E56*	ENST00000269305	NM_001126112.2	56	Gaa/Taa	4/11	1	2	FACETS	0.969	0.825	1	0.969	0.825	1	CLONAL	1	TRUE	1	0.18	2		796	608	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791223	42791223	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	48	805	0	ENST00000575354.2:c.283G>C	p.Glu95Gln	p.E95Q	ENST00000575354	NM_015125.3	95	Gag/Cag	3/20	1	2	FACETS	0.812	0.685	0.952	0.812	0.685	0.952	CLONAL	1	TRUE	1	0.18	2		805	657	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721114	61721114	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	49	522	0	ENST00000401558.2:c.1160C>G	p.Ser387Cys	p.S387C	ENST00000401558	NM_003400.3	387	tCt/tGt	12/25	1	2	FACETS	0.897	0.759	1	0.897	0.759	1	CLONAL	1	TRUE	1	0.18	2		522	607	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458323	12458323	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	66	734	0	ENST00000287820.6:c.940C>G	p.Gln314Glu	p.Q314E	ENST00000287820	NM_015869.4	314	Cag/Gag	6/7	1	2	FACETS	0.892	0.773	1	0.892	0.773	1	CLONAL	1	TRUE	1	0.18	2		734	822	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374998	149374998	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	84	859	1	ENST00000360632.3:c.96C>G	p.Phe32Leu	p.F32L	ENST00000360632	NM_015472.4	32	ttC/ttG	2/7	1	2	FACETS	0.99	0.872	1	0.99	0.872	1	CLONAL	1	TRUE	1	0.18	2		860	943	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293637	137293637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531899705	NA	P-0037546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	66	932	2	ENST00000481739.1:c.188C>T	p.Pro63Leu	p.P63L	ENST00000481739	NM_002957.4	63	cCg/cTg	2/10	0.14306524285273	1	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	0	0.18	1		934	659	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	81	541	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.397334279266003	2		541	365	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054221	30054221	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	180	483	0	ENST00000338641.4:c.643G>T	p.Glu215Ter	p.E215*	ENST00000338641	NM_000268.3	215	Gag/Tag	7/16	0.397334279266003	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.397334279266003	1		483	673	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888139	112888139	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	189	584	0	ENST00000351677.2:c.155C>G	p.Thr52Ser	p.T52S	ENST00000351677	NM_002834.3	52	aCc/aGc	3/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.397334279266003	2		584	869	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557514	21557515	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0037603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	232	673	0	ENST00000382592.4:c.2330dup	p.Leu777PhefsTer4	p.L777Ffs*4	ENST00000382592	NM_014572.2	777	ttg/ttTg	5/8	0.377599614617938	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.397334279266003	1		673	790	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007820	45007821	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0037603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	97	569	0	ENST00000558401.1:c.269dup	p.Thr91HisfsTer4	p.T91Hfs*4	ENST00000558401	NM_004048.2	89	-/T	2/4	0.397334279266003	1	FACETS	0.557	0.496	0.621	0.557	0.496	0.621	SUBCLONAL	1	TRUE	0	0.397334279266003	1		569	703	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095539	178095540	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0037608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	147	551	0	ENST00000397062.3:c.1791dup	p.Lys598Ter	p.K598*	ENST00000397062	NM_006164.4	597	-/T	5/5	0.20065826624528	4	FACETS	0.823	0.753	0.896	0.823	0.753	0.896	INDETERMINATE	2	FALSE	2	0.335446506834434	4		551	711	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97934323	97934323	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	64	339	1	ENST00000289081.3:c.452A>G	p.Lys151Arg	p.K151R	ENST00000289081	NM_000136.2	151	aAa/aGa	5/15	0.155690141733997	4	FACETS	1	0.954	1	0.614	0.533	0.701	INDETERMINATE	1	FALSE	2	0.335446506834434	4		340	415	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941825	44941825	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	128	198	0	ENST00000377967.4:c.3152del	p.Asn1051MetfsTer32	p.N1051Mfs*32	ENST00000377967	NM_021140.2	1050	gAa/ga	21/29	0.281594567000212	2	FACETS	0.877	0.809	0.946			1	CLONAL	3	FALSE	NA	0.335446506834434	2		198	290	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0037623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	166	388	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.878	0.81	0.948	0.878	0.81	0.948	CLONAL	1	TRUE	1	0.631411813089472	2		388	599	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436297	110436305	+	inframe_deletion	In_Frame_Del	DEL	CGGCGGCGG	CGGCGGCGG	-	rs34412495	NA	P-0037623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	50	61	0	ENST00000375856.3:c.2096_2104del	p.Ala699_Ala701del	p.A699_A701del	ENST00000375856	NM_003749.2	699	gCCGCCGCCGtg/gtg	1/2	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.631411813089472	2		61	154	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061208	38061208	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	62	290	1	ENST00000250448.2:c.781C>A	p.Arg261Ser	p.R261S	ENST00000250448	NM_004496.3	261	Cgc/Agc	2/2	1	2	FACETS	0.493	0.428	0.564	0.493	0.428	0.564	SUBCLONAL	1	TRUE	1	0.631411813089472	2		291	398	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023637	27023638	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTCCAAGCCGC	novel	NA	P-0037623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	32	107	0	ENST00000324856.7:c.748_758dup	p.Ser255ArgfsTer112	p.S255Rfs*112	ENST00000324856	NM_006015.4	248	ggc/ggCTCCAAGCCGCc	1/20	0.156212912608653	0	FACETS	0.187	0.153	0.225			1	INDETERMINATE	1	TRUE	0	0.631411813089472	0		107	200	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0037640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	84	388	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.190808603806885	2		388	865	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100727	8100728	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs771019738	NA	P-0037640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	53	770	1	ENST00000346208.3:c.708dup	p.Ser237GlnfsTer66	p.S237Qfs*66	ENST00000346208		234	ttc/ttCc	3/6	1	2	FACETS	0.903	0.77	1	0.903	0.77	1	CLONAL	1	TRUE	1	0.190808603806885	2		771	615	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845523	151845524	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0037640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	55	988	0	ENST00000262189.6:c.13488dup	p.Lys4497Ter	p.K4497*	ENST00000262189	NM_170606.2	4496	-/T	52/59	1	2	FACETS	0.725	0.619	0.842	0.725	0.619	0.842	SUBCLONAL	1	TRUE	1	0.190808603806885	2		988	795	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117308	115117308	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0037640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	28	406	0	ENST00000257566.3:c.864+2T>C		p.X288_splice	ENST00000257566	NM_016569.3	288			0.190808603806885	1	FACETS	0.752	0.601	0.924	0.752	0.601	0.924	CLONAL	1	TRUE	0	0.190808603806885	1		406	353	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178694	56178695	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0037640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	13	261	0	ENST00000399503.3:c.3666+2dup		p.X1222_splice	ENST00000399503	NM_005921.1	1222			0.190817931306644	3	FACETS	0.739	0.528	0.996	0.369	0.264	0.498	CLONAL	1	TRUE	1	0.190808603806885	3		261	202	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106314	27106331	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTCTTGCCAAGCGCTG	TTCTCTTGCCAAGCGCTG	AGAGAATC	novel	NA	P-0037640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	46	869	2	ENST00000324856.7:c.5925_5942delinsAGAGAATC	p.Asp1975GlufsTer37	p.D1975Efs*37	ENST00000324856	NM_006015.4	1975	gaTTCTCTTGCCAAGCGCTGc/gaAGAGAATCc	20/20	1	2	FACETS	0.645	0.542	0.76	0.645	0.542	0.76	SUBCLONAL	1	TRUE	1	0.190808603806885	2		871	747	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0037647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	242	272	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.394903332803748	3	FACETS	0.866	0.811	0.922	0.866	0.811	0.922	CLONAL	2	TRUE	1	0.419558452211553	3		272	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0037647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	216	836	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.419558452211553	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.419558452211553	1		836	779	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	125	540	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.390957894384835	3	FACETS	1	0.981	1	0.658	0.598	0.721	CLONAL	1	TRUE	1	0.390843195020137	3		540	581	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0037657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	162	500	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.390957894384835	3	FACETS	0.903	0.833	0.974	0.903	0.833	0.974	CLONAL	2	TRUE	1	0.390843195020137	3		500	549	SUCCESS
APC	324	MSKCC	GRCh37	5	112174058	112174058	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0037657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	42	325	0	ENST00000257430.4:c.2767A>T	p.Arg923Ter	p.R923*	ENST00000257430	NM_000038.5	923	Aga/Tga	16/16	0.390957894384835	3	FACETS	0.646	0.54	0.763	0.323	0.27	0.382	SUBCLONAL	1	TRUE	1	0.390843195020137	3		325	398	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665110	182665110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1361986556	NA	P-0037657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	53	378	0	ENST00000292782.4:c.616C>T	p.Arg206Ter	p.R206*	ENST00000292782	NM_020640.2	206	Cga/Tga	6/7	0.390957894384835	3	FACETS	0.585	0.499	0.68	0.293	0.249	0.34	SUBCLONAL	1	TRUE	1	0.390843195020137	3		378	554	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020866	26020866	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	92	347	0	ENST00000357647.3:c.149G>C	p.Arg50Pro	p.R50P	ENST00000357647	NM_003529.2	50	cGc/cCc	1/1	0.265193079226436	3	FACETS	0.935	0.841	1	0.623	0.56	0.689	CLONAL	2	TRUE	0	0.390843195020137	3		347	301	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911170	29911170	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs199474532	NA	P-0037657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	45	408	0	ENST00000376809.5:c.469T>G	p.Trp157Gly	p.W157G	ENST00000376809	NM_002116.7	157	Tgg/Ggg	3/8	0.265193079226436	3	FACETS	0.966	0.817	1	0.322	0.272	0.377	CLONAL	1	TRUE	0	0.390843195020137	3		408	285	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323208	31323208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	271	643	0	ENST00000412585.2:c.781G>A	p.Gly261Arg	p.G261R	ENST00000412585	NM_005514.6	261	Gga/Aga	4/8	0.265193079226436	3	FACETS	1	0.991	1	0.827	0.781	0.874	CLONAL	2	TRUE	0	0.390843195020137	3		643	668	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0037683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	13	418	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.192179059087166	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		418	295	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0037683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	31	566	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		567	335	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427231	49427231	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs746280829	NA	P-0037683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	40	778	0	ENST00000301067.7:c.11257A>G	p.Ile3753Val	p.I3753V	ENST00000301067	NM_003482.3	3753	Atc/Gtc	39/54	0.192179059087166	4	FACETS		NA	1			1	NA	NA	FALSE	2	NA	4		778	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0037689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	738	539	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.792358900634937	3	FACETS	0.981	0.965	0.997	0.981	0.965	0.997	CLONAL	3	TRUE	0	0.82689644950753	3		539	857	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	240539	240539	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	13	33	0	ENST00000264932.6:c.1499G>C	p.Arg500Thr	p.R500T	ENST00000264932	NM_004168.2	500	aGa/aCa	11/15	0.82689644950753	4	FACETS	0.857	0.625	1	0.286	0.208	0.376	CLONAL	1	TRUE	1	0.82689644950753	4		33	67	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428229	49428229	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs902898516	NA	P-0037689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	143	694	1	ENST00000301067.7:c.10471C>T	p.Arg3491Cys	p.R3491C	ENST00000301067	NM_003482.3	3491	Cgt/Tgt	37/54	0.174706700518829	2	FACETS	0.431	0.393	0.471	0.215	0.196	0.236	INDETERMINATE	1	TRUE	0	0.82689644950753	2		695	803	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349447	73349447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	576	543	0	ENST00000377767.4:c.889C>T	p.Leu297Phe	p.L297F	ENST00000377767	NM_014953.3	297	Ctc/Ttc	6/21	0.810360328550926	3	FACETS	0.996	0.978	1	0.996	0.978	1	CLONAL	3	TRUE	0	0.82689644950753	3		543	659	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134422	30134422	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	144	565	0	ENST00000263025.4:c.109G>C	p.Asp37His	p.D37H	ENST00000263025	NM_002746.2	37	Gac/Cac	1/9	0.787046483262822	2	FACETS	0.619	0.567	0.672	0.309	0.283	0.336	SUBCLONAL	1	TRUE	0	0.82689644950753	2		565	563	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375007	45375007	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	201	556	0	ENST00000262160.6:c.836A>G	p.Tyr279Cys	p.Y279C	ENST00000262160	NM_005901.5	279	tAt/tGt	8/11	0.822286744093775	1	FACETS	0.98	0.933	1	0.98	0.933	1	CLONAL	1	TRUE	0	0.82689644950753	1		556	291	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164458	36164458	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	37	197	0	ENST00000300305.3:c.1417G>C	p.Glu473Gln	p.E473Q	ENST00000300305		473	Gag/Cag	8/8	0.397209257018313	3	FACETS	0.56	0.465	0.664	0.187	0.155	0.222	INDETERMINATE	1	TRUE	0	0.82689644950753	3		197	226	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31401588	31401588	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	159	744	0	ENST00000344624.3:c.4076G>C	p.Arg1359Thr	p.R1359T	ENST00000344624		1359	aGa/aCa	33/33	0.82689644950753	4	FACETS	0.519	0.474	0.566	0.173	0.158	0.189	SUBCLONAL	1	TRUE	1	0.82689644950753	4		744	1355	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878177	48878181	+	frameshift_variant	Frame_Shift_Del	DEL	TCTCG	TCTCG	-	novel	NA	P-0037689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	57	87	0	ENST00000267163.4:c.131_135del	p.Leu44GlnfsTer3	p.L44Qfs*3	ENST00000267163	NM_000321.2	43	ccTCTCGtc/cctc	1/27	0.810360328550926	3	FACETS	0.866	0.796	0.929	0.866	0.796	0.929	CLONAL	3	TRUE	0	0.82689644950753	3		87	75	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0037700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	245	643	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	1	2	FACETS	1	0.952	1	1	0.996	1	CLONAL	3	FALSE	1	0.226307521783329	2		643	711	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631935	90631935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267606870	NA	P-0037700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	12	705	0	ENST00000330062.3:c.418C>T	p.Arg140Trp	p.R140W	ENST00000330062	NM_002168.2	140	Cgg/Tgg	4/11	1	2	FACETS	0.188	0.131	0.259	0.188	0.131	0.259	SUBCLONAL	1	FALSE	1	0.226307521783329	2		705	563	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259238	36259239	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0037700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	231	419	1	ENST00000300305.3:c.252_253insT	p.His85SerfsTer53	p.H85Sfs*53	ENST00000300305		84	-/T	3/8	1	2	FACETS	1	0.976	1	1	0.996	1	CLONAL	3	FALSE	1	0.226307521783329	2		420	630	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0037757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	132	364	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.584610730682528	3	FACETS	0.988	0.9	1	0.494	0.45	0.54	CLONAL	1	TRUE	1	0.580629648992676	3		364	594	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608346	43608346	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	226	986	1	ENST00000355710.3:c.1694G>T	p.Cys565Phe	p.C565F	ENST00000355710	NM_020975.4	565	tGc/tTc	9/20	0.505888872972098	3	FACETS	0.788	0.733	0.846	0.394	0.366	0.423	SUBCLONAL	1	TRUE	1	0.580629648992676	3		987	1274	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871836	12871836	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	107	375	0	ENST00000228872.4:c.553G>C	p.Glu185Gln	p.E185Q	ENST00000228872	NM_004064.3	185	Gag/Cag	2/3	0.556454609295767	3	FACETS	0.813	0.731	0.899	0.406	0.365	0.45	CLONAL	1	TRUE	1	0.580629648992676	3		375	585	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442705	99442705	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0037757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1398	128	547	0	ENST00000268035.6:c.1103-1G>A		p.X368_splice	ENST00000268035	NM_000875.3	368			0.580629648992676	7	FACETS	0.708	0.639	0.782			1	SUBCLONAL	1	TRUE	NA	0.580629648992676	7		547	1526	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944441	40944441	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	215	692	0	ENST00000373198.4:c.2061C>A	p.Tyr687Ter	p.Y687*	ENST00000373198	NM_133170.3	687	taC/taA	12/32	0.584610730682528	3	FACETS	0.981	0.912	1	0.491	0.456	0.526	CLONAL	1	TRUE	1	0.580629648992676	3		692	974	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554397	141554397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	275	837	4	ENST00000220592.5:c.1754C>T	p.Pro585Leu	p.P585L	ENST00000220592	NM_012154.3	585	cCg/cTg	14/19	NA	2	FACETS	0.986	0.927	1			1	INDETERMINATE	1	TRUE	NA	0.580629648992676	2		841	961	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0037769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	336	565	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	NA	2	FACETS	0.865	0.821	0.91			1	INDETERMINATE	1	TRUE	NA	0.864297365945434	2		565	899	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947827	178947827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	285	336	0	ENST00000263967.3:c.2702G>T	p.Cys901Phe	p.C901F	ENST00000263967	NM_006218.2	901	tGt/tTt	19/21	0.568658265803554	3	FACETS	0.886	0.843	0.929			1	CLONAL	2	TRUE	NA	0.864297365945434	3		336	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577524	7577524	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	503	504	0	ENST00000269305.4:c.757A>C	p.Thr253Pro	p.T253P	ENST00000269305	NM_001126112.2	253	Acc/Ccc	7/11	0.862647386102008	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.864297365945434	1		504	635	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247168	153247168	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1560758208	NA	P-0037769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	93	257	0	ENST00000281708.4:c.1634A>G	p.Tyr545Cys	p.Y545C	ENST00000281708	NM_033632.3	545	tAt/tGt	10/12	0.415084966415427	1	FACETS	0.354	0.318	0.392	0.354	0.318	0.392	INDETERMINATE	1	TRUE	0	0.864297365945434	1		257	345	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0037791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	58	908	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	1	2	FACETS	0.495	0.424	0.573	0.495	0.424	0.573	SUBCLONAL	1	FALSE	1	0.244090687602474	2		908	960	SUCCESS
APC	324	MSKCC	GRCh37	5	112175288	112175288	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0037791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	114	336	0	ENST00000257430.4:c.3997A>T	p.Lys1333Ter	p.K1333*	ENST00000257430	NM_000038.5	1333	Aaa/Taa	16/16	0.24089860960515	3	FACETS	0.867	0.787	0.95	0.867	0.787	0.95	CLONAL	3	FALSE	0	0.244090687602474	3		336	403	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636973	176636973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1215568879	NA	P-0037791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	59	752	1	ENST00000439151.2:c.1573C>T	p.Arg525Trp	p.R525W	ENST00000439151	NM_022455.4	525	Cgg/Tgg	5/23	0.24089860960515	3	FACETS	0.567	0.486	0.655	0.189	0.162	0.219	SUBCLONAL	1	FALSE	0	0.244090687602474	3		753	957	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578183	7578184	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCT	novel	NA	P-0037791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	128	889	0	ENST00000269305.4:c.662_665dup	p.Pro223AlafsTer3	p.P223Afs*3	ENST00000269305	NM_001126112.2	222	ccg/ccAGCCg	6/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.244090687602474	2		889	900	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58711302	58711302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	59	716	0	ENST00000305921.3:c.790G>T	p.Asp264Tyr	p.D264Y	ENST00000305921	NM_003620.3	264	Gac/Tac	3/6	1	2	FACETS	0.553	0.474	0.639	0.553	0.474	0.639	SUBCLONAL	1	FALSE	1	0.244090687602474	2		716	874	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645800	215645800	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1553622436	NA	P-0037791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	51	619	0	ENST00000260947.4:c.798G>C	p.Leu266Phe	p.L266F	ENST00000260947	NM_000465.2	266	ttG/ttC	4/11	0.244090687602474	1	FACETS	0.57	0.483	0.665	0.57	0.483	0.665	SUBCLONAL	1	FALSE	0	0.244090687602474	1		619	644	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	290	708	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.552601263239424	2		708	806	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	167	368	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.552601263239424	2		368	423	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	174	707	7	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.552601263239424	2		714	557	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	257	528	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.552601263239424	2		528	710	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437697	52437697	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1553644922	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	235	671	0	ENST00000460680.1:c.1464del	p.Ser489AlafsTer82	p.S489Afs*82	ENST00000460680	NM_004656.3	488	ccC/cc	13/17	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.552601263239424	2		671	678	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685330	86685330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	24	123	0	ENST00000274376.6:c.3046C>T	p.Arg1016Cys	p.R1016C	ENST00000274376	NM_002890.2	1016	Cgt/Tgt	24/25	0.413939785880794	1	FACETS	0.4	0.317	0.495	0.4	0.317	0.495	SUBCLONAL	1	TRUE	0	0.552601263239424	1		123	157	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	302	853	2	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.552601263239424	2		855	820	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	391	784	0	ENST00000269305.4:c.379T>C	p.Ser127Pro	p.S127P	ENST00000269305	NM_001126112.2	127	Tcc/Ccc	5/11	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.552601263239424	2		784	979	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500499	99500499	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771642071	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	230	285	1	ENST00000268035.6:c.3932C>T	p.Ser1311Leu	p.S1311L	ENST00000268035	NM_000875.3	1311	tCg/tTg	21/21	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.552601263239424	2		286	560	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	155	295	2	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.552601263239424	2		297	394	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944382	131944382	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs748536322	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	97	199	4	ENST00000265335.6:c.2801del	p.Asn934IlefsTer6	p.N934Ifs*6	ENST00000265335		932	Aaa/aa	17/25	0.413939785880794	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.552601263239424	1		203	229	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913253	39913253	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	221	517	0	ENST00000378444.4:c.4862del	p.Pro1621GlnfsTer53	p.P1621Qfs*53	ENST00000378444	NM_001123385.1	1621	cCa/ca	14/15	0.552601263239424	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.552601263239424	1		517	392	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248860	133248860	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs116260568	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	304	585	0	ENST00000320574.5:c.1735C>T	p.Arg579Cys	p.R579C	ENST00000320574	NM_006231.2	579	Cgc/Tgc	16/49	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.552601263239424	2		585	842	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	137	471	5	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.552601263239424	2		476	381	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512401	38512402	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs745553450	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	176	705	2	ENST00000254066.5:c.1319dup	p.Pro441AlafsTer5	p.P441Afs*5	ENST00000254066	NM_000964.3	438	gcc/gCcc	9/9	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.552601263239424	2		707	599	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925132	81925132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199636472	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	99	532	0	ENST00000359376.3:c.923C>T	p.Ala308Val	p.A308V	ENST00000359376	NM_002661.3	308	gCg/gTg	11/33	1	2	FACETS	0.629	0.562	0.699	0.629	0.562	0.699	SUBCLONAL	1	TRUE	1	0.552601263239424	2		532	570	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390120	89390120	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	142	302	0	ENST00000336596.2:c.869G>T	p.Cys290Phe	p.C290F	ENST00000336596	NM_005233.5	290	tGc/tTc	4/17	1	2	FACETS	0.751	0.695	0.809	1	0.989	1	SUBCLONAL	2	TRUE	1	0.552601263239424	2		302	342	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097830	8097830	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1425866094	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	275	635	0	ENST00000346208.3:c.212C>T	p.Thr71Met	p.T71M	ENST00000346208		71	aCg/aTg	2/6	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.552601263239424	2		635	676	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585494	29585494	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660428	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	74	232	0	ENST00000356175.3:c.4243G>A	p.Glu1415Lys	p.E1415K	ENST00000356175	NM_000267.3	1415	Gaa/Aaa	31/57	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.552601263239424	2		232	202	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041211	112041211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140762956	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	192	449	1	ENST00000368678.4:c.44C>T	p.Thr15Met	p.T15M	ENST00000368678		15	aCg/aTg	3/13	0.496430859098751	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.552601263239424	1		450	401	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	140	574	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.413939785880794	1	FACETS	0.592	0.541	0.646	0.592	0.541	0.646	SUBCLONAL	1	TRUE	0	0.552601263239424	1		580	619	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	475	874	2	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	0.219510232057517	3	FACETS	0.829	0.792	0.865	0.552	0.528	0.577	INDETERMINATE	2	TRUE	0	0.552601263239424	3		876	1324	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300040	137300040	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	111	726	0	ENST00000481739.1:c.331del	p.Leu111TrpfsTer57	p.L111Wfs*57	ENST00000481739	NM_002957.4	109	Ccc/cc	3/10	1	2	FACETS	0.507	0.456	0.562	0.507	0.456	0.562	SUBCLONAL	1	TRUE	1	0.552601263239424	2		726	792	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344955	118344955	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	109	243	1	ENST00000534358.1:c.3086del	p.Lys1029ArgfsTer65	p.K1029Rfs*65	ENST00000534358	NM_005933.3	1027	ctA/ct	3/36	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.552601263239424	2		244	282	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522590	176522590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765924274	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	165	768	0	ENST00000292408.4:c.1687C>T	p.Arg563Trp	p.R563W	ENST00000292408	NM_213647.1	563	Cgg/Tgg	13/18	0.552601263239424	1	FACETS	0.704	0.649	0.76	0.704	0.649	0.76	SUBCLONAL	1	TRUE	0	0.552601263239424	1		768	614	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197281	94197282	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs774440500	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	133	382	0	ENST00000323929.3:c.1222dup	p.Thr408AsnfsTer49	p.T408Nfs*49	ENST00000323929	NM_005591.3	408	aca/aAca	11/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.552601263239424	2		382	410	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287468	46287469	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	126	376	0	ENST00000334344.6:c.5333dup	p.Asn1778LysfsTer4	p.N1778Kfs*4	ENST00000334344	NM_152641.2	1776	tta/ttAa	20/21	1	2	FACETS	0.979	0.892	1	0.979	0.892	1	CLONAL	1	TRUE	1	0.552601263239424	2		376	466	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121888	2121888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779275341	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	258	780	0	ENST00000219476.3:c.2050G>A	p.Val684Met	p.V684M	ENST00000219476	NM_000548.3	684	Gtg/Atg	19/42	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.552601263239424	2		780	692	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1620979	1620979	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1329397192	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	361	845	3	ENST00000344749.5:c.1081del	p.Gln361ArgfsTer33	p.Q361Rfs*33	ENST00000344749	NM_001136139.2	361	Cag/ag	13/19	0.525107821742589	0	FACETS		NA	1			1	NA	2	TRUE	0	0.552601263239424	0		848	553	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258894	16258894	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	177	672	3	ENST00000375759.3:c.6164del	p.Pro2055LeufsTer9	p.P2055Lfs*9	ENST00000375759	NM_015001.2	2053	aaC/aa	11/15	1	2	FACETS	0.799	0.737	0.863	0.799	0.737	0.863	SUBCLONAL	1	TRUE	1	0.552601263239424	2		675	802	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437355	121437355	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	256	720	0	ENST00000257555.6:c.1693C>A	p.Leu565Ile	p.L565I	ENST00000257555		565	Ctc/Atc	9/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.552601263239424	2		720	725	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319305	11319305	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	39	462	0	ENST00000361445.4:c.162G>T	p.Glu54Asp	p.E54D	ENST00000361445	NM_004958.3	54	gaG/gaT	2/58	1	2	FACETS	0.292	0.242	0.348	0.292	0.242	0.348	SUBCLONAL	1	TRUE	1	0.552601263239424	2		462	483	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023193	27023193	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	37	150	0	ENST00000324856.7:c.299T>C	p.Leu100Pro	p.L100P	ENST00000324856	NM_006015.4	100	cTg/cCg	1/20	1	2	FACETS	0.93	0.78	1	0.93	0.78	1	CLONAL	1	TRUE	1	0.552601263239424	2		150	144	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65312372	65312372	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	172	441	0	ENST00000342505.4:c.1947C>A	p.His649Gln	p.H649Q	ENST00000342505	NM_002227.2	649	caC/caA	14/25	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.552601263239424	2		441	536	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446207	70446207	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	160	439	0	ENST00000373644.4:c.5147C>G	p.Thr1716Arg	p.T1716R	ENST00000373644	NM_030625.2	1716	aCa/aGa	11/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.552601263239424	2		439	423	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999024	100999024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	175	611	0	ENST00000325455.5:c.778del	p.Ala260ArgfsTer41	p.A260Rfs*41	ENST00000325455	NM_001202474.3	260	Gcg/cg	1/8	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.552601263239424	2		611	459	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246677	46246677	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	39	140	0	ENST00000334344.6:c.4771C>T	p.Gln1591Ter	p.Q1591*	ENST00000334344	NM_152641.2	1591	Cag/Tag	15/21	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.552601263239424	2		140	122	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421834	49421834	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs117904191	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	116	766	0	ENST00000301067.7:c.14473C>T	p.Arg4825Trp	p.R4825W	ENST00000301067	NM_003482.3	4825	Cgg/Tgg	46/54	1	2	FACETS	0.478	0.43	0.529	0.478	0.43	0.529	SUBCLONAL	1	TRUE	1	0.552601263239424	2		766	878	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434851	49434851	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1460481305	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	61	874	0	ENST00000301067.7:c.6702del	p.Arg2235AspfsTer29	p.R2235Dfs*29	ENST00000301067	NM_003482.3	2234	ccC/cc	31/54	1	2	FACETS	0.283	0.243	0.326	0.283	0.243	0.326	SUBCLONAL	1	TRUE	1	0.552601263239424	2		874	781	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443789	49443789	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	320	745	0	ENST00000301067.7:c.3582del	p.Thr1195HisfsTer17	p.T1195Hfs*17	ENST00000301067	NM_003482.3	1194	ccC/cc	11/54	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.552601263239424	2		745	889	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444006	49444006	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs541921137	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	235	660	1	ENST00000301067.7:c.3365C>T	p.Thr1122Ile	p.T1122I	ENST00000301067	NM_003482.3	1122	aCa/aTa	11/54	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.552601263239424	2		661	670	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484165	50484165	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	73	540	0	ENST00000394963.4:c.1015T>G	p.Cys339Gly	p.C339G	ENST00000394963	NM_003076.4	339	Tgt/Ggt	8/13	1	2	FACETS	0.484	0.424	0.549	0.484	0.424	0.549	SUBCLONAL	1	TRUE	1	0.552601263239424	2		540	546	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861804	57861804	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	44	521	0	ENST00000228682.2:c.1105T>C	p.Cys369Arg	p.C369R	ENST00000228682	NM_005269.2	369	Tgc/Cgc	10/12	1	2	FACETS	0.261	0.218	0.308	0.261	0.218	0.308	SUBCLONAL	1	TRUE	1	0.552601263239424	2		521	611	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345121	73345121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	123	284	0	ENST00000377767.4:c.1676C>T	p.Ala559Val	p.A559V	ENST00000377767	NM_014953.3	559	gCa/gTa	13/21	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.552601263239424	2		284	315	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996065	73996065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747735855	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	202	868	3	ENST00000318443.5:c.799C>T	p.Arg267Cys	p.R267C	ENST00000318443	NM_001024736.1	267	Cgc/Tgc	5/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.552601263239424	2		871	682	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646215	3646215	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1175366606	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	242	768	1	ENST00000294008.3:c.1863G>T	p.Glu621Asp	p.E621D	ENST00000294008	NM_032444.2	621	gaG/gaT	8/15	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.552601263239424	2		769	642	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349508	89349508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143417087	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	258	677	0	ENST00000301030.4:c.3442G>A	p.Gly1148Ser	p.G1148S	ENST00000301030	NM_001256183.1	1148	Ggc/Agc	9/13	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.552601263239424	2		677	671	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492830	56492832	+	inframe_deletion	In_Frame_Del	DEL	CCA	CCA	-	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	173	368	0	ENST00000407977.2:c.107_109del	p.Val36del	p.V36del	ENST00000407977		36	gTGGag/gag	2/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.552601263239424	2		368	480	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533094	63533094	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	201	581	0	ENST00000307078.5:c.1800del	p.Gly601AlafsTer88	p.G601Afs*88	ENST00000307078	NM_004655.3	600	ccC/cc	7/11	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.552601263239424	2		581	509	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211124	2211124	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	345	807	0	ENST00000398665.3:c.1378T>G	p.Phe460Val	p.F460V	ENST00000398665	NM_032482.2	460	Ttc/Gtc	15/28	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.552601263239424	2		807	954	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349715	15349715	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	239	621	0	ENST00000263377.2:c.3859C>G	p.Gln1287Glu	p.Q1287E	ENST00000263377	NM_058243.2	1287	Cag/Gag	19/20	1	2	FACETS	0.802	0.757	0.849	1	0.994	1	CLONAL	2	TRUE	1	0.552601263239424	2		621	539	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632276	215632276	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779468443	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	126	474	0	ENST00000260947.4:c.1498G>A	p.Asp500Asn	p.D500N	ENST00000260947	NM_000465.2	500	Gat/Aat	6/11	0.191162987296779	2	FACETS	0.869	0.79	0.95	0.434	0.395	0.475	INDETERMINATE	1	TRUE	0	0.552601263239424	2		474	525	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660748	227660748	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	278	685	0	ENST00000305123.5:c.2707A>G	p.Ser903Gly	p.S903G	ENST00000305123	NM_005544.2	903	Agt/Ggt	1/2	0.191162987296779	2	FACETS	0.817	0.774	0.86	0.817	0.774	0.86	INDETERMINATE	2	TRUE	0	0.552601263239424	2		685	616	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722777	49722777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381537507	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	13	63	0	ENST00000449682.2:c.1462C>T	p.Arg488Trp	p.R488W	ENST00000449682	NM_020998.3	488	Cgg/Tgg	13/18	1	2	FACETS	1	0.786	1	1	0.786	1	CLONAL	1	TRUE	1	0.552601263239424	2		63	44	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637650	52637650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752454573	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	187	417	0	ENST00000394830.3:c.2666C>T	p.Pro889Leu	p.P889L	ENST00000394830	NM_018313.4	889	cCg/cTg	18/30	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.552601263239424	2		417	511	SUCCESS
ATR	545	MSKCC	GRCh37	3	142222220	142222220	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	93	389	1	ENST00000350721.4:c.5272G>T	p.Gly1758Ter	p.G1758*	ENST00000350721	NM_001184.3	1758	Gga/Tga	30/47	1	2	FACETS	0.741	0.662	0.825	0.741	0.662	0.825	SUBCLONAL	1	TRUE	1	0.552601263239424	2		390	454	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191229	185191229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	127	444	0	ENST00000265026.3:c.2110G>A	p.Ala704Thr	p.A704T	ENST00000265026	NM_004721.4	704	Gct/Act	11/14	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.552601263239424	2		444	395	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245453	153245453	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	68	509	0	ENST00000281708.4:c.1738C>A	p.His580Asn	p.H580N	ENST00000281708	NM_033632.3	580	Cac/Aac	11/12	NA	2	FACETS	0.636	0.556	0.722			1	INDETERMINATE	1	TRUE	NA	0.552601263239424	2		509	387	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259052	153259052	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	58	163	0	ENST00000281708.4:c.763G>T	p.Glu255Ter	p.E255*	ENST00000281708	NM_033632.3	255	Gaa/Taa	5/12	NA	2	FACETS	0.755	0.667	0.845			1	INDETERMINATE	2	TRUE	NA	0.552601263239424	2		163	139	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665360	176665360	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	89	353	0	ENST00000439151.2:c.4044G>T	p.Glu1348Asp	p.E1348D	ENST00000439151	NM_022455.4	1348	gaG/gaT	7/23	0.552601263239424	1	FACETS	0.646	0.577	0.718	0.646	0.577	0.718	SUBCLONAL	1	TRUE	0	0.552601263239424	1		353	361	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985533	2985533	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	156	467	0	ENST00000396946.4:c.278A>G	p.Glu93Gly	p.E93G	ENST00000396946	NM_032415.4	93	gAg/gGg	4/25	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.552601263239424	2		467	506	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273281	55273281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	221	467	1	ENST00000275493.2:c.3604C>T	p.Pro1202Ser	p.P1202S	ENST00000275493	NM_005228.3	1202	Cca/Tca	28/28	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.552601263239424	2		468	552	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012235	152012235	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	140	357	0	ENST00000262189.6:c.578G>A	p.Arg193Lys	p.R193K	ENST00000262189	NM_170606.2	193	aGa/aAa	4/59	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.552601263239424	2		357	430	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006158	22006158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377452255	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	298	667	0	ENST00000276925.6:c.245G>A	p.Arg82Gln	p.R82Q	ENST00000276925	NM_004936.3	82	cGa/cAa	2/2	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.552601263239424	2		667	724	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760343	133760343	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	96	620	0	ENST00000318560.5:c.2666A>T	p.Lys889Met	p.K889M	ENST00000318560	NM_005157.4	889	aAg/aTg	11/11	1	2	FACETS	0.663	0.593	0.738	0.663	0.593	0.738	SUBCLONAL	1	TRUE	1	0.552601263239424	2		620	524	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564638	139564638	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778100938	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	311	866	0	ENST00000308874.7:c.427G>A	p.Ala143Thr	p.A143T	ENST00000308874		143	Gct/Act	7/10	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.552601263239424	2		866	810	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139804439	139804439	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199507094	NA	P-0037867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	257	571	0	ENST00000247668.2:c.596G>T	p.Arg199Leu	p.R199L	ENST00000247668	NM_021138.3	199	cGg/cTg	6/11	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.552601263239424	2		571	674	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0037903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	149	388	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.369751638673676	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	2	0.46566935920948	4		388	444	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	271	554	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	1	2	FACETS	0.964	0.909	1	0.964	0.909	1	CLONAL	1	TRUE	1	0.742525581422897	2		554	757	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236087	108236087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781894	NA	P-0037943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	371	539	1	ENST00000278616.4:c.9023G>A	p.Arg3008His	p.R3008H	ENST00000278616	NM_000051.3	3008	cGt/cAt	63/63	0.742525581422897	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.742525581422897	1		540	542	SUCCESS
APC	324	MSKCC	GRCh37	5	112174241	112174241	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1254176854	NA	P-0037943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	165	450	0	ENST00000257430.4:c.2950G>T	p.Glu984Ter	p.E984*	ENST00000257430	NM_000038.5	984	Gaa/Taa	16/16	1	2	FACETS	0.94	0.87	1	0.94	0.87	1	CLONAL	1	TRUE	1	0.742525581422897	2		450	473	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606096	81606096	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	305	534	0	ENST00000298171.2:c.766A>C	p.Asn256His	p.N256H	ENST00000298171	NM_000369.2	256	Aac/Cac	9/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.742525581422897	2		534	776	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882995	89882995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	140	137	0	ENST00000389301.3:c.29C>T	p.Ala10Val	p.A10V	ENST00000389301	NM_000135.2	10	gCc/gTc	1/43	0.742525581422897	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.742525581422897	1		137	198	SUCCESS
APC	324	MSKCC	GRCh37	5	112175760	112175760	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	166	363	0	ENST00000257430.4:c.4469A>C	p.His1490Pro	p.H1490P	ENST00000257430	NM_000038.5	1490	cAt/cCt	16/16	1	2	FACETS	0.911	0.843	0.98	0.911	0.843	0.98	CLONAL	1	TRUE	1	0.742525581422897	2		363	491	SUCCESS
APC	324	MSKCC	GRCh37	5	112175765	112175766	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	T	novel	NA	P-0037943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	148	352	0	ENST00000257430.4:c.4474_4475delinsT	p.Ala1492SerfsTer15	p.A1492Sfs*15	ENST00000257430	NM_000038.5	1492	GCc/Tc	16/16	1	2	FACETS	0.829	0.763	0.897	0.829	0.763	0.897	CLONAL	1	TRUE	1	0.742525581422897	2		352	481	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624294	89624295	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0037969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	57	528	0	ENST00000371953.3:c.69dup	p.Asp24ArgfsTer20	p.D24Rfs*20	ENST00000371953	NM_000314.4	23	tta/ttAa	1/9	0.181588132020478	4	FACETS	0.839	0.728	0.957	1	0.956	1	CLONAL	3	FALSE	2	0.235159450442983	4		528	238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578188	7578188	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201592	NA	P-0039148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	217	625	0	ENST00000269305.4:c.661G>T	p.Glu221Ter	p.E221*	ENST00000269305	NM_001126112.2	221	Gag/Tag	6/11	0.392194974014575	2	FACETS	0.92	0.862	0.978	0.92	0.862	0.978	CLONAL	2	TRUE	0	0.42060389095092	2		625	561	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201949	102201949	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	19	223	0	ENST00000263464.3:c.1301G>T	p.Arg434Ile	p.R434I	ENST00000263464	NM_001165.4	434	aGa/aTa	6/9	0.42060389095092	6	FACETS	0.475	0.36	0.611	0.119	0.09	0.153	SUBCLONAL	1	TRUE	2	0.42060389095092	6		223	350	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103498626	103498626	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	62	346	0	ENST00000355739.4:c.10C>A	p.Gln4Lys	p.Q4K	ENST00000355739	NM_000123.3	4	Cag/Aag	1/15	0.177449151328341	5	FACETS	1	0.947	1	0.396	0.343	0.453	INDETERMINATE	1	TRUE	2	0.42060389095092	5		346	405	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533854	533854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	244	795	0	ENST00000451590.1:c.202C>T	p.Arg68Trp	p.R68W	ENST00000451590	NM_001130442.1	68	Cgg/Tgg	3/5	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.70732224662067	2		795	633	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097734	8097734	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1348071008	NA	P-0039160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	154	597	2	ENST00000346208.3:c.116C>T	p.Ala39Val	p.A39V	ENST00000346208		39	gCg/gTg	2/6	1	2	FACETS	0.923	0.851	0.996	0.923	0.851	0.996	CLONAL	1	TRUE	1	0.70732224662067	2		599	472	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054233	30054233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555994816	NA	P-0039160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	152	465	0	ENST00000338641.4:c.655G>A	p.Val219Met	p.V219M	ENST00000338641	NM_000268.3	219	Gtg/Atg	7/16	0.70732224662067	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.70732224662067	1		465	274	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20152121	20152121	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	112	329	0	ENST00000379607.5:c.209G>C	p.Trp70Ser	p.W70S	ENST00000379607	NM_001412.3	70	tGg/tCg	4/7	0.687350292249759	1	FACETS	0.894	0.822	0.965	0.894	0.822	0.965	CLONAL	1	TRUE	0	0.70732224662067	1		329	229	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	84	540	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.813	0.721	0.911	0.813	0.721	0.911	CLONAL	1	TRUE	1	0.450027152850508	2		540	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0039192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	182	664	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.450027152850508	1	FACETS	0.888	0.822	0.956	0.888	0.822	0.956	CLONAL	1	TRUE	0	0.450027152850508	1		665	706	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089601	27089601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	199	825	0	ENST00000324856.7:c.2557C>T	p.Leu853Phe	p.L853F	ENST00000324856	NM_006015.4	853	Ctc/Ttc	8/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.450027152850508	2		825	849	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054364	42054367	+	frameshift_variant	Frame_Shift_Del	DEL	TATT	TATT	-	novel	NA	P-0039192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	105	468	0	ENST00000219905.7:c.7551_7554del	p.Ile2517MetfsTer7	p.I2517Mfs*7	ENST00000219905	NM_001164273.1	2516	taTATT/ta	22/24	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.450027152850508	2		468	447	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827909	72827909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369093764	NA	P-0039192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	241	757	0	ENST00000268489.5:c.8672C>T	p.Ser2891Leu	p.S2891L	ENST00000268489	NM_006885.3	2891	tCa/tTa	9/10	0.450027152850508	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.450027152850508	1		757	788	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604664	48604669	+	inframe_deletion	In_Frame_Del	DEL	CGTCGC	CGTCGC	-	novel	NA	P-0039192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	114	427	0	ENST00000342988.3:c.1486_1491del	p.Arg496_Arg497del	p.R496_R497del	ENST00000342988	NM_005359.5	496	CGTCGC/-	12/12	0.450027152850508	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.450027152850508	1		427	324	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117101	7117101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757977053	NA	P-0039192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	217	802	0	ENST00000302850.5:c.4115G>A	p.Arg1372Gln	p.R1372Q	ENST00000302850	NM_000208.2	1372	cGg/cAg	22/22	0.450027152850508	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.450027152850508	1		802	691	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050370	13050370	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	195	625	0	ENST00000316448.5:c.322G>A	p.Gly108Ser	p.G108S	ENST00000316448	NM_004343.3	108	Ggc/Agc	3/9	0.450027152850508	1	FACETS	0.991	0.921	1	0.991	0.921	1	CLONAL	1	TRUE	0	0.450027152850508	1		625	678	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0039210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	64	368	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		368	364	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140704	55140704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765271720	NA	P-0039210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	82	485	0	ENST00000257290.5:c.1565G>A	p.Arg522His	p.R522H	ENST00000257290	NM_006206.4	522	cGt/cAt	11/23	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		485	563	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0039260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	1066	719	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.304265418176971	9	FACETS	0.993	0.969	1			1	CLONAL	8	TRUE	NA	0.304265418176971	9		719	1822	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578397	7578397	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1555526004	NA	P-0039260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	144	554	0	ENST00000269305.4:c.533A>C	p.His178Pro	p.H178P	ENST00000269305	NM_001126112.2	178	cAc/cCc	5/11	0.304265418176971	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.304265418176971	1		554	714	SUCCESS
APC	324	MSKCC	GRCh37	5	112175358	112175358	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1554085480	NA	P-0039260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	116	220	0	ENST00000257430.4:c.4067C>G	p.Ser1356Ter	p.S1356*	ENST00000257430	NM_000038.5	1356	tCa/tGa	16/16	0.304265418176971	2	FACETS	0.97	0.882	1	0.97	0.882	1	CLONAL	2	TRUE	0	0.304265418176971	2		220	393	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695938	117695938	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142973937	NA	P-0039260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	50	486	3	ENST00000369458.3:c.499C>T	p.Arg167Trp	p.R167W	ENST00000369458	NM_024626.3	167	Cgg/Tgg	4/6	0.304265418176971	1	FACETS	0.361	0.305	0.422	0.361	0.305	0.422	SUBCLONAL	1	TRUE	0	0.304265418176971	1		489	772	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708159	117708159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	83	316	0	ENST00000368508.3:c.2018G>A	p.Ser673Asn	p.S673N	ENST00000368508	NM_002944.2	673	aGt/aAt	14/43	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.304265418176971	2		316	513	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0039406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	377	493	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	0.610312035554892	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.610312035554892	3		493	790	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	189	541	0				ENST00000310581	NM_198253.2	-/1132			0.444482995468839	3	FACETS	0.922	0.86	0.985	0.922	0.86	0.985	CLONAL	2	TRUE	1	0.514412460154185	3		541	501	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294054	1294054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	287	1133	0	ENST00000310581.5:c.947C>T	p.Pro316Leu	p.P316L	ENST00000310581	NM_198253.2	316	cCc/cTc	2/16	0.444482995468839	3	FACETS	0.989	0.928	1	0.494	0.464	0.526	CLONAL	1	TRUE	1	0.514412460154185	3		1133	1419	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214049	108214049	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	54	316	0	ENST00000278616.4:c.8369G>C	p.Arg2790Thr	p.R2790T	ENST00000278616	NM_000051.3	2790	aGa/aCa	57/63	0.214040509068135	1	FACETS	0.405	0.347	0.468	0.405	0.347	0.468	INDETERMINATE	1	TRUE	0	0.514412460154185	1		316	385	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947547	48947548	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	123	385	0	ENST00000267163.4:c.1135dup	p.Met379AsnfsTer16	p.M379Nfs*16	ENST00000267163	NM_000321.2	378	-/A	12/27	0.514412460154185	1	FACETS	0.987	0.902	1	0.987	0.902	1	CLONAL	1	TRUE	0	0.514412460154185	1		385	360	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913396	NA	P-0039634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	169	368	0	ENST00000349496.5:c.95A>G	p.Asp32Gly	p.D32G	ENST00000349496	NM_001904.3	32	gAc/gGc	3/15	0.376907045985347	1	FACETS	0.833	0.778	0.887	0.833	0.778	0.887	INDETERMINATE	1	TRUE	0	0.742214084637624	1		368	344	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098804	178098804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553487942	NA	P-0039634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	366	548	1	ENST00000397062.3:c.241G>A	p.Gly81Ser	p.G81S	ENST00000397062	NM_006164.4	81	Ggt/Agt	2/5	0.734167233970377	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.742214084637624	2		549	476	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245318	46245318	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	168	538	0	ENST00000334344.6:c.3416del	p.Gly1139GlufsTer17	p.G1139Efs*17	ENST00000334344	NM_152641.2	1138	Ggg/gg	15/21	1	2	FACETS	0.874	0.809	0.94	0.874	0.809	0.94	CLONAL	1	TRUE	1	0.742214084637624	2		538	518	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435982	110435983	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0039634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	250	973	0	ENST00000375856.3:c.2418dup	p.Pro807AlafsTer67	p.P807Afs*67	ENST00000375856	NM_003749.2	806	-/G	1/2	0.376907045985347	1	FACETS	0.415	0.388	0.442	0.415	0.388	0.442	INDETERMINATE	1	TRUE	0	0.742214084637624	1		973	1022	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953130	38953130	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	52	168	1	ENST00000357387.3:c.2854A>T	p.Ile952Leu	p.I952L	ENST00000357387	NM_152756.3	952	Ata/Tta	29/38	1	2	FACETS	0.839	0.728	0.956	0.839	0.728	0.956	CLONAL	1	TRUE	1	0.742214084637624	2		169	167	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953177	38953177	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0039634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	44	147	0	ENST00000357387.3:c.2807C>G	p.Ser936Ter	p.S936*	ENST00000357387	NM_152756.3	936	tCa/tGa	29/38	1	2	FACETS	0.785	0.671	0.906	0.785	0.671	0.906	CLONAL	1	TRUE	1	0.742214084637624	2		147	151	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717703	89717703	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	100	454	0	ENST00000371953.3:c.728T>C	p.Phe243Ser	p.F243S	ENST00000371953	NM_000314.4	243	tTc/tCc	7/9	0.379715545977258	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.379715545977258	1		454	402	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407561	139407563	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	rs587778561	NA	P-0039665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	83	668	0	ENST00000277541.6:c.2377_2379del	p.Asn793del	p.N793del	ENST00000277541	NM_017617.3	793	AAC/-	15/34	1	2	FACETS	0.734	0.648	0.825	0.734	0.648	0.825	SUBCLONAL	1	TRUE	1	0.379715545977258	2		668	596	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281360	49281360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201503697	NA	P-0039665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	138	758	0	ENST00000282018.3:c.407G>A	p.Arg136His	p.R136H	ENST00000282018	NM_020377.2	136	cGt/cAt	1/1	1	2	FACETS	0.861	0.784	0.943	0.861	0.784	0.943	CLONAL	1	TRUE	1	0.379715545977258	2		758	844	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0039665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	63	275	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.949	1			1	INDETERMINATE	1	TRUE	NA	0.379715545977258	2		275	281	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278878	1278878	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	112	664	0	ENST00000310581.5:c.2164C>A	p.Gln722Lys	p.Q722K	ENST00000310581	NM_198253.2	722	Cag/Aag	6/16	NA	2	FACETS	1	0.906	1			1	INDETERMINATE	1	TRUE	NA	0.379715545977258	2		664	587	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043905	180043905	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	102	659	0	ENST00000261937.6:c.3091C>T	p.Arg1031Ter	p.R1031*	ENST00000261937	NM_182925.4	1031	Cga/Tga	22/30	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.379715545977258	2		659	522	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0039732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	82	285	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.593323766860293	2		285	222	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944178	71944178	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs748455961	NA	P-0039732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	208	944	0	ENST00000298229.2:c.2011T>C	p.Tyr671His	p.Y671H	ENST00000298229	NM_001567.3	671	Tat/Cat	17/28	0.593323766860293	1	FACETS	0.917	0.858	0.976	0.917	0.858	0.976	CLONAL	1	TRUE	0	0.593323766860293	1		944	538	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900017	151900017	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0039732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	67	101	0	ENST00000262189.6:c.4092+2T>G		p.X1364_splice	ENST00000262189	NM_170606.2	1364			1	2	FACETS	0.969	0.854	1	0.969	0.854	1	CLONAL	1	TRUE	1	0.593323766860293	2		101	233	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396760	139396760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	274	1226	0	ENST00000277541.6:c.5348G>A	p.Arg1783Gln	p.R1783Q	ENST00000277541	NM_017617.3	1783	cGg/cAg	28/34	1	2	FACETS	0.989	0.93	1	0.989	0.93	1	CLONAL	1	TRUE	1	0.593323766860293	2		1226	934	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	116	415	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.320456507804111	6	FACETS	0.983	0.893	1	0.983	0.893	1	CLONAL	3	TRUE	3	0.320456507804111	6		415	403	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974695	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1554656253	NA	P-0039736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	169	431	0	ENST00000304494.5:c.132C>G	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	taC/taG	1/3	0.320456507804111	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	0	0.320456507804111	3		431	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578458	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGA	novel	NA	P-0039736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	267	784	0	ENST00000269305.4:c.470_472dup	p.Val157_Arg158insLeu	p.V157_R158insL	ENST00000269305	NM_001126112.2	158	cgc/cTCCgc	5/11	0.320456507804111	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.320456507804111	3		784	574	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286185	66286185	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs865985552	NA	P-0039736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	63	204	0	ENST00000273854.3:c.1501G>C	p.Glu501Gln	p.E501Q	ENST00000273854	NM_004439.5	501	Gag/Cag	6/18	0.320456507804111	5	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	3	0.320456507804111	5		204	245	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0039789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	46	719	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.715	0.6	0.842	0.715	0.6	0.842	SUBCLONAL	1	TRUE	1	0.173445492373786	2		719	742	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593397	48593397	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	30	216	0	ENST00000342988.3:c.1148T>G	p.Ile383Arg	p.I383R	ENST00000342988	NM_005359.5	383	aTa/aGa	10/12	1	2	FACETS	0.925	0.746	1	0.925	0.746	1	CLONAL	1	TRUE	1	0.173445492373786	2		216	374	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484233	8484233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200684369	NA	P-0039789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	33	369	0	ENST00000356435.5:c.3299C>T	p.Thr1100Met	p.T1100M	ENST00000356435		1100	aCg/aTg	19/35	1	2	FACETS	0.642	0.521	0.778	0.642	0.521	0.778	SUBCLONAL	1	TRUE	1	0.173445492373786	2		369	593	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207005	1207009	+	frameshift_variant	Frame_Shift_Del	DEL	CACCG	CACCG	-	novel	NA	P-0039789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	46	568	0	ENST00000326873.7:c.93_97del	p.Thr32GlyfsTer129	p.T32Gfs*129	ENST00000326873	NM_000455.4	31	tcCACCGag/tcag	1/10	1	2	FACETS	0.847	0.712	0.997	0.847	0.712	0.997	CLONAL	1	TRUE	1	0.173445492373786	2		568	626	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578411	7578412	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACAACCTCCGTCATGTGCTGTG	novel	NA	P-0039790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	62	655	0	ENST00000269305.4:c.497_518dup	p.Arg174ThrfsTer14	p.R174Tfs*14	ENST00000269305	NM_001126112.2	173	gtg/gtCACAGCACATGACGGAGGTTGTg	5/11	0.235506524319595	1	FACETS	0.543	0.467	0.625	0.543	0.467	0.625	SUBCLONAL	1	TRUE	0	0.235506524319595	1		655	856	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874728	151874734	+	frameshift_variant	Frame_Shift_Del	DEL	GTCTAGG	GTCTAGG	-	novel	NA	P-0039790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	47	385	0	ENST00000262189.6:c.7804_7810del	p.Pro2602ThrfsTer43	p.P2602Tfs*43	ENST00000262189	NM_170606.2	2602	CCTAGACac/ac	38/59	1	2	FACETS	0.741	0.625	0.869	0.741	0.625	0.869	SUBCLONAL	1	TRUE	1	0.235506524319595	2		385	539	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	24	541	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.856	0.676	1	0.856	0.676	1	CLONAL	1	FALSE	1	0.314993210793034	2		541	178	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0039815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	434	836	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.314993210793034	6	FACETS	0.939	0.899	0.978	0.939	0.899	0.978	CLONAL	5	FALSE	1	0.314993210793034	6		836	957	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0039815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	372	369	3	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.314993210793034	3	FACETS	0.994	0.959	1	1	0.997	1	CLONAL	5	FALSE	0	0.314993210793034	3		372	550	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346365	73346365	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	35	390	0	ENST00000377767.4:c.1435G>C	p.Asp479His	p.D479H	ENST00000377767	NM_014953.3	479	Gac/Cac	10/21	0.272378060013581	4	FACETS	0.958	0.788	1	0.479	0.394	0.574	CLONAL	1	FALSE	2	0.314993210793034	4		390	305	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150003	202150003	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	204	652	0	ENST00000358485.4:c.1444C>T	p.Gln482Ter	p.Q482*	ENST00000358485	NM_001080125.1	482	Cag/Tag	8/9	0.314993210793034	3	FACETS	0.988	0.919	1	0.988	0.919	1	CLONAL	2	FALSE	1	0.314993210793034	3		652	759	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843634	156843634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201035170	NA	P-0039815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	199	1084	0	ENST00000524377.1:c.1060G>A	p.Val354Ile	p.V354I	ENST00000524377	NM_002529.3	354	Gtc/Atc	8/17	0.182481223796306	2	FACETS	0.953	0.887	1	0.953	0.887	1	INDETERMINATE	2	FALSE	0	0.314993210793034	2		1084	663	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956170	175956170	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	40	475	0	ENST00000367669.3:c.2042A>G	p.Asp681Gly	p.D681G	ENST00000367669	NM_022457.5	681	gAt/gGt	18/20	0.182481223796306	2	FACETS	0.751	0.626	0.89	0.376	0.313	0.445	INDETERMINATE	1	FALSE	0	0.314993210793034	2		475	338	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743085	743085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	50	678	0	ENST00000314574.4:c.893G>A	p.Gly298Glu	p.G298E	ENST00000314574	NM_005433.3	298	gGa/gAa	8/12	0.199694945942742	3	FACETS	0.835	0.71	0.972	0.418	0.355	0.487	CLONAL	1	FALSE	1	0.314993210793034	3		678	440	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118629	11118629	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	171	816	0	ENST00000358026.2:c.2053G>C	p.Glu685Gln	p.E685Q	ENST00000358026	NM_001128849.1	685	Gag/Cag	14/36	0.199694945942742	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	FALSE	1	0.314993210793034	3		816	590	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023768	31023779	+	inframe_deletion	In_Frame_Del	DEL	ACTGAGTACCAG	ACTGAGTACCAG	-	novel	NA	P-0039815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	74	815	0	ENST00000375687.4:c.3253_3264del	p.Thr1085_Gln1088del	p.T1085_Q1088del	ENST00000375687	NM_015338.5	1085	ACTGAGTACCAG/-	13/13	0.314993210793034	8	FACETS	0.788	0.687	0.897			1	SUBCLONAL	1	FALSE	NA	0.314993210793034	8		815	1160	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	61	415	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.82	0.707	0.944	0.82	0.707	0.944	CLONAL	1	TRUE	1	0.225687820121125	2		415	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0039817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	110	664	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.225687820121125	2		665	842	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0039817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	53	476	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.225687820121125	1	FACETS	0.788	0.672	0.914	0.788	0.672	0.914	CLONAL	1	TRUE	0	0.225687820121125	1		476	529	SUCCESS
AR	367	MSKCC	GRCh37	X	66765159	66765188	+	inframe_deletion	In_Frame_Del	DEL	GCAGCAGCAGCAGCAGCAGCAGCAGCAGCA	GCAGCAGCAGCAGCAGCAGCAGCAGCAGCA	-	rs3032358	NA	P-0039817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	29	222	0	ENST00000374690.3:c.210_239del	p.Gln71_Gln80del	p.Q71_Q80del	ENST00000374690	NM_000044.3	57	ctGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAg/ctg	1/8	1	1	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	0	0.225687820121125	1		222	211	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923654	72923654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746242918	NA	P-0039817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	100	830	0	ENST00000268489.5:c.3424C>T	p.Arg1142Cys	p.R1142C	ENST00000268489	NM_006885.3	1142	Cgc/Tgc	4/10	1	2	FACETS	0.954	0.851	1	0.954	0.851	1	CLONAL	1	TRUE	1	0.225687820121125	2		830	929	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961253	15961253	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	89	524	0	ENST00000268712.3:c.6136C>T	p.His2046Tyr	p.H2046Y	ENST00000268712	NM_006311.3	2046	Cat/Tat	39/46	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.225687820121125	2		524	633	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023076	150023076	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs187759014	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	122	740	0	ENST00000253339.5:c.187C>T	p.Arg63Ter	p.R63*	ENST00000253339		63	Cga/Tga	1/7	0.164618513626956	4	FACETS	0.914	0.838	0.991	1	0.985	1	INDETERMINATE	3	FALSE	2	0.392022594634997	4		740	316	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	78	369	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.877	0.783	0.973	1	0.983	1	CLONAL	2	FALSE	1	0.392022594634997	2		369	227	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717777	89717777	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	123	410	0	ENST00000371953.3:c.801+1G>T		p.X267_splice	ENST00000371953	NM_000314.4	267			0.392022594634997	2	FACETS	1	0.954	1	1	0.993	1	CLONAL	4	FALSE	0	0.392022594634997	2		410	156	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	50	346	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	0.599	0.509	0.697	0.599	0.509	0.697	SUBCLONAL	1	FALSE	1	0.392022594634997	2		346	426	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	247	971	3	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	0.392022594634997	4	FACETS	0.897	0.839	0.956	0.598	0.559	0.638	CLONAL	2	FALSE	1	0.392022594634997	4		974	978	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	93	343	0	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.392022594634997	2		343	387	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	147	554	0	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	1	2	FACETS	0.889	0.819	0.96	1	0.991	1	CLONAL	2	FALSE	1	0.392022594634997	2		554	422	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	42	624	1	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.407	0.34	0.483	0.407	0.34	0.483	SUBCLONAL	1	FALSE	1	0.392022594634997	2		625	526	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	82	501	7	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.392022594634997	2	FACETS	1	0.969	1	0.634	0.564	0.708	CLONAL	1	FALSE	0	0.392022594634997	2		508	330	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214592	5214592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369295620	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	268	777	0	ENST00000357368.4:c.4474C>T	p.Arg1492Trp	p.R1492W	ENST00000357368	NM_002850.3	1492	Cgg/Tgg	29/38	1	2	FACETS	0.962	0.907	1	1	0.995	1	CLONAL	2	FALSE	1	0.392022594634997	2		777	711	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020764	37020764	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	31	551	2	ENST00000358127.4:c.81del	p.Phe27LeufsTer2	p.F27Lfs*2	ENST00000358127	NM_001280556.1	27	ttT/tt	2/10	0.121163967082422	0	FACETS	0.185	0.149	0.225			1	INDETERMINATE	1	FALSE	0	0.392022594634997	0		553	521	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129867	55129867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373126818	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	142	537	1	ENST00000257290.5:c.401C>T	p.Thr134Met	p.T134M	ENST00000257290	NM_006206.4	134	aCg/aTg	4/23	1	2	FACETS	1	0.958	1	1	0.992	1	CLONAL	2	FALSE	1	0.392022594634997	2		538	344	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263974	104263974	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776579	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	46	239	1	ENST00000369902.3:c.71del	p.Pro24ArgfsTer72	p.P24Rfs*72	ENST00000369902	NM_016169.3	22	gCc/gc	1/12	0.392022594634997	2	FACETS	0.785	0.665	0.916	0.392	0.332	0.458	CLONAL	1	FALSE	0	0.392022594634997	2		240	299	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667422	241667422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756990249	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	139	514	0	ENST00000366560.3:c.1028G>A	p.Arg343Gln	p.R343Q	ENST00000366560	NM_000143.3	343	cGa/cAa	7/10	1	2	FACETS	0.914	0.841	0.988	1	0.991	1	CLONAL	2	FALSE	1	0.392022594634997	2		514	388	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497944	25497944	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1203651882	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	437	598	0	ENST00000264709.3:c.505C>T	p.Arg169Trp	p.R169W	ENST00000264709	NM_175629.2	169	Cgg/Tgg	6/23	0.392022594634997	4	FACETS	1	0.983	1	1	0.996	1	CLONAL	4	FALSE	1	0.392022594634997	4		598	749	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435769	116435769	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780102059	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	37	656	2	ENST00000397752.3:c.3859G>A	p.Val1287Ile	p.V1287I	ENST00000397752	NM_000245.2	1287	Gta/Ata	20/21	1	2	FACETS	0.431	0.355	0.516	0.431	0.355	0.516	SUBCLONAL	1	FALSE	1	0.392022594634997	2		658	438	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	332	947	4	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	1	2	FACETS	0.944	0.896	0.993	1	0.996	1	CLONAL	2	FALSE	1	0.392022594634997	2		951	897	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	306	990	2	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.983	0.931	1	1	0.996	1	CLONAL	2	FALSE	1	0.392022594634997	2		992	794	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465976	69465976	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	251	765	0	ENST00000227507.2:c.814G>T	p.Glu272Ter	p.E272*	ENST00000227507	NM_053056.2	272	Gag/Tag	5/5	1	2	FACETS	1	0.97	1	1	0.995	1	CLONAL	2	FALSE	1	0.392022594634997	2		765	613	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097629	27097629	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	183	614	0	ENST00000324856.7:c.3218G>A	p.Trp1073Ter	p.W1073*	ENST00000324856	NM_006015.4	1073	tGg/tAg	12/20	1	2	FACETS	0.881	0.819	0.944	1	0.993	1	CLONAL	2	FALSE	1	0.392022594634997	2		614	530	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938155	36938155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765312095	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	287	865	0	ENST00000361632.4:c.806G>A	p.Arg269His	p.R269H	ENST00000361632		269	cGc/cAc	6/16	1	2	FACETS	1	0.965	1	1	0.996	1	CLONAL	2	FALSE	1	0.392022594634997	2		865	714	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748452	162748452	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	66	448	0	ENST00000367921.3:c.2366A>G	p.Tyr789Cys	p.Y789C	ENST00000367921	NM_006182.2	789	tAt/tGt	17/18	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.392022594634997	2		448	265	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962554	100962554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	161	566	1	ENST00000325455.5:c.1843C>T	p.Arg615Cys	p.R615C	ENST00000325455	NM_001202474.3	615	Cgc/Tgc	3/8	1	2	FACETS	0.929	0.861	0.999	1	0.992	1	CLONAL	2	FALSE	1	0.392022594634997	2		567	442	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444057	49444057	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	68	752	0	ENST00000301067.7:c.3314C>T	p.Ala1105Val	p.A1105V	ENST00000301067	NM_003482.3	1105	gCc/gTc	11/54	1	2	FACETS	0.634	0.552	0.723	0.634	0.552	0.723	SUBCLONAL	1	FALSE	1	0.392022594634997	2		752	547	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432009	121432009	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	360	1019	0	ENST00000257555.6:c.759del	p.Leu254TrpfsTer88	p.L254Wfs*88	ENST00000257555		252	caG/ca	4/10	1	2	FACETS	1	0.975	1	1	0.997	1	CLONAL	2	FALSE	1	0.392022594634997	2		1019	886	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042488	42042488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	144	692	0	ENST00000219905.7:c.6683G>A	p.Ser2228Asn	p.S2228N	ENST00000219905	NM_001164273.1	2228	aGt/aAt	17/24	0.121163967082422	0	FACETS	0.685	0.635	0.736			1	INDETERMINATE	2	FALSE	0	0.392022594634997	0		692	326	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654720	67654720	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	101	426	0	ENST00000264010.4:c.1207G>C	p.Gly403Arg	p.G403R	ENST00000264010	NM_006565.3	403	Ggg/Cgg	6/12	1	2	FACETS	0.821	0.742	0.901	1	0.986	1	CLONAL	2	FALSE	1	0.392022594634997	2		426	314	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832074	72832074	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	130	658	0	ENST00000268489.5:c.4507C>T	p.Gln1503Ter	p.Q1503*	ENST00000268489	NM_006885.3	1503	Cag/Tag	9/10	1	2	FACETS	0.861	0.789	0.935	1	0.989	1	CLONAL	2	FALSE	1	0.392022594634997	2		658	385	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559192	29559192	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	143	451	0	ENST00000356175.3:c.3299C>A	p.Ser1100Ter	p.S1100*	ENST00000356175	NM_000267.3	1100	tCa/tAa	25/57	1	2	FACETS	0.97	0.895	1	1	0.992	1	CLONAL	2	FALSE	1	0.392022594634997	2		451	376	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448272	56448272	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	257	644	0	ENST00000407977.2:c.375G>C	p.Lys125Asn	p.K125N	ENST00000407977		125	aaG/aaC	3/10	1	2	FACETS	0.947	0.892	1	1	0.995	1	CLONAL	2	FALSE	1	0.392022594634997	2		644	692	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223199	36223199	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	358	1055	0	ENST00000222270.7:c.5749A>G	p.Ser1917Gly	p.S1917G	ENST00000222270	NM_014727.1	1917	Agc/Ggc	28/37	1	2	FACETS	1	0.959	1	1	0.996	1	CLONAL	2	FALSE	1	0.392022594634997	2		1055	905	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798819	42798819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	331	913	1	ENST00000575354.2:c.4391G>A	p.Arg1464Gln	p.R1464Q	ENST00000575354	NM_015125.3	1464	cGg/cAg	19/20	1	2	FACETS	1	0.953	1	1	0.996	1	CLONAL	2	FALSE	1	0.392022594634997	2		914	841	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128016916	128016916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1192130599	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	430	664	0	ENST00000285398.2:c.2173G>A	p.Glu725Lys	p.E725K	ENST00000285398	NM_000122.1	725	Gag/Aag	14/15	0.392022594634997	4	FACETS	1	0.986	1	1	0.996	1	CLONAL	4	FALSE	1	0.392022594634997	4		664	727	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430201	181430201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	190	205	0	ENST00000325404.1:c.53C>T	p.Ser18Leu	p.S18L	ENST00000325404	NM_003106.3	18	tCg/tTg	1/1	0.392022594634997	3	FACETS	0.897	0.847	0.947	1	0.994	1	CLONAL	4	FALSE	1	0.392022594634997	3		205	323	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807132	1807132	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	352	1021	0	ENST00000260795.2:c.1463T>C	p.Met488Thr	p.M488T	ENST00000260795		488	aTg/aCg	10/17	1	2	FACETS	1	0.988	1	1	0.997	1	CLONAL	2	FALSE	1	0.392022594634997	2		1021	805	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959397	38959397	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	44	450	0	ENST00000357387.3:c.2078A>C	p.Asn693Thr	p.N693T	ENST00000357387	NM_152756.3	693	aAc/aCc	22/38	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	FALSE	1	0.392022594634997	2		450	203	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973857	131973857	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876659182	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	125	458	0	ENST00000265335.6:c.3560T>C	p.Val1187Ala	p.V1187A	ENST00000265335		1187	gTg/gCg	23/25	1	2	FACETS	0.975	0.895	1	1	0.99	1	CLONAL	2	FALSE	1	0.392022594634997	2		458	327	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818379	170818379	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	54	286	0	ENST00000296930.5:c.209G>C	p.Ser70Thr	p.S70T	ENST00000296930	NM_002520.6	70	aGt/aCt	3/11	1	2	FACETS	1	0.918	1	1	0.98	1	CLONAL	2	FALSE	1	0.392022594634997	2		286	130	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157495210	157495210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375023508	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	119	536	0	ENST00000346085.5:c.3094G>A	p.Gly1032Ser	p.G1032S	ENST00000346085	NM_020732.3	1032	Ggc/Agc	11/20	0.164618513626956	4	FACETS	0.833	0.756	0.914	0.833	0.756	0.914	INDETERMINATE	2	FALSE	2	0.392022594634997	4		536	507	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434494	140434494	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	132	418	0	ENST00000288602.6:c.2204G>T	p.Arg735Leu	p.R735L	ENST00000288602	NM_004333.4	735	cGg/cTg	18/18	1	2	FACETS	0.996	0.917	1	1	0.991	1	CLONAL	2	FALSE	1	0.392022594634997	2		418	338	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476779	140476779	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs551111837	NA	P-0039854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	48	514	0	ENST00000288602.6:c.1627A>G	p.Ile543Val	p.I543V	ENST00000288602	NM_004333.4	543	Atc/Gtc	13/18	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	FALSE	1	0.392022594634997	2		514	224	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955535	48955535	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	94	329	0	ENST00000267163.4:c.1651G>T	p.Glu551Ter	p.E551*	ENST00000267163	NM_000321.2	551	Gaa/Taa	17/27	0.328494767991037	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	0	0.328494767991037	2		329	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579846	7579848	+	frameshift_variant	Frame_Shift_Del	DEL	ATA	ATA	CT	novel	NA	P-0039899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	193	588	1	ENST00000269305.4:c.65_67delinsAG	p.Leu22GlnfsTer22	p.L22Qfs*22	ENST00000269305	NM_001126112.2	22	cTATgg/cAGgg	2/11	0.319529408131345	2	FACETS	0.915	0.851	0.981	0.915	0.851	0.981	CLONAL	2	TRUE	0	0.328494767991037	2		589	642	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449458	31449458	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	107	398	0	ENST00000344624.3:c.2751A>T	p.Leu917Phe	p.L917F	ENST00000344624		917	ttA/ttT	19/33	0.328494767991037	3	FACETS	0.817	0.737	0.901	0.817	0.737	0.901	CLONAL	2	TRUE	1	0.328494767991037	3		398	464	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740424	145740424	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	122	687	0	ENST00000428558.2:c.1516G>T	p.Ala506Ser	p.A506S	ENST00000428558	NM_004260.3	506	Gcc/Tcc	9/22	0.328494767991037	3	FACETS	1	0.94	1	0.527	0.476	0.581	CLONAL	1	TRUE	1	0.328494767991037	3		687	820	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	103	541	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.928	0.844	1	0.928	0.844	1	CLONAL	1	TRUE	1	0.803945107745711	2		541	276	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440062	99440062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	211	432	0	ENST00000268035.6:c.1030G>A	p.Val344Ile	p.V344I	ENST00000268035	NM_000875.3	344	Gtt/Att	4/21	1	2	FACETS	0.976	0.914	1	0.976	0.914	1	CLONAL	1	TRUE	1	0.803945107745711	2		432	538	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661542	227661542	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	297	651	0	ENST00000305123.5:c.1913A>G	p.Lys638Arg	p.K638R	ENST00000305123	NM_005544.2	638	aAg/aGg	1/2	1	2	FACETS	0.997	0.944	1	0.997	0.944	1	CLONAL	1	TRUE	1	0.803945107745711	2		651	741	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860664	151860664	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	228	458	0	ENST00000262189.6:c.9998C>G	p.Pro3333Arg	p.P3333R	ENST00000262189	NM_170606.2	3333	cCt/cGt	43/59	0.803945107745711	5	FACETS	0.832	0.778	0.887	0.555	0.518	0.592	CLONAL	2	TRUE	2	0.803945107745711	5		458	752	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	96	415	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.983	0.879	1	0.983	0.879	1	CLONAL	1	FALSE	1	0.397897093098697	2		415	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0039939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	244	703	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.397897093098697	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	0	0.397897093098697	1		703	920	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281250	15281250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184522923	NA	P-0039939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	247	891	2	ENST00000263388.2:c.5006G>A	p.Arg1669His	p.R1669H	ENST00000263388	NM_000435.2	1669	cGc/cAc	27/33	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.397897093098697	2		893	1201	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073773	8073774	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0039939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	42	360	0	ENST00000377482.5:c.885dup	p.Pro296AlafsTer4	p.P296Afs*4	ENST00000377482	NM_018948.3	295	-/G	4/4	1	2	FACETS	0.526	0.44	0.622	0.526	0.44	0.622	SUBCLONAL	1	FALSE	1	0.397897093098697	2		360	401	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974791	21974792	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0039939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	107	233	0	ENST00000304494.5:c.35_36insAG	p.Ala13GlyfsTer14	p.A13Gfs*14	ENST00000304494	NM_000077.4	12	tcg/tcAGg	1/3	0.397897093098697	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	0	0.397897093098697	1		233	330	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	73	415	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.201512321183401	2	FACETS	0.862	0.756	0.975	0.431	0.378	0.488	INDETERMINATE	1	TRUE	0	0.366669723942545	2		415	462	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	183	541	0				ENST00000310581	NM_198253.2	-/1132			0.366669723942545	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.366669723942545	3		541	545	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1563889584	NA	P-0039967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	98	397	0	ENST00000304494.5:c.238del	p.Arg80AspfsTer66	p.R80Dfs*66	ENST00000304494	NM_000077.4	80	Cga/ga	2/3	0.366669723942545	1	FACETS	0.896	0.803	0.995	0.896	0.803	0.995	CLONAL	1	TRUE	0	0.366669723942545	1		397	487	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206578	108206578	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	63	263	0	ENST00000278616.4:c.8158G>T	p.Asp2720Tyr	p.D2720Y	ENST00000278616	NM_000051.3	2720	Gat/Tat	56/63	0.366669723942545	1	FACETS	0.961	0.838	1	0.961	0.838	1	CLONAL	1	TRUE	0	0.366669723942545	1		263	292	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779289	3779289	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	241	575	0	ENST00000262367.5:c.5759G>T	p.Gly1920Val	p.G1920V	ENST00000262367	NM_004380.2	1920	gGc/gTc	31/31	0.339756057571638	2	FACETS	0.919	0.863	0.977	0.919	0.863	0.977	CLONAL	2	TRUE	0	0.366669723942545	2		575	715	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40857126	40857126	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1159977413	NA	P-0039967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	84	430	0	ENST00000428826.2:c.1915A>G	p.Ile639Val	p.I639V	ENST00000428826		639	Att/Gtt	17/21	0.339423860230224	3	FACETS	0.733	0.647	0.825	0.366	0.323	0.413	SUBCLONAL	1	TRUE	1	0.366669723942545	3		430	740	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262352	39262352	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0039967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	71	493	0	ENST00000402219.2:c.1074+1del		p.X358_splice	ENST00000402219	NM_005633.3	358			1	2	FACETS	0.733	0.641	0.833	0.733	0.641	0.833	SUBCLONAL	1	TRUE	1	0.366669723942545	2		493	528	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190656644	190656644	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs973362695	NA	P-0039967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	35	214	0	ENST00000441310.2:c.109G>T	p.Ala37Ser	p.A37S	ENST00000441310	NM_000534.4	37	Gcc/Tcc	2/13	1	2	FACETS	0.517	0.424	0.621	0.517	0.424	0.621	SUBCLONAL	1	TRUE	1	0.366669723942545	2		214	369	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561418	9561418	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	120	445	0	ENST00000353224.5:c.364G>C	p.Glu122Gln	p.E122Q	ENST00000353224	NM_177990.2	122	Gaa/Caa	4/10	1	2	FACETS	0.977	0.884	1	0.977	0.884	1	CLONAL	1	TRUE	1	0.366669723942545	2		445	670	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427568	72427568	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	66	245	0	ENST00000477973.2:c.922G>T	p.Asp308Tyr	p.D308Y	ENST00000477973	NM_012234.5	308	Gac/Tac	4/4	1	2	FACETS	0.997	0.871	1	0.997	0.871	1	CLONAL	1	TRUE	1	0.366669723942545	2		245	361	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205182	128205182	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	162	551	0	ENST00000341105.2:c.259C>A	p.Pro87Thr	p.P87T	ENST00000341105	NM_032638.4	87	Cca/Aca	3/6	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.366669723942545	2		551	863	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501521	149501522	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0039967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	114	642	0	ENST00000261799.4:c.2265_2266delinsTT	p.Asp756Tyr	p.D756Y	ENST00000261799	NM_002609.3	755	ctGGac/ctTTac	16/23	1	2	FACETS	0.781	0.703	0.864	0.781	0.703	0.864	SUBCLONAL	1	TRUE	1	0.366669723942545	2		642	796	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853349	151853349	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs778429633	NA	P-0039967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	108	410	0	ENST00000262189.6:c.11753A>G	p.Asn3918Ser	p.N3918S	ENST00000262189	NM_170606.2	3918	aAt/aGt	45/59	0.366669723942545	3	FACETS	0.937	0.841	1	0.468	0.42	0.519	CLONAL	1	TRUE	1	0.366669723942545	3		410	744	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650282	48650282	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	138	637	0	ENST00000376670.3:c.252G>C	p.Met84Ile	p.M84I	ENST00000376670	NM_002049.3	84	atG/atC	3/6	1	2	FACETS	0.851	0.775	0.932	0.851	0.775	0.932	CLONAL	1	TRUE	1	0.366669723942545	2		637	884	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501521	149501521	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	112	642	0	ENST00000261799.4:c.2266G>T	p.Asp756Tyr	p.D756Y	ENST00000261799	NM_002609.3	756	Gac/Tac	16/23	1	2	FACETS	0.767	0.69	0.849	0.767	0.69	0.849	SUBCLONAL	1	TRUE	1	0.366669723942545	2		642	796	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0040008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	622	808	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.858855790041754	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.858855790041754	2		808	672	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254527	1254527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765787352	NA	P-0040008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	674	994	0	ENST00000310581.5:c.3251G>A	p.Arg1084Gln	p.R1084Q	ENST00000310581	NM_198253.2	1084	cGa/cAa	15/16	0.858855790041754	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.858855790041754	2		994	716	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18276997	18277019	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGCCTTCAATGAGACTATCAA	GAGGCCTTCAATGAGACTATCAA	-	novel	NA	P-0040008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	180	518	1	ENST00000222254.8:c.1446_1468del	p.Glu482AspfsTer3	p.E482Dfs*3	ENST00000222254	NM_005027.3	482	GAGGCCTTCAATGAGACTATCAAg/g	12/16	0.858855790041754	3	FACETS	1	0.962	1	0.528	0.49	0.568	CLONAL	1	TRUE	1	0.858855790041754	3		519	567	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197842	66197842	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	46	255	0	ENST00000273854.3:c.2857T>C	p.Ser953Pro	p.S953P	ENST00000273854	NM_004439.5	953	Tct/Cct	17/18	0.580594501324246	4	FACETS	0.696	0.59	0.812			1	SUBCLONAL	1	TRUE	NA	0.858855790041754	4		255	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0040020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	107	956	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.235214604570984	2		956	781	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512270	38512270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866777491	NA	P-0040020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	93	627	0	ENST00000254066.5:c.1181G>A	p.Arg394Gln	p.R394Q	ENST00000254066	NM_000964.3	394	cGg/cAg	9/9	1	2	FACETS	0.9	0.799	1	0.9	0.799	1	CLONAL	1	TRUE	1	0.235214604570984	2		627	879	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814554	43814554	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	65	415	0	ENST00000372470.3:c.1349A>C	p.Glu450Ala	p.E450A	ENST00000372470	NM_005373.2	450	gAg/gCg	9/12	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.235214604570984	2		415	519	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263241	115263241	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0040020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	145	605	0	ENST00000438362.2:c.2109T>A	p.Cys703Ter	p.C703*	ENST00000438362	NM_001242891.1	703	tgT/tgA	17/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.235214604570984	2		605	907	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849452	68849452	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	98	532	0	ENST00000261769.5:c.1355T>A	p.Leu452Gln	p.L452Q	ENST00000261769	NM_004360.3	452	cTa/cAa	10/16	0.0533522541767288	3	FACETS	1	0.967	1	0.606	0.541	0.676	INDETERMINATE	1	TRUE	1	0.235214604570984	3		532	768	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578487	7578488	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAACCC	novel	NA	P-0040034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1477	158	899	0	ENST00000269305.4:c.437_442dup	p.Val147_Asp148insGlyVal	p.V147_D148insGV	ENST00000269305	NM_001126112.2	148	gat/gGGGTTGat	5/11	1	2	FACETS	0.773	0.706	0.844	0.773	0.706	0.844	SUBCLONAL	1	TRUE	1	0.25	2		899	1635	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862749	9862749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150316865	NA	P-0040080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	149	511	1	ENST00000330684.3:c.2554G>A	p.Val852Met	p.V852M	ENST00000330684	NM_001134407.1	852	Gtg/Atg	12/13	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.81623358678485	2		512	285	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805653	43805653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765133601	NA	P-0040080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	50	416	0	ENST00000372470.3:c.709G>A	p.Glu237Lys	p.E237K	ENST00000372470	NM_005373.2	237	Gag/Aag	5/12	0.216603641322065	3	FACETS	0.589	0.503	0.682	0.294	0.251	0.341	INDETERMINATE	1	TRUE	1	0.81623358678485	3		416	293	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0040112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	213	144	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.575143333835187	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.575143333835187	2		144	353	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235809	108235809	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	173	237	0	ENST00000278616.4:c.8851G>T	p.Val2951Phe	p.V2951F	ENST00000278616	NM_000051.3	2951	Gtc/Ttc	62/63	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.575143333835187	2		237	448	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098387	108098387	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	55	295	0	ENST00000278616.4:c.37del	p.Arg13ValfsTer3	p.R13Vfs*3	ENST00000278616	NM_000051.3	12	tgC/tg	2/63	1	2	FACETS	0.523	0.449	0.603	0.523	0.449	0.603	SUBCLONAL	1	TRUE	1	0.575143333835187	2		295	366	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197471	106197471	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	201	292	0	ENST00000380013.4:c.5804A>G	p.Tyr1935Cys	p.Y1935C	ENST00000380013	NM_001127208.2	1935	tAt/tGt	11/11	0.531970328112054	2	FACETS	0.892	0.839	0.944	0.892	0.839	0.944	CLONAL	2	TRUE	0	0.575143333835187	2		292	392	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0040150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	16	628	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.21	0.154	0.277	0.21	0.154	0.277	SUBCLONAL	1	TRUE	1	0.214629193259928	2		628	711	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553043	106553043	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	72	535	0	ENST00000369096.4:c.1011del	p.Ser338LeufsTer40	p.S338Lfs*40	ENST00000369096	NM_001198.3	336	agC/ag	5/7	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.214629193259928	2		535	670	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432283	432283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	74	499	0	ENST00000399788.2:c.2240C>T	p.Thr747Ile	p.T747I	ENST00000399788	NM_001042603.1	747	aCa/aTa	16/28	1	2	FACETS	0.926	0.809	1	0.926	0.809	1	CLONAL	1	TRUE	1	0.214629193259928	2		499	745	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	13	540	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.521	0.37	0.706	0.521	0.37	0.706	SUBCLONAL	1	TRUE	1	0.13	2		540	384	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	19	396	0	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	0.0779534299761808	0	FACETS	0.805	0.611	1			1	INDETERMINATE	1	TRUE	0	0.13	0		396	316	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974715	21974732	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCCCCCGCCTCCA	GCAGCGCCCCCGCCTCCA	-	novel	NA	P-0040178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	19	414	0	ENST00000304494.5:c.95_112del	p.Leu32_Leu37del	p.L32_L37del	ENST00000304494	NM_000077.4	32	cTGGAGGCGGGGGCGCTGCcc/ccc	1/3	0.256624153459911	0	FACETS	0.911	0.692	1			1	CLONAL	1	TRUE	0	0.13	0		414	279	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578225	+	frameshift_variant	Frame_Shift_Del	DEL	TCTG	TCTG	-	novel	NA	P-0040178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	50	715	1	ENST00000269305.4:c.624_627del	p.Asp208GlufsTer38	p.D208Efs*38	ENST00000269305	NM_001126112.2	208	gaCAGA/ga	6/11	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.13	2		716	654	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0040212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	364	896	1	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	0.355870813417543	4	FACETS	0.961	0.915	1	0.961	0.915	1	INDETERMINATE	2	TRUE	2	0.736677330895048	4		897	893	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0040212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	541	864	1	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	0.246029290589755	3	FACETS	0.892	0.867	0.916			1	INDETERMINATE	3	TRUE	NA	0.736677330895048	3		865	751	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	201	540	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	0.992	0.928	1			1	INDETERMINATE	2	TRUE	NA	0.396493945885799	2		540	511	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533556	63533556	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147716924	NA	P-0040241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	319	821	2	ENST00000307078.5:c.1598C>T	p.Ala533Val	p.A533V	ENST00000307078	NM_004655.3	533	gCg/gTg	6/11	0.30097715569899	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.396493945885799	4		823	1059	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974783	21974783	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658556	NA	P-0040241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	169	212	0	ENST00000304494.5:c.44G>A	p.Trp15Ter	p.W15*	ENST00000304494	NM_000077.4	15	tGg/tAg	1/3	NA	2	FACETS	0.92	0.863	0.976			1	INDETERMINATE	3	TRUE	NA	0.396493945885799	2		212	309	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820588	44820589	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	59	233	3	ENST00000377967.4:c.289dup	p.Cys97LeufsTer29	p.C97Lfs*29	ENST00000377967	NM_021140.2	95	-/T	3/29	1	1	FACETS	0.78	0.687	0.875	1	0.976	1	SUBCLONAL	2	TRUE	0	0.396493945885799	1		236	153	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578207	7578207	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	340	733	0	ENST00000269305.4:c.642del	p.His214GlnfsTer33	p.H214Qfs*33	ENST00000269305	NM_001126112.2	214	caT/ca	6/11	0.396493945885799	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.396493945885799	2		733	792	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0040294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	57	415	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.27	2		415	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0040294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	147	717	1	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	1	2	FACETS	0.96	0.875	1	0.96	0.875	1	CLONAL	1	TRUE	1	0.27	2		718	1134	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877066	151877066	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	50	483	0	ENST00000262189.6:c.7295del	p.Phe2432SerfsTer20	p.F2432Sfs*20	ENST00000262189	NM_170606.2	2432	tTc/tc	37/59	1	2	FACETS	0.411	0.347	0.481	0.411	0.347	0.481	SUBCLONAL	1	TRUE	1	0.27	2		483	902	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55124952	55124952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754092062	NA	P-0040311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	61	539	0	ENST00000257290.5:c.17C>T	p.Pro6Leu	p.P6L	ENST00000257290	NM_006206.4	6	cCg/cTg	2/23	0.136078120125573	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.944366447671893	0		539	858	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937328	76937329	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	68	306	0	ENST00000373344.5:c.3419dup	p.Leu1140PhefsTer8	p.L1140Ffs*8	ENST00000373344	NM_000489.3	1140	tta/ttTa	9/35	0.944366447671893	1	FACETS	0.864	0.801	0.92	0.864	0.801	0.92	CLONAL	1	TRUE	0	0.944366447671893	1		306	88	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407527	407527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs908661692	NA	P-0040331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	38	426	0	ENST00000380956.4:c.1285G>A	p.Asp429Asn	p.D429N	ENST00000380956	NM_001195286.1	429	Gat/Aat	9/9	NA	2	FACETS	0.996	0.824	1			1	INDETERMINATE	1	TRUE	NA	0.18	2		426	424	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115901	8115902	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	58	542	0	ENST00000346208.3:c.1248dup	p.Thr417AspfsTer90	p.T417Dfs*90	ENST00000346208		416	ctg/ctGg	6/6	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.18	2		542	454	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120683	115120684	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCA	novel	NA	P-0040331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	102	906	0	ENST00000257566.3:c.320_322dup	p.Leu107_Glu108insVal	p.L107_E108insV	ENST00000257566	NM_016569.3	108	gag/gTGGag	1/8	1	2	FACETS	0.777	0.695	0.864	1	0.983	1	SUBCLONAL	2	TRUE	1	0.18	2		906	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0040372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	109	514	0	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	1	2	FACETS	0.543	0.488	0.602	0.543	0.488	0.602	SUBCLONAL	1	TRUE	1	0.53	2		514	757	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542049	187542049	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	35	214	0	ENST00000441802.2:c.5691del	p.Val1898SerfsTer4	p.V1898Sfs*4	ENST00000441802	NM_005245.3	1897	aaA/aa	10/27	1	2	FACETS	0.347	0.284	0.417	0.347	0.284	0.417	SUBCLONAL	1	TRUE	1	0.53	2		214	381	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720649	89720649	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs587782455	NA	P-0040413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	42	189	1	ENST00000371953.3:c.802-2A>T		p.X268_splice	ENST00000371953	NM_000314.4	268			0.236814632621393	3	FACETS	0.954	0.805	1	0.954	0.805	1	CLONAL	2	TRUE	1	0.236814632621393	3		190	208	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028682	12028683	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	111	354	0	ENST00000353533.5:c.886dup	p.Thr296AsnfsTer4	p.T296Nfs*4	ENST00000353533	NM_003010.3	295	-/A	8/11	0.222944711158915	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	0	0.236814632621393	2		354	453	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119886	70119886	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	70	461	0	ENST00000245479.2:c.888G>T	p.Gln296His	p.Q296H	ENST00000245479	NM_000346.3	296	caG/caT	3/3	0.155268517721002	4	FACETS	1	0.957	1	0.618	0.539	0.703	CLONAL	1	TRUE	2	0.236814632621393	4		461	592	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247926	10247926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139918621	NA	P-0040413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	56	571	0	ENST00000340748.4:c.4276C>T	p.Arg1426Trp	p.R1426W	ENST00000340748		1426	Cgg/Tgg	36/40	0.236814632621393	3	FACETS	0.784	0.67	0.908	0.392	0.335	0.454	CLONAL	1	TRUE	1	0.236814632621393	3		571	675	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308112	30308112	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	82	650	0	ENST00000262643.3:c.249T>A	p.Asp83Glu	p.D83E	ENST00000262643	NM_001238.2	83	gaT/gaA	5/12	0.236814632621393	3	FACETS	1	0.948	1	0.57	0.502	0.642	CLONAL	1	TRUE	1	0.236814632621393	3		650	680	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936532	49936533	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0040413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	74	699	1	ENST00000296474.3:c.1394_1395delinsTT	p.Gly465Val	p.G465V	ENST00000296474	NM_002447.2	465	gGC/gTT	2/20	0.233350839595068	2	FACETS	0.992	0.869	1	0.496	0.434	0.563	CLONAL	1	TRUE	0	0.236814632621393	2		700	630	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0040508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	98	415	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.859	0.77	0.954	0.859	0.77	0.954	CLONAL	1	TRUE	1	0.46274351395341	2		415	493	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0040508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	55	384	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.52	0.446	0.601	0.52	0.446	0.601	SUBCLONAL	1	TRUE	1	0.46274351395341	2		384	457	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0040508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	94	214	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	1	2	FACETS	0.752	0.679	0.828	1	0.983	1	SUBCLONAL	2	TRUE	1	0.46274351395341	2		214	270	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579529	7579529	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658483	NA	P-0040508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	153	681	0	ENST00000269305.4:c.158G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tGg/tAg	4/11	1	2	FACETS	0.695	0.635	0.757	0.695	0.635	0.757	SUBCLONAL	1	TRUE	1	0.46274351395341	2		681	952	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0040508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	19	514	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.099	0.075	0.129	0.099	0.075	0.129	SUBCLONAL	1	TRUE	1	0.46274351395341	2		514	827	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573988	7573988	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	153	702	0	ENST00000269305.4:c.1039G>C	p.Ala347Pro	p.A347P	ENST00000269305	NM_001126112.2	347	Gcc/Ccc	10/11	1	2	FACETS	0.701	0.64	0.763	0.701	0.64	0.763	SUBCLONAL	1	TRUE	1	0.46274351395341	2		702	944	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220134	5220134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115469963	NA	P-0040508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	95	547	0	ENST00000357368.4:c.3581G>A	p.Arg1194His	p.R1194H	ENST00000357368	NM_002850.3	1194	cGc/cAc	22/38	1	2	FACETS	0.642	0.572	0.716	0.642	0.572	0.716	SUBCLONAL	1	TRUE	1	0.46274351395341	2		547	640	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119952	70119953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	107	375	0	ENST00000245479.2:c.955dup	p.Tyr319LeufsTer259	p.Y319Lfs*259	ENST00000245479	NM_000346.3	318	-/T	3/3	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.46274351395341	2		375	455	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240265	5240265	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	172	785	1	ENST00000357368.4:c.1649A>T	p.Gln550Leu	p.Q550L	ENST00000357368	NM_002850.3	550	cAg/cTg	12/38	1	2	FACETS	0.774	0.712	0.839	0.774	0.712	0.839	SUBCLONAL	1	TRUE	1	0.46274351395341	2		786	960	SUCCESS
APC	324	MSKCC	GRCh37	5	112137069	112137079	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GGTAATGGTCA	GGTAATGGTCA	-	novel	NA	P-0040508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	122	341	0	ENST00000257430.4:c.828_834+4del		p.GNGQ275fs	ENST00000257430	NM_000038.5	275	GGTAATGGTCAg/g	8/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.46274351395341	2		341	456	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508021	106508021	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	40	201	0	ENST00000359195.3:c.15C>A	p.Asn5Lys	p.N5K	ENST00000359195	NM_002649.2	5	aaC/aaA	2/11	1	2	FACETS	0.835	0.701	0.981	0.835	0.701	0.981	CLONAL	1	TRUE	1	0.46274351395341	2		201	207	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	207	541	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.948	0.883	1	0.948	0.883	1	CLONAL	1	TRUE	1	0.604825492348501	2		541	722	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0040512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	17462	1045	5	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.604825492348501	41	FACETS	1	0.999	1			1	CLONAL	40	TRUE	NA	0.604825492348501	41		1050	18279	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692769	89692769	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1057520208	NA	P-0040512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	43	377	2	ENST00000371953.3:c.254-1G>A		p.X85_splice	ENST00000371953	NM_000314.4	85			0.604825492348501	1	FACETS	0.927	0.8	1	0.927	0.8	1	CLONAL	1	TRUE	0	0.604825492348501	1		379	107	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0040593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	847	886	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.825671302649072	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.855435929264431	3		886	924	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163298659	163298659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368618280	NA	P-0040593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	73	557	0	ENST00000271452.3:c.299G>A	p.Arg100Gln	p.R100Q	ENST00000271452	NM_145697.2	100	cGg/cAg	5/14	0.666289206794397	5	FACETS	0.618	0.54	0.701	0.206	0.18	0.234	SUBCLONAL	1	TRUE	2	0.855435929264431	5		557	631	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391201	89391201	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1195505981	NA	P-0040593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	164	485	0	ENST00000336596.2:c.1267A>G	p.Arg423Gly	p.R423G	ENST00000336596	NM_005233.5	423	Aga/Gga	5/17	0.257002794287571	6	FACETS	1	0.986	1	0.334	0.307	0.362	INDETERMINATE	1	TRUE	2	0.855435929264431	6		485	778	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779199	135779199	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	176	463	0	ENST00000298552.3:c.2047C>G	p.Pro683Ala	p.P683A	ENST00000298552	NM_001162426.1	683	Cct/Gct	17/23	0.529464469580782	5	FACETS	1	0.989	1	0.481	0.445	0.519	CLONAL	1	TRUE	2	0.855435929264431	5		463	651	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0040622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	43	388	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.196859521103608	3	FACETS	0.783	0.655	0.925	0.391	0.327	0.463	CLONAL	1	TRUE	1	0.229292762638395	3		388	534	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115111972	115111972	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	139	722	0	ENST00000257566.3:c.1768C>T	p.Gln590Ter	p.Q590*	ENST00000257566	NM_016569.3	590	Cag/Tag	7/8	0.0679485072548014	4	FACETS	1	0.932	1	1	0.932	1	INDETERMINATE	2	TRUE	2	0.229292762638395	4		722	726	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913284	NA	P-0040622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	33	338	0	ENST00000263967.3:c.1035T>G	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaG	5/21	0.196859521103608	3	FACETS	0.978	0.799	1	0.489	0.399	0.59	CLONAL	1	TRUE	1	0.229292762638395	3		338	328	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109879	115109879	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1268167495	NA	P-0040622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	137	643	0	ENST00000257566.3:c.1999G>A	p.Ala667Thr	p.A667T	ENST00000257566	NM_016569.3	667	Gcg/Acg	8/8	0.0679485072548014	4	FACETS	0.846	0.772	0.922	1	0.981	1	INDETERMINATE	3	TRUE	2	0.229292762638395	4		643	579	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863669	68863694	+	frameshift_variant	Frame_Shift_Del	DEL	ATCCCGATGAAATTGGAAATTTTATT	ATCCCGATGAAATTGGAAATTTTATT	-	novel	NA	P-0040622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	127	506	0	ENST00000261769.5:c.2408_2433del	p.Asn803ArgfsTer2	p.N803Rfs*2	ENST00000261769	NM_004360.3	803	aATCCCGATGAAATTGGAAATTTTATT/a	15/16	0.203651266004355	2	FACETS	0.811	0.736	0.89	0.811	0.736	0.89	CLONAL	2	TRUE	0	0.229292762638395	2		506	683	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	180	541	0				ENST00000310581	NM_198253.2	-/1132			0.0952772807004591	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		541	387	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0040640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	159	364	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.805	0.745	0.865	0.805	0.745	0.865	CLONAL	1	TRUE	1	0.93	2		364	425	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624272	89624273	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs876661009	NA	P-0040640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	74	367	0	ENST00000371953.3:c.47dup	p.Tyr16Ter	p.Y16*	ENST00000371953	NM_000314.4	16	tat/tAat	1/9	1	2	FACETS	0.28	0.245	0.318	0.28	0.245	0.318	SUBCLONAL	1	TRUE	1	0.93	2		367	568	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793008	33793010	+	inframe_deletion	In_Frame_Del	DEL	CGC	CGC	-	rs780345232	NA	P-0040640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	10	75	0	ENST00000498907.2:c.311_313del	p.Gly104del	p.G104del	ENST00000498907	NM_004364.3	104	gGCGac/gac	1/1	1	2	FACETS	0.182	0.124	0.255	0.182	0.124	0.255	SUBCLONAL	1	TRUE	1	0.93	2		75	118	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653845	89653845	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	238	400	0	ENST00000371953.3:c.143A>G	p.Asn48Ser	p.N48S	ENST00000371953	NM_000314.4	48	aAc/aGc	2/9	1	2	FACETS	0.819	0.77	0.869	0.819	0.77	0.869	CLONAL	1	TRUE	1	0.93	2		400	625	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435270	49435270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376062022	NA	P-0040640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	411	723	1	ENST00000301067.7:c.6283C>T	p.Arg2095Cys	p.R2095C	ENST00000301067	NM_003482.3	2095	Cgt/Tgt	31/54	0.3	3	FACETS	1	0.995	1			1	INDETERMINATE	1	TRUE	NA	0.93	3		724	933	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0040673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	183	275	0				ENST00000310581	NM_198253.2	-/1132			0.451222824816384	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.451222824816384	3		275	454	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0040673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	214	369	3	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.451222824816384	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.451222824816384	2		372	425	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0040673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	388	523	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.451222824816384	4	FACETS	0.949	0.906	0.992	0.949	0.906	0.992	CLONAL	3	TRUE	1	0.451222824816384	4		523	877	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916248	9916248	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397518472	NA	P-0040673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	217	373	0	ENST00000330684.3:c.2041C>T	p.Arg681Ter	p.R681*	ENST00000330684	NM_001134407.1	681	Cga/Tga	10/13	0.325101514608529	4	FACETS	1	0.983	1			1	CLONAL	2	TRUE	NA	0.451222824816384	4		373	611	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206941988	206941988	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376415487	NA	P-0040673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	186	215	1	ENST00000423557.1:c.530G>A	p.Arg177Gln	p.R177Q	ENST00000423557	NM_000572.2	177	cGa/cAa	5/5	0.451222824816384	6	FACETS	1	0.957	1	1	0.957	1	CLONAL	3	TRUE	3	0.451222824816384	6		216	504	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876235	35876235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866784625	NA	P-0040673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	140	452	0	ENST00000303115.3:c.1027G>A	p.Asp343Asn	p.D343N	ENST00000303115	NM_002185.3	343	Gat/Aat	8/8	0.451222824816384	3	FACETS	1	0.978	1	0.608	0.556	0.663	CLONAL	1	TRUE	1	0.451222824816384	3		452	625	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485282	8485282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	76	377	0	ENST00000356435.5:c.3098C>T	p.Ser1033Phe	p.S1033F	ENST00000356435		1033	tCc/tTc	18/35	0.451222824816384	2	FACETS	0.734	0.646	0.828	0.367	0.323	0.414	SUBCLONAL	1	TRUE	0	0.451222824816384	2		377	459	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536160	41536160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	259	406	1	ENST00000263253.7:c.1777C>T	p.Pro593Ser	p.P593S	ENST00000263253	NM_001429.3	593	Cct/Tct	9/31	0.363307208064332	5	FACETS	0.892	0.84	0.946	0.892	0.84	0.946	CLONAL	3	TRUE	2	0.451222824816384	5		407	719	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214630	133214630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	111	429	0	ENST00000320574.5:c.5648C>T	p.Ala1883Val	p.A1883V	ENST00000320574	NM_006231.2	1883	gCc/gTc	41/49	0.451222824816384	3	FACETS	0.947	0.853	1	0.473	0.426	0.523	CLONAL	1	TRUE	1	0.451222824816384	3		429	637	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488718	212488718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267599191	NA	P-0040673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	133	461	0	ENST00000342788.4:c.2131C>T	p.Arg711Cys	p.R711C	ENST00000342788	NM_005235.2	711	Cgt/Tgt	18/28	0.226237789234381	5	FACETS	0.81	0.738	0.885	0.54	0.492	0.59	INDETERMINATE	2	TRUE	2	0.451222824816384	5		461	610	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858258	9858258	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	86	410	0	ENST00000330684.3:c.3143G>A	p.Ser1048Asn	p.S1048N	ENST00000330684	NM_001134407.1	1048	aGc/aAc	13/13	0.325101514608529	4	FACETS	0.947	0.839	1			1	CLONAL	1	TRUE	NA	0.451222824816384	4		410	584	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245080	53245080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1428740468	NA	P-0040673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	150	677	0	ENST00000375401.3:c.860C>T	p.Ser287Leu	p.S287L	ENST00000375401	NM_004187.3	287	tCg/tTg	7/26	0.373366733100418	4	FACETS	0.947	0.864	1	0.473	0.432	0.517	CLONAL	1	TRUE	2	0.451222824816384	4		677	1019	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408926	41408926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	97	397	0	ENST00000373198.4:c.500C>T	p.Ser167Phe	p.S167F	ENST00000373198	NM_133170.3	167	tCc/tTc	4/32	0.439470419030697	4	FACETS	0.987	0.881	1	0.494	0.44	0.55	CLONAL	1	TRUE	2	0.451222824816384	4		397	632	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644451	18644451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	85	357	0	ENST00000266497.5:c.2629C>T	p.Pro877Ser	p.P877S	ENST00000266497		877	Cct/Tct	18/31	0.451222824816384	3	FACETS	1	0.931	1	0.533	0.473	0.596	CLONAL	1	TRUE	1	0.451222824816384	3		357	433	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002814	69002814	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1213028913	NA	P-0040673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	58	208	0	ENST00000288368.4:c.2114G>A	p.Gly705Glu	p.G705E	ENST00000288368	NM_024870.2	705	gGa/gAa	20/40	0.451222824816384	4	FACETS	1	0.881	1	0.511	0.441	0.587	CLONAL	1	TRUE	2	0.451222824816384	4		208	365	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076967	41076967	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	173	413	0	ENST00000373198.4:c.1453C>T	p.Pro485Ser	p.P485S	ENST00000373198	NM_133170.3	485	Cca/Tca	9/32	0.439470419030697	4	FACETS	0.796	0.735	0.859	0.796	0.735	0.859	SUBCLONAL	2	TRUE	2	0.451222824816384	4		413	699	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100286	8100286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241255776	NA	P-0040673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	67	655	0	ENST00000346208.3:c.260C>T	p.Pro87Leu	p.P87L	ENST00000346208		87	cCg/cTg	3/6	1	2	FACETS	0.378	0.328	0.433	0.378	0.328	0.433	SUBCLONAL	1	TRUE	1	0.451222824816384	2		655	785	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606659	43606659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	146	500	0	ENST00000355710.3:c.1268G>A	p.Gly423Glu	p.G423E	ENST00000355710	NM_020975.4	423	gGg/gAg	7/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.451222824816384	2		500	605	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472493	88472493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	111	584	0	ENST00000360948.2:c.2062G>A	p.Gly688Arg	p.G688R	ENST00000360948	NM_001012338.2	688	Gga/Aga	16/19	NA	2	FACETS	0.682	0.614	0.755			1	INDETERMINATE	1	TRUE	NA	0.451222824816384	2		584	721	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807816	3807817	+	missense_variant	Missense_Mutation	DNP	TC	TC	CT	novel	NA	P-0040673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	163	318	0	ENST00000262367.5:c.3602_3603delinsAG	p.Gly1201Glu	p.G1201E	ENST00000262367	NM_004380.2	1201	gGA/gAG	18/31	0.400916429577898	5	FACETS	1	0.965	1			1	CLONAL	2	TRUE	NA	0.451222824816384	5		318	562	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646892	37646892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	185	674	0	ENST00000447079.4:c.2014C>T	p.Pro672Ser	p.P672S	ENST00000447079	NM_015083.1	672	Cct/Tct	3/14	0.363307208064332	5	FACETS	1	0.989	1	0.474	0.438	0.513	CLONAL	1	TRUE	2	0.451222824816384	5		674	966	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030613	11030614	+	missense_variant	Missense_Mutation	DNP	CT	CT	TA	novel	NA	P-0040673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	157	562	0	ENST00000327064.4:c.1167_1168delinsTA	p.Trp390Arg	p.W390R	ENST00000327064	NM_199141.1	389	ttCTgg/ttTAgg	10/16	0.439470419030697	4	FACETS	1	0.962	1	0.545	0.499	0.593	CLONAL	1	TRUE	2	0.451222824816384	4		562	927	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745078	41745078	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	364	627	0	ENST00000301178.4:c.1144G>A	p.Asp382Asn	p.D382N	ENST00000301178	NM_021913.4	382	Gac/Aac	9/20	0.439470419030697	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.451222824816384	4		627	1050	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650758	12650758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	131	484	0	ENST00000251849.4:c.397C>T	p.His133Tyr	p.H133Y	ENST00000251849	NM_002880.3	133	Cat/Tat	4/17	0.439470419030697	4	FACETS	1	0.944	1	0.528	0.479	0.579	CLONAL	1	TRUE	2	0.451222824816384	4		484	798	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272108	142272109	+	missense_variant	Missense_Mutation	DNP	CA	CA	AT	novel	NA	P-0040673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	145	379	1	ENST00000350721.4:c.2765_2766delinsAT	p.Leu922His	p.L922H	ENST00000350721	NM_001184.3	922	cTG/cAT	13/47	0.439470419030697	4	FACETS	1	0.985	1	0.69	0.631	0.751	CLONAL	1	TRUE	2	0.451222824816384	4		380	676	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867439	35867439	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	144	345	0	ENST00000303115.3:c.253T>C	p.Phe85Leu	p.F85L	ENST00000303115	NM_002185.3	85	Ttc/Ctc	3/8	0.451222824816384	3	FACETS	0.975	0.899	1	0.975	0.899	1	CLONAL	2	TRUE	1	0.451222824816384	3		345	401	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80024759	80024759	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	80	385	0	ENST00000265081.6:c.1543T>G	p.Leu515Val	p.L515V	ENST00000265081	NM_002439.4	515	Ttg/Gtg	10/24	1	2	FACETS	0.854	0.756	0.959	0.854	0.756	0.959	CLONAL	1	TRUE	1	0.451222824816384	2		385	415	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987415	2987416	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0040673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	88	425	0	ENST00000396946.4:c.13_14delinsAA	p.Gly5Lys	p.G5K	ENST00000396946	NM_032415.4	5	GGg/AAg	3/25	0.371991424531894	4	FACETS	0.864	0.766	0.969			1	CLONAL	1	TRUE	NA	0.451222824816384	4		425	655	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020486	69020486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	114	480	0	ENST00000288368.4:c.2858C>T	p.Ser953Phe	p.S953F	ENST00000288368	NM_024870.2	953	tCt/tTt	24/40	0.451222824816384	4	FACETS	0.791	0.711	0.876	0.396	0.355	0.438	SUBCLONAL	1	TRUE	2	0.451222824816384	4		480	927	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915978	127915978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	102	407	0	ENST00000373547.4:c.503C>T	p.Pro168Leu	p.P168L	ENST00000373547	NM_002721.4	168	cCt/cTt	6/7	0.446817976845689	2	FACETS	1	0.957	1	0.558	0.503	0.616	CLONAL	1	TRUE	0	0.451222824816384	2		407	405	SUCCESS
AR	367	MSKCC	GRCh37	X	66941743	66941743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	135	580	0	ENST00000374690.3:c.2387G>A	p.Gly796Glu	p.G796E	ENST00000374690	NM_000044.3	796	gGa/gAa	6/8	0.373366733100418	4	FACETS	0.961	0.873	1	0.48	0.436	0.527	CLONAL	1	TRUE	2	0.451222824816384	4		580	904	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306996	65306997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	53	341	2	ENST00000342505.4:c.2580dup	p.Pro861ThrfsTer4	p.P861Tfs*4	ENST00000342505	NM_002227.2	860	-/A	19/25	0.566502422581673	1	FACETS	0.612	0.529	0.702	0.612	0.529	0.702	SUBCLONAL	1	TRUE	0	0.566502422581673	1		343	219	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676214	37676214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267604833	NA	P-0040742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	117	474	0	ENST00000447079.4:c.2969C>T	p.Pro990Leu	p.P990L	ENST00000447079	NM_015083.1	990	cCt/cTt	11/14	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.566502422581673	2		474	330	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593250	67593250	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	38	257	0	ENST00000274335.5:c.1996G>T	p.Glu666Ter	p.E666*	ENST00000274335		666	Gaa/Taa	15/15	0.422064377996853	1	FACETS	0.597	0.501	0.701	0.597	0.501	0.701	SUBCLONAL	1	TRUE	0	0.566502422581673	1		257	161	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197459	26197459	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	93	329	0	ENST00000356476.2:c.20C>A	p.Thr7Asn	p.T7N	ENST00000356476		7	aCt/aAt	1/1	0.566502422581673	3	FACETS	0.889	0.794	0.989	0.444	0.397	0.495	CLONAL	1	TRUE	1	0.566502422581673	3		329	474	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	178	541	0				ENST00000310581	NM_198253.2	-/1132			0.511883809291778	4	FACETS	1	0.988	1	0.469	0.433	0.506	CLONAL	1	TRUE	1	0.511883809291778	4		541	748	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522475	187522476	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	160	530	0	ENST00000441802.2:c.11587dup	p.Ser3863PhefsTer13	p.S3863Ffs*13	ENST00000441802	NM_005245.3	3863	tcc/tTcc	21/27	0.511883809291778	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.511883809291778	1		530	455	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589186	67589186	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	133	303	0	ENST00000274335.5:c.1175del	p.Phe392SerfsTer5	p.F392Sfs*5	ENST00000274335		392	Ttc/tc	9/15	0.511883809291778	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.511883809291778	1		303	334	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0040756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	64	326	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.896	0.787	1	0.896	0.787	1	CLONAL	1	TRUE	1	0.637584213037616	2		326	224	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138729528	NA	P-0040756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	142	651	0	ENST00000269305.4:c.523C>G	p.Arg175Gly	p.R175G	ENST00000269305	NM_001126112.2	175	Cgc/Ggc	5/11	0.637584213037616	1	FACETS	0.671	0.617	0.728	0.671	0.617	0.728	SUBCLONAL	1	TRUE	0	0.637584213037616	1		651	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579409	7579410	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0040756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	195	743	0	ENST00000269305.4:c.277_278del	p.Leu93ValfsTer55	p.L93Vfs*55	ENST00000269305	NM_001126112.2	93	CTg/g	4/11	0.637584213037616	1	FACETS	0.74	0.69	0.792	0.74	0.69	0.792	SUBCLONAL	1	TRUE	0	0.637584213037616	1		743	563	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937403	76937403	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0040756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	121	296	0	ENST00000373344.5:c.3345T>G	p.Tyr1115Ter	p.Y1115*	ENST00000373344	NM_000489.3	1115	taT/taG	9/35	0.637584213037616	1	FACETS	0.842	0.772	0.913	0.842	0.772	0.913	CLONAL	1	TRUE	0	0.637584213037616	1		296	307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0040779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	349	688	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.430518404565899	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.430518404565899	2		688	695	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89871790	89871790	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	66	530	0	ENST00000389301.3:c.607A>T	p.Met203Leu	p.M203L	ENST00000389301	NM_000135.2	203	Atg/Ttg	7/43	0.252854810881357	2	FACETS	0.456	0.396	0.522	0.228	0.198	0.261	INDETERMINATE	1	TRUE	0	0.430518404565899	2		530	672	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672842	30672842	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	50	795	0	ENST00000376406.3:c.4118T>G	p.Leu1373Arg	p.L1373R	ENST00000376406	NM_014641.2	1373	cTc/cGc	10/15	0.102754081643518	4	FACETS	0.339	0.286	0.397	0.169	0.143	0.199	INDETERMINATE	1	TRUE	2	0.430518404565899	4		795	981	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832031	72832031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144091993	NA	P-0040786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	385	616	0	ENST00000268489.5:c.4550C>T	p.Ser1517Leu	p.S1517L	ENST00000268489	NM_006885.3	1517	tCg/tTg	9/10	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.78370547556631	2		616	935	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779578	3779578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	638	1044	4	ENST00000262367.5:c.5470G>A	p.Ala1824Thr	p.A1824T	ENST00000262367	NM_004380.2	1824	Gcc/Acc	31/31	1	2	FACETS	0.996	0.959	1	0.996	0.959	1	CLONAL	1	TRUE	1	0.78370547556631	2		1048	1635	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946340	71946340	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	170	802	1	ENST00000298229.2:c.2504G>T	p.Gly835Val	p.G835V	ENST00000298229	NM_001567.3	835	gGg/gTg	23/28	0.773971084769403	1	FACETS	0.334	0.308	0.362	0.334	0.308	0.362	SUBCLONAL	1	TRUE	0	0.78370547556631	1		803	789	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61722669	61722670	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	215	372	2	ENST00000401558.2:c.967dup	p.Ser323LysfsTer9	p.S323Kfs*9	ENST00000401558	NM_003400.3	323	agt/aAgt	11/25	1	2	FACETS	0.989	0.926	1	0.989	0.926	1	CLONAL	1	TRUE	1	0.78370547556631	2		374	555	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319690	62319692	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs779176651	NA	P-0040786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	171	887	0	ENST00000360203.5:c.1678_1680del	p.Phe560del	p.F560del	ENST00000360203	NM_001283009.1	558	aTCTtc/atc	20/35	1	2	FACETS	0.363	0.333	0.395	0.363	0.333	0.395	SUBCLONAL	1	TRUE	1	0.78370547556631	2		887	1201	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0040845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	204	272	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.299754726672185	4	FACETS	0.846	0.788	0.905	0.846	0.788	0.905	CLONAL	3	TRUE	1	0.32	4		272	663	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106366	27106366	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	278	572	0	ENST00000324856.7:c.5979del	p.Phe1993LeufsTer22	p.F1993Lfs*22	ENST00000324856	NM_006015.4	1993	Ttt/tt	20/20	NA	2	FACETS	1	0.954	1			1	INDETERMINATE	2	TRUE	NA	0.32	2		572	856	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578368	7578369	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	novel	NA	P-0040845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	298	590	0	ENST00000269305.4:c.559+2dup		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.299754726672185	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.32	2		590	877	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0040851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	53	415	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.903	0.769	1	0.903	0.769	1	CLONAL	1	TRUE	1	0.193086029013739	2		415	608	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0040851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	35	587	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.193086029013739	5	FACETS	0.995	0.815	1			1	CLONAL	1	TRUE	NA	0.193086029013739	5		587	470	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46736432	46736432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764014400	NA	P-0040851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	39	526	1	ENST00000371975.4:c.1144C>T	p.Arg382Trp	p.R382W	ENST00000371975	NM_003579.3	382	Cgg/Tgg	10/18	0.193086029013739	2	FACETS	0.953	0.79	1	0.476	0.395	0.567	CLONAL	1	TRUE	0	0.193086029013739	2		527	424	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139307	108139307	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	44	575	0	ENST00000278616.4:c.2809G>T	p.Glu937Ter	p.E937*	ENST00000278616	NM_000051.3	937	Gaa/Taa	18/63	1	2	FACETS	0.85	0.713	1	0.85	0.713	1	CLONAL	1	TRUE	1	0.193086029013739	2		575	536	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673781	37673781	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	56	540	0	ENST00000447079.4:c.2935C>T	p.Arg979Ter	p.R979*	ENST00000447079	NM_015083.1	979	Cga/Tga	10/14	1	2	FACETS	0.843	0.721	0.977	0.843	0.721	0.977	CLONAL	1	TRUE	1	0.193086029013739	2		540	688	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243460	41243460	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs398122680	NA	P-0040851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	42	567	0	ENST00000357654.3:c.4088C>G	p.Ser1363Ter	p.S1363*	ENST00000357654	NM_007294.3	1363	tCa/tGa	10/23	1	2	FACETS	0.633	0.527	0.751	0.633	0.527	0.751	SUBCLONAL	1	TRUE	1	0.193086029013739	2		567	687	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978980	25978989	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAACCTGGGT	CAACCTGGGT	-	novel	NA	P-0040851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	30	372	0	ENST00000435504.4:c.940-6_943del		p.X314_splice	ENST00000435504		314		10/13	0.193086029013739	1	FACETS	0.695	0.56	0.848	0.695	0.56	0.848	SUBCLONAL	1	TRUE	0	0.193086029013739	1		372	404	SUCCESS
APC	324	MSKCC	GRCh37	5	112175206	112175206	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	30	198	0	ENST00000257430.4:c.3915del	p.Glu1306LysfsTer2	p.E1306Kfs*2	ENST00000257430	NM_000038.5	1305	gcA/gc	16/16	0.193086029013739	5	FACETS	0.795	0.644	0.965			1	CLONAL	2	TRUE	NA	0.193086029013739	5		198	252	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818365	170818365	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	44	342	0	ENST00000296930.5:c.195G>C	p.Met65Ile	p.M65I	ENST00000296930	NM_002520.6	65	atG/atC	3/11	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.193086029013739	2		342	440	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591247	67591249	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GGT	GGT	-	rs1131692243	NA	P-0040858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	28	375	0	ENST00000274335.5:c.1748_1750del		p.X583_splice	ENST00000274335		583		13/15	0.168562377354288	0	FACETS	0.455	0.364	0.559			1	SUBCLONAL	1	TRUE	0	0.267980767588854	0		375	336	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591043	67591043	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	16	225	0	ENST00000274335.5:c.1636G>T	p.Glu546Ter	p.E546*	ENST00000274335		546	Gaa/Taa	12/15	0.168562377354288	0	FACETS	0.396	0.293	0.518			1	SUBCLONAL	1	TRUE	0	0.267980767588854	0		225	221	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	181	836	0	ENST00000269305.4:c.848del	p.Arg283ProfsTer62	p.R283Pfs*62	ENST00000269305	NM_001126112.2	283	cGc/cc	8/11	0.267980767588854	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.267980767588854	1		836	1037	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812301	43812301	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0040858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	88	521	0	ENST00000372470.3:c.1165+1G>T		p.X389_splice	ENST00000372470	NM_005373.2	389			0.267980767588854	3	FACETS	0.891	0.788	1			1	CLONAL	1	TRUE	NA	0.267980767588854	3		521	836	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144548	58144548	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	28	288	0	ENST00000257904.6:c.523G>T	p.Val175Phe	p.V175F	ENST00000257904	NM_000075.3	175	Gtt/Ttt	5/8	1	2	FACETS	0.44	0.351	0.542	0.44	0.351	0.542	SUBCLONAL	1	TRUE	1	0.267980767588854	2		288	475	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263866	133263866	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	80	203	0	ENST00000320574.5:c.36C>A	p.Asp12Glu	p.D12E	ENST00000320574	NM_006231.2	12	gaC/gaA	1/49	0.218414966792989	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.267980767588854	1		203	402	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740738	58740738	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	129	569	0	ENST00000305921.3:c.1643A>C	p.Lys548Thr	p.K548T	ENST00000305921	NM_003620.3	548	aAg/aCg	6/6	0.267980767588854	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.267980767588854	1		569	646	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274791	142274791	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	17	417	0	ENST00000350721.4:c.2269C>G	p.Gln757Glu	p.Q757E	ENST00000350721	NM_001184.3	757	Caa/Gaa	10/47	1	2	FACETS	0.388	0.289	0.506	0.388	0.289	0.506	SUBCLONAL	1	TRUE	1	0.267980767588854	2		417	327	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0040889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	67	681	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.273259270673393	1	FACETS	0.525	0.46	0.594	0.525	0.46	0.594	INDETERMINATE	1	TRUE	0	0.594462734214448	1		681	302	SUCCESS
APC	324	MSKCC	GRCh37	5	112154723	112154723	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775126020	NA	P-0040889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	104	348	0	ENST00000257430.4:c.994C>T	p.Arg332Ter	p.R332*	ENST00000257430	NM_000038.5	332	Cga/Tga	10/16	0.273259270673393	1	FACETS	0.487	0.438	0.539	0.487	0.438	0.539	INDETERMINATE	1	TRUE	0	0.594462734214448	1		348	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579317	7579317	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	230	445	0	ENST00000269305.4:c.370T>C	p.Cys124Arg	p.C124R	ENST00000269305	NM_001126112.2	124	Tgc/Cgc	4/11	0.594462734214448	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.594462734214448	1		445	499	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162680	47162680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757222335	NA	P-0040889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	172	297	0	ENST00000409792.3:c.3446G>A	p.Ser1149Asn	p.S1149N	ENST00000409792	NM_014159.6	1149	aGt/aAt	3/21	0.273259270673393	1	FACETS	0.833	0.773	0.895	0.833	0.773	0.895	INDETERMINATE	1	TRUE	0	0.594462734214448	1		297	488	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926897	112926897	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397507548	NA	P-0040889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	146	358	0	ENST00000351677.2:c.1517A>C	p.Gln506Pro	p.Q506P	ENST00000351677	NM_002834.3	506	cAg/cCg	13/16	1	2	FACETS	0.812	0.744	0.883	0.812	0.744	0.883	CLONAL	1	TRUE	1	0.594462734214448	2		358	605	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251653	212251653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	35	358	0	ENST00000342788.4:c.3406G>A	p.Ala1136Thr	p.A1136T	ENST00000342788	NM_005235.2	1136	Gcc/Acc	27/28	0.233340058160454	2	FACETS	0.191	0.156	0.231	0.096	0.078	0.116	INDETERMINATE	1	TRUE	0	0.594462734214448	2		358	616	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143326445	143326445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	73	287	0	ENST00000262992.4:c.169C>T	p.Arg57Cys	p.R57C	ENST00000262992	NM_001101669.1	57	Cgt/Tgt	4/24	0.350909534909798	1	FACETS	0.377	0.33	0.427	0.377	0.33	0.427	INDETERMINATE	1	TRUE	0	0.594462734214448	1		287	458	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0040915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	101	422	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.38	2		422	502	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468141	25468141	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	102	634	0	ENST00000264709.3:c.1535G>A	p.Gly512Glu	p.G512E	ENST00000264709	NM_175629.2	512	gGa/gAa	13/23	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.38	2		634	533	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407859	139407859	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756642176	NA	P-0040915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	28	517	0	ENST00000277541.6:c.2338C>T	p.Arg780Trp	p.R780W	ENST00000277541	NM_017617.3	780	Cgg/Tgg	14/34	1	2	FACETS	0.322	0.257	0.397	0.322	0.257	0.397	SUBCLONAL	1	TRUE	1	0.38	2		517	457	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0040958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	57	415	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.345121718775399	3	FACETS	0.819	0.704	0.944	0.409	0.352	0.472	CLONAL	1	TRUE	1	0.345121718775399	3		415	473	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0040958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	92	665	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.818	0.727	0.914	0.818	0.727	0.914	CLONAL	1	TRUE	1	0.345121718775399	2		665	652	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407923	139407923	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	103	836	0	ENST00000277541.6:c.2274A>T	p.Glu758Asp	p.E758D	ENST00000277541	NM_017617.3	758	gaA/gaT	14/34	0.299784277309909	2	FACETS	1	0.948	1	0.547	0.49	0.607	CLONAL	1	FALSE	0	0.3	2		836	628	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0041067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	233	665	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.531730757121834	3	FACETS	1	0.986	1	0.753	0.712	0.793	CLONAL	2	FALSE	0	0.610777942243795	3		665	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912664	NA	P-0041067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	403	830	0	ENST00000269305.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000269305	NM_001126112.2	337	cGc/cAc	10/11	0.397219535903856	3	FACETS	0.853	0.821	0.885	0.853	0.821	0.885	CLONAL	3	FALSE	0	0.610777942243795	3		830	673	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841123	15841124	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0041067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	122	740	0	ENST00000307771.7:c.1212dup	p.Lys405GlufsTer23	p.K405Efs*23	ENST00000307771	NM_005089.3	403	agg/aGgg	11/11	0.243638546471526	2	FACETS	0.688	0.623	0.755	0.344	0.311	0.378	INDETERMINATE	1	FALSE	0	0.610777942243795	2		740	581	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41999970	41999970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	105	726	0	ENST00000219905.7:c.2233C>T	p.Leu745Phe	p.L745F	ENST00000219905	NM_001164273.1	745	Ctt/Ttt	6/24	0.157058659985873	3	FACETS	0.722	0.648	0.8	0.241	0.216	0.267	INDETERMINATE	1	FALSE	0	0.610777942243795	3		726	622	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630061	47630333	+	coding_sequence_variant,5_prime_UTR_variant	In_Frame_Del	DEL	AAGGATGCGCGTCTGCGGGTTTCCGCGCGACCTAGGCGCAGGCATGCGCAGTAGCTAAAGTCACCAGCGTGCGCGGGAAGCTGGGCCGCGTCTGCTTATGATTGGTTGCCGCGGCAGACTCCCACCCACCGAAACGCAGCCCTGGAAGCTGATTGGGTGTGGTCGCCGTGGCCGGACGCCGCTCGGGGGACGTGGGAGGGGAGGCGGGAAACAGCTTAGTGGGTGTGGGGTCGCGCATTTTCTTCAACCAGGAGGTGAGGAGGTTTCGACATG	AAGGATGCGCGTCTGCGGGTTTCCGCGCGACCTAGGCGCAGGCATGCGCAGTAGCTAAAGTCACCAGCGTGCGCGGGAAGCTGGGCCGCGTCTGCTTATGATTGGTTGCCGCGGCAGACTCCCACCCACCGAAACGCAGCCCTGGAAGCTGATTGGGTGTGGTCGCCGTGGCCGGACGCCGCTCGGGGGACGTGGGAGGGGAGGCGGGAAACAGCTTAGTGGGTGTGGGGTCGCGCATTTTCTTCAACCAGGAGGTGAGGAGGTTTCGACATG	-	novel	NA	P-0041067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	97	37	0				ENST00000233146	NM_000251.2	?-1/934		1/16	0.535745031171116	4	FACETS	0.939	0.898	0.973	1	0.991	1	CLONAL	5	FALSE	1	0.610777942243795	4		37	109	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	236	541	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.865972032975821	2		541	494	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0041092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25574	1511	1045	5	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.865972032975821	28	FACETS	0.79	0.766	0.814			1	SUBCLONAL	2	TRUE	NA	0.865972032975821	28		1050	27085	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240690	55240690	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs772046081	NA	P-0041092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21843	5731	835	2	ENST00000275493.2:c.1934C>G	p.Ser645Cys	p.S645C	ENST00000275493	NM_005228.3	645	tCc/tGc	17/28	0.865972032975821	28	FACETS	0.981	0.967	0.995			1	CLONAL	6	TRUE	NA	0.865972032975821	28		837	27574	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517553	176517553	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149419025	NA	P-0041092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	141	937	3	ENST00000292408.4:c.254G>A	p.Arg85His	p.R85H	ENST00000292408	NM_213647.1	85	cGc/cAc	3/18	1	2	FACETS	0.285	0.259	0.313	0.285	0.259	0.313	SUBCLONAL	1	TRUE	1	0.865972032975821	2		940	1143	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624244	89624245	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs786204881	NA	P-0041092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	130	197	0	ENST00000371953.3:c.21_22del	p.Glu7AspfsTer3	p.E7Dfs*3	ENST00000371953	NM_000314.4	6	aaAGag/aaag	1/9	0.856377382483095	1	FACETS	0.915	0.862	0.966	0.915	0.862	0.966	CLONAL	1	TRUE	0	0.865972032975821	1		197	186	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	73	541	0				ENST00000310581	NM_198253.2	-/1132			0.316496608446713	3	FACETS	1	0.964	1	0.633	0.556	0.715	CLONAL	1	TRUE	1	0.316496608446713	3		541	422	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057988	27057988	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	130	805	0	ENST00000324856.7:c.1696C>T	p.Gln566Ter	p.Q566*	ENST00000324856	NM_006015.4	566	Cag/Tag	3/20	0.316496608446713	3	FACETS	0.865	0.788	0.945	0.865	0.788	0.945	CLONAL	2	TRUE	1	0.316496608446713	3		805	550	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918622	44918622	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	163	309	0	ENST00000377967.4:c.1105C>T	p.Gln369Ter	p.Q369*	ENST00000377967	NM_021140.2	369	Cag/Tag	12/29	0.096239028936984	3	FACETS	0.929	0.869	0.99			1	INDETERMINATE	4	TRUE	NA	0.316496608446713	3		309	321	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305328	65305328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	156	702	0	ENST00000342505.4:c.2800C>T	p.His934Tyr	p.H934Y	ENST00000342505	NM_002227.2	934	Cat/Tat	20/25	0.316496608446713	3	FACETS	0.978	0.9	1	0.978	0.9	1	CLONAL	2	TRUE	1	0.316496608446713	3		702	584	SUCCESS
APC	324	MSKCC	GRCh37	5	112136980	112136980	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554076133	NA	P-0041104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	95	442	0	ENST00000257430.4:c.734C>T	p.Ser245Leu	p.S245L	ENST00000257430	NM_000038.5	245	tCa/tTa	8/16	0.306890341528558	2	FACETS	0.772	0.692	0.855	0.772	0.692	0.855	SUBCLONAL	2	TRUE	0	0.316496608446713	2		442	389	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434665	110434665	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868494628	NA	P-0041104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	94	1071	2	ENST00000375856.3:c.3736G>A	p.Gly1246Ser	p.G1246S	ENST00000375856	NM_003749.2	1246	Ggc/Agc	1/2	0.205812835695887	5	FACETS	1	0.933	1	0.357	0.317	0.399	CLONAL	1	TRUE	2	0.316496608446713	5		1073	819	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265218	16265218	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	95	534	0	ENST00000375759.3:c.10710G>C	p.Glu3570Asp	p.E3570D	ENST00000375759	NM_015001.2	3570	gaG/gaC	14/15	0.316496608446713	3	FACETS	0.896	0.804	0.993	0.896	0.804	0.993	CLONAL	2	TRUE	1	0.316496608446713	3		534	388	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163325176	163325176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	39	436	0	ENST00000271452.3:c.1312G>A	p.Glu438Lys	p.E438K	ENST00000271452	NM_145697.2	438	Gaa/Aaa	14/14	0.205812835695887	5	FACETS	0.88	0.73	1	0.293	0.243	0.349	CLONAL	1	TRUE	2	0.316496608446713	5		436	413	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100466	102100466	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	88	647	0	ENST00000282441.5:c.1310A>T	p.Gln437Leu	p.Q437L	ENST00000282441	NM_001130145.2	437	cAg/cTg	9/9	0.115705530269449	5	FACETS	1	0.947	1	0.373	0.33	0.419	INDETERMINATE	1	TRUE	2	0.316496608446713	5		647	732	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061761	38061762	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCGGC	novel	NA	P-0041104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	65	968	0	ENST00000250448.2:c.223_227dup	p.Leu77ProfsTer3	p.L77Pfs*3	ENST00000250448	NM_004496.3	76	ggc/ggGCCGGc	2/2	0.271578873983675	2	FACETS	0.724	0.628	0.828	0.362	0.314	0.414	SUBCLONAL	1	TRUE	0	0.316496608446713	2		968	567	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830178	72830178	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	128	796	1	ENST00000268489.5:c.6403C>T	p.Gln2135Ter	p.Q2135*	ENST00000268489	NM_006885.3	2135	Cag/Tag	9/10	0.205812835695887	5	FACETS	1	0.943	1	0.699	0.636	0.765	CLONAL	2	TRUE	2	0.316496608446713	5		797	569	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223161	1223163	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0041104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	68	870	0	ENST00000326873.7:c.1098_1100del	p.Phe366_Thr367delinsLeu	p.F366_T367delinsL	ENST00000326873	NM_000455.4	366	ttCACg/ttg	8/10	0.155397805698364	3	FACETS	0.612	0.531	0.7	0.204	0.177	0.234	INDETERMINATE	1	TRUE	0	0.316496608446713	3		870	813	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265476	198265476	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	131	569	0	ENST00000335508.6:c.2681A>G	p.Asp894Gly	p.D894G	ENST00000335508	NM_012433.2	894	gAt/gGt	18/25	0.205812835695887	5	FACETS	1	0.972	1	0.772	0.704	0.843	CLONAL	2	TRUE	2	0.316496608446713	5		569	527	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321130	62321130	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	109	1196	2	ENST00000360203.5:c.2053C>T	p.Gln685Ter	p.Q685*	ENST00000360203	NM_001283009.1	685	Cag/Tag	24/35	0.316496608446713	5	FACETS	1	0.931	1	0.35	0.314	0.389	CLONAL	1	TRUE	2	0.316496608446713	5		1198	967	SUCCESS
ATR	545	MSKCC	GRCh37	3	142257453	142257453	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	141	442	0	ENST00000350721.4:c.3596T>G	p.Phe1199Cys	p.F1199C	ENST00000350721	NM_001184.3	1199	tTt/tGt	19/47	0.316496608446713	5	FACETS	0.854	0.783	0.928	0.854	0.783	0.928	CLONAL	3	TRUE	2	0.316496608446713	5		442	513	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599318	55599318	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	46	557	0	ENST00000288135.5:c.2444G>C	p.Arg815Thr	p.R815T	ENST00000288135	NM_000222.2	815	aGa/aCa	17/21	0.316496608446713	3	FACETS	0.842	0.71	0.986	0.421	0.355	0.493	CLONAL	1	TRUE	1	0.316496608446713	3		557	400	SUCCESS
APC	324	MSKCC	GRCh37	5	112137036	112137036	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1434813233	NA	P-0041104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	123	538	0	ENST00000257430.4:c.790C>G	p.Gln264Glu	p.Q264E	ENST00000257430	NM_000038.5	264	Caa/Gaa	8/16	0.306890341528558	2	FACETS	0.787	0.715	0.861	0.787	0.715	0.861	SUBCLONAL	2	TRUE	0	0.316496608446713	2		538	494	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254938	16254938	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	137	529	0	ENST00000375759.3:c.2203C>G	p.Gln735Glu	p.Q735E	ENST00000375759	NM_015001.2	735	Cag/Gag	11/15	1	2	FACETS	0.993	0.906	1	0.993	0.906	1	CLONAL	1	TRUE	1	0.436506159129828	2		529	632	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111495	8111496	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGGAGGG	novel	NA	P-0041157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	163	626	0	ENST00000346208.3:c.987_988insGTGGAGG	p.Arg330ValfsTer24	p.R330Vfs*24	ENST00000346208		327	-/TGGAGGG	5/6	1	2	FACETS	0.913	0.839	0.99	0.913	0.839	0.99	CLONAL	1	TRUE	1	0.436506159129828	2		626	818	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0041201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	45	388	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.436916894857186	2		388	174	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0041201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	106	760	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	0.436916894857186	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.436916894857186	1		760	298	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982941	201982962	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGGCTGGCCTTGCAGCGCCCA	GAGGCTGGCCTTGCAGCGCCCA	-	novel	NA	P-0041201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	45	560	0	ENST00000359651.3:c.806-11_816del		p.X269_splice	ENST00000359651		269		7/8	1	2	FACETS	0.698	0.59	0.816	0.698	0.59	0.816	SUBCLONAL	1	TRUE	1	0.436916894857186	2		560	295	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0041207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	159	240	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.719611522092068	2		240	425	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0041207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	137	515	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	0.581083881019608	1	FACETS	0.675	0.622	0.73	0.675	0.622	0.73	SUBCLONAL	1	TRUE	0	0.719611522092068	1		515	361	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682459	52682459	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0041207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	136	278	0	ENST00000394830.3:c.715-1G>C		p.X239_splice	ENST00000394830	NM_018313.4	239			1	2	FACETS	0.863	0.791	0.937	0.863	0.791	0.937	CLONAL	1	TRUE	1	0.719611522092068	2		278	438	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143326378	143326378	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1367554744	NA	P-0041207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	164	415	0	ENST00000262992.4:c.236C>G	p.Ser79Cys	p.S79C	ENST00000262992	NM_001101669.1	79	tCc/tGc	4/24	1	2	FACETS	0.913	0.845	0.984	0.913	0.845	0.984	CLONAL	1	TRUE	1	0.719611522092068	2		415	499	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588952	67588953	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0041207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	125	308	0	ENST00000274335.5:c.1045_1046del	p.Asp349TyrfsTer14	p.D349Yfs*14	ENST00000274335		348	cGA/c	8/15	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.719611522092068	2		308	346	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589589	67589612	+	inframe_deletion	In_Frame_Del	DEL	AATATAACACTCAGTTTCAAGAAA	AATATAACACTCAGTTTCAAGAAA	-	novel	NA	P-0041207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	123	260	0	ENST00000274335.5:c.1354_1377del	p.Tyr452_Lys459del	p.Y452_K459del	ENST00000274335		451	gAATATAACACTCAGTTTCAAGAAAaa/gaa	10/15	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.719611522092068	2		260	333	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591219	67591284	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAAAAGGTGTTCGGCAAAAGAAGTTG	TGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAAAAGGTGTTCGGCAAAAGAAGTTG	GGC	novel	NA	P-0041207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	80	444	2	ENST00000274335.5:c.1746-29_1782delinsGGC		p.X582_splice	ENST00000274335		582		13/15	1	2	FACETS	0.48	0.424	0.54	0.48	0.424	0.54	SUBCLONAL	1	TRUE	1	0.719611522092068	2		446	463	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225148	53225148	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	250	784	0	ENST00000375401.3:c.3070G>T	p.Glu1024Ter	p.E1024*	ENST00000375401	NM_004187.3	1024	Gag/Tag	20/26	1	2	FACETS	0.87	0.816	0.924	0.87	0.816	0.924	CLONAL	1	TRUE	1	0.719611522092068	2		784	799	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0041216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	56	415	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.396932949839872	1	FACETS	0.764	0.671	0.861	1	0.973	1	SUBCLONAL	2	TRUE	0	0.396932949839872	1		415	148	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0041216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	227	703	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.387819016507692	2	FACETS	0.786	0.735	0.838	0.786	0.735	0.838	SUBCLONAL	2	TRUE	0	0.396932949839872	2		703	728	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0041216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	368	341	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.387819016507692	2	FACETS	0.858	0.821	0.896	1	0.994	1	CLONAL	3	TRUE	0	0.396932949839872	2		341	720	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492796	56492796	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	162	524	0	ENST00000407977.2:c.143T>C	p.Ile48Thr	p.I48T	ENST00000407977		48	aTc/aCc	2/10	0.396932949839872	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.396932949839872	1		524	456	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593515	48593517	+	frameshift_variant	Frame_Shift_Del	DEL	TGG	TGG	C	novel	NA	P-0041216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	52	363	0	ENST00000342988.3:c.1266_1268delinsC	p.Gly423ArgfsTer5	p.G423Rfs*5	ENST00000342988	NM_005359.5	422	ccTGGa/ccCa	10/12	0.330043493982586	1	FACETS	0.781	0.67	0.9	0.781	0.67	0.9	SUBCLONAL	1	TRUE	0	0.396932949839872	1		363	269	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0041236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	2674	615	0	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.814098834297607	6	FACETS	1	0.997	1	1	0.997	1	CLONAL	6	TRUE	0	0.814098834297607	6		615	2861	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432382	78432382	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1284370233	NA	P-0041236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	44	364	0	ENST00000370768.2:c.469G>C	p.Val157Leu	p.V157L	ENST00000370768	NM_003902.3	157	Gtc/Ctc	7/20	1	2	FACETS	0.381	0.321	0.446	0.381	0.321	0.446	SUBCLONAL	1	TRUE	1	0.814098834297607	2		364	284	SUCCESS
APC	324	MSKCC	GRCh37	5	112179431	112179432	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	111	502	0	ENST00000257430.4:c.8140_8141insA	p.Arg2714GlnfsTer19	p.R2714Qfs*19	ENST00000257430	NM_000038.5	2714	cgt/cAgt	16/16	0.812275652892555	1	FACETS	0.539	0.491	0.588	0.539	0.491	0.588	SUBCLONAL	1	TRUE	0	0.814098834297607	1		502	300	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495726	72495726	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	37	387	0	ENST00000477973.2:c.346T>G	p.Cys116Gly	p.C116G	ENST00000477973	NM_012234.5	116	Tgt/Ggt	1/4	1	2	FACETS	0.682	0.562	0.817	0.682	0.562	0.817	SUBCLONAL	1	FALSE	1	0.220558847390289	2		387	492	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7978952	7978952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139689690	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	72	426	0	ENST00000319144.4:c.1615G>A	p.Glu539Lys	p.E539K	ENST00000319144	NM_001139.2	539	Gaa/Aaa	12/15	0.348483118398698	3	FACETS	0.671	0.587	0.762	0.336	0.293	0.381	SUBCLONAL	1	FALSE	1	0.447287441449463	3		426	587	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	146	365	1				ENST00000310581	NM_198253.2	-/1132			0.187766003723485	5	FACETS	1	0.956	1	0.707	0.65	0.767	INDETERMINATE	2	FALSE	2	0.447287441449463	5		366	514	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665053	29665053	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691093	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	89	357	0	ENST00000356175.3:c.6652C>T	p.Gln2218Ter	p.Q2218*	ENST00000356175	NM_000267.3	2218	Caa/Taa	44/57	0.365407263009684	3	FACETS	1	0.98	1	0.738	0.66	0.819	CLONAL	1	FALSE	1	0.447287441449463	3		357	330	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29422354	29422354	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	143	633	0	ENST00000356175.3:c.27G>A	p.Trp9Ter	p.W9*	ENST00000356175	NM_000267.3	9	tgG/tgA	1/57	0.365407263009684	3	FACETS	0.972	0.887	1	0.486	0.443	0.531	CLONAL	1	FALSE	1	0.447287441449463	3		633	805	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964510	93964510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1435219791	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	39	352	0	ENST00000369303.4:c.2387G>A	p.Gly796Glu	p.G796E	ENST00000369303	NM_004440.3	796	gGa/gAa	14/17	0.242526480526868	4	FACETS	0.895	0.746	1			1	INDETERMINATE	1	FALSE	NA	0.447287441449463	4		352	282	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713470	40713470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318044562	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	182	641	0	ENST00000373198.4:c.4045C>T	p.Arg1349Cys	p.R1349C	ENST00000373198	NM_133170.3	1349	Cgt/Tgt	30/32	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	FALSE	NA	0.447287441449463	2		641	676	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168991	32168991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	331	870	0	ENST00000375023.3:c.4042G>A	p.Glu1348Lys	p.E1348K	ENST00000375023	NM_004557.3	1348	Gaa/Aaa	22/30	0.447287441449463	5	FACETS	0.893	0.843	0.945	0.596	0.562	0.63	CLONAL	2	FALSE	2	0.447287441449463	5		870	1384	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979369	93979369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776583281	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	42	246	0	ENST00000369303.4:c.1459G>A	p.Glu487Lys	p.E487K	ENST00000369303	NM_004440.3	487	Gaa/Aaa	7/17	0.404025563929625	4	FACETS	0.795	0.673	0.925			1	CLONAL	2	FALSE	NA	0.447287441449463	4		246	171	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155094	108155094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	77	331	0	ENST00000278616.4:c.3887C>T	p.Pro1296Leu	p.P1296L	ENST00000278616	NM_000051.3	1296	cCt/cTt	26/63	0.394327747549821	2	FACETS	0.883	0.791	0.976	0.883	0.791	0.976	CLONAL	2	FALSE	0	0.447287441449463	2		331	195	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485307	8485307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	75	321	0	ENST00000356435.5:c.3073C>T	p.His1025Tyr	p.H1025Y	ENST00000356435		1025	Cat/Tat	18/35	0.192413800712723	3	FACETS	0.877	0.78	0.977	0.585	0.52	0.652	INDETERMINATE	2	FALSE	0	0.447287441449463	3		321	234	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420285	88420285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199690201	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	71	489	0	ENST00000360948.2:c.2401G>A	p.Asp801Asn	p.D801N	ENST00000360948	NM_001012338.2	801	Gat/Aat	19/19	0.192413800712723	3	FACETS	0.778	0.681	0.883	0.259	0.227	0.295	INDETERMINATE	1	FALSE	0	0.447287441449463	3		489	499	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964502	93964502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	67	386	0	ENST00000369303.4:c.2395C>T	p.Pro799Ser	p.P799S	ENST00000369303	NM_004440.3	799	Cca/Tca	14/17	0.242526480526868	4	FACETS	1	0.972	1			1	INDETERMINATE	1	FALSE	NA	0.447287441449463	4		386	302	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29195996	29195996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	179	767	0	ENST00000240100.2:c.602C>T	p.Pro201Leu	p.P201L	ENST00000240100	NM_001394.6	201	cCc/cTc	3/4	0.187766003723485	5	FACETS	1	0.982	1	0.41	0.377	0.444	INDETERMINATE	1	FALSE	2	0.447287441449463	5		767	1087	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546763	9546763	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	160	335	0	ENST00000353224.5:c.1259C>T	p.Ser420Phe	p.S420F	ENST00000353224	NM_177990.2	420	tCc/tTc	5/10	0.187766003723485	5	FACETS	0.974	0.904	1	0.974	0.904	1	INDETERMINATE	3	FALSE	2	0.447287441449463	5		335	409	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630587	187630587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770123806	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	110	616	0	ENST00000441802.2:c.395G>A	p.Arg132Gln	p.R132Q	ENST00000441802	NM_005245.3	132	cGa/cAa	2/27	0.365407263009684	3	FACETS	0.929	0.836	1	0.464	0.418	0.514	CLONAL	1	FALSE	1	0.447287441449463	3		616	648	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47607010	47607010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	42	406	0	ENST00000263735.4:c.760G>A	p.Glu254Lys	p.E254K	ENST00000263735	NM_002354.2	254	Gaa/Aaa	7/9	0.366960807641976	2	FACETS	0.602	0.505	0.709	0.301	0.252	0.355	SUBCLONAL	1	FALSE	0	0.447287441449463	2		406	312	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192078	108192078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200431631	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	134	468	0	ENST00000278616.4:c.6503C>T	p.Ser2168Leu	p.S2168L	ENST00000278616	NM_000051.3	2168	tCg/tTg	45/63	0.394327747549821	2	FACETS	1	0.987	1	0.718	0.659	0.78	CLONAL	1	FALSE	0	0.447287441449463	2		468	417	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432194	121432194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267603344	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	214	608	0	ENST00000257555.6:c.941C>T	p.Pro314Leu	p.P314L	ENST00000257555		314	cCc/cTc	4/10	0.434924130020889	2	FACETS	0.861	0.806	0.916	0.861	0.806	0.916	CLONAL	2	FALSE	0	0.447287441449463	2		608	556	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458559	12458559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	95	621	0	ENST00000287820.6:c.1176G>A	p.Met392Ile	p.M392I	ENST00000287820	NM_015869.4	392	atG/atA	6/7	0.377091397733231	4	FACETS	0.841	0.749	0.939	0.421	0.374	0.47	CLONAL	1	FALSE	2	0.447287441449463	4		621	731	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473708	67473708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906855	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	99	576	0	ENST00000327367.4:c.788C>T	p.Pro263Leu	p.P263L	ENST00000327367	NM_005902.3	263	cCc/cTc	6/9	0.192413800712723	3	FACETS	0.827	0.739	0.92	0.276	0.246	0.307	INDETERMINATE	1	FALSE	0	0.447287441449463	3		576	655	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257189	16257189	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	53	479	0	ENST00000375759.3:c.4454C>T	p.Ser1485Phe	p.S1485F	ENST00000375759	NM_015001.2	1485	tCt/tTt	11/15	0.202164459188895	5	FACETS	1	0.888	1	0.348	0.298	0.403	INDETERMINATE	1	FALSE	2	0.447287441449463	5		479	379	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105529	27105529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	127	389	0	ENST00000324856.7:c.5140G>A	p.Glu1714Lys	p.E1714K	ENST00000324856	NM_006015.4	1714	Gag/Aag	20/20	0.202164459188895	5	FACETS	1	0.977	1	0.799	0.731	0.869	INDETERMINATE	2	FALSE	2	0.447287441449463	5		389	396	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562247	21562247	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	102	845	0	ENST00000382592.4:c.1672C>G	p.Arg558Gly	p.R558G	ENST00000382592	NM_014572.2	558	Cgc/Ggc	4/8	0.192413800712723	3	FACETS	0.626	0.559	0.697	0.209	0.186	0.233	INDETERMINATE	1	FALSE	0	0.447287441449463	3		845	892	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895657	28895657	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	110	480	0	ENST00000282397.4:c.3117T>G	p.Cys1039Trp	p.C1039W	ENST00000282397	NM_002019.4	1039	tgT/tgG	23/30	0.192413800712723	3	FACETS	1	0.984	1	0.492	0.445	0.54	INDETERMINATE	1	FALSE	0	0.447287441449463	3		480	408	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872485	35872486	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AT	novel	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	145	502	0	ENST00000216797.5:c.417_418delinsAT	p.Arg140Ter	p.R140*	ENST00000216797	NM_020529.2	139	ctCCga/ctATga	3/6	0.365407263009684	3	FACETS	1	0.979	1	0.611	0.559	0.665	CLONAL	1	FALSE	1	0.447287441449463	3		502	649	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609990	81609990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	83	325	1	ENST00000298171.2:c.1588G>A	p.Asp530Asn	p.D530N	ENST00000298171	NM_000369.2	530	Gac/Aac	10/10	0.365407263009684	3	FACETS	1	0.972	1	0.651	0.579	0.726	CLONAL	1	FALSE	1	0.447287441449463	3		326	349	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820755	3820756	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	360	913	1	ENST00000262367.5:c.2695_2696delinsTT	p.Pro899Phe	p.P899F	ENST00000262367	NM_004380.2	899	CCc/TTc	14/31	0.192413800712723	3	FACETS	0.92	0.874	0.968	0.614	0.582	0.645	INDETERMINATE	2	FALSE	0	0.447287441449463	3		914	1070	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993527	72993527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766318192	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	111	667	1	ENST00000268489.5:c.518C>T	p.Ser173Phe	p.S173F	ENST00000268489	NM_006885.3	173	tCt/tTt	2/10	1	2	FACETS	0.755	0.68	0.835	0.755	0.68	0.835	SUBCLONAL	1	FALSE	1	0.447287441449463	2		668	657	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346440	89346441	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	115	670	2	ENST00000301030.4:c.6509_6510delinsTT	p.Ala2170Val	p.A2170V	ENST00000301030	NM_001256183.1	2170	gCC/gTT	9/13	1	2	FACETS	0.873	0.789	0.962	0.873	0.789	0.962	CLONAL	1	FALSE	1	0.447287441449463	2		672	589	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577596	7577596	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	197	536	0	ENST00000269305.4:c.685T>A	p.Cys229Ser	p.C229S	ENST00000269305	NM_001126112.2	229	Tgt/Agt	7/11	0.348483118398698	3	FACETS	0.862	0.803	0.923	0.862	0.803	0.923	CLONAL	2	FALSE	1	0.447287441449463	3		536	625	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714663	52714663	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	144	711	2	ENST00000322088.6:c.421T>C	p.Phe141Leu	p.F141L	ENST00000322088	NM_014225.5	141	Ttc/Ctc	4/15	0.348483118398698	3	FACETS	0.995	0.908	1	0.497	0.454	0.543	CLONAL	1	FALSE	1	0.447287441449463	3		713	792	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978906	25978907	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	99	316	0	ENST00000435504.4:c.1016_1017delinsAA	p.Trp339Ter	p.W339*	ENST00000435504		339	tGG/tAA	10/13	0.366960807641976	2	FACETS	0.889	0.808	0.972	0.889	0.808	0.972	CLONAL	2	FALSE	0	0.447287441449463	2		316	249	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248672	212248672	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780519461	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	47	404	0	ENST00000342788.4:c.3595G>A	p.Glu1199Lys	p.E1199K	ENST00000342788	NM_005235.2	1199	Gag/Aag	28/28	0.192413800712723	3	FACETS	0.664	0.562	0.777	0.221	0.187	0.259	INDETERMINATE	1	FALSE	0	0.447287441449463	3		404	387	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546785	9546785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	48	378	0	ENST00000353224.5:c.1237C>T	p.Pro413Ser	p.P413S	ENST00000353224	NM_177990.2	413	Ccg/Tcg	5/10	0.187766003723485	5	FACETS	0.894	0.758	1	0.298	0.252	0.348	INDETERMINATE	1	FALSE	2	0.447287441449463	5		378	401	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253814	30253814	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs558849192	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	136	596	0	ENST00000307677.4:c.640T>C	p.Phe214Leu	p.F214L	ENST00000307677	NM_138578.1	214	Ttc/Ctc	3/3	0.187766003723485	5	FACETS	1	0.972	1	0.391	0.355	0.429	INDETERMINATE	1	FALSE	2	0.447287441449463	5		596	866	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750569	41750569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	76	573	1	ENST00000226382.2:c.59G>A	p.Gly20Glu	p.G20E	ENST00000226382	NM_003924.3	20	gGg/gAg	1/3	0.192413800712723	3	FACETS	0.705	0.619	0.797	0.235	0.206	0.266	INDETERMINATE	1	FALSE	0	0.447287441449463	3		574	590	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190797	32190797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	295	813	0	ENST00000375023.3:c.140G>A	p.Gly47Glu	p.G47E	ENST00000375023	NM_004557.3	47	gGa/gAa	2/30	0.447287441449463	5	FACETS	0.833	0.783	0.885	0.555	0.522	0.59	CLONAL	2	FALSE	2	0.447287441449463	5		813	1323	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117737456	117737456	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	62	323	0	ENST00000368508.3:c.193A>T	p.Asn65Tyr	p.N65Y	ENST00000368508	NM_002944.2	65	Aac/Tac	3/43	0.187766003723485	5	FACETS	1	0.913	1	0.702	0.615	0.793	INDETERMINATE	2	FALSE	2	0.447287441449463	5		323	220	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843394	128843420	+	inframe_deletion	In_Frame_Del	DEL	GCGCTGCACTCCTGACCGCTTCCCTGA	GCGCTGCACTCCTGACCGCTTCCCTGA	-	novel	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	95	594	0	ENST00000249373.3:c.501_527del	p.Arg168_Glu176del	p.R168_E176del	ENST00000249373	NM_005631.4	167	ctGCGCTGCACTCCTGACCGCTTCCCTGAa/cta	2/12	0.365407263009684	3	FACETS	0.81	0.722	0.903	0.405	0.361	0.452	CLONAL	1	FALSE	1	0.447287441449463	3		594	642	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345912	152345913	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	135	458	0	ENST00000359321.1:c.657_658delinsAA	p.Asp220Asn	p.D220N	ENST00000359321	NM_005431.1	219	gtGGac/gtAAac	3/3	0.365407263009684	3	FACETS	0.863	0.791	0.937	0.863	0.791	0.937	CLONAL	2	FALSE	1	0.447287441449463	3		458	428	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371923	55371923	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	115	308	0	ENST00000297316.4:c.613G>A	p.Asp205Asn	p.D205N	ENST00000297316	NM_022454.3	205	Gac/Aac	2/2	0.187766003723485	5	FACETS	0.759	0.686	0.836	0.506	0.457	0.557	INDETERMINATE	2	FALSE	2	0.447287441449463	5		308	566	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389298	8389298	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	65	500	1	ENST00000356435.5:c.4320G>A	p.Trp1440Ter	p.W1440*	ENST00000356435		1440	tgG/tgA	26/35	0.192413800712723	3	FACETS	0.851	0.74	0.97	0.284	0.246	0.324	INDETERMINATE	1	FALSE	0	0.447287441449463	3		501	418	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0041329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	110	344	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.273469281134496	5	FACETS	1	0.983	1	0.494	0.445	0.546	CLONAL	1	TRUE	2	0.418799521436591	5		344	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0041329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	285	567	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.404039463287806	2	FACETS	0.979	0.927	1	0.979	0.927	1	CLONAL	2	TRUE	0	0.418799521436591	2		567	695	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0041359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	70	388	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.306443071570431	2	FACETS	0.352	0.306	0.402	0.176	0.153	0.201	SUBCLONAL	1	TRUE	0	0.473531953643599	2		388	839	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0041359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	159	275	0				ENST00000310581	NM_198253.2	-/1132			0.119743760453134	3	FACETS	0.966	0.894	1			1	INDETERMINATE	2	TRUE	NA	0.473531953643599	3		275	430	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447419	49447419	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	410	896	0	ENST00000301067.7:c.679del	p.Ala227LeufsTer34	p.A227Lfs*34	ENST00000301067	NM_003482.3	227	Gct/ct	6/54	0.473531953643599	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.473531953643599	2		896	866	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578507	7578507	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519977	NA	P-0041359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	501	1321	1	ENST00000269305.4:c.423C>G	p.Cys141Trp	p.C141W	ENST00000269305	NM_001126112.2	141	tgC/tgG	5/11	0.370258810447083	2	FACETS	0.906	0.869	0.942	0.906	0.869	0.942	CLONAL	2	TRUE	0	0.473531953643599	2		1322	1168	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796926	78796936	+	frameshift_variant	Frame_Shift_Del	DEL	TTTCGAAATTT	TTTCGAAATTT	A	novel	NA	P-0041359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	88	720	0	ENST00000306801.3:c.1039_1049delinsA	p.Phe347IlefsTer8	p.F347Ifs*8	ENST00000306801	NM_020761.2	347	TTTCGAAATTTt/At	9/34	1	2	FACETS	0.383	0.338	0.431	0.383	0.338	0.431	SUBCLONAL	1	TRUE	1	0.473531953643599	2		720	970	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19261496	19261496	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763146191	NA	P-0041359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	130	937	0	ENST00000162023.5:c.49C>T	p.Arg17Trp	p.R17W	ENST00000162023		17	Cgg/Tgg	6/13	0.402102200948944	1	FACETS	0.467	0.423	0.513	0.467	0.423	0.513	SUBCLONAL	1	TRUE	0	0.473531953643599	1		937	897	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371864	116371864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750256779	NA	P-0041359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	261	551	0	ENST00000397752.3:c.1343G>A	p.Gly448Glu	p.G448E	ENST00000397752	NM_000245.2	448	gGa/gAa	3/21	0.260275814053104	3	FACETS	0.96	0.904	1	0.96	0.904	1	INDETERMINATE	2	TRUE	1	0.473531953643599	3		551	710	SUCCESS
MET	4233	MSKCC	GRCh37	7	116414783	116414783	+	intron_variant	Intron	SNP	C	C	G	novel	NA	P-0041359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	158	351	0	ENST00000397752.3:c.3029-152C>G		p.*1010*	ENST00000397752	NM_000245.2	-/1390			0.260275814053104	3	FACETS	1	0.969	1	0.556	0.51	0.604	INDETERMINATE	1	TRUE	1	0.473531953643599	3		351	742	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500790	8500790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	85	600	1	ENST00000356435.5:c.2092G>A	p.Glu698Lys	p.E698K	ENST00000356435		698	Gag/Aag	13/35	1	2	FACETS	0.509	0.45	0.573	0.509	0.45	0.573	SUBCLONAL	1	TRUE	1	0.473531953643599	2		601	705	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400155	139400155	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	108	1221	0	ENST00000277541.6:c.4193A>G	p.Tyr1398Cys	p.Y1398C	ENST00000277541	NM_017617.3	1398	tAc/tGc	25/34	1	2	FACETS	0.462	0.413	0.513	0.462	0.413	0.513	SUBCLONAL	1	TRUE	1	0.473531953643599	2		1221	988	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	282	541	0				ENST00000310581	NM_198253.2	-/1132			0.807190120836417	10	FACETS	1	0.981	1	0.277	0.26	0.295	CLONAL	2	TRUE	2	0.807190120836417	10		541	1333	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402765	139402765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1386494518	NA	P-0041365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1409	380	883	0	ENST00000277541.6:c.3244C>T	p.Arg1082Cys	p.R1082C	ENST00000277541	NM_017617.3	1082	Cgc/Tgc	20/34	0.692127750943049	4	FACETS	0.951	0.9	1			1	CLONAL	1	TRUE	NA	0.807190120836417	4		883	1789	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651879	36651879	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0041365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	519	602	0	ENST00000244741.5:c.1A>G	p.Met1?	p.M1?	ENST00000244741	NM_000389.4	1	Atg/Gtg	2/3	0.399438387051139	5	FACETS	0.861	0.829	0.894	0.861	0.829	0.894	INDETERMINATE	3	TRUE	2	0.807190120836417	5		602	1100	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977883	131977883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561655417	NA	P-0041365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	138	355	0	ENST00000265335.6:c.3766C>T	p.Arg1256Cys	p.R1256C	ENST00000265335		1256	Cgc/Tgc	25/25	0.706352191727837	3	FACETS	0.956	0.875	1	0.478	0.437	0.52	CLONAL	1	TRUE	1	0.807190120836417	3		355	502	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201854	67201854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	278	688	0	ENST00000312629.5:c.1054G>C	p.Glu352Gln	p.E352Q	ENST00000312629	NM_003952.2	352	Gag/Cag	13/15	0.807190120836417	3	FACETS	0.983	0.924	1	0.491	0.462	0.521	CLONAL	1	TRUE	1	0.807190120836417	3		688	984	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0041365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	1103	659	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.771898214538954	4	FACETS	1	0.99	1			1	CLONAL	4	TRUE	NA	0.807190120836417	4		659	1231	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486587	56486587	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	580	640	0	ENST00000267101.3:c.1166C>T	p.Thr389Ile	p.T389I	ENST00000267101	NM_001982.3	389	aCa/aTa	10/28	0.791356541250082	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.807190120836417	4		640	1269	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342518	118342518	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	127	278	0	ENST00000534358.1:c.644C>G	p.Ser215Cys	p.S215C	ENST00000534358	NM_005933.3	215	tCt/tGt	3/36	0.807190120836417	3	FACETS	1	0.937	1	0.516	0.471	0.562	CLONAL	1	TRUE	1	0.807190120836417	3		278	428	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878077	48878114	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCCACCGCCGCCGCTGCCGCCGCGGAACCCCCGGCA	CCGCCACCGCCGCCGCTGCCGCCGCGGAACCCCCGGCA	-	novel	NA	P-0041365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	580	123	0	ENST00000267163.4:c.34_71del	p.Thr12AlafsTer6	p.T12Afs*6	ENST00000267163	NM_000321.2	10	gCCGCCACCGCCGCCGCTGCCGCCGCGGAACCCCCGGCA/g	1/27	0.807190120836417	6	FACETS	0.952	0.935	0.968			1	CLONAL	6	TRUE	NA	0.807190120836417	6		123	658	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266691	18266692	+	frameshift_variant,start_lost	Frame_Shift_Ins	INS	-	-	GGCG	novel	NA	P-0041365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	263	645	0	ENST00000222254.8:c.6_9dup	p.Pro4_?3	p.P4_?3	ENST00000222254	NM_005027.3	1	atg/atGGCGg	2/16	0.710502889452392	4	FACETS	0.935	0.875	0.997	0.468	0.437	0.499	CLONAL	1	TRUE	2	0.807190120836417	4		645	1259	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515327	149515327	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	187	669	0	ENST00000261799.4:c.155T>A	p.Leu52Gln	p.L52Q	ENST00000261799	NM_002609.3	52	cTg/cAg	3/23	0.735871228235798	3	FACETS	0.645	0.596	0.697	0.323	0.298	0.349	SUBCLONAL	1	TRUE	1	0.807190120836417	3		669	1008	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878869	117878869	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	133	422	0	ENST00000297338.2:c.100G>C	p.Glu34Gln	p.E34Q	ENST00000297338	NM_006265.2	34	Gag/Cag	2/14	0.807190120836417	3	FACETS	0.77	0.701	0.841	0.385	0.35	0.421	SUBCLONAL	1	TRUE	1	0.807190120836417	3		422	601	SUCCESS
ATM	472	MSKCC	GRCh37	11	108183215	108183233	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAAGTTTACAGGTAAATAT	TAAGTTTACAGGTAAATAT	-	novel	NA	P-0041384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	32	292	0	ENST00000278616.4:c.5998_6006+10del		p.X2000_splice	ENST00000278616	NM_000051.3	2000		40/63	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		292	230	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0041413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	505	703	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.54989236278552	2		703	855	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729642	162729683	+	inframe_deletion	In_Frame_Del	DEL	CCCAGACCCATGAATACCACGTGTGGCCCGGCTATGACTATG	CCCAGACCCATGAATACCACGTGTGGCCCGGCTATGACTATG	-	novel	NA	P-0041413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	128	607	0	ENST00000367921.3:c.728_769del	p.Thr243_Val257delinsMet	p.T243_V257delinsM	ENST00000367921	NM_006182.2	243	aCCCAGACCCATGAATACCACGTGTGGCCCGGCTATGACTATGtg/atg	8/18	0.217699401672199	3	FACETS	0.944	0.858	1	0.472	0.429	0.517	INDETERMINATE	1	TRUE	1	0.54989236278552	3		607	629	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68758694	68758694	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	72	221	0	ENST00000487270.1:c.850G>A	p.Glu284Lys	p.E284K	ENST00000487270	NM_133509.3	284	Gaa/Aaa	8/11	0.549333484716668	2	FACETS	0.956	0.844	1	0.478	0.422	0.537	CLONAL	1	TRUE	0	0.54989236278552	2		221	274	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905470	50905470	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	231	872	0	ENST00000440232.2:c.598G>C	p.Gly200Arg	p.G200R	ENST00000440232	NM_002691.3	200	Ggg/Cgg	6/27	1	2	FACETS	0.943	0.881	1	0.943	0.881	1	CLONAL	1	TRUE	1	0.54989236278552	2		872	891	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944487	40944487	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	57	577	0	ENST00000373198.4:c.2015A>T	p.Asn672Ile	p.N672I	ENST00000373198	NM_133170.3	672	aAc/aTc	12/32	0.388928602767438	1	FACETS	0.243	0.208	0.281	0.243	0.208	0.281	SUBCLONAL	1	TRUE	0	0.54989236278552	1		577	618	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37048520	37048520	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	55	422	0	ENST00000231790.2:c.419A>C	p.Lys140Thr	p.K140T	ENST00000231790	NM_000249.3	140	aAa/aCa	5/19	0.140855413086139	4	FACETS	0.61	0.522	0.706			1	INDETERMINATE	1	TRUE	NA	0.54989236278552	4		422	508	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275166	41275179	+	frameshift_variant	Frame_Shift_Del	DEL	AGAGGCTCTTGTGC	AGAGGCTCTTGTGC	GGCTCTT	novel	NA	P-0041413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	40	403	2	ENST00000349496.5:c.1332_1345delinsGGCTCTT	p.Ile444MetfsTer26	p.I444Mfs*26	ENST00000349496	NM_001904.3	444	atAGAGGCTCTTGTGCgt/atGGCTCTTgt	9/15	0.140855413086139	4	FACETS	0.504	0.419	0.599			1	INDETERMINATE	1	TRUE	NA	0.54989236278552	4		405	447	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189099	32189100	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	TC	TC	CT	novel	NA	P-0041413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	342	435	0	ENST00000375023.3:c.454_455delinsAG	p.Glu152Arg	p.E152R	ENST00000375023	NM_004557.3	152	GAg/AGg	4/30	0.529732539338115	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.54989236278552	3		435	509	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37141709	37141709	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0041413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	321	406	0	ENST00000373509.5:c.785-1G>A		p.X262_splice	ENST00000373509	NM_002648.3	262			0.529732539338115	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	0	0.54989236278552	3		406	488	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549392	5549392	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	68	603	0	ENST00000397747.3:c.419A>G	p.Glu140Gly	p.E140G	ENST00000397747	NM_025239.3	140	gAg/gGg	4/7	0.507301313490533	3	FACETS	0.389	0.337	0.445	0.13	0.112	0.149	SUBCLONAL	1	TRUE	0	0.54989236278552	3		603	811	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844207	68844217	+	frameshift_variant	Frame_Shift_Del	DEL	GGTCTTTAAGG	GGTCTTTAAGG	-	novel	NA	P-0041469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	35	589	0	ENST00000261769.5:c.800_810del	p.Phe267CysfsTer22	p.F267Cfs*22	ENST00000261769	NM_004360.3	265	gaGGTCTTTAAGGgg/gagg	6/16	0.223192151212929	2	FACETS	1	0.95	1	0.719	0.601	0.845	INDETERMINATE	1	TRUE	0	0.377544255508298	2		589	129	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15938164	15938165	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCCGTTCCGTTCCTA	novel	NA	P-0041469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	18	483	0	ENST00000268712.3:c.7034_7049dup	p.Ser2351ArgfsTer19	p.S2351Rfs*19	ENST00000268712	NM_006311.3	2350	ccc/ccTAGGAACGGAACGGCCc	45/46	0.223192151212929	2	FACETS	0.751	0.571	0.958	0.375	0.285	0.479	INDETERMINATE	1	TRUE	0	0.377544255508298	2		483	127	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717715	89717716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587782341	NA	P-0041474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	89	544	1	ENST00000371953.3:c.741dup	p.Pro248ThrfsTer5	p.P248Tfs*5	ENST00000371953	NM_000314.4	247	tta/ttAa	7/9	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.21	2		545	764	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591135	67591137	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0041474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	36	320	0	ENST00000274335.5:c.1728_1730del	p.Arg577del	p.R577del	ENST00000274335		576	acGAGa/aca	12/15	1	2	FACETS	0.581	0.477	0.699	0.581	0.477	0.699	SUBCLONAL	1	TRUE	1	0.21	2		320	590	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142134	108142134	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs192810283	NA	P-0041474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	50	240	0	ENST00000278616.4:c.3077+1G>A		p.X1026_splice	ENST00000278616	NM_000051.3	1026			1	2	FACETS	0.874	0.741	1	0.874	0.741	1	CLONAL	1	TRUE	1	0.21	2		240	545	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0041479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	79	388	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.372973481006372	3	FACETS	0.911	0.803	1	0.456	0.401	0.514	CLONAL	1	TRUE	1	0.384260598409327	3		388	538	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0041479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	186	513	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.214172101961023	3	FACETS	1	0.929	1	0.667	0.619	0.715	INDETERMINATE	2	TRUE	0	0.384260598409327	3		513	577	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0041479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	158	206	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.384260598409327	3	FACETS	0.844	0.784	0.906	0.844	0.784	0.906	CLONAL	3	TRUE	0	0.384260598409327	3		206	387	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242511	55242511	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs121913418	NA	P-0041479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	23	315	0	ENST00000275493.2:c.2281G>A	p.Asp761Asn	p.D761N	ENST00000275493	NM_005228.3	761	Gat/Aat	19/28	0.214172101961023	3	FACETS	0.268	0.208	0.338	0.089	0.069	0.113	INDETERMINATE	1	TRUE	0	0.384260598409327	3		315	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579514	7579514	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	335	599	0	ENST00000269305.4:c.173del	p.Pro58GlnfsTer65	p.P58Qfs*65	ENST00000269305	NM_001126112.2	58	cCa/ca	4/11	0.384260598409327	2	FACETS	0.942	0.894	0.992	0.942	0.894	0.992	CLONAL	2	TRUE	0	0.384260598409327	2		599	925	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247280	153247280	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	223	362	0	ENST00000281708.4:c.1522C>T	p.Gln508Ter	p.Q508*	ENST00000281708	NM_033632.3	508	Caa/Taa	10/12	0.384260598409327	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.384260598409327	2		362	543	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006417	12006418	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	133	464	0	ENST00000396373.4:c.391dup	p.Ser131PhefsTer23	p.S131Ffs*23	ENST00000396373	NM_001987.4	129	ctt/cTtt	4/8	0.214172101961023	3	FACETS	1	0.946	1	0.352	0.32	0.386	INDETERMINATE	1	TRUE	0	0.384260598409327	3		464	781	SUCCESS
ATR	545	MSKCC	GRCh37	3	142232354	142232361	+	frameshift_variant	Frame_Shift_Del	DEL	CTTCTTGA	CTTCTTGA	-	novel	NA	P-0041479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	84	359	0	ENST00000350721.4:c.4623_4630del	p.Asn1541LysfsTer16	p.N1541Kfs*16	ENST00000350721	NM_001184.3	1541	aaTCAAGAAGat/aaat	26/47	0.372973481006372	3	FACETS	0.883	0.781	0.992	0.442	0.39	0.496	CLONAL	1	TRUE	1	0.384260598409327	3		359	590	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866613	117866613	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0041479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	42	492	0	ENST00000297338.2:c.1032T>A	p.Tyr344Ter	p.Y344*	ENST00000297338	NM_006265.2	344	taT/taA	9/14	0.372973481006372	3	FACETS	0.34	0.283	0.404	0.17	0.141	0.202	SUBCLONAL	1	TRUE	1	0.384260598409327	3		492	766	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551454	141551454	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	120	441	0	ENST00000220592.5:c.1843G>A	p.Val615Met	p.V615M	ENST00000220592	NM_012154.3	615	Gtg/Atg	15/19	0.372973481006372	3	FACETS	1	0.959	1	0.556	0.502	0.612	CLONAL	1	TRUE	1	0.384260598409327	3		441	670	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0041483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	133	476	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.429636234242283	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.429636234242283	1		476	456	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	162	480	1	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	0.429636234242283	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.429636234242283	1		481	528	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212522509	212522509	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs532377012	NA	P-0041483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	90	474	1	ENST00000342788.4:c.1916C>T	p.Thr639Met	p.T639M	ENST00000342788	NM_005235.2	639	aCg/aTg	16/28	1	2	FACETS	0.732	0.651	0.819	0.732	0.651	0.819	SUBCLONAL	1	TRUE	1	0.429636234242283	2		475	572	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842746	68842746	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	146	471	0	ENST00000261769.5:c.682T>A	p.Tyr228Asn	p.Y228N	ENST00000261769	NM_004360.3	228	Tac/Aac	5/16	0.429636234242283	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.429636234242283	1		471	530	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936097	49936102	+	inframe_deletion	In_Frame_Del	DEL	GGCCTT	GGCCTT	-	novel	NA	P-0041483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	134	690	0	ENST00000296474.3:c.1568_1573del	p.Gln523_Gly524del	p.Q523_G524del	ENST00000296474	NM_002447.2	523	cAAGGCCct/cct	4/20	1	2	FACETS	0.767	0.697	0.841	0.767	0.697	0.841	SUBCLONAL	1	TRUE	1	0.429636234242283	2		690	813	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845583	128845583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764495218	NA	P-0041483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	158	613	0	ENST00000249373.3:c.880G>A	p.Val294Ile	p.V294I	ENST00000249373	NM_005631.4	294	Gtc/Atc	4/12	1	2	FACETS	0.964	0.885	1	0.964	0.885	1	CLONAL	1	TRUE	1	0.429636234242283	2		613	763	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0041514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	124	565	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.863	0.781	0.949	0.863	0.781	0.949	CLONAL	1	TRUE	1	0.373150274463519	2		565	770	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0041514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	143	807	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.373150274463519	1	FACETS	0.95	0.869	1	0.95	0.869	1	CLONAL	1	TRUE	0	0.373150274463519	1		807	656	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0041514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	208	373	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.315203186219192	3	FACETS	0.99	0.923	1	0.99	0.923	1	CLONAL	2	TRUE	1	0.373150274463519	3		373	668	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763458	41763458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372169583	NA	P-0041514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	160	748	0	ENST00000301178.4:c.2257G>A	p.Val753Met	p.V753M	ENST00000301178	NM_021913.4	753	Gtg/Atg	19/20	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.373150274463519	2		748	856	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs371769427	NA	P-0041514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	60	290	0	ENST00000291552.4:c.101C>A	p.Ser34Tyr	p.S34Y	ENST00000291552	NM_006758.2	34	tCt/tAt	2/8	1	2	FACETS	0.676	0.583	0.776	0.676	0.583	0.776	SUBCLONAL	1	TRUE	1	0.373150274463519	2		290	476	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057848	27057848	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	93	878	1	ENST00000324856.7:c.1558del	p.Gln520SerfsTer99	p.Q520Sfs*99	ENST00000324856	NM_006015.4	519	tCc/tc	3/20	1	2	FACETS	0.49	0.435	0.55	0.49	0.435	0.55	SUBCLONAL	1	TRUE	1	0.373150274463519	2		879	1017	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487584	56487584	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	328	686	0	ENST00000267101.3:c.1517C>T	p.Ser506Phe	p.S506F	ENST00000267101	NM_001982.3	506	tCt/tTt	13/28	0.315203186219192	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.373150274463519	3		686	923	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692964	89692964	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs786204934	NA	P-0041520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	71	560	0	ENST00000371953.3:c.448G>T	p.Glu150Ter	p.E150*	ENST00000371953	NM_000314.4	150	Gag/Tag	5/9	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.23	2		560	548	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022940	27022942	+	inframe_deletion	In_Frame_Del	DEL	CCG	CCG	-	rs748085214	NA	P-0041520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	10	34	0	ENST00000324856.7:c.60_62del	p.Pro21del	p.P21del	ENST00000324856	NM_006015.4	16	CCG/-	1/20	1	2	FACETS	1	0.814	1	1	0.814	1	CLONAL	1	TRUE	1	0.23	2		34	67	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692911	89692911	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	62	494	0	ENST00000371953.3:c.395G>C	p.Gly132Ala	p.G132A	ENST00000371953	NM_000314.4	132	gGt/gCt	5/9	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.23	2		494	524	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513223	44513223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	58	265	1	ENST00000291552.4:c.712G>A	p.Gly238Arg	p.G238R	ENST00000291552	NM_006758.2	238	Ggg/Agg	8/8	1	2	FACETS	0.974	0.837	1	0.974	0.837	1	CLONAL	1	TRUE	1	0.23	2		266	518	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024006	27024019	+	frameshift_variant	Frame_Shift_Del	DEL	GGCAGCCGCTCGCC	GGCAGCCGCTCGCC	-	novel	NA	P-0041520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	26	104	0	ENST00000324856.7:c.1112_1125del	p.Gly371AlafsTer24	p.G371Afs*24	ENST00000324856	NM_006015.4	371	gGGCAGCCGCTCGCC/g	1/20	1	2	FACETS	1	0.8	1	1	0.8	1	CLONAL	1	TRUE	1	0.23	2		104	225	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719754	190719754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566975683	NA	P-0041520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	31	251	1	ENST00000441310.2:c.1756C>T	p.Arg586Cys	p.R586C	ENST00000441310	NM_000534.4	586	Cgt/Tgt	9/13	1	2	FACETS	0.97	0.787	1	0.97	0.787	1	CLONAL	1	TRUE	1	0.23	2		252	278	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591084	67591085	+	inframe_insertion	In_Frame_Ins	INS	-	-	GACAAACGTATGAACAGCATTAAACCAGAC	novel	NA	P-0041520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	33	305	0	ENST00000274335.5:c.1678_1707dup	p.Asp560_Asp569dup	p.D560_D569dup	ENST00000274335		560	-/GACAAACGTATGAACAGCATTAAACCAGAC	12/15	1	2	FACETS	0.725	0.59	0.876	0.725	0.59	0.876	SUBCLONAL	1	TRUE	1	0.23	2		305	396	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112035605	112035605	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	36	412	0	ENST00000368678.4:c.289A>G	p.Thr97Ala	p.T97A	ENST00000368678		97	Aca/Gca	4/13	1	2	FACETS	0.591	0.485	0.71	0.591	0.485	0.71	SUBCLONAL	1	TRUE	1	0.23	2		412	530	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212185	98212185	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	43	377	0	ENST00000331920.6:c.3487G>C	p.Gly1163Arg	p.G1163R	ENST00000331920	NM_000264.3	1163	Ggc/Cgc	21/24	1	2	FACETS	0.526	0.439	0.623	0.526	0.439	0.623	SUBCLONAL	1	TRUE	1	0.23	2		377	711	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128420078	128420078	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	65	483	0	ENST00000265960.3:c.350C>G	p.Ala117Gly	p.A117G	ENST00000265960	NM_001006617.1	117	gCc/gGc	4/12	1	2	FACETS	0.966	0.838	1	0.966	0.838	1	CLONAL	1	TRUE	1	0.23	2		483	585	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240838	53240838	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0041520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	27	443	0	ENST00000375401.3:c.1243-1G>A		p.X415_splice	ENST00000375401	NM_004187.3	415			1	2	FACETS	0.452	0.359	0.56	0.452	0.359	0.56	SUBCLONAL	1	TRUE	1	0.23	2		443	519	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0041526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	187	368	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.908	0.844	0.974	0.908	0.844	0.974	CLONAL	1	TRUE	1	0.695725935358401	2		368	592	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293552	1293552	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	413	835	0	ENST00000310581.5:c.1449C>G	p.Asn483Lys	p.N483K	ENST00000310581	NM_198253.2	483	aaC/aaG	2/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.695725935358401	2		835	1164	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484298	8484298	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs7869444	NA	P-0041526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	275	491	0	ENST00000356435.5:c.3234G>T	p.Glu1078Asp	p.E1078D	ENST00000356435		1078	gaG/gaT	19/35	0.695725935358401	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.695725935358401	1		491	483	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710615	117710615	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs748189554	NA	P-0041526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	193	391	0	ENST00000368508.3:c.1657C>A	p.Gln553Lys	p.Q553K	ENST00000368508	NM_002944.2	553	Cag/Aag	12/43	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.695725935358401	2		391	526	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28600653	28600653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	304	634	0	ENST00000253063.3:c.1004C>T	p.Pro335Leu	p.P335L	ENST00000253063	NM_031459.4	335	cCt/cTt	7/10	1	2	FACETS	0.975	0.922	1	0.975	0.922	1	CLONAL	1	TRUE	1	0.695725935358401	2		634	896	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999567	100999567	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	423	870	0	ENST00000325455.5:c.235T>C	p.Ser79Pro	p.S79P	ENST00000325455	NM_001202474.3	79	Tcg/Ccg	1/8	1	2	FACETS	0.978	0.933	1	0.978	0.933	1	CLONAL	1	TRUE	1	0.695725935358401	2		870	1243	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472146	472194	+	frameshift_variant	Frame_Shift_Del	DEL	TTGTTCTCTTCGGCAGAATGTTCATCCTTGTGCCTGGCTCTGGGGAAGT	TTGTTCTCTTCGGCAGAATGTTCATCCTTGTGCCTGGCTCTGGGGAAGT	-	novel	NA	P-0041526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	85	503	0	ENST00000399788.2:c.607_655del	p.Thr203AspfsTer3	p.T203Dfs*3	ENST00000399788	NM_001042603.1	203	ACTTCCCCAGAGCCAGGCACAAGGATGAACATTCTGCCGAAGAGAACAAga/ga	5/28	1	2	FACETS	0.432	0.383	0.486	0.432	0.383	0.486	SUBCLONAL	1	TRUE	1	0.695725935358401	2		503	565	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912484	50912485	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	270	707	1	ENST00000440232.2:c.1998_1999delinsTT	p.Arg667Trp	p.R667W	ENST00000440232	NM_002691.3	666	gcCCgg/gcTTgg	16/27	1	2	FACETS	0.869	0.817	0.922	0.869	0.817	0.922	CLONAL	1	TRUE	1	0.695725935358401	2		708	893	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742758	39742758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	221	516	2	ENST00000361337.2:c.1601C>T	p.Ser534Phe	p.S534F	ENST00000361337	NM_003286.2	534	tCc/tTc	15/21	1	2	FACETS	0.93	0.87	0.992	0.93	0.87	0.992	CLONAL	1	TRUE	1	0.695725935358401	2		518	683	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31483681	31483681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	130	299	0	ENST00000344624.3:c.2051G>A	p.Arg684His	p.R684H	ENST00000344624		684	cGt/cAt	13/33	1	2	FACETS	0.834	0.762	0.908	0.834	0.762	0.908	CLONAL	1	TRUE	1	0.695725935358401	2		299	448	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288599	33288599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	224	507	0	ENST00000374542.5:c.953G>A	p.Arg318Gln	p.R318Q	ENST00000374542	NM_001141970.1	318	cGa/cAa	3/8	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.695725935358401	2		507	635	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955133	93955133	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	253	517	0	ENST00000369303.4:c.2765T>C	p.Phe922Ser	p.F922S	ENST00000369303	NM_004440.3	922	tTc/tCc	16/17	1	2	FACETS	0.943	0.886	1	0.943	0.886	1	CLONAL	1	TRUE	1	0.695725935358401	2		517	771	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874011	123874013	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs780061449	NA	P-0041539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	17	90	0	ENST00000330479.4:c.62_64del	p.Ala21del	p.A21del	ENST00000330479	NM_020382.3	14	gaGGCg/gag	2/9	0.111510118113272	4	FACETS	0.708	0.528	0.92	0.354	0.264	0.46	INDETERMINATE	1	FALSE	2	0.225607561577354	4		90	261	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032739	30032739	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0041556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	102	284	0	ENST00000338641.4:c.115-1G>A		p.X39_splice	ENST00000338641	NM_000268.3	39			0.285968261141971	2	FACETS	1	0.969	1	0.6	0.54	0.663	CLONAL	1	TRUE	0	0.397444086431804	2		284	428	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867305	68867305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	239	499	0	ENST00000261769.5:c.2552C>T	p.Ser851Leu	p.S851L	ENST00000261769	NM_004360.3	851	tCa/tTa	16/16	0.141180158136246	4	FACETS	0.958	0.896	1	0.958	0.896	1	INDETERMINATE	2	TRUE	2	0.397444086431804	4		499	877	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	28	320	0	ENST00000257430.4:c.904C>G	p.Arg302Gly	p.R302G	ENST00000257430	NM_000038.5	302	Cga/Gga	9/16	0.280621801357992	2	FACETS	0.31	0.247	0.382	0.155	0.123	0.191	SUBCLONAL	1	TRUE	0	0.397444086431804	2		320	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578520	7578521	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	C	novel	NA	P-0041556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	383	793	0	ENST00000269305.4:c.409_410delinsG	p.Leu137GlyfsTer33	p.L137Gfs*33	ENST00000269305	NM_001126112.2	137	CTg/Gg	5/11	0.272706635364447	2	FACETS	0.786	0.747	0.826	0.786	0.747	0.826	SUBCLONAL	2	TRUE	0	0.397444086431804	2		793	1226	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0041571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	216	508	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		508	673	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156739	20156741	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	TNP	ACC	ACC	TTT	novel	NA	P-0041571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	120	328	0	ENST00000379607.5:c.17-1_18delinsAAA		p.X6_splice	ENST00000379607	NM_001412.3	6		2/7	0.231943726010299	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		328	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0041591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	297	718	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.308992115230611	2	FACETS	0.948	0.896	1	0.948	0.896	1	CLONAL	2	TRUE	0	0.376117681266742	2		718	833	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383999	84383999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150371881	NA	P-0041591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	110	404	0	ENST00000321945.7:c.853C>T	p.Arg285Trp	p.R285W	ENST00000321945	NM_139076.2	285	Cgg/Tgg	9/9	0.376117681266742	3	FACETS	1	0.953	1	0.551	0.496	0.609	CLONAL	1	TRUE	1	0.376117681266742	3		404	631	SUCCESS
APC	324	MSKCC	GRCh37	5	112175147	112175147	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	46	164	0	ENST00000257430.4:c.3856G>T	p.Glu1286Ter	p.E1286*	ENST00000257430	NM_000038.5	1286	Gaa/Taa	16/16	0.376117681266742	3	FACETS	1	0.955	1	0.676	0.575	0.784	CLONAL	1	TRUE	1	0.376117681266742	3		164	215	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874147	151874148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs747256476	NA	P-0041591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	311	367	13	ENST00000262189.6:c.8390dup	p.Glu2798GlyfsTer11	p.E2798Gfs*11	ENST00000262189	NM_170606.2	2797	aag/aaAg	38/59	0.376117681266742	7	FACETS	0.899	0.851	0.949	0.719	0.681	0.759	CLONAL	4	TRUE	2	0.376117681266742	7		380	892	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041022	112041022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376255649	NA	P-0041591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	110	328	0	ENST00000368678.4:c.233C>T	p.Thr78Met	p.T78M	ENST00000368678		78	aCg/aTg	3/13	0.288881730994806	4	FACETS	0.828	0.748	0.912	0.828	0.748	0.912	CLONAL	2	TRUE	2	0.376117681266742	4		328	486	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106108	27106108	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	145	447	0	ENST00000324856.7:c.5719del	p.Ile1907SerfsTer16	p.I1907Sfs*16	ENST00000324856	NM_006015.4	1907	Atc/tc	20/20	0.349287325715897	4	FACETS	0.811	0.742	0.883	0.811	0.742	0.883	CLONAL	2	TRUE	2	0.376117681266742	4		447	654	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114917829	114917829	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0041591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	202	467	0	ENST00000543371.1:c.1318+1G>C		p.X440_splice	ENST00000543371	NM_001198531.1	440			0.376117681266742	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.376117681266742	3		467	541	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39216449	39216449	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	119	329	0	ENST00000402219.2:c.3353A>G	p.Asp1118Gly	p.D1118G	ENST00000402219	NM_005633.3	1118	gAt/gGt	21/23	0.349287325715897	4	FACETS	0.864	0.784	0.948	0.864	0.784	0.948	CLONAL	2	TRUE	2	0.376117681266742	4		329	504	SUCCESS
APC	324	MSKCC	GRCh37	5	112173263	112173263	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	48	131	0	ENST00000257430.4:c.1972G>T	p.Glu658Ter	p.E658*	ENST00000257430	NM_000038.5	658	Gag/Tag	16/16	0.376117681266742	3	FACETS	0.766	0.656	0.883	0.766	0.656	0.883	SUBCLONAL	2	TRUE	1	0.376117681266742	3		131	198	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0041598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	251	418	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.727663970264321	3	FACETS	0.956	0.906	1	0.956	0.906	1	CLONAL	2	TRUE	1	0.727663970264321	3		418	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0041598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	297	718	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.727663970264321	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.727663970264321	1		718	508	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599949	10599950	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0041598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	88	803	0	ENST00000171111.5:c.1626_1627del	p.Glu542AspfsTer31	p.E542Dfs*31	ENST00000171111	NM_203500.1	542	gaGAcg/gacg	5/6	0.727663970264321	1	FACETS	0.237	0.21	0.267	0.237	0.21	0.267	SUBCLONAL	1	TRUE	0	0.727663970264321	1		803	648	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016647	12016648	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0041598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	131	303	0	ENST00000353533.5:c.783_784del	p.Asp263CysfsTer4	p.D263Cfs*4	ENST00000353533	NM_003010.3	261	acAAga/acga	7/11	0.727663970264321	1	FACETS	0.801	0.74	0.862	0.801	0.74	0.862	CLONAL	1	TRUE	0	0.727663970264321	1		303	286	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626783	14626783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	527	522	0	ENST00000254322.2:c.992G>A	p.Arg331Lys	p.R331K	ENST00000254322	NM_006145.1	331	aGa/aAa	3/3	0.727663970264321	7	FACETS	1	0.995	1	0.415	0.397	0.433	CLONAL	2	TRUE	1	0.727663970264321	7		522	1640	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720678	89720679	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0041598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	133	160	0	ENST00000371953.3:c.830_831del	p.Thr277IlefsTer20	p.T277Ifs*20	ENST00000371953	NM_000314.4	277	ACa/a	8/9	0.727663970264321	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.727663970264321	1		160	160	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602922	10602922	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	90	858	0	ENST00000171111.5:c.656A>G	p.Glu219Gly	p.E219G	ENST00000171111	NM_203500.1	219	gAg/gGg	3/6	0.727663970264321	1	FACETS	0.194	0.172	0.218	0.194	0.172	0.218	SUBCLONAL	1	TRUE	0	0.727663970264321	1		858	810	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198312	138198312	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	32	270	0	ENST00000237289.4:c.905T>A	p.Leu302His	p.L302H	ENST00000237289	NM_001270507.1	302	cTc/cAc	6/9	1	2	FACETS	0.2	0.162	0.243	0.2	0.162	0.243	SUBCLONAL	1	TRUE	1	0.727663970264321	2		270	439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0041621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	409	593	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.652111119384316	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.652111119384316	2		595	599	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724406	117724406	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	161	566	0	ENST00000368508.3:c.473T>C	p.Leu158Pro	p.L158P	ENST00000368508	NM_002944.2	158	cTg/cCg	6/43	0.652111119384316	3	FACETS	0.979	0.901	1	0.489	0.45	0.53	CLONAL	1	TRUE	1	0.652111119384316	3		566	669	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651327	52651327	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	305	518	0	ENST00000394830.3:c.1769T>A	p.Met590Lys	p.M590K	ENST00000394830	NM_018313.4	590	aTg/aAg	15/30	0.48327305664383	2	FACETS	0.997	0.948	1	0.997	0.948	1	CLONAL	2	TRUE	0	0.491205302286684	2		518	623	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950244	38950244	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	150	491	0	ENST00000357387.3:c.3706C>G	p.Pro1236Ala	p.P1236A	ENST00000357387	NM_152756.3	1236	Cct/Gct	31/38	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.491205302286684	2		491	588	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0041645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	82	415	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	0.701	0.62	0.787			1	INDETERMINATE	1	FALSE	NA	0.479366467697144	2		415	488	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2111996	2111996	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	131	712	0	ENST00000219476.3:c.1244C>A	p.Ala415Glu	p.A415E	ENST00000219476	NM_000548.3	415	gCg/gAg	12/42	0.214845796620514	3	FACETS	0.676	0.613	0.743	0.338	0.306	0.372	INDETERMINATE	1	FALSE	1	0.479366467697144	3		712	1002	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579336	7579336	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	254	804	0	ENST00000269305.4:c.351del	p.Thr118GlnfsTer5	p.T118Qfs*5	ENST00000269305	NM_001126112.2	117	ggG/gg	4/11	0.409445325000087	1	FACETS	0.881	0.826	0.937	0.881	0.826	0.937	CLONAL	1	FALSE	0	0.479366467697144	1		804	915	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961297	15961297	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	158	613	1	ENST00000268712.3:c.6092C>T	p.Pro2031Leu	p.P2031L	ENST00000268712	NM_006311.3	2031	cCc/cTc	39/46	0.409445325000087	1	FACETS	0.901	0.831	0.974	0.901	0.831	0.974	CLONAL	1	FALSE	0	0.479366467697144	1		614	556	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967259	134967259	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	94	730	0	ENST00000398015.3:c.2598C>A	p.Asn866Lys	p.N866K	ENST00000398015	NM_004441.4	866	aaC/aaA	14/16	0.332104479410607	0	FACETS	0.479	0.429	0.532			1	SUBCLONAL	1	FALSE	0	0.479366467697144	0		730	426	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688747	47688747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	32	375	0	ENST00000347630.2:c.553C>T	p.Arg185Trp	p.R185W	ENST00000347630	NM_001007230.1	185	Cgg/Tgg	7/11	NA	2	FACETS	0.115	0.093	0.141			1	INDETERMINATE	1	TRUE	NA	0.897292265820229	2		375	619	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604569	43604569	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs906695652	NA	P-0041647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	66	809	0	ENST00000355710.3:c.1154G>A	p.Gly385Glu	p.G385E	ENST00000355710	NM_020975.4	385	gGa/gAa	6/20	1	2	FACETS	0.121	0.104	0.139	0.121	0.104	0.139	SUBCLONAL	1	TRUE	1	0.897292265820229	2		809	1220	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577107	7577129	+	frameshift_variant	Frame_Shift_Del	DEL	ACAGGCACAAACACGCACCTCAA	ACAGGCACAAACACGCACCTCAA	-	novel	NA	P-0041647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	418	793	0	ENST00000269305.4:c.809_831del	p.Phe270SerfsTer28	p.F270Sfs*28	ENST00000269305	NM_001126112.2	270	tTTGAGGTGCGTGTTTGTGCCTGT/t	8/11	NA	2	FACETS	0.851	0.812	0.89			1	INDETERMINATE	1	TRUE	NA	0.897292265820229	2		793	1095	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937123	76937144	+	frameshift_variant	Frame_Shift_Del	DEL	CTATATCAGAAGAAGATGAGGA	CTATATCAGAAGAAGATGAGGA	-	novel	NA	P-0041647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	149	269	0	ENST00000373344.5:c.3604_3625del	p.Ser1202LysfsTer8	p.S1202Kfs*8	ENST00000373344	NM_000489.3	1202	TCCTCATCTTCTTCTGATATAGaa/aa	9/35	0.897292265820229	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.897292265820229	1		269	173	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0041662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	124	719	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.24	2		719	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0041662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	80	910	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	1	2	FACETS	0.785	0.69	0.888	0.785	0.69	0.888	SUBCLONAL	1	TRUE	1	0.24	2		910	849	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0041663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	64	204	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.290304688151162	3	FACETS	1	0.971	1	0.732	0.637	0.833	CLONAL	1	TRUE	1	0.290304688151162	3		204	345	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0041666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	154	418	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.237288036954338	5	FACETS	0.9	0.83	0.972	0.72	0.664	0.778	CLONAL	4	TRUE	0	0.237288036954338	5		418	489	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0041666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	147	907	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.23013105431313	2	FACETS	0.864	0.79	0.941	0.864	0.79	0.941	CLONAL	2	TRUE	0	0.237288036954338	2		907	717	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025570	1025570	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	158	1071	3	ENST00000358495.3:c.805del	p.Arg269GlyfsTer28	p.R269Gfs*28	ENST00000358495	NM_134424.2	269	Cgg/gg	9/12	0.237288036954338	6	FACETS	0.794	0.726	0.866			1	SUBCLONAL	2	TRUE	NA	0.237288036954338	6		1074	1236	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916752	48916752	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	51	329	0	ENST00000267163.4:c.282del	p.Lys96ArgfsTer15	p.K96Rfs*15	ENST00000267163	NM_000321.2	94	aaG/aa	3/27	0.163481207442693	4	FACETS	1	0.963	1	0.737	0.628	0.854	CLONAL	1	TRUE	2	0.237288036954338	4		329	361	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138484	2138484	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs748936673	NA	P-0041666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	84	1169	0	ENST00000219476.3:c.5297C>G	p.Pro1766Arg	p.P1766R	ENST00000219476	NM_000548.3	1766	cCt/cGt	42/42	0.219679484160012	2	FACETS	0.885	0.781	0.997	0.443	0.39	0.499	CLONAL	1	TRUE	0	0.237288036954338	2		1169	800	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514430	148514430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	93	499	0	ENST00000320356.2:c.1294C>T	p.Pro432Ser	p.P432S	ENST00000320356	NM_004456.4	432	Cct/Tct	11/20	0.163481207442693	4	FACETS	0.785	0.699	0.876	0.785	0.699	0.876	SUBCLONAL	2	TRUE	2	0.237288036954338	4		499	618	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0041829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	181	417	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.554815101076695	2		417	641	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0041829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	718	377	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.425017676406979	5	FACETS	0.986	0.958	1			1	CLONAL	4	TRUE	NA	0.554815101076695	5		377	1202	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794886	42794886	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	547	836	2	ENST00000575354.2:c.1966G>T	p.Ala656Ser	p.A656S	ENST00000575354	NM_015125.3	656	Gcc/Tcc	10/20	0.518232154425361	3	FACETS	0.957	0.92	0.994	0.957	0.92	0.994	CLONAL	2	TRUE	1	0.554815101076695	3		838	1316	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0041865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	131	708	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.23849013963701	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.23849013963701	1		708	826	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469669	NA	P-0041865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	18	722	0	ENST00000374080.3:c.130G>A	p.Gly44Ser	p.G44S	ENST00000374080		44	Ggt/Agt	2/45	0.23849013963701	1	FACETS	0.223	0.167	0.29	0.223	0.167	0.29	SUBCLONAL	1	TRUE	0	0.23849013963701	1		722	595	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907684	111907684	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	43	515	0	ENST00000393256.3:c.458G>C	p.Arg153Pro	p.R153P	ENST00000393256	NM_006538.4	153	cGg/cCg	3/4	1	2	FACETS	0.679	0.568	0.803	0.679	0.568	0.803	SUBCLONAL	1	TRUE	1	0.23849013963701	2		515	531	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38194823	38194823	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	23	413	0	ENST00000317025.8:c.910G>T	p.Gly304Cys	p.G304C	ENST00000317025	NM_023034.1	304	Ggt/Tgt	4/24	1	2	FACETS	0.593	0.463	0.745	0.593	0.463	0.745	SUBCLONAL	1	TRUE	1	0.23849013963701	2		413	325	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291798	15291800	+	frameshift_variant	Frame_Shift_Del	DEL	CGA	CGA	G	novel	NA	P-0041865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	219	1033	0	ENST00000263388.2:c.2966_2968delinsC	p.Leu989ProfsTer45	p.L989Pfs*45	ENST00000263388	NM_000435.2	989	cTCGag/cCag	18/33	0.192180138376013	3	FACETS	0.928	0.863	0.996	0.928	0.863	0.996	CLONAL	2	TRUE	1	0.23849013963701	3		1033	1107	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0041873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	136	226	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	0.321318302143545	2	FACETS	0.897	0.823	0.973	0.897	0.823	0.973	CLONAL	2	TRUE	0	0.362729253400374	2		226	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0041873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	394	934	1	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.358212184441724	2	FACETS	0.992	0.945	1	0.992	0.945	1	CLONAL	2	TRUE	0	0.362729253400374	2		935	1095	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505331	186505331	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	182	386	0	ENST00000323963.5:c.958del	p.Arg320GlyfsTer8	p.R320Gfs*8	ENST00000323963		319	ttC/tt	9/11	1	2	FACETS	0.987	0.921	1	0.987	0.921	1	CLONAL	1	TRUE	1	0.870179930001269	2		386	424	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	218483	218483	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs770866830	NA	P-0041904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	81	129	0	ENST00000264932.6:c.13C>G	p.Arg5Gly	p.R5G	ENST00000264932	NM_004168.2	5	Cgg/Ggg	1/15	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.870179930001269	NA		129	410	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69011971	69011971	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	260	669	0	ENST00000288368.4:c.2608C>G	p.Leu870Val	p.L870V	ENST00000288368	NM_024870.2	870	Cta/Gta	23/40	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.870179930001269	2		669	561	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	160	541	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.81323293695724	2		541	389	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214422	5214422	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	204	605	0	ENST00000357368.4:c.4564G>C	p.Asp1522His	p.D1522H	ENST00000357368	NM_002850.3	1522	Gat/Cat	30/38	1	2	FACETS	0.94	0.879	1	0.94	0.879	1	CLONAL	1	TRUE	1	0.81323293695724	2		605	534	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994282	21994282	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3731190	NA	P-0041935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	224	565	0	ENST00000579755.1:c.49C>T	p.Pro17Ser	p.P17S	ENST00000579755		17	Ccg/Tcg	1/3	1				0.819	0.931				CLONAL	1	TRUE	1	0.81323293695724	2		565	630	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579317	7579317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	400	557	0	ENST00000269305.4:c.370del	p.Cys124AlafsTer46	p.C124Afs*46	ENST00000269305	NM_001126112.2	124	Tgc/gc	4/11	0.540876243141554	2	FACETS	0.937	0.898	0.976	0.937	0.898	0.976	CLONAL	2	TRUE	0	0.543106229591426	2		557	786	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207786	29207786	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	173	546	0	ENST00000240100.2:c.10A>G	p.Met4Val	p.M4V	ENST00000240100	NM_001394.6	4	Atg/Gtg	1/4	0.275575620537307	0	FACETS	0.443	0.409	0.478			1	INDETERMINATE	1	TRUE	0	0.543106229591426	0		546	657	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928077	178928084	+	protein_altering_variant	In_Frame_Del	DEL	TAGAAGAT	TAGAAGAT	CAGAA	novel	NA	P-0041937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	120	422	0	ENST00000263967.3:c.1355_1362delinsCAGAA	p.Leu452_Asp454delinsSerGlu	p.L452_D454delinsSE	ENST00000263967	NM_006218.2	452	tTAGAAGAT/tCAGAA	8/21	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.543106229591426	2		422	337	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247372	153247372	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	71	266	0	ENST00000281708.4:c.1430G>T	p.Gly477Val	p.G477V	ENST00000281708	NM_033632.3	477	gGt/gTt	10/12	0.428391178812632	1	FACETS	0.678	0.598	0.762	0.678	0.598	0.762	SUBCLONAL	1	TRUE	0	0.543106229591426	1		266	281	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836272	151836272	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	188	400	0	ENST00000262189.6:c.14533A>G	p.Arg4845Gly	p.R4845G	ENST00000262189	NM_170606.2	4845	Agg/Ggg	57/59	0.543106229591426	1	FACETS	0.852	0.792	0.914	0.852	0.792	0.914	CLONAL	1	TRUE	0	0.543106229591426	1		400	592	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787806	135787806	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	65	391	0	ENST00000298552.3:c.776G>T	p.Cys259Phe	p.C259F	ENST00000298552	NM_001162426.1	259	tGt/tTt	9/23	1	2	FACETS	0.554	0.482	0.632	0.554	0.482	0.632	SUBCLONAL	1	TRUE	1	0.543106229591426	2		391	432	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632620	3632620	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144057906	NA	P-0041943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	864	722	0	ENST00000294008.3:c.5228C>T	p.Ser1743Leu	p.S1743L	ENST00000294008	NM_032444.2	1743	tCg/tTg	15/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.932321465668895	2		722	1821	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057519990	NA	P-0041944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	586	459	1	ENST00000269305.4:c.796G>T	p.Gly266Ter	p.G266*	ENST00000269305	NM_001126112.2	266	Gga/Tga	8/11	0.667571672215676	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	0	0.677256034556911	3		460	759	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864700	68864700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	138	328	1	ENST00000288368.4:c.71G>A	p.Arg24His	p.R24H	ENST00000288368	NM_024870.2	24	cGc/cAc	1/40	0.677256034556911	6	FACETS	1	0.966	1	0.281	0.256	0.308	CLONAL	1	TRUE	2	0.677256034556911	6		329	853	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104606	69104606	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	163	484	0	ENST00000288368.4:c.4450C>G	p.Arg1484Gly	p.R1484G	ENST00000288368	NM_024870.2	1484	Cga/Gga	37/40	0.677256034556911	6	FACETS	0.94	0.861	1	0.235	0.215	0.256	CLONAL	1	TRUE	2	0.677256034556911	6		484	1206	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061137	38061167	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCCCGCTTCCGCTCCCGCCCCCGCCGCCG	GCCCCCGCTTCCGCTCCCGCCCCCGCCGCCG	-	novel	NA	P-0041955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	145	211	0	ENST00000250448.2:c.822_852del	p.Gly275AlafsTer36	p.G275Afs*36	ENST00000250448	NM_004496.3	274	gcCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGC/gc	2/2	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.762494277913456	2		211	311	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641214	3641214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs546657275	NA	P-0041955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	318	1016	2	ENST00000294008.3:c.2425G>A	p.Glu809Lys	p.E809K	ENST00000294008	NM_032444.2	809	Gaa/Aaa	12/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.762494277913456	2		1018	789	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618903	37618952	+	frameshift_variant	Frame_Shift_Del	DEL	GCACAAAGACCGGAGTAAAAGTCATCGAAAAAGGGAAACACCCAAAAGTT	GCACAAAGACCGGAGTAAAAGTCATCGAAAAAGGGAAACACCCAAAAGTT	-	novel	NA	P-0041955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	192	710	0	ENST00000447079.4:c.579_628del	p.His194GlnfsTer19	p.H194Qfs*19	ENST00000447079	NM_015083.1	193	ggGCACAAAGACCGGAGTAAAAGTCATCGAAAAAGGGAAACACCCAAAAGTTac/ggac	1/14	0.273017552057808	3	FACETS	1	0.991	1	1	0.991	1	INDETERMINATE	2	FALSE	1	0.762494277913456	3		710	279	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0041956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	138	540	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.211773033160764	4	FACETS	0.96	0.877	1	0.96	0.877	1	CLONAL	2	TRUE	2	0.310866513215505	4		540	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0041956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	152	1194	1	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.24391349340499	2	FACETS	0.872	0.801	0.944	0.872	0.801	0.944	CLONAL	2	TRUE	0	0.310866513215505	2		1195	561	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041991-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	75	541	0				ENST00000310581	NM_198253.2	-/1132			0.243542515310658	4	FACETS	0.804	0.708	0.907	0.804	0.708	0.907	CLONAL	2	TRUE	2	0.286232600000364	4		541	419	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549404	21549404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753026198	NA	P-0041991-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	56	525	0	ENST00000382592.4:c.2872C>T	p.Arg958Cys	p.R958C	ENST00000382592	NM_014572.2	958	Cgc/Tgc	8/8	1	2	FACETS	0.789	0.677	0.911	0.789	0.677	0.911	CLONAL	1	TRUE	1	0.286232600000364	2		525	496	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	374	415	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.386020225278612	4	FACETS	1	0.964	1	1	0.964	1	INDETERMINATE	2	TRUE	2	0.687848082168393	4		415	906	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108040	30108040	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs148748320	NA	P-0042067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	202	849	0	ENST00000331968.5:c.767C>A	p.Pro256Gln	p.P256Q	ENST00000331968	NM_002742.2	256	cCa/cAa	5/18	0.68637400868054	3	FACETS	0.911	0.846	0.979	0.456	0.423	0.49	CLONAL	1	TRUE	1	0.687848082168393	3		849	866	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577589	7577600	+	inframe_deletion	In_Frame_Del	DEL	GTGGTACAGTCA	GTGGTACAGTCA	-	novel	NA	P-0042067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	651	905	0	ENST00000269305.4:c.681_692del	p.Asp228_Thr231del	p.D228_T231del	ENST00000269305	NM_001126112.2	227	tcTGACTGTACCACc/tcc	7/11	0.68637400868054	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	0	0.687848082168393	3		905	836	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201708	66201708	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	505	705	0	ENST00000273854.3:c.2794T>A	p.Leu932Met	p.L932M	ENST00000273854	NM_004439.5	932	Ttg/Atg	16/18	0.324590106756705	4	FACETS	1	0.99	1	0.791	0.766	0.816	INDETERMINATE	3	TRUE	0	0.687848082168393	4		705	783	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0042080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	75	500	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.236082688453807	1	FACETS	0.636	0.559	0.718	0.636	0.559	0.718	INDETERMINATE	1	FALSE	0	0.414664804878944	1		500	451	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	98	415	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.414664804878944	4	FACETS	1	0.964	1	0.591	0.528	0.657	CLONAL	1	FALSE	2	0.414664804878944	4		415	566	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	25	541	0				ENST00000310581	NM_198253.2	-/1132			0.245905669314836	0	FACETS	0.574	0.459	0.701			1	INDETERMINATE	1	FALSE	0	0.414664804878944	0		541	123	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913783	32913783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	60	460	0	ENST00000380152.3:c.5291C>T	p.Ser1764Leu	p.S1764L	ENST00000380152		1764	tCa/tTa	11/27	0.173962196340267	4	FACETS	0.966	0.834	1	0.483	0.417	0.554	INDETERMINATE	1	FALSE	2	0.414664804878944	4		460	424	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81971431	81971431	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	86	657	0	ENST00000359376.3:c.3121G>C	p.Glu1041Gln	p.E1041Q	ENST00000359376	NM_002661.3	1041	Gag/Cag	28/33	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.414664804878944	2		657	352	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106526	27106529	+	frameshift_variant	Frame_Shift_Del	DEL	TGGA	TGGA	-	novel	NA	P-0042080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	107	940	0	ENST00000324856.7:c.6137_6140del	p.Val2046GlyfsTer88	p.V2046Gfs*88	ENST00000324856	NM_006015.4	2046	gTGGAg/gg	20/20	0.173962196340267	4	FACETS	0.985	0.884	1	0.493	0.442	0.546	INDETERMINATE	1	FALSE	2	0.414664804878944	4		940	741	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692883	89692883	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	48	414	0	ENST00000371953.3:c.367C>A	p.His123Asn	p.H123N	ENST00000371953	NM_000314.4	123	Cac/Aac	5/9	0.414664804878944	2	FACETS	0.516	0.436	0.603	0.258	0.218	0.302	SUBCLONAL	1	FALSE	0	0.414664804878944	2		414	449	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913651	32913651	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs80358740	NA	P-0042080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	48	426	0	ENST00000380152.3:c.5159C>G	p.Ser1720Ter	p.S1720*	ENST00000380152		1720	tCa/tGa	11/27	0.173962196340267	4	FACETS	0.978	0.83	1	0.489	0.415	0.57	INDETERMINATE	1	FALSE	2	0.414664804878944	4		426	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579442	7579575	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGTAGGAGCTGCTGGTGCAGGGGCCACGGGGGGAGCAGCCTCTGGCATTCTGGGAGCTTCATCTGGACCTGGGTCTTCAGTGAACCATTGTTCAATATCGTCCGGGGACAGCATCAAATCATCCATTGCTTG	GGTGTAGGAGCTGCTGGTGCAGGGGCCACGGGGGGAGCAGCCTCTGGCATTCTGGGAGCTTCATCTGGACCTGGGTCTTCAGTGAACCATTGTTCAATATCGTCCGGGGACAGCATCAAATCATCCATTGCTTG	-	novel	NA	P-0042080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	37	865	1	ENST00000269305.4:c.112_245del	p.Gln38GlyfsTer66	p.Q38Gfs*66	ENST00000269305	NM_001126112.2	38	CAAGCAATGGATGATTTGATGCTGTCCCCGGACGATATTGAACAATGGTTCACTGAAGACCCAGGTCCAGATGAAGCTCCCAGAATGCCAGAGGCTGCTCCCCCCGTGGCCCCTGCACCAGCAGCTCCTACACCg/g	4/11	0.183373032847178	1	FACETS	0.425	0.351	0.507	0.425	0.351	0.507	INDETERMINATE	1	FALSE	0	0.414664804878944	1		866	333	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075308	16075309	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0042080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	51	461	0	ENST00000268712.3:c.243dup	p.Pro82AlafsTer7	p.P82Afs*7	ENST00000268712	NM_006311.3	81	-/G	4/46	0.183373032847178	1	FACETS	0.684	0.585	0.791	0.684	0.585	0.791	INDETERMINATE	1	FALSE	0	0.414664804878944	1		461	285	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118632	11118632	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	82	701	0	ENST00000358026.2:c.2056G>T	p.Glu686Ter	p.E686*	ENST00000358026	NM_001128849.1	686	Gag/Tag	14/36	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	FALSE	1	0.414664804878944	2		701	375	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211859	36211859	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	114	1011	0	ENST00000222270.7:c.1610C>G	p.Ser537Cys	p.S537C	ENST00000222270	NM_014727.1	537	tCc/tGc	3/37	1	2	FACETS	0.847	0.764	0.935	0.847	0.764	0.935	CLONAL	1	FALSE	1	0.414664804878944	2		1011	649	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222823	36222823	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	91	996	0	ENST00000222270.7:c.5452G>T	p.Glu1818Ter	p.E1818*	ENST00000222270	NM_014727.1	1818	Gag/Tag	27/37	1	2	FACETS	0.874	0.779	0.975	0.874	0.779	0.975	CLONAL	1	FALSE	1	0.414664804878944	2		996	502	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871890	45871890	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	91	736	0	ENST00000391945.4:c.358G>C	p.Glu120Gln	p.E120Q	ENST00000391945	NM_000400.3	120	Gag/Cag	5/23	0.326703617565496	4	FACETS	1	0.978	1			1	CLONAL	1	FALSE	NA	0.414664804878944	4		736	441	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462662	29462662	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762395127	NA	P-0042080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	65	894	0	ENST00000389048.3:c.2239G>A	p.Gly747Arg	p.G747R	ENST00000389048	NM_004304.4	747	Ggg/Agg	13/29	0.414664804878944	0	FACETS	0.535	0.467	0.608			1	SUBCLONAL	1	FALSE	0	0.414664804878944	0		894	343	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164861	47164861	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	36	391	0	ENST00000409792.3:c.1265C>T	p.Ser422Leu	p.S422L	ENST00000409792	NM_014159.6	422	tCa/tTa	3/21	0.195330384732117	5	FACETS	1	0.916	1	0.396	0.328	0.472	INDETERMINATE	1	FALSE	2	0.414664804878944	5		391	237	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604332	189604332	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	32	502	1	ENST00000264731.3:c.1499G>C	p.Gly500Ala	p.G500A	ENST00000264731	NM_003722.4	500	gGa/gCa	11/14	0.195330384732117	5	FACETS	0.974	0.795	1	0.325	0.265	0.392	INDETERMINATE	1	FALSE	2	0.414664804878944	5		503	257	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286580	33286580	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0042080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	172	594	0	ENST00000374542.5:c.2164-1G>A		p.X722_splice	ENST00000374542	NM_001141970.1	722			0.414664804878944	6	FACETS	0.827	0.761	0.895	0.413	0.38	0.448	CLONAL	2	FALSE	2	0.414664804878944	6		594	918	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287189	33287189	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	139	754	1	ENST00000374542.5:c.1908G>T	p.Lys636Asn	p.K636N	ENST00000374542	NM_001141970.1	636	aaG/aaT	6/8	0.414664804878944	6	FACETS	0.751	0.684	0.822	0.376	0.342	0.411	SUBCLONAL	2	FALSE	2	0.414664804878944	6		755	816	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287395	33287395	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs943558347	NA	P-0042080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	118	681	0	ENST00000374542.5:c.1702G>C	p.Glu568Gln	p.E568Q	ENST00000374542	NM_001141970.1	568	Gag/Cag	6/8	0.414664804878944	6	FACETS	0.881	0.797	0.969	0.44	0.398	0.485	CLONAL	2	FALSE	2	0.414664804878944	6		681	591	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287461	33287461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	141	760	0	ENST00000374542.5:c.1636G>A	p.Glu546Lys	p.E546K	ENST00000374542	NM_001141970.1	546	Gaa/Aaa	6/8	0.414664804878944	6	FACETS	0.871	0.795	0.951	0.436	0.397	0.476	CLONAL	2	FALSE	2	0.414664804878944	6		760	714	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945204	44945205	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0042080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	93	370	0	ENST00000377967.4:c.3529_3530del	p.Leu1177GlufsTer2	p.L1177Efs*2	ENST00000377967	NM_021140.2	1176	gtTCtg/gttg	24/29	0.354683468600702	2	FACETS	1	0.979	1			1	CLONAL	1	FALSE	NA	0.414664804878944	2		370	322	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223512	53223512	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	24	402	0	ENST00000375401.3:c.3847G>C	p.Glu1283Gln	p.E1283Q	ENST00000375401	NM_004187.3	1283	Gag/Cag	23/26	0.354683468600702	2	FACETS	1	0.924	1			1	CLONAL	1	FALSE	NA	0.414664804878944	2		402	85	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954272	32954273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359752	NA	P-0042144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	147	451	0	ENST00000380152.3:c.9253dup	p.Thr3085AsnfsTer26	p.T3085Nfs*26	ENST00000380152		3082	-/A	24/27	1	2	FACETS	0.85	0.781	0.92	0.85	0.781	0.92	CLONAL	1	TRUE	1	0.697635411268592	2		451	496	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913409	NA	P-0042144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	10	470	0	ENST00000349496.5:c.134C>G	p.Ser45Cys	p.S45C	ENST00000349496	NM_001904.3	45	tCt/tGt	3/15	1	2	FACETS	0.069	0.046	0.098	0.069	0.046	0.098	SUBCLONAL	1	TRUE	1	0.697635411268592	2		470	416	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101378	27101378	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	238	722	0	ENST00000324856.7:c.4660C>T	p.Pro1554Ser	p.P1554S	ENST00000324856	NM_006015.4	1554	Cca/Tca	18/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.697635411268592	2		722	566	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383342	4383342	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	129	889	0	ENST00000261254.3:c.136T>G	p.Cys46Gly	p.C46G	ENST00000261254	NM_001759.3	46	Tgc/Ggc	1/5	0.231856055748961	1	FACETS	0.473	0.431	0.517	0.473	0.431	0.517	INDETERMINATE	1	TRUE	0	0.697635411268592	1		889	509	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912080	32912081	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs397507677	NA	P-0042144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	256	765	0	ENST00000380152.3:c.3593dup	p.Asn1198LysfsTer2	p.N1198Kfs*2	ENST00000380152		1196	-/A	11/27	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.697635411268592	2		765	724	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681066	37681066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	185	662	0	ENST00000447079.4:c.3235G>A	p.Val1079Met	p.V1079M	ENST00000447079	NM_015083.1	1079	Gtg/Atg	12/14	0.66552882040085	3	FACETS	0.999	0.925	1	0.5	0.462	0.538	CLONAL	1	TRUE	1	0.697635411268592	3		662	716	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265783	41266198	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAG	TGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAG	-	novel	NA	P-0042144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	23	69	0	ENST00000349496.5:c.13+214_198del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	1	2	FACETS	1	0.82	1	1	0.82	1	CLONAL	1	TRUE	1	0.697635411268592	2		69	65	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178601	56178601	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	124	351	0	ENST00000399503.3:c.3574G>C	p.Ala1192Pro	p.A1192P	ENST00000399503	NM_005921.1	1192	Gcc/Ccc	14/20	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.697635411268592	2		351	343	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864377	162864377	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs75860381	NA	P-0042144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	141	594	0	ENST00000366898.1:c.136G>T	p.Ala46Ser	p.A46S	ENST00000366898	NM_004562.2	46	Gca/Tca	2/12	1	2	FACETS	0.951	0.875	1	0.951	0.875	1	CLONAL	1	TRUE	1	0.697635411268592	2		594	425	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205516	38205516	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	270	913	0	ENST00000317025.8:c.174G>C	p.Gln58His	p.Q58H	ENST00000317025	NM_023034.1	58	caG/caC	2/24	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.697635411268592	2		913	727	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978599	70978599	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	424	768	0	ENST00000276594.2:c.1054A>C	p.Ser352Arg	p.S352R	ENST00000276594	NM_024504.3	352	Agc/Cgc	5/8	0.638322465472158	4	FACETS	0.995	0.951	1	0.995	0.951	1	CLONAL	2	TRUE	2	0.697635411268592	4		768	1037	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0042151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	657	837	0	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.860109182682245	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.860109182682245	2		837	733	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163313613	163313613	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	23	249	0	ENST00000271452.3:c.760T>C	p.Tyr254His	p.Y254H	ENST00000271452	NM_145697.2	254	Tat/Cat	10/14	0.860109182682245	2	FACETS	0.514	0.408	0.632	0.257	0.204	0.316	SUBCLONAL	1	TRUE	0	0.860109182682245	2		249	104	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955880	55955880	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	90	561	0	ENST00000263923.4:c.3282G>T	p.Leu1094Phe	p.L1094F	ENST00000263923	NM_002253.2	1094	ttG/ttT	24/30	1	2	FACETS	0.772	0.695	0.852	0.772	0.695	0.852	SUBCLONAL	1	TRUE	1	0.860109182682245	2		561	271	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911251	29911251	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	26	551	0	ENST00000376809.5:c.550C>G	p.Leu184Val	p.L184V	ENST00000376809	NM_002116.7	184	Ctg/Gtg	3/8	0.833878897128444	2	FACETS	0.535	0.432	0.649	0.268	0.216	0.325	SUBCLONAL	1	TRUE	0	0.860109182682245	2		551	113	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0042157-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	61	760	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.243401711842752	2	FACETS	0.381	0.328	0.439	0.191	0.164	0.22	SUBCLONAL	1	TRUE	0	0.400488614908831	2		760	799	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0042157-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	185	539	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.243401711842752	2	FACETS	1	0.988	1	0.671	0.622	0.722	CLONAL	1	TRUE	0	0.400488614908831	2		539	688	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910685	29910685	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs199474408	NA	P-0042157-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	191	943	0	ENST00000376809.5:c.225G>A	p.Trp75Ter	p.W75*	ENST00000376809	NM_002116.7	75	tgG/tgA	2/8	0.20052896666066	3	FACETS	0.869	0.802	0.94	0.435	0.401	0.47	INDETERMINATE	1	TRUE	1	0.400488614908831	3		943	1317	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339974	116339974	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042157-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	161	344	0	ENST00000397752.3:c.836T>C	p.Ile279Thr	p.I279T	ENST00000397752	NM_000245.2	279	aTc/aCc	2/21	1	2	FACETS	0.935	0.867	1	1	0.992	1	CLONAL	2	TRUE	1	0.400488614908831	2		344	430	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944258	81944258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750403828	NA	P-0042157-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	42	532	0	ENST00000359376.3:c.1867C>T	p.Arg623Cys	p.R623C	ENST00000359376	NM_002661.3	623	Cgc/Tgc	18/33	0.400488614908831	1	FACETS	0.271	0.225	0.321	0.271	0.225	0.321	SUBCLONAL	1	TRUE	0	0.400488614908831	1		532	620	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867698	45867698	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042157-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	35	550	0	ENST00000391945.4:c.702C>G	p.Asp234Glu	p.D234E	ENST00000391945	NM_000400.3	234	gaC/gaG	8/23	1	2	FACETS	0.25	0.204	0.302	0.25	0.204	0.302	SUBCLONAL	1	TRUE	1	0.400488614908831	2		550	698	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760618	133760618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769473644	NA	P-0042157-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	44	712	1	ENST00000318560.5:c.2941G>A	p.Val981Ile	p.V981I	ENST00000318560	NM_005157.4	981	Gtt/Att	11/11	1	2	FACETS	0.261	0.218	0.309	0.261	0.218	0.309	SUBCLONAL	1	TRUE	1	0.400488614908831	2		713	843	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0042162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	422	565	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.471907341622032	4	FACETS	0.94	0.897	0.983	0.94	0.897	0.983	CLONAL	2	TRUE	2	0.671298879083246	4		565	1118	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0042162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	466	327	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.61931585552976	2	FACETS	0.907	0.876	0.939	0.907	0.876	0.939	CLONAL	2	TRUE	0	0.671298879083246	2		327	765	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356269	66356269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200754741	NA	P-0042162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	342	612	2	ENST00000273854.3:c.1228G>A	p.Gly410Ser	p.G410S	ENST00000273854	NM_004439.5	410	Ggt/Agt	5/18	0.592832483034082	2	FACETS	0.837	0.801	0.872	0.837	0.801	0.872	CLONAL	2	TRUE	0	0.671298879083246	2		614	609	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519938	NA	P-0042162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	438	338	0	ENST00000263967.3:c.1034A>C	p.Asn345Thr	p.N345T	ENST00000263967	NM_006218.2	345	aAt/aCt	5/21	0.671298879083246	5	FACETS	0.916	0.89	0.941	0.916	0.89	0.941	CLONAL	5	TRUE	0	0.671298879083246	5		338	572	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720803	89720805	+	inframe_deletion	In_Frame_Del	DEL	TAC	TAC	-	novel	NA	P-0042162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	122	234	0	ENST00000371953.3:c.955_957del	p.Thr319del	p.T319del	ENST00000371953	NM_000314.4	318	ctTACt/ctt	8/9	0.592832483034082	2	FACETS	0.777	0.719	0.834	0.777	0.719	0.834	SUBCLONAL	2	TRUE	0	0.671298879083246	2		234	234	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0042168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	60	500	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.646214169879644	4	FACETS	0.398	0.342	0.459	0.199	0.171	0.23	SUBCLONAL	1	TRUE	2	0.661648940987981	4		500	758	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090868	5090868	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	25	231	0	ENST00000381652.3:c.3016G>T	p.Glu1006Ter	p.E1006*	ENST00000381652	NM_004972.3	1006	Gaa/Taa	22/25	0.570202113359734	4	FACETS	0.302	0.237	0.376			1	SUBCLONAL	1	TRUE	NA	0.661648940987981	4		231	416	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610211	81610211	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	165	524	0	ENST00000298171.2:c.1809G>C	p.Lys603Asn	p.K603N	ENST00000298171	NM_000369.2	603	aaG/aaC	10/10	0.646214169879644	4	FACETS	1	0.957	1	0.531	0.488	0.576	CLONAL	1	TRUE	2	0.661648940987981	4		524	780	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631590	119631590	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	147	440	0	ENST00000316626.5:c.676G>C	p.Glu226Gln	p.E226Q	ENST00000316626		226	Gag/Cag	6/12	0.646214169879644	4	FACETS	0.953	0.871	1	0.476	0.435	0.519	CLONAL	1	TRUE	2	0.661648940987981	4		440	775	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696616	176696616	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	76	302	0	ENST00000439151.2:c.5317G>C	p.Glu1773Gln	p.E1773Q	ENST00000439151	NM_022455.4	1773	Gag/Cag	16/23	0.660846889427271	4	FACETS	0.864	0.76	0.974			1	CLONAL	1	TRUE	NA	0.661648940987981	4		302	442	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922864	39922864	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	160	652	0	ENST00000378444.4:c.3844C>G	p.Gln1282Glu	p.Q1282E	ENST00000378444	NM_001123385.1	1282	Caa/Gaa	8/15	0.660846889427271	3	FACETS	0.91	0.837	0.987			1	CLONAL	1	TRUE	NA	0.661648940987981	3		652	707	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0042177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	108	364	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.885	0.805	0.968	0.885	0.805	0.968	CLONAL	1	TRUE	1	0.77934685388116	2		364	313	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710585	114710585	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	286	710	2	ENST00000543371.1:c.70G>T	p.Glu24Ter	p.E24*	ENST00000543371	NM_001198531.1	24	Gag/Tag	1/14	1	2	FACETS	0.979	0.925	1	0.979	0.925	1	CLONAL	1	TRUE	1	0.77934685388116	2		712	750	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478816	56478816	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	32	782	0	ENST00000267101.3:c.272T>C	p.Met91Thr	p.M91T	ENST00000267101	NM_001982.3	91	aTg/aCg	3/28	1	2	FACETS	0.087	0.069	0.106	0.087	0.069	0.106	SUBCLONAL	1	TRUE	1	0.77934685388116	2		782	949	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	128	415	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.436042118363082	2		415	557	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0042182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	238	360	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.436042118363082	1	FACETS	0.772	0.727	0.817	1	0.994	1	SUBCLONAL	2	TRUE	0	0.436042118363082	1		360	553	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0042182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	140	577	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.818	0.745	0.894	0.818	0.745	0.894	CLONAL	1	TRUE	1	0.436042118363082	2		577	785	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259397	11259397	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	164	683	0	ENST00000361445.4:c.4171C>G	p.Arg1391Gly	p.R1391G	ENST00000361445	NM_004958.3	1391	Cga/Gga	28/58	1	2	FACETS	0.953	0.876	1	0.953	0.876	1	CLONAL	1	TRUE	1	0.436042118363082	2		683	789	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850777	63850777	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	127	653	0	ENST00000279873.7:c.1555G>T	p.Glu519Ter	p.E519*	ENST00000279873	NM_032199.2	519	Gaa/Taa	10/10	1	2	FACETS	0.854	0.775	0.937	0.854	0.775	0.937	CLONAL	1	TRUE	1	0.436042118363082	2		653	682	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341251	89341251	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	130	511	0	ENST00000301030.4:c.7684G>A	p.Glu2562Lys	p.E2562K	ENST00000301030	NM_001256183.1	2562	Gag/Aag	11/13	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.436042118363082	2		511	579	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	213	918	0	ENST00000227507.2:c.859C>A	p.Pro287Thr	p.P287T	ENST00000227507	NM_053056.2	287	Ccc/Acc	5/5	1	2	FACETS	0.992	0.922	1	0.992	0.922	1	CLONAL	1	TRUE	1	0.436042118363082	2		918	985	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32182013	32182013	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141422504	NA	P-0042182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	193	990	0	ENST00000375023.3:c.2041G>A	p.Val681Met	p.V681M	ENST00000375023	NM_004557.3	681	Gtg/Atg	13/30	1	2	FACETS	0.836	0.773	0.902	0.836	0.773	0.902	CLONAL	1	TRUE	1	0.436042118363082	2		990	1059	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099361	27099361	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	159	712	0	ENST00000324856.7:c.3598C>T	p.Gln1200Ter	p.Q1200*	ENST00000324856	NM_006015.4	1200	Cag/Tag	14/20	1	2	FACETS	0.896	0.822	0.973	0.896	0.822	0.973	CLONAL	1	TRUE	1	0.436042118363082	2		712	814	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097665	27097665	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	175	719	0	ENST00000324856.7:c.3254C>A	p.Ser1085Ter	p.S1085*	ENST00000324856	NM_006015.4	1085	tCa/tAa	12/20	1	2	FACETS	0.928	0.855	1	0.928	0.855	1	CLONAL	1	TRUE	1	0.436042118363082	2		719	865	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982330	201982374	+	inframe_deletion	In_Frame_Del	DEL	AAGGGGGATCCCAAGCACGGGAAGCGGAAACGAGGCCGGCCCCGA	AAGGGGGATCCCAAGCACGGGAAGCGGAAACGAGGCCGGCCCCGA	-	novel	NA	P-0042182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	75	920	0	ENST00000359651.3:c.712_756del	p.Gly238_Lys252del	p.G238_K252del	ENST00000359651		237	AAGGGGGATCCCAAGCACGGGAAGCGGAAACGAGGCCGGCCCCGA/-	6/8	1	2	FACETS	0.32	0.279	0.364	0.32	0.279	0.364	SUBCLONAL	1	TRUE	1	0.436042118363082	2		920	1076	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845596	63845608	+	frameshift_variant	Frame_Shift_Del	DEL	ACATGAAATACCT	ACATGAAATACCT	-	novel	NA	P-0042182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	57	350	1	ENST00000279873.7:c.1336_1348del	p.His446LysfsTer29	p.H446Kfs*29	ENST00000279873	NM_032199.2	445	aaACATGAAATACCT/aa	9/10	1	2	FACETS	0.607	0.522	0.699	0.607	0.522	0.699	SUBCLONAL	1	TRUE	1	0.436042118363082	2		351	431	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851736	63851737	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGCCTCTACAGACACACCGAGC	novel	NA	P-0042182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	132	777	0	ENST00000279873.7:c.2516_2537dup	p.His846GlnfsTer12	p.H846Qfs*12	ENST00000279873	NM_032199.2	838	-/AGCCTCTACAGACACACCGAGC	10/10	1	2	FACETS	0.647	0.587	0.71	0.647	0.587	0.71	SUBCLONAL	1	TRUE	1	0.436042118363082	2		777	936	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42384929	42384935	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCAGGG	CCCAGGG	-	novel	NA	P-0042182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	112	678	0	ENST00000221972.3:c.568-3_571del		p.X190_splice	ENST00000221972	NM_021601.3	190		5/5	1	2	FACETS	0.755	0.68	0.835	0.755	0.68	0.835	SUBCLONAL	1	TRUE	1	0.436042118363082	2		678	680	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927978	178927988	+	protein_altering_variant	In_Frame_Del	DEL	ACTGTCCATTG	ACTGTCCATTG	GC	novel	NA	P-0042182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	94	387	1	ENST00000263967.3:c.1256_1266delinsGC	p.His419_Leu422delinsArg	p.H419_L422delinsR	ENST00000263967	NM_006218.2	419	cACTGTCCATTG/cGC	8/21	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.436042118363082	2		388	405	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891335	151891335	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	108	371	0	ENST00000262189.6:c.4519G>T	p.Gly1507Ter	p.G1507*	ENST00000262189	NM_170606.2	1507	Gga/Tga	30/59	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.436042118363082	2		371	424	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371744	55371744	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	131	569	0	ENST00000297316.4:c.434T>A	p.Val145Glu	p.V145E	ENST00000297316	NM_022454.3	145	gTg/gAg	2/2	1	2	FACETS	0.971	0.884	1	0.971	0.884	1	CLONAL	1	TRUE	1	0.436042118363082	2		569	619	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131685	2131685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0121447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	310	1049	0	ENST00000219476.3:c.3700G>A	p.Ala1234Thr	p.A1234T	ENST00000219476	NM_000548.3	1234	Gcc/Acc	31/42	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	NA	1	0.733000285810208	2		1049	837	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	132	528	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.49	2		528	492	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	15	204	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.196	0.143	0.26	0.196	0.143	0.26	SUBCLONAL	1	TRUE	1	0.49	2		204	312	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs371769427	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	125	290	0	ENST00000291552.4:c.101C>A	p.Ser34Tyr	p.S34Y	ENST00000291552	NM_006758.2	34	tCt/tAt	2/8	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.49	2		290	419	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609994	43609994	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148935214	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	65	978	2	ENST00000355710.3:c.1946C>T	p.Ser649Leu	p.S649L	ENST00000355710	NM_020975.4	649	tCg/tTg	11/20	1	2	FACETS	0.26	0.224	0.298	0.26	0.224	0.298	SUBCLONAL	1	TRUE	1	0.49	2		980	1022	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435317	56435317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200066146	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	214	673	0	ENST00000407977.2:c.1820C>T	p.Ser607Leu	p.S607L	ENST00000407977		607	tCg/tTg	9/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.49	2		673	847	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276316	15276316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372834264	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	113	777	0	ENST00000263388.2:c.5678G>A	p.Arg1893Gln	p.R1893Q	ENST00000263388	NM_000435.2	1893	cGa/cAa	31/33	1	2	FACETS	0.51	0.458	0.565	0.51	0.458	0.565	SUBCLONAL	1	TRUE	1	0.49	2		777	905	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636134	28636134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200841206	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	234	633	0	ENST00000241453.7:c.238G>A	p.Ala80Thr	p.A80T	ENST00000241453	NM_004119.2	80	Gct/Act	3/24	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.49	2		633	870	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721157	176721157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373571733	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	135	414	0	ENST00000439151.2:c.6788C>T	p.Ser2263Leu	p.S2263L	ENST00000439151	NM_022455.4	2263	tCg/tTg	23/23	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.49	2		414	520	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	124	503	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.964	0.876	1	0.964	0.876	1	CLONAL	1	TRUE	1	0.49	2		503	525	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177626	56177626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530669321	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	72	424	0	ENST00000399503.3:c.2599G>A	p.Glu867Lys	p.E867K	ENST00000399503	NM_005921.1	867	Gaa/Aaa	14/20	1	2	FACETS	0.515	0.45	0.584	0.515	0.45	0.584	SUBCLONAL	1	TRUE	1	0.49	2		424	571	SUCCESS
APC	324	MSKCC	GRCh37	5	112177049	112177049	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	28	442	0	ENST00000257430.4:c.5758C>T	p.Arg1920Ter	p.R1920*	ENST00000257430	NM_000038.5	1920	Cga/Tga	16/16	1	2	FACETS	0.211	0.168	0.26	0.211	0.168	0.26	SUBCLONAL	1	TRUE	1	0.49	2		442	542	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780209	9780209	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373779625	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	241	822	1	ENST00000377346.4:c.1379G>A	p.Arg460His	p.R460H	ENST00000377346	NM_005026.3	460	cGc/cAc	11/24	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.49	2		823	955	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807573	36807573	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs774376244	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	164	582	0	ENST00000373129.3:c.1091C>T	p.Ala364Val	p.A364V	ENST00000373129	NM_032017.1	364	gCg/gTg	12/12	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.49	2		582	669	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303028	15303028	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773630799	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	272	993	3	ENST00000263388.2:c.422G>A	p.Arg141His	p.R141H	ENST00000263388	NM_000435.2	141	cGc/cAc	4/33	1	2	FACETS	0.999	0.938	1	0.999	0.938	1	CLONAL	1	TRUE	1	0.49	2		996	1111	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909629	76909629	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs919106518	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	89	474	1	ENST00000373344.5:c.4276C>T	p.Arg1426Ter	p.R1426*	ENST00000373344	NM_000489.3	1426	Cga/Tga	14/35	1	2	FACETS	0.634	0.563	0.709	0.634	0.563	0.709	SUBCLONAL	1	TRUE	1	0.49	2		475	573	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495360	149495360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs114435947	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	202	773	0	ENST00000261799.4:c.3287C>T	p.Ala1096Val	p.A1096V	ENST00000261799	NM_002609.3	1096	gCg/gTg	23/23	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.49	2		773	771	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900288	101900288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111854391	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	33	404	0	ENST00000374994.4:c.722C>T	p.Ser241Leu	p.S241L	ENST00000374994	NM_004612.2	241	tCg/tTg	4/9	1	2	FACETS	0.286	0.232	0.346	0.286	0.232	0.346	SUBCLONAL	1	TRUE	1	0.49	2		404	471	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	161	537	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.49	2		537	593	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037474	12037474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	32	505	0	ENST00000396373.4:c.1105C>T	p.Arg369Trp	p.R369W	ENST00000396373	NM_001987.4	369	Cgg/Tgg	6/8	0.11969952485356	3	FACETS	0.294	0.237	0.357	0.147	0.118	0.179	INDETERMINATE	1	TRUE	1	0.49	3		505	554	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247028	53247028	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	58	677	0	ENST00000375401.3:c.472G>A	p.Glu158Lys	p.E158K	ENST00000375401	NM_004187.3	158	Gaa/Aaa	4/26	1	2	FACETS	0.245	0.21	0.284	0.245	0.21	0.284	SUBCLONAL	1	TRUE	1	0.49	2		677	965	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938029	76938029	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	141	621	2	ENST00000373344.5:c.2719C>T	p.Arg907Ter	p.R907*	ENST00000373344	NM_000489.3	907	Cga/Tga	9/35	1	2	FACETS	0.877	0.801	0.956	0.877	0.801	0.956	CLONAL	1	TRUE	1	0.49	2		623	656	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126393	5126393	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	105	314	0	ENST00000381652.3:c.3238G>T	p.Glu1080Ter	p.E1080*	ENST00000381652	NM_004972.3	1080	Gaa/Taa	24/25	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.49	2		314	384	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337650	73337650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	33	241	0	ENST00000377767.4:c.2066G>A	p.Arg689Gln	p.R689Q	ENST00000377767	NM_014953.3	689	cGa/cAa	16/21	1	2	FACETS	0.436	0.356	0.526	0.436	0.356	0.526	SUBCLONAL	1	TRUE	1	0.49	2		241	309	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	172	714	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.915	0.844	0.99	0.915	0.844	0.99	CLONAL	1	TRUE	1	0.49	2		714	767	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900171	101900171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564161322	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	18	313	1	ENST00000374994.4:c.605C>T	p.Ala202Val	p.A202V	ENST00000374994	NM_004612.2	202	gCg/gTg	4/9	1	2	FACETS	0.222	0.167	0.287	0.222	0.167	0.287	SUBCLONAL	1	TRUE	1	0.49	2		314	331	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900239	101900239	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564161544	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	37	443	0	ENST00000374994.4:c.673C>T	p.Arg225Trp	p.R225W	ENST00000374994	NM_004612.2	225	Cgg/Tgg	4/9	1	2	FACETS	0.301	0.248	0.361	0.301	0.248	0.361	SUBCLONAL	1	TRUE	1	0.49	2		443	501	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341196	8341196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	22	395	0	ENST00000356435.5:c.5020C>T	p.Arg1674Cys	p.R1674C	ENST00000356435		1674	Cgc/Tgc	30/35	1	2	FACETS	0.218	0.169	0.276	0.218	0.169	0.276	SUBCLONAL	1	TRUE	1	0.49	2		395	411	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440379	52440379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	84	564	0	ENST00000460680.1:c.673G>A	p.Asp225Asn	p.D225N	ENST00000460680	NM_004656.3	225	Gac/Aac	9/17	1	2	FACETS	0.552	0.488	0.621	0.552	0.488	0.621	SUBCLONAL	1	TRUE	1	0.49	2		564	621	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275399	142275399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202162034	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	79	352	0	ENST00000350721.4:c.1904G>A	p.Arg635Gln	p.R635Q	ENST00000350721	NM_001184.3	635	cGa/cAa	9/47	1	2	FACETS	0.888	0.787	0.996	0.888	0.787	0.996	CLONAL	1	TRUE	1	0.49	2		352	363	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657021	47657021	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146567853	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	129	319	0	ENST00000233146.2:c.1217G>A	p.Arg406Gln	p.R406Q	ENST00000233146	NM_000251.2	406	cGa/cAa	7/16	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.49	2		319	504	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532867	187532867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762890230	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	41	452	0	ENST00000441802.2:c.9526G>A	p.Glu3176Lys	p.E3176K	ENST00000441802	NM_005245.3	3176	Gaa/Aaa	14/27	1	2	FACETS	0.281	0.234	0.334	0.281	0.234	0.334	SUBCLONAL	1	TRUE	1	0.49	2		452	595	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012465	29012465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373801409	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	97	446	0	ENST00000282397.4:c.406G>A	p.Val136Ile	p.V136I	ENST00000282397	NM_002019.4	136	Gta/Ata	4/30	1	2	FACETS	0.792	0.709	0.88	0.792	0.709	0.88	SUBCLONAL	1	TRUE	1	0.49	2		446	500	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	142	589	0	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	1	2	FACETS	0.908	0.83	0.99	0.908	0.83	0.99	CLONAL	1	TRUE	1	0.49	2		589	638	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814713	139814713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753016580	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	106	688	0	ENST00000247668.2:c.706G>A	p.Glu236Lys	p.E236K	ENST00000247668	NM_021138.3	236	Gag/Aag	8/11	1	2	FACETS	0.547	0.49	0.607	0.547	0.49	0.607	SUBCLONAL	1	TRUE	1	0.49	2		688	791	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435219	110435219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746894027	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	70	623	0	ENST00000375856.3:c.3182C>T	p.Ser1061Leu	p.S1061L	ENST00000375856	NM_003749.2	1061	tCg/tTg	1/2	1	2	FACETS	0.357	0.311	0.408	0.357	0.311	0.408	SUBCLONAL	1	TRUE	1	0.49	2		623	800	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095836	178095836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1328262363	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	128	447	0	ENST00000397062.3:c.1495C>T	p.Arg499Trp	p.R499W	ENST00000397062	NM_006164.4	499	Cgg/Tgg	5/5	1	2	FACETS	0.931	0.848	1	0.931	0.848	1	CLONAL	1	TRUE	1	0.49	2		447	561	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435061	18435061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603400	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	30	344	0	ENST00000266497.5:c.46G>A	p.Glu16Lys	p.E16K	ENST00000266497		16	Gaa/Aaa	1/31	1	2	FACETS	0.323	0.26	0.394	0.323	0.26	0.394	SUBCLONAL	1	TRUE	1	0.49	2		344	379	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650710	67650710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243010179	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	168	689	0	ENST00000264010.4:c.1015C>T	p.Arg339Trp	p.R339W	ENST00000264010	NM_006565.3	339	Cgg/Tgg	5/12	1	2	FACETS	0.688	0.632	0.747	0.688	0.632	0.747	SUBCLONAL	1	TRUE	1	0.49	2		689	996	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961884	15961884	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs970987519	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	117	376	0	ENST00000268712.3:c.5911G>A	p.Asp1971Asn	p.D1971N	ENST00000268712	NM_006311.3	1971	Gat/Aat	38/46	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.49	2		376	477	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32899248	32899248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375125172	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	53	304	0	ENST00000380152.3:c.352C>T	p.Arg118Cys	p.R118C	ENST00000380152		118	Cgc/Tgc	4/27	1	2	FACETS	0.585	0.5	0.676	0.585	0.5	0.676	SUBCLONAL	1	TRUE	1	0.49	2		304	370	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436149	56436149	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	223	597	0	ENST00000407977.2:c.988C>T	p.Arg330Ter	p.R330*	ENST00000407977		330	Cga/Tga	9/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.49	2		597	801	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906958	32906958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358423	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	43	390	0	ENST00000380152.3:c.1343G>A	p.Arg448His	p.R448H	ENST00000380152		448	cGt/cAt	10/27	1	2	FACETS	0.438	0.367	0.516	0.438	0.367	0.516	SUBCLONAL	1	TRUE	1	0.49	2		390	401	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348535	70348535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	183	606	0	ENST00000374080.3:c.3442C>T	p.Arg1148Cys	p.R1148C	ENST00000374080		1148	Cgc/Tgc	24/45	1	2	FACETS	0.961	0.889	1	0.961	0.889	1	CLONAL	1	TRUE	1	0.49	2		606	777	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	89	344	2	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.951	0.849	1	0.951	0.849	1	CLONAL	1	TRUE	1	0.49	2		346	382	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120360	94120360	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs749418654	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	62	312	0	ENST00000369303.4:c.691C>T	p.Arg231Ter	p.R231*	ENST00000369303	NM_004440.3	231	Cga/Tga	3/17	1	2	FACETS	0.637	0.553	0.729	0.637	0.553	0.729	SUBCLONAL	1	TRUE	1	0.49	2		312	397	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400902	72400902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1450443698	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	100	359	0	ENST00000357731.5:c.269G>A	p.Arg90Gln	p.R90Q	ENST00000357731	NM_173808.2	90	cGa/cAa	2/7	1	2	FACETS	0.991	0.891	1	0.991	0.891	1	CLONAL	1	TRUE	1	0.49	2		359	412	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404693	70404693	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756914683	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	194	535	0	ENST00000373644.4:c.2207C>T	p.Ser736Leu	p.S736L	ENST00000373644	NM_030625.2	736	tCg/tTg	4/12	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.49	2		535	704	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453185	140453185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	80	270	0	ENST00000288602.6:c.1750C>T	p.Leu584Phe	p.L584F	ENST00000288602	NM_004333.4	584	Ctt/Ttt	15/18	1	2	FACETS	0.96	0.852	1	0.96	0.852	1	CLONAL	1	TRUE	1	0.49	2		270	340	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317921	8317921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150063446	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	119	430	1	ENST00000356435.5:c.5692C>T	p.Arg1898Cys	p.R1898C	ENST00000356435		1898	Cgt/Tgt	35/35	1	2	FACETS	0.929	0.842	1	0.929	0.842	1	CLONAL	1	TRUE	1	0.49	2		431	523	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508824	106508824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226994105	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	185	586	0	ENST00000359195.3:c.818G>A	p.Arg273His	p.R273H	ENST00000359195	NM_002649.2	273	cGc/cAc	2/11	1	2	FACETS	0.991	0.917	1	0.991	0.917	1	CLONAL	1	TRUE	1	0.49	2		586	762	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729733	41729733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	37	578	0	ENST00000242208.4:c.796G>A	p.Glu266Lys	p.E266K	ENST00000242208	NM_002192.2	266	Gag/Aag	3/3	1	2	FACETS	0.256	0.21	0.307	0.256	0.21	0.307	SUBCLONAL	1	TRUE	1	0.49	2		578	591	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637690	52637690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239654517	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	29	376	0	ENST00000394830.3:c.2626C>T	p.Arg876Cys	p.R876C	ENST00000394830	NM_018313.4	876	Cgt/Tgt	18/30	1	2	FACETS	0.216	0.173	0.266	0.216	0.173	0.266	SUBCLONAL	1	TRUE	1	0.49	2		376	548	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6031649	6031649	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs200640585	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	46	566	0	ENST00000265849.7:c.943C>T	p.Arg315Ter	p.R315*	ENST00000265849	NM_000535.5	315	Cga/Tga	9/15	1	2	FACETS	0.258	0.217	0.304	0.258	0.217	0.304	SUBCLONAL	1	TRUE	1	0.49	2		566	727	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203791	94203791	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs190142346	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	46	231	0	ENST00000323929.3:c.863G>A	p.Arg288His	p.R288H	ENST00000323929	NM_005591.3	288	cGt/cAt	9/20	1	2	FACETS	0.89	0.758	1	0.89	0.758	1	CLONAL	1	TRUE	1	0.49	2		231	211	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820617	3820617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	123	842	0	ENST00000262367.5:c.2834C>T	p.Ser945Leu	p.S945L	ENST00000262367	NM_004380.2	945	tCg/tTg	14/31	1	2	FACETS	0.42	0.379	0.464	0.42	0.379	0.464	SUBCLONAL	1	TRUE	1	0.49	2		842	1194	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120318	94120318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41273629	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	20	290	0	ENST00000369303.4:c.733G>A	p.Ala245Thr	p.A245T	ENST00000369303	NM_004440.3	245	Gcc/Acc	3/17	1	2	FACETS	0.206	0.157	0.264	0.206	0.157	0.264	SUBCLONAL	1	TRUE	1	0.49	2		290	396	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027043	48027043	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1553413305	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	92	388	0	ENST00000234420.5:c.1921G>T	p.Glu641Ter	p.E641*	ENST00000234420	NM_000179.2	641	Gaa/Taa	4/10	1	2	FACETS	0.873	0.78	0.971	0.873	0.78	0.971	CLONAL	1	TRUE	1	0.49	2		388	430	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74858992	74858992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	133	324	0	ENST00000284811.8:c.212C>T	p.Ser71Leu	p.S71L	ENST00000284811		71	tCg/tTg	4/4	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.49	2		324	408	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950648	38950648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776074870	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	8	339	0	ENST00000357387.3:c.3302C>T	p.Ser1101Leu	p.S1101L	ENST00000357387	NM_152756.3	1101	tCg/tTg	31/38	1	2	FACETS	0.083	0.053	0.122	0.083	0.053	0.122	SUBCLONAL	1	TRUE	1	0.49	2		339	394	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738094	145738094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561220929	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	89	941	2	ENST00000428558.2:c.2816C>T	p.Ala939Val	p.A939V	ENST00000428558	NM_004260.3	939	gCg/gTg	17/22	1	2	FACETS	0.37	0.327	0.416	0.37	0.327	0.416	SUBCLONAL	1	TRUE	1	0.49	2		943	982	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562641	29562641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854562	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	117	388	0	ENST00000356175.3:c.3721C>T	p.Arg1241Ter	p.R1241*	ENST00000356175	NM_000267.3	1241	Cga/Tga	28/57	1	2	FACETS	0.871	0.789	0.958	0.871	0.789	0.958	CLONAL	1	TRUE	1	0.49	2		388	548	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437275	220437275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370513243	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	76	1034	3	ENST00000243786.2:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000243786	NM_002191.3	60	cGa/cAa	1/2	1	2	FACETS	0.251	0.219	0.286	0.251	0.219	0.286	SUBCLONAL	1	TRUE	1	0.49	2		1037	1234	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	159	481	0	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	1	2	FACETS	0.976	0.897	1	0.976	0.897	1	CLONAL	1	TRUE	1	0.49	2		481	665	SUCCESS
RET	5979	MSKCC	GRCh37	10	43598056	43598056	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751572082	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	77	678	1	ENST00000355710.3:c.604G>A	p.Val202Met	p.V202M	ENST00000355710	NM_020975.4	202	Gtg/Atg	3/20	1	2	FACETS	0.364	0.318	0.413	0.364	0.318	0.413	SUBCLONAL	1	TRUE	1	0.49	2		679	864	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371797	116371797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774779741	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	58	434	1	ENST00000397752.3:c.1276C>T	p.Arg426Cys	p.R426C	ENST00000397752	NM_000245.2	426	Cgc/Tgc	3/21	1	2	FACETS	0.353	0.302	0.408	0.353	0.302	0.408	SUBCLONAL	1	TRUE	1	0.49	2		435	671	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024169	112024169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465963577	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	38	458	0	ENST00000368678.4:c.616C>T	p.Arg206Cys	p.R206C	ENST00000368678		206	Cgc/Tgc	7/13	1	2	FACETS	0.275	0.227	0.329	0.275	0.227	0.329	SUBCLONAL	1	TRUE	1	0.49	2		458	564	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228018	53228018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199422238	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	201	836	1	ENST00000375401.3:c.2296C>T	p.Arg766Trp	p.R766W	ENST00000375401	NM_004187.3	766	Cgg/Tgg	16/26	1	2	FACETS	0.844	0.782	0.908	0.844	0.782	0.908	CLONAL	1	TRUE	1	0.49	2		837	972	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521544	8521544	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	60	486	0	ENST00000356435.5:c.694C>T	p.Arg232Cys	p.R232C	ENST00000356435		232	Cgc/Tgc	9/35	1	2	FACETS	0.384	0.33	0.442	0.384	0.33	0.442	SUBCLONAL	1	TRUE	1	0.49	2		486	638	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124717	108124717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751515818	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	101	363	0	ENST00000278616.4:c.2075G>A	p.Arg692His	p.R692H	ENST00000278616	NM_000051.3	692	cGc/cAc	13/63	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.49	2		363	390	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636719	176636719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140095431	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	151	503	1	ENST00000439151.2:c.1319G>A	p.Arg440Gln	p.R440Q	ENST00000439151	NM_022455.4	440	cGa/cAa	5/23	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.49	2		504	593	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692940	89692940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746152219	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	171	572	0	ENST00000371953.3:c.424C>T	p.Arg142Trp	p.R142W	ENST00000371953	NM_000314.4	142	Cgg/Tgg	5/9	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.49	2		572	601	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041624	47041624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	84	780	0	ENST00000377604.3:c.1849C>T	p.Pro617Ser	p.P617S	ENST00000377604	NM_001204468.1	617	Ccc/Tcc	17/24	1	2	FACETS	0.384	0.338	0.433	0.384	0.338	0.433	SUBCLONAL	1	TRUE	1	0.49	2		780	893	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456497	99456497	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45553041	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	51	382	0	ENST00000268035.6:c.1814G>A	p.Arg605His	p.R605H	ENST00000268035	NM_000875.3	605	cGc/cAc	8/21	1	2	FACETS	0.446	0.379	0.519	0.446	0.379	0.519	SUBCLONAL	1	TRUE	1	0.49	2		382	467	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430786	181430786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	63	903	0	ENST00000325404.1:c.638C>T	p.Ser213Leu	p.S213L	ENST00000325404	NM_003106.3	213	tCg/tTg	1/1	1	2	FACETS	0.254	0.219	0.293	0.254	0.219	0.293	SUBCLONAL	1	TRUE	1	0.49	2		903	1012	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629400	187629400	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1018407179	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	51	796	0	ENST00000441802.2:c.1582G>A	p.Glu528Lys	p.E528K	ENST00000441802	NM_005245.3	528	Gaa/Aaa	2/27	1	2	FACETS	0.211	0.178	0.247	0.211	0.178	0.247	SUBCLONAL	1	TRUE	1	0.49	2		796	987	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513352	41513352	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	196	580	2	ENST00000263253.7:c.256C>T	p.Arg86Ter	p.R86*	ENST00000263253	NM_001429.3	86	Cga/Tga	2/31	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.49	2		582	800	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125634	47125634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1357325164	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	57	395	0	ENST00000409792.3:c.5636G>A	p.Arg1879His	p.R1879H	ENST00000409792	NM_014159.6	1879	cGc/cAc	12/21	1	2	FACETS	0.46	0.395	0.531	0.46	0.395	0.531	SUBCLONAL	1	TRUE	1	0.49	2		395	506	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957133	81957133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1476399695	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	199	587	0	ENST00000359376.3:c.2351G>A	p.Arg784Gln	p.R784Q	ENST00000359376	NM_002661.3	784	cGa/cAa	22/33	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.49	2		587	729	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136279	202136279	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	66	529	1	ENST00000358485.4:c.523G>T	p.Glu175Ter	p.E175*	ENST00000358485	NM_001080125.1	175	Gaa/Taa	3/9	1	2	FACETS	0.39	0.338	0.447	0.39	0.338	0.447	SUBCLONAL	1	TRUE	1	0.49	2		530	690	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729807	41729807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756546726	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	82	469	0	ENST00000242208.4:c.722G>A	p.Arg241Gln	p.R241Q	ENST00000242208	NM_002192.2	241	cGg/cAg	3/3	1	2	FACETS	0.723	0.64	0.811	0.723	0.64	0.811	SUBCLONAL	1	TRUE	1	0.49	2		469	463	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279465	1279465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866767063	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	250	891	0	ENST00000310581.5:c.2071C>T	p.Arg691Cys	p.R691C	ENST00000310581	NM_198253.2	691	Cgc/Tgc	5/16	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.49	2		891	989	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463578	25463578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770938712	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	233	655	2	ENST00000264709.3:c.2104G>A	p.Asp702Asn	p.D702N	ENST00000264709	NM_175629.2	702	Gat/Aat	18/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.49	2		657	800	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380346	14380346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	135	325	0	ENST00000256196.4:c.71G>A	p.Gly24Asp	p.G24D	ENST00000256196		24	gGc/gAc	1/6	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.49	2		325	539	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434122	12434122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1170672782	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	24	295	0	ENST00000287820.6:c.490C>T	p.Arg164Trp	p.R164W	ENST00000287820	NM_015869.4	164	Cgg/Tgg	4/7	1	2	FACETS	0.249	0.195	0.312	0.249	0.195	0.312	SUBCLONAL	1	TRUE	1	0.49	2		295	393	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630870	187630870	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751034262	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	193	543	0	ENST00000441802.2:c.112G>A	p.Glu38Lys	p.E38K	ENST00000441802	NM_005245.3	38	Gag/Aag	2/27	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.49	2		543	758	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965472	68965472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200682883	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	84	700	0	ENST00000288368.4:c.1084C>T	p.Arg362Trp	p.R362W	ENST00000288368	NM_024870.2	362	Cgg/Tgg	9/40	1	2	FACETS	0.485	0.428	0.546	0.485	0.428	0.546	SUBCLONAL	1	TRUE	1	0.49	2		700	707	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912075	56912075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	82	741	2	ENST00000519728.1:c.1303G>A	p.Glu435Lys	p.E435K	ENST00000519728	NM_002350.3	435	Gaa/Aaa	12/13	1	2	FACETS	0.43	0.379	0.486	0.43	0.379	0.486	SUBCLONAL	1	TRUE	1	0.49	2		743	778	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931862	68931862	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200600940	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	81	613	0	ENST00000288368.4:c.292G>A	p.Glu98Lys	p.E98K	ENST00000288368	NM_024870.2	98	Gaa/Aaa	3/40	1	2	FACETS	0.428	0.377	0.484	0.428	0.377	0.484	SUBCLONAL	1	TRUE	1	0.49	2		613	772	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495351	149495351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373655593	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	81	731	2	ENST00000261799.4:c.3296C>T	p.Ala1099Val	p.A1099V	ENST00000261799	NM_002609.3	1099	gCg/gTg	23/23	1	2	FACETS	0.46	0.405	0.52	0.46	0.405	0.52	SUBCLONAL	1	TRUE	1	0.49	2		733	718	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982134	93982134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773950345	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	41	290	0	ENST00000369303.4:c.1331C>T	p.Ser444Leu	p.S444L	ENST00000369303	NM_004440.3	444	tCg/tTg	6/17	1	2	FACETS	0.386	0.321	0.457	0.386	0.321	0.457	SUBCLONAL	1	TRUE	1	0.49	2		290	434	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153601	108153601	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	39	141	0	ENST00000278616.4:c.3741C>A	p.Phe1247Leu	p.F1247L	ENST00000278616	NM_000051.3	1247	ttC/ttA	25/63	1	2	FACETS	0.965	0.812	1	0.965	0.812	1	CLONAL	1	TRUE	1	0.49	2		141	165	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143065	58143065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531817742	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	251	800	0	ENST00000257904.6:c.719G>A	p.Arg240Gln	p.R240Q	ENST00000257904	NM_000075.3	240	cGa/cAa	7/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.49	2		800	955	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828503	72828503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	70	715	0	ENST00000268489.5:c.8078G>A	p.Arg2693Gln	p.R2693Q	ENST00000268489	NM_006885.3	2693	cGa/cAa	9/10	1	2	FACETS	0.315	0.274	0.36	0.315	0.274	0.36	SUBCLONAL	1	TRUE	1	0.49	2		715	906	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30302690	30302690	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	57	496	0	ENST00000322652.5:c.781G>T	p.Glu261Ter	p.E261*	ENST00000322652	NM_015355.2	261	Gag/Tag	7/16	1	2	FACETS	0.343	0.293	0.397	0.343	0.293	0.397	SUBCLONAL	1	TRUE	1	0.49	2		496	679	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267569	7267569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	103	838	0	ENST00000302850.5:c.439G>A	p.Glu147Lys	p.E147K	ENST00000302850	NM_000208.2	147	Gag/Aag	2/22	1	2	FACETS	0.405	0.362	0.452	0.405	0.362	0.452	SUBCLONAL	1	TRUE	1	0.49	2		838	1037	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799799	72799799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779590242	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	159	633	0	ENST00000325599.8:c.1370C>T	p.Ser457Leu	p.S457L	ENST00000325599	NM_018130.2	457	tCg/tTg	11/11	1	2	FACETS	0.878	0.807	0.953	0.878	0.807	0.953	CLONAL	1	TRUE	1	0.49	2		633	739	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38157028	38157028	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	191	719	0	ENST00000317025.8:c.2692C>T	p.Arg898Cys	p.R898C	ENST00000317025	NM_023034.1	898	Cgt/Tgt	15/24	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.49	2		719	672	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793317	139793317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755436517	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	113	755	1	ENST00000247668.2:c.125G>A	p.Arg42His	p.R42H	ENST00000247668	NM_021138.3	42	cGc/cAc	2/11	1	2	FACETS	0.479	0.431	0.531	0.479	0.431	0.531	SUBCLONAL	1	TRUE	1	0.49	2		756	962	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100133	30100133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370296777	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	103	683	0	ENST00000331968.5:c.1487C>T	p.Thr496Met	p.T496M	ENST00000331968	NM_002742.2	496	aCg/aTg	10/18	1	2	FACETS	0.472	0.421	0.525	0.472	0.421	0.525	SUBCLONAL	1	TRUE	1	0.49	2		683	891	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630251	187630251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773192852	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	144	596	0	ENST00000441802.2:c.731C>T	p.Thr244Met	p.T244M	ENST00000441802	NM_005245.3	244	aCg/aTg	2/27	1	2	FACETS	0.934	0.855	1	0.934	0.855	1	CLONAL	1	TRUE	1	0.49	2		596	629	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111134	193111134	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	45	385	0	ENST00000367435.3:c.667G>T	p.Asp223Tyr	p.D223Y	ENST00000367435	NM_024529.4	223	Gat/Tat	7/17	1	2	FACETS	0.45	0.379	0.529	0.45	0.379	0.529	SUBCLONAL	1	TRUE	1	0.49	2		385	408	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206943236	206943236	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs766492258	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	32	333	0	ENST00000423557.1:c.382C>T	p.Arg128Ter	p.R128*	ENST00000423557	NM_000572.2	128	Cga/Tga	4/5	1	2	FACETS	0.267	0.216	0.324	0.267	0.216	0.324	SUBCLONAL	1	TRUE	1	0.49	2		333	490	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100301	27100301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	46	714	0	ENST00000324856.7:c.4013C>T	p.Ser1338Phe	p.S1338F	ENST00000324856	NM_006015.4	1338	tCc/tTc	17/20	1	2	FACETS	0.23	0.192	0.271	0.23	0.192	0.271	SUBCLONAL	1	TRUE	1	0.49	2		714	818	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807914	3807914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	145	585	0	ENST00000262367.5:c.3505C>T	p.Arg1169Cys	p.R1169C	ENST00000262367	NM_004380.2	1169	Cgc/Tgc	18/31	1	2	FACETS	0.841	0.769	0.916	0.841	0.769	0.916	CLONAL	1	TRUE	1	0.49	2		585	704	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638731	176638731	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151165525	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	91	691	1	ENST00000439151.2:c.3331G>A	p.Asp1111Asn	p.D1111N	ENST00000439151	NM_022455.4	1111	Gat/Aat	5/23	1	2	FACETS	0.456	0.404	0.511	0.456	0.404	0.511	SUBCLONAL	1	TRUE	1	0.49	2		692	815	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023085	150023085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771059780	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	165	670	0	ENST00000253339.5:c.178G>A	p.Glu60Lys	p.E60K	ENST00000253339		60	Gaa/Aaa	1/7	1	2	FACETS	0.943	0.868	1	0.943	0.868	1	CLONAL	1	TRUE	1	0.49	2		670	714	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026133	71026133	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs775136381	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	35	362	0	ENST00000318789.4:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000318789	NM_032682.5	497	Cga/Tga	17/21	1	2	FACETS	0.224	0.182	0.27	0.224	0.182	0.27	SUBCLONAL	1	TRUE	1	0.49	2		362	639	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162959	47162959	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776300341	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	136	367	0	ENST00000409792.3:c.3167C>T	p.Ser1056Leu	p.S1056L	ENST00000409792	NM_014159.6	1056	tCg/tTg	3/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.49	2		367	467	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754575	57754575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751788063	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	23	359	0	ENST00000274289.3:c.472C>T	p.Leu158Phe	p.L158F	ENST00000274289	NM_006622.3	158	Ctc/Ttc	3/14	1	2	FACETS	0.204	0.158	0.257	0.204	0.158	0.257	SUBCLONAL	1	TRUE	1	0.49	2		359	460	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224529	224529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370481102	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	34	444	0	ENST00000264932.6:c.205G>A	p.Ala69Thr	p.A69T	ENST00000264932	NM_004168.2	69	Gct/Act	3/15	1	2	FACETS	0.213	0.173	0.257	0.213	0.173	0.257	SUBCLONAL	1	TRUE	1	0.49	2		444	653	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94209542	94209542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746932208	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	37	274	0	ENST00000323929.3:c.572G>A	p.Arg191Gln	p.R191Q	ENST00000323929	NM_005591.3	191	cGa/cAa	7/20	1	2	FACETS	0.369	0.304	0.442	0.369	0.304	0.442	SUBCLONAL	1	TRUE	1	0.49	2		274	409	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273209	115273209	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs990081919	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	45	569	0	ENST00000438362.2:c.1249C>T	p.Arg417Cys	p.R417C	ENST00000438362	NM_001242891.1	417	Cgt/Tgt	11/20	1	2	FACETS	0.291	0.244	0.343	0.291	0.244	0.343	SUBCLONAL	1	TRUE	1	0.49	2		569	631	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285173	212285173	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754420079	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	19	437	0	ENST00000342788.4:c.3128C>T	p.Ser1043Leu	p.S1043L	ENST00000342788	NM_005235.2	1043	tCg/tTg	25/28	1	2	FACETS	0.219	0.166	0.282	0.219	0.166	0.282	SUBCLONAL	1	TRUE	1	0.49	2		437	354	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233141	66233141	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs146757388	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	133	402	0	ENST00000273854.3:c.1858C>T	p.Arg620Trp	p.R620W	ENST00000273854	NM_004439.5	620	Cgg/Tgg	10/18	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.49	2		402	441	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422908	12422908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267599576	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	51	657	0	ENST00000287820.6:c.398C>T	p.Ser133Phe	p.S133F	ENST00000287820	NM_015869.4	133	tCc/tTc	3/7	1	2	FACETS	0.299	0.253	0.349	0.299	0.253	0.349	SUBCLONAL	1	TRUE	1	0.49	2		657	697	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652995	29652996	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1135402867	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	32	543	0	ENST00000356175.3:c.4935dup	p.Pro1646SerfsTer15	p.P1646Sfs*15	ENST00000356175	NM_000267.3	1644	gtt/gTtt	36/57	1	2	FACETS	0.218	0.176	0.266	0.218	0.176	0.266	SUBCLONAL	1	TRUE	1	0.49	2		543	598	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12653459	12653459	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs896491732	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	121	424	0	ENST00000251849.4:c.310G>A	p.Glu104Lys	p.E104K	ENST00000251849	NM_002880.3	104	Gaa/Aaa	3/17	1	2	FACETS	0.988	0.897	1	0.988	0.897	1	CLONAL	1	TRUE	1	0.49	2		424	500	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066740	5066740	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777015472	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	103	339	0	ENST00000381652.3:c.1277G>A	p.Arg426Gln	p.R426Q	ENST00000381652	NM_004972.3	426	cGa/cAa	10/25	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.49	2		339	405	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39237759	39237759	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	46	348	0	ENST00000402219.2:c.2476C>T	p.Arg826Ter	p.R826*	ENST00000402219	NM_005633.3	826	Cga/Tga	15/23	1	2	FACETS	0.341	0.286	0.401	0.341	0.286	0.401	SUBCLONAL	1	TRUE	1	0.49	2		348	551	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316076	14316076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782490571	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	82	287	0	ENST00000256196.4:c.349C>T	p.Arg117Cys	p.R117C	ENST00000256196		117	Cgt/Tgt	4/6	1	2	FACETS	0.94	0.835	1	0.94	0.835	1	CLONAL	1	TRUE	1	0.49	2		287	356	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252328	133252328	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	177	501	0	ENST00000320574.5:c.1099T>G	p.Phe367Val	p.F367V	ENST00000320574	NM_006231.2	367	Ttt/Gtt	11/49	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.49	2		501	705	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39638012	39638012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs893280651	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	143	621	1	ENST00000262039.4:c.2429G>A	p.Arg810Gln	p.R810Q	ENST00000262039	NM_002647.2	810	cGa/cAa	22/25	1	2	FACETS	0.871	0.796	0.949	0.871	0.796	0.949	CLONAL	1	TRUE	1	0.49	2		622	670	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026124	48026124	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	109	388	0	ENST00000234420.5:c.1002G>T	p.Lys334Asn	p.K334N	ENST00000234420	NM_000179.2	334	aaG/aaT	4/10	1	2	FACETS	0.833	0.751	0.92	0.833	0.751	0.92	CLONAL	1	TRUE	1	0.49	2		388	534	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808294	99808294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	31	387	1	ENST00000280892.6:c.395G>A	p.Arg132Gln	p.R132Q	ENST00000280892	NM_001130678.1	132	cGa/cAa	5/7	1	2	FACETS	0.292	0.235	0.355	0.292	0.235	0.355	SUBCLONAL	1	TRUE	1	0.49	2		388	434	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426771	212426771	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879060634	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	167	524	0	ENST00000342788.4:c.2344C>T	p.Arg782Trp	p.R782W	ENST00000342788	NM_005235.2	782	Cgg/Tgg	20/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.49	2		524	619	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271637	15271637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs996150018	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	86	1106	0	ENST00000263388.2:c.6802G>A	p.Glu2268Lys	p.E2268K	ENST00000263388	NM_000435.2	2268	Gaa/Aaa	33/33	1	2	FACETS	0.284	0.25	0.321	0.284	0.25	0.321	SUBCLONAL	1	TRUE	1	0.49	2		1106	1236	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951109	17951109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143038064	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	84	784	1	ENST00000458235.1:c.1184G>A	p.Arg395His	p.R395H	ENST00000458235	NM_000215.3	395	cGt/cAt	9/24	1	2	FACETS	0.301	0.265	0.34	0.301	0.265	0.34	SUBCLONAL	1	TRUE	1	0.49	2		785	1138	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120469211	120469211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs116408209	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	63	538	0	ENST00000256646.2:c.3916G>A	p.Asp1306Asn	p.D1306N	ENST00000256646	NM_024408.3	1306	Gat/Aat	24/34	1	2	FACETS	0.319	0.275	0.366	0.319	0.275	0.366	SUBCLONAL	1	TRUE	1	0.49	2		538	807	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934623	9934623	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267604688	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	140	411	0	ENST00000330684.3:c.1532C>T	p.Ser511Leu	p.S511L	ENST00000330684	NM_001134407.1	511	tCg/tTg	7/13	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.49	2		411	528	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176430	123176430	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150057715	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	34	236	0	ENST00000218089.9:c.397G>A	p.Ala133Thr	p.A133T	ENST00000218089	NM_001042749.1	133	Gca/Aca	7/35	1	2	FACETS	0.43	0.352	0.517	0.43	0.352	0.517	SUBCLONAL	1	TRUE	1	0.49	2		236	323	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150232	108150232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs189445371	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	38	437	0	ENST00000278616.4:c.3299C>T	p.Thr1100Met	p.T1100M	ENST00000278616	NM_000051.3	1100	aCg/aTg	23/63	1	2	FACETS	0.293	0.241	0.35	0.293	0.241	0.35	SUBCLONAL	1	TRUE	1	0.49	2		437	530	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797271	135797271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs118203410	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	23	353	1	ENST00000298552.3:c.598G>A	p.Val200Ile	p.V200I	ENST00000298552	NM_001162426.1	200	Gtc/Atc	7/23	1	2	FACETS	0.219	0.17	0.276	0.219	0.17	0.276	SUBCLONAL	1	TRUE	1	0.49	2		354	428	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916551	39916551	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	200	751	0	ENST00000378444.4:c.4452G>T	p.Glu1484Asp	p.E1484D	ENST00000378444	NM_001123385.1	1484	gaG/gaT	11/15	1	2	FACETS	0.953	0.884	1	0.953	0.884	1	CLONAL	1	TRUE	1	0.49	2		751	857	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710875	117710875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140178288	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	59	446	0	ENST00000368508.3:c.1397G>A	p.Arg466Gln	p.R466Q	ENST00000368508	NM_002944.2	466	cGa/cAa	12/43	1	2	FACETS	0.432	0.372	0.498	0.432	0.372	0.498	SUBCLONAL	1	TRUE	1	0.49	2		446	557	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662453	67662453	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs879255516	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	112	644	0	ENST00000264010.4:c.1699C>T	p.Arg567Trp	p.R567W	ENST00000264010	NM_006565.3	567	Cgg/Tgg	9/12	1	2	FACETS	0.452	0.406	0.502	0.452	0.406	0.502	SUBCLONAL	1	TRUE	1	0.49	2		644	1011	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740231	162740231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773598662	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	119	531	0	ENST00000367921.3:c.1433G>A	p.Arg478His	p.R478H	ENST00000367921	NM_006182.2	478	cGc/cAc	12/18	1	2	FACETS	0.781	0.706	0.859	0.781	0.706	0.859	SUBCLONAL	1	TRUE	1	0.49	2		531	622	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880126	151880126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146495785	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	140	401	0	ENST00000262189.6:c.5198C>T	p.Ser1733Leu	p.S1733L	ENST00000262189	NM_170606.2	1733	tCg/tTg	35/59	1	2	FACETS	0.996	0.911	1	0.996	0.911	1	CLONAL	1	TRUE	1	0.49	2		401	574	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342932	118342932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	92	388	0	ENST00000534358.1:c.1058G>A	p.Arg353Gln	p.R353Q	ENST00000534358	NM_005933.3	353	cGa/cAa	3/36	1	2	FACETS	0.916	0.819	1	0.916	0.819	1	CLONAL	1	TRUE	1	0.49	2		388	410	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683754	162683754	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	169	503	0	ENST00000366898.1:c.215G>T	p.Arg72Ile	p.R72I	ENST00000366898	NM_004562.2	72	aGa/aTa	3/12	1	2	FACETS	0.983	0.906	1	0.983	0.906	1	CLONAL	1	TRUE	1	0.49	2		503	702	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118806	115118806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754023417	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	72	573	0	ENST00000257566.3:c.535G>A	p.Glu179Lys	p.E179K	ENST00000257566	NM_016569.3	179	Gaa/Aaa	2/8	1	2	FACETS	0.384	0.334	0.437	0.384	0.334	0.437	SUBCLONAL	1	TRUE	1	0.49	2		573	766	SUCCESS
APC	324	MSKCC	GRCh37	5	112178633	112178633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561614782	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	39	388	0	ENST00000257430.4:c.7342C>T	p.Pro2448Ser	p.P2448S	ENST00000257430	NM_000038.5	2448	Cca/Tca	16/16	1	2	FACETS	0.442	0.367	0.525	0.442	0.367	0.525	SUBCLONAL	1	TRUE	1	0.49	2		388	360	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893590	28893590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752645756	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	35	443	0	ENST00000282397.4:c.3256G>A	p.Gly1086Arg	p.G1086R	ENST00000282397	NM_002019.4	1086	Gga/Aga	24/30	1	2	FACETS	0.245	0.2	0.296	0.245	0.2	0.296	SUBCLONAL	1	TRUE	1	0.49	2		443	582	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867575	45867575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777291413	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	286	972	1	ENST00000391945.4:c.733G>A	p.Asp245Asn	p.D245N	ENST00000391945	NM_000400.3	245	Gac/Aac	9/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.49	2		973	1064	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390715	118390715	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	114	402	0	ENST00000534358.1:c.11365C>T	p.Arg3789Cys	p.R3789C	ENST00000534358	NM_005933.3	3789	Cgt/Tgt	33/36	1	2	FACETS	0.772	0.696	0.851	0.772	0.696	0.851	SUBCLONAL	1	TRUE	1	0.49	2		402	603	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443481	49443481	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781156556	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	40	558	0	ENST00000301067.7:c.3890G>A	p.Arg1297His	p.R1297H	ENST00000301067	NM_003482.3	1297	cGt/cAt	11/54	1	2	FACETS	0.24	0.199	0.286	0.24	0.199	0.286	SUBCLONAL	1	TRUE	1	0.49	2		558	680	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879486	151879486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	157	452	0	ENST00000262189.6:c.5459C>T	p.Ser1820Phe	p.S1820F	ENST00000262189	NM_170606.2	1820	tCt/tTt	36/59	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.49	2		452	566	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240761	55240761	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1231769201	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	70	887	1	ENST00000275493.2:c.2005C>T	p.Arg669Ter	p.R669*	ENST00000275493	NM_005228.3	669	Cga/Tga	17/28	1	2	FACETS	0.269	0.234	0.308	0.269	0.234	0.308	SUBCLONAL	1	TRUE	1	0.49	2		888	1061	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591007	67591007	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	56	221	1	ENST00000274335.5:c.1600C>T	p.Arg534Ter	p.R534*	ENST00000274335		534	Cga/Tga	12/15	1	2	FACETS	0.989	0.858	1	0.989	0.858	1	CLONAL	1	TRUE	1	0.49	2		222	231	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131315	202131315	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	124	491	1	ENST00000358485.4:c.283G>T	p.Glu95Ter	p.E95*	ENST00000358485	NM_001080125.1	95	Gaa/Taa	2/9	1	2	FACETS	0.896	0.814	0.982	0.896	0.814	0.982	CLONAL	1	TRUE	1	0.49	2		492	565	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877425	40877425	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	45	607	0	ENST00000373198.4:c.2271G>T	p.Glu757Asp	p.E757D	ENST00000373198	NM_133170.3	757	gaG/gaT	15/32	1	2	FACETS	0.227	0.19	0.269	0.227	0.19	0.269	SUBCLONAL	1	TRUE	1	0.49	2		607	808	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130067	143130067	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	128	385	0	ENST00000262992.4:c.949G>T	p.Glu317Ter	p.E317*	ENST00000262992	NM_001101669.1	317	Gaa/Taa	11/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.49	2		385	429	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119666149	119666149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762056483	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	26	390	1	ENST00000316626.5:c.332G>A	p.Arg111Gln	p.R111Q	ENST00000316626		111	cGa/cAa	3/12	1	2	FACETS	0.235	0.185	0.292	0.235	0.185	0.292	SUBCLONAL	1	TRUE	1	0.49	2		391	452	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879228	151879228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200152380	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	138	512	0	ENST00000262189.6:c.5717G>A	p.Arg1906Gln	p.R1906Q	ENST00000262189	NM_170606.2	1906	cGa/cAa	36/59	1	2	FACETS	0.942	0.86	1	0.942	0.86	1	CLONAL	1	TRUE	1	0.49	2		512	598	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033865	49033865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369755801	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	64	450	0	ENST00000267163.4:c.2002C>T	p.Arg668Cys	p.R668C	ENST00000267163	NM_000321.2	668	Cgc/Tgc	20/27	1	2	FACETS	0.45	0.389	0.515	0.45	0.389	0.515	SUBCLONAL	1	TRUE	1	0.49	2		450	581	SUCCESS
AR	367	MSKCC	GRCh37	X	66766259	66766259	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs780162524	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	129	564	0	ENST00000374690.3:c.1271C>A	p.Ser424Tyr	p.S424Y	ENST00000374690	NM_000044.3	424	tCt/tAt	1/8	1	2	FACETS	0.9	0.819	0.985	0.9	0.819	0.985	CLONAL	1	TRUE	1	0.49	2		564	585	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705261	52705261	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770424653	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	42	568	0	ENST00000322088.6:c.143G>A	p.Arg48Gln	p.R48Q	ENST00000322088	NM_014225.5	48	cGa/cAa	2/15	1	2	FACETS	0.22	0.183	0.262	0.22	0.183	0.262	SUBCLONAL	1	TRUE	1	0.49	2		568	778	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952012	178952012	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	74	398	0	ENST00000263967.3:c.3067C>T	p.Arg1023Ter	p.R1023*	ENST00000263967	NM_006218.2	1023	Cga/Tga	21/21	1	2	FACETS	0.803	0.707	0.905	0.803	0.707	0.905	CLONAL	1	TRUE	1	0.49	2		398	376	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918482	94918482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368962287	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	103	506	1	ENST00000536441.1:c.700G>A	p.Val234Ile	p.V234I	ENST00000536441	NM_144665.3	234	Gtt/Att	5/10	1	2	FACETS	0.818	0.735	0.905	0.818	0.735	0.905	CLONAL	1	TRUE	1	0.49	2		507	514	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026513	6026513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780044	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	60	705	1	ENST00000265849.7:c.1883G>A	p.Arg628Gln	p.R628Q	ENST00000265849	NM_000535.5	628	cGa/cAa	11/15	1	2	FACETS	0.254	0.218	0.293	0.254	0.218	0.293	SUBCLONAL	1	TRUE	1	0.49	2		706	965	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368470	225368470	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	44	290	0	ENST00000264414.4:c.1276G>T	p.Asp426Tyr	p.D426Y	ENST00000264414	NM_003590.4	426	Gat/Tat	9/16	1	2	FACETS	0.412	0.346	0.485	0.412	0.346	0.485	SUBCLONAL	1	TRUE	1	0.49	2		290	436	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163313548	163313548	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	12	165	0	ENST00000271452.3:c.695C>A	p.Ser232Tyr	p.S232Y	ENST00000271452	NM_145697.2	232	tCt/tAt	10/14	1	2	FACETS	0.206	0.144	0.282	0.206	0.144	0.282	SUBCLONAL	1	TRUE	1	0.49	2		165	238	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266472	41266472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	32	446	0	ENST00000349496.5:c.269G>A	p.Arg90Gln	p.R90Q	ENST00000349496	NM_001904.3	90	cGa/cAa	4/15	1	2	FACETS	0.238	0.193	0.29	0.238	0.193	0.29	SUBCLONAL	1	TRUE	1	0.49	2		446	548	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245683	41245683	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56039126	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	44	631	2	ENST00000357654.3:c.1865C>T	p.Ala622Val	p.A622V	ENST00000357654	NM_007294.3	622	gCg/gTg	10/23	1	2	FACETS	0.243	0.203	0.288	0.243	0.203	0.288	SUBCLONAL	1	TRUE	1	0.49	2		633	739	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937713	17937713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752088869	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	49	560	0	ENST00000458235.1:c.3214G>A	p.Glu1072Lys	p.E1072K	ENST00000458235	NM_000215.3	1072	Gag/Aag	24/24	1	2	FACETS	0.294	0.248	0.344	0.294	0.248	0.344	SUBCLONAL	1	TRUE	1	0.49	2		560	681	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074431	8074431	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	99	371	0	ENST00000377482.5:c.228G>T	p.Met76Ile	p.M76I	ENST00000377482	NM_018948.3	76	atG/atT	4/4	1	2	FACETS	0.998	0.897	1	0.998	0.897	1	CLONAL	1	TRUE	1	0.49	2		371	405	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255380	16255380	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368635957	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	86	564	1	ENST00000375759.3:c.2645G>A	p.Arg882Gln	p.R882Q	ENST00000375759	NM_015001.2	882	cGa/cAa	11/15	1	2	FACETS	0.454	0.401	0.51	0.454	0.401	0.51	SUBCLONAL	1	TRUE	1	0.49	2		565	774	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17354346	17354346	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	20	344	0	ENST00000375499.3:c.438C>A	p.Phe146Leu	p.F146L	ENST00000375499	NM_003000.2	146	ttC/ttA	5/8	1	2	FACETS	0.206	0.157	0.263	0.206	0.157	0.263	SUBCLONAL	1	TRUE	1	0.49	2		344	397	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363634	40363634	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	34	442	0	ENST00000397332.2:c.595G>T	p.Glu199Ter	p.E199*	ENST00000397332	NM_001033082.2	199	Gaa/Taa	3/3	1	2	FACETS	0.236	0.192	0.285	0.236	0.192	0.285	SUBCLONAL	1	TRUE	1	0.49	2		442	589	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313318	65313318	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	180	548	0	ENST00000342505.4:c.1796C>A	p.Ser599Tyr	p.S599Y	ENST00000342505	NM_002227.2	599	tCt/tAt	13/25	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.49	2		548	699	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262316	115262317	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	124	442	1	ENST00000438362.2:c.2237dup	p.His747ProfsTer10	p.H747Pfs*10	ENST00000438362	NM_001242891.1	746	ttc/ttTc	18/20	1	2	FACETS	0.91	0.827	0.997	0.91	0.827	0.997	CLONAL	1	TRUE	1	0.49	2		443	556	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273248	115273248	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	152	493	0	ENST00000438362.2:c.1210G>T	p.Asp404Tyr	p.D404Y	ENST00000438362	NM_001242891.1	404	Gat/Tat	11/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.49	2		493	569	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458503	120458503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	74	687	0	ENST00000256646.2:c.6842G>A	p.Gly2281Asp	p.G2281D	ENST00000256646	NM_024408.3	2281	gGc/gAc	34/34	1	2	FACETS	0.464	0.406	0.526	0.464	0.406	0.526	SUBCLONAL	1	TRUE	1	0.49	2		687	651	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497808	120497808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782169028	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	41	661	0	ENST00000256646.2:c.2074C>T	p.Arg692Cys	p.R692C	ENST00000256646	NM_024408.3	692	Cgc/Tgc	13/34	1	2	FACETS	0.245	0.203	0.291	0.245	0.203	0.291	SUBCLONAL	1	TRUE	1	0.49	2		661	684	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851339	156851339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760974854	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	243	848	0	ENST00000524377.1:c.2296C>T	p.Arg766Trp	p.R766W	ENST00000524377	NM_002529.3	766	Cgg/Tgg	17/17	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.49	2		848	922	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956116	175956116	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	133	421	0	ENST00000367669.3:c.2096T>G	p.Phe699Cys	p.F699C	ENST00000367669	NM_022457.5	699	tTt/tGt	18/20	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.49	2		421	525	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091441	193091441	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	124	513	0	ENST00000367435.3:c.111G>T	p.Lys37Asn	p.K37N	ENST00000367435	NM_024529.4	37	aaG/aaT	1/17	1	2	FACETS	0.768	0.696	0.843	0.768	0.696	0.843	SUBCLONAL	1	TRUE	1	0.49	2		513	659	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248646	8248646	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	153	629	0	ENST00000335790.3:c.241C>T	p.Leu81Phe	p.L81F	ENST00000335790	NM_002315.2	81	Ctc/Ttc	3/4	1	2	FACETS	0.92	0.844	0.999	0.92	0.844	0.999	CLONAL	1	TRUE	1	0.49	2		629	679	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14300921	14300921	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	36	314	0	ENST00000256196.4:c.577G>T	p.Glu193Ter	p.E193*	ENST00000256196		193	Gaa/Taa	6/6	1	2	FACETS	0.354	0.291	0.425	0.354	0.291	0.425	SUBCLONAL	1	TRUE	1	0.49	2		314	415	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625289	69625289	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	250	910	2	ENST00000334134.2:c.504G>T	p.Lys168Asn	p.K168N	ENST00000334134	NM_005247.2	168	aaG/aaT	3/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.49	2		912	946	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940165	71940165	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747330824	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	52	893	1	ENST00000298229.2:c.550G>A	p.Asp184Asn	p.D184N	ENST00000298229	NM_001567.3	184	Gac/Aac	5/28	1	2	FACETS	0.212	0.179	0.247	0.212	0.179	0.247	SUBCLONAL	1	TRUE	1	0.49	2		894	1003	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918463	94918463	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	124	522	0	ENST00000536441.1:c.719A>G	p.Asp240Gly	p.D240G	ENST00000536441	NM_144665.3	240	gAc/gGc	5/10	1	2	FACETS	0.998	0.908	1	0.998	0.908	1	CLONAL	1	TRUE	1	0.49	2		522	507	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236197	108236197	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555152033	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	172	595	0	ENST00000278616.4:c.9133C>T	p.Leu3045Phe	p.L3045F	ENST00000278616	NM_000051.3	3045	Ctc/Ttc	63/63	1	2	FACETS	0.895	0.825	0.968	0.895	0.825	0.968	CLONAL	1	TRUE	1	0.49	2		595	784	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380737	118380737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1425093050	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	125	454	0	ENST00000534358.1:c.10975C>T	p.Arg3659Trp	p.R3659W	ENST00000534358	NM_005933.3	3659	Cgg/Tgg	30/36	1	2	FACETS	0.977	0.889	1	0.977	0.889	1	CLONAL	1	TRUE	1	0.49	2		454	522	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390416	118390416	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520053	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	216	598	0	ENST00000534358.1:c.11230C>T	p.Arg3744Ter	p.R3744*	ENST00000534358	NM_005933.3	3744	Cga/Tga	32/36	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.49	2		598	826	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103264	119103264	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	177	547	0	ENST00000264033.4:c.302G>A	p.Arg101Lys	p.R101K	ENST00000264033	NM_005188.3	101	aGa/aAa	2/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.49	2		547	630	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	430229	430229	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	31	402	0	ENST00000399788.2:c.2473G>T	p.Glu825Ter	p.E825*	ENST00000399788	NM_001042603.1	825	Gaa/Taa	18/28	1	2	FACETS	0.224	0.18	0.273	0.224	0.18	0.273	SUBCLONAL	1	TRUE	1	0.49	2		402	566	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	459933	459933	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	142	538	0	ENST00000399788.2:c.1162G>T	p.Glu388Ter	p.E388*	ENST00000399788	NM_001042603.1	388	Gaa/Taa	10/28	1	2	FACETS	0.919	0.84	1	0.919	0.84	1	CLONAL	1	TRUE	1	0.49	2		538	631	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464397	464397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746045026	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	80	532	1	ENST00000399788.2:c.797G>A	p.Arg266Gln	p.R266Q	ENST00000399788	NM_001042603.1	266	cGa/cAa	7/28	1	2	FACETS	0.551	0.485	0.621	0.551	0.485	0.621	SUBCLONAL	1	TRUE	1	0.49	2		533	593	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800831	18800831	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	89	318	0	ENST00000266497.5:c.4207G>T	p.Glu1403Ter	p.E1403*	ENST00000266497		1403	Gag/Tag	31/31	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.49	2		318	348	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69229696	69229696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	33	392	0	ENST00000462284.1:c.772G>A	p.Glu258Lys	p.E258K	ENST00000462284	NM_002392.5	258	Gaa/Aaa	9/11	1	2	FACETS	0.264	0.214	0.32	0.264	0.214	0.32	SUBCLONAL	1	TRUE	1	0.49	2		392	510	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233415	69233415	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	42	387	0	ENST00000462284.1:c.1280A>G	p.Asp427Gly	p.D427G	ENST00000462284	NM_002392.5	427	gAc/gGc	11/11	1	2	FACETS	0.364	0.304	0.431	0.364	0.304	0.431	SUBCLONAL	1	TRUE	1	0.49	2		387	471	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112131	115112131	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772620679	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	64	830	0	ENST00000257566.3:c.1609G>A	p.Ala537Thr	p.A537T	ENST00000257566	NM_016569.3	537	Gct/Act	7/8	1	2	FACETS	0.276	0.238	0.317	0.276	0.238	0.317	SUBCLONAL	1	TRUE	1	0.49	2		830	948	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578239	28578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	152	601	0	ENST00000241453.7:c.2932G>T	p.Glu978Ter	p.E978*	ENST00000241453	NM_004119.2	978	Gag/Tag	24/24	1	2	FACETS	0.828	0.759	0.901	0.828	0.759	0.901	CLONAL	1	TRUE	1	0.49	2		601	749	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609667	28609667	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	156	584	0	ENST00000241453.7:c.1562G>A	p.Gly521Asp	p.G521D	ENST00000241453	NM_004119.2	521	gGc/gAc	12/24	1	2	FACETS	0.989	0.909	1	0.989	0.909	1	CLONAL	1	TRUE	1	0.49	2		584	644	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936957	48936957	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	94	366	1	ENST00000267163.4:c.725C>T	p.Ala242Val	p.A242V	ENST00000267163	NM_000321.2	242	gCt/gTt	8/27	1	2	FACETS	0.925	0.828	1	0.925	0.828	1	CLONAL	1	TRUE	1	0.49	2		367	415	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434632	110434632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs940747787	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	109	824	1	ENST00000375856.3:c.3769G>A	p.Asp1257Asn	p.D1257N	ENST00000375856	NM_003749.2	1257	Gac/Aac	1/2	1	2	FACETS	0.489	0.438	0.543	0.489	0.438	0.543	SUBCLONAL	1	TRUE	1	0.49	2		825	910	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061691	38061691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754265844	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	121	445	0	ENST00000250448.2:c.298G>A	p.Gly100Ser	p.G100S	ENST00000250448	NM_004496.3	100	Ggc/Agc	2/2	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.49	2		445	439	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961791	41961791	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	136	416	0	ENST00000219905.7:c.699C>A	p.Phe233Leu	p.F233L	ENST00000219905	NM_001164273.1	233	ttC/ttA	2/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.49	2		416	495	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003099	42003099	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	175	671	0	ENST00000219905.7:c.2636C>T	p.Ser879Phe	p.S879F	ENST00000219905	NM_001164273.1	879	tCc/tTc	8/24	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.49	2		671	689	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749417	43749417	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	91	304	0	ENST00000382044.4:c.1390-1G>T		p.X464_splice	ENST00000382044	NM_001141980.1	464			1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.49	2		304	334	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73995362	73995362	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763918983	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	41	413	1	ENST00000318443.5:c.668G>A	p.Arg223His	p.R223H	ENST00000318443	NM_001024736.1	223	cGc/cAc	4/10	1	2	FACETS	0.345	0.287	0.409	0.345	0.287	0.409	SUBCLONAL	1	TRUE	1	0.49	2		414	485	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88671957	88671957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs574695821	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	69	286	0	ENST00000360948.2:c.1213G>A	p.Asp405Asn	p.D405N	ENST00000360948	NM_001012338.2	405	Gat/Aat	10/19	1	2	FACETS	0.782	0.685	0.886	0.782	0.685	0.886	SUBCLONAL	1	TRUE	1	0.49	2		286	360	SUCCESS
BLM	641	MSKCC	GRCh37	15	91341429	91341429	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	21	241	0	ENST00000355112.3:c.3220A>G	p.Thr1074Ala	p.T1074A	ENST00000355112	NM_000057.2	1074	Aca/Gca	17/22	1	2	FACETS	0.271	0.209	0.344	0.271	0.209	0.344	SUBCLONAL	1	TRUE	1	0.49	2		241	316	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250862	99250862	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	145	537	2	ENST00000268035.6:c.166G>A	p.Glu56Lys	p.E56K	ENST00000268035	NM_000875.3	56	Gag/Aag	2/21	1	2	FACETS	0.918	0.84	0.999	0.918	0.84	0.999	CLONAL	1	TRUE	1	0.49	2		539	645	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858021	9858021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	57	587	0	ENST00000330684.3:c.3380G>A	p.Gly1127Asp	p.G1127D	ENST00000330684	NM_001134407.1	1127	gGt/gAt	13/13	1	2	FACETS	0.325	0.278	0.376	0.325	0.278	0.376	SUBCLONAL	1	TRUE	1	0.49	2		587	716	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041854	14041854	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	105	445	0	ENST00000311895.7:c.2401C>A	p.Leu801Ile	p.L801I	ENST00000311895	NM_005236.2	801	Ctc/Atc	11/11	1	2	FACETS	0.92	0.828	1	0.92	0.828	1	CLONAL	1	TRUE	1	0.49	2		445	466	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832515	72832515	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	132	421	0	ENST00000268489.5:c.4066G>T	p.Glu1356Ter	p.E1356*	ENST00000268489	NM_006885.3	1356	Gaa/Taa	9/10	1	2	FACETS	0.883	0.804	0.966	0.883	0.804	0.966	CLONAL	1	TRUE	1	0.49	2		421	610	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993190	72993190	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	280	942	0	ENST00000268489.5:c.855C>A	p.Phe285Leu	p.F285L	ENST00000268489	NM_006885.3	285	ttC/ttA	2/10	1	2	FACETS	0.993	0.933	1	0.993	0.933	1	CLONAL	1	TRUE	1	0.49	2		942	1151	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819766	81819766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766974268	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	170	603	1	ENST00000359376.3:c.172G>A	p.Ala58Thr	p.A58T	ENST00000359376	NM_002661.3	58	Gct/Act	2/33	1	2	FACETS	0.935	0.862	1	0.935	0.862	1	CLONAL	1	TRUE	1	0.49	2		604	742	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942021	81942021	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	117	434	0	ENST00000359376.3:c.1558G>A	p.Asp520Asn	p.D520N	ENST00000359376	NM_002661.3	520	Gat/Aat	17/33	1	2	FACETS	0.913	0.827	1	0.913	0.827	1	CLONAL	1	TRUE	1	0.49	2		434	523	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984773	11984773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	54	424	0	ENST00000353533.5:c.319G>A	p.Glu107Lys	p.E107K	ENST00000353533	NM_003010.3	107	Gaa/Aaa	3/11	1	2	FACETS	0.419	0.358	0.486	0.419	0.358	0.486	SUBCLONAL	1	TRUE	1	0.49	2		424	526	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870628	40870628	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	197	590	0	ENST00000428826.2:c.775G>T	p.Glu259Ter	p.E259*	ENST00000428826		259	Gaa/Taa	9/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.49	2		590	710	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246842	41246842	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	51	388	0	ENST00000357654.3:c.706A>G	p.Thr236Ala	p.T236A	ENST00000357654	NM_007294.3	236	Act/Gct	10/23	1	2	FACETS	0.434	0.369	0.505	0.434	0.369	0.505	SUBCLONAL	1	TRUE	1	0.49	2		388	480	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740721	58740721	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	91	627	0	ENST00000305921.3:c.1626T>G	p.Asn542Lys	p.N542K	ENST00000305921	NM_003620.3	542	aaT/aaG	6/6	1	2	FACETS	0.468	0.415	0.525	0.468	0.415	0.525	SUBCLONAL	1	TRUE	1	0.49	2		627	793	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760889	59760889	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	173	411	0	ENST00000259008.2:c.3518T>G	p.Ile1173Ser	p.I1173S	ENST00000259008	NM_032043.2	1173	aTt/aGt	20/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.49	2		411	571	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853769	59853769	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	51	359	1	ENST00000259008.2:c.2090C>A	p.Ser697Tyr	p.S697Y	ENST00000259008	NM_032043.2	697	tCt/tAt	14/20	1	2	FACETS	0.477	0.406	0.555	0.477	0.406	0.555	SUBCLONAL	1	TRUE	1	0.49	2		360	436	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533730	63533730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs950007141	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	41	630	0	ENST00000307078.5:c.1424C>T	p.Ser475Leu	p.S475L	ENST00000307078	NM_004655.3	475	tCg/tTg	6/11	1	2	FACETS	0.249	0.207	0.296	0.249	0.207	0.296	SUBCLONAL	1	TRUE	1	0.49	2		630	672	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743020	743020	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	168	489	0	ENST00000314574.4:c.958G>T	p.Glu320Ter	p.E320*	ENST00000314574	NM_005433.3	320	Gaa/Taa	8/12	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.49	2		489	637	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39537620	39537620	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	64	362	0	ENST00000262039.4:c.154G>T	p.Glu52Ter	p.E52*	ENST00000262039	NM_002647.2	52	Gag/Tag	2/25	1	2	FACETS	0.819	0.714	0.931	0.819	0.714	0.931	CLONAL	1	TRUE	1	0.49	2		362	319	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122718	7122718	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	277	869	0	ENST00000302850.5:c.3436G>A	p.Gly1146Arg	p.G1146R	ENST00000302850	NM_000208.2	1146	Ggg/Agg	19/22	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.49	2		869	1053	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302271	15302271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	287	815	1	ENST00000263388.2:c.1000G>A	p.Ala334Thr	p.A334T	ENST00000263388	NM_000435.2	334	Gct/Act	6/33	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.49	2		816	1114	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15364975	15364975	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	48	517	0	ENST00000263377.2:c.2146G>T	p.Asp716Tyr	p.D716Y	ENST00000263377	NM_058243.2	716	Gac/Tac	11/20	1	2	FACETS	0.252	0.213	0.297	0.252	0.213	0.297	SUBCLONAL	1	TRUE	1	0.49	2		517	776	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765718	41765718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751040564	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	84	649	0	ENST00000301178.4:c.2594G>A	p.Arg865His	p.R865H	ENST00000301178	NM_021913.4	865	cGc/cAc	20/20	1	2	FACETS	0.503	0.444	0.566	0.503	0.444	0.566	SUBCLONAL	1	TRUE	1	0.49	2		649	682	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867361	45867361	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	244	788	0	ENST00000391945.4:c.832G>A	p.Glu278Lys	p.E278K	ENST00000391945	NM_000400.3	278	Gag/Aag	10/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.49	2		788	939	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973053	25973053	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	127	510	0	ENST00000435504.4:c.1372T>A	p.Ser458Thr	p.S458T	ENST00000435504		458	Tcc/Acc	12/13	1	2	FACETS	0.885	0.804	0.969	0.885	0.804	0.969	CLONAL	1	TRUE	1	0.49	2		510	586	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940498	29940498	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	142	528	0	ENST00000389048.3:c.733C>A	p.Leu245Ile	p.L245I	ENST00000389048	NM_004304.4	245	Ctc/Atc	2/29	1	2	FACETS	0.994	0.91	1	0.994	0.91	1	CLONAL	1	TRUE	1	0.49	2		528	583	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025925	48025925	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	112	387	0	ENST00000234420.5:c.803A>G	p.Asp268Gly	p.D268G	ENST00000234420	NM_000179.2	268	gAc/gGc	4/10	1	2	FACETS	0.945	0.854	1	0.945	0.854	1	CLONAL	1	TRUE	1	0.49	2		387	484	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711179	61711179	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	36	586	0	ENST00000401558.2:c.2570C>A	p.Ser857Tyr	p.S857Y	ENST00000401558	NM_003400.3	857	tCt/tAt	21/25	1	2	FACETS	0.25	0.205	0.301	0.25	0.205	0.301	SUBCLONAL	1	TRUE	1	0.49	2		586	588	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920731	96920731	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	142	416	0	ENST00000258439.3:c.249C>A	p.Phe83Leu	p.F83L	ENST00000258439	NM_001193304.2	83	ttC/ttA	3/4	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.49	2		416	546	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047330	128047330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	164	542	0	ENST00000285398.2:c.592C>T	p.Arg198Cys	p.R198C	ENST00000285398	NM_000122.1	198	Cgc/Tgc	5/15	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.49	2		542	648	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198272762	198272762	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	114	611	0	ENST00000335508.6:c.1199C>A	p.Ser400Tyr	p.S400Y	ENST00000335508	NM_012433.2	400	tCt/tAt	9/25	1	2	FACETS	0.648	0.584	0.716	0.648	0.584	0.716	SUBCLONAL	1	TRUE	1	0.49	2		611	718	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593720	215593720	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	92	298	0	ENST00000260947.4:c.2014T>C	p.Phe672Leu	p.F672L	ENST00000260947	NM_000465.2	672	Ttt/Ctt	11/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.49	2		298	331	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660315	227660315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	43	572	0	ENST00000305123.5:c.3140C>T	p.Pro1047Leu	p.P1047L	ENST00000305123	NM_005544.2	1047	cCt/cTt	1/2	1	2	FACETS	0.339	0.284	0.401	0.339	0.284	0.401	SUBCLONAL	1	TRUE	1	0.49	2		572	517	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662424	227662424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752842091	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	73	704	0	ENST00000305123.5:c.1031G>A	p.Gly344Asp	p.G344D	ENST00000305123	NM_005544.2	344	gGc/gAc	1/2	1	2	FACETS	0.416	0.363	0.472	0.416	0.363	0.472	SUBCLONAL	1	TRUE	1	0.49	2		704	717	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663168	227663168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	206	740	3	ENST00000305123.5:c.287C>T	p.Ala96Val	p.A96V	ENST00000305123	NM_005544.2	96	gCg/gTg	1/2	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.49	2		743	788	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019159	31019159	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1298870586	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	189	583	0	ENST00000375687.4:c.754T>G	p.Phe252Val	p.F252V	ENST00000375687	NM_015338.5	252	Ttt/Gtt	9/13	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.49	2		583	749	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39745033	39745033	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	65	541	1	ENST00000361337.2:c.1822+1G>A		p.X608_splice	ENST00000361337	NM_003286.2	608			1	2	FACETS	0.38	0.329	0.436	0.38	0.329	0.436	SUBCLONAL	1	TRUE	1	0.49	2		542	698	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39746856	39746856	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	126	380	0	ENST00000361337.2:c.1870C>T	p.Arg624Ter	p.R624*	ENST00000361337	NM_003286.2	624	Cga/Tga	18/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.49	2		380	450	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727188	40727188	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	105	552	0	ENST00000373198.4:c.3776A>G	p.His1259Arg	p.H1259R	ENST00000373198	NM_133170.3	1259	cAc/cGc	28/32	1	2	FACETS	0.549	0.492	0.61	0.549	0.492	0.61	SUBCLONAL	1	TRUE	1	0.49	2		552	780	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46255782	46255782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	48	436	0	ENST00000371998.3:c.394G>A	p.Gly132Arg	p.G132R	ENST00000371998		132	Gga/Aga	6/23	1	2	FACETS	0.371	0.313	0.435	0.371	0.313	0.435	SUBCLONAL	1	TRUE	1	0.49	2		436	528	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485083	57485083	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	120	449	1	ENST00000371085.3:c.917C>T	p.Ser306Leu	p.S306L	ENST00000371085	NM_000516.4	306	tCg/tTg	11/13	1	2	FACETS	0.964	0.875	1	0.964	0.875	1	CLONAL	1	TRUE	1	0.49	2		450	508	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171612	36171612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	47	306	0	ENST00000300305.3:c.953C>T	p.Ser318Phe	p.S318F	ENST00000300305		318	tCc/tTc	7/8	1	2	FACETS	0.426	0.36	0.499	0.426	0.36	0.499	SUBCLONAL	1	TRUE	1	0.49	2		306	450	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22153321	22153321	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	31	500	0	ENST00000215832.6:c.589G>T	p.Glu197Ter	p.E197*	ENST00000215832	NM_002745.4	197	Gaa/Taa	4/9	1	2	FACETS	0.212	0.17	0.259	0.212	0.17	0.259	SUBCLONAL	1	TRUE	1	0.49	2		500	598	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130706	29130706	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	54	417	0	ENST00000328354.6:c.4T>C	p.Ser2Pro	p.S2P	ENST00000328354	NM_007194.3	2	Tct/Cct	2/15	1	2	FACETS	0.424	0.362	0.492	0.424	0.362	0.492	SUBCLONAL	1	TRUE	1	0.49	2		417	520	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729963	30729963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1305853447	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	43	445	1	ENST00000295754.5:c.1484G>A	p.Arg495Gln	p.R495Q	ENST00000295754	NM_003242.5	495	cGa/cAa	6/7	1	2	FACETS	0.265	0.221	0.314	0.265	0.221	0.314	SUBCLONAL	1	TRUE	1	0.49	2		446	663	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070327	37070327	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	33	474	0	ENST00000231790.2:c.1462A>G	p.Lys488Glu	p.K488E	ENST00000231790	NM_000249.3	488	Aag/Gag	13/19	1	2	FACETS	0.24	0.195	0.291	0.24	0.195	0.291	SUBCLONAL	1	TRUE	1	0.49	2		474	561	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41279520	41279520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	44	428	0	ENST00000349496.5:c.2090G>A	p.Gly697Glu	p.G697E	ENST00000349496	NM_001904.3	697	gGa/gAa	14/15	1	2	FACETS	0.327	0.273	0.386	0.327	0.273	0.386	SUBCLONAL	1	TRUE	1	0.49	2		428	550	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427681	72427681	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772981068	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	95	401	0	ENST00000477973.2:c.809C>T	p.Ser270Leu	p.S270L	ENST00000477973	NM_012234.5	270	tCg/tTg	4/4	1	2	FACETS	0.771	0.689	0.858	0.771	0.689	0.858	SUBCLONAL	1	TRUE	1	0.49	2		401	503	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799463	72799463	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	65	733	0	ENST00000325599.8:c.1706G>T	p.Arg569Ile	p.R569I	ENST00000325599	NM_018130.2	569	aGa/aTa	11/11	1	2	FACETS	0.291	0.252	0.334	0.291	0.252	0.334	SUBCLONAL	1	TRUE	1	0.49	2		733	911	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242907	142242907	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	81	529	0	ENST00000350721.4:c.4080A>C	p.Glu1360Asp	p.E1360D	ENST00000350721	NM_001184.3	1360	gaA/gaC	22/47	1	2	FACETS	0.453	0.399	0.511	0.453	0.399	0.511	SUBCLONAL	1	TRUE	1	0.49	2		529	730	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268391	142268391	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	101	333	0	ENST00000350721.4:c.3101A>C	p.Lys1034Thr	p.K1034T	ENST00000350721	NM_001184.3	1034	aAa/aCa	15/47	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.49	2		333	341	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169953103	169953103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757899632	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	166	485	0	ENST00000295797.4:c.187G>A	p.Glu63Lys	p.E63K	ENST00000295797	NM_002740.5	63	Gaa/Aaa	2/18	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.49	2		485	665	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169977795	169977795	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	241	536	0	ENST00000295797.4:c.262G>T	p.Glu88Ter	p.E88*	ENST00000295797	NM_002740.5	88	Gaa/Taa	3/18	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.49	2		536	828	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430440	181430440	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	138	885	2	ENST00000325404.1:c.292C>T	p.Arg98Ter	p.R98*	ENST00000325404	NM_003106.3	98	Cga/Tga	1/1	1	2	FACETS	0.519	0.471	0.57	0.519	0.471	0.57	SUBCLONAL	1	TRUE	1	0.49	2		887	1085	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604293	189604293	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781366519	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	191	482	1	ENST00000264731.3:c.1460G>A	p.Arg487His	p.R487H	ENST00000264731	NM_003722.4	487	cGc/cAc	11/14	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.49	2		483	693	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592185	55592185	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	53	498	0	ENST00000288135.5:c.1509T>A	p.Tyr503Ter	p.Y503*	ENST00000288135	NM_000222.2	503	taT/taA	9/21	1	2	FACETS	0.352	0.3	0.41	0.352	0.3	0.41	SUBCLONAL	1	TRUE	1	0.49	2		498	614	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230917	66230917	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	16	281	0	ENST00000273854.3:c.2054A>C	p.Glu685Ala	p.E685A	ENST00000273854	NM_004439.5	685	gAa/gCa	12/18	1	2	FACETS	0.22	0.162	0.289	0.22	0.162	0.289	SUBCLONAL	1	TRUE	1	0.49	2		281	297	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467556	66467556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147719164	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	70	348	0	ENST00000273854.3:c.713G>A	p.Arg238Gln	p.R238Q	ENST00000273854	NM_004439.5	238	cGa/cAa	3/18	1	2	FACETS	0.714	0.626	0.809	0.714	0.626	0.809	SUBCLONAL	1	TRUE	1	0.49	2		348	400	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557209	187557209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	160	574	0	ENST00000441802.2:c.4153C>T	p.Pro1385Ser	p.P1385S	ENST00000441802	NM_005245.3	1385	Cct/Tct	6/27	1	2	FACETS	0.992	0.913	1	0.992	0.913	1	CLONAL	1	TRUE	1	0.49	2		574	658	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629372	187629372	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	109	772	0	ENST00000441802.2:c.1610G>T	p.Arg537Met	p.R537M	ENST00000441802	NM_005245.3	537	aGg/aTg	2/27	1	2	FACETS	0.442	0.396	0.491	0.442	0.396	0.491	SUBCLONAL	1	TRUE	1	0.49	2		772	1006	SUCCESS
APC	324	MSKCC	GRCh37	5	112178100	112178100	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	41	410	0	ENST00000257430.4:c.6809C>A	p.Ser2270Tyr	p.S2270Y	ENST00000257430	NM_000038.5	2270	tCt/tAt	16/16	1	2	FACETS	0.305	0.254	0.363	0.305	0.254	0.363	SUBCLONAL	1	TRUE	1	0.49	2		410	548	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170834711	170834711	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	42	352	0	ENST00000296930.5:c.779C>A	p.Ser260Tyr	p.S260Y	ENST00000296930	NM_002520.6	260	tCt/tAt	10/11	1	2	FACETS	0.416	0.348	0.492	0.416	0.348	0.492	SUBCLONAL	1	TRUE	1	0.49	2		352	412	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394929	394929	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	65	546	0	ENST00000380956.4:c.325G>T	p.Glu109Ter	p.E109*	ENST00000380956	NM_001195286.1	109	Gaa/Taa	3/9	1	2	FACETS	0.4	0.346	0.458	0.4	0.346	0.458	SUBCLONAL	1	TRUE	1	0.49	2		546	664	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488377	20488377	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1321986801	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	65	515	1	ENST00000346618.3:c.1033C>T	p.Pro345Ser	p.P345S	ENST00000346618	NM_001949.4	345	Ccc/Tcc	6/7	1	2	FACETS	0.439	0.381	0.503	0.439	0.381	0.503	SUBCLONAL	1	TRUE	1	0.49	2		516	604	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171942	32171942	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	70	474	0	ENST00000375023.3:c.3090C>A	p.Phe1030Leu	p.F1030L	ENST00000375023	NM_004557.3	1030	ttC/ttA	19/30	1	2	FACETS	0.493	0.43	0.561	0.493	0.43	0.561	SUBCLONAL	1	TRUE	1	0.49	2		474	580	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64288417	64288417	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	19	241	0	ENST00000370651.3:c.181G>A	p.Glu61Lys	p.E61K	ENST00000370651	NM_003463.4	61	Gaa/Aaa	3/6	1	2	FACETS	0.22	0.167	0.284	0.22	0.167	0.284	SUBCLONAL	1	TRUE	1	0.49	2		241	352	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64290033	64290033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779059610	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	140	523	0	ENST00000370651.3:c.476G>A	p.Arg159His	p.R159H	ENST00000370651	NM_003463.4	159	cGt/cAt	6/6	1	2	FACETS	0.911	0.833	0.993	0.911	0.833	0.993	CLONAL	1	TRUE	1	0.49	2		523	627	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94129005	94129005	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	45	428	1	ENST00000369303.4:c.55C>T	p.Leu19Phe	p.L19F	ENST00000369303	NM_004440.3	19	Ctc/Ttc	1/17	1	2	FACETS	0.284	0.238	0.335	0.284	0.238	0.335	SUBCLONAL	1	TRUE	1	0.49	2		429	646	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015677	112015677	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs751647014	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	36	482	0	ENST00000368678.4:c.1165C>T	p.Arg389Ter	p.R389*	ENST00000368678		389	Cga/Tga	11/13	1	2	FACETS	0.251	0.206	0.302	0.251	0.206	0.302	SUBCLONAL	1	TRUE	1	0.49	2		482	585	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663590	117663590	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	87	472	0	ENST00000368508.3:c.4642G>T	p.Glu1548Ter	p.E1548*	ENST00000368508	NM_002944.2	1548	Gag/Tag	28/43	1	2	FACETS	0.507	0.448	0.569	0.507	0.448	0.569	SUBCLONAL	1	TRUE	1	0.49	2		472	701	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663677	117663677	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	17	215	0	ENST00000368508.3:c.4555G>T	p.Asp1519Tyr	p.D1519Y	ENST00000368508	NM_002944.2	1519	Gat/Tat	28/43	1	2	FACETS	0.258	0.192	0.336	0.258	0.192	0.336	SUBCLONAL	1	TRUE	1	0.49	2		215	269	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117680986	117680986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780046038	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	96	351	0	ENST00000368508.3:c.3634C>T	p.Arg1212Cys	p.R1212C	ENST00000368508	NM_002944.2	1212	Cgc/Tgc	23/43	1	2	FACETS	0.992	0.89	1	0.992	0.89	1	CLONAL	1	TRUE	1	0.49	2		351	395	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510835	157510835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	62	743	1	ENST00000346085.5:c.3610G>A	p.Ala1204Thr	p.A1204T	ENST00000346085	NM_020732.3	1204	Gca/Aca	14/20	1	2	FACETS	0.281	0.242	0.324	0.281	0.242	0.324	SUBCLONAL	1	TRUE	1	0.49	2		744	901	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979561	2979561	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	54	369	0	ENST00000396946.4:c.686T>G	p.Ile229Ser	p.I229S	ENST00000396946	NM_032415.4	229	aTc/aGc	6/25	1	2	FACETS	0.42	0.358	0.487	0.42	0.358	0.487	SUBCLONAL	1	TRUE	1	0.49	2		369	525	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508776	106508776	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	174	570	0	ENST00000359195.3:c.770C>A	p.Ser257Tyr	p.S257Y	ENST00000359195	NM_002649.2	257	tCt/tAt	2/11	1	2	FACETS	0.995	0.918	1	0.995	0.918	1	CLONAL	1	TRUE	1	0.49	2		570	714	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339981	116339981	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	99	397	0	ENST00000397752.3:c.843C>A	p.Phe281Leu	p.F281L	ENST00000397752	NM_000245.2	281	ttC/ttA	2/21	1	2	FACETS	0.865	0.776	0.959	0.865	0.776	0.959	CLONAL	1	TRUE	1	0.49	2		397	467	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411568	116411568	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	27	357	0	ENST00000397752.3:c.2747C>A	p.Ser916Tyr	p.S916Y	ENST00000397752	NM_000245.2	916	tCt/tAt	13/21	1	2	FACETS	0.288	0.229	0.356	0.288	0.229	0.356	SUBCLONAL	1	TRUE	1	0.49	2		357	382	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874407	151874407	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	21	379	0	ENST00000262189.6:c.8131G>T	p.Asp2711Tyr	p.D2711Y	ENST00000262189	NM_170606.2	2711	Gac/Tac	38/59	1	2	FACETS	0.218	0.167	0.277	0.218	0.167	0.277	SUBCLONAL	1	TRUE	1	0.49	2		379	393	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945601	151945601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770827883	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	28	341	0	ENST00000262189.6:c.1918G>A	p.Glu640Lys	p.E640K	ENST00000262189	NM_170606.2	640	Gaa/Aaa	14/59	1	2	FACETS	0.229	0.182	0.282	0.229	0.182	0.282	SUBCLONAL	1	TRUE	1	0.49	2		341	500	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058450	69058450	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	19	372	0	ENST00000288368.4:c.4094C>A	p.Pro1365His	p.P1365H	ENST00000288368	NM_024870.2	1365	cCt/cAt	34/40	1	2	FACETS	0.217	0.164	0.28	0.217	0.164	0.28	SUBCLONAL	1	TRUE	1	0.49	2		372	357	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566378	141566378	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	20	333	0	ENST00000220592.5:c.1034A>G	p.Asn345Ser	p.N345S	ENST00000220592	NM_012154.3	345	aAc/aGc	9/19	1	2	FACETS	0.205	0.156	0.263	0.205	0.156	0.263	SUBCLONAL	1	TRUE	1	0.49	2		333	398	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572576	141572576	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	57	608	0	ENST00000220592.5:c.494T>C	p.Val165Ala	p.V165A	ENST00000220592	NM_012154.3	165	gTc/gCc	4/19	1	2	FACETS	0.319	0.273	0.37	0.319	0.273	0.37	SUBCLONAL	1	TRUE	1	0.49	2		608	729	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080332	5080332	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	82	312	0	ENST00000381652.3:c.2235A>C	p.Glu745Asp	p.E745D	ENST00000381652	NM_004972.3	745	gaA/gaC	17/25	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.49	2		312	332	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5465546	5465546	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	20	293	0	ENST00000381577.3:c.730C>A	p.Leu244Met	p.L244M	ENST00000381577	NM_014143.3	244	Ctg/Atg	5/7	1	2	FACETS	0.204	0.155	0.261	0.204	0.155	0.261	SUBCLONAL	1	TRUE	1	0.49	2		293	400	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206782	27206782	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	33	515	0	ENST00000380036.4:c.2567G>T	p.Arg856Ile	p.R856I	ENST00000380036	NM_000459.3	856	aGa/aTa	15/23	1	2	FACETS	0.218	0.176	0.264	0.218	0.176	0.264	SUBCLONAL	1	TRUE	1	0.49	2		515	619	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213590	27213590	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	52	463	0	ENST00000380036.4:c.2986A>G	p.Thr996Ala	p.T996A	ENST00000380036	NM_000459.3	996	Aca/Gca	18/23	1	2	FACETS	0.37	0.314	0.431	0.37	0.314	0.431	SUBCLONAL	1	TRUE	1	0.49	2		463	574	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409478	80409478	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	35	465	0	ENST00000286548.4:c.636G>T	p.Glu212Asp	p.E212D	ENST00000286548	NM_002072.3	212	gaG/gaT	5/7	1	2	FACETS	0.285	0.233	0.343	0.285	0.233	0.343	SUBCLONAL	1	TRUE	1	0.49	2		465	502	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128321916	128321916	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	154	551	0	ENST00000265960.3:c.844C>T	p.Arg282Ter	p.R282*	ENST00000265960	NM_001006617.1	282	Cga/Tga	6/12	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.49	2		551	621	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139438491	139438491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754666783	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	134	975	2	ENST00000277541.6:c.125G>A	p.Gly42Asp	p.G42D	ENST00000277541	NM_017617.3	42	gGc/gAc	2/34	1	2	FACETS	0.462	0.418	0.507	0.462	0.418	0.507	SUBCLONAL	1	TRUE	1	0.49	2		977	1185	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793347	139793347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	49	689	1	ENST00000247668.2:c.155G>A	p.Arg52Gln	p.R52Q	ENST00000247668	NM_021138.3	52	cGg/cAg	2/11	1	2	FACETS	0.232	0.195	0.272	0.232	0.195	0.272	SUBCLONAL	1	TRUE	1	0.49	2		690	863	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317500	1317500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	109	807	0	ENST00000400841.2:c.565G>A	p.Ala189Thr	p.A189T	ENST00000400841		189	Gct/Act	5/6	1	2	FACETS	0.472	0.423	0.524	0.472	0.423	0.524	SUBCLONAL	1	TRUE	1	0.49	2		807	943	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934198	39934198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	225	819	1	ENST00000378444.4:c.401C>T	p.Ala134Val	p.A134V	ENST00000378444	NM_001123385.1	134	gCt/gTt	4/15	1	2	FACETS	0.89	0.829	0.953	0.89	0.829	0.953	CLONAL	1	TRUE	1	0.49	2		820	1032	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934211	39934211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457205832	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	53	780	2	ENST00000378444.4:c.388G>A	p.Glu130Lys	p.E130K	ENST00000378444	NM_001123385.1	130	Gag/Aag	4/15	1	2	FACETS	0.208	0.177	0.243	0.208	0.177	0.243	SUBCLONAL	1	TRUE	1	0.49	2		782	1039	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040911	47040911	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	59	930	0	ENST00000377604.3:c.1441G>A	p.Glu481Lys	p.E481K	ENST00000377604	NM_001204468.1	481	Gag/Aag	14/24	1	2	FACETS	0.234	0.2	0.27	0.234	0.2	0.27	SUBCLONAL	1	TRUE	1	0.49	2		930	1031	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650311	48650311	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	179	804	0	ENST00000376670.3:c.281C>T	p.Ala94Val	p.A94V	ENST00000376670	NM_002049.3	94	gCc/gTc	3/6	1	2	FACETS	0.839	0.774	0.906	0.839	0.774	0.906	CLONAL	1	TRUE	1	0.49	2		804	871	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411275	63411275	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773684332	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	105	853	2	ENST00000330258.3:c.1892G>A	p.Arg631Gln	p.R631Q	ENST00000330258	NM_152424.3	631	cGa/cAa	2/2	1	2	FACETS	0.444	0.397	0.494	0.444	0.397	0.494	SUBCLONAL	1	TRUE	1	0.49	2		855	966	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412448	63412448	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1470153305	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	249	956	0	ENST00000330258.3:c.719C>A	p.Ser240Tyr	p.S240Y	ENST00000330258	NM_152424.3	240	tCt/tAt	2/2	1	2	FACETS	0.929	0.869	0.991	0.929	0.869	0.991	CLONAL	1	TRUE	1	0.49	2		956	1094	SUCCESS
AR	367	MSKCC	GRCh37	X	66931522	66931522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137852583	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	189	638	1	ENST00000374690.3:c.2164G>A	p.Ala722Thr	p.A722T	ENST00000374690	NM_000044.3	722	Gcc/Acc	4/8	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.49	2		639	748	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344943	70344943	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	240	769	0	ENST00000374080.3:c.2173C>A	p.Leu725Ile	p.L725I	ENST00000374080		725	Ctt/Att	15/45	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.49	2		769	930	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357641	70357642	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs879255527	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	234	941	0	ENST00000374080.3:c.5898dup	p.Ser1967GlnfsTer84	p.S1967Qfs*84	ENST00000374080		1964	-/C	41/45	1	2	FACETS	0.864	0.805	0.924	0.864	0.805	0.924	CLONAL	1	TRUE	1	0.49	2		941	1106	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76931740	76931740	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782344877	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	149	392	0	ENST00000373344.5:c.3790G>A	p.Asp1264Asn	p.D1264N	ENST00000373344	NM_000489.3	1264	Gac/Aac	10/35	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.49	2		392	548	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938221	76938221	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	73	547	0	ENST00000373344.5:c.2527A>C	p.Asn843His	p.N843H	ENST00000373344	NM_000489.3	843	Aat/Cat	9/35	1	2	FACETS	0.434	0.379	0.494	0.434	0.379	0.494	SUBCLONAL	1	TRUE	1	0.49	2		547	686	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939872	76939872	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	29	477	0	ENST00000373344.5:c.876G>T	p.Gln292His	p.Q292H	ENST00000373344	NM_000489.3	292	caG/caT	9/35	1	2	FACETS	0.217	0.174	0.267	0.217	0.174	0.267	SUBCLONAL	1	TRUE	1	0.49	2		477	545	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123025125	123025125	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs779388079	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	23	190	0	ENST00000355640.3:c.1015A>G	p.Ile339Val	p.I339V	ENST00000355640		339	Ata/Gta	4/7	1	2	FACETS	0.288	0.224	0.362	0.288	0.224	0.362	SUBCLONAL	1	TRUE	1	0.49	2		190	326	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164929	123164929	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	76	328	1	ENST00000218089.9:c.242A>G	p.Asn81Ser	p.N81S	ENST00000218089	NM_001042749.1	81	aAc/aGc	5/35	1	2	FACETS	0.823	0.726	0.926	0.823	0.726	0.926	CLONAL	1	TRUE	1	0.49	2		329	377	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518144	8518144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1158240950	NA	P-0042199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	34	447	0	ENST00000356435.5:c.1247C>T	p.Ala416Val	p.A416V	ENST00000356435		416	gCa/gTa	10/35	1	2	FACETS	0.237	0.193	0.287	0.237	0.193	0.287	SUBCLONAL	1	TRUE	1	0.49	2		447	585	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	359	541	0				ENST00000310581	NM_198253.2	-/1132			0.686327245190431	4	FACETS	0.945	0.9	0.991	0.945	0.9	0.991	CLONAL	2	TRUE	2	0.774720350095038	4		541	870	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0042206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	870	593	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.774720350095038	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.774720350095038	3		595	1039	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947596	48947596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1566196458	NA	P-0042206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	96	284	0	ENST00000267163.4:c.1183C>T	p.Gln395Ter	p.Q395*	ENST00000267163	NM_000321.2	395	Caa/Taa	12/27	0.774720350095038	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.774720350095038	1		284	149	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792545	33792545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746895795	NA	P-0042206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	95	198	1	ENST00000498907.2:c.776C>T	p.Ala259Val	p.A259V	ENST00000498907	NM_004364.3	259	gCg/gTg	1/1	0.667829259922424	3	FACETS	1	0.947	1	0.54	0.486	0.596	CLONAL	1	TRUE	1	0.774720350095038	3		199	315	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16090003	16090003	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0042206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	308	188	0	ENST00000268712.3:c.109-2A>G		p.X37_splice	ENST00000268712	NM_006311.3	37			0.774720350095038	3	FACETS	0.999	0.971	1	1	0.997	1	CLONAL	3	TRUE	1	0.774720350095038	3		188	368	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711932	89711945	+	frameshift_variant	Frame_Shift_Del	DEL	AATCATCTGGATTA	AATCATCTGGATTA	-	novel	NA	P-0042206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	126	395	0	ENST00000371953.3:c.550_563del	p.Asn184Ter	p.N184*	ENST00000371953	NM_000314.4	184	AATCATCTGGATTAt/t	6/9	0.774720350095038	2	FACETS	1	0.986	1	0.667	0.617	0.716	CLONAL	1	TRUE	0	0.774720350095038	2		395	244	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371667	225371667	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	308	453	0	ENST00000264414.4:c.937A>G	p.Met313Val	p.M313V	ENST00000264414	NM_003590.4	313	Atg/Gtg	7/16	0.774720350095038	2	FACETS	0.918	0.884	0.951	0.918	0.884	0.951	CLONAL	2	TRUE	0	0.774720350095038	2		453	433	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288533	33288533	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	222	388	0	ENST00000374542.5:c.1019T>C	p.Leu340Pro	p.L340P	ENST00000374542	NM_001141970.1	340	cTc/cCc	3/8	0.774720350095038	3	FACETS	1	0.933	1	0.5	0.466	0.535	CLONAL	1	TRUE	1	0.774720350095038	3		388	795	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975515	13975846	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATAGGCACTACCCAGGGGACAAAAGAAGAGAGAACATTTCTTTCTTTGGAGCAATTTTTTAAAAAAGTTTCTAATCCAAAGGAAGAAAAGATATTTTAGACTTAAGTCAAATGGAAATGAAAACTTTGTTGTTGCTATTGTTGTTTAAATCCAGAACAGATAAACTTCAAAATCACAACACCCTTAAACAGAAAATAGGATGATTAATGCAAAACCTTGTAACAGAACAAATATTAAATGTGTATTTTTAATGCATATACAAACAACTTAGTACAGGGAAAATTACGTCCAAAAAAGCAGTGGTATTTTTTCCATCTATTCTTGATATATCT	ATAGGCACTACCCAGGGGACAAAAGAAGAGAGAACATTTCTTTCTTTGGAGCAATTTTTTAAAAAAGTTTCTAATCCAAAGGAAGAAAAGATATTTTAGACTTAAGTCAAATGGAAATGAAAACTTTGTTGTTGCTATTGTTGTTTAAATCCAGAACAGATAAACTTCAAAATCACAACACCCTTAAACAGAAAATAGGATGATTAATGCAAAACCTTGTAACAGAACAAATATTAAATGTGTATTTTTAATGCATATACAAACAACTTAGTACAGGGAAAATTACGTCCAAAAAAGCAGTGGTATTTTTTCCATCTATTCTTGATATATCT	-	novel	NA	P-0042206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	291	259	1	ENST00000405192.2:c.366-325_372del		p.X122_splice	ENST00000405192	NM_001163147.1	122		7/12	0.774720350095038	6	FACETS	1	0.978	1	0.79	0.75	0.83	CLONAL	3	TRUE	2	0.774720350095038	6		260	606	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955548	90955548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	168	328	0	ENST00000265433.3:c.2117C>T	p.Ser706Leu	p.S706L	ENST00000265433	NM_002485.4	706	tCa/tTa	14/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.774720350095038	2		328	390	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855594	45855597	+	missense_variant	Missense_Mutation	ONP	TCCC	TCCC	ACCA	novel	NA	P-0042206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	328	727	1	ENST00000391945.4:c.2060_2063delinsTGGT	p.Gly687_Asp688delinsValVal	p.G687_D688delinsVV	ENST00000391945	NM_000400.3	687	gGGGAc/gTGGTc	22/23	0.667829259922424	3	FACETS	0.996	0.942	1	0.498	0.471	0.527	CLONAL	1	TRUE	1	0.774720350095038	3		728	1179	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203677	94203677	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	63	331	0	ENST00000323929.3:c.977C>G	p.Pro326Arg	p.P326R	ENST00000323929	NM_005591.3	326	cCt/cGt	9/20	1	2	FACETS	0.824	0.717	0.939	0.824	0.717	0.939	CLONAL	1	TRUE	1	0.435582817085328	2		331	351	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23625376	23625376	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	148	681	0	ENST00000261584.4:c.3150C>A	p.His1050Gln	p.H1050Q	ENST00000261584	NM_024675.3	1050	caC/caA	11/13	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.435582817085328	2		681	675	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39347481	39347481	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057517867	NA	P-0042230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	132	534	0	ENST00000402219.2:c.83A>G	p.Lys28Arg	p.K28R	ENST00000402219	NM_005633.3	28	aAa/aGa	1/23	1	2	FACETS	0.825	0.749	0.903	0.825	0.749	0.903	CLONAL	1	TRUE	1	0.435582817085328	2		534	735	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440924	52440924	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1553645729	NA	P-0042230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	150	662	0	ENST00000460680.1:c.581-1G>A		p.X194_splice	ENST00000460680	NM_004656.3	194			0.435582817085328	1	FACETS	0.947	0.87	1	0.947	0.87	1	CLONAL	1	TRUE	0	0.435582817085328	1		662	569	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149243900	149243900	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	176	631	0	ENST00000360632.3:c.918T>G	p.His306Gln	p.H306Q	ENST00000360632	NM_015472.4	306	caT/caG	6/7	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.435582817085328	2		631	755	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0042235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	44	388	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.503	0.421	0.594	0.503	0.421	0.594	SUBCLONAL	1	TRUE	1	0.26241130960406	2		388	667	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577578	7577578	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	132	837	0	ENST00000269305.4:c.703A>G	p.Asn235Asp	p.N235D	ENST00000269305	NM_001126112.2	235	Aac/Gac	7/11	0.26241130960406	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.26241130960406	1		837	784	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412898	49412898	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519954	NA	P-0042235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	216	907	0	ENST00000418115.1:c.125A>G	p.Tyr42Cys	p.Y42C	ENST00000418115	NM_001664.2	42	tAt/tGt	2/5	0.26241130960406	2	FACETS	0.889	0.827	0.953	0.889	0.827	0.953	CLONAL	2	TRUE	0	0.26241130960406	2		907	926	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244889	46244889	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	123	799	0	ENST00000334344.6:c.2983C>T	p.Gln995Ter	p.Q995*	ENST00000334344	NM_152641.2	995	Caa/Taa	15/21	1	2	FACETS	0.979	0.884	1	0.979	0.884	1	CLONAL	1	TRUE	1	0.26241130960406	2		799	958	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317081	87317081	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201490630	NA	P-0042235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	50	493	1	ENST00000277120.3:c.220G>A	p.Ala74Thr	p.A74T	ENST00000277120		74	Gca/Aca	3/19	1	2	FACETS	0.653	0.553	0.762	0.653	0.553	0.762	SUBCLONAL	1	TRUE	1	0.26241130960406	2		494	584	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245627	46245627	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	62	498	0	ENST00000334344.6:c.3724del	p.Ile1242Ter	p.I1242*	ENST00000334344	NM_152641.2	1241	Aaa/aa	15/21	1	2	FACETS	0.89	0.769	1	0.89	0.769	1	CLONAL	1	TRUE	1	0.26241130960406	2		498	531	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645087	67645087	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	88	957	0	ENST00000264010.4:c.352del	p.Val118TyrfsTer5	p.V118Yfs*5	ENST00000264010	NM_006565.3	118	Gta/ta	3/12	1	2	FACETS	0.734	0.649	0.825	0.734	0.649	0.825	SUBCLONAL	1	TRUE	1	0.26241130960406	2		957	914	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	232	541	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.917	0.862	0.973	0.917	0.862	0.973	CLONAL	1	TRUE	1	0.860694334561705	2		541	588	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0042236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	22504	1045	5	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.860694334561705	36	FACETS	0.99	0.988	0.992			1	CLONAL	35	TRUE	NA	0.860694334561705	36		1050	23589	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717715	89717716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587782341	NA	P-0042236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	288	544	1	ENST00000371953.3:c.741dup	p.Pro248ThrfsTer5	p.P248Tfs*5	ENST00000371953	NM_000314.4	247	tta/ttAa	7/9	0.860694334561705	1	FACETS	0.923	0.887	0.958	0.923	0.887	0.958	CLONAL	1	TRUE	0	0.860694334561705	1		545	413	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233055	69233055	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs748459725	NA	P-0042236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	109	273	0	ENST00000462284.1:c.920A>G	p.Asp307Gly	p.D307G	ENST00000462284	NM_002392.5	307	gAc/gGc	11/11	1	2	FACETS	0.709	0.644	0.778	0.709	0.644	0.778	SUBCLONAL	1	TRUE	1	0.860694334561705	2		273	357	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38064113	38064113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	250	486	0	ENST00000250448.2:c.65C>T	p.Thr22Met	p.T22M	ENST00000250448	NM_004496.3	22	aCg/aTg	1/2	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.860694334561705	2		486	544	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440760	56440760	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	311	602	0	ENST00000407977.2:c.458A>G	p.Gln153Arg	p.Q153R	ENST00000407977		153	cAg/cGg	5/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.860694334561705	2		602	714	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0042252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	335	593	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.145558268307181	4	FACETS	1	0.994	1			1	INDETERMINATE	3	TRUE	NA	0.751423153476141	4		595	449	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43817892	43817892	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	137	318	1	ENST00000372470.3:c.1571T>C	p.Leu524Pro	p.L524P	ENST00000372470	NM_005373.2	524	cTg/cCg	11/12	0.751423153476141	4	FACETS	0.935	0.852	1	0.468	0.426	0.511	CLONAL	1	TRUE	2	0.751423153476141	4		319	683	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912189	114912189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867720073	NA	P-0042252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	291	317	2	ENST00000543371.1:c.1259G>A	p.Arg420Gln	p.R420Q	ENST00000543371	NM_001198531.1	420	cGg/cAg	11/14	0.751423153476141	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.751423153476141	2		319	377	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060802	38060826	+	frameshift_variant	Frame_Shift_Del	DEL	AAGGAGTAGTGGGGGTCCCCTTTCA	AAGGAGTAGTGGGGGTCCCCTTTCA	-	novel	NA	P-0042252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	191	647	0	ENST00000250448.2:c.1163_1187del	p.Leu388ProfsTer44	p.L388Pfs*44	ENST00000250448	NM_004496.3	388	cTGAAAGGGGACCCCCACTACTCCTTc/cc	2/2	0.751423153476141	4	FACETS	0.715	0.659	0.772	0.357	0.329	0.386	SUBCLONAL	1	TRUE	2	0.751423153476141	4		647	1246	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952073	178952073	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519937	NA	P-0042275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	66	315	0	ENST00000263967.3:c.3128T>C	p.Met1043Thr	p.M1043T	ENST00000263967	NM_006218.2	1043	aTg/aCg	21/21	1	2	FACETS	0.976	0.849	1	0.976	0.849	1	CLONAL	1	TRUE	1	0.29469415443102	2		315	459	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599024	28599024	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	62	353	0	ENST00000241453.7:c.2264T>G	p.Leu755Arg	p.L755R	ENST00000241453	NM_004119.2	755	cTt/cGt	18/24	0.64076909656631	2	FACETS	0.698	0.609	0.793	0.349	0.304	0.397	SUBCLONAL	1	TRUE	0	0.643548102596926	2		353	276	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0042309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	107	285	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.590824039311343	3	FACETS	0.835	0.761	0.911	0.557	0.507	0.607	CLONAL	2	TRUE	0	0.590824039311343	3		285	281	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519938	NA	P-0042309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	24	338	0	ENST00000263967.3:c.1034A>C	p.Asn345Thr	p.N345T	ENST00000263967	NM_006218.2	345	aAt/aCt	5/21	1	2	FACETS	0.243	0.19	0.304	0.243	0.19	0.304	SUBCLONAL	1	TRUE	1	0.590824039311343	2		338	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0042309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	172	656	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.653	0.601	0.707	0.653	0.601	0.707	SUBCLONAL	1	TRUE	1	0.590824039311343	2		656	892	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0042309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	109	303	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	0.767	0.692	0.845	0.767	0.692	0.845	SUBCLONAL	1	TRUE	1	0.590824039311343	2		303	481	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052629	42052629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	205	615	1	ENST00000219905.7:c.7300C>T	p.Arg2434Trp	p.R2434W	ENST00000219905	NM_001164273.1	2434	Cgg/Tgg	20/24	1	2	FACETS	0.965	0.899	1	0.965	0.899	1	CLONAL	1	TRUE	1	0.590824039311343	2		616	719	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907683	111907684	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCGTATT	novel	NA	P-0042309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	103	564	0	ENST00000393256.3:c.460_467dup	p.Asp157ValfsTer16	p.D157Vfs*16	ENST00000393256	NM_006538.4	153	cgg/cGGCGTATTgg	3/4	1	2	FACETS	0.549	0.492	0.61	0.549	0.492	0.61	SUBCLONAL	1	TRUE	1	0.590824039311343	2		564	635	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0042324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	826	1042	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.872197273832267	2	FACETS	0.951	0.936	0.964	0.951	0.936	0.964	CLONAL	2	TRUE	0	0.925331662644307	2		1042	939	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061007	38061007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1388229958	NA	P-0042324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	122	168	0	ENST00000250448.2:c.982C>T	p.Pro328Ser	p.P328S	ENST00000250448	NM_004496.3	328	Ccc/Tcc	2/2	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.925331662644307	2		168	228	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317091	87317091	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	172	435	0	ENST00000277120.3:c.230A>T	p.Lys77Ile	p.K77I	ENST00000277120		77	aAa/aTa	3/19	0.897359021070379	2	FACETS	0.939	0.875	1	0.469	0.437	0.502	CLONAL	1	TRUE	0	0.925331662644307	2		435	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0042333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	489	593	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.854054791263395	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.953024311679486	1		595	518	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998307	100998308	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0042333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	103	74	0	ENST00000325455.5:c.1494dup	p.Ser499LeufsTer75	p.S499Lfs*75	ENST00000325455	NM_001202474.3	498	-/C	1/8	0.953024311679486	2	FACETS	0.992	0.96	1	0.992	0.96	1	CLONAL	2	TRUE	0	0.953024311679486	2		74	109	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864456	57864456	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	374	484	1	ENST00000228682.2:c.1933G>A	p.Ala645Thr	p.A645T	ENST00000228682	NM_005269.2	645	Gct/Act	12/12	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.953024311679486	2		485	778	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215796	133215796	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753627422	NA	P-0042333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	394	498	1	ENST00000320574.5:c.5467C>T	p.Arg1823Cys	p.R1823C	ENST00000320574	NM_006231.2	1823	Cgc/Tgc	40/49	1	2	FACETS	0.913	0.872	0.954	0.913	0.872	0.954	CLONAL	1	TRUE	1	0.953024311679486	2		499	906	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732934	30732935	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTTGA	novel	NA	P-0042333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	162	281	0	ENST00000295754.5:c.1548_1552dup	p.Thr518SerfsTer2	p.T518Sfs*2	ENST00000295754	NM_003242.5	516	acg/acGTTGAg	7/7	1	2	FACETS	0.813	0.755	0.873	0.813	0.755	0.873	CLONAL	1	TRUE	1	0.953024311679486	2		281	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0042351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	140	619	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.3918901158887	1	FACETS	0.909	0.832	0.99	0.909	0.832	0.99	CLONAL	1	TRUE	0	0.423665391041715	1		619	573	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs1057519842	NA	P-0042351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	76	327	0	ENST00000274335.5:c.1727_1729del	p.Thr576del	p.T576del	ENST00000274335		575	aaGACg/aag	12/15	0.3918901158887	1	FACETS	0.799	0.706	0.898	0.799	0.706	0.898	SUBCLONAL	1	TRUE	0	0.423665391041715	1		327	354	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250865	153250865	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	91	449	1	ENST00000281708.4:c.1195G>T	p.Asp399Tyr	p.D399Y	ENST00000281708	NM_033632.3	399	Gat/Tat	8/12	1	2	FACETS	0.842	0.75	0.94	0.842	0.75	0.94	CLONAL	1	TRUE	1	0.423665391041715	2		450	510	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992676	72992676	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	94	564	0	ENST00000268489.5:c.1369G>T	p.Glu457Ter	p.E457*	ENST00000268489	NM_006885.3	457	Gag/Tag	2/10	0.423665391041715	1	FACETS	0.866	0.775	0.961	0.866	0.775	0.961	CLONAL	1	TRUE	0	0.423665391041715	1		564	404	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0042356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	460	810	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.53375141045643	2	FACETS	0.934	0.898	0.969	0.934	0.898	0.969	CLONAL	2	TRUE	0	0.575607202950809	2		810	856	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	178	541	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.969	0.897	1	0.969	0.897	1	CLONAL	1	TRUE	1	0.575607202950809	2		541	638	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512383	38512383	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1188389540	NA	P-0042356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	175	323	0	ENST00000254066.5:c.1294C>T	p.Arg432Trp	p.R432W	ENST00000254066	NM_000964.3	432	Cgg/Tgg	9/9	0.575607202950809	3	FACETS	0.926	0.853	1	0.463	0.426	0.501	CLONAL	1	TRUE	1	0.575607202950809	3		323	846	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422521	225422521	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	37	227	0	ENST00000264414.4:c.119C>T	p.Ala40Val	p.A40V	ENST00000264414	NM_003590.4	40	gCa/gTa	2/16	1	2	FACETS	0.268	0.22	0.321	0.268	0.22	0.321	SUBCLONAL	1	TRUE	1	0.575607202950809	2		227	480	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346684	225346684	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	133	275	0	ENST00000264414.4:c.1954G>T	p.Glu652Ter	p.E652*	ENST00000264414	NM_003590.4	652	Gaa/Taa	14/16	1	2	FACETS	0.919	0.839	1	0.919	0.839	1	CLONAL	1	TRUE	1	0.575607202950809	2		275	503	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929570	44929570	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	179	127	0	ENST00000377967.4:c.2670C>A	p.Tyr890Ter	p.Y890*	ENST00000377967	NM_021140.2	890	taC/taA	17/29	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.575607202950809	1		127	324	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188251	10188251	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs5030813	NA	P-0042389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	67	689	0	ENST00000256474.2:c.394C>T	p.Gln132Ter	p.Q132*	ENST00000256474	NM_000551.3	132	Caa/Taa	2/3	0.20734959555504	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	FALSE	0	0.20734959555504	1		689	517	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748513	43748513	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	43	434	0	ENST00000523873.1:c.467A>C	p.Lys156Thr	p.K156T	ENST00000523873		156	aAg/aCg	6/8	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	FALSE	1	0.20734959555504	2		434	396	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0042398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	361	272	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.516302943337336	5	FACETS	0.985	0.951	1	0.985	0.951	1	CLONAL	5	TRUE	0	0.516145306631502	5		272	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0042398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	512	697	2	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.497230069030916	3	FACETS	0.937	0.905	0.969	0.937	0.905	0.969	CLONAL	3	TRUE	0	0.516145306631502	3		699	888	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729606	41729606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	225	499	0	ENST00000242208.4:c.923G>A	p.Arg308His	p.R308H	ENST00000242208	NM_002192.2	308	cGt/cAt	3/3	0.25760132840274	5	FACETS	1	0.981	1	0.746	0.698	0.795	INDETERMINATE	2	TRUE	2	0.516145306631502	5		499	691	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845397	151845397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779339485	NA	P-0042398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	146	596	1	ENST00000262189.6:c.13615G>A	p.Val4539Met	p.V4539M	ENST00000262189	NM_170606.2	4539	Gtg/Atg	52/59	0.25760132840274	5	FACETS	1	0.981	1	0.419	0.383	0.458	INDETERMINATE	1	TRUE	2	0.516145306631502	5		597	798	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983110	201983114	+	frameshift_variant	Frame_Shift_Del	DEL	AGAAC	AGAAC	-	novel	NA	P-0042398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	327	708	0	ENST00000359651.3:c.961_965del	p.Asn321GlnfsTer148	p.N321Qfs*148	ENST00000359651		320	aAGAAC/a	7/8	0.289755140433476	5	FACETS	1	0.963	1	0.682	0.645	0.72	INDETERMINATE	2	TRUE	2	0.516145306631502	5		708	1099	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045953	26045953	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1325561730	NA	P-0042398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	23	445	0	ENST00000540144.1:c.315C>G	p.Phe105Leu	p.F105L	ENST00000540144	NM_003531.2	105	ttC/ttG	1/1	NA	2	FACETS	0.221	0.171	0.278			1	INDETERMINATE	1	TRUE	NA	0.516145306631502	2		445	404	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930111	68930111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	89	342	0	ENST00000288368.4:c.172G>T	p.Ala58Ser	p.A58S	ENST00000288368	NM_024870.2	58	Gca/Tca	2/40	0.410953105336136	3	FACETS	1	0.91	1	0.512	0.456	0.57	CLONAL	1	TRUE	1	0.516145306631502	3		342	424	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042400-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	82	415	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.142414064149411	0	FACETS	0.748	0.663	0.837			1	INDETERMINATE	1	FALSE	0	0.357086050268121	0		415	395	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0042400-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	8	503	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.137	0.088	0.202	0.137	0.088	0.202	SUBCLONAL	1	FALSE	1	0.357086050268121	2		503	326	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982141	201982142	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0042400-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	197	807	0	ENST00000359651.3:c.666dup	p.Asp223Ter	p.D223*	ENST00000359651		222	act/acTt	5/8	0.199209037393392	0	FACETS	1	0.968	1			1	INDETERMINATE	1	FALSE	0	0.357086050268121	0		807	663	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111982980	111982980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042400-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	49	653	0	ENST00000368678.4:c.1567G>A	p.Ala523Thr	p.A523T	ENST00000368678		523	Gcg/Acg	13/13	1	2	FACETS	0.599	0.508	0.699	0.599	0.508	0.699	SUBCLONAL	1	FALSE	1	0.357086050268121	2		653	458	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0042404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	148	326	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.155490191454366	3	FACETS	1	0.976	1	0.59	0.54	0.643	INDETERMINATE	1	TRUE	1	0.402211387112309	3		326	749	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0042404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	183	727	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	0.376501025653581	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.402211387112309	1		727	713	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061636	38061636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	50	94	1	ENST00000250448.2:c.353C>T	p.Ala118Val	p.A118V	ENST00000250448	NM_004496.3	118	gCg/gTg	2/2	1	2	FACETS	0.834	0.723	0.95	1	0.973	1	CLONAL	2	TRUE	1	0.402211387112309	2		95	149	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604462	48604747	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGATAAAGTTTAGATCTACTGTTACTTCTTGGCACTTTAGCAGAGAAGTTATATGCTGAGGAGAATGAAATACAGAAAGCTGGTCACTTGATTAATTTAGAATGTAGGGAGGATGGGAAGAGATCACCCTGTCCCTCTGATGTCTTCCAAATCTTTTCTGTTAGGTCTGTCAGCTGCTGCTGGAATTGGTGTTGATGACCTTCGTCGCTTATGCATACTCAGGATGAGTTTTGTGAAAGGCTGGGGACCGGATTACCCAAGACAGAGCATCAAAGAAACACCTTGC	TGATAAAGTTTAGATCTACTGTTACTTCTTGGCACTTTAGCAGAGAAGTTATATGCTGAGGAGAATGAAATACAGAAAGCTGGTCACTTGATTAATTTAGAATGTAGGGAGGATGGGAAGAGATCACCCTGTCCCTCTGATGTCTTCCAAATCTTTTCTGTTAGGTCTGTCAGCTGCTGCTGGAATTGGTGTTGATGACCTTCGTCGCTTATGCATACTCAGGATGAGTTTTGTGAAAGGCTGGGGACCGGATTACCCAAGACAGAGCATCAAAGAAACACCTTGC	-	novel	NA	P-0042404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	58	43	0	ENST00000342988.3:c.1448-162_1571del		p.X483_splice	ENST00000342988	NM_005359.5	483		12/12	0.376501025653581	1	FACETS	0.972	0.891	1	1	0.986	1	CLONAL	3	TRUE	0	0.402211387112309	1		43	79	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212363	36212363	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	221	949	0	ENST00000222270.7:c.2114C>G	p.Pro705Arg	p.P705R	ENST00000222270	NM_014727.1	705	cCt/cGt	3/37	1	2	FACETS	0.954	0.887	1	0.954	0.887	1	CLONAL	1	TRUE	1	0.402211387112309	2		949	1152	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970972	21970973	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0042404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	167	635	0	ENST00000304494.5:c.385dup	p.Tyr129LeufsTer13	p.Y129Lfs*13	ENST00000304494	NM_000077.4	129	tac/tTac	2/3	0.402211387112309	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.402211387112309	1		635	613	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0042405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	147	311	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.50293570407853	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.50293570407853	2		311	268	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579410	7579411	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0042405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	684	715	0	ENST00000269305.4:c.276_277del	p.Leu93ValfsTer55	p.L93Vfs*55	ENST00000269305	NM_001126112.2	92	ccCCtg/cctg	4/11	0.50293570407853	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.50293570407853	3		715	1079	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799195	42799195	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	211	655	0	ENST00000575354.2:c.4679C>A	p.Thr1560Asn	p.T1560N	ENST00000575354	NM_015125.3	1560	aCc/aAc	20/20	0.287122122725088	3	FACETS	1	0.988	1	0.647	0.602	0.693	INDETERMINATE	1	TRUE	1	0.50293570407853	3		655	812	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0042420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	187	735	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.388810133203984	2		735	855	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0042420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	248	838	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.388810133203984	2		838	1223	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275465	38275465	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	177	624	0	ENST00000425967.3:c.1568T>C	p.Val523Ala	p.V523A	ENST00000425967	NM_001174067.1	523	gTg/gCg	12/19	0.388810133203984	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.388810133203984	1		624	728	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911895	32911895	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	130	439	0	ENST00000380152.3:c.3403del	p.Tyr1135ThrfsTer15	p.Y1135Tfs*15	ENST00000380152		1135	Tac/ac	11/27	0.388810133203984	1	FACETS	0.969	0.883	1	0.969	0.883	1	CLONAL	1	TRUE	0	0.388810133203984	1		439	556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882025	NA	P-0042485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	184	900	0	ENST00000269305.4:c.646G>T	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ttg	6/11	0.196313980512984	2	FACETS	1	0.988	1	0.696	0.642	0.752	CLONAL	1	TRUE	0	0.28	2		900	944	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523348	9523348	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	42	480	0	ENST00000353224.5:c.1889G>T	p.Gly630Val	p.G630V	ENST00000353224	NM_177990.2	630	gGg/gTg	9/10	1	2	FACETS	0.563	0.469	0.667	0.563	0.469	0.667	SUBCLONAL	1	TRUE	1	0.28	2		480	533	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0042489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	50	373	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.712	0.606	0.828	0.712	0.606	0.828	SUBCLONAL	1	FALSE	1	0.355640805303471	2		373	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0042489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	222	746	1	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	0.292550088113697	2	FACETS	0.878	0.821	0.937	0.878	0.821	0.937	CLONAL	2	FALSE	0	0.355640805303471	2		747	711	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609330	81609330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121908882	NA	P-0042489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	46	348	0	ENST00000298171.2:c.928C>T	p.Arg310Cys	p.R310C	ENST00000298171	NM_000369.2	310	Cgc/Tgc	10/10	1	2	FACETS	0.877	0.743	1	0.877	0.743	1	CLONAL	1	FALSE	1	0.355640805303471	2		348	295	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964992	15964992	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	80	643	0	ENST00000268712.3:c.5604G>C	p.Gln1868His	p.Q1868H	ENST00000268712	NM_006311.3	1868	caG/caC	37/46	0.292550088113697	2	FACETS	0.827	0.729	0.931	0.414	0.364	0.466	CLONAL	1	FALSE	0	0.355640805303471	2		643	544	SUCCESS
APC	324	MSKCC	GRCh37	5	112173607	112173608	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0042489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	24	300	0	ENST00000257430.4:c.2318_2319del	p.Phe773Ter	p.F773*	ENST00000257430	NM_000038.5	772	acTTtt/actt	16/16	1	2	FACETS	0.689	0.543	0.854	0.689	0.543	0.854	SUBCLONAL	1	FALSE	1	0.355640805303471	2		300	196	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911248	29911262	+	inframe_deletion	In_Frame_Del	DEL	TACCTGGATGGCACG	TACCTGGATGGCACG	-	novel	NA	P-0042489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	75	601	0	ENST00000376809.5:c.548_562del	p.Tyr183_Thr187del	p.Y183_T187del	ENST00000376809	NM_002116.7	183	TACCTGGATGGCACG/-	3/8	1	2	FACETS	0.771	0.677	0.872	0.771	0.677	0.872	SUBCLONAL	1	FALSE	1	0.355640805303471	2		601	547	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578206	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs886039484	NA	P-0042498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	1328	872	0	ENST00000269305.4:c.643A>G	p.Ser215Gly	p.S215G	ENST00000269305	NM_001126112.2	215	Agt/Ggt	6/11	0.816822538374471	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.816822538374471	3		872	1501	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045854	143045854	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	262	629	0	ENST00000262992.4:c.1780G>T	p.Val594Leu	p.V594L	ENST00000262992	NM_001101669.1	594	Gtg/Ttg	17/24	1	2	FACETS	0.959	0.904	1	0.959	0.904	1	CLONAL	1	TRUE	1	0.816822538374471	2		629	669	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013723	12013723	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	58	191	0	ENST00000353533.5:c.665A>T	p.Asn222Ile	p.N222I	ENST00000353533	NM_003010.3	222	aAc/aTc	6/11	0.816822538374471	3	FACETS	1	0.935	1	0.37	0.324	0.419	CLONAL	1	TRUE	0	0.816822538374471	3		191	180	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213959	2213959	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	805	838	0	ENST00000398665.3:c.1771G>T	p.Ala591Ser	p.A591S	ENST00000398665	NM_032482.2	591	Gcg/Tcg	18/28	0.816822538374471	2	FACETS	0.995	0.977	1	0.995	0.977	1	CLONAL	2	TRUE	0	0.816822538374471	2		838	990	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278071	18278071	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	954	1003	0	ENST00000222254.8:c.1691A>C	p.Lys564Thr	p.K564T	ENST00000222254	NM_005027.3	564	aAg/aCg	13/16	0.816822538374471	2	FACETS	0.997	0.98	1	0.997	0.98	1	CLONAL	2	TRUE	0	0.816822538374471	2		1003	1171	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443292	187443292	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370028442	NA	P-0042498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	163	313	1	ENST00000232014.4:c.1834G>A	p.Val612Ile	p.V612I	ENST00000232014	NM_001130845.1	612	Gta/Ata	8/10	0.771216039475365	4	FACETS	1	0.927	1	0.504	0.464	0.546	CLONAL	1	TRUE	2	0.816822538374471	4		314	719	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31451746	31451746	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	352	292	0	ENST00000344624.3:c.2576A>T	p.His859Leu	p.H859L	ENST00000344624		859	cAt/cTt	18/33	0.816822538374471	6	FACETS	1	0.975	1	1	0.975	1	CLONAL	4	TRUE	2	0.816822538374471	6		292	557	SUCCESS
APC	324	MSKCC	GRCh37	5	112154798	112154798	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1297299413	NA	P-0042498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	270	620	0	ENST00000257430.4:c.1069A>G	p.Ile357Val	p.I357V	ENST00000257430	NM_000038.5	357	Atc/Gtc	10/16	0.312012434308797	2	FACETS	1	0.965	1	0.514	0.486	0.543	INDETERMINATE	1	TRUE	0	0.816822538374471	2		620	643	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0042499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	144	368	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.614456112460709	2		368	458	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	206	541	0				ENST00000310581	NM_198253.2	-/1132			0.614456112460709	3	FACETS	0.955	0.896	1	0.955	0.896	1	CLONAL	2	TRUE	1	0.614456112460709	3		541	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	200	761	0	ENST00000269305.4:c.775G>C	p.Asp259His	p.D259H	ENST00000269305	NM_001126112.2	259	Gac/Cac	7/11	0.614456112460709	1	FACETS	0.867	0.811	0.925	0.867	0.811	0.925	CLONAL	1	TRUE	0	0.614456112460709	1		761	520	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900314	101900314	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	89	338	0	ENST00000374994.4:c.748C>T	p.Gln250Ter	p.Q250*	ENST00000374994	NM_004612.2	250	Caa/Taa	4/9	0.614456112460709	1	FACETS	0.592	0.53	0.657	0.592	0.53	0.657	SUBCLONAL	1	TRUE	0	0.614456112460709	1		338	339	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263856	133263856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241114520	NA	P-0042499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	13	277	0	ENST00000320574.5:c.46G>A	p.Asp16Asn	p.D16N	ENST00000320574	NM_006231.2	16	Gat/Aat	1/49	1	2	FACETS	0.163	0.116	0.22	0.163	0.116	0.22	SUBCLONAL	1	TRUE	1	0.614456112460709	2		277	260	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434922	56434922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	196	777	1	ENST00000407977.2:c.2215C>T	p.Pro739Ser	p.P739S	ENST00000407977		739	Cca/Tca	9/10	1	2	FACETS	0.991	0.922	1	0.991	0.922	1	CLONAL	1	TRUE	1	0.614456112460709	2		778	644	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256759	19256759	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	121	695	0	ENST00000162023.5:c.954C>G	p.Ile318Met	p.I318M	ENST00000162023		318	atC/atG	13/13	1		FACETS		0.599	0.726				SUBCLONAL	1	TRUE	1	0.614456112460709	2		695	596	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401189	139401189	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1247035429	NA	P-0042499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	242	815	0	ENST00000277541.6:c.3880G>A	p.Glu1294Lys	p.E1294K	ENST00000277541	NM_017617.3	1294	Gag/Aag	23/34	0.614456112460709	1	FACETS	0.879	0.827	0.932	0.879	0.827	0.932	CLONAL	1	TRUE	0	0.614456112460709	1		815	621	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	224	707	7	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.976	0.911	1	0.976	0.911	1	CLONAL	1	TRUE	1	0.553559041200677	2		714	829	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	105	471	5	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.526	0.471	0.584	0.526	0.471	0.584	SUBCLONAL	1	TRUE	1	0.553559041200677	2		476	721	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	95	214	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	1	2	FACETS	0.882	0.791	0.978	0.882	0.791	0.978	CLONAL	1	TRUE	1	0.553559041200677	2		214	389	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	113	681	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.553559041200677	2		681	392	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101267	27101268	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	252	674	0	ENST00000324856.7:c.4555dup	p.Gln1519ProfsTer13	p.Q1519Pfs*13	ENST00000324856	NM_006015.4	1517	gcc/gCcc	18/20	1	2	FACETS	0.889	0.832	0.948	0.889	0.832	0.948	CLONAL	1	TRUE	1	0.553559041200677	2		674	1024	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797418	45797418	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs768130289	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	298	775	1	ENST00000450313.1:c.1101del	p.Arg368GlyfsTer40	p.R368Gfs*40	ENST00000450313	NM_012222.2	367	ccC/cc	12/16	1	2	FACETS	0.906	0.853	0.961	0.906	0.853	0.961	CLONAL	1	TRUE	1	0.553559041200677	2		776	1188	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205266	61205266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753474292	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	252	533	0	ENST00000301761.2:c.206G>A	p.Arg69His	p.R69H	ENST00000301761	NM_017841.2	69	cGc/cAc	2/4	1	2	FACETS	0.992	0.929	1	0.992	0.929	1	CLONAL	1	TRUE	1	0.553559041200677	2		533	918	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199953	108199953	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	32	168	0	ENST00000278616.4:c.7295T>C	p.Ile2432Thr	p.I2432T	ENST00000278616	NM_000051.3	2432	aTt/aCt	49/63	1	2	FACETS	0.378	0.307	0.457	0.378	0.307	0.457	SUBCLONAL	1	TRUE	1	0.553559041200677	2		168	306	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641389	18641389	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1229278001	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	106	171	1	ENST00000266497.5:c.2393del	p.Asn798MetfsTer16	p.N798Mfs*16	ENST00000266497		796	ctA/ct	17/31	0.553559041200677	2	FACETS	1	0.96	1	0.555	0.503	0.609	CLONAL	1	TRUE	0	0.553559041200677	2		172	345	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425348	49425349	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	353	872	0	ENST00000301067.7:c.13139dup	p.Asp4381ArgfsTer29	p.D4381Rfs*29	ENST00000301067	NM_003482.3	4380	cca/ccCa	39/54	0.553559041200677	2	FACETS	1	0.96	1	0.508	0.481	0.536	CLONAL	1	TRUE	0	0.553559041200677	2		872	1255	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249213	133249213	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	239	538	0	ENST00000320574.5:c.1686G>T	p.Met562Ile	p.M562I	ENST00000320574	NM_006231.2	562	atG/atT	15/49	0.553559041200677	2	FACETS	1	0.976	1	0.543	0.508	0.579	CLONAL	1	TRUE	0	0.553559041200677	2		538	795	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	262	432	11	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.553559041200677	2		443	873	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2114280	2114280	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	307	650	0	ENST00000219476.3:c.1451T>C	p.Leu484Pro	p.L484P	ENST00000219476	NM_000548.3	484	cTg/cCg	15/42	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.553559041200677	2		650	978	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	108	423	3	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.535	0.48	0.593	0.535	0.48	0.593	SUBCLONAL	1	TRUE	1	0.553559041200677	2		426	730	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619279	23619279	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587776527	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	241	663	0	ENST00000261584.4:c.3256C>T	p.Arg1086Ter	p.R1086*	ENST00000261584	NM_024675.3	1086	Cga/Tga	12/13	1	2	FACETS	0.899	0.84	0.959	0.899	0.84	0.959	CLONAL	1	TRUE	1	0.553559041200677	2		663	969	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929493	81929493	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs746612517	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	240	555	0	ENST00000359376.3:c.1154T>C	p.Val385Ala	p.V385A	ENST00000359376	NM_002661.3	385	gTc/gCc	13/33	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.553559041200677	2		555	846	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351004	89351004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	375	750	1	ENST00000301030.4:c.1946G>A	p.Ser649Asn	p.S649N	ENST00000301030	NM_001256183.1	649	aGc/aAc	9/13	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.553559041200677	2		751	1346	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110505	8110505	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	168	396	0	ENST00000585124.1:c.387G>T	p.Gln129His	p.Q129H	ENST00000585124	NM_004217.3	129	caG/caT	5/9	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.553559041200677	2		396	586	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973765	15973765	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	84	450	0	ENST00000268712.3:c.4227del	p.Pro1410LeufsTer18	p.P1410Lfs*18	ENST00000268712	NM_006311.3	1409	ggG/gg	31/46	1	2	FACETS	0.408	0.36	0.46	0.408	0.36	0.46	SUBCLONAL	1	TRUE	1	0.553559041200677	2		450	744	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024417	16024417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771531803	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	168	371	1	ENST00000268712.3:c.1801G>A	p.Ala601Thr	p.A601T	ENST00000268712	NM_006311.3	601	Gca/Aca	16/46	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.553559041200677	2		372	602	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024476	16024476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	103	470	1	ENST00000268712.3:c.1742G>A	p.Arg581His	p.R581H	ENST00000268712	NM_006311.3	581	cGt/cAt	16/46	1	2	FACETS	0.509	0.455	0.566	0.509	0.455	0.566	SUBCLONAL	1	TRUE	1	0.553559041200677	2		471	731	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370254	40370254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750053820	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	333	714	0	ENST00000293328.3:c.1084G>A	p.Val362Met	p.V362M	ENST00000293328	NM_012448.3	362	Gtg/Atg	9/19	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.553559041200677	2		714	1025	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	294	855	4	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.888	0.835	0.942	0.888	0.835	0.942	CLONAL	1	TRUE	1	0.553559041200677	2		859	1196	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617669	39617669	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	53	260	0	ENST00000262039.4:c.1853C>A	p.Pro618His	p.P618H	ENST00000262039	NM_002647.2	618	cCt/cAt	17/25	1	2	FACETS	0.399	0.34	0.463	0.399	0.34	0.463	SUBCLONAL	1	TRUE	1	0.553559041200677	2		260	480	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125395	7125395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs185736681	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	323	853	0	ENST00000302850.5:c.3157C>T	p.Arg1053Cys	p.R1053C	ENST00000302850	NM_000208.2	1053	Cgc/Tgc	17/22	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.553559041200677	2		853	1091	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223614	36223614	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	363	938	1	ENST00000222270.7:c.6169del	p.Arg2057AlafsTer34	p.R2057Afs*34	ENST00000222270	NM_014727.1	2055	gCc/gc	28/37	1	2	FACETS	0.939	0.89	0.99	0.939	0.89	0.99	CLONAL	1	TRUE	1	0.553559041200677	2		939	1396	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794440	42794440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776806622	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	430	1017	0	ENST00000575354.2:c.1520G>A	p.Arg507His	p.R507H	ENST00000575354	NM_015125.3	507	cGc/cAc	10/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.553559041200677	2		1017	1378	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606123	47606123	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	64	290	0	ENST00000263735.4:c.587T>C	p.Val196Ala	p.V196A	ENST00000263735	NM_002354.2	196	gTt/gCt	6/9	1	2	FACETS	0.368	0.318	0.422	0.368	0.318	0.422	SUBCLONAL	1	TRUE	1	0.553559041200677	2		290	629	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152265	99152265	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	57	374	0	ENST00000074304.5:c.344T>C	p.Val115Ala	p.V115A	ENST00000074304	NM_001134224.1	115	gTc/gCc	6/26	1	2	FACETS	0.294	0.252	0.341	0.294	0.252	0.341	SUBCLONAL	1	TRUE	1	0.553559041200677	2		374	700	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434182	12434182	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776687	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	203	439	1	ENST00000287820.6:c.556del	p.Ser186ValfsTer47	p.S186Vfs*47	ENST00000287820	NM_015869.4	184	Aaa/aa	4/7	1	2	FACETS	0.944	0.877	1	0.944	0.877	1	CLONAL	1	TRUE	1	0.553559041200677	2		440	777	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932713	49932713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1156805771	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	367	784	1	ENST00000296474.3:c.3158G>A	p.Arg1053Gln	p.R1053Q	ENST00000296474	NM_002447.2	1053	cGg/cAg	14/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.553559041200677	2		785	1234	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588784	52588784	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1368022648	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	247	604	0	ENST00000394830.3:c.4244A>G	p.His1415Arg	p.H1415R	ENST00000394830	NM_018313.4	1415	cAt/cGt	27/30	1	2	FACETS	0.944	0.884	1	0.944	0.884	1	CLONAL	1	TRUE	1	0.553559041200677	2		604	945	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682400	52682400	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	174	292	0	ENST00000394830.3:c.773del	p.Asn258MetfsTer25	p.N258Mfs*25	ENST00000394830	NM_018313.4	258	aAt/at	8/30	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.553559041200677	2		292	619	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73047245	73047245	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	203	367	0	ENST00000356692.5:c.56del	p.Lys19ArgfsTer14	p.K19Rfs*14	ENST00000356692		18	Aaa/aa	2/9	1	2	FACETS	0.97	0.902	1	0.97	0.902	1	CLONAL	1	TRUE	1	0.553559041200677	2		367	756	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468398	89468398	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1467832547	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	82	242	0	ENST00000336596.2:c.1938del	p.Glu647ArgfsTer9	p.E647Rfs*9	ENST00000336596	NM_005233.5	644	tcA/tc	11/17	1	2	FACETS	0.784	0.696	0.877	0.784	0.696	0.877	SUBCLONAL	1	TRUE	1	0.553559041200677	2		242	378	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204873	128204873	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	356	913	1	ENST00000341105.2:c.568del	p.Ala190LeufsTer28	p.A190Lfs*28	ENST00000341105	NM_032638.4	190	Gct/ct	3/6	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.553559041200677	2		914	1270	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951929	178951929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	176	392	2	ENST00000263967.3:c.2984C>T	p.Ala995Val	p.A995V	ENST00000263967	NM_006218.2	995	gCc/gTc	21/21	1	2	FACETS	0.932	0.862	1	0.932	0.862	1	CLONAL	1	TRUE	1	0.553559041200677	2		394	682	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270105	66270105	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	131	344	0	ENST00000273854.3:c.1777C>A	p.Leu593Ile	p.L593I	ENST00000273854	NM_004439.5	593	Ctc/Atc	8/18	NA	2	FACETS	0.867	0.79	0.947			1	INDETERMINATE	1	TRUE	NA	0.553559041200677	2		344	546	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535316	66535316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	226	846	3	ENST00000273854.3:c.145G>A	p.Ala49Thr	p.A49T	ENST00000273854	NM_004439.5	49	Gca/Aca	1/18	NA	2	FACETS	0.927	0.865	0.991			1	INDETERMINATE	1	TRUE	NA	0.553559041200677	2		849	881	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157563	106157563	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	51	257	0	ENST00000380013.4:c.2464A>G	p.Thr822Ala	p.T822A	ENST00000380013	NM_001127208.2	822	Acc/Gcc	3/11	1	2	FACETS	0.35	0.297	0.408	0.35	0.297	0.408	SUBCLONAL	1	TRUE	1	0.553559041200677	2		257	526	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1268684	1268684	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	65	817	0	ENST00000310581.5:c.2533T>C	p.Cys845Arg	p.C845R	ENST00000310581	NM_198253.2	845	Tgc/Cgc	9/16	1	2	FACETS	0.193	0.167	0.223	0.193	0.167	0.223	SUBCLONAL	1	TRUE	1	0.553559041200677	2		817	1214	SUCCESS
APC	324	MSKCC	GRCh37	5	112163644	112163644	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	97	279	0	ENST00000257430.4:c.1567A>G	p.Lys523Glu	p.K523E	ENST00000257430	NM_000038.5	523	Aaa/Gaa	13/16	1	2	FACETS	0.738	0.661	0.819	0.738	0.661	0.819	SUBCLONAL	1	TRUE	1	0.553559041200677	2		279	475	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923673	131923673	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28903090	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	152	299	0	ENST00000265335.6:c.943G>T	p.Val315Leu	p.V315L	ENST00000265335		315	Gta/Tta	7/25	1	2	FACETS	0.981	0.902	1	0.981	0.902	1	CLONAL	1	TRUE	1	0.553559041200677	2		299	560	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518740	176518740	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1369223288	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	317	883	1	ENST00000292408.4:c.658G>A	p.Gly220Ser	p.G220S	ENST00000292408	NM_213647.1	220	Ggc/Agc	6/18	1	2	FACETS	0.935	0.882	0.989	0.935	0.882	0.989	CLONAL	1	TRUE	1	0.553559041200677	2		884	1225	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911117	29911117	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	194	1005	0	ENST00000376809.5:c.416A>C	p.Gln139Pro	p.Q139P	ENST00000376809	NM_002116.7	139	cAg/cCg	3/8	1	2	FACETS	0.505	0.466	0.546	0.505	0.466	0.546	SUBCLONAL	1	TRUE	1	0.553559041200677	2		1005	1388	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323352	31323352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1428341966	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	145	535	0	ENST00000412585.2:c.637G>A	p.Val213Met	p.V213M	ENST00000412585	NM_005514.6	213	Gtg/Atg	4/8	1	2	FACETS	0.737	0.673	0.803	0.737	0.673	0.803	SUBCLONAL	1	TRUE	1	0.553559041200677	2		535	711	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	151	562	1	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	0.725	0.664	0.789	0.725	0.664	0.789	SUBCLONAL	1	TRUE	1	0.553559041200677	2		563	752	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164794	32164794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	281	584	0	ENST00000375023.3:c.5108C>T	p.Thr1703Ile	p.T1703I	ENST00000375023	NM_004557.3	1703	aCa/aTa	28/30	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.553559041200677	2		584	1000	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192411	138192411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759654484	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	124	231	0	ENST00000237289.4:c.47G>A	p.Arg16Gln	p.R16Q	ENST00000237289	NM_001270507.1	16	cGg/cAg	2/9	1	2	FACETS	0.912	0.83	0.998	0.912	0.83	0.998	CLONAL	1	TRUE	1	0.553559041200677	2		231	491	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194824	29194824	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1347	397	1028	0	ENST00000240100.2:c.904A>G	p.Arg302Gly	p.R302G	ENST00000240100	NM_001394.6	302	Agg/Ggg	4/4	0.523214140301336	3	FACETS	1	0.976	1	0.525	0.498	0.553	CLONAL	1	TRUE	1	0.553559041200677	3		1028	1744	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033246	69033246	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	222	532	0	ENST00000288368.4:c.3686T>A	p.Val1229Asp	p.V1229D	ENST00000288368	NM_024870.2	1229	gTc/gAc	30/40	0.523214140301336	3	FACETS	1	0.974	1	0.545	0.508	0.584	CLONAL	1	TRUE	1	0.553559041200677	3		532	939	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982011	70982011	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1342056205	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1342	161	1027	0	ENST00000276594.2:c.85T>C	p.Tyr29His	p.Y29H	ENST00000276594	NM_024504.3	29	Tac/Cac	2/8	0.523214140301336	3	FACETS	0.494	0.451	0.539	0.247	0.225	0.27	SUBCLONAL	1	TRUE	1	0.553559041200677	3		1027	1503	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965738	90965738	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104895031	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	157	194	0	ENST00000265433.3:c.1579G>T	p.Asp527Tyr	p.D527Y	ENST00000265433	NM_002485.4	527	Gat/Tat	11/16	0.523214140301336	3	FACETS	1	0.983	1	0.627	0.577	0.678	CLONAL	1	TRUE	1	0.553559041200677	3		194	578	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752960	128752960	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	204	458	0	ENST00000377970.2:c.1121A>G	p.His374Arg	p.H374R	ENST00000377970	NM_002467.4	374	cAc/cGc	3/3	0.523214140301336	3	FACETS	0.998	0.926	1	0.499	0.463	0.537	CLONAL	1	TRUE	1	0.553559041200677	3		458	943	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741236	145741236	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1323	399	869	1	ENST00000428558.2:c.1170T>G	p.Phe390Leu	p.F390L	ENST00000428558	NM_004260.3	390	ttT/ttG	6/22	0.523214140301336	3	FACETS	1	0.981	1	0.534	0.507	0.563	CLONAL	1	TRUE	1	0.553559041200677	3		870	1722	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907157	101907157	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554701926	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	74	293	0	ENST00000374994.4:c.1117G>A	p.Val373Met	p.V373M	ENST00000374994	NM_004612.2	373	Gtg/Atg	6/9	0.553559041200677	3	FACETS	0.429	0.375	0.488	0.215	0.187	0.244	SUBCLONAL	1	TRUE	1	0.553559041200677	3		293	795	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128305433	128305433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	262	565	1	ENST00000265960.3:c.863G>A	p.Gly288Glu	p.G288E	ENST00000265960	NM_001006617.1	288	gGa/gAa	7/12	0.553559041200677	3	FACETS	1	0.978	1	0.546	0.511	0.582	CLONAL	1	TRUE	1	0.553559041200677	3		566	1107	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133748300	133748300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	255	651	2	ENST00000318560.5:c.961G>A	p.Gly321Arg	p.G321R	ENST00000318560	NM_005157.4	321	Ggg/Agg	6/11	0.553559041200677	3	FACETS	0.973	0.91	1	0.486	0.455	0.519	CLONAL	1	TRUE	1	0.553559041200677	3		653	1209	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217291	7217315	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTGTCCTCCAGGGCTCCCTAGAAAG	GTGTCCTCCAGGGCTCCCTAGAAAG	-	novel	NA	P-0042503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	213	648	0	ENST00000380728.2:c.398-8_414del		p.X133_splice	ENST00000380728		133		6/11	1	2	FACETS	0.832	0.774	0.892	0.832	0.774	0.892	CLONAL	1	TRUE	1	0.553559041200677	2		648	925	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	85	541	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.999	0.891	1	0.999	0.891	1	CLONAL	1	TRUE	1	0.530364120530891	2		541	321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs864622237	NA	P-0042525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	328	559	0	ENST00000269305.4:c.700T>A	p.Tyr234Asn	p.Y234N	ENST00000269305	NM_001126112.2	234	Tac/Aac	7/11	0.530364120530891	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.530364120530891	2		559	598	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs149840192	NA	P-0042525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6337	199	843	0	ENST00000275493.2:c.866C>A	p.Ala289Asp	p.A289D	ENST00000275493	NM_005228.3	289	gCc/gAc	7/28	0.530364120530891	25	FACETS	0.815	0.749	0.884			1	CLONAL	1	TRUE	NA	0.530364120530891	25		843	6536	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221783	55221783	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4836	1090	742	0	ENST00000275493.2:c.827A>T	p.Gln276Leu	p.Q276L	ENST00000275493	NM_005228.3	276	cAg/cTg	7/28	0.530364120530891	25	FACETS	0.985	0.953	1			1	CLONAL	5	TRUE	NA	0.530364120530891	25		742	5926	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221798	55221798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5041	1128	801	0	ENST00000275493.2:c.842C>T	p.Pro281Leu	p.P281L	ENST00000275493	NM_005228.3	281	cCc/cTc	7/28	0.530364120530891	25	FACETS	0.979	0.948	1			1	CLONAL	5	TRUE	NA	0.530364120530891	25		801	6169	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157239	106157239	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	127	382	0	ENST00000380013.4:c.2140T>C	p.Ser714Pro	p.S714P	ENST00000380013	NM_001127208.2	714	Tca/Cca	3/11	0.651274470605641	3	FACETS	0.956	0.87	1	0.478	0.435	0.523	CLONAL	1	TRUE	1	0.651274470605641	3		382	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578455	+	protein_altering_variant	In_Frame_Del	DEL	CCATGGC	CCATGGC	GATG	novel	NA	P-0042548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	525	909	3	ENST00000269305.4:c.475_481delinsCATC	p.Ala159_Ala161delinsHisPro	p.A159_A161delinsHP	ENST00000269305	NM_001126112.2	159	GCCATGGcc/CATCcc	5/11	0.651274470605641	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.651274470605641	2		912	784	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0042554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	282	836	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.490410676866317	1	FACETS	0.88	0.828	0.934	0.88	0.828	0.934	CLONAL	1	TRUE	0	0.490410676866317	1		836	986	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0042554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	98	597	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.490410676866317	1	FACETS	0.833	0.75	0.92	0.833	0.75	0.92	CLONAL	1	TRUE	0	0.490410676866317	1		597	362	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39763593	39763593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767696935	NA	P-0042554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	53	382	1	ENST00000288319.7:c.859C>T	p.Arg287Cys	p.R287C	ENST00000288319	NM_182918.3	287	Cgt/Tgt	8/10	1	2	FACETS	0.495	0.422	0.573	0.495	0.422	0.573	SUBCLONAL	1	TRUE	1	0.490410676866317	2		383	437	SUCCESS
ATR	545	MSKCC	GRCh37	3	142284971	142284971	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	63	474	0	ENST00000350721.4:c.284G>T	p.Ser95Ile	p.S95I	ENST00000350721	NM_001184.3	95	aGt/aTt	3/47	1	2	FACETS	0.612	0.531	0.699	0.612	0.531	0.699	SUBCLONAL	1	TRUE	1	0.490410676866317	2		474	420	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180646	56180677	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GATGGCAGGTATGTTAATGTTTTAAATTACAA	GATGGCAGGTATGTTAATGTTTTAAATTACAA	-	novel	NA	P-0042554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	30	331	0	ENST00000399503.3:c.3975_3982+24del		p.X1325_splice	ENST00000399503	NM_005921.1	1325		16/20	1	2	FACETS	0.559	0.453	0.677	0.559	0.453	0.677	SUBCLONAL	1	TRUE	1	0.490410676866317	2		331	219	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	46	541	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.365822998414989	2		541	180	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057520000	NA	P-0042591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	215	833	0	ENST00000269305.4:c.452C>G	p.Pro151Arg	p.P151R	ENST00000269305	NM_001126112.2	151	cCc/cGc	5/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.365822998414989	2		833	1001	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0042591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	126	520	0	ENST00000269305.4:c.994-1G>T		p.X332_splice	ENST00000269305	NM_001126112.2	332			1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.365822998414989	2		520	665	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015357	176015357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	73	310	0	ENST00000367669.3:c.1381C>T	p.His461Tyr	p.H461Y	ENST00000367669	NM_022457.5	461	Cat/Tat	12/20	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.365822998414989	2		310	378	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121082	11121082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	83	623	0	ENST00000358026.2:c.2149G>A	p.Glu717Lys	p.E717K	ENST00000358026	NM_001128849.1	717	Gaa/Aaa	15/36	0.167474297579662	0	FACETS	0.473	0.417	0.532			1	INDETERMINATE	1	TRUE	0	0.365822998414989	0		623	609	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209101872	209101872	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	24	373	0	ENST00000345146.2:c.1176G>C	p.Leu392Phe	p.L392F	ENST00000345146	NM_005896.2	392	ttG/ttC	10/10	0.365822998414989	1	FACETS	0.232	0.181	0.291	0.232	0.181	0.291	SUBCLONAL	1	TRUE	0	0.365822998414989	1		373	462	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513238	44513238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	29	344	0	ENST00000291552.4:c.697G>A	p.Asp233Asn	p.D233N	ENST00000291552	NM_006758.2	233	Gat/Aat	8/8	1	2	FACETS	0.349	0.28	0.428	0.349	0.28	0.428	SUBCLONAL	1	TRUE	1	0.365822998414989	2		344	454	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586432	189586432	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	122	406	0	ENST00000264731.3:c.1056G>C	p.Arg352Ser	p.R352S	ENST00000264731	NM_003722.4	352	agG/agC	8/14	0.123143092621207	3	FACETS	1	0.985	1	0.735	0.667	0.805	INDETERMINATE	1	TRUE	1	0.365822998414989	3		406	537	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295171	1295171	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0042591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	36	92	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.365822998414989	2		92	137	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0042621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	252	565	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.523937305307847	3	FACETS	0.835	0.785	0.885	0.835	0.785	0.885	CLONAL	2	TRUE	1	0.54764531894089	3		565	702	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0042621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	163	377	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.488490618024013	4	FACETS	0.811	0.748	0.876	0.811	0.748	0.876	CLONAL	2	TRUE	2	0.54764531894089	4		377	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0042621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	585	327	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.304132615700237	5	FACETS	0.958	0.933	0.983			1	INDETERMINATE	5	TRUE	NA	0.54764531894089	5		327	812	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150496	157150496	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs17318151	NA	P-0042621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	239	560	0	ENST00000346085.5:c.1678A>G	p.Ile560Val	p.I560V	ENST00000346085	NM_020732.3	560	Att/Gtt	2/20	0.438752850478134	4	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	2	0.54764531894089	4		560	668	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	290	430	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	0.54764531894089	3	FACETS	0.975	0.934	1	0.975	0.934	1	CLONAL	3	TRUE	0	0.54764531894089	3		430	461	SUCCESS
AR	367	MSKCC	GRCh37	X	66766208	66766208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	163	501	1	ENST00000374690.3:c.1220G>A	p.Arg407His	p.R407H	ENST00000374690	NM_000044.3	407	cGc/cAc	1/8	0.132561692360761	6	FACETS	0.875	0.81	0.942	0.875	0.81	0.942	INDETERMINATE	3	TRUE	3	0.54764531894089	6		502	475	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32899249	32899249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358603	NA	P-0042621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	77	283	2	ENST00000380152.3:c.353G>A	p.Arg118His	p.R118H	ENST00000380152		118	cGc/cAc	4/27	0.523937305307847	3	FACETS	1	0.897	1	0.507	0.448	0.57	CLONAL	1	TRUE	1	0.54764531894089	3		285	353	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0042628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	142	373	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.435865741591408	4	FACETS	0.844	0.774	0.916	0.844	0.774	0.916	CLONAL	2	TRUE	2	0.522914899699755	4		373	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0042628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	248	327	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.489994901552076	2	FACETS	0.841	0.794	0.889	0.841	0.794	0.889	CLONAL	2	TRUE	0	0.522914899699755	2		327	564	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710517	114710517	+	start_lost	Translation_Start_Site	SNP	T	T	A	novel	NA	P-0042628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	85	401	0	ENST00000543371.1:c.2T>A	p.Met1?	p.M1?	ENST00000543371	NM_001198531.1	1	aTg/aAg	1/14	0.522914899699755	3	FACETS	0.81	0.719	0.908	0.405	0.359	0.454	CLONAL	1	TRUE	1	0.522914899699755	3		401	506	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5239002	5239002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775100072	NA	P-0042628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	345	766	1	ENST00000357368.4:c.1777C>T	p.Arg593Cys	p.R593C	ENST00000357368	NM_002850.3	593	Cgc/Tgc	13/38	0.435865741591408	4	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	2	0.522914899699755	4		767	1004	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916948	178916950	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0042628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	165	369	0	ENST00000263967.3:c.337_339del	p.Leu113del	p.L113del	ENST00000263967	NM_006218.2	112	aTCCtc/atc	2/21	0.522914899699755	3	FACETS	0.921	0.855	0.989	0.921	0.855	0.989	CLONAL	2	TRUE	1	0.522914899699755	3		369	432	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628066	90628066	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	171	762	3	ENST00000330062.3:c.1253G>A	p.Cys418Tyr	p.C418Y	ENST00000330062	NM_002168.2	418	tGc/tAc	10/11	0.522914899699755	3	FACETS	0.891	0.82	0.965	0.445	0.41	0.483	CLONAL	1	TRUE	1	0.522914899699755	3		765	926	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115269657	115269657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	138	598	0	ENST00000438362.2:c.1549G>A	p.Ala517Thr	p.A517T	ENST00000438362	NM_001242891.1	517	Gct/Act	13/20	1	2	FACETS	0.961	0.879	1	0.961	0.879	1	CLONAL	1	TRUE	1	0.522914899699755	2		598	549	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263888	133263888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1167872104	NA	P-0042628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	187	372	1	ENST00000320574.5:c.14G>A	p.Ser5Asn	p.S5N	ENST00000320574	NM_006231.2	5	aGc/aAc	1/49	0.229871171994716	5	FACETS	1	0.985	1	0.803	0.747	0.859	INDETERMINATE	2	TRUE	2	0.522914899699755	5		373	530	SUCCESS
APC	324	MSKCC	GRCh37	5	112128141	112128141	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs777848503	NA	P-0042628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	153	258	0	ENST00000257430.4:c.646-2A>T		p.X216_splice	ENST00000257430	NM_000038.5	216			0.489994901552076	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.522914899699755	2		258	279	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750933	128750933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	251	505	0	ENST00000377970.2:c.470C>T	p.Ala157Val	p.A157V	ENST00000377970	NM_002467.4	157	gCc/gTc	2/3	0.435865741591408	4	FACETS	0.976	0.917	1	0.976	0.917	1	CLONAL	2	TRUE	2	0.522914899699755	4		505	749	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98009720	98009720	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	78	275	0	ENST00000289081.3:c.244G>A	p.Ala82Thr	p.A82T	ENST00000289081	NM_000136.2	82	Gca/Aca	3/15	0.522914899699755	3	FACETS	1	0.91	1	0.517	0.457	0.58	CLONAL	1	TRUE	1	0.522914899699755	3		275	364	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875950	76875950	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	49	330	0	ENST00000373344.5:c.5185T>A	p.Ser1729Thr	p.S1729T	ENST00000373344	NM_000489.3	1729	Tct/Act	20/35	0.522914899699755	3	FACETS	0.73	0.621	0.848	0.365	0.31	0.424	SUBCLONAL	1	TRUE	1	0.522914899699755	3		330	324	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0042629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	216	565	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.460028720284436	2		565	895	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419986	41419986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372989163	NA	P-0042629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	177	689	0	ENST00000373198.4:c.335G>A	p.Arg112His	p.R112H	ENST00000373198	NM_133170.3	112	cGt/cAt	3/32	0.460028720284436	3	FACETS	0.89	0.82	0.964	0.445	0.41	0.482	CLONAL	1	TRUE	1	0.460028720284436	3		689	1063	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0042629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	158	534	1	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.903	0.828	0.98	0.903	0.828	0.98	CLONAL	1	TRUE	1	0.460028720284436	2		535	761	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670339	134670339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1303716587	NA	P-0042629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	165	551	1	ENST00000398015.3:c.250C>T	p.Arg84Cys	p.R84C	ENST00000398015	NM_004441.4	84	Cgc/Tgc	3/16	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.460028720284436	2		552	701	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0042629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	113	404	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.460028720284436	1	FACETS	0.842	0.763	0.925	0.842	0.763	0.925	CLONAL	1	TRUE	0	0.460028720284436	1		404	449	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0042630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	156	540	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.225088829980003	4	FACETS	0.939	0.866	1			1	INDETERMINATE	2	TRUE	NA	0.500600166938043	4		540	498	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0042630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	70	384	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	0.500600166938043	3	FACETS	0.839	0.734	0.95	0.419	0.367	0.475	CLONAL	1	TRUE	1	0.500600166938043	3		384	417	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106720	27106720	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770028290	NA	P-0042630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	169	711	1	ENST00000324856.7:c.6331G>A	p.Val2111Ile	p.V2111I	ENST00000324856	NM_006015.4	2111	Gtc/Atc	20/20	1	2	FACETS	0.981	0.905	1	0.981	0.905	1	CLONAL	1	TRUE	1	0.500600166938043	2		712	688	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591895	48591895	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs377767346	NA	P-0042630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	105	499	1	ENST00000342988.3:c.1058A>G	p.Tyr353Cys	p.Y353C	ENST00000342988	NM_005359.5	353	tAc/tGc	9/12	0.500600166938043	1	FACETS	0.986	0.894	1	0.986	0.894	1	CLONAL	1	TRUE	0	0.500600166938043	1		500	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs967461896	NA	P-0042630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	377	797	4	ENST00000269305.4:c.526T>A	p.Cys176Ser	p.C176S	ENST00000269305	NM_001126112.2	176	Tgc/Agc	5/11	0.500600166938043	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.500600166938043	2		801	743	SUCCESS
APC	324	MSKCC	GRCh37	5	112173848	112173848	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	167	366	0	ENST00000257430.4:c.2557G>T	p.Glu853Ter	p.E853*	ENST00000257430	NM_000038.5	853	Gag/Tag	16/16	0.500600166938043	3	FACETS	0.991	0.921	1	0.991	0.921	1	CLONAL	2	TRUE	1	0.500600166938043	3		366	421	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478921	56478921	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	247	848	4	ENST00000267101.3:c.377A>T	p.Asn126Ile	p.N126I	ENST00000267101	NM_001982.3	126	aAc/aTc	3/28	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.500600166938043	2		852	849	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934315	81934315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367678289	NA	P-0042630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	199	825	1	ENST00000359376.3:c.1292C>T	p.Thr431Met	p.T431M	ENST00000359376	NM_002661.3	431	aCg/aTg	14/33	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.500600166938043	2		826	761	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	105	707	7	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.675	0.605	0.749	0.675	0.605	0.749	SUBCLONAL	1	TRUE	1	0.45	2		714	691	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	544	528	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.872	0.843	0.901	1	0.998	1	CLONAL	3	TRUE	1	0.45	2		528	924	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	94	574	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.829	0.74	0.923	0.829	0.74	0.923	CLONAL	1	TRUE	1	0.45	2		580	504	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	89	369	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.45	2		369	269	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	85	343	0	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.739	0.655	0.829	0.739	0.655	0.829	SUBCLONAL	1	TRUE	1	0.45	2		343	511	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	197	342	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.951	1	1	0.994	1	CLONAL	2	TRUE	1	0.45	2		342	431	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717769	89717770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	44	356	0	ENST00000371953.3:c.800dup	p.Asp268GlyfsTer30	p.D268Gfs*30	ENST00000371953	NM_000314.4	265	cta/ctAa	7/9	1	2	FACETS	0.993	0.843	1	0.993	0.843	1	CLONAL	1	TRUE	1	0.45	2		356	197	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	91	335	1	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.49	0.435	0.55	0.49	0.435	0.55	SUBCLONAL	1	TRUE	1	0.45	2		336	825	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	114	570	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.45	2		570	468	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101300	27101300	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	253	717	0	ENST00000324856.7:c.4582C>T	p.Arg1528Ter	p.R1528*	ENST00000324856	NM_006015.4	1528	Cga/Tga	18/20	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.45	2		717	783	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795103	242795104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768249210	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	147	982	0	ENST00000334409.5:c.105dup	p.Thr36HisfsTer70	p.T36Hfs*70	ENST00000334409	NM_005018.2	35	-/C	2/5	1	2	FACETS	0.598	0.545	0.654	0.598	0.545	0.654	SUBCLONAL	1	TRUE	1	0.45	2		982	1092	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374390	31374390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773207465	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	94	710	0	ENST00000328111.2:c.389G>A	p.Arg130His	p.R130H	ENST00000328111	NM_006892.3	130	cGc/cAc	5/23	1	2	FACETS	0.438	0.389	0.491	0.438	0.389	0.491	SUBCLONAL	1	TRUE	1	0.45	2		710	953	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	100	558	2	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.781	0.699	0.867	0.781	0.699	0.867	SUBCLONAL	1	TRUE	1	0.45	2		560	569	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890149	76890150	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	55	545	0	ENST00000373344.5:c.4744dup	p.Thr1582AsnfsTer19	p.T1582Nfs*19	ENST00000373344	NM_000489.3	1582	aca/aAca	17/35	1	2	FACETS	0.692	0.595	0.798	0.692	0.595	0.798	SUBCLONAL	1	TRUE	1	0.45	2		545	353	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	165	476	5	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	0.789	0.731	0.848	1	0.991	1	SUBCLONAL	2	TRUE	1	0.45	2		481	465	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	105	822	4	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	0.456	0.408	0.508	0.456	0.408	0.508	SUBCLONAL	1	TRUE	1	0.45	2		826	1023	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270530	98270530	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs751977093	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	40	239	0	ENST00000331920.6:c.114del	p.Leu39CysfsTer41	p.L39Cfs*41	ENST00000331920	NM_000264.3	38	ggG/gg	1/24	1	2	FACETS	0.549	0.457	0.65	0.549	0.457	0.65	SUBCLONAL	1	TRUE	1	0.45	2		239	324	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182050	11182050	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	77	575	0	ENST00000361445.4:c.6796C>T	p.Arg2266Cys	p.R2266C	ENST00000361445	NM_004958.3	2266	Cgc/Tgc	48/58	1	2	FACETS	0.446	0.391	0.506	0.446	0.391	0.506	SUBCLONAL	1	TRUE	1	0.45	2		575	767	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306553	41306553	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	81	666	1	ENST00000373198.4:c.1106del	p.Gly369ValfsTer28	p.G369Vfs*28	ENST00000373198	NM_133170.3	369	gGt/gt	7/32	1	2	FACETS	0.448	0.394	0.506	0.448	0.394	0.506	SUBCLONAL	1	TRUE	1	0.45	2		667	803	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	71	577	6	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.775	0.68	0.877	0.775	0.68	0.877	SUBCLONAL	1	TRUE	1	0.45	2		583	407	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38137094	38137094	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1351115556	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	192	726	0	ENST00000317025.8:c.3724C>T	p.Arg1242Ter	p.R1242*	ENST00000317025	NM_023034.1	1242	Cga/Tga	21/24	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.45	2		726	631	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609744	81609744	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201889708	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	44	478	0	ENST00000298171.2:c.1342G>A	p.Val448Ile	p.V448I	ENST00000298171	NM_000369.2	448	Gtc/Atc	10/10	1	2	FACETS	0.333	0.279	0.393	0.333	0.279	0.393	SUBCLONAL	1	TRUE	1	0.45	2		478	587	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209593	98209593	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	132	566	2	ENST00000331920.6:c.3945del	p.Tyr1316ThrfsTer56	p.Y1316Tfs*56	ENST00000331920	NM_000264.3	1315	ccC/cc	23/24	1	2	FACETS	0.965	0.879	1	0.965	0.879	1	CLONAL	1	TRUE	1	0.45	2		568	608	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405821	157405822	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	138	418	0	ENST00000346085.5:c.2067dup	p.Thr690HisfsTer73	p.T690Hfs*73	ENST00000346085	NM_020732.3	688	ctc/ctCc	6/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.45	2		418	523	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	276	862	1	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.45	2		863	1148	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370686	225370686	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1232071537	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	21	312	3	ENST00000264414.4:c.1193del	p.Lys398ArgfsTer6	p.K398Rfs*6	ENST00000264414	NM_003590.4	398	aAg/ag	8/16	1	2	FACETS	0.409	0.316	0.517	0.409	0.316	0.517	SUBCLONAL	1	TRUE	1	0.45	2		315	228	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425823	49425824	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs754290613	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	173	759	0	ENST00000301067.7:c.12662_12664dup	p.Gln4221dup	p.Q4221dup	ENST00000301067	NM_003482.3	4221	cta/cAGCta	39/54	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.45	2		759	727	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645373	67645373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1390969954	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	80	529	0	ENST00000264010.4:c.638G>A	p.Arg213His	p.R213H	ENST00000264010	NM_006565.3	213	cGt/cAt	3/12	1	2	FACETS	0.721	0.637	0.811	0.721	0.637	0.811	SUBCLONAL	1	TRUE	1	0.45	2		529	493	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605204	46605204	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1459319402	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	131	364	5	ENST00000263734.3:c.1421G>C	p.Ser474Thr	p.S474T	ENST00000263734	NM_001430.4	474	aGc/aCc	10/16	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.45	2		369	417	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247892	10247892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	175	952	1	ENST00000340748.4:c.4310G>A	p.Arg1437His	p.R1437H	ENST00000340748		1437	cGc/cAc	36/40	1	2	FACETS	0.7	0.644	0.759	0.7	0.644	0.759	SUBCLONAL	1	TRUE	1	0.45	2		953	1111	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891548	76891548	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	20	436	2	ENST00000373344.5:c.4558-1G>T		p.X1520_splice	ENST00000373344	NM_000489.3	1520			1	2	FACETS	0.28	0.213	0.357	0.28	0.213	0.357	SUBCLONAL	1	TRUE	1	0.45	2		438	318	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939496	76939496	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057523785	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	33	588	0	ENST00000373344.5:c.1252C>T	p.Arg418Ter	p.R418*	ENST00000373344	NM_000489.3	418	Cga/Tga	9/35	1	2	FACETS	0.46	0.375	0.555	0.46	0.375	0.555	SUBCLONAL	1	TRUE	1	0.45	2		588	319	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141084	55141084	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	60	416	0	ENST00000257290.5:c.1730C>A	p.Pro577Gln	p.P577Q	ENST00000257290	NM_006206.4	577	cCg/cAg	12/23	1	2	FACETS	0.67	0.579	0.768	0.67	0.579	0.768	SUBCLONAL	1	TRUE	1	0.45	2		416	398	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181390	38181390	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	81	423	0	ENST00000396334.3:c.403C>G	p.Gln135Glu	p.Q135E	ENST00000396334	NM_002468.4	135	Cag/Gag	2/5	1	2	FACETS	0.727	0.643	0.818	0.727	0.643	0.818	SUBCLONAL	1	TRUE	1	0.45	2		423	495	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105607	27105607	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	208	638	0	ENST00000324856.7:c.5218G>T	p.Gly1740Ter	p.G1740*	ENST00000324856	NM_006015.4	1740	Gga/Tga	20/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.45	2		638	666	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074377	8074378	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	50	434	0	ENST00000377482.5:c.281dup	p.Leu95SerfsTer7	p.L95Sfs*7	ENST00000377482	NM_018948.3	94	cct/ccCt	4/4	1	2	FACETS	0.505	0.429	0.588	0.505	0.429	0.588	SUBCLONAL	1	TRUE	1	0.45	2		434	440	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057975	27057975	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	85	650	0	ENST00000324856.7:c.1683G>C	p.Gln561His	p.Q561H	ENST00000324856	NM_006015.4	561	caG/caC	3/20	1	2	FACETS	0.509	0.45	0.573	0.509	0.45	0.573	SUBCLONAL	1	TRUE	1	0.45	2		650	742	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172379	108172379	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	26	366	0	ENST00000278616.4:c.5182A>G	p.Lys1728Glu	p.K1728E	ENST00000278616	NM_000051.3	1728	Aaa/Gaa	35/63	1	2	FACETS	0.472	0.375	0.582	0.472	0.375	0.582	SUBCLONAL	1	TRUE	1	0.45	2		366	245	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118339525	118339528	+	frameshift_variant	Frame_Shift_Del	DEL	AGTC	AGTC	-	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	91	526	0	ENST00000534358.1:c.470_473del	p.Val157GlufsTer42	p.V157Efs*42	ENST00000534358	NM_005933.3	156	gaAGTC/ga	2/36	1	2	FACETS	0.746	0.664	0.833	0.746	0.664	0.833	SUBCLONAL	1	TRUE	1	0.45	2		526	542	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225929	133225929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs550525366	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	156	893	0	ENST00000320574.5:c.3968C>T	p.Ala1323Val	p.A1323V	ENST00000320574	NM_006231.2	1323	gCc/gTc	31/49	1	2	FACETS	0.595	0.543	0.649	0.595	0.543	0.649	SUBCLONAL	1	TRUE	1	0.45	2		893	1166	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066760	30066760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	51	478	0	ENST00000331968.5:c.2371G>A	p.Asp791Asn	p.D791N	ENST00000331968	NM_002742.2	791	Gac/Aac	16/18	1	2	FACETS	0.626	0.534	0.726	0.626	0.534	0.726	SUBCLONAL	1	TRUE	1	0.45	2		478	362	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873759	35873759	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	126	673	0	ENST00000216797.5:c.92A>T	p.Asp31Val	p.D31V	ENST00000216797	NM_020529.2	31	gAc/gTc	1/6	1	2	FACETS	0.613	0.555	0.675	0.613	0.555	0.675	SUBCLONAL	1	TRUE	1	0.45	2		673	913	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988353	36988353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	59	284	0	ENST00000354822.5:c.300G>A	p.Met100Ile	p.M100I	ENST00000354822	NM_001079668.2	100	atG/atA	2/3	1	2	FACETS	0.581	0.501	0.668	0.581	0.501	0.668	SUBCLONAL	1	TRUE	1	0.45	2		284	451	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628058	90628058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1023592505	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	289	780	1	ENST00000330062.3:c.1261G>A	p.Gly421Ser	p.G421S	ENST00000330062	NM_002168.2	421	Ggc/Agc	10/11	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.45	2		781	974	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312770	91312770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	87	587	0	ENST00000355112.3:c.2509G>A	p.Val837Ile	p.V837I	ENST00000355112	NM_000057.2	837	Gta/Ata	12/22	1	2	FACETS	0.654	0.58	0.733	0.654	0.58	0.733	SUBCLONAL	1	TRUE	1	0.45	2		587	591	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658859	3658859	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs370082083	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	131	660	0	ENST00000294008.3:c.107A>G	p.Glu36Gly	p.E36G	ENST00000294008	NM_032444.2	36	gAa/gGa	2/15	1	2	FACETS	0.791	0.719	0.867	0.791	0.719	0.867	SUBCLONAL	1	TRUE	1	0.45	2		660	736	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627662	37627662	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	97	760	0	ENST00000447079.4:c.1577C>A	p.Pro526His	p.P526H	ENST00000447079	NM_015083.1	526	cCt/cAt	2/14	1	2	FACETS	0.522	0.465	0.583	0.522	0.465	0.583	SUBCLONAL	1	TRUE	1	0.45	2		760	826	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487544	38487544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	114	726	0	ENST00000254066.5:c.74C>T	p.Ala25Val	p.A25V	ENST00000254066	NM_000964.3	25	gCc/gTc	2/9	1	2	FACETS	0.588	0.529	0.651	0.588	0.529	0.651	SUBCLONAL	1	TRUE	1	0.45	2		726	861	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860582	45860582	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1218	103	1072	1	ENST00000391945.4:c.1425del	p.Val476SerfsTer8	p.V476Sfs*8	ENST00000391945	NM_000400.3	475	ccC/cc	15/23	1	2	FACETS	0.347	0.309	0.387	0.347	0.309	0.387	SUBCLONAL	1	TRUE	1	0.45	2		1073	1321	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46603700	46603700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	200	717	0	ENST00000263734.3:c.1057G>A	p.Val353Met	p.V353M	ENST00000263734	NM_001430.4	353	Gtg/Atg	9/16	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.45	2		717	698	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096022	178096022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs184287392	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	78	389	0	ENST00000397062.3:c.1309C>T	p.Arg437Trp	p.R437W	ENST00000397062	NM_006164.4	437	Cgg/Tgg	5/5	1	2	FACETS	0.738	0.65	0.831	0.738	0.65	0.831	SUBCLONAL	1	TRUE	1	0.45	2		389	470	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198260991	198260992	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	86	517	0	ENST00000335508.6:c.3327_3328del	p.Arg1109SerfsTer26	p.R1109Sfs*26	ENST00000335508	NM_012433.2	1109	agAGtt/agtt	23/25	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.45	2		517	310	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265148	198265150	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	96	336	0	ENST00000335508.6:c.2727_2729del	p.Met910del	p.M910del	ENST00000335508	NM_012433.2	909	gtAATg/gtg	19/25	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.45	2		336	313	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104640	209104640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	229	588	0	ENST00000345146.2:c.938C>T	p.Thr313Ile	p.T313I	ENST00000345146	NM_005896.2	313	aCc/aTc	8/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.45	2		588	790	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998043	169998043	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	79	720	1	ENST00000295797.4:c.734C>T	p.Ala245Val	p.A245V	ENST00000295797	NM_002740.5	245	gCt/gTt	9/18	1	2	FACETS	0.66	0.582	0.744	0.66	0.582	0.744	SUBCLONAL	1	TRUE	1	0.45	2		721	532	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916851	178916851	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	134	563	0	ENST00000263967.3:c.238G>A	p.Glu80Lys	p.E80K	ENST00000263967	NM_006218.2	80	Gaa/Aaa	2/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.45	2		563	469	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916862	178916862	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	132	652	0	ENST00000263967.3:c.249T>A	p.Phe83Leu	p.F83L	ENST00000263967	NM_006218.2	83	ttT/ttA	2/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.45	2		652	473	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951995	178951995	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	84	417	0	ENST00000263967.3:c.3050A>C	p.Asp1017Ala	p.D1017A	ENST00000263967	NM_006218.2	1017	gAt/gCt	21/21	1	2	FACETS	0.756	0.678	0.836	1	0.981	1	SUBCLONAL	2	TRUE	1	0.45	2		417	247	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696697	176696697	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	132	370	0	ENST00000439151.2:c.5398G>A	p.Gly1800Arg	p.G1800R	ENST00000439151	NM_022455.4	1800	Gga/Aga	16/23	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.45	2		370	397	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729726	41729727	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	45	527	0	ENST00000242208.4:c.802dup	p.Glu268GlyfsTer9	p.E268Gfs*9	ENST00000242208	NM_002192.2	268	gaa/gGaa	3/3	1	2	FACETS	0.313	0.262	0.369	0.313	0.262	0.369	SUBCLONAL	1	TRUE	1	0.45	2		527	640	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339164	116339164	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	52	313	0	ENST00000397752.3:c.26C>A	p.Pro9His	p.P9H	ENST00000397752	NM_000245.2	9	cCt/cAt	2/21	1	2	FACETS	0.59	0.503	0.684	0.59	0.503	0.684	SUBCLONAL	1	TRUE	1	0.45	2		313	392	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148516774	148516775	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	36	311	0	ENST00000320356.2:c.912dup	p.His305SerfsTer8	p.H305Sfs*8	ENST00000320356	NM_004456.4	304	-/T	9/20	1	2	FACETS	0.705	0.584	0.838	0.705	0.584	0.838	SUBCLONAL	1	TRUE	1	0.45	2		311	227	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151948046	151948046	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	33	334	0	ENST00000262189.6:c.1627A>G	p.Asn543Asp	p.N543D	ENST00000262189	NM_170606.2	543	Aac/Gac	12/59	1	2	FACETS	0.67	0.549	0.803	0.67	0.549	0.803	SUBCLONAL	1	TRUE	1	0.45	2		334	219	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759652	133759653	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0042644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	140	964	0	ENST00000318560.5:c.1979dup	p.Pro662AlafsTer87	p.P662Afs*87	ENST00000318560	NM_005157.4	659	tcc/tCcc	11/11	1	2	FACETS	0.594	0.54	0.651	0.594	0.54	0.651	SUBCLONAL	1	TRUE	1	0.45	2		964	1047	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0042654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	371	593	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.586287649181301	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.586287649181301	2		595	594	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166445	118166445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767537718	NA	P-0042654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	90	458	1	ENST00000369448.3:c.955G>A	p.Val319Met	p.V319M	ENST00000369448	NM_017709.3	319	Gtg/Atg	2/2	0.586287649181301	3	FACETS	1	0.939	1	0.537	0.48	0.596	CLONAL	1	TRUE	1	0.586287649181301	3		459	370	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533123	63533123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754833574	NA	P-0042654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	131	849	0	ENST00000307078.5:c.1771G>A	p.Ala591Thr	p.A591T	ENST00000307078	NM_004655.3	591	Gcc/Acc	7/11	0.586287649181301	4	FACETS	0.954	0.867	1	0.318	0.289	0.349	CLONAL	1	TRUE	1	0.586287649181301	4		849	743	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792113	42792113	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	123	663	0	ENST00000575354.2:c.917C>T	p.Ala306Val	p.A306V	ENST00000575354	NM_015125.3	306	gCt/gTt	6/20	0.586287649181301	6	FACETS	1	0.96	1			1	CLONAL	1	TRUE	NA	0.586287649181301	6		663	818	SUCCESS
AR	367	MSKCC	GRCh37	X	66765623	66765623	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	155	1180	0	ENST00000374690.3:c.635G>C	p.Arg212Thr	p.R212T	ENST00000374690	NM_000044.3	212	aGg/aCg	1/8	0.260756393919595	3	FACETS	0.908	0.833	0.987	0.303	0.277	0.329	INDETERMINATE	1	TRUE	0	0.586287649181301	3		1180	753	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0042667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	128	540	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.463888915267487	2		540	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0042667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	229	664	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.411365745603025	1	FACETS	0.811	0.757	0.867	0.811	0.757	0.867	CLONAL	1	TRUE	0	0.463888915267487	1		665	935	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971116	21971116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552823	NA	P-0042667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	175	507	0	ENST00000304494.5:c.242C>T	p.Pro81Leu	p.P81L	ENST00000304494	NM_000077.4	81	cCc/cTc	2/3	0.385520845718227	1	FACETS	0.829	0.766	0.894	0.829	0.766	0.894	CLONAL	1	TRUE	0	0.463888915267487	1		507	699	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202747	108202747	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	44	367	0	ENST00000278616.4:c.7771A>C	p.Ser2591Arg	p.S2591R	ENST00000278616	NM_000051.3	2591	Agc/Cgc	52/63	1	2	FACETS	0.464	0.389	0.546	0.464	0.389	0.546	SUBCLONAL	1	TRUE	1	0.463888915267487	2		367	409	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045741	26045741	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	64	326	0	ENST00000540144.1:c.103G>A	p.Gly35Ser	p.G35S	ENST00000540144	NM_003531.2	35	Ggc/Agc	1/1	1	2	FACETS	0.495	0.429	0.567	0.495	0.429	0.567	SUBCLONAL	1	TRUE	1	0.463888915267487	2		326	557	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551682	150551682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	291	423	0	ENST00000369026.2:c.325G>A	p.Glu109Lys	p.E109K	ENST00000369026	NM_021960.4	109	Gag/Aag	1/3	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.868962134220307	NA		423	518	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126729	5126729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774469142	NA	P-0042700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	175	495	0	ENST00000381652.3:c.3337C>T	p.Arg1113Cys	p.R1113C	ENST00000381652	NM_004972.3	1113	Cgc/Tgc	25/25	0.868962134220307	2	FACETS	0.876	0.814	0.938	0.438	0.407	0.469	CLONAL	1	TRUE	0	0.868962134220307	2		495	460	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985448	60985450	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0042700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	180	706	0	ENST00000333681.4:c.450_452del	p.Phe151del	p.F151del	ENST00000333681		150	ttCTTt/ttt	2/3	0.868962134220307	2	FACETS	0.544	0.503	0.587	0.272	0.251	0.294	SUBCLONAL	1	TRUE	0	0.868962134220307	2		706	761	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161906	47161907	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0042700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	106	387	1	ENST00000409792.3:c.4219dup	p.Arg1407LysfsTer8	p.R1407Kfs*8	ENST00000409792	NM_014159.6	1407	agg/aAgg	3/21	0.868962134220307	3	FACETS	0.476	0.427	0.528	0.238	0.213	0.264	SUBCLONAL	1	TRUE	1	0.868962134220307	3		388	735	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636486	21636486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	113	499	1	ENST00000421138.2:c.524C>T	p.Ala175Val	p.A175V	ENST00000421138		175	gCt/gTt	7/16	0.823941057328002	4	FACETS	0.512	0.46	0.568	0.256	0.23	0.284	SUBCLONAL	1	TRUE	2	0.868962134220307	4		500	949	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879798	123879799	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0042700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	138	502	0	ENST00000330479.4:c.494_495del	p.Gln165ArgfsTer36	p.Q165Rfs*36	ENST00000330479	NM_020382.3	165	cAG/c	4/9	0.868962134220307	3	FACETS	0.518	0.471	0.568	0.259	0.235	0.284	SUBCLONAL	1	TRUE	1	0.868962134220307	3		502	879	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799233	42799233	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	329	534	0	ENST00000575354.2:c.4717C>A	p.Pro1573Thr	p.P1573T	ENST00000575354	NM_015125.3	1573	Ccg/Acg	20/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.868962134220307	2		534	734	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574737	41574737	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	223	897	0	ENST00000263253.7:c.7022C>T	p.Ser2341Phe	p.S2341F	ENST00000263253	NM_001429.3	2341	tCc/tTc	31/31	0.848749051510343	2	FACETS	0.65	0.606	0.694	0.325	0.303	0.347	SUBCLONAL	1	TRUE	0	0.868962134220307	2		897	790	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924967	49924967	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	379	667	0	ENST00000296474.3:c.3976G>T	p.Ala1326Ser	p.A1326S	ENST00000296474	NM_002447.2	1326	Gca/Tca	20/20	0.868962134220307	3	FACETS	1	0.989	1	0.564	0.536	0.593	CLONAL	1	TRUE	1	0.868962134220307	3		667	1109	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480445	89480445	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	186	366	0	ENST00000336596.2:c.2282A>C	p.Lys761Thr	p.K761T	ENST00000336596	NM_005233.5	761	aAg/aCg	13/17	0.868962134220307	3	FACETS	0.9	0.835	0.968	0.45	0.417	0.484	CLONAL	1	TRUE	1	0.868962134220307	3		366	682	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878442	151878442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	404	827	0	ENST00000262189.6:c.6503C>T	p.Pro2168Leu	p.P2168L	ENST00000262189	NM_170606.2	2168	cCt/cTt	36/59	0.868962134220307	3	FACETS	1	0.975	1	0.346	0.329	0.364	CLONAL	1	TRUE	0	0.868962134220307	3		827	1284	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0042741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	101	388	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.439235097284815	2		388	411	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0042741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	68	368	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.826	0.722	0.936	0.826	0.722	0.936	CLONAL	1	TRUE	1	0.439235097284815	2		368	375	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0042741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	106	275	0				ENST00000310581	NM_198253.2	-/1132			0.439235097284815	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.439235097284815	1		275	319	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36934816	36934816	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	153	423	0	ENST00000361632.4:c.1517C>T	p.Pro506Leu	p.P506L	ENST00000361632		506	cCc/cTc	11/16	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.439235097284815	2		423	532	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176104212	176104212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	53	244	0	ENST00000367669.3:c.902G>A	p.Gly301Asp	p.G301D	ENST00000367669	NM_022457.5	301	gGc/gAc	8/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.439235097284815	2		244	206	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625435	69625435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376445217	NA	P-0042741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	117	535	0	ENST00000334134.2:c.358C>T	p.Arg120Trp	p.R120W	ENST00000334134	NM_005247.2	120	Cgg/Tgg	3/3	1	2	FACETS	0.769	0.694	0.848	0.769	0.694	0.848	SUBCLONAL	1	TRUE	1	0.439235097284815	2		535	693	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143570	108143570	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0042741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	65	284	0	ENST00000278616.4:c.3275C>G	p.Ser1092Ter	p.S1092*	ENST00000278616	NM_000051.3	1092	tCa/tGa	22/63	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.439235097284815	2		284	272	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199916	108199916	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	56	192	0	ENST00000278616.4:c.7258G>C	p.Ala2420Pro	p.A2420P	ENST00000278616	NM_000051.3	2420	Gcc/Ccc	49/63	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.439235097284815	2		192	234	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409115	4409115	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	166	460	0	ENST00000261254.3:c.810G>C	p.Lys270Asn	p.K270N	ENST00000261254	NM_001759.3	270	aaG/aaC	5/5	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.439235097284815	2		460	631	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601334	28601334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	38	334	0	ENST00000241453.7:c.2098C>T	p.Leu700Phe	p.L700F	ENST00000241453	NM_004119.2	700	Ctc/Ttc	17/24	0.24441109872288	3	FACETS	0.51	0.422	0.608	0.17	0.14	0.203	INDETERMINATE	1	TRUE	0	0.439235097284815	3		334	414	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727510	66727510	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	238	416	0	ENST00000307102.5:c.226G>A	p.Ala76Thr	p.A76T	ENST00000307102	NM_002755.3	76	Gct/Act	2/11	0.439235097284815	1	FACETS	0.751	0.707	0.795	1	0.993	1	SUBCLONAL	2	TRUE	0	0.439235097284815	1		416	563	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647419	23647419	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	44	448	0	ENST00000261584.4:c.448C>G	p.Gln150Glu	p.Q150E	ENST00000261584	NM_024675.3	150	Cag/Gag	4/13	1	2	FACETS	0.337	0.282	0.398	0.337	0.282	0.398	SUBCLONAL	1	TRUE	1	0.439235097284815	2		448	595	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577092	7577093	+	missense_variant	Missense_Mutation	DNP	CC	CC	GG	novel	NA	P-0042741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	205	491	2	ENST00000269305.4:c.845_846inv	p.Arg282Pro	p.R282P	ENST00000269305	NM_001126112.2	282	cGG/cCC	8/11	0.439235097284815	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.439235097284815	1		493	612	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865353	40865353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1454055017	NA	P-0042741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	61	547	0	ENST00000428826.2:c.1078C>T	p.Arg360Cys	p.R360C	ENST00000428826		360	Cgt/Tgt	11/21	1	2	FACETS	0.374	0.322	0.431	0.374	0.322	0.431	SUBCLONAL	1	TRUE	1	0.439235097284815	2		547	743	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210763	5210763	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	209	574	0	ENST00000357368.4:c.5288A>T	p.Asp1763Val	p.D1763V	ENST00000357368	NM_002850.3	1763	gAc/gTc	34/38	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.439235097284815	2		574	741	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223164	5223164	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	55	553	0	ENST00000357368.4:c.2639C>G	p.Thr880Ser	p.T880S	ENST00000357368	NM_002850.3	880	aCc/aGc	18/38	1	2	FACETS	0.355	0.303	0.412	0.355	0.303	0.412	SUBCLONAL	1	TRUE	1	0.439235097284815	2		553	705	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244386	5244386	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	179	516	0	ENST00000357368.4:c.1096G>T	p.Glu366Ter	p.E366*	ENST00000357368	NM_002850.3	366	Gaa/Taa	11/38	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.439235097284815	2		516	711	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259789	142259789	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	128	452	0	ENST00000350721.4:c.3538A>G	p.Thr1180Ala	p.T1180A	ENST00000350721	NM_001184.3	1180	Act/Gct	18/47	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.439235097284815	2		452	547	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968640	55968640	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	143	430	1	ENST00000263923.4:c.2023A>T	p.Asn675Tyr	p.N675Y	ENST00000263923	NM_002253.2	675	Aat/Tat	14/30	1	2	FACETS	0.903	0.825	0.985	0.903	0.825	0.985	CLONAL	1	TRUE	1	0.439235097284815	2		431	721	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295182	1295182	+	upstream_gene_variant	5'Flank	SNP	A	A	T	novel	NA	P-0042741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	72	202	0				ENST00000310581	NM_198253.2	-/1132			0.439235097284815	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.439235097284815	1		202	230	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962434	38962434	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	41	191	0	ENST00000357387.3:c.1698A>T	p.Lys566Asn	p.K566N	ENST00000357387	NM_152756.3	566	aaA/aaT	19/38	0.311706199370863	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.439235097284815	1		191	127	SUCCESS
APC	324	MSKCC	GRCh37	5	112175931	112175931	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	36	238	0	ENST00000257430.4:c.4643del	p.Asn1548ThrfsTer17	p.N1548Tfs*17	ENST00000257430	NM_000038.5	1547	gAa/ga	16/16	0.311706199370863	1	FACETS	0.695	0.578	0.823	0.695	0.578	0.823	SUBCLONAL	1	TRUE	0	0.439235097284815	1		238	184	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265479	152265479	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766779326	NA	P-0042741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	144	520	1	ENST00000206249.3:c.932C>T	p.Thr311Met	p.T311M	ENST00000206249	NM_000125.3	311	aCg/aTg	4/8	1	2	FACETS	0.987	0.903	1	0.987	0.903	1	CLONAL	1	TRUE	1	0.439235097284815	2		521	664	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741153	145741153	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs548957135	NA	P-0042741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	147	493	0	ENST00000428558.2:c.1253G>A	p.Arg418Gln	p.R418Q	ENST00000428558	NM_004260.3	418	cGg/cAg	6/22	0.439235097284815	3	FACETS	1	0.936	1	0.515	0.47	0.561	CLONAL	1	TRUE	1	0.439235097284815	3		493	793	SUCCESS
APC	324	MSKCC	GRCh37	5	112175934	112175934	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	41	228	0	ENST00000257430.4:c.4643A>T	p.Asn1548Ile	p.N1548I	ENST00000257430	NM_000038.5	1548	aAc/aTc	16/16	0.311706199370863	1	FACETS	0.792	0.668	0.925	0.792	0.668	0.925	CLONAL	1	TRUE	0	0.439235097284815	1		228	184	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589818	28589818	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	174	577	0	ENST00000241453.7:c.2562G>C	p.Trp854Cys	p.W854C	ENST00000241453	NM_004119.2	854	tgG/tgC	21/24	1	2	FACETS	0.854	0.787	0.923	0.854	0.787	0.923	CLONAL	1	TRUE	1	0.503830938999084	2		577	809	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578225	7578237	+	frameshift_variant	Frame_Shift_Del	DEL	GTCATCCAAATAC	GTCATCCAAATAC	-	novel	NA	P-0042759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	322	749	0	ENST00000269305.4:c.612_624del	p.Tyr205GlufsTer38	p.Y205Efs*38	ENST00000269305	NM_001126112.2	204	gaGTATTTGGATGAC/ga	6/11	0.503830938999084	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.503830938999084	1		749	693	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725455	117725455	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	32	507	0	ENST00000368508.3:c.426G>T	p.Trp142Cys	p.W142C	ENST00000368508	NM_002944.2	142	tgG/tgT	5/43	0.503830938999084	1	FACETS	0.316	0.257	0.382	0.316	0.257	0.382	SUBCLONAL	1	TRUE	0	0.503830938999084	1		507	301	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	146	528	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.784	0.716	0.855	0.784	0.716	0.855	SUBCLONAL	1	TRUE	1	0.456380312494391	2		528	816	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	68	577	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.548	0.477	0.624	0.548	0.477	0.624	SUBCLONAL	1	TRUE	1	0.456380312494391	2		577	544	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1232964733	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	21	65	0	ENST00000324856.7:c.1015del	p.Ala339LeufsTer24	p.A339Lfs*24	ENST00000324856	NM_006015.4	337	tGg/tg	1/20	1	2	FACETS	0.445	0.344	0.561	0.445	0.344	0.561	SUBCLONAL	1	TRUE	1	0.456380312494391	2		65	207	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374244	138374244	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	58	611	0	ENST00000289153.2:c.3200A>T	p.Asp1067Val	p.D1067V	ENST00000289153	NM_006219.2	1067	gAc/gTc	22/22	1	2	FACETS	0.462	0.397	0.533	0.462	0.397	0.533	SUBCLONAL	1	TRUE	1	0.456380312494391	2		611	550	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699360	47699360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	37	323	0	ENST00000347630.2:c.148G>A	p.Glu50Lys	p.E50K	ENST00000347630	NM_001007230.1	50	Gaa/Aaa	4/11	1	2	FACETS	0.512	0.423	0.61	0.512	0.423	0.61	SUBCLONAL	1	TRUE	1	0.456380312494391	2		323	317	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	14	445	1	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	1	2	FACETS	0.133	0.095	0.178	0.133	0.095	0.178	SUBCLONAL	1	TRUE	1	0.456380312494391	2		446	463	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120226	70120226	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	107	689	0	ENST00000245479.2:c.1228C>T	p.Gln410Ter	p.Q410*	ENST00000245479	NM_000346.3	410	Cag/Tag	3/3	1	2	FACETS	0.635	0.569	0.704	0.635	0.569	0.704	SUBCLONAL	1	TRUE	1	0.456380312494391	2		689	739	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	110	745	11	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.695	0.625	0.769	0.695	0.625	0.769	SUBCLONAL	1	TRUE	1	0.456380312494391	2		756	694	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	84	600	4	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	1	2	FACETS	0.539	0.476	0.607	0.539	0.476	0.607	SUBCLONAL	1	TRUE	1	0.456380312494391	2		604	683	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101612	27101612	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	136	773	2	ENST00000324856.7:c.4899del	p.Met1634Ter	p.M1634*	ENST00000324856	NM_006015.4	1632	Ccc/cc	18/20	1	2	FACETS	0.705	0.641	0.773	0.705	0.641	0.773	SUBCLONAL	1	TRUE	1	0.456380312494391	2		775	845	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991599	72991599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	113	786	1	ENST00000268489.5:c.2446G>A	p.Ala816Thr	p.A816T	ENST00000268489	NM_006885.3	816	Gcc/Acc	2/10	1	2	FACETS	0.576	0.518	0.637	0.576	0.518	0.637	SUBCLONAL	1	TRUE	1	0.456380312494391	2		787	860	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368262	31368262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	87	740	1	ENST00000328111.2:c.133G>A	p.Glu45Lys	p.E45K	ENST00000328111	NM_006892.3	45	Gag/Aag	2/23	1	2	FACETS	0.516	0.456	0.58	0.516	0.456	0.58	SUBCLONAL	1	TRUE	1	0.456380312494391	2		741	739	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612100	189612100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1455505991	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	111	711	1	ENST00000264731.3:c.1852C>T	p.Arg618Trp	p.R618W	ENST00000264731	NM_003722.4	618	Cgg/Tgg	14/14	1	2	FACETS	0.688	0.619	0.761	0.688	0.619	0.761	SUBCLONAL	1	TRUE	1	0.456380312494391	2		712	707	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016675	12016675	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	40	383	0	ENST00000353533.5:c.811G>A	p.Ala271Thr	p.A271T	ENST00000353533	NM_003010.3	271	Gca/Aca	7/11	1	2	FACETS	0.501	0.417	0.594	0.501	0.417	0.594	SUBCLONAL	1	TRUE	1	0.456380312494391	2		383	350	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260659	1260659	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	127	748	1	ENST00000310581.5:c.2900G>A	p.Gly967Glu	p.G967E	ENST00000310581	NM_198253.2	967	gGg/gAg	12/16	1	2	FACETS	0.64	0.58	0.704	0.64	0.58	0.704	SUBCLONAL	1	TRUE	1	0.456380312494391	2		749	869	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227012	53227012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	111	704	0	ENST00000375401.3:c.2563G>A	p.Ala855Thr	p.A855T	ENST00000375401	NM_004187.3	855	Gcc/Acc	18/26	1	2	FACETS	0.54	0.485	0.599	0.54	0.485	0.599	SUBCLONAL	1	TRUE	1	0.456380312494391	2		704	901	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932060	39932060	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	120	821	1	ENST00000378444.4:c.2539C>T	p.Gln847Ter	p.Q847*	ENST00000378444	NM_001123385.1	847	Cag/Tag	4/15	1	2	FACETS	0.628	0.567	0.693	0.628	0.567	0.693	SUBCLONAL	1	TRUE	1	0.456380312494391	2		822	837	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169852	32169852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs758030641	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	86	659	0	ENST00000375023.3:c.3755+1G>A		p.X1252_splice	ENST00000375023	NM_004557.3	1252			1	2	FACETS	0.516	0.456	0.58	0.516	0.456	0.58	SUBCLONAL	1	TRUE	1	0.456380312494391	2		659	730	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36217156	36217156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771289674	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	157	787	0	ENST00000222270.7:c.3905G>A	p.Arg1302His	p.R1302H	ENST00000222270	NM_014727.1	1302	cGc/cAc	14/37	1	2	FACETS	0.712	0.652	0.775	0.712	0.652	0.775	SUBCLONAL	1	TRUE	1	0.456380312494391	2		787	966	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821343	72821344	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs771413197	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	48	504	0	ENST00000268489.5:c.10831dup	p.His3611ProfsTer55	p.H3611Pfs*55	ENST00000268489	NM_006885.3	3611	cac/cCac	10/10	1	2	FACETS	0.484	0.409	0.565	0.484	0.409	0.565	SUBCLONAL	1	TRUE	1	0.456380312494391	2		504	435	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643770	52643771	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	63	684	1	ENST00000394830.3:c.2125dup	p.Ile709AsnfsTer14	p.I709Nfs*14	ENST00000394830	NM_018313.4	709	att/aAtt	17/30	1	2	FACETS	0.524	0.453	0.6	0.524	0.453	0.6	SUBCLONAL	1	TRUE	1	0.456380312494391	2		685	527	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776036	9776037	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1299016164	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	82	735	1	ENST00000377346.4:c.505dup	p.Leu169ProfsTer27	p.L169Pfs*27	ENST00000377346	NM_005026.3	167	ttc/ttCc	5/24	1	2	FACETS	0.522	0.46	0.589	0.522	0.46	0.589	SUBCLONAL	1	TRUE	1	0.456380312494391	2		736	688	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16247366	16247366	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	31	264	0	ENST00000375759.3:c.1637T>C	p.Val546Ala	p.V546A	ENST00000375759	NM_015001.2	546	gTg/gCg	9/15	1	2	FACETS	0.591	0.48	0.714	0.591	0.48	0.714	SUBCLONAL	1	TRUE	1	0.456380312494391	2		264	230	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257095	16257095	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	55	657	0	ENST00000375759.3:c.4360C>T	p.Leu1454Phe	p.L1454F	ENST00000375759	NM_015001.2	1454	Ctc/Ttc	11/15	1	2	FACETS	0.559	0.479	0.646	0.559	0.479	0.646	SUBCLONAL	1	TRUE	1	0.456380312494391	2		657	431	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743826	46743826	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	102	759	0	ENST00000371975.4:c.2116T>C	p.Trp706Arg	p.W706R	ENST00000371975	NM_003579.3	706	Tgg/Cgg	18/18	1	2	FACETS	0.562	0.502	0.625	0.562	0.502	0.625	SUBCLONAL	1	TRUE	1	0.456380312494391	2		759	796	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601959	43601959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	129	841	1	ENST00000355710.3:c.1003C>T	p.Pro335Ser	p.P335S	ENST00000355710	NM_020975.4	335	Ccc/Tcc	5/20	1	2	FACETS	0.637	0.577	0.7	0.637	0.577	0.7	SUBCLONAL	1	TRUE	1	0.456380312494391	2		842	888	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63699941	63699941	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	47	310	0	ENST00000279873.7:c.277-1G>A		p.X93_splice	ENST00000279873	NM_032199.2	93			1	2	FACETS	0.736	0.625	0.856	0.736	0.625	0.856	SUBCLONAL	1	TRUE	1	0.456380312494391	2		310	280	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70412266	70412266	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	24	263	0	ENST00000373644.4:c.4380del	p.Gly1461GlufsTer4	p.G1461Efs*4	ENST00000373644	NM_030625.2	1459	cAa/ca	6/12	1	2	FACETS	0.48	0.378	0.597	0.48	0.378	0.597	SUBCLONAL	1	TRUE	1	0.456380312494391	2		263	219	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711918	89711918	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	33	498	1	ENST00000371953.3:c.536G>T	p.Ser179Ile	p.S179I	ENST00000371953	NM_000314.4	179	aGc/aTc	6/9	1	2	FACETS	0.42	0.343	0.508	0.42	0.343	0.508	SUBCLONAL	1	TRUE	1	0.456380312494391	2		499	344	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711928	89711928	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	30	502	0	ENST00000371953.3:c.546A>C	p.Leu182Phe	p.L182F	ENST00000371953	NM_000314.4	182	ttA/ttC	6/9	1	2	FACETS	0.381	0.307	0.465	0.381	0.307	0.465	SUBCLONAL	1	TRUE	1	0.456380312494391	2		502	345	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725046	89725047	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAGCTGTA	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	17	242	0	ENST00000371953.3:c.1030_1037dup	p.Tyr346Ter	p.Y346*	ENST00000371953	NM_000314.4	343	-/AAGCTGTA	9/9	1	2	FACETS	0.428	0.321	0.554	0.428	0.321	0.554	SUBCLONAL	1	TRUE	1	0.456380312494391	2		242	174	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274768	123274768	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	85	736	0	ENST00000358487.5:c.1150G>T	p.Gly384Trp	p.G384W	ENST00000358487	NM_000141.4	384	Ggg/Tgg	9/18	1	2	FACETS	0.55	0.486	0.619	0.55	0.486	0.619	SUBCLONAL	1	TRUE	1	0.456380312494391	2		736	677	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577196	64577196	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	132	825	0	ENST00000312049.6:c.386T>C	p.Leu129Pro	p.L129P	ENST00000312049	NM_130799.2	129	cTc/cCc	2/10	1	2	FACETS	0.632	0.573	0.693	0.632	0.573	0.693	SUBCLONAL	1	TRUE	1	0.456380312494391	2		825	916	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342400	118342400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	40	388	0	ENST00000534358.1:c.526C>T	p.Arg176Cys	p.R176C	ENST00000534358	NM_005933.3	176	Cgt/Tgt	3/36	1	2	FACETS	0.556	0.464	0.659	0.556	0.464	0.659	SUBCLONAL	1	TRUE	1	0.456380312494391	2		388	315	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443863	18443863	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774001673	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	19	355	0	ENST00000266497.5:c.836C>T	p.Pro279Leu	p.P279L	ENST00000266497		279	cCg/cTg	3/31	1	2	FACETS	0.318	0.241	0.408	0.318	0.241	0.408	SUBCLONAL	1	TRUE	1	0.456380312494391	2		355	262	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491441	18491441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	21	235	0	ENST00000266497.5:c.1354G>A	p.Ala452Thr	p.A452T	ENST00000266497		452	Gca/Aca	8/31	1	2	FACETS	0.335	0.258	0.424	0.335	0.258	0.424	SUBCLONAL	1	TRUE	1	0.456380312494391	2		235	275	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211641	46211641	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	24	349	0	ENST00000334344.6:c.607C>A	p.Leu203Ile	p.L203I	ENST00000334344	NM_152641.2	203	Cta/Ata	5/21	1	2	FACETS	0.428	0.336	0.532	0.428	0.336	0.532	SUBCLONAL	1	TRUE	1	0.456380312494391	2		349	246	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447349	49447349	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	114	757	0	ENST00000301067.7:c.749A>T	p.His250Leu	p.H250L	ENST00000301067	NM_003482.3	250	cAc/cTc	6/54	1	2	FACETS	0.569	0.512	0.63	0.569	0.512	0.63	SUBCLONAL	1	TRUE	1	0.456380312494391	2		757	878	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448501	49448501	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	86	644	1	ENST00000301067.7:c.210C>A	p.Asn70Lys	p.N70K	ENST00000301067	NM_003482.3	70	aaC/aaA	3/54	1	2	FACETS	0.559	0.495	0.628	0.559	0.495	0.628	SUBCLONAL	1	TRUE	1	0.456380312494391	2		645	674	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481626	56481626	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	122	746	0	ENST00000267101.3:c.661C>A	p.Pro221Thr	p.P221T	ENST00000267101	NM_001982.3	221	Ccc/Acc	6/28	1	2	FACETS	0.67	0.606	0.738	0.67	0.606	0.738	SUBCLONAL	1	TRUE	1	0.456380312494391	2		746	798	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487226	56487226	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1385659523	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	95	730	0	ENST00000267101.3:c.1372G>A	p.Ala458Thr	p.A458T	ENST00000267101	NM_001982.3	458	Gcc/Acc	12/28	1	2	FACETS	0.615	0.548	0.686	0.615	0.548	0.686	SUBCLONAL	1	TRUE	1	0.456380312494391	2		730	677	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487233	56487233	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	84	725	0	ENST00000267101.3:c.1379G>A	p.Arg460Lys	p.R460K	ENST00000267101	NM_001982.3	460	aGg/aAg	12/28	1	2	FACETS	0.532	0.47	0.599	0.532	0.47	0.599	SUBCLONAL	1	TRUE	1	0.456380312494391	2		725	692	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492602	56492602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	100	606	0	ENST00000267101.3:c.2752G>A	p.Ala918Thr	p.A918T	ENST00000267101	NM_001982.3	918	Gct/Act	23/28	1	2	FACETS	0.621	0.555	0.691	0.621	0.555	0.691	SUBCLONAL	1	TRUE	1	0.456380312494391	2		606	706	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608500	28608500	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	44	634	0	ENST00000241453.7:c.1642A>T	p.Ile548Phe	p.I548F	ENST00000241453	NM_004119.2	548	Att/Ttt	13/24	1	2	FACETS	0.409	0.342	0.482	0.409	0.342	0.482	SUBCLONAL	1	TRUE	1	0.456380312494391	2		634	472	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951083	48951083	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1454134039	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	34	250	0	ENST00000267163.4:c.1245A>G	p.Ile415Met	p.I415M	ENST00000267163	NM_000321.2	415	atA/atG	13/27	1	2	FACETS	0.745	0.614	0.889	0.745	0.614	0.889	SUBCLONAL	1	TRUE	1	0.456380312494391	2		250	200	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519001	103519001	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	57	487	2	ENST00000355739.4:c.2339G>A	p.Gly780Asp	p.G780D	ENST00000355739	NM_000123.3	780	gGc/gAc	11/15	1	2	FACETS	0.467	0.401	0.539	0.467	0.401	0.539	SUBCLONAL	1	TRUE	1	0.456380312494391	2		489	535	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42002960	42002960	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1201355035	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	56	565	0	ENST00000219905.7:c.2497A>G	p.Asn833Asp	p.N833D	ENST00000219905	NM_001164273.1	833	Aat/Gat	8/24	1	2	FACETS	0.568	0.488	0.655	0.568	0.488	0.655	SUBCLONAL	1	TRUE	1	0.456380312494391	2		565	432	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929528	81929528	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	36	648	0	ENST00000359376.3:c.1189T>C	p.Ser397Pro	p.S397P	ENST00000359376	NM_002661.3	397	Tcg/Ccg	13/33	1	2	FACETS	0.224	0.184	0.27	0.224	0.184	0.27	SUBCLONAL	1	TRUE	1	0.456380312494391	2		648	703	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816246	89816246	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	107	727	2	ENST00000389301.3:c.3131A>G	p.Gln1044Arg	p.Q1044R	ENST00000389301	NM_000135.2	1044	cAg/cGg	32/43	1	2	FACETS	0.6	0.538	0.665	0.6	0.538	0.665	SUBCLONAL	1	TRUE	1	0.456380312494391	2		729	782	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89862329	89862329	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	110	689	0	ENST00000389301.3:c.991A>G	p.Ser331Gly	p.S331G	ENST00000389301	NM_000135.2	331	Agc/Ggc	11/43	1	2	FACETS	0.73	0.657	0.808	0.73	0.657	0.808	SUBCLONAL	1	TRUE	1	0.456380312494391	2		689	660	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15952204	15952204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	123	692	1	ENST00000268712.3:c.6491G>A	p.Ser2164Asn	p.S2164N	ENST00000268712	NM_006311.3	2164	aGc/aAc	41/46	1	2	FACETS	0.636	0.574	0.7	0.636	0.574	0.7	SUBCLONAL	1	TRUE	1	0.456380312494391	2		693	848	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983788	15983788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1344825664	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	36	636	0	ENST00000268712.3:c.3334C>T	p.Pro1112Ser	p.P1112S	ENST00000268712	NM_006311.3	1112	Ccc/Tcc	25/46	1	2	FACETS	0.23	0.188	0.277	0.23	0.188	0.277	SUBCLONAL	1	TRUE	1	0.456380312494391	2		636	686	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435618	56435618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	123	706	0	ENST00000407977.2:c.1519C>T	p.Pro507Ser	p.P507S	ENST00000407977		507	Ccc/Tcc	9/10	1	2	FACETS	0.701	0.634	0.771	0.701	0.634	0.771	SUBCLONAL	1	TRUE	1	0.456380312494391	2		706	769	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435906	56435906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	77	572	0	ENST00000407977.2:c.1231C>T	p.Pro411Ser	p.P411S	ENST00000407977		411	Ccc/Tcc	9/10	1	2	FACETS	0.648	0.57	0.731	0.648	0.57	0.731	SUBCLONAL	1	TRUE	1	0.456380312494391	2		572	521	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936826	78936826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	101	626	0	ENST00000306801.3:c.3908C>T	p.Ala1303Val	p.A1303V	ENST00000306801	NM_020761.2	1303	gCc/gTc	33/34	1	2	FACETS	0.683	0.611	0.759	0.683	0.611	0.759	SUBCLONAL	1	TRUE	1	0.456380312494391	2		626	648	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348455	56348455	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	60	417	0	ENST00000348428.3:c.263C>A	p.Pro88His	p.P88H	ENST00000348428	NM_006785.3	88	cCc/cAc	2/17	1	2	FACETS	0.628	0.542	0.72	0.628	0.542	0.72	SUBCLONAL	1	TRUE	1	0.456380312494391	2		417	419	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214744	5214744	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	58	518	0	ENST00000357368.4:c.4322T>A	p.Ile1441Asn	p.I1441N	ENST00000357368	NM_002850.3	1441	aTc/aAc	29/38	1	2	FACETS	0.46	0.396	0.531	0.46	0.396	0.531	SUBCLONAL	1	TRUE	1	0.456380312494391	2		518	552	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10267178	10267178	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	47	621	0	ENST00000340748.4:c.1240T>C	p.Cys414Arg	p.C414R	ENST00000340748		414	Tgt/Cgt	17/40	1	2	FACETS	0.289	0.243	0.34	0.289	0.243	0.34	SUBCLONAL	1	TRUE	1	0.456380312494391	2		621	712	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280004	18280004	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	77	570	0	ENST00000222254.8:c.2087A>G	p.Tyr696Cys	p.Y696C	ENST00000222254	NM_005027.3	696	tAc/tGc	16/16	1	2	FACETS	0.53	0.465	0.599	0.53	0.465	0.599	SUBCLONAL	1	TRUE	1	0.456380312494391	2		570	637	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976447	18976447	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	106	857	0	ENST00000262803.5:c.3097A>G	p.Thr1033Ala	p.T1033A	ENST00000262803	NM_002911.3	1033	Act/Gct	22/24	1	2	FACETS	0.535	0.479	0.594	0.535	0.479	0.594	SUBCLONAL	1	TRUE	1	0.456380312494391	2		857	869	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257847	19257847	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	83	845	1	ENST00000162023.5:c.539del	p.Pro180GlnfsTer43	p.P180Qfs*43	ENST00000162023		180	cCa/ca	9/13	1	2	FACETS	0.503	0.444	0.567	0.503	0.444	0.567	SUBCLONAL	1	TRUE	1	0.456380312494391	2		846	723	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228005	36228005	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	94	772	0	ENST00000222270.7:c.7391T>G	p.Leu2464Arg	p.L2464R	ENST00000222270	NM_014727.1	2464	cTc/cGc	33/37	1	2	FACETS	0.575	0.511	0.642	0.575	0.511	0.642	SUBCLONAL	1	TRUE	1	0.456380312494391	2		772	717	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905980	50905980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775232133	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	105	774	0	ENST00000440232.2:c.952G>A	p.Glu318Lys	p.E318K	ENST00000440232	NM_002691.3	318	Gag/Aag	8/27	1	2	FACETS	0.6	0.537	0.666	0.6	0.537	0.666	SUBCLONAL	1	TRUE	1	0.456380312494391	2		774	767	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469118	25469118	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	108	799	1	ENST00000264709.3:c.1340C>A	p.Ala447Asp	p.A447D	ENST00000264709	NM_175629.2	447	gCc/gAc	11/23	1	2	FACETS	0.522	0.468	0.58	0.522	0.468	0.58	SUBCLONAL	1	TRUE	1	0.456380312494391	2		800	906	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99162486	99162486	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	47	443	0	ENST00000074304.5:c.1004C>A	p.Pro335His	p.P335H	ENST00000074304	NM_001134224.1	335	cCc/cAc	12/26	1	2	FACETS	0.51	0.431	0.596	0.51	0.431	0.596	SUBCLONAL	1	TRUE	1	0.456380312494391	2		443	404	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044530	128044530	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	80	616	0	ENST00000285398.2:c.1091T>C	p.Leu364Pro	p.L364P	ENST00000285398	NM_000122.1	364	cTg/cCg	8/15	1	2	FACETS	0.527	0.464	0.595	0.527	0.464	0.595	SUBCLONAL	1	TRUE	1	0.456380312494391	2		616	665	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044561	128044561	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1558960995	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	86	567	0	ENST00000285398.2:c.1060G>A	p.Ala354Thr	p.A354T	ENST00000285398	NM_000122.1	354	Gca/Aca	8/15	1	2	FACETS	0.579	0.512	0.65	0.579	0.512	0.65	SUBCLONAL	1	TRUE	1	0.456380312494391	2		567	651	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530129	212530129	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	62	475	0	ENST00000342788.4:c.1790T>C	p.Leu597Ser	p.L597S	ENST00000342788	NM_005235.2	597	tTa/tCa	15/28	1	2	FACETS	0.686	0.595	0.784	0.686	0.595	0.784	SUBCLONAL	1	TRUE	1	0.456380312494391	2		475	396	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387964	31387964	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	23	383	0	ENST00000328111.2:c.1765C>A	p.Leu589Ile	p.L589I	ENST00000328111	NM_006892.3	589	Cta/Ata	17/23	1	2	FACETS	0.265	0.206	0.333	0.265	0.206	0.333	SUBCLONAL	1	TRUE	1	0.456380312494391	2		383	381	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419884	41419884	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	113	642	0	ENST00000373198.4:c.437G>A	p.Trp146Ter	p.W146*	ENST00000373198	NM_133170.3	146	tGg/tAg	3/32	1	2	FACETS	0.637	0.573	0.704	0.637	0.573	0.704	SUBCLONAL	1	TRUE	1	0.456380312494391	2		642	778	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265148	46265148	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	40	441	0	ENST00000371998.3:c.2018T>C	p.Met673Thr	p.M673T	ENST00000371998		673	aTg/aCg	12/23	1	2	FACETS	0.482	0.401	0.571	0.482	0.401	0.571	SUBCLONAL	1	TRUE	1	0.456380312494391	2		441	364	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267875	46267875	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	68	593	0	ENST00000371998.3:c.2636T>C	p.Leu879Ser	p.L879S	ENST00000371998		879	tTa/tCa	14/23	1	2	FACETS	0.542	0.472	0.617	0.542	0.472	0.617	SUBCLONAL	1	TRUE	1	0.456380312494391	2		593	550	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71019887	71019887	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	73	343	1	ENST00000318789.4:c.1722G>T	p.Gln574His	p.Q574H	ENST00000318789	NM_032682.5	574	caG/caT	19/21	1	2	FACETS	0.729	0.64	0.824	0.729	0.64	0.824	SUBCLONAL	1	TRUE	1	0.456380312494391	2		344	439	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178942595	178942595	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1261983174	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	33	306	0	ENST00000263967.3:c.2402T>G	p.Phe801Cys	p.F801C	ENST00000263967	NM_006218.2	801	tTt/tGt	16/21	1	2	FACETS	0.709	0.582	0.849	0.709	0.582	0.849	SUBCLONAL	1	TRUE	1	0.456380312494391	2		306	204	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607198	189607198	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276572584	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	118	738	0	ENST00000264731.3:c.1577C>T	p.Pro526Leu	p.P526L	ENST00000264731	NM_003722.4	526	cCt/cTt	12/14	1	2	FACETS	0.619	0.558	0.684	0.619	0.558	0.684	SUBCLONAL	1	TRUE	1	0.456380312494391	2		738	835	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612082	189612082	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	107	659	0	ENST00000264731.3:c.1834T>C	p.Ser612Pro	p.S612P	ENST00000264731	NM_003722.4	612	Tcc/Ccc	14/14	1	2	FACETS	0.713	0.64	0.789	0.713	0.64	0.789	SUBCLONAL	1	TRUE	1	0.456380312494391	2		659	658	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946239	55946239	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	63	497	0	ENST00000263923.4:c.3940A>T	p.Thr1314Ser	p.T1314S	ENST00000263923	NM_002253.2	1314	Aca/Tca	30/30	1	2	FACETS	0.461	0.398	0.529	0.461	0.398	0.529	SUBCLONAL	1	TRUE	1	0.456380312494391	2		497	599	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55991429	55991429	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	129	799	0	ENST00000263923.4:c.32T>C	p.Leu11Pro	p.L11P	ENST00000263923	NM_002253.2	11	cTg/cCg	1/30	1	2	FACETS	0.698	0.633	0.766	0.698	0.633	0.766	SUBCLONAL	1	TRUE	1	0.456380312494391	2		799	810	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538274	187538274	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	60	593	1	ENST00000441802.2:c.8960A>G	p.Glu2987Gly	p.E2987G	ENST00000441802	NM_005245.3	2987	gAa/gGa	11/27	1	2	FACETS	0.669	0.579	0.767	0.669	0.579	0.767	SUBCLONAL	1	TRUE	1	0.456380312494391	2		594	393	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959920	38959920	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	30	300	0	ENST00000357387.3:c.2012A>G	p.His671Arg	p.H671R	ENST00000357387	NM_152756.3	671	cAt/cGt	21/38	1	2	FACETS	0.648	0.526	0.784	0.648	0.526	0.784	SUBCLONAL	1	TRUE	1	0.456380312494391	2		300	203	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80169084	80169084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	32	473	1	ENST00000265081.6:c.3280G>A	p.Glu1094Lys	p.E1094K	ENST00000265081	NM_002439.4	1094	Gaa/Aaa	23/24	1	2	FACETS	0.523	0.426	0.632	0.523	0.426	0.632	SUBCLONAL	1	TRUE	1	0.456380312494391	2		474	268	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671723	30671723	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	91	735	0	ENST00000376406.3:c.5237del	p.Leu1746TrpfsTer16	p.L1746Wfs*16	ENST00000376406	NM_014641.2	1746	tTg/tg	10/15	1	2	FACETS	0.552	0.49	0.619	0.552	0.49	0.619	SUBCLONAL	1	TRUE	1	0.456380312494391	2		735	722	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178699	32178699	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	106	828	3	ENST00000375023.3:c.2695T>A	p.Ser899Thr	p.S899T	ENST00000375023	NM_004557.3	899	Tcc/Acc	18/30	1	2	FACETS	0.602	0.539	0.668	0.602	0.539	0.668	SUBCLONAL	1	TRUE	1	0.456380312494391	2		831	772	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845069	128845069	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1291088639	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	66	861	0	ENST00000249373.3:c.563A>G	p.Asn188Ser	p.N188S	ENST00000249373	NM_005631.4	188	aAc/aGc	3/12	1	2	FACETS	0.334	0.289	0.383	0.334	0.289	0.383	SUBCLONAL	1	TRUE	1	0.456380312494391	2		861	865	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866457	56866457	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	49	737	0	ENST00000519728.1:c.704G>T	p.Trp235Leu	p.W235L	ENST00000519728	NM_002350.3	235	tGg/tTg	8/13	1	2	FACETS	0.287	0.242	0.337	0.287	0.242	0.337	SUBCLONAL	1	TRUE	1	0.456380312494391	2		737	748	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376696	8376696	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	109	566	0	ENST00000356435.5:c.4417G>T	p.Gly1473Cys	p.G1473C	ENST00000356435		1473	Ggc/Tgc	27/35	1	2	FACETS	0.701	0.63	0.776	0.701	0.63	0.776	SUBCLONAL	1	TRUE	1	0.456380312494391	2		566	681	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015192	37015192	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	45	513	0	ENST00000358127.4:c.213-1G>T		p.X71_splice	ENST00000358127	NM_001280556.1	71			1	2	FACETS	0.448	0.377	0.527	0.448	0.377	0.527	SUBCLONAL	1	TRUE	1	0.456380312494391	2		513	440	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391244	139391244	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	139	865	0	ENST00000277541.6:c.6947G>T	p.Ser2316Ile	p.S2316I	ENST00000277541	NM_017617.3	2316	aGc/aTc	34/34	1	2	FACETS	0.674	0.613	0.738	0.674	0.613	0.738	SUBCLONAL	1	TRUE	1	0.456380312494391	2		865	904	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418371	139418371	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	117	867	0	ENST00000277541.6:c.201del	p.Cys68AlafsTer32	p.C68Afs*32	ENST00000277541	NM_017617.3	67	ccC/cc	3/34	1	2	FACETS	0.554	0.499	0.613	0.554	0.499	0.613	SUBCLONAL	1	TRUE	1	0.456380312494391	2		867	925	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932012	39932012	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	107	782	2	ENST00000378444.4:c.2587A>T	p.Ser863Cys	p.S863C	ENST00000378444	NM_001123385.1	863	Agt/Tgt	4/15	1	2	FACETS	0.576	0.516	0.639	0.576	0.516	0.639	SUBCLONAL	1	TRUE	1	0.456380312494391	2		784	814	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932482	39932482	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	120	792	0	ENST00000378444.4:c.2117T>C	p.Leu706Pro	p.L706P	ENST00000378444	NM_001123385.1	706	cTt/cCt	4/15	1	2	FACETS	0.588	0.531	0.649	0.588	0.531	0.649	SUBCLONAL	1	TRUE	1	0.456380312494391	2		792	894	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245038	53245038	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	111	806	0	ENST00000375401.3:c.902G>A	p.Ser301Asn	p.S301N	ENST00000375401	NM_004187.3	301	aGc/aAc	7/26	1	2	FACETS	0.575	0.516	0.637	0.575	0.516	0.637	SUBCLONAL	1	TRUE	1	0.456380312494391	2		806	846	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412301	63412301	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	142	934	0	ENST00000330258.3:c.866C>G	p.Thr289Arg	p.T289R	ENST00000330258	NM_152424.3	289	aCa/aGa	2/2	1	2	FACETS	0.66	0.601	0.722	0.66	0.601	0.722	SUBCLONAL	1	TRUE	1	0.456380312494391	2		934	943	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504164	123504164	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	54	443	0	ENST00000371139.4:c.340A>T	p.Thr114Ser	p.T114S	ENST00000371139	NM_001114937.2	114	Act/Tct	3/4	1	2	FACETS	0.924	0.797	1	0.924	0.797	1	CLONAL	1	TRUE	1	0.456380312494391	2		443	256	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0042788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	308	836	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.823458062564652	1	FACETS	0.861	0.826	0.895	0.861	0.826	0.895	CLONAL	1	TRUE	0	0.862250576801957	1		836	472	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094723	2094723	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs374489979	NA	P-0042788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	274	526	1	ENST00000219066.1:c.457C>T	p.Arg153Ter	p.R153*	ENST00000219066	NM_002528.5	153	Cga/Tga	3/6	0.781167296369545	1	FACETS	0.873	0.836	0.909	0.873	0.836	0.909	CLONAL	1	TRUE	0	0.862250576801957	1		527	414	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242673	46242673	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1469253969	NA	P-0042788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	165	284	0	ENST00000334344.6:c.1635G>A	p.Met545Ile	p.M545I	ENST00000334344	NM_152641.2	545	atG/atA	13/21	1	2	FACETS	0.94	0.874	1	0.94	0.874	1	CLONAL	1	TRUE	1	0.862250576801957	2		284	407	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044565	12044565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	113	409	0	ENST00000353533.5:c.1188G>A	p.Met396Ile	p.M396I	ENST00000353533	NM_003010.3	396	atG/atA	11/11	0.823458062564652	1	FACETS	0.893	0.835	0.948	0.893	0.835	0.948	CLONAL	1	TRUE	0	0.862250576801957	1		409	167	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209066	36209066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	57	88	0	ENST00000222270.7:c.146G>A	p.Arg49His	p.R49H	ENST00000222270	NM_014727.1	49	cGc/cAc	1/37	1	2	FACETS	0.778	0.681	0.879	0.778	0.681	0.879	SUBCLONAL	1	TRUE	1	0.862250576801957	2		88	170	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748153	41748153	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	150	295	0	ENST00000226382.2:c.616C>G	p.Pro206Ala	p.P206A	ENST00000226382	NM_003924.3	206	Ccc/Gcc	3/3	0.862250576801957	1	FACETS	0.884	0.833	0.932	0.884	0.833	0.932	CLONAL	1	TRUE	0	0.862250576801957	1		295	224	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0042815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	136	735	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.369780065612403	1	FACETS	0.964	0.879	1	0.964	0.879	1	CLONAL	1	TRUE	0	0.369780065612403	1		735	622	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0042815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	137	534	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.369780065612403	2		534	691	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47724984	47724984	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373478289	NA	P-0042815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	130	849	1	ENST00000449228.1:c.760G>A	p.Ala254Thr	p.A254T	ENST00000449228	NM_001127240.2	254	Gcg/Acg	4/4	1	2	FACETS	0.904	0.82	0.992	0.904	0.82	0.992	CLONAL	1	TRUE	1	0.369780065612403	2		850	778	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226467	41226467	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	114	576	0	ENST00000357654.3:c.4556del	p.Asn1519IlefsTer29	p.N1519Ifs*29	ENST00000357654	NM_007294.3	1519	aAt/at	14/23	0.369780065612403	1	FACETS	0.909	0.821	1	0.909	0.821	1	CLONAL	1	TRUE	0	0.369780065612403	1		576	553	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289950	15289950	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	105	855	0	ENST00000263388.2:c.3604T>A	p.Cys1202Ser	p.C1202S	ENST00000263388	NM_000435.2	1202	Tgc/Agc	22/33	1	2	FACETS	0.66	0.591	0.734	0.66	0.591	0.734	SUBCLONAL	1	TRUE	1	0.369780065612403	2		855	860	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715850	117715863	+	frameshift_variant	Frame_Shift_Del	DEL	TTTCTTAGAGAAGT	TTTCTTAGAGAAGT	-	novel	NA	P-0042815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	52	323	0	ENST00000368508.3:c.895_908del	p.Thr299GlufsTer9	p.T299Efs*9	ENST00000368508	NM_002944.2	299	ACTTCTCTAAGAAAg/g	9/43	1	2	FACETS	0.617	0.526	0.716	0.617	0.526	0.716	SUBCLONAL	1	TRUE	1	0.369780065612403	2		323	456	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873287	151873287	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	102	222	0	ENST00000262189.6:c.9251T>C	p.Phe3084Ser	p.F3084S	ENST00000262189	NM_170606.2	3084	tTc/tCc	38/59	0.111458412181347	4	FACETS	1	0.904	1	1	0.904	1	INDETERMINATE	2	TRUE	2	0.369780065612403	4		222	377	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0042818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	118	442	4	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.983	0.889	1	0.983	0.889	1	CLONAL	1	TRUE	1	0.396290005945764	2		446	606	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	255	554	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	0.169102883303859	2	FACETS	0.767	0.72	0.815	0.767	0.72	0.815	INDETERMINATE	2	TRUE	0	0.396290005945764	2		554	839	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0042818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	373	746	1	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	0.379088874353486	2	FACETS	0.96	0.914	1	0.96	0.914	1	CLONAL	2	TRUE	0	0.396290005945764	2		747	980	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372070	55372070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	264	587	0	ENST00000297316.4:c.760G>A	p.Ala254Thr	p.A254T	ENST00000297316	NM_022454.3	254	Gcg/Acg	2/2	0.11349116038081	4	FACETS	1	0.972	1	1	0.972	1	INDETERMINATE	2	TRUE	2	0.396290005945764	4		587	878	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971023	21971023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782797	NA	P-0042818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	59	581	0	ENST00000304494.5:c.335G>A	p.Arg112His	p.R112H	ENST00000304494	NM_000077.4	112	cGt/cAt	2/3	0.194679116676683	4	FACETS	0.415	0.356	0.48	0.207	0.178	0.24	INDETERMINATE	1	TRUE	2	0.396290005945764	4		581	1002	SUCCESS
APC	324	MSKCC	GRCh37	5	112175377	112175378	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0042818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	81	282	0	ENST00000257430.4:c.4090dup	p.Ser1364LysfsTer11	p.S1364Kfs*11	ENST00000257430	NM_000038.5	1362	-/A	16/16	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.396290005945764	2		282	390	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	188	541	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.94	0.878	1	0.94	0.878	1	CLONAL	1	TRUE	1	0.862084531600229	2		541	464	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944256	206944256	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374619208	NA	P-0042848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	130	511	0	ENST00000423557.1:c.374G>A	p.Arg125His	p.R125H	ENST00000423557	NM_000572.2	125	cGc/cAc	3/5	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.862084531600229	2		511	295	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617453	158617453	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	40	736	0	ENST00000263640.3:c.1203G>C	p.Arg401Ser	p.R401S	ENST00000263640	NM_001105.4	401	agG/agC	9/11	1	2	FACETS	0.251	0.208	0.298	0.251	0.208	0.298	SUBCLONAL	1	TRUE	1	0.862084531600229	2		736	370	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30946592	30946593	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0042848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	131	313	0	ENST00000375687.4:c.15_16del	p.Lys6GlufsTer67	p.K6Efs*67	ENST00000375687	NM_015338.5	5	cAG/c	1/13	0.540794614768439	3	FACETS	0.824	0.751	0.899	0.412	0.375	0.45	CLONAL	1	TRUE	1	0.862084531600229	3		313	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0042957-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	29	586	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	1	2	FACETS	0.576	0.461	0.708	0.576	0.461	0.708	SUBCLONAL	1	TRUE	1	0.15	2		586	671	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0042957-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	32	337	0	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	0.3	2	FACETS	1	0.914	1	0.618	0.503	0.749	CLONAL	1	TRUE	0	0.15	2		337	345	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106898	27106898	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042957-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	31	471	0	ENST00000324856.7:c.6509T>G	p.Leu2170Arg	p.L2170R	ENST00000324856	NM_006015.4	2170	cTg/cGg	20/20	1	2	FACETS	0.838	0.677	1	0.838	0.677	1	CLONAL	1	TRUE	1	0.15	2		471	493	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551215	29551215	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs777414641	NA	P-0042957-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	23	499	2	ENST00000389048.3:c.1414+1G>A		p.X472_splice	ENST00000389048	NM_004304.4	472			1	2	FACETS	0.757	0.59	0.952	0.757	0.59	0.952	CLONAL	1	TRUE	1	0.15	2		501	405	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646467	23646467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881906	NA	P-0042964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	88	596	2	ENST00000261584.4:c.1400G>A	p.Gly467Asp	p.G467D	ENST00000261584	NM_024675.3	467	gGc/gAc	4/13	0.286976592770409	3	FACETS	1	0.944	1	0.552	0.49	0.619	CLONAL	1	FALSE	1	0.3	3		598	611	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375431	40375431	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	98	625	0	ENST00000293328.3:c.519C>G	p.Ile173Met	p.I173M	ENST00000293328	NM_012448.3	173	atC/atG	5/19	0.286976592770409	3	FACETS	0.968	0.864	1	0.484	0.432	0.54	CLONAL	1	FALSE	1	0.3	3		625	776	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0042983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	25	272	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.728139623298874	1	FACETS	0.948	0.796	1	0.948	0.796	1	CLONAL	1	TRUE	0	0.72865724101265	1		272	46	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023465	27023549	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCTGGAGCCCTACGCGGGGCCCCAGCAGAACTCTCACGACCACGGCTTCCCCAACCACCAGTACAACTCCTACTACCCCAACC	GGCCTGGAGCCCTACGCGGGGCCCCAGCAGAACTCTCACGACCACGGCTTCCCCAACCACCAGTACAACTCCTACTACCCCAACC	-	novel	NA	P-0042983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	127	588	0	ENST00000324856.7:c.572_656del	p.Gly191AlafsTer13	p.G191Afs*13	ENST00000324856	NM_006015.4	191	GGCCTGGAGCCCTACGCGGGGCCCCAGCAGAACTCTCACGACCACGGCTTCCCCAACCACCAGTACAACTCCTACTACCCCAACCgc/gc	1/20	0.72865724101265	1	FACETS	0.507	0.463	0.553	0.507	0.463	0.553	SUBCLONAL	1	TRUE	0	0.72865724101265	1		588	437	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023602	27023609	+	protein_altering_variant	In_Frame_Del	DEL	TGGCACTC	TGGCACTC	CG	novel	NA	P-0042983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	113	415	2	ENST00000324856.7:c.708_715delinsCG	p.Gly237_Pro239delinsAla	p.G237_P239delinsA	ENST00000324856	NM_006015.4	236	ggTGGCACTCcg/ggCGcg	1/20	0.72865724101265	1	FACETS	0.546	0.496	0.598	0.546	0.496	0.598	SUBCLONAL	1	TRUE	0	0.72865724101265	1		417	361	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419049	419049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	13	670	0	ENST00000399788.2:c.3298G>A	p.Glu1100Lys	p.E1100K	ENST00000399788	NM_001042603.1	1100	Gaa/Aaa	22/28	0.728139623298874	1	FACETS	0.09	0.064	0.122	0.09	0.064	0.122	SUBCLONAL	1	TRUE	0	0.72865724101265	1		670	252	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0042983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	60	681	0	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	0.72865724101265	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.72865724101265	1		681	80	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591821	48591821	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	23	564	0	ENST00000342988.3:c.984C>A	p.Tyr328Ter	p.Y328*	ENST00000342988	NM_005359.5	328	taC/taA	9/12	0.723033630856386	1	FACETS	0.979	0.818	1	0.979	0.818	1	CLONAL	1	TRUE	0	0.72865724101265	1		564	41	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488657	212488657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374970657	NA	P-0042983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	19	522	0	ENST00000342788.4:c.2192C>T	p.Thr731Met	p.T731M	ENST00000342788	NM_005235.2	731	aCg/aTg	18/28	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.72865724101265	2		522	36	SUCCESS
APC	324	MSKCC	GRCh37	5	112151191	112151191	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0042983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	15	424	0	ENST00000257430.4:c.835-1G>A		p.X279_splice	ENST00000257430	NM_000038.5	279			0.627424405260744	1	FACETS	1	0.805	1	1	0.805	1	CLONAL	1	TRUE	0	0.72865724101265	1		424	26	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525016	157525016	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554236609	NA	P-0042983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	21	458	0	ENST00000346085.5:c.4911G>A	p.Trp1637Ter	p.W1637*	ENST00000346085	NM_020732.3	1637	tgG/tgA	19/20	0.723033630856386	1	FACETS	0.814	0.663	0.968	0.814	0.663	0.968	CLONAL	1	TRUE	0	0.72865724101265	1		458	45	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	67	708	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.241	0.208	0.276	0.241	0.208	0.276	SUBCLONAL	1	TRUE	1	0.630016146636737	2		708	884	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	159	368	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.630016146636737	2		368	439	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	132	418	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.630016146636737	2		418	376	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827927	40827927	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536150112	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	208	624	1	ENST00000373198.4:c.2501G>A	p.Arg834His	p.R834H	ENST00000373198	NM_133170.3	834	cGc/cAc	17/32	NA	2	FACETS	0.901	0.839	0.964			1	INDETERMINATE	1	TRUE	NA	0.630016146636737	2		625	733	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	200	528	0	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.943	0.878	1	0.943	0.878	1	CLONAL	1	TRUE	1	0.630016146636737	2		528	673	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	282	574	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.630016146636737	2		580	739	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	181	369	3	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.630016146636737	2		372	495	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	104	577	6	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.506	0.453	0.561	0.506	0.453	0.561	SUBCLONAL	1	TRUE	1	0.630016146636737	2		583	653	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	220	862	1	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.781	0.728	0.836	0.781	0.728	0.836	SUBCLONAL	1	TRUE	1	0.630016146636737	2		863	894	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	196	582	0	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	1	2	FACETS	0.965	0.897	1	0.965	0.897	1	CLONAL	1	TRUE	1	0.630016146636737	2		582	645	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294268	11294268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879251235	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	228	652	0	ENST00000361445.4:c.2263C>T	p.Arg755Cys	p.R755C	ENST00000361445	NM_004958.3	755	Cgc/Tgc	14/58	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.630016146636737	2		652	705	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256462	16256462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	243	683	0	ENST00000375759.3:c.3727C>T	p.Arg1243Trp	p.R1243W	ENST00000375759	NM_015001.2	1243	Cgg/Tgg	11/15	1	2	FACETS	0.992	0.93	1	0.992	0.93	1	CLONAL	1	TRUE	1	0.630016146636737	2		683	778	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699492	117699493	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	102	448	0	ENST00000369458.3:c.148dup	p.Glu50GlyfsTer10	p.E50Gfs*10	ENST00000369458	NM_024626.3	50	gag/gGag	3/6	1	2	FACETS	0.608	0.545	0.673	0.608	0.545	0.673	SUBCLONAL	1	TRUE	1	0.630016146636737	2		448	533	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851325	156851325	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	202	732	1	ENST00000524377.1:c.2285del	p.Gly762AlafsTer?	p.G762Afs*?	ENST00000524377	NM_002529.3	761	cGg/cg	17/17	1	2	FACETS	0.938	0.873	1	0.938	0.873	1	CLONAL	1	TRUE	1	0.630016146636737	2		733	684	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651613	206651613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782254432	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	333	875	0	ENST00000367120.3:c.923G>A	p.Arg308Gln	p.R308Q	ENST00000367120	NM_014002.3	308	cGa/cAa	9/22	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.630016146636737	2		875	961	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097701	8097702	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	63	502	0	ENST00000346208.3:c.86dup	p.Leu31ProfsTer22	p.L31Pfs*22	ENST00000346208		28	cac/caCc	2/6	1	2	FACETS	0.426	0.369	0.488	0.426	0.369	0.488	SUBCLONAL	1	TRUE	1	0.630016146636737	2		502	469	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8105989	8105989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	217	544	0	ENST00000346208.3:c.809C>T	p.Ser270Leu	p.S270L	ENST00000346208		270	tCg/tTg	4/6	1	2	FACETS	0.994	0.929	1	0.994	0.929	1	CLONAL	1	TRUE	1	0.630016146636737	2		544	693	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88676897	88676897	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782682	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	218	553	0	ENST00000372037.3:c.682C>T	p.Arg228Ter	p.R228*	ENST00000372037	NM_004329.2	228	Cga/Tga	9/13	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.630016146636737	2		553	690	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683357	88683357	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201040	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	250	761	0	ENST00000372037.3:c.1480C>T	p.Arg494Ter	p.R494*	ENST00000372037	NM_004329.2	494	Cga/Tga	13/13	1	2	FACETS	0.94	0.882	1	0.94	0.882	1	CLONAL	1	TRUE	1	0.630016146636737	2		761	844	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456690	32456690	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	102	429	0	ENST00000332351.3:c.202C>T	p.Gln68Ter	p.Q68*	ENST00000332351	NM_024426.4	68	Caa/Taa	1/10	1	2	FACETS	0.816	0.735	0.9	0.816	0.735	0.9	CLONAL	1	TRUE	1	0.630016146636737	2		429	397	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572092	64572093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767319284	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	167	680	4	ENST00000312049.6:c.1546dup	p.Arg516ProfsTer15	p.R516Pfs*15	ENST00000312049	NM_130799.2	516	cgg/cCgg	10/10	1	2	FACETS	0.85	0.784	0.917	0.85	0.784	0.917	CLONAL	1	TRUE	1	0.630016146636737	2		684	624	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	45	366	1	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	0.265	0.222	0.312	0.265	0.222	0.312	SUBCLONAL	1	TRUE	1	0.630016146636737	2		367	540	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170256	119170256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374672276	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	130	371	1	ENST00000264033.4:c.2486G>A	p.Arg829Gln	p.R829Q	ENST00000264033	NM_005188.3	829	cGg/cAg	16/16	1	2	FACETS	0.99	0.906	1	0.99	0.906	1	CLONAL	1	TRUE	1	0.630016146636737	2		372	417	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870961	12870962	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	117	445	0	ENST00000228872.4:c.192dup	p.Gln65SerfsTer60	p.Q65Sfs*60	ENST00000228872	NM_004064.3	63	gat/gaTt	1/3	1	2	FACETS	0.882	0.802	0.966	0.882	0.802	0.966	CLONAL	1	TRUE	1	0.630016146636737	2		445	421	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254721	46254721	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	54	378	0	ENST00000334344.6:c.4911G>T	p.Gln1637His	p.Q1637H	ENST00000334344	NM_152641.2	1637	caG/caT	16/21	1	2	FACETS	0.405	0.347	0.469	0.405	0.347	0.469	SUBCLONAL	1	TRUE	1	0.630016146636737	2		378	423	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416495	49416495	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	54	665	1	ENST00000301067.7:c.16216A>G	p.Ile5406Val	p.I5406V	ENST00000301067	NM_003482.3	5406	Atc/Gtc	51/54	1	2	FACETS	0.239	0.204	0.279	0.239	0.204	0.279	SUBCLONAL	1	TRUE	1	0.630016146636737	2		666	716	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562427	21562427	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	125	459	1	ENST00000382592.4:c.1492G>T	p.Gly498Cys	p.G498C	ENST00000382592	NM_014572.2	498	Ggc/Tgc	4/8	1	2	FACETS	0.949	0.867	1	0.949	0.867	1	CLONAL	1	TRUE	1	0.630016146636737	2		460	418	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895643	28895643	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	39	602	0	ENST00000282397.4:c.3131C>T	p.Ala1044Val	p.A1044V	ENST00000282397	NM_002019.4	1044	gCc/gTc	23/30	1	2	FACETS	0.19	0.157	0.227	0.19	0.157	0.227	SUBCLONAL	1	TRUE	1	0.630016146636737	2		602	651	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871633	35871634	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	116	383	0	ENST00000216797.5:c.872_873del	p.Thr291ArgfsTer15	p.T291Rfs*15	ENST00000216797	NM_020529.2	291	aCA/a	5/6	1	2	FACETS	0.918	0.835	1	0.918	0.835	1	CLONAL	1	TRUE	1	0.630016146636737	2		383	401	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343636	343636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs544557159	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	274	910	2	ENST00000262320.3:c.2038C>T	p.Arg680Trp	p.R680W	ENST00000262320	NM_003502.3	680	Cgg/Tgg	8/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.630016146636737	2		912	761	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3651016	3651016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	205	554	0	ENST00000294008.3:c.1127C>T	p.Ala376Val	p.A376V	ENST00000294008	NM_032444.2	376	gCa/gTa	5/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.630016146636737	2		554	616	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900423	3900423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	253	755	1	ENST00000262367.5:c.673C>T	p.Pro225Ser	p.P225S	ENST00000262367	NM_004380.2	225	Ccg/Tcg	2/31	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.630016146636737	2		756	717	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032029	10032029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747214620	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	111	699	0	ENST00000330684.3:c.794C>T	p.Thr265Met	p.T265M	ENST00000330684	NM_001134407.1	265	aCg/aTg	3/13	1	2	FACETS	0.479	0.431	0.531	0.479	0.431	0.531	SUBCLONAL	1	TRUE	1	0.630016146636737	2		699	735	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805074	89805074	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs74977201	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	192	704	1	ENST00000389301.3:c.4303G>A	p.Ala1435Thr	p.A1435T	ENST00000389301	NM_000135.2	1435	Gcc/Acc	43/43	1	2	FACETS	0.919	0.854	0.987	0.919	0.854	0.987	CLONAL	1	TRUE	1	0.630016146636737	2		705	663	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217705	7217707	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs757139280	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	40	534	0	ENST00000380728.2:c.220_222del	p.Glu74del	p.E74del	ENST00000380728		74	GAG/-	4/11	1	2	FACETS	0.211	0.175	0.252	0.211	0.175	0.252	SUBCLONAL	1	TRUE	1	0.630016146636737	2		534	601	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554265	29554265	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786202504	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	155	493	0	ENST00000356175.3:c.2281G>A	p.Ala761Thr	p.A761T	ENST00000356175	NM_000267.3	761	Gca/Aca	19/57	1	2	FACETS	0.913	0.841	0.987	0.913	0.841	0.987	CLONAL	1	TRUE	1	0.630016146636737	2		493	539	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687569	29687569	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	198	689	1	ENST00000356175.3:c.8162A>G	p.Tyr2721Cys	p.Y2721C	ENST00000356175	NM_000267.3	2721	tAc/tGc	56/57	1	2	FACETS	0.958	0.892	1	0.958	0.892	1	CLONAL	1	TRUE	1	0.630016146636737	2		690	656	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322639	30322639	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	176	583	0	ENST00000322652.5:c.1652T>C	p.Val551Ala	p.V551A	ENST00000322652	NM_015355.2	551	gTa/gCa	14/16	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.630016146636737	2		583	545	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627500	37627501	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	103	599	0	ENST00000447079.4:c.1421dup	p.Asn474LysfsTer12	p.N474Kfs*12	ENST00000447079	NM_015083.1	472	gta/gtAa	2/14	1	2	FACETS	0.484	0.434	0.538	0.484	0.434	0.538	SUBCLONAL	1	TRUE	1	0.630016146636737	2		599	675	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37863252	37863252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1284110310	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	62	636	3	ENST00000269571.5:c.83G>A	p.Gly28Asp	p.G28D	ENST00000269571		28	gGc/gAc	2/27	1	2	FACETS	0.303	0.261	0.348	0.303	0.261	0.348	SUBCLONAL	1	TRUE	1	0.630016146636737	2		639	650	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866112	37866112	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	273	684	0	ENST00000269571.5:c.621G>T	p.Glu207Asp	p.E207D	ENST00000269571		207	gaG/gaT	5/27	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.630016146636737	2		684	757	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883113	37883113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780434636	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	229	852	1	ENST00000269571.5:c.3016C>T	p.Arg1006Cys	p.R1006C	ENST00000269571		1006	Cgc/Tgc	25/27	1	2	FACETS	0.957	0.895	1	0.957	0.895	1	CLONAL	1	TRUE	1	0.630016146636737	2		853	760	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362446	40362447	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1202978138	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	202	645	0	ENST00000293328.3:c.1749dup	p.His584ThrfsTer8	p.H584Tfs*8	ENST00000293328	NM_012448.3	583	-/A	14/19	1	2	FACETS	0.877	0.816	0.94	0.877	0.816	0.94	CLONAL	1	TRUE	1	0.630016146636737	2		645	731	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448293	56448293	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	231	747	0	ENST00000407977.2:c.354del	p.Cys119AlafsTer39	p.C119Afs*39	ENST00000407977		118	ccC/cc	3/10	1	2	FACETS	0.885	0.827	0.944	0.885	0.827	0.944	CLONAL	1	TRUE	1	0.630016146636737	2		747	829	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780620	56780620	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200857129	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	178	584	1	ENST00000337432.4:c.635G>A	p.Arg212His	p.R212H	ENST00000337432	NM_058216.2	212	cGc/cAc	4/9	1	2	FACETS	0.928	0.86	0.998	0.928	0.86	0.998	CLONAL	1	TRUE	1	0.630016146636737	2		585	609	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545650	63545650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747647668	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	157	528	1	ENST00000307078.5:c.944C>T	p.Thr315Met	p.T315M	ENST00000307078	NM_004655.3	315	aCg/aTg	3/11	1	2	FACETS	0.93	0.857	1	0.93	0.857	1	CLONAL	1	TRUE	1	0.630016146636737	2		529	536	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119910	70119910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1297203260	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	130	547	0	ENST00000245479.2:c.916del	p.Val306CysfsTer77	p.V306Cfs*77	ENST00000245479	NM_000346.3	304	ccG/cc	3/3	1	2	FACETS	0.785	0.715	0.857	0.785	0.715	0.857	SUBCLONAL	1	TRUE	1	0.630016146636737	2		547	526	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221239	1221240	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	280	814	0	ENST00000326873.7:c.762_763insA	p.Phe255IlefsTer11	p.F255Ifs*11	ENST00000326873	NM_000455.4	254	-/A	6/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.630016146636737	2		814	828	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222967	5222967	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778392508	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	173	543	2	ENST00000357368.4:c.2836G>A	p.Val946Ile	p.V946I	ENST00000357368	NM_002850.3	946	Gtc/Atc	18/38	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.630016146636737	2		545	521	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600446	10600446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	100	757	0	ENST00000171111.5:c.1409G>A	p.Arg470His	p.R470H	ENST00000171111	NM_203500.1	470	cGt/cAt	4/6	1	2	FACETS	0.399	0.356	0.445	0.399	0.356	0.445	SUBCLONAL	1	TRUE	1	0.630016146636737	2		757	795	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602587	10602587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1197443517	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	120	703	1	ENST00000171111.5:c.991G>A	p.Ala331Thr	p.A331T	ENST00000171111	NM_203500.1	331	Gcg/Acg	3/6	1	2	FACETS	0.474	0.428	0.523	0.474	0.428	0.523	SUBCLONAL	1	TRUE	1	0.630016146636737	2		704	803	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031345	11031345	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752773089	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	249	785	1	ENST00000327064.4:c.1345G>A	p.Asp449Asn	p.D449N	ENST00000327064	NM_199141.1	449	Gac/Aac	12/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.630016146636737	2		786	782	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098351	11098351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763054014	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	167	545	0	ENST00000358026.2:c.869C>T	p.Ala290Val	p.A290V	ENST00000358026	NM_001128849.1	290	gCg/gTg	6/36	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.630016146636737	2		545	530	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136144	11136144	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	289	785	0	ENST00000358026.2:c.3128G>A	p.Arg1043Gln	p.R1043Q	ENST00000358026	NM_001128849.1	1043	cGg/cAg	22/36	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.630016146636737	2		785	865	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278138	15278138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756495084	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	153	772	0	ENST00000263388.2:c.5284G>A	p.Val1762Met	p.V1762M	ENST00000263388	NM_000435.2	1762	Gtg/Atg	29/33	1	2	FACETS	0.609	0.558	0.663	0.609	0.558	0.663	SUBCLONAL	1	TRUE	1	0.630016146636737	2		772	797	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218419	36218419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747829749	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	190	731	1	ENST00000222270.7:c.4198C>T	p.Arg1400Cys	p.R1400C	ENST00000222270	NM_014727.1	1400	Cgc/Tgc	16/37	1	2	FACETS	0.89	0.826	0.956	0.89	0.826	0.956	CLONAL	1	TRUE	1	0.630016146636737	2		732	678	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791001	42791001	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	195	651	0	ENST00000575354.2:c.146C>A	p.Pro49His	p.P49H	ENST00000575354	NM_015125.3	49	cCt/cAt	2/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.630016146636737	2		651	592	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798406	42798406	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	231	804	0	ENST00000575354.2:c.4281del	p.Lys1428ArgfsTer26	p.K1428Rfs*26	ENST00000575354	NM_015125.3	1426	aCc/ac	18/20	1	2	FACETS	0.88	0.823	0.94	0.88	0.823	0.94	CLONAL	1	TRUE	1	0.630016146636737	2		804	833	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798778	42798815	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGGAGCTAGAGTATGACAAGGTGCCATACTCCTCCC	TGGGGAGCTAGAGTATGACAAGGTGCCATACTCCTCCC	-	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	55	710	1	ENST00000575354.2:c.4352_4389del	p.Gly1451AlafsTer50	p.G1451Afs*50	ENST00000575354	NM_015125.3	1450	ctTGGGGAGCTAGAGTATGACAAGGTGCCATACTCCTCCCtg/cttg	19/20	1	2	FACETS	0.264	0.225	0.306	0.264	0.225	0.306	SUBCLONAL	1	TRUE	1	0.630016146636737	2		711	662	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902266	50902268	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs766482335	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	75	877	8	ENST00000440232.2:c.169_171del	p.Glu57del	p.E57del	ENST00000440232	NM_002691.3	53	cAGGag/cag	2/27	1	2	FACETS	0.266	0.232	0.303	0.266	0.232	0.303	SUBCLONAL	1	TRUE	1	0.630016146636737	2		885	895	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436865	29436865	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	51	617	0	ENST00000389048.3:c.3728del	p.Asn1243ThrfsTer15	p.N1243Tfs*15	ENST00000389048	NM_004304.4	1243	aAc/ac	24/29	1	2	FACETS	0.246	0.208	0.287	0.246	0.208	0.287	SUBCLONAL	1	TRUE	1	0.630016146636737	2		617	659	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027196	48027196	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs267608083	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	151	477	0	ENST00000234420.5:c.2079del	p.Lys693AsnfsTer43	p.K693Nfs*43	ENST00000234420	NM_000179.2	692	Aaa/aa	4/10	1	2	FACETS	0.917	0.843	0.992	0.917	0.843	0.992	CLONAL	1	TRUE	1	0.630016146636737	2		477	523	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047329	128047329	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748503195	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	46	592	0	ENST00000285398.2:c.593G>A	p.Arg198His	p.R198H	ENST00000285398	NM_000122.1	198	cGc/cAc	5/15	1	2	FACETS	0.225	0.188	0.265	0.225	0.188	0.265	SUBCLONAL	1	TRUE	1	0.630016146636737	2		592	650	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198272772	198272772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1360040192	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	178	650	0	ENST00000335508.6:c.1189C>T	p.Arg397Cys	p.R397C	ENST00000335508	NM_012433.2	397	Cgc/Tgc	9/25	1	2	FACETS	0.867	0.802	0.933	0.867	0.802	0.933	CLONAL	1	TRUE	1	0.630016146636737	2		650	652	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646085	215646085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	172	576	3	ENST00000260947.4:c.513del	p.Asp172MetfsTer40	p.D172Mfs*40	ENST00000260947	NM_000465.2	171	aaA/aa	4/11	1	2	FACETS	0.906	0.837	0.976	0.906	0.837	0.976	CLONAL	1	TRUE	1	0.630016146636737	2		579	603	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795061	242795061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1203794937	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	65	939	0	ENST00000334409.5:c.148G>A	p.Ala50Thr	p.A50T	ENST00000334409	NM_005018.2	50	Gcc/Acc	2/5	1	2	FACETS	0.228	0.197	0.262	0.228	0.197	0.262	SUBCLONAL	1	TRUE	1	0.630016146636737	2		939	904	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543581	9543581	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	242	666	0	ENST00000353224.5:c.1573T>G	p.Phe525Val	p.F525V	ENST00000353224	NM_177990.2	525	Ttt/Gtt	6/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.630016146636737	2		666	697	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961325	54961325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	40	598	1	ENST00000312783.6:c.307C>T	p.Pro103Ser	p.P103S	ENST00000312783	NM_198436.1	103	Cca/Tca	4/10	1	2	FACETS	0.181	0.15	0.216	0.181	0.15	0.216	SUBCLONAL	1	TRUE	1	0.630016146636737	2		599	701	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165283	47165283	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	37	397	0	ENST00000409792.3:c.843del	p.Glu282LysfsTer19	p.E282Kfs*19	ENST00000409792	NM_014159.6	281	aaA/aa	3/21	1	2	FACETS	0.324	0.267	0.387	0.324	0.267	0.387	SUBCLONAL	1	TRUE	1	0.630016146636737	2		397	363	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990415	69990415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764477527	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	88	409	0	ENST00000394351.3:c.374G>A	p.Ser125Asn	p.S125N	ENST00000394351	NM_000248.3	125	aGc/aAc	4/9	1	2	FACETS	0.751	0.67	0.836	0.751	0.67	0.836	SUBCLONAL	1	TRUE	1	0.630016146636737	2		409	372	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281238	142281238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886058056	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	85	497	1	ENST00000350721.4:c.1006C>T	p.Arg336Trp	p.R336W	ENST00000350721	NM_001184.3	336	Cgg/Tgg	4/47	1	2	FACETS	0.487	0.431	0.547	0.487	0.431	0.547	SUBCLONAL	1	TRUE	1	0.630016146636737	2		498	554	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	50	697	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.209	0.176	0.245	0.209	0.176	0.245	SUBCLONAL	1	TRUE	1	0.630016146636737	2		697	760	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519941	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	19	372	0	ENST00000263967.3:c.1031T>C	p.Val344Ala	p.V344A	ENST00000263967	NM_006218.2	344	gTg/gCg	5/21	1	2	FACETS	0.186	0.14	0.239	0.186	0.14	0.239	SUBCLONAL	1	TRUE	1	0.630016146636737	2		372	325	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198179	185198179	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	217	597	0	ENST00000265026.3:c.2661C>G	p.Asp887Glu	p.D887E	ENST00000265026	NM_004721.4	887	gaC/gaG	13/14	1	2	FACETS	0.966	0.902	1	0.966	0.902	1	CLONAL	1	TRUE	1	0.630016146636737	2		597	713	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164772	106164772	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761811530	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	197	553	0	ENST00000380013.4:c.3640C>T	p.Arg1214Trp	p.R1214W	ENST00000380013	NM_001127208.2	1214	Cgg/Tgg	6/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.630016146636737	2		553	579	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	21	272	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	0.243	0.187	0.308	0.243	0.187	0.308	SUBCLONAL	1	TRUE	1	0.630016146636737	2		272	274	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518216	187518216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	179	415	0	ENST00000441802.2:c.12478C>T	p.Arg4160Cys	p.R4160C	ENST00000441802	NM_005245.3	4160	Cgt/Tgt	25/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.630016146636737	2		415	496	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	92	388	1	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	1	2	FACETS	0.825	0.739	0.915	0.825	0.739	0.915	CLONAL	1	TRUE	1	0.630016146636737	2		389	354	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670061	86670061	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	139	419	0	ENST00000274376.6:c.1858C>A	p.Leu620Met	p.L620M	ENST00000274376	NM_002890.2	620	Ctg/Atg	14/25	1	2	FACETS	0.955	0.876	1	0.955	0.876	1	CLONAL	1	TRUE	1	0.630016146636737	2		419	462	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456995	149456995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41338945	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	155	467	0	ENST00000286301.3:c.733G>A	p.Ala245Thr	p.A245T	ENST00000286301	NM_005211.3	245	Gca/Aca	6/22	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.630016146636737	2		467	468	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721847	176721847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	192	575	2	ENST00000439151.2:c.7478C>T	p.Ala2493Val	p.A2493V	ENST00000439151	NM_022455.4	2493	gCc/gTc	23/23	1	2	FACETS	0.986	0.917	1	0.986	0.917	1	CLONAL	1	TRUE	1	0.630016146636737	2		577	618	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797707	32797707	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	183	521	0	ENST00000374899.4:c.1795G>T	p.Asp599Tyr	p.D599Y	ENST00000374899	NM_018833.2	599	Gat/Tat	10/12	1	2	FACETS	0.945	0.876	1	0.945	0.876	1	CLONAL	1	TRUE	1	0.630016146636737	2		521	615	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805738	32805739	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	170	708	0	ENST00000374899.4:c.272dup	p.Ala92SerfsTer75	p.A92Sfs*75	ENST00000374899	NM_018833.2	91	cca/ccCa	2/12	1	2	FACETS	0.843	0.779	0.91	0.843	0.779	0.91	CLONAL	1	TRUE	1	0.630016146636737	2		708	640	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508793	106508793	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370152741	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	170	681	0	ENST00000359195.3:c.787G>A	p.Glu263Lys	p.E263K	ENST00000359195	NM_002649.2	263	Gaa/Aaa	2/11	1	2	FACETS	0.823	0.759	0.888	0.823	0.759	0.888	CLONAL	1	TRUE	1	0.630016146636737	2		681	656	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538819	23538819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764325622	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	184	509	0	ENST00000380871.4:c.620G>A	p.Arg207Gln	p.R207Q	ENST00000380871	NM_006167.3	207	cGg/cAg	2/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.630016146636737	2		509	534	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271163	38271163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs17182456	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	148	562	0	ENST00000425967.3:c.2545G>A	p.Gly849Arg	p.G849R	ENST00000425967	NM_001174067.1	849	Gga/Aga	19/19	1	2	FACETS	0.932	0.857	1	0.932	0.857	1	CLONAL	1	TRUE	1	0.630016146636737	2		562	504	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964427	70964427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	219	555	0	ENST00000276594.2:c.1601G>A	p.Ser534Asn	p.S534N	ENST00000276594	NM_024504.3	534	aGc/aAc	8/8	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.630016146636737	2		555	660	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741649	145741649	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1292831710	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	242	802	0	ENST00000428558.2:c.854del	p.Pro285HisfsTer8	p.P285Hfs*8	ENST00000428558	NM_004260.3	285	cCa/ca	5/22	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.630016146636737	2		802	736	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971156	21971156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	148	519	0	ENST00000304494.5:c.202G>A	p.Ala68Thr	p.A68T	ENST00000304494	NM_000077.4	68	Gcg/Acg	2/3	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.630016146636737	2		519	443	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750371	133750372	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	201	639	0	ENST00000318560.5:c.1206dup	p.Ile403HisfsTer42	p.I403Hfs*42	ENST00000318560	NM_005157.4	401	ttc/ttCc	7/11	1	2	FACETS	0.899	0.836	0.963	0.899	0.836	0.963	CLONAL	1	TRUE	1	0.630016146636737	2		639	710	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409991	139409991	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	265	866	0	ENST00000277541.6:c.1847del	p.Gly616AlafsTer15	p.G616Afs*15	ENST00000277541	NM_017617.3	616	gGc/gc	11/34	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.630016146636737	2		866	835	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410102	139410102	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458789810	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	262	798	0	ENST00000277541.6:c.1736C>T	p.Ser579Phe	p.S579F	ENST00000277541	NM_017617.3	579	tCc/tTc	11/34	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.630016146636737	2		798	819	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417475	139417475	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761616770	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	66	778	4	ENST00000277541.6:c.569G>A	p.Arg190His	p.R190H	ENST00000277541	NM_017617.3	190	cGc/cAc	4/34	1	2	FACETS	0.293	0.254	0.336	0.293	0.254	0.336	SUBCLONAL	1	TRUE	1	0.630016146636737	2		782	715	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411246	63411246	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	58	722	0	ENST00000330258.3:c.1921C>T	p.Arg641Ter	p.R641*	ENST00000330258	NM_152424.3	641	Cga/Tga	2/2	1	2	FACETS	0.236	0.202	0.274	0.236	0.202	0.274	SUBCLONAL	1	TRUE	1	0.630016146636737	2		722	779	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411530	63411530	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	277	874	0	ENST00000330258.3:c.1637del	p.Leu546CysfsTer16	p.L546Cfs*16	ENST00000330258	NM_152424.3	546	tTg/tg	2/2	1	2	FACETS	0.958	0.901	1	0.958	0.901	1	CLONAL	1	TRUE	1	0.630016146636737	2		874	918	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182108	99182108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	51	462	0	ENST00000074304.5:c.2173G>A	p.Glu725Lys	p.E725K	ENST00000074304	NM_001134224.1	725	Gag/Aag	21/26	0.324657801534316	3	FACETS	1	0.908	1	0.541	0.463	0.625	CLONAL	1	FALSE	1	0.43074382761719	3		462	266	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261225	16261225	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	112	649	0	ENST00000375759.3:c.8490C>G	p.Ile2830Met	p.I2830M	ENST00000375759	NM_015001.2	2830	atC/atG	11/15	0.190615169870945	3	FACETS	0.85	0.771	0.93	0.85	0.771	0.93	INDETERMINATE	2	FALSE	1	0.43074382761719	3		649	372	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218059	108218059	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs771930635	NA	P-0043032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	22	215	0	ENST00000278616.4:c.8638G>T	p.Glu2880Ter	p.E2880*	ENST00000278616	NM_000051.3	2880	Gag/Tag	59/63	0.295112132757279	2	FACETS	1	0.911	1	0.655	0.522	0.8	CLONAL	1	FALSE	0	0.43074382761719	2		215	78	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989177	41989177	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	88	687	0	ENST00000219905.7:c.1969C>G	p.Leu657Val	p.L657V	ENST00000219905	NM_001164273.1	657	Ctg/Gtg	3/24	0.391982933631898	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	0	0.43074382761719	1		687	272	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348109	348109	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	64	931	0	ENST00000262320.3:c.1397del	p.Asn466ThrfsTer14	p.N466Tfs*14	ENST00000262320	NM_003502.3	466	aAc/ac	6/11	0.159682560614194	5	FACETS	1	0.952	1	0.405	0.352	0.462	INDETERMINATE	1	FALSE	2	0.43074382761719	5		931	403	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696703	47696703	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	89	539	1	ENST00000347630.2:c.245A>T	p.Asp82Val	p.D82V	ENST00000347630	NM_001007230.1	82	gAt/gTt	5/11	0.433793887500666	4	FACETS	0.857	0.766	0.952	0.571	0.511	0.635	CLONAL	2	FALSE	1	0.43074382761719	4		540	345	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966375	25966375	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	24	806	0	ENST00000435504.4:c.2831C>T	p.Ser944Phe	p.S944F	ENST00000435504		944	tCt/tTt	13/13	0.365090823586552	3	FACETS	0.344	0.269	0.43			1	SUBCLONAL	1	FALSE	NA	0.43074382761719	3		806	394	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744405	41744405	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	160	644	0	ENST00000301178.4:c.1025C>A	p.Ala342Asp	p.A342D	ENST00000301178	NM_021913.4	342	gCt/gAt	8/20	0.428129029120792	4	FACETS	1	0.985	1	0.831	0.77	0.894	CLONAL	2	TRUE	1	0.428129029120792	4		644	428	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50143285	50143285	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	21	159	0	ENST00000246792.3:c.71C>A	p.Pro24His	p.P24H	ENST00000246792	NM_006270.3	24	cCc/cAc	1/6	0.428129029120792	4	FACETS	0.91	0.707	1	0.303	0.235	0.381	CLONAL	1	TRUE	1	0.428129029120792	4		159	154	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175861	24175861	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	16	511	0	ENST00000263121.7:c.1089G>C	p.Lys363Asn	p.K363N	ENST00000263121	NM_003073.3	363	aaG/aaC	8/9	0.241481813903005	3	FACETS	0.318	0.235	0.418	0.106	0.078	0.14	INDETERMINATE	1	TRUE	0	0.428129029120792	3		511	285	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627241	86627241	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs752280214	NA	P-0043035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	38	298	0	ENST00000274376.6:c.616A>G	p.Ile206Val	p.I206V	ENST00000274376	NM_002890.2	206	Ata/Gta	2/25	0.424725445862677	1	FACETS	0.694	0.58	0.819	0.694	0.58	0.819	SUBCLONAL	1	TRUE	0	0.428129029120792	1		298	201	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370864	55370864	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs757881222	NA	P-0043035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	34	407	0	ENST00000297316.4:c.166G>T	p.Ala56Ser	p.A56S	ENST00000297316	NM_022454.3	56	Gcc/Tcc	1/2	1	2	FACETS	0.593	0.486	0.711	0.593	0.486	0.711	SUBCLONAL	1	TRUE	1	0.428129029120792	2		407	268	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0043040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	31	415	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.887	0.719	1	0.887	0.719	1	CLONAL	1	TRUE	1	0.23	2		415	304	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0043040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	40	388	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.805	0.669	0.956	0.805	0.669	0.956	CLONAL	1	TRUE	1	0.23	2		388	432	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0043040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	22	296	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	0.87	0.677	1	0.87	0.677	1	CLONAL	1	TRUE	1	0.23	2		296	220	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591092	67591092	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	25	251	0	ENST00000274335.5:c.1685G>C	p.Arg562Pro	p.R562P	ENST00000274335		562	cGt/cCt	12/15	1	2	FACETS	0.82	0.648	1	0.82	0.648	1	CLONAL	1	TRUE	1	0.23	2		251	265	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105744	27105745	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGGAGGA	novel	NA	P-0043040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	42	373	0	ENST00000324856.7:c.5361_5362insGAGAGGAG	p.Ile1788GlufsTer4	p.I1788Efs*4	ENST00000324856	NM_006015.4	1785	-/GAGGAGGA	20/20	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.23	2		373	359	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676254	29676254	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	33	302	0	ENST00000356175.3:c.7243del	p.Val2415TrpfsTer4	p.V2415Wfs*4	ENST00000356175	NM_000267.3	2415	Gtg/tg	48/57	1	2	FACETS	0.996	0.815	1	0.996	0.815	1	CLONAL	1	TRUE	1	0.23	2		302	288	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593348	67593348	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0043040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	34	247	0	ENST00000274335.5:c.2094C>G	p.Tyr698Ter	p.Y698*	ENST00000274335		698	taC/taG	15/15	1	2	FACETS	0.875	0.716	1	0.875	0.716	1	CLONAL	1	TRUE	1	0.23	2		247	338	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0043044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	69	566	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.472	0.411	0.538	0.472	0.411	0.538	SUBCLONAL	1	TRUE	1	0.479502997067656	2		567	610	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	49	295	2	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.461	0.391	0.538	0.461	0.391	0.538	SUBCLONAL	1	TRUE	1	0.479502997067656	2		297	443	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1232964733	NA	P-0043044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	25	65	0	ENST00000324856.7:c.1015del	p.Ala339LeufsTer24	p.A339Lfs*24	ENST00000324856	NM_006015.4	337	tGg/tg	1/20	1	2	FACETS	0.778	0.622	0.953	0.778	0.622	0.953	CLONAL	1	TRUE	1	0.479502997067656	2		65	134	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0043044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	57	260	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.503	0.432	0.58	0.503	0.432	0.58	SUBCLONAL	1	TRUE	1	0.479502997067656	2		260	473	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0043044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	41	323	0	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	1	2	FACETS	0.59	0.494	0.695	0.59	0.494	0.695	SUBCLONAL	1	TRUE	1	0.479502997067656	2		323	290	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519927	NA	P-0043044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	48	458	0	ENST00000263967.3:c.1625A>C	p.Glu542Ala	p.E542A	ENST00000263967	NM_006218.2	542	gAa/gCa	10/21	1	2	FACETS	0.674	0.573	0.784	0.674	0.573	0.784	SUBCLONAL	1	TRUE	1	0.479502997067656	2		458	297	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720711	89720712	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	15	122	2	ENST00000371953.3:c.867dup	p.Val290SerfsTer8	p.V290Sfs*8	ENST00000371953	NM_000314.4	288	gaa/gAaa	8/9	0.227987483164756	2	FACETS	0.745	0.554	0.965	0.372	0.277	0.483	INDETERMINATE	1	TRUE	0	0.479502997067656	2		124	84	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680522	241680522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778578307	NA	P-0043044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	49	332	0	ENST00000366560.3:c.227C>T	p.Thr76Met	p.T76M	ENST00000366560	NM_000143.3	76	aCg/aTg	2/10	0.479502997067656	5	FACETS	0.448	0.378	0.525	0.149	0.126	0.175	SUBCLONAL	1	TRUE	2	0.479502997067656	5		332	784	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0043044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	70	711	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.385	0.335	0.439	0.385	0.335	0.439	SUBCLONAL	1	TRUE	1	0.479502997067656	2		714	759	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012386	152012386	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	38	265	0	ENST00000262189.6:c.427del	p.Ser143ValfsTer3	p.S143Vfs*3	ENST00000262189	NM_170606.2	143	Agt/gt	4/59	1	2	FACETS	0.647	0.538	0.766	0.647	0.538	0.766	SUBCLONAL	1	TRUE	1	0.479502997067656	2		265	245	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013720	170013720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	36	353	2	ENST00000295797.4:c.1439G>A	p.Arg480His	p.R480H	ENST00000295797	NM_002740.5	480	cGc/cAc	15/18	1	2	FACETS	0.388	0.319	0.465	0.388	0.319	0.465	SUBCLONAL	1	TRUE	1	0.479502997067656	2		355	387	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504339	186504339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1560085211	NA	P-0043044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	20	291	0	ENST00000323963.5:c.681del	p.Lys227AsnfsTer3	p.K227Nfs*3	ENST00000323963		226	Aaa/aa	7/11	1	2	FACETS	0.381	0.292	0.484	0.381	0.292	0.484	SUBCLONAL	1	TRUE	1	0.479502997067656	2		291	219	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101375	27101375	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	108	478	0	ENST00000324856.7:c.4657C>T	p.Pro1553Ser	p.P1553S	ENST00000324856	NM_006015.4	1553	Ccc/Tcc	18/20	1	2	FACETS	0.734	0.66	0.812	0.734	0.66	0.812	SUBCLONAL	1	TRUE	1	0.479502997067656	2		478	614	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259382	16259382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	73	356	2	ENST00000375759.3:c.6647C>T	p.Ala2216Val	p.A2216V	ENST00000375759	NM_015001.2	2216	gCt/gTt	11/15	1	2	FACETS	0.741	0.651	0.837	0.741	0.651	0.837	SUBCLONAL	1	TRUE	1	0.479502997067656	2		358	411	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807438	36807438	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752175420	NA	P-0043044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	123	721	0	ENST00000373129.3:c.1226C>T	p.Pro409Leu	p.P409L	ENST00000373129	NM_032017.1	409	cCg/cTg	12/12	1	2	FACETS	0.604	0.546	0.666	0.604	0.546	0.666	SUBCLONAL	1	TRUE	1	0.479502997067656	2		721	849	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282343	115282343	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	31	385	0	ENST00000438362.2:c.307A>G	p.Asn103Asp	p.N103D	ENST00000438362	NM_001242891.1	103	Aat/Gat	3/20	1	2	FACETS	0.354	0.286	0.431	0.354	0.286	0.431	SUBCLONAL	1	TRUE	1	0.479502997067656	2		385	365	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367068	15367068	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	42	252	0	ENST00000263377.2:c.1558G>A	p.Ala520Thr	p.A520T	ENST00000263377	NM_058243.2	520	Gcc/Acc	9/20	1	2	FACETS	0.536	0.449	0.631	0.536	0.449	0.631	SUBCLONAL	1	TRUE	1	0.479502997067656	2		252	327	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723026	52723026	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	110	574	0	ENST00000322088.6:c.1211T>C	p.Leu404Pro	p.L404P	ENST00000322088	NM_014225.5	404	cTg/cCg	10/15	1	2	FACETS	0.596	0.535	0.66	0.596	0.535	0.66	SUBCLONAL	1	TRUE	1	0.479502997067656	2		574	770	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474004	29474004	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	110	675	1	ENST00000389048.3:c.2171A>G	p.Gln724Arg	p.Q724R	ENST00000389048	NM_004304.4	724	cAg/cGg	12/29	1	2	FACETS	0.532	0.478	0.59	0.532	0.478	0.59	SUBCLONAL	1	TRUE	1	0.479502997067656	2		676	862	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752969	128752970	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGAGCGCCAGAGGAGGAACGAGCA	novel	NA	P-0043044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	56	417	0	ENST00000377970.2:c.1153_1154insAGGAGCGCCAGAGGAGGAACGAGC	p.Glu384_Leu385insGlnGluArgGlnArgArgAsnGlu	p.E384_L385insQERQRRNE	ENST00000377970	NM_002467.4	377	ttg/ttGGAGCGCCAGAGGAGGAACGAGCAg	3/3	1	2	FACETS	0.353	0.302	0.409	0.353	0.302	0.409	SUBCLONAL	1	TRUE	1	0.479502997067656	2		417	662	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22008874	22008874	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780316323	NA	P-0043044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	41	507	0	ENST00000276925.6:c.79G>A	p.Val27Met	p.V27M	ENST00000276925	NM_004936.3	27	Gtg/Atg	1/2	1	2	FACETS	0.252	0.209	0.3	0.252	0.209	0.3	SUBCLONAL	1	TRUE	1	0.479502997067656	2		507	678	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0043118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	258	388	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.754434774875381	2		388	625	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0043118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	205	433	1	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.754434774875381	2		434	515	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877869	151877887	+	frameshift_variant	Frame_Shift_Del	DEL	ACAGGTCCAGGAAGTTGGG	ACAGGTCCAGGAAGTTGGG	-	novel	NA	P-0043118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	101	343	0	ENST00000262189.6:c.7058_7076del	p.Ser2353CysfsTer6	p.S2353Cfs*6	ENST00000262189	NM_170606.2	2353	tCCCAACTTCCTGGACCTGTg/tg	36/59	1	2	FACETS	0.705	0.635	0.777	0.705	0.635	0.777	SUBCLONAL	1	TRUE	1	0.754434774875381	2		343	380	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0043134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	48	566	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.718	0.608	0.838	0.718	0.608	0.838	SUBCLONAL	1	TRUE	1	0.341941511786524	2		567	391	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692805	89692805	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204928	NA	P-0043134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	68	348	0	ENST00000371953.3:c.289C>T	p.Gln97Ter	p.Q97*	ENST00000371953	NM_000314.4	97	Cag/Tag	5/9	0.314538050448496	3	FACETS	1	0.943	1	0.572	0.5	0.65	CLONAL	1	TRUE	1	0.341941511786524	3		348	407	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589625	67589627	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	novel	NA	P-0043134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	51	235	0	ENST00000274335.5:c.1390_1392del	p.Asp464del	p.D464del	ENST00000274335		463	tATGat/tat	10/15	1	2	FACETS	0.783	0.668	0.909	0.783	0.668	0.909	CLONAL	1	TRUE	1	0.341941511786524	2		235	381	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692806	89692806	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	115	347	0	ENST00000371953.3:c.290del	p.Gln97ArgfsTer2	p.Q97Rfs*2	ENST00000371953	NM_000314.4	97	cAg/cg	5/9	0.314538050448496	3	FACETS	0.98	0.89	1	0.98	0.89	1	CLONAL	2	TRUE	1	0.341941511786524	3		347	402	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114155	115114157	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs771239166	NA	P-0043134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	94	689	0	ENST00000257566.3:c.1060_1062del	p.Ser354del	p.S354del	ENST00000257566	NM_016569.3	354	TCT/-	6/8	1	2	FACETS	0.956	0.853	1	0.956	0.853	1	CLONAL	1	TRUE	1	0.341941511786524	2		689	575	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518710	176518710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1289445624	NA	P-0043134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	56	660	0	ENST00000292408.4:c.628G>A	p.Val210Met	p.V210M	ENST00000292408	NM_213647.1	210	Gtg/Atg	6/18	1	2	FACETS	0.671	0.576	0.775	0.671	0.576	0.775	SUBCLONAL	1	TRUE	1	0.341941511786524	2		660	488	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372518	55372519	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0043134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	254	908	1	ENST00000297316.4:c.1208_1209delinsTT	p.Ser403Ile	p.S403I	ENST00000297316	NM_022454.3	403	aGC/aTT	2/2	0.314538050448496	3	FACETS	0.93	0.872	0.99	0.93	0.872	0.99	CLONAL	2	TRUE	1	0.341941511786524	3		909	935	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993922	72993922	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	54	656	0	ENST00000268489.5:c.123G>T	p.Gln41His	p.Q41H	ENST00000268489	NM_006885.3	41	caG/caT	2/10	0.494719330152124	1	FACETS	0.224	0.191	0.261	0.224	0.191	0.261	SUBCLONAL	1	TRUE	0	0.494719330152124	1		656	732	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878115	48878117	+	inframe_deletion	In_Frame_Del	DEL	CCG	CCG	-	rs587778823	NA	P-0043186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	11	81	0	ENST00000267163.4:c.78_80del	p.Pro29del	p.P29del	ENST00000267163	NM_000321.2	23	CCG/-	1/27	0.309372985851311	1	FACETS	0.328	0.227	0.454	0.328	0.227	0.454	SUBCLONAL	1	TRUE	0	0.309372985851311	1		81	183	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795796	42795796	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	68	721	0	ENST00000575354.2:c.2785C>T	p.Pro929Ser	p.P929S	ENST00000575354	NM_015125.3	929	Cct/Tct	11/20	0.309372985851311	1	FACETS	0.434	0.377	0.497	0.434	0.377	0.497	SUBCLONAL	1	TRUE	0	0.309372985851311	1		721	856	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945227	54945227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	140	615	1	ENST00000312783.6:c.1199G>A	p.Ser400Asn	p.S400N	ENST00000312783	NM_198436.1	400	aGc/aAc	10/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.309372985851311	2		616	791	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541738	120541738	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	154	751	2	ENST00000229340.5:c.119C>T	p.Thr40Met	p.T40M	ENST00000229340	NM_006861.6	40	aCg/aTg	3/6	1	2	FACETS	0.812	0.746	0.881	0.812	0.746	0.881	CLONAL	1	TRUE	1	0.609708844865487	2		753	622	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612187	189612187	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	82	761	0	ENST00000264731.3:c.1939C>A	p.Arg647Ser	p.R647S	ENST00000264731	NM_003722.4	647	Cgc/Agc	14/14	1	2	FACETS	0.417	0.368	0.47	0.417	0.368	0.47	SUBCLONAL	1	TRUE	1	0.609708844865487	2		761	645	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0043337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	174	326	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.829	0.771	0.888	0.829	0.771	0.888	CLONAL	1	TRUE	1	0.922306122618915	2		326	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0043337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	377	660	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	1	2	FACETS	0.881	0.839	0.923	0.881	0.839	0.923	CLONAL	1	TRUE	1	0.922306122618915	2		660	928	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0043337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	281	513	0	ENST00000269305.4:c.97-1G>C		p.X33_splice	ENST00000269305	NM_001126112.2	33			1	2	FACETS	0.9	0.851	0.949	0.9	0.851	0.949	CLONAL	1	TRUE	1	0.922306122618915	2		513	677	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981277	201981277	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	403	672	1	ENST00000359651.3:c.356A>G	p.Asp119Gly	p.D119G	ENST00000359651		119	gAc/gGc	2/8	1	2	FACETS	0.871	0.831	0.911	0.871	0.831	0.911	CLONAL	1	TRUE	1	0.922306122618915	2		673	1003	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889142	76889142	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0043337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	256	186	0	ENST00000373344.5:c.4868T>A	p.Leu1623Ter	p.L1623*	ENST00000373344	NM_000489.3	1623	tTa/tAa	18/35	1	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.922306122618915	1		186	298	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0043347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	236	810	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.975	1	1	0.996	1	CLONAL	3	TRUE	1	0.209085986008224	2		810	701	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	213	541	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.98	1	1	0.996	1	CLONAL	4	TRUE	1	0.209085986008224	2		541	465	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0043347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	159	389	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.882	0.817	0.949	1	0.994	1	CLONAL	4	TRUE	1	0.209085986008224	2		389	431	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416062	49416062	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0043347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	303	666	1	ENST00000301067.7:c.16412+1G>A		p.X5471_splice	ENST00000301067	NM_003482.3	5471			1	2	FACETS	0.978	0.927	1	1	0.997	1	CLONAL	4	TRUE	1	0.209085986008224	2		667	741	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589521	69589521	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	72	85	0	ENST00000168712.1:c.332C>T	p.Thr111Ile	p.T111I	ENST00000168712	NM_002007.2	111	aCc/aTc	1/3	1	2	FACETS	0.9	0.809	0.992	1	0.988	1	CLONAL	5	TRUE	1	0.209085986008224	2		85	153	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440521	49440521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	384	834	0	ENST00000301067.7:c.4289G>A	p.Cys1430Tyr	p.C1430Y	ENST00000301067	NM_003482.3	1430	tGt/tAt	15/54	1	2	FACETS	0.959	0.914	1	1	0.997	1	CLONAL	4	TRUE	1	0.209085986008224	2		834	958	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058324	42058324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1028195551	NA	P-0043347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	185	318	0	ENST00000219905.7:c.8044G>A	p.Asp2682Asn	p.D2682N	ENST00000219905	NM_001164273.1	2682	Gac/Aac	24/24	1	2	FACETS	0.977	0.912	1	1	0.995	1	CLONAL	4	TRUE	1	0.209085986008224	2		318	453	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220975	36220978	+	frameshift_variant	Frame_Shift_Del	DEL	GGAT	GGAT	-	novel	NA	P-0043347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	35	549	0	ENST00000222270.7:c.5026_5029del	p.Asp1676ThrfsTer19	p.D1676Tfs*19	ENST00000222270	NM_014727.1	1675	caGGAT/ca	23/37	1	2	FACETS	0.506	0.414	0.611	0.506	0.414	0.611	SUBCLONAL	1	TRUE	1	0.209085986008224	2		549	661	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228089	36228090	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0043347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	57	758	0	ENST00000222270.7:c.7475_7476del	p.Tyr2492SerfsTer30	p.Y2492Sfs*30	ENST00000222270	NM_014727.1	2492	tAC/t	33/37	1	2	FACETS	0.58	0.496	0.672	0.58	0.496	0.672	SUBCLONAL	1	TRUE	1	0.209085986008224	2		758	940	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229309	36229309	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	46	653	0	ENST00000222270.7:c.7999G>T	p.Glu2667Ter	p.E2667*	ENST00000222270	NM_014727.1	2667	Gag/Tag	37/37	1	2	FACETS	0.498	0.418	0.588	0.498	0.418	0.588	SUBCLONAL	1	TRUE	1	0.209085986008224	2		653	883	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031213	36031213	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	375	768	0	ENST00000358208.4:c.1332C>G	p.Ile444Met	p.I444M	ENST00000358208		444	atC/atG	11/12	1	2	FACETS	0.963	0.918	1	1	0.997	1	CLONAL	4	TRUE	1	0.209085986008224	2		768	931	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62293295	62293295	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs769533935	NA	P-0043347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	255	502	0	ENST00000360203.5:c.394C>T	p.Arg132Trp	p.R132W	ENST00000360203	NM_001283009.1	132	Cgg/Tgg	4/35	1	2	FACETS	0.995	0.939	1	1	0.996	1	CLONAL	4	TRUE	1	0.209085986008224	2		502	613	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41562602	41562602	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0043347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	175	395	0	ENST00000263253.7:c.3807-1G>T		p.X1269_splice	ENST00000263253	NM_001429.3	1269			1	2	FACETS	1	0.96	1	1	0.995	1	CLONAL	4	TRUE	1	0.209085986008224	2		395	402	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612185	189612186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0043347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	57	554	0	ENST00000264731.3:c.1939dup	p.Arg647ProfsTer11	p.R647Pfs*11	ENST00000264731	NM_003722.4	646	ctc/ctCc	14/14	1	2	FACETS	0.745	0.638	0.862	0.745	0.638	0.862	SUBCLONAL	1	TRUE	1	0.209085986008224	2		554	732	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176671259	176671259	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	135	308	0	ENST00000439151.2:c.4366G>C	p.Asp1456His	p.D1456H	ENST00000439151	NM_022455.4	1456	Gat/Cat	9/23	1	2	FACETS	0.944	0.87	1	1	0.993	1	CLONAL	4	TRUE	1	0.209085986008224	2		308	342	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997744	149997744	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	43	487	0	ENST00000253339.5:c.2723del	p.His908LeufsTer49	p.H908Lfs*49	ENST00000253339		908	cAt/ct	5/7	1	2	FACETS	0.723	0.604	0.855	0.723	0.604	0.855	SUBCLONAL	1	TRUE	1	0.209085986008224	2		487	569	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845978	151845979	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	623	570	0	ENST00000262189.6:c.13033dup	p.Cys4345LeufsTer6	p.C4345Lfs*6	ENST00000262189	NM_170606.2	4345	tgc/tTgc	52/59	0.209742249286238	3	FACETS	0.956	0.936	0.976	1	0.998	1	CLONAL	9	TRUE	0	0.209085986008224	3		570	765	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101910003	101910003	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	105	235	0	ENST00000374994.4:c.1323G>A	p.Met441Ile	p.M441I	ENST00000374994	NM_004612.2	441	atG/atA	8/9	1	2	FACETS	1	0.913	1	1	0.992	1	CLONAL	4	TRUE	1	0.209085986008224	2		235	251	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	208	541	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.868	0.809	0.929	0.868	0.809	0.929	CLONAL	1	TRUE	1	0.670317441898943	2		541	715	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339576	70339576	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	246	546	0	ENST00000374080.3:c.245G>A	p.Arg82His	p.R82H	ENST00000374080		82	cGt/cAt	3/45	1	2	FACETS	0.928	0.87	0.987	0.928	0.87	0.987	CLONAL	1	TRUE	1	0.670317441898943	2		546	791	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717733	89717733	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	145	404	0	ENST00000371953.3:c.758T>C	p.Ile253Thr	p.I253T	ENST00000371953	NM_000314.4	253	aTc/aCc	7/9	0.625635465525657	1	FACETS	0.877	0.813	0.942	0.877	0.813	0.942	CLONAL	1	TRUE	0	0.670317441898943	1		404	328	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807895	3807895	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs28937315	NA	P-0043355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	282	468	0	ENST00000262367.5:c.3524A>G	p.Tyr1175Cys	p.Y1175C	ENST00000262367	NM_004380.2	1175	tAt/tGt	18/31	1	2	FACETS	0.909	0.856	0.963	0.909	0.856	0.963	CLONAL	1	TRUE	1	0.670317441898943	2		468	926	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562262	95562986	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCGATATAAGGTGATTCAGTGTTTTATCTGCATCTGGATGATCAAACATACATCTTGGTGGAATCTTCAAACAACCATATTCCGAGTCTTTCAATACAGAAGAGCGTGAACTGGCCACAGAAGCAGCAGCACAGCTCACTGAAAGGTTCTTTTGTTGGCTGTTGAAATTCTCCCGAGTAGGGCACAGGGCCTTTTCCCGATCAGTCCTTTTAATTACCGGGAGCACCTTCAGCCCCAGTGAACAGAGGAAAAGCTGAGCAGCCCTCTCCCCACAGCTGGTTAAATAGCAGCCCAGCAGGGCTTCCACACAGTCCGCTATGCTTTTGTCAGCAATACACTGCTCAGTGTGCAAGTCGTAAGAAATGGACTGCTTTCCCGTGTCAACACCACAGTTTTCTTCTGATGGATTCCAGAACCCCACCACAAAGTCATCTTCTTCAACAGCTTTGCTAGGATCCAGATAGCACATTGCATCCCAAGAGCTGTAGTCAAAATCCTCAAAATCTGATGAAAATGGCATACTACCTAAGGAGGATTTTTTGGGCATTTTCCATTCATATGCAGAATCAGTGGTTGAAAAAGGAGAAAGAGAGATTTTCTTTACAAAAGCTCCTGACCCCATTAACATATTATCTATAAATCTGATATGTTCCTGATCATACTCCAGGAAATCATCTTCATAGTCAGCCTCTTCCTTCGGAGCCCTCCACATCAGGCTCTCCT	CCCCGATATAAGGTGATTCAGTGTTTTATCTGCATCTGGATGATCAAACATACATCTTGGTGGAATCTTCAAACAACCATATTCCGAGTCTTTCAATACAGAAGAGCGTGAACTGGCCACAGAAGCAGCAGCACAGCTCACTGAAAGGTTCTTTTGTTGGCTGTTGAAATTCTCCCGAGTAGGGCACAGGGCCTTTTCCCGATCAGTCCTTTTAATTACCGGGAGCACCTTCAGCCCCAGTGAACAGAGGAAAAGCTGAGCAGCCCTCTCCCCACAGCTGGTTAAATAGCAGCCCAGCAGGGCTTCCACACAGTCCGCTATGCTTTTGTCAGCAATACACTGCTCAGTGTGCAAGTCGTAAGAAATGGACTGCTTTCCCGTGTCAACACCACAGTTTTCTTCTGATGGATTCCAGAACCCCACCACAAAGTCATCTTCTTCAACAGCTTTGCTAGGATCCAGATAGCACATTGCATCCCAAGAGCTGTAGTCAAAATCCTCAAAATCTGATGAAAATGGCATACTACCTAAGGAGGATTTTTTGGGCATTTTCCATTCATATGCAGAATCAGTGGTTGAAAAAGGAGAAAGAGAGATTTTCTTTACAAAAGCTCCTGACCCCATTAACATATTATCTATAAATCTGATATGTTCCTGATCATACTCCAGGAAATCATCTTCATAGTCAGCCTCTTCCTTCGGAGCCCTCCACATCAGGCTCTCCT	-	novel	NA	P-0043355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	91	389	0	ENST00000393063.1:c.4271_4995del	p.Glu1424ValfsTer2	p.E1424Vfs*2	ENST00000393063	NM_030621.3	1424	gAGGAGAGCCTGATGTGGAGGGCTCCGAAGGAAGAGGCTGACTATGAAGATGATTTCCTGGAGTATGATCAGGAACATATCAGATTTATAGATAATATGTTAATGGGGTCAGGAGCTTTTGTAAAGAAAATCTCTCTTTCTCCTTTTTCAACCACTGATTCTGCATATGAATGGAAAATGCCCAAAAAATCCTCCTTAGGTAGTATGCCATTTTCATCAGATTTTGAGGATTTTGACTACAGCTCTTGGGATGCAATGTGCTATCTGGATCCTAGCAAAGCTGTTGAAGAAGATGACTTTGTGGTGGGGTTCTGGAATCCATCAGAAGAAAACTGTGGTGTTGACACGGGAAAGCAGTCCATTTCTTACGACTTGCACACTGAGCAGTGTATTGCTGACAAAAGCATAGCGGACTGTGTGGAAGCCCTGCTGGGCTGCTATTTAACCAGCTGTGGGGAGAGGGCTGCTCAGCTTTTCCTCTGTTCACTGGGGCTGAAGGTGCTCCCGGTAATTAAAAGGACTGATCGGGAAAAGGCCCTGTGCCCTACTCGGGAGAATTTCAACAGCCAACAAAAGAACCTTTCAGTGAGCTGTGCTGCTGCTTCTGTGGCCAGTTCACGCTCTTCTGTATTGAAAGACTCGGAATATGGTTGTTTGAAGATTCCACCAAGATGTATGTTTGATCATCCAGATGCAGATAAAACACTGAATCACCTTATATCGGGG/g	24/28	1	2	FACETS	0.82	0.736	0.909	0.82	0.736	0.909	CLONAL	1	TRUE	1	0.670317441898943	2		389	331	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221828	55221828	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1220574404	NA	P-0043355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3477	434	633	0	ENST00000275493.2:c.872G>T	p.Cys291Phe	p.C291F	ENST00000275493	NM_005228.3	291	tGc/tTc	7/28	0.670317441898943	20	FACETS	1	0.99	1			1	CLONAL	2	TRUE	NA	0.670317441898943	20		633	3911	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306604	41306604	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	251	755	0	ENST00000373198.4:c.1055C>G	p.Pro352Arg	p.P352R	ENST00000373198	NM_133170.3	352	cCc/cGc	7/32	1	2	FACETS	0.828	0.774	0.884	0.828	0.774	0.884	CLONAL	1	TRUE	1	0.534015360477804	2		755	1135	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579417	7579426	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGGGGGCT	GGAGGGGGCT	-	novel	NA	P-0043376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	439	699	0	ENST00000269305.4:c.261_270del	p.Ala88GlyfsTer32	p.A88Gfs*32	ENST00000269305	NM_001126112.2	87	ccAGCCCCCTCC/cc	4/11	0.24850751308883	4	FACETS	0.968	0.928	1	0.968	0.928	1	CLONAL	4	TRUE	0	0.325327604206129	4		699	924	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266624	115267646	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTACAAAACAAAGGCAGGTACATCTTTCAATTTTATTTCATCTCTACTACATAGAAAGACAAGTAAGCAAAAAATAACAGCACAAATGTTAACAGGGTAGGTTGGCTGGCTGCTATTGAAATGGGGTAGGGAACCTGAAGCCAAGTTCTATTTTTAGAACAGCTGCTGGACTTTAAATACTTCTAAACTACCAAAATGCCTGCTTTTCCTAAATAGAATTGTTTAAATAAAATTGTTTAAGGAATTAATAAGTATTCATAAATAAAACATGCCTTGATCTCTTACTTTTTCCAGGTGACCATATGTCATTTTTTAAGAAGCCTTTCCTGGTCTCTAAAATGTAAATCACAATACTTACATACTGTCCTGATTCATCTTTATTACATGTATTGTTGTCTTTCTAAACATCATATACAGTATTTTACTCCTCTAGTCTGCCCCATATTTTCCACCAAAAAATAAGGTCAATGAATACAGGGATGTATCTGATTTCTTCACTGCTGTATCCCCAGTGTCTAAAACATAACACACACTTAAGAGTTCAGATGAGAGCCAAAAATAAGTTGCAGGTCTTTTAAAGTCAGAGATCCAAGATCCTAAATTACAATTAATTTTTTTAACTTCCCATTATTTTTCACATTTAGATTCATTCTTCTTCAAAACAATCTTCTAGGGAAATGCCTCTCTTCCCTACTCCATGGTGATGTATACATATCTTGGGGTTATTTTTGTTTTTTTCAGACAGTCTTGCTCTGTCACCCAGGTTGGAGTGCAGTGGTAGGATCATCATGGCTCACTGCAGTCTCAACCTACCAGCACAAGCGGCCCTCCCACCTCAGCCTCCCAAGTAACTGTGACTACAGGCATCCACTACCACAGCTGGCTATCCTGGGTTTATTTTTCAAAAGAAGACAATGAATTGAAAATATAAAGCAAATTTCCTAAAATATCTAGGCCAATCCTTCTCAAACTTCAGTGTATACCAGAATCACCTAAAGGATTTATTAAAAAAGAATGCCCACT	CTACAAAACAAAGGCAGGTACATCTTTCAATTTTATTTCATCTCTACTACATAGAAAGACAAGTAAGCAAAAAATAACAGCACAAATGTTAACAGGGTAGGTTGGCTGGCTGCTATTGAAATGGGGTAGGGAACCTGAAGCCAAGTTCTATTTTTAGAACAGCTGCTGGACTTTAAATACTTCTAAACTACCAAAATGCCTGCTTTTCCTAAATAGAATTGTTTAAATAAAATTGTTTAAGGAATTAATAAGTATTCATAAATAAAACATGCCTTGATCTCTTACTTTTTCCAGGTGACCATATGTCATTTTTTAAGAAGCCTTTCCTGGTCTCTAAAATGTAAATCACAATACTTACATACTGTCCTGATTCATCTTTATTACATGTATTGTTGTCTTTCTAAACATCATATACAGTATTTTACTCCTCTAGTCTGCCCCATATTTTCCACCAAAAAATAAGGTCAATGAATACAGGGATGTATCTGATTTCTTCACTGCTGTATCCCCAGTGTCTAAAACATAACACACACTTAAGAGTTCAGATGAGAGCCAAAAATAAGTTGCAGGTCTTTTAAAGTCAGAGATCCAAGATCCTAAATTACAATTAATTTTTTTAACTTCCCATTATTTTTCACATTTAGATTCATTCTTCTTCAAAACAATCTTCTAGGGAAATGCCTCTCTTCCCTACTCCATGGTGATGTATACATATCTTGGGGTTATTTTTGTTTTTTTCAGACAGTCTTGCTCTGTCACCCAGGTTGGAGTGCAGTGGTAGGATCATCATGGCTCACTGCAGTCTCAACCTACCAGCACAAGCGGCCCTCCCACCTCAGCCTCCCAAGTAACTGTGACTACAGGCATCCACTACCACAGCTGGCTATCCTGGGTTTATTTTTCAAAAGAAGACAATGAATTGAAAATATAAAGCAAATTTCCTAAAATATCTAGGCCAATCCTTCTCAAACTTCAGTGTATACCAGAATCACCTAAAGGATTTATTAAAAAAGAATGCCCACT	-	novel	NA	P-0043376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	77	493	0	ENST00000438362.2:c.1891+196_1892-1del		p.X631_splice	ENST00000438362	NM_001242891.1	631			0.141751191364337	3	FACETS	0.702	0.615	0.795	0.351	0.307	0.398	INDETERMINATE	1	TRUE	1	0.325327604206129	3		493	784	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115267955	115268831	+	splice_acceptor_variant,splice_donor_variant,intron_variant	Splice_Site	DEL	CTAAGGAGAAAGGAAATGACATTTAACTAAACATTACCATAAACATCAACAGTAACAGGCAGTCTTTATTTTACAGTAACAGTCATGGCATGGCATGCTTATTTACATTAGACACCATTTTAAGTAATTTCTATGTATTGACTCATTTAATCCTCAAGAATGCCCCATGAAGAGGTAACATTATCCCTAACTTCAGGATAATGAAACTAAGATACCAAGAAGTTATTTGGTAAAAATTACACAGGTATAAAGTGGCAGGGCCTGGATTCAAAAACTGAACTGTCTGGTTCTAAGAACCCTTACTTTCTATTTTTTTTTTTGAGACAGAGTCTCACTCTGTTGGCTAGGCTGGAGTACAGTGGTGCGATCTCAGCTTACTGCAACCTCTGCCTCCCAGGATCAAGTGGTCCTCCCACATCAGCCTCCTGAGTTGGTGAGACTACAGGTATGCACCACCATGTCAGGCTAATTTTGGTAATTTTTGTGGAGATGGAGTTTCACCGTGTTGCTCAGGCTGGCCTCGAACTCCTGGGCTCAAGGGATCCACCTGCCTCAGCCCCCAAAGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCAGACCCCTTACTCTTACACTACATTATACACCAAATGGCCAACTCTATGGTACCAACACAAAAAATAAGGTGGCACAGGCCTTTCTATTTCTTTTGGCCACAGGCTCTGTATATAGTAAGATCAGTGATTAACTTCAGTTTATATCTTGCCATAATTCTACCAATATGAAATCTGAACCTCAACAAGTATAATCAATCAATACTAAATGTTTTTTATTCCAACACCAAAGAATGGATGGTAAGTTAGCTGTAAAGTTCCTGAAAGTCACGCCTTAC	CTAAGGAGAAAGGAAATGACATTTAACTAAACATTACCATAAACATCAACAGTAACAGGCAGTCTTTATTTTACAGTAACAGTCATGGCATGGCATGCTTATTTACATTAGACACCATTTTAAGTAATTTCTATGTATTGACTCATTTAATCCTCAAGAATGCCCCATGAAGAGGTAACATTATCCCTAACTTCAGGATAATGAAACTAAGATACCAAGAAGTTATTTGGTAAAAATTACACAGGTATAAAGTGGCAGGGCCTGGATTCAAAAACTGAACTGTCTGGTTCTAAGAACCCTTACTTTCTATTTTTTTTTTTGAGACAGAGTCTCACTCTGTTGGCTAGGCTGGAGTACAGTGGTGCGATCTCAGCTTACTGCAACCTCTGCCTCCCAGGATCAAGTGGTCCTCCCACATCAGCCTCCTGAGTTGGTGAGACTACAGGTATGCACCACCATGTCAGGCTAATTTTGGTAATTTTTGTGGAGATGGAGTTTCACCGTGTTGCTCAGGCTGGCCTCGAACTCCTGGGCTCAAGGGATCCACCTGCCTCAGCCCCCAAAGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCAGACCCCTTACTCTTACACTACATTATACACCAAATGGCCAACTCTATGGTACCAACACAAAAAATAAGGTGGCACAGGCCTTTCTATTTCTTTTGGCCACAGGCTCTGTATATAGTAAGATCAGTGATTAACTTCAGTTTATATCTTGCCATAATTCTACCAATATGAAATCTGAACCTCAACAAGTATAATCAATCAATACTAAATGTTTTTTATTCCAACACCAAAGAATGGATGGTAAGTTAGCTGTAAAGTTCCTGAAAGTCACGCCTTAC	-	novel	NA	P-0043376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	78	368	0	ENST00000438362.2:c.1778+1_1779-1del		p.X593_splice	ENST00000438362	NM_001242891.1	593			0.141751191364337	3	FACETS	0.917	0.806	1	0.458	0.403	0.518	INDETERMINATE	1	TRUE	1	0.325327604206129	3		368	608	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115269007	115269602	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTGTGAAAATTAAGGATGCTCATTAACACCATATCACTTCCACACCAATCTCCTTAACTCAGAAAACAAGACCTATAACTCCCCCAGCGCATGCTTTTCATTCCAAATATCCTTTGTTATTACTTCAATGAAATTGATTTTCACCAAAACATTTATGTCTCATCCCACTTTTCACAAAGGATCAAACTTTTATCTTTCAGTCTGTATTCCTTATAGATTCTGAATTTCTCTAGAGGGCTATCCAAAAACCAAACATATTAAGTATGAGAAAAAATGAACAACAACGTAAAATCTTTGGTGTGCTTTTACTTTGATAATGTTTCAGTAGTAACTGTTTTAACTTTCTTACCAATAACGATTTTATTAAGCATGTTTTATCTAACGTTTAAACAGCTAGATTAACAAGGCTTTGATTAACAAAGAGCTTGACAGACACTTTTAATAAGCTGCTTTCAAATACAAGATATTCATGTATTTCTCTTAAACACAAAATATATTTCAGCAAAACTTGATAAAATTTGAAGAACCCATCCTGCAGGATTTATGATTAAGATGACAACTCTTAACCCTCTCTCGAATGAGCAGAATTATCTTG	CCTGTGAAAATTAAGGATGCTCATTAACACCATATCACTTCCACACCAATCTCCTTAACTCAGAAAACAAGACCTATAACTCCCCCAGCGCATGCTTTTCATTCCAAATATCCTTTGTTATTACTTCAATGAAATTGATTTTCACCAAAACATTTATGTCTCATCCCACTTTTCACAAAGGATCAAACTTTTATCTTTCAGTCTGTATTCCTTATAGATTCTGAATTTCTCTAGAGGGCTATCCAAAAACCAAACATATTAAGTATGAGAAAAAATGAACAACAACGTAAAATCTTTGGTGTGCTTTTACTTTGATAATGTTTCAGTAGTAACTGTTTTAACTTTCTTACCAATAACGATTTTATTAAGCATGTTTTATCTAACGTTTAAACAGCTAGATTAACAAGGCTTTGATTAACAAAGAGCTTGACAGACACTTTTAATAAGCTGCTTTCAAATACAAGATATTCATGTATTTCTCTTAAACACAAAATATATTTCAGCAAAACTTGATAAAATTTGAAGAACCCATCCTGCAGGATTTATGATTAAGATGACAACTCTTAACCCTCTCTCGAATGAGCAGAATTATCTTG	-	novel	NA	P-0043376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	90	309	0	ENST00000438362.2:c.1602+2_1603del		p.X534_splice	ENST00000438362	NM_001242891.1	534		14/20	0.141751191364337	3	FACETS	1	0.937	1	0.54	0.479	0.604	INDETERMINATE	1	TRUE	1	0.325327604206129	3		309	596	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225370	2225370	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	220	778	0	ENST00000326181.6:c.1456del	p.Val486SerfsTer12	p.V486Sfs*12	ENST00000326181	NM_032271.2	485	ctG/ct	16/21	0.131634904877545	5	FACETS	1	0.962	1	0.7	0.651	0.75	INDETERMINATE	2	TRUE	2	0.325327604206129	5		778	959	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096113	178096113	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	101	345	0	ENST00000397062.3:c.1218del	p.Leu407CysfsTer26	p.L407Cfs*26	ENST00000397062	NM_006164.4	406	ccC/cc	5/5	0.202973138686172	4	FACETS	0.776	0.696	0.861	0.776	0.696	0.861	SUBCLONAL	2	TRUE	2	0.325327604206129	4		345	530	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348705	118348705	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs71482146	NA	P-0043381-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	125	254	0	ENST00000534358.1:c.3358G>A	p.Glu1120Lys	p.E1120K	ENST00000534358	NM_005933.3	1120	Gaa/Aaa	5/36	0.70646894184401	1	FACETS	0.982	0.911	1	0.982	0.911	1	CLONAL	1	TRUE	0	0.70646894184401	1		254	233	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0043412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	17	172	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	1	2	FACETS	0.576	0.432	0.745	0.576	0.432	0.745	SUBCLONAL	1	TRUE	1	0.355486864289555	2		172	166	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653814	89653814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780004	NA	P-0043412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	8	167	0	ENST00000371953.3:c.112C>T	p.Pro38Ser	p.P38S	ENST00000371953	NM_000314.4	38	Cct/Tct	2/9	1	2	FACETS	0.405	0.262	0.589	0.405	0.262	0.589	SUBCLONAL	1	TRUE	1	0.355486864289555	2		167	111	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412905	49412905	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519951	NA	P-0043412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	120	513	0	ENST00000418115.1:c.118G>C	p.Glu40Gln	p.E40Q	ENST00000418115	NM_001664.2	40	Gag/Cag	2/5	0.355486864289555	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.355486864289555	1		513	482	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244079	46244079	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	107	318	0	ENST00000334344.6:c.2173C>T	p.Gln725Ter	p.Q725*	ENST00000334344	NM_152641.2	725	Cag/Tag	15/21	1	2	FACETS	0.971	0.882	1	1	0.989	1	CLONAL	2	TRUE	1	0.355486864289555	2		318	310	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032197	10032197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774932381	NA	P-0043412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	105	610	1	ENST00000330684.3:c.626C>T	p.Ser209Phe	p.S209F	ENST00000330684	NM_001134407.1	209	tCc/tTc	3/13	1	2	FACETS	0.932	0.836	1	0.932	0.836	1	CLONAL	1	TRUE	1	0.355486864289555	2		611	634	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554918	106554918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs529025464	NA	P-0043412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	98	477	0	ENST00000369096.4:c.2035C>T	p.Arg679Cys	p.R679C	ENST00000369096	NM_001198.3	679	Cgt/Tgt	7/7	1	2	FACETS	0.962	0.861	1	0.962	0.861	1	CLONAL	1	TRUE	1	0.355486864289555	2		477	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0043412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	95	599	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.355486864289555	1	FACETS	0.945	0.846	1	0.945	0.846	1	CLONAL	1	TRUE	0	0.355486864289555	1		599	465	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132751	152132751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	121	450	0	ENST00000262189.6:c.121C>T	p.Arg41Cys	p.R41C	ENST00000262189	NM_170606.2	41	Cgc/Tgc	1/59	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.355486864289555	2		450	554	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517394	176517394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	69	451	0	ENST00000292408.4:c.95C>T	p.Pro32Leu	p.P32L	ENST00000292408	NM_213647.1	32	cCc/cTc	3/18	1	2	FACETS	0.897	0.784	1	0.897	0.784	1	CLONAL	1	TRUE	1	0.355486864289555	2		451	433	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026897	6026897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	66	331	0	ENST00000265849.7:c.1499C>T	p.Ser500Phe	p.S500F	ENST00000265849	NM_000535.5	500	tCc/tTc	11/15	1	2	FACETS	0.938	0.818	1	0.938	0.818	1	CLONAL	1	TRUE	1	0.355486864289555	2		331	396	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026221	48026221	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	60	278	0	ENST00000234420.5:c.1099C>T	p.His367Tyr	p.H367Y	ENST00000234420	NM_000179.2	367	Cat/Tat	4/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.355486864289555	2		278	287	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100180	27100180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	93	444	0	ENST00000324856.7:c.3976C>T	p.Pro1326Ser	p.P1326S	ENST00000324856	NM_006015.4	1326	Ccg/Tcg	16/20	1	2	FACETS	0.973	0.867	1	0.973	0.867	1	CLONAL	1	TRUE	1	0.355486864289555	2		444	538	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510784	120510784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs312262794	NA	P-0043412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	74	441	0	ENST00000256646.2:c.1180C>T	p.Pro394Ser	p.P394S	ENST00000256646	NM_024408.3	394	Ccc/Tcc	7/34	1	2	FACETS	0.919	0.807	1	0.919	0.807	1	CLONAL	1	TRUE	1	0.355486864289555	2		441	453	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948344	71948344	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1424	180	957	0	ENST00000298229.2:c.3056T>A	p.Ile1019Asn	p.I1019N	ENST00000298229	NM_001567.3	1019	aTt/aAt	26/28	0.355486864289555	4	FACETS	0.856	0.786	0.929	0.285	0.262	0.31	CLONAL	1	TRUE	1	0.355486864289555	4		957	1604	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047165	77047165	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	371	493	0	ENST00000356341.3:c.1379G>A	p.Gly460Glu	p.G460E	ENST00000356341	NM_002576.4	460	gGg/gAg	13/15	0.355486864289555	4	FACETS	0.884	0.844	0.924	1	0.992	1	CLONAL	4	TRUE	1	0.355486864289555	4		493	800	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343739	118343739	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0043412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	67	355	0	ENST00000534358.1:c.1865T>A	p.Leu622Ter	p.L622*	ENST00000534358	NM_005933.3	622	tTa/tAa	3/36	0.355486864289555	1	FACETS	0.993	0.87	1	0.993	0.87	1	CLONAL	1	TRUE	0	0.355486864289555	1		355	312	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618776	37618776	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	113	547	1	ENST00000447079.4:c.452C>T	p.Ser151Leu	p.S151L	ENST00000447079	NM_015083.1	151	tCa/tTa	1/14	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.355486864289555	2		548	575	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221249	5221249	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	131	664	0	ENST00000357368.4:c.3217C>A	p.Leu1073Ile	p.L1073I	ENST00000357368	NM_002850.3	1073	Ctc/Atc	20/38	1	2	FACETS	0.984	0.894	1	0.984	0.894	1	CLONAL	1	TRUE	1	0.355486864289555	2		664	749	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965984	18965984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	151	681	1	ENST00000262803.5:c.1477C>T	p.Pro493Ser	p.P493S	ENST00000262803	NM_002911.3	493	Ccg/Tcg	11/24	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.355486864289555	2		682	777	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224559	36224560	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0043412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	181	902	1	ENST00000222270.7:c.7021_7022delinsAA	p.Gly2341Lys	p.G2341K	ENST00000222270	NM_014727.1	2341	GGg/AAg	29/37	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.355486864289555	2		903	989	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021717	31021718	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0043412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	83	429	1	ENST00000375687.4:c.1716_1717delinsTT	p.Arg573Trp	p.R573W	ENST00000375687	NM_015338.5	572	atCCgg/atTTgg	12/13	1	2	FACETS	0.953	0.844	1	0.953	0.844	1	CLONAL	1	TRUE	1	0.355486864289555	2		430	490	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070923	30070923	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	139	606	0	ENST00000338641.4:c.1439C>G	p.Thr480Arg	p.T480R	ENST00000338641	NM_000268.3	480	aCg/aGg	13/16	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.355486864289555	2		606	719	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202783	128202784	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0043412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	167	691	0	ENST00000341105.2:c.936_937delinsTT	p.His313Tyr	p.H313Y	ENST00000341105	NM_032638.4	312	ggCCac/ggTTac	4/6	0.276273862494139	3	FACETS	1	0.964	1	0.545	0.5	0.591	CLONAL	1	TRUE	1	0.355486864289555	3		691	1016	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979637	55979637	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	48	312	0	ENST00000263923.4:c.810del	p.Lys271AsnfsTer3	p.K271Nfs*3	ENST00000263923	NM_002253.2	270	aaG/aa	7/30	1	2	FACETS	0.88	0.748	1	0.88	0.748	1	CLONAL	1	TRUE	1	0.355486864289555	2		312	307	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873932	151873932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	44	275	0	ENST00000262189.6:c.8606C>T	p.Ser2869Phe	p.S2869F	ENST00000262189	NM_170606.2	2869	tCt/tTt	38/59	1	2	FACETS	0.924	0.78	1	0.924	0.78	1	CLONAL	1	TRUE	1	0.355486864289555	2		275	268	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346102	152346102	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	80	338	0	ENST00000359321.1:c.468G>A	p.Trp156Ter	p.W156*	ENST00000359321	NM_005431.1	156	tgG/tgA	3/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.355486864289555	2		338	339	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411724	139411725	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0043412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	129	718	0	ENST00000277541.6:c.1554_1555delinsAA	p.Gly519Ser	p.G519S	ENST00000277541	NM_017617.3	518	acGGgc/acAAgc	9/34	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.355486864289555	2		718	688	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76949379	76949379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	23	184	0	ENST00000373344.5:c.418G>A	p.Asp140Asn	p.D140N	ENST00000373344	NM_000489.3	140	Gat/Aat	6/35	1	2	FACETS	0.863	0.68	1	0.863	0.68	1	CLONAL	1	TRUE	1	0.355486864289555	2		184	150	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050664	30050686	+	frameshift_variant	Frame_Shift_Del	DEL	AGTGTTCACAAGCGGGGATTTTT	AGTGTTCACAAGCGGGGATTTTT	-	novel	NA	P-0043414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	47	275	0	ENST00000338641.4:c.466_488del	p.Ser156GlyfsTer39	p.S156Gfs*39	ENST00000338641	NM_000268.3	156	AGTGTTCACAAGCGGGGATTTTTg/g	5/16	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		275	368	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050689	30050690	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0043414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	79	283	0	ENST00000338641.4:c.492_493del	p.Gln165ArgfsTer37	p.Q165Rfs*37	ENST00000338641	NM_000268.3	164	gCC/g	5/16	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		283	352	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	346	721	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.654438123258741	3	FACETS	0.998	0.953	1	0.665	0.635	0.696	CLONAL	2	TRUE	0	0.654438123258741	3		721	703	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115853	8115854	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0043419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	559	604	0	ENST00000346208.3:c.1200dup	p.Ser401ValfsTer106	p.S401Vfs*106	ENST00000346208		400	atg/atGg	6/6	0.562724490361141	4	FACETS	0.913	0.882	0.944	0.913	0.882	0.944	CLONAL	3	TRUE	1	0.654438123258741	4		604	1032	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971128	21971128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	149	340	0	ENST00000304494.5:c.230C>T	p.Thr77Ile	p.T77I	ENST00000304494	NM_000077.4	77	aCt/aTt	2/3	0.654438123258741	3	FACETS	1	0.983	1	0.628	0.578	0.68	CLONAL	1	TRUE	1	0.654438123258741	3		340	481	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497562	125497562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	39	218	0	ENST00000428830.2:c.126G>A	p.Met42Ile	p.M42I	ENST00000428830	NM_001114121.2	42	atG/atA	3/14	0.654438123258741	2	FACETS	0.822	0.694	0.959	0.411	0.347	0.48	CLONAL	1	TRUE	0	0.654438123258741	2		218	145	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058566	72058566	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	165	415	0	ENST00000357731.5:c.874T>C	p.Phe292Leu	p.F292L	ENST00000357731	NM_173808.2	292	Ttc/Ctc	6/7	0.654438123258741	3	FACETS	0.943	0.868	1	0.471	0.434	0.51	CLONAL	1	TRUE	1	0.654438123258741	3		415	710	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736393	85736393	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	85	291	0	ENST00000370580.1:c.254C>G	p.Ser85Cys	p.S85C	ENST00000370580	NM_003921.4	85	tCt/tGt	2/3	0.654438123258741	3	FACETS	1	0.955	1	0.565	0.505	0.628	CLONAL	1	TRUE	1	0.654438123258741	3		291	305	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243708846	243708846	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	28	251	0	ENST00000263826.5:c.1217C>G	p.Ser406Cys	p.S406C	ENST00000263826	NM_005465.4	406	tCt/tGt	11/13	0.654438123258741	4	FACETS	0.73	0.588	0.889			1	SUBCLONAL	1	TRUE	NA	0.654438123258741	4		251	194	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198283251	198283251	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	84	428	0	ENST00000335508.6:c.477A>C	p.Gln159His	p.Q159H	ENST00000335508	NM_012433.2	159	caA/caC	5/25	0.471390016225742	4	FACETS	1	0.972	1	0.429	0.382	0.478	CLONAL	1	TRUE	1	0.654438123258741	4		428	330	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131893034	131893034	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	114	260	0	ENST00000265335.6:c.18G>C	p.Lys6Asn	p.K6N	ENST00000265335		6	aaG/aaC	1/25	0.606315905074254	4	FACETS	1	0.959	1	0.555	0.502	0.611	CLONAL	1	TRUE	2	0.654438123258741	4		260	519	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777909	27777909	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1165689563	NA	P-0043419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	86	313	0	ENST00000369163.2:c.58C>T	p.Gln20Ter	p.Q20*	ENST00000369163	NM_003536.2	20	Cag/Tag	1/1	0.654438123258741	5	FACETS	0.821	0.727	0.922	0.274	0.242	0.308	CLONAL	1	TRUE	2	0.654438123258741	5		313	634	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183822	10183823	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	49	472	0	ENST00000256474.2:c.292dup	p.Tyr98LeufsTer34	p.Y98Lfs*34	ENST00000256474	NM_000551.3	97	-/T	1/3	0.280960834181457	1	FACETS	0.931	0.793	1	0.931	0.793	1	CLONAL	1	TRUE	0	0.280960834181457	1		472	322	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106182958	106182958	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	42	276	0	ENST00000380013.4:c.3997del	p.Met1333TrpfsTer30	p.M1333Wfs*30	ENST00000380013	NM_001127208.2	1333	Atg/tg	8/11	0.136897669954967	3	FACETS	1	0.956	1	0.722	0.608	0.847	INDETERMINATE	1	TRUE	1	0.280960834181457	3		276	236	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	86	367	0	ENST00000425967.3:c.1731C>G	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaG	13/19	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.3254485194827	2		367	447	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209065	133209065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs58916399	NA	P-0043526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	178	431	3	ENST00000320574.5:c.6166G>A	p.Ala2056Thr	p.A2056T	ENST00000320574	NM_006231.2	2056	Gca/Aca	45/49	1	2	FACETS	1	0.984	1	1	0.994	1	CLONAL	2	TRUE	1	0.3254485194827	2		434	458	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468217	120468217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	72	640	0	ENST00000256646.2:c.4222G>A	p.Gly1408Ser	p.G1408S	ENST00000256646	NM_024408.3	1408	Ggt/Agt	25/34	1	2	FACETS	0.873	0.761	0.994	0.873	0.761	0.994	CLONAL	1	TRUE	1	0.202431616222332	2		640	815	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225972	133225972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555223943	NA	P-0043531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	70	688	0	ENST00000320574.5:c.3925G>A	p.Asp1309Asn	p.D1309N	ENST00000320574	NM_006231.2	1309	Gat/Aat	31/49	1	2	FACETS	0.763	0.664	0.871	0.763	0.664	0.871	SUBCLONAL	1	TRUE	1	0.202431616222332	2		688	906	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16005027	16005027	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	62	485	0	ENST00000268712.3:c.2227T>G	p.Ser743Ala	p.S743A	ENST00000268712	NM_006311.3	743	Tct/Gct	20/46	1	2	FACETS	0.828	0.714	0.952	0.828	0.714	0.952	CLONAL	1	TRUE	1	0.202431616222332	2		485	740	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633421	8633421	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	44	341	0	ENST00000356435.5:c.248G>A	p.Arg83Lys	p.R83K	ENST00000356435		83	aGa/aAa	3/35	0.202431616222332	1	FACETS	0.823	0.69	0.969	0.823	0.69	0.969	CLONAL	1	TRUE	0	0.202431616222332	1		341	475	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0043533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	34	500	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.472253613562883	3	FACETS	0.317	0.258	0.383	0.158	0.129	0.192	SUBCLONAL	1	TRUE	1	0.472253613562883	3		500	562	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842344	151842344	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs749571160	NA	P-0043533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	30	210	1	ENST00000262189.6:c.14068C>T	p.Arg4690Ter	p.R4690*	ENST00000262189	NM_170606.2	4690	Cga/Tga	54/59	1	2	FACETS	0.415	0.335	0.506	0.415	0.335	0.506	SUBCLONAL	1	TRUE	1	0.472253613562883	2		211	306	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796990	78796990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1301463689	NA	P-0043533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	27	408	0	ENST00000306801.3:c.1103C>T	p.Pro368Leu	p.P368L	ENST00000306801	NM_020761.2	368	cCg/cTg	9/34	0.296980235396031	2	FACETS	0.214	0.17	0.265	0.107	0.085	0.133	SUBCLONAL	1	TRUE	0	0.472253613562883	2		408	534	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431364	49431364	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	21	416	0	ENST00000301067.7:c.9775G>C	p.Glu3259Gln	p.E3259Q	ENST00000301067	NM_003482.3	3259	Gag/Cag	34/54	1	2	FACETS	0.225	0.172	0.286	0.225	0.172	0.286	SUBCLONAL	1	TRUE	1	0.472253613562883	2		416	396	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431373	49431373	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	26	445	0	ENST00000301067.7:c.9766G>C	p.Glu3256Gln	p.E3256Q	ENST00000301067	NM_003482.3	3256	Gag/Cag	34/54	1	2	FACETS	0.266	0.21	0.33	0.266	0.21	0.33	SUBCLONAL	1	TRUE	1	0.472253613562883	2		445	414	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443575	49443575	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	69	490	0	ENST00000301067.7:c.3796G>T	p.Glu1266Ter	p.E1266*	ENST00000301067	NM_003482.3	1266	Gag/Tag	11/54	1	2	FACETS	0.603	0.526	0.685	0.603	0.526	0.685	SUBCLONAL	1	TRUE	1	0.472253613562883	2		490	485	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40478145	40478146	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTTGAGGCCTTGGTGATACAC	novel	NA	P-0043533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	73	364	0	ENST00000264657.5:c.1333_1353dup	p.Val445_Lys451dup	p.V445_K451dup	ENST00000264657	NM_139276.2	445	-/GTGTATCACCAAGGCCTCAAG	15/24	1	2	FACETS	0.583	0.511	0.661	0.583	0.511	0.661	SUBCLONAL	1	TRUE	1	0.472253613562883	2		364	530	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054620	13054620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	44	320	0	ENST00000316448.5:c.1147G>A	p.Glu383Lys	p.E383K	ENST00000316448	NM_004343.3	383	Gag/Aag	9/9	1	2	FACETS	0.447	0.375	0.526	0.447	0.375	0.526	SUBCLONAL	1	TRUE	1	0.472253613562883	2		320	417	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940134	31940134	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	42	581	0	ENST00000375333.2:c.276C>G	p.Phe92Leu	p.F92L	ENST00000375333	NM_032454.1	92	ttC/ttG	2/8	1	2	FACETS	0.271	0.225	0.321	0.271	0.225	0.321	SUBCLONAL	1	TRUE	1	0.472253613562883	2		581	657	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005713	150005713	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0043533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	43	207	0	ENST00000253339.5:c.512C>G	p.Ser171Ter	p.S171*	ENST00000253339		171	tCa/tGa	3/7	1	2	FACETS	0.677	0.57	0.794	0.677	0.57	0.794	SUBCLONAL	1	TRUE	1	0.472253613562883	2		207	269	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410364	63410364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	67	621	1	ENST00000330258.3:c.2803G>A	p.Glu935Lys	p.E935K	ENST00000330258	NM_152424.3	935	Gag/Aag	2/2	0.159771578620726	3	FACETS	0.496	0.43	0.567	0.248	0.215	0.284	INDETERMINATE	1	TRUE	1	0.472253613562883	3		622	707	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0043534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	28	540	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.684	0.545	0.843	0.684	0.545	0.843	SUBCLONAL	1	TRUE	1	0.15	2		540	546	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0043592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	118	442	4	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.268223691239473	3	FACETS	0.896	0.818	0.976	0.896	0.818	0.976	CLONAL	3	TRUE	0	0.298498015333758	3		446	338	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0043592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	521	838	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.298498015333758	4	FACETS	0.881	0.846	0.917	1	0.994	1	CLONAL	4	TRUE	1	0.298498015333758	4		838	1286	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741472	145741472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745874353	NA	P-0043592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	203	1040	0	ENST00000428558.2:c.1031G>A	p.Arg344Gln	p.R344Q	ENST00000428558	NM_004260.3	344	cGg/cAg	5/22	0.298498015333758	5	FACETS	1	0.99	1	0.296	0.274	0.32	CLONAL	1	TRUE	0	0.298498015333758	5		1040	1329	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	273	627	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	1	2	FACETS	0.979	0.92	1	0.979	0.92	1	CLONAL	1	TRUE	1	0.535110709848033	2		627	1042	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467386	66467386	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	82	179	0	ENST00000273854.3:c.883T>C	p.Tyr295His	p.Y295H	ENST00000273854	NM_004439.5	295	Tat/Cat	3/18	1	2	FACETS	0.982	0.875	1	0.982	0.875	1	CLONAL	1	TRUE	1	0.535110709848033	2		179	312	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720828	89720828	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	41	174	0	ENST00000371953.3:c.981del	p.Ala328GlnfsTer16	p.A328Qfs*16	ENST00000371953	NM_000314.4	327	Aaa/aa	8/9	1	2	FACETS	0.886	0.746	1	0.886	0.746	1	CLONAL	1	TRUE	1	0.434307575266481	2		174	213	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499655	18499655	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	100	374	0	ENST00000266497.5:c.1510G>T	p.Asp504Tyr	p.D504Y	ENST00000266497		504	Gat/Tat	10/31	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.434307575266481	2		374	451	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67459123	67459123	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	145	878	0	ENST00000327367.4:c.539C>A	p.Pro180Gln	p.P180Q	ENST00000327367	NM_005902.3	180	cCa/cAa	4/9	1	2	FACETS	0.69	0.629	0.754	0.69	0.629	0.754	SUBCLONAL	1	TRUE	1	0.434307575266481	2		878	968	SUCCESS
YES1	7525	MSKCC	GRCh37	18	739732	739733	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	novel	NA	P-0043655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	94	266	0	ENST00000314574.4:c.1137+2dup		p.X379_splice	ENST00000314574	NM_005433.3	379			1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.434307575266481	2		266	413	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871349	35872208	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAATAACTCTTGGACTCCATTCTCCATAGCCCAAATATAATGAACTTTACAGGCTGAGAGAGTTTGCCTTTAATGCTTCTCTTTAAAAAAAGAGGGGGGGCAGGTACATTCTTGGGATACTGGTTATGCACAGAAATTTGAGAGACTCATTATGTAGATACCCCTCTGATAAGGAGCAGCTCTAGGGGCCTGGGAGGGTGAAGGGAATGGCACCTCATTAGTTAGAGCGCCGAAGGAGTTCACAGACTCACCTCGTCCTCTGTGAACTCCGTGAACTCTGACTCTGTGTCATAGCTCTCCTCATCCTCACTCTCTGGCAGCATCTGAAGGTTTTCTAGTGTCAGCTGGCCCAGCTGCTGCTGTATCCGGGTGCTTGGGCGGCCCCAGGTGAGCTGGTAGGGAGAATAGCCCTGGTAGGTAACTCTGTTGACATCAGCCCCACACTTCAACAGGAGTGACACCAGGTCAGGATTTTGCAGGTCCACTGCGAGGTGAAGGGCAGTCCGGCCATTACAGGGCTCCTGAAACCAAAAGGAATTTGAGATGCTTATGGCTGCATTTGGAATTTCTGCTCACAACATAAGCACGAGGAGCCTGACTCAGTGCGTCGGGGGCAGGAAGCACCAACCTGAGCATTGACATCAGCACCCAAGGACACCAAAAGCTCCACGATGCCCAGGTAGCCATGGATAGAGGCTAAGTGTAGACACGTGTGGCCTGGAAGAACAAAAGGAAAAAAGTATAACCACCTGTTTCAACCCTCACTCCTTTCACCTATTCTTTTATGGAACAAGTAGTCTTATCTTCTGAATTTTAAGAACCCACAGTCTGGGTTCTGAAAGAACTTTATAAAGGCATCC	AAATAACTCTTGGACTCCATTCTCCATAGCCCAAATATAATGAACTTTACAGGCTGAGAGAGTTTGCCTTTAATGCTTCTCTTTAAAAAAAGAGGGGGGGCAGGTACATTCTTGGGATACTGGTTATGCACAGAAATTTGAGAGACTCATTATGTAGATACCCCTCTGATAAGGAGCAGCTCTAGGGGCCTGGGAGGGTGAAGGGAATGGCACCTCATTAGTTAGAGCGCCGAAGGAGTTCACAGACTCACCTCGTCCTCTGTGAACTCCGTGAACTCTGACTCTGTGTCATAGCTCTCCTCATCCTCACTCTCTGGCAGCATCTGAAGGTTTTCTAGTGTCAGCTGGCCCAGCTGCTGCTGTATCCGGGTGCTTGGGCGGCCCCAGGTGAGCTGGTAGGGAGAATAGCCCTGGTAGGTAACTCTGTTGACATCAGCCCCACACTTCAACAGGAGTGACACCAGGTCAGGATTTTGCAGGTCCACTGCGAGGTGAAGGGCAGTCCGGCCATTACAGGGCTCCTGAAACCAAAAGGAATTTGAGATGCTTATGGCTGCATTTGGAATTTCTGCTCACAACATAAGCACGAGGAGCCTGACTCAGTGCGTCGGGGGCAGGAAGCACCAACCTGAGCATTGACATCAGCACCCAAGGACACCAAAAGCTCCACGATGCCCAGGTAGCCATGGATAGAGGCTAAGTGTAGACACGTGTGGCCTGGAAGAACAAAAGGAAAAAAGTATAACCACCTGTTTCAACCCTCACTCCTTTCACCTATTCTTTTATGGAACAAGTAGTCTTATCTTCTGAATTTTAAGAACCCACAGTCTGGGTTCTGAAAGAACTTTATAAAGGCATCC	-	novel	NA	P-0043684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	89	80	0	ENST00000216797.5:c.548-143_907-83del		p.X183_splice	ENST00000216797	NM_020529.2	183		4-5/6	0.767987379289638	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.767987379289638	2		80	108	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579339	7579339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	284	423	0	ENST00000269305.4:c.348del	p.Thr118GlnfsTer5	p.T118Qfs*5	ENST00000269305	NM_001126112.2	116	tcT/tc	4/11	0.767987379289638	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.767987379289638	2		423	366	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935008	49935008	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs535567428	NA	P-0043684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	286	480	1	ENST00000296474.3:c.1991C>T	p.Pro664Leu	p.P664L	ENST00000296474	NM_002447.2	664	cCg/cTg	6/20	0.767987379289638	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.767987379289638	2		481	369	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0043706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	68	388	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.20647436826553	5	FACETS	1	0.967	1	0.46	0.4	0.525	CLONAL	1	TRUE	2	0.20647436826553	5		388	625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0043706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	71	515	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.20647436826553	2		515	568	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696597	47696597	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	36	320	0	ENST00000347630.2:c.351G>A	p.Met117Ile	p.M117I	ENST00000347630	NM_001007230.1	117	atG/atA	5/11	1	2	FACETS	0.766	0.63	0.92	0.766	0.63	0.92	CLONAL	1	TRUE	1	0.20647436826553	2		320	455	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503813	149503813	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1283745894	NA	P-0043706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	53	495	0	ENST00000261799.4:c.2023G>A	p.Gly675Arg	p.G675R	ENST00000261799	NM_002609.3	675	Gga/Aga	14/23	0.20647436826553	3	FACETS	1	0.931	1	0.579	0.494	0.672	CLONAL	1	TRUE	1	0.20647436826553	3		495	489	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0043710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	110	226	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	0.135907790878183	6	FACETS	1	0.963	1	0.754	0.682	0.828	INDETERMINATE	2	TRUE	3	0.453694336627952	6		226	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057519990	NA	P-0043710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	219	459	1	ENST00000269305.4:c.796G>T	p.Gly266Ter	p.G266*	ENST00000269305	NM_001126112.2	266	Gga/Tga	8/11	0.295491723863742	3	FACETS	1	0.949	1	0.676	0.633	0.719	CLONAL	2	TRUE	0	0.453694336627952	3		460	584	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913237	NA	P-0043710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	213	273	0	ENST00000369535.4:c.35G>T	p.Gly12Val	p.G12V	ENST00000369535	NM_002524.4	12	gGt/gTt	2/7	0.313504872823355	3	FACETS	1	0.987	1	0.795	0.747	0.844	CLONAL	2	TRUE	0	0.453694336627952	3		273	483	SUCCESS
APC	324	MSKCC	GRCh37	5	112174154	112174154	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	118	279	0	ENST00000257430.4:c.2863G>T	p.Glu955Ter	p.E955*	ENST00000257430	NM_000038.5	955	Gaa/Taa	16/16	0.135907790878183	6	FACETS	1	0.966	1	0.755	0.686	0.827	INDETERMINATE	2	TRUE	3	0.453694336627952	6		279	438	SUCCESS
AR	367	MSKCC	GRCh37	X	66765620	66765620	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370893700	NA	P-0043710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	163	726	1	ENST00000374690.3:c.632C>T	p.Ala211Val	p.A211V	ENST00000374690	NM_000044.3	211	gCg/gTg	1/8	0.453694336627952	3	FACETS	0.981	0.9	1	0.49	0.45	0.533	CLONAL	1	TRUE	1	0.453694336627952	3		727	899	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111959732	111959732	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	236	478	0	ENST00000375549.3:c.311A>G	p.His104Arg	p.H104R	ENST00000375549	NM_003002.3	104	cAc/cGc	3/4	0.135907790878183	6	FACETS	1	0.974	1	0.722	0.675	0.771	INDETERMINATE	2	TRUE	3	0.453694336627952	6		478	916	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0043718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	13	513	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.29	0.206	0.394	0.29	0.206	0.394	SUBCLONAL	1	TRUE	1	0.233720037570734	2		513	383	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0043718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	30	373	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.65	0.524	0.793	0.65	0.524	0.793	SUBCLONAL	1	TRUE	1	0.233720037570734	2		373	395	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247367	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747241612	NA	P-0043718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	38	203	0	ENST00000281708.4:c.1435C>G	p.Arg479Gly	p.R479G	ENST00000281708	NM_033632.3	479	Cga/Gga	10/12	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.233720037570734	2		203	252	SUCCESS
APC	324	MSKCC	GRCh37	5	112175756	112175756	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	69	157	0	ENST00000257430.4:c.4466del	p.Leu1489TyrfsTer18	p.L1489Yfs*18	ENST00000257430	NM_000038.5	1489	Tta/ta	16/16	0.207238641444167	2	FACETS	0.879	0.777	0.985	1	0.969	1	CLONAL	3	TRUE	0	0.233720037570734	2		157	224	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282215	38282215	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	68	431	0	ENST00000425967.3:c.841C>T	p.Arg281Trp	p.R281W	ENST00000425967	NM_001174067.1	281	Cgg/Tgg	8/19	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.233720037570734	2		431	440	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989385	7989385	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200663524	NA	P-0043718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	83	638	1	ENST00000319144.4:c.301G>A	p.Ala101Thr	p.A101T	ENST00000319144	NM_001139.2	101	Gcc/Acc	2/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.233720037570734	2		639	545	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625252	69625252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782761826	NA	P-0043718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	63	977	0	ENST00000334134.2:c.541C>T	p.Arg181Cys	p.R181C	ENST00000334134	NM_005247.2	181	Cgc/Tgc	3/3	1	2	FACETS	0.908	0.785	1	0.908	0.785	1	CLONAL	1	TRUE	1	0.233720037570734	2		977	594	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431404	121431404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780357	NA	P-0043718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	71	517	0	ENST00000257555.6:c.608G>A	p.Arg203His	p.R203H	ENST00000257555		203	cGt/cAt	3/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.233720037570734	2		517	484	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248215	59248216	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	15	23	0	ENST00000371222.2:c.527dup	p.Asn177GlnfsTer133	p.N177Qfs*133	ENST00000371222	NM_002228.3	176	ttc/ttTc	1/1	0.233720037570734	2	FACETS	0.93	0.709	1	1	0.894	1	CLONAL	3	TRUE	0	0.233720037570734	2		23	46	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900969	114900969	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	37	342	0	ENST00000543371.1:c.581del	p.Pro194LeufsTer31	p.P194Lfs*31	ENST00000543371	NM_001198531.1	193	caC/ca	6/14	0.233720037570734	1	FACETS	0.647	0.534	0.774	0.647	0.534	0.774	SUBCLONAL	1	TRUE	0	0.233720037570734	1		342	432	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983936	15983936	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	40	237	0	ENST00000268712.3:c.3283G>T	p.Glu1095Ter	p.E1095*	ENST00000268712	NM_006311.3	1095	Gaa/Taa	24/46	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.233720037570734	2		237	318	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120159	70120160	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0043718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	35	319	0	ENST00000245479.2:c.1163_1164dup	p.Pro389SerfsTer15	p.P389Sfs*15	ENST00000245479	NM_000346.3	387	-/GA	3/3	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.233720037570734	2		319	257	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268713	46268713	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	67	363	0	ENST00000371998.3:c.2998C>A	p.Gln1000Lys	p.Q1000K	ENST00000371998		1000	Caa/Aaa	16/23	NA	2	FACETS	1	0.944	1			1	INDETERMINATE	1	TRUE	NA	0.233720037570734	2		363	495	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589204	67589221	+	inframe_deletion	In_Frame_Del	DEL	TTCAGTTCTGTGGTTGAA	TTCAGTTCTGTGGTTGAA	-	novel	NA	P-0043718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	59	201	0	ENST00000274335.5:c.1194_1211del	p.Phe398_Glu403del	p.F398_E403del	ENST00000274335		398	TTCAGTTCTGTGGTTGAA/-	9/15	0.207238641444167	2	FACETS	0.758	0.656	0.868	0.758	0.656	0.868	SUBCLONAL	2	TRUE	0	0.233720037570734	2		201	333	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994246	21994246	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1316222103	NA	P-0043718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	40	504	0	ENST00000579755.1:c.85C>T	p.Arg29Trp	p.R29W	ENST00000579755		29	Cgg/Tgg	1/3	1				0.55	0.787				SUBCLONAL	1	TRUE	1	0.233720037570734	2		504	517	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915929	127915929	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	56	311	0	ENST00000373547.4:c.552A>T	p.Glu184Asp	p.E184D	ENST00000373547	NM_002721.4	184	gaA/gaT	6/7	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.233720037570734	2		311	430	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039297	47039297	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	82	591	0	ENST00000377604.3:c.920T>C	p.Leu307Pro	p.L307P	ENST00000377604	NM_001204468.1	307	cTg/cCg	10/24	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.233720037570734	2		591	595	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0043732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	76	263	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.37393176749144	3	FACETS	1	0.959	1	0.595	0.526	0.667	CLONAL	1	TRUE	1	0.491374403749918	3		263	324	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0043732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	3272	635	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.491374403749918	17	FACETS	0.993	0.984	1			1	CLONAL	16	TRUE	NA	0.491374403749918	17		635	3926	SUCCESS
APC	324	MSKCC	GRCh37	5	112175630	112175630	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	64	255	0	ENST00000257430.4:c.4339del	p.Gln1447LysfsTer26	p.Q1447Kfs*26	ENST00000257430	NM_000038.5	1447	Caa/aa	16/16	0.37393176749144	3	FACETS	0.702	0.61	0.802	0.351	0.305	0.401	SUBCLONAL	1	TRUE	1	0.491374403749918	3		255	462	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553260	41553260	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	155	448	0	ENST00000263253.7:c.3349T>G	p.Tyr1117Asp	p.Y1117D	ENST00000263253	NM_001429.3	1117	Tat/Gat	18/31	0.0718182345323792	4	FACETS	1	0.987	1	0.704	0.647	0.764	INDETERMINATE	1	TRUE	2	0.491374403749918	4		448	668	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386614	81386614	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	37	262	0	ENST00000222390.5:c.373A>T	p.Ile125Phe	p.I125F	ENST00000222390	NM_000601.4	125	Att/Ttt	4/18	0.137790498026349	5	FACETS	0.802	0.663	0.957	0.267	0.221	0.319	INDETERMINATE	1	TRUE	2	0.491374403749918	5		262	326	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0043735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	140	418	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.293684612321622	2	FACETS	0.928	0.853	1	1	0.986	1	CLONAL	3	TRUE	0	0.24	2		418	419	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662338	227662338	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147944503	NA	P-0043783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	263	571	0	ENST00000305123.5:c.1117C>T	p.Arg373Cys	p.R373C	ENST00000305123	NM_005544.2	373	Cgc/Tgc	1/2	1	2	FACETS	0.957	0.898	1	0.957	0.898	1	CLONAL	1	TRUE	1	0.589168271674417	2		571	933	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110150	3110150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762714189	NA	P-0043783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	203	356	0	ENST00000078429.4:c.140C>T	p.Thr47Met	p.T47M	ENST00000078429	NM_002067.2	47	aCg/aTg	2/7	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.589168271674417	2		356	683	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795881	42795905	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCAGCCCCCCAGCAAGGTGAGGGC	CCCAGCCCCCCAGCAAGGTGAGGGC	-	novel	NA	P-0043783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	285	673	0	ENST00000575354.2:c.2871_2886+9del		p.X957_splice	ENST00000575354	NM_015125.3	957		11/20	1	2	FACETS	0.858	0.806	0.911	0.858	0.806	0.911	CLONAL	1	TRUE	1	0.589168271674417	2		673	1128	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277867	41277867	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	137	386	0	ENST00000349496.5:c.1831C>T	p.Gln611Ter	p.Q611*	ENST00000349496	NM_001904.3	611	Caa/Taa	12/15	0.57187885629996	1	FACETS	0.818	0.752	0.886	0.818	0.752	0.886	CLONAL	1	TRUE	0	0.589168271674417	1		386	401	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059231	47059231	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0043783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	126	286	0	ENST00000409792.3:c.7432-2A>G		p.X2478_splice	ENST00000409792	NM_014159.6	2478			0.57187885629996	1	FACETS	0.955	0.877	1	0.955	0.877	1	CLONAL	1	TRUE	0	0.589168271674417	1		286	316	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225494	26225494	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	167	368	0	ENST00000360408.1:c.112A>C	p.Lys38Gln	p.K38Q	ENST00000360408	NM_003532.2	38	Aag/Cag	1/1	1	2	FACETS	0.829	0.764	0.896	0.829	0.764	0.896	CLONAL	1	TRUE	1	0.589168271674417	2		368	684	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184023	123184061	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCCCCCATTCAGTGATGCGATAGCTGAAATTCGAGCTA	TTCCCCCATTCAGTGATGCGATAGCTGAAATTCGAGCTA	-	novel	NA	P-0043783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	93	94	0	ENST00000218089.9:c.894-11_921del		p.X298_splice	ENST00000218089	NM_001042749.1	298		11/35	1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.589168271674417	1		94	175	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0043788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	18	415	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.673	0.505	0.872	0.673	0.505	0.872	SUBCLONAL	1	TRUE	1	0.12	2		415	446	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578448	7578448	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1064795691	NA	P-0043788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	45	561	0	ENST00000269305.4:c.482C>A	p.Ala161Asp	p.A161D	ENST00000269305	NM_001126112.2	161	gCc/gAc	5/11	1	2	FACETS	0.656	0.548	0.775	0.656	0.548	0.775	SUBCLONAL	1	TRUE	1	0.12	2		561	1144	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920652	96920652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767739392	NA	P-0043788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	47	422	0	ENST00000258439.3:c.328G>A	p.Ala110Thr	p.A110T	ENST00000258439	NM_001193304.2	110	Gct/Act	3/4	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.12	2		422	766	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244280	153244280	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	18	206	0	ENST00000281708.4:c.1877C>T	p.Ala626Val	p.A626V	ENST00000281708	NM_033632.3	626	gCt/gTt	12/12	1	2	FACETS	0.845	0.635	1	0.845	0.635	1	CLONAL	1	TRUE	1	0.12	2		206	355	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225180	53225180	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	58	251	0	ENST00000375401.3:c.3038C>T	p.Pro1013Leu	p.P1013L	ENST00000375401	NM_004187.3	1013	cCt/cTt	20/26	1	1	FACETS	0.798	0.686	0.921	1	0.971	1	CLONAL	2	TRUE	0	0.12	1		251	569	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	102	541	0				ENST00000310581	NM_198253.2	-/1132			0.499158565924442	3	FACETS	1	0.938	1			1	CLONAL	2	FALSE	NA	0.711279965206747	3		541	190	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355779	73355779	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs771930385	NA	P-0043803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	202	367	0	ENST00000377767.4:c.192C>G	p.His64Gln	p.H64Q	ENST00000377767	NM_014953.3	64	caC/caG	1/21	0.711279965206747	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	FALSE	0	0.711279965206747	2		367	261	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624246	89624246	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	79	163	0	ENST00000371953.3:c.20del	p.Glu7GlyfsTer17	p.E7Gfs*17	ENST00000371953	NM_000314.4	7	gAg/gg	1/9	0.711279965206747	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	FALSE	0	0.711279965206747	2		163	92	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953788	48953788	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0043803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	89	160	0	ENST00000267163.4:c.1389+2T>G		p.X463_splice	ENST00000267163	NM_000321.2	463			0.711279965206747	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	FALSE	0	0.711279965206747	2		160	107	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27172633	27172633	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	167	464	0	ENST00000380036.4:c.648G>A	p.Trp216Ter	p.W216*	ENST00000380036	NM_000459.3	216	tgG/tgA	5/23	0.708620890391276	4	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	FALSE	2	0.711279965206747	4		464	392	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0043811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	342	418	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.758318979140662	4	FACETS	0.921	0.883	0.959	0.921	0.883	0.959	CLONAL	3	TRUE	1	0.758318979140662	4		418	574	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579355	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519997	NA	P-0043811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	329	636	0	ENST00000269305.4:c.332T>C	p.Leu111Pro	p.L111P	ENST00000269305	NM_001126112.2	111	cTg/cCg	4/11	0.758318979140662	1	FACETS	0.95	0.909	0.99	0.95	0.909	0.99	CLONAL	1	TRUE	0	0.758318979140662	1		636	567	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753334	42753334	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2103	132	862	0	ENST00000222329.4:c.930G>A	p.Met310Ile	p.M310I	ENST00000222329	NM_006494.2	310	atG/atA	4/4	0.701493988175738	4	FACETS	0.274	0.247	0.302			1	SUBCLONAL	1	TRUE	NA	0.758318979140662	4		862	2235	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39607453	39607453	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	108	151	0	ENST00000262039.4:c.1531C>G	p.Pro511Ala	p.P511A	ENST00000262039	NM_002647.2	511	Cca/Gca	14/25	0.463283243537477	4	FACETS	1	0.939	1	0.351	0.317	0.388	CLONAL	1	TRUE	1	0.758318979140662	4		151	475	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752709	42752709	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1273385423	NA	P-0043811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1814	112	722	0	ENST00000222329.4:c.1555G>T	p.Gly519Trp	p.G519W	ENST00000222329	NM_006494.2	519	Ggg/Tgg	4/4	0.701493988175738	4	FACETS	0.27	0.241	0.3			1	SUBCLONAL	1	TRUE	NA	0.758318979140662	4		722	1926	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752865	42752865	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1862	115	702	0	ENST00000222329.4:c.1399G>C	p.Glu467Gln	p.E467Q	ENST00000222329	NM_006494.2	467	Gag/Cag	4/4	0.701493988175738	4	FACETS	0.27	0.241	0.3			1	SUBCLONAL	1	TRUE	NA	0.758318979140662	4		702	1977	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753672	42753672	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2069	132	764	0	ENST00000222329.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000222329	NM_006494.2	198	Gaa/Taa	4/4	0.701493988175738	4	FACETS	0.278	0.251	0.307			1	SUBCLONAL	1	TRUE	NA	0.758318979140662	4		764	2201	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909291	41909291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778979671	NA	P-0043811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2228	535	514	0	ENST00000372991.4:c.97C>T	p.Arg33Cys	p.R33C	ENST00000372991	NM_001760.3	33	Cgc/Tgc	1/5	0.758318979140662	6	FACETS	1	0.995	1	0.428	0.409	0.449	CLONAL	1	TRUE	3	0.758318979140662	6		514	2763	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	231	946	0	ENST00000269305.4:c.380C>A	p.Ser127Tyr	p.S127Y	ENST00000269305	NM_001126112.2	127	tCc/tAc	5/11	0.736790566926583	1	FACETS	0.891	0.844	0.937	0.891	0.844	0.937	CLONAL	1	TRUE	0	0.76916516386516	1		946	415	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346147	89346147	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	73	336	0	ENST00000301030.4:c.6803T>C	p.Leu2268Pro	p.L2268P	ENST00000301030	NM_001256183.1	2268	cTc/cCc	9/13	1	2	FACETS	0.722	0.639	0.809	0.722	0.639	0.809	SUBCLONAL	1	TRUE	1	0.76916516386516	2		336	263	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0043930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	12	418	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.582	0.408	0.798	0.582	0.408	0.798	SUBCLONAL	1	TRUE	1	0.13	2		418	317	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481806	56481806	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	33	484	0	ENST00000267101.3:c.734C>T	p.Ala245Val	p.A245V	ENST00000267101	NM_001982.3	245	gCc/gTc	7/28	1	2	FACETS	0.781	0.634	0.947	0.781	0.634	0.947	CLONAL	1	TRUE	1	0.13	2		484	650	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266112	41266112	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913228	NA	P-0043930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	22	288	0	ENST00000349496.5:c.109T>G	p.Ser37Ala	p.S37A	ENST00000349496	NM_001904.3	37	Tct/Gct	3/15	1	2	FACETS	0.935	0.724	1	0.935	0.724	1	CLONAL	1	TRUE	1	0.13	2		288	362	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	275	396	0	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	0.519591116268052	2	FACETS	0.989	0.94	1	0.989	0.94	1	CLONAL	2	TRUE	0	0.519591116268052	2		396	535	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0043934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	82	311	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	1	2	FACETS	0.962	0.856	1	0.962	0.856	1	CLONAL	1	TRUE	1	0.519591116268052	2		311	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0043934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	647	735	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.46706687106868	3	FACETS	1	0.986	1			1	CLONAL	3	TRUE	NA	0.519591116268052	3		735	1021	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120239	70120239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	670	560	0	ENST00000245479.2:c.1241C>A	p.Ser414Ter	p.S414*	ENST00000245479	NM_000346.3	414	tCg/tAg	3/3	0.519591116268052	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.519591116268052	3		560	1040	SUCCESS
APC	324	MSKCC	GRCh37	5	112174213	112174214	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554084587	NA	P-0043934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	96	617	0	ENST00000257430.4:c.2926dup	p.Arg976LysfsTer9	p.R976Kfs*9	ENST00000257430	NM_000038.5	974	-/A	16/16	1	2	FACETS	0.899	0.806	0.996	0.899	0.806	0.996	CLONAL	1	TRUE	1	0.519591116268052	2		617	411	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323270	31323273	+	frameshift_variant	Frame_Shift_Del	DEL	GTCA	GTCA	-	novel	NA	P-0043934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	110	245	0	ENST00000412585.2:c.716_719del	p.Leu239ProfsTer57	p.L239Pfs*57	ENST00000412585	NM_005514.6	239	cTGACc/cc	4/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.519591116268052	2		245	372	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105562	27105563	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	146	436	0	ENST00000324856.7:c.5175dup	p.Glu1726Ter	p.E1726*	ENST00000324856	NM_006015.4	1725	att/aTtt	20/20	1	2	FACETS	0.862	0.789	0.938	0.862	0.789	0.938	CLONAL	1	TRUE	1	0.519591116268052	2		436	652	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435901	49435901	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	176	681	0	ENST00000301067.7:c.6080A>G	p.Asn2027Ser	p.N2027S	ENST00000301067	NM_003482.3	2027	aAt/aGt	28/54	1	2	FACETS	0.806	0.743	0.871	0.806	0.743	0.871	CLONAL	1	TRUE	1	0.519591116268052	2		681	841	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879504	151879504	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	153	378	0	ENST00000262189.6:c.5441C>G	p.Pro1814Arg	p.P1814R	ENST00000262189	NM_170606.2	1814	cCt/cGt	36/59	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.519591116268052	2		378	512	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0043951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	42	267	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	0.471	0.393	0.559	0.471	0.393	0.559	SUBCLONAL	1	TRUE	1	0.287454978767242	2		267	620	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0043951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	173	369	3	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.982	1	1	0.994	1	CLONAL	2	TRUE	1	0.287454978767242	2		372	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0043951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	32	593	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.287454978767242	1	FACETS	0.246	0.198	0.3	0.246	0.198	0.3	SUBCLONAL	1	TRUE	0	0.287454978767242	1		595	776	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0043951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	19	971	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.287454978767242	1	FACETS	0.128	0.096	0.166	0.128	0.096	0.166	SUBCLONAL	1	TRUE	0	0.287454978767242	1		972	882	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602314	10602314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1307	74	571	0	ENST00000171111.5:c.1264G>A	p.Asp422Asn	p.D422N	ENST00000171111	NM_203500.1	422	Gat/Aat	3/6	0.287454978767242	5	FACETS	0.534	0.465	0.608			1	SUBCLONAL	1	TRUE	NA	0.287454978767242	5		571	1381	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649052	37649052	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	113	390	1	ENST00000447079.4:c.2157G>A	p.Trp719Ter	p.W719*	ENST00000447079	NM_015083.1	719	tgG/tgA	4/14	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.287454978767242	2		391	735	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257552	19257552	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	93	571	0	ENST00000162023.5:c.674C>T	p.Ser225Phe	p.S225F	ENST00000162023		225	tCc/tTc	10/13	0.262097295156211	3	FACETS	0.694	0.615	0.778	0.347	0.307	0.389	SUBCLONAL	1	TRUE	1	0.287454978767242	3		571	1067	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713544	30713546	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0043951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	75	547	0	ENST00000295754.5:c.871_873del	p.Lys291del	p.K291del	ENST00000295754	NM_003242.5	290	gAGAag/gag	4/7	0.287454978767242	1	FACETS	0.878	0.771	0.992	0.878	0.771	0.992	CLONAL	1	TRUE	0	0.287454978767242	1		547	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0043951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	93	383	4	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.287454978767242	1	FACETS	0.907	0.808	1	0.907	0.808	1	CLONAL	1	TRUE	0	0.287454978767242	1		387	611	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849053	156849053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369353892	NA	P-0043951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	49	579	0	ENST00000524377.1:c.1945C>T	p.Arg649Trp	p.R649W	ENST00000524377	NM_002529.3	649	Cgg/Tgg	15/17	1	2	FACETS	0.35	0.295	0.411	0.35	0.295	0.411	SUBCLONAL	1	TRUE	1	0.287454978767242	2		579	974	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440154	49440154	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	121	523	0	ENST00000301067.7:c.4472G>A	p.Trp1491Ter	p.W1491*	ENST00000301067	NM_003482.3	1491	tGg/tAg	16/54	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.287454978767242	2		523	806	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396838	396838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759464398	NA	P-0043951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	101	606	1	ENST00000262320.3:c.188G>A	p.Arg63His	p.R63H	ENST00000262320	NM_003502.3	63	cGc/cAc	2/11	1	2	FACETS	0.73	0.651	0.814	0.73	0.651	0.814	SUBCLONAL	1	TRUE	1	0.287454978767242	2		607	963	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462965	120462965	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	58	389	0	ENST00000256646.2:c.5366G>A	p.Trp1789Ter	p.W1789*	ENST00000256646	NM_024408.3	1789	tGg/tAg	30/34	1	2	FACETS	0.601	0.515	0.694	0.601	0.515	0.694	SUBCLONAL	1	TRUE	1	0.287454978767242	2		389	672	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877348	28877348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772567599	NA	P-0043951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	108	426	2	ENST00000282397.4:c.3973C>T	p.Pro1325Ser	p.P1325S	ENST00000282397	NM_002019.4	1325	Cca/Tca	30/30	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.287454978767242	2		428	744	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821605	72821605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769543239	NA	P-0043951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	10	53	0	ENST00000268489.5:c.10570G>A	p.Gly3524Ser	p.G3524S	ENST00000268489	NM_006885.3	3524	Ggc/Agc	10/10	1	2	FACETS	0.87	0.597	1	0.87	0.597	1	CLONAL	1	TRUE	1	0.287454978767242	2		53	80	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991711	25991711	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	46	280	0	ENST00000435504.4:c.531G>T	p.Lys177Asn	p.K177N	ENST00000435504		177	aaG/aaT	7/13	0.287454978767242	1	FACETS	0.533	0.449	0.626	0.533	0.449	0.626	SUBCLONAL	1	TRUE	0	0.287454978767242	1		280	514	SUCCESS
ATR	545	MSKCC	GRCh37	3	142234348	142234348	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	62	217	0	ENST00000350721.4:c.4392T>G	p.Ser1464Arg	p.S1464R	ENST00000350721	NM_001184.3	1464	agT/agG	25/47	1	2	FACETS	0.961	0.832	1	0.961	0.832	1	CLONAL	1	TRUE	1	0.287454978767242	2		217	449	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397655	139397656	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0043951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	78	534	0	ENST00000277541.6:c.5145dup	p.Tyr1716LeufsTer9	p.Y1716Lfs*9	ENST00000277541	NM_017617.3	1715	-/C	27/34	0.287454978767242	0	FACETS	0.549	0.482	0.62			1	SUBCLONAL	1	TRUE	0	0.287454978767242	0		534	705	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399933	139399933	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	108	609	1	ENST00000277541.6:c.4415G>T	p.Cys1472Phe	p.C1472F	ENST00000277541	NM_017617.3	1472	tGc/tTc	25/34	0.287454978767242	0	FACETS	0.746	0.67	0.826			1	SUBCLONAL	1	TRUE	0	0.287454978767242	0		610	718	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0043958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	119	836	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.852	0.778	0.928	0.852	0.778	0.928	CLONAL	1	TRUE	1	0.800495953217904	2		836	349	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211827	123211828	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	53	167	0	ENST00000218089.9:c.2695dup	p.Ile899AsnfsTer8	p.I899Nfs*8	ENST00000218089	NM_001042749.1	898	-/A	27/35	1	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.800495953217904	1		167	71	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0043968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	397	327	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.40653039800226	3	FACETS	0.987	0.953	1	1	0.996	1	CLONAL	4	TRUE	0	0.40653039800226	3		327	595	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	291	593	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.40653039800226	5	FACETS	0.84	0.792	0.888	0.84	0.792	0.888	CLONAL	3	TRUE	2	0.40653039800226	5		593	915	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590997	67590997	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	17	117	0	ENST00000274335.5:c.1590G>T	p.Lys530Asn	p.K530N	ENST00000274335		530	aaG/aaT	12/15	0.40653039800226	3	FACETS	1	0.785	1	0.519	0.393	0.663	CLONAL	1	TRUE	1	0.40653039800226	3		117	97	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	73	540	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.223618296816097	4	FACETS	0.799	0.704	0.901	0.799	0.704	0.901	CLONAL	2	TRUE	2	0.345049842580176	4		540	356	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0044008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	102	261	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.345049842580176	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.345049842580176	3		261	306	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0044008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	59	597	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.345049842580176	3	FACETS	0.891	0.768	1	0.446	0.384	0.512	CLONAL	1	TRUE	1	0.345049842580176	3		597	450	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916946	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0044008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	105	358	0	ENST00000263967.3:c.332_334del	p.Lys111del	p.K111del	ENST00000263967	NM_006218.2	111	AAG/-	2/21	0.345049842580176	2	FACETS	0.936	0.849	1	0.936	0.849	1	CLONAL	2	TRUE	0	0.345049842580176	2		358	325	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411678	63411678	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	313	288	0	ENST00000330258.3:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000330258	NM_152424.3	497	Cga/Tga	2/2	0.345049842580176	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.345049842580176	3		288	917	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0044012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	73	240	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.815	0.715	0.921	0.815	0.715	0.921	CLONAL	1	TRUE	1	0.407286323106179	2		240	440	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653805	89653805	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659443	NA	P-0044012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	73	305	0	ENST00000371953.3:c.103A>G	p.Met35Val	p.M35V	ENST00000371953	NM_000314.4	35	Atg/Gtg	2/9	1	2	FACETS	0.996	0.877	1	0.996	0.877	1	CLONAL	1	TRUE	1	0.407286323106179	2		305	360	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653860	89653860	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	60	286	0	ENST00000371953.3:c.158T>C	p.Val53Ala	p.V53A	ENST00000371953	NM_000314.4	53	gTa/gCa	2/9	1	2	FACETS	0.896	0.776	1	0.896	0.776	1	CLONAL	1	TRUE	1	0.407286323106179	2		286	329	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916945	178916956	+	inframe_deletion	In_Frame_Del	DEL	AGATCCTCAATC	AGATCCTCAATC	-	novel	NA	P-0044012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	60	302	0	ENST00000263967.3:c.332_343del	p.Lys111_Asn114del	p.K111_N114del	ENST00000263967	NM_006218.2	111	aAGATCCTCAATCga/aga	2/21	1	2	FACETS	0.708	0.612	0.812	0.708	0.612	0.812	SUBCLONAL	1	TRUE	1	0.407286323106179	2		302	416	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986559	36986560	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0044015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	34	479	0	ENST00000354822.5:c.1129dup	p.Leu377ProfsTer62	p.L377Pfs*62	ENST00000354822	NM_001079668.2	377	ctg/cCtg	3/3	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		479	568	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0044027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	87	204	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.941	1	1	0.987	1	CLONAL	2	TRUE	1	0.3	2		204	271	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134252	11134252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	358	574	0	ENST00000358026.2:c.2918G>A	p.Arg973Gln	p.R973Q	ENST00000358026	NM_001128849.1	973	cGg/cAg	20/36	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.814760334544044	2		574	818	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098816	178098816	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	554	560	0	ENST00000397062.3:c.229G>T	p.Asp77Tyr	p.D77Y	ENST00000397062	NM_006164.4	77	Gat/Tat	2/5	0.814760334544044	4	FACETS	0.932	0.903	0.96	0.932	0.903	0.96	CLONAL	3	TRUE	1	0.814760334544044	4		560	883	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0044050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	265	444	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	0.291314332034389	3	FACETS	0.963	0.913	1	1	0.992	1	CLONAL	4	TRUE	0	0.291314332034389	3		444	541	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121909229	NA	P-0044050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	56	329	0	ENST00000371953.3:c.389G>C	p.Arg130Pro	p.R130P	ENST00000371953	NM_000314.4	130	cGa/cCa	5/9	0.291314332034389	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	3	TRUE	0	0.291314332034389	3		329	127	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916949	+	inframe_deletion	In_Frame_Del	DEL	AAGATC	AAGATC	-	novel	NA	P-0044050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	11	259	0	ENST00000263967.3:c.331_336del	p.Lys111_Ile112del	p.K111_I112del	ENST00000263967	NM_006218.2	111	AAGATC/-	2/21	1	2	FACETS	0.899	0.629	1	0.899	0.629	1	CLONAL	1	TRUE	1	0.291314332034389	2		259	84	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220545	133220545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768504121	NA	P-0044050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	94	423	0	ENST00000320574.5:c.4168C>T	p.Arg1390Cys	p.R1390C	ENST00000320574	NM_006231.2	1390	Cgc/Tgc	33/49	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.291314332034389	2		423	512	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971166	21971176	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCAGCAGCT	CAGCAGCAGCT	-	novel	NA	P-0044050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	199	277	0	ENST00000304494.5:c.182_192del	p.Glu61AlafsTer55	p.E61Afs*55	ENST00000304494	NM_000077.4	61	gAGCTGCTGCTG/g	2/3	0.291314332034389	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.291314332034389	2		277	589	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670668	67670668	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1396410914	NA	P-0044050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	138	407	0	ENST00000264010.4:c.1913C>T	p.Pro638Leu	p.P638L	ENST00000264010	NM_006565.3	638	cCt/cTt	11/12	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.291314332034389	2		407	788	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	103	541	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.93	1	1	0.988	1	CLONAL	2	TRUE	1	0.18	2		541	547	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0044060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	73	719	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.843	0.735	0.96	0.843	0.735	0.96	CLONAL	1	TRUE	1	0.18	2		719	962	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579529	7579529	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658483	NA	P-0044060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	77	681	0	ENST00000269305.4:c.158G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tGg/tAg	4/11	1	2	FACETS	0.956	0.838	1	0.956	0.838	1	CLONAL	1	TRUE	1	0.18	2		681	895	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101612	27101612	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	191	773	2	ENST00000324856.7:c.4899del	p.Met1634Ter	p.M1634*	ENST00000324856	NM_006015.4	1632	Ccc/cc	18/20	0.153290020079008	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.18	3		775	1009	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0044060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	146	476	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	1	2	FACETS	0.878	0.801	0.959	1	0.99	1	CLONAL	2	TRUE	1	0.18	2		476	924	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0044060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	27	235	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.822	0.654	1	0.822	0.654	1	CLONAL	1	TRUE	1	0.18	2		235	365	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027160	49027160	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0044060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	34	410	0	ENST00000267163.4:c.1727C>G	p.Ser576Ter	p.S576*	ENST00000267163	NM_000321.2	576	tCa/tGa	18/27	0.228019896904103	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	0	0.18	1		410	294	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890267	72890267	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	36	472	0	ENST00000325599.8:c.415G>C	p.Glu139Gln	p.E139Q	ENST00000325599	NM_018130.2	139	Gaa/Caa	4/11	1	2	FACETS	0.618	0.507	0.744	0.618	0.507	0.744	SUBCLONAL	1	TRUE	1	0.18	2		472	647	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578215	7578215	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	58	604	0	ENST00000269305.4:c.634T>G	p.Phe212Val	p.F212V	ENST00000269305	NM_001126112.2	212	Ttt/Gtt	6/11	1	2	FACETS	0.734	0.629	0.849	0.734	0.629	0.849	SUBCLONAL	1	TRUE	1	0.18	2		604	878	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842468	68842468	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1555515232	NA	P-0044060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	56	510	0	ENST00000261769.5:c.529C>T	p.Gln177Ter	p.Q177*	ENST00000261769	NM_004360.3	177	Cag/Tag	4/16	0.3	1	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	0	0.18	1		510	553	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27172700	27172700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	68	554	0	ENST00000380036.4:c.715G>A	p.Glu239Lys	p.E239K	ENST00000380036	NM_000459.3	239	Gaa/Aaa	5/23	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.18	2		554	731	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965421	18965421	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	51	345	0	ENST00000262803.5:c.1168G>C	p.Glu390Gln	p.E390Q	ENST00000262803	NM_002911.3	390	Gag/Cag	9/24	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.18	2		345	473	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406235	70406235	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	58	537	0	ENST00000373644.4:c.3749C>T	p.Ser1250Leu	p.S1250L	ENST00000373644	NM_030625.2	1250	tCa/tTa	4/12	NA	2	FACETS	0.923	0.792	1			1	INDETERMINATE	1	TRUE	NA	0.18	2		537	698	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406543	70406543	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	63	632	0	ENST00000373644.4:c.4057C>G	p.Leu1353Val	p.L1353V	ENST00000373644	NM_030625.2	1353	Ctc/Gtc	4/12	NA	2	FACETS	0.8	0.69	0.92			1	INDETERMINATE	1	TRUE	NA	0.18	2		632	875	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307583	118307583	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	49	445	0	ENST00000534358.1:c.356C>A	p.Ser119Ter	p.S119*	ENST00000534358	NM_005933.3	119	tCg/tAg	1/36	1	2	FACETS	0.853	0.722	0.999	0.853	0.722	0.999	CLONAL	1	TRUE	1	0.18	2		445	638	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784613	43784613	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	52	466	0	ENST00000382044.4:c.61G>C	p.Asp21His	p.D21H	ENST00000382044	NM_001141980.1	21	Gat/Cat	2/28	0.3	1	FACETS	0.875	0.744	1	0.875	0.744	1	CLONAL	1	TRUE	0	0.18	1		466	601	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842376	68842376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	52	552	0	ENST00000261769.5:c.437C>T	p.Ser146Phe	p.S146F	ENST00000261769	NM_004360.3	146	tCt/tTt	4/16	0.3	1	FACETS	0.872	0.742	1	0.872	0.742	1	CLONAL	1	TRUE	0	0.18	1		552	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576872	7576872	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	114	607	0	ENST00000269305.4:c.974G>C	p.Gly325Ala	p.G325A	ENST00000269305	NM_001126112.2	325	gGa/gCa	9/11	1	2	FACETS	0.788	0.709	0.871	1	0.985	1	SUBCLONAL	2	TRUE	1	0.18	2		607	804	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761243	59761243	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	46	581	1	ENST00000259008.2:c.3164C>A	p.Ser1055Tyr	p.S1055Y	ENST00000259008	NM_032043.2	1055	tCc/tAc	20/20	1	2	FACETS	0.688	0.578	0.81	0.688	0.578	0.81	SUBCLONAL	1	TRUE	1	0.18	2		582	743	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56377272	56377272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779297336	NA	P-0044060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	18	250	0	ENST00000348428.3:c.893G>A	p.Ser298Asn	p.S298N	ENST00000348428	NM_006785.3	298	aGt/aAt	6/17	0.153290020079008	3	FACETS	0.634	0.476	0.82	0.317	0.238	0.41	SUBCLONAL	1	TRUE	1	0.18	3		250	344	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965026	25965026	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	45	494	0	ENST00000435504.4:c.4180G>C	p.Glu1394Gln	p.E1394Q	ENST00000435504		1394	Gag/Cag	13/13	1	2	FACETS	0.826	0.694	0.974	0.826	0.694	0.974	CLONAL	1	TRUE	1	0.18	2		494	605	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966179	25966179	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	66	579	0	ENST00000435504.4:c.3027G>C	p.Glu1009Asp	p.E1009D	ENST00000435504		1009	gaG/gaC	13/13	1	2	FACETS	0.888	0.769	1	0.888	0.769	1	CLONAL	1	TRUE	1	0.18	2		579	826	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72897392	72897392	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	56	467	0	ENST00000325599.8:c.100G>C	p.Glu34Gln	p.E34Q	ENST00000325599	NM_018130.2	34	Gag/Cag	1/11	1	2	FACETS	0.809	0.692	0.938	0.809	0.692	0.938	CLONAL	1	TRUE	1	0.18	2		467	769	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510036	187510036	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	37	419	0	ENST00000441802.2:c.13477T>A	p.Phe4493Ile	p.F4493I	ENST00000441802	NM_005245.3	4493	Ttt/Att	27/27	1	2	FACETS	0.78	0.642	0.935	0.78	0.642	0.935	CLONAL	1	TRUE	1	0.18	2		419	527	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293529	137293529	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	77	781	0	ENST00000481739.1:c.80C>G	p.Ser27Cys	p.S27C	ENST00000481739	NM_002957.4	27	tCc/tGc	2/10	1	2	FACETS	0.825	0.722	0.936	0.825	0.722	0.936	CLONAL	1	TRUE	1	0.18	2		781	1037	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390822	139390822	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	74	679	0	ENST00000277541.6:c.7369C>A	p.Leu2457Met	p.L2457M	ENST00000277541	NM_017617.3	2457	Ctg/Atg	34/34	1	2	FACETS	0.908	0.793	1	0.908	0.793	1	CLONAL	1	TRUE	1	0.18	2		679	906	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402705	139402705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	62	671	1	ENST00000277541.6:c.3304G>A	p.Glu1102Lys	p.E1102K	ENST00000277541	NM_017617.3	1102	Gag/Aag	20/34	1	2	FACETS	0.771	0.665	0.888	0.771	0.665	0.888	SUBCLONAL	1	TRUE	1	0.18	2		672	893	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76953113	76953113	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	30	214	0	ENST00000373344.5:c.200C>G	p.Ser67Cys	p.S67C	ENST00000373344	NM_000489.3	67	tCt/tGt	4/35	0.291475784018931	2	FACETS	1	0.922	1			1	CLONAL	1	TRUE	NA	0.18	2		214	256	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860626	3860630	+	stop_gained	Nonsense_Mutation	ONP	GAAGT	GAAGT	TAAGG	novel	NA	P-0044060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	65	620	1	ENST00000262367.5:c.949_953delinsCCTTA	p.Thr317_Ser318delinsProTer	p.T317_S318delinsP*	ENST00000262367	NM_004380.2	317	ACTTCa/CCTTAa	3/31	0.3	2	FACETS	0.884	0.765	1	0.442	0.382	0.507	CLONAL	1	TRUE	0	0.18	2		621	817	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0044131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	501	708	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.338802221388723	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	0	0.338802221388723	3		708	1126	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042536	42042536	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	210	558	0	ENST00000219905.7:c.6731G>A	p.Trp2244Ter	p.W2244*	ENST00000219905	NM_001164273.1	2244	tGg/tAg	17/24	0.338802221388723	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.338802221388723	3		558	703	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	306	541	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.808328878559454	2		541	636	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032356	10032356	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763500409	NA	P-0044136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	132	615	0	ENST00000330684.3:c.467C>T	p.Thr156Met	p.T156M	ENST00000330684	NM_001134407.1	156	aCg/aTg	3/13	0.410464693334405	2	FACETS	0.461	0.419	0.505	0.231	0.209	0.253	INDETERMINATE	1	TRUE	0	0.808328878559454	2		615	708	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699372	47699372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	884	476	0	ENST00000347630.2:c.136G>A	p.Glu46Lys	p.E46K	ENST00000347630	NM_001007230.1	46	Gag/Aag	4/11	0.808328878559454	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.808328878559454	3		476	1020	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982416	201982417	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	564	987	0	ENST00000359651.3:c.796dup	p.Ser266LysfsTer35	p.S266Kfs*35	ENST00000359651		265	-/A	6/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.808328878559454	2		987	1345	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589607	67589607	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	212	272	0	ENST00000274335.5:c.1370A>C	p.Gln457Pro	p.Q457P	ENST00000274335		457	cAa/cCa	10/15	1	2	FACETS	0.95	0.89	1	0.95	0.89	1	CLONAL	1	TRUE	1	0.808328878559454	2		272	552	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259308	89259308	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	111	473	0	ENST00000336596.2:c.452del	p.Ser151IlefsTer12	p.S151Ifs*12	ENST00000336596	NM_005233.5	151	aGt/at	3/17	0.416826232139258	1	FACETS	0.431	0.39	0.472	0.431	0.39	0.472	INDETERMINATE	1	TRUE	0	0.808328878559454	1		473	380	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295266	1295266	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0044136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	350	451	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.808328878559454	2		452	754	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	366	415	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.363690642369214	6	FACETS	1	0.974	1			1	CLONAL	5	TRUE	NA	0.363690642369214	6		415	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0044137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	201	327	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.343253247072436	2	FACETS	0.923	0.86	0.986	0.923	0.86	0.986	CLONAL	2	TRUE	0	0.363690642369214	2		327	599	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248357	212248357	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879163362	NA	P-0044137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	26	245	0	ENST00000342788.4:c.3910C>T	p.Arg1304Trp	p.R1304W	ENST00000342788	NM_005235.2	1304	Cgg/Tgg	28/28	0.326580914184065	4	FACETS	0.863	0.687	1	0.431	0.343	0.531	CLONAL	1	TRUE	2	0.363690642369214	4		245	226	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112455	115112455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	102	779	0	ENST00000257566.3:c.1285G>A	p.Asp429Asn	p.D429N	ENST00000257566	NM_016569.3	429	Gac/Aac	7/8	0.363690642369214	3	FACETS	1	0.949	1	0.549	0.492	0.609	CLONAL	1	TRUE	1	0.363690642369214	3		779	604	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190850	185190851	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0044137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	203	791	1	ENST00000265026.3:c.1731_1732del	p.Ser578Ter	p.S578*	ENST00000265026	NM_004721.4	577	acTTct/acct	11/14	0.354431732502013	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.363690642369214	3		792	632	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974739	21974753	+	inframe_deletion	In_Frame_Del	DEL	CCCGCACCTCCTCTA	CCCGCACCTCCTCTA	-	novel	NA	P-0044137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	86	398	0	ENST00000304494.5:c.74_88del	p.Val25_Arg29del	p.V25_R29del	ENST00000304494	NM_000077.4	25	gTAGAGGAGGTGCGGGcg/gcg	1/3	0.363690642369214	2	FACETS	0.886	0.794	0.98	0.886	0.794	0.98	CLONAL	2	TRUE	0	0.363690642369214	2		398	267	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932833	36932833	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs756056579	NA	P-0044146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	203	740	1	ENST00000361632.4:c.2038G>A	p.Glu680Lys	p.E680K	ENST00000361632		680	Gag/Aag	15/16	1	2	FACETS	0.672	0.623	0.723	0.672	0.623	0.723	SUBCLONAL	1	TRUE	1	0.585469732438767	2		741	1032	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937115	36937115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	304	735	0	ENST00000361632.4:c.1204G>A	p.Glu402Lys	p.E402K	ENST00000361632		402	Gaa/Aaa	9/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.585469732438767	2		735	982	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864514	57864514	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	273	782	0	ENST00000228682.2:c.1991A>T	p.His664Leu	p.H664L	ENST00000228682	NM_005269.2	664	cAt/cTt	12/12	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.585469732438767	2		782	912	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782082	NA	P-0044146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	266	571	0	ENST00000269305.4:c.745A>T	p.Arg249Trp	p.R249W	ENST00000269305	NM_001126112.2	249	Agg/Tgg	7/11	0.585469732438767	1	FACETS	0.929	0.876	0.982	0.929	0.876	0.982	CLONAL	1	TRUE	0	0.585469732438767	1		571	692	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750764	39750764	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	249	644	0	ENST00000361337.2:c.2164A>C	p.Asn722His	p.N722H	ENST00000361337	NM_003286.2	722	Aat/Cat	20/21	0.381852318537532	1	FACETS	0.715	0.671	0.761	0.715	0.671	0.761	SUBCLONAL	1	TRUE	0	0.585469732438767	1		644	841	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056437	26056437	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	16	295	0	ENST00000343677.2:c.220G>C	p.Glu74Gln	p.E74Q	ENST00000343677	NM_005319.3	74	Gag/Cag	1/1	0.427365940774213	4	FACETS	0.308	0.227	0.404	0.154	0.113	0.202	SUBCLONAL	1	TRUE	2	0.533803972374441	4		295	299	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713544	30713546	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0044188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	141	547	0	ENST00000295754.5:c.871_873del	p.Lys291del	p.K291del	ENST00000295754	NM_003242.5	290	gAGAag/gag	4/7	1	2	FACETS	0.952	0.871	1	0.952	0.871	1	CLONAL	1	TRUE	1	0.496938144114749	2		547	596	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0044188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	476	815	1	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.496938144114749	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.496938144114749	2		816	937	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101030	4101030	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730880511	NA	P-0044188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	355	696	0	ENST00000262948.5:c.692G>T	p.Arg231Leu	p.R231L	ENST00000262948	NM_030662.3	231	cGc/cTc	6/11	0.496938144114749	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.496938144114749	2		696	695	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987147	69987147	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760770591	NA	P-0044188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	143	524	1	ENST00000394351.3:c.208G>A	p.Ala70Thr	p.A70T	ENST00000394351	NM_000248.3	70	Gca/Aca	2/9	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.496938144114749	2		525	574	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266054	41266649	+	splice_donor_variant,splice_acceptor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	CAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCAAGATGATGCAGAACTTGC	CAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCAAGATGATGCAGAACTTGC	-	novel	NA	P-0044188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	78	336	0	ENST00000349496.5:c.53_448del		p.X18_splice	ENST00000349496	NM_001904.3	18	gaCAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCAAGATGATGCAGAACTTGCc/gac	3-4/15	1	2	FACETS	0.842	0.744	0.945	0.842	0.744	0.945	CLONAL	1	TRUE	1	0.496938144114749	2		336	373	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937850	76937850	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs138256318	NA	P-0044188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	112	333	0	ENST00000373344.5:c.2898G>T	p.Glu966Asp	p.E966D	ENST00000373344	NM_000489.3	966	gaG/gaT	9/35	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.496938144114749	1		333	226	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981563	201981565	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TGG	TGG	-	rs995289305	NA	P-0044188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	268	1023	2	ENST00000359651.3:c.478+1_478+3del		p.X160_splice	ENST00000359651		160		3/8	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.496938144114749	2		1025	1050	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981243	201981245	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0044188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	306	999	0	ENST00000359651.3:c.325_327del	p.Glu109del	p.E109del	ENST00000359651		108	GAG/-	2/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.496938144114749	2		999	1136	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446440	49446441	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0044188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	196	725	1	ENST00000301067.7:c.1164_1165del	p.Tyr389ArgfsTer26	p.Y389Rfs*26	ENST00000301067	NM_003482.3	388	ctGTac/ctac	9/54	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.496938144114749	2		726	769	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001946	29001946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	99	433	0	ENST00000282397.4:c.1219C>A	p.Leu407Met	p.L407M	ENST00000282397	NM_002019.4	407	Ctg/Atg	9/30	1	2	FACETS	0.908	0.815	1	0.908	0.815	1	CLONAL	1	TRUE	1	0.496938144114749	2		433	439	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663412	67663415	+	frameshift_variant	Frame_Shift_Del	DEL	AAGA	AAGA	-	novel	NA	P-0044188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	68	353	0	ENST00000264010.4:c.1818_1821del	p.Glu607IlefsTer23	p.E607Ifs*23	ENST00000264010	NM_006565.3	605	AAGAaa/aa	10/12	1	2	FACETS	0.791	0.693	0.896	0.791	0.693	0.896	SUBCLONAL	1	TRUE	1	0.496938144114749	2		353	346	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117719	70117720	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0044188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	569	1009	0	ENST00000245479.2:c.190_191del	p.Ser64ArgfsTer187	p.S64Rfs*187	ENST00000245479	NM_000346.3	63	GAg/g	1/3	0.496938144114749	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.496938144114749	2		1009	1050	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117564	4117566	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0044188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	83	651	0	ENST00000262948.5:c.154_156del	p.Lys52del	p.K52del	ENST00000262948	NM_030662.3	52	AAG/-	2/11	0.496938144114749	2	FACETS	0.879	0.781	0.983	0.44	0.39	0.492	CLONAL	1	TRUE	0	0.496938144114749	2		651	380	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144001	11144003	+	inframe_deletion	In_Frame_Del	DEL	GCA	GCA	-	novel	NA	P-0044188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	173	671	0	ENST00000358026.2:c.3586_3588del	p.Gln1196del	p.Q1196del	ENST00000358026	NM_001128849.1	1194	ggGCAg/ggg	26/36	NA	5	FACETS	1	0.96	1			1	INDETERMINATE	2	TRUE	NA	0.496938144114749	5		671	575	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295182	1295183	+	upstream_gene_variant	5'Flank	INS	-	-	GGGCGGGGCCGCGGAAAGGAAG	novel	NA	P-0044188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	41	295	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.444	0.37	0.525	0.444	0.37	0.525	SUBCLONAL	1	TRUE	1	0.496938144114749	2		295	372	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508527	106508527	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	100	377	0	ENST00000359195.3:c.521A>T	p.Glu174Val	p.E174V	ENST00000359195	NM_002649.2	174	gAg/gTg	2/11	1	2	FACETS	0.898	0.807	0.994	0.898	0.807	0.994	CLONAL	1	TRUE	1	0.496938144114749	2		377	448	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391370	139391371	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0044188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	278	1004	0	ENST00000277541.6:c.6820_6821del	p.Ser2274ProfsTer79	p.S2274Pfs*79	ENST00000277541	NM_017617.3	2274	TCc/c	34/34	1	2	FACETS	0.966	0.907	1	0.966	0.907	1	CLONAL	1	TRUE	1	0.496938144114749	2		1004	1158	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0044211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	188	368	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.440689710350375	2		368	586	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0044211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	44	335	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.340821761767643	1	FACETS	0.32	0.268	0.377	0.32	0.268	0.377	SUBCLONAL	1	TRUE	0	0.440689710350375	1		335	487	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729163	66729163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516792	NA	P-0044211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	303	613	0	ENST00000307102.5:c.371C>T	p.Pro124Leu	p.P124L	ENST00000307102	NM_002755.3	124	cCg/cTg	3/11	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.440689710350375	2		613	988	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858184	9858184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	237	506	0	ENST00000330684.3:c.3217G>A	p.Glu1073Lys	p.E1073K	ENST00000330684	NM_001134407.1	1073	Gaa/Aaa	13/13	1	2	FACETS	0.761	0.713	0.809	1	0.993	1	SUBCLONAL	2	TRUE	1	0.440689710350375	2		506	707	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0044211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	219	343	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.82	0.768	0.873	1	0.993	1	CLONAL	2	TRUE	1	0.440689710350375	2		344	606	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262827	46262827	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	220	451	1	ENST00000371998.3:c.1000C>T	p.Arg334Ter	p.R334*	ENST00000371998		334	Cga/Tga	10/23	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.440689710350375	2		452	725	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337254	89337255	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0044211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	339	600	0	ENST00000301030.4:c.7776_7777delinsAA	p.Asp2593Asn	p.D2593N	ENST00000301030	NM_001256183.1	2592	caGGac/caAAac	12/13	1	2	FACETS	0.756	0.716	0.796	1	0.995	1	SUBCLONAL	2	TRUE	1	0.440689710350375	2		600	1018	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2202766	2202766	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	391	551	0	ENST00000398665.3:c.775A>T	p.Asn259Tyr	p.N259Y	ENST00000398665	NM_032482.2	259	Aac/Tac	9/28	1	2	FACETS	0.822	0.782	0.861	1	0.996	1	CLONAL	2	TRUE	1	0.440689710350375	2		551	1080	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21553836	21553836	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	140	540	0	ENST00000382592.4:c.2766G>C	p.Gln922His	p.Q922H	ENST00000382592	NM_014572.2	922	caG/caC	7/8	1	2	FACETS	0.843	0.769	0.921	0.843	0.769	0.921	CLONAL	1	TRUE	1	0.448871052558988	2		540	740	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0044257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	45	418	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.86	0.729	1	0.86	0.729	1	CLONAL	1	TRUE	1	0.430523249339878	2		418	243	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678727	52678727	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	46	425	1	ENST00000394830.3:c.892C>T	p.Arg298Ter	p.R298*	ENST00000394830	NM_018313.4	298	Cga/Tga	9/30	0.430523249339878	1	FACETS	0.584	0.495	0.682	0.584	0.495	0.682	SUBCLONAL	1	TRUE	0	0.430523249339878	1		426	287	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183771	10183771	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	107	638	0	ENST00000256474.2:c.240T>A	p.Ser80Arg	p.S80R	ENST00000256474	NM_000551.3	80	agT/agA	1/3	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.430523249339878	NA		638	396	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433514	49433514	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	147	834	0	ENST00000301067.7:c.8039A>G	p.Gln2680Arg	p.Q2680R	ENST00000301067	NM_003482.3	2680	cAa/cGa	31/54	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.430523249339878	2		834	633	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493513	56493513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376939275	NA	P-0044257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	60	457	0	ENST00000267101.3:c.2921G>A	p.Arg974Gln	p.R974Q	ENST00000267101	NM_001982.3	974	cGg/cAg	24/28	1	2	FACETS	0.749	0.648	0.858	0.749	0.648	0.858	SUBCLONAL	1	TRUE	1	0.430523249339878	2		457	372	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118639	11118639	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	133	710	0	ENST00000358026.2:c.2063A>C	p.Lys688Thr	p.K688T	ENST00000358026	NM_001128849.1	688	aAg/aCg	14/36	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.430523249339878	2		710	600	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721149	61721149	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	63	528	0	ENST00000401558.2:c.1125T>A	p.His375Gln	p.H375Q	ENST00000401558	NM_003400.3	375	caT/caA	12/25	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.430523249339878	2		528	284	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163640	47163640	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	29	333	0	ENST00000409792.3:c.2486del	p.Leu829TrpfsTer13	p.L829Wfs*13	ENST00000409792	NM_014159.6	829	tTg/tg	3/21	0.430523249339878	1	FACETS	0.846	0.691	1	0.846	0.691	1	CLONAL	1	TRUE	0	0.430523249339878	1		333	125	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956167	55956167	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	89	494	0	ENST00000263923.4:c.3148G>C	p.Ala1050Pro	p.A1050P	ENST00000263923	NM_002253.2	1050	Gcc/Ccc	23/30	1	2	FACETS	0.973	0.867	1	0.973	0.867	1	CLONAL	1	TRUE	1	0.430523249339878	2		494	425	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271202	153271202	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	29	250	0	ENST00000281708.4:c.576del	p.Glu192AspfsTer47	p.E192Dfs*47	ENST00000281708	NM_033632.3	192	gaA/ga	3/12	1	2	FACETS	0.869	0.706	1	0.869	0.706	1	CLONAL	1	TRUE	1	0.430523249339878	2		250	155	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223867	53223868	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0044257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	182	470	0	ENST00000375401.3:c.3491_3492del	p.Leu1164ProfsTer39	p.L1164Pfs*39	ENST00000375401	NM_004187.3	1164	cTG/c	23/26	1	1	FACETS	0.773	0.722	0.825	1	0.992	1	SUBCLONAL	2	TRUE	0	0.430523249339878	1		470	429	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	58	540	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.856	0.735	0.987	0.856	0.735	0.987	CLONAL	1	TRUE	1	0.239942501748275	2		540	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0044259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	82	956	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.239942501748275	1	FACETS	0.758	0.667	0.855	0.758	0.667	0.855	SUBCLONAL	1	TRUE	0	0.239942501748275	1		956	794	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0044259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	63	280	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.239942501748275	1	FACETS	0.867	0.751	0.993	0.867	0.751	0.993	CLONAL	1	TRUE	0	0.239942501748275	1		280	533	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054525	42054525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	54	355	0	ENST00000219905.7:c.7709C>T	p.Pro2570Leu	p.P2570L	ENST00000219905	NM_001164273.1	2570	cCt/cTt	22/24	1	2	FACETS	0.716	0.611	0.831	0.716	0.611	0.831	SUBCLONAL	1	TRUE	1	0.239942501748275	2		355	629	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782067	9782070	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	novel	NA	P-0044291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	190	648	0	ENST00000377346.4:c.2090_2093del	p.Asp697AlafsTer4	p.D697Afs*4	ENST00000377346	NM_005026.3	697	gACTTc/gc	17/24	0.299114503804849	2	FACETS	0.844	0.782	0.907	0.844	0.782	0.907	CLONAL	2	TRUE	0	0.299114503804849	2		648	753	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593616	+	protein_altering_variant	In_Frame_Del	DEL	AGTGGAAGGTTGTTGA	AGTGGAAGGTTGTTGA	C	novel	NA	P-0044291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	98	326	0	ENST00000288135.5:c.1667_1682delinsC	p.Gln556_Glu561delinsPro	p.Q556_E561delinsP	ENST00000288135	NM_000222.2	556	cAGTGGAAGGTTGTTGAg/cCg	11/21	0.299114503804849	2	FACETS	0.972	0.876	1	0.972	0.876	1	CLONAL	2	TRUE	0	0.299114503804849	2		326	337	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620566	52620566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746373271	NA	P-0044295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	178	376	0	ENST00000394830.3:c.3187C>T	p.Arg1063Trp	p.R1063W	ENST00000394830	NM_018313.4	1063	Cgg/Tgg	21/30	0.639157127520992	1	FACETS	0.938	0.876	1	0.938	0.876	1	CLONAL	1	TRUE	0	0.639157127520992	1		376	404	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0044304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	180	621	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.283256913612909	5	FACETS	1	0.966	1			1	CLONAL	2	TRUE	NA	0.283256913612909	5		621	838	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0044304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	242	568	0	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.283256913612909	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.283256913612909	2		568	717	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061184	38061184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778808721	NA	P-0044304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	147	366	0	ENST00000250448.2:c.805G>A	p.Glu269Lys	p.E269K	ENST00000250448	NM_004496.3	269	Gag/Aag	2/2	0.252758527742691	5	FACETS	1	0.978	1	0.799	0.732	0.868	CLONAL	2	TRUE	2	0.283256913612909	5		366	617	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772211	68772211	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786203576	NA	P-0044304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	240	615	0	ENST00000261769.5:c.60G>A	p.Trp20Ter	p.W20*	ENST00000261769	NM_004360.3	20	tgG/tgA	2/16	0.283256913612909	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.283256913612909	2		615	782	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849095	156849095	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	132	748	0	ENST00000524377.1:c.1987G>T	p.Val663Leu	p.V663L	ENST00000524377	NM_002529.3	663	Gtg/Ttg	15/17	0.283256913612909	4	FACETS	1	0.906	1	0.333	0.302	0.367	CLONAL	1	TRUE	1	0.283256913612909	4		748	1196	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061663	38061663	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	128	284	0	ENST00000250448.2:c.326G>C	p.Ser109Thr	p.S109T	ENST00000250448	NM_004496.3	109	aGc/aCc	2/2	0.252758527742691	5	FACETS	0.885	0.807	0.966	0.885	0.807	0.966	CLONAL	3	TRUE	2	0.283256913612909	5		284	485	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47596666	47596666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	45	258	0	ENST00000263735.4:c.22G>A	p.Ala8Thr	p.A8T	ENST00000263735	NM_002354.2	8	Gcg/Acg	1/9	1	2	FACETS	0.957	0.808	1	0.957	0.808	1	CLONAL	1	TRUE	1	0.283256913612909	2		258	332	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0044318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	148	513	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.726467677243731	2		513	385	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030314	180030314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777755208	NA	P-0044318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	374	692	1	ENST00000261937.6:c.3970C>T	p.Arg1324Trp	p.R1324W	ENST00000261937	NM_182925.4	1324	Cgg/Tgg	30/30	0.695893761963874	4	FACETS	1	0.985	1	0.535	0.51	0.559	CLONAL	2	TRUE	0	0.726467677243731	4		693	831	SUCCESS
APC	324	MSKCC	GRCh37	5	112175417	112175418	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	rs1554085533	NA	P-0044318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	118	292	0	ENST00000257430.4:c.4127_4128del	p.Tyr1376CysfsTer9	p.Y1376Cfs*9	ENST00000257430	NM_000038.5	1376	TAt/t	16/16	0.726467677243731	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.726467677243731	2		292	148	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508557	106508557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	121	332	0	ENST00000359195.3:c.551G>A	p.Arg184His	p.R184H	ENST00000359195	NM_002649.2	184	cGc/cAc	2/11	0.618311018704335	4	FACETS	0.861	0.788	0.936	0.861	0.788	0.936	CLONAL	2	TRUE	2	0.726467677243731	4		332	334	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939512	71939512	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	206	795	0	ENST00000298229.2:c.367C>G	p.Pro123Ala	p.P123A	ENST00000298229	NM_001567.3	123	Ccg/Gcg	3/28	0.618311018704335	4	FACETS	0.833	0.772	0.897	0.417	0.386	0.449	CLONAL	1	TRUE	2	0.726467677243731	4		795	1175	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444238	49444238	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	414	906	0	ENST00000301067.7:c.3133C>T	p.Pro1045Ser	p.P1045S	ENST00000301067	NM_003482.3	1045	Cct/Tct	11/54	0.726467677243731	4	FACETS	0.868	0.828	0.909	0.868	0.828	0.909	CLONAL	2	TRUE	2	0.726467677243731	4		906	1133	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260163	19260163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	195	704	0	ENST00000162023.5:c.130G>A	p.Ala44Thr	p.A44T	ENST00000162023		44	Gcc/Acc	7/13	0.662341437243743	3	FACETS	0.859	0.796	0.924	0.429	0.398	0.462	CLONAL	1	TRUE	1	0.726467677243731	3		704	852	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750520	41750520	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	220	513	0	ENST00000226382.2:c.108C>A	p.Cys36Ter	p.C36*	ENST00000226382	NM_003924.3	36	tgC/tgA	1/3	0.726467677243731	2	FACETS	0.971	0.927	1	0.971	0.927	1	CLONAL	2	TRUE	0	0.726467677243731	2		513	312	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206709	27206709	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	168	518	0	ENST00000380036.4:c.2494G>A	p.Glu832Lys	p.E832K	ENST00000380036	NM_000459.3	832	Gag/Aag	15/23	0.726467677243731	4	FACETS	0.921	0.847	0.998	0.307	0.282	0.333	CLONAL	1	TRUE	1	0.726467677243731	4		518	867	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390984	139390984	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	644	835	0	ENST00000277541.6:c.7207C>T	p.Gln2403Ter	p.Q2403*	ENST00000277541	NM_017617.3	2403	Cag/Tag	34/34	0.726467677243731	4	FACETS	0.943	0.915	0.971			1	CLONAL	3	TRUE	NA	0.726467677243731	4		835	1082	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0044330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	101	656	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.24246149236532	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.24246149236532	1		656	640	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101401	27101402	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0044330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	51	288	0	ENST00000324856.7:c.4689dup	p.Met1564HisfsTer8	p.M1564Hfs*8	ENST00000324856	NM_006015.4	1561	-/C	18/20	1	2	FACETS	0.871	0.741	1	0.871	0.741	1	CLONAL	1	TRUE	1	0.24246149236532	2		288	483	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293605	1293605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	138	557	1	ENST00000310581.5:c.1396C>T	p.Arg466Trp	p.R466W	ENST00000310581	NM_198253.2	466	Cgg/Tgg	2/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.24246149236532	2		558	817	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881620	37881620	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196082930	NA	P-0044330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	107	442	1	ENST00000269571.5:c.2690G>A	p.Arg897Gln	p.R897Q	ENST00000269571		897	cGg/cAg	22/27	0.24246149236532	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.24246149236532	1		443	719	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964504	93964504	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	28	276	0	ENST00000369303.4:c.2393T>A	p.Ile798Asn	p.I798N	ENST00000369303	NM_004440.3	798	aTt/aAt	14/17	1	2	FACETS	0.895	0.718	1	0.895	0.718	1	CLONAL	1	TRUE	1	0.24246149236532	2		276	258	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547303	106547303	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	55	311	0	ENST00000369096.4:c.540G>T	p.Met180Ile	p.M180I	ENST00000369096	NM_001198.3	180	atG/atT	4/7	1	2	FACETS	0.913	0.782	1	0.913	0.782	1	CLONAL	1	TRUE	1	0.24246149236532	2		311	497	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856013	111856013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	38	317	0	ENST00000341259.2:c.64G>A	p.Ala22Thr	p.A22T	ENST00000341259	NM_005475.2	22	Gcc/Acc	2/8	1	2	FACETS	0.495	0.408	0.593	0.495	0.408	0.593	SUBCLONAL	1	TRUE	1	0.24246149236532	2		317	633	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350203	15350203	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	107	506	4	ENST00000263377.2:c.3576G>T	p.Lys1192Asn	p.K1192N	ENST00000263377	NM_058243.2	1192	aaG/aaT	17/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.24246149236532	2		510	718	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266076	41266111	+	inframe_deletion	In_Frame_Del	DEL	TGGCAGCAACAGTCTTACCTGGACTCTGGAATCCAT	TGGCAGCAACAGTCTTACCTGGACTCTGGAATCCAT	-	novel	NA	P-0044330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	60	269	0	ENST00000349496.5:c.74_109del	p.Trp25_His36del	p.W25_H36del	ENST00000349496	NM_001904.3	25	TGGCAGCAACAGTCTTACCTGGACTCTGGAATCCAT/-	3/15	0.24246149236532	2	FACETS	1	0.969	1	0.739	0.64	0.844	CLONAL	1	TRUE	0	0.24246149236532	2		269	335	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	235	541	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.56475031273662	2		541	644	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0044395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	183	278	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.112955218323171	3	FACETS	0.76	0.706	0.815	0.76	0.706	0.815	INDETERMINATE	2	TRUE	1	0.56475031273662	3		278	547	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168682	32168682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs935064991	NA	P-0044395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	332	670	0	ENST00000375023.3:c.4241C>T	p.Ala1414Val	p.A1414V	ENST00000375023	NM_004557.3	1414	gCg/gTg	23/30	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.56475031273662	2		670	1062	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913409	NA	P-0044395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	32	293	0	ENST00000349496.5:c.134C>A	p.Ser45Tyr	p.S45Y	ENST00000349496	NM_001904.3	45	tCt/tAt	3/15	1	2	FACETS	0.21	0.17	0.256	0.21	0.17	0.256	SUBCLONAL	1	TRUE	1	0.56475031273662	2		293	539	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523088	25523088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758534627	NA	P-0044395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	111	514	0	ENST00000264709.3:c.97C>T	p.Arg33Cys	p.R33C	ENST00000264709	NM_175629.2	33	Cgt/Tgt	3/23	1	2	FACETS	0.439	0.394	0.487	0.439	0.394	0.487	SUBCLONAL	1	TRUE	1	0.56475031273662	2		514	895	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89828391	89828391	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1185836546	NA	P-0044395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	196	396	0	ENST00000389301.3:c.2818C>G	p.Gln940Glu	p.Q940E	ENST00000389301	NM_000135.2	940	Caa/Gaa	29/43	1	2	FACETS	0.986	0.916	1	0.986	0.916	1	CLONAL	1	TRUE	1	0.56475031273662	2		396	704	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435759	56435759	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	242	443	0	ENST00000407977.2:c.1378G>C	p.Asp460His	p.D460H	ENST00000407977		460	Gat/Cat	9/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.56475031273662	2		443	736	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110556	4110556	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs727504370	NA	P-0044395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	303	549	0	ENST00000262948.5:c.401A>G	p.Tyr134Cys	p.Y134C	ENST00000262948	NM_030662.3	134	tAc/tGc	3/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.56475031273662	2		549	977	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651426	52651426	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	168	395	0	ENST00000394830.3:c.1670A>T	p.Asp557Val	p.D557V	ENST00000394830	NM_018313.4	557	gAt/gTt	15/30	0.56475031273662	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.56475031273662	1		395	391	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481457	140481457	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	267	383	0	ENST00000288602.6:c.1351G>C	p.Glu451Gln	p.E451Q	ENST00000288602	NM_004333.4	451	Gag/Cag	11/18	0.112955218323171	3	FACETS	0.791	0.745	0.838	0.791	0.745	0.838	INDETERMINATE	2	TRUE	1	0.56475031273662	3		383	766	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371708	225371708	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	24	383	0	ENST00000264414.4:c.896T>G	p.Met299Arg	p.M299R	ENST00000264414	NM_003590.4	299	aTg/aGg	7/16	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		383	381	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073643	8073643	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	38	473	1	ENST00000377482.5:c.1016del	p.Pro339ArgfsTer113	p.P339Rfs*113	ENST00000377482	NM_018948.3	339	cCg/cg	4/4	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		474	623	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	193	466	2	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	0.927	0.881	0.971	1	0.995	1	CLONAL	4	TRUE	1	0.365329128016978	2		468	285	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	141	423	3	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	1	0.939	1	1	0.992	1	CLONAL	2	TRUE	1	0.365329128016978	2		426	378	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143994	11143994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	164	603	1	ENST00000358026.2:c.3575G>A	p.Arg1192His	p.R1192H	ENST00000358026	NM_001128849.1	1192	cGc/cAc	26/36	0.158426238499293	6	FACETS	1	0.982	1			1	INDETERMINATE	2	TRUE	NA	0.365329128016978	6		604	631	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442579	52442579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1312611941	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	172	376	1	ENST00000460680.1:c.166C>T	p.Arg56Cys	p.R56C	ENST00000460680	NM_004656.3	56	Cgc/Tgc	4/17	0.365329128016978	6	FACETS	0.904	0.836	0.974	0.678	0.627	0.731	CLONAL	3	TRUE	2	0.365329128016978	6		377	601	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216560	2216560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777525091	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	378	840	0	ENST00000398665.3:c.2204C>T	p.Thr735Met	p.T735M	ENST00000398665	NM_032482.2	735	aCg/aTg	20/28	0.114671234604183	5	FACETS	1	0.988	1			1	INDETERMINATE	4	TRUE	NA	0.365329128016978	5		840	736	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220476	123220476	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	254	251	0	ENST00000218089.9:c.3133C>T	p.Arg1045Ter	p.R1045*	ENST00000218089	NM_001042749.1	1045	Cga/Tga	30/35	0.254150987103847	2	FACETS	1	0.988	1			1	CLONAL	4	TRUE	NA	0.365329128016978	2		251	328	SUCCESS
APC	324	MSKCC	GRCh37	5	112154969	112154969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137854567	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	223	662	0	ENST00000257430.4:c.1240C>T	p.Arg414Cys	p.R414C	ENST00000257430	NM_000038.5	414	Cgc/Tgc	10/16	0.196010408480805	4	FACETS	0.886	0.83	0.943	1	0.99	1	INDETERMINATE	3	TRUE	2	0.365329128016978	4		662	627	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164914	106164914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771761785	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	144	365	1	ENST00000380013.4:c.3782G>A	p.Arg1261His	p.R1261H	ENST00000380013	NM_001127208.2	1261	cGc/cAc	6/11	0.196010408480805	4	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	2	TRUE	2	0.365329128016978	4		366	455	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	127	576	4	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	0.365329128016978	5	FACETS	1	0.942	1	0.522	0.476	0.571	CLONAL	2	TRUE	1	0.365329128016978	5		580	515	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746002	162746002	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1056323839	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	112	392	0	ENST00000367921.3:c.2125C>T	p.Arg709Ter	p.R709*	ENST00000367921	NM_006182.2	709	Cga/Tga	16/18	0.365329128016978	7	FACETS	1	0.916	1	0.339	0.305	0.374	CLONAL	2	TRUE	1	0.365329128016978	7		392	577	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242904	142242904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	172	503	0	ENST00000350721.4:c.4083G>T	p.Leu1361Phe	p.L1361F	ENST00000350721	NM_001184.3	1361	ttG/ttT	22/47	0.365329128016978	5	FACETS	1	0.957	1	0.702	0.648	0.758	CLONAL	2	TRUE	2	0.365329128016978	5		503	692	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200961	108200961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782310	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	110	349	0	ENST00000278616.4:c.7328G>A	p.Arg2443Gln	p.R2443Q	ENST00000278616	NM_000051.3	2443	cGa/cAa	50/63	0.0812692101112469	4	FACETS	0.849	0.772	0.927	1	0.979	1	INDETERMINATE	3	TRUE	2	0.365329128016978	4		349	323	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820836	36820836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1452017656	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	139	560	0	ENST00000373129.3:c.541G>A	p.Val181Met	p.V181M	ENST00000373129	NM_032017.1	181	Gtg/Atg	6/12	NA	2	FACETS	0.968	0.891	1			1	INDETERMINATE	2	TRUE	NA	0.365329128016978	2		560	393	SUCCESS
APC	324	MSKCC	GRCh37	5	112173495	112173495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147655929	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	105	314	0	ENST00000257430.4:c.2204C>T	p.Ala735Val	p.A735V	ENST00000257430	NM_000038.5	735	gCg/gTg	16/16	0.196010408480805	4	FACETS	0.912	0.829	0.996	1	0.982	1	INDETERMINATE	3	TRUE	2	0.365329128016978	4		314	287	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285059	15285059	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs367543285	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	234	696	0	ENST00000263388.2:c.4556T>C	p.Leu1519Pro	p.L1519P	ENST00000263388	NM_000435.2	1519	cTg/cCg	25/33	0.365329128016978	7	FACETS	0.998	0.933	1			1	CLONAL	3	TRUE	NA	0.365329128016978	7		696	819	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149973	202149973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1272714323	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	185	610	1	ENST00000358485.4:c.1414C>T	p.Arg472Ter	p.R472*	ENST00000358485	NM_001080125.1	472	Cga/Tga	8/9	0.118835250522437	4	FACETS	0.893	0.832	0.956	1	0.989	1	INDETERMINATE	3	TRUE	2	0.365329128016978	4		611	516	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041242	112041242	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	93	296	0	ENST00000368678.4:c.13C>T	p.Gln5Ter	p.Q5*	ENST00000368678		5	Caa/Taa	3/13	1	2	FACETS	0.798	0.717	0.882	1	0.984	1	SUBCLONAL	2	TRUE	1	0.365329128016978	2		296	319	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233024	55233024	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144943614	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	161	427	0	ENST00000275493.2:c.1774G>A	p.Val592Ile	p.V592I	ENST00000275493	NM_005228.3	592	Gtc/Atc	15/28	1	2	FACETS	0.964	0.893	1	1	0.992	1	CLONAL	2	TRUE	1	0.365329128016978	2		427	457	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955112	17955112	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755706305	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	162	747	11	ENST00000458235.1:c.115del	p.Gln39SerfsTer108	p.Q39Sfs*108	ENST00000458235	NM_000215.3	39	Cag/ag	2/24	0.365329128016978	1	FACETS	0.859	0.797	0.922	1	0.992	1	CLONAL	2	TRUE	0	0.365329128016978	1		758	422	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186757	108186757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs864622251	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	141	394	0	ENST00000278616.4:c.6115G>A	p.Glu2039Lys	p.E2039K	ENST00000278616	NM_000051.3	2039	Gaa/Aaa	42/63	0.0812692101112469	4	FACETS	1	0.981	1	1	0.981	1	INDETERMINATE	2	TRUE	2	0.365329128016978	4		394	431	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866710	37866710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258412021	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	492	716	3	ENST00000269571.5:c.877G>A	p.Ala293Thr	p.A293T	ENST00000269571		293	Gcc/Acc	7/27	0.365329128016978	5	FACETS	0.989	0.955	1	1	0.996	1	CLONAL	5	TRUE	1	0.365329128016978	5		719	843	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258595	19258595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377026490	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	166	789	0	ENST00000162023.5:c.305C>T	p.Pro102Leu	p.P102L	ENST00000162023		102	cCg/cTg	8/13	0.118150123892394	3	FACETS	0.982	0.908	1	0.982	0.908	1	INDETERMINATE	2	TRUE	1	0.365329128016978	3		789	547	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30303560	30303560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	12	60	0	ENST00000322652.5:c.844G>A	p.Ala282Thr	p.A282T	ENST00000322652	NM_015355.2	282	Gcc/Acc	8/16	0.365329128016978	5	FACETS	0.959	0.694	1	0.48	0.347	0.633	CLONAL	2	TRUE	1	0.365329128016978	5		60	53	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11019828	11019828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	222	588	0	ENST00000327064.4:c.503G>A	p.Arg168Gln	p.R168Q	ENST00000327064	NM_199141.1	168	cGg/cAg	4/16	0.158426238499293	6	FACETS	0.93	0.868	0.993			1	INDETERMINATE	3	TRUE	NA	0.365329128016978	6		588	754	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420670	49420670	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs797045659	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	384	663	0	ENST00000301067.7:c.15079C>T	p.Arg5027Ter	p.R5027*	ENST00000301067	NM_003482.3	5027	Cga/Tga	48/54	0.365329128016978	6	FACETS	0.989	0.947	1	1	0.994	1	CLONAL	5	TRUE	2	0.365329128016978	6		663	736	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928292	69928292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752026814	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	151	383	1	ENST00000352241.4:c.112G>A	p.Ala38Thr	p.A38T	ENST00000352241	NM_198159.2	38	Gcc/Acc	2/10	0.365329128016978	6	FACETS	1	0.967	1	0.554	0.508	0.601	CLONAL	2	TRUE	2	0.365329128016978	6		384	646	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622120	43622120	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	100	517	0	ENST00000355710.3:c.3142del	p.Leu1048SerfsTer61	p.L1048Sfs*61	ENST00000355710	NM_020975.4	1046	gCc/gc	19/20	0.217926592032728	1	FACETS	1	0.973	1	1	0.973	1	INDETERMINATE	1	TRUE	0	0.365329128016978	1		517	363	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416115	49416115	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs267607239	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	170	448	0	ENST00000301067.7:c.16360C>T	p.Arg5454Ter	p.R5454*	ENST00000301067	NM_003482.3	5454	Cga/Tga	52/54	0.365329128016978	6	FACETS	0.908	0.84	0.979	0.681	0.63	0.735	CLONAL	3	TRUE	2	0.365329128016978	6		448	591	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281179	15281179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1172987380	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	298	845	2	ENST00000263388.2:c.5077C>T	p.Arg1693Trp	p.R1693W	ENST00000263388	NM_000435.2	1693	Cgg/Tgg	27/33	0.365329128016978	7	FACETS	1	0.975	1			1	CLONAL	3	TRUE	NA	0.365329128016978	7		847	983	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455533	189455533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144315591	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	283	385	0	ENST00000264731.3:c.67G>A	p.Val23Ile	p.V23I	ENST00000264731	NM_003722.4	23	Gta/Ata	2/14	0.365329128016978	8	FACETS	1	0.979	1	1	0.979	1	CLONAL	6	TRUE	2	0.365329128016978	8		385	516	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521177	187521177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778434346	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	177	548	0	ENST00000441802.2:c.11978C>T	p.Pro3993Leu	p.P3993L	ENST00000441802	NM_005245.3	3993	cCc/cTc	22/27	0.196010408480805	4	FACETS	0.882	0.819	0.946	1	0.988	1	INDETERMINATE	3	TRUE	2	0.365329128016978	4		548	500	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526271	31526271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545917535	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	231	890	0	ENST00000344624.3:c.769G>A	p.Asp257Asn	p.D257N	ENST00000344624		257	Gac/Aac	2/33	0.118150123892394	3	FACETS	1	0.987	1	1	0.987	1	INDETERMINATE	2	TRUE	1	0.365329128016978	3		890	626	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873308	151873308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs549101307	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	90	292	1	ENST00000262189.6:c.9230G>A	p.Arg3077His	p.R3077H	ENST00000262189	NM_170606.2	3077	cGt/cAt	38/59	0.0812692101112469	4	FACETS	1	0.97	1	1	0.97	1	INDETERMINATE	2	TRUE	2	0.365329128016978	4		293	276	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59871074	59871074	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780227	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	57	264	0	ENST00000259008.2:c.1357G>A	p.Ala453Thr	p.A453T	ENST00000259008	NM_032043.2	453	Gct/Act	10/20	0.357848594771334	4	FACETS	0.772	0.668	0.883	0.515	0.445	0.589	SUBCLONAL	2	TRUE	1	0.365329128016978	4		264	276	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730876	40730876	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	100	730	0	ENST00000373198.4:c.3659G>T	p.Arg1220Leu	p.R1220L	ENST00000373198	NM_133170.3	1220	cGg/cTg	27/32	0.365329128016978	0	FACETS	1	0.955	1			1	CLONAL	1	TRUE	0	0.365329128016978	0		730	316	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100143	30100143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs191202207	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	182	646	0	ENST00000331968.5:c.1477G>A	p.Glu493Lys	p.E493K	ENST00000331968	NM_002742.2	493	Gaa/Aaa	10/18	0.0852555770919983	3	FACETS	1	0.955	1			1	INDETERMINATE	2	TRUE	NA	0.365329128016978	3		646	567	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7168037	7168037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866529817	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	119	588	1	ENST00000302850.5:c.1552C>T	p.Pro518Ser	p.P518S	ENST00000302850	NM_000208.2	518	Ccg/Tcg	7/22	0.200136469982366	3	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.365329128016978	3		589	587	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951138	48951138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771421892	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	76	340	0	ENST00000267163.4:c.1300G>A	p.Val434Met	p.V434M	ENST00000267163	NM_000321.2	434	Gtg/Atg	13/27	0.196010408480805	4	FACETS	1	0.887	1	1	0.887	1	INDETERMINATE	2	TRUE	2	0.365329128016978	4		340	284	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16248740	16248740	+	splice_region_variant,intron_variant	Splice_Region	DEL	A	A	-	novel	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	17	269	0	ENST00000375759.3:c.1750-2del		p.X584_splice	ENST00000375759	NM_015001.2	584			0.142499568815365	5	FACETS	0.55	0.41	0.715	0.183	0.136	0.239	INDETERMINATE	1	TRUE	2	0.365329128016978	5		269	262	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262663	16262663	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747459170	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	139	404	0	ENST00000375759.3:c.9928G>A	p.Asp3310Asn	p.D3310N	ENST00000375759	NM_015001.2	3310	Gac/Aac	11/15	0.142499568815365	5	FACETS	0.977	0.898	1	0.977	0.898	1	INDETERMINATE	3	TRUE	2	0.365329128016978	5		404	402	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65311209	65311209	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs117679986	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	110	404	0	ENST00000342505.4:c.2102C>T	p.Ala701Val	p.A701V	ENST00000342505	NM_002227.2	701	gCc/gTc	15/25	0.118835250522437	4	FACETS	1	0.971	1	1	0.971	1	INDETERMINATE	2	TRUE	2	0.365329128016978	4		404	349	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65312350	65312350	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	126	489	0	ENST00000342505.4:c.1969T>C	p.Cys657Arg	p.C657R	ENST00000342505	NM_002227.2	657	Tgt/Cgt	14/25	0.118835250522437	4	FACETS	1	0.953	1	1	0.953	1	INDETERMINATE	2	TRUE	2	0.365329128016978	4		489	441	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325882	65325882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1490560356	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	142	510	1	ENST00000342505.4:c.1240C>T	p.Arg414Trp	p.R414W	ENST00000342505	NM_002227.2	414	Cgg/Tgg	9/25	0.118835250522437	4	FACETS	1	0.976	1	1	0.976	1	INDETERMINATE	2	TRUE	2	0.365329128016978	4		511	457	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846355	156846355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775718859	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	497	687	2	ENST00000524377.1:c.1796G>A	p.Arg599His	p.R599H	ENST00000524377	NM_002529.3	599	cGc/cAc	14/17	0.365329128016978	7	FACETS	1	0.992	1	1	0.992	1	CLONAL	6	TRUE	1	0.365329128016978	7		689	802	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348808	118348808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1131691799	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	123	376	0	ENST00000534358.1:c.3461G>A	p.Arg1154Gln	p.R1154Q	ENST00000534358	NM_005933.3	1154	cGg/cAg	5/36	0.0812692101112469	4	FACETS	1	0.979	1	1	0.979	1	INDETERMINATE	2	TRUE	2	0.365329128016978	4		376	370	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719895	18719895	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	216	356	0	ENST00000266497.5:c.3792G>A	p.Trp1264Ter	p.W1264*	ENST00000266497		1264	tgG/tgA	27/31	0.35209814501851	4	FACETS	0.943	0.889	0.997	1	0.99	1	CLONAL	4	TRUE	1	0.365329128016978	4		356	428	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918750	32918750	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	66	213	0	ENST00000380152.3:c.6897T>A	p.Asn2299Lys	p.N2299K	ENST00000380152		2299	aaT/aaA	12/27	0.196010408480805	4	FACETS	1	0.949	1	1	0.949	1	INDETERMINATE	2	TRUE	2	0.365329128016978	4		213	215	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370284	40370284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	168	770	0	ENST00000293328.3:c.1054G>A	p.Val352Met	p.V352M	ENST00000293328	NM_012448.3	352	Gtg/Atg	9/19	0.357848594771334	4	FACETS	0.979	0.904	1	0.653	0.602	0.705	CLONAL	2	TRUE	1	0.365329128016978	4		770	641	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274331	5274331	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	114	615	0	ENST00000357368.4:c.116C>T	p.Pro39Leu	p.P39L	ENST00000357368	NM_002850.3	39	cCc/cTc	3/38	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.365329128016978	2		615	515	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250809	10250809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	183	746	3	ENST00000340748.4:c.3671C>T	p.Pro1224Leu	p.P1224L	ENST00000340748		1224	cCg/cTg	32/40	0.200136469982366	3	FACETS	0.923	0.855	0.992			1	INDETERMINATE	2	TRUE	NA	0.365329128016978	3		749	642	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11027439	11027439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	459	739	3	ENST00000327064.4:c.1006C>T	p.Arg336Trp	p.R336W	ENST00000327064	NM_199141.1	336	Cgg/Tgg	8/16	0.158426238499293	6	FACETS	1	0.98	1			1	INDETERMINATE	5	TRUE	NA	0.365329128016978	6		742	846	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141528	11141528	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	223	728	0	ENST00000358026.2:c.3505G>A	p.Asp1169Asn	p.D1169N	ENST00000358026	NM_001128849.1	1169	Gac/Aac	25/36	0.158426238499293	6	FACETS	0.985	0.921	1			1	INDETERMINATE	3	TRUE	NA	0.365329128016978	6		728	715	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302984	15302984	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs745367307	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	252	852	1	ENST00000263388.2:c.466C>T	p.Arg156Ter	p.R156*	ENST00000263388	NM_000435.2	156	Cga/Tga	4/33	0.365329128016978	7	FACETS	0.908	0.85	0.967			1	CLONAL	3	TRUE	NA	0.365329128016978	7		853	969	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030692	48030693	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	rs267608092	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	106	346	0	ENST00000234420.5:c.3311_3312del	p.Phe1104TrpfsTer3	p.F1104Wfs*3	ENST00000234420	NM_000179.2	1102	acTTtt/actt	5/10	0.118835250522437	4	FACETS	1	0.946	1	1	0.946	1	INDETERMINATE	2	TRUE	2	0.365329128016978	4		346	371	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436874	52436874	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	336	582	0	ENST00000460680.1:c.1904T>C	p.Leu635Pro	p.L635P	ENST00000460680	NM_004656.3	635	cTg/cCg	15/17	0.365329128016978	6	FACETS	1	0.967	1	1	0.994	1	CLONAL	5	TRUE	2	0.365329128016978	6		582	628	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539294	187539294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	96	400	0	ENST00000441802.2:c.8446G>A	p.Ala2816Thr	p.A2816T	ENST00000441802	NM_005245.3	2816	Gca/Aca	10/27	0.196010408480805	4	FACETS	1	0.932	1	1	0.932	1	INDETERMINATE	2	TRUE	2	0.365329128016978	4		400	343	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407587	407587	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	80	268	0	ENST00000380956.4:c.1345A>G	p.Ile449Val	p.I449V	ENST00000380956	NM_001195286.1	449	Att/Gtt	9/9	0.0852555770919983	3	FACETS	1	0.944	1			1	INDETERMINATE	2	TRUE	NA	0.365329128016978	3		268	238	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841838	151841838	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	100	309	0	ENST00000262189.6:c.14303A>G	p.Glu4768Gly	p.E4768G	ENST00000262189	NM_170606.2	4768	gAa/gGa	55/59	0.0812692101112469	4	FACETS	1	0.958	1	1	0.958	1	INDETERMINATE	2	TRUE	2	0.365329128016978	4		309	335	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942801	44942829	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCATGAACACAGTTCAACTATACATGA	GGGCATGAACACAGTTCAACTATACATGA	-	novel	NA	P-0044415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	185	294	0	ENST00000377967.4:c.3381_3409del	p.Gly1128SerfsTer13	p.G1128Sfs*13	ENST00000377967	NM_021140.2	1127	ttGGGCATGAACACAGTTCAACTATACATGAaa/ttaa	23/29	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.365329128016978	NA		294	250	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	33	541	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.779	0.632	0.945	0.779	0.632	0.945	CLONAL	1	TRUE	1	0.13	2		541	652	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667635	29667638	+	frameshift_variant	Frame_Shift_Del	DEL	TAGA	TAGA	-	novel	NA	P-0044443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	47	381	0	ENST00000356175.3:c.6974_6977del	p.Asp2325ValfsTer49	p.D2325Vfs*49	ENST00000356175	NM_000267.3	2324	tTAGAt/tt	46/57	1	2	FACETS	1	0.842	1	1	0.842	1	CLONAL	1	TRUE	1	0.13	2		381	723	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0044443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	76	394	0	ENST00000304494.5:c.151-1G>A		p.X51_splice	ENST00000304494	NM_000077.4	51			1	2	FACETS	0.879	0.771	0.995	1	0.98	1	CLONAL	2	TRUE	1	0.13	2		394	665	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547843	41547843	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	34	339	0	ENST00000263253.7:c.2824C>T	p.Gln942Ter	p.Q942*	ENST00000263253	NM_001429.3	942	Cag/Tag	15/31	1	2	FACETS	0.822	0.67	0.995	0.822	0.67	0.995	CLONAL	1	TRUE	1	0.13	2		339	636	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191427	185191427	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs183571847	NA	P-0044443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1228	75	747	1	ENST00000265026.3:c.2308G>A	p.Ala770Thr	p.A770T	ENST00000265026	NM_004721.4	770	Gcc/Acc	11/14	1	2	FACETS	0.886	0.773	1	0.886	0.773	1	CLONAL	1	TRUE	1	0.13	2		748	1303	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589588	67589620	+	inframe_deletion	In_Frame_Del	DEL	GAATATAACACTCAGTTTCAAGAAAAAAGTCGA	GAATATAACACTCAGTTTCAAGAAAAAAGTCGA	-	novel	NA	P-0044443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	18	254	0	ENST00000274335.5:c.1357_1389del	p.Asn453_Tyr463del	p.N453_Y463del	ENST00000274335		451	GAATATAACACTCAGTTTCAAGAAAAAAGTCGA/-	10/15	1	2	FACETS	0.789	0.593	1	0.789	0.593	1	CLONAL	1	TRUE	1	0.13	2		254	351	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562641	29562641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854562	NA	P-0044468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	95	388	0	ENST00000356175.3:c.3721C>T	p.Arg1241Ter	p.R1241*	ENST00000356175	NM_000267.3	1241	Cga/Tga	28/57	0.221720451817456	1	FACETS	0.723	0.645	0.806	0.723	0.645	0.806	SUBCLONAL	1	TRUE	0	0.367185025107387	1		388	584	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625252	69625252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782761826	NA	P-0044468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	290	977	0	ENST00000334134.2:c.541C>T	p.Arg181Cys	p.R181C	ENST00000334134	NM_005247.2	181	Cgc/Tgc	3/3	0.302698439598421	3	FACETS	0.977	0.921	1	0.977	0.921	1	CLONAL	2	TRUE	1	0.367185025107387	3		977	957	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681160	117681160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	79	237	0	ENST00000368508.3:c.3460C>T	p.Pro1154Ser	p.P1154S	ENST00000368508	NM_002944.2	1154	Cct/Tct	23/43	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.367185025107387	2		237	425	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164832	47164832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1017636782	NA	P-0044468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	62	358	0	ENST00000409792.3:c.1294C>T	p.Arg432Cys	p.R432C	ENST00000409792	NM_014159.6	432	Cgt/Tgt	3/21	1	2	FACETS	0.938	0.815	1	0.938	0.815	1	CLONAL	1	TRUE	1	0.367185025107387	2		358	360	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829806	76829806	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	129	224	1	ENST00000373344.5:c.6235C>T	p.Arg2079Ter	p.R2079*	ENST00000373344	NM_000489.3	2079	Cga/Tga	28/35	1	1	FACETS	0.79	0.725	0.857	1	0.988	1	SUBCLONAL	2	TRUE	0	0.367185025107387	1		225	363	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460582	149460582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	126	734	0	ENST00000286301.3:c.55G>A	p.Gly19Arg	p.G19R	ENST00000286301	NM_005211.3	19	Gga/Aga	3/22	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.367185025107387	2		734	680	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0044468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	297	1006	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	0.278117278867774	4	FACETS	0.818	0.769	0.869	0.818	0.769	0.869	CLONAL	2	TRUE	2	0.367185025107387	4		1006	1352	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109314067	109314067	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs557313505	NA	P-0044468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	95	234	0	ENST00000436639.2:c.1156C>T	p.Arg386Cys	p.R386C	ENST00000436639	NM_014454.2	386	Cgt/Tgt	7/10	1	2	FACETS	0.943	0.842	1	0.943	0.842	1	CLONAL	1	TRUE	1	0.367185025107387	2		234	549	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112910775	112910775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	96	295	0	ENST00000351677.2:c.784C>T	p.Leu262Phe	p.L262F	ENST00000351677	NM_002834.3	262	Ctc/Ttc	7/16	1	2	FACETS	0.972	0.869	1	0.972	0.869	1	CLONAL	1	TRUE	1	0.367185025107387	2		295	538	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420083	420083	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	129	558	0	ENST00000399788.2:c.3184C>T	p.Leu1062Phe	p.L1062F	ENST00000399788	NM_001042603.1	1062	Ctt/Ttt	21/28	1	2	FACETS	0.938	0.851	1	0.938	0.851	1	CLONAL	1	TRUE	1	0.367185025107387	2		558	749	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420188	420188	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	109	427	0	ENST00000399788.2:c.3079T>C	p.Ser1027Pro	p.S1027P	ENST00000399788	NM_001042603.1	1027	Tct/Cct	21/28	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.367185025107387	2		427	522	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906541	32906541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	75	114	0	ENST00000380152.3:c.926C>T	p.Ser309Leu	p.S309L	ENST00000380152		309	tCa/tTa	10/27	1	2	FACETS	0.966	0.85	1	0.966	0.85	1	CLONAL	1	TRUE	1	0.367185025107387	2		114	423	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10288034	10288034	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	39	511	0	ENST00000340748.4:c.455C>T	p.Ser152Leu	p.S152L	ENST00000340748		152	tCa/tTa	5/40	1	2	FACETS	0.301	0.248	0.36	0.301	0.248	0.36	SUBCLONAL	1	TRUE	1	0.367185025107387	2		511	706	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890269	72890269	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	114	446	0	ENST00000325599.8:c.413C>T	p.Ser138Leu	p.S138L	ENST00000325599	NM_018130.2	138	tCa/tTa	4/11	1	2	FACETS	0.815	0.734	0.901	0.815	0.734	0.901	CLONAL	1	TRUE	1	0.367185025107387	2		446	762	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456543	189456543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	108	492	0	ENST00000264731.3:c.304G>A	p.Asp102Asn	p.D102N	ENST00000264731	NM_003722.4	102	Gac/Aac	3/14	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.367185025107387	2		492	527	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955058	55955058	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761176323	NA	P-0044468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	100	531	0	ENST00000263923.4:c.3487C>T	p.Leu1163Phe	p.L1163F	ENST00000263923	NM_002253.2	1163	Ctc/Ttc	26/30	1	2	FACETS	0.886	0.793	0.984	0.886	0.793	0.984	CLONAL	1	TRUE	1	0.367185025107387	2		531	615	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112029201	112029202	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0044468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	88	421	0	ENST00000368678.4:c.366_367del	p.Arg123LeufsTer19	p.R123Lfs*19	ENST00000368678		122	gcCCgc/gcgc	5/13	1	2	FACETS	0.903	0.802	1	0.903	0.802	1	CLONAL	1	TRUE	1	0.367185025107387	2		421	531	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467742	50467742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	96	777	0	ENST00000331340.3:c.977C>T	p.Ser326Phe	p.S326F	ENST00000331340	NM_006060.4	326	tCc/tTc	8/8	1	2	FACETS	0.827	0.738	0.922	0.827	0.738	0.922	CLONAL	1	TRUE	1	0.367185025107387	2		777	632	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229315	55229400	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCTGGAGGGGTAGGAGGTTATTTCTTTAATCCCCTTGCGTTGATCAAAAATAAGGCTCCAGGTTGTTGTTATAGCTTTACAGGCA	TTCTGGAGGGGTAGGAGGTTATTTCTTTAATCCCCTTGCGTTGATCAAAAATAAGGCTCCAGGTTGTTGTTATAGCTTTACAGGCA	-	novel	NA	P-0044468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	86	620	0	ENST00000275493.2:c.1627_1631+81del		p.X543_splice	ENST00000275493	NM_005228.3	543		13/28	1	2	FACETS	0.748	0.662	0.84	0.748	0.662	0.84	SUBCLONAL	1	TRUE	1	0.367185025107387	2		620	626	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245057	53245057	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	113	436	0	ENST00000375401.3:c.883A>G	p.Lys295Glu	p.K295E	ENST00000375401	NM_004187.3	295	Aag/Gag	7/26	1	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.367185025107387	1		436	463	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0044472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	39	369	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.98	0.813	1	0.98	0.813	1	CLONAL	1	TRUE	1	0.2	2		369	398	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0044472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	42	597	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.2	2		597	308	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0044472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	26	280	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.751	0.595	0.93	0.751	0.595	0.93	CLONAL	1	TRUE	1	0.2	2		280	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0044472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	43	516	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	1	2	FACETS	0.609	0.508	0.721	0.609	0.508	0.721	SUBCLONAL	1	TRUE	1	0.2	2		516	706	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020768	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs926053251	NA	P-0044472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	67	507	1	ENST00000358127.4:c.77T>G	p.Val26Gly	p.V26G	ENST00000358127	NM_001280556.1	26	gTt/gGt	2/10	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.2	2		508	574	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555687605	NA	P-0044472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	13	259	0	ENST00000342988.3:c.1610A>G	p.Asp537Gly	p.D537G	ENST00000342988	NM_005359.5	537	gAc/gGc	12/12	1	2	FACETS	0.409	0.291	0.554	0.409	0.291	0.554	SUBCLONAL	1	TRUE	1	0.2	2		259	318	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0044472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	21	266	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	1	2	FACETS	0.592	0.455	0.751	0.592	0.455	0.751	SUBCLONAL	1	TRUE	1	0.2	2		266	355	SUCCESS
APC	324	MSKCC	GRCh37	5	112173912	112173912	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	18	276	0	ENST00000257430.4:c.2621C>A	p.Ser874Ter	p.S874*	ENST00000257430	NM_000038.5	874	tCa/tAa	16/16	1	2	FACETS	0.525	0.394	0.679	0.525	0.394	0.679	SUBCLONAL	1	TRUE	1	0.2	2		276	343	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938397	76938397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	10	582	0	ENST00000373344.5:c.2351C>T	p.Ser784Phe	p.S784F	ENST00000373344	NM_000489.3	784	tCt/tTt	9/35	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.747252629899848	NA		582	177	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578531	7578531	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	519	1077	0	ENST00000269305.4:c.399del	p.Met133IlefsTer37	p.M133Ifs*37	ENST00000269305	NM_001126112.2	133	atG/at	5/11	0.627381696634656	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.747252629899848	1		1077	818	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985492	2985492	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	250	539	0	ENST00000396946.4:c.319A>C	p.Thr107Pro	p.T107P	ENST00000396946	NM_032415.4	107	Act/Cct	4/25	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.747252629899848	NA		539	687	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871868	12871869	+	frameshift_variant	Frame_Shift_Ins	INS	AC	AC	CTTT	novel	NA	P-0044482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	153	291	0	ENST00000228872.4:c.585_586delinsCTTT	p.Arg195SerfsTer31	p.R195Sfs*31	ENST00000228872	NM_004064.3	195	agACgt/agCTTTgt	2/3	NA	2	FACETS	0.77	0.721	0.818			1	INDETERMINATE	2	TRUE	NA	0.747252629899848	2		291	266	SUCCESS
EED	8726	MSKCC	GRCh37	11	85963281	85963281	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	20	257	0	ENST00000263360.6:c.359G>C	p.Arg120Thr	p.R120T	ENST00000263360	NM_003797.3	120	aGa/aCa	3/12	1	2	FACETS	0.201	0.154	0.257	0.201	0.154	0.257	SUBCLONAL	1	TRUE	1	0.6	2		257	331	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	59	540	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.921	0.796	1	0.921	0.796	1	CLONAL	1	TRUE	1	0.340818561940584	2		540	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0044538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	179	327	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.340818561940584	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.340818561940584	1		327	717	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436149	56436149	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	54	597	0	ENST00000407977.2:c.988C>T	p.Arg330Ter	p.R330*	ENST00000407977		330	Cga/Tga	9/10	0.340818561940584	1	FACETS	0.398	0.34	0.463	0.398	0.34	0.463	SUBCLONAL	1	TRUE	0	0.340818561940584	1		597	660	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604706	48604706	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	25	392	0	ENST00000342988.3:c.1528G>A	p.Gly510Arg	p.G510R	ENST00000342988	NM_005359.5	510	Gga/Aga	12/12	0.323202604714074	1	FACETS	0.278	0.218	0.346	0.278	0.218	0.346	SUBCLONAL	1	TRUE	0	0.340818561940584	1		392	438	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437606	56437606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886926322	NA	P-0044538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	63	407	0	ENST00000407977.2:c.856C>T	p.Arg286Trp	p.R286W	ENST00000407977		286	Cgg/Tgg	8/10	0.340818561940584	1	FACETS	0.592	0.513	0.678	0.592	0.513	0.678	SUBCLONAL	1	TRUE	0	0.340818561940584	1		407	518	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6029571	6029571	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs200513014	NA	P-0044538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	88	342	0	ENST00000265849.7:c.1004A>G	p.Asn335Ser	p.N335S	ENST00000265849	NM_000535.5	335	aAt/aGt	10/15	1	2	FACETS	0.987	0.877	1	0.987	0.877	1	CLONAL	1	TRUE	1	0.340818561940584	2		342	523	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438192	49438192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	131	633	0	ENST00000301067.7:c.5077C>T	p.Arg1693Trp	p.R1693W	ENST00000301067	NM_003482.3	1693	Cgg/Tgg	20/54	1	2	FACETS	0.838	0.76	0.921	0.838	0.76	0.921	CLONAL	1	TRUE	1	0.340818561940584	2		633	917	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058542	72058542	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	102	403	1	ENST00000357731.5:c.898G>A	p.Ala300Thr	p.A300T	ENST00000357731	NM_173808.2	300	Gcc/Acc	6/7	1	2	FACETS	0.983	0.881	1	0.983	0.881	1	CLONAL	1	TRUE	1	0.340818561940584	2		404	609	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458173	120458173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	85	618	0	ENST00000256646.2:c.7172G>A	p.Ser2391Asn	p.S2391N	ENST00000256646	NM_024408.3	2391	aGt/aAt	34/34	1	2	FACETS	0.67	0.592	0.754	0.67	0.592	0.754	SUBCLONAL	1	TRUE	1	0.340818561940584	2		618	744	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098540	108098540	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	28	156	0	ENST00000278616.4:c.110C>A	p.Pro37His	p.P37H	ENST00000278616	NM_000051.3	37	cCt/cAt	3/63	1	2	FACETS	0.657	0.527	0.804	0.657	0.527	0.804	SUBCLONAL	1	TRUE	1	0.340818561940584	2		156	250	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967620	26967620	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	68	294	0	ENST00000381527.3:c.763A>G	p.Ile255Val	p.I255V	ENST00000381527	NM_001260.1	255	Ata/Gta	7/13	1	2	FACETS	0.913	0.797	1	0.913	0.797	1	CLONAL	1	TRUE	1	0.340818561940584	2		294	437	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162475176	162475176	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761430731	NA	P-0044538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	84	373	0	ENST00000366898.1:c.565C>T	p.Pro189Ser	p.P189S	ENST00000366898	NM_004562.2	189	Cca/Tca	5/12	0.323202604714074	1	FACETS	0.725	0.641	0.814	0.725	0.641	0.814	SUBCLONAL	1	TRUE	0	0.340818561940584	1		373	564	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2972184	2972184	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	59	559	1	ENST00000396946.4:c.1555A>T	p.Thr519Ser	p.T519S	ENST00000396946	NM_032415.4	519	Aca/Tca	11/25	1	2	FACETS	0.389	0.333	0.449	0.389	0.333	0.449	SUBCLONAL	1	TRUE	1	0.340818561940584	2		560	891	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806089	1806089	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913479	NA	P-0044552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	798	656	1	ENST00000260795.2:c.1108G>T	p.Gly370Cys	p.G370C	ENST00000260795		370	Ggc/Tgc	8/17	0.798067787751063	3	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.798067787751063	3		657	1335	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026871	71026871	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	145	240	0	ENST00000318789.4:c.1351G>A	p.Asp451Asn	p.D451N	ENST00000318789	NM_032682.5	451	Gat/Aat	16/21	0.798067787751063	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.798067787751063	1		240	208	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119720	108119720	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1555069657	NA	P-0044552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	130	256	0	ENST00000278616.4:c.1126G>T	p.Glu376Ter	p.E376*	ENST00000278616	NM_000051.3	376	Gaa/Taa	9/63	0.798067787751063	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.798067787751063	1		256	184	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76764023	76764023	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	661	312	0	ENST00000373344.5:c.7285C>T	p.Gln2429Ter	p.Q2429*	ENST00000373344	NM_000489.3	2429	Caa/Taa	35/35	0.724681584807727	2	FACETS	1	0.998	1			1	CLONAL	2	TRUE	NA	0.798067787751063	2		312	737	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099434	27099492	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTCCTATGAGCCAAATAAGGATCCTTATGGCAGCATGAGGAAAGGTGACTGATCTGAT	TGTCCTATGAGCCAAATAAGGATCCTTATGGCAGCATGAGGAAAGGTGACTGATCTGAT	-	novel	NA	P-0044552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	48	483	0	ENST00000324856.7:c.3673_3715+16del		p.X1225_splice	ENST00000324856	NM_006015.4	1225		14/20	1	2	FACETS	0.19	0.16	0.223	0.19	0.16	0.223	SUBCLONAL	1	TRUE	1	0.798067787751063	2		483	632	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145758	11145758	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1447890611	NA	P-0044552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	440	673	0	ENST00000358026.2:c.4120C>T	p.Arg1374Cys	p.R1374C	ENST00000358026	NM_001128849.1	1374	Cgc/Tgc	29/36	0.140772447186845	4	FACETS	0.908	0.868	0.948	0.908	0.868	0.948	INDETERMINATE	2	TRUE	2	0.798067787751063	4		673	1092	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623131	52623131	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	350	441	0	ENST00000394830.3:c.2920C>T	p.Gln974Ter	p.Q974*	ENST00000394830	NM_018313.4	974	Caa/Taa	19/30	0.798067787751063	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.798067787751063	1		441	474	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490491	20490491	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1474	459	495	2	ENST00000346618.3:c.1228A>T	p.Thr410Ser	p.T410S	ENST00000346618	NM_001949.4	410	Act/Tct	7/7	0.798067787751063	6	FACETS	0.772	0.735	0.81			1	SUBCLONAL	2	TRUE	NA	0.798067787751063	6		497	1933	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0044554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	117	500	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.993	0.901	1	0.993	0.901	1	CLONAL	1	TRUE	1	0.496906492282798	2		500	474	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0044554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	170	810	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.952	0.877	1	0.952	0.877	1	CLONAL	1	TRUE	1	0.496906492282798	2		810	719	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	102	541	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.95	0.855	1	0.95	0.855	1	CLONAL	1	TRUE	1	0.496906492282798	2		541	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0044554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	179	971	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.668	0.615	0.723	0.668	0.615	0.723	SUBCLONAL	1	TRUE	1	0.496906492282798	2		972	1079	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	99	214	0	ENST00000397062.3:c.92G>A	p.Gly31Glu	p.G31E	ENST00000397062	NM_006164.4	31	gGa/gAa	2/5	1	2	FACETS	0.94	0.844	1	0.94	0.844	1	CLONAL	1	TRUE	1	0.496906492282798	2		214	424	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591891	48591891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912581	NA	P-0044554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	256	327	2	ENST00000342988.3:c.1054G>A	p.Gly352Arg	p.G352R	ENST00000342988	NM_005359.5	352	Gga/Aga	9/12	0.496906492282798	2	FACETS	0.835	0.788	0.883	0.835	0.788	0.883	CLONAL	2	TRUE	0	0.496906492282798	2		329	617	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733044	74733044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	207	354	1	ENST00000359995.5:c.199G>A	p.Asp67Asn	p.D67N	ENST00000359995	NM_001195427.1	67	Gac/Aac	1/3	1	2	FACETS	0.965	0.897	1	0.965	0.897	1	CLONAL	1	TRUE	1	0.496906492282798	2		355	863	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115277125	115277125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770606954	NA	P-0044554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	97	277	0	ENST00000438362.2:c.658C>T	p.Arg220Cys	p.R220C	ENST00000438362	NM_001242891.1	220	Cgc/Tgc	7/20	1	2	FACETS	0.649	0.579	0.722	0.649	0.579	0.722	SUBCLONAL	1	TRUE	1	0.496906492282798	2		277	602	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741925	162741925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	165	315	0	ENST00000367921.3:c.1616C>T	p.Ser539Leu	p.S539L	ENST00000367921	NM_006182.2	539	tCa/tTa	13/18	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.496906492282798	2		315	616	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478795	56478795	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1425922004	NA	P-0044554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	175	372	0	ENST00000267101.3:c.251C>G	p.Thr84Arg	p.T84R	ENST00000267101	NM_001982.3	84	aCa/aGa	3/28	1	2	FACETS	0.873	0.805	0.943	0.873	0.805	0.943	CLONAL	1	TRUE	1	0.496906492282798	2		372	807	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794460	42794460	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	283	584	0	ENST00000575354.2:c.1540C>A	p.Pro514Thr	p.P514T	ENST00000575354	NM_015125.3	514	Ccc/Acc	10/20	1	2	FACETS	0.968	0.909	1	0.968	0.909	1	CLONAL	1	TRUE	1	0.496906492282798	2		584	1177	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715373	117715373	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	77	295	0	ENST00000368508.3:c.1116C>G	p.Ile372Met	p.I372M	ENST00000368508	NM_002944.2	372	atC/atG	10/43	NA	2	FACETS	0.716	0.631	0.806			1	INDETERMINATE	1	TRUE	NA	0.496906492282798	2		295	433	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0044566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	173	275	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.420553224981106	3	FACETS	0.887	0.829	0.945	0.887	0.829	0.945	CLONAL	3	TRUE	0	0.436451094865788	3		275	363	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	304	383	1	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.436451094865788	2	FACETS	0.944	0.895	0.993	0.944	0.895	0.993	CLONAL	2	TRUE	0	0.436451094865788	2		384	738	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857679	9857679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886042648	NA	P-0044566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	97	296	0	ENST00000330684.3:c.3722G>A	p.Arg1241Gln	p.R1241Q	ENST00000330684	NM_001134407.1	1241	cGg/cAg	13/13	0.408833850234586	4	FACETS	0.985	0.88	1	0.493	0.44	0.549	CLONAL	1	TRUE	2	0.436451094865788	4		296	648	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151893008	151893008	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	76	181	0	ENST00000262189.6:c.4362del	p.Lys1454AsnfsTer30	p.K1454Nfs*30	ENST00000262189	NM_170606.2	1454	aaA/aa	28/59	0.408833850234586	4	FACETS	0.815	0.721	0.913	0.815	0.721	0.913	CLONAL	2	TRUE	2	0.436451094865788	4		181	307	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858150	9858150	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	134	397	1	ENST00000330684.3:c.3251A>G	p.Asp1084Gly	p.D1084G	ENST00000330684	NM_001134407.1	1084	gAc/gGc	13/13	0.408833850234586	4	FACETS	1	0.931	1	0.515	0.467	0.564	CLONAL	1	TRUE	2	0.436451094865788	4		398	857	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979533	7979533	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs144747081	NA	P-0044566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	321	424	0	ENST00000319144.4:c.1492T>C	p.Tyr498His	p.Y498H	ENST00000319144	NM_001139.2	498	Tac/Cac	11/15	0.436451094865788	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.436451094865788	2		424	709	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151893012	151893012	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	81	188	0	ENST00000262189.6:c.4358C>G	p.Ala1453Gly	p.A1453G	ENST00000262189	NM_170606.2	1453	gCa/gGa	28/59	0.408833850234586	4	FACETS	0.841	0.748	0.939	0.841	0.748	0.939	CLONAL	2	TRUE	2	0.436451094865788	4		188	317	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0044568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	106	760	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.263562610047418	1	FACETS	0.772	0.692	0.858	0.772	0.692	0.858	SUBCLONAL	1	TRUE	0	0.277516482539817	1		760	852	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164079	108164079	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	30	147	0	ENST00000278616.4:c.4651G>C	p.Asp1551His	p.D1551H	ENST00000278616	NM_000051.3	1551	Gat/Cat	31/63	1	2	FACETS	0.68	0.549	0.828	0.68	0.549	0.828	SUBCLONAL	1	TRUE	1	0.277516482539817	2		147	318	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40856618	40856618	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0044568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	43	322	0	ENST00000428826.2:c.2017+2T>C		p.X673_splice	ENST00000428826		673			1	2	FACETS	0.539	0.45	0.637	0.539	0.45	0.637	SUBCLONAL	1	TRUE	1	0.277516482539817	2		322	575	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222082	2222082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	117	625	1	ENST00000398665.3:c.2914G>A	p.Gly972Arg	p.G972R	ENST00000398665	NM_032482.2	972	Ggg/Agg	24/28	1	2	FACETS	0.932	0.839	1	0.932	0.839	1	CLONAL	1	TRUE	1	0.277516482539817	2		626	905	SUCCESS
APC	324	MSKCC	GRCh37	5	112175075	112175076	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs863225345	NA	P-0044568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	17	132	0	ENST00000257430.4:c.3785dup	p.Tyr1262Ter	p.Y1262*	ENST00000257430	NM_000038.5	1262	tat/tAat	16/16	1	2	FACETS	0.479	0.357	0.622	0.479	0.357	0.622	SUBCLONAL	1	TRUE	1	0.277516482539817	2		132	256	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92300746	92300746	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	36	228	0	ENST00000265734.4:c.641G>A	p.Arg214His	p.R214H	ENST00000265734	NM_001259.6	214	cGt/cAt	5/8	1	2	FACETS	0.66	0.543	0.791	0.66	0.543	0.791	SUBCLONAL	1	TRUE	1	0.277516482539817	2		228	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0044601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	26	760	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.472	0.372	0.587	0.472	0.372	0.587	SUBCLONAL	1	TRUE	1	0.16	2		760	689	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	59	643	0	ENST00000347630.2:c.399C>A	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttA	6/11	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.16	2		643	731	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821956	72821956	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	21	322	0	ENST00000268489.5:c.10219del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3407	Gct/ct	10/10	0.3	3	FACETS	0.854	0.657	1			1	CLONAL	1	TRUE	NA	0.16	3		322	332	SUCCESS
ATM	472	MSKCC	GRCh37	11	108225571	108225572	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555143538	NA	P-0044601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	42	386	0	ENST00000278616.4:c.8823_8824del	p.Gln2942GlyfsTer13	p.Q2942Gfs*13	ENST00000278616	NM_000051.3	2940	aaCTct/aact	61/63	1	2	FACETS	0.839	0.699	0.994	0.839	0.699	0.994	CLONAL	1	TRUE	1	0.16	2		386	626	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035227	42035227	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	87	677	0	ENST00000219905.7:c.5070del	p.Ala1691LeufsTer8	p.A1691Lfs*8	ENST00000219905	NM_001164273.1	1690	gTt/gt	15/24	1	2	FACETS	0.75	0.664	0.842	1	0.978	1	SUBCLONAL	2	TRUE	1	0.16	2		677	725	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176330	24176330	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1057517825	NA	P-0044643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	44	617	1	ENST00000263121.7:c.1121G>A	p.Arg374Gln	p.R374Q	ENST00000263121	NM_003073.3	374	cGg/cAg	9/9	1	2	FACETS	0.445	0.372	0.526	0.445	0.372	0.526	SUBCLONAL	1	TRUE	1	0.286707541845813	2		618	690	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224504	108224504	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs769951912	NA	P-0044643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	17	208	0	ENST00000278616.4:c.8683G>T	p.Glu2895Ter	p.E2895*	ENST00000278616	NM_000051.3	2895	Gaa/Taa	60/63	1	2	FACETS	0.513	0.384	0.667	0.513	0.384	0.667	SUBCLONAL	1	TRUE	1	0.286707541845813	2		208	231	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964925	55964925	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	87	324	0	ENST00000263923.4:c.2312C>G	p.Thr771Arg	p.T771R	ENST00000263923	NM_002253.2	771	aCg/aGg	16/30	1	2	FACETS	0.809	0.72	0.903	0.809	0.72	0.903	CLONAL	1	TRUE	1	0.509761913933032	2		324	422	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942035	44942036	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0044665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	87	127	0	ENST00000377967.4:c.3284+2dup		p.X1095_splice	ENST00000377967	NM_021140.2	1095			1	1	FACETS	0.752	0.686	0.819	1	0.984	1	SUBCLONAL	2	TRUE	0	0.509761913933032	1		127	169	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	128	541	0				ENST00000310581	NM_198253.2	-/1132			0.33959044666956	5	FACETS	1	0.957	1	0.724	0.659	0.791	CLONAL	2	TRUE	2	0.33959044666956	5		541	524	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81914540	81914540	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770601419	NA	P-0044697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	62	323	0	ENST00000359376.3:c.674C>T	p.Ser225Leu	p.S225L	ENST00000359376	NM_002661.3	225	tCg/tTg	8/33	0.157174907400069	3	FACETS	1	0.888	1	0.513	0.445	0.587	INDETERMINATE	1	TRUE	1	0.33959044666956	3		323	416	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202462	123202462	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs762388218	NA	P-0044697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	113	370	0	ENST00000218089.9:c.2314T>C	p.Cys772Arg	p.C772R	ENST00000218089	NM_001042749.1	772	Tgt/Cgt	24/35	0.280174664051654	2	FACETS	0.804	0.729	0.882	0.804	0.729	0.882	CLONAL	2	TRUE	0	0.33959044666956	2		370	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs878854073	NA	P-0044697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	202	441	0	ENST00000269305.4:c.673-1G>A		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.33959044666956	4	FACETS	0.929	0.867	0.992	0.929	0.867	0.992	CLONAL	3	TRUE	1	0.33959044666956	4		441	572	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983019	201983019	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	248	756	0	ENST00000359651.3:c.868G>T	p.Glu290Ter	p.E290*	ENST00000359651		290	Gag/Tag	7/8	0.11076617598275	6	FACETS	0.851	0.796	0.907	0.851	0.796	0.907	INDETERMINATE	3	TRUE	3	0.33959044666956	6		756	961	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983094	201983094	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	130	721	0	ENST00000359651.3:c.943T>C	p.Trp315Arg	p.W315R	ENST00000359651		315	Tgg/Cgg	7/8	0.11076617598275	6	FACETS	0.799	0.724	0.876	0.532	0.483	0.584	INDETERMINATE	2	TRUE	3	0.33959044666956	6		721	805	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81914526	81914529	+	frameshift_variant	Frame_Shift_Del	DEL	ATTC	ATTC	-	novel	NA	P-0044697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	61	331	1	ENST00000359376.3:c.661_664del	p.Phe221LysfsTer41	p.F221Kfs*41	ENST00000359376	NM_002661.3	220	gaATTC/ga	8/33	0.157174907400069	3	FACETS	1	0.868	1	0.501	0.434	0.575	INDETERMINATE	1	TRUE	1	0.33959044666956	3		332	419	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59934575	59934576	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0044697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	28	238	0	ENST00000259008.2:c.222_223delinsCT	p.Glu74_Gly75delinsAspCys	p.E74_G75delinsDC	ENST00000259008	NM_032043.2	74	gaGGgc/gaCTgc	4/20	0.115400077706154	6	FACETS	0.824	0.659	1	0.275	0.219	0.338	INDETERMINATE	1	TRUE	3	0.33959044666956	6		238	336	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229360	36229360	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	125	525	0	ENST00000222270.7:c.8050G>T	p.Glu2684Ter	p.E2684*	ENST00000222270	NM_014727.1	2684	Gag/Tag	37/37	0.195987460550834	3	FACETS	1	0.984	1	0.72	0.654	0.79	INDETERMINATE	1	TRUE	1	0.33959044666956	3		525	598	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090684	71090684	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0044697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	100	181	0	ENST00000318789.4:c.665-1G>A		p.X222_splice	ENST00000318789	NM_032682.5	222			0.33959044666956	5	FACETS	0.882	0.802	0.964	0.882	0.802	0.964	CLONAL	4	TRUE	1	0.33959044666956	5		181	252	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250837	153250837	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	32	308	0	ENST00000281708.4:c.1223C>A	p.Ala408Glu	p.A408E	ENST00000281708	NM_033632.3	408	gCa/gAa	8/12	0.280174664051654	2	FACETS	0.553	0.449	0.669	0.276	0.224	0.335	SUBCLONAL	1	TRUE	0	0.33959044666956	2		308	341	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915008	131915009	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0044697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	20	295	0	ENST00000265335.6:c.366-1_366delinsTT		p.X122_splice	ENST00000265335		122		4/25	0.33959044666956	3	FACETS	0.447	0.342	0.571	0.224	0.171	0.286	SUBCLONAL	1	TRUE	1	0.33959044666956	3		295	308	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839979	27839979	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	43	504	0	ENST00000328488.2:c.115C>G	p.Pro39Ala	p.P39A	ENST00000328488	NM_003533.2	39	Ccc/Gcc	1/1	0.271945927914441	4	FACETS	0.615	0.514	0.727	0.154	0.128	0.182	SUBCLONAL	1	TRUE	0	0.33959044666956	4		504	552	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450331	50450331	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	42	537	0	ENST00000331340.3:c.515C>A	p.Pro172His	p.P172H	ENST00000331340	NM_006060.4	172	cCc/cAc	5/8	0.33959044666956	3	FACETS	0.563	0.47	0.667	0.281	0.235	0.334	SUBCLONAL	1	TRUE	1	0.33959044666956	3		537	514	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132775	152132775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	69	530	0	ENST00000262189.6:c.97G>A	p.Asp33Asn	p.D33N	ENST00000262189	NM_170606.2	33	Gac/Aac	1/59	NA	2	FACETS	0.788	0.687	0.896			1	INDETERMINATE	1	TRUE	NA	0.33959044666956	2		530	516	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772912	135772913	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	223	510	0	ENST00000298552.3:c.2710dup	p.Thr904AsnfsTer46	p.T904Nfs*46	ENST00000298552	NM_001162426.1	904	acc/aAcc	21/23	0.283658684528835	3	FACETS	1	0.986	1	0.79	0.74	0.842	CLONAL	2	TRUE	0	0.33959044666956	3		510	648	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949155	44949155	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	167	336	0	ENST00000377967.4:c.3717del	p.Trp1239Ter	p.W1239*	ENST00000377967	NM_021140.2	1239	tGg/tg	25/29	0.313234058765665	3	FACETS	1	0.984	1	0.813	0.753	0.873	CLONAL	2	TRUE	0	0.33959044666956	3		336	472	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196809	123196810	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAAA	novel	NA	P-0044697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	125	494	0	ENST00000218089.9:c.1696_1697insAAAA	p.Leu566GlnfsTer23	p.L566Qfs*23	ENST00000218089	NM_001042749.1	566	ctt/cAAAAtt	18/35	0.280174664051654	2	FACETS	0.885	0.808	0.965	0.885	0.808	0.965	CLONAL	2	TRUE	0	0.33959044666956	2		494	416	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	154	540	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.280795846307331	4	FACETS	0.908	0.836	0.981	0.908	0.836	0.981	CLONAL	3	TRUE	1	0.280795846307331	4		540	516	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0044742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	235	341	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.280795846307331	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	1	0.280795846307331	4		341	639	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100175	27100176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0044742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	84	565	0	ENST00000324856.7:c.3977dup	p.Gln1327AlafsTer11	p.Q1327Afs*11	ENST00000324856	NM_006015.4	1324	tac/taCc	16/20	0.202345310617663	3	FACETS	1	0.938	1	0.548	0.484	0.616	CLONAL	1	TRUE	1	0.280795846307331	3		565	623	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576851	7576851	+	splice_donor_variant	Splice_Site	DEL	A	A	-	novel	NA	P-0044742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	121	578	0	ENST00000269305.4:c.993+2del		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.187495828867252	2	FACETS	1	0.983	1	0.696	0.63	0.765	CLONAL	1	TRUE	0	0.280795846307331	2		578	619	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604650	48604651	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0044742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	60	307	0	ENST00000342988.3:c.1474_1475del	p.Val492Ter	p.V492*	ENST00000342988	NM_005359.5	491	gGT/g	12/12	0.187495828867252	2	FACETS	1	0.953	1	0.619	0.536	0.708	CLONAL	1	TRUE	0	0.280795846307331	2		307	345	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0044747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	49	418	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.997	0.847	1	0.997	0.847	1	CLONAL	1	TRUE	1	0.26	2		418	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0044747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	76	688	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.26	2		688	565	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80171602	80171602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576204286	NA	P-0044747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	27	316	0	ENST00000265081.6:c.3335C>T	p.Thr1112Met	p.T1112M	ENST00000265081	NM_002439.4	1112	aCg/aTg	24/24	0.0922438165281765	3	FACETS	0.473	0.376	0.585	0.237	0.188	0.293	INDETERMINATE	1	TRUE	1	0.26	3		316	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576858	7576858	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	353	487	0	ENST00000269305.4:c.988del	p.Leu330PhefsTer15	p.L330Ffs*15	ENST00000269305	NM_001126112.2	330	Ctt/tt	9/11	NA	2	FACETS	0.902	0.862	0.941			1	INDETERMINATE	2	TRUE	NA	0.581564001179145	2		487	673	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462003	120462003	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	87	499	0	ENST00000256646.2:c.5713G>T	p.Ala1905Ser	p.A1905S	ENST00000256646	NM_024408.3	1905	Gcc/Tcc	31/34	0.408825126023072	1	FACETS	0.315	0.279	0.354	0.315	0.279	0.354	SUBCLONAL	1	TRUE	0	0.581564001179145	1		499	673	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553560	29553561	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0044770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	138	254	0	ENST00000356175.3:c.2110_2111del	p.Leu704GlyfsTer11	p.L704Gfs*11	ENST00000356175	NM_000267.3	703	gtTCtg/gttg	18/57	0.578684313495696	1	FACETS	0.993	0.916	1	0.993	0.916	1	CLONAL	1	TRUE	0	0.581564001179145	1		254	339	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245890	41245902	+	frameshift_variant	Frame_Shift_Del	DEL	TGACCACTATTAG	TGACCACTATTAG	-	novel	NA	P-0044770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	117	554	1	ENST00000357654.3:c.1646_1658del	p.Thr549MetfsTer19	p.T549Mfs*19	ENST00000357654	NM_007294.3	549	aCTAATAGTGGTCAt/at	10/23	0.578684313495696	1	FACETS	0.921	0.842	1	0.921	0.842	1	CLONAL	1	TRUE	0	0.581564001179145	1		555	310	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729380	41729381	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0044770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	239	529	0	ENST00000242208.4:c.1148_1149delinsAA	p.Pro383Gln	p.P383Q	ENST00000242208	NM_002192.2	383	cCC/cAA	3/3	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.581564001179145	2		529	819	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0044772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	313	760	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.674762313667595	2		760	726	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0044772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	343	534	1	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.674762313667595	4	FACETS		NA	1	1	0.997	1	NA	5	TRUE	0	0.674762313667595	4		535	364	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793881	NA	P-0044772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	309	726	0	ENST00000269305.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGg/gAg	8/11	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.674762313667595	2		726	685	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457158	25457158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1459396018	NA	P-0044772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	221	558	0	ENST00000264709.3:c.2729C>T	p.Ala910Val	p.A910V	ENST00000264709	NM_175629.2	910	gCg/gTg	23/23	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.674762313667595	2		558	507	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133311	30133311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200617125	NA	P-0044772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	248	567	0	ENST00000263025.4:c.187G>A	p.Val63Met	p.V63M	ENST00000263025	NM_002746.2	63	Gtg/Atg	2/9	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.674762313667595	2		567	589	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204499812	204499812	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	271	305	0	ENST00000367182.3:c.154G>T	p.Val52Phe	p.V52F	ENST00000367182	NM_001278516.1	52	Gtc/Ttc	4/11	0.674762313667595	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.674762313667595	3		305	437	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425295	49425305	+	frameshift_variant	Frame_Shift_Del	DEL	TGCCCAGGTAC	TGCCCAGGTAC	-	novel	NA	P-0044772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	301	788	0	ENST00000301067.7:c.13183_13193del	p.Val4395SerfsTer11	p.V4395Sfs*11	ENST00000301067	NM_003482.3	4395	GTACCTGGGCAt/t	39/54	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.674762313667595	2		788	710	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349207	70349207	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	222	702	0	ENST00000374080.3:c.3619C>A	p.Leu1207Met	p.L1207M	ENST00000374080		1207	Ctg/Atg	26/45	0.420607413706328	1	FACETS	0.724	0.679	0.771	0.724	0.679	0.771	SUBCLONAL	1	TRUE	0	0.674762313667595	1		702	602	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0044782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	102	311	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.310094178469546	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	0	0.315578120041087	2		311	312	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259034	89259034	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	37	238	1	ENST00000336596.2:c.178G>T	p.Glu60Ter	p.E60*	ENST00000336596	NM_005233.5	60	Gaa/Taa	3/17	1	2	FACETS	0.862	0.714	1	0.862	0.714	1	CLONAL	1	TRUE	1	0.315578120041087	2		239	272	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600595	43600595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	139	640	0	ENST00000355710.3:c.821C>T	p.Ala274Val	p.A274V	ENST00000355710	NM_020975.4	274	gCg/gTg	4/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.315578120041087	2		640	822	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204866	94204866	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	45	378	0	ENST00000323929.3:c.719T>A	p.Leu240His	p.L240H	ENST00000323929	NM_005591.3	240	cTt/cAt	8/20	0.310094178469546	2	FACETS	0.745	0.627	0.874	0.372	0.313	0.437	SUBCLONAL	1	TRUE	0	0.315578120041087	2		378	383	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420798	49420798	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	85	553	0	ENST00000301067.7:c.14951G>C	p.Gly4984Ala	p.G4984A	ENST00000301067	NM_003482.3	4984	gGa/gCa	48/54	1	2	FACETS	0.615	0.543	0.693	0.615	0.543	0.693	SUBCLONAL	1	TRUE	1	0.315578120041087	2		553	876	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066946	30066946	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	68	348	0	ENST00000331968.5:c.2185G>T	p.Gly729Cys	p.G729C	ENST00000331968	NM_002742.2	729	Ggt/Tgt	16/18	1	2	FACETS	0.902	0.786	1	0.902	0.786	1	CLONAL	1	TRUE	1	0.315578120041087	2		348	478	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416701	29416701	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	79	462	0	ENST00000389048.3:c.4252C>G	p.Pro1418Ala	p.P1418A	ENST00000389048	NM_004304.4	1418	Cct/Gct	29/29	1	2	FACETS	0.874	0.77	0.985	0.874	0.77	0.985	CLONAL	1	TRUE	1	0.315578120041087	2		462	573	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023993	31023993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	122	611	0	ENST00000375687.4:c.3478G>A	p.Gly1160Ser	p.G1160S	ENST00000375687	NM_015338.5	1160	Ggc/Agc	13/13	0.315578120041087	6	FACETS	1	0.929	1	0.26	0.234	0.287	CLONAL	1	TRUE	2	0.315578120041087	6		611	1215	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751083	128751083	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	116	611	0	ENST00000377970.2:c.620C>T	p.Ser207Leu	p.S207L	ENST00000377970	NM_002467.4	207	tCg/tTg	2/3	0.315578120041087	4	FACETS	1	0.906	1	0.335	0.302	0.371	CLONAL	1	TRUE	1	0.315578120041087	4		611	961	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97888833	97888833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1306075116	NA	P-0044782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	47	418	0	ENST00000289081.3:c.874C>T	p.Arg292Trp	p.R292W	ENST00000289081	NM_000136.2	292	Cgg/Tgg	9/15	0.255863707979754	2	FACETS	0.531	0.448	0.623	0.265	0.224	0.312	SUBCLONAL	1	TRUE	0	0.315578120041087	2		418	561	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	26	540	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.574367418756719	8	FACETS	0.913	0.762	1	0.761	0.635	0.888	CLONAL	5	FALSE	2	0.574367418756719	8		540	54	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0044801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	303	760	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.396197612583668	5	FACETS	1	0.989	1			1	CLONAL	5	FALSE	NA	0.574367418756719	5		760	374	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27192565	27192565	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	55	496	0	ENST00000380036.4:c.1568G>C	p.Gly523Ala	p.G523A	ENST00000380036	NM_000459.3	523	gGa/gCa	11/23	0.574367418756719	1	FACETS	0.91	0.797	1	0.91	0.797	1	CLONAL	1	FALSE	0	0.574367418756719	1		496	150	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0044804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	134	364	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.643301113078437	4	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	FALSE	2	0.764528330210066	4		364	301	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577068	7577069	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0044804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	386	731	1	ENST00000269305.4:c.869_870del	p.Arg290GlnfsTer15	p.R290Qfs*15	ENST00000269305	NM_001126112.2	290	cGC/c	8/11	0.607211514190991	2	FACETS	0.752	0.722	0.782	0.752	0.722	0.782	SUBCLONAL	2	FALSE	0	0.764528330210066	2		732	671	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0044815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	118	719	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.777	0.7	0.859	0.777	0.7	0.859	SUBCLONAL	1	FALSE	1	0.292783056502745	2		719	1037	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0044815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	38	373	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.557	0.46	0.665	0.557	0.46	0.665	SUBCLONAL	1	FALSE	1	0.292783056502745	2		373	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0044815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	278	838	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.220668175425411	2	FACETS	1	0.992	1	0.682	0.639	0.726	CLONAL	1	FALSE	0	0.292783056502745	2		838	1393	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777670	9777670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760642664	NA	P-0044815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	110	732	0	ENST00000377346.4:c.1006G>A	p.Asp336Asn	p.D336N	ENST00000377346	NM_005026.3	336	Gac/Aac	8/24	1	2	FACETS	0.717	0.643	0.796	0.717	0.643	0.796	SUBCLONAL	1	FALSE	1	0.292783056502745	2		732	1048	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282480	115282480	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs777883903	NA	P-0044815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	47	361	0	ENST00000438362.2:c.170A>G	p.Asn57Ser	p.N57S	ENST00000438362	NM_001242891.1	57	aAt/aGt	3/20	1	2	FACETS	0.626	0.528	0.734	0.626	0.528	0.734	SUBCLONAL	1	FALSE	1	0.292783056502745	2		361	513	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231166	46231166	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0044815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	49	293	0	ENST00000334344.6:c.1086T>A	p.Cys362Ter	p.C362*	ENST00000334344	NM_152641.2	362	tgT/tgA	9/21	1	2	FACETS	0.893	0.758	1	0.893	0.758	1	CLONAL	1	FALSE	1	0.292783056502745	2		293	375	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620092	21620092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	94	538	1	ENST00000382592.4:c.74G>A	p.Gly25Glu	p.G25E	ENST00000382592	NM_014572.2	25	gGg/gAg	2/8	1	2	FACETS	0.686	0.609	0.768	0.686	0.609	0.768	SUBCLONAL	1	FALSE	1	0.292783056502745	2		539	936	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592650	28592650	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	135	497	0	ENST00000241453.7:c.2495T>C	p.Leu832Ser	p.L832S	ENST00000241453	NM_004119.2	832	tTg/tCg	20/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.292783056502745	2		497	792	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041375	42041375	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	173	613	0	ENST00000219905.7:c.5570C>A	p.Ser1857Ter	p.S1857*	ENST00000219905	NM_001164273.1	1857	tCg/tAg	17/24	0.186033468410322	3	FACETS	1	0.988	1	0.72	0.662	0.78	CLONAL	1	FALSE	1	0.292783056502745	3		613	941	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214372	5214372	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	71	490	0	ENST00000357368.4:c.4614G>T	p.Lys1538Asn	p.K1538N	ENST00000357368	NM_002850.3	1538	aaG/aaT	30/38	1	2	FACETS	0.744	0.649	0.846	0.744	0.649	0.846	SUBCLONAL	1	FALSE	1	0.292783056502745	2		490	652	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247165	153247165	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0044815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	39	241	0	ENST00000281708.4:c.1637C>G	p.Ser546Ter	p.S546*	ENST00000281708	NM_033632.3	546	tCa/tGa	10/12	1	2	FACETS	0.633	0.525	0.753	0.633	0.525	0.753	SUBCLONAL	1	FALSE	1	0.292783056502745	2		241	421	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393189	393189	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	93	548	0	ENST00000380956.4:c.37G>A	p.Gly13Ser	p.G13S	ENST00000380956	NM_001195286.1	13	Ggc/Agc	2/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.292783056502745	NA		548	796	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271703	38271703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1415925468	NA	P-0044815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	117	865	4	ENST00000425967.3:c.2246G>A	p.Arg749His	p.R749H	ENST00000425967	NM_001174067.1	749	cGc/cAc	17/19	1	2	FACETS	0.613	0.551	0.679	0.613	0.551	0.679	SUBCLONAL	1	FALSE	1	0.292783056502745	2		869	1304	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0044821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	290	388	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.993	0.941	1	0.993	0.941	1	CLONAL	1	TRUE	1	0.850171829587993	2		388	687	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	299	309	0	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	0.850171829587993	1	FACETS	0.965	0.929	1	0.965	0.929	1	CLONAL	1	TRUE	0	0.850171829587993	1		309	419	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662023	227662023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776903727	NA	P-0044821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	334	553	1	ENST00000305123.5:c.1432G>A	p.Ala478Thr	p.A478T	ENST00000305123	NM_005544.2	478	Gcc/Acc	1/2	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.850171829587993	2		554	781	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106644	27106644	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	382	619	0	ENST00000324856.7:c.6256del	p.Asp2086ThrfsTer49	p.D2086Tfs*49	ENST00000324856	NM_006015.4	2085	ctG/ct	20/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.850171829587993	2		619	879	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439660	140439660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	133	313	0	ENST00000288602.6:c.2079G>A	p.Met693Ile	p.M693I	ENST00000288602	NM_004333.4	693	atG/atA	17/18	1	2	FACETS	0.542	0.494	0.592	0.542	0.494	0.592	SUBCLONAL	1	TRUE	1	0.850171829587993	2		313	577	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0044825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	57	500	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.981	0.846	1	0.981	0.846	1	CLONAL	1	TRUE	1	0.33	2		500	352	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0044825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	178	971	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.33	2		972	1010	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0044825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	67	235	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.33	2		235	386	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578513	7578513	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	201	746	0	ENST00000269305.4:c.417G>C	p.Lys139Asn	p.K139N	ENST00000269305	NM_001126112.2	139	aaG/aaC	5/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.33	2		746	1167	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031973	26031973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	65	312	0	ENST00000244661.2:c.316G>C	p.Glu106Gln	p.E106Q	ENST00000244661	NM_003537.3	106	Gag/Cag	1/1	1	2	FACETS	0.816	0.709	0.931	0.816	0.709	0.931	CLONAL	1	TRUE	1	0.33	2		312	483	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294454	1294454	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	139	601	0	ENST00000310581.5:c.547C>G	p.Gln183Glu	p.Q183E	ENST00000310581	NM_198253.2	183	Cag/Gag	2/16	1	2	FACETS	0.98	0.892	1	0.98	0.892	1	CLONAL	1	TRUE	1	0.33	2		601	860	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720741	89720741	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs371387815	NA	P-0044825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	13	167	0	ENST00000371953.3:c.892C>T	p.Gln298Ter	p.Q298*	ENST00000371953	NM_000314.4	298	Caa/Taa	8/9	0.296225991610491	1	FACETS	0.396	0.283	0.533	0.396	0.283	0.533	SUBCLONAL	1	TRUE	0	0.33	1		167	166	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588942	67588942	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	33	214	0	ENST00000274335.5:c.1033G>A	p.Glu345Lys	p.E345K	ENST00000274335		345	Gaa/Aaa	8/15	1	2	FACETS	0.83	0.68	0.997	0.83	0.68	0.997	CLONAL	1	TRUE	1	0.33	2		214	241	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023354	31023354	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	96	467	0	ENST00000375687.4:c.2839G>C	p.Glu947Gln	p.E947Q	ENST00000375687	NM_015338.5	947	Gag/Cag	13/13	1	2	FACETS	0.928	0.828	1	0.928	0.828	1	CLONAL	1	TRUE	1	0.33	2		467	627	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029128	14029128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748206066	NA	P-0044825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	36	203	0	ENST00000311895.7:c.1339G>A	p.Glu447Lys	p.E447K	ENST00000311895	NM_005236.2	447	Gaa/Aaa	8/11	0.277457890530514	3	FACETS	0.691	0.569	0.827	0.345	0.284	0.414	SUBCLONAL	1	TRUE	1	0.33	3		203	368	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852174	63852174	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	88	481	0	ENST00000279873.7:c.2952G>C	p.Glu984Asp	p.E984D	ENST00000279873	NM_032199.2	984	gaG/gaC	10/10	1	2	FACETS	0.804	0.713	0.902	0.804	0.713	0.902	CLONAL	1	TRUE	1	0.33	2		481	663	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376528	118376528	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	63	307	0	ENST00000534358.1:c.9921G>C	p.Gln3307His	p.Q3307H	ENST00000534358	NM_005933.3	3307	caG/caC	27/36	1	2	FACETS	0.848	0.736	0.97	0.848	0.736	0.97	CLONAL	1	TRUE	1	0.33	2		307	450	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864774	57864774	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	136	693	0	ENST00000228682.2:c.2251C>A	p.Leu751Met	p.L751M	ENST00000228682	NM_005269.2	751	Ctg/Atg	12/12	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.33	2		693	821	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100431	2100431	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	88	406	0	ENST00000219476.3:c.169C>G	p.Arg57Gly	p.R57G	ENST00000219476	NM_000548.3	57	Cgc/Ggc	3/42	0.277457890530514	3	FACETS	0.807	0.714	0.906	0.403	0.357	0.453	CLONAL	1	TRUE	1	0.33	3		406	770	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579838	7579838	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0044825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	107	601	0	ENST00000269305.4:c.74+1G>A		p.X25_splice	ENST00000269305	NM_001126112.2	25			1	2	FACETS	0.872	0.782	0.967	0.872	0.782	0.967	CLONAL	1	TRUE	1	0.33	2		601	744	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678029	58678029	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	88	307	0	ENST00000305921.3:c.254C>G	p.Ser85Trp	p.S85W	ENST00000305921	NM_003620.3	85	tCg/tGg	1/6	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.33	2		307	435	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526312	189526312	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	106	438	0	ENST00000264731.3:c.576G>C	p.Trp192Cys	p.W192C	ENST00000264731	NM_003722.4	192	tgG/tgC	4/14	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.33	2		438	593	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391410	84391410	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	58	406	0	ENST00000321945.7:c.422C>A	p.Thr141Lys	p.T141K	ENST00000321945	NM_139076.2	141	aCa/aAa	5/9	1	2	FACETS	0.754	0.649	0.868	0.754	0.649	0.868	SUBCLONAL	1	TRUE	1	0.33	2		406	466	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127916195	127916195	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	56	305	0	ENST00000373547.4:c.449C>G	p.Thr150Arg	p.T150R	ENST00000373547	NM_002721.4	150	aCa/aGa	5/7	1	2	FACETS	0.886	0.762	1	0.886	0.762	1	CLONAL	1	TRUE	1	0.33	2		305	383	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	50	285	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	1	2	FACETS	0.489	0.416	0.567	0.489	0.416	0.567	SUBCLONAL	1	TRUE	1	0.61093388174383	2		285	335	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591092	67591092	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	79	251	0	ENST00000274335.5:c.1685G>C	p.Arg562Pro	p.R562P	ENST00000274335		562	cGt/cCt	12/15	1	2	FACETS	0.947	0.843	1	0.947	0.843	1	CLONAL	1	TRUE	1	0.61093388174383	2		251	273	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0044830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	97	313	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.604	0.54	0.671	0.604	0.54	0.671	SUBCLONAL	1	TRUE	1	0.61093388174383	2		313	526	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0044830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	33	324	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	0.207	0.168	0.251	0.207	0.168	0.251	SUBCLONAL	1	TRUE	1	0.61093388174383	2		324	522	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589597	67589597	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	46	208	0	ENST00000274335.5:c.1360A>C	p.Thr454Pro	p.T454P	ENST00000274335		454	Act/Cct	10/15	1	2	FACETS	0.886	0.758	1	0.886	0.758	1	CLONAL	1	TRUE	1	0.61093388174383	2		208	170	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945637	71945637	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	202	537	0	ENST00000298229.2:c.2393G>A	p.Trp798Ter	p.W798*	ENST00000298229	NM_001567.3	798	tGg/tAg	21/28	1	2	FACETS	0.975	0.908	1	0.975	0.908	1	CLONAL	1	TRUE	1	0.61093388174383	2		537	678	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685289	89685289	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554897267	NA	P-0044830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	42	171	0	ENST00000371953.3:c.188del	p.Asn63ThrfsTer36	p.N63Tfs*36	ENST00000371953	NM_000314.4	62	Aaa/aa	3/9	0.61093388174383	3	FACETS	0.823	0.694	0.964	0.412	0.347	0.482	CLONAL	1	TRUE	1	0.61093388174383	3		171	218	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258036	123258036	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	310	476	0	ENST00000358487.5:c.1645A>G	p.Asn549Asp	p.N549D	ENST00000358487	NM_000141.4	549	Aat/Gat	12/18	0.61093388174383	3	FACETS	0.978	0.93	1	0.978	0.93	1	CLONAL	2	TRUE	1	0.61093388174383	3		476	677	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101109	27101113	+	frameshift_variant	Frame_Shift_Del	DEL	TCTCT	TCTCT	-	novel	NA	P-0044830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	72	765	0	ENST00000324856.7:c.4391_4395del	p.Val1464GlyfsTer25	p.V1464Gfs*25	ENST00000324856	NM_006015.4	1464	gTCTCT/g	18/20	1	2	FACETS	0.239	0.208	0.273	0.239	0.208	0.273	SUBCLONAL	1	TRUE	1	0.61093388174383	2		765	986	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720744	89720745	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	19	193	0	ENST00000371953.3:c.898dup	p.Ile300AsnfsTer3	p.I300Nfs*3	ENST00000371953	NM_000314.4	299	gaa/gAaa	8/9	0.61093388174383	3	FACETS	0.511	0.39	0.65	0.255	0.195	0.325	SUBCLONAL	1	TRUE	1	0.61093388174383	3		193	159	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192627	94192627	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs780001540	NA	P-0044830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	153	466	0	ENST00000323929.3:c.1447C>T	p.Arg483Ter	p.R483*	ENST00000323929	NM_005591.3	483	Cga/Tga	13/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.61093388174383	2		466	492	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444566	187444566	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	252	615	0	ENST00000232014.4:c.1661C>A	p.Ser554Tyr	p.S554Y	ENST00000232014	NM_001130845.1	554	tCc/tAc	7/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.5	2		615	912	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539195	187539195	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	146	418	0	ENST00000441802.2:c.8545G>C	p.Asp2849His	p.D2849H	ENST00000441802	NM_005245.3	2849	Gat/Cat	10/27	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.5	2		418	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0044884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	239	539	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.564579823983999	1	FACETS	0.941	0.884	0.998	0.941	0.884	0.998	CLONAL	1	FALSE	0	0.564579823983999	1		539	646	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061098	38061202	+	inframe_deletion	In_Frame_Del	DEL	GGGGTCCTTGCGGCTCTCAGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTG	GGGGTCCTTGCGGCTCTCAGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTG	-	novel	NA	P-0044884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	94	154	0	ENST00000250448.2:c.787_891del	p.Gln263_Pro297del	p.Q263_P297del	ENST00000250448	NM_004496.3	263	CAGAAGCGCTTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGGCGCCAAGGGCGGCCCTGAGAGCCGCAAGGACCCC/-	2/2	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	1	0.564579823983999	2		154	323	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198263211	198263211	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	153	404	0	ENST00000335508.6:c.3108T>G	p.Ile1036Met	p.I1036M	ENST00000335508	NM_012433.2	1036	atT/atG	21/25	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	1	0.564579823983999	2		404	537	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24133970	24133970	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	54	301	0	ENST00000263121.7:c.121G>T	p.Gly41Cys	p.G41C	ENST00000263121	NM_003073.3	41	Ggt/Tgt	2/9	1	2	FACETS	0.392	0.335	0.454	0.392	0.335	0.454	SUBCLONAL	1	FALSE	1	0.564579823983999	2		301	488	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0044921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	166	369	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.601310941087962	2		369	510	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424409	47424409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779648831	NA	P-0044921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	229	576	2	ENST00000377045.4:c.329C>T	p.Ala110Val	p.A110V	ENST00000377045	NM_001654.4	110	gCg/gTg	5/16	1	2	FACETS	0.863	0.805	0.922	0.863	0.805	0.922	CLONAL	1	TRUE	1	0.601310941087962	2		578	883	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631129	69631129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs281860303	NA	P-0044921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	310	655	8	ENST00000334134.2:c.283C>T	p.Arg95Trp	p.R95W	ENST00000334134	NM_005247.2	95	Cgg/Tgg	2/3	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.601310941087962	2		663	1002	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200467	67200467	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	238	705	3	ENST00000312629.5:c.661C>T	p.His221Tyr	p.H221Y	ENST00000312629	NM_003952.2	221	Cat/Tat	8/15	1	2	FACETS	0.839	0.784	0.895	0.839	0.784	0.895	CLONAL	1	TRUE	1	0.601310941087962	2		708	944	SUCCESS
APC	324	MSKCC	GRCh37	5	112173388	112173388	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1060503282	NA	P-0044921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	107	286	0	ENST00000257430.4:c.2097G>A	p.Trp699Ter	p.W699*	ENST00000257430	NM_000038.5	699	tgG/tgA	16/16	1	2	FACETS	0.986	0.893	1	0.986	0.893	1	CLONAL	1	TRUE	1	0.601310941087962	2		286	361	SUCCESS
ATM	472	MSKCC	GRCh37	11	108100002	108100002	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781545	NA	P-0044921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	97	237	0	ENST00000278616.4:c.283C>T	p.Gln95Ter	p.Q95*	ENST00000278616	NM_000051.3	95	Cag/Tag	4/63	0.601310941087962	1	FACETS	0.826	0.748	0.907	0.826	0.748	0.907	CLONAL	1	TRUE	0	0.601310941087962	1		237	273	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431380	49431381	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	187	588	3	ENST00000301067.7:c.9758dup	p.Leu3253PhefsTer4	p.L3253Ffs*4	ENST00000301067	NM_003482.3	3253	ttg/ttTg	34/54	1	2	FACETS	0.894	0.828	0.961	0.894	0.828	0.961	CLONAL	1	TRUE	1	0.601310941087962	2		591	696	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554660	63554660	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	255	554	4	ENST00000307078.5:c.79C>T	p.Pro27Ser	p.P27S	ENST00000307078	NM_004655.3	27	Cca/Tca	2/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.601310941087962	2		558	778	SUCCESS
APC	324	MSKCC	GRCh37	5	112175441	112175442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTAGCAGATGTACTTCTGTCAGTTCACTTGATAG	novel	NA	P-0044921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	65	252	1	ENST00000257430.4:c.4153_4186dup	p.Phe1396Ter	p.F1396*	ENST00000257430	NM_000038.5	1384	ttt/tTTAGCAGATGTACTTCTGTCAGTTCACTTGATAGtt	16/16	1	2	FACETS	0.534	0.464	0.608	0.534	0.464	0.608	SUBCLONAL	1	TRUE	1	0.601310941087962	2		253	405	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019996	123019996	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	241	612	1	ENST00000355640.3:c.484A>G	p.Ser162Gly	p.S162G	ENST00000355640		162	Agt/Ggt	2/7	1	2	FACETS	0.951	0.89	1	0.951	0.89	1	CLONAL	1	TRUE	1	0.601310941087962	2		613	843	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0044961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	669	664	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.775674457984821	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.775674457984821	2		665	840	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0044961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	301	369	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.770440921626454	3	FACETS	0.997	0.952	1	0.997	0.952	1	CLONAL	2	TRUE	1	0.775674457984821	3		369	540	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928846	49928846	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371791811	NA	P-0044961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	724	743	0	ENST00000296474.3:c.3520C>T	p.Arg1174Cys	p.R1174C	ENST00000296474	NM_002447.2	1174	Cgc/Tgc	16/20	0.770440921626454	3	FACETS	0.986	0.956	1	0.986	0.956	1	CLONAL	2	TRUE	1	0.775674457984821	3		743	1314	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176590	142176590	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	40	302	0	ENST00000350721.4:c.7511C>A	p.Thr2504Asn	p.T2504N	ENST00000350721	NM_001184.3	2504	aCc/aAc	45/47	0.770440921626454	3	FACETS	0.235	0.195	0.28	0.118	0.097	0.14	SUBCLONAL	1	TRUE	1	0.775674457984821	3		302	609	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860104	151860120	+	frameshift_variant	Frame_Shift_Del	DEL	GTGAATCAGGAACAAAT	GTGAATCAGGAACAAAT	-	novel	NA	P-0044961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	150	362	0	ENST00000262189.6:c.10542_10558del	p.Phe3515IlefsTer45	p.F3515Ifs*45	ENST00000262189	NM_170606.2	3514	tcATTTGTTCCTGATTCACca/tcca	43/59	0.775674457984821	3	FACETS	0.937	0.86	1	0.312	0.286	0.339	CLONAL	1	TRUE	0	0.775674457984821	3		362	573	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0044972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	42	272	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	NA	2	FACETS	1	0.854	1			1	INDETERMINATE	1	TRUE	NA	0.346055611917801	2		272	239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0044972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	103	660	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.346055611917801	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.346055611917801	1		660	385	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0045002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	92	534	1	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.409360787220206	2	FACETS	1	0.982	1	0.678	0.618	0.739	INDETERMINATE	1	TRUE	0	0.710158604181799	2		535	191	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	61	541	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.34	2		541	358	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589586	67589591	+	inframe_deletion	In_Frame_Del	DEL	ATGAAT	ATGAAT	-	novel	NA	P-0045003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	24	122	0	ENST00000274335.5:c.1351_1356del	p.Glu451_Tyr452del	p.E451_Y452del	ENST00000274335		450	cATGAATat/cat	10/15	0.0849512276877928	3	FACETS	1	0.881	1	0.586	0.465	0.722	INDETERMINATE	1	TRUE	1	0.34	3		122	141	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37637646	37637646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	101	970	0	ENST00000249071.6:c.88G>A	p.Gly30Arg	p.G30R	ENST00000249071	NM_002872.4	30	Gga/Aga	2/7	1	2	FACETS	0.826	0.739	0.919	0.826	0.739	0.919	CLONAL	1	TRUE	1	0.34	2		970	719	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437729	52437729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1559586864	NA	P-0045003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	84	790	0	ENST00000460680.1:c.1432G>A	p.Val478Met	p.V478M	ENST00000460680	NM_004656.3	478	Gtg/Atg	13/17	1	2	FACETS	0.837	0.741	0.941	0.837	0.741	0.941	CLONAL	1	TRUE	1	0.34	2		790	590	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	228	540	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.303832059492758	3	FACETS	0.865	0.811	0.92	0.865	0.811	0.92	INDETERMINATE	2	TRUE	1	0.529133021853364	3		540	630	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	245	707	7	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.529133021853364	2		714	800	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	124	418	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.309578600733339	1	FACETS	0.877	0.801	0.955	0.877	0.801	0.955	INDETERMINATE	1	TRUE	0	0.529133021853364	1		418	393	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	199	566	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.529343361919803	1	FACETS	0.979	0.914	1	0.979	0.914	1	CLONAL	1	TRUE	0	0.529133021853364	1		567	565	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637555	52637555	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	146	503	0	ENST00000394830.3:c.2761C>T	p.Arg921Ter	p.R921*	ENST00000394830	NM_018313.4	921	Cga/Tga	18/30	0.529133021853364	2	FACETS	0.802	0.743	0.862	0.802	0.743	0.862	CLONAL	2	TRUE	0	0.529133021853364	2		503	344	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	99	502	0	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	0.309578600733339	1	FACETS	0.541	0.484	0.6	0.541	0.484	0.6	INDETERMINATE	1	TRUE	0	0.529133021853364	1		502	509	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278865	1278865	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149566858	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	300	917	0	ENST00000310581.5:c.2177C>T	p.Thr726Met	p.T726M	ENST00000310581	NM_198253.2	726	aCg/aTg	6/16	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.529133021853364	2		917	989	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631629	90631629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367982647	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	133	818	4	ENST00000330062.3:c.640G>A	p.Ala214Thr	p.A214T	ENST00000330062	NM_002168.2	214	Gca/Aca	5/11	0.302184233175326	2	FACETS	0.581	0.527	0.638	0.291	0.263	0.319	INDETERMINATE	1	TRUE	0	0.529133021853364	2		822	865	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725019	47725019	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs762488821	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	146	1032	0	ENST00000449228.1:c.725del	p.Gly242AlafsTer48	p.G242Afs*48	ENST00000449228	NM_001127240.2	242	gGc/gc	4/4	0.309578600733339	1	FACETS	0.445	0.406	0.487	0.445	0.406	0.487	INDETERMINATE	1	TRUE	0	0.529133021853364	1		1032	911	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40468879	40468879	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	219	519	1	ENST00000264657.5:c.2185del	p.Arg729AlafsTer3	p.R729Afs*3	ENST00000264657	NM_139276.2	729	Cgc/gc	23/24	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.529133021853364	2		520	657	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845518	128845518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748004767	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	281	929	2	ENST00000249373.3:c.815C>T	p.Ala272Val	p.A272V	ENST00000249373	NM_005631.4	272	gCg/gTg	4/12	0.309578600733339	1	FACETS	0.948	0.894	1	0.948	0.894	1	INDETERMINATE	1	TRUE	0	0.529133021853364	1		931	824	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276289	15276289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755817475	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	160	892	2	ENST00000263388.2:c.5705G>A	p.Arg1902His	p.R1902H	ENST00000263388	NM_000435.2	1902	cGc/cAc	31/33	0.309578600733339	1	FACETS	0.535	0.49	0.581	0.535	0.49	0.581	INDETERMINATE	1	TRUE	0	0.529133021853364	1		894	832	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850777	63850777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374377066	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	194	693	1	ENST00000279873.7:c.1555G>A	p.Glu519Lys	p.E519K	ENST00000279873	NM_032199.2	519	Gaa/Aaa	10/10	0.309578600733339	1	FACETS	0.948	0.883	1	0.948	0.883	1	INDETERMINATE	1	TRUE	0	0.529133021853364	1		694	569	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724280	52724280	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	139	784	0	ENST00000322088.6:c.1415del	p.Lys472SerfsTer28	p.K472Sfs*28	ENST00000322088	NM_014225.5	471	gAa/ga	12/15	0.309578600733339	1	FACETS	0.529	0.482	0.578	0.529	0.482	0.578	INDETERMINATE	1	TRUE	0	0.529133021853364	1		784	730	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677762	47677762	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1380705599	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	100	647	0	ENST00000347630.2:c.1103G>A	p.Arg368His	p.R368H	ENST00000347630	NM_001007230.1	368	cGc/cAc	11/11	1	2	FACETS	0.553	0.495	0.616	0.553	0.495	0.616	SUBCLONAL	1	TRUE	1	0.529133021853364	2		647	683	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834537	156834537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374170641	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	142	1058	0	ENST00000524377.1:c.305G>A	p.Gly102Asp	p.G102D	ENST00000524377	NM_002529.3	102	gGt/gAt	3/17	1	2	FACETS	0.52	0.473	0.569	0.52	0.473	0.569	SUBCLONAL	1	TRUE	1	0.529133021853364	2		1058	1033	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597883	43597883	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	147	1011	1	ENST00000355710.3:c.431G>T	p.Arg144Leu	p.R144L	ENST00000355710	NM_020975.4	144	cGc/cTc	3/20	0.309578600733339	1	FACETS	0.455	0.415	0.497	0.455	0.415	0.497	INDETERMINATE	1	TRUE	0	0.529133021853364	1		1012	898	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431114	49431114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1397945395	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	278	844	1	ENST00000301067.7:c.10025G>A	p.Arg3342His	p.R3342H	ENST00000301067	NM_003482.3	3342	cGc/cAc	34/54	0.303832059492758	3	FACETS	1	0.99	1	0.626	0.588	0.665	INDETERMINATE	1	TRUE	1	0.529133021853364	3		845	1061	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144997	58144997	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501931	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	240	717	0	ENST00000257904.6:c.347C>T	p.Thr116Met	p.T116M	ENST00000257904	NM_000075.3	116	aCg/aTg	3/8	0.303832059492758	3	FACETS	1	0.988	1	0.619	0.579	0.661	INDETERMINATE	1	TRUE	1	0.529133021853364	3		717	926	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822611	72822611	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	234	738	0	ENST00000268489.5:c.9564G>T	p.Met3188Ile	p.M3188I	ENST00000268489	NM_006885.3	3188	atG/atT	10/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.529133021853364	2		738	788	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110078	8110078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751644642	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	242	633	0	ENST00000585124.1:c.527G>A	p.Arg176Gln	p.R176Q	ENST00000585124	NM_004217.3	176	cGa/cAa	6/9	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.529133021853364	2		633	731	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857743	59857743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	116	455	3	ENST00000259008.2:c.1814G>A	p.Gly605Asp	p.G605D	ENST00000259008	NM_032043.2	605	gGc/gAc	13/20	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.529133021853364	2		458	427	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968142	18968142	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	130	796	0	ENST00000262803.5:c.1982G>A	p.Gly661Asp	p.G661D	ENST00000262803	NM_002911.3	661	gGc/gAc	15/24	0.309578600733339	1	FACETS	0.522	0.474	0.572	0.522	0.474	0.572	INDETERMINATE	1	TRUE	0	0.529133021853364	1		796	692	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918076	50918076	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	144	881	1	ENST00000440232.2:c.2393A>C	p.Tyr798Ser	p.Y798S	ENST00000440232	NM_002691.3	798	tAc/tCc	20/27	0.309578600733339	1	FACETS	0.497	0.454	0.543	0.497	0.454	0.543	INDETERMINATE	1	TRUE	0	0.529133021853364	1		882	805	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027670	48027670	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1558665790	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	64	410	0	ENST00000234420.5:c.2548T>C	p.Tyr850His	p.Y850H	ENST00000234420	NM_000179.2	850	Tac/Cac	4/10	1	2	FACETS	0.514	0.446	0.587	0.514	0.446	0.587	SUBCLONAL	1	TRUE	1	0.529133021853364	2		410	471	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149222	61149223	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	165	436	0	ENST00000295025.8:c.1414dup	p.Met472AsnfsTer16	p.M472Nfs*16	ENST00000295025	NM_002908.2	471	gga/ggAa	11/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.529133021853364	2		436	477	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070355	37070355	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs63751435	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	166	562	0	ENST00000231790.2:c.1491del	p.Arg498GlufsTer10	p.R498Efs*10	ENST00000231790	NM_000249.3	497	cGg/cg	13/19	0.529343361919803	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.529133021853364	1		562	431	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142993	47142993	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	102	685	0	ENST00000409792.3:c.4970C>A	p.Pro1657His	p.P1657H	ENST00000409792	NM_014159.6	1657	cCt/cAt	8/21	0.529133021853364	2	FACETS	0.604	0.541	0.671	0.302	0.27	0.336	SUBCLONAL	1	TRUE	0	0.529133021853364	2		685	638	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436674	52436676	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	367	838	0	ENST00000460680.1:c.1998_2000del	p.Arg667del	p.R667del	ENST00000460680	NM_004656.3	666	agAAGg/agg	16/17	0.529133021853364	2	FACETS	0.958	0.916	1	0.958	0.916	1	CLONAL	2	TRUE	0	0.529133021853364	2		838	724	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643470	52643470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	87	662	0	ENST00000394830.3:c.2426C>T	p.Ala809Val	p.A809V	ENST00000394830	NM_018313.4	809	gCt/gTt	17/30	0.529133021853364	2	FACETS	0.628	0.557	0.703	0.314	0.278	0.352	SUBCLONAL	1	TRUE	0	0.529133021853364	2		662	524	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607155	189607155	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1261217150	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	157	967	0	ENST00000264731.3:c.1534A>G	p.Met512Val	p.M512V	ENST00000264731	NM_003722.4	512	Atg/Gtg	12/14	0.309578600733339	1	FACETS	0.56	0.513	0.608	0.56	0.513	0.608	INDETERMINATE	1	TRUE	0	0.529133021853364	1		967	780	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950120	38950120	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	213	670	0	ENST00000357387.3:c.3830T>C	p.Leu1277Pro	p.L1277P	ENST00000357387	NM_152756.3	1277	cTg/cCg	31/38	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.529133021853364	2		670	710	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722246	176722246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	98	603	1	ENST00000439151.2:c.7877C>T	p.Ala2626Val	p.A2626V	ENST00000439151	NM_022455.4	2626	gCc/gTc	23/23	1	2	FACETS	0.505	0.45	0.563	0.505	0.45	0.563	SUBCLONAL	1	TRUE	1	0.529133021853364	2		604	734	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140508746	140508746	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	104	679	0	ENST00000288602.6:c.554T>C	p.Leu185Pro	p.L185P	ENST00000288602	NM_004333.4	185	cTg/cCg	4/18	0.309578600733339	1	FACETS	0.488	0.438	0.541	0.488	0.438	0.541	INDETERMINATE	1	TRUE	0	0.529133021853364	1		679	592	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	163	480	1	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	1	2	FACETS	0.95	0.874	1	0.95	0.874	1	CLONAL	1	TRUE	1	0.475350920343062	2		481	722	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0046846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	182	373	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	NA	2	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.475350920343062	2		373	690	SUCCESS
APC	324	MSKCC	GRCh37	5	112175328	112175328	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0046846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	163	267	0	ENST00000257430.4:c.4037C>G	p.Ser1346Ter	p.S1346*	ENST00000257430	NM_000038.5	1346	tCa/tGa	16/16	0.475350920343062	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.475350920343062	2		267	333	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367797	15367797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1195390127	NA	P-0046846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	373	686	2	ENST00000263377.2:c.1529G>A	p.Arg510Gln	p.R510Q	ENST00000263377	NM_058243.2	510	cGg/cAg	8/20	0.437625181855364	3	FACETS	0.913	0.868	0.958	0.913	0.868	0.958	CLONAL	2	TRUE	1	0.475350920343062	3		688	1064	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	275	728	0	ENST00000269305.4:c.376T>C	p.Tyr126His	p.Y126H	ENST00000269305	NM_001126112.2	126	Tac/Cac	5/11	0.475350920343062	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.475350920343062	1		728	779	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442566	52442566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553646022	NA	P-0046846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	208	432	0	ENST00000460680.1:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000460680	NM_004656.3	60	cGa/cAa	4/17	0.154226909937038	3	FACETS	0.771	0.719	0.825	0.771	0.719	0.825	INDETERMINATE	2	TRUE	1	0.475350920343062	3		432	702	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793433	18793433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202143029	NA	P-0046846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	140	399	1	ENST00000266497.5:c.4130G>A	p.Arg1377His	p.R1377H	ENST00000266497		1377	cGt/cAt	30/31	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.475350920343062	2		400	537	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925326	114925326	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	196	466	0	ENST00000543371.1:c.1404G>C	p.Lys468Asn	p.K468N	ENST00000543371	NM_001198531.1	468	aaG/aaC	14/14	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.475350920343062	2		466	603	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805561	46805561	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1286034091	NA	P-0046846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	403	829	3	ENST00000290295.7:c.395G>A	p.Gly132Glu	p.G132E	ENST00000290295	NM_006361.5	132	gGa/gAa	1/2	0.169702176922821	4	FACETS	0.914	0.869	0.96	0.914	0.869	0.96	INDETERMINATE	2	TRUE	2	0.475350920343062	4		832	1369	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101071	26101071	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	204	592	0	ENST00000435504.4:c.21del	p.Lys8ArgfsTer14	p.K8Rfs*14	ENST00000435504		7	agG/ag	1/13	1	2	FACETS	0.983	0.913	1	0.983	0.913	1	CLONAL	1	TRUE	1	0.475350920343062	2		592	873	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149237	61149237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1233682212	NA	P-0049133-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	125	298	0	ENST00000295025.8:c.1427C>T	p.Ser476Phe	p.S476F	ENST00000295025	NM_002908.2	476	tCc/tTc	11/11	0.276308112322455	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.383381913347324	4		298	385	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591291	67591291	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049133-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	121	317	0	ENST00000274335.5:c.1789T>C	p.Trp597Arg	p.W597R	ENST00000274335		597	Tgg/Cgg	13/15	0.385935810900705	4	FACETS	0.815	0.739	0.893	0.815	0.739	0.893	CLONAL	2	TRUE	2	0.383381913347324	4		317	536	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25458622	25458622	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049133-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	158	488	0	ENST00000264709.3:c.2551T>G	p.Phe851Val	p.F851V	ENST00000264709	NM_175629.2	851	Ttc/Gtc	22/23	0.276308112322455	4	FACETS	0.992	0.913	1	0.992	0.913	1	CLONAL	2	TRUE	2	0.383381913347324	4		488	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0049188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	494	643	1	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.751978505964344	2		644	1293	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061389	38061389	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	368	808	0	ENST00000250448.2:c.600C>G	p.Ile200Met	p.I200M	ENST00000250448	NM_004496.3	200	atC/atG	2/2	0.324261581821155	3	FACETS	1	0.993	1	0.639	0.608	0.672	INDETERMINATE	1	TRUE	1	0.751978505964344	3		808	1053	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977949	134977949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56186270	NA	P-0051005-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	224	395	0	ENST00000398015.3:c.2942C>T	p.Thr981Met	p.T981M	ENST00000398015	NM_004441.4	981	aCg/aTg	16/16	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.451984648031127	2		395	668	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432435	49432435	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051005-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	300	678	0	ENST00000301067.7:c.8704C>T	p.Gln2902Ter	p.Q2902*	ENST00000301067	NM_003482.3	2902	Cag/Tag	34/54	0.374084505985381	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.451984648031127	1		678	917	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456650	138456650	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs750830394	NA	P-0051005-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	129	419	0	ENST00000289153.2:c.700A>G	p.Ile234Val	p.I234V	ENST00000289153	NM_006219.2	234	Att/Gtt	4/22	1	2	FACETS	0.933	0.848	1	0.933	0.848	1	CLONAL	1	TRUE	1	0.451984648031127	2		419	612	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457823	69457823	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051005-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	133	536	0	ENST00000227507.2:c.223G>T	p.Glu75Ter	p.E75*	ENST00000227507	NM_053056.2	75	Gag/Tag	2/5	1	2	FACETS	0.857	0.779	0.937	0.857	0.779	0.937	CLONAL	1	TRUE	1	0.451984648031127	2		536	687	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432335	49432335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051005-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	354	747	0	ENST00000301067.7:c.8804C>T	p.Ser2935Leu	p.S2935L	ENST00000301067	NM_003482.3	2935	tCa/tTa	34/54	0.374084505985381	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.451984648031127	1		747	990	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432354	49432354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051005-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	332	714	0	ENST00000301067.7:c.8785C>T	p.Leu2929Phe	p.L2929F	ENST00000301067	NM_003482.3	2929	Ctt/Ttt	34/54	0.374084505985381	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.451984648031127	1		714	968	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432359	49432359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051005-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	333	725	0	ENST00000301067.7:c.8780C>T	p.Ser2927Leu	p.S2927L	ENST00000301067	NM_003482.3	2927	tCa/tTa	34/54	0.374084505985381	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.451984648031127	1		725	982	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432703	49432704	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCTG	novel	NA	P-0051005-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	96	669	0	ENST00000301067.7:c.8431_8435dup	p.Gln2812HisfsTer41	p.Q2812Hfs*41	ENST00000301067	NM_003482.3	2812	cag/caCAGCAg	34/54	0.374084505985381	1	FACETS	0.381	0.339	0.427	0.381	0.339	0.427	SUBCLONAL	1	TRUE	0	0.451984648031127	1		669	862	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346386	89346387	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0051005-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	89	633	0	ENST00000301030.4:c.6562_6563dup	p.Ala2189ArgfsTer30	p.A2189Rfs*30	ENST00000301030	NM_001256183.1	2188	ccg/ccCCg	9/13	0.377917185722804	1	FACETS	0.432	0.383	0.485	0.432	0.383	0.485	SUBCLONAL	1	TRUE	0	0.451984648031127	1		633	705	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1627360	1627360	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051005-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	139	511	0	ENST00000344749.5:c.364C>G	p.Gln122Glu	p.Q122E	ENST00000344749	NM_001136139.2	122	Cag/Gag	6/19	0.454940784663938	1	FACETS	0.858	0.785	0.934	0.858	0.785	0.934	CLONAL	1	TRUE	0	0.451984648031127	1		511	555	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141568662	141568662	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051005-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	103	628	0	ENST00000220592.5:c.800T>A	p.Val267Glu	p.V267E	ENST00000220592	NM_012154.3	267	gTg/gAg	7/19	0.440259652709819	3	FACETS	0.655	0.586	0.729	0.218	0.195	0.243	SUBCLONAL	1	TRUE	0	0.451984648031127	3		628	853	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0051015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	199	738	1	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.553471766830662	1	FACETS	0.942	0.879	1	0.942	0.879	1	CLONAL	1	TRUE	0	0.553471766830662	1		739	552	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989018	41989018	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	141	615	1	ENST00000219905.7:c.1810C>T	p.Gln604Ter	p.Q604*	ENST00000219905	NM_001164273.1	604	Cag/Tag	3/24	0.553471766830662	1	FACETS	0.863	0.794	0.934	0.863	0.794	0.934	CLONAL	1	TRUE	0	0.553471766830662	1		616	427	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534726	18534726	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	138	526	1	ENST00000266497.5:c.1784T>A	p.Phe595Tyr	p.F595Y	ENST00000266497		595	tTc/tAc	12/31	0.518255181188756	1	FACETS	0.882	0.81	0.955	0.882	0.81	0.955	CLONAL	1	TRUE	0	0.553471766830662	1		527	409	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001075	150001075	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	102	543	1	ENST00000253339.5:c.2529A>T	p.Lys843Asn	p.K843N	ENST00000253339		843	aaA/aaT	4/7	0.486068897493402	1	FACETS	0.425	0.381	0.472	0.425	0.381	0.472	SUBCLONAL	1	TRUE	0	0.553471766830662	1		544	627	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0051041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	85	565	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.935	0.826	1	0.935	0.826	1	CLONAL	1	TRUE	1	0.262436263075103	2		565	693	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0051041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	157	347	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	0.248715140323544	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.262436263075103	2		347	534	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519985	NA	P-0051041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	99	545	0	ENST00000269305.4:c.857A>G	p.Glu286Gly	p.E286G	ENST00000269305	NM_001126112.2	286	gAa/gGa	8/11	0.262436263075103	1	FACETS	0.919	0.821	1	0.919	0.821	1	CLONAL	1	TRUE	0	0.262436263075103	1		545	713	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051239-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	209	541	0				ENST00000310581	NM_198253.2	-/1132			0.476015086860308	4	FACETS	0.932	0.87	0.996	0.932	0.87	0.996	CLONAL	2	TRUE	2	0.512223502803231	4		541	662	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916851	178916851	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051239-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	352	563	0	ENST00000263967.3:c.238G>A	p.Glu80Lys	p.E80K	ENST00000263967	NM_006218.2	80	Gaa/Aaa	2/21	0.512797404054306	4	FACETS	0.995	0.951	1	0.995	0.951	1	CLONAL	3	TRUE	1	0.512223502803231	4		563	696	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059194	27059194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051239-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	366	547	0	ENST00000324856.7:c.1831C>T	p.Gln611Ter	p.Q611*	ENST00000324856	NM_006015.4	611	Cag/Tag	4/20	0.512797404054306	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.512223502803231	3		547	570	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182505	99182505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051239-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	125	660	2	ENST00000074304.5:c.2308G>A	p.Val770Met	p.V770M	ENST00000074304	NM_001134224.1	770	Gtg/Atg	22/26	0.512797404054306	4	FACETS	1	0.911	1			1	CLONAL	1	TRUE	NA	0.512223502803231	4		662	734	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630442	47630442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051239-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	151	773	0	ENST00000233146.2:c.112G>A	p.Asp38Asn	p.D38N	ENST00000233146	NM_000251.2	38	Gac/Aac	1/16	0.512797404054306	3	FACETS	0.935	0.856	1	0.468	0.428	0.509	CLONAL	1	TRUE	1	0.512223502803231	3		773	792	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18276981	18276981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051239-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	153	732	0	ENST00000222254.8:c.1428G>A	p.Met476Ile	p.M476I	ENST00000222254	NM_005027.3	476	atG/atA	12/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.512223502803231	2		732	571	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279522	123279522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370877537	NA	P-0051239-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	165	723	0	ENST00000358487.5:c.910G>A	p.Asp304Asn	p.D304N	ENST00000358487	NM_000141.4	304	Gac/Aac	7/18	0.512797404054306	3	FACETS	1	0.953	1	0.525	0.483	0.57	CLONAL	1	TRUE	1	0.512223502803231	3		723	770	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260643	16260643	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051239-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	597	929	0	ENST00000375759.3:c.7908G>C	p.Lys2636Asn	p.K2636N	ENST00000375759	NM_015001.2	2636	aaG/aaC	11/15	0.512797404054306	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.512223502803231	3		929	908	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851255	156851255	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051239-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	135	673	0	ENST00000524377.1:c.2212G>C	p.Asp738His	p.D738H	ENST00000524377	NM_002529.3	738	Gac/Cac	17/17	0.512797404054306	5	FACETS	1	0.929	1	0.342	0.311	0.375	CLONAL	1	TRUE	2	0.512223502803231	5		673	908	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725030	162725030	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051239-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	161	801	0	ENST00000367921.3:c.502C>T	p.Pro168Ser	p.P168S	ENST00000367921	NM_006182.2	168	Cca/Tca	6/18	0.512797404054306	5	FACETS	1	0.947	1	0.348	0.319	0.379	CLONAL	1	TRUE	2	0.512223502803231	5		801	1064	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981210	201981210	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051239-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	178	891	0	ENST00000359651.3:c.289A>G	p.Met97Val	p.M97V	ENST00000359651		97	Atg/Gtg	2/8	0.512797404054306	3	FACETS	1	0.951	1	0.52	0.48	0.562	CLONAL	1	TRUE	1	0.512223502803231	3		891	839	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600624	43600624	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051239-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	166	887	0	ENST00000355710.3:c.850G>C	p.Glu284Gln	p.E284Q	ENST00000355710	NM_020975.4	284	Gag/Cag	4/20	0.458868940572668	4	FACETS	1	0.925	1			1	CLONAL	1	TRUE	NA	0.512223502803231	4		887	972	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217654	7217654	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051239-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	310	686	0	ENST00000380728.2:c.273G>C	p.Lys91Asn	p.K91N	ENST00000380728		91	aaG/aaC	4/11	0.512797404054306	2	FACETS	0.981	0.934	1	0.981	0.934	1	CLONAL	2	TRUE	0	0.512223502803231	2		686	617	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662752	227662752	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051239-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	179	934	0	ENST00000305123.5:c.703G>C	p.Glu235Gln	p.E235Q	ENST00000305123	NM_005544.2	235	Gag/Cag	1/2	1	2	FACETS	0.998	0.923	1	0.998	0.923	1	CLONAL	1	TRUE	1	0.512223502803231	2		934	700	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31393193	31393193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051239-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	118	635	0	ENST00000328111.2:c.2281G>A	p.Glu761Lys	p.E761K	ENST00000328111	NM_006892.3	761	Gaa/Aaa	21/23	0.505348004634703	4	FACETS	0.929	0.839	1	0.464	0.419	0.512	CLONAL	1	TRUE	2	0.512223502803231	4		635	750	SUCCESS
APC	324	MSKCC	GRCh37	5	112179677	112179677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051239-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	132	749	0	ENST00000257430.4:c.8386G>A	p.Asp2796Asn	p.D2796N	ENST00000257430	NM_000038.5	2796	Gat/Aat	16/16	0.512797404054306	3	FACETS	0.84	0.763	0.92	0.42	0.381	0.46	CLONAL	1	TRUE	1	0.512223502803231	3		749	771	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673673	30673673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051239-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	181	841	0	ENST00000376406.3:c.3287C>T	p.Ser1096Leu	p.S1096L	ENST00000376406	NM_014641.2	1096	tCa/tTa	10/15	0.492398348473128	3	FACETS	1	0.946	1			1	CLONAL	1	TRUE	NA	0.512223502803231	3		841	862	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168996	32168996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs8192573	NA	P-0051239-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	162	941	0	ENST00000375023.3:c.4037G>A	p.Arg1346Gln	p.R1346Q	ENST00000375023	NM_004557.3	1346	cGg/cAg	22/30	1	2	FACETS	0.95	0.874	1	0.95	0.874	1	CLONAL	1	TRUE	1	0.512223502803231	2		941	666	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47597189	47597189	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1488259580	NA	P-0051239-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	897	535	0	ENST00000430070.2:c.700G>C	p.Glu234Gln	p.E234Q	ENST00000430070	NM_018095.4	234	Gag/Cag	3/4	0.512223502803231	9	FACETS	0.995	0.974	1			1	CLONAL	8	TRUE	NA	0.512223502803231	9		535	1229	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462803	69462803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051239-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	150	766	0	ENST00000227507.2:c.616G>A	p.Gly206Arg	p.G206R	ENST00000227507	NM_053056.2	206	Ggg/Agg	4/5	0.512223502803231	5	FACETS	0.9	0.821	0.983	0.3	0.273	0.328	CLONAL	1	TRUE	2	0.512223502803231	5		766	1151	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670053	29670053	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051239-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	112	446	0	ENST00000356175.3:c.7026C>G	p.Ile2342Met	p.I2342M	ENST00000356175	NM_000267.3	2342	atC/atG	47/57	0.512797404054306	4	FACETS	1	0.92	1	0.512	0.461	0.565	CLONAL	1	TRUE	2	0.512223502803231	4		446	646	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468908	25468908	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051239-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	116	572	0	ENST00000264709.3:c.1455G>T	p.Gln485His	p.Q485H	ENST00000264709	NM_175629.2	485	caG/caT	12/23	0.490657328491717	3	FACETS	0.995	0.899	1	0.497	0.449	0.548	CLONAL	1	TRUE	1	0.512223502803231	3		572	572	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488730	212488730	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1358626425	NA	P-0051239-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	153	828	0	ENST00000342788.4:c.2119C>G	p.Gln707Glu	p.Q707E	ENST00000342788	NM_005235.2	707	Caa/Gaa	18/28	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.512223502803231	2		828	545	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721160	176721160	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051239-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	167	896	0	ENST00000439151.2:c.6791T>A	p.Leu2264His	p.L2264H	ENST00000439151	NM_022455.4	2264	cTc/cAc	23/23	0.512797404054306	3	FACETS	1	0.968	1	0.548	0.505	0.594	CLONAL	1	TRUE	1	0.512223502803231	3		896	747	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056430	26056430	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051239-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	281	769	0	ENST00000343677.2:c.227del	p.Asn76ThrfsTer13	p.N76Tfs*13	ENST00000343677	NM_005319.3	76	aAc/ac	1/1	0.512797404054306	3	FACETS	0.952	0.899	1	0.952	0.899	1	CLONAL	2	TRUE	1	0.512223502803231	3		769	724	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181537	32181537	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051239-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	130	689	0	ENST00000375023.3:c.2248G>T	p.Gly750Cys	p.G750C	ENST00000375023	NM_004557.3	750	Ggc/Tgc	14/30	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.512223502803231	2		689	500	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225219	53225219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051239-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	60	398	0	ENST00000375401.3:c.2999C>T	p.Ala1000Val	p.A1000V	ENST00000375401	NM_004187.3	1000	gCc/gTc	20/26	0.492398348473128	2	FACETS	0.551	0.476	0.632			1	SUBCLONAL	1	TRUE	NA	0.512223502803231	2		398	425	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0051591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	197	438	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	0.313190738593834	2	FACETS	0.929	0.865	0.994	0.929	0.865	0.994	CLONAL	2	TRUE	0	0.342721640907204	2		438	619	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	66	540	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.913	0.792	1	0.913	0.792	1	CLONAL	1	TRUE	1	0.2167799147739	2		540	667	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0054285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	113	341	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.2167799147739	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.2167799147739	1		341	775	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0054285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	149	588	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.2167799147739	2		588	1345	SUCCESS
EED	8726	MSKCC	GRCh37	11	85975306	85975306	+	splice_donor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0058733-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	98	443	0	ENST00000263360.6:c.726+1del		p.X242_splice	ENST00000263360	NM_003797.3	242			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		443	407	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0059959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	32	261	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.52179057180707	1	FACETS	0.728	0.603	0.863	0.728	0.603	0.863	SUBCLONAL	1	TRUE	0	0.535933214909214	1		261	120	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781504	NA	P-0059959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	328	679	0	ENST00000269305.4:c.314G>T	p.Gly105Val	p.G105V	ENST00000269305	NM_001126112.2	105	gGc/gTc	4/11	0.517590179577885	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.535933214909214	3		679	490	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735470	40735470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761910971	NA	P-0059959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	159	552	0	ENST00000373198.4:c.3403G>A	p.Val1135Met	p.V1135M	ENST00000373198	NM_133170.3	1135	Gtg/Atg	25/32	0.535933214909214	7	FACETS	0.842	0.773	0.915	0.421	0.386	0.458	CLONAL	2	TRUE	3	0.535933214909214	7		552	824	SUCCESS
AR	367	MSKCC	GRCh37	X	66766199	66766199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035114992	NA	P-0059959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	77	578	0	ENST00000374690.3:c.1211C>T	p.Ala404Val	p.A404V	ENST00000374690	NM_000044.3	404	gCg/gTg	1/8	0.163428406708733	6	FACETS	1	0.976	1	0.49	0.432	0.551	INDETERMINATE	1	TRUE	3	0.535933214909214	6		578	405	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29497003	29497003	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397514641	NA	P-0060769-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	64	373	0	ENST00000356175.3:c.574C>T	p.Arg192Ter	p.R192*	ENST00000356175	NM_000267.3	192	Cga/Tga	5/57	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		373	316	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577595	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0060946-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	160	398	0	ENST00000269305.4:c.686_687del	p.Cys229TyrfsTer10	p.C229Yfs*10	ENST00000269305	NM_001126112.2	229	tGT/t	7/11	0.361947895537304	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	0	0.364536151365486	2		398	438	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981635	70981635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060946-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	99	571	0	ENST00000276594.2:c.461C>T	p.Pro154Leu	p.P154L	ENST00000276594	NM_024504.3	154	cCt/cTt	2/8	0.364536151365486	5	FACETS	1	0.925	1	0.349	0.311	0.389	CLONAL	1	TRUE	2	0.364536151365486	5		571	803	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554397	141554397	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060946-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	87	389	0	ENST00000220592.5:c.1754del	p.Pro585ArgfsTer110	p.P585Rfs*110	ENST00000220592	NM_012154.3	585	cCg/cg	14/19	0.364536151365486	5	FACETS	1	0.915	1	0.347	0.307	0.389	CLONAL	1	TRUE	2	0.364536151365486	5		389	710	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0061020-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	60	660	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	1	2	FACETS	0.91	0.782	1	0.91	0.782	1	CLONAL	1	TRUE	1	0.16	2		660	824	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0061020-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	52	513	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.16	2		513	633	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420184	49420184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555185701	NA	P-0061020-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	125	663	0	ENST00000301067.7:c.15565G>A	p.Gly5189Arg	p.G5189R	ENST00000301067	NM_003482.3	5189	Gga/Aga	48/54	0.153872608568028	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	1	0.16	3		663	782	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0061030-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	26	594	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	1	2	FACETS	0.337	0.265	0.419	0.337	0.265	0.419	SUBCLONAL	1	TRUE	1	0.19	2		594	813	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061276-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	359	340	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.828483441824535	2		340	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0061343-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	184	735	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.521081800576216	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.521081800576216	1		735	515	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881002	37881003	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCTCCCCA	rs397516982	NA	P-0061440-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	146	742	0	ENST00000269571.5:c.2332_2340dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	-/GGCTCCCCA	20/27	0.421863151574851	3	FACETS	0.909	0.836	0.984	0.909	0.836	0.984	CLONAL	2	TRUE	1	0.421863151574851	3		742	461	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863677	68863683	+	frameshift_variant	Frame_Shift_Del	DEL	GAAATTG	GAAATTG	-	novel	NA	P-0061440-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	57	484	0	ENST00000261769.5:c.2422_2428del	p.Gly808LeufsTer6	p.G808Lfs*6	ENST00000261769	NM_004360.3	806	GAAATTGga/ga	15/16	0.421863151574851	1	FACETS	0.881	0.764	1	0.881	0.764	1	CLONAL	1	TRUE	0	0.421863151574851	1		484	242	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0121619-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	184	541	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.805	0.749	0.862	0.805	0.749	0.862	CLONAL	1	NA	1	0.875733457106561	2		541	522	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10796822	10796822	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372648972	NA	P-0061584-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	182	570	0	ENST00000361367.2:c.2954G>A	p.Arg985His	p.R985H	ENST00000361367	NM_014633.3	985	cGt/cAt	23/25	1	2	FACETS	0.841	0.779	0.905	0.841	0.779	0.905	CLONAL	1	TRUE	1	0.65258361154531	2		570	663	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	80	541	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.771	0.682	0.866	0.771	0.682	0.866	SUBCLONAL	1	TRUE	1	0.484772153172694	2		541	428	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134270	11134270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs797045981	NA	P-0061661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	139	455	0	ENST00000358026.2:c.2936G>A	p.Arg979Gln	p.R979Q	ENST00000358026	NM_001128849.1	979	cGa/cAa	20/36	0.434303497374831	4	FACETS	1	0.976	1	0.598	0.545	0.653	CLONAL	1	TRUE	2	0.484772153172694	4		455	712	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22161969	22161969	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs530183395	NA	P-0061661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	100	446	0	ENST00000215832.6:c.286G>C	p.Glu96Gln	p.E96Q	ENST00000215832	NM_002745.4	96	Gag/Cag	2/9	0.348339424828075	4	FACETS	1	0.936	1	0.532	0.476	0.591	CLONAL	1	TRUE	2	0.484772153172694	4		446	576	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288942	33288942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747846898	NA	P-0061661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	160	605	0	ENST00000374542.5:c.610C>T	p.Arg204Trp	p.R204W	ENST00000374542	NM_001141970.1	204	Cgg/Tgg	3/8	0.484772153172694	3	FACETS	1	0.975	1	0.575	0.528	0.624	CLONAL	1	TRUE	1	0.484772153172694	3		605	713	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64288930	64288930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	56	358	0	ENST00000370651.3:c.326G>A	p.Gly109Glu	p.G109E	ENST00000370651	NM_003463.4	109	gGg/gAg	4/6	0.484772153172694	3	FACETS	0.872	0.752	1	0.436	0.376	0.502	CLONAL	1	TRUE	1	0.484772153172694	3		358	329	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0061662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	69	956	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.741	0.646	0.844	0.741	0.646	0.844	SUBCLONAL	1	TRUE	1	0.314442818586868	2		956	592	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469985	157469985	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554226099	NA	P-0061662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	75	832	0	ENST00000346085.5:c.2779G>T	p.Gly927Ter	p.G927*	ENST00000346085	NM_020732.3	927	Gga/Tga	9/20	1	2	FACETS	0.723	0.633	0.819	0.723	0.633	0.819	SUBCLONAL	1	TRUE	1	0.314442818586868	2		832	660	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039230	49039230	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	46	436	0	ENST00000267163.4:c.2308C>T	p.Gln770Ter	p.Q770*	ENST00000267163	NM_000321.2	770	Cag/Tag	22/27	1	2	FACETS	0.9	0.762	1	0.9	0.762	1	CLONAL	1	TRUE	1	0.314442818586868	2		436	325	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056247	27056247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	37	838	0	ENST00000324856.7:c.1243C>T	p.His415Tyr	p.H415Y	ENST00000324856	NM_006015.4	415	Cat/Tat	2/20	1	2	FACETS	0.358	0.294	0.429	0.358	0.294	0.429	SUBCLONAL	1	TRUE	1	0.314442818586868	2		838	658	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135637	64135638	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0061662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	73	754	0	ENST00000334205.4:c.1105_1106delinsTT	p.Asp369Phe	p.D369F	ENST00000334205	NM_003942.2	369	GAc/TTc	10/17	1	2	FACETS	0.683	0.597	0.776	0.683	0.597	0.776	SUBCLONAL	1	TRUE	1	0.314442818586868	2		754	680	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005395	29005395	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	35	509	0	ENST00000282397.4:c.866C>G	p.Ala289Gly	p.A289G	ENST00000282397	NM_002019.4	289	gCc/gGc	7/30	1	2	FACETS	0.62	0.509	0.744	0.62	0.509	0.744	SUBCLONAL	1	TRUE	1	0.314442818586868	2		509	359	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868048	56868048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1025198458	NA	P-0061662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	37	713	0	ENST00000308159.5:c.1546G>A	p.Glu516Lys	p.E516K	ENST00000308159	NM_014669.4	516	Gag/Aag	14/22	1	2	FACETS	0.421	0.346	0.505	0.421	0.346	0.505	SUBCLONAL	1	TRUE	1	0.314442818586868	2		713	559	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29563023	29563023	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	50	499	2	ENST00000356175.3:c.3958G>C	p.Glu1320Gln	p.E1320Q	ENST00000356175	NM_000267.3	1320	Gaa/Caa	29/57	1	2	FACETS	0.75	0.638	0.873	0.75	0.638	0.873	SUBCLONAL	1	TRUE	1	0.314442818586868	2		501	424	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045954	26045954	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	61	991	0	ENST00000540144.1:c.316G>C	p.Glu106Gln	p.E106Q	ENST00000540144	NM_003531.2	106	Gaa/Caa	1/1	0.136349632606349	5	FACETS	0.735	0.633	0.846	0.245	0.211	0.282	INDETERMINATE	1	TRUE	2	0.314442818586868	5		991	777	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061663-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	114	541	0				ENST00000310581	NM_198253.2	-/1132			0.118851611387752	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.884179021943191	0		541	300	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720666	89720666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061663-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	56	161	0	ENST00000371953.3:c.820del	p.Trp274GlyfsTer2	p.W274Gfs*2	ENST00000371953	NM_000314.4	273	Ttt/tt	8/9	0.884179021943191	1	FACETS	0.872	0.793	0.946	0.872	0.793	0.946	CLONAL	1	TRUE	0	0.884179021943191	1		161	81	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754268	57754268	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061663-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	208	502	0	ENST00000274289.3:c.583T>C	p.Tyr195His	p.Y195H	ENST00000274289	NM_006622.3	195	Tac/Cac	4/14	0.191949972873842	4	FACETS	1	0.966	1	1	0.966	1	INDETERMINATE	2	TRUE	2	0.884179021943191	4		502	427	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754877	57754877	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061663-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	152	391	0	ENST00000274289.3:c.313A>T	p.Asn105Tyr	p.N105Y	ENST00000274289	NM_006622.3	105	Aac/Tac	2/14	0.191949972873842	4	FACETS	0.887	0.823	0.953	0.887	0.823	0.953	INDETERMINATE	2	TRUE	2	0.884179021943191	4		391	365	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526151	189526151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061664-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	266	768	0	ENST00000264731.3:c.415G>A	p.Ala139Thr	p.A139T	ENST00000264731	NM_003722.4	139	Gcg/Acg	4/14	0.668870140305158	4	FACETS	1	0.962	1	0.519	0.486	0.553	CLONAL	1	TRUE	2	0.739077274587315	4		768	1207	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061665-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	81	541	0				ENST00000310581	NM_198253.2	-/1132			0.184888965174089	4	FACETS	0.767	0.678	0.861	0.767	0.678	0.861	SUBCLONAL	2	TRUE	2	0.293856839640873	4		541	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0061665-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	39	539	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.525	0.434	0.625	0.525	0.434	0.625	SUBCLONAL	1	TRUE	1	0.293856839640873	2		539	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0061665-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	77	595	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	1	2	FACETS	0.989	0.87	1	0.989	0.87	1	CLONAL	1	TRUE	1	0.293856839640873	2		595	530	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941653	48941653	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0061665-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	37	252	0	ENST00000267163.4:c.963C>G	p.Tyr321Ter	p.Y321*	ENST00000267163	NM_000321.2	321	taC/taG	10/27	1	2	FACETS	0.972	0.806	1	0.972	0.806	1	CLONAL	1	TRUE	1	0.293856839640873	2		252	259	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777635	9777635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773473376	NA	P-0061665-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	38	668	1	ENST00000377346.4:c.971G>A	p.Arg324His	p.R324H	ENST00000377346	NM_005026.3	324	cGc/cAc	8/24	1	2	FACETS	0.396	0.326	0.474	0.396	0.326	0.474	SUBCLONAL	1	TRUE	1	0.293856839640873	2		669	653	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056214	27056214	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061665-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	100	613	0	ENST00000324856.7:c.1210C>T	p.Gln404Ter	p.Q404*	ENST00000324856	NM_006015.4	404	Caa/Taa	2/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.293856839640873	2		613	578	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0061666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	89	206	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.248772175997263	1	FACETS	0.996	0.884	1	0.996	0.884	1	CLONAL	1	TRUE	0	0.248772175997263	1		206	629	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057520006	NA	P-0061666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	114	615	0	ENST00000269305.4:c.821T>A	p.Val274Asp	p.V274D	ENST00000269305	NM_001126112.2	274	gTt/gAt	8/11	0.219779534229572	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.248772175997263	1		615	784	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467192	99467192	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	50	476	0	ENST00000268035.6:c.2573C>A	p.Pro858His	p.P858H	ENST00000268035	NM_000875.3	858	cCc/cAc	12/21	1	2	FACETS	0.572	0.484	0.669	0.572	0.484	0.669	SUBCLONAL	1	TRUE	1	0.248772175997263	2		476	703	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127427	17127427	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	48	556	0	ENST00000285071.4:c.427T>C	p.Phe143Leu	p.F143L	ENST00000285071	NM_144997.5	143	Ttc/Ctc	6/14	0.219779534229572	1	FACETS	0.486	0.41	0.57	0.486	0.41	0.57	SUBCLONAL	1	TRUE	0	0.248772175997263	1		556	695	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370952	55370952	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs775421817	NA	P-0061666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	118	569	0	ENST00000297316.4:c.254G>T	p.Arg85Leu	p.R85L	ENST00000297316	NM_022454.3	85	cGg/cTg	1/2	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.248772175997263	2		569	754	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0061667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	64	326	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.280454850393883	2		326	399	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044877	47044877	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	90	355	0	ENST00000377604.3:c.2203G>T	p.Glu735Ter	p.E735*	ENST00000377604	NM_001204468.1	735	Gag/Tag	20/24	0.051055581315961	2	FACETS	1	0.962	1			1	INDETERMINATE	2	TRUE	NA	0.280454850393883	2		355	280	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317012	11317012	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs151205593	NA	P-0061667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	27	595	0	ENST00000361445.4:c.482A>G	p.Asn161Ser	p.N161S	ENST00000361445	NM_004958.3	161	aAt/aGt	4/58	1	2	FACETS	0.419	0.332	0.517	0.419	0.332	0.517	SUBCLONAL	1	TRUE	1	0.280454850393883	2		595	460	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399245	139399245	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375018022	NA	P-0061667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	26	580	0	ENST00000277541.6:c.4898G>A	p.Arg1633His	p.R1633H	ENST00000277541	NM_017617.3	1633	cGt/cAt	26/34	1	2	FACETS	0.44	0.348	0.546	0.44	0.348	0.546	SUBCLONAL	1	TRUE	1	0.280454850393883	2		580	421	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641301	23641301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567217931	NA	P-0061667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	47	606	0	ENST00000261584.4:c.2174C>T	p.Ser725Leu	p.S725L	ENST00000261584	NM_024675.3	725	tCa/tTa	5/13	1	2	FACETS	0.662	0.559	0.777	0.662	0.559	0.777	SUBCLONAL	1	TRUE	1	0.280454850393883	2		606	506	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749594	41749594	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1366012932	NA	P-0061667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	80	517	0	ENST00000301178.4:c.1519C>T	p.Arg507Trp	p.R507W	ENST00000301178	NM_021913.4	507	Cgg/Tgg	12/20	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.280454850393883	2		517	543	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155192	108155192	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	39	360	0	ENST00000278616.4:c.3985G>T	p.Gly1329Ter	p.G1329*	ENST00000278616	NM_000051.3	1329	Gga/Tga	26/63	0.280454850393883	1	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	0	0.280454850393883	1		360	232	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120733	115120733	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	37	639	0	ENST00000257566.3:c.273G>T	p.Lys91Asn	p.K91N	ENST00000257566	NM_016569.3	91	aaG/aaT	1/8	1	2	FACETS	0.602	0.497	0.721	0.602	0.497	0.721	SUBCLONAL	1	TRUE	1	0.280454850393883	2		639	438	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610165	81610165	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	76	611	1	ENST00000298171.2:c.1763C>A	p.Thr588Lys	p.T588K	ENST00000298171	NM_000369.2	588	aCg/aAg	10/10	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.280454850393883	2		612	510	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041874	42041874	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	88	555	0	ENST00000219905.7:c.6070del	p.Ser2024ProfsTer78	p.S2024Pfs*78	ENST00000219905	NM_001164273.1	2023	gaT/ga	17/24	0.280454850393883	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.280454850393883	1		555	386	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024679	14024680	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0061667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	52	376	0	ENST00000311895.7:c.905_906insAT	p.Asp302GlufsTer13	p.D302Efs*13	ENST00000311895	NM_005236.2	302	gat/gaATt	5/11	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.280454850393883	2		376	333	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050383	37050383	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1248251121	NA	P-0061667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	51	334	0	ENST00000231790.2:c.532G>A	p.Glu178Lys	p.E178K	ENST00000231790	NM_000249.3	178	Gaa/Aaa	6/19	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.280454850393883	2		334	356	SUCCESS
ATR	545	MSKCC	GRCh37	3	142180838	142180838	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	22	346	0	ENST00000350721.4:c.7136G>T	p.Trp2379Leu	p.W2379L	ENST00000350721	NM_001184.3	2379	tGg/tTg	42/47	1	2	FACETS	0.679	0.528	0.853	0.679	0.528	0.853	SUBCLONAL	1	TRUE	1	0.280454850393883	2		346	231	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681111	117681111	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	22	478	0	ENST00000368508.3:c.3509A>G	p.Asp1170Gly	p.D1170G	ENST00000368508	NM_002944.2	1170	gAt/gGt	23/43	1	2	FACETS	0.415	0.321	0.524	0.415	0.321	0.524	SUBCLONAL	1	TRUE	1	0.280454850393883	2		478	378	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528596	8528596	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	34	451	0	ENST00000356435.5:c.536G>C	p.Arg179Pro	p.R179P	ENST00000356435		179	cGa/cCa	4/35	0.280454850393883	1	FACETS	0.547	0.447	0.659	0.547	0.447	0.659	SUBCLONAL	1	TRUE	0	0.280454850393883	1		451	381	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128748844	128748845	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1198480500	NA	P-0061669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	35	375	0	ENST00000377970.2:c.12dup	p.Arg5SerfsTer17	p.R5Sfs*17	ENST00000377970	NM_002467.4	2	gat/gaTt	1/3	0.226438316458042	4	FACETS	0.808	0.661	0.973	0.404	0.33	0.487	CLONAL	1	TRUE	2	0.2	4		375	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0061669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	124	593	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.198613068206434	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	2	TRUE	0	0.2	2		593	620	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0061670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	74	540	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.435455782450035	2		540	279	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0061670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	109	593	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.435455782450035	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.435455782450035	1		595	360	SUCCESS
APC	324	MSKCC	GRCh37	5	112174213	112174214	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554084587	NA	P-0061670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	112	617	0	ENST00000257430.4:c.2926dup	p.Arg976LysfsTer9	p.R976Kfs*9	ENST00000257430	NM_000038.5	974	-/A	16/16	1	2	FACETS	0.972	0.878	1	0.972	0.878	1	CLONAL	1	TRUE	1	0.435455782450035	2		617	529	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604785	48604787	+	inframe_deletion	In_Frame_Del	DEL	TAG	TAG	-	novel	NA	P-0061670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	147	561	0	ENST00000342988.3:c.1607_1609del	p.Leu536_Asp537delinsHis	p.L536_D537delinsH	ENST00000342988	NM_005359.5	536	cTAGac/cac	12/12	0.435455782450035	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.435455782450035	1		561	469	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919237	178919237	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	65	372	0	ENST00000263967.3:c.722T>G	p.Leu241Arg	p.L241R	ENST00000263967	NM_006218.2	241	cTc/cGc	4/21	1	2	FACETS	0.786	0.684	0.894	0.786	0.684	0.894	SUBCLONAL	1	TRUE	1	0.435455782450035	2		372	380	SUCCESS
APC	324	MSKCC	GRCh37	5	112175740	112175762	+	frameshift_variant	Frame_Shift_Del	DEL	AGATGCTGATACTTTATTACATT	AGATGCTGATACTTTATTACATT	-	novel	NA	P-0061670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	130	633	0	ENST00000257430.4:c.4449_4471del	p.Asp1484CysfsTer22	p.D1484Cfs*22	ENST00000257430	NM_000038.5	1483	ccAGATGCTGATACTTTATTACATTtt/cctt	16/16	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.435455782450035	2		633	573	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0061671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	124	566	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.687	0.623	0.754	0.687	0.623	0.754	SUBCLONAL	1	TRUE	1	0.574591703068842	2		567	628	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0061671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	181	373	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.52953536250776	3	FACETS	0.97	0.906	1	0.97	0.906	1	CLONAL	2	TRUE	1	0.574591703068842	3		373	418	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0061671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	145	597	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.854	0.782	0.928	0.854	0.782	0.928	CLONAL	1	TRUE	1	0.574591703068842	2		597	591	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0061671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	141	534	1	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.52953536250776	3	FACETS	0.978	0.905	1	0.978	0.905	1	CLONAL	2	TRUE	1	0.574591703068842	3		535	323	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368208	45368208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	222	378	1	ENST00000262160.6:c.1394G>A	p.Ser465Asn	p.S465N	ENST00000262160	NM_005901.5	465	aGc/aAc	11/11	0.543673321754019	2	FACETS	0.929	0.878	0.979	0.929	0.878	0.979	CLONAL	2	TRUE	0	0.574591703068842	2		379	416	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412110	63412110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852216	NA	P-0061671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	178	586	1	ENST00000330258.3:c.1057C>T	p.Arg353Ter	p.R353*	ENST00000330258	NM_152424.3	353	Cga/Tga	2/2	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.574591703068842	2		587	553	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934222	39934222	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1358504792	NA	P-0061671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	164	551	1	ENST00000378444.4:c.377C>T	p.Pro126Leu	p.P126L	ENST00000378444	NM_001123385.1	126	cCg/cTg	4/15	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.574591703068842	2		552	552	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473616	67473616	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs778356642	NA	P-0061671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	302	454	3	ENST00000327367.4:c.696G>A	p.Trp232Ter	p.W232*	ENST00000327367	NM_005902.3	232	tgG/tgA	6/9	0.560660996536271	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.574591703068842	2		457	492	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78426108	78426108	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	149	535	2	ENST00000370768.2:c.1417G>A	p.Gly473Arg	p.G473R	ENST00000370768	NM_003902.3	473	Ggg/Agg	15/20	1	2	FACETS	0.896	0.822	0.972	0.896	0.822	0.972	CLONAL	1	TRUE	1	0.574591703068842	2		537	579	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554445	63554445	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs765473342	NA	P-0061671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	211	606	1	ENST00000307078.5:c.294C>A	p.Phe98Leu	p.F98L	ENST00000307078	NM_004655.3	98	ttC/ttA	2/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.574591703068842	2		607	666	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120283	70120284	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCCC	novel	NA	P-0061671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	183	568	0	ENST00000245479.2:c.1286_1290dup	p.Ser431AlafsTer41	p.S431Afs*41	ENST00000245479	NM_000346.3	429	agc/aGCCCCgc	3/3	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.574591703068842	2		568	629	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120284	70120285	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0061671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	185	571	0	ENST00000245479.2:c.1290dup	p.Ser431LeufsTer147	p.S431Lfs*147	ENST00000245479	NM_000346.3	429	agc/agCc	3/3	1	2	FACETS	0.929	0.861	1	0.929	0.861	1	CLONAL	1	TRUE	1	0.574591703068842	2		571	693	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548328	41548328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770254783	NA	P-0061671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	94	471	0	ENST00000263253.7:c.3116C>T	p.Pro1039Leu	p.P1039L	ENST00000263253	NM_001429.3	1039	cCg/cTg	16/31	1	2	FACETS	0.586	0.523	0.654	0.586	0.523	0.654	SUBCLONAL	1	TRUE	1	0.574591703068842	2		471	558	SUCCESS
APC	324	MSKCC	GRCh37	5	112170743	112170744	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0061671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	160	461	1	ENST00000257430.4:c.1840dup	p.Ala614GlyfsTer20	p.A614Gfs*20	ENST00000257430	NM_000038.5	613	-/G	15/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.574591703068842	2		462	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0061672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	18	471	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	1	2	FACETS	0.564	0.423	0.733	0.564	0.423	0.733	SUBCLONAL	1	TRUE	1	0.11	2		471	580	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0061672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	15	272	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.687	0.501	0.912	0.687	0.501	0.912	SUBCLONAL	1	TRUE	1	0.11	2		272	397	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0061673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	156	369	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.817459888640055	2		369	370	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	311	589	0	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.817459888640055	2		589	715	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0061673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	395	532	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.817459888640055	2		532	893	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0061673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	128	317	1	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.817459888640055	2		318	311	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106559	27106559	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	407	870	0	ENST00000324856.7:c.6170G>C	p.Arg2057Pro	p.R2057P	ENST00000324856	NM_006015.4	2057	cGg/cCg	20/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.817459888640055	2		870	941	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100458	157100459	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0061673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	45	192	0	ENST00000346085.5:c.1397dup	p.Gln467ProfsTer68	p.Q467Pfs*68	ENST00000346085	NM_020732.3	465	-/G	1/20	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.817459888640055	2		192	110	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061674-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	476	733	0	ENST00000269305.4:c.166del	p.Glu56LysfsTer67	p.E56Kfs*67	ENST00000269305	NM_001126112.2	56	Gaa/aa	4/11	0.712681265907388	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.712681265907388	2		733	628	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432743	49432743	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1356426477	NA	P-0061674-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	209	633	0	ENST00000301067.7:c.8396A>G	p.Tyr2799Cys	p.Y2799C	ENST00000301067	NM_003482.3	2799	tAt/tGt	34/54	1	2	FACETS	0.968	0.904	1	0.968	0.904	1	CLONAL	1	TRUE	1	0.712681265907388	2		633	606	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288680	33288680	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061674-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	412	547	0	ENST00000374542.5:c.872G>C	p.Arg291Pro	p.R291P	ENST00000374542	NM_001141970.1	291	cGg/cCg	3/8	0.712681265907388	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.712681265907388	2		547	570	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763984	76763984	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061674-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	138	511	0	ENST00000373344.5:c.7324C>G	p.Pro2442Ala	p.P2442A	ENST00000373344	NM_000489.3	2442	Cca/Gca	35/35	0.510912963187179	3	FACETS	0.712	0.648	0.778	0.356	0.324	0.389	SUBCLONAL	1	TRUE	1	0.712681265907388	3		511	738	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874347	151874347	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	81	663	0	ENST00000262189.6:c.8191G>T	p.Glu2731Ter	p.E2731*	ENST00000262189	NM_170606.2	2731	Gaa/Taa	38/59	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.360351103846382	2		663	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0061676-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	76	622	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.19	2		622	750	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014071	14014071	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs368281878	NA	P-0061676-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	29	519	0	ENST00000311895.7:c.49G>T	p.Glu17Ter	p.E17*	ENST00000311895	NM_005236.2	17	Gag/Tag	1/11	1	2	FACETS	0.552	0.442	0.678	0.552	0.442	0.678	SUBCLONAL	1	TRUE	1	0.19	2		519	553	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913351	NA	P-0061676-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	17	439	0	ENST00000288602.6:c.1397G>C	p.Gly466Ala	p.G466A	ENST00000288602	NM_004333.4	466	gGa/gCa	11/18	1	2	FACETS	0.663	0.495	0.862	0.663	0.495	0.862	SUBCLONAL	1	TRUE	1	0.19	2		439	270	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678349	88678349	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061676-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	48	603	0	ENST00000360948.2:c.1187T>A	p.Leu396His	p.L396H	ENST00000360948	NM_001012338.2	396	cTc/cAc	9/19	1	2	FACETS	0.915	0.773	1	0.915	0.773	1	CLONAL	1	TRUE	1	0.19	2		603	552	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	338142	338142	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061676-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	33	642	0	ENST00000262320.3:c.2569A>G	p.Lys857Glu	p.K857E	ENST00000262320	NM_003502.3	857	Aaa/Gaa	11/11	1	2	FACETS	0.55	0.446	0.667	0.55	0.446	0.667	SUBCLONAL	1	TRUE	1	0.19	2		642	632	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754863	29754863	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061676-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	67	714	0	ENST00000389048.3:c.1072T>A	p.Ser358Thr	p.S358T	ENST00000389048	NM_004304.4	358	Tct/Act	4/29	1	2	FACETS	0.988	0.858	1	0.988	0.858	1	CLONAL	1	TRUE	1	0.19	2		714	714	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380506	31380506	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061676-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	43	687	0	ENST00000328111.2:c.996G>T	p.Met332Ile	p.M332I	ENST00000328111	NM_006892.3	332	atG/atT	9/23	1	2	FACETS	0.659	0.55	0.78	0.659	0.55	0.78	SUBCLONAL	1	TRUE	1	0.19	2		687	687	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564423	139564423	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061676-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	48	629	0	ENST00000308874.7:c.371G>T	p.Arg124Leu	p.R124L	ENST00000308874		124	cGc/cTc	6/10	1	2	FACETS	0.831	0.702	0.974	0.831	0.702	0.974	CLONAL	1	TRUE	1	0.19	2		629	608	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916414	39916415	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0061676-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	32	451	0	ENST00000378444.4:c.4588_4589delinsTT	p.Gly1530Leu	p.G1530L	ENST00000378444	NM_001123385.1	1530	GGa/TTa	11/15	0.148475543717206	1	FACETS	0.561	0.455	0.682	0.561	0.455	0.682	SUBCLONAL	1	TRUE	0	0.19	1		451	543	SUCCESS
AR	367	MSKCC	GRCh37	X	66765982	66765982	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061676-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	49	695	0	ENST00000374690.3:c.994G>T	p.Ala332Ser	p.A332S	ENST00000374690	NM_000044.3	332	Gca/Tca	1/8	0.148475543717206	1	FACETS	0.773	0.654	0.904	0.773	0.654	0.904	CLONAL	1	TRUE	0	0.19	1		695	604	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76953099	76953099	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0061676-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	11	339	0	ENST00000373344.5:c.214A>T	p.Lys72Ter	p.K72*	ENST00000373344	NM_000489.3	72	Aag/Tag	4/35	0.148475543717206	1	FACETS	0.838	0.583	1	0.838	0.583	1	CLONAL	1	TRUE	0	0.19	1		339	125	SUCCESS
YES1	7525	MSKCC	GRCh37	18	751704	751704	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs368508541	NA	P-0061678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	25	319	0	ENST00000314574.4:c.371+1G>A		p.X124_splice	ENST00000314574	NM_005433.3	124			1	2	FACETS	0.704	0.563	0.86	0.704	0.563	0.86	SUBCLONAL	1	TRUE	1	0.55944405728502	2		319	127	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179465	56179465	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	47	518	2	ENST00000399503.3:c.3778G>A	p.Ala1260Thr	p.A1260T	ENST00000399503	NM_005921.1	1260	Gct/Act	15/20	1	2	FACETS	0.939	0.804	1	0.939	0.804	1	CLONAL	1	TRUE	1	0.55944405728502	2		520	179	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588174	67588174	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	36	476	0	ENST00000274335.5:c.1004G>T	p.Trp335Leu	p.W335L	ENST00000274335		335	tGg/tTg	7/15	1	2	FACETS	0.858	0.717	1	0.858	0.717	1	CLONAL	1	TRUE	1	0.55944405728502	2		476	150	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0061679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	245	476	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	0.40720069044158	1	FACETS	0.854	0.806	0.903	1	0.994	1	CLONAL	2	TRUE	0	0.40720069044158	1		476	561	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0061679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	286	465	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	0.40720069044158	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.40720069044158	3		465	492	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221607	36221607	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0061679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	167	760	0	ENST00000222270.7:c.5277-1G>A		p.X1759_splice	ENST00000222270	NM_014727.1	1759			0.154151695087174	3	FACETS	1	0.986	1	0.67	0.617	0.725	INDETERMINATE	1	TRUE	1	0.40720069044158	3		760	737	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0061680-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	152	1006	3	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	0.317221383719486	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.317221383719486	1		1009	791	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199955	108199955	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061680-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	12	516	0	ENST00000278616.4:c.7297C>T	p.Gln2433Ter	p.Q2433*	ENST00000278616	NM_000051.3	2433	Cag/Tag	49/63	0.219059458142905	0	FACETS	0.276	0.194	0.377			1	SUBCLONAL	1	TRUE	0	0.317221383719486	0		516	187	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255302	16255302	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061680-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	158	884	0	ENST00000375759.3:c.2567A>C	p.Lys856Thr	p.K856T	ENST00000375759	NM_015001.2	856	aAa/aCa	11/15	0.182708477086008	3	FACETS	1	0.987	1	0.72	0.66	0.782	INDETERMINATE	1	TRUE	1	0.317221383719486	3		884	802	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183752	10183753	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0061680-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	87	766	1	ENST00000256474.2:c.221_222delinsAT	p.Val74Asp	p.V74D	ENST00000256474	NM_000551.3	74	gTC/gAT	1/3	0.317221383719486	1	FACETS	0.961	0.854	1	0.961	0.854	1	CLONAL	1	TRUE	0	0.317221383719486	1		767	480	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643916	52643916	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061680-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	52	513	0	ENST00000394830.3:c.1980del	p.Lys661AsnfsTer2	p.K661Nfs*2	ENST00000394830	NM_018313.4	660	caG/ca	17/30	0.317221383719486	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.317221383719486	1		513	201	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151866329	151866330	+	stop_gained,inframe_insertion	Nonsense_Mutation	INS	-	-	CCATCCTAA	novel	NA	P-0061680-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	32	544	0	ENST00000262189.6:c.9454-4_9458dup	p.Gly3153_Ser3154insTer	p.G3153_S3154ins*	ENST00000262189	NM_170606.2	3153	ggc/ggTTAGGATGGc	41/59	1	2	FACETS	0.885	0.723	1	0.885	0.723	1	CLONAL	1	TRUE	1	0.317221383719486	2		544	228	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0061681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	194	681	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.637468081748634	1	FACETS	0.909	0.851	0.968	0.909	0.851	0.968	CLONAL	1	TRUE	0	0.637468081748634	1		681	456	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940012	76940012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs122445105	NA	P-0061681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	200	268	0	ENST00000373344.5:c.736C>T	p.Arg246Cys	p.R246C	ENST00000373344	NM_000489.3	246	Cgc/Tgc	9/35	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.637468081748634	1		268	309	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696431	47696431	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519969	NA	P-0061681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	182	618	0	ENST00000347630.2:c.392G>C	p.Trp131Ser	p.W131S	ENST00000347630	NM_001007230.1	131	tGg/tCg	6/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.637468081748634	2		618	511	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639056	3639056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	133	695	0	ENST00000294008.3:c.4583C>T	p.Ala1528Val	p.A1528V	ENST00000294008	NM_032444.2	1528	gCc/gTc	12/15	1	2	FACETS	0.942	0.862	1	0.942	0.862	1	CLONAL	1	TRUE	1	0.637468081748634	2		695	443	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500606	99500606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs909142461	NA	P-0061681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	53	661	0	ENST00000268035.6:c.4039G>A	p.Ala1347Thr	p.A1347T	ENST00000268035	NM_000875.3	1347	Gcc/Acc	21/21	1	2	FACETS	0.359	0.306	0.417	0.359	0.306	0.417	SUBCLONAL	1	TRUE	1	0.637468081748634	2		661	463	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436557	110436557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	188	787	0	ENST00000375856.3:c.1844C>T	p.Ser615Phe	p.S615F	ENST00000375856	NM_003749.2	615	tCc/tTc	1/2	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.637468081748634	2		787	477	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061155	38061167	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCCCGCCGCCG	GCCCCCGCCGCCG	-	novel	NA	P-0061681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	171	755	0	ENST00000250448.2:c.822_834del	p.Gly276AlafsTer41	p.G276Afs*41	ENST00000250448	NM_004496.3	274	gcCGGCGGCGGGGGC/gc	2/2	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.637468081748634	2		755	533	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40469222	40469222	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	128	486	0	ENST00000264657.5:c.2122A>G	p.Thr708Ala	p.T708A	ENST00000264657	NM_139276.2	708	Acc/Gcc	22/24	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.637468081748634	2		486	383	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688699	47688699	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	176	525	0	ENST00000347630.2:c.601G>C	p.Asp201His	p.D201H	ENST00000347630	NM_001007230.1	201	Gac/Cac	7/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.637468081748634	2		525	547	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637537	52637537	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	31	313	0	ENST00000394830.3:c.2779G>T	p.Glu927Ter	p.E927*	ENST00000394830	NM_018313.4	927	Gaa/Taa	18/30	0.394238740196992	1	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	0	0.394238740196992	1		313	121	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90949290	90949299	+	frameshift_variant	Frame_Shift_Del	DEL	TGTTGATTTT	TGTTGATTTT	-	novel	NA	P-0061682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	10	197	0	ENST00000265433.3:c.2189_2198del	p.Gln730LeufsTer18	p.Q730Lfs*18	ENST00000265433	NM_002485.4	730	cAAAATCAACAt/ct	15/16	1	2	FACETS	0.564	0.386	0.782	0.564	0.386	0.782	SUBCLONAL	1	TRUE	1	0.394238740196992	2		197	90	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967510	90967510	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0061682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	30	409	0	ENST00000265433.3:c.1397+1G>T		p.X466_splice	ENST00000265433	NM_002485.4	466			1	2	FACETS	1	0.828	1	1	0.828	1	CLONAL	1	TRUE	1	0.394238740196992	2		409	150	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231061	53231061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	97	338	0	ENST00000375401.3:c.1841C>T	p.Ala614Val	p.A614V	ENST00000375401	NM_004187.3	614	gCt/gTt	13/26	1	1	FACETS	0.803	0.729	0.879	1	0.985	1	CLONAL	2	TRUE	0	0.394238740196992	1		338	246	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191513	10191513	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1131690962	NA	P-0061683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	39	477	0	ENST00000256474.2:c.506T>C	p.Leu169Pro	p.L169P	ENST00000256474	NM_000551.3	169	cTa/cCa	3/3	0.21396123602889	1	FACETS	0.482	0.399	0.576	0.482	0.399	0.576	SUBCLONAL	1	TRUE	0	0.21396123602889	1		477	675	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349606	15349616	+	frameshift_variant	Frame_Shift_Del	DEL	TGGTCCAGCAT	TGGTCCAGCAT	-	novel	NA	P-0061683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	56	661	0	ENST00000263377.2:c.3958_3968del	p.Met1320AlafsTer23	p.M1320Afs*23	ENST00000263377	NM_058243.2	1320	ATGCTGGACCAg/g	19/20	1	2	FACETS	0.75	0.641	0.869	0.75	0.641	0.869	SUBCLONAL	1	TRUE	1	0.21396123602889	2		661	698	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162546	47162546	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	43	452	0	ENST00000409792.3:c.3580del	p.Ile1194TyrfsTer42	p.I1194Yfs*42	ENST00000409792	NM_014159.6	1194	Ata/ta	3/21	0.21396123602889	1	FACETS	0.799	0.669	0.943	0.799	0.669	0.943	CLONAL	1	TRUE	0	0.21396123602889	1		452	449	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209034	133209034	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	97	515	0	ENST00000320574.5:c.6197T>C	p.Ile2066Thr	p.I2066T	ENST00000320574	NM_006231.2	2066	aTc/aCc	45/49	1	2	FACETS	0.803	0.72	0.89	0.803	0.72	0.89	CLONAL	1	TRUE	1	0.548115350571903	2		515	441	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56339043	56339044	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTGGCGGAG	novel	NA	P-0061684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	85	472	0	ENST00000348428.3:c.176_184dup	p.Glu59_Ala61dup	p.E59_A61dup	ENST00000348428	NM_006785.3	59	-/CTGGCGGAG	1/17	1	2	FACETS	0.571	0.506	0.641	0.571	0.506	0.641	SUBCLONAL	1	TRUE	1	0.548115350571903	2		472	543	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183748	10183767	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGTCATCTTCTGCAATCG	CAGGTCATCTTCTGCAATCG	-	novel	NA	P-0061684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	108	570	0	ENST00000256474.2:c.220_239del	p.Val74SerfsTer51	p.V74Sfs*51	ENST00000256474	NM_000551.3	73	CAGGTCATCTTCTGCAATCGc/c	1/3	0.473722048122749	1	FACETS	0.636	0.574	0.7	0.636	0.574	0.7	SUBCLONAL	1	TRUE	0	0.548115350571903	1		570	450	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	63	643	0	ENST00000347630.2:c.399C>A	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttA	6/11	0.13419239437249	4	FACETS	0.873	0.755	1	0.436	0.377	0.501	INDETERMINATE	1	TRUE	2	0.326066094206697	4		643	587	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184667	11184670	+	frameshift_variant	Frame_Shift_Del	DEL	AAAC	AAAC	-	novel	NA	P-0061685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	29	533	0	ENST00000361445.4:c.6547_6550del	p.Val2183SerfsTer3	p.V2183Sfs*3	ENST00000361445	NM_004958.3	2183	GTTTtc/tc	47/58	0.163848127753263	3	FACETS	0.5	0.401	0.612	0.25	0.2	0.306	INDETERMINATE	1	TRUE	1	0.326066094206697	3		533	414	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254967	16254968	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0061685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	98	663	0	ENST00000375759.3:c.2236_2237del	p.Arg746ValfsTer4	p.R746Vfs*4	ENST00000375759	NM_015001.2	744	gcAGag/gcag	11/15	0.163848127753263	3	FACETS	1	0.948	1	0.55	0.492	0.613	INDETERMINATE	1	TRUE	1	0.326066094206697	3		663	635	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717757	89717758	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1554825249	NA	P-0061685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	34	324	0	ENST00000371953.3:c.783_784del	p.Asn262GlnfsTer35	p.N262Qfs*35	ENST00000371953	NM_000314.4	261	cAG/c	7/9	1	2	FACETS	0.66	0.541	0.793	0.66	0.541	0.793	SUBCLONAL	1	TRUE	1	0.326066094206697	2		324	316	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112577	115112591	+	frameshift_variant	Frame_Shift_Del	DEL	TCGGGGCCATGCTCC	TCGGGGCCATGCTCC	AAGA	novel	NA	P-0061685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	62	751	1	ENST00000257566.3:c.1149_1163delinsTCTT	p.Glu383AspfsTer20	p.E383Dfs*20	ENST00000257566	NM_016569.3	383	gaGGAGCATGGCCCCGAg/gaTCTTg	7/8	0.158390413991769	3	FACETS	0.793	0.685	0.909	0.396	0.342	0.455	INDETERMINATE	1	TRUE	1	0.326066094206697	3		752	558	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061111	38061112	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0061685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	42	764	0	ENST00000250448.2:c.877_878del	p.Ser293ProfsTer9	p.S293Pfs*9	ENST00000250448	NM_004496.3	293	AGc/c	2/2	0.163848127753263	3	FACETS	0.619	0.517	0.733	0.31	0.258	0.367	INDETERMINATE	1	TRUE	1	0.326066094206697	3		764	484	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041106	42041110	+	frameshift_variant	Frame_Shift_Del	DEL	TGTCA	TGTCA	-	novel	NA	P-0061685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	80	720	0	ENST00000219905.7:c.5487_5491del	p.Met1830SerfsTer19	p.M1830Sfs*19	ENST00000219905	NM_001164273.1	1828	ccTGTCAtg/cctg	16/24	0.107249445679597	4	FACETS	1	0.967	1	0.64	0.565	0.721	INDETERMINATE	1	TRUE	2	0.326066094206697	4		720	508	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046641	42046642	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0061685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	57	395	0	ENST00000219905.7:c.7018_7019del	p.Val2340ArgfsTer4	p.V2340Rfs*4	ENST00000219905	NM_001164273.1	2339	TGt/t	18/24	0.107249445679597	4	FACETS	1	0.907	1	0.535	0.46	0.617	INDETERMINATE	1	TRUE	2	0.326066094206697	4		395	433	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892261	9892261	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	36	704	0	ENST00000330684.3:c.2229A>T	p.Glu743Asp	p.E743D	ENST00000330684	NM_001134407.1	743	gaA/gaT	11/13	0.326066094206697	0	FACETS	0.397	0.326	0.475			1	SUBCLONAL	1	TRUE	0	0.326066094206697	0		704	375	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029594	14029595	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0061685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	55	511	0	ENST00000311895.7:c.1807_1808del	p.Leu603GlufsTer12	p.L603Efs*12	ENST00000311895	NM_005236.2	602	cCT/c	8/11	0.107249445679597	4	FACETS	0.893	0.765	1	0.446	0.382	0.517	INDETERMINATE	1	TRUE	2	0.326066094206697	4		511	501	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832603	72832604	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0061685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	57	487	0	ENST00000268489.5:c.3977_3978del	p.Glu1326GlyfsTer24	p.E1326Gfs*24	ENST00000268489	NM_006885.3	1326	gAG/g	9/10	0.163848127753263	3	FACETS	1	0.931	1	0.566	0.488	0.651	INDETERMINATE	1	TRUE	1	0.326066094206697	3		487	359	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950272	15950273	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0061685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	84	519	0	ENST00000268712.3:c.6671_6672del	p.Ser2224Ter	p.S2224*	ENST00000268712	NM_006311.3	2224	tCT/t	42/46	0.13419239437249	4	FACETS	1	0.971	1	0.658	0.583	0.739	INDETERMINATE	1	TRUE	2	0.326066094206697	4		519	519	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132485	11132486	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0061685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	72	854	0	ENST00000358026.2:c.2702_2703del	p.Tyr901CysfsTer43	p.Y901Cfs*43	ENST00000358026	NM_001128849.1	901	TAt/t	19/36	0.163848127753263	3	FACETS	0.955	0.835	1	0.477	0.417	0.542	INDETERMINATE	1	TRUE	1	0.326066094206697	3		854	538	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449884	29449885	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CA	CA	-	novel	NA	P-0061685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	69	882	0	ENST00000389048.3:c.2970_2971del	p.Cys990Ter	p.C990*	ENST00000389048	NM_004304.4	990	tgTGag/tgag	18/29	0.326066094206697	1	FACETS	0.86	0.752	0.975	0.86	0.752	0.975	CLONAL	1	TRUE	0	0.326066094206697	1		882	412	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639588	47639588	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63749897	NA	P-0061685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	54	324	0	ENST00000233146.2:c.687del	p.Ala230LeufsTer16	p.A230Lfs*16	ENST00000233146	NM_000251.2	227	agA/ag	4/16	0.107249445679597	4	FACETS	1	0.953	1	0.64	0.549	0.739	INDETERMINATE	1	TRUE	2	0.326066094206697	4		324	343	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067423	37067424	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1114167435	NA	P-0061685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	83	701	0	ENST00000231790.2:c.1336_1337del	p.Ser446LeufsTer32	p.S446Lfs*32	ENST00000231790	NM_000249.3	445	cAG/c	12/19	0.13419239437249	4	FACETS	0.977	0.862	1	0.488	0.431	0.55	INDETERMINATE	1	TRUE	2	0.326066094206697	4		701	691	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952145	178952149	+	frameshift_variant	Frame_Shift_Del	DEL	TGAAC	TGAAC	-	novel	NA	P-0061685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	56	434	0	ENST00000263967.3:c.3204_*1del		p.LN1067fs	ENST00000263967	NM_006218.2	1067	tTGAAC/t	21/21	0.163848127753263	3	FACETS	0.865	0.742	0.998	0.432	0.371	0.499	INDETERMINATE	1	TRUE	1	0.326066094206697	3		434	462	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803560	1803561	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	novel	NA	P-0061685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	51	840	0	ENST00000260795.2:c.740_741del		p.X247_splice	ENST00000260795		247			1	2	FACETS	0.729	0.621	0.848	0.729	0.621	0.848	SUBCLONAL	1	TRUE	1	0.326066094206697	2		840	429	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559376	141559377	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0061685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	62	612	0	ENST00000220592.5:c.1424_1425del	p.Arg475LysfsTer198	p.R475Kfs*198	ENST00000220592	NM_012154.3	475	aGA/a	12/19	0.163848127753263	3	FACETS	1	0.903	1	0.525	0.455	0.601	INDETERMINATE	1	TRUE	1	0.326066094206697	3		612	421	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739013	145739014	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs746222099	NA	P-0061685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	88	805	0	ENST00000428558.2:c.2141_2142del	p.Glu714AlafsTer94	p.E714Afs*94	ENST00000428558	NM_004260.3	714	gAG/g	13/22	0.163848127753263	3	FACETS	1	0.889	1	0.501	0.444	0.562	INDETERMINATE	1	TRUE	1	0.326066094206697	3		805	626	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518610	204518610	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	111	585	0	ENST00000367182.3:c.1273G>A	p.Glu425Lys	p.E425K	ENST00000367182	NM_001278516.1	425	Gaa/Aaa	11/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.31	2		585	645	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145292	58145292	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	100	745	0	ENST00000257904.6:c.209A>G	p.Asn70Ser	p.N70S	ENST00000257904	NM_000075.3	70	aAt/aGt	2/8	1	2	FACETS	0.756	0.675	0.843	0.756	0.675	0.843	SUBCLONAL	1	TRUE	1	0.31	2		745	853	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0061687-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	76	546	1	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	1	2	FACETS	0.816	0.717	0.921	0.816	0.717	0.921	CLONAL	1	TRUE	1	0.368279347612714	2		547	506	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112412	115112412	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061687-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	29	756	0	ENST00000257566.3:c.1328C>T	p.Ser443Leu	p.S443L	ENST00000257566	NM_016569.3	443	tCg/tTg	7/8	1	2	FACETS	0.378	0.303	0.463	0.378	0.303	0.463	SUBCLONAL	1	TRUE	1	0.368279347612714	2		756	417	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870929	12870929	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061687-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	98	616	0	ENST00000228872.4:c.157del	p.Glu53LysfsTer18	p.E53Kfs*18	ENST00000228872	NM_004064.3	52	atG/at	1/3	0.252147129697445	4	FACETS	1	0.937	1	0.535	0.478	0.597	CLONAL	1	TRUE	2	0.368279347612714	4		616	680	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118720	115118721	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0061687-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	99	593	0	ENST00000257566.3:c.620_621del	p.Leu207GlnfsTer19	p.L207Qfs*19	ENST00000257566	NM_016569.3	207	cTG/c	2/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.368279347612714	2		593	485	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221084	5221084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371881792	NA	P-0061687-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	69	679	1	ENST00000357368.4:c.3382G>A	p.Val1128Ile	p.V1128I	ENST00000357368	NM_002850.3	1128	Gtc/Atc	20/38	1	2	FACETS	0.953	0.834	1	0.953	0.834	1	CLONAL	1	TRUE	1	0.368279347612714	2		680	393	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849512	68849512	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061687-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	92	620	0	ENST00000261769.5:c.1416del	p.Val473SerfsTer8	p.V473Sfs*8	ENST00000261769	NM_004360.3	472	aCc/ac	10/16	0.368279347612714	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.368279347612714	1		620	372	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029309	143029309	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061687-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	14	266	0	ENST00000262992.4:c.2311C>G	p.Gln771Glu	p.Q771E	ENST00000262992	NM_001101669.1	771	Cag/Gag	21/24	1	2	FACETS	0.28	0.202	0.374	0.28	0.202	0.374	SUBCLONAL	1	TRUE	1	0.368279347612714	2		266	272	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949168	151949168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061687-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	50	279	0	ENST00000262189.6:c.1477C>T	p.His493Tyr	p.H493Y	ENST00000262189	NM_170606.2	493	Cac/Tac	11/59	0.230728339202779	3	FACETS	1	0.881	1	0.519	0.442	0.601	CLONAL	1	TRUE	1	0.368279347612714	3		279	310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0061688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	90	539	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.461845237881167	1	FACETS	0.937	0.84	1	0.937	0.84	1	CLONAL	1	TRUE	0	0.461845237881167	1		539	320	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0061688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	136	597	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.461845237881167	2		597	526	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0061688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	67	260	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.461845237881167	2		260	285	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411678	63411678	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	98	288	0	ENST00000330258.3:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000330258	NM_152424.3	497	Cga/Tga	2/2	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.461845237881167	1		288	228	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581229	48581229	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs377767331	NA	P-0061688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	106	516	0	ENST00000342988.3:c.533C>G	p.Ser178Ter	p.S178*	ENST00000342988	NM_005359.5	178	tCa/tGa	5/12	0.436153356772577	1	FACETS	0.983	0.89	1	0.983	0.89	1	CLONAL	1	TRUE	0	0.461845237881167	1		516	359	SUCCESS
APC	324	MSKCC	GRCh37	5	112174096	112174096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs137854575	NA	P-0061688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	65	494	0	ENST00000257430.4:c.2805C>A	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	taC/taA	16/16	1	2	FACETS	0.954	0.835	1	0.954	0.835	1	CLONAL	1	TRUE	1	0.461845237881167	2		494	295	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275768	38275768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781310679	NA	P-0061688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	112	538	0	ENST00000425967.3:c.1501C>T	p.Arg501Cys	p.R501C	ENST00000425967	NM_001174067.1	501	Cgc/Tgc	11/19	0.436153356772577	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.461845237881167	1		538	348	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343550	118343550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	163	645	3	ENST00000534358.1:c.1676C>T	p.Ser559Leu	p.S559L	ENST00000534358	NM_005933.3	559	tCg/tTg	3/36	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.461845237881167	2		648	598	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914550	32914550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358842	NA	P-0061688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	55	583	0	ENST00000380152.3:c.6058G>A	p.Glu2020Lys	p.E2020K	ENST00000380152		2020	Gaa/Aaa	11/27	1	2	FACETS	0.794	0.684	0.912	0.794	0.684	0.912	CLONAL	1	TRUE	1	0.461845237881167	2		583	300	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061689-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	95	541	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.74	0.665	0.819	0.74	0.665	0.819	SUBCLONAL	1	TRUE	1	0.725093039581964	2		541	354	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981305	201981306	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061689-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	164	707	0	ENST00000359651.3:c.385dup	p.Thr129AsnfsTer6	p.T129Nfs*6	ENST00000359651		128	-/A	2/8	1	2	FACETS	0.862	0.796	0.929	0.862	0.796	0.929	CLONAL	1	TRUE	1	0.725093039581964	2		707	525	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099980	27099981	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGT	novel	NA	P-0061689-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	250	810	0	ENST00000324856.7:c.3863_3866dup	p.Arg1289SerfsTer10	p.R1289Sfs*10	ENST00000324856	NM_006015.4	1287	aga/aGAGTga	15/20	0.667564807326579	1	FACETS	0.829	0.784	0.875	0.829	0.784	0.875	CLONAL	1	TRUE	0	0.725093039581964	1		810	530	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878419	151878419	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061689-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	264	746	0	ENST00000262189.6:c.6526C>T	p.Gln2176Ter	p.Q2176*	ENST00000262189	NM_170606.2	2176	Cag/Tag	36/59	0.665065049542986	4	FACETS	1	0.963	1	0.52	0.487	0.555	CLONAL	1	TRUE	2	0.725093039581964	4		746	1207	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0061690-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	303	621	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.402999901358993	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	3	TRUE	0	0.402999901358993	3		621	600	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0061690-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	60	665	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.402999901358993	3	FACETS	1	0.924	1	0.549	0.476	0.627	CLONAL	1	TRUE	1	0.402999901358993	3		665	326	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918694	44918694	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061690-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	40	442	0	ENST00000377967.4:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000377967	NM_021140.2	393	Cga/Tga	12/29	0.399246602536554	1	FACETS	0.891	0.75	1	0.891	0.75	1	CLONAL	1	TRUE	0	0.402999901358993	1		442	178	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs530941076	NA	P-0061690-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	380	729	0	ENST00000269305.4:c.658T>C	p.Tyr220His	p.Y220H	ENST00000269305	NM_001126112.2	220	Tat/Cat	6/11	0.402999901358993	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	0	0.402999901358993	3		729	722	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016678	12016678	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0061690-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	146	505	0	ENST00000353533.5:c.813+1G>A		p.X271_splice	ENST00000353533	NM_003010.3	271			0.402999901358993	3	FACETS	0.942	0.875	1	0.942	0.875	1	CLONAL	3	TRUE	0	0.402999901358993	3		505	308	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47679360	47679360	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061690-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	58	531	0	ENST00000347630.2:c.847G>T	p.Glu283Ter	p.E283*	ENST00000347630	NM_001007230.1	283	Gag/Tag	10/11	0.402999901358993	3	FACETS	0.839	0.723	0.965	0.28	0.241	0.322	CLONAL	1	TRUE	0	0.402999901358993	3		531	412	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184513	7184513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061690-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	116	569	0	ENST00000302850.5:c.788G>A	p.Arg263Lys	p.R263K	ENST00000302850	NM_000208.2	263	aGg/aAg	3/22	0.402999901358993	3	FACETS	1	0.956	1	0.552	0.498	0.608	CLONAL	1	TRUE	1	0.402999901358993	3		569	627	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291052	15291052	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061690-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	101	868	0	ENST00000263388.2:c.3158A>G	p.Gln1053Arg	p.Q1053R	ENST00000263388	NM_000435.2	1053	cAg/cGg	20/33	0.402999901358993	3	FACETS	0.801	0.716	0.891	0.4	0.358	0.446	CLONAL	1	TRUE	1	0.402999901358993	3		868	752	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093423	30093423	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061691-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	18	348	0	ENST00000331968.5:c.1840A>T	p.Ile614Phe	p.I614F	ENST00000331968	NM_002742.2	614	Att/Ttt	13/18	1	2	FACETS	0.354	0.266	0.457	0.354	0.266	0.457	SUBCLONAL	1	TRUE	1	0.348623866445129	2		348	292	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221657	36221657	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061691-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	193	718	0	ENST00000222270.7:c.5326T>C	p.Tyr1776His	p.Y1776H	ENST00000222270	NM_014727.1	1776	Tat/Cat	26/37	0.145913791864629	3	FACETS	1	0.968	1	0.713	0.663	0.764	INDETERMINATE	2	TRUE	0	0.348623866445129	3		718	608	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660324	227660324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748385460	NA	P-0061691-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	24	614	0	ENST00000305123.5:c.3131C>T	p.Pro1044Leu	p.P1044L	ENST00000305123	NM_005544.2	1044	cCg/cTg	1/2	0.203411152347799	3	FACETS	0.372	0.291	0.465	0.186	0.145	0.233	INDETERMINATE	1	TRUE	1	0.348623866445129	3		614	435	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821548	32821548	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061691-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	27	676	0	ENST00000354258.4:c.46T>A	p.Phe16Ile	p.F16I	ENST00000354258	NM_000593.5	16	Ttt/Att	1/11	1	2	FACETS	0.317	0.251	0.392	0.317	0.251	0.392	SUBCLONAL	1	TRUE	1	0.348623866445129	2		676	489	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061692-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	255	596	1	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.288321338740903	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	0	0.383140551585819	2		597	662	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0061692-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	526	372	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.383140551585819	7	FACETS	0.997	0.968	1	0.997	0.968	1	CLONAL	7	TRUE	0	0.383140551585819	7		372	770	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102199658	102199658	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061692-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	66	221	0	ENST00000263464.3:c.1063G>T	p.Glu355Ter	p.E355*	ENST00000263464	NM_001165.4	355	Gaa/Taa	5/9	0.3076675244673	4	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	2	0.383140551585819	4		221	210	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986800	36986800	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061692-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	122	533	0	ENST00000354822.5:c.889G>T	p.Gly297Cys	p.G297C	ENST00000354822	NM_001079668.2	297	Ggc/Tgc	3/3	0.383140551585819	3	FACETS	0.968	0.875	1	0.484	0.437	0.533	CLONAL	1	TRUE	1	0.383140551585819	3		533	784	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177896	56177910	+	inframe_deletion	In_Frame_Del	DEL	CAAACAAAAGGCAGA	CAAACAAAAGGCAGA	-	novel	NA	P-0061692-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	246	539	0	ENST00000399503.3:c.2870_2884del	p.Gln957_Arg961del	p.Q957_R961del	ENST00000399503	NM_005921.1	957	CAAACAAAAGGCAGA/-	14/20	0.359982645591493	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.383140551585819	4		539	845	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737065	145737076	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GATGCCGTGGAA	GATGCCGTGGAA	-	novel	NA	P-0061692-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	242	535	0	ENST00000428558.2:c.3490_3501del	p.Phe1164_Ile1167del	p.F1164_I1167del	ENST00000428558	NM_004260.3	1164	TTCCACGGCATC/-	21/22	0.383140551585819	5	FACETS	1	0.938	1	0.669	0.625	0.714	CLONAL	2	TRUE	2	0.383140551585819	5		535	991	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227041	53227041	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061692-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	176	360	0	ENST00000375401.3:c.2534G>T	p.Gly845Val	p.G845V	ENST00000375401	NM_004187.3	845	gGt/gTt	18/26	0.351159980490603	3	FACETS	0.939	0.87	1	0.939	0.87	1	CLONAL	2	TRUE	1	0.383140551585819	3		360	583	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0061693-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	21	147	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.206051856330677	1	FACETS	1	0.828	1	1	0.828	1	CLONAL	1	TRUE	0	0.206051856330677	1		147	169	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0061693-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	67	393	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	0.206051856330677	1	FACETS	0.756	0.66	0.858	1	0.973	1	SUBCLONAL	2	TRUE	0	0.206051856330677	1		393	386	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420399	49420399	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061693-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	81	609	0	ENST00000301067.7:c.15350G>T	p.Cys5117Phe	p.C5117F	ENST00000301067	NM_003482.3	5117	tGt/tTt	48/54	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.206051856330677	2		609	761	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0061695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	15	540	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.809	0.591	1	0.809	0.591	1	CLONAL	1	TRUE	1	0.12	2		540	309	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346338	73346338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	17	197	0	ENST00000377767.4:c.1462G>A	p.Asp488Asn	p.D488N	ENST00000377767	NM_014953.3	488	Gat/Aat	10/21	1	2	FACETS	0.772	0.575	1	0.772	0.575	1	CLONAL	1	TRUE	1	0.12	2		197	367	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5239008	5239008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138765579	NA	P-0061695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	28	755	0	ENST00000357368.4:c.1771G>A	p.Ala591Thr	p.A591T	ENST00000357368	NM_002850.3	591	Gcc/Acc	13/38	1	2	FACETS	1	0.814	1	1	0.814	1	CLONAL	1	TRUE	1	0.12	2		755	457	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143008	47143008	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	18	205	0	ENST00000409792.3:c.4955C>T	p.Thr1652Ile	p.T1652I	ENST00000409792	NM_014159.6	1652	aCc/aTc	8/21	1	2	FACETS	0.838	0.63	1	0.838	0.63	1	CLONAL	1	TRUE	1	0.12	2		205	358	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	364553	364553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	28	674	0	ENST00000262320.3:c.1009G>A	p.Asp337Asn	p.D337N	ENST00000262320	NM_003502.3	337	Gac/Aac	3/11	1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	TRUE	1	0.12	2		674	437	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591893	48591893	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	14	413	0	ENST00000342988.3:c.1056del	p.Tyr353ThrfsTer31	p.Y353Tfs*31	ENST00000342988	NM_005359.5	352	ggA/gg	9/12	0.153608001918808	1	FACETS	0.436	0.314	0.586	0.436	0.314	0.586	SUBCLONAL	1	TRUE	0	0.12	1		413	503	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691100	18691100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372642230	NA	P-0061696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	178	483	0	ENST00000266497.5:c.3211C>T	p.Pro1071Ser	p.P1071S	ENST00000266497		1071	Cct/Tct	23/31	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.625726044346008	2		483	499	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162742038	162742038	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0061696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	154	658	0	ENST00000367921.3:c.1728+1G>C		p.X576_splice	ENST00000367921	NM_006182.2	576			1	2	FACETS	0.982	0.906	1	0.982	0.906	1	CLONAL	1	TRUE	1	0.625726044346008	2		658	501	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63699948	63699948	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	181	561	0	ENST00000279873.7:c.283G>T	p.Val95Phe	p.V95F	ENST00000279873	NM_032199.2	95	Gtc/Ttc	3/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.625726044346008	2		561	528	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224595	108224595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769959260	NA	P-0061696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	171	527	0	ENST00000278616.4:c.8774G>A	p.Gly2925Asp	p.G2925D	ENST00000278616	NM_000051.3	2925	gGt/gAt	60/63	0.625726044346008	1	FACETS	0.994	0.927	1	0.994	0.927	1	CLONAL	1	TRUE	0	0.625726044346008	1		527	378	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416108	49416134	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TTTATTCGGAACATGTAGATGCCTCGA	TTTATTCGGAACATGTAGATGCCTCGA	-	novel	NA	P-0061696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	131	575	0	ENST00000301067.7:c.16341_16367del	p.Arg5448_Asn5456del	p.R5448_N5456del	ENST00000301067	NM_003482.3	5447	aaTCGAGGCATCTACATGTTCCGAATAAAc/aac	52/54	1	2	FACETS	0.9	0.823	0.981	0.9	0.823	0.981	CLONAL	1	TRUE	1	0.625726044346008	2		575	465	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151919131	151919131	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	110	440	2	ENST00000262189.6:c.3454G>T	p.Glu1152Ter	p.E1152*	ENST00000262189	NM_170606.2	1152	Gaa/Taa	22/59	1	2	FACETS	0.886	0.802	0.972	0.886	0.802	0.972	CLONAL	1	TRUE	1	0.625726044346008	2		442	397	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0061698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	85	368	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.38674242243236	2		368	307	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	48	541	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.38674242243236	2		541	191	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337717	73337717	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	66	417	0	ENST00000377767.4:c.1999A>T	p.Met667Leu	p.M667L	ENST00000377767	NM_014953.3	667	Atg/Ttg	16/21	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.38674242243236	2		417	278	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628343	187628343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	73	706	0	ENST00000441802.2:c.2639C>T	p.Ala880Val	p.A880V	ENST00000441802	NM_005245.3	880	gCa/gTa	2/27	1	2	FACETS	0.66	0.578	0.749	0.66	0.578	0.749	SUBCLONAL	1	TRUE	1	0.38674242243236	2		706	572	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	13	541	0				ENST00000310581	NM_198253.2	-/1132			0.286898433308438	0	FACETS	0.395	0.284	0.526			1	SUBCLONAL	1	TRUE	0	0.39	0		541	103	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	129	664	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.250285205560466	3	FACETS	1	0.965	1	0.732	0.671	0.794	CLONAL	2	TRUE	0	0.39	3		665	360	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	42	659	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	0.18310254135092	3	FACETS	0.79	0.662	0.93	0.395	0.331	0.465	INDETERMINATE	1	TRUE	1	0.39	3		659	326	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050425	13050425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536586990	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	80	647	0	ENST00000316448.5:c.377C>T	p.Ser126Leu	p.S126L	ENST00000316448	NM_004343.3	126	tCa/tTa	3/9	0.274126563223716	4	FACETS	0.999	0.88	1	0.333	0.293	0.375	CLONAL	1	TRUE	1	0.39	4		647	571	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486178	99486178	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	41	669	0	ENST00000268035.6:c.3484G>C	p.Glu1162Gln	p.E1162Q	ENST00000268035	NM_000875.3	1162	Gag/Cag	19/21	1	2	FACETS	0.828	0.694	0.974	0.828	0.694	0.974	CLONAL	1	TRUE	1	0.39	2		669	254	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733218	74733218	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	36	733	0	ENST00000359995.5:c.25G>A	p.Asp9Asn	p.D9N	ENST00000359995	NM_001195427.1	9	Gat/Aat	1/3	1	2	FACETS	0.457	0.376	0.548	0.457	0.376	0.548	SUBCLONAL	1	TRUE	1	0.39	2		733	404	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035147	37035147	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs63751012	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	36	532	0	ENST00000231790.2:c.109G>C	p.Glu37Gln	p.E37Q	ENST00000231790	NM_000249.3	37	Gag/Cag	1/19	0.18310254135092	3	FACETS	0.537	0.441	0.644	0.268	0.22	0.322	INDETERMINATE	1	TRUE	1	0.39	3		532	411	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682991	241682991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226883651	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	54	641	0	ENST00000366560.3:c.32C>T	p.Ser11Leu	p.S11L	ENST00000366560	NM_000143.3	11	tCg/tTg	1/10	1	2	FACETS	0.885	0.76	1	0.885	0.76	1	CLONAL	1	TRUE	1	0.39	2		641	313	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624428	140624428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507457	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	27	596	0	ENST00000288602.6:c.76G>A	p.Glu26Lys	p.E26K	ENST00000288602	NM_004333.4	26	Gag/Aag	1/18	0.167725869315369	4	FACETS	0.687	0.548	0.845			1	INDETERMINATE	1	TRUE	NA	0.39	4		596	280	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982373	201982373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398134258	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	52	798	1	ENST00000359651.3:c.752G>A	p.Arg251Gln	p.R251Q	ENST00000359651		251	cGa/cAa	6/8	1	2	FACETS	0.886	0.759	1	0.886	0.759	1	CLONAL	1	TRUE	1	0.39	2		799	301	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216753	7216753	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs745671551	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	97	813	0	ENST00000380728.2:c.670C>T	p.Gln224Ter	p.Q224*	ENST00000380728		224	Cag/Tag	8/11	0.250285205560466	3	FACETS	0.754	0.677	0.835	0.503	0.451	0.557	SUBCLONAL	2	TRUE	0	0.39	3		813	394	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165711	108165711	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	50	479	0	ENST00000278616.4:c.4834G>C	p.Glu1612Gln	p.E1612Q	ENST00000278616	NM_000051.3	1612	Gaa/Caa	32/63	0.175547762887496	3	FACETS	1	0.933	1	0.583	0.498	0.674	INDETERMINATE	1	TRUE	1	0.39	3		479	263	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27192526	27192526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776631444	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	41	569	0	ENST00000380036.4:c.1529G>A	p.Arg510Gln	p.R510Q	ENST00000380036	NM_000459.3	510	cGg/cAg	11/23	0.3	0	FACETS	0.475	0.398	0.56			1	SUBCLONAL	1	TRUE	0	0.39	0		569	270	SUCCESS
APC	324	MSKCC	GRCh37	5	112176884	112176884	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1064794887	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	67	576	0	ENST00000257430.4:c.5593C>G	p.Leu1865Val	p.L1865V	ENST00000257430	NM_000038.5	1865	Cta/Gta	16/16	0.175547762887496	3	FACETS	1	0.952	1	0.595	0.52	0.675	INDETERMINATE	1	TRUE	1	0.39	3		576	345	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921533	178921533	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	30	351	0	ENST00000263967.3:c.1015C>G	p.Leu339Val	p.L339V	ENST00000263967	NM_006218.2	339	Ctt/Gtt	5/21	0.186966805694475	3	FACETS	0.699	0.565	0.849	0.35	0.282	0.425	INDETERMINATE	1	TRUE	1	0.39	3		351	263	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577260	64577260	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs794728647	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	54	837	0	ENST00000312049.6:c.322C>T	p.Arg108Ter	p.R108*	ENST00000312049	NM_130799.2	108	Cga/Tga	2/10	0.18310254135092	3	FACETS	0.907	0.778	1	0.453	0.389	0.524	INDETERMINATE	1	TRUE	1	0.39	3		837	365	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63898320	63898320	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	84	519	0	ENST00000398590.3:c.46G>A	p.Ala16Thr	p.A16T	ENST00000398590	NM_001177387.1	16	Gcg/Acg	3/14	0.18310254135092	3	FACETS	1	0.972	1	0.653	0.58	0.73	INDETERMINATE	1	TRUE	1	0.39	3		519	394	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363628	40363628	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	82	577	0	ENST00000397332.2:c.601G>A	p.Asp201Asn	p.D201N	ENST00000397332	NM_001033082.2	201	Gat/Aat	3/3	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.39	2		577	287	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115279392	115279392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	21	375	0	ENST00000438362.2:c.625G>A	p.Asp209Asn	p.D209N	ENST00000438362	NM_001242891.1	209	Gat/Aat	6/20	0.186966805694475	3	FACETS	0.47	0.362	0.595	0.235	0.181	0.298	INDETERMINATE	1	TRUE	1	0.39	3		375	274	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175772	176175772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1456199578	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	44	745	0	ENST00000367669.3:c.343C>T	p.Leu115Phe	p.L115F	ENST00000367669	NM_022457.5	115	Ctc/Ttc	1/20	1	2	FACETS	0.603	0.507	0.709	0.603	0.507	0.709	SUBCLONAL	1	TRUE	1	0.39	2		745	374	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574692	64574692	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	31	676	0	ENST00000312049.6:c.784-1G>A		p.X262_splice	ENST00000312049	NM_130799.2	262			0.18310254135092	3	FACETS	0.748	0.608	0.905	0.374	0.304	0.453	INDETERMINATE	1	TRUE	1	0.39	3		676	254	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577180	64577180	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1244702530	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	58	810	0	ENST00000312049.6:c.402C>G	p.Phe134Leu	p.F134L	ENST00000312049	NM_130799.2	134	ttC/ttG	2/10	0.18310254135092	3	FACETS	1	0.893	1	0.52	0.449	0.596	INDETERMINATE	1	TRUE	1	0.39	3		810	342	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392038	118392038	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	34	755	0	ENST00000534358.1:c.11549G>C	p.Arg3850Thr	p.R3850T	ENST00000534358	NM_005933.3	3850	aGa/aCa	35/36	0.175547762887496	3	FACETS	0.645	0.528	0.776	0.323	0.264	0.388	INDETERMINATE	1	TRUE	1	0.39	3		755	323	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142554	119142554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	33	486	0	ENST00000264033.4:c.553G>A	p.Asp185Asn	p.D185N	ENST00000264033	NM_005188.3	185	Gat/Aat	3/16	0.175547762887496	3	FACETS	0.674	0.551	0.812	0.337	0.275	0.406	INDETERMINATE	1	TRUE	1	0.39	3		486	300	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716403	18716403	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	52	573	0	ENST00000266497.5:c.3750G>C	p.Gln1250His	p.Q1250H	ENST00000266497		1250	caG/caC	26/31	0.18310254135092	3	FACETS	0.996	0.853	1	0.498	0.426	0.576	INDETERMINATE	1	TRUE	1	0.39	3		573	320	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445998	49445998	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	40	1082	0	ENST00000301067.7:c.1468G>A	p.Glu490Lys	p.E490K	ENST00000301067	NM_003482.3	490	Gag/Aag	10/54	0.18310254135092	3	FACETS	0.621	0.516	0.736	0.31	0.258	0.368	INDETERMINATE	1	TRUE	1	0.39	3		1082	395	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046668	42046668	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	31	516	0	ENST00000219905.7:c.7042G>C	p.Glu2348Gln	p.E2348Q	ENST00000219905	NM_001164273.1	2348	Gag/Cag	18/24	1	2	FACETS	0.459	0.372	0.558	0.459	0.372	0.558	SUBCLONAL	1	TRUE	1	0.39	2		516	346	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634364	23634364	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	45	511	0	ENST00000261584.4:c.2922G>C	p.Lys974Asn	p.K974N	ENST00000261584	NM_024675.3	974	aaG/aaC	9/13	0.18310254135092	3	FACETS	1	0.89	1	0.532	0.451	0.621	INDETERMINATE	1	TRUE	1	0.39	3		511	259	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134446	30134446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	31	759	0	ENST00000263025.4:c.85G>A	p.Glu29Lys	p.E29K	ENST00000263025	NM_002746.2	29	Gag/Aag	1/9	0.270487770548264	1	FACETS	0.343	0.277	0.417	0.343	0.277	0.417	SUBCLONAL	1	TRUE	0	0.39	1		759	373	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211635	5211635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	20	671	0	ENST00000357368.4:c.5200G>A	p.Asp1734Asn	p.D1734N	ENST00000357368	NM_002850.3	1734	Gac/Aac	33/38	0.240872427012473	0	FACETS	0.266	0.204	0.339			1	SUBCLONAL	1	TRUE	0	0.39	0		671	235	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6222367	6222367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1221083899	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	28	737	0	ENST00000252674.7:c.875C>T	p.Ser292Leu	p.S292L	ENST00000252674	NM_005934.3	292	tCg/tTg	6/12	0.240872427012473	0	FACETS	0.409	0.329	0.5			1	SUBCLONAL	1	TRUE	0	0.39	0		737	214	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11114057	11114057	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	90	582	0	ENST00000358026.2:c.1985C>G	p.Ser662Ter	p.S662*	ENST00000358026	NM_001128849.1	662	tCa/tGa	13/36	0.274126563223716	4	FACETS	0.922	0.825	1	0.615	0.55	0.682	CLONAL	2	TRUE	1	0.39	4		582	348	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288706	15288706	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	32	512	0	ENST00000263388.2:c.4033C>T	p.Leu1345Phe	p.L1345F	ENST00000263388	NM_000435.2	1345	Ctc/Ttc	24/33	1	2	FACETS	0.949	0.779	1	0.949	0.779	1	CLONAL	1	TRUE	1	0.39	2		512	173	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218344	36218344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	26	745	0	ENST00000222270.7:c.4123G>A	p.Asp1375Asn	p.D1375N	ENST00000222270	NM_014727.1	1375	Gac/Aac	16/37	0.3	6	FACETS	0.598	0.473	0.741	0.12	0.094	0.149	SUBCLONAL	1	TRUE	1	0.39	6		745	397	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250062	39250062	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1264856949	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	33	430	0	ENST00000402219.2:c.1507G>C	p.Asp503His	p.D503H	ENST00000402219	NM_005633.3	503	Gat/Cat	10/23	0.248706923210508	4	FACETS	0.709	0.578	0.855	0.236	0.192	0.285	SUBCLONAL	1	TRUE	1	0.39	4		430	332	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21304110	21304110	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	92	611	0	ENST00000354336.3:c.889C>G	p.Gln297Glu	p.Q297E	ENST00000354336	NM_005207.3	297	Caa/Gaa	3/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.39	2		611	323	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027124	71027124	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	43	799	0	ENST00000318789.4:c.1203G>C	p.Gln401His	p.Q401H	ENST00000318789	NM_032682.5	401	caG/caC	15/21	0.18310254135092	3	FACETS	0.533	0.446	0.63	0.267	0.223	0.315	INDETERMINATE	1	TRUE	1	0.39	3		799	494	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799764	72799764	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374852297	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	77	725	0	ENST00000325599.8:c.1405G>A	p.Glu469Lys	p.E469K	ENST00000325599	NM_018130.2	469	Gaa/Aaa	11/11	0.18310254135092	3	FACETS	1	0.966	1	0.629	0.556	0.707	INDETERMINATE	1	TRUE	1	0.39	3		725	375	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295173	1295173	+	upstream_gene_variant	5'Flank	SNP	C	C	G	novel	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	32	681	0				ENST00000310581	NM_198253.2	-/1132			0.286898433308438	0	FACETS	0.681	0.561	0.812			1	SUBCLONAL	1	TRUE	0	0.39	0		681	147	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962448	38962448	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs750067124	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	29	256	0	ENST00000357387.3:c.1684C>G	p.Leu562Val	p.L562V	ENST00000357387	NM_152756.3	562	Cta/Gta	19/38	0.175547762887496	3	FACETS	0.756	0.61	0.921	0.378	0.305	0.461	INDETERMINATE	1	TRUE	1	0.39	3		256	235	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189031	38189031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752471679	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	62	498	0	ENST00000317025.8:c.983G>A	p.Arg328Gln	p.R328Q	ENST00000317025	NM_023034.1	328	cGa/cAa	5/24	0.18310254135092	3	FACETS	1	0.941	1	0.576	0.5	0.656	INDETERMINATE	1	TRUE	1	0.39	3		498	330	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528780	8528780	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	19	529	0	ENST00000356435.5:c.353-1G>C		p.X118_splice	ENST00000356435		118			0.240872427012473	0	FACETS	0.248	0.188	0.317			1	SUBCLONAL	1	TRUE	0	0.39	0		529	240	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918711	44918711	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	72	235	0	ENST00000377967.4:c.1194G>C	p.Gln398His	p.Q398H	ENST00000377967	NM_021140.2	398	caG/caC	12/29	0.230169831135927	2	FACETS	1	0.928	1			1	INDETERMINATE	2	TRUE	NA	0.39	2		235	176	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428494	78428582	+	stop_gained	Nonsense_Mutation	DEL	CTGTTGTGGAGTGCCACGAATTGTAAATAACTTCATATTAGGATCTGCATTTGGTGGAGGATTTCTCTGAAGTTCTATTCTTGCACCAG	CTGTTGTGGAGTGCCACGAATTGTAAATAACTTCATATTAGGATCTGCATTTGGTGGAGGATTTCTCTGAAGTTCTATTCTTGCACCAG	TGCACCATACTGCT	novel	NA	P-0061699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	61	518	1	ENST00000370768.2:c.1217_1305delinsAGCAGTATGGTGCA	p.Ser406_Gln435delinsTer	p.S406_Q435delins*	ENST00000370768	NM_003902.3	406	tCTGGTGCAAGAATAGAACTTCAGAGAAATCCTCCACCAAATGCAGATCCTAATATGAAGTTATTTACAATTCGTGGCACTCCACAACAG/tAGCAGTATGGTGCA	14/20	0.186966805694475	3	FACETS	1	0.914	1	0.536	0.464	0.612	INDETERMINATE	1	TRUE	1	0.39	3		519	349	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	39	541	0				ENST00000310581	NM_198253.2	-/1132			0.307005108257249	4	FACETS	1	0.866	1	1	0.866	1	INDETERMINATE	2	TRUE	2	0.770324961190041	4		541	89	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0061700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	174	719	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.57110742333501	4	FACETS	0.916	0.863	0.968	0.916	0.863	0.968	CLONAL	3	TRUE	1	0.770324961190041	4		719	291	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0061700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	161	595	0	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	0.57110742333501	4	FACETS	0.89	0.836	0.944	0.89	0.836	0.944	CLONAL	3	TRUE	1	0.770324961190041	4		595	277	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136172	11136172	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	124	586	0	ENST00000358026.2:c.3156C>G	p.Phe1052Leu	p.F1052L	ENST00000358026	NM_001128849.1	1052	ttC/ttG	22/36	0.70546841559901	5	FACETS	1	0.957	1	0.712	0.653	0.772	CLONAL	2	TRUE	2	0.770324961190041	5		586	325	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356353	66356353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	119	689	0	ENST00000273854.3:c.1144G>A	p.Asp382Asn	p.D382N	ENST00000273854	NM_004439.5	382	Gac/Aac	5/18	0.505884091579338	4	FACETS	0.925	0.861	0.988	0.925	0.861	0.988	CLONAL	3	TRUE	1	0.770324961190041	4		689	197	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982309	201982309	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0061735-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	74	657	0	ENST00000359651.3:c.689-1G>A		p.X230_splice	ENST00000359651		230			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.13	2		657	905	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143993	11143993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568509370	NA	P-0061735-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	48	580	0	ENST00000358026.2:c.3574C>T	p.Arg1192Cys	p.R1192C	ENST00000358026	NM_001128849.1	1192	Cgc/Tgc	26/36	1	2	FACETS	0.953	0.804	1	0.953	0.804	1	CLONAL	1	TRUE	1	0.13	2		580	775	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43766910	43766911	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061735-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	38	453	0	ENST00000382044.4:c.1140dup	p.Ile381TyrfsTer4	p.I381Yfs*4	ENST00000382044	NM_001141980.1	380	-/T	10/28	1	2	FACETS	0.913	0.753	1	0.913	0.753	1	CLONAL	1	TRUE	1	0.13	2		453	640	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124481161	124481161	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061735-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	19	417	0	ENST00000357628.3:c.1235A>G	p.Lys412Arg	p.K412R	ENST00000357628	NM_015450.2	412	aAg/aGg	14/19	1	2	FACETS	0.897	0.68	1	0.897	0.68	1	CLONAL	1	TRUE	1	0.13	2		417	326	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0061736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	135	272	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.221611496353104	5	FACETS	0.989	0.907	1	0.989	0.907	1	CLONAL	3	TRUE	2	0.330391316671339	5		272	412	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226165	2226165	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	48	659	0	ENST00000326181.6:c.1862A>G	p.Tyr621Cys	p.Y621C	ENST00000326181	NM_032271.2	621	tAc/tGc	19/21	0.112845381094947	3	FACETS	0.468	0.395	0.55	0.234	0.197	0.275	INDETERMINATE	1	TRUE	1	0.330391316671339	3		659	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578424	7578425	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	274	653	0	ENST00000269305.4:c.505dup	p.Met169AsnfsTer12	p.M169Nfs*12	ENST00000269305	NM_001126112.2	169	atg/aAtg	5/11	0.326405843038964	2	FACETS	0.993	0.935	1	0.993	0.935	1	CLONAL	2	TRUE	0	0.330391316671339	2		653	835	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0061738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	242	539	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.472227424896277	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	FALSE	0	0.533740081511585	2		539	451	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0061738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	193	543	1	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.457464294734795	3	FACETS	0.911	0.85	0.972	0.911	0.85	0.972	CLONAL	2	FALSE	1	0.533740081511585	3		544	503	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925334	114925334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	336	479	0	ENST00000543371.1:c.1412G>A	p.Arg471His	p.R471H	ENST00000543371	NM_001198531.1	471	cGc/cAc	14/14	0.483368458102034	3	FACETS	0.943	0.903	0.981	0.943	0.903	0.981	CLONAL	3	FALSE	0	0.533740081511585	3		479	564	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392694	118392694	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	115	496	0	ENST00000534358.1:c.11726A>G	p.Asn3909Ser	p.N3909S	ENST00000534358	NM_005933.3	3909	aAt/aGt	36/36	0.453048450716182	3	FACETS	0.977	0.883	1	0.488	0.441	0.538	CLONAL	1	FALSE	1	0.533740081511585	3		496	559	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252014	133252014	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500853	NA	P-0061738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	112	520	0	ENST00000320574.5:c.1196C>T	p.Ala399Val	p.A399V	ENST00000320574	NM_006231.2	399	gCg/gTg	12/49	0.457464294734795	3	FACETS	0.88	0.794	0.971	0.44	0.397	0.486	CLONAL	1	FALSE	1	0.533740081511585	3		520	604	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518940	187518940	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs940602352	NA	P-0061738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	70	372	0	ENST00000441802.2:c.12264G>T	p.Gln4088His	p.Q4088H	ENST00000441802	NM_005245.3	4088	caG/caT	24/27	1	2	FACETS	0.701	0.615	0.794	0.701	0.615	0.794	SUBCLONAL	1	FALSE	1	0.533740081511585	2		372	374	SUCCESS
APC	324	MSKCC	GRCh37	5	112175345	112175349	+	frameshift_variant	Frame_Shift_Del	DEL	GTTGA	GTTGA	-	novel	NA	P-0061738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	97	437	0	ENST00000257430.4:c.4054_4058del	p.Val1352IlefsTer21	p.V1352Ifs*21	ENST00000257430	NM_000038.5	1352	GTTGAa/a	16/16	0.457464294734795	3	FACETS	0.901	0.806	1	0.451	0.403	0.501	CLONAL	1	FALSE	1	0.533740081511585	3		437	511	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149440455	149440455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771977143	NA	P-0061738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	118	412	0	ENST00000286301.3:c.1939G>A	p.Val647Ile	p.V647I	ENST00000286301	NM_005211.3	647	Gtc/Atc	14/22	0.526754978017733	5	FACETS	1	0.946	1	0.268	0.241	0.295	CLONAL	1	FALSE	1	0.533740081511585	5		412	744	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	52	541	0				ENST00000310581	NM_198253.2	-/1132			0.199660090682916	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.757243631144877	0		541	156	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233037	55233037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1477025000	NA	P-0061739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6280	963	468	0	ENST00000275493.2:c.1787C>T	p.Pro596Leu	p.P596L	ENST00000275493	NM_005228.3	596	cCg/cTg	15/28	0.757243631144877	37	FACETS	1	0.965	1	0.139	0.134	0.144	CLONAL	5	TRUE	1	0.757243631144877	37		468	7243	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0061740-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	380	588	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.50876441118879	3	FACETS	0.998	0.964	1			1	CLONAL	3	TRUE	NA	0.623808335803427	3		588	534	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765576	41765576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763066660	NA	P-0061740-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	138	571	0	ENST00000301178.4:c.2452G>A	p.Glu818Lys	p.E818K	ENST00000301178	NM_021913.4	818	Gaa/Aaa	20/20	NA	2	FACETS	0.975	0.894	1			1	INDETERMINATE	1	TRUE	NA	0.623808335803427	2		571	454	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872532	136872532	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061740-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	212	453	0	ENST00000241393.3:c.966A>T	p.Arg322Ser	p.R322S	ENST00000241393	NM_003467.2	322	agA/agT	2/2	0.622116660402353	3	FACETS	0.795	0.744	0.846	0.795	0.744	0.846	SUBCLONAL	2	TRUE	1	0.623808335803427	3		453	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0061742-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	29	539	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.679	0.543	0.835	0.679	0.543	0.835	SUBCLONAL	1	TRUE	1	0.13	2		539	657	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0061742-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	12	373	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.348	0.243	0.479	0.348	0.243	0.479	SUBCLONAL	1	TRUE	1	0.13	2		373	530	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410522	63410522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751427137	NA	P-0061742-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	74	751	0	ENST00000330258.3:c.2645C>T	p.Pro882Leu	p.P882L	ENST00000330258	NM_152424.3	882	cCt/cTt	2/2	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.13	2		751	1023	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061743-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	98	541	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.782	0.7	0.867	0.782	0.7	0.867	SUBCLONAL	1	TRUE	1	0.522461005448983	2		541	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0061743-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	79	476	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	1	2	FACETS	0.419	0.368	0.474	0.419	0.368	0.474	SUBCLONAL	1	TRUE	1	0.522461005448983	2		476	722	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375882	118375882	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061743-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	56	623	0	ENST00000534358.1:c.9275A>G	p.Tyr3092Cys	p.Y3092C	ENST00000534358	NM_005933.3	3092	tAt/tGt	27/36	1	2	FACETS	0.365	0.312	0.423	0.365	0.312	0.423	SUBCLONAL	1	TRUE	1	0.522461005448983	2		623	587	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061743-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	65	660	0	ENST00000222270.7:c.515C>G	p.Thr172Ser	p.T172S	ENST00000222270	NM_014727.1	172	aCc/aGc	3/37	1	2	FACETS	0.297	0.256	0.34	0.297	0.256	0.34	SUBCLONAL	1	TRUE	1	0.522461005448983	2		660	839	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21348270	21348270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1366650212	NA	P-0061743-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	37	639	0	ENST00000215739.8:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000215739	NM_006767.3	471	Cgc/Tgc	13/21	1	2	FACETS	0.236	0.194	0.284	0.236	0.194	0.284	SUBCLONAL	1	TRUE	1	0.522461005448983	2		639	599	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565885	55565885	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061743-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	20	321	0	ENST00000288135.5:c.709G>C	p.Asp237His	p.D237H	ENST00000288135	NM_000222.2	237	Gat/Cat	4/21	1	2	FACETS	0.21	0.16	0.268	0.21	0.16	0.268	SUBCLONAL	1	TRUE	1	0.522461005448983	2		321	365	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	50	415	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.350800070005315	4	FACETS	1	0.939	1	1	0.939	1	CLONAL	3	TRUE	1	0.350800070005315	4		415	114	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0061744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	22	836	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.350800070005315	1	FACETS	0.923	0.727	1	0.923	0.727	1	CLONAL	1	TRUE	0	0.350800070005315	1		836	112	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200266	67200266	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	15	718	0	ENST00000312629.5:c.574T>C	p.Tyr192His	p.Y192H	ENST00000312629	NM_003952.2	192	Tac/Cac	7/15	0.245721227132107	3	FACETS	0.661	0.486	0.869	0.22	0.162	0.29	SUBCLONAL	1	TRUE	0	0.350800070005315	3		718	152	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288609	15288609	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	19	376	1	ENST00000263388.2:c.4130C>T	p.Ala1377Val	p.A1377V	ENST00000263388	NM_000435.2	1377	gCg/gTg	24/33	0.19728472339485	1	FACETS	1	0.811	1	1	0.811	1	INDETERMINATE	1	TRUE	0	0.350800070005315	1		377	85	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273923	18273923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	15	797	0	ENST00000222254.8:c.1256C>T	p.Thr419Ile	p.T419I	ENST00000222254	NM_005027.3	419	aCa/aTa	10/16	0.19728472339485	1	FACETS	0.569	0.42	0.744	0.569	0.42	0.744	INDETERMINATE	1	TRUE	0	0.350800070005315	1		797	124	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839968	27839969	+	missense_variant	Missense_Mutation	DNP	GT	GT	CC	novel	NA	P-0061744-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	15	1152	1	ENST00000328488.2:c.125_126delinsGG	p.Tyr42Trp	p.Y42W	ENST00000328488	NM_003533.2	42	tAC/tGG	1/1	1	2	FACETS	0.57	0.419	0.749	0.57	0.419	0.749	SUBCLONAL	1	TRUE	1	0.350800070005315	2		1153	150	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696432	47696432	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519968	NA	P-0061757-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	200	458	0	ENST00000347630.2:c.391T>G	p.Trp131Gly	p.W131G	ENST00000347630	NM_001007230.1	131	Tgg/Ggg	6/11	0.292173261529283	1	FACETS	0.867	0.81	0.925	0.867	0.81	0.925	INDETERMINATE	1	TRUE	0	0.605808234922354	1		458	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0061758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	210	836	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.35134285573613	1	FACETS	1	0.989	1	1	0.995	1	CLONAL	2	TRUE	0	0.35134285573613	1		836	410	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0061758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	230	514	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	0.35134285573613	3	FACETS	0.91	0.855	0.965	1	0.992	1	CLONAL	3	TRUE	1	0.35134285573613	3		514	564	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591151	67591154	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ATGT	ATGT	C	novel	NA	P-0061758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	55	369	0	ENST00000274335.5:c.1744_1745+2delinsC		p.X582_splice	ENST00000274335		582		12/15	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.35134285573613	2		369	238	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100916	41100917	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0061758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	173	433	0	ENST00000373198.4:c.1439dup	p.Glu481Ter	p.E481*	ENST00000373198	NM_133170.3	480	act/acCt	8/32	1	2	FACETS	0.971	0.901	1	1	0.993	1	CLONAL	2	TRUE	1	0.35134285573613	2		433	507	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0061761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	333	326	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.577030317177634	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.577030317177634	3		326	706	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201506	67201506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	240	734	0	ENST00000312629.5:c.947C>T	p.Pro316Leu	p.P316L	ENST00000312629	NM_003952.2	316	cCa/cTa	11/15	1	2	FACETS	0.984	0.921	1	0.984	0.921	1	CLONAL	1	TRUE	1	0.577030317177634	2		734	845	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs121913370	NA	P-0061761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	103	379	0	ENST00000288602.6:c.1742A>C	p.Asn581Thr	p.N581T	ENST00000288602	NM_004333.4	581	aAt/aCt	15/18	1	2	FACETS	0.978	0.883	1	0.978	0.883	1	CLONAL	1	TRUE	1	0.577030317177634	2		379	365	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620694	52620695	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0061761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	120	414	0	ENST00000394830.3:c.3058_3059del	p.Lys1020ValfsTer9	p.K1020Vfs*9	ENST00000394830	NM_018313.4	1020	AAg/g	21/30	0.577030317177634	1	FACETS	0.945	0.866	1	0.945	0.866	1	CLONAL	1	TRUE	0	0.577030317177634	1		414	313	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0061762-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	131	810	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.856	0.783	0.932	0.856	0.783	0.932	CLONAL	1	TRUE	1	0.682997087856068	2		810	448	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788651	3788651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061762-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	396	465	0	ENST00000262367.5:c.4303G>A	p.Asp1435Asn	p.D1435N	ENST00000262367	NM_004380.2	1435	Gat/Aat	26/31	0.653517471499442	4	FACETS	0.928	0.891	0.965	0.928	0.891	0.965	CLONAL	3	TRUE	1	0.682997087856068	4		465	701	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061762-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	128	481	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	0.928	0.849	1	0.928	0.849	1	CLONAL	1	TRUE	1	0.682997087856068	2		481	404	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188271	142188271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202193482	NA	P-0061762-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	106	466	1	ENST00000350721.4:c.6460G>A	p.Asp2154Asn	p.D2154N	ENST00000350721	NM_001184.3	2154	Gat/Aat	38/47	0.682997087856068	6	FACETS	0.96	0.861	1	0.192	0.172	0.213	CLONAL	1	TRUE	1	0.682997087856068	6		467	765	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220147	5220147	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061762-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	122	683	0	ENST00000357368.4:c.3568C>T	p.Arg1190Trp	p.R1190W	ENST00000357368	NM_002850.3	1190	Cgg/Tgg	22/38	1	2	FACETS	0.806	0.734	0.881	0.806	0.734	0.881	CLONAL	1	TRUE	1	0.682997087856068	2		683	443	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378279	225378279	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061762-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	114	380	0	ENST00000264414.4:c.616G>C	p.Glu206Gln	p.E206Q	ENST00000264414	NM_003590.4	206	Gag/Cag	5/16	1	2	FACETS	0.845	0.768	0.926	0.845	0.768	0.926	CLONAL	1	TRUE	1	0.682997087856068	2		380	395	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295287	1295287	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0061762-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	129	806	1				ENST00000310581	NM_198253.2	-/1132			0.644988356214251	4	FACETS	0.971	0.882	1	0.324	0.294	0.355	CLONAL	1	TRUE	1	0.682997087856068	4		807	655	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31238218	31238218	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061762-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	68	352	0	ENST00000376228.5:c.664G>A	p.Glu222Lys	p.E222K	ENST00000376228	NM_002117.5	222	Gag/Aag	4/8	1	2	FACETS	0.844	0.744	0.948	0.844	0.744	0.948	CLONAL	1	TRUE	1	0.682997087856068	2		352	236	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31238888	31238888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061762-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	22	190	0	ENST00000376228.5:c.581G>A	p.Arg194Lys	p.R194K	ENST00000376228	NM_002117.5	194	aGa/aAa	3/8	1	2	FACETS	0.693	0.548	0.852	0.693	0.548	0.852	SUBCLONAL	1	TRUE	1	0.682997087856068	2		190	93	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266611	198266611	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs755415626	NA	P-0061763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	259	477	0	ENST00000335508.6:c.2225G>A	p.Gly742Asp	p.G742D	ENST00000335508	NM_012433.2	742	gGt/gAt	16/25	0.864725995607682	3	FACETS	1	0.976	1	0.537	0.504	0.57	CLONAL	1	TRUE	1	0.864725995607682	3		477	799	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554645	63554645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1173490917	NA	P-0061763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	704	646	0	ENST00000307078.5:c.94G>A	p.Glu32Lys	p.E32K	ENST00000307078	NM_004655.3	32	Gag/Aag	2/11	0.864725995607682	5	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	2	0.864725995607682	5		646	1230	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878166	48878166	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	500	518	0	ENST00000267163.4:c.118G>T	p.Glu40Ter	p.E40*	ENST00000267163	NM_000321.2	40	Gag/Tag	1/27	0.864725995607682	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.864725995607682	3		518	804	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553788	106553788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1281186824	NA	P-0061763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	501	494	0	ENST00000369096.4:c.1753G>A	p.Gly585Ser	p.G585S	ENST00000369096	NM_001198.3	585	Ggc/Agc	5/7	0.327667123102017	6	FACETS	0.882	0.851	0.914	0.882	0.851	0.914	INDETERMINATE	4	TRUE	2	0.864725995607682	6		494	896	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17354346	17354346	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	193	373	0	ENST00000375499.3:c.438C>G	p.Phe146Leu	p.F146L	ENST00000375499	NM_003000.2	146	ttC/ttG	5/8	0.864725995607682	3	FACETS	1	0.963	1			1	CLONAL	1	TRUE	NA	0.864725995607682	3		373	607	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322627	39322627	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	490	485	0	ENST00000373001.3:c.365A>C	p.Asp122Ala	p.D122A	ENST00000373001	NM_022157.3	122	gAc/gCc	2/7	0.864725995607682	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.864725995607682	3		485	791	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934262	48934262	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0061763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	139	350	0	ENST00000267163.4:c.717T>G	p.Tyr239Ter	p.Y239*	ENST00000267163	NM_000321.2	239	taT/taG	7/27	0.864725995607682	3	FACETS	0.951	0.872	1	0.476	0.436	0.517	CLONAL	1	TRUE	1	0.864725995607682	3		350	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578186	7578210	+	frameshift_variant	Frame_Shift_Del	DEL	CTCATAGGGCACCACCACACTATGT	CTCATAGGGCACCACCACACTATGT	-	novel	NA	P-0061763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	589	596	0	ENST00000269305.4:c.639_663del	p.His214ArgfsTer25	p.H214Rfs*25	ENST00000269305	NM_001126112.2	213	cgACATAGTGTGGTGGTGCCCTATGAG/cg	6/11	0.864725995607682	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.864725995607682	2		596	656	SUCCESS
APC	324	MSKCC	GRCh37	5	112090612	112090612	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	327	307	0	ENST00000257430.4:c.26del	p.Leu9CysfsTer2	p.L9Cfs*2	ENST00000257430	NM_000038.5	9	Ttg/tg	2/16	0.864725995607682	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.864725995607682	2		307	359	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729478	41729478	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	597	614	0	ENST00000242208.4:c.1051G>C	p.Glu351Gln	p.E351Q	ENST00000242208	NM_002192.2	351	Gag/Cag	3/3	0.864725995607682	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.864725995607682	3		614	930	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0061764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	73	643	1	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.357994574332897	1	FACETS	0.678	0.594	0.768	0.678	0.594	0.768	SUBCLONAL	1	TRUE	0	0.357994574332897	1		644	494	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43771625	43771625	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	108	498	1	ENST00000382044.4:c.758T>A	p.Val253Asp	p.V253D	ENST00000382044	NM_001141980.1	253	gTt/gAt	7/28	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.357994574332897	2		499	472	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0019392-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	526	414	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.833978707735156	6	FACETS	0.978	0.953	1	0.978	0.953	1	CLONAL	5	TRUE	1	0.833978707735156	6		414	688	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578504	7578540	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTG	AGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTG	-	novel	NA	P-0019392-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	337	633	0	ENST00000269305.4:c.390_426del	p.Asn131CysfsTer27	p.N131Cfs*27	ENST00000269305	NM_001126112.2	130	ctCAACAAGATGTTTTGCCAACTGGCCAAGACCTGCCCT/ct	5/11	0.801513035878319	3	FACETS	0.902	0.875	0.928	0.902	0.875	0.928	CLONAL	3	TRUE	0	0.833978707735156	3		633	423	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111959704	111959704	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019392-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	84	370	0	ENST00000375549.3:c.283C>G	p.Leu95Val	p.L95V	ENST00000375549	NM_003002.3	95	Ctg/Gtg	3/4	0.651317400988967	3	FACETS	0.876	0.781	0.975	0.438	0.39	0.488	CLONAL	1	TRUE	1	0.833978707735156	3		370	326	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492739	56492739	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019392-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	498	555	0	ENST00000407977.2:c.200del	p.Gly67ValfsTer9	p.G67Vfs*9	ENST00000407977		67	gGt/gt	2/10	0.801513035878319	3	FACETS	0.964	0.944	0.984	0.964	0.944	0.984	CLONAL	3	TRUE	0	0.833978707735156	3		555	585	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214046	108214046	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019392-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	150	462	0	ENST00000278616.4:c.8366A>T	p.Lys2789Ile	p.K2789I	ENST00000278616	NM_000051.3	2789	aAa/aTa	57/63	0.651317400988967	3	FACETS	0.96	0.883	1	0.48	0.441	0.52	CLONAL	1	TRUE	1	0.833978707735156	3		462	531	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533641	63533641	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019392-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	116	687	0	ENST00000307078.5:c.1513T>C	p.Phe505Leu	p.F505L	ENST00000307078	NM_004655.3	505	Ttt/Ctt	6/11	0.801513035878319	3	FACETS	0.941	0.855	1	0.314	0.285	0.344	CLONAL	1	TRUE	0	0.833978707735156	3		687	419	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214357	36214357	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019392-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	142	518	0	ENST00000222270.7:c.3011A>C	p.Lys1004Thr	p.K1004T	ENST00000222270	NM_014727.1	1004	aAg/aCg	7/37	0.816341313566101	3	FACETS	1	0.968	1	0.551	0.506	0.597	CLONAL	1	TRUE	1	0.833978707735156	3		518	438	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141589	202141589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019392-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	33	463	0	ENST00000358485.4:c.877G>A	p.Gly293Arg	p.G293R	ENST00000358485	NM_001080125.1	293	Gga/Aga	7/9	0.833303527795146	4	FACETS	0.225	0.182	0.273	0.112	0.091	0.137	SUBCLONAL	1	TRUE	2	0.833978707735156	4		463	646	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478752	57478752	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019392-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	132	604	1	ENST00000371085.3:c.338T>C	p.Leu113Pro	p.L113P	ENST00000371085	NM_000516.4	113	cTg/cCg	5/13	0.656585662873733	4	FACETS	0.828	0.753	0.907	0.414	0.376	0.454	CLONAL	1	TRUE	2	0.833978707735156	4		605	701	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30061037	30061037	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019392-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	101	339	0	ENST00000338641.4:c.869T>G	p.Leu290Arg	p.L290R	ENST00000338641	NM_000268.3	290	cTt/cGt	9/16	0.796009360378474	2	FACETS	1	0.929	1	0.511	0.466	0.557	CLONAL	1	TRUE	0	0.833978707735156	2		339	237	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394853	394853	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019392-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	145	611	0	ENST00000380956.4:c.249A>C	p.Glu83Asp	p.E83D	ENST00000380956	NM_001195286.1	83	gaA/gaC	3/9	0.801060743116027	3	FACETS	1	0.966	1	0.364	0.335	0.394	CLONAL	1	TRUE	0	0.833978707735156	3		611	451	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289592	33289592	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019392-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	110	548	0	ENST00000374542.5:c.111A>C	p.Glu37Asp	p.E37D	ENST00000374542	NM_001141970.1	37	gaA/gaC	2/8	0.801060743116027	3	FACETS	1	0.916	1	0.337	0.305	0.369	CLONAL	1	TRUE	0	0.833978707735156	3		548	370	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0024830-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	218	458	0				ENST00000310581	NM_198253.2	-/1132			0.288175169850102	5	FACETS	1	0.988	1	0.82	0.768	0.873	INDETERMINATE	2	TRUE	2	0.543163878691924	5		458	592	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0024830-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	386	461	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.543163878691924	5	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	2	0.543163878691924	5		461	801	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105676	27105678	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs753766136	NA	P-0024830-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	172	643	1	ENST00000324856.7:c.5299_5301del	p.Glu1767del	p.E1767del	ENST00000324856	NM_006015.4	1763	GAA/-	20/20	0.543163878691924	3	FACETS	0.93	0.856	1	0.465	0.428	0.504	CLONAL	1	TRUE	1	0.543163878691924	3		644	866	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074171	8074171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024830-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	199	679	0	ENST00000377482.5:c.488C>T	p.Ser163Phe	p.S163F	ENST00000377482	NM_018948.3	163	tCt/tTt	4/4	0.543163878691924	3	FACETS	1	0.981	1	0.58	0.538	0.623	CLONAL	1	TRUE	1	0.543163878691924	3		679	803	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858001	9858001	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs748967552	NA	P-0024830-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	119	666	0	ENST00000330684.3:c.3400C>A	p.Gln1134Lys	p.Q1134K	ENST00000330684	NM_001134407.1	1134	Cag/Aag	13/13	0.543163878691924	3	FACETS	0.791	0.715	0.872	0.396	0.357	0.436	SUBCLONAL	1	TRUE	1	0.543163878691924	3		666	704	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156135	99156135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024830-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	267	573	0	ENST00000074304.5:c.815C>T	p.Ala272Val	p.A272V	ENST00000074304	NM_001134224.1	272	gCc/gTc	10/26	0.194477240213943	5	FACETS	0.9	0.849	0.951	0.9	0.849	0.951	INDETERMINATE	3	TRUE	2	0.543163878691924	5		573	661	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128849139	128849139	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024830-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	157	521	0	ENST00000249373.3:c.1367G>C	p.Gly456Ala	p.G456A	ENST00000249373	NM_005631.4	456	gGc/gCc	8/12	0.543163878691924	5	FACETS	1	0.98	1	0.408	0.373	0.443	CLONAL	1	TRUE	2	0.543163878691924	5		521	858	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008428	71008428	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034290-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	168	428	0	ENST00000318789.4:c.2004del	p.Asp669MetfsTer4	p.D669Mfs*4	ENST00000318789	NM_032682.5	668	gaA/ga	21/21	0.419022594623069	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.598668798074806	4		428	386	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257873	16257873	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034290-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	92	589	0	ENST00000375759.3:c.5139del	p.Met1714Ter	p.M1714*	ENST00000375759	NM_015001.2	1713	gCc/gc	11/15	0.508384268042566	4	FACETS	1	0.932	1	0.529	0.472	0.59	CLONAL	1	TRUE	2	0.598668798074806	4		589	464	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56854497	56854498	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0034290-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	36	288	0	ENST00000519728.1:c.79_80del	p.Thr27Ter	p.T27*	ENST00000519728	NM_002350.3	27	ACt/t	2/13	0.508384268042566	4	FACETS	0.61	0.503	0.73	0.305	0.251	0.365	SUBCLONAL	1	TRUE	2	0.598668798074806	4		288	315	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982031	70982035	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCT	CTGCT	-	novel	NA	P-0034290-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	78	508	0	ENST00000276594.2:c.61_65del	p.Ser21ProfsTer105	p.S21Pfs*105	ENST00000276594	NM_024504.3	21	AGCAGc/c	2/8	0.508384268042566	4	FACETS	1	0.942	1	0.554	0.49	0.622	CLONAL	1	TRUE	2	0.598668798074806	4		508	376	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0034872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	95	547	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.450446578093565	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.450446578093565	1		547	256	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577493	7577497	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CCTGA	CCTGA	-	rs1567548832	NA	P-0034872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	246	544	0	ENST00000269305.4:c.782+2_782+6del		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.450446578093565	3	FACETS	1	0.99	1	0.817	0.771	0.863	CLONAL	2	TRUE	0	0.450446578093565	3		544	546	SUCCESS
YES1	7525	MSKCC	GRCh37	18	751795	751795	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	50	291	0	ENST00000314574.4:c.281C>A	p.Thr94Asn	p.T94N	ENST00000314574	NM_005433.3	94	aCt/aAt	3/12	0.208878043643445	4	FACETS	0.982	0.837	1	0.491	0.418	0.57	INDETERMINATE	1	TRUE	2	0.450446578093565	4		291	328	SUCCESS
YES1	7525	MSKCC	GRCh37	18	751801	751801	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	52	303	0	ENST00000314574.4:c.275G>T	p.Gly92Val	p.G92V	ENST00000314574	NM_005433.3	92	gGt/gTt	3/12	0.208878043643445	4	FACETS	0.973	0.833	1	0.487	0.416	0.563	INDETERMINATE	1	TRUE	2	0.450446578093565	4		303	344	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756706	756706	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	121	493	0	ENST00000314574.4:c.122C>T	p.Pro41Leu	p.P41L	ENST00000314574	NM_005433.3	41	cCa/cTa	2/12	0.208878043643445	4	FACETS	0.782	0.711	0.857	0.782	0.711	0.857	INDETERMINATE	2	TRUE	2	0.450446578093565	4		493	498	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0037087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	201	773	2	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.292278205860768	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.391601718651457	2		775	490	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353989	15353989	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	12	164	0	ENST00000263377.2:c.2891C>G	p.Pro964Arg	p.P964R	ENST00000263377	NM_058243.2	964	cCc/cGc	14/20	0.391601718651457	5	FACETS	0.537	0.378	0.733	0.179	0.126	0.245	SUBCLONAL	1	TRUE	2	0.391601718651457	5		164	181	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200151	128200187	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCCTGTTAACCTAGAGGCAACCACCAGTTTTCAGAG	GGCCTGTTAACCTAGAGGCAACCACCAGTTTTCAGAG	-	novel	NA	P-0037087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	44	489	0	ENST00000341105.2:c.1144-26_1154del		p.X382_splice	ENST00000341105	NM_032638.4	382		6/6	0.391601718651457	6	FACETS	0.499	0.417	0.59	0.166	0.139	0.197	SUBCLONAL	1	TRUE	3	0.391601718651457	6		489	803	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900033	151900033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	75	345	0	ENST00000262189.6:c.4078C>T	p.Pro1360Ser	p.P1360S	ENST00000262189	NM_170606.2	1360	Cct/Tct	26/59	0.391601718651457	6	FACETS	0.711	0.621	0.808	0.178	0.155	0.202	SUBCLONAL	1	TRUE	2	0.391601718651457	6		345	961	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs539507291	NA	P-0037097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	174	812	1	ENST00000257555.6:c.862G>A	p.Gly288Arg	p.G288R	ENST00000257555		288	Ggg/Agg	4/10	0.101539151787505	0	FACETS	0.379	0.351	0.409			1	INDETERMINATE	1	TRUE	0	0.60139520512521	0		813	608	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845321	151845321	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1327155514	NA	P-0037097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	174	699	0	ENST00000262189.6:c.13691A>G	p.Gln4564Arg	p.Q4564R	ENST00000262189	NM_170606.2	4564	cAg/cGg	52/59	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.60139520512521	2		699	517	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350264	89350264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	185	865	0	ENST00000301030.4:c.2686G>A	p.Glu896Lys	p.E896K	ENST00000301030	NM_001256183.1	896	Gag/Aag	9/13	1	2	FACETS	0.874	0.806	0.945	0.874	0.806	0.945	CLONAL	1	TRUE	1	0.378884588697175	2		865	1117	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0037113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	56	387	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	1	2	FACETS	0.223	0.191	0.259	0.223	0.191	0.259	SUBCLONAL	1	TRUE	1	0.697879942332775	2		387	719	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0037113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	232	558	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	1	2	FACETS	0.745	0.696	0.796	0.745	0.696	0.796	SUBCLONAL	1	TRUE	1	0.697879942332775	2		558	892	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790455	3790455	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783490	NA	P-0037113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	358	414	0	ENST00000262367.5:c.4078C>T	p.Arg1360Ter	p.R1360*	ENST00000262367	NM_004380.2	1360	Cga/Tga	24/31	0.275274687298494	3	FACETS	0.857	0.817	0.898	0.572	0.545	0.599	INDETERMINATE	2	TRUE	0	0.697879942332775	3		414	807	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087896	27087920	+	frameshift_variant	Frame_Shift_Del	DEL	CACCCAGTGGCCAGTCGGACAGCAT	CACCCAGTGGCCAGTCGGACAGCAT	-	novel	NA	P-0037113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	154	477	0	ENST00000324856.7:c.2185_2209del	p.Pro729CysfsTer5	p.P729Cfs*5	ENST00000324856	NM_006015.4	728	cCACCCAGTGGCCAGTCGGACAGCATc/cc	6/20	0.38301681685192	1	FACETS	0.419	0.384	0.455	0.419	0.384	0.455	INDETERMINATE	1	TRUE	0	0.697879942332775	1		477	686	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544167	18544167	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	49	242	0	ENST00000266497.5:c.1984C>T	p.Gln662Ter	p.Q662*	ENST00000266497		662	Cag/Tag	13/31	1	2	FACETS	0.345	0.293	0.402	0.345	0.293	0.402	SUBCLONAL	1	TRUE	1	0.697879942332775	2		242	407	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094470	27094470	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	103	433	0	ENST00000324856.7:c.3178G>T	p.Glu1060Ter	p.E1060*	ENST00000324856	NM_006015.4	1060	Gag/Tag	11/20	0.38301681685192	1	FACETS	0.317	0.284	0.352	0.317	0.284	0.352	INDETERMINATE	1	TRUE	0	0.697879942332775	1		433	606	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023555	27023555	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	38	462	0	ENST00000324856.7:c.661del	p.Ala221ProfsTer11	p.A221Pfs*11	ENST00000324856	NM_006015.4	221	Gcc/cc	1/20	0.38301681685192	1	FACETS	0.105	0.086	0.126	0.105	0.086	0.126	INDETERMINATE	1	TRUE	0	0.697879942332775	1		462	678	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092967	27092968	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0037113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	25	190	0	ENST00000324856.7:c.2899_2900dup	p.Met967IlefsTer2	p.M967Ifs*2	ENST00000324856	NM_006015.4	966	-/AT	10/20	0.38301681685192	1	FACETS	0.134	0.105	0.167	0.134	0.105	0.167	INDETERMINATE	1	TRUE	0	0.697879942332775	1		190	348	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759909	63759909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	26	207	0	ENST00000279873.7:c.562C>T	p.Arg188Cys	p.R188C	ENST00000279873	NM_032199.2	188	Cgc/Tgc	4/10	1	2	FACETS	0.197	0.155	0.244	0.197	0.155	0.244	SUBCLONAL	1	TRUE	1	0.697879942332775	2		207	379	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497678	125497678	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	188	315	1	ENST00000428830.2:c.242A>G	p.Tyr81Cys	p.Y81C	ENST00000428830	NM_001114121.2	81	tAt/tGt	3/14	0.38301681685192	1	FACETS	0.713	0.665	0.762	0.713	0.665	0.762	INDETERMINATE	1	TRUE	0	0.697879942332775	1		316	492	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828870	26828870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	73	246	0	ENST00000381527.3:c.92C>T	p.Thr31Ile	p.T31I	ENST00000381527	NM_001260.1	31	aCt/aTt	1/13	1	2	FACETS	0.399	0.35	0.453	0.399	0.35	0.453	SUBCLONAL	1	TRUE	1	0.697879942332775	2		246	524	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527404	137527404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	42	261	0	ENST00000367739.4:c.242C>T	p.Ser81Phe	p.S81F	ENST00000367739	NM_000416.2	81	tCt/tTt	3/7	1	2	FACETS	0.307	0.257	0.363	0.307	0.257	0.363	SUBCLONAL	1	TRUE	1	0.697879942332775	2		261	392	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468322	50468322	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	112	253	1	ENST00000331340.3:c.1557C>A	p.Ser519Arg	p.S519R	ENST00000331340	NM_006060.4	519	agC/agA	8/8	1	2	FACETS	0.654	0.591	0.72	0.654	0.591	0.72	SUBCLONAL	1	TRUE	1	0.697879942332775	2		254	491	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117861253	117861254	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0037113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	152	382	0	ENST00000297338.2:c.1635_1636del	p.Gly547ArgfsTer26	p.G547Rfs*26	ENST00000297338	NM_006265.2	545	tcAGgg/tcgg	13/14	1	2	FACETS	0.675	0.62	0.733	0.675	0.62	0.733	SUBCLONAL	1	TRUE	1	0.697879942332775	2		382	645	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842323	68842337	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTAGGCCTCCGTTTC	TTAGGCCTCCGTTTC	-	novel	NA	P-0037114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	138	488	0	ENST00000261769.5:c.388-3_399del		p.X130_splice	ENST00000261769	NM_004360.3	130		4/16	0.629371245806853	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.629371245806853	1		488	296	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740599	58740599	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	169	592	0	ENST00000305921.3:c.1504A>T	p.Asn502Tyr	p.N502Y	ENST00000305921	NM_003620.3	502	Aat/Tat	6/6	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.629371245806853	2		592	489	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0037114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	181	494	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.846	0.783	0.911	0.846	0.783	0.911	CLONAL	1	TRUE	1	0.629371245806853	2		494	680	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0037114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	122	441	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.629371245806853	2		441	351	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748086	72748086	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0121556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	42	478	0	ENST00000357731.5:c.92G>C	p.Cys31Ser	p.C31S	ENST00000357731	NM_173808.2	31	tGc/tCc	1/7	0.510984070755655	2	FACETS	0.445	0.373	0.526	0.223	0.186	0.263	SUBCLONAL	1	NA	0	0.510984070755655	2		478	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0037126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	220	565	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.392195947607476	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	0	0.406301356252955	2		565	540	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696430	47696430	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	244	571	0	ENST00000347630.2:c.393G>C	p.Trp131Cys	p.W131C	ENST00000347630	NM_001007230.1	131	tgG/tgC	6/11	1	2	FACETS	0.833	0.783	0.883	0.833	0.783	0.883	CLONAL	1	TRUE	1	0.895987716968353	2		571	654	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427984	49427984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	30	741	0	ENST00000301067.7:c.10606C>T	p.Arg3536Cys	p.R3536C	ENST00000301067	NM_003482.3	3536	Cgc/Tgc	38/54	1	2	FACETS	0.112	0.09	0.138	0.112	0.09	0.138	SUBCLONAL	1	TRUE	1	0.895987716968353	2		741	596	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026157	71026157	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	230	513	0	ENST00000318789.4:c.1465A>G	p.Asn489Asp	p.N489D	ENST00000318789	NM_032682.5	489	Aat/Gat	17/21	0.606479263815678	3	FACETS	1	0.986	1	0.588	0.552	0.625	CLONAL	1	TRUE	1	0.895987716968353	3		513	632	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0037152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	397	389	1	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.749520407517205	4	FACETS	0.955	0.92	0.989	0.955	0.92	0.989	CLONAL	3	TRUE	1	0.79954044231319	4		390	624	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577507	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0037152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	493	488	0	ENST00000269305.4:c.774dup	p.Asp259ArgfsTer5	p.D259Rfs*5	ENST00000269305	NM_001126112.2	258	-/A	7/11	NA	2	FACETS	0.92	0.894	0.945			1	INDETERMINATE	2	TRUE	NA	0.79954044231319	2		488	670	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164631	36164632	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0037152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	381	410	0	ENST00000300305.3:c.1243dup	p.Gln415ProfsTer185	p.Q415Pfs*185	ENST00000300305		415	cag/cCag	8/8	0.79954044231319	3	FACETS	1	0.99	1	0.58	0.551	0.609	CLONAL	1	TRUE	1	0.79954044231319	3		410	1150	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0037160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	337	549	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.905750541784645	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.905750541784645	1		552	382	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999749	100999761	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCCGCCCGCCA	GGGCCGCCCGCCA	CC	novel	NA	P-0037160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	231	578	2	ENST00000325455.5:c.41_53delinsGG	p.Val14GlyfsTer30	p.V14Gfs*30	ENST00000325455	NM_001202474.3	14	gTGGCGGGCGGCCCg/gGGg	1/8	1	2	FACETS	0.936	0.881	0.992	0.936	0.881	0.992	CLONAL	1	TRUE	1	0.905750541784645	2		580	545	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41199682	41199682	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397509284	NA	P-0037160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	276	535	0	ENST00000357654.3:c.5445G>A	p.Trp1815Ter	p.W1815*	ENST00000357654	NM_007294.3	1815	tgG/tgA	22/23	0.905750541784645	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.905750541784645	1		535	312	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967502	38967502	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	82	309	1	ENST00000357387.3:c.1088G>T	p.Arg363Met	p.R363M	ENST00000357387	NM_152756.3	363	aGg/aTg	13/38	0.173765717545585	1	FACETS	0.516	0.465	0.568	0.516	0.465	0.568	INDETERMINATE	1	TRUE	0	0.905750541784645	1		310	192	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115871	8115872	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0037175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	138	499	0	ENST00000346208.3:c.1219_1220del	p.Ser407AlafsTer99	p.S407Afs*99	ENST00000346208		406	aTC/a	6/6	1	2	FACETS	0.939	0.859	1	0.939	0.859	1	CLONAL	1	TRUE	1	0.53824092558233	2		499	546	SUCCESS
AR	367	MSKCC	GRCh37	X	66863220	66863221	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0037175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	83	484	0	ENST00000374690.3:c.1740dup	p.Lys581GlnfsTer9	p.K581Qfs*9	ENST00000374690	NM_000044.3	580	tgc/tgCc	2/8	0.53824092558233	1	FACETS	0.716	0.638	0.797	0.716	0.638	0.797	SUBCLONAL	1	TRUE	0	0.53824092558233	1		484	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0037180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	212	715	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.433742210015784	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.433742210015784	1		715	752	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0037180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	74	522	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.241574627044645	1	FACETS	0.9	0.795	1	0.9	0.795	1	INDETERMINATE	1	TRUE	0	0.433742210015784	1		522	297	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946435	2946435	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751651073	NA	P-0037180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	476	632	0	ENST00000396946.4:c.3302G>A	p.Arg1101His	p.R1101H	ENST00000396946	NM_032415.4	1101	cGc/cAc	25/25	0.364566524925765	5	FACETS	1	0.99	1	0.82	0.786	0.854	CLONAL	3	TRUE	1	0.433742210015784	5		632	1105	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134512	30134512	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	29	243	0	ENST00000263025.4:c.19C>T	p.Gln7Ter	p.Q7*	ENST00000263025	NM_002746.2	7	Cag/Tag	1/9	0.150969299916006	3	FACETS	0.563	0.453	0.687	0.282	0.226	0.344	INDETERMINATE	1	TRUE	1	0.433742210015784	3		243	289	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88651956	88651957	+	stop_gained	Nonsense_Mutation	DNP	GA	GA	TT	novel	NA	P-0037180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	58	374	0	ENST00000372037.3:c.303_304delinsTT	p.Met101_Lys102delinsIleTer	p.M101_K102delinsI*	ENST00000372037	NM_004329.2	101	atGAaa/atTTaa	5/13	1	2	FACETS	0.651	0.561	0.748	0.651	0.561	0.748	SUBCLONAL	1	TRUE	1	0.433742210015784	2		374	411	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593391	48593391	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	59	304	0	ENST00000342988.3:c.1142T>C	p.Leu381Ser	p.L381S	ENST00000342988	NM_005359.5	381	tTg/tCg	10/12	0.335309542574405	1	FACETS	0.775	0.673	0.884	0.775	0.673	0.884	SUBCLONAL	1	TRUE	0	0.433742210015784	1		304	275	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004945	150004945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	145	443	0	ENST00000253339.5:c.1280C>G	p.Pro427Arg	p.P427R	ENST00000253339		427	cCt/cGt	3/7	0.188770798024574	3	FACETS	1	0.985	1	0.452	0.414	0.492	INDETERMINATE	1	TRUE	0	0.433742210015784	3		443	600	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913250	NA	P-0037224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	129	268	0	ENST00000369535.4:c.34G>A	p.Gly12Ser	p.G12S	ENST00000369535	NM_002524.4	12	Ggt/Agt	2/7	0.202763128726353	3	FACETS	1	0.981	1	0.651	0.591	0.714	INDETERMINATE	1	TRUE	1	0.34335092903256	3		268	676	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0037224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	131	436	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.34335092903256	3	FACETS	0.839	0.765	0.916	0.839	0.765	0.916	CLONAL	2	TRUE	1	0.34335092903256	3		436	533	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251754	212251754	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	105	428	0	ENST00000342788.4:c.3305T>G	p.Phe1102Cys	p.F1102C	ENST00000342788	NM_005235.2	1102	tTt/tGt	27/28	0.202763128726353	3	FACETS	1	0.981	1	0.704	0.633	0.778	INDETERMINATE	1	TRUE	1	0.34335092903256	3		428	509	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047995	180047995	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762560832	NA	P-0037224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	148	842	0	ENST00000261937.6:c.2180C>T	p.Ala727Val	p.A727V	ENST00000261937	NM_182925.4	727	gCg/gTg	15/30	0.30534794321662	3	FACETS	1	0.919	1	0.504	0.459	0.55	CLONAL	1	TRUE	1	0.34335092903256	3		842	1003	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579592	7579592	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0037224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	233	610	0	ENST00000269305.4:c.97-2A>T		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.34335092903256	2	FACETS	0.994	0.932	1	0.994	0.932	1	CLONAL	2	TRUE	0	0.34335092903256	2		610	683	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88679151	88679151	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	25	68	0	ENST00000372037.3:c.1091A>G	p.Lys364Arg	p.K364R	ENST00000372037	NM_004329.2	364	aAg/aGg	10/13	0.202763128726353	3	FACETS	0.889	0.717	1	0.889	0.717	1	INDETERMINATE	2	TRUE	1	0.34335092903256	3		68	96	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593505	48593505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	181	379	0	ENST00000342988.3:c.1256G>A	p.Gly419Glu	p.G419E	ENST00000342988	NM_005359.5	419	gGg/gAg	10/12	0.34335092903256	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.34335092903256	2		379	482	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332865	152332865	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	282	577	0	ENST00000206249.3:c.1171C>A	p.Leu391Ile	p.L391I	ENST00000206249	NM_000125.3	391	Ctc/Atc	5/8	0.34335092903256	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.34335092903256	3		577	887	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783214	9783214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	180	565	0	ENST00000377346.4:c.2458G>A	p.Asp820Asn	p.D820N	ENST00000377346	NM_005026.3	820	Gac/Aac	20/24	0.152117817878408	4	FACETS	0.876	0.809	0.945	0.876	0.809	0.945	INDETERMINATE	2	TRUE	2	0.34335092903256	4		565	804	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436181	56436197	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCTCTGGAAAAAAGAA	CCCTCTGGAAAAAAGAA	-	novel	NA	P-0037224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	180	482	0	ENST00000407977.2:c.953-13_956del		p.X318_splice	ENST00000407977		318		9/10	0.34335092903256	2	FACETS	0.875	0.811	0.941	0.875	0.811	0.941	CLONAL	2	TRUE	0	0.34335092903256	2		482	599	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467958	50467958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1219777993	NA	P-0037224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	129	633	3	ENST00000331340.3:c.1193C>T	p.Thr398Met	p.T398M	ENST00000331340	NM_006060.4	398	aCg/aTg	8/8	0.34335092903256	3	FACETS	1	0.972	1	0.589	0.534	0.646	CLONAL	1	TRUE	1	0.34335092903256	3		636	748	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	63	522	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.957	0.83	1	0.957	0.83	1	CLONAL	1	TRUE	1	0.278296088609437	2		522	473	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	78	711	0	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	0.732	0.642	0.828	0.732	0.642	0.828	SUBCLONAL	1	TRUE	1	0.278296088609437	2		711	766	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	45	438	1	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	0.614	0.515	0.722	0.614	0.515	0.722	SUBCLONAL	1	TRUE	1	0.278296088609437	2		439	527	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	33	355	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.765	0.625	0.922	0.765	0.625	0.922	CLONAL	1	TRUE	1	0.278296088609437	2		355	310	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	79	517	3	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.762	0.67	0.862	0.762	0.67	0.862	SUBCLONAL	1	TRUE	1	0.278296088609437	2		520	745	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045772	143045772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145209328	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	66	658	0	ENST00000262992.4:c.1862C>T	p.Thr621Met	p.T621M	ENST00000262992	NM_001101669.1	621	aCg/aTg	17/24	1	2	FACETS	0.674	0.584	0.771	0.674	0.584	0.771	SUBCLONAL	1	TRUE	1	0.278296088609437	2		658	704	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	113	877	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.874	0.786	0.968	0.874	0.786	0.968	CLONAL	1	TRUE	1	0.278296088609437	2		883	929	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	99	514	2	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.278296088609437	2		516	562	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	97	559	3	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	0.878	0.782	0.98	0.878	0.782	0.98	CLONAL	1	TRUE	1	0.278296088609437	2		562	794	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484611	57484611	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	106	769	0	ENST00000371085.3:c.695G>A	p.Arg232His	p.R232H	ENST00000371085	NM_000516.4	232	cGc/cAc	9/13	1	2	FACETS	0.983	0.881	1	0.983	0.881	1	CLONAL	1	TRUE	1	0.278296088609437	2		769	775	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	73	680	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	0.777	0.679	0.883	0.777	0.679	0.883	SUBCLONAL	1	TRUE	1	0.278296088609437	2		680	675	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	83	524	0	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	1	2	FACETS	0.76	0.67	0.857	0.76	0.67	0.857	SUBCLONAL	1	TRUE	1	0.278296088609437	2		524	785	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332273	70332273	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	47	441	1	ENST00000373644.4:c.184del	p.Thr62GlnfsTer13	p.T62Qfs*13	ENST00000373644	NM_030625.2	60	Aaa/aa	2/12	1	2	FACETS	0.669	0.564	0.784	0.669	0.564	0.784	SUBCLONAL	1	TRUE	1	0.278296088609437	2		442	505	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456467	99456467	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56248469	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	56	539	0	ENST00000268035.6:c.1784G>A	p.Arg595His	p.R595H	ENST00000268035	NM_000875.3	595	cGt/cAt	8/21	1	2	FACETS	0.709	0.607	0.82	0.709	0.607	0.82	SUBCLONAL	1	TRUE	1	0.278296088609437	2		539	568	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289196	33289196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771284147	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	100	624	0	ENST00000374542.5:c.356G>A	p.Arg119Gln	p.R119Q	ENST00000374542	NM_001141970.1	119	cGg/cAg	3/8	1	2	FACETS	0.911	0.813	1	0.911	0.813	1	CLONAL	1	TRUE	1	0.278296088609437	2		624	789	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	108	790	3	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	1	2	FACETS	0.889	0.797	0.987	0.889	0.797	0.987	CLONAL	1	TRUE	1	0.278296088609437	2		793	873	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781122	161781122	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	105	686	3	ENST00000366898.1:c.1283del	p.Asn428MetfsTer7	p.N428Mfs*7	ENST00000366898	NM_004562.2	428	aAt/at	11/12	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.278296088609437	2		689	747	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261555	142261555	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	36	508	1	ENST00000350721.4:c.3402del	p.Phe1134LeufsTer6	p.F1134Lfs*6	ENST00000350721	NM_001184.3	1134	ttT/tt	17/47	1	2	FACETS	0.539	0.443	0.647	0.539	0.443	0.647	SUBCLONAL	1	TRUE	1	0.278296088609437	2		509	480	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347484	91347484	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	72	443	0	ENST00000355112.3:c.3651del	p.Lys1217AsnfsTer62	p.K1217Nfs*62	ENST00000355112	NM_000057.2	1216	Aaa/aa	19/22	1	2	FACETS	0.709	0.619	0.806	0.709	0.619	0.806	SUBCLONAL	1	TRUE	1	0.278296088609437	2		443	730	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	173	627	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.821	0.757	0.887	1	0.991	1	CLONAL	2	TRUE	1	0.278296088609437	2		633	757	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231610	5231611	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	19	178	0	ENST00000357368.4:c.1865dup	p.Gln623SerfsTer4	p.Q623Sfs*4	ENST00000357368	NM_002850.3	622	cct/ccCt	14/38	1	2	FACETS	0.683	0.52	0.872	0.683	0.52	0.872	SUBCLONAL	1	TRUE	1	0.278296088609437	2		178	200	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209593	98209593	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	89	628	2	ENST00000331920.6:c.3945del	p.Tyr1316ThrfsTer56	p.Y1316Tfs*56	ENST00000331920	NM_000264.3	1315	ccC/cc	23/24	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.278296088609437	2		630	628	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259043	16259043	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	75	679	0	ENST00000375759.3:c.6313del	p.Ala2105LeufsTer33	p.A2105Lfs*33	ENST00000375759	NM_015001.2	2103	aGg/ag	11/15	1	2	FACETS	0.786	0.688	0.891	0.786	0.688	0.891	SUBCLONAL	1	TRUE	1	0.278296088609437	2		679	686	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431545	49431545	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	99	852	0	ENST00000301067.7:c.9594del	p.Ser3199AlafsTer3	p.S3199Afs*3	ENST00000301067	NM_003482.3	3198	ccC/cc	34/54	1	2	FACETS	0.816	0.727	0.91	0.816	0.727	0.91	CLONAL	1	TRUE	1	0.278296088609437	2		852	872	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214871	36214871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	134	906	0	ENST00000222270.7:c.3302del	p.Pro1101LeufsTer81	p.P1101Lfs*81	ENST00000222270	NM_014727.1	1099	ggC/gg	8/37	1	2	FACETS	0.986	0.895	1	0.986	0.895	1	CLONAL	1	TRUE	1	0.278296088609437	2		906	977	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166821	32166821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1041758474	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	112	957	1	ENST00000375023.3:c.4417C>T	p.Arg1473Cys	p.R1473C	ENST00000375023	NM_004557.3	1473	Cgt/Tgt	24/30	1	2	FACETS	0.832	0.747	0.923	0.832	0.747	0.923	CLONAL	1	TRUE	1	0.278296088609437	2		958	967	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284970	15284970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	126	968	1	ENST00000263388.2:c.4645G>A	p.Ala1549Thr	p.A1549T	ENST00000263388	NM_000435.2	1549	Gcg/Acg	25/33	1	2	FACETS	0.901	0.815	0.992	0.901	0.815	0.992	CLONAL	1	TRUE	1	0.278296088609437	2		969	1005	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244148	153244148	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	89	717	0	ENST00000281708.4:c.2009del	p.Gly670GlufsTer37	p.G670Efs*37	ENST00000281708	NM_033632.3	670	gGa/ga	12/12	1	2	FACETS	0.863	0.765	0.968	0.863	0.765	0.968	CLONAL	1	TRUE	1	0.278296088609437	2		717	741	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47685288	47685288	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	56	500	0	ENST00000347630.2:c.662G>A	p.Arg221His	p.R221H	ENST00000347630	NM_001007230.1	221	cGt/cAt	8/11	1	2	FACETS	0.811	0.696	0.937	0.811	0.696	0.937	CLONAL	1	TRUE	1	0.278296088609437	2		500	496	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214714	36214714	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	86	646	0	ENST00000222270.7:c.3145del	p.Ala1049ArgfsTer133	p.A1049Rfs*133	ENST00000222270	NM_014727.1	1047	cGg/cg	8/37	1	2	FACETS	0.941	0.833	1	0.941	0.833	1	CLONAL	1	TRUE	1	0.278296088609437	2		646	657	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793290	242793291	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	126	1109	0	ENST00000334409.5:c.786dup	p.Ala263ArgfsTer7	p.A263Rfs*7	ENST00000334409	NM_005018.2	262	-/C	5/5	1	2	FACETS	0.872	0.788	0.96	0.872	0.788	0.96	CLONAL	1	TRUE	1	0.278296088609437	2		1109	1039	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105737	27105737	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1064794151	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	57	454	0	ENST00000324856.7:c.5351del	p.Asn1784MetfsTer5	p.N1784Mfs*5	ENST00000324856	NM_006015.4	1783	gAa/ga	20/20	1	2	FACETS	0.789	0.678	0.911	0.789	0.678	0.911	CLONAL	1	TRUE	1	0.278296088609437	2		454	519	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724362	112724362	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	99	681	1	ENST00000369452.4:c.252del	p.Lys84AsnfsTer7	p.K84Nfs*7	ENST00000369452	NM_007373.3	82	agA/ag	2/9	1	2	FACETS	0.951	0.849	1	0.951	0.849	1	CLONAL	1	TRUE	1	0.278296088609437	2		682	748	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416191	416191	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	77	556	0	ENST00000399788.2:c.3995del	p.Pro1332LeufsTer26	p.P1332Lfs*26	ENST00000399788	NM_001042603.1	1332	cCt/ct	24/28	1	2	FACETS	0.912	0.801	1	0.912	0.801	1	CLONAL	1	TRUE	1	0.278296088609437	2		556	607	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870838	12870838	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	50	249	0	ENST00000228872.4:c.65A>C	p.Glu22Ala	p.E22A	ENST00000228872	NM_004064.3	22	gAg/gCg	1/3	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.278296088609437	2		249	290	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658322	18658322	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	94	717	0	ENST00000266497.5:c.3127A>G	p.Lys1043Glu	p.K1043E	ENST00000266497		1043	Aag/Gag	22/31	1	2	FACETS	0.985	0.877	1	0.985	0.877	1	CLONAL	1	TRUE	1	0.278296088609437	2		717	686	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244983	46244983	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	95	775	0	ENST00000334344.6:c.3077T>C	p.Val1026Ala	p.V1026A	ENST00000334344	NM_152641.2	1026	gTa/gCa	15/21	1	2	FACETS	0.823	0.732	0.92	0.823	0.732	0.92	CLONAL	1	TRUE	1	0.278296088609437	2		775	830	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426664	49426664	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	47	507	0	ENST00000301067.7:c.11824C>T	p.Gln3942Ter	p.Q3942*	ENST00000301067	NM_003482.3	3942	Caa/Taa	39/54	1	2	FACETS	0.705	0.595	0.826	0.705	0.595	0.826	SUBCLONAL	1	TRUE	1	0.278296088609437	2		507	479	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484319	50484319	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150612896	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	99	823	0	ENST00000394963.4:c.1079G>A	p.Arg360Gln	p.R360Q	ENST00000394963	NM_003076.4	360	cGg/cAg	9/13	1	2	FACETS	0.8	0.713	0.893	0.8	0.713	0.893	SUBCLONAL	1	TRUE	1	0.278296088609437	2		823	889	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349480	73349480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1048864282	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	65	586	0	ENST00000377767.4:c.856G>A	p.Ala286Thr	p.A286T	ENST00000377767	NM_014953.3	286	Gct/Act	6/21	1	2	FACETS	0.779	0.675	0.891	0.779	0.675	0.891	SUBCLONAL	1	TRUE	1	0.278296088609437	2		586	600	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56792460	56792460	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	71	618	0	ENST00000308159.5:c.190C>A	p.Leu64Ile	p.L64I	ENST00000308159	NM_014669.4	64	Ctc/Atc	3/22	1	2	FACETS	0.787	0.687	0.896	0.787	0.687	0.896	SUBCLONAL	1	TRUE	1	0.278296088609437	2		618	648	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771353	68771353	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	71	489	0	ENST00000261769.5:c.35T>G	p.Leu12Arg	p.L12R	ENST00000261769	NM_004360.3	12	cTg/cGg	1/16	1	2	FACETS	0.985	0.861	1	0.985	0.861	1	CLONAL	1	TRUE	1	0.278296088609437	2		489	518	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883239	37883239	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377602610	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	125	846	5	ENST00000269571.5:c.3142C>T	p.Arg1048Cys	p.R1048C	ENST00000269571		1048	Cgc/Tgc	25/27	1	2	FACETS	0.983	0.889	1	0.983	0.889	1	CLONAL	1	TRUE	1	0.278296088609437	2		851	914	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120399	70120400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	163	1161	0	ENST00000245479.2:c.1402dup	p.Tyr468LeufsTer110	p.Y468Lfs*110	ENST00000245479	NM_000346.3	467	-/T	3/3	1	2	FACETS	0.952	0.872	1	0.952	0.872	1	CLONAL	1	TRUE	1	0.278296088609437	2		1161	1230	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732431	74732431	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	66	407	0	ENST00000359995.5:c.478A>G	p.Thr160Ala	p.T160A	ENST00000359995	NM_001195427.1	160	Acc/Gcc	2/3	1	2	FACETS	0.898	0.781	1	0.898	0.781	1	CLONAL	1	TRUE	1	0.278296088609437	2		407	528	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222076	2222076	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	151	1121	0	ENST00000398665.3:c.2908A>G	p.Ser970Gly	p.S970G	ENST00000398665	NM_032482.2	970	Agc/Ggc	24/28	1	2	FACETS	0.989	0.903	1	0.989	0.903	1	CLONAL	1	TRUE	1	0.278296088609437	2		1121	1097	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254608	10254608	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs760683699	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	106	772	0	ENST00000340748.4:c.2902C>A	p.Leu968Met	p.L968M	ENST00000340748		968	Ctg/Atg	28/40	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.278296088609437	2		772	738	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169557	11169557	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	92	615	0	ENST00000358026.2:c.4723G>T	p.Gly1575Cys	p.G1575C	ENST00000358026	NM_001128849.1	1575	Ggc/Tgc	33/36	1	2	FACETS	0.923	0.821	1	0.923	0.821	1	CLONAL	1	TRUE	1	0.278296088609437	2		615	716	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276860	15276861	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	73	889	0	ENST00000263388.2:c.5403_5404dup	p.Ala1802GlyfsTer24	p.A1802Gfs*24	ENST00000263388	NM_000435.2	1802	gct/gGGct	30/33	1	2	FACETS	0.573	0.5	0.653	0.573	0.5	0.653	SUBCLONAL	1	TRUE	1	0.278296088609437	2		889	915	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211494	36211495	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	64	672	2	ENST00000222270.7:c.1249dup	p.Leu417ProfsTer133	p.L417Pfs*133	ENST00000222270	NM_014727.1	415	-/C	3/37	1	2	FACETS	0.629	0.544	0.722	0.629	0.544	0.722	SUBCLONAL	1	TRUE	1	0.278296088609437	2		674	731	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220945	36220945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	52	502	0	ENST00000222270.7:c.4995G>A	p.Met1665Ile	p.M1665I	ENST00000222270	NM_014727.1	1665	atG/atA	23/37	1	2	FACETS	0.664	0.565	0.772	0.664	0.565	0.772	SUBCLONAL	1	TRUE	1	0.278296088609437	2		502	563	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213183	39213185	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	107	1181	0	ENST00000402219.2:c.3782_3784del	p.Pro1261del	p.P1261del	ENST00000402219	NM_005633.3	1261	cCTCaa/caa	23/23	1	2	FACETS	0.646	0.577	0.719	0.646	0.577	0.719	SUBCLONAL	1	TRUE	1	0.278296088609437	2		1181	1191	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39294858	39294858	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	62	460	0	ENST00000402219.2:c.124G>T	p.Asp42Tyr	p.D42Y	ENST00000402219	NM_005633.3	42	Gat/Tat	2/23	1	2	FACETS	0.915	0.792	1	0.915	0.792	1	CLONAL	1	TRUE	1	0.278296088609437	2		460	487	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116254	209116254	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	53	361	0	ENST00000345146.2:c.22G>T	p.Gly8Cys	p.G8C	ENST00000345146	NM_005896.2	8	Ggt/Tgt	3/10	1	2	FACETS	0.898	0.768	1	0.898	0.768	1	CLONAL	1	TRUE	1	0.278296088609437	2		361	424	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484753	57484753	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	85	732	0	ENST00000371085.3:c.733A>G	p.Ile245Val	p.I245V	ENST00000371085	NM_000516.4	245	Atc/Gtc	10/13	1	2	FACETS	0.797	0.704	0.897	0.797	0.704	0.897	SUBCLONAL	1	TRUE	1	0.278296088609437	2		732	766	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163157	47163157	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1211480425	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	63	552	0	ENST00000409792.3:c.2969T>C	p.Val990Ala	p.V990A	ENST00000409792	NM_014159.6	990	gTg/gCg	3/21	1	2	FACETS	0.866	0.75	0.991	0.866	0.75	0.991	CLONAL	1	TRUE	1	0.278296088609437	2		552	523	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090585	71090585	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	88	657	0	ENST00000318789.4:c.763A>C	p.Thr255Pro	p.T255P	ENST00000318789	NM_032682.5	255	Acc/Ccc	11/21	1	2	FACETS	0.914	0.81	1	0.914	0.81	1	CLONAL	1	TRUE	1	0.278296088609437	2		657	692	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902779	1902779	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs140401180	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	88	759	2	ENST00000382891.5:c.398T>C	p.Met133Thr	p.M133T	ENST00000382891	NM_133335.3	133	aTg/aCg	2/22	1	2	FACETS	0.782	0.692	0.878	0.782	0.692	0.878	SUBCLONAL	1	TRUE	1	0.278296088609437	2		761	809	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981508	55981509	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	71	659	0	ENST00000263923.4:c.428dup	p.Asn143LysfsTer31	p.N143Kfs*31	ENST00000263923	NM_002253.2	143	aac/aaAc	4/30	1	2	FACETS	0.753	0.656	0.856	0.753	0.656	0.856	SUBCLONAL	1	TRUE	1	0.278296088609437	2		659	678	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178659	56178659	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	34	305	0	ENST00000399503.3:c.3635del	p.Asn1212MetfsTer33	p.N1212Mfs*33	ENST00000399503	NM_005921.1	1211	gAa/ga	14/20	1	2	FACETS	0.677	0.554	0.815	0.677	0.554	0.815	SUBCLONAL	1	TRUE	1	0.278296088609437	2		305	361	SUCCESS
APC	324	MSKCC	GRCh37	5	112137003	112137003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772806807	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	61	500	0	ENST00000257430.4:c.757G>A	p.Gly253Ser	p.G253S	ENST00000257430	NM_000038.5	253	Ggc/Agc	8/16	1	2	FACETS	0.749	0.646	0.861	0.749	0.646	0.861	SUBCLONAL	1	TRUE	1	0.278296088609437	2		500	585	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948472	31948472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745355598	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	46	530	0	ENST00000375333.2:c.955C>T	p.Arg319Trp	p.R319W	ENST00000375333	NM_032454.1	319	Cgg/Tgg	7/8	1	2	FACETS	0.668	0.562	0.784	0.668	0.562	0.784	SUBCLONAL	1	TRUE	1	0.278296088609437	2		530	495	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300039	137300040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0037227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	86	940	0	ENST00000481739.1:c.330_331dup	p.Leu111ProfsTer58	p.L111Pfs*58	ENST00000481739	NM_002957.4	108	-/CC	3/10	1	2	FACETS	0.647	0.571	0.729	0.647	0.571	0.729	SUBCLONAL	1	TRUE	1	0.278296088609437	2		940	955	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0037253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	317	414	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.607226958338969	3	FACETS	0.988	0.951	1	0.988	0.951	1	CLONAL	3	TRUE	0	0.607226958338969	3		414	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0037253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	296	670	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.607226958338969	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.607226958338969	2		670	438	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953760	48953760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913302	NA	P-0037253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	145	257	0	ENST00000267163.4:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000267163	NM_000321.2	455	Cga/Tga	14/27	0.607226958338969	2	FACETS	0.915	0.855	0.975	0.915	0.855	0.975	CLONAL	2	TRUE	0	0.607226958338969	2		257	261	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799162	88799162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	72	423	1	ENST00000360948.2:c.223G>A	p.Asp75Asn	p.D75N	ENST00000360948	NM_001012338.2	75	Gac/Aac	2/19	1	2	FACETS	0.865	0.765	0.972	0.865	0.765	0.972	CLONAL	1	TRUE	1	0.607226958338969	2		424	274	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0037257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	141	315	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.95	0.869	1	0.95	0.869	1	CLONAL	1	TRUE	1	0.535110550801655	2		315	555	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575671	48575671	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0037257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	230	452	0	ENST00000342988.3:c.431C>G	p.Ser144Ter	p.S144*	ENST00000342988	NM_005359.5	144	tCa/tGa	4/12	0.535110550801655	1	FACETS	0.93	0.871	0.99	0.93	0.871	0.99	CLONAL	1	TRUE	0	0.535110550801655	1		452	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0037257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	291	578	1	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.535110550801655	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.535110550801655	1		579	751	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984423	201984424	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0037257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	177	479	0	ENST00000359651.3:c.1090dup	p.Glu364GlyfsTer107	p.E364Gfs*107	ENST00000359651		363	gag/gaGg	8/8	0.435895121419143	3	FACETS	0.954	0.88	1	0.477	0.44	0.516	CLONAL	1	TRUE	1	0.535110550801655	3		479	879	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023708	27023715	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGCCAT	GGGGCCAT	-	novel	NA	P-0037261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	69	225	0	ENST00000324856.7:c.818_825del	p.Ala273GlyfsTer124	p.A273Gfs*124	ENST00000324856	NM_006015.4	272	GGGGCCATg/g	1/20	0.493800092349508	1	FACETS	0.782	0.691	0.878	0.782	0.691	0.878	SUBCLONAL	1	TRUE	0	0.547393655029156	1		225	234	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004217	150004217	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1431439182	NA	P-0037263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	148	394	2	ENST00000253339.5:c.2008C>T	p.Arg670Trp	p.R670W	ENST00000253339		670	Cgg/Tgg	3/7	0.883512608921875	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.89766280479048	1		396	166	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	241	501	0	ENST00000269305.4:c.672G>C	p.Glu224Asp	p.E224D	ENST00000269305	NM_001126112.2	224	gaG/gaC	6/11	0.89766280479048	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.89766280479048	1		501	277	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438364	110438437	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	CCGGCCCGGGCGGCCCGTGCCGCGGCGGGCTCGCCATCGCGGGCGCTTCAGGCCGCGCGGCCCGGGCCCGGCGC	CCGGCCCGGGCGGCCCGTGCCGCGGCGGGCTCGCCATCGCGGGCGCTTCAGGCCGCGCGGCCCGGGCCCGGCGC	-	novel	NA	P-0037263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	59	83	0	ENST00000375856.3:c.-37_37del		p.*13*	ENST00000375856	NM_003749.2	?-13/1338		1/2	0.89766280479048	2	FACETS	1	0.928	1	0.53	0.471	0.589	CLONAL	1	TRUE	0	0.89766280479048	2		83	124	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978367	2978367	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	91	618	0	ENST00000396946.4:c.963C>A	p.Asn321Lys	p.N321K	ENST00000396946	NM_032415.4	321	aaC/aaA	7/25	0.89766280479048	1	FACETS	0.405	0.364	0.447	0.405	0.364	0.447	SUBCLONAL	1	TRUE	0	0.89766280479048	1		618	276	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061229	38061237	+	inframe_deletion	In_Frame_Del	DEL	ACATGTTGC	ACATGTTGC	-	novel	NA	P-0037277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	195	596	0	ENST00000250448.2:c.752_760del	p.Gly251_Phe254delinsVal	p.G251_F254delinsV	ENST00000250448	NM_004496.3	251	gGCAACATGTtc/gtc	2/2	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.370008573357213	2		596	773	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524215	18524215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769408892	NA	P-0037283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	36	585	0	ENST00000266497.5:c.1727C>T	p.Ala576Val	p.A576V	ENST00000266497		576	gCg/gTg	11/31	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		585	663	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0037292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	69	414	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.274272350312068	4	FACETS	0.849	0.745	0.959	0.849	0.745	0.959	CLONAL	2	FALSE	2	0.340551118266448	4		414	320	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0037292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	71	547	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.644	0.562	0.733	0.644	0.562	0.733	SUBCLONAL	1	FALSE	1	0.340551118266448	2		547	647	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916929	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519931	NA	P-0037292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	25	544	0	ENST00000263967.3:c.316G>C	p.Gly106Arg	p.G106R	ENST00000263967	NM_006218.2	106	Ggc/Cgc	2/21	1	2	FACETS	0.602	0.476	0.745	0.602	0.476	0.745	SUBCLONAL	1	FALSE	1	0.340551118266448	2		544	244	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0037292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	24	313	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	1	2	FACETS	0.684	0.539	0.849	0.684	0.539	0.849	SUBCLONAL	1	FALSE	1	0.340551118266448	2		313	206	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246445	105246445	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	176	749	0	ENST00000349310.3:c.155T>G	p.Leu52Arg	p.L52R	ENST00000349310	NM_001014432.1	52	cTc/cGc	4/15	0.211857585650105	2	FACETS	1	0.989	1	0.708	0.654	0.764	CLONAL	1	FALSE	0	0.340551118266448	2		749	730	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50815230	50815230	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	56	737	0	ENST00000398568.2:c.1583C>A	p.Ala528Glu	p.A528E	ENST00000398568	NM_001042412.1	528	gCg/gAg	9/18	1	2	FACETS	0.417	0.356	0.483	0.417	0.356	0.483	SUBCLONAL	1	FALSE	1	0.340551118266448	2		737	789	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209101817	209101817	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	48	605	0	ENST00000345146.2:c.1231C>G	p.Gln411Glu	p.Q411E	ENST00000345146	NM_005896.2	411	Cag/Gag	10/10	1	2	FACETS	0.921	0.783	1	0.921	0.783	1	CLONAL	1	FALSE	1	0.340551118266448	2		605	306	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182679076	182679076	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	14	613	0	ENST00000292782.4:c.458G>T	p.Arg153Leu	p.R153L	ENST00000292782	NM_020640.2	153	cGa/cTa	4/7	1	2	FACETS	0.326	0.235	0.436	0.326	0.235	0.436	SUBCLONAL	1	FALSE	1	0.340551118266448	2		613	252	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680197	30680197	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	73	944	2	ENST00000376406.3:c.1522A>T	p.Ile508Phe	p.I508F	ENST00000376406	NM_014641.2	508	Atc/Ttc	5/15	0.340551118266448	4	FACETS	0.795	0.695	0.903	0.397	0.347	0.452	CLONAL	1	FALSE	2	0.340551118266448	4		946	723	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190557	32190557	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753044693	NA	P-0037292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	78	760	0	ENST00000375023.3:c.182C>T	p.Thr61Met	p.T61M	ENST00000375023	NM_004557.3	61	aCg/aTg	3/30	0.340551118266448	4	FACETS	0.88	0.773	0.995	0.44	0.386	0.498	CLONAL	1	FALSE	2	0.340551118266448	4		760	698	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266112	41266112	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913228	NA	P-0037329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	220	219	0	ENST00000349496.5:c.109T>G	p.Ser37Ala	p.S37A	ENST00000349496	NM_001904.3	37	Tct/Gct	3/15	0.506442203541172	1	FACETS	0.828	0.784	0.873	0.828	0.784	0.873	CLONAL	1	TRUE	0	0.799246072784551	1		219	399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0037351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	239	467	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.59927230765046	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.59927230765046	1		467	501	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0037351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	198	545	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.935	0.869	1	0.935	0.869	1	CLONAL	1	TRUE	1	0.59927230765046	2		545	707	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057936	27057937	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1415146710	NA	P-0037351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	180	671	0	ENST00000324856.7:c.1650dup	p.Tyr551LeufsTer72	p.Y551Lfs*72	ENST00000324856	NM_006015.4	548	-/C	3/20	0.109385033941038	4	FACETS	1	0.99	1	0.745	0.69	0.802	INDETERMINATE	1	TRUE	2	0.59927230765046	4		671	645	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0037351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	80	301	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.716	0.634	0.802	0.716	0.634	0.802	SUBCLONAL	1	TRUE	1	0.59927230765046	2		301	373	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184589	11184589	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	202	729	0	ENST00000361445.4:c.6628G>C	p.Ala2210Pro	p.A2210P	ENST00000361445	NM_004958.3	2210	Gcc/Ccc	47/58	0.419982428986406	1	FACETS	0.721	0.671	0.772	0.721	0.671	0.772	SUBCLONAL	1	TRUE	0	0.59927230765046	1		729	655	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730904	40730904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770182876	NA	P-0037351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	128	649	1	ENST00000373198.4:c.3631G>A	p.Glu1211Lys	p.E1211K	ENST00000373198	NM_133170.3	1211	Gag/Aag	27/32	0.570346452884624	3	FACETS	0.938	0.853	1	0.469	0.426	0.514	CLONAL	1	TRUE	1	0.59927230765046	3		650	592	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665709	86665709	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	115	348	0	ENST00000274376.6:c.1690C>A	p.Gln564Lys	p.Q564K	ENST00000274376	NM_002890.2	564	Caa/Aaa	12/25	1	2	FACETS	0.938	0.852	1	0.938	0.852	1	CLONAL	1	TRUE	1	0.59927230765046	2		348	409	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	117	350	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.311019534113703	3	FACETS	0.888	0.807	0.973	0.888	0.807	0.973	CLONAL	2	TRUE	1	0.365706886608562	3		350	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0037366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	305	668	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.361874281049289	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.365706886608562	2		668	769	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120509086	120509086	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	174	317	0	ENST00000256646.2:c.1480G>C	p.Glu494Gln	p.E494Q	ENST00000256646	NM_024408.3	494	Gaa/Caa	9/34	0.361874281049289	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.365706886608562	2		317	434	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923156	48923156	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	116	264	0	ENST00000267163.4:c.606del	p.Glu204LysfsTer10	p.E204Kfs*10	ENST00000267163	NM_000321.2	202	Aaa/aa	6/27	0.363398904146497	3	FACETS	0.985	0.905	1	0.985	0.905	1	CLONAL	3	TRUE	0	0.365706886608562	3		264	254	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0037380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	251	438	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.929	0.873	0.987	0.929	0.873	0.987	CLONAL	1	TRUE	1	0.722161268986696	2		438	748	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306689	41306689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868376470	NA	P-0037380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	230	717	0	ENST00000373198.4:c.970G>A	p.Glu324Lys	p.E324K	ENST00000373198	NM_133170.3	324	Gaa/Aaa	7/32	1	2	FACETS	0.995	0.934	1	0.995	0.934	1	CLONAL	1	TRUE	1	0.722161268986696	2		717	640	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467675	50467675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759124417	NA	P-0037380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	18	316	0	ENST00000331340.3:c.910G>A	p.Glu304Lys	p.E304K	ENST00000331340	NM_006060.4	304	Gaa/Aaa	8/8	1	2	FACETS	0.144	0.108	0.187	0.144	0.108	0.187	SUBCLONAL	1	TRUE	1	0.722161268986696	2		316	345	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468158	50468158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	152	618	0	ENST00000331340.3:c.1393G>A	p.Glu465Lys	p.E465K	ENST00000331340	NM_006060.4	465	Gaa/Aaa	8/8	1	2	FACETS	0.952	0.879	1	0.952	0.879	1	CLONAL	1	TRUE	1	0.722161268986696	2		618	442	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031970	10031970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	207	450	0	ENST00000330684.3:c.853G>A	p.Asp285Asn	p.D285N	ENST00000330684	NM_001134407.1	285	Gac/Aac	3/13	1	2	FACETS	0.935	0.873	0.999	0.935	0.873	0.999	CLONAL	1	TRUE	1	0.722161268986696	2		450	613	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389318	8389318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	60	437	0	ENST00000356435.5:c.4300G>A	p.Glu1434Lys	p.E1434K	ENST00000356435		1434	Gaa/Aaa	26/35	1	2	FACETS	0.233	0.2	0.269	0.233	0.2	0.269	SUBCLONAL	1	TRUE	1	0.722161268986696	2		437	712	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0037380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	109	458	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.722161268986696	2		458	245	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406233	70406233	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs781235061	NA	P-0037380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	40	403	0	ENST00000373644.4:c.3747A>C	p.Glu1249Asp	p.E1249D	ENST00000373644	NM_030625.2	1249	gaA/gaC	4/12	0.621841388207119	1	FACETS	0.175	0.145	0.208	0.175	0.145	0.208	SUBCLONAL	1	TRUE	0	0.722161268986696	1		403	405	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425665	49425666	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0037380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	174	500	2	ENST00000301067.7:c.12822_12823delinsTT	p.Gln4275Ter	p.Q4275*	ENST00000301067	NM_003482.3	4274	ctCCag/ctTTag	39/54	1	2	FACETS	0.966	0.896	1	0.966	0.896	1	CLONAL	1	TRUE	1	0.722161268986696	2		502	499	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290246	15290247	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0037380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	158	595	1	ENST00000263388.2:c.3388_3389delinsTT	p.Pro1130Phe	p.P1130F	ENST00000263388	NM_000435.2	1130	CCc/TTc	21/33	1	2	FACETS	0.571	0.524	0.62	0.571	0.524	0.62	SUBCLONAL	1	TRUE	1	0.722161268986696	2		596	766	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222832	36222832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	344	672	3	ENST00000222270.7:c.5461C>T	p.Pro1821Ser	p.P1821S	ENST00000222270	NM_014727.1	1821	Cca/Tca	27/37	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.722161268986696	2		675	899	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202176	138202176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763346708	NA	P-0037380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	157	272	0	ENST00000237289.4:c.2093C>T	p.Ser698Leu	p.S698L	ENST00000237289	NM_001270507.1	698	tCg/tTg	9/9	0.722161268986696	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.722161268986696	1		272	269	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971123	21971123	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1554654113	NA	P-0037384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	53	232	0	ENST00000304494.5:c.235A>C	p.Thr79Pro	p.T79P	ENST00000304494	NM_000077.4	79	Acc/Ccc	2/3	0.561435581913804	1	FACETS	0.725	0.63	0.825	0.725	0.63	0.825	SUBCLONAL	1	TRUE	0	0.598890651156447	1		232	171	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577567	7577568	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs1555525539	NA	P-0037384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	351	555	0	ENST00000269305.4:c.713_714del	p.Cys238Ter	p.C238*	ENST00000269305	NM_001126112.2	238	tGT/t	7/11	0.547148186890631	2	FACETS	0.881	0.843	0.92	0.881	0.843	0.92	CLONAL	2	TRUE	0	0.598890651156447	2		555	665	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349356	89349356	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	291	870	0	ENST00000301030.4:c.3594A>T	p.Lys1198Asn	p.K1198N	ENST00000301030	NM_001256183.1	1198	aaA/aaT	9/13	0.582369957763868	2	FACETS	0.865	0.813	0.917	0.432	0.406	0.459	CLONAL	1	TRUE	0	0.598890651156447	2		870	1124	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966665	44966667	+	inframe_deletion	In_Frame_Del	DEL	CTA	CTA	-	novel	NA	P-0037384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	93	294	0	ENST00000377967.4:c.3889_3891del	p.Leu1297del	p.L1297del	ENST00000377967	NM_021140.2	1297	CTA/-	27/29	1	2	FACETS	0.887	0.796	0.983	0.887	0.796	0.983	CLONAL	1	TRUE	1	0.598890651156447	2		294	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0037391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	246	743	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.825336162179731	1	FACETS	0.62	0.584	0.655	0.62	0.584	0.655	SUBCLONAL	1	TRUE	0	0.825336162179731	1		743	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579871	7579872	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0037391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	68	610	0	ENST00000269305.4:c.41dup	p.Ser15GlufsTer14	p.S15Efs*14	ENST00000269305	NM_001126112.2	14	ctg/ctTg	2/11	0.825336162179731	1	FACETS	0.164	0.143	0.188	0.164	0.143	0.188	SUBCLONAL	1	TRUE	0	0.825336162179731	1		610	589	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	65	350	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.254757504179886	0	FACETS	0.642	0.557	0.735			1	SUBCLONAL	1	FALSE	0	0.254757504179886	0		350	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750600586	NA	P-0037400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	46	746	0	ENST00000269305.4:c.413C>T	p.Ala138Val	p.A138V	ENST00000269305	NM_001126112.2	138	gCc/gTc	5/11	0.162767725800364	2	FACETS	0.661	0.557	0.777	0.331	0.278	0.389	SUBCLONAL	1	FALSE	0	0.254757504179886	2		746	546	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	42	347	0	ENST00000304494.5:c.172del	p.Arg58GlufsTer88	p.R58Efs*88	ENST00000304494	NM_000077.4	58	Cga/ga	2/3	0.193816654819345	0	FACETS	0.793	0.665	0.933			1	CLONAL	1	FALSE	0	0.254757504179886	0		347	310	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955109	17955109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140784576	NA	P-0037400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	46	677	2	ENST00000458235.1:c.118C>T	p.Arg40Cys	p.R40C	ENST00000458235	NM_000215.3	40	Cgc/Tgc	2/24	0.162767725800364	2	FACETS	0.813	0.686	0.954	0.407	0.343	0.477	CLONAL	1	FALSE	0	0.254757504179886	2		679	444	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974676	21974676	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0037400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	34	404	0	ENST00000304494.5:c.150+1G>C		p.X50_splice	ENST00000304494	NM_000077.4	50			0.193816654819345	0	FACETS	0.603	0.494	0.725			1	SUBCLONAL	1	FALSE	0	0.254757504179886	0		404	330	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0037401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	90	441	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.866	0.775	0.962	0.866	0.775	0.962	CLONAL	1	TRUE	1	0.582175463274182	2		441	357	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879229	151879229	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763438739	NA	P-0037401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	70	411	0	ENST00000262189.6:c.5716C>T	p.Arg1906Ter	p.R1906*	ENST00000262189	NM_170606.2	1906	Cga/Tga	36/59	1	2	FACETS	0.477	0.417	0.542	0.477	0.417	0.542	SUBCLONAL	1	TRUE	1	0.582175463274182	2		411	504	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111564	8111564	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	C	novel	NA	P-0037401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	133	400	1	ENST00000346208.3:c.1047+3A>C		p.X349_splice	ENST00000346208		349			1	2	FACETS	0.968	0.885	1	0.968	0.885	1	CLONAL	1	TRUE	1	0.582175463274182	2		401	472	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063633	67063633	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	104	244	1	ENST00000412916.2:c.83del	p.Lys28SerfsTer61	p.K28Sfs*61	ENST00000412916		28	Aag/ag	2/6	0.582175463274182	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.582175463274182	1		245	242	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636993	158636993	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	169	456	0	ENST00000263640.3:c.187T>C	p.Phe63Leu	p.F63L	ENST00000263640	NM_001105.4	63	Ttc/Ctc	4/11	1	2	FACETS	0.966	0.893	1	0.966	0.893	1	CLONAL	1	TRUE	1	0.582175463274182	2		456	601	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	14	441	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.194	0.139	0.259	0.194	0.139	0.259	SUBCLONAL	1	TRUE	1	0.521928828937962	2		441	277	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347484	91347484	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	68	443	0	ENST00000355112.3:c.3651del	p.Lys1217AsnfsTer62	p.K1217Nfs*62	ENST00000355112	NM_000057.2	1216	Aaa/aa	19/22	1	2	FACETS	0.454	0.395	0.518	0.454	0.395	0.518	SUBCLONAL	1	TRUE	1	0.521928828937962	2		443	574	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	217	627	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.521928828937962	2		633	637	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	51	350	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	0.451	0.384	0.525			1	INDETERMINATE	1	TRUE	NA	0.521928828937962	2		350	433	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775782	9775782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767750196	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	42	679	0	ENST00000377346.4:c.325G>A	p.Val109Met	p.V109M	ENST00000377346	NM_005026.3	109	Gtg/Atg	4/24	1	2	FACETS	0.261	0.217	0.31	0.261	0.217	0.31	SUBCLONAL	1	TRUE	1	0.521928828937962	2		679	617	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256679	16256679	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	24	469	0	ENST00000375759.3:c.3944G>A	p.Ser1315Asn	p.S1315N	ENST00000375759	NM_015001.2	1315	aGc/aAc	11/15	1	2	FACETS	0.227	0.177	0.284	0.227	0.177	0.284	SUBCLONAL	1	TRUE	1	0.521928828937962	2		469	406	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	86	527	1	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	0.688	0.611	0.77	0.688	0.611	0.77	SUBCLONAL	1	TRUE	1	0.521928828937962	2		528	479	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100833	27100834	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	32	456	0	ENST00000324856.7:c.4117dup	p.Met1373AsnfsTer72	p.M1373Nfs*72	ENST00000324856	NM_006015.4	1372	cca/ccAa	18/20	1	2	FACETS	0.318	0.258	0.386	0.318	0.258	0.386	SUBCLONAL	1	TRUE	1	0.521928828937962	2		456	385	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599234	28599234	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	58	799	0	ENST00000253063.3:c.685del	p.Gln229ArgfsTer18	p.Q229Rfs*18	ENST00000253063	NM_031459.4	227	gCc/gc	5/10	1	2	FACETS	0.314	0.269	0.363	0.314	0.269	0.363	SUBCLONAL	1	TRUE	1	0.521928828937962	2		799	708	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807433	36807433	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	47	713	2	ENST00000373129.3:c.1231C>T	p.Arg411Ter	p.R411*	ENST00000373129	NM_032017.1	411	Cga/Tga	12/12	1	2	FACETS	0.272	0.228	0.319	0.272	0.228	0.319	SUBCLONAL	1	TRUE	1	0.521928828937962	2		715	663	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809504	36809504	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1412240338	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	52	693	0	ENST00000373129.3:c.961G>A	p.Ala321Thr	p.A321T	ENST00000373129	NM_032017.1	321	Gcc/Acc	10/12	1	2	FACETS	0.26	0.221	0.304	0.26	0.221	0.304	SUBCLONAL	1	TRUE	1	0.521928828937962	2		693	765	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724526	162724526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	87	512	0	ENST00000367921.3:c.298G>A	p.Val100Met	p.V100M	ENST00000367921	NM_006182.2	100	Gtg/Atg	5/18	1	2	FACETS	0.668	0.593	0.747	0.668	0.593	0.747	SUBCLONAL	1	TRUE	1	0.521928828937962	2		512	499	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740213	162740213	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	24	415	0	ENST00000367921.3:c.1415A>G	p.Asp472Gly	p.D472G	ENST00000367921	NM_006182.2	472	gAt/gGt	12/18	1	2	FACETS	0.199	0.155	0.25	0.199	0.155	0.25	SUBCLONAL	1	TRUE	1	0.521928828937962	2		415	462	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980293	201980293	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	48	698	1	ENST00000359651.3:c.33del	p.Phe11LeufsTer32	p.F11Lfs*32	ENST00000359651		10	aTt/at	1/8	1	2	FACETS	0.265	0.224	0.312	0.265	0.224	0.312	SUBCLONAL	1	TRUE	1	0.521928828937962	2		699	693	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600556	43600556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	44	712	0	ENST00000355710.3:c.782C>T	p.Thr261Ile	p.T261I	ENST00000355710	NM_020975.4	261	aCc/aTc	4/20	1	2	FACETS	0.246	0.206	0.291	0.246	0.206	0.291	SUBCLONAL	1	TRUE	1	0.521928828937962	2		712	685	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104268987	104268987	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	144	640	1	ENST00000369902.3:c.244G>A	p.Ala82Thr	p.A82T	ENST00000369902	NM_016169.3	82	Gct/Act	2/12	1	2	FACETS	0.784	0.716	0.854	0.784	0.716	0.854	SUBCLONAL	1	TRUE	1	0.521928828937962	2		641	704	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	103	348	10	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.924	0.833	1	0.924	0.833	1	CLONAL	1	TRUE	1	0.521928828937962	2		358	427	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	170	1121	2	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.749	0.689	0.811	0.749	0.689	0.811	SUBCLONAL	1	TRUE	1	0.521928828937962	2		1123	870	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	129	605	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.842	0.766	0.921	0.842	0.766	0.921	CLONAL	1	TRUE	1	0.521928828937962	2		608	587	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	118	726	0	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	1	2	FACETS	0.651	0.588	0.717	0.651	0.588	0.717	SUBCLONAL	1	TRUE	1	0.521928828937962	2		726	695	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	66	255	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	NA	2	FACETS	0.57	0.496	0.649			1	INDETERMINATE	1	TRUE	NA	0.521928828937962	2		255	444	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	47	549	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.111544717949413	3	FACETS	0.399	0.336	0.469	0.2	0.168	0.235	INDETERMINATE	1	TRUE	1	0.521928828937962	3		549	569	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856655	111856655	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1014425313	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	35	318	0	ENST00000341259.2:c.706G>A	p.Val236Met	p.V236M	ENST00000341259	NM_005475.2	236	Gtg/Atg	2/8	0.111544717949413	3	FACETS	0.437	0.358	0.525	0.218	0.179	0.263	INDETERMINATE	1	TRUE	1	0.521928828937962	3		318	387	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115111992	115111992	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	56	533	0	ENST00000257566.3:c.1748A>C	p.Gln583Pro	p.Q583P	ENST00000257566	NM_016569.3	583	cAg/cCg	7/8	0.111544717949413	3	FACETS	0.463	0.397	0.536	0.232	0.198	0.268	INDETERMINATE	1	TRUE	1	0.521928828937962	3		533	584	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	160	423	4	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.521928828937962	2		427	566	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201517	133201517	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	58	666	0	ENST00000320574.5:c.6721G>T	p.Asp2241Tyr	p.D2241Y	ENST00000320574	NM_006231.2	2241	Gac/Tac	48/49	1	2	FACETS	0.321	0.275	0.371	0.321	0.275	0.371	SUBCLONAL	1	TRUE	1	0.521928828937962	2		666	692	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828867	26828867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	49	323	0	ENST00000381527.3:c.89G>A	p.Gly30Asp	p.G30D	ENST00000381527	NM_001260.1	30	gGc/gAc	1/13	0.415173716053573	4	FACETS	0.605	0.513	0.707	0.202	0.171	0.236	SUBCLONAL	1	TRUE	1	0.521928828937962	4		323	472	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881488	48881489	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	224	263	0	ENST00000267163.4:c.219_220dup	p.Ala74GlufsTer4	p.A74Efs*4	ENST00000267163	NM_000321.2	70	-/AG	2/27	0.415173716053573	4	FACETS	0.85	0.8	0.901	0.85	0.8	0.901	CLONAL	3	TRUE	1	0.521928828937962	4		263	512	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951110	48951110	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	27	275	0	ENST00000267163.4:c.1272C>A	p.Tyr424Ter	p.Y424*	ENST00000267163	NM_000321.2	424	taC/taA	13/27	0.415173716053573	4	FACETS	0.383	0.304	0.473	0.128	0.101	0.158	SUBCLONAL	1	TRUE	1	0.521928828937962	4		275	411	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434746	110434746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	50	708	0	ENST00000375856.3:c.3655C>T	p.Pro1219Ser	p.P1219S	ENST00000375856	NM_003749.2	1219	Ccg/Tcg	1/2	0.415173716053573	4	FACETS	0.324	0.274	0.38	0.108	0.091	0.127	SUBCLONAL	1	TRUE	1	0.521928828937962	4		708	900	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986896	36986896	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	79	437	0	ENST00000354822.5:c.793G>T	p.Gly265Cys	p.G265C	ENST00000354822	NM_001079668.2	265	Ggc/Tgc	3/3	1	2	FACETS	0.66	0.582	0.742	0.66	0.582	0.742	SUBCLONAL	1	TRUE	1	0.521928828937962	2		437	459	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614463	38614463	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	29	432	0	ENST00000299084.4:c.234del	p.Asp79ThrfsTer42	p.D79Tfs*42	ENST00000299084	NM_152594.2	77	Aaa/aa	3/7	1	2	FACETS	0.241	0.193	0.296	0.241	0.193	0.296	SUBCLONAL	1	TRUE	1	0.521928828937962	2		432	461	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43730536	43730536	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	81	441	0	ENST00000382044.4:c.3177del	p.Thr1060ProfsTer36	p.T1060Pfs*36	ENST00000382044	NM_001141980.1	1059	ccC/cc	16/28	1	2	FACETS	0.643	0.568	0.722	0.643	0.568	0.722	SUBCLONAL	1	TRUE	1	0.521928828937962	2		441	483	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99451928	99451928	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	66	282	0	ENST00000268035.6:c.1262A>G	p.Tyr421Cys	p.Y421C	ENST00000268035	NM_000875.3	421	tAc/tGc	6/21	1	2	FACETS	0.757	0.662	0.859	0.757	0.662	0.859	SUBCLONAL	1	TRUE	1	0.521928828937962	2		282	334	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639789	3639789	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373107728	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	43	805	0	ENST00000294008.3:c.3850G>A	p.Val1284Met	p.V1284M	ENST00000294008	NM_032444.2	1284	Gtg/Atg	12/15	1	2	FACETS	0.228	0.19	0.271	0.228	0.19	0.271	SUBCLONAL	1	TRUE	1	0.521928828937962	2		805	722	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641093	3641093	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	67	1079	0	ENST00000294008.3:c.2546C>T	p.Ala849Val	p.A849V	ENST00000294008	NM_032444.2	849	gCa/gTa	12/15	1	2	FACETS	0.226	0.196	0.26	0.226	0.196	0.26	SUBCLONAL	1	TRUE	1	0.521928828937962	2		1079	1134	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647657	3647657	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs774532876	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	48	792	1	ENST00000294008.3:c.1406del	p.Pro469HisfsTer4	p.P469Hfs*4	ENST00000294008	NM_032444.2	469	cCa/ca	7/15	1	2	FACETS	0.21	0.177	0.247	0.21	0.177	0.247	SUBCLONAL	1	TRUE	1	0.521928828937962	2		793	875	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779057	3779057	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	53	549	0	ENST00000262367.5:c.5991del	p.Val1998Ter	p.V1998*	ENST00000262367	NM_004380.2	1997	ccC/cc	31/31	1	2	FACETS	0.433	0.37	0.502	0.433	0.37	0.502	SUBCLONAL	1	TRUE	1	0.521928828937962	2		549	469	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779211	3779211	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783507	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	50	449	0	ENST00000262367.5:c.5837del	p.Pro1946HisfsTer30	p.P1946Hfs*30	ENST00000262367	NM_004380.2	1946	cCa/ca	31/31	1	2	FACETS	0.603	0.514	0.699	0.603	0.514	0.699	SUBCLONAL	1	TRUE	1	0.521928828937962	2		449	318	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842405	68842405	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	51	518	0	ENST00000261769.5:c.466T>C	p.Trp156Arg	p.W156R	ENST00000261769	NM_004360.3	156	Tgg/Cgg	4/16	1	2	FACETS	0.364	0.309	0.424	0.364	0.309	0.424	SUBCLONAL	1	TRUE	1	0.521928828937962	2		518	537	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	19	335	4	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.27	0.205	0.346	0.27	0.205	0.346	SUBCLONAL	1	TRUE	1	0.521928828937962	2		339	270	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827213	72827213	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	36	492	0	ENST00000268489.5:c.9368C>A	p.Pro3123His	p.P3123H	ENST00000268489	NM_006885.3	3123	cCt/cAt	9/10	1	2	FACETS	0.327	0.269	0.392	0.327	0.269	0.392	SUBCLONAL	1	TRUE	1	0.521928828937962	2		492	422	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827414	72827414	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs374608671	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	54	755	0	ENST00000268489.5:c.9167T>C	p.Ile3056Thr	p.I3056T	ENST00000268489	NM_006885.3	3056	aTt/aCt	9/10	1	2	FACETS	0.28	0.238	0.326	0.28	0.238	0.326	SUBCLONAL	1	TRUE	1	0.521928828937962	2		755	739	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953271	81953271	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	20	231	0	ENST00000359376.3:c.2235+2T>C		p.X745_splice	ENST00000359376	NM_002661.3	745			1	2	FACETS	0.268	0.205	0.342	0.268	0.205	0.342	SUBCLONAL	1	TRUE	1	0.521928828937962	2		231	286	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845372	89845372	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	42	581	0	ENST00000389301.3:c.1755del	p.Ala586ProfsTer19	p.A586Pfs*19	ENST00000389301	NM_000135.2	585	ccC/cc	19/43	1	2	FACETS	0.235	0.195	0.279	0.235	0.195	0.279	SUBCLONAL	1	TRUE	1	0.521928828937962	2		581	686	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	33	714	0	ENST00000269305.4:c.569del	p.Pro190LeufsTer57	p.P190Lfs*57	ENST00000269305	NM_001126112.2	190	cCt/ct	6/11	1	2	FACETS	0.237	0.193	0.288	0.237	0.193	0.288	SUBCLONAL	1	TRUE	1	0.521928828937962	2		714	533	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950396	15950396	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201721277	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	73	509	0	ENST00000268712.3:c.6548G>A	p.Arg2183His	p.R2183H	ENST00000268712	NM_006311.3	2183	cGc/cAc	42/46	1	2	FACETS	0.696	0.611	0.786	0.696	0.611	0.786	SUBCLONAL	1	TRUE	1	0.521928828937962	2		509	402	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995345	15995345	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs367874483	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	21	419	0	ENST00000268712.3:c.2848A>G	p.Ile950Val	p.I950V	ENST00000268712	NM_006311.3	950	Att/Gtt	22/46	1	2	FACETS	0.195	0.15	0.249	0.195	0.15	0.249	SUBCLONAL	1	TRUE	1	0.521928828937962	2		419	412	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	72	685	5	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.724	0.636	0.818	0.724	0.636	0.818	SUBCLONAL	1	TRUE	1	0.521928828937962	2		690	381	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17129540	17129540	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	145	710	1	ENST00000285071.4:c.346del	p.Gln116SerfsTer14	p.Q116Sfs*14	ENST00000285071	NM_144997.5	116	Cag/ag	5/14	1	2	FACETS	0.756	0.691	0.824	0.756	0.691	0.824	SUBCLONAL	1	TRUE	1	0.521928828937962	2		711	735	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40476850	40476850	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	39	483	1	ENST00000264657.5:c.1479del	p.Phe493LeufsTer16	p.F493Lfs*16	ENST00000264657	NM_139276.2	493	ttT/tt	17/24	0.521928828937962	2	FACETS	0.3	0.248	0.358	0.15	0.124	0.179	SUBCLONAL	1	TRUE	0	0.521928828937962	2		484	498	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63537572	63537572	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	267	398	0	ENST00000307078.5:c.1059+1G>A		p.X353_splice	ENST00000307078	NM_004655.3	353			0.521928828937962	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.521928828937962	2		398	493	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119910	70119910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1297203260	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	184	452	0	ENST00000245479.2:c.916del	p.Val306CysfsTer77	p.V306Cfs*77	ENST00000245479	NM_000346.3	304	ccG/cc	3/3	0.521928828937962	2	FACETS	1	0.991	1	0.736	0.686	0.787	CLONAL	1	TRUE	0	0.521928828937962	2		452	479	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619172	1619172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374199541	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	89	776	0	ENST00000344749.5:c.1388C>T	p.Ala463Val	p.A463V	ENST00000344749	NM_001136139.2	463	gCg/gTg	16/19	1	2	FACETS	0.421	0.373	0.473	0.421	0.373	0.473	SUBCLONAL	1	TRUE	1	0.521928828937962	2		776	810	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2193700	2193700	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	38	621	1	ENST00000398665.3:c.506T>C	p.Val169Ala	p.V169A	ENST00000398665	NM_032482.2	169	gTc/gCc	6/28	1	2	FACETS	0.215	0.177	0.257	0.215	0.177	0.257	SUBCLONAL	1	TRUE	1	0.521928828937962	2		622	678	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222730	5222731	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs756013055	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	52	512	3	ENST00000357368.4:c.3072dup	p.Val1025ArgfsTer34	p.V1025Rfs*34	ENST00000357368	NM_002850.3	1024	-/C	18/38	1	2	FACETS	0.406	0.346	0.472	0.406	0.346	0.472	SUBCLONAL	1	TRUE	1	0.521928828937962	2		515	491	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296322	15296322	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772994625	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	117	698	2	ENST00000263388.2:c.2120G>A	p.Gly707Asp	p.G707D	ENST00000263388	NM_000435.2	707	gGc/gAc	13/33	1	2	FACETS	0.781	0.707	0.859	0.781	0.707	0.859	SUBCLONAL	1	TRUE	1	0.521928828937962	2		700	574	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296373	15296373	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1381914938	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	41	832	0	ENST00000263388.2:c.2069C>A	p.Pro690Gln	p.P690Q	ENST00000263388	NM_000435.2	690	cCa/cAa	13/33	1	2	FACETS	0.244	0.202	0.29	0.244	0.202	0.29	SUBCLONAL	1	TRUE	1	0.521928828937962	2		832	644	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18958551	18958551	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	48	519	1	ENST00000262803.5:c.372-2A>G		p.X124_splice	ENST00000262803	NM_002911.3	124			1	2	FACETS	0.263	0.221	0.309	0.263	0.221	0.309	SUBCLONAL	1	TRUE	1	0.521928828937962	2		520	700	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967091	18967092	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1384543747	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	37	676	0	ENST00000262803.5:c.1814_1815del	p.Glu605AlafsTer17	p.E605Afs*17	ENST00000262803	NM_002911.3	602	gcAGag/gcag	13/24	1	2	FACETS	0.208	0.171	0.25	0.208	0.171	0.25	SUBCLONAL	1	TRUE	1	0.521928828937962	2		676	681	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	113	727	4	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.621	0.559	0.686	0.621	0.559	0.686	SUBCLONAL	1	TRUE	1	0.521928828937962	2		731	697	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211288	36211288	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	55	865	0	ENST00000222270.7:c.1039G>A	p.Gly347Arg	p.G347R	ENST00000222270	NM_014727.1	347	Gga/Aga	3/37	1	2	FACETS	0.217	0.184	0.252	0.217	0.184	0.252	SUBCLONAL	1	TRUE	1	0.521928828937962	2		865	973	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752804	42752804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1286494808	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	155	760	0	ENST00000222329.4:c.1460G>A	p.Arg487His	p.R487H	ENST00000222329	NM_006494.2	487	cGc/cAc	4/4	1	2	FACETS	0.861	0.79	0.934	0.861	0.79	0.934	CLONAL	1	TRUE	1	0.521928828937962	2		760	690	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753594	42753594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1320701373	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	31	620	2	ENST00000222329.4:c.670C>T	p.Arg224Cys	p.R224C	ENST00000222329	NM_006494.2	224	Cgc/Tgc	4/4	1	2	FACETS	0.238	0.192	0.29	0.238	0.192	0.29	SUBCLONAL	1	TRUE	1	0.521928828937962	2		622	500	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791355	42791355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	29	604	1	ENST00000575354.2:c.415C>T	p.Arg139Trp	p.R139W	ENST00000575354	NM_015125.3	139	Cgg/Tgg	3/20	1	2	FACETS	0.208	0.166	0.255	0.208	0.166	0.255	SUBCLONAL	1	TRUE	1	0.521928828937962	2		605	535	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965688	25965689	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	138	695	0	ENST00000435504.4:c.3517_3518del	p.Ser1173Ter	p.S1173*	ENST00000435504		1173	AGt/t	13/13	1	2	FACETS	0.614	0.559	0.672	0.614	0.559	0.672	SUBCLONAL	1	TRUE	1	0.521928828937962	2		695	861	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222519	39222520	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	30	502	0	ENST00000402219.2:c.3090dup	p.Tyr1031IlefsTer2	p.Y1031Ifs*2	ENST00000402219	NM_005633.3	1030	-/A	20/23	1	2	FACETS	0.212	0.17	0.26	0.212	0.17	0.26	SUBCLONAL	1	TRUE	1	0.521928828937962	2		502	541	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010482	48010482	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1558644995	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	73	456	0	ENST00000234420.5:c.114del	p.Ala40ProfsTer41	p.A40Pfs*41	ENST00000234420	NM_000179.2	37	gCc/gc	1/10	1	2	FACETS	0.75	0.66	0.846	0.75	0.66	0.846	SUBCLONAL	1	TRUE	1	0.521928828937962	2		456	373	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	57	486	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.378	0.324	0.437	0.378	0.324	0.437	SUBCLONAL	1	TRUE	1	0.521928828937962	2		488	578	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170887	99170887	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	102	601	0	ENST00000074304.5:c.1516A>G	p.Met506Val	p.M506V	ENST00000074304	NM_001134224.1	506	Atg/Gtg	16/26	1	2	FACETS	0.693	0.621	0.769	0.693	0.621	0.769	SUBCLONAL	1	TRUE	1	0.521928828937962	2		601	564	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99181152	99181152	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1303725216	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	47	586	0	ENST00000074304.5:c.2093A>G	p.His698Arg	p.H698R	ENST00000074304	NM_001134224.1	698	cAt/cGt	20/26	1	2	FACETS	0.273	0.23	0.321	0.273	0.23	0.321	SUBCLONAL	1	TRUE	1	0.521928828937962	2		586	660	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149596	202149596	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	100	488	0	ENST00000358485.4:c.1037G>A	p.Cys346Tyr	p.C346Y	ENST00000358485	NM_001080125.1	346	tGc/tAc	8/9	1	2	FACETS	0.81	0.727	0.897	0.81	0.727	0.897	CLONAL	1	TRUE	1	0.521928828937962	2		488	473	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439511	220439511	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs577636996	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	29	589	0	ENST00000243786.2:c.364C>T	p.Arg122Cys	p.R122C	ENST00000243786	NM_002191.3	122	Cgc/Tgc	2/2	1	2	FACETS	0.219	0.175	0.269	0.219	0.175	0.269	SUBCLONAL	1	TRUE	1	0.521928828937962	2		589	508	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793363	242793363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	44	803	0	ENST00000334409.5:c.714del	p.Val239CysfsTer39	p.V239Cfs*39	ENST00000334409	NM_005018.2	238	ccC/cc	5/5	1	2	FACETS	0.263	0.22	0.311	0.263	0.22	0.311	SUBCLONAL	1	TRUE	1	0.521928828937962	2		803	641	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206777	36206777	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	44	492	0	ENST00000300305.3:c.735del	p.Thr246ArgfsTer8	p.T246Rfs*8	ENST00000300305		245	ccC/cc	6/8	1	2	FACETS	0.311	0.26	0.367	0.311	0.26	0.367	SUBCLONAL	1	TRUE	1	0.521928828937962	2		492	543	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656840	45656840	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	38	513	1	ENST00000407780.3:c.316del	p.Gln106ArgfsTer11	p.Q106Rfs*11	ENST00000407780	NM_001283052.1	106	Cag/ag	3/7	1	2	FACETS	0.263	0.217	0.315	0.263	0.217	0.315	SUBCLONAL	1	TRUE	1	0.521928828937962	2		514	553	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573680	41573680	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	48	588	1	ENST00000263253.7:c.5965A>G	p.Met1989Val	p.M1989V	ENST00000263253	NM_001429.3	1989	Atg/Gtg	31/31	1	2	FACETS	0.327	0.276	0.383	0.327	0.276	0.383	SUBCLONAL	1	TRUE	1	0.521928828937962	2		589	563	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574470	41574470	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	108	624	0	ENST00000263253.7:c.6755A>T	p.Glu2252Val	p.E2252V	ENST00000263253	NM_001429.3	2252	gAg/gTg	31/31	1	2	FACETS	0.93	0.84	1	0.93	0.84	1	CLONAL	1	TRUE	1	0.521928828937962	2		624	445	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475455	12475455	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	132	564	0	ENST00000287820.6:c.1329A>C	p.Gln443His	p.Q443H	ENST00000287820	NM_015869.4	443	caA/caC	7/7	0.48833990651307	2	FACETS	0.771	0.702	0.844	0.386	0.351	0.422	SUBCLONAL	1	TRUE	0	0.521928828937962	2		564	656	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732957	30732957	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504421	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	30	256	0	ENST00000295754.5:c.1570G>A	p.Asp524Asn	p.D524N	ENST00000295754	NM_003242.5	524	Gac/Aac	7/7	0.48833990651307	2	FACETS	0.322	0.259	0.393	0.161	0.129	0.197	SUBCLONAL	1	TRUE	0	0.521928828937962	2		256	357	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084146	47084146	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	30	468	0	ENST00000409792.3:c.7143del	p.Ser2382LeufsTer29	p.S2382Lfs*29	ENST00000409792	NM_014159.6	2381	ccC/cc	17/21	0.48833990651307	2	FACETS	0.24	0.193	0.294	0.12	0.096	0.147	SUBCLONAL	1	TRUE	0	0.521928828937962	2		468	479	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161907	47161907	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	27	444	3	ENST00000409792.3:c.4219del	p.Arg1407GlyfsTer5	p.R1407Gfs*5	ENST00000409792	NM_014159.6	1407	Agg/gg	3/21	0.48833990651307	2	FACETS	0.2	0.159	0.248	0.1	0.079	0.124	SUBCLONAL	1	TRUE	0	0.521928828937962	2		447	517	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936002	49936004	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	45	682	0	ENST00000296474.3:c.1666_1668del	p.Lys556del	p.K556del	ENST00000296474	NM_002447.2	556	AAG/-	4/20	1	2	FACETS	0.261	0.218	0.308	0.261	0.218	0.308	SUBCLONAL	1	TRUE	1	0.521928828937962	2		682	661	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443613	52443613	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	104	458	0	ENST00000460680.1:c.79del	p.Val27CysfsTer45	p.V27Cfs*45	ENST00000460680	NM_004656.3	27	Gtg/tg	3/17	1	2	FACETS	0.829	0.745	0.916	0.829	0.745	0.916	CLONAL	1	TRUE	1	0.521928828937962	2		458	481	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021818	71021818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869025203	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	44	219	0	ENST00000318789.4:c.1540C>T	p.Arg514Cys	p.R514C	ENST00000318789	NM_032682.5	514	Cgt/Tgt	18/21	1	2	FACETS	0.721	0.61	0.841	0.721	0.61	0.841	SUBCLONAL	1	TRUE	1	0.521928828937962	2		219	234	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428542	72428544	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs768490904	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	61	417	0	ENST00000477973.2:c.458_460del	p.Gln154del	p.Q154del	ENST00000477973	NM_012234.5	154	CAA/-	2/4	1	2	FACETS	0.653	0.566	0.746	0.653	0.566	0.746	SUBCLONAL	1	TRUE	1	0.521928828937962	2		417	358	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204873	128204873	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	36	800	1	ENST00000341105.2:c.568del	p.Ala190LeufsTer28	p.A190Lfs*28	ENST00000341105	NM_032638.4	190	Gct/ct	3/6	1	2	FACETS	0.219	0.179	0.264	0.219	0.179	0.264	SUBCLONAL	1	TRUE	1	0.521928828937962	2		801	630	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916644	178916644	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	38	311	0	ENST00000263967.3:c.31T>C	p.Trp11Arg	p.W11R	ENST00000263967	NM_006218.2	11	Tgg/Cgg	2/21	1	2	FACETS	0.703	0.587	0.831	0.703	0.587	0.831	SUBCLONAL	1	TRUE	1	0.521928828937962	2		311	207	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916875	178916875	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	25	536	0	ENST00000263967.3:c.262C>T	p.Arg88Ter	p.R88*	ENST00000263967	NM_006218.2	88	Cga/Tga	2/21	1	2	FACETS	0.159	0.124	0.198	0.159	0.124	0.198	SUBCLONAL	1	TRUE	1	0.521928828937962	2		536	604	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928039	178928039	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	25	434	0	ENST00000263967.3:c.1321del	p.Met441TrpfsTer3	p.M441Wfs*3	ENST00000263967	NM_006218.2	439	ggA/gg	8/21	1	2	FACETS	0.203	0.16	0.254	0.203	0.16	0.254	SUBCLONAL	1	TRUE	1	0.521928828937962	2		434	471	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430629	181430629	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	28	530	0	ENST00000325404.1:c.481G>A	p.Ala161Thr	p.A161T	ENST00000325404	NM_003106.3	161	Gcg/Acg	1/1	1	2	FACETS	0.258	0.206	0.318	0.258	0.206	0.318	SUBCLONAL	1	TRUE	1	0.521928828937962	2		530	416	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535360	66535360	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	57	583	1	ENST00000273854.3:c.101C>T	p.Ala34Val	p.A34V	ENST00000273854	NM_004439.5	34	gCa/gTa	1/18	1	2	FACETS	0.387	0.332	0.448	0.387	0.332	0.448	SUBCLONAL	1	TRUE	1	0.521928828937962	2		584	564	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143324184	143324185	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	42	237	0	ENST00000262992.4:c.278dup	p.Leu93PhefsTer9	p.L93Ffs*9	ENST00000262992	NM_001101669.1	93	ttg/ttTg	5/24	1	2	FACETS	0.587	0.493	0.69	0.587	0.493	0.69	SUBCLONAL	1	TRUE	1	0.521928828937962	2		237	274	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519145	187519145	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	26	355	0	ENST00000441802.2:c.12238G>T	p.Gly4080Ter	p.G4080*	ENST00000441802	NM_005245.3	4080	Gga/Tga	23/27	1	2	FACETS	0.231	0.183	0.287	0.231	0.183	0.287	SUBCLONAL	1	TRUE	1	0.521928828937962	2		355	431	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293851	1293851	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	61	960	0	ENST00000310581.5:c.1150del	p.Gln384SerfsTer125	p.Q384Sfs*125	ENST00000310581	NM_198253.2	384	Cag/ag	2/16	1	2	FACETS	0.275	0.236	0.317	0.275	0.236	0.317	SUBCLONAL	1	TRUE	1	0.521928828937962	2		960	851	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515149	31515149	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	134	774	1	ENST00000344624.3:c.1236G>A	p.Trp412Ter	p.W412*	ENST00000344624		412	tgG/tgA	5/33	1	2	FACETS	0.608	0.553	0.667	0.608	0.553	0.667	SUBCLONAL	1	TRUE	1	0.521928828937962	2		775	844	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38949958	38949958	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	22	378	0	ENST00000357387.3:c.3992C>T	p.Ala1331Val	p.A1331V	ENST00000357387	NM_152756.3	1331	gCt/gTt	31/38	1	2	FACETS	0.282	0.218	0.356	0.282	0.218	0.356	SUBCLONAL	1	TRUE	1	0.521928828937962	2		378	299	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38954947	38954947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771642192	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	22	288	0	ENST00000357387.3:c.2626G>A	p.Val876Ile	p.V876I	ENST00000357387	NM_152756.3	876	Gtc/Atc	27/38	1	2	FACETS	0.353	0.274	0.444	0.353	0.274	0.444	SUBCLONAL	1	TRUE	1	0.521928828937962	2		288	239	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	80	409	4	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.937	0.833	1	0.937	0.833	1	CLONAL	1	TRUE	1	0.521928828937962	2		413	327	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645084	86645084	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	57	335	0	ENST00000274376.6:c.1156T>C	p.Tyr386His	p.Y386H	ENST00000274376	NM_002890.2	386	Tat/Cat	8/25	1	2	FACETS	0.635	0.547	0.729	0.635	0.547	0.729	SUBCLONAL	1	TRUE	1	0.521928828937962	2		335	344	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562876	176562876	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1268581071	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	121	411	0	ENST00000439151.2:c.772T>C	p.Phe258Leu	p.F258L	ENST00000439151	NM_022455.4	258	Ttt/Ctt	2/23	1	2	FACETS	0.818	0.741	0.898	0.818	0.741	0.898	CLONAL	1	TRUE	1	0.521928828937962	2		411	567	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030307	180030308	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs772530628	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	111	734	0	ENST00000261937.6:c.3976dup	p.Ala1326GlyfsTer118	p.A1326Gfs*118	ENST00000261937	NM_182925.4	1326	gcc/gGcc	30/30	1	2	FACETS	0.61	0.549	0.675	0.61	0.549	0.675	SUBCLONAL	1	TRUE	1	0.521928828937962	2		734	697	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	121	620	8	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	1	2	FACETS	0.716	0.648	0.787	0.716	0.648	0.787	SUBCLONAL	1	TRUE	1	0.521928828937962	2		628	648	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322267	31322267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1478537435	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	12	225	0	ENST00000412585.2:c.1082C>T	p.Thr361Ile	p.T361I	ENST00000412585	NM_005514.6	361	aCa/aTa	7/8	1	2	FACETS	0.251	0.177	0.343	0.251	0.177	0.343	SUBCLONAL	1	TRUE	1	0.521928828937962	2		225	183	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168664	32168664	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	57	541	0	ENST00000375023.3:c.4259C>T	p.Ala1420Val	p.A1420V	ENST00000375023	NM_004557.3	1420	gCc/gTc	23/30	1	2	FACETS	0.404	0.347	0.467	0.404	0.347	0.467	SUBCLONAL	1	TRUE	1	0.521928828937962	2		541	540	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553296	106553296	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	72	412	0	ENST00000369096.4:c.1261A>G	p.Asn421Asp	p.N421D	ENST00000369096	NM_001198.3	421	Aat/Gat	5/7	1	2	FACETS	0.59	0.516	0.668	0.59	0.516	0.668	SUBCLONAL	1	TRUE	1	0.521928828937962	2		412	468	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229234	55229234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	41	337	0	ENST00000275493.2:c.1541G>A	p.Gly514Asp	p.G514D	ENST00000275493	NM_005228.3	514	gGc/gAc	13/28	1	2	FACETS	0.417	0.348	0.493	0.417	0.348	0.493	SUBCLONAL	1	TRUE	1	0.521928828937962	2		337	377	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508508	106508508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	15	218	0	ENST00000359195.3:c.502G>A	p.Val168Met	p.V168M	ENST00000359195	NM_002649.2	168	Gtg/Atg	2/11	1	2	FACETS	0.327	0.239	0.43	0.327	0.239	0.43	SUBCLONAL	1	TRUE	1	0.521928828937962	2		218	176	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285495	38285495	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223331	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	148	657	0	ENST00000425967.3:c.658C>T	p.Arg220Cys	p.R220C	ENST00000425967	NM_001174067.1	220	Cgc/Tgc	6/19	1	2	FACETS	0.691	0.631	0.753	0.691	0.631	0.753	SUBCLONAL	1	TRUE	1	0.521928828937962	2		657	821	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739881	145739881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764297840	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	134	700	0	ENST00000428558.2:c.1649C>T	p.Ala550Val	p.A550V	ENST00000428558	NM_004260.3	550	gCg/gTg	10/22	1	2	FACETS	0.747	0.68	0.818	0.747	0.68	0.818	SUBCLONAL	1	TRUE	1	0.521928828937962	2		700	687	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738279	133738279	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	23	469	0	ENST00000318560.5:c.679G>T	p.Gly227Cys	p.G227C	ENST00000318560	NM_005157.4	227	Ggt/Tgt	4/11	1	2	FACETS	0.194	0.15	0.244	0.194	0.15	0.244	SUBCLONAL	1	TRUE	1	0.521928828937962	2		469	455	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771719	135771720	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	122	624	0	ENST00000298552.3:c.3397dup	p.Leu1133ProfsTer26	p.L1133Pfs*26	ENST00000298552	NM_001162426.1	1133	ctg/cCtg	23/23	1	2	FACETS	0.684	0.62	0.753	0.684	0.62	0.753	SUBCLONAL	1	TRUE	1	0.521928828937962	2		624	683	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933593	39933594	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	76	490	1	ENST00000378444.4:c.1005dup	p.Ser336LeufsTer45	p.S336Lfs*45	ENST00000378444	NM_001123385.1	335	-/C	4/15	1	2	FACETS	0.698	0.615	0.787	0.698	0.615	0.787	SUBCLONAL	1	TRUE	1	0.521928828937962	2		491	417	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411518	63411518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	35	799	0	ENST00000330258.3:c.1649C>T	p.Pro550Leu	p.P550L	ENST00000330258	NM_152424.3	550	cCa/cTa	2/2	1	2	FACETS	0.201	0.164	0.243	0.201	0.164	0.243	SUBCLONAL	1	TRUE	1	0.521928828937962	2		799	667	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339230	70339230	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	109	479	0	ENST00000374080.3:c.107T>C	p.Leu36Pro	p.L36P	ENST00000374080		36	cTg/cCg	2/45	1	2	FACETS	0.847	0.764	0.934	0.847	0.764	0.934	CLONAL	1	TRUE	1	0.521928828937962	2		479	493	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444808	49444809	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	38	731	0	ENST00000301067.7:c.2657dup	p.Gly887TrpfsTer16	p.G887Wfs*16	ENST00000301067	NM_003482.3	886	cct/ccCt	10/54	0.111544717949413	3	FACETS	0.278	0.229	0.333	0.139	0.114	0.167	INDETERMINATE	1	TRUE	1	0.521928828937962	3		731	660	SUCCESS
AR	367	MSKCC	GRCh37	X	66766424	66766424	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	13	186	0	ENST00000374690.3:c.1440del	p.Tyr481ThrfsTer29	p.Y481Tfs*29	ENST00000374690	NM_000044.3	479	gCc/gc	1/8	1	2	FACETS	0.344	0.246	0.461	0.344	0.246	0.461	SUBCLONAL	1	TRUE	1	0.521928828937962	2		186	145	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0037424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	88	414	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.297880851918732	3	FACETS	1	0.957	1	0.723	0.659	0.787	INDETERMINATE	2	TRUE	0	0.617558190503882	3		414	172	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933367	39933367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754579483	NA	P-0037424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	11	622	1	ENST00000378444.4:c.1232G>A	p.Arg411Gln	p.R411Q	ENST00000378444	NM_001123385.1	411	cGg/cAg	4/15	0.617558190503882	1	FACETS	0.123	0.085	0.171	0.123	0.085	0.171	SUBCLONAL	1	TRUE	0	0.617558190503882	1		623	200	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841488	156841488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1023556915	NA	P-0037424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	14	608	1	ENST00000524377.1:c.791C>T	p.Thr264Met	p.T264M	ENST00000524377	NM_002529.3	264	aCg/aTg	7/17	0.246942131551725	4	FACETS	0.175	0.126	0.236	0.058	0.042	0.079	INDETERMINATE	1	TRUE	1	0.617558190503882	4		609	418	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533581	63533582	+	missense_variant	Missense_Mutation	DNP	GG	GG	AC	novel	NA	P-0037424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	55	686	1	ENST00000307078.5:c.1572_1573delinsGT	p.Pro525Ser	p.P525S	ENST00000307078	NM_004655.3	524	gtCCcc/gtGTcc	6/11	0.520122886820371	2	FACETS	0.869	0.754	0.991	0.434	0.377	0.496	CLONAL	1	TRUE	0	0.617558190503882	2		687	205	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0037458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	85	557	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.479123348543716	2		557	288	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138407755	138407755	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	78	372	0	ENST00000289153.2:c.2098C>G	p.Arg700Gly	p.R700G	ENST00000289153	NM_006219.2	700	Cgg/Ggg	14/22	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.479123348543716	2		372	298	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783216	9783216	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121480-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	138	535	0	ENST00000377346.4:c.2460C>A	p.Asp820Glu	p.D820E	ENST00000377346	NM_005026.3	820	gaC/gaA	20/24	0.618585831846105	3	FACETS	0.937	0.855	1	0.468	0.427	0.511	CLONAL	1	NA	1	0.629847492341511	3		535	615	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417167	417167	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121480-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	47	157	0	ENST00000399788.2:c.3383C>A	p.Ala1128Glu	p.A1128E	ENST00000399788	NM_001042603.1	1128	gCa/gAa	23/28	0.562259833262816	5	FACETS	0.971	0.824	1	0.324	0.274	0.377	CLONAL	1	NA	2	0.629847492341511	5		157	299	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871133	12871134	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0121480-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	49	267	0	ENST00000228872.4:c.361_362dup	p.Pro122LeufsTer24	p.P122Lfs*24	ENST00000228872	NM_004064.3	120	-/GC	1/3	0.562259833262816	5	FACETS	0.77	0.654	0.897	0.257	0.218	0.299	SUBCLONAL	1	NA	2	0.629847492341511	5		267	393	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432516	49432516	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121480-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	131	581	0	ENST00000301067.7:c.8623G>T	p.Ala2875Ser	p.A2875S	ENST00000301067	NM_003482.3	2875	Gcc/Tcc	34/54	0.562259833262816	5	FACETS	0.955	0.867	1	0.318	0.289	0.35	CLONAL	1	NA	2	0.629847492341511	5		581	847	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435156	49435156	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121480-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	83	536	0	ENST00000301067.7:c.6397G>T	p.Ala2133Ser	p.A2133S	ENST00000301067	NM_003482.3	2133	Gcc/Tcc	31/54	0.562259833262816	5	FACETS	0.715	0.631	0.805	0.238	0.21	0.269	SUBCLONAL	1	NA	2	0.629847492341511	5		536	717	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772478	56772478	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0121480-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	116	342	0	ENST00000337432.4:c.332T>C	p.Leu111Pro	p.L111P	ENST00000337432	NM_058216.2	111	cTt/cCt	2/9	0.539196319597586	5	FACETS	0.976	0.88	1	0.325	0.293	0.359	CLONAL	1	NA	2	0.629847492341511	5		342	734	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796972	78796973	+	missense_variant	Missense_Mutation	DNP	GC	GC	CT	novel	NA	P-0121480-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	141	395	1	ENST00000306801.3:c.1085_1086delinsCT	p.Cys362Ser	p.C362S	ENST00000306801	NM_020761.2	362	tGC/tCT	9/34	0.539196319597586	5	FACETS	1	0.944	1	0.35	0.318	0.383	CLONAL	1	NA	2	0.629847492341511	5		396	830	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636934	158636934	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121480-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	121	388	0	ENST00000263640.3:c.246G>T	p.Lys82Asn	p.K82N	ENST00000263640	NM_001105.4	82	aaG/aaT	4/11	0.53932783001156	3	FACETS	1	0.935	1	0.518	0.47	0.567	CLONAL	1	NA	1	0.629847492341511	3		388	488	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326263	62326263	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121480-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	223	846	0	ENST00000360203.5:c.3279C>A	p.Asp1093Glu	p.D1093E	ENST00000360203	NM_001283009.1	1093	gaC/gaA	32/35	0.61346544734529	4	FACETS	1	0.941	1	0.337	0.314	0.362	CLONAL	1	NA	1	0.629847492341511	4		846	1140	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117717425	117717425	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0121480-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	73	236	0	ENST00000368508.3:c.782T>A	p.Phe261Tyr	p.F261Y	ENST00000368508	NM_002944.2	261	tTt/tAt	8/43	0.629847492341511	3	FACETS	1	0.95	1	0.569	0.503	0.638	CLONAL	1	NA	1	0.629847492341511	3		236	268	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468213	50468213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0121480-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	275	591	1	ENST00000331340.3:c.1448G>A	p.Cys483Tyr	p.C483Y	ENST00000331340	NM_006060.4	483	tGc/tAc	8/8	0.489066034320851	4	FACETS	0.91	0.858	0.963	0.91	0.858	0.963	CLONAL	2	NA	2	0.629847492341511	4		592	782	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58725318	58725318	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121480-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	88	317	0	ENST00000305921.3:c.892G>T	p.Val298Phe	p.V298F	ENST00000305921	NM_003620.3	298	Gtc/Ttc	4/6	0.539196319597586	5	FACETS	0.852	0.755	0.955	0.284	0.251	0.319	CLONAL	1	NA	2	0.629847492341511	5		317	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0037473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	982	670	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.936561663400602	2	FACETS	0.999	0.988	1	0.999	0.988	1	CLONAL	2	TRUE	0	0.936561663400602	2		670	1050	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0037473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	123	100	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	0.936561663400602	3	FACETS	0.984	0.919	1	0.984	0.919	1	CLONAL	2	TRUE	1	0.936561663400602	3		100	196	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648217	206648217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149591181	NA	P-0037473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	331	452	0	ENST00000367120.3:c.238C>T	p.Arg80Trp	p.R80W	ENST00000367120	NM_014002.3	80	Cgg/Tgg	5/22	0.936561663400602	3	FACETS	1	0.964	1	0.511	0.484	0.539	CLONAL	1	TRUE	1	0.936561663400602	3		452	1015	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653815	89653815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	259	511	0	ENST00000371953.3:c.113C>T	p.Pro38Leu	p.P38L	ENST00000371953	NM_000314.4	38	cCt/cTt	2/9	0.936561663400602	1	FACETS	0.946	0.916	0.973	0.946	0.916	0.973	CLONAL	1	TRUE	0	0.936561663400602	1		511	311	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0037492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	69	561	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.231749698721568	3	FACETS	0.9	0.783	1	0.45	0.391	0.514	CLONAL	1	TRUE	1	0.243959975117	3		561	705	SUCCESS
APC	324	MSKCC	GRCh37	5	112175524	112175524	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	59	364	0	ENST00000257430.4:c.4233del	p.Ser1411ArgfsTer4	p.S1411Rfs*4	ENST00000257430	NM_000038.5	1411	agT/ag	16/16	0.243959975117	1	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	0	0.243959975117	1		364	419	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391214	89391214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs530556931	NA	P-0037492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	59	408	0	ENST00000336596.2:c.1280C>T	p.Ala427Val	p.A427V	ENST00000336596	NM_005233.5	427	gCg/gTg	5/17	0.243959975117	3	FACETS	0.998	0.859	1	0.499	0.429	0.575	CLONAL	1	TRUE	1	0.243959975117	3		408	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0037492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	219	655	0	ENST00000269305.4:c.838A>T	p.Arg280Ter	p.R280*	ENST00000269305	NM_001126112.2	280	Aga/Tga	8/11	0.243959975117	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.243959975117	2		655	815	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332814	65332817	+	frameshift_variant	Frame_Shift_Del	DEL	TTAT	TTAT	-	novel	NA	P-0037533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	168	438	0	ENST00000342505.4:c.722_725del	p.Asn241MetfsTer7	p.N241Mfs*7	ENST00000342505	NM_002227.2	241	aATAAt/at	7/25	0.483860334658098	2	FACETS	0.868	0.808	0.929	0.868	0.808	0.929	CLONAL	2	TRUE	0	0.483942653712367	2		438	400	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575080	48575080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	126	486	0	ENST00000342988.3:c.274C>T	p.His92Tyr	p.H92Y	ENST00000342988	NM_005359.5	92	Cat/Tat	3/12	0.483860334658098	2	FACETS	0.794	0.729	0.86	0.794	0.729	0.86	SUBCLONAL	2	TRUE	0	0.483942653712367	2		486	328	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0037533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	175	248	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.483860334658098	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	2	0.483942653712367	4		248	513	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0037533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	101	314	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.483860334658098	4	FACETS	0.846	0.763	0.933	0.846	0.763	0.933	CLONAL	2	TRUE	2	0.483942653712367	4		314	366	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628215	187628215	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	113	722	0	ENST00000441802.2:c.2767A>T	p.Asn923Tyr	p.N923Y	ENST00000441802	NM_005245.3	923	Aac/Tac	2/27	1	2	FACETS	0.955	0.864	1	0.955	0.864	1	CLONAL	1	TRUE	1	0.483942653712367	2		722	489	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001200	150001200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	115	668	0	ENST00000253339.5:c.2404G>A	p.Glu802Lys	p.E802K	ENST00000253339		802	Gaa/Aaa	4/7	0.483860334658098	3	FACETS	0.662	0.596	0.733			1	SUBCLONAL	1	TRUE	NA	0.483942653712367	3		668	891	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0037543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	450	441	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.495355193700298	6	FACETS	0.905	0.872	0.937	0.905	0.872	0.937	CLONAL	5	TRUE	1	0.540621498497328	6		441	766	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257158	16257158	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	58	489	0	ENST00000375759.3:c.4423C>T	p.Arg1475Ter	p.R1475*	ENST00000375759	NM_015001.2	1475	Cga/Tga	11/15	1	2	FACETS	0.343	0.294	0.396	0.343	0.294	0.396	SUBCLONAL	1	TRUE	1	0.540621498497328	2		489	626	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203791	94203819	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGCAGCAAACCAACATGTCTGAAGTGGAG	CGCAGCAAACCAACATGTCTGAAGTGGAG	-	novel	NA	P-0037543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	61	253	0	ENST00000323929.3:c.846-11_863del		p.X282_splice	ENST00000323929	NM_005591.3	282		9/20	1	2	FACETS	0.786	0.684	0.895	0.786	0.684	0.895	SUBCLONAL	1	TRUE	1	0.540621498497328	2		253	287	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0037545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	380	535	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.746380935486872	2	FACETS	0.973	0.942	1	0.973	0.942	1	CLONAL	2	TRUE	0	0.746380935486872	2		535	523	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247294	153247294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	107	297	1	ENST00000281708.4:c.1508C>T	p.Ala503Val	p.A503V	ENST00000281708	NM_033632.3	503	gCa/gTa	10/12	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.746380935486872	2		298	281	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438210	49438210	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	177	771	0	ENST00000301067.7:c.5059del	p.Arg1687AlafsTer35	p.R1687Afs*35	ENST00000301067	NM_003482.3	1687	Cgc/gc	20/54	0.687855247961814	3	FACETS	0.866	0.8	0.935	0.433	0.4	0.468	CLONAL	1	TRUE	1	0.746380935486872	3		771	752	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40477081	40477081	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0037545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	115	400	0	ENST00000264657.5:c.1366-2A>G		p.X456_splice	ENST00000264657	NM_139276.2	456			1	2	FACETS	0.985	0.899	1	0.985	0.899	1	CLONAL	1	TRUE	1	0.746380935486872	2		400	313	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271252	26271252	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs937808792	NA	P-0037545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	80	483	0	ENST00000305910.3:c.361A>G	p.Met121Val	p.M121V	ENST00000305910	NM_003534.2	121	Atg/Gtg	1/1	1	2	FACETS	0.607	0.538	0.68	0.607	0.538	0.68	SUBCLONAL	1	TRUE	1	0.746380935486872	2		483	353	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0037548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	94	353	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.465685290075576	1	FACETS	0.502	0.45	0.558	0.502	0.45	0.558	SUBCLONAL	1	TRUE	0	0.615329747581997	1		353	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576890	7576890	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	346	687	0	ENST00000269305.4:c.956del	p.Lys319ArgfsTer26	p.K319Rfs*26	ENST00000269305	NM_001126112.2	319	aAg/ag	9/11	0.615329747581997	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.615329747581997	1		687	726	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912654	NA	P-0037548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	77	635	0	ENST00000269305.4:c.469G>A	p.Val157Ile	p.V157I	ENST00000269305	NM_001126112.2	157	Gtc/Atc	5/11	0.615329747581997	1	FACETS	0.249	0.218	0.282	0.249	0.218	0.282	SUBCLONAL	1	TRUE	0	0.615329747581997	1		635	696	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085924	16085924	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1251450674	NA	P-0037548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	171	458	0	ENST00000281043.3:c.1100C>G	p.Ala367Gly	p.A367G	ENST00000281043	NM_005378.4	367	gCt/gGt	3/3	0.465685290075576	1	FACETS	0.96	0.894	1	0.96	0.894	1	CLONAL	1	TRUE	0	0.615329747581997	1		458	401	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43742126	43742126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1193943585	NA	P-0037579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	184	621	1	ENST00000523873.1:c.115G>A	p.Glu39Lys	p.E39K	ENST00000523873		39	Gaa/Aaa	2/8	1	2	FACETS	0.587	0.542	0.635	0.587	0.542	0.635	SUBCLONAL	1	TRUE	1	0.639188197345981	2		622	980	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66779628	66779628	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	107	514	0	ENST00000307102.5:c.958G>A	p.Glu320Lys	p.E320K	ENST00000307102	NM_002755.3	320	Gag/Aag	8/11	1	2	FACETS	0.519	0.466	0.575	0.519	0.466	0.575	SUBCLONAL	1	TRUE	1	0.639188197345981	2		514	645	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863700	68863701	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0037579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	80	302	0	ENST00000261769.5:c.2439+1dup		p.-813fs	ENST00000261769	NM_004360.3	813	-/G		0.318995056074024	1	FACETS	0.529	0.47	0.591	0.529	0.47	0.591	INDETERMINATE	1	TRUE	0	0.639188197345981	1		302	322	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964361	70964361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	72	401	0	ENST00000276594.2:c.1667C>T	p.Ser556Leu	p.S556L	ENST00000276594	NM_024504.3	556	tCa/tTa	8/8	0.639188197345981	4	FACETS	0.441	0.385	0.503	0.147	0.128	0.168	SUBCLONAL	1	TRUE	1	0.639188197345981	4		401	837	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	76	517	3	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.45	2		520	337	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	118	627	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.966	0.875	1	0.966	0.875	1	CLONAL	1	TRUE	1	0.45	2		633	543	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	61	348	10	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.958	0.834	1	0.958	0.834	1	CLONAL	1	TRUE	1	0.45	2		358	283	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161907	47161907	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	92	444	3	ENST00000409792.3:c.4219del	p.Arg1407GlyfsTer5	p.R1407Gfs*5	ENST00000409792	NM_014159.6	1407	Agg/gg	3/21	1	2	FACETS	0.921	0.823	1	0.921	0.823	1	CLONAL	1	TRUE	1	0.45	2		447	444	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	83	248	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.854	0.757	0.956	0.854	0.757	0.956	CLONAL	1	TRUE	1	0.45	2		248	432	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	45	754	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.775	0.656	0.904	0.775	0.656	0.904	CLONAL	1	TRUE	1	0.45	2		754	258	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143260	24143260	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	122	712	0	ENST00000263121.7:c.496del	p.Leu166PhefsTer10	p.L166Ffs*10	ENST00000263121	NM_003073.3	164	ttC/tt	4/9	1	2	FACETS	0.854	0.774	0.938	0.854	0.774	0.938	CLONAL	1	TRUE	1	0.45	2		712	635	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	59	273	1	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.778	0.673	0.891	0.778	0.673	0.891	SUBCLONAL	1	TRUE	1	0.45	2		274	337	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752800	57752800	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	57	375	3	ENST00000274289.3:c.1128del	p.Asp377ThrfsTer26	p.D377Tfs*26	ENST00000274289	NM_006622.3	376	aaA/aa	8/14	1	2	FACETS	0.787	0.679	0.903	0.787	0.679	0.903	CLONAL	1	TRUE	1	0.45	2		378	322	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500625	99500625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149470389	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	67	365	1	ENST00000268035.6:c.4058G>A	p.Arg1353His	p.R1353H	ENST00000268035	NM_000875.3	1353	cGc/cAc	21/21	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.45	2		366	290	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795103	242795104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768249210	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	72	607	1	ENST00000334409.5:c.105dup	p.Thr36HisfsTer70	p.T36Hfs*70	ENST00000334409	NM_005018.2	35	-/C	2/5	1	2	FACETS	0.564	0.493	0.641	0.564	0.493	0.641	SUBCLONAL	1	TRUE	1	0.45	2		608	567	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007332	143007332	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	68	425	1	ENST00000262992.4:c.2452del	p.Arg818GlufsTer4	p.R818Efs*4	ENST00000262992	NM_001101669.1	818	Aga/ga	22/24	1	2	FACETS	0.684	0.597	0.777	0.684	0.597	0.777	SUBCLONAL	1	TRUE	1	0.45	2		426	442	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	159	444	0	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.45	2		444	643	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	70	635	6	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	1	2	FACETS	0.96	0.844	1	0.96	0.844	1	CLONAL	1	TRUE	1	0.45	2		641	324	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905055	50905055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	81	510	5	ENST00000440232.2:c.342del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	113	Ggg/gg	4/27	1	2	FACETS	0.872	0.772	0.977	0.872	0.772	0.977	CLONAL	1	TRUE	1	0.45	2		515	413	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120115	70120115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	27	597	0	ENST00000245479.2:c.1121del	p.Pro374ArgfsTer9	p.P374Rfs*9	ENST00000245479	NM_000346.3	373	Ccc/cc	3/3	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.45	2		597	93	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885939	111885939	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	73	513	1	ENST00000341259.2:c.1566del	p.Glu523SerfsTer25	p.E523Sfs*25	ENST00000341259	NM_005475.2	521	Ccc/cc	8/8	1	2	FACETS	0.765	0.672	0.865	0.765	0.672	0.865	SUBCLONAL	1	TRUE	1	0.45	2		514	424	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333991	70333993	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	rs903550402	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	40	195	0	ENST00000373644.4:c.1902_1904del	p.Val635del	p.V635del	ENST00000373644	NM_030625.2	632	tcTGTt/tct	2/12	1	2	FACETS	0.907	0.762	1	0.907	0.762	1	CLONAL	1	TRUE	1	0.45	2		195	196	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165569	47165569	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs78759480	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	108	483	0	ENST00000409792.3:c.557C>T	p.Pro186Leu	p.P186L	ENST00000409792	NM_014159.6	186	cCg/cTg	3/21	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.45	2		483	453	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031815	10031815	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs397518465	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	90	534	1	ENST00000330684.3:c.1007+1G>A		p.X336_splice	ENST00000330684	NM_001134407.1	336			1	2	FACETS	0.875	0.78	0.976	0.875	0.78	0.976	CLONAL	1	TRUE	1	0.45	2		535	457	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29090060	29090060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121908706	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	48	208	0	ENST00000328354.6:c.1421G>A	p.Arg474His	p.R474H	ENST00000328354	NM_007194.3	474	cGt/cAt	13/15	1	2	FACETS	0.793	0.675	0.921	0.793	0.675	0.921	CLONAL	1	TRUE	1	0.45	2		208	269	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127694	2127694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660733	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	89	512	0	ENST00000219476.3:c.2933G>A	p.Arg978His	p.R978H	ENST00000219476	NM_000548.3	978	cGc/cAc	26/42	1	2	FACETS	0.899	0.801	1	0.899	0.801	1	CLONAL	1	TRUE	1	0.45	2		512	440	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324886	31324887	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760037174	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	32	380	0	ENST00000412585.2:c.49_50insG	p.Leu17ArgfsTer82	p.L17Rfs*82	ENST00000412585	NM_005514.6	17	ctg/cGtg	1/8	1	2	FACETS	0.453	0.368	0.548	0.453	0.368	0.548	SUBCLONAL	1	TRUE	1	0.45	2		380	314	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250839	99250839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774734018	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	62	401	0	ENST00000268035.6:c.143G>A	p.Arg48His	p.R48H	ENST00000268035	NM_000875.3	48	cGc/cAc	2/21	1	2	FACETS	0.875	0.761	0.996	0.875	0.761	0.996	CLONAL	1	TRUE	1	0.45	2		401	315	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762431	41762431	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748730668	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	95	486	1	ENST00000301178.4:c.2111G>A	p.Arg704His	p.R704H	ENST00000301178	NM_021913.4	704	cGc/cAc	18/20	1	2	FACETS	0.878	0.785	0.976	0.878	0.785	0.976	CLONAL	1	TRUE	1	0.45	2		487	481	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793676	89793677	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	50	246	0	ENST00000336032.3:c.752dup	p.Pro252AlafsTer3	p.P252Afs*3	ENST00000336032	NM_006813.2	249	gaa/gAaa	2/2	1	2	FACETS	0.845	0.723	0.977	0.845	0.723	0.977	CLONAL	1	TRUE	1	0.45	2		246	263	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994829	73994829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751833994	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	40	306	1	ENST00000318443.5:c.313G>A	p.Ala105Thr	p.A105T	ENST00000318443	NM_001024736.1	105	Gca/Aca	3/10	1	2	FACETS	0.912	0.766	1	0.912	0.766	1	CLONAL	1	TRUE	1	0.45	2		307	195	SUCCESS
AR	367	MSKCC	GRCh37	X	66765350	66765350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749864595	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	105	644	0	ENST00000374690.3:c.362C>T	p.Ser121Leu	p.S121L	ENST00000374690	NM_000044.3	121	tCg/tTg	1/8	1	2	FACETS	0.915	0.823	1	0.915	0.823	1	CLONAL	1	TRUE	1	0.45	2		644	510	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074168	8074169	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	70	315	1	ENST00000377482.5:c.490_491del	p.Leu164GlyfsTer2	p.L164Gfs*2	ENST00000377482	NM_018948.3	164	CTg/g	4/4	1	2	FACETS	0.904	0.794	1	0.904	0.794	1	CLONAL	1	TRUE	1	0.45	2		316	344	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925582	114925582	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	138	558	0	ENST00000543371.1:c.1663del	p.Ala555ProfsTer47	p.A555Pfs*47	ENST00000543371	NM_001198531.1	554	Ggg/gg	14/14	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.45	2		558	537	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151869	108151869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555091402	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	77	428	0	ENST00000278616.4:c.3550G>A	p.Gly1184Arg	p.G1184R	ENST00000278616	NM_000051.3	1184	Gga/Aga	24/63	1	2	FACETS	0.908	0.802	1	0.908	0.802	1	CLONAL	1	TRUE	1	0.45	2		428	377	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434981	49434981	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572145631	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	54	378	0	ENST00000301067.7:c.6572C>T	p.Thr2191Met	p.T2191M	ENST00000301067	NM_003482.3	2191	aCg/aTg	31/54	1	2	FACETS	0.968	0.835	1	0.968	0.835	1	CLONAL	1	TRUE	1	0.45	2		378	248	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209301	133209302	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	121	616	0	ENST00000320574.5:c.6084_6085insA	p.Gly2029ArgfsTer30	p.G2029Rfs*30	ENST00000320574	NM_006231.2	2028	-/A	44/49	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.45	2		616	501	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937016	48937016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs556201144	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	49	270	2	ENST00000267163.4:c.784C>T	p.Arg262Trp	p.R262W	ENST00000267163	NM_000321.2	262	Cgg/Tgg	8/27	1	2	FACETS	0.624	0.53	0.726	0.624	0.53	0.726	SUBCLONAL	1	TRUE	1	0.45	2		272	349	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396565	30396565	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	75	401	0	ENST00000331968.5:c.154C>A	p.His52Asn	p.H52N	ENST00000331968	NM_002742.2	52	Cat/Aat	1/18	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.45	2		401	298	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582827	95582827	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	56	302	0	ENST00000393063.1:c.1715T>A	p.Phe572Tyr	p.F572Y	ENST00000393063	NM_030621.3	572	tTt/tAt	11/28	1	2	FACETS	0.78	0.673	0.896	0.78	0.673	0.896	SUBCLONAL	1	TRUE	1	0.45	2		302	319	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925161	81925161	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1384764686	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	94	499	0	ENST00000359376.3:c.952C>A	p.Leu318Met	p.L318M	ENST00000359376	NM_002661.3	318	Ctg/Atg	11/33	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.45	2		499	412	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110189	8110189	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753106886	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	82	445	0	ENST00000585124.1:c.416G>A	p.Arg139His	p.R139H	ENST00000585124	NM_004217.3	139	cGt/cAt	6/9	1	2	FACETS	0.83	0.735	0.931	0.83	0.735	0.931	CLONAL	1	TRUE	1	0.45	2		445	439	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576049	29576049	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	101	405	0	ENST00000356175.3:c.4022A>G	p.Gln1341Arg	p.Q1341R	ENST00000356175	NM_000267.3	1341	cAg/cGg	30/57	1	2	FACETS	0.978	0.879	1	0.978	0.879	1	CLONAL	1	TRUE	1	0.45	2		405	459	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581325	48581325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	90	456	1	ENST00000342988.3:c.629G>A	p.Ser210Asn	p.S210N	ENST00000342988	NM_005359.5	210	aGc/aAc	5/12	1	2	FACETS	0.998	0.891	1	0.998	0.891	1	CLONAL	1	TRUE	1	0.45	2		457	401	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224199	36224199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775887663	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	113	647	0	ENST00000222270.7:c.6749G>A	p.Arg2250His	p.R2250H	ENST00000222270	NM_014727.1	2250	cGc/cAc	28/37	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.45	2		647	469	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796799	42796799	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	133	802	2	ENST00000575354.2:c.3261del	p.Gly1088GlufsTer5	p.G1088Efs*5	ENST00000575354	NM_015125.3	1086	gCc/gc	14/20	1	2	FACETS	0.915	0.833	1	0.915	0.833	1	CLONAL	1	TRUE	1	0.45	2		804	646	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721118	61721118	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	120	454	0	ENST00000401558.2:c.1156T>C	p.Phe386Leu	p.F386L	ENST00000401558	NM_003400.3	386	Ttc/Ctc	12/25	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.45	2		454	462	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149727	202149728	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	108	579	0	ENST00000358485.4:c.1173dup	p.Ile392HisfsTer3	p.I392Hfs*3	ENST00000358485	NM_001080125.1	390	gcc/gCcc	8/9	1	2	FACETS	0.825	0.742	0.912	0.825	0.742	0.912	CLONAL	1	TRUE	1	0.45	2		579	582	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568866	212568866	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	86	416	0	ENST00000342788.4:c.1252del	p.Ser418LeufsTer4	p.S418Lfs*4	ENST00000342788	NM_005235.2	418	Tct/ct	11/28	1	2	FACETS	0.948	0.844	1	0.948	0.844	1	CLONAL	1	TRUE	1	0.45	2		416	403	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46255845	46255845	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	78	351	0	ENST00000371998.3:c.457G>A	p.Val153Ile	p.V153I	ENST00000371998		153	Gtt/Att	6/23	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.45	2		351	324	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288173	21288173	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	102	516	0	ENST00000354336.3:c.418G>A	p.Glu140Lys	p.E140K	ENST00000354336	NM_005207.3	140	Gaa/Aaa	2/3	1	2	FACETS	0.877	0.787	0.971	0.877	0.787	0.971	CLONAL	1	TRUE	1	0.45	2		516	517	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521507	187521507	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	61	337	0	ENST00000441802.2:c.11648A>G	p.His3883Arg	p.H3883R	ENST00000441802	NM_005245.3	3883	cAt/cGt	22/27	1	2	FACETS	0.955	0.831	1	0.955	0.831	1	CLONAL	1	TRUE	1	0.45	2		337	284	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131926963	131926963	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	31	136	1	ENST00000265335.6:c.1504del	p.Met502TrpfsTer3	p.M502Wfs*3	ENST00000265335		500	ttA/tt	10/25	1	2	FACETS	0.721	0.589	0.869	0.721	0.589	0.869	SUBCLONAL	1	TRUE	1	0.45	2		137	191	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323149	31323150	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	82	520	0	ENST00000412585.2:c.839_840del	p.Arg280IlefsTer8	p.R280Ifs*8	ENST00000412585	NM_005514.6	280	aGA/a	4/8	1	2	FACETS	0.772	0.683	0.867	0.772	0.683	0.867	SUBCLONAL	1	TRUE	1	0.45	2		520	472	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117730804	117730804	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs140860347	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	116	441	0	ENST00000368508.3:c.230G>A	p.Arg77Gln	p.R77Q	ENST00000368508	NM_002944.2	77	cGg/cAg	4/43	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.45	2		441	471	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845457	128845457	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	153	676	0	ENST00000249373.3:c.754T>A	p.Phe252Ile	p.F252I	ENST00000249373	NM_005631.4	252	Ttc/Atc	4/12	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.45	2		676	643	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80646066	80646066	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	25	166	0	ENST00000286548.4:c.86T>C	p.Leu29Pro	p.L29P	ENST00000286548	NM_002072.3	29	cTc/cCc	1/7	1	2	FACETS	0.799	0.638	0.979	0.799	0.638	0.979	CLONAL	1	TRUE	1	0.45	2		166	139	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239622	53239622	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	127	645	1	ENST00000375401.3:c.1720A>G	p.Asn574Asp	p.N574D	ENST00000375401	NM_004187.3	574	Aac/Gac	12/26	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.45	2		646	563	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412248	63412248	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	142	515	1	ENST00000330258.3:c.919del	p.Asp307ThrfsTer3	p.D307Tfs*3	ENST00000330258	NM_152424.3	307	Gac/ac	2/2	1	2	FACETS	0.948	0.866	1	0.948	0.866	1	CLONAL	1	TRUE	1	0.45	2		516	666	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205129	123205129	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	117	522	0	ENST00000218089.9:c.2489T>C	p.Leu830Ser	p.L830S	ENST00000218089	NM_001042749.1	830	tTg/tCg	25/35	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.45	2		522	460	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229240	123229240	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867285087	NA	P-0037604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	84	157	0	ENST00000218089.9:c.3724C>T	p.Arg1242Ter	p.R1242*	ENST00000218089	NM_001042749.1	1242	Cga/Tga	34/35	1	1	FACETS	0.774	0.695	0.856	1	0.982	1	SUBCLONAL	2	TRUE	0	0.372519624522477	1		157	237	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519966	NA	P-0037604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	187	624	0	ENST00000347630.2:c.397T>A	p.Phe133Ile	p.F133I	ENST00000347630	NM_001007230.1	133	Ttc/Atc	6/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.372519624522477	2		624	808	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675074	40675074	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	161	664	0	ENST00000249776.8:c.38T>G	p.Phe13Cys	p.F13C	ENST00000249776	NM_033286.3	13	tTc/tGc	1/9	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.372519624522477	2		664	837	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0037614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	52	414	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.118567400956338	3	FACETS	0.875	0.743	1	0.437	0.371	0.51	CLONAL	1	TRUE	1	0.18	3		414	720	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0037614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	78	523	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.18	2		523	653	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	136	350	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.393883843249396	2		350	622	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0037616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	232	743	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.963	1	1	0.995	1	CLONAL	2	TRUE	1	0.393883843249396	2		743	570	SUCCESS
APC	324	MSKCC	GRCh37	5	112175606	112175606	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	112	235	0	ENST00000257430.4:c.4316del	p.Pro1439LeufsTer34	p.P1439Lfs*34	ENST00000257430	NM_000038.5	1439	Cct/ct	16/16	0.393883843249396	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	0	0.393883843249396	2		235	281	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849863	156849863	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747855434	NA	P-0037616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	201	449	0	ENST00000524377.1:c.2119G>A	p.Glu707Lys	p.E707K	ENST00000524377	NM_002529.3	707	Gag/Aag	16/17	0.166363400476043	3	FACETS	1	0.956	1	0.688	0.641	0.735	INDETERMINATE	2	TRUE	0	0.393883843249396	3		449	592	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922695	44922695	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	203	220	0	ENST00000377967.4:c.1556G>C	p.Arg519Pro	p.R519P	ENST00000377967	NM_021140.2	519	cGa/cCa	16/29	0.393883843249396	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.393883843249396	3		220	499	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046548	30046548	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	105	444	0	ENST00000331968.5:c.2635C>A	p.Gln879Lys	p.Q879K	ENST00000331968	NM_002742.2	879	Cag/Aag	18/18	1	2	FACETS	0.871	0.782	0.965	0.871	0.782	0.965	CLONAL	1	TRUE	1	0.393883843249396	2		444	612	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119865	70119866	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GATG	novel	NA	P-0037616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	68	388	0	ENST00000245479.2:c.868_871dup	p.Val291GlyfsTer6	p.V291Gfs*6	ENST00000245479	NM_000346.3	289	-/GATG	3/3	0.337293958350247	3	FACETS	0.804	0.701	0.915	0.402	0.35	0.458	CLONAL	1	TRUE	1	0.393883843249396	3		388	514	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845616	68845616	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	280	308	0	ENST00000261769.5:c.862G>A	p.Asp288Asn	p.D288N	ENST00000261769	NM_004360.3	288	Gac/Aac	7/16	0.874706370281039	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.874706370281039	1		308	348	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207633	2207633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752264656	NA	P-0037686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	274	407	1	ENST00000398665.3:c.917C>T	p.Thr306Met	p.T306M	ENST00000398665	NM_032482.2	306	aCg/aTg	11/28	1	2	FACETS	0.901	0.851	0.952	0.901	0.851	0.952	CLONAL	1	TRUE	1	0.874706370281039	2		408	695	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356413	66356413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764384268	NA	P-0037686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	122	199	0	ENST00000273854.3:c.1084C>T	p.Arg362Trp	p.R362W	ENST00000273854	NM_004439.5	362	Cgg/Tgg	5/18	1	2	FACETS	0.891	0.817	0.967	0.891	0.817	0.967	CLONAL	1	TRUE	1	0.874706370281039	2		199	313	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426842	70426842	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	206	230	0	ENST00000373644.4:c.4502T>C	p.Leu1501Ser	p.L1501S	ENST00000373644	NM_030625.2	1501	tTg/tCg	7/12	1	2	FACETS	0.871	0.814	0.928	0.871	0.814	0.928	CLONAL	1	TRUE	1	0.874706370281039	2		230	541	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228288	53228288	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	341	381	0	ENST00000375401.3:c.2114G>T	p.Arg705Leu	p.R705L	ENST00000375401	NM_004187.3	705	cGc/cTc	15/26	0.202980001519462	1	FACETS	0.569	0.541	0.597	0.569	0.541	0.597	INDETERMINATE	1	TRUE	0	0.874706370281039	1		381	771	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0037694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	45	494	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.369752932914394	4	FACETS	1	0.96	1	0.723	0.616	0.839	CLONAL	1	FALSE	2	0.461470321588561	4		494	197	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0037694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	9	441	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.465634378753179	4	FACETS	0.328	0.217	0.469	0.164	0.108	0.235	SUBCLONAL	1	FALSE	2	0.461470321588561	4		441	174	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0037694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	38	613	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.399284487940595	2	FACETS	0.807	0.688	0.932	0.807	0.688	0.932	CLONAL	2	FALSE	0	0.461470321588561	2		613	102	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0037694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	76	370	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.465634378753179	4	FACETS	0.967	0.871	1	1	0.98	1	CLONAL	3	FALSE	2	0.461470321588561	4		370	166	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411258	63411258	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	15	748	0	ENST00000330258.3:c.1909G>A	p.Glu637Lys	p.E637K	ENST00000330258	NM_152424.3	637	Gag/Aag	2/2	0.296954422763679	1	FACETS	0.625	0.466	0.808	0.625	0.466	0.808	SUBCLONAL	1	FALSE	0	0.461470321588561	1		748	80	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0037754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	110	414	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.935	0.842	1	0.935	0.842	1	CLONAL	1	TRUE	1	0.377729298675898	2		414	623	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0037754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	434	670	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.377729298675898	2		670	1069	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971177	21971177	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913382	NA	P-0037754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	104	486	0	ENST00000304494.5:c.181G>T	p.Glu61Ter	p.E61*	ENST00000304494	NM_000077.4	61	Gag/Tag	2/3	0.377729298675898	1	FACETS	0.958	0.863	1	0.958	0.863	1	CLONAL	1	TRUE	0	0.377729298675898	1		486	466	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111012	193111012	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	120	311	0	ENST00000367435.3:c.545T>A	p.Ile182Asn	p.I182N	ENST00000367435	NM_024529.4	182	aTt/aAt	7/17	0.371414578659799	2	FACETS	0.892	0.815	0.972	0.892	0.815	0.972	CLONAL	2	TRUE	0	0.377729298675898	2		311	356	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247793	59247794	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0037754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	209	912	0	ENST00000371222.2:c.949_950del	p.Asn317GlnfsTer30	p.N317Qfs*30	ENST00000371222	NM_002228.3	317	AAc/c	1/1	1	2	FACETS	0.977	0.906	1	0.977	0.906	1	CLONAL	1	TRUE	1	0.377729298675898	2		912	1133	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400950	72400950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	80	438	0	ENST00000357731.5:c.221G>A	p.Arg74Gln	p.R74Q	ENST00000357731	NM_173808.2	74	cGg/cAg	2/7	1	2	FACETS	0.766	0.675	0.863	0.766	0.675	0.863	SUBCLONAL	1	TRUE	1	0.377729298675898	2		438	553	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554129	63554129	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	141	835	0	ENST00000307078.5:c.610G>T	p.Gly204Ter	p.G204*	ENST00000307078	NM_004655.3	204	Gga/Tga	2/11	1	2	FACETS	0.759	0.69	0.831	0.759	0.69	0.831	SUBCLONAL	1	TRUE	1	0.377729298675898	2		835	984	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530094	212530094	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	67	391	0	ENST00000342788.4:c.1825G>C	p.Asp609His	p.D609H	ENST00000342788	NM_005235.2	609	Gat/Cat	15/28	1	2	FACETS	0.752	0.655	0.856	0.752	0.655	0.856	SUBCLONAL	1	TRUE	1	0.377729298675898	2		391	472	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0037778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	111	370	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.586391586161543	5	FACETS	0.912	0.844	0.979			1	CLONAL	4	TRUE	NA	0.586391586161543	5		370	195	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097719	27097719	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	169	674	0	ENST00000324856.7:c.3308T>C	p.Phe1103Ser	p.F1103S	ENST00000324856	NM_006015.4	1103	tTt/tCt	12/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.586391586161543	2		674	484	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111461	8111492	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGTGCGAACTGTCAGACCACCACAACCACA	CCTGTGCGAACTGTCAGACCACCACAACCACA	-	novel	NA	P-0037778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	206	612	0	ENST00000346208.3:c.948_979del	p.Cys317LeufsTer24	p.C317Lfs*24	ENST00000346208		316	tCCTGTGCGAACTGTCAGACCACCACAACCACA/t	5/6	1	2	FACETS	0.994	0.926	1	0.994	0.926	1	CLONAL	1	TRUE	1	0.586391586161543	2		612	707	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346261	89346262	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0037778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	165	400	0	ENST00000301030.4:c.6688_6689del	p.Arg2230GlyfsTer29	p.R2230Gfs*29	ENST00000301030	NM_001256183.1	2230	AGg/g	9/13	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.586391586161543	2		400	509	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386444	31386444	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	115	697	0	ENST00000328111.2:c.1669G>C	p.Glu557Gln	p.E557Q	ENST00000328111	NM_006892.3	557	Gaa/Caa	15/23	0.38441346499782	1	FACETS	0.449	0.405	0.495	0.449	0.405	0.495	SUBCLONAL	1	TRUE	0	0.586391586161543	1		697	617	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	351	350	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.345049354059903	5	FACETS	0.974	0.934	1			1	CLONAL	4	TRUE	NA	0.544395000737111	5		350	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577530	7577530	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	387	776	0	ENST00000269305.4:c.751A>T	p.Ile251Phe	p.I251F	ENST00000269305	NM_001126112.2	251	Atc/Ttc	7/11	0.544395000737111	2	FACETS	0.979	0.939	1	0.979	0.939	1	CLONAL	2	TRUE	0	0.544395000737111	2		776	726	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257860	198257860	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	55	572	0	ENST00000335508.6:c.3592G>C	p.Gly1198Arg	p.G1198R	ENST00000335508	NM_012433.2	1198	Ggg/Cgg	24/25	0.544395000737111	3	FACETS	0.31	0.264	0.36	0.155	0.132	0.18	SUBCLONAL	1	TRUE	1	0.544395000737111	3		572	829	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025621	1025621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763842232	NA	P-0037834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	425	760	0	ENST00000358495.3:c.754G>A	p.Glu252Lys	p.E252K	ENST00000358495	NM_134424.2	252	Gag/Aag	9/12	0.0947590984412576	5	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.521926955533715	5		760	1189	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646980	23646981	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0037834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	374	804	0	ENST00000261584.4:c.886dup	p.Met296AsnfsTer7	p.M296Nfs*7	ENST00000261584	NM_024675.3	296	atg/aAtg	4/13	0.31761612445891	4	FACETS	0.84	0.796	0.884	0.84	0.796	0.884	CLONAL	2	TRUE	2	0.521926955533715	4		804	1299	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577148	7577148	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1060501194	NA	P-0037834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	616	724	0	ENST00000269305.4:c.790del	p.Leu264TyrfsTer81	p.L264Yfs*81	ENST00000269305	NM_001126112.2	264	Cta/ta	8/11	0.460033539258636	3	FACETS	0.863	0.835	0.892	0.863	0.835	0.892	CLONAL	3	TRUE	0	0.521926955533715	3		724	1149	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982394	201982394	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	380	972	0	ENST00000359651.3:c.773G>A	p.Trp258Ter	p.W258*	ENST00000359651		258	tGg/tAg	6/8	1	2	FACETS	0.99	0.939	1	0.99	0.939	1	CLONAL	1	TRUE	1	0.521926955533715	2		972	1471	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999773	100999773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1025431009	NA	P-0037834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	207	895	1	ENST00000325455.5:c.29G>A	p.Arg10Gln	p.R10Q	ENST00000325455	NM_001202474.3	10	cGg/cAg	1/8	1	2	FACETS	0.751	0.697	0.808	0.751	0.697	0.808	SUBCLONAL	1	TRUE	1	0.521926955533715	2		896	1056	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799326	88799327	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0037834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	343	611	0	ENST00000360948.2:c.58dup	p.Ser20LysfsTer23	p.S20Kfs*23	ENST00000360948	NM_001012338.2	20	agc/aAgc	2/19	0.521926955533715	6	FACETS	1	0.983	1			1	CLONAL	2	TRUE	NA	0.521926955533715	6		611	1235	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0037857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	107	245	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.727558927387712	2		245	275	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023307	27023307	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0037857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	112	173	0	ENST00000324856.7:c.413C>G	p.Ser138Ter	p.S138*	ENST00000324856	NM_006015.4	138	tCa/tGa	1/20	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.727558927387712	2		173	300	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729968	30729968	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs863223852	NA	P-0037857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	211	405	0	ENST00000295754.5:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000295754	NM_003242.5	497	Cga/Tga	6/7	0.727558927387712	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.727558927387712	1		405	366	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69229729	69229729	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	36	265	0	ENST00000462284.1:c.805G>A	p.Glu269Lys	p.E269K	ENST00000462284	NM_002392.5	269	Gaa/Aaa	9/11	0.370003885633936	2	FACETS	0.385	0.316	0.462	0.192	0.158	0.231	SUBCLONAL	1	TRUE	0	0.370003885633936	2		265	506	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619955	21619955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756666534	NA	P-0037890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	134	556	1	ENST00000382592.4:c.211G>A	p.Gly71Arg	p.G71R	ENST00000382592	NM_014572.2	71	Gga/Aga	2/8	1	2	FACETS	0.85	0.772	0.932	0.85	0.772	0.932	CLONAL	1	TRUE	1	0.370003885633936	2		557	852	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998899	11998899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	48	234	0	ENST00000353533.5:c.401G>A	p.Arg134Gln	p.R134Q	ENST00000353533	NM_003010.3	134	cGg/cAg	4/11	0.266195886135529	2	FACETS	0.754	0.64	0.879	0.377	0.32	0.44	SUBCLONAL	1	TRUE	0	0.370003885633936	2		234	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579539	7579541	+	frameshift_variant	Frame_Shift_Del	DEL	TAT	TAT	A	novel	NA	P-0037890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	254	690	1	ENST00000269305.4:c.146_148delinsT	p.Asp49ValfsTer2	p.D49Vfs*2	ENST00000269305	NM_001126112.2	49	gATAtt/gTtt	4/11	0.266195886135529	2	FACETS	0.759	0.711	0.807	0.759	0.711	0.807	SUBCLONAL	2	TRUE	0	0.370003885633936	2		691	905	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0037908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	72	414	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.883	0.777	0.996	0.883	0.777	0.996	CLONAL	1	TRUE	1	0.455461252217875	2		414	358	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0037908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	86	248	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.455461252217875	2		248	364	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855984	68855984	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121964877	NA	P-0037908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	79	318	0	ENST00000261769.5:c.1792C>T	p.Arg598Ter	p.R598*	ENST00000261769	NM_004360.3	598	Cga/Tga	12/16	0.455461252217875	1	FACETS	0.864	0.767	0.966	0.864	0.767	0.966	CLONAL	1	TRUE	0	0.455461252217875	1		318	310	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256000	16256000	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	89	351	0	ENST00000375759.3:c.3265G>T	p.Gly1089Ter	p.G1089*	ENST00000375759	NM_015001.2	1089	Gga/Tga	11/15	1	2	FACETS	0.992	0.885	1	0.992	0.885	1	CLONAL	1	TRUE	1	0.455461252217875	2		351	394	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178143	56178143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1444422239	NA	P-0037908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	84	208	0	ENST00000399503.3:c.3116C>T	p.Ser1039Leu	p.S1039L	ENST00000399503	NM_005921.1	1039	tCa/tTa	14/20	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.455461252217875	2		208	351	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223654	53223654	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	116	483	0	ENST00000375401.3:c.3705G>C	p.Trp1235Cys	p.W1235C	ENST00000375401	NM_004187.3	1235	tgG/tgC	23/26	0.455461252217875	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.455461252217875	1		483	381	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112055	115112059	+	frameshift_variant	Frame_Shift_Del	DEL	GCCAT	GCCAT	A	novel	NA	P-0037908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	94	451	0	ENST00000257566.3:c.1681_1685delinsT	p.Met561SerfsTer70	p.M561Sfs*70	ENST00000257566	NM_016569.3	561	ATGGCc/Tc	7/8	1	2	FACETS	0.86	0.768	0.957	0.86	0.768	0.957	CLONAL	1	TRUE	1	0.455461252217875	2		451	480	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0037956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	387	441	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.502226168835587	5	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	2	0.502226168835587	5		441	843	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691022	NA	P-0037956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	387	848	2	ENST00000269305.4:c.1024del	p.Arg342GlufsTer3	p.R342Efs*3	ENST00000269305	NM_001126112.2	342	Cga/ga	10/11	0.480301772150405	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.502226168835587	2		850	753	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270519	10270519	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	331	718	0	ENST00000340748.4:c.1121C>T	p.Ala374Val	p.A374V	ENST00000340748		374	gCg/gTg	15/40	0.445092149643116	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.502226168835587	4		718	934	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041229	29041229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	288	646	0	ENST00000282397.4:c.199G>A	p.Val67Met	p.V67M	ENST00000282397	NM_002019.4	67	Gtg/Atg	3/30	0.378060718587343	4	FACETS	0.967	0.912	1	0.967	0.912	1	CLONAL	2	TRUE	2	0.502226168835587	4		646	891	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656564	3656564	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	367	863	0	ENST00000294008.3:c.671T>G	p.Leu224Trp	p.L224W	ENST00000294008	NM_032444.2	224	tTg/tGg	3/15	0.445092149643116	4	FACETS	0.96	0.911	1	0.96	0.911	1	CLONAL	2	TRUE	2	0.502226168835587	4		863	1144	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056226	26056226	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1383675761	NA	P-0037956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	301	633	0	ENST00000343677.2:c.431G>A	p.Gly144Asp	p.G144D	ENST00000343677	NM_005319.3	144	gGc/gAc	1/1	0.445092149643116	4	FACETS	0.966	0.912	1	0.966	0.912	1	CLONAL	2	TRUE	2	0.502226168835587	4		633	932	SUCCESS
AR	367	MSKCC	GRCh37	X	66765159	66765191	+	inframe_deletion	In_Frame_Del	DEL	GCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA	GCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA	-	rs3032358	NA	P-0037960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	34	180	0	ENST00000374690.3:c.207_239del	p.Gln70_Gln80del	p.Q70_Q80del	ENST00000374690	NM_000044.3	57	ctGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAg/ctg	1/8	0.357804902101484	3	FACETS	0.852	0.7	1			1	CLONAL	1	TRUE	NA	0.357804902101484	3		180	263	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86686687	86686689	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	novel	NA	P-0037960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	73	399	0	ENST00000274376.6:c.3134_3136del	p.Asp1045del	p.D1045del	ENST00000274376	NM_002890.2	1044	aATGat/aat	25/25	1	2	FACETS	0.831	0.729	0.941	0.831	0.729	0.941	CLONAL	1	TRUE	1	0.357804902101484	2		399	491	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216499	108216499	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	160	336	0	ENST00000278616.4:c.8448A>T	p.Lys2816Asn	p.K2816N	ENST00000278616	NM_000051.3	2816	aaA/aaT	58/63	0.335399663470502	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.357804902101484	2		336	432	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81960738	81960738	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0037960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	46	721	0	ENST00000359376.3:c.2469C>G	p.Tyr823Ter	p.Y823*	ENST00000359376	NM_002661.3	823	taC/taG	23/33	0.335399663470502	2	FACETS	0.385	0.324	0.454	0.193	0.162	0.227	SUBCLONAL	1	TRUE	0	0.357804902101484	2		721	667	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022253	26022253	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0037960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	346	578	0	ENST00000435504.4:c.403+1G>A		p.X135_splice	ENST00000435504		135			0.357804902101484	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	TRUE	1	0.357804902101484	4		578	853	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617424	158617424	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	92	631	0	ENST00000263640.3:c.1232T>G	p.Leu411Trp	p.L411W	ENST00000263640	NM_001105.4	411	tTg/tGg	9/11	0.357804902101484	5	FACETS	0.81	0.718	0.908	0.202	0.179	0.227	CLONAL	1	TRUE	1	0.357804902101484	5		631	976	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576870	212576870	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	88	492	0	ENST00000342788.4:c.1029G>T	p.Met343Ile	p.M343I	ENST00000342788	NM_005235.2	343	atG/atT	9/28	0.357804902101484	6	FACETS	0.708	0.625	0.797			1	SUBCLONAL	1	TRUE	NA	0.357804902101484	6		492	1192	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179185	123179185	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	313	302	0	ENST00000218089.9:c.634G>T	p.Val212Phe	p.V212F	ENST00000218089	NM_001042749.1	212	Gtc/Ttc	8/35	0.357804902101484	3	FACETS	0.984	0.942	1			1	CLONAL	4	TRUE	NA	0.357804902101484	3		302	524	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265469	152265469	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038005-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	179	686	0	ENST00000206249.3:c.922T>G	p.Leu308Val	p.L308V	ENST00000206249	NM_000125.3	308	Ttg/Gtg	4/8	1	2	FACETS	0.882	0.814	0.951	0.882	0.814	0.951	CLONAL	1	TRUE	1	0.532215155767728	2		686	763	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	17	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.584	0.436	0.76	0.584	0.436	0.76	SUBCLONAL	1	TRUE	1	0.23	2		126	253	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591247	67591249	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GGT	GGT	-	rs1131692243	NA	P-0038039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	50	310	0	ENST00000274335.5:c.1748_1750del		p.X583_splice	ENST00000274335		583		13/15	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.23	2		310	326	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426123	138426123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217537873	NA	P-0038039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	24	259	0	ENST00000289153.2:c.1408G>A	p.Glu470Lys	p.E470K	ENST00000289153	NM_006219.2	470	Gaa/Aaa	9/22	1	2	FACETS	0.962	0.758	1	0.962	0.758	1	CLONAL	1	TRUE	1	0.23	2		259	217	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2957015	2957015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	37	432	1	ENST00000396946.4:c.2612C>T	p.Thr871Ile	p.T871I	ENST00000396946	NM_032415.4	871	aCc/aTc	20/25	0.212923696083267	3	FACETS	0.743	0.612	0.889	0.371	0.306	0.445	SUBCLONAL	1	TRUE	1	0.23	3		433	483	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665755	29665756	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs876657715	NA	P-0038039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	25	271	0	ENST00000356175.3:c.6791dup	p.Tyr2264Ter	p.Y2264*	ENST00000356175	NM_000267.3	2264	tac/tAac	45/57	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.23	2		271	146	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428200	47428200	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	78	726	0	ENST00000377045.4:c.1160G>A	p.Gly387Asp	p.G387D	ENST00000377045	NM_001654.4	387	gGc/gAc	11/16	1	2	FACETS	0.885	0.777	1	0.885	0.777	1	CLONAL	1	TRUE	1	0.23	2		726	766	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	10	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.713	0.484	1	0.713	0.484	1	CLONAL	1	TRUE	1	0.17	2		126	165	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0038350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	58	658	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.17	2		658	628	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517201	NA	P-0038350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	37	624	0	ENST00000263967.3:c.1637A>C	p.Gln546Pro	p.Q546P	ENST00000263967	NM_006218.2	546	cAg/cCg	10/21	1	2	FACETS	0.485	0.398	0.583	0.485	0.398	0.583	SUBCLONAL	1	TRUE	1	0.17	2		624	897	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983086	201983086	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	50	692	0	ENST00000359651.3:c.935C>G	p.Ala312Gly	p.A312G	ENST00000359651		312	gCc/gGc	7/8	1	2	FACETS	0.819	0.694	0.958	0.819	0.694	0.958	CLONAL	1	TRUE	1	0.17	2		692	718	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143079	7143079	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	41	575	0	ENST00000302850.5:c.2290C>G	p.Leu764Val	p.L764V	ENST00000302850	NM_000208.2	764	Ctt/Gtt	12/22	0.138654435488974	1	FACETS	0.765	0.636	0.908	0.765	0.636	0.908	CLONAL	1	TRUE	0	0.17	1		575	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579400	7579400	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	222	882	0	ENST00000269305.4:c.287del	p.Ser96LeufsTer27	p.S96Lfs*27	ENST00000269305	NM_001126112.2	96	tCt/tt	4/11	0.510417653931557	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.510417653931557	1		882	560	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380350	14380350	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	62	253	0	ENST00000256196.4:c.67G>T	p.Gly23Cys	p.G23C	ENST00000256196		23	Ggc/Tgc	1/6	0.506115366436826	3	FACETS	0.881	0.766	1	0.441	0.383	0.503	CLONAL	1	TRUE	1	0.510417653931557	3		253	346	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737115	162737115	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	230	474	0	ENST00000367921.3:c.1259T>C	p.Leu420Pro	p.L420P	ENST00000367921	NM_006182.2	420	cTc/cCc	11/18	0.510417653931557	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.510417653931557	3		474	517	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131231	202131232	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0038696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	106	490	0	ENST00000358485.4:c.200_201del	p.Tyr67Ter	p.Y67*	ENST00000358485	NM_001080125.1	67	TAt/t	2/9	1	2	FACETS	0.864	0.778	0.953	0.864	0.778	0.953	CLONAL	1	TRUE	1	0.510417653931557	2		490	481	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661765	227662331	+	inframe_deletion	In_Frame_Del	DEL	TGCCACCTCCTGGTGGGTAGGCAGGCATCATCTCTGTGTACTCCTCAATGGAAGCCACTGAGGACTGGGACGGGGTCTTCTGGTGGGTAATGGTAGGGGATGTGCCTGCCGAGTGAGTTCTCTTTCGGAACCGATTATCCAGATCTGCAGCACTGGCTGCTTCATCCCCAGCCAAGGCTGGACTCGTGCCCAAGCCTGTTCCTGGGGTGCAGCGGTGGCCATTGCCACCCCGAGACAAAATGTAGTGACCGTTGGGGGCGGTCAGGGTGGAGGGCCCCTTGCCACCCATGCAGATATAGTTGCTTAGCTCCTCCTCACCGCGGGCTGGTGGGGTGTGGCCCAGGGAATCCGGAGTGACACTGCGGAAGGAACTCCGGAAATCGCAGGGACTGGAGCCATACTCATCCGAGGAGATGAAACCGCCATCGCTGGGGGAACCAGACACCGAAGCACTAGATCGCCGTGGGAAGAGACAATCCGAGGTGGAGCCATGGCCACTGGTGCTACTGGACGACAGACTGACCGGGCTGGTGGCCGAAGGCGAGCAGCGGGAAGCCGGCATGGGGA	TGCCACCTCCTGGTGGGTAGGCAGGCATCATCTCTGTGTACTCCTCAATGGAAGCCACTGAGGACTGGGACGGGGTCTTCTGGTGGGTAATGGTAGGGGATGTGCCTGCCGAGTGAGTTCTCTTTCGGAACCGATTATCCAGATCTGCAGCACTGGCTGCTTCATCCCCAGCCAAGGCTGGACTCGTGCCCAAGCCTGTTCCTGGGGTGCAGCGGTGGCCATTGCCACCCCGAGACAAAATGTAGTGACCGTTGGGGGCGGTCAGGGTGGAGGGCCCCTTGCCACCCATGCAGATATAGTTGCTTAGCTCCTCCTCACCGCGGGCTGGTGGGGTGTGGCCCAGGGAATCCGGAGTGACACTGCGGAAGGAACTCCGGAAATCGCAGGGACTGGAGCCATACTCATCCGAGGAGATGAAACCGCCATCGCTGGGGGAACCAGACACCGAAGCACTAGATCGCCGTGGGAAGAGACAATCCGAGGTGGAGCCATGGCCACTGGTGCTACTGGACGACAGACTGACCGGGCTGGTGGCCGAAGGCGAGCAGCGGGAAGCCGGCATGGGGA	-	novel	NA	P-0038696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	182	848	0	ENST00000305123.5:c.1124_1690del	p.Ile375_Gly563del	p.I375_G563del	ENST00000305123	NM_005544.2	375	aTCCCCATGCCGGCTTCCCGCTGCTCGCCTTCGGCCACCAGCCCGGTCAGTCTGTCGTCCAGTAGCACCAGTGGCCATGGCTCCACCTCGGATTGTCTCTTCCCACGGCGATCTAGTGCTTCGGTGTCTGGTTCCCCCAGCGATGGCGGTTTCATCTCCTCGGATGAGTATGGCTCCAGTCCCTGCGATTTCCGGAGTTCCTTCCGCAGTGTCACTCCGGATTCCCTGGGCCACACCCCACCAGCCCGCGGTGAGGAGGAGCTAAGCAACTATATCTGCATGGGTGGCAAGGGGCCCTCCACCCTGACCGCCCCCAACGGTCACTACATTTTGTCTCGGGGTGGCAATGGCCACCGCTGCACCCCAGGAACAGGCTTGGGCACGAGTCCAGCCTTGGCTGGGGATGAAGCAGCCAGTGCTGCAGATCTGGATAATCGGTTCCGAAAGAGAACTCACTCGGCAGGCACATCCCCTACCATTACCCACCAGAAGACCCCGTCCCAGTCCTCAGTGGCTTCCATTGAGGAGTACACAGAGATGATGCCTGCCTACCCACCAGGAGGTGGCAgt/agt	1/2	0.510417653931557	2	FACETS	0.845	0.789	0.901	0.845	0.789	0.901	CLONAL	2	TRUE	0	0.510417653931557	2		848	422	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146590	55146590	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	132	521	1	ENST00000257290.5:c.2264C>A	p.Ser755Tyr	p.S755Y	ENST00000257290	NM_006206.4	755	tCc/tAc	16/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.510417653931557	2		522	478	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579400	7579400	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038696-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	193	882	0	ENST00000269305.4:c.287del	p.Ser96LeufsTer27	p.S96Lfs*27	ENST00000269305	NM_001126112.2	96	tCt/tt	4/11	0.244959144150541	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.244959144150541	1		882	1041	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380350	14380350	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038696-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	120	253	0	ENST00000256196.4:c.67G>T	p.Gly23Cys	p.G23C	ENST00000256196		23	Ggc/Tgc	1/6	1	2	FACETS	1	0.912	1	1	0.989	1	CLONAL	2	TRUE	1	0.244959144150541	2		253	488	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737115	162737115	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038696-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	176	474	0	ENST00000367921.3:c.1259T>C	p.Leu420Pro	p.L420P	ENST00000367921	NM_006182.2	420	cTc/cCc	11/18	0.210389517629332	3	FACETS	0.999	0.922	1	0.999	0.922	1	CLONAL	2	TRUE	1	0.244959144150541	3		474	807	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131231	202131232	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0038696-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	84	490	0	ENST00000358485.4:c.200_201del	p.Tyr67Ter	p.Y67*	ENST00000358485	NM_001080125.1	67	TAt/t	2/9	NA	2	FACETS	1	0.941	1			1	INDETERMINATE	1	TRUE	NA	0.244959144150541	2		490	622	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661765	227662331	+	inframe_deletion	In_Frame_Del	DEL	TGCCACCTCCTGGTGGGTAGGCAGGCATCATCTCTGTGTACTCCTCAATGGAAGCCACTGAGGACTGGGACGGGGTCTTCTGGTGGGTAATGGTAGGGGATGTGCCTGCCGAGTGAGTTCTCTTTCGGAACCGATTATCCAGATCTGCAGCACTGGCTGCTTCATCCCCAGCCAAGGCTGGACTCGTGCCCAAGCCTGTTCCTGGGGTGCAGCGGTGGCCATTGCCACCCCGAGACAAAATGTAGTGACCGTTGGGGGCGGTCAGGGTGGAGGGCCCCTTGCCACCCATGCAGATATAGTTGCTTAGCTCCTCCTCACCGCGGGCTGGTGGGGTGTGGCCCAGGGAATCCGGAGTGACACTGCGGAAGGAACTCCGGAAATCGCAGGGACTGGAGCCATACTCATCCGAGGAGATGAAACCGCCATCGCTGGGGGAACCAGACACCGAAGCACTAGATCGCCGTGGGAAGAGACAATCCGAGGTGGAGCCATGGCCACTGGTGCTACTGGACGACAGACTGACCGGGCTGGTGGCCGAAGGCGAGCAGCGGGAAGCCGGCATGGGGA	TGCCACCTCCTGGTGGGTAGGCAGGCATCATCTCTGTGTACTCCTCAATGGAAGCCACTGAGGACTGGGACGGGGTCTTCTGGTGGGTAATGGTAGGGGATGTGCCTGCCGAGTGAGTTCTCTTTCGGAACCGATTATCCAGATCTGCAGCACTGGCTGCTTCATCCCCAGCCAAGGCTGGACTCGTGCCCAAGCCTGTTCCTGGGGTGCAGCGGTGGCCATTGCCACCCCGAGACAAAATGTAGTGACCGTTGGGGGCGGTCAGGGTGGAGGGCCCCTTGCCACCCATGCAGATATAGTTGCTTAGCTCCTCCTCACCGCGGGCTGGTGGGGTGTGGCCCAGGGAATCCGGAGTGACACTGCGGAAGGAACTCCGGAAATCGCAGGGACTGGAGCCATACTCATCCGAGGAGATGAAACCGCCATCGCTGGGGGAACCAGACACCGAAGCACTAGATCGCCGTGGGAAGAGACAATCCGAGGTGGAGCCATGGCCACTGGTGCTACTGGACGACAGACTGACCGGGCTGGTGGCCGAAGGCGAGCAGCGGGAAGCCGGCATGGGGA	-	novel	NA	P-0038696-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	286	848	0	ENST00000305123.5:c.1124_1690del	p.Ile375_Gly563del	p.I375_G563del	ENST00000305123	NM_005544.2	375	aTCCCCATGCCGGCTTCCCGCTGCTCGCCTTCGGCCACCAGCCCGGTCAGTCTGTCGTCCAGTAGCACCAGTGGCCATGGCTCCACCTCGGATTGTCTCTTCCCACGGCGATCTAGTGCTTCGGTGTCTGGTTCCCCCAGCGATGGCGGTTTCATCTCCTCGGATGAGTATGGCTCCAGTCCCTGCGATTTCCGGAGTTCCTTCCGCAGTGTCACTCCGGATTCCCTGGGCCACACCCCACCAGCCCGCGGTGAGGAGGAGCTAAGCAACTATATCTGCATGGGTGGCAAGGGGCCCTCCACCCTGACCGCCCCCAACGGTCACTACATTTTGTCTCGGGGTGGCAATGGCCACCGCTGCACCCCAGGAACAGGCTTGGGCACGAGTCCAGCCTTGGCTGGGGATGAAGCAGCCAGTGCTGCAGATCTGGATAATCGGTTCCGAAAGAGAACTCACTCGGCAGGCACATCCCCTACCATTACCCACCAGAAGACCCCGTCCCAGTCCTCAGTGGCTTCCATTGAGGAGTACACAGAGATGATGCCTGCCTACCCACCAGGAGGTGGCAgt/agt	1/2	0.210389517629332	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.244959144150541	3		848	1137	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146590	55146590	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038696-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	106	521	1	ENST00000257290.5:c.2264C>A	p.Ser755Tyr	p.S755Y	ENST00000257290	NM_006206.4	755	tCc/tAc	16/23	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.244959144150541	2		522	744	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041072	29041072	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038696-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	61	572	0	ENST00000282397.4:c.356A>C	p.Glu119Ala	p.E119A	ENST00000282397	NM_002019.4	119	gAa/gCa	3/30	0.198274266870491	2	FACETS	0.613	0.527	0.706	0.306	0.263	0.353	SUBCLONAL	1	TRUE	0	0.244959144150541	2		572	813	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976443	18976443	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038696-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	197	912	0	ENST00000262803.5:c.3093C>G	p.Ser1031Arg	p.S1031R	ENST00000262803	NM_002911.3	1031	agC/agG	22/24	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.244959144150541	2		912	1340	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039385	49039385	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs794727372	NA	P-0038841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	317	543	0	ENST00000267163.4:c.2370C>A	p.Tyr790Ter	p.Y790*	ENST00000267163	NM_000321.2	790	taC/taA	23/27	0.727396931306068	2	FACETS	0.962	0.926	0.997	0.962	0.926	0.997	CLONAL	2	TRUE	0	0.727396931306068	2		543	453	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509422	149509422	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	292	639	0	ENST00000261799.4:c.1477A>T	p.Ser493Cys	p.S493C	ENST00000261799	NM_002609.3	493	Agc/Tgc	10/23	0.727396931306068	2	FACETS	1	0.987	1	0.562	0.532	0.593	CLONAL	1	TRUE	0	0.727396931306068	2		639	714	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891549	76891549	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0038841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	194	163	0	ENST00000373344.5:c.4558-2A>G		p.X1520_splice	ENST00000373344	NM_000489.3	1520			0.693720466456055	2	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.727396931306068	2		163	232	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	91	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	1	0.259712176837908	2		126	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578281	7578281	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660254	NA	P-0038855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	141	486	0	ENST00000269305.4:c.568C>A	p.Pro190Thr	p.P190T	ENST00000269305	NM_001126112.2	190	Cct/Act	6/11	0.259712176837908	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	0	0.259712176837908	1		486	751	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254962	16254962	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	41	329	0	ENST00000375759.3:c.2227C>T	p.Gln743Ter	p.Q743*	ENST00000375759	NM_015001.2	743	Cag/Tag	11/15	1	2	FACETS	0.553	0.46	0.657	0.553	0.46	0.657	SUBCLONAL	1	FALSE	1	0.259712176837908	2		329	571	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881544	48881544	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0038855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	92	211	0	ENST00000267163.4:c.264+2T>C		p.X88_splice	ENST00000267163	NM_000321.2	88			0.21608224019278	2	FACETS	0.947	0.848	1	0.947	0.848	1	CLONAL	2	FALSE	0	0.259712176837908	2		211	374	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175987	176175987	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	48	234	0	ENST00000367669.3:c.128C>T	p.Ser43Leu	p.S43L	ENST00000367669	NM_022457.5	43	tCg/tTg	1/20	1	2	FACETS	0.78	0.66	0.912	0.78	0.66	0.912	CLONAL	1	FALSE	1	0.259712176837908	2		234	474	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051598	30051598	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	68	220	0	ENST00000338641.4:c.532C>T	p.Gln178Ter	p.Q178*	ENST00000338641	NM_000268.3	178	Cag/Tag	6/16	0.259712176837908	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	FALSE	0	0.259712176837908	1		220	419	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180076488	180076488	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs749884420	NA	P-0038855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	26	116	0	ENST00000261937.6:c.58G>T	p.Gly20Cys	p.G20C	ENST00000261937	NM_182925.4	20	Ggc/Tgc	1/30	0.259712176837908	1	FACETS	0.875	0.698	1	0.875	0.698	1	CLONAL	1	FALSE	0	0.259712176837908	1		116	199	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652034	36652035	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	138	609	0	ENST00000244741.5:c.159dup	p.Val54CysfsTer9	p.V54Cfs*9	ENST00000244741	NM_000389.4	52	-/T	2/3	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	FALSE	1	0.259712176837908	2		609	1054	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225896	53225896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	75	349	0	ENST00000375401.3:c.2953G>A	p.Glu985Lys	p.E985K	ENST00000375401	NM_004187.3	985	Gag/Aag	19/26	1	1	FACETS	0.959	0.842	1	0.959	0.842	1	CLONAL	1	FALSE	0	0.259712176837908	1		349	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0039051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	269	428	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.48677338377094	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.48677338377094	1		428	752	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997744	149997798	+	frameshift_variant	Frame_Shift_Del	DEL	TGTGCTAGACATCGCTGGTGCTGGCGTGCAGCTCTCCGCTCTAATGGCTTCAGTC	TGTGCTAGACATCGCTGGTGCTGGCGTGCAGCTCTCCGCTCTAATGGCTTCAGTC	-	novel	NA	P-0039051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	57	382	0	ENST00000253339.5:c.2669_2723del	p.Arg890IlefsTer49	p.R890Ifs*49	ENST00000253339		890	aGACTGAAGCCATTAGAGCGGAGAGCTGCACGCCAGCACCAGCGATGTCTAGCACAt/at	5/7	1	2	FACETS	0.42	0.361	0.486	0.42	0.361	0.486	SUBCLONAL	1	TRUE	1	0.48677338377094	2		382	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0039173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	54	467	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.88	0.75	1	0.88	0.75	1	CLONAL	1	TRUE	1	0.15	2		467	818	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	33	350	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.144322826263625	3	FACETS	1	0.91	1	0.603	0.491	0.729	CLONAL	1	TRUE	1	0.15	3		350	392	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553761	106553761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	73	379	4	ENST00000369096.4:c.1726G>A	p.Glu576Lys	p.E576K	ENST00000369096	NM_001198.3	576	Gaa/Aaa	5/7	0.144322826263625	3	FACETS	0.862	0.754	0.978	0.862	0.754	0.978	CLONAL	2	TRUE	1	0.15	3		383	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781288	NA	P-0039173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	106	794	0	ENST00000269305.4:c.422G>T	p.Cys141Phe	p.C141F	ENST00000269305	NM_001126112.2	141	tGc/tTc	5/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.15	2		794	1130	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175436	+	frameshift_variant	Frame_Shift_Del	DEL	GAGACCCCACT	GAGACCCCACT	-	novel	NA	P-0039173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	45	296	0	ENST00000257430.4:c.4135_4145del	p.Glu1379HisfsTer3	p.E1379Hfs*3	ENST00000257430	NM_000038.5	1379	GAGACCCCACTc/c	16/16	0.144322826263625	3	FACETS	1	0.885	1	1	0.885	1	CLONAL	2	TRUE	1	0.15	3		296	305	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593603	55593603	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913235	NA	P-0039199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	247	578	2	ENST00000288135.5:c.1669T>A	p.Trp557Arg	p.W557R	ENST00000288135	NM_000222.2	557	Tgg/Agg	11/21	1	2	FACETS	0.896	0.842	0.95	0.896	0.842	0.95	CLONAL	1	TRUE	1	0.813454249744509	2		580	678	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037932	49037933	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0039199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	15	228	0	ENST00000267163.4:c.2173_2174del	p.Val725AsnfsTer25	p.V725Nfs*25	ENST00000267163	NM_000321.2	724	atTGta/atta	21/27	1	2	FACETS	0.395	0.288	0.524	0.395	0.288	0.524	SUBCLONAL	1	FALSE	1	0.263624547537709	2		228	288	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647272	23647272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660851	NA	P-0039199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	48	489	0	ENST00000261584.4:c.595C>T	p.Leu199Phe	p.L199F	ENST00000261584	NM_024675.3	199	Ctt/Ttt	4/13	1	2	FACETS	0.58	0.489	0.68	0.58	0.489	0.68	SUBCLONAL	1	FALSE	1	0.263624547537709	2		489	628	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876455	35876455	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	52	457	0	ENST00000303115.3:c.1247C>G	p.Pro416Arg	p.P416R	ENST00000303115	NM_002185.3	416	cCc/cGc	8/8	1	2	FACETS	0.769	0.655	0.894	0.769	0.655	0.894	SUBCLONAL	1	FALSE	1	0.263624547537709	2		457	513	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434681	128434681	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039199-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	35	457	0	ENST00000265960.3:c.173A>C	p.Asn58Thr	p.N58T	ENST00000265960	NM_001006617.1	58	aAt/aCt	2/12	1	2	FACETS	0.511	0.418	0.615	0.511	0.418	0.615	SUBCLONAL	1	FALSE	1	0.263624547537709	2		457	520	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	110	877	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.934	0.839	1	1	0.987	1	CLONAL	2	TRUE	1	0.15	2		883	785	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	56	547	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.15	2		547	689	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	54	350	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.15	2		350	608	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	35	464	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.817	0.669	0.985	0.817	0.669	0.985	CLONAL	1	TRUE	1	0.15	2		464	571	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	31	461	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.796	0.643	0.971	0.796	0.643	0.971	CLONAL	1	TRUE	1	0.15	2		461	519	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670774	134670774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1435725610	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	47	463	0	ENST00000398015.3:c.685G>A	p.Ala229Thr	p.A229T	ENST00000398015	NM_004441.4	229	Gca/Aca	3/16	1	2	FACETS	0.963	0.811	1	0.963	0.811	1	CLONAL	1	TRUE	1	0.15	2		463	651	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	48	471	1	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.868	0.732	1	0.868	0.732	1	CLONAL	1	TRUE	1	0.15	2		472	737	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101751	71101751	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	24	219	0	ENST00000318789.4:c.447del	p.Lys149AsnfsTer57	p.K149Nfs*57	ENST00000318789	NM_032682.5	149	aaA/aa	9/21	1	2	FACETS	0.792	0.62	0.991	0.792	0.62	0.991	CLONAL	1	TRUE	1	0.15	2		219	404	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101327	27101327	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	55	597	1	ENST00000324856.7:c.4609C>T	p.Gln1537Ter	p.Q1537*	ENST00000324856	NM_006015.4	1537	Cag/Tag	18/20	1	2	FACETS	0.918	0.783	1	0.918	0.783	1	CLONAL	1	TRUE	1	0.15	2		598	799	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149250	119149250	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200341293	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	52	485	0	ENST00000264033.4:c.1258C>T	p.Arg420Ter	p.R420*	ENST00000264033	NM_005188.3	420	Cga/Tga	9/16	1	2	FACETS	0.918	0.78	1	0.918	0.78	1	CLONAL	1	TRUE	1	0.15	2		485	755	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137033	64137033	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759826654	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	56	537	1	ENST00000334205.4:c.1544C>T	p.Ser515Leu	p.S515L	ENST00000334205	NM_003942.2	515	tCg/tTg	13/17	1	2	FACETS	0.977	0.836	1	0.977	0.836	1	CLONAL	1	TRUE	1	0.15	2		538	764	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508673	106508673	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs554272230	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	37	518	0	ENST00000359195.3:c.667G>A	p.Val223Ile	p.V223I	ENST00000359195	NM_002649.2	223	Gtc/Atc	2/11	1	2	FACETS	0.672	0.552	0.807	0.672	0.552	0.807	SUBCLONAL	1	TRUE	1	0.15	2		518	734	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380973	116380973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	40	480	0	ENST00000397752.3:c.1595C>T	p.Ala532Val	p.A532V	ENST00000397752	NM_000245.2	532	gCc/gTc	5/21	1	2	FACETS	0.732	0.606	0.872	0.732	0.606	0.872	SUBCLONAL	1	TRUE	1	0.15	2		480	729	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778282	3778282	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	40	547	2	ENST00000262367.5:c.6766del	p.Leu2256SerfsTer46	p.L2256Sfs*46	ENST00000262367	NM_004380.2	2256	Ctc/tc	31/31	1	2	FACETS	0.72	0.596	0.858	0.72	0.596	0.858	SUBCLONAL	1	TRUE	1	0.15	2		549	741	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851687	134851687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	41	473	1	ENST00000398015.3:c.1093G>A	p.Ala365Thr	p.A365T	ENST00000398015	NM_004441.4	365	Gca/Aca	5/16	1	2	FACETS	0.842	0.7	1	0.842	0.7	1	CLONAL	1	TRUE	1	0.15	2		474	649	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184534	7184534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775222338	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	42	499	0	ENST00000302850.5:c.767G>A	p.Arg256His	p.R256H	ENST00000302850	NM_000208.2	256	cGc/cAc	3/22	1	2	FACETS	0.802	0.668	0.952	0.802	0.668	0.952	CLONAL	1	TRUE	1	0.15	2		499	698	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161277	56161277	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	24	285	0	ENST00000399503.3:c.1149del	p.Phe383LeufsTer53	p.F383Lfs*53	ENST00000399503	NM_005921.1	382	aaT/aa	5/20	1	2	FACETS	0.688	0.538	0.862	0.688	0.538	0.862	SUBCLONAL	1	TRUE	1	0.15	2		285	465	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604704	48604704	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1060500744	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	38	394	1	ENST00000342988.3:c.1529del	p.Gly510AspfsTer27	p.G510Dfs*27	ENST00000342988	NM_005359.5	509	tGg/tg	12/12	1	2	FACETS	0.881	0.727	1	0.881	0.727	1	CLONAL	1	TRUE	1	0.15	2		395	575	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921550	178921551	+	inframe_insertion	In_Frame_Ins	INS	-	-	AATGTA	novel	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	42	306	0	ENST00000263967.3:c.1036_1041dup	p.Val346_Asn347dup	p.V346_N347dup	ENST00000263967	NM_006218.2	346	-/AATGTA	5/21	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.15	2		306	482	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330639	65330639	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	29	309	0	ENST00000342505.4:c.1007del	p.Lys336ArgfsTer6	p.K336Rfs*6	ENST00000342505	NM_002227.2	336	aAg/ag	8/25	1	2	FACETS	0.811	0.65	0.994	0.811	0.65	0.994	CLONAL	1	TRUE	1	0.15	2		309	477	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11270909	11270909	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	55	385	0	ENST00000361445.4:c.3616C>A	p.His1206Asn	p.H1206N	ENST00000361445	NM_004958.3	1206	Cat/Aat	24/58	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.15	2		385	659	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258436	16258436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	48	567	0	ENST00000375759.3:c.5701C>T	p.Arg1901Cys	p.R1901C	ENST00000375759	NM_015001.2	1901	Cgc/Tgc	11/15	1	2	FACETS	0.75	0.632	0.881	0.75	0.632	0.881	SUBCLONAL	1	TRUE	1	0.15	2		567	853	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739048	46739049	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	44	469	0	ENST00000371975.4:c.1397_1398insCT	p.Lys466AsnfsTer43	p.K466Nfs*43	ENST00000371975	NM_003579.3	466	aag/aaCTg	13/18	1	2	FACETS	0.927	0.776	1	0.927	0.776	1	CLONAL	1	TRUE	1	0.15	2		469	633	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076800	102076800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768834182	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	60	679	0	ENST00000282441.5:c.979C>T	p.Arg327Trp	p.R327W	ENST00000282441	NM_001130145.2	327	Cgg/Tgg	5/9	1	2	FACETS	0.89	0.765	1	0.89	0.765	1	CLONAL	1	TRUE	1	0.15	2		679	899	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003481	42003481	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	41	512	0	ENST00000219905.7:c.3021del	p.Lys1007AsnfsTer15	p.K1007Nfs*15	ENST00000219905	NM_001164273.1	1006	ggA/gg	8/24	1	2	FACETS	0.8	0.665	0.952	0.8	0.665	0.952	CLONAL	1	TRUE	1	0.15	2		512	683	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832120	72832124	+	frameshift_variant	Frame_Shift_Del	DEL	TATGG	TATGG	-	novel	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	35	435	0	ENST00000268489.5:c.4457_4461del	p.Thr1486AsnfsTer3	p.T1486Nfs*3	ENST00000268489	NM_006885.3	1486	aCCATA/a	9/10	1	2	FACETS	0.735	0.601	0.886	0.735	0.601	0.886	SUBCLONAL	1	TRUE	1	0.15	2		435	635	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923799	72923799	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	49	613	0	ENST00000268489.5:c.3279C>A	p.Cys1093Ter	p.C1093*	ENST00000268489	NM_006885.3	1093	tgC/tgA	4/10	1	2	FACETS	0.895	0.756	1	0.895	0.756	1	CLONAL	1	TRUE	1	0.15	2		613	730	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341520	89341520	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	46	460	0	ENST00000301030.4:c.7550T>A	p.Leu2517Gln	p.L2517Q	ENST00000301030	NM_001256183.1	2517	cTa/cAa	10/13	1	2	FACETS	0.914	0.768	1	0.914	0.768	1	CLONAL	1	TRUE	1	0.15	2		460	671	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131218	17131219	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	62	640	0	ENST00000285071.4:c.233dup	p.Ser79ValfsTer21	p.S79Vfs*21	ENST00000285071	NM_144997.5	78	aag/aaAg	4/14	1	2	FACETS	0.898	0.773	1	0.898	0.773	1	CLONAL	1	TRUE	1	0.15	2		640	921	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118915	70118915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1469442385	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	61	592	1	ENST00000245479.2:c.487G>A	p.Val163Met	p.V163M	ENST00000245479	NM_000346.3	163	Gtg/Atg	2/3	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.15	2		593	778	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218423	1218423	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs757841535	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	44	508	0	ENST00000326873.7:c.298C>G	p.Gln100Glu	p.Q100E	ENST00000326873	NM_000455.4	100	Caa/Gaa	2/10	1	2	FACETS	0.801	0.67	0.947	0.801	0.67	0.947	CLONAL	1	TRUE	1	0.15	2		508	732	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602938	10602938	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	46	593	0	ENST00000171111.5:c.640G>T	p.Val214Leu	p.V214L	ENST00000171111	NM_203500.1	214	Gtg/Ttg	3/6	1	2	FACETS	0.768	0.645	0.904	0.768	0.645	0.904	CLONAL	1	TRUE	1	0.15	2		593	799	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032083	11032083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764885947	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	49	603	1	ENST00000327064.4:c.1648C>T	p.Arg550Trp	p.R550W	ENST00000327064	NM_199141.1	550	Cgg/Tgg	15/16	1	2	FACETS	0.86	0.726	1	0.86	0.726	1	CLONAL	1	TRUE	1	0.15	2		604	760	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661419	227661420	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	41	522	0	ENST00000305123.5:c.2035_2036delinsAG	p.Pro679Ser	p.P679S	ENST00000305123	NM_005544.2	679	CCc/AGc	1/2	1	2	FACETS	0.87	0.724	1	0.87	0.724	1	CLONAL	1	TRUE	1	0.15	2		522	628	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306593	41306593	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	64	584	0	ENST00000373198.4:c.1066T>C	p.Tyr356His	p.Y356H	ENST00000373198	NM_133170.3	356	Tat/Cat	7/32	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.15	2		584	774	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266017	41266017	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	20	233	0	ENST00000349496.5:c.14C>A	p.Ala5Asp	p.A5D	ENST00000349496	NM_001904.3	5	gCt/gAt	3/15	1	2	FACETS	0.747	0.571	0.954	0.747	0.571	0.954	CLONAL	1	TRUE	1	0.15	2		233	357	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164209	47164209	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	35	310	0	ENST00000409792.3:c.1917A>C	p.Glu639Asp	p.E639D	ENST00000409792	NM_014159.6	639	gaA/gaC	3/21	1	2	FACETS	0.839	0.687	1	0.839	0.687	1	CLONAL	1	TRUE	1	0.15	2		310	556	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138407716	138407716	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	27	307	0	ENST00000289153.2:c.2136+1G>T		p.X712_splice	ENST00000289153	NM_006219.2	712			1	2	FACETS	0.726	0.576	0.897	0.726	0.576	0.897	SUBCLONAL	1	TRUE	1	0.15	2		307	496	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902780	1902780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	59	543	0	ENST00000382891.5:c.399G>A	p.Met133Ile	p.M133I	ENST00000382891	NM_133335.3	133	atG/atA	2/22	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.15	2		543	770	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522451	187522451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	39	521	0	ENST00000441802.2:c.11612C>T	p.Ala3871Val	p.A3871V	ENST00000441802	NM_005245.3	3871	gCt/gTt	21/27	1	2	FACETS	0.72	0.595	0.86	0.72	0.595	0.86	SUBCLONAL	1	TRUE	1	0.15	2		521	722	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162886	38162886	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	54	531	0	ENST00000317025.8:c.2320del	p.Tyr774IlefsTer43	p.Y774Ifs*43	ENST00000317025	NM_023034.1	774	Tat/at	13/24	1	2	FACETS	0.823	0.701	0.957	0.823	0.701	0.957	CLONAL	1	TRUE	1	0.15	2		531	875	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922268	39922276	+	inframe_deletion	In_Frame_Del	DEL	CTGCACTGG	CTGCACTGG	-	novel	NA	P-0039294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	38	397	0	ENST00000378444.4:c.3896_3904del	p.Thr1299_Gly1302delinsSer	p.T1299_G1302delinsS	ENST00000378444	NM_001123385.1	1299	aCCAGTGCAGgc/agc	9/15	1	2	FACETS	0.839	0.692	1	0.839	0.692	1	CLONAL	1	TRUE	1	0.15	2		397	604	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711876	89711876	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	162	394	0	ENST00000371953.3:c.494G>A	p.Gly165Glu	p.G165E	ENST00000371953	NM_000314.4	165	gGa/gAa	6/9	0.505709676923984	2	FACETS	0.959	0.895	1	0.959	0.895	1	CLONAL	2	TRUE	0	0.505709676923984	2		394	334	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222726	5222726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779918003	NA	P-0039435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	271	462	1	ENST00000357368.4:c.3077G>A	p.Arg1026His	p.R1026H	ENST00000357368	NM_002850.3	1026	cGc/cAc	18/38	0.462404218529243	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.505709676923984	4		463	743	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572289	64572289	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs794728629	NA	P-0039435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	255	559	0	ENST00000312049.6:c.1351-1G>C		p.X451_splice	ENST00000312049	NM_130799.2	451			0.505709676923984	2	FACETS	0.934	0.883	0.984	0.934	0.883	0.984	CLONAL	2	TRUE	0	0.505709676923984	2		559	540	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288561	33288561	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	222	466	0	ENST00000374542.5:c.991G>C	p.Asp331His	p.D331H	ENST00000374542	NM_001141970.1	331	Gat/Cat	3/8	0.505709676923984	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.505709676923984	2		466	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0039467-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	248	467	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.85995443956103	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.85995443956103	1		467	300	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951156	48951156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060503078	NA	P-0039467-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	56	361	1	ENST00000267163.4:c.1318G>A	p.Glu440Lys	p.E440K	ENST00000267163	NM_000321.2	440	Gaa/Aaa	13/27	0.408794060230269	3	FACETS	0.991	0.863	1	0.495	0.431	0.563	INDETERMINATE	1	TRUE	1	0.85995443956103	3		362	188	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857968	9857968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779746293	NA	P-0039467-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	53	610	1	ENST00000330684.3:c.3433G>A	p.Val1145Met	p.V1145M	ENST00000330684	NM_001134407.1	1145	Gtg/Atg	13/13	0.539885081851208	1	FACETS	0.346	0.299	0.396	0.346	0.299	0.396	SUBCLONAL	1	TRUE	0	0.85995443956103	1		611	203	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420871	49420871	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555185969	NA	P-0039467-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	224	647	0	ENST00000301067.7:c.14878C>T	p.Arg4960Ter	p.R4960*	ENST00000301067	NM_003482.3	4960	Cga/Tga	48/54	0.30395450565125	4	FACETS	1	0.985	1	1	0.985	1	INDETERMINATE	2	TRUE	2	0.85995443956103	4		647	432	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390766	139390766	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039467-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	291	874	0	ENST00000277541.6:c.7425del	p.Val2476Ter	p.V2476*	ENST00000277541	NM_017617.3	2475	ccC/cc	34/34	0.359000518353809	1	FACETS	0.721	0.687	0.755	0.721	0.687	0.755	INDETERMINATE	1	TRUE	0	0.85995443956103	1		874	535	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732806	44732807	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039467-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	274	594	0	ENST00000377967.4:c.10dup	p.Cys4LeufsTer17	p.C4Lfs*17	ENST00000377967	NM_021140.2	3	-/T	1/29	0.85995443956103	1	FACETS	0.976	0.94	1	0.976	0.94	1	CLONAL	1	TRUE	0	0.85995443956103	1		594	372	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641653	12641653	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039467-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	41	384	0	ENST00000251849.4:c.988A>T	p.Ile330Phe	p.I330F	ENST00000251849	NM_002880.3	330	Att/Ttt	9/17	1	2	FACETS	0.226	0.188	0.269	0.226	0.188	0.269	SUBCLONAL	1	TRUE	1	0.85995443956103	2		384	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0039467-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	398	467	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.775321501934476	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.775321501934476	1		467	610	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951156	48951156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060503078	NA	P-0039467-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	165	361	1	ENST00000267163.4:c.1318G>A	p.Glu440Lys	p.E440K	ENST00000267163	NM_000321.2	440	Gaa/Aaa	13/27	1	2	FACETS	0.896	0.83	0.964	0.896	0.83	0.964	CLONAL	1	TRUE	1	0.775321501934476	2		362	475	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857968	9857968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779746293	NA	P-0039467-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	180	610	1	ENST00000330684.3:c.3433G>A	p.Val1145Met	p.V1145M	ENST00000330684	NM_001134407.1	1145	Gtg/Atg	13/13	0.48248326168484	1	FACETS	0.414	0.383	0.447	0.414	0.383	0.447	SUBCLONAL	1	TRUE	0	0.775321501934476	1		611	686	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420871	49420871	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555185969	NA	P-0039467-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	391	647	0	ENST00000301067.7:c.14878C>T	p.Arg4960Ter	p.R4960*	ENST00000301067	NM_003482.3	4960	Cga/Tga	48/54	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.775321501934476	2		647	950	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390766	139390766	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039467-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	456	874	0	ENST00000277541.6:c.7425del	p.Val2476Ter	p.V2476*	ENST00000277541	NM_017617.3	2475	ccC/cc	34/34	0.323765354895818	1	FACETS	0.658	0.63	0.687	0.658	0.63	0.687	INDETERMINATE	1	TRUE	0	0.775321501934476	1		874	1094	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732806	44732807	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039467-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	324	594	0	ENST00000377967.4:c.10dup	p.Cys4LeufsTer17	p.C4Lfs*17	ENST00000377967	NM_021140.2	3	-/T	1/29	0.775321501934476	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.775321501934476	1		594	507	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0039546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	95	389	1	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.644747781624736	2		390	248	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0039546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	121	363	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.869	0.791	0.95	0.869	0.791	0.95	CLONAL	1	TRUE	1	0.644747781624736	2		363	432	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560476	95560476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	201	404	0	ENST00000393063.1:c.5113G>A	p.Glu1705Lys	p.E1705K	ENST00000393063	NM_030621.3	1705	Gaa/Aaa	25/28	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.644747781624736	2		404	542	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624296	89624296	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786201995	NA	P-0039546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	164	396	0	ENST00000371953.3:c.70G>T	p.Asp24Tyr	p.D24Y	ENST00000371953	NM_000314.4	24	Gac/Tac	1/9	1	2	FACETS	0.923	0.853	0.996	0.923	0.853	0.996	CLONAL	1	TRUE	1	0.644747781624736	2		396	551	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916618	178916618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	71	280	0	ENST00000263967.3:c.5C>T	p.Pro2Leu	p.P2L	ENST00000263967	NM_006218.2	2	cCt/cTt	2/21	1	2	FACETS	0.922	0.816	1	0.922	0.816	1	CLONAL	1	TRUE	1	0.644747781624736	2		280	239	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717687	89717690	+	frameshift_variant	Frame_Shift_Del	DEL	TTCA	TTCA	-	novel	NA	P-0039546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	139	350	0	ENST00000371953.3:c.713_716del	p.Phe238CysfsTer17	p.F238Cfs*17	ENST00000371953	NM_000314.4	238	TTCAtg/tg	7/9	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.644747781624736	2		350	405	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680606	241680606	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	106	310	0	ENST00000366560.3:c.143A>T	p.Asn48Ile	p.N48I	ENST00000366560	NM_000143.3	48	aAt/aTt	2/10	0.644747781624736	4	FACETS	0.923	0.829	1	0.308	0.276	0.341	CLONAL	1	TRUE	1	0.644747781624736	4		310	586	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692944	89692944	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786202047	NA	P-0039546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	118	411	0	ENST00000371953.3:c.428G>A	p.Gly143Asp	p.G143D	ENST00000371953	NM_000314.4	143	gGc/gAc	5/9	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.644747781624736	2		411	322	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992795	72992805	+	stop_gained	Nonsense_Mutation	DEL	GAGGTAATGGG	GAGGTAATGGG	TA	novel	NA	P-0039546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	32	541	2	ENST00000268489.5:c.1240_1250delinsTA	p.Pro414_Ser417delinsTer	p.P414_S417delins*	ENST00000268489	NM_006885.3	414	CCCATTACCTCa/TAa	2/10	0.644747781624736	1	FACETS	0.141	0.114	0.171	0.141	0.114	0.171	SUBCLONAL	1	TRUE	0	0.644747781624736	1		543	478	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149679	202149679	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	167	471	0	ENST00000358485.4:c.1120C>A	p.Leu374Ile	p.L374I	ENST00000358485	NM_001080125.1	374	Ctc/Atc	8/9	1	2	FACETS	0.935	0.864	1	0.935	0.864	1	CLONAL	1	TRUE	1	0.644747781624736	2		471	554	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992797	72992805	+	inframe_deletion	In_Frame_Del	DEL	GGTAATGGG	GGTAATGGG	-	novel	NA	P-0039546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	31	530	0	ENST00000268489.5:c.1240_1248del	p.Pro414_Thr416del	p.P414_T416del	ENST00000268489	NM_006885.3	414	CCCATTACC/-	2/10	0.644747781624736	1	FACETS	0.139	0.112	0.169	0.139	0.112	0.169	SUBCLONAL	1	TRUE	0	0.644747781624736	1		530	470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578504	7578512	+	inframe_deletion	In_Frame_Del	DEL	AGGGCAGGT	AGGGCAGGT	-	novel	NA	P-0039563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	384	774	0	ENST00000269305.4:c.418_426del	p.Thr140_Pro142del	p.T140_P142del	ENST00000269305	NM_001126112.2	140	ACCTGCCCT/-	5/11	0.244126629755539	5	FACETS	0.985	0.941	1	0.788	0.753	0.823	CLONAL	4	TRUE	0	0.356038063811287	5		774	840	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0039632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	23	522	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		522	333	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	121	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.761	0.695	0.83	1	0.987	1	SUBCLONAL	2	TRUE	1	0.42838433727326	2		126	371	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0039664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	224	771	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.326969581773715	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.42838433727326	2		771	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0039664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	98	722	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.42838433727326	1	FACETS	0.512	0.457	0.571	0.512	0.457	0.571	SUBCLONAL	1	TRUE	0	0.42838433727326	1		724	702	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0039664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	99	853	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.42838433727326	1	FACETS	0.594	0.531	0.661	0.594	0.531	0.661	SUBCLONAL	1	TRUE	0	0.42838433727326	1		853	611	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398260	25398260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	56	404	0	ENST00000311936.3:c.59C>T	p.Thr20Met	p.T20M	ENST00000311936	NM_004985.3	20	aCg/aTg	2/5	NA	4	FACETS	0.999	0.859	1	0.499	0.429	0.575	INDETERMINATE	1	TRUE	2	0.42838433727326	4		404	374	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120460287	120460287	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0039664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	47	426	1	ENST00000256646.2:c.6027+1G>A		p.X2009_splice	ENST00000256646	NM_024408.3	2009			1	2	FACETS	0.378	0.319	0.444	0.378	0.319	0.444	SUBCLONAL	1	TRUE	1	0.42838433727326	2		427	580	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911561	134911561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757883750	NA	P-0039664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	65	519	0	ENST00000398015.3:c.2026G>A	p.Asp676Asn	p.D676N	ENST00000398015	NM_004441.4	676	Gac/Aac	11/16	1	2	FACETS	0.482	0.417	0.552	0.482	0.417	0.552	SUBCLONAL	1	TRUE	1	0.42838433727326	2		519	630	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396941	139396942	+	splice_acceptor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0039664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	189	256	0	ENST00000277541.6:c.5168-2dup		p.X1723_splice	ENST00000277541	NM_017617.3	1723			0.372439283610551	3	FACETS	0.995	0.936	1	0.995	0.936	1	CLONAL	3	TRUE	0	0.42838433727326	3		256	359	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112441	115112448	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCGACG	GGGCGACG	-	novel	NA	P-0039753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	147	601	0	ENST00000257566.3:c.1292_1299del	p.Ala431GlyfsTer5	p.A431Gfs*5	ENST00000257566	NM_016569.3	431	gCGTCGCCC/g	7/8	1	2	FACETS	0.909	0.831	0.99	0.909	0.831	0.99	CLONAL	1	TRUE	1	0.446747931601722	2		601	724	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263889	133263889	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	94	275	0	ENST00000320574.5:c.13A>T	p.Ser5Cys	p.S5C	ENST00000320574	NM_006231.2	5	Agc/Tgc	1/49	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.446747931601722	2		275	394	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950889	32950889	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0039753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	91	333	0	ENST00000380152.3:c.8715T>A	p.Tyr2905Ter	p.Y2905*	ENST00000380152		2905	taT/taA	21/27	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.446747931601722	2		333	390	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448386	56448387	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0039753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	104	791	0	ENST00000407977.2:c.259_260dup	p.Leu88ArgfsTer71	p.L88Rfs*71	ENST00000407977		87	ccg/ccCCg	3/10	0.446747931601722	1	FACETS	0.592	0.531	0.656	0.592	0.531	0.656	SUBCLONAL	1	TRUE	0	0.446747931601722	1		791	611	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242762	66242762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	57	272	0	ENST00000273854.3:c.1810G>A	p.Gly604Arg	p.G604R	ENST00000273854	NM_004439.5	604	Ggg/Agg	9/18	1	2	FACETS	0.942	0.815	1	0.942	0.815	1	CLONAL	1	TRUE	1	0.446747931601722	2		272	271	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11301616	11301616	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	196	627	0	ENST00000361445.4:c.1535G>C	p.Gly512Ala	p.G512A	ENST00000361445	NM_004958.3	512	gGa/gCa	10/58	0.376535838140881	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.376535838140881	1		627	771	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46270960	46270962	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0039782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	104	394	0	ENST00000371998.3:c.3088_3090del	p.Leu1030del	p.L1030del	ENST00000371998		1028	ccTCTt/cct	17/23	0.221904710025677	5	FACETS	1	0.948	1	0.366	0.327	0.407	INDETERMINATE	1	TRUE	2	0.376535838140881	5		394	788	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034909	42034909	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	194	507	0	ENST00000219905.7:c.4751del	p.Ser1584LeufsTer10	p.S1584Lfs*10	ENST00000219905	NM_001164273.1	1584	tCt/tt	15/24	0.271748423292784	3	FACETS	0.782	0.725	0.841	0.782	0.725	0.841	SUBCLONAL	2	TRUE	1	0.376535838140881	3		507	783	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10244936	10244936	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	181	694	1	ENST00000340748.4:c.4773G>T	p.Glu1591Asp	p.E1591D	ENST00000340748		1591	gaG/gaT	39/40	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.376535838140881	2		695	958	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14017054	14017054	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	47	344	0	ENST00000405192.2:c.233G>T	p.Ser78Ile	p.S78I	ENST00000405192	NM_001163147.1	78	aGt/aTt	5/12	1	2	FACETS	0.939	0.798	1	0.939	0.798	1	CLONAL	1	TRUE	1	0.376535838140881	2		344	266	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0039784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	100	523	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.265	0.236	0.295	0.265	0.236	0.295	SUBCLONAL	1	TRUE	1	0.91	2		523	830	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099928	157099929	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	58	360	0	ENST00000346085.5:c.865_866insA	p.Gly289GlufsTer246	p.G289Efs*246	ENST00000346085	NM_020732.3	289	ggg/gAgg	1/20	1	2	FACETS	0.208	0.178	0.241	0.208	0.178	0.241	SUBCLONAL	1	TRUE	1	0.91	2		360	612	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139438543	139438543	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	90	734	0	ENST00000277541.6:c.73T>C	p.Ser25Pro	p.S25P	ENST00000277541	NM_017617.3	25	Tcc/Ccc	2/34	1	2	FACETS	0.2	0.177	0.225	0.2	0.177	0.225	SUBCLONAL	1	TRUE	1	0.91	2		734	989	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0039804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	579	741	1	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.877829137895792	1	FACETS	0.969	0.945	0.992	0.969	0.945	0.992	CLONAL	1	TRUE	0	0.881116405458572	1		742	759	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303295	11303295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	539	1033	1	ENST00000361445.4:c.1288C>T	p.Arg430Cys	p.R430C	ENST00000361445	NM_004958.3	430	Cgt/Tgt	9/58	1	2	FACETS	0.86	0.825	0.895	0.86	0.825	0.895	CLONAL	1	TRUE	1	0.881116405458572	2		1034	1423	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556654	41556670	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGTGAGAAGTGTTTC	TCTGTGAGAAGTGTTTC	-	novel	NA	P-0039804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	159	601	1	ENST00000263253.7:c.3599_3615del	p.Phe1200Ter	p.F1200*	ENST00000263253	NM_001429.3	1200	tTCTGTGAGAAGTGTTTC/t	20/31	1	2	FACETS	0.56	0.515	0.607	0.56	0.515	0.607	SUBCLONAL	1	TRUE	1	0.881116405458572	2		602	644	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509612	106509612	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1353	436	807	0	ENST00000359195.3:c.1606C>A	p.Pro536Thr	p.P536T	ENST00000359195	NM_002649.2	536	Cct/Act	2/11	0.885739423355592	4	FACETS	1	0.976	1	0.347	0.33	0.365	CLONAL	1	TRUE	1	0.881116405458572	4		807	1789	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0039870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	163	382	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	1	2	FACETS	0.931	0.864	0.998	0.931	0.864	0.998	CLONAL	1	TRUE	1	0.85657633737034	2		382	409	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274794	123274794	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913478	NA	P-0039870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	312	669	0	ENST00000358487.5:c.1124A>G	p.Tyr375Cys	p.Y375C	ENST00000358487	NM_000141.4	375	tAc/tGc	9/18	0.85657633737034	2	FACETS	0.997	0.946	1	0.498	0.473	0.524	CLONAL	1	TRUE	0	0.85657633737034	2		669	731	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720650	89720650	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1257124719	NA	P-0039870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	269	316	0	ENST00000371953.3:c.802-1G>A		p.X268_splice	ENST00000371953	NM_000314.4	268			0.85657633737034	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.85657633737034	2		316	306	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159750	20159750	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	287	717	0	ENST00000379607.5:c.9G>T	p.Lys3Asn	p.K3N	ENST00000379607	NM_001412.3	3	aaG/aaT	1/7	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.85657633737034	2		717	648	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641019	3641019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113420526	NA	P-0039870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	531	1113	0	ENST00000294008.3:c.2620G>A	p.Gly874Ser	p.G874S	ENST00000294008	NM_032444.2	874	Ggc/Agc	12/15	1	2	FACETS	0.987	0.948	1	0.987	0.948	1	CLONAL	1	TRUE	1	0.85657633737034	2		1113	1256	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918160	50918160	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	372	1107	0	ENST00000440232.2:c.2477G>T	p.Cys826Phe	p.C826F	ENST00000440232	NM_002691.3	826	tGc/tTc	20/27	1	2	FACETS	0.998	0.952	1	0.998	0.952	1	CLONAL	1	TRUE	1	0.85657633737034	2		1107	870	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393207	393207	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	255	644	0	ENST00000380956.4:c.55del	p.Cys19AlafsTer10	p.C19Afs*10	ENST00000380956	NM_001195286.1	19	Tgc/gc	2/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.85657633737034	NA		644	644	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186501404	186501404	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764605841	NA	P-0039874-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	155	289	0	ENST00000323963.5:c.5C>G	p.Ser2Cys	p.S2C	ENST00000323963		2	tCt/tGt	1/11	1	2	FACETS	0.848	0.785	0.912	0.848	0.785	0.912	CLONAL	1	TRUE	1	0.898686244381089	2		289	407	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0039890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	333	771	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.544817504152974	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.609903953587333	2		771	493	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633223	12633223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	240	672	0	ENST00000251849.4:c.1177G>A	p.Glu393Lys	p.E393K	ENST00000251849	NM_002880.3	393	Gag/Aag	11/17	0.50527138134873	2	FACETS	0.805	0.761	0.849	0.805	0.761	0.849	CLONAL	2	TRUE	0	0.609903953587333	2		672	489	SUCCESS
AR	367	MSKCC	GRCh37	X	66942818	66942818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137852564	NA	P-0039890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	237	370	0	ENST00000374690.3:c.2599G>A	p.Val867Met	p.V867M	ENST00000374690	NM_000044.3	867	Gtg/Atg	7/8	0.569982984130186	2	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.609903953587333	2		370	348	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724409	112724410	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0039890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	150	769	1	ENST00000369452.4:c.293_294delinsTT	p.Arg98Leu	p.R98L	ENST00000369452	NM_007373.3	98	cGG/cTT	2/9	0.337945023377443	3	FACETS	0.97	0.889	1	0.485	0.444	0.527	INDETERMINATE	1	TRUE	1	0.609903953587333	3		770	662	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434578	99434578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199789940	NA	P-0039890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	174	719	1	ENST00000268035.6:c.665G>A	p.Arg222Gln	p.R222Q	ENST00000268035	NM_000875.3	222	cGg/cAg	3/21	0.609903953587333	3	FACETS	1	0.946	1	0.516	0.476	0.557	CLONAL	1	TRUE	1	0.609903953587333	3		720	722	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943766	9943766	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	216	776	0	ENST00000330684.3:c.1175G>C	p.Arg392Thr	p.R392T	ENST00000330684	NM_001134407.1	392	aGg/aCg	5/13	0.58316344931436	2	FACETS	0.849	0.802	0.897	0.849	0.802	0.897	CLONAL	2	TRUE	0	0.609903953587333	2		776	417	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031971	10031971	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	238	889	1	ENST00000330684.3:c.852G>T	p.Trp284Cys	p.W284C	ENST00000330684	NM_001134407.1	284	tgG/tgT	3/13	0.58316344931436	2	FACETS	0.883	0.836	0.929	0.883	0.836	0.929	CLONAL	2	TRUE	0	0.609903953587333	2		890	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576896	7576897	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	326	874	0	ENST00000269305.4:c.949dup	p.Gln317ProfsTer20	p.Q317Pfs*20	ENST00000269305	NM_001126112.2	317	cag/cCag	9/11	0.58316344931436	2	FACETS	0.811	0.773	0.849	0.811	0.773	0.849	CLONAL	2	TRUE	0	0.609903953587333	2		874	659	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362496	40362496	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	360	758	0	ENST00000293328.3:c.1700A>T	p.Asn567Ile	p.N567I	ENST00000293328	NM_012448.3	567	aAt/aTt	14/19	0.50473038807256	3	FACETS	0.901	0.858	0.944	0.901	0.858	0.944	CLONAL	2	TRUE	1	0.609903953587333	3		758	855	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11015647	11015647	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0039890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	297	717	0	ENST00000327064.4:c.241A>T	p.Lys81Ter	p.K81*	ENST00000327064	NM_199141.1	81	Aag/Tag	2/16	0.544817504152974	2	FACETS	0.982	0.939	1	0.982	0.939	1	CLONAL	2	TRUE	0	0.609903953587333	2		717	496	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918169	50918169	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	225	1033	0	ENST00000440232.2:c.2486T>C	p.Leu829Pro	p.L829P	ENST00000440232	NM_002691.3	829	cTg/cCg	20/27	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.609903953587333	2		1033	674	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131291	202131291	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	398	583	0	ENST00000358485.4:c.259G>T	p.Asp87Tyr	p.D87Y	ENST00000358485	NM_001080125.1	87	Gac/Tac	2/9	0.603698380571818	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.609903953587333	2		583	625	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306685	41306685	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	208	909	0	ENST00000373198.4:c.974T>A	p.Val325Glu	p.V325E	ENST00000373198	NM_133170.3	325	gTg/gAg	7/32	0.546609648983682	3	FACETS	1	0.991	1	0.702	0.655	0.75	CLONAL	1	TRUE	1	0.609903953587333	3		909	634	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732947	30732947	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	229	516	0	ENST00000295754.5:c.1560C>A	p.Cys520Ter	p.C520*	ENST00000295754	NM_003242.5	520	tgC/tgA	7/7	0.50527138134873	2	FACETS	0.991	0.941	1	0.991	0.941	1	CLONAL	2	TRUE	0	0.609903953587333	2		516	379	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138382852	138382852	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	188	592	0	ENST00000289153.2:c.2692A>G	p.Ile898Val	p.I898V	ENST00000289153	NM_006219.2	898	Att/Gtt	19/22	0.609903953587333	6	FACETS	1	0.99	1	0.369	0.341	0.398	CLONAL	1	TRUE	2	0.609903953587333	6		592	927	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687097	176687097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	139	648	0	ENST00000439151.2:c.5074C>T	p.His1692Tyr	p.H1692Y	ENST00000439151	NM_022455.4	1692	Cac/Tac	14/23	1	2	FACETS	0.735	0.671	0.802	0.735	0.671	0.802	SUBCLONAL	1	TRUE	1	0.609903953587333	2		648	620	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707755	176707755	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0039890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	246	647	1	ENST00000439151.2:c.5812A>T	p.Lys1938Ter	p.K1938*	ENST00000439151	NM_022455.4	1938	Aag/Tag	18/23	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.609903953587333	2		648	677	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528619	157528619	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0039890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	156	926	0	ENST00000346085.5:c.6344T>G	p.Leu2115Ter	p.L2115*	ENST00000346085	NM_020732.3	2115	tTa/tGa	20/20	0.337945023377443	3	FACETS	1	0.953	1	0.526	0.484	0.571	INDETERMINATE	1	TRUE	1	0.609903953587333	3		926	634	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129929	69129929	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	173	518	1	ENST00000288368.4:c.4683G>T	p.Gln1561His	p.Q1561H	ENST00000288368	NM_024870.2	1561	caG/caT	38/40	0.497807154957782	4	FACETS	1	0.976	1	0.574	0.529	0.62	CLONAL	1	TRUE	2	0.609903953587333	4		519	796	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981522	70981522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	205	1113	1	ENST00000276594.2:c.574C>T	p.Pro192Ser	p.P192S	ENST00000276594	NM_024504.3	192	Cct/Tct	2/8	0.497807154957782	4	FACETS	0.845	0.782	0.91	0.422	0.391	0.455	CLONAL	1	TRUE	2	0.609903953587333	4		1114	1281	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633390	8633390	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	233	636	0	ENST00000356435.5:c.279G>T	p.Glu93Asp	p.E93D	ENST00000356435		93	gaG/gaT	3/35	0.544817504152974	2	FACETS	0.878	0.831	0.925	0.878	0.831	0.925	CLONAL	2	TRUE	0	0.609903953587333	2		636	435	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028689	12028689	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0039898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	165	325	0	ENST00000353533.5:c.891+1G>C		p.X297_splice	ENST00000353533	NM_003010.3	297			0.504364727622208	2	FACETS	0.988	0.924	1	0.988	0.924	1	CLONAL	2	TRUE	0	0.504364727622208	2		325	331	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858168	152858168	+	synonymous_variant	Silent	SNP	G	G	A	rs1557026101	NA	P-0039898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	177	727	1	ENST00000406277.2:c.447C>T	p.Ser149=	p.S149=	ENST00000406277	NM_152274.4	149	tcC/tcT	6/7	0.462866916024527	5	FACETS	0.991	0.911	1	0.33	0.303	0.359	CLONAL	1	TRUE	2	0.504364727622208	5		728	1244	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0039906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	92	545	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.201432151831889	2		545	646	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0039906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	22	400	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.149538805141822	1	FACETS	0.574	0.445	0.725	0.574	0.445	0.725	SUBCLONAL	1	TRUE	0	0.201432151831889	1		400	342	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955592	55955592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560674167	NA	P-0039906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	47	394	2	ENST00000263923.4:c.3353G>A	p.Arg1118Gln	p.R1118Q	ENST00000263923	NM_002253.2	1118	cGa/cAa	25/30	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.201432151831889	2		396	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578473	7578473	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064795860	NA	P-0039906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	154	720	1	ENST00000269305.4:c.457C>T	p.Pro153Ser	p.P153S	ENST00000269305	NM_001126112.2	153	Ccc/Tcc	5/11	0.201432151831889	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.201432151831889	1		721	1001	SUCCESS
APC	324	MSKCC	GRCh37	5	112175799	112175799	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0039906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	20	230	0	ENST00000257430.4:c.4508C>G	p.Ser1503Ter	p.S1503*	ENST00000257430	NM_000038.5	1503	tCa/tGa	16/16	0.149538805141822	1	FACETS	0.597	0.457	0.762	0.597	0.457	0.762	SUBCLONAL	1	TRUE	0	0.201432151831889	1		230	299	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	365	350	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.393206047562544	6	FACETS	0.904	0.861	0.948	0.904	0.861	0.948	CLONAL	4	FALSE	2	0.393206047562544	6		350	917	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0039944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	116	248	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.393206047562544	4	FACETS	1	0.975	1	0.312	0.282	0.345	CLONAL	1	FALSE	0	0.393206047562544	4		248	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0039944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	373	523	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.357808444490861	3	FACETS	0.839	0.799	0.879	0.839	0.799	0.879	CLONAL	3	FALSE	0	0.393206047562544	3		523	902	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0039944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	237	328	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.393206047562544	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	FALSE	2	0.393206047562544	4		328	785	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858493	9858493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765257420	NA	P-0039944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	134	466	1	ENST00000330684.3:c.2908C>T	p.Arg970Trp	p.R970W	ENST00000330684	NM_001134407.1	970	Cgg/Tgg	13/13	0.393206047562544	4	FACETS	1	0.94	1	0.523	0.475	0.574	CLONAL	1	FALSE	2	0.393206047562544	4		467	908	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	360001	360001	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs771361430	NA	P-0039944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	156	583	0	ENST00000262320.3:c.1088A>G	p.Asn363Ser	p.N363S	ENST00000262320	NM_003502.3	363	aAt/aGt	4/11	0.393206047562544	4	FACETS	0.859	0.784	0.937	0.429	0.392	0.469	CLONAL	1	FALSE	2	0.393206047562544	4		583	1287	SUCCESS
APC	324	MSKCC	GRCh37	5	112175641	112175641	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	100	306	0	ENST00000257430.4:c.4350del	p.Glu1451LysfsTer22	p.E1451Kfs*22	ENST00000257430	NM_000038.5	1450	cgA/cg	16/16	0.393206047562544	4	FACETS	1	0.938	1	0.535	0.478	0.595	CLONAL	1	FALSE	2	0.393206047562544	4		306	662	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873545	151873545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	493	512	0	ENST00000262189.6:c.8993C>T	p.Ser2998Leu	p.S2998L	ENST00000262189	NM_170606.2	2998	tCa/tTa	38/59	0.393206047562544	6	FACETS	0.988	0.949	1	0.988	0.949	1	CLONAL	4	FALSE	2	0.393206047562544	6		512	1133	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98222017	98222017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	145	423	0	ENST00000331920.6:c.2752G>A	p.Ala918Thr	p.A918T	ENST00000331920	NM_000264.3	918	Gct/Act	17/24	0.28258382034892	5	FACETS	1	0.987	1			1	CLONAL	1	FALSE	NA	0.393206047562544	5		423	791	SUCCESS
AR	367	MSKCC	GRCh37	X	66863193	66863193	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	58	260	0	ENST00000374690.3:c.1712A>C	p.His571Pro	p.H571P	ENST00000374690	NM_000044.3	571	cAc/cCc	2/8	0.393206047562544	4	FACETS	0.525	0.45	0.607			1	SUBCLONAL	1	FALSE	NA	0.393206047562544	4		260	783	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582237	52582237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779331178	NA	P-0039996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	19	276	0	ENST00000394830.3:c.4591G>A	p.Val1531Ile	p.V1531I	ENST00000394830	NM_018313.4	1531	Gtc/Atc	30/30	0.437844712475713	2	FACETS	0.344	0.261	0.441	0.172	0.13	0.221	SUBCLONAL	1	TRUE	0	0.445046471913963	2		276	248	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577074	7577075	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTCTC	novel	NA	P-0039996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	267	693	0	ENST00000269305.4:c.859_863dup	p.Asn288LysfsTer59	p.N288Kfs*59	ENST00000269305	NM_001126112.2	288	aat/aaGAGAAt	8/11	0.402135682361569	2	FACETS	0.985	0.932	1	0.985	0.932	1	CLONAL	2	TRUE	0	0.445046471913963	2		693	609	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0040028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	57	414	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.309326597895963	2		414	302	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482843	67482843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	57	534	0	ENST00000327367.4:c.1247C>T	p.Ser416Phe	p.S416F	ENST00000327367	NM_005902.3	416	tCc/tTc	9/9	0.206422085191559	2	FACETS	0.624	0.535	0.721	0.312	0.267	0.361	SUBCLONAL	1	TRUE	0	0.309326597895963	2		534	591	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510850	120510850	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	55	284	0	ENST00000256646.2:c.1114C>G	p.Leu372Val	p.L372V	ENST00000256646	NM_024408.3	372	Ctg/Gtg	7/34	0.309326597895963	3	FACETS	1	0.959	1	0.664	0.572	0.764	CLONAL	1	TRUE	1	0.309326597895963	3		284	309	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138375009	138375009	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0040028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	48	359	0	ENST00000289153.2:c.3050C>G	p.Ser1017Ter	p.S1017*	ENST00000289153	NM_006219.2	1017	tCa/tGa	21/22	1	2	FACETS	0.732	0.62	0.855	0.732	0.62	0.855	SUBCLONAL	1	TRUE	1	0.309326597895963	2		359	424	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0040031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	28	245	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.879	0.702	1	0.879	0.702	1	CLONAL	1	TRUE	1	0.14	2		245	455	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443864	52443864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	52	778	1	ENST00000460680.1:c.31G>A	p.Asp11Asn	p.D11N	ENST00000460680	NM_004656.3	11	Gac/Aac	1/17	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.14	2		779	695	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375220	15375220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs913018426	NA	P-0040031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	34	496	0	ENST00000263377.2:c.1207A>G	p.Ile403Val	p.I403V	ENST00000263377	NM_058243.2	403	Atc/Gtc	6/20	1	2	FACETS	0.934	0.762	1	0.934	0.762	1	CLONAL	1	TRUE	1	0.14	2		496	520	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0040083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	634	476	0	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	0.329314610461597	7	FACETS	0.948	0.919	0.976			1	CLONAL	7	TRUE	NA	0.329314610461597	7		476	1058	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993861	72993861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756319969	NA	P-0040083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	94	508	0	ENST00000268489.5:c.184G>A	p.Ala62Thr	p.A62T	ENST00000268489	NM_006885.3	62	Gcg/Acg	2/10	0.235567690777726	4	FACETS	0.983	0.874	1	0.492	0.437	0.55	CLONAL	1	TRUE	2	0.329314610461597	4		508	772	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185195165	185195165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	49	306	0	ENST00000265026.3:c.2482G>A	p.Glu828Lys	p.E828K	ENST00000265026	NM_004721.4	828	Gaa/Aaa	12/14	0.329314610461597	7	FACETS	0.661	0.558	0.775	0.165	0.139	0.194	SUBCLONAL	1	TRUE	3	0.329314610461597	7		306	821	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170046	32170046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768387019	NA	P-0040083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1366	174	954	0	ENST00000375023.3:c.3562G>A	p.Asp1188Asn	p.D1188N	ENST00000375023	NM_004557.3	1188	Gat/Aat	21/30	0.29632699308358	4	FACETS	0.912	0.837	0.991	0.456	0.418	0.496	CLONAL	1	TRUE	2	0.329314610461597	4		954	1540	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202721	108202721	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	70	315	0	ENST00000278616.4:c.7745G>T	p.Arg2582Ile	p.R2582I	ENST00000278616	NM_000051.3	2582	aGa/aTa	52/63	0.329314610461597	2	FACETS	0.877	0.766	0.995	0.438	0.383	0.498	CLONAL	1	TRUE	0	0.329314610461597	2		315	485	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115484	8115846	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTAGACGGGGCTGTAATCTGGTAACTGTATGTATTTTAGTTCTTCAGTCCCTGGGAAGGAGACAGGAGAAGGTGGGAGGGAGGAAGGGGCCAGCTGAAATGGAAACAGATCCCTGATCCGGGGCGGTCAGTGGAACCCTTCTTGGTGTGCGAGAGCCTGTGCATTTCAGAGGCAGCAAAAAAGTAAAAAAAAAAAAAAAAAATTGATCTTTGTTTAGATTAACAGACCCCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGGCCGCCCTCTCCA	ACTAGACGGGGCTGTAATCTGGTAACTGTATGTATTTTAGTTCTTCAGTCCCTGGGAAGGAGACAGGAGAAGGTGGGAGGGAGGAAGGGGCCAGCTGAAATGGAAACAGATCCCTGATCCGGGGCGGTCAGTGGAACCCTTCTTGGTGTGCGAGAGCCTGTGCATTTCAGAGGCAGCAAAAAAGTAAAAAAAAAAAAAAAAAATTGATCTTTGTTTAGATTAACAGACCCCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGGCCGCCCTCTCCA	-	novel	NA	P-0040083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	147	25	1	ENST00000346208.3:c.1048-218_1192del		p.X350_splice	ENST00000346208		350		6/6	0.329314610461597	3	FACETS	1	0.99	1	1	0.995	1	CLONAL	6	TRUE	1	0.329314610461597	3		26	160	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514499	125514499	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	62	298	0	ENST00000428830.2:c.1194G>C	p.Glu398Asp	p.E398D	ENST00000428830	NM_001114121.2	398	gaG/gaC	11/14	NA	2	FACETS	0.983	0.853	1			1	INDETERMINATE	1	TRUE	NA	0.329314610461597	2		298	383	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990429	81990429	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1567549863	NA	P-0040083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	109	535	0	ENST00000359376.3:c.3700G>C	p.Glu1234Gln	p.E1234Q	ENST00000359376	NM_002661.3	1234	Gag/Cag	32/33	0.096608337210295	3	FACETS	0.833	0.747	0.924	0.416	0.373	0.462	INDETERMINATE	1	TRUE	1	0.329314610461597	3		535	926	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639025	176639025	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	130	610	0	ENST00000439151.2:c.3625C>T	p.Pro1209Ser	p.P1209S	ENST00000439151	NM_022455.4	1209	Cct/Tct	5/23	0.235567690777726	4	FACETS	1	0.932	1	0.518	0.469	0.57	CLONAL	1	TRUE	2	0.329314610461597	4		610	1013	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169207	32169207	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139568674	NA	P-0040083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	163	713	0	ENST00000375023.3:c.3826G>A	p.Glu1276Lys	p.E1276K	ENST00000375023	NM_004557.3	1276	Gag/Aag	22/30	0.29632699308358	4	FACETS	1	0.919	1	0.502	0.459	0.547	CLONAL	1	TRUE	2	0.329314610461597	4		713	1311	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868450	117868450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148308569	NA	P-0040083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	106	514	0	ENST00000297338.2:c.892C>T	p.Pro298Ser	p.P298S	ENST00000297338	NM_006265.2	298	Cca/Tca	8/14	0.29632699308358	4	FACETS	0.862	0.771	0.958	0.431	0.385	0.479	CLONAL	1	TRUE	2	0.329314610461597	4		514	993	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117870663	117870663	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	80	420	0	ENST00000297338.2:c.409C>T	p.Gln137Ter	p.Q137*	ENST00000297338	NM_006265.2	137	Cag/Tag	5/14	0.29632699308358	4	FACETS	0.931	0.819	1	0.465	0.409	0.525	CLONAL	1	TRUE	2	0.329314610461597	4		420	694	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0040096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	64	314	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.164511662422332	4	FACETS	0.972	0.842	1	0.486	0.421	0.557	INDETERMINATE	1	TRUE	2	0.29	4		314	586	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916728	178916728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	13	280	0	ENST00000263967.3:c.115G>A	p.Glu39Lys	p.E39K	ENST00000263967	NM_006218.2	39	Gag/Aag	2/21	0.164511662422332	4	FACETS	0.292	0.207	0.396	0.146	0.103	0.198	INDETERMINATE	1	TRUE	2	0.29	4		280	396	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79968073	79968073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760032154	NA	P-0040096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	69	357	0	ENST00000265081.6:c.803G>A	p.Arg268Gln	p.R268Q	ENST00000265081	NM_002439.4	268	cGa/cAa	5/24	1	2	FACETS	0.991	0.866	1	0.991	0.866	1	CLONAL	1	TRUE	1	0.29	2		357	480	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38506081	38506081	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	114	552	0	ENST00000254066.5:c.373C>G	p.His125Asp	p.H125D	ENST00000254066	NM_000964.3	125	Cac/Gac	4/9	0.205154077504821	3	FACETS	1	0.957	1			1	CLONAL	1	TRUE	NA	0.29	3		552	807	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016276	150016276	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	55	385	0	ENST00000253339.5:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000253339		144	Caa/Taa	2/7	0.303853907441127	2	FACETS	0.892	0.765	1	0.446	0.382	0.516	CLONAL	1	TRUE	0	0.29	2		385	425	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444393	50444393	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	40	329	0	ENST00000331340.3:c.323G>A	p.Gly108Glu	p.G108E	ENST00000331340	NM_006060.4	108	gGa/gAa	4/8	0.303853907441127	4	FACETS	0.584	0.485	0.696	0.195	0.161	0.232	SUBCLONAL	1	TRUE	1	0.29	4		329	609	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877996	151877996	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	31	316	0	ENST00000262189.6:c.6949C>T	p.Gln2317Ter	p.Q2317*	ENST00000262189	NM_170606.2	2317	Caa/Taa	36/59	0.303853907441127	2	FACETS	0.57	0.461	0.693	0.285	0.23	0.347	SUBCLONAL	1	TRUE	0	0.29	2		316	375	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222474	53222475	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0040096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	111	785	3	ENST00000375401.3:c.4357_4358delinsTT	p.Arg1453Leu	p.R1453L	ENST00000375401	NM_004187.3	1453	CGg/TTg	26/26	NA	2	FACETS	0.686	0.615	0.761			1	INDETERMINATE	1	TRUE	NA	0.29	2		788	1116	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354317	70354317	+	splice_donor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0040096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	86	804	0	ENST00000374080.3:c.4727+1del		p.X1576_splice	ENST00000374080		1576			0.259744798392595	3	FACETS	0.553	0.488	0.624	0.277	0.244	0.312	SUBCLONAL	1	TRUE	1	0.29	3		804	1227	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944665	32944665	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	139	375	0	ENST00000380152.3:c.8458del	p.Val2820Ter	p.V2820*	ENST00000380152		2820	Gta/ta	19/27	0.554156846238189	1	FACETS	0.97	0.893	1	0.97	0.893	1	CLONAL	1	TRUE	0	0.554156846238189	1		375	374	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556087	29556139	+	frameshift_variant	Frame_Shift_Del	DEL	CCATGTGAGTGGAGGAGGATCCATAGATTTGTCTGACACAGACTCCCTACAGG	CCATGTGAGTGGAGGAGGATCCATAGATTTGTCTGACACAGACTCCCTACAGG	-	novel	NA	P-0040119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	44	164	0	ENST00000356175.3:c.2454_2506del	p.His819MetfsTer28	p.H819Mfs*28	ENST00000356175	NM_000267.3	818	tcCCATGTGAGTGGAGGAGGATCCATAGATTTGTCTGACACAGACTCCCTACAGGaa/tcaa	21/57	0.554156846238189	1	FACETS	0.696	0.593	0.805	0.696	0.593	0.805	SUBCLONAL	1	TRUE	0	0.554156846238189	1		164	165	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156867	106156867	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	92	372	0	ENST00000380013.4:c.1768C>G	p.Leu590Val	p.L590V	ENST00000380013	NM_001127208.2	590	Ctt/Gtt	3/11	0.554156846238189	1	FACETS	0.674	0.604	0.748	0.674	0.604	0.748	SUBCLONAL	1	TRUE	0	0.554156846238189	1		372	356	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	209	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.768	0.722	0.814	1	0.993	1	SUBCLONAL	2	TRUE	1	0.6115509337605	2		126	445	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0040139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	802	1232	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	0.6115509337605	3	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.6115509337605	3		1232	1424	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235840	108235840	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	221	495	1	ENST00000278616.4:c.8882C>T	p.Thr2961Ile	p.T2961I	ENST00000278616	NM_000051.3	2961	aCc/aTc	62/63	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.6115509337605	2		496	624	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632653	3632653	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	404	828	2	ENST00000294008.3:c.5195G>T	p.Gly1732Val	p.G1732V	ENST00000294008	NM_032444.2	1732	gGt/gTt	15/15	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.6115509337605	2		830	1188	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808921	3808921	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	348	724	2	ENST00000262367.5:c.3303del	p.Tyr1102IlefsTer14	p.Y1102Ifs*14	ENST00000262367	NM_004380.2	1101	ctG/ct	17/31	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.6115509337605	2		726	858	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197719	123197720	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	58	241	0	ENST00000218089.9:c.1844dup	p.Ile616AspfsTer19	p.I616Dfs*19	ENST00000218089	NM_001042749.1	615	cag/cAag	20/35	1	1	FACETS	0.386	0.333	0.443	0.386	0.333	0.443	SUBCLONAL	1	TRUE	0	0.6115509337605	1		241	341	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	85	715	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.2	2		715	807	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	11	313	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	1	2	FACETS	0.261	0.179	0.363	0.261	0.179	0.363	SUBCLONAL	1	TRUE	1	0.2	2		313	422	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	42	255	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.779	0.65	0.923	0.779	0.65	0.923	CLONAL	1	TRUE	1	0.2	2		255	539	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	82	584	0	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.972	0.855	1	0.972	0.855	1	CLONAL	1	TRUE	1	0.2	2		584	844	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202627	67202627	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1028574404	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	60	466	5	ENST00000312629.5:c.1436G>A	p.Arg479His	p.R479H	ENST00000312629	NM_003952.2	479	cGt/cAt	15/15	1	2	FACETS	0.81	0.696	0.933	0.81	0.696	0.933	CLONAL	1	TRUE	1	0.2	2		471	741	SUCCESS
APC	324	MSKCC	GRCh37	5	112175675	112175676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	21	289	2	ENST00000257430.4:c.4393_4394dup	p.Ser1465ArgfsTer9	p.S1465Rfs*9	ENST00000257430	NM_000038.5	1462	aag/aAGag	16/16	1	2	FACETS	0.505	0.388	0.642	0.505	0.388	0.642	SUBCLONAL	1	TRUE	1	0.2	2		291	416	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	10	490	1	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.212	0.142	0.3	0.212	0.142	0.3	SUBCLONAL	1	TRUE	1	0.2	2		491	472	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	42	390	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	1	2	FACETS	0.625	0.521	0.741	0.625	0.521	0.741	SUBCLONAL	1	TRUE	1	0.2	2		390	672	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	36	441	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.713	0.585	0.856	0.713	0.585	0.856	SUBCLONAL	1	TRUE	1	0.2	2		441	505	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	34	329	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.634	0.517	0.766	0.634	0.517	0.766	SUBCLONAL	1	TRUE	1	0.2	2		329	536	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679547	86679547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	35	320	1	ENST00000274376.6:c.2708G>A	p.Arg903Gln	p.R903Q	ENST00000274376	NM_002890.2	903	cGa/cAa	21/25	1	2	FACETS	0.816	0.669	0.981	0.816	0.669	0.981	CLONAL	1	TRUE	1	0.2	2		321	429	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341448	70341448	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	107	309	1	ENST00000374080.3:c.883C>T	p.Arg295Cys	p.R295C	ENST00000374080		295	Cgc/Tgc	7/45	1	1	FACETS	1	0.961	1	1	0.989	1	CLONAL	2	TRUE	0	0.2	1		310	428	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100998	41100998	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772057709	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	74	533	2	ENST00000373198.4:c.1358G>A	p.Arg453His	p.R453H	ENST00000373198	NM_133170.3	453	cGc/cAc	8/32	1	2	FACETS	0.995	0.87	1	0.995	0.87	1	CLONAL	1	TRUE	1	0.2	2		535	744	SUCCESS
AR	367	MSKCC	GRCh37	X	66765117	66765117	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	56	255	0	ENST00000374690.3:c.129G>T	p.Glu43Asp	p.E43D	ENST00000374690	NM_000044.3	43	gaG/gaT	1/8	1	1	FACETS	0.897	0.775	1	1	0.975	1	CLONAL	2	TRUE	0	0.2	1		255	281	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029408	14029408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368830992	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	27	365	2	ENST00000311895.7:c.1619C>T	p.Ser540Leu	p.S540L	ENST00000311895	NM_005236.2	540	tCg/tTg	8/11	1	2	FACETS	0.513	0.407	0.635	0.513	0.407	0.635	SUBCLONAL	1	TRUE	1	0.2	2		367	526	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522274	157522274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567836947	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	41	506	0	ENST00000346085.5:c.4546G>A	p.Val1516Ile	p.V1516I	ENST00000346085	NM_020732.3	1516	Gtc/Atc	18/20	1	2	FACETS	0.533	0.443	0.634	0.533	0.443	0.634	SUBCLONAL	1	TRUE	1	0.2	2		506	769	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288851	33288851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs913125455	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	31	391	0	ENST00000374542.5:c.701G>A	p.Arg234His	p.R234H	ENST00000374542	NM_001141970.1	234	cGc/cAc	3/8	0.3	3	FACETS	0.605	0.488	0.737			1	SUBCLONAL	1	TRUE	NA	0.2	3		391	564	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856187	111856187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs73428142	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	29	340	1	ENST00000341259.2:c.238C>T	p.Arg80Cys	p.R80C	ENST00000341259	NM_005475.2	80	Cgc/Tgc	2/8	1	2	FACETS	0.679	0.545	0.832	0.679	0.545	0.832	SUBCLONAL	1	TRUE	1	0.2	2		341	427	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164862	36164862	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1273605678	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	110	711	3	ENST00000300305.3:c.1013C>T	p.Ala338Val	p.A338V	ENST00000300305		338	gCg/gTg	8/8	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.2	2		714	923	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872552	136872552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145335491	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	23	431	1	ENST00000241393.3:c.946G>A	p.Ala316Thr	p.A316T	ENST00000241393	NM_003467.2	316	Gca/Aca	2/2	1	2	FACETS	0.561	0.437	0.705	0.561	0.437	0.705	SUBCLONAL	1	TRUE	1	0.2	2		432	410	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393440	139393440	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs932710972	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	54	535	3	ENST00000277541.6:c.6091G>A	p.Ala2031Thr	p.A2031T	ENST00000277541	NM_017617.3	2031	Gcc/Acc	33/34	1	2	FACETS	0.682	0.581	0.793	0.682	0.581	0.793	SUBCLONAL	1	TRUE	1	0.2	2		538	792	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231576	5231576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	24	317	1	ENST00000357368.4:c.1900G>A	p.Ala634Thr	p.A634T	ENST00000357368	NM_002850.3	634	Gcc/Acc	14/38	1	2	FACETS	0.533	0.417	0.668	0.533	0.417	0.668	SUBCLONAL	1	TRUE	1	0.2	2		318	450	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458270	12458270	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	42	438	1	ENST00000287820.6:c.892del	p.Leu298CysfsTer38	p.L298Cfs*38	ENST00000287820	NM_015869.4	296	aCc/ac	6/7	0.3	2	FACETS	0.647	0.539	0.768			1	SUBCLONAL	1	TRUE	NA	0.2	2		439	649	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793332	139793332	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376801177	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	77	544	3	ENST00000247668.2:c.140C>T	p.Ala47Val	p.A47V	ENST00000247668	NM_021138.3	47	gCg/gTg	2/11	1	2	FACETS	0.948	0.831	1	0.948	0.831	1	CLONAL	1	TRUE	1	0.2	2		547	812	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	74	683	3	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.845	0.738	0.96	0.845	0.738	0.96	CLONAL	1	TRUE	1	0.2	2		686	876	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738359	190738359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143554211	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	26	269	2	ENST00000441310.2:c.2611C>T	p.Arg871Cys	p.R871C	ENST00000441310	NM_000534.4	871	Cgc/Tgc	12/13	1	2	FACETS	0.67	0.53	0.83	0.67	0.53	0.83	SUBCLONAL	1	TRUE	1	0.2	2		271	388	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445203	49445203	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	85	617	11	ENST00000301067.7:c.2263del	p.Arg755GlyfsTer175	p.R755Gfs*175	ENST00000301067	NM_003482.3	755	Cgg/gg	10/54	1	2	FACETS	0.928	0.819	1	0.928	0.819	1	CLONAL	1	TRUE	1	0.2	2		628	916	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426498	47426498	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372763934	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	69	242	2	ENST00000377045.4:c.841C>T	p.Arg281Trp	p.R281W	ENST00000377045	NM_001654.4	281	Cgg/Tgg	9/16	1	1	FACETS	0.761	0.666	0.863	1	0.974	1	SUBCLONAL	2	TRUE	0	0.2	1		244	408	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917680	151917680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	53	248	0	ENST00000262189.6:c.3640G>A	p.Val1214Met	p.V1214M	ENST00000262189	NM_170606.2	1214	Gtg/Atg	23/59	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.2	2		248	397	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713340	40713340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1272852268	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	70	483	5	ENST00000373198.4:c.4175G>A	p.Arg1392His	p.R1392H	ENST00000373198	NM_133170.3	1392	cGt/cAt	30/32	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.2	2		488	652	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730008	41730008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537531066	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	76	527	1	ENST00000242208.4:c.521G>A	p.Arg174His	p.R174H	ENST00000242208	NM_002192.2	174	cGc/cAc	3/3	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.2	2		528	702	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50138844	50138844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748655822	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	102	656	5	ENST00000246792.3:c.646G>A	p.Val216Ile	p.V216I	ENST00000246792	NM_006270.3	216	Gtc/Atc	6/6	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.2	2		661	1015	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163784	47163784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1313153861	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	48	326	0	ENST00000409792.3:c.2342C>T	p.Thr781Met	p.T781M	ENST00000409792	NM_014159.6	781	aCg/aTg	3/21	1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	1	0.2	2		326	480	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509756	187509756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376922855	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	28	236	0	ENST00000441802.2:c.13757C>T	p.Thr4586Met	p.T4586M	ENST00000441802	NM_005245.3	4586	aCg/aTg	27/27	1	2	FACETS	0.809	0.647	0.994	0.809	0.647	0.994	CLONAL	1	TRUE	1	0.2	2		236	346	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101923	11101923	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502063	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	111	574	3	ENST00000358026.2:c.1343G>A	p.Arg448His	p.R448H	ENST00000358026	NM_001128849.1	448	cGc/cAc	8/36	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.2	2		577	888	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245723	46245723	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	59	382	4	ENST00000334344.6:c.3817C>T	p.Arg1273Ter	p.R1273*	ENST00000334344	NM_152641.2	1273	Cga/Tga	15/21	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.2	2		386	557	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114701	108114701	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs372694758	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	23	305	1	ENST00000278616.4:c.518G>T	p.Arg173Met	p.R173M	ENST00000278616	NM_000051.3	173	aGg/aTg	6/63	1	2	FACETS	0.574	0.446	0.721	0.574	0.446	0.721	SUBCLONAL	1	TRUE	1	0.2	2		306	401	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905439	11905439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764237239	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	47	379	3	ENST00000396373.4:c.89C>T	p.Ser30Leu	p.S30L	ENST00000396373	NM_001987.4	30	tCg/tTg	2/8	1	2	FACETS	0.827	0.698	0.971	0.827	0.698	0.971	CLONAL	1	TRUE	1	0.2	2		382	568	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109650	115109650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751905018	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	92	640	1	ENST00000257566.3:c.2228C>T	p.Pro743Leu	p.P743L	ENST00000257566	NM_016569.3	743	cCg/cTg	8/8	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.2	2		641	861	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663439	29663439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	109	438	1	ENST00000356175.3:c.6032C>T	p.Ala2011Val	p.A2011V	ENST00000356175	NM_000267.3	2011	gCa/gTa	40/57	0.22037089075768	3	FACETS	0.865	0.778	0.958	0.865	0.778	0.958	CLONAL	2	TRUE	1	0.2	3		439	693	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665809	29665809	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	45	243	0	ENST00000356175.3:c.6844C>T	p.Pro2282Ser	p.P2282S	ENST00000356175	NM_000267.3	2282	Cca/Tca	45/57	0.22037089075768	3	FACETS	0.804	0.679	0.94	0.804	0.679	0.94	CLONAL	2	TRUE	1	0.2	3		243	308	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673791	37673791	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	73	459	0	ENST00000447079.4:c.2945T>C	p.Leu982Pro	p.L982P	ENST00000447079	NM_015083.1	982	cTa/cCa	10/14	0.22037089075768	3	FACETS	1	0.898	1	0.516	0.451	0.587	CLONAL	1	TRUE	1	0.2	3		459	778	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11022924	11022924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1377302649	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	88	625	0	ENST00000327064.4:c.623G>A	p.Arg208Gln	p.R208Q	ENST00000327064	NM_199141.1	208	cGg/cAg	5/16	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.2	2		625	878	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793025	33793025	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	10	141	0	ENST00000498907.2:c.296G>T	p.Gly99Val	p.G99V	ENST00000498907	NM_004364.3	99	gGc/gTc	1/1	1	2	FACETS	0.541	0.366	0.759	0.541	0.366	0.759	SUBCLONAL	1	TRUE	1	0.2	2		141	185	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902666	50902666	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752124373	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	98	625	3	ENST00000440232.2:c.241C>T	p.Arg81Trp	p.R81W	ENST00000440232	NM_002691.3	81	Cgg/Tgg	3/27	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.2	2		628	869	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919867	50919867	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs749159160	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	65	496	2	ENST00000440232.2:c.2954G>A	p.Arg985Gln	p.R985Q	ENST00000440232	NM_002691.3	985	cGg/cAg	24/27	1	2	FACETS	0.898	0.777	1	0.898	0.777	1	CLONAL	1	TRUE	1	0.2	2		498	724	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657068	47657068	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63751712	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	28	256	0	ENST00000233146.2:c.1264G>T	p.Glu422Ter	p.E422*	ENST00000233146	NM_000251.2	422	Gaa/Taa	7/16	1	2	FACETS	0.856	0.685	1	0.856	0.685	1	CLONAL	1	TRUE	1	0.2	2		256	327	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703591	47703591	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	72	514	1	ENST00000233146.2:c.2091T>G	p.Cys697Trp	p.C697W	ENST00000233146	NM_000251.2	697	tgT/tgG	13/16	1	2	FACETS	0.999	0.872	1	0.999	0.872	1	CLONAL	1	TRUE	1	0.2	2		515	721	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321546	62321546	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	104	616	2	ENST00000360203.5:c.2248C>T	p.Arg750Cys	p.R750C	ENST00000360203	NM_001283009.1	750	Cgt/Tgt	25/35	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.2	2		618	846	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391081	89391081	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	72	579	3	ENST00000336596.2:c.1147C>A	p.Leu383Ile	p.L383I	ENST00000336596	NM_005233.5	383	Ctc/Atc	5/17	1	2	FACETS	0.945	0.825	1	0.945	0.825	1	CLONAL	1	TRUE	1	0.2	2		582	762	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119585438	119585438	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1174225568	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	27	287	0	ENST00000316626.5:c.947G>A	p.Arg316Gln	p.R316Q	ENST00000316626		316	cGg/cAg	9/12	1	2	FACETS	0.783	0.623	0.965	0.783	0.623	0.965	CLONAL	1	TRUE	1	0.2	2		287	345	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007355	143007357	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs1357813195	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	41	263	0	ENST00000262992.4:c.2427_2429del	p.Leu810del	p.L810del	ENST00000262992	NM_001101669.1	809	ctCCTt/ctt	22/24	1	2	FACETS	0.976	0.814	1	0.976	0.814	1	CLONAL	1	TRUE	1	0.2	2		263	420	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534301	187534301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753059895	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	44	468	1	ENST00000441802.2:c.9425C>T	p.Thr3142Met	p.T3142M	ENST00000441802	NM_005245.3	3142	aCg/aTg	13/27	1	2	FACETS	0.642	0.537	0.759	0.642	0.537	0.759	SUBCLONAL	1	TRUE	1	0.2	2		469	685	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500554	149500554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	60	538	5	ENST00000261799.4:c.2483C>T	p.Ala828Val	p.A828V	ENST00000261799	NM_002609.3	828	gCg/gTg	18/23	1	2	FACETS	0.801	0.689	0.924	0.801	0.689	0.924	CLONAL	1	TRUE	1	0.2	2		543	749	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798544	32798544	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	62	528	0	ENST00000374899.4:c.1312G>T	p.Gly438Ter	p.G438*	ENST00000374899	NM_018833.2	438	Gga/Tga	8/12	1	2	FACETS	0.854	0.737	0.982	0.854	0.737	0.982	CLONAL	1	TRUE	1	0.2	2		528	726	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553776	106553776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs941078758	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	29	339	3	ENST00000369096.4:c.1741G>A	p.Ala581Thr	p.A581T	ENST00000369096	NM_001198.3	581	Gcc/Acc	5/7	1	2	FACETS	0.534	0.427	0.656	0.534	0.427	0.656	SUBCLONAL	1	TRUE	1	0.2	2		342	543	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752799	128752799	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs146971340	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	38	282	0	ENST00000377970.2:c.960T>A	p.His320Gln	p.H320Q	ENST00000377970	NM_002467.4	320	caT/caA	3/3	1	2	FACETS	0.876	0.724	1	0.876	0.724	1	CLONAL	1	TRUE	1	0.2	2		282	434	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740812	145740812	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773561522	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	44	576	0	ENST00000428558.2:c.1288C>T	p.Pro430Ser	p.P430S	ENST00000428558	NM_004260.3	430	Cct/Tct	7/22	1	2	FACETS	0.509	0.425	0.602	0.509	0.425	0.602	SUBCLONAL	1	TRUE	1	0.2	2		576	865	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249321	110249321	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	90	693	1	ENST00000374672.4:c.1252C>T	p.Arg418Ter	p.R418*	ENST00000374672	NM_004235.4	418	Cga/Tga	4/5	1	2	FACETS	0.965	0.854	1	0.965	0.854	1	CLONAL	1	TRUE	1	0.2	2		694	933	SUCCESS
AR	367	MSKCC	GRCh37	X	66765673	66765673	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	38	396	0	ENST00000374690.3:c.685A>G	p.Thr229Ala	p.T229A	ENST00000374690	NM_000044.3	229	Act/Gct	1/8	1	1	FACETS	0.737	0.609	0.88	0.737	0.609	0.88	SUBCLONAL	1	TRUE	0	0.2	1		396	464	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805589	46805589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	73	619	4	ENST00000290295.7:c.367C>T	p.Arg123Cys	p.R123C	ENST00000290295	NM_006361.5	123	Cgc/Tgc	1/2	0.22037089075768	3	FACETS	0.816	0.712	0.929	0.408	0.356	0.465	CLONAL	1	TRUE	1	0.2	3		623	984	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974652	21974676	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CTCCCGCTGCAGACCCTCTACCCAC	CTCCCGCTGCAGACCCTCTACCCAC	-	novel	NA	P-0040147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	57	447	2	ENST00000304494.5:c.150+1_150+25del		p.X50_splice	ENST00000304494	NM_000077.4	50			1	2	FACETS	0.991	0.851	1	0.991	0.851	1	CLONAL	1	TRUE	1	0.2	2		449	575	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040152-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	105	350	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.512347859602044	2	FACETS	0.82	0.748	0.892	0.82	0.748	0.892	CLONAL	2	TRUE	0	0.512347859602044	2		350	250	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0040152-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	184	707	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.512347859602044	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.512347859602044	1		707	498	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221161	5221161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs575201235	NA	P-0040152-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	203	914	3	ENST00000357368.4:c.3305G>A	p.Arg1102His	p.R1102H	ENST00000357368	NM_002850.3	1102	cGc/cAc	20/38	0.512347859602044	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.512347859602044	1		917	504	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573556	48573556	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040152-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	35	271	0	ENST00000342988.3:c.140T>C	p.Leu47Pro	p.L47P	ENST00000342988	NM_005359.5	47	cTg/cCg	2/12	0.512347859602044	1	FACETS	0.932	0.784	1	0.932	0.784	1	CLONAL	1	TRUE	0	0.512347859602044	1		271	109	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830786	72830786	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040152-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	156	751	0	ENST00000268489.5:c.5795T>A	p.Leu1932His	p.L1932H	ENST00000268489	NM_006885.3	1932	cTc/cAc	9/10	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.512347859602044	2		751	577	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974687	21974688	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCGG	novel	NA	P-0040152-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	143	569	0	ENST00000304494.5:c.139_140insCCGA	p.Arg47ThrfsTer74	p.R47Tfs*74	ENST00000304494	NM_000077.4	47	agg/aCCGAgg	1/3	0.512347859602044	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.512347859602044	1		569	396	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0040155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	82	389	1	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.972	0.867	1	0.972	0.867	1	CLONAL	1	TRUE	1	0.574005709676225	2		390	294	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0040155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	105	282	0	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	1	2	FACETS	0.884	0.797	0.974	0.884	0.797	0.974	CLONAL	1	TRUE	1	0.574005709676225	2		282	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1555525367	NA	P-0040155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	197	401	0	ENST00000269305.4:c.783-1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.574005709676225	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.574005709676225	1		401	487	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732912	44732912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	59	253	0	ENST00000377967.4:c.115C>T	p.Pro39Ser	p.P39S	ENST00000377967	NM_021140.2	39	Ccc/Tcc	1/29	0.449316538785551	2	FACETS	0.278	0.239	0.321			1	SUBCLONAL	1	TRUE	NA	0.574005709676225	2		253	739	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161690	56161690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	70	369	0	ENST00000399503.3:c.1187G>A	p.Arg396His	p.R396H	ENST00000399503	NM_005921.1	396	cGt/cAt	6/20	NA	2	FACETS	0.794	0.699	0.896			1	INDETERMINATE	1	TRUE	NA	0.574005709676225	2		369	307	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222467	2222467	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs768713660	NA	P-0040155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	218	575	0	ENST00000326181.6:c.661G>A	p.Asp221Asn	p.D221N	ENST00000326181	NM_032271.2	221	Gac/Aac	9/21	0.519635812514429	3	FACETS	1	0.948	1	0.511	0.475	0.548	CLONAL	1	TRUE	1	0.574005709676225	3		575	957	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573531	48573531	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	38	274	0	ENST00000342988.3:c.115G>C	p.Ala39Pro	p.A39P	ENST00000342988	NM_005359.5	39	Gca/Cca	2/12	0.559370308978406	1	FACETS	0.732	0.618	0.853	0.732	0.618	0.853	SUBCLONAL	1	TRUE	0	0.574005709676225	1		274	129	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277910	41277936	+	inframe_deletion	In_Frame_Del	DEL	AGGAAGCTGCAGAAGCTATTGAAGCTG	AGGAAGCTGCAGAAGCTATTGAAGCTG	-	novel	NA	P-0040155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	106	363	0	ENST00000349496.5:c.1877_1903del	p.Glu626_Glu634del	p.E626_E634del	ENST00000349496	NM_001904.3	625	aAGGAAGCTGCAGAAGCTATTGAAGCTGag/aag	12/15	1	2	FACETS	0.912	0.824	1	0.912	0.824	1	CLONAL	1	TRUE	1	0.574005709676225	2		363	405	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651520	52651520	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	69	384	0	ENST00000394830.3:c.1576T>G	p.Leu526Val	p.L526V	ENST00000394830	NM_018313.4	526	Tta/Gta	15/30	0.551413252884049	1	FACETS	0.678	0.597	0.762	0.678	0.597	0.762	SUBCLONAL	1	TRUE	0	0.574005709676225	1		384	253	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576519	67576519	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	56	257	0	ENST00000274335.5:c.798A>C	p.Glu266Asp	p.E266D	ENST00000274335		266	gaA/gaC	5/15	1	2	FACETS	0.848	0.735	0.968	0.848	0.735	0.968	CLONAL	1	TRUE	1	0.574005709676225	2		257	230	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683791	162683791	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	36	273	0	ENST00000366898.1:c.178G>T	p.Asp60Tyr	p.D60Y	ENST00000366898	NM_004562.2	60	Gac/Tac	3/12	0.574005709676225	3	FACETS	0.605	0.499	0.721	0.302	0.249	0.361	SUBCLONAL	1	TRUE	1	0.574005709676225	3		273	267	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636245	87636245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	461	450	0	ENST00000277120.3:c.2410G>A	p.Gly804Arg	p.G804R	ENST00000277120		804	Ggg/Agg	19/19	0.574005709676225	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.574005709676225	2		450	702	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0040198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	207	414	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.267858196238658	5	FACETS	1	0.988	1			1	INDETERMINATE	3	TRUE	NA	0.951855061908809	5		414	311	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0040198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	144	314	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.852	0.788	0.918	0.852	0.788	0.918	CLONAL	1	TRUE	1	0.951855061908809	2		314	355	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527817	157527817	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	270	760	2	ENST00000346085.5:c.5547del	p.Leu1850Ter	p.L1850*	ENST00000346085	NM_020732.3	1848	Ccc/cc	20/20	0.120566382196867	3	FACETS	1	0.983	1	0.552	0.52	0.585	INDETERMINATE	1	TRUE	1	0.951855061908809	3		762	758	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469779	157469779	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	424	1017	0	ENST00000346085.5:c.2573del	p.Ala858GlyfsTer56	p.A858Gfs*56	ENST00000346085	NM_020732.3	858	gCg/gg	9/20	0.120566382196867	3	FACETS	1	0.995	1	0.667	0.638	0.696	INDETERMINATE	1	TRUE	1	0.951855061908809	3		1017	986	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs886039483	NA	P-0040209-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	1139	667	0	ENST00000269305.4:c.376T>G	p.Tyr126Asp	p.Y126D	ENST00000269305	NM_001126112.2	126	Tac/Gac	5/11	0.486035462814808	4	FACETS	1	0.997	1	1	0.997	1	CLONAL	4	TRUE	0	0.486035462814808	4		667	1603	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194766	30194766	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370180862	NA	P-0040209-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	169	479	0	ENST00000331968.5:c.379G>A	p.Asp127Asn	p.D127N	ENST00000331968	NM_002742.2	127	Gat/Aat	2/18	0.106197060895378	5	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.486035462814808	5		479	887	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942661	48942661	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0040209-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	107	194	0	ENST00000267163.4:c.1050-2A>T		p.X350_splice	ENST00000267163	NM_000321.2	350			0.433509586948613	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.486035462814808	1		194	241	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028168	69028168	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0040209-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	122	411	0	ENST00000288368.4:c.3326+1G>T		p.X1109_splice	ENST00000288368	NM_024870.2	1109			0.486035462814808	5	FACETS	0.991	0.895	1	0.33	0.298	0.364	CLONAL	1	TRUE	2	0.486035462814808	5		411	876	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906420	32906421	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	T	novel	NA	P-0040209-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	103	278	0	ENST00000380152.3:c.805_806delinsT	p.Thr269TyrfsTer8	p.T269Yfs*8	ENST00000380152		269	ACa/Ta	10/27	0.486035462814808	5	FACETS	1	0.956	1	0.281	0.252	0.313	CLONAL	1	TRUE	1	0.486035462814808	5		278	651	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321379	65321379	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0121526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	68	424	0	ENST00000342505.4:c.1461G>C	p.Gln487His	p.Q487H	ENST00000342505	NM_002227.2	487	caG/caC	11/25	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	NA	1	0.230605092943367	2		424	546	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511412	66511595	+	splice_acceptor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	AACAAAATCTACTTAGAAAAAAATCCCTGTGAATCAGTTGTCTAATGAATTTAGCAAGTTAAATGCCAGATTGACATTTTGCTTTATAGTTTATACAAGCATGTGTGTGTTTTTTTCTCGCAGAGAACCATGGAGTCTGGCAGTACCGCCGCCAGTGAGGAGGCACGCAGCCTTCGAGAATGTG	AACAAAATCTACTTAGAAAAAAATCCCTGTGAATCAGTTGTCTAATGAATTTAGCAAGTTAAATGCCAGATTGACATTTTGCTTTATAGTTTATACAAGCATGTGTGTGTTTTTTTCTCGCAGAGAACCATGGAGTCTGGCAGTACCGCCGCCAGTGAGGAGGCACGCAGCCTTCGAGAATGTG	-	novel	NA	P-0040282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	84	85	0	ENST00000358598.2:c.-6-122_56del		p.X2_splice	ENST00000358598	NM_212471.2	2		2/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		85	146	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0040287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	36	389	1	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	TRUE	1	0.29	2		390	244	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	59	646	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.163281971564718	1	FACETS	0.725	0.625	0.834	0.725	0.625	0.834	INDETERMINATE	1	TRUE	0	0.29	1		646	480	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9786967	9786967	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	21	446	0	ENST00000377346.4:c.2998G>T	p.Asp1000Tyr	p.D1000Y	ENST00000377346	NM_005026.3	1000	Gac/Tac	24/24	1	2	FACETS	0.506	0.39	0.642	0.506	0.39	0.642	SUBCLONAL	1	TRUE	1	0.29	2		446	286	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984827	11984827	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	35	482	0	ENST00000353533.5:c.375del	p.Gln126LysfsTer2	p.Q126Kfs*2	ENST00000353533	NM_003010.3	125	Ggg/gg	3/11	0.163281971564718	1	FACETS	0.871	0.719	1	0.871	0.719	1	INDETERMINATE	1	TRUE	0	0.29	1		482	237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0040326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	177	549	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.19162748791651	2	FACETS	0.785	0.722	0.849	0.785	0.722	0.849	SUBCLONAL	2	TRUE	0	0.226289927334105	2		552	997	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793008	33793010	+	inframe_deletion	In_Frame_Del	DEL	CGC	CGC	-	rs780345232	NA	P-0040326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	11	121	0	ENST00000498907.2:c.311_313del	p.Gly104del	p.G104del	ENST00000498907	NM_004364.3	104	gGCGac/gac	1/1	1	2	FACETS	0.549	0.38	0.759	0.549	0.38	0.759	SUBCLONAL	1	TRUE	1	0.226289927334105	2		121	177	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879448	151879448	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	126	409	1	ENST00000262189.6:c.5497C>T	p.Gln1833Ter	p.Q1833*	ENST00000262189	NM_170606.2	1833	Cag/Tag	36/59	0.221601027120327	2	FACETS	0.95	0.863	1	0.95	0.863	1	CLONAL	2	TRUE	0	0.226289927334105	2		410	586	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0040347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	193	482	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.221302303591006	3	FACETS	1	0.984	1	0.755	0.711	0.8	INDETERMINATE	2	TRUE	0	0.610837027324073	3		482	364	SUCCESS
BLM	641	MSKCC	GRCh37	15	91290653	91290653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	26	253	0	ENST00000355112.3:c.31G>A	p.Glu11Lys	p.E11K	ENST00000355112	NM_000057.2	11	Gag/Aag	2/22	1	2	FACETS	0.205	0.162	0.255	0.205	0.162	0.255	SUBCLONAL	1	TRUE	1	0.610837027324073	2		253	415	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	67	441	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.34	2		441	287	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	251	877	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.97	1	1	0.995	1	CLONAL	2	TRUE	1	0.34	2		883	704	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	180	685	5	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.988	0.917	1	1	0.993	1	CLONAL	2	TRUE	1	0.34	2		690	536	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	98	409	4	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.848	0.764	0.935	1	0.985	1	CLONAL	2	TRUE	1	0.34	2		413	340	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258203	16258203	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763428386	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	231	271	0	ENST00000375759.3:c.5468G>A	p.Arg1823His	p.R1823H	ENST00000375759	NM_015001.2	1823	cGt/cAt	11/15	1	2	FACETS	1	0.947	1	1	0.995	1	CLONAL	2	TRUE	1	0.34	2		271	672	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264495	16264495	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	242	300	0	ENST00000375759.3:c.10698G>T	p.Arg3566Ser	p.R3566S	ENST00000375759	NM_015001.2	3566	agG/agT	13/15	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.34	2		300	631	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	175	644	1	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	0.95	0.881	1	1	0.993	1	CLONAL	2	TRUE	1	0.34	2		645	542	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099936	27099936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773264329	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	253	344	1	ENST00000324856.7:c.3815C>T	p.Ala1272Val	p.A1272V	ENST00000324856	NM_006015.4	1272	gCg/gTg	15/20	1	2	FACETS	1	0.964	1	1	0.995	1	CLONAL	2	TRUE	1	0.34	2		345	720	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	177	621	2	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.94	0.872	1	1	0.993	1	CLONAL	2	TRUE	1	0.34	2		623	554	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521525	46521525	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	240	372	0	ENST00000262741.5:c.883del	p.Met295Ter	p.M295*	ENST00000262741	NM_003629.3	295	Atg/tg	7/10	1	2	FACETS	1	0.978	1	1	0.995	1	CLONAL	2	TRUE	1	0.34	2		372	650	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156836707	156836707	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	299	333	0	ENST00000524377.1:c.365T>C	p.Leu122Pro	p.L122P	ENST00000524377	NM_002529.3	122	cTc/cCc	4/17	1	2	FACETS	1	0.982	1	1	0.996	1	CLONAL	2	TRUE	1	0.34	2		333	812	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	80	129	0	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	1	2	FACETS	0.96	0.858	1	1	0.985	1	CLONAL	2	TRUE	1	0.34	2		129	245	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136051	64136051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	214	279	0	ENST00000334205.4:c.1312G>A	p.Ala438Thr	p.A438T	ENST00000334205	NM_003942.2	438	Gca/Aca	11/17	1	2	FACETS	0.823	0.767	0.88	1	0.993	1	CLONAL	2	TRUE	1	0.34	2		279	765	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77043861	77043861	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	261	307	0	ENST00000356341.3:c.1465A>G	p.Lys489Glu	p.K489E	ENST00000356341	NM_002576.4	489	Aag/Gag	14/15	1	2	FACETS	0.996	0.937	1	1	0.995	1	CLONAL	2	TRUE	1	0.34	2		307	771	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998688	100998688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	236	323	0	ENST00000325455.5:c.1114G>A	p.Asp372Asn	p.D372N	ENST00000325455	NM_001202474.3	372	Gac/Aac	1/8	1	2	FACETS	0.859	0.804	0.916	1	0.994	1	CLONAL	2	TRUE	1	0.34	2		323	808	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999603	100999603	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	263	364	0	ENST00000325455.5:c.199del	p.Gln67ArgfsTer99	p.Q67Rfs*99	ENST00000325455	NM_001202474.3	67	Cag/ag	1/8	1	2	FACETS	0.979	0.921	1	1	0.995	1	CLONAL	2	TRUE	1	0.34	2		364	790	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114817	108114817	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786204543	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	70	377	2	ENST00000278616.4:c.640del	p.Ser214ProfsTer16	p.S214Pfs*16	ENST00000278616	NM_000051.3	212	Ttt/tt	6/63	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.34	2		379	275	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427309	49427309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs566069597	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	189	268	0	ENST00000301067.7:c.11179C>T	p.Arg3727Cys	p.R3727C	ENST00000301067	NM_003482.3	3727	Cgt/Tgt	39/54	1	2	FACETS	1	0.967	1	1	0.994	1	CLONAL	2	TRUE	1	0.34	2		268	523	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884755	111884755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772497470	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	218	262	0	ENST00000341259.2:c.844C>T	p.Arg282Trp	p.R282W	ENST00000341259	NM_005475.2	282	Cgg/Tgg	4/8	1	2	FACETS	0.946	0.884	1	1	0.994	1	CLONAL	2	TRUE	1	0.34	2		262	678	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562552	21562552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	34	56	0	ENST00000382592.4:c.1367C>T	p.Thr456Met	p.T456M	ENST00000382592	NM_014572.2	456	aCg/aTg	4/8	1	2	FACETS	0.752	0.626	0.888	1	0.952	1	SUBCLONAL	2	TRUE	1	0.34	2		56	133	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054027	42054027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1384151590	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	75	154	1	ENST00000219905.7:c.7489C>T	p.Arg2497Trp	p.R2497W	ENST00000219905	NM_001164273.1	2497	Cgg/Tgg	21/24	1	2	FACETS	1	0.943	1	1	0.985	1	CLONAL	2	TRUE	1	0.34	2		155	203	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500606	99500606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs909142461	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	176	266	0	ENST00000268035.6:c.4039G>A	p.Ala1347Thr	p.A1347T	ENST00000268035	NM_000875.3	1347	Gcc/Acc	21/21	1	2	FACETS	0.87	0.806	0.936	1	0.992	1	CLONAL	2	TRUE	1	0.34	2		266	595	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343595	343595	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	257	313	0	ENST00000262320.3:c.2079del	p.Thr694ProfsTer11	p.T694Pfs*11	ENST00000262320	NM_003502.3	693	ccC/cc	8/11	1	2	FACETS	0.959	0.902	1	1	0.995	1	CLONAL	2	TRUE	1	0.34	2		313	788	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	160	419	2	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.997	0.922	1	1	0.992	1	CLONAL	2	TRUE	1	0.34	2		421	472	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020478	14020478	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377014538	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	129	191	0	ENST00000311895.7:c.449G>A	p.Arg150His	p.R150H	ENST00000311895	NM_005236.2	150	cGc/cAc	3/11	1	2	FACETS	0.921	0.843	1	1	0.99	1	CLONAL	2	TRUE	1	0.34	2		191	412	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348899	89348899	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	298	424	1	ENST00000301030.4:c.4051A>G	p.Arg1351Gly	p.R1351G	ENST00000301030	NM_001256183.1	1351	Aga/Gga	9/13	1	2	FACETS	0.975	0.921	1	1	0.996	1	CLONAL	2	TRUE	1	0.34	2		425	899	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857933	89857933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780135578	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	208	242	0	ENST00000389301.3:c.1237C>T	p.Arg413Cys	p.R413C	ENST00000389301	NM_000135.2	413	Cgt/Tgt	14/43	1	2	FACETS	1	0.953	1	1	0.994	1	CLONAL	2	TRUE	1	0.34	2		242	597	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654820	29654820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786203416	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	96	159	1	ENST00000356175.3:c.5509G>A	p.Ala1837Thr	p.A1837T	ENST00000356175	NM_000267.3	1837	Gca/Aca	37/57	1	2	FACETS	0.866	0.78	0.956	1	0.986	1	CLONAL	2	TRUE	1	0.34	2		160	326	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245587	41245587	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357522	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	160	295	2	ENST00000357654.3:c.1961del	p.Lys654SerfsTer47	p.K654Sfs*47	ENST00000357654	NM_007294.3	654	aAg/ag	10/23	1	2	FACETS	0.794	0.731	0.858	1	0.99	1	SUBCLONAL	2	TRUE	1	0.34	2		297	593	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448310	56448310	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567880628	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	250	348	0	ENST00000407977.2:c.337C>T	p.Arg113Ter	p.R113*	ENST00000407977		113	Cga/Tga	3/10	1	2	FACETS	0.935	0.878	0.994	1	0.995	1	CLONAL	2	TRUE	1	0.34	2		348	786	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56339057	56339058	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	45	60	0	ENST00000348428.3:c.186dup	p.Ser63GlufsTer18	p.S63Efs*18	ENST00000348428	NM_006785.3	61	gcg/gcGg	1/17	1	2	FACETS	0.761	0.649	0.88	1	0.964	1	SUBCLONAL	2	TRUE	1	0.34	2		60	174	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251481	10251482	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	228	312	2	ENST00000340748.4:c.3450dup	p.Leu1151ValfsTer12	p.L1151Vfs*12	ENST00000340748		1150	-/G	31/40	1	2	FACETS	0.903	0.844	0.962	1	0.994	1	CLONAL	2	TRUE	1	0.34	2		314	743	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952243	17952243	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	218	314	0	ENST00000458235.1:c.1097del	p.Pro366ArgfsTer99	p.P366Rfs*99	ENST00000458235	NM_000215.3	366	cCg/cg	8/24	1	2	FACETS	0.881	0.822	0.941	1	0.993	1	CLONAL	2	TRUE	1	0.34	2		314	728	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793082	33793082	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	156	151	0	ENST00000498907.2:c.239A>G	p.Asp80Gly	p.D80G	ENST00000498907	NM_004364.3	80	gAc/gGc	1/1	1	2	FACETS	1	0.947	1	1	0.992	1	CLONAL	2	TRUE	1	0.34	2		151	445	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219700	36219700	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	236	302	0	ENST00000222270.7:c.4601del	p.Pro1534HisfsTer112	p.P1534Hfs*112	ENST00000222270	NM_014727.1	1533	Ccc/cc	20/37	1	2	FACETS	0.934	0.875	0.994	1	0.994	1	CLONAL	2	TRUE	1	0.34	2		302	743	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	268	590	0	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.971	0.914	1	1	0.995	1	CLONAL	2	TRUE	1	0.34	2		590	812	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131403	202131403	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	130	240	0	ENST00000358485.4:c.371T>C	p.Leu124Pro	p.L124P	ENST00000358485	NM_001080125.1	124	cTg/cCg	2/9	1	2	FACETS	0.859	0.785	0.936	1	0.989	1	CLONAL	2	TRUE	1	0.34	2		240	445	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394039	31394039	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	29	196	0	ENST00000328111.2:c.2326A>G	p.Thr776Ala	p.T776A	ENST00000328111	NM_006892.3	776	Acc/Gcc	22/23	1	2	FACETS	0.333	0.266	0.408	0.333	0.266	0.408	SUBCLONAL	1	TRUE	1	0.34	2		196	513	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279864	46279866	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	rs112826888	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	99	198	4	ENST00000371998.3:c.3792_3794del	p.Gln1276del	p.Q1276del	ENST00000371998		1264	CAA/-	20/23	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.34	2		202	536	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72873690	72873690	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1217408412	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	35	180	0	ENST00000325599.8:c.612del	p.Phe204LeufsTer10	p.F204Lfs*10	ENST00000325599	NM_018130.2	204	ttT/tt	6/11	1	2	FACETS	0.811	0.678	0.953	1	0.959	1	CLONAL	2	TRUE	1	0.34	2		180	127	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	222	708	8	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	1	2	FACETS	0.902	0.843	0.962	1	0.994	1	CLONAL	2	TRUE	1	0.34	2		716	724	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197444	106197444	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1316795626	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	102	149	0	ENST00000380013.4:c.5777G>A	p.Arg1926His	p.R1926H	ENST00000380013	NM_001127208.2	1926	cGt/cAt	11/11	1	2	FACETS	0.943	0.854	1	1	0.988	1	CLONAL	2	TRUE	1	0.34	2		149	318	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542414	187542414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	111	204	0	ENST00000441802.2:c.5326G>A	p.Glu1776Lys	p.E1776K	ENST00000441802	NM_005245.3	1776	Gaa/Aaa	10/27	1	2	FACETS	0.98	0.892	1	1	0.989	1	CLONAL	2	TRUE	1	0.34	2		204	333	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970914	79970915	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587776701	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	85	270	1	ENST00000265081.6:c.1148dup	p.Asn385GlnfsTer19	p.N385Qfs*19	ENST00000265081	NM_002439.4	380	-/A	7/24	1	2	FACETS	0.76	0.678	0.846	1	0.98	1	SUBCLONAL	2	TRUE	1	0.34	2		271	329	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80160739	80160739	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	122	233	0	ENST00000265081.6:c.3108G>T	p.Glu1036Asp	p.E1036D	ENST00000265081	NM_002439.4	1036	gaG/gaT	22/24	1	2	FACETS	0.922	0.842	1	1	0.989	1	CLONAL	2	TRUE	1	0.34	2		233	389	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564679	86564680	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1425668686	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	201	307	0	ENST00000274376.6:c.416dup	p.Pro140SerfsTer18	p.P140Sfs*18	ENST00000274376	NM_002890.2	137	-/C	1/25	1	2	FACETS	0.786	0.731	0.843	1	0.992	1	SUBCLONAL	2	TRUE	1	0.34	2		307	752	SUCCESS
APC	324	MSKCC	GRCh37	5	112137078	112137078	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1554076217	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	114	156	0	ENST00000257430.4:c.832C>T	p.Gln278Ter	p.Q278*	ENST00000257430	NM_000038.5	278	Cag/Tag	8/16	1	2	FACETS	1	0.949	1	1	0.99	1	CLONAL	2	TRUE	1	0.34	2		156	317	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	110	393	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.901	0.818	0.987	1	0.988	1	CLONAL	2	TRUE	1	0.34	2		393	359	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944381	131944382	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs748536322	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	29	105	2	ENST00000265335.6:c.2801dup	p.Asn934LysfsTer10	p.N934Kfs*10	ENST00000265335		931	-/A	17/25	1	2	FACETS	0.797	0.654	0.952	1	0.949	1	CLONAL	2	TRUE	1	0.34	2		107	107	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056466	26056466	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs760631461	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	76	129	0	ENST00000343677.2:c.191A>G	p.Lys64Arg	p.K64R	ENST00000343677	NM_005319.3	64	aAa/aGa	1/1	1	2	FACETS	0.86	0.764	0.96	1	0.982	1	CLONAL	2	TRUE	1	0.34	2		129	260	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910346	29910346	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	206	351	0	ENST00000376809.5:c.19del	p.Arg7GlufsTer13	p.R7Efs*13	ENST00000376809	NM_002116.7	6	Ccc/cc	1/8	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.34	2		351	898	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910741	29910741	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs199474449	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	265	353	0	ENST00000376809.5:c.281A>G	p.Gln94Arg	p.Q94R	ENST00000376809	NM_002116.7	94	cAg/cGg	2/8	1	2	FACETS	0.993	0.935	1	1	0.995	1	CLONAL	2	TRUE	1	0.34	2		353	785	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940280	31940280	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	239	291	0	ENST00000375333.2:c.422G>A	p.Gly141Asp	p.G141D	ENST00000375333	NM_032454.1	141	gGt/gAt	2/8	1	2	FACETS	1	0.942	1	1	0.995	1	CLONAL	2	TRUE	1	0.34	2		291	700	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188297	32188297	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs753855314	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	249	353	2	ENST00000375023.3:c.1044del	p.Gly349AlafsTer49	p.G349Afs*49	ENST00000375023	NM_004557.3	348	ggC/gg	6/30	1	2	FACETS	0.973	0.913	1	1	0.995	1	CLONAL	2	TRUE	1	0.34	2		355	753	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	268	648	2	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	1	0.944	1	1	0.995	1	CLONAL	2	TRUE	1	0.34	2		650	786	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982082	70982082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	196	244	0	ENST00000276594.2:c.14G>A	p.Arg5Gln	p.R5Q	ENST00000276594	NM_024504.3	5	cGg/cAg	2/8	0.296868855150074	4	FACETS	1	0.979	1	0.755	0.702	0.81	CLONAL	2	TRUE	1	0.34	4		244	682	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752893	128752893	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	95	254	0	ENST00000377970.2:c.1054A>G	p.Ser352Gly	p.S352G	ENST00000377970	NM_002467.4	352	Agc/Ggc	3/3	0.296868855150074	4	FACETS	0.812	0.722	0.909	0.271	0.24	0.303	CLONAL	1	TRUE	1	0.34	4		254	922	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGG	novel	NA	P-0040355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	168	406	0	ENST00000220592.5:c.1804_1806dup	p.Pro602dup	p.P602dup	ENST00000220592	NM_012154.3	602	-/CCC	14/19	0.296868855150074	4	FACETS	1	0.971	1	0.375	0.344	0.408	CLONAL	1	TRUE	1	0.34	4		406	1177	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0040365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	207	549	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.518695469856016	2	FACETS	0.94	0.888	0.992	0.94	0.888	0.992	CLONAL	2	FALSE	0	0.595012829528129	2		552	370	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17349197	17349197	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	34	324	0	ENST00000375499.3:c.671A>T	p.Asp224Val	p.D224V	ENST00000375499	NM_003000.2	224	gAt/gTt	7/8	0.35774586373387	4	FACETS	0.502	0.411	0.605	0.251	0.205	0.303	SUBCLONAL	1	FALSE	2	0.595012829528129	4		324	363	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0040367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	124	523	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.459136178053779	1	FACETS	0.933	0.85	1	0.933	0.85	1	CLONAL	1	TRUE	0	0.459136178053779	1		523	446	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462655	40462655	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	29	319	0	ENST00000345506.4:c.2353C>G	p.Leu785Val	p.L785V	ENST00000345506	NM_003152.3	785	Ctt/Gtt	20/20	0.459136178053779	1	FACETS	0.233	0.186	0.286	0.233	0.186	0.286	SUBCLONAL	1	TRUE	0	0.459136178053779	1		319	418	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224351	36224351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	48	527	2	ENST00000222270.7:c.6901G>A	p.Asp2301Asn	p.D2301N	ENST00000222270	NM_014727.1	2301	Gat/Aat	28/37	0.459136178053779	3	FACETS	0.308	0.259	0.361	0.154	0.129	0.181	SUBCLONAL	1	TRUE	1	0.459136178053779	3		529	836	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922657	44922689	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTTGACAGATGAGACCAACAGGAGTTGCACA	TTTTTGACAGATGAGACCAACAGGAGTTGCACA	-	novel	NA	P-0040367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	44	164	0	ENST00000377967.4:c.1528-10_1550del		p.X510_splice	ENST00000377967	NM_021140.2	510		16/29	0.40203372557016	1	FACETS	0.773	0.657	0.898	0.773	0.657	0.898	SUBCLONAL	1	TRUE	0	0.459136178053779	1		164	191	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0040442-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	286	467	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.50467809652029	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.513710001507353	1		467	823	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224456	123224456	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040442-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	193	213	0	ENST00000218089.9:c.3309G>A	p.Trp1103Ter	p.W1103*	ENST00000218089	NM_001042749.1	1103	tgG/tgA	31/35	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.513710001507353	1		213	402	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	70	612	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	0.335	0.291	0.382	0.335	0.291	0.382	SUBCLONAL	1	TRUE	1	0.462415165146474	2		612	905	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578528	7578528	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	345	1024	0	ENST00000269305.4:c.402T>G	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	ttT/ttG	5/11	0.462415165146474	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.462415165146474	1		1024	1126	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929133	44929133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	199	674	1	ENST00000377967.4:c.2233G>A	p.Glu745Lys	p.E745K	ENST00000377967	NM_021140.2	745	Gag/Aag	17/29	0.462415165146474	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.462415165146474	1		675	655	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140507833	140507833	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	116	473	0	ENST00000288602.6:c.638A>G	p.Asp213Gly	p.D213G	ENST00000288602	NM_004333.4	213	gAt/gGt	5/18	1	2	FACETS	0.914	0.827	1	0.914	0.827	1	CLONAL	1	TRUE	1	0.462415165146474	2		473	549	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0040495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	41	414	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.300808392449087	1	FACETS	0.828	0.693	0.976	0.828	0.693	0.976	CLONAL	1	TRUE	0	0.29	1		414	292	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172272	99172272	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs374507988	NA	P-0040495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	48	509	0	ENST00000074304.5:c.1837+1G>A		p.X613_splice	ENST00000074304	NM_001134224.1	613			1	2	FACETS	0.609	0.514	0.713	0.609	0.514	0.713	SUBCLONAL	1	TRUE	1	0.29	2		509	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579442	7579443	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0040495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	102	812	0	ENST00000269305.4:c.243_244dup	p.Pro82HisfsTer42	p.P82Hfs*42	ENST00000269305	NM_001126112.2	82	ccg/cACcg	4/11	0.166112108953427	2	FACETS	0.801	0.716	0.892	0.401	0.358	0.446	INDETERMINATE	1	TRUE	0	0.29	2		812	878	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577047	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTGGTGA	novel	NA	P-0040554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	421	527	0	ENST00000269305.4:c.885_891dup	p.Glu298SerfsTer10	p.E298Sfs*10	ENST00000269305	NM_001126112.2	297	-/TCACCAC	8/11	0.673303838163477	2	FACETS	0.881	0.848	0.913	0.881	0.848	0.913	CLONAL	2	TRUE	0	0.675902782389604	2		527	707	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0040572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	446	549	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.484172815539946	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.492502258923674	2		552	890	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	244	350	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.492502258923674	3	FACETS	0.959	0.902	1	0.959	0.902	1	CLONAL	2	TRUE	1	0.492502258923674	3		350	644	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	131	569	0	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	0.492502258923674	3	FACETS	0.852	0.774	0.935	0.426	0.387	0.468	CLONAL	1	TRUE	1	0.492502258923674	3		569	778	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106238	27106238	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	410	700	0	ENST00000324856.7:c.5850del	p.Asn1951ThrfsTer5	p.N1951Tfs*5	ENST00000324856	NM_006015.4	1950	cGg/cg	20/20	0.484172815539946	2	FACETS	0.995	0.953	1	0.995	0.953	1	CLONAL	2	TRUE	0	0.492502258923674	2		700	837	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740258	162740258	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	72	490	0	ENST00000367921.3:c.1460T>C	p.Leu487Pro	p.L487P	ENST00000367921	NM_006182.2	487	cTg/cCg	12/18	0.492502258923674	3	FACETS	0.53	0.462	0.602	0.265	0.231	0.301	SUBCLONAL	1	TRUE	1	0.492502258923674	3		490	688	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175729	176175729	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	194	853	0	ENST00000367669.3:c.386A>G	p.Asp129Gly	p.D129G	ENST00000367669	NM_022457.5	129	gAc/gGc	1/20	0.492502258923674	3	FACETS	0.829	0.766	0.895	0.415	0.383	0.448	CLONAL	1	TRUE	1	0.492502258923674	3		853	1184	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910797	32910797	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	230	426	1	ENST00000380152.3:c.2305C>A	p.Leu769Ile	p.L769I	ENST00000380152		769	Ctt/Att	11/27	0.484172815539946	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.492502258923674	2		427	467	SUCCESS
APC	324	MSKCC	GRCh37	5	112173383	112173383	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1060503279	NA	P-0040572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	78	349	0	ENST00000257430.4:c.2092T>G	p.Leu698Val	p.L698V	ENST00000257430	NM_000038.5	698	Tta/Gta	16/16	0.492502258923674	3	FACETS	0.817	0.72	0.921	0.409	0.36	0.461	CLONAL	1	TRUE	1	0.492502258923674	3		349	483	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517484	176517484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754036845	NA	P-0040611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	52	701	0	ENST00000292408.4:c.185G>A	p.Arg62His	p.R62H	ENST00000292408	NM_213647.1	62	cGt/cAt	3/18	1	2	FACETS	0.169	0.143	0.198	0.169	0.143	0.198	SUBCLONAL	1	TRUE	1	0.639840360430623	2		701	960	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15838365	15838365	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	23	194	0	ENST00000307771.7:c.863A>G	p.Asn288Ser	p.N288S	ENST00000307771	NM_005089.3	288	aAc/aGc	10/11	1	1	FACETS	0.189	0.147	0.237	0.189	0.147	0.237	SUBCLONAL	1	TRUE	0	0.639840360430623	1		194	259	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	128	126	0				ENST00000310581	NM_198253.2	-/1132			0.461872172989122	3	FACETS	0.969	0.889	1	0.969	0.889	1	CLONAL	2	TRUE	1	0.461872172989122	3		126	352	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508856	106508856	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376958957	NA	P-0040648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	176	485	0	ENST00000359195.3:c.850G>A	p.Glu284Lys	p.E284K	ENST00000359195	NM_002649.2	284	Gaa/Aaa	2/11	0.461872172989122	2	FACETS	0.97	0.905	1	0.97	0.905	1	CLONAL	2	TRUE	0	0.461872172989122	2		485	393	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414251	32414251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121907910	NA	P-0040648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	188	410	0	ENST00000332351.3:c.1300C>T	p.Arg434Cys	p.R434C	ENST00000332351	NM_024426.4	434	Cgt/Tgt	8/10	0.461872172989122	3	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	1	0.461872172989122	3		410	498	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376107	118376107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	174	464	1	ENST00000534358.1:c.9500C>T	p.Ser3167Phe	p.S3167F	ENST00000534358	NM_005933.3	3167	tCc/tTc	27/36	0.461872172989122	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.461872172989122	2		465	370	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864404	162864404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	195	452	0	ENST00000366898.1:c.109C>T	p.Pro37Ser	p.P37S	ENST00000366898	NM_004562.2	37	Ccg/Tcg	2/12	0.457618049536559	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.461872172989122	2		452	397	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472559	88472559	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	140	536	0	ENST00000360948.2:c.1996G>A	p.Gly666Ser	p.G666S	ENST00000360948	NM_001012338.2	666	Ggt/Agt	16/19	0.251755263743738	4	FACETS	0.876	0.802	0.952	0.876	0.802	0.952	INDETERMINATE	2	TRUE	2	0.461872172989122	4		536	506	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843748	156843748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537263008	NA	P-0040648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	273	827	0	ENST00000524377.1:c.1174C>T	p.Pro392Ser	p.P392S	ENST00000524377	NM_002529.3	392	Cct/Tct	8/17	0.432866775300308	3	FACETS	0.908	0.856	0.962	0.908	0.856	0.962	CLONAL	2	TRUE	1	0.461872172989122	3		827	801	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50481167	50481167	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	71	384	0	ENST00000394963.4:c.553T>C	p.Phe185Leu	p.F185L	ENST00000394963	NM_003076.4	185	Ttc/Ctc	5/13	0.461872172989122	3	FACETS	0.864	0.757	0.979	0.432	0.378	0.49	CLONAL	1	TRUE	1	0.461872172989122	3		384	438	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112940024	112940024	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1253971623	NA	P-0040648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	276	590	0	ENST00000351677.2:c.1676C>G	p.Pro559Arg	p.P559R	ENST00000351677	NM_002834.3	559	cCt/cGt	14/16	0.461872172989122	3	FACETS	0.931	0.878	0.985	0.931	0.878	0.985	CLONAL	2	TRUE	1	0.461872172989122	3		590	790	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483101	29483123	+	frameshift_variant	Frame_Shift_Del	DEL	TTATAAGCGGCCTCACTACTATT	TTATAAGCGGCCTCACTACTATT	-	novel	NA	P-0040648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	70	407	1	ENST00000356175.3:c.164_186del	p.Ile55LysfsTer4	p.I55Kfs*4	ENST00000356175	NM_000267.3	54	gTTATAAGCGGCCTCACTACTATT/g	2/57	0.461872172989122	4	FACETS	0.806	0.703	0.916	0.403	0.351	0.458	CLONAL	1	TRUE	2	0.461872172989122	4		408	550	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585473	29585473	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0040648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	104	357	0	ENST00000356175.3:c.4222A>T	p.Lys1408Ter	p.K1408*	ENST00000356175	NM_000267.3	1408	Aaa/Taa	31/57	0.461872172989122	4	FACETS	0.809	0.73	0.892	0.809	0.73	0.892	CLONAL	2	TRUE	2	0.461872172989122	4		357	407	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349926	15349926	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	230	624	0	ENST00000263377.2:c.3726G>T	p.Lys1242Asn	p.K1242N	ENST00000263377	NM_058243.2	1242	aaG/aaT	18/20	0.350259149511485	4	FACETS	0.982	0.919	1	0.982	0.919	1	CLONAL	2	TRUE	2	0.461872172989122	4		624	741	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228965	36228965	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	229	634	0	ENST00000222270.7:c.7745C>T	p.Ser2582Leu	p.S2582L	ENST00000222270	NM_014727.1	2582	tCa/tTa	36/37	0.350259149511485	4	FACETS	0.935	0.874	0.998	0.935	0.874	0.998	CLONAL	2	TRUE	2	0.461872172989122	4		634	775	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867579	45867579	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	255	736	0	ENST00000391945.4:c.729C>A	p.Cys243Ter	p.C243*	ENST00000391945	NM_000400.3	243	tgC/tgA	9/23	0.350259149511485	4	FACETS	0.935	0.878	0.994	0.935	0.878	0.994	CLONAL	2	TRUE	2	0.461872172989122	4		736	863	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919917	50919917	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	226	672	0	ENST00000440232.2:c.3004C>A	p.Leu1002Ile	p.L1002I	ENST00000440232	NM_002691.3	1002	Ctc/Atc	24/27	0.350259149511485	4	FACETS	0.955	0.893	1	0.955	0.893	1	CLONAL	2	TRUE	2	0.461872172989122	4		672	749	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606191	47606191	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs757963724	NA	P-0040648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	25	280	0	ENST00000263735.4:c.655G>A	p.Asp219Asn	p.D219N	ENST00000263735	NM_002354.2	219	Gat/Aat	6/9	0.220501867826916	3	FACETS	0.503	0.397	0.624	0.168	0.132	0.208	INDETERMINATE	1	TRUE	0	0.461872172989122	3		280	265	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268440	198268440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	36	412	0	ENST00000335508.6:c.1588C>T	p.Pro530Ser	p.P530S	ENST00000335508	NM_012433.2	530	Cct/Tct	12/25	0.220501867826916	3	FACETS	0.465	0.382	0.557	0.155	0.127	0.186	INDETERMINATE	1	TRUE	0	0.461872172989122	3		412	413	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39751881	39751881	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	173	394	0	ENST00000361337.2:c.2242C>T	p.Gln748Ter	p.Q748*	ENST00000361337	NM_003286.2	748	Cag/Tag	21/21	0.244766319727188	5	FACETS	1	0.951	1	0.691	0.639	0.744	INDETERMINATE	2	TRUE	2	0.461872172989122	5		394	612	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877379	40877379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763387029	NA	P-0040648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	179	534	0	ENST00000373198.4:c.2317C>T	p.Leu773Phe	p.L773F	ENST00000373198	NM_133170.3	773	Ctc/Ttc	15/32	0.284104435761973	3	FACETS	0.861	0.799	0.925			1	CLONAL	2	TRUE	NA	0.461872172989122	3		534	554	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721567	49721567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	120	508	0	ENST00000449682.2:c.2072G>A	p.Gly691Glu	p.G691E	ENST00000449682	NM_020998.3	691	gGa/gAa	18/18	0.244766319727188	5	FACETS	1	0.984	1	0.481	0.435	0.529	INDETERMINATE	1	TRUE	2	0.461872172989122	5		508	610	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178943785	178943785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	105	305	0	ENST00000263967.3:c.2452C>T	p.Arg818Cys	p.R818C	ENST00000263967	NM_006218.2	818	Cgt/Tgt	17/21	0.244766319727188	5	FACETS	1	0.962	1	0.748	0.677	0.821	INDETERMINATE	2	TRUE	2	0.461872172989122	5		305	343	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271312	1271312	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	107	680	0	ENST00000310581.5:c.2390C>T	p.Ser797Phe	p.S797F	ENST00000310581	NM_198253.2	797	tCc/tTc	8/16	0.461872172989122	3	FACETS	1	0.914	1	0.508	0.457	0.562	CLONAL	1	TRUE	1	0.461872172989122	3		680	561	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665362	176665362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	176	337	0	ENST00000439151.2:c.4046C>T	p.Ala1349Val	p.A1349V	ENST00000439151	NM_022455.4	1349	gCt/gTt	7/23	0.432866775300308	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.461872172989122	3		337	411	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109315715	109315715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	194	514	0	ENST00000436639.2:c.1070C>T	p.Ala357Val	p.A357V	ENST00000436639	NM_014454.2	357	gCt/gTt	6/10	0.457618049536559	2	FACETS	0.879	0.821	0.937	0.879	0.821	0.937	CLONAL	2	TRUE	0	0.461872172989122	2		514	478	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117645515	117645515	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	183	492	0	ENST00000368508.3:c.5621T>C	p.Val1874Ala	p.V1874A	ENST00000368508	NM_002944.2	1874	gTt/gCt	34/43	0.457618049536559	2	FACETS	0.946	0.884	1	0.946	0.884	1	CLONAL	2	TRUE	0	0.461872172989122	2		492	419	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0040651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	165	657	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.474851299139155	2		657	518	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441424	52441443	+	frameshift_variant	Frame_Shift_Del	DEL	CTATTATGGGCCTTGGCCAA	CTATTATGGGCCTTGGCCAA	-	novel	NA	P-0040651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	115	426	0	ENST00000460680.1:c.409_428del	p.Leu137ProfsTer11	p.L137Pfs*11	ENST00000460680	NM_004656.3	137	TTGGCCAAGGCCCATAATAGc/c	6/17	0.474851299139155	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.474851299139155	1		426	281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0040702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	488	707	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.665250135397135	3	FACETS	0.998	0.97	1			1	CLONAL	3	TRUE	NA	0.665250135397135	3		707	653	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790168	40790168	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745346735	NA	P-0040702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	54	643	0	ENST00000373198.4:c.2563G>A	p.Gly855Arg	p.G855R	ENST00000373198	NM_133170.3	855	Ggg/Agg	18/32	0.653117769769115	3	FACETS	0.662	0.568	0.763	0.331	0.284	0.382	SUBCLONAL	1	TRUE	1	0.665250135397135	3		643	327	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0040753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	208	441	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.299664038577609	3	FACETS	0.968	0.905	1			1	CLONAL	2	TRUE	NA	0.429906995014305	3		441	607	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550494	29550497	+	frameshift_variant	Frame_Shift_Del	DEL	TAAC	TAAC	-	rs786202782	NA	P-0040753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	98	298	0	ENST00000356175.3:c.1756_1759del	p.Thr586ValfsTer18	p.T586Vfs*18	ENST00000356175	NM_000267.3	585	tTAACt/tt	16/57	0.429906995014305	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.429906995014305	1		298	346	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928226	178928226	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519872	NA	P-0040753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	237	420	1	ENST00000263967.3:c.1412C>T	p.Pro471Leu	p.P471L	ENST00000263967	NM_006218.2	471	cCa/cTa	9/21	0.299664038577609	3	FACETS	0.928	0.87	0.987			1	CLONAL	2	TRUE	NA	0.429906995014305	3		421	722	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179362	56179363	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0040753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	66	214	0	ENST00000399503.3:c.3676_3677dup	p.Pro1228TyrfsTer18	p.P1228Yfs*18	ENST00000399503	NM_005921.1	1225	-/AC	15/20	0.429906995014305	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.429906995014305	1		214	227	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602764	10602764	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	216	906	1	ENST00000171111.5:c.814C>T	p.Arg272Cys	p.R272C	ENST00000171111	NM_203500.1	272	Cgc/Tgc	3/6	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.13	2		907	1332	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167738	56167738	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs753326217	NA	P-0040799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	30	310	0	ENST00000399503.3:c.1303A>G	p.Ile435Val	p.I435V	ENST00000399503	NM_005921.1	435	Ata/Gta	7/20	1	2	FACETS	1	0.815	1	1	0.815	1	CLONAL	1	TRUE	1	0.13	2		310	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579350	7579350	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587781642	NA	P-0040803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	307	765	0	ENST00000269305.4:c.337T>G	p.Phe113Val	p.F113V	ENST00000269305	NM_001126112.2	113	Ttc/Gtc	4/11	0.610293706204275	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.606812974711109	1		765	565	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946342	71946342	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	133	867	0	ENST00000298229.2:c.2506G>T	p.Glu836Ter	p.E836*	ENST00000298229	NM_001567.3	836	Gag/Tag	23/28	1	2	FACETS	0.635	0.578	0.695	0.635	0.578	0.695	SUBCLONAL	1	TRUE	1	0.606812974711109	2		867	690	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652239	36652239	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	92	659	2	ENST00000244741.5:c.361C>A	p.Pro121Thr	p.P121T	ENST00000244741	NM_000389.4	121	Cct/Act	2/3	1	2	FACETS	0.532	0.474	0.594	0.532	0.474	0.594	SUBCLONAL	1	TRUE	1	0.606812974711109	2		661	570	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246113	41246113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064794100	NA	P-0040817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	196	696	0	ENST00000357654.3:c.1435G>A	p.Glu479Lys	p.E479K	ENST00000357654	NM_007294.3	479	Gaa/Aaa	10/23	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.490388310095661	2		696	768	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821086	32821086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs2228108	NA	P-0040817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	374	1115	0	ENST00000354258.4:c.508C>T	p.Leu170Phe	p.L170F	ENST00000354258	NM_000593.5	170	Ctt/Ttt	1/11	0.47115527482102	2	FACETS	0.987	0.943	1	0.987	0.943	1	CLONAL	2	TRUE	0	0.490388310095661	2		1115	773	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868444	117868444	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	150	691	0	ENST00000297338.2:c.898G>C	p.Glu300Gln	p.E300Q	ENST00000297338	NM_006265.2	300	Gag/Cag	8/14	0.489206646021011	3	FACETS	0.856	0.782	0.933	0.428	0.391	0.467	CLONAL	1	TRUE	1	0.490388310095661	3		691	890	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321065	137321065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	155	738	0	ENST00000481739.1:c.1022G>A	p.Gly341Glu	p.G341E	ENST00000481739	NM_002957.4	341	gGg/gAg	7/10	0.490388310095661	3	FACETS	1	0.972	1	0.567	0.52	0.616	CLONAL	1	TRUE	1	0.490388310095661	3		738	694	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409053	139409053	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	174	1080	0	ENST00000277541.6:c.2116G>T	p.Glu706Ter	p.E706*	ENST00000277541	NM_017617.3	706	Gag/Tag	13/34	0.490388310095661	3	FACETS	0.937	0.863	1	0.469	0.431	0.508	CLONAL	1	TRUE	1	0.490388310095661	3		1080	943	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411748	139411748	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	104	942	0	ENST00000277541.6:c.1531G>C	p.Glu511Gln	p.E511Q	ENST00000277541	NM_017617.3	511	Gag/Cag	9/34	NA	2	FACETS	0.5	0.447	0.556			1	INDETERMINATE	1	TRUE	NA	0.490388310095661	2		942	849	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929578	44929578	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0040817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	94	383	0	ENST00000377967.4:c.2678C>G	p.Ser893Ter	p.S893*	ENST00000377967	NM_021140.2	893	tCa/tGa	17/29	0.490388310095661	1	FACETS	0.806	0.723	0.892	0.806	0.723	0.892	CLONAL	1	TRUE	0	0.490388310095661	1		383	359	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652290	48652290	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs782391440	NA	P-0040817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	182	1101	0	ENST00000376670.3:c.961C>G	p.Leu321Val	p.L321V	ENST00000376670	NM_002049.3	321	Ctg/Gtg	6/6	0.490388310095661	1	FACETS	0.869	0.805	0.934	0.869	0.805	0.934	CLONAL	1	TRUE	0	0.490388310095661	1		1101	645	SUCCESS
AR	367	MSKCC	GRCh37	X	66766446	66766447	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0040817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	95	499	1	ENST00000374690.3:c.1458_1459delinsTA	p.Pro487Thr	p.P487T	ENST00000374690	NM_000044.3	486	ccCCct/ccTAct	1/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.490388310095661	2		500	341	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	108	350	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.411521542415186	3	FACETS	0.865	0.778	0.956	0.432	0.389	0.478	CLONAL	1	TRUE	1	0.535836944560673	3		350	591	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988489	36988489	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	56	551	0	ENST00000354822.5:c.164A>T	p.Lys55Met	p.K55M	ENST00000354822	NM_001079668.2	55	aAg/aTg	2/3	1	2	FACETS	0.357	0.306	0.414	0.357	0.306	0.414	SUBCLONAL	1	TRUE	1	0.535836944560673	2		551	585	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218852	36218852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs549211601	NA	P-0040919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	197	672	3	ENST00000222270.7:c.4463G>A	p.Arg1488Gln	p.R1488Q	ENST00000222270	NM_014727.1	1488	cGg/cAg	18/37	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.535836944560673	2		675	659	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198283292	198283292	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	150	496	0	ENST00000335508.6:c.436A>C	p.Lys146Gln	p.K146Q	ENST00000335508	NM_012433.2	146	Aaa/Caa	5/25	0.411521542415186	3	FACETS	1	0.961	1	0.541	0.496	0.588	CLONAL	1	TRUE	1	0.535836944560673	3		496	656	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927405	178927405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	95	361	0	ENST00000263967.3:c.1168G>A	p.Asp390Asn	p.D390N	ENST00000263967	NM_006218.2	390	Gat/Aat	7/21	1	2	FACETS	0.923	0.828	1	0.923	0.828	1	CLONAL	1	TRUE	1	0.535836944560673	2		361	384	SUCCESS
APC	324	MSKCC	GRCh37	5	112151195	112151215	+	frameshift_variant	Frame_Shift_Del	DEL	TCAACTACACGAATGGACCAT	TCAACTACACGAATGGACCAT	ACCAC	novel	NA	P-0040919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	71	383	1	ENST00000257430.4:c.838_858delinsACCAC	p.Ser280ThrfsTer8	p.S280Tfs*8	ENST00000257430	NM_000038.5	280	TCAACTACACGAATGGACCAT/ACCAC	9/16	1	2	FACETS	0.593	0.519	0.672	0.593	0.519	0.672	SUBCLONAL	1	TRUE	1	0.535836944560673	2		384	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0041051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	144	549	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.399107078599002	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.399107078599002	1		552	577	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	110	544	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.226236265897862	1	FACETS	0.758	0.683	0.837	0.758	0.683	0.837	INDETERMINATE	1	TRUE	0	0.399107078599002	1		544	582	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0041051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	130	372	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	0.211689992411071	3	FACETS	1	0.985	1	0.717	0.653	0.783	INDETERMINATE	1	TRUE	1	0.399107078599002	3		372	545	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928225	178928225	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	125	309	0	ENST00000263967.3:c.1411C>G	p.Pro471Ala	p.P471A	ENST00000263967	NM_006218.2	471	Cca/Gca	9/21	0.211689992411071	3	FACETS	0.85	0.775	0.928	0.85	0.775	0.928	INDETERMINATE	2	TRUE	1	0.399107078599002	3		309	442	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843386	3843386	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0041051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	30	237	0	ENST00000262367.5:c.1216+1del		p.X406_splice	ENST00000262367	NM_004380.2	406			0.269408781076042	3	FACETS	0.49	0.395	0.598			1	SUBCLONAL	1	TRUE	NA	0.399107078599002	3		237	368	SUCCESS
YES1	7525	MSKCC	GRCh37	18	742970	742971	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0041051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	114	301	0	ENST00000314574.4:c.1007_1008del	p.Tyr336CysfsTer5	p.Y336Cfs*5	ENST00000314574	NM_005433.3	336	tAT/t	8/12	0.399107078599002	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.399107078599002	1		301	423	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378245	15378245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	43	336	0	ENST00000263377.2:c.541C>T	p.Arg181Cys	p.R181C	ENST00000263377	NM_058243.2	181	Cgt/Tgt	4/20	0.226236265897862	1	FACETS	0.423	0.354	0.499	0.423	0.354	0.499	INDETERMINATE	1	TRUE	0	0.399107078599002	1		336	408	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860666	151860667	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	104	359	0	ENST00000262189.6:c.9995dup	p.Leu3332PhefsTer19	p.L3332Ffs*19	ENST00000262189	NM_170606.2	3332	tta/ttTa	43/59	0.226236265897862	1	FACETS	0.946	0.852	1	0.946	0.852	1	INDETERMINATE	1	TRUE	0	0.399107078599002	1		359	441	SUCCESS
AR	367	MSKCC	GRCh37	X	66943552	66943552	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137852578	NA	P-0041059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	64	184	0	ENST00000374690.3:c.2632A>G	p.Thr878Ala	p.T878A	ENST00000374690	NM_000044.3	878	Act/Gct	8/8	0.192281153024456	2	FACETS	0.847	0.741	0.959			1	CLONAL	3	TRUE	NA	0.192281153024456	2		184	262	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349274	70349274	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	190	348	0	ENST00000374080.3:c.3686T>C	p.Val1229Ala	p.V1229A	ENST00000374080		1229	gTa/gCa	26/45	0.192281153024456	2	FACETS	0.893	0.832	0.956			1	CLONAL	4	TRUE	NA	0.192281153024456	2		348	553	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437605	56437605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329721997	NA	P-0041064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	104	570	0	ENST00000407977.2:c.857G>A	p.Arg286Gln	p.R286Q	ENST00000407977		286	cGg/cAg	8/10	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.3150172176792	2		570	656	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435010	110435010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	183	890	1	ENST00000375856.3:c.3391C>T	p.Arg1131Cys	p.R1131C	ENST00000375856	NM_003749.2	1131	Cgc/Tgc	1/2	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.3150172176792	2		891	1111	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426722	212426722	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	104	625	0	ENST00000342788.4:c.2393T>G	p.Leu798Arg	p.L798R	ENST00000342788	NM_005235.2	798	cTt/cGt	20/28	1	2	FACETS	0.958	0.859	1	0.958	0.859	1	CLONAL	1	TRUE	1	0.3150172176792	2		625	689	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230605	46230605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303729294	NA	P-0041064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	161	499	0	ENST00000334344.6:c.854G>A	p.Arg285Gln	p.R285Q	ENST00000334344	NM_152641.2	285	cGg/cAg	8/21	0.246521000716339	3	FACETS	0.975	0.898	1	0.975	0.898	1	CLONAL	2	TRUE	1	0.3150172176792	3		499	607	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210565	5210565	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770322238	NA	P-0041064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	158	768	2	ENST00000357368.4:c.5402G>A	p.Arg1801His	p.R1801H	ENST00000357368	NM_002850.3	1801	cGc/cAc	35/38	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.3150172176792	2		770	901	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490554	20490554	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	87	590	0	ENST00000346618.3:c.1291C>T	p.Gln431Ter	p.Q431*	ENST00000346618	NM_001949.4	431	Caa/Taa	7/7	1	2	FACETS	0.688	0.608	0.773	0.688	0.608	0.773	SUBCLONAL	1	TRUE	1	0.3150172176792	2		590	803	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455121	50455121	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	83	386	0	ENST00000331340.3:c.668G>T	p.Cys223Phe	p.C223F	ENST00000331340	NM_006060.4	223	tGc/tTc	6/8	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.3150172176792	2		386	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0041070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4	111	668	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.784588688418146	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.784588688418146	2		668	115	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0041070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	8	568	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.135444995375795	4	FACETS	1	0.759	1	0.587	0.394	0.812	INDETERMINATE	1	TRUE	2	0.784588688418146	4		568	31	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542779	187542779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369592206	NA	P-0041070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	14	548	1	ENST00000441802.2:c.4961G>A	p.Arg1654His	p.R1654H	ENST00000441802	NM_005245.3	1654	cGt/cAt	10/27	1	2	FACETS	0.939	0.714	1	0.939	0.714	1	CLONAL	1	TRUE	1	0.784588688418146	2		549	38	SUCCESS
ATM	472	MSKCC	GRCh37	11	108127022	108127022	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	15	573	0	ENST00000278616.4:c.2205A>G	p.Ile735Met	p.I735M	ENST00000278616	NM_000051.3	735	atA/atG	14/63	1	2	FACETS	1	0.776	1	1	0.776	1	CLONAL	1	TRUE	1	0.784588688418146	2		573	38	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989682	15989682	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	32	504	0	ENST00000268712.3:c.3091A>G	p.Arg1031Gly	p.R1031G	ENST00000268712	NM_006311.3	1031	Agg/Ggg	23/46	0.784588688418146	2	FACETS	1	0.929	1	0.591	0.502	0.682	CLONAL	1	TRUE	0	0.784588688418146	2		504	69	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989700	15989700	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	30	465	0	ENST00000268712.3:c.3073C>G	p.Pro1025Ala	p.P1025A	ENST00000268712	NM_006311.3	1025	Ccg/Gcg	23/46	0.784588688418146	2	FACETS	1	0.932	1	0.607	0.513	0.702	CLONAL	1	TRUE	0	0.784588688418146	2		465	63	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918969	76918969	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2	20	301	0	ENST00000373344.5:c.4022del	p.Leu1341CysfsTer5	p.L1341Cfs*5	ENST00000373344	NM_000489.3	1341	tTg/tg	12/35	1	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.784588688418146	1		301	22	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0041119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	291	539	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.68415312466491	1	FACETS	0.987	0.939	1	0.987	0.939	1	CLONAL	1	TRUE	0	0.68415312466491	1		539	567	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0041119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	477	485	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.68415312466491	2		485	979	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404813	404813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368604945	NA	P-0041119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	300	454	0	ENST00000399788.2:c.4381G>A	p.Glu1461Lys	p.E1461K	ENST00000399788	NM_001042603.1	1461	Gag/Aag	26/28	0.68415312466491	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.68415312466491	1		454	540	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630639	187630639	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	285	611	0	ENST00000441802.2:c.343C>A	p.His115Asn	p.H115N	ENST00000441802	NM_005245.3	115	Cac/Aac	2/27	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.68415312466491	2		611	788	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	38	743	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.451	0.371	0.541	0.451	0.371	0.541	SUBCLONAL	1	TRUE	1	0.18	2		743	936	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	166	585	0	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	1	2	FACETS	0.984	0.907	1	1	0.994	1	CLONAL	3	TRUE	1	0.18	2		585	625	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217225	11217225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	32	611	1	ENST00000361445.4:c.4453G>A	p.Glu1485Lys	p.E1485K	ENST00000361445	NM_004958.3	1485	Gag/Aag	30/58	1	2	FACETS	0.556	0.45	0.676	0.556	0.45	0.676	SUBCLONAL	1	TRUE	1	0.18	2		612	640	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276387	115276387	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779453730	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	195	575	0	ENST00000438362.2:c.941C>T	p.Thr314Ile	p.T314I	ENST00000438362	NM_001242891.1	314	aCc/aTc	9/20	1	2	FACETS	1	0.979	1	1	0.995	1	CLONAL	3	TRUE	1	0.18	2		575	639	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165970	118165970	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1422217522	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	171	501	0	ENST00000369448.3:c.480G>T	p.Lys160Asn	p.K160N	ENST00000369448	NM_017709.3	160	aaG/aaT	2/2	1	2	FACETS	0.888	0.822	0.955	1	0.994	1	CLONAL	4	TRUE	1	0.18	2		501	535	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462975	120462975	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1435723160	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	172	614	1	ENST00000256646.2:c.5356C>T	p.Arg1786Ter	p.R1786*	ENST00000256646	NM_024408.3	1786	Cga/Tga	30/34	1	2	FACETS	1	0.977	1	1	0.994	1	CLONAL	3	TRUE	1	0.18	2		615	561	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849887	156849887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759190964	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	257	937	0	ENST00000524377.1:c.2143G>A	p.Val715Met	p.V715M	ENST00000524377	NM_002529.3	715	Gtg/Atg	16/17	1	2	FACETS	1	0.984	1	1	0.996	1	CLONAL	3	TRUE	1	0.18	2		937	836	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176153796	176153796	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	124	345	0	ENST00000367669.3:c.440A>G	p.Tyr147Cys	p.Y147C	ENST00000367669	NM_022457.5	147	tAc/tGc	2/20	1	2	FACETS	1	0.951	1	1	0.992	1	CLONAL	3	TRUE	1	0.18	2		345	432	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104712	193104712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	126	358	0	ENST00000367435.3:c.416G>A	p.Arg139Gln	p.R139Q	ENST00000367435	NM_024529.4	139	cGa/cAa	5/17	1	2	FACETS	0.888	0.812	0.967	1	0.993	1	CLONAL	4	TRUE	1	0.18	2		358	394	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246493799	246493799	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	154	340	0	ENST00000388985.4:c.377T>G	p.Phe126Cys	p.F126C	ENST00000388985		126	tTt/tGt	4/12	1	2	FACETS	0.951	0.878	1	1	0.994	1	CLONAL	4	TRUE	1	0.18	2		340	450	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115975	8115975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	127	388	0	ENST00000346208.3:c.1321G>A	p.Ala441Thr	p.A441T	ENST00000346208		441	Gcc/Acc	6/6	1	2	FACETS	0.919	0.841	0.999	1	0.993	1	CLONAL	4	TRUE	1	0.18	2		388	384	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619124	43619124	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	199	588	0	ENST00000355710.3:c.2807C>A	p.Ser936Tyr	p.S936Y	ENST00000355710	NM_020975.4	936	tCt/tAt	17/20	1	2	FACETS	0.973	0.908	1	1	0.995	1	CLONAL	4	TRUE	1	0.18	2		588	568	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624245	89624245	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554890335	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	114	215	0	ENST00000371953.3:c.19G>T	p.Glu7Ter	p.E7*	ENST00000371953	NM_000314.4	7	Gag/Tag	1/9	1	2	FACETS	0.925	0.847	1	1	0.992	1	CLONAL	5	TRUE	1	0.18	2		215	274	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690835	89690835	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs876661177	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	132	362	0	ENST00000371953.3:c.242T>G	p.Phe81Cys	p.F81C	ENST00000371953	NM_000314.4	81	tTt/tGt	4/9	1	2	FACETS	0.894	0.82	0.971	1	0.993	1	CLONAL	4	TRUE	1	0.18	2		362	410	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692892	89692892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554898129	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	128	456	0	ENST00000371953.3:c.376G>A	p.Ala126Thr	p.A126T	ENST00000371953	NM_000314.4	126	Gct/Act	5/9	1	2	FACETS	1	0.973	1	1	0.993	1	CLONAL	3	TRUE	1	0.18	2		456	410	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769557	112769557	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	235	731	0	ENST00000369452.4:c.1509G>T	p.Glu503Asp	p.E503D	ENST00000369452	NM_007373.3	503	gaG/gaT	8/9	1	2	FACETS	0.88	0.824	0.937	1	0.996	1	CLONAL	4	TRUE	1	0.18	2		731	742	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414253	32414253	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	219	492	0	ENST00000332351.3:c.1298C>A	p.Ser433Tyr	p.S433Y	ENST00000332351	NM_024426.4	433	tCt/tAt	8/10	1	2	FACETS	0.923	0.863	0.984	1	0.996	1	CLONAL	4	TRUE	1	0.18	2		492	659	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77069944	77069944	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	42	530	1	ENST00000356341.3:c.596C>A	p.Ser199Tyr	p.S199Y	ENST00000356341	NM_002576.4	199	tCt/tAt	6/15	1	2	FACETS	0.712	0.594	0.845	0.712	0.594	0.845	SUBCLONAL	1	TRUE	1	0.18	2		531	655	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203640	94203640	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	67	285	0	ENST00000323929.3:c.1014G>T	p.Glu338Asp	p.E338D	ENST00000323929	NM_005591.3	338	gaG/gaT	9/20	1	2	FACETS	0.936	0.823	1	1	0.985	1	CLONAL	3	TRUE	1	0.18	2		285	265	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143321	108143321	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	131	414	0	ENST00000278616.4:c.3140A>C	p.Lys1047Thr	p.K1047T	ENST00000278616	NM_000051.3	1047	aAa/aCa	21/63	1	2	FACETS	0.99	0.904	1	1	0.992	1	CLONAL	3	TRUE	1	0.18	2		414	490	SUCCESS
ATM	472	MSKCC	GRCh37	11	108168100	108168100	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	19	338	0	ENST00000278616.4:c.4996G>T	p.Glu1666Ter	p.E1666*	ENST00000278616	NM_000051.3	1666	Gaa/Taa	33/63	1	2	FACETS	0.605	0.458	0.777	0.605	0.458	0.777	SUBCLONAL	1	TRUE	1	0.18	2		338	349	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178711	108178711	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	92	250	1	ENST00000278616.4:c.5762G>A	p.Arg1921Lys	p.R1921K	ENST00000278616	NM_000051.3	1921	aGa/aAa	38/63	1	2	FACETS	0.929	0.837	1	1	0.99	1	CLONAL	4	TRUE	1	0.18	2		251	275	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186743	108186743	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3218670	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	172	454	0	ENST00000278616.4:c.6101G>A	p.Arg2034Gln	p.R2034Q	ENST00000278616	NM_000051.3	2034	cGa/cAa	42/63	1	2	FACETS	1	0.978	1	1	0.994	1	CLONAL	3	TRUE	1	0.18	2		454	558	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118370029	118370029	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	19	289	1	ENST00000534358.1:c.5973G>T	p.Glu1991Asp	p.E1991D	ENST00000534358	NM_005933.3	1991	gaG/gaT	23/36	1	2	FACETS	0.648	0.491	0.832	0.648	0.491	0.832	SUBCLONAL	1	TRUE	1	0.18	2		290	326	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372513	118372513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782124549	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	40	660	0	ENST00000534358.1:c.6446G>A	p.Arg2149Gln	p.R2149Q	ENST00000534358	NM_005933.3	2149	cGa/cAa	26/36	1	2	FACETS	0.581	0.481	0.693	0.581	0.481	0.693	SUBCLONAL	1	TRUE	1	0.18	2		660	765	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416748	416748	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	27	435	0	ENST00000399788.2:c.3802G>A	p.Glu1268Lys	p.E1268K	ENST00000399788	NM_001042603.1	1268	Gaa/Aaa	23/28	0.3	1	FACETS	0.752	0.599	0.927	0.752	0.599	0.927	CLONAL	1	TRUE	0	0.18	1		435	363	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422312	422312	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	126	630	1	ENST00000399788.2:c.2946G>T	p.Lys982Asn	p.K982N	ENST00000399788	NM_001042603.1	982	aaG/aaT	20/28	0.3	1	FACETS	1	0.925	1	1	0.99	1	CLONAL	2	TRUE	0	0.18	1		631	624	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	493204	493204	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	142	503	0	ENST00000399788.2:c.359T>C	p.Leu120Ser	p.L120S	ENST00000399788	NM_001042603.1	120	tTg/tCg	3/28	0.3	1	FACETS	1	0.961	1	1	0.993	1	CLONAL	3	TRUE	0	0.18	1		503	445	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435508	18435508	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	102	295	0	ENST00000266497.5:c.493C>A	p.His165Asn	p.H165N	ENST00000266497		165	Cat/Aat	1/31	1	2	FACETS	1	0.915	1	1	0.991	1	CLONAL	4	TRUE	1	0.18	2		295	281	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552635	18552635	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	171	600	0	ENST00000266497.5:c.2046C>A	p.Phe682Leu	p.F682L	ENST00000266497		682	ttC/ttA	14/31	0.3	1	FACETS	1	0.97	1	1	0.994	1	CLONAL	3	TRUE	0	0.18	1		600	529	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415845	49415845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	140	457	0	ENST00000301067.7:c.16502G>A	p.Arg5501Gln	p.R5501Q	ENST00000301067	NM_003482.3	5501	cGa/cAa	53/54	0.3	1	FACETS	0.979	0.898	1	1	0.993	1	CLONAL	3	TRUE	0	0.18	1		457	482	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416114	49416114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	118	548	0	ENST00000301067.7:c.16361G>A	p.Arg5454Gln	p.R5454Q	ENST00000301067	NM_003482.3	5454	cGa/cAa	52/54	0.3	1	FACETS	1	0.917	1	1	0.989	1	CLONAL	2	TRUE	0	0.18	1		548	588	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416118	49416118	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	121	510	1	ENST00000301067.7:c.16357T>C	p.Phe5453Leu	p.F5453L	ENST00000301067	NM_003482.3	5453	Ttc/Ctc	52/54	0.3	1	FACETS	1	0.946	1	1	0.99	1	CLONAL	2	TRUE	0	0.18	1		511	576	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865826	57865826	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	128	674	0	ENST00000228682.2:c.3303C>A	p.Phe1101Leu	p.F1101L	ENST00000228682	NM_005269.2	1101	ttC/ttA	12/12	0.3	1	FACETS	0.889	0.811	0.971	1	0.992	1	CLONAL	3	TRUE	0	0.18	1		674	485	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145001	58145001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772938517	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	39	763	0	ENST00000257904.6:c.343G>A	p.Glu115Lys	p.E115K	ENST00000257904	NM_000075.3	115	Gaa/Aaa	3/8	0.3	1	FACETS	0.566	0.468	0.676	0.566	0.468	0.676	SUBCLONAL	1	TRUE	0	0.18	1		763	697	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218408	69218408	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	170	496	0	ENST00000462284.1:c.500G>T	p.Arg167Ile	p.R167I	ENST00000462284	NM_002392.5	167	aGa/aTa	7/11	0.3	1	FACETS	1	0.928	1	1	0.994	1	CLONAL	3	TRUE	0	0.18	1		496	571	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112919920	112919920	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	87	269	0	ENST00000351677.2:c.1135G>T	p.Glu379Ter	p.E379*	ENST00000351677	NM_002834.3	379	Gaa/Taa	10/16	0.3	1	FACETS	1	0.958	1	1	0.989	1	CLONAL	3	TRUE	0	0.18	1		269	260	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	189	745	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	0.3	1	FACETS	0.994	0.923	1	1	0.995	1	CLONAL	3	TRUE	0	0.18	1		745	641	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601310	28601310	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	192	455	0	ENST00000241453.7:c.2122G>T	p.Glu708Ter	p.E708*	ENST00000241453	NM_004119.2	708	Gaa/Taa	17/24	1	2	FACETS	0.901	0.838	0.965	1	0.995	1	CLONAL	4	TRUE	1	0.18	2		455	592	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602393	28602393	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753200838	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	141	489	0	ENST00000241453.7:c.1975A>G	p.Met659Val	p.M659V	ENST00000241453	NM_004119.2	659	Atg/Gtg	16/24	1	2	FACETS	0.913	0.835	0.994	1	0.992	1	CLONAL	3	TRUE	1	0.18	2		489	572	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919595	28919595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs553261958	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	173	517	1	ENST00000282397.4:c.2342G>A	p.Arg781Gln	p.R781Q	ENST00000282397	NM_002019.4	781	cGa/cAa	16/30	1	2	FACETS	0.942	0.87	1	1	0.994	1	CLONAL	3	TRUE	1	0.18	2		518	680	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964148	28964148	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	151	433	0	ENST00000282397.4:c.1754G>T	p.Arg585Ile	p.R585I	ENST00000282397	NM_002019.4	585	aGa/aTa	13/30	1	2	FACETS	0.955	0.882	1	1	0.994	1	CLONAL	4	TRUE	1	0.18	2		433	439	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964205	28964206	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	108	342	0	ENST00000282397.4:c.1696dup	p.Met566AsnfsTer15	p.M566Nfs*15	ENST00000282397	NM_002019.4	566	atg/aAtg	13/30	1	2	FACETS	1	0.952	1	1	0.991	1	CLONAL	3	TRUE	1	0.18	2		342	370	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906539	32906539	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	37	387	0	ENST00000380152.3:c.924T>G	p.Phe308Leu	p.F308L	ENST00000380152		308	ttT/ttG	10/27	1	2	FACETS	0.858	0.707	1	0.858	0.707	1	CLONAL	1	TRUE	1	0.18	2		387	479	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907011	32907011	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	138	486	0	ENST00000380152.3:c.1396A>C	p.Asn466His	p.N466H	ENST00000380152		466	Aat/Cat	10/27	1	2	FACETS	0.937	0.861	1	1	0.993	1	CLONAL	4	TRUE	1	0.18	2		486	409	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913196	32913196	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs863224589	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	180	645	0	ENST00000380152.3:c.4704G>T	p.Lys1568Asn	p.K1568N	ENST00000380152		1568	aaG/aaT	11/27	1	2	FACETS	1	0.978	1	1	0.995	1	CLONAL	3	TRUE	1	0.18	2		645	588	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913525	32913525	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs28897733	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	170	490	0	ENST00000380152.3:c.5033A>C	p.Lys1678Thr	p.K1678T	ENST00000380152		1678	aAa/aCa	11/27	1	2	FACETS	1	0.958	1	1	0.994	1	CLONAL	3	TRUE	1	0.18	2		490	598	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937591	32937591	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1555287065	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	198	573	0	ENST00000380152.3:c.8252T>G	p.Ile2751Ser	p.I2751S	ENST00000380152		2751	aTt/aGt	18/27	1	2	FACETS	0.899	0.837	0.962	1	0.995	1	CLONAL	4	TRUE	1	0.18	2		573	612	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945130	32945130	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80359105	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	157	368	0	ENST00000380152.3:c.8525G>A	p.Arg2842His	p.R2842H	ENST00000380152		2842	cGc/cAc	20/27	1	2	FACETS	0.973	0.9	1	1	0.994	1	CLONAL	4	TRUE	1	0.18	2		368	448	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438352	110438352	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	45	123	0	ENST00000375856.3:c.49G>T	p.Gly17Cys	p.G17C	ENST00000375856	NM_003749.2	17	Ggc/Tgc	1/2	1	2	FACETS	1	0.917	1	1	0.98	1	CLONAL	3	TRUE	1	0.18	2		123	151	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991104	41991104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	43	574	0	ENST00000219905.7:c.2057C>T	p.Ser686Phe	p.S686F	ENST00000219905	NM_001164273.1	686	tCt/tTt	4/24	1	2	FACETS	0.8	0.669	0.947	0.8	0.669	0.947	CLONAL	1	TRUE	1	0.18	2		574	597	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43769818	43769818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	51	574	0	ENST00000382044.4:c.928G>A	p.Asp310Asn	p.D310N	ENST00000382044	NM_001141980.1	310	Gac/Aac	8/28	1	2	FACETS	0.76	0.644	0.887	0.76	0.644	0.887	SUBCLONAL	1	TRUE	1	0.18	2		574	746	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098655	2098655	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs766814650	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	234	689	1	ENST00000219476.3:c.39G>T	p.Glu13Asp	p.E13D	ENST00000219476	NM_000548.3	13	gaG/gaT	2/42	1	2	FACETS	0.925	0.867	0.984	1	0.996	1	CLONAL	4	TRUE	1	0.18	2		690	703	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647143	2647143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	38	561	0	ENST00000342085.4:c.1421G>A	p.Arg474Gln	p.R474Q	ENST00000342085	NM_002613.4	474	cGa/cAa	13/14	1	2	FACETS	0.662	0.546	0.792	0.662	0.546	0.792	SUBCLONAL	1	TRUE	1	0.18	2		561	638	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641493	23641493	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	42	787	0	ENST00000261584.4:c.1982C>A	p.Pro661His	p.P661H	ENST00000261584	NM_024675.3	661	cCt/cAt	5/13	1	2	FACETS	0.637	0.53	0.756	0.637	0.53	0.756	SUBCLONAL	1	TRUE	1	0.18	2		787	733	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50788288	50788288	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	278	615	0	ENST00000398568.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000398568	NM_001042412.1	289	gCg/gTg	5/18	1	2	FACETS	0.891	0.839	0.944	1	0.996	1	CLONAL	4	TRUE	1	0.18	2		615	867	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650710	67650710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243010179	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	263	666	0	ENST00000264010.4:c.1015C>T	p.Arg339Trp	p.R339W	ENST00000264010	NM_006565.3	339	Cgg/Tgg	5/12	1	2	FACETS	1	0.98	1	1	0.996	1	CLONAL	3	TRUE	1	0.18	2		666	887	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821193	72821193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200911275	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	300	786	2	ENST00000268489.5:c.10982C>T	p.Ser3661Leu	p.S3661L	ENST00000268489	NM_006885.3	3661	tCg/tTg	10/10	1	2	FACETS	0.876	0.827	0.927	1	0.997	1	CLONAL	4	TRUE	1	0.18	2		788	951	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830931	72830931	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	183	545	0	ENST00000268489.5:c.5650G>T	p.Glu1884Ter	p.E1884*	ENST00000268489	NM_006885.3	1884	Gaa/Taa	9/10	1	2	FACETS	0.928	0.862	0.995	1	0.995	1	CLONAL	4	TRUE	1	0.18	2		545	548	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832072	72832072	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	215	633	0	ENST00000268489.5:c.4509G>T	p.Gln1503His	p.Q1503H	ENST00000268489	NM_006885.3	1503	caG/caT	9/10	1	2	FACETS	0.927	0.867	0.989	1	0.995	1	CLONAL	4	TRUE	1	0.18	2		633	644	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346961	89346961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775491352	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	104	490	0	ENST00000301030.4:c.5989G>A	p.Ala1997Thr	p.A1997T	ENST00000301030	NM_001256183.1	1997	Gcg/Acg	9/13	1	2	FACETS	1	0.935	1	1	0.991	1	CLONAL	3	TRUE	1	0.18	2		490	369	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350856	89350856	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	328	800	0	ENST00000301030.4:c.2094G>T	p.Glu698Asp	p.E698D	ENST00000301030	NM_001256183.1	698	gaG/gaT	9/13	1	2	FACETS	1	0.988	1	1	0.997	1	CLONAL	3	TRUE	1	0.18	2		800	1057	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877154	89877154	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	207	525	0	ENST00000389301.3:c.483C>A	p.Phe161Leu	p.F161L	ENST00000389301	NM_000135.2	161	ttC/ttA	5/43	1	2	FACETS	1	0.982	1	1	0.995	1	CLONAL	3	TRUE	1	0.18	2		525	668	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	38	.	.	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	1	2	FACETS	0.415	0.341	0.498	0.415	0.341	0.498	SUBCLONAL	1	TRUE	1	0.18	2		0	1018	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15952253	15952253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767227910	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	275	735	1	ENST00000268712.3:c.6442G>A	p.Glu2148Lys	p.E2148K	ENST00000268712	NM_006311.3	2148	Gag/Aag	41/46	1	2	FACETS	0.904	0.851	0.958	1	0.996	1	CLONAL	4	TRUE	1	0.18	2		736	845	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049857	16049857	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs781575973	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	106	309	0	ENST00000268712.3:c.915A>C	p.Gln305His	p.Q305H	ENST00000268712	NM_006311.3	305	caA/caC	10/46	1	2	FACETS	0.895	0.812	0.981	1	0.991	1	CLONAL	4	TRUE	1	0.18	2		309	329	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29497004	29497004	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781670	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	50	276	0	ENST00000356175.3:c.575G>A	p.Arg192Gln	p.R192Q	ENST00000356175	NM_000267.3	192	cGa/cAa	5/57	1	2	FACETS	0.908	0.775	1	1	0.972	1	CLONAL	2	TRUE	1	0.18	2		276	306	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528084	29528084	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	23	278	0	ENST00000356175.3:c.1092C>A	p.Phe364Leu	p.F364L	ENST00000356175	NM_000267.3	364	ttC/ttA	10/57	1	2	FACETS	0.878	0.686	1	0.878	0.686	1	CLONAL	1	TRUE	1	0.18	2		278	291	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684380	29684380	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781791	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	169	411	0	ENST00000356175.3:c.7900C>A	p.Pro2634Thr	p.P2634T	ENST00000356175	NM_000267.3	2634	Cct/Act	53/57	1	2	FACETS	0.95	0.881	1	1	0.994	1	CLONAL	4	TRUE	1	0.18	2		411	494	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38504619	38504619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1240210247	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	235	825	2	ENST00000254066.5:c.230C>T	p.Ser77Leu	p.S77L	ENST00000254066	NM_000964.3	77	tCg/tTg	3/9	1	2	FACETS	1	0.98	1	1	0.996	1	CLONAL	3	TRUE	1	0.18	2		827	782	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59871053	59871053	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	139	363	0	ENST00000259008.2:c.1378G>T	p.Asp460Tyr	p.D460Y	ENST00000259008	NM_032043.2	460	Gat/Tat	10/20	1	2	FACETS	1	0.975	1	1	0.993	1	CLONAL	3	TRUE	1	0.18	2		363	443	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39567848	39567848	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	22	226	0	ENST00000262039.4:c.604G>T	p.Glu202Ter	p.E202*	ENST00000262039	NM_002647.2	202	Gaa/Taa	5/25	1	2	FACETS	0.892	0.693	1	0.892	0.693	1	CLONAL	1	TRUE	1	0.18	2		226	274	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229332	5229332	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1417612381	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	318	866	2	ENST00000357368.4:c.2371G>A	p.Glu791Lys	p.E791K	ENST00000357368	NM_002850.3	791	Gaa/Aaa	16/38	1	2	FACETS	0.993	0.94	1	1	0.997	1	CLONAL	4	TRUE	1	0.18	2		868	890	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7141795	7141795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149536206	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	227	761	2	ENST00000302850.5:c.2575C>T	p.His859Tyr	p.H859Y	ENST00000302850	NM_000208.2	859	Cat/Tat	13/22	1	2	FACETS	0.889	0.832	0.948	1	0.996	1	CLONAL	4	TRUE	1	0.18	2		763	709	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792263	33792263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	259	864	2	ENST00000498907.2:c.1058C>T	p.Ala353Val	p.A353V	ENST00000498907	NM_004364.3	353	gCc/gTc	1/1	1	2	FACETS	0.963	0.906	1	1	0.996	1	CLONAL	4	TRUE	1	0.18	2		866	747	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793305	33793305	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	86	262	0	ENST00000498907.2:c.16T>G	p.Phe6Val	p.F6V	ENST00000498907	NM_004364.3	6	Ttc/Gtc	1/1	1	2	FACETS	0.971	0.873	1	1	0.99	1	CLONAL	4	TRUE	1	0.18	2		262	246	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212215	36212215	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	283	856	1	ENST00000222270.7:c.1966G>T	p.Glu656Ter	p.E656*	ENST00000222270	NM_014727.1	656	Gaa/Taa	3/37	1	2	FACETS	0.899	0.848	0.952	1	0.996	1	CLONAL	4	TRUE	1	0.18	2		857	874	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965416	25965416	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	218	821	0	ENST00000435504.4:c.3790G>T	p.Asp1264Tyr	p.D1264Y	ENST00000435504		1264	Gat/Tat	13/13	1	2	FACETS	1	0.982	1	1	0.995	1	CLONAL	3	TRUE	1	0.18	2		821	705	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606641	29606641	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	176	619	1	ENST00000389048.3:c.1239C>A	p.Ser413Arg	p.S413R	ENST00000389048	NM_004304.4	413	agC/agA	5/29	1	2	FACETS	0.977	0.904	1	1	0.994	1	CLONAL	3	TRUE	1	0.18	2		620	667	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213223	39213223	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	150	942	1	ENST00000402219.2:c.3744C>A	p.Phe1248Leu	p.F1248L	ENST00000402219	NM_005633.3	1248	ttC/ttA	23/23	1	2	FACETS	0.922	0.842	1	1	0.99	1	CLONAL	2	TRUE	1	0.18	2		943	904	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249941	39249941	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	245	662	1	ENST00000402219.2:c.1628C>A	p.Ser543Tyr	p.S543Y	ENST00000402219	NM_005633.3	543	tCt/tAt	10/23	1	2	FACETS	0.92	0.863	0.977	1	0.996	1	CLONAL	4	TRUE	1	0.18	2		663	740	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705457	47705457	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	135	333	0	ENST00000233146.2:c.2257G>T	p.Gly753Ter	p.G753*	ENST00000233146	NM_000251.2	753	Gga/Tga	14/16	1	2	FACETS	0.995	0.914	1	1	0.993	1	CLONAL	4	TRUE	1	0.18	2		333	377	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026606	48026606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1358771617	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	153	499	0	ENST00000234420.5:c.1484G>A	p.Arg495Gln	p.R495Q	ENST00000234420	NM_000179.2	495	cGa/cAa	4/10	1	2	FACETS	0.9	0.83	0.972	1	0.994	1	CLONAL	4	TRUE	1	0.18	2		499	472	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	190	400	0	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	0.942	0.877	1	1	0.995	1	CLONAL	4	TRUE	1	0.18	2		400	560	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719724	61719724	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	229	651	0	ENST00000401558.2:c.1544G>A	p.Arg515Gln	p.R515Q	ENST00000401558	NM_003400.3	515	cGa/cAa	14/25	1	2	FACETS	1	0.984	1	1	0.996	1	CLONAL	3	TRUE	1	0.18	2		651	730	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99137182	99137182	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	92	268	0	ENST00000074304.5:c.139G>T	p.Glu47Ter	p.E47*	ENST00000074304	NM_001134224.1	47	Gaa/Taa	4/26	1	2	FACETS	0.901	0.807	1	1	0.989	1	CLONAL	3	TRUE	1	0.18	2		268	378	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622495	158622495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316254232	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	199	526	0	ENST00000263640.3:c.1004G>A	p.Arg335Gln	p.R335Q	ENST00000263640	NM_001105.4	335	cGa/cAa	8/11	1	2	FACETS	0.935	0.872	1	1	0.995	1	CLONAL	4	TRUE	1	0.18	2		526	591	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095761	178095761	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	134	360	0	ENST00000397062.3:c.1570G>T	p.Glu524Ter	p.E524*	ENST00000397062	NM_006164.4	524	Gaa/Taa	5/5	1	2	FACETS	0.919	0.843	0.997	1	0.993	1	CLONAL	4	TRUE	1	0.18	2		360	405	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178129274	178129274	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	192	452	0	ENST00000397062.3:c.31C>T	p.Leu11Phe	p.L11F	ENST00000397062	NM_006164.4	11	Ctc/Ttc	1/5	1	2	FACETS	1	0.959	1	1	0.995	1	CLONAL	4	TRUE	1	0.18	2		452	514	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738308	190738308	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	130	307	0	ENST00000441310.2:c.2560C>A	p.Leu854Ile	p.L854I	ENST00000441310	NM_000534.4	854	Ctt/Att	12/13	1	2	FACETS	1	0.965	1	1	0.993	1	CLONAL	3	TRUE	1	0.18	2		307	435	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257737	198257737	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	156	442	0	ENST00000335508.6:c.3715G>A	p.Val1239Ile	p.V1239I	ENST00000335508	NM_012433.2	1239	Gtt/Att	24/25	1	2	FACETS	0.95	0.878	1	1	0.994	1	CLONAL	4	TRUE	1	0.18	2		442	456	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198262785	198262785	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	52	442	1	ENST00000335508.6:c.3190G>T	p.Glu1064Ter	p.E1064*	ENST00000335508	NM_012433.2	1064	Gag/Tag	22/25	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.18	2		443	511	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131315	202131315	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	184	540	0	ENST00000358485.4:c.283G>T	p.Glu95Ter	p.E95*	ENST00000358485	NM_001080125.1	95	Gaa/Taa	2/9	1	2	FACETS	1	0.981	1	1	0.995	1	CLONAL	3	TRUE	1	0.18	2		540	586	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566733	212566733	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	130	336	0	ENST00000342788.4:c.1448A>C	p.Gln483Pro	p.Q483P	ENST00000342788	NM_005235.2	483	cAg/cCg	12/28	1	2	FACETS	1	0.959	1	1	0.993	1	CLONAL	3	TRUE	1	0.18	2		336	445	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812293	212812293	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569995088	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	149	318	0	ENST00000342788.4:c.283C>T	p.Arg95Cys	p.R95C	ENST00000342788	NM_005235.2	95	Cgt/Tgt	3/28	1	2	FACETS	0.939	0.865	1	1	0.994	1	CLONAL	4	TRUE	1	0.18	2		318	441	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657093	215657093	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1444375563	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	181	495	0	ENST00000260947.4:c.292A>C	p.Asn98His	p.N98H	ENST00000260947	NM_000465.2	98	Aat/Cat	3/11	1	2	FACETS	1	0.978	1	1	0.995	1	CLONAL	3	TRUE	1	0.18	2		495	590	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543547	9543547	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760772824	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	183	508	0	ENST00000353224.5:c.1607C>T	p.Thr536Ile	p.T536I	ENST00000353224	NM_177990.2	536	aCt/aTt	6/10	1	2	FACETS	0.918	0.853	0.984	1	0.995	1	CLONAL	4	TRUE	1	0.18	2		508	554	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30946596	30946596	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	146	337	0	ENST00000375687.4:c.18G>T	p.Lys6Asn	p.K6N	ENST00000375687	NM_015338.5	6	aaG/aaT	1/13	1	2	FACETS	0.92	0.847	0.994	1	0.994	1	CLONAL	4	TRUE	1	0.18	2		337	441	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376816	31376816	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	101	570	1	ENST00000328111.2:c.811G>A	p.Glu271Lys	p.E271K	ENST00000328111	NM_006892.3	271	Gag/Aag	7/23	1	2	FACETS	1	0.947	1	1	0.988	1	CLONAL	2	TRUE	1	0.18	2		571	516	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728698	39728698	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	94	254	0	ENST00000361337.2:c.978A>C	p.Lys326Asn	p.K326N	ENST00000361337	NM_003286.2	326	aaA/aaC	12/21	1	2	FACETS	1	0.927	1	1	0.99	1	CLONAL	3	TRUE	1	0.18	2		254	335	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46266513	46266513	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	36	348	0	ENST00000371998.3:c.2498G>T	p.Gly833Val	p.G833V	ENST00000371998		833	gGa/gTa	13/23	1	2	FACETS	0.873	0.718	1	0.873	0.718	1	CLONAL	1	TRUE	1	0.18	2		348	458	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252865	36252865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060499616	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	142	429	0	ENST00000300305.3:c.497G>A	p.Arg166Gln	p.R166Q	ENST00000300305		166	cGa/cAa	4/8	1	2	FACETS	1	0.961	1	1	0.993	1	CLONAL	3	TRUE	1	0.18	2		429	487	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24158958	24158958	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs142218902	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	242	687	0	ENST00000263121.7:c.630G>T	p.Glu210Asp	p.E210D	ENST00000263121	NM_003073.3	210	gaG/gaT	6/9	1	2	FACETS	0.986	0.926	1	1	0.996	1	CLONAL	4	TRUE	1	0.18	2		687	682	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37055937	37055937	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	124	347	1	ENST00000231790.2:c.692T>G	p.Ile231Ser	p.I231S	ENST00000231790	NM_000249.3	231	aTt/aGt	9/19	1	2	FACETS	1	0.972	1	1	0.992	1	CLONAL	3	TRUE	1	0.18	2		348	398	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275019	41275019	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	58	424	0	ENST00000349496.5:c.1186-1G>T		p.X396_splice	ENST00000349496	NM_001904.3	396			1	2	FACETS	0.903	0.779	1	1	0.976	1	CLONAL	2	TRUE	1	0.18	2		424	357	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47061257	47061257	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	165	428	0	ENST00000409792.3:c.7424G>T	p.Arg2475Ile	p.R2475I	ENST00000409792	NM_014159.6	2475	aGa/aTa	19/21	1	2	FACETS	1	0.969	1	1	0.994	1	CLONAL	3	TRUE	1	0.18	2		428	558	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164267	47164267	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	131	374	1	ENST00000409792.3:c.1859G>A	p.Arg620Gln	p.R620Q	ENST00000409792	NM_014159.6	620	cGa/cAa	3/21	1	2	FACETS	0.943	0.865	1	1	0.993	1	CLONAL	4	TRUE	1	0.18	2		375	386	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165279	47165279	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	26	379	0	ENST00000409792.3:c.847G>T	p.Asp283Tyr	p.D283Y	ENST00000409792	NM_014159.6	283	Gat/Tat	3/21	1	2	FACETS	0.672	0.531	0.833	0.672	0.531	0.833	SUBCLONAL	1	TRUE	1	0.18	2		379	430	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436344	52436344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765539314	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	243	841	2	ENST00000460680.1:c.2150G>A	p.Arg717Gln	p.R717Q	ENST00000460680	NM_004656.3	717	cGg/cAg	17/17	1	2	FACETS	0.963	0.904	1	1	0.996	1	CLONAL	4	TRUE	1	0.18	2		843	701	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597438	52597438	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	128	560	0	ENST00000394830.3:c.3872T>G	p.Phe1291Cys	p.F1291C	ENST00000394830	NM_018313.4	1291	tTt/tGt	25/30	1	2	FACETS	1	0.975	1	1	0.991	1	CLONAL	2	TRUE	1	0.18	2		560	589	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637690	52637690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239654517	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	170	406	0	ENST00000394830.3:c.2626C>T	p.Arg876Cys	p.R876C	ENST00000394830	NM_018313.4	876	Cgt/Tgt	18/30	1	2	FACETS	1	0.967	1	1	0.994	1	CLONAL	3	TRUE	1	0.18	2		406	583	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990420	69990420	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	170	385	0	ENST00000394351.3:c.379G>A	p.Glu127Lys	p.E127K	ENST00000394351	NM_000248.3	127	Gaa/Aaa	4/9	1	2	FACETS	1	0.961	1	1	0.995	1	CLONAL	4	TRUE	1	0.18	2		385	449	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70005661	70005661	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	158	462	0	ENST00000394351.3:c.690G>T	p.Leu230Phe	p.L230F	ENST00000394351	NM_000248.3	230	ttG/ttT	7/9	1	2	FACETS	1	0.978	1	1	0.994	1	CLONAL	3	TRUE	1	0.18	2		462	504	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448552	89448552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	200	568	0	ENST00000336596.2:c.1516G>A	p.Val506Ile	p.V506I	ENST00000336596	NM_005233.5	506	Gta/Ata	7/17	1	2	FACETS	1	0.979	1	1	0.995	1	CLONAL	3	TRUE	1	0.18	2		568	657	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457270	89457270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	127	402	1	ENST00000336596.2:c.1751G>A	p.Gly584Asp	p.G584D	ENST00000336596	NM_005233.5	584	gGc/gAc	9/17	1	2	FACETS	0.889	0.813	0.967	1	0.993	1	CLONAL	4	TRUE	1	0.18	2		403	397	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960109	134960109	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	194	703	0	ENST00000398015.3:c.2466G>T	p.Glu822Asp	p.E822D	ENST00000398015	NM_004441.4	822	gaG/gaT	13/16	1	2	FACETS	1	0.968	1	1	0.995	1	CLONAL	3	TRUE	1	0.18	2		703	670	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426006	138426006	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755672708	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	155	413	0	ENST00000289153.2:c.1525G>A	p.Asp509Asn	p.D509N	ENST00000289153	NM_006219.2	509	Gat/Aat	9/22	1	2	FACETS	0.906	0.837	0.978	1	0.994	1	CLONAL	4	TRUE	1	0.18	2		413	475	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238521	142238521	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	70	269	1	ENST00000350721.4:c.4372C>A	p.Leu1458Ile	p.L1458I	ENST00000350721	NM_001184.3	1458	Cta/Ata	24/47	1	2	FACETS	1	0.908	1	1	0.986	1	CLONAL	3	TRUE	1	0.18	2		270	251	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238542	142238542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148064542	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	133	300	0	ENST00000350721.4:c.4351C>T	p.Arg1451Trp	p.R1451W	ENST00000350721	NM_001184.3	1451	Cgg/Tgg	24/47	1	2	FACETS	0.927	0.854	1	1	0.993	1	CLONAL	5	TRUE	1	0.18	2		300	319	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259876	142259876	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	144	391	0	ENST00000350721.4:c.3451G>A	p.Ala1151Thr	p.A1151T	ENST00000350721	NM_001184.3	1151	Gcc/Acc	18/47	1	2	FACETS	0.957	0.881	1	1	0.994	1	CLONAL	4	TRUE	1	0.18	2		391	418	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278200	142278200	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	236	574	0	ENST00000350721.4:c.1625A>G	p.Lys542Arg	p.K542R	ENST00000350721	NM_001184.3	542	aAa/aGa	7/47	1	2	FACETS	0.951	0.892	1	1	0.996	1	CLONAL	4	TRUE	1	0.18	2		574	689	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279247	142279247	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	114	520	0	ENST00000350721.4:c.1399A>C	p.Lys467Gln	p.K467Q	ENST00000350721	NM_001184.3	467	Aaa/Caa	6/47	1	2	FACETS	1	0.964	1	1	0.99	1	CLONAL	2	TRUE	1	0.18	2		520	556	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013719	170013719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388201066	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	159	421	1	ENST00000295797.4:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000295797	NM_002740.5	480	Cgc/Tgc	15/18	1	2	FACETS	1	0.968	1	1	0.994	1	CLONAL	3	TRUE	1	0.18	2		422	539	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	124	450	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	1	0.953	1	1	0.992	1	CLONAL	3	TRUE	1	0.18	2		450	430	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191446	185191446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756793616	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	289	864	0	ENST00000265026.3:c.2327C>T	p.Thr776Met	p.T776M	ENST00000265026	NM_004721.4	776	aCg/aTg	11/14	1	2	FACETS	1	0.983	1	1	0.996	1	CLONAL	3	TRUE	1	0.18	2		864	964	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133597	55133597	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	185	613	0	ENST00000257290.5:c.901G>T	p.Glu301Ter	p.E301*	ENST00000257290	NM_006206.4	301	Gaa/Taa	6/23	1	2	FACETS	0.877	0.814	0.941	1	0.995	1	CLONAL	4	TRUE	1	0.18	2		613	586	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133718	55133718	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	176	589	0	ENST00000257290.5:c.932-1G>A		p.X311_splice	ENST00000257290	NM_006206.4	311			1	2	FACETS	1	0.931	1	1	0.995	1	CLONAL	4	TRUE	1	0.18	2		589	488	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593395	55593395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1560416964	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	122	364	0	ENST00000288135.5:c.1552C>T	p.Pro518Ser	p.P518S	ENST00000288135	NM_000222.2	518	Ccc/Tcc	10/21	1	2	FACETS	0.911	0.832	0.992	1	0.992	1	CLONAL	4	TRUE	1	0.18	2		364	372	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955605	55955605	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	78	477	0	ENST00000263923.4:c.3340G>T	p.Glu1114Ter	p.E1114*	ENST00000263923	NM_002253.2	1114	Gaa/Taa	25/30	1	2	FACETS	0.959	0.846	1	1	0.983	1	CLONAL	2	TRUE	1	0.18	2		477	452	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961092	55961092	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	180	739	0	ENST00000263923.4:c.2848G>T	p.Asp950Tyr	p.D950Y	ENST00000263923	NM_002253.2	950	Gac/Tac	21/30	1	2	FACETS	1	0.977	1	1	0.993	1	CLONAL	2	TRUE	1	0.18	2		739	872	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968610	55968610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374980446	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	268	622	0	ENST00000263923.4:c.2053G>A	p.Glu685Lys	p.E685K	ENST00000263923	NM_002253.2	685	Gaa/Aaa	14/30	1	2	FACETS	1	0.984	1	1	0.996	1	CLONAL	3	TRUE	1	0.18	2		622	882	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970985	55970985	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	59	662	0	ENST00000263923.4:c.1812G>T	p.Lys604Asn	p.K604N	ENST00000263923	NM_002253.2	604	aaG/aaT	13/30	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.18	2		662	626	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972005	55972005	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761405036	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	155	471	0	ENST00000263923.4:c.1639G>A	p.Val547Met	p.V547M	ENST00000263923	NM_002253.2	547	Gtg/Atg	12/30	1	2	FACETS	0.891	0.822	0.962	1	0.994	1	CLONAL	4	TRUE	1	0.18	2		471	483	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193974	106193974	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	55	306	0	ENST00000380013.4:c.4436T>G	p.Leu1479Arg	p.L1479R	ENST00000380013	NM_001127208.2	1479	cTt/cGt	10/11	1	2	FACETS	0.83	0.713	0.957	1	0.972	1	CLONAL	2	TRUE	1	0.18	2		306	368	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114277	143114277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs76891221	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	118	397	0	ENST00000262992.4:c.1144C>T	p.Arg382Trp	p.R382W	ENST00000262992	NM_001101669.1	382	Cgg/Tgg	13/24	1	2	FACETS	0.881	0.803	0.962	1	0.992	1	CLONAL	4	TRUE	1	0.18	2		397	372	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159104	143159104	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1405228238	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	95	469	0	ENST00000262992.4:c.749G>A	p.Arg250Gln	p.R250Q	ENST00000262992	NM_001101669.1	250	cGa/cAa	10/24	1	2	FACETS	0.865	0.775	0.959	1	0.989	1	CLONAL	3	TRUE	1	0.18	2		469	407	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630299	187630299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	205	630	1	ENST00000441802.2:c.683G>A	p.Gly228Asp	p.G228D	ENST00000441802	NM_005245.3	228	gGc/gAc	2/27	1	2	FACETS	1	0.982	1	1	0.995	1	CLONAL	3	TRUE	1	0.18	2		631	657	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228414	228414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	172	543	0	ENST00000264932.6:c.736C>T	p.Arg246Cys	p.R246C	ENST00000264932	NM_004168.2	246	Cgc/Tgc	6/15	1	2	FACETS	1	0.969	1	1	0.994	1	CLONAL	3	TRUE	1	0.18	2		543	585	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526411	31526411	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	389	1200	0	ENST00000344624.3:c.629A>G	p.Tyr210Cys	p.Y210C	ENST00000344624		210	tAc/tGc	2/33	1	2	FACETS	0.923	0.878	0.969	1	0.997	1	CLONAL	4	TRUE	1	0.18	2		1200	1171	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967461	38967461	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	141	377	0	ENST00000357387.3:c.1129C>A	p.Leu377Ile	p.L377I	ENST00000357387	NM_152756.3	377	Ctt/Att	13/38	1	2	FACETS	0.89	0.818	0.964	1	0.993	1	CLONAL	4	TRUE	1	0.18	2		377	440	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168741	56168741	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	134	511	1	ENST00000399503.3:c.1595G>T	p.Arg532Leu	p.R532L	ENST00000399503	NM_005921.1	532	cGa/cTa	9/20	1	2	FACETS	0.863	0.787	0.942	1	0.992	1	CLONAL	3	TRUE	1	0.18	2		512	575	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588949	67588949	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	127	284	0	ENST00000274335.5:c.1040T>G	p.Leu347Arg	p.L347R	ENST00000274335		347	cTt/cGt	8/15	1	2	FACETS	0.9	0.823	0.979	1	0.993	1	CLONAL	4	TRUE	1	0.18	2		284	392	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633825	86633825	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	120	294	0	ENST00000274376.6:c.934G>T	p.Glu312Ter	p.E312*	ENST00000274376	NM_002890.2	312	Gaa/Taa	5/25	1	2	FACETS	0.998	0.913	1	1	0.993	1	CLONAL	4	TRUE	1	0.18	2		294	334	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681186	86681186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	84	323	0	ENST00000274376.6:c.2827C>T	p.Leu943Phe	p.L943F	ENST00000274376	NM_002890.2	943	Ctt/Ttt	22/25	1	2	FACETS	1	0.901	1	1	0.988	1	CLONAL	3	TRUE	1	0.18	2		323	308	SUCCESS
APC	324	MSKCC	GRCh37	5	112174502	112174502	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876659539	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	118	351	0	ENST00000257430.4:c.3211C>T	p.Gln1071Ter	p.Q1071*	ENST00000257430	NM_000038.5	1071	Caa/Taa	16/16	1	2	FACETS	0.9	0.821	0.982	1	0.992	1	CLONAL	4	TRUE	1	0.18	2		351	364	SUCCESS
APC	324	MSKCC	GRCh37	5	112175921	112175921	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	109	235	0	ENST00000257430.4:c.4630G>T	p.Glu1544Ter	p.E1544*	ENST00000257430	NM_000038.5	1544	Gaa/Taa	16/16	1	2	FACETS	1	0.924	1	1	0.992	1	CLONAL	4	TRUE	1	0.18	2		235	298	SUCCESS
APC	324	MSKCC	GRCh37	5	112176581	112176581	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	139	338	0	ENST00000257430.4:c.5290C>A	p.Gln1764Lys	p.Q1764K	ENST00000257430	NM_000038.5	1764	Cag/Aag	16/16	1	2	FACETS	0.924	0.849	1	1	0.993	1	CLONAL	4	TRUE	1	0.18	2		338	418	SUCCESS
APC	324	MSKCC	GRCh37	5	112177377	112177377	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	106	323	0	ENST00000257430.4:c.6086C>A	p.Ser2029Tyr	p.S2029Y	ENST00000257430	NM_000038.5	2029	tCt/tAt	16/16	1	2	FACETS	1	0.949	1	1	0.991	1	CLONAL	3	TRUE	1	0.18	2		323	365	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562399	176562399	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	38	740	0	ENST00000439151.2:c.295G>T	p.Asp99Tyr	p.D99Y	ENST00000439151	NM_022455.4	99	Gac/Tac	2/23	1	2	FACETS	0.563	0.464	0.674	0.563	0.464	0.674	SUBCLONAL	1	TRUE	1	0.18	2		740	750	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631272	176631272	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	123	347	0	ENST00000439151.2:c.1215A>T	p.Lys405Asn	p.K405N	ENST00000439151	NM_022455.4	405	aaA/aaT	4/23	1	2	FACETS	0.881	0.804	0.959	1	0.992	1	CLONAL	4	TRUE	1	0.18	2		347	388	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665317	176665317	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	167	424	1	ENST00000439151.2:c.4001C>A	p.Ser1334Tyr	p.S1334Y	ENST00000439151	NM_022455.4	1334	tCt/tAt	7/23	1	2	FACETS	1	0.979	1	1	0.994	1	CLONAL	3	TRUE	1	0.18	2		425	535	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046683	180046683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	274	993	1	ENST00000261937.6:c.2629G>A	p.Ala877Thr	p.A877T	ENST00000261937	NM_182925.4	877	Gcc/Acc	18/30	1	2	FACETS	1	0.978	1	1	0.996	1	CLONAL	3	TRUE	1	0.18	2		994	940	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048561	180048561	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	214	892	0	ENST00000261937.6:c.2001G>T	p.Lys667Asn	p.K667N	ENST00000261937	NM_182925.4	667	aaG/aaT	13/30	1	2	FACETS	1	0.972	1	1	0.995	1	CLONAL	3	TRUE	1	0.18	2		892	736	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398884	398884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375133421	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	179	588	0	ENST00000380956.4:c.694G>A	p.Gly232Arg	p.G232R	ENST00000380956	NM_001195286.1	232	Gga/Aga	6/9	1	2	FACETS	0.875	0.812	0.94	1	0.995	1	CLONAL	4	TRUE	1	0.18	2		588	568	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488359	20488359	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	202	493	0	ENST00000346618.3:c.1015T>G	p.Leu339Val	p.L339V	ENST00000346618	NM_001949.4	339	Ttg/Gtg	6/7	1	2	FACETS	0.906	0.845	0.969	1	0.995	1	CLONAL	4	TRUE	1	0.18	2		493	619	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250666	26250666	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	201	746	0	ENST00000446824.2:c.168G>T	p.Gln56His	p.Q56H	ENST00000446824	NM_021018.2	56	caG/caT	1/1	1	2	FACETS	0.927	0.865	0.992	1	0.995	1	CLONAL	4	TRUE	1	0.18	2		746	602	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681100	30681100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765107298	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	169	422	1	ENST00000376406.3:c.619G>A	p.Gly207Ser	p.G207S	ENST00000376406	NM_014641.2	207	Ggc/Agc	5/15	1	2	FACETS	1	0.946	1	1	0.995	1	CLONAL	4	TRUE	1	0.18	2		423	459	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681661	30681661	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	196	633	0	ENST00000376406.3:c.436A>G	p.Thr146Ala	p.T146A	ENST00000376406	NM_014641.2	146	Aca/Gca	3/15	1	2	FACETS	0.891	0.83	0.954	1	0.995	1	CLONAL	4	TRUE	1	0.18	2		633	611	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815404	32815404	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	75	786	0	ENST00000354258.4:c.1969G>T	p.Glu657Ter	p.E657*	ENST00000354258	NM_000593.5	657	Gaa/Taa	9/11	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.18	2		786	790	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552763	106552763	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	209	627	0	ENST00000369096.4:c.728T>A	p.Val243Asp	p.V243D	ENST00000369096	NM_001198.3	243	gTc/gAc	5/7	1	2	FACETS	0.882	0.823	0.943	1	0.995	1	CLONAL	4	TRUE	1	0.18	2		627	658	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638398	117638398	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	132	483	0	ENST00000368508.3:c.6043G>A	p.Val2015Ile	p.V2015I	ENST00000368508	NM_002944.2	2015	Gtt/Att	38/43	1	2	FACETS	0.89	0.815	0.967	1	0.993	1	CLONAL	4	TRUE	1	0.18	2		483	412	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117645576	117645576	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	199	546	1	ENST00000368508.3:c.5560G>T	p.Asp1854Tyr	p.D1854Y	ENST00000368508	NM_002944.2	1854	Gat/Tat	34/43	1	2	FACETS	0.95	0.886	1	1	0.995	1	CLONAL	4	TRUE	1	0.18	2		547	582	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647547	117647547	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	173	583	0	ENST00000368508.3:c.5397G>T	p.Gln1799His	p.Q1799H	ENST00000368508	NM_002944.2	1799	caG/caT	33/43	1	2	FACETS	1	0.967	1	1	0.994	1	CLONAL	3	TRUE	1	0.18	2		583	593	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662631	117662631	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	83	535	0	ENST00000368508.3:c.4834G>T	p.Glu1612Ter	p.E1612*	ENST00000368508	NM_002944.2	1612	Gaa/Taa	29/43	1	2	FACETS	0.901	0.797	1	1	0.983	1	CLONAL	2	TRUE	1	0.18	2		535	512	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665230	117665230	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1258207555	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	98	238	0	ENST00000368508.3:c.4517G>T	p.Arg1506Ile	p.R1506I	ENST00000368508	NM_002944.2	1506	aGa/aTa	27/43	1	2	FACETS	0.898	0.812	0.988	1	0.991	1	CLONAL	4	TRUE	1	0.18	2		238	303	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674327	117674327	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	157	422	0	ENST00000368508.3:c.4147A>C	p.Lys1383Gln	p.K1383Q	ENST00000368508	NM_002944.2	1383	Aaa/Caa	26/43	1	2	FACETS	0.892	0.823	0.962	1	0.994	1	CLONAL	4	TRUE	1	0.18	2		422	489	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704605	117704605	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	118	449	1	ENST00000368508.3:c.2371G>T	p.Asp791Tyr	p.D791Y	ENST00000368508	NM_002944.2	791	Gac/Tac	16/43	1	2	FACETS	1	0.909	1	1	0.992	1	CLONAL	3	TRUE	1	0.18	2		450	437	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715410	117715410	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769599473	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	136	457	0	ENST00000368508.3:c.1079G>T	p.Arg360Ile	p.R360I	ENST00000368508	NM_002944.2	360	aGa/aTa	10/43	1	2	FACETS	0.935	0.859	1	1	0.993	1	CLONAL	4	TRUE	1	0.18	2		457	404	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864478	162864478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	158	546	0	ENST00000366898.1:c.35G>A	p.Gly12Asp	p.G12D	ENST00000366898	NM_004562.2	12	gGt/gAt	2/12	1	2	FACETS	0.926	0.856	0.998	1	0.994	1	CLONAL	4	TRUE	1	0.18	2		546	474	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259533	55259533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	192	656	0	ENST00000275493.2:c.2591C>T	p.Ala864Val	p.A864V	ENST00000275493	NM_005228.3	864	gCg/gTg	21/28	1	2	FACETS	0.962	0.893	1	1	0.994	1	CLONAL	3	TRUE	1	0.18	2		656	739	SUCCESS
MET	4233	MSKCC	GRCh37	7	116413948	116413948	+	intron_variant	Intron	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	72	1114	0	ENST00000397752.3:c.3029-987G>T		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.68	0.592	0.776	0.68	0.592	0.776	SUBCLONAL	1	TRUE	1	0.18	2		1114	1176	SUCCESS
MET	4233	MSKCC	GRCh37	7	116414246	116414246	+	intron_variant	Intron	SNP	T	T	C	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	250	926	0	ENST00000397752.3:c.3029-689T>C		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	1	0.985	1	1	0.996	1	CLONAL	3	TRUE	1	0.18	2		926	801	SUCCESS
MET	4233	MSKCC	GRCh37	7	116414566	116414566	+	intron_variant	Intron	SNP	A	A	C	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	189	805	0	ENST00000397752.3:c.3029-369A>C		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	1	0.971	1	1	0.993	1	CLONAL	2	TRUE	1	0.18	2		805	956	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836803	151836803	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	51	616	0	ENST00000262189.6:c.14417G>T	p.Arg4806Leu	p.R4806L	ENST00000262189	NM_170606.2	4806	cGa/cTa	56/59	1	2	FACETS	0.917	0.779	1	0.917	0.779	1	CLONAL	1	TRUE	1	0.18	2		616	618	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859299	151859299	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	34	341	0	ENST00000262189.6:c.11363C>A	p.Ser3788Tyr	p.S3788Y	ENST00000262189	NM_170606.2	3788	tCt/tAt	43/59	1	2	FACETS	0.889	0.726	1	0.889	0.726	1	CLONAL	1	TRUE	1	0.18	2		341	425	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880069	151880069	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	148	426	0	ENST00000262189.6:c.5255A>C	p.Lys1752Thr	p.K1752T	ENST00000262189	NM_170606.2	1752	aAa/aCa	35/59	1	2	FACETS	1	0.975	1	1	0.994	1	CLONAL	3	TRUE	1	0.18	2		426	477	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945021	151945021	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs756918375	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	12	79	0	ENST00000262189.6:c.2498G>T	p.Arg833Ile	p.R833I	ENST00000262189	NM_170606.2	833	aGa/aTa	14/59	1	2	FACETS	0.939	0.663	1	0.939	0.663	1	CLONAL	1	TRUE	1	0.18	2		79	142	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012244	152012244	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748254163	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	146	417	0	ENST00000262189.6:c.569G>A	p.Arg190Gln	p.R190Q	ENST00000262189	NM_170606.2	190	cGa/cAa	4/59	1	2	FACETS	1	0.967	1	1	0.993	1	CLONAL	3	TRUE	1	0.18	2		417	492	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273576	38273576	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	112	529	0	ENST00000425967.3:c.1759C>T	p.Pro587Ser	p.P587S	ENST00000425967	NM_001174067.1	587	Ccc/Tcc	14/19	1	2	FACETS	1	0.965	1	1	0.992	1	CLONAL	3	TRUE	1	0.18	2		529	367	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275837	38275837	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	256	783	0	ENST00000425967.3:c.1432T>G	p.Ser478Ala	p.S478A	ENST00000425967	NM_001174067.1	478	Tca/Gca	11/19	1	2	FACETS	1	0.985	1	1	0.996	1	CLONAL	3	TRUE	1	0.18	2		783	821	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277205	38277205	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	272	824	0	ENST00000425967.3:c.1223T>C	p.Ile408Thr	p.I408T	ENST00000425967	NM_001174067.1	408	aTc/aCc	10/19	1	2	FACETS	0.925	0.871	0.98	1	0.996	1	CLONAL	4	TRUE	1	0.18	2		824	817	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56854504	56854504	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1285322860	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	173	550	0	ENST00000519728.1:c.86G>T	p.Arg29Ile	p.R29I	ENST00000519728	NM_002350.3	29	aGa/aTa	2/13	1	2	FACETS	1	0.949	1	1	0.994	1	CLONAL	3	TRUE	1	0.18	2		550	620	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56910929	56910929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1218543185	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	187	534	1	ENST00000519728.1:c.1075G>A	p.Glu359Lys	p.E359K	ENST00000519728	NM_002350.3	359	Gag/Aag	11/13	1	2	FACETS	1	0.958	1	1	0.995	1	CLONAL	3	TRUE	1	0.18	2		535	662	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995547	68995547	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	175	703	2	ENST00000288368.4:c.1951G>T	p.Glu651Ter	p.E651*	ENST00000288368	NM_024870.2	651	Gaa/Taa	18/40	1	2	FACETS	1	0.983	1	1	0.993	1	CLONAL	2	TRUE	1	0.18	2		705	786	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5078415	5078415	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	161	436	0	ENST00000381652.3:c.2102G>A	p.Gly701Asp	p.G701D	ENST00000381652	NM_004972.3	701	gGc/gAc	16/25	1	2	FACETS	0.94	0.869	1	1	0.994	1	CLONAL	4	TRUE	1	0.18	2		436	476	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27168520	27168520	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	132	583	0	ENST00000380036.4:c.392T>C	p.Met131Thr	p.M131T	ENST00000380036	NM_000459.3	131	aTg/aCg	3/23	1	2	FACETS	1	0.965	1	1	0.991	1	CLONAL	2	TRUE	1	0.18	2		583	655	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27209165	27209165	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	190	573	0	ENST00000380036.4:c.2622A>C	p.Glu874Asp	p.E874D	ENST00000380036	NM_000459.3	874	gaA/gaC	16/23	1	2	FACETS	0.89	0.828	0.954	1	0.995	1	CLONAL	4	TRUE	1	0.18	2		573	593	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268780	98268780	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	178	609	0	ENST00000331920.6:c.303C>A	p.Phe101Leu	p.F101L	ENST00000331920	NM_000264.3	101	ttC/ttA	2/24	1	2	FACETS	0.856	0.791	0.924	1	0.994	1	CLONAL	3	TRUE	1	0.18	2		609	770	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128305385	128305385	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs913099145	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	256	645	0	ENST00000265960.3:c.911T>C	p.Ile304Thr	p.I304T	ENST00000265960	NM_001006617.1	304	aTc/aCc	7/12	1	2	FACETS	1	0.983	1	1	0.996	1	CLONAL	3	TRUE	1	0.18	2		645	844	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753909	133753909	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746156716	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	175	626	0	ENST00000318560.5:c.1378C>T	p.Arg460Cys	p.R460C	ENST00000318560	NM_005157.4	460	Cgc/Tgc	8/11	1	2	FACETS	0.988	0.913	1	1	0.994	1	CLONAL	3	TRUE	1	0.18	2		626	656	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755478	133755478	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355584861	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	219	746	1	ENST00000318560.5:c.1447C>T	p.Arg483Trp	p.R483W	ENST00000318560	NM_005157.4	483	Cgg/Tgg	9/11	1	2	FACETS	1	0.975	1	1	0.995	1	CLONAL	3	TRUE	1	0.18	2		747	746	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918695	44918695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746746824	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	166	519	0	ENST00000377967.4:c.1178G>A	p.Arg393Gln	p.R393Q	ENST00000377967	NM_021140.2	393	cGa/cAa	12/29	1	2	FACETS	0.945	0.875	1	1	0.994	1	CLONAL	4	TRUE	1	0.18	2		519	488	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426524	47426524	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	191	748	0	ENST00000377045.4:c.867G>T	p.Lys289Asn	p.K289N	ENST00000377045	NM_001654.4	289	aaG/aaT	9/16	1	2	FACETS	1	0.937	1	1	0.995	1	CLONAL	3	TRUE	1	0.18	2		748	700	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228207	53228207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	265	785	1	ENST00000375401.3:c.2195C>T	p.Ser732Phe	p.S732F	ENST00000375401	NM_004187.3	732	tCc/tTc	15/26	1	2	FACETS	0.924	0.869	0.979	1	0.996	1	CLONAL	4	TRUE	1	0.18	2		786	797	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411963	63411963	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	222	864	0	ENST00000330258.3:c.1204G>T	p.Glu402Ter	p.E402*	ENST00000330258	NM_152424.3	402	Gaa/Taa	2/2	1	2	FACETS	1	0.982	1	1	0.995	1	CLONAL	3	TRUE	1	0.18	2		864	725	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357172	70357172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1367861836	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	253	821	1	ENST00000374080.3:c.5687C>T	p.Ser1896Phe	p.S1896F	ENST00000374080		1896	tCt/tTt	39/45	1	2	FACETS	0.901	0.846	0.957	1	0.996	1	CLONAL	4	TRUE	1	0.18	2		822	780	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776380	76776380	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	42	526	0	ENST00000373344.5:c.7086G>T	p.Met2362Ile	p.M2362I	ENST00000373344	NM_000489.3	2362	atG/atT	34/35	1	2	FACETS	0.943	0.787	1	0.943	0.787	1	CLONAL	1	TRUE	1	0.18	2		526	495	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814252	76814252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs122445101	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	101	384	0	ENST00000373344.5:c.6392G>A	p.Arg2131Gln	p.R2131Q	ENST00000373344	NM_000489.3	2131	cGa/cAa	29/35	1	2	FACETS	1	0.91	1	1	0.987	1	CLONAL	2	TRUE	1	0.18	2		384	552	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909659	76909659	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	152	436	1	ENST00000373344.5:c.4246C>A	p.Gln1416Lys	p.Q1416K	ENST00000373344	NM_000489.3	1416	Cag/Aag	14/35	1	2	FACETS	0.891	0.821	0.962	1	0.994	1	CLONAL	4	TRUE	1	0.18	2		437	474	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937850	76937850	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs138256318	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	33	619	0	ENST00000373344.5:c.2898G>T	p.Glu966Asp	p.E966D	ENST00000373344	NM_000489.3	966	gaG/gaT	9/35	1	2	FACETS	0.564	0.458	0.684	0.564	0.458	0.684	SUBCLONAL	1	TRUE	1	0.18	2		619	650	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938094	76938094	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	197	681	1	ENST00000373344.5:c.2654G>T	p.Arg885Ile	p.R885I	ENST00000373344	NM_000489.3	885	aGa/aTa	9/35	1	2	FACETS	1	0.976	1	1	0.995	1	CLONAL	3	TRUE	1	0.18	2		682	659	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939072	76939072	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	186	559	0	ENST00000373344.5:c.1676C>A	p.Ser559Ter	p.S559*	ENST00000373344	NM_000489.3	559	tCa/tAa	9/35	1	2	FACETS	1	0.979	1	1	0.995	1	CLONAL	3	TRUE	1	0.18	2		559	604	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939806	76939806	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	232	588	0	ENST00000373344.5:c.942A>C	p.Arg314Ser	p.R314S	ENST00000373344	NM_000489.3	314	agA/agC	9/35	1	2	FACETS	0.935	0.877	0.995	1	0.996	1	CLONAL	4	TRUE	1	0.18	2		588	689	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020384	123020384	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	101	331	0	ENST00000355640.3:c.872C>G	p.Ala291Gly	p.A291G	ENST00000355640		291	gCt/gGt	2/7	1	2	FACETS	0.92	0.833	1	1	0.991	1	CLONAL	4	TRUE	1	0.18	2		331	305	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202443	123202443	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	98	461	0	ENST00000218089.9:c.2295G>T	p.Met765Ile	p.M765I	ENST00000218089	NM_001042749.1	765	atG/atT	24/35	1	2	FACETS	0.91	0.814	1	1	0.985	1	CLONAL	2	TRUE	1	0.18	2		461	598	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123499661	123499661	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	32	612	0	ENST00000371139.4:c.188C>A	p.Ser63Tyr	p.S63Y	ENST00000371139	NM_001114937.2	63	tCt/tAt	2/4	1	2	FACETS	0.578	0.468	0.703	0.578	0.468	0.703	SUBCLONAL	1	TRUE	1	0.18	2		612	615	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0041154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	485	722	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.437981832149126	2	FACETS	0.966	0.934	0.998	1	0.997	1	CLONAL	3	TRUE	0	0.437981832149126	2		724	764	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0041154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	100	568	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.833	0.756	0.913	1	0.986	1	CLONAL	2	TRUE	1	0.437981832149126	2		568	274	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469590	25469591	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0041154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	94	884	0	ENST00000264709.3:c.1177_1178del	p.Ser393Ter	p.S393*	ENST00000264709	NM_175629.2	393	AGt/t	10/23	1	2	FACETS	0.566	0.503	0.632	0.566	0.503	0.632	SUBCLONAL	1	TRUE	1	0.437981832149126	2		884	759	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527838	157527841	+	frameshift_variant	Frame_Shift_Del	DEL	AGAA	AGAA	-	rs886041706	NA	P-0041154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	27	597	0	ENST00000346085.5:c.5570_5573del	p.Lys1857SerfsTer17	p.K1857Sfs*17	ENST00000346085	NM_020732.3	1855	AGAAag/ag	20/20	1	2	FACETS	0.311	0.247	0.385	0.311	0.247	0.385	SUBCLONAL	1	TRUE	1	0.437981832149126	2		597	396	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0041200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	40	387	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.13	2		387	498	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920381	134920381	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	45	561	0	ENST00000398015.3:c.2196G>A	p.Met732Ile	p.M732I	ENST00000398015	NM_004441.4	732	atG/atA	12/16	1	2	FACETS	0.95	0.796	1	0.95	0.796	1	CLONAL	1	TRUE	1	0.13	2		561	729	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453987	140453987	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	25	240	0	ENST00000288602.6:c.1741A>T	p.Asn581Tyr	p.N581Y	ENST00000288602	NM_004333.4	581	Aat/Tat	14/18	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.13	2		240	303	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381516	81381516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	40	302	0	ENST00000222390.5:c.545G>A	p.Gly182Glu	p.G182E	ENST00000222390	NM_000601.4	182	gGg/gAg	5/18	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.13	2		302	493	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350514	15350514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	60	721	1	ENST00000263377.2:c.3401C>T	p.Pro1134Leu	p.P1134L	ENST00000263377	NM_058243.2	1134	cCc/cTc	16/20	1	2	FACETS	0.909	0.781	1	0.909	0.781	1	CLONAL	1	TRUE	1	0.13	2		722	1015	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675119	40675119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766760890	NA	P-0041200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	58	875	2	ENST00000249776.8:c.83C>T	p.Pro28Leu	p.P28L	ENST00000249776	NM_033286.3	28	cCg/cTg	1/9	0.0771747826348792	0	FACETS	0.729	0.624	0.844			1	INDETERMINATE	1	TRUE	0	0.13	0		877	1065	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299917	15299917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555729068	NA	P-0041200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	68	835	3	ENST00000263388.2:c.1261C>T	p.Arg421Cys	p.R421C	ENST00000263388	NM_000435.2	421	Cgt/Tgt	8/33	1	2	FACETS	0.926	0.803	1	0.926	0.803	1	CLONAL	1	TRUE	1	0.13	2		838	1130	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625656	1625656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	66	890	1	ENST00000344749.5:c.418C>T	p.Pro140Ser	p.P140S	ENST00000344749	NM_001136139.2	140	Cct/Tct	7/19	1	2	FACETS	0.813	0.703	0.933	0.813	0.703	0.933	CLONAL	1	TRUE	1	0.13	2		891	1249	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120296	70120296	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1338	132	744	0	ENST00000245479.2:c.1298C>T	p.Pro433Leu	p.P433L	ENST00000245479	NM_000346.3	433	cCg/cTg	3/3	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.13	2		744	1470	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351157	89351157	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	48	646	0	ENST00000301030.4:c.1793A>C	p.His598Pro	p.H598P	ENST00000301030	NM_001256183.1	598	cAc/cCc	9/13	1	2	FACETS	0.811	0.683	0.952	0.811	0.683	0.952	CLONAL	1	TRUE	1	0.13	2		646	911	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794096	42794096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568511345	NA	P-0041200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	42	494	1	ENST00000575354.2:c.1457G>A	p.Gly486Asp	p.G486D	ENST00000575354	NM_015125.3	486	gGc/gAc	9/20	1	2	FACETS	0.95	0.792	1	0.95	0.792	1	CLONAL	1	TRUE	1	0.13	2		495	680	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624838	9624838	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	40	467	0	ENST00000353224.5:c.139G>A	p.Ala47Thr	p.A47T	ENST00000353224	NM_177990.2	47	Gcc/Acc	3/10	1	2	FACETS	0.941	0.78	1	0.941	0.78	1	CLONAL	1	TRUE	1	0.13	2		467	654	SUCCESS
APC	324	MSKCC	GRCh37	5	112173828	112173828	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	20	357	0	ENST00000257430.4:c.2537C>T	p.Ser846Phe	p.S846F	ENST00000257430	NM_000038.5	846	tCt/tTt	16/16	1	2	FACETS	0.805	0.615	1	0.805	0.615	1	CLONAL	1	TRUE	1	0.13	2		357	382	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468218	50468218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	88	668	1	ENST00000331340.3:c.1453G>A	p.Gly485Ser	p.G485S	ENST00000331340	NM_006060.4	485	Ggc/Agc	8/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.13	2		669	998	SUCCESS
BTK	695	MSKCC	GRCh37	X	100614312	100614312	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555978277	NA	P-0041200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	40	272	0	ENST00000308731.7:c.863G>A	p.Arg288Gln	p.R288Q	ENST00000308731	NM_000061.2	288	cGg/cAg	10/19	1	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.13	1		272	392	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961602	18961603	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	T	novel	NA	P-0041200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	47	606	0	ENST00000262803.5:c.735_736delinsT	p.Ser247ProfsTer74	p.S247Pfs*74	ENST00000262803	NM_002911.3	245	atCCcc/atTcc	5/24	1	2	FACETS	0.833	0.701	0.98	0.833	0.701	0.98	CLONAL	1	TRUE	1	0.13	2		606	868	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	193	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.948	0.885	1	0.948	0.885	1	CLONAL	1	TRUE	1	0.773731788027672	2		126	526	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0041221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17922	16221	750	2	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.773731788027672	34	FACETS	1	0.999	1			1	CLONAL	16	TRUE	NA	0.773731788027672	34		752	34143	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315513	30315513	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs774753677	NA	P-0041221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	58	470	0	ENST00000322652.5:c.1198A>G	p.Ile400Val	p.I400V	ENST00000322652	NM_015355.2	400	Att/Gtt	10/16	1	2	FACETS	0.211	0.18	0.244	0.211	0.18	0.244	SUBCLONAL	1	TRUE	1	0.773731788027672	2		470	712	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210237	123210237	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	282	354	0	ENST00000218089.9:c.2591del	p.Leu864TyrfsTer8	p.L864Yfs*8	ENST00000218089	NM_001042749.1	863	aaT/aa	26/35	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.773731788027672	1		354	394	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0041232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	27	414	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.827	1	1	0.827	1	CLONAL	1	TRUE	1	0.09	2		414	573	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0041232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	27	485	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.844	0.669	1	0.844	0.669	1	CLONAL	1	TRUE	1	0.09	2		485	711	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0041232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	26	416	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.899	0.709	1	0.899	0.709	1	CLONAL	1	TRUE	1	0.09	2		416	643	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0041232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	12	350	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	0.534	0.374	0.734	0.534	0.374	0.734	SUBCLONAL	1	TRUE	1	0.09	2		350	499	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591099	67591099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs773686816	NA	P-0041232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	24	295	1	ENST00000274335.5:c.1692C>A	p.Asn564Lys	p.N564K	ENST00000274335		564	aaC/aaA	12/15	1	2	FACETS	0.982	0.768	1	0.982	0.768	1	CLONAL	1	TRUE	1	0.09	2		296	543	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0041252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	153	414	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.94	0.863	1	0.94	0.863	1	CLONAL	1	TRUE	1	0.504692081790905	2		414	645	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0041252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	122	311	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	0.504692081790905	1	FACETS	0.835	0.76	0.912	0.835	0.76	0.912	CLONAL	1	TRUE	0	0.504692081790905	1		311	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0041252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	306	823	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.504692081790905	1	FACETS	0.977	0.923	1	0.977	0.923	1	CLONAL	1	TRUE	0	0.504692081790905	1		823	928	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041037	112041037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761032788	NA	P-0041252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	166	516	0	ENST00000368678.4:c.218C>T	p.Thr73Met	p.T73M	ENST00000368678		73	aCg/aTg	3/13	1	2	FACETS	0.871	0.802	0.943	0.871	0.802	0.943	CLONAL	1	TRUE	1	0.504692081790905	2		516	755	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227954	53227954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1192107564	NA	P-0041252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	240	793	1	ENST00000375401.3:c.2360G>A	p.Arg787Gln	p.R787Q	ENST00000375401	NM_004187.3	787	cGg/cAg	16/26	0.504692081790905	1	FACETS	0.951	0.891	1	0.951	0.891	1	CLONAL	1	TRUE	0	0.504692081790905	1		794	748	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964487	93964487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1219702649	NA	P-0041252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	162	476	0	ENST00000369303.4:c.2410G>A	p.Ala804Thr	p.A804T	ENST00000369303	NM_004440.3	804	Gca/Aca	14/17	1	2	FACETS	0.961	0.885	1	0.961	0.885	1	CLONAL	1	TRUE	1	0.504692081790905	2		476	668	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397553	116397553	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	211	307	0	ENST00000397752.3:c.1925A>T	p.Asn642Ile	p.N642I	ENST00000397752	NM_000245.2	642	aAt/aTt	7/21	1	2	FACETS	0.983	0.914	1	0.983	0.914	1	CLONAL	1	TRUE	1	0.504692081790905	2		307	851	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468158	50468158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	463	618	0	ENST00000331340.3:c.1393G>A	p.Glu465Lys	p.E465K	ENST00000331340	NM_006060.4	465	Gaa/Aaa	8/8	0.375565519378636	4	FACETS	0.84	0.804	0.878			1	CLONAL	3	TRUE	NA	0.421271245838221	4		618	1239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747342068	NA	P-0041255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	386	817	1	ENST00000269305.4:c.394A>G	p.Lys132Glu	p.K132E	ENST00000269305	NM_001126112.2	132	Aag/Gag	5/11	0.415652518826565	2	FACETS	0.995	0.949	1	0.995	0.949	1	CLONAL	2	TRUE	0	0.421271245838221	2		818	921	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247899	59247899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	54	747	0	ENST00000371222.2:c.844G>A	p.Glu282Lys	p.E282K	ENST00000371222	NM_002228.3	282	Gaa/Aaa	1/1	1	2	FACETS	0.263	0.224	0.307	0.263	0.224	0.307	SUBCLONAL	1	TRUE	1	0.421271245838221	2		747	973	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503056	125503056	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0041255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	65	233	0	ENST00000428830.2:c.425-2A>C		p.X142_splice	ENST00000428830	NM_001114121.2	142			0.421271245838221	3	FACETS	1	0.904	1	0.348	0.303	0.396	CLONAL	1	TRUE	0	0.421271245838221	3		233	358	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786663	3786663	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	110	593	0	ENST00000262367.5:c.4548C>G	p.Ile1516Met	p.I1516M	ENST00000262367	NM_004380.2	1516	atC/atG	27/31	0.374539382420799	4	FACETS	0.841	0.754	0.932	0.42	0.377	0.466	CLONAL	1	TRUE	2	0.421271245838221	4		593	883	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516915	187516915	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	93	508	0	ENST00000441802.2:c.13066T>C	p.Tyr4356His	p.Y4356H	ENST00000441802	NM_005245.3	4356	Tac/Cac	26/27	0.324752319851864	4	FACETS	0.824	0.732	0.921	0.275	0.244	0.307	CLONAL	1	TRUE	1	0.421271245838221	4		508	762	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0041276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	1283	549	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.844600914253235	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.844313727249254	3		552	1418	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0041276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	469	508	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	0.844600914253235	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.844313727249254	1		508	580	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095917	29095917	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780192	NA	P-0041276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	346	620	1	ENST00000328354.6:c.917G>A	p.Gly306Glu	p.G306E	ENST00000328354	NM_007194.3	306	gGg/gAg	9/15	1	2	FACETS	0.963	0.916	1	0.963	0.916	1	CLONAL	1	TRUE	1	0.844313727249254	2		621	851	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306689	41306689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868376470	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	395	717	0	ENST00000373198.4:c.970G>A	p.Glu324Lys	p.E324K	ENST00000373198	NM_133170.3	324	Gaa/Aaa	7/32	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.710247152876966	2		717	991	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	305	458	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.710247152876966	2		458	691	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117870663	117870663	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	177	420	0	ENST00000297338.2:c.409C>T	p.Gln137Ter	p.Q137*	ENST00000297338	NM_006265.2	137	Cag/Tag	5/14	1	2	FACETS	0.937	0.87	1	0.937	0.87	1	CLONAL	1	TRUE	1	0.710247152876966	2		420	532	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462975	120462975	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1435723160	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	384	614	1	ENST00000256646.2:c.5356C>T	p.Arg1786Ter	p.R1786*	ENST00000256646	NM_024408.3	1786	Cga/Tga	30/34	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.710247152876966	2		615	908	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5246054	5246054	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	285	427	0	ENST00000357368.4:c.721C>T	p.Arg241Cys	p.R241C	ENST00000357368	NM_002850.3	241	Cgc/Tgc	10/38	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.710247152876966	2		427	724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	536	754	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.710247152876966	2		754	1335	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151625	55151625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571523023	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	330	684	0	ENST00000257290.5:c.2411G>A	p.Arg804Gln	p.R804Q	ENST00000257290	NM_006206.4	804	cGa/cAa	17/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.710247152876966	2		684	873	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973911	55973911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs941528100	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	382	581	2	ENST00000263923.4:c.1405G>A	p.Glu469Lys	p.E469K	ENST00000263923	NM_002253.2	469	Gag/Aag	10/30	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.710247152876966	2		583	987	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641526	18641526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1331057234	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	162	434	0	ENST00000266497.5:c.2525G>A	p.Gly842Glu	p.G842E	ENST00000266497		842	gGg/gAg	17/31	0.710247152876966	1	FACETS	0.67	0.621	0.72	0.67	0.621	0.72	SUBCLONAL	1	TRUE	0	0.710247152876966	1		434	439	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490340	29490340	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	358	539	0	ENST00000356175.3:c.425T>A	p.Leu142Ter	p.L142*	ENST00000356175	NM_000267.3	142	tTa/tAa	4/57	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.710247152876966	2		539	954	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756634	756634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1387077624	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	332	649	0	ENST00000314574.4:c.194C>T	p.Ser65Phe	p.S65F	ENST00000314574	NM_005433.3	65	tCc/tTc	2/12	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.710247152876966	2		649	930	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645693	12645693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397516827	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	232	381	0	ENST00000251849.4:c.776C>T	p.Ser259Phe	p.S259F	ENST00000251849	NM_002880.3	259	tCc/tTc	7/17	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.710247152876966	2		381	642	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	712	534	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.997	1	1	0.998	1	CLONAL	2	TRUE	1	0.710247152876966	2		534	897	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729163	66729163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516792	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	407	756	0	ENST00000307102.5:c.371C>T	p.Pro124Leu	p.P124L	ENST00000307102	NM_002755.3	124	cCg/cTg	3/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.710247152876966	2		756	1137	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335121	65335121	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	318	636	0	ENST00000342505.4:c.520C>T	p.Arg174Ter	p.R174*	ENST00000342505	NM_002227.2	174	Cga/Tga	6/25	1	2	FACETS	0.937	0.886	0.988	0.937	0.886	0.988	CLONAL	1	TRUE	1	0.710247152876966	2		636	956	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067153	37067153	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782467	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	184	300	0	ENST00000231790.2:c.1064C>T	p.Pro355Leu	p.P355L	ENST00000231790	NM_000249.3	355	cCc/cTc	12/19	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.710247152876966	2		300	428	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248746	212248746	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762661533	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	166	451	0	ENST00000342788.4:c.3521G>A	p.Arg1174Gln	p.R1174Q	ENST00000342788	NM_005235.2	1174	cGg/cAg	28/28	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.710247152876966	2		451	454	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693886	47693886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750029	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	159	460	0	ENST00000233146.2:c.1600C>T	p.Arg534Cys	p.R534C	ENST00000233146	NM_000251.2	534	Cgt/Tgt	10/16	1	2	FACETS	0.975	0.902	1	0.975	0.902	1	CLONAL	1	TRUE	1	0.710247152876966	2		460	459	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892205	9892205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	485	683	0	ENST00000330684.3:c.2285G>A	p.Gly762Glu	p.G762E	ENST00000330684	NM_001134407.1	762	gGa/gAa	11/13	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.710247152876966	2		683	1163	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713427	40713427	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752787425	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	442	740	0	ENST00000373198.4:c.4088G>A	p.Arg1363Gln	p.R1363Q	ENST00000373198	NM_133170.3	1363	cGg/cAg	30/32	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.710247152876966	2		740	1137	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355282	15355282	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572537806	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	410	489	0	ENST00000263377.2:c.2341C>T	p.Pro781Ser	p.P781S	ENST00000263377	NM_058243.2	781	Ccc/Tcc	13/20	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.710247152876966	2		489	834	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508619	106508619	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	377	616	0	ENST00000359195.3:c.613A>G	p.Lys205Glu	p.K205E	ENST00000359195	NM_002649.2	205	Aag/Gag	2/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.710247152876966	2		616	941	SUCCESS
CBL	867	MSKCC	GRCh37	11	119168158	119168158	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1565272311	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	246	552	1	ENST00000264033.4:c.2218C>T	p.Gln740Ter	p.Q740*	ENST00000264033	NM_005188.3	740	Cag/Tag	14/16	1	2	FACETS	0.992	0.933	1	0.992	0.933	1	CLONAL	1	TRUE	1	0.710247152876966	2		553	698	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589732	28589732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	250	511	0	ENST00000241453.7:c.2648C>T	p.Ser883Leu	p.S883L	ENST00000241453	NM_004119.2	883	tCa/tTa	21/24	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.710247152876966	2		511	694	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166811	32166811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142608082	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	497	713	2	ENST00000375023.3:c.4427G>A	p.Arg1476Gln	p.R1476Q	ENST00000375023	NM_004557.3	1476	cGa/cAa	24/30	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.710247152876966	2		715	1281	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740215	162740215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771675675	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	423	637	0	ENST00000367921.3:c.1417C>T	p.Arg473Cys	p.R473C	ENST00000367921	NM_006182.2	473	Cgc/Tgc	12/18	0.710247152876966	3	FACETS	1	0.987	1	0.552	0.526	0.58	CLONAL	1	TRUE	1	0.710247152876966	3		637	1461	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552823	106552823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1042709746	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	378	787	0	ENST00000369096.4:c.788G>A	p.Gly263Glu	p.G263E	ENST00000369096	NM_001198.3	263	gGa/gAa	5/7	1	2	FACETS	0.922	0.876	0.969	0.922	0.876	0.969	CLONAL	1	TRUE	1	0.710247152876966	2		787	1154	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579475	7579475	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	469	806	0	ENST00000269305.4:c.212C>T	p.Pro71Leu	p.P71L	ENST00000269305	NM_001126112.2	71	cCc/cTc	4/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.710247152876966	2		806	1274	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664894	29664894	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1567617727	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	139	438	0	ENST00000356175.3:c.6637C>T	p.Gln2213Ter	p.Q2213*	ENST00000356175	NM_000267.3	2213	Caa/Taa	43/57	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.710247152876966	2		438	382	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032173	26032173	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765944241	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	257	520	0	ENST00000244661.2:c.116C>T	p.Pro39Leu	p.P39L	ENST00000244661	NM_003537.3	39	cCt/cTt	1/1	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.710247152876966	2		520	671	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026984	71026984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763413735	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	327	608	0	ENST00000318789.4:c.1343C>T	p.Ser448Leu	p.S448L	ENST00000318789	NM_032682.5	448	tCg/tTg	15/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.710247152876966	2		608	885	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78599593	78599593	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs772240053	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	300	449	0	ENST00000306801.3:c.265G>A	p.Asp89Asn	p.D89N	ENST00000306801	NM_020761.2	89	Gat/Aat	2/34	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.710247152876966	2		449	701	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163486	108163486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770590652	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	164	545	0	ENST00000278616.4:c.4577C>T	p.Pro1526Leu	p.P1526L	ENST00000278616	NM_000051.3	1526	cCc/cTc	30/63	0.382765446934525	1	FACETS	0.612	0.566	0.658	0.612	0.566	0.658	INDETERMINATE	1	TRUE	0	0.710247152876966	1		545	487	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341130	8341130	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	153	519	0	ENST00000356435.5:c.5086G>A	p.Gly1696Arg	p.G1696R	ENST00000356435		1696	Gga/Aga	30/35	1	2	FACETS	0.867	0.799	0.937	0.867	0.799	0.937	CLONAL	1	TRUE	1	0.710247152876966	2		519	497	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151558	55151558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	212	486	1	ENST00000257290.5:c.2344C>T	p.Leu782Phe	p.L782F	ENST00000257290	NM_006206.4	782	Ctt/Ttt	17/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.710247152876966	2		487	549	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615595	43615595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	395	678	0	ENST00000355710.3:c.2674G>A	p.Asp892Asn	p.D892N	ENST00000355710	NM_020975.4	892	Gat/Aat	15/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.710247152876966	2		678	1084	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551100	41551100	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	356	631	0	ENST00000263253.7:c.3244C>T	p.Gln1082Ter	p.Q1082*	ENST00000263253	NM_001429.3	1082	Cag/Tag	17/31	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.710247152876966	2		631	968	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352462	89352462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	492	751	0	ENST00000301030.4:c.877G>A	p.Glu293Lys	p.E293K	ENST00000301030	NM_001256183.1	293	Gag/Aag	8/13	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.710247152876966	2		751	1187	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944956	31944956	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	345	581	1	ENST00000340398.3:c.145C>T	p.Arg49Ter	p.R49*	ENST00000340398	NM_001013699.2	49	Cga/Tga	1/1	0.710247152876966	1	FACETS	0.702	0.666	0.737	0.702	0.666	0.737	SUBCLONAL	1	TRUE	0	0.710247152876966	1		582	893	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874635	35874635	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs752967041	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	266	429	0	ENST00000303115.3:c.791G>A	p.Trp264Ter	p.W264*	ENST00000303115	NM_002185.3	264	tGg/tAg	6/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.710247152876966	2		429	689	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8338945	8338945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	235	527	0	ENST00000356435.5:c.5356G>A	p.Glu1786Lys	p.E1786K	ENST00000356435		1786	Gaa/Aaa	32/35	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.710247152876966	2		527	630	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794781	42794781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1284125732	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	437	805	0	ENST00000575354.2:c.1861C>T	p.Pro621Ser	p.P621S	ENST00000575354	NM_015125.3	621	Ccc/Tcc	10/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.710247152876966	2		805	1111	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374311	31374311	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	373	586	0	ENST00000328111.2:c.310C>T	p.Arg104Ter	p.R104*	ENST00000328111	NM_006892.3	104	Cga/Tga	5/23	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.710247152876966	2		586	946	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111855978	111855978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1484288251	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	397	550	0	ENST00000341259.2:c.29C>T	p.Ser10Leu	p.S10L	ENST00000341259	NM_005475.2	10	tCg/tTg	2/8	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.710247152876966	2		550	1026	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515151	106515151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	226	425	0	ENST00000359195.3:c.2294C>T	p.Ser765Leu	p.S765L	ENST00000359195	NM_002649.2	765	tCa/tTa	5/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.710247152876966	2		425	626	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956164	55956164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780209077	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	338	609	0	ENST00000263923.4:c.3151C>T	p.Arg1051Trp	p.R1051W	ENST00000263923	NM_002253.2	1051	Cgg/Tgg	23/30	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.710247152876966	2		609	890	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275836	38275836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	417	764	0	ENST00000425967.3:c.1433C>T	p.Ser478Leu	p.S478L	ENST00000425967	NM_001174067.1	478	tCa/tTa	11/19	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.710247152876966	2		764	1072	SUCCESS
AR	367	MSKCC	GRCh37	X	66765072	66765072	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	463	353	0	ENST00000374690.3:c.84G>C	p.Gln28His	p.Q28H	ENST00000374690	NM_000044.3	28	caG/caC	1/8	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.710247152876966	1		353	584	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770630	40770630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	268	443	0	ENST00000373198.4:c.2752G>A	p.Gly918Arg	p.G918R	ENST00000373198	NM_133170.3	918	Ggg/Agg	19/32	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.710247152876966	2		443	689	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061517	38061517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771653601	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	301	408	0	ENST00000250448.2:c.472G>A	p.Asp158Asn	p.D158N	ENST00000250448	NM_004496.3	158	Gac/Aac	2/2	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.710247152876966	2		408	722	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471007	8471007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764232627	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	207	471	0	ENST00000356435.5:c.3492G>A	p.Met1164Ile	p.M1164I	ENST00000356435		1164	atG/atA	20/35	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.710247152876966	2		471	496	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857805	9857805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	389	705	0	ENST00000330684.3:c.3596C>T	p.Pro1199Leu	p.P1199L	ENST00000330684	NM_001134407.1	1199	cCg/cTg	13/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.710247152876966	2		705	1054	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710974	117710974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	192	378	0	ENST00000368508.3:c.1298G>A	p.Arg433Lys	p.R433K	ENST00000368508	NM_002944.2	433	aGa/aAa	12/43	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.710247152876966	2		378	532	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198260807	198260807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	156	582	0	ENST00000335508.6:c.3512C>T	p.Pro1171Leu	p.P1171L	ENST00000335508	NM_012433.2	1171	cCg/cTg	23/25	1	2	FACETS	0.957	0.884	1	0.957	0.884	1	CLONAL	1	TRUE	1	0.710247152876966	2		582	459	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259646	89259646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	183	392	0	ENST00000336596.2:c.790G>A	p.Glu264Lys	p.E264K	ENST00000336596	NM_005233.5	264	Gaa/Aaa	3/17	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.710247152876966	2		392	470	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189349321	189349321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	145	439	0	ENST00000264731.3:c.17C>T	p.Ser6Leu	p.S6L	ENST00000264731	NM_003722.4	6	tCa/tTa	1/14	1	2	FACETS	0.928	0.854	1	0.928	0.854	1	CLONAL	1	TRUE	1	0.710247152876966	2		439	440	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762875	40762875	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763646270	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	506	744	0	ENST00000392038.2:c.133C>T	p.Pro45Ser	p.P45S	ENST00000392038	NM_001626.4	45	Cct/Tct	3/14	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.710247152876966	2		744	1215	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612101	189612101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778606951	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	423	665	1	ENST00000264731.3:c.1853G>A	p.Arg618Gln	p.R618Q	ENST00000264731	NM_003722.4	618	cGg/cAg	14/14	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.710247152876966	2		666	1009	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93607866	93607866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	251	504	0	ENST00000375746.1:c.568G>A	p.Gly190Arg	p.G190R	ENST00000375746	NM_001174167.1	190	Gga/Aga	3/14	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.710247152876966	2		504	656	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100405	8100405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	432	836	0	ENST00000346208.3:c.379C>T	p.Pro127Ser	p.P127S	ENST00000346208		127	Ccg/Tcg	3/6	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.710247152876966	2		836	1195	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647776	206647776	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	393	686	1	ENST00000367120.3:c.190C>T	p.His64Tyr	p.H64Y	ENST00000367120	NM_014002.3	64	Cac/Tac	4/22	0.710247152876966	3	FACETS	0.987	0.936	1	0.493	0.468	0.519	CLONAL	1	TRUE	1	0.710247152876966	3		687	1520	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984810	55984810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	329	614	0	ENST00000263923.4:c.319G>A	p.Glu107Lys	p.E107K	ENST00000263923	NM_002253.2	107	Gaa/Aaa	3/30	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.710247152876966	2		614	916	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357508	89357508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	493	806	0	ENST00000301030.4:c.310G>A	p.Gly104Arg	p.G104R	ENST00000301030	NM_001256183.1	104	Gga/Aga	5/13	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.710247152876966	2		806	1294	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962929	2962929	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147006022	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	530	878	0	ENST00000396946.4:c.1979G>A	p.Arg660Gln	p.R660Q	ENST00000396946	NM_032415.4	660	cGg/cAg	16/25	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.710247152876966	2		878	1418	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561325	9561325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	285	573	1	ENST00000353224.5:c.457G>A	p.Gly153Arg	p.G153R	ENST00000353224	NM_177990.2	153	Gga/Aga	4/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.710247152876966	2		574	741	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912693	100912693	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	223	468	0	ENST00000325455.5:c.2629C>T	p.Leu877Phe	p.L877F	ENST00000325455	NM_001202474.3	877	Ctt/Ttt	7/8	0.382765446934525	1	FACETS	0.74	0.695	0.786	0.74	0.695	0.786	INDETERMINATE	1	TRUE	0	0.710247152876966	1		468	547	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306584	41306584	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	454	785	1	ENST00000373198.4:c.1075C>T	p.Arg359Ter	p.R359*	ENST00000373198	NM_133170.3	359	Cga/Tga	7/32	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.710247152876966	2		786	1154	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615724	100615724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375531341	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	435	321	0	ENST00000308731.7:c.608C>T	p.Pro203Leu	p.P203L	ENST00000308731	NM_000061.2	203	cCg/cTg	8/19	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.710247152876966	1		321	556	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244256	46244256	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	220	574	0	ENST00000334344.6:c.2350C>T	p.Pro784Ser	p.P784S	ENST00000334344	NM_152641.2	784	Cct/Tct	15/21	1	2	FACETS	0.979	0.916	1	0.979	0.916	1	CLONAL	1	TRUE	1	0.710247152876966	2		574	633	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528767	8528767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752353348	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	264	398	1	ENST00000356435.5:c.365C>T	p.Pro122Leu	p.P122L	ENST00000356435		122	cCc/cTc	4/35	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.710247152876966	2		399	646	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727179	40727179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	427	555	1	ENST00000373198.4:c.3785C>T	p.Pro1262Leu	p.P1262L	ENST00000373198	NM_133170.3	1262	cCt/cTt	28/32	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.710247152876966	2		556	1079	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313232	30313232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	370	692	0	ENST00000262643.3:c.926C>T	p.Ser309Leu	p.S309L	ENST00000262643	NM_001238.2	309	tCa/tTa	10/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.710247152876966	2		692	982	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372442	55372442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	484	836	0	ENST00000297316.4:c.1132C>T	p.Pro378Ser	p.P378S	ENST00000297316	NM_022454.3	378	Ccc/Tcc	2/2	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.710247152876966	2		836	1256	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170061	32170061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	516	882	0	ENST00000375023.3:c.3547G>A	p.Gly1183Arg	p.G1183R	ENST00000375023	NM_004557.3	1183	Gga/Aga	21/30	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.710247152876966	2		882	1262	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101913	11101913	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	484	904	1	ENST00000358026.2:c.1333C>T	p.Gln445Ter	p.Q445*	ENST00000358026	NM_001128849.1	445	Cag/Tag	8/36	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.710247152876966	2		905	1231	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354375	354375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910854855	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	528	782	0	ENST00000262320.3:c.1183C>T	p.Arg395Cys	p.R395C	ENST00000262320	NM_003502.3	395	Cgc/Tgc	5/11	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.710247152876966	2		782	1339	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78882691	78882691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	479	710	1	ENST00000306801.3:c.2482G>A	p.Asp828Asn	p.D828N	ENST00000306801	NM_020761.2	828	Gac/Aac	21/34	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.710247152876966	2		711	1217	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843676	156843676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866261145	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1362	534	910	1	ENST00000524377.1:c.1102G>A	p.Gly368Ser	p.G368S	ENST00000524377	NM_002529.3	368	Ggc/Agc	8/17	0.710247152876966	3	FACETS	1	0.987	1	0.537	0.514	0.561	CLONAL	1	TRUE	1	0.710247152876966	3		911	1896	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879010	151879010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	739	667	1	ENST00000262189.6:c.5935C>T	p.Pro1979Ser	p.P1979S	ENST00000262189	NM_170606.2	1979	Ccc/Tcc	36/59	0.710247152876966	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.710247152876966	3		668	1319	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753849	133753849	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	377	725	0	ENST00000318560.5:c.1318T>C	p.Tyr440His	p.Y440H	ENST00000318560	NM_005157.4	440	Tac/Cac	8/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.710247152876966	2		725	989	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251707	212251707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	289	534	0	ENST00000342788.4:c.3352C>T	p.His1118Tyr	p.H1118Y	ENST00000342788	NM_005235.2	1118	Cat/Tat	27/28	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.710247152876966	2		534	793	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893590	28893590	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	306	543	0	ENST00000282397.4:c.3256G>T	p.Gly1086Ter	p.G1086*	ENST00000282397	NM_002019.4	1086	Gga/Tga	24/30	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.710247152876966	2		543	755	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563152	21563152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774128777	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	458	832	0	ENST00000382592.4:c.767C>T	p.Pro256Leu	p.P256L	ENST00000382592	NM_014572.2	256	cCg/cTg	4/8	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.710247152876966	2		832	1129	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518223	8518223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	255	462	0	ENST00000356435.5:c.1168G>A	p.Glu390Lys	p.E390K	ENST00000356435		390	Gaa/Aaa	10/35	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.710247152876966	2		462	658	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383653	42383653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555843732	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	444	683	0	ENST00000221972.3:c.428G>A	p.Arg143Gln	p.R143Q	ENST00000221972	NM_021601.3	143	cGa/cAa	3/5	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.710247152876966	2		683	1131	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156321	106156321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	213	426	0	ENST00000380013.4:c.1222C>T	p.Pro408Ser	p.P408S	ENST00000380013	NM_001127208.2	408	Ccc/Tcc	3/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.710247152876966	2		426	545	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612783	228612783	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1202634115	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	447	757	2	ENST00000366696.1:c.244G>A	p.Asp82Asn	p.D82N	ENST00000366696	NM_003493.2	82	Gac/Aac	1/1	0.710247152876966	3	FACETS	1	0.985	1	0.538	0.512	0.564	CLONAL	1	TRUE	1	0.710247152876966	3		759	1586	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389287	8389287	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	246	645	0	ENST00000356435.5:c.4331G>A	p.Trp1444Ter	p.W1444*	ENST00000356435		1444	tGg/tAg	26/35	1	2	FACETS	0.955	0.897	1	0.955	0.897	1	CLONAL	1	TRUE	1	0.710247152876966	2		645	725	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748601	40748601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200545231	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	304	582	0	ENST00000373198.4:c.2915G>A	p.Arg972Gln	p.R972Q	ENST00000373198	NM_133170.3	972	cGa/cAa	21/32	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.710247152876966	2		582	816	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722210	49722210	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1288496355	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	295	481	1	ENST00000449682.2:c.1730G>A	p.Gly577Glu	p.G577E	ENST00000449682	NM_020998.3	577	gGg/gAg	15/18	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.710247152876966	2		482	674	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945009	151945009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	12	43	0	ENST00000262189.6:c.2510C>T	p.Pro837Leu	p.P837L	ENST00000262189	NM_170606.2	837	cCt/cTt	14/59	0.710247152876966	3	FACETS	0.526	0.375	0.707	0.263	0.187	0.354	SUBCLONAL	1	TRUE	1	0.710247152876966	3		43	87	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743906	41743906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	501	831	0	ENST00000301178.4:c.841G>A	p.Glu281Lys	p.E281K	ENST00000301178	NM_021913.4	281	Gag/Aag	7/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.710247152876966	2		831	1356	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729400	41729400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	415	725	0	ENST00000242208.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000242208	NM_002192.2	377	Cgc/Tgc	3/3	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.710247152876966	2		725	1161	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292591	15292591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758913191	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	545	873	0	ENST00000263388.2:c.2588C>T	p.Ser863Leu	p.S863L	ENST00000263388	NM_000435.2	863	tCg/tTg	17/33	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.710247152876966	2		873	1305	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743975	41743975	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	497	881	0	ENST00000301178.4:c.910C>T	p.Pro304Ser	p.P304S	ENST00000301178	NM_021913.4	304	Cct/Tct	7/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.710247152876966	2		881	1296	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968102	68968102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	217	603	0	ENST00000288368.4:c.1131G>A	p.Met377Ile	p.M377I	ENST00000288368	NM_024870.2	377	atG/atA	10/40	1	2	FACETS	0.975	0.912	1	0.975	0.912	1	CLONAL	1	TRUE	1	0.710247152876966	2		603	627	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551240	29551240	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55706535	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	440	805	0	ENST00000389048.3:c.1390G>A	p.Gly464Arg	p.G464R	ENST00000389048	NM_004304.4	464	Gga/Aga	6/29	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.710247152876966	2		805	1091	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517766	176517766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370322847	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	440	815	0	ENST00000292408.4:c.376G>A	p.Asp126Asn	p.D126N	ENST00000292408	NM_213647.1	126	Gat/Aat	4/18	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.710247152876966	2		815	1144	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897016	28897016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	401	637	0	ENST00000282397.4:c.2864C>T	p.Pro955Leu	p.P955L	ENST00000282397	NM_002019.4	955	cCa/cTa	21/30	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.710247152876966	2		637	1047	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028504	42028504	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751169367	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	275	517	2	ENST00000219905.7:c.4042C>T	p.Arg1348Trp	p.R1348W	ENST00000219905	NM_001164273.1	1348	Cgg/Tgg	13/24	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.710247152876966	2		519	735	SUCCESS
APC	324	MSKCC	GRCh37	5	112178282	112178282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	227	511	0	ENST00000257430.4:c.6991C>T	p.Pro2331Ser	p.P2331S	ENST00000257430	NM_000038.5	2331	Cct/Tct	16/16	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.710247152876966	2		511	627	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560854	9560854	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	413	620	0	ENST00000353224.5:c.928G>A	p.Gly310Arg	p.G310R	ENST00000353224	NM_177990.2	310	Gga/Aga	4/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.710247152876966	2		620	1072	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099959	27099959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	446	693	0	ENST00000324856.7:c.3838C>T	p.Pro1280Ser	p.P1280S	ENST00000324856	NM_006015.4	1280	Ccc/Tcc	15/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.710247152876966	2		693	1171	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012211	16012211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1391053845	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	204	496	0	ENST00000268712.3:c.2071C>T	p.Arg691Cys	p.R691C	ENST00000268712	NM_006311.3	691	Cgt/Tgt	19/46	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.710247152876966	2		496	563	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508580	106508580	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs796052174	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	297	510	1	ENST00000359195.3:c.574G>A	p.Asp192Asn	p.D192N	ENST00000359195	NM_002649.2	192	Gac/Aac	2/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.710247152876966	2		511	744	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074195	8074195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1299729594	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	321	612	1	ENST00000377482.5:c.464C>T	p.Pro155Leu	p.P155L	ENST00000377482	NM_018948.3	155	cCg/cTg	4/4	1	2	FACETS	0.98	0.928	1	0.98	0.928	1	CLONAL	1	TRUE	1	0.710247152876966	2		613	922	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500827	149500827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748872294	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	489	766	1	ENST00000261799.4:c.2403G>A	p.Met801Ile	p.M801I	ENST00000261799	NM_002609.3	801	atG/atA	17/23	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.710247152876966	2		767	1209	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223545	36223545	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	511	858	0	ENST00000222270.7:c.6095C>A	p.Ser2032Tyr	p.S2032Y	ENST00000222270	NM_014727.1	2032	tCc/tAc	28/37	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.710247152876966	2		858	1340	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743889	40743889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	385	669	0	ENST00000373198.4:c.3106G>A	p.Glu1036Lys	p.E1036K	ENST00000373198	NM_133170.3	1036	Gaa/Aaa	23/32	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.710247152876966	2		669	1004	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250217	110250217	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760599521	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	436	791	0	ENST00000374672.4:c.458C>T	p.Pro153Leu	p.P153L	ENST00000374672	NM_004235.4	153	cCg/cTg	3/5	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.710247152876966	2		791	1037	SUCCESS
APC	324	MSKCC	GRCh37	5	112174559	112174559	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	155	511	0	ENST00000257430.4:c.3268C>T	p.Gln1090Ter	p.Q1090*	ENST00000257430	NM_000038.5	1090	Caa/Taa	16/16	1	2	FACETS	0.887	0.818	0.958	0.887	0.818	0.958	CLONAL	1	TRUE	1	0.710247152876966	2		511	492	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436002	56436002	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1366537134	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	266	588	1	ENST00000407977.2:c.1135C>T	p.Gln379Ter	p.Q379*	ENST00000407977		379	Cag/Tag	9/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.710247152876966	2		589	697	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857958	9857958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140536516	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	390	739	0	ENST00000330684.3:c.3443C>T	p.Pro1148Leu	p.P1148L	ENST00000330684	NM_001134407.1	1148	cCg/cTg	13/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.710247152876966	2		739	1029	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627691	37627691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	512	807	1	ENST00000447079.4:c.1606C>T	p.Pro536Ser	p.P536S	ENST00000447079	NM_015083.1	536	Cca/Tca	2/14	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.710247152876966	2		808	1259	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335792	73335792	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	159	359	0	ENST00000377767.4:c.2503C>T	p.His835Tyr	p.H835Y	ENST00000377767	NM_014953.3	835	Cat/Tat	18/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.710247152876966	2		359	415	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686929	37686929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	399	585	0	ENST00000447079.4:c.3833C>T	p.Pro1278Leu	p.P1278L	ENST00000447079	NM_015083.1	1278	cCa/cTa	14/14	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.710247152876966	2		585	1056	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497530	125497530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	116	351	0	ENST00000428830.2:c.94G>A	p.Glu32Lys	p.E32K	ENST00000428830	NM_001114121.2	32	Gaa/Aaa	3/14	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.710247152876966	2		351	325	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444263	50444263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	214	383	0	ENST00000331340.3:c.193G>A	p.Glu65Lys	p.E65K	ENST00000331340	NM_006060.4	65	Gaa/Aaa	4/8	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.710247152876966	2		383	577	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641043	23641043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	418	747	1	ENST00000261584.4:c.2432C>T	p.Pro811Leu	p.P811L	ENST00000261584	NM_024675.3	811	cCa/cTa	5/13	1	2	FACETS	0.991	0.945	1	0.991	0.945	1	CLONAL	1	TRUE	1	0.710247152876966	2		748	1188	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251601	212251601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs905120734	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	285	517	0	ENST00000342788.4:c.3458C>T	p.Pro1153Leu	p.P1153L	ENST00000342788	NM_005235.2	1153	cCt/cTt	27/28	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.710247152876966	2		517	779	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180629	32180629	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1278741655	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	428	529	0	ENST00000375023.3:c.2498C>T	p.Pro833Leu	p.P833L	ENST00000375023	NM_004557.3	833	cCc/cTc	16/30	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.710247152876966	2		529	1056	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622494	28622494	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	177	650	0	ENST00000241453.7:c.1123G>A	p.Ala375Thr	p.A375T	ENST00000241453	NM_004119.2	375	Gcc/Acc	9/24	1	2	FACETS	0.868	0.805	0.934	0.868	0.805	0.934	CLONAL	1	TRUE	1	0.710247152876966	2		650	574	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149447870	149447870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	510	927	0	ENST00000286301.3:c.1534G>A	p.Glu512Lys	p.E512K	ENST00000286301	NM_005211.3	512	Gag/Aag	11/22	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.710247152876966	2		927	1349	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456486	189456486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	328	594	0	ENST00000264731.3:c.247G>A	p.Asp83Asn	p.D83N	ENST00000264731	NM_003722.4	83	Gat/Aat	3/14	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.710247152876966	2		594	826	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858468	57858468	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763536538	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	375	647	1	ENST00000228682.2:c.206C>T	p.Ser69Phe	p.S69F	ENST00000228682	NM_005269.2	69	tCt/tTt	4/12	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.710247152876966	2		648	1022	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041745	29041745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1377493987	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	212	421	1	ENST00000282397.4:c.74C>T	p.Ser25Leu	p.S25L	ENST00000282397	NM_002019.4	25	tCa/tTa	2/30	1	2	FACETS	0.992	0.927	1	0.992	0.927	1	CLONAL	1	TRUE	1	0.710247152876966	2		422	602	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965359	25965359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377609636	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	407	803	0	ENST00000435504.4:c.3847C>T	p.Arg1283Cys	p.R1283C	ENST00000435504		1283	Cgt/Tgt	13/13	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.710247152876966	2		803	1088	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533688	63533688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	329	709	0	ENST00000307078.5:c.1466C>T	p.Pro489Leu	p.P489L	ENST00000307078	NM_004655.3	489	cCc/cTc	6/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.710247152876966	2		709	886	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893590	28893590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752645756	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	276	543	0	ENST00000282397.4:c.3256G>A	p.Gly1086Arg	p.G1086R	ENST00000282397	NM_002019.4	1086	Gga/Aga	24/30	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.710247152876966	2		543	755	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923465	9923465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771688818	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	321	670	0	ENST00000330684.3:c.1822C>T	p.Leu608Phe	p.L608F	ENST00000330684	NM_001134407.1	608	Ctt/Ttt	9/13	1	2	FACETS	0.99	0.938	1	0.99	0.938	1	CLONAL	1	TRUE	1	0.710247152876966	2		670	913	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800940	18800940	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	121	450	0	ENST00000266497.5:c.4316C>T	p.Pro1439Leu	p.P1439L	ENST00000266497		1439	cCa/cTa	31/31	0.710247152876966	1	FACETS	0.617	0.564	0.672	0.617	0.564	0.672	SUBCLONAL	1	TRUE	0	0.710247152876966	1		450	356	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440365	187440365	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	411	611	0	ENST00000232014.4:c.2002C>T	p.Arg668Cys	p.R668C	ENST00000232014	NM_001130845.1	668	Cgt/Tgt	10/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.710247152876966	2		611	1008	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005900	69005900	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	242	572	0	ENST00000288368.4:c.2311T>C	p.Ser771Pro	p.S771P	ENST00000288368	NM_024870.2	771	Tct/Cct	21/40	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.710247152876966	2		572	680	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490506	20490506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	442	647	1	ENST00000346618.3:c.1243C>T	p.Pro415Ser	p.P415S	ENST00000346618	NM_001949.4	415	Cct/Tct	7/7	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.710247152876966	2		648	1059	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	479	913	1	ENST00000375333.2:c.265G>T	p.Asp89Tyr	p.D89Y	ENST00000375333	NM_032454.1	89	Gac/Tac	2/8	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.710247152876966	2		914	1228	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500796	8500796	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	323	579	1	ENST00000356435.5:c.2086G>A	p.Gly696Ser	p.G696S	ENST00000356435		696	Ggc/Agc	13/35	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.710247152876966	2		580	893	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546546	9546546	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	289	444	0	ENST00000353224.5:c.1476C>A	p.Phe492Leu	p.F492L	ENST00000353224	NM_177990.2	492	ttC/ttA	5/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.710247152876966	2		444	752	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463579	25463579	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	405	663	0	ENST00000264709.3:c.2103C>A	p.Phe701Leu	p.F701L	ENST00000264709	NM_175629.2	701	ttC/ttA	18/23	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.710247152876966	2		663	1039	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808323	1808323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	472	975	0	ENST00000260795.2:c.2081C>T	p.Pro694Leu	p.P694L	ENST00000260795		694	cCg/cTg	15/17	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.710247152876966	2		975	1239	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749987	162749987	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	347	586	0	ENST00000367921.3:c.2519C>T	p.Pro840Leu	p.P840L	ENST00000367921	NM_006182.2	840	cCc/cTc	18/18	0.710247152876966	3	FACETS	0.987	0.934	1	0.494	0.467	0.521	CLONAL	1	TRUE	1	0.710247152876966	3		586	1341	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811738	102811738	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1490271682	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	447	755	3	ENST00000307046.8:c.446G>A	p.Arg149Lys	p.R149K	ENST00000307046	NM_001111285.1	149	aGg/aAg	4/4	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.710247152876966	2		758	1163	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11308034	11308034	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	451	706	0	ENST00000361445.4:c.958C>T	p.Gln320Ter	p.Q320*	ENST00000361445	NM_004958.3	320	Cag/Tag	7/58	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.710247152876966	2		706	1181	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254957	16254957	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	355	508	0	ENST00000375759.3:c.2222C>T	p.Pro741Leu	p.P741L	ENST00000375759	NM_015001.2	741	cCc/cTc	11/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.710247152876966	2		508	908	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28605624	28605624	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	349	644	0	ENST00000253063.3:c.1228T>A	p.Tyr410Asn	p.Y410N	ENST00000253063	NM_031459.4	410	Tat/Aat	9/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.710247152876966	2		644	892	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809755	36809756	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	361	727	0	ENST00000373129.3:c.849_850delinsTT	p.Arg284Cys	p.R284C	ENST00000373129	NM_032017.1	283	ttCCgc/ttTTgc	9/12	1	2	FACETS	0.955	0.907	1	0.955	0.907	1	CLONAL	1	TRUE	1	0.710247152876966	2		727	1064	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36931979	36931979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	405	753	1	ENST00000361632.4:c.2490G>A	p.Met830Ile	p.M830I	ENST00000361632		830	atG/atA	16/16	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.710247152876966	2		754	1055	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46738357	46738357	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	369	586	0	ENST00000371975.4:c.1258C>T	p.Gln420Ter	p.Q420*	ENST00000371975	NM_003579.3	420	Cag/Tag	12/18	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.710247152876966	2		586	936	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739081	46739082	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	465	739	1	ENST00000371975.4:c.1430_1431delinsTT	p.Ala477Val	p.A477V	ENST00000371975	NM_003579.3	477	gCC/gTT	13/18	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.710247152876966	2		740	1178	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282391	115282391	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	233	624	0	ENST00000438362.2:c.259C>T	p.Gln87Ter	p.Q87*	ENST00000438362	NM_001242891.1	87	Cag/Tag	3/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.710247152876966	2		624	645	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699322	117699322	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	375	593	1	ENST00000369458.3:c.319C>T	p.Gln107Ter	p.Q107*	ENST00000369458	NM_024626.3	107	Caa/Taa	3/6	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.710247152876966	2		594	991	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844702	156844702	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1569	597	929	2	ENST00000524377.1:c.1256C>A	p.Ser419Ter	p.S419*	ENST00000524377	NM_002529.3	419	tCg/tAg	11/17	0.710247152876966	3	FACETS	1	0.984	1	0.526	0.504	0.548	CLONAL	1	TRUE	1	0.710247152876966	3		931	2166	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741965	162741965	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	363	586	0	ENST00000367921.3:c.1656T>G	p.Asp552Glu	p.D552E	ENST00000367921	NM_006182.2	552	gaT/gaG	13/18	0.710247152876966	3	FACETS	1	0.982	1	0.54	0.511	0.569	CLONAL	1	TRUE	1	0.710247152876966	3		586	1283	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982963	201982963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	428	756	0	ENST00000359651.3:c.812G>A	p.Arg271Lys	p.R271K	ENST00000359651		271	aGa/aAa	7/8	0.710247152876966	3	FACETS	1	0.978	1	0.524	0.498	0.55	CLONAL	1	TRUE	1	0.710247152876966	3		756	1559	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206943200	206943200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	290	433	0	ENST00000423557.1:c.418G>A	p.Glu140Lys	p.E140K	ENST00000423557	NM_000572.2	140	Gag/Aag	4/5	0.710247152876966	3	FACETS	0.959	0.902	1	0.479	0.451	0.509	CLONAL	1	TRUE	1	0.710247152876966	3		433	1154	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944751	206944751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	368	612	0	ENST00000423557.1:c.175G>A	p.Asp59Asn	p.D59N	ENST00000423557	NM_000572.2	59	Gat/Aat	2/5	0.710247152876966	3	FACETS	1	0.984	1	0.545	0.517	0.574	CLONAL	1	TRUE	1	0.710247152876966	3		612	1288	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945687	206945687	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376787667	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	397	639	0	ENST00000423557.1:c.94C>T	p.His32Tyr	p.H32Y	ENST00000423557	NM_000572.2	32	Cac/Tac	1/5	0.710247152876966	3	FACETS	1	0.964	1	0.51	0.484	0.536	CLONAL	1	TRUE	1	0.710247152876966	3		639	1486	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567811	226567811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs552397377	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1268	430	800	2	ENST00000366794.5:c.1355G>A	p.Arg452Gln	p.R452Q	ENST00000366794	NM_001618.3	452	cGa/cAa	10/23	0.710247152876966	3	FACETS	0.966	0.919	1	0.483	0.459	0.508	CLONAL	1	TRUE	1	0.710247152876966	3		802	1698	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570787	226570788	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	339	629	0	ENST00000366794.5:c.1108_1109delinsTT	p.Pro370Leu	p.P370L	ENST00000366794	NM_001618.3	370	CCg/TTg	8/23	0.710247152876966	3	FACETS	0.856	0.808	0.905	0.428	0.404	0.453	CLONAL	1	TRUE	1	0.710247152876966	3		629	1511	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246027167	246027167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	263	614	0	ENST00000388985.4:c.835G>A	p.Asp279Asn	p.D279N	ENST00000388985		279	Gat/Aat	9/12	0.710247152876966	3	FACETS	0.959	0.9	1	0.48	0.45	0.511	CLONAL	1	TRUE	1	0.710247152876966	3		614	1046	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612057	43612057	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356141763	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	410	790	1	ENST00000355710.3:c.2162G>A	p.Arg721Gln	p.R721Q	ENST00000355710	NM_020975.4	721	cGg/cAg	12/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.710247152876966	2		791	1111	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623595	43623595	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	290	523	1	ENST00000355710.3:c.3223G>T	p.Val1075Leu	p.V1075L	ENST00000355710	NM_020975.4	1075	Gta/Tta	20/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.710247152876966	2		524	816	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332531	70332531	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774343833	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	256	725	0	ENST00000373644.4:c.436C>T	p.Pro146Ser	p.P146S	ENST00000373644	NM_030625.2	146	Cct/Tct	2/12	1	2	FACETS	0.939	0.882	0.996	0.939	0.882	0.996	CLONAL	1	TRUE	1	0.710247152876966	2		725	768	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405797	70405797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	215	609	0	ENST00000373644.4:c.3311C>T	p.Pro1104Leu	p.P1104L	ENST00000373644	NM_030625.2	1104	cCa/cTa	4/12	1	2	FACETS	0.989	0.925	1	0.989	0.925	1	CLONAL	1	TRUE	1	0.710247152876966	2		609	612	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70432699	70432699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	201	591	0	ENST00000373644.4:c.4721C>T	p.Ser1574Leu	p.S1574L	ENST00000373644	NM_030625.2	1574	tCa/tTa	8/12	1	2	FACETS	0.948	0.884	1	0.948	0.884	1	CLONAL	1	TRUE	1	0.710247152876966	2		591	597	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769482	112769482	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	136	525	0	ENST00000369452.4:c.1434G>T	p.Leu478Phe	p.L478F	ENST00000369452	NM_007373.3	478	ttG/ttT	8/9	1	2	FACETS	0.868	0.796	0.943	0.868	0.796	0.943	CLONAL	1	TRUE	1	0.710247152876966	2		525	441	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771482	112771482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1208150244	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	406	681	0	ENST00000369452.4:c.1655C>T	p.Pro552Leu	p.P552L	ENST00000369452	NM_007373.3	552	cCa/cTa	9/9	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.710247152876966	2		681	942	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32439124	32439124	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	153	597	0	ENST00000332351.3:c.949G>T	p.Gly317Ter	p.G317*	ENST00000332351	NM_024426.4	317	Gga/Tga	4/10	1	2	FACETS	0.886	0.817	0.958	0.886	0.817	0.958	CLONAL	1	TRUE	1	0.710247152876966	2		597	486	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205131	61205131	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	341	682	0	ENST00000301761.2:c.71C>T	p.Pro24Leu	p.P24L	ENST00000301761	NM_017841.2	24	cCt/cTt	2/4	1	2	FACETS	0.95	0.9	1	0.95	0.9	1	CLONAL	1	TRUE	1	0.710247152876966	2		682	1011	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136033	64136033	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	510	789	0	ENST00000334205.4:c.1294C>T	p.Gln432Ter	p.Q432*	ENST00000334205	NM_003942.2	432	Cag/Tag	11/17	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.710247152876966	2		789	1224	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573765	64573765	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	458	746	0	ENST00000312049.6:c.988C>A	p.Arg330Ser	p.R330S	ENST00000312049	NM_130799.2	330	Cgc/Agc	7/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.710247152876966	2		746	1207	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514311	69514311	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	358	660	0	ENST00000294312.3:c.370G>A	p.Glu124Lys	p.E124K	ENST00000294312	NM_005117.2	124	Gag/Aag	3/3	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.710247152876966	2		660	960	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948792	71948792	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	489	858	0	ENST00000298229.2:c.3504C>A	p.Phe1168Leu	p.F1168L	ENST00000298229	NM_001567.3	1168	ttC/ttA	26/28	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.710247152876966	2		858	1231	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922235	100922235	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	141	574	0	ENST00000325455.5:c.2277G>A	p.Met759Ile	p.M759I	ENST00000325455	NM_001202474.3	759	atG/atA	5/8	0.382765446934525	1	FACETS	0.634	0.583	0.686	0.634	0.583	0.686	INDETERMINATE	1	TRUE	0	0.710247152876966	1		574	404	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999244	100999245	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	413	767	1	ENST00000325455.5:c.557_558delinsTT	p.Pro186Leu	p.P186L	ENST00000325455	NM_001202474.3	186	cCC/cTT	1/8	0.382765446934525	1	FACETS	0.738	0.705	0.772	0.738	0.705	0.772	INDETERMINATE	1	TRUE	0	0.710247152876966	1		768	1016	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102196232	102196232	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	99	413	0	ENST00000263464.3:c.889G>A	p.Gly297Ser	p.G297S	ENST00000263464	NM_001165.4	297	Ggt/Agt	3/9	0.382765446934525	1	FACETS	0.558	0.504	0.615	0.558	0.504	0.615	INDETERMINATE	1	TRUE	0	0.710247152876966	1		413	322	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175459	108175459	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs754562056	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	195	470	0	ENST00000278616.4:c.5554C>T	p.Gln1852Ter	p.Q1852*	ENST00000278616	NM_000051.3	1852	Caa/Taa	37/63	0.382765446934525	1	FACETS	0.673	0.628	0.719	0.673	0.628	0.719	INDETERMINATE	1	TRUE	0	0.710247152876966	1		470	526	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352532	118352532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	387	723	0	ENST00000534358.1:c.3737C>T	p.Pro1246Leu	p.P1246L	ENST00000534358	NM_005933.3	1246	cCa/cTa	7/36	1	2	FACETS	0.938	0.892	0.985	0.938	0.892	0.985	CLONAL	1	TRUE	1	0.710247152876966	2		723	1162	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372434	118372435	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	297	690	0	ENST00000534358.1:c.6367_6368delinsTT	p.Pro2123Leu	p.P2123L	ENST00000534358	NM_005933.3	2123	CCa/TTa	26/36	1	2	FACETS	0.925	0.873	0.978	0.925	0.873	0.978	CLONAL	1	TRUE	1	0.710247152876966	2		690	904	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376107	118376107	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	326	660	0	ENST00000534358.1:c.9500C>A	p.Ser3167Tyr	p.S3167Y	ENST00000534358	NM_005933.3	3167	tCc/tAc	27/36	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.710247152876966	2		660	907	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	430268	430269	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	168	374	1	ENST00000399788.2:c.2433_2434delinsTT	p.Pro812Ser	p.P812S	ENST00000399788	NM_001042603.1	811	agCCca/agTTca	18/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.710247152876966	2		375	433	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	443491	443492	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	185	532	2	ENST00000399788.2:c.1405_1406delinsTT	p.Pro469Leu	p.P469L	ENST00000399788	NM_001042603.1	469	CCg/TTg	11/28	1	2	FACETS	0.848	0.787	0.911	0.848	0.787	0.911	CLONAL	1	TRUE	1	0.710247152876966	2		534	614	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	459854	459854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565542593	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	322	771	0	ENST00000399788.2:c.1241C>T	p.Ser414Phe	p.S414F	ENST00000399788	NM_001042603.1	414	tCc/tTc	10/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.710247152876966	2		771	869	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	493255	493255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	258	537	0	ENST00000399788.2:c.308C>T	p.Ser103Phe	p.S103F	ENST00000399788	NM_001042603.1	103	tCt/tTt	3/28	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.710247152876966	2		537	711	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435596	18435596	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	119	421	0	ENST00000266497.5:c.581G>A	p.Arg194Lys	p.R194K	ENST00000266497		194	aGg/aAg	1/31	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.710247152876966	2		421	328	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656268	18656268	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	179	555	0	ENST00000266497.5:c.2947T>A	p.Ser983Thr	p.S983T	ENST00000266497		983	Tct/Act	21/31	0.710247152876966	1	FACETS	0.595	0.552	0.639	0.595	0.552	0.639	SUBCLONAL	1	TRUE	0	0.710247152876966	1		555	546	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285594	46285594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	201	415	1	ENST00000334344.6:c.4954C>T	p.His1652Tyr	p.H1652Y	ENST00000334344	NM_152641.2	1652	Cat/Tat	17/21	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.710247152876966	2		416	559	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420826	49420826	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781012274	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	408	720	2	ENST00000301067.7:c.14923C>T	p.Arg4975Cys	p.R4975C	ENST00000301067	NM_003482.3	4975	Cgt/Tgt	48/54	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.710247152876966	2		722	1043	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433754	49433754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	561	974	1	ENST00000301067.7:c.7799C>T	p.Ser2600Phe	p.S2600F	ENST00000301067	NM_003482.3	2600	tCc/tTc	31/54	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.710247152876966	2		975	1341	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433904	49433904	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368698254	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	534	925	0	ENST00000301067.7:c.7649C>T	p.Pro2550Leu	p.P2550L	ENST00000301067	NM_003482.3	2550	cCt/cTt	31/54	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.710247152876966	2		925	1292	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434273	49434273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	636	937	0	ENST00000301067.7:c.7280C>T	p.Pro2427Leu	p.P2427L	ENST00000301067	NM_003482.3	2427	cCc/cTc	31/54	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.710247152876966	2		937	1605	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435261	49435261	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	468	808	0	ENST00000301067.7:c.6292G>T	p.Asp2098Tyr	p.D2098Y	ENST00000301067	NM_003482.3	2098	Gac/Tac	31/54	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.710247152876966	2		808	1240	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436940	49436940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	421	805	0	ENST00000301067.7:c.5563C>T	p.Pro1855Ser	p.P1855S	ENST00000301067	NM_003482.3	1855	Cca/Tca	25/54	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.710247152876966	2		805	1158	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859028	57859028	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	435	730	0	ENST00000228682.2:c.524C>A	p.Pro175Gln	p.P175Q	ENST00000228682	NM_005269.2	175	cCa/cAa	5/12	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.710247152876966	2		730	1106	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864229	57864229	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	338	679	0	ENST00000228682.2:c.1706C>A	p.Ser569Tyr	p.S569Y	ENST00000228682	NM_005269.2	569	tCc/tAc	12/12	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.710247152876966	2		679	938	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145435	58145435	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	308	574	0	ENST00000257904.6:c.66G>T	p.Lys22Asn	p.K22N	ENST00000257904	NM_000075.3	22	aaG/aaT	2/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.710247152876966	2		574	830	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811706	102811706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	481	811	0	ENST00000307046.8:c.478G>A	p.Glu160Lys	p.E160K	ENST00000307046	NM_001111285.1	160	Gaa/Aaa	4/4	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.710247152876966	2		811	1288	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112436	115112436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369654422	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	475	612	1	ENST00000257566.3:c.1304C>T	p.Ser435Leu	p.S435L	ENST00000257566	NM_016569.3	435	tCa/tTa	7/8	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.710247152876966	2		613	1139	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536659	120536659	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	485	766	0	ENST00000229340.5:c.433C>T	p.Gln145Ter	p.Q145*	ENST00000229340	NM_006861.6	145	Cag/Tag	5/6	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.710247152876966	2		766	1220	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120783953	120783953	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	382	685	1	ENST00000257552.2:c.1032C>A	p.Phe344Leu	p.F344L	ENST00000257552	NM_002442.3	344	ttC/ttA	13/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.710247152876966	2		686	992	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120805871	120805871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	558	826	0	ENST00000257552.2:c.207G>A	p.Met69Ile	p.M69I	ENST00000257552	NM_002442.3	69	atG/atA	4/15	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.710247152876966	2		826	1340	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426660	121426660	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	463	682	0	ENST00000257555.6:c.351G>T	p.Lys117Asn	p.K117N	ENST00000257555		117	aaG/aaT	2/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.710247152876966	2		682	1165	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620147	21620147	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	297	604	0	ENST00000382592.4:c.19C>T	p.Pro7Ser	p.P7S	ENST00000382592	NM_014572.2	7	Cct/Tct	2/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.710247152876966	2		604	776	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597612	28597612	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	213	467	0	ENST00000241453.7:c.2293G>A	p.Glu765Lys	p.E765K	ENST00000241453	NM_004119.2	765	Gaa/Aaa	19/24	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.710247152876966	2		467	559	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601340	28601340	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	188	509	0	ENST00000241453.7:c.2092G>T	p.Asp698Tyr	p.D698Y	ENST00000241453	NM_004119.2	698	Gat/Tat	17/24	1	2	FACETS	0.926	0.861	0.992	0.926	0.861	0.992	CLONAL	1	TRUE	1	0.710247152876966	2		509	572	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001963	29001963	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	274	569	0	ENST00000282397.4:c.1202G>T	p.Gly401Val	p.G401V	ENST00000282397	NM_002019.4	401	gGg/gTg	9/30	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.710247152876966	2		569	660	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041192	29041192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	341	738	0	ENST00000282397.4:c.236C>T	p.Ser79Phe	p.S79F	ENST00000282397	NM_002019.4	79	tCt/tTt	3/30	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.710247152876966	2		738	925	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913887	32913887	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	180	604	1	ENST00000380152.3:c.5395G>T	p.Ala1799Ser	p.A1799S	ENST00000380152		1799	Gca/Tca	11/27	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.710247152876966	2		605	489	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515168	103515168	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	159	402	0	ENST00000355739.4:c.1669G>T	p.Asp557Tyr	p.D557Y	ENST00000355739	NM_000123.3	557	Gat/Tat	8/15	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.710247152876966	2		402	441	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515177	103515178	+	missense_variant	Missense_Mutation	DNP	CT	CT	TA	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	149	437	0	ENST00000355739.4:c.1678_1679delinsTA	p.Leu560Tyr	p.L560Y	ENST00000355739	NM_000123.3	560	CTt/TAt	8/15	1	2	FACETS	0.978	0.902	1	0.978	0.902	1	CLONAL	1	TRUE	1	0.710247152876966	2		437	429	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434821	110434821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573895037	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	481	791	0	ENST00000375856.3:c.3580C>T	p.Pro1194Ser	p.P1194S	ENST00000375856	NM_003749.2	1194	Cct/Tct	1/2	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.710247152876966	2		791	1144	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422090	81422090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	366	611	0	ENST00000298171.2:c.66G>A	p.Met22Ile	p.M22I	ENST00000298171	NM_000369.2	22	atG/atA	1/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.710247152876966	2		611	946	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81574784	81574784	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	156	489	0	ENST00000298171.2:c.680G>A	p.Gly227Glu	p.G227E	ENST00000298171	NM_000369.2	227	gGa/gAa	8/10	1	2	FACETS	0.943	0.871	1	0.943	0.871	1	CLONAL	1	TRUE	1	0.710247152876966	2		489	466	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606054	81606054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	347	615	0	ENST00000298171.2:c.724C>T	p.Pro242Ser	p.P242S	ENST00000298171	NM_000369.2	242	Cca/Tca	9/10	1	2	FACETS	0.986	0.936	1	0.986	0.936	1	CLONAL	1	TRUE	1	0.710247152876966	2		615	991	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562677	95562677	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	259	478	0	ENST00000393063.1:c.4580T>C	p.Phe1527Ser	p.F1527S	ENST00000393063	NM_030621.3	1527	tTc/tCc	24/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.710247152876966	2		478	653	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988839	41988839	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	210	594	0	ENST00000219905.7:c.1631C>T	p.Pro544Leu	p.P544L	ENST00000219905	NM_001164273.1	544	cCc/cTc	3/24	1	2	FACETS	0.927	0.865	0.99	0.927	0.865	0.99	CLONAL	1	TRUE	1	0.710247152876966	2		594	638	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028627	42028627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	406	747	1	ENST00000219905.7:c.4165C>T	p.Pro1389Ser	p.P1389S	ENST00000219905	NM_001164273.1	1389	Cct/Tct	13/24	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.710247152876966	2		748	1059	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041099	42041099	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	332	682	0	ENST00000219905.7:c.5477T>A	p.Leu1826Ter	p.L1826*	ENST00000219905	NM_001164273.1	1826	tTa/tAa	16/24	1	2	FACETS	0.991	0.94	1	0.991	0.94	1	CLONAL	1	TRUE	1	0.710247152876966	2		682	943	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720261	43720261	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	343	552	0	ENST00000382044.4:c.3781G>A	p.Asp1261Asn	p.D1261N	ENST00000382044	NM_001141980.1	1261	Gat/Aat	18/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.710247152876966	2		552	905	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748853	43748853	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	505	825	0	ENST00000382044.4:c.1953A>T	p.Glu651Asp	p.E651D	ENST00000382044	NM_001141980.1	651	gaA/gaT	12/28	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.710247152876966	2		825	1160	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88428950	88428950	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1331800469	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	105	428	0	ENST00000360948.2:c.2150G>A	p.Gly717Glu	p.G717E	ENST00000360948	NM_001012338.2	717	gGa/gAa	17/19	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.710247152876966	2		428	279	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472492	88472492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	422	768	0	ENST00000360948.2:c.2063G>A	p.Gly688Glu	p.G688E	ENST00000360948	NM_001012338.2	688	gGa/gAa	16/19	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.710247152876966	2		768	1114	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680752	88680752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1461541348	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	488	771	2	ENST00000360948.2:c.505C>T	p.Arg169Cys	p.R169C	ENST00000360948	NM_001012338.2	169	Cgc/Tgc	6/19	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.710247152876966	2		773	1234	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303979	91303979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1302320494	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	285	713	0	ENST00000355112.3:c.1376C>T	p.Pro459Leu	p.P459L	ENST00000355112	NM_000057.2	459	cCc/cTc	7/22	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.710247152876966	2		713	772	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99192818	99192818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs577151797	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	263	338	2	ENST00000268035.6:c.8C>T	p.Ser3Phe	p.S3F	ENST00000268035	NM_000875.3	3	tCt/tTt	1/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.710247152876966	2		340	722	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251003	99251003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	400	739	1	ENST00000268035.6:c.307C>T	p.Leu103Phe	p.L103F	ENST00000268035	NM_000875.3	103	Ctc/Ttc	2/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.710247152876966	2		740	1082	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347735	347735	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	437	717	0	ENST00000262320.3:c.1771G>T	p.Gly591Cys	p.G591C	ENST00000262320	NM_003502.3	591	Ggc/Tgc	6/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.710247152876966	2		717	1151	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396668	396668	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	426	764	0	ENST00000262320.3:c.358G>T	p.Ala120Ser	p.A120S	ENST00000262320	NM_003502.3	120	Gcc/Tcc	2/11	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.710247152876966	2		764	1046	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2090197	2090197	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1184801355	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	462	860	0	ENST00000219066.1:c.752G>A	p.Trp251Ter	p.W251*	ENST00000219066	NM_002528.5	251	tGg/tAg	5/6	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.710247152876966	2		860	1227	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2115528	2115529	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	413	649	0	ENST00000219476.3:c.1608_1609delinsTT	p.Arg537Cys	p.R537C	ENST00000219476	NM_000548.3	536	gcCCgc/gcTTgc	16/42	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.710247152876966	2		649	1102	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639935	3639935	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	489	809	0	ENST00000294008.3:c.3704C>T	p.Pro1235Leu	p.P1235L	ENST00000294008	NM_032444.2	1235	cCc/cTc	12/15	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.710247152876966	2		809	1149	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658884	3658884	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	424	671	0	ENST00000294008.3:c.82C>A	p.Pro28Thr	p.P28T	ENST00000294008	NM_032444.2	28	Cct/Act	2/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.710247152876966	2		671	1102	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808874	3808874	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	358	591	0	ENST00000262367.5:c.3350C>T	p.Pro1117Leu	p.P1117L	ENST00000262367	NM_004380.2	1117	cCc/cTc	17/31	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.710247152876966	2		591	908	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858555	9858555	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	320	696	0	ENST00000330684.3:c.2846T>C	p.Phe949Ser	p.F949S	ENST00000330684	NM_001134407.1	949	tTt/tCt	13/13	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.710247152876966	2		696	798	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984849	9984850	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	333	635	1	ENST00000330684.3:c.1115_1116delinsAA	p.Trp372Ter	p.W372*	ENST00000330684	NM_001134407.1	372	tGG/tAA	4/13	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.710247152876966	2		636	925	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032369	10032369	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555455829	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	293	533	0	ENST00000330684.3:c.454C>T	p.Gln152Ter	p.Q152*	ENST00000330684	NM_001134407.1	152	Cag/Tag	3/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.710247152876966	2		533	756	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041839	14041839	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	308	532	0	ENST00000311895.7:c.2386C>T	p.Pro796Ser	p.P796S	ENST00000311895	NM_005236.2	796	Ccc/Tcc	11/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.710247152876966	2		532	802	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647656	23647656	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	121	318	0	ENST00000261584.4:c.212-1G>A		p.X71_splice	ENST00000261584	NM_024675.3	71			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.710247152876966	2		318	293	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782276	56782277	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	386	673	1	ENST00000308159.5:c.117_118delinsAA	p.Gly40Arg	p.G40R	ENST00000308159	NM_014669.4	39	gcGGga/gcAAga	2/22	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.710247152876966	2		674	1071	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644809	67644809	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	337	679	0	ENST00000264010.4:c.74A>T	p.Tyr25Phe	p.Y25F	ENST00000264010	NM_006565.3	25	tAc/tTc	3/12	1	2	FACETS	0.921	0.873	0.971	0.921	0.873	0.971	CLONAL	1	TRUE	1	0.710247152876966	2		679	1030	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827804	72827805	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	321	740	1	ENST00000268489.5:c.8776_8777delinsTT	p.Pro2926Leu	p.P2926L	ENST00000268489	NM_006885.3	2926	CCg/TTg	9/10	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.710247152876966	2		741	894	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991664	72991664	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760236892	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	245	474	0	ENST00000268489.5:c.2381C>T	p.Ser794Leu	p.S794L	ENST00000268489	NM_006885.3	794	tCg/tTg	2/10	1	2	FACETS	0.977	0.918	1	0.977	0.918	1	CLONAL	1	TRUE	1	0.710247152876966	2		474	706	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350815	89350815	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	357	871	0	ENST00000301030.4:c.2135T>G	p.Phe712Cys	p.F712C	ENST00000301030	NM_001256183.1	712	tTt/tGt	9/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.710247152876966	2		871	962	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849467	89849467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	456	822	0	ENST00000389301.3:c.1514C>T	p.Ser505Phe	p.S505F	ENST00000389301	NM_000135.2	505	tCc/tTc	16/43	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.710247152876966	2		822	1172	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849482	89849482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867433570	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	400	751	0	ENST00000389301.3:c.1499C>T	p.Pro500Leu	p.P500L	ENST00000389301	NM_000135.2	500	cCc/cTc	16/43	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.710247152876966	2		751	1014	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849500	89849501	+	missense_variant	Missense_Mutation	DNP	AG	AG	TA	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	302	640	1	ENST00000389301.3:c.1480_1481delinsTA	p.Leu494Tyr	p.L494Y	ENST00000389301	NM_000135.2	494	CTc/TAc	16/43	1	2	FACETS	0.98	0.926	1	0.98	0.926	1	CLONAL	1	TRUE	1	0.710247152876966	2		641	868	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579508	7579508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	489	838	0	ENST00000269305.4:c.179C>T	p.Pro60Leu	p.P60L	ENST00000269305	NM_001126112.2	60	cCa/cTa	4/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.710247152876966	2		838	1267	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984455	7984455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	445	793	0	ENST00000319144.4:c.403G>A	p.Glu135Lys	p.E135K	ENST00000319144	NM_001139.2	135	Gag/Aag	3/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.710247152876966	2		793	1158	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990619	7990619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	305	512	0	ENST00000319144.4:c.142G>A	p.Gly48Arg	p.G48R	ENST00000319144	NM_001139.2	48	Ggg/Agg	1/15	1	2	FACETS	0.94	0.888	0.992	0.94	0.888	0.992	CLONAL	1	TRUE	1	0.710247152876966	2		512	914	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971271	15971271	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	409	672	0	ENST00000268712.3:c.4678T>C	p.Tyr1560His	p.Y1560H	ENST00000268712	NM_006311.3	1560	Tat/Cat	32/46	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.710247152876966	2		672	1064	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559182	29559182	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	224	464	0	ENST00000356175.3:c.3289G>T	p.Glu1097Ter	p.E1097*	ENST00000356175	NM_000267.3	1097	Gaa/Taa	25/57	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.710247152876966	2		464	600	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562966	29562966	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	166	521	0	ENST00000356175.3:c.3901C>A	p.Leu1301Met	p.L1301M	ENST00000356175	NM_000267.3	1301	Ctg/Atg	29/57	1	2	FACETS	0.98	0.908	1	0.98	0.908	1	CLONAL	1	TRUE	1	0.710247152876966	2		521	477	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665143	29665143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555534961	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	230	600	0	ENST00000356175.3:c.6742C>T	p.Arg2248Cys	p.R2248C	ENST00000356175	NM_000267.3	2248	Cgt/Tgt	44/57	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.710247152876966	2		600	633	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33427980	33427980	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786203974	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	364	605	0	ENST00000345365.6:c.979C>T	p.Gln327Ter	p.Q327*	ENST00000345365	NM_002878.3	327	Cag/Tag	10/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.710247152876966	2		605	996	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667873	37667873	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	229	571	0	ENST00000447079.4:c.2758T>A	p.Trp920Arg	p.W920R	ENST00000447079	NM_015083.1	920	Tgg/Agg	8/14	1	2	FACETS	0.924	0.865	0.984	0.924	0.865	0.984	CLONAL	1	TRUE	1	0.710247152876966	2		571	698	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511610	38511610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs976585948	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	443	829	0	ENST00000254066.5:c.1108C>T	p.Arg370Cys	p.R370C	ENST00000254066	NM_000964.3	370	Cgc/Tgc	8/9	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.710247152876966	2		829	1152	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40457698	40457699	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	401	692	2	ENST00000345506.4:c.1451_1452delinsAT	p.Trp484Tyr	p.W484Y	ENST00000345506	NM_003152.3	484	tGG/tAT	13/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.710247152876966	2		694	1009	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440925	56440925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	486	676	0	ENST00000407977.2:c.412C>T	p.Leu138Phe	p.L138F	ENST00000407977		138	Ctc/Ttc	4/10	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.710247152876966	2		676	1214	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760865	59760865	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	205	661	0	ENST00000259008.2:c.3542C>A	p.Ser1181Ter	p.S1181*	ENST00000259008	NM_032043.2	1181	tCa/tAa	20/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.710247152876966	2		661	529	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59870969	59870969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1450320184	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	153	455	0	ENST00000259008.2:c.1462C>T	p.Pro488Ser	p.P488S	ENST00000259008	NM_032043.2	488	Ccc/Tcc	10/20	1	2	FACETS	0.957	0.884	1	0.957	0.884	1	CLONAL	1	TRUE	1	0.710247152876966	2		455	450	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59878817	59878817	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	109	332	0	ENST00000259008.2:c.937T>A	p.Tyr313Asn	p.Y313N	ENST00000259008	NM_032043.2	313	Tat/Aat	8/20	1	2	FACETS	0.984	0.895	1	0.984	0.895	1	CLONAL	1	TRUE	1	0.710247152876966	2		332	312	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006815	62006815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758150594	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	425	740	1	ENST00000392795.3:c.573G>A	p.Met191Ile	p.M191I	ENST00000392795	NM_001039933.1	191	atG/atA	5/6	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.710247152876966	2		741	1120	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211159	2211160	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	481	892	1	ENST00000398665.3:c.1413_1414delinsTT	p.Pro472Ser	p.P472S	ENST00000398665	NM_032482.2	471	tcCCcc/tcTTcc	15/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.710247152876966	2		893	1283	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216397	2216397	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	418	816	0	ENST00000398665.3:c.2041C>A	p.Arg681Ser	p.R681S	ENST00000398665	NM_032482.2	681	Cgc/Agc	20/28	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.710247152876966	2		816	1099	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119279	3119279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	499	833	0	ENST00000078429.4:c.811C>T	p.Leu271Phe	p.L271F	ENST00000078429	NM_002067.2	271	Ctc/Ttc	6/7	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.710247152876966	2		833	1303	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248671	10248671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	374	593	0	ENST00000340748.4:c.4082C>T	p.Pro1361Leu	p.P1361L	ENST00000340748		1361	cCt/cTt	35/40	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.710247152876966	2		593	893	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144025	11144026	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	384	754	2	ENST00000358026.2:c.3606_3607delinsTT	p.Arg1203Cys	p.R1203C	ENST00000358026	NM_001128849.1	1202	ctCCgc/ctTTgc	26/36	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.710247152876966	2		756	1029	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144179	11144179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	405	722	0	ENST00000358026.2:c.3760G>A	p.Glu1254Lys	p.E1254K	ENST00000358026	NM_001128849.1	1254	Gag/Aag	26/36	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.710247152876966	2		722	1119	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272498	15272498	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200541224	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	444	678	1	ENST00000263388.2:c.5941C>T	p.Arg1981Cys	p.R1981C	ENST00000263388	NM_000435.2	1981	Cgc/Tgc	33/33	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.710247152876966	2		679	1119	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349970	15349970	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	473	795	2	ENST00000263377.2:c.3682C>T	p.Arg1228Cys	p.R1228C	ENST00000263377	NM_058243.2	1228	Cgc/Tgc	18/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.710247152876966	2		797	1211	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968208	18968208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	459	737	0	ENST00000262803.5:c.2048C>T	p.Ser683Leu	p.S683L	ENST00000262803	NM_002911.3	683	tCg/tTg	15/24	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.710247152876966	2		737	1138	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212033	36212033	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	565	944	0	ENST00000222270.7:c.1784C>T	p.Pro595Leu	p.P595L	ENST00000222270	NM_014727.1	595	cCa/cTa	3/37	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.710247152876966	2		944	1455	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212240	36212240	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	442	771	0	ENST00000222270.7:c.1991C>T	p.Ser664Leu	p.S664L	ENST00000222270	NM_014727.1	664	tCg/tTg	3/37	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.710247152876966	2		771	1138	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212516	36212516	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568369908	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	545	853	0	ENST00000222270.7:c.2267C>T	p.Pro756Leu	p.P756L	ENST00000222270	NM_014727.1	756	cCa/cTa	3/37	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.710247152876966	2		853	1324	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214158	36214159	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	432	887	1	ENST00000222270.7:c.2984_2985delinsTT	p.Thr995Ile	p.T995I	ENST00000222270	NM_014727.1	995	aCC/aTT	6/37	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.710247152876966	2		888	1200	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219772	36219772	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	489	866	0	ENST00000222270.7:c.4669C>T	p.Pro1557Ser	p.P1557S	ENST00000222270	NM_014727.1	1557	Cca/Tca	20/37	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.710247152876966	2		866	1236	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224114	36224114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	505	791	0	ENST00000222270.7:c.6664C>T	p.Pro2222Ser	p.P2222S	ENST00000222270	NM_014727.1	2222	Ccc/Tcc	28/37	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.710247152876966	2		791	1218	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227996	36227996	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	459	778	0	ENST00000222270.7:c.7382G>T	p.Gly2461Val	p.G2461V	ENST00000222270	NM_014727.1	2461	gGg/gTg	33/37	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.710247152876966	2		778	1156	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753477	42753477	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	517	847	0	ENST00000222329.4:c.787C>T	p.Gln263Ter	p.Q263*	ENST00000222329	NM_006494.2	263	Cag/Tag	4/4	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.710247152876966	2		847	1311	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795445	42795445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1480893310	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	320	572	0	ENST00000575354.2:c.2525C>T	p.Pro842Leu	p.P842L	ENST00000575354	NM_015125.3	842	cCa/cTa	10/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.710247152876966	2		572	783	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797159	42797159	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs189391255	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	551	901	3	ENST00000575354.2:c.3521C>T	p.Pro1174Leu	p.P1174L	ENST00000575354	NM_015125.3	1174	cCg/cTg	15/20	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.710247152876966	2		904	1297	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873477	45873477	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs773936050	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	346	622	1	ENST00000391945.4:c.19G>T	p.Gly7Trp	p.G7W	ENST00000391945	NM_000400.3	7	Ggg/Tgg	2/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.710247152876966	2		623	931	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27016077	27016077	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194974108	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	411	665	1	ENST00000335756.4:c.353G>A	p.Arg118Gln	p.R118Q	ENST00000335756	NM_001809.3	118	cGa/cAa	4/5	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.710247152876966	2		666	1047	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416461	29416461	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	540	918	0	ENST00000389048.3:c.4492A>T	p.Lys1498Ter	p.K1498*	ENST00000389048	NM_004304.4	1498	Aag/Tag	29/29	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.710247152876966	2		918	1404	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446353	29446353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	540	853	0	ENST00000389048.3:c.3214G>A	p.Glu1072Lys	p.E1072K	ENST00000389048	NM_004304.4	1072	Gag/Aag	20/29	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.710247152876966	2		853	1321	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606684	29606684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	384	738	1	ENST00000389048.3:c.1196C>T	p.Pro399Leu	p.P399L	ENST00000389048	NM_004304.4	399	cCa/cTa	5/29	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.710247152876966	2		739	1057	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285843	39285843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	184	579	0	ENST00000402219.2:c.316C>T	p.Pro106Ser	p.P106S	ENST00000402219	NM_005633.3	106	Cca/Tca	3/23	1	2	FACETS	0.974	0.906	1	0.974	0.906	1	CLONAL	1	TRUE	1	0.710247152876966	2		579	532	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47604184	47604184	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs878854491	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	163	490	0	ENST00000263735.4:c.523C>T	p.Gln175Ter	p.Q175*	ENST00000263735	NM_002354.2	175	Caa/Taa	5/9	1	2	FACETS	0.871	0.805	0.939	0.871	0.805	0.939	CLONAL	1	TRUE	1	0.710247152876966	2		490	527	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046245	128046245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	369	521	0	ENST00000285398.2:c.1018C>T	p.Leu340Phe	p.L340F	ENST00000285398	NM_000122.1	340	Ctt/Ttt	7/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.710247152876966	2		521	950	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251794	212251794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	285	445	0	ENST00000342788.4:c.3265C>T	p.Pro1089Ser	p.P1089S	ENST00000342788	NM_005235.2	1089	Cca/Tca	27/28	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.710247152876966	2		445	697	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295752	212295752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	203	672	0	ENST00000342788.4:c.2561C>T	p.Pro854Leu	p.P854L	ENST00000342788	NM_005235.2	854	cCa/cTa	21/28	1	2	FACETS	0.958	0.893	1	0.958	0.893	1	CLONAL	1	TRUE	1	0.710247152876966	2		672	597	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212522534	212522534	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878927700	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	226	475	0	ENST00000342788.4:c.1891C>T	p.His631Tyr	p.H631Y	ENST00000342788	NM_005235.2	631	Cat/Tat	16/28	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.710247152876966	2		475	611	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439829	220439829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1390732250	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	489	897	0	ENST00000243786.2:c.682G>A	p.Glu228Lys	p.E228K	ENST00000243786	NM_002191.3	228	Gag/Aag	2/2	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.710247152876966	2		897	1209	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346648	225346648	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	141	470	1	ENST00000264414.4:c.1990C>T	p.Gln664Ter	p.Q664*	ENST00000264414	NM_003590.4	664	Caa/Taa	14/16	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.710247152876966	2		471	391	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794104	242794105	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	436	760	2	ENST00000334409.5:c.623_624delinsTT	p.Pro208Leu	p.P208L	ENST00000334409	NM_005018.2	208	cCC/cTT	4/5	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.710247152876966	2		762	1146	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794499	242794499	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772850929	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	492	759	1	ENST00000334409.5:c.443G>A	p.Arg148Lys	p.R148K	ENST00000334409	NM_005018.2	148	aGg/aAg	3/5	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.710247152876966	2		760	1195	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523364	9523365	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	219	485	0	ENST00000353224.5:c.1872_1873delinsTA	p.Asp625Asn	p.D625N	ENST00000353224	NM_177990.2	624	gtGGac/gtTAac	9/10	1	2	FACETS	0.925	0.864	0.986	0.925	0.864	0.986	CLONAL	1	TRUE	1	0.710247152876966	2		485	667	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546971	9546971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	295	465	0	ENST00000353224.5:c.1051C>T	p.Pro351Ser	p.P351S	ENST00000353224	NM_177990.2	351	Ccc/Tcc	5/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.710247152876966	2		465	767	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024805	31024806	+	missense_variant	Missense_Mutation	DNP	CC	CC	TG	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	362	700	0	ENST00000375687.4:c.4290_4291delinsTG	p.Pro1431Ala	p.P1431A	ENST00000375687	NM_015338.5	1430	ctCCcc/ctTGcc	13/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.710247152876966	2		700	1002	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374389	31374389	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	479	668	0	ENST00000328111.2:c.388C>A	p.Arg130Ser	p.R130S	ENST00000328111	NM_006892.3	130	Cgc/Agc	5/23	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.710247152876966	2		668	1243	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375094	31375094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	520	839	0	ENST00000328111.2:c.491C>T	p.Ser164Phe	p.S164F	ENST00000328111	NM_006892.3	164	tCt/tTt	6/23	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.710247152876966	2		839	1285	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39708727	39708727	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs752185915	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	115	451	1	ENST00000361337.2:c.338C>T	p.Pro113Leu	p.P113L	ENST00000361337	NM_003286.2	113	cCa/cTa	6/21	1	2	FACETS	0.846	0.769	0.925	0.846	0.769	0.925	CLONAL	1	TRUE	1	0.710247152876966	2		452	383	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944422	40944422	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	349	672	0	ENST00000373198.4:c.2080C>G	p.Pro694Ala	p.P694A	ENST00000373198	NM_133170.3	694	Cct/Gct	12/32	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.710247152876966	2		672	945	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979274	40979274	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	389	588	0	ENST00000373198.4:c.1859C>T	p.Pro620Leu	p.P620L	ENST00000373198	NM_133170.3	620	cCt/cTt	11/32	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.710247152876966	2		588	945	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979299	40979299	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	416	679	0	ENST00000373198.4:c.1834A>T	p.Lys612Ter	p.K612*	ENST00000373198	NM_133170.3	612	Aaa/Taa	11/32	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.710247152876966	2		679	1116	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961519	54961519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	347	629	0	ENST00000312783.6:c.113C>T	p.Pro38Leu	p.P38L	ENST00000312783	NM_198436.1	38	cCt/cTt	4/10	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.710247152876966	2		629	976	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485861	57485861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	321	501	0	ENST00000371085.3:c.1162C>T	p.Leu388Phe	p.L388F	ENST00000371085	NM_000516.4	388	Ctt/Ttt	13/13	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.710247152876966	2		501	819	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62320407	62320407	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	354	694	0	ENST00000360203.5:c.1801-1G>A		p.X601_splice	ENST00000360203	NM_001283009.1	601			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.710247152876966	2		694	953	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866339	42866339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	515	810	0	ENST00000398585.3:c.293C>T	p.Ser98Phe	p.S98F	ENST00000398585	NM_001135099.1	98	tCc/tTc	3/14	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.710247152876966	2		810	1328	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866397	42866398	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	517	805	2	ENST00000398585.3:c.234_235delinsAA	p.Ala79Thr	p.A79T	ENST00000398585	NM_001135099.1	78	ccGGct/ccAAct	3/14	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.710247152876966	2		807	1297	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656866	45656866	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	477	682	0	ENST00000407780.3:c.290C>A	p.Ser97Tyr	p.S97Y	ENST00000407780	NM_001283052.1	97	tCc/tAc	3/7	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.710247152876966	2		682	1170	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543909	41543909	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	471	713	0	ENST00000263253.7:c.2200C>T	p.Gln734Ter	p.Q734*	ENST00000263253	NM_001429.3	734	Cag/Tag	12/31	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.710247152876966	2		713	1241	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564859	41564859	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	348	650	0	ENST00000263253.7:c.4160C>T	p.Pro1387Leu	p.P1387L	ENST00000263253	NM_001429.3	1387	cCa/cTa	25/31	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.710247152876966	2		650	917	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12393116	12393116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	301	734	1	ENST00000287820.6:c.25C>T	p.Pro9Ser	p.P9S	ENST00000287820	NM_015869.4	9	Cct/Tct	1/7	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.710247152876966	2		735	814	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035111	37035111	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs63749838	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	391	571	0	ENST00000231790.2:c.73A>T	p.Ile25Phe	p.I25F	ENST00000231790	NM_000249.3	25	Atc/Ttc	1/19	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.710247152876966	2		571	946	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274912	41274912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	214	437	0	ENST00000349496.5:c.1162C>T	p.Leu388Phe	p.L388F	ENST00000349496	NM_001904.3	388	Ctt/Ttt	8/15	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.710247152876966	2		437	590	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098412	47098412	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	312	608	0	ENST00000409792.3:c.6862C>T	p.Pro2288Ser	p.P2288S	ENST00000409792	NM_014159.6	2288	Cct/Tct	15/21	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.710247152876966	2		608	813	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164852	47164852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs973506863	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	213	385	0	ENST00000409792.3:c.1274C>T	p.Ser425Phe	p.S425F	ENST00000409792	NM_014159.6	425	tCt/tTt	3/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.710247152876966	2		385	524	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165543	47165543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	438	583	0	ENST00000409792.3:c.583C>T	p.Pro195Ser	p.P195S	ENST00000409792	NM_014159.6	195	Cca/Tca	3/21	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.710247152876966	2		583	1066	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924798	49924798	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	532	905	0	ENST00000296474.3:c.4145C>A	p.Pro1382His	p.P1382H	ENST00000296474	NM_002447.2	1382	cCc/cAc	20/20	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.710247152876966	2		905	1363	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933462	49933463	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	424	801	1	ENST00000296474.3:c.2727_2728delinsTT	p.Arg910Trp	p.R910W	ENST00000296474	NM_002447.2	909	ttCCgg/ttTTgg	11/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.710247152876966	2		802	1155	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015100	71015100	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	312	457	0	ENST00000318789.4:c.1830G>A	p.Met610Ile	p.M610I	ENST00000318789	NM_032682.5	610	atG/atA	20/21	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.710247152876966	2		457	844	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468402	89468402	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	206	361	0	ENST00000336596.2:c.1936A>T	p.Lys646Ter	p.K646*	ENST00000336596	NM_005233.5	646	Aaa/Taa	11/17	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.710247152876966	2		361	470	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426045	138426045	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	156	588	0	ENST00000289153.2:c.1486C>T	p.Pro496Ser	p.P496S	ENST00000289153	NM_006219.2	496	Cca/Tca	9/22	1	2	FACETS	0.953	0.88	1	0.953	0.88	1	CLONAL	1	TRUE	1	0.710247152876966	2		588	461	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238554	142238554	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	180	371	0	ENST00000350721.4:c.4339C>A	p.Pro1447Thr	p.P1447T	ENST00000350721	NM_001184.3	1447	Cct/Act	24/47	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.710247152876966	2		371	465	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526080	189526080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	369	610	0	ENST00000264731.3:c.344G>A	p.Gly115Glu	p.G115E	ENST00000264731	NM_003722.4	115	gGg/gAg	4/14	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.710247152876966	2		610	977	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801175	1801175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs558935109	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	524	805	1	ENST00000260795.2:c.304G>A	p.Glu102Lys	p.E102K	ENST00000260795		102	Gag/Aag	2/17	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.710247152876966	2		806	1303	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803390	1803390	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	484	784	1	ENST00000260795.2:c.659C>T	p.Pro220Leu	p.P220L	ENST00000260795		220	cCc/cTc	5/17	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.710247152876966	2		785	1233	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806689	1806689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	469	705	1	ENST00000260795.2:c.1405C>T	p.Arg469Trp	p.R469W	ENST00000260795		469	Cgg/Tgg	9/17	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.710247152876966	2		706	1208	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957788	1957789	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	383	783	0	ENST00000382891.5:c.2754_2755delinsTT	p.Pro919Ser	p.P919S	ENST00000382891	NM_133335.3	918	ttCCct/ttTTct	15/22	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.710247152876966	2		783	1034	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1959701	1959701	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	279	409	0	ENST00000382891.5:c.2923C>T	p.Gln975Ter	p.Q975*	ENST00000382891	NM_133335.3	975	Cag/Tag	16/22	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.710247152876966	2		409	699	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964395	55964395	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	305	615	0	ENST00000263923.4:c.2418G>T	p.Met806Ile	p.M806I	ENST00000263923	NM_002253.2	806	atG/atT	17/30	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.710247152876966	2		615	805	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973999	55974000	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	392	691	1	ENST00000263923.4:c.1316_1317delinsAT	p.Thr439Asn	p.T439N	ENST00000263923	NM_002253.2	439	aCC/aAT	10/30	1	2	FACETS	0.998	0.95	1	0.998	0.95	1	CLONAL	1	TRUE	1	0.710247152876966	2		692	1106	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99823111	99823111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	137	388	0	ENST00000280892.6:c.101C>T	p.Pro34Leu	p.P34L	ENST00000280892	NM_001130678.1	34	cCc/cTc	2/7	1	2	FACETS	0.899	0.825	0.975	0.899	0.825	0.975	CLONAL	1	TRUE	1	0.710247152876966	2		388	429	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157306	106157306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	217	602	0	ENST00000380013.4:c.2207C>T	p.Ser736Leu	p.S736L	ENST00000380013	NM_001127208.2	736	tCa/tTa	3/11	1	2	FACETS	0.979	0.916	1	0.979	0.916	1	CLONAL	1	TRUE	1	0.710247152876966	2		602	624	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158491	106158491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	125	404	0	ENST00000380013.4:c.3392C>T	p.Pro1131Leu	p.P1131L	ENST00000380013	NM_001127208.2	1131	cCa/cTa	3/11	1	2	FACETS	0.848	0.774	0.925	0.848	0.774	0.925	CLONAL	1	TRUE	1	0.710247152876966	2		404	415	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268105	153268105	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	293	377	0	ENST00000281708.4:c.703C>T	p.Gln235Ter	p.Q235*	ENST00000281708	NM_033632.3	235	Cag/Tag	4/12	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.710247152876966	2		377	698	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519213	187519213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	433	701	0	ENST00000441802.2:c.12170C>T	p.Ser4057Phe	p.S4057F	ENST00000441802	NM_005245.3	4057	tCc/tTc	23/27	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.710247152876966	2		701	1098	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251181	251182	+	missense_variant	Missense_Mutation	DNP	CT	CT	TA	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	133	359	0	ENST00000264932.6:c.1626_1627delinsTA	p.Tyr543Asn	p.Y543N	ENST00000264932	NM_004168.2	542	ctCTat/ctTAat	12/15	1	2	FACETS	0.695	0.634	0.758	0.695	0.634	0.758	SUBCLONAL	1	TRUE	1	0.710247152876966	2		359	539	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	T	rs943069833	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	242	320	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.710247152876966	2		320	590	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871311	35871311	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs753635194	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	115	425	1	ENST00000303115.3:c.533G>A	p.Trp178Ter	p.W178*	ENST00000303115	NM_002185.3	178	tGg/tAg	4/8	1	2	FACETS	0.818	0.743	0.895	0.818	0.743	0.895	CLONAL	1	TRUE	1	0.710247152876966	2		426	396	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873729	35873730	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	180	425	0	ENST00000303115.3:c.685_686delinsTT	p.Pro229Leu	p.P229L	ENST00000303115	NM_002185.3	229	CCa/TTa	5/8	1	2	FACETS	0.953	0.885	1	0.953	0.885	1	CLONAL	1	TRUE	1	0.710247152876966	2		425	532	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874587	35874587	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	291	524	0	ENST00000303115.3:c.743T>C	p.Leu248Ser	p.L248S	ENST00000303115	NM_002185.3	248	tTg/tCg	6/8	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.710247152876966	2		524	797	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80063837	80063837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1267678112	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	175	685	0	ENST00000265081.6:c.1982C>T	p.Ser661Phe	p.S661F	ENST00000265081	NM_002439.4	661	tCc/tTc	14/24	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.710247152876966	2		685	478	SUCCESS
APC	324	MSKCC	GRCh37	5	112177620	112177620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	138	438	0	ENST00000257430.4:c.6329C>T	p.Ser2110Phe	p.S2110F	ENST00000257430	NM_000038.5	2110	tCc/tTc	16/16	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.710247152876966	2		438	377	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503857	149503857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	391	737	0	ENST00000261799.4:c.1979C>T	p.Pro660Leu	p.P660L	ENST00000261799	NM_002609.3	660	cCc/cTc	14/23	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.710247152876966	2		737	1000	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515268	149515268	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	454	841	0	ENST00000261799.4:c.214G>C	p.Glu72Gln	p.E72Q	ENST00000261799	NM_002609.3	72	Gaa/Caa	3/23	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.710247152876966	2		841	1164	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518074	176518074	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	428	800	0	ENST00000292408.4:c.572T>A	p.Phe191Tyr	p.F191Y	ENST00000292408	NM_213647.1	191	tTt/tAt	5/18	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.710247152876966	2		800	1175	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522554	176522554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	453	815	0	ENST00000292408.4:c.1651G>A	p.Glu551Lys	p.E551K	ENST00000292408	NM_213647.1	551	Gag/Aag	13/18	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.710247152876966	2		815	1108	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524564	176524565	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	475	952	2	ENST00000292408.4:c.2296_2297delinsTT	p.Pro766Phe	p.P766F	ENST00000292408	NM_213647.1	766	CCc/TTc	18/18	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.710247152876966	2		954	1325	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637472	176637473	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	225	637	0	ENST00000439151.2:c.2072_2073delinsTT	p.Ala691Val	p.A691V	ENST00000439151	NM_022455.4	691	gCC/gTT	5/23	1	2	FACETS	0.944	0.884	1	0.944	0.884	1	CLONAL	1	TRUE	1	0.710247152876966	2		637	671	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176684012	176684012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	428	708	0	ENST00000439151.2:c.4826C>T	p.Pro1609Leu	p.P1609L	ENST00000439151	NM_022455.4	1609	cCc/cTc	13/23	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.710247152876966	2		708	1060	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046041	180046042	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	153	170	2	ENST00000261937.6:c.2829_2830delinsAA	p.Asp944Asn	p.D944N	ENST00000261937	NM_182925.4	943	cgGGac/cgAAac	20/30	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.710247152876966	2		172	382	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046364	180046364	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	373	622	0	ENST00000261937.6:c.2650G>A	p.Gly884Ser	p.G884S	ENST00000261937	NM_182925.4	884	Ggc/Agc	19/30	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.710247152876966	2		622	970	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047969	180047969	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	455	844	1	ENST00000261937.6:c.2206C>T	p.Gln736Ter	p.Q736*	ENST00000261937	NM_182925.4	736	Cag/Tag	15/30	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.710247152876966	2		845	1151	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056776	180056776	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	550	873	0	ENST00000261937.6:c.736G>A	p.Glu246Lys	p.E246K	ENST00000261937	NM_182925.4	246	Gag/Aag	6/30	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.710247152876966	2		873	1399	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681897	30681897	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	395	657	0	ENST00000376406.3:c.200C>G	p.Pro67Arg	p.P67R	ENST00000376406	NM_014641.2	67	cCc/cGc	3/15	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.710247152876966	2		657	979	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30682894	30682894	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	344	690	0	ENST00000376406.3:c.59C>T	p.Ser20Phe	p.S20F	ENST00000376406	NM_014641.2	20	tCc/tTc	2/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.710247152876966	2		690	926	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166446	32166446	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	506	793	0	ENST00000375023.3:c.4597G>C	p.Glu1533Gln	p.E1533Q	ENST00000375023	NM_004557.3	1533	Gag/Cag	25/30	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.710247152876966	2		793	1310	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188625	32188625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	318	706	1	ENST00000375023.3:c.830C>T	p.Pro277Leu	p.P277L	ENST00000375023	NM_004557.3	277	cCa/cTa	5/30	1	2	FACETS	0.859	0.812	0.908	0.859	0.812	0.908	CLONAL	1	TRUE	1	0.710247152876966	2		707	1042	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818755	32818755	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	447	734	0	ENST00000354258.4:c.1196T>A	p.Phe399Tyr	p.F399Y	ENST00000354258	NM_000593.5	399	tTc/tAc	4/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.710247152876966	2		734	1161	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286836	33286836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	376	676	1	ENST00000374542.5:c.2101C>T	p.Pro701Ser	p.P701S	ENST00000374542	NM_001141970.1	701	Cct/Tct	7/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.710247152876966	2		677	1028	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287337	33287337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760084261	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	308	688	0	ENST00000374542.5:c.1760C>T	p.Ser587Phe	p.S587F	ENST00000374542	NM_001141970.1	587	tCc/tTc	6/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.710247152876966	2		688	829	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288350	33288350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141322869	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	353	615	0	ENST00000374542.5:c.1058C>T	p.Ser353Leu	p.S353L	ENST00000374542	NM_001141970.1	353	tCa/tTa	4/8	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.710247152876966	2		615	875	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956663	93956663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	230	532	1	ENST00000369303.4:c.2573C>T	p.Pro858Leu	p.P858L	ENST00000369303	NM_004440.3	858	cCc/cTc	15/17	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.710247152876966	2		533	639	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967241	93967241	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	119	360	0	ENST00000369303.4:c.2111G>A	p.Gly704Glu	p.G704E	ENST00000369303	NM_004440.3	704	gGg/gAg	12/17	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.710247152876966	2		360	290	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066680	94066680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	332	620	0	ENST00000369303.4:c.1079G>A	p.Arg360Lys	p.R360K	ENST00000369303	NM_004440.3	360	aGa/aAa	5/17	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.710247152876966	2		620	901	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553676	106553676	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	302	588	2	ENST00000369096.4:c.1641G>A	p.Met547Ile	p.M547I	ENST00000369096	NM_001198.3	547	atG/atA	5/7	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.710247152876966	2		590	780	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112029183	112029183	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370983835	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	279	570	0	ENST00000368678.4:c.385G>A	p.Glu129Lys	p.E129K	ENST00000368678		129	Gag/Aag	5/13	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.710247152876966	2		570	758	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622245	117622245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	168	521	0	ENST00000368508.3:c.6625C>T	p.His2209Tyr	p.H2209Y	ENST00000368508	NM_002944.2	2209	Cat/Tat	42/43	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.710247152876966	2		521	427	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117645569	117645569	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	172	632	0	ENST00000368508.3:c.5567G>A	p.Trp1856Ter	p.W1856*	ENST00000368508	NM_002944.2	1856	tGg/tAg	34/43	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.710247152876966	2		632	410	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678974	117678974	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs750581358	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	76	338	0	ENST00000368508.3:c.3847C>A	p.Leu1283Ile	p.L1283I	ENST00000368508	NM_002944.2	1283	Ctt/Att	24/43	1	2	FACETS	0.955	0.852	1	0.955	0.852	1	CLONAL	1	TRUE	1	0.710247152876966	2		338	224	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686345	117686345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	125	329	0	ENST00000368508.3:c.2996C>T	p.Ser999Phe	p.S999F	ENST00000368508	NM_002944.2	999	tCt/tTt	20/43	1	2	FACETS	0.994	0.911	1	0.994	0.911	1	CLONAL	1	TRUE	1	0.710247152876966	2		329	354	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687449	117687449	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	201	403	0	ENST00000368508.3:c.2602G>A	p.Gly868Arg	p.G868R	ENST00000368508	NM_002944.2	868	Ggg/Agg	18/43	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.710247152876966	2		403	546	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714412	117714412	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	152	527	0	ENST00000368508.3:c.1237A>C	p.Lys413Gln	p.K413Q	ENST00000368508	NM_002944.2	413	Aaa/Caa	11/43	1	2	FACETS	0.966	0.892	1	0.966	0.892	1	CLONAL	1	TRUE	1	0.710247152876966	2		527	443	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138197261	138197261	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	256	359	0	ENST00000237289.4:c.763C>T	p.His255Tyr	p.H255Y	ENST00000237289	NM_001270507.1	255	Cat/Tat	5/9	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.710247152876966	2		359	648	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382133	152382133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	184	370	0	ENST00000206249.3:c.1243G>A	p.Gly415Arg	p.G415R	ENST00000206249	NM_000125.3	415	Gga/Aga	6/8	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.710247152876966	2		370	518	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420100	152420100	+	stop_lost	Nonstop_Mutation	SNP	G	G	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	226	471	0	ENST00000206249.3:c.1787G>T	p.Ter596LeuextTer23	p.*596Lext*23	ENST00000206249	NM_000125.3	596	tGa/tTa	8/8	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.710247152876966	2		471	626	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222630	157222630	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554265316	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	397	610	0	ENST00000346085.5:c.1897C>T	p.Gln633Ter	p.Q633*	ENST00000346085	NM_020732.3	633	Cag/Tag	4/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.710247152876966	2		610	1070	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683574	162683574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	323	568	0	ENST00000366898.1:c.395C>T	p.Pro132Leu	p.P132L	ENST00000366898	NM_004562.2	132	cCa/cTa	3/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.710247152876966	2		568	876	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963942	2963942	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	439	812	1	ENST00000396946.4:c.1865C>T	p.Ser622Phe	p.S622F	ENST00000396946	NM_032415.4	622	tCc/tTc	15/25	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.710247152876966	2		813	1114	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977629	2977629	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	470	861	0	ENST00000396946.4:c.1055C>A	p.Ser352Ter	p.S352*	ENST00000396946	NM_032415.4	352	tCg/tAg	8/25	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.710247152876966	2		861	1199	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987360	2987360	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	427	781	1	ENST00000396946.4:c.69G>A	p.Trp23Ter	p.W23*	ENST00000396946	NM_032415.4	23	tgG/tgA	3/25	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.710247152876966	2		782	1165	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729673	41729673	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	402	635	0	ENST00000242208.4:c.856G>T	p.Glu286Ter	p.E286*	ENST00000242208	NM_002192.2	286	Gag/Tag	3/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.710247152876966	2		635	1094	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739622	41739622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	331	706	0	ENST00000242208.4:c.351G>A	p.Met117Ile	p.M117I	ENST00000242208	NM_002192.2	117	atG/atA	2/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.710247152876966	2		706	893	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50358689	50358689	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	146	305	0	ENST00000331340.3:c.32A>G	p.Gln11Arg	p.Q11R	ENST00000331340	NM_006060.4	11	cAa/cGa	2/8	1	2	FACETS	0.993	0.916	1	0.993	0.916	1	CLONAL	1	TRUE	1	0.710247152876966	2		305	414	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444438	50444438	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	284	441	1	ENST00000331340.3:c.368G>A	p.Gly123Glu	p.G123E	ENST00000331340	NM_006060.4	123	gGg/gAg	4/8	1	2	FACETS	0.984	0.928	1	0.984	0.928	1	CLONAL	1	TRUE	1	0.710247152876966	2		442	813	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455114	50455114	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	274	483	0	ENST00000331340.3:c.661G>A	p.Glu221Lys	p.E221K	ENST00000331340	NM_006060.4	221	Gag/Aag	6/8	1	2	FACETS	0.993	0.936	1	0.993	0.936	1	CLONAL	1	TRUE	1	0.710247152876966	2		483	777	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332018	81332018	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	134	378	0	ENST00000222390.5:c.2066G>A	p.Gly689Asp	p.G689D	ENST00000222390	NM_000601.4	689	gGt/gAt	18/18	1	2	FACETS	0.939	0.861	1	0.939	0.861	1	CLONAL	1	TRUE	1	0.710247152876966	2		378	402	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339484	81339484	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	141	520	0	ENST00000222390.5:c.1520G>A	p.Trp507Ter	p.W507*	ENST00000222390	NM_000601.4	507	tGg/tAg	13/18	1	2	FACETS	0.847	0.777	0.918	0.847	0.777	0.918	CLONAL	1	TRUE	1	0.710247152876966	2		520	469	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92247508	92247509	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	187	370	0	ENST00000265734.4:c.711_712delinsTT	p.Pro238Ser	p.P238S	ENST00000265734	NM_001259.6	237	ctCCca/ctTTca	7/8	1	2	FACETS	0.921	0.856	0.987	0.921	0.856	0.987	CLONAL	1	TRUE	1	0.710247152876966	2		370	572	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509529	106509529	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	405	677	0	ENST00000359195.3:c.1523C>A	p.Pro508Gln	p.P508Q	ENST00000359195	NM_002649.2	508	cCa/cAa	2/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.710247152876966	2		677	1015	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509694	106509694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779178136	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	298	666	2	ENST00000359195.3:c.1688C>T	p.Pro563Leu	p.P563L	ENST00000359195	NM_002649.2	563	cCa/cTa	2/11	1	2	FACETS	0.983	0.929	1	0.983	0.929	1	CLONAL	1	TRUE	1	0.710247152876966	2		668	854	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380103	116380103	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	302	664	0	ENST00000397752.3:c.1492C>A	p.Gln498Lys	p.Q498K	ENST00000397752	NM_000245.2	498	Caa/Aaa	4/21	0.710247152876966	3	FACETS	1	0.973	1	0.527	0.497	0.558	CLONAL	1	TRUE	1	0.710247152876966	3		664	1093	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397493	116397493	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	279	415	0	ENST00000397752.3:c.1865T>A	p.Leu622Ter	p.L622*	ENST00000397752	NM_000245.2	622	tTg/tAg	7/21	0.710247152876966	3	FACETS	0.979	0.93	1	0.979	0.93	1	CLONAL	2	TRUE	1	0.710247152876966	3		415	544	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501243	140501243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	166	602	0	ENST00000288602.6:c.829C>T	p.Pro277Ser	p.P277S	ENST00000288602	NM_004333.4	277	Cca/Tca	6/18	0.710247152876966	3	FACETS	0.929	0.856	1	0.464	0.428	0.502	CLONAL	1	TRUE	1	0.710247152876966	3		602	682	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853119	151853119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	330	508	0	ENST00000262189.6:c.11836C>T	p.Pro3946Ser	p.P3946S	ENST00000262189	NM_170606.2	3946	Cca/Tca	46/59	0.710247152876966	3	FACETS	0.975	0.921	1	0.488	0.46	0.516	CLONAL	1	TRUE	1	0.710247152876966	3		508	1291	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878793	151878793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	588	604	0	ENST00000262189.6:c.6152C>T	p.Pro2051Leu	p.P2051L	ENST00000262189	NM_170606.2	2051	cCa/cTa	36/59	0.710247152876966	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.710247152876966	3		604	1081	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945117	151945117	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	65	433	0	ENST00000262189.6:c.2402C>T	p.Pro801Leu	p.P801L	ENST00000262189	NM_170606.2	801	cCt/cTt	14/59	0.710247152876966	3	FACETS	0.494	0.429	0.564	0.247	0.214	0.282	SUBCLONAL	1	TRUE	1	0.710247152876966	3		433	502	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205554	38205554	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	428	840	0	ENST00000317025.8:c.136C>T	p.Gln46Ter	p.Q46*	ENST00000317025	NM_023034.1	46	Cag/Tag	2/24	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.710247152876966	2		840	1107	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272368	38272368	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	399	679	0	ENST00000425967.3:c.1999G>T	p.Val667Leu	p.V667L	ENST00000425967	NM_001174067.1	667	Gtg/Ttg	15/19	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.710247152876966	2		679	975	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939476	68939476	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	112	551	0	ENST00000288368.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000288368	NM_024870.2	154	gGa/gTa	5/40	1	2	FACETS	0.909	0.827	0.994	0.909	0.827	0.994	CLONAL	1	TRUE	1	0.710247152876966	2		551	347	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956797	68956797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	374	712	1	ENST00000288368.4:c.915G>A	p.Met305Ile	p.M305I	ENST00000288368	NM_024870.2	305	atG/atA	8/40	1	2	FACETS	0.961	0.913	1	0.961	0.913	1	CLONAL	1	TRUE	1	0.710247152876966	2		713	1096	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995486	68995486	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	132	568	0	ENST00000288368.4:c.1890G>T	p.Met630Ile	p.M630I	ENST00000288368	NM_024870.2	630	atG/atT	18/40	1	2	FACETS	0.9	0.825	0.978	0.9	0.825	0.978	CLONAL	1	TRUE	1	0.710247152876966	2		568	413	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009341	69009341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	334	579	0	ENST00000288368.4:c.2458G>A	p.Gly820Ser	p.G820S	ENST00000288368	NM_024870.2	820	Ggt/Agt	22/40	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.710247152876966	2		579	849	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030868	69030868	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	330	432	0	ENST00000288368.4:c.3410A>T	p.Glu1137Val	p.E1137V	ENST00000288368	NM_024870.2	1137	gAa/gTa	27/40	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.710247152876966	2		432	807	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69103986	69103986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	197	632	0	ENST00000288368.4:c.4376C>T	p.Pro1459Leu	p.P1459L	ENST00000288368	NM_024870.2	1459	cCa/cTa	36/40	1	2	FACETS	0.915	0.853	0.98	0.915	0.853	0.98	CLONAL	1	TRUE	1	0.710247152876966	2		632	606	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970908	70970908	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	379	645	0	ENST00000276594.2:c.1353T>G	p.Ile451Met	p.I451M	ENST00000276594	NM_024504.3	451	atT/atG	6/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.710247152876966	2		645	1016	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958438	90958438	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374638426	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	150	448	0	ENST00000265433.3:c.2000C>T	p.Ser667Phe	p.S667F	ENST00000265433	NM_002485.4	667	tCt/tTt	13/16	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.710247152876966	2		448	405	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376033	8376033	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	255	444	1	ENST00000356435.5:c.4564C>A	p.His1522Asn	p.H1522N	ENST00000356435		1522	Cat/Aat	28/35	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.710247152876966	2		445	661	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436684	8436685	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	102	467	0	ENST00000356435.5:c.3993_3994delinsAA	p.Met1331_Ala1332delinsIleThr	p.M1331_A1332delinsIT	ENST00000356435		1331	atGGct/atAAct	24/35	1	2	FACETS	0.984	0.892	1	0.984	0.892	1	CLONAL	1	TRUE	1	0.710247152876966	2		467	292	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471025	8471025	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	191	519	0	ENST00000356435.5:c.3474G>A	p.Trp1158Ter	p.W1158*	ENST00000356435		1158	tgG/tgA	20/35	1	2	FACETS	0.976	0.909	1	0.976	0.909	1	CLONAL	1	TRUE	1	0.710247152876966	2		519	551	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484270	8484271	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	306	637	1	ENST00000356435.5:c.3261_3262delinsAT	p.Asn1087_Arg1088delinsLysCys	p.N1087_R1088delinsKC	ENST00000356435		1087	aaTCgt/aaATgt	19/35	1	2	FACETS	0.977	0.924	1	0.977	0.924	1	CLONAL	1	TRUE	1	0.710247152876966	2		638	882	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484351	8484351	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	222	483	0	ENST00000356435.5:c.3181G>T	p.Glu1061Ter	p.E1061*	ENST00000356435		1061	Gaa/Taa	19/35	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.710247152876966	2		483	570	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486309	8486309	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159858	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	207	416	0	ENST00000356435.5:c.2508G>A	p.Met836Ile	p.M836I	ENST00000356435		836	atG/atA	17/35	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.710247152876966	2		416	536	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492904	8492904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	427	661	0	ENST00000356435.5:c.2425G>A	p.Gly809Ser	p.G809S	ENST00000356435		809	Ggt/Agt	16/35	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.710247152876966	2		661	1079	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492909	8492909	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	404	668	0	ENST00000356435.5:c.2420G>C	p.Gly807Ala	p.G807A	ENST00000356435		807	gGa/gCa	16/35	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.710247152876966	2		668	1066	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492958	8492958	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	311	561	0	ENST00000356435.5:c.2371C>T	p.Gln791Ter	p.Q791*	ENST00000356435		791	Cag/Tag	16/35	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.710247152876966	2		561	840	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499688	8499688	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774424685	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	353	574	0	ENST00000356435.5:c.2281G>A	p.Gly761Ser	p.G761S	ENST00000356435		761	Ggc/Agc	14/35	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.710247152876966	2		574	861	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517880	8517880	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	194	423	0	ENST00000356435.5:c.1511C>T	p.Ser504Leu	p.S504L	ENST00000356435		504	tCa/tTa	10/35	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.710247152876966	2		423	490	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27172731	27172731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	218	585	0	ENST00000380036.4:c.746G>A	p.Arg249Lys	p.R249K	ENST00000380036	NM_000459.3	249	aGg/aAg	5/23	1	2	FACETS	0.861	0.804	0.919	0.861	0.804	0.919	CLONAL	1	TRUE	1	0.710247152876966	2		585	713	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27228232	27228232	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	258	629	0	ENST00000380036.4:c.3229G>A	p.Glu1077Lys	p.E1077K	ENST00000380036	NM_000459.3	1077	Gag/Aag	22/23	1	2	FACETS	0.976	0.919	1	0.976	0.919	1	CLONAL	1	TRUE	1	0.710247152876966	2		629	744	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923436	36923436	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	494	863	1	ENST00000358127.4:c.826G>T	p.Asp276Tyr	p.D276Y	ENST00000358127	NM_001280556.1	276	Gac/Tac	7/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.710247152876966	2		864	1312	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015046	37015046	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	372	660	0	ENST00000358127.4:c.358G>A	p.Ala120Thr	p.A120T	ENST00000358127	NM_001280556.1	120	Gca/Aca	3/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.710247152876966	2		660	959	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339253	87339253	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	266	567	0	ENST00000277120.3:c.835G>T	p.Val279Phe	p.V279F	ENST00000277120		279	Gtc/Ttc	8/19	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.710247152876966	2		567	714	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606567	93606568	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	287	695	0	ENST00000375746.1:c.387_388delinsAA	p.Glu130Lys	p.E130K	ENST00000375746	NM_001174167.1	129	agGGaa/agAAaa	2/14	1	2	FACETS	0.885	0.834	0.937	0.885	0.834	0.937	CLONAL	1	TRUE	1	0.710247152876966	2		695	913	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624514	93624515	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	294	540	1	ENST00000375746.1:c.605_606delinsTT	p.Ser202Phe	p.S202F	ENST00000375746	NM_001174167.1	202	tCC/tTT	4/14	1	2	FACETS	0.991	0.937	1	0.991	0.937	1	CLONAL	1	TRUE	1	0.710247152876966	2		541	835	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650867	93650867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	356	666	0	ENST00000375746.1:c.1793C>T	p.Pro598Leu	p.P598L	ENST00000375746	NM_001174167.1	598	cCa/cTa	13/14	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.710247152876966	2		666	918	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215898	98215898	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	482	686	0	ENST00000331920.6:c.3311T>G	p.Phe1104Cys	p.F1104C	ENST00000331920	NM_000264.3	1104	tTt/tGt	20/24	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.710247152876966	2		686	1206	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229693	98229693	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	198	313	0	ENST00000331920.6:c.2265C>A	p.Phe755Leu	p.F755L	ENST00000331920	NM_000264.3	755	ttC/ttA	15/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.710247152876966	2		313	477	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98247992	98247992	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554702047	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	337	554	0	ENST00000331920.6:c.559C>T	p.Arg187Cys	p.R187C	ENST00000331920	NM_000264.3	187	Cgt/Tgt	3/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.710247152876966	2		554	870	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248066	98248066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	368	617	0	ENST00000331920.6:c.485C>T	p.Pro162Leu	p.P162L	ENST00000331920	NM_000264.3	162	cCt/cTt	3/24	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.710247152876966	2		617	926	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101909987	101909987	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	93	352	0	ENST00000374994.4:c.1307C>A	p.Pro436Gln	p.P436Q	ENST00000374994	NM_004612.2	436	cCa/cAa	8/9	1	2	FACETS	0.909	0.819	1	0.909	0.819	1	CLONAL	1	TRUE	1	0.710247152876966	2		352	288	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249725	110249726	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	422	853	0	ENST00000374672.4:c.949_950delinsTT	p.Pro317Leu	p.P317L	ENST00000374672	NM_004235.4	317	CCg/TTg	3/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.710247152876966	2		853	1157	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249798	110249798	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	477	805	0	ENST00000374672.4:c.877C>T	p.Pro293Ser	p.P293S	ENST00000374672	NM_004235.4	293	Cct/Tct	3/5	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.710247152876966	2		805	1167	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931636	39931636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	419	346	0	ENST00000378444.4:c.2963C>T	p.Ser988Phe	p.S988F	ENST00000378444	NM_001123385.1	988	tCc/tTc	4/15	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.710247152876966	1		346	532	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410331	63410332	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	481	482	1	ENST00000330258.3:c.2835_2836delinsTT	p.Leu946Phe	p.L946F	ENST00000330258	NM_152424.3	945	ccCCtt/ccTTtt	2/2	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.710247152876966	1		483	601	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411000	63411000	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	400	420	0	ENST00000330258.3:c.2167C>T	p.Gln723Ter	p.Q723*	ENST00000330258	NM_152424.3	723	Cag/Tag	2/2	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.710247152876966	1		420	513	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0041280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	42	504	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.666	0.554	0.79	0.666	0.554	0.79	SUBCLONAL	1	TRUE	1	0.18	2		506	701	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0041280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	53	458	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	0.919	0.783	1	0.919	0.783	1	CLONAL	1	TRUE	1	0.18	2		458	641	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727453	66727453	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397516790	NA	P-0041280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	54	659	0	ENST00000307102.5:c.169A>G	p.Lys57Glu	p.K57E	ENST00000307102	NM_002755.3	57	Aag/Gag	2/11	1	2	FACETS	0.9	0.767	1	0.9	0.767	1	CLONAL	1	TRUE	1	0.18	2		659	667	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62293296	62293296	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs762587175	NA	P-0041280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	59	568	2	ENST00000360203.5:c.395G>A	p.Arg132Gln	p.R132Q	ENST00000360203	NM_001283009.1	132	cGg/cAg	4/35	1	2	FACETS	0.993	0.854	1	0.993	0.854	1	CLONAL	1	TRUE	1	0.18	2		570	660	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577500	7577500	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	62	743	0	ENST00000269305.4:c.781del	p.Ser261ValfsTer84	p.S261Vfs*84	ENST00000269305	NM_001126112.2	261	Agt/gt	7/11	1	2	FACETS	0.885	0.763	1	0.885	0.763	1	CLONAL	1	TRUE	1	0.18	2		743	778	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	156	467	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.272530278178465	5	FACETS	0.893	0.818	0.972	0.595	0.545	0.648	CLONAL	2	TRUE	2	0.272530278178465	5		467	903	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	113	458	0				ENST00000310581	NM_198253.2	-/1132			0.199963969393083	3	FACETS	0.886	0.8	0.975	0.886	0.8	0.975	CLONAL	2	TRUE	1	0.272530278178465	3		458	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	349	733	0	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	0.272530278178465	5	FACETS	0.927	0.877	0.978	0.927	0.877	0.978	CLONAL	3	TRUE	2	0.272530278178465	5		733	1297	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540074	187540074	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs921535768	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	50	372	0	ENST00000441802.2:c.7666C>T	p.Arg2556Ter	p.R2556*	ENST00000441802	NM_005245.3	2556	Cga/Tga	10/27	0.272530278178465	3	FACETS	1	0.858	1	0.505	0.429	0.588	CLONAL	1	TRUE	1	0.272530278178465	3		372	413	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259496	89259496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	96	370	0	ENST00000336596.2:c.640G>A	p.Asp214Asn	p.D214N	ENST00000336596	NM_005233.5	214	Gac/Aac	3/17	0.181445837500709	5	FACETS	0.962	0.86	1	0.641	0.573	0.713	CLONAL	2	TRUE	2	0.272530278178465	5		370	516	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164832	47164832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1017636782	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	91	257	0	ENST00000409792.3:c.1294C>T	p.Arg432Cys	p.R432C	ENST00000409792	NM_014159.6	432	Cgt/Tgt	3/21	0.181445837500709	5	FACETS	0.852	0.763	0.946	0.852	0.763	0.946	CLONAL	3	TRUE	2	0.272530278178465	5		257	368	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353815	15353815	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780028668	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	68	501	1	ENST00000263377.2:c.3065C>T	p.Pro1022Leu	p.P1022L	ENST00000263377	NM_058243.2	1022	cCg/cTg	14/20	0.271298352729141	3	FACETS	0.816	0.709	0.931	0.408	0.354	0.466	CLONAL	1	TRUE	1	0.272530278178465	3		502	695	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494960	56494960	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	161	428	0	ENST00000267101.3:c.3317C>T	p.Ala1106Val	p.A1106V	ENST00000267101	NM_001982.3	1106	gCt/gTt	27/28	0.272530278178465	6	FACETS	1	0.97	1	0.559	0.513	0.607	CLONAL	2	TRUE	2	0.272530278178465	6		428	816	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602613	10602613	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	204	646	0	ENST00000171111.5:c.965C>T	p.Pro322Leu	p.P322L	ENST00000171111	NM_203500.1	322	cCc/cTc	3/6	0.271298352729141	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.272530278178465	3		646	799	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485448	57485448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	51	301	0	ENST00000371085.3:c.1030G>A	p.Glu344Lys	p.E344K	ENST00000371085	NM_000516.4	344	Gag/Aag	12/13	0.272530278178465	3	FACETS	0.996	0.848	1	0.498	0.424	0.579	CLONAL	1	TRUE	1	0.272530278178465	3		301	427	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127723	2127723	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763047420	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	48	388	0	ENST00000219476.3:c.2962C>T	p.Arg988Cys	p.R988C	ENST00000219476	NM_000548.3	988	Cgc/Tgc	26/42	0.199963969393083	3	FACETS	0.814	0.688	0.952	0.407	0.344	0.476	CLONAL	1	TRUE	1	0.272530278178465	3		388	492	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932269	39932269	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	237	858	0	ENST00000378444.4:c.2330C>T	p.Pro777Leu	p.P777L	ENST00000378444	NM_001123385.1	777	cCa/cTa	4/15	0.179674825049105	4	FACETS	0.959	0.894	1	0.959	0.894	1	CLONAL	2	TRUE	2	0.272530278178465	4		858	1154	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486128	8486128	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1274347777	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	114	408	1	ENST00000356435.5:c.2689G>A	p.Ala897Thr	p.A897T	ENST00000356435		897	Gcc/Acc	17/35	0.219411026972333	4	FACETS	0.864	0.78	0.953	0.864	0.78	0.953	CLONAL	2	TRUE	2	0.272530278178465	4		409	616	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268805	41268805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	121	355	0	ENST00000349496.5:c.1043C>T	p.Ser348Phe	p.S348F	ENST00000349496	NM_001904.3	348	tCt/tTt	7/15	0.181445837500709	5	FACETS	1	0.976	1	0.816	0.741	0.894	CLONAL	2	TRUE	2	0.272530278178465	5		355	511	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974679	21974680	+	stop_gained,splice_region_variant	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	145	433	0	ENST00000304494.5:c.147_148delinsTT	p.Gln50Ter	p.Q50*	ENST00000304494	NM_000077.4	49	atCCag/atTTag	1/3	0.219411026972333	4	FACETS	0.866	0.795	0.94	1	0.984	1	CLONAL	3	TRUE	2	0.272530278178465	4		433	521	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783313	9783313	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	162	527	0	ENST00000377346.4:c.2557G>A	p.Asp853Asn	p.D853N	ENST00000377346	NM_005026.3	853	Gat/Aat	20/24	0.271298352729141	3	FACETS	0.989	0.91	1	0.989	0.91	1	CLONAL	2	TRUE	1	0.272530278178465	3		527	683	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316131	11316132	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	155	552	0	ENST00000361445.4:c.622_623delinsAA	p.Gly208Lys	p.G208K	ENST00000361445	NM_004958.3	208	GGa/AAa	5/58	0.271298352729141	3	FACETS	0.872	0.8	0.947	0.872	0.8	0.947	CLONAL	2	TRUE	1	0.272530278178465	3		552	741	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22413013	22413013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	54	144	0	ENST00000344548.3:c.260C>T	p.Pro87Leu	p.P87L	ENST00000344548	NM_001039802.1	87	cCa/cTa	5/7	0.271298352729141	3	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	1	0.272530278178465	3		144	198	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551499	150551499	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1314309745	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	426	721	0	ENST00000369026.2:c.508G>A	p.Glu170Lys	p.E170K	ENST00000369026	NM_021960.4	170	Gag/Aag	1/3	0.181445837500709	5	FACETS	0.977	0.933	1	1	0.995	1	CLONAL	4	TRUE	2	0.272530278178465	5		721	1127	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204506606	204506606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	210	321	0	ENST00000367182.3:c.392C>T	p.Pro131Leu	p.P131L	ENST00000367182	NM_001278516.1	131	cCa/cTa	6/11	0.268335561630576	3	FACETS	1	0.941	1	1	0.941	1	CLONAL	3	TRUE	0	0.272530278178465	3		321	580	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606777	43606778	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	175	639	2	ENST00000355710.3:c.1386_1387delinsAA	p.Gly463Arg	p.G463R	ENST00000355710	NM_020975.4	462	tcGGgg/tcAAgg	7/20	0.271298352729141	3	FACETS	0.934	0.862	1	0.934	0.862	1	CLONAL	2	TRUE	1	0.272530278178465	3		641	781	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63700144	63700144	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	31	149	0	ENST00000279873.7:c.479T>A	p.Val160Asp	p.V160D	ENST00000279873	NM_032199.2	160	gTt/gAt	3/10	0.271298352729141	3	FACETS	0.917	0.744	1	0.458	0.372	0.556	CLONAL	1	TRUE	1	0.272530278178465	3		149	282	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154254	2154255	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	173	684	1	ENST00000434045.2:c.673_674delinsAA	p.Gly225Lys	p.G225K	ENST00000434045	NM_001127598.1	225	GGg/AAg	5/5	0.199963969393083	3	FACETS	0.822	0.756	0.889	0.822	0.756	0.889	CLONAL	2	TRUE	1	0.272530278178465	3		685	878	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154447	2154448	+	missense_variant	Missense_Mutation	DNP	AG	AG	TA	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	76	539	0	ENST00000434045.2:c.480_481delinsTA	p.Phe161Ile	p.F161I	ENST00000434045	NM_001127598.1	160	aaCTtc/aaTAtc	5/5	0.199963969393083	3	FACETS	0.956	0.838	1	0.478	0.419	0.541	CLONAL	1	TRUE	1	0.272530278178465	3		539	663	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135631	64135631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	106	623	0	ENST00000334205.4:c.1099C>T	p.Leu367Phe	p.L367F	ENST00000334205	NM_003942.2	367	Ctc/Ttc	10/17	0.199963969393083	3	FACETS	0.927	0.83	1	0.464	0.415	0.516	CLONAL	1	TRUE	1	0.272530278178465	3		623	953	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571979	64571980	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	206	701	2	ENST00000312049.6:c.1659_1660delinsTT	p.Gln554Ter	p.Q554*	ENST00000312049	NM_130799.2	553	ttCCag/ttTTag	10/10	0.199963969393083	3	FACETS	0.938	0.871	1	0.938	0.871	1	CLONAL	2	TRUE	1	0.272530278178465	3		703	916	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575044	64575045	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	70	402	0	ENST00000312049.6:c.762_763delinsAA	p.Glu255Lys	p.E255K	ENST00000312049	NM_130799.2	254	ctGGag/ctAAag	4/10	0.199963969393083	3	FACETS	1	0.92	1	0.536	0.468	0.61	CLONAL	1	TRUE	1	0.272530278178465	3		402	544	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984930	101984930	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	51	284	0	ENST00000282441.5:c.377A>G	p.His126Arg	p.H126R	ENST00000282441	NM_001130145.2	126	cAt/cGt	2/9	0.199963969393083	3	FACETS	1	0.939	1	0.601	0.512	0.697	CLONAL	1	TRUE	1	0.272530278178465	3		284	354	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984936	101984936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1192221094	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	45	246	0	ENST00000282441.5:c.383C>T	p.Ser128Phe	p.S128F	ENST00000282441	NM_001130145.2	128	tCt/tTt	2/9	0.199963969393083	3	FACETS	1	0.924	1	0.583	0.492	0.682	CLONAL	1	TRUE	1	0.272530278178465	3		246	322	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376129	118376131	+	missense_variant	Missense_Mutation	TNP	TAG	TAG	ATT	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	60	443	1	ENST00000534358.1:c.9522_9524delinsATT	p.Ser3174_Ser3175delinsArgPhe	p.S3174_S3175delinsRF	ENST00000534358	NM_005933.3	3174	agTAGt/agATTt	27/36	0.199963969393083	3	FACETS	1	0.867	1	0.502	0.433	0.577	CLONAL	1	TRUE	1	0.272530278178465	3		444	498	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417170	417170	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	61	169	0	ENST00000399788.2:c.3380T>A	p.Val1127Glu	p.V1127E	ENST00000399788	NM_001042603.1	1127	gTg/gAg	23/28	0.181445837500709	5	FACETS	1	0.938	1	0.756	0.658	0.861	CLONAL	2	TRUE	2	0.272530278178465	5		169	278	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425320	49425320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	374	695	0	ENST00000301067.7:c.13168G>A	p.Glu4390Lys	p.E4390K	ENST00000301067	NM_003482.3	4390	Gag/Aag	39/54	0.272530278178465	6	FACETS	1	0.974	1	1	0.974	1	CLONAL	4	TRUE	2	0.272530278178465	6		695	1023	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431724	49431724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs551794772	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	186	617	1	ENST00000301067.7:c.9415C>T	p.Pro3139Ser	p.P3139S	ENST00000301067	NM_003482.3	3139	Ccc/Tcc	34/54	0.272530278178465	6	FACETS	0.986	0.91	1	0.493	0.455	0.533	CLONAL	2	TRUE	2	0.272530278178465	6		618	1069	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555646	21555646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	171	515	0	ENST00000382592.4:c.2624G>A	p.Gly875Glu	p.G875E	ENST00000382592	NM_014572.2	875	gGg/gAg	6/8	0.272530278178465	3	FACETS	0.949	0.875	1	0.949	0.875	1	CLONAL	2	TRUE	1	0.272530278178465	3		515	751	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557392	21557392	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	53	335	0	ENST00000382592.4:c.2453G>A	p.Trp818Ter	p.W818*	ENST00000382592	NM_014572.2	818	tGg/tAg	5/8	0.272530278178465	3	FACETS	0.98	0.837	1	0.49	0.418	0.568	CLONAL	1	TRUE	1	0.272530278178465	3		335	451	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514770	103514771	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	56	361	0	ENST00000355739.4:c.1271_1272delinsTT	p.Ser424Phe	p.S424F	ENST00000355739	NM_000123.3	424	tCC/tTT	8/15	0.272530278178465	3	FACETS	1	0.898	1	0.528	0.453	0.61	CLONAL	1	TRUE	1	0.272530278178465	3		361	442	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872995	35872995	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	85	305	0	ENST00000216797.5:c.237C>G	p.His79Gln	p.H79Q	ENST00000216797	NM_020529.2	79	caC/caG	2/6	0.272530278178465	5	FACETS	1	0.961	1	0.402	0.355	0.452	CLONAL	1	TRUE	2	0.272530278178465	5		305	729	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95599762	95599762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	84	285	0	ENST00000393063.1:c.34G>A	p.Ala12Thr	p.A12T	ENST00000393063	NM_030621.3	12	Gca/Aca	3/28	0.272530278178465	5	FACETS	0.877	0.777	0.984	0.585	0.518	0.656	CLONAL	2	TRUE	2	0.272530278178465	5		285	495	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675112	40675113	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	105	708	0	ENST00000249776.8:c.76_77delinsTT	p.Pro26Leu	p.P26L	ENST00000249776	NM_033286.3	26	CCa/TTa	1/9	1	2	FACETS	0.89	0.796	0.989	0.89	0.796	0.989	CLONAL	1	TRUE	1	0.272530278178465	2		708	866	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961291	41961292	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	42	374	1	ENST00000219905.7:c.199_200delinsTT	p.Pro67Leu	p.P67L	ENST00000219905	NM_001164273.1	67	CCa/TTa	2/24	1	2	FACETS	0.813	0.68	0.96	0.813	0.68	0.96	CLONAL	1	TRUE	1	0.272530278178465	2		375	379	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343497	343497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	206	678	0	ENST00000262320.3:c.2177C>T	p.Ser726Phe	p.S726F	ENST00000262320	NM_003502.3	726	tCc/tTc	8/11	0.199963969393083	3	FACETS	0.969	0.9	1	0.969	0.9	1	CLONAL	2	TRUE	1	0.272530278178465	3		678	886	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396570	396570	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs780104760	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	160	572	0	ENST00000262320.3:c.456C>A	p.Asn152Lys	p.N152K	ENST00000262320	NM_003502.3	152	aaC/aaA	2/11	0.199963969393083	3	FACETS	0.886	0.814	0.961	0.886	0.814	0.961	CLONAL	2	TRUE	1	0.272530278178465	3		572	753	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396909	396910	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	123	601	1	ENST00000262320.3:c.116_117delinsTT	p.Pro39Leu	p.P39L	ENST00000262320	NM_003502.3	39	cCC/cTT	2/11	0.199963969393083	3	FACETS	1	0.952	1	0.543	0.49	0.599	CLONAL	1	TRUE	1	0.272530278178465	3		602	944	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122859	2122860	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	126	508	1	ENST00000219476.3:c.2230_2231delinsTT	p.Pro744Leu	p.P744L	ENST00000219476	NM_000548.3	744	CCa/TTa	21/42	0.199963969393083	3	FACETS	0.781	0.708	0.857	0.781	0.708	0.857	SUBCLONAL	2	TRUE	1	0.272530278178465	3		509	673	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56873485	56873485	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	74	440	0	ENST00000308159.5:c.2189G>A	p.Arg730Lys	p.R730K	ENST00000308159	NM_014669.4	730	aGa/aAa	20/22	0.272530278178465	3	FACETS	1	0.945	1	0.57	0.5	0.646	CLONAL	1	TRUE	1	0.272530278178465	3		440	541	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733223	74733223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	180	473	0	ENST00000359995.5:c.20C>T	p.Pro7Leu	p.P7L	ENST00000359995	NM_001195427.1	7	cCt/cTt	1/3	0.271298352729141	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.272530278178465	3		473	730	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375037	45375037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	45	275	0	ENST00000262160.6:c.806C>T	p.Ser269Leu	p.S269L	ENST00000262160	NM_005901.5	269	tCa/tTa	8/11	0.272530278178465	3	FACETS	1	0.909	1	0.557	0.47	0.652	CLONAL	1	TRUE	1	0.272530278178465	3		275	337	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610322	10610323	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	98	745	0	ENST00000171111.5:c.387_388delinsTT	p.Pro130Ser	p.P130S	ENST00000171111	NM_203500.1	129	caCCcc/caTTcc	2/6	0.271298352729141	3	FACETS	0.855	0.761	0.955	0.427	0.38	0.478	CLONAL	1	TRUE	1	0.272530278178465	3		745	956	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289675	15289676	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	222	688	0	ENST00000263388.2:c.3795_3796delinsAA	p.Gly1266Ser	p.G1266S	ENST00000263388	NM_000435.2	1265	ccGGgt/ccAAgt	23/33	0.271298352729141	3	FACETS	0.92	0.856	0.986	0.92	0.856	0.986	CLONAL	2	TRUE	1	0.272530278178465	3		688	1006	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354116	15354116	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	205	553	0	ENST00000263377.2:c.2764C>T	p.Pro922Ser	p.P922S	ENST00000263377	NM_058243.2	922	Ccc/Tcc	14/20	0.271298352729141	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.272530278178465	3		553	780	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224007	36224008	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	284	769	1	ENST00000222270.7:c.6557_6558delinsTT	p.Pro2186Leu	p.P2186L	ENST00000222270	NM_014727.1	2186	cCC/cTT	28/37	0.181445837500709	5	FACETS	1	0.986	1	0.775	0.727	0.824	CLONAL	2	TRUE	2	0.272530278178465	5		770	1263	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051099	128051100	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	121	426	1	ENST00000285398.2:c.223_224delinsTT	p.Pro75Phe	p.P75F	ENST00000285398	NM_000122.1	75	CCc/TTc	2/15	0.272530278178465	3	FACETS	0.82	0.743	0.901	0.82	0.743	0.901	CLONAL	2	TRUE	1	0.272530278178465	3		427	615	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376275	225376275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	22	232	0	ENST00000264414.4:c.679G>A	p.Glu227Lys	p.E227K	ENST00000264414	NM_003590.4	227	Gaa/Aaa	6/16	0.272530278178465	3	FACETS	0.758	0.589	0.953	0.379	0.294	0.477	CLONAL	1	TRUE	1	0.272530278178465	3		232	242	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513581	41513582	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	143	485	1	ENST00000263253.7:c.485_486delinsTT	p.Ala162Val	p.A162V	ENST00000263253	NM_001429.3	162	gCC/gTT	2/31	0.181445837500709	5	FACETS	1	0.945	1	0.697	0.637	0.76	CLONAL	2	TRUE	2	0.272530278178465	5		486	707	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119642315	119642315	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	39	291	0	ENST00000316626.5:c.382C>G	p.Leu128Val	p.L128V	ENST00000316626		128	Ctt/Gtt	4/12	0.181445837500709	5	FACETS	0.854	0.708	1	0.285	0.236	0.339	CLONAL	1	TRUE	2	0.272530278178465	5		291	472	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188274	142188274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747991579	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	108	308	0	ENST00000350721.4:c.6457C>T	p.His2153Tyr	p.H2153Y	ENST00000350721	NM_001184.3	2153	Cac/Tac	38/47	0.181445837500709	5	FACETS	0.876	0.791	0.964	0.876	0.791	0.964	CLONAL	3	TRUE	2	0.272530278178465	5		308	425	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953829	55953829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	134	405	0	ENST00000263923.4:c.3607G>A	p.Glu1203Lys	p.E1203K	ENST00000263923	NM_002253.2	1203	Gag/Aag	27/30	0.272530278178465	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	1	0.272530278178465	3		405	527	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111597	56111598	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	40	135	1	ENST00000399503.3:c.197_198delinsAA	p.Arg66Gln	p.R66Q	ENST00000399503	NM_005921.1	66	cGG/cAA	1/20	0.272530278178465	3	FACETS	1	0.955	1	0.738	0.618	0.868	CLONAL	1	TRUE	1	0.272530278178465	3		136	226	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680188	30680188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	146	596	0	ENST00000376406.3:c.1531G>A	p.Glu511Lys	p.E511K	ENST00000376406	NM_014641.2	511	Gag/Aag	5/15	0.272530278178465	6	FACETS	0.824	0.751	0.9	0.412	0.375	0.45	CLONAL	2	TRUE	2	0.272530278178465	6		596	1005	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004901	150004901	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	125	343	0	ENST00000253339.5:c.1324C>T	p.Gln442Ter	p.Q442*	ENST00000253339		442	Cag/Tag	3/7	0.272530278178465	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	0	0.272530278178465	2		343	450	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508111	106508111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	32	198	0	ENST00000359195.3:c.105G>A	p.Met35Ile	p.M35I	ENST00000359195	NM_002649.2	35	atG/atA	2/11	1	2	FACETS	0.799	0.65	0.965	0.799	0.65	0.965	CLONAL	1	TRUE	1	0.272530278178465	2		198	294	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287448	38287449	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	101	462	2	ENST00000425967.3:c.208_209delinsTT	p.Pro70Phe	p.P70F	ENST00000425967	NM_001174067.1	70	CCt/TTt	4/19	0.222349027261027	2	FACETS	0.752	0.675	0.833	0.752	0.675	0.833	SUBCLONAL	2	TRUE	0	0.272530278178465	2		464	493	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104678	69104678	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	121	484	0	ENST00000288368.4:c.4522G>T	p.Val1508Phe	p.V1508F	ENST00000288368	NM_024870.2	1508	Gtt/Ttt	37/40	0.181445837500709	5	FACETS	0.979	0.886	1	0.653	0.591	0.717	CLONAL	2	TRUE	2	0.272530278178465	5		484	639	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413102	139413102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	162	637	0	ENST00000277541.6:c.1040G>A	p.Gly347Asp	p.G347D	ENST00000277541	NM_017617.3	347	gGc/gAc	6/34	0.219411026972333	4	FACETS	0.865	0.794	0.94	0.865	0.794	0.94	CLONAL	2	TRUE	2	0.272530278178465	4		637	874	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314878	1314882	+	downstream_gene_variant	3'Flank	DEL	CAGGA	CAGGA	-	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	21	283	0				ENST00000400841		-/233			0.179674825049105	4	FACETS	0.492	0.378	0.625	0.246	0.189	0.313	SUBCLONAL	1	TRUE	2	0.272530278178465	4		283	399	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938396	44938397	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	76	274	0	ENST00000377967.4:c.2944_2945delinsAA	p.Gly982Lys	p.G982K	ENST00000377967	NM_021140.2	982	GGa/AAa	20/29	0.179674825049105	4	FACETS	0.825	0.727	0.93	0.825	0.727	0.93	CLONAL	2	TRUE	2	0.272530278178465	4		274	430	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411318	63411318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756872620	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	177	682	0	ENST00000330258.3:c.1849G>A	p.Glu617Lys	p.E617K	ENST00000330258	NM_152424.3	617	Gaa/Aaa	2/2	0.179674825049105	4	FACETS	0.891	0.821	0.963	0.891	0.821	0.963	CLONAL	2	TRUE	2	0.272530278178465	4		682	928	SUCCESS
AR	367	MSKCC	GRCh37	X	66941742	66941743	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	141	504	1	ENST00000374690.3:c.2386_2387delinsAA	p.Gly796Lys	p.G796K	ENST00000374690	NM_000044.3	796	GGa/AAa	6/8	0.179674825049105	4	FACETS	0.96	0.876	1	0.96	0.876	1	CLONAL	2	TRUE	2	0.272530278178465	4		505	686	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	78	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.762	0.67	0.86	0.762	0.67	0.86	SUBCLONAL	1	TRUE	1	0.359885736953353	2		126	569	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074393	8074393	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	60	358	0	ENST00000377482.5:c.266del	p.Lys89SerfsTer32	p.K89Sfs*32	ENST00000377482	NM_018948.3	89	aAg/ag	4/4	1	2	FACETS	0.995	0.863	1	0.995	0.863	1	CLONAL	1	TRUE	1	0.359885736953353	2		358	335	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624289	89624297	+	inframe_deletion	In_Frame_Del	DEL	CGACTTAGA	CGACTTAGA	-	novel	NA	P-0041342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	70	437	1	ENST00000371953.3:c.64_72del	p.Asp22_Asp24del	p.D22_D24del	ENST00000371953	NM_000314.4	21	ttCGACTTAGAc/ttc	1/9	0.359885736953353	1	FACETS	0.725	0.634	0.822	0.725	0.634	0.822	SUBCLONAL	1	TRUE	0	0.359885736953353	1		438	440	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560103	29560104	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0041342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	26	267	1	ENST00000356175.3:c.3580_3581del	p.Asp1194HisfsTer9	p.D1194Hfs*9	ENST00000356175	NM_000267.3	1194	GAc/c	27/57	1	2	FACETS	0.471	0.373	0.582	0.471	0.373	0.582	SUBCLONAL	1	TRUE	1	0.359885736953353	2		268	307	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796784	135796784	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	26	256	0	ENST00000298552.3:c.703A>C	p.Thr235Pro	p.T235P	ENST00000298552	NM_001162426.1	235	Act/Cct	8/23	0.359885736953353	1	FACETS	0.57	0.454	0.701	0.57	0.454	0.701	SUBCLONAL	1	TRUE	0	0.359885736953353	1		256	208	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs864622237	NA	P-0041410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	399	545	0	ENST00000269305.4:c.700T>C	p.Tyr234His	p.Y234H	ENST00000269305	NM_001126112.2	234	Tac/Cac	7/11	0.719667347523161	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.799912705659623	1		545	585	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263323	115263323	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	380	596	0	ENST00000438362.2:c.2027A>T	p.Glu676Val	p.E676V	ENST00000438362	NM_001242891.1	676	gAg/gTg	17/20	1	2	FACETS	0.98	0.934	1	0.98	0.934	1	CLONAL	1	TRUE	1	0.799912705659623	2		596	969	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115978	8116009	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	ATGGGTTAGAGCCCTGCTCGATGCTCACAGGG	ATGGGTTAGAGCCCTGCTCGATGCTCACAGGG	CAT	novel	NA	P-0041410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	183	297	2	ENST00000346208.3:c.1324_*23delinsCAT		p.*442*	ENST00000346208		442		6/6	1	2	FACETS	0.811	0.753	0.87	0.811	0.753	0.87	CLONAL	1	TRUE	1	0.799912705659623	2		299	564	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225636	133225636	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	221	621	0	ENST00000320574.5:c.4028G>T	p.Gly1343Val	p.G1343V	ENST00000320574	NM_006231.2	1343	gGc/gTc	32/49	0.799912705659623	1	FACETS	0.56	0.525	0.596	0.56	0.525	0.596	SUBCLONAL	1	TRUE	0	0.799912705659623	1		621	592	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0041433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	26	464	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.332	0.262	0.413	0.332	0.262	0.413	SUBCLONAL	1	TRUE	1	0.29	2		464	540	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0041433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	63	373	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.983	0.853	1	0.983	0.853	1	CLONAL	1	TRUE	1	0.29	2		373	442	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884482	151884482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1418271614	NA	P-0041433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	62	303	0	ENST00000262189.6:c.4873G>A	p.Glu1625Lys	p.E1625K	ENST00000262189	NM_170606.2	1625	Gaa/Aaa	33/59	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.29	2		303	362	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827835	72827835	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	30	469	0	ENST00000268489.5:c.8746G>A	p.Glu2916Lys	p.E2916K	ENST00000268489	NM_006885.3	2916	Gaa/Aaa	9/10	0.0887322641748176	0	FACETS	0.385	0.31	0.469			1	INDETERMINATE	1	TRUE	0	0.29	0		469	382	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016549	12016549	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0041433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	16	152	0	ENST00000353533.5:c.686-1G>C		p.X229_splice	ENST00000353533	NM_003010.3	229			0.216864203753466	1	FACETS	0.447	0.331	0.585	0.447	0.331	0.585	SUBCLONAL	1	TRUE	0	0.29	1		152	211	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098969	178098969	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	34	272	0	ENST00000397062.3:c.76C>A	p.Gln26Lys	p.Q26K	ENST00000397062	NM_006164.4	26	Caa/Aaa	2/5	1	2	FACETS	0.827	0.676	0.997	0.827	0.676	0.997	CLONAL	1	TRUE	1	0.203417876385524	2		272	404	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591888	48591888	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519739	NA	P-0041518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	50	454	0	ENST00000342988.3:c.1051G>C	p.Asp351His	p.D351H	ENST00000342988	NM_005359.5	351	Gat/Cat	9/12	0.203417876385524	1	FACETS	0.718	0.608	0.839	0.718	0.608	0.839	SUBCLONAL	1	TRUE	0	0.203417876385524	1		454	615	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851765	134851765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	49	474	0	ENST00000398015.3:c.1171G>A	p.Val391Ile	p.V391I	ENST00000398015	NM_004441.4	391	Gtc/Atc	5/16	1	2	FACETS	0.804	0.68	0.941	0.804	0.68	0.941	CLONAL	1	TRUE	1	0.203417876385524	2		474	599	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070871	30070871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs74315503	NA	P-0041518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	73	607	0	ENST00000338641.4:c.1387G>A	p.Glu463Lys	p.E463K	ENST00000338641	NM_000268.3	463	Gag/Aag	13/16	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.203417876385524	2		607	700	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260482	16260482	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs764911348	NA	P-0041518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	44	444	0	ENST00000375759.3:c.7747G>C	p.Glu2583Gln	p.E2583Q	ENST00000375759	NM_015001.2	2583	Gaa/Caa	11/15	0.203417876385524	1	FACETS	0.845	0.709	0.995	0.845	0.709	0.995	CLONAL	1	TRUE	0	0.203417876385524	1		444	460	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233605	69233605	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	52	280	0	ENST00000462284.1:c.1470G>C	p.Met490Ile	p.M490I	ENST00000462284	NM_002392.5	490	atG/atC	11/11	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.203417876385524	2		280	434	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112524	115112524	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	48	696	0	ENST00000257566.3:c.1216G>A	p.Asp406Asn	p.D406N	ENST00000257566	NM_016569.3	406	Gac/Aac	7/8	1	2	FACETS	0.655	0.553	0.769	0.655	0.553	0.769	SUBCLONAL	1	TRUE	1	0.203417876385524	2		696	720	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287305	38287305	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	71	768	1	ENST00000425967.3:c.352G>T	p.Glu118Ter	p.E118*	ENST00000425967	NM_001174067.1	118	Gag/Tag	4/19	1	2	FACETS	0.919	0.801	1	0.919	0.801	1	CLONAL	1	TRUE	1	0.203417876385524	2		769	760	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56910951	56910951	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	72	575	0	ENST00000519728.1:c.1097G>C	p.Arg366Pro	p.R366P	ENST00000519728	NM_002350.3	366	cGg/cCg	11/13	1	2	FACETS	0.829	0.723	0.944	0.829	0.723	0.944	CLONAL	1	TRUE	1	0.203417876385524	2		575	854	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342675	70342675	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	68	644	0	ENST00000374080.3:c.1436C>G	p.Ser479Cys	p.S479C	ENST00000374080		479	tCc/tGc	10/45	1	2	FACETS	0.795	0.69	0.909	0.795	0.69	0.909	CLONAL	1	TRUE	1	0.203417876385524	2		644	841	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578530	7578530	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs267605077	NA	P-0041523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	412	857	0	ENST00000269305.4:c.400T>C	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	Ttt/Ctt	5/11	0.490025077746269	2	FACETS	0.97	0.931	1	0.97	0.931	1	CLONAL	2	TRUE	0	0.544264399684089	2		857	780	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856439	111856439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	80	256	3	ENST00000341259.2:c.490G>A	p.Gly164Arg	p.G164R	ENST00000341259	NM_005475.2	164	Ggg/Agg	2/8	0.473671245955093	5	FACETS	0.996	0.879	1	0.332	0.293	0.374	CLONAL	1	TRUE	2	0.544264399684089	5		259	536	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787769	135787769	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs118203452	NA	P-0041523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	142	581	1	ENST00000298552.3:c.813T>A	p.Tyr271Ter	p.Y271*	ENST00000298552	NM_001162426.1	271	taT/taA	9/23	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.544264399684089	2		582	509	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0041528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	56	277	1	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	1	2	FACETS	0.961	0.826	1	0.961	0.826	1	CLONAL	1	TRUE	1	0.290017871564379	2		278	402	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346338	73346338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	92	345	0	ENST00000377767.4:c.1462G>A	p.Asp488Asn	p.D488N	ENST00000377767	NM_014953.3	488	Gat/Aat	10/21	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.290017871564379	2		345	611	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468912	25468912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780672407	NA	P-0041528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	164	744	0	ENST00000264709.3:c.1451G>A	p.Arg484Gln	p.R484Q	ENST00000264709	NM_175629.2	484	cGg/cAg	12/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.290017871564379	2		744	961	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577106	+	inframe_insertion	In_Frame_Ins	INS	-	-	GACAGGCACAAACACGCACCTCAAAGCTGTTCCGTCCCAGTAGATTACCAT	novel	NA	P-0041528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	76	761	0	ENST00000269305.4:c.832_833insATGGTAATCTACTGGGACGGAACAGCTTTGAGGTGCGTGTTTGTGCCTGTC	p.Cys277_Pro278insHisGlyAsnLeuLeuGlyArgAsnSerPheGluValArgValCysAlaCys	p.C277_P278insHGNLLGRNSFEVRVCAC	ENST00000269305	NM_001126112.2	278	cct/cATGGTAATCTACTGGGACGGAACAGCTTTGAGGTGCGTGTTTGTGCCTGTCct	8/11	0.290017871564379	1	FACETS	0.46	0.402	0.523	0.46	0.402	0.523	SUBCLONAL	1	TRUE	0	0.290017871564379	1		761	974	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011106	12011106	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0041528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	69	293	0	ENST00000353533.5:c.514-1G>A		p.X172_splice	ENST00000353533	NM_003010.3	172			0.290017871564379	1	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	0	0.290017871564379	1		293	395	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554451	63554452	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0041528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	160	770	1	ENST00000307078.5:c.287_288delinsTT	p.Arg96Leu	p.R96L	ENST00000307078	NM_004655.3	96	cGA/cTT	2/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.290017871564379	2		771	964	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31424568	31424569	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CG	novel	NA	P-0041528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	130	744	0	ENST00000344624.3:c.3225_3226dup	p.Glu1076AlafsTer42	p.E1076Afs*42	ENST00000344624		1076	gaa/gCGaa	25/33	1	2	FACETS	0.873	0.791	0.96	0.873	0.791	0.96	CLONAL	1	TRUE	1	0.290017871564379	2		744	1027	SUCCESS
APC	324	MSKCC	GRCh37	5	112174774	112174774	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	71	360	0	ENST00000257430.4:c.3484del	p.Tyr1162IlefsTer3	p.Y1162Ifs*3	ENST00000257430	NM_000038.5	1161	aaT/aa	16/16	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.290017871564379	2		360	489	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	83	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.329561608076033	2		126	495	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405951	49405951	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	34	674	2	ENST00000418115.1:c.187C>A	p.Gln63Lys	p.Q63K	ENST00000418115	NM_001664.2	63	Cag/Aag	3/5	0.25223330792863	1	FACETS	0.264	0.215	0.32	0.264	0.215	0.32	SUBCLONAL	1	TRUE	0	0.329561608076033	1		676	653	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715979	52715979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205227	NA	P-0041531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	31	814	3	ENST00000322088.6:c.544C>T	p.Arg182Trp	p.R182W	ENST00000322088	NM_014225.5	182	Cgg/Tgg	5/15	1	2	FACETS	0.22	0.177	0.27	0.22	0.177	0.27	SUBCLONAL	1	TRUE	1	0.329561608076033	2		817	854	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738828	145738828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201883228	NA	P-0041531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	124	1002	0	ENST00000428558.2:c.2237C>T	p.Ala746Val	p.A746V	ENST00000428558	NM_004260.3	746	gCg/gTg	14/22	1	2	FACETS	0.618	0.558	0.683	0.618	0.558	0.683	SUBCLONAL	1	TRUE	1	0.329561608076033	2		1002	1217	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215276	123215276	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	45	386	0	ENST00000218089.9:c.2822C>T	p.Ser941Leu	p.S941L	ENST00000218089	NM_001042749.1	941	tCa/tTa	28/35	1	2	FACETS	0.59	0.496	0.694	0.59	0.496	0.694	SUBCLONAL	1	TRUE	1	0.329561608076033	2		386	463	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276400	115276400	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs534189855	NA	P-0041531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	81	475	0	ENST00000438362.2:c.928G>C	p.Glu310Gln	p.E310Q	ENST00000438362	NM_001242891.1	310	Gaa/Caa	9/20	1	2	FACETS	0.922	0.814	1	0.922	0.814	1	CLONAL	1	TRUE	1	0.329561608076033	2		475	533	SUCCESS
H3C13	653604	MSKCC	GRCh37	1	149784867	149784867	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	40	292	0	ENST00000331491.1:c.370G>C	p.Asp124His	p.D124H	ENST00000331491	NM_001123375.2	124	Gac/Cac	1/1	1	2	FACETS	0.983	0.823	1	0.983	0.823	1	CLONAL	1	TRUE	1	0.329561608076033	2		292	247	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981119	201981119	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	120	858	0	ENST00000359651.3:c.198C>G	p.Phe66Leu	p.F66L	ENST00000359651		66	ttC/ttG	2/8	1	2	FACETS	0.919	0.83	1	0.919	0.83	1	CLONAL	1	TRUE	1	0.329561608076033	2		858	792	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104359190	104359190	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	87	478	1	ENST00000369902.3:c.911A>T	p.Asp304Val	p.D304V	ENST00000369902	NM_016169.3	304	gAc/gTc	8/12	1	2	FACETS	0.958	0.85	1	0.958	0.85	1	CLONAL	1	TRUE	1	0.329561608076033	2		479	551	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343514	118343514	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0041531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	83	462	0	ENST00000534358.1:c.1640C>G	p.Ser547Ter	p.S547*	ENST00000534358	NM_005933.3	547	tCa/tGa	3/36	0.25223330792863	1	FACETS	0.913	0.809	1	0.913	0.809	1	CLONAL	1	TRUE	0	0.329561608076033	1		462	461	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482340	56482341	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0041531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	43	566	0	ENST00000267101.3:c.888_889delinsTT	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	296	gtGGat/gtTTat	8/28	0.322016708566393	3	FACETS	0.46	0.384	0.544	0.23	0.192	0.272	SUBCLONAL	1	TRUE	1	0.329561608076033	3		566	661	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042076	42042076	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1337789886	NA	P-0041531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	76	542	0	ENST00000219905.7:c.6271G>C	p.Glu2091Gln	p.E2091Q	ENST00000219905	NM_001164273.1	2091	Gaa/Caa	17/24	0.267478587363752	3	FACETS	0.828	0.726	0.937	0.414	0.363	0.469	CLONAL	1	TRUE	1	0.329561608076033	3		542	649	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058693	42058693	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	54	269	0	ENST00000219905.7:c.8413G>C	p.Asp2805His	p.D2805H	ENST00000219905	NM_001164273.1	2805	Gat/Cat	24/24	0.267478587363752	3	FACETS	1	0.874	1	0.51	0.437	0.59	CLONAL	1	TRUE	1	0.329561608076033	3		269	374	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946800	17946800	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	126	989	0	ENST00000458235.1:c.1847G>C	p.Gly616Ala	p.G616A	ENST00000458235	NM_000215.3	616	gGc/gCc	14/24	1	2	FACETS	0.831	0.752	0.915	0.831	0.752	0.915	CLONAL	1	TRUE	1	0.329561608076033	2		989	920	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976406	18976406	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1327509370	NA	P-0041531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	116	1137	0	ENST00000262803.5:c.3056G>C	p.Gly1019Ala	p.G1019A	ENST00000262803	NM_002911.3	1019	gGa/gCa	22/24	1	2	FACETS	0.645	0.58	0.714	0.645	0.58	0.714	SUBCLONAL	1	TRUE	1	0.329561608076033	2		1137	1092	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657132	215657132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	69	354	0	ENST00000260947.4:c.253G>A	p.Val85Met	p.V85M	ENST00000260947	NM_000465.2	85	Gtg/Atg	3/11	1	2	FACETS	0.983	0.859	1	0.983	0.859	1	CLONAL	1	TRUE	1	0.329561608076033	2		354	426	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651392	52651392	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	60	476	0	ENST00000394830.3:c.1704G>C	p.Leu568Phe	p.L568F	ENST00000394830	NM_018313.4	568	ttG/ttC	15/30	0.25223330792863	1	FACETS	0.667	0.576	0.766	0.667	0.576	0.766	SUBCLONAL	1	TRUE	0	0.329561608076033	1		476	456	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499032	149499032	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	132	635	0	ENST00000261799.4:c.2796G>C	p.Glu932Asp	p.E932D	ENST00000261799	NM_002609.3	932	gaG/gaC	20/23	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.329561608076033	2		635	723	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031889	26031889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	35	252	0	ENST00000244661.2:c.400G>A	p.Glu134Lys	p.E134K	ENST00000244661	NM_003537.3	134	Gaa/Aaa	1/1	1	2	FACETS	0.694	0.571	0.832	0.694	0.571	0.832	SUBCLONAL	1	TRUE	1	0.329561608076033	2		252	306	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859377	151859377	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	53	485	0	ENST00000262189.6:c.11285C>G	p.Ser3762Cys	p.S3762C	ENST00000262189	NM_170606.2	3762	tCt/tGt	43/59	1	2	FACETS	0.654	0.558	0.759	0.654	0.558	0.759	SUBCLONAL	1	TRUE	1	0.329561608076033	2		485	492	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0041538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	655	482	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.881848065591834	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.887873035589232	2		482	730	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0041538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	267	330	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.999	0.945	1	0.999	0.945	1	CLONAL	1	TRUE	1	0.887873035589232	2		330	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0041538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	382	814	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.887873035589232	1	FACETS	0.913	0.884	0.942	0.913	0.884	0.942	CLONAL	1	TRUE	0	0.887873035589232	1		814	524	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117858	70117858	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	343	792	0	ENST00000245479.2:c.326T>C	p.Met109Thr	p.M109T	ENST00000245479	NM_000346.3	109	aTg/aCg	1/3	1	2	FACETS	0.925	0.88	0.971	0.925	0.88	0.971	CLONAL	1	TRUE	1	0.887873035589232	2		792	835	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458650	120458650	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	330	808	0	ENST00000256646.2:c.6695C>A	p.Ser2232Tyr	p.S2232Y	ENST00000256646	NM_024408.3	2232	tCt/tAt	34/34	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.887873035589232	2		808	724	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881495	48881495	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0041538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	129	247	0	ENST00000267163.4:c.217A>T	p.Arg73Ter	p.R73*	ENST00000267163	NM_000321.2	73	Aga/Tga	2/27	0.887873035589232	1	FACETS	0.973	0.923	1	0.973	0.923	1	CLONAL	1	TRUE	0	0.887873035589232	1		247	166	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862722	9862722	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	395	702	0	ENST00000330684.3:c.2581T>A	p.Phe861Ile	p.F861I	ENST00000330684	NM_001134407.1	861	Ttc/Atc	12/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.887873035589232	2		702	875	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298035	15298035	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	537	1129	1	ENST00000263388.2:c.1721A>G	p.Tyr574Cys	p.Y574C	ENST00000263388	NM_000435.2	574	tAc/tGc	11/33	1	2	FACETS	0.977	0.939	1	0.977	0.939	1	CLONAL	1	TRUE	1	0.887873035589232	2		1130	1238	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155225	106155225	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	199	457	0	ENST00000380013.4:c.126G>T	p.Glu42Asp	p.E42D	ENST00000380013	NM_001127208.2	42	gaG/gaT	3/11	1	2	FACETS	0.946	0.885	1	0.946	0.885	1	CLONAL	1	TRUE	1	0.887873035589232	2		457	474	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222047	2222049	+	stop_gained	Nonsense_Mutation	TNP	CCG	CCG	GCT	novel	NA	P-0041538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	909	1045	0	ENST00000398665.3:c.2879_2881delinsGCT	p.Ala960_Glu961delinsGlyTer	p.A960_E961delinsG*	ENST00000398665	NM_032482.2	960	gCCGag/gGCTag	24/28	0.887873035589232	2	FACETS	0.995	0.981	1	0.995	0.981	1	CLONAL	2	TRUE	0	0.887873035589232	2		1045	1029	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0041541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	213	458	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.932	0.871	0.994	0.932	0.871	0.994	CLONAL	1	TRUE	1	0.729303818881078	2		458	627	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0041541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	75	255	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.729303818881078	3	FACETS	0.826	0.729	0.928	0.413	0.364	0.464	CLONAL	1	TRUE	1	0.729303818881078	3		255	340	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861144	57861144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373249560	NA	P-0041541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	225	658	0	ENST00000228682.2:c.941G>A	p.Arg314His	p.R314H	ENST00000228682	NM_005269.2	314	cGc/cAc	9/12	1	2	FACETS	0.807	0.754	0.861	0.807	0.754	0.861	CLONAL	1	TRUE	1	0.729303818881078	2		658	765	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107093	27107093	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	474	682	0	ENST00000324856.7:c.6706del	p.Arg2236AlafsTer31	p.R2236Afs*31	ENST00000324856	NM_006015.4	2235	gCc/gc	20/20	0.681100059965558	2	FACETS	0.937	0.907	0.965	0.937	0.907	0.965	CLONAL	2	TRUE	0	0.729303818881078	2		682	694	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696770	176696770	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	39	394	0	ENST00000439151.2:c.5471A>T	p.Asp1824Val	p.D1824V	ENST00000439151	NM_022455.4	1824	gAt/gTt	16/23	1	2	FACETS	0.258	0.213	0.307	0.258	0.213	0.307	SUBCLONAL	1	TRUE	1	0.729303818881078	2		394	415	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222638	53222638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	342	982	1	ENST00000375401.3:c.4298G>A	p.Arg1433Lys	p.R1433K	ENST00000375401	NM_004187.3	1433	aGg/aAg	25/26	1	2	FACETS	0.897	0.851	0.945	0.897	0.851	0.945	CLONAL	1	TRUE	1	0.729303818881078	2		983	1045	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907620	76907620	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	148	445	0	ENST00000373344.5:c.4541G>T	p.Arg1514Leu	p.R1514L	ENST00000373344	NM_000489.3	1514	cGa/cTa	15/35	1	2	FACETS	0.844	0.776	0.913	0.844	0.776	0.913	CLONAL	1	TRUE	1	0.729303818881078	2		445	481	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0041550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	48	245	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.9	0.763	1	0.9	0.763	1	CLONAL	1	TRUE	1	0.28	2		245	381	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945656	206945656	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767158016	NA	P-0041550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	60	497	0	ENST00000423557.1:c.125G>A	p.Arg42Gln	p.R42Q	ENST00000423557	NM_000572.2	42	cGa/cAa	1/5	1	2	FACETS	0.831	0.716	0.955	0.831	0.716	0.955	CLONAL	1	TRUE	1	0.28	2		497	516	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057936	27057937	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1415146710	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	81	671	0	ENST00000324856.7:c.1650dup	p.Tyr551LeufsTer72	p.Y551Lfs*72	ENST00000324856	NM_006015.4	548	-/C	3/20	1	2	FACETS	0.549	0.483	0.62	0.549	0.483	0.62	SUBCLONAL	1	TRUE	1	0.359619596475651	2		671	821	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391214	89391214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs530556931	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	79	408	0	ENST00000336596.2:c.1280C>T	p.Ala427Val	p.A427V	ENST00000336596	NM_005233.5	427	gCg/gTg	5/17	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.359619596475651	2		408	422	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	49	353	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.774	0.658	0.901	0.774	0.658	0.901	CLONAL	1	TRUE	1	0.359619596475651	2		353	352	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	114	621	2	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.995	0.898	1	0.995	0.898	1	CLONAL	1	TRUE	1	0.359619596475651	2		623	637	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211674	5211674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1351895585	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	179	780	0	ENST00000357368.4:c.5161C>T	p.Arg1721Trp	p.R1721W	ENST00000357368	NM_002850.3	1721	Cgg/Tgg	33/38	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.359619596475651	2		780	921	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545585	106545585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376453517	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	66	432	0	ENST00000359195.3:c.3062G>A	p.Arg1021His	p.R1021H	ENST00000359195	NM_002649.2	1021	cGt/cAt	11/11	0.303349286446284	3	FACETS	1	0.909	1	0.527	0.459	0.6	CLONAL	1	TRUE	1	0.359619596475651	3		432	411	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588988	67588988	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	44	296	0	ENST00000274335.5:c.1079C>T	p.Ala360Val	p.A360V	ENST00000274335		360	gCg/gTg	8/15	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.359619596475651	2		296	235	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308382	15308383	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs749829137	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	122	760	2	ENST00000263388.2:c.125dup	p.Cys43LeufsTer32	p.C43Lfs*32	ENST00000263388	NM_000435.2	42	cct/ccCt	2/33	1	2	FACETS	0.752	0.679	0.829	0.752	0.679	0.829	SUBCLONAL	1	TRUE	1	0.359619596475651	2		762	902	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604736	48604736	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	55	443	0	ENST00000342988.3:c.1558G>T	p.Glu520Ter	p.E520*	ENST00000342988	NM_005359.5	520	Gaa/Taa	12/12	1	2	FACETS	0.508	0.434	0.589	0.508	0.434	0.589	SUBCLONAL	1	TRUE	1	0.359619596475651	2		443	602	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032553	12032553	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	63	463	0	ENST00000353533.5:c.989A>C	p.Asn330Thr	p.N330T	ENST00000353533	NM_003010.3	330	aAt/aCt	9/11	1	2	FACETS	0.842	0.731	0.962	0.842	0.731	0.962	CLONAL	1	TRUE	1	0.359619596475651	2		463	416	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671529	30671529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763745278	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	151	794	0	ENST00000376406.3:c.5431C>T	p.Arg1811Cys	p.R1811C	ENST00000376406	NM_014641.2	1811	Cgc/Tgc	10/15	1	2	FACETS	0.909	0.831	0.991	0.909	0.831	0.991	CLONAL	1	TRUE	1	0.359619596475651	2		794	924	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842734	68842734	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200310662	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	112	557	0	ENST00000261769.5:c.670C>T	p.Arg224Cys	p.R224C	ENST00000261769	NM_004360.3	224	Cgc/Tgc	5/16	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.359619596475651	2		557	590	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645983	215645984	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1559425604	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	56	468	0	ENST00000260947.4:c.614dup	p.Gln206AlafsTer8	p.Q206Afs*8	ENST00000260947	NM_000465.2	205	aag/aaAg	4/11	1	2	FACETS	0.839	0.722	0.966	0.839	0.722	0.966	CLONAL	1	TRUE	1	0.359619596475651	2		468	371	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	60	302	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	1	2	FACETS	0.981	0.851	1	0.981	0.851	1	CLONAL	1	TRUE	1	0.359619596475651	2		302	340	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907683	111907683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146318804	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	104	429	2	ENST00000393256.3:c.457C>T	p.Arg153Trp	p.R153W	ENST00000393256	NM_006538.4	153	Cgg/Tgg	3/4	1	2	FACETS	0.979	0.878	1	0.979	0.878	1	CLONAL	1	TRUE	1	0.359619596475651	2		431	591	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005460	42005460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	154	665	1	ENST00000219905.7:c.3196C>T	p.Arg1066Cys	p.R1066C	ENST00000219905	NM_001164273.1	1066	Cgc/Tgc	9/24	1	2	FACETS	0.96	0.879	1	0.96	0.879	1	CLONAL	1	TRUE	1	0.359619596475651	2		666	892	SUCCESS
AR	367	MSKCC	GRCh37	X	66766187	66766187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	60	580	2	ENST00000374690.3:c.1199C>T	p.Ala400Val	p.A400V	ENST00000374690	NM_000044.3	400	gCg/gTg	1/8	1	2	FACETS	0.642	0.553	0.738	0.642	0.553	0.738	SUBCLONAL	1	TRUE	1	0.359619596475651	2		582	520	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300155	15300155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768208563	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	201	923	0	ENST00000263388.2:c.1121G>A	p.Arg374Gln	p.R374Q	ENST00000263388	NM_000435.2	374	cGg/cAg	7/33	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.359619596475651	2		923	1061	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298770	15298770	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	225	918	0	ENST00000263388.2:c.1528G>A	p.Glu510Lys	p.E510K	ENST00000263388	NM_000435.2	510	Gaa/Aaa	10/33	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.359619596475651	2		918	1061	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066627	94066627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	34	536	1	ENST00000369303.4:c.1132G>A	p.Glu378Lys	p.E378K	ENST00000369303	NM_004440.3	378	Gaa/Aaa	5/17	1	2	FACETS	0.305	0.249	0.37	0.305	0.249	0.37	SUBCLONAL	1	TRUE	1	0.359619596475651	2		537	619	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021728	71021728	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1559602356	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	79	413	1	ENST00000318789.4:c.1630C>T	p.Arg544Ter	p.R544*	ENST00000318789	NM_032682.5	544	Cga/Tga	18/21	1	2	FACETS	0.867	0.764	0.976	0.867	0.764	0.976	CLONAL	1	TRUE	1	0.359619596475651	2		414	507	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442575	52442575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	112	384	0	ENST00000460680.1:c.170G>A	p.Arg57Gln	p.R57Q	ENST00000460680	NM_004656.3	57	cGg/cAg	4/17	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.359619596475651	2		384	580	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231119	142231119	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs55894265	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	95	417	0	ENST00000350721.4:c.4835A>G	p.Asn1612Ser	p.N1612S	ENST00000350721	NM_001184.3	1612	aAt/aGt	27/47	1	2	FACETS	0.966	0.862	1	0.966	0.862	1	CLONAL	1	TRUE	1	0.359619596475651	2		417	547	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749983	162749983	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	105	529	0	ENST00000367921.3:c.2515C>T	p.Arg839Cys	p.R839C	ENST00000367921	NM_006182.2	839	Cgt/Tgt	18/18	1	2	FACETS	0.875	0.785	0.971	0.875	0.785	0.971	CLONAL	1	TRUE	1	0.359619596475651	2		529	667	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209264	98209264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778630	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	104	928	2	ENST00000331920.6:c.4274C>T	p.Ser1425Leu	p.S1425L	ENST00000331920	NM_000264.3	1425	tCg/tTg	23/24	1	2	FACETS	0.642	0.574	0.714	0.642	0.574	0.714	SUBCLONAL	1	TRUE	1	0.359619596475651	2		930	901	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591125	67591125	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	48	339	0	ENST00000274335.5:c.1718T>C	p.Leu573Pro	p.L573P	ENST00000274335		573	cTg/cCg	12/15	1	2	FACETS	0.875	0.744	1	0.875	0.744	1	CLONAL	1	TRUE	1	0.359619596475651	2		339	305	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576097	29576098	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	48	467	0	ENST00000356175.3:c.4076dup	p.Gln1360SerfsTer14	p.Q1360Sfs*14	ENST00000356175	NM_000267.3	1357	ttc/ttCc	30/57	1	2	FACETS	0.53	0.448	0.62	0.53	0.448	0.62	SUBCLONAL	1	TRUE	1	0.359619596475651	2		467	504	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458147	120458147	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1325403451	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	97	700	2	ENST00000256646.2:c.7198C>T	p.Arg2400Ter	p.R2400*	ENST00000256646	NM_024408.3	2400	Cga/Tga	34/34	1	2	FACETS	0.676	0.602	0.755	0.676	0.602	0.755	SUBCLONAL	1	TRUE	1	0.359619596475651	2		702	798	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834588	156834588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778566154	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	177	890	2	ENST00000524377.1:c.356G>A	p.Arg119His	p.R119H	ENST00000524377	NM_002529.3	119	cGc/cAc	3/17	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.359619596475651	2		892	975	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366309	15366309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	119	708	0	ENST00000263377.2:c.1846C>T	p.Arg616Trp	p.R616W	ENST00000263377	NM_058243.2	616	Cgg/Tgg	10/20	1	2	FACETS	0.969	0.876	1	0.969	0.876	1	CLONAL	1	TRUE	1	0.359619596475651	2		708	683	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879580	37879580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	129	697	1	ENST00000269571.5:c.1955C>T	p.Thr652Met	p.T652M	ENST00000269571		652	aCg/aTg	17/27	1	2	FACETS	0.9	0.816	0.988	0.9	0.816	0.988	CLONAL	1	TRUE	1	0.359619596475651	2		698	797	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480083	20480083	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	78	346	3	ENST00000346618.3:c.400C>T	p.Arg134Ter	p.R134*	ENST00000346618	NM_001949.4	134	Cga/Tga	2/7	1	2	FACETS	0.997	0.88	1	0.997	0.88	1	CLONAL	1	TRUE	1	0.359619596475651	2		349	435	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355310	81355310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	47	239	0	ENST00000222390.5:c.1064G>A	p.Arg355Gln	p.R355Q	ENST00000222390	NM_000601.4	355	cGa/cAa	9/18	0.303349286446284	3	FACETS	1	0.934	1	0.593	0.504	0.689	CLONAL	1	TRUE	1	0.359619596475651	3		239	260	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604665	48604665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660045	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	27	387	1	ENST00000342988.3:c.1487G>A	p.Arg496His	p.R496H	ENST00000342988	NM_005359.5	496	cGt/cAt	12/12	1	2	FACETS	0.363	0.288	0.448	0.363	0.288	0.448	SUBCLONAL	1	TRUE	1	0.359619596475651	2		388	414	SUCCESS
AR	367	MSKCC	GRCh37	X	66941679	66941679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852562	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	102	596	1	ENST00000374690.3:c.2323C>T	p.Arg775Cys	p.R775C	ENST00000374690	NM_000044.3	775	Cgc/Tgc	6/8	1	2	FACETS	0.878	0.786	0.975	0.878	0.786	0.975	CLONAL	1	TRUE	1	0.359619596475651	2		597	646	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586099	29586099	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754639587	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	84	392	0	ENST00000356175.3:c.4319T>C	p.Met1440Thr	p.M1440T	ENST00000356175	NM_000267.3	1440	aTg/aCg	32/57	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.359619596475651	2		392	419	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164475	36164475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1442794209	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	129	531	3	ENST00000300305.3:c.1400C>T	p.Ala467Val	p.A467V	ENST00000300305		467	gCg/gTg	8/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.359619596475651	2		534	542	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176329	24176329	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1568963596	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	186	809	2	ENST00000263121.7:c.1120C>T	p.Arg374Trp	p.R374W	ENST00000263121	NM_003073.3	374	Cgg/Tgg	9/9	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.359619596475651	2		811	872	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802585	139802585	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs956492484	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	155	889	0	ENST00000247668.2:c.430C>T	p.Arg144Cys	p.R144C	ENST00000247668	NM_021138.3	144	Cgc/Tgc	5/11	1	2	FACETS	0.872	0.797	0.95	0.872	0.797	0.95	CLONAL	1	TRUE	1	0.359619596475651	2		889	989	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779703	3779703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	136	740	1	ENST00000262367.5:c.5345C>T	p.Ala1782Val	p.A1782V	ENST00000262367	NM_004380.2	1782	gCg/gTg	31/31	1	2	FACETS	0.911	0.829	0.998	0.911	0.829	0.998	CLONAL	1	TRUE	1	0.359619596475651	2		741	830	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858337	9858337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560057284	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	69	425	0	ENST00000330684.3:c.3064C>T	p.Arg1022Cys	p.R1022C	ENST00000330684	NM_001134407.1	1022	Cgc/Tgc	13/13	1	2	FACETS	0.866	0.757	0.983	0.866	0.757	0.983	CLONAL	1	TRUE	1	0.359619596475651	2		425	443	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285669	46285669	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1368075571	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	52	428	0	ENST00000334344.6:c.5029C>T	p.Arg1677Ter	p.R1677*	ENST00000334344	NM_152641.2	1677	Cga/Tga	17/21	1	2	FACETS	0.799	0.683	0.925	0.799	0.683	0.925	CLONAL	1	TRUE	1	0.359619596475651	2		428	362	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051057	180051057	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756924526	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	115	696	0	ENST00000261937.6:c.1426C>T	p.Arg476Trp	p.R476W	ENST00000261937	NM_182925.4	476	Cgg/Tgg	11/30	1	2	FACETS	0.936	0.845	1	0.936	0.845	1	CLONAL	1	TRUE	1	0.359619596475651	2		696	683	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446845	187446845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201771435	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	130	652	0	ENST00000232014.4:c.1348G>A	p.Val450Ile	p.V450I	ENST00000232014	NM_001130845.1	450	Gtt/Att	5/10	1	2	FACETS	0.89	0.808	0.977	0.89	0.808	0.977	CLONAL	1	TRUE	1	0.359619596475651	2		652	812	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219839	133219839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766511597	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	120	681	0	ENST00000320574.5:c.4522C>T	p.Arg1508Cys	p.R1508C	ENST00000320574	NM_006231.2	1508	Cgc/Tgc	35/49	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.359619596475651	2		681	656	SUCCESS
APC	324	MSKCC	GRCh37	5	112176654	112176654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201472075	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	42	294	0	ENST00000257430.4:c.5363G>A	p.Arg1788His	p.R1788H	ENST00000257430	NM_000038.5	1788	cGt/cAt	16/16	1	2	FACETS	0.934	0.786	1	0.934	0.786	1	CLONAL	1	TRUE	1	0.359619596475651	2		294	250	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098422	11098422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764188556	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	147	600	2	ENST00000358026.2:c.940G>A	p.Ala314Thr	p.A314T	ENST00000358026	NM_001128849.1	314	Gcg/Acg	6/36	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.359619596475651	2		602	678	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740668	58740668	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs759850701	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	130	652	0	ENST00000305921.3:c.1573G>T	p.Glu525Ter	p.E525*	ENST00000305921	NM_003620.3	525	Gaa/Taa	6/6	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.359619596475651	2		652	660	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029072	14029072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763619616	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	56	285	0	ENST00000311895.7:c.1283C>T	p.Ala428Val	p.A428V	ENST00000311895	NM_005236.2	428	gCg/gTg	8/11	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.359619596475651	2		285	278	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405201	139405201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767886377	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	104	961	1	ENST00000277541.6:c.2644G>A	p.Ala882Thr	p.A882T	ENST00000277541	NM_017617.3	882	Gca/Aca	17/34	1	2	FACETS	0.601	0.537	0.669	0.601	0.537	0.669	SUBCLONAL	1	TRUE	1	0.359619596475651	2		962	962	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707797	176707797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886041219	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	109	461	0	ENST00000439151.2:c.5854C>T	p.Arg1952Trp	p.R1952W	ENST00000439151	NM_022455.4	1952	Cgg/Tgg	18/23	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.359619596475651	2		461	535	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923000	44923000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139486036	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	130	731	0	ENST00000377967.4:c.1861C>T	p.Arg621Cys	p.R621C	ENST00000377967	NM_021140.2	621	Cgc/Tgc	16/29	1	2	FACETS	0.775	0.702	0.852	0.775	0.702	0.852	SUBCLONAL	1	TRUE	1	0.359619596475651	2		731	933	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569823	67569823	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1230037871	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	48	287	0	ENST00000274335.5:c.484C>T	p.Arg162Ter	p.R162*	ENST00000274335		162	Cga/Tga	3/15	1	2	FACETS	0.748	0.634	0.872	0.748	0.634	0.872	SUBCLONAL	1	TRUE	1	0.359619596475651	2		287	357	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349070	11349070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	95	476	0	ENST00000332029.2:c.266C>T	p.Ala89Val	p.A89V	ENST00000332029	NM_003745.1	89	gCg/gTg	2/2	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.359619596475651	2		476	508	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890251	72890251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200658486	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	81	475	0	ENST00000325599.8:c.431C>T	p.Pro144Leu	p.P144L	ENST00000325599	NM_018130.2	144	cCg/cTg	4/11	1	2	FACETS	0.88	0.777	0.989	0.88	0.777	0.989	CLONAL	1	TRUE	1	0.359619596475651	2		475	512	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242743	16242743	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756096700	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	112	577	1	ENST00000375759.3:c.1364G>A	p.Arg455His	p.R455H	ENST00000375759	NM_015001.2	455	cGc/cAc	6/15	1	2	FACETS	0.952	0.858	1	0.952	0.858	1	CLONAL	1	TRUE	1	0.359619596475651	2		578	654	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045802	143045802	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766650822	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	127	659	0	ENST00000262992.4:c.1832C>T	p.Ala611Val	p.A611V	ENST00000262992	NM_001101669.1	611	gCg/gTg	17/24	1	2	FACETS	0.924	0.838	1	0.924	0.838	1	CLONAL	1	TRUE	1	0.359619596475651	2		659	764	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025856	48025857	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs267608041	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	67	358	0	ENST00000234420.5:c.741dup	p.Arg248ThrfsTer8	p.R248Tfs*8	ENST00000234420	NM_000179.2	245	ata/atAa	4/10	1	2	FACETS	0.929	0.811	1	0.929	0.811	1	CLONAL	1	TRUE	1	0.359619596475651	2		358	401	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682692	86682692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757298110	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	30	204	0	ENST00000274376.6:c.2897G>A	p.Arg966His	p.R966H	ENST00000274376	NM_002890.2	966	cGt/cAt	23/25	1	2	FACETS	0.953	0.776	1	0.953	0.776	1	CLONAL	1	TRUE	1	0.359619596475651	2		204	175	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231148	53231148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	132	554	1	ENST00000375401.3:c.1754G>A	p.Arg585His	p.R585H	ENST00000375401	NM_004187.3	585	cGc/cAc	13/26	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.359619596475651	2		555	646	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941475	71941475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200043222	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	168	872	0	ENST00000298229.2:c.1160G>A	p.Arg387Gln	p.R387Q	ENST00000298229	NM_001567.3	387	cGg/cAg	10/28	1	2	FACETS	0.921	0.845	0.999	0.921	0.845	0.999	CLONAL	1	TRUE	1	0.359619596475651	2		872	1015	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860058	152860058	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	81	780	0	ENST00000406277.2:c.370C>T	p.Leu124Phe	p.L124F	ENST00000406277	NM_152274.4	124	Ctt/Ttt	5/7	1		FACETS		0.422	0.544				SUBCLONAL	1	TRUE	1	0.359619596475651	2		780	937	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383903	15383903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324868843	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	93	445	0	ENST00000263377.2:c.8C>T	p.Ala3Val	p.A3V	ENST00000263377	NM_058243.2	3	gCg/gTg	2/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.359619596475651	2		445	442	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349928	70349928	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	175	871	0	ENST00000374080.3:c.3911G>T	p.Ser1304Ile	p.S1304I	ENST00000374080		1304	aGc/aTc	28/45	1	2	FACETS	0.97	0.893	1	0.97	0.893	1	CLONAL	1	TRUE	1	0.359619596475651	2		871	1003	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606811	43606811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775842917	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	122	913	0	ENST00000355710.3:c.1420C>T	p.Arg474Trp	p.R474W	ENST00000355710	NM_020975.4	474	Cgg/Tgg	7/20	1	2	FACETS	0.697	0.629	0.769	0.697	0.629	0.769	SUBCLONAL	1	TRUE	1	0.359619596475651	2		913	974	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350054	70350054	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs966195679	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	51	496	1	ENST00000374080.3:c.4037G>A	p.Arg1346His	p.R1346H	ENST00000374080		1346	cGc/cAc	28/45	1	2	FACETS	0.565	0.48	0.658	0.565	0.48	0.658	SUBCLONAL	1	TRUE	1	0.359619596475651	2		497	502	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435634	110435634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	140	544	2	ENST00000375856.3:c.2767G>A	p.Asp923Asn	p.D923N	ENST00000375856	NM_003749.2	923	Gac/Aac	1/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.359619596475651	2		546	607	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266955	18266955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs532391308	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	75	451	2	ENST00000222254.8:c.266G>A	p.Arg89His	p.R89H	ENST00000222254	NM_005027.3	89	cGc/cAc	2/16	1	2	FACETS	0.862	0.757	0.974	0.862	0.757	0.974	CLONAL	1	TRUE	1	0.359619596475651	2		453	484	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622369	1622369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143406385	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	165	1046	0	ENST00000344749.5:c.595G>A	p.Ala199Thr	p.A199T	ENST00000344749	NM_001136139.2	199	Gcc/Acc	9/19	1	2	FACETS	0.899	0.825	0.976	0.899	0.825	0.976	CLONAL	1	TRUE	1	0.359619596475651	2		1046	1021	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212857	27212857	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs906836493	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	95	863	0	ENST00000380036.4:c.2839G>A	p.Asp947Asn	p.D947N	ENST00000380036	NM_000459.3	947	Gac/Aac	17/23	1	2	FACETS	0.526	0.467	0.589	0.526	0.467	0.589	SUBCLONAL	1	TRUE	1	0.359619596475651	2		863	1005	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125365	7125365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759020723	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	114	816	0	ENST00000302850.5:c.3187G>A	p.Ala1063Thr	p.A1063T	ENST00000302850	NM_000208.2	1063	Gcc/Acc	17/22	1	2	FACETS	0.669	0.602	0.741	0.669	0.602	0.741	SUBCLONAL	1	TRUE	1	0.359619596475651	2		816	947	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085680	16085680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776847158	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	46	771	0	ENST00000281043.3:c.856C>T	p.Arg286Cys	p.R286C	ENST00000281043	NM_005378.4	286	Cgt/Tgt	3/3	1	2	FACETS	0.281	0.235	0.331	0.281	0.235	0.331	SUBCLONAL	1	TRUE	1	0.359619596475651	2		771	912	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095665	178095666	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	77	396	1	ENST00000397062.3:c.1665dup	p.Gln556ThrfsTer15	p.Q556Tfs*15	ENST00000397062	NM_006164.4	555	-/A	5/5	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.359619596475651	2		397	416	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	109	877	0	ENST00000293328.3:c.1101_1102dup	p.Gln368ProfsTer3	p.Q368Pfs*3	ENST00000293328	NM_012448.3	368	cag/cCCag	9/19	1	2	FACETS	0.641	0.575	0.712	0.641	0.575	0.712	SUBCLONAL	1	TRUE	1	0.359619596475651	2		877	945	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096209	2096209	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148104494	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	126	954	1	ENST00000219066.1:c.298C>T	p.Arg100Cys	p.R100C	ENST00000219066	NM_002528.5	100	Cgt/Tgt	2/6	1	2	FACETS	0.63	0.569	0.695	0.63	0.569	0.695	SUBCLONAL	1	TRUE	1	0.359619596475651	2		955	1112	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798765	135798765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554819886	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	56	293	0	ENST00000298552.3:c.478C>T	p.Arg160Cys	p.R160C	ENST00000298552	NM_001162426.1	160	Cgt/Tgt	6/23	1	2	FACETS	0.903	0.777	1	0.903	0.777	1	CLONAL	1	TRUE	1	0.359619596475651	2		293	345	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900336	3900336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148781922	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	224	722	1	ENST00000262367.5:c.760G>A	p.Ala254Thr	p.A254T	ENST00000262367	NM_004380.2	254	Gcg/Acg	2/31	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.359619596475651	2		723	911	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204927	128204927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	216	906	1	ENST00000341105.2:c.514G>A	p.Gly172Ser	p.G172S	ENST00000341105	NM_032638.4	172	Ggc/Agc	3/6	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.359619596475651	2		907	1044	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209699	98209699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201595274	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	99	853	2	ENST00000331920.6:c.3839C>T	p.Ser1280Leu	p.S1280L	ENST00000331920	NM_000264.3	1280	tCg/tTg	23/24	1	2	FACETS	0.597	0.532	0.667	0.597	0.532	0.667	SUBCLONAL	1	TRUE	1	0.359619596475651	2		855	922	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16055260	16055260	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1446410092	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	65	398	0	ENST00000268712.3:c.842C>T	p.Thr281Ile	p.T281I	ENST00000268712	NM_006311.3	281	aCa/aTa	8/46	1	2	FACETS	0.927	0.807	1	0.927	0.807	1	CLONAL	1	TRUE	1	0.359619596475651	2		398	390	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242099	105242099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768800433	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	105	880	2	ENST00000349310.3:c.325G>A	p.Gly109Ser	p.G109S	ENST00000349310	NM_001014432.1	109	Ggc/Agc	6/15	1	2	FACETS	0.645	0.577	0.717	0.645	0.577	0.717	SUBCLONAL	1	TRUE	1	0.359619596475651	2		882	906	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78831653	78831653	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758599889	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	158	829	3	ENST00000306801.3:c.1462C>T	p.Arg488Trp	p.R488W	ENST00000306801	NM_020761.2	488	Cgg/Tgg	13/34	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.359619596475651	2		832	847	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710875	117710875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140178288	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	109	489	0	ENST00000368508.3:c.1397G>A	p.Arg466Gln	p.R466Q	ENST00000368508	NM_002944.2	466	cGa/cAa	12/43	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.359619596475651	2		489	466	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566114	141566114	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	124	553	0	ENST00000220592.5:c.1150C>T	p.Arg384Ter	p.R384*	ENST00000220592	NM_012154.3	384	Cga/Tga	10/19	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.359619596475651	2		553	639	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943750	71943750	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780875030	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	167	866	0	ENST00000298229.2:c.1793G>A	p.Arg598His	p.R598H	ENST00000298229	NM_001567.3	598	cGt/cAt	15/28	1	2	FACETS	0.969	0.89	1	0.969	0.89	1	CLONAL	1	TRUE	1	0.359619596475651	2		866	958	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288996	33288996	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773506568	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	71	635	0	ENST00000374542.5:c.556C>T	p.Arg186Trp	p.R186W	ENST00000374542	NM_001141970.1	186	Cgg/Tgg	3/8	1	2	FACETS	0.513	0.447	0.585	0.513	0.447	0.585	SUBCLONAL	1	TRUE	1	0.359619596475651	2		635	769	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40874920	40874920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756635466	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	77	544	0	ENST00000428826.2:c.380C>T	p.Thr127Met	p.T127M	ENST00000428826		127	aCg/aTg	6/21	1	2	FACETS	0.571	0.501	0.647	0.571	0.501	0.647	SUBCLONAL	1	TRUE	1	0.359619596475651	2		544	750	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109680	115109680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	224	1063	2	ENST00000257566.3:c.2198C>T	p.Ala733Val	p.A733V	ENST00000257566	NM_016569.3	733	gCc/gTc	8/8	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.359619596475651	2		1065	1161	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856200	111856200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1365917986	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	63	423	1	ENST00000341259.2:c.251C>T	p.Ala84Val	p.A84V	ENST00000341259	NM_005475.2	84	gCg/gTg	2/8	1	2	FACETS	0.644	0.557	0.738	0.644	0.557	0.738	SUBCLONAL	1	TRUE	1	0.359619596475651	2		424	544	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252327	133252327	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	101	513	1	ENST00000320574.5:c.1100T>C	p.Phe367Ser	p.F367S	ENST00000320574	NM_006231.2	367	tTt/tCt	11/49	1	2	FACETS	0.955	0.856	1	0.955	0.856	1	CLONAL	1	TRUE	1	0.359619596475651	2		514	588	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226388	2226388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs112052747	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	291	942	4	ENST00000398665.3:c.3868G>A	p.Ala1290Thr	p.A1290T	ENST00000398665	NM_032482.2	1290	Gct/Act	27/28	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.359619596475651	2		946	1115	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345803	152345803	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	36	433	0	ENST00000359321.1:c.767T>C	p.Val256Ala	p.V256A	ENST00000359321	NM_005431.1	256	gTt/gCt	3/3	0.303349286446284	3	FACETS	0.397	0.325	0.478	0.198	0.162	0.239	SUBCLONAL	1	TRUE	1	0.359619596475651	3		433	595	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40682086	40682086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201422345	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	148	657	0	ENST00000249776.8:c.641G>A	p.Arg214Gln	p.R214Q	ENST00000249776	NM_033286.3	214	cGg/cAg	6/9	1	2	FACETS	0.989	0.904	1	0.989	0.904	1	CLONAL	1	TRUE	1	0.359619596475651	2		657	832	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852250	63852250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	78	596	1	ENST00000279873.7:c.3028C>T	p.Arg1010Trp	p.R1010W	ENST00000279873	NM_032199.2	1010	Cgg/Tgg	10/10	1	2	FACETS	0.631	0.554	0.713	0.631	0.554	0.713	SUBCLONAL	1	TRUE	1	0.359619596475651	2		597	688	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52692235	52692236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	89	408	0	ENST00000394830.3:c.624dup	p.Gln209SerfsTer6	p.Q209Sfs*6	ENST00000394830	NM_018313.4	208	-/T	6/30	1	2	FACETS	0.959	0.853	1	0.959	0.853	1	CLONAL	1	TRUE	1	0.359619596475651	2		408	516	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118929	115118929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	50	303	0	ENST00000257566.3:c.412G>A	p.Val138Met	p.V138M	ENST00000257566	NM_016569.3	138	Gtg/Atg	2/8	1	2	FACETS	0.838	0.714	0.972	0.838	0.714	0.972	CLONAL	1	TRUE	1	0.359619596475651	2		303	332	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552921	106552921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	194	920	0	ENST00000369096.4:c.886C>T	p.Arg296Trp	p.R296W	ENST00000369096	NM_001198.3	296	Cgg/Tgg	5/7	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.359619596475651	2		920	1033	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103887	209103887	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	59	440	0	ENST00000345146.2:c.1062C>A	p.Phe354Leu	p.F354L	ENST00000345146	NM_005896.2	354	ttC/ttA	9/10	1	2	FACETS	0.848	0.732	0.973	0.848	0.732	0.973	CLONAL	1	TRUE	1	0.359619596475651	2		440	387	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222899	36222899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	203	1135	3	ENST00000222270.7:c.5528C>T	p.Pro1843Leu	p.P1843L	ENST00000222270	NM_014727.1	1843	cCt/cTt	27/37	1	2	FACETS	0.942	0.872	1	0.942	0.872	1	CLONAL	1	TRUE	1	0.359619596475651	2		1138	1198	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940025	76940025	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	79	577	1	ENST00000373344.5:c.723G>T	p.Lys241Asn	p.K241N	ENST00000373344	NM_000489.3	241	aaG/aaT	9/35	1	2	FACETS	0.915	0.808	1	0.915	0.808	1	CLONAL	1	TRUE	1	0.359619596475651	2		578	480	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651187	45651187	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs749300015	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	203	686	1	ENST00000407780.3:c.838C>T	p.Arg280Ter	p.R280*	ENST00000407780	NM_001283052.1	280	Cga/Tga	5/7	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.359619596475651	2		687	814	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277996	18277996	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs919917611	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	163	734	1	ENST00000222254.8:c.1616G>A	p.Arg539His	p.R539H	ENST00000222254	NM_005027.3	539	cGc/cAc	13/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.359619596475651	2		735	867	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175481	108175481	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1060501568	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	51	365	0	ENST00000278616.4:c.5576G>T	p.Arg1859Ile	p.R1859I	ENST00000278616	NM_000051.3	1859	aGa/aTa	37/63	1	2	FACETS	0.852	0.727	0.987	0.852	0.727	0.987	CLONAL	1	TRUE	1	0.359619596475651	2		365	333	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841300	15841300	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	150	637	4	ENST00000307771.7:c.1384C>T	p.Arg462Ter	p.R462*	ENST00000307771	NM_005089.3	462	Cga/Tga	11/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.359619596475651	2		641	798	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650027	206650027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201666998	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	75	505	0	ENST00000367120.3:c.547G>A	p.Asp183Asn	p.D183N	ENST00000367120	NM_014002.3	183	Gac/Aac	7/22	1	2	FACETS	0.64	0.56	0.725	0.64	0.56	0.725	SUBCLONAL	1	TRUE	1	0.359619596475651	2		505	652	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328427	137328427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	144	1030	0	ENST00000481739.1:c.1356G>A	p.Met452Ile	p.M452I	ENST00000481739	NM_002957.4	452	atG/atA	10/10	1	2	FACETS	0.844	0.769	0.923	0.844	0.769	0.923	CLONAL	1	TRUE	1	0.359619596475651	2		1030	949	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40498651	40498651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	95	511	0	ENST00000264657.5:c.209G>A	p.Arg70His	p.R70H	ENST00000264657	NM_139276.2	70	cGc/cAc	3/24	1	2	FACETS	0.891	0.795	0.993	0.891	0.795	0.993	CLONAL	1	TRUE	1	0.359619596475651	2		511	593	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572100	95572100	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	57	436	0	ENST00000393063.1:c.3008G>A	p.Arg1003Gln	p.R1003Q	ENST00000393063	NM_030621.3	1003	cGa/cAa	20/28	1	2	FACETS	0.647	0.556	0.746	0.647	0.556	0.746	SUBCLONAL	1	TRUE	1	0.359619596475651	2		436	490	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720297	43720297	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	42	566	0	ENST00000382044.4:c.3745C>T	p.Arg1249Trp	p.R1249W	ENST00000382044	NM_001141980.1	1249	Cgg/Tgg	18/28	1	2	FACETS	0.344	0.286	0.408	0.344	0.286	0.408	SUBCLONAL	1	TRUE	1	0.359619596475651	2		566	679	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435457	49435457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748389081	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	178	753	2	ENST00000301067.7:c.6215G>A	p.Arg2072His	p.R2072H	ENST00000301067	NM_003482.3	2072	cGc/cAc	30/54	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.359619596475651	2		755	854	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249242	133249242	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854844	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	131	743	0	ENST00000320574.5:c.1657C>T	p.Arg553Cys	p.R553C	ENST00000320574	NM_006231.2	553	Cgc/Tgc	15/49	1	2	FACETS	0.852	0.773	0.935	0.852	0.773	0.935	CLONAL	1	TRUE	1	0.359619596475651	2		743	855	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074254	8074255	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	101	516	0	ENST00000377482.5:c.404dup	p.Asn135LysfsTer13	p.N135Kfs*13	ENST00000377482	NM_018948.3	135	aac/aaAc	4/4	1	2	FACETS	0.987	0.885	1	0.987	0.885	1	CLONAL	1	TRUE	1	0.359619596475651	2		516	569	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307745	11307745	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	127	554	0	ENST00000361445.4:c.1162A>C	p.Ile388Leu	p.I388L	ENST00000361445	NM_004958.3	388	Atc/Ctc	8/58	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.359619596475651	2		554	664	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263680	16263680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759376315	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	78	503	0	ENST00000375759.3:c.10049C>T	p.Pro3350Leu	p.P3350L	ENST00000375759	NM_015001.2	3350	cCc/cTc	12/15	1	2	FACETS	0.828	0.729	0.934	0.828	0.729	0.934	CLONAL	1	TRUE	1	0.359619596475651	2		503	524	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363110	40363110	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	105	579	0	ENST00000397332.2:c.1119G>T	p.Glu373Asp	p.E373D	ENST00000397332	NM_001033082.2	373	gaG/gaT	3/3	1	2	FACETS	0.894	0.802	0.992	0.894	0.802	0.992	CLONAL	1	TRUE	1	0.359619596475651	2		579	653	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798257	45798257	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369854269	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	135	718	2	ENST00000450313.1:c.679G>A	p.Ala227Thr	p.A227T	ENST00000450313	NM_012222.2	227	Gcc/Acc	8/16	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.359619596475651	2		720	723	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798439	45798439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369677603	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	143	769	1	ENST00000450313.1:c.572G>A	p.Arg191Gln	p.R191Q	ENST00000450313	NM_012222.2	191	cGg/cAg	7/16	1	2	FACETS	0.93	0.848	1	0.93	0.848	1	CLONAL	1	TRUE	1	0.359619596475651	2		770	855	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115272920	115272920	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	127	685	0	ENST00000438362.2:c.1453del	p.Ser485ProfsTer28	p.S485Pfs*28	ENST00000438362	NM_001242891.1	485	Tcc/cc	12/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.359619596475651	2		685	648	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458455	120458455	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	84	677	0	ENST00000256646.2:c.6890C>T	p.Pro2297Leu	p.P2297L	ENST00000256646	NM_024408.3	2297	cCt/cTt	34/34	1	2	FACETS	0.689	0.609	0.775	0.689	0.609	0.775	SUBCLONAL	1	TRUE	1	0.359619596475651	2		677	678	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512325	120512325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	60	492	0	ENST00000256646.2:c.917C>T	p.Pro306Leu	p.P306L	ENST00000256646	NM_024408.3	306	cCc/cTc	6/34	1	2	FACETS	0.568	0.49	0.654	0.568	0.49	0.654	SUBCLONAL	1	TRUE	1	0.359619596475651	2		492	587	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551433	150551433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1047911810	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	113	944	2	ENST00000369026.2:c.574G>A	p.Gly192Ser	p.G192S	ENST00000369026	NM_021960.4	192	Ggc/Agc	1/3	1	2	FACETS	0.599	0.537	0.664	0.599	0.537	0.664	SUBCLONAL	1	TRUE	1	0.359619596475651	2		946	1050	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838342	156838342	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1038009599	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	97	963	0	ENST00000524377.1:c.620T>C	p.Val207Ala	p.V207A	ENST00000524377	NM_002529.3	207	gTg/gCg	6/17	1	2	FACETS	0.508	0.452	0.568	0.508	0.452	0.568	SUBCLONAL	1	TRUE	1	0.359619596475651	2		963	1062	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740140	162740140	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1212920521	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	113	554	1	ENST00000367921.3:c.1342C>A	p.Pro448Thr	p.P448T	ENST00000367921	NM_006182.2	448	Cca/Aca	12/18	1	2	FACETS	0.979	0.883	1	0.979	0.883	1	CLONAL	1	TRUE	1	0.359619596475651	2		555	642	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175781	176175781	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	74	778	0	ENST00000367669.3:c.334A>G	p.Lys112Glu	p.K112E	ENST00000367669	NM_022457.5	112	Aag/Gag	1/20	1	2	FACETS	0.511	0.446	0.58	0.511	0.446	0.58	SUBCLONAL	1	TRUE	1	0.359619596475651	2		778	806	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518751	204518751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	45	346	0	ENST00000367182.3:c.1414G>A	p.Ala472Thr	p.A472T	ENST00000367182	NM_001278516.1	472	Gct/Act	11/11	1	2	FACETS	0.878	0.742	1	0.878	0.742	1	CLONAL	1	TRUE	1	0.359619596475651	2		346	285	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100351	8100351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776412274	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	153	898	1	ENST00000346208.3:c.325G>A	p.Ala109Thr	p.A109T	ENST00000346208		109	Gcc/Acc	3/6	1	2	FACETS	0.971	0.889	1	0.971	0.889	1	CLONAL	1	TRUE	1	0.359619596475651	2		899	876	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845573	63845573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	36	259	0	ENST00000279873.7:c.1312G>A	p.Val438Ile	p.V438I	ENST00000279873	NM_032199.2	438	Gta/Ata	9/10	1	2	FACETS	0.62	0.511	0.741	0.62	0.511	0.741	SUBCLONAL	1	TRUE	1	0.359619596475651	2		259	323	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243220	123243220	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	160	928	1	ENST00000358487.5:c.2293A>G	p.Thr765Ala	p.T765A	ENST00000358487	NM_000141.4	765	Acc/Gcc	17/18	1	2	FACETS	0.937	0.858	1	0.937	0.858	1	CLONAL	1	TRUE	1	0.359619596475651	2		929	950	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156654	2156654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	112	799	1	ENST00000434045.2:c.268G>A	p.Gly90Ser	p.G90S	ENST00000434045	NM_001127598.1	90	Ggc/Agc	3/5	1	2	FACETS	0.672	0.603	0.745	0.672	0.603	0.745	SUBCLONAL	1	TRUE	1	0.359619596475651	2		800	927	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200429	67200429	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	147	628	0	ENST00000312629.5:c.623T>C	p.Ile208Thr	p.I208T	ENST00000312629	NM_003952.2	208	aTc/aCc	8/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.359619596475651	2		628	747	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201723	67201723	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	41	672	0	ENST00000312629.5:c.1024G>A	p.Asp342Asn	p.D342N	ENST00000312629	NM_003952.2	342	Gac/Aac	12/15	1	2	FACETS	0.347	0.288	0.413	0.347	0.288	0.413	SUBCLONAL	1	TRUE	1	0.359619596475651	2		672	657	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102094388	102094388	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	45	524	0	ENST00000282441.5:c.1068G>T	p.Glu356Asp	p.E356D	ENST00000282441	NM_001130145.2	356	gaG/gaT	7/9	1	2	FACETS	0.495	0.415	0.582	0.495	0.415	0.582	SUBCLONAL	1	TRUE	1	0.359619596475651	2		524	506	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139319	108139319	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	74	581	0	ENST00000278616.4:c.2821T>C	p.Ser941Pro	p.S941P	ENST00000278616	NM_000051.3	941	Tcc/Ccc	18/63	1	2	FACETS	0.818	0.718	0.926	0.818	0.718	0.926	CLONAL	1	TRUE	1	0.359619596475651	2		581	503	SUCCESS
ATM	472	MSKCC	GRCh37	11	108154955	108154955	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	rs1555093268	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	41	233	0	ENST00000278616.4:c.3748T>A	p.Ser1250Thr	p.S1250T	ENST00000278616	NM_000051.3	1250	Tct/Act	26/63	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.359619596475651	2		233	200	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118391551	118391551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	62	365	0	ENST00000534358.1:c.11464C>T	p.Arg3822Cys	p.R3822C	ENST00000534358	NM_005933.3	3822	Cgc/Tgc	34/36	1	2	FACETS	0.833	0.722	0.952	0.833	0.722	0.952	CLONAL	1	TRUE	1	0.359619596475651	2		365	414	SUCCESS
CBL	867	MSKCC	GRCh37	11	119077147	119077147	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	88	517	0	ENST00000264033.4:c.20A>G	p.Lys7Arg	p.K7R	ENST00000264033	NM_005188.3	7	aAg/aGg	1/16	1	2	FACETS	0.866	0.769	0.97	0.866	0.769	0.97	CLONAL	1	TRUE	1	0.359619596475651	2		517	565	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18747431	18747431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	57	327	0	ENST00000266497.5:c.3892G>A	p.Asp1298Asn	p.D1298N	ENST00000266497		1298	Gat/Aat	28/31	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.359619596475651	2		327	288	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421896	49421896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1357291847	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	172	692	0	ENST00000301067.7:c.14411C>T	p.Ala4804Val	p.A4804V	ENST00000301067	NM_003482.3	4804	gCg/gTg	46/54	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.359619596475651	2		692	857	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422867	49422868	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	120	755	0	ENST00000301067.7:c.14227dup	p.Leu4743ProfsTer39	p.L4743Pfs*39	ENST00000301067	NM_003482.3	4743	ctc/cCtc	44/54	1	2	FACETS	0.931	0.841	1	0.931	0.841	1	CLONAL	1	TRUE	1	0.359619596475651	2		755	717	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437373	121437373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750897215	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	165	855	0	ENST00000257555.6:c.1711G>A	p.Asp571Asn	p.D571N	ENST00000257555		571	Gac/Aac	9/10	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.359619596475651	2		855	882	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202814	133202814	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	151	761	0	ENST00000320574.5:c.6420G>T	p.Glu2140Asp	p.E2140D	ENST00000320574	NM_006231.2	2140	gaG/gaT	46/49	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.359619596475651	2		761	813	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562918	21562918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223540790	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	151	927	3	ENST00000382592.4:c.1001G>A	p.Arg334His	p.R334H	ENST00000382592	NM_014572.2	334	cGc/cAc	4/8	1	2	FACETS	0.896	0.819	0.977	0.896	0.819	0.977	CLONAL	1	TRUE	1	0.359619596475651	2		930	937	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28883055	28883055	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	26	367	0	ENST00000282397.4:c.3645T>G	p.Asn1215Lys	p.N1215K	ENST00000282397	NM_002019.4	1215	aaT/aaG	28/30	1	2	FACETS	0.305	0.241	0.379	0.305	0.241	0.379	SUBCLONAL	1	TRUE	1	0.359619596475651	2		367	474	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32905114	32905114	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs80358962	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	24	401	0	ENST00000380152.3:c.740T>C	p.Ile247Thr	p.I247T	ENST00000380152		247	aTc/aCc	9/27	1	2	FACETS	0.306	0.239	0.383	0.306	0.239	0.383	SUBCLONAL	1	TRUE	1	0.359619596475651	2		401	436	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906647	32906648	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	58	397	0	ENST00000380152.3:c.1037dup	p.Asn346LysfsTer12	p.N346Kfs*12	ENST00000380152		344	-/A	10/27	1	2	FACETS	0.996	0.861	1	0.996	0.861	1	CLONAL	1	TRUE	1	0.359619596475651	2		397	324	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49051531	49051531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	55	310	0	ENST00000267163.4:c.2704G>A	p.Ala902Thr	p.A902T	ENST00000267163	NM_000321.2	902	Gca/Aca	26/27	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.359619596475651	2		310	272	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435906	110435906	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780869475	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	138	767	0	ENST00000375856.3:c.2495G>A	p.Arg832His	p.R832H	ENST00000375856	NM_003749.2	832	cGc/cAc	1/2	1	2	FACETS	0.999	0.91	1	0.999	0.91	1	CLONAL	1	TRUE	1	0.359619596475651	2		767	768	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061636	38061636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	87	387	1	ENST00000250448.2:c.353C>T	p.Ala118Val	p.A118V	ENST00000250448	NM_004496.3	118	gCg/gTg	2/2	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.359619596475651	2		388	378	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582858	95582858	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	59	313	0	ENST00000393063.1:c.1684A>T	p.Met562Leu	p.M562L	ENST00000393063	NM_030621.3	562	Atg/Ttg	11/28	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.359619596475651	2		313	271	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105237149	105237149	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	86	769	0	ENST00000349310.3:c.1296G>T	p.Glu432Asp	p.E432D	ENST00000349310	NM_001014432.1	432	gaG/gaT	14/15	1	2	FACETS	0.597	0.528	0.672	0.597	0.528	0.672	SUBCLONAL	1	TRUE	1	0.359619596475651	2		769	801	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242033	105242033	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	188	969	1	ENST00000349310.3:c.391G>A	p.Ala131Thr	p.A131T	ENST00000349310	NM_001014432.1	131	Gct/Act	6/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.359619596475651	2		970	969	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058636	42058636	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	51	259	0	ENST00000219905.7:c.8356T>A	p.Ser2786Thr	p.S2786T	ENST00000219905	NM_001164273.1	2786	Tca/Aca	24/24	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.359619596475651	2		259	281	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43785238	43785238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559128141	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	151	707	0	ENST00000382044.4:c.4C>T	p.Pro2Ser	p.P2S	ENST00000382044	NM_001141980.1	2	Cct/Tct	1/28	1	2	FACETS	0.978	0.894	1	0.978	0.894	1	CLONAL	1	TRUE	1	0.359619596475651	2		707	859	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423503	88423503	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	101	529	0	ENST00000360948.2:c.2332G>T	p.Glu778Ter	p.E778*	ENST00000360948	NM_001012338.2	778	Gag/Tag	18/19	1	2	FACETS	0.872	0.781	0.969	0.872	0.781	0.969	CLONAL	1	TRUE	1	0.359619596475651	2		529	644	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293055	91293056	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	81	501	1	ENST00000355112.3:c.563dup	p.Lys190Ter	p.K190*	ENST00000355112	NM_000057.2	186	tca/tcAa	3/22	1	2	FACETS	0.986	0.872	1	0.986	0.872	1	CLONAL	1	TRUE	1	0.359619596475651	2		502	457	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465456	99465456	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	108	553	0	ENST00000268035.6:c.2281G>A	p.Asp761Asn	p.D761N	ENST00000268035	NM_000875.3	761	Gac/Aac	11/21	1	2	FACETS	0.916	0.823	1	0.916	0.823	1	CLONAL	1	TRUE	1	0.359619596475651	2		553	656	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339512	339512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867213399	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	179	918	2	ENST00000262320.3:c.2390G>A	p.Arg797His	p.R797H	ENST00000262320	NM_003502.3	797	cGc/cAc	10/11	1	2	FACETS	0.965	0.889	1	0.965	0.889	1	CLONAL	1	TRUE	1	0.359619596475651	2		920	1032	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104324	2104324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1175373447	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	74	697	1	ENST00000219476.3:c.364C>T	p.Leu122Phe	p.L122F	ENST00000219476	NM_000548.3	122	Ctc/Ttc	5/42	1	2	FACETS	0.569	0.498	0.646	0.569	0.498	0.646	SUBCLONAL	1	TRUE	1	0.359619596475651	2		698	723	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220679	2220679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	138	742	0	ENST00000326181.6:c.296C>T	p.Ser99Phe	p.S99F	ENST00000326181	NM_032271.2	99	tCc/tTc	5/21	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.359619596475651	2		742	705	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222203	2222203	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751318317	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	171	843	2	ENST00000326181.6:c.487G>A	p.Val163Met	p.V163M	ENST00000326181	NM_032271.2	163	Gtg/Atg	8/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.359619596475651	2		845	824	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639257	3639257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1186678343	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	271	873	0	ENST00000294008.3:c.4382C>T	p.Ala1461Val	p.A1461V	ENST00000294008	NM_032444.2	1461	gCc/gTc	12/15	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.359619596475651	2		873	1024	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3651163	3651163	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	205	890	0	ENST00000294008.3:c.980G>T	p.Arg327Ile	p.R327I	ENST00000294008	NM_032444.2	327	aGa/aTa	5/15	1	2	FACETS	0.945	0.875	1	0.945	0.875	1	CLONAL	1	TRUE	1	0.359619596475651	2		890	1206	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779746	3779746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	218	720	0	ENST00000262367.5:c.5302C>T	p.Arg1768Cys	p.R1768C	ENST00000262367	NM_004380.2	1768	Cgc/Tgc	31/31	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.359619596475651	2		720	823	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823871	3823871	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1159173242	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	75	765	0	ENST00000262367.5:c.2344A>G	p.Asn782Asp	p.N782D	ENST00000262367	NM_004380.2	782	Aac/Gac	13/31	1	2	FACETS	0.405	0.353	0.46	0.405	0.353	0.46	SUBCLONAL	1	TRUE	1	0.359619596475651	2		765	1031	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645965	67645965	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	60	622	0	ENST00000264010.4:c.893T>G	p.Leu298Arg	p.L298R	ENST00000264010	NM_006565.3	298	cTc/cGc	4/12	1	2	FACETS	0.423	0.364	0.489	0.423	0.364	0.489	SUBCLONAL	1	TRUE	1	0.359619596475651	2		622	788	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822401	72822401	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs898512837	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	177	1008	0	ENST00000268489.5:c.9774G>T	p.Lys3258Asn	p.K3258N	ENST00000268489	NM_006885.3	3258	aaG/aaT	10/10	1	2	FACETS	0.932	0.858	1	0.932	0.858	1	CLONAL	1	TRUE	1	0.359619596475651	2		1008	1056	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553525	29553525	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	119	575	0	ENST00000356175.3:c.2074T>C	p.Tyr692His	p.Y692H	ENST00000356175	NM_000267.3	692	Tac/Cac	18/57	1	2	FACETS	0.958	0.866	1	0.958	0.866	1	CLONAL	1	TRUE	1	0.359619596475651	2		575	691	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676219	29676219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	68	351	0	ENST00000356175.3:c.7208G>A	p.Arg2403Lys	p.R2403K	ENST00000356175	NM_000267.3	2403	aGa/aAa	48/57	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.359619596475651	2		351	347	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474416	40474416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	115	547	1	ENST00000264657.5:c.1985C>T	p.Ala662Val	p.A662V	ENST00000264657	NM_139276.2	662	gCt/gTt	21/24	1	2	FACETS	0.992	0.895	1	0.992	0.895	1	CLONAL	1	TRUE	1	0.359619596475651	2		548	645	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40477063	40477063	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	86	502	0	ENST00000264657.5:c.1382T>G	p.Val461Gly	p.V461G	ENST00000264657	NM_139276.2	461	gTt/gGt	16/24	1	2	FACETS	0.751	0.665	0.843	0.751	0.665	0.843	SUBCLONAL	1	TRUE	1	0.359619596475651	2		502	637	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245683	41245683	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56039126	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	71	683	0	ENST00000357654.3:c.1865C>T	p.Ala622Val	p.A622V	ENST00000357654	NM_007294.3	622	gCg/gTg	10/23	1	2	FACETS	0.723	0.632	0.821	0.723	0.632	0.821	SUBCLONAL	1	TRUE	1	0.359619596475651	2		683	546	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41247935	41247935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	80	420	0	ENST00000357654.3:c.598G>A	p.Gly200Arg	p.G200R	ENST00000357654	NM_007294.3	200	Gga/Aga	9/23	1	2	FACETS	0.915	0.808	1	0.915	0.808	1	CLONAL	1	TRUE	1	0.359619596475651	2		420	486	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805483	46805483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	200	956	0	ENST00000290295.7:c.473C>T	p.Pro158Leu	p.P158L	ENST00000290295	NM_006361.5	158	cCg/cTg	1/2	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.359619596475651	2		956	1016	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699375	47699375	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	79	398	0	ENST00000347630.2:c.133C>T	p.Arg45Trp	p.R45W	ENST00000347630	NM_001007230.1	45	Cgg/Tgg	4/11	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.359619596475651	2		398	412	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55693437	55693437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	57	681	0	ENST00000284073.2:c.644G>A	p.Gly215Glu	p.G215E	ENST00000284073	NM_138962.2	215	gGg/gAg	9/14	1	2	FACETS	0.389	0.333	0.451	0.389	0.333	0.451	SUBCLONAL	1	TRUE	1	0.359619596475651	2		681	815	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2194554	2194555	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	110	533	0	ENST00000398665.3:c.635dup	p.His213AlafsTer30	p.H213Afs*30	ENST00000398665	NM_032482.2	210	gga/ggAa	7/28	1	2	FACETS	0.926	0.833	1	0.926	0.833	1	CLONAL	1	TRUE	1	0.359619596475651	2		533	661	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210424	2210424	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867592560	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	163	763	0	ENST00000398665.3:c.1031G>A	p.Arg344His	p.R344H	ENST00000398665	NM_032482.2	344	cGc/cAc	13/28	1	2	FACETS	0.967	0.888	1	0.967	0.888	1	CLONAL	1	TRUE	1	0.359619596475651	2		763	937	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5225812	5225812	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	198	901	0	ENST00000357368.4:c.2420T>A	p.Ile807Asn	p.I807N	ENST00000357368	NM_002850.3	807	aTc/aAc	17/38	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.359619596475651	2		901	971	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184532	7184532	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	71	666	0	ENST00000302850.5:c.769A>G	p.Asn257Asp	p.N257D	ENST00000302850	NM_000208.2	257	Aac/Gac	3/22	1	2	FACETS	0.52	0.453	0.593	0.52	0.453	0.593	SUBCLONAL	1	TRUE	1	0.359619596475651	2		666	759	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123778	11123778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502056	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	81	609	1	ENST00000358026.2:c.2428G>A	p.Val810Met	p.V810M	ENST00000358026	NM_001128849.1	810	Gtg/Atg	16/36	1	2	FACETS	0.675	0.595	0.762	0.675	0.595	0.762	SUBCLONAL	1	TRUE	1	0.359619596475651	2		610	667	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627586	14627586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764446419	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	36	522	0	ENST00000254322.2:c.484C>T	p.Pro162Ser	p.P162S	ENST00000254322	NM_006145.1	162	Ccc/Tcc	2/3	1	2	FACETS	0.308	0.252	0.37	0.308	0.252	0.37	SUBCLONAL	1	TRUE	1	0.359619596475651	2		522	651	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271689	15271689	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	209	1121	1	ENST00000263388.2:c.6750A>C	p.Glu2250Asp	p.E2250D	ENST00000263388	NM_000435.2	2250	gaA/gaC	33/33	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.359619596475651	2		1122	1109	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281184	15281184	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	212	1073	0	ENST00000263388.2:c.5072A>C	p.Lys1691Thr	p.K1691T	ENST00000263388	NM_000435.2	1691	aAg/aCg	27/33	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.359619596475651	2		1073	1119	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350069	15350069	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	96	907	0	ENST00000263377.2:c.3583A>C	p.Lys1195Gln	p.K1195Q	ENST00000263377	NM_058243.2	1195	Aaa/Caa	18/20	1	2	FACETS	0.605	0.538	0.677	0.605	0.538	0.677	SUBCLONAL	1	TRUE	1	0.359619596475651	2		907	882	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375240	15375240	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	99	600	0	ENST00000263377.2:c.1187A>G	p.His396Arg	p.H396R	ENST00000263377	NM_058243.2	396	cAc/cGc	6/20	1	2	FACETS	0.789	0.704	0.878	0.789	0.704	0.878	SUBCLONAL	1	TRUE	1	0.359619596475651	2		600	698	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387307	17387307	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	83	754	1	ENST00000359435.4:c.573G>T	p.Gln191His	p.Q191H	ENST00000359435	NM_001033549.1	191	caG/caT	7/9	1	2	FACETS	0.571	0.503	0.644	0.571	0.503	0.644	SUBCLONAL	1	TRUE	1	0.359619596475651	2		755	808	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971130	18971130	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs141708625	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	155	779	1	ENST00000262803.5:c.2183C>T	p.Ala728Val	p.A728V	ENST00000262803	NM_002911.3	728	gCg/gTg	16/24	1	2	FACETS	0.987	0.904	1	0.987	0.904	1	CLONAL	1	TRUE	1	0.359619596475651	2		780	873	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210812	36210812	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763797736	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	59	1023	2	ENST00000222270.7:c.563G>A	p.Arg188Gln	p.R188Q	ENST00000222270	NM_014727.1	188	cGg/cAg	3/37	1	2	FACETS	0.312	0.267	0.361	0.312	0.267	0.361	SUBCLONAL	1	TRUE	1	0.359619596475651	2		1025	1051	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215985	36215985	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	106	888	0	ENST00000222270.7:c.3525T>A	p.Phe1175Leu	p.F1175L	ENST00000222270	NM_014727.1	1175	ttT/ttA	10/37	1	2	FACETS	0.606	0.542	0.674	0.606	0.542	0.674	SUBCLONAL	1	TRUE	1	0.359619596475651	2		888	973	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867724	45867724	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753696173	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	73	1004	2	ENST00000391945.4:c.676G>A	p.Ala226Thr	p.A226T	ENST00000391945	NM_000400.3	226	Gcc/Acc	8/23	1	2	FACETS	0.41	0.357	0.467	0.41	0.357	0.467	SUBCLONAL	1	TRUE	1	0.359619596475651	2		1006	990	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085822	16085822	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	107	609	1	ENST00000281043.3:c.998C>T	p.Ala333Val	p.A333V	ENST00000281043	NM_005378.4	333	gCc/gTc	3/3	1	2	FACETS	0.969	0.871	1	0.969	0.871	1	CLONAL	1	TRUE	1	0.359619596475651	2		610	614	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416423	29416423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	78	850	0	ENST00000389048.3:c.4530G>A	p.Trp1510Ter	p.W1510*	ENST00000389048	NM_004304.4	1510	tgG/tgA	29/29	1	2	FACETS	0.42	0.368	0.476	0.42	0.368	0.476	SUBCLONAL	1	TRUE	1	0.359619596475651	2		850	1033	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46588202	46588202	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	127	636	0	ENST00000263734.3:c.752A>G	p.Asp251Gly	p.D251G	ENST00000263734	NM_001430.4	251	gAc/gGc	6/16	1	2	FACETS	0.972	0.881	1	0.972	0.881	1	CLONAL	1	TRUE	1	0.359619596475651	2		636	727	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607663	46607663	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1259062822	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	94	879	1	ENST00000263734.3:c.1852C>T	p.Pro618Ser	p.P618S	ENST00000263734	NM_001430.4	618	Cca/Tca	12/16	1	2	FACETS	0.539	0.478	0.604	0.539	0.478	0.604	SUBCLONAL	1	TRUE	1	0.359619596475651	2		880	970	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630514	47630514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767140240	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	123	711	0	ENST00000233146.2:c.184G>A	p.Gly62Arg	p.G62R	ENST00000233146	NM_000251.2	62	Ggg/Agg	1/16	1	2	FACETS	0.923	0.835	1	0.923	0.835	1	CLONAL	1	TRUE	1	0.359619596475651	2		711	741	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026364	48026364	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	84	449	1	ENST00000234420.5:c.1242G>A	p.Trp414Ter	p.W414*	ENST00000234420	NM_000179.2	414	tgG/tgA	4/10	1	2	FACETS	0.938	0.831	1	0.938	0.831	1	CLONAL	1	TRUE	1	0.359619596475651	2		450	498	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198283297	198283297	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	83	446	0	ENST00000335508.6:c.431A>G	p.Asp144Gly	p.D144G	ENST00000335508	NM_012433.2	144	gAt/gGt	5/25	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.359619596475651	2		446	451	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288656	198288656	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	84	511	0	ENST00000335508.6:c.71C>A	p.Ala24Asp	p.A24D	ENST00000335508	NM_012433.2	24	gCt/gAt	2/25	1	2	FACETS	0.851	0.753	0.955	0.851	0.753	0.955	CLONAL	1	TRUE	1	0.359619596475651	2		511	549	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150042	202150042	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs768000891	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	138	557	0	ENST00000358485.4:c.1481+2T>C		p.X494_splice	ENST00000358485	NM_001080125.1	494			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.359619596475651	2		557	721	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735470	204735470	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	91	472	0	ENST00000302823.3:c.271A>G	p.Met91Val	p.M91V	ENST00000302823	NM_005214.4	91	Atg/Gtg	2/4	1	2	FACETS	0.879	0.782	0.982	0.879	0.782	0.982	CLONAL	1	TRUE	1	0.359619596475651	2		472	576	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023213	31023213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	149	726	2	ENST00000375687.4:c.2698C>T	p.Pro900Ser	p.P900S	ENST00000375687	NM_015338.5	900	Ccc/Tcc	13/13	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.359619596475651	2		728	797	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46275817	46275817	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	93	471	0	ENST00000371998.3:c.3253G>A	p.Gly1085Arg	p.G1085R	ENST00000371998		1085	Gga/Aga	18/23	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.359619596475651	2		471	504	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42843835	42843835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781290787	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	110	519	1	ENST00000398585.3:c.1084G>A	p.Gly362Arg	p.G362R	ENST00000398585	NM_001135099.1	362	Gga/Aga	10/14	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.359619596475651	2		520	598	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655194	45655194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218803422	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	109	682	0	ENST00000407780.3:c.658G>A	p.Val220Met	p.V220M	ENST00000407780	NM_001283052.1	220	Gtg/Atg	4/7	1	2	FACETS	0.885	0.796	0.98	0.885	0.796	0.98	CLONAL	1	TRUE	1	0.359619596475651	2		682	685	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545901	41545901	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	168	827	0	ENST00000263253.7:c.2516C>G	p.Thr839Ser	p.T839S	ENST00000263253	NM_001429.3	839	aCc/aGc	14/31	1	2	FACETS	0.903	0.829	0.98	0.903	0.829	0.98	CLONAL	1	TRUE	1	0.359619596475651	2		827	1035	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421310	12421310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	111	736	2	ENST00000287820.6:c.190C>T	p.Pro64Ser	p.P64S	ENST00000287820	NM_015869.4	64	Ccc/Tcc	2/7	1	2	FACETS	0.824	0.741	0.912	0.824	0.741	0.912	CLONAL	1	TRUE	1	0.359619596475651	2		738	749	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266062	41266062	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	84	364	0	ENST00000349496.5:c.59C>A	p.Ala20Glu	p.A20E	ENST00000349496	NM_001904.3	20	gCg/gAg	3/15	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.359619596475651	2		364	443	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933198	49933198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415030187	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	164	732	1	ENST00000296474.3:c.2912C>T	p.Ala971Val	p.A971V	ENST00000296474	NM_002447.2	971	gCa/gTa	12/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.359619596475651	2		733	748	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439245	52439245	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	164	877	0	ENST00000460680.1:c.997A>G	p.Lys333Glu	p.K333E	ENST00000460680	NM_004656.3	333	Aag/Gag	11/17	1	2	FACETS	0.929	0.852	1	0.929	0.852	1	CLONAL	1	TRUE	1	0.359619596475651	2		877	982	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242891	142242891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	76	551	1	ENST00000350721.4:c.4096C>T	p.Pro1366Ser	p.P1366S	ENST00000350721	NM_001184.3	1366	Cca/Tca	22/47	1	2	FACETS	0.943	0.831	1	0.943	0.831	1	CLONAL	1	TRUE	1	0.359619596475651	2		552	448	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169981188	169981188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs980860031	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	94	488	0	ENST00000295797.4:c.335G>A	p.Arg112His	p.R112H	ENST00000295797	NM_002740.5	112	cGt/cAt	4/18	1	2	FACETS	0.745	0.663	0.832	0.745	0.663	0.832	SUBCLONAL	1	TRUE	1	0.359619596475651	2		488	702	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449510	187449510	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	72	325	0	ENST00000232014.4:c.370T>G	p.Phe124Val	p.F124V	ENST00000232014	NM_001130845.1	124	Ttt/Gtt	4/10	1	2	FACETS	0.981	0.861	1	0.981	0.861	1	CLONAL	1	TRUE	1	0.359619596475651	2		325	408	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801012	1801012	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	177	1026	2	ENST00000260795.2:c.141G>T	p.Glu47Asp	p.E47D	ENST00000260795		47	gaG/gaT	2/17	1	2	FACETS	0.924	0.851	1	0.924	0.851	1	CLONAL	1	TRUE	1	0.359619596475651	2		1028	1065	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133837	55133838	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	80	505	0	ENST00000257290.5:c.1050_1051insC	p.Lys351GlnfsTer8	p.K351Qfs*8	ENST00000257290	NM_006206.4	350	-/C	7/23	1	2	FACETS	0.888	0.784	0.999	0.888	0.784	0.999	CLONAL	1	TRUE	1	0.359619596475651	2		505	501	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152078	55152078	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	79	687	0	ENST00000257290.5:c.2510T>G	p.Phe837Cys	p.F837C	ENST00000257290	NM_006206.4	837	tTt/tGt	18/23	1	2	FACETS	0.544	0.478	0.616	0.544	0.478	0.616	SUBCLONAL	1	TRUE	1	0.359619596475651	2		687	807	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971129	55971129	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	122	599	0	ENST00000263923.4:c.1668A>T	p.Gln556His	p.Q556H	ENST00000263923	NM_002253.2	556	caA/caT	13/30	1	2	FACETS	0.971	0.879	1	0.971	0.879	1	CLONAL	1	TRUE	1	0.359619596475651	2		599	699	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972076	55972076	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	106	483	0	ENST00000263923.4:c.1568A>C	p.Asn523Thr	p.N523T	ENST00000263923	NM_002253.2	523	aAt/aCt	12/30	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.359619596475651	2		483	556	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155356	106155356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	83	429	0	ENST00000380013.4:c.257C>T	p.Ser86Phe	p.S86F	ENST00000380013	NM_001127208.2	86	tCc/tTc	3/11	1	2	FACETS	0.976	0.864	1	0.976	0.864	1	CLONAL	1	TRUE	1	0.359619596475651	2		429	473	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510249	187510249	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1248948388	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	84	480	0	ENST00000441802.2:c.13264A>G	p.Thr4422Ala	p.T4422A	ENST00000441802	NM_005245.3	4422	Acg/Gcg	27/27	1	2	FACETS	0.834	0.738	0.937	0.834	0.738	0.937	CLONAL	1	TRUE	1	0.359619596475651	2		480	560	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525673	187525673	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	71	507	0	ENST00000441802.2:c.10406C>A	p.Ser3469Tyr	p.S3469Y	ENST00000441802	NM_005245.3	3469	tCt/tAt	18/27	1	2	FACETS	0.83	0.726	0.941	0.83	0.726	0.941	CLONAL	1	TRUE	1	0.359619596475651	2		507	476	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549439	187549439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374571513	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	129	560	0	ENST00000441802.2:c.4679C>T	p.Pro1560Leu	p.P1560L	ENST00000441802	NM_005245.3	1560	cCg/cTg	9/27	1	2	FACETS	0.851	0.771	0.935	0.851	0.771	0.935	CLONAL	1	TRUE	1	0.359619596475651	2		560	843	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225584	225584	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	17	191	0	ENST00000264932.6:c.363G>A	p.Trp121Ter	p.W121*	ENST00000264932	NM_004168.2	121	tgG/tgA	4/15	1	2	FACETS	0.391	0.292	0.508	0.391	0.292	0.508	SUBCLONAL	1	TRUE	1	0.359619596475651	2		191	242	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31429596	31429596	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	76	505	0	ENST00000344624.3:c.3202C>T	p.Leu1068Phe	p.L1068F	ENST00000344624		1068	Ctc/Ttc	24/33	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.359619596475651	2		505	417	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515141	31515141	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	157	801	1	ENST00000344624.3:c.1244G>A	p.Cys415Tyr	p.C415Y	ENST00000344624		415	tGc/tAc	5/33	1	2	FACETS	0.983	0.901	1	0.983	0.901	1	CLONAL	1	TRUE	1	0.359619596475651	2		802	888	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589538	67589538	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	26	171	0	ENST00000274335.5:c.1301A>C	p.Asp434Ala	p.D434A	ENST00000274335		434	gAt/gCt	10/15	1	2	FACETS	0.846	0.676	1	0.846	0.676	1	CLONAL	1	TRUE	1	0.359619596475651	2		171	171	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564774	86564774	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	100	950	0	ENST00000274376.6:c.506T>C	p.Val169Ala	p.V169A	ENST00000274376	NM_002890.2	169	gTg/gCg	1/25	1	2	FACETS	0.572	0.509	0.638	0.572	0.509	0.638	SUBCLONAL	1	TRUE	1	0.359619596475651	2		950	973	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670026	86670026	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	64	317	0	ENST00000274376.6:c.1823T>C	p.Val608Ala	p.V608A	ENST00000274376	NM_002890.2	608	gTa/gCa	14/25	1	2	FACETS	0.975	0.849	1	0.975	0.849	1	CLONAL	1	TRUE	1	0.359619596475651	2		317	365	SUCCESS
APC	324	MSKCC	GRCh37	5	112154766	112154766	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	105	499	0	ENST00000257430.4:c.1037C>T	p.Ser346Phe	p.S346F	ENST00000257430	NM_000038.5	346	tCc/tTc	10/16	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.359619596475651	2		499	545	SUCCESS
APC	324	MSKCC	GRCh37	5	112173492	112173492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	54	320	0	ENST00000257430.4:c.2201C>T	p.Pro734Leu	p.P734L	ENST00000257430	NM_000038.5	734	cCt/cTt	16/16	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.359619596475651	2		320	257	SUCCESS
APC	324	MSKCC	GRCh37	5	112174826	112174826	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs751249843	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	32	268	0	ENST00000257430.4:c.3535T>C	p.Tyr1179His	p.Y1179H	ENST00000257430	NM_000038.5	1179	Tat/Cat	16/16	1	2	FACETS	0.839	0.687	1	0.839	0.687	1	CLONAL	1	TRUE	1	0.359619596475651	2		268	212	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435642	149435642	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	72	732	0	ENST00000286301.3:c.2501T>C	p.Val834Ala	p.V834A	ENST00000286301	NM_005211.3	834	gTt/gCt	19/22	1	2	FACETS	0.476	0.415	0.542	0.476	0.415	0.542	SUBCLONAL	1	TRUE	1	0.359619596475651	2		732	841	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435648	149435648	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	171	746	0	ENST00000286301.3:c.2495A>G	p.Tyr832Cys	p.Y832C	ENST00000286301	NM_005211.3	832	tAc/tGc	19/22	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.359619596475651	2		746	852	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497244	149497245	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	156	782	0	ENST00000261799.4:c.3073dup	p.Leu1025ProfsTer3	p.L1025Pfs*3	ENST00000261799	NM_002609.3	1025	ctg/cCtg	22/23	1	2	FACETS	0.911	0.834	0.992	0.911	0.834	0.992	CLONAL	1	TRUE	1	0.359619596475651	2		782	952	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523083	176523083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs2301344	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	158	813	1	ENST00000292408.4:c.1847G>A	p.Arg616His	p.R616H	ENST00000292408	NM_213647.1	616	cGc/cAc	14/18	1	2	FACETS	0.959	0.879	1	0.959	0.879	1	CLONAL	1	TRUE	1	0.359619596475651	2		814	916	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176662910	176662911	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	33	363	0	ENST00000439151.2:c.3891dup	p.Gln1298ThrfsTer16	p.Q1298Tfs*16	ENST00000439151	NM_022455.4	1295	-/A	6/23	1	2	FACETS	0.57	0.465	0.687	0.57	0.465	0.687	SUBCLONAL	1	TRUE	1	0.359619596475651	2		363	322	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480173	20480173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	76	332	0	ENST00000346618.3:c.490C>T	p.Pro164Ser	p.P164S	ENST00000346618	NM_001949.4	164	Cca/Tca	2/7	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.359619596475651	2		332	377	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675426	30675426	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776398578	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	78	684	0	ENST00000376406.3:c.2930C>T	p.Pro977Leu	p.P977L	ENST00000376406	NM_014641.2	977	cCg/cTg	8/15	1	2	FACETS	0.548	0.48	0.62	0.548	0.48	0.62	SUBCLONAL	1	TRUE	1	0.359619596475651	2		684	792	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190479	32190479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1418529062	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	176	980	1	ENST00000375023.3:c.260C>T	p.Pro87Leu	p.P87L	ENST00000375023	NM_004557.3	87	cCc/cTc	3/30	1	2	FACETS	0.987	0.908	1	0.987	0.908	1	CLONAL	1	TRUE	1	0.359619596475651	2		981	992	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140804	37140804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752976281	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	127	563	0	ENST00000373509.5:c.640C>T	p.Arg214Cys	p.R214C	ENST00000373509	NM_002648.3	214	Cgc/Tgc	5/6	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.359619596475651	2		563	632	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015619	112015619	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	61	461	0	ENST00000368678.4:c.1223T>C	p.Leu408Ser	p.L408S	ENST00000368678		408	tTg/tCg	11/13	1	2	FACETS	0.605	0.522	0.695	0.605	0.522	0.695	SUBCLONAL	1	TRUE	1	0.359619596475651	2		461	561	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020733	112020733	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs989052808	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	37	349	1	ENST00000368678.4:c.838G>A	p.Ala280Thr	p.A280T	ENST00000368678		280	Gct/Act	8/13	1	2	FACETS	0.396	0.326	0.474	0.396	0.326	0.474	SUBCLONAL	1	TRUE	1	0.359619596475651	2		350	520	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647572	117647572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759533205	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	88	474	0	ENST00000368508.3:c.5372G>A	p.Ser1791Asn	p.S1791N	ENST00000368508	NM_002944.2	1791	aGc/aAc	33/43	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.359619596475651	2		474	465	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005257	150005257	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	89	469	0	ENST00000253339.5:c.968T>C	p.Val323Ala	p.V323A	ENST00000253339		323	gTt/gCt	3/7	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.359619596475651	2		469	488	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005485	150005485	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	66	414	0	ENST00000253339.5:c.740C>T	p.Pro247Leu	p.P247L	ENST00000253339		247	cCt/cTt	3/7	1	2	FACETS	0.768	0.668	0.876	0.768	0.668	0.876	SUBCLONAL	1	TRUE	1	0.359619596475651	2		414	478	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953023	2953023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754645078	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	79	816	1	ENST00000396946.4:c.2917C>T	p.Arg973Cys	p.R973C	ENST00000396946	NM_032415.4	973	Cgc/Tgc	22/25	0.359619596475651	1	FACETS	0.447	0.392	0.506	0.447	0.392	0.506	SUBCLONAL	1	TRUE	0	0.359619596475651	1		817	806	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508068	106508068	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755613711	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	23	282	1	ENST00000359195.3:c.62G>A	p.Arg21Gln	p.R21Q	ENST00000359195	NM_002649.2	21	cGg/cAg	2/11	0.303349286446284	3	FACETS	0.476	0.371	0.597	0.238	0.185	0.299	SUBCLONAL	1	TRUE	1	0.359619596475651	3		283	317	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439689	140439689	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	55	416	0	ENST00000288602.6:c.2050A>G	p.Asn684Asp	p.N684D	ENST00000288602	NM_004333.4	684	Aac/Gac	17/18	0.303349286446284	3	FACETS	0.902	0.774	1	0.451	0.387	0.521	CLONAL	1	TRUE	1	0.359619596475651	3		416	400	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494254	140494254	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	155	918	0	ENST00000288602.6:c.994A>G	p.Thr332Ala	p.T332A	ENST00000288602	NM_004333.4	332	Acc/Gcc	8/18	0.303349286446284	3	FACETS	0.88	0.804	0.96	0.44	0.402	0.48	CLONAL	1	TRUE	1	0.359619596475651	3		918	1156	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148526822	148526822	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	40	337	0	ENST00000320356.2:c.482G>T	p.Arg161Ile	p.R161I	ENST00000320356	NM_004456.4	161	aGa/aTa	5/20	0.303349286446284	3	FACETS	0.725	0.604	0.859	0.363	0.302	0.43	SUBCLONAL	1	TRUE	1	0.359619596475651	3		337	362	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880115	151880116	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	92	457	0	ENST00000262189.6:c.5208dup	p.Lys1737Ter	p.K1737*	ENST00000262189	NM_170606.2	1736	-/T	35/59	0.303349286446284	3	FACETS	1	0.954	1	0.566	0.504	0.632	CLONAL	1	TRUE	1	0.359619596475651	3		457	533	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005949	69005949	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	97	549	0	ENST00000288368.4:c.2360A>C	p.Lys787Thr	p.K787T	ENST00000288368	NM_024870.2	787	aAa/aCa	21/40	1	2	FACETS	0.972	0.869	1	0.972	0.869	1	CLONAL	1	TRUE	1	0.359619596475651	2		549	555	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981975	70981975	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	175	1034	0	ENST00000276594.2:c.121A>G	p.Asn41Asp	p.N41D	ENST00000276594	NM_024504.3	41	Aac/Gac	2/8	1	2	FACETS	0.95	0.875	1	0.95	0.875	1	CLONAL	1	TRUE	1	0.359619596475651	2		1034	1024	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864929	117864929	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	53	301	0	ENST00000297338.2:c.1180A>G	p.Thr394Ala	p.T394A	ENST00000297338	NM_006265.2	394	Aca/Gca	10/14	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.359619596475651	2		301	261	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868893	117868893	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	15	319	0	ENST00000297338.2:c.806A>G	p.Asn269Ser	p.N269S	ENST00000297338	NM_006265.2	269	aAt/aGt	7/14	1	2	FACETS	0.281	0.205	0.372	0.281	0.205	0.372	SUBCLONAL	1	TRUE	1	0.359619596475651	2		319	297	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27183575	27183575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	79	453	0	ENST00000380036.4:c.1149G>A	p.Met383Ile	p.M383I	ENST00000380036	NM_000459.3	383	atG/atA	8/23	1	2	FACETS	0.847	0.746	0.954	0.847	0.746	0.954	CLONAL	1	TRUE	1	0.359619596475651	2		453	519	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93607822	93607822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	60	479	2	ENST00000375746.1:c.524G>A	p.Arg175Gln	p.R175Q	ENST00000375746	NM_001174167.1	175	cGg/cAg	3/14	1	2	FACETS	0.618	0.533	0.711	0.618	0.533	0.711	SUBCLONAL	1	TRUE	1	0.359619596475651	2		481	540	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434664	128434664	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	119	651	0	ENST00000265960.3:c.190T>C	p.Tyr64His	p.Y64H	ENST00000265960	NM_001006617.1	64	Tat/Cat	2/12	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.359619596475651	2		651	646	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771908	135771908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060503200	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	134	685	2	ENST00000298552.3:c.3209C>T	p.Ala1070Val	p.A1070V	ENST00000298552	NM_001162426.1	1070	gCg/gTg	23/23	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.359619596475651	2		687	741	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411832	139411832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748102038	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	110	852	0	ENST00000277541.6:c.1447G>A	p.Glu483Lys	p.E483K	ENST00000277541	NM_017617.3	483	Gag/Aag	9/34	1	2	FACETS	0.606	0.543	0.672	0.606	0.543	0.672	SUBCLONAL	1	TRUE	1	0.359619596475651	2		852	1010	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966726	44966726	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	63	508	0	ENST00000377967.4:c.3950T>G	p.Ile1317Ser	p.I1317S	ENST00000377967	NM_021140.2	1317	aTt/aGt	27/29	1	2	FACETS	0.75	0.65	0.858	0.75	0.65	0.858	SUBCLONAL	1	TRUE	1	0.359619596475651	2		508	467	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040660	47040660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1477871550	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	62	854	1	ENST00000377604.3:c.1295C>T	p.Pro432Leu	p.P432L	ENST00000377604	NM_001204468.1	432	cCg/cTg	13/24	1	2	FACETS	0.381	0.328	0.438	0.381	0.328	0.438	SUBCLONAL	1	TRUE	1	0.359619596475651	2		855	906	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041633	47041633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	188	827	0	ENST00000377604.3:c.1858G>A	p.Glu620Lys	p.E620K	ENST00000377604	NM_001204468.1	620	Gag/Aag	17/24	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.359619596475651	2		827	880	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424670	47424670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	171	799	0	ENST00000377045.4:c.478G>A	p.Asp160Asn	p.D160N	ENST00000377045	NM_001654.4	160	Gat/Aat	6/16	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.359619596475651	2		799	905	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650563	48650563	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	181	855	0	ENST00000376670.3:c.533G>T	p.Ser178Ile	p.S178I	ENST00000376670	NM_002049.3	178	aGc/aTc	3/6	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.359619596475651	2		855	981	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651601	48651601	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	152	788	0	ENST00000376670.3:c.767C>A	p.Thr256Asn	p.T256N	ENST00000376670	NM_002049.3	256	aCt/aAt	5/6	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.359619596475651	2		788	845	SUCCESS
AR	367	MSKCC	GRCh37	X	66766217	66766217	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	56	598	0	ENST00000374690.3:c.1229A>G	p.Asp410Gly	p.D410G	ENST00000374690	NM_000044.3	410	gAc/gGc	1/8	1	2	FACETS	0.59	0.505	0.682	0.59	0.505	0.682	SUBCLONAL	1	TRUE	1	0.359619596475651	2		598	528	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356192	70356192	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1211195670	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	232	944	1	ENST00000374080.3:c.5087C>T	p.Pro1696Leu	p.P1696L	ENST00000374080		1696	cCg/cTg	37/45	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.359619596475651	2		945	1127	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356405	70356405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	138	741	1	ENST00000374080.3:c.5300C>T	p.Pro1767Leu	p.P1767L	ENST00000374080		1767	cCc/cTc	37/45	1	2	FACETS	0.971	0.885	1	0.971	0.885	1	CLONAL	1	TRUE	1	0.359619596475651	2		742	790	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357060	70357060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759956340	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	135	890	1	ENST00000374080.3:c.5575C>T	p.Arg1859Cys	p.R1859C	ENST00000374080		1859	Cgt/Tgt	39/45	1	2	FACETS	0.667	0.605	0.733	0.667	0.605	0.733	SUBCLONAL	1	TRUE	1	0.359619596475651	2		891	1125	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939004	76939004	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	75	589	0	ENST00000373344.5:c.1744G>T	p.Val582Leu	p.V582L	ENST00000373344	NM_000489.3	582	Gta/Tta	9/35	1	2	FACETS	0.887	0.78	1	0.887	0.78	1	CLONAL	1	TRUE	1	0.359619596475651	2		589	470	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939202	76939202	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	89	619	0	ENST00000373344.5:c.1546G>T	p.Asp516Tyr	p.D516Y	ENST00000373344	NM_000489.3	516	Gat/Tat	9/35	1	2	FACETS	0.967	0.86	1	0.967	0.86	1	CLONAL	1	TRUE	1	0.359619596475651	2		619	512	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613319	100613319	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	136	622	0	ENST00000308731.7:c.1081T>C	p.Tyr361His	p.Y361H	ENST00000308731	NM_000061.2	361	Tac/Cac	12/19	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.359619596475651	2		622	675	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179153	123179153	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	72	487	0	ENST00000218089.9:c.602T>G	p.Ile201Ser	p.I201S	ENST00000218089	NM_001042749.1	201	aTt/aGt	8/35	1	2	FACETS	0.977	0.857	1	0.977	0.857	1	CLONAL	1	TRUE	1	0.359619596475651	2		487	410	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504045	123504045	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	21	332	0	ENST00000371139.4:c.221A>G	p.Lys74Arg	p.K74R	ENST00000371139	NM_001114937.2	74	aAa/aGa	3/4	1	2	FACETS	0.393	0.303	0.499	0.393	0.303	0.499	SUBCLONAL	1	TRUE	1	0.359619596475651	2		332	297	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252112	226252112	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	15	65	0	ENST00000366813.1:c.60A>C	p.Gln20His	p.Q20H	ENST00000366813		20	caA/caC	1/3	1	2	FACETS	1	0.838	1	1	0.838	1	CLONAL	1	TRUE	1	0.359619596475651	2		65	71	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637555	52637555	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	70	346	0	ENST00000394830.3:c.2761C>T	p.Arg921Ter	p.R921*	ENST00000394830	NM_018313.4	921	Cga/Tga	18/30	0.470148744689376	1	FACETS	0.86	0.758	0.966	0.86	0.758	0.966	CLONAL	1	TRUE	0	0.470148744689376	1		346	265	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139408984	139408984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	143	686	0	ENST00000277541.6:c.2185G>A	p.Ala729Thr	p.A729T	ENST00000277541	NM_017617.3	729	Gcc/Acc	13/34	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.470148744689376	2		686	582	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106211	27106211	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	95	604	0	ENST00000324856.7:c.5822T>A	p.Phe1941Tyr	p.F1941Y	ENST00000324856	NM_006015.4	1941	tTt/tAt	20/20	0.335329976573322	1	FACETS	0.562	0.502	0.626	0.562	0.502	0.626	SUBCLONAL	1	TRUE	0	0.470148744689376	1		604	550	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562624	21562624	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	105	403	0	ENST00000382592.4:c.1295T>A	p.Val432Glu	p.V432E	ENST00000382592	NM_014572.2	432	gTg/gAg	4/8	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.470148744689376	2		403	435	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191516	10191516	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1437199117	NA	P-0041599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	111	476	0	ENST00000256474.2:c.509del	p.Val170AlafsTer32	p.V170Afs*32	ENST00000256474	NM_000551.3	170	gTc/gc	3/3	0.470148744689376	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.470148744689376	1		476	357	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059230	47059230	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs777018406	NA	P-0041599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	100	346	0	ENST00000409792.3:c.7432-1G>A		p.X2478_splice	ENST00000409792	NM_014159.6	2478			0.470148744689376	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.470148744689376	1		346	309	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	102	348	10	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.529706656711051	2		358	308	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	93	471	1	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.989	0.887	1	0.989	0.887	1	CLONAL	1	FALSE	1	0.529706656711051	2		472	355	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087503	27087503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	222	703	1	ENST00000324856.7:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000324856	NM_006015.4	693	Cga/Tga	5/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.529706656711051	2		704	694	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176710828	176710828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587784177	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	87	402	1	ENST00000439151.2:c.6050G>A	p.Arg2017Gln	p.R2017Q	ENST00000439151	NM_022455.4	2017	cGg/cAg	20/23	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.529706656711051	2		403	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780068	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	282	721	2	ENST00000269305.4:c.472C>T	p.Arg158Cys	p.R158C	ENST00000269305	NM_001126112.2	158	Cgc/Tgc	5/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.529706656711051	2		723	861	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260214	16260214	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	99	472	0	ENST00000375759.3:c.7484del	p.Pro2495LeufsTer4	p.P2495Lfs*4	ENST00000375759	NM_015001.2	2493	agC/ag	11/15	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	FALSE	1	0.529706656711051	2		472	364	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057937	27057937	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	155	622	2	ENST00000324856.7:c.1650del	p.Tyr551ThrfsTer68	p.Y551Tfs*68	ENST00000324856	NM_006015.4	549	Ccc/cc	3/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.529706656711051	2		624	556	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913274	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	13	647	0	ENST00000263967.3:c.1634A>C	p.Glu545Ala	p.E545A	ENST00000263967	NM_006218.2	545	gAg/gCg	10/21	0.529706656711051	2	FACETS	0.42	0.302	0.561	0.21	0.151	0.281	SUBCLONAL	1	FALSE	0	0.529706656711051	2		647	117	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394848	394848	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1302327519	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	96	419	0	ENST00000380956.4:c.244C>T	p.Arg82Ter	p.R82*	ENST00000380956	NM_001195286.1	82	Cga/Tga	3/9	1	2	FACETS	0.964	0.866	1	0.964	0.866	1	CLONAL	1	FALSE	1	0.529706656711051	2		419	376	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528611	8528611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201846121	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	58	390	0	ENST00000356435.5:c.521G>A	p.Arg174His	p.R174H	ENST00000356435		174	cGt/cAt	4/35	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	FALSE	1	0.529706656711051	2		390	205	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509082	106509082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144565710	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	105	595	1	ENST00000359195.3:c.1076G>A	p.Arg359His	p.R359H	ENST00000359195	NM_002649.2	359	cGc/cAc	2/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.529706656711051	2		596	363	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288969	212288969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148791072	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	74	520	0	ENST00000342788.4:c.2777C>T	p.Thr926Met	p.T926M	ENST00000342788	NM_005235.2	926	aCg/aTg	23/28	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.529706656711051	2		520	245	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138382857	138382857	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142933486	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	41	347	0	ENST00000289153.2:c.2687G>A	p.Arg896Gln	p.R896Q	ENST00000289153	NM_006219.2	896	cGa/cAa	19/22	0.529706656711051	2	FACETS	0.741	0.623	0.868	0.37	0.311	0.434	SUBCLONAL	1	FALSE	0	0.529706656711051	2		347	209	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445149	49445149	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	182	779	4	ENST00000301067.7:c.2317del	p.Gln773SerfsTer157	p.Q773Sfs*157	ENST00000301067	NM_003482.3	773	Cag/ag	10/54	0.529706656711051	3	FACETS	0.754	0.7	0.81	0.754	0.7	0.81	SUBCLONAL	2	FALSE	1	0.529706656711051	3		783	576	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692949	89692949	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167627	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	95	525	1	ENST00000371953.3:c.437del	p.Leu146Ter	p.L146*	ENST00000371953	NM_000314.4	145	Ttt/tt	5/9	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.529706656711051	2		526	278	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637008	93637008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201479078	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	148	456	0	ENST00000375746.1:c.1058C>T	p.Ala353Val	p.A353V	ENST00000375746	NM_001174167.1	353	gCg/gTg	9/14	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.529706656711051	2		456	436	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225626	26225626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373685271	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	107	535	0	ENST00000360408.1:c.244G>A	p.Asp82Asn	p.D82N	ENST00000360408	NM_003532.2	82	Gac/Aac	1/1	1	2	FACETS	0.81	0.729	0.894	0.81	0.729	0.894	CLONAL	1	FALSE	1	0.529706656711051	2		535	499	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187104	38187104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758646155	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	146	656	1	ENST00000317025.8:c.1373C>T	p.Ala458Val	p.A458V	ENST00000317025	NM_023034.1	458	gCg/gTg	6/24	0.529706656711051	3	FACETS	0.919	0.84	1	0.459	0.42	0.501	CLONAL	1	FALSE	1	0.529706656711051	3		657	759	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509373	149509373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766614995	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	154	606	0	ENST00000261799.4:c.1526C>T	p.Thr509Met	p.T509M	ENST00000261799	NM_002609.3	509	aCg/aTg	10/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.529706656711051	2		606	504	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129868	69129868	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776942401	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	134	294	1	ENST00000288368.4:c.4622C>T	p.Thr1541Met	p.T1541M	ENST00000288368	NM_024870.2	1541	aCg/aTg	38/40	0.529706656711051	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	FALSE	1	0.529706656711051	3		295	307	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610129	28610129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	72	529	1	ENST00000241453.7:c.1361C>T	p.Ser454Leu	p.S454L	ENST00000241453	NM_004119.2	454	tCg/tTg	11/24	1	2	FACETS	0.842	0.741	0.948	0.842	0.741	0.948	CLONAL	1	FALSE	1	0.529706656711051	2		530	323	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731544	47731544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	31	26	1	ENST00000449228.1:c.248G>A	p.Arg83His	p.R83H	ENST00000449228	NM_001127240.2	83	cGc/cAc	2/4	1	2	FACETS	0.76	0.638	0.886	1	0.954	1	SUBCLONAL	2	FALSE	1	0.529706656711051	2		27	77	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400191	139400191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367710569	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	188	796	0	ENST00000277541.6:c.4157C>T	p.Pro1386Leu	p.P1386L	ENST00000277541	NM_017617.3	1386	cCg/cTg	25/34	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.529706656711051	2		796	567	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251216	115251216	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	107	527	0	ENST00000369535.4:c.510del	p.Lys170AsnfsTer19	p.K170Nfs*19	ENST00000369535	NM_002524.4	170	aaA/aa	5/7	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.529706656711051	2		527	318	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317192	11317192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	95	540	0	ENST00000361445.4:c.302C>T	p.Ala101Val	p.A101V	ENST00000361445	NM_004958.3	101	gCc/gTc	4/58	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	FALSE	1	0.529706656711051	2		540	356	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648209	206648209	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	85	359	0	ENST00000367120.3:c.230G>A	p.Gly77Asp	p.G77D	ENST00000367120	NM_014002.3	77	gGc/gAc	5/22	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.529706656711051	2		359	281	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434408	49434408	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	210	802	2	ENST00000301067.7:c.7145del	p.Pro2382HisfsTer2	p.P2382Hfs*2	ENST00000301067	NM_003482.3	2382	cCa/ca	31/54	0.529706656711051	3	FACETS	0.83	0.776	0.886	0.83	0.776	0.886	CLONAL	2	FALSE	1	0.529706656711051	3		804	604	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112919971	112919971	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	99	517	0	ENST00000351677.2:c.1186T>C	p.Tyr396His	p.Y396H	ENST00000351677	NM_002834.3	396	Tat/Cat	10/16	0.529706656711051	3	FACETS	1	0.979	1	0.677	0.61	0.747	CLONAL	1	FALSE	1	0.529706656711051	3		517	349	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972892	32972893	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs776212316	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	33	276	0	ENST00000380152.3:c.10248dup	p.Tyr3417IlefsTer21	p.Y3417Ifs*21	ENST00000380152		3414	-/A	27/27	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	FALSE	1	0.529706656711051	2		276	97	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131629	2131629	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	180	753	0	ENST00000219476.3:c.3644C>A	p.Pro1215Gln	p.P1215Q	ENST00000219476	NM_000548.3	1215	cCg/cAg	31/42	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.529706656711051	2		753	608	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346256	89346256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760007187	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	88	399	0	ENST00000301030.4:c.6694C>T	p.Arg2232Cys	p.R2232C	ENST00000301030	NM_001256183.1	2232	Cgt/Tgt	9/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.529706656711051	2		399	262	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574002	7574002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375338359	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	191	707	1	ENST00000269305.4:c.1025G>A	p.Arg342Gln	p.R342Q	ENST00000269305	NM_001126112.2	342	cGa/cAa	10/11	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	FALSE	1	0.529706656711051	2		708	720	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33430503	33430503	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	151	708	0	ENST00000345365.6:c.637T>C	p.Ser213Pro	p.S213P	ENST00000345365	NM_002878.3	213	Tcc/Ccc	7/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.529706656711051	2		708	521	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223613	36223614	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs765758919	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	201	907	1	ENST00000222270.7:c.6169dup	p.Arg2057ProfsTer3	p.R2057Pfs*3	ENST00000222270	NM_014727.1	2055	gcc/gCcc	28/37	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.529706656711051	2		908	692	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637373	47637374	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	77	691	0	ENST00000233146.2:c.508_509del	p.Gln170GlufsTer7	p.Q170Efs*7	ENST00000233146	NM_000251.2	169	atACag/atag	3/16	1	2	FACETS	0.923	0.818	1	0.923	0.818	1	CLONAL	1	FALSE	1	0.529706656711051	2		691	315	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131382	202131382	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	99	517	0	ENST00000358485.4:c.350A>T	p.Asn117Ile	p.N117I	ENST00000358485	NM_001080125.1	117	aAt/aTt	2/9	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.529706656711051	2		517	288	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141683	202141683	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	60	321	0	ENST00000358485.4:c.971T>C	p.Leu324Ser	p.L324S	ENST00000358485	NM_001080125.1	324	tTg/tCg	7/9	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.529706656711051	2		321	192	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730925	40730925	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	91	544	0	ENST00000373198.4:c.3610G>T	p.Val1204Leu	p.V1204L	ENST00000373198	NM_133170.3	1204	Gtg/Ttg	27/32	0.529706656711051	3	FACETS	1	0.935	1	0.533	0.476	0.592	CLONAL	1	FALSE	1	0.529706656711051	3		544	408	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518872	187518872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	59	454	1	ENST00000441802.2:c.12332C>T	p.Ala4111Val	p.A4111V	ENST00000441802	NM_005245.3	4111	gCc/gTc	24/27	1	2	FACETS	0.753	0.652	0.86	0.753	0.652	0.86	SUBCLONAL	1	FALSE	1	0.529706656711051	2		455	296	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672752	86672753	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	54	305	0	ENST00000274376.6:c.2241dup	p.Asp748ArgfsTer19	p.D748Rfs*19	ENST00000274376	NM_002890.2	747	caa/cAaa	17/25	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	1	0.529706656711051	2		305	167	SUCCESS
APC	324	MSKCC	GRCh37	5	112176856	112176856	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1064795688	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	29	341	0	ENST00000257430.4:c.5569del	p.Ser1857HisfsTer6	p.S1857Hfs*6	ENST00000257430	NM_000038.5	1855	tgT/tg	16/16	1	2	FACETS	0.766	0.623	0.923	0.766	0.623	0.923	CLONAL	1	FALSE	1	0.529706656711051	2		341	143	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449544	149449544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	132	672	1	ENST00000286301.3:c.1402G>A	p.Val468Met	p.V468M	ENST00000286301	NM_005211.3	468	Gtg/Atg	10/22	1	2	FACETS	0.942	0.86	1	0.942	0.86	1	CLONAL	1	FALSE	1	0.529706656711051	2		673	529	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827893	170827893	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	87	516	1	ENST00000296930.5:c.636del	p.Asp213ThrfsTer32	p.D213Tfs*32	ENST00000296930	NM_002520.6	211	ggA/gg	8/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.529706656711051	2		517	286	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43746640	43746640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	118	550	1	ENST00000523873.1:c.407G>A	p.Arg136Lys	p.R136K	ENST00000523873		136	aGa/aAa	5/8	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.529706656711051	2		551	404	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200293	138200293	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748312513	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	94	429	0	ENST00000237289.4:c.1711G>A	p.Val571Ile	p.V571I	ENST00000237289	NM_001270507.1	571	Gtc/Atc	7/9	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	FALSE	1	0.529706656711051	2		429	338	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099063	157099088	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	CATGGCCCATAACGCGGGCGCCGCGG	CATGGCCCATAACGCGGGCGCCGCGG	-	novel	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	41	247	0	ENST00000346085.5:c.1_26del	p.Met1_?9	p.M1_?9	ENST00000346085	NM_020732.3	1		1/20	1	2	FACETS	0.67	0.563	0.787	0.67	0.563	0.787	SUBCLONAL	1	FALSE	1	0.529706656711051	2		247	231	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231160	98231160	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502290	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	162	632	0	ENST00000331920.6:c.2123C>T	p.Thr708Ile	p.T708I	ENST00000331920	NM_000264.3	708	aCa/aTa	14/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.529706656711051	2		632	483	SUCCESS
AR	367	MSKCC	GRCh37	X	66765119	66765119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs962089572	NA	P-0041619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	79	570	0	ENST00000374690.3:c.131C>T	p.Ala44Val	p.A44V	ENST00000374690	NM_000044.3	44	gCc/gTc	1/8	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	1	0.529706656711051	2		570	281	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0041626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	116	464	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.997	0.899	1	0.997	0.899	1	CLONAL	1	TRUE	1	0.313067232324458	2		464	743	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862207	68862207	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	113	575	0	ENST00000261769.5:c.2295G>C	p.Gln765His	p.Q765H	ENST00000261769	NM_004360.3	765	caG/caC	14/16	0.313067232324458	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.313067232324458	1		575	574	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0041636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	194	547	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.679725516733451	2		547	525	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0041636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	342	508	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	0.657287063001047	3	FACETS	1	0.96	1	0.671	0.64	0.701	CLONAL	2	TRUE	0	0.679725516733451	3		508	670	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088788	27088788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	355	563	3	ENST00000324856.7:c.2402del	p.Gly801ValfsTer32	p.G801Vfs*32	ENST00000324856	NM_006015.4	799	caG/ca	7/20	1	2	FACETS	0.969	0.933	1	1	0.997	1	CLONAL	2	TRUE	1	0.679725516733451	2		566	539	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100727	8100728	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs771019738	NA	P-0041636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	208	649	0	ENST00000346208.3:c.708dup	p.Ser237GlnfsTer66	p.S237Qfs*66	ENST00000346208		234	ttc/ttCc	3/6	0.679725516733451	3	FACETS	0.887	0.824	0.953	0.444	0.412	0.477	CLONAL	1	TRUE	1	0.679725516733451	3		649	924	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683175	88683175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1418504897	NA	P-0041636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	16	357	0	ENST00000372037.3:c.1385C>T	p.Pro462Leu	p.P462L	ENST00000372037	NM_004329.2	462	cCg/cTg	12/13	0.657287063001047	3	FACETS	0.238	0.176	0.313	0.079	0.058	0.105	SUBCLONAL	1	TRUE	0	0.679725516733451	3		357	265	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0041636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	85	127	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.657287063001047	3	FACETS	1	0.974	1	0.781	0.716	0.844	CLONAL	2	TRUE	0	0.679725516733451	3		127	143	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212865	94212865	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	29	356	0	ENST00000323929.3:c.377A>G	p.His126Arg	p.H126R	ENST00000323929	NM_005591.3	126	cAt/cGt	5/20	1	2	FACETS	0.408	0.33	0.496	0.408	0.33	0.496	SUBCLONAL	1	TRUE	1	0.679725516733451	2		356	209	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427960	49427961	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0041636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	222	566	0	ENST00000301067.7:c.10629_10630del	p.Ala3544GlnfsTer11	p.A3544Qfs*11	ENST00000301067	NM_003482.3	3543	tgTGcc/tgcc	38/54	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.679725516733451	2		566	622	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120806011	120806011	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	234	631	1	ENST00000257552.2:c.166del	p.Leu56Ter	p.L56*	ENST00000257552	NM_002442.3	56	Ctg/tg	3/15	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.679725516733451	2		632	682	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562267	21562267	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	277	827	0	ENST00000382592.4:c.1652C>A	p.Pro551His	p.P551H	ENST00000382592	NM_014572.2	551	cCc/cAc	4/8	1	2	FACETS	0.98	0.923	1	0.98	0.923	1	CLONAL	1	TRUE	1	0.679725516733451	2		827	832	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435153	110435153	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	228	583	0	ENST00000375856.3:c.3248del	p.Pro1083ArgfsTer23	p.P1083Rfs*23	ENST00000375856	NM_003749.2	1083	cCg/cg	1/2	1	2	FACETS	0.945	0.884	1	0.945	0.884	1	CLONAL	1	TRUE	1	0.679725516733451	2		583	710	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562524	95562524	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	77	329	0	ENST00000393063.1:c.4733C>A	p.Ala1578Asp	p.A1578D	ENST00000393063	NM_030621.3	1578	gCt/gAt	24/28	1	2	FACETS	0.849	0.754	0.947	0.849	0.754	0.947	CLONAL	1	TRUE	1	0.679725516733451	2		329	267	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292902	91292902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	86	506	0	ENST00000355112.3:c.404C>T	p.Ala135Val	p.A135V	ENST00000355112	NM_000057.2	135	gCt/gTt	3/22	1	2	FACETS	0.948	0.85	1	0.948	0.85	1	CLONAL	1	TRUE	1	0.679725516733451	2		506	267	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122323	2122323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	216	735	0	ENST00000219476.3:c.2179C>A	p.Pro727Thr	p.P727T	ENST00000219476	NM_000548.3	727	Cct/Act	20/42	1	2	FACETS	0.951	0.889	1	0.951	0.889	1	CLONAL	1	TRUE	1	0.679725516733451	2		735	668	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640548	3640548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	186	823	0	ENST00000294008.3:c.3091C>T	p.His1031Tyr	p.H1031Y	ENST00000294008	NM_032444.2	1031	Cac/Tac	12/15	1	2	FACETS	0.682	0.631	0.735	0.682	0.631	0.735	SUBCLONAL	1	TRUE	1	0.679725516733451	2		823	802	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257144	19257144	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	189	671	1	ENST00000162023.5:c.819del	p.Thr274ProfsTer?	p.T274Pfs*?	ENST00000162023		273	ccC/cc	12/13	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.679725516733451	2		672	536	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160365	99160365	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	156	441	0	ENST00000074304.5:c.844G>T	p.Glu282Ter	p.E282*	ENST00000074304	NM_001134224.1	282	Gag/Tag	11/26	0.679725516733451	3	FACETS	0.976	0.897	1	0.488	0.448	0.529	CLONAL	1	TRUE	1	0.679725516733451	3		441	630	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182187	99182187	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	430	569	0	ENST00000074304.5:c.2253del	p.Ser752AlafsTer79	p.S752Afs*79	ENST00000074304	NM_001134224.1	751	tCc/tc	21/26	0.679725516733451	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.679725516733451	3		569	843	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437288	220437288	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1190141661	NA	P-0041636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	260	902	1	ENST00000243786.2:c.197del	p.Gly66AlafsTer61	p.G66Afs*61	ENST00000243786	NM_002191.3	64	ctG/ct	1/2	0.679725516733451	3	FACETS	0.935	0.876	0.996	0.468	0.438	0.498	CLONAL	1	TRUE	1	0.679725516733451	3		903	1096	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661762	227661762	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	160	693	0	ENST00000305123.5:c.1693G>T	p.Gly565Ter	p.G565*	ENST00000305123	NM_005544.2	565	Gga/Tga	1/2	0.679725516733451	3	FACETS	0.96	0.883	1	0.48	0.441	0.52	CLONAL	1	TRUE	1	0.679725516733451	3		693	657	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643569	52643570	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0041636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	73	417	0	ENST00000394830.3:c.2326_2327del	p.Leu776AlafsTer19	p.L776Afs*19	ENST00000394830	NM_018313.4	776	TTg/g	17/30	1	2	FACETS	0.888	0.787	0.992	0.888	0.787	0.992	CLONAL	1	TRUE	1	0.679725516733451	2		417	242	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916873	178916875	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	novel	NA	P-0041636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	79	580	0	ENST00000263967.3:c.263_265del	p.Arg88del	p.R88del	ENST00000263967	NM_006218.2	87	aGACga/aga	2/21	1	2	FACETS	0.775	0.688	0.865	0.775	0.688	0.865	SUBCLONAL	1	TRUE	1	0.679725516733451	2		580	300	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55597498	55597498	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769701248	NA	P-0041636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	47	299	0	ENST00000288135.5:c.2146G>A	p.Asp716Asn	p.D716N	ENST00000288135	NM_000222.2	716	Gat/Aat	15/21	1	2	FACETS	0.786	0.674	0.905	0.786	0.674	0.905	CLONAL	1	TRUE	1	0.679725516733451	2		299	176	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361190	66361190	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	84	289	1	ENST00000273854.3:c.982A>G	p.Thr328Ala	p.T328A	ENST00000273854	NM_004439.5	328	Acc/Gcc	4/18	1	2	FACETS	0.943	0.845	1	0.943	0.845	1	CLONAL	1	TRUE	1	0.679725516733451	2		290	262	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157520036	157520036	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554235028	NA	P-0041636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	182	428	0	ENST00000346085.5:c.4105C>T	p.Gln1369Ter	p.Q1369*	ENST00000346085	NM_020732.3	1369	Cag/Tag	17/20	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.679725516733451	2		428	528	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0041636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	123	408	10	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	1	2	FACETS	0.754	0.698	0.81	1	0.989	1	SUBCLONAL	2	TRUE	1	0.679725516733451	2		418	240	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1327796	1327798	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs761286705	NA	P-0041636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	70	516	0	ENST00000400841.2:c.83_85del	p.Glu28del	p.E28del	ENST00000400841		28	gAAGga/gga	2/6	1	2	FACETS	0.604	0.53	0.683	0.604	0.53	0.683	SUBCLONAL	1	TRUE	1	0.679725516733451	2		516	341	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240702	53240702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372082304	NA	P-0041636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	143	590	0	ENST00000375401.3:c.1378C>T	p.Arg460Trp	p.R460W	ENST00000375401	NM_004187.3	460	Cgg/Tgg	10/26	1	2	FACETS	0.805	0.738	0.874	0.805	0.738	0.874	CLONAL	1	TRUE	1	0.679725516733451	2		590	523	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	200	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.913	0.854	0.972	0.913	0.854	0.972	CLONAL	1	TRUE	1	0.892614862626572	2		126	491	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151932990	151932990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs76844681	NA	P-0041649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	57	67	1	ENST00000262189.6:c.2681G>A	p.Arg894Gln	p.R894Q	ENST00000262189	NM_170606.2	894	cGg/cAg	16/59	0.50765861170136	4	FACETS	1	0.972	1	0.497	0.436	0.561	INDETERMINATE	1	TRUE	1	0.892614862626572	4		68	162	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	104	522	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.892	0.807	0.981	0.892	0.807	0.981	CLONAL	1	TRUE	1	0.645704381163769	2		522	361	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	133	517	3	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.569	0.517	0.623	0.569	0.517	0.623	SUBCLONAL	1	TRUE	1	0.645704381163769	2		520	724	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	618	877	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.992	1	1	0.998	1	CLONAL	2	TRUE	1	0.645704381163769	2		883	906	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	185	627	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.879	0.815	0.945	0.879	0.815	0.945	CLONAL	1	TRUE	1	0.645704381163769	2		633	652	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	129	644	1	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	0.44	0.398	0.483	0.44	0.398	0.483	SUBCLONAL	1	TRUE	1	0.645704381163769	2		645	909	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913559	32913559	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359479	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	95	390	3	ENST00000380152.3:c.5073del	p.Lys1691AsnfsTer15	p.K1691Nfs*15	ENST00000380152		1689	gcA/gc	11/27	1	2	FACETS	0.829	0.745	0.917	0.829	0.745	0.917	CLONAL	1	TRUE	1	0.645704381163769	2		393	355	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	227	362	7	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.645704381163769	2		369	629	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346158	89346158	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs878855327	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	127	297	3	ENST00000301030.4:c.6792del	p.Ala2265ProfsTer72	p.A2265Pfs*72	ENST00000301030	NM_001256183.1	2264	ccC/cc	9/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.645704381163769	2		300	368	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715624	30715624	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	100	256	1	ENST00000295754.5:c.1282G>A	p.Glu428Lys	p.E428K	ENST00000295754	NM_003242.5	428	Gaa/Aaa	5/7	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.645704381163769	2		257	298	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803222	1803222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	492	863	0	ENST00000260795.2:c.574G>A	p.Gly192Ser	p.G192S	ENST00000260795		192	Ggc/Agc	4/17	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.645704381163769	2		863	1245	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411082	63411082	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	268	284	0	ENST00000330258.3:c.2085G>A	p.Trp695Ter	p.W695*	ENST00000330258	NM_152424.3	695	tgG/tgA	2/2	1	1	FACETS	0.77	0.74	0.798	1	0.996	1	SUBCLONAL	2	TRUE	0	0.645704381163769	1		284	365	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437427	110437427	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	254	514	0	ENST00000375856.3:c.974A>G	p.His325Arg	p.H325R	ENST00000375856	NM_003749.2	325	cAc/cGc	1/2	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.645704381163769	2		514	728	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416952	416953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs771545848	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	161	400	2	ENST00000399788.2:c.3597dup	p.Gly1200ArgfsTer7	p.G1200Rfs*7	ENST00000399788	NM_001042603.1	1199	-/A	23/28	1	2	FACETS	0.857	0.79	0.926	0.857	0.79	0.926	CLONAL	1	TRUE	1	0.645704381163769	2		402	582	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	158	758	4	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.578	0.53	0.629	0.578	0.53	0.629	SUBCLONAL	1	TRUE	1	0.645704381163769	2		762	846	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523731	176523731	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	307	657	0	ENST00000292408.4:c.2147del	p.Pro716GlnfsTer6	p.P716Qfs*6	ENST00000292408	NM_213647.1	714	tgC/tg	16/18	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.645704381163769	2		657	909	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29686010	29686010	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757391670	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	87	255	0	ENST00000356175.3:c.8074C>T	p.Arg2692Trp	p.R2692W	ENST00000356175	NM_000267.3	2692	Cgg/Tgg	55/57	1	2	FACETS	0.973	0.873	1	0.973	0.873	1	CLONAL	1	TRUE	1	0.645704381163769	2		255	277	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042041	42042041	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	157	551	0	ENST00000219905.7:c.6240del	p.Val2081TrpfsTer21	p.V2081Wfs*21	ENST00000219905	NM_001164273.1	2079	gAa/ga	17/24	1	2	FACETS	0.978	0.903	1	0.978	0.903	1	CLONAL	1	TRUE	1	0.645704381163769	2		551	497	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817720	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	102	417	0	ENST00000262367.5:c.3250dup	p.Ile1084AsnfsTer3	p.I1084Nfs*3	ENST00000262367	NM_004380.2	1084	atc/aAtc		1	2	FACETS	0.526	0.471	0.584	0.526	0.471	0.584	SUBCLONAL	1	TRUE	1	0.645704381163769	2		417	601	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500576	99500576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141802822	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	316	586	0	ENST00000268035.6:c.4009C>T	p.Arg1337Cys	p.R1337C	ENST00000268035	NM_000875.3	1337	Cgc/Tgc	21/21	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.645704381163769	2		586	841	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416076	49416076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	353	667	1	ENST00000301067.7:c.16399G>A	p.Gly5467Ser	p.G5467S	ENST00000301067	NM_003482.3	5467	Ggc/Agc	52/54	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.645704381163769	2		668	990	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158637068	158637069	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CA	CA	-	rs141073095	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	244	554	3	ENST00000263640.3:c.111_112del	p.Cys37Ter	p.C37*	ENST00000263640	NM_001105.4	37	tgTGaa/tgaa	4/11	1	2	FACETS	0.885	0.829	0.943	0.885	0.829	0.943	CLONAL	1	TRUE	1	0.645704381163769	2		557	854	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163985	47163985	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	75	267	0	ENST00000409792.3:c.2141G>A	p.Cys714Tyr	p.C714Y	ENST00000409792	NM_014159.6	714	tGc/tAc	3/21	1	2	FACETS	0.952	0.846	1	0.952	0.846	1	CLONAL	1	TRUE	1	0.645704381163769	2		267	244	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900783	3900783	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	260	556	0	ENST00000262367.5:c.313G>T	p.Gly105Trp	p.G105W	ENST00000262367	NM_004380.2	105	Ggg/Tgg	2/31	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.645704381163769	2		556	719	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142480	119142480	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	150	400	0	ENST00000264033.4:c.479A>G	p.His160Arg	p.H160R	ENST00000264033	NM_005188.3	160	cAc/cGc	3/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.645704381163769	2		400	448	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165888	118165889	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	187	395	0	ENST00000369448.3:c.400_401del	p.Leu134GlufsTer16	p.L134Efs*16	ENST00000369448	NM_017709.3	133	aCT/a	2/2	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.645704381163769	2		395	476	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243675647	243675647	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	33	203	0	ENST00000263826.5:c.1333A>T	p.Thr445Ser	p.T445S	ENST00000263826	NM_005465.4	445	Aca/Tca	12/13	1	2	FACETS	0.501	0.411	0.6	0.501	0.411	0.6	SUBCLONAL	1	TRUE	1	0.645704381163769	2		203	204	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115757	8115757	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	229	463	0	ENST00000346208.3:c.1103T>C	p.Met368Thr	p.M368T	ENST00000346208		368	aTg/aCg	6/6	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.645704381163769	2		463	677	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998741	100998741	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	435	899	1	ENST00000325455.5:c.1061C>T	p.Ala354Val	p.A354V	ENST00000325455	NM_001202474.3	354	gCt/gTt	1/8	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.645704381163769	2		900	1125	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905423	11905423	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	220	401	3	ENST00000396373.4:c.73C>T	p.Pro25Ser	p.P25S	ENST00000396373	NM_001987.4	25	Ccg/Tcg	2/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.645704381163769	2		404	597	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445883	49445883	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1248	243	1111	0	ENST00000301067.7:c.1583del	p.Pro528HisfsTer402	p.P528Hfs*402	ENST00000301067	NM_003482.3	528	cCa/ca	10/54	1	2	FACETS	0.505	0.47	0.541	0.505	0.47	0.541	SUBCLONAL	1	TRUE	1	0.645704381163769	2		1111	1491	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543206	65543206	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	187	320	0	ENST00000358664.4:c.471G>T	p.Met157Ile	p.M157I	ENST00000358664	NM_002382.4	157	atG/atT	5/5	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.645704381163769	2		320	454	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475340	40475340	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	263	543	0	ENST00000264657.5:c.1686G>A	p.Trp562Ter	p.W562*	ENST00000264657	NM_139276.2	562	tgG/tgA	19/24	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.645704381163769	2		543	737	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55729508	55729508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	494	867	0	ENST00000284073.2:c.776C>T	p.Ala259Val	p.A259V	ENST00000284073	NM_138962.2	259	gCa/gTa	11/14	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.645704381163769	2		867	1392	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265607	10265607	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	272	597	0	ENST00000340748.4:c.1570T>A	p.Tyr524Asn	p.Y524N	ENST00000340748		524	Tat/Aat	19/40	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.645704381163769	2		597	741	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963941	2963943	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	rs780842262	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	247	686	15	ENST00000396946.4:c.1864_1866del	p.Ser622del	p.S622del	ENST00000396946	NM_032415.4	622	TCC/-	15/25	1	2	FACETS	0.898	0.841	0.956	0.898	0.841	0.956	CLONAL	1	TRUE	1	0.645704381163769	2		701	852	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268945	55268945	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	360	802	0	ENST00000275493.2:c.3011A>G	p.Glu1004Gly	p.E1004G	ENST00000275493	NM_005228.3	1004	gAa/gGa	25/28	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.645704381163769	2		802	978	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0041661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	124	301	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.330927887853432	2	FACETS	0.934	0.853	1	0.934	0.853	1	CLONAL	2	TRUE	0	0.330927887853432	2		301	401	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0041661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	294	743	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.330927887853432	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.330927887853432	2		743	825	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0041661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	194	485	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.310211714774222	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.330927887853432	3		485	660	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0041661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	86	550	4	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.11661479085153	5	FACETS	1	0.971	1	0.328	0.29	0.368	INDETERMINATE	1	TRUE	1	0.330927887853432	5		554	593	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814667	43814667	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1302209849	NA	P-0041661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	78	508	0	ENST00000372470.3:c.1462G>C	p.Glu488Gln	p.E488Q	ENST00000372470	NM_005373.2	488	Gag/Cag	9/12	0.170819950264748	4	FACETS	0.949	0.834	1	0.475	0.417	0.537	INDETERMINATE	1	TRUE	2	0.330927887853432	4		508	661	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251753	212251753	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	63	392	0	ENST00000342788.4:c.3306T>G	p.Phe1102Leu	p.F1102L	ENST00000342788	NM_005235.2	1102	ttT/ttG	27/28	0.310211714774222	3	FACETS	1	0.93	1	0.556	0.483	0.635	CLONAL	1	TRUE	1	0.330927887853432	3		392	399	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71064703	71064703	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	76	422	0	ENST00000318789.4:c.971T>C	p.Leu324Pro	p.L324P	ENST00000318789	NM_032682.5	324	cTa/cCa	12/21	0.310211714774222	3	FACETS	0.926	0.813	1	0.463	0.406	0.524	CLONAL	1	TRUE	1	0.330927887853432	3		422	578	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005560	150005560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	22	355	0	ENST00000253339.5:c.665C>T	p.Ala222Val	p.A222V	ENST00000253339		222	gCa/gTa	3/7	0.110600120556391	4	FACETS	0.448	0.347	0.566	0.224	0.173	0.283	INDETERMINATE	1	TRUE	2	0.330927887853432	4		355	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0041665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	115	853	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.245014264610376	1	FACETS	0.991	0.893	1	0.991	0.893	1	CLONAL	1	TRUE	0	0.253665274210565	1		853	799	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0041665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	92	881	2	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	0.225353043676581	1	FACETS	0.856	0.76	0.958	0.856	0.76	0.958	CLONAL	1	TRUE	0	0.253665274210565	1		883	740	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238958	5238958	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	64	728	0	ENST00000357368.4:c.1821del	p.Val608TrpfsTer30	p.V608Wfs*30	ENST00000357368	NM_002850.3	607	ccC/cc	13/38	0.225353043676581	1	FACETS	0.768	0.665	0.879	0.768	0.665	0.879	SUBCLONAL	1	TRUE	0	0.253665274210565	1		728	574	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468036	120468036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs919872084	NA	P-0041665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	82	774	0	ENST00000256646.2:c.4403C>T	p.Ser1468Phe	p.S1468F	ENST00000256646	NM_024408.3	1468	tCc/tTc	25/34	1	2	FACETS	0.871	0.768	0.982	0.871	0.768	0.982	CLONAL	1	TRUE	1	0.253665274210565	2		774	742	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198278	185198278	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	78	650	0	ENST00000265026.3:c.2760G>T	p.Met920Ile	p.M920I	ENST00000265026	NM_004721.4	920	atG/atT	13/14	1	2	FACETS	0.896	0.788	1	0.896	0.788	1	CLONAL	1	TRUE	1	0.253665274210565	2		650	686	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0041678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	152	441	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.460880628658239	2		441	518	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100738	8100738	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	85	700	0	ENST00000346208.3:c.712A>T	p.Ser238Cys	p.S238C	ENST00000346208		238	Agc/Tgc	3/6	1	2	FACETS	0.389	0.343	0.439	0.389	0.343	0.439	SUBCLONAL	1	TRUE	1	0.460880628658239	2		700	948	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621148	1621148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	280	803	2	ENST00000344749.5:c.998G>A	p.Gly333Asp	p.G333D	ENST00000344749	NM_001136139.2	333	gGc/gAc	12/19	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.460880628658239	2		805	1001	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566086	141566086	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	212	580	0	ENST00000220592.5:c.1178A>T	p.Tyr393Phe	p.Y393F	ENST00000220592	NM_012154.3	393	tAc/tTc	10/19	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.460880628658239	2		580	823	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183755	10183757	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs5030648	NA	P-0041690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	91	638	0	ENST00000256474.2:c.227_229del	p.Phe76del	p.F76del	ENST00000256474	NM_000551.3	75	aTCTtc/atc	1/3	0.527948535223941	1	FACETS	0.725	0.65	0.803	0.725	0.65	0.803	SUBCLONAL	1	TRUE	0	0.556088943516265	1		638	326	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201089	108201089	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779865	NA	P-0041690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	30	317	0	ENST00000278616.4:c.7456C>T	p.Arg2486Ter	p.R2486*	ENST00000278616	NM_000051.3	2486	Cga/Tga	50/63	1	2	FACETS	0.5	0.405	0.605	0.5	0.405	0.605	SUBCLONAL	1	TRUE	1	0.556088943516265	2		317	216	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52621381	52621382	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0041690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	56	325	0	ENST00000394830.3:c.3035_3036delinsAT	p.Val1012Asp	p.V1012D	ENST00000394830	NM_018313.4	1012	gTC/gAT	20/30	0.527948535223941	1	FACETS	0.881	0.771	0.997	0.881	0.771	0.997	CLONAL	1	TRUE	0	0.556088943516265	1		325	165	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763884	76763884	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	26	503	0	ENST00000373344.5:c.7424C>T	p.Ala2475Val	p.A2475V	ENST00000373344	NM_000489.3	2475	gCa/gTa	35/35	1	2	FACETS	0.233	0.184	0.289	0.233	0.184	0.289	SUBCLONAL	1	TRUE	1	0.556088943516265	2		503	402	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0041701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	58	301	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.250193567758662	4	FACETS	0.958	0.823	1			1	CLONAL	1	FALSE	NA	0.268433256301379	4		301	572	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0041701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	168	423	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	0.250193567758662	4	FACETS	0.954	0.882	1			1	CLONAL	3	FALSE	NA	0.268433256301379	4		423	555	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659245	86659245	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554048066	NA	P-0041701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	32	277	1	ENST00000274376.6:c.1534C>T	p.Arg512Ter	p.R512*	ENST00000274376	NM_002890.2	512	Cga/Tga	11/25	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	FALSE	1	0.268433256301379	2		278	225	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	125	807	0	ENST00000267101.3:c.310G>C	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ctg	3/28	0.268433256301379	3	FACETS	1	0.904	1	0.5	0.452	0.552	CLONAL	1	FALSE	1	0.268433256301379	3		807	1056	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612752	228612752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	244	771	0	ENST00000366696.1:c.275C>T	p.Ala92Val	p.A92V	ENST00000366696	NM_003493.2	92	gCg/gTg	1/1	0.235656622407854	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	FALSE	1	0.268433256301379	3		771	960	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196191	108196191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	150	553	0	ENST00000278616.4:c.6727C>T	p.Gln2243Ter	p.Q2243*	ENST00000278616	NM_000051.3	2243	Caa/Taa	46/63	0.257276448953701	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	FALSE	0	0.268433256301379	2		553	538	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610118	28610118	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	132	614	0	ENST00000241453.7:c.1372C>T	p.Pro458Ser	p.P458S	ENST00000241453	NM_004119.2	458	Cca/Tca	11/24	0.268433256301379	4	FACETS	0.755	0.686	0.828	0.503	0.457	0.552	SUBCLONAL	2	FALSE	1	0.268433256301379	4		614	826	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225365137	225365137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	63	486	0	ENST00000264414.4:c.1553C>T	p.Ala518Val	p.A518V	ENST00000264414	NM_003590.4	518	gCc/gTc	11/16	0.235656622407854	3	FACETS	0.902	0.781	1	0.451	0.39	0.518	CLONAL	1	FALSE	1	0.268433256301379	3		486	590	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020808	112020808	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	73	412	0	ENST00000368678.4:c.763G>A	p.Gly255Arg	p.G255R	ENST00000368678		255	Gga/Aga	8/13	1	2	FACETS	0.911	0.797	1	0.911	0.797	1	CLONAL	1	FALSE	1	0.268433256301379	2		412	597	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815601	139815601	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	130	783	0	ENST00000247668.2:c.1072A>T	p.Ile358Phe	p.I358F	ENST00000247668	NM_021138.3	358	Atc/Ttc	9/11	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	FALSE	1	0.268433256301379	2		783	936	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11313952	11313952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	181	843	0	ENST00000361445.4:c.784C>T	p.His262Tyr	p.H262Y	ENST00000361445	NM_004958.3	262	Cat/Tat	6/58	0.492279073078143	3	FACETS	1	0.949	1	0.518	0.478	0.56	CLONAL	1	TRUE	1	0.520322471277522	3		843	846	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255014	16255014	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778549803	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	116	424	0	ENST00000375759.3:c.2279C>T	p.Ser760Leu	p.S760L	ENST00000375759	NM_015001.2	760	tCa/tTa	11/15	0.492279073078143	3	FACETS	1	0.963	1	0.563	0.51	0.619	CLONAL	1	TRUE	1	0.520322471277522	3		424	499	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416104	49416104	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	228	656	0	ENST00000301067.7:c.16371T>G	p.Asn5457Lys	p.N5457K	ENST00000301067	NM_003482.3	5457	aaT/aaG	52/54	0.374818552652989	4	FACETS	0.905	0.847	0.965			1	CLONAL	2	TRUE	NA	0.520322471277522	4		656	736	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426174	49426174	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	202	889	1	ENST00000301067.7:c.12314T>C	p.Val4105Ala	p.V4105A	ENST00000301067	NM_003482.3	4105	gTt/gCt	39/54	0.374818552652989	4	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.520322471277522	4		890	1011	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859574	57859574	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	102	713	0	ENST00000228682.2:c.628C>T	p.Pro210Ser	p.P210S	ENST00000228682	NM_005269.2	210	Ccc/Tcc	7/12	0.381191871892994	4	FACETS	0.78	0.698	0.868	0.39	0.349	0.434	SUBCLONAL	1	TRUE	2	0.520322471277522	4		713	764	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218320	133218320	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1285538355	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	338	924	0	ENST00000320574.5:c.5291C>T	p.Ala1764Val	p.A1764V	ENST00000320574	NM_006231.2	1764	gCc/gTc	39/49	0.438324690975826	3	FACETS	0.949	0.901	0.997	0.949	0.901	0.997	CLONAL	2	TRUE	1	0.520322471277522	3		924	863	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225568	133225568	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	116	920	0	ENST00000320574.5:c.4096T>A	p.Phe1366Ile	p.F1366I	ENST00000320574	NM_006231.2	1366	Ttc/Atc	32/49	0.438324690975826	3	FACETS	0.739	0.666	0.816	0.37	0.333	0.408	SUBCLONAL	1	TRUE	1	0.520322471277522	3		920	760	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28624322	28624322	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866313760	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	247	608	0	ENST00000241453.7:c.652G>A	p.Glu218Lys	p.E218K	ENST00000241453	NM_004119.2	218	Gaa/Aaa	6/24	0.498322262115035	4	FACETS	0.929	0.872	0.987	0.929	0.872	0.987	CLONAL	2	TRUE	2	0.520322471277522	4		608	777	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001434	29001434	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	75	393	0	ENST00000282397.4:c.1298A>C	p.Lys433Thr	p.K433T	ENST00000282397	NM_002019.4	433	aAg/aCg	10/30	0.498322262115035	4	FACETS	0.915	0.804	1	0.457	0.402	0.517	CLONAL	1	TRUE	2	0.520322471277522	4		393	479	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008327	29008327	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	91	350	0	ENST00000282397.4:c.544A>T	p.Lys182Ter	p.K182*	ENST00000282397	NM_002019.4	182	Aaa/Taa	5/30	0.498322262115035	4	FACETS	1	0.959	1	0.578	0.515	0.644	CLONAL	1	TRUE	2	0.520322471277522	4		350	460	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041183	29041183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	144	791	0	ENST00000282397.4:c.245G>A	p.Gly82Glu	p.G82E	ENST00000282397	NM_002019.4	82	gGa/gAa	3/30	0.498322262115035	4	FACETS	0.908	0.827	0.992	0.454	0.413	0.496	CLONAL	1	TRUE	2	0.520322471277522	4		791	927	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068872	30068872	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	148	685	0	ENST00000331968.5:c.2057T>C	p.Leu686Ser	p.L686S	ENST00000331968	NM_002742.2	686	tTa/tCa	14/18	0.381191871892994	4	FACETS	1	0.959	1	0.541	0.494	0.589	CLONAL	1	TRUE	2	0.520322471277522	4		685	800	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614532	38614533	+	missense_variant	Missense_Mutation	DNP	GG	GG	AC	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	143	743	1	ENST00000299084.4:c.298_299delinsAC	p.Gly100Thr	p.G100T	ENST00000299084	NM_152594.2	100	GGt/ACt	3/7	0.364740480935148	3	FACETS	0.887	0.809	0.968	0.443	0.404	0.484	CLONAL	1	TRUE	1	0.520322471277522	3		744	781	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032353	42032353	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779785984	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	171	627	0	ENST00000219905.7:c.4537C>T	p.Arg1513Cys	p.R1513C	ENST00000219905	NM_001164273.1	1513	Cgc/Tgc	14/24	0.364740480935148	3	FACETS	1	0.983	1	0.618	0.57	0.667	CLONAL	1	TRUE	1	0.520322471277522	3		627	670	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43766957	43766957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	44	229	0	ENST00000382044.4:c.1094C>T	p.Ser365Leu	p.S365L	ENST00000382044	NM_001141980.1	365	tCa/tTa	10/28	0.364740480935148	3	FACETS	0.692	0.583	0.811	0.346	0.291	0.406	SUBCLONAL	1	TRUE	1	0.520322471277522	3		229	308	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630407	90630407	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	150	755	0	ENST00000330062.3:c.904G>A	p.Gly302Ser	p.G302S	ENST00000330062	NM_002168.2	302	Ggt/Agt	7/11	0.520322471277522	5	FACETS	0.869	0.793	0.95	0.217	0.198	0.238	CLONAL	1	TRUE	1	0.520322471277522	5		755	1181	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99491843	99491843	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	110	730	0	ENST00000268035.6:c.3628G>T	p.Glu1210Ter	p.E1210*	ENST00000268035	NM_000875.3	1210	Gag/Tag	20/21	0.520322471277522	5	FACETS	0.698	0.625	0.775	0.174	0.156	0.194	SUBCLONAL	1	TRUE	1	0.520322471277522	5		730	1079	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094704	2094704	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	177	988	0	ENST00000219066.1:c.476T>G	p.Leu159Arg	p.L159R	ENST00000219066	NM_002528.5	159	cTg/cGg	3/6	0.381191871892994	4	FACETS	0.878	0.808	0.952	0.439	0.404	0.476	CLONAL	1	TRUE	2	0.520322471277522	4		988	1178	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639374	3639374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	192	969	1	ENST00000294008.3:c.4265C>T	p.Pro1422Leu	p.P1422L	ENST00000294008	NM_032444.2	1422	cCa/cTa	12/15	0.381191871892994	4	FACETS	1	0.964	1	0.535	0.494	0.577	CLONAL	1	TRUE	2	0.520322471277522	4		970	1049	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892299	9892299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs796052549	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	177	512	0	ENST00000330684.3:c.2191G>A	p.Asp731Asn	p.D731N	ENST00000330684	NM_001134407.1	731	Gat/Aat	11/13	0.381191871892994	4	FACETS	0.961	0.892	1	0.961	0.892	1	CLONAL	2	TRUE	2	0.520322471277522	4		512	538	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588830	29588830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	98	424	0	ENST00000356175.3:c.4616C>T	p.Ser1539Phe	p.S1539F	ENST00000356175	NM_000267.3	1539	tCc/tTc	34/57	0.498322262115035	4	FACETS	0.919	0.821	1	0.46	0.41	0.512	CLONAL	1	TRUE	2	0.520322471277522	4		424	623	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879857	37879857	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	380	845	0	ENST00000269571.5:c.2152A>T	p.Thr718Ser	p.T718S	ENST00000269571		718	Acg/Tcg	18/27	0.498322262115035	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.520322471277522	4		845	1065	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245006	41245006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	359	866	0	ENST00000357654.3:c.2542G>A	p.Glu848Lys	p.E848K	ENST00000357654	NM_007294.3	848	Gaa/Aaa	10/23	0.498322262115035	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.520322471277522	4		866	1015	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761133	59761133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768065626	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	169	697	0	ENST00000259008.2:c.3274C>T	p.Pro1092Ser	p.P1092S	ENST00000259008	NM_032043.2	1092	Ccg/Tcg	20/20	0.498322262115035	4	FACETS	1	0.965	1	0.544	0.5	0.59	CLONAL	1	TRUE	2	0.520322471277522	4		697	908	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119234	3119234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775040372	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	393	990	0	ENST00000078429.4:c.766C>T	p.Arg256Trp	p.R256W	ENST00000078429	NM_002067.2	256	Cgg/Tgg	6/7	0.454507194498805	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.520322471277522	4		990	1121	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172347	7172347	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	169	681	0	ENST00000302850.5:c.1222T>A	p.Phe408Ile	p.F408I	ENST00000302850	NM_000208.2	408	Ttc/Atc	5/22	0.454507194498805	4	FACETS	1	0.966	1	0.547	0.503	0.593	CLONAL	1	TRUE	2	0.520322471277522	4		681	903	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291170	10291171	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	208	942	1	ENST00000340748.4:c.300_301delinsTT	p.Arg101Trp	p.R101W	ENST00000340748		100	aaCCgg/aaTTgg	4/40	0.492279073078143	3	FACETS	1	0.97	1	0.54	0.501	0.58	CLONAL	1	TRUE	1	0.520322471277522	3		943	933	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260213	19260213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	190	924	0	ENST00000162023.5:c.80G>A	p.Gly27Glu	p.G27E	ENST00000162023		27	gGg/gAg	7/13	0.492279073078143	3	FACETS	1	0.936	1	0.506	0.468	0.546	CLONAL	1	TRUE	1	0.520322471277522	3		924	909	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758775	41758775	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374737642	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	400	967	0	ENST00000301178.4:c.1829G>A	p.Arg610Gln	p.R610Q	ENST00000301178	NM_021913.4	610	cGa/cAa	16/20	0.454507194498805	4	FACETS	0.987	0.94	1	0.987	0.94	1	CLONAL	2	TRUE	2	0.520322471277522	4		967	1184	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086010	16086010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	104	751	0	ENST00000281043.3:c.1186G>A	p.Asp396Asn	p.D396N	ENST00000281043	NM_005378.4	396	Gac/Aac	3/3	0.381191871892994	4	FACETS	0.784	0.702	0.871	0.392	0.351	0.436	SUBCLONAL	1	TRUE	2	0.520322471277522	4		751	775	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086052	16086052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	130	795	0	ENST00000281043.3:c.1228G>A	p.Glu410Lys	p.E410K	ENST00000281043	NM_005378.4	410	Gag/Aag	3/3	0.381191871892994	4	FACETS	0.848	0.769	0.931	0.424	0.384	0.466	CLONAL	1	TRUE	2	0.520322471277522	4		795	896	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622630	158622630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	241	598	1	ENST00000263640.3:c.869C>T	p.Ser290Leu	p.S290L	ENST00000263640	NM_001105.4	290	tCg/tTg	8/11	0.381191871892994	4	FACETS	0.94	0.882	1	0.94	0.882	1	CLONAL	2	TRUE	2	0.520322471277522	4		599	749	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057302	30057302	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315496	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	239	557	0	ENST00000338641.4:c.784C>T	p.Arg262Ter	p.R262*	ENST00000338641	NM_000268.3	262	Cga/Tga	8/16	0.520322471277522	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.520322471277522	2		557	444	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627277	37627277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2676	202	987	0	ENST00000249071.6:c.442G>A	p.Glu148Lys	p.E148K	ENST00000249071	NM_002872.4	148	Gag/Aag	5/7	0.520322471277522	11	FACETS	0.901	0.831	0.976			1	CLONAL	1	TRUE	NA	0.520322471277522	11		987	2878	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	63	458	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	0.498322262115035	4	FACETS	0.655	0.567	0.751	0.328	0.283	0.376	SUBCLONAL	1	TRUE	2	0.520322471277522	4		458	562	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391084	89391084	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	357	851	0	ENST00000336596.2:c.1150C>T	p.Pro384Ser	p.P384S	ENST00000336596	NM_005233.5	384	Cct/Tct	5/17	0.498322262115035	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.520322471277522	4		851	982	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238559	142238559	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	84	339	1	ENST00000350721.4:c.4334G>A	p.Arg1445Lys	p.R1445K	ENST00000350721	NM_001184.3	1445	aGa/aAa	24/47	0.520322471277522	3	FACETS	0.976	0.866	1	0.488	0.433	0.546	CLONAL	1	TRUE	1	0.520322471277522	3		340	417	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937476	178937476	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	138	695	0	ENST00000263967.3:c.1864T>G	p.Tyr622Asp	p.Y622D	ENST00000263967	NM_006218.2	622	Tat/Gat	12/21	0.520322471277522	3	FACETS	0.986	0.899	1	0.493	0.449	0.539	CLONAL	1	TRUE	1	0.520322471277522	3		695	678	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532623	187532623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1331743336	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	235	518	1	ENST00000441802.2:c.9770G>A	p.Arg3257Gln	p.R3257Q	ENST00000441802	NM_005245.3	3257	cGg/cAg	14/27	0.454507194498805	4	FACETS	0.988	0.926	1	0.988	0.926	1	CLONAL	2	TRUE	2	0.520322471277522	4		519	695	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540005	187540005	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	118	518	0	ENST00000441802.2:c.7735T>A	p.Phe2579Ile	p.F2579I	ENST00000441802	NM_005245.3	2579	Ttc/Atc	10/27	0.454507194498805	4	FACETS	1	0.948	1	0.536	0.485	0.591	CLONAL	1	TRUE	2	0.520322471277522	4		518	643	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264520	1264520	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	107	582	0	ENST00000310581.5:c.2842A>T	p.Ser948Cys	p.S948C	ENST00000310581	NM_198253.2	948	Agc/Tgc	11/16	0.454507194498805	4	FACETS	1	0.916	1	0.511	0.459	0.566	CLONAL	1	TRUE	2	0.520322471277522	4		582	612	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	144	478	1				ENST00000310581	NM_198253.2	-/1132			0.454507194498805	4	FACETS	1	0.985	1	0.689	0.63	0.749	CLONAL	1	TRUE	2	0.520322471277522	4		479	611	SUCCESS
APC	324	MSKCC	GRCh37	5	112179054	112179054	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1554088648	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	112	407	0	ENST00000257430.4:c.7763A>G	p.Asp2588Gly	p.D2588G	ENST00000257430	NM_000038.5	2588	gAt/gGt	16/16	0.520322471277522	3	FACETS	1	0.963	1	0.565	0.511	0.622	CLONAL	1	TRUE	1	0.520322471277522	3		407	480	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923285	131923285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	139	262	0	ENST00000265335.6:c.788C>T	p.Ser263Phe	p.S263F	ENST00000265335		263	tCt/tTt	6/25	0.520322471277522	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.520322471277522	3		262	298	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	709	1017	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	0.520322471277522	5	FACETS	0.989	0.955	1	0.989	0.955	1	CLONAL	3	TRUE	2	0.520322471277522	5		1017	1636	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978784	13978784	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	220	722	1	ENST00000405192.2:c.323C>T	p.Pro108Leu	p.P108L	ENST00000405192	NM_001163147.1	108	cCc/cTc	6/12	0.400687286135454	5	FACETS	1	0.991	1	0.475	0.441	0.509	CLONAL	1	TRUE	2	0.520322471277522	5		723	1057	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913355	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	97	531	1	ENST00000288602.6:c.1406G>A	p.Gly469Glu	p.G469E	ENST00000288602	NM_004333.4	469	gGa/gAa	11/18	0.357010216609949	6	FACETS	1	0.926	1	0.35	0.312	0.39	CLONAL	1	TRUE	3	0.520322471277522	6		532	725	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38157094	38157095	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	153	714	3	ENST00000317025.8:c.2625_2626delinsAA	p.Asp876Asn	p.D876N	ENST00000317025	NM_023034.1	875	caGGac/caAAac	15/24	0.48943671551243	5	FACETS	0.923	0.842	1			1	CLONAL	1	TRUE	NA	0.520322471277522	5		717	1135	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970945	70970945	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242917883	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	177	892	2	ENST00000276594.2:c.1316G>A	p.Arg439Gln	p.R439Q	ENST00000276594	NM_024504.3	439	cGa/cAa	6/8	0.454507194498805	4	FACETS	0.964	0.887	1	0.482	0.443	0.522	CLONAL	1	TRUE	2	0.520322471277522	4		894	1073	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595234	141595234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	170	807	0	ENST00000220592.5:c.199C>T	p.Pro67Ser	p.P67S	ENST00000220592	NM_012154.3	67	Ccg/Tcg	2/19	0.454507194498805	4	FACETS	0.897	0.823	0.973	0.448	0.411	0.487	CLONAL	1	TRUE	2	0.520322471277522	4		807	1108	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918578	44918578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	96	537	0	ENST00000377967.4:c.1061C>T	p.Ala354Val	p.A354V	ENST00000377967	NM_021140.2	354	gCc/gTc	12/29	0.505075550097374	3	FACETS	0.86	0.768	0.956			1	CLONAL	1	TRUE	NA	0.520322471277522	3		537	541	SUCCESS
AR	367	MSKCC	GRCh37	X	66766136	66766136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	157	770	0	ENST00000374690.3:c.1148C>T	p.Pro383Leu	p.P383L	ENST00000374690	NM_000044.3	383	cCc/cTc	1/8	0.333709271390665	3	FACETS	1	0.95	1			1	CLONAL	1	TRUE	NA	0.520322471277522	3		770	726	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0041740-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	27	512	1	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		513	496	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414399	6414399	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041740-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	61	232	0	ENST00000356142.4:c.33C>A	p.Asp11Glu	p.D11E	ENST00000356142	NM_018890.3	11	gaC/gaA	1/7	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		232	434	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425787	49425788	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0041740-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	33	751	0	ENST00000301067.7:c.12700_12701del	p.Gln4235GlyfsTer98	p.Q4235Gfs*98	ENST00000301067	NM_003482.3	4234	AGt/t	39/54	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		751	576	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444181	49444181	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041740-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	55	1054	1	ENST00000301067.7:c.3190del	p.Val1064SerfsTer55	p.V1064Sfs*55	ENST00000301067	NM_003482.3	1064	Gtc/tc	11/54	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		1055	1065	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252155	226252156	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0041740-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	17	153	0	ENST00000366813.1:c.103_104delinsTT	p.Gly35Leu	p.G35L	ENST00000366813		35	GGg/TTg	1/3	0.25441795045112	3	FACETS		NA	1			1	NA	NA	TRUE	1	NA	3		153	245	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741846	17741846	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041740-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	20	182	0	ENST00000250003.3:c.517G>T	p.Gly173Cys	p.G173C	ENST00000250003	NM_002478.4	173	Ggc/Tgc	1/3	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		182	221	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0041871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	259	535	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.438821506226031	2		535	1135	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0041871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	288	370	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.991	0.93	1	0.991	0.93	1	CLONAL	1	TRUE	1	0.438821506226031	2		370	1325	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0041871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	107	417	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.865	0.778	0.956	0.865	0.778	0.956	CLONAL	1	TRUE	1	0.438821506226031	2		417	564	SUCCESS
APC	324	MSKCC	GRCh37	5	112154935	112154935	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	203	656	0	ENST00000257430.4:c.1206del	p.Glu403LysfsTer51	p.E403Kfs*51	ENST00000257430	NM_000038.5	402	cgT/cg	10/16	1	2	FACETS	0.922	0.854	0.991	0.922	0.854	0.991	CLONAL	1	TRUE	1	0.438821506226031	2		656	1004	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380283	25380283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913528	NA	P-0041871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	125	501	2	ENST00000311936.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000311936	NM_004985.3	59	Gca/Aca	3/5	0.183622613317066	1	FACETS	0.699	0.634	0.767	0.699	0.634	0.767	INDETERMINATE	1	TRUE	0	0.438821506226031	1		503	636	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs121913468	NA	P-0041871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	197	537	1	ENST00000269571.5:c.2305G>A	p.Asp769Asn	p.D769N	ENST00000269571		769	Gac/Aac	19/27	1	2	FACETS	0.951	0.881	1	0.951	0.881	1	CLONAL	1	TRUE	1	0.438821506226031	2		538	944	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966652	36966652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749999635	NA	P-0041871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	190	535	0	ENST00000358127.4:c.674G>A	p.Arg225Gln	p.R225Q	ENST00000358127	NM_001280556.1	225	cGg/cAg	6/10	1	2	FACETS	0.972	0.899	1	0.972	0.899	1	CLONAL	1	TRUE	1	0.438821506226031	2		535	891	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280683	41280683	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	122	689	0	ENST00000349496.5:c.2199del	p.Met734Ter	p.M734*	ENST00000349496	NM_001904.3	732	gaC/ga	15/15	1	2	FACETS	0.59	0.532	0.65	0.59	0.532	0.65	SUBCLONAL	1	TRUE	1	0.438821506226031	2		689	943	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0041878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	124	522	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.640193369949578	3	FACETS	1	0.941	1	0.522	0.475	0.571	CLONAL	1	TRUE	1	0.657847348215036	3		522	480	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0041878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	295	458	0				ENST00000310581	NM_198253.2	-/1132			0.547709998150654	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.657847348215036	3		458	587	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909523	50909523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	495	1044	0	ENST00000440232.2:c.1327C>T	p.Arg443Trp	p.R443W	ENST00000440232	NM_002691.3	443	Cgg/Tgg	11/27	1	2	FACETS	0.972	0.93	1	0.972	0.93	1	CLONAL	1	TRUE	1	0.657847348215036	2		1044	1548	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492909	8492909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	375	694	0	ENST00000356435.5:c.2420G>A	p.Gly807Glu	p.G807E	ENST00000356435		807	gGa/gAa	16/35	0.657847348215036	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.657847348215036	1		694	715	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852222	128852222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1424	421	1050	1	ENST00000249373.3:c.2294G>A	p.Gly765Asp	p.G765D	ENST00000249373	NM_005631.4	765	gGc/gAc	12/12	0.640193369949578	3	FACETS	0.922	0.875	0.969	0.461	0.437	0.485	CLONAL	1	TRUE	1	0.657847348215036	3		1051	1845	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343429	118343430	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	227	573	1	ENST00000534358.1:c.1555_1556delinsTT	p.Pro519Leu	p.P519L	ENST00000534358	NM_005933.3	519	CCa/TTa	3/36	1	2	FACETS	0.89	0.832	0.95	0.89	0.832	0.95	CLONAL	1	TRUE	1	0.657847348215036	2		574	775	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231466	46231466	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	75	350	0	ENST00000334344.6:c.1306A>G	p.Ile436Val	p.I436V	ENST00000334344	NM_152641.2	436	Att/Gtt	10/21	0.657847348215036	1	FACETS	0.814	0.729	0.901	0.814	0.729	0.901	CLONAL	1	TRUE	0	0.657847348215036	1		350	188	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987190	36987190	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	348	755	0	ENST00000354822.5:c.499A>G	p.Met167Val	p.M167V	ENST00000354822	NM_001079668.2	167	Atg/Gtg	3/3	1	2	FACETS	0.997	0.946	1	0.997	0.946	1	CLONAL	1	TRUE	1	0.657847348215036	2		755	1061	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774113	66774113	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	428	1136	0	ENST00000307102.5:c.589C>G	p.Leu197Val	p.L197V	ENST00000307102	NM_002755.3	197	Cta/Gta	6/11	1	2	FACETS	0.898	0.855	0.942	0.898	0.855	0.942	CLONAL	1	TRUE	1	0.657847348215036	2		1136	1449	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2113022	2113022	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	380	777	0	ENST00000219476.3:c.1411T>C	p.Phe471Leu	p.F471L	ENST00000219476	NM_000548.3	471	Ttt/Ctt	14/42	1	2	FACETS	0.95	0.902	0.999	0.95	0.902	0.999	CLONAL	1	TRUE	1	0.657847348215036	2		777	1216	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683632	162683632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	312	627	0	ENST00000366898.1:c.337C>T	p.Pro113Ser	p.P113S	ENST00000366898	NM_004562.2	113	Cca/Tca	3/12	1	2	FACETS	0.946	0.893	0.999	0.946	0.893	0.999	CLONAL	1	TRUE	1	0.657847348215036	2		627	1003	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151935870	151935871	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	26	8	0	ENST00000262189.6:c.2573_2574delinsAA	p.Trp858Ter	p.W858*	ENST00000262189	NM_170606.2	858	tGG/tAA	15/59	0.640193369949578	3	FACETS	1	0.921	1	1	0.964	1	CLONAL	3	TRUE	1	0.657847348215036	3		8	33	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760660	133760660	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1162	521	1236	0	ENST00000318560.5:c.2983G>A	p.Asp995Asn	p.D995N	ENST00000318560	NM_005157.4	995	Gac/Aac	11/11	1	2	FACETS	0.941	0.901	0.982	0.941	0.901	0.982	CLONAL	1	TRUE	1	0.657847348215036	2		1236	1683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0041879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	364	668	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.277876634581366	3	FACETS	1	0.987	1	0.736	0.699	0.773	CLONAL	2	FALSE	0	0.388730710099386	3		668	1013	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846339	156846339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238297758	NA	P-0041879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	98	694	1	ENST00000524377.1:c.1780C>T	p.His594Tyr	p.H594Y	ENST00000524377	NM_002529.3	594	Cac/Tac	14/17	0.260100948951718	5	FACETS	0.665	0.591	0.744	0.222	0.197	0.248	SUBCLONAL	1	FALSE	2	0.388730710099386	5		695	1200	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560829	9560829	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	146	534	0	ENST00000353224.5:c.953A>G	p.Tyr318Cys	p.Y318C	ENST00000353224	NM_177990.2	318	tAc/tGc	4/10	0.37300057674494	4	FACETS	1	0.976	1			1	CLONAL	1	FALSE	NA	0.388730710099386	4		534	875	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259193	36259193	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	104	656	0	ENST00000300305.3:c.298T>G	p.Ser100Ala	p.S100A	ENST00000300305		100	Tcc/Gcc	3/8	0.338176299427518	3	FACETS	0.834	0.747	0.927	0.417	0.373	0.464	CLONAL	1	FALSE	1	0.388730710099386	3		656	766	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952091	178952091	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	104	338	0	ENST00000263967.3:c.3146G>A	p.Gly1049Asp	p.G1049D	ENST00000263967	NM_006218.2	1049	gGt/gAt	21/21	0.319066921810233	5	FACETS	1	0.965	1	0.765	0.691	0.842	CLONAL	2	FALSE	2	0.388730710099386	5		338	369	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750514	41750514	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	57	729	0	ENST00000226382.2:c.114G>C	p.Gln38His	p.Q38H	ENST00000226382	NM_003924.3	38	caG/caC	1/3	0.388730710099386	3	FACETS	0.424	0.363	0.491	0.212	0.181	0.246	SUBCLONAL	1	FALSE	1	0.388730710099386	3		729	826	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959925	38959925	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	100	289	0	ENST00000357387.3:c.2007C>G	p.His669Gln	p.H669Q	ENST00000357387	NM_152756.3	669	caC/caG	21/38	0.319066921810233	5	FACETS	1	0.968	1	0.785	0.708	0.865	CLONAL	2	FALSE	2	0.388730710099386	5		289	346	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962915	2962915	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	443	884	0	ENST00000396946.4:c.1993T>A	p.Ser665Thr	p.S665T	ENST00000396946	NM_032415.4	665	Tcg/Acg	16/25	0.375163025613908	5	FACETS	0.879	0.838	0.92	0.879	0.838	0.92	CLONAL	3	FALSE	2	0.388730710099386	5		884	1369	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729475	41729475	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	87	804	0	ENST00000242208.4:c.1054G>C	p.Gly352Arg	p.G352R	ENST00000242208	NM_002192.2	352	Ggt/Cgt	3/3	0.375163025613908	5	FACETS	0.598	0.528	0.674	0.199	0.176	0.225	SUBCLONAL	1	FALSE	2	0.388730710099386	5		804	1185	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390877	139390877	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	606	757	0	ENST00000277541.6:c.7314del	p.Ser2439AlafsTer38	p.S2439Afs*38	ENST00000277541	NM_017617.3	2438	ccG/cc	34/34	0.349157612153793	4	FACETS	0.9	0.869	0.931	0.9	0.869	0.931	CLONAL	4	FALSE	0	0.388730710099386	4		757	1203	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0041879-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	309	668	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.520360438264654	1	FACETS	0.843	0.797	0.889	0.843	0.797	0.889	CLONAL	1	TRUE	0	0.578005516596942	1		668	902	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846339	156846339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238297758	NA	P-0041879-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	325	694	1	ENST00000524377.1:c.1780C>T	p.His594Tyr	p.H594Y	ENST00000524377	NM_002529.3	594	Cac/Tac	14/17	1	2	FACETS	0.919	0.867	0.971	0.919	0.867	0.971	CLONAL	1	TRUE	1	0.578005516596942	2		695	1224	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952091	178952091	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041879-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	116	338	0	ENST00000263967.3:c.3146G>A	p.Gly1049Asp	p.G1049D	ENST00000263967	NM_006218.2	1049	gGt/gAt	21/21	1	2	FACETS	0.994	0.903	1	0.994	0.903	1	CLONAL	1	TRUE	1	0.578005516596942	2		338	404	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959925	38959925	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041879-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	58	289	0	ENST00000357387.3:c.2007C>G	p.His669Gln	p.H669Q	ENST00000357387	NM_152756.3	669	caC/caG	21/38	NA	2	FACETS	0.933	0.813	1			1	INDETERMINATE	1	TRUE	NA	0.578005516596942	2		289	215	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962915	2962915	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041879-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	674	884	0	ENST00000396946.4:c.1993T>A	p.Ser665Thr	p.S665T	ENST00000396946	NM_032415.4	665	Tcg/Acg	16/25	0.51344060845499	2	FACETS	0.885	0.857	0.914	0.885	0.857	0.914	CLONAL	2	TRUE	0	0.578005516596942	2		884	1317	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390877	139390877	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041879-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	579	757	0	ENST00000277541.6:c.7314del	p.Ser2439AlafsTer38	p.S2439Afs*38	ENST00000277541	NM_017617.3	2438	ccG/cc	34/34	0.51344060845499	2	FACETS	0.794	0.765	0.824	0.794	0.765	0.824	SUBCLONAL	2	TRUE	0	0.578005516596942	2		757	1261	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495527	56495527	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041879-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	56	639	0	ENST00000267101.3:c.3717G>T	p.Gln1239His	p.Q1239H	ENST00000267101	NM_001982.3	1239	caG/caT	28/28	1	2	FACETS	0.202	0.173	0.235	0.202	0.173	0.235	SUBCLONAL	1	TRUE	1	0.578005516596942	2		639	957	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012657	36012657	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1447509893	NA	P-0041879-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	45	170	0	ENST00000358208.4:c.101C>A	p.Ala34Asp	p.A34D	ENST00000358208		34	gCc/gAc	2/12	0.224547016785105	4	FACETS	0.67	0.564	0.785			1	INDETERMINATE	1	TRUE	NA	0.578005516596942	4		170	367	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224220	53224220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041879-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	40	400	0	ENST00000375401.3:c.3331G>T	p.Asp1111Tyr	p.D1111Y	ENST00000375401	NM_004187.3	1111	Gac/Tac	22/26	1	1	FACETS	0.141	0.116	0.168	0.141	0.116	0.168	SUBCLONAL	1	TRUE	0	0.578005516596942	1		400	699	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115952	8115953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCAC	novel	NA	P-0041881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	123	509	1	ENST00000346208.3:c.1301_1304dup	p.Ser436ProfsTer72	p.S436Pfs*72	ENST00000346208		433	cac/caCCACc	6/6	1	2	FACETS	0.824	0.75	0.902	0.824	0.75	0.902	CLONAL	1	TRUE	1	0.630896283053881	2		510	473	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246517	41246517	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	107	844	0	ENST00000357654.3:c.1031C>G	p.Ala344Gly	p.A344G	ENST00000357654	NM_007294.3	344	gCt/gGt	10/23	0.583024326156381	2	FACETS	0.852	0.786	0.918	0.852	0.786	0.918	CLONAL	2	TRUE	0	0.630896283053881	2		844	199	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583434	46583434	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	61	475	0	ENST00000263734.3:c.362T>A	p.Leu121His	p.L121H	ENST00000263734	NM_001430.4	121	cTt/cAt	3/16	1	2	FACETS	0.502	0.435	0.575	0.502	0.435	0.575	SUBCLONAL	1	TRUE	1	0.630896283053881	2		475	385	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779210	3779211	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs587783507	NA	P-0041885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	17	458	0	ENST00000262367.5:c.5837dup	p.Pro1947ThrfsTer19	p.P1947Tfs*19	ENST00000262367	NM_004380.2	1946	cca/ccCa	31/31	0.883016020416018	1	FACETS	0.078	0.058	0.102	0.078	0.058	0.102	SUBCLONAL	1	TRUE	0	0.883016020416018	1		458	276	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033867	49033867	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	22	473	0	ENST00000267163.4:c.2005del	p.Leu669PhefsTer8	p.L669Ffs*8	ENST00000267163	NM_000321.2	668	cgC/cg	20/27	0.883016020416018	1	FACETS	0.072	0.055	0.092	0.072	0.055	0.092	SUBCLONAL	1	TRUE	0	0.883016020416018	1		473	386	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343603	343603	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	126	920	0	ENST00000262320.3:c.2071del	p.Gln691LysfsTer14	p.Q691Kfs*14	ENST00000262320	NM_003502.3	691	Caa/aa	8/11	0.883016020416018	1	FACETS	0.302	0.275	0.331	0.302	0.275	0.331	SUBCLONAL	1	TRUE	0	0.883016020416018	1		920	527	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	364542	364542	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0041885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	41	849	0	ENST00000262320.3:c.1019+1G>A		p.X340_splice	ENST00000262320	NM_003502.3	340			0.883016020416018	1	FACETS	0.084	0.07	0.101	0.084	0.07	0.101	SUBCLONAL	1	TRUE	0	0.883016020416018	1		849	615	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587413	29587414	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0041885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	161	423	0	ENST00000356175.3:c.4394_4395insA	p.Cys1465Ter	p.C1465*	ENST00000356175	NM_000267.3	1465	tgt/tgAt	33/57	0.883016020416018	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.883016020416018	1		423	199	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0041886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	251	605	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.559256147493047	1	FACETS	0.981	0.924	1	0.981	0.924	1	CLONAL	1	TRUE	0	0.559256147493047	1		605	659	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936093	178936093	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913275	NA	P-0041886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	397	177	0	ENST00000263967.3:c.1635G>T	p.Glu545Asp	p.E545D	ENST00000263967	NM_006218.2	545	gaG/gaT	10/21	0.559256147493047	5	FACETS	1	0.993	1	0.604	0.575	0.633	CLONAL	2	TRUE	1	0.559256147493047	5		177	1081	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602863	10602863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	307	1045	3	ENST00000171111.5:c.715G>A	p.Val239Met	p.V239M	ENST00000171111	NM_203500.1	239	Gtg/Atg	3/6	0.559256147493047	2	FACETS	0.966	0.911	1	0.483	0.455	0.512	CLONAL	1	TRUE	0	0.559256147493047	2		1048	1136	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937914	36937914	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	91	1038	0	ENST00000361632.4:c.922C>G	p.Arg308Gly	p.R308G	ENST00000361632		308	Cgc/Ggc	7/16	0.238468617933297	5	FACETS	0.475	0.42	0.534	0.158	0.14	0.178	INDETERMINATE	1	TRUE	2	0.559256147493047	5		1038	1259	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428205	49428205	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	106	837	1	ENST00000301067.7:c.10495C>T	p.Gln3499Ter	p.Q3499*	ENST00000301067	NM_003482.3	3499	Cag/Tag	37/54	0.559256147493047	3	FACETS	0.451	0.403	0.502	0.15	0.134	0.168	SUBCLONAL	1	TRUE	0	0.559256147493047	3		838	1076	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	88	454	0	ENST00000295754.5:c.1583G>C	p.Arg528Pro	p.R528P	ENST00000295754	NM_003242.5	528	cGt/cCt	7/7	0.559256147493047	2	FACETS	0.69	0.614	0.771	0.345	0.307	0.386	SUBCLONAL	1	TRUE	0	0.559256147493047	2		454	456	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717678	89717678	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554825200	NA	P-0041901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	35	216	0	ENST00000371953.3:c.703G>T	p.Glu235Ter	p.E235*	ENST00000371953	NM_000314.4	235	Gaa/Taa	7/9	0.166911246816292	4	FACETS	1	0.851	1	0.522	0.427	0.629	CLONAL	1	TRUE	2	0.15	4		216	514	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588648	28588648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	31	224	0	ENST00000241453.7:c.2800C>T	p.Pro934Ser	p.P934S	ENST00000241453	NM_004119.2	934	Cca/Tca	23/24	0.166911246816292	4	FACETS	1	0.891	1	0.578	0.467	0.704	CLONAL	1	TRUE	2	0.15	4		224	411	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293806	1293806	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	48	419	0	ENST00000310581.5:c.1195A>C	p.Asn399His	p.N399H	ENST00000310581	NM_198253.2	399	Aac/Cac	2/16	0.25823089626813	0	FACETS	0.982	0.83	1			1	CLONAL	1	TRUE	0	0.15	0		419	554	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591112	67591134	+	frameshift_variant	Frame_Shift_Del	DEL	GACCTTATCCAGCTGAGAAAGAC	GACCTTATCCAGCTGAGAAAGAC	-	novel	NA	P-0041901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	21	144	0	ENST00000274335.5:c.1707_1729del	p.Asp569GlufsTer25	p.D569Efs*25	ENST00000274335		569	GACCTTATCCAGCTGAGAAAGACg/g	12/15	0.166911246816292	4	FACETS	0.912	0.702	1	0.456	0.351	0.579	CLONAL	1	TRUE	2	0.15	4		144	353	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591247	67591247	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0041901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	36	164	0	ENST00000274335.5:c.1746-1G>A		p.X582_splice	ENST00000274335		582			0.166911246816292	4	FACETS	1	0.886	1	0.554	0.455	0.666	CLONAL	1	TRUE	2	0.15	4		164	498	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372518	55372519	+	missense_variant	Missense_Mutation	DNP	GC	GC	TA	novel	NA	P-0041901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	113	372	0	ENST00000297316.4:c.1208_1209delinsTA	p.Ser403Ile	p.S403I	ENST00000297316	NM_022454.3	403	aGC/aTA	2/2	0.166911246816292	4	FACETS	0.779	0.699	0.864	0.779	0.699	0.864	SUBCLONAL	2	TRUE	2	0.15	4		372	1112	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028084	48028084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753795	NA	P-0041947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	18	323	0	ENST00000234420.5:c.2962C>T	p.Arg988Cys	p.R988C	ENST00000234420	NM_000179.2	988	Cgc/Tgc	4/10	1	2	FACETS	0.73	0.55	0.943	0.73	0.55	0.943	CLONAL	1	TRUE	1	0.17	2		323	290	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028670	12028670	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	128	405	0	ENST00000353533.5:c.873G>T	p.Trp291Cys	p.W291C	ENST00000353533	NM_003010.3	291	tgG/tgT	8/11	0.543738495238417	1	FACETS	0.762	0.695	0.831	0.762	0.695	0.831	SUBCLONAL	1	TRUE	0	0.543738495238417	1		405	450	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913284	NA	P-0041953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	114	274	0	ENST00000263967.3:c.1035T>G	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaG	5/21	1	2	FACETS	0.89	0.806	0.978	0.89	0.806	0.978	CLONAL	1	TRUE	1	0.543738495238417	2		274	471	SUCCESS
APC	324	MSKCC	GRCh37	5	112175987	112175987	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	112	241	0	ENST00000257430.4:c.4696G>A	p.Asp1566Asn	p.D1566N	ENST00000257430	NM_000038.5	1566	Gat/Aat	16/16	1	2	FACETS	0.936	0.848	1	0.936	0.848	1	CLONAL	1	TRUE	1	0.543738495238417	2		241	440	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557936	29557936	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	35	178	0	ENST00000356175.3:c.3190C>A	p.Leu1064Ile	p.L1064I	ENST00000356175	NM_000267.3	1064	Ctt/Att	24/57	0.543738495238417	1	FACETS	0.633	0.527	0.748	0.633	0.527	0.748	SUBCLONAL	1	TRUE	0	0.543738495238417	1		178	148	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0041959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	134	329	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.463823039954174	3	FACETS	0.958	0.871	1	0.479	0.435	0.525	CLONAL	1	TRUE	1	0.46307266366411	3		329	744	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0041959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	149	277	1	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.463823039954174	3	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	1	0.46307266366411	3		278	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0041959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	481	812	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.463823039954174	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.46307266366411	3		812	1207	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913255	NA	P-0041959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	336	493	0	ENST00000369535.4:c.183A>T	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caT	3/7	0.463823039954174	3	FACETS	0.996	0.945	1	0.996	0.945	1	CLONAL	2	TRUE	1	0.46307266366411	3		493	897	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584696	187584696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144526682	NA	P-0041959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	242	574	0	ENST00000441802.2:c.3337G>A	p.Asp1113Asn	p.D1113N	ENST00000441802	NM_005245.3	1113	Gat/Aat	3/27	0.463823039954174	3	FACETS	0.852	0.799	0.907	0.852	0.799	0.907	CLONAL	2	TRUE	1	0.46307266366411	3		574	755	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431178	49431178	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs793888512	NA	P-0041959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	332	678	0	ENST00000301067.7:c.9961C>T	p.Arg3321Ter	p.R3321*	ENST00000301067	NM_003482.3	3321	Cga/Tga	34/54	0.463823039954174	4	FACETS	0.936	0.885	0.987	0.936	0.885	0.987	CLONAL	2	TRUE	2	0.46307266366411	4		678	1121	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122706	7122706	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	183	768	0	ENST00000302850.5:c.3448C>G	p.Leu1150Val	p.L1150V	ENST00000302850	NM_000208.2	1150	Ctg/Gtg	19/22	0.463823039954174	3	FACETS	0.877	0.808	0.949	0.438	0.404	0.475	CLONAL	1	TRUE	1	0.46307266366411	3		768	1110	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574749	41574749	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1260684837	NA	P-0041959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	174	876	0	ENST00000263253.7:c.7034G>C	p.Ser2345Thr	p.S2345T	ENST00000263253	NM_001429.3	2345	aGt/aCt	31/31	0.463823039954174	4	FACETS	0.856	0.786	0.93	0.428	0.393	0.465	CLONAL	1	TRUE	2	0.46307266366411	4		876	1284	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258976	153258976	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	154	210	0	ENST00000281708.4:c.839T>C	p.Phe280Ser	p.F280S	ENST00000281708	NM_033632.3	280	tTc/tCc	5/12	0.463823039954174	3	FACETS	0.992	0.917	1	0.992	0.917	1	CLONAL	2	TRUE	1	0.46307266366411	3		210	413	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460572	149460572	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	332	664	0	ENST00000286301.3:c.65T>G	p.Val22Gly	p.V22G	ENST00000286301	NM_005211.3	22	gTg/gGg	3/22	0.463823039954174	3	FACETS	0.969	0.919	1	0.969	0.919	1	CLONAL	2	TRUE	1	0.46307266366411	3		664	911	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960179	151960179	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	203	358	0	ENST00000262189.6:c.1221T>A	p.Asp407Glu	p.D407E	ENST00000262189	NM_170606.2	407	gaT/gaA	9/59	0.463823039954174	4	FACETS	0.988	0.921	1	0.988	0.921	1	CLONAL	2	TRUE	2	0.46307266366411	4		358	649	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69103971	69103971	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	302	600	0	ENST00000288368.4:c.4361A>G	p.Asp1454Gly	p.D1454G	ENST00000288368	NM_024870.2	1454	gAc/gGc	36/40	0.401136504423184	4	FACETS	0.965	0.91	1	0.965	0.91	1	CLONAL	2	TRUE	2	0.46307266366411	4		600	989	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512473	38512473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	123	701	1	ENST00000254066.5:c.1384C>T	p.Pro462Ser	p.P462S	ENST00000254066	NM_000964.3	462	Ccg/Tcg	9/9	0.396787818289147	5	FACETS	0.809	0.729	0.892	0.202	0.182	0.223	CLONAL	1	TRUE	1	0.452326573222346	5		702	1129	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249501	153249501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1316840275	NA	P-0041974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	102	364	0	ENST00000281708.4:c.1277C>T	p.Ser426Leu	p.S426L	ENST00000281708	NM_033632.3	426	tCa/tTa	9/12	1	2	FACETS	0.819	0.734	0.907	0.819	0.734	0.907	CLONAL	1	TRUE	1	0.452326573222346	2		364	551	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855493	45855493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913026	NA	P-0041974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	140	781	0	ENST00000391945.4:c.2164C>T	p.Arg722Trp	p.R722W	ENST00000391945	NM_000400.3	722	Cgg/Tgg	22/23	1	2	FACETS	0.984	0.899	1	0.984	0.899	1	CLONAL	1	TRUE	1	0.452326573222346	2		781	629	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967555	26967555	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	162	309	0	ENST00000381527.3:c.698T>A	p.Ile233Lys	p.I233K	ENST00000381527	NM_001260.1	233	aTa/aAa	7/13	0.324538720674088	3	FACETS	1	0.988	1	0.712	0.656	0.77	CLONAL	1	TRUE	1	0.452326573222346	3		309	617	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579386	7579400	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	TCTGGGAAGGGACAG	TCTGGGAAGGGACAG	-	novel	NA	P-0041974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	314	729	0	ENST00000269305.4:c.287_301del	p.Ser96_Lys101delinsTer	p.S96_K101delins*	ENST00000269305	NM_001126112.2	96	tCTGTCCCTTCCCAGAaa/taa	4/11	NA	2	FACETS	0.877	0.831	0.922			1	INDETERMINATE	2	TRUE	NA	0.452326573222346	2		729	792	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56402540	56402540	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	43	122	0	ENST00000348428.3:c.1582T>G	p.Leu528Val	p.L528V	ENST00000348428	NM_006785.3	528	Tta/Gta	13/17	1	2	FACETS	0.901	0.762	1	0.901	0.762	1	CLONAL	1	TRUE	1	0.452326573222346	2		122	211	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027087	71027094	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGGGCG	GGGGGGCG	-	novel	NA	P-0041974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	160	479	0	ENST00000318789.4:c.1233_1240del	p.Ala412AspfsTer46	p.A412Dfs*46	ENST00000318789	NM_032682.5	411	acCGCCCCCCtg/actg	15/21	0.317391421940649	2	FACETS	1	0.988	1	0.694	0.64	0.748	CLONAL	1	TRUE	0	0.452326573222346	2		479	510	SUCCESS
APC	324	MSKCC	GRCh37	5	112151196	112151196	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs137854569	NA	P-0041974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	95	271	0	ENST00000257430.4:c.839C>G	p.Ser280Ter	p.S280*	ENST00000257430	NM_000038.5	280	tCa/tGa	9/16	0.13137518226559	3	FACETS	1	0.976	1	0.439	0.394	0.487	INDETERMINATE	1	TRUE	0	0.452326573222346	3		271	391	SUCCESS
APC	324	MSKCC	GRCh37	5	112175755	112175759	+	frameshift_variant	Frame_Shift_Del	DEL	ATTAC	ATTAC	-	novel	NA	P-0041974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	29	231	0	ENST00000257430.4:c.4467_4471del	p.Leu1489PhefsTer23	p.L1489Ffs*23	ENST00000257430	NM_000038.5	1488	ttATTACat/ttat	16/16	0.13137518226559	3	FACETS	0.533	0.429	0.651	0.178	0.143	0.217	INDETERMINATE	1	TRUE	0	0.452326573222346	3		231	295	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0041980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	171	414	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.225342306401013	5	FACETS	1	0.97	1	0.725	0.672	0.78	INDETERMINATE	2	TRUE	2	0.543509571791247	5		414	525	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0041980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	417	853	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.531511397464422	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.543509571791247	2		853	763	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928358	69928358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774545277	NA	P-0041980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	25	324	0	ENST00000352241.4:c.178C>T	p.Arg60Cys	p.R60C	ENST00000352241	NM_198159.2	60	Cgc/Tgc	2/10	0.323938362867427	3	FACETS	0.318	0.25	0.396	0.159	0.125	0.198	INDETERMINATE	1	TRUE	1	0.543509571791247	3		324	368	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944369	76944369	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123425	NA	P-0041980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	214	172	0	ENST00000373344.5:c.536A>G	p.Asn179Ser	p.N179S	ENST00000373344	NM_000489.3	179	aAt/aGt	7/35	0.245863358492663	3	FACETS	1	0.975	1			1	INDETERMINATE	3	TRUE	NA	0.543509571791247	3		172	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0042116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	87	772	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.4432076899878	3	FACETS	0.743	0.658	0.833	0.371	0.329	0.417	SUBCLONAL	1	TRUE	1	0.440426943886306	3		772	649	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0042120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	17	852	1	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.406414798334283	5	FACETS	0.235	0.174	0.308			1	SUBCLONAL	1	TRUE	NA	0.41	5		853	570	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038526	47038526	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	26	441	0	ENST00000377604.3:c.688C>T	p.Arg230Ter	p.R230*	ENST00000377604	NM_001204468.1	230	Cga/Tga	8/24	0.406414798334283	2	FACETS	0.613	0.488	0.754	0.306	0.244	0.377	SUBCLONAL	1	TRUE	0	0.41	2		441	207	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220540	123220540	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	11	379	0	ENST00000218089.9:c.3201del	p.Ser1068GlnfsTer37	p.S1068Qfs*37	ENST00000218089	NM_001042749.1	1066	cGg/cg	30/35	0.406414798334283	3	FACETS	0.32	0.221	0.443	0.107	0.073	0.148	SUBCLONAL	1	TRUE	0	0.41	3		379	202	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44733215	44733228	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGGCCCTACTGG	GAAGGCCCTACTGG	A	novel	NA	P-0042120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	12	366	0	ENST00000377967.4:c.207_220delinsA	p.Lys70AlafsTer10	p.K70Afs*10	ENST00000377967	NM_021140.2	69	acGAAGGCCCTACTGGgc/acAgc	2/29	0.406414798334283	3	FACETS	0.369	0.26	0.504	0.123	0.086	0.168	SUBCLONAL	1	TRUE	0	0.41	3		366	191	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	256	464	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.881	0.828	0.935	0.881	0.828	0.935	CLONAL	1	TRUE	1	0.738606269630757	2		464	787	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868444	117868444	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	306	691	0	ENST00000297338.2:c.898G>C	p.Glu300Gln	p.E300Q	ENST00000297338	NM_006265.2	300	Gag/Cag	8/14	1	2	FACETS	0.886	0.837	0.936	0.886	0.837	0.936	CLONAL	1	TRUE	1	0.738606269630757	2		691	935	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493443	56493443	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	233	577	0	ENST00000267101.3:c.2851G>C	p.Asp951His	p.D951H	ENST00000267101	NM_001982.3	951	Gat/Cat	24/28	1	2	FACETS	0.863	0.808	0.919	0.863	0.808	0.919	CLONAL	1	TRUE	1	0.738606269630757	2		577	731	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70432668	70432668	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	149	469	0	ENST00000373644.4:c.4690C>G	p.Gln1564Glu	p.Q1564E	ENST00000373644	NM_030625.2	1564	Caa/Gaa	8/12	1	2	FACETS	0.62	0.568	0.674	0.62	0.568	0.674	SUBCLONAL	1	TRUE	1	0.738606269630757	2		469	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578223	7578223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	295	894	0	ENST00000269305.4:c.626G>A	p.Arg209Lys	p.R209K	ENST00000269305	NM_001126112.2	209	aGa/aAa	6/11	1	2	FACETS	0.718	0.676	0.761	0.718	0.676	0.761	SUBCLONAL	1	TRUE	1	0.738606269630757	2		894	1113	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	38	336	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.189	0.155	0.226	0.189	0.155	0.226	SUBCLONAL	1	TRUE	1	0.738606269630757	2		336	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578227	7578227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	288	924	0	ENST00000269305.4:c.622G>A	p.Asp208Asn	p.D208N	ENST00000269305	NM_001126112.2	208	Gac/Aac	6/11	1	2	FACETS	0.71	0.667	0.753	0.71	0.667	0.753	SUBCLONAL	1	TRUE	1	0.738606269630757	2		924	1099	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627889	37627889	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	290	778	0	ENST00000447079.4:c.1804C>T	p.Gln602Ter	p.Q602*	ENST00000447079	NM_015083.1	602	Cag/Tag	2/14	1	2	FACETS	0.784	0.739	0.831	0.784	0.739	0.831	SUBCLONAL	1	TRUE	1	0.738606269630757	2		778	1001	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	380	658	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.738606269630757	2		658	1014	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81528560	81528560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	99	278	0	ENST00000298171.2:c.239G>A	p.Arg80Lys	p.R80K	ENST00000298171	NM_000369.2	80	aGa/aAa	2/10	1	2	FACETS	0.702	0.631	0.775	0.702	0.631	0.775	SUBCLONAL	1	TRUE	1	0.738606269630757	2		278	382	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175869	24175869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555881572	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	204	724	0	ENST00000263121.7:c.1097G>A	p.Arg366His	p.R366H	ENST00000263121	NM_003073.3	366	cGc/cAc	8/9	1	2	FACETS	0.652	0.606	0.7	0.652	0.606	0.7	SUBCLONAL	1	TRUE	1	0.738606269630757	2		724	847	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37680952	37680952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	189	587	0	ENST00000447079.4:c.3121G>A	p.Glu1041Lys	p.E1041K	ENST00000447079	NM_015083.1	1041	Gag/Aag	12/14	1	2	FACETS	0.717	0.664	0.771	0.717	0.664	0.771	SUBCLONAL	1	TRUE	1	0.738606269630757	2		587	714	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448705	49448705	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	66	694	0	ENST00000301067.7:c.154C>T	p.Gln52Ter	p.Q52*	ENST00000301067	NM_003482.3	52	Cag/Tag	2/54	1	2	FACETS	0.223	0.193	0.256	0.223	0.193	0.256	SUBCLONAL	1	TRUE	1	0.738606269630757	2		694	802	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121313	29121313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	264	853	0	ENST00000328354.6:c.362G>A	p.Cys121Tyr	p.C121Y	ENST00000328354	NM_007194.3	121	tGt/tAt	3/15	1	2	FACETS	0.671	0.629	0.714	0.671	0.629	0.714	SUBCLONAL	1	TRUE	1	0.738606269630757	2		853	1066	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342965	118342965	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	79	341	0	ENST00000534358.1:c.1091C>G	p.Ser364Ter	p.S364*	ENST00000534358	NM_005933.3	364	tCa/tGa	3/36	1	2	FACETS	0.413	0.364	0.465	0.413	0.364	0.465	SUBCLONAL	1	TRUE	1	0.738606269630757	2		341	518	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003117	42003117	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	82	742	0	ENST00000219905.7:c.2654C>G	p.Ser885Cys	p.S885C	ENST00000219905	NM_001164273.1	885	tCt/tGt	8/24	0.738606269630757	1	FACETS	0.221	0.194	0.249	0.221	0.194	0.249	SUBCLONAL	1	TRUE	0	0.738606269630757	1		742	635	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041449	42041449	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	201	629	0	ENST00000219905.7:c.5644C>G	p.Gln1882Glu	p.Q1882E	ENST00000219905	NM_001164273.1	1882	Cag/Gag	17/24	0.738606269630757	1	FACETS	0.62	0.578	0.662	0.62	0.578	0.662	SUBCLONAL	1	TRUE	0	0.738606269630757	1		629	554	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43700226	43700226	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	76	768	0	ENST00000382044.4:c.5661G>C	p.Gln1887His	p.Q1887H	ENST00000382044	NM_001141980.1	1887	caG/caC	27/28	0.738606269630757	1	FACETS	0.233	0.205	0.264	0.233	0.205	0.264	SUBCLONAL	1	TRUE	0	0.738606269630757	1		768	556	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627670	37627670	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	258	815	0	ENST00000447079.4:c.1585C>G	p.Leu529Val	p.L529V	ENST00000447079	NM_015083.1	529	Ctt/Gtt	2/14	1	2	FACETS	0.644	0.603	0.686	0.644	0.603	0.686	SUBCLONAL	1	TRUE	1	0.738606269630757	2		815	1085	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526089	66526089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	42	408	0	ENST00000358598.2:c.920C>T	p.Ser307Leu	p.S307L	ENST00000358598	NM_212471.2	307	tCa/tTa	10/11	1	2	FACETS	0.183	0.152	0.217	0.183	0.152	0.217	SUBCLONAL	1	TRUE	1	0.738606269630757	2		408	623	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291541	10291541	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1234060339	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	49	596	0	ENST00000340748.4:c.138G>T	p.Leu46Phe	p.L46F	ENST00000340748		46	ttG/ttT	3/40	1	2	FACETS	0.21	0.177	0.246	0.21	0.177	0.246	SUBCLONAL	1	TRUE	1	0.738606269630757	2		596	631	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227600	36227600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367682204	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	213	538	0	ENST00000222270.7:c.7169C>T	p.Ser2390Leu	p.S2390L	ENST00000222270	NM_014727.1	2390	tCg/tTg	31/37	1	2	FACETS	0.854	0.798	0.913	0.854	0.798	0.913	CLONAL	1	TRUE	1	0.738606269630757	2		538	675	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470997	25470997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	100	926	2	ENST00000264709.3:c.764C>T	p.Ser255Phe	p.S255F	ENST00000264709	NM_175629.2	255	tCc/tTc	7/23	1	2	FACETS	0.251	0.224	0.281	0.251	0.224	0.281	SUBCLONAL	1	TRUE	1	0.738606269630757	2		928	1077	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378305	225378305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	155	407	0	ENST00000264414.4:c.590G>A	p.Gly197Glu	p.G197E	ENST00000264414	NM_003590.4	197	gGa/gAa	5/16	1	2	FACETS	0.748	0.688	0.81	0.748	0.688	0.81	SUBCLONAL	1	TRUE	1	0.738606269630757	2		407	561	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321767	62321767	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs774200190	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	93	817	0	ENST00000360203.5:c.2386G>C	p.Val796Leu	p.V796L	ENST00000360203	NM_001283009.1	796	Gtc/Ctc	26/35	1	2	FACETS	0.252	0.224	0.283	0.252	0.224	0.283	SUBCLONAL	1	TRUE	1	0.738606269630757	2		817	998	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247353	71247353	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	75	614	0	ENST00000318789.4:c.180G>C	p.Gln60His	p.Q60H	ENST00000318789	NM_032682.5	60	caG/caC	6/21	1	2	FACETS	0.236	0.206	0.269	0.236	0.206	0.269	SUBCLONAL	1	TRUE	1	0.738606269630757	2		614	859	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295235	1295235	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	177	598	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.67	0.619	0.723	0.67	0.619	0.723	SUBCLONAL	1	TRUE	1	0.738606269630757	2		598	715	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672483	30672483	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	317	842	0	ENST00000376406.3:c.4477G>T	p.Ala1493Ser	p.A1493S	ENST00000376406	NM_014641.2	1493	Gcc/Tcc	10/15	1	2	FACETS	0.871	0.823	0.919	0.871	0.823	0.919	CLONAL	1	TRUE	1	0.738606269630757	2		842	986	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652070	36652071	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	493	1086	0	ENST00000244741.5:c.193dup	p.Trp65LeufsTer24	p.W65Lfs*24	ENST00000244741	NM_000389.4	64	-/T	2/3	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.738606269630757	2		1086	1266	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652200	36652201	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	358	916	0	ENST00000244741.5:c.324dup	p.Asp109ArgfsTer20	p.D109Rfs*20	ENST00000244741	NM_000389.4	108	gaa/gAaa	2/3	1	2	FACETS	0.904	0.858	0.951	0.904	0.858	0.951	CLONAL	1	TRUE	1	0.738606269630757	2		916	1072	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140929	37140929	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	47	573	0	ENST00000373509.5:c.765C>G	p.Phe255Leu	p.F255L	ENST00000373509	NM_002648.3	255	ttC/ttG	5/6	1	2	FACETS	0.167	0.14	0.196	0.167	0.14	0.196	SUBCLONAL	1	TRUE	1	0.738606269630757	2		573	763	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140946	37140946	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1426492223	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	33	480	1	ENST00000373509.5:c.782C>T	p.Ser261Leu	p.S261L	ENST00000373509	NM_002648.3	261	tCa/tTa	5/6	1	2	FACETS	0.139	0.112	0.168	0.139	0.112	0.168	SUBCLONAL	1	TRUE	1	0.738606269630757	2		481	645	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202309	138202309	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	312	759	0	ENST00000237289.4:c.2226G>T	p.Arg742Ser	p.R742S	ENST00000237289	NM_001270507.1	742	agG/agT	9/9	1	2	FACETS	0.94	0.889	0.991	0.94	0.889	0.991	CLONAL	1	TRUE	1	0.738606269630757	2		759	899	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386620	81386620	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	154	362	0	ENST00000222390.5:c.368-1G>C		p.X123_splice	ENST00000222390	NM_000601.4	123			1	2	FACETS	0.836	0.77	0.903	0.836	0.77	0.903	CLONAL	1	TRUE	1	0.738606269630757	2		362	499	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851500	128851500	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	281	954	0	ENST00000249373.3:c.1825G>T	p.Glu609Ter	p.E609*	ENST00000249373	NM_005631.4	609	Gag/Tag	11/12	1	2	FACETS	0.782	0.736	0.829	0.782	0.736	0.829	SUBCLONAL	1	TRUE	1	0.738606269630757	2		954	973	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44919321	44919321	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	157	257	0	ENST00000377967.4:c.1249C>G	p.Pro417Ala	p.P417A	ENST00000377967	NM_021140.2	417	Cct/Gct	13/29	1	1	FACETS	0.882	0.824	0.94	0.882	0.824	0.94	CLONAL	1	TRUE	0	0.738606269630757	1		257	304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0042152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	334	845	1	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.773247585276213	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.773247585276213	2		846	395	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217333	11217333	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	174	732	0	ENST00000361445.4:c.4345T>C	p.Trp1449Arg	p.W1449R	ENST00000361445	NM_004958.3	1449	Tgg/Cgg	30/58	0.60682796130451	5	FACETS	0.811	0.751	0.874	0.541	0.5	0.583	CLONAL	2	TRUE	2	0.773247585276213	5		732	599	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362443	40362443	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	90	730	0	ENST00000293328.3:c.1753C>A	p.Leu585Ile	p.L585I	ENST00000293328	NM_012448.3	585	Ctc/Atc	14/19	0.773247585276213	1	FACETS	0.523	0.47	0.578	0.523	0.47	0.578	SUBCLONAL	1	TRUE	0	0.773247585276213	1		730	273	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348421	56348421	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	92	397	0	ENST00000348428.3:c.229T>C	p.Cys77Arg	p.C77R	ENST00000348428	NM_006785.3	77	Tgt/Cgt	2/17	0.515737462019526	4	FACETS	1	0.964	1	0.588	0.526	0.652	CLONAL	1	TRUE	2	0.773247585276213	4		397	359	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875663	35875663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	46	480	0	ENST00000303115.3:c.850G>A	p.Glu284Lys	p.E284K	ENST00000303115	NM_002185.3	284	Gaa/Aaa	7/8	0.773247585276213	3	FACETS	0.431	0.363	0.505	0.215	0.181	0.253	SUBCLONAL	1	TRUE	1	0.773247585276213	3		480	383	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045733	26045733	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	58	345	0	ENST00000540144.1:c.95C>G	p.Ala32Gly	p.A32G	ENST00000540144	NM_003531.2	32	gCc/gGc	1/1	0.599583735736412	3	FACETS	0.963	0.839	1	0.482	0.419	0.547	CLONAL	1	TRUE	1	0.773247585276213	3		345	216	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137320996	137320996	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	132	812	1	ENST00000481739.1:c.953T>C	p.Ile318Thr	p.I318T	ENST00000481739	NM_002957.4	318	aTc/aCc	7/10	0.367365644657206	2	FACETS	0.722	0.66	0.786	0.361	0.33	0.393	INDETERMINATE	1	TRUE	0	0.773247585276213	2		813	473	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0042175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	43	255	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.234285399288908	3	FACETS	1	0.893	1	1	0.893	1	INDETERMINATE	2	FALSE	1	0.450455952351964	3		255	112	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0042175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	169	920	1	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	2	FALSE	NA	0.450455952351964	2		921	335	SUCCESS
APC	324	MSKCC	GRCh37	5	112175174	112175174	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	17	323	0	ENST00000257430.4:c.3883G>T	p.Glu1295Ter	p.E1295*	ENST00000257430	NM_000038.5	1295	Gaa/Taa	16/16	0.450455952351964	1	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	FALSE	0	0.450455952351964	1		323	52	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001422	29001422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752383804	NA	P-0042175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	213	482	1	ENST00000282397.4:c.1310C>T	p.Ser437Leu	p.S437L	ENST00000282397	NM_002019.4	437	tCg/tTg	10/30	0.33800004648799	6	FACETS	1	0.963	1	1	0.963	1	CLONAL	4	FALSE	2	0.450455952351964	6		483	436	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066846	30066846	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758982696	NA	P-0042175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	26	752	2	ENST00000331968.5:c.2285G>A	p.Arg762His	p.R762H	ENST00000331968	NM_002742.2	762	cGc/cAc	16/18	0.152864509294973	6	FACETS	0.631	0.5	0.781	0.21	0.166	0.261	INDETERMINATE	1	FALSE	3	0.450455952351964	6		754	348	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781413	3781413	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	79	770	0	ENST00000262367.5:c.4952A>T	p.Asp1651Val	p.D1651V	ENST00000262367	NM_004380.2	1651	gAc/gTc	30/31	0.162594055429717	3	FACETS	1	0.936	1	0.363	0.32	0.407	INDETERMINATE	1	FALSE	0	0.450455952351964	3		770	395	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0042208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	100	350	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.242048752238218	5	FACETS	0.927	0.834	1	0.695	0.625	0.768	CLONAL	3	TRUE	1	0.242048752238218	5		350	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0042208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	199	843	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.242048752238218	2		843	1137	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133793	41133793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	38	367	0	ENST00000379561.5:c.1835G>A	p.Cys612Tyr	p.C612Y	ENST00000379561	NM_002015.3	612	tGt/tAt	2/3	1	2	FACETS	0.737	0.61	0.879	0.737	0.61	0.879	SUBCLONAL	1	TRUE	1	0.242048752238218	2		367	426	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928439	69928439	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	104	645	1	ENST00000352241.4:c.259C>T	p.Gln87Ter	p.Q87*	ENST00000352241	NM_198159.2	87	Caa/Taa	2/10	1	2	FACETS	0.952	0.851	1	0.952	0.851	1	CLONAL	1	TRUE	1	0.242048752238218	2		646	903	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0042233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	33	343	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.88	0.721	1	0.88	0.721	1	CLONAL	1	FALSE	1	0.3	2		343	250	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715612	30715612	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1559467821	NA	P-0042233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	20	267	0	ENST00000295754.5:c.1270T>C	p.Tyr424His	p.Y424H	ENST00000295754	NM_003242.5	424	Tac/Cac	5/7	0.3	1	FACETS	0.537	0.412	0.682	0.537	0.412	0.682	SUBCLONAL	1	FALSE	0	0.3	1		267	211	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951805	2951805	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0042233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	62	732	1	ENST00000396946.4:c.3144+1G>A		p.X1048_splice	ENST00000396946	NM_032415.4	1048			0.227465718566827	3	FACETS	0.593	0.511	0.683	0.297	0.255	0.342	SUBCLONAL	1	FALSE	1	0.3	3		733	801	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0042258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	150	482	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.549192500881284	2		482	412	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063718	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0042258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	85	231	0	ENST00000412916.2:c.165+2dup		p.X55_splice	ENST00000412916		55			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.549192500881284	2		231	238	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878176	151878176	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	239	514	0	ENST00000262189.6:c.6769C>T	p.Arg2257Ter	p.R2257*	ENST00000262189	NM_170606.2	2257	Cga/Tga	36/59	0.355603186078765	5	FACETS	1	0.989	1	0.829	0.779	0.88	CLONAL	2	TRUE	2	0.549192500881284	5		514	638	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042392	16042393	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0042258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	102	379	0	ENST00000268712.3:c.1281dup	p.Met428TyrfsTer5	p.M428Yfs*5	ENST00000268712	NM_006311.3	427	-/T	12/46	0.549192500881284	1	FACETS	0.962	0.874	1	0.962	0.874	1	CLONAL	1	TRUE	0	0.549192500881284	1		379	280	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0042261-T11-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	455	482	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.591436326054473	2	FACETS	0.989	0.955	1	0.989	0.955	1	CLONAL	2	TRUE	0	0.632030972374878	2		482	728	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673130	30673130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042261-T11-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	303	648	0	ENST00000376406.3:c.3830C>T	p.Ser1277Phe	p.S1277F	ENST00000376406	NM_014641.2	1277	tCt/tTt	10/15	1	2	FACETS	0.93	0.877	0.984	0.93	0.877	0.984	CLONAL	1	TRUE	1	0.632030972374878	2		648	1031	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422703	49422703	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042261-T11-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	268	540	0	ENST00000301067.7:c.14290G>C	p.Glu4764Gln	p.E4764Q	ENST00000301067	NM_003482.3	4764	Gag/Cag	45/54	0.622972529055348	1	FACETS	0.997	0.944	1	0.997	0.944	1	CLONAL	1	TRUE	0	0.632030972374878	1		540	582	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10284510	10284546	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CGTAGAACAAAAAGAAAGGTATAGTAACTATTCTTAC	CGTAGAACAAAAAGAAAGGTATAGTAACTATTCTTAC	-	novel	NA	P-0042261-T11-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	119	227	0	ENST00000340748.4:c.635+1_635+37del		p.X212_splice	ENST00000340748		212			0.59404352531528	3	FACETS	0.909	0.824	0.999	0.455	0.412	0.5	CLONAL	1	TRUE	1	0.632030972374878	3		227	545	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176618953	176618953	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042261-T11-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	194	395	0	ENST00000439151.2:c.996G>C	p.Lys332Asn	p.K332N	ENST00000439151	NM_022455.4	332	aaG/aaC	3/23	1	2	FACETS	0.929	0.863	0.996	0.929	0.863	0.996	CLONAL	1	TRUE	1	0.632030972374878	2		395	661	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949731	151949731	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042261-T11-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	234	424	0	ENST00000262189.6:c.1369G>C	p.Asp457His	p.D457H	ENST00000262189	NM_170606.2	457	Gac/Cac	10/59	1	2	FACETS	0.999	0.936	1	0.999	0.936	1	CLONAL	1	TRUE	1	0.632030972374878	2		424	741	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964526	70964526	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042261-T11-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	236	554	0	ENST00000276594.2:c.1502C>G	p.Ser501Cys	p.S501C	ENST00000276594	NM_024504.3	501	tCc/tGc	8/8	0.581748971926041	3	FACETS	0.921	0.859	0.985	0.461	0.429	0.493	CLONAL	1	TRUE	1	0.632030972374878	3		554	1067	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606214	93606214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042261-T11-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	189	529	0	ENST00000375746.1:c.34C>T	p.His12Tyr	p.H12Y	ENST00000375746	NM_001174167.1	12	Cac/Tac	2/14	1	2	FACETS	0.867	0.804	0.931	0.867	0.804	0.931	CLONAL	1	TRUE	1	0.632030972374878	2		529	690	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528086	29528086	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs864622107	NA	P-0042261-T11-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	78	169	0	ENST00000356175.3:c.1094C>G	p.Ser365Ter	p.S365*	ENST00000356175	NM_000267.3	365	tCa/tGa	10/57	0.622972529055348	1	FACETS	0.918	0.825	1	0.918	0.825	1	CLONAL	1	TRUE	0	0.632030972374878	1		169	184	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131281	202131281	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042261-T11-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	232	485	1	ENST00000358485.4:c.249C>A	p.Phe83Leu	p.F83L	ENST00000358485	NM_001080125.1	83	ttC/ttA	2/9	0.622972529055348	1	FACETS	0.902	0.848	0.956	0.902	0.848	0.956	CLONAL	1	TRUE	0	0.632030972374878	1		486	557	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178646	56178646	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042261-T11-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	38	439	0	ENST00000399503.3:c.3619C>G	p.Gln1207Glu	p.Q1207E	ENST00000399503	NM_005921.1	1207	Cag/Gag	14/20	1	2	FACETS	0.163	0.134	0.195	0.163	0.134	0.195	SUBCLONAL	1	TRUE	1	0.632030972374878	2		439	739	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969991	161969991	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042261-T11-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	34	384	0	ENST00000366898.1:c.978G>T	p.Gln326His	p.Q326H	ENST00000366898	NM_004562.2	326	caG/caT	9/12	0.632030972374878	2	FACETS	0.2	0.163	0.242	0.1	0.081	0.121	SUBCLONAL	1	TRUE	0	0.632030972374878	2		384	538	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0042273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	149	441	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.698516181328392	3	FACETS	0.902	0.838	0.966	0.902	0.838	0.966	CLONAL	2	FALSE	1	0.698516181328392	3		441	319	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0042273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	361	1011	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	FALSE	1	0.698516181328392	2		1011	793	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0042273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	106	265	1	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	0.698516181328392	3	FACETS	1	0.985	1	0.739	0.673	0.807	CLONAL	1	FALSE	1	0.698516181328392	3		266	277	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519886	NA	P-0042273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	83	299	0	ENST00000349496.5:c.97T>G	p.Ser33Ala	p.S33A	ENST00000349496	NM_001904.3	33	Tct/Gct	3/15	1	2	FACETS	0.743	0.662	0.828	0.743	0.662	0.828	SUBCLONAL	1	FALSE	1	0.698516181328392	2		299	320	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573941	41573941	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766166888	NA	P-0042273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	132	665	0	ENST00000263253.7:c.6226G>A	p.Ala2076Thr	p.A2076T	ENST00000263253	NM_001429.3	2076	Gcc/Acc	31/31	1	2	FACETS	0.847	0.775	0.922	0.847	0.775	0.922	CLONAL	1	FALSE	1	0.698516181328392	2		665	446	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188174	11188174	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	108	418	0	ENST00000361445.4:c.5920T>C	p.Tyr1974His	p.Y1974H	ENST00000361445	NM_004958.3	1974	Tac/Cac	43/58	1	2	FACETS	0.825	0.747	0.905	0.825	0.747	0.905	CLONAL	1	FALSE	1	0.698516181328392	2		418	375	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437758	49437758	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	95	503	0	ENST00000301067.7:c.5212G>T	p.Glu1738Ter	p.E1738*	ENST00000301067	NM_003482.3	1738	Gag/Tag	22/54	1	2	FACETS	0.668	0.599	0.741	0.668	0.599	0.741	SUBCLONAL	1	FALSE	1	0.698516181328392	2		503	407	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520333	176520333	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0042273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	144	768	0	ENST00000292408.4:c.1251+1G>A		p.X417_splice	ENST00000292408	NM_213647.1	417			1	2	FACETS	0.91	0.837	0.985	0.91	0.837	0.985	CLONAL	1	FALSE	1	0.698516181328392	2		768	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0042315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	261	467	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.297989698027509	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.298034266417864	2		467	804	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266490	55266490	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	51	523	0	ENST00000275493.2:c.2782G>C	p.Glu928Gln	p.E928Q	ENST00000275493	NM_005228.3	928	Gag/Cag	23/28	0.298034266417864	5	FACETS	0.491	0.416	0.575	0.164	0.138	0.192	SUBCLONAL	1	TRUE	2	0.298034266417864	5		523	1008	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984428	201984428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	115	593	1	ENST00000359651.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000359651		365	Gag/Aag	8/8	0.208928385408067	4	FACETS	0.988	0.888	1	0.494	0.444	0.547	CLONAL	1	TRUE	2	0.298034266417864	4		594	1014	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877385	40877385	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	87	522	0	ENST00000373198.4:c.2311G>T	p.Ala771Ser	p.A771S	ENST00000373198	NM_133170.3	771	Gct/Tct	15/32	0.208928385408067	4	FACETS	0.903	0.799	1	0.452	0.399	0.508	CLONAL	1	TRUE	2	0.298034266417864	4		522	839	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178942531	178942531	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	84	275	0	ENST00000263967.3:c.2338T>C	p.Trp780Arg	p.W780R	ENST00000263967	NM_006218.2	780	Tgg/Cgg	16/21	0.298034266417864	3	FACETS	0.822	0.73	0.919	0.822	0.73	0.919	CLONAL	2	TRUE	1	0.298034266417864	3		275	394	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0042317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	65	365	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	1	2	FACETS	0.649	0.564	0.74	0.649	0.564	0.74	SUBCLONAL	1	TRUE	1	0.44431583664348	2		365	451	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508257	106508257	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766854286	NA	P-0042317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	56	516	0	ENST00000359195.3:c.251C>T	p.Ala84Val	p.A84V	ENST00000359195	NM_002649.2	84	gCg/gTg	2/11	1	2	FACETS	0.443	0.379	0.513	0.443	0.379	0.513	SUBCLONAL	1	TRUE	1	0.44431583664348	2		516	569	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052725	42052725	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	94	385	0	ENST00000219905.7:c.7396C>T	p.Arg2466Ter	p.R2466*	ENST00000219905	NM_001164273.1	2466	Cga/Tga	20/24	0.44431583664348	1	FACETS	0.859	0.77	0.953	0.859	0.77	0.953	CLONAL	1	TRUE	0	0.44431583664348	1		385	383	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793146	33793146	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1210600080	NA	P-0042317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	44	367	1	ENST00000498907.2:c.175G>T	p.Glu59Ter	p.E59*	ENST00000498907	NM_004364.3	59	Gag/Tag	1/1	0.252674627174953	1	FACETS	0.439	0.369	0.516	0.439	0.369	0.516	INDETERMINATE	1	TRUE	0	0.44431583664348	1		368	351	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041151	47041152	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0042317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	179	750	1	ENST00000377604.3:c.1581_1582del	p.Thr528HisfsTer10	p.T528Hfs*10	ENST00000377604	NM_001204468.1	527	TAt/t	15/24	0.44431583664348	1	FACETS	0.906	0.838	0.976	0.906	0.838	0.976	CLONAL	1	TRUE	0	0.44431583664348	1		751	692	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0042339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	115	416	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.24074506571732	2	FACETS	0.854	0.777	0.933	1	0.979	1	CLONAL	3	FALSE	0	0.24074506571732	2		416	373	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913400	NA	P-0042339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	9	305	0	ENST00000349496.5:c.98C>A	p.Ser33Tyr	p.S33Y	ENST00000349496	NM_001904.3	33	tCt/tAt	3/15	1	2	FACETS	0.203	0.133	0.292	0.203	0.133	0.292	SUBCLONAL	1	FALSE	1	0.24074506571732	2		305	369	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0042339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	48	289	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	1	0.24074506571732	2		289	348	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	44	554	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.734	0.615	0.865	0.734	0.615	0.865	SUBCLONAL	1	FALSE	1	0.24074506571732	2		554	498	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097630	27097630	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	68	471	1	ENST00000324856.7:c.3219G>A	p.Trp1073Ter	p.W1073*	ENST00000324856	NM_006015.4	1073	tgG/tgA	12/20	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	FALSE	1	0.24074506571732	2		472	562	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099888	27099888	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	79	490	0	ENST00000324856.7:c.3767del	p.Met1256ArgfsTer13	p.M1256Rfs*13	ENST00000324856	NM_006015.4	1256	aTg/ag	15/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	FALSE	1	0.24074506571732	2		490	598	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619427	1619427	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201296678	NA	P-0042339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	81	569	2	ENST00000344749.5:c.1214G>A	p.Arg405His	p.R405H	ENST00000344749	NM_001136139.2	405	cGc/cAc	15/19	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	1	0.24074506571732	2		571	633	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967032	18967032	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	88	552	0	ENST00000262803.5:c.1747G>A	p.Glu583Lys	p.E583K	ENST00000262803	NM_002911.3	583	Gag/Aag	13/24	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.24074506571732	2		552	592	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182279	38182279	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	57	504	0	ENST00000396334.3:c.715G>T	p.Asp239Tyr	p.D239Y	ENST00000396334	NM_002468.4	239	Gat/Tat	4/5	1	2	FACETS	0.916	0.786	1	0.916	0.786	1	CLONAL	1	FALSE	1	0.24074506571732	2		504	517	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371789	55371790	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0042339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	14	196	0	ENST00000297316.4:c.480_481dup	p.Glu161ValfsTer227	p.E161Vfs*227	ENST00000297316	NM_022454.3	160	gct/gcTGt	2/2	1	2	FACETS	0.75	0.545	0.996	0.75	0.545	0.996	CLONAL	1	FALSE	1	0.24074506571732	2		196	155	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0042340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	407	590	0	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.672829903166119	2	FACETS	0.959	0.925	0.992	0.959	0.925	0.992	CLONAL	2	TRUE	0	0.672829903166119	2		590	631	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933198	100933198	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	167	285	0	ENST00000325455.5:c.2192A>T	p.Lys731Met	p.K731M	ENST00000325455	NM_001202474.3	731	aAg/aTg	4/8	0.672829903166119	3	FACETS	0.933	0.86	1	0.467	0.43	0.505	CLONAL	1	TRUE	1	0.672829903166119	3		285	711	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446443	49446443	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	259	373	0	ENST00000301067.7:c.1162C>G	p.Leu388Val	p.L388V	ENST00000301067	NM_003482.3	388	Ctg/Gtg	9/54	0.667069989284117	3	FACETS	1	0.975	1	0.537	0.503	0.571	CLONAL	1	TRUE	1	0.672829903166119	3		373	958	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936983	48936983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	335	331	0	ENST00000267163.4:c.751del	p.Arg251GlufsTer13	p.R251Efs*13	ENST00000267163	NM_000321.2	251	Cga/ga	8/27	0.66901747851038	2	FACETS	0.917	0.88	0.954	0.917	0.88	0.954	CLONAL	2	TRUE	0	0.672829903166119	2		331	543	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186501400	186501400	+	start_lost	Translation_Start_Site	SNP	A	A	T	rs571299759	NA	P-0042340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	121	241	0	ENST00000323963.5:c.1A>T	p.Met1?	p.M1?	ENST00000323963		1	Atg/Ttg	1/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.672829903166119	NA		241	741	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0042341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	78	311	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.383745804169308	2		311	329	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56376762	56376762	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	91	372	0	ENST00000348428.3:c.802A>G	p.Thr268Ala	p.T268A	ENST00000348428	NM_006785.3	268	Aca/Gca	5/17	1	2	FACETS	0.812	0.73	0.897	1	0.984	1	CLONAL	2	FALSE	1	0.383745804169308	2		372	292	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845523	151845524	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0042358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	82	668	0	ENST00000262189.6:c.13488dup	p.Lys4497Ter	p.K4497*	ENST00000262189	NM_170606.2	4496	-/T	52/59	1	2	FACETS	0.751	0.66	0.848	0.751	0.66	0.848	SUBCLONAL	1	TRUE	1	0.23	2		668	950	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981156	201981156	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	265	860	0	ENST00000359651.3:c.235C>T	p.Gln79Ter	p.Q79*	ENST00000359651		79	Caa/Taa	2/8	0.3	3	FACETS	0.952	0.891	1	0.952	0.891	1	CLONAL	2	TRUE	1	0.23	3		860	1349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0042372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	433	670	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.536292409380724	2	FACETS	0.933	0.896	0.971	0.933	0.896	0.971	CLONAL	2	TRUE	0	0.536292409380724	2		670	865	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0042372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	103	550	4	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.536292409380724	3	FACETS	0.801	0.718	0.889	0.401	0.359	0.445	CLONAL	1	TRUE	1	0.536292409380724	3		554	608	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913338	NA	P-0042372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	242	390	0	ENST00000288602.6:c.1781A>C	p.Asp594Ala	p.D594A	ENST00000288602	NM_004333.4	594	gAt/gCt	15/18	0.509449834647255	5	FACETS	1	0.984	1	0.757	0.71	0.805	CLONAL	2	TRUE	2	0.536292409380724	5		390	717	SUCCESS
APC	324	MSKCC	GRCh37	5	112175162	112175162	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561588104	NA	P-0042372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	143	275	0	ENST00000257430.4:c.3871C>T	p.Gln1291Ter	p.Q1291*	ENST00000257430	NM_000038.5	1291	Cag/Tag	16/16	0.526062823637366	2	FACETS	0.977	0.91	1	0.977	0.91	1	CLONAL	2	TRUE	0	0.536292409380724	2		275	273	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138135	2138135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201206500	NA	P-0042372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	430	702	0	ENST00000219476.3:c.5155G>A	p.Ala1719Thr	p.A1719T	ENST00000219476	NM_000548.3	1719	Gca/Aca	40/42	0.536292409380724	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.536292409380724	2		702	794	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770576	40770576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	273	504	2	ENST00000373198.4:c.2806C>T	p.Arg936Ter	p.R936*	ENST00000373198	NM_133170.3	936	Cga/Tga	19/32	0.509449834647255	5	FACETS	0.937	0.881	0.995	0.625	0.587	0.664	CLONAL	2	TRUE	2	0.536292409380724	5		506	980	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491376	18491376	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	58	303	0	ENST00000266497.5:c.1289T>A	p.Ile430Asn	p.I430N	ENST00000266497		430	aTt/aAt	8/31	0.307768281061869	4	FACETS	0.835	0.72	0.959	0.417	0.36	0.48	INDETERMINATE	1	TRUE	2	0.536292409380724	4		303	398	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0042391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	39	494	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.57	0.472	0.679	0.57	0.472	0.679	SUBCLONAL	1	TRUE	1	0.277751056432329	2		494	493	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0042391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	31	506	0	ENST00000311936.3:c.180_181delinsAA	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggAAaa	3/5	0.277751056432329	3	FACETS	0.461	0.371	0.562	0.23	0.185	0.281	SUBCLONAL	1	TRUE	1	0.277751056432329	3		506	552	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691943	30691943	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	31	356	0	ENST00000295754.5:c.445T>G	p.Phe149Val	p.F149V	ENST00000295754	NM_003242.5	149	Ttc/Gtc	3/7	1	2	FACETS	0.643	0.521	0.781	0.643	0.521	0.781	SUBCLONAL	1	TRUE	1	0.277751056432329	2		356	347	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs397518442	NA	P-0042399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	238	650	1	ENST00000326873.7:c.650del	p.Pro217ArgfsTer70	p.P217Rfs*70	ENST00000326873	NM_000455.4	216	tCc/tc	5/10	0.333795047359805	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	0	0.333795047359805	2		651	706	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002946	69002946	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146486437	NA	P-0042399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	97	277	0	ENST00000288368.4:c.2246C>T	p.Thr749Met	p.T749M	ENST00000288368	NM_024870.2	749	aCg/aTg	20/40	0.30954277674723	4	FACETS	1	0.9	1	1	0.9	1	CLONAL	2	TRUE	2	0.333795047359805	4		277	387	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253421	226253425	+	frameshift_variant	Frame_Shift_Del	DEL	AAACT	AAACT	-	novel	NA	P-0042399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	34	87	0	ENST00000366813.1:c.193_197del	p.Lys65SerfsTer14	p.K65Sfs*14	ENST00000366813		65	AAACTt/t	2/3	0.333795047359805	3	FACETS	1	0.913	1	1	0.913	1	CLONAL	2	TRUE	1	0.333795047359805	3		87	104	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827991	40827991	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	32	321	1	ENST00000373198.4:c.2437G>T	p.Ala813Ser	p.A813S	ENST00000373198	NM_133170.3	813	Gcc/Tcc	17/32	1	2	FACETS	0.17	0.137	0.207	0.17	0.137	0.207	SUBCLONAL	1	TRUE	1	0.758564024047434	2		322	497	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509550	29509550	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0042418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	161	276	0	ENST00000356175.3:c.755T>A	p.Leu252Ter	p.L252*	ENST00000356175	NM_000267.3	252	tTg/tAg	8/57	0.727836062225053	1	FACETS	0.991	0.932	1	0.991	0.932	1	CLONAL	1	TRUE	0	0.758564024047434	1		276	266	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651167	206651167	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	300	602	0	ENST00000367120.3:c.777G>T	p.Trp259Cys	p.W259C	ENST00000367120	NM_014002.3	259	tgG/tgT	8/22	0.758564024047434	4	FACETS	0.908	0.853	0.965	0.303	0.284	0.322	CLONAL	1	TRUE	1	0.758564024047434	4		602	1532	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144505	58144505	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	137	236	0	ENST00000257904.6:c.566C>G	p.Ser189Cys	p.S189C	ENST00000257904	NM_000075.3	189	tCc/tGc	5/8	1	2	FACETS	0.99	0.911	1	0.99	0.911	1	CLONAL	1	TRUE	1	0.758564024047434	2		236	365	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250244	133250244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	54	458	0	ENST00000320574.5:c.1276G>A	p.Ala426Thr	p.A426T	ENST00000320574	NM_006231.2	426	Gcg/Acg	13/49	1	2	FACETS	0.196	0.167	0.228	0.196	0.167	0.228	SUBCLONAL	1	TRUE	1	0.758564024047434	2		458	726	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805605	46805609	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGG	CCCGG	-	novel	NA	P-0042418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	315	560	0	ENST00000290295.7:c.347_351del	p.Ala116GlyfsTer9	p.A116Gfs*9	ENST00000290295	NM_006361.5	116	gCCGGG/g	1/2	1	2	FACETS	0.973	0.921	1	0.973	0.921	1	CLONAL	1	TRUE	1	0.758564024047434	2		560	854	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119942	70119942	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	157	298	0	ENST00000245479.2:c.944A>G	p.Tyr315Cys	p.Y315C	ENST00000245479	NM_000346.3	315	tAc/tGc	3/3	0.758564024047434	3	FACETS	0.868	0.797	0.941	0.434	0.398	0.471	CLONAL	1	TRUE	1	0.758564024047434	3		298	658	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221147	5221147	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	291	453	0	ENST00000357368.4:c.3319G>C	p.Gly1107Arg	p.G1107R	ENST00000357368	NM_002850.3	1107	Ggc/Cgc	20/38	1	2	FACETS	0.994	0.94	1	0.994	0.94	1	CLONAL	1	TRUE	1	0.758564024047434	2		453	772	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331997	81331997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	96	212	0	ENST00000222390.5:c.2087G>A	p.Gly696Glu	p.G696E	ENST00000222390	NM_000601.4	696	gGa/gAa	18/18	1	2	FACETS	0.92	0.832	1	0.92	0.832	1	CLONAL	1	TRUE	1	0.758564024047434	2		212	275	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123040993	123040993	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs61757636	NA	P-0042418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	13	65	0	ENST00000355640.3:c.1456A>G	p.Thr486Ala	p.T486A	ENST00000355640		486	Aca/Gca	7/7	1	2	FACETS	0.369	0.266	0.49	0.369	0.266	0.49	SUBCLONAL	1	TRUE	1	0.758564024047434	2		65	93	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0042511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	544	549	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.744799489438497	2	FACETS	0.994	0.967	1	0.994	0.967	1	CLONAL	2	TRUE	0	0.745969371762908	2		552	734	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032554	47032554	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	274	857	0	ENST00000377604.3:c.460G>C	p.Val154Leu	p.V154L	ENST00000377604	NM_001204468.1	154	Gtg/Ctg	5/24	1	2	FACETS	0.885	0.834	0.938	0.885	0.834	0.938	CLONAL	1	TRUE	1	0.745969371762908	2		857	830	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0042517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	77	350	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.11777081116421	3	FACETS	0.787	0.692	0.888			1	INDETERMINATE	2	TRUE	NA	0.210827011262969	3		350	513	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0042517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	127	707	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.1874004671499	2	FACETS	0.753	0.682	0.827	0.753	0.682	0.827	SUBCLONAL	2	TRUE	0	0.210827011262969	2		707	800	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0042517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	119	504	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.210827011262969	2	FACETS	0.927	0.839	1	0.927	0.839	1	CLONAL	2	TRUE	0	0.210827011262969	2		506	609	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592251	29592251	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs797044942	NA	P-0042517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	12	142	0	ENST00000356175.3:c.4666C>T	p.Gln1556Ter	p.Q1556*	ENST00000356175	NM_000267.3	1556	Cag/Tag	35/57	0.131260928233668	3	FACETS	0.608	0.427	0.83	0.304	0.213	0.415	SUBCLONAL	1	TRUE	1	0.210827011262969	3		142	207	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971167	21971167	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	42	442	0	ENST00000304494.5:c.191T>C	p.Leu64Pro	p.L64P	ENST00000304494	NM_000077.4	64	cTg/cCg	2/3	1	2	FACETS	0.713	0.594	0.844	0.713	0.594	0.844	SUBCLONAL	1	TRUE	1	0.210827011262969	2		442	559	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974776	21974794	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCAGCCAGTCAGCCGAA	GGCCAGCCAGTCAGCCGAA	-	novel	NA	P-0042517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	29	183	0	ENST00000304494.5:c.33_51del	p.Ser12ArgfsTer8	p.S12Rfs*8	ENST00000304494	NM_000077.4	11	ccTTCGGCTGACTGGCTGGCC/cc	1/3	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.210827011262969	2		183	228	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81534602	81534602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151211603	NA	P-0042517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	45	313	0	ENST00000298171.2:c.247G>A	p.Val83Ile	p.V83I	ENST00000298171	NM_000369.2	83	Gta/Ata	3/10	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.210827011262969	2		313	380	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859921	151859922	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0042517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	48	386	0	ENST00000262189.6:c.10740_10741del	p.His3580GlnfsTer15	p.H3580Qfs*15	ENST00000262189	NM_170606.2	3580	caCAgt/cagt	43/59	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.210827011262969	2		386	390	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	133	126	0				ENST00000310581	NM_198253.2	-/1132			0.224342752228569	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.925903826476255	0		126	273	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0042551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	187	623	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.926	0.866	0.988	0.926	0.866	0.988	CLONAL	1	TRUE	1	0.925903826476255	2		623	436	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0042551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	65	365	6	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	0.949	0.845	1	0.949	0.845	1	CLONAL	1	TRUE	1	0.925903826476255	2		371	148	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870260	44870260	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	68	426	0	ENST00000377967.4:c.439C>T	p.Gln147Ter	p.Q147*	ENST00000377967	NM_021140.2	147	Cag/Tag	5/29	0.925903826476255	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.925903826476255	1		426	77	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916223	9916223	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	59	710	0	ENST00000330684.3:c.2066G>T	p.Ser689Ile	p.S689I	ENST00000330684	NM_001134407.1	689	aGc/aTc	10/13	1	2	FACETS	0.496	0.431	0.565	0.496	0.431	0.565	SUBCLONAL	1	TRUE	1	0.925903826476255	2		710	257	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115849	8115850	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0042556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	305	766	0	ENST00000346208.3:c.1196dup	p.His399GlnfsTer108	p.H399Qfs*108	ENST00000346208		399	cac/cAac	6/6	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.588028937763875	2		766	946	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0042583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	145	467	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.454250326714338	1	FACETS	0.755	0.692	0.82	0.755	0.692	0.82	SUBCLONAL	1	TRUE	0	0.510748750307484	1		467	560	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042595-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	29	414	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.854	0.687	1	1	0.963	1	CLONAL	3	TRUE	1	0.08	2		414	283	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933700	39933709	+	frameshift_variant	Frame_Shift_Del	DEL	TCAACAGGAT	TCAACAGGAT	-	novel	NA	P-0042595-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	20	320	0	ENST00000378444.4:c.890_899del	p.Asn297IlefsTer78	p.N297Ifs*78	ENST00000378444	NM_001123385.1	297	aATCCTGTTGAt/at	4/15	1	1	FACETS	0.934	0.715	1	1	0.933	1	CLONAL	2	TRUE	0	0.08	1		320	257	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	63	441	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.906	0.79	1	0.906	0.79	1	CLONAL	1	TRUE	1	0.44	2		441	316	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	133	627	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.44	2		633	598	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	206	467	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.44	2		467	907	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	269	348	10	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.963	1	1	0.996	1	CLONAL	2	TRUE	1	0.44	2		358	598	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	190	423	4	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.924	0.854	0.996	0.924	0.854	0.996	CLONAL	1	TRUE	1	0.44	2		427	935	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	192	714	0	ENST00000269305.4:c.569del	p.Pro190LeufsTer57	p.P190Lfs*57	ENST00000269305	NM_001126112.2	190	cCt/ct	6/11	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.44	2		714	860	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	174	685	5	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.44	2		690	718	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412248	63412248	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	209	515	1	ENST00000330258.3:c.919del	p.Asp307ThrfsTer3	p.D307Tfs*3	ENST00000330258	NM_152424.3	307	Gac/ac	2/2	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.44	1		516	538	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	158	621	2	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.44	2		623	691	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	75	393	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.861	0.758	0.97	0.861	0.758	0.97	CLONAL	1	TRUE	1	0.44	2		393	396	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123778	11123778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502056	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	179	609	1	ENST00000358026.2:c.2428G>A	p.Val810Met	p.V810M	ENST00000358026	NM_001128849.1	810	Gtg/Atg	16/36	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.44	2		610	752	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682399	52682400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	52	308	0	ENST00000394830.3:c.773dup	p.Asn258LysfsTer6	p.N258Kfs*6	ENST00000394830	NM_018313.4	258	aat/aaAt	8/30	1	2	FACETS	0.77	0.659	0.889	0.77	0.659	0.889	SUBCLONAL	1	TRUE	1	0.44	2		308	307	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261554	142261555	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1043355995	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	72	317	0	ENST00000350721.4:c.3402dup	p.Asn1135Ter	p.N1135*	ENST00000350721	NM_001184.3	1134	-/T	17/47	1	2	FACETS	0.974	0.857	1	0.974	0.857	1	CLONAL	1	TRUE	1	0.44	2		317	336	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	170	556	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.44	2		556	751	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	222	1000	7	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	0.441662547014809	2	FACETS	0.917	0.852	0.983	0.458	0.426	0.492	CLONAL	1	TRUE	0	0.44	2		1007	1101	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741760	145741760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759352592	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	209	825	0	ENST00000428558.2:c.743G>A	p.Arg248His	p.R248H	ENST00000428558	NM_004260.3	248	cGt/cAt	5/22	1	2	FACETS	0.974	0.905	1	0.974	0.905	1	CLONAL	1	TRUE	1	0.44	2		825	975	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349641	89349641	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs772267579	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	224	841	6	ENST00000301030.4:c.3309del	p.Asp1104MetfsTer214	p.D1104Mfs*214	ENST00000301030	NM_001256183.1	1103	aaA/aa	9/13	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.44	2		847	895	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593651	215593651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111367604	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	73	367	0	ENST00000260947.4:c.2083G>A	p.Val695Ile	p.V695I	ENST00000260947	NM_000465.2	695	Gtc/Atc	11/11	1	2	FACETS	0.794	0.697	0.897	0.794	0.697	0.897	SUBCLONAL	1	TRUE	1	0.44	2		367	418	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	121	451	4	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.44	2		455	468	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378244	15378244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	109	458	1	ENST00000263377.2:c.542G>A	p.Arg181His	p.R181H	ENST00000263377	NM_058243.2	181	cGt/cAt	4/20	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.44	2		459	482	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712520	52712520	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	64	511	0	ENST00000394830.3:c.232C>T	p.Arg78Ter	p.R78*	ENST00000394830	NM_018313.4	78	Cga/Tga	3/30	1	2	FACETS	0.505	0.437	0.578	0.505	0.437	0.578	SUBCLONAL	1	TRUE	1	0.44	2		511	576	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98247991	98247991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138034434	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	122	427	2	ENST00000331920.6:c.560G>A	p.Arg187His	p.R187H	ENST00000331920	NM_000264.3	187	cGt/cAt	3/24	1	2	FACETS	0.999	0.907	1	0.999	0.907	1	CLONAL	1	TRUE	1	0.44	2		429	555	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003767	45003767	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	135	541	0	ENST00000558401.1:c.23C>A	p.Ala8Asp	p.A8D	ENST00000558401	NM_004048.2	8	gCt/gAt	1/4	1	2	FACETS	0.831	0.757	0.91	0.831	0.757	0.91	CLONAL	1	TRUE	1	0.44	2		541	738	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678541	88678541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145157285	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	120	500	1	ENST00000360948.2:c.995C>T	p.Thr332Met	p.T332M	ENST00000360948	NM_001012338.2	332	aCg/aTg	9/19	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.44	2		501	523	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356423	66356423	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	75	315	1	ENST00000273854.3:c.1074del	p.Ser359LeufsTer63	p.S359Lfs*63	ENST00000273854	NM_004439.5	358	ccC/cc	5/18	1	2	FACETS	0.968	0.855	1	0.968	0.855	1	CLONAL	1	TRUE	1	0.44	2		316	352	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211461	46211461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	10	203	0	ENST00000334344.6:c.427C>T	p.Arg143Cys	p.R143C	ENST00000334344	NM_152641.2	143	Cgt/Tgt	5/21	1	2	FACETS	0.275	0.187	0.387	0.275	0.187	0.387	SUBCLONAL	1	TRUE	1	0.44	2		203	165	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235935	108235935	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770641163	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	81	426	0	ENST00000278616.4:c.8977C>T	p.Arg2993Ter	p.R2993*	ENST00000278616	NM_000051.3	2993	Cga/Tga	62/63	1	2	FACETS	0.92	0.816	1	0.92	0.816	1	CLONAL	1	TRUE	1	0.44	2		426	400	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001091	150001091	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753995655	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	71	450	1	ENST00000253339.5:c.2513G>A	p.Arg838His	p.R838H	ENST00000253339		838	cGt/cAt	4/7	1	2	FACETS	0.966	0.85	1	0.966	0.85	1	CLONAL	1	TRUE	1	0.44	2		451	334	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948796	17948796	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201972084	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	231	847	1	ENST00000458235.1:c.1646G>A	p.Arg549Gln	p.R549Q	ENST00000458235	NM_000215.3	549	cGa/cAa	12/24	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.44	2		848	1037	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351595	89351595	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	213	873	2	ENST00000301030.4:c.1355del	p.Asn452IlefsTer3	p.N452Ifs*3	ENST00000301030	NM_001256183.1	452	aAt/at	9/13	1	2	FACETS	0.991	0.921	1	0.991	0.921	1	CLONAL	1	TRUE	1	0.44	2		875	977	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390732	139390732	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	296	991	0	ENST00000277541.6:c.7459C>T	p.Gln2487Ter	p.Q2487*	ENST00000277541	NM_017617.3	2487	Cag/Tag	34/34	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.44	2		991	1240	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840564	36840564	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771002648	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	252	971	2	ENST00000358127.4:c.1169G>A	p.Arg390His	p.R390H	ENST00000358127	NM_001280556.1	390	cGt/cAt	10/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.44	2		973	1089	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165309	32165309	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	287	992	0	ENST00000375023.3:c.4819G>T	p.Gly1607Trp	p.G1607W	ENST00000375023	NM_004557.3	1607	Ggg/Tgg	27/30	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.44	2		992	1263	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610306	10610306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	312	998	0	ENST00000171111.5:c.404G>A	p.Arg135His	p.R135H	ENST00000171111	NM_203500.1	135	cGc/cAc	2/6	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.44	2		998	1226	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224111	36224111	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	204	676	0	ENST00000222270.7:c.6666del	p.Thr2223ProfsTer38	p.T2223Pfs*38	ENST00000222270	NM_014727.1	2221	Ccc/cc	28/37	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.44	2		676	868	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905505	11905505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774396176	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	68	304	2	ENST00000396373.4:c.155C>T	p.Ala52Val	p.A52V	ENST00000396373	NM_001987.4	52	gCg/gTg	2/8	1	2	FACETS	0.724	0.632	0.822	0.724	0.632	0.822	SUBCLONAL	1	TRUE	1	0.44	2		306	427	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732985	30732985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	119	464	0	ENST00000295754.5:c.1598G>A	p.Cys533Tyr	p.C533Y	ENST00000295754	NM_003242.5	533	tGt/tAt	7/7	1	2	FACETS	0.98	0.888	1	0.98	0.888	1	CLONAL	1	TRUE	1	0.44	2		464	552	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508860	106508860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1251220989	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	160	617	3	ENST00000359195.3:c.854C>T	p.Thr285Met	p.T285M	ENST00000359195	NM_002649.2	285	aCg/aTg	2/11	1	2	FACETS	0.992	0.912	1	0.992	0.912	1	CLONAL	1	TRUE	1	0.44	2		620	733	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874709	151874709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139770288	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	135	457	1	ENST00000262189.6:c.7829G>A	p.Arg2610Gln	p.R2610Q	ENST00000262189	NM_170606.2	2610	cGa/cAa	38/59	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.44	2		458	534	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882000	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	275	853	0	ENST00000269305.4:c.475G>A	p.Ala159Thr	p.A159T	ENST00000269305	NM_001126112.2	159	Gcc/Acc	5/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.44	2		853	1210	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855967	68855967	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	34	597	1	ENST00000261769.5:c.1779del	p.Ile594TyrfsTer19	p.I594Yfs*19	ENST00000261769	NM_004360.3	592	gCc/gc	12/16	1	2	FACETS	0.237	0.193	0.287	0.237	0.193	0.287	SUBCLONAL	1	TRUE	1	0.44	2		598	651	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250136	110250136	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	142	560	0	ENST00000374672.4:c.539del	p.Pro180LeufsTer14	p.P180Lfs*14	ENST00000374672	NM_004235.4	180	cCt/ct	3/5	1	2	FACETS	0.883	0.806	0.964	0.883	0.806	0.964	CLONAL	1	TRUE	1	0.44	2		560	731	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883773	37883774	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs766671083	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	65	887	0	ENST00000269571.5:c.3391dup	p.Leu1131ProfsTer8	p.L1131Pfs*8	ENST00000269571		1129	gcc/gCcc	26/27	1	2	FACETS	0.249	0.215	0.287	0.249	0.215	0.287	SUBCLONAL	1	TRUE	1	0.44	2		887	1186	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79968139	79968142	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs763478027	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	102	633	0	ENST00000265081.6:c.873_876del	p.Val292MetfsTer15	p.V292Mfs*15	ENST00000265081	NM_002439.4	290	cTGTTt/ct	5/24	1	2	FACETS	0.805	0.722	0.893	0.805	0.722	0.893	CLONAL	1	TRUE	1	0.44	2		633	576	SUCCESS
APC	324	MSKCC	GRCh37	5	112173848	112173849	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	rs794727160	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	87	393	0	ENST00000257430.4:c.2563_2564del	p.Glu855ThrfsTer56	p.E855Tfs*56	ENST00000257430	NM_000038.5	853	GAg/g	16/16	1	2	FACETS	0.939	0.836	1	0.939	0.836	1	CLONAL	1	TRUE	1	0.44	2		393	421	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633486	3633486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs181782315	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	229	941	0	ENST00000294008.3:c.4765C>T	p.Arg1589Cys	p.R1589C	ENST00000294008	NM_032444.2	1589	Cgc/Tgc	14/15	1	2	FACETS	0.924	0.86	0.989	0.924	0.86	0.989	CLONAL	1	TRUE	1	0.44	2		941	1127	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244038	5244038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771439798	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	251	794	0	ENST00000357368.4:c.1444G>A	p.Asp482Asn	p.D482N	ENST00000357368	NM_002850.3	482	Gac/Aac	11/38	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.44	2		794	1031	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387420	17387420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757371052	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	253	843	0	ENST00000359435.4:c.686C>T	p.Thr229Met	p.T229M	ENST00000359435	NM_001033549.1	229	aCg/aTg	7/9	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.44	2		843	1055	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812270	43812270	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	169	634	0	ENST00000372470.3:c.1135C>A	p.Leu379Met	p.L379M	ENST00000372470	NM_005373.2	379	Ctg/Atg	7/12	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.44	2		634	756	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681435	88681435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554891354	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	161	679	0	ENST00000372037.3:c.1325G>A	p.Arg442His	p.R442H	ENST00000372037	NM_004329.2	442	cGt/cAt	11/13	1	2	FACETS	0.955	0.878	1	0.955	0.878	1	CLONAL	1	TRUE	1	0.44	2		679	766	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066749	77066749	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	99	412	0	ENST00000356341.3:c.736C>T	p.Pro246Ser	p.P246S	ENST00000356341	NM_002576.4	246	Cct/Tct	7/15	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.44	2		412	417	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008202	29008202	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	70	354	0	ENST00000282397.4:c.669T>A	p.His223Gln	p.H223Q	ENST00000282397	NM_002019.4	223	caT/caA	5/30	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.44	2		354	307	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396549	30396549	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	143	499	0	ENST00000331968.5:c.170T>C	p.Leu57Pro	p.L57P	ENST00000331968	NM_002742.2	57	cTg/cCg	1/18	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.44	2		499	640	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341226	341226	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1290523788	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	269	943	0	ENST00000262320.3:c.2258T>C	p.Val753Ala	p.V753A	ENST00000262320	NM_003502.3	753	gTa/gCa	9/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.44	2		943	1115	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223188	2223188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373051088	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	221	737	1	ENST00000326181.6:c.800C>T	p.Thr267Met	p.T267M	ENST00000326181	NM_032271.2	267	aCg/aTg	10/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.44	2		738	915	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026160	36026160	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	207	937	1	ENST00000358208.4:c.762G>T	p.Gln254His	p.Q254H	ENST00000358208		254	caG/caT	7/12	1	2	FACETS	0.813	0.754	0.875	0.813	0.754	0.875	CLONAL	1	TRUE	1	0.44	2		938	1157	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940765	49940765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540212347	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	179	688	0	ENST00000296474.3:c.278C>T	p.Thr93Met	p.T93M	ENST00000296474	NM_002447.2	93	aCg/aTg	1/20	1	2	FACETS	0.998	0.922	1	0.998	0.922	1	CLONAL	1	TRUE	1	0.44	2		688	815	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627780	187627780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767098741	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	163	592	0	ENST00000441802.2:c.3202G>A	p.Glu1068Lys	p.E1068K	ENST00000441802	NM_005245.3	1068	Gag/Aag	2/27	0.441662547014809	3	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.44	3		592	678	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956595	93956595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	73	362	0	ENST00000369303.4:c.2641C>T	p.Pro881Ser	p.P881S	ENST00000369303	NM_004440.3	881	Cca/Tca	15/17	1	2	FACETS	0.904	0.796	1	0.904	0.796	1	CLONAL	1	TRUE	1	0.44	2		362	367	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843323	128843323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	256	890	0	ENST00000249373.3:c.430C>T	p.Arg144Cys	p.R144C	ENST00000249373	NM_005631.4	144	Cgt/Tgt	2/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.44	2		890	1108	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	239	544	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.309266837166318	5	FACETS	1	0.979	1	0.743	0.694	0.794	CLONAL	2	TRUE	2	0.309266837166318	5		544	1015	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0042647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	286	866	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.184245136643521	2	FACETS	0.924	0.87	0.979	0.924	0.87	0.979	INDETERMINATE	2	TRUE	0	0.309266837166318	2		866	1001	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983017	149983017	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757876116	NA	P-0042647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	52	542	0	ENST00000253339.5:c.3241C>T	p.Arg1081Ter	p.R1081*	ENST00000253339		1081	Cga/Tga	7/7	0.309266837166318	3	FACETS	0.991	0.879	1	1	0.968	1	CLONAL	4	TRUE	0	0.309266837166318	3		542	98	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0042662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	68	485	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.815	0.712	0.925	0.815	0.712	0.925	CLONAL	1	FALSE	1	0.420261524220452	2		485	397	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0042666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	171	590	0	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.521115377031764	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.521115377031764	1		590	420	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0042666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	578	274	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.521115377031764	5	FACETS	0.886	0.856	0.917			1	CLONAL	4	TRUE	NA	0.521115377031764	5		274	1115	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974795	21974795	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	57	187	0	ENST00000304494.5:c.32del	p.Pro11LeufsTer15	p.P11Lfs*15	ENST00000304494	NM_000077.4	11	cCt/ct	1/3	0.521115377031764	1	FACETS	0.963	0.843	1	0.963	0.843	1	CLONAL	1	TRUE	0	0.521115377031764	1		187	168	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0042668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	15	326	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.358	0.26	0.477	0.358	0.26	0.477	SUBCLONAL	1	TRUE	1	0.13	2		326	644	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515241	106515241	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143259740	NA	P-0042680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	33	328	0	ENST00000359195.3:c.2384C>T	p.Ala795Val	p.A795V	ENST00000359195	NM_002649.2	795	gCg/gTg	5/11	1	2	FACETS	0.393	0.32	0.474	0.393	0.32	0.474	SUBCLONAL	1	TRUE	1	0.495368944030119	2		328	339	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984913	55984913	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	149	489	0	ENST00000263923.4:c.216A>T	p.Gln72His	p.Q72H	ENST00000263923	NM_002253.2	72	caA/caT	3/30	1	2	FACETS	0.815	0.746	0.887	0.815	0.746	0.887	CLONAL	1	TRUE	1	0.495368944030119	2		489	738	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	90	441	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.933	0.832	1	0.933	0.832	1	CLONAL	1	TRUE	1	0.444704213308177	2		441	434	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	353	790	3	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	0.444704213308177	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.444704213308177	2		793	794	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	144	627	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.884	0.807	0.963	0.884	0.807	0.963	CLONAL	1	TRUE	1	0.444704213308177	2		633	733	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	157	605	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.444704213308177	2		608	695	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	212	255	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.944	0.886	1	1	0.994	1	CLONAL	2	TRUE	1	0.444704213308177	2		255	505	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	116	486	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	0.444704213308177	2	FACETS	0.92	0.832	1	0.46	0.416	0.506	CLONAL	1	TRUE	0	0.444704213308177	2		488	567	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201089	108201089	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779865	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	105	317	0	ENST00000278616.4:c.7456C>T	p.Arg2486Ter	p.R2486*	ENST00000278616	NM_000051.3	2486	Cga/Tga	50/63	1	2	FACETS	0.978	0.88	1	0.978	0.88	1	CLONAL	1	TRUE	1	0.444704213308177	2		317	483	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914592	32914592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1799954	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	111	387	0	ENST00000380152.3:c.6100C>T	p.Arg2034Cys	p.R2034C	ENST00000380152		2034	Cgt/Tgt	11/27	1	2	FACETS	0.779	0.701	0.861	0.779	0.701	0.861	SUBCLONAL	1	TRUE	1	0.444704213308177	2		387	641	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308383	15308383	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	153	499	1	ENST00000263388.2:c.125del	p.Pro42LeufsTer194	p.P42Lfs*194	ENST00000263388	NM_000435.2	42	cCt/ct	2/33	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.444704213308177	2		500	646	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460354	149460354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437040009	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	142	415	1	ENST00000286301.3:c.283G>A	p.Ala95Thr	p.A95T	ENST00000286301	NM_005211.3	95	Gcc/Acc	3/22	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.444704213308177	2		416	553	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852118	63852118	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	149	477	0	ENST00000279873.7:c.2901del	p.Lys967AsnfsTer15	p.K967Nfs*15	ENST00000279873	NM_032199.2	966	Aaa/aa	10/10	1	2	FACETS	0.96	0.879	1	0.96	0.879	1	CLONAL	1	TRUE	1	0.444704213308177	2		477	698	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	145	407	0	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.444704213308177	2		407	569	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796882	42796883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761345552	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	169	597	1	ENST00000575354.2:c.3347dup	p.Ser1117LysfsTer34	p.S1117Kfs*34	ENST00000575354	NM_015125.3	1114	gcc/gCcc	14/20	1	2	FACETS	0.903	0.831	0.978	0.903	0.831	0.978	CLONAL	1	TRUE	1	0.444704213308177	2		598	842	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	152	435	0	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.994	0.911	1	0.994	0.911	1	CLONAL	1	TRUE	1	0.444704213308177	2		435	688	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715678	30715678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039551	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	109	256	0	ENST00000295754.5:c.1336G>A	p.Asp446Asn	p.D446N	ENST00000295754	NM_003242.5	446	Gat/Aat	5/7	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.444704213308177	2		256	469	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178635	32178635	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs761063325	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	62	606	2	ENST00000375023.3:c.2759del	p.Pro920LeufsTer12	p.P920Lfs*12	ENST00000375023	NM_004557.3	920	cCt/ct	18/30	0.444704213308177	1	FACETS	0.315	0.271	0.362	0.315	0.271	0.362	SUBCLONAL	1	TRUE	0	0.444704213308177	1		608	689	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166010	118166010	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767827215	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	110	411	0	ENST00000369448.3:c.520C>T	p.Arg174Trp	p.R174W	ENST00000369448	NM_017709.3	174	Cgg/Tgg	2/2	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.444704213308177	2		411	494	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044408	128044408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373790042	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	155	541	1	ENST00000285398.2:c.1213G>A	p.Val405Ile	p.V405I	ENST00000285398	NM_000122.1	405	Gtt/Att	8/15	1	2	FACETS	0.936	0.858	1	0.936	0.858	1	CLONAL	1	TRUE	1	0.444704213308177	2		542	745	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439282	149439282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766586864	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	128	415	0	ENST00000286301.3:c.2113G>A	p.Glu705Lys	p.E705K	ENST00000286301	NM_005211.3	705	Gag/Aag	15/22	1	2	FACETS	0.926	0.841	1	0.926	0.841	1	CLONAL	1	TRUE	1	0.444704213308177	2		415	622	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460538	8460538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772029273	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	129	374	1	ENST00000356435.5:c.3748G>A	p.Val1250Met	p.V1250M	ENST00000356435		1250	Gtg/Atg	22/35	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.444704213308177	2		375	577	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561492	141561492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	148	465	0	ENST00000220592.5:c.1313G>A	p.Arg438Gln	p.R438Q	ENST00000220592	NM_012154.3	438	cGg/cAg	11/19	0.444704213308177	3	FACETS	0.947	0.865	1	0.474	0.432	0.517	CLONAL	1	TRUE	1	0.444704213308177	3		465	859	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223175	36223175	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	179	575	1	ENST00000222270.7:c.5730del	p.Arg1911AspfsTer23	p.R1911Dfs*23	ENST00000222270	NM_014727.1	1909	Ccc/cc	28/37	1	2	FACETS	0.91	0.839	0.983	0.91	0.839	0.983	CLONAL	1	TRUE	1	0.444704213308177	2		576	885	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441816	49441816	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	171	484	3	ENST00000301067.7:c.4168del	p.Ala1390GlnfsTer27	p.A1390Qfs*27	ENST00000301067	NM_003482.3	1390	Gca/ca	14/54	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.444704213308177	2		487	754	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911587	114911587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	169	437	0	ENST00000543371.1:c.1105G>A	p.Val369Ile	p.V369I	ENST00000543371	NM_001198531.1	369	Gta/Ata	10/14	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.444704213308177	2		437	719	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	159	520	4	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.444704213308177	2		524	661	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467921	50467921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	132	415	0	ENST00000331340.3:c.1156C>T	p.Arg386Cys	p.R386C	ENST00000331340	NM_006060.4	386	Cgc/Tgc	8/8	1	2	FACETS	0.928	0.844	1	0.928	0.844	1	CLONAL	1	TRUE	1	0.444704213308177	2		415	640	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976689	55976689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747477930	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	121	405	0	ENST00000263923.4:c.1136C>T	p.Ala379Val	p.A379V	ENST00000263923	NM_002253.2	379	gCg/gTg	9/30	1	2	FACETS	0.979	0.888	1	0.979	0.888	1	CLONAL	1	TRUE	1	0.444704213308177	2		405	556	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483963	212483963	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	100	318	0	ENST00000342788.4:c.2240C>A	p.Pro747His	p.P747H	ENST00000342788	NM_005235.2	747	cCt/cAt	19/28	NA	2	FACETS	0.831	0.745	0.923			1	INDETERMINATE	1	TRUE	NA	0.444704213308177	2		318	541	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797401	45797401	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35352891	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	163	540	0	ENST00000450313.1:c.1118C>T	p.Ala373Val	p.A373V	ENST00000450313	NM_012222.2	373	gCc/gTc	12/16	1	2	FACETS	0.979	0.9	1	0.979	0.9	1	CLONAL	1	TRUE	1	0.444704213308177	2		540	749	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458578	120458578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148759277	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	161	440	0	ENST00000256646.2:c.6767G>A	p.Arg2256His	p.R2256H	ENST00000256646	NM_024408.3	2256	cGc/cAc	34/34	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.444704213308177	2		440	663	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912356	97912356	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs769039987	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	114	285	0	ENST00000289081.3:c.535C>T	p.Arg179Ter	p.R179*	ENST00000289081	NM_000136.2	179	Cga/Tga	7/15	1	2	FACETS	0.89	0.804	0.981	0.89	0.804	0.981	CLONAL	1	TRUE	1	0.444704213308177	2		285	576	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223431	36223431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs546000224	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	241	637	0	ENST00000222270.7:c.5981C>T	p.Ala1994Val	p.A1994V	ENST00000222270	NM_014727.1	1994	gCg/gTg	28/37	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.444704213308177	2		637	944	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778817	9778817	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	162	516	0	ENST00000377346.4:c.1086G>T	p.Glu362Asp	p.E362D	ENST00000377346	NM_005026.3	362	gaG/gaT	9/24	1	2	FACETS	0.885	0.813	0.961	0.885	0.813	0.961	CLONAL	1	TRUE	1	0.444704213308177	2		516	823	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180582	94180582	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	47	359	0	ENST00000323929.3:c.1586T>C	p.Leu529Pro	p.L529P	ENST00000323929	NM_005591.3	529	cTc/cCc	15/20	1	2	FACETS	0.443	0.374	0.519	0.443	0.374	0.519	SUBCLONAL	1	TRUE	1	0.444704213308177	2		359	477	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022550	12022550	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs752454285	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	153	510	0	ENST00000396373.4:c.656A>G	p.Gln219Arg	p.Q219R	ENST00000396373	NM_001987.4	219	cAg/cGg	5/8	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.444704213308177	2		510	685	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434812	99434812	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	120	459	0	ENST00000268035.6:c.899A>C	p.Asp300Ala	p.D300A	ENST00000268035	NM_000875.3	300	gAc/gCc	3/21	1	2	FACETS	0.812	0.734	0.893	0.812	0.734	0.893	CLONAL	1	TRUE	1	0.444704213308177	2		459	665	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339524	339524	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	189	573	0	ENST00000262320.3:c.2378C>A	p.Pro793His	p.P793H	ENST00000262320	NM_003502.3	793	cCc/cAc	10/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.444704213308177	2		573	818	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56871563	56871563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1269746871	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	139	384	0	ENST00000308159.5:c.1943C>T	p.Pro648Leu	p.P648L	ENST00000308159	NM_014669.4	648	cCt/cTt	18/22	1	2	FACETS	0.994	0.908	1	0.994	0.908	1	CLONAL	1	TRUE	1	0.444704213308177	2		384	629	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829079	72829079	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	136	526	0	ENST00000268489.5:c.7502C>A	p.Pro2501His	p.P2501H	ENST00000268489	NM_006885.3	2501	cCt/cAt	9/10	1	2	FACETS	0.968	0.883	1	0.968	0.883	1	CLONAL	1	TRUE	1	0.444704213308177	2		526	632	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805344	89805344	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	143	428	1	ENST00000389301.3:c.4206del	p.Leu1403CysfsTer4	p.L1403Cfs*4	ENST00000389301	NM_000135.2	1402	ttT/tt	42/43	1	2	FACETS	0.906	0.827	0.988	0.906	0.827	0.988	CLONAL	1	TRUE	1	0.444704213308177	2		429	710	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877377	89877377	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs577625130	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	168	436	1	ENST00000389301.3:c.386C>T	p.Ala129Val	p.A129V	ENST00000389301	NM_000135.2	129	gCg/gTg	4/43	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.444704213308177	2		437	746	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752347	55752347	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1485302383	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	164	507	0	ENST00000284073.2:c.805C>T	p.Arg269Trp	p.R269W	ENST00000284073	NM_138962.2	269	Cgg/Tgg	12/14	0.444704213308177	2	FACETS	0.964	0.887	1	0.482	0.443	0.523	CLONAL	1	TRUE	0	0.444704213308177	2		507	765	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2214544	2214544	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	192	539	0	ENST00000398665.3:c.1872G>T	p.Gln624His	p.Q624H	ENST00000398665	NM_032482.2	624	caG/caT	19/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.444704213308177	2		539	781	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46588037	46588037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780349023	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	156	484	1	ENST00000263734.3:c.587C>T	p.Thr196Met	p.T196M	ENST00000263734	NM_001430.4	196	aCg/aTg	6/16	0.444704213308177	2	FACETS	0.987	0.906	1	0.493	0.453	0.536	CLONAL	1	TRUE	0	0.444704213308177	2		485	711	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161945	47161945	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	107	249	0	ENST00000409792.3:c.4181A>G	p.Glu1394Gly	p.E1394G	ENST00000409792	NM_014159.6	1394	gAa/gGa	3/21	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.444704213308177	2		249	450	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505038	186505039	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	78	251	0	ENST00000323963.5:c.896_897del	p.Thr299SerfsTer7	p.T299Sfs*7	ENST00000323963		298	ttCAca/ttca	8/11	1	2	FACETS	0.858	0.758	0.964	0.858	0.758	0.964	CLONAL	1	TRUE	1	0.444704213308177	2		251	409	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99812387	99812387	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	87	317	0	ENST00000280892.6:c.281+1G>A		p.X94_splice	ENST00000280892	NM_001130678.1	94			1	2	FACETS	0.754	0.669	0.844	0.754	0.669	0.844	SUBCLONAL	1	TRUE	1	0.444704213308177	2		317	519	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540268	187540268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760291675	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	122	331	0	ENST00000441802.2:c.7472C>T	p.Ala2491Val	p.A2491V	ENST00000441802	NM_005245.3	2491	gCt/gTt	10/27	1	2	FACETS	0.994	0.902	1	0.994	0.902	1	CLONAL	1	TRUE	1	0.444704213308177	2		331	552	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236639	236639	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770028533	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	124	395	0	ENST00000264932.6:c.1357G>A	p.Gly453Arg	p.G453R	ENST00000264932	NM_004168.2	453	Ggg/Agg	10/15	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.444704213308177	2		395	517	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589652	67589652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1383740979	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	57	114	0	ENST00000274335.5:c.1415G>A	p.Arg472His	p.R472H	ENST00000274335		472	cGc/cAc	10/15	1	2	FACETS	0.946	0.819	1	0.946	0.819	1	CLONAL	1	TRUE	1	0.444704213308177	2		114	271	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517800	176517800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199792541	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	142	496	0	ENST00000292408.4:c.410C>T	p.Ser137Leu	p.S137L	ENST00000292408	NM_213647.1	137	tCg/tTg	4/18	1	2	FACETS	0.901	0.822	0.983	0.901	0.822	0.983	CLONAL	1	TRUE	1	0.444704213308177	2		496	709	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041155	180041155	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	176	583	0	ENST00000261937.6:c.3244G>A	p.Ala1082Thr	p.A1082T	ENST00000261937	NM_182925.4	1082	Gcc/Acc	24/30	1	2	FACETS	0.966	0.891	1	0.966	0.891	1	CLONAL	1	TRUE	1	0.444704213308177	2		583	819	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324660	31324660	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	185	419	0	ENST00000412585.2:c.148G>T	p.Gly50Cys	p.G50C	ENST00000412585	NM_005514.6	50	Ggc/Tgc	2/8	0.444704213308177	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.444704213308177	1		419	468	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800486	32800486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773325619	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	221	602	3	ENST00000374899.4:c.1061G>A	p.Arg354His	p.R354H	ENST00000374899	NM_018833.2	354	cGc/cAc	6/12	0.444704213308177	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.444704213308177	1		605	705	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818233	32818234	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs879888996	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	207	523	0	ENST00000354258.4:c.1291_1292del	p.Leu431ValfsTer20	p.L431Vfs*20	ENST00000354258	NM_000593.5	431	CTg/g	5/11	0.444704213308177	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.444704213308177	1		523	613	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141557613	141557613	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	61	577	0	ENST00000220592.5:c.1702A>G	p.Asn568Asp	p.N568D	ENST00000220592	NM_012154.3	568	Aac/Gac	13/19	0.444704213308177	3	FACETS	0.32	0.275	0.369	0.16	0.137	0.185	SUBCLONAL	1	TRUE	1	0.444704213308177	3		577	1048	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27168522	27168522	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	122	374	0	ENST00000380036.4:c.394A>G	p.Thr132Ala	p.T132A	ENST00000380036	NM_000459.3	132	Act/Gct	3/23	1	2	FACETS	0.932	0.845	1	0.932	0.845	1	CLONAL	1	TRUE	1	0.444704213308177	2		374	589	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041936	14041936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	164	298	0	ENST00000311895.7:c.2483C>T	p.Ala828Val	p.A828V	ENST00000311895	NM_005236.2	828	gCa/gTa	11/11	1	2	FACETS	0.965	0.897	1	0.965	0.897	1	CLONAL	1	TRUE	1	0.828608406669245	2		298	410	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0042763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	152	486	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	0.494098207860993	1	FACETS	0.788	0.724	0.854	0.788	0.724	0.854	SUBCLONAL	1	TRUE	0	0.494098207860993	1		488	588	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777652	9777652	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	253	688	0	ENST00000377346.4:c.988G>T	p.Gly330Cys	p.G330C	ENST00000377346	NM_005026.3	330	Ggc/Tgc	8/24	0.32087551479875	1	FACETS	0.864	0.81	0.92	0.864	0.81	0.92	CLONAL	1	TRUE	0	0.494098207860993	1		688	892	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416542	49416542	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	112	566	0	ENST00000301067.7:c.16169G>A	p.Arg5390Gln	p.R5390Q	ENST00000301067	NM_003482.3	5390	cGg/cAg	51/54	1	2	FACETS	0.597	0.537	0.661	0.597	0.537	0.661	SUBCLONAL	1	TRUE	1	0.494098207860993	2		566	759	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427974	49427974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	173	668	1	ENST00000301067.7:c.10616G>A	p.Arg3539Gln	p.R3539Q	ENST00000301067	NM_003482.3	3539	cGg/cAg	38/54	1	2	FACETS	0.898	0.828	0.97	0.898	0.828	0.97	CLONAL	1	TRUE	1	0.494098207860993	2		669	780	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431154	49431154	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	75	616	0	ENST00000301067.7:c.9985C>G	p.Leu3329Val	p.L3329V	ENST00000301067	NM_003482.3	3329	Ctg/Gtg	34/54	1	2	FACETS	0.369	0.323	0.42	0.369	0.323	0.42	SUBCLONAL	1	TRUE	1	0.494098207860993	2		616	822	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120676	115120676	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	120	735	0	ENST00000257566.3:c.330A>C	p.Lys110Asn	p.K110N	ENST00000257566	NM_016569.3	110	aaA/aaC	1/8	1	2	FACETS	0.48	0.433	0.531	0.48	0.433	0.531	SUBCLONAL	1	TRUE	1	0.494098207860993	2		735	1011	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562919	21562919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770192145	NA	P-0042763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	213	631	1	ENST00000382592.4:c.1000C>T	p.Arg334Cys	p.R334C	ENST00000382592	NM_014572.2	334	Cgc/Tgc	4/8	0.494098207860993	1	FACETS	0.86	0.801	0.92	0.86	0.801	0.92	CLONAL	1	TRUE	0	0.494098207860993	1		632	755	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039339	49039339	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0042763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	127	554	0	ENST00000267163.4:c.2326-2A>G		p.X776_splice	ENST00000267163	NM_000321.2	776			0.494098207860993	1	FACETS	0.552	0.501	0.606	0.552	0.501	0.606	SUBCLONAL	1	TRUE	0	0.494098207860993	1		554	701	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984856	9984856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	99	531	1	ENST00000330684.3:c.1109G>A	p.Arg370Gln	p.R370Q	ENST00000330684	NM_001134407.1	370	cGg/cAg	4/13	0.32087551479875	1	FACETS	0.475	0.425	0.529	0.475	0.425	0.529	SUBCLONAL	1	TRUE	0	0.494098207860993	1		532	635	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993864	72993864	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	81	501	1	ENST00000268489.5:c.181C>A	p.Leu61Ile	p.L61I	ENST00000268489	NM_006885.3	61	Ctc/Atc	2/10	0.32087551479875	1	FACETS	0.478	0.422	0.538	0.478	0.422	0.538	SUBCLONAL	1	TRUE	0	0.494098207860993	1		502	516	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438223	56438223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	81	660	0	ENST00000407977.2:c.770G>A	p.Gly257Asp	p.G257D	ENST00000407977		257	gGt/gAt	7/10	0.32087551479875	1	FACETS	0.346	0.304	0.39	0.346	0.304	0.39	SUBCLONAL	1	TRUE	0	0.494098207860993	1		660	714	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448328	56448328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199909371	NA	P-0042763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	130	750	2	ENST00000407977.2:c.319G>A	p.Val107Ile	p.V107I	ENST00000407977		107	Gtc/Atc	3/10	0.32087551479875	1	FACETS	0.464	0.421	0.51	0.464	0.421	0.51	SUBCLONAL	1	TRUE	0	0.494098207860993	1		752	853	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530076	63530076	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	39	630	1	ENST00000307078.5:c.2359A>G	p.Thr787Ala	p.T787A	ENST00000307078	NM_004655.3	787	Acc/Gcc	10/11	0.32087551479875	1	FACETS	0.158	0.13	0.19	0.158	0.13	0.19	SUBCLONAL	1	TRUE	0	0.494098207860993	1		631	751	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240290	5240290	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	130	737	0	ENST00000357368.4:c.1624A>G	p.Thr542Ala	p.T542A	ENST00000357368	NM_002850.3	542	Acg/Gcg	12/38	1	2	FACETS	0.492	0.445	0.542	0.492	0.445	0.542	SUBCLONAL	1	TRUE	1	0.494098207860993	2		737	1069	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243944	5243944	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	83	526	0	ENST00000357368.4:c.1538C>T	p.Ser513Leu	p.S513L	ENST00000357368	NM_002850.3	513	tCg/tTg	11/38	1	2	FACETS	0.377	0.332	0.426	0.377	0.332	0.426	SUBCLONAL	1	TRUE	1	0.494098207860993	2		526	890	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446385	29446385	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs72852032	NA	P-0042763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	265	755	1	ENST00000389048.3:c.3182G>A	p.Arg1061Gln	p.R1061Q	ENST00000389048	NM_004304.4	1061	cGg/cAg	20/29	0.120021307861353	5	FACETS	0.8	0.749	0.852			1	INDETERMINATE	2	TRUE	NA	0.494098207860993	5		756	1168	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027496	48027496	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	157	421	0	ENST00000234420.5:c.2374C>G	p.Leu792Val	p.L792V	ENST00000234420	NM_000179.2	792	Cta/Gta	4/10	0.494098207860993	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.494098207860993	1		421	426	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99163069	99163069	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs775824571	NA	P-0042763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	69	450	0	ENST00000074304.5:c.1075A>G	p.Thr359Ala	p.T359A	ENST00000074304	NM_001134224.1	359	Acc/Gcc	13/26	1	2	FACETS	0.42	0.365	0.479	0.42	0.365	0.479	SUBCLONAL	1	TRUE	1	0.494098207860993	2		450	665	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439722	220439722	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	96	726	0	ENST00000243786.2:c.575C>A	p.Pro192His	p.P192H	ENST00000243786	NM_002191.3	192	cCc/cAc	2/2	0.494098207860993	1	FACETS	0.401	0.357	0.448	0.401	0.357	0.448	SUBCLONAL	1	TRUE	0	0.494098207860993	1		726	730	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008519	70008519	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	78	411	0	ENST00000394351.3:c.806A>C	p.Asn269Thr	p.N269T	ENST00000394351	NM_000248.3	269	aAc/aCc	8/9	0.494098207860993	1	FACETS	0.475	0.419	0.536	0.475	0.419	0.536	SUBCLONAL	1	TRUE	0	0.494098207860993	1		411	500	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911587	134911587	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	92	485	0	ENST00000398015.3:c.2052G>T	p.Glu684Asp	p.E684D	ENST00000398015	NM_004441.4	684	gaG/gaT	11/16	0.141760415998448	6	FACETS	0.71	0.629	0.797			1	INDETERMINATE	1	TRUE	NA	0.494098207860993	6		485	1043	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231113	142231113	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	150	358	0	ENST00000350721.4:c.4841T>C	p.Val1614Ala	p.V1614A	ENST00000350721	NM_001184.3	1614	gTa/gCa	27/47	0.494098207860993	4	FACETS	1	0.931	1	0.511	0.467	0.557	CLONAL	1	TRUE	2	0.494098207860993	4		358	888	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442853	187442853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766041104	NA	P-0042763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	69	411	0	ENST00000232014.4:c.1853G>A	p.Arg618His	p.R618H	ENST00000232014	NM_001130845.1	618	cGt/cAt	9/10	0.494098207860993	4	FACETS	0.499	0.433	0.57	0.249	0.216	0.285	SUBCLONAL	1	TRUE	2	0.494098207860993	4		411	837	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247373	153247373	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	51	283	0	ENST00000281708.4:c.1429G>T	p.Gly477Cys	p.G477C	ENST00000281708	NM_033632.3	477	Ggt/Tgt	10/12	0.494098207860993	1	FACETS	0.456	0.389	0.528	0.456	0.389	0.528	SUBCLONAL	1	TRUE	0	0.494098207860993	1		283	341	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517762	187517762	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	18	249	0	ENST00000441802.2:c.12932del	p.Pro4311HisfsTer38	p.P4311Hfs*38	ENST00000441802	NM_005245.3	4311	cCa/ca	25/27	0.494098207860993	1	FACETS	0.173	0.13	0.224	0.173	0.13	0.224	SUBCLONAL	1	TRUE	0	0.494098207860993	1		249	317	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950501	38950501	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	89	455	0	ENST00000357387.3:c.3449T>C	p.Ile1150Thr	p.I1150T	ENST00000357387	NM_152756.3	1150	aTa/aCa	31/38	0.235224955238431	2	FACETS	0.585	0.519	0.655	0.292	0.259	0.328	INDETERMINATE	1	TRUE	0	0.494098207860993	2		455	616	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43746254	43746254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	194	551	0	ENST00000523873.1:c.373C>T	p.His125Tyr	p.H125Y	ENST00000523873		125	Cac/Tac	4/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.494098207860993	2		551	725	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13949304	13949304	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	54	327	0	ENST00000405192.2:c.824C>A	p.Pro275His	p.P275H	ENST00000405192	NM_001163147.1	275	cCc/cAc	9/12	0.32087551479875	1	FACETS	0.41	0.351	0.475	0.41	0.351	0.475	SUBCLONAL	1	TRUE	0	0.494098207860993	1		327	401	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877031	151877031	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	74	470	1	ENST00000262189.6:c.7330A>G	p.Arg2444Gly	p.R2444G	ENST00000262189	NM_170606.2	2444	Agg/Ggg	37/59	0.32087551479875	1	FACETS	0.408	0.357	0.462	0.408	0.357	0.462	SUBCLONAL	1	TRUE	0	0.494098207860993	1		471	553	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559308	141559308	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	198	688	2	ENST00000220592.5:c.1493C>T	p.Ala498Val	p.A498V	ENST00000220592	NM_012154.3	498	gCg/gTg	12/19	1	2	FACETS	0.943	0.874	1	0.943	0.874	1	CLONAL	1	TRUE	1	0.494098207860993	2		690	850	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030529	47030529	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	124	700	1	ENST00000377604.3:c.304T>C	p.Tyr102His	p.Y102H	ENST00000377604	NM_001204468.1	102	Tat/Cat	4/24	1	2	FACETS	0.564	0.51	0.621	0.564	0.51	0.621	SUBCLONAL	1	TRUE	1	0.494098207860993	2		701	890	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228014	53228014	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	237	700	1	ENST00000375401.3:c.2300C>T	p.Ala767Val	p.A767V	ENST00000375401	NM_004187.3	767	gCt/gTt	16/26	1	2	FACETS	0.993	0.928	1	0.993	0.928	1	CLONAL	1	TRUE	1	0.494098207860993	2		701	966	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938326	76938326	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	185	605	0	ENST00000373344.5:c.2422C>T	p.Arg808Ter	p.R808*	ENST00000373344	NM_000489.3	808	Cga/Tga	9/35	1	2	FACETS	0.98	0.907	1	0.98	0.907	1	CLONAL	1	TRUE	1	0.494098207860993	2		605	764	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0042765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	154	393	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.967	0.894	1	0.967	0.894	1	CLONAL	1	TRUE	1	0.749814672673993	2		393	425	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0042765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	152	326	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA	2	FACETS	0.839	0.774	0.907			1	INDETERMINATE	1	TRUE	NA	0.749814672673993	2		326	483	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0042765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	167	428	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.942	0.873	1	0.942	0.873	1	CLONAL	1	TRUE	1	0.749814672673993	2		428	473	SUCCESS
APC	324	MSKCC	GRCh37	5	112173926	112173926	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060503287	NA	P-0042765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	174	417	0	ENST00000257430.4:c.2635C>T	p.Gln879Ter	p.Q879*	ENST00000257430	NM_000038.5	879	Cag/Tag	16/16	1	2	FACETS	0.987	0.918	1	0.987	0.918	1	CLONAL	1	TRUE	1	0.749814672673993	2		417	470	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900291	101900291	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	181	445	0	ENST00000374994.4:c.725G>A	p.Trp242Ter	p.W242*	ENST00000374994	NM_004612.2	242	tGg/tAg	4/9	0.749814672673993	1	FACETS	0.917	0.863	0.971	0.917	0.863	0.971	CLONAL	1	TRUE	0	0.749814672673993	1		445	329	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589209	67589223	+	inframe_deletion	In_Frame_Del	DEL	TTCTGTGGTTGAATT	TTCTGTGGTTGAATT	-	novel	NA	P-0042765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	143	404	0	ENST00000274335.5:c.1197_1211del	p.Ser399_Leu404delinsArg	p.S399_L404delinsR	ENST00000274335		399	agTTCTGTGGTTGAATTa/aga	9/15	1	2	FACETS	0.79	0.725	0.856	0.79	0.725	0.856	SUBCLONAL	1	TRUE	1	0.749814672673993	2		404	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0042784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	271	619	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.310503600997234	2	FACETS	0.949	0.892	1	0.949	0.892	1	CLONAL	2	FALSE	0	0.310503600997234	2		619	920	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682303	37682303	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121541-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	122	874	0	ENST00000447079.4:c.3494C>A	p.Ser1165Tyr	p.S1165Y	ENST00000447079	NM_015083.1	1165	tCc/tAc	13/14	0.270958522818418	2	FACETS	0.69	0.627	0.756	0.345	0.313	0.378	INDETERMINATE	1	NA	0	0.717049341039129	2		874	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0042805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	432	1033	5	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.640927481409969	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.640927481409969	1		1038	913	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908179	28908179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	109	572	0	ENST00000282397.4:c.2576C>T	p.Ala859Val	p.A859V	ENST00000282397	NM_002019.4	859	gCt/gTt	18/30	0.303227639048513	1	FACETS	0.546	0.494	0.601	0.546	0.494	0.601	INDETERMINATE	1	TRUE	0	0.640927481409969	1		572	423	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967932	93967932	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	20	595	0	ENST00000369303.4:c.1995A>T	p.Lys665Asn	p.K665N	ENST00000369303	NM_004440.3	665	aaA/aaT	11/17	1	2	FACETS	0.167	0.127	0.214	0.167	0.127	0.214	SUBCLONAL	1	TRUE	1	0.640927481409969	2		595	374	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342636	70342636	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	188	785	0	ENST00000374080.3:c.1397A>G	p.His466Arg	p.H466R	ENST00000374080		466	cAt/cGt	10/45	1	2	FACETS	0.796	0.737	0.856	0.796	0.737	0.856	SUBCLONAL	1	TRUE	1	0.640927481409969	2		785	737	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0042820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	213	773	2	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.18210700906045	3	FACETS	1	0.981	1	0.751	0.703	0.8	INDETERMINATE	2	TRUE	0	0.389477382870163	3		775	580	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955382	48955382	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0042820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	20	215	0	ENST00000267163.4:c.1499del		p.X500_splice	ENST00000267163	NM_000321.2	500			0.389477382870163	2	FACETS	0.917	0.73	1	0.917	0.73	1	CLONAL	2	TRUE	0	0.389477382870163	2		215	56	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	98	414	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.0827565200454095	5	FACETS	0.783	0.7	0.872	0.522	0.466	0.581	INDETERMINATE	2	TRUE	2	0.27543385740743	5		414	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0042855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	312	670	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.27543385740743	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.27543385740743	2		670	1087	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955070	93955070	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1399866665	NA	P-0042855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	38	432	0	ENST00000369303.4:c.2828A>G	p.Asn943Ser	p.N943S	ENST00000369303	NM_004440.3	943	aAt/aGt	16/17	0.236313569621072	2	FACETS	0.831	0.689	0.989	0.416	0.344	0.495	CLONAL	1	TRUE	0	0.27543385740743	2		432	332	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339225	87339225	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	82	688	0	ENST00000277120.3:c.807A>C	p.Glu269Asp	p.E269D	ENST00000277120		269	gaA/gaC	8/19	0.27543385740743	2	FACETS	0.824	0.726	0.928	0.412	0.363	0.464	CLONAL	1	TRUE	0	0.27543385740743	2		688	723	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0042857-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	19	464	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.757	0.575	0.97	0.757	0.575	0.97	CLONAL	1	TRUE	1	0.2	2		464	251	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115955	8115956	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0042857-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	69	568	0	ENST00000346208.3:c.1305dup	p.Ser436LeufsTer71	p.S436Lfs*71	ENST00000346208		434	cac/caCc	6/6	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.2	2		568	632	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636098	73636098	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042857-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	135	446	0	ENST00000377687.4:c.361G>C	p.Asp121His	p.D121H	ENST00000377687	NM_001730.3	121	Gac/Cac	2/4	0.270797542616524	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.2	3		446	656	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583295	46583295	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042857-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	33	298	0	ENST00000263734.3:c.223T>G	p.Ser75Ala	p.S75A	ENST00000263734	NM_001430.4	75	Tct/Gct	3/16	0.270797542616524	3	FACETS	0.769	0.626	0.931	0.385	0.313	0.466	CLONAL	1	TRUE	1	0.2	3		298	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0042861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	199	535	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.222624957819488	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	0	0.222624957819488	2		535	891	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0042861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	51	343	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.222624957819488	2		343	336	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460401	149460401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	79	920	0	ENST00000286301.3:c.236C>T	p.Thr79Met	p.T79M	ENST00000286301	NM_005211.3	79	aCg/aTg	3/22	0.222624957819488	0	FACETS	0.691	0.607	0.782			1	SUBCLONAL	1	TRUE	0	0.222624957819488	0		920	798	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158417	26158417	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs368384735	NA	P-0042861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	79	1202	0	ENST00000289316.2:c.20C>G	p.Ser7Cys	p.S7C	ENST00000289316	NM_138720.2	7	tCt/tGt	1/2	1	2	FACETS	0.646	0.566	0.732	0.646	0.566	0.732	SUBCLONAL	1	TRUE	1	0.222624957819488	2		1202	1099	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224174	36224174	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368273689	NA	P-0042861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	100	854	1	ENST00000222270.7:c.6724G>A	p.Val2242Met	p.V2242M	ENST00000222270	NM_014727.1	2242	Gtg/Atg	28/37	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.222624957819488	2		855	815	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422176	81422176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758059665	NA	P-0042861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	96	597	1	ENST00000298171.2:c.152C>T	p.Pro51Leu	p.P51L	ENST00000298171	NM_000369.2	51	cCg/cTg	1/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.222624957819488	2		598	658	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994649	73994649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs541095307	NA	P-0042861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	56	1338	1	ENST00000318443.5:c.133G>A	p.Asp45Asn	p.D45N	ENST00000318443	NM_001024736.1	45	Gat/Aat	3/10	1	2	FACETS	0.519	0.443	0.603	0.519	0.443	0.603	SUBCLONAL	1	TRUE	1	0.222624957819488	2		1339	969	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256611	19256611	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	144	650	0	ENST00000162023.5:c.1102C>G	p.Arg368Gly	p.R368G	ENST00000162023		368	Cgg/Ggg	13/13	1	2	FACETS	0.998	0.913	1	1	0.991	1	CLONAL	2	TRUE	1	0.222624957819488	2		650	648	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211132	36211132	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	284	1335	1	ENST00000222270.7:c.883C>A	p.Arg295Ser	p.R295S	ENST00000222270	NM_014727.1	295	Cgc/Agc	3/37	1	2	FACETS	0.943	0.885	1	1	0.995	1	CLONAL	2	TRUE	1	0.222624957819488	2		1336	1353	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	33	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.814	1	1	0.814	1	CLONAL	1	TRUE	1	0.15	2		126	440	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0042869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	105	1232	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	0.771	0.69	0.857	1	0.983	1	SUBCLONAL	2	TRUE	1	0.15	2		1232	908	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0042869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	37	1001	1	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	1	2	FACETS	0.777	0.639	0.932	0.777	0.639	0.932	CLONAL	1	TRUE	1	0.15	2		1002	635	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001366	29001366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779189056	NA	P-0042869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	23	544	0	ENST00000282397.4:c.1366G>A	p.Ala456Thr	p.A456T	ENST00000282397	NM_002019.4	456	Gca/Aca	10/30	1	2	FACETS	0.918	0.716	1	0.918	0.716	1	CLONAL	1	TRUE	1	0.15	2		544	334	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820648	3820648	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	67	1092	0	ENST00000262367.5:c.2803C>T	p.Gln935Ter	p.Q935*	ENST00000262367	NM_004380.2	935	Cag/Tag	14/31	1	2	FACETS	0.793	0.687	0.909	0.793	0.687	0.909	CLONAL	1	TRUE	1	0.15	2		1092	1126	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446967	187446967	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763470720	NA	P-0042869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	46	1003	4	ENST00000232014.4:c.1226C>T	p.Thr409Met	p.T409M	ENST00000232014	NM_001130845.1	409	aCg/aTg	5/10	1	2	FACETS	0.735	0.617	0.866	0.735	0.617	0.866	SUBCLONAL	1	TRUE	1	0.15	2		1007	835	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878133	48878133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	15	143	0	ENST00000267163.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000267163	NM_000321.2	29	Cct/Tct	1/27	1	2	FACETS	0.833	0.61	1	0.833	0.61	1	CLONAL	1	TRUE	1	0.15	2		143	240	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950004	44950004	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	10	347	0	ENST00000377967.4:c.3774del	p.Trp1258Ter	p.W1258*	ENST00000377967	NM_021140.2	1258	tGg/tg	26/29	1	1	FACETS	1	0.694	1	1	0.694	1	CLONAL	1	TRUE	0	0.15	1		347	121	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224542	123224542	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0042869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	20	402	0	ENST00000218089.9:c.3395T>G	p.Leu1132Ter	p.L1132*	ENST00000218089	NM_001042749.1	1132	tTa/tGa	31/35	1	1	FACETS	0.828	0.639	1	1	0.926	1	CLONAL	2	TRUE	0	0.15	1		402	149	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	122	877	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.313680980836323	2		883	762	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	93	514	2	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.313680980836323	2		516	497	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	100	685	5	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.313680980836323	2		690	608	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120115	70120115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	33	597	0	ENST00000245479.2:c.1121del	p.Pro374ArgfsTer9	p.P374Rfs*9	ENST00000245479	NM_000346.3	373	Ccc/cc	3/3	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.313680980836323	2		597	160	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114817	108114817	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786204543	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	101	377	2	ENST00000278616.4:c.640del	p.Ser214ProfsTer16	p.S214Pfs*16	ENST00000278616	NM_000051.3	212	Ttt/tt	6/63	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.313680980836323	2		379	590	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55597498	55597498	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769701248	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	50	299	0	ENST00000288135.5:c.2146G>A	p.Asp716Asn	p.D716N	ENST00000288135	NM_000222.2	716	Gat/Aat	15/21	1	2	FACETS	0.766	0.652	0.892	0.766	0.652	0.892	SUBCLONAL	1	TRUE	1	0.313680980836323	2		299	416	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	106	492	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.313680980836323	2		492	630	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103755	47103756	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	114	407	0	ENST00000409792.3:c.6190_6191del	p.Asp2064ProfsTer8	p.D2064Pfs*8	ENST00000409792	NM_014159.6	2064	GAc/c	14/21	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.313680980836323	2		407	681	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	175	480	0	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.313680980836323	2		480	1000	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874637	35874637	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	54	282	1	ENST00000303115.3:c.799del	p.Arg267GlyfsTer28	p.R267Gfs*28	ENST00000303115	NM_002185.3	265	Aaa/aa	6/8	1	2	FACETS	0.834	0.714	0.964	0.834	0.714	0.964	CLONAL	1	TRUE	1	0.313680980836323	2		283	413	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989482	212989482	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	54	285	0	ENST00000342788.4:c.229C>A	p.Leu77Met	p.L77M	ENST00000342788	NM_005235.2	77	Ctg/Atg	2/28	1	2	FACETS	0.97	0.832	1	0.97	0.832	1	CLONAL	1	TRUE	1	0.313680980836323	2		285	355	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890150	76890150	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	83	373	0	ENST00000373344.5:c.4744del	p.Thr1582GlnfsTer24	p.T1582Qfs*24	ENST00000373344	NM_000489.3	1582	Aca/ca	17/35	1	2	FACETS	0.952	0.842	1	0.952	0.842	1	CLONAL	1	TRUE	1	0.313680980836323	2		373	556	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136949	64136949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749917386	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	109	528	0	ENST00000334205.4:c.1460G>A	p.Arg487Gln	p.R487Q	ENST00000334205	NM_003942.2	487	cGg/cAg	13/17	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.313680980836323	2		528	635	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129338	152129338	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1361952517	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	105	522	1	ENST00000206249.3:c.296del	p.Pro99HisfsTer10	p.P99Hfs*10	ENST00000206249	NM_000125.3	97	ttC/tt	1/8	1	2	FACETS	0.959	0.86	1	0.959	0.86	1	CLONAL	1	TRUE	1	0.313680980836323	2		523	698	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533939	63533940	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs771001164	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	75	379	0	ENST00000307078.5:c.1214_1215del	p.Glu405GlyfsTer56	p.E405Gfs*56	ENST00000307078	NM_004655.3	405	gAG/g	6/11	1	2	FACETS	0.978	0.859	1	0.978	0.859	1	CLONAL	1	TRUE	1	0.313680980836323	2		379	489	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	360055	360055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	137	576	0	ENST00000262320.3:c.1034del	p.Pro345HisfsTer69	p.P345Hfs*69	ENST00000262320	NM_003502.3	345	cCa/ca	4/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.313680980836323	2		576	675	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253377	226253377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	48	203	0	ENST00000366813.1:c.149G>A	p.Arg50His	p.R50H	ENST00000366813		50	cGt/cAt	2/3	1	2	FACETS	0.959	0.815	1	0.959	0.815	1	CLONAL	1	TRUE	1	0.313680980836323	2		203	319	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044511	47044511	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	95	617	0	ENST00000377604.3:c.2012del	p.Asn671IlefsTer33	p.N671Ifs*33	ENST00000377604	NM_001204468.1	670	Aaa/aa	18/24	1	2	FACETS	0.786	0.699	0.878	0.786	0.699	0.878	SUBCLONAL	1	TRUE	1	0.313680980836323	2		617	771	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572092	64572093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767319284	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	120	655	2	ENST00000312049.6:c.1546dup	p.Arg516ProfsTer15	p.R516Pfs*15	ENST00000312049	NM_130799.2	516	cgg/cCgg	10/10	1	2	FACETS	0.959	0.866	1	0.959	0.866	1	CLONAL	1	TRUE	1	0.313680980836323	2		657	798	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498235	498235	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	53	235	2	ENST00000399788.2:c.23del	p.Gly8AlafsTer58	p.G8Afs*58	ENST00000399788	NM_001042603.1	8	gGc/gc	1/28	NA	2	FACETS	1	0.913	1			1	INDETERMINATE	1	TRUE	NA	0.313680980836323	2		237	310	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781321	3781321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200112956	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	186	806	0	ENST00000262367.5:c.5044C>T	p.Arg1682Cys	p.R1682C	ENST00000262367	NM_004380.2	1682	Cgc/Tgc	30/31	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.313680980836323	2		806	994	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	87	420	1	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	0.313680980836323	1	FACETS	0.997	0.887	1	0.997	0.887	1	CLONAL	1	TRUE	0	0.313680980836323	1		421	469	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339722	70339722	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	102	552	2	ENST00000374080.3:c.395del	p.Lys132ArgfsTer15	p.K132Rfs*15	ENST00000374080		131	Aaa/aa	3/45	1	2	FACETS	0.89	0.796	0.989	0.89	0.796	0.989	CLONAL	1	TRUE	1	0.313680980836323	2		554	731	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2492097	2492097	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs772088410	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	132	611	2	ENST00000355716.4:c.500del	p.Pro167ArgfsTer23	p.P167Rfs*23	ENST00000355716	NM_003820.2	165	tgC/tg	5/8	1	2	FACETS	0.933	0.847	1	0.933	0.847	1	CLONAL	1	TRUE	1	0.313680980836323	2		613	902	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240163	41240163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	28	77	0	ENST00000379561.5:c.187G>A	p.Ala63Thr	p.A63T	ENST00000379561	NM_002015.3	63	Gct/Act	1/3	1	2	FACETS	0.797	0.65	0.957	1	0.947	1	CLONAL	2	TRUE	1	0.313680980836323	2		77	112	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214398	36214398	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs868041281	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	113	494	0	ENST00000222270.7:c.3057del	p.Gly1020AlafsTer4	p.G1020Afs*4	ENST00000222270	NM_014727.1	1018	Aaa/aa	7/37	1	2	FACETS	0.946	0.851	1	0.946	0.851	1	CLONAL	1	TRUE	1	0.313680980836323	2		494	762	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	359972	359972	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	96	563	0	ENST00000262320.3:c.1116+1G>A		p.X372_splice	ENST00000262320	NM_003502.3	372			1	2	FACETS	0.981	0.875	1	0.981	0.875	1	CLONAL	1	TRUE	1	0.313680980836323	2		563	624	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929495	81929495	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769180169	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	110	420	0	ENST00000359376.3:c.1156G>A	p.Val386Met	p.V386M	ENST00000359376	NM_002661.3	386	Gtg/Atg	13/33	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.313680980836323	2		420	682	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925402	114925402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748822481	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	148	661	2	ENST00000543371.1:c.1485del	p.Ser496ProfsTer5	p.S496Pfs*5	ENST00000543371	NM_001198531.1	494	Ccc/cc	14/14	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.313680980836323	2		663	820	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347191	89347191	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	106	565	0	ENST00000301030.4:c.5759C>T	p.Thr1920Met	p.T1920M	ENST00000301030	NM_001256183.1	1920	aCg/aTg	9/13	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.313680980836323	2		565	550	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918125	50918127	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs763850764	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	142	710	0	ENST00000440232.2:c.2446_2448del	p.Ser816del	p.S816del	ENST00000440232	NM_002691.3	814	ttCTCc/ttc	20/27	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.313680980836323	2		710	835	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356254	66356254	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	73	466	0	ENST00000273854.3:c.1243C>A	p.Leu415Ile	p.L415I	ENST00000273854	NM_004439.5	415	Ctt/Att	5/18	1	2	FACETS	0.824	0.721	0.934	0.824	0.721	0.934	CLONAL	1	TRUE	1	0.313680980836323	2		466	565	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187222	38187222	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	297	654	0	ENST00000317025.8:c.1255del	p.Thr419ProfsTer8	p.T419Pfs*8	ENST00000317025	NM_023034.1	419	Acc/cc	6/24	0.313680980836323	3	FACETS	0.959	0.903	1	0.959	0.903	1	CLONAL	2	TRUE	1	0.313680980836323	3		654	1142	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374338	81374338	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202185530	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	78	284	0	ENST00000222390.5:c.724C>T	p.Arg242Trp	p.R242W	ENST00000222390	NM_000601.4	242	Cgg/Tgg	6/18	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.313680980836323	2		284	465	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741646	145741646	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757320755	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	132	637	0	ENST00000428558.2:c.857C>T	p.Ser286Leu	p.S286L	ENST00000428558	NM_004260.3	286	tCg/tTg	5/22	0.313680980836323	3	FACETS	1	0.931	1	0.516	0.468	0.567	CLONAL	1	TRUE	1	0.313680980836323	3		637	943	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563285	21563285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1207863433	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	146	710	3	ENST00000382592.4:c.634G>A	p.Val212Met	p.V212M	ENST00000382592	NM_014572.2	212	Gtg/Atg	4/8	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.313680980836323	2		713	922	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248139	59248139	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	27	113	0	ENST00000371222.2:c.604del	p.Gln202SerfsTer24	p.Q202Sfs*24	ENST00000371222	NM_002228.3	202	Cag/ag	1/1	1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	1	0.313680980836323	2		113	162	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218901	193218901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	44	203	0	ENST00000367435.3:c.1459C>T	p.Pro487Ser	p.P487S	ENST00000367435	NM_024529.4	487	Cca/Tca	16/17	1	2	FACETS	0.899	0.758	1	0.899	0.758	1	CLONAL	1	TRUE	1	0.313680980836323	2		203	312	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226579958	226579958	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	96	471	0	ENST00000366794.5:c.344C>T	p.Ala115Val	p.A115V	ENST00000366794	NM_001618.3	115	gCa/gTa	3/23	1	2	FACETS	0.857	0.764	0.957	0.857	0.764	0.957	CLONAL	1	TRUE	1	0.313680980836323	2		471	714	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415936	49415936	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	35	366	0	ENST00000301067.7:c.16413-2A>G		p.X5471_splice	ENST00000301067	NM_003482.3	5471			1	2	FACETS	0.457	0.374	0.551	0.457	0.374	0.551	SUBCLONAL	1	TRUE	1	0.313680980836323	2		366	488	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493620	56493621	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	rs766102716	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	60	324	0	ENST00000267101.3:c.2944_2945del		p.X982_splice	ENST00000267101	NM_001982.3	982			1	2	FACETS	0.933	0.807	1	0.933	0.807	1	CLONAL	1	TRUE	1	0.313680980836323	2		324	410	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240345	41240345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	36	313	1	ENST00000379561.5:c.5C>T	p.Ala2Val	p.A2V	ENST00000379561	NM_002015.3	2	gCc/gTc	1/3	1	2	FACETS	0.473	0.389	0.568	0.473	0.389	0.568	SUBCLONAL	1	TRUE	1	0.313680980836323	2		314	485	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724871	43724872	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	78	339	0	ENST00000382044.4:c.3195dup	p.Asn1066GlufsTer20	p.N1066Efs*20	ENST00000382044	NM_001141980.1	1065	-/G	17/28	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.313680980836323	2		339	423	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43769865	43769865	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	79	367	0	ENST00000382044.4:c.881T>G	p.Leu294Arg	p.L294R	ENST00000382044	NM_001141980.1	294	cTg/cGg	8/28	1	2	FACETS	0.839	0.739	0.947	0.839	0.739	0.947	CLONAL	1	TRUE	1	0.313680980836323	2		367	600	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348954	11348954	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	121	486	0	ENST00000332029.2:c.382G>A	p.Val128Met	p.V128M	ENST00000332029	NM_003745.1	128	Gtg/Atg	2/2	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.313680980836323	2		486	724	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829466	72829466	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1337139331	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	120	505	0	ENST00000268489.5:c.7115T>C	p.Met2372Thr	p.M2372T	ENST00000268489	NM_006885.3	2372	aTg/aCg	9/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.313680980836323	2		505	645	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350510	89350510	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	170	607	0	ENST00000301030.4:c.2440T>C	p.Phe814Leu	p.F814L	ENST00000301030	NM_001256183.1	814	Ttt/Ctt	9/13	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.313680980836323	2		607	910	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533648	63533649	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	106	628	0	ENST00000307078.5:c.1505dup	p.Lys503GlnfsTer125	p.K503Qfs*125	ENST00000307078	NM_004655.3	502	ggc/ggGc	6/11	1	2	FACETS	0.936	0.84	1	0.936	0.84	1	CLONAL	1	TRUE	1	0.313680980836323	2		628	722	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309511	30309511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	315	584	0	ENST00000307677.4:c.511G>A	p.Ala171Thr	p.A171T	ENST00000307677	NM_138578.1	171	Gcc/Acc	2/3	0.313680980836323	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.313680980836323	3		584	981	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391023	89391024	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	88	438	0	ENST00000336596.2:c.1095dup	p.Cys366MetfsTer9	p.C366Mfs*9	ENST00000336596	NM_005233.5	363	-/A	5/17	1	2	FACETS	0.93	0.826	1	0.93	0.826	1	CLONAL	1	TRUE	1	0.313680980836323	2		438	603	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1272361	1272361	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	143	758	0	ENST00000310581.5:c.2321G>A	p.Arg774Gln	p.R774Q	ENST00000310581	NM_198253.2	774	cGa/cAa	7/16	1	2	FACETS	0.996	0.908	1	0.996	0.908	1	CLONAL	1	TRUE	1	0.313680980836323	2		758	915	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790754	89790754	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	141	722	0	ENST00000336032.3:c.145del	p.Arg49GlyfsTer13	p.R49Gfs*13	ENST00000336032	NM_006813.2	47	gaC/ga	1/2	1	2	FACETS	0.837	0.761	0.917	0.837	0.761	0.917	CLONAL	1	TRUE	1	0.313680980836323	2		722	1074	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663641	117663641	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	41	339	1	ENST00000368508.3:c.4591G>T	p.Ala1531Ser	p.A1531S	ENST00000368508	NM_002944.2	1531	Gct/Tct	28/43	1	2	FACETS	0.406	0.337	0.483	0.406	0.337	0.483	SUBCLONAL	1	TRUE	1	0.313680980836323	2		340	644	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339939	116339939	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	71	289	0	ENST00000397752.3:c.801A>C	p.Glu267Asp	p.E267D	ENST00000397752	NM_000245.2	267	gaA/gaC	2/21	1	2	FACETS	0.967	0.847	1	0.967	0.847	1	CLONAL	1	TRUE	1	0.313680980836323	2		289	468	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343060	70343060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	86	431	0	ENST00000374080.3:c.1601C>T	p.Ala534Val	p.A534V	ENST00000374080		534	gCg/gTg	11/45	1	2	FACETS	0.972	0.862	1	0.972	0.862	1	CLONAL	1	TRUE	1	0.313680980836323	2		431	564	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344618	70344618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	88	441	0	ENST00000374080.3:c.1979C>T	p.Pro660Leu	p.P660L	ENST00000374080		660	cCa/cTa	14/45	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.313680980836323	2		441	543	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108827	2108834	+	frameshift_variant	Frame_Shift_Del	DEL	TATTCTCT	TATTCTCT	C	novel	NA	P-0042880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	96	645	0	ENST00000219476.3:c.928_935delinsC	p.Tyr310ProfsTer51	p.Y310Pfs*51	ENST00000219476	NM_000548.3	310	TATTCTCTc/Cc	10/42	1	2	FACETS	0.827	0.737	0.923	0.827	0.737	0.923	CLONAL	1	TRUE	1	0.313680980836323	2		645	740	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	81	414	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.25351266195008	3	FACETS	0.826	0.731	0.927			1	CLONAL	2	TRUE	NA	0.251996308306513	3		414	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0042882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	216	721	0	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.251996308306513	6	FACETS	1	0.974	1	0.817	0.761	0.874	CLONAL	3	TRUE	2	0.251996308306513	6		721	789	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575194	48575194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555685186	NA	P-0042882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	28	235	0	ENST00000342988.3:c.388C>T	p.Pro130Ser	p.P130S	ENST00000342988	NM_005359.5	130	Cca/Tca	3/12	0.162897290350542	2	FACETS	1	0.908	1	0.617	0.498	0.751	CLONAL	1	TRUE	0	0.251996308306513	2		235	180	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247764	59247764	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	48	562	0	ENST00000371222.2:c.979C>T	p.Gln327Ter	p.Q327*	ENST00000371222	NM_002228.3	327	Cag/Tag	1/1	0.147049794505163	3	FACETS	0.892	0.754	1	0.446	0.377	0.522	INDETERMINATE	1	TRUE	1	0.251996308306513	3		562	481	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041356	42041356	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	65	497	0	ENST00000219905.7:c.5551A>T	p.Thr1851Ser	p.T1851S	ENST00000219905	NM_001164273.1	1851	Act/Tct	17/24	0.251996308306513	6	FACETS	1	0.957	1	0.315	0.273	0.361	CLONAL	1	TRUE	2	0.251996308306513	6		497	616	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266577	142266577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	44	290	0	ENST00000350721.4:c.3347C>T	p.Pro1116Leu	p.P1116L	ENST00000350721	NM_001184.3	1116	cCt/cTt	16/47	0.187510417245874	4	FACETS	0.919	0.777	1	0.612	0.518	0.715	CLONAL	2	TRUE	1	0.251996308306513	4		290	238	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960150	151960150	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	32	383	0	ENST00000262189.6:c.1250G>T	p.Cys417Phe	p.C417F	ENST00000262189	NM_170606.2	417	tGt/tTt	9/59	0.205191673724282	1	FACETS	0.782	0.637	0.944	0.782	0.637	0.944	CLONAL	1	TRUE	0	0.251996308306513	1		383	284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0042906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	125	668	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.370614346883701	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.370614346883701	1		668	532	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741822	162741822	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs115169993	NA	P-0042906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	64	284	0	ENST00000367921.3:c.1513G>A	p.Gly505Ser	p.G505S	ENST00000367921	NM_006182.2	505	Ggt/Agt	13/18	0.370614346883701	3	FACETS	1	0.918	1	0.537	0.467	0.612	CLONAL	1	TRUE	1	0.370614346883701	3		284	381	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959064	2959064	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	102	523	1	ENST00000396946.4:c.2452C>T	p.Arg818Trp	p.R818W	ENST00000396946	NM_032415.4	818	Cgg/Tgg	18/25	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.370614346883701	2		524	540	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117737446	117737446	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	88	264	0	ENST00000368508.3:c.203A>G	p.Asp68Gly	p.D68G	ENST00000368508	NM_002944.2	68	gAt/gGt	3/43	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.370614346883701	2		264	390	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063717	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0042911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	50	166	0	ENST00000412916.2:c.165+1G>C		p.X55_splice	ENST00000412916		55			0.509504064865089	1	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	0	0.509504064865089	1		166	144	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115705	8115706	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0042911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	63	273	0	ENST00000346208.3:c.1053_1054dup	p.Arg352ThrfsTer4	p.R352Tfs*4	ENST00000346208		351	aac/aACac	6/6	1	2	FACETS	0.803	0.7	0.913	0.803	0.7	0.913	CLONAL	1	TRUE	1	0.509504064865089	2		273	308	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032467	12032475	+	inframe_deletion	In_Frame_Del	DEL	CACAGGCCG	CACAGGCCG	-	novel	NA	P-0042911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	36	303	0	ENST00000353533.5:c.903_911del	p.Thr302_Arg304del	p.T302_R304del	ENST00000353533	NM_003010.3	301	gcCACAGGCCGa/gca	9/11	1	2	FACETS	0.533	0.441	0.636	0.533	0.441	0.636	SUBCLONAL	1	TRUE	1	0.509504064865089	2		303	265	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923140	48923140	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	21	340	1	ENST00000267163.4:c.588del	p.Thr197HisfsTer4	p.T197Hfs*4	ENST00000267163	NM_000321.2	196	atC/at	6/27	0.3	1	FACETS	0.472	0.364	0.598	0.472	0.364	0.598	SUBCLONAL	1	FALSE	0	0.3	1		341	252	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	275	414	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.4743725276344	5	FACETS	0.964	0.911	1	0.964	0.911	1	CLONAL	3	TRUE	2	0.4743725276344	5		414	686	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0042982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	283	836	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.454979698644075	2	FACETS	0.973	0.923	1	0.973	0.923	1	CLONAL	2	TRUE	0	0.4743725276344	2		836	613	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741894	17741894	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	33	135	0	ENST00000250003.3:c.565G>A	p.Gly189Ser	p.G189S	ENST00000250003	NM_002478.4	189	Ggc/Agc	1/3	0.415317394604697	3	FACETS	1	0.942	1	0.683	0.567	0.808	CLONAL	1	TRUE	1	0.4743725276344	3		135	126	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29068968	29068968	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	27	263	0	ENST00000282397.4:c.13T>G	p.Trp5Gly	p.W5G	ENST00000282397	NM_002019.4	5	Tgg/Ggg	1/30	0.415317394604697	3	FACETS	0.557	0.444	0.684	0.278	0.222	0.342	SUBCLONAL	1	TRUE	1	0.4743725276344	3		263	253	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	70	605	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.751	0.652	0.858	0.751	0.652	0.858	SUBCLONAL	1	TRUE	1	0.16	2		608	1165	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	59	461	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	0.158533959923975	3	FACETS	1	0.941	1	0.592	0.508	0.683	CLONAL	1	TRUE	1	0.16	3		461	673	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460516	149460516	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	70	788	0	ENST00000286301.3:c.121C>T	p.Arg41Ter	p.R41*	ENST00000286301	NM_005211.3	41	Cga/Tga	3/22	1	2	FACETS	0.785	0.682	0.898	0.785	0.682	0.898	SUBCLONAL	1	TRUE	1	0.16	2		788	1114	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	47	390	1	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	0.158533959923975	3	FACETS	0.867	0.73	1	0.433	0.365	0.51	CLONAL	1	TRUE	1	0.16	3		391	732	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	49	487	2	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	0.977	0.826	1	0.977	0.826	1	CLONAL	1	TRUE	1	0.16	2		489	627	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028632	12028632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753665559	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	32	447	1	ENST00000353533.5:c.835G>A	p.Ala279Thr	p.A279T	ENST00000353533	NM_003010.3	279	Gca/Aca	8/11	0.151470765581605	3	FACETS	0.715	0.579	0.87	0.358	0.289	0.435	SUBCLONAL	1	TRUE	1	0.16	3		448	604	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160488	108160488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730881369	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	30	561	0	ENST00000278616.4:c.4396C>T	p.Arg1466Ter	p.R1466*	ENST00000278616	NM_000051.3	1466	Cga/Tga	29/63	1	2	FACETS	0.775	0.623	0.947	0.775	0.623	0.947	CLONAL	1	TRUE	1	0.16	2		561	484	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371662	55371662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	54	632	0	ENST00000297316.4:c.352G>A	p.Val118Met	p.V118M	ENST00000297316	NM_022454.3	118	Gtg/Atg	2/2	0.290366061317443	1	FACETS	0.766	0.652	0.89	0.766	0.652	0.89	SUBCLONAL	1	TRUE	0	0.16	1		632	811	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790819	89790819	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1370	80	687	5	ENST00000336032.3:c.211del	p.Gln71SerfsTer112	p.Q71Sfs*112	ENST00000336032	NM_006813.2	69	aCc/ac	1/2	0.144327998450027	3	FACETS	0.745	0.653	0.844			1	SUBCLONAL	1	TRUE	NA	0.16	3		692	1450	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945659	54945659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753238269	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	21	244	1	ENST00000312783.6:c.911G>A	p.Arg304Gln	p.R304Q	ENST00000312783	NM_198436.1	304	cGg/cAg	9/10	1	2	FACETS	0.643	0.494	0.818	0.643	0.494	0.818	SUBCLONAL	1	TRUE	1	0.16	2		245	408	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1396	97	605	1	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	NA	3	FACETS	0.877	0.779	0.983	0.439	0.389	0.492	INDETERMINATE	1	TRUE	1	0.16	3		606	1493	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021815	71021815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	30	264	0	ENST00000318789.4:c.1543C>T	p.His515Tyr	p.H515Y	ENST00000318789	NM_032682.5	515	Cat/Tat	18/21	1	2	FACETS	1	0.827	1	1	0.827	1	CLONAL	1	TRUE	1	0.16	2		264	365	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969369	44969369	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1318649487	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	25	264	0	ENST00000377967.4:c.4051C>T	p.Arg1351Ter	p.R1351*	ENST00000377967	NM_021140.2	1351	Cga/Tga	28/29	0.138661871769235	2	FACETS	1	0.898	1			1	CLONAL	1	TRUE	NA	0.16	2		264	251	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121912	2121912	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201769220	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	86	768	0	ENST00000219476.3:c.2074G>A	p.Val692Ile	p.V692I	ENST00000219476	NM_000548.3	692	Gtc/Atc	19/42	1	2	FACETS	0.932	0.822	1	0.932	0.822	1	CLONAL	1	TRUE	1	0.16	2		768	1153	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55269020	55269020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182857647	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	63	753	0	ENST00000275493.2:c.3086C>T	p.Thr1029Met	p.T1029M	ENST00000275493	NM_005228.3	1029	aCg/aTg	25/28	0.158533959923975	3	FACETS	0.748	0.645	0.861	0.374	0.322	0.431	SUBCLONAL	1	TRUE	1	0.16	3		753	1137	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258894	16258894	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	130	737	2	ENST00000375759.3:c.6164del	p.Pro2055LeufsTer9	p.P2055Lfs*9	ENST00000375759	NM_015001.2	2053	aaC/aa	11/15	0.158533959923975	3	FACETS	1	0.982	1	0.69	0.624	0.76	CLONAL	1	TRUE	1	0.16	3		739	1271	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112388	115112388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs565848855	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	46	435	0	ENST00000257566.3:c.1352C>T	p.Ala451Val	p.A451V	ENST00000257566	NM_016569.3	451	gCg/gTg	7/8	1	2	FACETS	0.712	0.597	0.838	0.712	0.597	0.838	SUBCLONAL	1	TRUE	1	0.16	2		435	808	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480543	50480543	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147034181	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	62	520	0	ENST00000394963.4:c.413G>A	p.Arg138His	p.R138H	ENST00000394963	NM_003076.4	138	cGt/cAt	4/13	0.138661871769235	4	FACETS	1	0.9	1			1	CLONAL	1	TRUE	NA	0.16	4		520	852	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149375074	149375074	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1646	106	847	0	ENST00000360632.3:c.20C>G	p.Pro7Arg	p.P7R	ENST00000360632	NM_015472.4	7	cCc/cGc	2/7	1	2	FACETS	0.756	0.675	0.844	0.756	0.675	0.844	SUBCLONAL	1	TRUE	1	0.16	2		847	1752	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939062	48939062	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	13	275	0	ENST00000267163.4:c.897del	p.Phe299LeufsTer2	p.F299Lfs*2	ENST00000267163	NM_000321.2	298	ccT/cc	9/27	0.3	1	FACETS	0.683	0.487	0.921	0.683	0.487	0.921	SUBCLONAL	1	TRUE	0	0.16	1		275	219	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940513	71940513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	113	646	0	ENST00000298229.2:c.664G>A	p.Val222Met	p.V222M	ENST00000298229	NM_001567.3	222	Gtg/Atg	6/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.16	2		646	1077	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427092	49427093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	43	614	0	ENST00000301067.7:c.11395dup	p.Gln3799ProfsTer213	p.Q3799Pfs*213	ENST00000301067	NM_003482.3	3799	cag/cCag	39/54	0.138661871769235	4	FACETS	0.732	0.61	0.867			1	SUBCLONAL	1	TRUE	NA	0.16	4		614	852	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500650	99500651	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	43	506	0	ENST00000268035.6:c.4087dup	p.Gln1363ProfsTer11	p.Q1363Pfs*11	ENST00000268035	NM_000875.3	1361	-/C	21/21	1	2	FACETS	0.811	0.677	0.96	0.811	0.677	0.96	CLONAL	1	TRUE	1	0.16	2		506	663	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108253	8108253	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1281	68	738	0	ENST00000585124.1:c.971A>G	p.His324Arg	p.H324R	ENST00000585124	NM_004217.3	324	cAc/cGc	9/9	0.151470765581605	3	FACETS	0.681	0.589	0.78	0.34	0.294	0.39	SUBCLONAL	1	TRUE	1	0.16	3		738	1349	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1627401	1627401	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs771302868	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	66	736	0	ENST00000344749.5:c.323A>G	p.Tyr108Cys	p.Y108C	ENST00000344749	NM_001136139.2	108	tAt/tGt	6/19	1	2	FACETS	0.711	0.615	0.816	0.711	0.615	0.816	SUBCLONAL	1	TRUE	1	0.16	2		736	1160	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855589	45855589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751956427	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	71	750	2	ENST00000391945.4:c.2068C>T	p.Arg690Trp	p.R690W	ENST00000391945	NM_000400.3	690	Cgg/Tgg	22/23	NA	3	FACETS	0.877	0.763	1	0.438	0.381	0.501	INDETERMINATE	1	TRUE	1	0.16	3		752	1093	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965358	25965358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs572342520	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	67	699	0	ENST00000435504.4:c.3848G>A	p.Arg1283His	p.R1283H	ENST00000435504		1283	cGt/cAt	13/13	1	2	FACETS	0.732	0.634	0.839	0.732	0.634	0.839	SUBCLONAL	1	TRUE	1	0.16	2		699	1144	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416185	29416185	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	77	609	0	ENST00000389048.3:c.4768G>T	p.Gly1590Cys	p.G1590C	ENST00000389048	NM_004304.4	1590	Ggc/Tgc	29/29	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.16	2		609	938	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639566	47639566	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	18	391	0	ENST00000233146.2:c.659G>C	p.Gly220Ala	p.G220A	ENST00000233146	NM_000251.2	220	gGa/gCa	4/16	0.3	1	FACETS	0.852	0.642	1	0.852	0.642	1	CLONAL	1	TRUE	0	0.16	1		391	243	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660673	190660673	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	19	343	0	ENST00000441310.2:c.311C>T	p.Ala104Val	p.A104V	ENST00000441310	NM_000534.4	104	gCt/gTt	3/13	1	2	FACETS	0.625	0.473	0.804	0.625	0.473	0.804	SUBCLONAL	1	TRUE	1	0.16	2		343	380	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530120	212530120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	40	405	0	ENST00000342788.4:c.1799C>T	p.Ala600Val	p.A600V	ENST00000342788	NM_005235.2	600	gCa/gTa	15/28	1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	1	0.16	2		405	489	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484608	57484608	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137854538	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	51	585	1	ENST00000371085.3:c.692G>A	p.Arg231His	p.R231H	ENST00000371085	NM_000516.4	231	cGc/cAc	9/13	1	2	FACETS	0.644	0.545	0.753	0.644	0.545	0.753	SUBCLONAL	1	TRUE	1	0.16	2		586	990	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021823	71021823	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	24	249	0	ENST00000318789.4:c.1535C>G	p.Ala512Gly	p.A512G	ENST00000318789	NM_032682.5	512	gCa/gGa	18/21	1	2	FACETS	0.926	0.726	1	0.926	0.726	1	CLONAL	1	TRUE	1	0.16	2		249	324	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401712	401712	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	48	688	0	ENST00000380956.4:c.1034A>G	p.Asp345Gly	p.D345G	ENST00000380956	NM_001195286.1	345	gAc/gGc	7/9	0.13078481936217	4	FACETS	0.741	0.624	0.871	0.371	0.312	0.436	SUBCLONAL	1	TRUE	2	0.16	4		688	939	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748555	43748555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772901865	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	43	482	1	ENST00000523873.1:c.509G>A	p.Arg170His	p.R170H	ENST00000523873		170	cGc/cAc	6/8	NA	2	FACETS	0.71	0.592	0.841			1	INDETERMINATE	1	TRUE	NA	0.16	2		483	757	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099187	157099189	+	inframe_deletion	In_Frame_Del	DEL	GCG	GCG	-	novel	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	58	414	0	ENST00000346085.5:c.129_131del	p.Ala47del	p.A47del	ENST00000346085	NM_020732.3	42	GCG/-	1/20	NA	3	FACETS	0.892	0.764	1	0.446	0.382	0.516	INDETERMINATE	1	TRUE	1	0.16	3		414	878	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56860234	56860234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760301322	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	50	577	0	ENST00000519728.1:c.236C>T	p.Pro79Leu	p.P79L	ENST00000519728	NM_002350.3	79	cCg/cTg	4/13	0.290366061317443	1	FACETS	0.667	0.564	0.781	0.667	0.564	0.781	SUBCLONAL	1	TRUE	0	0.16	1		577	862	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046408	69046408	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	57	588	0	ENST00000288368.4:c.3881A>G	p.Lys1294Arg	p.K1294R	ENST00000288368	NM_024870.2	1294	aAg/aGg	32/40	0.290366061317443	1	FACETS	0.793	0.678	0.918	0.793	0.678	0.918	CLONAL	1	TRUE	0	0.16	1		588	827	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760465	133760465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758209901	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	62	720	0	ENST00000318560.5:c.2788G>A	p.Ala930Thr	p.A930T	ENST00000318560	NM_005157.4	930	Gca/Aca	11/11	1	2	FACETS	0.76	0.654	0.875	0.76	0.654	0.875	SUBCLONAL	1	TRUE	1	0.16	2		720	1020	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139811029	139811029	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	62	677	0	ENST00000247668.2:c.640G>A	p.Val214Ile	p.V214I	ENST00000247668	NM_021138.3	214	Gtc/Atc	7/11	1	2	FACETS	0.649	0.558	0.748	0.649	0.558	0.748	SUBCLONAL	1	TRUE	1	0.16	2		677	1194	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0043001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	170	441	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.426923604602681	3	FACETS	0.888	0.822	0.956	0.888	0.822	0.956	CLONAL	2	TRUE	1	0.426923604602681	3		441	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0043001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	193	662	1	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.426923604602681	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.426923604602681	1		663	672	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175481	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0043001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	84	374	0	ENST00000257430.4:c.4192_4193del	p.Arg1399PhefsTer9	p.R1399Ffs*9	ENST00000257430	NM_000038.5	1397	GAg/g	16/16	0.426923604602681	3	FACETS	0.901	0.798	1	0.45	0.399	0.506	CLONAL	1	TRUE	1	0.426923604602681	3		374	530	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627445	37627445	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	198	572	0	ENST00000447079.4:c.1360G>T	p.Glu454Ter	p.E454*	ENST00000447079	NM_015083.1	454	Gaa/Taa	2/14	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.426923604602681	2		572	798	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390436	56390436	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	108	376	0	ENST00000348428.3:c.1175del	p.Arg392LeufsTer11	p.R392Lfs*11	ENST00000348428	NM_006785.3	392	cGt/ct	10/17	0.426923604602681	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.426923604602681	1		376	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0043019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	316	707	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.221207510385233	3	FACETS	1	0.986	1	0.743	0.703	0.784	CLONAL	2	TRUE	0	0.359966783429189	3		707	929	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0043019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	121	326	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.359966783429189	2		326	571	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0043019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	26	455	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.685	0.545	0.842	0.685	0.545	0.842	SUBCLONAL	1	TRUE	1	0.359966783429189	2		455	211	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175420	108175420	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204751	NA	P-0043019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	28	263	0	ENST00000278616.4:c.5515C>T	p.Gln1839Ter	p.Q1839*	ENST00000278616	NM_000051.3	1839	Cag/Tag	37/63	0.149174655253974	3	FACETS	0.497	0.398	0.611	0.166	0.132	0.204	INDETERMINATE	1	TRUE	0	0.359966783429189	3		263	369	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475134	40475134	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	96	694	0	ENST00000264657.5:c.1776G>T	p.Glu592Asp	p.E592D	ENST00000264657	NM_139276.2	592	gaG/gaT	20/24	0.359966783429189	5	FACETS	0.684	0.608	0.767	0.342	0.304	0.384	SUBCLONAL	1	TRUE	3	0.359966783429189	5		694	1200	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553685	106553686	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	86	570	0	ENST00000369096.4:c.1655dup	p.Asn552LysfsTer81	p.N552Kfs*81	ENST00000369096	NM_001198.3	550	-/A	5/7	0.359966783429189	5	FACETS	1	0.911	1			1	CLONAL	1	TRUE	NA	0.359966783429189	5		570	711	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	189	400	0	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	0.540968407483699	3	FACETS	1	0.987	1	0.618	0.577	0.66	INDETERMINATE	1	TRUE	1	0.978784403506562	3		400	465	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812293	212812293	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569995088	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	66	318	0	ENST00000342788.4:c.283C>T	p.Arg95Cys	p.R95C	ENST00000342788	NM_005235.2	95	Cgt/Tgt	3/28	0.540968407483699	3	FACETS	0.459	0.399	0.523	0.229	0.199	0.262	INDETERMINATE	1	TRUE	1	0.978784403506562	3		318	438	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	134	554	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.51	0.465	0.556	0.51	0.465	0.556	SUBCLONAL	1	TRUE	1	0.978784403506562	2		554	537	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242646	16242646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	25	447	0	ENST00000375759.3:c.1267C>T	p.Arg423Cys	p.R423C	ENST00000375759	NM_015001.2	423	Cgc/Tgc	6/15	1	2	FACETS	0.127	0.099	0.158	0.127	0.099	0.158	SUBCLONAL	1	TRUE	1	0.978784403506562	2		447	403	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255458	16255458	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	160	481	0	ENST00000375759.3:c.2723T>G	p.Val908Gly	p.V908G	ENST00000375759	NM_015001.2	908	gTc/gGc	11/15	1	2	FACETS	0.549	0.506	0.594	0.549	0.506	0.594	SUBCLONAL	1	TRUE	1	0.978784403506562	2		481	595	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258680	16258680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	178	534	1	ENST00000375759.3:c.5945G>A	p.Arg1982Gln	p.R1982Q	ENST00000375759	NM_015001.2	1982	cGg/cAg	11/15	1	2	FACETS	0.573	0.53	0.617	0.573	0.53	0.617	SUBCLONAL	1	TRUE	1	0.978784403506562	2		535	635	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261434	16261434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	172	576	0	ENST00000375759.3:c.8699C>T	p.Ser2900Leu	p.S2900L	ENST00000375759	NM_015001.2	2900	tCg/tTg	11/15	1	2	FACETS	0.549	0.507	0.592	0.549	0.507	0.592	SUBCLONAL	1	TRUE	1	0.978784403506562	2		576	640	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057704	27057704	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	184	716	0	ENST00000324856.7:c.1412A>G	p.Tyr471Cys	p.Y471C	ENST00000324856	NM_006015.4	471	tAc/tGc	3/20	1	2	FACETS	0.481	0.445	0.519	0.481	0.445	0.519	SUBCLONAL	1	TRUE	1	0.978784403506562	2		716	781	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100292	27100292	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	178	585	0	ENST00000324856.7:c.4005-1G>T		p.X1335_splice	ENST00000324856	NM_006015.4	1335			1	2	FACETS	0.536	0.496	0.578	0.536	0.496	0.578	SUBCLONAL	1	TRUE	1	0.978784403506562	2		585	678	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105688	27105688	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	96	584	0	ENST00000324856.7:c.5299G>T	p.Glu1767Ter	p.E1767*	ENST00000324856	NM_006015.4	1767	Gaa/Taa	20/20	1	2	FACETS	0.57	0.513	0.63	0.57	0.513	0.63	SUBCLONAL	1	TRUE	1	0.978784403506562	2		584	344	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938116	36938116	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	217	663	0	ENST00000361632.4:c.843+2T>C		p.X281_splice	ENST00000361632		281			1	2	FACETS	0.599	0.559	0.64	0.599	0.559	0.64	SUBCLONAL	1	TRUE	1	0.978784403506562	2		663	740	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46597593	46597593	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	151	396	0	ENST00000262741.5:c.32A>G	p.Asp11Gly	p.D11G	ENST00000262741	NM_003629.3	11	gAt/gGt	1/10	1	2	FACETS	0.556	0.511	0.603	0.556	0.511	0.603	SUBCLONAL	1	TRUE	1	0.978784403506562	2		396	555	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309871	65309871	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	122	443	2	ENST00000342505.4:c.2279C>T	p.Ala760Val	p.A760V	ENST00000342505	NM_002227.2	760	gCt/gTt	17/25	1	2	FACETS	0.474	0.43	0.52	0.474	0.43	0.52	SUBCLONAL	1	TRUE	1	0.978784403506562	2		445	526	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339110	65339111	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	81	413	3	ENST00000342505.4:c.425dup	p.Ile143AspfsTer9	p.I143Dfs*9	ENST00000342505	NM_002227.2	142	aag/aaAg	5/25	1	2	FACETS	0.32	0.282	0.36	0.32	0.282	0.36	SUBCLONAL	1	TRUE	1	0.978784403506562	2		416	517	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339172	65339172	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	56	382	0	ENST00000342505.4:c.364A>G	p.Asn122Asp	p.N122D	ENST00000342505	NM_002227.2	122	Aat/Gat	5/25	1	2	FACETS	0.259	0.222	0.3	0.259	0.222	0.3	SUBCLONAL	1	TRUE	1	0.978784403506562	2		382	441	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428511	78428511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408536007	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	87	410	0	ENST00000370768.2:c.1288C>T	p.Arg430Cys	p.R430C	ENST00000370768	NM_003902.3	430	Cgt/Tgt	14/20	1	2	FACETS	0.509	0.455	0.567	0.509	0.455	0.567	SUBCLONAL	1	TRUE	1	0.978784403506562	2		410	349	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844182	156844182	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs143438931	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	269	781	0	ENST00000524377.1:c.1185C>A	p.Phe395Leu	p.F395L	ENST00000524377	NM_002529.3	395	ttC/ttA	9/17	1	2	FACETS	0.62	0.583	0.658	0.62	0.583	0.658	SUBCLONAL	1	TRUE	1	0.978784403506562	2		781	886	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746018	162746018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	98	363	0	ENST00000367921.3:c.2141G>A	p.Arg714Gln	p.R714Q	ENST00000367921	NM_006182.2	714	cGa/cAa	16/18	1	2	FACETS	0.483	0.433	0.534	0.483	0.433	0.534	SUBCLONAL	1	TRUE	1	0.978784403506562	2		363	415	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099353	193099353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	97	297	0	ENST00000367435.3:c.287G>A	p.Gly96Glu	p.G96E	ENST00000367435	NM_024529.4	96	gGa/gAa	3/17	1	2	FACETS	0.53	0.476	0.586	0.53	0.476	0.586	SUBCLONAL	1	TRUE	1	0.978784403506562	2		297	374	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518425	204518425	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761828808	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	115	365	0	ENST00000367182.3:c.1088G>A	p.Arg363Gln	p.R363Q	ENST00000367182	NM_001278516.1	363	cGa/cAa	11/11	1	2	FACETS	0.604	0.549	0.661	0.604	0.549	0.661	SUBCLONAL	1	TRUE	1	0.978784403506562	2		365	389	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518480	204518480	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	39	316	0	ENST00000367182.3:c.1143A>C	p.Glu381Asp	p.E381D	ENST00000367182	NM_001278516.1	381	gaA/gaC	11/11	1	2	FACETS	0.244	0.203	0.29	0.244	0.203	0.29	SUBCLONAL	1	TRUE	1	0.978784403506562	2		316	326	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944257	206944257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	126	325	0	ENST00000423557.1:c.373C>T	p.Arg125Cys	p.R125C	ENST00000423557	NM_000572.2	125	Cgc/Tgc	3/5	1	2	FACETS	0.55	0.501	0.601	0.55	0.501	0.601	SUBCLONAL	1	TRUE	1	0.978784403506562	2		325	468	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567748	226567748	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	201	613	0	ENST00000366794.5:c.1418T>C	p.Phe473Ser	p.F473S	ENST00000366794	NM_001618.3	473	tTc/tCc	10/23	1	2	FACETS	0.538	0.5	0.578	0.538	0.5	0.578	SUBCLONAL	1	TRUE	1	0.978784403506562	2		613	763	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615542	43615542	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	162	484	1	ENST00000355710.3:c.2621A>G	p.Asp874Gly	p.D874G	ENST00000355710	NM_020975.4	874	gAc/gGc	15/20	0.397832616796004	3	FACETS	0.681	0.626	0.738	0.34	0.313	0.369	INDETERMINATE	1	TRUE	1	0.978784403506562	3		485	724	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405499	70405499	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs779775444	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	184	469	0	ENST00000373644.4:c.3013C>A	p.Leu1005Ile	p.L1005I	ENST00000373644	NM_030625.2	1005	Ctt/Att	4/12	0.397832616796004	3	FACETS	1	0.983	1	0.585	0.545	0.625	INDETERMINATE	1	TRUE	1	0.978784403506562	3		469	479	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70412277	70412277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	35	257	0	ENST00000373644.4:c.4387G>A	p.Ala1463Thr	p.A1463T	ENST00000373644	NM_030625.2	1463	Gca/Aca	6/12	0.397832616796004	3	FACETS	0.284	0.233	0.341	0.142	0.116	0.171	INDETERMINATE	1	TRUE	1	0.978784403506562	3		257	375	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	111	290	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.397832616796004	3	FACETS	0.704	0.636	0.775	0.352	0.318	0.388	INDETERMINATE	1	TRUE	1	0.978784403506562	3		290	480	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692932	89692932	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs1085308048	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	244	578	0	ENST00000371953.3:c.416T>G	p.Leu139Ter	p.L139*	ENST00000371953	NM_000314.4	139	tTa/tGa	5/9	0.397832616796004	3	FACETS	1	0.991	1	0.647	0.61	0.684	INDETERMINATE	1	TRUE	1	0.978784403506562	3		578	574	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720870	89720870	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1554825652	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	196	370	0	ENST00000371953.3:c.1021T>G	p.Phe341Val	p.F341V	ENST00000371953	NM_000314.4	341	Ttt/Gtt	8/9	0.397832616796004	3	FACETS	1	0.989	1	0.651	0.61	0.693	INDETERMINATE	1	TRUE	1	0.978784403506562	3		370	458	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112767343	112767343	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	94	429	0	ENST00000369452.4:c.1216G>T	p.Glu406Ter	p.E406*	ENST00000369452	NM_007373.3	406	Gaa/Taa	6/9	0.397832616796004	3	FACETS	0.539	0.481	0.6	0.269	0.24	0.3	INDETERMINATE	1	TRUE	1	0.978784403506562	3		429	531	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239388	123239388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144176428	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	97	352	0	ENST00000358487.5:c.2449G>A	p.Gly817Ser	p.G817S	ENST00000358487	NM_000141.4	817	Ggc/Agc	18/18	0.397832616796004	3	FACETS	0.65	0.583	0.721	0.325	0.291	0.361	INDETERMINATE	1	TRUE	1	0.978784403506562	3		352	454	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127996	64127996	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	243	743	0	ENST00000334205.4:c.394T>C	p.Tyr132His	p.Y132H	ENST00000334205	NM_003942.2	132	Tac/Cac	4/17	1	2	FACETS	0.586	0.549	0.625	0.586	0.549	0.625	SUBCLONAL	1	TRUE	1	0.978784403506562	2		743	847	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128018	64128018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781570977	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	279	735	2	ENST00000334205.4:c.416G>A	p.Arg139His	p.R139H	ENST00000334205	NM_003942.2	139	cGc/cAc	4/17	1	2	FACETS	0.61	0.574	0.647	0.61	0.574	0.647	SUBCLONAL	1	TRUE	1	0.978784403506562	2		737	934	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514117	69514117	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	221	656	0	ENST00000294312.3:c.564C>A	p.Phe188Leu	p.F188L	ENST00000294312	NM_005117.2	188	ttC/ttA	3/3	1	2	FACETS	0.59	0.55	0.63	0.59	0.55	0.63	SUBCLONAL	1	TRUE	1	0.978784403506562	2		656	766	SUCCESS
EED	8726	MSKCC	GRCh37	11	85968614	85968614	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs767913799	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	69	278	0	ENST00000263360.6:c.610A>C	p.Asn204His	p.N204H	ENST00000263360	NM_003797.3	204	Aat/Cat	6/12	1	2	FACETS	0.495	0.435	0.558	0.495	0.435	0.558	SUBCLONAL	1	TRUE	1	0.978784403506562	2		278	285	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94910992	94910992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	44	581	0	ENST00000536441.1:c.1138C>T	p.Arg380Trp	p.R380W	ENST00000536441	NM_144665.3	380	Cgg/Tgg	8/10	1	2	FACETS	0.182	0.153	0.215	0.182	0.153	0.215	SUBCLONAL	1	TRUE	1	0.978784403506562	2		581	493	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933481	100933481	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs1209629034	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	51	208	0	ENST00000325455.5:c.1909C>T	p.Arg637Ter	p.R637*	ENST00000325455	NM_001202474.3	637	Cga/Tga	4/8	1	2	FACETS	0.506	0.435	0.581	0.506	0.435	0.581	SUBCLONAL	1	TRUE	1	0.978784403506562	2		208	206	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201966	102201966	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	24	177	0	ENST00000263464.3:c.1318G>T	p.Glu440Ter	p.E440*	ENST00000263464	NM_001165.4	440	Gaa/Taa	6/9	1	2	FACETS	0.331	0.262	0.409	0.331	0.262	0.409	SUBCLONAL	1	TRUE	1	0.978784403506562	2		177	148	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121531	108121531	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779815	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	119	400	0	ENST00000278616.4:c.1339C>T	p.Arg447Ter	p.R447*	ENST00000278616	NM_000051.3	447	Cga/Tga	10/63	1	2	FACETS	0.534	0.485	0.585	0.534	0.485	0.585	SUBCLONAL	1	TRUE	1	0.978784403506562	2		400	455	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172385	108172385	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764389018	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	101	333	0	ENST00000278616.4:c.5188C>T	p.Arg1730Ter	p.R1730*	ENST00000278616	NM_000051.3	1730	Cga/Tga	35/63	1	2	FACETS	0.559	0.504	0.617	0.559	0.504	0.617	SUBCLONAL	1	TRUE	1	0.978784403506562	2		333	369	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103322	119103322	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	102	488	1	ENST00000264033.4:c.360G>T	p.Glu120Asp	p.E120D	ENST00000264033	NM_005188.3	120	gaG/gaT	2/16	1	2	FACETS	0.475	0.427	0.525	0.475	0.427	0.525	SUBCLONAL	1	TRUE	1	0.978784403506562	2		489	439	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419049	419049	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	50	449	1	ENST00000399788.2:c.3298G>T	p.Glu1100Ter	p.E1100*	ENST00000399788	NM_001042603.1	1100	Gaa/Taa	22/28	1	2	FACETS	0.215	0.182	0.251	0.215	0.182	0.251	SUBCLONAL	1	TRUE	1	0.978784403506562	2		450	475	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573894	18573894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759658584	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	24	321	0	ENST00000266497.5:c.2212C>T	p.Arg738Cys	p.R738C	ENST00000266497		738	Cgt/Tgt	15/31	1	2	FACETS	0.155	0.121	0.194	0.155	0.121	0.194	SUBCLONAL	1	TRUE	1	0.978784403506562	2		321	316	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378546	25378546	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	77	306	0	ENST00000311936.3:c.450+2T>C		p.X150_splice	ENST00000311936	NM_004985.3	150			1	2	FACETS	0.514	0.456	0.576	0.514	0.456	0.576	SUBCLONAL	1	TRUE	1	0.978784403506562	2		306	306	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446708	49446708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	160	434	0	ENST00000301067.7:c.1102G>A	p.Val368Met	p.V368M	ENST00000301067	NM_003482.3	368	Gtg/Atg	8/54	1	2	FACETS	0.567	0.522	0.613	0.567	0.522	0.613	SUBCLONAL	1	TRUE	1	0.978784403506562	2		434	577	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493470	56493470	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	59	483	1	ENST00000267101.3:c.2878G>T	p.Glu960Ter	p.E960*	ENST00000267101	NM_001982.3	960	Gaa/Taa	24/28	1	2	FACETS	0.21	0.18	0.242	0.21	0.18	0.242	SUBCLONAL	1	TRUE	1	0.978784403506562	2		484	575	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112919983	112919983	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	63	636	0	ENST00000351677.2:c.1198G>T	p.Glu400Ter	p.E400*	ENST00000351677	NM_002834.3	400	Gaa/Taa	10/16	1	2	FACETS	0.188	0.162	0.217	0.188	0.162	0.217	SUBCLONAL	1	TRUE	1	0.978784403506562	2		636	683	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	134	623	0	ENST00000320574.5:c.1231G>C	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ctg	13/49	1	2	FACETS	0.559	0.511	0.609	0.559	0.511	0.609	SUBCLONAL	1	TRUE	1	0.978784403506562	2		623	490	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611388	28611388	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	94	379	0	ENST00000241453.7:c.1243G>T	p.Glu415Ter	p.E415*	ENST00000241453	NM_004119.2	415	Gaa/Taa	10/24	1	2	FACETS	0.512	0.459	0.568	0.512	0.459	0.568	SUBCLONAL	1	TRUE	1	0.978784403506562	2		379	375	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004277	29004277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370686484	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	56	307	0	ENST00000282397.4:c.1016G>A	p.Arg339Gln	p.R339Q	ENST00000282397	NM_002019.4	339	cGa/cAa	8/30	1	2	FACETS	0.304	0.261	0.35	0.304	0.261	0.35	SUBCLONAL	1	TRUE	1	0.978784403506562	2		307	377	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911322	32911322	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	94	434	0	ENST00000380152.3:c.2830A>C	p.Lys944Gln	p.K944Q	ENST00000380152		944	Aaa/Caa	11/27	1	2	FACETS	0.508	0.455	0.563	0.508	0.455	0.563	SUBCLONAL	1	TRUE	1	0.978784403506562	2		434	378	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134681	41134681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	96	361	0	ENST00000379561.5:c.947G>A	p.Arg316Gln	p.R316Q	ENST00000379561	NM_002015.3	316	cGa/cAa	2/3	1	2	FACETS	0.526	0.472	0.582	0.526	0.472	0.582	SUBCLONAL	1	TRUE	1	0.978784403506562	2		361	373	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134988	41134988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	15	207	0	ENST00000379561.5:c.640C>T	p.Arg214Cys	p.R214C	ENST00000379561	NM_002015.3	214	Cgt/Tgt	2/3	1	2	FACETS	0.119	0.087	0.158	0.119	0.087	0.158	SUBCLONAL	1	TRUE	1	0.978784403506562	2		207	257	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108091	30108091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80271647	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	125	517	0	ENST00000331968.5:c.716C>T	p.Ser239Leu	p.S239L	ENST00000331968	NM_002742.2	239	tCg/tTg	5/18	1	2	FACETS	0.518	0.471	0.567	0.518	0.471	0.567	SUBCLONAL	1	TRUE	1	0.978784403506562	2		517	493	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560286	95560286	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	105	380	0	ENST00000393063.1:c.5303T>C	p.Val1768Ala	p.V1768A	ENST00000393063	NM_030621.3	1768	gTc/gCc	25/28	1	2	FACETS	0.463	0.417	0.512	0.463	0.417	0.512	SUBCLONAL	1	TRUE	1	0.978784403506562	2		380	463	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562862	95562862	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	69	264	0	ENST00000393063.1:c.4395G>T	p.Lys1465Asn	p.K1465N	ENST00000393063	NM_030621.3	1465	aaG/aaT	24/28	1	2	FACETS	0.551	0.485	0.62	0.551	0.485	0.62	SUBCLONAL	1	TRUE	1	0.978784403506562	2		264	256	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961364	41961364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	40	395	0	ENST00000219905.7:c.272G>A	p.Arg91Gln	p.R91Q	ENST00000219905	NM_001164273.1	91	cGa/cAa	2/24	1	2	FACETS	0.218	0.181	0.259	0.218	0.181	0.259	SUBCLONAL	1	TRUE	1	0.978784403506562	2		395	375	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059155	42059155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561561375	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	102	354	0	ENST00000219905.7:c.8875G>A	p.Glu2959Lys	p.E2959K	ENST00000219905	NM_001164273.1	2959	Gaa/Aaa	24/24	1	2	FACETS	0.525	0.473	0.579	0.525	0.473	0.579	SUBCLONAL	1	TRUE	1	0.978784403506562	2		354	397	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720315	43720315	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752274598	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	158	584	0	ENST00000382044.4:c.3727C>T	p.Arg1243Cys	p.R1243C	ENST00000382044	NM_001141980.1	1243	Cgt/Tgt	18/28	1	2	FACETS	0.56	0.515	0.605	0.56	0.515	0.605	SUBCLONAL	1	TRUE	1	0.978784403506562	2		584	577	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43769929	43769929	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	28	353	0	ENST00000382044.4:c.817G>T	p.Ala273Ser	p.A273S	ENST00000382044	NM_001141980.1	273	Gca/Tca	8/28	1	2	FACETS	0.136	0.108	0.168	0.136	0.108	0.168	SUBCLONAL	1	TRUE	1	0.978784403506562	2		353	421	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628243	90628243	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	205	721	0	ENST00000330062.3:c.1168G>T	p.Asp390Tyr	p.D390Y	ENST00000330062	NM_002168.2	390	Gac/Tac	9/11	1	2	FACETS	0.497	0.462	0.534	0.497	0.462	0.534	SUBCLONAL	1	TRUE	1	0.978784403506562	2		721	842	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396379	396379	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1157096242	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	183	656	0	ENST00000262320.3:c.647A>G	p.Glu216Gly	p.E216G	ENST00000262320	NM_003502.3	216	gAg/gGg	2/11	0.978784403506562	3	FACETS	0.509	0.469	0.551	0.255	0.234	0.276	SUBCLONAL	1	TRUE	1	0.978784403506562	3		656	1094	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636813	2636813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs547797391	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	223	675	0	ENST00000342085.4:c.1262C>T	p.Ser421Leu	p.S421L	ENST00000342085	NM_002613.4	421	tCg/tTg	11/14	0.978784403506562	3	FACETS	0.492	0.457	0.529	0.246	0.228	0.265	SUBCLONAL	1	TRUE	1	0.978784403506562	3		675	1379	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779181	3779181	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	123	487	0	ENST00000262367.5:c.5867T>C	p.Val1956Ala	p.V1956A	ENST00000262367	NM_004380.2	1956	gTg/gCg	31/31	0.978784403506562	3	FACETS	0.491	0.444	0.54	0.245	0.222	0.27	SUBCLONAL	1	TRUE	1	0.978784403506562	3		487	763	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857016	9857016	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	51	236	0	ENST00000330684.3:c.4385C>A	p.Ser1462Tyr	p.S1462Y	ENST00000330684	NM_001134407.1	1462	tCt/tAt	13/13	0.978784403506562	3	FACETS	0.484	0.413	0.56	0.242	0.206	0.28	SUBCLONAL	1	TRUE	1	0.978784403506562	3		236	321	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274185	10274185	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	125	473	0	ENST00000330684.3:c.84G>T	p.Glu28Asp	p.E28D	ENST00000330684	NM_001134407.1	28	gaG/gaT	2/13	0.978784403506562	3	FACETS	0.523	0.474	0.575	0.262	0.237	0.288	SUBCLONAL	1	TRUE	1	0.978784403506562	3		473	727	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56832433	56832433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367699010	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	98	327	1	ENST00000308159.5:c.343G>A	p.Glu115Lys	p.E115K	ENST00000308159	NM_014669.4	115	Gaa/Aaa	4/22	1	2	FACETS	0.52	0.467	0.575	0.52	0.467	0.575	SUBCLONAL	1	TRUE	1	0.978784403506562	2		328	385	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645414	67645414	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772804334	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	124	435	0	ENST00000264010.4:c.679G>A	p.Asp227Asn	p.D227N	ENST00000264010	NM_006565.3	227	Gat/Aat	3/12	1	2	FACETS	0.557	0.507	0.608	0.557	0.507	0.608	SUBCLONAL	1	TRUE	1	0.978784403506562	2		435	455	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650701	67650701	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	200	539	0	ENST00000264010.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000264010	NM_006565.3	336	Gaa/Taa	5/12	1	2	FACETS	0.514	0.477	0.552	0.514	0.477	0.552	SUBCLONAL	1	TRUE	1	0.978784403506562	2		539	795	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827732	72827732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241554729	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	149	524	0	ENST00000268489.5:c.8849G>A	p.Arg2950His	p.R2950H	ENST00000268489	NM_006885.3	2950	cGc/cAc	9/10	1	2	FACETS	0.539	0.495	0.585	0.539	0.495	0.585	SUBCLONAL	1	TRUE	1	0.978784403506562	2		524	565	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830535	72830535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776901666	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	165	536	0	ENST00000268489.5:c.6046G>A	p.Glu2016Lys	p.E2016K	ENST00000268489	NM_006885.3	2016	Gag/Aag	9/10	1	2	FACETS	0.469	0.431	0.508	0.469	0.431	0.508	SUBCLONAL	1	TRUE	1	0.978784403506562	2		536	719	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108557	8108557	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1466818032	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	190	613	0	ENST00000585124.1:c.838G>A	p.Glu280Lys	p.E280K	ENST00000585124	NM_004217.3	280	Gag/Aag	8/9	1	2	FACETS	0.504	0.467	0.543	0.504	0.467	0.543	SUBCLONAL	1	TRUE	1	0.978784403506562	2		613	770	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032475	12032475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194360851	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	61	258	0	ENST00000353533.5:c.911G>A	p.Arg304Gln	p.R304Q	ENST00000353533	NM_003010.3	304	cGa/cAa	9/11	1	2	FACETS	0.463	0.403	0.527	0.463	0.403	0.527	SUBCLONAL	1	TRUE	1	0.978784403506562	2		258	269	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068429	16068429	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765365064	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	18	94	0	ENST00000268712.3:c.482C>T	p.Ser161Leu	p.S161L	ENST00000268712	NM_006311.3	161	tCg/tTg	5/46	1	2	FACETS	0.372	0.284	0.471	0.372	0.284	0.471	SUBCLONAL	1	TRUE	1	0.978784403506562	2		94	99	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	115	426	0	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	1	2	FACETS	0.484	0.438	0.531	0.484	0.438	0.531	SUBCLONAL	1	TRUE	1	0.978784403506562	2		426	486	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	72	405	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.463	0.407	0.521	0.463	0.407	0.521	SUBCLONAL	1	TRUE	1	0.978784403506562	2		405	318	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627509	37627509	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs371684674	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	136	483	0	ENST00000447079.4:c.1424C>A	p.Ser475Tyr	p.S475Y	ENST00000447079	NM_015083.1	475	tCt/tAt	2/14	1	2	FACETS	0.52	0.475	0.567	0.52	0.475	0.567	SUBCLONAL	1	TRUE	1	0.978784403506562	2		483	534	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38506064	38506064	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	186	578	0	ENST00000254066.5:c.356A>G	p.Asn119Ser	p.N119S	ENST00000254066	NM_000964.3	119	aAc/aGc	4/9	1	2	FACETS	0.497	0.46	0.536	0.497	0.46	0.536	SUBCLONAL	1	TRUE	1	0.978784403506562	2		578	764	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118901	70118901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	229	666	1	ENST00000245479.2:c.473C>T	p.Ala158Val	p.A158V	ENST00000245479	NM_000346.3	158	gCg/gTg	2/3	1	2	FACETS	0.544	0.508	0.581	0.544	0.508	0.581	SUBCLONAL	1	TRUE	1	0.978784403506562	2		667	860	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375016	45375016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226662382	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	82	373	0	ENST00000262160.6:c.827C>T	p.Ser276Leu	p.S276L	ENST00000262160	NM_005901.5	276	tCg/tTg	8/11	1	2	FACETS	0.514	0.457	0.574	0.514	0.457	0.574	SUBCLONAL	1	TRUE	1	0.978784403506562	2		373	326	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222487	2222487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	242	623	1	ENST00000398665.3:c.3319C>T	p.Arg1107Cys	p.R1107C	ENST00000398665	NM_032482.2	1107	Cgc/Tgc	24/28	1	2	FACETS	0.59	0.552	0.629	0.59	0.552	0.629	SUBCLONAL	1	TRUE	1	0.978784403506562	2		624	838	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125493	7125493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913148	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	195	601	1	ENST00000302850.5:c.3059G>A	p.Arg1020Gln	p.R1020Q	ENST00000302850	NM_000208.2	1020	cGa/cAa	17/22	1	2	FACETS	0.51	0.473	0.549	0.51	0.473	0.549	SUBCLONAL	1	TRUE	1	0.978784403506562	2		602	781	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10267136	10267136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	168	510	0	ENST00000340748.4:c.1282G>A	p.Glu428Lys	p.E428K	ENST00000340748		428	Gag/Aag	17/40	1	2	FACETS	0.511	0.471	0.552	0.511	0.471	0.552	SUBCLONAL	1	TRUE	1	0.978784403506562	2		510	672	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169001	11169001	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	141	658	0	ENST00000358026.2:c.4591G>A	p.Glu1531Lys	p.E1531K	ENST00000358026	NM_001128849.1	1531	Gag/Aag	32/36	1	2	FACETS	0.333	0.303	0.364	0.333	0.303	0.364	SUBCLONAL	1	TRUE	1	0.978784403506562	2		658	866	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210808	36210808	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	276	834	1	ENST00000222270.7:c.559G>T	p.Glu187Ter	p.E187*	ENST00000222270	NM_014727.1	187	Gaa/Taa	3/37	1	2	FACETS	0.574	0.539	0.609	0.574	0.539	0.609	SUBCLONAL	1	TRUE	1	0.978784403506562	2		835	983	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211219	36211219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765836382	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	322	975	1	ENST00000222270.7:c.970G>A	p.Glu324Lys	p.E324K	ENST00000222270	NM_014727.1	324	Gaa/Aaa	3/37	1	2	FACETS	0.565	0.534	0.598	0.565	0.534	0.598	SUBCLONAL	1	TRUE	1	0.978784403506562	2		976	1164	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765694	41765694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61737385	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	198	582	0	ENST00000301178.4:c.2570C>T	p.Ala857Val	p.A857V	ENST00000301178	NM_021913.4	857	gCg/gTg	20/20	1	2	FACETS	0.567	0.527	0.609	0.567	0.527	0.609	SUBCLONAL	1	TRUE	1	0.978784403506562	2		582	713	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972993	25972993	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	101	332	0	ENST00000435504.4:c.1432C>A	p.Leu478Ile	p.L478I	ENST00000435504		478	Ctt/Att	12/13	0.540968407483699	3	FACETS	0.615	0.552	0.681	0.307	0.276	0.341	INDETERMINATE	1	TRUE	1	0.978784403506562	3		332	500	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234206	39234206	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	113	457	0	ENST00000402219.2:c.2639C>A	p.Ser880Ter	p.S880*	ENST00000402219	NM_005633.3	880	tCa/tAa	16/23	0.540968407483699	3	FACETS	0.584	0.527	0.644	0.292	0.263	0.322	INDETERMINATE	1	TRUE	1	0.978784403506562	3		457	589	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262542	39262542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	52	411	0	ENST00000402219.2:c.964C>T	p.Leu322Phe	p.L322F	ENST00000402219	NM_005633.3	322	Ctt/Ttt	7/23	0.540968407483699	3	FACETS	0.356	0.304	0.414	0.178	0.152	0.207	INDETERMINATE	1	TRUE	1	0.978784403506562	3		411	444	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690287	47690287	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	98	375	0	ENST00000233146.2:c.1504G>T	p.Asp502Tyr	p.D502Y	ENST00000233146	NM_000251.2	502	Gat/Tat	9/16	0.540968407483699	3	FACETS	0.707	0.634	0.783	0.353	0.317	0.392	INDETERMINATE	1	TRUE	1	0.978784403506562	3		375	422	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026015	48026015	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765237563	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	233	386	0	ENST00000234420.5:c.893G>A	p.Arg298Gln	p.R298Q	ENST00000234420	NM_000179.2	298	cGa/cAa	4/10	0.540968407483699	3	FACETS	1	0.99	1	0.634	0.597	0.672	INDETERMINATE	1	TRUE	1	0.978784403506562	3		386	559	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147532	61147532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543671237	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	11	37	0	ENST00000295025.8:c.937C>T	p.Arg313Cys	p.R313C	ENST00000295025	NM_002908.2	313	Cgc/Tgc	9/11	0.540968407483699	3	FACETS	0.67	0.476	0.894	0.335	0.238	0.447	INDETERMINATE	1	TRUE	1	0.978784403506562	3		37	50	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149129	61149129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144119768	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	87	405	0	ENST00000295025.8:c.1319C>T	p.Ser440Leu	p.S440L	ENST00000295025	NM_002908.2	440	tCg/tTg	11/11	0.540968407483699	3	FACETS	0.547	0.486	0.612	0.274	0.243	0.306	INDETERMINATE	1	TRUE	1	0.978784403506562	3		405	484	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172018	99172018	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	291	452	1	ENST00000074304.5:c.1584G>T	p.Glu528Asp	p.E528D	ENST00000074304	NM_001134224.1	528	gaG/gaT	17/26	0.540968407483699	3	FACETS	1	0.99	1	0.601	0.568	0.634	INDETERMINATE	1	TRUE	1	0.978784403506562	3		453	737	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617503	158617503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1034717563	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	124	478	0	ENST00000263640.3:c.1153G>A	p.Glu385Lys	p.E385K	ENST00000263640	NM_001105.4	385	Gaa/Aaa	9/11	0.540968407483699	3	FACETS	0.518	0.469	0.57	0.259	0.234	0.285	INDETERMINATE	1	TRUE	1	0.978784403506562	3		478	728	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266128	198266128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	85	327	1	ENST00000335508.6:c.2492G>A	p.Arg831Gln	p.R831Q	ENST00000335508	NM_012433.2	831	cGa/cAa	17/25	0.540968407483699	3	FACETS	0.626	0.557	0.7	0.313	0.278	0.35	INDETERMINATE	1	TRUE	1	0.978784403506562	3		328	413	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137653	202137653	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	77	356	0	ENST00000358485.4:c.760G>T	p.Glu254Ter	p.E254*	ENST00000358485	NM_001080125.1	254	Gaa/Taa	5/9	0.540968407483699	3	FACETS	0.525	0.463	0.592	0.263	0.231	0.296	INDETERMINATE	1	TRUE	1	0.978784403506562	3		356	446	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587128	212587128	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	137	326	0	ENST00000342788.4:c.873G>T	p.Lys291Asn	p.K291N	ENST00000342788	NM_005235.2	291	aaG/aaT	7/28	0.540968407483699	3	FACETS	1	0.981	1	0.603	0.555	0.65	INDETERMINATE	1	TRUE	1	0.978784403506562	3		326	346	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587164	212587164	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	108	424	0	ENST00000342788.4:c.837C>A	p.Phe279Leu	p.F279L	ENST00000342788	NM_005235.2	279	ttC/ttA	7/28	0.540968407483699	3	FACETS	0.661	0.596	0.73	0.331	0.298	0.365	INDETERMINATE	1	TRUE	1	0.978784403506562	3		424	497	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379426	225379426	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	29	530	0	ENST00000264414.4:c.442C>T	p.Arg148Ter	p.R148*	ENST00000264414	NM_003590.4	148	Cga/Tga	4/16	0.540968407483699	3	FACETS	0.157	0.125	0.193	0.079	0.062	0.097	INDETERMINATE	1	TRUE	1	0.978784403506562	3		530	562	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394071	31394071	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs868828837	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	121	409	1	ENST00000328111.2:c.2358C>A	p.Asn786Lys	p.N786K	ENST00000328111	NM_006892.3	786	aaC/aaA	22/23	1	2	FACETS	0.471	0.427	0.517	0.471	0.427	0.517	SUBCLONAL	1	TRUE	1	0.978784403506562	2		410	525	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742679	39742679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	127	332	1	ENST00000361337.2:c.1522C>T	p.Arg508Cys	p.R508C	ENST00000361337	NM_003286.2	508	Cgt/Tgt	15/21	1	2	FACETS	0.565	0.516	0.617	0.565	0.516	0.617	SUBCLONAL	1	TRUE	1	0.978784403506562	2		333	459	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877358	40877358	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	124	467	0	ENST00000373198.4:c.2338C>A	p.Leu780Ile	p.L780I	ENST00000373198	NM_133170.3	780	Ctc/Atc	15/32	1	2	FACETS	0.454	0.412	0.498	0.454	0.412	0.498	SUBCLONAL	1	TRUE	1	0.978784403506562	2		467	558	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980858	40980858	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	162	541	0	ENST00000373198.4:c.1628T>C	p.Phe543Ser	p.F543S	ENST00000373198	NM_133170.3	543	tTc/tCc	10/32	1	2	FACETS	0.554	0.51	0.598	0.554	0.51	0.598	SUBCLONAL	1	TRUE	1	0.978784403506562	2		541	598	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264158	46264158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375357603	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	88	284	0	ENST00000371998.3:c.1205G>A	p.Ser402Asn	p.S402N	ENST00000371998		402	aGt/aAt	11/23	1	2	FACETS	0.527	0.471	0.586	0.527	0.471	0.586	SUBCLONAL	1	TRUE	1	0.978784403506562	2		284	341	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46271024	46271024	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772403773	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	227	453	0	ENST00000371998.3:c.3148G>A	p.Glu1050Lys	p.E1050K	ENST00000371998		1050	Gaa/Aaa	17/23	1	2	FACETS	0.748	0.702	0.796	0.748	0.702	0.796	SUBCLONAL	1	TRUE	1	0.978784403506562	2		453	620	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945650	54945650	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	22	289	0	ENST00000312783.6:c.920A>C	p.Asp307Ala	p.D307A	ENST00000312783	NM_198436.1	307	gAt/gCt	9/10	1	2	FACETS	0.156	0.121	0.197	0.156	0.121	0.197	SUBCLONAL	1	TRUE	1	0.978784403506562	2		289	288	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62309650	62309650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753838163	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	214	583	0	ENST00000360203.5:c.988G>A	p.Asp330Asn	p.D330N	ENST00000360203	NM_001283009.1	330	Gat/Aat	12/35	1	2	FACETS	0.606	0.566	0.648	0.606	0.566	0.648	SUBCLONAL	1	TRUE	1	0.978784403506562	2		583	721	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231773	36231773	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1569061762	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	22	565	2	ENST00000300305.3:c.611G>A	p.Arg204Gln	p.R204Q	ENST00000300305		204	cGa/cAa	5/8	1	2	FACETS	0.059	0.045	0.076	0.059	0.045	0.076	SUBCLONAL	1	TRUE	1	0.978784403506562	2		567	756	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755666	39755666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	198	676	0	ENST00000288319.7:c.1099C>T	p.Arg367Cys	p.R367C	ENST00000288319	NM_182918.3	367	Cgc/Tgc	10/10	1	2	FACETS	0.518	0.481	0.557	0.518	0.481	0.557	SUBCLONAL	1	TRUE	1	0.978784403506562	2		676	781	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513324	44513324	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	59	626	1	ENST00000291552.4:c.611C>A	p.Ser204Tyr	p.S204Y	ENST00000291552	NM_006758.2	204	tCt/tAt	8/8	1	2	FACETS	0.12	0.103	0.139	0.12	0.103	0.139	SUBCLONAL	1	TRUE	1	0.978784403506562	2		627	1003	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077447	30077447	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	102	319	0	ENST00000338641.4:c.1594A>C	p.Ser532Arg	p.S532R	ENST00000338641	NM_000268.3	532	Agc/Cgc	15/16	1	2	FACETS	0.569	0.514	0.627	0.569	0.514	0.627	SUBCLONAL	1	TRUE	1	0.978784403506562	2		319	366	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191488	10191488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs5030818	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	142	405	0	ENST00000256474.2:c.481C>T	p.Arg161Ter	p.R161*	ENST00000256474	NM_000551.3	161	Cga/Tga	3/3	1	2	FACETS	0.561	0.514	0.61	0.561	0.514	0.61	SUBCLONAL	1	TRUE	1	0.978784403506562	2		405	517	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458536	12458536	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs780238349	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	219	566	2	ENST00000287820.6:c.1153C>T	p.Arg385Ter	p.R385*	ENST00000287820	NM_015869.4	385	Cga/Tga	6/7	1	2	FACETS	0.684	0.64	0.73	0.684	0.64	0.73	SUBCLONAL	1	TRUE	1	0.978784403506562	2		568	654	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641905	12641905	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs755926381	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	116	254	0	ENST00000251849.4:c.844C>T	p.Arg282Ter	p.R282*	ENST00000251849	NM_002880.3	282	Cga/Tga	8/17	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.978784403506562	2		254	236	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275255	41275255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	127	320	0	ENST00000349496.5:c.1421G>A	p.Arg474Gln	p.R474Q	ENST00000349496	NM_001904.3	474	cGa/cAa	9/15	1	2	FACETS	0.563	0.513	0.614	0.563	0.513	0.614	SUBCLONAL	1	TRUE	1	0.978784403506562	2		320	461	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275649	41275649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	110	369	0	ENST00000349496.5:c.1544G>A	p.Arg515Gln	p.R515Q	ENST00000349496	NM_001904.3	515	cGa/cAa	10/15	1	2	FACETS	0.473	0.427	0.521	0.473	0.427	0.521	SUBCLONAL	1	TRUE	1	0.978784403506562	2		369	475	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163387	47163387	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	53	293	0	ENST00000409792.3:c.2739G>T	p.Lys913Asn	p.K913N	ENST00000409792	NM_014159.6	913	aaG/aaT	3/21	1	2	FACETS	0.495	0.427	0.567	0.495	0.427	0.567	SUBCLONAL	1	TRUE	1	0.978784403506562	2		293	219	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413009	49413009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519953	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	172	590	0	ENST00000418115.1:c.14G>A	p.Arg5Gln	p.R5Q	ENST00000418115	NM_001664.2	5	cGg/cAg	2/5	1	2	FACETS	0.499	0.46	0.539	0.499	0.46	0.539	SUBCLONAL	1	TRUE	1	0.978784403506562	2		590	704	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391088	89391088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767254790	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	152	614	1	ENST00000336596.2:c.1154G>A	p.Arg385Gln	p.R385Q	ENST00000336596	NM_005233.5	385	cGa/cAa	5/17	1	2	FACETS	0.43	0.393	0.467	0.43	0.393	0.467	SUBCLONAL	1	TRUE	1	0.978784403506562	2		615	723	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480466	89480466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446890859	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	88	315	0	ENST00000336596.2:c.2303C>T	p.Ser768Leu	p.S768L	ENST00000336596	NM_005233.5	768	tCg/tTg	13/17	1	2	FACETS	0.456	0.407	0.509	0.456	0.407	0.509	SUBCLONAL	1	TRUE	1	0.978784403506562	2		315	394	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453531	138453531	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372119491	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	105	319	0	ENST00000289153.2:c.917G>A	p.Arg306Gln	p.R306Q	ENST00000289153	NM_006219.2	306	cGa/cAa	5/22	1	2	FACETS	0.588	0.531	0.646	0.588	0.531	0.646	SUBCLONAL	1	TRUE	1	0.978784403506562	2		319	365	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281346	142281346	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	115	503	0	ENST00000350721.4:c.898A>C	p.Lys300Gln	p.K300Q	ENST00000350721	NM_001184.3	300	Aag/Cag	4/47	1	2	FACETS	0.528	0.479	0.579	0.528	0.479	0.579	SUBCLONAL	1	TRUE	1	0.978784403506562	2		503	445	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951949	178951949	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	99	403	1	ENST00000263967.3:c.3004T>G	p.Phe1002Val	p.F1002V	ENST00000263967	NM_006218.2	1002	Ttc/Gtc	21/21	1	2	FACETS	0.556	0.5	0.613	0.556	0.5	0.613	SUBCLONAL	1	TRUE	1	0.978784403506562	2		404	364	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146724	185146724	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs537804181	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	220	645	0	ENST00000265026.3:c.355C>A	p.Gln119Lys	p.Q119K	ENST00000265026	NM_004721.4	119	Cag/Aag	2/14	1	2	FACETS	0.56	0.522	0.599	0.56	0.522	0.599	SUBCLONAL	1	TRUE	1	0.978784403506562	2		645	803	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526268	189526268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	185	567	0	ENST00000264731.3:c.532G>A	p.Asp178Asn	p.D178N	ENST00000264731	NM_003722.4	178	Gac/Aac	4/14	1	2	FACETS	0.529	0.489	0.569	0.529	0.489	0.569	SUBCLONAL	1	TRUE	1	0.978784403506562	2		567	715	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587161	189587161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173679499	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	22	397	1	ENST00000264731.3:c.1178G>A	p.Arg393Gln	p.R393Q	ENST00000264731	NM_003722.4	393	cGa/cAa	9/14	1	2	FACETS	0.112	0.086	0.142	0.112	0.086	0.142	SUBCLONAL	1	TRUE	1	0.978784403506562	2		398	402	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748309	41748309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs894529129	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	54	733	0	ENST00000226382.2:c.460C>T	p.Arg154Cys	p.R154C	ENST00000226382	NM_003924.3	154	Cgc/Tgc	3/3	1	2	FACETS	0.108	0.092	0.127	0.108	0.092	0.127	SUBCLONAL	1	TRUE	1	0.978784403506562	2		733	1017	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136805	55136805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41279521	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	61	311	0	ENST00000257290.5:c.1127G>A	p.Arg376Gln	p.R376Q	ENST00000257290	NM_006206.4	376	cGa/cAa	8/23	1	2	FACETS	0.507	0.442	0.575	0.507	0.442	0.575	SUBCLONAL	1	TRUE	1	0.978784403506562	2		311	246	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151628	55151628	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	129	568	0	ENST00000257290.5:c.2414G>T	p.Gly805Val	p.G805V	ENST00000257290	NM_006206.4	805	gGa/gTa	17/23	1	2	FACETS	0.467	0.425	0.511	0.467	0.425	0.511	SUBCLONAL	1	TRUE	1	0.978784403506562	2		568	564	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156639	55156639	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768291477	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	139	511	0	ENST00000257290.5:c.3040G>A	p.Ala1014Thr	p.A1014T	ENST00000257290	NM_006206.4	1014	Gct/Act	22/23	1	2	FACETS	0.478	0.437	0.521	0.478	0.437	0.521	SUBCLONAL	1	TRUE	1	0.978784403506562	2		511	594	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979589	55979589	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	147	468	0	ENST00000263923.4:c.858G>T	p.Lys286Asn	p.K286N	ENST00000263923	NM_002253.2	286	aaG/aaT	7/30	1	2	FACETS	0.601	0.552	0.651	0.601	0.552	0.651	SUBCLONAL	1	TRUE	1	0.978784403506562	2		468	500	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233097	66233097	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	95	327	0	ENST00000273854.3:c.1902G>T	p.Lys634Asn	p.K634N	ENST00000273854	NM_004439.5	634	aaG/aaT	10/18	1	2	FACETS	0.484	0.434	0.537	0.484	0.434	0.537	SUBCLONAL	1	TRUE	1	0.978784403506562	2		327	401	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007310	143007310	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	84	301	0	ENST00000262992.4:c.2474G>A	p.Trp825Ter	p.W825*	ENST00000262992	NM_001101669.1	825	tGg/tAg	22/24	1	2	FACETS	0.52	0.463	0.58	0.52	0.463	0.58	SUBCLONAL	1	TRUE	1	0.978784403506562	2		301	330	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143350363	143350363	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	54	179	0	ENST00000262992.4:c.99G>T	p.Gln33His	p.Q33H	ENST00000262992	NM_001101669.1	33	caG/caT	3/24	1	2	FACETS	0.645	0.561	0.733	0.645	0.561	0.733	SUBCLONAL	1	TRUE	1	0.978784403506562	2		179	171	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352400	143352400	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	33	473	0	ENST00000262992.4:c.13G>T	p.Glu5Ter	p.E5*	ENST00000262992	NM_001101669.1	5	Gag/Tag	2/24	1	2	FACETS	0.117	0.095	0.142	0.117	0.095	0.142	SUBCLONAL	1	TRUE	1	0.978784403506562	2		473	576	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249534	153249534	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	65	348	0	ENST00000281708.4:c.1244G>A	p.Arg415Lys	p.R415K	ENST00000281708	NM_033632.3	415	aGa/aAa	9/12	1	2	FACETS	0.384	0.335	0.437	0.384	0.335	0.437	SUBCLONAL	1	TRUE	1	0.978784403506562	2		348	346	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540917	187540917	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558300184	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	18	302	0	ENST00000441802.2:c.6823G>A	p.Asp2275Asn	p.D2275N	ENST00000441802	NM_005245.3	2275	Gac/Aac	10/27	1	2	FACETS	0.123	0.092	0.159	0.123	0.092	0.159	SUBCLONAL	1	TRUE	1	0.978784403506562	2		302	300	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282725	1282725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	161	510	0	ENST00000310581.5:c.1588C>T	p.Pro530Ser	p.P530S	ENST00000310581	NM_198253.2	530	Ccg/Tcg	3/16	1	2	FACETS	0.5	0.46	0.542	0.5	0.46	0.542	SUBCLONAL	1	TRUE	1	0.978784403506562	2		510	658	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38978751	38978751	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1432686344	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	55	216	0	ENST00000357387.3:c.755G>T	p.Arg252Ile	p.R252I	ENST00000357387	NM_152756.3	252	aGa/aTa	9/38	1	2	FACETS	0.576	0.501	0.656	0.576	0.501	0.656	SUBCLONAL	1	TRUE	1	0.978784403506562	2		216	195	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168656	56168656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764525244	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	108	341	0	ENST00000399503.3:c.1510G>A	p.Glu504Lys	p.E504K	ENST00000399503	NM_005921.1	504	Gag/Aag	9/20	1	2	FACETS	0.542	0.49	0.596	0.542	0.49	0.596	SUBCLONAL	1	TRUE	1	0.978784403506562	2		341	407	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79952287	79952287	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	26	386	0	ENST00000265081.6:c.295A>C	p.Lys99Gln	p.K99Q	ENST00000265081	NM_002439.4	99	Aag/Cag	2/24	1	2	FACETS	0.111	0.087	0.138	0.111	0.087	0.138	SUBCLONAL	1	TRUE	1	0.978784403506562	2		386	480	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961030	79961030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138381683	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	128	434	0	ENST00000265081.6:c.427G>A	p.Asp143Asn	p.D143N	ENST00000265081	NM_002439.4	143	Gat/Aat	3/24	1	2	FACETS	0.533	0.485	0.582	0.533	0.485	0.582	SUBCLONAL	1	TRUE	1	0.978784403506562	2		434	491	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961137	79961137	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs569679162	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	110	490	0	ENST00000265081.6:c.534G>T	p.Lys178Asn	p.K178N	ENST00000265081	NM_002439.4	178	aaG/aaT	3/24	1	2	FACETS	0.474	0.428	0.522	0.474	0.428	0.522	SUBCLONAL	1	TRUE	1	0.978784403506562	2		490	474	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86668007	86668007	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	57	256	0	ENST00000274376.6:c.1771C>T	p.Arg591Cys	p.R591C	ENST00000274376	NM_002890.2	591	Cgt/Tgt	13/25	1	2	FACETS	0.464	0.402	0.53	0.464	0.402	0.53	SUBCLONAL	1	TRUE	1	0.978784403506562	2		256	251	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670010	86670010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	50	242	0	ENST00000274376.6:c.1807G>A	p.Ala603Thr	p.A603T	ENST00000274376	NM_002890.2	603	Gcc/Acc	14/25	1	2	FACETS	0.422	0.361	0.488	0.422	0.361	0.488	SUBCLONAL	1	TRUE	1	0.978784403506562	2		242	242	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672345	86672345	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	75	325	0	ENST00000274376.6:c.2147A>C	p.Lys716Thr	p.K716T	ENST00000274376	NM_002890.2	716	aAa/aCa	16/25	1	2	FACETS	0.528	0.468	0.592	0.528	0.468	0.592	SUBCLONAL	1	TRUE	1	0.978784403506562	2		325	290	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86676414	86676414	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	30	176	0	ENST00000274376.6:c.2690+2T>C		p.X897_splice	ENST00000274376	NM_002890.2	897			1	2	FACETS	0.39	0.318	0.47	0.39	0.318	0.47	SUBCLONAL	1	TRUE	1	0.978784403506562	2		176	157	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679546	86679546	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554050230	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	82	317	0	ENST00000274376.6:c.2707C>T	p.Arg903Ter	p.R903*	ENST00000274376	NM_002890.2	903	Cga/Tga	21/25	1	2	FACETS	0.54	0.481	0.603	0.54	0.481	0.603	SUBCLONAL	1	TRUE	1	0.978784403506562	2		317	310	SUCCESS
APC	324	MSKCC	GRCh37	5	112177677	112177677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782301	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	56	310	0	ENST00000257430.4:c.6386C>T	p.Ser2129Leu	p.S2129L	ENST00000257430	NM_000038.5	2129	tCg/tTg	16/16	1	2	FACETS	0.481	0.416	0.549	0.481	0.416	0.549	SUBCLONAL	1	TRUE	1	0.978784403506562	2		310	238	SUCCESS
APC	324	MSKCC	GRCh37	5	112178781	112178781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141010008	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	99	371	0	ENST00000257430.4:c.7490C>T	p.Ser2497Leu	p.S2497L	ENST00000257430	NM_000038.5	2497	tCg/tTg	16/16	1	2	FACETS	0.516	0.464	0.57	0.516	0.464	0.57	SUBCLONAL	1	TRUE	1	0.978784403506562	2		371	392	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940521	131940521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs181961360	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	87	273	0	ENST00000265335.6:c.2548C>T	p.Arg850Cys	p.R850C	ENST00000265335		850	Cgt/Tgt	16/25	1	2	FACETS	0.554	0.495	0.615	0.554	0.495	0.615	SUBCLONAL	1	TRUE	1	0.978784403506562	2		273	321	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441394	149441394	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370624765	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	173	492	0	ENST00000286301.3:c.1645C>T	p.Arg549Cys	p.R549C	ENST00000286301	NM_005211.3	549	Cgc/Tgc	12/22	1	2	FACETS	0.52	0.48	0.561	0.52	0.48	0.561	SUBCLONAL	1	TRUE	1	0.978784403506562	2		492	680	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500816	149500816	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	95	690	0	ENST00000261799.4:c.2414G>A	p.Gly805Asp	p.G805D	ENST00000261799	NM_002609.3	805	gGc/gAc	17/23	1	2	FACETS	0.275	0.244	0.307	0.275	0.244	0.307	SUBCLONAL	1	TRUE	1	0.978784403506562	2		690	707	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176618958	176618958	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	131	499	0	ENST00000439151.2:c.1001G>A	p.Arg334His	p.R334H	ENST00000439151	NM_022455.4	334	cGc/cAc	3/23	1	2	FACETS	0.461	0.419	0.504	0.461	0.419	0.504	SUBCLONAL	1	TRUE	1	0.978784403506562	2		499	581	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636883	176636883	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752490855	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	115	445	0	ENST00000439151.2:c.1483G>A	p.Ala495Thr	p.A495T	ENST00000439151	NM_022455.4	495	Gct/Act	5/23	1	2	FACETS	0.538	0.488	0.59	0.538	0.488	0.59	SUBCLONAL	1	TRUE	1	0.978784403506562	2		445	437	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637408	176637408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554189230	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	119	424	1	ENST00000439151.2:c.2008G>A	p.Asp670Asn	p.D670N	ENST00000439151	NM_022455.4	670	Gat/Aat	5/23	1	2	FACETS	0.532	0.483	0.583	0.532	0.483	0.583	SUBCLONAL	1	TRUE	1	0.978784403506562	2		425	457	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709523	176709523	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs797045057	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	90	284	0	ENST00000439151.2:c.5950C>T	p.Arg1984Ter	p.R1984*	ENST00000439151	NM_022455.4	1984	Cga/Tga	19/23	1	2	FACETS	0.63	0.566	0.696	0.63	0.566	0.696	SUBCLONAL	1	TRUE	1	0.978784403506562	2		284	292	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046749	180046749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121909657	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	232	784	0	ENST00000261937.6:c.2563G>A	p.Ala855Thr	p.A855T	ENST00000261937	NM_182925.4	855	Gcc/Acc	18/30	1	2	FACETS	0.544	0.508	0.581	0.544	0.508	0.581	SUBCLONAL	1	TRUE	1	0.978784403506562	2		784	872	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20486948	20486948	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs773975473	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	219	275	0	ENST00000346618.3:c.913C>T	p.Arg305Ter	p.R305*	ENST00000346618	NM_001949.4	305	Cga/Tga	5/7	0.978784403506562	3	FACETS	0.797	0.753	0.841	0.797	0.753	0.841	SUBCLONAL	2	TRUE	1	0.978784403506562	3		275	418	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056588	26056588	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	41	239	0	ENST00000343677.2:c.69G>T	p.Lys23Asn	p.K23N	ENST00000343677	NM_005319.3	23	aaG/aaT	1/1	0.978784403506562	3	FACETS	0.26	0.216	0.309	0.13	0.108	0.155	SUBCLONAL	1	TRUE	1	0.978784403506562	3		239	480	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911048	29911048	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs765200653	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	106	368	0	ENST00000376809.5:c.347C>A	p.Ser116Tyr	p.S116Y	ENST00000376809	NM_002116.7	116	tCt/tAt	3/8	0.978784403506562	3	FACETS	0.564	0.507	0.624	0.282	0.253	0.312	SUBCLONAL	1	TRUE	1	0.978784403506562	3		368	572	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672671	30672671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	663	711	1	ENST00000376406.3:c.4289C>A	p.Ser1430Tyr	p.S1430Y	ENST00000376406	NM_014641.2	1430	tCt/tAt	10/15	0.978784403506562	3	FACETS	0.755	0.73	0.78	0.755	0.73	0.78	SUBCLONAL	2	TRUE	1	0.978784403506562	3		712	1337	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672767	30672767	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1300485516	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	90	691	1	ENST00000376406.3:c.4193G>T	p.Arg1398Ile	p.R1398I	ENST00000376406	NM_014641.2	1398	aGa/aTa	10/15	0.978784403506562	3	FACETS	0.223	0.197	0.251	0.111	0.098	0.126	SUBCLONAL	1	TRUE	1	0.978784403506562	3		692	1230	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30682823	30682823	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	97	531	0	ENST00000376406.3:c.130G>T	p.Glu44Ter	p.E44*	ENST00000376406	NM_014641.2	44	Gaa/Taa	2/15	0.978784403506562	3	FACETS	0.366	0.326	0.409	0.183	0.163	0.205	SUBCLONAL	1	TRUE	1	0.978784403506562	3		531	807	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948260	31948260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs534517982	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	170	629	1	ENST00000375333.2:c.848G>A	p.Arg283Gln	p.R283Q	ENST00000375333	NM_032454.1	283	cGa/cAa	6/8	0.978784403506562	3	FACETS	0.432	0.396	0.469	0.216	0.198	0.235	SUBCLONAL	1	TRUE	1	0.978784403506562	3		630	1199	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803500	32803500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550712305	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1336	109	755	2	ENST00000374899.4:c.659G>A	p.Arg220Gln	p.R220Q	ENST00000374899	NM_018833.2	220	cGa/cAa	4/12	0.978784403506562	3	FACETS	0.23	0.205	0.256	0.115	0.102	0.128	SUBCLONAL	1	TRUE	1	0.978784403506562	3		757	1445	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32814855	32814855	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	208	673	1	ENST00000354258.4:c.2210G>A	p.Ser737Asn	p.S737N	ENST00000354258	NM_000593.5	737	aGc/aAc	10/11	0.978784403506562	3	FACETS	0.488	0.452	0.526	0.244	0.226	0.263	SUBCLONAL	1	TRUE	1	0.978784403506562	3		674	1296	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066675	94066675	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	141	423	0	ENST00000369303.4:c.1084G>T	p.Asp362Tyr	p.D362Y	ENST00000369303	NM_004440.3	362	Gat/Tat	5/17	1	2	FACETS	0.497	0.454	0.541	0.497	0.454	0.541	SUBCLONAL	1	TRUE	1	0.978784403506562	2		423	580	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415228	109415228	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	39	687	0	ENST00000436639.2:c.49G>T	p.Asp17Tyr	p.D17Y	ENST00000436639	NM_014454.2	17	Gat/Tat	1/10	1	2	FACETS	0.109	0.09	0.131	0.109	0.09	0.131	SUBCLONAL	1	TRUE	1	0.978784403506562	2		687	728	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527294	137527294	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	30	517	0	ENST00000367739.4:c.352G>T	p.Glu118Ter	p.E118*	ENST00000367739	NM_000416.2	118	Gaa/Taa	3/7	1	2	FACETS	0.119	0.095	0.145	0.119	0.095	0.145	SUBCLONAL	1	TRUE	1	0.978784403506562	2		517	517	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527358	157527358	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	75	328	0	ENST00000346085.5:c.5083T>A	p.Phe1695Ile	p.F1695I	ENST00000346085	NM_020732.3	1695	Ttt/Att	20/20	1	2	FACETS	0.435	0.384	0.49	0.435	0.384	0.49	SUBCLONAL	1	TRUE	1	0.978784403506562	2		328	352	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739609	41739609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	117	419	0	ENST00000242208.4:c.364G>A	p.Glu122Lys	p.E122K	ENST00000242208	NM_002192.2	122	Gag/Aag	2/3	1	2	FACETS	0.51	0.462	0.559	0.51	0.462	0.559	SUBCLONAL	1	TRUE	1	0.978784403506562	2		419	469	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467841	50467841	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752909152	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	124	435	0	ENST00000331340.3:c.1076C>T	p.Pro359Leu	p.P359L	ENST00000331340	NM_006060.4	359	cCg/cTg	8/8	1	2	FACETS	0.474	0.431	0.52	0.474	0.431	0.52	SUBCLONAL	1	TRUE	1	0.978784403506562	2		435	534	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508517	106508517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs549157001	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	61	293	0	ENST00000359195.3:c.511G>A	p.Asp171Asn	p.D171N	ENST00000359195	NM_002649.2	171	Gat/Aat	2/11	1	2	FACETS	0.442	0.384	0.503	0.442	0.384	0.503	SUBCLONAL	1	TRUE	1	0.978784403506562	2		293	282	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340162	116340162	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	74	217	0	ENST00000397752.3:c.1024C>A	p.Leu342Ile	p.L342I	ENST00000397752	NM_000245.2	342	Ctt/Att	2/21	1	2	FACETS	0.494	0.436	0.555	0.494	0.436	0.555	SUBCLONAL	1	TRUE	1	0.978784403506562	2		217	306	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395504	116395504	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	95	358	0	ENST00000397752.3:c.1797G>T	p.Lys599Asn	p.K599N	ENST00000397752	NM_000245.2	599	aaG/aaT	6/21	1	2	FACETS	0.479	0.429	0.532	0.479	0.429	0.532	SUBCLONAL	1	TRUE	1	0.978784403506562	2		358	405	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836298	151836298	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	194	472	0	ENST00000262189.6:c.14507A>G	p.Asp4836Gly	p.D4836G	ENST00000262189	NM_170606.2	4836	gAc/gGc	57/59	1	2	FACETS	0.622	0.579	0.667	0.622	0.579	0.667	SUBCLONAL	1	TRUE	1	0.978784403506562	2		472	637	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129946	69129946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759522634	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	77	298	0	ENST00000288368.4:c.4700G>A	p.Arg1567Gln	p.R1567Q	ENST00000288368	NM_024870.2	1567	cGg/cAg	38/40	1	2	FACETS	0.402	0.355	0.453	0.402	0.355	0.453	SUBCLONAL	1	TRUE	1	0.978784403506562	2		298	391	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141565993	141565993	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	140	383	0	ENST00000220592.5:c.1269+2T>C		p.X423_splice	ENST00000220592	NM_012154.3	423			1	2	FACETS	0.613	0.562	0.665	0.613	0.562	0.665	SUBCLONAL	1	TRUE	1	0.978784403506562	2		383	467	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740573	145740573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573164516	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	74	718	0	ENST00000428558.2:c.1444C>T	p.Arg482Cys	p.R482C	ENST00000428558	NM_004260.3	482	Cgc/Tgc	8/22	1	2	FACETS	0.159	0.138	0.181	0.159	0.138	0.181	SUBCLONAL	1	TRUE	1	0.978784403506562	2		718	952	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054649	5054649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373174105	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	55	278	1	ENST00000381652.3:c.701G>A	p.Arg234His	p.R234H	ENST00000381652	NM_004972.3	234	cGc/cAc	7/25	1	2	FACETS	0.446	0.385	0.511	0.446	0.385	0.511	SUBCLONAL	1	TRUE	1	0.978784403506562	2		279	252	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528596	8528596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	93	332	1	ENST00000356435.5:c.536G>A	p.Arg179Gln	p.R179Q	ENST00000356435		179	cGa/cAa	4/35	1	2	FACETS	0.529	0.475	0.587	0.529	0.475	0.587	SUBCLONAL	1	TRUE	1	0.978784403506562	2		333	359	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020670	37020670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	162	434	0	ENST00000358127.4:c.175C>T	p.Arg59Trp	p.R59W	ENST00000358127	NM_001280556.1	59	Cgg/Tgg	2/10	1	2	FACETS	0.578	0.533	0.624	0.578	0.533	0.624	SUBCLONAL	1	TRUE	1	0.978784403506562	2		434	573	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97897737	97897737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs889715188	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	134	387	0	ENST00000289081.3:c.734G>A	p.Arg245Gln	p.R245Q	ENST00000289081	NM_000136.2	245	cGg/cAg	8/15	1	2	FACETS	0.554	0.507	0.604	0.554	0.507	0.604	SUBCLONAL	1	TRUE	1	0.978784403506562	2		387	494	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772845	135772845	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	164	549	0	ENST00000298552.3:c.2778G>T	p.Gln926His	p.Q926H	ENST00000298552	NM_001162426.1	926	caG/caT	21/23	1	2	FACETS	0.462	0.425	0.501	0.462	0.425	0.501	SUBCLONAL	1	TRUE	1	0.978784403506562	2		549	725	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409980	139409980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	242	851	0	ENST00000277541.6:c.1858G>A	p.Asp620Asn	p.D620N	ENST00000277541	NM_017617.3	620	Gac/Aac	11/34	1	2	FACETS	0.499	0.467	0.533	0.499	0.467	0.533	SUBCLONAL	1	TRUE	1	0.978784403506562	2		851	990	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156719	20156719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	103	363	1	ENST00000379607.5:c.38G>A	p.Arg13His	p.R13H	ENST00000379607	NM_001412.3	13	cGc/cAc	2/7	1	2	FACETS	0.444	0.399	0.491	0.444	0.399	0.491	SUBCLONAL	1	TRUE	1	0.978784403506562	2		364	474	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650546	48650546	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	198	778	0	ENST00000376670.3:c.516C>A	p.Phe172Leu	p.F172L	ENST00000376670	NM_002049.3	172	ttC/ttA	3/6	1	2	FACETS	0.467	0.432	0.502	0.467	0.432	0.502	SUBCLONAL	1	TRUE	1	0.978784403506562	2		778	867	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230825	53230825	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	192	748	1	ENST00000375401.3:c.1968G>T	p.Glu656Asp	p.E656D	ENST00000375401	NM_004187.3	656	gaG/gaT	14/26	1	2	FACETS	0.481	0.446	0.518	0.481	0.446	0.518	SUBCLONAL	1	TRUE	1	0.978784403506562	2		749	815	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412634	63412634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753930754	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	176	576	0	ENST00000330258.3:c.533G>A	p.Arg178His	p.R178H	ENST00000330258	NM_152424.3	178	cGt/cAt	2/2	1	2	FACETS	0.52	0.48	0.561	0.52	0.48	0.561	SUBCLONAL	1	TRUE	1	0.978784403506562	2		576	692	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814238	76814238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	93	355	0	ENST00000373344.5:c.6406G>A	p.Asp2136Asn	p.D2136N	ENST00000373344	NM_000489.3	2136	Gac/Aac	29/35	1	2	FACETS	0.617	0.555	0.682	0.617	0.555	0.682	SUBCLONAL	1	TRUE	1	0.978784403506562	2		355	308	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890161	76890161	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	44	442	1	ENST00000373344.5:c.4733C>A	p.Ser1578Tyr	p.S1578Y	ENST00000373344	NM_000489.3	1578	tCt/tAt	17/35	1	2	FACETS	0.203	0.17	0.24	0.203	0.17	0.24	SUBCLONAL	1	TRUE	1	0.978784403506562	2		443	442	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937505	76937505	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	90	403	0	ENST00000373344.5:c.3243G>T	p.Lys1081Asn	p.K1081N	ENST00000373344	NM_000489.3	1081	aaG/aaT	9/35	1	2	FACETS	0.566	0.507	0.627	0.566	0.507	0.627	SUBCLONAL	1	TRUE	1	0.978784403506562	2		403	325	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210230	123210230	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	130	489	1	ENST00000218089.9:c.2582G>A	p.Arg861Lys	p.R861K	ENST00000218089	NM_001042749.1	861	aGa/aAa	26/35	1	2	FACETS	0.58	0.53	0.632	0.58	0.53	0.632	SUBCLONAL	1	TRUE	1	0.978784403506562	2		490	458	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211837	123211837	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	54	349	0	ENST00000218089.9:c.2704G>T	p.Glu902Ter	p.E902*	ENST00000218089	NM_001042749.1	902	Gaa/Taa	27/35	1	2	FACETS	0.415	0.357	0.477	0.415	0.357	0.477	SUBCLONAL	1	TRUE	1	0.978784403506562	2		349	266	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944760	206944760	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	119	525	0	ENST00000423557.1:c.166C>T	p.Gln56Ter	p.Q56*	ENST00000423557	NM_000572.2	56	Caa/Taa	2/5	0.616435785896075	3	FACETS	0.668	0.604	0.737	0.334	0.302	0.369	SUBCLONAL	1	TRUE	1	0.637062090632209	3		525	737	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	41	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.963	0.803	1	0.963	0.803	1	CLONAL	1	TRUE	1	0.19	2		126	448	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653867	89653867	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0043068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	45	436	0	ENST00000371953.3:c.164+1G>A		p.X55_splice	ENST00000371953	NM_000314.4	55			1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.19	2		436	430	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690835	89690835	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs876661177	NA	P-0043068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	40	451	0	ENST00000371953.3:c.242T>A	p.Phe81Tyr	p.F81Y	ENST00000371953	NM_000314.4	81	tTt/tAt	4/9	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.19	2		451	323	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942575	71942575	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	67	739	0	ENST00000298229.2:c.1531G>C	p.Ala511Pro	p.A511P	ENST00000298229	NM_001567.3	511	Gca/Cca	13/28	1	2	FACETS	0.814	0.706	0.932	0.814	0.706	0.932	CLONAL	1	TRUE	1	0.19	2		739	866	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	63	494	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.255	0.219	0.293	0.255	0.219	0.293	SUBCLONAL	1	TRUE	1	0.59	2		494	839	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	162	290	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.851	0.784	0.921	0.851	0.784	0.921	CLONAL	1	TRUE	1	0.59	2		290	645	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	123	623	0	ENST00000320574.5:c.1231G>C	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ctg	13/49	1	2	FACETS	0.881	0.802	0.964	0.881	0.802	0.964	CLONAL	1	TRUE	1	0.59	2		623	473	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	257	770	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.966	0.906	1	0.966	0.906	1	CLONAL	1	TRUE	1	0.59	2		770	902	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660469	67660469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	131	414	0	ENST00000264010.4:c.1369C>T	p.Arg457Ter	p.R457*	ENST00000264010	NM_006565.3	457	Cga/Tga	8/12	1	2	FACETS	0.919	0.84	1	0.919	0.84	1	CLONAL	1	TRUE	1	0.59	2		414	483	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208010	5208010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	180	829	1	ENST00000357368.4:c.5701C>T	p.Arg1901Trp	p.R1901W	ENST00000357368	NM_002850.3	1901	Cgg/Tgg	37/38	0.127185167938153	0	FACETS	0.341	0.315	0.368			1	INDETERMINATE	1	TRUE	0	0.59	0		830	734	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	111	421	0	ENST00000257430.4:c.4199C>A	p.Ser1400Ter	p.S1400*	ENST00000257430	NM_000038.5	1400	tCg/tAg	16/16	1	2	FACETS	0.871	0.788	0.957	0.871	0.788	0.957	CLONAL	1	TRUE	1	0.59	2		421	432	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685272	89685272	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs748031178	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	80	273	0	ENST00000371953.3:c.167T>G	p.Phe56Cys	p.F56C	ENST00000371953	NM_000314.4	56	tTt/tGt	3/9	1	2	FACETS	0.955	0.85	1	0.955	0.85	1	CLONAL	1	TRUE	1	0.59	2		273	284	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120360	94120360	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs749418654	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	108	349	0	ENST00000369303.4:c.691C>T	p.Arg231Ter	p.R231*	ENST00000369303	NM_004440.3	231	Cga/Tga	3/17	1	2	FACETS	0.939	0.85	1	0.939	0.85	1	CLONAL	1	TRUE	1	0.59	2		349	390	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898755	134898755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs546798910	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	124	433	0	ENST00000398015.3:c.1813G>A	p.Glu605Lys	p.E605K	ENST00000398015	NM_004441.4	605	Gaa/Aaa	10/16	1	2	FACETS	0.86	0.782	0.94	0.86	0.782	0.94	CLONAL	1	TRUE	1	0.59	2		433	489	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672842	86672842	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	106	301	0	ENST00000274376.6:c.2329G>T	p.Glu777Ter	p.E777*	ENST00000274376	NM_002890.2	777	Gaa/Taa	17/25	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.59	2		301	355	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709529	176709529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777258117	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	131	399	0	ENST00000439151.2:c.5956C>T	p.Arg1986Cys	p.R1986C	ENST00000439151	NM_022455.4	1986	Cgc/Tgc	19/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.59	2		399	388	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851456	63851456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201542647	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	193	598	0	ENST00000279873.7:c.2234C>T	p.Ala745Val	p.A745V	ENST00000279873	NM_032199.2	745	gCg/gTg	10/10	1	2	FACETS	0.92	0.854	0.988	0.92	0.854	0.988	CLONAL	1	TRUE	1	0.59	2		598	711	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692978	89692978	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	133	673	0	ENST00000371953.3:c.462C>A	p.Phe154Leu	p.F154L	ENST00000371953	NM_000314.4	154	ttC/ttA	5/9	1	2	FACETS	0.689	0.627	0.754	0.689	0.627	0.754	SUBCLONAL	1	TRUE	1	0.59	2		673	654	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519009	66519009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	44	631	0	ENST00000358598.2:c.290G>A	p.Arg97Gln	p.R97Q	ENST00000358598	NM_212471.2	97	cGa/cAa	3/11	1	2	FACETS	0.217	0.182	0.257	0.217	0.182	0.257	SUBCLONAL	1	TRUE	1	0.59	2		631	686	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967186	134967186	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200311306	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	156	582	1	ENST00000398015.3:c.2525G>A	p.Arg842Gln	p.R842Q	ENST00000398015	NM_004441.4	842	cGg/cAg	14/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.59	2		583	509	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692931	89692931	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	276	745	0	ENST00000371953.3:c.415T>G	p.Leu139Val	p.L139V	ENST00000371953	NM_000314.4	139	Tta/Gta	5/9	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.59	2		745	781	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230680	46230680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1325578765	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	29	474	0	ENST00000334344.6:c.929G>A	p.Arg310His	p.R310H	ENST00000334344	NM_152641.2	310	cGt/cAt	8/21	1	2	FACETS	0.183	0.146	0.225	0.183	0.146	0.225	SUBCLONAL	1	TRUE	1	0.59	2		474	538	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80343451	80343451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	128	405	2	ENST00000286548.4:c.868G>A	p.Asp290Asn	p.D290N	ENST00000286548	NM_002072.3	290	Gac/Aac	6/7	1	2	FACETS	0.964	0.88	1	0.964	0.88	1	CLONAL	1	TRUE	1	0.59	2		407	450	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504512	103504512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs569799893	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	129	400	0	ENST00000355739.4:c.133C>T	p.Arg45Cys	p.R45C	ENST00000355739	NM_000123.3	45	Cgc/Tgc	2/15	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.59	2		400	432	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248592	8248592	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	204	936	1	ENST00000335790.3:c.295G>A	p.Glu99Lys	p.E99K	ENST00000335790	NM_002315.2	99	Gag/Aag	3/4	1	2	FACETS	0.864	0.803	0.927	0.864	0.803	0.927	CLONAL	1	TRUE	1	0.59	2		937	800	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571498	95571498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	53	514	0	ENST00000393063.1:c.3179G>A	p.Arg1060His	p.R1060H	ENST00000393063	NM_030621.3	1060	cGc/cAc	21/28	1	2	FACETS	0.296	0.252	0.344	0.296	0.252	0.344	SUBCLONAL	1	TRUE	1	0.59	2		514	607	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992217	11992217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	147	466	0	ENST00000396373.4:c.307C>T	p.Arg103Cys	p.R103C	ENST00000396373	NM_001987.4	103	Cgc/Tgc	3/8	1	2	FACETS	0.909	0.835	0.987	0.909	0.835	0.987	CLONAL	1	TRUE	1	0.59	2		466	548	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255400	16255400	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	125	656	0	ENST00000375759.3:c.2665A>C	p.Lys889Gln	p.K889Q	ENST00000375759	NM_015001.2	889	Aag/Cag	11/15	1	2	FACETS	0.569	0.515	0.625	0.569	0.515	0.625	SUBCLONAL	1	TRUE	1	0.59	2		656	745	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332883	65332883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764523308	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	80	261	0	ENST00000342505.4:c.656G>A	p.Arg219Gln	p.R219Q	ENST00000342505	NM_002227.2	219	cGa/cAa	7/25	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.59	2		261	267	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058631	72058631	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	139	490	0	ENST00000357731.5:c.809G>T	p.Gly270Val	p.G270V	ENST00000357731	NM_173808.2	270	gGa/gTa	6/7	1	2	FACETS	0.911	0.835	0.991	0.911	0.835	0.991	CLONAL	1	TRUE	1	0.59	2		490	517	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332889	70332889	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	245	781	0	ENST00000373644.4:c.794A>G	p.Asn265Ser	p.N265S	ENST00000373644	NM_030625.2	265	aAc/aGc	2/12	1	2	FACETS	0.981	0.919	1	0.981	0.919	1	CLONAL	1	TRUE	1	0.59	2		781	847	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653812	89653812	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	144	512	0	ENST00000371953.3:c.110T>G	p.Phe37Cys	p.F37C	ENST00000371953	NM_000314.4	37	tTt/tGt	2/9	1	2	FACETS	0.919	0.843	0.998	0.919	0.843	0.998	CLONAL	1	TRUE	1	0.59	2		512	531	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94169050	94169050	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	92	347	0	ENST00000323929.3:c.1942G>T	p.Glu648Ter	p.E648*	ENST00000323929	NM_005591.3	648	Gaa/Taa	18/20	1	2	FACETS	0.829	0.743	0.92	0.829	0.743	0.92	CLONAL	1	TRUE	1	0.59	2		347	376	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28980032	28980032	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	123	361	0	ENST00000282397.4:c.1437-1G>A		p.X479_splice	ENST00000282397	NM_002019.4	479			1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.59	2		361	397	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028859	42028859	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	184	670	0	ENST00000219905.7:c.4397A>C	p.Lys1466Thr	p.K1466T	ENST00000219905	NM_001164273.1	1466	aAa/aCa	13/24	1	2	FACETS	0.957	0.887	1	0.957	0.887	1	CLONAL	1	TRUE	1	0.59	2		670	652	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858430	9858430	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	64	633	0	ENST00000330684.3:c.2971T>C	p.Ser991Pro	p.S991P	ENST00000330684	NM_001134407.1	991	Tcc/Ccc	13/13	1	2	FACETS	0.36	0.312	0.413	0.36	0.312	0.413	SUBCLONAL	1	TRUE	1	0.59	2		633	602	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50811830	50811830	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	187	517	0	ENST00000398568.2:c.1107A>C	p.Lys369Asn	p.K369N	ENST00000398568	NM_001042412.1	369	aaA/aaC	7/18	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.59	2		517	628	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017721	31017721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	161	646	1	ENST00000375687.4:c.583G>A	p.Ala195Thr	p.A195T	ENST00000375687	NM_015338.5	195	Gcc/Acc	8/13	1	2	FACETS	0.943	0.869	1	0.943	0.869	1	CLONAL	1	TRUE	1	0.59	2		647	579	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024251	31024251	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	167	688	1	ENST00000375687.4:c.3736G>A	p.Val1246Ile	p.V1246I	ENST00000375687	NM_015338.5	1246	Gtc/Atc	13/13	1	2	FACETS	0.9	0.83	0.972	0.9	0.83	0.972	CLONAL	1	TRUE	1	0.59	2		689	629	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721205	39721205	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	52	564	0	ENST00000361337.2:c.708G>T	p.Glu236Asp	p.E236D	ENST00000361337	NM_003286.2	236	gaG/gaT	9/21	1	2	FACETS	0.275	0.234	0.321	0.275	0.234	0.321	SUBCLONAL	1	TRUE	1	0.59	2		564	640	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114163	73114163	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780289621	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	183	551	0	ENST00000356692.5:c.799G>A	p.Glu267Lys	p.E267K	ENST00000356692		267	Gaa/Aaa	8/9	1	2	FACETS	0.986	0.915	1	0.986	0.915	1	CLONAL	1	TRUE	1	0.59	2		551	629	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952075	178952075	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	122	441	0	ENST00000263967.3:c.3130A>T	p.Asn1044Tyr	p.N1044Y	ENST00000263967	NM_006218.2	1044	Aat/Tat	21/21	1	2	FACETS	0.927	0.844	1	0.927	0.844	1	CLONAL	1	TRUE	1	0.59	2		441	446	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748186	41748186	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	187	713	0	ENST00000226382.2:c.583A>G	p.Thr195Ala	p.T195A	ENST00000226382	NM_003924.3	195	Act/Gct	3/3	1	2	FACETS	0.927	0.859	0.996	0.927	0.859	0.996	CLONAL	1	TRUE	1	0.59	2		713	684	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561932	55561932	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	91	297	0	ENST00000288135.5:c.322T>C	p.Tyr108His	p.Y108H	ENST00000288135	NM_000222.2	108	Tat/Cat	2/21	1	2	FACETS	0.986	0.885	1	0.986	0.885	1	CLONAL	1	TRUE	1	0.59	2		297	313	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38949931	38949931	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	85	408	0	ENST00000357387.3:c.4019G>T	p.Arg1340Ile	p.R1340I	ENST00000357387	NM_152756.3	1340	aGa/aTa	31/38	1	2	FACETS	0.604	0.536	0.677	0.604	0.536	0.677	SUBCLONAL	1	TRUE	1	0.59	2		408	477	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670128	86670128	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	131	427	0	ENST00000274376.6:c.1925T>C	p.Phe642Ser	p.F642S	ENST00000274376	NM_002890.2	642	tTt/tCt	14/25	1	2	FACETS	0.925	0.845	1	0.925	0.845	1	CLONAL	1	TRUE	1	0.59	2		427	480	SUCCESS
APC	324	MSKCC	GRCh37	5	112175754	112175754	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	102	380	0	ENST00000257430.4:c.4463T>G	p.Leu1488Ter	p.L1488*	ENST00000257430	NM_000038.5	1488	tTa/tGa	16/16	1	2	FACETS	0.845	0.761	0.933	0.845	0.761	0.933	CLONAL	1	TRUE	1	0.59	2		380	409	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662436	117662436	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	44	608	0	ENST00000368508.3:c.4941G>T	p.Glu1647Asp	p.E1647D	ENST00000368508	NM_002944.2	1647	gaG/gaT	30/43	1	2	FACETS	0.238	0.199	0.282	0.238	0.199	0.282	SUBCLONAL	1	TRUE	1	0.59	2		608	626	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976776	2976776	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	215	1011	0	ENST00000396946.4:c.1236G>T	p.Glu412Asp	p.E412D	ENST00000396946	NM_032415.4	412	gaG/gaT	9/25	0.3	1	FACETS	0.551	0.513	0.591	0.551	0.513	0.591	INDETERMINATE	1	TRUE	0	0.59	1		1011	932	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486335	8486335	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141603921	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	19	354	0	ENST00000356435.5:c.2482C>T	p.Arg828Trp	p.R828W	ENST00000356435		828	Cgg/Tgg	17/35	1	2	FACETS	0.187	0.142	0.241	0.187	0.142	0.241	SUBCLONAL	1	TRUE	1	0.59	2		354	344	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15838431	15838431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	180	497	1	ENST00000307771.7:c.929C>T	p.Ala310Val	p.A310V	ENST00000307771	NM_005089.3	310	gCg/gTg	10/11	1	2	FACETS	0.942	0.872	1	0.942	0.872	1	CLONAL	1	TRUE	1	0.59	2		498	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0043081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	199	676	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.288620940264264	3	FACETS	0.887	0.831	0.942	1	0.986	1	CLONAL	4	FALSE	0	0.288620940264264	3		676	445	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934285	49934285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	70	786	0	ENST00000296474.3:c.2222G>A	p.Gly741Glu	p.G741E	ENST00000296474	NM_002447.2	741	gGg/gAg	8/20	0.288620940264264	5	FACETS	1	0.911	1	0.352	0.307	0.401	CLONAL	1	FALSE	2	0.288620940264264	5		786	658	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872243	45872243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773453200	NA	P-0043081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	60	853	0	ENST00000391945.4:c.191C>T	p.Pro64Leu	p.P64L	ENST00000391945	NM_000400.3	64	cCg/cTg	4/23	0.288620940264264	4	FACETS	1	0.887	1	0.344	0.296	0.396	CLONAL	1	FALSE	1	0.288620940264264	4		853	519	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868267	37868267	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761376658	NA	P-0043081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	256	681	0	ENST00000269571.5:c.988C>T	p.Arg330Trp	p.R330W	ENST00000269571		330	Cgg/Tgg	8/27	0.288620940264264	3	FACETS	0.924	0.874	0.975	1	0.991	1	CLONAL	4	FALSE	0	0.288620940264264	3		681	549	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243887	41243887	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs80357310	NA	P-0043081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	46	630	0	ENST00000357654.3:c.3661G>C	p.Glu1221Gln	p.E1221Q	ENST00000357654	NM_007294.3	1221	Gaa/Caa	10/23	0.288620940264264	3	FACETS	0.926	0.781	1	0.309	0.26	0.362	CLONAL	1	FALSE	0	0.288620940264264	3		630	394	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36846928	36847038	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TGTGTATGGTGGGTGGAGAGAGAAACAGGAACCAAACGTCAAATCCAGTTCAGAAAAGGCCCTGGGTCCCAGCCAGCCTGGTTGCCAATGGCATTTGCCTCTTCCGTGAGT	TGTGTATGGTGGGTGGAGAGAGAAACAGGAACCAAACGTCAAATCCAGTTCAGAAAAGGCCCTGGGTCCCAGCCAGCCTGGTTGCCAATGGCATTTGCCTCTTCCGTGAGT	-	novel	NA	P-0043081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	34	537	0	ENST00000358127.4:c.1013-112_1013-2del		p.X338_splice	ENST00000358127	NM_001280556.1	338			0.220781762670227	3	FACETS	0.63	0.515	0.76	0.21	0.171	0.254	SUBCLONAL	1	FALSE	0	0.288620940264264	3		537	428	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	181	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.58433457183811	2		126	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0043121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	266	593	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.58433457183811	1	FACETS	0.982	0.928	1	0.982	0.928	1	CLONAL	1	TRUE	0	0.58433457183811	1		593	656	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325164	123325164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	93	511	0	ENST00000358487.5:c.164G>A	p.Gly55Glu	p.G55E	ENST00000358487	NM_000141.4	55	gGg/gAg	3/18	1	2	FACETS	0.391	0.347	0.438	0.391	0.347	0.438	SUBCLONAL	1	TRUE	1	0.58433457183811	2		511	814	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918622	44918622	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	200	202	0	ENST00000377967.4:c.1105C>T	p.Gln369Ter	p.Q369*	ENST00000377967	NM_021140.2	369	Cag/Tag	12/29	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.58433457183811	1		202	362	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376071	8376071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	29	225	0	ENST00000356435.5:c.4526G>A	p.Arg1509Lys	p.R1509K	ENST00000356435		1509	aGa/aAa	28/35	1	2	FACETS	0.251	0.201	0.308	0.251	0.201	0.308	SUBCLONAL	1	TRUE	1	0.58433457183811	2		225	395	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628266	187628266	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	320	530	0	ENST00000441802.2:c.2716C>T	p.Gln906Ter	p.Q906*	ENST00000441802	NM_005245.3	906	Cag/Tag	2/27	0.58433457183811	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.58433457183811	1		530	684	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223356	2223356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1376643409	NA	P-0043121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	301	576	0	ENST00000326181.6:c.968C>T	p.Ser323Leu	p.S323L	ENST00000326181	NM_032271.2	323	tCg/tTg	10/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.58433457183811	2		576	962	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799626	3799626	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0043121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	211	353	0	ENST00000262367.5:c.3836+2T>G		p.X1279_splice	ENST00000262367	NM_004380.2	1279			1	2	FACETS	0.929	0.866	0.995	0.929	0.866	0.995	CLONAL	1	TRUE	1	0.58433457183811	2		353	777	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981763	201981779	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCAGACCAGGGCAGCC	CCCAGACCAGGGCAGCC	-	novel	NA	P-0043121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	319	588	1	ENST00000359651.3:c.479-3_492del		p.X160_splice	ENST00000359651		160		4/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.58433457183811	2		589	1041	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992795	72992795	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0043121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	255	541	0	ENST00000268489.5:c.1250C>G	p.Ser417Ter	p.S417*	ENST00000268489	NM_006885.3	417	tCa/tGa	2/10	1	2	FACETS	0.944	0.885	1	0.944	0.885	1	CLONAL	1	TRUE	1	0.58433457183811	2		541	925	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551003	41551003	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	81	292	0	ENST00000263253.7:c.3147C>G	p.Phe1049Leu	p.F1049L	ENST00000263253	NM_001429.3	1049	ttC/ttG	17/31	0.33045079319631	2	FACETS	0.506	0.446	0.57	0.253	0.223	0.285	INDETERMINATE	1	TRUE	0	0.58433457183811	2		292	548	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947413	38947413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	104	223	0	ENST00000357387.3:c.4267G>A	p.Asp1423Asn	p.D1423N	ENST00000357387	NM_152756.3	1423	Gat/Aat	32/38	1	2	FACETS	0.937	0.846	1	0.937	0.846	1	CLONAL	1	TRUE	1	0.58433457183811	2		223	380	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604835	48604835	+	stop_lost	Nonstop_Mutation	SNP	T	T	A	novel	NA	P-0043128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	34	286	0	ENST00000342988.3:c.1657T>A	p.Ter553ArgextTer40	p.*553Rext*40	ENST00000342988	NM_005359.5	553	Tga/Aga	12/12	0.197035098441949	1	FACETS	0.594	0.486	0.716	0.594	0.486	0.716	SUBCLONAL	1	TRUE	0	0.255849262422836	1		286	390	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332844	70332844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	82	668	0	ENST00000373644.4:c.749C>T	p.Ala250Val	p.A250V	ENST00000373644	NM_030625.2	250	gCt/gTt	2/12	1	2	FACETS	0.702	0.618	0.793	0.702	0.618	0.793	SUBCLONAL	1	TRUE	1	0.255849262422836	2		668	913	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39763599	39763599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	37	340	0	ENST00000288319.7:c.853G>A	p.Asp285Asn	p.D285N	ENST00000288319	NM_182918.3	285	Gac/Aac	8/10	1	2	FACETS	0.563	0.463	0.674	0.563	0.463	0.674	SUBCLONAL	1	TRUE	1	0.255849262422836	2		340	514	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608577	189608577	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0043128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	72	500	0	ENST00000264731.3:c.1653-1G>T		p.X551_splice	ENST00000264731	NM_003722.4	551			0.174866454434941	2	FACETS	0.915	0.8	1	0.458	0.4	0.52	CLONAL	1	TRUE	0	0.255849262422836	2		500	615	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948148	55948148	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	65	454	0	ENST00000263923.4:c.3823A>G	p.Arg1275Gly	p.R1275G	ENST00000263923	NM_002253.2	1275	Aga/Gga	29/30	1	2	FACETS	0.851	0.738	0.974	0.851	0.738	0.974	CLONAL	1	TRUE	1	0.255849262422836	2		454	597	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101985017	101985017	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	83	531	0	ENST00000282441.5:c.464C>A	p.Pro155His	p.P155H	ENST00000282441	NM_001130145.2	155	cCc/cAc	2/9	1	2	FACETS	0.384	0.339	0.433	0.384	0.339	0.433	SUBCLONAL	1	TRUE	1	0.666277519135616	2		531	648	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830844	3830845	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0043135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	228	497	0	ENST00000262367.5:c.1710_1711dup	p.Ile571ThrfsTer19	p.I571Tfs*19	ENST00000262367	NM_004380.2	571	att/aCAtt	8/31	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.666277519135616	2		497	636	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166740	32166740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	197	807	0	ENST00000375023.3:c.4498C>T	p.Arg1500Cys	p.R1500C	ENST00000375023	NM_004557.3	1500	Cgc/Tgc	24/30	1	2	FACETS	0.758	0.704	0.814	0.758	0.704	0.814	SUBCLONAL	1	TRUE	1	0.666277519135616	2		807	780	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0043137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	153	458	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		458	440	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0043146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	77	522	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.846083286943337	2		522	166	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	173	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.846083286943337	2		126	379	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577266	64577273	+	frameshift_variant	Frame_Shift_Del	DEL	AGAGGGAC	AGAGGGAC	-	novel	NA	P-0043146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	205	603	1	ENST00000312049.6:c.309_316del	p.Leu105SerfsTer9	p.L105Sfs*9	ENST00000312049	NM_130799.2	103	ctGTCCCTCTat/ctat	2/10	0.846083286943337	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.846083286943337	1		604	279	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831197	3831209	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTCTTACTTTGT	GGTCTTACTTTGT	-	novel	NA	P-0043146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	16	271	0	ENST00000262367.5:c.1672_1676+8del		p.X558_splice	ENST00000262367	NM_004380.2	558		7/31	1	2	FACETS	0.222	0.165	0.29	0.222	0.165	0.29	SUBCLONAL	1	TRUE	1	0.846083286943337	2		271	170	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022391	26022391	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	36	342	0	ENST00000435504.4:c.266A>G	p.Asp89Gly	p.D89G	ENST00000435504		89	gAt/gGt	5/13	1	2	FACETS	0.375	0.31	0.446	0.375	0.31	0.446	SUBCLONAL	1	TRUE	1	0.846083286943337	2		342	227	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272121	142272121	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	48	350	0	ENST00000350721.4:c.2753A>T	p.Lys918Ile	p.K918I	ENST00000350721	NM_001184.3	918	aAa/aTa	13/47	1	2	FACETS	0.623	0.535	0.718	0.623	0.535	0.718	SUBCLONAL	1	TRUE	1	0.846083286943337	2		350	182	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31511280	31511280	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	26	509	0	ENST00000344624.3:c.1294G>C	p.Asp432His	p.D432H	ENST00000344624		432	Gat/Cat	6/33	1	2	FACETS	0.205	0.162	0.254	0.205	0.162	0.254	SUBCLONAL	1	TRUE	1	0.846083286943337	2		509	300	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0043162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	28	350	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.0403696334735444	3	FACETS	0.41	0.327	0.506	0.205	0.163	0.253	INDETERMINATE	1	FALSE	1	0.266963758450464	3		350	580	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338701	70338701	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs769202858	NA	P-0043162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	35	636	0	ENST00000374080.3:c.97G>A	p.Glu33Lys	p.E33K	ENST00000374080		33	Gag/Aag	1/45	1	2	FACETS	0.471	0.385	0.567	0.471	0.385	0.567	SUBCLONAL	1	FALSE	1	0.266963758450464	2		636	557	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	37	787	0	ENST00000267101.3:c.273G>T	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atT	3/28	0.0403696334735444	3	FACETS	0.472	0.388	0.566	0.236	0.194	0.283	INDETERMINATE	1	FALSE	1	0.266963758450464	3		787	666	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482864	67482864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555414503	NA	P-0043162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	54	523	0	ENST00000327367.4:c.1268G>A	p.Ser423Asn	p.S423N	ENST00000327367	NM_005902.3	423	aGt/aAt	9/9	1	2	FACETS	0.829	0.709	0.96	0.829	0.709	0.96	CLONAL	1	FALSE	1	0.266963758450464	2		523	488	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435170	56435171	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	71	890	0	ENST00000407977.2:c.1966dup	p.Arg656LysfsTer91	p.R656Kfs*91	ENST00000407977		656	agg/aAgg	9/10	0.266963758450464	1	FACETS	0.787	0.687	0.894	0.787	0.687	0.894	SUBCLONAL	1	FALSE	0	0.266963758450464	1		890	586	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183797	10183797	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	125	705	0	ENST00000256474.2:c.266T>G	p.Leu89Arg	p.L89R	ENST00000256474	NM_000551.3	89	cTc/cGc	1/3	0.441539635429301	1	FACETS	0.795	0.722	0.871	0.795	0.722	0.871	SUBCLONAL	1	TRUE	0	0.441539635429301	1		705	555	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609707	28609718	+	inframe_deletion	In_Frame_Del	DEL	TTATGGCTTCAC	TTATGGCTTCAC	-	novel	NA	P-0043202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	146	687	0	ENST00000241453.7:c.1511_1522del	p.Ser504_Ile507del	p.S504_I507del	ENST00000241453	NM_004119.2	504	aGTGAAGCCATAAaa/aaa	12/24	1	2	FACETS	0.933	0.853	1	0.933	0.853	1	CLONAL	1	TRUE	1	0.441539635429301	2		687	709	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125859	47125859	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	49	256	1	ENST00000409792.3:c.5411T>G	p.Leu1804Trp	p.L1804W	ENST00000409792	NM_014159.6	1804	tTg/tGg	12/21	0.441539635429301	1	FACETS	0.824	0.706	0.949	0.824	0.706	0.949	CLONAL	1	TRUE	0	0.441539635429301	1		257	210	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651508	52651508	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	115	566	0	ENST00000394830.3:c.1588del	p.Val530PhefsTer39	p.V530Ffs*39	ENST00000394830	NM_018313.4	530	Gtt/tt	15/30	0.441539635429301	1	FACETS	0.944	0.857	1	0.944	0.857	1	CLONAL	1	TRUE	0	0.441539635429301	1		566	430	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89176359	89176359	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	47	320	0	ENST00000336596.2:c.89T>A	p.Val30Asp	p.V30D	ENST00000336596	NM_005233.5	30	gTc/gAc	2/17	1	2	FACETS	0.752	0.639	0.876	0.752	0.639	0.876	SUBCLONAL	1	TRUE	1	0.441539635429301	2		320	283	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924562	131924562	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1254198489	NA	P-0043202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	93	445	0	ENST00000265335.6:c.1235A>G	p.Asn412Ser	p.N412S	ENST00000265335		412	aAc/aGc	8/25	1	2	FACETS	0.798	0.712	0.889	0.798	0.712	0.889	SUBCLONAL	1	TRUE	1	0.441539635429301	2		445	528	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0043225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	171	441	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.974	0.904	1	0.974	0.904	1	CLONAL	1	TRUE	1	0.755421118205671	2		441	465	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12043921	12043921	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	1209	434	0	ENST00000396373.4:c.1300C>G	p.Leu434Val	p.L434V	ENST00000396373	NM_001987.4	434	Ctg/Gtg	8/8	0.755421118205671	8	FACETS	1	0.996	1	0.902	0.886	0.919	CLONAL	6	TRUE	1	0.755421118205671	8		434	1655	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72893575	72893575	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0043225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	200	439	0	ENST00000325599.8:c.144-1G>A		p.X48_splice	ENST00000325599	NM_018130.2	48			1	2	FACETS	0.881	0.821	0.942	0.881	0.821	0.942	CLONAL	1	TRUE	1	0.755421118205671	2		439	601	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803120	1803120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1162571458	NA	P-0043225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	271	663	0	ENST00000260795.2:c.472C>T	p.Arg158Trp	p.R158W	ENST00000260795		158	Cgg/Tgg	4/17	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.755421118205671	2		663	714	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0043274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	86	469	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.261554422010282	2		469	524	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928078	178928080	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs587776933	NA	P-0043274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	39	612	0	ENST00000263967.3:c.1359_1361del	p.Glu453del	p.E453del	ENST00000263967	NM_006218.2	452	ttAGAa/tta	8/21	1	2	FACETS	0.448	0.37	0.535	0.448	0.37	0.535	SUBCLONAL	1	TRUE	1	0.261554422010282	2		612	666	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0043326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	129	668	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.91863661850713	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.926919382493226	2		668	134	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346550	81346550	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs148293411	NA	P-0043326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	84	434	0	ENST00000222390.5:c.1403G>A	p.Arg468His	p.R468H	ENST00000222390	NM_000601.4	468	cGt/cAt	11/18	0.829934690216159	3	FACETS	0.867	0.791	0.941	0.867	0.791	0.941	CLONAL	2	TRUE	1	0.926919382493226	3		434	153	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992708	68992708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	97	778	0	ENST00000288368.4:c.1673C>T	p.Pro558Leu	p.P558L	ENST00000288368	NM_024870.2	558	cCc/cTc	16/40	0.568711841921878	6	FACETS	0.784	0.704	0.867	0.523	0.469	0.578	SUBCLONAL	2	TRUE	3	0.926919382493226	6		778	381	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992747	68992747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	88	830	0	ENST00000288368.4:c.1712G>A	p.Gly571Glu	p.G571E	ENST00000288368	NM_024870.2	571	gGa/gAa	16/40	0.568711841921878	6	FACETS	0.753	0.672	0.837	0.502	0.448	0.558	SUBCLONAL	2	TRUE	3	0.926919382493226	6		830	360	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857376	9857376	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	71	715	0	ENST00000330684.3:c.4025C>G	p.Ser1342Cys	p.S1342C	ENST00000330684	NM_001134407.1	1342	tCc/tGc	13/13	0.79211151028575	4	FACETS	0.886	0.779	1	0.443	0.389	0.5	CLONAL	1	TRUE	2	0.926919382493226	4		715	333	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858072	9858072	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1244209721	NA	P-0043326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	88	753	0	ENST00000330684.3:c.3329C>G	p.Ser1110Ter	p.S1110*	ENST00000330684	NM_001134407.1	1110	tCa/tGa	13/13	0.79211151028575	4	FACETS	0.992	0.885	1	0.496	0.442	0.552	CLONAL	1	TRUE	2	0.926919382493226	4		753	369	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543640	29543640	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs995433670	NA	P-0043326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	19	789	1	ENST00000389048.3:c.1523A>T	p.Asp508Val	p.D508V	ENST00000389048	NM_004304.4	508	gAt/gTt	7/29	0.926919382493226	4	FACETS	0.295	0.224	0.378	0.098	0.074	0.126	SUBCLONAL	1	TRUE	1	0.926919382493226	4		790	268	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540260	187540260	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	69	555	0	ENST00000441802.2:c.7480C>T	p.Gln2494Ter	p.Q2494*	ENST00000441802	NM_005245.3	2494	Cag/Tag	10/27	0.922795529820299	4	FACETS	1	0.929	1	0.539	0.475	0.607	CLONAL	1	TRUE	2	0.926919382493226	4		555	266	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	168	461	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.84	0.776	0.907	0.84	0.776	0.907	CLONAL	1	FALSE	1	0.645927089397834	2		461	619	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0043336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	335	683	3	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	NA	2	FACETS	0.916	0.866	0.966			1	INDETERMINATE	1	FALSE	NA	0.645927089397834	2		686	1133	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577035	7577036	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0043336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	369	687	0	ENST00000269305.4:c.902dup	p.Gly302ArgfsTer4	p.G302Rfs*4	ENST00000269305	NM_001126112.2	301	cca/ccCa	8/11	0.6043638813566	1	FACETS	0.861	0.821	0.903	0.861	0.821	0.903	CLONAL	1	FALSE	0	0.645927089397834	1		687	898	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0043336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	255	475	2	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.894	0.839	0.951	0.894	0.839	0.951	CLONAL	1	FALSE	1	0.645927089397834	2		477	883	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0043336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	112	494	4	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.717	0.648	0.788	0.717	0.648	0.788	SUBCLONAL	1	FALSE	1	0.645927089397834	2		498	484	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438316	110438317	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	rs532810290	NA	P-0043336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	85	162	0	ENST00000375856.3:c.82_84dup	p.Asn28dup	p.N28dup	ENST00000375856	NM_003749.2	28	-/AAC	1/2	0.645927089397834	1	FACETS	0.6	0.536	0.667	0.6	0.536	0.667	SUBCLONAL	1	FALSE	0	0.645927089397834	1		162	297	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693003	89693003	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs786204900	NA	P-0043336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	149	437	0	ENST00000371953.3:c.491del	p.Lys164ArgfsTer3	p.K164Rfs*3	ENST00000371953	NM_000314.4	163	Aaa/aa	5/9	0.645927089397834	1	FACETS	0.783	0.723	0.844	0.783	0.723	0.844	SUBCLONAL	1	FALSE	0	0.645927089397834	1		437	399	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351359	89351359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756332789	NA	P-0043336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	376	769	0	ENST00000301030.4:c.1591G>A	p.Ala531Thr	p.A531T	ENST00000301030	NM_001256183.1	531	Gcc/Acc	9/13	1	2	FACETS	0.931	0.883	0.979	0.931	0.883	0.979	CLONAL	1	FALSE	1	0.645927089397834	2		769	1251	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0043336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	59	498	2	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	0.177937418284224	2	FACETS	0.233	0.199	0.269	0.116	0.099	0.135	INDETERMINATE	1	FALSE	0	0.645927089397834	2		500	785	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549835	187549835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	161	449	1	ENST00000441802.2:c.4406C>T	p.Thr1469Ile	p.T1469I	ENST00000441802	NM_005245.3	1469	aCa/aTa	8/27	0.193896999157711	1	FACETS	0.605	0.558	0.653	0.605	0.558	0.653	INDETERMINATE	1	FALSE	0	0.645927089397834	1		450	558	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783211	9783211	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	272	541	0	ENST00000377346.4:c.2455G>A	p.Gly819Arg	p.G819R	ENST00000377346	NM_005026.3	819	Ggg/Agg	20/24	NA	2	FACETS	0.813	0.763	0.864			1	INDETERMINATE	1	FALSE	NA	0.645927089397834	2		541	1036	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs753143066	NA	P-0043336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	261	681	1	ENST00000295797.4:c.826dup	p.Thr276AsnfsTer16	p.T276Nfs*16	ENST00000295797	NM_002740.5	273	tta/ttAa	9/18	1	2	FACETS	0.745	0.698	0.793	0.745	0.698	0.793	SUBCLONAL	1	FALSE	1	0.645927089397834	2		682	1085	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164508	47164508	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs201756643	NA	P-0043336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	171	410	1	ENST00000409792.3:c.1618C>T	p.Arg540Ter	p.R540*	ENST00000409792	NM_014159.6	540	Cga/Tga	3/21	0.247240359511868	1	FACETS	0.771	0.716	0.827	0.771	0.716	0.827	INDETERMINATE	1	FALSE	0	0.645927089397834	1		411	465	SUCCESS
BTK	695	MSKCC	GRCh37	X	100629549	100629549	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	196	308	0	ENST00000308731.7:c.215del	p.Asn72IlefsTer49	p.N72Ifs*49	ENST00000308731	NM_000061.2	72	aAt/at	3/19	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	0	0.645927089397834	1		308	330	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186697	11186697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780210598	NA	P-0043336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	227	490	0	ENST00000361445.4:c.6508C>T	p.Arg2170Trp	p.R2170W	ENST00000361445	NM_004958.3	2170	Cgg/Tgg	46/58	NA	2	FACETS	0.916	0.857	0.978			1	INDETERMINATE	1	FALSE	NA	0.645927089397834	2		490	767	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47643462	47643462	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750502	NA	P-0043336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	157	539	1	ENST00000233146.2:c.970C>T	p.Gln324Ter	p.Q324*	ENST00000233146	NM_000251.2	324	Cag/Tag	6/16	0.645927089397834	1	FACETS	0.745	0.689	0.802	0.745	0.689	0.802	SUBCLONAL	1	FALSE	0	0.645927089397834	1		540	442	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987388	2987388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1192456063	NA	P-0043336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	229	552	1	ENST00000396946.4:c.41C>T	p.Thr14Met	p.T14M	ENST00000396946	NM_032415.4	14	aCg/aTg	3/25	NA	2	FACETS	0.76	0.709	0.813			1	INDETERMINATE	1	FALSE	NA	0.645927089397834	2		553	933	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186625	108186625	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876659454	NA	P-0043336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	31	411	0	ENST00000278616.4:c.6082C>T	p.Gln2028Ter	p.Q2028*	ENST00000278616	NM_000051.3	2028	Caa/Taa	41/63	1	2	FACETS	0.177	0.143	0.216	0.177	0.143	0.216	SUBCLONAL	1	FALSE	1	0.645927089397834	2		411	542	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245405	133245405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565966539	NA	P-0043336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	297	671	1	ENST00000320574.5:c.1915C>T	p.Arg639Cys	p.R639C	ENST00000320574	NM_006231.2	639	Cgc/Tgc	17/49	NA	2	FACETS	0.891	0.84	0.944			1	INDETERMINATE	1	FALSE	NA	0.645927089397834	2		672	1032	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753384	42753385	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0043336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	377	694	0	ENST00000222329.4:c.879dup	p.Pro294AlafsTer15	p.P294Afs*15	ENST00000222329	NM_006494.2	293	-/G	4/4	1	2	FACETS	0.899	0.853	0.945	0.899	0.853	0.945	CLONAL	1	FALSE	1	0.645927089397834	2		694	1299	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798163	42798163	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	295	643	0	ENST00000575354.2:c.4117del	p.Ser1373ProfsTer42	p.S1373Pfs*42	ENST00000575354	NM_015125.3	1373	Tcc/cc	17/20	1	2	FACETS	0.796	0.749	0.844	0.796	0.749	0.844	SUBCLONAL	1	FALSE	1	0.645927089397834	2		643	1148	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530072	212530072	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	294	311	0	ENST00000342788.4:c.1847C>A	p.Pro616Gln	p.P616Q	ENST00000342788	NM_005235.2	616	cCa/cAa	15/28	NA	2	FACETS	0.785	0.746	0.823			1	INDETERMINATE	2	FALSE	NA	0.645927089397834	2		311	580	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051644	30051644	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	184	310	0	ENST00000338641.4:c.578del	p.Ala193GlufsTer16	p.A193Efs*16	ENST00000338641	NM_000268.3	193	gCa/ga	6/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.645927089397834	2		310	531	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643863	52643863	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1187519621	NA	P-0043336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	121	480	0	ENST00000394830.3:c.2033G>A	p.Arg678His	p.R678H	ENST00000394830	NM_018313.4	678	cGc/cAc	17/30	0.247240359511868	1	FACETS	0.383	0.347	0.422	0.383	0.347	0.422	INDETERMINATE	1	FALSE	0	0.645927089397834	1		480	662	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884563	151884563	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0043336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	189	381	0	ENST00000262189.6:c.4794-2A>G		p.X1598_splice	ENST00000262189	NM_170606.2	1598			0.210164693637166	3	FACETS	1	0.99	1	0.714	0.665	0.765	INDETERMINATE	1	FALSE	1	0.645927089397834	3		381	542	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239040	98239040	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1060502277	NA	P-0043336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	157	352	1	ENST00000331920.6:c.1602+1G>A		p.X534_splice	ENST00000331920	NM_000264.3	534			1	2	FACETS	0.892	0.822	0.964	0.892	0.822	0.964	CLONAL	1	FALSE	1	0.645927089397834	2		353	545	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0043339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	740	522	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.335009462088955	6	FACETS	0.972	0.951	0.993	0.81	0.792	0.828	INDETERMINATE	5	TRUE	0	0.847671491619328	6		522	968	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0043339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	631	523	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.837960567634882	2	FACETS	0.981	0.961	1	0.981	0.961	1	CLONAL	2	TRUE	0	0.847671491619328	2		523	759	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001420	29001420	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	225	383	0	ENST00000282397.4:c.1312T>C	p.Phe438Leu	p.F438L	ENST00000282397	NM_002019.4	438	Ttt/Ctt	10/30	0.661201119202988	1	FACETS	0.953	0.898	1	0.953	0.898	1	CLONAL	1	TRUE	0	0.661201119202988	1		383	478	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0043348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	29	248	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.300941670131986	4	FACETS	0.357	0.285	0.439	0.119	0.095	0.147	SUBCLONAL	1	TRUE	1	0.32	4		248	671	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	233	126	0				ENST00000310581	NM_198253.2	-/1132			0.300941670131986	6	FACETS	0.929	0.876	0.983	1	0.987	1	CLONAL	5	TRUE	2	0.32	6		126	514	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0043348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	16	464	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.300941670131986	4	FACETS	0.172	0.126	0.228	0.057	0.042	0.076	SUBCLONAL	1	TRUE	1	0.32	4		464	767	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0043348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	53	255	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.300941670131986	4	FACETS	0.919	0.784	1	0.306	0.261	0.355	CLONAL	1	TRUE	1	0.32	4		255	476	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526287	189526287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	291	794	0	ENST00000264731.3:c.551C>T	p.Ser184Leu	p.S184L	ENST00000264731	NM_003722.4	184	tCg/tTg	4/14	0.300941670131986	4	FACETS	0.907	0.859	0.954	1	0.991	1	CLONAL	4	TRUE	1	0.32	4		794	662	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039340	49039340	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0043348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	342	566	0	ENST00000267163.4:c.2326-1del		p.X776_splice	ENST00000267163	NM_000321.2	776			0.298157083534476	4	FACETS	1	0.99	1	0.863	0.821	0.906	CLONAL	3	TRUE	0	0.32	4		566	817	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991999	72991999	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	39	618	1	ENST00000268489.5:c.2046C>A	p.Tyr682Ter	p.Y682*	ENST00000268489	NM_006885.3	682	taC/taA	2/10	1	2	FACETS	0.429	0.355	0.512	0.429	0.355	0.512	SUBCLONAL	1	TRUE	1	0.32	2		619	568	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859911	151859911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	37	478	0	ENST00000262189.6:c.10751G>A	p.Gly3584Glu	p.G3584E	ENST00000262189	NM_170606.2	3584	gGa/gAa	43/59	0.186006156462238	4	FACETS	0.51	0.42	0.612	0.255	0.21	0.306	INDETERMINATE	1	TRUE	2	0.32	4		478	598	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860404	151860404	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	54	629	0	ENST00000262189.6:c.10258G>A	p.Asp3420Asn	p.D3420N	ENST00000262189	NM_170606.2	3420	Gat/Aat	43/59	0.186006156462238	4	FACETS	0.553	0.471	0.643	0.276	0.235	0.322	INDETERMINATE	1	TRUE	2	0.32	4		629	806	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0043362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	11	522	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		522	469	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0043369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	167	547	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.322417804962936	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.322417804962936	1		547	857	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0043369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	214	754	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.322417804962936	1	FACETS	0.92	0.854	0.989	0.92	0.854	0.989	CLONAL	1	TRUE	0	0.322417804962936	1		754	1210	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0043369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	137	591	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.836	0.759	0.916	0.836	0.759	0.916	CLONAL	1	TRUE	1	0.322417804962936	2		591	1017	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091809	29091809	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs202089930	NA	P-0043369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	119	503	0	ENST00000328354.6:c.1148C>A	p.Thr383Asn	p.T383N	ENST00000328354	NM_007194.3	383	aCc/aAc	11/15	0.322417804962936	1	FACETS	0.907	0.819	0.998	0.907	0.819	0.998	CLONAL	1	TRUE	0	0.322417804962936	1		503	683	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955527	48955544	+	inframe_deletion	In_Frame_Del	DEL	AACATTTAGAACGATGTG	AACATTTAGAACGATGTG	-	novel	NA	P-0043369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	51	358	0	ENST00000267163.4:c.1648_1665del	p.Leu550_His555del	p.L550_H555del	ENST00000267163	NM_000321.2	548	aAACATTTAGAACGATGTGaa/aaa	17/27	0.322417804962936	1	FACETS	0.79	0.674	0.915	0.79	0.674	0.915	CLONAL	1	TRUE	0	0.322417804962936	1		358	336	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624258	89624258	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	116	248	0	ENST00000371953.3:c.32del	p.Arg11LysfsTer13	p.R11Kfs*13	ENST00000371953	NM_000314.4	11	aGa/aa	1/9	0.154653274093898	3	FACETS	0.918	0.833	1	0.612	0.555	0.672	INDETERMINATE	2	TRUE	0	0.322417804962936	3		248	455	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717696	89717696	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	85	442	0	ENST00000371953.3:c.723del	p.Phe241LeufsTer15	p.F241Lfs*15	ENST00000371953	NM_000314.4	241	Ttt/tt	7/9	0.154653274093898	3	FACETS	0.918	0.812	1	0.306	0.27	0.344	INDETERMINATE	1	TRUE	0	0.322417804962936	3		442	667	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005170	150005170	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	149	422	0	ENST00000253339.5:c.1055del	p.Gly352AspfsTer6	p.G352Dfs*6	ENST00000253339		352	gGa/ga	3/7	0.201105221338182	3	FACETS	0.756	0.692	0.822	0.756	0.692	0.822	SUBCLONAL	2	TRUE	1	0.322417804962936	3		422	710	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0043371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	102	350	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.533789788949115	3	FACETS	0.783	0.709	0.86	0.783	0.709	0.86	SUBCLONAL	2	TRUE	1	0.533789788949115	3		350	309	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258744	115258744	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121434596	NA	P-0043371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	136	414	0	ENST00000369535.4:c.38G>T	p.Gly13Val	p.G13V	ENST00000369535	NM_002524.4	13	gGt/gTt	2/7	0.451510110520874	3	FACETS	1	0.981	1	0.632	0.578	0.688	CLONAL	1	TRUE	1	0.533789788949115	3		414	511	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692901	89692901	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs786204929	NA	P-0043371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	121	387	0	ENST00000371953.3:c.385G>T	p.Gly129Ter	p.G129*	ENST00000371953	NM_000314.4	129	Gga/Tga	5/9	0.503551977003643	2	FACETS	0.889	0.82	0.958	0.889	0.82	0.958	CLONAL	2	TRUE	0	0.533789788949115	2		387	255	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0043371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	274	498	0	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	0.503551977003643	2	FACETS	0.854	0.809	0.9	0.854	0.809	0.9	CLONAL	2	TRUE	0	0.533789788949115	2		498	601	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825518	50825519	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1219062549	NA	P-0043371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	69	318	0	ENST00000398568.2:c.2156dup	p.Asn719LysfsTer2	p.N719Kfs*2	ENST00000398568	NM_001042412.1	717	gaa/gAaa	14/18	0.53160614093874	4	FACETS	1	0.975	1	0.74	0.651	0.833	CLONAL	1	TRUE	2	0.533789788949115	4		318	268	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63531801	63531801	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	492	584	0	ENST00000307078.5:c.2180C>A	p.Ser727Ter	p.S727*	ENST00000307078	NM_004655.3	727	tCg/tAg	9/11	0.533789788949115	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.533789788949115	3		584	1116	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs80338963	NA	P-0043371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	17	363	0	ENST00000342988.3:c.1081C>A	p.Arg361Ser	p.R361S	ENST00000342988	NM_005359.5	361	Cgc/Agc	9/12	0.533789788949115	1	FACETS	0.175	0.13	0.228	0.175	0.13	0.228	SUBCLONAL	1	TRUE	0	0.533789788949115	1		363	267	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139754	55139754	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs201223501	NA	P-0043371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	177	533	0	ENST00000257290.5:c.1415T>G	p.Ile472Ser	p.I472S	ENST00000257290	NM_006206.4	472	aTc/aGc	10/23	0.331642193775516	3	FACETS	1	0.968	1	0.544	0.502	0.588	CLONAL	1	TRUE	1	0.533789788949115	3		533	772	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876448	35876448	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	318	555	0	ENST00000303115.3:c.1240del	p.Thr414ArgfsTer13	p.T414Rfs*13	ENST00000303115	NM_002185.3	414	Acg/cg	8/8	0.2210599825224	5	FACETS	1	0.971	1	0.694	0.656	0.733	INDETERMINATE	2	TRUE	2	0.533789788949115	5		555	1030	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0043371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	104	311	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	0.2210599825224	5	FACETS	0.941	0.85	1	0.627	0.566	0.69	INDETERMINATE	2	TRUE	2	0.533789788949115	5		311	373	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225683	26225683	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs750903931	NA	P-0043371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	57	583	0	ENST00000360408.1:c.301T>G	p.Leu101Val	p.L101V	ENST00000360408	NM_003532.2	101	Ttg/Gtg	1/1	0.533789788949115	3	FACETS	0.28	0.239	0.324	0.14	0.119	0.162	SUBCLONAL	1	TRUE	1	0.533789788949115	3		583	968	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411678	63411678	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	451	721	2	ENST00000330258.3:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000330258	NM_152424.3	497	Cga/Tga	2/2	0.494900979283544	2	FACETS	0.932	0.894	0.969	0.932	0.894	0.969	CLONAL	2	TRUE	0	0.533789788949115	2		723	907	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510672	38510672	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	127	639	0	ENST00000254066.5:c.926T>G	p.Val309Gly	p.V309G	ENST00000254066	NM_000964.3	309	gTc/gGc	7/9	1	2	FACETS	0.855	0.781	0.931	0.855	0.781	0.931	CLONAL	1	TRUE	1	0.70899388859066	2		639	419	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930413	39930413	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0043372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	86	133	0	ENST00000378444.4:c.3052-1G>A		p.X1018_splice	ENST00000378444	NM_001123385.1	1018			1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.70899388859066	1		133	105	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813032	76813032	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	165	246	0	ENST00000373344.5:c.6589C>T	p.Arg2197Cys	p.R2197C	ENST00000373344	NM_000489.3	2197	Cgt/Tgt	30/35	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.70899388859066	1		246	236	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0043399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	83	547	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.387	0.342	0.436	0.387	0.342	0.436	SUBCLONAL	1	TRUE	1	0.677352323617369	2		547	633	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0043399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	189	248	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.677352323617369	2		248	513	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0043399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	150	479	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.677352323617369	2		479	443	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435481	110435481	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	248	503	0	ENST00000375856.3:c.2920C>G	p.Pro974Ala	p.P974A	ENST00000375856	NM_003749.2	974	Ccg/Gcg	1/2	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.677352323617369	2		503	720	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456487	29456487	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	305	667	0	ENST00000389048.3:c.2431G>C	p.Val811Leu	p.V811L	ENST00000389048	NM_004304.4	811	Gtg/Ctg	14/29	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.677352323617369	2		667	862	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367339	50367339	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	175	444	0	ENST00000331340.3:c.146G>T	p.Ser49Ile	p.S49I	ENST00000331340	NM_006060.4	49	aGt/aTt	3/8	1	2	FACETS	0.939	0.871	1	0.939	0.871	1	CLONAL	1	TRUE	1	0.677352323617369	2		444	550	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8339040	8339040	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	164	398	0	ENST00000356435.5:c.5261G>A	p.Cys1754Tyr	p.C1754Y	ENST00000356435		1754	tGt/tAt	32/35	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.677352323617369	2		398	448	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996824	100996830	+	frameshift_variant	Frame_Shift_Del	DEL	AAACAAA	AAACAAA	TGT	novel	NA	P-0043399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	157	519	1	ENST00000325455.5:c.1697_1703delinsACA	p.Ile566AsnfsTer82	p.I566Nfs*82	ENST00000325455	NM_001202474.3	566	aTTTGTTTa/aACAa	2/8	0.258299941912813	2	FACETS	0.832	0.767	0.9	0.416	0.383	0.45	INDETERMINATE	1	TRUE	0	0.677352323617369	2		520	557	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654624	67654624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	92	408	1	ENST00000264010.4:c.1111C>T	p.Arg371Cys	p.R371C	ENST00000264010	NM_006565.3	371	Cgc/Tgc	6/12	0.379345124433572	1	FACETS	0.995	0.89	1	0.995	0.89	1	CLONAL	1	TRUE	0	0.379345124433572	1		409	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0043427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	247	501	0	ENST00000269305.4:c.96+1G>A		p.X32_splice	ENST00000269305	NM_001126112.2	32			0.379345124433572	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.379345124433572	2		501	644	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939033	48939033	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1131690901	NA	P-0043427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	118	188	0	ENST00000267163.4:c.869del	p.Asn290MetfsTer11	p.N290Mfs*11	ENST00000267163	NM_000321.2	289	Aaa/aa	9/27	0.379345124433572	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.379345124433572	3		188	300	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225607	133225607	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	421	632	0	ENST00000320574.5:c.4057A>T	p.Ser1353Cys	p.S1353C	ENST00000320574	NM_006231.2	1353	Agt/Tgt	32/49	0.295627335762628	3	FACETS	1	0.987	1			1	CLONAL	3	TRUE	NA	0.379345124433572	3		632	824	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647224	2647224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	104	532	0	ENST00000342085.4:c.1502C>T	p.Ser501Leu	p.S501L	ENST00000342085	NM_002613.4	501	tCa/tTa	13/14	1	2	FACETS	0.959	0.861	1	0.959	0.861	1	CLONAL	1	TRUE	1	0.379345124433572	2		532	572	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541579	29541580	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0043427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	154	337	0	ENST00000356175.3:c.1504dup	p.Ala502GlyfsTer9	p.A502Gfs*9	ENST00000356175	NM_000267.3	501	-/G	13/57	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	2	TRUE	NA	0.379345124433572	2		337	371	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665135	138665135	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	230	495	1	ENST00000330315.3:c.430C>T	p.Arg144Trp	p.R144W	ENST00000330315	NM_023067.3	144	Cgg/Tgg	1/1	0.379345124433572	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	2	0.379345124433572	4		496	788	SUCCESS
ATR	545	MSKCC	GRCh37	3	142218521	142218521	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	80	337	0	ENST00000350721.4:c.5328A>C	p.Glu1776Asp	p.E1776D	ENST00000350721	NM_001184.3	1776	gaA/gaC	31/47	0.379345124433572	4	FACETS	0.903	0.796	1	0.452	0.398	0.51	CLONAL	1	TRUE	2	0.379345124433572	4		337	644	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948165	178948165	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0043427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	76	164	0	ENST00000263967.3:c.2936+1G>A		p.X979_splice	ENST00000263967	NM_006218.2	979			0.379345124433572	4	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	2	0.379345124433572	4		164	260	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231750	66231750	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	48	340	0	ENST00000273854.3:c.1950C>A	p.Tyr650Ter	p.Y650*	ENST00000273854	NM_004439.5	650	taC/taA	11/18	1	2	FACETS	0.801	0.68	0.932	0.801	0.68	0.932	CLONAL	1	TRUE	1	0.379345124433572	2		340	316	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521277	187521277	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	125	591	0	ENST00000441802.2:c.11878G>T	p.Gly3960Ter	p.G3960*	ENST00000441802	NM_005245.3	3960	Gga/Tga	22/27	1	2	FACETS	0.985	0.893	1	0.985	0.893	1	CLONAL	1	TRUE	1	0.379345124433572	2		591	669	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0043485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	23	568	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.725	0.576	0.889	0.725	0.576	0.889	SUBCLONAL	1	TRUE	1	0.634591186577445	2		568	100	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413070	139413072	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0043485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	43	686	0	ENST00000277541.6:c.1070_1072del	p.Phe357del	p.F357del	ENST00000277541	NM_017617.3	357	tTCTac/tac	6/34	1	2	FACETS	0.368	0.309	0.434	0.368	0.309	0.434	SUBCLONAL	1	TRUE	1	0.634591186577445	2		686	368	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413073	139413075	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0043485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	51	517	0	ENST00000277541.6:c.1067_1069del	p.Ser356del	p.S356del	ENST00000277541	NM_017617.3	356	tCCTtc/ttc	6/34	1	2	FACETS	0.422	0.359	0.49	0.422	0.359	0.49	SUBCLONAL	1	TRUE	1	0.634591186577445	2		517	381	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797278	42797278	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs968289754	NA	P-0043485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	28	685	0	ENST00000575354.2:c.3640C>T	p.Arg1214Ter	p.R1214*	ENST00000575354	NM_015125.3	1214	Cga/Tga	15/20	0.640182922234517	1	FACETS	0.3	0.241	0.366	0.3	0.241	0.366	SUBCLONAL	1	TRUE	0	0.634591186577445	1		685	201	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795712	42795715	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CAGT	CAGT	-	novel	NA	P-0043485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	48	799	0	ENST00000575354.2:c.2705_2708del	p.Ser902PhefsTer21	p.S902Ffs*21	ENST00000575354	NM_015125.3	901	CAGTca/ca	11/20	0.640182922234517	1	FACETS	0.443	0.378	0.513	0.443	0.378	0.513	SUBCLONAL	1	TRUE	0	0.634591186577445	1		799	233	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0043487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	213	467	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.565094167121093	1	FACETS	0.926	0.867	0.987	0.926	0.867	0.987	CLONAL	1	TRUE	0	0.565094167121093	1		467	584	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0043487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	94	754	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.855	0.767	0.948	0.855	0.767	0.948	CLONAL	1	TRUE	1	0.565094167121093	2		754	389	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0043487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	95	464	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.549197964838064	2	FACETS	0.851	0.763	0.943	0.426	0.381	0.472	CLONAL	1	TRUE	0	0.565094167121093	2		464	395	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0043487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	171	310	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.55987667179995	2	FACETS	0.882	0.826	0.939	0.882	0.826	0.939	CLONAL	2	TRUE	0	0.565094167121093	2		310	343	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398831	398831	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs538810711	NA	P-0043487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	112	429	1	ENST00000380956.4:c.641G>T	p.Cys214Phe	p.C214F	ENST00000380956	NM_001195286.1	214	tGc/tTc	6/9	1	2	FACETS	0.873	0.79	0.96	0.873	0.79	0.96	CLONAL	1	TRUE	1	0.565094167121093	2		430	454	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980007	7980007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147992320	NA	P-0043487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	196	740	0	ENST00000319144.4:c.1330G>A	p.Val444Ile	p.V444I	ENST00000319144	NM_001139.2	444	Gtt/Att	10/15	0.565094167121093	1	FACETS	0.892	0.832	0.953	0.892	0.832	0.953	CLONAL	1	TRUE	0	0.565094167121093	1		740	558	SUCCESS
APC	324	MSKCC	GRCh37	5	112174437	112174437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs876658667	NA	P-0043487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	78	261	0	ENST00000257430.4:c.3146G>A	p.Trp1049Ter	p.W1049*	ENST00000257430	NM_000038.5	1049	tGg/tAg	16/16	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.565094167121093	2		261	267	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632363	1632363	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143787476	NA	P-0043487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	234	812	1	ENST00000344749.5:c.187G>A	p.Asp63Asn	p.D63N	ENST00000344749	NM_001136139.2	63	Gac/Aac	4/19	1	2	FACETS	0.962	0.899	1	0.962	0.899	1	CLONAL	1	TRUE	1	0.565094167121093	2		813	861	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662551	227662551	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	169	565	3	ENST00000305123.5:c.904C>T	p.Arg302Ter	p.R302*	ENST00000305123	NM_005544.2	302	Cga/Tga	1/2	1	2	FACETS	0.999	0.923	1	0.999	0.923	1	CLONAL	1	TRUE	1	0.565094167121093	2		568	599	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991122	41991123	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0043487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	133	518	2	ENST00000219905.7:c.2075_2076del	p.Ser692TyrfsTer4	p.S692Yfs*4	ENST00000219905	NM_001164273.1	692	tCA/t	4/24	1	2	FACETS	0.94	0.858	1	0.94	0.858	1	CLONAL	1	TRUE	1	0.565094167121093	2		520	501	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916247	9916247	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	123	486	0	ENST00000330684.3:c.2042G>C	p.Arg681Pro	p.R681P	ENST00000330684	NM_001134407.1	681	cGa/cCa	10/13	1	2	FACETS	0.899	0.818	0.984	0.899	0.818	0.984	CLONAL	1	TRUE	1	0.565094167121093	2		486	484	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356422	66356423	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0043487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	86	303	0	ENST00000273854.3:c.1074dup	p.Ser359LeufsTer11	p.S359Lfs*11	ENST00000273854	NM_004439.5	358	-/C	5/18	1	2	FACETS	0.882	0.787	0.982	0.882	0.787	0.982	CLONAL	1	TRUE	1	0.565094167121093	2		303	345	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0043522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	576	482	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.401978727557403	6	FACETS	1	0.982	1	1	0.998	1	CLONAL	7	TRUE	1	0.401978727557403	6		482	733	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727451	66727451	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519729	NA	P-0043522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	87	420	0	ENST00000307102.5:c.167A>C	p.Gln56Pro	p.Q56P	ENST00000307102	NM_002755.3	56	cAg/cCg	2/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.401978727557403	2		420	387	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575209	48575209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767326	NA	P-0043522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	77	228	0	ENST00000342988.3:c.403C>T	p.Arg135Ter	p.R135*	ENST00000342988	NM_005359.5	135	Cga/Tga	3/12	1	2	FACETS	0.757	0.674	0.844	1	0.979	1	SUBCLONAL	2	TRUE	1	0.401978727557403	2		228	253	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577529	7577529	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs730882027	NA	P-0043522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	244	510	0	ENST00000269305.4:c.752T>G	p.Ile251Ser	p.I251S	ENST00000269305	NM_001126112.2	251	aTc/aGc	7/11	0.402804176072102	2	FACETS	0.84	0.795	0.884	1	0.991	1	CLONAL	3	TRUE	0	0.401978727557403	2		510	482	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604750	48604750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	116	333	0	ENST00000342988.3:c.1572G>T	p.Trp524Cys	p.W524C	ENST00000342988	NM_005359.5	524	tgG/tgT	12/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.401978727557403	2		333	430	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411522	63411522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746279756	NA	P-0043522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	574	636	2	ENST00000330258.3:c.1645C>T	p.Arg549Trp	p.R549W	ENST00000330258	NM_152424.3	549	Cgg/Tgg	2/2	0.401978727557403	6	FACETS	1	0.983	1	1	0.983	1	CLONAL	5	TRUE	1	0.401978727557403	6		638	1004	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420011	41420011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773011187	NA	P-0043522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	159	381	2	ENST00000373198.4:c.310G>A	p.Asp104Asn	p.D104N	ENST00000373198	NM_133170.3	104	Gac/Aac	3/32	0.252269411448812	4	FACETS	0.992	0.914	1	0.992	0.914	1	CLONAL	2	TRUE	2	0.401978727557403	4		383	559	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021340	31021340	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	180	453	0	ENST00000375687.4:c.1342del	p.Leu448SerfsTer14	p.L448Sfs*14	ENST00000375687	NM_015338.5	447	Ccc/cc	12/13	0.252269411448812	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.401978727557403	4		453	564	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89478284	89478284	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	56	293	0	ENST00000336596.2:c.2103C>A	p.Tyr701Ter	p.Y701*	ENST00000336596	NM_005233.5	701	taC/taA	12/17	0.402804176072102	3	FACETS	1	0.954	1	0.627	0.542	0.718	CLONAL	1	TRUE	1	0.401978727557403	3		293	267	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004885	150004885	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	156	349	0	ENST00000253339.5:c.1340G>C	p.Ser447Thr	p.S447T	ENST00000253339		447	aGt/aCt	3/7	0.317253452089241	4	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	2	0.401978727557403	4		349	530	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519920	NA	P-0043560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	158	316	0	ENST00000397062.3:c.85G>A	p.Asp29Asn	p.D29N	ENST00000397062	NM_006164.4	29	Gat/Aat	2/5	0.435955931118622	3	FACETS	1	0.986	1	0.833	0.775	0.891	CLONAL	2	TRUE	0	0.447204547716297	3		316	346	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11308102	11308102	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1304123826	NA	P-0043560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	90	688	0	ENST00000361445.4:c.890A>G	p.Asp297Gly	p.D297G	ENST00000361445	NM_004958.3	297	gAc/gGc	7/58	0.447204547716297	3	FACETS	0.63	0.558	0.706	0.315	0.279	0.353	SUBCLONAL	1	TRUE	1	0.447204547716297	3		688	782	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552687	18552687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	139	684	1	ENST00000266497.5:c.2098G>A	p.Gly700Arg	p.G700R	ENST00000266497		700	Gga/Aga	14/31	0.271498018475523	5	FACETS	0.866	0.791	0.943	0.577	0.527	0.629	CLONAL	2	TRUE	2	0.447204547716297	5		685	600	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212425	36212425	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	183	848	1	ENST00000222270.7:c.2176G>T	p.Ala726Ser	p.A726S	ENST00000222270	NM_014727.1	726	Gct/Tct	3/37	0.417414684016783	4	FACETS	1	0.921	1	0.333	0.307	0.361	CLONAL	1	TRUE	1	0.447204547716297	4		849	1185	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715762	61715762	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	66	364	0	ENST00000401558.2:c.2167T>C	p.Cys723Arg	p.C723R	ENST00000401558	NM_003400.3	723	Tgc/Cgc	18/25	0.447204547716297	3	FACETS	0.948	0.827	1	0.316	0.275	0.36	CLONAL	1	TRUE	0	0.447204547716297	3		364	381	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146702	185146702	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	107	627	0	ENST00000265026.3:c.333C>A	p.Ser111Arg	p.S111R	ENST00000265026	NM_004721.4	111	agC/agA	2/14	0.447204547716297	5	FACETS	0.749	0.67	0.833	0.187	0.167	0.209	SUBCLONAL	1	TRUE	1	0.447204547716297	5		627	1068	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1255431	1255431	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	133	585	0	ENST00000310581.5:c.3128G>T	p.Cys1043Phe	p.C1043F	ENST00000310581	NM_198253.2	1043	tGc/tTc	14/16	0.35558756505221	3	FACETS	0.918	0.834	1	0.459	0.417	0.503	CLONAL	1	TRUE	1	0.447204547716297	3		585	793	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871271	35871271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	77	394	0	ENST00000303115.3:c.493C>T	p.His165Tyr	p.H165Y	ENST00000303115	NM_002185.3	165	Cac/Tac	4/8	0.447204547716297	3	FACETS	0.895	0.788	1	0.447	0.394	0.504	CLONAL	1	TRUE	1	0.447204547716297	3		394	471	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997768	149997768	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs575740406	NA	P-0043560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	120	505	0	ENST00000253339.5:c.2699G>A	p.Arg900His	p.R900H	ENST00000253339		900	cGc/cAc	5/7	0.447204547716297	3	FACETS	0.983	0.889	1	0.328	0.296	0.361	CLONAL	1	TRUE	0	0.447204547716297	3		505	668	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0043574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	38	245	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.973	0.804	1	0.973	0.804	1	CLONAL	1	TRUE	1	0.160104045641612	2		245	488	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670750	134670750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	56	525	0	ENST00000398015.3:c.661G>T	p.Ala221Ser	p.A221S	ENST00000398015	NM_004441.4	221	Gct/Tct	3/16	0.040168753897226	4	FACETS	1	0.909	1	1	0.909	1	INDETERMINATE	2	TRUE	2	0.160104045641612	4		525	377	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166371	118166373	+	inframe_deletion	In_Frame_Del	DEL	ACC	ACC	-	novel	NA	P-0043574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	16	362	0	ENST00000369448.3:c.883_885del	p.His295del	p.H295del	ENST00000369448	NM_017709.3	294	aACCac/aac	2/2	0.160104045641612	5	FACETS	0.787	0.581	1	0.393	0.29	0.517	CLONAL	1	TRUE	3	0.160104045641612	5		362	315	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0043584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	288	877	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.622642733755818	2		883	895	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0043584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	129	348	10	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.622642733755818	2	FACETS	0.919	0.839	1	0.459	0.419	0.501	CLONAL	1	TRUE	0	0.622642733755818	2		358	451	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	341	1121	2	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.622642733755818	2		1123	1042	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0043584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	272	605	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.975	0.917	1	0.975	0.917	1	CLONAL	1	TRUE	1	0.622642733755818	2		608	896	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0043584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	95	492	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.765	0.686	0.848	0.765	0.686	0.848	SUBCLONAL	1	TRUE	1	0.622642733755818	2		492	399	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0043584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	106	338	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.622642733755818	2		338	311	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0043584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	278	457	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	0.622642733755818	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.622642733755818	2		457	386	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929022	44929022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	135	576	2	ENST00000377967.4:c.2122G>A	p.Gly708Arg	p.G708R	ENST00000377967	NM_021140.2	708	Gga/Aga	17/29	1	2	FACETS	0.836	0.764	0.91	0.836	0.764	0.91	CLONAL	1	TRUE	1	0.622642733755818	2		578	519	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549095	87549095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	111	449	0	ENST00000277120.3:c.1652G>A	p.Arg551Gln	p.R551Q	ENST00000277120		551	cGa/cAa	15/19	1	2	FACETS	0.921	0.836	1	0.921	0.836	1	CLONAL	1	TRUE	1	0.622642733755818	2		449	387	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189472	94189473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs757691558	NA	P-0043584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	68	159	1	ENST00000323929.3:c.1532dup	p.Asn511LysfsTer3	p.N511Kfs*3	ENST00000323929	NM_005591.3	511	aat/aaAt	14/20	1	2	FACETS	0.78	0.685	0.88	0.78	0.685	0.88	SUBCLONAL	1	TRUE	1	0.622642733755818	2		160	280	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228384	228384	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774160524	NA	P-0043584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	129	434	0	ENST00000264932.6:c.706G>A	p.Ala236Thr	p.A236T	ENST00000264932	NM_004168.2	236	Gca/Aca	6/15	1	2	FACETS	0.867	0.791	0.946	0.867	0.791	0.946	CLONAL	1	TRUE	1	0.622642733755818	2		434	478	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29197675	29197675	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	293	598	1	ENST00000240100.2:c.519del	p.Ser174ValfsTer53	p.S174Vfs*53	ENST00000240100	NM_001394.6	173	ccC/cc	2/4	1	2	FACETS	0.981	0.925	1	0.981	0.925	1	CLONAL	1	TRUE	1	0.622642733755818	2		599	959	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444809	49444809	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	61	786	1	ENST00000301067.7:c.2657del	p.Pro886LeufsTer44	p.P886Lfs*44	ENST00000301067	NM_003482.3	886	cCt/ct	10/54	1	2	FACETS	0.193	0.165	0.223	0.193	0.165	0.223	SUBCLONAL	1	TRUE	1	0.622642733755818	2		787	1016	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16235908	16235908	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	130	427	0	ENST00000375759.3:c.974C>T	p.Ser325Phe	p.S325F	ENST00000375759	NM_015001.2	325	tCt/tTt	4/15	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.622642733755818	2		427	415	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111527	8111527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	186	575	1	ENST00000346208.3:c.1013G>A	p.Cys338Tyr	p.C338Y	ENST00000346208		338	tGc/tAc	5/6	1	2	FACETS	0.971	0.902	1	0.971	0.902	1	CLONAL	1	TRUE	1	0.622642733755818	2		576	615	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717640	89717641	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0043584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	214	418	0	ENST00000371953.3:c.666dup	p.Lys223GlufsTer20	p.K223Efs*20	ENST00000371953	NM_000314.4	222	gtg/gtGg	7/9	0.622642733755818	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.622642733755818	2		418	324	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912793	100912795	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0043584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	102	396	0	ENST00000325455.5:c.2527_2529del	p.Glu843del	p.E843del	ENST00000325455	NM_001202474.3	843	GAG/-	7/8	1	2	FACETS	0.981	0.887	1	0.981	0.887	1	CLONAL	1	TRUE	1	0.622642733755818	2		396	334	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592261	29592261	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	11	88	0	ENST00000356175.3:c.4680del	p.Glu1561LysfsTer6	p.E1561Kfs*6	ENST00000356175	NM_000267.3	1559	gAa/ga	35/57	1	2	FACETS	0.318	0.221	0.437	0.318	0.221	0.437	SUBCLONAL	1	TRUE	1	0.622642733755818	2		88	111	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413710	138413710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753827615	NA	P-0043584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	32	491	0	ENST00000289153.2:c.1810C>T	p.Arg604Trp	p.R604W	ENST00000289153	NM_006219.2	604	Cgg/Tgg	12/22	1	2	FACETS	0.216	0.175	0.263	0.216	0.175	0.263	SUBCLONAL	1	TRUE	1	0.622642733755818	2		491	475	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433374	138433375	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	83	181	0	ENST00000289153.2:c.1237dup	p.Thr413AsnfsTer9	p.T413Nfs*9	ENST00000289153	NM_006219.2	413	acg/aAcg	7/22	1	2	FACETS	0.913	0.815	1	0.913	0.815	1	CLONAL	1	TRUE	1	0.622642733755818	2		181	292	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80168997	80168997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	88	470	0	ENST00000265081.6:c.3193G>A	p.Ala1065Thr	p.A1065T	ENST00000265081	NM_002439.4	1065	Gca/Aca	23/24	1	2	FACETS	0.817	0.73	0.908	0.817	0.73	0.908	CLONAL	1	TRUE	1	0.622642733755818	2		470	346	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681532	117681532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	69	362	0	ENST00000368508.3:c.3418G>A	p.Ala1140Thr	p.A1140T	ENST00000368508	NM_002944.2	1140	Gct/Act	22/43	1	2	FACETS	0.923	0.815	1	0.923	0.815	1	CLONAL	1	TRUE	1	0.622642733755818	2		362	240	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371895	55371896	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0043584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	138	240	0	ENST00000297316.4:c.587dup	p.Pro197SerfsTer168	p.P197Sfs*168	ENST00000297316	NM_022454.3	195	-/C	2/2	1	2	FACETS	0.949	0.87	1	0.949	0.87	1	CLONAL	1	TRUE	1	0.622642733755818	2		240	467	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413985	139413985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763187824	NA	P-0043584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	307	633	0	ENST00000277541.6:c.775G>A	p.Asp259Asn	p.D259N	ENST00000277541	NM_017617.3	259	Gac/Aac	5/34	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.622642733755818	2		633	939	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651679	48651679	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	241	697	1	ENST00000376670.3:c.845G>A	p.Cys282Tyr	p.C282Y	ENST00000376670	NM_002049.3	282	tGc/tAc	5/6	1	2	FACETS	0.922	0.863	0.982	0.922	0.863	0.982	CLONAL	1	TRUE	1	0.622642733755818	2		698	840	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347778	70347778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	139	514	1	ENST00000374080.3:c.3017G>A	p.Cys1006Tyr	p.C1006Y	ENST00000374080		1006	tGc/tAc	22/45	1	2	FACETS	0.865	0.792	0.941	0.865	0.792	0.941	CLONAL	1	TRUE	1	0.622642733755818	2		515	516	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909991	100909995	+	frameshift_variant	Frame_Shift_Del	DEL	TTGTT	TTGTT	C	novel	NA	P-0043584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	73	271	0	ENST00000325455.5:c.2654_2658delinsG	p.Lys885SerfsTer7	p.K885Sfs*7	ENST00000325455	NM_001202474.3	885	aAACAA/aG	8/8	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.622642733755818	2		271	208	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206612	108206612	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	150	272	0	ENST00000278616.4:c.8192T>G	p.Val2731Gly	p.V2731G	ENST00000278616	NM_000051.3	2731	gTc/gGc	56/63	0.758598387293677	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.758598387293677	1		272	231	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913250	NA	P-0043620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	271	268	0	ENST00000369535.4:c.34G>A	p.Gly12Ser	p.G12S	ENST00000369535	NM_002524.4	12	Ggt/Agt	2/7	0.571534643870785	3	FACETS	0.915	0.874	0.956	0.915	0.874	0.956	CLONAL	3	TRUE	0	0.571534643870785	3		268	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0043620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	309	707	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.571534643870785	2	FACETS	0.967	0.923	1	0.967	0.923	1	CLONAL	2	TRUE	0	0.571534643870785	2		707	559	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0043620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	145	183	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.544153059205238	3	FACETS	0.863	0.807	0.918	0.863	0.807	0.918	CLONAL	3	TRUE	0	0.571534643870785	3		183	252	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	18	225	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	0.708	0.543	0.894	0.708	0.543	0.894	SUBCLONAL	1	TRUE	1	0.571534643870785	2		225	89	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0043661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	60	414	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.74	0.637	0.852	0.74	0.637	0.852	SUBCLONAL	1	TRUE	1	0.25	2		414	649	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755128667	NA	P-0043661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	123	760	1	ENST00000407977.2:c.1976dup	p.Pro660SerfsTer87	p.P660Sfs*87	ENST00000407977		659	ggt/ggGt	9/10	1	2	FACETS	0.753	0.679	0.832	0.753	0.679	0.832	SUBCLONAL	1	TRUE	1	0.25	2		761	1306	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217651	7217651	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	79	461	0	ENST00000380728.2:c.276del	p.Val93PhefsTer16	p.V93Ffs*16	ENST00000380728		92	aaA/aa	4/11	1	2	FACETS	0.706	0.62	0.799	0.706	0.62	0.799	SUBCLONAL	1	TRUE	1	0.25	2		461	895	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219121	94219121	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	56	389	0	ENST00000323929.3:c.283A>T	p.Ser95Cys	p.S95C	ENST00000323929	NM_005591.3	95	Agt/Tgt	4/20	1	2	FACETS	0.855	0.733	0.988	0.855	0.733	0.988	CLONAL	1	TRUE	1	0.25	2		389	524	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	149	807	0	ENST00000267101.3:c.310G>C	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ctg	3/28	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.21680204194018	2		807	967	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0043665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	48	326	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.21680204194018	2		326	300	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0043665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	108	588	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.798	0.718	0.883	1	0.984	1	SUBCLONAL	2	TRUE	1	0.21680204194018	2		588	624	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916946	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0043665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	108	414	0	ENST00000263967.3:c.332_334del	p.Lys111del	p.K111del	ENST00000263967	NM_006218.2	111	AAG/-	2/21	0.21680204194018	2	FACETS	0.952	0.863	1	1	0.983	1	CLONAL	3	TRUE	0	0.21680204194018	2		414	349	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692790	89692790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	35	323	1	ENST00000371953.3:c.274G>A	p.Asp92Asn	p.D92N	ENST00000371953	NM_000314.4	92	Gac/Aac	5/9	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.21680204194018	2		324	240	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0043687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	85	350	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.497836602198902	2		350	325	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0043687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	125	270	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.497836602198902	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.497836602198902	1		270	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577017	7577017	+	splice_donor_variant	Splice_Site	SNP	A	A	T	rs1131691016	NA	P-0043687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	157	480	0	ENST00000269305.4:c.919+2T>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.497836602198902	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.497836602198902	1		480	443	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093362	30093362	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	56	142	0	ENST00000331968.5:c.1901T>G	p.Leu634Arg	p.L634R	ENST00000331968	NM_002742.2	634	cTa/cGa	13/18	0.497836602198902	1	FACETS	0.858	0.746	0.975	0.858	0.746	0.975	CLONAL	1	TRUE	0	0.497836602198902	1		142	197	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111417	56111417	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	70	206	0	ENST00000399503.3:c.17G>C	p.Gly6Ala	p.G6A	ENST00000399503	NM_005921.1	6	gGg/gCg	1/20	1	2	FACETS	0.868	0.763	0.98	0.868	0.763	0.98	CLONAL	1	TRUE	1	0.497836602198902	2		206	324	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101909967	101909967	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0043687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	30	46	0	ENST00000374994.4:c.1287T>A	p.Tyr429Ter	p.Y429*	ENST00000374994	NM_004612.2	429	taT/taA	8/9	0.497836602198902	1	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	0	0.497836602198902	1		46	88	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0043688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	171	494	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.108605427829957	4	FACETS	1	0.966	1	1	0.966	1	INDETERMINATE	2	TRUE	2	0.484727357830437	4		494	489	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243045	105243046	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTGCAGGCAGCGGATGATGAAGGTGTTGGGCCGGGGCCGCTCCGT	novel	NA	P-0043688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	180	565	0	ENST00000349310.3:c.193_237dup	p.Thr65_Gln79dup	p.T65_Q79dup	ENST00000349310	NM_001014432.1	65	-/ACGGAGCGGCCCCGGCCCAACACCTTCATCATCCGCTGCCTGCAG	5/15	NA	2	FACETS	0.72	0.664	0.779			1	INDETERMINATE	1	TRUE	NA	0.484727357830437	2		565	1031	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576214	88576214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750565995	NA	P-0043688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	222	433	1	ENST00000360948.2:c.1459G>A	p.Gly487Ser	p.G487S	ENST00000360948	NM_001012338.2	487	Ggc/Agc	13/19	0.167000022151594	4	FACETS	1	0.984	1	1	0.984	1	INDETERMINATE	2	TRUE	2	0.484727357830437	4		434	595	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982016	70982016	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	217	580	0	ENST00000276594.2:c.80C>A	p.Ala27Asp	p.A27D	ENST00000276594	NM_024504.3	27	gCc/gAc	2/8	0.450714866897539	5	FACETS	0.813	0.756	0.872	0.542	0.504	0.581	CLONAL	2	TRUE	2	0.484727357830437	5		580	951	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0043712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	122	715	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.350414173518463	1	FACETS	0.884	0.8	0.971	0.884	0.8	0.971	CLONAL	1	TRUE	0	0.350414173518463	1		715	650	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0043712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	62	350	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.975	0.846	1	0.975	0.846	1	CLONAL	1	TRUE	1	0.350414173518463	2		350	363	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593505	48593505	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	54	324	0	ENST00000342988.3:c.1256G>T	p.Gly419Val	p.G419V	ENST00000342988	NM_005359.5	419	gGg/gTg	10/12	0.350414173518463	1	FACETS	0.911	0.784	1	0.911	0.784	1	CLONAL	1	TRUE	0	0.350414173518463	1		324	279	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555271	226555272	+	missense_variant	Missense_Mutation	DNP	CT	CT	AC	novel	NA	P-0043712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	46	395	1	ENST00000366794.5:c.2315_2316delinsGT	p.Glu772Gly	p.E772G	ENST00000366794	NM_001618.3	772	gAG/gGT	17/23	0.350414173518463	1	FACETS	0.502	0.423	0.589	0.502	0.423	0.589	SUBCLONAL	1	TRUE	0	0.350414173518463	1		396	431	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266025	41266222	+	inframe_deletion	In_Frame_Del	DEL	ATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCC	ATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCC	-	novel	NA	P-0043712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	10	228	0	ENST00000349496.5:c.22_219del	p.Met8_Ser73del	p.M8_S73del	ENST00000349496	NM_001904.3	8	ATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCC/-	3/15	0.342535222802753	2	FACETS	0.348	0.236	0.488	0.174	0.118	0.244	SUBCLONAL	1	TRUE	0	0.350414173518463	2		228	164	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199892	138199892	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	28	404	0	ENST00000237289.4:c.1310C>A	p.Ala437Asp	p.A437D	ENST00000237289	NM_001270507.1	437	gCc/gAc	7/9	1	2	FACETS	0.379	0.302	0.466	0.379	0.302	0.466	SUBCLONAL	1	TRUE	1	0.350414173518463	2		404	422	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397756	116397756	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0043712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	83	415	0	ENST00000397752.3:c.2030T>G	p.Leu677Ter	p.L677*	ENST00000397752	NM_000245.2	677	tTa/tGa	8/21	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.350414173518463	2		415	428	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183827	10183836	+	frameshift_variant	Frame_Shift_Del	DEL	CAACGCTGCC	CAACGCTGCC	TACCTGCA	novel	NA	P-0043738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	93	598	1	ENST00000256474.2:c.296_305delinsTACCTGCA	p.Pro99LeufsTer32	p.P99Lfs*32	ENST00000256474	NM_000551.3	99	cCAACGCTGCCg/cTACCTGCAg	1/3	0.3	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.29	1		599	519	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231291	142231291	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	196	309	0	ENST00000350721.4:c.4663G>C	p.Val1555Leu	p.V1555L	ENST00000350721	NM_001184.3	1555	Gtt/Ctt	27/47	1	2	FACETS	0.947	0.883	1	0.947	0.883	1	CLONAL	1	TRUE	1	0.744347334475169	2		309	556	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0043840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	307	656	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	0.218664186290466	1	FACETS	1	0.982	1	1	0.997	1	CLONAL	3	TRUE	0	0.218664186290466	1		656	771	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699351	47699351	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	259	443	0	ENST00000347630.2:c.157A>G	p.Lys53Glu	p.K53E	ENST00000347630	NM_001007230.1	53	Aaa/Gaa	4/11	0.218664186290466	1	FACETS	1	0.979	1	1	0.996	1	CLONAL	3	TRUE	0	0.218664186290466	1		443	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0043853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	212	467	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.708	0.659	0.758	0.708	0.659	0.758	SUBCLONAL	1	TRUE	1	0.759225211025309	2		467	789	SUCCESS
APC	324	MSKCC	GRCh37	5	112175225	112175225	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	56	227	0	ENST00000257430.4:c.3934G>T	p.Gly1312Ter	p.G1312*	ENST00000257430	NM_000038.5	1312	Gga/Tga	16/16	0.645359893814285	1	FACETS	0.863	0.769	0.956	0.863	0.769	0.956	CLONAL	1	TRUE	0	0.759225211025309	1		227	106	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871807	12871807	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	155	283	0	ENST00000228872.4:c.524del	p.Ser175Ter	p.S175*	ENST00000228872	NM_004064.3	175	tCa/ta	2/3	0.625374398241168	1	FACETS	0.804	0.75	0.859	0.804	0.75	0.859	CLONAL	1	TRUE	0	0.759225211025309	1		283	315	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696456	47696456	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	126	428	0	ENST00000347630.2:c.367T>G	p.Tyr123Asp	p.Y123D	ENST00000347630	NM_001007230.1	123	Tat/Gat	6/11	1	2	FACETS	0.849	0.776	0.924	0.849	0.776	0.924	CLONAL	1	TRUE	1	0.759225211025309	2		428	391	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653780	89653781	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	rs1554893747	NA	P-0043903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	106	226	0	ENST00000371953.3:c.80-1_80del		p.X27_splice	ENST00000371953	NM_000314.4	27			0.772646518776087	1	FACETS	0.806	0.741	0.871	0.806	0.741	0.871	CLONAL	1	TRUE	0	0.772646518776087	1		226	209	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577257	64577257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	403	651	0	ENST00000312049.6:c.325G>T	p.Glu109Ter	p.E109*	ENST00000312049	NM_130799.2	109	Gaa/Taa	2/10	0.772646518776087	1	FACETS	0.944	0.908	0.98	0.944	0.908	0.98	CLONAL	1	TRUE	0	0.772646518776087	1		651	678	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0043914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	325	549	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.574286465242646	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.594639876076211	2		552	546	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18963802	18963802	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	77	326	0	ENST00000262803.5:c.979G>C	p.Asp327His	p.D327H	ENST00000262803	NM_002911.3	327	Gat/Cat	7/24	0.594639876076211	3	FACETS	0.819	0.723	0.922	0.41	0.361	0.461	CLONAL	1	TRUE	1	0.594639876076211	3		326	410	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902491	1902491	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	106	591	0	ENST00000382891.5:c.110G>T	p.Ser37Ile	p.S37I	ENST00000382891	NM_133335.3	37	aGc/aTc	2/22	0.594639876076211	2	FACETS	0.644	0.579	0.712	0.322	0.289	0.356	SUBCLONAL	1	TRUE	0	0.594639876076211	2		591	554	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525531	187525532	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	67	312	0	ENST00000441802.2:c.10547dup	p.Val3517GlyfsTer4	p.V3517Gfs*4	ENST00000441802	NM_005245.3	3516	aag/aaAg	18/27	0.594639876076211	2	FACETS	1	0.939	1	0.55	0.486	0.616	CLONAL	1	TRUE	0	0.594639876076211	2		312	205	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	123	627	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.500906458731459	2		633	348	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	73	350	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.672	0.59	0.759	0.672	0.59	0.759	SUBCLONAL	1	TRUE	1	0.500906458731459	2		350	434	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222730	5222731	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs756013055	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	83	512	3	ENST00000357368.4:c.3072dup	p.Val1025ArgfsTer34	p.V1025Rfs*34	ENST00000357368	NM_002850.3	1024	-/C	18/38	1	2	FACETS	0.614	0.543	0.69	0.614	0.543	0.69	SUBCLONAL	1	TRUE	1	0.500906458731459	2		515	540	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	128	461	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.500906458731459	2		461	363	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	144	584	0	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.828	0.757	0.903	0.828	0.757	0.903	CLONAL	1	TRUE	1	0.500906458731459	2		584	694	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852118	63852118	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	118	477	0	ENST00000279873.7:c.2901del	p.Lys967AsnfsTer15	p.K967Nfs*15	ENST00000279873	NM_032199.2	966	Aaa/aa	10/10	0.384903934066977	3	FACETS	0.885	0.799	0.974	0.442	0.399	0.487	CLONAL	1	TRUE	1	0.500906458731459	3		477	666	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925402	114925402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748822481	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	128	661	2	ENST00000543371.1:c.1485del	p.Ser496ProfsTer5	p.S496Pfs*5	ENST00000543371	NM_001198531.1	494	Ccc/cc	14/14	0.431330288388696	3	FACETS	0.786	0.712	0.864	0.262	0.237	0.288	SUBCLONAL	1	TRUE	0	0.500906458731459	3		663	813	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	120	475	2	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.812	0.736	0.892	0.812	0.736	0.892	CLONAL	1	TRUE	1	0.500906458731459	2		477	590	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	46	349	3	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.505	0.426	0.591	0.505	0.426	0.591	SUBCLONAL	1	TRUE	1	0.500906458731459	2		352	364	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073616	8073616	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	82	388	0	ENST00000377482.5:c.1043del	p.Pro348ArgfsTer104	p.P348Rfs*104	ENST00000377482	NM_018948.3	348	cCg/cg	4/4	1	2	FACETS	0.744	0.659	0.834	0.744	0.659	0.834	SUBCLONAL	1	TRUE	1	0.500906458731459	2		388	440	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567646	226567647	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1159330096	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	102	543	0	ENST00000366794.5:c.1519dup	p.Ser507LysfsTer14	p.S507Kfs*14	ENST00000366794	NM_001618.3	507	agc/aAgc	10/23	0.379578986843786	4	FACETS	0.738	0.66	0.822	0.246	0.22	0.274	SUBCLONAL	1	TRUE	1	0.500906458731459	4		543	828	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348566	89348568	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs753054998	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	121	698	5	ENST00000301030.4:c.4382_4384del	p.Lys1461del	p.K1461del	ENST00000301030	NM_001256183.1	1461	aAGAga/aga	9/13	1	2	FACETS	0.672	0.608	0.74	0.672	0.608	0.74	SUBCLONAL	1	TRUE	1	0.500906458731459	2		703	719	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662450	67662450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	118	552	1	ENST00000264010.4:c.1696C>T	p.Arg566Cys	p.R566C	ENST00000264010	NM_006565.3	566	Cgt/Tgt	9/12	1	2	FACETS	0.65	0.587	0.717	0.65	0.587	0.717	SUBCLONAL	1	TRUE	1	0.500906458731459	2		553	725	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248123	59248123	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs370122841	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	23	144	0	ENST00000371222.2:c.620C>A	p.Pro207Gln	p.P207Q	ENST00000371222	NM_002228.3	207	cCg/cAg	1/1	1	2	FACETS	0.712	0.562	0.88	0.712	0.562	0.88	SUBCLONAL	1	TRUE	1	0.500906458731459	2		144	129	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	143	581	0	ENST00000397062.3:c.246A>C	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaC	2/5	0.364455955826905	3	FACETS	0.831	0.758	0.908	0.416	0.379	0.454	CLONAL	1	TRUE	1	0.500906458731459	3		581	859	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996755	100996757	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	64	323	0	ENST00000325455.5:c.1770_1772del	p.Phe591del	p.F591del	ENST00000325455	NM_001202474.3	590	ttCTTt/ttt	2/8	1	2	FACETS	0.606	0.526	0.691	0.606	0.526	0.691	SUBCLONAL	1	TRUE	1	0.500906458731459	2		323	422	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55603380	55603380	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	63	340	1	ENST00000288135.5:c.2740del	p.Arg914AspfsTer10	p.R914Dfs*10	ENST00000288135	NM_000222.2	912	ctA/ct	20/21	1	2	FACETS	0.779	0.678	0.886	0.779	0.678	0.886	SUBCLONAL	1	TRUE	1	0.500906458731459	2		341	323	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278070	18278070	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs886041602	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	156	620	0	ENST00000222254.8:c.1690A>G	p.Lys564Glu	p.K564E	ENST00000222254	NM_005027.3	564	Aag/Gag	13/16	1	2	FACETS	0.823	0.755	0.894	0.823	0.755	0.894	CLONAL	1	TRUE	1	0.500906458731459	2		620	757	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437222	220437223	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1286117855	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	91	714	0	ENST00000243786.2:c.132dup	p.Ala45ArgfsTer29	p.A45Rfs*29	ENST00000243786	NM_002191.3	42	-/C	1/2	0.364455955826905	3	FACETS	0.557	0.494	0.624	0.278	0.247	0.312	SUBCLONAL	1	TRUE	1	0.500906458731459	3		714	816	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610601	10610601	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	162	635	0	ENST00000171111.5:c.109G>T	p.Glu37Ter	p.E37*	ENST00000171111	NM_203500.1	37	Gag/Tag	2/6	1	2	FACETS	0.875	0.805	0.949	0.875	0.805	0.949	CLONAL	1	TRUE	1	0.500906458731459	2		635	739	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089462	27089462	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	123	530	0	ENST00000324856.7:c.2420-2A>G		p.X807_splice	ENST00000324856	NM_006015.4	807			1	2	FACETS	0.847	0.768	0.929	0.847	0.768	0.929	CLONAL	1	TRUE	1	0.500906458731459	2		530	580	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717712	89717713	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	GTAA	novel	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	264	377	0	ENST00000371953.3:c.739_740insAAGT	p.Leu247Ter	p.L247*	ENST00000371953	NM_000314.4	246	ccg/ccGTAAg	7/9	0.431330288388696	3	FACETS	1	0.984	1	0.735	0.695	0.775	CLONAL	2	TRUE	0	0.500906458731459	3		377	598	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944205	71944205	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	113	525	0	ENST00000298229.2:c.2040+1del		p.G680fs	ENST00000298229	NM_001567.3	680	Ggg/gg	17/28	1	2	FACETS	0.892	0.806	0.981	0.892	0.806	0.981	CLONAL	1	TRUE	1	0.500906458731459	2		525	506	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946344	71946345	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	157	633	0	ENST00000298229.2:c.2513_2514del	p.Val838GlyfsTer45	p.V838Gfs*45	ENST00000298229	NM_001567.3	836	gaGTgt/gagt	23/28	1	2	FACETS	0.854	0.784	0.927	0.854	0.784	0.927	CLONAL	1	TRUE	1	0.500906458731459	2		633	734	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343322	118343322	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	65	297	0	ENST00000534358.1:c.1448G>A	p.Ser483Asn	p.S483N	ENST00000534358	NM_005933.3	483	aGt/aAt	3/36	1	2	FACETS	0.688	0.6	0.784	0.688	0.6	0.784	SUBCLONAL	1	TRUE	1	0.500906458731459	2		297	377	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495319	56495319	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	113	507	0	ENST00000267101.3:c.3509C>A	p.Pro1170His	p.P1170H	ENST00000267101	NM_001982.3	1170	cCc/cAc	28/28	1	2	FACETS	0.738	0.666	0.815	0.738	0.666	0.815	SUBCLONAL	1	TRUE	1	0.500906458731459	2		507	611	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26978214	26978214	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	65	359	0	ENST00000381527.3:c.1391A>G	p.Tyr464Cys	p.Y464C	ENST00000381527	NM_001260.1	464	tAc/tGc	13/13	1	2	FACETS	0.608	0.529	0.693	0.608	0.529	0.693	SUBCLONAL	1	TRUE	1	0.500906458731459	2		359	427	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046548	30046548	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763088813	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	125	562	1	ENST00000331968.5:c.2635C>T	p.Gln879Ter	p.Q879*	ENST00000331968	NM_002742.2	879	Cag/Tag	18/18	1	2	FACETS	0.821	0.745	0.9	0.821	0.745	0.9	CLONAL	1	TRUE	1	0.500906458731459	2		563	608	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647656	3647657	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs774532876	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	114	734	0	ENST00000294008.3:c.1406dup	p.Leu470IlefsTer8	p.L470Ifs*8	ENST00000294008	NM_032444.2	469	cca/ccCa	7/15	1	2	FACETS	0.575	0.517	0.635	0.575	0.517	0.635	SUBCLONAL	1	TRUE	1	0.500906458731459	2		734	792	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8113526	8113526	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs779961970	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	112	655	0	ENST00000585124.1:c.17A>G	p.Asn6Ser	p.N6S	ENST00000585124	NM_004217.3	6	aAc/aGc	2/9	1	2	FACETS	0.619	0.557	0.684	0.619	0.557	0.684	SUBCLONAL	1	TRUE	1	0.500906458731459	2		655	723	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553666	29553666	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	78	444	0	ENST00000356175.3:c.2215A>G	p.Met739Val	p.M739V	ENST00000356175	NM_000267.3	739	Atg/Gtg	18/57	1	2	FACETS	0.729	0.644	0.82	0.729	0.644	0.82	SUBCLONAL	1	TRUE	1	0.500906458731459	2		444	427	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41247864	41247865	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	rs80357537	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	69	362	0	ENST00000357654.3:c.668dup	p.Ala224GlyfsTer4	p.A224Gfs*4	ENST00000357654	NM_007294.3	223	aag/aaAg	9/23	1	2	FACETS	0.625	0.546	0.709	0.625	0.546	0.709	SUBCLONAL	1	TRUE	1	0.500906458731459	2		362	441	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007448	62007448	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	99	471	0	ENST00000392795.3:c.419A>C	p.Glu140Ala	p.E140A	ENST00000392795	NM_001039933.1	140	gAg/gCg	3/6	1	2	FACETS	0.689	0.616	0.765	0.689	0.616	0.765	SUBCLONAL	1	TRUE	1	0.500906458731459	2		471	574	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979284	40979284	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764919361	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	113	442	0	ENST00000373198.4:c.1849C>T	p.Arg617Trp	p.R617W	ENST00000373198	NM_133170.3	617	Cgg/Tgg	11/32	1	2	FACETS	0.716	0.646	0.79	0.716	0.646	0.79	SUBCLONAL	1	TRUE	1	0.500906458731459	2		442	630	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49724669	49724669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	65	315	0	ENST00000449682.2:c.520C>A	p.Pro174Thr	p.P174T	ENST00000449682	NM_020998.3	174	Cct/Act	5/18	1	2	FACETS	0.806	0.704	0.915	0.806	0.704	0.915	CLONAL	1	TRUE	1	0.500906458731459	2		315	322	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260187	149260187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374427935	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	115	458	0	ENST00000360632.3:c.706C>T	p.Arg236Trp	p.R236W	ENST00000360632	NM_015472.4	236	Cgg/Tgg	4/7	1	2	FACETS	0.82	0.741	0.903	0.82	0.741	0.903	CLONAL	1	TRUE	1	0.500906458731459	2		458	560	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622282	162622282	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	65	286	0	ENST00000366898.1:c.415G>C	p.Gly139Arg	p.G139R	ENST00000366898	NM_004562.2	139	Ggt/Cgt	4/12	1	2	FACETS	0.7	0.61	0.796	0.7	0.61	0.796	SUBCLONAL	1	TRUE	1	0.500906458731459	2		286	371	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993675	90993676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	41	303	0	ENST00000265433.3:c.247dup	p.Met83AsnfsTer23	p.M83Nfs*23	ENST00000265433	NM_002485.4	83	atg/aAtg	3/16	1	2	FACETS	0.54	0.452	0.638	0.54	0.452	0.638	SUBCLONAL	1	TRUE	1	0.500906458731459	2		303	303	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650082	93650082	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	122	521	0	ENST00000375746.1:c.1633A>G	p.Asn545Asp	p.N545D	ENST00000375746	NM_001174167.1	545	Aac/Gac	12/14	1	2	FACETS	0.812	0.736	0.891	0.812	0.736	0.891	CLONAL	1	TRUE	1	0.500906458731459	2		521	600	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393359	139393359	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs760123789	NA	P-0043940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	144	531	0	ENST00000277541.6:c.6172A>G	p.Asn2058Asp	p.N2058D	ENST00000277541	NM_017617.3	2058	Aac/Gac	33/34	1	2	FACETS	0.857	0.783	0.933	0.857	0.783	0.933	CLONAL	1	TRUE	1	0.500906458731459	2		531	671	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	116	414	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.935	0.849	1	0.935	0.849	1	CLONAL	1	TRUE	1	0.554993916099019	2		414	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0044007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	492	670	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.211885314855263	1	FACETS	1	0.996	1	1	0.996	1	INDETERMINATE	1	TRUE	0	0.554993916099019	1		670	916	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0044007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	9	242	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.540687501902907	1	FACETS	0.078	0.051	0.113	0.078	0.051	0.113	SUBCLONAL	1	TRUE	0	0.554993916099019	1		242	299	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0044007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	109	331	0	ENST00000304494.5:c.151-1G>A		p.X51_splice	ENST00000304494	NM_000077.4	51			0.554993916099019	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.554993916099019	1		331	261	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678559	88678559	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764882745	NA	P-0044007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	77	363	1	ENST00000360948.2:c.977G>A	p.Arg326His	p.R326H	ENST00000360948	NM_001012338.2	326	cGt/cAt	9/19	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.554993916099019	2		364	266	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938116	76938116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	66	512	0	ENST00000373344.5:c.2632G>A	p.Asp878Asn	p.D878N	ENST00000373344	NM_000489.3	878	Gat/Aat	9/35	1	2	FACETS	0.364	0.316	0.417	0.364	0.316	0.417	SUBCLONAL	1	TRUE	1	0.554993916099019	2		512	653	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	315	126	0				ENST00000310581	NM_198253.2	-/1132			0.275800001082499	7	FACETS	1	0.982	1			1	CLONAL	7	TRUE	NA	0.275800001082499	7		126	527	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799254	42799254	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	332	576	0	ENST00000575354.2:c.4738G>C	p.Glu1580Gln	p.E1580Q	ENST00000575354	NM_015125.3	1580	Gag/Cag	20/20	0.275800001082499	5	FACETS	1	0.956	1	0.806	0.765	0.847	CLONAL	4	TRUE	0	0.275800001082499	5		576	845	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200023	123200023	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0044014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	78	95	0	ENST00000218089.9:c.2097-2A>G		p.X699_splice	ENST00000218089	NM_001042749.1	699			0.275800001082499	2	FACETS	1	0.946	1			1	CLONAL	5	TRUE	NA	0.275800001082499	2		95	110	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438226	110438226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	10	84	0	ENST00000375856.3:c.175G>A	p.Glu59Lys	p.E59K	ENST00000375856	NM_003749.2	59	Gag/Aag	1/2	0.275800001082499	5	FACETS	0.717	0.487	1	0.239	0.162	0.335	CLONAL	1	TRUE	2	0.275800001082499	5		84	143	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857255	9857255	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	47	413	0	ENST00000330684.3:c.4146C>G	p.Cys1382Trp	p.C1382W	ENST00000330684	NM_001134407.1	1382	tgC/tgG	13/13	1	2	FACETS	0.727	0.614	0.851	0.727	0.614	0.851	SUBCLONAL	1	TRUE	1	0.275800001082499	2		413	469	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858905	89858905	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1449343629	NA	P-0044014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	26	478	1	ENST00000389301.3:c.1057C>A	p.Pro353Thr	p.P353T	ENST00000389301	NM_000135.2	353	Cct/Act	12/43	1	2	FACETS	0.405	0.32	0.503	0.405	0.32	0.503	SUBCLONAL	1	TRUE	1	0.275800001082499	2		479	465	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556298	29556298	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1314766383	NA	P-0044014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	30	384	0	ENST00000356175.3:c.2665A>G	p.Thr889Ala	p.T889A	ENST00000356175	NM_000267.3	889	Aca/Gca	21/57	0.221819078121205	2	FACETS	0.377	0.303	0.462	0.189	0.151	0.231	SUBCLONAL	1	TRUE	0	0.275800001082499	2		384	577	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474460	40474460	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	25	388	0	ENST00000264657.5:c.1941C>A	p.Asn647Lys	p.N647K	ENST00000264657	NM_139276.2	647	aaC/aaA	21/24	0.221819078121205	2	FACETS	0.413	0.325	0.515	0.206	0.162	0.258	SUBCLONAL	1	TRUE	0	0.275800001082499	2		388	439	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873160	136873160	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	56	304	0	ENST00000241393.3:c.338A>G	p.His113Arg	p.H113R	ENST00000241393	NM_003467.2	113	cAt/cGt	2/2	0.275800001082499	3	FACETS	1	0.95	1	0.414	0.356	0.477	CLONAL	1	TRUE	0	0.275800001082499	3		304	372	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747047	40747047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	43	427	1	ENST00000373198.4:c.3035G>A	p.Gly1012Asp	p.G1012D	ENST00000373198	NM_133170.3	1012	gGc/gAc	22/32	0.197740956057376	4	FACETS	0.786	0.658	0.929	0.393	0.329	0.465	CLONAL	1	TRUE	2	0.275800001082499	4		428	506	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55597510	55597510	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	20	325	0	ENST00000288135.5:c.2158G>A	p.Glu720Lys	p.E720K	ENST00000288135	NM_000222.2	720	Gag/Aag	15/21	1	2	FACETS	0.394	0.301	0.504	0.394	0.301	0.504	SUBCLONAL	1	TRUE	1	0.275800001082499	2		325	368	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295295	1295295	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0044014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	75	330	1				ENST00000310581	NM_198253.2	-/1132			0.275800001082499	7	FACETS	1	0.969	1			1	CLONAL	1	TRUE	NA	0.275800001082499	7		331	679	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287961	33287961	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	41	467	0	ENST00000374542.5:c.1292C>A	p.Ser431Tyr	p.S431Y	ENST00000374542	NM_001141970.1	431	tCc/tAc	5/8	0.275800001082499	3	FACETS	0.493	0.41	0.587	0.247	0.205	0.294	SUBCLONAL	1	TRUE	1	0.275800001082499	3		467	686	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755455	133755455	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	41	434	0	ENST00000318560.5:c.1424G>A	p.Cys475Tyr	p.C475Y	ENST00000318560	NM_005157.4	475	tGt/tAt	9/11	0.209850245418224	2	FACETS	0.649	0.541	0.77	0.325	0.27	0.385	SUBCLONAL	1	TRUE	0	0.275800001082499	2		434	458	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344087	70344087	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	181	358	0	ENST00000374080.3:c.1823T>A	p.Val608Asp	p.V608D	ENST00000374080		608	gTt/gAt	13/45	0.275800001082499	2	FACETS	0.848	0.788	0.909			1	CLONAL	3	TRUE	NA	0.275800001082499	2		358	516	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	207	414	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.221333128381065	4	FACETS	0.879	0.831	0.927	0.659	0.623	0.695	INDETERMINATE	3	TRUE	0	0.74748170613083	4		414	367	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0044037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	77	274	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	1	2	FACETS	0.821	0.735	0.909	0.821	0.735	0.909	CLONAL	1	TRUE	1	0.92	2		274	204	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0044083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	108	464	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.856	0.77	0.946	0.856	0.77	0.946	CLONAL	1	TRUE	1	0.445937681021347	2		464	566	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148930	119148930	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs387906664	NA	P-0044083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	11	393	1	ENST00000264033.4:c.1150T>C	p.Cys384Arg	p.C384R	ENST00000264033	NM_005188.3	384	Tgt/Cgt	8/16	1	2	FACETS	0.091	0.062	0.127	0.091	0.062	0.127	SUBCLONAL	1	TRUE	1	0.445937681021347	2		394	541	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475078	40475078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	144	541	0	ENST00000264657.5:c.1832G>A	p.Ser611Asn	p.S611N	ENST00000264657	NM_139276.2	611	aGt/aAt	20/24	1	2	FACETS	0.927	0.847	1	0.927	0.847	1	CLONAL	1	TRUE	1	0.445937681021347	2		541	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0044175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	271	535	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.74471436538825	2	FACETS	0.807	0.771	0.842	0.807	0.771	0.842	CLONAL	2	TRUE	0	0.779341184397728	2		535	431	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893668	28893668	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs374452662	NA	P-0044175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	39	292	0	ENST00000282397.4:c.3178C>T	p.Arg1060Ter	p.R1060*	ENST00000282397	NM_002019.4	1060	Cga/Tga	24/30	0.272254578263682	3	FACETS	0.638	0.533	0.752	0.319	0.266	0.376	INDETERMINATE	1	TRUE	1	0.779341184397728	3		292	218	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534444	140534444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1258111302	NA	P-0044175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	35	386	0	ENST00000288602.6:c.469G>A	p.Val157Ile	p.V157I	ENST00000288602	NM_004333.4	157	Gtt/Att	3/18	0.272254578263682	3	FACETS	0.77	0.64	0.912	0.385	0.32	0.456	INDETERMINATE	1	TRUE	1	0.779341184397728	3		386	162	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372202	55372202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764648837	NA	P-0044175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	108	302	0	ENST00000297316.4:c.892G>A	p.Gly298Ser	p.G298S	ENST00000297316	NM_022454.3	298	Ggc/Agc	2/2	0.262851384630103	4	FACETS	0.783	0.704	0.866	0.391	0.352	0.433	INDETERMINATE	1	TRUE	2	0.779341184397728	4		302	630	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919731	96919731	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1324266357	NA	P-0044175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	113	504	0	ENST00000258439.3:c.532T>C	p.Tyr178His	p.Y178H	ENST00000258439	NM_001193304.2	178	Tac/Cac	4/4	1	2	FACETS	0.603	0.545	0.663	0.603	0.545	0.663	SUBCLONAL	1	TRUE	1	0.779341184397728	2		504	481	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931907	68931907	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0044175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	82	381	0	ENST00000288368.4:c.336+1G>T		p.X112_splice	ENST00000288368	NM_024870.2	112			0.262851384630103	4	FACETS	1	0.942	1	1	0.942	1	INDETERMINATE	2	TRUE	2	0.779341184397728	4		381	177	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0044182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	108	441	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.503477755590672	2		441	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0044182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	226	887	0	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.503477755590672	1	FACETS	0.877	0.82	0.936	0.877	0.82	0.936	CLONAL	1	TRUE	0	0.503477755590672	1		887	766	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510160	149510160	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772355478	NA	P-0044182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	220	786	1	ENST00000261799.4:c.1309C>T	p.Arg437Cys	p.R437C	ENST00000261799	NM_002609.3	437	Cgt/Tgt	9/23	1	2	FACETS	0.907	0.845	0.972	0.907	0.845	0.972	CLONAL	1	TRUE	1	0.503477755590672	2		787	963	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0044182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	248	470	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.467566010494704	2	FACETS	0.928	0.877	0.979	0.928	0.877	0.979	CLONAL	2	TRUE	0	0.503477755590672	2		470	531	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229444	36229444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	146	548	2	ENST00000222270.7:c.8134C>T	p.Arg2712Trp	p.R2712W	ENST00000222270	NM_014727.1	2712	Cgg/Tgg	37/37	1	2	FACETS	0.975	0.893	1	0.975	0.893	1	CLONAL	1	TRUE	1	0.503477755590672	2		550	595	SUCCESS
APC	324	MSKCC	GRCh37	5	112178001	112178001	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1299714632	NA	P-0044182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	37	438	0	ENST00000257430.4:c.6710G>A	p.Arg2237Gln	p.R2237Q	ENST00000257430	NM_000038.5	2237	cGa/cAa	16/16	1	2	FACETS	0.273	0.224	0.327	0.273	0.224	0.327	SUBCLONAL	1	TRUE	1	0.503477755590672	2		438	539	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447433	12447433	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	167	634	0	ENST00000287820.6:c.672G>T	p.Glu224Asp	p.E224D	ENST00000287820	NM_015869.4	224	gaG/gaT	5/7	1	2	FACETS	0.857	0.789	0.928	0.857	0.789	0.928	CLONAL	1	TRUE	1	0.503477755590672	2		634	774	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362470	118362470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	83	298	0	ENST00000534358.1:c.4831G>A	p.Glu1611Lys	p.E1611K	ENST00000534358	NM_005933.3	1611	Gag/Aag	15/36	1	2	FACETS	0.778	0.69	0.871	0.778	0.69	0.871	SUBCLONAL	1	TRUE	1	0.503477755590672	2		298	424	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245567	46245567	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	98	369	0	ENST00000334344.6:c.3661C>T	p.Gln1221Ter	p.Q1221*	ENST00000334344	NM_152641.2	1221	Caa/Taa	15/21	1	2	FACETS	0.893	0.801	0.989	0.893	0.801	0.989	CLONAL	1	TRUE	1	0.503477755590672	2		369	436	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246008	46246008	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	92	382	0	ENST00000334344.6:c.4102G>A	p.Asp1368Asn	p.D1368N	ENST00000334344	NM_152641.2	1368	Gat/Aat	15/21	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.503477755590672	2		382	363	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632726	23632726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	122	537	0	ENST00000261584.4:c.3070G>A	p.Glu1024Lys	p.E1024K	ENST00000261584	NM_024675.3	1024	Gaa/Aaa	10/13	1	2	FACETS	0.873	0.792	0.958	0.873	0.792	0.958	CLONAL	1	TRUE	1	0.503477755590672	2		537	555	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845621	68845621	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	183	679	0	ENST00000261769.5:c.868del	p.Asp290ThrfsTer4	p.D290Tfs*4	ENST00000261769	NM_004360.3	289	gcG/gc	7/16	0.503477755590672	1	FACETS	0.875	0.811	0.94	0.875	0.811	0.94	CLONAL	1	TRUE	0	0.503477755590672	1		679	622	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72863759	72863759	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0044182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	132	459	0	ENST00000268489.5:c.3449-1G>A		p.X1150_splice	ENST00000268489	NM_006885.3	1150			0.503477755590672	1	FACETS	0.981	0.899	1	0.981	0.899	1	CLONAL	1	TRUE	0	0.503477755590672	1		459	400	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5216734	5216734	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	138	509	0	ENST00000357368.4:c.4093G>C	p.Glu1365Gln	p.E1365Q	ENST00000357368	NM_002850.3	1365	Gaa/Caa	26/38	1	2	FACETS	0.839	0.766	0.916	0.839	0.766	0.916	CLONAL	1	TRUE	1	0.503477755590672	2		509	653	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22143055	22143055	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	139	463	0	ENST00000215832.6:c.652C>G	p.Leu218Val	p.L218V	ENST00000215832	NM_002745.4	218	Ctg/Gtg	5/9	1	2	FACETS	0.934	0.854	1	0.934	0.854	1	CLONAL	1	TRUE	1	0.503477755590672	2		463	591	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191535	10191535	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	125	568	0	ENST00000256474.2:c.528G>C	p.Arg176Ser	p.R176S	ENST00000256474	NM_000551.3	176	agG/agC	3/3	1	2	FACETS	0.74	0.671	0.812	0.74	0.671	0.812	SUBCLONAL	1	TRUE	1	0.503477755590672	2		568	671	SUCCESS
ATR	545	MSKCC	GRCh37	3	142168353	142168353	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	108	431	0	ENST00000350721.4:c.7853G>C	p.Gly2618Ala	p.G2618A	ENST00000350721	NM_001184.3	2618	gGa/gCa	47/47	1	2	FACETS	0.892	0.805	0.983	0.892	0.805	0.983	CLONAL	1	TRUE	1	0.503477755590672	2		431	481	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749533	41749533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1402111533	NA	P-0044182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	159	617	1	ENST00000226382.2:c.262G>A	p.Asp88Asn	p.D88N	ENST00000226382	NM_003924.3	88	Gac/Aac	2/3	1	2	FACETS	0.898	0.826	0.974	0.898	0.826	0.974	CLONAL	1	TRUE	1	0.503477755590672	2		618	703	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394992	394992	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	116	548	0	ENST00000380956.4:c.388G>C	p.Glu130Gln	p.E130Q	ENST00000380956	NM_001195286.1	130	Gag/Cag	3/9	1	2	FACETS	0.803	0.726	0.884	0.803	0.726	0.884	CLONAL	1	TRUE	1	0.503477755590672	2		548	574	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864720	68864720	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	114	493	0	ENST00000288368.4:c.91C>G	p.Leu31Val	p.L31V	ENST00000288368	NM_024870.2	31	Ctc/Gtc	1/40	0.503477755590672	1	FACETS	0.654	0.591	0.72	0.654	0.591	0.72	SUBCLONAL	1	TRUE	0	0.503477755590672	1		493	518	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	119	877	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.67	0.604	0.741	0.67	0.604	0.741	SUBCLONAL	1	FALSE	1	0.360874233332273	2		883	984	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	128	627	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.75	0.679	0.825	0.75	0.679	0.825	SUBCLONAL	1	FALSE	1	0.360874233332273	2		633	946	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1387	104	1121	2	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.387	0.344	0.432	0.387	0.344	0.432	SUBCLONAL	1	FALSE	1	0.360874233332273	2		1123	1491	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	134	685	5	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.978	0.89	1	0.978	0.89	1	CLONAL	1	FALSE	1	0.360874233332273	2		690	759	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992721	68992721	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs764112302	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	58	594	3	ENST00000288368.4:c.1693del	p.Ser565ArgfsTer10	p.S565Rfs*10	ENST00000288368	NM_024870.2	562	cgT/cg	16/40	NA	2	FACETS	0.416	0.357	0.482			1	INDETERMINATE	1	FALSE	NA	0.360874233332273	2		597	772	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	28	392	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.3	0.239	0.369	0.3	0.239	0.369	SUBCLONAL	1	FALSE	1	0.360874233332273	2		392	518	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	30	336	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.405	0.326	0.494	0.405	0.326	0.494	SUBCLONAL	1	FALSE	1	0.360874233332273	2		336	411	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	18	689	1	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.117	0.087	0.152	0.117	0.087	0.152	SUBCLONAL	1	FALSE	1	0.360874233332273	2		690	856	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	53	683	1	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	NA	2	FACETS	0.344	0.292	0.401			1	INDETERMINATE	1	FALSE	NA	0.360874233332273	2		684	854	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649922	88649922	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786201038	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	52	504	0	ENST00000372037.3:c.176del	p.Leu59Ter	p.L59*	ENST00000372037	NM_004329.2	57	ccT/cc	4/13	1	2	FACETS	0.393	0.333	0.458	0.393	0.333	0.458	SUBCLONAL	1	FALSE	1	0.360874233332273	2		504	734	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	119	347	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.360874233332273	2	FACETS	1	0.985	1	0.726	0.66	0.795	CLONAL	1	FALSE	0	0.360874233332273	2		347	454	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692981	89692982	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	60	483	0	ENST00000371953.3:c.469dup	p.Glu157GlyfsTer23	p.E157Gfs*23	ENST00000371953	NM_000314.4	155	-/G	5/9	1	2	FACETS	0.523	0.45	0.602	0.523	0.45	0.602	SUBCLONAL	1	FALSE	1	0.360874233332273	2		483	636	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	55	746	0	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	0.3	0.256	0.349	0.3	0.256	0.349	SUBCLONAL	1	FALSE	1	0.360874233332273	2		746	1015	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	30	470	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	0.287	0.23	0.352	0.287	0.23	0.352	SUBCLONAL	1	FALSE	1	0.360874233332273	2		470	579	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518112	8518112	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs533774328	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	36	467	1	ENST00000356435.5:c.1279C>T	p.Arg427Ter	p.R427*	ENST00000356435		427	Cga/Tga	10/35	1	2	FACETS	0.358	0.293	0.43	0.358	0.293	0.43	SUBCLONAL	1	FALSE	1	0.360874233332273	2		468	558	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053023	180053023	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	121	903	2	ENST00000261937.6:c.1267del	p.Gln423ArgfsTer70	p.Q423Rfs*70	ENST00000261937	NM_182925.4	423	Cag/ag	10/30	1	2	FACETS	0.583	0.525	0.644	0.583	0.525	0.644	SUBCLONAL	1	FALSE	1	0.360874233332273	2		905	1151	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932492	39932492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	125	858	2	ENST00000378444.4:c.2107C>T	p.Pro703Ser	p.P703S	ENST00000378444	NM_001123385.1	703	Ccc/Tcc	4/15	NA	2	FACETS	0.603	0.544	0.665			1	INDETERMINATE	1	FALSE	NA	0.360874233332273	2		860	1149	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488225	56488225	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	53	609	1	ENST00000267101.3:c.1744G>T	p.Gly582Trp	p.G582W	ENST00000267101	NM_001982.3	582	Ggg/Tgg	15/28	1	2	FACETS	0.336	0.285	0.392	0.336	0.285	0.392	SUBCLONAL	1	FALSE	1	0.360874233332273	2		610	874	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661945	29661945	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854552	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	47	494	1	ENST00000356175.3:c.5839C>T	p.Arg1947Ter	p.R1947*	ENST00000356175	NM_000267.3	1947	Cga/Tga	39/57	1	2	FACETS	0.408	0.344	0.48	0.408	0.344	0.48	SUBCLONAL	1	FALSE	1	0.360874233332273	2		495	638	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905873	50905873	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756829126	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	94	887	0	ENST00000440232.2:c.845C>T	p.Thr282Met	p.T282M	ENST00000440232	NM_002691.3	282	aCg/aTg	8/27	1	2	FACETS	0.449	0.398	0.504	0.449	0.398	0.504	SUBCLONAL	1	FALSE	1	0.360874233332273	2		887	1160	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs770248150	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	13	397	0	ENST00000311936.3:c.351A>T	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaT	4/5	1	2	FACETS	0.143	0.101	0.194	0.143	0.101	0.194	SUBCLONAL	1	FALSE	1	0.360874233332273	2		397	505	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142885	30142885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766999851	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	65	854	3	ENST00000389048.3:c.641G>A	p.Arg214His	p.R214H	ENST00000389048	NM_004304.4	214	cGc/cAc	1/29	NA	2	FACETS	0.366	0.316	0.421			1	INDETERMINATE	1	FALSE	NA	0.360874233332273	2		857	983	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268793	98268793	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1554708751	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	53	591	1	ENST00000331920.6:c.290del	p.Asn97ThrfsTer20	p.N97Tfs*20	ENST00000331920	NM_000264.3	97	aAc/ac	2/24	1	2	FACETS	0.385	0.327	0.448	0.385	0.327	0.448	SUBCLONAL	1	FALSE	1	0.360874233332273	2		592	763	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099080	157099080	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	18	137	0	ENST00000346085.5:c.17G>C	p.Gly6Ala	p.G6A	ENST00000346085	NM_020732.3	6	gGc/gCc	1/20	1	2	FACETS	0.46	0.347	0.592	0.46	0.347	0.592	SUBCLONAL	1	FALSE	1	0.360874233332273	2		137	217	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250046	53250047	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs782600511	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	92	654	0	ENST00000375401.3:c.202dup	p.Arg68ProfsTer7	p.R68Pfs*7	ENST00000375401	NM_004187.3	68	cga/cCga	2/26	NA	2	FACETS	0.549	0.487	0.615			1	INDETERMINATE	1	FALSE	NA	0.360874233332273	2		654	929	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366129	15366129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1468704458	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	48	547	1	ENST00000263377.2:c.2026C>T	p.Arg676Trp	p.R676W	ENST00000263377	NM_058243.2	676	Cgg/Tgg	10/20	1	2	FACETS	0.354	0.298	0.416	0.354	0.298	0.416	SUBCLONAL	1	FALSE	1	0.360874233332273	2		548	751	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212182	98212182	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371346118	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	36	398	0	ENST00000331920.6:c.3490G>A	p.Val1164Ile	p.V1164I	ENST00000331920	NM_000264.3	1164	Gtt/Att	21/24	1	2	FACETS	0.374	0.306	0.449	0.374	0.306	0.449	SUBCLONAL	1	FALSE	1	0.360874233332273	2		398	534	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342743	87342743	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	41	497	0	ENST00000277120.3:c.1028A>G	p.His343Arg	p.H343R	ENST00000277120		343	cAc/cGc	9/19	1	2	FACETS	0.359	0.298	0.427	0.359	0.298	0.427	SUBCLONAL	1	FALSE	1	0.360874233332273	2		497	633	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572555	95572555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	22	227	0	ENST00000393063.1:c.2810G>A	p.Arg937His	p.R937H	ENST00000393063	NM_030621.3	937	cGc/cAc	19/28	1	2	FACETS	0.398	0.309	0.502	0.398	0.309	0.502	SUBCLONAL	1	FALSE	1	0.360874233332273	2		227	306	SUCCESS
AR	367	MSKCC	GRCh37	X	66937403	66937403	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886039558	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	52	650	0	ENST00000374690.3:c.2257C>T	p.Arg753Ter	p.R753*	ENST00000374690	NM_000044.3	753	Cga/Tga	5/8	0.3566149034245	1	FACETS	0.296	0.251	0.346	0.296	0.251	0.346	SUBCLONAL	1	FALSE	0	0.360874233332273	1		650	797	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025857	48025857	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs267608041	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	44	355	0	ENST00000234420.5:c.741del	p.Lys247AsnfsTer32	p.K247Nfs*32	ENST00000234420	NM_000179.2	245	atA/at	4/10	1	2	FACETS	0.544	0.457	0.641	0.544	0.457	0.641	SUBCLONAL	1	FALSE	1	0.360874233332273	2		355	448	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131403	17131403	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs758385503	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	66	783	0	ENST00000285071.4:c.49del	p.Arg17AlafsTer38	p.R17Afs*38	ENST00000285071	NM_144997.5	17	Cgc/gc	4/14	1	2	FACETS	0.406	0.351	0.465	0.406	0.351	0.465	SUBCLONAL	1	FALSE	1	0.360874233332273	2		783	902	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661917	29661917	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	40	488	0	ENST00000356175.3:c.5815del	p.Cys1939AlafsTer19	p.C1939Afs*19	ENST00000356175	NM_000267.3	1937	cgT/cg	39/57	1	2	FACETS	0.348	0.288	0.415	0.348	0.288	0.415	SUBCLONAL	1	FALSE	1	0.360874233332273	2		488	637	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11172947	11172947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759011563	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	49	515	1	ENST00000361445.4:c.7328G>A	p.Arg2443Gln	p.R2443Q	ENST00000361445	NM_004958.3	2443	cGa/cAa	54/58	1	2	FACETS	0.34	0.287	0.399	0.34	0.287	0.399	SUBCLONAL	1	FALSE	1	0.360874233332273	2		516	799	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231449	5231449	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	61	892	1	ENST00000357368.4:c.2027del	p.Pro676ArgfsTer134	p.P676Rfs*134	ENST00000357368	NM_002850.3	676	cCg/cg	14/38	1	2	FACETS	0.313	0.269	0.361	0.313	0.269	0.361	SUBCLONAL	1	FALSE	1	0.360874233332273	2		893	1081	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845190	151845190	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764910946	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	49	558	0	ENST00000262189.6:c.13822C>T	p.Arg4608Cys	p.R4608C	ENST00000262189	NM_170606.2	4608	Cgc/Tgc	52/59	1	2	FACETS	0.365	0.309	0.428	0.365	0.309	0.428	SUBCLONAL	1	FALSE	1	0.360874233332273	2		558	743	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395216	139395216	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	76	970	0	ENST00000277541.6:c.5722G>A	p.Ala1908Thr	p.A1908T	ENST00000277541	NM_017617.3	1908	Gcc/Acc	31/34	1	2	FACETS	0.345	0.301	0.392	0.345	0.301	0.392	SUBCLONAL	1	FALSE	1	0.360874233332273	2		970	1221	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832793	3832793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	63	598	0	ENST00000262367.5:c.1465G>A	p.Gly489Arg	p.G489R	ENST00000262367	NM_004380.2	489	Gga/Aga	6/31	1	2	FACETS	0.447	0.386	0.514	0.447	0.386	0.514	SUBCLONAL	1	FALSE	1	0.360874233332273	2		598	781	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100171	27100171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778051	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	47	583	0	ENST00000324856.7:c.3967C>T	p.Arg1323Cys	p.R1323C	ENST00000324856	NM_006015.4	1323	Cgc/Tgc	16/20	1	2	FACETS	0.324	0.272	0.381	0.324	0.272	0.381	SUBCLONAL	1	FALSE	1	0.360874233332273	2		583	805	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127670	64127670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1181	93	975	1	ENST00000334205.4:c.163G>A	p.Gly55Arg	p.G55R	ENST00000334205	NM_003942.2	55	Ggg/Agg	3/17	1	2	FACETS	0.405	0.358	0.454	0.405	0.358	0.454	SUBCLONAL	1	FALSE	1	0.360874233332273	2		976	1274	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257665	16257665	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	74	536	0	ENST00000375759.3:c.4930G>A	p.Val1644Ile	p.V1644I	ENST00000375759	NM_015001.2	1644	Gtc/Atc	11/15	1	2	FACETS	0.496	0.433	0.564	0.496	0.433	0.564	SUBCLONAL	1	FALSE	1	0.360874233332273	2		536	827	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812526	43812526	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	66	626	0	ENST00000372470.3:c.1229G>T	p.Trp410Leu	p.W410L	ENST00000372470	NM_005373.2	410	tGg/tTg	8/12	1	2	FACETS	0.413	0.357	0.473	0.413	0.357	0.473	SUBCLONAL	1	FALSE	1	0.360874233332273	2		626	886	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333092	70333092	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	66	759	0	ENST00000373644.4:c.997G>T	p.Gly333Cys	p.G333C	ENST00000373644	NM_030625.2	333	Ggc/Tgc	2/12	1	2	FACETS	0.372	0.321	0.427	0.372	0.321	0.427	SUBCLONAL	1	FALSE	1	0.360874233332273	2		759	984	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903715	114903715	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	59	625	0	ENST00000543371.1:c.722del	p.Pro241ArgfsTer10	p.P241Rfs*10	ENST00000543371	NM_001198531.1	240	tCc/tc	7/14	1	2	FACETS	0.37	0.317	0.428	0.37	0.317	0.428	SUBCLONAL	1	FALSE	1	0.360874233332273	2		625	883	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77043827	77043827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752626713	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	83	727	2	ENST00000356341.3:c.1499G>A	p.Arg500His	p.R500H	ENST00000356341	NM_002576.4	500	cGc/cAc	14/15	1	2	FACETS	0.484	0.426	0.547	0.484	0.426	0.547	SUBCLONAL	1	FALSE	1	0.360874233332273	2		729	950	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981819	101981820	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	88	811	0	ENST00000282441.5:c.244dup	p.Gln82ProfsTer30	p.Q82Pfs*30	ENST00000282441	NM_001130145.2	80	-/C	1/9	1	2	FACETS	0.453	0.4	0.51	0.453	0.4	0.51	SUBCLONAL	1	FALSE	1	0.360874233332273	2		811	1076	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856145	111856145	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	65	398	0	ENST00000341259.2:c.196C>T	p.Gln66Ter	p.Q66*	ENST00000341259	NM_005475.2	66	Cag/Tag	2/8	1	2	FACETS	0.639	0.554	0.73	0.639	0.554	0.73	SUBCLONAL	1	FALSE	1	0.360874233332273	2		398	564	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219169	133219169	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	58	806	0	ENST00000320574.5:c.4875G>T	p.Gln1625His	p.Q1625H	ENST00000320574	NM_006231.2	1625	caG/caT	37/49	1	2	FACETS	0.291	0.248	0.337	0.291	0.248	0.337	SUBCLONAL	1	FALSE	1	0.360874233332273	2		806	1106	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597587	28597588	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	48	506	1	ENST00000241453.7:c.2317dup	p.Arg773LysfsTer14	p.R773Kfs*14	ENST00000241453	NM_004119.2	773	agg/aAgg	19/24	1	2	FACETS	0.35	0.295	0.412	0.35	0.295	0.412	SUBCLONAL	1	FALSE	1	0.360874233332273	2		507	759	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911213	32911213	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	40	512	0	ENST00000380152.3:c.2721G>T	p.Lys907Asn	p.K907N	ENST00000380152		907	aaG/aaT	11/27	1	2	FACETS	0.309	0.256	0.369	0.309	0.256	0.369	SUBCLONAL	1	FALSE	1	0.360874233332273	2		512	717	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823897	3823897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1273214954	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	57	805	1	ENST00000262367.5:c.2318C>T	p.Pro773Leu	p.P773L	ENST00000262367	NM_004380.2	773	cCg/cTg	13/31	1	2	FACETS	0.287	0.245	0.334	0.287	0.245	0.334	SUBCLONAL	1	FALSE	1	0.360874233332273	2		806	1099	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274130	10274130	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	64	708	1	ENST00000330684.3:c.139A>T	p.Thr47Ser	p.T47S	ENST00000330684	NM_001134407.1	47	Aca/Tca	2/13	1	2	FACETS	0.416	0.359	0.478	0.416	0.359	0.478	SUBCLONAL	1	FALSE	1	0.360874233332273	2		709	852	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663346	67663346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771793540	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	54	391	0	ENST00000264010.4:c.1747G>A	p.Val583Ile	p.V583I	ENST00000264010	NM_006565.3	583	Gta/Ata	10/12	1	2	FACETS	0.441	0.376	0.513	0.441	0.376	0.513	SUBCLONAL	1	FALSE	1	0.360874233332273	2		391	678	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89865609	89865609	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	52	569	1	ENST00000389301.3:c.858G>T	p.Gln286His	p.Q286H	ENST00000389301	NM_000135.2	286	caG/caT	10/43	1	2	FACETS	0.364	0.309	0.425	0.364	0.309	0.425	SUBCLONAL	1	FALSE	1	0.360874233332273	2		570	791	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131295	17131295	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	87	967	1	ENST00000285071.4:c.157C>T	p.Gln53Ter	p.Q53*	ENST00000285071	NM_144997.5	53	Cag/Tag	4/14	1	2	FACETS	0.404	0.356	0.455	0.404	0.356	0.455	SUBCLONAL	1	FALSE	1	0.360874233332273	2		968	1194	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368295	45368295	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	30	388	0	ENST00000262160.6:c.1307G>A	p.Cys436Tyr	p.C436Y	ENST00000262160	NM_005901.5	436	tGc/tAc	11/11	1	2	FACETS	0.291	0.233	0.356	0.291	0.233	0.356	SUBCLONAL	1	FALSE	1	0.360874233332273	2		388	572	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288832	15288832	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	12	166	1	ENST00000263388.2:c.3907C>A	p.Pro1303Thr	p.P1303T	ENST00000263388	NM_000435.2	1303	Cca/Aca	24/33	1	2	FACETS	0.288	0.202	0.394	0.288	0.202	0.394	SUBCLONAL	1	FALSE	1	0.360874233332273	2		167	231	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942172	17942172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1462715334	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	83	706	1	ENST00000458235.1:c.2843G>A	p.Arg948His	p.R948H	ENST00000458235	NM_000215.3	948	cGc/cAc	21/24	1	2	FACETS	0.47	0.414	0.531	0.47	0.414	0.531	SUBCLONAL	1	FALSE	1	0.360874233332273	2		707	978	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799228	42799228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	62	781	0	ENST00000575354.2:c.4712C>T	p.Ala1571Val	p.A1571V	ENST00000575354	NM_015125.3	1571	gCt/gTt	20/20	1	2	FACETS	0.347	0.298	0.4	0.347	0.298	0.4	SUBCLONAL	1	FALSE	1	0.360874233332273	2		781	991	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467074	25467074	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	62	854	0	ENST00000264709.3:c.1801T>G	p.Trp601Gly	p.W601G	ENST00000264709	NM_175629.2	601	Tgg/Ggg	15/23	1	2	FACETS	0.35	0.301	0.403	0.35	0.301	0.403	SUBCLONAL	1	FALSE	1	0.360874233332273	2		854	982	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965820	25965820	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	57	757	0	ENST00000435504.4:c.3386C>T	p.Ser1129Phe	p.S1129F	ENST00000435504		1129	tCt/tTt	13/13	1	2	FACETS	0.348	0.297	0.403	0.348	0.297	0.403	SUBCLONAL	1	FALSE	1	0.360874233332273	2		757	909	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543642	29543642	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	65	739	0	ENST00000389048.3:c.1521G>T	p.Lys507Asn	p.K507N	ENST00000389048	NM_004304.4	507	aaG/aaT	7/29	NA	2	FACETS	0.418	0.361	0.48			1	INDETERMINATE	1	FALSE	NA	0.360874233332273	2		739	862	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018201	48018202	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1057524912	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	76	644	0	ENST00000234420.5:c.402dup	p.Asp135Ter	p.D135*	ENST00000234420	NM_000179.2	132	-/T	2/10	1	2	FACETS	0.459	0.402	0.522	0.459	0.402	0.522	SUBCLONAL	1	FALSE	1	0.360874233332273	2		644	917	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190708718	190708718	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	59	397	0	ENST00000441310.2:c.611C>T	p.Ser204Leu	p.S204L	ENST00000441310	NM_000534.4	204	tCa/tTa	6/13	1	2	FACETS	0.616	0.53	0.709	0.616	0.53	0.709	SUBCLONAL	1	FALSE	1	0.360874233332273	2		397	531	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022640	31022640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868859861	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	58	701	0	ENST00000375687.4:c.2125G>A	p.Ala709Thr	p.A709T	ENST00000375687	NM_015338.5	709	Gcc/Acc	13/13	1	2	FACETS	0.352	0.302	0.408	0.352	0.302	0.408	SUBCLONAL	1	FALSE	1	0.360874233332273	2		701	912	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs749415085	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	28	386	0	ENST00000263967.3:c.112C>A	p.Arg38Ser	p.R38S	ENST00000263967	NM_006218.2	38	Cgt/Agt	2/21	1	2	FACETS	0.364	0.291	0.448	0.364	0.291	0.448	SUBCLONAL	1	FALSE	1	0.360874233332273	2		386	426	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1800992	1800992	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1236	80	1059	0	ENST00000260795.2:c.121C>A	p.Pro41Thr	p.P41T	ENST00000260795		41	Cca/Aca	2/17	1	2	FACETS	0.337	0.295	0.382	0.337	0.295	0.382	SUBCLONAL	1	FALSE	1	0.360874233332273	2		1059	1316	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1936967	1936967	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146509878	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	60	565	1	ENST00000382891.5:c.1652C>T	p.Thr551Met	p.T551M	ENST00000382891	NM_133335.3	551	aCg/aTg	7/22	1	2	FACETS	0.399	0.343	0.461	0.399	0.343	0.461	SUBCLONAL	1	FALSE	1	0.360874233332273	2		566	833	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946146	55946146	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	37	361	0	ENST00000263923.4:c.4033C>A	p.Pro1345Thr	p.P1345T	ENST00000263923	NM_002253.2	1345	Cct/Act	30/30	NA	2	FACETS	0.401	0.33	0.48			1	INDETERMINATE	1	FALSE	NA	0.360874233332273	2		361	512	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628392	187628392	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	79	753	0	ENST00000441802.2:c.2590G>C	p.Asp864His	p.D864H	ENST00000441802	NM_005245.3	864	Gac/Cac	2/27	1	2	FACETS	0.448	0.393	0.508	0.448	0.393	0.508	SUBCLONAL	1	FALSE	1	0.360874233332273	2		753	977	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235429	235429	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	66	767	1	ENST00000264932.6:c.1235G>T	p.Gly412Val	p.G412V	ENST00000264932	NM_004168.2	412	gGc/gTc	9/15	1	2	FACETS	0.42	0.364	0.482	0.42	0.364	0.482	SUBCLONAL	1	FALSE	1	0.360874233332273	2		768	870	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046672	180046672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	109	947	0	ENST00000261937.6:c.2640G>A	p.Met880Ile	p.M880I	ENST00000261937	NM_182925.4	880	atG/atA	18/30	1	2	FACETS	0.5	0.447	0.556	0.5	0.447	0.556	SUBCLONAL	1	FALSE	1	0.360874233332273	2		947	1209	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435839	116435839	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1390590380	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	62	651	0	ENST00000397752.3:c.3929A>G	p.Asp1310Gly	p.D1310G	ENST00000397752	NM_000245.2	1310	gAc/gGc	20/21	1	2	FACETS	0.376	0.324	0.434	0.376	0.324	0.434	SUBCLONAL	1	FALSE	1	0.360874233332273	2		651	913	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760613	133760613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1320	86	1078	1	ENST00000318560.5:c.2936C>T	p.Ala979Val	p.A979V	ENST00000318560	NM_005157.4	979	gCc/gTc	11/11	1	2	FACETS	0.339	0.298	0.383	0.339	0.298	0.383	SUBCLONAL	1	FALSE	1	0.360874233332273	2		1079	1406	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413157	139413157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1384	78	1006	0	ENST00000277541.6:c.985G>A	p.Gly329Ser	p.G329S	ENST00000277541	NM_017617.3	329	Ggt/Agt	6/34	1	2	FACETS	0.296	0.258	0.336	0.296	0.258	0.336	SUBCLONAL	1	FALSE	1	0.360874233332273	2		1006	1462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0044185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	451	775	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.679443776513781	3	FACETS	0.977	0.948	1	0.977	0.948	1	CLONAL	3	FALSE	0	0.679443776513781	3		775	607	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533309	29533309	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs752789273	NA	P-0044185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	29	289	1	ENST00000356175.3:c.1312G>T	p.Glu438Ter	p.E438*	ENST00000356175	NM_000267.3	438	Gaa/Taa	12/57	0.650556084924685	4	FACETS	0.549	0.442	0.67	0.137	0.11	0.168	SUBCLONAL	1	FALSE	0	0.679443776513781	4		290	261	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472633	88472633	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	21	424	0	ENST00000360948.2:c.1922A>G	p.Asp641Gly	p.D641G	ENST00000360948	NM_001012338.2	641	gAt/gGt	16/19	0.374435903846796	5	FACETS	0.443	0.341	0.561	0.148	0.113	0.187	INDETERMINATE	1	FALSE	2	0.679443776513781	5		424	282	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934267	81934267	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	66	788	0	ENST00000359376.3:c.1244G>T	p.Arg415Leu	p.R415L	ENST00000359376	NM_002661.3	415	cGt/cTt	14/33	0.589176357432064	3	FACETS	0.549	0.478	0.626	0.183	0.159	0.209	SUBCLONAL	1	FALSE	0	0.679443776513781	3		788	474	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979982	7979982	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	215	777	0	ENST00000319144.4:c.1355C>G	p.Ser452Cys	p.S452C	ENST00000319144	NM_001139.2	452	tCt/tGt	10/15	0.679443776513781	3	FACETS	0.757	0.709	0.806	0.505	0.473	0.537	SUBCLONAL	2	FALSE	0	0.679443776513781	3		777	560	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534329	63534329	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	98	817	0	ENST00000307078.5:c.1192A>C	p.Ile398Leu	p.I398L	ENST00000307078	NM_004655.3	398	Atc/Ctc	5/11	0.650556084924685	4	FACETS	0.598	0.533	0.667	0.15	0.133	0.167	SUBCLONAL	1	FALSE	0	0.679443776513781	4		817	810	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637984	39637984	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	125	633	0	ENST00000262039.4:c.2401C>A	p.Gln801Lys	p.Q801K	ENST00000262039	NM_002647.2	801	Cag/Aag	22/25	0.679443776513781	7	FACETS	1	0.982	1	0.273	0.247	0.3	CLONAL	1	FALSE	2	0.679443776513781	7		633	727	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048862	180048862	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	196	1065	0	ENST00000261937.6:c.1700A>T	p.Glu567Val	p.E567V	ENST00000261937	NM_182925.4	567	gAg/gTg	13/30	0.635764622250084	4	FACETS	1	0.973	1	0.368	0.341	0.397	CLONAL	1	FALSE	1	0.679443776513781	4		1065	877	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	37	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.183916642138538	2		126	336	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931862	68931862	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200600940	NA	P-0044195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	39	584	0	ENST00000288368.4:c.292G>A	p.Glu98Lys	p.E98K	ENST00000288368	NM_024870.2	98	Gaa/Aaa	3/40	1	2	FACETS	0.938	0.778	1	0.938	0.778	1	CLONAL	1	TRUE	1	0.183916642138538	2		584	452	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693006	89693006	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	A	A	T	rs1554898237	NA	P-0044195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	35	384	0	ENST00000371953.3:c.490A>T	p.Lys164Ter	p.K164*	ENST00000371953	NM_000314.4	164	Aag/Tag	5/9	1	2	FACETS	0.78	0.643	0.931	1	0.952	1	CLONAL	2	TRUE	1	0.183916642138538	2		384	244	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162645	47162645	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	26	336	0	ENST00000409792.3:c.3481del	p.Ser1161LeufsTer16	p.S1161Lfs*16	ENST00000409792	NM_014159.6	1161	Tct/ct	3/21	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.183916642138538	2		336	228	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613184	52613184	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	67	560	0	ENST00000394830.3:c.3344del	p.Asn1115MetfsTer19	p.N1115Mfs*19	ENST00000394830	NM_018313.4	1115	aAt/at	22/30	1	2	FACETS	0.772	0.672	0.879	1	0.974	1	SUBCLONAL	2	TRUE	1	0.183916642138538	2		560	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0044199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	238	701	1	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.23777576179822	3	FACETS	0.986	0.924	1	0.986	0.924	1	CLONAL	3	TRUE	0	0.246974258092722	3		702	732	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971151	55971151	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	42	501	0	ENST00000263923.4:c.1646G>A	p.Arg549Lys	p.R549K	ENST00000263923	NM_002253.2	549	aGg/aAg	13/30	0.246974258092722	3	FACETS	0.685	0.571	0.811	0.342	0.285	0.406	SUBCLONAL	1	TRUE	1	0.246974258092722	3		501	558	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046378	69046378	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375506738	NA	P-0044199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	90	580	0	ENST00000288368.4:c.3851C>T	p.Ala1284Val	p.A1284V	ENST00000288368	NM_024870.2	1284	gCg/gTg	32/40	0.154020148828689	4	FACETS	1	0.969	1	0.422	0.374	0.473	CLONAL	1	TRUE	1	0.246974258092722	4		580	718	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522616	157522616	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs375949587	NA	P-0044199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	103	575	0	ENST00000346085.5:c.4888G>C	p.Asp1630His	p.D1630H	ENST00000346085	NM_020732.3	1630	Gat/Cat	18/20	0.246974258092722	3	FACETS	1	0.963	1	0.39	0.349	0.435	CLONAL	1	TRUE	0	0.246974258092722	3		575	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0044208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	369	773	2	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.381734701015945	2	FACETS	0.933	0.888	0.98	0.933	0.888	0.98	CLONAL	2	TRUE	0	0.391406701167149	2		775	1010	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864914	117864914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	137	277	0	ENST00000297338.2:c.1195G>A	p.Glu399Lys	p.E399K	ENST00000297338	NM_006265.2	399	Gaa/Aaa	10/14	0.391406701167149	4	FACETS	0.912	0.834	0.993	0.912	0.834	0.993	CLONAL	2	TRUE	2	0.391406701167149	4		277	534	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0044219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	71	522	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.278631800112334	4	FACETS	1	0.943	1	1	0.943	1	CLONAL	3	TRUE	1	0.278631800112334	4		522	198	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460504	8460504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148300682	NA	P-0044219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	56	471	1	ENST00000356435.5:c.3782C>T	p.Thr1261Met	p.T1261M	ENST00000356435		1261	aCg/aTg	22/35	0.278631800112334	1	FACETS	0.901	0.775	1	0.901	0.775	1	CLONAL	1	TRUE	0	0.278631800112334	1		472	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0044219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	120	619	0	ENST00000269305.4:c.97-1G>A		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.278631800112334	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.278631800112334	2		619	387	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188404	32188404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763926116	NA	P-0044219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	52	542	0	ENST00000375023.3:c.937G>A	p.Glu313Lys	p.E313K	ENST00000375023	NM_004557.3	313	Gaa/Aaa	6/30	0.278631800112334	3	FACETS	1	0.866	1	0.507	0.433	0.589	CLONAL	1	TRUE	1	0.278631800112334	3		542	419	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421540	32421540	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760654956	NA	P-0044219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	161	650	1	ENST00000332351.3:c.1052G>A	p.Gly351Glu	p.G351E	ENST00000332351	NM_024426.4	351	gGa/gAa	6/10	0.278631800112334	3	FACETS	0.942	0.866	1	0.942	0.866	1	CLONAL	2	TRUE	1	0.278631800112334	3		651	699	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346364	73346364	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	40	210	0	ENST00000377767.4:c.1436A>G	p.Asp479Gly	p.D479G	ENST00000377767	NM_014953.3	479	gAc/gGc	10/21	1	2	FACETS	0.971	0.82	1	0.971	0.82	1	CLONAL	1	TRUE	1	0.505381863575527	2		210	163	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	210	350	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.341909295102326	6	FACETS	0.939	0.889	0.989			1	CLONAL	6	TRUE	NA	0.341909295102326	6		350	367	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577123	7577123	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876660333	NA	P-0044286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	73	563	0	ENST00000269305.4:c.815T>A	p.Val272Glu	p.V272E	ENST00000269305	NM_001126112.2	272	gTg/gAg	8/11	0.341909295102326	1	FACETS	0.944	0.831	1	0.944	0.831	1	CLONAL	1	TRUE	0	0.341909295102326	1		563	375	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971099	21971099	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	63	301	0	ENST00000304494.5:c.259del	p.Arg87GlyfsTer59	p.R87Gfs*59	ENST00000304494	NM_000077.4	87	Cgg/gg	2/3	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.341909295102326	2		301	273	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0044289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	94	441	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.326083252105092	4	FACETS	1	0.945	1	1	0.983	1	CLONAL	4	TRUE	1	0.326083252105092	4		441	183	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254906	16254906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	25	446	0	ENST00000375759.3:c.2171G>A	p.Arg724Gln	p.R724Q	ENST00000375759	NM_015001.2	724	cGa/cAa	11/15	0.246544919196677	3	FACETS	0.362	0.285	0.452	0.181	0.142	0.226	SUBCLONAL	1	TRUE	1	0.326083252105092	3		446	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577128	7577128	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	151	612	0	ENST00000269305.4:c.810T>A	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	ttT/ttA	8/11	0.281259613732345	2	FACETS	1	0.985	1	0.668	0.612	0.726	CLONAL	1	TRUE	0	0.326083252105092	2		612	693	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104386977	104386977	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	12	286	0	ENST00000369902.3:c.1342G>C	p.Glu448Gln	p.E448Q	ENST00000369902	NM_016169.3	448	Gaa/Caa	11/12	1	2	FACETS	0.377	0.265	0.515	0.377	0.265	0.515	SUBCLONAL	1	TRUE	1	0.326083252105092	2		286	195	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55704588	55704588	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0044289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	86	621	1	ENST00000284073.2:c.653-2A>G		p.X218_splice	ENST00000284073	NM_138962.2	218			0.281259613732345	2	FACETS	0.713	0.63	0.801	0.356	0.315	0.401	SUBCLONAL	1	TRUE	0	0.326083252105092	2		622	740	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383868	15383868	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	54	490	0	ENST00000263377.2:c.43C>G	p.Pro15Ala	p.P15A	ENST00000263377	NM_058243.2	15	Cca/Gca	2/20	0.239627910925206	5	FACETS	0.734	0.626	0.852	0.245	0.208	0.284	SUBCLONAL	1	TRUE	2	0.326083252105092	5		490	672	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846345	128846345	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	84	607	0	ENST00000249373.3:c.1181A>G	p.Tyr394Cys	p.Y394C	ENST00000249373	NM_005631.4	394	tAc/tGc	6/12	1	2	FACETS	0.471	0.414	0.532	0.471	0.414	0.532	SUBCLONAL	1	TRUE	1	0.326083252105092	2		607	1094	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	83	126	0				ENST00000310581	NM_198253.2	-/1132			0.280448310949819	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.413402362815027	1		126	265	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0044320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	344	310	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.111059685947807	5	FACETS	0.994	0.949	1			1	INDETERMINATE	4	TRUE	NA	0.413402362815027	5		310	678	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0044320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	100	572	2	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	0.413402362815027	6	FACETS	1	0.922	1	0.26	0.232	0.29	CLONAL	1	TRUE	2	0.413402362815027	6		574	849	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911769	26911769	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	33	200	0	ENST00000381527.3:c.194G>C	p.Arg65Thr	p.R65T	ENST00000381527	NM_001260.1	65	aGa/aCa	2/13	0.280448310949819	1	FACETS	0.435	0.355	0.524	0.435	0.355	0.524	SUBCLONAL	1	TRUE	0	0.413402362815027	1		200	291	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4102403	4102403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457335620	NA	P-0044320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	362	736	0	ENST00000262948.5:c.499G>A	p.Glu167Lys	p.E167K	ENST00000262948	NM_030662.3	167	Gag/Aag	4/11	0.397537479899677	4	FACETS	0.868	0.825	0.911	1	0.994	1	CLONAL	3	TRUE	2	0.413402362815027	4		736	951	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956772	68956772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199819614	NA	P-0044320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	208	700	1	ENST00000288368.4:c.890G>A	p.Arg297His	p.R297H	ENST00000288368	NM_024870.2	297	cGt/cAt	8/40	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.413402362815027	2		701	795	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981382	201981563	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCCCTGGAGCTCTGGGCCAGCTGCACAGCCAGAGAGAGCCCTTGAGGGAGGGATTAGGGGAGTGTGACCCTTCCTTCCTTCCTTGTCAGCTTCCAGCTCTTCTGATGAGCTCAGTTGGATCATTGAGCTGCTGGAGAAGGATGGCATGGCCTTCCAGGAGGCCCTAGACCCAGGGCCCTTT	GGCCCTGGAGCTCTGGGCCAGCTGCACAGCCAGAGAGAGCCCTTGAGGGAGGGATTAGGGGAGTGTGACCCTTCCTTCCTTCCTTGTCAGCTTCCAGCTCTTCTGATGAGCTCAGTTGGATCATTGAGCTGCTGGAGAAGGATGGCATGGCCTTCCAGGAGGCCCTAGACCCAGGGCCCTTT	-	novel	NA	P-0044320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	140	434	0	ENST00000359651.3:c.385+78_478+1del		p.X129_splice	ENST00000359651		129		3/8	0.404526274480124	3	FACETS	0.877	0.821	0.932	1	0.984	1	CLONAL	4	TRUE	0	0.413402362815027	3		434	233	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490293	56490293	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	54	341	0	ENST00000267101.3:c.2062G>C	p.Glu688Gln	p.E688Q	ENST00000267101	NM_001982.3	688	Gag/Cag	18/28	0.413402362815027	6	FACETS	1	0.864	1	0.253	0.216	0.293	CLONAL	1	TRUE	2	0.413402362815027	6		341	472	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027219	49027219	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	42	385	0	ENST00000267163.4:c.1786C>G	p.Leu596Val	p.L596V	ENST00000267163	NM_000321.2	596	Ctc/Gtc	18/27	0.215981773902009	5	FACETS	0.689	0.575	0.815	0.23	0.191	0.272	INDETERMINATE	1	TRUE	2	0.413402362815027	5		385	478	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38545417	38545417	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	170	662	0	ENST00000299084.4:c.31G>C	p.Asp11His	p.D11H	ENST00000299084	NM_152594.2	11	Gat/Cat	1/7	0.195729278970365	5	FACETS	0.897	0.826	0.97	0.598	0.551	0.647	INDETERMINATE	2	TRUE	2	0.413402362815027	5		662	743	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658818	3658818	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	223	666	0	ENST00000294008.3:c.148G>C	p.Asp50His	p.D50H	ENST00000294008	NM_032444.2	50	Gac/Cac	2/15	0.215981773902009	5	FACETS	1	0.981	1	0.753	0.703	0.804	INDETERMINATE	2	TRUE	2	0.413402362815027	5		666	774	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10288004	10288004	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	47	576	0	ENST00000340748.4:c.485C>G	p.Thr162Ser	p.T162S	ENST00000340748		162	aCc/aGc	5/40	0.397537479899677	4	FACETS	0.375	0.316	0.442	0.188	0.158	0.221	SUBCLONAL	1	TRUE	2	0.413402362815027	4		576	856	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748569	40748569	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	58	727	0	ENST00000392038.2:c.313A>G	p.Met105Val	p.M105V	ENST00000392038	NM_001626.4	105	Atg/Gtg	5/14	0.397537479899677	4	FACETS	0.494	0.423	0.571	0.247	0.211	0.286	SUBCLONAL	1	TRUE	2	0.413402362815027	4		727	803	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562482	21562483	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGGCG	rs550642106	NA	P-0044362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	10	68	0	ENST00000382592.4:c.1431_1436dup	p.Pro479_Ala480dup	p.P479_A480dup	ENST00000382592	NM_014572.2	479	ccg/ccCGCCCCg	4/8	0.153798456441892	3	FACETS	0.612	0.414	0.859	0.306	0.207	0.43	SUBCLONAL	1	TRUE	1	0.19164808355254	3		68	187	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100414	157100414	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1438676618	NA	P-0044362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	15	36	0	ENST00000346085.5:c.1351T>C	p.Ser451Pro	p.S451P	ENST00000346085	NM_020732.3	451	Tcg/Ccg	1/20	0.19164808355254	5	FACETS	0.904	0.662	1	0.301	0.22	0.398	CLONAL	1	TRUE	2	0.19164808355254	5		36	223	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514495	NA	P-0044376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	228	698	0	ENST00000269305.4:c.542G>A	p.Arg181His	p.R181H	ENST00000269305	NM_001126112.2	181	cGc/cAc	5/11	0.741233433692477	1	FACETS	0.985	0.935	1	0.985	0.935	1	CLONAL	1	TRUE	0	0.752104421007438	1		698	384	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038893	12038893	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	176	414	0	ENST00000396373.4:c.1186A>G	p.Arg396Gly	p.R396G	ENST00000396373	NM_001987.4	396	Aga/Gga	7/8	0.752104421007438	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.752104421007438	1		414	287	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300846	137300846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	272	898	2	ENST00000481739.1:c.491G>A	p.Arg164His	p.R164H	ENST00000481739	NM_002957.4	164	cGc/cAc	4/10	1	2	FACETS	0.975	0.919	1	0.975	0.919	1	CLONAL	1	TRUE	1	0.752104421007438	2		900	742	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440961	56440961	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	56	642	0	ENST00000407977.2:c.376G>A	p.Ala126Thr	p.A126T	ENST00000407977		126	Gct/Act	4/10	0.752104421007438	1	FACETS	0.246	0.211	0.283	0.246	0.211	0.283	SUBCLONAL	1	TRUE	0	0.752104421007438	1		642	378	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	111	471	1	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.836	0.763	0.911	0.836	0.763	0.911	CLONAL	1	TRUE	1	0.9	2		472	295	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	544	584	0	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.917	0.881	0.953	0.917	0.881	0.953	CLONAL	1	TRUE	1	0.9	2		584	1318	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	478	708	8	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	1	2	FACETS	0.874	0.837	0.911	0.874	0.837	0.911	CLONAL	1	TRUE	1	0.9	2		716	1216	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	93	372	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	1	2	FACETS	0.85	0.769	0.933	0.85	0.769	0.933	CLONAL	1	TRUE	1	0.9	2		372	243	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913255	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	153	493	0	ENST00000369535.4:c.183A>T	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caT	3/7	1	2	FACETS	0.939	0.871	1	0.939	0.871	1	CLONAL	1	TRUE	1	0.9	2		493	362	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517762	187517762	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	207	249	0	ENST00000441802.2:c.12932del	p.Pro4311HisfsTer38	p.P4311Hfs*38	ENST00000441802	NM_005245.3	4311	cCa/ca	25/27	1	2	FACETS	0.943	0.884	1	0.943	0.884	1	CLONAL	1	TRUE	1	0.9	2		249	488	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	216	390	1	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.9	2		391	446	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	385	684	0	ENST00000324856.7:c.4555del	p.Gln1519ArgfsTer8	p.Q1519Rfs*8	ENST00000324856	NM_006015.4	1517	gCc/gc	18/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.9	2		684	847	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446283	70446284	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	256	498	3	ENST00000373644.4:c.5230dup	p.Arg1744LysfsTer26	p.R1744Kfs*26	ENST00000373644	NM_030625.2	1741	-/A	11/12	1	2	FACETS	0.84	0.791	0.89	0.84	0.791	0.89	CLONAL	1	TRUE	1	0.9	2		501	677	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	132	334	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	0.962	0.888	1	0.962	0.888	1	CLONAL	1	TRUE	1	0.9	2		334	305	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899272	78899272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368064754	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	427	481	0	ENST00000306801.3:c.2911G>A	p.Val971Ile	p.V971I	ENST00000306801	NM_020761.2	971	Gtc/Atc	24/34	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.9	2		481	923	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285320	212285320	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	81	357	0	ENST00000342788.4:c.2981A>G	p.Lys994Arg	p.K994R	ENST00000342788	NM_005235.2	994	aAg/aGg	25/28	1	2	FACETS	0.978	0.883	1	0.978	0.883	1	CLONAL	1	TRUE	1	0.9	2		357	184	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202855	133202855	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057517583	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	399	612	1	ENST00000320574.5:c.6379C>T	p.Arg2127Ter	p.R2127*	ENST00000320574	NM_006231.2	2127	Cga/Tga	46/49	1	2	FACETS	0.986	0.943	1	0.986	0.943	1	CLONAL	1	TRUE	1	0.9	2		613	899	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154241	2154242	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755455183	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	476	774	2	ENST00000434045.2:c.686dup	p.Glu230ArgfsTer50	p.E230Rfs*50	ENST00000434045	NM_001127598.1	229	cca/ccCa	5/5	1	2	FACETS	0.844	0.808	0.881	0.844	0.808	0.881	CLONAL	1	TRUE	1	0.9	2		776	1253	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806180	1806181	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760502257	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	596	778	2	ENST00000260795.2:c.1206dup	p.Lys403GlnfsTer93	p.K403Qfs*93	ENST00000260795		400	agc/agCc	8/17	1	2	FACETS	0.885	0.852	0.919	0.885	0.852	0.919	CLONAL	1	TRUE	1	0.9	2		780	1496	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052632	42052632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779811318	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	265	458	0	ENST00000219905.7:c.7303C>T	p.Arg2435Trp	p.R2435W	ENST00000219905	NM_001164273.1	2435	Cgg/Tgg	20/24	1	2	FACETS	0.822	0.775	0.871	0.822	0.775	0.871	CLONAL	1	TRUE	1	0.9	2		458	716	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337684	73337684	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771690280	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	47	200	1	ENST00000377767.4:c.2032del	p.Ile678PhefsTer59	p.I678Ffs*59	ENST00000377767	NM_014953.3	678	Att/tt	16/21	1	2	FACETS	0.757	0.653	0.865	0.757	0.653	0.865	SUBCLONAL	1	TRUE	1	0.9	2		201	138	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572556	95572556	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1354833117	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	72	187	0	ENST00000393063.1:c.2809C>T	p.Arg937Cys	p.R937C	ENST00000393063	NM_030621.3	937	Cgc/Tgc	19/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.9	2		187	128	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992721	68992721	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs764112302	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	139	594	3	ENST00000288368.4:c.1693del	p.Ser565ArgfsTer10	p.S565Rfs*10	ENST00000288368	NM_024870.2	562	cgT/cg	16/40	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.9	2		597	309	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434182	12434182	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776687	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	120	410	0	ENST00000287820.6:c.556del	p.Ser186ValfsTer47	p.S186Vfs*47	ENST00000287820	NM_015869.4	184	Aaa/aa	4/7	1	2	FACETS	0.966	0.888	1	0.966	0.888	1	CLONAL	1	TRUE	1	0.9	2		410	276	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438211	49438211	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	435	710	1	ENST00000301067.7:c.5058del	p.Lys1686AsnfsTer36	p.K1686Nfs*36	ENST00000301067	NM_003482.3	1686	aaA/aa	20/54	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.9	2		711	959	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445040	49445041	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	349	643	1	ENST00000301067.7:c.2425dup	p.Gln809ProfsTer3	p.Q809Pfs*3	ENST00000301067	NM_003482.3	809	cag/cCag	10/54	1	2	FACETS	0.872	0.829	0.916	0.872	0.829	0.916	CLONAL	1	TRUE	1	0.9	2		644	889	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560476	95560476	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	210	475	0	ENST00000393063.1:c.5113G>C	p.Glu1705Gln	p.E1705Q	ENST00000393063	NM_030621.3	1705	Gaa/Caa	25/28	1	2	FACETS	0.989	0.929	1	0.989	0.929	1	CLONAL	1	TRUE	1	0.9	2		475	472	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225669	225669	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542980860	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	507	854	0	ENST00000264932.6:c.448G>A	p.Val150Met	p.V150M	ENST00000264932	NM_004168.2	150	Gtg/Atg	4/15	1	2	FACETS	0.831	0.797	0.867	0.831	0.797	0.867	CLONAL	1	TRUE	1	0.9	2		854	1355	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748399150	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	599	857	6	ENST00000220592.5:c.1806del	p.Ala603ProfsTer92	p.A603Pfs*92	ENST00000220592	NM_012154.3	602	ccC/cc	14/19	1	2	FACETS	0.896	0.863	0.93	0.896	0.863	0.93	CLONAL	1	TRUE	1	0.9	2		863	1485	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781420	3781421	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	398	604	1	ENST00000262367.5:c.4944dup	p.Ile1649HisfsTer11	p.I1649Hfs*11	ENST00000262367	NM_004380.2	1648	-/C	30/31	1	2	FACETS	0.792	0.754	0.83	0.792	0.754	0.83	SUBCLONAL	1	TRUE	1	0.9	2		605	1117	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170834728	170834728	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	72	345	0	ENST00000296930.5:c.796G>T	p.Ala266Ser	p.A266S	ENST00000296930	NM_002520.6	266	Gcc/Tcc	10/11	1	2	FACETS	0.97	0.869	1	0.97	0.869	1	CLONAL	1	TRUE	1	0.9	2		345	165	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850965	63850965	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	554	535	0	ENST00000279873.7:c.1746del	p.Phe582LeufsTer47	p.F582Lfs*47	ENST00000279873	NM_032199.2	581	tgT/tg	10/10	0.3	7	FACETS	1	0.994	1			1	INDETERMINATE	4	TRUE	NA	0.9	7		535	909	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097703	27097704	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	229	517	0	ENST00000324856.7:c.3292_3293del	p.Gln1098ValfsTer6	p.Q1098Vfs*6	ENST00000324856	NM_006015.4	1098	CAg/g	12/20	1	2	FACETS	0.975	0.918	1	0.975	0.918	1	CLONAL	1	TRUE	1	0.9	2		517	522	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717666	89717666	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1554825189	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	159	456	1	ENST00000371953.3:c.693del	p.Thr232HisfsTer24	p.T232Hfs*24	ENST00000371953	NM_000314.4	231	Ccc/cc	7/9	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.9	2		457	300	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625399	69625399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372402801	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	578	792	0	ENST00000334134.2:c.394C>T	p.Arg132Trp	p.R132W	ENST00000334134	NM_005247.2	132	Cgg/Tgg	3/3	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.9	2		792	1274	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241465	105241465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748789094	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	463	644	0	ENST00000349310.3:c.515C>T	p.Thr172Ile	p.T172I	ENST00000349310	NM_001014432.1	172	aCa/aTa	7/15	1	2	FACETS	0.935	0.895	0.974	0.935	0.895	0.974	CLONAL	1	TRUE	1	0.9	2		644	1101	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782909	66782909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750934083	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	182	468	0	ENST00000307102.5:c.1138G>A	p.Gly380Ser	p.G380S	ENST00000307102	NM_002755.3	380	Ggc/Agc	11/11	1	2	FACETS	0.837	0.78	0.896	0.837	0.78	0.896	CLONAL	1	TRUE	1	0.9	2		468	483	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994865	73994865	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200105637	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	27	23	0	ENST00000318443.5:c.349G>A	p.Glu117Lys	p.E117K	ENST00000318443	NM_001024736.1	117	Gag/Aag	3/10	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.9	2		23	54	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935617	15935618	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	24	274	0	ENST00000268712.3:c.7315dup	p.Asp2439GlyfsTer2	p.D2439Gfs*2	ENST00000268712	NM_006311.3	2439	gat/gGat	46/46	1	2	FACETS	0.186	0.146	0.232	0.186	0.146	0.232	SUBCLONAL	1	TRUE	1	0.9	2		274	287	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315376	30315376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370824521	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	139	447	0	ENST00000322652.5:c.1061C>T	p.Thr354Met	p.T354M	ENST00000322652	NM_015355.2	354	aCg/aTg	10/16	1	2	FACETS	0.939	0.868	1	0.939	0.868	1	CLONAL	1	TRUE	1	0.9	2		447	329	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530042	63530042	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	205	424	0	ENST00000307078.5:c.2393del	p.Lys798ArgfsTer63	p.K798Rfs*63	ENST00000307078	NM_004655.3	798	aAg/ag	10/11	1	2	FACETS	0.967	0.907	1	0.967	0.907	1	CLONAL	1	TRUE	1	0.9	2		424	471	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216581	2216581	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1366871233	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	655	815	0	ENST00000398665.3:c.2225C>A	p.Pro742His	p.P742H	ENST00000398665	NM_032482.2	742	cCc/cAc	20/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.9	2		815	1420	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36217169	36217169	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	416	753	0	ENST00000222270.7:c.3918del	p.Cys1306TrpfsTer49	p.C1306Wfs*49	ENST00000222270	NM_014727.1	1306	tgT/tg	14/37	1	2	FACETS	0.929	0.888	0.971	0.929	0.888	0.971	CLONAL	1	TRUE	1	0.9	2		753	995	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119634939	119634939	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	91	276	0	ENST00000316626.5:c.560T>G	p.Leu187Arg	p.L187R	ENST00000316626		187	cTc/cGc	5/12	1	2	FACETS	0.936	0.849	1	0.936	0.849	1	CLONAL	1	TRUE	1	0.9	2		276	216	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950306	38950306	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	89	434	1	ENST00000357387.3:c.3644T>C	p.Ile1215Thr	p.I1215T	ENST00000357387	NM_152756.3	1215	aTa/aCa	31/38	1	2	FACETS	0.907	0.821	0.996	0.907	0.821	0.996	CLONAL	1	TRUE	1	0.9	2		435	218	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340229	116340229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	71	279	0	ENST00000397752.3:c.1091C>T	p.Ala364Val	p.A364V	ENST00000397752	NM_000245.2	364	gCa/gTa	2/21	1	2	FACETS	0.826	0.736	0.919	0.826	0.736	0.919	CLONAL	1	TRUE	1	0.9	2		279	191	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336379	80336379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	145	398	0	ENST00000286548.4:c.940G>A	p.Val314Met	p.V314M	ENST00000286548	NM_002072.3	314	Gtg/Atg	7/7	1	2	FACETS	0.959	0.888	1	0.959	0.888	1	CLONAL	1	TRUE	1	0.9	2		398	336	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424713	47424714	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	353	633	0	ENST00000377045.4:c.526dup	p.Leu176ProfsTer3	p.L176Pfs*3	ENST00000377045	NM_001654.4	174	cgc/cgCc	6/16	1	2	FACETS	0.974	0.928	1	0.974	0.928	1	CLONAL	1	TRUE	1	0.9	2		633	805	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354648	70354648	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	289	647	0	ENST00000374080.3:c.4813A>C	p.Ser1605Arg	p.S1605R	ENST00000374080		1605	Agc/Cgc	35/45	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.9	2		647	613	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	245	414	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.303884614016247	5	FACETS	1	0.977	1			1	CLONAL	3	TRUE	NA	0.402238387241195	5		414	608	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0044390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	259	435	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.402238387241195	2		435	934	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578412	7578412	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519747	NA	P-0044390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	355	468	0	ENST00000269305.4:c.518T>G	p.Val173Gly	p.V173G	ENST00000269305	NM_001126112.2	173	gTg/gGg	5/11	0.402238387241195	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.402238387241195	2		468	868	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641076	3641076	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	235	638	0	ENST00000294008.3:c.2563T>G	p.Tyr855Asp	p.Y855D	ENST00000294008	NM_032444.2	855	Tat/Gat	12/15	0.402238387241195	2	FACETS	1	0.941	1	0.505	0.471	0.541	CLONAL	1	TRUE	0	0.402238387241195	2		638	1156	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262096	10262096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	179	619	0	ENST00000340748.4:c.2195C>T	p.Ser732Phe	p.S732F	ENST00000340748		732	tCt/tTt	23/40	0.419245713478787	6	FACETS	1	0.945	1			1	CLONAL	1	TRUE	NA	0.624803708925277	6		619	1247	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578468	7578468	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	524	798	0	ENST00000269305.4:c.462del	p.Thr155ProfsTer15	p.T155Pfs*15	ENST00000269305	NM_001126112.2	154	ggC/gg	5/11	NA	2	FACETS	0.931	0.899	0.962			1	INDETERMINATE	2	TRUE	NA	0.624803708925277	2		798	901	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447023	49447041	+	frameshift_variant	Frame_Shift_Del	DEL	CATGGGTGGTTTTAGGCAG	CATGGGTGGTTTTAGGCAG	-	novel	NA	P-0044397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	237	450	0	ENST00000301067.7:c.903_921del	p.Phe301LeufsTer27	p.F301Lfs*27	ENST00000301067	NM_003482.3	301	ttCTGCCTAAAACCACCCATG/tt	7/54	0.618421481860125	3	FACETS	0.892	0.84	0.945	0.892	0.84	0.945	CLONAL	2	TRUE	1	0.624803708925277	3		450	558	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447036	49447036	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	146	457	0	ENST00000301067.7:c.908del	p.Leu303GlnfsTer31	p.L303Qfs*31	ENST00000301067	NM_003482.3	303	cTa/ca	7/54	0.618421481860125	3	FACETS	1	0.96	1	0.538	0.493	0.585	CLONAL	1	TRUE	1	0.624803708925277	3		457	570	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656493	3656493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148547201	NA	P-0044397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	211	712	0	ENST00000294008.3:c.742G>A	p.Glu248Lys	p.E248K	ENST00000294008	NM_032444.2	248	Gag/Aag	3/15	0.621647467994431	3	FACETS	0.878	0.815	0.943	0.439	0.407	0.472	CLONAL	1	TRUE	1	0.624803708925277	3		712	1010	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923661	72923661	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	154	618	1	ENST00000268489.5:c.3417C>A	p.Phe1139Leu	p.F1139L	ENST00000268489	NM_006885.3	1139	ttC/ttA	4/10	0.621647467994431	3	FACETS	0.782	0.716	0.851	0.391	0.358	0.426	SUBCLONAL	1	TRUE	1	0.624803708925277	3		619	827	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968622	55968622	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	31	593	0	ENST00000263923.4:c.2041G>T	p.Gly681Trp	p.G681W	ENST00000263923	NM_002253.2	681	Ggg/Tgg	14/30	1	2	FACETS	0.171	0.137	0.208	0.171	0.137	0.208	SUBCLONAL	1	TRUE	1	0.624803708925277	2		593	582	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	55	517	3	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.14	2		520	768	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	21	350	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.525	0.403	0.669	0.525	0.403	0.669	SUBCLONAL	1	TRUE	1	0.14	2		350	571	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847282	68847282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	64	555	1	ENST00000261769.5:c.1204G>A	p.Asp402Asn	p.D402N	ENST00000261769	NM_004360.3	402	Gat/Aat	9/16	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.14	2		556	795	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857656	9857656	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754286517	NA	P-0044401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	31	452	1	ENST00000330684.3:c.3745G>A	p.Asp1249Asn	p.D1249N	ENST00000330684	NM_001134407.1	1249	Gat/Aat	13/13	1	2	FACETS	0.795	0.642	0.97	0.795	0.642	0.97	CLONAL	1	TRUE	1	0.14	2		453	557	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404809	70404809	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	53	464	1	ENST00000373644.4:c.2328del	p.Lys776AsnfsTer19	p.K776Nfs*19	ENST00000373644	NM_030625.2	775	Aaa/aa	4/12	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.14	2		465	627	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822586	72822586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	42	601	2	ENST00000268489.5:c.9589del	p.Gln3197SerfsTer44	p.Q3197Sfs*44	ENST00000268489	NM_006885.3	3197	Cag/ag	10/10	1	2	FACETS	0.862	0.718	1	0.862	0.718	1	CLONAL	1	TRUE	1	0.14	2		603	696	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633601	69633601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	10	103	0	ENST00000334134.2:c.101G>A	p.Gly34Asp	p.G34D	ENST00000334134	NM_005247.2	34	gGc/gAc	1/3	1	2	FACETS	0.748	0.507	1	0.748	0.507	1	CLONAL	1	TRUE	1	0.14	2		103	191	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553456	29553456	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	45	525	0	ENST00000356175.3:c.2005A>G	p.Ser669Gly	p.S669G	ENST00000356175	NM_000267.3	669	Agt/Ggt	18/57	1	2	FACETS	0.829	0.695	0.979	0.829	0.695	0.979	CLONAL	1	TRUE	1	0.14	2		525	775	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220995	36220995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	82	660	0	ENST00000222270.7:c.5045G>A	p.Cys1682Tyr	p.C1682Y	ENST00000222270	NM_014727.1	1682	tGc/tAc	23/37	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.14	2		660	845	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589591	67589591	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	17	193	0	ENST00000274335.5:c.1354T>C	p.Tyr452His	p.Y452H	ENST00000274335		452	Tat/Cat	10/15	1	2	FACETS	0.88	0.657	1	0.88	0.657	1	CLONAL	1	TRUE	1	0.14	2		193	276	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861607	152861607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	64	377	0	ENST00000406277.2:c.145G>A	p.Ala49Thr	p.A49T	ENST00000406277	NM_152274.4	49	Gct/Act	4/7	1		FACETS		0.694	0.916				CLONAL	2	TRUE	0	0.14	1		377	531	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0044412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	110	522	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.405690980712713	4	FACETS	0.94	0.853	1	0.94	0.853	1	CLONAL	2	TRUE	2	0.466459408129879	4		522	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576919	7576919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	331	555	0	ENST00000269305.4:c.927del	p.Asn310ThrfsTer35	p.N310Tfs*35	ENST00000269305	NM_001126112.2	309	ccC/cc	9/11	0.376885524275289	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.466459408129879	2		555	701	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0044412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	110	206	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.466459408129879	2	FACETS	0.943	0.864	1	0.943	0.864	1	CLONAL	2	TRUE	0	0.466459408129879	2		206	250	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	234	409	2	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	0.466459408129879	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.466459408129879	3		411	587	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137020	64137020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1174133485	NA	P-0044412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	335	618	1	ENST00000334205.4:c.1531C>T	p.Arg511Cys	p.R511C	ENST00000334205	NM_003942.2	511	Cgc/Tgc	13/17	0.466459408129879	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.466459408129879	3		619	871	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279668	123279668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	96	373	0	ENST00000358487.5:c.764G>A	p.Arg255Gln	p.R255Q	ENST00000358487	NM_000141.4	255	cGg/cAg	7/18	0.466459408129879	3	FACETS	0.952	0.851	1	0.476	0.425	0.53	CLONAL	1	TRUE	1	0.466459408129879	3		373	533	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418445	49418445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745599611	NA	P-0044412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	74	633	1	ENST00000301067.7:c.15968G>A	p.Arg5323His	p.R5323H	ENST00000301067	NM_003482.3	5323	cGc/cAc	50/54	0.463212870148958	4	FACETS	0.434	0.379	0.495	0.217	0.189	0.248	SUBCLONAL	1	TRUE	2	0.466459408129879	4		634	1071	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377246	118377246	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	222	438	0	ENST00000534358.1:c.10639C>T	p.Gln3547Ter	p.Q3547*	ENST00000534358	NM_005933.3	3547	Cag/Tag	27/36	0.466459408129879	3	FACETS	0.975	0.914	1	0.975	0.914	1	CLONAL	2	TRUE	1	0.466459408129879	3		438	602	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741528	145741531	+	frameshift_variant	Frame_Shift_Del	DEL	GGAG	GGAG	-	novel	NA	P-0044412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	208	916	0	ENST00000428558.2:c.972_975del	p.Ser325ValfsTer33	p.S325Vfs*33	ENST00000428558	NM_004260.3	324	ccCTCC/cc	5/22	0.466459408129879	3	FACETS	0.901	0.835	0.97	0.451	0.417	0.485	CLONAL	1	TRUE	1	0.466459408129879	3		916	1220	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0044449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	104	436	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.117116532553869	4	FACETS	0.811	0.73	0.896			1	INDETERMINATE	2	TRUE	NA	0.369974993306117	4		436	475	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0044449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	210	.	.	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.129026778128263	5	FACETS	1	0.966	1	0.709	0.659	0.76	INDETERMINATE	2	TRUE	2	0.369974993306117	5		0	830	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0044449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	199	183	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.369974993306117	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	3	TRUE	0	0.369974993306117	3		183	418	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920337	134920337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141607080	NA	P-0044449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	46	577	0	ENST00000398015.3:c.2152G>A	p.Val718Met	p.V718M	ENST00000398015	NM_004441.4	718	Gtg/Atg	12/16	0.369974993306117	1	FACETS	0.669	0.566	0.781	0.669	0.566	0.781	SUBCLONAL	1	TRUE	0	0.369974993306117	1		577	303	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115726	108115726	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	67	223	0	ENST00000278616.4:c.875del	p.Pro292ArgfsTer28	p.P292Rfs*28	ENST00000278616	NM_000051.3	292	Ccg/cg	7/63	0.129026778128263	5	FACETS	1	0.88	1	0.668	0.586	0.755	INDETERMINATE	2	TRUE	2	0.369974993306117	5		223	281	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941740	48941740	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776782	NA	P-0044449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	65	180	0	ENST00000267163.4:c.1049+1G>A		p.X350_splice	ENST00000267163	NM_000321.2	350			0.129026778128263	5	FACETS	0.859	0.757	0.966	0.859	0.757	0.966	INDETERMINATE	3	TRUE	2	0.369974993306117	5		180	212	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632566	3632566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1205902549	NA	P-0044449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	120	1013	0	ENST00000294008.3:c.5282G>A	p.Arg1761His	p.R1761H	ENST00000294008	NM_032444.2	1761	cGc/cAc	15/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.369974993306117	2		1013	557	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0044467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	112	441	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.46224626961083	2		441	380	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950099	44950099	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	65	74	0	ENST00000377967.4:c.3868G>T	p.Glu1290Ter	p.E1290*	ENST00000377967	NM_021140.2	1290	Gaa/Taa	26/29	1	2	FACETS	0.899	0.785	1	0.899	0.785	1	CLONAL	1	TRUE	1	0.46224626961083	2		74	313	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224170	39224170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1558460622	NA	P-0044467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	25	72	0	ENST00000402219.2:c.2974G>A	p.Glu992Lys	p.E992K	ENST00000402219	NM_005633.3	992	Gaa/Aaa	19/23	1	2	FACETS	0.746	0.595	0.915	0.746	0.595	0.915	CLONAL	1	TRUE	1	0.46224626961083	2		72	145	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11168338	11168338	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	138	368	3	ENST00000361445.4:c.7534G>T	p.Asp2512Tyr	p.D2512Y	ENST00000361445	NM_004958.3	2512	Gac/Tac	57/58	1	2	FACETS	0.931	0.85	1	0.931	0.85	1	CLONAL	1	TRUE	1	0.46224626961083	2		371	641	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061226	38061226	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	255	794	0	ENST00000250448.2:c.763G>C	p.Glu255Gln	p.E255Q	ENST00000250448	NM_004496.3	255	Gag/Cag	2/2	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.46224626961083	2		794	1075	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863691	68863692	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATTG	novel	NA	P-0044467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	134	517	0	ENST00000261769.5:c.2433_2436dup	p.Glu813Ter	p.E813*	ENST00000261769	NM_004360.3	810	-/ATTG	15/16	0.46224626961083	1	FACETS	0.796	0.726	0.869	0.796	0.726	0.869	SUBCLONAL	1	TRUE	0	0.46224626961083	1		517	560	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0044479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	132	545	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.963	0.875	1	0.963	0.875	1	CLONAL	1	TRUE	1	0.357458636796335	2		545	767	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0044479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	33	210	0	ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	4/10	1	2	FACETS	0.676	0.553	0.814	0.676	0.553	0.814	SUBCLONAL	1	TRUE	1	0.357458636796335	2		210	273	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240285	41240285	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	24	495	0	ENST00000379561.5:c.65C>G	p.Ser22Trp	p.S22W	ENST00000379561	NM_002015.3	22	tCg/tGg	1/3	1	2	FACETS	0.283	0.221	0.354	0.283	0.221	0.354	SUBCLONAL	1	TRUE	1	0.357458636796335	2		495	475	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620605	52620606	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	77	425	0	ENST00000394830.3:c.3147dup	p.Leu1050ThrfsTer32	p.L1050Tfs*32	ENST00000394830	NM_018313.4	1049	-/A	21/30	0.312848316414383	1	FACETS	0.785	0.691	0.884	0.785	0.691	0.884	SUBCLONAL	1	TRUE	0	0.357458636796335	1		425	451	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681164	86681164	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	45	224	0	ENST00000274376.6:c.2805A>T	p.Lys935Asn	p.K935N	ENST00000274376	NM_002890.2	935	aaA/aaT	22/25	0.312848316414383	1	FACETS	0.757	0.641	0.885	0.757	0.641	0.885	SUBCLONAL	1	TRUE	0	0.357458636796335	1		224	273	SUCCESS
AR	367	MSKCC	GRCh37	X	66766373	66766373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	10	57	0	ENST00000374690.3:c.1385G>A	p.Gly462Asp	p.G462D	ENST00000374690	NM_000044.3	462	gGc/gAc	1/8	1	2	FACETS	0.658	0.451	0.912	0.658	0.451	0.912	SUBCLONAL	1	TRUE	1	0.357458636796335	2		57	85	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	145	522	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.56	2		522	518	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	164	517	3	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.914	0.842	0.988	0.914	0.842	0.988	CLONAL	1	TRUE	1	0.56	2		520	641	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	178	877	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.858	0.793	0.926	0.858	0.793	0.926	CLONAL	1	TRUE	1	0.56	2		883	741	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	233	549	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.993	0.928	1	0.993	0.928	1	CLONAL	1	TRUE	1	0.56	2		549	838	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	156	419	2	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.56	2		421	556	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257144	19257144	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	131	671	1	ENST00000162023.5:c.819del	p.Thr274ProfsTer?	p.T274Pfs*?	ENST00000162023		273	ccC/cc	12/13	1	2	FACETS	0.812	0.74	0.888	0.812	0.74	0.888	CLONAL	1	TRUE	1	0.56	2		672	576	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	118	390	1	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	1	2	FACETS	0.937	0.851	1	0.937	0.851	1	CLONAL	1	TRUE	1	0.56	2		391	450	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434367	121434367	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	190	777	0	ENST00000257555.6:c.1136del	p.Pro379LeufsTer5	p.P379Lfs*5	ENST00000257555		377	ctC/ct	6/10	1	2	FACETS	0.936	0.868	1	0.936	0.868	1	CLONAL	1	TRUE	1	0.56	2		777	725	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	152	448	0	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	1	2	FACETS	0.856	0.786	0.929	0.856	0.786	0.929	CLONAL	1	TRUE	1	0.56	2		448	634	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154242	2154242	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755455183	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	47	897	1	ENST00000434045.2:c.686del	p.Pro229GlnfsTer27	p.P229Qfs*27	ENST00000434045	NM_001127598.1	229	cCa/ca	5/5	1	2	FACETS	0.22	0.185	0.259	0.22	0.185	0.259	SUBCLONAL	1	TRUE	1	0.56	2		898	762	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118885	70118885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	201	736	0	ENST00000245479.2:c.457C>T	p.Pro153Ser	p.P153S	ENST00000245479	NM_000346.3	153	Ccc/Tcc	2/3	1	2	FACETS	0.924	0.858	0.991	0.924	0.858	0.991	CLONAL	1	TRUE	1	0.56	2		736	777	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670357	134670357	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369940994	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	133	486	0	ENST00000398015.3:c.268C>T	p.Arg90Cys	p.R90C	ENST00000398015	NM_004441.4	90	Cgc/Tgc	3/16	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.56	2		486	462	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277254	41277254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs797044875	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	113	373	1	ENST00000349496.5:c.1723G>A	p.Gly575Arg	p.G575R	ENST00000349496	NM_001904.3	575	Gga/Aga	11/15	1	2	FACETS	0.79	0.714	0.869	0.79	0.714	0.869	SUBCLONAL	1	TRUE	1	0.56	2		374	511	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885145	111885145	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs892433462	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	169	709	1	ENST00000341259.2:c.1038del	p.Leu347CysfsTer26	p.L347Cfs*26	ENST00000341259	NM_005475.2	345	Ggg/gg	6/8	1	2	FACETS	0.909	0.839	0.982	0.909	0.839	0.982	CLONAL	1	TRUE	1	0.56	2		710	664	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920173	76920173	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	167	456	3	ENST00000373344.5:c.3904del	p.Arg1302GlufsTer44	p.R1302Efs*44	ENST00000373344	NM_000489.3	1302	Aga/ga	11/35	1	2	FACETS	0.909	0.838	0.982	0.909	0.838	0.982	CLONAL	1	TRUE	1	0.56	2		459	656	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661663	227661664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761880048	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	150	663	16	ENST00000305123.5:c.1791dup	p.His598AlafsTer13	p.H598Afs*13	ENST00000305123	NM_005544.2	597	-/G	1/2	1	2	FACETS	0.91	0.835	0.987	0.91	0.835	0.987	CLONAL	1	TRUE	1	0.56	2		679	589	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103754	47103755	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	rs749901643	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	210	528	0	ENST00000409792.3:c.6190_6191dup	p.Asp2064GlufsTer84	p.D2064Efs*84	ENST00000409792	NM_014159.6	2064	gac/gaGAc	14/21	1	2	FACETS	0.949	0.884	1	0.949	0.884	1	CLONAL	1	TRUE	1	0.56	2		528	790	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047959	180047959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs933223149	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	262	951	0	ENST00000261937.6:c.2216G>A	p.Arg739His	p.R739H	ENST00000261937	NM_182925.4	739	cGc/cAc	15/30	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.56	2		951	884	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913558	32913559	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359479	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	124	379	0	ENST00000380152.3:c.5073dup	p.Trp1692MetfsTer3	p.W1692Mfs*3	ENST00000380152		1689	gca/gcAa	11/27	1	2	FACETS	0.889	0.809	0.973	0.889	0.809	0.973	CLONAL	1	TRUE	1	0.56	2		379	498	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448297	56448298	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1567880599	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	227	845	3	ENST00000407977.2:c.349dup	p.Arg117ProfsTer8	p.R117Pfs*8	ENST00000407977		117	cgc/cCgc	3/10	1	2	FACETS	0.872	0.813	0.932	0.872	0.813	0.932	CLONAL	1	TRUE	1	0.56	2		848	930	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183609	185183609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	147	415	0	ENST00000265026.3:c.1463C>T	p.Ala488Val	p.A488V	ENST00000265026	NM_004721.4	488	gCc/gTc	9/14	1	2	FACETS	0.958	0.879	1	0.958	0.879	1	CLONAL	1	TRUE	1	0.56	2		415	548	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058500	72058500	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1428865181	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	137	400	0	ENST00000357731.5:c.940C>T	p.Pro314Ser	p.P314S	ENST00000357731	NM_173808.2	314	Cct/Tct	6/7	1	2	FACETS	0.956	0.874	1	0.956	0.874	1	CLONAL	1	TRUE	1	0.56	2		400	512	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622330	1622330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377067150	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	234	939	4	ENST00000344749.5:c.634G>A	p.Ala212Thr	p.A212T	ENST00000344749	NM_001136139.2	212	Gcc/Acc	9/19	1	2	FACETS	0.983	0.919	1	0.983	0.919	1	CLONAL	1	TRUE	1	0.56	2		943	850	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933617	39933617	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	179	661	1	ENST00000378444.4:c.982del	p.Asp328ThrfsTer50	p.D328Tfs*50	ENST00000378444	NM_001123385.1	328	Gac/ac	4/15	1	2	FACETS	0.932	0.862	1	0.932	0.862	1	CLONAL	1	TRUE	1	0.56	2		662	686	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119562149	119562149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149631706	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	138	445	0	ENST00000316626.5:c.1187G>A	p.Arg396Gln	p.R396Q	ENST00000316626		396	cGg/cAg	11/12	1	2	FACETS	0.805	0.735	0.878	0.805	0.735	0.878	CLONAL	1	TRUE	1	0.56	2		445	612	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	rs267608078	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	92	456	0	ENST00000234420.5:c.3260_3261dup	p.Phe1088ProfsTer3	p.F1088Pfs*3	ENST00000234420	NM_000179.2	1085	acc/aCCcc	5/10	1	2	FACETS	0.474	0.421	0.531	0.474	0.421	0.531	SUBCLONAL	1	TRUE	1	0.56	2		456	693	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670340	134670340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415689583	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	115	485	0	ENST00000398015.3:c.251G>A	p.Arg84His	p.R84H	ENST00000398015	NM_004441.4	84	cGc/cAc	3/16	1	2	FACETS	0.868	0.787	0.953	0.868	0.787	0.953	CLONAL	1	TRUE	1	0.56	2		485	473	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739894	41739894	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	140	487	1	ENST00000242208.4:c.79G>A	p.Glu27Lys	p.E27K	ENST00000242208	NM_002192.2	27	Gag/Aag	2/3	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.56	2		488	461	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216189	36216189	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	216	826	1	ENST00000222270.7:c.3602del	p.Pro1201ArgfsTer154	p.P1201Rfs*154	ENST00000222270	NM_014727.1	1199	ggC/gg	11/37	1	2	FACETS	0.975	0.909	1	0.975	0.909	1	CLONAL	1	TRUE	1	0.56	2		827	791	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146944	38146945	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	220	810	0	ENST00000317025.8:c.3197dup	p.Asn1066LysfsTer14	p.N1066Kfs*14	ENST00000317025	NM_023034.1	1066	aac/aaAc	18/24	1	2	FACETS	0.779	0.725	0.836	0.779	0.725	0.836	SUBCLONAL	1	TRUE	1	0.56	2		810	1008	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241924	72241924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs552625764	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	121	360	0	ENST00000357731.5:c.466G>A	p.Val156Ile	p.V156I	ENST00000357731	NM_173808.2	156	Gtc/Atc	3/7	1	2	FACETS	0.873	0.793	0.956	0.873	0.793	0.956	CLONAL	1	TRUE	1	0.56	2		360	495	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210769	5210769	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770699501	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	209	790	0	ENST00000357368.4:c.5282C>T	p.Thr1761Met	p.T1761M	ENST00000357368	NM_002850.3	1761	aCg/aTg	34/38	1	2	FACETS	0.953	0.887	1	0.953	0.887	1	CLONAL	1	TRUE	1	0.56	2		790	783	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497322	149497322	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs987244289	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	206	756	1	ENST00000261799.4:c.2996G>A	p.Arg999Gln	p.R999Q	ENST00000261799	NM_002609.3	999	cGa/cAa	22/23	1	2	FACETS	0.944	0.879	1	0.944	0.879	1	CLONAL	1	TRUE	1	0.56	2		757	779	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647400	3647400	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763869769	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	163	740	4	ENST00000294008.3:c.1663G>A	p.Val555Met	p.V555M	ENST00000294008	NM_032444.2	555	Gtg/Atg	7/15	1	2	FACETS	0.852	0.785	0.923	0.852	0.785	0.923	CLONAL	1	TRUE	1	0.56	2		744	683	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970916	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	244	637	0	ENST00000265081.6:c.1147_1148del	p.Lys383GlyfsTer20	p.K383Gfs*20	ENST00000265081	NM_002439.4	381	AAa/a	7/24	1	2	FACETS	0.872	0.816	0.931	0.872	0.816	0.931	CLONAL	1	TRUE	1	0.56	2		637	999	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338703	70338703	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	183	659	0	ENST00000374080.3:c.99G>T	p.Glu33Asp	p.E33D	ENST00000374080		33	gaG/gaT	1/45	1	2	FACETS	0.981	0.909	1	0.981	0.909	1	CLONAL	1	TRUE	1	0.56	2		659	666	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89825027	89825027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773070418	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	196	678	2	ENST00000389301.3:c.2939C>T	p.Ala980Val	p.A980V	ENST00000389301	NM_000135.2	980	gCg/gTg	30/43	1	2	FACETS	0.875	0.812	0.94	0.875	0.812	0.94	CLONAL	1	TRUE	1	0.56	2		680	800	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746161	162746161	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	72	237	0	ENST00000367921.3:c.2283+1G>A		p.X761_splice	ENST00000367921	NM_006182.2	761			1	2	FACETS	0.832	0.733	0.937	0.832	0.733	0.937	CLONAL	1	TRUE	1	0.56	2		237	309	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204623	128204623	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	254	865	1	ENST00000341105.2:c.818del	p.Gly273AspfsTer53	p.G273Dfs*53	ENST00000341105	NM_032638.4	273	gGa/ga	3/6	1	2	FACETS	0.981	0.919	1	0.981	0.919	1	CLONAL	1	TRUE	1	0.56	2		866	925	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978495	70978495	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	107	457	0	ENST00000276594.2:c.1158del	p.Lys387SerfsTer90	p.K387Sfs*90	ENST00000276594	NM_024504.3	386	ggG/gg	5/8	1	2	FACETS	0.889	0.803	0.979	0.889	0.803	0.979	CLONAL	1	TRUE	1	0.56	2		457	430	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780272	9780273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	180	752	0	ENST00000377346.4:c.1446dup	p.Val483ArgfsTer43	p.V483Rfs*43	ENST00000377346	NM_005026.3	481	cac/caCc	11/24	1	2	FACETS	0.916	0.847	0.987	0.916	0.847	0.987	CLONAL	1	TRUE	1	0.56	2		752	702	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094386	27094388	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	147	620	0	ENST00000324856.7:c.3097_3099del	p.Glu1033del	p.E1033del	ENST00000324856	NM_006015.4	1032	GAG/-	11/20	1	2	FACETS	0.794	0.727	0.864	0.794	0.727	0.864	SUBCLONAL	1	TRUE	1	0.56	2		620	661	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405011	70405011	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	155	555	0	ENST00000373644.4:c.2525T>C	p.Ile842Thr	p.I842T	ENST00000373644	NM_030625.2	842	aTc/aCc	4/12	1	2	FACETS	0.932	0.857	1	0.932	0.857	1	CLONAL	1	TRUE	1	0.56	2		555	594	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137183	64137183	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	189	688	0	ENST00000334205.4:c.1615G>A	p.Ala539Thr	p.A539T	ENST00000334205	NM_003942.2	539	Gcc/Acc	14/17	1	2	FACETS	0.86	0.796	0.926	0.86	0.796	0.926	CLONAL	1	TRUE	1	0.56	2		688	785	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998937	100998937	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	165	667	0	ENST00000325455.5:c.865A>G	p.Met289Val	p.M289V	ENST00000325455	NM_001202474.3	289	Atg/Gtg	1/8	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.56	2		667	587	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170319	119170319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	118	305	0	ENST00000264033.4:c.2549C>T	p.Ala850Val	p.A850V	ENST00000264033	NM_005188.3	850	gCt/gTt	16/16	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.56	2		305	412	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658371	18658371	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	90	357	0	ENST00000266497.5:c.3176C>A	p.Ala1059Glu	p.A1059E	ENST00000266497		1059	gCa/gAa	22/31	1	2	FACETS	0.913	0.817	1	0.913	0.817	1	CLONAL	1	TRUE	1	0.56	2		357	352	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438045	49438045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1331807800	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	262	775	1	ENST00000301067.7:c.5126G>A	p.Arg1709His	p.R1709H	ENST00000301067	NM_003482.3	1709	cGc/cAc	21/54	1	2	FACETS	0.976	0.916	1	0.976	0.916	1	CLONAL	1	TRUE	1	0.56	2		776	959	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105240287	105240287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs551254461	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	244	803	0	ENST00000349310.3:c.664C>T	p.Arg222Cys	p.R222C	ENST00000349310	NM_001014432.1	222	Cgc/Tgc	9/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.56	2		803	828	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827588	72827588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	201	651	0	ENST00000268489.5:c.8993G>A	p.Arg2998Gln	p.R2998Q	ENST00000268489	NM_006885.3	2998	cGg/cAg	9/10	1	2	FACETS	0.918	0.853	0.985	0.918	0.853	0.985	CLONAL	1	TRUE	1	0.56	2		651	782	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347020	89347020	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867065526	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	35	650	0	ENST00000301030.4:c.5930C>T	p.Ser1977Leu	p.S1977L	ENST00000301030	NM_001256183.1	1977	tCg/tTg	9/13	1	2	FACETS	0.224	0.183	0.271	0.224	0.183	0.271	SUBCLONAL	1	TRUE	1	0.56	2		650	557	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231479	5231479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1377623190	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	239	890	0	ENST00000357368.4:c.1997C>T	p.Pro666Leu	p.P666L	ENST00000357368	NM_002850.3	666	cCg/cTg	14/38	1	2	FACETS	0.979	0.916	1	0.979	0.916	1	CLONAL	1	TRUE	1	0.56	2		890	872	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228148	36228148	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867668452	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	228	850	0	ENST00000222270.7:c.7534G>A	p.Ala2512Thr	p.A2512T	ENST00000222270	NM_014727.1	2512	Gca/Aca	33/37	1	2	FACETS	0.876	0.817	0.936	0.876	0.817	0.936	CLONAL	1	TRUE	1	0.56	2		850	930	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967123	25967123	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	114	531	0	ENST00000435504.4:c.2083C>T	p.Pro695Ser	p.P695S	ENST00000435504		695	Cca/Tca	13/13	1	2	FACETS	0.905	0.82	0.993	0.905	0.82	0.993	CLONAL	1	TRUE	1	0.56	2		531	450	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222423	39222423	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	228	682	0	ENST00000402219.2:c.3187del	p.Ile1063LeufsTer25	p.I1063Lfs*25	ENST00000402219	NM_005633.3	1063	Att/tt	20/23	1	2	FACETS	0.874	0.815	0.934	0.874	0.815	0.934	CLONAL	1	TRUE	1	0.56	2		682	932	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022395	31022395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1162384519	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	79	339	0	ENST00000375687.4:c.1880C>T	p.Ala627Val	p.A627V	ENST00000375687	NM_015338.5	627	gCg/gTg	13/13	1	2	FACETS	0.827	0.733	0.926	0.827	0.733	0.926	CLONAL	1	TRUE	1	0.56	2		339	341	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164896	106164896	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	38	516	0	ENST00000380013.4:c.3764A>G	p.Tyr1255Cys	p.Y1255C	ENST00000380013	NM_001127208.2	1255	tAc/tGc	6/11	1	2	FACETS	0.206	0.169	0.247	0.206	0.169	0.247	SUBCLONAL	1	TRUE	1	0.56	2		516	659	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541216	187541216	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	126	387	0	ENST00000441802.2:c.6524T>C	p.Met2175Thr	p.M2175T	ENST00000441802	NM_005245.3	2175	aTg/aCg	10/27	1	2	FACETS	0.898	0.818	0.982	0.898	0.818	0.982	CLONAL	1	TRUE	1	0.56	2		387	501	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629124	187629125	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	161	576	0	ENST00000441802.2:c.1857dup	p.Asn620GlnfsTer56	p.N620Qfs*56	ENST00000441802	NM_005245.3	619	-/C	2/27	1	2	FACETS	0.848	0.78	0.919	0.848	0.78	0.919	CLONAL	1	TRUE	1	0.56	2		576	678	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945803	38945803	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	49	213	0	ENST00000357387.3:c.4423C>A	p.Leu1475Ile	p.L1475I	ENST00000357387	NM_152756.3	1475	Ctt/Att	34/38	1	2	FACETS	0.854	0.732	0.983	0.854	0.732	0.983	CLONAL	1	TRUE	1	0.56	2		213	205	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188970	32188970	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1227775066	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	250	951	0	ENST00000375023.3:c.584T>C	p.Val195Ala	p.V195A	ENST00000375023	NM_004557.3	195	gTc/gCc	4/30	1	2	FACETS	0.966	0.905	1	0.966	0.905	1	CLONAL	1	TRUE	1	0.56	2		951	924	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70967546	70967547	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	142	647	0	ENST00000276594.2:c.1476_1477del	p.Tyr493LeufsTer3	p.Y493Lfs*3	ENST00000276594	NM_024504.3	492	gtGTat/gtat	7/8	1	2	FACETS	0.739	0.675	0.806	0.739	0.675	0.806	SUBCLONAL	1	TRUE	1	0.56	2		647	686	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5466786	5466787	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	49	136	0	ENST00000381577.3:c.813dup	p.Cys272MetfsTer13	p.C272Mfs*13	ENST00000381577	NM_014143.3	269	-/A	6/7	1	2	FACETS	0.956	0.823	1	0.956	0.823	1	CLONAL	1	TRUE	1	0.56	2		136	183	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212816	27212816	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199701926	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	272	906	0	ENST00000380036.4:c.2798C>T	p.Ala933Val	p.A933V	ENST00000380036	NM_000459.3	933	gCg/gTg	17/23	1	2	FACETS	0.988	0.928	1	0.988	0.928	1	CLONAL	1	TRUE	1	0.56	2		906	983	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37034003	37034003	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	146	408	0	ENST00000358127.4:c.26C>A	p.Thr9Asn	p.T9N	ENST00000358127	NM_001280556.1	9	aCt/aAt	1/10	1	2	FACETS	0.83	0.76	0.903	0.83	0.76	0.903	CLONAL	1	TRUE	1	0.56	2		408	628	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246350	53246350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	277	699	1	ENST00000375401.3:c.632G>A	p.Arg211Gln	p.R211Q	ENST00000375401	NM_004187.3	211	cGg/cAg	5/26	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.56	2		700	953	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345347	70345347	+	splice_donor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0044484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	203	750	0	ENST00000374080.3:c.2371+2del		p.X791_splice	ENST00000374080		791			1	2	FACETS	0.872	0.81	0.937	0.872	0.81	0.937	CLONAL	1	TRUE	1	0.56	2		750	831	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	52	414	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.162210302552055	3	FACETS	1	0.95	1	0.637	0.544	0.739	CLONAL	1	FALSE	1	0.218600134556333	3		414	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0044487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	89	723	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	1	2	FACETS	0.781	0.695	0.873	1	0.981	1	SUBCLONAL	2	FALSE	1	0.218600134556333	2		723	521	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813023	89813023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142833057	NA	P-0044487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	85	809	1	ENST00000389301.3:c.3482C>T	p.Thr1161Met	p.T1161M	ENST00000389301	NM_000135.2	1161	aCg/aTg	35/43	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.218600134556333	2		810	652	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0044500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	203	866	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.152056872255023	2	FACETS	1	0.99	1	0.717	0.664	0.772	CLONAL	1	TRUE	0	0.25	2		866	1133	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0044500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	83	435	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.968	0.854	1	0.968	0.854	1	CLONAL	1	TRUE	1	0.25	2		435	686	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519927	NA	P-0044500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	69	640	0	ENST00000263967.3:c.1625A>G	p.Glu542Gly	p.E542G	ENST00000263967	NM_006218.2	542	gAa/gGa	10/21	1	2	FACETS	0.998	0.87	1	0.998	0.87	1	CLONAL	1	TRUE	1	0.25	2		640	553	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380347	14380347	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	103	343	0	ENST00000256196.4:c.70G>C	p.Gly24Arg	p.G24R	ENST00000256196		24	Ggc/Cgc	1/6	1	2	FACETS	0.826	0.742	0.914	1	0.985	1	CLONAL	2	TRUE	1	0.25	2		343	499	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712676	43712676	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1341837884	NA	P-0044500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	105	872	0	ENST00000382044.4:c.4508A>G	p.Asn1503Ser	p.N1503S	ENST00000382044	NM_001141980.1	1503	aAt/aGt	21/28	1	2	FACETS	0.841	0.752	0.936	0.841	0.752	0.936	CLONAL	1	TRUE	1	0.25	2		872	999	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475159	40475193	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TACCTGGAGCCAAGGAGGAGGAACAATGTTGTTAT	TACCTGGAGCCAAGGAGGAGGAACAATGTTGTTAT	-	novel	NA	P-0044500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	44	483	0	ENST00000264657.5:c.1749-32_1751del		p.X583_splice	ENST00000264657	NM_139276.2	583		20/24	1	2	FACETS	0.615	0.515	0.726	0.615	0.515	0.726	SUBCLONAL	1	TRUE	1	0.25	2		483	572	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0044514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	36	301	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.194339519416209	3	FACETS	0.715	0.587	0.86	0.358	0.293	0.43	SUBCLONAL	1	TRUE	1	0.19	3		301	580	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	31	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.19	2		126	270	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0044514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	84	841	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	1	2	FACETS	0.771	0.679	0.87	0.771	0.679	0.87	SUBCLONAL	1	TRUE	1	0.19	2		841	1147	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028895	47028895	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	25	285	0	ENST00000377604.3:c.199G>T	p.Glu67Ter	p.E67*	ENST00000377604	NM_001204468.1	67	Gag/Tag	3/24	0.3	2	FACETS	0.812	0.641	1	0.406	0.32	0.505	CLONAL	1	TRUE	0	0.19	2		285	324	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023897	27023897	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	10	88	0	ENST00000324856.7:c.1003C>T	p.Gln335Ter	p.Q335*	ENST00000324856	NM_006015.4	335	Cag/Tag	1/20	1	2	FACETS	0.78	0.53	1	0.78	0.53	1	CLONAL	1	TRUE	1	0.19	2		88	135	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217417	7217417	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	53	492	0	ENST00000380728.2:c.379C>G	p.His127Asp	p.H127D	ENST00000380728		127	Cat/Gat	5/11	1	2	FACETS	0.661	0.562	0.77	0.661	0.562	0.77	SUBCLONAL	1	TRUE	1	0.19	2		492	844	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	129	790	3	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.267104805459561	2		793	897	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0044516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	207	741	1	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.267104805459561	3	FACETS	0.946	0.878	1	0.946	0.878	1	CLONAL	2	TRUE	1	0.267104805459561	3		742	929	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494627	2494635	+	inframe_deletion	In_Frame_Del	DEL	AGGCCCTGC	AGGCCCTGC	-	novel	NA	P-0044516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	124	680	0	ENST00000355716.4:c.773_781del	p.Leu258_Ala260del	p.L258_A260del	ENST00000355716	NM_003820.2	256	gAGGCCCTGCag/gag	8/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.267104805459561	2		680	745	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118379849	118379849	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0044516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	19	226	0	ENST00000534358.1:c.10836-2A>T		p.X3612_splice	ENST00000534358	NM_005933.3	3612			0.224736307348595	2	FACETS	0.463	0.351	0.595	0.232	0.175	0.298	SUBCLONAL	1	TRUE	0	0.267104805459561	2		226	307	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244946	46244946	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	80	532	0	ENST00000334344.6:c.3040C>T	p.Gln1014Ter	p.Q1014*	ENST00000334344	NM_152641.2	1014	Cag/Tag	15/21	0.267104805459561	3	FACETS	0.888	0.781	1	0.444	0.39	0.502	CLONAL	1	TRUE	1	0.267104805459561	3		532	765	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287489	46287489	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0044516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	100	257	0	ENST00000334344.6:c.5348C>G	p.Ser1783Ter	p.S1783*	ENST00000334344	NM_152641.2	1783	tCa/tGa	20/21	0.267104805459561	3	FACETS	0.935	0.84	1	0.935	0.84	1	CLONAL	2	TRUE	1	0.267104805459561	3		257	454	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944552	32944552	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749770064	NA	P-0044516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	189	439	0	ENST00000380152.3:c.8345G>A	p.Ser2782Asn	p.S2782N	ENST00000380152		2782	aGt/aAt	19/27	0.267104805459561	5	FACETS	0.951	0.882	1	0.951	0.882	1	CLONAL	3	TRUE	2	0.267104805459561	5		439	695	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578260	7578260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204041	NA	P-0044516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	116	665	0	ENST00000269305.4:c.589G>A	p.Val197Met	p.V197M	ENST00000269305	NM_001126112.2	197	Gtg/Atg	6/11	0.267104805459561	3	FACETS	1	0.977	1	0.644	0.581	0.711	CLONAL	1	TRUE	1	0.267104805459561	3		665	764	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436107	56436107	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	106	688	0	ENST00000407977.2:c.1030C>T	p.Gln344Ter	p.Q344*	ENST00000407977		344	Cag/Tag	9/10	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.267104805459561	2		688	753	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105678	11105678	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0044516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	82	563	0	ENST00000358026.2:c.1593+1G>A		p.X531_splice	ENST00000358026	NM_001128849.1	531			0.267104805459561	3	FACETS	0.986	0.869	1	0.493	0.434	0.556	CLONAL	1	TRUE	1	0.267104805459561	3		563	706	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477807	140477807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs180177038	NA	P-0044516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	184	441	0	ENST00000288602.6:c.1501G>A	p.Glu501Lys	p.E501K	ENST00000288602	NM_004333.4	501	Gaa/Aaa	12/18	0.267104805459561	4	FACETS	1	0.95	1	1	0.95	1	CLONAL	3	TRUE	1	0.267104805459561	4		441	566	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0044535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	55	255	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.51918640216697	2		255	182	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772290	68772290	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	217	529	1	ENST00000261769.5:c.139G>T	p.Glu47Ter	p.E47*	ENST00000261769	NM_004360.3	47	Gag/Tag	2/16	0.51918640216697	1	FACETS	0.932	0.871	0.994	0.932	0.871	0.994	CLONAL	1	TRUE	0	0.51918640216697	1		530	664	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	51	522	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.689	0.587	0.799	0.689	0.587	0.799	SUBCLONAL	1	TRUE	1	0.402540799744289	2		522	368	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	253	877	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.915	0.861	0.97	1	0.995	1	CLONAL	2	TRUE	1	0.402540799744289	2		883	687	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	146	514	2	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.83	0.764	0.897	1	0.99	1	CLONAL	2	TRUE	1	0.402540799744289	2		516	437	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	235	627	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.857	0.804	0.912	1	0.994	1	CLONAL	2	TRUE	1	0.402540799744289	2		633	681	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	134	584	0	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.948	0.863	1	0.948	0.863	1	CLONAL	1	TRUE	1	0.402540799744289	2		584	702	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	66	490	1	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.788	0.687	0.897	0.788	0.687	0.897	SUBCLONAL	1	TRUE	1	0.402540799744289	2		491	416	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	45	255	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.968	0.821	1	0.968	0.821	1	CLONAL	1	TRUE	1	0.402540799744289	2		255	231	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258928	16258928	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	168	486	0	ENST00000375759.3:c.6198del	p.Lys2066AsnfsTer20	p.K2066Nfs*20	ENST00000375759	NM_015001.2	2065	Aaa/aa	11/15	1	2	FACETS	0.935	0.859	1	0.935	0.859	1	CLONAL	1	TRUE	1	0.402540799744289	2		486	893	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22417937	22417937	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	47	150	0	ENST00000344548.3:c.503T>C	p.Val168Ala	p.V168A	ENST00000344548	NM_001039802.1	168	gTa/gCa	7/7	1	2	FACETS	0.84	0.714	0.977	0.84	0.714	0.977	CLONAL	1	TRUE	1	0.402540799744289	2		150	278	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101267	27101268	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	125	448	0	ENST00000324856.7:c.4555dup	p.Gln1519ProfsTer13	p.Q1519Pfs*13	ENST00000324856	NM_006015.4	1517	gcc/gCcc	18/20	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.402540799744289	2		448	615	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36823851	36823851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772996133	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	95	294	1	ENST00000373129.3:c.331G>A	p.Gly111Ser	p.G111S	ENST00000373129	NM_032017.1	111	Ggc/Agc	5/12	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.402540799744289	2		295	416	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276644	115276644	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	90	377	0	ENST00000438362.2:c.815G>T	p.Gly272Val	p.G272V	ENST00000438362	NM_001242891.1	272	gGc/gTc	8/20	1	2	FACETS	0.943	0.841	1	0.943	0.841	1	CLONAL	1	TRUE	1	0.402540799744289	2		377	474	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246498701	246498701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771269963	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	98	380	1	ENST00000388985.4:c.304G>A	p.Val102Ile	p.V102I	ENST00000388985		102	Gtt/Att	3/12	1	2	FACETS	0.743	0.664	0.828	0.743	0.664	0.828	SUBCLONAL	1	TRUE	1	0.402540799744289	2		381	655	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845529	63845529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771981107	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	67	244	0	ENST00000279873.7:c.1268G>A	p.Arg423Gln	p.R423Q	ENST00000279873	NM_032199.2	423	cGg/cAg	9/10	1	2	FACETS	0.905	0.79	1	0.905	0.79	1	CLONAL	1	TRUE	1	0.402540799744289	2		244	368	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851143	63851143	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	124	449	0	ENST00000279873.7:c.1921G>T	p.Ala641Ser	p.A641S	ENST00000279873	NM_032199.2	641	Gcg/Tcg	10/10	1	2	FACETS	0.903	0.819	0.992	0.903	0.819	0.992	CLONAL	1	TRUE	1	0.402540799744289	2		449	682	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710595	114710597	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs754968616	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	254	382	0	ENST00000543371.1:c.85_87del	p.Glu29del	p.E29del	ENST00000543371	NM_001198531.1	27	cAGGag/cag	1/14	0.402540799744289	2	FACETS	0.98	0.923	1	0.98	0.923	1	CLONAL	2	TRUE	0	0.402540799744289	2		382	644	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138915	64138915	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	62	170	0	ENST00000334205.4:c.2287del	p.Arg763AlafsTer21	p.R763Afs*21	ENST00000334205	NM_003942.2	761	gCc/gc	17/17	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.402540799744289	2		170	298	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589662	69589662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	22	86	0	ENST00000168712.1:c.191C>A	p.Pro64His	p.P64H	ENST00000168712	NM_002007.2	64	cCc/cAc	1/3	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.402540799744289	2		86	85	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425623	49425623	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs751148266	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	155	519	0	ENST00000301067.7:c.12865C>A	p.Leu4289Ile	p.L4289I	ENST00000301067	NM_003482.3	4289	Ctc/Atc	39/54	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.402540799744289	2		519	655	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434005	49434005	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	140	558	0	ENST00000301067.7:c.7548del	p.Asn2517IlefsTer26	p.N2517Ifs*26	ENST00000301067	NM_003482.3	2516	ccC/cc	31/54	1	2	FACETS	0.988	0.902	1	0.988	0.902	1	CLONAL	1	TRUE	1	0.402540799744289	2		558	704	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490962	56490962	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	39	443	1	ENST00000267101.3:c.2413del	p.Ala805HisfsTer95	p.A805Hfs*95	ENST00000267101	NM_001982.3	803	cGg/cg	20/28	1	2	FACETS	0.259	0.213	0.309	0.259	0.213	0.309	SUBCLONAL	1	TRUE	1	0.402540799744289	2		444	749	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120785306	120785306	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	114	444	0	ENST00000257552.2:c.802A>G	p.Thr268Ala	p.T268A	ENST00000257552	NM_002442.3	268	Act/Gct	12/15	1	2	FACETS	0.845	0.762	0.933	0.845	0.762	0.933	CLONAL	1	TRUE	1	0.402540799744289	2		444	670	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707822	43707822	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs746063219	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	142	541	1	ENST00000382044.4:c.5059C>T	p.Arg1687Ter	p.R1687*	ENST00000382044	NM_001141980.1	1687	Cga/Tga	23/28	1	2	FACETS	0.828	0.755	0.905	0.828	0.755	0.905	CLONAL	1	TRUE	1	0.402540799744289	2		542	852	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	169	609	1	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	1	2	FACETS	0.908	0.835	0.984	0.908	0.835	0.984	CLONAL	1	TRUE	1	0.402540799744289	2		610	925	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003813	45003813	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	91	304	0	ENST00000558401.1:c.67+2T>C		p.X23_splice	ENST00000558401	NM_004048.2	23			1	2	FACETS	0.855	0.761	0.954	0.855	0.761	0.954	CLONAL	1	TRUE	1	0.402540799744289	2		304	529	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007688	45007688	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	72	251	0	ENST00000558401.1:c.135C>A	p.Cys45Ter	p.C45*	ENST00000558401	NM_004048.2	45	tgC/tgA	2/4	1	2	FACETS	0.879	0.771	0.994	0.879	0.771	0.994	CLONAL	1	TRUE	1	0.402540799744289	2		251	407	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343582	343582	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	182	592	0	ENST00000262320.3:c.2092del	p.His698ThrfsTer7	p.H698Tfs*7	ENST00000262320	NM_003502.3	698	Cac/ac	8/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.402540799744289	2		592	807	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347983	347983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760961378	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	187	532	3	ENST00000262320.3:c.1523del	p.Gly508ValfsTer197	p.G508Vfs*197	ENST00000262320	NM_003502.3	508	gGt/gt	6/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.402540799744289	2		535	872	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226264	2226264	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	111	529	0	ENST00000326181.6:c.1879-2A>G		p.X627_splice	ENST00000326181	NM_032271.2	627			1	2	FACETS	0.746	0.671	0.826	0.746	0.671	0.826	SUBCLONAL	1	TRUE	1	0.402540799744289	2		529	739	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647209	2647209	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	124	416	0	ENST00000342085.4:c.1487G>T	p.Gly496Val	p.G496V	ENST00000342085	NM_002613.4	496	gGt/gTt	13/14	1	2	FACETS	0.967	0.877	1	0.967	0.877	1	CLONAL	1	TRUE	1	0.402540799744289	2		416	637	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370173	40370173	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	181	562	0	ENST00000293328.3:c.1165C>T	p.Arg389Cys	p.R389C	ENST00000293328	NM_012448.3	389	Cgc/Tgc	9/19	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.402540799744289	2		562	886	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	167	465	1	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.988	0.908	1	0.988	0.908	1	CLONAL	1	TRUE	1	0.402540799744289	2		466	840	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554218	63554218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555583417	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	117	441	0	ENST00000307078.5:c.521C>T	p.Ala174Val	p.A174V	ENST00000307078	NM_004655.3	174	gCg/gTg	2/11	1	2	FACETS	0.816	0.737	0.9	0.816	0.737	0.9	CLONAL	1	TRUE	1	0.402540799744289	2		441	712	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272337	15272337	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs771517374	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	170	552	6	ENST00000263388.2:c.6102del	p.Gly2035ValfsTer50	p.G2035Vfs*50	ENST00000263388	NM_000435.2	2034	ccC/cc	33/33	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.402540799744289	2		558	782	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281200	15281200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	123	553	1	ENST00000263388.2:c.5056G>A	p.Val1686Met	p.V1686M	ENST00000263388	NM_000435.2	1686	Gtg/Atg	27/33	1	2	FACETS	0.743	0.672	0.819	0.743	0.672	0.819	SUBCLONAL	1	TRUE	1	0.402540799744289	2		554	822	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366174	15366174	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	135	493	0	ENST00000263377.2:c.1981C>G	p.Pro661Ala	p.P661A	ENST00000263377	NM_058243.2	661	Ccg/Gcg	10/20	1	2	FACETS	0.883	0.803	0.966	0.883	0.803	0.966	CLONAL	1	TRUE	1	0.402540799744289	2		493	760	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953983	17953983	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	122	477	0	ENST00000458235.1:c.421-2A>G		p.X141_splice	ENST00000458235	NM_000215.3	141			1	2	FACETS	0.975	0.883	1	0.975	0.883	1	CLONAL	1	TRUE	1	0.402540799744289	2		477	622	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753555	42753555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762723221	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	203	547	0	ENST00000222329.4:c.709C>T	p.Arg237Trp	p.R237W	ENST00000222329	NM_006494.2	237	Cgg/Tgg	4/4	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.402540799744289	2		547	904	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082313	16082314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs780080562	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	125	567	3	ENST00000281043.3:c.134dup	p.Glu47GlyfsTer8	p.E47Gfs*8	ENST00000281043	NM_005378.4	43	acc/aCcc	2/3	1	2	FACETS	0.746	0.675	0.82	0.746	0.675	0.82	SUBCLONAL	1	TRUE	1	0.402540799744289	2		570	833	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030648	48030648	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	48	335	0	ENST00000234420.5:c.3263del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1088	Ttc/tc	5/10	1	2	FACETS	0.42	0.354	0.492	0.42	0.354	0.492	SUBCLONAL	1	TRUE	1	0.402540799744289	2		335	568	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646085	215646085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	79	371	2	ENST00000260947.4:c.513del	p.Asp172MetfsTer40	p.D172Mfs*40	ENST00000260947	NM_000465.2	171	aaA/aa	4/11	1	2	FACETS	0.777	0.685	0.875	0.777	0.685	0.875	SUBCLONAL	1	TRUE	1	0.402540799744289	2		373	505	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961367	54961367	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	94	311	0	ENST00000312783.6:c.265T>C	p.Ser89Pro	p.S89P	ENST00000312783	NM_198436.1	89	Tcc/Ccc	4/10	1	2	FACETS	0.851	0.759	0.948	0.851	0.759	0.948	CLONAL	1	TRUE	1	0.402540799744289	2		311	549	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198192	185198192	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs552226638	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	138	378	1	ENST00000265026.3:c.2674A>G	p.Thr892Ala	p.T892A	ENST00000265026	NM_004721.4	892	Acg/Gcg	13/14	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.402540799744289	2		379	680	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55603385	55603385	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	76	258	0	ENST00000288135.5:c.2741G>T	p.Arg914Ile	p.R914I	ENST00000288135	NM_000222.2	914	aGa/aTa	20/21	1	2	FACETS	0.942	0.83	1	0.942	0.83	1	CLONAL	1	TRUE	1	0.402540799744289	2		258	401	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197563	106197563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745668941	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	76	272	0	ENST00000380013.4:c.5896C>T	p.Arg1966Cys	p.R1966C	ENST00000380013	NM_001127208.2	1966	Cgt/Tgt	11/11	1	2	FACETS	0.832	0.732	0.938	0.832	0.732	0.938	CLONAL	1	TRUE	1	0.402540799744289	2		272	454	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323362	31323363	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748204482	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	51	255	0	ENST00000412585.2:c.626dup	p.Thr211AspfsTer10	p.T211Dfs*10	ENST00000412585	NM_005514.6	209	cca/ccCa	4/8	1	2	FACETS	0.656	0.56	0.762	0.656	0.56	0.762	SUBCLONAL	1	TRUE	1	0.402540799744289	2		255	386	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508116	106508116	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	37	184	0	ENST00000359195.3:c.110T>G	p.Leu37Arg	p.L37R	ENST00000359195	NM_002649.2	37	cTc/cGc	2/11	1	2	FACETS	0.727	0.603	0.863	0.727	0.603	0.863	SUBCLONAL	1	TRUE	1	0.402540799744289	2		184	253	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494247	140494247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730880418	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	170	608	0	ENST00000288602.6:c.1001C>T	p.Pro334Leu	p.P334L	ENST00000288602	NM_004333.4	334	cCg/cTg	8/18	1	2	FACETS	0.776	0.712	0.842	0.776	0.712	0.842	SUBCLONAL	1	TRUE	1	0.402540799744289	2		608	1089	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859801	117859801	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	67	203	0	ENST00000297338.2:c.1834A>G	p.Thr612Ala	p.T612A	ENST00000297338	NM_006265.2	612	Aca/Gca	14/14	1	2	FACETS	0.932	0.815	1	0.932	0.815	1	CLONAL	1	TRUE	1	0.402540799744289	2		203	357	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185545	27185545	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1564083506	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	154	433	1	ENST00000380036.4:c.1250del	p.Pro417LeufsTer10	p.P417Lfs*10	ENST00000380036	NM_000459.3	415	ctC/ct	9/23	1	2	FACETS	0.995	0.912	1	0.995	0.912	1	CLONAL	1	TRUE	1	0.402540799744289	2		434	769	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238357	98238357	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146616780	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	130	408	1	ENST00000331920.6:c.1687G>A	p.Ala563Thr	p.A563T	ENST00000331920	NM_000264.3	563	Gcg/Acg	12/24	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.402540799744289	2		409	614	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405177	139405177	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1248255443	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	150	533	0	ENST00000277541.6:c.2668G>A	p.Gly890Ser	p.G890S	ENST00000277541	NM_017617.3	890	Ggc/Agc	17/34	1	2	FACETS	0.937	0.858	1	0.937	0.858	1	CLONAL	1	TRUE	1	0.402540799744289	2		533	795	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	125	242	1	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.402540799744289	1		243	352	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0044585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	97	441	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.463495293432435	2		441	411	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0044585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	193	547	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.463495293432435	2		547	769	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0044585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	108	561	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.463495293432435	2		561	385	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0044585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	131	458	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.463495293432435	2		458	561	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152857997	152857997	+	synonymous_variant	Silent	SNP	G	G	A	rs201983563	NA	P-0044585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	28	304	0	ENST00000406277.2:c.618C>T	p.Pro206=	p.P206=	ENST00000406277	NM_152274.4	206	ccC/ccT	6/7	1	2	FACETS	0.316	0.252	0.389	0.316	0.252	0.389	SUBCLONAL	1	TRUE	1	0.463495293432435	2		304	382	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056169	27056169	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0044585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	28	643	1	ENST00000324856.7:c.1165A>T	p.Lys389Ter	p.K389*	ENST00000324856	NM_006015.4	389	Aag/Tag	2/20	0.463495293432435	1	FACETS	0.183	0.146	0.226	0.183	0.146	0.226	SUBCLONAL	1	TRUE	0	0.463495293432435	1		644	507	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597451	10597451	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	546	865	0	ENST00000171111.5:c.1752del	p.Tyr584Ter	p.Y584*	ENST00000171111	NM_203500.1	584	taC/ta	6/6	0.463495293432435	2	FACETS	0.947	0.911	0.983	0.947	0.911	0.983	CLONAL	2	TRUE	0	0.463495293432435	2		865	1244	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021471	31021480	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGGCTGAG	CCAGGCTGAG	-	novel	NA	P-0044585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	106	645	0	ENST00000375687.4:c.1474_1483del	p.Ala492ThrfsTer208	p.A492Tfs*208	ENST00000375687	NM_015338.5	490	atCCAGGCTGAG/at	12/13	1	2	FACETS	0.607	0.544	0.673	0.607	0.544	0.673	SUBCLONAL	1	TRUE	1	0.463495293432435	2		645	754	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252155	226252155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	18	126	0	ENST00000366813.1:c.103G>T	p.Gly35Trp	p.G35W	ENST00000366813		35	Ggg/Tgg	1/3	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		126	278	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0044589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	856	853	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.510518343227429	3	FACETS	0.984	0.958	1	0.984	0.958	1	CLONAL	3	TRUE	0	0.510588184089731	3		853	1426	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724121	61724121	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	51	291	0	ENST00000401558.2:c.781C>T	p.Arg261Ter	p.R261*	ENST00000401558	NM_003400.3	261	Cga/Tga	10/25	0.512427996642552	3	FACETS	0.351	0.298	0.41	0.117	0.099	0.137	SUBCLONAL	1	TRUE	0	0.510588184089731	3		291	714	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751225	57751225	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358636691	NA	P-0044589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	138	382	0	ENST00000274289.3:c.1642G>A	p.Ala548Thr	p.A548T	ENST00000274289	NM_006622.3	548	Gca/Aca	12/14	0.512028381752277	2	FACETS	0.88	0.804	0.96	0.44	0.402	0.48	CLONAL	1	TRUE	0	0.510588184089731	2		382	614	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256493	115256493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	230	506	0	ENST00000369535.4:c.218G>A	p.Arg73Lys	p.R73K	ENST00000369535	NM_002524.4	73	aGg/aAg	3/7	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.510588184089731	2		506	855	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376896	118376896	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555048277	NA	P-0044589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	296	345	0	ENST00000534358.1:c.10289G>C	p.Cys3430Ser	p.C3430S	ENST00000534358	NM_005933.3	3430	tGt/tCt	27/36	0.510518343227429	3	FACETS	0.959	0.907	1	0.639	0.605	0.674	CLONAL	2	TRUE	0	0.510588184089731	3		345	759	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724484	43724484	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	327	751	0	ENST00000382044.4:c.3583G>A	p.Gly1195Arg	p.G1195R	ENST00000382044	NM_001141980.1	1195	Gga/Aga	17/28	0.512427996642552	2	FACETS	1	0.973	1	0.524	0.495	0.554	CLONAL	1	TRUE	0	0.510588184089731	2		751	1222	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214560	5214579	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCAAGGCTCACCCGTGACT	TCCAAGGCTCACCCGTGACT	-	novel	NA	P-0044589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	247	530	0	ENST00000357368.4:c.4487_4494+12del		p.X1496_splice	ENST00000357368	NM_002850.3	1496		29/38	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.510588184089731	2		530	884	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349658	15349658	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	610	684	3	ENST00000263377.2:c.3916G>A	p.Ala1306Thr	p.A1306T	ENST00000263377	NM_058243.2	1306	Gcc/Acc	19/20	0.499446021341043	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.510588184089731	3		687	1401	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032805	30032805	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs780872661	NA	P-0044589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	186	431	0	ENST00000338641.4:c.180G>C	p.Trp60Cys	p.W60C	ENST00000338641	NM_000268.3	60	tgG/tgC	2/16	0.512427996642552	2	FACETS	0.944	0.874	1	0.472	0.437	0.508	CLONAL	1	TRUE	0	0.510588184089731	2		431	772	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467852	66467865	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGTTGCAGTCCC	GCTGTTGCAGTCCC	-	novel	NA	P-0044589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	89	328	0	ENST00000273854.3:c.404_417del	p.Arg135ProfsTer9	p.R135Pfs*9	ENST00000273854	NM_004439.5	135	cGGGACTGCAACAGC/c	3/18	0.38875749279242	4	FACETS	0.752	0.667	0.843	0.376	0.333	0.422	SUBCLONAL	1	TRUE	2	0.510588184089731	4		328	700	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31511172	31511172	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1286	250	591	0	ENST00000344624.3:c.1402C>G	p.Pro468Ala	p.P468A	ENST00000344624		468	Cct/Gct	6/33	0.423377910582502	4	FACETS	0.963	0.898	1	0.482	0.449	0.515	CLONAL	1	TRUE	2	0.510588184089731	4		591	1536	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	101	414	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.219600842958669	3	FACETS	1	0.919	1	1	0.919	1	CLONAL	2	TRUE	1	0.219599646051001	3		414	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0044655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	170	700	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	NA	2	FACETS	0.821	0.755	0.89			1	INDETERMINATE	2	TRUE	NA	0.219599646051001	2		700	943	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0044663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	134	245	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.0982303849385535	3	FACETS	0.984	0.898	1	0.984	0.898	1	INDETERMINATE	2	TRUE	1	0.286883551308023	3		245	543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0044663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	197	1033	5	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.286883551308023	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.286883551308023	1		1038	958	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586236	48586236	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs1555686071	NA	P-0044663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	19	342	0	ENST00000342988.3:c.905G>A	p.Trp302Ter	p.W302*	ENST00000342988	NM_005359.5	302	tGg/tAg	8/12	0.286883551308023	1	FACETS	0.364	0.276	0.467	0.364	0.276	0.467	SUBCLONAL	1	TRUE	0	0.286883551308023	1		342	312	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42879888	42879894	+	frameshift_variant	Frame_Shift_Del	DEL	CGCTCCT	CGCTCCT	-	novel	NA	P-0044663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	51	199	0	ENST00000398585.3:c.38_44del	p.Glu13AlafsTer26	p.E13Afs*26	ENST00000398585	NM_001135099.1	13	gAGGAGCGc/gc	1/14	1	2	FACETS	0.861	0.733	1	0.861	0.733	1	CLONAL	1	TRUE	1	0.286883551308023	2		199	413	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660205	12660205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044668-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	121	467	0	ENST00000251849.4:c.16G>A	p.Gly6Arg	p.G6R	ENST00000251849	NM_002880.3	6	Gga/Aga	2/17	1	2	FACETS	0.937	0.858	1	0.937	0.858	1	CLONAL	1	TRUE	1	0.775318303422977	2		467	333	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0044736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	228	558	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.283137136969087	3	FACETS	0.822	0.766	0.881	0.822	0.766	0.881	CLONAL	2	TRUE	1	0.283137136969087	3		558	1118	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578410	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCGCCT	CAGCGCCT	-	novel	NA	P-0044736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	72	567	0	ENST00000269305.4:c.520_527del	p.Arg174ProfsTer4	p.R174Pfs*4	ENST00000269305	NM_001126112.2	174	AGGCGCTGc/c	5/11	0.283137136969087	1	FACETS	0.569	0.496	0.648	0.569	0.496	0.648	SUBCLONAL	1	TRUE	0	0.283137136969087	1		567	767	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	107	414	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.148208475818303	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.17	3		414	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501195	NA	P-0044738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	62	610	0	ENST00000269305.4:c.313G>A	p.Gly105Ser	p.G105S	ENST00000269305	NM_001126112.2	105	Ggc/Agc	4/11	1	2	FACETS	0.821	0.708	0.946	0.821	0.708	0.946	CLONAL	1	TRUE	1	0.17	2		610	888	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941290	71941290	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	58	611	0	ENST00000298229.2:c.1065C>G	p.Asp355Glu	p.D355E	ENST00000298229	NM_001567.3	355	gaC/gaG	9/28	1	2	FACETS	0.774	0.663	0.895	0.774	0.663	0.895	SUBCLONAL	1	TRUE	1	0.17	2		611	882	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292806	91292806	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	47	371	0	ENST00000355112.3:c.308G>T	p.Gly103Val	p.G103V	ENST00000355112	NM_000057.2	103	gGa/gTa	3/22	1	2	FACETS	0.855	0.72	1	0.855	0.72	1	CLONAL	1	TRUE	1	0.17	2		371	647	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866543	78866543	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	66	455	0	ENST00000306801.3:c.2116A>T	p.Thr706Ser	p.T706S	ENST00000306801	NM_020761.2	706	Acc/Tcc	19/34	0.148208475818303	3	FACETS	1	0.926	1	0.552	0.478	0.632	CLONAL	1	TRUE	1	0.17	3		455	763	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794728	42794728	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	69	612	0	ENST00000575354.2:c.1808C>G	p.Pro603Arg	p.P603R	ENST00000575354	NM_015125.3	603	cCc/cGc	10/20	1	2	FACETS	0.986	0.858	1	0.986	0.858	1	CLONAL	1	TRUE	1	0.17	2		612	823	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139517	47139517	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	62	406	0	ENST00000409792.3:c.5070del	p.Gly1691GlufsTer14	p.G1691Efs*14	ENST00000409792	NM_014159.6	1690	ggA/gg	9/21	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.17	2		406	554	SUCCESS
ATR	545	MSKCC	GRCh37	3	142172019	142172019	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	35	416	0	ENST00000350721.4:c.7712G>C	p.Gly2571Ala	p.G2571A	ENST00000350721	NM_001184.3	2571	gGg/gCg	46/47	1	2	FACETS	0.639	0.523	0.771	0.639	0.523	0.771	SUBCLONAL	1	TRUE	1	0.17	2		416	644	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938356	76938356	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	47	456	0	ENST00000373344.5:c.2392G>C	p.Ala798Pro	p.A798P	ENST00000373344	NM_000489.3	798	Gct/Cct	9/35	1	2	FACETS	0.801	0.675	0.942	0.801	0.675	0.942	CLONAL	1	TRUE	1	0.17	2		456	690	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989159	41989159	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	39	435	0	ENST00000219905.7:c.1951C>G	p.Pro651Ala	p.P651A	ENST00000219905	NM_001164273.1	651	Cca/Gca	3/24	1	2	FACETS	0.668	0.552	0.798	0.668	0.552	0.798	SUBCLONAL	1	TRUE	1	0.17	2		435	687	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989155	41989156	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	37	436	0	ENST00000219905.7:c.1950dup	p.Pro651SerfsTer6	p.P651Sfs*6	ENST00000219905	NM_001164273.1	649	-/T	3/24	1	2	FACETS	0.635	0.522	0.762	0.635	0.522	0.762	SUBCLONAL	1	TRUE	1	0.17	2		436	686	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs28934577	NA	P-0044744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	225	700	0	ENST00000269305.4:c.770T>G	p.Leu257Arg	p.L257R	ENST00000269305	NM_001126112.2	257	cTg/cGg	7/11	0.388566266846024	2	FACETS	0.942	0.885	1	0.942	0.885	1	CLONAL	2	TRUE	0	0.418961594064684	2		700	570	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543901	212543901	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	97	400	0	ENST00000342788.4:c.1498G>T	p.Gly500Ter	p.G500*	ENST00000342788	NM_005235.2	500	Gga/Tga	13/28	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.418961594064684	2		400	447	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911545	114911545	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	166	446	0	ENST00000543371.1:c.1063A>C	p.Asn355His	p.N355H	ENST00000543371	NM_001198531.1	355	Aat/Cat	10/14	0.418961594064684	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	1	0.418961594064684	3		446	465	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885293	111885293	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	198	639	0	ENST00000341259.2:c.1181G>A	p.Ser394Asn	p.S394N	ENST00000341259	NM_005475.2	394	aGc/aAc	6/8	0.416698881342514	3	FACETS	0.998	0.93	1	0.998	0.93	1	CLONAL	2	TRUE	1	0.418961594064684	3		639	573	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234426	41234426	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs949793708	NA	P-0044744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	90	507	0	ENST00000357654.3:c.4352A>G	p.Glu1451Gly	p.E1451G	ENST00000357654	NM_007294.3	1451	gAa/gGa	12/23	0.114960555761208	3	FACETS	0.955	0.85	1	0.318	0.283	0.356	INDETERMINATE	1	TRUE	0	0.418961594064684	3		507	544	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812210	212812210	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	63	373	0	ENST00000342788.4:c.366C>G	p.Asn122Lys	p.N122K	ENST00000342788	NM_005235.2	122	aaC/aaG	3/28	1	2	FACETS	0.769	0.668	0.878	0.769	0.668	0.878	SUBCLONAL	1	TRUE	1	0.418961594064684	2		373	391	SUCCESS
APC	324	MSKCC	GRCh37	5	112173839	112173839	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0044744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	223	453	0	ENST00000257430.4:c.2548A>T	p.Arg850Ter	p.R850*	ENST00000257430	NM_000038.5	850	Aga/Tga	16/16	0.418961594064684	3	FACETS	0.971	0.917	1	0.971	0.917	1	CLONAL	3	TRUE	0	0.418961594064684	3		453	442	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111549	8111550	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	194	615	0	ENST00000346208.3:c.1037dup	p.Leu347AlafsTer5	p.L347Afs*5	ENST00000346208		345	-/A	5/6	0.198449373328541	4	FACETS	0.876	0.815	0.938	1	0.993	1	CLONAL	4	TRUE	2	0.228227778307119	4		615	596	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255141	16255142	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0044746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	44	501	1	ENST00000375759.3:c.2417_2418dup	p.Arg807AspfsTer3	p.R807Dfs*3	ENST00000375759	NM_015001.2	802	-/GA	11/15	0.228227778307119	3	FACETS	1	0.876	1	0.525	0.441	0.618	CLONAL	1	TRUE	1	0.228227778307119	3		502	409	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118902	115118903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	107	360	0	ENST00000257566.3:c.438dup	p.Ala147SerfsTer13	p.A147Sfs*13	ENST00000257566	NM_016569.3	146	-/A	2/8	0.15364176888349	4	FACETS	1	0.962	1	1	0.987	1	CLONAL	3	TRUE	2	0.228227778307119	4		360	343	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024017	31024017	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1291218446	NA	P-0044746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	49	661	0	ENST00000375687.4:c.3502A>C	p.Ser1168Arg	p.S1168R	ENST00000375687	NM_015338.5	1168	Agt/Cgt	13/13	0.228227778307119	3	FACETS	0.949	0.804	1	0.475	0.402	0.555	CLONAL	1	TRUE	1	0.228227778307119	3		661	504	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115947	8115948	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0044751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	202	371	1	ENST00000346208.3:c.1295dup	p.His433ThrfsTer74	p.H433Tfs*74	ENST00000346208		431	-/C	6/6	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.816204949686446	2		372	475	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682931	241682931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659347	NA	P-0044751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	199	483	0	ENST00000366560.3:c.92C>T	p.Ala31Val	p.A31V	ENST00000366560	NM_000143.3	31	gCg/gTg	1/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.816204949686446	2		483	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578245	7578245	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	293	639	0	ENST00000269305.4:c.604del	p.Arg202ValfsTer45	p.R202Vfs*45	ENST00000269305	NM_001126112.2	202	Cgt/gt	6/11	0.816204949686446	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.816204949686446	1		639	390	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420460	49420460	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	558	557	3	ENST00000301067.7:c.15289C>T	p.Arg5097Ter	p.R5097*	ENST00000301067	NM_003482.3	5097	Cga/Tga	48/54	0.807797608669793	3	FACETS	1	0.991	1	0.71	0.687	0.732	CLONAL	2	TRUE	0	0.807797608669793	3		560	911	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933687	39933687	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0044768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	621	543	2	ENST00000378444.4:c.912T>G	p.Tyr304Ter	p.Y304*	ENST00000378444	NM_001123385.1	304	taT/taG	4/15	0.807797608669793	4	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.807797608669793	4		545	1142	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	471	126	0				ENST00000310581	NM_198253.2	-/1132			0.433630794073246	9	FACETS	0.947	0.913	0.981	1	0.992	1	CLONAL	7	TRUE	3	0.433630794073246	9		126	825	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0044769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	348	648	1	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.433630794073246	3	FACETS	0.994	0.95	1	0.994	0.95	1	CLONAL	3	TRUE	0	0.433630794073246	3		649	655	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200961	108200961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782310	NA	P-0044769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	56	354	0	ENST00000278616.4:c.7328G>A	p.Arg2443Gln	p.R2443Q	ENST00000278616	NM_000051.3	2443	cGa/cAa	50/63	0.414413624739261	4	FACETS	0.926	0.796	1	0.309	0.265	0.356	CLONAL	1	TRUE	1	0.433630794073246	4		354	400	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968233	134968233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753895808	NA	P-0044769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	271	661	0	ENST00000398015.3:c.2746G>A	p.Val916Met	p.V916M	ENST00000398015	NM_004441.4	916	Gtg/Atg	15/16	0.433630794073246	6	FACETS	0.913	0.859	0.968	0.913	0.859	0.968	CLONAL	3	TRUE	3	0.433630794073246	6		661	852	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978499	70978499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141769540	NA	P-0044769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	35	414	0	ENST00000276594.2:c.1154C>T	p.Pro385Leu	p.P385L	ENST00000276594	NM_024504.3	385	cCg/cTg	5/8	0.433630794073246	5	FACETS	0.502	0.41	0.605	0.167	0.136	0.202	SUBCLONAL	1	TRUE	2	0.433630794073246	5		414	531	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045527	47045527	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	347	338	1	ENST00000377604.3:c.2494G>T	p.Glu832Ter	p.E832*	ENST00000377604	NM_001204468.1	832	Gag/Tag	22/24	0.433630794073246	3	FACETS	1	0.98	1			1	CLONAL	4	TRUE	NA	0.433630794073246	3		339	477	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971127	55971127	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	82	508	0	ENST00000263923.4:c.1670C>T	p.Pro557Leu	p.P557L	ENST00000263923	NM_002253.2	557	cCt/cTt	13/30	0.325858120105645	3	FACETS	0.957	0.847	1	0.478	0.423	0.537	CLONAL	1	TRUE	1	0.433630794073246	3		508	481	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262429	16262429	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	52	373	0	ENST00000375759.3:c.9694G>T	p.Glu3232Ter	p.E3232*	ENST00000375759	NM_015001.2	3232	Gaa/Taa	11/15	0.412192797781728	4	FACETS	0.9	0.769	1	0.45	0.384	0.522	CLONAL	1	TRUE	2	0.433630794073246	4		373	382	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193202280	193202280	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	70	372	0	ENST00000367435.3:c.1312G>A	p.Asp438Asn	p.D438N	ENST00000367435	NM_024529.4	438	Gac/Aac	14/17	0.433630794073246	5	FACETS	1	0.931	1	0.366	0.32	0.416	CLONAL	1	TRUE	2	0.433630794073246	5		372	485	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307510	118307510	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	115	674	0	ENST00000534358.1:c.283T>C	p.Ser95Pro	p.S95P	ENST00000534358	NM_005933.3	95	Tca/Cca	1/36	0.414413624739261	4	FACETS	1	0.913	1	0.338	0.304	0.374	CLONAL	1	TRUE	1	0.433630794073246	4		674	750	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937084	48937085	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	92	219	0	ENST00000267163.4:c.853dup	p.Ile285AsnfsTer3	p.I285Nfs*3	ENST00000267163	NM_000321.2	284	-/A	8/27	0.178726601678562	4	FACETS	0.911	0.835	0.985			1	INDETERMINATE	4	TRUE	NA	0.433630794073246	4		219	167	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56855431	56855431	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	45	298	0	ENST00000308159.5:c.580G>C	p.Glu194Gln	p.E194Q	ENST00000308159	NM_014669.4	194	Gag/Cag	7/22	0.426853227524778	2	FACETS	0.851	0.721	0.991	0.425	0.36	0.496	CLONAL	1	TRUE	0	0.433630794073246	2		298	244	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56870600	56870600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	81	413	0	ENST00000308159.5:c.1870G>A	p.Glu624Lys	p.E624K	ENST00000308159	NM_014669.4	624	Gag/Aag	17/22	0.426853227524778	2	FACETS	1	0.906	1	0.512	0.454	0.573	CLONAL	1	TRUE	0	0.433630794073246	2		413	365	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223102	41223102	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	94	613	0	ENST00000357654.3:c.4829C>A	p.Ser1610Tyr	p.S1610Y	ENST00000357654	NM_007294.3	1610	tCt/tAt	15/23	0.433630794073246	8	FACETS	0.884	0.785	0.991			1	CLONAL	1	TRUE	NA	0.433630794073246	8		613	1128	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243523	41243523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	58	570	0	ENST00000357654.3:c.4025C>T	p.Ser1342Leu	p.S1342L	ENST00000357654	NM_007294.3	1342	tCa/tTa	10/23	0.433630794073246	8	FACETS	0.59	0.505	0.683			1	SUBCLONAL	1	TRUE	NA	0.433630794073246	8		570	1044	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243922	41243922	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	444	607	0	ENST00000357654.3:c.3626T>C	p.Leu1209Ser	p.L1209S	ENST00000357654	NM_007294.3	1209	tTa/tCa	10/23	0.433630794073246	8	FACETS	0.949	0.909	0.989			1	CLONAL	5	TRUE	NA	0.433630794073246	8		607	993	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212043	36212043	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	112	1044	0	ENST00000222270.7:c.1794G>C	p.Glu598Asp	p.E598D	ENST00000222270	NM_014727.1	598	gaG/gaC	3/37	0.265894649158921	6	FACETS	0.785	0.704	0.872			1	SUBCLONAL	1	TRUE	NA	0.433630794073246	6		1044	1228	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095962	178095962	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	51	397	0	ENST00000397062.3:c.1369G>C	p.Asp457His	p.D457H	ENST00000397062	NM_006164.4	457	Gat/Cat	5/5	0.376796827423796	3	FACETS	0.732	0.624	0.85	0.366	0.312	0.425	SUBCLONAL	1	TRUE	1	0.433630794073246	3		397	391	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274959	142274959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1301785134	NA	P-0044769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	66	340	0	ENST00000350721.4:c.2101G>A	p.Asp701Asn	p.D701N	ENST00000350721	NM_001184.3	701	Gac/Aac	10/47	0.433630794073246	6	FACETS	1	0.954	1	0.408	0.355	0.466	CLONAL	1	TRUE	3	0.433630794073246	6		340	464	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590686	189590686	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	75	434	0	ENST00000264731.3:c.1251C>G	p.Ile417Met	p.I417M	ENST00000264731	NM_003722.4	417	atC/atG	10/14	0.433630794073246	6	FACETS	0.97	0.85	1	0.323	0.283	0.367	CLONAL	1	TRUE	3	0.433630794073246	6		434	666	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976711	55976711	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	81	481	0	ENST00000263923.4:c.1114G>C	p.Glu372Gln	p.E372Q	ENST00000263923	NM_002253.2	372	Gag/Cag	9/30	0.325858120105645	3	FACETS	1	0.904	1	0.512	0.453	0.575	CLONAL	1	TRUE	1	0.433630794073246	3		481	444	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345728	152345728	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0044769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	32	175	0	ENST00000359321.1:c.842G>C	p.Ter281SerextTer4	p.*281Sext*4	ENST00000359321	NM_005431.1	281	tGa/tCa	3/3	0.426208475666594	4	FACETS	1	0.862	1			1	CLONAL	1	TRUE	NA	0.433630794073246	4		175	199	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484121	8484121	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	53	355	0	ENST00000356435.5:c.3411A>G	p.Ile1137Met	p.I1137M	ENST00000356435		1137	atA/atG	19/35	0.386833678132135	4	FACETS	1	0.903	1	0.356	0.305	0.411	CLONAL	1	TRUE	1	0.433630794073246	4		355	328	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180357	27180357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	55	354	0	ENST00000380036.4:c.1021G>A	p.Glu341Lys	p.E341K	ENST00000380036	NM_000459.3	341	Gag/Aag	7/23	0.386833678132135	4	FACETS	0.838	0.718	0.968	0.279	0.239	0.323	CLONAL	1	TRUE	1	0.433630794073246	4		354	434	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922689	44922690	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0044769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	162	166	0	ENST00000377967.4:c.1552dup	p.Val518GlyfsTer8	p.V518Gfs*8	ENST00000377967	NM_021140.2	517	cag/caGg	16/29	0.433630794073246	3	FACETS	1	0.984	1			1	CLONAL	3	TRUE	NA	0.433630794073246	3		166	265	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0044783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	81	441	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.975	0.862	1	0.975	0.862	1	CLONAL	1	TRUE	1	0.330195031298015	2		441	503	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204864	NA	P-0044783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	38	285	0	ENST00000371953.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000371953	NM_000314.4	171	Cag/Tag	6/9	1	2	FACETS	0.445	0.367	0.532	0.445	0.367	0.532	SUBCLONAL	1	TRUE	1	0.330195031298015	2		285	517	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468187	25468187	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	186	544	0	ENST00000264709.3:c.1489T>C	p.Cys497Arg	p.C497R	ENST00000264709	NM_175629.2	497	Tgt/Cgt	13/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.330195031298015	2		544	867	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176992	56176993	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0044783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	128	261	0	ENST00000399503.3:c.2263_2264del	p.Leu755TrpfsTer8	p.L755Wfs*8	ENST00000399503	NM_005921.1	754	ctTCtt/cttt	13/20	0.330195031298015	3	FACETS	0.879	0.801	0.96	0.879	0.801	0.96	CLONAL	2	TRUE	1	0.330195031298015	3		261	514	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180629	32180629	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1278741655	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	78	529	0	ENST00000375023.3:c.2498C>T	p.Pro833Leu	p.P833L	ENST00000375023	NM_004557.3	833	cCc/cTc	16/30	0.54310321126623	3	FACETS	0.358	0.313	0.406	0.179	0.156	0.203	SUBCLONAL	1	TRUE	1	0.547435335947138	3		529	1014	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170021	32170021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	143	733	0	ENST00000375023.3:c.3587G>A	p.Gly1196Glu	p.G1196E	ENST00000375023	NM_004557.3	1196	gGa/gAa	21/30	0.54310321126623	3	FACETS	0.542	0.493	0.594	0.271	0.246	0.297	SUBCLONAL	1	TRUE	1	0.547435335947138	3		733	1227	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827982	40827982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	73	446	0	ENST00000373198.4:c.2446G>A	p.Glu816Lys	p.E816K	ENST00000373198	NM_133170.3	816	Gag/Aag	17/32	1	2	FACETS	0.412	0.36	0.468	0.412	0.36	0.468	SUBCLONAL	1	TRUE	1	0.547435335947138	2		446	647	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230641	46230641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	82	348	0	ENST00000334344.6:c.890C>T	p.Ser297Phe	p.S297F	ENST00000334344	NM_152641.2	297	tCc/tTc	8/21	1	2	FACETS	0.517	0.457	0.582	0.517	0.457	0.582	SUBCLONAL	1	TRUE	1	0.547435335947138	2		348	579	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435407	18435407	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	47	240	0	ENST00000266497.5:c.392G>A	p.Gly131Glu	p.G131E	ENST00000266497		131	gGa/gAa	1/31	1	2	FACETS	0.394	0.332	0.461	0.394	0.332	0.461	SUBCLONAL	1	TRUE	1	0.547435335947138	2		240	436	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491360	18491360	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	24	198	0	ENST00000266497.5:c.1273G>A	p.Glu425Lys	p.E425K	ENST00000266497		425	Gaa/Aaa	8/31	1	2	FACETS	0.292	0.229	0.365	0.292	0.229	0.365	SUBCLONAL	1	TRUE	1	0.547435335947138	2		198	300	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	179	461	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.54310321126623	3	FACETS	1	0.974	1	0.561	0.518	0.605	CLONAL	1	TRUE	1	0.547435335947138	3		461	743	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612028	189612028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs900140738	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	67	443	0	ENST00000264731.3:c.1780C>T	p.Arg594Ter	p.R594*	ENST00000264731	NM_003722.4	594	Cga/Tga	14/14	1	2	FACETS	0.345	0.299	0.395	0.345	0.299	0.395	SUBCLONAL	1	TRUE	1	0.547435335947138	2		443	709	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372497	55372497	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	137	709	0	ENST00000297316.4:c.1187C>T	p.Ser396Phe	p.S396F	ENST00000297316	NM_022454.3	396	tCc/tTc	2/2	0.233677449874598	3	FACETS	0.504	0.457	0.553	0.252	0.228	0.277	INDETERMINATE	1	TRUE	1	0.547435335947138	3		709	1266	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264412	46264412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746670862	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	78	318	2	ENST00000371998.3:c.1459C>T	p.Arg487Cys	p.R487C	ENST00000371998		487	Cgt/Tgt	11/23	1	2	FACETS	0.463	0.407	0.524	0.463	0.407	0.524	SUBCLONAL	1	TRUE	1	0.547435335947138	2		320	615	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522095	157522095	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	108	516	1	ENST00000346085.5:c.4367C>T	p.Ser1456Phe	p.S1456F	ENST00000346085	NM_020732.3	1456	tCc/tTc	18/20	1	2	FACETS	0.51	0.457	0.565	0.51	0.457	0.565	SUBCLONAL	1	TRUE	1	0.547435335947138	2		517	774	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271831	15271831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779902629	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	143	778	0	ENST00000263388.2:c.6608C>T	p.Ser2203Phe	p.S2203F	ENST00000263388	NM_000435.2	2203	tCc/tTc	33/33	1	2	FACETS	0.51	0.464	0.558	0.51	0.464	0.558	SUBCLONAL	1	TRUE	1	0.547435335947138	2		778	1024	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876352	35876352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	81	441	0	ENST00000303115.3:c.1144C>T	p.Leu382Phe	p.L382F	ENST00000303115	NM_002185.3	382	Ctc/Ttc	8/8	1	2	FACETS	0.41	0.361	0.463	0.41	0.361	0.463	SUBCLONAL	1	TRUE	1	0.547435335947138	2		441	721	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732855	44732855	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1271145433	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	87	228	0	ENST00000377967.4:c.58G>A	p.Asp20Asn	p.D20N	ENST00000377967	NM_021140.2	20	Gat/Aat	1/29	1	1	FACETS	0.614	0.547	0.684	0.614	0.547	0.684	SUBCLONAL	1	TRUE	0	0.547435335947138	1		228	376	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69011995	69011995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	91	430	0	ENST00000288368.4:c.2632C>T	p.Pro878Ser	p.P878S	ENST00000288368	NM_024870.2	878	Cct/Tct	23/40	0.233677449874598	3	FACETS	0.433	0.383	0.486	0.216	0.191	0.243	INDETERMINATE	1	TRUE	1	0.547435335947138	3		430	978	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259167	89259167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753700696	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	63	310	0	ENST00000336596.2:c.311G>A	p.Arg104Gln	p.R104Q	ENST00000336596	NM_005233.5	104	cGa/cAa	3/17	1	2	FACETS	0.438	0.379	0.502	0.438	0.379	0.502	SUBCLONAL	1	TRUE	1	0.547435335947138	2		310	525	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636826	8636826	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1353675904	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	81	369	0	ENST00000356435.5:c.83G>A	p.Arg28Gln	p.R28Q	ENST00000356435		28	cGa/cAa	2/35	1	2	FACETS	0.441	0.388	0.498	0.441	0.388	0.498	SUBCLONAL	1	TRUE	1	0.547435335947138	2		369	671	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602269	10602269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751899258	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	102	619	0	ENST00000171111.5:c.1309C>T	p.His437Tyr	p.H437Y	ENST00000171111	NM_203500.1	437	Cac/Tac	3/6	1	2	FACETS	0.411	0.367	0.458	0.411	0.367	0.458	SUBCLONAL	1	TRUE	1	0.547435335947138	2		619	906	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235281	235281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	70	303	0	ENST00000264932.6:c.1087C>T	p.His363Tyr	p.H363Y	ENST00000264932	NM_004168.2	363	Cac/Tac	9/15	1	2	FACETS	0.446	0.389	0.508	0.446	0.389	0.508	SUBCLONAL	1	TRUE	1	0.547435335947138	2		303	573	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964325	55964325	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145905001	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	55	335	0	ENST00000263923.4:c.2488C>T	p.Pro830Ser	p.P830S	ENST00000263923	NM_002253.2	830	Ccc/Tcc	17/30	1	2	FACETS	0.339	0.289	0.393	0.339	0.289	0.393	SUBCLONAL	1	TRUE	1	0.547435335947138	2		335	593	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979602	55979602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	69	390	0	ENST00000263923.4:c.845G>A	p.Gly282Glu	p.G282E	ENST00000263923	NM_002253.2	282	gGg/gAg	7/30	1	2	FACETS	0.369	0.32	0.421	0.369	0.32	0.421	SUBCLONAL	1	TRUE	1	0.547435335947138	2		390	684	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023301	33023301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	93	574	0	ENST00000300177.4:c.410C>T	p.Ser137Phe	p.S137F	ENST00000300177	NM_001191322.1	137	tCc/tTc	2/2	0.375032941201999	1	FACETS	0.298	0.265	0.334	0.298	0.265	0.334	SUBCLONAL	1	TRUE	0	0.547435335947138	1		574	827	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249511	153249512	+	stop_gained	Nonsense_Mutation	DNP	CA	CA	AC	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	67	371	2	ENST00000281708.4:c.1266_1267delinsGT	p.Gly423Ter	p.G423*	ENST00000281708	NM_033632.3	422	ggTGga/ggGTga	9/12	1	2	FACETS	0.35	0.303	0.4	0.35	0.303	0.4	SUBCLONAL	1	TRUE	1	0.547435335947138	2		373	700	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195745	102195745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	55	274	0	ENST00000263464.3:c.505G>A	p.Glu169Lys	p.E169K	ENST00000263464	NM_001165.4	169	Gaa/Aaa	2/9	1	2	FACETS	0.379	0.324	0.439	0.379	0.324	0.439	SUBCLONAL	1	TRUE	1	0.547435335947138	2		274	530	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714445	117714445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1307627482	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	55	315	0	ENST00000368508.3:c.1204G>A	p.Glu402Lys	p.E402K	ENST00000368508	NM_002944.2	402	Gaa/Aaa	11/43	1	2	FACETS	0.376	0.321	0.435	0.376	0.321	0.435	SUBCLONAL	1	TRUE	1	0.547435335947138	2		315	535	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671269	30671269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	86	475	0	ENST00000376406.3:c.5608G>A	p.Glu1870Lys	p.E1870K	ENST00000376406	NM_014641.2	1870	Gag/Aag	11/15	0.54310321126623	3	FACETS	0.411	0.362	0.463	0.205	0.181	0.232	SUBCLONAL	1	TRUE	1	0.547435335947138	3		475	974	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288813	11288813	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	95	484	0	ENST00000361445.4:c.2942C>T	p.Ser981Phe	p.S981F	ENST00000361445	NM_004958.3	981	tCc/tTc	19/58	1	2	FACETS	0.428	0.381	0.479	0.428	0.381	0.479	SUBCLONAL	1	TRUE	1	0.547435335947138	2		484	810	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608349	43608349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1319956362	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	119	795	0	ENST00000355710.3:c.1697C>T	p.Pro566Leu	p.P566L	ENST00000355710	NM_020975.4	566	cCc/cTc	9/20	1	2	FACETS	0.394	0.355	0.436	0.394	0.355	0.436	SUBCLONAL	1	TRUE	1	0.547435335947138	2		795	1103	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610091	43610092	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	104	648	0	ENST00000355710.3:c.2043_2044delinsAA	p.Ala682Thr	p.A682T	ENST00000355710	NM_020975.4	681	caGGcc/caAAcc	11/20	1	2	FACETS	0.428	0.382	0.476	0.428	0.382	0.476	SUBCLONAL	1	TRUE	1	0.547435335947138	2		648	888	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114724328	114724328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	95	336	0	ENST00000543371.1:c.395C>T	p.Ser132Phe	p.S132F	ENST00000543371	NM_001198531.1	132	tCc/tTc	4/14	1	2	FACETS	0.422	0.375	0.472	0.422	0.375	0.472	SUBCLONAL	1	TRUE	1	0.547435335947138	2		336	823	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864753	57864753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	124	606	0	ENST00000228682.2:c.2230G>A	p.Gly744Arg	p.G744R	ENST00000228682	NM_005269.2	744	Gga/Aga	12/12	1	2	FACETS	0.575	0.52	0.633	0.575	0.52	0.633	SUBCLONAL	1	TRUE	1	0.547435335947138	2		606	788	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914920	32914920	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149330893	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	62	301	0	ENST00000380152.3:c.6428C>T	p.Ser2143Leu	p.S2143L	ENST00000380152		2143	tCa/tTa	11/27	1	2	FACETS	0.455	0.393	0.522	0.455	0.393	0.522	SUBCLONAL	1	TRUE	1	0.547435335947138	2		301	498	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968942	32968942	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555289566	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	56	320	0	ENST00000380152.3:c.9373C>T	p.Leu3125Phe	p.L3125F	ENST00000380152		3125	Ctc/Ttc	25/27	1	2	FACETS	0.341	0.292	0.395	0.341	0.292	0.395	SUBCLONAL	1	TRUE	1	0.547435335947138	2		320	600	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060886	38060886	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	71	549	0	ENST00000250448.2:c.1103C>G	p.Ala368Gly	p.A368G	ENST00000250448	NM_004496.3	368	gCc/gGc	2/2	1	2	FACETS	0.333	0.29	0.38	0.333	0.29	0.38	SUBCLONAL	1	TRUE	1	0.547435335947138	2		549	778	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41962111	41962111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	60	294	0	ENST00000219905.7:c.1019C>T	p.Ser340Leu	p.S340L	ENST00000219905	NM_001164273.1	340	tCa/tTa	2/24	0.375032941201999	1	FACETS	0.352	0.304	0.405	0.352	0.304	0.405	SUBCLONAL	1	TRUE	0	0.547435335947138	1		294	452	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663416	67663416	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	63	250	0	ENST00000264010.4:c.1817A>G	p.Lys606Arg	p.K606R	ENST00000264010	NM_006565.3	606	aAa/aGa	10/12	1	2	FACETS	0.424	0.367	0.486	0.424	0.367	0.486	SUBCLONAL	1	TRUE	1	0.547435335947138	2		250	543	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984501	72984501	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	132	613	0	ENST00000268489.5:c.3083G>C	p.Arg1028Thr	p.R1028T	ENST00000268489	NM_006885.3	1028	aGg/aCg	3/10	1	2	FACETS	0.464	0.42	0.51	0.464	0.42	0.51	SUBCLONAL	1	TRUE	1	0.547435335947138	2		613	1040	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222554	2222554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	107	492	0	ENST00000398665.3:c.3386C>T	p.Ser1129Phe	p.S1129F	ENST00000398665	NM_032482.2	1129	tCc/tTc	24/28	1	2	FACETS	0.469	0.42	0.521	0.469	0.42	0.521	SUBCLONAL	1	TRUE	1	0.547435335947138	2		492	833	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223380	2223380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	107	666	0	ENST00000398665.3:c.3491C>T	p.Pro1164Leu	p.P1164L	ENST00000398665	NM_032482.2	1164	cCc/cTc	25/28	1	2	FACETS	0.419	0.375	0.466	0.419	0.375	0.466	SUBCLONAL	1	TRUE	1	0.547435335947138	2		666	933	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226350	2226350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	105	733	1	ENST00000398665.3:c.3830C>T	p.Pro1277Leu	p.P1277L	ENST00000398665	NM_032482.2	1277	cCc/cTc	27/28	1	2	FACETS	0.393	0.351	0.438	0.393	0.351	0.438	SUBCLONAL	1	TRUE	1	0.547435335947138	2		734	976	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257609	19257609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	129	702	1	ENST00000162023.5:c.617G>A	p.Gly206Glu	p.G206E	ENST00000162023		206	gGg/gAg	10/13	1	2	FACETS	0.435	0.393	0.479	0.435	0.393	0.479	SUBCLONAL	1	TRUE	1	0.547435335947138	2		703	1084	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745099	41745099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	109	617	0	ENST00000301178.4:c.1165G>A	p.Val389Met	p.V389M	ENST00000301178	NM_021913.4	389	Gtg/Atg	9/20	1	2	FACETS	0.399	0.357	0.443	0.399	0.357	0.443	SUBCLONAL	1	TRUE	1	0.547435335947138	2		617	998	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754482	41754482	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	125	599	0	ENST00000301178.4:c.1601A>C	p.His534Pro	p.H534P	ENST00000301178	NM_021913.4	534	cAc/cCc	13/20	1	2	FACETS	0.436	0.394	0.481	0.436	0.394	0.481	SUBCLONAL	1	TRUE	1	0.547435335947138	2		599	1047	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794443	242794443	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	140	797	0	ENST00000334409.5:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000334409	NM_005018.2	167	Caa/Taa	3/5	1	2	FACETS	0.527	0.48	0.578	0.527	0.48	0.578	SUBCLONAL	1	TRUE	1	0.547435335947138	2		797	970	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546995	9546995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	44	329	0	ENST00000353224.5:c.1027C>T	p.Pro343Ser	p.P343S	ENST00000353224	NM_177990.2	343	Cca/Tca	5/10	1	2	FACETS	0.367	0.308	0.432	0.367	0.308	0.432	SUBCLONAL	1	TRUE	1	0.547435335947138	2		329	438	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408909	41408909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	72	390	0	ENST00000373198.4:c.517C>T	p.His173Tyr	p.H173Y	ENST00000373198	NM_133170.3	173	Cat/Tat	4/32	1	2	FACETS	0.393	0.343	0.447	0.393	0.343	0.447	SUBCLONAL	1	TRUE	1	0.547435335947138	2		390	669	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206881	36206881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	49	227	0	ENST00000300305.3:c.631G>A	p.Asp211Asn	p.D211N	ENST00000300305		211	Gat/Aat	6/8	1	2	FACETS	0.402	0.341	0.47	0.402	0.341	0.47	SUBCLONAL	1	TRUE	1	0.547435335947138	2		227	445	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39772565	39772565	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	43	329	0	ENST00000288319.7:c.676G>A	p.Gly226Ser	p.G226S	ENST00000288319	NM_182918.3	226	Ggt/Agt	6/10	1	2	FACETS	0.29	0.242	0.344	0.29	0.242	0.344	SUBCLONAL	1	TRUE	1	0.547435335947138	2		329	541	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267267	41267267	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	70	300	0	ENST00000349496.5:c.851C>T	p.Ala284Val	p.A284V	ENST00000349496	NM_001904.3	284	gCc/gTc	6/15	1	2	FACETS	0.385	0.335	0.438	0.385	0.335	0.438	SUBCLONAL	1	TRUE	1	0.547435335947138	2		300	665	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165542	47165542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	97	401	0	ENST00000409792.3:c.584C>T	p.Pro195Leu	p.P195L	ENST00000409792	NM_014159.6	195	cCa/cTa	3/21	1	2	FACETS	0.429	0.381	0.479	0.429	0.381	0.479	SUBCLONAL	1	TRUE	1	0.547435335947138	2		401	827	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922331	178922331	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	91	319	0	ENST00000263967.3:c.1100T>G	p.Leu367Ter	p.L367*	ENST00000263967	NM_006218.2	367	tTa/tGa	6/21	1	2	FACETS	0.512	0.455	0.573	0.512	0.455	0.573	SUBCLONAL	1	TRUE	1	0.547435335947138	2		319	649	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259036	153259036	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	24	202	0	ENST00000281708.4:c.779G>C	p.Cys260Ser	p.C260S	ENST00000281708	NM_033632.3	260	tGt/tCt	5/12	1	2	FACETS	0.248	0.194	0.31	0.248	0.194	0.31	SUBCLONAL	1	TRUE	1	0.547435335947138	2		202	354	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435858	149435858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	121	584	0	ENST00000286301.3:c.2366G>A	p.Gly789Asp	p.G789D	ENST00000286301	NM_005211.3	789	gGt/gAt	18/22	1	2	FACETS	0.454	0.41	0.502	0.454	0.41	0.502	SUBCLONAL	1	TRUE	1	0.547435335947138	2		584	973	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397153	397153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	72	457	0	ENST00000380956.4:c.538G>A	p.Asp180Asn	p.D180N	ENST00000380956	NM_001195286.1	180	Gac/Aac	5/9	0.54310321126623	3	FACETS	0.384	0.335	0.438	0.192	0.167	0.219	SUBCLONAL	1	TRUE	1	0.547435335947138	3		457	872	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271545	26271545	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	80	347	0	ENST00000305910.3:c.68C>G	p.Thr23Ser	p.T23S	ENST00000305910	NM_003534.2	23	aCt/aGt	1/1	0.54310321126623	3	FACETS	0.605	0.533	0.683	0.303	0.266	0.342	SUBCLONAL	1	TRUE	1	0.547435335947138	3		347	615	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910377	29910377	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41554816	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	126	777	0	ENST00000376809.5:c.47C>T	p.Ala16Val	p.A16V	ENST00000376809	NM_002116.7	16	gCc/gTc	1/8	0.54310321126623	3	FACETS	0.499	0.45	0.55	0.25	0.225	0.275	SUBCLONAL	1	TRUE	1	0.547435335947138	3		777	1175	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120547	94120547	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	59	315	0	ENST00000369303.4:c.504C>G	p.Asn168Lys	p.N168K	ENST00000369303	NM_004440.3	168	aaC/aaG	3/17	1	2	FACETS	0.413	0.355	0.476	0.413	0.355	0.476	SUBCLONAL	1	TRUE	1	0.547435335947138	2		315	522	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715380	117715380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	59	284	0	ENST00000368508.3:c.1109C>T	p.Ser370Phe	p.S370F	ENST00000368508	NM_002944.2	370	tCt/tTt	10/43	1	2	FACETS	0.466	0.401	0.535	0.466	0.401	0.535	SUBCLONAL	1	TRUE	1	0.547435335947138	2		284	463	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259511	55259511	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	115	535	0	ENST00000275493.2:c.2569G>A	p.Gly857Arg	p.G857R	ENST00000275493	NM_005228.3	857	Ggg/Agg	21/28	1	2	FACETS	0.464	0.417	0.513	0.464	0.417	0.513	SUBCLONAL	1	TRUE	1	0.547435335947138	2		535	906	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372010	55372011	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	151	400	1	ENST00000297316.4:c.700_701delinsTT	p.Pro234Leu	p.P234L	ENST00000297316	NM_022454.3	234	CCg/TTg	2/2	0.233677449874598	3	FACETS	0.917	0.84	0.998	0.459	0.42	0.499	INDETERMINATE	1	TRUE	1	0.547435335947138	3		401	766	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158117	27158117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760573137	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	106	407	0	ENST00000380036.4:c.341G>A	p.Arg114Gln	p.R114Q	ENST00000380036	NM_000459.3	114	cGa/cAa	2/23	1	2	FACETS	0.521	0.467	0.579	0.521	0.467	0.579	SUBCLONAL	1	TRUE	1	0.547435335947138	2		407	743	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223704	36223707	+	frameshift_variant	Frame_Shift_Del	DEL	CTTC	CTTC	TTT	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	137	789	1	ENST00000222270.7:c.6254_6257delinsTTT	p.Pro2085LeufsTer6	p.P2085Lfs*6	ENST00000222270	NM_014727.1	2085	cCTTCg/cTTTg	28/37	1	2	FACETS	0.433	0.393	0.476	0.433	0.393	0.476	SUBCLONAL	1	TRUE	1	0.547435335947138	2		790	1155	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295253	+	upstream_gene_variant	5'Flank	ONP	GAGG	GAGG	AAGA	novel	NA	P-0044788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	53	273	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.533	0.457	0.617	0.533	0.457	0.617	SUBCLONAL	1	TRUE	1	0.547435335947138	2		274	363	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	142	877	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.892	0.814	0.974	0.892	0.814	0.974	CLONAL	1	TRUE	1	0.42122877820037	2		883	756	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	140	627	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.789	0.718	0.862	0.789	0.718	0.862	SUBCLONAL	1	TRUE	1	0.42122877820037	2		633	843	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	291	605	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.84	0.794	0.888	1	0.995	1	CLONAL	2	TRUE	1	0.42122877820037	2		608	822	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	87	461	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.779	0.692	0.873	0.779	0.692	0.873	SUBCLONAL	1	TRUE	1	0.42122877820037	2		461	530	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	84	329	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.7	0.619	0.786	0.7	0.619	0.786	SUBCLONAL	1	TRUE	1	0.42122877820037	2		329	570	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	134	492	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.885	0.805	0.968	0.885	0.805	0.968	CLONAL	1	TRUE	1	0.42122877820037	2		492	719	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775780	9775780	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765031777	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	133	637	0	ENST00000377346.4:c.323G>A	p.Arg108His	p.R108H	ENST00000377346	NM_005026.3	108	cGc/cAc	4/24	1	2	FACETS	0.673	0.61	0.738	0.673	0.61	0.738	SUBCLONAL	1	TRUE	1	0.42122877820037	2		637	939	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11206776	11206776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	127	421	0	ENST00000361445.4:c.4643C>T	p.Ala1548Val	p.A1548V	ENST00000361445	NM_004958.3	1548	gCt/gTt	32/58	1	2	FACETS	0.827	0.75	0.908	0.827	0.75	0.908	CLONAL	1	TRUE	1	0.42122877820037	2		421	729	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307989	11307989	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	152	434	0	ENST00000361445.4:c.1003G>T	p.Gly335Trp	p.G335W	ENST00000361445	NM_004958.3	335	Ggg/Tgg	7/58	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.42122877820037	2		434	699	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199451	16199451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	99	299	1	ENST00000375759.3:c.224G>A	p.Arg75His	p.R75H	ENST00000375759	NM_015001.2	75	cGc/cAc	2/15	1	2	FACETS	0.902	0.808	1	0.902	0.808	1	CLONAL	1	TRUE	1	0.42122877820037	2		300	521	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257354	16257354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	111	395	0	ENST00000375759.3:c.4619C>T	p.Ser1540Phe	p.S1540F	ENST00000375759	NM_015001.2	1540	tCc/tTc	11/15	1	2	FACETS	0.749	0.673	0.828	0.749	0.673	0.828	SUBCLONAL	1	TRUE	1	0.42122877820037	2		395	704	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257729	16257729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199930614	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	97	375	0	ENST00000375759.3:c.4994C>T	p.Ala1665Val	p.A1665V	ENST00000375759	NM_015001.2	1665	gCg/gTg	11/15	1	2	FACETS	0.706	0.63	0.787	0.706	0.63	0.787	SUBCLONAL	1	TRUE	1	0.42122877820037	2		375	652	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257980	16257980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761228108	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	87	423	1	ENST00000375759.3:c.5245G>A	p.Val1749Ile	p.V1749I	ENST00000375759	NM_015001.2	1749	Gta/Ata	11/15	1	2	FACETS	0.699	0.62	0.784	0.699	0.62	0.784	SUBCLONAL	1	TRUE	1	0.42122877820037	2		424	591	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259270	16259270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774668447	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	73	357	0	ENST00000375759.3:c.6535G>A	p.Ala2179Thr	p.A2179T	ENST00000375759	NM_015001.2	2179	Gca/Aca	11/15	1	2	FACETS	0.719	0.631	0.814	0.719	0.631	0.814	SUBCLONAL	1	TRUE	1	0.42122877820037	2		357	482	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262348	16262348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	57	294	0	ENST00000375759.3:c.9613G>A	p.Ala3205Thr	p.A3205T	ENST00000375759	NM_015001.2	3205	Gca/Aca	11/15	1	2	FACETS	0.616	0.53	0.71	0.616	0.53	0.71	SUBCLONAL	1	TRUE	1	0.42122877820037	2		294	439	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099430	27099430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1227227387	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	81	371	1	ENST00000324856.7:c.3667C>T	p.Arg1223Cys	p.R1223C	ENST00000324856	NM_006015.4	1223	Cgc/Tgc	14/20	1	2	FACETS	0.633	0.558	0.713	0.633	0.558	0.713	SUBCLONAL	1	TRUE	1	0.42122877820037	2		372	608	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937880	36937880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	84	769	0	ENST00000361632.4:c.956G>A	p.Ser319Asn	p.S319N	ENST00000361632		319	aGc/aAc	7/16	1	2	FACETS	0.395	0.348	0.446	0.395	0.348	0.446	SUBCLONAL	1	TRUE	1	0.42122877820037	2		769	1010	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797139	45797139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150792276	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	178	711	0	ENST00000450313.1:c.1276C>T	p.Arg426Cys	p.R426C	ENST00000450313	NM_012222.2	426	Cgt/Tgt	13/16	1	2	FACETS	0.825	0.759	0.893	0.825	0.759	0.893	CLONAL	1	TRUE	1	0.42122877820037	2		711	1025	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726956	46726956	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	93	358	1	ENST00000371975.4:c.790G>A	p.Ala264Thr	p.A264T	ENST00000371975	NM_003579.3	264	Gcc/Acc	8/18	1	2	FACETS	0.699	0.622	0.78	0.699	0.622	0.78	SUBCLONAL	1	TRUE	1	0.42122877820037	2		359	632	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429956	78429956	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	38	255	0	ENST00000370768.2:c.923G>A	p.Arg308His	p.R308H	ENST00000370768	NM_003902.3	308	cGc/cAc	11/20	1	2	FACETS	0.366	0.302	0.437	0.366	0.302	0.437	SUBCLONAL	1	TRUE	1	0.42122877820037	2		255	493	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115260813	115260813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768724629	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	80	374	0	ENST00000438362.2:c.2512C>T	p.Arg838Cys	p.R838C	ENST00000438362	NM_001242891.1	838	Cgt/Tgt	20/20	1	2	FACETS	0.693	0.611	0.781	0.693	0.611	0.781	SUBCLONAL	1	TRUE	1	0.42122877820037	2		374	548	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843439	156843439	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	148	565	0	ENST00000524377.1:c.865C>T	p.Gln289Ter	p.Q289*	ENST00000524377	NM_002529.3	289	Cag/Tag	8/17	0.395310948583586	4	FACETS	1	0.947	1	0.35	0.32	0.383	CLONAL	1	TRUE	1	0.42122877820037	4		565	950	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163325170	163325170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144589776	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	55	266	0	ENST00000271452.3:c.1306G>A	p.Gly436Ser	p.G436S	ENST00000271452	NM_145697.2	436	Ggt/Agt	14/14	0.395310948583586	4	FACETS	0.676	0.578	0.783	0.225	0.192	0.261	SUBCLONAL	1	TRUE	1	0.42122877820037	4		266	549	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015383	176015383	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	69	264	0	ENST00000367669.3:c.1355C>T	p.Thr452Ile	p.T452I	ENST00000367669	NM_022457.5	452	aCt/aTt	12/20	0.395310948583586	4	FACETS	0.859	0.749	0.978	0.286	0.249	0.326	CLONAL	1	TRUE	1	0.42122877820037	4		264	542	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204499872	204499872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	101	364	1	ENST00000367182.3:c.214C>T	p.His72Tyr	p.H72Y	ENST00000367182	NM_001278516.1	72	Cat/Tat	4/11	0.395310948583586	4	FACETS	0.724	0.646	0.807	0.241	0.215	0.269	SUBCLONAL	1	TRUE	1	0.42122877820037	4		365	942	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253371	226253371	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	46	338	2	ENST00000366813.1:c.143C>T	p.Ala48Val	p.A48V	ENST00000366813		48	gCg/gTg	2/3	0.395310948583586	4	FACETS	0.594	0.5	0.697	0.198	0.166	0.233	SUBCLONAL	1	TRUE	1	0.42122877820037	4		340	523	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226573322	226573322	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	101	423	0	ENST00000366794.5:c.894C>A	p.Cys298Ter	p.C298*	ENST00000366794	NM_001618.3	298	tgC/tgA	7/23	0.395310948583586	4	FACETS	0.731	0.653	0.815	0.244	0.217	0.272	SUBCLONAL	1	TRUE	1	0.42122877820037	4		423	932	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727057	243727057	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	88	334	0	ENST00000263826.5:c.913A>C	p.Thr305Pro	p.T305P	ENST00000263826	NM_005465.4	305	Aca/Cca	9/13	0.395310948583586	4	FACETS	0.742	0.657	0.834	0.247	0.219	0.278	SUBCLONAL	1	TRUE	1	0.42122877820037	4		334	800	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612161	43612161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	47	244	0	ENST00000355710.3:c.2266G>A	p.Ala756Thr	p.A756T	ENST00000355710	NM_020975.4	756	Gcc/Acc	12/20	1	2	FACETS	0.687	0.582	0.801	0.687	0.582	0.801	SUBCLONAL	1	TRUE	1	0.42122877820037	2		244	325	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450805	70450805	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759636615	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	83	406	0	ENST00000373644.4:c.5645C>T	p.Thr1882Met	p.T1882M	ENST00000373644	NM_030625.2	1882	aCg/aTg	12/12	1	2	FACETS	0.688	0.608	0.773	0.688	0.608	0.773	SUBCLONAL	1	TRUE	1	0.42122877820037	2		406	573	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624296	89624296	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs786201995	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	121	341	0	ENST00000371953.3:c.70G>C	p.Asp24His	p.D24H	ENST00000371953	NM_000314.4	24	Gac/Cac	1/9	1	2	FACETS	0.915	0.829	1	0.915	0.829	1	CLONAL	1	TRUE	1	0.42122877820037	2		341	628	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685289	89685289	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554897267	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	53	176	0	ENST00000371953.3:c.188del	p.Asn63ThrfsTer36	p.N63Tfs*36	ENST00000371953	NM_000314.4	62	Aaa/aa	3/9	1	2	FACETS	0.814	0.699	0.939	0.814	0.699	0.939	CLONAL	1	TRUE	1	0.42122877820037	2		176	309	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717661	89717661	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	114	364	0	ENST00000371953.3:c.686C>A	p.Ser229Ter	p.S229*	ENST00000371953	NM_000314.4	229	tCa/tAa	7/9	1	2	FACETS	0.889	0.802	0.98	0.889	0.802	0.98	CLONAL	1	TRUE	1	0.42122877820037	2		364	609	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533535	533535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	172	595	1	ENST00000451590.1:c.368G>A	p.Arg123His	p.R123H	ENST00000451590	NM_001130442.1	123	cGc/cAc	4/5	1	2	FACETS	0.85	0.782	0.921	0.85	0.782	0.921	CLONAL	1	TRUE	1	0.42122877820037	2		596	961	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939260	71939260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	130	588	1	ENST00000298229.2:c.209G>A	p.Arg70His	p.R70H	ENST00000298229	NM_001567.3	70	cGc/cAc	2/28	1	2	FACETS	0.738	0.67	0.811	0.738	0.67	0.811	SUBCLONAL	1	TRUE	1	0.42122877820037	2		589	836	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941429	71941429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754156985	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	152	614	3	ENST00000298229.2:c.1114C>T	p.Arg372Cys	p.R372C	ENST00000298229	NM_001567.3	372	Cgt/Tgt	10/28	1	2	FACETS	0.788	0.72	0.859	0.788	0.72	0.859	SUBCLONAL	1	TRUE	1	0.42122877820037	2		617	916	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076650	102076650	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	87	285	0	ENST00000282441.5:c.829G>A	p.Ala277Thr	p.A277T	ENST00000282441	NM_001130145.2	277	Gct/Act	5/9	1	2	FACETS	0.801	0.711	0.896	0.801	0.711	0.896	CLONAL	1	TRUE	1	0.42122877820037	2		285	516	SUCCESS
ATM	472	MSKCC	GRCh37	11	108213967	108213967	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876659872	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	54	211	0	ENST00000278616.4:c.8287C>T	p.Arg2763Ter	p.R2763*	ENST00000278616	NM_000051.3	2763	Cga/Tga	57/63	1	2	FACETS	0.633	0.542	0.732	0.633	0.542	0.732	SUBCLONAL	1	TRUE	1	0.42122877820037	2		211	405	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402328	402328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	30	259	0	ENST00000399788.2:c.4463G>A	p.Ser1488Asn	p.S1488N	ENST00000399788	NM_001042603.1	1488	aGc/aAc	27/28	1	2	FACETS	0.288	0.232	0.353	0.288	0.232	0.353	SUBCLONAL	1	TRUE	1	0.42122877820037	2		259	494	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1036408	1036408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778385100	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	110	417	0	ENST00000358495.3:c.370G>A	p.Val124Ile	p.V124I	ENST00000358495	NM_134424.2	124	Gtt/Att	6/12	1	2	FACETS	0.776	0.698	0.858	0.776	0.698	0.858	SUBCLONAL	1	TRUE	1	0.42122877820037	2		417	673	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21630862	21630862	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202110155	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	41	393	0	ENST00000421138.2:c.742G>A	p.Ala248Thr	p.A248T	ENST00000421138		248	Gca/Aca	8/16	1	2	FACETS	0.244	0.202	0.29	0.244	0.202	0.29	SUBCLONAL	1	TRUE	1	0.42122877820037	2		393	799	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420108	49420108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123729	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	153	448	0	ENST00000301067.7:c.15641G>A	p.Arg5214His	p.R5214H	ENST00000301067	NM_003482.3	5214	cGc/cAc	48/54	1	2	FACETS	0.948	0.869	1	0.948	0.869	1	CLONAL	1	TRUE	1	0.42122877820037	2		448	766	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427588	49427588	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	125	496	0	ENST00000301067.7:c.10900C>T	p.Gln3634Ter	p.Q3634*	ENST00000301067	NM_003482.3	3634	Cag/Tag	39/54	1	2	FACETS	0.956	0.867	1	0.956	0.867	1	CLONAL	1	TRUE	1	0.42122877820037	2		496	621	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481947	56481947	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs755433568	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	83	360	0	ENST00000267101.3:c.874+1G>A		p.X292_splice	ENST00000267101	NM_001982.3	292			1	2	FACETS	0.561	0.494	0.631	0.561	0.494	0.631	SUBCLONAL	1	TRUE	1	0.42122877820037	2		360	703	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864545	57864545	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	154	631	1	ENST00000228682.2:c.2022G>T	p.Gln674His	p.Q674H	ENST00000228682	NM_005269.2	674	caG/caT	12/12	1	2	FACETS	0.774	0.708	0.843	0.774	0.708	0.843	SUBCLONAL	1	TRUE	1	0.42122877820037	2		632	945	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864610	57864610	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	190	641	0	ENST00000228682.2:c.2087C>A	p.Ala696Asp	p.A696D	ENST00000228682	NM_005269.2	696	gCt/gAt	12/12	1	2	FACETS	0.9	0.832	0.971	0.9	0.832	0.971	CLONAL	1	TRUE	1	0.42122877820037	2		641	1002	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112323	115112323	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	14	151	0	ENST00000257566.3:c.1417C>T	p.Leu473Phe	p.L473F	ENST00000257566	NM_016569.3	473	Ctc/Ttc	7/8	1	2	FACETS	0.249	0.179	0.333	0.249	0.179	0.333	SUBCLONAL	1	TRUE	1	0.42122877820037	2		151	267	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249829	133249829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555228490	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	97	355	0	ENST00000320574.5:c.1394C>T	p.Ala465Val	p.A465V	ENST00000320574	NM_006231.2	465	gCc/gTc	14/49	1	2	FACETS	0.751	0.671	0.837	0.751	0.671	0.837	SUBCLONAL	1	TRUE	1	0.42122877820037	2		355	613	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253214	133253214	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	108	411	0	ENST00000320574.5:c.827T>A	p.Ile276Asn	p.I276N	ENST00000320574	NM_006231.2	276	aTt/aAt	9/49	1	2	FACETS	0.743	0.668	0.823	0.743	0.668	0.823	SUBCLONAL	1	TRUE	1	0.42122877820037	2		411	690	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549289	21549289	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	136	543	0	ENST00000382592.4:c.2987C>A	p.Pro996His	p.P996H	ENST00000382592	NM_014572.2	996	cCc/cAc	8/8	1	2	FACETS	0.805	0.732	0.882	0.805	0.732	0.882	CLONAL	1	TRUE	1	0.42122877820037	2		543	802	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877387	28877387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747687298	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	92	331	0	ENST00000282397.4:c.3934G>A	p.Ala1312Thr	p.A1312T	ENST00000282397	NM_002019.4	1312	Gct/Act	30/30	1	2	FACETS	0.656	0.583	0.733	0.656	0.583	0.733	SUBCLONAL	1	TRUE	1	0.42122877820037	2		331	666	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005282	29005282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	71	245	2	ENST00000282397.4:c.979C>T	p.His327Tyr	p.H327Y	ENST00000282397	NM_002019.4	327	Cat/Tat	7/30	1	2	FACETS	0.763	0.668	0.864	0.763	0.668	0.864	SUBCLONAL	1	TRUE	1	0.42122877820037	2		247	442	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910789	32910789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	62	267	0	ENST00000380152.3:c.2297C>T	p.Ala766Val	p.A766V	ENST00000380152		766	gCc/gTc	11/27	1	2	FACETS	0.708	0.613	0.809	0.708	0.613	0.809	SUBCLONAL	1	TRUE	1	0.42122877820037	2		267	416	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930610	32930610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358973	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	90	409	0	ENST00000380152.3:c.7481G>A	p.Arg2494Gln	p.R2494Q	ENST00000380152		2494	cGa/cAa	15/27	1	2	FACETS	0.773	0.687	0.864	0.773	0.687	0.864	SUBCLONAL	1	TRUE	1	0.42122877820037	2		409	553	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435390	110435390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1398081220	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	123	390	0	ENST00000375856.3:c.3011G>A	p.Gly1004Asp	p.G1004D	ENST00000375856	NM_003749.2	1004	gGc/gAc	1/2	1	2	FACETS	0.864	0.783	0.949	0.864	0.783	0.949	CLONAL	1	TRUE	1	0.42122877820037	2		390	676	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40682064	40682064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs963577856	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	151	432	0	ENST00000249776.8:c.619G>A	p.Val207Ile	p.V207I	ENST00000249776	NM_033286.3	207	Gta/Ata	6/9	1	2	FACETS	0.895	0.819	0.975	0.895	0.819	0.975	CLONAL	1	TRUE	1	0.42122877820037	2		432	801	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032375	42032375	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	110	351	0	ENST00000219905.7:c.4559C>T	p.Ala1520Val	p.A1520V	ENST00000219905	NM_001164273.1	1520	gCg/gTg	14/24	1	2	FACETS	0.795	0.715	0.879	0.795	0.715	0.879	SUBCLONAL	1	TRUE	1	0.42122877820037	2		351	657	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477178	67477178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	120	425	2	ENST00000327367.4:c.985G>A	p.Ala329Thr	p.A329T	ENST00000327367	NM_005902.3	329	Gcc/Acc	7/9	1	2	FACETS	0.752	0.679	0.828	0.752	0.679	0.828	SUBCLONAL	1	TRUE	1	0.42122877820037	2		427	758	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112008	2112008	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	100	373	1	ENST00000219476.3:c.1256C>A	p.Pro419His	p.P419H	ENST00000219476	NM_000548.3	419	cCt/cAt	12/42	1	2	FACETS	0.73	0.653	0.812	0.73	0.653	0.812	SUBCLONAL	1	TRUE	1	0.42122877820037	2		374	650	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223541	2223541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs942789564	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	128	615	3	ENST00000326181.6:c.1072G>A	p.Ala358Thr	p.A358T	ENST00000326181	NM_032271.2	358	Gca/Aca	11/21	1	2	FACETS	0.687	0.622	0.755	0.687	0.622	0.755	SUBCLONAL	1	TRUE	1	0.42122877820037	2		618	885	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633218	3633218	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	164	733	0	ENST00000294008.3:c.5033del	p.Pro1678GlnfsTer37	p.P1678Qfs*37	ENST00000294008	NM_032444.2	1678	cCa/ca	14/15	1	2	FACETS	0.781	0.716	0.849	0.781	0.716	0.849	SUBCLONAL	1	TRUE	1	0.42122877820037	2		733	997	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656601	3656601	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1395992833	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	213	585	1	ENST00000294008.3:c.634C>T	p.Arg212Ter	p.R212*	ENST00000294008	NM_032444.2	212	Cga/Tga	3/15	1	2	FACETS	0.984	0.914	1	0.984	0.914	1	CLONAL	1	TRUE	1	0.42122877820037	2		586	1028	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781369	3781369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1159046430	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	134	646	1	ENST00000262367.5:c.4996G>A	p.Ala1666Thr	p.A1666T	ENST00000262367	NM_004380.2	1666	Gcc/Acc	30/31	1	2	FACETS	0.667	0.605	0.732	0.667	0.605	0.732	SUBCLONAL	1	TRUE	1	0.42122877820037	2		647	954	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781375	3781375	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	156	646	3	ENST00000262367.5:c.4990C>T	p.Arg1664Cys	p.R1664C	ENST00000262367	NM_004380.2	1664	Cgc/Tgc	30/31	1	2	FACETS	0.801	0.733	0.872	0.801	0.733	0.872	CLONAL	1	TRUE	1	0.42122877820037	2		649	925	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031933	10031933	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775591257	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	101	518	0	ENST00000330684.3:c.890G>A	p.Gly297Asp	p.G297D	ENST00000330684	NM_001134407.1	297	gGc/gAc	3/13	1	2	FACETS	0.721	0.645	0.802	0.721	0.645	0.802	SUBCLONAL	1	TRUE	1	0.42122877820037	2		518	665	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649398	23649398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144944814	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	60	270	0	ENST00000261584.4:c.101G>A	p.Arg34His	p.R34H	ENST00000261584	NM_024675.3	34	cGc/cAc	2/13	1	2	FACETS	0.552	0.476	0.635	0.552	0.476	0.635	SUBCLONAL	1	TRUE	1	0.42122877820037	2		270	516	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865830	56865830	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145146218	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	80	275	0	ENST00000308159.5:c.1162C>T	p.Arg388Trp	p.R388W	ENST00000308159	NM_014669.4	388	Cgg/Tgg	11/22	1	2	FACETS	0.74	0.653	0.833	0.74	0.653	0.833	SUBCLONAL	1	TRUE	1	0.42122877820037	2		275	513	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865834	56865834	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	85	277	0	ENST00000308159.5:c.1166C>T	p.Ala389Val	p.A389V	ENST00000308159	NM_014669.4	389	gCc/gTc	11/22	1	2	FACETS	0.773	0.685	0.867	0.773	0.685	0.867	SUBCLONAL	1	TRUE	1	0.42122877820037	2		277	522	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650654	67650654	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	114	321	0	ENST00000264010.4:c.959G>A	p.Arg320His	p.R320H	ENST00000264010	NM_006565.3	320	cGt/cAt	5/12	1	2	FACETS	0.837	0.755	0.923	0.837	0.755	0.923	CLONAL	1	TRUE	1	0.42122877820037	2		321	647	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822199	72822199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781682309	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	139	589	0	ENST00000268489.5:c.9976G>A	p.Ala3326Thr	p.A3326T	ENST00000268489	NM_006885.3	3326	Gcc/Acc	10/10	1	2	FACETS	0.748	0.681	0.819	0.748	0.681	0.819	SUBCLONAL	1	TRUE	1	0.42122877820037	2		589	882	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993161	72993161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754613484	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	174	593	0	ENST00000268489.5:c.884G>A	p.Arg295His	p.R295H	ENST00000268489	NM_006885.3	295	cGt/cAt	2/10	1	2	FACETS	0.781	0.718	0.846	0.781	0.718	0.846	SUBCLONAL	1	TRUE	1	0.42122877820037	2		593	1058	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965107	81965107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760133960	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	93	322	0	ENST00000359376.3:c.2587G>A	p.Ala863Thr	p.A863T	ENST00000359376	NM_002661.3	863	Gcc/Acc	25/33	1	2	FACETS	0.856	0.763	0.954	0.856	0.763	0.954	CLONAL	1	TRUE	1	0.42122877820037	2		322	516	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983137	7983137	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	135	514	0	ENST00000319144.4:c.877A>C	p.Met293Leu	p.M293L	ENST00000319144	NM_001139.2	293	Atg/Ctg	7/15	1	2	FACETS	0.783	0.711	0.857	0.783	0.711	0.857	SUBCLONAL	1	TRUE	1	0.42122877820037	2		514	819	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131262	17131262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778587763	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	192	662	2	ENST00000285071.4:c.190G>A	p.Ala64Thr	p.A64T	ENST00000285071	NM_144997.5	64	Gca/Aca	4/14	1	2	FACETS	0.82	0.757	0.885	0.82	0.757	0.885	CLONAL	1	TRUE	1	0.42122877820037	2		664	1112	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553583	29553583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1479669686	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	39	151	0	ENST00000356175.3:c.2132G>A	p.Arg711His	p.R711H	ENST00000356175	NM_000267.3	711	cGc/cAc	18/57	1	2	FACETS	0.699	0.583	0.827	0.699	0.583	0.827	SUBCLONAL	1	TRUE	1	0.42122877820037	2		151	265	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375496	40375496	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121908502	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	144	495	0	ENST00000293328.3:c.454C>T	p.Arg152Ter	p.R152*	ENST00000293328	NM_012448.3	152	Cga/Tga	5/19	1	2	FACETS	0.761	0.694	0.832	0.761	0.694	0.832	SUBCLONAL	1	TRUE	1	0.42122877820037	2		495	898	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234451	41234451	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs41293455	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	126	341	0	ENST00000357654.3:c.4327C>T	p.Arg1443Ter	p.R1443*	ENST00000357654	NM_007294.3	1443	Cga/Tga	12/23	1	2	FACETS	0.876	0.795	0.961	0.876	0.795	0.961	CLONAL	1	TRUE	1	0.42122877820037	2		341	683	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62009579	62009579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	152	519	0	ENST00000392795.3:c.43G>A	p.Val15Met	p.V15M	ENST00000392795	NM_001039933.1	15	Gtg/Atg	1/6	1	2	FACETS	0.884	0.809	0.963	0.884	0.809	0.963	CLONAL	1	TRUE	1	0.42122877820037	2		519	816	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120178	70120178	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057518216	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	95	347	1	ENST00000245479.2:c.1180C>T	p.Arg394Ter	p.R394*	ENST00000245479	NM_000346.3	394	Cga/Tga	3/3	1	2	FACETS	0.958	0.857	1	0.958	0.857	1	CLONAL	1	TRUE	1	0.42122877820037	2		348	471	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39575960	39575960	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	59	208	0	ENST00000262039.4:c.891+2T>C		p.X297_splice	ENST00000262039	NM_002647.2	297			1	2	FACETS	0.678	0.585	0.779	0.678	0.585	0.779	SUBCLONAL	1	TRUE	1	0.42122877820037	2		208	413	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395736	45395736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	47	294	0	ENST00000262160.6:c.398G>A	p.Arg133His	p.R133H	ENST00000262160	NM_005901.5	133	cGc/cAc	4/11	1	2	FACETS	0.399	0.336	0.469	0.399	0.336	0.469	SUBCLONAL	1	TRUE	1	0.42122877820037	2		294	559	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603020	48603020	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	37	215	1	ENST00000342988.3:c.1321C>T	p.Arg441Cys	p.R441C	ENST00000342988	NM_005359.5	441	Cgt/Tgt	11/12	1	2	FACETS	0.397	0.327	0.475	0.397	0.327	0.475	SUBCLONAL	1	TRUE	1	0.42122877820037	2		216	443	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390327	56390327	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	56	216	0	ENST00000348428.3:c.1066C>T	p.His356Tyr	p.H356Y	ENST00000348428	NM_006785.3	356	Cac/Tac	10/17	1	2	FACETS	0.655	0.563	0.755	0.655	0.563	0.755	SUBCLONAL	1	TRUE	1	0.42122877820037	2		216	406	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60795922	60795922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	115	439	0	ENST00000333681.4:c.656C>T	p.Thr219Ile	p.T219I	ENST00000333681		219	aCt/aTt	3/3	1	2	FACETS	0.772	0.696	0.852	0.772	0.696	0.852	SUBCLONAL	1	TRUE	1	0.42122877820037	2		439	707	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129635	11129635	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	128	478	0	ENST00000358026.2:c.2441C>T	p.Thr814Met	p.T814M	ENST00000358026	NM_001128849.1	814	aCg/aTg	17/36	1	2	FACETS	0.726	0.658	0.798	0.726	0.658	0.798	SUBCLONAL	1	TRUE	1	0.42122877820037	2		478	837	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627627	14627627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	132	448	1	ENST00000254322.2:c.443G>A	p.Arg148His	p.R148H	ENST00000254322	NM_006145.1	148	cGc/cAc	2/3	1	2	FACETS	0.919	0.836	1	0.919	0.836	1	CLONAL	1	TRUE	1	0.42122877820037	2		449	682	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266970	18266970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757629395	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	70	190	2	ENST00000222254.8:c.281G>A	p.Arg94His	p.R94H	ENST00000222254	NM_005027.3	94	cGc/cAc	2/16	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.42122877820037	2		192	268	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211040	36211040	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	158	721	1	ENST00000222270.7:c.791G>A	p.Gly264Asp	p.G264D	ENST00000222270	NM_014727.1	264	gGc/gAc	3/37	1	2	FACETS	0.723	0.662	0.788	0.723	0.662	0.788	SUBCLONAL	1	TRUE	1	0.42122877820037	2		722	1037	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36217221	36217221	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	152	556	0	ENST00000222270.7:c.3970C>A	p.Leu1324Ile	p.L1324I	ENST00000222270	NM_014727.1	1324	Ctc/Atc	14/37	1	2	FACETS	0.777	0.71	0.847	0.777	0.71	0.847	SUBCLONAL	1	TRUE	1	0.42122877820037	2		556	929	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221666	36221666	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1568379151	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	177	685	1	ENST00000222270.7:c.5335C>T	p.Arg1779Ter	p.R1779*	ENST00000222270	NM_014727.1	1779	Cga/Tga	26/37	1	2	FACETS	0.848	0.781	0.918	0.848	0.781	0.918	CLONAL	1	TRUE	1	0.42122877820037	2		686	991	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752913	42752913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750229302	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	184	691	0	ENST00000222329.4:c.1351G>A	p.Gly451Arg	p.G451R	ENST00000222329	NM_006494.2	451	Ggg/Agg	4/4	1	2	FACETS	0.882	0.813	0.952	0.882	0.813	0.952	CLONAL	1	TRUE	1	0.42122877820037	2		691	991	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799003	42799003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200799936	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	146	669	1	ENST00000575354.2:c.4487G>A	p.Arg1496His	p.R1496H	ENST00000575354	NM_015125.3	1496	cGc/cAc	20/20	1	2	FACETS	0.637	0.58	0.697	0.637	0.58	0.697	SUBCLONAL	1	TRUE	1	0.42122877820037	2		670	1088	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905773	50905773	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	117	632	0	ENST00000440232.2:c.821C>T	p.Ala274Val	p.A274V	ENST00000440232	NM_002691.3	274	gCc/gTc	7/27	1	2	FACETS	0.684	0.617	0.755	0.684	0.617	0.755	SUBCLONAL	1	TRUE	1	0.42122877820037	2		632	812	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497902	25497902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1311728146	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	167	570	0	ENST00000264709.3:c.547C>T	p.Arg183Trp	p.R183W	ENST00000264709	NM_175629.2	183	Cgg/Tgg	6/23	1	2	FACETS	0.9	0.827	0.976	0.9	0.827	0.976	CLONAL	1	TRUE	1	0.42122877820037	2		570	881	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432668	29432668	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45502292	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	122	481	1	ENST00000389048.3:c.3820G>A	p.Ala1274Thr	p.A1274T	ENST00000389048	NM_004304.4	1274	Gcc/Acc	25/29	1	2	FACETS	0.664	0.6	0.732	0.664	0.6	0.732	SUBCLONAL	1	TRUE	1	0.42122877820037	2		482	872	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281489	198281489	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	124	338	0	ENST00000335508.6:c.642del	p.Lys214AsnfsTer17	p.K214Nfs*17	ENST00000335508	NM_012433.2	214	aaA/aa	6/25	1	2	FACETS	0.755	0.683	0.83	0.755	0.683	0.83	SUBCLONAL	1	TRUE	1	0.42122877820037	2		338	780	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661035	227661035	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	101	575	0	ENST00000305123.5:c.2420C>A	p.Ser807Tyr	p.S807Y	ENST00000305123	NM_005544.2	807	tCt/tAt	1/2	1	2	FACETS	0.71	0.635	0.79	0.71	0.635	0.79	SUBCLONAL	1	TRUE	1	0.42122877820037	2		575	675	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	135	711	3	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.716	0.651	0.785	0.716	0.651	0.785	SUBCLONAL	1	TRUE	1	0.42122877820037	2		714	895	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31381362	31381362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113400552	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	127	293	1	ENST00000328111.2:c.1087C>T	p.Arg363Cys	p.R363C	ENST00000328111	NM_006892.3	363	Cgt/Tgt	10/23	1	2	FACETS	0.944	0.857	1	0.944	0.857	1	CLONAL	1	TRUE	1	0.42122877820037	2		294	639	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388006	31388006	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908943	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	89	297	0	ENST00000328111.2:c.1807G>A	p.Ala603Thr	p.A603T	ENST00000328111	NM_006892.3	603	Gct/Act	17/23	1	2	FACETS	0.808	0.718	0.903	0.808	0.718	0.903	CLONAL	1	TRUE	1	0.42122877820037	2		297	523	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012672	36012672	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1479413147	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	42	127	1	ENST00000358208.4:c.116G>A	p.Ser39Asn	p.S39N	ENST00000358208		39	aGc/aAc	2/12	1	2	FACETS	0.968	0.817	1	0.968	0.817	1	CLONAL	1	TRUE	1	0.42122877820037	2		128	206	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012792	36012792	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764609637	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	34	122	0	ENST00000358208.4:c.236C>T	p.Ala79Val	p.A79V	ENST00000358208		79	gCg/gTg	2/12	1	2	FACETS	0.654	0.537	0.783	0.654	0.537	0.783	SUBCLONAL	1	TRUE	1	0.42122877820037	2		122	247	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961394	54961394	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	54	189	0	ENST00000312783.6:c.238C>T	p.Gln80Ter	p.Q80*	ENST00000312783	NM_198436.1	80	Cag/Tag	4/10	1	2	FACETS	0.77	0.661	0.888	0.77	0.661	0.888	SUBCLONAL	1	TRUE	1	0.42122877820037	2		189	333	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57470688	57470688	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	67	217	0	ENST00000371085.3:c.161G>T	p.Ser54Ile	p.S54I	ENST00000371085	NM_000516.4	54	aGc/aTc	2/13	1	2	FACETS	0.767	0.669	0.872	0.767	0.669	0.872	SUBCLONAL	1	TRUE	1	0.42122877820037	2		217	415	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069382	30069382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	162	529	2	ENST00000338641.4:c.1247C>T	p.Ala416Val	p.A416V	ENST00000338641	NM_000268.3	416	gCg/gTg	12/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.42122877820037	2		531	738	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574775	41574775	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	156	538	1	ENST00000263253.7:c.7060G>A	p.Ala2354Thr	p.A2354T	ENST00000263253	NM_001429.3	2354	Gcc/Acc	31/31	1	2	FACETS	0.703	0.643	0.766	0.703	0.643	0.766	SUBCLONAL	1	TRUE	1	0.42122877820037	2		539	1054	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098642	47098642	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	125	466	0	ENST00000409792.3:c.6632G>T	p.Gly2211Val	p.G2211V	ENST00000409792	NM_014159.6	2211	gGa/gTa	15/21	1	2	FACETS	0.825	0.748	0.907	0.825	0.748	0.907	CLONAL	1	TRUE	1	0.42122877820037	2		466	719	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127731	47127731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	144	337	0	ENST00000409792.3:c.5351C>T	p.Ala1784Val	p.A1784V	ENST00000409792	NM_014159.6	1784	gCa/gTa	11/21	1	2	FACETS	0.857	0.782	0.935	0.857	0.782	0.935	CLONAL	1	TRUE	1	0.42122877820037	2		337	798	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162904	47162904	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs757432733	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	94	301	0	ENST00000409792.3:c.3222G>T	p.Lys1074Asn	p.K1074N	ENST00000409792	NM_014159.6	1074	aaG/aaT	3/21	1	2	FACETS	0.834	0.744	0.929	0.834	0.744	0.929	CLONAL	1	TRUE	1	0.42122877820037	2		301	535	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721600	49721600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	33	161	0	ENST00000449682.2:c.2039C>T	p.Ala680Val	p.A680V	ENST00000449682	NM_020998.3	680	gCc/gTc	18/18	1	2	FACETS	0.67	0.549	0.804	0.67	0.549	0.804	SUBCLONAL	1	TRUE	1	0.42122877820037	2		161	234	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723507	49723507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	16	65	0	ENST00000449682.2:c.1135G>A	p.Val379Met	p.V379M	ENST00000449682	NM_020998.3	379	Gtg/Atg	9/18	1	2	FACETS	0.938	0.707	1	0.938	0.707	1	CLONAL	1	TRUE	1	0.42122877820037	2		65	81	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936659	49936659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376534011	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	105	481	1	ENST00000296474.3:c.1268G>A	p.Arg423His	p.R423H	ENST00000296474	NM_002447.2	423	cGc/cAc	2/20	1	2	FACETS	0.679	0.609	0.754	0.679	0.609	0.754	SUBCLONAL	1	TRUE	1	0.42122877820037	2		482	734	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247353	71247353	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	111	385	0	ENST00000318789.4:c.180G>T	p.Gln60His	p.Q60H	ENST00000318789	NM_032682.5	60	caG/caT	6/21	1	2	FACETS	0.912	0.822	1	0.912	0.822	1	CLONAL	1	TRUE	1	0.42122877820037	2		385	578	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720910	119720910	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	67	305	0	ENST00000316626.5:c.265C>T	p.Gln89Ter	p.Q89*	ENST00000316626		89	Cag/Tag	2/12	1	2	FACETS	0.586	0.51	0.668	0.586	0.51	0.668	SUBCLONAL	1	TRUE	1	0.42122877820037	2		305	543	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204747	128204747	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	142	725	0	ENST00000341105.2:c.694G>T	p.Gly232Cys	p.G232C	ENST00000341105	NM_032638.4	232	Ggc/Tgc	3/6	1	2	FACETS	0.728	0.663	0.796	0.728	0.663	0.796	SUBCLONAL	1	TRUE	1	0.42122877820037	2		725	926	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807841	1807841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	162	725	0	ENST00000260795.2:c.1900G>A	p.Ala634Thr	p.A634T	ENST00000260795		634	Gca/Aca	13/17	1	2	FACETS	0.786	0.72	0.854	0.786	0.72	0.854	SUBCLONAL	1	TRUE	1	0.42122877820037	2		725	979	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980527	1980527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760185069	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	88	539	1	ENST00000382891.5:c.3989C>T	p.Ala1330Val	p.A1330V	ENST00000382891	NM_133335.3	1330	gCg/gTg	22/22	1	2	FACETS	0.465	0.411	0.523	0.465	0.411	0.523	SUBCLONAL	1	TRUE	1	0.42122877820037	2		540	899	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594061	55594061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs891140054	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	100	308	0	ENST00000288135.5:c.1847C>T	p.Ala616Val	p.A616V	ENST00000288135	NM_000222.2	616	gCg/gTg	12/21	1	2	FACETS	0.86	0.771	0.955	0.86	0.771	0.955	CLONAL	1	TRUE	1	0.42122877820037	2		308	552	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467859	66467859	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	62	237	0	ENST00000273854.3:c.410G>A	p.Cys137Tyr	p.C137Y	ENST00000273854	NM_004439.5	137	tGc/tAc	3/18	1	2	FACETS	0.663	0.574	0.759	0.663	0.574	0.759	SUBCLONAL	1	TRUE	1	0.42122877820037	2		237	444	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391521	84391521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542570943	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	76	255	0	ENST00000321945.7:c.311G>A	p.Arg104His	p.R104H	ENST00000321945	NM_139076.2	104	cGt/cAt	5/9	1	2	FACETS	0.689	0.605	0.778	0.689	0.605	0.778	SUBCLONAL	1	TRUE	1	0.42122877820037	2		255	524	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268140	153268140	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs185892035	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	98	267	0	ENST00000281708.4:c.668G>A	p.Arg223His	p.R223H	ENST00000281708	NM_033632.3	223	cGc/cAc	4/12	1	2	FACETS	0.716	0.639	0.797	0.716	0.639	0.797	SUBCLONAL	1	TRUE	1	0.42122877820037	2		267	650	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522466	187522466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781093382	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	93	338	3	ENST00000441802.2:c.11597C>T	p.Ala3866Val	p.A3866V	ENST00000441802	NM_005245.3	3866	gCg/gTg	21/27	1	2	FACETS	0.592	0.526	0.662	0.592	0.526	0.662	SUBCLONAL	1	TRUE	1	0.42122877820037	2		341	746	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527264	187527264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754008095	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	81	409	0	ENST00000441802.2:c.10310C>T	p.Ala3437Val	p.A3437V	ENST00000441802	NM_005245.3	3437	gCg/gTg	17/27	1	2	FACETS	0.518	0.456	0.584	0.518	0.456	0.584	SUBCLONAL	1	TRUE	1	0.42122877820037	2		409	743	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627774	187627774	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1183516785	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	97	345	0	ENST00000441802.2:c.3208C>T	p.Arg1070Ter	p.R1070*	ENST00000441802	NM_005245.3	1070	Cga/Tga	2/27	1	2	FACETS	0.76	0.679	0.846	0.76	0.679	0.846	SUBCLONAL	1	TRUE	1	0.42122877820037	2		345	606	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515156	31515156	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	79	490	0	ENST00000344624.3:c.1229C>A	p.Pro410His	p.P410H	ENST00000344624		410	cCt/cAt	5/33	1	2	FACETS	0.434	0.381	0.492	0.434	0.381	0.492	SUBCLONAL	1	TRUE	1	0.42122877820037	2		490	864	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876515	35876515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	105	429	0	ENST00000303115.3:c.1307C>T	p.Pro436Leu	p.P436L	ENST00000303115	NM_002185.3	436	cCc/cTc	8/8	1	2	FACETS	0.73	0.655	0.81	0.73	0.655	0.81	SUBCLONAL	1	TRUE	1	0.42122877820037	2		429	683	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522813	67522813	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	76	221	0	ENST00000274335.5:c.310A>T	p.Thr104Ser	p.T104S	ENST00000274335		104	Act/Tct	1/15	1	2	FACETS	0.884	0.78	0.996	0.884	0.78	0.996	CLONAL	1	TRUE	1	0.42122877820037	2		221	408	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593263	67593263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	72	203	0	ENST00000274335.5:c.2009G>A	p.Cys670Tyr	p.C670Y	ENST00000274335		670	tGt/tAt	15/15	1	2	FACETS	0.855	0.75	0.966	0.855	0.75	0.966	CLONAL	1	TRUE	1	0.42122877820037	2		203	400	SUCCESS
APC	324	MSKCC	GRCh37	5	112176555	112176555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771967537	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	43	272	0	ENST00000257430.4:c.5264C>T	p.Ala1755Val	p.A1755V	ENST00000257430	NM_000038.5	1755	gCg/gTg	16/16	1	2	FACETS	0.418	0.349	0.493	0.418	0.349	0.493	SUBCLONAL	1	TRUE	1	0.42122877820037	2		272	489	SUCCESS
APC	324	MSKCC	GRCh37	5	112176676	112176676	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	54	199	0	ENST00000257430.4:c.5390del	p.Asn1797IlefsTer3	p.N1797Ifs*3	ENST00000257430	NM_000038.5	1795	tcA/tc	16/16	1	2	FACETS	0.675	0.578	0.779	0.675	0.578	0.779	SUBCLONAL	1	TRUE	1	0.42122877820037	2		199	380	SUCCESS
APC	324	MSKCC	GRCh37	5	112178764	112178764	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554088389	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	85	287	0	ENST00000257430.4:c.7473G>A	p.Met2491Ile	p.M2491I	ENST00000257430	NM_000038.5	2491	atG/atA	16/16	1	2	FACETS	0.756	0.67	0.848	0.756	0.67	0.848	SUBCLONAL	1	TRUE	1	0.42122877820037	2		287	534	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924480	131924480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139372231	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	94	314	0	ENST00000265335.6:c.1153C>T	p.Arg385Cys	p.R385C	ENST00000265335		385	Cgt/Tgt	8/25	1	2	FACETS	0.857	0.765	0.954	0.857	0.765	0.954	CLONAL	1	TRUE	1	0.42122877820037	2		314	521	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523291	176523291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776973649	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	124	618	1	ENST00000292408.4:c.1948C>T	p.Arg650Cys	p.R650C	ENST00000292408	NM_213647.1	650	Cgc/Tgc	15/18	1	2	FACETS	0.735	0.665	0.809	0.735	0.665	0.809	SUBCLONAL	1	TRUE	1	0.42122877820037	2		619	801	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	85	275	2	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.801	0.71	0.897	0.801	0.71	0.897	CLONAL	1	TRUE	1	0.42122877820037	2		277	504	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393321	393321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	106	396	0	ENST00000380956.4:c.169G>A	p.Ala57Thr	p.A57T	ENST00000380956	NM_001195286.1	57	Gcg/Acg	2/9	1	2	FACETS	0.793	0.712	0.878	0.793	0.712	0.878	SUBCLONAL	1	TRUE	1	0.42122877820037	2		396	635	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26046027	26046027	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	60	254	0	ENST00000540144.1:c.389G>A	p.Arg130His	p.R130H	ENST00000540144	NM_003531.2	130	cGc/cAc	1/1	1	2	FACETS	0.744	0.643	0.852	0.744	0.643	0.852	SUBCLONAL	1	TRUE	1	0.42122877820037	2		254	383	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197213	26197213	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210592442	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	90	376	0	ENST00000356476.2:c.266C>T	p.Ala89Val	p.A89V	ENST00000356476		89	gCg/gTg	1/1	1	2	FACETS	0.758	0.674	0.847	0.758	0.674	0.847	SUBCLONAL	1	TRUE	1	0.42122877820037	2		376	564	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858252	27858252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	162	467	0	ENST00000359303.2:c.319G>A	p.Asp107Asn	p.D107N	ENST00000359303	NM_003535.2	107	Gac/Aac	1/1	1	2	FACETS	0.867	0.796	0.942	0.867	0.796	0.942	CLONAL	1	TRUE	1	0.42122877820037	2		467	887	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820271	32820271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	101	436	0	ENST00000354258.4:c.787G>A	p.Ala263Thr	p.A263T	ENST00000354258	NM_000593.5	263	Gcc/Acc	2/11	1	2	FACETS	0.621	0.555	0.692	0.621	0.555	0.692	SUBCLONAL	1	TRUE	1	0.42122877820037	2		436	772	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287204	33287204	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1562719507	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	123	505	0	ENST00000374542.5:c.1893del	p.Lys631AsnfsTer14	p.K631Nfs*14	ENST00000374542	NM_001141970.1	631	aaA/aa	6/8	1	2	FACETS	0.711	0.643	0.783	0.711	0.643	0.783	SUBCLONAL	1	TRUE	1	0.42122877820037	2		505	821	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287520	33287520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141395832	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	124	442	2	ENST00000374542.5:c.1577G>A	p.Arg526His	p.R526H	ENST00000374542	NM_001141970.1	526	cGc/cAc	6/8	1	2	FACETS	0.695	0.629	0.765	0.695	0.629	0.765	SUBCLONAL	1	TRUE	1	0.42122877820037	2		444	847	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289056	33289056	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	162	544	0	ENST00000374542.5:c.496T>G	p.Leu166Val	p.L166V	ENST00000374542	NM_001141970.1	166	Ttg/Gtg	3/8	1	2	FACETS	0.853	0.782	0.926	0.853	0.782	0.926	CLONAL	1	TRUE	1	0.42122877820037	2		544	902	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956607	93956607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777383467	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	49	271	0	ENST00000369303.4:c.2629C>T	p.Arg877Cys	p.R877C	ENST00000369303	NM_004440.3	877	Cgt/Tgt	15/17	1	2	FACETS	0.459	0.389	0.536	0.459	0.389	0.536	SUBCLONAL	1	TRUE	1	0.42122877820037	2		271	507	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958135	2958135	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150990488	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	133	588	0	ENST00000396946.4:c.2597G>A	p.Arg866Gln	p.R866Q	ENST00000396946	NM_032415.4	866	cGg/cAg	19/25	1	2	FACETS	0.775	0.704	0.849	0.775	0.704	0.849	SUBCLONAL	1	TRUE	1	0.42122877820037	2		588	815	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6031676	6031676	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780063	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	93	341	0	ENST00000265849.7:c.916G>A	p.Val306Met	p.V306M	ENST00000265849	NM_000535.5	306	Gtg/Atg	9/15	1	2	FACETS	0.681	0.606	0.761	0.681	0.606	0.761	SUBCLONAL	1	TRUE	1	0.42122877820037	2		341	648	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441985	6441985	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	109	367	1	ENST00000356142.4:c.544C>T	p.Arg182Ter	p.R182*	ENST00000356142	NM_018890.3	182	Cga/Tga	7/7	1	2	FACETS	0.812	0.731	0.899	0.812	0.731	0.899	CLONAL	1	TRUE	1	0.42122877820037	2		368	637	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729709	41729709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768547360	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	100	430	0	ENST00000242208.4:c.820G>A	p.Gly274Arg	p.G274R	ENST00000242208	NM_002192.2	274	Gga/Aga	3/3	1	2	FACETS	0.715	0.639	0.795	0.715	0.639	0.795	SUBCLONAL	1	TRUE	1	0.42122877820037	2		430	664	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435817	116435817	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	130	444	0	ENST00000397752.3:c.3907C>A	p.Leu1303Ile	p.L1303I	ENST00000397752	NM_000245.2	1303	Cta/Ata	20/21	1	2	FACETS	0.783	0.711	0.86	0.783	0.711	0.86	SUBCLONAL	1	TRUE	1	0.42122877820037	2		444	788	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435985	116435985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1443741792	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	135	447	0	ENST00000397752.3:c.3980G>A	p.Arg1327His	p.R1327H	ENST00000397752	NM_000245.2	1327	cGc/cAc	21/21	1	2	FACETS	0.79	0.719	0.866	0.79	0.719	0.866	SUBCLONAL	1	TRUE	1	0.42122877820037	2		447	811	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852125	128852125	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	174	709	0	ENST00000249373.3:c.2197G>A	p.Val733Ile	p.V733I	ENST00000249373	NM_005631.4	733	Gtc/Atc	12/12	1	2	FACETS	0.876	0.806	0.949	0.876	0.806	0.949	CLONAL	1	TRUE	1	0.42122877820037	2		709	943	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515059	148515059	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	82	312	0	ENST00000320356.2:c.1150G>T	p.Asp384Tyr	p.D384Y	ENST00000320356	NM_004456.4	384	Gac/Tac	10/20	1	2	FACETS	0.699	0.617	0.786	0.699	0.617	0.786	SUBCLONAL	1	TRUE	1	0.42122877820037	2		312	557	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133214	38133214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	112	402	0	ENST00000317025.8:c.4259G>A	p.Ser1420Asn	p.S1420N	ENST00000317025	NM_023034.1	1420	aGc/aAc	24/24	1	2	FACETS	0.743	0.668	0.821	0.743	0.668	0.821	SUBCLONAL	1	TRUE	1	0.42122877820037	2		402	716	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38153388	38153388	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	127	458	0	ENST00000317025.8:c.2841G>A	p.Trp947Ter	p.W947*	ENST00000317025	NM_023034.1	947	tgG/tgA	16/24	1	2	FACETS	0.747	0.677	0.821	0.747	0.677	0.821	SUBCLONAL	1	TRUE	1	0.42122877820037	2		458	807	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271162	38271162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437821654	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	92	416	0	ENST00000425967.3:c.2546G>A	p.Gly849Glu	p.G849E	ENST00000425967	NM_001174067.1	849	gGa/gAa	19/19	1	2	FACETS	0.837	0.746	0.933	0.837	0.746	0.933	CLONAL	1	TRUE	1	0.42122877820037	2		416	522	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866514	56866514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	157	528	0	ENST00000519728.1:c.761G>A	p.Gly254Asp	p.G254D	ENST00000519728	NM_002350.3	254	gGc/gAc	8/13	1	2	FACETS	0.748	0.685	0.815	0.748	0.685	0.815	SUBCLONAL	1	TRUE	1	0.42122877820037	2		528	996	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981360	68981360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1474820456	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	68	238	0	ENST00000288368.4:c.1432G>A	p.Val478Met	p.V478M	ENST00000288368	NM_024870.2	478	Gtg/Atg	12/40	1	2	FACETS	0.866	0.757	0.982	0.866	0.757	0.982	CLONAL	1	TRUE	1	0.42122877820037	2		238	373	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028025	69028025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200550325	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	67	331	0	ENST00000288368.4:c.3184C>T	p.Arg1062Cys	p.R1062C	ENST00000288368	NM_024870.2	1062	Cgt/Tgt	26/40	1	2	FACETS	0.684	0.596	0.779	0.684	0.596	0.779	SUBCLONAL	1	TRUE	1	0.42122877820037	2		331	465	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031691	69031691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748595305	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	85	242	0	ENST00000288368.4:c.3446G>A	p.Arg1149His	p.R1149H	ENST00000288368	NM_024870.2	1149	cGc/cAc	28/40	1	2	FACETS	0.689	0.61	0.773	0.689	0.61	0.773	SUBCLONAL	1	TRUE	1	0.42122877820037	2		242	586	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869692	117869692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1337189031	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	36	214	0	ENST00000297338.2:c.502C>T	p.Arg168Cys	p.R168C	ENST00000297338	NM_006265.2	168	Cgt/Tgt	6/14	1	2	FACETS	0.453	0.373	0.543	0.453	0.373	0.543	SUBCLONAL	1	TRUE	1	0.42122877820037	2		214	377	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737110	145737110	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	180	671	0	ENST00000428558.2:c.3456G>T	p.Glu1152Asp	p.E1152D	ENST00000428558	NM_004260.3	1152	gaG/gaT	21/22	1	2	FACETS	0.964	0.889	1	0.964	0.889	1	CLONAL	1	TRUE	1	0.42122877820037	2		671	887	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739026	145739026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781121286	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	81	531	0	ENST00000428558.2:c.2129G>A	p.Arg710His	p.R710H	ENST00000428558	NM_004260.3	710	cGc/cAc	13/22	1	2	FACETS	0.462	0.406	0.522	0.462	0.406	0.522	SUBCLONAL	1	TRUE	1	0.42122877820037	2		531	833	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741761	145741761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540719285	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	141	574	0	ENST00000428558.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000428558	NM_004260.3	248	Cgt/Tgt	5/22	1	2	FACETS	0.742	0.676	0.812	0.742	0.676	0.812	SUBCLONAL	1	TRUE	1	0.42122877820037	2		574	902	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341839	8341839	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	84	405	0	ENST00000356435.5:c.4801C>A	p.Gln1601Lys	p.Q1601K	ENST00000356435		1601	Caa/Aaa	29/35	1	2	FACETS	0.618	0.546	0.695	0.618	0.546	0.695	SUBCLONAL	1	TRUE	1	0.42122877820037	2		405	645	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484181	8484181	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1025234387	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	95	375	0	ENST00000356435.5:c.3351G>T	p.Lys1117Asn	p.K1117N	ENST00000356435		1117	aaG/aaT	19/35	1	2	FACETS	0.767	0.684	0.855	0.767	0.684	0.855	SUBCLONAL	1	TRUE	1	0.42122877820037	2		375	588	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507344	8507344	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573381420	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	102	272	0	ENST00000356435.5:c.1634C>T	p.Ala545Val	p.A545V	ENST00000356435		545	gCc/gTc	11/35	1	2	FACETS	0.882	0.791	0.978	0.882	0.791	0.978	CLONAL	1	TRUE	1	0.42122877820037	2		272	549	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215787	98215787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376844749	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	129	446	1	ENST00000331920.6:c.3422C>T	p.Ala1141Val	p.A1141V	ENST00000331920	NM_000264.3	1141	gCg/gTg	20/24	1	2	FACETS	0.819	0.743	0.898	0.819	0.743	0.898	CLONAL	1	TRUE	1	0.42122877820037	2		447	748	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755914	133755914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1476512998	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	124	457	0	ENST00000318560.5:c.1541G>A	p.Gly514Asp	p.G514D	ENST00000318560	NM_005157.4	514	gGc/gAc	10/11	1	2	FACETS	0.726	0.657	0.799	0.726	0.657	0.799	SUBCLONAL	1	TRUE	1	0.42122877820037	2		457	811	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399159	139399159	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1456612268	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	129	584	0	ENST00000277541.6:c.4984C>T	p.Arg1662Trp	p.R1662W	ENST00000277541	NM_017617.3	1662	Cgg/Tgg	26/34	1	2	FACETS	0.8	0.725	0.878	0.8	0.725	0.878	SUBCLONAL	1	TRUE	1	0.42122877820037	2		584	766	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409968	139409968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372771179	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	175	692	0	ENST00000277541.6:c.1870G>A	p.Ala624Thr	p.A624T	ENST00000277541	NM_017617.3	624	Gcc/Acc	11/34	1	2	FACETS	0.865	0.796	0.936	0.865	0.796	0.936	CLONAL	1	TRUE	1	0.42122877820037	2		692	961	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230758	53230758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782683492	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	164	511	0	ENST00000375401.3:c.2035C>T	p.Arg679Cys	p.R679C	ENST00000375401	NM_004187.3	679	Cgt/Tgt	14/26	1	2	FACETS	0.914	0.84	0.992	0.914	0.84	0.992	CLONAL	1	TRUE	1	0.42122877820037	2		511	852	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247490	53247490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782091438	NA	P-0044790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	97	436	0	ENST00000375401.3:c.319C>T	p.Arg107Trp	p.R107W	ENST00000375401	NM_004187.3	107	Cgg/Tgg	3/26	1	2	FACETS	0.571	0.508	0.637	0.571	0.508	0.637	SUBCLONAL	1	TRUE	1	0.42122877820037	2		436	807	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0044793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	109	494	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.315137355411962	2		494	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578476	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTGCCGGGCGG	GGGTGCCGGGCGG	-	rs876659215	NA	P-0044793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	230	801	0	ENST00000269305.4:c.454_466del	p.Pro152AlafsTer14	p.P152Afs*14	ENST00000269305	NM_001126112.2	152	CCGCCCGGCACCCgc/gc	5/11	0.2110717659109	3	FACETS	0.876	0.821	0.931	0.876	0.821	0.931	CLONAL	3	TRUE	0	0.315137355411962	3		801	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0044796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	100	606	1	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.203293973575754	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.203293973575754	1		607	676	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562181	21562181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	160	801	1	ENST00000382592.4:c.1738G>A	p.Val580Ile	p.V580I	ENST00000382592	NM_014572.2	580	Gtc/Atc	4/8	0.203293973575754	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.203293973575754	1		802	1133	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050809	49050910	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTAAAGTAAAGAATTCTGTAATTTGTAGACTTCTGAGAAGTTCCAGAAAATAAATCAGATGGTATGTAACAGCGACCGTGTGCTCAAAAGAAGTGCTGAAGG	TTAAAGTAAAGAATTCTGTAATTTGTAGACTTCTGAGAAGTTCCAGAAAATAAATCAGATGGTATGTAACAGCGACCGTGTGCTCAAAAGAAGTGCTGAAGG	-	novel	NA	P-0044796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	33	160	0	ENST00000267163.4:c.2521-28_2594del		p.X841_splice	ENST00000267163	NM_000321.2	841		25/27	0.203293973575754	3	FACETS	0.755	0.618	0.906	0.503	0.412	0.604	CLONAL	2	TRUE	0	0.203293973575754	3		160	237	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650662	67650662	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0044796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	121	418	0	ENST00000264010.4:c.967A>T	p.Lys323Ter	p.K323*	ENST00000264010	NM_006565.3	323	Aag/Tag	5/12	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.203293973575754	2		418	815	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243868	41243868	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1295353818	NA	P-0044796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	76	472	0	ENST00000357654.3:c.3680A>G	p.Gln1227Arg	p.Q1227R	ENST00000357654	NM_007294.3	1227	cAa/cGa	10/23	0.203293973575754	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.203293973575754	1		472	638	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499710	8499710	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	57	501	0	ENST00000356435.5:c.2259G>T	p.Arg753Ser	p.R753S	ENST00000356435		753	agG/agT	14/35	1	2	FACETS	0.74	0.633	0.856	0.74	0.633	0.856	SUBCLONAL	1	TRUE	1	0.203293973575754	2		501	758	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0044809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	205	467	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.229059703561591	1	FACETS	1	0.949	1	1	0.994	1	CLONAL	2	FALSE	0	0.229059703561591	1		467	773	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	77	126	0				ENST00000310581	NM_198253.2	-/1132			0.229059703561591	3	FACETS	0.794	0.699	0.895	0.794	0.699	0.895	SUBCLONAL	2	FALSE	1	0.229059703561591	3		126	472	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107236	193107236	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	25	265	0	ENST00000367435.3:c.445G>C	p.Asp149His	p.D149H	ENST00000367435	NM_024529.4	149	Gat/Cat	6/17	0.189847536742256	3	FACETS	0.808	0.638	1	0.269	0.212	0.335	CLONAL	1	FALSE	0	0.229059703561591	3		265	301	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63699984	63699984	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	42	286	0	ENST00000279873.7:c.319G>C	p.Glu107Gln	p.E107Q	ENST00000279873	NM_032199.2	107	Gaa/Caa	3/10	0.169310799925446	0	FACETS	0.732	0.613	0.865			1	SUBCLONAL	1	FALSE	0	0.229059703561591	0		286	386	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94922999	94922999	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	38	458	1	ENST00000536441.1:c.469G>A	p.Glu157Lys	p.E157K	ENST00000536441	NM_144665.3	157	Gaa/Aaa	4/10	1	2	FACETS	0.857	0.71	1	0.857	0.71	1	CLONAL	1	FALSE	1	0.229059703561591	2		459	387	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504561	103504561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774884182	NA	P-0044809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	34	333	0	ENST00000355739.4:c.182G>A	p.Arg61Gln	p.R61Q	ENST00000355739	NM_000123.3	61	cGg/cAg	2/15	1	2	FACETS	0.771	0.631	0.929	0.771	0.631	0.929	CLONAL	1	FALSE	1	0.229059703561591	2		333	385	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40861904	40861904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	56	560	0	ENST00000428826.2:c.1453G>A	p.Glu485Lys	p.E485K	ENST00000428826		485	Gag/Aag	13/21	1	2	FACETS	0.567	0.484	0.657	0.567	0.484	0.657	SUBCLONAL	1	FALSE	1	0.229059703561591	2		560	863	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226510	41226510	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	51	433	0	ENST00000357654.3:c.4513G>T	p.Asp1505Tyr	p.D1505Y	ENST00000357654	NM_007294.3	1505	Gat/Tat	14/23	1	2	FACETS	0.69	0.586	0.805	0.69	0.586	0.805	SUBCLONAL	1	FALSE	1	0.229059703561591	2		433	645	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761283	59761283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776002434	NA	P-0044809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	71	597	1	ENST00000259008.2:c.3124G>A	p.Glu1042Lys	p.E1042K	ENST00000259008	NM_032043.2	1042	Gaa/Aaa	20/20	0.229059703561591	3	FACETS	0.741	0.645	0.845	0.37	0.322	0.423	SUBCLONAL	1	FALSE	1	0.229059703561591	3		598	933	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598102	55598102	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	58	548	0	ENST00000288135.5:c.2299G>T	p.Glu767Ter	p.E767*	ENST00000288135	NM_000222.2	767	Gaa/Taa	16/21	1	2	FACETS	0.659	0.565	0.762	0.659	0.565	0.762	SUBCLONAL	1	FALSE	1	0.229059703561591	2		548	768	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380914	116380914	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	161	530	0	ENST00000397752.3:c.1536G>C	p.Lys512Asn	p.K512N	ENST00000397752	NM_000245.2	512	aaG/aaC	5/21	1	2	FACETS	0.949	0.872	1	1	0.992	1	CLONAL	2	FALSE	1	0.229059703561591	2		530	741	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163307857	163307857	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	74	297	0	ENST00000271452.3:c.483G>C	p.Glu161Asp	p.E161D	ENST00000271452	NM_145697.2	161	gaG/gaC	7/14	0.563889975177826	3	FACETS	0.825	0.725	0.931	0.412	0.362	0.466	CLONAL	1	TRUE	1	0.563889975177826	3		297	408	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380749	118380749	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	122	392	0	ENST00000534358.1:c.10987A>G	p.Ile3663Val	p.I3663V	ENST00000534358	NM_005933.3	3663	Att/Gtt	30/36	0.529201383817972	3	FACETS	1	0.961	1	0.554	0.503	0.606	CLONAL	1	TRUE	1	0.563889975177826	3		392	501	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811728	102811728	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	181	632	0	ENST00000307046.8:c.456G>T	p.Trp152Cys	p.W152C	ENST00000307046	NM_001111285.1	152	tgG/tgT	4/4	0.529201383817972	3	FACETS	0.996	0.92	1	0.498	0.46	0.538	CLONAL	1	TRUE	1	0.563889975177826	3		632	826	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900288	32900288	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs81002797	NA	P-0044812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	95	284	0	ENST00000380152.3:c.475+1G>A		p.X159_splice	ENST00000380152		159			0.563889975177826	2	FACETS	0.842	0.768	0.917	0.842	0.768	0.917	CLONAL	2	TRUE	0	0.563889975177826	2		284	200	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358489	91358489	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	80	444	0	ENST00000355112.3:c.4234C>G	p.Pro1412Ala	p.P1412A	ENST00000355112	NM_000057.2	1412	Cct/Gct	22/22	0.52481411139568	4	FACETS	0.629	0.553	0.71	0.314	0.276	0.355	SUBCLONAL	1	TRUE	2	0.563889975177826	4		444	706	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490221	29490227	+	frameshift_variant	Frame_Shift_Del	DEL	GAGATTA	GAGATTA	-	novel	NA	P-0044812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	85	297	0	ENST00000356175.3:c.308_314del	p.Arg103MetfsTer60	p.R103Mfs*60	ENST00000356175	NM_000267.3	102	atGAGATTA/at	4/57	0.563889975177826	1	FACETS	0.975	0.878	1	0.975	0.878	1	CLONAL	1	TRUE	0	0.563889975177826	1		297	222	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091719	29091719	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1248967885	NA	P-0044812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	68	49	0	ENST00000328354.6:c.1238T>C	p.Leu413Ser	p.L413S	ENST00000328354	NM_007194.3	413	tTa/tCa	11/15	0.534688958495098	3	FACETS	1	0.939	1	1	0.939	1	CLONAL	3	TRUE	0	0.563889975177826	3		49	100	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543946	41543946	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs766548877	NA	P-0044812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	142	582	0	ENST00000263253.7:c.2237A>G	p.Asn746Ser	p.N746S	ENST00000263253	NM_001429.3	746	aAc/aGc	12/31	0.563889975177826	2	FACETS	0.781	0.714	0.851	0.39	0.357	0.426	SUBCLONAL	1	TRUE	0	0.563889975177826	2		582	645	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935563	13935563	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs773216548	NA	P-0044812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	230	396	0	ENST00000405192.2:c.1293T>A	p.Asp431Glu	p.D431E	ENST00000405192	NM_001163147.1	431	gaT/gaA	12/12	0.543767649315069	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.563889975177826	2		396	396	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851109	151851128	+	frameshift_variant	Frame_Shift_Del	DEL	GATGCAGAGTAATTGCTACA	GATGCAGAGTAATTGCTACA	-	novel	NA	P-0044812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	37	236	0	ENST00000262189.6:c.12243_12262del	p.Val4082TyrfsTer4	p.V4082Yfs*4	ENST00000262189	NM_170606.2	4081	tcTGTAGCAATTACTCTGCATCct/tcct	48/59	0.497561750194461	5	FACETS	0.799	0.662	0.952	0.266	0.22	0.318	CLONAL	1	TRUE	2	0.563889975177826	5		236	303	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974784	+	frameshift_variant	Frame_Shift_Del	DEL	GCCAGCCA	GCCAGCCA	-	novel	NA	P-0044812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	34	241	0	ENST00000304494.5:c.43_50del	p.Trp15HisfsTer26	p.W15Hfs*26	ENST00000304494	NM_000077.4	15	TGGCTGGCc/c	1/3	0.563889975177826	1	FACETS	0.57	0.472	0.676	0.57	0.472	0.676	SUBCLONAL	1	TRUE	0	0.563889975177826	1		241	152	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0044820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	87	314	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.392704087861746	5	FACETS	0.842	0.745	0.946	0.281	0.248	0.316	CLONAL	1	TRUE	2	0.473036337244951	5		314	747	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229240	123229240	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867285087	NA	P-0044820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	89	157	0	ENST00000218089.9:c.3724C>T	p.Arg1242Ter	p.R1242*	ENST00000218089	NM_001042749.1	1242	Cga/Tga	34/35	1	1	FACETS	0.76	0.691	0.83	1	0.984	1	SUBCLONAL	2	TRUE	0	0.473036337244951	1		157	189	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	135	126	0				ENST00000310581	NM_198253.2	-/1132			0.223643766090437	5	FACETS	1	0.944	1	0.694	0.635	0.754	INDETERMINATE	2	TRUE	2	0.473036337244951	5		126	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0044820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	453	428	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.437595585990902	2	FACETS	0.976	0.936	1	0.976	0.936	1	CLONAL	2	TRUE	0	0.473036337244951	2		428	981	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0044820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	107	464	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.392704087861746	5	FACETS	0.877	0.786	0.974	0.292	0.262	0.325	CLONAL	1	TRUE	2	0.473036337244951	5		464	882	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196999	106196999	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	140	268	0	ENST00000380013.4:c.5332C>T	p.His1778Tyr	p.H1778Y	ENST00000380013	NM_001127208.2	1778	Cat/Tat	11/11	0.473036337244951	3	FACETS	0.895	0.823	0.968	0.895	0.823	0.968	CLONAL	2	TRUE	1	0.473036337244951	3		268	409	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821594	72821596	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs374416547	NA	P-0044820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	10	124	0	ENST00000268489.5:c.10579_10581del	p.Gly3527del	p.G3527del	ENST00000268489	NM_006885.3	3527	GGC/-	10/10	0.351799066815546	3	FACETS	0.263	0.178	0.37	0.131	0.089	0.185	SUBCLONAL	1	TRUE	1	0.473036337244951	3		124	199	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295176	1295176	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1475402448	NA	P-0044820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	151	230	0				ENST00000310581	NM_198253.2	-/1132			0.223643766090437	5	FACETS	1	0.982	1	0.816	0.753	0.881	INDETERMINATE	2	TRUE	2	0.473036337244951	5		230	446	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32932053	32932053	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1135401919	NA	P-0044820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	147	251	0	ENST00000380152.3:c.7792G>T	p.Glu2598Ter	p.E2598*	ENST00000380152		2598	Gaa/Taa	16/27	0.429202955107003	3	FACETS	1	0.98	1	0.779	0.722	0.836	CLONAL	2	TRUE	0	0.473036337244951	3		251	329	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872582	136872582	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	77	336	0	ENST00000241393.3:c.916G>T	p.Gly306Ter	p.G306*	ENST00000241393	NM_003467.2	306	Gga/Tga	2/2	0.415585086176086	3	FACETS	0.724	0.637	0.818	0.241	0.212	0.273	SUBCLONAL	1	TRUE	0	0.473036337244951	3		336	556	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140790	55140805	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGGTAGATATTTTCT	CAGGTAGATATTTTCT	-	novel	NA	P-0044820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	66	371	0	ENST00000257290.5:c.1653_1653+15del		p.X551_splice	ENST00000257290	NM_006206.4	551		11/23	0.473036337244951	3	FACETS	0.74	0.644	0.844	0.37	0.322	0.422	SUBCLONAL	1	TRUE	1	0.473036337244951	3		371	466	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170148	32170148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	131	921	1	ENST00000375023.3:c.3460G>A	p.Gly1154Ser	p.G1154S	ENST00000375023	NM_004557.3	1154	Ggc/Agc	21/30	0.473036337244951	3	FACETS	0.552	0.5	0.608	0.276	0.25	0.304	SUBCLONAL	1	TRUE	1	0.473036337244951	3		922	1240	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099925	157099925	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	155	453	0	ENST00000346085.5:c.862G>C	p.Glu288Gln	p.E288Q	ENST00000346085	NM_020732.3	288	Gaa/Caa	1/20	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.473036337244951	2		453	639	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050770	5050770	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	71	390	0	ENST00000381652.3:c.553G>C	p.Asp185His	p.D185H	ENST00000381652	NM_004972.3	185	Gat/Cat	6/25	0.473036337244951	1	FACETS	0.594	0.521	0.672	0.594	0.521	0.672	SUBCLONAL	1	TRUE	0	0.473036337244951	1		390	386	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923011	44923011	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	283	288	0	ENST00000377967.4:c.1872del	p.Thr625ProfsTer66	p.T625Pfs*66	ENST00000377967	NM_021140.2	624	ctG/ct	16/29	0.382575717807976	2	FACETS	1	0.99	1			1	CLONAL	2	TRUE	NA	0.473036337244951	2		288	516	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430793	47430793	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	132	392	0	ENST00000377045.4:c.1758G>C	p.Leu586Phe	p.L586F	ENST00000377045	NM_001654.4	586	ttG/ttC	16/16	0.382575717807976	2	FACETS	0.86	0.783	0.941			1	CLONAL	1	TRUE	NA	0.473036337244951	2		392	649	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0044860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	279	523	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.207578598420078	3	FACETS	1	0.978	1	1	0.995	1	CLONAL	5	FALSE	0	0.207578598420078	3		523	563	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0044860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	73	277	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	0.934	0.828	1	1	0.986	1	CLONAL	3	FALSE	1	0.207578598420078	2		277	251	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61712995	61712995	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1460782822	NA	P-0044860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	40	375	0	ENST00000401558.2:c.2416A>G	p.Ile806Val	p.I806V	ENST00000401558	NM_003400.3	806	Ata/Gta	20/25	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	1	0.207578598420078	2		375	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0044907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	178	467	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.351551315988415	2	FACETS	0.91	0.845	0.978	0.91	0.845	0.978	CLONAL	2	TRUE	0	0.354913648698759	2		467	551	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0044907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	150	550	4	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.131732464870052	4	FACETS	1	0.952	1	0.7	0.644	0.759	INDETERMINATE	2	TRUE	1	0.354913648698759	4		554	545	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478902	56478902	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	295	826	0	ENST00000267101.3:c.358A>G	p.Met120Val	p.M120V	ENST00000267101	NM_001982.3	120	Atg/Gtg	3/28	0.14306543000279	6	FACETS	0.916	0.863	0.971	0.916	0.863	0.971	INDETERMINATE	3	TRUE	3	0.354913648698759	6		826	1034	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928076	178928084	+	inframe_deletion	In_Frame_Del	DEL	TTAGAAGAT	TTAGAAGAT	-	novel	NA	P-0044907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	141	515	0	ENST00000263967.3:c.1356_1364del	p.Glu453_Leu455del	p.E453_L455del	ENST00000263967	NM_006218.2	452	TTAGAAGAT/-	8/21	0.131732464870052	4	FACETS	0.822	0.751	0.896	0.548	0.5	0.597	INDETERMINATE	2	TRUE	1	0.354913648698759	4		515	655	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514729	103514729	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	61	444	0	ENST00000355739.4:c.1230G>T	p.Gln410His	p.Q410H	ENST00000355739	NM_000123.3	410	caG/caT	8/15	0.257670600245585	3	FACETS	1	0.911	1	0.356	0.308	0.407	CLONAL	1	TRUE	0	0.354913648698759	3		444	379	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41021765	41021765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	177	473	0	ENST00000267868.3:c.707G>A	p.Gly236Asp	p.G236D	ENST00000267868	NM_002875.4	236	gGt/gAt	8/10	0.0856650239339845	4	FACETS	1	0.942	1	1	0.942	1	INDETERMINATE	2	TRUE	2	0.354913648698759	4		473	662	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0044914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	161	248	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.750114108025703	3	FACETS	0.591	0.541	0.642	0.295	0.27	0.321	SUBCLONAL	1	TRUE	1	0.777176089476211	3		248	974	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0044914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	113	464	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.750114108025703	3	FACETS	0.368	0.33	0.409	0.184	0.165	0.205	SUBCLONAL	1	TRUE	1	0.777176089476211	3		464	1096	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252866	36252866	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	197	501	0	ENST00000300305.3:c.496C>G	p.Arg166Gly	p.R166G	ENST00000300305		166	Cga/Gga	4/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.777176089476211	2		501	477	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245858	46245858	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	103	343	0	ENST00000334344.6:c.3952C>T	p.Gln1318Ter	p.Q1318*	ENST00000334344	NM_152641.2	1318	Cag/Tag	15/21	1	2	FACETS	0.539	0.484	0.596	0.539	0.484	0.596	SUBCLONAL	1	TRUE	1	0.777176089476211	2		343	492	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649679	48649679	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150572851	NA	P-0044914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	434	789	1	ENST00000376670.3:c.163G>A	p.Ala55Thr	p.A55T	ENST00000376670	NM_002049.3	55	Gct/Act	2/6	0.315794807729977	1	FACETS	0.739	0.708	0.77	0.739	0.708	0.77	INDETERMINATE	1	TRUE	0	0.777176089476211	1		790	924	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245027	46245027	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	181	563	0	ENST00000334344.6:c.3121C>T	p.Gln1041Ter	p.Q1041*	ENST00000334344	NM_152641.2	1041	Caa/Taa	15/21	1	2	FACETS	0.597	0.552	0.644	0.597	0.552	0.644	SUBCLONAL	1	TRUE	1	0.777176089476211	2		563	780	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133747537	133747537	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	128	419	0	ENST00000318560.5:c.844G>C	p.Glu282Gln	p.E282Q	ENST00000318560	NM_005157.4	282	Gag/Cag	5/11	0.771643305225185	2	FACETS	0.6	0.546	0.656	0.3	0.273	0.328	SUBCLONAL	1	TRUE	0	0.777176089476211	2		419	549	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041361	47041361	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782440714	NA	P-0044914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	256	720	0	ENST00000377604.3:c.1705G>A	p.Val569Ile	p.V569I	ENST00000377604	NM_001204468.1	569	Gtc/Atc	16/24	0.315794807729977	1	FACETS	0.457	0.428	0.486	0.457	0.428	0.486	INDETERMINATE	1	TRUE	0	0.777176089476211	1		720	882	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532590	187532590	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0044914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	178	329	0	ENST00000441802.2:c.9803C>G	p.Ser3268Ter	p.S3268*	ENST00000441802	NM_005245.3	3268	tCa/tGa	14/27	0.777176089476211	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.777176089476211	1		329	242	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245765	46245765	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	116	413	2	ENST00000334344.6:c.3859G>T	p.Glu1287Ter	p.E1287*	ENST00000334344	NM_152641.2	1287	Gaa/Taa	15/21	1	2	FACETS	0.538	0.486	0.592	0.538	0.486	0.592	SUBCLONAL	1	TRUE	1	0.777176089476211	2		415	555	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445485	49445485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371225040	NA	P-0044914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	305	866	0	ENST00000301067.7:c.1981C>T	p.Arg661Cys	p.R661C	ENST00000301067	NM_003482.3	661	Cgc/Tgc	10/54	1	2	FACETS	0.599	0.564	0.636	0.599	0.564	0.636	SUBCLONAL	1	TRUE	1	0.777176089476211	2		866	1310	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs149680468	NA	P-0044914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	78	303	0	ENST00000281708.4:c.1513C>A	p.Arg505Ser	p.R505S	ENST00000281708	NM_033632.3	505	Cgc/Agc	10/12	1	2	FACETS	0.415	0.365	0.468	0.415	0.365	0.468	SUBCLONAL	1	TRUE	1	0.777176089476211	2		303	484	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38991161	38991161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1346388651	NA	P-0044914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	109	318	0	ENST00000357387.3:c.473C>T	p.Ala158Val	p.A158V	ENST00000357387	NM_152756.3	158	gCt/gTt	7/38	NA	2	FACETS	0.531	0.479	0.586			1	INDETERMINATE	1	TRUE	NA	0.777176089476211	2		318	528	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779014	3779014	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765101871	NA	P-0044914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	327	627	0	ENST00000262367.5:c.6034G>A	p.Val2012Ile	p.V2012I	ENST00000262367	NM_004380.2	2012	Gtc/Atc	31/31	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.777176089476211	2		627	776	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244257	46244257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	113	365	0	ENST00000334344.6:c.2351C>G	p.Pro784Arg	p.P784R	ENST00000334344	NM_152641.2	784	cCt/cGt	15/21	1	2	FACETS	0.634	0.573	0.696	0.634	0.573	0.696	SUBCLONAL	1	TRUE	1	0.777176089476211	2		365	459	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245865	46245865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	95	336	0	ENST00000334344.6:c.3959C>T	p.Ser1320Leu	p.S1320L	ENST00000334344	NM_152641.2	1320	tCa/tTa	15/21	1	2	FACETS	0.521	0.466	0.579	0.521	0.466	0.579	SUBCLONAL	1	TRUE	1	0.777176089476211	2		336	469	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245907	46245907	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	79	316	0	ENST00000334344.6:c.4001G>A	p.Gly1334Glu	p.G1334E	ENST00000334344	NM_152641.2	1334	gGa/gAa	15/21	1	2	FACETS	0.468	0.414	0.527	0.468	0.414	0.527	SUBCLONAL	1	TRUE	1	0.777176089476211	2		316	434	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103437	2103437	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	464	824	0	ENST00000219476.3:c.320C>G	p.Ala107Gly	p.A107G	ENST00000219476	NM_000548.3	107	gCc/gGc	4/42	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.777176089476211	2		824	1167	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733038	74733038	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1686	113	546	0	ENST00000359995.5:c.205G>T	p.Glu69Ter	p.E69*	ENST00000359995	NM_001195427.1	69	Gag/Tag	1/3	0.777176089476211	6	FACETS	0.413	0.37	0.459			1	SUBCLONAL	1	TRUE	NA	0.777176089476211	6		546	1799	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266845	18266845	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	182	493	0	ENST00000222254.8:c.156G>T	p.Gln52His	p.Q52H	ENST00000222254	NM_005027.3	52	caG/caT	2/16	1	2	FACETS	0.602	0.556	0.649	0.602	0.556	0.649	SUBCLONAL	1	TRUE	1	0.777176089476211	2		493	778	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982502	25982502	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	171	222	0	ENST00000435504.4:c.788G>C	p.Arg263Thr	p.R263T	ENST00000435504		263	aGa/aCa	9/13	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.777176089476211	2		222	429	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52692235	52692235	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	79	317	0	ENST00000394830.3:c.625C>T	p.Gln209Ter	p.Q209*	ENST00000394830	NM_018313.4	209	Cag/Tag	6/30	0.777176089476211	1	FACETS	0.414	0.368	0.463	0.414	0.368	0.463	SUBCLONAL	1	TRUE	0	0.777176089476211	1		317	300	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054886	5054886	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0044914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	147	252	0	ENST00000381652.3:c.936+2T>C		p.X312_splice	ENST00000381652	NM_004972.3	312			0.777176089476211	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.777176089476211	1		252	223	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994276	21994276	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	46	551	0	ENST00000579755.1:c.55C>T	p.Arg19Ter	p.R19*	ENST00000579755		19	Cga/Tga	1/3	0.777176089476211				0.105	0.148				SUBCLONAL	1	TRUE	0	0.777176089476211	1		551	576	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932077	39932077	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0044914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	402	721	0	ENST00000378444.4:c.2522C>G	p.Ser841Ter	p.S841*	ENST00000378444	NM_001123385.1	841	tCa/tGa	4/15	0.315794807729977	1	FACETS	0.758	0.725	0.79	0.758	0.725	0.79	INDETERMINATE	1	TRUE	0	0.777176089476211	1		721	835	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575098	48575113	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTGGAGGTGGCCTG	CTCTGGAGGTGGCCTG	-	novel	NA	P-0044914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	65	285	0	ENST00000342988.3:c.292_307del	p.Leu98IlefsTer7	p.L98Ifs*7	ENST00000342988	NM_005359.5	98	CTCTGGAGGTGGCCTGat/at	3/12	0.315794807729977	1	FACETS	0.299	0.261	0.34	0.299	0.261	0.34	INDETERMINATE	1	TRUE	0	0.777176089476211	1		285	342	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575122	48575122	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	65	273	0	ENST00000342988.3:c.320del	p.Asn107MetfsTer3	p.N107Mfs*3	ENST00000342988	NM_005359.5	106	Aaa/aa	3/12	0.315794807729977	1	FACETS	0.303	0.265	0.345	0.303	0.265	0.345	INDETERMINATE	1	TRUE	0	0.777176089476211	1		273	337	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453145	140453146	+	missense_variant	Missense_Mutation	DNP	AG	AG	GA	rs121913368	NA	P-0044915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	318	371	1	ENST00000288602.6:c.1789_1790delinsTC	p.Leu597Ser	p.L597S	ENST00000288602	NM_004333.4	597	CTa/TCa	15/18	0.753043295672588	5	FACETS	0.923	0.886	0.959	0.923	0.886	0.959	CLONAL	4	TRUE	1	0.753043295672588	5		372	487	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307003	65307003	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	48	363	0	ENST00000342505.4:c.2574A>C	p.Glu858Asp	p.E858D	ENST00000342505	NM_002227.2	858	gaA/gaC	19/25	0.367933473739182	3	FACETS	0.756	0.646	0.875	0.378	0.323	0.438	INDETERMINATE	1	TRUE	1	0.753043295672588	3		363	232	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112555	2112555	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	80	895	0	ENST00000219476.3:c.1315G>C	p.Asp439His	p.D439H	ENST00000219476	NM_000548.3	439	Gac/Cac	13/42	0.648316613486459	3	FACETS	0.578	0.51	0.651	0.289	0.255	0.326	SUBCLONAL	1	TRUE	1	0.753043295672588	3		895	506	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828801	3828801	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	249	603	0	ENST00000262367.5:c.1841C>G	p.Pro614Arg	p.P614R	ENST00000262367	NM_004380.2	614	cCa/cGa	9/31	0.648316613486459	3	FACETS	0.987	0.937	1	0.987	0.937	1	CLONAL	2	TRUE	1	0.753043295672588	3		603	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577541	7577544	+	frameshift_variant	Frame_Shift_Del	DEL	TTCA	TTCA	-	novel	NA	P-0044915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	250	769	0	ENST00000269305.4:c.737_740del	p.Met246ThrfsTer98	p.M246Tfs*98	ENST00000269305	NM_001126112.2	246	aTGAAc/ac	7/11	0.701111213829649	2	FACETS	0.938	0.899	0.975	0.938	0.899	0.975	CLONAL	2	TRUE	0	0.753043295672588	2		769	354	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31421465	31421465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	184	419	0	ENST00000344624.3:c.3439G>A	p.Glu1147Lys	p.E1147K	ENST00000344624		1147	Gaa/Aaa	27/33	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.603141145474208	2		419	478	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0044957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	825	698	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.885224701087134	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.885224701087134	1		698	973	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268760	41268760	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	414	411	0	ENST00000349496.5:c.998A>T	p.Tyr333Phe	p.Y333F	ENST00000349496	NM_001904.3	333	tAc/tTc	7/15	0.885224701087134	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.885224701087134	1		411	483	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716229	52716229	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	212	713	0	ENST00000322088.6:c.673G>T	p.Val225Leu	p.V225L	ENST00000322088	NM_014225.5	225	Gtg/Ttg	6/15	0.125673384065926	3	FACETS	0.591	0.548	0.636	0.197	0.182	0.212	INDETERMINATE	1	TRUE	0	0.885224701087134	3		713	1169	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413274	139413274	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	498	754	2	ENST00000277541.6:c.868C>T	p.Gln290Ter	p.Q290*	ENST00000277541	NM_017617.3	290	Cag/Tag	6/34	1	2	FACETS	0.826	0.791	0.862	0.826	0.791	0.862	CLONAL	1	TRUE	1	0.885224701087134	2		756	1362	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545835	41545835	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	325	760	0	ENST00000263253.7:c.2450T>A	p.Ile817Asn	p.I817N	ENST00000263253	NM_001429.3	817	aTt/aAt	14/31	0.861617323511819	2	FACETS	0.668	0.631	0.705	0.334	0.315	0.353	SUBCLONAL	1	TRUE	0	0.885224701087134	2		760	1100	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840078	27840078	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1443072275	NA	P-0044957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	111	221	0	ENST00000328488.2:c.16C>G	p.Gln6Glu	p.Q6E	ENST00000328488	NM_003533.2	6	Caa/Gaa	1/1	0.40678104154217	3	FACETS	0.661	0.597	0.729	0.331	0.298	0.365	INDETERMINATE	1	TRUE	1	0.885224701087134	3		221	547	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519713	137519713	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	258	269	0	ENST00000367739.4:c.925A>G	p.Thr309Ala	p.T309A	ENST00000367739	NM_000416.2	309	Acg/Gcg	7/7	0.443132743524112	3	FACETS	0.836	0.793	0.879	0.836	0.793	0.879	INDETERMINATE	2	TRUE	1	0.885224701087134	3		269	503	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510886	157510886	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	449	575	0	ENST00000346085.5:c.3661G>T	p.Gly1221Cys	p.G1221C	ENST00000346085	NM_020732.3	1221	Ggc/Tgc	14/20	0.443132743524112	3	FACETS	1	0.989	1	0.554	0.529	0.58	INDETERMINATE	1	TRUE	1	0.885224701087134	3		575	1321	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	172	414	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.683551901150401	2		414	472	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0044971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	125	458	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.683551901150401	1	FACETS	0.919	0.849	0.989	0.919	0.849	0.989	CLONAL	1	TRUE	0	0.683551901150401	1		458	262	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0044971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	172	330	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.85	0.786	0.916	0.85	0.786	0.916	CLONAL	1	TRUE	1	0.683551901150401	2		330	592	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851286	156851286	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745776726	NA	P-0044971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	114	773	1	ENST00000524377.1:c.2243G>A	p.Arg748Gln	p.R748Q	ENST00000524377	NM_002529.3	748	cGg/cAg	17/17	1	2	FACETS	0.487	0.439	0.538	0.487	0.439	0.538	SUBCLONAL	1	TRUE	1	0.683551901150401	2		774	685	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548243	41548243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775368605	NA	P-0044971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	106	300	0	ENST00000263253.7:c.3031G>A	p.Glu1011Lys	p.E1011K	ENST00000263253	NM_001429.3	1011	Gaa/Aaa	16/31	1	2	FACETS	0.756	0.683	0.833	0.756	0.683	0.833	SUBCLONAL	1	TRUE	1	0.683551901150401	2		300	410	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949076	44949076	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	75	246	1	ENST00000377967.4:c.3637C>T	p.Arg1213Ter	p.R1213*	ENST00000377967	NM_021140.2	1213	Cga/Tga	25/29	1	1	FACETS	0.488	0.432	0.547	0.488	0.432	0.547	SUBCLONAL	1	TRUE	0	0.683551901150401	1		247	296	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056964	180056964	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	116	826	2	ENST00000261937.6:c.655C>A	p.Pro219Thr	p.P219T	ENST00000261937	NM_182925.4	219	Ccc/Acc	5/30	1	2	FACETS	0.43	0.387	0.475	0.43	0.387	0.475	SUBCLONAL	1	TRUE	1	0.683551901150401	2		828	789	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593405	48593405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519962	NA	P-0044971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	12	343	0	ENST00000342988.3:c.1156G>A	p.Gly386Ser	p.G386S	ENST00000342988	NM_005359.5	386	Ggt/Agt	10/12	0.683551901150401	1	FACETS	0.07	0.048	0.096	0.07	0.048	0.096	SUBCLONAL	1	TRUE	0	0.683551901150401	1		343	331	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49423020	49423020	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0044971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	36	688	0	ENST00000301067.7:c.14076-1G>T		p.X4692_splice	ENST00000301067	NM_003482.3	4692			1	2	FACETS	0.168	0.137	0.202	0.168	0.137	0.202	SUBCLONAL	1	TRUE	1	0.683551901150401	2		688	627	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492800	56492800	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	101	552	0	ENST00000407977.2:c.139A>T	p.Ile47Phe	p.I47F	ENST00000407977		47	Att/Ttt	2/10	1	2	FACETS	0.461	0.412	0.513	0.461	0.412	0.513	SUBCLONAL	1	TRUE	1	0.683551901150401	2		552	641	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936096	+	missense_variant	Missense_Mutation	DNP	AG	AG	GT	novel	NA	P-0044971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	21	638	0	ENST00000263967.3:c.1637_1638delinsGT	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAG/cGT	10/21	1	2	FACETS	0.088	0.067	0.113	0.088	0.067	0.113	SUBCLONAL	1	TRUE	1	0.683551901150401	2		638	695	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249341	110249341	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	398	1067	3	ENST00000374672.4:c.1232C>A	p.Ser411Tyr	p.S411Y	ENST00000374672	NM_004235.4	411	tCc/tAc	4/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.683551901150401	2		1070	1117	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942658	44942768	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTATTTGTAGCAGAGTTTCACTTTTGATGTGTTATTTTATTGCAGGTGGAAGTTGCAGCTACATGAGCTGACTAAACTTCCTGCTTTTGTGCGTGTCGTATCAGCAGGA	AGGTATTTGTAGCAGAGTTTCACTTTTGATGTGTTATTTTATTGCAGGTGGAAGTTGCAGCTACATGAGCTGACTAAACTTCCTGCTTTTGTGCGTGTCGTATCAGCAGGA	-	novel	NA	P-0044971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	10	130	0	ENST00000377967.4:c.3285-46_3349del		p.X1095_splice	ENST00000377967	NM_021140.2	1095		23/29	1	1	FACETS	0.129	0.087	0.181	0.129	0.087	0.181	SUBCLONAL	1	TRUE	0	0.683551901150401	1		130	149	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0044991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	16	330	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.427	0.314	0.563	0.427	0.314	0.563	SUBCLONAL	1	TRUE	1	0.13	2		330	577	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0044991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	28	280	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	1	2	FACETS	1	0.802	1	1	0.802	1	CLONAL	1	TRUE	1	0.13	2		280	429	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311619	15311621	+	inframe_deletion	In_Frame_Del	DEL	AGC	AGC	-	rs746497955	NA	P-0044991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	11	117	1	ENST00000263388.2:c.96_98del	p.Leu33del	p.L33del	ENST00000263388	NM_000435.2	32	ctGCTa/cta	1/33	1	2	FACETS	0.973	0.673	1	0.973	0.673	1	CLONAL	1	TRUE	1	0.13	2		118	174	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149290705	149290705	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	134	538	0	ENST00000360632.3:c.514G>T	p.Val172Phe	p.V172F	ENST00000360632	NM_015472.4	172	Gtc/Ttc	3/7	1	2	FACETS	0.947	0.86	1	0.947	0.86	1	CLONAL	1	TRUE	1	0.323156502203565	2		538	876	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982453	25982453	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	166	350	0	ENST00000435504.4:c.837del	p.Asn280IlefsTer7	p.N280Ifs*7	ENST00000435504		279	gtT/gt	9/13	0.693958734543726	1	FACETS	0.838	0.78	0.895	0.838	0.78	0.895	CLONAL	1	TRUE	0	0.693958734543726	1		350	373	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0046166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	197	441	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.436356308358349	4	FACETS	1	0.949	1			1	CLONAL	3	TRUE	NA	0.436356308358349	4		441	427	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	145	507	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.436356308358349	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.436356308358349	1		507	451	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061191	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	102	379	0	ENST00000250448.2:c.798C>G	p.Phe266Leu	p.F266L	ENST00000250448	NM_004496.3	266	ttC/ttG	2/2	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.436356308358349	2		379	455	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536697	120536697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768711168	NA	P-0046166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	157	630	0	ENST00000229340.5:c.395C>T	p.Thr132Met	p.T132M	ENST00000229340	NM_006861.6	132	aCg/aTg	5/6	1	2	FACETS	0.994	0.912	1	0.994	0.912	1	CLONAL	1	TRUE	1	0.436356308358349	2		630	724	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180556	56180562	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAATG	AAGAATG	-	novel	NA	P-0046166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	124	208	0	ENST00000399503.3:c.3886_3892del	p.Arg1296Ter	p.R1296*	ENST00000399503	NM_005921.1	1295	atAAGAATG/at	16/20	NA	2	FACETS	1	0.946	1			1	INDETERMINATE	2	TRUE	NA	0.436356308358349	2		208	275	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041623	14041623	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1204895453	NA	P-0046209-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	48	581	0	ENST00000311895.7:c.2170G>A	p.Val724Met	p.V724M	ENST00000311895	NM_005236.2	724	Gtg/Atg	11/11	0.731993738824232	2	FACETS	0.242	0.205	0.284	0.121	0.102	0.142	SUBCLONAL	1	TRUE	0	0.731993738824232	2		581	541	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78797023	78797023	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046209-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	143	536	0	ENST00000306801.3:c.1136G>A	p.Trp379Ter	p.W379*	ENST00000306801	NM_020761.2	379	tGg/tAg	9/34	0.731993738824232	3	FACETS	0.998	0.915	1	0.499	0.457	0.542	CLONAL	1	TRUE	1	0.731993738824232	3		536	535	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626117	12626118	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046209-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	269	620	0	ENST00000251849.4:c.1842_1843insT	p.Lys615Ter	p.K615*	ENST00000251849	NM_002880.3	614	-/T	17/17	0.488274479846651	3	FACETS	1	0.986	1	0.574	0.539	0.609	CLONAL	1	TRUE	1	0.731993738824232	3		620	875	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411886	116411896	+	splice_region_variant,intron_variant	Splice_Region	DEL	TTTCTCTCTGT	TTTCTCTCTGT	-	novel	NA	P-0046209-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	9868	610	0	ENST00000397752.3:c.2888-14_2888-4del		p.X963_splice	ENST00000397752	NM_000245.2	963			0.731993738824232	16	FACETS	0.976	0.972	0.979	0.976	0.972	0.979	CLONAL	16	TRUE	0	0.731993738824232	16		610	10577	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040652	47040653	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0046209-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	120	268	0	ENST00000377604.3:c.1287_1288delinsTT	p.Glu429_Glu430delinsAspTer	p.E429_E430delinsD*	ENST00000377604	NM_001204468.1	429	gaGGag/gaTTag	13/24	0.20091328023538	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	NA	0.731993738824232	0		268	164	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054993	176054993	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046209-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	198	319	0	ENST00000367669.3:c.1060G>C	p.Ala354Pro	p.A354P	ENST00000367669	NM_022457.5	354	Gca/Cca	10/20	0.390195468835332	3	FACETS	1	0.982	1	0.727	0.687	0.766	INDETERMINATE	2	TRUE	0	0.731993738824232	3		319	339	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961687	41961687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	126	451	0	ENST00000219905.7:c.595C>T	p.Arg199Cys	p.R199C	ENST00000219905	NM_001164273.1	199	Cgt/Tgt	2/24	0.392344379546568	1	FACETS	0.965	0.878	1	0.965	0.878	1	CLONAL	1	TRUE	0	0.392344379546568	1		451	535	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403570	138403570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	202	660	0	ENST00000289153.2:c.2212G>A	p.Gly738Arg	p.G738R	ENST00000289153	NM_006219.2	738	Ggg/Agg	15/22	1	2	FACETS	0.984	0.912	1	0.984	0.912	1	CLONAL	1	TRUE	1	0.392344379546568	2		660	1046	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134660	41134660	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	120	384	0	ENST00000379561.5:c.968C>G	p.Thr323Ser	p.T323S	ENST00000379561	NM_002015.3	323	aCt/aGt	2/3	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.392344379546568	2		384	612	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007830	45007830	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	99	431	0	ENST00000558401.1:c.277del	p.Thr93LeufsTer10	p.T93Lfs*10	ENST00000558401	NM_004048.2	93	Act/ct	2/4	0.392344379546568	1	FACETS	0.828	0.742	0.918	0.828	0.742	0.918	CLONAL	1	TRUE	0	0.392344379546568	1		431	490	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849475	89849475	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	179	702	0	ENST00000389301.3:c.1506G>C	p.Lys502Asn	p.K502N	ENST00000389301	NM_000135.2	502	aaG/aaC	16/43	1	2	FACETS	0.882	0.812	0.954	0.882	0.812	0.954	CLONAL	1	TRUE	1	0.392344379546568	2		702	1035	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209101895	209101895	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0046216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	90	287	0	ENST00000345146.2:c.1155-2A>C		p.X385_splice	ENST00000345146	NM_005896.2	385			1	2	FACETS	0.995	0.887	1	0.995	0.887	1	CLONAL	1	TRUE	1	0.392344379546568	2		287	461	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188212	10188213	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCAGAGATGCAGGGACACACGATGGGCTTCTGGTTAACCAAACTGAAATGTG	novel	NA	P-0046216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	88	592	0	ENST00000256474.2:c.402_403insATGTGTCAGAGATGCAGGGACACACGATGGGCTTCTGGTTAACCAAACTGAA	p.Leu135MetfsTer14	p.L135Mfs*14	ENST00000256474	NM_000551.3	119	ttc/tTCAGAGATGCAGGGACACACGATGGGCTTCTGGTTAACCAAACTGAAATGTGtc	2/3	0.382997834761841	1	FACETS	0.466	0.412	0.523	0.466	0.412	0.523	SUBCLONAL	1	TRUE	0	0.392344379546568	1		592	774	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400043	49400043	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	150	551	0	ENST00000418115.1:c.294G>T	p.Lys98Asn	p.K98N	ENST00000418115	NM_001664.2	98	aaG/aaT	4/5	0.382997834761841	1	FACETS	0.956	0.877	1	0.956	0.877	1	CLONAL	1	TRUE	0	0.392344379546568	1		551	643	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52692304	52692304	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	130	432	0	ENST00000394830.3:c.556del	p.Leu186TrpfsTer8	p.L186Wfs*8	ENST00000394830	NM_018313.4	186	Ctg/tg	6/30	0.382997834761841	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.392344379546568	1		432	525	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138407718	138407718	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	99	306	0	ENST00000289153.2:c.2135A>G	p.Gln712Arg	p.Q712R	ENST00000289153	NM_006219.2	712	cAg/cGg	14/22	1	2	FACETS	0.926	0.829	1	0.926	0.829	1	CLONAL	1	TRUE	1	0.392344379546568	2		306	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0046449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	366	467	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.998	0.951	1	0.998	0.951	1	CLONAL	1	TRUE	1	0.808486277908845	2		467	907	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	139	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.808486277908845	2		126	325	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0046449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	293	475	1	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	0.808486277908845	1	FACETS	0.995	0.955	1	0.995	0.955	1	CLONAL	1	TRUE	0	0.808486277908845	1		476	434	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657025	45657025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542311532	NA	P-0046449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	240	577	0	ENST00000407780.3:c.131G>A	p.Arg44His	p.R44H	ENST00000407780	NM_001283052.1	44	cGt/cAt	3/7	1	2	FACETS	0.909	0.854	0.965	0.909	0.854	0.965	CLONAL	1	TRUE	1	0.808486277908845	2		577	653	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55272964	55272964	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2367	14740	523	0	ENST00000275493.2:c.3287C>G	p.Ser1096Cys	p.S1096C	ENST00000275493	NM_005228.3	1096	tCc/tGc	28/28	0.808486277908845	30	FACETS	1	0.999	1			1	CLONAL	26	TRUE	NA	0.808486277908845	30		523	17107	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273020	55273020	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2734	18437	686	0	ENST00000275493.2:c.3343C>G	p.Leu1115Val	p.L1115V	ENST00000275493	NM_005228.3	1115	Ctg/Gtg	28/28	0.808486277908845	30	FACETS	0.983	0.979	0.986			1	CLONAL	27	TRUE	NA	0.808486277908845	30		686	21171	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194830	29194830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	460	1036	2	ENST00000240100.2:c.898C>T	p.Arg300Trp	p.R300W	ENST00000240100	NM_001394.6	300	Cgg/Tgg	4/4	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.808486277908845	2		1038	1100	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610564	10610564	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	75	1206	0	ENST00000171111.5:c.146A>G	p.Asn49Ser	p.N49S	ENST00000171111	NM_203500.1	49	aAc/aGc	2/6	0.145149600798273	0	FACETS	0.93	0.816	1			1	CLONAL	1	FALSE	0	0.209089414477554	0		1206	610	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	78	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.82	0.728	0.917	0.82	0.728	0.917	CLONAL	1	TRUE	1	0.63	2		126	302	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0047087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	304	785	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	0.885	0.834	0.936	0.885	0.834	0.936	CLONAL	1	TRUE	1	0.63	2		785	1091	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	30	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.735	0.596	0.891	0.735	0.596	0.891	SUBCLONAL	1	TRUE	1	0.359517517803278	2		126	227	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575507	67575507	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	102	393	0	ENST00000274335.5:c.581del	p.Pro194GlnfsTer13	p.P194Qfs*13	ENST00000274335		194	Cca/ca	4/15	1	2	FACETS	0.88	0.788	0.977	0.88	0.788	0.977	CLONAL	1	TRUE	1	0.359517517803278	2		393	645	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417862	138417862	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	120	481	0	ENST00000289153.2:c.1657A>G	p.Asn553Asp	p.N553D	ENST00000289153	NM_006219.2	553	Aat/Gat	11/22	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.359517517803278	2		481	620	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591281	67591292	+	inframe_deletion	In_Frame_Del	DEL	GTTGAACGAGTG	GTTGAACGAGTG	-	novel	NA	P-0047122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	86	324	0	ENST00000274335.5:c.1783_1794del	p.Asn595_Leu598del	p.N595_L598del	ENST00000274335		593	aaGTTGAACGAGTGg/aag	13/15	1	2	FACETS	0.832	0.737	0.933	0.832	0.737	0.933	CLONAL	1	TRUE	1	0.359517517803278	2		324	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0047948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	275	715	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.3	2	FACETS	0.989	0.932	1	0.989	0.932	1	CLONAL	2	TRUE	0	0.34	2		715	818	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	84	275	0	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	0.193974609194628	2	FACETS	1	0.977	1	0.712	0.634	0.794	INDETERMINATE	1	TRUE	0	0.34	2		275	347	SUCCESS
APC	324	MSKCC	GRCh37	5	112157650	112157650	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1060503333	NA	P-0047948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	29	380	0	ENST00000257430.4:c.1370C>A	p.Ser457Ter	p.S457*	ENST00000257430	NM_000038.5	457	tCa/tAa	11/16	0.193974609194628	2	FACETS	0.4	0.32	0.49	0.2	0.16	0.245	INDETERMINATE	1	TRUE	0	0.34	2		380	427	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933480	100933480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766277966	NA	P-0047948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	31	177	0	ENST00000325455.5:c.1910G>A	p.Arg637Gln	p.R637Q	ENST00000325455	NM_001202474.3	637	cGa/cAa	4/8	1	2	FACETS	0.779	0.634	0.942	0.779	0.634	0.942	CLONAL	1	TRUE	1	0.34	2		177	234	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744489	41744489	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767925068	NA	P-0047948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	90	923	2	ENST00000301178.4:c.1109C>T	p.Ala370Val	p.A370V	ENST00000301178	NM_021913.4	370	gCg/gTg	8/20	0.209692523553247	2	FACETS	0.577	0.511	0.648	0.289	0.255	0.324	SUBCLONAL	1	TRUE	0	0.34	2		925	917	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646292	3646300	+	inframe_deletion	In_Frame_Del	DEL	CACAGCCTG	CACAGCCTG	-	novel	NA	P-0047948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	73	1166	0	ENST00000294008.3:c.1778_1786del	p.Ala593_Cys595del	p.A593_C595del	ENST00000294008	NM_032444.2	593	gCAGGCTGTGgc/ggc	8/15	0.209692523553247	2	FACETS	0.396	0.345	0.451	0.198	0.172	0.226	SUBCLONAL	1	TRUE	0	0.34	2		1166	1085	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52675997	52675997	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	60	541	0	ENST00000394830.3:c.1060G>T	p.Glu354Ter	p.E354*	ENST00000394830	NM_018313.4	354	Gaa/Taa	11/30	0.3	1	FACETS	0.513	0.442	0.59	0.513	0.442	0.59	SUBCLONAL	1	TRUE	0	0.34	1		541	571	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572521	64572522	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	A	novel	NA	P-0047948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	74	807	0	ENST00000312049.6:c.1334_1335delinsT	p.Gly445ValfsTer13	p.G445Vfs*13	ENST00000312049	NM_130799.2	445	gGC/gT	9/10	1	2	FACETS	0.568	0.496	0.645	0.568	0.496	0.645	SUBCLONAL	1	TRUE	1	0.34	2		807	767	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0048299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	135	414	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.735417957151099	3	FACETS	0.756	0.697	0.816	0.756	0.697	0.816	SUBCLONAL	2	FALSE	1	0.735417957151099	3		414	332	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0048299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	54	183	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.735417957151099	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	FALSE	0	0.735417957151099	2		183	72	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0048299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	253	851	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.735417957151099	3	FACETS	0.939	0.879	1	0.47	0.439	0.501	CLONAL	1	FALSE	1	0.735417957151099	3		851	1002	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0048299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	378	587	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.735417957151099	2	FACETS	0.987	0.954	1	0.987	0.954	1	CLONAL	2	FALSE	0	0.735417957151099	2		587	521	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589618	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519838	NA	P-0048299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	60	108	0	ENST00000274335.5:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000274335		461	Cga/Tga	10/15	0.735417957151099	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	FALSE	0	0.735417957151099	2		108	77	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411937	63411937	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	421	924	0	ENST00000330258.3:c.1230G>A	p.Trp410Ter	p.W410*	ENST00000330258	NM_152424.3	410	tgG/tgA	2/2	0.287032671948192	3	FACETS	1	0.989	1	0.713	0.686	0.74	INDETERMINATE	2	FALSE	0	0.735417957151099	3		924	732	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970924	70970924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1277239045	NA	P-0048299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	310	570	1	ENST00000276594.2:c.1337G>A	p.Arg446Gln	p.R446Q	ENST00000276594	NM_024504.3	446	cGg/cAg	6/8	0.482346412279851	1	FACETS	0.917	0.875	0.96	0.917	0.875	0.96	CLONAL	1	FALSE	0	0.735417957151099	1		571	581	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134513	41134513	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	187	379	1	ENST00000379561.5:c.1115A>G	p.Glu372Gly	p.E372G	ENST00000379561	NM_002015.3	372	gAa/gGa	2/3	0.735417957151099	8	FACETS	0.751	0.693	0.812	0.25	0.231	0.271	SUBCLONAL	2	FALSE	2	0.735417957151099	8		380	1085	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	143	464	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.238332716599096	2	FACETS	0.92	0.841	1	0.92	0.841	1	CLONAL	2	TRUE	0	0.238332716599096	2		464	652	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0048822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	170	1033	5	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.16349467906191	2	FACETS	1	0.988	1	0.716	0.658	0.777	CLONAL	1	TRUE	0	0.238332716599096	2		1038	996	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142927	30142927	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs978946990	NA	P-0048822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	89	1249	2	ENST00000389048.3:c.599G>A	p.Arg200Lys	p.R200K	ENST00000389048	NM_004304.4	200	aGa/aAa	1/29	1	2	FACETS	0.688	0.609	0.774	0.688	0.609	0.774	SUBCLONAL	1	TRUE	1	0.238332716599096	2		1251	1085	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031889	26031889	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	44	443	0	ENST00000244661.2:c.400G>C	p.Glu134Gln	p.E134Q	ENST00000244661	NM_003537.3	134	Gaa/Caa	1/1	0.238332716599096	4	FACETS	0.868	0.727	1	0.434	0.363	0.512	CLONAL	1	TRUE	2	0.238332716599096	4		443	527	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42759146	42759146	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	62	607	3	ENST00000222329.4:c.6G>C	p.Lys2Asn	p.K2N	ENST00000222329	NM_006494.2	2	aaG/aaC	1/4	0.238332716599096	1	FACETS	0.766	0.662	0.88	0.766	0.662	0.88	SUBCLONAL	1	TRUE	0	0.238332716599096	1		610	598	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132935	64132935	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	69	774	1	ENST00000334205.4:c.1069C>T	p.Gln357Ter	p.Q357*	ENST00000334205	NM_003942.2	357	Cag/Tag	9/17	0.208973428429283	3	FACETS	0.749	0.651	0.856	0.25	0.217	0.286	SUBCLONAL	1	TRUE	0	0.238332716599096	3		775	865	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615018	43615018	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587778657	NA	P-0048822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	77	1061	2	ENST00000355710.3:c.2432C>G	p.Ser811Cys	p.S811C	ENST00000355710	NM_020975.4	811	tCc/tGc	14/20	0.16349467906191	2	FACETS	0.648	0.567	0.735	0.324	0.283	0.368	SUBCLONAL	1	TRUE	0	0.238332716599096	2		1063	997	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18649027	18649027	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	43	364	0	ENST00000266497.5:c.2702C>T	p.Pro901Leu	p.P901L	ENST00000266497		901	cCa/cTa	19/31	0.238332716599096	2	FACETS	0.685	0.573	0.809	0.342	0.286	0.405	SUBCLONAL	1	TRUE	0	0.238332716599096	2		364	527	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40467773	40467773	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	63	604	1	ENST00000264657.5:c.2303C>A	p.Ser768Tyr	p.S768Y	ENST00000264657	NM_139276.2	768	tCc/tAc	24/24	0.16349467906191	2	FACETS	0.735	0.635	0.844	0.368	0.317	0.422	SUBCLONAL	1	TRUE	0	0.238332716599096	2		605	719	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40880852	40880852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1194330891	NA	P-0048822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	45	500	1	ENST00000428826.2:c.108G>A	p.Met36Ile	p.M36I	ENST00000428826		36	atG/atA	3/21	0.16349467906191	2	FACETS	0.508	0.425	0.599	0.254	0.212	0.3	SUBCLONAL	1	TRUE	0	0.238332716599096	2		501	744	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210818	2210818	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	63	829	0	ENST00000398665.3:c.1315C>T	p.Gln439Ter	p.Q439*	ENST00000398665	NM_032482.2	439	Cag/Tag	14/28	0.238332716599096	2	FACETS	0.649	0.56	0.747	0.325	0.28	0.374	SUBCLONAL	1	TRUE	0	0.238332716599096	2		829	814	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605856	46605856	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	55	774	0	ENST00000263734.3:c.1504G>C	p.Glu502Gln	p.E502Q	ENST00000263734	NM_001430.4	502	Gag/Cag	11/16	1	2	FACETS	0.52	0.443	0.604	0.52	0.443	0.604	SUBCLONAL	1	TRUE	1	0.238332716599096	2		774	888	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99175925	99175925	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0048822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	51	553	1	ENST00000074304.5:c.1838-1G>A		p.X613_splice	ENST00000074304	NM_001134224.1	613			1	2	FACETS	0.7	0.595	0.817	0.7	0.595	0.817	SUBCLONAL	1	TRUE	1	0.238332716599096	2		554	611	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026853	71026853	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	28	259	0	ENST00000318789.4:c.1369G>C	p.Glu457Gln	p.E457Q	ENST00000318789	NM_032682.5	457	Gaa/Caa	16/21	0.238332716599096	2	FACETS	0.559	0.447	0.688	0.28	0.223	0.344	SUBCLONAL	1	TRUE	0	0.238332716599096	2		259	420	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953158	38953158	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	23	237	0	ENST00000357387.3:c.2826G>C	p.Leu942Phe	p.L942F	ENST00000357387	NM_152756.3	942	ttG/ttC	29/38	0.238332716599096	6	FACETS	0.652	0.507	0.82	0.163	0.126	0.205	SUBCLONAL	1	TRUE	2	0.238332716599096	6		237	437	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109314103	109314103	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0048822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	28	349	0	ENST00000436639.2:c.1121-1G>C		p.X374_splice	ENST00000436639	NM_014454.2	374			0.18577539030152	3	FACETS	0.53	0.423	0.653			1	SUBCLONAL	1	TRUE	NA	0.238332716599096	3		349	496	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559377	141559377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	72	965	6	ENST00000220592.5:c.1424G>A	p.Arg475Lys	p.R475K	ENST00000220592	NM_012154.3	475	aGa/aAa	12/19	1	2	FACETS	0.64	0.558	0.729	0.64	0.558	0.729	SUBCLONAL	1	TRUE	1	0.238332716599096	2		971	944	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050695	5050695	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	3535	339	6	ENST00000381652.3:c.478G>A	p.Asp160Asn	p.D160N	ENST00000381652	NM_004972.3	160	Gat/Aat	6/25	0.238332716599096	73	FACETS	0.998	0.99	1	0.97	0.963	0.977	CLONAL	70	TRUE	1	0.238332716599096	73		345	4019	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449799	8449799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61733196	NA	P-0048822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	46	446	0	ENST00000356435.5:c.3914C>T	p.Pro1305Leu	p.P1305L	ENST00000356435		1305	cCg/cTg	23/35	1	2	FACETS	0.58	0.488	0.683	0.58	0.488	0.683	SUBCLONAL	1	TRUE	1	0.238332716599096	2		446	665	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342772	87342772	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	37	502	0	ENST00000277120.3:c.1057C>G	p.His353Asp	p.H353D	ENST00000277120		353	Cac/Gac	9/19	0.216421813123334	3	FACETS	0.542	0.446	0.65	0.271	0.223	0.325	SUBCLONAL	1	TRUE	1	0.238332716599096	3		502	641	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149237	61149237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1233682212	NA	P-0049133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	59	349	0	ENST00000295025.8:c.1427C>T	p.Ser476Phe	p.S476F	ENST00000295025	NM_002908.2	476	tCc/tTc	11/11	0.213220852979357	3	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	1	0.213220852979357	3		349	265	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591291	67591291	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	67	325	0	ENST00000274335.5:c.1789T>C	p.Trp597Arg	p.W597R	ENST00000274335		597	Tgg/Cgg	13/15	0.213220852979357	4	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	2	0.213220852979357	4		325	326	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25458622	25458622	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	61	421	0	ENST00000264709.3:c.2551T>G	p.Phe851Val	p.F851V	ENST00000264709	NM_175629.2	851	Ttc/Gtc	22/23	1	2	FACETS	0.914	0.794	1	1	0.978	1	CLONAL	2	TRUE	1	0.213220852979357	2		421	313	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0049409-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	102	414	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.267758800466904	4	FACETS	1	0.953	1	0.371	0.332	0.411	INDETERMINATE	1	FALSE	1	0.460538871172774	4		414	582	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882005	NA	P-0049409-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	53	443	0	ENST00000269305.4:c.713G>C	p.Cys238Ser	p.C238S	ENST00000269305	NM_001126112.2	238	tGt/tCt	7/11	1	2	FACETS	0.362	0.308	0.421	0.362	0.308	0.421	SUBCLONAL	1	FALSE	1	0.460538871172774	2		443	636	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2949769	2949769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376446854	NA	P-0049409-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	82	450	0	ENST00000396946.4:c.3175G>A	p.Gly1059Ser	p.G1059S	ENST00000396946	NM_032415.4	1059	Ggc/Agc	24/25	1	2	FACETS	0.544	0.479	0.613	0.544	0.479	0.613	SUBCLONAL	1	FALSE	1	0.460538871172774	2		450	655	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992692	68992692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529924687	NA	P-0049409-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	37	369	0	ENST00000288368.4:c.1657G>A	p.Glu553Lys	p.E553K	ENST00000288368	NM_024870.2	553	Gaa/Aaa	16/40	1	2	FACETS	0.263	0.216	0.316	0.263	0.216	0.316	SUBCLONAL	1	FALSE	1	0.460538871172774	2		369	610	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0049459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	159	328	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.397746525929128	2	FACETS	0.886	0.82	0.954	0.886	0.82	0.954	CLONAL	2	TRUE	0	0.397746525929128	2		328	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0049459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	304	707	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.397746525929128	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.397746525929128	2		707	726	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225940	2225940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	133	708	1	ENST00000326181.6:c.1732G>A	p.Glu578Lys	p.E578K	ENST00000326181	NM_032271.2	578	Gag/Aag	18/21	0.342388760861117	4	FACETS	0.82	0.743	0.901	0.41	0.371	0.451	CLONAL	1	TRUE	2	0.397746525929128	4		709	1140	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477184	67477184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1320208623	NA	P-0049459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	84	466	1	ENST00000327367.4:c.991G>A	p.Val331Ile	p.V331I	ENST00000327367	NM_005902.3	331	Gtc/Atc	7/9	1	2	FACETS	0.696	0.615	0.782	0.696	0.615	0.782	SUBCLONAL	1	TRUE	1	0.397746525929128	2		467	607	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861023	35861023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138482569	NA	P-0049459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	85	343	0	ENST00000303115.3:c.152C>T	p.Ser51Leu	p.S51L	ENST00000303115	NM_002185.3	51	tCg/tTg	2/8	0.342388760861117	4	FACETS	0.931	0.823	1	0.465	0.411	0.523	CLONAL	1	TRUE	2	0.397746525929128	4		343	642	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143976	11143976	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	134	513	0	ENST00000358026.2:c.3557C>T	p.Ala1186Val	p.A1186V	ENST00000358026	NM_001128849.1	1186	gCg/gTg	26/36	0.397746525929128	3	FACETS	1	0.956	1	0.541	0.492	0.593	CLONAL	1	TRUE	1	0.397746525929128	3		513	746	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247964	59247964	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	103	612	0	ENST00000371222.2:c.779T>C	p.Met260Thr	p.M260T	ENST00000371222	NM_002228.3	260	aTg/aCg	1/1	0.397746525929128	3	FACETS	0.605	0.54	0.674	0.302	0.27	0.337	SUBCLONAL	1	TRUE	1	0.397746525929128	3		612	1027	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0050679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	422	326	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.572879108727309	7	FACETS	0.913	0.877	0.949	0.913	0.877	0.949	CLONAL	5	FALSE	2	0.572879108727309	7		326	785	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239420	105239420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	346	926	3	ENST00000349310.3:c.967G>A	p.Asp323Asn	p.D323N	ENST00000349310	NM_001014432.1	323	Gac/Aac	12/15	0.572879108727309	4	FACETS	0.958	0.909	1	0.958	0.909	1	CLONAL	2	FALSE	2	0.572879108727309	4		929	992	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577529	7577529	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs730882027	NA	P-0050679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	536	884	0	ENST00000269305.4:c.752T>C	p.Ile251Thr	p.I251T	ENST00000269305	NM_001126112.2	251	aTc/aCc	7/11	0.501368958391685	3	FACETS	1	0.991	1			1	CLONAL	3	FALSE	NA	0.572879108727309	3		884	763	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	80	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.727372333325041	2		126	218	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717630	89717630	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554825168	NA	P-0050952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	188	562	0	ENST00000371953.3:c.655C>T	p.Gln219Ter	p.Q219*	ENST00000371953	NM_000314.4	219	Cag/Tag	7/9	0.727372333325041	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.727372333325041	1		562	296	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562710	29562710	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs863224660	NA	P-0050952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	62	618	0	ENST00000356175.3:c.3790G>T	p.Glu1264Ter	p.E1264*	ENST00000356175	NM_000267.3	1264	Gaa/Taa	28/57	0.296522647409176	1	FACETS	0.256	0.222	0.294	0.256	0.222	0.294	INDETERMINATE	1	TRUE	0	0.727372333325041	1		618	423	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451294	70451294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	235	805	0	ENST00000373644.4:c.6134C>T	p.Ser2045Phe	p.S2045F	ENST00000373644	NM_030625.2	2045	tCc/tTc	12/12	0.727372333325041	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.727372333325041	1		805	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577147	7577161	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGATTACCACTACTC	AGATTACCACTACTC	-	novel	NA	P-0050952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	191	786	0	ENST00000269305.4:c.783-6_791del		p.X261_splice	ENST00000269305	NM_001126112.2	261		8/11	0.727372333325041	1	FACETS	0.921	0.866	0.975	0.921	0.866	0.975	CLONAL	1	TRUE	0	0.727372333325041	1		786	363	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0051493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	82	458	0				ENST00000310581	NM_198253.2	-/1132			0.696428846240848	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.696428846240848	1		458	139	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0051493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	173	349	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.696428846240848	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.696428846240848	1		349	291	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926248	112926249	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0051493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	131	513	0	ENST00000351677.2:c.1381_1382delinsAA	p.Ala461Asn	p.A461N	ENST00000351677	NM_002834.3	461	GCt/AAt	12/16	1	2	FACETS	0.718	0.655	0.784	0.718	0.655	0.784	SUBCLONAL	1	TRUE	1	0.696428846240848	2		513	524	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955531	48955531	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	153	357	1	ENST00000267163.4:c.1649del	p.Leu550Ter	p.L550*	ENST00000267163	NM_000321.2	549	caT/ca	17/27	0.673848303477788	1	FACETS	0.927	0.864	0.99	0.927	0.864	0.99	CLONAL	1	TRUE	0	0.696428846240848	1		358	309	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266107	41266107	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052146-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	100	272	0	ENST00000349496.5:c.104T>G	p.Ile35Ser	p.I35S	ENST00000349496	NM_001904.3	35	aTc/aGc	3/15	0.391221067920489	1	FACETS	0.892	0.801	0.988	0.892	0.801	0.988	CLONAL	1	TRUE	0	0.391221067920489	1		272	461	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038867	47038867	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052146-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	71	442	0	ENST00000377604.3:c.874G>T	p.Glu292Ter	p.E292*	ENST00000377604	NM_001204468.1	292	Gag/Tag	9/24	1	2	FACETS	0.963	0.845	1	0.963	0.845	1	CLONAL	1	TRUE	1	0.391221067920489	2		442	377	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457283	5457283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778072834	NA	P-0052146-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	54	403	0	ENST00000381577.3:c.257G>A	p.Arg86Gln	p.R86Q	ENST00000381577	NM_014143.3	86	cGg/cAg	3/7	1	2	FACETS	0.53	0.453	0.614	0.53	0.453	0.614	SUBCLONAL	1	TRUE	1	0.391221067920489	2		403	521	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155692	119155692	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052146-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	90	531	0	ENST00000264033.4:c.1445C>T	p.Pro482Leu	p.P482L	ENST00000264033	NM_005188.3	482	cCt/cTt	10/16	1	2	FACETS	0.813	0.723	0.909	0.813	0.723	0.909	CLONAL	1	TRUE	1	0.391221067920489	2		531	566	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575108	48575108	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052146-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	42	163	0	ENST00000342988.3:c.303del	p.Trp101CysfsTer9	p.W101Cfs*9	ENST00000342988	NM_005359.5	101	tGg/tg	3/12	0.391221067920489	1	FACETS	0.628	0.527	0.738	0.628	0.527	0.738	SUBCLONAL	1	TRUE	0	0.391221067920489	1		163	275	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165486	47165492	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCCAC	AGGCCAC	-	novel	NA	P-0052146-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	128	596	0	ENST00000409792.3:c.634_640del	p.Val212CysfsTer6	p.V212Cfs*6	ENST00000409792	NM_014159.6	212	GTGGCCTtg/tg	3/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.391221067920489	2		596	532	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485103	57485103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052522-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	27	438	1	ENST00000371085.3:c.937C>T	p.Pro313Ser	p.P313S	ENST00000371085	NM_000516.4	313	Cca/Tca	11/13	0.597739347498117	3	FACETS	1	0.843	1	0.519	0.423	0.623	CLONAL	1	TRUE	1	0.722344302032516	3		439	98	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426784	121426784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765432081	NA	P-0052522-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	67	550	1	ENST00000257555.6:c.475C>T	p.Arg159Trp	p.R159W	ENST00000257555		159	Cgg/Tgg	2/10	0.722344302032516	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	0	0.722344302032516	2		551	92	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578234	7578234	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs786202222	NA	P-0052522-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	64	491	1	ENST00000269305.4:c.615T>A	p.Tyr205Ter	p.Y205*	ENST00000269305	NM_001126112.2	205	taT/taA	6/11	0.722344302032516	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.722344302032516	2		492	78	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033965	49033965	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052522-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	58	382	0	ENST00000267163.4:c.2102A>G	p.Asp701Gly	p.D701G	ENST00000267163	NM_000321.2	701	gAc/gGc	20/27	0.722344302032516	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	0	0.722344302032516	3		382	64	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982426	201982426	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052522-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	33	465	0	ENST00000359651.3:c.805G>T	p.Ala269Ser	p.A269S	ENST00000359651		269	Gcg/Tcg	6/8	1	2	FACETS	0.714	0.592	0.845	0.714	0.592	0.845	SUBCLONAL	1	TRUE	1	0.722344302032516	2		465	128	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0052881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	232	715	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.516127951064045	3	FACETS	0.927	0.872	0.984	0.927	0.872	0.984	CLONAL	2	TRUE	1	0.557270694050328	3		715	574	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436297	110436308	+	inframe_deletion	In_Frame_Del	DEL	CGGCGGCGGCGG	CGGCGGCGGCGG	-	rs34412495	NA	P-0052881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	88	194	0	ENST00000375856.3:c.2093_2104del	p.Ala698_Ala701del	p.A698_A701del	ENST00000375856	NM_003749.2	698	gCCGCCGCCGCCGtg/gtg	1/2	0.556024898369302	5	FACETS	0.97	0.869	1	0.646	0.579	0.716	CLONAL	2	TRUE	2	0.557270694050328	5		194	299	SUCCESS
APC	324	MSKCC	GRCh37	5	112175177	112175187	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGATTCTGC	GCAGATTCTGC	A	novel	NA	P-0052881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	91	212	0	ENST00000257430.4:c.3886_3896delinsA	p.Ala1296IlefsTer6	p.A1296Ifs*6	ENST00000257430	NM_000038.5	1296	GCAGATTCTGCt/At	16/16	0.557270694050328	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	0	0.557270694050328	2		212	158	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0054312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	523	887	0	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.369918519294669	5	FACETS	1	0.983	1	0.829	0.798	0.86	CLONAL	4	FALSE	0	0.369918519294669	5		887	1061	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536156	106536156	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	56	423	0	ENST00000369096.4:c.123G>C	p.Met41Ile	p.M41I	ENST00000369096	NM_001198.3	41	atG/atC	2/7	0.344589524983712	3	FACETS	0.775	0.665	0.894	0.387	0.332	0.447	SUBCLONAL	1	FALSE	1	0.369918519294669	3		423	463	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0054407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	62	490	1	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.807	0.699	0.924	0.807	0.699	0.924	CLONAL	1	TRUE	1	0.358917886566289	2		491	428	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593505	48593505	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	42	324	0	ENST00000342988.3:c.1256G>T	p.Gly419Val	p.G419V	ENST00000342988	NM_005359.5	419	gGg/gTg	10/12	1	2	FACETS	0.686	0.575	0.809	0.686	0.575	0.809	SUBCLONAL	1	TRUE	1	0.358917886566289	2		324	341	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0054407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	50	435	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.496	0.42	0.579	0.496	0.42	0.579	SUBCLONAL	1	TRUE	1	0.358917886566289	2		435	562	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0054407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	157	465	1	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.917	0.84	0.998	0.917	0.84	0.998	CLONAL	1	TRUE	1	0.358917886566289	2		466	954	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0054407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	70	392	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.358917886566289	2		392	385	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862749	9862749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150316865	NA	P-0054407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	103	677	0	ENST00000330684.3:c.2554G>A	p.Val852Met	p.V852M	ENST00000330684	NM_001134407.1	852	Gtg/Atg	12/13	1	2	FACETS	0.978	0.877	1	0.978	0.877	1	CLONAL	1	TRUE	1	0.358917886566289	2		677	587	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244257	5244257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	63	1041	2	ENST00000357368.4:c.1225G>A	p.Gly409Ser	p.G409S	ENST00000357368	NM_002850.3	409	Ggc/Agc	11/38	1	2	FACETS	0.389	0.335	0.448	0.389	0.335	0.448	SUBCLONAL	1	TRUE	1	0.358917886566289	2		1043	902	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198888	67198888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751194292	NA	P-0054407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	104	605	1	ENST00000312629.5:c.359G>A	p.Arg120Gln	p.R120Q	ENST00000312629	NM_003952.2	120	cGg/cAg	5/15	1	2	FACETS	0.958	0.86	1	0.958	0.86	1	CLONAL	1	TRUE	1	0.358917886566289	2		606	605	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920444	114920444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1219807932	NA	P-0054407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	98	536	0	ENST00000543371.1:c.1385C>T	p.Pro462Leu	p.P462L	ENST00000543371	NM_001198531.1	462	cCg/cTg	13/14	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.358917886566289	2		536	542	SUCCESS
APC	324	MSKCC	GRCh37	5	112174516	112174516	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0054407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	58	330	0	ENST00000257430.4:c.3225T>A	p.Tyr1075Ter	p.Y1075*	ENST00000257430	NM_000038.5	1075	taT/taA	16/16	1	2	FACETS	0.979	0.847	1	0.979	0.847	1	CLONAL	1	TRUE	1	0.358917886566289	2		330	330	SUCCESS
APC	324	MSKCC	GRCh37	5	112175775	112175778	+	frameshift_variant	Frame_Shift_Ins	INS	GTAC	GTAC	AATCCAGACGGAAAA	novel	NA	P-0054407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	46	338	0	ENST00000257430.4:c.4484_4487delinsAATCCAGACGGAAAA	p.Ser1495LysfsTer16	p.S1495Kfs*16	ENST00000257430	NM_000038.5	1495	aGTACt/aAATCCAGACGGAAAAt	16/16	1	2	FACETS	0.84	0.711	0.981	0.84	0.711	0.981	CLONAL	1	TRUE	1	0.358917886566289	2		338	305	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054542-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	9	350	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.682	0.452	0.975	0.682	0.452	0.975	SUBCLONAL	1	TRUE	1	0.15	2		350	176	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577569	7577569	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519981	NA	P-0054542-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	27	454	0	ENST00000269305.4:c.712T>A	p.Cys238Ser	p.C238S	ENST00000269305	NM_001126112.2	238	Tgt/Agt	7/11	1	2	FACETS	0.902	0.718	1	0.902	0.718	1	CLONAL	1	TRUE	1	0.15	2		454	399	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056466-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	111	126	0				ENST00000310581	NM_198253.2	-/1132			0.388290996997489	5	FACETS	1	0.965	1	0.758	0.687	0.831	CLONAL	2	TRUE	2	0.388290996997489	5		126	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0056466-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	137	428	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.220028995848444	3	FACETS	0.796	0.728	0.867	0.531	0.485	0.578	INDETERMINATE	2	TRUE	0	0.388290996997489	3		428	529	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0056466-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	41	464	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.828	0.695	0.974	0.828	0.695	0.974	CLONAL	1	TRUE	1	0.388290996997489	2		464	255	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179050	123179050	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056466-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	43	438	0	ENST00000218089.9:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000218089	NM_001042749.1	167	Cag/Tag	8/35	0.388290996997489	1	FACETS	0.866	0.733	1	0.866	0.733	1	CLONAL	1	TRUE	0	0.388290996997489	1		438	206	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923342	9923342	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397514557	NA	P-0056466-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	52	526	0	ENST00000330684.3:c.1945C>G	p.Leu649Val	p.L649V	ENST00000330684	NM_001134407.1	649	Ctg/Gtg	9/13	0.118488666577683	4	FACETS	0.721	0.614	0.838	0.36	0.307	0.419	INDETERMINATE	1	TRUE	2	0.388290996997489	4		526	516	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757393	40757393	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs763353429	NA	P-0056466-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	107	469	0	ENST00000373198.4:c.2904+1G>A		p.X968_splice	ENST00000373198	NM_133170.3	968			0.227050301506653	3	FACETS	1	0.97	1	0.6	0.54	0.664	INDETERMINATE	1	TRUE	1	0.388290996997489	3		469	548	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920386	134920386	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056466-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	153	678	0	ENST00000398015.3:c.2201A>T	p.Tyr734Phe	p.Y734F	ENST00000398015	NM_004441.4	734	tAc/tTc	12/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.388290996997489	2		678	682	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	105	517	3	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.835	0.749	0.926	0.835	0.749	0.926	CLONAL	1	TRUE	1	0.37	2		520	680	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	87	627	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.37	2		633	442	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	94	423	4	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.854	0.761	0.952	0.854	0.761	0.952	CLONAL	1	TRUE	1	0.37	2		427	595	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119910	70119910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1297203260	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	79	452	0	ENST00000245479.2:c.916del	p.Val306CysfsTer77	p.V306Cfs*77	ENST00000245479	NM_000346.3	304	ccG/cc	3/3	1	2	FACETS	0.832	0.734	0.938	0.832	0.734	0.938	CLONAL	1	TRUE	1	0.37	2		452	513	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	113	486	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.83	0.747	0.917	0.83	0.747	0.917	CLONAL	1	TRUE	1	0.37	2		488	736	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	52	420	1	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	0.48	0.409	0.559	0.48	0.409	0.559	SUBCLONAL	1	TRUE	1	0.37	2		421	585	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	117	605	1	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.9	0.812	0.992	0.9	0.812	0.992	CLONAL	1	TRUE	1	0.37	2		606	703	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	107	465	1	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.843	0.757	0.934	0.843	0.757	0.934	CLONAL	1	TRUE	1	0.37	2		466	686	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	55	357	2	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.592	0.507	0.685	0.592	0.507	0.685	SUBCLONAL	1	TRUE	1	0.37	2		359	502	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533939	63533942	+	frameshift_variant	Frame_Shift_Del	DEL	CTCT	CTCT	-	rs771001164	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	96	407	0	ENST00000307078.5:c.1212_1215del	p.Glu405AlafsTer52	p.E405Afs*52	ENST00000307078	NM_004655.3	404	agAGAG/ag	6/11	1	2	FACETS	0.896	0.8	0.998	0.896	0.8	0.998	CLONAL	1	TRUE	1	0.37	2		407	579	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459245	120459246	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	100	444	0	ENST00000256646.2:c.6099dup	p.Ala2034CysfsTer24	p.A2034Cfs*24	ENST00000256646	NM_024408.3	2033	-/T	34/34	1	2	FACETS	0.778	0.695	0.866	0.778	0.695	0.866	SUBCLONAL	1	TRUE	1	0.37	2		444	695	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846265	156846265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs746910337	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	100	413	0	ENST00000524377.1:c.1706A>G	p.His569Arg	p.H569R	ENST00000524377	NM_002529.3	569	cAc/cGc	14/17	1	2	FACETS	0.869	0.778	0.966	0.869	0.778	0.966	CLONAL	1	TRUE	1	0.37	2		413	622	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743362	162743362	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372362070	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	110	419	1	ENST00000367921.3:c.1832G>A	p.Arg611Gln	p.R611Q	ENST00000367921	NM_006182.2	611	cGa/cAa	14/18	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.37	2		420	577	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318812	163318812	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	101	343	0	ENST00000271452.3:c.1202T>A	p.Ile401Asn	p.I401N	ENST00000271452	NM_145697.2	401	aTt/aAt	13/14	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.37	2		343	417	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851326	63851326	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	125	468	0	ENST00000279873.7:c.2104G>A	p.Ala702Thr	p.A702T	ENST00000279873	NM_032199.2	702	Gcc/Acc	10/10	1	2	FACETS	0.923	0.836	1	0.923	0.836	1	CLONAL	1	TRUE	1	0.37	2		468	732	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685270	89685271	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	45	209	0	ENST00000371953.3:c.170dup	p.Leu57PhefsTer6	p.L57Ffs*6	ENST00000371953	NM_000314.4	55	-/T	3/9	1	2	FACETS	0.875	0.74	1	0.875	0.74	1	CLONAL	1	TRUE	1	0.37	2		209	278	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717618	89717619	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	77	331	0	ENST00000371953.3:c.644_645del	p.Phe215CysfsTer27	p.F215Cfs*27	ENST00000371953	NM_000314.4	215	TTt/t	7/9	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.37	2		331	383	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392858	118392858	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781866935	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	119	432	0	ENST00000534358.1:c.11890G>A	p.Ala3964Thr	p.A3964T	ENST00000534358	NM_005933.3	3964	Gcc/Acc	36/36	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.37	2		432	606	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624396	21624398	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs749841294	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	84	372	0	ENST00000421138.2:c.1631_1633del	p.Lys544del	p.K544del	ENST00000421138		544	aAGAtt/att	14/16	1	2	FACETS	0.842	0.746	0.945	0.842	0.746	0.945	CLONAL	1	TRUE	1	0.37	2		372	539	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536918	120536918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1367775509	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	104	394	0	ENST00000229340.5:c.268G>A	p.Val90Ile	p.V90I	ENST00000229340	NM_006861.6	90	Gtc/Atc	4/6	1	2	FACETS	0.983	0.882	1	0.983	0.882	1	CLONAL	1	TRUE	1	0.37	2		394	572	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	112	467	5	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.37	2		472	587	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209298	133209298	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060500809	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	32	444	0	ENST00000320574.5:c.6088del	p.Ala2030ProfsTer18	p.A2030Pfs*18	ENST00000320574	NM_006231.2	2030	Gcc/cc	44/49	1	2	FACETS	0.288	0.233	0.35	0.288	0.233	0.35	SUBCLONAL	1	TRUE	1	0.37	2		444	601	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914049	32914049	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1238686039	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	84	381	0	ENST00000380152.3:c.5557T>C	p.Cys1853Arg	p.C1853R	ENST00000380152		1853	Tgt/Cgt	11/27	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.37	2		381	395	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636580	73636581	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	153	467	0	ENST00000377687.4:c.848dup	p.Cys284LeufsTer31	p.C284Lfs*31	ENST00000377687	NM_001730.3	281	-/C	2/4	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.37	2		467	784	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987135	36987135	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	86	363	0	ENST00000354822.5:c.554del	p.Pro185ArgfsTer43	p.P185Rfs*43	ENST00000354822	NM_001079668.2	185	cCg/cg	3/3	1	2	FACETS	0.998	0.886	1	0.998	0.886	1	CLONAL	1	TRUE	1	0.37	2		363	466	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562174	95562174	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	53	389	0	ENST00000393063.1:c.5083A>G	p.Asn1695Asp	p.N1695D	ENST00000393063	NM_030621.3	1695	Aat/Gat	24/28	1	2	FACETS	0.545	0.464	0.632	0.545	0.464	0.632	SUBCLONAL	1	TRUE	1	0.37	2		389	526	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348711	11348712	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	74	379	0	ENST00000332029.2:c.624dup	p.Phe209LeufsTer44	p.F209Lfs*44	ENST00000332029	NM_003745.1	208	-/C	2/2	1	2	FACETS	0.789	0.692	0.893	0.789	0.692	0.893	SUBCLONAL	1	TRUE	1	0.37	2		379	507	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041867	14041869	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs1567253994	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	124	430	0	ENST00000311895.7:c.2417_2419del	p.Pro806del	p.P806del	ENST00000311895	NM_005236.2	805	tCTCct/tct	11/11	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.37	2		430	661	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990331	81990331	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768299957	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	88	425	0	ENST00000359376.3:c.3602G>A	p.Arg1201His	p.R1201H	ENST00000359376	NM_002661.3	1201	cGc/cAc	32/33	1	2	FACETS	0.748	0.663	0.838	0.748	0.663	0.838	SUBCLONAL	1	TRUE	1	0.37	2		425	636	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805935	89805937	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	rs927201841	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	120	470	0	ENST00000389301.3:c.3959_3961del	p.Leu1320del	p.L1320del	ENST00000389301	NM_000135.2	1320	cTCCgt/cgt	40/43	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.37	2		470	633	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508267	38508267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754292583	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	88	376	1	ENST00000254066.5:c.575G>A	p.Arg192His	p.R192H	ENST00000254066	NM_000964.3	192	cGc/cAc	5/9	1	2	FACETS	0.92	0.818	1	0.92	0.818	1	CLONAL	1	TRUE	1	0.37	2		377	517	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	98	377	0	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	0.845	0.755	0.94	0.845	0.755	0.94	CLONAL	1	TRUE	1	0.37	2		377	627	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40364063	40364063	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	15	62	0	ENST00000293328.3:c.1619A>G	p.Asn540Ser	p.N540S	ENST00000293328	NM_012448.3	540	aAc/aGc	13/19	1	2	FACETS	0.943	0.701	1	0.943	0.701	1	CLONAL	1	TRUE	1	0.37	2		62	86	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435700	56435701	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	123	414	0	ENST00000407977.2:c.1436_1437del	p.Val479GlyfsTer25	p.V479Gfs*25	ENST00000407977		479	gTG/g	9/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.37	2		414	557	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438206	56438207	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	92	432	0	ENST00000407977.2:c.786_787del	p.Gly263GlufsTer18	p.G263Efs*18	ENST00000407977		262	tcAGgg/tcgg	7/10	1	2	FACETS	0.883	0.787	0.986	0.883	0.787	0.986	CLONAL	1	TRUE	1	0.37	2		432	563	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534379	63534379	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	149	488	0	ENST00000307078.5:c.1142T>C	p.Leu381Pro	p.L381P	ENST00000307078	NM_004655.3	381	cTg/cCg	5/11	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.37	2		488	779	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511578	66511578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	76	353	0	ENST00000358598.2:c.38G>A	p.Arg13His	p.R13H	ENST00000358598	NM_212471.2	13	cGc/cAc	2/11	1	2	FACETS	0.752	0.661	0.85	0.752	0.661	0.85	SUBCLONAL	1	TRUE	1	0.37	2		353	546	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117848	70117848	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs886042523	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	95	440	0	ENST00000245479.2:c.316A>G	p.Lys106Glu	p.K106E	ENST00000245479	NM_000346.3	106	Aag/Gag	1/3	1	2	FACETS	0.98	0.875	1	0.98	0.875	1	CLONAL	1	TRUE	1	0.37	2		440	524	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896525	78896525	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	101	371	0	ENST00000306801.3:c.2522C>T	p.Ala841Val	p.A841V	ENST00000306801	NM_020761.2	841	gCc/gTc	22/34	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.37	2		371	497	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985377	60985377	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	59	431	0	ENST00000333681.4:c.523C>A	p.Leu175Met	p.L175M	ENST00000333681		175	Ctg/Atg	2/3	1	2	FACETS	0.532	0.458	0.614	0.532	0.458	0.614	SUBCLONAL	1	TRUE	1	0.37	2		431	599	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6230591	6230591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1481816585	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	79	359	0	ENST00000252674.7:c.410G>A	p.Arg137Gln	p.R137Q	ENST00000252674	NM_005934.3	137	cGg/cAg	4/12	1	2	FACETS	0.914	0.807	1	0.914	0.807	1	CLONAL	1	TRUE	1	0.37	2		359	467	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610591	10610591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173824866	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	115	396	0	ENST00000171111.5:c.119C>T	p.Ala40Val	p.A40V	ENST00000171111	NM_203500.1	40	gCg/gTg	2/6	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.37	2		396	581	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223686	36223686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775158252	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	122	560	0	ENST00000222270.7:c.6236G>A	p.Arg2079Gln	p.R2079Q	ENST00000222270	NM_014727.1	2079	cGg/cAg	28/37	1	2	FACETS	0.937	0.848	1	0.937	0.848	1	CLONAL	1	TRUE	1	0.37	2		560	704	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029193	26029195	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	59	341	0	ENST00000435504.4:c.155_157del	p.Pro52del	p.P52del	ENST00000435504		52	cCTCtt/ctt	4/13	1	2	FACETS	0.862	0.745	0.988	0.862	0.745	0.988	CLONAL	1	TRUE	1	0.37	2		341	370	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705527	47705528	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1573574188	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	76	378	0	ENST00000233146.2:c.2332dup	p.Cys778LeufsTer9	p.C778Lfs*9	ENST00000233146	NM_000251.2	776	gct/gcTt	14/16	1	2	FACETS	0.882	0.776	0.995	0.882	0.776	0.995	CLONAL	1	TRUE	1	0.37	2		378	466	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920667	96920667	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	112	360	0	ENST00000258439.3:c.313C>A	p.Leu105Met	p.L105M	ENST00000258439	NM_001193304.2	105	Ctg/Atg	3/4	1	2	FACETS	0.988	0.89	1	0.988	0.89	1	CLONAL	1	TRUE	1	0.37	2		360	613	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178129303	178129303	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1437398564	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	76	249	0	ENST00000397062.3:c.2T>C	p.Met1?	p.M1?	ENST00000397062	NM_006164.4	1	aTg/aCg	1/5	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.37	2		249	329	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513282	44513287	+	inframe_deletion	In_Frame_Del	DEL	CCACCG	CCACCG	-	rs745888281	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	83	396	0	ENST00000291552.4:c.648_653del	p.Gly222_Gly223del	p.G222_G223del	ENST00000291552	NM_006758.2	216	ggCGGTGGt/ggt	8/8	1	2	FACETS	0.653	0.576	0.735	0.653	0.576	0.735	SUBCLONAL	1	TRUE	1	0.37	2		396	687	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29442702	29442702	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	101	297	0	ENST00000544604.2:c.745-2A>C		p.X249_splice	ENST00000544604	NM_001206998.1	249			1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.37	2		297	523	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090446	37090446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750217	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	76	329	0	ENST00000231790.2:c.2041G>A	p.Ala681Thr	p.A681T	ENST00000231790	NM_000249.3	681	Gct/Act	18/19	1	2	FACETS	0.813	0.715	0.919	0.813	0.715	0.919	CLONAL	1	TRUE	1	0.37	2		329	505	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933456	49933456	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	85	549	4	ENST00000296474.3:c.2734del	p.Asp912ThrfsTer24	p.D912Tfs*24	ENST00000296474	NM_002447.2	912	Gac/ac	11/20	1	2	FACETS	0.737	0.652	0.828	0.737	0.652	0.828	SUBCLONAL	1	TRUE	1	0.37	2		553	623	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586470	189586470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147148566	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	115	403	0	ENST00000264731.3:c.1094C>T	p.Ser365Leu	p.S365L	ENST00000264731	NM_003722.4	365	tCg/tTg	8/14	1	2	FACETS	0.979	0.884	1	0.979	0.884	1	CLONAL	1	TRUE	1	0.37	2		403	635	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294665	1294665	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	93	395	3	ENST00000310581.5:c.336del	p.Glu113ArgfsTer15	p.E113Rfs*15	ENST00000310581	NM_198253.2	112	ccC/cc	2/16	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.37	2		398	467	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589135	67589135	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	37	333	0	ENST00000274335.5:c.1127del	p.Gly376GlufsTer5	p.G376Efs*5	ENST00000274335		375	Ggg/gg	9/15	1	2	FACETS	0.639	0.528	0.762	0.639	0.528	0.762	SUBCLONAL	1	TRUE	1	0.37	2		333	313	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512355	149512355	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	83	499	0	ENST00000261799.4:c.1085C>T	p.Ala362Val	p.A362V	ENST00000261799	NM_002609.3	362	gCt/gTt	7/23	1	2	FACETS	0.615	0.542	0.692	0.615	0.542	0.692	SUBCLONAL	1	TRUE	1	0.37	2		499	730	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522560	176522560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201831200	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	99	481	0	ENST00000292408.4:c.1657G>A	p.Ala553Thr	p.A553T	ENST00000292408	NM_213647.1	553	Gcc/Acc	13/18	1	2	FACETS	0.896	0.802	0.997	0.896	0.802	0.997	CLONAL	1	TRUE	1	0.37	2		481	597	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032174	26032174	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	130	550	0	ENST00000244661.2:c.115C>G	p.Pro39Ala	p.P39A	ENST00000244661	NM_003537.3	39	Cct/Gct	1/1	1	2	FACETS	0.951	0.863	1	0.951	0.863	1	CLONAL	1	TRUE	1	0.37	2		550	739	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163554	32163554	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	63	392	1	ENST00000375023.3:c.5672del	p.Gly1891AlafsTer13	p.G1891Afs*13	ENST00000375023	NM_004557.3	1891	gGc/gc	30/30	1	2	FACETS	0.908	0.789	1	0.908	0.789	1	CLONAL	1	TRUE	1	0.37	2		393	375	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813426	32813426	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	89	457	0	ENST00000354258.4:c.2357A>G	p.His786Arg	p.H786R	ENST00000354258	NM_000593.5	786	cAc/cGc	11/11	1	2	FACETS	0.856	0.761	0.958	0.856	0.761	0.958	CLONAL	1	TRUE	1	0.37	2		457	562	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431577	6431577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	57	178	0	ENST00000356142.4:c.130G>A	p.Val44Ile	p.V44I	ENST00000356142	NM_018890.3	44	Gtt/Att	3/7	1	2	FACETS	0.972	0.839	1	0.972	0.839	1	CLONAL	1	TRUE	1	0.37	2		178	317	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508205	106508205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	93	397	0	ENST00000359195.3:c.199G>A	p.Val67Met	p.V67M	ENST00000359195	NM_002649.2	67	Gtg/Atg	2/11	1	2	FACETS	0.901	0.803	1	0.901	0.803	1	CLONAL	1	TRUE	1	0.37	2		397	558	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874092	151874093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	90	414	0	ENST00000262189.6:c.8445dup	p.Ser2816IlefsTer6	p.S2816Ifs*6	ENST00000262189	NM_170606.2	2815	-/A	38/59	1	2	FACETS	0.855	0.76	0.956	0.855	0.76	0.956	CLONAL	1	TRUE	1	0.37	2		414	569	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923086	39923087	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058146-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	83	199	0	ENST00000378444.4:c.3621dup	p.Gln1208ThrfsTer8	p.Q1208Tfs*8	ENST00000378444	NM_001123385.1	1207	-/A	8/15	1	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.37	1		199	319	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0058230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	49	350	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.834	0.709	0.971	1	0.968	1	CLONAL	2	TRUE	1	0.16	2		350	367	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577595	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0058230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	109	514	0	ENST00000269305.4:c.686_687del	p.Cys229TyrfsTer10	p.C229Yfs*10	ENST00000269305	NM_001126112.2	229	tGT/t	7/11	1	2	FACETS	0.983	0.884	1	1	0.988	1	CLONAL	2	TRUE	1	0.16	2		514	693	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971142	21971142	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	61	599	0	ENST00000304494.5:c.216C>A	p.Cys72Ter	p.C72*	ENST00000304494	NM_000077.4	72	tgC/tgA	2/3	0.3	1	FACETS	0.945	0.814	1	0.945	0.814	1	CLONAL	1	TRUE	0	0.16	1		599	742	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106175	27106175	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	124	569	0	ENST00000324856.7:c.5786G>C	p.Ser1929Thr	p.S1929T	ENST00000324856	NM_006015.4	1929	aGt/aCt	20/20	1	2	FACETS	1	0.909	1	1	0.989	1	CLONAL	2	TRUE	1	0.16	2		569	772	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948085	178948085	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	39	445	0	ENST00000263967.3:c.2857C>G	p.Pro953Ala	p.P953A	ENST00000263967	NM_006218.2	953	Cca/Gca	20/21	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.16	2		445	441	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401321	139401321	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771192471	NA	P-0058230-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	58	615	0	ENST00000277541.6:c.3748G>A	p.Gly1250Ser	p.G1250S	ENST00000277541	NM_017617.3	1250	Ggc/Agc	23/34	1	2	FACETS	0.94	0.806	1	0.94	0.806	1	CLONAL	1	TRUE	1	0.16	2		615	771	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0058338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	11	127	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.565303172036877	1	FACETS	0.872	0.635	1	0.872	0.635	1	CLONAL	1	TRUE	0	0.565303172036877	1		127	32	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682991	241682991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226883651	NA	P-0058338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	50	565	1	ENST00000366560.3:c.32C>T	p.Ser11Leu	p.S11L	ENST00000366560	NM_000143.3	11	tCg/tTg	1/10	1	2	FACETS	0.871	0.749	1	0.871	0.749	1	CLONAL	1	TRUE	1	0.565303172036877	2		566	203	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103270	119103270	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058338-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	48	487	0	ENST00000264033.4:c.308A>T	p.Glu103Val	p.E103V	ENST00000264033	NM_005188.3	103	gAg/gTg	2/16	0.565303172036877	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.565303172036877	1		487	112	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059297-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	107	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.847127530778254	2		126	249	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0059297-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	168	479	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.801	0.742	0.862	0.801	0.742	0.862	CLONAL	1	TRUE	1	0.847127530778254	2		479	495	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564512	41564512	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555911075	NA	P-0059297-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	180	327	0	ENST00000263253.7:c.3934C>T	p.Arg1312Ter	p.R1312*	ENST00000263253	NM_001429.3	1312	Cga/Tga	24/31	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.847127530778254	2		327	406	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577125	64577147	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGGGCTCCAACCTGTGATGAAG	CTGGGCTCCAACCTGTGATGAAG	-	novel	NA	P-0059297-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	230	384	0	ENST00000312049.6:c.435_445+12del		p.X145_splice	ENST00000312049	NM_130799.2	145		2/10	0.847127530778254	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.847127530778254	1		384	285	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574693	64574693	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0059471-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	521	499	0	ENST00000312049.6:c.784-2A>C		p.X262_splice	ENST00000312049	NM_130799.2	262			0.688323909039225	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.688323909039225	2		499	748	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61324582	61324582	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059471-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	186	429	0	ENST00000283752.5:c.534C>G	p.Asn178Lys	p.N178K	ENST00000283752	NM_006919.2	178	aaC/aaG	6/8	0.688323909039225	3	FACETS	0.895	0.838	0.952	0.596	0.558	0.635	CLONAL	2	TRUE	0	0.688323909039225	3		429	406	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909587	76909587	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0059471-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	42	136	0	ENST00000373344.5:c.4317+1G>T		p.X1439_splice	ENST00000373344	NM_000489.3	1439			1	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.688323909039225	1		136	55	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0059936-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	183	467	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.501305109418877	2	FACETS	0.937	0.879	0.994	0.937	0.879	0.994	CLONAL	2	TRUE	0	0.544219074505147	2		467	359	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637631	23637631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45476495	NA	P-0059936-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	187	399	0	ENST00000261584.4:c.2674G>A	p.Glu892Lys	p.E892K	ENST00000261584	NM_024675.3	892	Gaa/Aaa	7/13	0.544219074505147	4	FACETS	0.984	0.916	1	0.984	0.916	1	CLONAL	2	TRUE	2	0.544219074505147	4		399	539	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471692	120471692	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059936-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3643	232	458	0	ENST00000256646.2:c.3799G>T	p.Glu1267Ter	p.E1267*	ENST00000256646	NM_024408.3	1267	Gag/Tag	23/34	0.544219074505147	33	FACETS	1	0.953	1			1	CLONAL	2	TRUE	NA	0.544219074505147	33		458	3875	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046540	30046540	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059936-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	141	523	0	ENST00000331968.5:c.2643del	p.Thr882HisfsTer3	p.T882Hfs*3	ENST00000331968	NM_002742.2	881	ccC/cc	18/18	0.544219074505147	3	FACETS	0.849	0.783	0.918	0.849	0.783	0.918	CLONAL	2	TRUE	1	0.544219074505147	3		523	388	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478112	99478113	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCAGGGGTCGTTTGGGATGGTCTATGAA	novel	NA	P-0059936-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	63	506	0	ENST00000268035.6:c.3019_3047dup	p.Val1017ArgfsTer16	p.V1017Rfs*16	ENST00000268035	NM_000875.3	1006	ggg/gGGCAGGGGTCGTTTGGGATGGTCTATGAAgg	16/21	0.544219074505147	3	FACETS	0.596	0.516	0.683	0.298	0.258	0.342	SUBCLONAL	1	TRUE	1	0.544219074505147	3		506	494	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188072	11188072	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060465-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	59	657	0	ENST00000361445.4:c.6022C>A	p.Gln2008Lys	p.Q2008K	ENST00000361445	NM_004958.3	2008	Cag/Aag	43/58	1	2	FACETS	0.599	0.517	0.689	0.599	0.517	0.689	SUBCLONAL	1	TRUE	1	0.441394315645689	2		657	446	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087379	27087379	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060465-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	52	565	1	ENST00000324856.7:c.1953G>T	p.Met651Ile	p.M651I	ENST00000324856	NM_006015.4	651	atG/atT	5/20	1	2	FACETS	0.727	0.622	0.841	0.727	0.622	0.841	SUBCLONAL	1	TRUE	1	0.441394315645689	2		566	324	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948545	71948545	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060465-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	130	849	0	ENST00000298229.2:c.3257G>T	p.Arg1086Leu	p.R1086L	ENST00000298229	NM_001567.3	1086	cGt/cTt	26/28	0.240131750218863	5	FACETS	0.969	0.884	1	0.646	0.589	0.705	INDETERMINATE	2	TRUE	2	0.441394315645689	5		849	505	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800884	120800884	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060465-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	137	594	0	ENST00000257552.2:c.364G>T	p.Val122Leu	p.V122L	ENST00000257552	NM_002442.3	122	Gtg/Ttg	6/15	0.240131750218863	5	FACETS	1	0.972	1	0.758	0.694	0.823	INDETERMINATE	2	TRUE	2	0.441394315645689	5		594	454	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628119	90628119	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs754284825	NA	P-0060465-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	39	866	0	ENST00000330062.3:c.1200G>T	p.Lys400Asn	p.K400N	ENST00000330062	NM_002168.2	400	aaG/aaT	10/11	0.380535313418538	3	FACETS	0.479	0.397	0.571	0.16	0.132	0.191	SUBCLONAL	1	TRUE	0	0.441394315645689	3		866	450	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644791	67644792	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0060465-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	81	671	0	ENST00000264010.4:c.59dup	p.Glu21GlyfsTer29	p.E21Gfs*29	ENST00000264010	NM_006565.3	19	gga/ggAa	3/12	0.388210578036195	3	FACETS	0.898	0.793	1	0.449	0.396	0.505	CLONAL	1	TRUE	1	0.441394315645689	3		671	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0060465-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	266	603	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.363012646693174	3	FACETS	0.924	0.876	0.971	0.924	0.876	0.971	CLONAL	3	TRUE	0	0.441394315645689	3		603	531	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872790	37872790	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060465-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	132	759	0	ENST00000269571.5:c.1669G>T	p.Ala557Ser	p.A557S	ENST00000269571		557	Gcc/Tcc	14/27	0.441394315645689	5	FACETS	0.81	0.737	0.885	0.54	0.491	0.59	CLONAL	2	TRUE	2	0.441394315645689	5		759	614	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223048	1223048	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0060465-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	115	677	0	ENST00000326873.7:c.985A>T	p.Lys329Ter	p.K329*	ENST00000326873	NM_000455.4	329	Aag/Tag	8/10	0.437599777011979	2	FACETS	0.773	0.705	0.843	0.773	0.705	0.843	SUBCLONAL	2	TRUE	0	0.441394315645689	2		677	337	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597496	10597496	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0060465-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	107	467	0	ENST00000171111.5:c.1709-2A>T		p.X570_splice	ENST00000171111	NM_203500.1	570			0.437599777011979	2	FACETS	0.848	0.772	0.925	0.848	0.772	0.925	CLONAL	2	TRUE	0	0.441394315645689	2		467	286	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257150	19257150	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060465-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	41	416	0	ENST00000162023.5:c.813G>T	p.Gln271His	p.Q271H	ENST00000162023		271	caG/caT	12/13	0.388210578036195	3	FACETS	1	0.898	1	0.545	0.459	0.639	CLONAL	1	TRUE	1	0.441394315645689	3		416	208	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306664	41306664	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060465-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	102	553	0	ENST00000373198.4:c.995G>C	p.Gly332Ala	p.G332A	ENST00000373198	NM_133170.3	332	gGc/gCc	7/32	0.355003286532751	4	FACETS	0.827	0.745	0.912	0.827	0.745	0.912	CLONAL	2	TRUE	2	0.441394315645689	4		553	403	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167526	24167526	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060465-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	122	641	0	ENST00000263121.7:c.910G>T	p.Gly304Cys	p.G304C	ENST00000263121	NM_003073.3	304	Ggc/Tgc	7/9	0.403541705801325	3	FACETS	0.798	0.727	0.871	0.798	0.727	0.871	SUBCLONAL	2	TRUE	1	0.441394315645689	3		641	423	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167779	56167779	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060465-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	88	556	0	ENST00000399503.3:c.1344G>T	p.Leu448Phe	p.L448F	ENST00000399503	NM_005921.1	448	ttG/ttT	7/20	0.292985788066182	5	FACETS	1	0.961	1	0.396	0.351	0.443	CLONAL	1	TRUE	2	0.441394315645689	5		556	558	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047966	180047966	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060465-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	39	864	0	ENST00000261937.6:c.2209C>T	p.Arg737Cys	p.R737C	ENST00000261937	NM_182925.4	737	Cgc/Tgc	15/30	1	2	FACETS	0.561	0.467	0.665	0.561	0.467	0.665	SUBCLONAL	1	TRUE	1	0.441394315645689	2		864	315	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922478	56922478	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060465-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	133	501	0	ENST00000519728.1:c.1348G>T	p.Ala450Ser	p.A450S	ENST00000519728	NM_002350.3	450	Gcc/Tcc	13/13	0.441394315645689	5	FACETS	1	0.951	1	0.706	0.645	0.769	CLONAL	2	TRUE	2	0.441394315645689	5		501	473	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317499	1317499	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060465-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	90	439	0	ENST00000400841.2:c.566C>A	p.Ala189Asp	p.A189D	ENST00000400841		189	gCt/gAt	5/6	0.399252716792583	2	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.441394315645689	2		439	311	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155742	119155742	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778927765	NA	P-0060478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	55	662	0	ENST00000264033.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000264033	NM_005188.3	499	Cga/Tga	10/16	1	2	FACETS	0.991	0.846	1	0.991	0.846	1	CLONAL	1	TRUE	1	0.14	2		662	793	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0060519-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	65	522	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.917	0.796	1	0.917	0.796	1	CLONAL	1	TRUE	1	0.25	2		522	567	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753176	42753176	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs538236832	NA	P-0060519-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	100	338	0	ENST00000222329.4:c.1088C>T	p.Ser363Leu	p.S363L	ENST00000222329	NM_006494.2	363	tCg/tTg	4/4	1	2	FACETS	0.99	0.884	1	0.99	0.884	1	CLONAL	1	TRUE	1	0.25	2		338	808	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060657-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	68	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.827	0.728	0.931	0.827	0.728	0.931	CLONAL	1	TRUE	1	0.632760715734229	2		126	260	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099420	157099421	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCAA	rs750911844	NA	P-0060657-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	53	729	0	ENST00000346085.5:c.363_368dup	p.Gln130_Gln131dup	p.Q130_Q131dup	ENST00000346085	NM_020732.3	130	-/CAGCAA	1/20	1	2	FACETS	0.313	0.267	0.364	0.313	0.267	0.364	SUBCLONAL	1	TRUE	1	0.632760715734229	2		729	535	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692911	89692911	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121909241	NA	P-0060657-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	78	429	0	ENST00000371953.3:c.395G>T	p.Gly132Val	p.G132V	ENST00000371953	NM_000314.4	132	gGt/gTt	5/9	1	2	FACETS	0.77	0.683	0.863	0.77	0.683	0.863	SUBCLONAL	1	TRUE	1	0.632760715734229	2		429	320	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624305	89624305	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	rs746128825	NA	P-0060657-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	108	457	0	ENST00000371953.3:c.79T>A	p.Tyr27Asn	p.Y27N	ENST00000371953	NM_000314.4	27	Tat/Aat	1/9	1	2	FACETS	0.908	0.822	0.997	0.908	0.822	0.997	CLONAL	1	TRUE	1	0.632760715734229	2		457	376	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591148	67591154	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TTGATGT	TTGATGT	-	novel	NA	P-0060657-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	101	480	0	ENST00000274335.5:c.1741_1745+2del		p.X581_splice	ENST00000274335		581		12/15	1	2	FACETS	0.925	0.835	1	0.925	0.835	1	CLONAL	1	TRUE	1	0.632760715734229	2		480	345	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772821	135772821	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060657-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	25	567	0	ENST00000298552.3:c.2802del	p.Lys934AsnfsTer21	p.K934Nfs*21	ENST00000298552	NM_001162426.1	934	aaA/aa	21/23	0.632760715734229	1	FACETS	0.173	0.136	0.215	0.173	0.136	0.215	SUBCLONAL	1	TRUE	0	0.632760715734229	1		567	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs878854073	NA	P-0060658-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	131	333	0	ENST00000269305.4:c.673-1G>A		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.687786552288436	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.687786552288436	2		333	168	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866396	56866396	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060658-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	81	281	0	ENST00000519728.1:c.643G>T	p.Ala215Ser	p.A215S	ENST00000519728	NM_002350.3	215	Gca/Tca	8/13	0.590208298293764	5	FACETS	1	0.913	1	0.346	0.306	0.389	CLONAL	1	TRUE	2	0.687786552288436	5		281	461	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397712	139397712	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060658-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	97	460	0	ENST00000277541.6:c.5089A>G	p.Thr1697Ala	p.T1697A	ENST00000277541	NM_017617.3	1697	Acc/Gcc	27/34	0.687786552288436	4	FACETS	1	0.959	1			1	CLONAL	1	TRUE	NA	0.687786552288436	4		460	418	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060685-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	227	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.928	0.873	0.983	0.928	0.873	0.983	CLONAL	1	TRUE	1	0.924992873111043	2		126	529	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0060685-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	571	623	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	1	TRUE	NA	0.924992873111043	2		623	1010	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041606	47041606	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060685-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	474	319	0	ENST00000377604.3:c.1831G>T	p.Glu611Ter	p.E611*	ENST00000377604	NM_001204468.1	611	Gag/Tag	17/24	1	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.924992873111043	1		319	490	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966766	44966766	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060685-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	283	192	0	ENST00000377967.4:c.3990C>A	p.Tyr1330Ter	p.Y1330*	ENST00000377967	NM_021140.2	1330	taC/taA	27/29	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.924992873111043	1		192	304	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828057	3828057	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060685-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	374	382	0	ENST00000262367.5:c.2068del	p.Ala690LeufsTer5	p.A690Lfs*5	ENST00000262367	NM_004380.2	690	Gct/ct	10/31	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.924992873111043	2		382	727	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980291	201980292	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0060685-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	359	473	0	ENST00000359651.3:c.28_29dup	p.Ser12LeufsTer32	p.S12Lfs*32	ENST00000359651		9	-/AT	1/8	1	2	FACETS	0.916	0.873	0.96	0.916	0.873	0.96	CLONAL	1	TRUE	1	0.924992873111043	2		473	847	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231489066	231489066	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060685-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	336	358	0	ENST00000295050.7:c.1429G>C	p.Glu477Gln	p.E477Q	ENST00000295050	NM_032018.5	477	Gaa/Caa	5/5	1	2	FACETS	0.969	0.922	1	0.969	0.922	1	CLONAL	1	TRUE	1	0.924992873111043	2		358	750	SUCCESS
BLM	641	MSKCC	GRCh37	15	91334000	91334000	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060685-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	361	445	0	ENST00000355112.3:c.2945G>T	p.Arg982Ile	p.R982I	ENST00000355112	NM_000057.2	982	aGa/aTa	15/22	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.924992873111043	2		445	740	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7977069	7977069	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060685-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	252	343	0	ENST00000319144.4:c.1661C>A	p.Pro554His	p.P554H	ENST00000319144	NM_001139.2	554	cCt/cAt	13/15	1	2	FACETS	0.959	0.906	1	0.959	0.906	1	CLONAL	1	TRUE	1	0.924992873111043	2		343	568	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250281	39250281	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060685-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	310	383	0	ENST00000402219.2:c.1288G>C	p.Asp430His	p.D430H	ENST00000402219	NM_005633.3	430	Gat/Cat	10/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.924992873111043	2		383	644	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162186	47162186	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060685-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	358	530	0	ENST00000409792.3:c.3940C>A	p.Pro1314Thr	p.P1314T	ENST00000409792	NM_014159.6	1314	Cct/Act	3/21	1	2	FACETS	0.927	0.883	0.971	0.927	0.883	0.971	CLONAL	1	TRUE	1	0.924992873111043	2		530	835	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109311862	109311862	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060685-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	237	341	0	ENST00000436639.2:c.1410C>A	p.Cys470Ter	p.C470*	ENST00000436639	NM_014454.2	470	tgC/tgA	8/10	1	2	FACETS	0.949	0.894	1	0.949	0.894	1	CLONAL	1	TRUE	1	0.924992873111043	2		341	540	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143994	11143994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060685-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	177	508	1	ENST00000358026.2:c.3575G>A	p.Arg1192His	p.R1192H	ENST00000358026	NM_001128849.1	1192	cGc/cAc	26/36	1	2	FACETS	0.417	0.384	0.451	0.417	0.384	0.451	SUBCLONAL	1	TRUE	1	0.924992873111043	2		509	918	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	161	877	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.969	0.895	1	1	0.992	1	CLONAL	2	TRUE	1	0.333683799987938	2		883	498	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	51	559	3	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	0.300579930239361	3	FACETS	0.828	0.705	0.962	0.414	0.352	0.481	CLONAL	1	TRUE	1	0.333683799987938	3		562	431	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	110	627	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.333683799987938	2		633	449	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	92	527	1	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.333683799987938	2		528	522	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	58	348	10	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.333683799987938	2		358	340	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	89	549	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.333683799987938	2		549	444	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119910	70119910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1297203260	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	146	452	0	ENST00000245479.2:c.916del	p.Val306CysfsTer77	p.V306Cfs*77	ENST00000245479	NM_000346.3	304	ccG/cc	3/3	1	2	FACETS	0.873	0.809	0.938	1	0.993	1	CLONAL	3	TRUE	1	0.333683799987938	2		452	334	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	75	409	4	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.856	0.752	0.968	0.856	0.752	0.968	CLONAL	1	TRUE	1	0.333683799987938	2		413	525	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	128	390	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	0.327711910316242	2	FACETS	0.938	0.858	1	0.938	0.858	1	CLONAL	2	TRUE	0	0.333683799987938	2		390	409	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872552	136872552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145335491	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	88	431	1	ENST00000241393.3:c.946G>A	p.Ala316Thr	p.A316T	ENST00000241393	NM_003467.2	316	Gca/Aca	2/2	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.333683799987938	2		432	495	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	142	590	0	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.941	0.865	1	1	0.991	1	CLONAL	2	TRUE	1	0.333683799987938	2		590	452	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851765	134851765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	65	474	0	ENST00000398015.3:c.1171G>A	p.Val391Ile	p.V391I	ENST00000398015	NM_004441.4	391	Gtc/Atc	5/16	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.333683799987938	2		474	378	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	56	451	4	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	0.327711910316242	2	FACETS	0.784	0.674	0.904	0.392	0.337	0.452	CLONAL	1	TRUE	0	0.333683799987938	2		455	428	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	73	480	0	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.985	0.865	1	0.985	0.865	1	CLONAL	1	TRUE	1	0.333683799987938	2		480	444	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	58	494	4	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.952	0.822	1	0.952	0.822	1	CLONAL	1	TRUE	1	0.333683799987938	2		498	365	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024505	16024505	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	83	386	0	ENST00000268712.3:c.1713del	p.Arg572GlufsTer18	p.R572Efs*18	ENST00000268712	NM_006311.3	571	ggG/gg	16/46	1	2	FACETS	0.953	0.843	1	0.953	0.843	1	CLONAL	1	TRUE	1	0.333683799987938	2		386	522	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	78	467	5	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.333683799987938	2		472	387	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253974	133253974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61732929	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	75	374	0	ENST00000320574.5:c.776G>A	p.Arg259His	p.R259H	ENST00000320574	NM_006231.2	259	cGc/cAc	8/49	1	2	FACETS	0.931	0.818	1	0.931	0.818	1	CLONAL	1	TRUE	1	0.333683799987938	2		374	483	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	92	465	2	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.333683799987938	2		467	481	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730831	40730831	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372700928	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	56	451	0	ENST00000373198.4:c.3704G>A	p.Arg1235His	p.R1235H	ENST00000373198	NM_133170.3	1235	cGc/cAc	27/32	1	2	FACETS	0.867	0.746	0.999	0.867	0.746	0.999	CLONAL	1	TRUE	1	0.333683799987938	2		451	387	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136309	202136309	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	57	324	0	ENST00000358485.4:c.553G>T	p.Glu185Ter	p.E185*	ENST00000358485	NM_001080125.1	185	Gag/Tag	3/9	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.333683799987938	2		324	336	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934243	49934243	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1407832113	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	74	508	1	ENST00000296474.3:c.2264del	p.Gly755ValfsTer19	p.G755Vfs*19	ENST00000296474	NM_002447.2	755	gGt/gt	8/20	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.333683799987938	2		509	415	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968597	55968597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34038364	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	73	373	0	ENST00000263923.4:c.2066C>T	p.Thr689Met	p.T689M	ENST00000263923	NM_002253.2	689	aCg/aTg	14/30	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.333683799987938	2		373	423	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020769	37020769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	45	369	0	ENST00000358127.4:c.76del	p.Val26PhefsTer3	p.V26Ffs*3	ENST00000358127	NM_001280556.1	26	Gtt/tt	2/10	1	2	FACETS	0.685	0.576	0.804	0.685	0.576	0.804	SUBCLONAL	1	TRUE	1	0.333683799987938	2		369	394	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467064	25467064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759818409	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	60	473	1	ENST00000264709.3:c.1811G>A	p.Arg604Gln	p.R604Q	ENST00000264709	NM_175629.2	604	cGg/cAg	15/23	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.333683799987938	2		474	354	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955112	17955112	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755706305	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	67	410	1	ENST00000458235.1:c.115del	p.Gln39SerfsTer108	p.Q39Sfs*108	ENST00000458235	NM_000215.3	39	Cag/ag	2/24	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.333683799987938	2		411	380	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413100	139413100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201236538	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	68	466	0	ENST00000277541.6:c.1042G>A	p.Ala348Thr	p.A348T	ENST00000277541	NM_017617.3	348	Gcc/Acc	6/34	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.333683799987938	2		466	398	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729888	41729888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1043609570	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	118	405	0	ENST00000242208.4:c.641G>A	p.Arg214Gln	p.R214Q	ENST00000242208	NM_002192.2	214	cGg/cAg	3/3	0.121340052947168	3	FACETS	1	0.923	1	0.678	0.616	0.741	INDETERMINATE	2	TRUE	0	0.333683799987938	3		405	406	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249361	153249361	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	62	307	2	ENST00000281708.4:c.1417del	p.Arg473GlufsTer25	p.R473Efs*25	ENST00000281708	NM_033632.3	473	Aga/ga	9/12	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.333683799987938	2		309	348	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740727	58740727	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	96	459	2	ENST00000305921.3:c.1636del	p.Leu546Ter	p.L546*	ENST00000305921	NM_003620.3	544	ggC/gg	6/6	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.333683799987938	2		461	554	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279922	18279922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1254390009	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	41	377	0	ENST00000222254.8:c.2005G>A	p.Val669Ile	p.V669I	ENST00000222254	NM_005027.3	669	Gtc/Atc	16/16	1	2	FACETS	0.85	0.712	1	0.85	0.712	1	CLONAL	1	TRUE	1	0.333683799987938	2		377	289	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306553	41306553	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	35	342	0	ENST00000373198.4:c.1106del	p.Gly369ValfsTer28	p.G369Vfs*28	ENST00000373198	NM_133170.3	369	gGt/gt	7/32	1	2	FACETS	0.69	0.567	0.827	0.69	0.567	0.827	SUBCLONAL	1	TRUE	1	0.333683799987938	2		342	304	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538257	9538257	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs746240534	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	75	384	0	ENST00000353224.5:c.1741C>T	p.Arg581Trp	p.R581W	ENST00000353224	NM_177990.2	581	Cgg/Tgg	7/10	1	2	FACETS	0.995	0.875	1	0.995	0.875	1	CLONAL	1	TRUE	1	0.333683799987938	2		384	452	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396234	396234	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	64	431	1	ENST00000262320.3:c.792del	p.Gly265GlufsTer149	p.G265Efs*149	ENST00000262320	NM_003502.3	264	ccC/cc	2/11	1	2	FACETS	0.924	0.803	1	0.924	0.803	1	CLONAL	1	TRUE	1	0.333683799987938	2		432	415	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140309	50140309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755565332	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	76	394	0	ENST00000246792.3:c.232C>T	p.Arg78Trp	p.R78W	ENST00000246792	NM_006270.3	78	Cgg/Tgg	2/6	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.333683799987938	2		394	365	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731468	47731468	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1284528511	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	29	386	0	ENST00000449228.1:c.324del	p.Phe109SerfsTer120	p.F109Sfs*120	ENST00000449228	NM_001127240.2	108	ggG/gg	2/4	1	2	FACETS	0.661	0.532	0.806	0.661	0.532	0.806	SUBCLONAL	1	TRUE	1	0.333683799987938	2		386	263	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350532	15350532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748633137	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	46	374	0	ENST00000263377.2:c.3383C>T	p.Ser1128Leu	p.S1128L	ENST00000263377	NM_058243.2	1128	tCg/tTg	16/20	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.333683799987938	2		374	232	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039374	47039374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	64	425	0	ENST00000377604.3:c.997G>A	p.Val333Ile	p.V333I	ENST00000377604	NM_001204468.1	333	Gtc/Atc	10/24	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.333683799987938	2		425	375	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42842590	42842590	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs771443342	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	63	367	0	ENST00000398585.3:c.1267del	p.Ala423ProfsTer12	p.A423Pfs*12	ENST00000398585	NM_001135099.1	423	Gcc/cc	11/14	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.333683799987938	2		367	345	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948747	71948748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760925109	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	64	567	5	ENST00000298229.2:c.3466dup	p.Arg1156ProfsTer59	p.R1156Pfs*59	ENST00000298229	NM_001567.3	1153	-/C	26/28	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.333683799987938	2		572	343	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133898	41133898	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	68	456	0	ENST00000379561.5:c.1730del	p.Gly577AlafsTer5	p.G577Afs*5	ENST00000379561	NM_002015.3	577	gGc/gc	2/3	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.333683799987938	2		456	400	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712796	43712796	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs186678492	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	172	492	0	ENST00000382044.4:c.4388G>A	p.Arg1463His	p.R1463H	ENST00000382044	NM_001141980.1	1463	cGt/cAt	21/28	0.327711910316242	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.333683799987938	2		492	502	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231497	5231497	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200771602	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	61	406	0	ENST00000357368.4:c.1979C>T	p.Pro660Leu	p.P660L	ENST00000357368	NM_002850.3	660	cCg/cTg	14/38	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.333683799987938	2		406	321	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349179	89349180	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	rs886039477	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	87	448	0	ENST00000301030.4:c.3770_3771del	p.Lys1257ArgfsTer25	p.K1257Rfs*25	ENST00000301030	NM_001256183.1	1257	aAA/a	9/13	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.333683799987938	2		448	504	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797114	45797114	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780084	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	57	538	0	ENST00000450313.1:c.1301C>T	p.Thr434Met	p.T434M	ENST00000450313	NM_012222.2	434	aCg/aTg	13/16	1	2	FACETS	0.827	0.712	0.952	0.827	0.712	0.952	CLONAL	1	TRUE	1	0.333683799987938	2		538	413	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164884	106164884	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1339287432	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	61	314	0	ENST00000380013.4:c.3752C>T	p.Thr1251Met	p.T1251M	ENST00000380013	NM_001127208.2	1251	aCg/aTg	6/11	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.333683799987938	2		314	361	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266670	41266670	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	87	395	0	ENST00000349496.5:c.467T>C	p.Leu156Pro	p.L156P	ENST00000349496	NM_001904.3	156	cTg/cCg	4/15	0.327711910316242	2	FACETS	1	0.903	1	0.509	0.452	0.57	CLONAL	1	TRUE	0	0.333683799987938	2		395	512	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521157	187521157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373469759	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	73	395	0	ENST00000441802.2:c.11998G>A	p.Glu4000Lys	p.E4000K	ENST00000441802	NM_005245.3	4000	Gaa/Aaa	22/27	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.333683799987938	2		395	401	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981862	201981862	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	62	475	0	ENST00000359651.3:c.573del	p.Gly192AlafsTer62	p.G192Afs*62	ENST00000359651		191	ccT/cc	4/8	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.333683799987938	2		475	340	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131276	17131276	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374969279	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	63	445	0	ENST00000285071.4:c.176G>A	p.Arg59His	p.R59H	ENST00000285071	NM_144997.5	59	cGt/cAt	4/14	1	2	FACETS	0.872	0.757	0.997	0.872	0.757	0.997	CLONAL	1	TRUE	1	0.333683799987938	2		445	433	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258735	16258735	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	72	553	0	ENST00000375759.3:c.6005del	p.Asn2002MetfsTer20	p.N2002Mfs*20	ENST00000375759	NM_015001.2	2000	ggA/gg	11/15	1	2	FACETS	0.833	0.729	0.945	0.833	0.729	0.945	CLONAL	1	TRUE	1	0.333683799987938	2		553	518	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526647	106526648	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	121	344	0	ENST00000359195.3:c.2946_2947del	p.Arg982SerfsTer8	p.R982Sfs*8	ENST00000359195	NM_002649.2	980	aaAGag/aaag	10/11	0.326295206616376	3	FACETS	0.942	0.857	1	0.942	0.857	1	CLONAL	2	TRUE	1	0.333683799987938	3		344	449	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872067	37872067	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	49	541	0	ENST00000269571.5:c.1388G>A	p.Ser463Asn	p.S463N	ENST00000269571		463	aGt/aAt	12/27	1	2	FACETS	0.753	0.639	0.877	0.753	0.639	0.877	SUBCLONAL	1	TRUE	1	0.333683799987938	2		541	390	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246525	10246525	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	46	334	0	ENST00000340748.4:c.4612C>T	p.Arg1538Cys	p.R1538C	ENST00000340748		1538	Cgc/Tgc	38/40	1	2	FACETS	0.916	0.776	1	0.916	0.776	1	CLONAL	1	TRUE	1	0.333683799987938	2		334	301	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216693	36216693	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765981100	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	58	498	0	ENST00000222270.7:c.3859C>T	p.Arg1287Trp	p.R1287W	ENST00000222270	NM_014727.1	1287	Cgg/Tgg	13/37	1	2	FACETS	0.88	0.759	1	0.88	0.759	1	CLONAL	1	TRUE	1	0.333683799987938	2		498	395	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630539	187630539	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	118	431	0	ENST00000441802.2:c.443T>C	p.Leu148Ser	p.L148S	ENST00000441802	NM_005245.3	148	tTa/tCa	2/27	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.333683799987938	2		431	598	SUCCESS
MAD2L2	10459	MSKCC	GRCh37	1	11736959	11736959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151024263	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	45	390	0	ENST00000235310.3:c.278G>A	p.Arg93His	p.R93H	ENST00000235310		93	cGc/cAc	7/11	1	2	FACETS	0.753	0.635	0.883	0.753	0.635	0.883	SUBCLONAL	1	TRUE	1	0.333683799987938	2		390	358	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424841	47424841	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	104	422	1	ENST00000404338.3:c.2914del	p.Arg972GlyfsTer55	p.R972Gfs*55	ENST00000404338	NM_004491.4	970	tCc/tc	1/6	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.333683799987938	2		423	521	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107045	27107045	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	87	526	0	ENST00000324856.7:c.6656A>G	p.Gln2219Arg	p.Q2219R	ENST00000324856	NM_006015.4	2219	cAg/cGg	20/20	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.333683799987938	2		526	467	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981530	201981530	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	57	394	0	ENST00000359651.3:c.445del	p.Ala149ProfsTer6	p.A149Pfs*6	ENST00000359651		148	atG/at	3/8	1	2	FACETS	0.987	0.852	1	0.987	0.852	1	CLONAL	1	TRUE	1	0.333683799987938	2		394	346	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115920	8115920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	58	503	1	ENST00000346208.3:c.1266G>A	p.Met422Ile	p.M422I	ENST00000346208		422	atG/atA	6/6	1	2	FACETS	0.779	0.671	0.897	0.779	0.671	0.897	SUBCLONAL	1	TRUE	1	0.333683799987938	2		504	446	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852263	63852263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1236991649	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	85	414	0	ENST00000279873.7:c.3041G>A	p.Arg1014His	p.R1014H	ENST00000279873	NM_032199.2	1014	cGc/cAc	10/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.333683799987938	2		414	407	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482372	56482372	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	76	403	0	ENST00000267101.3:c.920C>A	p.Pro307His	p.P307H	ENST00000267101	NM_001982.3	307	cCt/cAt	8/28	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.333683799987938	2		403	405	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235901	133235901	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	64	606	1	ENST00000320574.5:c.3255G>T	p.Glu1085Asp	p.E1085D	ENST00000320574	NM_006231.2	1085	gaG/gaT	26/49	1	2	FACETS	0.92	0.799	1	0.92	0.799	1	CLONAL	1	TRUE	1	0.333683799987938	2		607	417	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30095735	30095736	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	24	235	0	ENST00000331968.5:c.1752dup	p.Pro585SerfsTer2	p.P585Sfs*2	ENST00000331968	NM_002742.2	584	-/T	12/18	0.300579930239361	3	FACETS	0.552	0.433	0.689	0.276	0.216	0.345	SUBCLONAL	1	TRUE	1	0.333683799987938	3		235	304	SUCCESS
BLM	641	MSKCC	GRCh37	15	91326089	91326089	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	41	289	0	ENST00000355112.3:c.2593T>C	p.Tyr865His	p.Y865H	ENST00000355112	NM_000057.2	865	Tat/Cat	13/22	0.327711910316242	2	FACETS	0.783	0.655	0.924	0.391	0.327	0.462	CLONAL	1	TRUE	0	0.333683799987938	2		289	314	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396439	396439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	77	431	0	ENST00000262320.3:c.587del	p.Asn196ThrfsTer46	p.N196Tfs*46	ENST00000262320	NM_003502.3	196	aAc/ac	2/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.333683799987938	2		431	400	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138132	2138132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	60	546	0	ENST00000219476.3:c.5152C>T	p.His1718Tyr	p.H1718Y	ENST00000219476	NM_000548.3	1718	Cac/Tac	40/42	1	2	FACETS	0.906	0.783	1	0.906	0.783	1	CLONAL	1	TRUE	1	0.333683799987938	2		546	397	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30323853	30323853	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	67	258	0	ENST00000322652.5:c.1831A>G	p.Lys611Glu	p.K611E	ENST00000322652	NM_015355.2	611	Aaa/Gaa	15/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.333683799987938	2		258	307	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554587	63554588	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	70	463	0	ENST00000307078.5:c.151_152del	p.Val51LeufsTer89	p.V51Lfs*89	ENST00000307078	NM_004655.3	51	GTc/c	2/11	1	2	FACETS	0.91	0.796	1	0.91	0.796	1	CLONAL	1	TRUE	1	0.333683799987938	2		463	461	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554665	63554665	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs746837986	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	119	497	0	ENST00000307078.5:c.74del	p.Pro25GlnfsTer51	p.P25Qfs*51	ENST00000307078	NM_004655.3	25	cCa/ca	2/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.333683799987938	2		497	547	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221303	1221303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1461580063	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	57	476	0	ENST00000326873.7:c.826G>A	p.Gly276Ser	p.G276S	ENST00000326873	NM_000455.4	276	Ggc/Agc	6/10	1	2	FACETS	0.913	0.787	1	0.913	0.787	1	CLONAL	1	TRUE	1	0.333683799987938	2		476	374	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6216446	6216446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293851158	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	49	409	0	ENST00000252674.7:c.1277C>T	p.Ala426Val	p.A426V	ENST00000252674	NM_005934.3	426	gCc/gTc	8/12	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.333683799987938	2		409	283	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172380	7172380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	60	391	0	ENST00000302850.5:c.1189del	p.Ile397SerfsTer18	p.I397Sfs*18	ENST00000302850	NM_000208.2	397	Atc/tc	5/22	1	2	FACETS	0.831	0.718	0.953	0.831	0.718	0.953	CLONAL	1	TRUE	1	0.333683799987938	2		391	433	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610585	10610585	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	47	510	0	ENST00000171111.5:c.125T>C	p.Val42Ala	p.V42A	ENST00000171111	NM_203500.1	42	gTg/gCg	2/6	1	2	FACETS	0.787	0.666	0.919	0.787	0.666	0.919	CLONAL	1	TRUE	1	0.333683799987938	2		510	358	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121134	11121134	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	69	421	0	ENST00000358026.2:c.2201T>C	p.Val734Ala	p.V734A	ENST00000358026	NM_001128849.1	734	gTg/gCg	15/36	1	2	FACETS	0.942	0.823	1	0.942	0.823	1	CLONAL	1	TRUE	1	0.333683799987938	2		421	439	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144468	11144468	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	66	289	0	ENST00000358026.2:c.3800G>A	p.Gly1267Asp	p.G1267D	ENST00000358026	NM_001128849.1	1267	gGc/gAc	27/36	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.333683799987938	2		289	331	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292526	15292526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	52	441	0	ENST00000263388.2:c.2653G>A	p.Ala885Thr	p.A885T	ENST00000263388	NM_000435.2	885	Gcc/Acc	17/33	1	2	FACETS	0.816	0.697	0.945	0.816	0.697	0.945	CLONAL	1	TRUE	1	0.333683799987938	2		441	382	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425335	47425335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	77	438	0	ENST00000404338.3:c.3403G>A	p.Asp1135Asn	p.D1135N	ENST00000404338	NM_004491.4	1135	Gac/Aac	1/6	1	2	FACETS	0.946	0.833	1	0.946	0.833	1	CLONAL	1	TRUE	1	0.333683799987938	2		438	488	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47503884	47503884	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	61	405	1	ENST00000404338.3:c.4444del	p.Gln1482SerfsTer317	p.Q1482Sfs*317	ENST00000404338	NM_004491.4	1480	aCc/ac	6/6	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.333683799987938	2		406	355	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439418	220439418	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	49	387	0	ENST00000243786.2:c.271G>A	p.Ala91Thr	p.A91T	ENST00000243786	NM_002191.3	91	Gcc/Acc	2/2	1	2	FACETS	0.996	0.849	1	0.996	0.849	1	CLONAL	1	TRUE	1	0.333683799987938	2		387	295	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660120	227660120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544798746	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	87	532	0	ENST00000305123.5:c.3335G>A	p.Arg1112Gln	p.R1112Q	ENST00000305123	NM_005544.2	1112	cGg/cAg	1/2	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.333683799987938	2		532	435	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662376	227662376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770400020	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	62	460	0	ENST00000305123.5:c.1079G>A	p.Arg360Gln	p.R360Q	ENST00000305123	NM_005544.2	360	cGg/cAg	1/2	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.333683799987938	2		460	351	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445079	89445079	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs752088339	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	56	415	0	ENST00000336596.2:c.1399A>G	p.Ile467Val	p.I467V	ENST00000336596	NM_005233.5	467	Ata/Gta	6/17	1	2	FACETS	0.912	0.785	1	0.912	0.785	1	CLONAL	1	TRUE	1	0.333683799987938	2		415	368	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920141	1920141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1211896693	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	86	470	1	ENST00000382891.5:c.1201C>T	p.Arg401Trp	p.R401W	ENST00000382891	NM_133335.3	401	Cgg/Tgg	5/22	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.333683799987938	2		471	514	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138567	55138567	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	54	317	0	ENST00000257290.5:c.1244C>A	p.Ser415Ter	p.S415*	ENST00000257290	NM_006206.4	415	tCa/tAa	9/23	1	2	FACETS	0.938	0.805	1	0.938	0.805	1	CLONAL	1	TRUE	1	0.333683799987938	2		317	345	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509124	66509124	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	34	269	0	ENST00000273854.3:c.203C>G	p.Thr68Ser	p.T68S	ENST00000273854	NM_004439.5	68	aCt/aGt	2/18	1	2	FACETS	0.787	0.646	0.943	0.787	0.646	0.943	CLONAL	1	TRUE	1	0.333683799987938	2		269	259	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532903	187533240	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTGAGTATAAAATCTTCCGATTTAATCCTATGAAGACATAAAAACATGTCAAAAGATTTTAAATAAAAAAGTTTAACACTTTTTTTTTTTTTTGAGATGGAGTCTCCCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGTGATCTTGGCTCACTGCAACCTCTGTCCCCCAGGTTCAAGCAATTCTCCTGCCTCAGCCTCCCGAGTGGCTGGGGTTACAGACACACTGTAATTTTTGTATTTTTATTAGAGACGGGGTTTCTCCATGTTGGCCAGGCTGGTCTTGAACTCCTGACCTCGTGATCCACCCGCCTCGGCCTCCCAAAGTGCCAGGATCCCAG	GTGAGTATAAAATCTTCCGATTTAATCCTATGAAGACATAAAAACATGTCAAAAGATTTTAAATAAAAAAGTTTAACACTTTTTTTTTTTTTTGAGATGGAGTCTCCCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGTGATCTTGGCTCACTGCAACCTCTGTCCCCCAGGTTCAAGCAATTCTCCTGCCTCAGCCTCCCGAGTGGCTGGGGTTACAGACACACTGTAATTTTTGTATTTTTATTAGAGACGGGGTTTCTCCATGTTGGCCAGGCTGGTCTTGAACTCCTGACCTCGTGATCCACCCGCCTCGGCCTCCCAAAGTGCCAGGATCCCAG	-	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	32	341	0	ENST00000441802.2:c.9464-311_9490del		p.X3155_splice	ENST00000441802	NM_005245.3	3155		14/27	1	2	FACETS	0.573	0.465	0.693	0.573	0.465	0.693	SUBCLONAL	1	TRUE	1	0.333683799987938	2		341	335	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31464359	31464359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1339947335	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	54	345	0	ENST00000344624.3:c.2558G>A	p.Arg853His	p.R853H	ENST00000344624		853	cGt/cAt	17/33	1	2	FACETS	0.776	0.665	0.898	0.776	0.665	0.898	SUBCLONAL	1	TRUE	1	0.333683799987938	2		345	417	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953135	38953135	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	44	309	0	ENST00000357387.3:c.2849C>T	p.Pro950Leu	p.P950L	ENST00000357387	NM_152756.3	950	cCa/cTa	29/38	1	2	FACETS	0.727	0.611	0.854	0.727	0.611	0.854	SUBCLONAL	1	TRUE	1	0.333683799987938	2		309	363	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170929	56170929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748356370	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	77	424	0	ENST00000399503.3:c.1757G>A	p.Arg586His	p.R586H	ENST00000399503	NM_005921.1	586	cGt/cAt	10/20	1	2	FACETS	0.923	0.812	1	0.923	0.812	1	CLONAL	1	TRUE	1	0.333683799987938	2		424	500	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86686632	86686634	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	59	309	0	ENST00000274376.6:c.3078_3080del	p.Leu1027del	p.L1027del	ENST00000274376	NM_002890.2	1026	CTT/-	25/25	1	2	FACETS	0.974	0.842	1	0.974	0.842	1	CLONAL	1	TRUE	1	0.333683799987938	2		309	363	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86686660	86686660	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	55	341	0	ENST00000274376.6:c.3108del	p.Lys1036AsnfsTer?	p.K1036Nfs*?	ENST00000274376	NM_002890.2	1035	cAa/ca	25/25	1	2	FACETS	0.826	0.709	0.953	0.826	0.709	0.953	CLONAL	1	TRUE	1	0.333683799987938	2		341	399	SUCCESS
APC	324	MSKCC	GRCh37	5	112179446	112179446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	81	429	0	ENST00000257430.4:c.8155G>A	p.Glu2719Lys	p.E2719K	ENST00000257430	NM_000038.5	2719	Gaa/Aaa	16/16	1	2	FACETS	0.925	0.817	1	0.925	0.817	1	CLONAL	1	TRUE	1	0.333683799987938	2		429	525	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120454	94120455	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	76	431	0	ENST00000369303.4:c.596_597del	p.Lys199SerfsTer11	p.K199Sfs*11	ENST00000369303	NM_004440.3	199	aAA/a	3/17	1	2	FACETS	0.943	0.83	1	0.943	0.83	1	CLONAL	1	TRUE	1	0.333683799987938	2		431	483	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877054	151877054	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	87	450	0	ENST00000262189.6:c.7307del	p.Pro2436HisfsTer16	p.P2436Hfs*16	ENST00000262189	NM_170606.2	2436	cCa/ca	37/59	0.326295206616376	3	FACETS	1	0.928	1	0.531	0.471	0.595	CLONAL	1	TRUE	1	0.333683799987938	3		450	573	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738784	145738784	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs941552175	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	53	646	0	ENST00000428558.2:c.2281A>G	p.Met761Val	p.M761V	ENST00000428558	NM_004260.3	761	Atg/Gtg	14/22	0.300579930239361	3	FACETS	0.588	0.501	0.684	0.294	0.25	0.342	SUBCLONAL	1	TRUE	1	0.333683799987938	3		646	630	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867574	101867574	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1264167074	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	20	198	0	ENST00000374994.4:c.91del	p.Ala31ArgfsTer19	p.A31Rfs*19	ENST00000374994	NM_004612.2	29	ccG/cc	1/9	1	2	FACETS	0.838	0.647	1	0.838	0.647	1	CLONAL	1	TRUE	1	0.333683799987938	2		198	143	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797300	135797300	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs118203402	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	82	393	0	ENST00000298552.3:c.569G>A	p.Arg190His	p.R190H	ENST00000298552	NM_001162426.1	190	cGc/cAc	7/23	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.333683799987938	2		393	475	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15809109	15809109	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060747-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	67	369	0	ENST00000307771.7:c.94C>T	p.Gln32Ter	p.Q32*	ENST00000307771	NM_005089.3	32	Cag/Tag	2/11	1	2	FACETS	0.898	0.783	1	0.898	0.783	1	CLONAL	1	TRUE	1	0.333683799987938	2		369	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0060877-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	346	715	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.35949690990251	2	FACETS	1	0.985	1	1	0.996	1	CLONAL	3	TRUE	0	0.35949690990251	2		715	604	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0060877-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	58	566	0	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	0.309949436323408	2	FACETS	0.639	0.549	0.736	0.319	0.274	0.368	SUBCLONAL	1	TRUE	0	0.35949690990251	2		566	505	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0060877-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	89	484	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	0.309949436323408	2	FACETS	0.806	0.723	0.893	0.806	0.723	0.893	CLONAL	2	TRUE	0	0.35949690990251	2		484	307	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119884	70119884	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060877-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	335	700	0	ENST00000245479.2:c.886C>T	p.Gln296Ter	p.Q296*	ENST00000245479	NM_000346.3	296	Cag/Tag	3/3	0.35949690990251	3	FACETS	1	0.966	1	1	0.995	1	CLONAL	3	TRUE	1	0.35949690990251	3		700	720	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003749	45003749	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs368160918	NA	P-0060877-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	131	591	0	ENST00000558401.1:c.5C>G	p.Ser2Cys	p.S2C	ENST00000558401	NM_004048.2	2	tCt/tGt	1/4	1	2	FACETS	0.779	0.711	0.848	1	0.988	1	SUBCLONAL	2	TRUE	1	0.35949690990251	2		591	468	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0060921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	245	255	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.428409305984648	3	FACETS	0.896	0.846	0.945	1	0.992	1	CLONAL	3	TRUE	1	0.428320491867569	3		255	517	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0060921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	185	455	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.424042851428586	2	FACETS	0.816	0.76	0.875	0.816	0.76	0.875	CLONAL	2	TRUE	0	0.428320491867569	2		455	529	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920401	114920401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1422891742	NA	P-0060921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	104	363	0	ENST00000543371.1:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000543371	NM_001198531.1	448	Cgg/Tgg	13/14	1	2	FACETS	0.872	0.783	0.966	0.872	0.783	0.966	CLONAL	1	TRUE	1	0.428320491867569	2		363	557	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245524	153245524	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	89	323	0	ENST00000281708.4:c.1667G>A	p.Ser556Asn	p.S556N	ENST00000281708	NM_033632.3	556	aGt/aAt	11/12	1	2	FACETS	0.98	0.874	1	0.98	0.874	1	CLONAL	1	TRUE	1	0.428320491867569	2		323	424	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467988	50467988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	141	540	0	ENST00000331340.3:c.1223G>A	p.Arg408His	p.R408H	ENST00000331340	NM_006060.4	408	cGc/cAc	8/8	0.36200777620308	3	FACETS	1	0.923	1	0.507	0.462	0.554	CLONAL	1	TRUE	1	0.428320491867569	3		540	789	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420073	420075	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0060921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	227	446	0	ENST00000399788.2:c.3192_3194del	p.Lys1064del	p.K1064del	ENST00000399788	NM_001042603.1	1064	aaGAAt/aat	21/28	0.423981330583163	4	FACETS	0.848	0.791	0.906	0.565	0.527	0.604	CLONAL	2	TRUE	1	0.428320491867569	4		446	893	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120428	70120429	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0060921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	157	534	0	ENST00000245479.2:c.1431dup	p.Thr478HisfsTer100	p.T478Hfs*100	ENST00000245479	NM_000346.3	477	tac/taCc	3/3	1	2	FACETS	0.945	0.867	1	0.945	0.867	1	CLONAL	1	TRUE	1	0.428320491867569	2		534	776	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872365	45872365	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060921-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	146	504	0	ENST00000391945.4:c.146C>T	p.Thr49Ile	p.T49I	ENST00000391945	NM_000400.3	49	aCa/aTa	3/23	0.423981330583163	4	FACETS	0.955	0.87	1	0.318	0.29	0.348	CLONAL	1	TRUE	1	0.428320491867569	4		504	1020	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0061004-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	265	535	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.950395059993051	2	FACETS	0.996	0.977	1	0.996	0.977	1	CLONAL	2	TRUE	0	0.950395059993051	2		535	280	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28929495	NA	P-0061004-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	603	390	0	ENST00000275493.2:c.2155G>A	p.Gly719Ser	p.G719S	ENST00000275493	NM_005228.3	719	Ggc/Agc	18/28	0.556672857903223	6	FACETS	0.923	0.895	0.951	1	0.996	1	INDETERMINATE	4	TRUE	3	0.950395059993051	6		390	997	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202644	108202647	+	frameshift_variant	Frame_Shift_Del	DEL	TTTG	TTTG	-	rs1555124506	NA	P-0061004-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	78	344	0	ENST00000278616.4:c.7671_7674del	p.Phe2558LeufsTer5	p.F2558Lfs*5	ENST00000278616	NM_000051.3	2556	acTTTG/ac	52/63	1	2	FACETS	0.421	0.372	0.473	0.421	0.372	0.473	SUBCLONAL	1	TRUE	1	0.950395059993051	2		344	390	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145743153	145743153	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061004-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	140	461	0	ENST00000428558.2:c.16del	p.Asp6ThrfsTer43	p.D6Tfs*43	ENST00000428558	NM_004260.3	6	Gac/ac	1/22	0.950395059993051	2	FACETS	0.413	0.376	0.451	0.206	0.188	0.226	SUBCLONAL	1	TRUE	0	0.950395059993051	2		461	714	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346940	70346940	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061004-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	109	510	0	ENST00000374080.3:c.2807G>T	p.Cys936Phe	p.C936F	ENST00000374080		936	tGc/tTc	20/45	0.678940126136266	3	FACETS	0.418	0.375	0.464	0.209	0.187	0.232	SUBCLONAL	1	TRUE	1	0.950395059993051	3		510	809	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374244	138374244	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061005-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	31	492	0	ENST00000289153.2:c.3200A>T	p.Asp1067Val	p.D1067V	ENST00000289153	NM_006219.2	1067	gAc/gTc	22/22	1	2	FACETS	0.463	0.373	0.564	0.463	0.373	0.564	SUBCLONAL	1	TRUE	1	0.262170257332972	2		492	511	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045016	47045016	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061005-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	56	759	0	ENST00000377604.3:c.2342C>A	p.Ser781Ter	p.S781*	ENST00000377604	NM_001204468.1	781	tCa/tAa	20/24	1	2	FACETS	0.678	0.58	0.785	0.678	0.58	0.785	SUBCLONAL	1	TRUE	1	0.262170257332972	2		759	630	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979532	55979532	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061005-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	44	525	0	ENST00000263923.4:c.915C>A	p.Tyr305Ter	p.Y305*	ENST00000263923	NM_002253.2	305	taC/taA	7/30	1	2	FACETS	0.627	0.526	0.74	0.627	0.526	0.74	SUBCLONAL	1	TRUE	1	0.262170257332972	2		525	535	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200946	108200946	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs147604227	NA	P-0061005-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	35	518	0	ENST00000278616.4:c.7313C>G	p.Thr2438Arg	p.T2438R	ENST00000278616	NM_000051.3	2438	aCa/aGa	50/63	0.262170257332972	1	FACETS	0.53	0.434	0.637	0.53	0.434	0.637	SUBCLONAL	1	TRUE	0	0.262170257332972	1		518	438	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729771	41729771	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061005-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	61	662	0	ENST00000242208.4:c.758G>A	p.Ser253Asn	p.S253N	ENST00000242208	NM_002192.2	253	aGc/aAc	3/3	1	2	FACETS	0.709	0.611	0.816	0.709	0.611	0.816	SUBCLONAL	1	TRUE	1	0.262170257332972	2		662	656	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999158	100999158	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061005-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	41	749	0	ENST00000325455.5:c.644A>T	p.Gln215Leu	p.Q215L	ENST00000325455	NM_001202474.3	215	cAg/cTg	1/8	0.262170257332972	1	FACETS	0.485	0.404	0.576	0.485	0.404	0.576	SUBCLONAL	1	TRUE	0	0.262170257332972	1		749	560	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864561	57864561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061005-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	154	735	0	ENST00000228682.2:c.2038C>T	p.Leu680Phe	p.L680F	ENST00000228682	NM_005269.2	680	Ctc/Ttc	12/12	0.262170257332972	3	FACETS	0.941	0.863	1	0.941	0.863	1	CLONAL	2	TRUE	1	0.262170257332972	3		735	706	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991307	41991308	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061005-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	29	560	0	ENST00000219905.7:c.2141dup	p.Leu714PhefsTer31	p.L714Ffs*31	ENST00000219905	NM_001164273.1	713	gat/gaTt	5/24	0.262170257332972	1	FACETS	0.465	0.373	0.57	0.465	0.373	0.57	SUBCLONAL	1	TRUE	0	0.262170257332972	1		560	413	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155486	47155486	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061005-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	28	463	0	ENST00000409792.3:c.4595G>C	p.Arg1532Pro	p.R1532P	ENST00000409792	NM_014159.6	1532	cGg/cCg	5/21	1	2	FACETS	0.538	0.43	0.662	0.538	0.43	0.662	SUBCLONAL	1	TRUE	1	0.262170257332972	2		463	397	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144378884	144378884	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs373393887	NA	P-0061005-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	20	372	0	ENST00000262995.4:c.1637A>T	p.Asp546Val	p.D546V	ENST00000262995	NM_207123.2	546	gAt/gTt	7/11	1	2	FACETS	0.454	0.347	0.58	0.454	0.347	0.58	SUBCLONAL	1	TRUE	1	0.262170257332972	2		372	336	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952479	38952480	+	missense_variant	Missense_Mutation	DNP	AC	AC	GA	novel	NA	P-0061005-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	31	566	0	ENST00000357387.3:c.2945_2946delinsTC	p.Cys982Phe	p.C982F	ENST00000357387	NM_152756.3	982	tGT/tTC	30/38	1	2	FACETS	0.473	0.382	0.577	0.473	0.382	0.577	SUBCLONAL	1	TRUE	1	0.262170257332972	2		566	500	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401207	139401207	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061005-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	36	750	0	ENST00000277541.6:c.3862G>T	p.Val1288Phe	p.V1288F	ENST00000277541	NM_017617.3	1288	Gtc/Ttc	23/34	1	2	FACETS	0.449	0.368	0.54	0.449	0.368	0.54	SUBCLONAL	1	TRUE	1	0.262170257332972	2		750	612	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	113	438	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.256907951554173	3	FACETS	0.944	0.851	1	0.472	0.425	0.521	INDETERMINATE	1	FALSE	1	0.463737769179379	3		438	636	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	42	126	0				ENST00000310581	NM_198253.2	-/1132			0.1681940118264	0	FACETS	0.376	0.316	0.442			1	INDETERMINATE	1	FALSE	0	0.463737769179379	0		126	258	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517766	176517766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370322847	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	104	815	0	ENST00000292408.4:c.376G>A	p.Asp126Asn	p.D126N	ENST00000292408	NM_213647.1	126	Gat/Aat	4/18	0.256907951554173	3	FACETS	1	0.941	1	0.533	0.479	0.59	INDETERMINATE	1	FALSE	1	0.463737769179379	3		815	518	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508728	148508728	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs267601395	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	71	428	0	ENST00000320356.2:c.1936T>A	p.Tyr646Asn	p.Y646N	ENST00000320356	NM_004456.4	646	Tac/Aac	16/20	1	2	FACETS	0.712	0.624	0.807	0.712	0.624	0.807	SUBCLONAL	1	FALSE	1	0.463737769179379	2		428	430	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956220	55956220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190050670	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	71	479	0	ENST00000263923.4:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000263923	NM_002253.2	1032	cGa/cAa	23/30	0.1681940118264	0	FACETS	0.377	0.33	0.427			1	INDETERMINATE	1	FALSE	0	0.463737769179379	0		479	436	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128016978	128016978	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs4150521	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	78	585	0	ENST00000285398.2:c.2111C>T	p.Ser704Leu	p.S704L	ENST00000285398	NM_000122.1	704	tCg/tTg	14/15	0.1681940118264	0	FACETS	0.364	0.32	0.41			1	INDETERMINATE	1	FALSE	0	0.463737769179379	0		585	496	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211097	55211097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219568637	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	32	514	0	ENST00000275493.2:c.340G>A	p.Glu114Lys	p.E114K	ENST00000275493	NM_005228.3	114	Gaa/Aaa	3/28	0.40455742801022	0	FACETS	0.248	0.202	0.3			1	SUBCLONAL	1	FALSE	0	0.463737769179379	0		514	298	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732484	74732484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755334722	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	484	715	0	ENST00000359995.5:c.425C>T	p.Ser142Phe	p.S142F	ENST00000359995	NM_001195427.1	142	tCt/tTt	2/3	0.328369545263203	3	FACETS	0.992	0.95	1	0.992	0.95	1	CLONAL	2	FALSE	1	0.463737769179379	3		715	1296	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912795	100912795	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	55	442	0	ENST00000325455.5:c.2527G>A	p.Glu843Lys	p.E843K	ENST00000325455	NM_001202474.3	843	Gag/Aag	7/8	1	2	FACETS	0.494	0.423	0.572	0.494	0.423	0.572	SUBCLONAL	1	FALSE	1	0.463737769179379	2		442	480	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715890	117715890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371206741	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	93	377	0	ENST00000368508.3:c.868G>A	p.Glu290Lys	p.E290K	ENST00000368508	NM_002944.2	290	Gaa/Aaa	9/43	0.227397830198595	1	FACETS	0.627	0.56	0.699	0.627	0.56	0.699	INDETERMINATE	1	FALSE	0	0.463737769179379	1		377	491	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319853	8319853	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	62	490	0	ENST00000356435.5:c.5648G>A	p.Arg1883Gln	p.R1883Q	ENST00000356435		1883	cGa/cAa	34/35	1	2	FACETS	0.532	0.46	0.609	0.532	0.46	0.609	SUBCLONAL	1	FALSE	1	0.463737769179379	2		490	503	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622446	28622446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	42	515	0	ENST00000241453.7:c.1171C>T	p.Pro391Ser	p.P391S	ENST00000241453	NM_004119.2	391	Cct/Tct	9/24	0.1681940118264	0	FACETS	0.153	0.127	0.182			1	INDETERMINATE	1	FALSE	0	0.463737769179379	0		515	634	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683508	182683508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	60	330	0	ENST00000292782.4:c.37C>T	p.Arg13Cys	p.R13C	ENST00000292782	NM_020640.2	13	Cgt/Tgt	2/7	1	2	FACETS	0.521	0.449	0.598	0.521	0.449	0.598	SUBCLONAL	1	FALSE	1	0.463737769179379	2		330	497	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982038	70982038	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	34	683	0	ENST00000276594.2:c.58G>A	p.Glu20Lys	p.E20K	ENST00000276594	NM_024504.3	20	Gag/Aag	2/8	0.463737769179379	1	FACETS	0.386	0.316	0.463	0.386	0.316	0.463	SUBCLONAL	1	FALSE	0	0.463737769179379	1		683	292	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	200	688	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	0.221929772353819	4	FACETS	1	0.99	1	0.714	0.662	0.768	INDETERMINATE	1	FALSE	2	0.463737769179379	4		688	884	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	46	643	0				ENST00000310581	NM_198253.2	-/1132			0.1681940118264	0	FACETS	0.417	0.354	0.486			1	INDETERMINATE	1	FALSE	0	0.463737769179379	0		643	255	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432368	432368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1362895739	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	46	204	0	ENST00000399788.2:c.2155C>T	p.Arg719Cys	p.R719C	ENST00000399788	NM_001042603.1	719	Cgc/Tgc	16/28	0.221929772353819	4	FACETS	1	0.947	1	0.637	0.541	0.74	INDETERMINATE	1	FALSE	2	0.463737769179379	4		204	228	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372783	81372783	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs865828369	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	51	473	0	ENST00000222390.5:c.751C>T	p.Pro251Ser	p.P251S	ENST00000222390	NM_000601.4	251	Ccc/Tcc	7/18	1	2	FACETS	0.421	0.357	0.49	0.421	0.357	0.49	SUBCLONAL	1	FALSE	1	0.463737769179379	2		473	523	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367248	50367248	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	40	601	0	ENST00000331340.3:c.55C>T	p.Pro19Ser	p.P19S	ENST00000331340	NM_006060.4	19	Cct/Tct	3/8	0.227397830198595	1	FACETS	0.179	0.148	0.214	0.179	0.148	0.214	INDETERMINATE	1	FALSE	0	0.463737769179379	1		601	740	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968619	55968619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775179342	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	86	539	0	ENST00000263923.4:c.2044G>A	p.Glu682Lys	p.E682K	ENST00000263923	NM_002253.2	682	Gaa/Aaa	14/30	0.1681940118264	0	FACETS	0.43	0.381	0.481			1	INDETERMINATE	1	FALSE	0	0.463737769179379	0		539	463	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27173277	27173277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1364054872	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	109	617	0	ENST00000380036.4:c.818G>A	p.Gly273Glu	p.G273E	ENST00000380036	NM_000459.3	273	gGa/gAa	6/23	0.143295656787822	0	FACETS	0.431	0.388	0.476			1	INDETERMINATE	1	FALSE	0	0.463737769179379	0		617	585	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965586	93965586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372024057	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	103	479	1	ENST00000369303.4:c.2342G>A	p.Arg781Gln	p.R781Q	ENST00000369303	NM_004440.3	781	cGa/cAa	13/17	0.256907951554173	3	FACETS	0.939	0.842	1	0.469	0.421	0.521	INDETERMINATE	1	FALSE	1	0.463737769179379	3		480	583	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445961	49445961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1449395575	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	241	951	0	ENST00000301067.7:c.1505C>T	p.Pro502Leu	p.P502L	ENST00000301067	NM_003482.3	502	cCt/cTt	10/54	0.463737769179379	4	FACETS	0.873	0.817	0.931	0.873	0.817	0.931	CLONAL	2	FALSE	2	0.463737769179379	4		951	871	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913323	28913323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751180218	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	55	535	0	ENST00000282397.4:c.2470C>T	p.Arg824Trp	p.R824W	ENST00000282397	NM_002019.4	824	Cgg/Tgg	17/30	0.1681940118264	0	FACETS	0.282	0.241	0.326			1	INDETERMINATE	1	FALSE	0	0.463737769179379	0		535	451	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386522	81386522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	76	415	2	ENST00000222390.5:c.465G>A	p.Met155Ile	p.M155I	ENST00000222390	NM_000601.4	155	atG/atA	4/18	1	2	FACETS	0.57	0.5	0.645	0.57	0.5	0.645	SUBCLONAL	1	FALSE	1	0.463737769179379	2		417	575	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396812	139396812	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	96	680	0	ENST00000277541.6:c.5296C>T	p.Gln1766Ter	p.Q1766*	ENST00000277541	NM_017617.3	1766	Cag/Tag	28/34	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	FALSE	1	0.463737769179379	2		680	408	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873285	151873285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	105	525	0	ENST00000262189.6:c.9253C>T	p.Pro3085Ser	p.P3085S	ENST00000262189	NM_170606.2	3085	Cct/Tct	38/59	1	2	FACETS	0.785	0.705	0.869	0.785	0.705	0.869	SUBCLONAL	1	FALSE	1	0.463737769179379	2		525	577	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164071	106164071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	71	360	0	ENST00000380013.4:c.3581C>T	p.Pro1194Leu	p.P1194L	ENST00000380013	NM_001127208.2	1194	cCt/cTt	5/11	1	2	FACETS	0.625	0.547	0.709	0.625	0.547	0.709	SUBCLONAL	1	FALSE	1	0.463737769179379	2		360	490	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981328	68981328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	49	293	0	ENST00000288368.4:c.1400G>A	p.Gly467Glu	p.G467E	ENST00000288368	NM_024870.2	467	gGa/gAa	12/40	0.463737769179379	1	FACETS	0.479	0.407	0.557	0.479	0.407	0.557	SUBCLONAL	1	FALSE	0	0.463737769179379	1		293	339	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167710	185167710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	135	508	0	ENST00000265026.3:c.1033G>A	p.Glu345Lys	p.E345K	ENST00000265026	NM_004721.4	345	Gag/Aag	6/14	1	2	FACETS	0.882	0.804	0.964	0.882	0.804	0.964	CLONAL	1	FALSE	1	0.463737769179379	2		508	660	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638362	117638362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	116	610	0	ENST00000368508.3:c.6079G>A	p.Glu2027Lys	p.E2027K	ENST00000368508	NM_002944.2	2027	Gaa/Aaa	38/43	0.227397830198595	1	FACETS	0.751	0.68	0.825	0.751	0.68	0.825	INDETERMINATE	1	FALSE	0	0.463737769179379	1		610	512	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172349	7172349	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	52	564	0	ENST00000302850.5:c.1220C>T	p.Ser407Phe	p.S407F	ENST00000302850	NM_000208.2	407	tCc/tTc	5/22	0.26500629280197	0	FACETS	0.275	0.234	0.32			1	INDETERMINATE	1	FALSE	0	0.463737769179379	0		564	437	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436095	116436095	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765332671	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	158	579	0	ENST00000397752.3:c.4090C>T	p.Pro1364Ser	p.P1364S	ENST00000397752	NM_000245.2	1364	Ccg/Tcg	21/21	0.326367691873746	4	FACETS	1	0.986	1	0.678	0.622	0.735	CLONAL	1	FALSE	2	0.463737769179379	4		579	736	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28586440	28586440	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1205769705	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	127	546	0	ENST00000253063.3:c.82C>T	p.Pro28Ser	p.P28S	ENST00000253063	NM_031459.4	28	Ccc/Tcc	1/10	0.412779697647484	4	FACETS	1	0.982	1			1	CLONAL	1	FALSE	NA	0.463737769179379	4		546	593	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111541	8111541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	40	573	0	ENST00000346208.3:c.1027C>T	p.Leu343Phe	p.L343F	ENST00000346208		343	Ctc/Ttc	5/6	0.239139332725532	0	FACETS	0.228	0.19	0.271			1	INDETERMINATE	1	FALSE	0	0.463737769179379	0		573	405	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347622	118347622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	135	551	0	ENST00000534358.1:c.3259C>T	p.Pro1087Ser	p.P1087S	ENST00000534358	NM_005933.3	1087	Cct/Tct	4/36	0.221929772353819	4	FACETS	1	0.967	1	0.566	0.515	0.62	INDETERMINATE	1	FALSE	2	0.463737769179379	4		551	753	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390449	118390449	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	163	682	0	ENST00000534358.1:c.11263G>A	p.Glu3755Lys	p.E3755K	ENST00000534358	NM_005933.3	3755	Gag/Aag	32/36	0.221929772353819	4	FACETS	1	0.988	1	0.711	0.654	0.77	INDETERMINATE	1	FALSE	2	0.463737769179379	4		682	724	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	465635	465635	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	126	420	0	ENST00000399788.2:c.741G>C	p.Lys247Asn	p.K247N	ENST00000399788	NM_001042603.1	247	aaG/aaC	6/28	0.221929772353819	4	FACETS	1	0.969	1	0.58	0.526	0.637	INDETERMINATE	1	FALSE	2	0.463737769179379	4		420	686	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435037	18435037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	44	475	0	ENST00000266497.5:c.22G>A	p.Asp8Asn	p.D8N	ENST00000266497		8	Gat/Aat	1/31	0.313443315498665	0	FACETS	0.217	0.181	0.255			1	SUBCLONAL	1	FALSE	0	0.463737769179379	0		475	470	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435389	18435389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764761797	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	54	567	0	ENST00000266497.5:c.374C>T	p.Ser125Phe	p.S125F	ENST00000266497		125	tCc/tTc	1/31	0.313443315498665	0	FACETS	0.242	0.206	0.28			1	SUBCLONAL	1	FALSE	0	0.463737769179379	0		567	517	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944998	31944998	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748979871	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	137	862	0	ENST00000340398.3:c.103G>A	p.Gly35Arg	p.G35R	ENST00000340398	NM_001013699.2	35	Ggg/Agg	1/1	1	2	FACETS	0.659	0.599	0.722	0.659	0.599	0.722	SUBCLONAL	1	FALSE	1	0.463737769179379	2		862	897	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215739	133215739	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1193250579	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	72	607	0	ENST00000320574.5:c.5524C>T	p.His1842Tyr	p.H1842Y	ENST00000320574	NM_006231.2	1842	Cac/Tac	40/49	1	2	FACETS	0.754	0.661	0.852	0.754	0.661	0.852	SUBCLONAL	1	FALSE	1	0.463737769179379	2		607	412	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913504	32913504	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	124	480	0	ENST00000380152.3:c.5012T>A	p.Phe1671Tyr	p.F1671Y	ENST00000380152		1671	tTt/tAt	11/27	0.160480917360517	4	FACETS	1	0.972	1	0.591	0.536	0.649	INDETERMINATE	1	FALSE	2	0.463737769179379	4		480	662	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50774242	50774242	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200518441	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	150	510	0	ENST00000307179.4:c.1783G>A	p.Gly595Arg	p.G595R	ENST00000307179		595	Ggg/Agg	11/20	0.221929772353819	4	FACETS	1	0.983	1	0.649	0.594	0.706	INDETERMINATE	1	FALSE	2	0.463737769179379	4		510	730	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647697	3647697	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	105	580	0	ENST00000294008.3:c.1367-1G>A		p.X456_splice	ENST00000294008	NM_032444.2	456			1	2	FACETS	0.906	0.815	1	0.906	0.815	1	CLONAL	1	FALSE	1	0.463737769179379	2		580	500	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984842	9984842	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	53	527	0	ENST00000330684.3:c.1122+1G>A		p.X374_splice	ENST00000330684	NM_001134407.1	374			1	2	FACETS	0.556	0.475	0.644	0.556	0.475	0.644	SUBCLONAL	1	FALSE	1	0.463737769179379	2		527	411	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89871795	89871795	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	109	471	0	ENST00000389301.3:c.602C>T	p.Pro201Leu	p.P201L	ENST00000389301	NM_000135.2	201	cCc/cTc	7/43	0.289271656409071	2	FACETS	1	0.953	1	0.545	0.493	0.6	CLONAL	1	FALSE	0	0.463737769179379	2		471	431	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541468	29541468	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1131691131	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	42	75	0	ENST00000356175.3:c.1393-1G>A		p.X465_splice	ENST00000356175	NM_000267.3	465			0.412779697647484	4	FACETS	0.89	0.757	1			1	CLONAL	2	FALSE	NA	0.463737769179379	4		75	149	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546068	29546068	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	188	583	0	ENST00000356175.3:c.1574del	p.Leu525Ter	p.L525*	ENST00000356175	NM_000267.3	525	Tta/ta	14/57	0.412779697647484	4	FACETS	1	0.987	1			1	CLONAL	1	FALSE	NA	0.463737769179379	4		583	891	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690618	33690618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	110	718	0	ENST00000308377.4:c.209C>T	p.Pro70Leu	p.P70L	ENST00000308377	NM_152270.3	70	cCc/cTc	2/5	0.328369545263203	3	FACETS	0.724	0.65	0.802	0.362	0.325	0.401	SUBCLONAL	1	FALSE	1	0.463737769179379	3		718	807	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78854279	78854279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756025816	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	217	573	0	ENST00000306801.3:c.1574C>T	p.Pro525Leu	p.P525L	ENST00000306801	NM_020761.2	525	cCc/cTc	14/34	0.328369545263203	3	FACETS	0.928	0.869	0.989	0.928	0.869	0.989	CLONAL	2	FALSE	1	0.463737769179379	3		573	621	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61306990	61306990	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746310287	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	41	446	0	ENST00000341074.5:c.490C>T	p.Pro164Ser	p.P164S	ENST00000341074	NM_002974.2	164	Cct/Tct	6/8	0.143295656787822	0	FACETS	0.291	0.243	0.344			1	INDETERMINATE	1	FALSE	0	0.463737769179379	0		446	326	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223320	2223320	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1174739572	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	140	750	0	ENST00000398665.3:c.3431C>T	p.Ser1144Leu	p.S1144L	ENST00000398665	NM_032482.2	1144	tCg/tTg	25/28	0.256907951554173	3	FACETS	1	0.979	1	0.611	0.558	0.666	INDETERMINATE	1	FALSE	1	0.463737769179379	3		750	609	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270077	198270077	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	106	447	0	ENST00000335508.6:c.1359G>A	p.Met453Ile	p.M453I	ENST00000335508	NM_012433.2	453	atG/atA	10/25	0.256907951554173	3	FACETS	0.79	0.708	0.876	0.395	0.354	0.438	INDETERMINATE	1	FALSE	1	0.463737769179379	3		447	713	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587181	212587181	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	79	620	0	ENST00000342788.4:c.820C>T	p.Gln274Ter	p.Q274*	ENST00000342788	NM_005235.2	274	Caa/Taa	7/28	0.143295656787822	0	FACETS	0.29	0.255	0.328			1	INDETERMINATE	1	FALSE	0	0.463737769179379	0		620	629	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561492	9561492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	50	699	0	ENST00000353224.5:c.290C>T	p.Ser97Phe	p.S97F	ENST00000353224	NM_177990.2	97	tCc/tTc	4/10	0.197570233499071	0	FACETS	0.224	0.19	0.262			1	INDETERMINATE	1	FALSE	0	0.463737769179379	0		699	516	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175861	24175862	+	stop_gained	Nonsense_Mutation	DNP	GA	GA	AT	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	81	643	0	ENST00000263121.7:c.1089_1090delinsAT	p.Lys364Ter	p.K364*	ENST00000263121	NM_003073.3	363	aaGAag/aaATag	8/9	0.17429419793938	3	FACETS	0.818	0.722	0.92	0.273	0.24	0.307	INDETERMINATE	1	FALSE	0	0.463737769179379	3		643	526	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713669	30713669	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	84	800	0	ENST00000295754.5:c.994A>G	p.Asn332Asp	p.N332D	ENST00000295754	NM_003242.5	332	Aac/Gac	4/7	1	2	FACETS	0.539	0.476	0.607	0.539	0.476	0.607	SUBCLONAL	1	FALSE	1	0.463737769179379	2		800	672	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63985171	63985171	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	106	527	0	ENST00000398590.3:c.2774A>T	p.Asn925Ile	p.N925I	ENST00000398590	NM_001177387.1	925	aAt/aTt	14/14	1	2	FACETS	0.751	0.674	0.831	0.751	0.674	0.831	SUBCLONAL	1	FALSE	1	0.463737769179379	2		527	609	SUCCESS
ALB	213	MSKCC	GRCh37	4	74270862	74270862	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374543070	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	63	347	0	ENST00000295897.4:c.109G>A	p.Asp37Asn	p.D37N	ENST00000295897	NM_000477.5	37	Gat/Aat	2/15	0.1681940118264	0	FACETS	0.375	0.325	0.428			1	INDETERMINATE	1	FALSE	0	0.463737769179379	0		347	389	SUCCESS
APC	324	MSKCC	GRCh37	5	112177874	112177874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1165586440	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	51	476	1	ENST00000257430.4:c.6583T>C	p.Tyr2195His	p.Y2195H	ENST00000257430	NM_000038.5	2195	Tat/Cat	16/16	1	2	FACETS	0.606	0.517	0.703	0.606	0.517	0.703	SUBCLONAL	1	FALSE	1	0.463737769179379	2		477	363	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433969	149433969	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs866905513	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	106	587	0	ENST00000286301.3:c.2679G>A	p.Trp893Ter	p.W893*	ENST00000286301	NM_005211.3	893	tgG/tgA	21/22	1	2	FACETS	0.907	0.817	1	0.907	0.817	1	CLONAL	1	FALSE	1	0.463737769179379	2		587	504	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456956	149456956	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	95	692	0	ENST00000286301.3:c.772C>T	p.Gln258Ter	p.Q258*	ENST00000286301	NM_005211.3	258	Caa/Taa	6/22	1	2	FACETS	0.815	0.728	0.906	0.815	0.728	0.906	CLONAL	1	FALSE	1	0.463737769179379	2		692	503	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166279	32166279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	202	697	0	ENST00000375023.3:c.4675G>A	p.Gly1559Arg	p.G1559R	ENST00000375023	NM_004557.3	1559	Ggg/Agg	26/30	0.369339995656419	4	FACETS	0.822	0.764	0.882	0.822	0.764	0.882	CLONAL	2	FALSE	2	0.463737769179379	4		697	776	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198287	138198287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	131	470	0	ENST00000237289.4:c.880C>T	p.Pro294Ser	p.P294S	ENST00000237289	NM_001270507.1	294	Cct/Tct	6/9	0.328369545263203	3	FACETS	1	0.977	1	0.607	0.553	0.664	CLONAL	1	FALSE	1	0.463737769179379	3		470	573	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372728	81372728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	70	501	0	ENST00000222390.5:c.806C>T	p.Pro269Leu	p.P269L	ENST00000222390	NM_000601.4	269	cCa/cTa	7/18	1	2	FACETS	0.536	0.468	0.61	0.536	0.468	0.61	SUBCLONAL	1	FALSE	1	0.463737769179379	2		501	563	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958424	90958424	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	86	303	0	ENST00000265433.3:c.2014C>T	p.Pro672Ser	p.P672S	ENST00000265433	NM_002485.4	672	Cca/Tca	13/16	1	2	FACETS	0.923	0.821	1	0.923	0.821	1	CLONAL	1	FALSE	1	0.463737769179379	2		303	402	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331666	8331666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	60	570	0	ENST00000356435.5:c.5450G>A	p.Gly1817Glu	p.G1817E	ENST00000356435		1817	gGa/gAa	33/35	0.143295656787822	0	FACETS	0.286	0.246	0.328			1	INDETERMINATE	1	FALSE	0	0.463737769179379	0		570	486	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521516	8521516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748982864	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	69	541	0	ENST00000356435.5:c.722C>T	p.Pro241Leu	p.P241L	ENST00000356435		241	cCa/cTa	9/35	0.143295656787822	0	FACETS	0.34	0.297	0.387			1	INDETERMINATE	1	FALSE	0	0.463737769179379	0		541	469	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239096	98239096	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	94	558	0	ENST00000331920.6:c.1547T>A	p.Phe516Tyr	p.F516Y	ENST00000331920	NM_000264.3	516	tTt/tAt	11/24	0.143295656787822	0	FACETS	0.449	0.401	0.5			1	INDETERMINATE	1	FALSE	0	0.463737769179379	0		558	484	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391502	139391502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	99	910	0	ENST00000277541.6:c.6689C>T	p.Pro2230Leu	p.P2230L	ENST00000277541	NM_017617.3	2230	cCc/cTc	34/34	1	2	FACETS	0.844	0.756	0.936	0.844	0.756	0.936	CLONAL	1	FALSE	1	0.463737769179379	2		910	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0061302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	20	722	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.709218440588457	1	FACETS	0.109	0.083	0.14	0.109	0.083	0.14	SUBCLONAL	1	TRUE	0	0.746478143124073	1		724	307	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383225	4383225	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	90	516	0	ENST00000261254.3:c.19G>C	p.Glu7Gln	p.E7Q	ENST00000261254	NM_001759.3	7	Gag/Cag	1/5	0.287709800756985	2	FACETS	0.877	0.789	0.968	0.438	0.394	0.484	INDETERMINATE	1	TRUE	0	0.746478143124073	2		516	275	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014344	70014344	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	25	453	0	ENST00000394351.3:c.1205A>T	p.Lys402Ile	p.K402I	ENST00000394351	NM_000248.3	402	aAa/aTa	9/9	0.677221920965895	1	FACETS	0.143	0.113	0.178	0.143	0.113	0.178	SUBCLONAL	1	TRUE	0	0.746478143124073	1		453	293	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248998	55248999	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCAGCG	rs727504263	NA	P-0061304-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	1010	557	0	ENST00000275493.2:c.2300_2308dup	p.Ala767_Val769dup	p.A767_V769dup	ENST00000275493	NM_005228.3	767	atg/aTGGCCAGCGtg	20/28	0.420963866189527	10	FACETS	1	0.991	1	0.779	0.758	0.8	CLONAL	6	TRUE	2	0.420963866189527	10		557	2066	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793881	NA	P-0061304-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	180	577	0	ENST00000269305.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGg/gAg	8/11	0.420963866189527	1	FACETS	0.996	0.922	1	0.996	0.922	1	CLONAL	1	TRUE	0	0.420963866189527	1		577	678	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165698	118165698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1432369724	NA	P-0061330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	193	611	0	ENST00000369448.3:c.208C>T	p.Arg70Trp	p.R70W	ENST00000369448	NM_017709.3	70	Cgg/Tgg	2/2	0.134530978276792	4	FACETS	1	0.943	1	1	0.943	1	INDETERMINATE	2	TRUE	2	0.225899833099766	4		611	1024	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7590694	7590694	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0061330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	200	459	0	ENST00000269305.4:c.-29+1G>A		p.X10_splice	ENST00000269305	NM_001126112.2	10			0.225899833099766	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.225899833099766	2		459	748	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267651	198267853	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTAGAAATTAAATGTAAATACCTTTGCCAAATTAGAAATGATCTCTCGGCCTTCCACTCTAGCATAGTAATCTTCATCAATCAATAGCGGTTCAATGACCACGAGGATCTGAAAAAGAGAAAAGAGAAGAAGCTACACTTTCACATCAATTACTGATGAAATGCTCATGTACAGAATTAAACATACATAAGAAATTTAGAAT	TCTAGAAATTAAATGTAAATACCTTTGCCAAATTAGAAATGATCTCTCGGCCTTCCACTCTAGCATAGTAATCTTCATCAATCAATAGCGGTTCAATGACCACGAGGATCTGAAAAAGAGAAAAGAGAAGAAGCTACACTTTCACATCAATTACTGATGAAATGCTCATGTACAGAATTAAACATACATAAGAAATTTAGAAT	-	novel	NA	P-0061330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	54	376	0	ENST00000335508.6:c.1720-94_1806+22del		p.X574_splice	ENST00000335508	NM_012433.2	574		13/25	0.192421812769655	4	FACETS	0.92	0.785	1	0.46	0.392	0.534	CLONAL	1	TRUE	2	0.225899833099766	4		376	637	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869601	117869601	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061330-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	191	399	0	ENST00000297338.2:c.593G>T	p.Ser198Ile	p.S198I	ENST00000297338	NM_006265.2	198	aGc/aTc	6/14	0.225899833099766	7	FACETS	0.906	0.837	0.977	0.679	0.628	0.733	CLONAL	3	TRUE	3	0.225899833099766	7		399	974	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0061336-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	510	668	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	NA	2	FACETS	1	0.968	1			1	INDETERMINATE	2	TRUE	NA	0.568515042189718	2		668	894	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634309	23634309	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061336-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	168	245	0	ENST00000261584.4:c.2977A>T	p.Thr993Ser	p.T993S	ENST00000261584	NM_024675.3	993	Acg/Tcg	9/13	1	2	FACETS	0.905	0.835	0.978	0.905	0.835	0.978	CLONAL	1	TRUE	1	0.568515042189718	2		245	653	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56866241	56866241	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061336-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	164	270	0	ENST00000308159.5:c.1286G>C	p.Ser429Thr	p.S429T	ENST00000308159	NM_014669.4	429	aGc/aCc	12/22	0.563750594090678	1	FACETS	0.857	0.793	0.922	0.857	0.793	0.922	CLONAL	1	TRUE	0	0.568515042189718	1		270	482	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321792	62321792	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0061336-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	143	243	0	ENST00000360203.5:c.2411C>G	p.Ser804Ter	p.S804*	ENST00000360203	NM_001283009.1	804	tCa/tGa	26/35	0.513924711862419	3	FACETS	1	0.972	1	0.38	0.348	0.413	CLONAL	1	TRUE	0	0.568515042189718	3		243	567	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945445	151945445	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061336-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	54	250	0	ENST00000262189.6:c.2074G>C	p.Val692Leu	p.V692L	ENST00000262189	NM_170606.2	692	Gtc/Ctc	14/59	0.568515042189718	3	FACETS	0.335	0.285	0.39	0.168	0.142	0.195	SUBCLONAL	1	TRUE	1	0.568515042189718	3		250	728	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0061387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	528	549	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.35022125936939	3	FACETS	1	0.988	1	0.715	0.686	0.744	CLONAL	2	TRUE	0	0.469124370321918	3		552	1296	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0061387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	130	245	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.448289239502583	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	3	TRUE	0	0.469124370321918	3		245	218	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440757	56440757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774211426	NA	P-0061387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	516	570	1	ENST00000407977.2:c.461C>T	p.Pro154Leu	p.P154L	ENST00000407977		154	cCg/cTg	5/10	0.35022125936939	3	FACETS	1	0.994	1	0.779	0.749	0.81	CLONAL	2	TRUE	0	0.469124370321918	3		571	1162	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974695	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	186	556	0	ENST00000304494.5:c.132C>A	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	taC/taA	1/3	0.458733820844482	1	FACETS	0.774	0.716	0.834	0.774	0.716	0.834	SUBCLONAL	1	TRUE	0	0.469124370321918	1		556	784	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916913	178916924	+	inframe_deletion	In_Frame_Del	DEL	AGTAATTGAACC	AGTAATTGAACC	-	novel	NA	P-0061387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	17	176	0	ENST00000263967.3:c.304_315del	p.Ile102_Val105del	p.I102_V105del	ENST00000263967	NM_006218.2	100	aaAGTAATTGAACCa/aaa	2/21	0.393409455335786	3	FACETS	0.785	0.593	1	0.392	0.296	0.504	CLONAL	1	TRUE	1	0.469124370321918	3		176	114	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424494	49424494	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	167	485	0	ENST00000301067.7:c.13729G>A	p.Ala4577Thr	p.A4577T	ENST00000301067	NM_003482.3	4577	Gcc/Acc	41/54	0.448289239502583	3	FACETS	0.791	0.726	0.86	0.264	0.242	0.287	SUBCLONAL	1	TRUE	0	0.469124370321918	3		485	1111	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967252	25967252	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	137	506	2	ENST00000435504.4:c.1954A>G	p.Thr652Ala	p.T652A	ENST00000435504		652	Aca/Gca	13/13	1	2	FACETS	0.638	0.58	0.7	0.638	0.58	0.7	SUBCLONAL	1	TRUE	1	0.469124370321918	2		508	915	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	77	126	0				ENST00000310581	NM_198253.2	-/1132			0.339269314797596	2	FACETS	1	0.909	1			1	CLONAL	1	TRUE	NA	0.34	2		126	437	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631839	90631839	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519906	NA	P-0061403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	126	914	2	ENST00000330062.3:c.514A>G	p.Arg172Gly	p.R172G	ENST00000330062	NM_002168.2	172	Agg/Ggg	4/11	1	2	FACETS	0.942	0.853	1	0.942	0.853	1	CLONAL	1	TRUE	1	0.34	2		916	787	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495297	212495297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	91	613	0	ENST00000342788.4:c.1969G>A	p.Val657Ile	p.V657I	ENST00000342788	NM_005235.2	657	Gta/Ata	17/28	1	2	FACETS	0.997	0.888	1	0.997	0.888	1	CLONAL	1	TRUE	1	0.34	2		613	537	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555180	226555180	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0061403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	63	587	0	ENST00000366794.5:c.2406+1G>A		p.X802_splice	ENST00000366794	NM_001618.3	802			1	2	FACETS	0.809	0.702	0.925	0.809	0.702	0.925	CLONAL	1	TRUE	1	0.34	2		587	458	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003529	57003529	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	C	C	T	rs200854787	NA	P-0061403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	137	815	0	ENST00000257254.3:c.950G>A	p.Arg317His	p.R317H	ENST00000257254		317	cGc/cAc	1/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.34	2		815	691	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190708717	190708717	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	93	496	0	ENST00000441310.2:c.610T>A	p.Ser204Thr	p.S204T	ENST00000441310	NM_000534.4	204	Tca/Aca	6/13	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.34	2		496	467	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	222	126	0				ENST00000310581	NM_198253.2	-/1132			0.319911290653981	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.319911290653981	3		126	765	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0061405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	177	393	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.319911290653981	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.319911290653981	1		393	644	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338683	70338683	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	124	162	0	ENST00000374080.3:c.79C>G	p.Gln27Glu	p.Q27E	ENST00000374080		27	Cag/Gag	1/45	1	1	FACETS	0.885	0.809	0.962	1	0.989	1	CLONAL	2	TRUE	0	0.319911290653981	1		162	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577077	7577077	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs748891343	NA	P-0061405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	174	391	0	ENST00000269305.4:c.861G>C	p.Glu287Asp	p.E287D	ENST00000269305	NM_001126112.2	287	gaG/gaC	8/11	0.319911290653981	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.319911290653981	1		391	651	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831324	72831324	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs139598608	NA	P-0061405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	74	437	0	ENST00000268489.5:c.5257C>G	p.Gln1753Glu	p.Q1753E	ENST00000268489	NM_006885.3	1753	Caa/Gaa	9/10	1	2	FACETS	0.669	0.585	0.759	0.669	0.585	0.759	SUBCLONAL	1	TRUE	1	0.319911290653981	2		437	692	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870778	12870778	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0061405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	62	406	0	ENST00000228872.4:c.5C>G	p.Ser2Ter	p.S2*	ENST00000228872	NM_004064.3	2	tCa/tGa	1/3	1	2	FACETS	0.535	0.462	0.616	0.535	0.462	0.616	SUBCLONAL	1	TRUE	1	0.319911290653981	2		406	724	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268503	46268503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777114269	NA	P-0061405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	52	362	0	ENST00000371998.3:c.2890C>T	p.Arg964Trp	p.R964W	ENST00000371998		964	Cgg/Tgg	15/23	0.12153354135835	0	FACETS	0.441	0.376	0.513			1	INDETERMINATE	1	TRUE	0	0.319911290653981	0		362	501	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831455	89831455	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	79	339	0	ENST00000389301.3:c.2621G>C	p.Arg874Thr	p.R874T	ENST00000389301	NM_000135.2	874	aGa/aCa	28/43	1	2	FACETS	0.918	0.809	1	0.918	0.809	1	CLONAL	1	TRUE	1	0.319911290653981	2		339	538	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509460	46509460	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	99	306	0	ENST00000262741.5:c.1271C>G	p.Ser424Cys	p.S424C	ENST00000262741	NM_003629.3	424	tCt/tGt	10/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.319911290653981	2		306	523	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462900	120462900	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	52	380	1	ENST00000256646.2:c.5431C>G	p.Gln1811Glu	p.Q1811E	ENST00000256646	NM_024408.3	1811	Cag/Gag	30/34	1	2	FACETS	0.51	0.433	0.594	0.51	0.433	0.594	SUBCLONAL	1	TRUE	1	0.319911290653981	2		381	638	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033902	49033902	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	58	266	0	ENST00000267163.4:c.2039del	p.Ile680ThrfsTer16	p.I680Tfs*16	ENST00000267163	NM_000321.2	680	aTc/ac	20/27	0.319911290653981	1	FACETS	0.973	0.842	1	0.973	0.842	1	CLONAL	1	TRUE	0	0.319911290653981	1		266	313	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964971	15964971	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	94	385	0	ENST00000268712.3:c.5625G>C	p.Lys1875Asn	p.K1875N	ENST00000268712	NM_006311.3	1875	aaG/aaC	37/46	0.319911290653981	3	FACETS	1	0.977	1	0.683	0.61	0.76	CLONAL	1	TRUE	1	0.319911290653981	3		385	499	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873579	37873579	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	157	434	0	ENST00000269571.5:c.1744G>C	p.Asp582His	p.D582H	ENST00000269571		582	Gac/Cac	15/27	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.319911290653981	2		434	717	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215951	41215951	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	13	177	0	ENST00000357654.3:c.5092G>T	p.Glu1698Ter	p.E1698*	ENST00000357654	NM_007294.3	1698	Gaa/Taa	17/23	1	2	FACETS	0.447	0.319	0.601	0.447	0.319	0.601	SUBCLONAL	1	TRUE	1	0.319911290653981	2		177	182	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78704504	78704504	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	53	326	0	ENST00000306801.3:c.652G>C	p.Glu218Gln	p.E218Q	ENST00000306801	NM_020761.2	218	Gag/Cag	5/34	0.225614295485692	3	FACETS	0.553	0.471	0.644	0.184	0.157	0.215	SUBCLONAL	1	TRUE	0	0.319911290653981	3		326	695	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602662	10602662	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	190	459	0	ENST00000171111.5:c.916G>A	p.Glu306Lys	p.E306K	ENST00000171111	NM_203500.1	306	Gag/Aag	3/6	0.156438346943101	3	FACETS	1	0.989	1	0.706	0.652	0.761	INDETERMINATE	1	TRUE	1	0.319911290653981	3		459	976	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467908	66467908	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	30	238	0	ENST00000273854.3:c.361G>A	p.Glu121Lys	p.E121K	ENST00000273854	NM_004439.5	121	Gaa/Aaa	3/18	1	2	FACETS	0.747	0.605	0.907	0.747	0.605	0.907	CLONAL	1	TRUE	1	0.319911290653981	2		238	251	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519235	187519235	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	66	249	0	ENST00000441802.2:c.12148G>A	p.Glu4050Lys	p.E4050K	ENST00000441802	NM_005245.3	4050	Gag/Aag	23/27	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.319911290653981	2		249	377	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969111	93969111	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	52	262	0	ENST00000369303.4:c.1885G>C	p.Asp629His	p.D629H	ENST00000369303	NM_004440.3	629	Gat/Cat	10/17	0.319911290653981	1	FACETS	0.962	0.825	1	0.962	0.825	1	CLONAL	1	TRUE	0	0.319911290653981	1		262	284	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214352	55214352	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	119	399	0	ENST00000275493.2:c.478G>A	p.Glu160Lys	p.E160K	ENST00000275493	NM_005228.3	160	Gag/Aag	4/28	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.319911290653981	2		399	708	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	80	126	0				ENST00000310581	NM_198253.2	-/1132			0.300692344870791	4	FACETS	0.866	0.775	0.96	1	0.973	1	CLONAL	3	TRUE	2	0.361318094233388	4		126	232	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0061406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	64	372	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.361318094233388	3	FACETS	0.807	0.707	0.914	0.807	0.707	0.914	CLONAL	2	TRUE	1	0.361318094233388	3		372	259	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7978952	7978952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139689690	NA	P-0061406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	39	397	0	ENST00000319144.4:c.1615G>A	p.Glu539Lys	p.E539K	ENST00000319144	NM_001139.2	539	Gaa/Aaa	12/15	0.361318094233388	3	FACETS	0.977	0.814	1	0.488	0.407	0.578	CLONAL	1	TRUE	1	0.361318094233388	3		397	261	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230459181	230459181	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138064546	NA	P-0061406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	226	378	0	ENST00000391860.1:c.1220C>T	p.Pro407Leu	p.P407L	ENST00000391860	NM_001258311.1	407	cCg/cTg	7/7	0.361318094233388	7	FACETS	0.925	0.875	0.975	1	0.984	1	CLONAL	6	TRUE	2	0.361318094233388	7		378	429	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106057	27106057	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	117	503	0	ENST00000324856.7:c.5670del	p.Thr1891GlnfsTer32	p.T1891Qfs*32	ENST00000324856	NM_006015.4	1890	Ggg/gg	20/20	0.361318094233388	2	FACETS	0.853	0.785	0.922	1	0.983	1	CLONAL	3	TRUE	0	0.361318094233388	2		503	253	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29444432	29444432	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	109	412	0	ENST00000544604.2:c.968G>T	p.Trp323Leu	p.W323L	ENST00000544604	NM_001206998.1	323	tGg/tTg	7/9	0.300692344870791	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.361318094233388	4		412	356	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0061407-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	54	458	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.459152523895409	2		458	226	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0061407-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	91	430	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.459152523895409	2		430	343	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964965	55964965	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061407-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	29	186	0	ENST00000263923.4:c.2272C>T	p.Gln758Ter	p.Q758*	ENST00000263923	NM_002253.2	758	Cag/Tag	16/30	0.236549446821789	1	FACETS	0.667	0.542	0.804	0.667	0.542	0.804	INDETERMINATE	1	TRUE	0	0.459152523895409	1		186	146	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579896	7579896	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0061407-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	108	450	0	ENST00000269305.4:c.17C>G	p.Ser6Ter	p.S6*	ENST00000269305	NM_001126112.2	6	tCa/tGa	2/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.459152523895409	2		450	334	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842707	68842707	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0061408-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	101	325	0	ENST00000261769.5:c.643A>T	p.Lys215Ter	p.K215*	ENST00000261769	NM_004360.3	215	Aag/Tag	5/16	0.27020201966796	2	FACETS	0.993	0.898	1	0.993	0.898	1	CLONAL	2	TRUE	0	0.326161937498397	2		325	312	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1936892	1936892	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061408-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	57	276	0	ENST00000382891.5:c.1577G>C	p.Arg526Thr	p.R526T	ENST00000382891	NM_133335.3	526	aGa/aCa	7/22	0.288497699113639	3	FACETS	1	0.959	1	0.658	0.568	0.754	CLONAL	1	TRUE	1	0.326161937498397	3		276	309	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599320	55599320	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913506	NA	P-0061419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	77	362	0	ENST00000288135.5:c.2446G>C	p.Asp816His	p.D816H	ENST00000288135	NM_000222.2	816	Gac/Cac	17/21	0.389430520498757	1	FACETS	0.813	0.727	0.903	0.813	0.727	0.903	CLONAL	1	TRUE	0	0.605580123263509	1		362	218	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398222	25398222	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061419-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	58	266	0	ENST00000311936.3:c.97G>C	p.Asp33His	p.D33H	ENST00000311936	NM_004985.3	33	Gat/Cat	2/5	0.605580123263509	3	FACETS	0.719	0.621	0.825	0.36	0.31	0.413	SUBCLONAL	1	TRUE	1	0.605580123263509	3		266	347	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992805	72992805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	124	540	0	ENST00000268489.5:c.1240C>T	p.Pro414Ser	p.P414S	ENST00000268489	NM_006885.3	414	Ccc/Tcc	2/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.603108799470667	2		540	340	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618661	37618665	+	frameshift_variant	Frame_Shift_Del	DEL	CACCA	CACCA	-	novel	NA	P-0061420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	179	689	0	ENST00000447079.4:c.338_342del	p.His113ProfsTer12	p.H113Pfs*12	ENST00000447079	NM_015083.1	113	CACCAc/c	1/14	0.231858102148963	4	FACETS	1	0.985	1			1	INDETERMINATE	1	FALSE	NA	0.603108799470667	4		689	755	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657643	37657643	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	131	429	0	ENST00000447079.4:c.2561del	p.Asn854IlefsTer14	p.N854Ifs*14	ENST00000447079	NM_015083.1	854	Aat/at	6/14	0.231858102148963	4	FACETS	0.857	0.793	0.92			1	INDETERMINATE	3	FALSE	NA	0.603108799470667	4		429	271	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37637626	37637626	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0061420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	115	544	0	ENST00000249071.6:c.107+1G>A		p.X36_splice	ENST00000249071	NM_002872.4	36			1	2	FACETS	0.915	0.83	1	0.915	0.83	1	CLONAL	1	FALSE	1	0.603108799470667	2		544	417	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933777	49933777	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	169	618	0	ENST00000296474.3:c.2500C>A	p.Pro834Thr	p.P834T	ENST00000296474	NM_002447.2	834	Ccc/Acc	10/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.603108799470667	2		618	473	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608579	189608579	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1340744193	NA	P-0061420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	117	395	0	ENST00000264731.3:c.1654T>C	p.Phe552Leu	p.F552L	ENST00000264731	NM_003722.4	552	Ttc/Ctc	13/14	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	FALSE	NA	0.603108799470667	2		395	272	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564484	55564484	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	116	408	0	ENST00000288135.5:c.372G>T	p.Leu124Phe	p.L124F	ENST00000288135	NM_000222.2	124	ttG/ttT	3/21	0.267297223707694	0	FACETS	0.581	0.533	0.629			1	INDETERMINATE	1	FALSE	0	0.603108799470667	0		408	263	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680297	30680297	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	119	514	0	ENST00000376406.3:c.1422C>A	p.His474Gln	p.H474Q	ENST00000376406	NM_014641.2	474	caC/caA	5/15	0.136713963622584	3	FACETS	0.753	0.688	0.82	0.502	0.458	0.547	INDETERMINATE	2	FALSE	0	0.603108799470667	3		514	341	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061235	38061242	+	frameshift_variant	Frame_Shift_Del	DEL	TGCCGGAG	TGCCGGAG	C	novel	NA	P-0061420-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	124	634	0	ENST00000250448.2:c.747_754delinsG	p.Asp249GlufsTer70	p.D249Efs*70	ENST00000250448	NM_004496.3	249	gaCTCCGGCAac/gaGac	2/2	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.603108799470667	2		634	367	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	246	458	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.951	1	1	0.996	1	CLONAL	5	TRUE	1	0.163354168551106	2		458	596	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	51	807	0	ENST00000267101.3:c.310G>C	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ctg	3/28	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.163354168551106	2		807	582	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	245	435	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.979	1	1	0.996	1	CLONAL	5	TRUE	1	0.163354168551106	2		435	556	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652129	36652129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34916193	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	293	540	0	ENST00000244741.5:c.251G>A	p.Arg84Gln	p.R84Q	ENST00000244741	NM_000389.4	84	cGa/cAa	2/3	1	2	FACETS	0.94	0.889	0.992	1	0.997	1	CLONAL	5	TRUE	1	0.163354168551106	2		540	763	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164851	36164852	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	714	631	0	ENST00000300305.3:c.1023dup	p.Ile342HisfsTer258	p.I342Hfs*258	ENST00000300305		341	-/C	8/8	0.163354168551106	2	FACETS	1	0.993	1			1	CLONAL	9	TRUE	0	0.163354168551106	2		631	938	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68301849	68301849	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	189	363	0	ENST00000487270.1:c.251C>A	p.Ser84Tyr	p.S84Y	ENST00000487270	NM_133509.3	84	tCt/tAt	4/11	1	2	FACETS	1	0.971	1	1	0.995	1	CLONAL	4	TRUE	1	0.163354168551106	2		363	536	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712823	43712823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28903077	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	294	523	0	ENST00000382044.4:c.4361G>A	p.Arg1454Gln	p.R1454Q	ENST00000382044	NM_001141980.1	1454	cGa/cAa	21/28	1	2	FACETS	1	0.974	1	1	0.997	1	CLONAL	5	TRUE	1	0.163354168551106	2		523	690	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652021	36652021	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs12721594	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	323	581	0	ENST00000244741.5:c.143G>A	p.Arg48Gln	p.R48Q	ENST00000244741	NM_000389.4	48	cGa/cAa	2/3	1	2	FACETS	0.924	0.876	0.973	1	0.997	1	CLONAL	5	TRUE	1	0.163354168551106	2		581	856	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501249	140501249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	210	309	0	ENST00000288602.6:c.823G>A	p.Glu275Lys	p.E275K	ENST00000288602	NM_004333.4	275	Gaa/Aaa	6/18	0.163354168551106	0	FACETS	0.881	0.835	0.926			1	CLONAL	7	TRUE	0	0.163354168551106	0		309	349	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245389	153245389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	198	324	0	ENST00000281708.4:c.1802C>T	p.Ser601Phe	p.S601F	ENST00000281708	NM_033632.3	601	tCt/tTt	11/12	1	2	FACETS	0.903	0.843	0.964	1	0.995	1	CLONAL	5	TRUE	1	0.163354168551106	2		324	537	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981202	201981202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750329636	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	316	548	0	ENST00000359651.3:c.281G>A	p.Arg94Gln	p.R94Q	ENST00000359651		94	cGa/cAa	2/8	1	2	FACETS	1	0.958	1	1	0.997	1	CLONAL	5	TRUE	1	0.163354168551106	2		548	766	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233619	233619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457666982	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	85	151	0	ENST00000264932.6:c.923C>T	p.Thr308Met	p.T308M	ENST00000264932	NM_004168.2	308	aCg/aTg	8/15	1	2	FACETS	1	0.936	1	1	0.99	1	CLONAL	4	TRUE	1	0.163354168551106	2		151	246	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531767	46531767	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	255	329	0	ENST00000262741.5:c.580G>T	p.Glu194Ter	p.E194*	ENST00000262741	NM_003629.3	194	Gag/Tag	5/10	1	2	FACETS	0.921	0.87	0.972	1	0.996	1	CLONAL	6	TRUE	1	0.163354168551106	2		329	565	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495696	56495696	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	280	484	0	ENST00000267101.3:c.3886C>T	p.Gln1296Ter	p.Q1296*	ENST00000267101	NM_001982.3	1296	Cag/Tag	28/28	1	2	FACETS	1	0.959	1	1	0.997	1	CLONAL	5	TRUE	1	0.163354168551106	2		484	675	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425638	49425638	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	340	592	0	ENST00000301067.7:c.12850C>T	p.Gln4284Ter	p.Q4284*	ENST00000301067	NM_003482.3	4284	Cag/Tag	39/54	1	2	FACETS	1	0.951	1	1	0.997	1	CLONAL	5	TRUE	1	0.163354168551106	2		592	832	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771658	135771658	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	202	440	0	ENST00000298552.3:c.3459C>G	p.Ile1153Met	p.I1153M	ENST00000298552	NM_001162426.1	1153	atC/atG	23/23	0.163354168551106	2	FACETS	1	0.965	1	1	0.994	1	CLONAL	4	TRUE	0	0.163354168551106	2		440	587	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79974795	79974795	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	218	404	0	ENST00000265081.6:c.1223C>G	p.Ser408Cys	p.S408C	ENST00000265081	NM_002439.4	408	tCt/tGt	8/24	1	2	FACETS	0.976	0.915	1	1	0.996	1	CLONAL	5	TRUE	1	0.163354168551106	2		404	547	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993363	72993363	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	322	521	0	ENST00000268489.5:c.682C>A	p.Leu228Met	p.L228M	ENST00000268489	NM_006885.3	228	Ctg/Atg	2/10	0.163354168551106	5	FACETS	1	0.965	1	1	0.992	1	CLONAL	5	TRUE	1	0.163354168551106	5		521	957	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652025	36652025	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	319	547	0	ENST00000244741.5:c.147G>C	p.Trp49Cys	p.W49C	ENST00000244741	NM_000389.4	49	tgG/tgC	2/3	1	2	FACETS	0.949	0.9	0.999	1	0.997	1	CLONAL	5	TRUE	1	0.163354168551106	2		547	823	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060990	38060990	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	339	599	0	ENST00000250448.2:c.999G>C	p.Gln333His	p.Q333H	ENST00000250448	NM_004496.3	333	caG/caC	2/2	1	2	FACETS	0.917	0.874	0.962	1	0.997	1	CLONAL	6	TRUE	1	0.163354168551106	2		599	754	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202849	16202849	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	274	450	0	ENST00000375759.3:c.557C>T	p.Ser186Phe	p.S186F	ENST00000375759	NM_015001.2	186	tCt/tTt	3/15	1	2	FACETS	1	0.959	1	1	0.997	1	CLONAL	5	TRUE	1	0.163354168551106	2		450	660	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925655	114925655	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	220	458	0	ENST00000543371.1:c.1733C>G	p.Ser578Cys	p.S578C	ENST00000543371	NM_001198531.1	578	tCt/tGt	14/14	0.163354168551106	1	FACETS	1	0.94	1	1	0.996	1	CLONAL	4	TRUE	0	0.163354168551106	1		458	616	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398262	25398262	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913538	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	187	256	0	ENST00000311936.3:c.57G>C	p.Leu19Phe	p.L19F	ENST00000311936	NM_004985.3	19	ttG/ttC	2/5	1	2	FACETS	0.991	0.925	1	1	0.995	1	CLONAL	5	TRUE	1	0.163354168551106	2		256	462	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26927896	26927896	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	183	333	0	ENST00000381527.3:c.335G>C	p.Arg112Thr	p.R112T	ENST00000381527	NM_001260.1	112	aGa/aCa	4/13	1	2	FACETS	1	0.964	1	1	0.995	1	CLONAL	4	TRUE	1	0.163354168551106	2		333	529	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465506	99465506	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	209	452	0	ENST00000268035.6:c.2331C>G	p.Phe777Leu	p.F777L	ENST00000268035	NM_000875.3	777	ttC/ttG	11/21	1	2	FACETS	1	0.965	1	1	0.996	1	CLONAL	4	TRUE	1	0.163354168551106	2		452	609	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042127	14042127	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	267	462	0	ENST00000311895.7:c.2674G>A	p.Ala892Thr	p.A892T	ENST00000311895	NM_005236.2	892	Gca/Aca	11/11	1	2	FACETS	0.933	0.88	0.986	1	0.996	1	CLONAL	5	TRUE	1	0.163354168551106	2		462	701	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984484	7984484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1276974165	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	261	435	0	ENST00000319144.4:c.374C>T	p.Ser125Leu	p.S125L	ENST00000319144	NM_001139.2	125	tCg/tTg	3/15	1	2	FACETS	1	0.964	1	1	0.996	1	CLONAL	5	TRUE	1	0.163354168551106	2		435	622	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486070	29486070	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs746824139	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	180	328	0	ENST00000356175.3:c.247C>T	p.Gln83Ter	p.Q83*	ENST00000356175	NM_000267.3	83	Cag/Tag	3/57	1	2	FACETS	0.975	0.909	1	1	0.995	1	CLONAL	5	TRUE	1	0.163354168551106	2		328	452	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217906	2217906	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	34	466	0	ENST00000398665.3:c.2680G>T	p.Ala894Ser	p.A894S	ENST00000398665	NM_032482.2	894	Gcc/Tcc	22/28	1	2	FACETS	0.693	0.565	0.837	0.693	0.565	0.837	SUBCLONAL	1	TRUE	1	0.163354168551106	2		466	601	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627307	14627307	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	346	581	0	ENST00000254322.2:c.763A>G	p.Ile255Val	p.I255V	ENST00000254322	NM_006145.1	255	Att/Gtt	2/3	1	2	FACETS	1	0.958	1	1	0.997	1	CLONAL	5	TRUE	1	0.163354168551106	2		581	841	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795356	39795356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528221936	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	202	474	0	ENST00000288319.7:c.364G>A	p.Glu122Lys	p.E122K	ENST00000288319	NM_182918.3	122	Gag/Aag	3/10	0.163354168551106	2	FACETS	0.974	0.907	1	1	0.994	1	CLONAL	4	TRUE	0	0.163354168551106	2		474	635	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651992	36651992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	298	556	0	ENST00000244741.5:c.114G>A	p.Met38Ile	p.M38I	ENST00000244741	NM_000389.4	38	atG/atA	2/3	1	2	FACETS	0.911	0.862	0.961	1	0.997	1	CLONAL	5	TRUE	1	0.163354168551106	2		556	801	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860728	151860728	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	331	600	0	ENST00000262189.6:c.9934C>A	p.Gln3312Lys	p.Q3312K	ENST00000262189	NM_170606.2	3312	Cag/Aag	43/59	0.163354168551106	0	FACETS	0.863	0.827	0.899			1	CLONAL	7	TRUE	0	0.163354168551106	0		600	561	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913562	39913562	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	31	359	0	ENST00000378444.4:c.4766G>T	p.Arg1589Leu	p.R1589L	ENST00000378444	NM_001123385.1	1589	cGc/cTc	13/15	0.163354168551106	3	FACETS	0.688	0.555	0.839	0.229	0.185	0.28	SUBCLONAL	1	TRUE	0	0.163354168551106	3		359	597	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929017	44929017	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	329	350	0	ENST00000377967.4:c.2117C>G	p.Ser706Ter	p.S706*	ENST00000377967	NM_021140.2	706	tCa/tGa	17/29	0.163354168551106	3	FACETS	1	0.969	1	1	0.997	1	CLONAL	7	TRUE	0	0.163354168551106	3		350	611	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039288	47039296	+	inframe_deletion	In_Frame_Del	DEL	TGCGCAACC	TGCGCAACC	-	novel	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	369	515	0	ENST00000377604.3:c.913_921del	p.Arg305_Leu307del	p.R305_L307del	ENST00000377604	NM_001204468.1	304	tTGCGCAACCtg/ttg	10/24	0.163354168551106	3	FACETS	0.954	0.912	0.995	1	0.997	1	CLONAL	7	TRUE	0	0.163354168551106	3		515	732	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222271	53222271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	429	576	0	ENST00000375401.3:c.4561G>A	p.Glu1521Lys	p.E1521K	ENST00000375401	NM_004187.3	1521	Gag/Aag	26/26	0.163354168551106	3	FACETS	1	0.976	1	1	0.997	1	CLONAL	7	TRUE	0	0.163354168551106	3		576	794	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0061423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	141	467	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.607572275218999	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.607572275218999	1		467	323	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0061423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	39	382	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.510702438736736	1	FACETS	0.377	0.315	0.446	0.377	0.315	0.446	SUBCLONAL	1	TRUE	0	0.607572275218999	1		382	237	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	121	275	0	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	1	2	FACETS	0.953	0.868	1	0.953	0.868	1	CLONAL	1	TRUE	1	0.607572275218999	2		275	418	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604790	48604790	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1568211615	NA	P-0061423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	136	417	0	ENST00000342988.3:c.1612G>T	p.Glu538Ter	p.E538*	ENST00000342988	NM_005359.5	538	Gaa/Taa	12/12	0.607572275218999	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.607572275218999	1		417	305	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920413	114920413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767830105	NA	P-0061423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	151	354	0	ENST00000543371.1:c.1354G>A	p.Gly452Arg	p.G452R	ENST00000543371	NM_001198531.1	452	Ggg/Agg	13/14	0.458460838296747	1	FACETS	0.766	0.706	0.827	0.766	0.706	0.827	SUBCLONAL	1	TRUE	0	0.607572275218999	1		354	452	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332919	153332919	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs781123562	NA	P-0061423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	119	372	0	ENST00000281708.4:c.37C>T	p.Arg13Ter	p.R13*	ENST00000281708	NM_033632.3	13	Cga/Tga	2/12	0.607572275218999	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.607572275218999	1		372	266	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649553	206649553	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147688366	NA	P-0061423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	141	517	0	ENST00000367120.3:c.388G>A	p.Gly130Ser	p.G130S	ENST00000367120	NM_014002.3	130	Ggc/Agc	6/22	0.416608129312384	1	FACETS	0.731	0.672	0.792	0.731	0.672	0.792	SUBCLONAL	1	TRUE	0	0.607572275218999	1		517	442	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210586	5210586	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	134	520	0	ENST00000357368.4:c.5381G>T	p.Trp1794Leu	p.W1794L	ENST00000357368	NM_002850.3	1794	tGg/tTg	35/38	1	2	FACETS	0.915	0.837	0.996	0.915	0.837	0.996	CLONAL	1	TRUE	1	0.607572275218999	2		520	482	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956187	55956187	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	110	376	0	ENST00000263923.4:c.3128A>G	p.Lys1043Arg	p.K1043R	ENST00000263923	NM_002253.2	1043	aAa/aGa	23/30	0.510702438736736	1	FACETS	0.724	0.658	0.793	0.724	0.658	0.793	SUBCLONAL	1	TRUE	0	0.607572275218999	1		376	348	SUCCESS
APC	324	MSKCC	GRCh37	5	112173480	112173480	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	78	401	0	ENST00000257430.4:c.2189del	p.Met730ArgfsTer31	p.M730Rfs*31	ENST00000257430	NM_000038.5	730	aTg/ag	16/16	1	2	FACETS	0.937	0.833	1	0.937	0.833	1	CLONAL	1	TRUE	1	0.607572275218999	2		401	274	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845325	76845325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	162	310	0	ENST00000373344.5:c.6196G>A	p.Asp2066Asn	p.D2066N	ENST00000373344	NM_000489.3	2066	Gat/Aat	27/35	0.302700544067576	3	FACETS	0.856	0.788	0.927	0.856	0.788	0.927	CLONAL	2	TRUE	1	0.326069107688385	3		310	675	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135415	30135415	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0061424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	73	350	1	ENST00000331968.5:c.404-1G>A		p.X135_splice	ENST00000331968	NM_002742.2	135			0.326069107688385	1	FACETS	0.848	0.744	0.959	0.848	0.744	0.959	CLONAL	1	TRUE	0	0.326069107688385	1		351	442	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395183	139395191	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCGCCCT	TGGCGCCCT	A	novel	NA	P-0061424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	140	605	0	ENST00000277541.6:c.5747_5755delinsT	p.Gln1916LeufsTer24	p.Q1916Lfs*24	ENST00000277541	NM_017617.3	1916	cAGGGCGCCAgc/cTgc	31/34	0.326069107688385	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.326069107688385	1		605	656	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0061425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	22	326	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.430915752999987	4	FACETS	0.987	0.788	1	0.658	0.525	0.802	CLONAL	2	TRUE	1	0.430915752999987	4		326	74	SUCCESS
APC	324	MSKCC	GRCh37	5	112175536	112175536	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	18	397	13	ENST00000257430.4:c.4245del	p.Ser1415ArgfsTer4	p.S1415Rfs*4	ENST00000257430	NM_000038.5	1415	agT/ag	16/16	0.311670535642615	1	FACETS	0.978	0.758	1	0.978	0.758	1	CLONAL	1	TRUE	0	0.430915752999987	1		410	67	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165299	32165299	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061425-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	20	421	6	ENST00000375023.3:c.4829T>G	p.Leu1610Trp	p.L1610W	ENST00000375023	NM_004557.3	1610	tTg/tGg	27/30	0.197392858043322	0	FACETS	0.839	0.664	1			1	INDETERMINATE	1	TRUE	0	0.430915752999987	0		427	63	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061426-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	186	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.897	0.831	0.964	0.897	0.831	0.964	CLONAL	1	TRUE	1	0.60397326700881	2		126	687	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057600	180057600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1267101992	NA	P-0061426-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	247	449	1	ENST00000261937.6:c.355C>T	p.Arg119Cys	p.R119C	ENST00000261937	NM_182925.4	119	Cgc/Tgc	3/30	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.60397326700881	2		450	778	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075389	8075390	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061426-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	272	369	0	ENST00000377482.5:c.180dup	p.Gln61SerfsTer41	p.Q61Sfs*41	ENST00000377482	NM_018948.3	60	-/T	3/4	0.60397326700881	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.60397326700881	1		369	564	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227708	36227708	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061426-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	130	542	0	ENST00000222270.7:c.7277T>G	p.Val2426Gly	p.V2426G	ENST00000222270	NM_014727.1	2426	gTt/gGt	31/37	0.293229794113816	1	FACETS	0.378	0.343	0.416	0.378	0.343	0.416	INDETERMINATE	1	TRUE	0	0.60397326700881	1		542	794	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651918	36651918	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061426-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	391	488	0	ENST00000244741.5:c.41del	p.Gly14AlafsTer17	p.G14Afs*17	ENST00000244741	NM_000389.4	14	Ggc/gc	2/3	0.532691463156764	2	FACETS	0.856	0.82	0.892	0.856	0.82	0.892	CLONAL	2	TRUE	0	0.60397326700881	2		488	756	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0061464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	79	547	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.259736138171169	2		547	431	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0061464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	80	605	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.259736138171169	2		608	503	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43730536	43730536	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	81	441	0	ENST00000382044.4:c.3177del	p.Thr1060ProfsTer36	p.T1060Pfs*36	ENST00000382044	NM_001141980.1	1059	ccC/cc	16/28	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.259736138171169	2		441	489	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0061464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	59	490	1	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.259736138171169	2		491	411	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	60	648	2	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	0.759	0.653	0.873	0.759	0.653	0.873	SUBCLONAL	1	TRUE	1	0.259736138171169	2		650	609	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0061464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	49	416	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.259736138171169	2		416	375	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	70	554	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.259736138171169	2		554	454	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0061464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	84	561	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.259736138171169	2		561	539	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266494	198266494	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs756424171	NA	P-0061464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	44	467	0	ENST00000335508.6:c.2342A>G	p.Asp781Gly	p.D781G	ENST00000335508	NM_012433.2	781	gAt/gGt	16/25	1	2	FACETS	0.828	0.696	0.975	0.828	0.696	0.975	CLONAL	1	TRUE	1	0.259736138171169	2		467	409	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828383	72828383	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1277890729	NA	P-0061464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	94	622	0	ENST00000268489.5:c.8198G>A	p.Arg2733His	p.R2733H	ENST00000268489	NM_006885.3	2733	cGt/cAt	9/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.259736138171169	2		622	599	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466031	69466031	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	65	565	0	ENST00000227507.2:c.869T>G	p.Val290Gly	p.V290G	ENST00000227507	NM_053056.2	290	gTg/gGg	5/5	1	2	FACETS	0.941	0.817	1	0.941	0.817	1	CLONAL	1	TRUE	1	0.259736138171169	2		565	532	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119767	70119767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	40	454	0	ENST00000245479.2:c.769C>T	p.Arg257Cys	p.R257C	ENST00000245479	NM_000346.3	257	Cgc/Tgc	3/3	1	2	FACETS	0.883	0.735	1	0.883	0.735	1	CLONAL	1	TRUE	1	0.259736138171169	2		454	349	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513037	106513037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765837588	NA	P-0061464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	70	511	0	ENST00000359195.3:c.2051G>A	p.Arg684His	p.R684H	ENST00000359195	NM_002649.2	684	cGt/cAt	3/11	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.259736138171169	2		511	529	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948755	71948755	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1565399032	NA	P-0061464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	57	616	1	ENST00000298229.2:c.3470del	p.Gly1157AspfsTer45	p.G1157Dfs*45	ENST00000298229	NM_001567.3	1156	cGg/cg	26/28	1	2	FACETS	0.854	0.733	0.985	0.854	0.733	0.985	CLONAL	1	TRUE	1	0.259736138171169	2		617	514	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723381	49723381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1440228604	NA	P-0061464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	34	466	0	ENST00000449682.2:c.1162G>A	p.Ala388Thr	p.A388T	ENST00000449682	NM_020998.3	388	Gca/Aca	10/18	1	2	FACETS	0.648	0.53	0.781	0.648	0.53	0.781	SUBCLONAL	1	TRUE	1	0.259736138171169	2		466	404	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087888	27087906	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTCGGCCACCCAGTGGC	ACCTCGGCCACCCAGTGGC	TGG	novel	NA	P-0061464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	140	494	2	ENST00000324856.7:c.2175_2193delinsTGG	p.Pro726GlyfsTer11	p.P726Gfs*11	ENST00000324856	NM_006015.4	725	ccACCTCGGCCACCCAGTGGC/ccTGG	6/20	0.255090674903561	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.259736138171169	2		496	484	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717629	89717649	+	inframe_deletion	In_Frame_Del	DEL	CCAGCTAAAGGTGAAGATATA	CCAGCTAAAGGTGAAGATATA	-	novel	NA	P-0061464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	45	474	0	ENST00000371953.3:c.654_674del	p.Gln219_Tyr225del	p.Q219_Y225del	ENST00000371953	NM_000314.4	218	tgCCAGCTAAAGGTGAAGATATAt/tgt	7/9	1	2	FACETS	0.827	0.696	0.971	0.827	0.696	0.971	CLONAL	1	TRUE	1	0.259736138171169	2		474	419	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428020	49428021	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0061464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	75	555	0	ENST00000301067.7:c.10569dup	p.Gln3524AlafsTer32	p.Q3524Afs*32	ENST00000301067	NM_003482.3	3523	-/G	38/54	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.259736138171169	2		555	512	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68878165	68878165	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	57	603	0	ENST00000487270.1:c.878T>A	p.Ile293Lys	p.I293K	ENST00000487270	NM_133509.3	293	aTa/aAa	9/11	1	2	FACETS	0.816	0.7	0.942	0.816	0.7	0.942	CLONAL	1	TRUE	1	0.259736138171169	2		603	538	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95556996	95556996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	44	404	0	ENST00000393063.1:c.5608G>A	p.Ala1870Thr	p.A1870T	ENST00000393063	NM_030621.3	1870	Gct/Act	28/28	1	2	FACETS	0.693	0.581	0.817	0.693	0.581	0.817	SUBCLONAL	1	TRUE	1	0.259736138171169	2		404	489	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145715	11145716	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAG	novel	NA	P-0061464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	53	549	0	ENST00000358026.2:c.4090_4092dup	p.Glu1364dup	p.E1364dup	ENST00000358026	NM_001128849.1	1364	-/GAG	29/36	1	2	FACETS	0.763	0.651	0.886	0.763	0.651	0.886	SUBCLONAL	1	TRUE	1	0.259736138171169	2		549	535	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145679	61145679	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761338053	NA	P-0061464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	82	495	0	ENST00000295025.8:c.791G>A	p.Arg264Gln	p.R264Q	ENST00000295025	NM_002908.2	264	cGg/cAg	7/11	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.259736138171169	2		495	604	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524720	187524720	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1235406566	NA	P-0061464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	62	680	0	ENST00000441802.2:c.10960G>T	p.Glu3654Ter	p.E3654*	ENST00000441802	NM_005245.3	3654	Gaa/Taa	19/27	0.168936760930591	0	FACETS	0.608	0.525	0.698			1	SUBCLONAL	1	TRUE	0	0.259736138171169	0		680	581	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405926	157405926	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs758625736	NA	P-0061464-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	71	653	0	ENST00000346085.5:c.2168A>G	p.His723Arg	p.H723R	ENST00000346085	NM_020732.3	723	cAt/cGt	6/20	0.259736138171169	1	FACETS	0.73	0.637	0.83	0.73	0.637	0.83	SUBCLONAL	1	TRUE	0	0.259736138171169	1		653	652	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0061467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	33	467	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.698	0.569	0.843	0.698	0.569	0.843	SUBCLONAL	1	TRUE	1	0.254846150418474	2		467	371	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55269026	55269026	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs570295933	NA	P-0061467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	56	680	0	ENST00000275493.2:c.3092G>A	p.Arg1031Gln	p.R1031Q	ENST00000275493	NM_005228.3	1031	cGg/cAg	25/28	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.254846150418474	2		680	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs967461896	NA	P-0061467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	67	624	1	ENST00000269305.4:c.526T>C	p.Cys176Arg	p.C176R	ENST00000269305	NM_001126112.2	176	Tgc/Cgc	5/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.254846150418474	2		625	431	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857926	9857926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	62	695	0	ENST00000330684.3:c.3475C>T	p.Arg1159Cys	p.R1159C	ENST00000330684	NM_001134407.1	1159	Cgc/Tgc	13/13	0.254846150418474	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.254846150418474	1		695	365	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094456	27094456	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	50	600	0	ENST00000324856.7:c.3164A>G	p.Tyr1055Cys	p.Y1055C	ENST00000324856	NM_006015.4	1055	tAt/tGt	11/20	0.254846150418474	1	FACETS	0.975	0.831	1	0.975	0.831	1	CLONAL	1	TRUE	0	0.254846150418474	1		600	351	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998585	100998585	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	37	551	0	ENST00000325455.5:c.1217T>C	p.Val406Ala	p.V406A	ENST00000325455	NM_001202474.3	406	gTg/gCg	1/8	1	2	FACETS	0.787	0.65	0.94	0.787	0.65	0.94	CLONAL	1	TRUE	1	0.254846150418474	2		551	369	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134230	11134230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1227826852	NA	P-0061467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	37	475	0	ENST00000358026.2:c.2896C>T	p.Arg966Trp	p.R966W	ENST00000358026	NM_001128849.1	966	Cgg/Tgg	20/36	1	2	FACETS	0.91	0.753	1	0.91	0.753	1	CLONAL	1	TRUE	1	0.254846150418474	2		475	319	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770627	40770627	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	43	518	0	ENST00000373198.4:c.2755C>A	p.Gln919Lys	p.Q919K	ENST00000373198	NM_133170.3	919	Cag/Aag	19/32	0.213716613230917	3	FACETS	0.942	0.789	1	0.471	0.394	0.555	CLONAL	1	TRUE	1	0.254846150418474	3		518	404	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670414	134670414	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061467-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	37	532	0	ENST00000398015.3:c.325A>G	p.Thr109Ala	p.T109A	ENST00000398015	NM_004441.4	109	Acc/Gcc	3/16	1	2	FACETS	0.949	0.785	1	0.949	0.785	1	CLONAL	1	TRUE	1	0.254846150418474	2		532	306	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188200	10188200	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061475-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	137	284	0	ENST00000256474.2:c.343C>A	p.His115Asn	p.H115N	ENST00000256474	NM_000551.3	115	Cac/Aac	2/3	0.690307827352648	1	FACETS	0.97	0.901	1	0.97	0.901	1	CLONAL	1	TRUE	0	0.690307827352648	1		284	268	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814973	43814973	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061475-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	28	435	0	ENST00000372470.3:c.1508G>A	p.Gly503Asp	p.G503D	ENST00000372470	NM_005373.2	503	gGc/gAc	10/12	0.690307827352648	1	FACETS	0.122	0.097	0.15	0.122	0.097	0.15	SUBCLONAL	1	TRUE	0	0.690307827352648	1		435	437	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845607	63845607	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061475-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	182	340	0	ENST00000279873.7:c.1346C>G	p.Pro449Arg	p.P449R	ENST00000279873	NM_032199.2	449	cCt/cGt	9/10	1	2	FACETS	0.901	0.836	0.968	0.901	0.836	0.968	CLONAL	1	TRUE	1	0.690307827352648	2		340	585	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912700	32912700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061475-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	114	331	0	ENST00000380152.3:c.4208C>T	p.Thr1403Ile	p.T1403I	ENST00000380152		1403	aCt/aTt	11/27	1	2	FACETS	0.902	0.821	0.987	0.902	0.821	0.987	CLONAL	1	TRUE	1	0.690307827352648	2		331	366	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860923	45860923	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061475-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	220	477	0	ENST00000391945.4:c.1272A>C	p.Arg424Ser	p.R424S	ENST00000391945	NM_000400.3	424	agA/agC	13/23	1	2	FACETS	0.924	0.863	0.985	0.924	0.863	0.985	CLONAL	1	TRUE	1	0.690307827352648	2		477	690	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814256	76814256	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061475-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	98	271	0	ENST00000373344.5:c.6388A>G	p.Asn2130Asp	p.N2130D	ENST00000373344	NM_000489.3	2130	Aat/Gat	29/35	1	2	FACETS	0.825	0.744	0.91	0.825	0.744	0.91	CLONAL	1	TRUE	1	0.690307827352648	2		271	344	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0061479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	101	545	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.162564399954403	2	FACETS	1	0.978	1	0.698	0.624	0.777	CLONAL	1	TRUE	0	0.196651926002064	2		545	736	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28886135	28886135	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs145693340	NA	P-0061479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	34	352	0	ENST00000282397.4:c.3487C>A	p.Gln1163Lys	p.Q1163K	ENST00000282397	NM_002019.4	1163	Caa/Aaa	26/30	1	2	FACETS	0.753	0.615	0.909	0.753	0.615	0.909	CLONAL	1	TRUE	1	0.196651926002064	2		352	459	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0061480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	79	248	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.317493587323916	4	FACETS	0.867	0.774	0.965	0.65	0.58	0.724	CLONAL	3	TRUE	0	0.317493587323916	4		248	252	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0061480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	197	444	0	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	0.223608827140616	4	FACETS	0.853	0.79	0.919	0.853	0.79	0.919	CLONAL	2	TRUE	2	0.317493587323916	4		444	958	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191488	10191488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs5030818	NA	P-0061480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	238	405	0	ENST00000256474.2:c.481C>T	p.Arg161Ter	p.R161*	ENST00000256474	NM_000551.3	161	Cga/Tga	3/3	0.246121346575419	3	FACETS	1	0.985	1	0.777	0.728	0.827	CLONAL	2	TRUE	0	0.317493587323916	3		405	745	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440912	52440912	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1205668341	NA	P-0061480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	232	495	2	ENST00000460680.1:c.592del	p.Glu198ArgfsTer33	p.E198Rfs*33	ENST00000460680	NM_004656.3	198	Gag/ag	8/17	0.246121346575419	3	FACETS	1	0.955	1	0.684	0.639	0.73	CLONAL	2	TRUE	0	0.317493587323916	3		497	825	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027020	71027020	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	103	558	0	ENST00000318789.4:c.1307G>A	p.Arg436His	p.R436H	ENST00000318789	NM_032682.5	436	cGc/cAc	15/21	0.246121346575419	3	FACETS	0.787	0.703	0.877	0.262	0.234	0.293	SUBCLONAL	1	TRUE	0	0.317493587323916	3		558	955	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226592	2226592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376766280	NA	P-0061480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	78	582	0	ENST00000398665.3:c.4072G>A	p.Gly1358Ser	p.G1358S	ENST00000398665	NM_032482.2	1358	Ggc/Agc	27/28	0.223608827140616	4	FACETS	0.619	0.543	0.703	0.31	0.271	0.352	SUBCLONAL	1	TRUE	2	0.317493587323916	4		582	1045	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2208957	2208958	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	56	395	0	ENST00000398665.3:c.992dup	p.Asn331LysfsTer28	p.N331Kfs*28	ENST00000398665	NM_032482.2	329	-/A	12/28	0.223608827140616	4	FACETS	0.759	0.65	0.879	0.38	0.325	0.44	SUBCLONAL	1	TRUE	2	0.317493587323916	4		395	612	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343707	343707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758124815	NA	P-0061480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	68	456	0	ENST00000262320.3:c.1967C>T	p.Thr656Met	p.T656M	ENST00000262320	NM_003502.3	656	aCg/aTg	8/11	0.223608827140616	4	FACETS	0.69	0.599	0.789	0.345	0.299	0.395	SUBCLONAL	1	TRUE	2	0.317493587323916	4		456	818	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251109	99251109	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs746570875	NA	P-0061480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	134	573	0	ENST00000268035.6:c.418del	p.Ala140ProfsTer20	p.A140Pfs*20	ENST00000268035	NM_000875.3	138	cGg/cg	2/21	0.223608827140616	4	FACETS	1	0.983	1	0.681	0.619	0.747	CLONAL	1	TRUE	2	0.317493587323916	4		573	816	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276215	15276215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748889237	NA	P-0061480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	39	491	0	ENST00000263388.2:c.5779G>A	p.Ala1927Thr	p.A1927T	ENST00000263388	NM_000435.2	1927	Gcc/Acc	31/33	0.223608827140616	4	FACETS	0.433	0.357	0.517	0.216	0.178	0.259	SUBCLONAL	1	TRUE	2	0.317493587323916	4		491	748	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17389736	17389736	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	83	541	0	ENST00000359435.4:c.869A>G	p.Glu290Gly	p.E290G	ENST00000359435	NM_001033549.1	290	gAg/gGg	9/9	0.223608827140616	4	FACETS	0.755	0.665	0.852	0.378	0.332	0.426	SUBCLONAL	1	TRUE	2	0.317493587323916	4		541	912	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965299	25965299	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	115	332	0	ENST00000435504.4:c.3907del	p.His1303ThrfsTer21	p.H1303Tfs*21	ENST00000435504		1303	Cac/ac	13/13	0.231940620722221	5	FACETS	0.751	0.677	0.829	0.501	0.451	0.553	SUBCLONAL	2	TRUE	2	0.317493587323916	5		332	712	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643545	52643545	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	245	413	0	ENST00000394830.3:c.2351del	p.Asn784IlefsTer7	p.N784Ifs*7	ENST00000394830	NM_018313.4	784	aAt/at	17/30	0.246121346575419	3	FACETS	1	0.989	1	0.815	0.765	0.866	CLONAL	2	TRUE	0	0.317493587323916	3		413	731	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0061481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	250	565	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.438474917306876	3	FACETS	0.835	0.792	0.878	0.835	0.792	0.878	CLONAL	3	TRUE	0	0.539196148038893	3		565	470	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098966	178098966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	261	365	0	ENST00000397062.3:c.79G>A	p.Asp27Asn	p.D27N	ENST00000397062	NM_006164.4	27	Gat/Aat	2/5	0.522472156339948	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	1	0.539196148038893	4		365	463	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56872901	56872901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748209131	NA	P-0061481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	26	378	0	ENST00000308159.5:c.2056G>A	p.Asp686Asn	p.D686N	ENST00000308159	NM_014669.4	686	Gac/Aac	19/22	0.498250677689707	3	FACETS	0.676	0.54	0.83	0.338	0.27	0.415	SUBCLONAL	1	TRUE	1	0.539196148038893	3		378	181	SUCCESS
ATR	545	MSKCC	GRCh37	3	142254950	142254950	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	41	232	0	ENST00000350721.4:c.3819G>T	p.Lys1273Asn	p.K1273N	ENST00000350721	NM_001184.3	1273	aaG/aaT	20/47	0.539196148038893	6	FACETS	0.859	0.725	1	0.573	0.483	0.669	CLONAL	2	TRUE	3	0.539196148038893	6		232	184	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003323	143003324	+	missense_variant	Missense_Mutation	DNP	TC	TC	CA	novel	NA	P-0061481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	64	293	1	ENST00000262992.4:c.2502_2503delinsTG	p.Asn835Asp	p.N835D	ENST00000262992	NM_001101669.1	834	ctGAat/ctTGat	23/24	0.430251740460017	2	FACETS	0.813	0.724	0.904	0.813	0.724	0.904	CLONAL	2	TRUE	0	0.539196148038893	2		294	146	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0061483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	371	558	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.524855765283183	3	FACETS	1	0.991	1	0.769	0.734	0.803	CLONAL	2	TRUE	0	0.524855765283183	3		558	774	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468919	25468919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	141	392	0	ENST00000264709.3:c.1444G>A	p.Glu482Lys	p.E482K	ENST00000264709	NM_175629.2	482	Gag/Aag	12/23	0.46313798624772	3	FACETS	1	0.966	1	0.555	0.507	0.605	CLONAL	1	TRUE	1	0.524855765283183	3		392	611	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799224	42799224	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	119	395	0	ENST00000575354.2:c.4708C>T	p.Gln1570Ter	p.Q1570*	ENST00000575354	NM_015125.3	1570	Cag/Tag	20/20	0.524855765283183	3	FACETS	0.951	0.861	1	0.475	0.43	0.523	CLONAL	1	TRUE	1	0.524855765283183	3		395	602	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954339	48954339	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	82	258	0	ENST00000267163.4:c.1460T>C	p.Leu487Ser	p.L487S	ENST00000267163	NM_000321.2	487	tTg/tCg	16/27	1	2	FACETS	0.973	0.866	1	0.973	0.866	1	CLONAL	1	TRUE	1	0.524855765283183	2		258	321	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	16	414	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.643	0.475	0.843	0.643	0.475	0.843	SUBCLONAL	1	TRUE	1	0.17173745336862	2		414	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0061484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	47	589	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.17173745336862	1	FACETS	0.806	0.679	0.946	0.806	0.679	0.946	CLONAL	1	TRUE	0	0.17173745336862	1		589	621	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074249	30074279	+	frameshift_variant	Frame_Shift_Del	DEL	GCCTGTCTTTCGACTTCAAAGATACTGACAT	GCCTGTCTTTCGACTTCAAAGATACTGACAT	-	novel	NA	P-0061484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	68	462	0	ENST00000338641.4:c.1512_1542del	p.Ser504ArgfsTer8	p.S504Rfs*8	ENST00000338641	NM_000268.3	504	aGCCTGTCTTTCGACTTCAAAGATACTGACATg/ag	14/16	0.17173745336862	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.17173745336862	1		462	490	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0061486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	104	365	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.403832251003437	2		365	510	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210075	55210075	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	167	438	0	ENST00000275493.2:c.185T>G	p.Leu62Arg	p.L62R	ENST00000275493	NM_005228.3	62	cTt/cGt	2/28	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.403832251003437	2		438	635	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100340	27100340	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	169	579	0	ENST00000324856.7:c.4052G>A	p.Gly1351Asp	p.G1351D	ENST00000324856	NM_006015.4	1351	gGc/gAc	17/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.403832251003437	2		579	786	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2058343	2058343	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	121	456	0	ENST00000349721.2:c.1400G>T	p.Arg467Leu	p.R467L	ENST00000349721	NM_003070.3	467	cGg/cTg	8/34	1	2	FACETS	0.96	0.87	1	0.96	0.87	1	CLONAL	1	TRUE	1	0.403832251003437	2		456	624	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0061487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	311	715	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.542697759300139	2	FACETS	0.967	0.923	1	0.967	0.923	1	CLONAL	2	TRUE	0	0.569443356436723	2		715	565	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922321	178922321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	252	235	0	ENST00000263967.3:c.1090G>A	p.Gly364Arg	p.G364R	ENST00000263967	NM_006218.2	364	Gga/Aga	6/21	0.569093579738842	5	FACETS	0.9	0.854	0.945	0.9	0.854	0.945	CLONAL	4	TRUE	1	0.569443356436723	5		235	456	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740432	58740432	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs775750934	NA	P-0061487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	310	444	0	ENST00000305921.3:c.1337C>G	p.Ser446Ter	p.S446*	ENST00000305921	NM_003620.3	446	tCa/tGa	6/6	1	2	FACETS	0.774	0.735	0.814	1	0.995	1	SUBCLONAL	2	TRUE	1	0.569443356436723	2		444	703	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716325	52716325	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	258	412	0	ENST00000322088.6:c.769T>G	p.Trp257Gly	p.W257G	ENST00000322088	NM_014225.5	257	Tgg/Ggg	6/15	0.471577249927039	4	FACETS	0.938	0.882	0.995	0.938	0.882	0.995	CLONAL	2	TRUE	2	0.569443356436723	4		412	758	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851013	63851013	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	175	494	0	ENST00000279873.7:c.1791C>A	p.Ser597Arg	p.S597R	ENST00000279873	NM_032199.2	597	agC/agA	10/10	1	2	FACETS	0.928	0.858	1	0.928	0.858	1	CLONAL	1	TRUE	1	0.569443356436723	2		494	662	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47503727	47503727	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	295	515	0	ENST00000404338.3:c.4284del	p.Phe1428LeufsTer371	p.F1428Lfs*371	ENST00000404338	NM_004491.4	1428	Ttt/tt	6/6	0.471577249927039	4	FACETS	0.876	0.827	0.927	0.876	0.827	0.927	CLONAL	2	TRUE	2	0.569443356436723	4		515	928	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47503727	47503727	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	339	515	0	ENST00000404338.3:c.4282T>G	p.Phe1428Val	p.F1428V	ENST00000404338	NM_004491.4	1428	Ttt/Gtt	6/6	0.471577249927039	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	2	0.569443356436723	4		515	928	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390197	89390197	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	162	382	0	ENST00000336596.2:c.946G>C	p.Asp316His	p.D316H	ENST00000336596	NM_005233.5	316	Gac/Cac	4/17	0.521973733051816	3	FACETS	0.832	0.763	0.903	0.416	0.381	0.452	CLONAL	1	TRUE	1	0.569443356436723	3		382	879	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937439	76937439	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	81	412	0	ENST00000373344.5:c.3309G>T	p.Lys1103Asn	p.K1103N	ENST00000373344	NM_000489.3	1103	aaG/aaT	9/35	0.418985296889439	3	FACETS	0.774	0.685	0.87	0.387	0.342	0.435	SUBCLONAL	1	TRUE	1	0.569443356436723	3		412	472	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0061488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	132	479	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	0.470675476482339	3	FACETS	0.864	0.784	0.947	0.432	0.392	0.474	CLONAL	1	TRUE	1	0.476042289133604	3		479	795	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223488	53223488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	116	241	0	ENST00000375401.3:c.3871C>T	p.Arg1291Cys	p.R1291C	ENST00000375401	NM_004187.3	1291	Cgc/Tgc	23/26	0.442873150533291	2	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.476042289133604	2		241	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577027	7577069	+	frameshift_variant	Frame_Shift_Del	DEL	GTGCTCCCTGGGGGCAGCTCGTGGTGAGGCTCCCCTTTCTTGC	GTGCTCCCTGGGGGCAGCTCGTGGTGAGGCTCCCCTTTCTTGC	-	novel	NA	P-0061488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	321	631	0	ENST00000269305.4:c.869_911del	p.Arg290LeufsTer41	p.R290Lfs*41	ENST00000269305	NM_001126112.2	290	cGCAAGAAAGGGGAGCCTCACCACGAGCTGCCCCCAGGGAGCACt/ct	8/11	0.474938568673706	2	FACETS	0.911	0.866	0.957	0.911	0.866	0.957	CLONAL	2	TRUE	0	0.476042289133604	2		631	740	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6270673	6270673	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	293	531	0	ENST00000252674.7:c.110G>A	p.Arg37His	p.R37H	ENST00000252674	NM_005934.3	37	cGc/cAc	2/12	0.42504166461162	4	FACETS	0.917	0.864	0.971	0.917	0.864	0.971	CLONAL	2	TRUE	2	0.476042289133604	4		531	991	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271366	26271366	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs75254483	NA	P-0061488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	193	643	1	ENST00000305910.3:c.247C>A	p.Leu83Met	p.L83M	ENST00000305910	NM_003534.2	83	Ctg/Atg	1/1	0.470675476482339	3	FACETS	0.918	0.848	0.99	0.459	0.424	0.495	CLONAL	1	TRUE	1	0.476042289133604	3		644	1094	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31239382	31239382	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	44	382	0	ENST00000376228.5:c.337G>C	p.Glu113Gln	p.E113Q	ENST00000376228	NM_002117.5	113	Gag/Cag	2/8	0.470675476482339	3	FACETS	0.44	0.369	0.519	0.22	0.184	0.26	SUBCLONAL	1	TRUE	1	0.476042289133604	3		382	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0061489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	160	535	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.199573042867129	4	FACETS	1	0.972	1			1	CLONAL	2	TRUE	NA	0.237294201925385	4		535	740	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0061489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	173	534	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.201442129522695	3	FACETS	0.902	0.831	0.977	0.902	0.831	0.977	CLONAL	2	TRUE	1	0.237294201925385	3		534	904	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0061489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	70	481	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.199573042867129	4	FACETS	0.823	0.716	0.939			1	CLONAL	1	TRUE	NA	0.237294201925385	4		481	887	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857692	9857692	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1389208302	NA	P-0061489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	323	602	0	ENST00000330684.3:c.3709G>A	p.Asp1237Asn	p.D1237N	ENST00000330684	NM_001134407.1	1237	Gat/Aat	13/13	0.237294201925385	3	FACETS	0.948	0.896	1	0.948	0.896	1	CLONAL	3	TRUE	0	0.237294201925385	3		602	1071	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521483	46521483	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs968243629	NA	P-0061489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	120	337	0	ENST00000262741.5:c.925C>T	p.Arg309Ter	p.R309*	ENST00000262741	NM_003629.3	309	Cga/Tga	7/10	0.201442129522695	3	FACETS	0.809	0.732	0.891	0.809	0.732	0.891	CLONAL	2	TRUE	1	0.237294201925385	3		337	699	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724542	162724542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1041487062	NA	P-0061489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	87	603	0	ENST00000367921.3:c.314G>A	p.Arg105His	p.R105H	ENST00000367921	NM_006182.2	105	cGc/cAc	5/18	0.0710261250203776	3	FACETS	0.904	0.799	1	0.452	0.399	0.509	INDETERMINATE	1	TRUE	1	0.237294201925385	3		603	907	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661614	227661614	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	218	594	1	ENST00000305123.5:c.1841C>T	p.Pro614Leu	p.P614L	ENST00000305123	NM_005544.2	614	cCc/cTc	1/2	0.237294201925385	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.237294201925385	3		595	930	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357481	89357481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	305	548	0	ENST00000301030.4:c.337G>A	p.Glu113Lys	p.E113K	ENST00000301030	NM_001256183.1	113	Gag/Aag	5/13	0.237294201925385	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	3	TRUE	0	0.237294201925385	3		548	930	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486202	8486202	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	129	550	0	ENST00000356435.5:c.2615A>C	p.Glu872Ala	p.E872A	ENST00000356435		872	gAg/gCg	17/35	0.201442129522695	3	FACETS	0.784	0.711	0.86	0.784	0.711	0.86	SUBCLONAL	2	TRUE	1	0.237294201925385	3		550	776	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750510	57750510	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	58	479	0	ENST00000274289.3:c.1958C>G	p.Thr653Arg	p.T653R	ENST00000274289	NM_006622.3	653	aCa/aGa	14/14	0.201442129522695	3	FACETS	0.688	0.59	0.795	0.344	0.295	0.398	SUBCLONAL	1	TRUE	1	0.237294201925385	3		479	795	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910766	29910766	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	175	375	0	ENST00000376809.5:c.309del	p.Thr104ProfsTer18	p.T104Pfs*18	ENST00000376809	NM_002116.7	102	ctG/ct	2/8	0.129846629917974	4	FACETS	0.956	0.885	1	1	0.989	1	INDETERMINATE	3	TRUE	2	0.237294201925385	4		375	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0061490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	278	707	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.829703958181573	2		707	666	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944558	32944558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80359076	NA	P-0061490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	201	321	0	ENST00000380152.3:c.8351G>A	p.Arg2784Gln	p.R2784Q	ENST00000380152		2784	cGg/cAg	19/27	1	2	FACETS	0.987	0.924	1	0.987	0.924	1	CLONAL	1	TRUE	1	0.829703958181573	2		321	491	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152276	99152276	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772559256	NA	P-0061490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	232	419	0	ENST00000074304.5:c.355G>A	p.Val119Met	p.V119M	ENST00000074304	NM_001134224.1	119	Gtg/Atg	6/26	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.829703958181573	2		419	515	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890149	76890150	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	194	209	0	ENST00000373344.5:c.4744dup	p.Thr1582AsnfsTer19	p.T1582Nfs*19	ENST00000373344	NM_000489.3	1582	aca/aAca	17/35	1	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.829703958181573	1		209	268	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578201	7578202	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0061490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	362	634	0	ENST00000269305.4:c.647_648del	p.Val216GlyfsTer5	p.V216Gfs*5	ENST00000269305	NM_001126112.2	216	gTG/g	6/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.829703958181573	2		634	868	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098913	47098913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	341	496	0	ENST00000409792.3:c.6361C>T	p.Arg2121Cys	p.R2121C	ENST00000409792	NM_014159.6	2121	Cgc/Tgc	15/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.829703958181573	2		496	788	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976706	2976706	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1044557293	NA	P-0061490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	539	479	0	ENST00000396946.4:c.1306C>T	p.Arg436Trp	p.R436W	ENST00000396946	NM_032415.4	436	Cgg/Tgg	9/25	0.829703958181573	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.829703958181573	3		479	843	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662442	227662442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	278	587	1	ENST00000305123.5:c.1013G>A	p.Arg338His	p.R338H	ENST00000305123	NM_005544.2	338	cGc/cAc	1/2	1	2	FACETS	0.931	0.879	0.983	0.931	0.879	0.983	CLONAL	1	TRUE	1	0.829703958181573	2		588	720	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955111	17955112	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755706305	NA	P-0061490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	230	522	0	ENST00000458235.1:c.115dup	p.Gln39ProfsTer13	p.Q39Pfs*13	ENST00000458235	NM_000215.3	39	cag/cCag	2/24	1	2	FACETS	0.883	0.828	0.938	0.883	0.828	0.938	CLONAL	1	TRUE	1	0.829703958181573	2		522	628	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164760	47164760	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	275	570	0	ENST00000409792.3:c.1366C>T	p.Arg456Ter	p.R456*	ENST00000409792	NM_014159.6	456	Cga/Tga	3/21	1	2	FACETS	0.893	0.843	0.945	0.893	0.843	0.945	CLONAL	1	TRUE	1	0.829703958181573	2		570	742	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574055	46574055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	288	519	0	ENST00000263734.3:c.70C>T	p.Arg24Trp	p.R24W	ENST00000263734	NM_001430.4	24	Cgg/Tgg	2/16	0.829703958181573	2	FACETS	0.933	0.882	0.985	0.467	0.441	0.493	CLONAL	1	TRUE	0	0.829703958181573	2		519	744	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62009575	62009575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs114330958	NA	P-0061490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	53	501	0	ENST00000392795.3:c.47C>T	p.Ala16Val	p.A16V	ENST00000392795	NM_001039933.1	16	gCg/gTg	1/6	1	2	FACETS	0.21	0.178	0.244	0.21	0.178	0.244	SUBCLONAL	1	TRUE	1	0.829703958181573	2		501	609	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25462009	25462009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757083492	NA	P-0061490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	306	466	0	ENST00000264709.3:c.2398G>A	p.Gly800Ser	p.G800S	ENST00000264709	NM_175629.2	800	Ggt/Agt	20/23	0.829703958181573	2	FACETS	0.994	0.943	1	0.497	0.471	0.523	CLONAL	1	TRUE	0	0.829703958181573	2		466	742	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639767	3639767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754761366	NA	P-0061490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	260	529	0	ENST00000294008.3:c.3872C>T	p.Thr1291Met	p.T1291M	ENST00000294008	NM_032444.2	1291	aCg/aTg	12/15	1	2	FACETS	0.958	0.904	1	0.958	0.904	1	CLONAL	1	TRUE	1	0.829703958181573	2		529	654	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868492	117868492	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760261220	NA	P-0061490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	239	427	0	ENST00000297338.2:c.850G>A	p.Val284Ile	p.V284I	ENST00000297338	NM_006265.2	284	Gtt/Att	8/14	1	2	FACETS	0.976	0.919	1	0.976	0.919	1	CLONAL	1	TRUE	1	0.829703958181573	2		427	590	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351238	89351238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1266962947	NA	P-0061490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	45	558	0	ENST00000301030.4:c.1712C>T	p.Thr571Met	p.T571M	ENST00000301030	NM_001256183.1	571	aCg/aTg	9/13	1	2	FACETS	0.155	0.129	0.183	0.155	0.129	0.183	SUBCLONAL	1	TRUE	1	0.829703958181573	2		558	701	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465940	69465940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755986542	NA	P-0061490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	284	574	0	ENST00000227507.2:c.778C>T	p.Arg260Cys	p.R260C	ENST00000227507	NM_053056.2	260	Cgc/Tgc	5/5	1	2	FACETS	0.963	0.911	1	0.963	0.911	1	CLONAL	1	TRUE	1	0.829703958181573	2		574	711	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554147	63554147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	386	611	0	ENST00000307078.5:c.592G>A	p.Glu198Lys	p.E198K	ENST00000307078	NM_004655.3	198	Gaa/Aaa	2/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.829703958181573	2		611	876	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169498	27169498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	291	440	0	ENST00000380036.4:c.499C>T	p.Arg167Trp	p.R167W	ENST00000380036	NM_000459.3	167	Cgg/Tgg	4/23	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.829703958181573	2		440	644	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17359572	17359572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs570278423	NA	P-0061490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	255	337	0	ENST00000375499.3:c.269G>A	p.Arg90Gln	p.R90Q	ENST00000375499	NM_003000.2	90	cGa/cAa	3/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.829703958181573	2		337	587	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798130	45798130	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34126013	NA	P-0061490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	328	546	0	ENST00000450313.1:c.721C>T	p.Arg241Trp	p.R241W	ENST00000450313	NM_012222.2	241	Cgg/Tgg	9/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.829703958181573	2		546	790	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510763	120510763	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	53	481	0	ENST00000256646.2:c.1201T>C	p.Cys401Arg	p.C401R	ENST00000256646	NM_024408.3	401	Tgc/Cgc	7/34	1	2	FACETS	0.167	0.141	0.194	0.167	0.141	0.194	SUBCLONAL	1	TRUE	1	0.829703958181573	2		481	767	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150923484	150923484	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	310	536	0	ENST00000271640.5:c.2131C>T	p.Arg711Cys	p.R711C	ENST00000271640	NM_001145415.1	711	Cgt/Tgt	13/22	1	2	FACETS	0.991	0.94	1	0.991	0.94	1	CLONAL	1	TRUE	1	0.829703958181573	2		536	754	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094942	11094942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764312409	NA	P-0061490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	245	562	1	ENST00000358026.2:c.115G>A	p.Ala39Thr	p.A39T	ENST00000358026	NM_001128849.1	39	Gcc/Acc	2/36	1	2	FACETS	0.967	0.91	1	0.967	0.91	1	CLONAL	1	TRUE	1	0.829703958181573	2		563	611	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302276	15302276	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774985086	NA	P-0061490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	264	450	0	ENST00000263388.2:c.995G>A	p.Arg332His	p.R332H	ENST00000263388	NM_000435.2	332	cGc/cAc	6/33	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.829703958181573	2		450	633	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57470706	57470706	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	277	376	0	ENST00000371085.3:c.179T>C	p.Met60Thr	p.M60T	ENST00000371085	NM_000516.4	60	aTg/aCg	2/13	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.829703958181573	2		376	668	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136801	55136801	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	187	290	0	ENST00000257290.5:c.1123T>C	p.Tyr375His	p.Y375H	ENST00000257290	NM_006206.4	375	Tat/Cat	8/23	1	2	FACETS	0.924	0.861	0.987	0.924	0.861	0.987	CLONAL	1	TRUE	1	0.829703958181573	2		290	488	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417580	139417580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	472	509	0	ENST00000277541.6:c.464G>A	p.Cys155Tyr	p.C155Y	ENST00000277541	NM_017617.3	155	tGc/tAc	4/34	0.796680835112669	2	FACETS	0.945	0.92	0.969	0.945	0.92	0.969	CLONAL	2	TRUE	0	0.829703958181573	2		509	602	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0061494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	160	485	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.527566491471689	2	FACETS	0.896	0.842	0.949	0.896	0.842	0.949	CLONAL	2	TRUE	0	0.659032561646493	2		485	271	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	318	752	0	ENST00000269305.4:c.503A>T	p.His168Leu	p.H168L	ENST00000269305	NM_001126112.2	168	cAc/cTc	5/11	0.537866880383451	2	FACETS	0.81	0.773	0.847	0.81	0.773	0.847	CLONAL	2	TRUE	0	0.659032561646493	2		752	596	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784029	9784029	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	109	440	0	ENST00000377346.4:c.2597A>C	p.Glu866Ala	p.E866A	ENST00000377346	NM_005026.3	866	gAg/gCg	21/24	0.526223626105225	3	FACETS	0.811	0.731	0.896	0.406	0.365	0.448	CLONAL	1	TRUE	1	0.659032561646493	3		440	542	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643351	52643351	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	115	465	0	ENST00000394830.3:c.2545G>T	p.Glu849Ter	p.E849*	ENST00000394830	NM_018313.4	849	Gaa/Taa	17/30	0.527566491471689	2	FACETS	0.855	0.793	0.917	0.855	0.793	0.917	CLONAL	2	TRUE	0	0.659032561646493	2		465	204	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0061494-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	690	485	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.458067902114289	6	FACETS	1	0.994	1	1	0.994	1	CLONAL	6	TRUE	0	0.458067902114289	6		485	914	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061494-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	319	752	0	ENST00000269305.4:c.503A>T	p.His168Leu	p.H168L	ENST00000269305	NM_001126112.2	168	cAc/cTc	5/11	0.458067902114289	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.458067902114289	2		752	680	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643351	52643351	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061494-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	186	465	0	ENST00000394830.3:c.2545G>T	p.Glu849Ter	p.E849*	ENST00000394830	NM_018313.4	849	Gaa/Taa	17/30	0.458067902114289	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.458067902114289	2		465	364	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0061495-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	77	522	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.958	0.848	1	1	0.987	1	CLONAL	3	TRUE	1	0.16	2		522	335	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061495-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	15	126	0				ENST00000310581	NM_198253.2	-/1132			0.3	0	FACETS	0.905	0.673	1			1	CLONAL	2	TRUE	0	0.16	0		126	87	SUCCESS
MAD2L2	10459	MSKCC	GRCh37	1	11737635	11737635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061495-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	13	418	0	ENST00000235310.3:c.196G>A	p.Asp66Asn	p.D66N	ENST00000235310		66	Gac/Aac	6/11	0.172724943606885	0	FACETS	0.533	0.38	0.721			1	SUBCLONAL	1	TRUE	0	0.16	0		418	256	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038275	30038275	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0061496-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	99	408	0	ENST00000338641.4:c.447+1G>A		p.X149_splice	ENST00000338641	NM_000268.3	149			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		408	326	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074313	30074313	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0061496-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	65	412	0	ENST00000338641.4:c.1574+1G>A		p.X525_splice	ENST00000338641	NM_000268.3	525			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		412	256	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061497-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	66	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.793	0.69	0.905	0.793	0.69	0.905	CLONAL	1	TRUE	1	0.336233573728914	2		126	495	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0061497-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	123	771	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.336233573728914	2		771	705	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0061497-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	135	534	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.336233573728914	2		534	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0061497-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	103	370	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.336233573728914	1	FACETS	0.954	0.857	1	0.954	0.857	1	CLONAL	1	TRUE	0	0.336233573728914	1		370	534	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149751	202149751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061497-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	158	528	0	ENST00000358485.4:c.1192C>T	p.Gln398Ter	p.Q398*	ENST00000358485	NM_001080125.1	398	Cag/Tag	8/9	1	2	FACETS	0.988	0.905	1	0.988	0.905	1	CLONAL	1	TRUE	1	0.336233573728914	2		528	951	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183644	10183644	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs867958699	NA	P-0061497-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	129	496	0	ENST00000256474.2:c.113C>A	p.Ser38Tyr	p.S38Y	ENST00000256474	NM_000551.3	38	tCc/tAc	1/3	0.336233573728914	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.336233573728914	1		496	558	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	148	877	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.872	0.799	0.948	1	0.993	1	CLONAL	3	TRUE	1	0.177871586705847	2		883	636	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	70	514	2	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.816	0.714	0.927	1	0.977	1	CLONAL	2	TRUE	1	0.177871586705847	2		516	482	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	16	524	0	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	1	2	FACETS	0.31	0.228	0.409	0.31	0.228	0.409	SUBCLONAL	1	TRUE	1	0.177871586705847	2		524	580	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	74	348	10	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.883	0.78	0.992	1	0.986	1	CLONAL	3	TRUE	1	0.177871586705847	2		358	314	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119910	70119910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1297203260	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	114	452	0	ENST00000245479.2:c.916del	p.Val306CysfsTer77	p.V306Cfs*77	ENST00000245479	NM_000346.3	304	ccG/cc	3/3	1	2	FACETS	0.923	0.836	1	1	0.991	1	CLONAL	3	TRUE	1	0.177871586705847	2		452	463	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120115	70120115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	92	597	0	ENST00000245479.2:c.1121del	p.Pro374ArgfsTer9	p.P374Rfs*9	ENST00000245479	NM_000346.3	373	Ccc/cc	3/3	1	2	FACETS	1	0.96	1	1	0.988	1	CLONAL	2	TRUE	1	0.177871586705847	2		597	446	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521525	46521525	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	51	372	0	ENST00000262741.5:c.883del	p.Met295Ter	p.M295*	ENST00000262741	NM_003629.3	295	Atg/tg	7/10	1	2	FACETS	0.864	0.738	1	1	0.971	1	CLONAL	2	TRUE	1	0.177871586705847	2		372	332	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	98	494	4	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	0.177871586705847	1	FACETS	1	0.96	1	1	0.988	1	CLONAL	2	TRUE	0	0.177871586705847	1		498	439	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460504	8460504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148300682	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	75	471	1	ENST00000356435.5:c.3782C>T	p.Thr1261Met	p.T1261M	ENST00000356435		1261	aCg/aTg	22/35	1	2	FACETS	0.873	0.767	0.986	1	0.98	1	CLONAL	2	TRUE	1	0.177871586705847	2		472	483	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	19	448	0	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	0.177871586705847	1	FACETS	0.564	0.428	0.725	0.564	0.428	0.725	SUBCLONAL	1	TRUE	0	0.177871586705847	1		448	345	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023769	27023769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	69	534	1	ENST00000324856.7:c.879del	p.Thr294ProfsTer69	p.T294Pfs*69	ENST00000324856	NM_006015.4	292	aCc/ac	1/20	1	2	FACETS	0.793	0.692	0.902	1	0.976	1	CLONAL	2	TRUE	1	0.177871586705847	2		535	489	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097621	27097622	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	76	474	0	ENST00000324856.7:c.3216dup	p.Trp1073MetfsTer32	p.W1073Mfs*32	ENST00000324856	NM_006015.4	1070	-/A	12/20	1	2	FACETS	0.811	0.713	0.916	1	0.978	1	CLONAL	2	TRUE	1	0.177871586705847	2		474	527	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459187	120459187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	97	553	0	ENST00000256646.2:c.6158G>A	p.Arg2053His	p.R2053H	ENST00000256646	NM_024408.3	2053	cGc/cAc	34/34	1	2	FACETS	0.986	0.882	1	1	0.986	1	CLONAL	2	TRUE	1	0.177871586705847	2		553	553	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981161	201981163	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	100	492	0	ENST00000359651.3:c.241_243del	p.Glu81del	p.E81del	ENST00000359651		80	gtGGAg/gtg	2/8	1	2	FACETS	1	0.965	1	1	0.989	1	CLONAL	2	TRUE	1	0.177871586705847	2		492	478	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620366	43620366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758191409	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	43	481	2	ENST00000355710.3:c.2975C>T	p.Pro992Leu	p.P992L	ENST00000355710	NM_020975.4	992	cCg/cTg	18/20	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.177871586705847	2		483	439	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10781744	10781744	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	60	382	0	ENST00000361367.2:c.617A>G	p.His206Arg	p.H206R	ENST00000361367	NM_014633.3	206	cAt/cGt	6/25	1	2	FACETS	0.817	0.706	0.936	1	0.973	1	CLONAL	2	TRUE	1	0.177871586705847	2		382	413	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392805	118392805	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	65	518	0	ENST00000534358.1:c.11837A>G	p.Asp3946Gly	p.D3946G	ENST00000534358	NM_005933.3	3946	gAc/gGc	36/36	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.177871586705847	2		518	494	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	38	357	2	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.177871586705847	2		359	320	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428387	49428387	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	68	544	0	ENST00000301067.7:c.10418A>G	p.His3473Arg	p.H3473R	ENST00000301067	NM_003482.3	3473	cAt/cGt	36/54	0.161957713413181	4	FACETS	0.948	0.827	1	0.948	0.827	1	CLONAL	2	TRUE	2	0.177871586705847	4		544	475	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50769161	50769161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148200969	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	51	389	0	ENST00000307179.4:c.965G>A	p.Arg322Gln	p.R322Q	ENST00000307179		322	cGa/cAa	9/20	1	2	FACETS	0.907	0.776	1	1	0.973	1	CLONAL	2	TRUE	1	0.177871586705847	2		389	316	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347982	347983	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760961378	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	79	613	0	ENST00000262320.3:c.1523dup	p.Ala509CysfsTer82	p.A509Cfs*82	ENST00000262320	NM_003502.3	508	ggt/ggGt	6/11	1	2	FACETS	1	0.943	1	1	0.985	1	CLONAL	2	TRUE	1	0.177871586705847	2		613	400	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223314	2223314	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	48	570	0	ENST00000326181.6:c.926A>G	p.Asp309Gly	p.D309G	ENST00000326181	NM_032271.2	309	gAc/gGc	10/21	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.177871586705847	2		570	416	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642772	3642772	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	58	462	0	ENST00000294008.3:c.2255T>C	p.Leu752Pro	p.L752P	ENST00000294008	NM_032444.2	752	cTg/cCg	11/15	1	2	FACETS	0.764	0.658	0.878	1	0.969	1	SUBCLONAL	2	TRUE	1	0.177871586705847	2		462	427	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830604	72830604	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	62	551	1	ENST00000268489.5:c.5977del	p.Ser1993ProfsTer4	p.S1993Pfs*4	ENST00000268489	NM_006885.3	1993	Tcc/cc	9/10	1	2	FACETS	0.996	0.865	1	1	0.979	1	CLONAL	2	TRUE	1	0.177871586705847	2		552	350	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024505	16024505	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	69	386	0	ENST00000268712.3:c.1713del	p.Arg572GlufsTer18	p.R572Efs*18	ENST00000268712	NM_006311.3	571	ggG/gg	16/46	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.177871586705847	2		386	604	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439919	56439919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	112	498	0	ENST00000407977.2:c.673del	p.Arg225AlafsTer194	p.R225Afs*194	ENST00000407977		225	Cgc/gc	6/10	1	2	FACETS	1	0.942	1	1	0.989	1	CLONAL	2	TRUE	1	0.177871586705847	2		498	593	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58701017	58701017	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	54	482	0	ENST00000305921.3:c.608C>A	p.Pro203Gln	p.P203Q	ENST00000305921	NM_003620.3	203	cCg/cAg	2/6	1	2	FACETS	0.821	0.704	0.947	1	0.971	1	CLONAL	2	TRUE	1	0.177871586705847	2		482	370	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533905	63533905	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	114	536	0	ENST00000307078.5:c.1249del	p.Ala417ArgfsTer41	p.A417Rfs*41	ENST00000307078	NM_004655.3	417	Gcg/cg	6/11	1	2	FACETS	0.913	0.827	1	1	0.991	1	CLONAL	3	TRUE	1	0.177871586705847	2		536	468	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533939	63533942	+	frameshift_variant	Frame_Shift_Del	DEL	CTCT	CTCT	-	rs771001164	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	65	407	0	ENST00000307078.5:c.1212_1215del	p.Glu405AlafsTer52	p.E405Afs*52	ENST00000307078	NM_004655.3	404	agAGAG/ag	6/11	1	2	FACETS	0.947	0.825	1	1	0.979	1	CLONAL	2	TRUE	1	0.177871586705847	2		407	386	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222128	2222128	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs748754858	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	57	568	0	ENST00000398665.3:c.2960A>G	p.His987Arg	p.H987R	ENST00000398665	NM_032482.2	987	cAc/cGc	24/28	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.177871586705847	2		568	450	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231557	5231557	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150939732	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	66	420	0	ENST00000357368.4:c.1919G>A	p.Arg640His	p.R640H	ENST00000357368	NM_002850.3	640	cGc/cAc	14/38	1	2	FACETS	1	0.92	1	1	0.982	1	CLONAL	2	TRUE	1	0.177871586705847	2		420	346	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250885	10250885	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	44	487	0	ENST00000340748.4:c.3595A>G	p.Met1199Val	p.M1199V	ENST00000340748		1199	Atg/Gtg	32/40	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.177871586705847	2		487	387	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383640	15383640	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	54	417	0	ENST00000263377.2:c.271A>G	p.Lys91Glu	p.K91E	ENST00000263377	NM_058243.2	91	Aag/Gag	2/20	1	2	FACETS	0.901	0.773	1	1	0.974	1	CLONAL	2	TRUE	1	0.177871586705847	2		417	337	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211448	36211448	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	53	629	0	ENST00000222270.7:c.1199A>G	p.Lys400Arg	p.K400R	ENST00000222270	NM_014727.1	400	aAg/aGg	3/37	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.177871586705847	2		629	484	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794441	42794441	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	71	604	0	ENST00000575354.2:c.1526del	p.Pro509HisfsTer14	p.P509Hfs*14	ENST00000575354	NM_015125.3	507	cgC/cg	10/20	1	2	FACETS	0.911	0.798	1	1	0.98	1	CLONAL	2	TRUE	1	0.177871586705847	2		604	438	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795269	42795269	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs34000070	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	64	542	0	ENST00000575354.2:c.2353del	p.Ala785ProfsTer139	p.A785Pfs*139	ENST00000575354	NM_015125.3	783	caG/ca	10/20	1	2	FACETS	1	0.948	1	1	0.983	1	CLONAL	2	TRUE	1	0.177871586705847	2		542	307	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523009	25523009	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	36	432	4	ENST00000264709.3:c.176del	p.Pro59ArgfsTer13	p.P59Rfs*13	ENST00000264709	NM_175629.2	59	cCg/cg	3/23	1	2	FACETS	0.926	0.762	1	0.926	0.762	1	CLONAL	1	TRUE	1	0.177871586705847	2		436	437	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143048	30143048	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	50	636	0	ENST00000389048.3:c.478del	p.Glu160ArgfsTer26	p.E160Rfs*26	ENST00000389048	NM_004304.4	160	Gag/ag	1/29	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.177871586705847	2		636	457	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426752	212426752	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	66	499	0	ENST00000342788.4:c.2363T>G	p.Leu788Arg	p.L788R	ENST00000342788	NM_005235.2	788	cTg/cGg	20/28	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.177871586705847	2		499	521	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663330	227663330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	81	437	0	ENST00000305123.5:c.125C>T	p.Ala42Val	p.A42V	ENST00000305123	NM_005544.2	42	gCg/gTg	1/2	1	2	FACETS	1	0.949	1	1	0.986	1	CLONAL	2	TRUE	1	0.177871586705847	2		437	404	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713414	40713414	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	53	583	0	ENST00000373198.4:c.4101del	p.Ser1368ProfsTer31	p.S1368Pfs*31	ENST00000373198	NM_133170.3	1367	ccC/cc	30/32	0.177871586705847	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.177871586705847	1		583	444	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279789	46279789	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs969825525	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	81	571	0	ENST00000371998.3:c.3715C>T	p.Arg1239Ter	p.R1239*	ENST00000371998		1239	Cga/Tga	20/23	0.177871586705847	1	FACETS	0.84	0.742	0.944	1	0.981	1	CLONAL	2	TRUE	0	0.177871586705847	1		571	494	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29383127	29383127	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	69	528	0	ENST00000544604.2:c.364G>T	p.Gly122Ter	p.G122*	ENST00000544604	NM_001206998.1	122	Gga/Tga	2/9	0.141420533522294	0	FACETS	0.862	0.755	0.976			1	CLONAL	2	TRUE	0	0.177871586705847	0		528	370	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536145	41536145	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1457616974	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	46	318	0	ENST00000263253.7:c.1762G>A	p.Val588Ile	p.V588I	ENST00000263253	NM_001429.3	588	Gtc/Atc	9/31	0.141420533522294	0	FACETS	1	0.947	1			1	CLONAL	1	TRUE	0	0.177871586705847	0		318	327	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035151	37035151	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	60	379	0	ENST00000231790.2:c.113A>T	p.Asn38Ile	p.N38I	ENST00000231790	NM_000249.3	38	aAc/aTc	1/19	1	2	FACETS	0.767	0.662	0.88	1	0.97	1	SUBCLONAL	2	TRUE	1	0.177871586705847	2		379	440	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528621	89528621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780470195	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	50	398	0	ENST00000336596.2:c.2921C>T	p.Thr974Met	p.T974M	ENST00000336596	NM_005233.5	974	aCg/aTg	17/17	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.177871586705847	2		398	402	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186817	142186817	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	32	329	0	ENST00000350721.4:c.6646A>G	p.Thr2216Ala	p.T2216A	ENST00000350721	NM_001184.3	2216	Act/Gct	39/47	1	2	FACETS	0.756	0.617	0.911	1	0.946	1	CLONAL	2	TRUE	1	0.177871586705847	2		329	238	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	34	444	0	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.177871586705847	2		444	343	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542144	187542144	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	57	612	0	ENST00000441802.2:c.5596A>G	p.Thr1866Ala	p.T1866A	ENST00000441802	NM_005245.3	1866	Aca/Gca	10/27	0.107751243181826	4	FACETS	1	0.897	1	1	0.897	1	CLONAL	2	TRUE	2	0.177871586705847	4		612	360	SUCCESS
APC	324	MSKCC	GRCh37	5	112179813	112179813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	63	474	0	ENST00000257430.4:c.8522C>T	p.Thr2841Ile	p.T2841I	ENST00000257430	NM_000038.5	2841	aCa/aTa	16/16	0.177871586705847	4	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	2	0.177871586705847	4		474	343	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721235	176721235	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	51	528	0	ENST00000439151.2:c.6866G>T	p.Arg2289Met	p.R2289M	ENST00000439151	NM_022455.4	2289	aGg/aTg	23/23	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.177871586705847	2		528	461	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323144	31323144	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	108	716	0	ENST00000412585.2:c.845del	p.Thr282AsnfsTer15	p.T282Nfs*15	ENST00000412585	NM_005514.6	282	aCa/aa	4/8	0.165193335207585	4	FACETS	0.999	0.897	1	0.999	0.897	1	CLONAL	2	TRUE	2	0.177871586705847	4		716	716	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168969	32168969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs567483221	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	68	594	0	ENST00000375023.3:c.4064G>A	p.Arg1355Gln	p.R1355Q	ENST00000375023	NM_004557.3	1355	cGg/cAg	22/30	0.165193335207585	4	FACETS	0.839	0.73	0.955	0.839	0.73	0.955	CLONAL	2	TRUE	2	0.177871586705847	4		594	537	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704479	117704479	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	34	359	0	ENST00000368508.3:c.2496+1G>A		p.X832_splice	ENST00000368508	NM_002944.2	832			1	2	FACETS	0.861	0.709	1	1	0.957	1	CLONAL	2	TRUE	1	0.177871586705847	2		359	222	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741861	145741862	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	202	545	0	ENST00000428558.2:c.641_642del	p.Ser214Ter	p.S214*	ENST00000428558	NM_004260.3	214	tCA/t	5/22	0.177871586705847	5	FACETS	0.933	0.87	0.997	1	0.983	1	CLONAL	5	TRUE	1	0.177871586705847	5		545	617	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2060867	2060867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	88	550	0	ENST00000349721.2:c.1573C>T	p.Arg525Cys	p.R525C	ENST00000349721	NM_003070.3	525	Cgt/Tgt	9/34	1	2	FACETS	1	0.923	1	1	0.986	1	CLONAL	2	TRUE	1	0.177871586705847	2		550	472	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15821896	15821896	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	36	408	0	ENST00000307771.7:c.294del	p.Lys98AsnfsTer10	p.K98Nfs*10	ENST00000307771	NM_005089.3	97	Aaa/aa	4/11	0.177871586705847	1	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	0	0.177871586705847	1		408	339	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045698	47045698	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	50	641	0	ENST00000377604.3:c.2579A>G	p.Asn860Ser	p.N860S	ENST00000377604	NM_001204468.1	860	aAc/aGc	23/24	0.177871586705847	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.177871586705847	1		641	377	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411864	63411864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767572122	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	54	639	1	ENST00000330258.3:c.1303G>A	p.Gly435Ser	p.G435S	ENST00000330258	NM_152424.3	435	Ggc/Agc	2/2	0.177871586705847	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.177871586705847	1		640	442	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224461	123224461	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	54	457	0	ENST00000218089.9:c.3314G>A	p.Ser1105Asn	p.S1105N	ENST00000218089	NM_001042749.1	1105	aGc/aAc	31/35	0.177871586705847	1	FACETS	0.931	0.801	1	1	0.975	1	CLONAL	2	TRUE	0	0.177871586705847	1		457	297	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324917	31324917	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	44	434	0	ENST00000412585.2:c.19del	p.Arg7GlufsTer13	p.R7Efs*13	ENST00000412585	NM_005514.6	7	Cga/ga	1/8	0.165193335207585	4	FACETS	1	0.914	1	0.571	0.479	0.674	CLONAL	1	TRUE	2	0.177871586705847	4		434	510	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660807	227660808	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs747646240	NA	P-0061498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	78	590	0	ENST00000305123.5:c.2645_2647dup	p.Gln882dup	p.Q882dup	ENST00000305123	NM_005544.2	882	ccc/cAGCcc	1/2	1	2	FACETS	0.797	0.702	0.9	1	0.978	1	SUBCLONAL	2	TRUE	1	0.177871586705847	2		590	550	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589575	67589576	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	9	385	0	ENST00000274335.5:c.1344dup	p.Leu449IlefsTer3	p.L449Ifs*3	ENST00000274335		446	-/A	10/15	1	2	FACETS	0.27	0.178	0.389	0.27	0.178	0.389	SUBCLONAL	1	TRUE	1	0.16	2		385	416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0061501-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	359	605	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	NA	2	FACETS	0.956	0.922	0.99			1	INDETERMINATE	2	TRUE	NA	0.710890095448911	2		605	528	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256192	133256192	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061501-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	45	432	0	ENST00000320574.5:c.469T>A	p.Phe157Ile	p.F157I	ENST00000320574	NM_006231.2	157	Ttc/Atc	6/49	0.324733344017969	2	FACETS	0.333	0.28	0.391	0.167	0.14	0.196	INDETERMINATE	1	TRUE	0	0.710890095448911	2		432	380	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745734	745734	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061501-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	15	466	0	ENST00000314574.4:c.698T>C	p.Leu233Pro	p.L233P	ENST00000314574	NM_005433.3	233	cTg/cCg	6/12	0.710890095448911	2	FACETS	0.227	0.166	0.299	0.113	0.083	0.15	SUBCLONAL	1	TRUE	0	0.710890095448911	2		466	186	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0061507-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	151	467	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.477795251693221	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.477795251693221	1		467	461	SUCCESS
APC	324	MSKCC	GRCh37	5	112157650	112157650	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1060503333	NA	P-0061507-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	35	380	0	ENST00000257430.4:c.1370C>A	p.Ser457Ter	p.S457*	ENST00000257430	NM_000038.5	457	tCa/tAa	11/16	1	2	FACETS	0.823	0.683	0.977	0.823	0.683	0.977	CLONAL	1	TRUE	1	0.477795251693221	2		380	178	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845374	76845374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061507-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	24	414	0	ENST00000373344.5:c.6147G>T	p.Leu2049Phe	p.L2049F	ENST00000373344	NM_000489.3	2049	ttG/ttT	27/35	1	2	FACETS	0.707	0.561	0.872	0.707	0.561	0.872	SUBCLONAL	1	TRUE	1	0.477795251693221	2		414	142	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912189	114912189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867720073	NA	P-0061507-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	134	428	0	ENST00000543371.1:c.1259G>A	p.Arg420Gln	p.R420Q	ENST00000543371	NM_001198531.1	420	cGg/cAg	11/14	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.477795251693221	2		428	486	SUCCESS
APC	324	MSKCC	GRCh37	5	112175168	112175169	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0061507-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	51	533	0	ENST00000257430.4:c.3880_3881del	p.Gln1294GlyfsTer6	p.Q1294Gfs*6	ENST00000257430	NM_000038.5	1293	ACa/a	16/16	1	2	FACETS	0.998	0.858	1	0.998	0.858	1	CLONAL	1	TRUE	1	0.477795251693221	2		533	214	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110664	2110676	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTTCCAGGCCATG	GTTCCAGGCCATG	CCAGCCCTGTGT	novel	NA	P-0061507-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	155	632	1	ENST00000219476.3:c.976-7_981delinsCCAGCCCTGTGT		p.X326_splice	ENST00000219476	NM_000548.3	326		11/42	0.477795251693221	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.477795251693221	1		633	460	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0061508-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	62	464	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.774	0.674	0.879	0.774	0.674	0.879	SUBCLONAL	1	TRUE	1	0.56642957446701	2		464	283	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844202	68844202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061508-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	151	600	0	ENST00000261769.5:c.790C>T	p.Gln264Ter	p.Q264*	ENST00000261769	NM_004360.3	264	Cag/Tag	6/16	0.56642957446701	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.56642957446701	1		600	365	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604499	43604499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061508-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	135	684	0	ENST00000355710.3:c.1084C>T	p.Leu362Phe	p.L362F	ENST00000355710	NM_020975.4	362	Ctc/Ttc	6/20	1	2	FACETS	0.816	0.745	0.891	0.816	0.745	0.891	CLONAL	1	TRUE	1	0.56642957446701	2		684	584	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518326	187518326	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0061508-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	130	533	0	ENST00000441802.2:c.12369-1G>T		p.X4123_splice	ENST00000441802	NM_005245.3	4123			1	2	FACETS	0.946	0.864	1	0.946	0.864	1	CLONAL	1	TRUE	1	0.56642957446701	2		533	485	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0061509-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	53	255	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.333861724213743	2		255	279	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050644	30050644	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0061509-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	88	459	0	ENST00000338641.4:c.448-2A>C		p.X150_splice	ENST00000338641	NM_000268.3	150			0.333861724213743	1	FACETS	0.911	0.81	1	0.911	0.81	1	CLONAL	1	TRUE	0	0.333861724213743	1		459	482	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0061510-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	104	350	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.987	0.895	1	0.987	0.895	1	CLONAL	1	TRUE	1	0.664849693306367	2		350	317	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0061510-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	184	726	0	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	1	2	FACETS	0.773	0.716	0.832	0.773	0.716	0.832	SUBCLONAL	1	TRUE	1	0.664849693306367	2		726	716	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0061510-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	37	464	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.752	0.63	0.883	0.752	0.63	0.883	SUBCLONAL	1	TRUE	1	0.664849693306367	2		464	148	SUCCESS
APC	324	MSKCC	GRCh37	5	112174266	112174267	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061510-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	112	566	0	ENST00000257430.4:c.2976dup	p.Lys993Ter	p.K993*	ENST00000257430	NM_000038.5	992	agt/agTt	16/16	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.664849693306367	2		566	337	SUCCESS
APC	324	MSKCC	GRCh37	5	112128142	112128142	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs78847145	NA	P-0061510-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	38	237	0	ENST00000257430.4:c.646-1G>T		p.X216_splice	ENST00000257430	NM_000038.5	216			1	2	FACETS	0.668	0.56	0.786	0.668	0.56	0.786	SUBCLONAL	1	TRUE	1	0.664849693306367	2		237	171	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105968	27105977	+	frameshift_variant	Frame_Shift_Del	DEL	AGAGCAAGAC	AGAGCAAGAC	-	novel	NA	P-0061510-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	453	705	0	ENST00000324856.7:c.5584_5593del	p.Lys1862CysfsTer18	p.K1862Cfs*18	ENST00000324856	NM_006015.4	1860	gAGAGCAAGACa/ga	20/20	0.657620483045906	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.664849693306367	2		705	665	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516864	187516864	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061510-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	36	532	0	ENST00000441802.2:c.13117T>C	p.Ser4373Pro	p.S4373P	ENST00000441802	NM_005245.3	4373	Tcc/Ccc	26/27	1	2	FACETS	0.183	0.15	0.221	0.183	0.15	0.221	SUBCLONAL	1	TRUE	1	0.664849693306367	2		532	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0061511-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	377	715	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.570053609810778	2	FACETS	0.971	0.931	1	0.971	0.931	1	CLONAL	2	TRUE	0	0.577835370188908	2		715	672	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039133	49039133	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs587776786	NA	P-0061511-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	98	164	0	ENST00000267163.4:c.2212-1G>A		p.X738_splice	ENST00000267163	NM_000321.2	738			0.57544921077383	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.577835370188908	2		164	153	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911254	29911254	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs41541015	NA	P-0061511-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	50	173	0	ENST00000376809.5:c.553G>T	p.Asp185Tyr	p.D185Y	ENST00000376809	NM_002116.7	185	Gat/Tat	3/8	0.561414426147186	1	FACETS	0.826	0.716	0.941	0.826	0.716	0.941	CLONAL	1	TRUE	0	0.577835370188908	1		173	149	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679718	88679718	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061511-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	120	453	0	ENST00000360948.2:c.745C>G	p.Gln249Glu	p.Q249E	ENST00000360948	NM_001012338.2	249	Cag/Gag	7/19	1	2	FACETS	0.827	0.751	0.907	0.827	0.751	0.907	CLONAL	1	TRUE	1	0.577835370188908	2		453	502	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828308	50828308	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061511-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	160	517	0	ENST00000398568.2:c.2646G>T	p.Trp882Cys	p.W882C	ENST00000398568	NM_001042412.1	882	tgG/tgT	17/18	0.577835370188908	1	FACETS	0.873	0.808	0.94	0.873	0.808	0.94	CLONAL	1	TRUE	0	0.577835370188908	1		517	451	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946338	2946339	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0061511-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	168	563	0	ENST00000396946.4:c.3398_3399delinsTT	p.Arg1133Leu	p.R1133L	ENST00000396946	NM_032415.4	1133	cGC/cTT	25/25	1	2	FACETS	0.922	0.851	0.995	0.922	0.851	0.995	CLONAL	1	TRUE	1	0.577835370188908	2		563	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0061512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	55	590	0	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.239093686284303	1	FACETS	0.856	0.734	0.99	0.856	0.734	0.99	CLONAL	1	TRUE	0	0.239093686284303	1		590	473	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526287	189526287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	85	794	0	ENST00000264731.3:c.551C>T	p.Ser184Leu	p.S184L	ENST00000264731	NM_003722.4	184	tCg/tTg	4/14	0.239093686284303	3	FACETS	0.807	0.712	0.91	0.404	0.356	0.455	CLONAL	1	TRUE	1	0.239093686284303	3		794	986	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278135	142278135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	23	415	0	ENST00000350721.4:c.1690G>A	p.Asp564Asn	p.D564N	ENST00000350721	NM_001184.3	564	Gat/Aat	7/47	0.239093686284303	3	FACETS	0.699	0.546	0.877	0.35	0.273	0.439	SUBCLONAL	1	TRUE	1	0.239093686284303	3		415	308	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771344	68771344	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	51	539	0	ENST00000261769.5:c.26C>G	p.Ser9Trp	p.S9W	ENST00000261769	NM_004360.3	9	tCg/tGg	1/16	0.239093686284303	1	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	0	0.239093686284303	1		539	363	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974695	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1554656253	NA	P-0061512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	82	842	0	ENST00000304494.5:c.132C>G	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	taC/taG	1/3	0.239093686284303	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.239093686284303	1		842	553	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324058	123324058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs938460066	NA	P-0061512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	60	471	0	ENST00000358487.5:c.412G>A	p.Asp138Asn	p.D138N	ENST00000358487	NM_000141.4	138	Gat/Aat	4/18	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.239093686284303	2		471	438	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324627	31324627	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs41561613	NA	P-0061512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	58	791	0	ENST00000412585.2:c.181G>C	p.Asp61His	p.D61H	ENST00000412585	NM_005514.6	61	Gac/Cac	2/8	0.239093686284303	1	FACETS	0.785	0.675	0.905	0.785	0.675	0.905	CLONAL	1	TRUE	0	0.239093686284303	1		791	544	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075565	8075565	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	61	571	0	ENST00000377482.5:c.115G>C	p.Glu39Gln	p.E39Q	ENST00000377482	NM_018948.3	39	Gag/Cag	2/4	0.239093686284303	3	FACETS	1	0.911	1	0.537	0.463	0.617	CLONAL	1	TRUE	1	0.239093686284303	3		571	532	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873041	136873041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	73	812	0	ENST00000241393.3:c.457G>A	p.Glu153Lys	p.E153K	ENST00000241393	NM_003467.2	153	Gaa/Aaa	2/2	1	2	FACETS	0.858	0.749	0.974	0.858	0.749	0.974	CLONAL	1	TRUE	1	0.239093686284303	2		812	712	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196062	67196062	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	50	492	0	ENST00000312629.5:c.46G>C	p.Glu16Gln	p.E16Q	ENST00000312629	NM_003952.2	16	Gag/Cag	1/15	1	2	FACETS	0.966	0.821	1	0.966	0.821	1	CLONAL	1	TRUE	1	0.239093686284303	2		492	433	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160338	108160338	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057516311	NA	P-0061512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	20	264	0	ENST00000278616.4:c.4246C>T	p.Gln1416Ter	p.Q1416*	ENST00000278616	NM_000051.3	1416	Cag/Tag	29/63	1	2	FACETS	0.99	0.762	1	0.99	0.762	1	CLONAL	1	TRUE	1	0.239093686284303	2		264	169	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417059	417059	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	90	704	0	ENST00000399788.2:c.3491G>C	p.Cys1164Ser	p.C1164S	ENST00000399788	NM_001042603.1	1164	tGc/tCc	23/28	0.234548957498235	3	FACETS	1	0.903	1	0.51	0.452	0.573	CLONAL	1	TRUE	1	0.239093686284303	3		704	826	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003184	42003184	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	53	621	0	ENST00000219905.7:c.2721C>G	p.Phe907Leu	p.F907L	ENST00000219905	NM_001164273.1	907	ttC/ttG	8/24	1	2	FACETS	0.866	0.739	1	0.866	0.739	1	CLONAL	1	TRUE	1	0.239093686284303	2		621	512	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845405	89845405	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	76	719	0	ENST00000389301.3:c.1722C>G	p.Phe574Leu	p.F574L	ENST00000389301	NM_000135.2	574	ttC/ttG	19/43	0.239093686284303	1	FACETS	0.924	0.811	1	0.924	0.811	1	CLONAL	1	TRUE	0	0.239093686284303	1		719	606	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858936	89858936	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	81	510	0	ENST00000389301.3:c.1026G>T	p.Met342Ile	p.M342I	ENST00000389301	NM_000135.2	342	atG/atT	12/43	0.239093686284303	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.239093686284303	1		510	566	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872963	136872963	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	85	727	0	ENST00000241393.3:c.535G>C	p.Glu179Gln	p.E179Q	ENST00000241393	NM_003467.2	179	Gag/Cag	2/2	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.239093686284303	2		727	671	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735657	204735657	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0061512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	45	576	0	ENST00000302823.3:c.457+1G>T		p.X153_splice	ENST00000302823	NM_005214.4	153			1	2	FACETS	0.751	0.631	0.884	0.751	0.631	0.884	SUBCLONAL	1	TRUE	1	0.239093686284303	2		576	501	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503774	186503774	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	57	521	0	ENST00000323963.5:c.451G>A	p.Glu151Lys	p.E151K	ENST00000323963		151	Gaa/Aaa	5/11	0.239093686284303	3	FACETS	0.905	0.776	1	0.452	0.388	0.523	CLONAL	1	TRUE	1	0.239093686284303	3		521	590	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324621	31324621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41563012	NA	P-0061512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	65	811	0	ENST00000412585.2:c.187G>A	p.Asp63Asn	p.D63N	ENST00000412585	NM_005514.6	63	Gac/Aac	2/8	0.239093686284303	1	FACETS	0.849	0.736	0.971	0.849	0.736	0.971	CLONAL	1	TRUE	0	0.239093686284303	1		811	564	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339865	116339865	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	106	601	0	ENST00000397752.3:c.727G>C	p.Asp243His	p.D243H	ENST00000397752	NM_000245.2	243	Gat/Cat	2/21	0.239093686284303	5	FACETS	1	0.953	1	0.551	0.495	0.609	CLONAL	2	TRUE	1	0.239093686284303	5		601	547	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874314	151874314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	32	519	0	ENST00000262189.6:c.8224G>A	p.Asp2742Asn	p.D2742N	ENST00000262189	NM_170606.2	2742	Gat/Aat	38/59	0.239093686284303	1	FACETS	0.783	0.637	0.946	0.783	0.637	0.946	CLONAL	1	TRUE	0	0.239093686284303	1		519	301	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229547	98229547	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	55	598	0	ENST00000331920.6:c.2411A>C	p.Tyr804Ser	p.Y804S	ENST00000331920	NM_000264.3	804	tAt/tCt	15/24	0.239093686284303	2	FACETS	0.911	0.78	1	0.456	0.39	0.527	CLONAL	1	TRUE	0	0.239093686284303	2		598	505	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039359	47039359	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	96	872	0	ENST00000377604.3:c.982T>A	p.Ser328Thr	p.S328T	ENST00000377604	NM_001204468.1	328	Tcc/Acc	10/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.239093686284303	2		872	661	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342424	70342424	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	60	627	0	ENST00000374080.3:c.1315T>A	p.Trp439Arg	p.W439R	ENST00000374080		439	Tgg/Agg	9/45	1	2	FACETS	0.82	0.706	0.944	0.82	0.706	0.944	CLONAL	1	TRUE	1	0.239093686284303	2		627	612	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504151	123504151	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	25	402	0	ENST00000371139.4:c.327A>C	p.Arg109Ser	p.R109S	ENST00000371139	NM_001114937.2	109	agA/agC	3/4	0.239093686284303	1	FACETS	0.745	0.59	0.923	0.745	0.59	0.923	CLONAL	1	TRUE	0	0.239093686284303	1		402	247	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31237842	31237842	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs774464615	NA	P-0061513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	204	591	0	ENST00000376228.5:c.916A>G	p.Ile306Val	p.I306V	ENST00000376228	NM_002117.5	306	Atc/Gtc	5/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.530243613351641	2		591	704	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	22	569	0	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	1	2	FACETS	0.125	0.096	0.158	0.125	0.096	0.158	SUBCLONAL	1	TRUE	1	0.529686277907623	2		569	667	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	11	400	0	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	0.089	0.061	0.124	0.089	0.061	0.124	SUBCLONAL	1	TRUE	1	0.529686277907623	2		400	467	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105688	27105688	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	48	584	0	ENST00000324856.7:c.5299G>T	p.Glu1767Ter	p.E1767*	ENST00000324856	NM_006015.4	1767	Gaa/Taa	20/20	1	2	FACETS	0.28	0.236	0.329	0.28	0.236	0.329	SUBCLONAL	1	TRUE	1	0.529686277907623	2		584	647	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573894	18573894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759658584	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	18	321	0	ENST00000266497.5:c.2212C>T	p.Arg738Cys	p.R738C	ENST00000266497		738	Cgt/Tgt	15/31	1	2	FACETS	0.241	0.181	0.312	0.241	0.181	0.312	SUBCLONAL	1	TRUE	1	0.529686277907623	2		321	282	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	88	426	0	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	1	2	FACETS	0.585	0.519	0.655	0.585	0.519	0.655	SUBCLONAL	1	TRUE	1	0.529686277907623	2		426	568	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	114	405	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.529686277907623	2		405	375	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	32	435	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.246	0.199	0.299	0.246	0.199	0.299	SUBCLONAL	1	TRUE	1	0.529686277907623	2		435	491	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930610	32930610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358973	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	36	409	0	ENST00000380152.3:c.7481G>A	p.Arg2494Gln	p.R2494Q	ENST00000380152		2494	cGa/cAa	15/27	1	2	FACETS	0.249	0.204	0.299	0.249	0.204	0.299	SUBCLONAL	1	TRUE	1	0.529686277907623	2		409	547	SUCCESS
MAD2L2	10459	MSKCC	GRCh37	1	11735743	11735743	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760862974	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	45	607	2	ENST00000235310.3:c.473G>A	p.Arg158His	p.R158H	ENST00000235310		158	cGc/cAc	9/11	1	2	FACETS	0.25	0.209	0.295	0.25	0.209	0.295	SUBCLONAL	1	TRUE	1	0.529686277907623	2		609	680	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255797	16255797	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs778318005	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	37	598	1	ENST00000375759.3:c.3062A>G	p.Asp1021Gly	p.D1021G	ENST00000375759	NM_015001.2	1021	gAc/gGc	11/15	1	2	FACETS	0.192	0.158	0.231	0.192	0.158	0.231	SUBCLONAL	1	TRUE	1	0.529686277907623	2		599	727	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094291	27094291	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	32	442	0	ENST00000324856.7:c.2999C>A	p.Ser1000Tyr	p.S1000Y	ENST00000324856	NM_006015.4	1000	tCt/tAt	11/20	1	2	FACETS	0.221	0.179	0.269	0.221	0.179	0.269	SUBCLONAL	1	TRUE	1	0.529686277907623	2		442	547	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106316	27106316	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	39	592	0	ENST00000324856.7:c.5927C>A	p.Ser1976Tyr	p.S1976Y	ENST00000324856	NM_006015.4	1976	tCt/tAt	20/20	1	2	FACETS	0.203	0.168	0.243	0.203	0.168	0.243	SUBCLONAL	1	TRUE	1	0.529686277907623	2		592	724	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	151	588	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.79	0.723	0.859	0.79	0.723	0.859	SUBCLONAL	1	TRUE	1	0.529686277907623	2		588	722	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937198	36937198	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	56	651	0	ENST00000361632.4:c.1121C>A	p.Ser374Tyr	p.S374Y	ENST00000361632		374	tCt/tAt	9/16	1	2	FACETS	0.287	0.245	0.333	0.287	0.245	0.333	SUBCLONAL	1	TRUE	1	0.529686277907623	2		651	737	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366821	40366821	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	38	757	0	ENST00000397332.2:c.376T>C	p.Trp126Arg	p.W126R	ENST00000397332	NM_001033082.2	126	Tgg/Cgg	2/3	1	2	FACETS	0.191	0.157	0.229	0.191	0.157	0.229	SUBCLONAL	1	TRUE	1	0.529686277907623	2		757	753	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46724371	46724371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745591449	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	46	392	0	ENST00000371975.4:c.224G>A	p.Arg75Gln	p.R75Q	ENST00000371975	NM_003579.3	75	cGa/cAa	4/18	1	2	FACETS	0.39	0.329	0.458	0.39	0.329	0.458	SUBCLONAL	1	TRUE	1	0.529686277907623	2		392	445	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733451	85733451	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	35	545	0	ENST00000370580.1:c.561C>A	p.Phe187Leu	p.F187L	ENST00000370580	NM_003921.4	187	ttC/ttA	3/3	1	2	FACETS	0.221	0.18	0.266	0.221	0.18	0.266	SUBCLONAL	1	TRUE	1	0.529686277907623	2		545	599	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733537	85733537	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	38	485	0	ENST00000370580.1:c.475G>A	p.Glu159Lys	p.E159K	ENST00000370580	NM_003921.4	159	Gaa/Aaa	3/3	1	2	FACETS	0.258	0.213	0.309	0.258	0.213	0.309	SUBCLONAL	1	TRUE	1	0.529686277907623	2		485	556	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462186	120462186	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1364033989	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	50	577	0	ENST00000256646.2:c.5530T>G	p.Leu1844Val	p.L1844V	ENST00000256646	NM_024408.3	1844	Ttg/Gtg	31/34	1	2	FACETS	0.281	0.237	0.328	0.281	0.237	0.328	SUBCLONAL	1	TRUE	1	0.529686277907623	2		577	673	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150935124	150935124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147846533	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	31	458	0	ENST00000271640.5:c.3220C>T	p.Arg1074Cys	p.R1074C	ENST00000271640	NM_001145415.1	1074	Cgc/Tgc	18/22	1	2	FACETS	0.217	0.175	0.265	0.217	0.175	0.265	SUBCLONAL	1	TRUE	1	0.529686277907623	2		458	540	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843644	156843644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	56	812	0	ENST00000524377.1:c.1070G>A	p.Gly357Asp	p.G357D	ENST00000524377	NM_002529.3	357	gGc/gAc	8/17	1	2	FACETS	0.232	0.198	0.27	0.232	0.198	0.27	SUBCLONAL	1	TRUE	1	0.529686277907623	2		812	910	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846230	156846230	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	43	627	0	ENST00000524377.1:c.1671C>A	p.Phe557Leu	p.F557L	ENST00000524377	NM_002529.3	557	ttC/ttA	14/17	1	2	FACETS	0.24	0.2	0.285	0.24	0.2	0.285	SUBCLONAL	1	TRUE	1	0.529686277907623	2		627	676	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111168	193111168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1452051467	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	142	482	1	ENST00000367435.3:c.701G>A	p.Arg234Gln	p.R234Q	ENST00000367435	NM_024529.4	234	cGa/cAa	7/17	1	2	FACETS	0.959	0.878	1	0.959	0.878	1	CLONAL	1	TRUE	1	0.529686277907623	2		483	559	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193116996	193116996	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	16	196	0	ENST00000367435.3:c.730-1G>T		p.X244_splice	ENST00000367435	NM_024529.4	244			1	2	FACETS	0.215	0.158	0.282	0.215	0.158	0.282	SUBCLONAL	1	TRUE	1	0.529686277907623	2		196	281	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193172924	193172924	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	78	361	0	ENST00000367435.3:c.973-1G>T		p.X325_splice	ENST00000367435	NM_024529.4	325			1	2	FACETS	0.679	0.599	0.764	0.679	0.599	0.764	SUBCLONAL	1	TRUE	1	0.529686277907623	2		361	434	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567747	226567747	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	42	611	0	ENST00000366794.5:c.1419C>A	p.Phe473Leu	p.F473L	ENST00000366794	NM_001618.3	473	ttC/ttA	10/23	1	2	FACETS	0.241	0.2	0.286	0.241	0.2	0.286	SUBCLONAL	1	TRUE	1	0.529686277907623	2		611	659	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231488782	231488782	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	32	406	0	ENST00000295050.7:c.1145C>A	p.Ser382Tyr	p.S382Y	ENST00000295050	NM_032018.5	382	tCt/tAt	5/5	1	2	FACETS	0.23	0.186	0.28	0.23	0.186	0.28	SUBCLONAL	1	TRUE	1	0.529686277907623	2		406	525	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246078896	246078896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs987211168	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	52	499	0	ENST00000388985.4:c.749G>A	p.Arg250Gln	p.R250Q	ENST00000388985		250	cGg/cAg	8/12	1	2	FACETS	0.336	0.286	0.392	0.336	0.286	0.392	SUBCLONAL	1	TRUE	1	0.529686277907623	2		499	584	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850704	63850705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	315	475	1	ENST00000279873.7:c.1489dup	p.Ile497AsnfsTer31	p.I497Nfs*31	ENST00000279873	NM_032199.2	494	-/A	10/10	0.529686277907623	2	FACETS	0.942	0.898	0.987	0.942	0.898	0.987	CLONAL	2	TRUE	0	0.529686277907623	2		476	631	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851560	63851560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	35	585	0	ENST00000279873.7:c.2338C>T	p.Arg780Ter	p.R780*	ENST00000279873	NM_032199.2	780	Cga/Tga	10/10	0.529686277907623	2	FACETS	0.201	0.164	0.243	0.101	0.082	0.122	SUBCLONAL	1	TRUE	0	0.529686277907623	2		585	657	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332109	70332109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777837034	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	28	393	1	ENST00000373644.4:c.14G>A	p.Arg5His	p.R5H	ENST00000373644	NM_030625.2	5	cGc/cAc	2/12	0.529686277907623	2	FACETS	0.218	0.174	0.269	0.109	0.087	0.135	SUBCLONAL	1	TRUE	0	0.529686277907623	2		394	485	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406048	70406048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199726871	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	45	442	0	ENST00000373644.4:c.3562G>A	p.Asp1188Asn	p.D1188N	ENST00000373644	NM_030625.2	1188	Gac/Aac	4/12	0.529686277907623	2	FACETS	0.291	0.244	0.343	0.145	0.122	0.172	SUBCLONAL	1	TRUE	0	0.529686277907623	2		442	584	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653803	89653803	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	100	249	0	ENST00000371953.3:c.101C>A	p.Ala34Asp	p.A34D	ENST00000371953	NM_000314.4	34	gCt/gAt	2/9	0.529686277907623	2	FACETS	0.874	0.799	0.95	0.874	0.799	0.95	CLONAL	2	TRUE	0	0.529686277907623	2		249	216	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104386990	104386990	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	32	413	0	ENST00000369902.3:c.1355C>A	p.Ser452Tyr	p.S452Y	ENST00000369902	NM_016169.3	452	tCt/tAt	11/12	0.529686277907623	2	FACETS	0.231	0.187	0.281	0.116	0.093	0.141	SUBCLONAL	1	TRUE	0	0.529686277907623	2		413	523	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910883	114910883	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1477809102	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	40	465	0	ENST00000543371.1:c.1001+1G>A		p.X334_splice	ENST00000543371	NM_001198531.1	334			0.529686277907623	2	FACETS	0.253	0.209	0.301	0.126	0.104	0.151	SUBCLONAL	1	TRUE	0	0.529686277907623	2		465	598	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925316	114925316	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	32	395	0	ENST00000543371.1:c.1394G>T	p.Arg465Ile	p.R465I	ENST00000543371	NM_001198531.1	465	aGa/aTa	14/14	0.529686277907623	2	FACETS	0.238	0.192	0.289	0.119	0.096	0.145	SUBCLONAL	1	TRUE	0	0.529686277907623	2		395	508	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47597180	47597180	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	31	428	0	ENST00000430070.2:c.709G>T	p.Glu237Ter	p.E237*	ENST00000430070	NM_018095.4	237	Gag/Tag	3/4	1	2	FACETS	0.218	0.175	0.266	0.218	0.175	0.266	SUBCLONAL	1	TRUE	1	0.529686277907623	2		428	538	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57004108	57004108	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	45	669	0	ENST00000257254.3:c.371G>A	p.Ser124Asn	p.S124N	ENST00000257254		124	aGc/aAc	1/2	1	2	FACETS	0.24	0.201	0.283	0.24	0.201	0.283	SUBCLONAL	1	TRUE	1	0.529686277907623	2		669	709	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577558	64577558	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	34	528	0	ENST00000312049.6:c.24G>T	p.Lys8Asn	p.K8N	ENST00000312049	NM_130799.2	8	aaG/aaT	2/10	1	2	FACETS	0.248	0.202	0.3	0.248	0.202	0.3	SUBCLONAL	1	TRUE	1	0.529686277907623	2		528	518	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948179	71948179	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	37	641	0	ENST00000298229.2:c.2891A>T	p.Glu964Val	p.E964V	ENST00000298229	NM_001567.3	964	gAg/gTg	26/28	1	2	FACETS	0.215	0.176	0.258	0.215	0.176	0.258	SUBCLONAL	1	TRUE	1	0.529686277907623	2		641	650	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204753	94204753	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1160887570	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	19	370	0	ENST00000323929.3:c.832G>T	p.Glu278Ter	p.E278*	ENST00000323929	NM_005591.3	278	Gaa/Taa	8/20	1	2	FACETS	0.21	0.159	0.27	0.21	0.159	0.27	SUBCLONAL	1	TRUE	1	0.529686277907623	2		370	342	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94211920	94211920	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	21	348	0	ENST00000323929.3:c.525G>T	p.Lys175Asn	p.K175N	ENST00000323929	NM_005591.3	175	aaG/aaT	6/20	1	2	FACETS	0.21	0.161	0.267	0.21	0.161	0.267	SUBCLONAL	1	TRUE	1	0.529686277907623	2		348	377	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195697	102195697	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	34	531	0	ENST00000263464.3:c.457G>T	p.Asp153Tyr	p.D153Y	ENST00000263464	NM_001165.4	153	Gat/Tat	2/9	1	2	FACETS	0.192	0.156	0.232	0.192	0.156	0.232	SUBCLONAL	1	TRUE	1	0.529686277907623	2		531	670	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117732	108117732	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	30	287	0	ENST00000278616.4:c.943T>G	p.Leu315Val	p.L315V	ENST00000278616	NM_000051.3	315	Tta/Gta	8/63	1	2	FACETS	0.331	0.267	0.404	0.331	0.267	0.404	SUBCLONAL	1	TRUE	1	0.529686277907623	2		287	342	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416675	416675	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	47	496	0	ENST00000399788.2:c.3875C>A	p.Thr1292Asn	p.T1292N	ENST00000399788	NM_001042603.1	1292	aCt/aAt	23/28	1	2	FACETS	0.277	0.233	0.326	0.277	0.233	0.326	SUBCLONAL	1	TRUE	1	0.529686277907623	2		496	640	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427551	427551	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	101	528	0	ENST00000399788.2:c.2618A>C	p.Lys873Thr	p.K873T	ENST00000399788	NM_001042603.1	873	aAa/aCa	19/28	1	2	FACETS	0.581	0.52	0.646	0.581	0.52	0.646	SUBCLONAL	1	TRUE	1	0.529686277907623	2		528	656	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	443516	443516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	63	469	0	ENST00000399788.2:c.1381G>A	p.Val461Met	p.V461M	ENST00000399788	NM_001042603.1	461	Gtg/Atg	11/28	1	2	FACETS	0.46	0.398	0.527	0.46	0.398	0.527	SUBCLONAL	1	TRUE	1	0.529686277907623	2		469	517	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644417	18644417	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	27	336	0	ENST00000266497.5:c.2595A>T	p.Glu865Asp	p.E865D	ENST00000266497		865	gaA/gaT	18/31	1	2	FACETS	0.255	0.202	0.315	0.255	0.202	0.315	SUBCLONAL	1	TRUE	1	0.529686277907623	2		336	400	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25362815	25362815	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	15	287	0	ENST00000311936.3:c.481C>T	p.Arg161Ter	p.R161*	ENST00000311936	NM_004985.3	161	Cga/Tga	5/5	1	2	FACETS	0.218	0.159	0.289	0.218	0.159	0.289	SUBCLONAL	1	TRUE	1	0.529686277907623	2		287	260	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398237	25398237	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	23	300	0	ENST00000311936.3:c.82T>G	p.Phe28Val	p.F28V	ENST00000311936	NM_004985.3	28	Ttt/Gtt	2/5	1	2	FACETS	0.247	0.192	0.311	0.247	0.192	0.311	SUBCLONAL	1	TRUE	1	0.529686277907623	2		300	351	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424810	49424810	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	47	612	0	ENST00000301067.7:c.13537G>T	p.Ala4513Ser	p.A4513S	ENST00000301067	NM_003482.3	4513	Gca/Tca	40/54	1	2	FACETS	0.251	0.211	0.296	0.251	0.211	0.296	SUBCLONAL	1	TRUE	1	0.529686277907623	2		612	706	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487277	56487277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035001455	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	147	541	0	ENST00000267101.3:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000267101	NM_001982.3	475	Cgg/Tgg	12/28	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.529686277907623	2		541	545	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487629	56487629	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779911233	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	51	570	0	ENST00000267101.3:c.1562G>A	p.Arg521Gln	p.R521Q	ENST00000267101	NM_001982.3	521	cGa/cAa	13/28	1	2	FACETS	0.295	0.25	0.345	0.295	0.25	0.345	SUBCLONAL	1	TRUE	1	0.529686277907623	2		570	652	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864115	57864115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147758271	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	41	633	1	ENST00000228682.2:c.1592G>A	p.Arg531His	p.R531H	ENST00000228682	NM_005269.2	531	cGc/cAc	12/12	1	2	FACETS	0.224	0.186	0.267	0.224	0.186	0.267	SUBCLONAL	1	TRUE	1	0.529686277907623	2		634	690	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112939961	112939961	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	37	349	0	ENST00000351677.2:c.1613A>C	p.Lys538Thr	p.K538T	ENST00000351677	NM_002834.3	538	aAa/aCa	14/16	1	2	FACETS	0.311	0.256	0.373	0.311	0.256	0.373	SUBCLONAL	1	TRUE	1	0.529686277907623	2		349	449	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114228	115114228	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	42	450	0	ENST00000257566.3:c.989A>C	p.Lys330Thr	p.K330T	ENST00000257566	NM_016569.3	330	aAa/aCa	6/8	1	2	FACETS	0.276	0.23	0.328	0.276	0.23	0.328	SUBCLONAL	1	TRUE	1	0.529686277907623	2		450	574	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118949	115118949	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	28	421	0	ENST00000257566.3:c.392G>A	p.Arg131Gln	p.R131Q	ENST00000257566	NM_016569.3	131	cGa/cAa	2/8	1	2	FACETS	0.228	0.182	0.281	0.228	0.182	0.281	SUBCLONAL	1	TRUE	1	0.529686277907623	2		421	463	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123888144	123888144	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	75	419	0	ENST00000330479.4:c.622G>T	p.Glu208Ter	p.E208*	ENST00000330479	NM_020382.3	208	Gaa/Taa	6/9	1	2	FACETS	0.525	0.461	0.594	0.525	0.461	0.594	SUBCLONAL	1	TRUE	1	0.529686277907623	2		419	539	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215787	133215787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762000608	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	32	482	0	ENST00000320574.5:c.5476C>T	p.Arg1826Trp	p.R1826W	ENST00000320574	NM_006231.2	1826	Cgg/Tgg	40/49	1	2	FACETS	0.218	0.176	0.265	0.218	0.176	0.265	SUBCLONAL	1	TRUE	1	0.529686277907623	2		482	554	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249857	133249857	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1565972665	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	153	456	0	ENST00000320574.5:c.1366G>C	p.Ala456Pro	p.A456P	ENST00000320574	NM_006231.2	456	Gcc/Ccc	14/49	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.529686277907623	2		456	533	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609752	28609752	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	33	515	1	ENST00000241453.7:c.1477G>T	p.Gly493Ter	p.G493*	ENST00000241453	NM_004119.2	493	Gga/Tga	12/24	1	2	FACETS	0.203	0.165	0.247	0.203	0.165	0.247	SUBCLONAL	1	TRUE	1	0.529686277907623	2		516	613	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900651	32900651	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	39	344	0	ENST00000380152.3:c.532A>C	p.Lys178Gln	p.K178Q	ENST00000380152		178	Aaa/Caa	7/27	1	2	FACETS	0.328	0.272	0.391	0.328	0.272	0.391	SUBCLONAL	1	TRUE	1	0.529686277907623	2		344	449	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910522	32910522	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	23	313	0	ENST00000380152.3:c.2030C>A	p.Ser677Tyr	p.S677Y	ENST00000380152		677	tCt/tAt	11/27	1	2	FACETS	0.219	0.17	0.276	0.219	0.17	0.276	SUBCLONAL	1	TRUE	1	0.529686277907623	2		313	396	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954155	32954155	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	27	394	0	ENST00000380152.3:c.9129A>C	p.Glu3043Asp	p.E3043D	ENST00000380152		3043	gaA/gaC	24/27	1	2	FACETS	0.225	0.178	0.278	0.225	0.178	0.278	SUBCLONAL	1	TRUE	1	0.529686277907623	2		394	454	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134925	41134925	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	44	456	0	ENST00000379561.5:c.703T>G	p.Ser235Ala	p.S235A	ENST00000379561	NM_002015.3	235	Tct/Gct	2/3	1	2	FACETS	0.289	0.242	0.341	0.289	0.242	0.341	SUBCLONAL	1	TRUE	1	0.529686277907623	2		456	575	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916845	48916845	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	22	251	0	ENST00000267163.4:c.375A>C	p.Glu125Asp	p.E125D	ENST00000267163	NM_000321.2	125	gaA/gaC	3/27	1	2	FACETS	0.366	0.284	0.46	0.366	0.284	0.46	SUBCLONAL	1	TRUE	1	0.529686277907623	2		251	227	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953748	48953748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759079385	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	16	198	0	ENST00000267163.4:c.1351C>T	p.Arg451Cys	p.R451C	ENST00000267163	NM_000321.2	451	Cgc/Tgc	14/27	1	2	FACETS	0.21	0.155	0.277	0.21	0.155	0.277	SUBCLONAL	1	TRUE	1	0.529686277907623	2		198	287	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093381	30093381	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1469866177	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	28	292	0	ENST00000331968.5:c.1882C>T	p.Arg628Cys	p.R628C	ENST00000331968	NM_002742.2	628	Cgt/Tgt	13/18	1	2	FACETS	0.441	0.353	0.539	0.441	0.353	0.539	SUBCLONAL	1	TRUE	1	0.529686277907623	2		292	240	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352644	68352644	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	33	383	0	ENST00000487270.1:c.511C>A	p.Leu171Ile	p.L171I	ENST00000487270	NM_133509.3	171	Ctt/Att	6/11	1	2	FACETS	0.272	0.221	0.33	0.272	0.221	0.33	SUBCLONAL	1	TRUE	1	0.529686277907623	2		383	458	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610326	81610326	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	184	562	0	ENST00000298171.2:c.1924T>C	p.Phe642Leu	p.F642L	ENST00000298171	NM_000369.2	642	Ttc/Ctc	10/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.529686277907623	2		562	658	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95598897	95598897	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	31	397	0	ENST00000393063.1:c.262G>T	p.Asp88Tyr	p.D88Y	ENST00000393063	NM_030621.3	88	Gac/Tac	4/28	1	2	FACETS	0.252	0.203	0.308	0.252	0.203	0.308	SUBCLONAL	1	TRUE	1	0.529686277907623	2		397	464	SUCCESS
SCG5	6447	MSKCC	GRCh37	15	32976805	32976805	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs771862859	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	34	424	0	ENST00000300175.4:c.424C>T	p.Arg142Ter	p.R142*	ENST00000300175	NM_001144757.1	142	Cga/Tga	4/6	1	2	FACETS	0.249	0.203	0.301	0.249	0.203	0.301	SUBCLONAL	1	TRUE	1	0.529686277907623	2		424	516	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675070	40675070	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	31	512	0	ENST00000249776.8:c.34G>T	p.Val12Phe	p.V12F	ENST00000249776	NM_033286.3	12	Gtt/Ttt	1/9	1	2	FACETS	0.199	0.16	0.243	0.199	0.16	0.243	SUBCLONAL	1	TRUE	1	0.529686277907623	2		512	589	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019570	42019570	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	35	475	0	ENST00000219905.7:c.3623C>A	p.Ser1208Tyr	p.S1208Y	ENST00000219905	NM_001164273.1	1208	tCt/tAt	10/24	1	2	FACETS	0.227	0.185	0.274	0.227	0.185	0.274	SUBCLONAL	1	TRUE	1	0.529686277907623	2		475	582	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035008	42035008	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	176	489	0	ENST00000219905.7:c.4850C>T	p.Ala1617Val	p.A1617V	ENST00000219905	NM_001164273.1	1617	gCt/gTt	15/24	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.529686277907623	2		489	664	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748220	43748220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	37	483	0	ENST00000382044.4:c.2586G>T	p.Glu862Asp	p.E862D	ENST00000382044	NM_001141980.1	862	gaG/gaT	12/28	1	2	FACETS	0.226	0.186	0.271	0.226	0.186	0.271	SUBCLONAL	1	TRUE	1	0.529686277907623	2		483	618	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748582	43748582	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	43	553	1	ENST00000382044.4:c.2224G>T	p.Glu742Ter	p.E742*	ENST00000382044	NM_001141980.1	742	Gaa/Taa	12/28	1	2	FACETS	0.244	0.204	0.289	0.244	0.204	0.289	SUBCLONAL	1	TRUE	1	0.529686277907623	2		554	665	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457674	67457674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749178459	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	58	639	0	ENST00000327367.4:c.484G>A	p.Glu162Lys	p.E162K	ENST00000327367	NM_005902.3	162	Gaa/Aaa	3/9	1	2	FACETS	0.291	0.249	0.337	0.291	0.249	0.337	SUBCLONAL	1	TRUE	1	0.529686277907623	2		639	752	SUCCESS
BLM	641	MSKCC	GRCh37	15	91290720	91290720	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs139282091	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	38	301	0	ENST00000355112.3:c.98C>T	p.Ser33Leu	p.S33L	ENST00000355112	NM_000057.2	33	tCa/tTa	2/22	1	2	FACETS	0.361	0.299	0.431	0.361	0.299	0.431	SUBCLONAL	1	TRUE	1	0.529686277907623	2		301	397	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304059	91304059	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	39	573	0	ENST00000355112.3:c.1456C>A	p.Leu486Ile	p.L486I	ENST00000355112	NM_000057.2	486	Ctt/Att	7/22	1	2	FACETS	0.23	0.19	0.275	0.23	0.19	0.275	SUBCLONAL	1	TRUE	1	0.529686277907623	2		573	639	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347499	91347499	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	31	420	0	ENST00000355112.3:c.3661G>T	p.Glu1221Ter	p.E1221*	ENST00000355112	NM_000057.2	1221	Gaa/Taa	19/22	1	2	FACETS	0.212	0.171	0.259	0.212	0.171	0.259	SUBCLONAL	1	TRUE	1	0.529686277907623	2		420	551	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250820	99250820	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	35	557	0	ENST00000268035.6:c.124G>A	p.Asp42Asn	p.D42N	ENST00000268035	NM_000875.3	42	Gac/Aac	2/21	1	2	FACETS	0.195	0.159	0.236	0.195	0.159	0.236	SUBCLONAL	1	TRUE	1	0.529686277907623	2		557	677	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354440	354440	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs138744096	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	38	506	0	ENST00000262320.3:c.1118G>A	p.Arg373His	p.R373H	ENST00000262320	NM_003502.3	373	cGc/cAc	5/11	1	2	FACETS	0.239	0.197	0.286	0.239	0.197	0.286	SUBCLONAL	1	TRUE	1	0.529686277907623	2		506	600	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640425	3640425	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1187558674	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	49	619	0	ENST00000294008.3:c.3214A>G	p.Thr1072Ala	p.T1072A	ENST00000294008	NM_032444.2	1072	Acc/Gcc	12/15	1	2	FACETS	0.237	0.2	0.278	0.237	0.2	0.278	SUBCLONAL	1	TRUE	1	0.529686277907623	2		619	781	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640689	3640689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750906921	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	52	675	0	ENST00000294008.3:c.2950G>A	p.Glu984Lys	p.E984K	ENST00000294008	NM_032444.2	984	Gaa/Aaa	12/15	1	2	FACETS	0.249	0.211	0.291	0.249	0.211	0.291	SUBCLONAL	1	TRUE	1	0.529686277907623	2		675	788	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857653	9857653	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1555482239	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	153	658	0	ENST00000330684.3:c.3748G>T	p.Glu1250Ter	p.E1250*	ENST00000330684	NM_001134407.1	1250	Gaa/Taa	13/13	1	2	FACETS	0.811	0.744	0.882	0.811	0.744	0.882	CLONAL	1	TRUE	1	0.529686277907623	2		658	712	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029458	14029458	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	59	540	0	ENST00000311895.7:c.1669C>A	p.Leu557Ile	p.L557I	ENST00000311895	NM_005236.2	557	Ctt/Att	8/11	1	2	FACETS	0.314	0.269	0.362	0.314	0.269	0.362	SUBCLONAL	1	TRUE	1	0.529686277907623	2		540	710	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647343	23647343	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	27	427	0	ENST00000261584.4:c.524G>T	p.Arg175Ile	p.R175I	ENST00000261584	NM_024675.3	175	aGa/aTa	4/13	1	2	FACETS	0.203	0.161	0.252	0.203	0.161	0.252	SUBCLONAL	1	TRUE	1	0.529686277907623	2		427	501	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50830304	50830304	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	50	498	0	ENST00000398568.2:c.2747C>A	p.Ser916Tyr	p.S916Y	ENST00000398568	NM_001042412.1	916	tCt/tAt	18/18	1	2	FACETS	0.309	0.262	0.362	0.309	0.262	0.362	SUBCLONAL	1	TRUE	1	0.529686277907623	2		498	610	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645069	67645069	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	51	521	0	ENST00000264010.4:c.334G>T	p.Glu112Ter	p.E112*	ENST00000264010	NM_006565.3	112	Gaa/Taa	3/12	1	2	FACETS	0.319	0.27	0.372	0.319	0.27	0.372	SUBCLONAL	1	TRUE	1	0.529686277907623	2		521	604	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827964	72827964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768307205	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	39	547	0	ENST00000268489.5:c.8617G>A	p.Glu2873Lys	p.E2873K	ENST00000268489	NM_006885.3	2873	Gaa/Aaa	9/10	1	2	FACETS	0.225	0.186	0.269	0.225	0.186	0.269	SUBCLONAL	1	TRUE	1	0.529686277907623	2		547	654	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992930	72992930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1398839726	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	61	549	0	ENST00000268489.5:c.1115G>A	p.Arg372Gln	p.R372Q	ENST00000268489	NM_006885.3	372	cGa/cAa	2/10	1	2	FACETS	0.37	0.319	0.426	0.37	0.319	0.426	SUBCLONAL	1	TRUE	1	0.529686277907623	2		549	622	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81904473	81904473	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	20	304	0	ENST00000359376.3:c.581A>C	p.Lys194Thr	p.K194T	ENST00000359376	NM_002661.3	194	aAa/aCa	7/33	1	2	FACETS	0.215	0.164	0.275	0.215	0.164	0.275	SUBCLONAL	1	TRUE	1	0.529686277907623	2		304	351	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351577	89351577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778960311	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	164	545	0	ENST00000301030.4:c.1373G>A	p.Arg458Gln	p.R458Q	ENST00000301030	NM_001256183.1	458	cGa/cAa	9/13	1	2	FACETS	0.963	0.887	1	0.963	0.887	1	CLONAL	1	TRUE	1	0.529686277907623	2		545	643	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89807267	89807267	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	25	374	0	ENST00000389301.3:c.3773T>C	p.Val1258Ala	p.V1258A	ENST00000389301	NM_000135.2	1258	gTt/gCt	38/43	1	2	FACETS	0.218	0.171	0.272	0.218	0.171	0.272	SUBCLONAL	1	TRUE	1	0.529686277907623	2		374	433	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89815091	89815091	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	37	468	0	ENST00000389301.3:c.3324C>A	p.Phe1108Leu	p.F1108L	ENST00000389301	NM_000135.2	1108	ttC/ttA	33/43	1	2	FACETS	0.248	0.204	0.298	0.248	0.204	0.298	SUBCLONAL	1	TRUE	1	0.529686277907623	2		468	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579568	7579568	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782877	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	46	653	0	ENST00000269305.4:c.119T>C	p.Met40Thr	p.M40T	ENST00000269305	NM_001126112.2	40	aTg/aCg	4/11	1	2	FACETS	0.231	0.194	0.273	0.231	0.194	0.273	SUBCLONAL	1	TRUE	1	0.529686277907623	2		653	751	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979529	7979529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768784091	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	52	508	1	ENST00000319144.4:c.1496G>A	p.Arg499His	p.R499H	ENST00000319144	NM_001139.2	499	cGc/cAc	11/15	1	2	FACETS	0.337	0.287	0.393	0.337	0.287	0.393	SUBCLONAL	1	TRUE	1	0.529686277907623	2		509	582	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983784	15983784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150513105	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	40	461	0	ENST00000268712.3:c.3338G>A	p.Arg1113Gln	p.R1113Q	ENST00000268712	NM_006311.3	1113	cGa/cAa	25/46	1	2	FACETS	0.246	0.204	0.293	0.246	0.204	0.293	SUBCLONAL	1	TRUE	1	0.529686277907623	2		461	614	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496961	29496961	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	21	216	0	ENST00000356175.3:c.532G>T	p.Glu178Ter	p.E178*	ENST00000356175	NM_000267.3	178	Gaa/Taa	5/57	1	2	FACETS	0.279	0.215	0.354	0.279	0.215	0.354	SUBCLONAL	1	TRUE	1	0.529686277907623	2		216	284	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509612	29509612	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	31	452	0	ENST00000356175.3:c.817C>A	p.Leu273Ile	p.L273I	ENST00000356175	NM_000267.3	273	Ctc/Atc	8/57	1	2	FACETS	0.224	0.18	0.273	0.224	0.18	0.273	SUBCLONAL	1	TRUE	1	0.529686277907623	2		452	523	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552212	29552212	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	26	380	1	ENST00000356175.3:c.1945G>T	p.Glu649Ter	p.E649*	ENST00000356175	NM_000267.3	649	Gaa/Taa	17/57	1	2	FACETS	0.227	0.179	0.282	0.227	0.179	0.282	SUBCLONAL	1	TRUE	1	0.529686277907623	2		381	432	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696704	47696704	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	45	417	0	ENST00000347630.2:c.244G>T	p.Asp82Tyr	p.D82Y	ENST00000347630	NM_001007230.1	82	Gat/Tat	5/11	1	2	FACETS	0.305	0.256	0.36	0.305	0.256	0.36	SUBCLONAL	1	TRUE	1	0.529686277907623	2		417	557	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492761	56492761	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	46	560	0	ENST00000407977.2:c.178A>C	p.Lys60Gln	p.K60Q	ENST00000407977		60	Aaa/Caa	2/10	1	2	FACETS	0.281	0.236	0.331	0.281	0.236	0.331	SUBCLONAL	1	TRUE	1	0.529686277907623	2		560	618	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740416	58740416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777279856	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	121	468	0	ENST00000305921.3:c.1321C>T	p.Arg441Cys	p.R441C	ENST00000305921	NM_003620.3	441	Cgt/Tgt	6/6	1	2	FACETS	0.765	0.693	0.841	0.765	0.693	0.841	SUBCLONAL	1	TRUE	1	0.529686277907623	2		468	597	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861668	59861668	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	34	338	0	ENST00000259008.2:c.1591T>A	p.Phe531Ile	p.F531I	ENST00000259008	NM_032043.2	531	Ttt/Att	11/20	1	2	FACETS	0.323	0.263	0.389	0.323	0.263	0.389	SUBCLONAL	1	TRUE	1	0.529686277907623	2		338	398	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876642	59876642	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	22	330	0	ENST00000259008.2:c.1159G>T	p.Glu387Ter	p.E387*	ENST00000259008	NM_032043.2	387	Gaa/Taa	9/20	1	2	FACETS	0.206	0.159	0.261	0.206	0.159	0.261	SUBCLONAL	1	TRUE	1	0.529686277907623	2		330	403	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756643	756643	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	35	499	0	ENST00000314574.4:c.185T>C	p.Phe62Ser	p.F62S	ENST00000314574	NM_005433.3	62	tTt/tCt	2/12	1	2	FACETS	0.218	0.178	0.263	0.218	0.178	0.263	SUBCLONAL	1	TRUE	1	0.529686277907623	2		499	607	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61305174	61305174	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs2144461673	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	31	565	0	ENST00000341074.5:c.952A>G	p.Thr318Ala	p.T318A	ENST00000341074	NM_002974.2	318	Acc/Gcc	8/8	1	2	FACETS	0.19	0.153	0.232	0.19	0.153	0.232	SUBCLONAL	1	TRUE	1	0.529686277907623	2		565	616	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247805	10247805	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770535972	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	37	602	1	ENST00000340748.4:c.4397G>A	p.Arg1466His	p.R1466H	ENST00000340748		1466	cGc/cAc	36/40	1	2	FACETS	0.202	0.166	0.243	0.202	0.166	0.243	SUBCLONAL	1	TRUE	1	0.529686277907623	2		603	691	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10267124	10267124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751093624	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	31	366	2	ENST00000340748.4:c.1294G>A	p.Glu432Lys	p.E432K	ENST00000340748		432	Gaa/Aaa	17/40	1	2	FACETS	0.232	0.187	0.283	0.232	0.187	0.283	SUBCLONAL	1	TRUE	1	0.529686277907623	2		368	505	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270733	10270733	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	37	498	0	ENST00000340748.4:c.1002G>T	p.Glu334Asp	p.E334D	ENST00000340748		334	gaG/gaT	14/40	1	2	FACETS	0.219	0.18	0.263	0.219	0.18	0.263	SUBCLONAL	1	TRUE	1	0.529686277907623	2		498	638	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602918	10602918	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	43	503	0	ENST00000171111.5:c.660C>A	p.Phe220Leu	p.F220L	ENST00000171111	NM_203500.1	220	ttC/ttA	3/6	1	2	FACETS	0.25	0.208	0.296	0.25	0.208	0.296	SUBCLONAL	1	TRUE	1	0.529686277907623	2		503	650	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11114047	11114047	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	28	403	0	ENST00000358026.2:c.1975G>T	p.Glu659Ter	p.E659*	ENST00000358026	NM_001128849.1	659	Gaa/Taa	13/36	1	2	FACETS	0.194	0.154	0.239	0.194	0.154	0.239	SUBCLONAL	1	TRUE	1	0.529686277907623	2		403	545	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214401	36214401	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	30	495	0	ENST00000222270.7:c.3055A>T	p.Lys1019Ter	p.K1019*	ENST00000222270	NM_014727.1	1019	Aaa/Taa	7/37	1	2	FACETS	0.205	0.165	0.251	0.205	0.165	0.251	SUBCLONAL	1	TRUE	1	0.529686277907623	2		495	552	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741894	40741894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs930976777	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	40	698	0	ENST00000392038.2:c.1078G>A	p.Glu360Lys	p.E360K	ENST00000392038	NM_001626.4	360	Gag/Aag	11/14	1	2	FACETS	0.194	0.16	0.232	0.194	0.16	0.232	SUBCLONAL	1	TRUE	1	0.529686277907623	2		698	778	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758852	41758852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756510536	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	39	523	0	ENST00000301178.4:c.1906C>T	p.Arg636Trp	p.R636W	ENST00000301178	NM_021913.4	636	Cgg/Tgg	16/20	1	2	FACETS	0.221	0.183	0.265	0.221	0.183	0.265	SUBCLONAL	1	TRUE	1	0.529686277907623	2		523	665	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793207	42793207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	54	654	0	ENST00000575354.2:c.1099G>T	p.Glu367Ter	p.E367*	ENST00000575354	NM_015125.3	367	Gaa/Taa	7/20	1	2	FACETS	0.253	0.215	0.295	0.253	0.215	0.295	SUBCLONAL	1	TRUE	1	0.529686277907623	2		654	806	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912440	50912440	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	38	523	0	ENST00000440232.2:c.1954C>T	p.Arg652Trp	p.R652W	ENST00000440232	NM_002691.3	652	Cgg/Tgg	16/27	1	2	FACETS	0.265	0.218	0.317	0.265	0.218	0.317	SUBCLONAL	1	TRUE	1	0.529686277907623	2		523	542	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467086	25467086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757492795	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	39	628	0	ENST00000264709.3:c.1789C>T	p.Arg597Trp	p.R597W	ENST00000264709	NM_175629.2	597	Cgg/Tgg	15/23	1	2	FACETS	0.218	0.179	0.26	0.218	0.179	0.26	SUBCLONAL	1	TRUE	1	0.529686277907623	2		628	677	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965877	25965877	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	53	550	0	ENST00000435504.4:c.3329T>G	p.Phe1110Cys	p.F1110C	ENST00000435504		1110	tTt/tGt	13/13	1	2	FACETS	0.306	0.261	0.357	0.306	0.261	0.357	SUBCLONAL	1	TRUE	1	0.529686277907623	2		550	653	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416563	29416563	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs374135358	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	58	712	0	ENST00000389048.3:c.4390C>T	p.Arg1464Ter	p.R1464*	ENST00000389048	NM_004304.4	1464	Cga/Tga	29/29	1	2	FACETS	0.292	0.25	0.338	0.292	0.25	0.338	SUBCLONAL	1	TRUE	1	0.529686277907623	2		712	750	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250133	39250133	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	33	391	0	ENST00000402219.2:c.1436G>T	p.Arg479Ile	p.R479I	ENST00000402219	NM_005633.3	479	aGa/aTa	10/23	1	2	FACETS	0.271	0.22	0.328	0.271	0.22	0.328	SUBCLONAL	1	TRUE	1	0.529686277907623	2		391	460	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47600957	47600957	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	28	425	0	ENST00000263735.4:c.195A>C	p.Lys65Asn	p.K65N	ENST00000263735	NM_002354.2	65	aaA/aaC	3/9	1	2	FACETS	0.206	0.164	0.254	0.206	0.164	0.254	SUBCLONAL	1	TRUE	1	0.529686277907623	2		425	513	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656909	47656909	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	17	257	0	ENST00000233146.2:c.1105G>T	p.Asp369Tyr	p.D369Y	ENST00000233146	NM_000251.2	369	Gat/Tat	7/16	1	2	FACETS	0.218	0.163	0.285	0.218	0.163	0.285	SUBCLONAL	1	TRUE	1	0.529686277907623	2		257	294	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027681	48027681	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	33	451	0	ENST00000234420.5:c.2559G>T	p.Lys853Asn	p.K853N	ENST00000234420	NM_000179.2	853	aaG/aaT	4/10	1	2	FACETS	0.225	0.182	0.272	0.225	0.182	0.272	SUBCLONAL	1	TRUE	1	0.529686277907623	2		451	555	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033753	48033753	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1553333707	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	115	368	0	ENST00000234420.5:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000234420	NM_000179.2	1322	Gaa/Taa	9/10	1	2	FACETS	0.963	0.873	1	0.963	0.873	1	CLONAL	1	TRUE	1	0.529686277907623	2		368	451	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	9	339	0	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	0.088	0.058	0.127	0.088	0.058	0.127	SUBCLONAL	1	TRUE	1	0.529686277907623	2		339	385	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128028923	128028923	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1366074068	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	133	404	1	ENST00000285398.2:c.1934G>A	p.Arg645Gln	p.R645Q	ENST00000285398	NM_000122.1	645	cGa/cAa	12/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.529686277907623	2		405	458	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630626	158630626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912678	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	30	441	0	ENST00000263640.3:c.617G>A	p.Arg206His	p.R206H	ENST00000263640	NM_001105.4	206	cGc/cAc	6/11	1	2	FACETS	0.208	0.167	0.255	0.208	0.167	0.255	SUBCLONAL	1	TRUE	1	0.529686277907623	2		441	544	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257160	198257160	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	23	350	0	ENST00000335508.6:c.3782T>C	p.Val1261Ala	p.V1261A	ENST00000335508	NM_012433.2	1261	gTc/gCc	25/25	1	2	FACETS	0.214	0.167	0.27	0.214	0.167	0.27	SUBCLONAL	1	TRUE	1	0.529686277907623	2		350	405	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131412	202131412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339962485	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	36	470	0	ENST00000358485.4:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000358485	NM_001080125.1	127	cGa/cAa	2/9	1	2	FACETS	0.252	0.206	0.303	0.252	0.206	0.303	SUBCLONAL	1	TRUE	1	0.529686277907623	2		470	540	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812165	212812165	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	20	352	0	ENST00000342788.4:c.411G>T	p.Lys137Asn	p.K137N	ENST00000342788	NM_005235.2	137	aaG/aaT	3/28	1	2	FACETS	0.2	0.152	0.256	0.2	0.152	0.256	SUBCLONAL	1	TRUE	1	0.529686277907623	2		352	378	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645327	215645327	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	29	450	0	ENST00000260947.4:c.1271G>T	p.Arg424Ile	p.R424I	ENST00000260947	NM_000465.2	424	aGa/aTa	4/11	1	2	FACETS	0.198	0.158	0.243	0.198	0.158	0.243	SUBCLONAL	1	TRUE	1	0.529686277907623	2		450	553	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306710	41306710	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	30	466	0	ENST00000373198.4:c.949G>T	p.Asp317Tyr	p.D317Y	ENST00000373198	NM_133170.3	317	Gat/Tat	7/32	1	2	FACETS	0.194	0.155	0.237	0.194	0.155	0.237	SUBCLONAL	1	TRUE	1	0.529686277907623	2		466	585	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46251038	46251038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1348905384	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	129	318	0	ENST00000371998.3:c.47G>A	p.Arg16Gln	p.R16Q	ENST00000371998		16	cGa/cAa	3/23	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.529686277907623	2		318	443	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46254199	46254199	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	27	324	0	ENST00000371998.3:c.331G>T	p.Asp111Tyr	p.D111Y	ENST00000371998		111	Gac/Tac	5/23	1	2	FACETS	0.246	0.195	0.304	0.246	0.195	0.304	SUBCLONAL	1	TRUE	1	0.529686277907623	2		324	415	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288420	21288420	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	48	572	1	ENST00000354336.3:c.665C>A	p.Ser222Tyr	p.S222Y	ENST00000354336	NM_005207.3	222	tCt/tAt	2/3	1	2	FACETS	0.239	0.201	0.281	0.239	0.201	0.281	SUBCLONAL	1	TRUE	1	0.529686277907623	2		573	758	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21344752	21344752	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	150	462	0	ENST00000215739.8:c.729C>A	p.Phe243Leu	p.F243L	ENST00000215739	NM_006767.3	243	ttC/ttA	8/21	1	2	FACETS	0.95	0.872	1	0.95	0.872	1	CLONAL	1	TRUE	1	0.529686277907623	2		462	596	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421355	12421355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777334819	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	51	486	0	ENST00000287820.6:c.235G>A	p.Glu79Lys	p.E79K	ENST00000287820	NM_015869.4	79	Gaa/Aaa	2/7	1	2	FACETS	0.312	0.264	0.364	0.312	0.264	0.364	SUBCLONAL	1	TRUE	1	0.529686277907623	2		486	618	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650355	12650355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	49	427	0	ENST00000251849.4:c.491G>A	p.Arg164Gln	p.R164Q	ENST00000251849	NM_002880.3	164	cGa/cAa	5/17	1	2	FACETS	0.318	0.269	0.372	0.318	0.269	0.372	SUBCLONAL	1	TRUE	1	0.529686277907623	2		427	582	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650743	12650743	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1559434089	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	29	369	0	ENST00000251849.4:c.412A>G	p.Thr138Ala	p.T138A	ENST00000251849	NM_002880.3	138	Aca/Gca	4/17	1	2	FACETS	0.237	0.19	0.291	0.237	0.19	0.291	SUBCLONAL	1	TRUE	1	0.529686277907623	2		369	462	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686336	30686336	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	42	552	0	ENST00000295754.5:c.192G>T	p.Gln64His	p.Q64H	ENST00000295754	NM_003242.5	64	caG/caT	2/7	1	2	FACETS	0.237	0.197	0.281	0.237	0.197	0.281	SUBCLONAL	1	TRUE	1	0.529686277907623	2		552	670	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165122	47165122	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	31	370	0	ENST00000409792.3:c.1004G>T	p.Arg335Ile	p.R335I	ENST00000409792	NM_014159.6	335	aGa/aTa	3/21	1	2	FACETS	0.265	0.214	0.323	0.265	0.214	0.323	SUBCLONAL	1	TRUE	1	0.529686277907623	2		370	441	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643554	52643554	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	38	480	0	ENST00000394830.3:c.2342T>G	p.Leu781Arg	p.L781R	ENST00000394830	NM_018313.4	781	cTt/cGt	17/30	1	2	FACETS	0.245	0.202	0.293	0.245	0.202	0.293	SUBCLONAL	1	TRUE	1	0.529686277907623	2		480	586	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63967873	63967873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	28	474	0	ENST00000398590.3:c.764C>A	p.Ser255Tyr	p.S255Y	ENST00000398590	NM_001177387.1	255	tCt/tAt	7/14	1	2	FACETS	0.203	0.161	0.25	0.203	0.161	0.25	SUBCLONAL	1	TRUE	1	0.529686277907623	2		474	521	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73108276	73108276	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	16	124	0	ENST00000356692.5:c.376G>T	p.Glu126Ter	p.E126*	ENST00000356692		126	Gaa/Taa	4/9	1	2	FACETS	0.395	0.293	0.514	0.395	0.293	0.514	SUBCLONAL	1	TRUE	1	0.529686277907623	2		124	153	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259104	89259104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1019076961	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	32	506	0	ENST00000336596.2:c.248G>T	p.Arg83Ile	p.R83I	ENST00000336596	NM_005233.5	83	aGa/aTa	3/17	1	2	FACETS	0.204	0.165	0.248	0.204	0.165	0.248	SUBCLONAL	1	TRUE	1	0.529686277907623	2		506	593	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456470	89456470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147450955	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	30	408	0	ENST00000336596.2:c.1646C>T	p.Ala549Val	p.A549V	ENST00000336596	NM_005233.5	549	gCg/gTg	8/17	1	2	FACETS	0.229	0.184	0.281	0.229	0.184	0.281	SUBCLONAL	1	TRUE	1	0.529686277907623	2		408	494	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457258	89457258	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779282250	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	29	361	0	ENST00000336596.2:c.1739G>T	p.Arg580Ile	p.R580I	ENST00000336596	NM_005233.5	580	aGa/aTa	9/17	1	2	FACETS	0.268	0.214	0.328	0.268	0.214	0.328	SUBCLONAL	1	TRUE	1	0.529686277907623	2		361	409	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499354	89499354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	201	536	1	ENST00000336596.2:c.2524C>T	p.Arg842Ter	p.R842*	ENST00000336596	NM_005233.5	842	Cga/Tga	15/17	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.529686277907623	2		537	669	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898809	134898809	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	32	435	0	ENST00000398015.3:c.1867G>T	p.Glu623Ter	p.E623*	ENST00000398015	NM_004441.4	623	Gag/Tag	10/16	1	2	FACETS	0.248	0.2	0.301	0.248	0.2	0.301	SUBCLONAL	1	TRUE	1	0.529686277907623	2		435	488	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	11	359	0	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	1	2	FACETS	0.092	0.063	0.128	0.092	0.063	0.128	SUBCLONAL	1	TRUE	1	0.529686277907623	2		359	452	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	14	558	1	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	1	2	FACETS	0.079	0.056	0.107	0.079	0.056	0.107	SUBCLONAL	1	TRUE	1	0.529686277907623	2		559	668	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979637	55979637	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	36	358	0	ENST00000263923.4:c.810G>T	p.Lys270Asn	p.K270N	ENST00000263923	NM_002253.2	270	aaG/aaT	7/30	1	2	FACETS	0.299	0.246	0.36	0.299	0.246	0.36	SUBCLONAL	1	TRUE	1	0.529686277907623	2		358	454	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217294	66217294	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	49	400	0	ENST00000273854.3:c.2321T>C	p.Val774Ala	p.V774A	ENST00000273854	NM_004439.5	774	gTg/gCg	14/18	1	2	FACETS	0.352	0.298	0.412	0.352	0.298	0.412	SUBCLONAL	1	TRUE	1	0.529686277907623	2		400	525	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286185	66286185	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	19	377	0	ENST00000273854.3:c.1501G>T	p.Glu501Ter	p.E501*	ENST00000273854	NM_004439.5	501	Gag/Tag	6/18	1	2	FACETS	0.212	0.161	0.273	0.212	0.161	0.273	SUBCLONAL	1	TRUE	1	0.529686277907623	2		377	338	SUCCESS
ALB	213	MSKCC	GRCh37	4	74276102	74276102	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	22	332	0	ENST00000295897.4:c.689T>G	p.Phe230Cys	p.F230C	ENST00000295897	NM_000477.5	230	tTt/tGt	6/15	1	2	FACETS	0.206	0.159	0.26	0.206	0.159	0.26	SUBCLONAL	1	TRUE	1	0.529686277907623	2		332	404	SUCCESS
ALB	213	MSKCC	GRCh37	4	74283364	74283364	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1356780437	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	37	361	0	ENST00000295897.4:c.1406G>T	p.Arg469Ile	p.R469I	ENST00000295897	NM_000477.5	469	aGa/aTa	11/15	1	2	FACETS	0.316	0.26	0.378	0.316	0.26	0.378	SUBCLONAL	1	TRUE	1	0.529686277907623	2		361	442	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808250	99808250	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	17	217	0	ENST00000280892.6:c.439G>T	p.Asp147Tyr	p.D147Y	ENST00000280892	NM_001130678.1	147	Gat/Tat	5/7	1	2	FACETS	0.205	0.153	0.268	0.205	0.153	0.268	SUBCLONAL	1	TRUE	1	0.529686277907623	2		217	313	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244184	153244184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759610249	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	34	572	0	ENST00000281708.4:c.1973G>A	p.Arg658Gln	p.R658Q	ENST00000281708	NM_033632.3	658	cGa/cAa	12/12	1	2	FACETS	0.195	0.158	0.236	0.195	0.158	0.236	SUBCLONAL	1	TRUE	1	0.529686277907623	2		572	659	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258970	153258970	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	96	383	1	ENST00000281708.4:c.845C>A	p.Ser282Ter	p.S282*	ENST00000281708	NM_033632.3	282	tCa/tAa	5/12	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.529686277907623	2		384	327	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332790	153332790	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	47	600	0	ENST00000281708.4:c.166A>C	p.Asn56His	p.N56H	ENST00000281708	NM_033632.3	56	Aat/Cat	2/12	1	2	FACETS	0.246	0.207	0.29	0.246	0.207	0.29	SUBCLONAL	1	TRUE	1	0.529686277907623	2		600	720	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332865	153332865	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	46	526	0	ENST00000281708.4:c.91G>T	p.Glu31Ter	p.E31*	ENST00000281708	NM_033632.3	31	Gaa/Taa	2/12	1	2	FACETS	0.258	0.216	0.304	0.258	0.216	0.304	SUBCLONAL	1	TRUE	1	0.529686277907623	2		526	674	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525100	187525100	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	27	418	0	ENST00000441802.2:c.10580C>A	p.Ser3527Tyr	p.S3527Y	ENST00000441802	NM_005245.3	3527	tCt/tAt	19/27	1	2	FACETS	0.211	0.167	0.261	0.211	0.167	0.261	SUBCLONAL	1	TRUE	1	0.529686277907623	2		418	483	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541861	187541861	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	49	567	0	ENST00000441802.2:c.5879C>T	p.Ala1960Val	p.A1960V	ENST00000441802	NM_005245.3	1960	gCc/gTc	10/27	1	2	FACETS	0.284	0.24	0.333	0.284	0.24	0.333	SUBCLONAL	1	TRUE	1	0.529686277907623	2		567	651	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549397	187549397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769656312	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	196	581	0	ENST00000441802.2:c.4721C>T	p.Ser1574Leu	p.S1574L	ENST00000441802	NM_005245.3	1574	tCg/tTg	9/27	1	2	FACETS	0.976	0.906	1	0.976	0.906	1	CLONAL	1	TRUE	1	0.529686277907623	2		581	758	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549725	187549725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199516712	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	36	513	0	ENST00000441802.2:c.4516C>T	p.Arg1506Cys	p.R1506C	ENST00000441802	NM_005245.3	1506	Cgt/Tgt	8/27	1	2	FACETS	0.234	0.192	0.282	0.234	0.192	0.282	SUBCLONAL	1	TRUE	1	0.529686277907623	2		513	581	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630411	187630411	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	37	530	0	ENST00000441802.2:c.571C>T	p.Arg191Ter	p.R191*	ENST00000441802	NM_005245.3	191	Cga/Tga	2/27	1	2	FACETS	0.212	0.174	0.254	0.212	0.174	0.254	SUBCLONAL	1	TRUE	1	0.529686277907623	2		530	660	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294532	1294532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1360708027	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	42	704	0	ENST00000310581.5:c.469G>A	p.Ala157Thr	p.A157T	ENST00000310581	NM_198253.2	157	Gcg/Acg	2/16	1	2	FACETS	0.222	0.185	0.264	0.222	0.185	0.264	SUBCLONAL	1	TRUE	1	0.529686277907623	2		704	713	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295889	1295889	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	64	787	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.28	0.242	0.322	0.28	0.242	0.322	SUBCLONAL	1	TRUE	1	0.529686277907623	2		787	862	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950689	38950689	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	72	406	0	ENST00000357387.3:c.3261C>A	p.Phe1087Leu	p.F1087L	ENST00000357387	NM_152756.3	1087	ttC/ttA	31/38	1	2	FACETS	0.526	0.46	0.596	0.526	0.46	0.596	SUBCLONAL	1	TRUE	1	0.529686277907623	2		406	517	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576373	67576373	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	25	318	0	ENST00000274335.5:c.652G>T	p.Glu218Ter	p.E218*	ENST00000274335		218	Gaa/Taa	5/15	1	2	FACETS	0.27	0.212	0.336	0.27	0.212	0.336	SUBCLONAL	1	TRUE	1	0.529686277907623	2		318	350	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	16	346	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	0.144	0.106	0.19	0.144	0.106	0.19	SUBCLONAL	1	TRUE	1	0.529686277907623	2		346	420	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589168	67589168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	29	336	0	ENST00000274335.5:c.1156C>T	p.Arg386Ter	p.R386*	ENST00000274335		386	Cga/Tga	9/15	1	2	FACETS	0.294	0.235	0.36	0.294	0.235	0.36	SUBCLONAL	1	TRUE	1	0.529686277907623	2		336	373	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590992	67590992	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	26	312	0	ENST00000274335.5:c.1585G>T	p.Asp529Tyr	p.D529Y	ENST00000274335		529	Gat/Tat	12/15	1	2	FACETS	0.251	0.198	0.311	0.251	0.198	0.311	SUBCLONAL	1	TRUE	1	0.529686277907623	2		312	391	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592108	67592108	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1419325070	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	36	419	0	ENST00000274335.5:c.1924C>T	p.Arg642Ter	p.R642*	ENST00000274335		642	Cga/Tga	14/15	1	2	FACETS	0.244	0.2	0.294	0.244	0.2	0.294	SUBCLONAL	1	TRUE	1	0.529686277907623	2		419	557	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685209	86685209	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	59	329	0	ENST00000274376.6:c.2926-1G>T		p.X976_splice	ENST00000274376	NM_002890.2	976			1	2	FACETS	0.592	0.512	0.68	0.592	0.512	0.68	SUBCLONAL	1	TRUE	1	0.529686277907623	2		329	376	SUCCESS
APC	324	MSKCC	GRCh37	5	112136980	112136980	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1554076133	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	103	303	0	ENST00000257430.4:c.734C>A	p.Ser245Ter	p.S245*	ENST00000257430	NM_000038.5	245	tCa/tAa	8/16	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.529686277907623	2		303	384	SUCCESS
APC	324	MSKCC	GRCh37	5	112174663	112174663	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	43	477	0	ENST00000257430.4:c.3372T>A	p.Asn1124Lys	p.N1124K	ENST00000257430	NM_000038.5	1124	aaT/aaA	16/16	1	2	FACETS	0.306	0.255	0.362	0.306	0.255	0.362	SUBCLONAL	1	TRUE	1	0.529686277907623	2		477	531	SUCCESS
APC	324	MSKCC	GRCh37	5	112175228	112175228	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs863225349	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	31	482	0	ENST00000257430.4:c.3937A>G	p.Thr1313Ala	p.T1313A	ENST00000257430	NM_000038.5	1313	Act/Gct	16/16	1	2	FACETS	0.2	0.161	0.244	0.2	0.161	0.244	SUBCLONAL	1	TRUE	1	0.529686277907623	2		482	586	SUCCESS
APC	324	MSKCC	GRCh37	5	112175486	112175486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424719678	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	39	515	0	ENST00000257430.4:c.4195C>T	p.Arg1399Cys	p.R1399C	ENST00000257430	NM_000038.5	1399	Cgt/Tgt	16/16	1	2	FACETS	0.234	0.194	0.28	0.234	0.194	0.28	SUBCLONAL	1	TRUE	1	0.529686277907623	2		515	628	SUCCESS
APC	324	MSKCC	GRCh37	5	112175852	112175852	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	50	489	0	ENST00000257430.4:c.4561G>T	p.Glu1521Ter	p.E1521*	ENST00000257430	NM_000038.5	1521	Gaa/Taa	16/16	1	2	FACETS	0.304	0.257	0.355	0.304	0.257	0.355	SUBCLONAL	1	TRUE	1	0.529686277907623	2		489	622	SUCCESS
APC	324	MSKCC	GRCh37	5	112175925	112175925	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs863225356	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	110	463	0	ENST00000257430.4:c.4634C>A	p.Ser1545Ter	p.S1545*	ENST00000257430	NM_000038.5	1545	tCa/tAa	16/16	1	2	FACETS	0.682	0.614	0.754	0.682	0.614	0.754	SUBCLONAL	1	TRUE	1	0.529686277907623	2		463	609	SUCCESS
APC	324	MSKCC	GRCh37	5	112177049	112177049	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	63	546	0	ENST00000257430.4:c.5758C>T	p.Arg1920Ter	p.R1920*	ENST00000257430	NM_000038.5	1920	Cga/Tga	16/16	1	2	FACETS	0.34	0.293	0.39	0.34	0.293	0.39	SUBCLONAL	1	TRUE	1	0.529686277907623	2		546	700	SUCCESS
APC	324	MSKCC	GRCh37	5	112178000	112178000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768922431	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	86	495	0	ENST00000257430.4:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000257430	NM_000038.5	2237	Cga/Tga	16/16	1	2	FACETS	0.619	0.548	0.693	0.619	0.548	0.693	SUBCLONAL	1	TRUE	1	0.529686277907623	2		495	525	SUCCESS
APC	324	MSKCC	GRCh37	5	112179011	112179011	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876659753	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	126	376	0	ENST00000257430.4:c.7720C>A	p.Leu2574Ile	p.L2574I	ENST00000257430	NM_000038.5	2574	Ctt/Att	16/16	1	2	FACETS	0.927	0.844	1	0.927	0.844	1	CLONAL	1	TRUE	1	0.529686277907623	2		376	513	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911514	131911514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143802516	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	30	370	0	ENST00000265335.6:c.259C>T	p.Arg87Cys	p.R87C	ENST00000265335		87	Cgt/Tgt	3/25	1	2	FACETS	0.278	0.223	0.339	0.278	0.223	0.339	SUBCLONAL	1	TRUE	1	0.529686277907623	2		370	408	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923334	131923334	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1561638972	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	23	336	0	ENST00000265335.6:c.837G>T	p.Lys279Asn	p.K279N	ENST00000265335		279	aaG/aaT	6/25	1	2	FACETS	0.242	0.188	0.304	0.242	0.188	0.304	SUBCLONAL	1	TRUE	1	0.529686277907623	2		336	359	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637208	176637208	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	48	562	0	ENST00000439151.2:c.1808C>A	p.Ser603Tyr	p.S603Y	ENST00000439151	NM_022455.4	603	tCt/tAt	5/23	1	2	FACETS	0.239	0.201	0.281	0.239	0.201	0.281	SUBCLONAL	1	TRUE	1	0.529686277907623	2		562	758	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638146	176638146	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	36	493	0	ENST00000439151.2:c.2746G>T	p.Asp916Tyr	p.D916Y	ENST00000439151	NM_022455.4	916	Gat/Tat	5/23	1	2	FACETS	0.223	0.182	0.268	0.223	0.182	0.268	SUBCLONAL	1	TRUE	1	0.529686277907623	2		493	610	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696681	176696681	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	32	494	0	ENST00000439151.2:c.5382C>A	p.Phe1794Leu	p.F1794L	ENST00000439151	NM_022455.4	1794	ttC/ttA	16/23	1	2	FACETS	0.19	0.153	0.231	0.19	0.153	0.231	SUBCLONAL	1	TRUE	1	0.529686277907623	2		494	637	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721717	176721717	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	36	597	0	ENST00000439151.2:c.7348A>G	p.Asn2450Asp	p.N2450D	ENST00000439151	NM_022455.4	2450	Aat/Gat	23/23	1	2	FACETS	0.207	0.169	0.249	0.207	0.169	0.249	SUBCLONAL	1	TRUE	1	0.529686277907623	2		597	658	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225461	26225461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	58	856	0	ENST00000360408.1:c.79C>T	p.Arg27Cys	p.R27C	ENST00000360408	NM_003532.2	27	Cgc/Tgc	1/1	1	2	FACETS	0.238	0.204	0.276	0.238	0.204	0.276	SUBCLONAL	1	TRUE	1	0.529686277907623	2		856	920	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225776	26225776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1186783518	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	43	617	0	ENST00000360408.1:c.394C>T	p.Arg132Cys	p.R132C	ENST00000360408	NM_003532.2	132	Cgt/Tgt	1/1	1	2	FACETS	0.226	0.188	0.268	0.226	0.188	0.268	SUBCLONAL	1	TRUE	1	0.529686277907623	2		617	719	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910556	29910556	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	58	669	1	ENST00000376809.5:c.96C>A	p.Phe32Leu	p.F32L	ENST00000376809	NM_002116.7	32	ttC/ttA	2/8	1	2	FACETS	0.318	0.273	0.368	0.318	0.273	0.368	SUBCLONAL	1	TRUE	1	0.529686277907623	2		670	688	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675604	30675604	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	48	523	0	ENST00000376406.3:c.2752G>T	p.Glu918Ter	p.E918*	ENST00000376406	NM_014641.2	918	Gaa/Taa	8/15	1	2	FACETS	0.276	0.232	0.324	0.276	0.232	0.324	SUBCLONAL	1	TRUE	1	0.529686277907623	2		523	657	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675799	30675799	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	41	505	0	ENST00000376406.3:c.2557A>G	p.Thr853Ala	p.T853A	ENST00000376406	NM_014641.2	853	Acc/Gcc	8/15	1	2	FACETS	0.245	0.203	0.291	0.245	0.203	0.291	SUBCLONAL	1	TRUE	1	0.529686277907623	2		505	632	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166874	32166874	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	38	570	0	ENST00000375023.3:c.4364C>T	p.Ala1455Val	p.A1455V	ENST00000375023	NM_004557.3	1455	gCc/gTc	24/30	1	2	FACETS	0.218	0.179	0.261	0.218	0.179	0.261	SUBCLONAL	1	TRUE	1	0.529686277907623	2		570	658	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169953	32169953	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202197092	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	118	570	0	ENST00000375023.3:c.3655C>T	p.Arg1219Trp	p.R1219W	ENST00000375023	NM_004557.3	1219	Cgg/Tgg	21/30	1	2	FACETS	0.729	0.659	0.802	0.729	0.659	0.802	SUBCLONAL	1	TRUE	1	0.529686277907623	2		570	611	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32802938	32802938	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140654840	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	31	434	2	ENST00000374899.4:c.938G>A	p.Arg313His	p.R313H	ENST00000374899	NM_018833.2	313	cGc/cAc	5/12	1	2	FACETS	0.197	0.159	0.241	0.197	0.159	0.241	SUBCLONAL	1	TRUE	1	0.529686277907623	2		436	594	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32819896	32819896	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	35	409	0	ENST00000354258.4:c.1014G>T	p.Gln338His	p.Q338H	ENST00000354258	NM_000593.5	338	caG/caT	3/11	1	2	FACETS	0.23	0.188	0.277	0.23	0.188	0.277	SUBCLONAL	1	TRUE	1	0.529686277907623	2		409	575	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748479	43748479	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45533131	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	32	428	0	ENST00000523873.1:c.433C>T	p.Arg145Ter	p.R145*	ENST00000523873		145	Cga/Tga	6/8	1	2	FACETS	0.245	0.198	0.298	0.245	0.198	0.298	SUBCLONAL	1	TRUE	1	0.529686277907623	2		428	493	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553582	106553582	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs755787471	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	41	666	1	ENST00000369096.4:c.1547C>A	p.Ser516Tyr	p.S516Y	ENST00000369096	NM_001198.3	516	tCt/tAt	5/7	1	2	FACETS	0.211	0.175	0.252	0.211	0.175	0.252	SUBCLONAL	1	TRUE	1	0.529686277907623	2		667	733	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020771	112020771	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374907658	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	49	493	0	ENST00000368678.4:c.800C>T	p.Ser267Leu	p.S267L	ENST00000368678		267	tCg/tTg	8/13	1	2	FACETS	0.297	0.251	0.348	0.297	0.251	0.348	SUBCLONAL	1	TRUE	1	0.529686277907623	2		493	623	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663595	117663595	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	70	307	0	ENST00000368508.3:c.4637G>T	p.Gly1546Val	p.G1546V	ENST00000368508	NM_002944.2	1546	gGa/gTa	28/43	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.529686277907623	2		307	240	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681126	117681126	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs759618879	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	33	414	0	ENST00000368508.3:c.3494T>C	p.Val1165Ala	p.V1165A	ENST00000368508	NM_002944.2	1165	gTt/gCt	23/43	1	2	FACETS	0.253	0.205	0.306	0.253	0.205	0.306	SUBCLONAL	1	TRUE	1	0.529686277907623	2		414	493	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715410	117715410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	93	369	0	ENST00000368508.3:c.1079G>A	p.Arg360Lys	p.R360K	ENST00000368508	NM_002944.2	360	aGa/aAa	10/43	1	2	FACETS	0.882	0.79	0.979	0.882	0.79	0.979	CLONAL	1	TRUE	1	0.529686277907623	2		369	398	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026513	6026513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780044	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	24	282	0	ENST00000265849.7:c.1883G>A	p.Arg628Gln	p.R628Q	ENST00000265849	NM_000535.5	628	cGa/cAa	11/15	1	2	FACETS	0.23	0.18	0.288	0.23	0.18	0.288	SUBCLONAL	1	TRUE	1	0.529686277907623	2		282	394	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468280	50468280	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	34	556	0	ENST00000331340.3:c.1515C>A	p.Phe505Leu	p.F505L	ENST00000331340	NM_006060.4	505	ttC/ttA	8/8	1	2	FACETS	0.206	0.168	0.25	0.206	0.168	0.25	SUBCLONAL	1	TRUE	1	0.529686277907623	2		556	622	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509660	106509660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757849968	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	36	564	0	ENST00000359195.3:c.1654C>T	p.Arg552Cys	p.R552C	ENST00000359195	NM_002649.2	552	Cgc/Tgc	2/11	1	2	FACETS	0.213	0.174	0.256	0.213	0.174	0.256	SUBCLONAL	1	TRUE	1	0.529686277907623	2		564	639	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509747	106509747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761655879	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	30	497	0	ENST00000359195.3:c.1741G>A	p.Glu581Lys	p.E581K	ENST00000359195	NM_002649.2	581	Gaa/Aaa	2/11	1	2	FACETS	0.194	0.155	0.237	0.194	0.155	0.237	SUBCLONAL	1	TRUE	1	0.529686277907623	2		497	585	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545631	106545631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	31	471	0	ENST00000359195.3:c.3108G>T	p.Met1036Ile	p.M1036I	ENST00000359195	NM_002649.2	1036	atG/atT	11/11	1	2	FACETS	0.199	0.16	0.243	0.199	0.16	0.243	SUBCLONAL	1	TRUE	1	0.529686277907623	2		471	588	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339217	116339217	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	137	488	0	ENST00000397752.3:c.79A>G	p.Lys27Glu	p.K27E	ENST00000397752	NM_000245.2	27	Aaa/Gaa	2/21	1	2	FACETS	0.944	0.863	1	0.944	0.863	1	CLONAL	1	TRUE	1	0.529686277907623	2		488	548	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411608	116411608	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	35	471	0	ENST00000397752.3:c.2787G>T	p.Gln929His	p.Q929H	ENST00000397752	NM_000245.2	929	caG/caT	13/21	1	2	FACETS	0.23	0.188	0.278	0.23	0.188	0.278	SUBCLONAL	1	TRUE	1	0.529686277907623	2		471	574	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205681	38205681	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	138	396	0	ENST00000317025.8:c.9C>A	p.Phe3Leu	p.F3L	ENST00000317025	NM_023034.1	3	ttC/ttA	2/24	1	2	FACETS	0.989	0.905	1	0.989	0.905	1	CLONAL	1	TRUE	1	0.529686277907623	2		396	527	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371909	55371909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1200403075	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	38	629	0	ENST00000297316.4:c.599G>A	p.Gly200Asp	p.G200D	ENST00000297316	NM_022454.3	200	gGc/gAc	2/2	1	2	FACETS	0.23	0.189	0.275	0.23	0.189	0.275	SUBCLONAL	1	TRUE	1	0.529686277907623	2		629	624	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69012034	69012034	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	22	312	0	ENST00000288368.4:c.2671G>T	p.Glu891Ter	p.E891*	ENST00000288368	NM_024870.2	891	Gaa/Taa	23/40	1	2	FACETS	0.191	0.147	0.241	0.191	0.147	0.241	SUBCLONAL	1	TRUE	1	0.529686277907623	2		312	436	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90960096	90960096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs962092255	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	14	193	0	ENST00000265433.3:c.1870C>T	p.Arg624Cys	p.R624C	ENST00000265433	NM_002485.4	624	Cgt/Tgt	12/16	1	2	FACETS	0.239	0.173	0.319	0.239	0.173	0.319	SUBCLONAL	1	TRUE	1	0.529686277907623	2		193	221	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2077760	2077760	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs775121610	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	38	478	0	ENST00000349721.2:c.2168C>A	p.Thr723Asn	p.T723N	ENST00000349721	NM_003070.3	723	aCc/aAc	14/34	1	2	FACETS	0.258	0.212	0.308	0.258	0.212	0.308	SUBCLONAL	1	TRUE	1	0.529686277907623	2		478	557	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2096702	2096702	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	39	385	0	ENST00000349721.2:c.2929C>A	p.Leu977Met	p.L977M	ENST00000349721	NM_003070.3	977	Ctg/Atg	20/34	1	2	FACETS	0.324	0.269	0.387	0.324	0.269	0.387	SUBCLONAL	1	TRUE	1	0.529686277907623	2		385	454	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2161878	2161878	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764576819	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	33	442	0	ENST00000349721.2:c.4174G>A	p.Asp1392Asn	p.D1392N	ENST00000349721	NM_003070.3	1392	Gat/Aat	28/34	1	2	FACETS	0.227	0.184	0.276	0.227	0.184	0.276	SUBCLONAL	1	TRUE	1	0.529686277907623	2		442	548	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072541	5072541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368927897	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	28	408	0	ENST00000381652.3:c.1691G>A	p.Arg564Gln	p.R564Q	ENST00000381652	NM_004972.3	564	cGa/cAa	13/25	1	2	FACETS	0.265	0.211	0.326	0.265	0.211	0.326	SUBCLONAL	1	TRUE	1	0.529686277907623	2		408	399	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126378	5126378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775568041	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	29	349	1	ENST00000381652.3:c.3223G>A	p.Val1075Met	p.V1075M	ENST00000381652	NM_004972.3	1075	Gtg/Atg	24/25	1	2	FACETS	0.253	0.203	0.311	0.253	0.203	0.311	SUBCLONAL	1	TRUE	1	0.529686277907623	2		350	432	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341105	8341105	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs141770150	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	37	375	0	ENST00000356435.5:c.5111T>G	p.Phe1704Cys	p.F1704C	ENST00000356435		1704	tTt/tGt	30/35	1	2	FACETS	0.308	0.253	0.369	0.308	0.253	0.369	SUBCLONAL	1	TRUE	1	0.529686277907623	2		375	454	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633425	8633425	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	28	397	0	ENST00000356435.5:c.244C>A	p.Leu82Ile	p.L82I	ENST00000356435		82	Ctc/Atc	3/35	1	2	FACETS	0.213	0.17	0.263	0.213	0.17	0.263	SUBCLONAL	1	TRUE	1	0.529686277907623	2		397	496	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325640	87325640	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	30	390	0	ENST00000277120.3:c.517G>T	p.Asp173Tyr	p.D173Y	ENST00000277120		173	Gat/Tat	6/19	1	2	FACETS	0.228	0.183	0.28	0.228	0.183	0.28	SUBCLONAL	1	TRUE	1	0.529686277907623	2		390	496	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342815	87342815	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	34	491	0	ENST00000277120.3:c.1100A>C	p.Tyr367Ser	p.Y367S	ENST00000277120		367	tAt/tCt	9/19	1	2	FACETS	0.212	0.173	0.257	0.212	0.173	0.257	SUBCLONAL	1	TRUE	1	0.529686277907623	2		491	605	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606379	93606379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757250931	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	50	688	0	ENST00000375746.1:c.199G>A	p.Glu67Lys	p.E67K	ENST00000375746	NM_001174167.1	67	Gag/Aag	2/14	1	2	FACETS	0.281	0.238	0.329	0.281	0.238	0.329	SUBCLONAL	1	TRUE	1	0.529686277907623	2		688	672	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220333	98220333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138458710	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	35	504	1	ENST00000331920.6:c.3130G>A	p.Ala1044Thr	p.A1044T	ENST00000331920	NM_000264.3	1044	Gct/Act	18/24	1	2	FACETS	0.226	0.184	0.273	0.226	0.184	0.273	SUBCLONAL	1	TRUE	1	0.529686277907623	2		505	585	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229689	98229689	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	34	398	0	ENST00000331920.6:c.2269T>G	p.Phe757Val	p.F757V	ENST00000331920	NM_000264.3	757	Ttt/Gtt	15/24	1	2	FACETS	0.234	0.19	0.283	0.234	0.19	0.283	SUBCLONAL	1	TRUE	1	0.529686277907623	2		398	549	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771747	135771747	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	40	566	0	ENST00000298552.3:c.3370G>T	p.Asp1124Tyr	p.D1124Y	ENST00000298552	NM_001162426.1	1124	Gac/Tac	23/23	1	2	FACETS	0.213	0.176	0.254	0.213	0.176	0.254	SUBCLONAL	1	TRUE	1	0.529686277907623	2		566	709	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781078	135781078	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	44	531	0	ENST00000298552.3:c.1887G>T	p.Lys629Asn	p.K629N	ENST00000298552	NM_001162426.1	629	aaG/aaT	15/23	1	2	FACETS	0.267	0.223	0.315	0.267	0.223	0.315	SUBCLONAL	1	TRUE	1	0.529686277907623	2		531	623	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786028	135786028	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs918660416	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	192	612	0	ENST00000298552.3:c.1193C>T	p.Ala398Val	p.A398V	ENST00000298552	NM_001162426.1	398	gCc/gTc	12/23	1	2	FACETS	0.939	0.871	1	0.939	0.871	1	CLONAL	1	TRUE	1	0.529686277907623	2		612	772	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787679	135787679	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	34	354	0	ENST00000298552.3:c.903G>T	p.Gln301His	p.Q301H	ENST00000298552	NM_001162426.1	301	caG/caT	9/23	1	2	FACETS	0.293	0.239	0.354	0.293	0.239	0.354	SUBCLONAL	1	TRUE	1	0.529686277907623	2		354	438	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1327788	1327788	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	26	350	1	ENST00000400841.2:c.93G>T	p.Gln31His	p.Q31H	ENST00000400841		31	caG/caT	2/6	1	2	FACETS	0.234	0.185	0.291	0.234	0.185	0.291	SUBCLONAL	1	TRUE	1	0.529686277907623	2		351	419	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911462	39911462	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	36	461	0	ENST00000378444.4:c.5168T>G	p.Leu1723Arg	p.L1723R	ENST00000378444	NM_001123385.1	1723	cTg/cGg	15/15	1	2	FACETS	0.212	0.174	0.256	0.212	0.174	0.256	SUBCLONAL	1	TRUE	1	0.529686277907623	2		461	640	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032591	47032591	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	36	511	0	ENST00000377604.3:c.497C>A	p.Ser166Tyr	p.S166Y	ENST00000377604	NM_001204468.1	166	tCt/tAt	5/24	1	2	FACETS	0.218	0.179	0.263	0.218	0.179	0.263	SUBCLONAL	1	TRUE	1	0.529686277907623	2		511	623	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044713	47044713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs887995752	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	52	738	0	ENST00000377604.3:c.2113G>A	p.Glu705Lys	p.E705K	ENST00000377604	NM_001204468.1	705	Gag/Aag	19/24	1	2	FACETS	0.245	0.208	0.286	0.245	0.208	0.286	SUBCLONAL	1	TRUE	1	0.529686277907623	2		738	802	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410597	63410597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758807218	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	46	641	0	ENST00000330258.3:c.2570G>A	p.Arg857Gln	p.R857Q	ENST00000330258	NM_152424.3	857	cGa/cAa	2/2	1	2	FACETS	0.245	0.205	0.288	0.245	0.205	0.288	SUBCLONAL	1	TRUE	1	0.529686277907623	2		641	710	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412761	63412761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	31	582	0	ENST00000330258.3:c.406G>A	p.Ala136Thr	p.A136T	ENST00000330258	NM_152424.3	136	Gct/Act	2/2	1	2	FACETS	0.19	0.153	0.232	0.19	0.153	0.232	SUBCLONAL	1	TRUE	1	0.529686277907623	2		582	616	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413141	63413141	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	41	488	0	ENST00000330258.3:c.26C>T	p.Ala9Val	p.A9V	ENST00000330258	NM_152424.3	9	gCt/gTt	2/2	1	2	FACETS	0.261	0.216	0.31	0.261	0.216	0.31	SUBCLONAL	1	TRUE	1	0.529686277907623	2		488	594	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342687	70342687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	42	506	0	ENST00000374080.3:c.1448G>A	p.Arg483Gln	p.R483Q	ENST00000374080		483	cGa/cAa	10/45	1	2	FACETS	0.279	0.232	0.331	0.279	0.232	0.331	SUBCLONAL	1	TRUE	1	0.529686277907623	2		506	569	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918898	76918898	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	29	380	0	ENST00000373344.5:c.4093G>T	p.Glu1365Ter	p.E1365*	ENST00000373344	NM_000489.3	1365	Gaa/Taa	12/35	1	2	FACETS	0.225	0.18	0.276	0.225	0.18	0.276	SUBCLONAL	1	TRUE	1	0.529686277907623	2		380	487	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938995	76938995	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs886044898	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	27	374	0	ENST00000373344.5:c.1753G>T	p.Glu585Ter	p.E585*	ENST00000373344	NM_000489.3	585	Gaa/Taa	9/35	1	2	FACETS	0.226	0.179	0.28	0.226	0.179	0.28	SUBCLONAL	1	TRUE	1	0.529686277907623	2		374	451	SUCCESS
BTK	695	MSKCC	GRCh37	X	100629567	100629567	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	32	383	0	ENST00000308731.7:c.197C>T	p.Thr66Ile	p.T66I	ENST00000308731	NM_000061.2	66	aCa/aTa	3/19	1	2	FACETS	0.236	0.191	0.286	0.236	0.191	0.286	SUBCLONAL	1	TRUE	1	0.529686277907623	2		383	513	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020225	123020225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	46	460	0	ENST00000355640.3:c.713G>A	p.Arg238Gln	p.R238Q	ENST00000355640		238	cGa/cAa	2/7	1	2	FACETS	0.292	0.245	0.344	0.292	0.245	0.344	SUBCLONAL	1	TRUE	1	0.529686277907623	2		460	595	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191750	123191750	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	73	347	0	ENST00000218089.9:c.1339A>C	p.Met447Leu	p.M447L	ENST00000218089	NM_001042749.1	447	Atg/Ctg	15/35	1	2	FACETS	0.875	0.772	0.984	0.875	0.772	0.984	CLONAL	1	TRUE	1	0.529686277907623	2		347	315	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227825	36227825	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	107	680	0	ENST00000222270.7:c.7310C>T	p.Thr2437Ile	p.T2437I	ENST00000222270	NM_014727.1	2437	aCt/aTt	32/37	0.0795168654231044	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		680	739	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	60	126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.732	0.633	0.839	0.732	0.633	0.839	SUBCLONAL	1	TRUE	1	0.41	2		126	400	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0061516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	34	373	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.842	0.694	1	0.842	0.694	1	CLONAL	1	TRUE	1	0.41	2		373	197	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs104886003	NA	P-0061516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	27	238	0	ENST00000263967.3:c.1633G>C	p.Glu545Gln	p.E545Q	ENST00000263967	NM_006218.2	545	Gag/Cag	10/21	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.41	2		238	109	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0061516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	53	282	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.41	2		282	244	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725043	89725043	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0061516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	17	250	0	ENST00000371953.3:c.1027del		p.X343_splice	ENST00000371953	NM_000314.4	343			1	2	FACETS	0.643	0.484	0.827	0.643	0.484	0.827	SUBCLONAL	1	TRUE	1	0.41	2		250	129	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347959	89347959	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201160642	NA	P-0061516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	101	621	0	ENST00000301030.4:c.4991C>T	p.Ala1664Val	p.A1664V	ENST00000301030	NM_001256183.1	1664	gCg/gTg	9/13	1	2	FACETS	0.813	0.728	0.903	0.813	0.728	0.903	CLONAL	1	TRUE	1	0.41	2		621	606	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058015	27058015	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	149	613	0	ENST00000324856.7:c.1723C>T	p.Gln575Ter	p.Q575*	ENST00000324856	NM_006015.4	575	Cag/Tag	3/20	1	2	FACETS	0.992	0.908	1	0.992	0.908	1	CLONAL	1	TRUE	1	0.41	2		613	733	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050896	49050898	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0061516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	54	435	0	ENST00000267163.4:c.2583_2585del	p.Arg861del	p.R861del	ENST00000267163	NM_000321.2	860	aaAAGa/aaa	25/27	1	2	FACETS	0.775	0.665	0.894	0.775	0.665	0.894	SUBCLONAL	1	TRUE	1	0.41	2		435	340	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645096	67645096	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	128	613	0	ENST00000264010.4:c.362del	p.Pro121LeufsTer2	p.P121Lfs*2	ENST00000264010	NM_006565.3	121	Cct/ct	3/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.41	2		613	576	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481660	40481660	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs113994136	NA	P-0061516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	99	563	0	ENST00000264657.5:c.1145G>T	p.Arg382Leu	p.R382L	ENST00000264657	NM_139276.2	382	cGg/cTg	13/24	1	2	FACETS	0.903	0.808	1	0.903	0.808	1	CLONAL	1	TRUE	1	0.41	2		563	535	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229242	36229248	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCAAT	TGGCAAT	-	novel	NA	P-0061516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	151	756	0	ENST00000222270.7:c.7932_7938del	p.His2644GlnfsTer92	p.H2644Qfs*92	ENST00000222270	NM_014727.1	2644	caTGGCAAT/ca	37/37	0.0768664637504985	3	FACETS	1	0.982	1	0.631	0.578	0.686	INDETERMINATE	1	TRUE	1	0.41	3		756	703	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811693	102811693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061520-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	80	844	0	ENST00000307046.8:c.491G>A	p.Gly164Glu	p.G164E	ENST00000307046	NM_001111285.1	164	gGg/gAg	4/4	0.479496571165519	3	FACETS	0.475	0.418	0.538	0.238	0.209	0.269	SUBCLONAL	1	TRUE	1	0.479496571165519	3		844	870	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485136	57485387	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTGTGTATGGCTTCCACTCTTGCTGGCTGTTCATTGCGGTGGTTCTTTTTCAAACGGTCAGGCTGAAAACCCCCATCCCCCTCCCACCACCAAACCATAAAGGATCTATAAGAGAAGCAAGAAAAACGCACTCCCACTAATTCTCATATGGAAAAATCAGGGTTTTGAAGACTTCAGGAGCTACAGAGATGCTAGCACCCCAGCTCTGCTTGAATTTTAAATTACATTAATATGTATTCCCTTTTTATATA	GGTGTGTATGGCTTCCACTCTTGCTGGCTGTTCATTGCGGTGGTTCTTTTTCAAACGGTCAGGCTGAAAACCCCCATCCCCCTCCCACCACCAAACCATAAAGGATCTATAAGAGAAGCAAGAAAAACGCACTCCCACTAATTCTCATATGGAAAAATCAGGGTTTTGAAGACTTCAGGAGCTACAGAGATGCTAGCACCCCAGCTCTGCTTGAATTTTAAATTACATTAATATGTATTCCCTTTTTATATA	-	novel	NA	P-0061520-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	48	676	0	ENST00000371085.3:c.970+1_971-1del		p.X324_splice	ENST00000371085	NM_000516.4	324		11/13	0.412065514865605	3	FACETS	0.303	0.255	0.356	0.151	0.127	0.178	SUBCLONAL	1	TRUE	1	0.479496571165519	3		676	820	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577544	7577544	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587780074	NA	P-0061520-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	240	582	0	ENST00000269305.4:c.737T>G	p.Met246Arg	p.M246R	ENST00000269305	NM_001126112.2	246	aTg/aGg	7/11	0.479496571165519	2	FACETS	0.902	0.85	0.954	0.902	0.85	0.954	CLONAL	2	TRUE	0	0.479496571165519	2		582	555	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485456	57485736	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTGAGTCGAGCCTGTCTTTAGTTTCCTCTCTTGTTCCTCCTCTTTTTCTCATGGATGTAAATTTACTTAATTCCAAATTCAGGGGTTCAGCTACCCAGTTCCATGGTTTTAGTTCACGCACATCCAGTGTGGATTTGAGCTCTTTGCGCCCCTCTTTTTGCTTTTGTTTTCATATGACATCAGAGGCTGGCTGACAGCCGTCCCTGGTAGGTGTCCCCATCAGGGATAGGGTGGTTCCTGGCGAGGGTGTCACTGACAAGTCCCCTTGTTTGTGCCCGCA	GGTGAGTCGAGCCTGTCTTTAGTTTCCTCTCTTGTTCCTCCTCTTTTTCTCATGGATGTAAATTTACTTAATTCCAAATTCAGGGGTTCAGCTACCCAGTTCCATGGTTTTAGTTCACGCACATCCAGTGTGGATTTGAGCTCTTTGCGCCCCTCTTTTTGCTTTTGTTTTCATATGACATCAGAGGCTGGCTGACAGCCGTCCCTGGTAGGTGTCCCCATCAGGGATAGGGTGGTTCCTGGCGAGGGTGTCACTGACAAGTCCCCTTGTTTGTGCCCGCA	-	novel	NA	P-0061520-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	56	592	0	ENST00000371085.3:c.1038+1_1039-1del		p.X346_splice	ENST00000371085	NM_000516.4	346		12/13	0.412065514865605	3	FACETS	0.353	0.301	0.409	0.176	0.15	0.205	SUBCLONAL	1	TRUE	1	0.479496571165519	3		592	821	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639960	93639960	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061520-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	128	693	0	ENST00000375746.1:c.1289C>T	p.Pro430Leu	p.P430L	ENST00000375746	NM_001174167.1	430	cCg/cTg	10/14	0.468540341565268	3	FACETS	0.883	0.801	0.969	0.294	0.267	0.323	CLONAL	1	TRUE	0	0.479496571165519	3		693	750	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447295	49447295	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061520-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	194	764	1	ENST00000301067.7:c.803G>A	p.Trp268Ter	p.W268*	ENST00000301067	NM_003482.3	268	tGg/tAg	6/54	0.479496571165519	3	FACETS	1	0.979	1	0.573	0.531	0.617	CLONAL	1	TRUE	1	0.479496571165519	3		765	875	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944653	32944653	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061520-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	178	513	0	ENST00000380152.3:c.8446G>T	p.Gly2816Cys	p.G2816C	ENST00000380152		2816	Ggt/Tgt	19/27	0.479496571165519	2	FACETS	0.937	0.876	1	0.937	0.876	1	CLONAL	2	TRUE	0	0.479496571165519	2		513	396	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78811736	78811736	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061520-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	111	566	0	ENST00000306801.3:c.1151T>A	p.Leu384Gln	p.L384Q	ENST00000306801	NM_020761.2	384	cTg/cAg	10/34	0.479496571165519	3	FACETS	0.775	0.697	0.857	0.258	0.232	0.286	SUBCLONAL	1	TRUE	0	0.479496571165519	3		566	741	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31472225	31472225	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061520-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	78	639	0	ENST00000344624.3:c.2186A>T	p.Glu729Val	p.E729V	ENST00000344624		729	gAg/gTg	14/33	0.457156391930724	4	FACETS	0.555	0.487	0.629	0.185	0.162	0.21	SUBCLONAL	1	TRUE	1	0.479496571165519	4		639	867	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861050	35861051	+	missense_variant	Missense_Mutation	DNP	AG	AG	TT	novel	NA	P-0061520-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	184	512	0	ENST00000303115.3:c.179_180delinsTT	p.Glu60Val	p.E60V	ENST00000303115	NM_002185.3	60	gAG/gTT	2/8	0.457156391930724	4	FACETS	0.778	0.72	0.838	0.518	0.48	0.559	SUBCLONAL	2	TRUE	1	0.479496571165519	4		512	730	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509436	106509436	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200175951	NA	P-0061520-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	501	745	0	ENST00000359195.3:c.1430G>T	p.Arg477Leu	p.R477L	ENST00000359195	NM_002649.2	477	cGt/cTt	2/11	0.479496571165519	5	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	2	0.479496571165519	5		745	1096	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0061522-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	212	681	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		681	612	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0061523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	76	350	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.374867241070699	2		350	402	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974809	21974809	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	117	969	0	ENST00000304494.5:c.18del	p.Ser7AlafsTer19	p.S7Afs*19	ENST00000304494	NM_000077.4	6	ggG/gg	1/3	0.374867241070699	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.374867241070699	1		969	444	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891277	101891277	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	75	658	0	ENST00000374994.4:c.238C>T	p.Arg80Ter	p.R80*	ENST00000374994	NM_004612.2	80	Cga/Tga	2/9	0.374867241070699	1	FACETS	0.793	0.698	0.894	0.793	0.698	0.894	SUBCLONAL	1	TRUE	0	0.374867241070699	1		658	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578234	7578234	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0061523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	137	893	0	ENST00000269305.4:c.615T>G	p.Tyr205Ter	p.Y205*	ENST00000269305	NM_001126112.2	205	taT/taG	6/11	0.374867241070699	1	FACETS	0.998	0.911	1	0.998	0.911	1	CLONAL	1	TRUE	0	0.374867241070699	1		893	595	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0061524-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	332	681	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	0.702707607140014	3	FACETS	0.984	0.939	1	0.984	0.939	1	CLONAL	2	TRUE	1	0.702707607140014	3		681	649	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0061525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	306	853	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	1	TRUE	NA	0.558515309268462	2		853	736	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0061525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	170	806	0	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	0.558515309268462	1	FACETS	0.932	0.865	1	0.932	0.865	1	CLONAL	1	TRUE	0	0.558515309268462	1		806	471	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561756	55561756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376469897	NA	P-0061525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	142	598	0	ENST00000288135.5:c.146G>A	p.Arg49His	p.R49H	ENST00000288135	NM_000222.2	49	cGc/cAc	2/21	1	2	FACETS	0.883	0.808	0.96	0.883	0.808	0.96	CLONAL	1	TRUE	1	0.558515309268462	2		598	576	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097686	27097686	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0061525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	343	669	0	ENST00000324856.7:c.3275T>A	p.Leu1092Ter	p.L1092*	ENST00000324856	NM_006015.4	1092	tTg/tAg	12/20	0.486409423781838	2	FACETS	0.841	0.802	0.881	0.841	0.802	0.881	CLONAL	2	TRUE	0	0.558515309268462	2		669	730	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120785311	120785311	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	161	688	0	ENST00000257552.2:c.797C>T	p.Pro266Leu	p.P266L	ENST00000257552	NM_002442.3	266	cCt/cTt	12/15	1	2	FACETS	0.845	0.778	0.916	0.845	0.778	0.916	CLONAL	1	TRUE	1	0.558515309268462	2		688	682	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357237	89357420	+	splice_acceptor_variant,splice_donor_variant,intron_variant	Splice_Site	DEL	CTGCAGGCCAAGGAGGGGACAGATGGGCATTACTGTGGGGTGGTCCTGCTTTGTCCAATCTTCAAGAGCCCAGGCCACCATCACGAGGTCCCTTTGCACAGGGCTTGTCCTCAGCACAGCCATGAGGCTGCGACCAGGCAGAGCCCCTTCCCTGCGCCAGGGACCACCCACAGGCCGGGCTCAC	CTGCAGGCCAAGGAGGGGACAGATGGGCATTACTGTGGGGTGGTCCTGCTTTGTCCAATCTTCAAGAGCCCAGGCCACCATCACGAGGTCCCTTTGCACAGGGCTTGTCCTCAGCACAGCCATGAGGCTGCGACCAGGCAGAGCCCCTTCCCTGCGCCAGGGACCACCCACAGGCCGGGCTCAC	-	novel	NA	P-0061525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	161	809	0	ENST00000301030.4:c.397+1_398-1del		p.X133_splice	ENST00000301030	NM_001256183.1	133			0.347386778329395	3	FACETS	0.828	0.759	0.899	0.276	0.253	0.3	CLONAL	1	TRUE	0	0.558515309268462	3		809	891	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89839751	89839754	+	frameshift_variant	Frame_Shift_Del	DEL	CCTC	CCTC	-	novel	NA	P-0061525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	73	712	0	ENST00000389301.3:c.1939_1942del	p.Glu647SerfsTer13	p.E647Sfs*13	ENST00000389301	NM_000135.2	647	GAGGag/ag	22/43	0.347386778329395	3	FACETS	0.431	0.377	0.491	0.144	0.125	0.164	SUBCLONAL	1	TRUE	0	0.558515309268462	3		712	775	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940784	49940784	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	215	862	0	ENST00000296474.3:c.259T>C	p.Ser87Pro	p.S87P	ENST00000296474	NM_002447.2	87	Tct/Cct	1/20	0.476420457554237	1	FACETS	0.984	0.922	1	0.984	0.922	1	CLONAL	1	TRUE	0	0.558515309268462	1		862	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0061526-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	91	535	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.245802676338579	4	FACETS	0.846	0.755	0.943	0.564	0.503	0.629	CLONAL	2	FALSE	1	0.3	4		535	466	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675071	40675071	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061526-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	71	565	0	ENST00000249776.8:c.35T>G	p.Val12Gly	p.V12G	ENST00000249776	NM_033286.3	12	gTt/gGt	1/9	0.164670423099071	3	FACETS	1	0.927	1	0.543	0.475	0.617	INDETERMINATE	1	FALSE	1	0.3	3		565	501	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573513	48573513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061526-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	90	540	0	ENST00000342988.3:c.97G>T	p.Glu33Ter	p.E33*	ENST00000342988	NM_005359.5	33	Gaa/Taa	2/12	0.213821898688544	2	FACETS	0.792	0.707	0.88	0.792	0.707	0.88	SUBCLONAL	2	FALSE	0	0.3	2		540	379	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849470	68849470	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061526-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	118	579	0	ENST00000261769.5:c.1373A>T	p.Asn458Ile	p.N458I	ENST00000261769	NM_004360.3	458	aAt/aTt	10/16	0.226150510731878	2	FACETS	0.816	0.74	0.895	0.816	0.74	0.895	CLONAL	2	FALSE	0	0.3	2		579	482	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100487	2100487	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061526-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	87	375	0	ENST00000219476.3:c.225G>C	p.Glu75Asp	p.E75D	ENST00000219476	NM_000548.3	75	gaG/gaC	3/42	0.122583288613941	5	FACETS	0.821	0.729	0.919	0.548	0.486	0.613	INDETERMINATE	2	FALSE	2	0.3	5		375	512	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805564	46805564	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061526-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	63	657	0	ENST00000290295.7:c.392C>A	p.Pro131Gln	p.P131Q	ENST00000290295	NM_006361.5	131	cCg/cAg	1/2	0.132113119172723	3	FACETS	1	0.92	1	0.362	0.313	0.414	INDETERMINATE	1	FALSE	0	0.3	3		657	445	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113181	209113181	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061526-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	93	514	0	ENST00000345146.2:c.326G>C	p.Arg109Thr	p.R109T	ENST00000345146	NM_005896.2	109	aGa/aCa	4/10	0.0795592589357632	3	FACETS	1	0.961	1	0.589	0.525	0.658	INDETERMINATE	1	FALSE	1	0.3	3		514	605	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0061527-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	22	255	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.14	2		255	263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0061527-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	34	606	1	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	1	2	FACETS	0.655	0.534	0.793	0.655	0.534	0.793	SUBCLONAL	1	TRUE	1	0.14	2		607	741	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552730	106552730	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061527-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	44	572	0	ENST00000369096.4:c.695G>T	p.Ser232Ile	p.S232I	ENST00000369096	NM_001198.3	232	aGc/aTc	5/7	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.14	2		572	612	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0061560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	488	772	0	ENST00000269305.4:c.920-2A>C		p.X307_splice	ENST00000269305	NM_001126112.2	307			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		772	623	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0061561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	119	350	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.988	0.9	1	0.988	0.9	1	CLONAL	1	TRUE	1	0.605307327386136	2		350	398	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0061561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	248	754	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.595784848274612	1	FACETS	0.964	0.908	1	0.964	0.908	1	CLONAL	1	TRUE	0	0.605307327386136	1		754	593	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0061561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	224	635	6	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	0.605307327386136	1	FACETS	0.788	0.738	0.839	0.788	0.738	0.839	SUBCLONAL	1	TRUE	0	0.605307327386136	1		641	655	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874463	151874463	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	240	615	0	ENST00000262189.6:c.8075A>G	p.Asp2692Gly	p.D2692G	ENST00000262189	NM_170606.2	2692	gAt/gGt	38/59	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.605307327386136	2		615	748	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993741	72993741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544655521	NA	P-0061561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	275	807	0	ENST00000268489.5:c.304G>A	p.Ala102Thr	p.A102T	ENST00000268489	NM_006885.3	102	Gcg/Acg	2/10	1	2	FACETS	0.852	0.8	0.906	0.852	0.8	0.906	CLONAL	1	TRUE	1	0.605307327386136	2		807	1066	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568862	212568862	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	53	486	0	ENST00000342788.4:c.1256A>C	p.Asn419Thr	p.N419T	ENST00000342788	NM_005235.2	419	aAc/aCc	11/28	1	2	FACETS	0.357	0.305	0.415	0.357	0.305	0.415	SUBCLONAL	1	TRUE	1	0.605307327386136	2		486	490	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121110	11121110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749349816	NA	P-0061562-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	159	569	0	ENST00000358026.2:c.2177G>A	p.Arg726His	p.R726H	ENST00000358026	NM_001128849.1	726	cGt/cAt	15/36	0.614559818816871	4	FACETS	0.819	0.757	0.883	0.819	0.757	0.883	CLONAL	2	TRUE	2	0.67153676577316	4		569	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0061563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	162	549	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.540598149650654	1	FACETS	0.994	0.921	1	0.994	0.921	1	CLONAL	1	TRUE	0	0.540598149650654	1		552	440	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0061563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	32	350	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.995	0.824	1	0.995	0.824	1	CLONAL	1	TRUE	1	0.540598149650654	2		350	119	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258744	115258744	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121434596	NA	P-0061563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	64	414	0	ENST00000369535.4:c.38G>T	p.Gly13Val	p.G13V	ENST00000369535	NM_002524.4	13	gGt/gTt	2/7	1	2	FACETS	0.925	0.81	1	0.925	0.81	1	CLONAL	1	TRUE	1	0.540598149650654	2		414	256	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563167	21563167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371775408	NA	P-0061563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	118	630	0	ENST00000382592.4:c.752C>T	p.Ala251Val	p.A251V	ENST00000382592	NM_014572.2	251	gCg/gTg	4/8	0.540598149650654	3	FACETS	0.923	0.835	1	0.461	0.417	0.508	CLONAL	1	TRUE	1	0.540598149650654	3		630	601	SUCCESS
APC	324	MSKCC	GRCh37	5	112174472	112174475	+	frameshift_variant	Frame_Shift_Del	DEL	AAAC	AAAC	-	rs1114167551	NA	P-0061563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	31	469	0	ENST00000257430.4:c.3184_3187del	p.Gln1062ValfsTer63	p.Q1062Vfs*63	ENST00000257430	NM_000038.5	1061	AAACaa/aa	16/16	1	2	FACETS	0.882	0.726	1	0.882	0.726	1	CLONAL	1	TRUE	1	0.540598149650654	2		469	130	SUCCESS
APC	324	MSKCC	GRCh37	5	112175757	112175758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	68	545	0	ENST00000257430.4:c.4467dup	p.His1490ThrfsTer24	p.H1490Tfs*24	ENST00000257430	NM_000038.5	1489	tta/ttAa	16/16	1	2	FACETS	0.998	0.879	1	0.998	0.879	1	CLONAL	1	TRUE	1	0.540598149650654	2		545	252	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981777	201981778	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0061563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	134	601	0	ENST00000359651.3:c.492dup	p.Phe165LeufsTer31	p.F165Lfs*31	ENST00000359651		163	agc/agCc	4/8	1	2	FACETS	0.974	0.89	1	0.974	0.89	1	CLONAL	1	TRUE	1	0.540598149650654	2		601	509	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923028	39923028	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	181	551	0	ENST00000378444.4:c.3680G>T	p.Gly1227Val	p.G1227V	ENST00000378444	NM_001123385.1	1227	gGc/gTc	8/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.540598149650654	2		551	619	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174828	56174829	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0061565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	96	463	0	ENST00000399503.3:c.1992_1993dup	p.Thr665IlefsTer7	p.T665Ifs*7	ENST00000399503	NM_005921.1	663	gta/gTAta	11/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.529306246651208	2		463	310	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696638	47696638	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061566-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	166	590	0	ENST00000347630.2:c.310T>A	p.Phe104Ile	p.F104I	ENST00000347630	NM_001007230.1	104	Ttc/Atc	5/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.512243310733255	2		590	588	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061204	38061204	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061566-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	67	669	0	ENST00000250448.2:c.785G>T	p.Arg262Leu	p.R262L	ENST00000250448	NM_004496.3	262	cGc/cTc	2/2	1	2	FACETS	0.558	0.486	0.635	0.558	0.486	0.635	SUBCLONAL	1	TRUE	1	0.512243310733255	2		669	469	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	364565	364565	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061567-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	26	690	0	ENST00000262320.3:c.997del	p.Leu333CysfsTer81	p.L333Cfs*81	ENST00000262320	NM_003502.3	333	Ctg/tg	3/11	1	2	FACETS	1	0.824	1	1	0.957	1	CLONAL	2	FALSE	1	0.322216135532271	2		690	80	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955137	1955137	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs767239709	NA	P-0061567-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	10	688	0	ENST00000382891.5:c.2224G>T	p.Ala742Ser	p.A742S	ENST00000382891	NM_133335.3	742	Gct/Tct	12/22	0.323378814513577	1	FACETS	0.814	0.561	1	0.814	0.561	1	CLONAL	1	FALSE	0	0.322216135532271	1		688	64	SUCCESS
APC	324	MSKCC	GRCh37	5	112137012	112137022	+	frameshift_variant	Frame_Shift_Del	DEL	GATGCTGAGCG	GATGCTGAGCG	-	novel	NA	P-0061568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	28	514	0	ENST00000257430.4:c.767_777del	p.Asp256AlafsTer3	p.D256Afs*3	ENST00000257430	NM_000038.5	256	GATGCTGAGCGg/g	8/16	1	2	FACETS	0.169	0.135	0.208	0.169	0.135	0.208	SUBCLONAL	1	TRUE	1	0.763564859213812	2		514	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0061571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	65	743	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.968	0.838	1	0.968	0.838	1	CLONAL	1	TRUE	1	0.16	2		743	839	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0061571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	14	402	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	0.0946544103057182	0	FACETS	0.304	0.219	0.409			1	INDETERMINATE	1	TRUE	0	0.16	0		402	483	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028690	12028690	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0061571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	25	501	0	ENST00000353533.5:c.891+2T>C		p.X297_splice	ENST00000353533	NM_003010.3	297			1	2	FACETS	0.631	0.496	0.787	0.631	0.496	0.787	SUBCLONAL	1	TRUE	1	0.16	2		501	495	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432664	29432664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113994087	NA	P-0061572-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	178	528	0	ENST00000389048.3:c.3824G>A	p.Arg1275Gln	p.R1275Q	ENST00000389048	NM_004304.4	1275	cGa/cAa	25/29	1	2	FACETS	0.987	0.917	1	0.987	0.917	1	CLONAL	1	TRUE	1	0.675138134873673	2		528	534	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61323221	61323221	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061572-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	39	186	0	ENST00000283752.5:c.843T>A	p.Asp281Glu	p.D281E	ENST00000283752	NM_006919.2	281	gaT/gaA	8/8	0.675138134873673	3	FACETS	0.736	0.616	0.867	0.368	0.308	0.434	SUBCLONAL	1	TRUE	1	0.675138134873673	3		186	210	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748034	41748047	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCGCTGCTGCTG	CGCCGCTGCTGCTG	-	novel	NA	P-0061572-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	20	226	0	ENST00000226382.2:c.722_735del	p.Ala241GlyfsTer114	p.A241Gfs*114	ENST00000226382	NM_003924.3	241	gCAGCAGCAGCGGCG/g	3/3	1	2	FACETS	0.617	0.481	0.77	0.617	0.481	0.77	SUBCLONAL	1	TRUE	1	0.675138134873673	2		226	96	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188196	10188196	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0061573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	49	440	0	ENST00000256474.2:c.341-2A>T		p.X114_splice	ENST00000256474	NM_000551.3	114			0.197684639408095	1	FACETS	0.921	0.781	1	0.921	0.781	1	CLONAL	1	FALSE	0	0.197684639408095	1		440	485	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205302	61205302	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	50	526	0	ENST00000301761.2:c.245del	p.Asn82ThrfsTer16	p.N82Tfs*16	ENST00000301761	NM_017841.2	81	gAa/ga	2/4	1	2	FACETS	0.778	0.659	0.909	0.778	0.659	0.909	CLONAL	1	FALSE	1	0.197684639408095	2		526	650	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41022055	41022055	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	55	565	0	ENST00000267868.3:c.779G>A	p.Gly260Asp	p.G260D	ENST00000267868	NM_002875.4	260	gGt/gAt	9/10	1	2	FACETS	0.803	0.686	0.931	0.803	0.686	0.931	CLONAL	1	FALSE	1	0.197684639408095	2		565	693	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132567	11132567	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	99	755	0	ENST00000358026.2:c.2783T>G	p.Leu928Arg	p.L928R	ENST00000358026	NM_001128849.1	928	cTg/cGg	19/36	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.197684639408095	2		755	918	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141499	11141499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	56	712	0	ENST00000358026.2:c.3476G>A	p.Gly1159Glu	p.G1159E	ENST00000358026	NM_001128849.1	1159	gGg/gAg	25/36	1	2	FACETS	0.714	0.611	0.828	0.714	0.611	0.828	SUBCLONAL	1	FALSE	1	0.197684639408095	2		712	793	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671617	30671624	+	frameshift_variant	Frame_Shift_Del	DEL	TGTCTCAA	TGTCTCAA	-	novel	NA	P-0061573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	57	738	0	ENST00000376406.3:c.5336_5343del	p.Leu1779ProfsTer15	p.L1779Pfs*15	ENST00000376406	NM_014641.2	1779	cTTGAGACA/c	10/15	1	2	FACETS	0.736	0.63	0.853	0.736	0.63	0.853	SUBCLONAL	1	FALSE	1	0.197684639408095	2		738	783	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263932	104263948	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCCCCCGGCCCCACC	GCGCCCCCGGCCCCACC	-	novel	NA	P-0061575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	21	549	0	ENST00000369902.3:c.37_53del	p.Thr13TrpfsTer29	p.T13Wfs*29	ENST00000369902	NM_016169.3	8	gGCGCCCCCGGCCCCACC/g	1/12	0.590930686210217	1	FACETS	0.227	0.175	0.286	0.227	0.175	0.286	SUBCLONAL	1	TRUE	0	0.590930686210217	1		549	221	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527461	29527461	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786203950	NA	P-0061575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	121	421	0	ENST00000356175.3:c.910C>T	p.Arg304Ter	p.R304*	ENST00000356175	NM_000267.3	304	Cga/Tga	9/57	0.584047521499425	4	FACETS	0.814	0.742	0.889	0.814	0.742	0.889	CLONAL	2	TRUE	2	0.590930686210217	4		421	400	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320926	30320926	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	106	431	0	ENST00000322652.5:c.1336G>C	p.Asp446His	p.D446H	ENST00000322652	NM_015355.2	446	Gat/Cat	12/16	0.584047521499425	4	FACETS	1	0.977	1	0.644	0.581	0.71	CLONAL	1	TRUE	2	0.590930686210217	4		431	443	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0061577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	368	522	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.828957119438762	3	FACETS	0.957	0.918	0.996	0.957	0.918	0.996	CLONAL	2	TRUE	1	0.828957119438762	3		522	656	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720741	89720741	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs371387815	NA	P-0061577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	15	107	0	ENST00000371953.3:c.892C>T	p.Gln298Ter	p.Q298*	ENST00000371953	NM_000314.4	298	Caa/Taa	8/9	0.828957119438762	1	FACETS	0.684	0.536	0.832	0.684	0.536	0.832	SUBCLONAL	1	TRUE	0	0.828957119438762	1		107	31	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940061	49940061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1440811627	NA	P-0061578-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	118	909	0	ENST00000296474.3:c.982C>T	p.Pro328Ser	p.P328S	ENST00000296474	NM_002447.2	328	Cca/Tca	1/20	0.312345915048836	1	FACETS	0.678	0.611	0.748	0.678	0.611	0.748	SUBCLONAL	1	TRUE	0	0.330680300963216	1		909	879	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114203	115114204	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061578-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	256	676	0	ENST00000257566.3:c.1013dup	p.Ser339ValfsTer4	p.S339Vfs*4	ENST00000257566	NM_016569.3	338	gag/gaAg	6/8	0.330680300963216	2	FACETS	0.913	0.857	0.97	0.913	0.857	0.97	CLONAL	2	TRUE	0	0.330680300963216	2		676	848	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578244	7578244	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061578-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	206	790	0	ENST00000269305.4:c.605del	p.Arg202LeufsTer45	p.R202Lfs*45	ENST00000269305	NM_001126112.2	202	cGt/ct	6/11	0.238267511606823	2	FACETS	1	0.99	1	0.698	0.648	0.75	CLONAL	1	TRUE	0	0.330680300963216	2		790	892	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103720	47103720	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0061578-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	47	672	0	ENST00000409792.3:c.6226A>T	p.Lys2076Ter	p.K2076*	ENST00000409792	NM_014159.6	2076	Aaa/Taa	14/21	0.234921160443674	3	FACETS	0.385	0.323	0.453	0.128	0.107	0.151	SUBCLONAL	1	TRUE	0	0.330680300963216	3		672	861	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	604	126	0				ENST00000310581	NM_198253.2	-/1132			0.706286749269224	5	FACETS	0.884	0.859	0.91	0.884	0.859	0.91	CLONAL	4	TRUE	1	0.82748940867177	5		126	925	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0061579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	535	461	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.82748940867177	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.82748940867177	2		461	643	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0061579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	106	215	0	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	0.82748940867177	1	FACETS	0.945	0.881	1	0.945	0.881	1	CLONAL	1	TRUE	0	0.82748940867177	1		215	159	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922763	44922763	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	449	261	0	ENST00000377967.4:c.1624C>T	p.Gln542Ter	p.Q542*	ENST00000377967	NM_021140.2	542	Cag/Tag	16/29	0.492637410125782	2	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.82748940867177	2		261	496	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924289	11924289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	343	771	0	ENST00000353533.5:c.86C>T	p.Pro29Leu	p.P29L	ENST00000353533	NM_003010.3	29	cCa/cTa	1/11	0.82748940867177	2	FACETS	0.96	0.912	1	0.48	0.456	0.504	CLONAL	1	TRUE	0	0.82748940867177	2		771	864	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855029	76855029	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1557085898	NA	P-0061579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	8	190	0	ENST00000373344.5:c.5807A>G	p.Lys1936Arg	p.K1936R	ENST00000373344	NM_000489.3	1936	aAg/aGg	25/35	1	1	FACETS	0.045	0.029	0.067	0.045	0.029	0.067	SUBCLONAL	1	TRUE	0	0.82748940867177	1		190	251	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867571	45867571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	331	699	0	ENST00000391945.4:c.737C>T	p.Ser246Phe	p.S246F	ENST00000391945	NM_000400.3	246	tCc/tTc	9/23	1	2	FACETS	0.995	0.945	1	0.995	0.945	1	CLONAL	1	TRUE	1	0.82748940867177	2		699	804	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582935	95582935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs965350808	NA	P-0061579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	37	495	0	ENST00000393063.1:c.1607G>A	p.Arg536His	p.R536H	ENST00000393063	NM_030621.3	536	cGt/cAt	11/28	1	2	FACETS	0.161	0.132	0.194	0.161	0.132	0.194	SUBCLONAL	1	TRUE	1	0.82748940867177	2		495	554	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058444	42058444	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	162	510	0	ENST00000219905.7:c.8164A>C	p.Asn2722His	p.N2722H	ENST00000219905	NM_001164273.1	2722	Aac/Cac	24/24	0.225054111174165	1	FACETS	0.361	0.333	0.391	0.361	0.333	0.391	INDETERMINATE	1	TRUE	0	0.82748940867177	1		510	635	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37876039	37876039	+	splice_acceptor_variant	In_Frame_Del	SNP	G	G	C	rs113161321	NA	P-0061579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	644	523	0	ENST00000269571.5:c.1899-1G>C		p.C634_S649del	ENST00000269571		634			0.530586222855032	4	FACETS	0.943	0.916	0.969			1	CLONAL	3	TRUE	NA	0.82748940867177	4		523	1006	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936367	78936367	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	93	558	0	ENST00000306801.3:c.3799C>A	p.Leu1267Met	p.L1267M	ENST00000306801	NM_020761.2	1267	Ctg/Atg	32/34	1	2	FACETS	0.308	0.274	0.345	0.308	0.274	0.345	SUBCLONAL	1	TRUE	1	0.82748940867177	2		558	729	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423445	47423445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	260	466	0	ENST00000404338.3:c.1513G>A	p.Glu505Lys	p.E505K	ENST00000404338	NM_004491.4	505	Gaa/Aaa	1/6	1	2	FACETS	0.985	0.929	1	0.985	0.929	1	CLONAL	1	TRUE	1	0.82748940867177	2		466	638	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424422	47424422	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	327	534	0	ENST00000404338.3:c.2490G>C	p.Lys830Asn	p.K830N	ENST00000404338	NM_004491.4	830	aaG/aaC	1/6	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.82748940867177	2		534	749	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022527	31022527	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	342	599	0	ENST00000375687.4:c.2012C>A	p.Ala671Asp	p.A671D	ENST00000375687	NM_015338.5	671	gCc/gAc	13/13	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.82748940867177	2		599	825	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578247	7578247	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061580-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	371	662	0	ENST00000269305.4:c.602del	p.Leu201CysfsTer46	p.L201Cfs*46	ENST00000269305	NM_001126112.2	201	tTg/tg	6/11	0.786873749644655	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.786873749644655	1		662	552	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007162	62007162	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061580-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	49	609	0	ENST00000392795.3:c.520A>G	p.Ile174Val	p.I174V	ENST00000392795	NM_001039933.1	174	Atc/Gtc	4/6	0.786873749644655	2	FACETS	0.164	0.138	0.193	0.082	0.069	0.097	SUBCLONAL	1	TRUE	0	0.786873749644655	2		609	759	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606100	47606100	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061580-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	111	257	0	ENST00000263735.4:c.564T>G	p.Asn188Lys	p.N188K	ENST00000263735	NM_002354.2	188	aaT/aaG	6/9	0.786873749644655	3	FACETS	0.954	0.864	1	0.477	0.432	0.524	CLONAL	1	TRUE	1	0.786873749644655	3		257	412	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0061581-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	236	557	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	1	2	FACETS	0.78	0.73	0.831	1	0.993	1	SUBCLONAL	2	TRUE	1	0.393097431829328	2		557	770	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841048	15841048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061581-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	205	360	0	ENST00000307771.7:c.1132C>T	p.Arg378Trp	p.R378W	ENST00000307771	NM_005089.3	378	Cgg/Tgg	11/11	0.324440559062129	2	FACETS	1	0.939	1			1	CLONAL	2	TRUE	NA	0.393097431829328	2		360	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577586	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCCCATGCAGGAACTGTTACACATGTAGTTGTAGTGGA	CCGCCCATGCAGGAACTGTTACACATGTAGTTGTAGTGGA	-	novel	NA	P-0061581-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	156	608	0	ENST00000269305.4:c.695_734del	p.Ile232ThrfsTer2	p.I232Tfs*2	ENST00000269305	NM_001126112.2	232	aTCCACTACAACTACATGTGTAACAGTTCCTGCATGGGCGGc/ac	7/11	0.393097431829328	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.393097431829328	1		608	508	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128849164	128849168	+	frameshift_variant	Frame_Shift_Del	DEL	CATTA	CATTA	-	novel	NA	P-0061581-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	499	632	2	ENST00000249373.3:c.1393_1397del	p.Ile465LeufsTer13	p.I465Lfs*13	ENST00000249373	NM_005631.4	464	ctCATTAcc/ctcc	8/12	0.393097431829328	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	1	0.393097431829328	4		634	1071	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860515	151860515	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1563205536	NA	P-0061581-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	242	788	0	ENST00000262189.6:c.10147G>T	p.Val3383Leu	p.V3383L	ENST00000262189	NM_170606.2	3383	Gta/Tta	43/59	0.393097431829328	4	FACETS	1	0.989	1	0.434	0.405	0.465	CLONAL	1	TRUE	1	0.393097431829328	4		788	1316	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0061582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	52	722	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.996	0.847	1	0.996	0.847	1	CLONAL	1	TRUE	1	0.15	2		724	696	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252866	36252866	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	34	501	0	ENST00000300305.3:c.496C>G	p.Arg166Gly	p.R166G	ENST00000300305		166	Cga/Gga	4/8	1	2	FACETS	0.83	0.677	1	0.83	0.677	1	CLONAL	1	TRUE	1	0.15	2		501	546	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0061582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	46	501	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	1	2	FACETS	0.984	0.828	1	0.984	0.828	1	CLONAL	1	TRUE	1	0.15	2		501	623	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945133	44945133	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	26	351	0	ENST00000377967.4:c.3457T>C	p.Cys1153Arg	p.C1153R	ENST00000377967	NM_021140.2	1153	Tgt/Cgt	24/29	1	2	FACETS	0.818	0.647	1	0.818	0.647	1	CLONAL	1	TRUE	1	0.15	2		351	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0061583-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	197	812	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.495675040131471	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.495675040131471	1		812	587	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374882	45374882	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs776149698	NA	P-0061583-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	93	598	0	ENST00000262160.6:c.961C>T	p.Arg321Ter	p.R321*	ENST00000262160	NM_005901.5	321	Cga/Tga	8/11	0.495675040131471	1	FACETS	0.62	0.554	0.69	0.62	0.554	0.69	SUBCLONAL	1	TRUE	0	0.495675040131471	1		598	455	SUCCESS
APC	324	MSKCC	GRCh37	5	112174129	112174135	+	frameshift_variant	Frame_Shift_Del	DEL	ATGTTCT	ATGTTCT	-	novel	NA	P-0061583-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	130	580	0	ENST00000257430.4:c.2841_2847del	p.Ser948LeufsTer5	p.S948Lfs*5	ENST00000257430	NM_000038.5	946	acATGTTCT/ac	16/16	0.34778679217596	1	FACETS	0.778	0.71	0.849	0.778	0.71	0.849	SUBCLONAL	1	TRUE	0	0.495675040131471	1		580	507	SUCCESS
APC	324	MSKCC	GRCh37	5	112175760	112175760	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061583-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	81	636	2	ENST00000257430.4:c.4469del	p.His1490LeufsTer17	p.H1490Lfs*17	ENST00000257430	NM_000038.5	1490	cAt/ct	16/16	0.34778679217596	1	FACETS	0.401	0.353	0.452	0.401	0.353	0.452	SUBCLONAL	1	TRUE	0	0.495675040131471	1		638	613	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150530	157150530	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061583-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	127	603	0	ENST00000346085.5:c.1713del	p.Gly572GlufsTer21	p.G572Efs*21	ENST00000346085	NM_020732.3	571	gCc/gc	2/20	1	2	FACETS	0.824	0.748	0.903	0.824	0.748	0.903	CLONAL	1	TRUE	1	0.495675040131471	2		603	622	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10796822	10796822	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372648972	NA	P-0061584-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	89	666	0	ENST00000361367.2:c.2954G>A	p.Arg985His	p.R985H	ENST00000361367	NM_014633.3	985	cGt/cAt	23/25	0.424445136060134	3	FACETS	1	0.935	1	0.535	0.476	0.598	CLONAL	1	TRUE	1	0.427654233882993	3		666	472	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	106	414	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.329144934154301	3	FACETS	0.832	0.75	0.917	0.832	0.75	0.917	CLONAL	2	TRUE	1	0.329144934154301	3		414	451	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0061585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	138	333	5	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.329144934154301	3	FACETS	0.894	0.824	0.966	0.894	0.824	0.966	CLONAL	3	TRUE	0	0.329144934154301	3		338	364	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120062	70120062	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	64	489	0	ENST00000245479.2:c.1067del	p.Pro356ArgfsTer27	p.P356Rfs*27	ENST00000245479	NM_000346.3	355	gCc/gc	3/3	0.329144934154301	2	FACETS	0.815	0.707	0.932	0.408	0.353	0.466	CLONAL	1	TRUE	0	0.329144934154301	2		489	477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577518	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGATGG	novel	NA	P-0061585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	202	589	0	ENST00000269305.4:c.758_763dup	p.Thr253_Ile254dup	p.T253_I254dup	ENST00000269305	NM_001126112.2	253	atc/aCCATCAtc	7/11	0.329144934154301	2	FACETS	0.936	0.871	1	0.936	0.871	1	CLONAL	2	TRUE	0	0.329144934154301	2		589	656	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533261	29533261	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786202145	NA	P-0061585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	215	597	2	ENST00000356175.3:c.1264G>A	p.Ala422Thr	p.A422T	ENST00000356175	NM_000267.3	422	Gca/Aca	12/57	0.329144934154301	2	FACETS	0.966	0.902	1	0.966	0.902	1	CLONAL	2	TRUE	0	0.329144934154301	2		599	676	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023494	31023494	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	240	689	0	ENST00000375687.4:c.2979del	p.Pro994LeufsTer30	p.P994Lfs*30	ENST00000375687	NM_015338.5	993	agT/ag	13/13	0.208922510929426	4	FACETS	0.974	0.91	1	0.974	0.91	1	CLONAL	2	TRUE	2	0.329144934154301	4		689	995	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0061587-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	64	441	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.626	0.542	0.718	0.626	0.542	0.718	SUBCLONAL	1	TRUE	1	0.322988702408767	2		441	633	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0061587-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	51	326	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.71	0.604	0.825	0.71	0.604	0.825	SUBCLONAL	1	TRUE	1	0.322988702408767	2		326	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0061587-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	86	455	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	1	2	FACETS	0.99	0.878	1	0.99	0.878	1	CLONAL	1	TRUE	1	0.322988702408767	2		455	538	SUCCESS
APC	324	MSKCC	GRCh37	5	112173830	112173830	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061587-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	82	466	0	ENST00000257430.4:c.2539G>T	p.Glu847Ter	p.E847*	ENST00000257430	NM_000038.5	847	Gaa/Taa	16/16	1	2	FACETS	0.824	0.727	0.928	0.824	0.727	0.928	CLONAL	1	TRUE	1	0.322988702408767	2		466	616	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727501	88727501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147992979	NA	P-0061587-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	79	570	0	ENST00000360948.2:c.278C>T	p.Thr93Met	p.T93M	ENST00000360948	NM_001012338.2	93	aCg/aTg	3/19	1	2	FACETS	0.708	0.622	0.8	0.708	0.622	0.8	SUBCLONAL	1	TRUE	1	0.322988702408767	2		570	691	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793183	42793183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777585940	NA	P-0061587-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	112	695	0	ENST00000575354.2:c.1075G>A	p.Gly359Arg	p.G359R	ENST00000575354	NM_015125.3	359	Ggg/Agg	7/20	1	2	FACETS	0.802	0.721	0.888	0.802	0.721	0.888	CLONAL	1	TRUE	1	0.322988702408767	2		695	865	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710522	114710522	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061587-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	99	490	0	ENST00000543371.1:c.7C>T	p.Gln3Ter	p.Q3*	ENST00000543371	NM_001198531.1	3	Cag/Tag	1/14	1	2	FACETS	0.844	0.754	0.941	0.844	0.754	0.941	CLONAL	1	TRUE	1	0.322988702408767	2		490	726	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	186	126	0				ENST00000310581	NM_198253.2	-/1132			0.548008455247752	4	FACETS	0.859	0.799	0.92	0.859	0.799	0.92	CLONAL	2	FALSE	2	0.647574156907822	4		126	551	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	403	292	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	0.572498100390532	2	FACETS	1	0.996	1			1	CLONAL	2	FALSE	NA	0.647574156907822	2		292	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	33	680	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.647574156907822	2	FACETS	0.178	0.144	0.216	0.089	0.072	0.108	SUBCLONAL	1	FALSE	0	0.647574156907822	2		680	572	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45854910	45854910	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs200022901	NA	P-0061588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	350	542	0	ENST00000391945.4:c.2260G>C	p.Glu754Gln	p.E754Q	ENST00000391945	NM_000400.3	754	Gag/Cag	23/23	0.637503059688685	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	FALSE	1	0.647574156907822	3		542	683	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	288	328	0	ENST00000335508.6:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000335508	NM_012433.2	902	Gaa/Aaa	18/25	0.620960579941878	5	FACETS	1	0.98	1			1	CLONAL	2	FALSE	NA	0.647574156907822	5		328	813	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229229	123229229	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0061588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	312	194	0	ENST00000218089.9:c.3713C>G	p.Ser1238Ter	p.S1238*	ENST00000218089	NM_001042749.1	1238	tCa/tGa	34/35	0.531936165103222	2	FACETS	1	0.995	1			1	CLONAL	2	FALSE	NA	0.647574156907822	2		194	393	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095620	178095620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	204	582	0	ENST00000397062.3:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000397062	NM_006164.4	571	Gaa/Aaa	5/5	0.596888869091458	4	FACETS	1	0.971	1	0.363	0.337	0.391	CLONAL	1	FALSE	1	0.647574156907822	4		582	952	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351208	89351208	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	417	642	0	ENST00000301030.4:c.1742C>G	p.Ser581Cys	p.S581C	ENST00000301030	NM_001256183.1	581	tCt/tGt	9/13	0.637503059688685	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	FALSE	1	0.647574156907822	3		642	803	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244517	46244517	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	358	612	1	ENST00000334344.6:c.2611C>T	p.Gln871Ter	p.Q871*	ENST00000334344	NM_152641.2	871	Cag/Tag	15/21	0.330586938826624	5	FACETS	1	0.99	1	0.764	0.726	0.802	INDETERMINATE	2	FALSE	2	0.647574156907822	5		613	951	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463320	25463320	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0061588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	436	621	0	ENST00000264709.3:c.2174-1G>T		p.X725_splice	ENST00000264709	NM_175629.2	725			0.596888869091458	4	FACETS	0.92	0.884	0.955	0.92	0.884	0.955	CLONAL	3	FALSE	1	0.647574156907822	4		621	804	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401285	139401285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	386	742	0	ENST00000277541.6:c.3784G>A	p.Glu1262Lys	p.E1262K	ENST00000277541	NM_017617.3	1262	Gag/Aag	23/34	0.647574156907822	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	FALSE	0	0.647574156907822	2		742	573	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971164	21971166	+	inframe_deletion	In_Frame_Del	DEL	AGC	AGC	-	novel	NA	P-0061588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	368	655	0	ENST00000304494.5:c.192_194del	p.Leu65del	p.L65del	ENST00000304494	NM_000077.4	64	ctGCTc/ctc	2/3	0.647574156907822	2	FACETS	0.936	0.899	0.972	0.936	0.899	0.972	CLONAL	2	FALSE	0	0.647574156907822	2		655	607	SUCCESS
MET	4233	MSKCC	GRCh37	7	116381073	116381073	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	534	551	0	ENST00000397752.3:c.1695C>G	p.Ile565Met	p.I565M	ENST00000397752	NM_000245.2	565	atC/atG	5/21	0.596888869091458	4	FACETS	0.934	0.901	0.966	0.934	0.901	0.966	CLONAL	3	FALSE	1	0.647574156907822	4		551	970	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102198787	102198787	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	146	295	0	ENST00000263464.3:c.958G>C	p.Glu320Gln	p.E320Q	ENST00000263464	NM_001165.4	320	Gag/Cag	4/9	0.637503059688685	3	FACETS	1	0.982	1	0.624	0.574	0.676	CLONAL	1	FALSE	1	0.647574156907822	3		295	478	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691118	18691118	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	257	417	0	ENST00000266497.5:c.3229G>C	p.Glu1077Gln	p.E1077Q	ENST00000266497		1077	Gag/Cag	23/31	0.330586938826624	5	FACETS	1	0.99	1	0.824	0.777	0.871	INDETERMINATE	2	FALSE	2	0.647574156907822	5		417	633	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636409	73636409	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	684	655	0	ENST00000377687.4:c.672G>T	p.Gln224His	p.Q224H	ENST00000377687	NM_001730.3	224	caG/caT	2/4	0.38975157225846	6	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	FALSE	3	0.647574156907822	6		655	1394	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14022063	14022063	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	153	369	0	ENST00000311895.7:c.763G>C	p.Glu255Gln	p.E255Q	ENST00000311895	NM_005236.2	255	Gaa/Caa	4/11	0.637503059688685	3	FACETS	1	0.952	1	0.526	0.483	0.57	CLONAL	1	FALSE	1	0.647574156907822	3		369	595	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831312	89831312	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	117	586	0	ENST00000389301.3:c.2764G>C	p.Glu922Gln	p.E922Q	ENST00000389301	NM_000135.2	922	Gag/Cag	28/43	0.637503059688685	3	FACETS	0.617	0.557	0.681	0.309	0.278	0.341	SUBCLONAL	1	FALSE	1	0.647574156907822	3		586	775	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578432	7578433	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0061588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	429	758	0	ENST00000269305.4:c.497dup	p.Gln167ThrfsTer14	p.Q167Tfs*14	ENST00000269305	NM_001126112.2	166	tca/tcCa	5/11	0.647574156907822	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	FALSE	0	0.647574156907822	2		758	658	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438152	56438152	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	344	619	0	ENST00000407977.2:c.841G>C	p.Glu281Gln	p.E281Q	ENST00000407977		281	Gag/Cag	7/10	0.594098740605488	4	FACETS	0.96	0.911	1	0.96	0.911	1	CLONAL	2	FALSE	2	0.647574156907822	4		619	912	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212281	36212281	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	289	695	0	ENST00000222270.7:c.2032G>T	p.Glu678Ter	p.E678*	ENST00000222270	NM_014727.1	678	Gag/Tag	3/37	0.637503059688685	3	FACETS	1	0.994	1	0.728	0.687	0.769	CLONAL	1	FALSE	1	0.647574156907822	3		695	812	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423409	47423409	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	192	485	0	ENST00000404338.3:c.1477C>T	p.Gln493Ter	p.Q493*	ENST00000404338	NM_004491.4	493	Cag/Tag	1/6	0.637503059688685	3	FACETS	1	0.97	1	0.543	0.503	0.583	CLONAL	1	FALSE	1	0.647574156907822	3		485	723	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424006	47424006	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs375267312	NA	P-0061588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	236	551	0	ENST00000404338.3:c.2074C>G	p.His692Asp	p.H692D	ENST00000404338	NM_004491.4	692	Cat/Gat	1/6	0.637503059688685	3	FACETS	1	0.982	1	0.566	0.529	0.603	CLONAL	1	FALSE	1	0.647574156907822	3		551	853	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424267	47424267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	275	510	0	ENST00000404338.3:c.2335G>A	p.Asp779Asn	p.D779N	ENST00000404338	NM_004491.4	779	Gat/Aat	1/6	0.637503059688685	3	FACETS	1	0.991	1	0.652	0.614	0.691	CLONAL	1	FALSE	1	0.647574156907822	3		510	862	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425230	47425230	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	250	595	0	ENST00000404338.3:c.3298G>A	p.Glu1100Lys	p.E1100K	ENST00000404338	NM_004491.4	1100	Gaa/Aaa	1/6	0.637503059688685	3	FACETS	1	0.976	1	0.543	0.508	0.578	CLONAL	1	FALSE	1	0.647574156907822	3		595	942	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023162	31023162	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	256	599	0	ENST00000375687.4:c.2647G>C	p.Glu883Gln	p.E883Q	ENST00000375687	NM_015338.5	883	Gaa/Caa	13/13	0.637503059688685	3	FACETS	1	0.988	1	0.609	0.571	0.647	CLONAL	1	FALSE	1	0.647574156907822	3		599	860	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014214	70014214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150995386	NA	P-0061588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	1451	663	0	ENST00000394351.3:c.1075G>A	p.Glu359Lys	p.E359K	ENST00000394351	NM_000248.3	359	Gag/Aag	9/9	0.647574156907822	7	FACETS	1	0.995	1			1	CLONAL	6	FALSE	NA	0.647574156907822	7		663	1909	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144354748	144354748	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1381835671	NA	P-0061588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	160	451	0	ENST00000262995.4:c.472C>G	p.Leu158Val	p.L158V	ENST00000262995	NM_207123.2	158	Cta/Gta	3/11	1	2	FACETS	0.996	0.921	1	0.996	0.921	1	CLONAL	1	FALSE	1	0.647574156907822	2		451	496	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553261	106553261	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	234	802	0	ENST00000369096.4:c.1226A>C	p.His409Pro	p.H409P	ENST00000369096	NM_001198.3	409	cAc/cCc	5/7	0.647574156907822	3	FACETS	0.977	0.912	1	0.489	0.456	0.522	CLONAL	1	FALSE	1	0.647574156907822	3		802	979	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922857	44922857	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765545282	NA	P-0061588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	371	314	0	ENST00000377967.4:c.1718C>T	p.Ser573Phe	p.S573F	ENST00000377967	NM_021140.2	573	tCt/tTt	16/29	0.572498100390532	2	FACETS	0.839	0.816	0.861			1	CLONAL	3	FALSE	NA	0.647574156907822	2		314	455	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842405	68842405	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	77	638	0	ENST00000261769.5:c.466T>G	p.Trp156Gly	p.W156G	ENST00000261769	NM_004360.3	156	Tgg/Ggg	4/16	0.269816992639069	1	FACETS	0.824	0.724	0.932	0.824	0.724	0.932	CLONAL	1	TRUE	0	0.269816992639069	1		638	599	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579378	7579379	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0061589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	105	842	0	ENST00000269305.4:c.308dup	p.Tyr103Ter	p.Y103*	ENST00000269305	NM_001126112.2	103	tac/taAc	4/11	0.269816992639069	1	FACETS	0.947	0.849	1	0.947	0.849	1	CLONAL	1	TRUE	0	0.269816992639069	1		842	711	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376376	15376376	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1055405627	NA	P-0061589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	150	786	0	ENST00000263377.2:c.638C>T	p.Pro213Leu	p.P213L	ENST00000263377	NM_058243.2	213	cCg/cTg	5/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.269816992639069	2		786	808	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190830	106190830	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	224	527	0	ENST00000380013.4:c.4108G>T	p.Gly1370Trp	p.G1370W	ENST00000380013	NM_001127208.2	1370	Ggg/Tgg	9/11	0.455564907257536	2	FACETS	0.924	0.869	0.98	0.924	0.869	0.98	CLONAL	2	TRUE	0	0.455564907257536	2		527	532	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230492839	230492839	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	172	674	0	ENST00000391860.1:c.215G>C	p.Ser72Thr	p.S72T	ENST00000391860	NM_001258311.1	72	aGc/aCc	2/7	0.261154474663085	4	FACETS	1	0.984	1	0.63	0.58	0.682	INDETERMINATE	1	TRUE	2	0.455564907257536	4		674	872	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028796	42028799	+	frameshift_variant	Frame_Shift_Del	DEL	ATGG	ATGG	-	novel	NA	P-0061591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	192	686	0	ENST00000219905.7:c.4335_4338del	p.His1445GlnfsTer34	p.H1445Qfs*34	ENST00000219905	NM_001164273.1	1445	cATGGa/ca	13/24	0.261154474663085	4	FACETS	1	0.988	1	0.673	0.623	0.726	INDETERMINATE	1	TRUE	2	0.455564907257536	4		686	911	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864560	56864560	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	277	529	0	ENST00000308159.5:c.1048A>T	p.Thr350Ser	p.T350S	ENST00000308159	NM_014669.4	350	Acc/Tcc	10/22	0.455564907257536	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.455564907257536	2		529	582	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579499	7579500	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CTTCATC	novel	NA	P-0061591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	350	837	0	ENST00000269305.4:c.181_187dup	p.Ala63GlyfsTer2	p.A63Gfs*2	ENST00000269305	NM_001126112.2	63	gct/gGATGAAGct	4/11	0.453522370121961	2	FACETS	0.862	0.82	0.905	0.862	0.82	0.905	CLONAL	2	TRUE	0	0.455564907257536	2		837	891	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213914	36213914	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	286	681	2	ENST00000222270.7:c.2740G>C	p.Glu914Gln	p.E914Q	ENST00000222270	NM_014727.1	914	Gag/Cag	6/37	0.407376004419938	4	FACETS	0.897	0.844	0.951	0.897	0.844	0.951	CLONAL	2	TRUE	2	0.455564907257536	4		683	1019	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864451	162864451	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs530092788	NA	P-0061591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	166	544	0	ENST00000366898.1:c.62C>A	p.Thr21Asn	p.T21N	ENST00000366898	NM_004562.2	21	aCc/aAc	2/12	0.270655526557458	4	FACETS	1	0.989	1	0.745	0.686	0.806	INDETERMINATE	1	TRUE	2	0.455564907257536	4		544	712	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0061592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	442	539	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.732656877236762	2	FACETS	0.959	0.929	0.988	0.959	0.929	0.988	CLONAL	2	TRUE	0	0.732656877236762	2		539	629	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926888	112926888	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507546	NA	P-0061592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	332	409	2	ENST00000351677.2:c.1508G>T	p.Gly503Val	p.G503V	ENST00000351677	NM_002834.3	503	gGg/gTg	13/16	0.732078793444894	2	FACETS	0.952	0.917	0.986	0.952	0.917	0.986	CLONAL	2	TRUE	0	0.732656877236762	2		411	476	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674234	86674234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	192	401	0	ENST00000274376.6:c.2366G>A	p.Arg789Gln	p.R789Q	ENST00000274376	NM_002890.2	789	cGa/cAa	18/25	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.732656877236762	2		401	516	SUCCESS
AR	367	MSKCC	GRCh37	X	66766603	66766603	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs753693014	NA	P-0061592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	333	490	3	ENST00000374690.3:c.1615C>A	p.Arg539Ser	p.R539S	ENST00000374690	NM_000044.3	539	Cgt/Agt	1/8	0.732656877236762	2	FACETS	0.957	0.922	0.991	0.957	0.922	0.991	CLONAL	2	TRUE	0	0.732656877236762	2		493	475	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282315	115282315	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	220	318	2	ENST00000438362.2:c.335G>A	p.Gly112Glu	p.G112E	ENST00000438362	NM_001242891.1	112	gGa/gAa	3/20	0.732656877236762	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.732656877236762	1		320	335	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547011	9547011	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	249	558	1	ENST00000353224.5:c.1011G>T	p.Gln337His	p.Q337H	ENST00000353224	NM_177990.2	337	caG/caT	5/10	0.651813845606346	4	FACETS	1	0.979	1	0.554	0.518	0.592	CLONAL	1	TRUE	2	0.732656877236762	4		559	1062	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733349	40733349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	396	462	3	ENST00000373198.4:c.3457G>T	p.Val1153Leu	p.V1153L	ENST00000373198	NM_133170.3	1153	Gtg/Ttg	26/32	0.368812201265542	3	FACETS	0.973	0.933	1	0.649	0.622	0.676	INDETERMINATE	2	TRUE	0	0.732656877236762	3		465	759	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940054	49940054	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	280	717	1	ENST00000296474.3:c.989del	p.Gly330ValfsTer8	p.G330Vfs*8	ENST00000296474	NM_002447.2	330	gGt/gt	1/20	1	2	FACETS	0.858	0.808	0.909	0.858	0.808	0.909	CLONAL	1	TRUE	1	0.732656877236762	2		718	891	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480459	89480459	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	180	447	0	ENST00000336596.2:c.2296G>C	p.Gly766Arg	p.G766R	ENST00000336596	NM_005233.5	766	Gga/Cga	13/17	1	2	FACETS	0.908	0.843	0.975	0.908	0.843	0.975	CLONAL	1	TRUE	1	0.732656877236762	2		447	541	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670261	134670261	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	231	573	0	ENST00000398015.3:c.172T>G	p.Tyr58Asp	p.Y58D	ENST00000398015	NM_004441.4	58	Tac/Gac	3/16	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.732656877236762	2		573	586	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825392	134825392	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	212	483	0	ENST00000398015.3:c.908G>A	p.Cys303Tyr	p.C303Y	ENST00000398015	NM_004441.4	303	tGt/tAt	4/16	1	2	FACETS	0.927	0.867	0.989	0.927	0.867	0.989	CLONAL	1	TRUE	1	0.732656877236762	2		483	624	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238578	142238578	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	196	411	1	ENST00000350721.4:c.4315G>T	p.Gly1439Cys	p.G1439C	ENST00000350721	NM_001184.3	1439	Ggt/Tgt	24/47	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.732656877236762	2		412	482	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861089	35861089	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1263850945	NA	P-0061592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	206	433	0	ENST00000303115.3:c.218T>C	p.Ile73Thr	p.I73T	ENST00000303115	NM_002185.3	73	aTa/aCa	2/8	0.732656877236762	3	FACETS	1	0.97	1	0.537	0.499	0.575	CLONAL	1	TRUE	1	0.732656877236762	3		433	716	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945130	151945130	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	55	289	0	ENST00000262189.6:c.2389C>G	p.Leu797Val	p.L797V	ENST00000262189	NM_170606.2	797	Ctg/Gtg	14/59	0.235705031791152	5	FACETS	0.868	0.746	1	0.289	0.248	0.334	INDETERMINATE	1	TRUE	2	0.732656877236762	5		289	363	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104616	69104616	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	183	542	0	ENST00000288368.4:c.4460C>A	p.Ala1487Asp	p.A1487D	ENST00000288368	NM_024870.2	1487	gCc/gAc	37/40	0.732656877236762	3	FACETS	0.839	0.775	0.904	0.419	0.387	0.452	CLONAL	1	TRUE	1	0.732656877236762	3		542	814	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486219	8486219	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061592-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	297	566	0	ENST00000356435.5:c.2598G>T	p.Glu866Asp	p.E866D	ENST00000356435		866	gaG/gaT	17/35	0.579454614288529	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.732656877236762	1		566	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0061593-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	85	722	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.237851548086858	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.237851548086858	1		724	565	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0061593-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	71	550	4	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.237851548086858	2		554	565	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0061593-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	60	512	1	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	1	2	FACETS	0.903	0.778	1	0.903	0.778	1	CLONAL	1	TRUE	1	0.237851548086858	2		513	559	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0061593-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	56	455	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.776	0.664	0.898	0.776	0.664	0.898	SUBCLONAL	1	TRUE	1	0.237851548086858	2		455	607	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253371	226253371	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061593-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	32	338	2	ENST00000366813.1:c.143C>T	p.Ala48Val	p.A48V	ENST00000366813		48	gCg/gTg	2/3	1	2	FACETS	0.773	0.628	0.936	0.773	0.628	0.936	CLONAL	1	TRUE	1	0.237851548086858	2		340	348	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0061593-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	38	333	5	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.805	0.666	0.959	0.805	0.666	0.959	CLONAL	1	TRUE	1	0.237851548086858	2		338	397	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129867	55129867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373126818	NA	P-0061593-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	56	608	7	ENST00000257290.5:c.401C>T	p.Thr134Met	p.T134M	ENST00000257290	NM_006206.4	134	aCg/aTg	4/23	1	2	FACETS	0.74	0.634	0.857	0.74	0.634	0.857	SUBCLONAL	1	TRUE	1	0.237851548086858	2		615	636	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920401	114920401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1422891742	NA	P-0061593-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	53	363	0	ENST00000543371.1:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000543371	NM_001198531.1	448	Cgg/Tgg	13/14	1	2	FACETS	0.838	0.715	0.973	0.838	0.715	0.973	CLONAL	1	TRUE	1	0.237851548086858	2		363	532	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434564	140434564	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1481562268	NA	P-0061593-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	60	400	4	ENST00000288602.6:c.2134G>A	p.Ala712Thr	p.A712T	ENST00000288602	NM_004333.4	712	Gcc/Acc	18/18	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.237851548086858	2		404	447	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0061595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	27	248	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.295387358187658	3	FACETS	0.892	0.713	1	0.446	0.356	0.548	CLONAL	1	TRUE	1	0.29	3		248	239	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	188	126	0				ENST00000310581	NM_198253.2	-/1132			0.252327052243204	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.29	4		126	760	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0061595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	187	310	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.295387358187658	5	FACETS	1	0.941	1	1	0.941	1	CLONAL	4	TRUE	1	0.29	5		310	459	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201902	67201902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55642995	NA	P-0061595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	122	707	1	ENST00000312629.5:c.1102G>A	p.Val368Met	p.V368M	ENST00000312629	NM_003952.2	368	Gtg/Atg	13/15	0.295387358187658	5	FACETS	1	0.948	1			1	CLONAL	1	TRUE	NA	0.29	5		708	1118	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578179	7578179	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	311	675	0	ENST00000269305.4:c.670G>T	p.Glu224Ter	p.E224*	ENST00000269305	NM_001126112.2	224	Gag/Tag	6/11	0.295387358187658	3	FACETS	1	0.948	1			1	CLONAL	3	TRUE	NA	0.29	3		675	818	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0061595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	86	407	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	0.295377267736186	3	FACETS	1	0.936	1	0.542	0.48	0.609	CLONAL	1	TRUE	1	0.29	3		407	626	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651906	36651906	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1581	288	681	0	ENST00000244741.5:c.28C>T	p.Gln10Ter	p.Q10*	ENST00000244741	NM_000389.4	10	Cag/Tag	2/3	0.295387358187658	8	FACETS	0.994	0.931	1			1	CLONAL	2	TRUE	NA	0.29	8		681	1869	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873724	35873724	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs999467784	NA	P-0061595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	93	568	0	ENST00000216797.5:c.127G>C	p.Glu43Gln	p.E43Q	ENST00000216797	NM_020529.2	43	Gag/Cag	1/6	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.29	2		568	596	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371781	118371781	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	84	534	0	ENST00000534358.1:c.6238C>G	p.Pro2080Ala	p.P2080A	ENST00000534358	NM_005933.3	2080	Cca/Gca	25/36	1	2	FACETS	0.966	0.854	1	0.966	0.854	1	CLONAL	1	TRUE	1	0.29	2		534	600	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185028	32185028	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs140082058	NA	P-0061595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	105	693	0	ENST00000375023.3:c.1640G>T	p.Arg547Leu	p.R547L	ENST00000375023	NM_004557.3	547	cGa/cTa	10/30	0.295387358187658	2	FACETS	1	0.942	1	0.537	0.482	0.596	CLONAL	1	TRUE	0	0.29	2		693	674	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212200	36212200	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	212	522	0	ENST00000222270.7:c.1951C>T	p.Gln651Ter	p.Q651*	ENST00000222270	NM_014727.1	651	Cag/Tag	3/37	0.295387358187658	5	FACETS	1	0.935	1	1	0.935	1	CLONAL	3	TRUE	2	0.29	5		522	698	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911979	32911979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	113	499	0	ENST00000380152.3:c.3487G>A	p.Asp1163Asn	p.D1163N	ENST00000380152		1163	Gat/Aat	11/27	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.29	2		499	590	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363489	40363489	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749442938	NA	P-0061595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	868	733	0	ENST00000397332.2:c.740G>A	p.Arg247His	p.R247H	ENST00000397332	NM_001033082.2	247	cGt/cAt	3/3	0.295387358187658	10	FACETS	1	0.989	1			1	CLONAL	8	TRUE	NA	0.29	10		733	1565	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245724	46245724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565624116	NA	P-0061595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	381	718	0	ENST00000334344.6:c.3818G>A	p.Arg1273Gln	p.R1273Q	ENST00000334344	NM_152641.2	1273	cGa/cAa	15/21	0.270952226068713	4	FACETS	0.952	0.908	0.996			1	CLONAL	4	TRUE	NA	0.29	4		718	890	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614556	38614556	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	90	351	0	ENST00000299084.4:c.322G>C	p.Asp108His	p.D108H	ENST00000299084	NM_152594.2	108	Gat/Cat	3/7	0.295377267736186	3	FACETS	0.945	0.845	1	0.945	0.845	1	CLONAL	2	TRUE	1	0.29	3		351	376	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50788108	50788108	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	46	356	0	ENST00000307179.4:c.2722G>C	p.Glu908Gln	p.E908Q	ENST00000307179		908	Gaa/Caa	17/20	0.295377267736186	3	FACETS	0.982	0.829	1	0.491	0.414	0.575	CLONAL	1	TRUE	1	0.29	3		356	370	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250888	99250888	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	110	611	0	ENST00000268035.6:c.192C>G	p.Ile64Met	p.I64M	ENST00000268035	NM_000875.3	64	atC/atG	2/21	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.29	2		611	742	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390468	56390468	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	111	381	0	ENST00000348428.3:c.1207G>C	p.Asp403His	p.D403H	ENST00000348428	NM_006785.3	403	Gac/Cac	10/17	0.295377267736186	3	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	1	0.29	3		381	428	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602859	10602859	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	116	714	0	ENST00000171111.5:c.719G>C	p.Arg240Pro	p.R240P	ENST00000171111	NM_203500.1	240	cGc/cCc	3/6	0.271812671393232	2	FACETS	0.966	0.871	1	0.483	0.435	0.534	CLONAL	1	TRUE	0	0.29	2		714	828	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094979	11094979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	262	709	0	ENST00000358026.2:c.152C>T	p.Ser51Leu	p.S51L	ENST00000358026	NM_001128849.1	51	tCa/tTa	2/36	0.271812671393232	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.29	2		709	766	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152056	11152056	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854225	NA	P-0061595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	94	710	0	ENST00000358026.2:c.4340G>A	p.Arg1447Gln	p.R1447Q	ENST00000358026	NM_001128849.1	1447	cGa/cAa	31/36	0.271812671393232	2	FACETS	0.794	0.706	0.889	0.397	0.353	0.445	SUBCLONAL	1	TRUE	0	0.29	2		710	816	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982426	25982426	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	190	454	0	ENST00000435504.4:c.864C>G	p.Asn288Lys	p.N288K	ENST00000435504		288	aaC/aaG	9/13	0.252327052243204	4	FACETS	0.835	0.775	0.897	1	0.986	1	CLONAL	3	TRUE	2	0.29	4		454	675	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982482	25982482	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	132	461	0	ENST00000435504.4:c.808G>C	p.Asp270His	p.D270H	ENST00000435504		270	Gac/Cac	9/13	0.252327052243204	4	FACETS	0.894	0.813	0.978	0.894	0.813	0.978	CLONAL	2	TRUE	2	0.29	4		461	657	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026506	48026506	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876658726	NA	P-0061595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	92	647	0	ENST00000234420.5:c.1384C>T	p.Pro462Ser	p.P462S	ENST00000234420	NM_000179.2	462	Cct/Tct	4/10	0.252327052243204	4	FACETS	1	0.897	1	0.505	0.448	0.566	CLONAL	1	TRUE	2	0.29	4		647	810	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042470	37042470	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	69	347	0	ENST00000231790.2:c.232G>C	p.Glu78Gln	p.E78Q	ENST00000231790	NM_000249.3	78	Gaa/Caa	3/19	0.295377267736186	3	FACETS	1	0.953	1	0.6	0.524	0.682	CLONAL	1	TRUE	1	0.29	3		347	454	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249465	153249465	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	87	443	0	ENST00000281708.4:c.1313C>G	p.Ser438Cys	p.S438C	ENST00000281708	NM_033632.3	438	tCt/tGt	9/12	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.29	2		443	531	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295188	1295188	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0061595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	77	609	0				ENST00000310581	NM_198253.2	-/1132			0.252327052243204	4	FACETS	0.879	0.771	0.996	0.44	0.385	0.498	CLONAL	1	TRUE	2	0.29	4		609	779	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38996959	38996959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	294	442	0	ENST00000357387.3:c.418G>A	p.Glu140Lys	p.E140K	ENST00000357387	NM_152756.3	140	Gag/Aag	6/38	0.295387358187658	6	FACETS	0.913	0.865	0.961			1	CLONAL	5	TRUE	NA	0.29	6		442	702	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38137127	38137127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	102	491	0	ENST00000317025.8:c.3691G>A	p.Glu1231Lys	p.E1231K	ENST00000317025	NM_023034.1	1231	Gaa/Aaa	21/24	0.257565428954196	4	FACETS	1	0.97	1	0.411	0.367	0.457	CLONAL	1	TRUE	1	0.29	4		491	736	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38184356	38184356	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs778367894	NA	P-0061595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	75	514	0	ENST00000317025.8:c.1600G>C	p.Glu534Gln	p.E534Q	ENST00000317025	NM_023034.1	534	Gaa/Caa	7/24	0.257565428954196	4	FACETS	1	0.946	1	0.381	0.334	0.431	CLONAL	1	TRUE	1	0.29	4		514	584	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205566	38205566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	90	603	0	ENST00000317025.8:c.124G>A	p.Glu42Lys	p.E42K	ENST00000317025	NM_023034.1	42	Gaa/Aaa	2/24	0.257565428954196	4	FACETS	0.949	0.841	1	0.316	0.28	0.355	CLONAL	1	TRUE	1	0.29	4		603	844	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041403	47041403	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	275	421	0	ENST00000377604.3:c.1747G>A	p.Asp583Asn	p.D583N	ENST00000377604	NM_001204468.1	583	Gac/Aac	16/24	0.280087022750258	2	FACETS	1	0.985	1			1	CLONAL	3	TRUE	NA	0.29	2		421	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0061596-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	324	715	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.415563530598593	2		715	661	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0061596-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	460	771	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.415563530598593	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.415563530598593	3		771	811	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0061596-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	1067	662	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.415563530598593	8	FACETS	1	0.995	1			1	CLONAL	6	TRUE	NA	0.415563530598593	8		662	1808	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105603	27105604	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061596-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	179	671	0	ENST00000324856.7:c.5214_5215insA	p.Pro1739ThrfsTer17	p.P1739Tfs*17	ENST00000324856	NM_006015.4	1738	-/A	20/20	0.363881333242632	3	FACETS	0.858	0.796	0.923	0.858	0.796	0.923	CLONAL	2	TRUE	1	0.415563530598593	3		671	606	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746075	162746075	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061596-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	207	659	0	ENST00000367921.3:c.2198G>T	p.Arg733Met	p.R733M	ENST00000367921	NM_006182.2	733	aGg/aTg	16/18	0.276163177353842	4	FACETS	0.804	0.747	0.863	0.804	0.747	0.863	CLONAL	2	TRUE	2	0.415563530598593	4		659	877	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462549	29462549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061596-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	216	626	0	ENST00000389048.3:c.2352del	p.Ser785ValfsTer5	p.S785Vfs*5	ENST00000389048	NM_004304.4	784	ccC/cc	13/29	0.279135676632091	4	FACETS	0.911	0.849	0.974	0.911	0.849	0.974	CLONAL	2	TRUE	2	0.415563530598593	4		626	808	SUCCESS
APC	324	MSKCC	GRCh37	5	112179357	112179360	+	frameshift_variant	Frame_Shift_Del	DEL	AGGC	AGGC	-	novel	NA	P-0061596-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	209	557	0	ENST00000257430.4:c.8067_8070del	p.Ala2690IlefsTer32	p.A2690Ifs*32	ENST00000257430	NM_000038.5	2689	aAGGCa/aa	16/16	0.415563530598593	2	FACETS	0.882	0.825	0.941	0.882	0.825	0.941	CLONAL	2	TRUE	0	0.415563530598593	2		557	570	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0061597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	148	458	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.749970426216493	2		458	331	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0061597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	195	568	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.965	0.9	1	0.965	0.9	1	CLONAL	1	TRUE	1	0.749970426216493	2		568	539	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413070	139413072	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0061597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	14	686	0	ENST00000277541.6:c.1070_1072del	p.Phe357del	p.F357del	ENST00000277541	NM_017617.3	357	tTCTac/tac	6/34	1	2	FACETS	0.063	0.045	0.086	0.063	0.045	0.086	SUBCLONAL	1	TRUE	1	0.749970426216493	2		686	589	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799063	42799065	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs751580245	NA	P-0061597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	20	801	0	ENST00000575354.2:c.4550_4552del	p.Lys1517del	p.K1517del	ENST00000575354	NM_015125.3	1516	cAGAag/cag	20/20	0.749970426216493	1	FACETS	0.118	0.09	0.151	0.118	0.09	0.151	SUBCLONAL	1	TRUE	0	0.749970426216493	1		801	283	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798888	42798888	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0061597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	41	886	0	ENST00000575354.2:c.4459+1G>A		p.X1487_splice	ENST00000575354	NM_015125.3	1487			0.749970426216493	1	FACETS	0.163	0.135	0.193	0.163	0.135	0.193	SUBCLONAL	1	TRUE	0	0.749970426216493	1		886	420	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794522	42794523	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0061597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	116	851	0	ENST00000575354.2:c.1604_1605del	p.Ser535CysfsTer154	p.S535Cfs*154	ENST00000575354	NM_015125.3	534	tcCTct/tcct	10/20	0.749970426216493	1	FACETS	0.54	0.492	0.59	0.54	0.492	0.59	SUBCLONAL	1	TRUE	0	0.749970426216493	1		851	358	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412737	139412739	+	inframe_deletion	In_Frame_Del	DEL	CAG	CAG	-	novel	NA	P-0061597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	27	760	0	ENST00000277541.6:c.1105_1107del	p.Leu369del	p.L369del	ENST00000277541	NM_017617.3	369	CTG/-	7/34	1	2	FACETS	0.136	0.108	0.169	0.136	0.108	0.169	SUBCLONAL	1	TRUE	1	0.749970426216493	2		760	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578551	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061601-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	85	470	0	ENST00000269305.4:c.379T>A	p.Ser127Thr	p.S127T	ENST00000269305	NM_001126112.2	127	Tcc/Acc	5/11	0.294918607273356	5	FACETS	1	0.934	1			1	CLONAL	1	TRUE	NA	0.294918607273356	5		470	767	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291798	15291798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759991207	NA	P-0061601-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	80	591	0	ENST00000263388.2:c.2968G>A	p.Glu990Lys	p.E990K	ENST00000263388	NM_000435.2	990	Gag/Aag	18/33	0.209629057690622	5	FACETS	0.661	0.58	0.749	0.22	0.193	0.25	SUBCLONAL	1	TRUE	2	0.294918607273356	5		591	1183	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435258	49435258	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1452715535	NA	P-0061602-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	216	556	0	ENST00000301067.7:c.6295C>T	p.Arg2099Ter	p.R2099*	ENST00000301067	NM_003482.3	2099	Cga/Tga	31/54	0.830171744580725	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.830171744580725	1		556	289	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	25	544	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.106141255987373	5	FACETS	0.611	0.481	0.761	0.153	0.12	0.191	INDETERMINATE	1	TRUE	1	0.285974943389826	5		544	409	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0061603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	176	591	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.106141255987373	5	FACETS	0.962	0.895	1	0.962	0.895	1	INDETERMINATE	4	TRUE	1	0.285974943389826	5		591	457	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922364	178922364	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	14	216	0	ENST00000263967.3:c.1133G>T	p.Cys378Phe	p.C378F	ENST00000263967	NM_006218.2	378	tGt/tTt	6/21	0.285974943389826	3	FACETS	0.506	0.366	0.676	0.253	0.183	0.338	SUBCLONAL	1	TRUE	1	0.285974943389826	3		216	221	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0061603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	99	437	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	0.285974943389826	1	FACETS	1	0.937	1	1	0.988	1	CLONAL	2	TRUE	0	0.285974943389826	1		437	284	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668637	52668637	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs764729828	NA	P-0061603-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	49	366	0	ENST00000394830.3:c.1282A>G	p.Ile428Val	p.I428V	ENST00000394830	NM_018313.4	428	Ata/Gta	12/30	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.285974943389826	2		366	339	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0061605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	235	274	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.59082459706123	5	FACETS	0.942	0.888	0.997			1	CLONAL	3	TRUE	NA	0.59082459706123	5		274	531	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955113	55955113	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	243	348	0	ENST00000263923.4:c.3432C>A	p.His1144Gln	p.H1144Q	ENST00000263923	NM_002253.2	1144	caC/caA	26/30	0.598971043480309	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.59082459706123	3		348	485	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155333	185155333	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	169	412	0	ENST00000265026.3:c.574G>T	p.Val192Leu	p.V192L	ENST00000265026	NM_004721.4	192	Gtg/Ttg	3/14	0.598971043480309	3	FACETS	1	0.986	1	0.644	0.596	0.695	CLONAL	1	TRUE	1	0.59082459706123	3		412	575	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041022	47041022	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	681	579	0	ENST00000377604.3:c.1552C>T	p.Gln518Ter	p.Q518*	ENST00000377604	NM_001204468.1	518	Cag/Tag	14/24	0.215430473890918	6	FACETS	0.992	0.971	1			1	INDETERMINATE	6	TRUE	NA	0.59082459706123	6		579	845	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236215	108236215	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	308	423	1	ENST00000278616.4:c.9151G>A	p.Gly3051Arg	p.G3051R	ENST00000278616	NM_000051.3	3051	Gga/Aga	63/63	0.598971043480309	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.59082459706123	2		424	425	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46597560	46597561	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0061605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	326	352	0	ENST00000262741.5:c.64_65insGG	p.Tyr22TrpfsTer6	p.Y22Wfs*6	ENST00000262741	NM_003629.3	22	tat/tGGat	1/10	0.372852200098012	5	FACETS	0.972	0.925	1	0.972	0.925	1	CLONAL	3	TRUE	2	0.59082459706123	5		352	714	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551556	150551556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1278	90	570	0	ENST00000369026.2:c.451G>A	p.Gly151Ser	p.G151S	ENST00000369026	NM_021960.4	151	Ggt/Agt	1/3	0.59082459706123	5	FACETS	0.42	0.371	0.473	0.14	0.123	0.158	SUBCLONAL	1	TRUE	2	0.59082459706123	5		570	1368	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50769515	50769622	+	inframe_deletion	In_Frame_Del	DEL	AACCTGCTGCCCAGACGCCACCTGCATCTATAGAAGTAGATGAAAATATAGAATTGATAAGTGGTCAAAATGAGAGAATGGGACCACTGAATATATCAACTCCAGTTG	AACCTGCTGCCCAGACGCCACCTGCATCTATAGAAGTAGATGAAAATATAGAATTGATAAGTGGTCAAAATGAGAGAATGGGACCACTGAATATATCAACTCCAGTTG	-	novel	NA	P-0061605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	33	299	0	ENST00000307179.4:c.1041_1148del	p.Ala348_Pro383del	p.A348_P383del	ENST00000307179		346	aAACCTGCTGCCCAGACGCCACCTGCATCTATAGAAGTAGATGAAAATATAGAATTGATAAGTGGTCAAAATGAGAGAATGGGACCACTGAATATATCAACTCCAGTTGaa/aaa	10/20	0.598971043480309	2	FACETS	0.393	0.321	0.474	0.197	0.16	0.237	SUBCLONAL	1	TRUE	0	0.59082459706123	2		299	284	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348104	348104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	53	591	0	ENST00000262320.3:c.1402G>A	p.Glu468Lys	p.E468K	ENST00000262320	NM_003502.3	468	Gag/Aag	6/11	0.301773362689834	3	FACETS	0.341	0.29	0.397	0.114	0.096	0.133	INDETERMINATE	1	TRUE	0	0.59082459706123	3		591	681	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627232	37627232	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	109	418	0	ENST00000447079.4:c.1147A>T	p.Ser383Cys	p.S383C	ENST00000447079	NM_015083.1	383	Agt/Tgt	2/14	0.160162674795311	3	FACETS	1	0.908	1	0.335	0.303	0.37	INDETERMINATE	1	TRUE	0	0.59082459706123	3		418	475	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56409145	56409145	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	75	221	0	ENST00000348428.3:c.1652G>T	p.Arg551Leu	p.R551L	ENST00000348428	NM_006785.3	551	cGa/cTa	14/17	0.414265460135476	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.59082459706123	1		221	147	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470964	25470964	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	279	596	0	ENST00000264709.3:c.797G>T	p.Gly266Val	p.G266V	ENST00000264709	NM_175629.2	266	gGg/gTg	7/23	0.464494135547114	4	FACETS	0.864	0.814	0.916	0.864	0.814	0.916	CLONAL	2	TRUE	2	0.59082459706123	4		596	869	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11301713	11301713	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	133	371	0	ENST00000361445.4:c.1438G>T	p.Ala480Ser	p.A480S	ENST00000361445	NM_004958.3	480	Gcc/Tcc	10/58	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.59082459706123	2		371	441	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	244	517	3	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.948	0.891	1	0.948	0.891	1	CLONAL	1	TRUE	1	0.73	2		520	705	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	259	877	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.911	0.857	0.966	0.911	0.857	0.966	CLONAL	1	TRUE	1	0.73	2		883	779	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	250	605	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.976	0.917	1	0.976	0.917	1	CLONAL	1	TRUE	1	0.73	2		608	702	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	204	409	4	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.904	0.844	0.967	0.904	0.844	0.967	CLONAL	1	TRUE	1	0.73	2		413	618	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795103	242795104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768249210	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	168	607	1	ENST00000334409.5:c.105dup	p.Thr36HisfsTer70	p.T36Hfs*70	ENST00000334409	NM_005018.2	35	-/C	2/5	1	2	FACETS	0.67	0.618	0.724	0.67	0.618	0.724	SUBCLONAL	1	TRUE	1	0.73	2		608	687	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	210	461	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.868	0.81	0.927	0.868	0.81	0.927	CLONAL	1	TRUE	1	0.73	2		461	663	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	296	590	0	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.965	0.912	1	0.965	0.912	1	CLONAL	1	TRUE	1	0.73	2		590	840	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	273	492	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.987	0.93	1	0.987	0.93	1	CLONAL	1	TRUE	1	0.73	2		492	758	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	208	487	2	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	0.905	0.844	0.966	0.905	0.844	0.966	CLONAL	1	TRUE	1	0.73	2		489	630	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	154	290	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.73	2		290	409	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996755	100996757	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	176	323	0	ENST00000325455.5:c.1770_1772del	p.Phe591del	p.F591del	ENST00000325455	NM_001202474.3	590	ttCTTt/ttt	2/8	1	2	FACETS	0.949	0.881	1	0.949	0.881	1	CLONAL	1	TRUE	1	0.73	2		323	508	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	198	282	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.73	2		282	504	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112154	115112154	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	193	575	1	ENST00000257566.3:c.1586del	p.Gly529AlafsTer103	p.G529Afs*103	ENST00000257566	NM_016569.3	529	gGc/gc	7/8	1	2	FACETS	0.834	0.775	0.894	0.834	0.775	0.894	CLONAL	1	TRUE	1	0.73	2		576	634	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675268	176675269	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	229	415	0	ENST00000439151.2:c.4591dup	p.Met1531AsnfsTer4	p.M1531Nfs*4	ENST00000439151	NM_022455.4	1528	-/A	11/23	1	2	FACETS	0.919	0.86	0.978	0.919	0.86	0.978	CLONAL	1	TRUE	1	0.73	2		415	683	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	248	591	1	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.917	0.861	0.974	0.917	0.861	0.974	CLONAL	1	TRUE	1	0.73	2		592	741	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056277	27056277	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	311	524	0	ENST00000324856.7:c.1273C>T	p.Gln425Ter	p.Q425*	ENST00000324856	NM_006015.4	425	Cag/Tag	2/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.73	2		524	723	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435128	110435129	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs772322568	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	190	614	1	ENST00000375856.3:c.3272dup	p.Lys1092GlufsTer233	p.K1092Efs*233	ENST00000375856	NM_003749.2	1091	ccg/ccCg	1/2	1	2	FACETS	0.794	0.737	0.852	0.794	0.737	0.852	SUBCLONAL	1	TRUE	1	0.73	2		615	656	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219487	133219487	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	220	482	0	ENST00000320574.5:c.4647del	p.Lys1550AsnfsTer12	p.K1550Nfs*12	ENST00000320574	NM_006231.2	1549	ccC/cc	36/49	1	2	FACETS	0.889	0.831	0.948	0.889	0.831	0.948	CLONAL	1	TRUE	1	0.73	2		482	678	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263974	104263974	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776579	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	157	401	3	ENST00000369902.3:c.71del	p.Pro24ArgfsTer72	p.P24Rfs*72	ENST00000369902	NM_016169.3	22	gCc/gc	1/12	1	2	FACETS	0.971	0.898	1	0.971	0.898	1	CLONAL	1	TRUE	1	0.73	2		404	443	SUCCESS
AR	367	MSKCC	GRCh37	X	66765666	66765667	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	245	604	0	ENST00000374690.3:c.683dup	p.Thr229HisfsTer6	p.T229Hfs*6	ENST00000374690	NM_000044.3	226	-/G	1/8	1	2	FACETS	0.958	0.9	1	0.958	0.9	1	CLONAL	1	TRUE	1	0.73	2		604	701	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193850	106193850	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	200	362	1	ENST00000380013.4:c.4317del	p.Lys1439AsnfsTer9	p.K1439Nfs*9	ENST00000380013	NM_001127208.2	1438	Aaa/aa	10/11	1	2	FACETS	0.943	0.88	1	0.943	0.88	1	CLONAL	1	TRUE	1	0.73	2		363	581	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	101	220	0	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	1	2	FACETS	0.957	0.868	1	0.957	0.868	1	CLONAL	1	TRUE	1	0.73	2		220	289	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391376	139391376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs972658026	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	220	597	0	ENST00000277541.6:c.6815G>A	p.Arg2272His	p.R2272H	ENST00000277541	NM_017617.3	2272	cGt/cAt	34/34	1	2	FACETS	0.932	0.872	0.993	0.932	0.872	0.993	CLONAL	1	TRUE	1	0.73	2		597	647	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936058	71936058	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	83	280	0	ENST00000298229.2:c.35del	p.Gly12AlafsTer15	p.G12Afs*15	ENST00000298229	NM_001567.3	10	ccG/cc	1/28	1	2	FACETS	0.827	0.739	0.918	0.827	0.739	0.918	CLONAL	1	TRUE	1	0.73	2		280	275	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135804187	135804187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1230244328	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	204	403	0	ENST00000298552.3:c.73G>A	p.Val25Met	p.V25M	ENST00000298552	NM_001162426.1	25	Gtg/Atg	3/23	1	2	FACETS	0.891	0.831	0.953	0.891	0.831	0.953	CLONAL	1	TRUE	1	0.73	2		403	627	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922221	100922221	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	128	314	0	ENST00000325455.5:c.2291G>T	p.Gly764Val	p.G764V	ENST00000325455	NM_001202474.3	764	gGa/gTa	5/8	1	2	FACETS	0.899	0.823	0.977	0.899	0.823	0.977	CLONAL	1	TRUE	1	0.73	2		314	390	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944554	40944554	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	187	455	0	ENST00000373198.4:c.1948del	p.Val650Ter	p.V650*	ENST00000373198	NM_133170.3	650	Gtg/tg	12/32	1	2	FACETS	0.959	0.893	1	0.959	0.893	1	CLONAL	1	TRUE	1	0.73	2		455	534	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476770	140476770	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	64	282	0	ENST00000288602.6:c.1636A>G	p.Thr546Ala	p.T546A	ENST00000288602	NM_004333.4	546	Acc/Gcc	13/18	1	2	FACETS	0.433	0.376	0.494	0.433	0.376	0.494	SUBCLONAL	1	TRUE	1	0.73	2		282	405	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528064	157528065	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	51	494	0	ENST00000346085.5:c.5791_5792del	p.Leu1931ValfsTer12	p.L1931Vfs*12	ENST00000346085	NM_020732.3	1930	cCT/c	20/20	0.3	2	FACETS	0.18	0.152	0.211			1	INDETERMINATE	1	TRUE	NA	0.73	2		494	776	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692982	89692985	+	frameshift_variant	Frame_Shift_Del	DEL	GGGG	GGGG	-	novel	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	150	378	0	ENST00000371953.3:c.466_469del	p.Gly156LysfsTer2	p.G156Kfs*2	ENST00000371953	NM_000314.4	156	GGGGaa/aa	5/9	1	2	FACETS	0.93	0.858	1	0.93	0.858	1	CLONAL	1	TRUE	1	0.73	2		378	442	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658865	3658865	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1567178416	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	183	374	0	ENST00000294008.3:c.101A>G	p.Gln34Arg	p.Q34R	ENST00000294008	NM_032444.2	34	cAg/cGg	2/15	1	2	FACETS	0.955	0.888	1	0.955	0.888	1	CLONAL	1	TRUE	1	0.73	2		374	525	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38787005	38787005	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755389218	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	254	415	0	ENST00000348513.6:c.988G>A	p.Glu330Lys	p.E330K	ENST00000348513	NM_003079.4	330	Gag/Aag	10/11	1	2	FACETS	0.96	0.903	1	0.96	0.903	1	CLONAL	1	TRUE	1	0.73	2		415	725	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023065	48023065	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	200	345	0	ENST00000234420.5:c.490C>A	p.His164Asn	p.H164N	ENST00000234420	NM_000179.2	164	Cat/Aat	3/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.73	2		345	536	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661123	227661123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752902060	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	246	566	0	ENST00000305123.5:c.2332G>A	p.Gly778Arg	p.G778R	ENST00000305123	NM_005544.2	778	Ggg/Agg	1/2	1	2	FACETS	0.988	0.929	1	0.988	0.929	1	CLONAL	1	TRUE	1	0.73	2		566	682	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29444454	29444454	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	253	492	0	ENST00000544604.2:c.994del	p.His332ThrfsTer7	p.H332Tfs*7	ENST00000544604	NM_001206998.1	330	tgC/tg	7/9	1	2	FACETS	0.963	0.905	1	0.963	0.905	1	CLONAL	1	TRUE	1	0.73	2		492	720	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183561	185183561	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	188	331	0	ENST00000265026.3:c.1415A>G	p.Tyr472Cys	p.Y472C	ENST00000265026	NM_004721.4	472	tAt/tGt	9/14	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.73	2		331	496	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31504721	31504721	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	236	385	0	ENST00000344624.3:c.1609A>G	p.Lys537Glu	p.K537E	ENST00000344624		537	Aaa/Gaa	8/33	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.73	2		385	572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578484	7578485	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1064793929	NA	P-0061615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	356	690	0	ENST00000269305.4:c.445dup	p.Ser149PhefsTer32	p.S149Ffs*32	ENST00000269305	NM_001126112.2	149	tcc/tTcc	5/11	0.389325680227504	3	FACETS	0.888	0.848	0.928	0.888	0.848	0.928	CLONAL	3	TRUE	0	0.45506180910947	3		690	721	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133806	55133806	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs77524207	NA	P-0061615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	99	504	0	ENST00000257290.5:c.1019G>A	p.Arg340Gln	p.R340Q	ENST00000257290	NM_006206.4	340	cGg/cAg	7/23	1	2	FACETS	0.971	0.872	1	0.971	0.872	1	CLONAL	1	TRUE	1	0.45506180910947	2		504	448	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144509	11144509	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778685	NA	P-0061615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	106	444	0	ENST00000358026.2:c.3841G>A	p.Val1281Ile	p.V1281I	ENST00000358026	NM_001128849.1	1281	Gtc/Atc	27/36	0.423040443202256	3	FACETS	1	0.943	1	0.535	0.482	0.592	CLONAL	1	TRUE	1	0.45506180910947	3		444	534	SUCCESS
ALB	213	MSKCC	GRCh37	4	74279198	74279198	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	95	451	0	ENST00000295897.4:c.905G>T	p.Cys302Phe	p.C302F	ENST00000295897	NM_000477.5	302	tGc/tTc	8/15	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.45506180910947	2		451	385	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158406	108158406	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	66	364	0	ENST00000278616.4:c.4073G>C	p.Ser1358Thr	p.S1358T	ENST00000278616	NM_000051.3	1358	aGt/aCt	27/63	0.45506180910947	2	FACETS	0.795	0.694	0.903	0.397	0.347	0.452	CLONAL	1	TRUE	0	0.45506180910947	2		364	365	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926885	112926885	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0061615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	57	470	0	ENST00000351677.2:c.1505C>G	p.Ser502Ter	p.S502*	ENST00000351677	NM_002834.3	502	tCa/tGa	13/16	0.45506180910947	4	FACETS	0.663	0.569	0.765	0.221	0.189	0.255	SUBCLONAL	1	TRUE	1	0.45506180910947	4		470	550	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593398	48593403	+	inframe_deletion	In_Frame_Del	DEL	AGGCAA	AGGCAA	-	novel	NA	P-0061615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	45	352	0	ENST00000342988.3:c.1152_1157del	p.Lys385_Gly386del	p.K385_G386del	ENST00000342988	NM_005359.5	383	atAGGCAAa/ata	10/12	0.45506180910947	1	FACETS	0.536	0.453	0.627	0.536	0.453	0.627	SUBCLONAL	1	TRUE	0	0.45506180910947	1		352	285	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096012	178096012	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	85	677	0	ENST00000397062.3:c.1319del	p.Pro440HisfsTer31	p.P440Hfs*31	ENST00000397062	NM_006164.4	440	cCa/ca	5/5	0.45506180910947	2	FACETS	0.664	0.588	0.745	0.332	0.294	0.373	SUBCLONAL	1	TRUE	0	0.45506180910947	2		677	563	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948026	178948027	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	65	334	0	ENST00000263967.3:c.2802dup	p.Gly935TrpfsTer14	p.G935Wfs*14	ENST00000263967	NM_006218.2	933	gat/gaTt	20/21	1	2	FACETS	0.736	0.641	0.838	0.736	0.641	0.838	SUBCLONAL	1	TRUE	1	0.45506180910947	2		334	388	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361162	70361162	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	18	383	0	ENST00000374080.3:c.6350A>C	p.Gln2117Pro	p.Q2117P	ENST00000374080		2117	cAg/cCg	43/45	1	1	FACETS	0.191	0.143	0.247	0.191	0.143	0.247	SUBCLONAL	1	TRUE	0	0.45506180910947	1		383	320	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431178	49431178	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs793888512	NA	P-0061616-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	39	678	0	ENST00000301067.7:c.9961C>T	p.Arg3321Ter	p.R3321*	ENST00000301067	NM_003482.3	3321	Cga/Tga	34/54	1	2	FACETS	0.897	0.742	1	0.897	0.742	1	CLONAL	1	TRUE	1	0.15	2		678	580	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625251	69625251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782147248	NA	P-0061616-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	42	667	0	ENST00000334134.2:c.542G>A	p.Arg181His	p.R181H	ENST00000334134	NM_005247.2	181	cGc/cAc	3/3	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.15	2		667	441	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351422	70351422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061616-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	28	191	0	ENST00000374080.3:c.4070G>A	p.Arg1357His	p.R1357H	ENST00000374080		1357	cGc/cAc	29/45	1	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.15	1		191	236	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867286	45867286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061616-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	28	647	0	ENST00000391945.4:c.907G>A	p.Ala303Thr	p.A303T	ENST00000391945	NM_000400.3	303	Gcc/Acc	10/23	1	2	FACETS	0.753	0.6	0.927	0.753	0.6	0.927	CLONAL	1	TRUE	1	0.15	2		647	496	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612061	189612061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777373892	NA	P-0061616-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	23	548	0	ENST00000264731.3:c.1813C>T	p.Arg605Trp	p.R605W	ENST00000264731	NM_003722.4	605	Cgg/Tgg	14/14	1	2	FACETS	0.697	0.542	0.877	0.697	0.542	0.877	SUBCLONAL	1	TRUE	1	0.15	2		548	440	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609111	43609111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767402	NA	P-0061616-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	29	748	0	ENST00000355710.3:c.1867G>A	p.Glu623Lys	p.E623K	ENST00000355710	NM_020975.4	623	Gaa/Aaa	10/20	1	2	FACETS	0.72	0.577	0.884	0.72	0.577	0.884	SUBCLONAL	1	TRUE	1	0.15	2		748	537	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610144	28610144	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061616-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	30	383	0	ENST00000241453.7:c.1346A>G	p.Gln449Arg	p.Q449R	ENST00000241453	NM_004119.2	449	cAg/cGg	11/24	1	2	FACETS	0.915	0.737	1	0.915	0.737	1	CLONAL	1	TRUE	1	0.15	2		383	437	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456394	40456394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061616-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	35	525	0	ENST00000345506.4:c.1204G>A	p.Val402Met	p.V402M	ENST00000345506	NM_003152.3	402	Gtg/Atg	11/20	1	2	FACETS	0.968	0.793	1	0.968	0.793	1	CLONAL	1	TRUE	1	0.15	2		525	482	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63985174	63985174	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769269406	NA	P-0061616-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	34	457	0	ENST00000398590.3:c.2777C>T	p.Ala926Val	p.A926V	ENST00000398590	NM_001177387.1	926	gCg/gTg	14/14	1	2	FACETS	0.994	0.812	1	0.994	0.812	1	CLONAL	1	TRUE	1	0.15	2		457	456	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141549543	141549543	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061616-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	37	466	0	ENST00000220592.5:c.2045A>C	p.His682Pro	p.H682P	ENST00000220592	NM_012154.3	682	cAc/cCc	16/19	1	2	FACETS	0.931	0.767	1	0.931	0.767	1	CLONAL	1	TRUE	1	0.15	2		466	530	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	183	126	0				ENST00000310581	NM_198253.2	-/1132			0.905168944981825	6	FACETS	0.942	0.881	1	0.942	0.881	1	CLONAL	3	TRUE	3	0.905168944981825	6		126	402	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348822	118348822	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	132	508	0	ENST00000534358.1:c.3477del	p.Gly1160AlafsTer15	p.G1160Afs*15	ENST00000534358	NM_005933.3	1159	Ccc/cc	5/36	0.827309630229522	3	FACETS	0.852	0.779	0.929	0.426	0.389	0.465	CLONAL	1	TRUE	1	0.905168944981825	3		508	497	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378681	25378681	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	43	344	0	ENST00000311936.3:c.317C>T	p.Ser106Phe	p.S106F	ENST00000311936	NM_004985.3	106	tCt/tTt	4/5	0.814940648054166	3	FACETS	0.775	0.675	0.876	0.775	0.675	0.876	SUBCLONAL	2	TRUE	1	0.905168944981825	3		344	89	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037859	49037875	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTACTAGATTATGATG	TTTACTAGATTATGATG	-	novel	NA	P-0061617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	25	253	0	ENST00000267163.4:c.2107-7_2116del		p.X703_splice	ENST00000267163	NM_000321.2	703		21/27	NA	2	FACETS	0.767	0.662	0.861			1	INDETERMINATE	2	TRUE	NA	0.905168944981825	2		253	36	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222294	2222294	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	41	692	0	ENST00000398665.3:c.3126G>C	p.Lys1042Asn	p.K1042N	ENST00000398665	NM_032482.2	1042	aaG/aaC	24/28	0.428444429819664	5	FACETS	0.703	0.588	0.829	0.234	0.196	0.277	INDETERMINATE	1	TRUE	2	0.905168944981825	5		692	304	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2225391	2225391	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	17	443	0	ENST00000398665.3:c.3601G>T	p.Glu1201Ter	p.E1201*	ENST00000398665	NM_032482.2	1201	Gag/Tag	26/28	0.428444429819664	5	FACETS	0.459	0.343	0.595	0.153	0.114	0.199	INDETERMINATE	1	TRUE	2	0.905168944981825	5		443	193	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753627	42753627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	42	839	0	ENST00000222329.4:c.637G>A	p.Asp213Asn	p.D213N	ENST00000222329	NM_006494.2	213	Gat/Aat	4/4	0.428444429819664	5	FACETS	0.488	0.408	0.578	0.163	0.136	0.193	INDETERMINATE	1	TRUE	2	0.905168944981825	5		839	448	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46602910	46602910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	36	643	0	ENST00000263734.3:c.968G>A	p.Gly323Glu	p.G323E	ENST00000263734	NM_001430.4	323	gGg/gAg	8/16	0.719001202872528	3	FACETS	0.275	0.226	0.33	0.138	0.113	0.165	SUBCLONAL	1	TRUE	1	0.905168944981825	3		643	420	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403251	116403251	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	69	439	0	ENST00000397752.3:c.2512A>T	p.Asn838Tyr	p.N838Y	ENST00000397752	NM_000245.2	838	Aat/Tat	11/21	0.695679189467345	4	FACETS	0.844	0.753	0.938	0.844	0.753	0.938	CLONAL	2	TRUE	2	0.905168944981825	4		439	172	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050731	5050731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	21	383	0	ENST00000381652.3:c.514C>T	p.His172Tyr	p.H172Y	ENST00000381652	NM_004972.3	172	Cat/Tat	6/25	0.346027695381913	5	FACETS	0.647	0.502	0.814	0.216	0.167	0.272	INDETERMINATE	1	TRUE	2	0.905168944981825	5		383	169	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0061618-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	283	549	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.461563026472913	2	FACETS	0.84	0.801	0.879	1	0.993	1	CLONAL	3	TRUE	0	0.460147625064077	2		552	488	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061618-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	121	414	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.460586856478483	4	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	2	0.460147625064077	4		414	370	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777134	9777134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1445282622	NA	P-0061618-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	278	520	0	ENST00000377346.4:c.898C>T	p.Arg300Cys	p.R300C	ENST00000377346	NM_005026.3	300	Cgt/Tgt	7/24	0.460586856478483	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.460147625064077	4		520	827	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139215	37139215	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061618-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1206	73	504	0	ENST00000373509.5:c.555C>G	p.Ile185Met	p.I185M	ENST00000373509	NM_002648.3	185	atC/atG	4/6	0.460147625064077	7	FACETS	0.533	0.465	0.608			1	SUBCLONAL	1	TRUE	NA	0.460147625064077	7		504	1279	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs377622327	NA	P-0061619-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	197	680	0	ENST00000324856.7:c.3972C>A	p.Tyr1324Ter	p.Y1324*	ENST00000324856	NM_006015.4	1324	taC/taA	16/20	1	2	FACETS	0.922	0.859	0.987	0.922	0.859	0.987	CLONAL	1	TRUE	1	0.686911943972124	2		680	622	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	60	711	3	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.829	0.713	0.956	0.829	0.713	0.956	CLONAL	1	TRUE	1	0.19	2		714	762	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0061620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	57	530	0	ENST00000269305.4:c.375+1G>T		p.X125_splice	ENST00000269305	NM_001126112.2	125			1	2	FACETS	0.997	0.855	1	0.997	0.855	1	CLONAL	1	TRUE	1	0.19	2		530	602	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212425	36212425	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1321602732	NA	P-0061620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	69	705	0	ENST00000222270.7:c.2176G>C	p.Ala726Pro	p.A726P	ENST00000222270	NM_014727.1	726	Gct/Cct	3/37	1	2	FACETS	0.867	0.753	0.99	0.867	0.753	0.99	CLONAL	1	TRUE	1	0.19	2		705	838	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0061621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	399	603	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.431443034248298	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	4	TRUE	0	0.428065570904386	4		603	620	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937367	32937367	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80359691	NA	P-0061621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	142	425	0	ENST00000380152.3:c.8029del	p.Glu2677LysfsTer17	p.E2677Kfs*17	ENST00000380152		2676	atG/at	18/27	0.431443034248298	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.428065570904386	2		425	291	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225598	2225598	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	46	572	0	ENST00000326181.6:c.1601A>G	p.Tyr534Cys	p.Y534C	ENST00000326181	NM_032271.2	534	tAc/tGc	17/21	0.431443034248298	2	FACETS	0.572	0.483	0.669	0.286	0.241	0.335	SUBCLONAL	1	TRUE	0	0.428065570904386	2		572	376	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496935	29496935	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	123	242	0	ENST00000356175.3:c.506A>T	p.Glu169Val	p.E169V	ENST00000356175	NM_000267.3	169	gAa/gTa	5/57	0.431443034248298	3	FACETS	0.998	0.925	1	0.998	0.925	1	CLONAL	3	TRUE	0	0.428065570904386	3		242	233	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883132	37883132	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	211	558	0	ENST00000269571.5:c.3035A>T	p.Asp1012Val	p.D1012V	ENST00000269571		1012	gAt/gTt	25/27	0.431443034248298	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	3	TRUE	0	0.428065570904386	3		558	386	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576831	212576831	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	17	360	0	ENST00000342788.4:c.1068C>G	p.Phe356Leu	p.F356L	ENST00000342788	NM_005235.2	356	ttC/ttG	9/28	0.431443034248298	2	FACETS	0.313	0.233	0.407	0.156	0.116	0.204	SUBCLONAL	1	TRUE	0	0.428065570904386	2		360	254	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62320962	62320962	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	124	554	0	ENST00000360203.5:c.1986C>G	p.Phe662Leu	p.F662L	ENST00000360203	NM_001283009.1	662	ttC/ttG	23/35	0.348593509470657	3	FACETS	0.89	0.813	0.97	0.89	0.813	0.97	CLONAL	2	TRUE	1	0.428065570904386	3		554	395	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933255	49933255	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	160	621	0	ENST00000296474.3:c.2855G>C	p.Gly952Ala	p.G952A	ENST00000296474	NM_002447.2	952	gGg/gCg	12/20	0.431443034248298	3	FACETS	1	0.946	1	0.684	0.634	0.736	CLONAL	2	TRUE	0	0.428065570904386	3		621	442	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595807	52595816	+	frameshift_variant	Frame_Shift_Del	DEL	TCTCAAGATT	TCTCAAGATT	-	novel	NA	P-0061621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	31	504	0	ENST00000394830.3:c.4099_4108del	p.Asn1367GlnfsTer10	p.N1367Qfs*10	ENST00000394830	NM_018313.4	1367	AATCTTGAGAca/ca	26/30	0.431443034248298	3	FACETS	0.384	0.31	0.468	0.128	0.103	0.156	SUBCLONAL	1	TRUE	0	0.428065570904386	3		504	458	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205161	128205161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1357122451	NA	P-0061621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	25	643	0	ENST00000341105.2:c.280G>A	p.Gly94Ser	p.G94S	ENST00000341105	NM_032638.4	94	Ggt/Agt	3/6	0.297702955819409	4	FACETS	0.352	0.277	0.439	0.176	0.138	0.22	SUBCLONAL	1	TRUE	2	0.428065570904386	4		643	474	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467968	66467968	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	102	362	0	ENST00000273854.3:c.301G>T	p.Val101Leu	p.V101L	ENST00000273854	NM_004439.5	101	Gta/Tta	3/18	0.431443034248298	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	0	0.428065570904386	2		362	235	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542574	187542574	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	158	473	0	ENST00000441802.2:c.5166G>T	p.Gln1722His	p.Q1722H	ENST00000441802	NM_005245.3	1722	caG/caT	10/27	0.431443034248298	2	FACETS	0.987	0.917	1	0.987	0.917	1	CLONAL	2	TRUE	0	0.428065570904386	2		473	374	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170832346	170832346	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	27	136	0	ENST00000296930.5:c.710C>G	p.Thr237Arg	p.T237R	ENST00000296930	NM_002520.6	237	aCa/aGa	9/11	0.431443034248298	2	FACETS	1	0.89	1	0.573	0.465	0.691	CLONAL	1	TRUE	0	0.428065570904386	2		136	110	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001323	150001323	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	30	448	0	ENST00000253339.5:c.2281G>C	p.Asp761His	p.D761H	ENST00000253339		761	Gac/Cac	4/7	1	2	FACETS	0.363	0.292	0.443	0.363	0.292	0.443	SUBCLONAL	1	TRUE	1	0.428065570904386	2		448	386	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527998	157527998	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	115	625	0	ENST00000346085.5:c.5723A>T	p.Gln1908Leu	p.Q1908L	ENST00000346085	NM_020732.3	1908	cAg/cTg	20/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.428065570904386	2		625	441	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845133	151845133	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	115	477	0	ENST00000262189.6:c.13879G>C	p.Asp4627His	p.D4627H	ENST00000262189	NM_170606.2	4627	Gac/Cac	52/59	0.430025077327347	2	FACETS	0.85	0.776	0.926	0.85	0.776	0.926	CLONAL	2	TRUE	0	0.428065570904386	2		477	316	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878842	151878842	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	77	486	0	ENST00000262189.6:c.6103C>G	p.Pro2035Ala	p.P2035A	ENST00000262189	NM_170606.2	2035	Cct/Gct	36/59	0.430025077327347	2	FACETS	1	0.917	1	0.523	0.462	0.587	CLONAL	1	TRUE	0	0.428065570904386	2		486	344	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200217	123200217	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061621-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	54	152	0	ENST00000218089.9:c.2196C>G	p.His732Gln	p.H732Q	ENST00000218089	NM_001042749.1	732	caC/caG	23/35	0.428065570904386	3	FACETS	1	0.941	1			1	CLONAL	1	TRUE	NA	0.428065570904386	3		152	260	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0061622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	113	370	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.297071216764101	2	FACETS	0.972	0.884	1	0.972	0.884	1	CLONAL	2	TRUE	0	0.32188459723577	2		370	361	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	52	275	0	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	1	2	FACETS	0.784	0.669	0.91	0.784	0.669	0.91	CLONAL	1	TRUE	1	0.32188459723577	2		275	412	SUCCESS
APC	324	MSKCC	GRCh37	5	112173947	112173947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs755806668	NA	P-0061622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	55	499	0	ENST00000257430.4:c.2656C>T	p.Gln886Ter	p.Q886*	ENST00000257430	NM_000038.5	886	Cag/Tag	16/16	1	2	FACETS	0.8	0.686	0.924	0.8	0.686	0.924	CLONAL	1	TRUE	1	0.32188459723577	2		499	427	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450876	70450876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757931991	NA	P-0061622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	47	502	0	ENST00000373644.4:c.5716G>A	p.Glu1906Lys	p.E1906K	ENST00000373644	NM_030625.2	1906	Gaa/Aaa	12/12	1	2	FACETS	0.711	0.601	0.831	0.711	0.601	0.831	SUBCLONAL	1	TRUE	1	0.32188459723577	2		502	411	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149436861	149436861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs281860271	NA	P-0061622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	18	450	0	ENST00000286301.3:c.2308G>A	p.Ala770Thr	p.A770T	ENST00000286301	NM_005211.3	770	Gct/Act	17/22	1	2	FACETS	0.338	0.254	0.437	0.338	0.254	0.437	SUBCLONAL	1	TRUE	1	0.32188459723577	2		450	331	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119769	70119794	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCTTGCCAGAGGGGGGCAGACAGC	CCCCTTGCCAGAGGGGGGCAGACAGC	-	novel	NA	P-0061622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	87	425	0	ENST00000245479.2:c.776_801del	p.Leu259TyrfsTer28	p.L259Yfs*28	ENST00000245479	NM_000346.3	257	cgCCCCTTGCCAGAGGGGGGCAGACAGCcc/cgcc	3/3	0.227910901463109	3	FACETS	0.832	0.742	0.927	0.832	0.742	0.927	CLONAL	2	TRUE	1	0.32188459723577	3		425	377	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611167	100611167	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	42	456	0	ENST00000308731.7:c.1439G>T	p.Gly480Val	p.G480V	ENST00000308731	NM_000061.2	480	gGc/gTc	15/19	0.227910901463109	3	FACETS	0.687	0.574	0.812	0.343	0.287	0.406	SUBCLONAL	1	TRUE	1	0.32188459723577	3		456	441	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346338	73346338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	47	345	0	ENST00000377767.4:c.1462G>A	p.Asp488Asn	p.D488N	ENST00000377767	NM_014953.3	488	Gat/Aat	10/21	1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	1	0.313188302776587	2		345	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0061623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	139	670	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.313188302776587	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.313188302776587	1		670	609	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0061623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	150	482	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.769	0.705	0.835	1	0.989	1	SUBCLONAL	2	TRUE	1	0.313188302776587	2		482	623	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589589	67589591	+	inframe_deletion	In_Frame_Del	DEL	AAT	AAT	-	novel	NA	P-0061623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	27	271	0	ENST00000274335.5:c.1353_1355del	p.Glu451_Tyr452delinsAsp	p.E451_Y452delinsD	ENST00000274335		451	gAATat/gat	10/15	1	2	FACETS	0.753	0.602	0.923	0.753	0.602	0.923	CLONAL	1	TRUE	1	0.313188302776587	2		271	229	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061204	38061204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	37	590	0	ENST00000250448.2:c.785G>A	p.Arg262His	p.R262H	ENST00000250448	NM_004496.3	262	cGc/cAc	2/2	1	2	FACETS	0.407	0.335	0.489	0.407	0.335	0.489	SUBCLONAL	1	TRUE	1	0.313188302776587	2		590	580	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954643	17954643	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	61	608	0	ENST00000458235.1:c.251del	p.Pro84ArgfsTer63	p.P84Rfs*63	ENST00000458235	NM_000215.3	84	cCg/cg	3/24	0.313188302776587	1	FACETS	0.581	0.502	0.668	0.581	0.502	0.668	SUBCLONAL	1	TRUE	0	0.313188302776587	1		608	565	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs371769427	NA	P-0061623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	45	368	0	ENST00000291552.4:c.101C>A	p.Ser34Tyr	p.S34Y	ENST00000291552	NM_006758.2	34	tCt/tAt	2/8	1	2	FACETS	0.676	0.569	0.794	0.676	0.569	0.794	SUBCLONAL	1	TRUE	1	0.313188302776587	2		368	425	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591054	67591056	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0061623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	36	392	0	ENST00000274335.5:c.1651_1653del	p.Lys551del	p.K551del	ENST00000274335		549	ttGAAg/ttg	12/15	1	2	FACETS	0.524	0.43	0.628	0.524	0.43	0.628	SUBCLONAL	1	TRUE	1	0.313188302776587	2		392	439	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067433	37067433	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	108	501	0	ENST00000231790.2:c.1348del	p.Asp450IlefsTer41	p.D450Ifs*41	ENST00000231790	NM_000249.3	448	gaG/ga	12/19	0.313188302776587	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.313188302776587	1		501	569	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957465	175957465	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	34	401	0	ENST00000367669.3:c.1931del	p.Asn644ThrfsTer3	p.N644Tfs*3	ENST00000367669	NM_022457.5	644	aAc/ac	17/20	1	2	FACETS	0.446	0.364	0.538	0.446	0.364	0.538	SUBCLONAL	1	TRUE	1	0.313188302776587	2		401	487	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1039255	1039255	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs760209331	NA	P-0061623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	41	440	0	ENST00000358495.3:c.242A>G	p.Tyr81Cys	p.Y81C	ENST00000358495	NM_134424.2	81	tAc/tGc	4/12	1	2	FACETS	0.433	0.36	0.515	0.433	0.36	0.515	SUBCLONAL	1	TRUE	1	0.313188302776587	2		440	604	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557837	21557837	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	47	469	2	ENST00000382592.4:c.2008A>G	p.Lys670Glu	p.K670E	ENST00000382592	NM_014572.2	670	Aag/Gag	5/8	1	2	FACETS	0.514	0.433	0.603	0.514	0.433	0.603	SUBCLONAL	1	TRUE	1	0.313188302776587	2		471	584	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610320	10610320	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	99	602	1	ENST00000171111.5:c.390del	p.Lys131ArgfsTer26	p.K131Rfs*26	ENST00000171111	NM_203500.1	130	ccC/cc	2/6	0.313188302776587	1	FACETS	0.964	0.863	1	0.964	0.863	1	CLONAL	1	TRUE	0	0.313188302776587	1		603	553	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144081	11144081	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	43	534	0	ENST00000358026.2:c.3662A>G	p.Lys1221Arg	p.K1221R	ENST00000358026	NM_001128849.1	1221	aAg/aGg	26/36	0.313188302776587	1	FACETS	0.458	0.383	0.541	0.458	0.383	0.541	SUBCLONAL	1	TRUE	0	0.313188302776587	1		534	506	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067423	37067423	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	122	516	0	ENST00000231790.2:c.1334A>T	p.Gln445Leu	p.Q445L	ENST00000231790	NM_000249.3	445	cAg/cTg	12/19	0.313188302776587	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.313188302776587	1		516	576	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247173	153247173	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	78	385	0	ENST00000281708.4:c.1629A>C	p.Arg543Ser	p.R543S	ENST00000281708	NM_033632.3	543	agA/agC	10/12	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.313188302776587	2		385	445	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803488	32803488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1436892267	NA	P-0061623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	40	486	0	ENST00000374899.4:c.671G>A	p.Arg224Gln	p.R224Q	ENST00000374899	NM_018833.2	224	cGg/cAg	4/12	1	2	FACETS	0.434	0.36	0.516	0.434	0.36	0.516	SUBCLONAL	1	TRUE	1	0.313188302776587	2		486	589	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853056	151853057	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0061623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	39	455	0	ENST00000262189.6:c.11898dup	p.Lys3967GlnfsTer4	p.K3967Qfs*4	ENST00000262189	NM_170606.2	3966	-/C	46/59	1	2	FACETS	0.449	0.371	0.535	0.449	0.371	0.535	SUBCLONAL	1	TRUE	1	0.313188302776587	2		455	555	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730301	133730301	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	97	441	0	ENST00000318560.5:c.367G>T	p.Glu123Ter	p.E123*	ENST00000318560	NM_005157.4	123	Gag/Tag	3/11	0.22023708868972	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.313188302776587	1		441	485	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932791	39932791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	41	621	0	ENST00000378444.4:c.1808C>T	p.Ala603Val	p.A603V	ENST00000378444	NM_001123385.1	603	gCc/gTc	4/15	0.313188302776587	1	FACETS	0.362	0.301	0.43	0.362	0.301	0.43	SUBCLONAL	1	TRUE	0	0.313188302776587	1		621	610	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	49	517	3	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.256	0.216	0.3	0.256	0.216	0.3	SUBCLONAL	1	TRUE	1	0.71	2		520	539	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	402	877	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.903	0.87	0.935	1	0.997	1	CLONAL	2	TRUE	1	0.71	2		883	627	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	136	627	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.98	0.9	1	0.98	0.9	1	CLONAL	1	TRUE	1	0.71	2		633	391	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	126	685	5	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.822	0.75	0.896	0.822	0.75	0.896	CLONAL	1	TRUE	1	0.71	2		690	432	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	165	409	4	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.926	0.857	0.997	0.926	0.857	0.997	CLONAL	1	TRUE	1	0.71	2		413	502	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	58	377	0	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	0.364	0.313	0.419	0.364	0.313	0.419	SUBCLONAL	1	TRUE	1	0.71	2		377	449	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150931823	150931823	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	141	400	0	ENST00000271640.5:c.2500G>T	p.Gly834Cys	p.G834C	ENST00000271640	NM_001145415.1	834	Ggc/Tgc	15/22	1	2	FACETS	0.971	0.894	1	0.971	0.894	1	CLONAL	1	TRUE	1	0.71	2		400	409	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870251	155870251	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	65	478	0	ENST00000368323.3:c.588del	p.Lys196AsnfsTer12	p.K196Nfs*12	ENST00000368323	NM_006912.5	196	aaA/aa	6/6	1	2	FACETS	0.353	0.306	0.403	0.353	0.306	0.403	SUBCLONAL	1	TRUE	1	0.71	2		478	519	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	99	506	5	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	0.512	0.458	0.568	0.512	0.458	0.568	SUBCLONAL	1	TRUE	1	0.71	2		511	545	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432409	49432412	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	novel	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	241	599	0	ENST00000301067.7:c.8727_8730del	p.Ser2910ArgfsTer32	p.S2910Rfs*32	ENST00000301067	NM_003482.3	2909	gtAAGT/gt	34/54	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.71	2		599	645	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636462	73636462	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	209	518	0	ENST00000377687.4:c.725C>G	p.Ser242Cys	p.S242C	ENST00000377687	NM_001730.3	242	tCt/tGt	2/4	1	2	FACETS	0.954	0.891	1	0.954	0.891	1	CLONAL	1	TRUE	1	0.71	2		518	617	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438216	110438216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1273204122	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	155	420	0	ENST00000375856.3:c.185C>T	p.Ala62Val	p.A62V	ENST00000375856	NM_003749.2	62	gCg/gTg	1/2	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.71	2		420	374	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347093	347093	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	73	400	0	ENST00000262320.3:c.1918del	p.Glu640LysfsTer65	p.E640Kfs*65	ENST00000262320	NM_003502.3	640	Gaa/aa	7/11	1	2	FACETS	0.556	0.489	0.627	0.556	0.489	0.627	SUBCLONAL	1	TRUE	1	0.71	2		400	370	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217888	2217888	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	86	457	0	ENST00000398665.3:c.2662G>T	p.Val888Leu	p.V888L	ENST00000398665	NM_032482.2	888	Gtg/Ttg	22/28	1	2	FACETS	0.53	0.471	0.593	0.53	0.471	0.593	SUBCLONAL	1	TRUE	1	0.71	2		457	457	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7293850	7293850	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	161	711	1	ENST00000302850.5:c.53T>G	p.Val18Gly	p.V18G	ENST00000302850	NM_000208.2	18	gTg/gGg	1/22	1	2	FACETS	0.882	0.815	0.952	0.882	0.815	0.952	CLONAL	1	TRUE	1	0.71	2		712	514	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250813	10250813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	154	482	0	ENST00000340748.4:c.3667G>A	p.Gly1223Arg	p.G1223R	ENST00000340748		1223	Ggg/Agg	32/40	1	2	FACETS	0.908	0.837	0.98	0.908	0.837	0.98	CLONAL	1	TRUE	1	0.71	2		482	478	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753149	42753151	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs199960550	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	184	613	4	ENST00000222329.4:c.1113_1115del	p.Ser373del	p.S373del	ENST00000222329	NM_006494.2	371	tcTTCc/tcc	4/4	1	2	FACETS	0.891	0.827	0.956	0.891	0.827	0.956	CLONAL	1	TRUE	1	0.71	2		617	582	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	203	659	0	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	0.991	0.925	1	0.991	0.925	1	CLONAL	1	TRUE	1	0.71	2		659	577	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713413	40713414	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	150	598	0	ENST00000373198.4:c.4101dup	p.Ser1368LeufsTer20	p.S1368Lfs*20	ENST00000373198	NM_133170.3	1367	-/C	30/32	0.698607339844211	2	FACETS	0.832	0.765	0.9			1	CLONAL	1	TRUE	NA	0.71	2		598	508	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877357	40877357	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	124	403	0	ENST00000373198.4:c.2339T>C	p.Leu780Pro	p.L780P	ENST00000373198	NM_133170.3	780	cTc/cCc	15/32	0.698607339844211	2	FACETS	0.834	0.761	0.909			1	CLONAL	1	TRUE	NA	0.71	2		403	419	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41560079	41560079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373249130	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	113	334	0	ENST00000263253.7:c.3751G>A	p.Gly1251Arg	p.G1251R	ENST00000263253	NM_001429.3	1251	Gga/Aga	22/31	1	2	FACETS	0.865	0.786	0.947	0.865	0.786	0.947	CLONAL	1	TRUE	1	0.71	2		334	368	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519886	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	110	442	0	ENST00000349496.5:c.97T>C	p.Ser33Pro	p.S33P	ENST00000349496	NM_001904.3	33	Tct/Cct	3/15	1	2	FACETS	0.629	0.567	0.693	0.629	0.567	0.693	SUBCLONAL	1	TRUE	1	0.71	2		442	493	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981832	63981832	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	42	527	3	ENST00000398590.3:c.2340del	p.Thr781ProfsTer11	p.T781Pfs*11	ENST00000398590	NM_001177387.1	778	ggC/gg	12/14	1	2	FACETS	0.2	0.166	0.237	0.2	0.166	0.237	SUBCLONAL	1	TRUE	1	0.71	2		530	593	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430600	181430600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1372564199	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	89	566	0	ENST00000325404.1:c.452C>T	p.Ala151Val	p.A151V	ENST00000325404	NM_003106.3	151	gCg/gTg	1/1	1	2	FACETS	0.517	0.46	0.577	0.517	0.46	0.577	SUBCLONAL	1	TRUE	1	0.71	2		566	485	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980398	1980398	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	183	448	0	ENST00000382891.5:c.3860T>C	p.Val1287Ala	p.V1287A	ENST00000382891	NM_133335.3	1287	gTg/gCg	22/22	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.71	2		448	452	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84393376	84393376	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs761514478	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	41	216	0	ENST00000321945.7:c.281A>G	p.Lys94Arg	p.K94R	ENST00000321945	NM_139076.2	94	aAg/aGg	4/9	1	2	FACETS	0.453	0.38	0.533	0.453	0.38	0.533	SUBCLONAL	1	TRUE	1	0.71	2		216	255	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534309	187534310	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	183	431	0	ENST00000441802.2:c.9416_9417del	p.Glu3139AlafsTer27	p.E3139Afs*27	ENST00000441802	NM_005245.3	3139	gAG/g	13/27	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.71	2		431	479	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671952	30671952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200530869	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	207	582	0	ENST00000376406.3:c.5008G>A	p.Val1670Ile	p.V1670I	ENST00000376406	NM_014641.2	1670	Gtc/Atc	10/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.71	2		582	554	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798160	32798160	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	81	481	0	ENST00000374899.4:c.1519T>C	p.Ser507Pro	p.S507P	ENST00000374899	NM_018833.2	507	Tct/Cct	9/12	1	2	FACETS	0.424	0.374	0.477	0.424	0.374	0.477	SUBCLONAL	1	TRUE	1	0.71	2		481	538	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129329	152129329	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	83	481	1	ENST00000206249.3:c.287del	p.Gly96ValfsTer13	p.G96Vfs*13	ENST00000206249	NM_000125.3	94	ctG/ct	1/8	1	2	FACETS	0.518	0.459	0.581	0.518	0.459	0.581	SUBCLONAL	1	TRUE	1	0.71	2		482	451	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	124	457	2	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.79	0.72	0.863	0.79	0.72	0.863	SUBCLONAL	1	TRUE	1	0.71	2		459	442	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124532331	124532331	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	112	285	0	ENST00000357628.3:c.113G>A	p.Ser38Asn	p.S38N	ENST00000357628	NM_015450.2	38	aGc/aAc	6/19	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.71	2		285	292	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877153	151877153	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	78	479	0	ENST00000262189.6:c.7208G>A	p.Arg2403Gln	p.R2403Q	ENST00000262189	NM_170606.2	2403	cGa/cAa	37/59	1	2	FACETS	0.521	0.459	0.586	0.521	0.459	0.586	SUBCLONAL	1	TRUE	1	0.71	2		479	422	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008881	152008881	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	159	325	0	ENST00000262189.6:c.739+2T>C		p.X247_splice	ENST00000262189	NM_170606.2	247			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.71	2		325	402	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399333	139399333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763765573	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	174	522	0	ENST00000277541.6:c.4810G>A	p.Val1604Met	p.V1604M	ENST00000277541	NM_017617.3	1604	Gtg/Atg	26/34	1	2	FACETS	0.998	0.927	1	0.998	0.927	1	CLONAL	1	TRUE	1	0.71	2		522	491	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361151	70361151	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs757508922	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	147	287	0	ENST00000374080.3:c.6339A>C	p.Gln2113His	p.Q2113H	ENST00000374080		2113	caA/caC	43/45	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.71	1		287	235	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361160	70361160	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs79912241	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	137	273	0	ENST00000374080.3:c.6348C>A	p.His2116Gln	p.H2116Q	ENST00000374080		2116	caC/caA	43/45	1	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.71	1		273	227	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0061624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	48	158	0	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	1	FACETS	0.815	0.713	0.919	0.815	0.713	0.919	CLONAL	1	TRUE	0	0.71	1		158	107	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157306	106157306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	80	602	0	ENST00000380013.4:c.2207C>T	p.Ser736Leu	p.S736L	ENST00000380013	NM_001127208.2	736	tCa/tTa	3/11	1	2	FACETS	0.783	0.689	0.885	0.783	0.689	0.885	SUBCLONAL	1	TRUE	1	0.25250137095263	2		602	809	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	42	407	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	1	2	FACETS	0.652	0.544	0.772	0.652	0.544	0.772	SUBCLONAL	1	TRUE	1	0.25250137095263	2		407	510	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	61	549	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	1	2	FACETS	0.689	0.594	0.793	0.689	0.594	0.793	SUBCLONAL	1	TRUE	1	0.25250137095263	2		549	701	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97876927	97876927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	129	451	0	ENST00000289081.3:c.1138G>A	p.Glu380Lys	p.E380K	ENST00000289081	NM_000136.2	380	Gaa/Aaa	12/15	0.212576229173052	2	FACETS	0.884	0.804	0.967	0.884	0.804	0.967	CLONAL	2	TRUE	0	0.25250137095263	2		451	578	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860557	45860557	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	109	670	0	ENST00000391945.4:c.1450A>G	p.Thr484Ala	p.T484A	ENST00000391945	NM_000400.3	484	Acg/Gcg	15/23	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.25250137095263	2		670	791	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796929	78796929	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	79	486	0	ENST00000306801.3:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000306801	NM_020761.2	348	Cga/Tga	9/34	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.25250137095263	2		486	576	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252909	36252909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	67	476	0	ENST00000300305.3:c.453G>A	p.Met151Ile	p.M151I	ENST00000300305		151	atG/atA	4/8	1	2	FACETS	0.925	0.804	1	0.925	0.804	1	CLONAL	1	TRUE	1	0.25250137095263	2		476	574	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619037	37619037	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	128	734	0	ENST00000447079.4:c.713C>A	p.Ser238Ter	p.S238*	ENST00000447079	NM_015083.1	238	tCg/tAg	1/14	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.25250137095263	2		734	861	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805705	46805705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138213197	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	105	.	.	ENST00000290295.7:c.251G>A	p.Gly84Glu	p.G84E	ENST00000290295	NM_006361.5	84	gGa/gAa	1/2	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.25250137095263	2		0	826	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916917	178916917	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	67	408	0	ENST00000263967.3:c.304A>T	p.Ile102Phe	p.I102F	ENST00000263967	NM_006218.2	102	Att/Ttt	2/21	1	2	FACETS	0.846	0.735	0.967	0.846	0.735	0.967	CLONAL	1	TRUE	1	0.25250137095263	2		408	627	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324070	31324070	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs151341262	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	112	580	0	ENST00000412585.2:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000412585	NM_005514.6	165	Cag/Tag	3/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.25250137095263	2		580	646	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641356	23641356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	41	538	0	ENST00000261584.4:c.2119C>T	p.Pro707Ser	p.P707S	ENST00000261584	NM_024675.3	707	Cct/Tct	5/13	1	2	FACETS	0.465	0.386	0.553	0.465	0.386	0.553	SUBCLONAL	1	TRUE	1	0.25250137095263	2		538	699	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436152	51436152	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	56	457	0	ENST00000262662.1:c.112G>A	p.Gly38Arg	p.G38R	ENST00000262662		38	Gga/Aga	3/4	1	2	FACETS	0.758	0.649	0.877	0.758	0.649	0.877	SUBCLONAL	1	TRUE	1	0.25250137095263	2		457	585	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111794	56111794	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs557606535	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	65	417	0	ENST00000399503.3:c.394G>A	p.Asp132Asn	p.D132N	ENST00000399503	NM_005921.1	132	Gac/Aac	1/20	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.25250137095263	2		417	467	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29115398	29115398	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs769193111	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	36	261	0	ENST00000328354.6:c.668C>G	p.Ser223Ter	p.S223*	ENST00000328354	NM_007194.3	223	tCa/tGa	5/15	1	2	FACETS	0.902	0.744	1	0.902	0.744	1	CLONAL	1	TRUE	1	0.25250137095263	2		261	316	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279452	38279452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	47	456	0	ENST00000425967.3:c.1037G>A	p.Gly346Glu	p.G346E	ENST00000425967	NM_001174067.1	346	gGa/gAa	9/19	1	2	FACETS	0.573	0.482	0.673	0.573	0.482	0.673	SUBCLONAL	1	TRUE	1	0.25250137095263	2		456	650	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554000	63554000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755206242	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	105	567	0	ENST00000307078.5:c.739G>A	p.Val247Met	p.V247M	ENST00000307078	NM_004655.3	247	Gtg/Atg	2/11	1	2	FACETS	0.953	0.853	1	0.953	0.853	1	CLONAL	1	TRUE	1	0.25250137095263	2		567	873	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021497	42021497	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	108	577	0	ENST00000219905.7:c.3793C>T	p.Gln1265Ter	p.Q1265*	ENST00000219905	NM_001164273.1	1265	Cag/Tag	11/24	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.25250137095263	2		577	825	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244124	153244124	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	100	628	0	ENST00000281708.4:c.2033C>T	p.Ser678Leu	p.S678L	ENST00000281708	NM_033632.3	678	tCa/tTa	12/12	1	2	FACETS	0.986	0.881	1	0.986	0.881	1	CLONAL	1	TRUE	1	0.25250137095263	2		628	803	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505488	157505488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	49	569	0	ENST00000346085.5:c.3469G>A	p.Glu1157Lys	p.E1157K	ENST00000346085	NM_020732.3	1157	Gaa/Aaa	13/20	1	2	FACETS	0.62	0.524	0.726	0.62	0.524	0.726	SUBCLONAL	1	TRUE	1	0.25250137095263	2		569	626	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1720609	1720609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	95	566	0	ENST00000378609.4:c.799G>A	p.Asp267Asn	p.D267N	ENST00000378609	NM_002074.3	267	Gac/Aac	10/12	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.25250137095263	2		566	740	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106098	8106098	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs759593548	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	97	502	0	ENST00000346208.3:c.918G>C	p.Arg306Ser	p.R306S	ENST00000346208		306	agG/agC	4/6	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.25250137095263	2		502	737	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456411	32456411	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	63	621	0	ENST00000332351.3:c.481A>G	p.Thr161Ala	p.T161A	ENST00000332351	NM_024426.4	161	Act/Gct	1/10	1	2	FACETS	0.688	0.594	0.791	0.688	0.594	0.791	SUBCLONAL	1	TRUE	1	0.25250137095263	2		621	725	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912791	100912791	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	86	469	0	ENST00000325455.5:c.2531T>C	p.Met844Thr	p.M844T	ENST00000325455	NM_001202474.3	844	aTg/aCg	7/8	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.25250137095263	2		469	576	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420157	49420157	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	100	693	0	ENST00000301067.7:c.15592G>T	p.Asp5198Tyr	p.D5198Y	ENST00000301067	NM_003482.3	5198	Gac/Tac	48/54	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.25250137095263	2		693	759	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434461	121434461	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	108	686	0	ENST00000257555.6:c.1225C>A	p.Pro409Thr	p.P409T	ENST00000257555		409	Cct/Act	6/10	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.25250137095263	2		686	810	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896437	28896437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	60	400	0	ENST00000282397.4:c.3013C>T	p.Gln1005Ter	p.Q1005*	ENST00000282397	NM_002019.4	1005	Caa/Taa	22/30	1	2	FACETS	0.877	0.756	1	0.877	0.756	1	CLONAL	1	TRUE	1	0.25250137095263	2		400	542	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953511	32953511	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	58	444	0	ENST00000380152.3:c.8812G>A	p.Asp2938Asn	p.D2938N	ENST00000380152		2938	Gat/Aat	22/27	1	2	FACETS	0.727	0.624	0.839	0.727	0.624	0.839	SUBCLONAL	1	TRUE	1	0.25250137095263	2		444	632	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866444	37866444	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	105	698	0	ENST00000269571.5:c.749C>G	p.Ser250Cys	p.S250C	ENST00000269571		250	tCt/tGt	6/27	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.25250137095263	2		698	798	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435387	56435387	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs539442891	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	122	797	0	ENST00000407977.2:c.1750C>T	p.Arg584Trp	p.R584W	ENST00000407977		584	Cgg/Tgg	9/10	1	2	FACETS	0.979	0.884	1	0.979	0.884	1	CLONAL	1	TRUE	1	0.25250137095263	2		797	987	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976929	18976930	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	63	557	0	ENST00000262803.5:c.3314_3315delinsTT	p.Arg1105Leu	p.R1105L	ENST00000262803	NM_002911.3	1105	cGG/cTT	23/24	1	2	FACETS	0.758	0.655	0.87	0.758	0.655	0.87	SUBCLONAL	1	TRUE	1	0.25250137095263	2		557	658	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209065	36209065	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	35	356	0	ENST00000222270.7:c.145C>A	p.Arg49Ser	p.R49S	ENST00000222270	NM_014727.1	49	Cgc/Agc	1/37	1	2	FACETS	0.735	0.603	0.883	0.735	0.603	0.883	SUBCLONAL	1	TRUE	1	0.25250137095263	2		356	377	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422564	47422564	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	78	517	0	ENST00000404338.3:c.632G>A	p.Arg211Lys	p.R211K	ENST00000404338	NM_004491.4	211	aGa/aAa	1/6	1	2	FACETS	0.946	0.832	1	0.946	0.832	1	CLONAL	1	TRUE	1	0.25250137095263	2		517	653	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424448	47424448	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	92	555	0	ENST00000404338.3:c.2516C>T	p.Ser839Leu	p.S839L	ENST00000404338	NM_004491.4	839	tCa/tTa	1/6	1	2	FACETS	0.882	0.783	0.988	0.882	0.783	0.988	CLONAL	1	TRUE	1	0.25250137095263	2		555	826	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424886	47424886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	95	600	0	ENST00000404338.3:c.2954C>T	p.Ser985Leu	p.S985L	ENST00000404338	NM_004491.4	985	tCa/tTa	1/6	1	2	FACETS	0.915	0.814	1	0.915	0.814	1	CLONAL	1	TRUE	1	0.25250137095263	2		600	822	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965850	25965875	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGGTTTGGATGTCCTTCTGCCAGC	GCAGGTTTGGATGTCCTTCTGCCAGC	-	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	97	549	0	ENST00000435504.4:c.3331_3356del	p.Ala1111AsnfsTer20	p.A1111Nfs*20	ENST00000435504		1111	GCTGGCAGAAGGACATCCAAACCTGCa/a	13/13	1	2	FACETS	0.984	0.877	1	0.984	0.877	1	CLONAL	1	TRUE	1	0.25250137095263	2		549	781	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702376	47702376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	71	335	0	ENST00000233146.2:c.1972G>A	p.Glu658Lys	p.E658K	ENST00000233146	NM_000251.2	658	Gaa/Aaa	12/16	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.25250137095263	2		335	508	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446255	29446255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	74	677	0	ENST00000544604.2:c.2086G>A	p.Asp696Asn	p.D696N	ENST00000544604	NM_001206998.1	696	Gac/Aac	8/9	1	2	FACETS	0.753	0.659	0.856	0.753	0.659	0.856	SUBCLONAL	1	TRUE	1	0.25250137095263	2		677	778	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561815	55561815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	66	486	0	ENST00000288135.5:c.205G>A	p.Glu69Lys	p.E69K	ENST00000288135	NM_000222.2	69	Gag/Aag	2/21	1	2	FACETS	0.804	0.698	0.92	0.804	0.698	0.92	CLONAL	1	TRUE	1	0.25250137095263	2		486	650	SUCCESS
ALB	213	MSKCC	GRCh37	4	74277799	74277799	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774958805	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	95	451	0	ENST00000295897.4:c.800C>T	p.Thr267Met	p.T267M	ENST00000295897	NM_000477.5	267	aCg/aTg	7/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.25250137095263	2		451	619	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180792	106180792	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	73	428	0	ENST00000380013.4:c.3820C>G	p.Gln1274Glu	p.Q1274E	ENST00000380013	NM_001127208.2	1274	Cag/Gag	7/11	1	2	FACETS	0.997	0.873	1	0.997	0.873	1	CLONAL	1	TRUE	1	0.25250137095263	2		428	580	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531044	187531044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	62	485	0	ENST00000441802.2:c.9979G>A	p.Asp3327Asn	p.D3327N	ENST00000441802	NM_005245.3	3327	Gat/Aat	15/27	1	2	FACETS	0.77	0.664	0.884	0.77	0.664	0.884	SUBCLONAL	1	TRUE	1	0.25250137095263	2		485	638	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254492	1254492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	57	505	0	ENST00000310581.5:c.3286C>T	p.Leu1096Phe	p.L1096F	ENST00000310581	NM_198253.2	1096	Ctc/Ttc	15/16	1	2	FACETS	0.72	0.617	0.832	0.72	0.617	0.832	SUBCLONAL	1	TRUE	1	0.25250137095263	2		505	627	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515132	31515132	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	77	509	0	ENST00000344624.3:c.1253C>T	p.Ser418Leu	p.S418L	ENST00000344624		418	tCa/tTa	5/33	1	2	FACETS	0.901	0.791	1	0.901	0.791	1	CLONAL	1	TRUE	1	0.25250137095263	2		509	677	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627297	86627297	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	66	429	0	ENST00000274376.6:c.672G>A	p.Met224Ile	p.M224I	ENST00000274376	NM_002890.2	224	atG/atA	2/25	1	2	FACETS	0.917	0.797	1	0.917	0.797	1	CLONAL	1	TRUE	1	0.25250137095263	2		429	570	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104607	69104607	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	128	522	0	ENST00000288368.4:c.4451G>C	p.Arg1484Pro	p.R1484P	ENST00000288368	NM_024870.2	1484	cGa/cCa	37/40	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.25250137095263	2		522	705	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922747	44922748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCAGTCT	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	109	270	0	ENST00000377967.4:c.1609_1615dup	p.Ser539PhefsTer16	p.S539Ffs*16	ENST00000377967	NM_021140.2	536	-/TCAGTCT	16/29	0.146491031872329	2	FACETS	1	0.952	1			1	INDETERMINATE	2	TRUE	NA	0.25250137095263	2		270	399	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028853	47028869	+	frameshift_variant	Frame_Shift_Del	DEL	GGCAAGCATGACTATGA	GGCAAGCATGACTATGA	-	novel	NA	P-0061625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	117	302	0	ENST00000377604.3:c.157_173del	p.Gly53ArgfsTer4	p.G53Rfs*4	ENST00000377604	NM_001204468.1	53	GGCAAGCATGACTATGAc/c	3/24	0.146491031872329	2	FACETS	1	0.958	1			1	INDETERMINATE	2	TRUE	NA	0.25250137095263	2		302	424	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0061626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	165	458	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.462712439631561	2		458	599	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374293	138374293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	139	376	0	ENST00000289153.2:c.3151G>A	p.Glu1051Lys	p.E1051K	ENST00000289153	NM_006219.2	1051	Gaa/Aaa	22/22	1	2	FACETS	0.943	0.861	1	0.943	0.861	1	CLONAL	1	TRUE	1	0.462712439631561	2		376	637	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008324	29008324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770377283	NA	P-0061626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	66	314	0	ENST00000282397.4:c.547C>T	p.Arg183Cys	p.R183C	ENST00000282397	NM_002019.4	183	Cgc/Tgc	5/30	0.274904825373926	1	FACETS	0.402	0.349	0.46	0.402	0.349	0.46	INDETERMINATE	1	TRUE	0	0.462712439631561	1		314	545	SUCCESS
ATM	472	MSKCC	GRCh37	11	108099904	108099904	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0061626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	82	198	0	ENST00000278616.4:c.186-1G>C		p.X62_splice	ENST00000278616	NM_000051.3	62			0.462712439631561	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	0	0.462712439631561	1		198	269	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115953	8115953	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	197	506	0	ENST00000346208.3:c.1300del	p.His434ThrfsTer41	p.H434Tfs*41	ENST00000346208		433	caC/ca	6/6	0.245132786917348	1	FACETS	0.877	0.815	0.942	0.877	0.815	0.942	INDETERMINATE	1	TRUE	0	0.462712439631561	1		506	746	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420399	49420399	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	224	519	0	ENST00000301067.7:c.15350G>T	p.Cys5117Phe	p.C5117F	ENST00000301067	NM_003482.3	5117	tGt/tTt	48/54	0.245132786917348	1	FACETS	0.943	0.881	1	0.943	0.881	1	INDETERMINATE	1	TRUE	0	0.462712439631561	1		519	789	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49449058	49449058	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0061626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	74	345	0	ENST00000301067.7:c.49+1G>A		p.X17_splice	ENST00000301067	NM_003482.3	17			0.245132786917348	1	FACETS	0.48	0.421	0.544	0.48	0.421	0.544	INDETERMINATE	1	TRUE	0	0.462712439631561	1		345	512	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350537	89350537	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs747437062	NA	P-0061626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	143	291	0	ENST00000301030.4:c.2413G>C	p.Glu805Gln	p.E805Q	ENST00000301030	NM_001256183.1	805	Gaa/Caa	9/13	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.462712439631561	2		291	542	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526534	66526534	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	101	399	0	ENST00000358598.2:c.1090G>C	p.Asp364His	p.D364H	ENST00000358598	NM_212471.2	364	Gac/Cac	11/11	0.245132786917348	1	FACETS	0.499	0.447	0.555	0.499	0.447	0.555	INDETERMINATE	1	TRUE	0	0.462712439631561	1		399	672	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226806	2226806	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	184	710	0	ENST00000398665.3:c.4286C>A	p.Ser1429Tyr	p.S1429Y	ENST00000398665	NM_032482.2	1429	tCt/tAt	27/28	1	2	FACETS	0.896	0.827	0.967	0.896	0.827	0.967	CLONAL	1	TRUE	1	0.462712439631561	2		710	888	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548256	41548256	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	187	374	0	ENST00000263253.7:c.3044G>C	p.Arg1015Thr	p.R1015T	ENST00000263253	NM_001429.3	1015	aGa/aCa	16/31	0.462712439631561	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.462712439631561	1		374	507	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553365	41553365	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	177	345	0	ENST00000263253.7:c.3454G>C	p.Glu1152Gln	p.E1152Q	ENST00000263253	NM_001429.3	1152	Gaa/Caa	18/31	0.462712439631561	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.462712439631561	1		345	503	SUCCESS
ATR	545	MSKCC	GRCh37	3	142297489	142297489	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	123	358	0	ENST00000350721.4:c.58A>T	p.Ser20Cys	p.S20C	ENST00000350721	NM_001184.3	20	Agt/Tgt	1/47	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.462712439631561	2		358	494	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796105	57796105	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1208548556	NA	P-0061626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	213	387	0	ENST00000309042.7:c.1081C>T	p.Leu361Phe	p.L361F	ENST00000309042	NM_005612.4	361	Ctt/Ttt	4/4	0.462712439631561	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.462712439631561	1		387	545	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630888	187630888	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	175	509	0	ENST00000441802.2:c.94del	p.Leu32CysfsTer39	p.L32Cfs*39	ENST00000441802	NM_005245.3	32	Ctg/tg	2/27	0.462712439631561	1	FACETS	0.964	0.892	1	0.964	0.892	1	CLONAL	1	TRUE	0	0.462712439631561	1		509	603	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045759	26045759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	238	688	0	ENST00000540144.1:c.121C>T	p.Arg41Cys	p.R41C	ENST00000540144	NM_003531.2	41	Cgc/Tgc	1/1	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.462712439631561	2		688	1019	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0000113-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	989	465	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.962524707583607	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.962524707583607	2		465	1001	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044904	47044904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000113-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	1041	1098	0	ENST00000377604.3:c.2230C>T	p.Arg744Cys	p.R744C	ENST00000377604	NM_001204468.1	744	Cgt/Tgt	20/24	0.26765427488314	3	FACETS	0.836	0.815	0.857	0.836	0.815	0.857	INDETERMINATE	2	TRUE	1	0.962524707583607	3		1098	1916	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990409	81990409	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000113-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	301	735	0	ENST00000359376.3:c.3680A>T	p.Asn1227Ile	p.N1227I	ENST00000359376	NM_002661.3	1227	aAc/aTc	32/33	0.962524707583607	1	FACETS	0.516	0.49	0.542	0.516	0.49	0.542	SUBCLONAL	1	TRUE	0	0.962524707583607	1		735	629	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934055	39934055	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000113-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	902	812	0	ENST00000378444.4:c.544A>C	p.Asn182His	p.N182H	ENST00000378444	NM_001123385.1	182	Aat/Cat	4/15	0.26765427488314	3	FACETS	0.864	0.841	0.887	0.864	0.841	0.887	INDETERMINATE	2	TRUE	1	0.962524707583607	3		812	1606	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0000113-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	328	749	15	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	0.955	0.905	1	0.955	0.905	1	CLONAL	1	TRUE	1	0.772904202401995	2		764	889	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000113-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	371	843	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	1	2	FACETS	0.912	0.867	0.957	0.912	0.867	0.957	CLONAL	1	TRUE	1	0.772904202401995	2		843	1053	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594221	55594221	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913512	NA	P-0000113-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	246	444	0	ENST00000288135.5:c.1924A>C	p.Lys642Gln	p.K642Q	ENST00000288135	NM_000222.2	642	Aaa/Caa	13/21	0.745592946434621	1	FACETS	0.969	0.923	1	0.969	0.923	1	CLONAL	1	TRUE	0	0.772904202401995	1		444	403	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000113-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	371	778	0	ENST00000304494.5:c.143C>T	p.Pro48Leu	p.P48L	ENST00000304494	NM_000077.4	48	cCg/cTg	1/3	0.772904202401995	1	FACETS	0.928	0.89	0.964	0.928	0.89	0.964	CLONAL	1	TRUE	0	0.772904202401995	1		778	635	SUCCESS
AR	367	MSKCC	GRCh37	X	66765127	66765127	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000113-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	203	586	0	ENST00000374690.3:c.139G>A	p.Ala47Thr	p.A47T	ENST00000374690	NM_000044.3	47	Gca/Aca	1/8	1	2	FACETS	0.814	0.759	0.871	0.814	0.759	0.871	CLONAL	1	TRUE	1	0.772904202401995	2		586	645	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916529	39916529	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000113-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	201	557	0	ENST00000378444.4:c.4474C>A	p.His1492Asn	p.H1492N	ENST00000378444	NM_001123385.1	1492	Cat/Aat	11/15	1	2	FACETS	0.824	0.768	0.882	0.824	0.768	0.882	CLONAL	1	TRUE	1	0.772904202401995	2		557	631	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506389	120506389	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000113-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	630	663	0	ENST00000256646.2:c.1723G>C	p.Asp575His	p.D575H	ENST00000256646	NM_024408.3	575	Gac/Cac	11/34	0.728942997667198	2	FACETS	0.924	0.9	0.948	0.924	0.9	0.948	CLONAL	2	TRUE	0	0.772904202401995	2		663	882	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505386	125505386	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000113-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	171	418	0	ENST00000428830.2:c.676A>C	p.Thr226Pro	p.T226P	ENST00000428830	NM_001114121.2	226	Aca/Cca	7/14	1	2	FACETS	0.97	0.901	1	0.97	0.901	1	CLONAL	1	TRUE	1	0.772904202401995	2		418	456	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418445	49418445	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000113-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	305	778	0	ENST00000301067.7:c.15968G>T	p.Arg5323Leu	p.R5323L	ENST00000301067	NM_003482.3	5323	cGc/cTc	50/54	1	2	FACETS	0.883	0.834	0.932	0.883	0.834	0.932	CLONAL	1	TRUE	1	0.772904202401995	2		778	894	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144478	58144478	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000113-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	311	630	0	ENST00000257904.6:c.593G>A	p.Trp198Ter	p.W198*	ENST00000257904	NM_000075.3	198	tGg/tAg	5/8	1	2	FACETS	0.98	0.929	1	0.98	0.929	1	CLONAL	1	TRUE	1	0.772904202401995	2		630	821	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579431	7579432	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000113-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	387	850	0	ENST00000269305.4:c.255dup	p.Ala86CysfsTer63	p.A86Cfs*63	ENST00000269305	NM_001126112.2	85	-/T	4/11	1	2	FACETS	0.886	0.843	0.93	0.886	0.843	0.93	CLONAL	1	TRUE	1	0.772904202401995	2		850	1130	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292555	15292555	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000113-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	609	737	0	ENST00000263388.2:c.2624G>T	p.Cys875Phe	p.C875F	ENST00000263388	NM_000435.2	875	tGc/tTc	17/33	0.728942997667198	2	FACETS	0.908	0.883	0.932	0.908	0.883	0.932	CLONAL	2	TRUE	0	0.772904202401995	2		737	868	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424878	47425304	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGGATTCAGAAGAAGATATCGAGCCATCTTACAGCCTGTTTCGAGAAGACACATCACTGCCTTCTCTGTCCAAAGACCATTCTAAGCTCTCTATGGAACTGGAGGGAAATGATGGGCTGTCTTTCATTATGAGCAATTTTGAGAGTAAACTGAACAACAAAGTACCTCCGCCAGTCAAACCAAAGCCTCCTGTCCATTTTGAAATTACAAAGGGGGATCTATCTTATTTAGACCAAGGCCATAGGGATGGACAGAGGAAGTCTGTGTCTTCTAGCCCCTGGCTGCCTCAGGATGGGTTTGATCCTTCTGACTATGCTGAACCCATGGATGCTGTGGTGAAGCCAAGGAATGAAGAAGAAAACATATACTCCGTGCCCCATGACAGCACCCAAGGCAAAATCATCACCATTCGGAATATCAACAAA	GCAGGATTCAGAAGAAGATATCGAGCCATCTTACAGCCTGTTTCGAGAAGACACATCACTGCCTTCTCTGTCCAAAGACCATTCTAAGCTCTCTATGGAACTGGAGGGAAATGATGGGCTGTCTTTCATTATGAGCAATTTTGAGAGTAAACTGAACAACAAAGTACCTCCGCCAGTCAAACCAAAGCCTCCTGTCCATTTTGAAATTACAAAGGGGGATCTATCTTATTTAGACCAAGGCCATAGGGATGGACAGAGGAAGTCTGTGTCTTCTAGCCCCTGGCTGCCTCAGGATGGGTTTGATCCTTCTGACTATGCTGAACCCATGGATGCTGTGGTGAAGCCAAGGAATGAAGAAGAAAACATATACTCCGTGCCCCATGACAGCACCCAAGGCAAAATCATCACCATTCGGAATATCAACAAA	-	novel	NA	P-0000113-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	212	714	0	ENST00000404338.3:c.2948_3374del	p.Gln983ProfsTer19	p.Q983Pfs*19	ENST00000404338	NM_004491.4	982	ctGCAGGATTCAGAAGAAGATATCGAGCCATCTTACAGCCTGTTTCGAGAAGACACATCACTGCCTTCTCTGTCCAAAGACCATTCTAAGCTCTCTATGGAACTGGAGGGAAATGATGGGCTGTCTTTCATTATGAGCAATTTTGAGAGTAAACTGAACAACAAAGTACCTCCGCCAGTCAAACCAAAGCCTCCTGTCCATTTTGAAATTACAAAGGGGGATCTATCTTATTTAGACCAAGGCCATAGGGATGGACAGAGGAAGTCTGTGTCTTCTAGCCCCTGGCTGCCTCAGGATGGGTTTGATCCTTCTGACTATGCTGAACCCATGGATGCTGTGGTGAAGCCAAGGAATGAAGAAGAAAACATATACTCCGTGCCCCATGACAGCACCCAAGGCAAAATCATCACCATTCGGAATATCAACAAA/ct	1/6	NA	2	FACETS	0.656	0.611	0.703			1	INDETERMINATE	1	TRUE	NA	0.772904202401995	2		714	836	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917866	29917866	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000113-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	249	620	0	ENST00000389048.3:c.802T>G	p.Phe268Val	p.F268V	ENST00000389048	NM_004304.4	268	Ttt/Gtt	3/29	1	2	FACETS	0.899	0.844	0.954	0.899	0.844	0.954	CLONAL	1	TRUE	1	0.772904202401995	2		620	717	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379425	225379425	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000113-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	108	428	0	ENST00000264414.4:c.443G>C	p.Arg148Pro	p.R148P	ENST00000264414	NM_003590.4	148	cGa/cCa	4/16	1	2	FACETS	0.863	0.784	0.944	0.863	0.784	0.944	CLONAL	1	TRUE	1	0.772904202401995	2		428	324	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796243	57796243	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000113-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	22	529	0	ENST00000309042.7:c.1219C>T	p.His407Tyr	p.H407Y	ENST00000309042	NM_005612.4	407	Cac/Tac	4/4	0.745592946434621	1	FACETS	0.085	0.065	0.108	0.085	0.065	0.108	SUBCLONAL	1	TRUE	0	0.772904202401995	1		529	412	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467599	66467599	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000113-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	242	553	0	ENST00000273854.3:c.670G>T	p.Val224Phe	p.V224F	ENST00000273854	NM_004439.5	224	Gtt/Ttt	3/18	0.745592946434621	1	FACETS	0.844	0.8	0.889	0.844	0.8	0.889	CLONAL	1	TRUE	0	0.772904202401995	1		553	455	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628865	187628865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000113-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	296	635	0	ENST00000441802.2:c.2117C>T	p.Ser706Phe	p.S706F	ENST00000441802	NM_005245.3	706	tCt/tTt	2/27	0.745592946434621	1	FACETS	0.931	0.889	0.972	0.931	0.889	0.972	CLONAL	1	TRUE	0	0.772904202401995	1		635	505	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97869347	97869347	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0000113-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	280	598	0	ENST00000289081.3:c.1533+1G>T		p.X511_splice	ENST00000289081	NM_000136.2	511			1	2	FACETS	0.869	0.819	0.92	0.869	0.819	0.92	CLONAL	1	TRUE	1	0.772904202401995	2		598	834	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404193	139404193	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000113-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	334	724	0	ENST00000277541.6:c.2961C>A	p.Cys987Ter	p.C987*	ENST00000277541	NM_017617.3	987	tgC/tgA	18/34	1	2	FACETS	0.928	0.88	0.977	0.928	0.88	0.977	CLONAL	1	TRUE	1	0.772904202401995	2		724	931	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418174	139418174	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000113-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	324	637	0	ENST00000277541.6:c.398G>A	p.Trp133Ter	p.W133*	ENST00000277541	NM_017617.3	133	tGg/tAg	3/34	1	2	FACETS	0.933	0.884	0.982	0.933	0.884	0.982	CLONAL	1	TRUE	1	0.772904202401995	2		637	899	SUCCESS
AR	367	MSKCC	GRCh37	X	66766351	66766351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000113-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	108	468	0	ENST00000374690.3:c.1363G>A	p.Gly455Ser	p.G455S	ENST00000374690	NM_000044.3	455	Ggt/Agt	1/8	1	2	FACETS	0.507	0.457	0.561	0.507	0.457	0.561	SUBCLONAL	1	TRUE	1	0.772904202401995	2		468	551	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345895	70345895	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000113-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	192	506	0	ENST00000374080.3:c.2432A>G	p.Asp811Gly	p.D811G	ENST00000374080		811	gAt/gGt	18/45	1	2	FACETS	0.776	0.721	0.833	0.776	0.721	0.833	SUBCLONAL	1	TRUE	1	0.772904202401995	2		506	640	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268361	198268361	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000675-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	222	378	0	ENST00000335508.6:c.1667T>C	p.Ile556Thr	p.I556T	ENST00000335508	NM_012433.2	556	aTt/aCt	12/25	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.542078834849408	2		378	767	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034435	123034435	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000675-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	127	123	0	ENST00000355640.3:c.1192C>T	p.Gln398Ter	p.Q398*	ENST00000355640		398	Cag/Tag	6/7	0.542078834849408	2	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.542078834849408	2		123	347	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0002880-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	92	579	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.316064877725944	3	FACETS	1	0.94	1	0.542	0.482	0.606	CLONAL	1	FALSE	1	0.333305664188617	3		579	594	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002880-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	104	828	0	ENST00000361445.4:c.5930C>G	p.Thr1977Arg	p.T1977R	ENST00000361445	NM_004958.3	1977	aCa/aGa	43/58	0.320979939764843	3	FACETS	0.804	0.719	0.895	0.402	0.359	0.448	CLONAL	1	FALSE	1	0.333305664188617	3		828	905	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0003166-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	181	329	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.369151835491745	2		329	791	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679366	29679366	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs866445127	NA	P-0003166-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	169	507	0	ENST00000356175.3:c.7486C>T	p.Arg2496Ter	p.R2496*	ENST00000356175	NM_000267.3	2496	Cga/Tga	50/57	0.369151835491745	1	FACETS	0.93	0.856	1	0.93	0.856	1	CLONAL	1	TRUE	0	0.369151835491745	1		507	803	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0004524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	625	499	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.537844780245858	4	FACETS	0.953	0.926	0.979			1	CLONAL	4	TRUE	NA	0.537844780245858	4		500	938	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226574044	226574044	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	148	418	0	ENST00000366794.5:c.817C>G	p.Pro273Ala	p.P273A	ENST00000366794	NM_001618.3	273	Cct/Gct	6/23	0.302991403661486	5	FACETS	1	0.952	1	0.354	0.323	0.387	INDETERMINATE	1	TRUE	2	0.537844780245858	5		418	936	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244244	46244244	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	255	412	0	ENST00000334344.6:c.2338C>G	p.Pro780Ala	p.P780A	ENST00000334344	NM_152641.2	780	Cca/Gca	15/21	0.529692385045319	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.537844780245858	4		412	700	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40447688	40447688	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	475	781	0	ENST00000345506.4:c.427C>G	p.Gln143Glu	p.Q143E	ENST00000345506	NM_003152.3	143	Cag/Gag	6/20	0.537844780245858	2	FACETS	0.966	0.93	1	0.966	0.93	1	CLONAL	2	TRUE	0	0.537844780245858	2		781	914	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939403	76939403	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1557141862	NA	P-0004524-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	212	708	0	ENST00000373344.5:c.1345C>G	p.Pro449Ala	p.P449A	ENST00000373344	NM_000489.3	449	Cct/Gct	9/35	NA	2	FACETS	1	0.932	1			1	INDETERMINATE	1	TRUE	NA	0.537844780245858	2		708	788	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0004524-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	1035	499	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.693411026984341	4	FACETS	0.983	0.968	0.999			1	CLONAL	4	TRUE	NA	0.727051518585393	4		500	1250	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226574044	226574044	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004524-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	325	418	0	ENST00000366794.5:c.817C>G	p.Pro273Ala	p.P273A	ENST00000366794	NM_001618.3	273	Cct/Gct	6/23	0.727051518585393	3	FACETS	1	0.988	1	0.575	0.544	0.607	CLONAL	1	TRUE	1	0.727051518585393	3		418	1060	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244244	46244244	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004524-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	420	412	0	ENST00000334344.6:c.2338C>G	p.Pro780Ala	p.P780A	ENST00000334344	NM_152641.2	780	Cca/Gca	15/21	0.42041409410915	6	FACETS	0.978	0.936	1	0.978	0.936	1	INDETERMINATE	3	TRUE	3	0.727051518585393	6		412	966	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40447688	40447688	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004524-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	865	781	0	ENST00000345506.4:c.427C>G	p.Gln143Glu	p.Q143E	ENST00000345506	NM_003152.3	143	Cag/Gag	6/20	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.727051518585393	2		781	1164	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939403	76939403	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1557141862	NA	P-0004524-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	304	708	0	ENST00000373344.5:c.1345C>G	p.Pro449Ala	p.P449A	ENST00000373344	NM_000489.3	449	Cct/Gct	9/35	0.140443182020235	2	FACETS	0.715	0.673	0.757	0.357	0.336	0.379	INDETERMINATE	1	TRUE	0	0.727051518585393	2		708	1170	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262222	16262222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004524-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	52	102	0	ENST00000375759.3:c.9487C>T	p.His3163Tyr	p.H3163Y	ENST00000375759	NM_015001.2	3163	Cac/Tac	11/15	0.686573290338721	5	FACETS	0.912	0.78	1			1	CLONAL	1	TRUE	NA	0.727051518585393	5		102	328	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646039	215646039	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004524-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	179	524	0	ENST00000260947.4:c.559C>G	p.Pro187Ala	p.P187A	ENST00000260947	NM_000465.2	187	Cct/Gct	4/11	0.727051518585393	1	FACETS	0.689	0.641	0.737	0.689	0.641	0.737	SUBCLONAL	1	TRUE	0	0.727051518585393	1		524	455	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713491	30713491	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004524-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	38	280	0	ENST00000295754.5:c.816G>C	p.Glu272Asp	p.E272D	ENST00000295754	NM_003242.5	272	gaG/gaC	4/7	0.727051518585393	3	FACETS	0.208	0.171	0.249	0.104	0.085	0.125	SUBCLONAL	1	TRUE	1	0.727051518585393	3		280	686	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843537	3843537	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004524-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	44	413	0	ENST00000262367.5:c.1066C>T	p.Gln356Ter	p.Q356*	ENST00000262367	NM_004380.2	356	Cag/Tag	4/31	0.727051518585393	1	FACETS	0.164	0.137	0.194	0.164	0.137	0.194	SUBCLONAL	1	TRUE	0	0.727051518585393	1		413	470	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599341	55599341	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519761	NA	P-0004760-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	190	356	0	ENST00000288135.5:c.2467T>G	p.Tyr823Asp	p.Y823D	ENST00000288135	NM_000222.2	823	Tat/Gat	17/21	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.919578259808676	2		356	369	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593667	55593669	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	rs1060502543	NA	P-0004760-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	258	387	0	ENST00000288135.5:c.1735_1737del	p.Asp579del	p.D579del	ENST00000288135	NM_000222.2	578	tATGat/tat	11/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.919578259808676	2		387	532	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593615	+	inframe_deletion	In_Frame_Del	DEL	AGTGGAAGGTTGTTG	AGTGGAAGGTTGTTG	-	novel	NA	P-0004760-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	277	342	0	ENST00000288135.5:c.1669_1683del	p.Trp557_Glu561del	p.W557_E561del	ENST00000288135	NM_000222.2	556	cAGTGGAAGGTTGTTGag/cag	11/21	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.919578259808676	2		342	560	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0005813-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	743	319	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.634651774512298	8	FACETS	0.953	0.924	0.982	0.794	0.77	0.818	CLONAL	5	FALSE	2	0.634651774512298	8		319	1427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0005813-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	401	472	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.608644371849357	2	FACETS	0.995	0.959	1	0.995	0.959	1	CLONAL	2	FALSE	0	0.634651774512298	2		472	635	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0005813-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	694	299	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.634651774512298	8	FACETS	0.932	0.905	0.958	0.932	0.905	0.958	CLONAL	6	FALSE	2	0.634651774512298	8		299	1136	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039377	49039378	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCCTTACAAGTTTCCTAGTTC	novel	NA	P-0005813-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	316	270	0	ENST00000267163.4:c.2363_2384dup	p.Arg798GlnfsTer4	p.R798Qfs*4	ENST00000267163	NM_000321.2	788	agc/aGCCCTTACAAGTTTCCTAGTTCgc	23/27	0.608644371849357	2	FACETS	1	0.994	1	0.696	0.662	0.731	CLONAL	1	FALSE	0	0.634651774512298	2		270	715	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249092	55249092	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005813-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	438	323	0	ENST00000275493.2:c.2390G>C	p.Cys797Ser	p.C797S	ENST00000275493	NM_005228.3	797	tGc/tCc	20/28	0.634651774512298	8	FACETS	0.948	0.904	0.993	0.474	0.452	0.497	CLONAL	3	FALSE	2	0.634651774512298	8		323	1409	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134283	2134283	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005813-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	202	572	0	ENST00000219476.3:c.4060G>T	p.Gly1354Cys	p.G1354C	ENST00000219476	NM_000548.3	1354	Ggc/Tgc	34/42	0.570803352488779	4	FACETS	1	0.967	1	0.536	0.497	0.577	CLONAL	1	FALSE	2	0.634651774512298	4		572	970	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247028	53247028	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005813-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	161	355	1	ENST00000375401.3:c.472G>T	p.Glu158Ter	p.E158*	ENST00000375401	NM_004187.3	158	Gaa/Taa	4/26	0.634651774512298	3	FACETS	0.849	0.78	0.921	0.425	0.39	0.461	CLONAL	1	FALSE	1	0.634651774512298	3		356	787	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	184	321	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.969	0.901	1	0.969	0.901	1	CLONAL	1	TRUE	1	0.694056517309556	2		321	547	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0007013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	179	271	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.964	0.895	1	0.964	0.895	1	CLONAL	1	TRUE	1	0.694056517309556	2		272	535	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	70	544	0	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	0.694056517309556	1	FACETS	0.193	0.168	0.221	0.193	0.168	0.221	SUBCLONAL	1	TRUE	0	0.694056517309556	1		544	681	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101402	27101402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	174	576	0	ENST00000324856.7:c.4689del	p.Met1564Ter	p.M1564*	ENST00000324856	NM_006015.4	1562	Ccc/cc	18/20	0.694056517309556	1	FACETS	0.492	0.455	0.531	0.492	0.455	0.531	SUBCLONAL	1	TRUE	0	0.694056517309556	1		576	665	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106916	27106917	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0007013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	31	368	0	ENST00000324856.7:c.6527_6528del	p.Gln2176ArgfsTer48	p.Q2176Rfs*48	ENST00000324856	NM_006015.4	2176	cAG/c	20/20	0.694056517309556	1	FACETS	0.123	0.099	0.15	0.123	0.099	0.15	SUBCLONAL	1	TRUE	0	0.694056517309556	1		368	476	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816193	89816193	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142379991	NA	P-0007013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	195	634	0	ENST00000389301.3:c.3184G>A	p.Gly1062Arg	p.G1062R	ENST00000389301	NM_000135.2	1062	Ggg/Agg	32/43	1	2	FACETS	0.524	0.484	0.565	0.524	0.484	0.565	SUBCLONAL	1	TRUE	1	0.694056517309556	2		634	1072	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40376841	40376841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1468	345	1087	2	ENST00000293328.3:c.331C>T	p.His111Tyr	p.H111Y	ENST00000293328	NM_012448.3	111	Cat/Tat	4/19	1	2	FACETS	0.548	0.517	0.581	0.548	0.517	0.581	SUBCLONAL	1	TRUE	1	0.694056517309556	2		1089	1813	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791728	42791728	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	55	487	0	ENST00000575354.2:c.614A>G	p.Asn205Ser	p.N205S	ENST00000575354	NM_015125.3	205	aAt/aGt	5/20	0.694056517309556	1	FACETS	0.172	0.147	0.2	0.172	0.147	0.2	SUBCLONAL	1	TRUE	0	0.694056517309556	1		487	601	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429989	78429989	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	142	248	0	ENST00000370768.2:c.890del	p.Met297ArgfsTer26	p.M297Rfs*26	ENST00000370768	NM_003902.3	297	aTg/ag	11/20	0.694056517309556	1	FACETS	0.903	0.838	0.968	0.903	0.838	0.968	CLONAL	1	TRUE	0	0.694056517309556	1		248	296	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443593	52443595	+	inframe_deletion	In_Frame_Del	DEL	GTA	GTA	-	novel	NA	P-0007013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	47	404	0	ENST00000460680.1:c.97_99del	p.Tyr33del	p.Y33del	ENST00000460680	NM_004656.3	33	TAC/-	3/17	1	2	FACETS	0.171	0.143	0.201	0.171	0.143	0.201	SUBCLONAL	1	TRUE	1	0.694056517309556	2		404	792	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128748844	128748845	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1198480500	NA	P-0007013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	336	753	1	ENST00000377970.2:c.12dup	p.Arg5SerfsTer17	p.R5Sfs*17	ENST00000377970	NM_002467.4	2	gat/gaTt	1/3	1	2	FACETS	0.864	0.817	0.911	0.864	0.817	0.911	CLONAL	1	TRUE	1	0.694056517309556	2		754	1121	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288651	33288652	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0007013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	48	291	0	ENST00000374542.5:c.900_901del	p.His300GlnfsTer43	p.H300Qfs*43	ENST00000374542	NM_001141970.1	300	caCAgc/cagc	3/8	1	2	FACETS	0.274	0.232	0.321	0.274	0.232	0.321	SUBCLONAL	1	TRUE	1	0.694056517309556	2		291	504	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917495	178917496	+	missense_variant	Missense_Mutation	DNP	CC	CC	GA	novel	NA	P-0007013-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	34	198	0	ENST00000263967.3:c.370_371delinsGA	p.Pro124Glu	p.P124E	ENST00000263967	NM_006218.2	124	CCa/GAa	3/21	1	2	FACETS	0.268	0.219	0.323	0.268	0.219	0.323	SUBCLONAL	1	TRUE	1	0.694056517309556	2		198	366	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577520	7577520	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1330865474	NA	P-0008181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	146	614	0	ENST00000269305.4:c.761T>G	p.Ile254Ser	p.I254S	ENST00000269305	NM_001126112.2	254	aTc/aGc	7/11	0.332215035567976	1	FACETS	0.997	0.912	1	0.997	0.912	1	CLONAL	1	TRUE	0	0.332215035567976	1		614	735	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584607	48584607	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	164	663	0	ENST00000342988.3:c.780C>A	p.Tyr260Ter	p.Y260*	ENST00000342988	NM_005359.5	260	taC/taA	6/12	0.332215035567976	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.332215035567976	1		663	794	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0008181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	60	341	0	ENST00000311936.3:c.34_35delinsCT	p.Gly12Leu	p.G12L	ENST00000311936	NM_004985.3	12	GGt/CTt	2/5	1	2	FACETS	0.707	0.61	0.812	0.707	0.61	0.812	SUBCLONAL	1	TRUE	1	0.332215035567976	2		341	511	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	155	321	0				ENST00000310581	NM_198253.2	-/1132			0.579948879723532	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.614295545113914	3		321	287	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0008337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	139	271	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.889	0.814	0.967	0.889	0.814	0.967	CLONAL	1	TRUE	1	0.614295545113914	2		272	509	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0008337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	172	304	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.614295545113914	2		304	525	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175857	24175859	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs875989800	NA	P-0008337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	162	454	0	ENST00000263121.7:c.1091_1093del	p.Lys364del	p.K364del	ENST00000263121	NM_003073.3	362	gAGAag/gag	8/9	1	2	FACETS	0.858	0.79	0.927	0.858	0.79	0.927	CLONAL	1	TRUE	1	0.614295545113914	2		454	615	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578326	212578326	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	163	497	0	ENST00000342788.4:c.931T>C	p.Ser311Pro	p.S311P	ENST00000342788	NM_005235.2	311	Tcc/Ccc	8/28	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.614295545113914	2		497	518	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052888	180052888	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	83	476	0	ENST00000261937.6:c.1402A>G	p.Met468Val	p.M468V	ENST00000261937	NM_182925.4	468	Atg/Gtg	10/30	0.579948879723532	3	FACETS	0.59	0.521	0.663	0.295	0.26	0.332	SUBCLONAL	1	TRUE	1	0.614295545113914	3		476	599	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095893	178095895	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	novel	NA	P-0008337-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	63	417	0	ENST00000397062.3:c.1436_1438del	p.Val479del	p.V479del	ENST00000397062	NM_006164.4	479	gTTGac/gac	5/5	1	2	FACETS	0.348	0.301	0.4	0.348	0.301	0.4	SUBCLONAL	1	TRUE	1	0.614295545113914	2		417	589	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845757	68845757	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587780784	NA	P-0008398-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	267	559	2	ENST00000261769.5:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000261769	NM_004360.3	335	Cga/Tga	7/16	0.534529756416367	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.575752923678788	1		561	591	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267698	198267698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008398-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	107	449	0	ENST00000335508.6:c.1781G>A	p.Arg594Gln	p.R594Q	ENST00000335508	NM_012433.2	594	cGa/cAa	13/25	1	2	FACETS	0.856	0.773	0.943	0.856	0.773	0.943	CLONAL	1	TRUE	1	0.575752923678788	2		449	434	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259368	89259368	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008398-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	195	688	0	ENST00000336596.2:c.512T>C	p.Val171Ala	p.V171A	ENST00000336596	NM_005233.5	171	gTa/gCa	3/17	1	2	FACETS	0.986	0.916	1	0.986	0.916	1	CLONAL	1	TRUE	1	0.575752923678788	2		688	687	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873518	151873518	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008398-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	325	766	0	ENST00000262189.6:c.9020del	p.Gly3007GlufsTer25	p.G3007Efs*25	ENST00000262189	NM_170606.2	3007	gGa/ga	38/59	0.109302262413442	3	FACETS	1	0.99	1	0.603	0.57	0.638	INDETERMINATE	1	TRUE	1	0.575752923678788	3		766	1205	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780677	56780677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502588	NA	P-0008398-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	113	400	0	ENST00000337432.4:c.692C>T	p.Ser231Leu	p.S231L	ENST00000337432	NM_058216.2	231	tCa/tTa	4/9	1	2	FACETS	0.935	0.847	1	0.935	0.847	1	CLONAL	1	TRUE	1	0.575752923678788	2		400	420	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878356	151878356	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008398-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	299	784	0	ENST00000262189.6:c.6589C>T	p.Gln2197Ter	p.Q2197*	ENST00000262189	NM_170606.2	2197	Cag/Tag	36/59	0.109302262413442	3	FACETS	1	0.992	1	0.647	0.61	0.685	INDETERMINATE	1	TRUE	1	0.575752923678788	3		784	1034	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878785	151878785	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008398-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	273	695	0	ENST00000262189.6:c.6160C>G	p.Gln2054Glu	p.Q2054E	ENST00000262189	NM_170606.2	2054	Cag/Gag	36/59	0.109302262413442	3	FACETS	1	0.989	1	0.615	0.578	0.653	INDETERMINATE	1	TRUE	1	0.575752923678788	3		695	993	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150933155	150933155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008398-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1559	351	752	0	ENST00000271640.5:c.2617G>T	p.Asp873Tyr	p.D873Y	ENST00000271640	NM_001145415.1	873	Gat/Tat	16/22	0.531938853488911	4	FACETS	1	0.949	1	0.503	0.474	0.532	CLONAL	1	TRUE	2	0.575752923678788	4		752	1910	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94923016	94923016	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008398-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	78	466	0	ENST00000536441.1:c.452G>A	p.Arg151Lys	p.R151K	ENST00000536441	NM_144665.3	151	aGa/aAa	4/10	0.568063299126169	1	FACETS	0.694	0.617	0.775	0.694	0.617	0.775	SUBCLONAL	1	TRUE	0	0.575752923678788	1		466	278	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490326	56490326	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008398-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	76	671	0	ENST00000267101.3:c.2095G>C	p.Val699Leu	p.V699L	ENST00000267101	NM_001982.3	699	Gtc/Ctc	18/28	1	2	FACETS	0.26	0.227	0.296	0.26	0.227	0.296	SUBCLONAL	1	TRUE	1	0.575752923678788	2		671	1015	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799551	72799551	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008398-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	114	555	0	ENST00000325599.8:c.1618G>C	p.Glu540Gln	p.E540Q	ENST00000325599	NM_018130.2	540	Gag/Cag	11/11	1	2	FACETS	0.368	0.331	0.408	0.368	0.331	0.408	SUBCLONAL	1	TRUE	1	0.575752923678788	2		555	1075	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796105	57796105	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008398-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	216	571	0	ENST00000309042.7:c.1081C>G	p.Leu361Val	p.L361V	ENST00000309042	NM_005612.4	361	Ctt/Gtt	4/4	0.138944951480676	0	FACETS	0.424	0.396	0.454			1	INDETERMINATE	1	TRUE	0	0.575752923678788	0		571	750	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628094	187628094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008398-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	73	811	0	ENST00000441802.2:c.2888G>A	p.Arg963Lys	p.R963K	ENST00000441802	NM_005245.3	963	aGa/aAa	2/27	0.165496793540653	0	FACETS	0.115	0.1	0.131			1	INDETERMINATE	1	TRUE	0	0.575752923678788	0		811	937	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0010079-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	5840	534	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.865247157783091	30	FACETS	1	0.997	1			1	CLONAL	27	TRUE	NA	0.865247157783091	30		534	6528	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004630	16004630	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0010079-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3179	670	675	0	ENST00000268712.3:c.2624C>G	p.Ser875Ter	p.S875*	ENST00000268712	NM_006311.3	875	tCa/tGa	20/46	0.865247157783091	19	FACETS	1	0.992	1			1	CLONAL	3	TRUE	NA	0.865247157783091	19		675	3849	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112569	115112569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180836314	NA	P-0010079-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	42	670	0	ENST00000257566.3:c.1171G>A	p.Asp391Asn	p.D391N	ENST00000257566	NM_016569.3	391	Gac/Aac	7/8	0.803882704450883	4	FACETS	0.266	0.221	0.315	0.133	0.11	0.158	SUBCLONAL	1	TRUE	2	0.865247157783091	4		670	682	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004707	16004708	+	missense_variant	Missense_Mutation	DNP	GG	GG	TA	novel	NA	P-0010079-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2207	954	621	1	ENST00000268712.3:c.2546_2547delinsTA	p.Ala849Val	p.A849V	ENST00000268712	NM_006311.3	849	gCC/gTA	20/46	0.865247157783091	19	FACETS	0.971	0.94	1			1	CLONAL	6	TRUE	NA	0.865247157783091	19		622	3161	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836768	151836768	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010079-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	82	498	0	ENST00000262189.6:c.14452G>C	p.Glu4818Gln	p.E4818Q	ENST00000262189	NM_170606.2	4818	Gag/Cag	56/59	0.419027965054725	4	FACETS	0.838	0.742	0.939	0.419	0.371	0.47	INDETERMINATE	1	TRUE	2	0.865247157783091	4		498	422	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707872	43707872	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0010079-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	52	692	0	ENST00000382044.4:c.5009C>G	p.Ser1670Ter	p.S1670*	ENST00000382044	NM_001141980.1	1670	tCa/tGa	23/28	0.865247157783091	3	FACETS	0.345	0.294	0.401	0.173	0.147	0.201	SUBCLONAL	1	TRUE	1	0.865247157783091	3		692	499	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528086	29528086	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs864622107	NA	P-0010079-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	25	223	0	ENST00000356175.3:c.1094C>G	p.Ser365Ter	p.S365*	ENST00000356175	NM_000267.3	365	tCa/tGa	10/57	0.865247157783091	4	FACETS	0.521	0.413	0.643	0.26	0.206	0.322	SUBCLONAL	1	TRUE	2	0.865247157783091	4		223	207	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6222292	6222292	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs770746045	NA	P-0010079-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	71	912	0	ENST00000252674.7:c.950G>C	p.Arg317Pro	p.R317P	ENST00000252674	NM_005934.3	317	cGc/cCc	6/12	0.550492499556106	3	FACETS	0.368	0.321	0.419	0.184	0.16	0.21	SUBCLONAL	1	TRUE	1	0.865247157783091	3		912	639	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462350	89462350	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010079-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	81	512	0	ENST00000336596.2:c.1822G>C	p.Ala608Pro	p.A608P	ENST00000336596	NM_005233.5	608	Gct/Cct	10/17	0.865247157783091	4	FACETS	0.741	0.656	0.833	0.371	0.328	0.417	SUBCLONAL	1	TRUE	2	0.865247157783091	4		512	471	SUCCESS
ALB	213	MSKCC	GRCh37	4	74280834	74280834	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010079-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	99	545	0	ENST00000295897.4:c.1141C>G	p.Leu381Val	p.L381V	ENST00000295897	NM_000477.5	381	Cta/Gta	9/15	0.503142089061806	5	FACETS	1	0.942	1	0.358	0.321	0.398	INDETERMINATE	1	TRUE	2	0.865247157783091	5		545	489	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176683980	176683980	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010079-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	61	532	0	ENST00000439151.2:c.4794G>T	p.Gln1598His	p.Q1598H	ENST00000439151	NM_022455.4	1598	caG/caT	13/23	1	2	FACETS	0.507	0.441	0.577	0.507	0.441	0.577	SUBCLONAL	1	TRUE	1	0.865247157783091	2		532	278	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1296046	1296046	+	upstream_gene_variant	5'Flank	SNP	A	A	C	novel	NA	P-0010079-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	17	812	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.865247157783091	NA		812	149	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	52	321	0				ENST00000310581	NM_198253.2	-/1132			0.338427301951661	1	FACETS	1	0.903	1	1	0.903	1	INDETERMINATE	1	TRUE	0	0.642841425517297	1		321	107	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929157	44929157	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	143	277	0	ENST00000377967.4:c.2257C>T	p.Gln753Ter	p.Q753*	ENST00000377967	NM_021140.2	753	Cag/Tag	17/29	0.547511154671423	2	FACETS	0.893	0.835	0.951			1	CLONAL	2	TRUE	NA	0.642841425517297	2		277	249	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143293	30143293	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs748978993	NA	P-0010316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	91	659	0	ENST00000389048.3:c.233C>G	p.Ser78Trp	p.S78W	ENST00000389048	NM_004304.4	78	tCg/tGg	1/29	0.642841425517297	3	FACETS	0.751	0.678	0.827	0.501	0.452	0.551	SUBCLONAL	2	TRUE	0	0.642841425517297	3		659	249	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939718	76939718	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	46	265	1	ENST00000373344.5:c.1030T>C	p.Ser344Pro	p.S344P	ENST00000373344	NM_000489.3	344	Tcc/Ccc	9/35	1	1	FACETS	0.925	0.806	1	0.925	0.806	1	CLONAL	1	TRUE	0	0.642841425517297	1		266	105	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2164229	2164229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	60	631	0	ENST00000398665.3:c.46G>A	p.Glu16Lys	p.E16K	ENST00000398665	NM_032482.2	16	Gag/Aag	1/28	1	2	FACETS	0.428	0.37	0.491	0.428	0.37	0.491	SUBCLONAL	1	TRUE	1	0.642841425517297	2		631	436	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589552	69589552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	31	1140	1	ENST00000168712.1:c.301G>A	p.Asp101Asn	p.D101N	ENST00000168712	NM_002007.2	101	Gac/Aac	1/3	0.642841425517297	1	FACETS	0.555	0.458	0.659	0.555	0.458	0.659	SUBCLONAL	1	TRUE	0	0.642841425517297	1		1141	118	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928076	178928084	+	inframe_deletion	In_Frame_Del	DEL	TTAGAAGAT	TTAGAAGAT	-	novel	NA	P-0010316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	57	438	0	ENST00000263967.3:c.1356_1364del	p.Glu453_Leu455del	p.E453_L455del	ENST00000263967	NM_006218.2	452	TTAGAAGAT/-	8/21	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.642841425517297	2		438	164	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864693	68864693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	16	496	1	ENST00000288368.4:c.64C>T	p.Arg22Cys	p.R22C	ENST00000288368	NM_024870.2	22	Cgc/Tgc	1/40	0.442888932996601	2	FACETS	0.265	0.196	0.346	0.132	0.098	0.173	SUBCLONAL	1	TRUE	0	0.642841425517297	2		497	188	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164816	123164817	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	34	226	1	ENST00000218089.9:c.135dup	p.Gly46ArgfsTer41	p.G46Rfs*41	ENST00000218089	NM_001042749.1	43	-/A	5/35	1	1	FACETS	0.561	0.467	0.662	0.561	0.467	0.662	SUBCLONAL	1	TRUE	0	0.642841425517297	1		227	128	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273176	115273176	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	152	600	0	ENST00000438362.2:c.1282G>A	p.Gly428Arg	p.G428R	ENST00000438362	NM_001242891.1	428	Ggg/Agg	11/20	0.642841425517297	4	FACETS	0.85	0.784	0.918			1	CLONAL	2	TRUE	NA	0.642841425517297	4		600	457	SUCCESS
FH	2271	MSKCC	GRCh37	1	241676913	241676913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	38	391	0	ENST00000366560.3:c.368C>T	p.Ala123Val	p.A123V	ENST00000366560	NM_000143.3	123	gCa/gTa	3/10	0.338427301951661	1	FACETS	0.341	0.284	0.404	0.341	0.284	0.404	INDETERMINATE	1	TRUE	0	0.642841425517297	1		391	235	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200942	108200942	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1565529213	NA	P-0010316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	39	494	0	ENST00000278616.4:c.7309T>C	p.Tyr2437His	p.Y2437H	ENST00000278616	NM_000051.3	2437	Tac/Cac	50/63	0.262342194524244	0	FACETS	0.276	0.232	0.323			1	INDETERMINATE	1	TRUE	0	0.642841425517297	0		494	157	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205785	108205785	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs778601472	NA	P-0010316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	44	470	0	ENST00000278616.4:c.8100A>C	p.Lys2700Asn	p.K2700N	ENST00000278616	NM_000051.3	2700	aaA/aaC	55/63	0.262342194524244	0	FACETS	0.263	0.223	0.306			1	INDETERMINATE	1	TRUE	0	0.642841425517297	0		470	186	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118365076	118365076	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	45	461	0	ENST00000534358.1:c.5252A>G	p.Lys1751Arg	p.K1751R	ENST00000534358	NM_005933.3	1751	aAa/aGa	17/36	0.262342194524244	0	FACETS	0.239	0.203	0.278			1	INDETERMINATE	1	TRUE	0	0.642841425517297	0		461	209	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416788	416788	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	203	724	0	ENST00000399788.2:c.3762G>C	p.Met1254Ile	p.M1254I	ENST00000399788	NM_001042603.1	1254	atG/atC	23/28	0.250468330856416	5	FACETS	1	0.979	1	0.445	0.415	0.475	INDETERMINATE	2	TRUE	0	0.642841425517297	5		724	558	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434909	49434909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	69	804	0	ENST00000301067.7:c.6644C>T	p.Ser2215Leu	p.S2215L	ENST00000301067	NM_003482.3	2215	tCa/tTa	31/54	NA	2	FACETS	0.801	0.705	0.902			1	INDETERMINATE	1	TRUE	NA	0.642841425517297	2		804	268	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26927973	26927973	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	35	521	0	ENST00000381527.3:c.412G>A	p.Gly138Ser	p.G138S	ENST00000381527	NM_001260.1	138	Ggt/Agt	4/13	0.587397563303104	2	FACETS	0.576	0.477	0.685	0.288	0.238	0.343	SUBCLONAL	1	TRUE	0	0.642841425517297	2		521	189	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574288	95574288	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	11	446	0	ENST00000393063.1:c.2579T>C	p.Leu860Pro	p.L860P	ENST00000393063	NM_030621.3	860	cTt/cCt	17/28	0.266349911529664	1	FACETS	0.135	0.093	0.187	0.135	0.093	0.187	INDETERMINATE	1	TRUE	0	0.642841425517297	1		446	172	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038608	14038608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	36	401	0	ENST00000311895.7:c.1933G>A	p.Glu645Lys	p.E645K	ENST00000311895	NM_005236.2	645	Gaa/Aaa	10/11	0.383060014065008	1	FACETS	0.314	0.26	0.374	0.314	0.26	0.374	INDETERMINATE	1	TRUE	0	0.642841425517297	1		401	242	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995242	15995242	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	46	569	0	ENST00000268712.3:c.2951A>C	p.Asp984Ala	p.D984A	ENST00000268712	NM_006311.3	984	gAt/gCt	22/46	0.289447969742917	2	FACETS	0.425	0.359	0.497	0.212	0.179	0.249	INDETERMINATE	1	TRUE	0	0.642841425517297	2		569	337	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075239	16075239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	62	575	0	ENST00000268712.3:c.313G>A	p.Glu105Lys	p.E105K	ENST00000268712	NM_006311.3	105	Gaa/Aaa	4/46	0.289447969742917	2	FACETS	0.473	0.41	0.541	0.236	0.205	0.271	INDETERMINATE	1	TRUE	0	0.642841425517297	2		575	408	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325805	30325806	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TATTAGCA	novel	NA	P-0010316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	31	427	0	ENST00000322652.5:c.2006_2013dup	p.Met672LeufsTer3	p.M672Lfs*3	ENST00000322652	NM_015355.2	668	ctt/ctTATTAGCAt	16/16	0.488367163979714	4	FACETS	0.508	0.412	0.616	0.254	0.206	0.308	SUBCLONAL	1	TRUE	2	0.642841425517297	4		427	312	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17941428	17941478	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCTGGAGAGGGGACAAGGTCTTGAGATGCGAGGGTGTAGAAAGGACAGGA	ACCTGGAGAGGGGACAAGGTCTTGAGATGCGAGGGTGTAGAAAGGACAGGA	-	novel	NA	P-0010316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	126	678	0	ENST00000458235.1:c.2979-49_2980del		p.X993_splice	ENST00000458235	NM_000215.3	993		22/24	0.326085819676268	4	FACETS	1	0.984	1	0.688	0.627	0.751	INDETERMINATE	1	TRUE	2	0.642841425517297	4		678	468	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37059052	37059114	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTATTTGCCCAAAAACACACACCCATTCCTGTACCTCAGGTAATGTAGCACCAAACTCCTCAA	CTATTTGCCCAAAAACACACACCCATTCCTGTACCTCAGGTAATGTAGCACCAAACTCCTCAA	-	novel	NA	P-0010316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	20	576	0	ENST00000231790.2:c.847_884+25del		p.X283_splice	ENST00000231790	NM_000249.3	283		10/19	0.205679368810574	5	FACETS	0.437	0.334	0.556	0.087	0.066	0.112	INDETERMINATE	1	TRUE	0	0.642841425517297	5		576	280	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169991080	169991080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	37	341	0	ENST00000295797.4:c.598G>A	p.Val200Met	p.V200M	ENST00000295797	NM_002740.5	200	Gtg/Atg	7/18	1	2	FACETS	0.408	0.338	0.486	0.408	0.338	0.486	SUBCLONAL	1	TRUE	1	0.642841425517297	2		341	282	SUCCESS
APC	324	MSKCC	GRCh37	5	112163704	112163704	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0010316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	41	333	0	ENST00000257430.4:c.1626+1G>C		p.X542_splice	ENST00000257430	NM_000038.5	542			0.377780755932963	2	FACETS	0.534	0.448	0.627	0.267	0.224	0.314	INDETERMINATE	1	TRUE	0	0.642841425517297	2		333	239	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709550	176709550	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	108	419	0	ENST00000439151.2:c.5977A>G	p.Ile1993Val	p.I1993V	ENST00000439151	NM_022455.4	1993	Atc/Gtc	19/23	0.377780755932963	2	FACETS	0.812	0.747	0.875	0.812	0.747	0.875	INDETERMINATE	2	TRUE	0	0.642841425517297	2		419	207	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750936	128750945	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTCGTCTC	AGCTCGTCTC	-	novel	NA	P-0010316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	88	648	0	ENST00000377970.2:c.475_484del	p.Leu159ArgfsTer35	p.L159Rfs*35	ENST00000377970	NM_002467.4	158	aAGCTCGTCTCa/aa	2/3	0.394716500846918	5	FACETS	1	0.954	1	0.228	0.202	0.255	CLONAL	1	TRUE	0	0.642841425517297	5		648	472	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180294	27180294	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	59	688	0	ENST00000380036.4:c.958G>C	p.Gly320Arg	p.G320R	ENST00000380036	NM_000459.3	320	Ggg/Cgg	7/23	0.642841425517297	1	FACETS	0.389	0.337	0.446	0.389	0.337	0.446	SUBCLONAL	1	TRUE	0	0.642841425517297	1		688	320	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929234	44929253	+	frameshift_variant	Frame_Shift_Del	DEL	TCAGCTCTCTGCCTTGTTGA	TCAGCTCTCTGCCTTGTTGA	C	novel	NA	P-0010316-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	14	263	0	ENST00000377967.4:c.2334_2353delinsC	p.Gln779TrpfsTer82	p.Q779Wfs*82	ENST00000377967	NM_021140.2	778	ccTCAGCTCTCTGCCTTGTTGAtg/ccCtg	17/29	0.547511154671423	2	FACETS	0.174	0.125	0.232			1	SUBCLONAL	1	TRUE	NA	0.642841425517297	2		263	251	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982356	25982356	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011155-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	136	359	0	ENST00000435504.4:c.934C>T	p.Arg312Ter	p.R312*	ENST00000435504		312	Cga/Tga	9/13	1	2	FACETS	0.889	0.815	0.964	0.889	0.815	0.964	CLONAL	1	TRUE	1	0.705348858746231	2		359	434	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0011155-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	40	661	2	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	1	2	FACETS	0.162	0.134	0.194	0.162	0.134	0.194	SUBCLONAL	1	TRUE	1	0.705348858746231	2		663	698	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130397	29130421	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCAAATCCATCCTGAAGGGCCCA	TGGCAAATCCATCCTGAAGGGCCCA	-	novel	NA	P-0011155-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	65	605	0	ENST00000328354.6:c.289_313del	p.Trp97IlefsTer5	p.W97Ifs*5	ENST00000328354	NM_007194.3	97	TGGGCCCTTCAGGATGGATTTGCCAat/at	2/15	0.705348858746231	1	FACETS	0.318	0.277	0.362	0.318	0.277	0.362	SUBCLONAL	1	TRUE	0	0.705348858746231	1		605	375	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2033082	2033082	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0011155-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	69	517	0	ENST00000349721.2:c.355+1G>A		p.X119_splice	ENST00000349721	NM_003070.3	119			1	2	FACETS	0.302	0.263	0.344	0.302	0.263	0.344	SUBCLONAL	1	TRUE	1	0.705348858746231	2		517	648	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271892	15271892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011523-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	430	915	0	ENST00000263388.2:c.6547C>T	p.Pro2183Ser	p.P2183S	ENST00000263388	NM_000435.2	2183	Ccc/Tcc	33/33	0.500411945877596	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.500411945877596	3		915	675	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969322	44969322	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0011523-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	57	330	0	ENST00000377967.4:c.4006-2A>T		p.X1336_splice	ENST00000377967	NM_021140.2	1336			0.446975225761655	2	FACETS	0.791	0.696	0.889	0.791	0.696	0.889	SUBCLONAL	2	TRUE	0	0.500411945877596	2		330	144	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433650	49433650	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs794727549	NA	P-0011523-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	266	813	0	ENST00000301067.7:c.7903C>T	p.Arg2635Ter	p.R2635*	ENST00000301067	NM_003482.3	2635	Cga/Tga	31/54	0.230027026679784	3	FACETS	1	0.987	1	0.76	0.719	0.801	INDETERMINATE	2	TRUE	0	0.500411945877596	3		813	583	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426132	138426132	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0011523-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	31	304	0	ENST00000289153.2:c.1400-1G>C		p.X467_splice	ENST00000289153	NM_006219.2	467			0.500411945877596	4	FACETS	0.902	0.736	1	0.301	0.245	0.363	CLONAL	1	TRUE	1	0.500411945877596	4		304	206	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629949	187629949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349314438	NA	P-0011523-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	92	688	0	ENST00000441802.2:c.1033C>T	p.Pro345Ser	p.P345S	ENST00000441802	NM_005245.3	345	Ccc/Tcc	2/27	0.446975225761655	2	FACETS	1	0.946	1	0.542	0.486	0.601	CLONAL	1	TRUE	0	0.500411945877596	2		688	339	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814946	139814946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011523-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	111	611	0	ENST00000247668.2:c.939G>T	p.Lys313Asn	p.K313N	ENST00000247668	NM_021138.3	313	aaG/aaT	8/11	0.473645170730979	2	FACETS	0.911	0.823	1	0.455	0.411	0.502	CLONAL	1	TRUE	0	0.500411945877596	2		611	487	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139818308	139818308	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011523-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	88	461	0	ENST00000247668.2:c.1143C>G	p.Phe381Leu	p.F381L	ENST00000247668	NM_021138.3	381	ttC/ttG	10/11	0.473645170730979	2	FACETS	0.906	0.809	1	0.453	0.404	0.505	CLONAL	1	TRUE	0	0.500411945877596	2		461	388	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106094	8106094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011523-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	88	605	0	ENST00000346208.3:c.914G>A	p.Arg305Gln	p.R305Q	ENST00000346208		305	cGa/cAa	4/6	0.493351827800931	3	FACETS	0.799	0.71	0.895	0.4	0.355	0.448	SUBCLONAL	1	TRUE	1	0.500411945877596	3		605	550	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143341	30143341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011523-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	44	672	0	ENST00000389048.3:c.185C>T	p.Ser62Leu	p.S62L	ENST00000389048	NM_004304.4	62	tCg/tTg	1/29	0.285089843800344	4	FACETS	0.656	0.551	0.772	0.328	0.275	0.386	INDETERMINATE	1	TRUE	2	0.500411945877596	4		672	402	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543793	41543928	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCAATTTCACAAAGGCATTCAGATCTAACATTTTGCTCATATTCACAGGTTTGAATCAATTTGGCCAGATGAGCATGGCCCAGCCCCCTATTGTACCCCGGCAAACCCCTCCTCTTCAGCACCATGGACAGTTGGC	TCAATTTCACAAAGGCATTCAGATCTAACATTTTGCTCATATTCACAGGTTTGAATCAATTTGGCCAGATGAGCATGGCCCAGCCCCCTATTGTACCCCGGCAAACCCCTCCTCTTCAGCACCATGGACAGTTGGC	-	novel	NA	P-0011523-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	63	269	0	ENST00000263253.7:c.2132-44_2223del		p.X711_splice	ENST00000263253	NM_001429.3	711		12/31	0.458081410885276	3	FACETS	0.787	0.692	0.886	0.787	0.692	0.886	SUBCLONAL	2	TRUE	1	0.500411945877596	3		269	200	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197221	26197221	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011523-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	97	968	0	ENST00000356476.2:c.258G>C	p.Gln86His	p.Q86H	ENST00000356476		86	caG/caC	1/1	0.500411945877596	5	FACETS	0.636	0.566	0.712	0.212	0.188	0.238	SUBCLONAL	1	TRUE	2	0.500411945877596	5		968	1067	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271892	15271892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011523-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	276	915	0	ENST00000263388.2:c.6547C>T	p.Pro2183Ser	p.P2183S	ENST00000263388	NM_000435.2	2183	Ccc/Tcc	33/33	0.407967755311798	3	FACETS	0.912	0.864	0.96	0.912	0.864	0.96	CLONAL	3	TRUE	0	0.406761549190408	3		915	597	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969322	44969322	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0011523-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	76	330	0	ENST00000377967.4:c.4006-2A>T		p.X1336_splice	ENST00000377967	NM_021140.2	1336			0.337157852245713	2	FACETS	0.816	0.727	0.908	0.816	0.727	0.908	CLONAL	2	TRUE	0	0.406761549190408	2		330	229	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433650	49433650	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs794727549	NA	P-0011523-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	221	813	0	ENST00000301067.7:c.7903C>T	p.Arg2635Ter	p.R2635*	ENST00000301067	NM_003482.3	2635	Cga/Tga	31/54	0.337157852245713	2	FACETS	0.95	0.891	1	0.95	0.891	1	CLONAL	2	TRUE	0	0.406761549190408	2		813	572	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818442	43818442	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0011523-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	81	494	0	ENST00000372470.3:c.1907G>C	p.Ter636SerextTer?	p.*636Sext*?	ENST00000372470	NM_005373.2	636	tGa/tCa	12/12	0.338640197462148	2	FACETS	0.779	0.688	0.876	0.39	0.344	0.438	SUBCLONAL	1	TRUE	0	0.406761549190408	2		494	511	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426132	138426132	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0011523-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	29	304	0	ENST00000289153.2:c.1400-1G>C		p.X467_splice	ENST00000289153	NM_006219.2	467			0.407967755311798	4	FACETS	0.685	0.551	0.836	0.228	0.183	0.279	SUBCLONAL	1	TRUE	1	0.406761549190408	4		304	293	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629949	187629949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349314438	NA	P-0011523-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	93	688	0	ENST00000441802.2:c.1033C>T	p.Pro345Ser	p.P345S	ENST00000441802	NM_005245.3	345	Ccc/Tcc	2/27	0.337157852245713	2	FACETS	0.878	0.783	0.978	0.439	0.391	0.489	CLONAL	1	TRUE	0	0.406761549190408	2		688	521	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814946	139814946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011523-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	83	611	0	ENST00000247668.2:c.939G>T	p.Lys313Asn	p.K313N	ENST00000247668	NM_021138.3	313	aaG/aaT	8/11	0.338640197462148	2	FACETS	0.841	0.745	0.944	0.421	0.372	0.472	CLONAL	1	TRUE	0	0.406761549190408	2		611	485	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139818308	139818308	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011523-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	60	461	0	ENST00000247668.2:c.1143C>G	p.Phe381Leu	p.F381L	ENST00000247668	NM_021138.3	381	ttC/ttG	10/11	0.338640197462148	2	FACETS	0.756	0.654	0.867	0.378	0.327	0.434	SUBCLONAL	1	TRUE	0	0.406761549190408	2		461	390	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979566	7979566	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011523-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	86	439	0	ENST00000319144.4:c.1459G>T	p.Glu487Ter	p.E487*	ENST00000319144	NM_001139.2	487	Gag/Tag	11/15	0.407967755311798	3	FACETS	0.92	0.816	1	0.46	0.408	0.516	CLONAL	1	TRUE	1	0.406761549190408	3		439	553	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566537	41566537	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011523-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	63	401	0	ENST00000263253.7:c.4414G>C	p.Asp1472His	p.D1472H	ENST00000263253	NM_001429.3	1472	Gac/Cac	27/31	0.33305789921546	3	FACETS	0.89	0.772	1	0.445	0.386	0.508	CLONAL	1	TRUE	1	0.406761549190408	3		401	419	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118833	61118833	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs868755436	NA	P-0012008-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	233	167	0	ENST00000295025.8:c.26A>G	p.Tyr9Cys	p.Y9C	ENST00000295025	NM_002908.2	9	tAt/tGt	2/11	0.374579791657716	4	FACETS	1	0.981	1			1	CLONAL	2	TRUE	NA	0.374579791657716	4		167	762	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295195	1295195	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0012008-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	35	94	0				ENST00000310581	NM_198253.2	-/1132			0.374579791657716	5	FACETS	0.871	0.716	1	0.29	0.238	0.349	CLONAL	1	TRUE	2	0.374579791657716	5		94	335	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10267166	10267166	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012008-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	116	341	0	ENST00000340748.4:c.1252C>T	p.His418Tyr	p.H418Y	ENST00000340748		418	Cac/Tac	17/40	1	2	FACETS	0.951	0.859	1	0.951	0.859	1	CLONAL	1	TRUE	1	0.374579791657716	2		341	651	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118833	61118833	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs868755436	NA	P-0012008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	194	167	0	ENST00000295025.8:c.26A>G	p.Tyr9Cys	p.Y9C	ENST00000295025	NM_002908.2	9	tAt/tGt	2/11	0.407939838485083	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	3	TRUE	0	0.407939838485083	3		167	374	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10267166	10267166	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	129	341	0	ENST00000340748.4:c.1252C>T	p.His418Tyr	p.H418Y	ENST00000340748		418	Cac/Tac	17/40	0.339513734538722	3	FACETS	1	0.973	1	0.592	0.538	0.649	CLONAL	1	TRUE	1	0.407939838485083	3		341	643	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784335	9784335	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	73	408	0	ENST00000377346.4:c.2720T>A	p.Leu907Gln	p.L907Q	ENST00000377346	NM_005026.3	907	cTg/cAg	22/24	NA	2	FACETS	0.621	0.544	0.705			1	INDETERMINATE	1	TRUE	NA	0.407939838485083	2		408	576	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363358	40363388	+	frameshift_variant	Frame_Shift_Del	DEL	CTACAGGTGGGGGACTCACAATCTCTTCATC	CTACAGGTGGGGGACTCACAATCTCTTCATC	-	novel	NA	P-0012008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	95	592	0	ENST00000397332.2:c.841_871del	p.Asp281LysfsTer20	p.D281Kfs*20	ENST00000397332	NM_001033082.2	281	GATGAAGAGATTGTGAGTCCCCCACCTGTAGaa/aa	3/3	0.369492677123789	3	FACETS	0.719	0.64	0.803	0.24	0.213	0.268	SUBCLONAL	1	TRUE	0	0.407939838485083	3		592	780	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435408	121435422	+	inframe_deletion	In_Frame_Del	DEL	CAGAGCCATGTGACC	CAGAGCCATGTGACC	-	novel	NA	P-0012008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	83	631	0	ENST00000257555.6:c.1448_1462del	p.His483_Ser487del	p.H483_S487del	ENST00000257555		481	CAGAGCCATGTGACC/-	7/10	0.407939838485083	3	FACETS	0.518	0.456	0.585	0.259	0.228	0.293	SUBCLONAL	1	TRUE	1	0.407939838485083	3		631	946	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094832	11094842	+	frameshift_variant	Frame_Shift_Del	DEL	CCACTCCAGAC	CCACTCCAGAC	-	novel	NA	P-0012008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	144	620	0	ENST00000358026.2:c.9_19del	p.Asp5GlyfsTer23	p.D5Gfs*23	ENST00000358026	NM_001128849.1	2	tCCACTCCAGAC/t	2/36	0.339513734538722	3	FACETS	0.992	0.905	1	0.496	0.452	0.542	CLONAL	1	TRUE	1	0.407939838485083	3		620	857	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149000	61149000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1166562398	NA	P-0012008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	107	393	0	ENST00000295025.8:c.1190G>A	p.Gly397Glu	p.G397E	ENST00000295025	NM_002908.2	397	gGa/gAa	11/11	0.407939838485083	3	FACETS	1	0.912	1	0.338	0.304	0.375	CLONAL	1	TRUE	0	0.407939838485083	3		393	622	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744029	39744029	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	122	356	0	ENST00000361337.2:c.1657C>G	p.Leu553Val	p.L553V	ENST00000361337	NM_003286.2	553	Cta/Gta	16/21	0.219070235226978	3	FACETS	1	0.983	1	0.463	0.42	0.507	INDETERMINATE	1	TRUE	0	0.407939838485083	3		356	519	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820905	32820905	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	113	680	0	ENST00000354258.4:c.689G>C	p.Gly230Ala	p.G230A	ENST00000354258	NM_000593.5	230	gGa/gCa	1/11	1	2	FACETS	0.632	0.568	0.699	0.632	0.568	0.699	SUBCLONAL	1	TRUE	1	0.407939838485083	2		680	877	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141568640	141568640	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	83	527	0	ENST00000220592.5:c.822G>C	p.Gln274His	p.Q274H	ENST00000220592	NM_012154.3	274	caG/caC	7/19	0.190012432358197	5	FACETS	0.76	0.67	0.857			1	INDETERMINATE	1	TRUE	NA	0.407939838485083	5		527	863	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030436	47030436	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	99	316	0	ENST00000377604.3:c.211G>C	p.Glu71Gln	p.E71Q	ENST00000377604	NM_001204468.1	71	Gag/Cag	4/24	0.389737906685518	2	FACETS	0.95	0.851	1			1	CLONAL	1	TRUE	NA	0.407939838485083	2		316	511	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	497	575	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.568869379320065	3	FACETS	0.983	0.952	1	0.983	0.952	1	CLONAL	3	TRUE	0	0.568869379320065	3		575	761	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	44	240	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.568869379320065	3	FACETS	0.849	0.719	0.991	0.283	0.239	0.331	CLONAL	1	TRUE	0	0.568869379320065	3		240	234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	349	552	1	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.543932719275456	2	FACETS	0.951	0.91	0.992	0.951	0.91	0.992	CLONAL	2	TRUE	0	0.568869379320065	2		553	645	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314925	1314925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	116	568	0	ENST00000400841.2:c.736C>T	p.Leu246Phe	p.L246F	ENST00000400841		246	Ctc/Ttc	6/6	1	2	FACETS	0.673	0.608	0.741	0.673	0.608	0.741	SUBCLONAL	1	TRUE	1	0.568869379320065	2		568	606	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138409963	138409963	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	108	422	0	ENST00000289153.2:c.1915C>G	p.Leu639Val	p.L639V	ENST00000289153	NM_006219.2	639	Ctt/Gtt	13/22	0.568869379320065	3	FACETS	1	0.931	1	0.347	0.312	0.382	CLONAL	1	TRUE	0	0.568869379320065	3		422	469	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586262	48586262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658694	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	84	402	0	ENST00000342988.3:c.931C>T	p.Gln311Ter	p.Q311*	ENST00000342988	NM_005359.5	311	Cag/Tag	8/12	0.53096218179321	1	FACETS	0.873	0.784	0.966	0.873	0.784	0.966	CLONAL	1	TRUE	0	0.568869379320065	1		402	242	SUCCESS
APC	324	MSKCC	GRCh37	5	112174760	112174760	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1554085038	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	118	512	0	ENST00000257430.4:c.3469G>C	p.Glu1157Gln	p.E1157Q	ENST00000257430	NM_000038.5	1157	Gag/Cag	16/16	0.553372854888218	3	FACETS	0.769	0.695	0.847	0.384	0.347	0.424	SUBCLONAL	1	TRUE	1	0.568869379320065	3		512	693	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740215	162740215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771675675	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	187	695	0	ENST00000367921.3:c.1417C>T	p.Arg473Cys	p.R473C	ENST00000367921	NM_006182.2	473	Cgc/Tgc	12/18	0.53413559312169	4	FACETS	0.869	0.801	0.94	0.29	0.267	0.314	CLONAL	1	TRUE	1	0.568869379320065	4		695	1187	SUCCESS
APC	324	MSKCC	GRCh37	5	112174529	112174529	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	94	574	2	ENST00000257430.4:c.3238G>T	p.Glu1080Ter	p.E1080*	ENST00000257430	NM_000038.5	1080	Gag/Tag	16/16	0.553372854888218	3	FACETS	0.641	0.571	0.716	0.321	0.285	0.358	SUBCLONAL	1	TRUE	1	0.568869379320065	3		576	662	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579506	7579506	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	135	833	0	ENST00000269305.4:c.181G>C	p.Asp61His	p.D61H	ENST00000269305	NM_001126112.2	61	Gat/Cat	4/11	0.543932719275456	2	FACETS	0.519	0.471	0.57	0.26	0.235	0.285	SUBCLONAL	1	TRUE	0	0.568869379320065	2		833	914	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752799	57752799	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	198	453	0	ENST00000274289.3:c.1129G>C	p.Asp377His	p.D377H	ENST00000274289	NM_006622.3	377	Gac/Cac	8/14	0.553372854888218	3	FACETS	0.894	0.836	0.953	0.894	0.836	0.953	CLONAL	2	TRUE	1	0.568869379320065	3		453	500	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525940	148525940	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	255	504	0	ENST00000320356.2:c.517G>C	p.Glu173Gln	p.E173Q	ENST00000320356	NM_004456.4	173	Gag/Cag	6/20	0.535093010600119	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.568869379320065	2		504	444	SUCCESS
ATM	472	MSKCC	GRCh37	11	108099946	108099946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	161	378	0	ENST00000278616.4:c.227G>T	p.Arg76Ile	p.R76I	ENST00000278616	NM_000051.3	76	aGa/aTa	4/63	0.535093010600119	2	FACETS	0.913	0.854	0.972	0.913	0.854	0.972	CLONAL	2	TRUE	0	0.568869379320065	2		378	310	SUCCESS
ATM	472	MSKCC	GRCh37	11	108127029	108127029	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	221	411	0	ENST00000278616.4:c.2212G>C	p.Glu738Gln	p.E738Q	ENST00000278616	NM_000051.3	738	Gag/Cag	14/63	0.535093010600119	2	FACETS	0.964	0.912	1	0.964	0.912	1	CLONAL	2	TRUE	0	0.568869379320065	2		411	403	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3094752	3094752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	402	612	0	ENST00000078429.4:c.103G>A	p.Asp35Asn	p.D35N	ENST00000078429	NM_002067.2	35	Gac/Aac	1/7	0.553372854888218	3	FACETS	0.962	0.918	1	0.962	0.918	1	CLONAL	2	TRUE	1	0.568869379320065	3		612	944	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435159	56435159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1275	213	915	0	ENST00000407977.2:c.1978C>T	p.Pro660Ser	p.P660S	ENST00000407977		660	Ccc/Tcc	9/10	0.553768483773565	4	FACETS	0.79	0.731	0.85	0.197	0.182	0.213	SUBCLONAL	1	TRUE	0	0.568869379320065	4		915	1488	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223349	53223349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	149	606	0	ENST00000375401.3:c.4010G>A	p.Arg1337Lys	p.R1337K	ENST00000375401	NM_004187.3	1337	aGa/aAa	23/26	1	2	FACETS	0.734	0.672	0.798	0.734	0.672	0.798	SUBCLONAL	1	TRUE	1	0.568869379320065	2		606	714	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873855	151873855	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	167	618	0	ENST00000262189.6:c.8683C>T	p.Gln2895Ter	p.Q2895*	ENST00000262189	NM_170606.2	2895	Cag/Tag	38/59	0.535093010600119	2	FACETS	0.882	0.813	0.953	0.441	0.406	0.477	CLONAL	1	TRUE	0	0.568869379320065	2		618	666	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029128	14029128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748206066	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	134	594	0	ENST00000311895.7:c.1339G>A	p.Glu447Lys	p.E447K	ENST00000311895	NM_005236.2	447	Gaa/Aaa	8/11	0.568869379320065	3	FACETS	0.721	0.655	0.791	0.361	0.327	0.396	SUBCLONAL	1	TRUE	1	0.568869379320065	3		594	839	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260068	16260068	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	193	844	0	ENST00000375759.3:c.7333C>T	p.Gln2445Ter	p.Q2445*	ENST00000375759	NM_015001.2	2445	Caa/Taa	11/15	1	2	FACETS	0.706	0.653	0.761	0.706	0.653	0.761	SUBCLONAL	1	TRUE	1	0.568869379320065	2		844	961	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37048481	37048481	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs267607744	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	93	400	0	ENST00000231790.2:c.381-1G>C		p.X127_splice	ENST00000231790	NM_000249.3	127			0.568869379320065	3	FACETS	0.835	0.745	0.93	0.278	0.248	0.31	CLONAL	1	TRUE	0	0.568869379320065	3		400	503	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177075	56177075	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	29	450	1	ENST00000399503.3:c.2345C>G	p.Ser782Ter	p.S782*	ENST00000399503	NM_005921.1	782	tCa/tGa	13/20	0.553372854888218	3	FACETS	0.236	0.188	0.29	0.118	0.094	0.145	SUBCLONAL	1	TRUE	1	0.568869379320065	3		451	556	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091830	29091830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	64	293	0	ENST00000328354.6:c.1127G>A	p.Gly376Glu	p.G376E	ENST00000328354	NM_007194.3	376	gGa/gAa	11/15	0.562851221763679	4	FACETS	0.934	0.813	1	0.467	0.406	0.532	CLONAL	1	TRUE	2	0.568869379320065	4		293	378	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164512	36164512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	163	698	0	ENST00000300305.3:c.1363G>A	p.Ala455Thr	p.A455T	ENST00000300305		455	Gcc/Acc	8/8	1	2	FACETS	0.795	0.731	0.861	0.795	0.731	0.861	SUBCLONAL	1	TRUE	1	0.568869379320065	2		698	721	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41219690	41219690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	65	394	0	ENST00000357654.3:c.5009G>A	p.Arg1670Lys	p.R1670K	ENST00000357654	NM_007294.3	1670	aGa/aAa	16/23	0.543932719275456	2	FACETS	0.628	0.547	0.714	0.314	0.273	0.357	SUBCLONAL	1	TRUE	0	0.568869379320065	2		394	364	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446798	49446798	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	184	743	0	ENST00000301067.7:c.1012G>C	p.Glu338Gln	p.E338Q	ENST00000301067	NM_003482.3	338	Gag/Cag	8/54	0.423334062762931	3	FACETS	0.797	0.735	0.861			1	SUBCLONAL	1	TRUE	NA	0.568869379320065	3		743	1043	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190510	32190510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746522697	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	162	825	0	ENST00000375023.3:c.229G>A	p.Gly77Arg	p.G77R	ENST00000375023	NM_004557.3	77	Gga/Aga	3/30	0.543932719275456	2	FACETS	0.691	0.635	0.75	0.346	0.317	0.375	SUBCLONAL	1	TRUE	0	0.568869379320065	2		825	824	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17350507	17350507	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	137	506	0	ENST00000375499.3:c.603G>T	p.Trp201Cys	p.W201C	ENST00000375499	NM_003000.2	201	tgG/tgT	6/8	1	2	FACETS	0.706	0.644	0.772	0.706	0.644	0.772	SUBCLONAL	1	TRUE	1	0.568869379320065	2		506	682	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332655	65332655	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	130	558	0	ENST00000342505.4:c.884C>G	p.Ser295Ter	p.S295*	ENST00000342505	NM_002227.2	295	tCa/tGa	7/25	1	2	FACETS	0.836	0.761	0.913	0.836	0.761	0.913	CLONAL	1	TRUE	1	0.568869379320065	2		558	547	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483269	120483269	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	143	632	0	ENST00000256646.2:c.3092C>G	p.Ser1031Cys	p.S1031C	ENST00000256646	NM_024408.3	1031	tCt/tGt	19/34	1	2	FACETS	0.746	0.682	0.813	0.746	0.682	0.813	SUBCLONAL	1	TRUE	1	0.568869379320065	2		632	674	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63760021	63760021	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	176	651	0	ENST00000279873.7:c.674G>T	p.Cys225Phe	p.C225F	ENST00000279873	NM_032199.2	225	tGt/tTt	4/10	1	2	FACETS	0.855	0.789	0.922	0.855	0.789	0.922	CLONAL	1	TRUE	1	0.568869379320065	2		651	724	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417920	32417920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	177	665	0	ENST00000332351.3:c.1132C>T	p.Leu378Phe	p.L378F	ENST00000332351	NM_024426.4	378	Ctt/Ttt	7/10	0.539773181746237	2	FACETS	0.933	0.863	1	0.466	0.431	0.503	CLONAL	1	TRUE	0	0.568869379320065	2		665	667	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	465702	465702	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	59	386	0	ENST00000399788.2:c.674C>G	p.Ser225Ter	p.S225*	ENST00000399788	NM_001042603.1	225	tCa/tGa	6/28	0.553372854888218	3	FACETS	0.592	0.51	0.681	0.296	0.255	0.341	SUBCLONAL	1	TRUE	1	0.568869379320065	3		386	450	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022792	12022792	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	216	986	0	ENST00000396373.4:c.898G>A	p.Glu300Lys	p.E300K	ENST00000396373	NM_001987.4	300	Gaa/Aaa	5/8	0.553372854888218	3	FACETS	0.766	0.711	0.824	0.383	0.355	0.412	SUBCLONAL	1	TRUE	1	0.568869379320065	3		986	1273	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466940	18466940	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	101	472	0	ENST00000266497.5:c.1079C>G	p.Ser360Cys	p.S360C	ENST00000266497		360	tCt/tGt	5/31	0.553372854888218	3	FACETS	0.914	0.82	1	0.457	0.41	0.507	CLONAL	1	TRUE	1	0.568869379320065	3		472	499	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415640	49415640	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	146	582	0	ENST00000301067.7:c.16537C>T	p.Gln5513Ter	p.Q5513*	ENST00000301067	NM_003482.3	5513	Cag/Tag	54/54	0.423334062762931	3	FACETS	0.76	0.694	0.83			1	SUBCLONAL	1	TRUE	NA	0.568869379320065	3		582	867	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120796810	120796810	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs868119585	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	170	467	0	ENST00000257552.2:c.449G>T	p.Arg150Leu	p.R150L	ENST00000257552	NM_002442.3	150	cGa/cTa	7/15	0.553372854888218	3	FACETS	1	0.966	1	0.543	0.5	0.587	CLONAL	1	TRUE	1	0.568869379320065	3		467	707	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907044	32907044	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	19	603	0	ENST00000380152.3:c.1429C>G	p.His477Asp	p.H477D	ENST00000380152		477	Cat/Gat	10/27	0.557669135021465	1	FACETS	0.131	0.099	0.169	0.131	0.099	0.169	SUBCLONAL	1	TRUE	0	0.568869379320065	1		603	364	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527979	103527979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	139	643	0	ENST00000355739.4:c.3287C>T	p.Ser1096Leu	p.S1096L	ENST00000355739	NM_000123.3	1096	tCa/tTa	15/15	0.557669135021465	1	FACETS	0.786	0.721	0.852	0.786	0.721	0.852	SUBCLONAL	1	TRUE	0	0.568869379320065	1		643	445	SUCCESS
SCG5	6447	MSKCC	GRCh37	15	32976806	32976806	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775294814	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	133	526	0	ENST00000300175.4:c.425G>A	p.Arg142Gln	p.R142Q	ENST00000300175	NM_001144757.1	142	cGa/cAa	4/6	0.468240907690521	2	FACETS	0.782	0.713	0.854	0.391	0.356	0.427	SUBCLONAL	1	TRUE	0	0.568869379320065	2		526	598	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059374	42059374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	178	769	0	ENST00000219905.7:c.9094G>A	p.Gly3032Arg	p.G3032R	ENST00000219905	NM_001164273.1	3032	Ggg/Agg	24/24	0.468240907690521	2	FACETS	0.753	0.695	0.814	0.377	0.347	0.407	SUBCLONAL	1	TRUE	0	0.568869379320065	2		769	831	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748399	43748399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	168	661	0	ENST00000382044.4:c.2407G>A	p.Ala803Thr	p.A803T	ENST00000382044	NM_001141980.1	803	Gct/Act	12/28	0.468240907690521	2	FACETS	0.883	0.814	0.954	0.441	0.407	0.477	CLONAL	1	TRUE	0	0.568869379320065	2		661	669	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748825	43748825	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	218	689	0	ENST00000382044.4:c.1981G>C	p.Glu661Gln	p.E661Q	ENST00000382044	NM_001141980.1	661	Gag/Cag	12/28	0.468240907690521	2	FACETS	0.96	0.896	1	0.48	0.448	0.514	CLONAL	1	TRUE	0	0.568869379320065	2		689	798	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310177	91310177	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	68	321	0	ENST00000355112.3:c.2231C>G	p.Ser744Ter	p.S744*	ENST00000355112	NM_000057.2	744	tCa/tGa	10/22	0.535093010600119	2	FACETS	0.781	0.685	0.883	0.391	0.342	0.442	SUBCLONAL	1	TRUE	0	0.568869379320065	2		321	306	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2089993	2089993	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	199	775	0	ENST00000219066.1:c.871C>G	p.Leu291Val	p.L291V	ENST00000219066	NM_002528.5	291	Ctg/Gtg	6/6	0.568869379320065	3	FACETS	0.867	0.803	0.934	0.434	0.401	0.467	CLONAL	1	TRUE	1	0.568869379320065	3		775	1036	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133206	30133206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	201	643	0	ENST00000263025.4:c.292G>A	p.Glu98Lys	p.E98K	ENST00000263025	NM_002746.2	98	Gag/Aag	2/9	0.568869379320065	3	FACETS	0.866	0.802	0.932	0.433	0.401	0.466	CLONAL	1	TRUE	1	0.568869379320065	3		643	1048	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89842224	89842224	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	126	512	0	ENST00000389301.3:c.1827-1G>C		p.X609_splice	ENST00000389301	NM_000135.2	609			0.535093010600119	2	FACETS	0.804	0.731	0.88	0.402	0.365	0.44	CLONAL	1	TRUE	0	0.568869379320065	2		512	551	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646847	37646847	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	114	436	0	ENST00000447079.4:c.1969G>C	p.Glu657Gln	p.E657Q	ENST00000447079	NM_015083.1	657	Gag/Cag	3/14	0.543932719275456	2	FACETS	0.844	0.764	0.927	0.422	0.382	0.464	CLONAL	1	TRUE	0	0.568869379320065	2		436	475	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512450	38512450	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	218	669	0	ENST00000254066.5:c.1361G>T	p.Arg454Ile	p.R454I	ENST00000254066	NM_000964.3	454	aGa/aTa	9/9	0.543932719275456	2	FACETS	0.957	0.892	1	0.478	0.446	0.512	CLONAL	1	TRUE	0	0.568869379320065	2		669	801	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435351	56435351	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	198	784	0	ENST00000407977.2:c.1786C>T	p.Gln596Ter	p.Q596*	ENST00000407977		596	Cag/Tag	9/10	0.553768483773565	4	FACETS	0.8	0.738	0.863	0.2	0.184	0.216	SUBCLONAL	1	TRUE	0	0.568869379320065	4		784	1366	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435653	56435653	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	197	690	0	ENST00000407977.2:c.1484C>G	p.Ser495Cys	p.S495C	ENST00000407977		495	tCt/tGt	9/10	0.553768483773565	4	FACETS	0.882	0.815	0.952	0.22	0.203	0.238	CLONAL	1	TRUE	0	0.568869379320065	4		690	1232	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678029	58678033	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCG	CGCCG	TGCC	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	281	720	2	ENST00000305921.3:c.254_258delinsTGCC	p.Ser85LeufsTer80	p.S85Lfs*80	ENST00000305921	NM_003620.3	85	tCGCCG/tTGCC	1/6	0.553768483773565	4	FACETS	1	0.983	1	0.283	0.265	0.302	CLONAL	1	TRUE	0	0.568869379320065	4		722	1367	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59793383	59793383	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	58	365	0	ENST00000259008.2:c.2421G>C	p.Leu807Phe	p.L807F	ENST00000259008	NM_032043.2	807	ttG/ttC	17/20	0.553768483773565	4	FACETS	0.84	0.724	0.964	0.21	0.181	0.241	CLONAL	1	TRUE	0	0.568869379320065	4		365	381	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3094667	3094667	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	248	400	0	ENST00000078429.4:c.18G>C	p.Met6Ile	p.M6I	ENST00000078429	NM_002067.2	6	atG/atC	1/7	0.553372854888218	3	FACETS	0.86	0.809	0.912	0.86	0.809	0.912	CLONAL	2	TRUE	1	0.568869379320065	3		400	651	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209233	36209233	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs565240074	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	207	948	0	ENST00000222270.7:c.313C>G	p.Arg105Gly	p.R105G	ENST00000222270	NM_014727.1	105	Cga/Gga	1/37	0.468240907690521	2	FACETS	0.676	0.626	0.727	0.338	0.313	0.364	SUBCLONAL	1	TRUE	0	0.568869379320065	2		948	1077	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085831	16085831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	140	707	0	ENST00000281043.3:c.1007C>T	p.Ser336Phe	p.S336F	ENST00000281043	NM_005378.4	336	tCt/tTt	3/3	0.535093010600119	2	FACETS	0.724	0.661	0.79	0.362	0.33	0.395	SUBCLONAL	1	TRUE	0	0.568869379320065	2		707	680	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309548	30309548	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	201	743	0	ENST00000307677.4:c.474G>C	p.Glu158Asp	p.E158D	ENST00000307677	NM_138578.1	158	gaG/gaC	2/3	0.347492080382073	5	FACETS	0.963	0.89	1	0.321	0.296	0.347	CLONAL	1	TRUE	2	0.568869379320065	5		743	1360	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548238	41548238	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	83	459	0	ENST00000263253.7:c.3026C>G	p.Ser1009Cys	p.S1009C	ENST00000263253	NM_001429.3	1009	tCt/tGt	16/31	0.562851221763679	4	FACETS	0.649	0.573	0.731	0.325	0.286	0.366	SUBCLONAL	1	TRUE	2	0.568869379320065	4		459	705	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191259	185191259	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	68	652	0	ENST00000265026.3:c.2140G>C	p.Asp714His	p.D714H	ENST00000265026	NM_004721.4	714	Gac/Cac	11/14	0.568869379320065	3	FACETS	0.306	0.265	0.351	0.102	0.088	0.117	SUBCLONAL	1	TRUE	0	0.568869379320065	3		652	1003	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807322	1807322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	206	788	0	ENST00000260795.2:c.1571C>T	p.Ser524Phe	p.S524F	ENST00000260795		524	tCt/tTt	11/17	0.539773181746237	2	FACETS	0.893	0.83	0.958	0.447	0.415	0.479	CLONAL	1	TRUE	0	0.568869379320065	2		788	811	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164927	106164927	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	143	531	0	ENST00000380013.4:c.3795G>C	p.Leu1265Phe	p.L1265F	ENST00000380013	NM_001127208.2	1265	ttG/ttC	6/11	0.543932719275456	2	FACETS	0.844	0.772	0.918	0.422	0.386	0.459	CLONAL	1	TRUE	0	0.568869379320065	2		531	596	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517739	187517739	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	128	653	0	ENST00000441802.2:c.12955G>A	p.Asp4319Asn	p.D4319N	ENST00000441802	NM_005245.3	4319	Gac/Aac	25/27	0.524738792065471	2	FACETS	0.798	0.726	0.873	0.399	0.363	0.437	SUBCLONAL	1	TRUE	0	0.568869379320065	2		653	564	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293490	1293490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	160	637	0	ENST00000310581.5:c.1511C>T	p.Ser504Leu	p.S504L	ENST00000310581	NM_198253.2	504	tCg/tTg	2/16	0.553372854888218	3	FACETS	0.878	0.806	0.953	0.439	0.403	0.477	CLONAL	1	TRUE	1	0.568869379320065	3		637	823	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184094	56184094	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	85	541	0	ENST00000399503.3:c.4299G>C	p.Trp1433Cys	p.W1433C	ENST00000399503	NM_005921.1	1433	tgG/tgC	19/20	0.553372854888218	3	FACETS	0.641	0.567	0.72	0.32	0.283	0.36	SUBCLONAL	1	TRUE	1	0.568869379320065	3		541	599	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915741	131915741	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	65	343	0	ENST00000265335.6:c.739G>C	p.Glu247Gln	p.E247Q	ENST00000265335		247	Gaa/Caa	5/25	0.499495036017873	4	FACETS	0.905	0.788	1	0.302	0.262	0.344	CLONAL	1	TRUE	1	0.568869379320065	4		343	396	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953979	131953979	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	74	301	0	ENST00000265335.6:c.3382C>G	p.Leu1128Val	p.L1128V	ENST00000265335		1128	Ctt/Gtt	21/25	0.499495036017873	4	FACETS	0.872	0.766	0.986	0.291	0.255	0.329	CLONAL	1	TRUE	1	0.568869379320065	4		301	468	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495418	149495418	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	195	745	0	ENST00000261799.4:c.3229G>C	p.Glu1077Gln	p.E1077Q	ENST00000261799	NM_002609.3	1077	Gag/Cag	23/23	0.499495036017873	4	FACETS	0.85	0.785	0.918	0.283	0.261	0.306	CLONAL	1	TRUE	1	0.568869379320065	4		745	1265	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020961	26020961	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	258	861	0	ENST00000357647.3:c.244G>C	p.Asp82His	p.D82H	ENST00000357647	NM_003529.2	82	Gac/Cac	1/1	0.543932719275456	2	FACETS	0.876	0.821	0.933	0.438	0.41	0.467	CLONAL	1	TRUE	0	0.568869379320065	2		861	1035	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197187	26197187	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	226	916	0	ENST00000356476.2:c.292G>C	p.Glu98Gln	p.E98Q	ENST00000356476		98	Gag/Cag	1/1	0.543932719275456	2	FACETS	0.684	0.637	0.734	0.342	0.318	0.367	SUBCLONAL	1	TRUE	0	0.568869379320065	2		916	1161	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680956	30680956	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	184	664	0	ENST00000376406.3:c.763G>C	p.Glu255Gln	p.E255Q	ENST00000376406	NM_014641.2	255	Gaa/Caa	5/15	0.543932719275456	2	FACETS	0.794	0.734	0.856	0.397	0.367	0.428	SUBCLONAL	1	TRUE	0	0.568869379320065	2		664	815	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815740	32815740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	159	685	0	ENST00000354258.4:c.1876G>A	p.Gly626Arg	p.G626R	ENST00000354258	NM_000593.5	626	Ggg/Agg	8/11	0.543932719275456	2	FACETS	0.67	0.615	0.728	0.335	0.307	0.364	SUBCLONAL	1	TRUE	0	0.568869379320065	2		685	834	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265613	152265613	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	136	613	0	ENST00000206249.3:c.1066C>G	p.His356Asp	p.H356D	ENST00000206249	NM_000125.3	356	Cac/Gac	4/8	0.543932719275456	2	FACETS	0.666	0.606	0.728	0.333	0.303	0.364	SUBCLONAL	1	TRUE	0	0.568869379320065	2		613	718	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026397	6026397	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587780045	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	44	191	0	ENST00000265849.7:c.1999G>C	p.Glu667Gln	p.E667Q	ENST00000265849	NM_000535.5	667	Gag/Cag	11/15	0.535093010600119	2	FACETS	0.926	0.79	1	0.463	0.395	0.536	CLONAL	1	TRUE	0	0.568869379320065	2		191	167	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273254	55273254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749441331	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	150	642	0	ENST00000275493.2:c.3577G>A	p.Glu1193Lys	p.E1193K	ENST00000275493	NM_005228.3	1193	Gaa/Aaa	28/28	0.492354879719897	2	FACETS	0.841	0.771	0.913	0.421	0.385	0.457	CLONAL	1	TRUE	0	0.568869379320065	2		642	627	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994143	21994143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780425629	NA	P-0012515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	202	578	0	ENST00000579755.1:c.188G>A	p.Arg63Lys	p.R63K	ENST00000579755		63	aGa/aAa	1/3	0.553372854888218		FACETS		0.93	1				CLONAL	1	TRUE	1	0.568869379320065	3		578	910	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	153	321	0				ENST00000310581	NM_198253.2	-/1132			0.231139226087207	2	FACETS	1	0.988	1	0.705	0.65	0.761	INDETERMINATE	1	TRUE	0	0.460935591351984	2		321	471	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0013150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	345	396	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	0.443724845989135	2	FACETS	0.976	0.93	1	0.976	0.93	1	CLONAL	2	TRUE	0	0.460935591351984	2		396	767	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276860	15276861	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs753725730	NA	P-0013150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	79	764	3	ENST00000263388.2:c.5404dup	p.Ala1802GlyfsTer8	p.A1802Gfs*8	ENST00000263388	NM_000435.2	1802	gct/gGct	30/33	1	2	FACETS	0.459	0.404	0.52	0.459	0.404	0.52	SUBCLONAL	1	TRUE	1	0.460935591351984	2		767	746	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820697	3820703	+	frameshift_variant	Frame_Shift_Del	DEL	GACTGTA	GACTGTA	-	novel	NA	P-0013150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	192	439	0	ENST00000262367.5:c.2748_2754del	p.Thr917ArgfsTer8	p.T917Rfs*8	ENST00000262367	NM_004380.2	916	ccTACAGTC/cc	14/31	0.260144026598628	1	FACETS	0.855	0.793	0.919	0.855	0.793	0.919	INDETERMINATE	1	TRUE	0	0.460935591351984	1		439	750	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099864	27099864	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	203	320	1	ENST00000324856.7:c.3743C>A	p.Ser1248Ter	p.S1248*	ENST00000324856	NM_006015.4	1248	tCa/tAa	15/20	0.231139226087207	2	FACETS	1	0.991	1	0.717	0.669	0.767	INDETERMINATE	1	TRUE	0	0.460935591351984	2		321	614	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833925	44833925	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	91	81	0	ENST00000377967.4:c.349C>G	p.Gln117Glu	p.Q117E	ENST00000377967	NM_021140.2	117	Cag/Gag	4/29	1	1	FACETS	0.763	0.694	0.834	1	0.984	1	SUBCLONAL	2	TRUE	0	0.460935591351984	1		81	199	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132542	11132542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	183	580	0	ENST00000358026.2:c.2758G>A	p.Glu920Lys	p.E920K	ENST00000358026	NM_001128849.1	920	Gag/Aag	19/36	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.460935591351984	2		580	732	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394821	394821	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	48	294	0	ENST00000380956.4:c.217G>A	p.Ala73Thr	p.A73T	ENST00000380956	NM_001195286.1	73	Gct/Act	3/9	1	2	FACETS	0.355	0.3	0.417	0.355	0.3	0.417	SUBCLONAL	1	TRUE	1	0.460935591351984	2		294	586	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587781702	NA	P-0013379-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	361	727	1	ENST00000269305.4:c.920-1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.542661835190279	2	FACETS	0.978	0.936	1	0.978	0.936	1	CLONAL	2	TRUE	0	0.542661835190279	2		728	680	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013379-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	140	460	0	ENST00000397062.3:c.101G>C	p.Arg34Pro	p.R34P	ENST00000397062	NM_006164.4	34	cGa/cCa	2/5	0.348845557588675	4	FACETS	0.84	0.77	0.911	0.84	0.77	0.911	CLONAL	2	TRUE	2	0.542661835190279	4		460	474	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508334	106508334	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013379-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	178	649	2	ENST00000359195.3:c.328T>A	p.Tyr110Asn	p.Y110N	ENST00000359195	NM_002649.2	110	Tac/Aac	2/11	0.542661835190279	3	FACETS	1	0.981	1	0.591	0.546	0.637	CLONAL	1	TRUE	1	0.542661835190279	3		651	706	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971053	21971053	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs137854598	NA	P-0013379-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	329	688	0	ENST00000304494.5:c.305C>A	p.Ala102Glu	p.A102E	ENST00000304494	NM_000077.4	102	gCg/gAg	2/3	0.542661835190279	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.542661835190279	2		688	578	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946245	55946245	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243160272	NA	P-0013379-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	288	626	0	ENST00000263923.4:c.3934G>A	p.Asp1312Asn	p.D1312N	ENST00000263923	NM_002253.2	1312	Gat/Aat	30/30	0.468158173102138	4	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	2	0.542661835190279	4		626	813	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499771	8499771	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs748340591	NA	P-0013379-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	245	568	0	ENST00000356435.5:c.2198G>T	p.Arg733Leu	p.R733L	ENST00000356435		733	cGc/cTc	14/35	0.542661835190279	2	FACETS	0.905	0.856	0.954	0.905	0.856	0.954	CLONAL	2	TRUE	0	0.542661835190279	2		568	499	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245189	133245701	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCGAGTGCCCACCCAGGCGGCCGACACTCACTGAACTCGCCCCTCCACTGCCAGGCCATCTTCCGCTGGCAGTTTGCTCCAGGCTTATTGAAGTCACAGGCAGCACAGGTGGCTTCGTCCACCATGGCAGAGGGCTGGGAGGGGTGAGAAAGCACTTAGGGCTGGGCAGAGAGAGCTCCGACTCTGACACGGGAAGTAAAGTCTCACCTGCAGGCGGTTGGTCAGGATGATGTTGGGGTACATGGCCCCCACGTCCAGGTGGTAGATGAGTGGACACTCGATGCGGCTGGGAACGTCCTTCAGGGAGGCAAGCTTGCTCTTAATCTCATCACACACCTGCAGAGAAAGCGAAACTCAGTAGAGGCTGGTGACCAAGCTTGCCTCGTGTGCAGTTCACCAACCCCTTTTAGACATTCAGGAGAGGAAAAAGCTGAAAAATATATAAATAGAGCAAAAACTAGCCAGAAGAAAAAAGTTAAGAAGGGTTGCCATCATTTCTATGAAATACATTA	ACCGAGTGCCCACCCAGGCGGCCGACACTCACTGAACTCGCCCCTCCACTGCCAGGCCATCTTCCGCTGGCAGTTTGCTCCAGGCTTATTGAAGTCACAGGCAGCACAGGTGGCTTCGTCCACCATGGCAGAGGGCTGGGAGGGGTGAGAAAGCACTTAGGGCTGGGCAGAGAGAGCTCCGACTCTGACACGGGAAGTAAAGTCTCACCTGCAGGCGGTTGGTCAGGATGATGTTGGGGTACATGGCCCCCACGTCCAGGTGGTAGATGAGTGGACACTCGATGCGGCTGGGAACGTCCTTCAGGGAGGCAAGCTTGCTCTTAATCTCATCACACACCTGCAGAGAAAGCGAAACTCAGTAGAGGCTGGTGACCAAGCTTGCCTCGTGTGCAGTTCACCAACCCCTTTTAGACATTCAGGAGAGGAAAAAGCTGAAAAATATATAAATAGAGCAAAAACTAGCCAGAAGAAAAAAGTTAAGAAGGGTTGCCATCATTTCTATGAAATACATTA	-	novel	NA	P-0013379-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	70	696	0	ENST00000320574.5:c.1795-176_2026+32del		p.X599_splice	ENST00000320574	NM_006231.2	599		17-18/49	0.468158173102138	4	FACETS	0.524	0.456	0.597	0.262	0.228	0.299	SUBCLONAL	1	TRUE	2	0.542661835190279	4		696	760	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281297	49281297	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013379-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	223	578	0	ENST00000282018.3:c.344C>G	p.Ser115Cys	p.S115C	ENST00000282018	NM_020377.2	115	tCt/tGt	1/1	0.542661835190279	2	FACETS	0.967	0.914	1	0.967	0.914	1	CLONAL	2	TRUE	0	0.542661835190279	2		578	425	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51529147	51529147	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013379-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	251	515	0	ENST00000260433.2:c.205G>C	p.Gly69Arg	p.G69R	ENST00000260433		69	Ggg/Cgg	3/10	0.542661835190279	2	FACETS	0.912	0.864	0.961	0.912	0.864	0.961	CLONAL	2	TRUE	0	0.542661835190279	2		515	507	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299084	15299084	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013379-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	278	512	0	ENST00000263388.2:c.1454del	p.Lys485ArgfsTer114	p.K485Rfs*114	ENST00000263388	NM_000435.2	485	aAg/ag	9/33	0.542661835190279	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	1	0.542661835190279	3		512	650	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793280	33793280	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1007915253	NA	P-0013379-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	542	466	0	ENST00000498907.2:c.41C>G	p.Pro14Arg	p.P14R	ENST00000498907	NM_004364.3	14	cCg/cGg	1/1	0.542661835190279	6	FACETS	0.919	0.888	0.948	0.919	0.888	0.948	CLONAL	5	TRUE	1	0.542661835190279	6		466	907	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687409	117687409	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013379-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	187	475	0	ENST00000368508.3:c.2642C>A	p.Ser881Tyr	p.S881Y	ENST00000368508	NM_002944.2	881	tCt/tAt	18/43	0.542661835190279	2	FACETS	0.987	0.929	1	0.987	0.929	1	CLONAL	2	TRUE	0	0.542661835190279	2		475	349	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615719	100615719	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013379-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	282	330	0	ENST00000308731.7:c.613G>C	p.Glu205Gln	p.E205Q	ENST00000308731	NM_000061.2	205	Gag/Cag	8/19	0.477138345203673	2	FACETS	0.873	0.839	0.905			1	CLONAL	3	TRUE	NA	0.542661835190279	2		330	397	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	132	321	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.877	0.806	0.948	0.877	0.806	0.948	CLONAL	1	TRUE	1	0.870405684111288	2		321	346	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	274	271	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.923	0.872	0.975	0.923	0.872	0.975	CLONAL	1	TRUE	1	0.870405684111288	2		272	682	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499772	8499772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773166856	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	257	525	0	ENST00000356435.5:c.2197C>T	p.Arg733Cys	p.R733C	ENST00000356435		733	Cgc/Tgc	14/35	1	2	FACETS	0.713	0.67	0.758	0.713	0.67	0.758	SUBCLONAL	1	TRUE	1	0.870405684111288	2		525	828	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256521	115256521	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs752508313	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	231	436	0	ENST00000369535.4:c.190T>G	p.Tyr64Asp	p.Y64D	ENST00000369535	NM_002524.4	64	Tac/Gac	3/7	0.870405684111288	1	FACETS	0.777	0.738	0.815	0.777	0.738	0.815	SUBCLONAL	1	TRUE	0	0.870405684111288	1		436	386	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843704	156843704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	250	797	0	ENST00000524377.1:c.1130C>T	p.Ala377Val	p.A377V	ENST00000524377	NM_002529.3	377	gCc/gTc	8/17	1	2	FACETS	0.709	0.665	0.754	0.709	0.665	0.754	SUBCLONAL	1	TRUE	1	0.870405684111288	2		797	810	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851379	156851379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	202	633	0	ENST00000524377.1:c.2336C>T	p.Ala779Val	p.A779V	ENST00000524377	NM_002529.3	779	gCc/gTc	17/17	1	2	FACETS	0.736	0.685	0.787	0.736	0.685	0.787	SUBCLONAL	1	TRUE	1	0.870405684111288	2		633	631	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161310406	161310406	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	209	430	1	ENST00000367975.2:c.202T>C	p.Ser68Pro	p.S68P	ENST00000367975	NM_003001.3	68	Tcc/Ccc	4/6	1	2	FACETS	0.629	0.585	0.673	0.629	0.585	0.673	SUBCLONAL	1	TRUE	1	0.870405684111288	2		431	764	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115946	8115946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs949032380	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	265	621	0	ENST00000346208.3:c.1292G>A	p.Gly431Glu	p.G431E	ENST00000346208		431	gGa/gAa	6/6	1	2	FACETS	0.853	0.804	0.903	0.853	0.804	0.903	CLONAL	1	TRUE	1	0.870405684111288	2		621	714	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333651	70333651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	232	566	0	ENST00000373644.4:c.1556C>T	p.Pro519Leu	p.P519L	ENST00000373644	NM_030625.2	519	cCt/cTt	2/12	1	2	FACETS	0.745	0.697	0.793	0.745	0.697	0.793	SUBCLONAL	1	TRUE	1	0.870405684111288	2		566	716	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256195	123256195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371854567	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	33	452	0	ENST00000358487.5:c.1714C>T	p.Leu572Phe	p.L572F	ENST00000358487	NM_000141.4	572	Ctc/Ttc	13/18	1	2	FACETS	0.122	0.099	0.148	0.122	0.099	0.148	SUBCLONAL	1	TRUE	1	0.870405684111288	2		452	622	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205218	61205218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs562958122	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	189	457	0	ENST00000301761.2:c.158C>T	p.Pro53Leu	p.P53L	ENST00000301761	NM_017841.2	53	cCt/cTt	2/4	1	2	FACETS	0.67	0.622	0.72	0.67	0.622	0.72	SUBCLONAL	1	TRUE	1	0.870405684111288	2		457	648	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192717	94192717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	39	337	0	ENST00000323929.3:c.1357G>A	p.Gly453Arg	p.G453R	ENST00000323929	NM_005591.3	453	Ggg/Agg	13/20	1	2	FACETS	0.154	0.127	0.184	0.154	0.127	0.184	SUBCLONAL	1	TRUE	1	0.870405684111288	2		337	581	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114842	108114842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145355104	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	184	337	0	ENST00000278616.4:c.659C>T	p.Ala220Val	p.A220V	ENST00000278616	NM_000051.3	220	gCg/gTg	6/63	1	2	FACETS	0.723	0.671	0.776	0.723	0.671	0.776	SUBCLONAL	1	TRUE	1	0.870405684111288	2		337	585	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118370103	118370103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1397000127	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	197	418	0	ENST00000534358.1:c.6047G>A	p.Gly2016Asp	p.G2016D	ENST00000534358	NM_005933.3	2016	gGc/gAc	23/36	1	2	FACETS	0.692	0.644	0.742	0.692	0.644	0.742	SUBCLONAL	1	TRUE	1	0.870405684111288	2		418	654	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245880	46245880	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	275	554	0	ENST00000334344.6:c.3974G>A	p.Gly1325Glu	p.G1325E	ENST00000334344	NM_152641.2	1325	gGg/gAg	15/21	1	2	FACETS	0.742	0.698	0.786	0.742	0.698	0.786	SUBCLONAL	1	TRUE	1	0.870405684111288	2		554	852	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422724	49422724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	244	649	0	ENST00000301067.7:c.14269C>T	p.Pro4757Ser	p.P4757S	ENST00000301067	NM_003482.3	4757	Cct/Tct	45/54	1	2	FACETS	0.707	0.663	0.752	0.707	0.663	0.752	SUBCLONAL	1	TRUE	1	0.870405684111288	2		649	793	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422852	49422852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	235	734	0	ENST00000301067.7:c.14243G>A	p.Ser4748Asn	p.S4748N	ENST00000301067	NM_003482.3	4748	aGc/aAc	44/54	1	2	FACETS	0.692	0.648	0.738	0.692	0.648	0.738	SUBCLONAL	1	TRUE	1	0.870405684111288	2		734	780	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426192	49426192	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781695699	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	223	711	0	ENST00000301067.7:c.12296G>A	p.Gly4099Glu	p.G4099E	ENST00000301067	NM_003482.3	4099	gGa/gAa	39/54	1	2	FACETS	0.708	0.661	0.755	0.708	0.661	0.755	SUBCLONAL	1	TRUE	1	0.870405684111288	2		711	724	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433823	49433823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1286278528	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	183	639	0	ENST00000301067.7:c.7730G>A	p.Ser2577Asn	p.S2577N	ENST00000301067	NM_003482.3	2577	aGc/aAc	31/54	1	2	FACETS	0.629	0.583	0.677	0.629	0.583	0.677	SUBCLONAL	1	TRUE	1	0.870405684111288	2		639	668	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416752	121416752	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1251482432	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	199	713	0	ENST00000257555.6:c.181C>T	p.Pro61Ser	p.P61S	ENST00000257555		61	Ccc/Tcc	1/10	1	2	FACETS	0.756	0.704	0.809	0.756	0.704	0.809	SUBCLONAL	1	TRUE	1	0.870405684111288	2		713	605	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219270	133219270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	188	583	0	ENST00000320574.5:c.4774G>A	p.Glu1592Lys	p.E1592K	ENST00000320574	NM_006231.2	1592	Gag/Aag	37/49	1	2	FACETS	0.702	0.652	0.754	0.702	0.652	0.754	SUBCLONAL	1	TRUE	1	0.870405684111288	2		583	615	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597507	28597507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	258	446	0	ENST00000241453.7:c.2398G>A	p.Glu800Lys	p.E800K	ENST00000241453	NM_004119.2	800	Gaa/Aaa	19/24	1	2	FACETS	0.782	0.735	0.83	0.782	0.735	0.83	SUBCLONAL	1	TRUE	1	0.870405684111288	2		446	758	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610142	28610142	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	232	489	0	ENST00000241453.7:c.1348G>A	p.Ala450Thr	p.A450T	ENST00000241453	NM_004119.2	450	Gcg/Acg	11/24	1	2	FACETS	0.759	0.711	0.808	0.759	0.711	0.808	SUBCLONAL	1	TRUE	1	0.870405684111288	2		489	702	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914430	32914430	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	203	483	0	ENST00000380152.3:c.5938A>G	p.Thr1980Ala	p.T1980A	ENST00000380152		1980	Aca/Gca	11/27	1	2	FACETS	0.756	0.705	0.808	0.756	0.705	0.808	SUBCLONAL	1	TRUE	1	0.870405684111288	2		483	617	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972609	32972609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	220	455	0	ENST00000380152.3:c.9959C>T	p.Pro3320Leu	p.P3320L	ENST00000380152		3320	cCt/cTt	27/27	1	2	FACETS	0.657	0.613	0.703	0.657	0.613	0.703	SUBCLONAL	1	TRUE	1	0.870405684111288	2		455	769	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347892	73347892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	196	419	1	ENST00000377767.4:c.1169C>T	p.Ala390Val	p.A390V	ENST00000377767	NM_014953.3	390	gCt/gTt	8/21	1	2	FACETS	0.71	0.661	0.761	0.71	0.661	0.761	SUBCLONAL	1	TRUE	1	0.870405684111288	2		420	634	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105512	30105512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768104173	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	248	516	0	ENST00000331968.5:c.1174G>A	p.Ala392Thr	p.A392T	ENST00000331968	NM_002742.2	392	Gcc/Acc	7/18	1	2	FACETS	0.741	0.695	0.788	0.741	0.695	0.788	SUBCLONAL	1	TRUE	1	0.870405684111288	2		516	769	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005394	42005394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	44	588	0	ENST00000219905.7:c.3130G>A	p.Ala1044Thr	p.A1044T	ENST00000219905	NM_001164273.1	1044	Gcc/Acc	9/24	1	2	FACETS	0.12	0.099	0.142	0.12	0.099	0.142	SUBCLONAL	1	TRUE	1	0.870405684111288	2		588	846	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041122	42041122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1428280674	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	268	524	0	ENST00000219905.7:c.5500C>T	p.Pro1834Ser	p.P1834S	ENST00000219905	NM_001164273.1	1834	Cca/Tca	16/24	1	2	FACETS	0.757	0.712	0.802	0.757	0.712	0.802	SUBCLONAL	1	TRUE	1	0.870405684111288	2		524	814	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51529101	51529101	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	212	438	0	ENST00000260433.2:c.251T>C	p.Phe84Ser	p.F84S	ENST00000260433		84	tTc/tCc	3/10	1	2	FACETS	0.795	0.743	0.848	0.795	0.743	0.848	SUBCLONAL	1	TRUE	1	0.870405684111288	2		438	613	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782062	66782062	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	197	431	0	ENST00000307102.5:c.1034del	p.Asn345ThrfsTer8	p.N345Tfs*8	ENST00000307102	NM_002755.3	343	atA/at	10/11	1	2	FACETS	0.722	0.672	0.773	0.722	0.672	0.773	SUBCLONAL	1	TRUE	1	0.870405684111288	2		431	627	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221295	2221295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757325627	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	30	489	0	ENST00000326181.6:c.379G>A	p.Val127Met	p.V127M	ENST00000326181	NM_032271.2	127	Gtg/Atg	6/21	1	2	FACETS	0.132	0.105	0.161	0.132	0.105	0.161	SUBCLONAL	1	TRUE	1	0.870405684111288	2		489	524	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032111	10032111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs899780729	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	39	479	0	ENST00000330684.3:c.712C>T	p.Leu238Phe	p.L238F	ENST00000330684	NM_001134407.1	238	Ctc/Ttc	3/13	1	2	FACETS	0.153	0.127	0.183	0.153	0.127	0.183	SUBCLONAL	1	TRUE	1	0.870405684111288	2		479	584	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029564	14029564	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	223	479	0	ENST00000311895.7:c.1775A>C	p.Glu592Ala	p.E592A	ENST00000311895	NM_005236.2	592	gAa/gCa	8/11	1	2	FACETS	0.71	0.663	0.757	0.71	0.663	0.757	SUBCLONAL	1	TRUE	1	0.870405684111288	2		479	722	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641632	23641632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1019525144	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	205	439	0	ENST00000261584.4:c.1843C>T	p.Pro615Ser	p.P615S	ENST00000261584	NM_024675.3	615	Cct/Tct	5/13	1	2	FACETS	0.688	0.64	0.736	0.688	0.64	0.736	SUBCLONAL	1	TRUE	1	0.870405684111288	2		439	685	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647011	23647011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45585833	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	38	499	0	ENST00000261584.4:c.856C>T	p.Pro286Ser	p.P286S	ENST00000261584	NM_024675.3	286	Cct/Tct	4/13	1	2	FACETS	0.115	0.094	0.138	0.115	0.094	0.138	SUBCLONAL	1	TRUE	1	0.870405684111288	2		499	760	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821907	72821907	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	204	574	0	ENST00000268489.5:c.10268A>G	p.Glu3423Gly	p.E3423G	ENST00000268489	NM_006885.3	3423	gAa/gGa	10/10	1	2	FACETS	0.719	0.67	0.769	0.719	0.67	0.769	SUBCLONAL	1	TRUE	1	0.870405684111288	2		574	652	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830777	72830777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752574946	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	229	636	0	ENST00000268489.5:c.5804G>A	p.Arg1935His	p.R1935H	ENST00000268489	NM_006885.3	1935	cGc/cAc	9/10	1	2	FACETS	0.685	0.641	0.731	0.685	0.641	0.731	SUBCLONAL	1	TRUE	1	0.870405684111288	2		636	768	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969983	81969983	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	39	546	0	ENST00000359376.3:c.3052G>A	p.Asp1018Asn	p.D1018N	ENST00000359376	NM_002661.3	1018	Gat/Aat	27/33	1	2	FACETS	0.137	0.113	0.164	0.137	0.113	0.164	SUBCLONAL	1	TRUE	1	0.870405684111288	2		546	656	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348928	89348928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	38	699	0	ENST00000301030.4:c.4022C>T	p.Pro1341Leu	p.P1341L	ENST00000301030	NM_001256183.1	1341	cCt/cTt	9/13	1	2	FACETS	0.123	0.101	0.147	0.123	0.101	0.147	SUBCLONAL	1	TRUE	1	0.870405684111288	2		699	711	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	233	607	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			1	2	FACETS	0.633	0.591	0.675	0.633	0.591	0.675	SUBCLONAL	1	TRUE	1	0.870405684111288	2		607	846	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973593	15973593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	49	563	0	ENST00000268712.3:c.4399C>T	p.Pro1467Ser	p.P1467S	ENST00000268712	NM_006311.3	1467	Ccc/Tcc	31/46	1	2	FACETS	0.136	0.115	0.16	0.136	0.115	0.16	SUBCLONAL	1	TRUE	1	0.870405684111288	2		563	826	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16046922	16046922	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	150	292	0	ENST00000268712.3:c.1171G>A	p.Glu391Lys	p.E391K	ENST00000268712	NM_006311.3	391	Gag/Aag	11/46	1	2	FACETS	0.735	0.677	0.794	0.735	0.677	0.794	SUBCLONAL	1	TRUE	1	0.870405684111288	2		292	469	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16062136	16062136	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	164	453	0	ENST00000268712.3:c.670T>C	p.Ser224Pro	p.S224P	ENST00000268712	NM_006311.3	224	Tcc/Ccc	6/46	1	2	FACETS	0.583	0.537	0.631	0.583	0.537	0.631	SUBCLONAL	1	TRUE	1	0.870405684111288	2		453	646	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068463	16068463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs74453660	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	10	107	1	ENST00000268712.3:c.448G>A	p.Gly150Arg	p.G150R	ENST00000268712	NM_006311.3	150	Gga/Aga	5/46	1	2	FACETS	0.129	0.087	0.182	0.129	0.087	0.182	SUBCLONAL	1	TRUE	1	0.870405684111288	2		108	178	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353824	40353824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	229	638	0	ENST00000293328.3:c.2296G>A	p.Ala766Thr	p.A766T	ENST00000293328	NM_012448.3	766	Gcg/Acg	19/19	1	2	FACETS	0.731	0.684	0.779	0.731	0.684	0.779	SUBCLONAL	1	TRUE	1	0.870405684111288	2		638	720	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226450	41226450	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886040237	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	48	522	0	ENST00000357654.3:c.4573C>T	p.Gln1525Ter	p.Q1525*	ENST00000357654	NM_007294.3	1525	Caa/Taa	14/23	1	2	FACETS	0.143	0.12	0.168	0.143	0.12	0.168	SUBCLONAL	1	TRUE	1	0.870405684111288	2		522	773	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007460	62007460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	229	633	0	ENST00000392795.3:c.407G>A	p.Gly136Asp	p.G136D	ENST00000392795	NM_001039933.1	136	gGc/gAc	3/6	1	2	FACETS	0.724	0.677	0.771	0.724	0.677	0.771	SUBCLONAL	1	TRUE	1	0.870405684111288	2		633	727	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533871	63533871	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	40	646	0	ENST00000307078.5:c.1283C>T	p.Ser428Phe	p.S428F	ENST00000307078	NM_004655.3	428	tCc/tTc	6/11	1	2	FACETS	0.136	0.112	0.162	0.136	0.112	0.162	SUBCLONAL	1	TRUE	1	0.870405684111288	2		646	678	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78820354	78820354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	195	594	0	ENST00000306801.3:c.1294C>T	p.Gln432Ter	p.Q432*	ENST00000306801	NM_020761.2	432	Cag/Tag	11/34	1	2	FACETS	0.671	0.623	0.719	0.671	0.623	0.719	SUBCLONAL	1	TRUE	1	0.870405684111288	2		594	668	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39575949	39575949	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	202	323	1	ENST00000262039.4:c.882T>G	p.Asp294Glu	p.D294E	ENST00000262039	NM_002647.2	294	gaT/gaG	8/25	1	2	FACETS	0.705	0.657	0.755	0.705	0.657	0.755	SUBCLONAL	1	TRUE	1	0.870405684111288	2		324	658	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591978	48591978	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	102	461	0	ENST00000342988.3:c.1139+2T>C		p.X380_splice	ENST00000342988	NM_005359.5	380			1	2	FACETS	0.332	0.296	0.369	0.332	0.296	0.369	SUBCLONAL	1	TRUE	1	0.870405684111288	2		461	707	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61325770	61325770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	56	83	0	ENST00000283752.5:c.446C>T	p.Ser149Phe	p.S149F	ENST00000283752	NM_006919.2	149	tCc/tTc	5/8	1	2	FACETS	0.875	0.768	0.986	0.875	0.768	0.986	CLONAL	1	TRUE	1	0.870405684111288	2		83	147	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221987	1221987	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370222210	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	27	512	1	ENST00000326873.7:c.902G>A	p.Arg301Gln	p.R301Q	ENST00000326873	NM_000455.4	301	cGg/cAg	7/10	1	2	FACETS	0.115	0.091	0.143	0.115	0.091	0.143	SUBCLONAL	1	TRUE	1	0.870405684111288	2		513	540	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212238	5212238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	214	664	0	ENST00000357368.4:c.4793G>A	p.Cys1598Tyr	p.C1598Y	ENST00000357368	NM_002850.3	1598	tGc/tAc	32/38	1	2	FACETS	0.748	0.699	0.799	0.748	0.699	0.799	SUBCLONAL	1	TRUE	1	0.870405684111288	2		664	657	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229684	5229684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	86	377	0	ENST00000357368.4:c.2167C>T	p.Pro723Ser	p.P723S	ENST00000357368	NM_002850.3	723	Ccg/Tcg	15/38	1	2	FACETS	0.65	0.581	0.722	0.65	0.581	0.722	SUBCLONAL	1	TRUE	1	0.870405684111288	2		377	304	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245935	5245935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	223	660	0	ENST00000357368.4:c.840G>T	p.Gln280His	p.Q280H	ENST00000357368	NM_002850.3	280	caG/caT	10/38	1	2	FACETS	0.659	0.615	0.704	0.659	0.615	0.704	SUBCLONAL	1	TRUE	1	0.870405684111288	2		660	778	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262426	10262426	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	201	476	0	ENST00000340748.4:c.2069G>A	p.Arg690Lys	p.R690K	ENST00000340748		690	aGg/aAg	22/40	1	2	FACETS	0.678	0.631	0.727	0.678	0.631	0.727	SUBCLONAL	1	TRUE	1	0.870405684111288	2		476	681	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11019811	11019811	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	49	625	0	ENST00000327064.4:c.486G>A	p.Met162Ile	p.M162I	ENST00000327064	NM_199141.1	162	atG/atA	4/16	1	2	FACETS	0.158	0.133	0.186	0.158	0.133	0.186	SUBCLONAL	1	TRUE	1	0.870405684111288	2		625	711	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276846	15276846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	227	676	0	ENST00000263388.2:c.5419C>T	p.Pro1807Ser	p.P1807S	ENST00000263388	NM_000435.2	1807	Cca/Tca	30/33	1	2	FACETS	0.698	0.653	0.745	0.698	0.653	0.745	SUBCLONAL	1	TRUE	1	0.870405684111288	2		676	747	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297746	15297746	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	201	545	0	ENST00000263388.2:c.1894G>A	p.Gly632Arg	p.G632R	ENST00000263388	NM_000435.2	632	Gga/Aga	12/33	1	2	FACETS	0.734	0.684	0.786	0.734	0.684	0.786	SUBCLONAL	1	TRUE	1	0.870405684111288	2		545	629	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302280	15302280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	184	608	0	ENST00000263388.2:c.991G>A	p.Asp331Asn	p.D331N	ENST00000263388	NM_000435.2	331	Gac/Aac	6/33	1	2	FACETS	0.675	0.626	0.726	0.675	0.626	0.726	SUBCLONAL	1	TRUE	1	0.870405684111288	2		608	626	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311608	30311608	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	24	278	0	ENST00000262643.3:c.463-1G>A		p.X155_splice	ENST00000262643	NM_001238.2	155			0.870405684111288	1	FACETS	0.103	0.081	0.129	0.103	0.081	0.129	SUBCLONAL	1	TRUE	0	0.870405684111288	1		278	302	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791718	42791718	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1344635105	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	43	677	3	ENST00000575354.2:c.604C>T	p.Arg202Trp	p.R202W	ENST00000575354	NM_015125.3	202	Cgg/Tgg	5/20	0.870405684111288	1	FACETS	0.117	0.098	0.139	0.117	0.098	0.139	SUBCLONAL	1	TRUE	0	0.870405684111288	1		680	475	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147185	61147185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408969857	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	229	328	0	ENST00000295025.8:c.863G>A	p.Gly288Asp	p.G288D	ENST00000295025	NM_002908.2	288	gGc/gAc	8/11	NA	2	FACETS	0.697	0.652	0.743			1	INDETERMINATE	1	TRUE	NA	0.870405684111288	2		328	755	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630963	67630963	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	237	470	0	ENST00000272342.5:c.1149G>A	p.Trp383Ter	p.W383*	ENST00000272342	NM_019002.3	383	tgG/tgA	5/6	1	2	FACETS	0.821	0.771	0.873	0.821	0.771	0.873	CLONAL	1	TRUE	1	0.870405684111288	2		470	663	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755584	39755584	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	233	672	0	ENST00000288319.7:c.1181G>A	p.Gly394Glu	p.G394E	ENST00000288319	NM_182918.3	394	gGg/gAg	10/10	1	2	FACETS	0.704	0.659	0.751	0.704	0.659	0.751	SUBCLONAL	1	TRUE	1	0.870405684111288	2		672	760	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37081731	37081731	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587778933	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	242	528	0	ENST00000231790.2:c.1613G>A	p.Trp538Ter	p.W538*	ENST00000231790	NM_000249.3	538	tGg/tAg	14/19	0.635754344851831	1	FACETS	0.583	0.55	0.616	0.583	0.55	0.616	SUBCLONAL	1	TRUE	0	0.870405684111288	1		528	539	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165579	47165579	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	289	696	0	ENST00000409792.3:c.547del	p.Val183Ter	p.V183*	ENST00000409792	NM_014159.6	183	Gta/ta	3/21	0.635754344851831	1	FACETS	0.576	0.546	0.606	0.576	0.546	0.606	SUBCLONAL	1	TRUE	0	0.870405684111288	1		696	651	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682399	52682400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	26	416	0	ENST00000394830.3:c.773dup	p.Asn258LysfsTer6	p.N258Kfs*6	ENST00000394830	NM_018313.4	258	aat/aaAt	8/30	0.635754344851831	1	FACETS	0.066	0.052	0.082	0.066	0.052	0.082	SUBCLONAL	1	TRUE	0	0.870405684111288	1		416	512	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215210	142215210	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	122	215	0	ENST00000350721.4:c.5891G>A	p.Trp1964Ter	p.W1964*	ENST00000350721	NM_001184.3	1964	tGg/tAg	34/47	1	2	FACETS	0.884	0.811	0.959	0.884	0.811	0.959	CLONAL	1	TRUE	1	0.870405684111288	2		215	317	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268991	142268991	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	192	320	0	ENST00000350721.4:c.2959C>T	p.Leu987Phe	p.L987F	ENST00000350721	NM_001184.3	987	Ctt/Ttt	14/47	1	2	FACETS	0.779	0.726	0.834	0.779	0.726	0.834	SUBCLONAL	1	TRUE	1	0.870405684111288	2		320	566	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374918	149374918	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	162	526	0	ENST00000360632.3:c.176G>A	p.Gly59Asp	p.G59D	ENST00000360632	NM_015472.4	59	gGc/gAc	2/7	1	2	FACETS	0.664	0.612	0.717	0.664	0.612	0.717	SUBCLONAL	1	TRUE	1	0.870405684111288	2		526	561	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182681805	182681805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	197	367	0	ENST00000292782.4:c.253G>A	p.Gly85Ser	p.G85S	ENST00000292782	NM_020640.2	85	Ggc/Agc	3/7	1	2	FACETS	0.69	0.642	0.74	0.69	0.642	0.74	SUBCLONAL	1	TRUE	1	0.870405684111288	2		367	656	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561846	55561846	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	38	505	0	ENST00000288135.5:c.236A>G	p.Gln79Arg	p.Q79R	ENST00000288135	NM_000222.2	79	cAg/cGg	2/21	1	2	FACETS	0.129	0.106	0.155	0.129	0.106	0.155	SUBCLONAL	1	TRUE	1	0.870405684111288	2		505	678	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467590	66467590	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746706656	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	231	455	0	ENST00000273854.3:c.679C>T	p.Arg227Cys	p.R227C	ENST00000273854	NM_004439.5	227	Cgt/Tgt	3/18	1	2	FACETS	0.702	0.657	0.748	0.702	0.657	0.748	SUBCLONAL	1	TRUE	1	0.870405684111288	2		455	756	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525132	187525132	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	197	381	0	ENST00000441802.2:c.10549-1G>A		p.X3517_splice	ENST00000441802	NM_005245.3	3517			1	2	FACETS	0.722	0.672	0.773	0.722	0.672	0.773	SUBCLONAL	1	TRUE	1	0.870405684111288	2		381	627	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629076	187629076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202140013	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	46	544	0	ENST00000441802.2:c.1906G>A	p.Ala636Thr	p.A636T	ENST00000441802	NM_005245.3	636	Gca/Aca	2/27	1	2	FACETS	0.142	0.119	0.168	0.142	0.119	0.168	SUBCLONAL	1	TRUE	1	0.870405684111288	2		544	744	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31405831	31405831	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	25	193	0	ENST00000344624.3:c.3948-1G>A		p.X1316_splice	ENST00000344624		1316			1	2	FACETS	0.137	0.108	0.172	0.137	0.108	0.172	SUBCLONAL	1	TRUE	1	0.870405684111288	2		193	418	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589211	67589211	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	172	405	0	ENST00000274335.5:c.1199C>T	p.Ser400Phe	p.S400F	ENST00000274335		400	tCt/tTt	9/15	1	2	FACETS	0.717	0.664	0.772	0.717	0.664	0.772	SUBCLONAL	1	TRUE	1	0.870405684111288	2		405	551	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86669980	86669980	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	126	236	0	ENST00000274376.6:c.1777G>A	p.Val593Ile	p.V593I	ENST00000274376	NM_002890.2	593	Gtc/Atc	14/25	1	2	FACETS	0.76	0.695	0.826	0.76	0.695	0.826	SUBCLONAL	1	TRUE	1	0.870405684111288	2		236	381	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675472	30675472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775063662	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	256	758	0	ENST00000376406.3:c.2884G>A	p.Ala962Thr	p.A962T	ENST00000376406	NM_014641.2	962	Gcc/Acc	8/15	1	2	FACETS	0.767	0.721	0.814	0.767	0.721	0.814	SUBCLONAL	1	TRUE	1	0.870405684111288	2		758	767	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31239024	31239024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs281860481	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	81	382	0	ENST00000376228.5:c.445G>A	p.Ala149Thr	p.A149T	ENST00000376228	NM_002117.5	149	Gcc/Acc	3/8	1	2	FACETS	0.504	0.447	0.565	0.504	0.447	0.565	SUBCLONAL	1	TRUE	1	0.870405684111288	2		382	369	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816840	32816840	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	182	530	0	ENST00000354258.4:c.1484C>T	p.Thr495Ile	p.T495I	ENST00000354258	NM_000593.5	495	aCc/aTc	6/11	1	2	FACETS	0.689	0.639	0.74	0.689	0.639	0.74	SUBCLONAL	1	TRUE	1	0.870405684111288	2		530	607	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068102	94068102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	219	419	0	ENST00000369303.4:c.860C>T	p.Ser287Phe	p.S287F	ENST00000369303	NM_004440.3	287	tCc/tTc	4/17	1	2	FACETS	0.792	0.741	0.844	0.792	0.741	0.844	SUBCLONAL	1	TRUE	1	0.870405684111288	2		419	635	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555303	106555303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	200	493	0	ENST00000369096.4:c.2420C>T	p.Pro807Leu	p.P807L	ENST00000369096	NM_001198.3	807	cCa/cTa	7/7	1	2	FACETS	0.747	0.696	0.799	0.747	0.696	0.799	SUBCLONAL	1	TRUE	1	0.870405684111288	2		493	615	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137522028	137522028	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	30	220	0	ENST00000367739.4:c.851C>T	p.Pro284Leu	p.P284L	ENST00000367739	NM_000416.2	284	cCc/cTc	6/7	0.652675637330924	1	FACETS	0.108	0.087	0.132	0.108	0.087	0.132	SUBCLONAL	1	TRUE	0	0.870405684111288	1		220	361	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192602	138192602	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	27	502	0	ENST00000237289.4:c.238C>T	p.Gln80Ter	p.Q80*	ENST00000237289	NM_001270507.1	80	Cag/Tag	2/9	0.652675637330924	1	FACETS	0.066	0.052	0.083	0.066	0.052	0.083	SUBCLONAL	1	TRUE	0	0.870405684111288	1		502	528	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005276	150005276	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	32	561	0	ENST00000253339.5:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000253339		317	Cag/Tag	3/7	0.652675637330924	1	FACETS	0.078	0.063	0.095	0.078	0.063	0.095	SUBCLONAL	1	TRUE	0	0.870405684111288	1		561	532	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522386	157522386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762698567	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	280	706	0	ENST00000346085.5:c.4658C>T	p.Ala1553Val	p.A1553V	ENST00000346085	NM_020732.3	1553	gCg/gTg	18/20	0.652675637330924	1	FACETS	0.631	0.599	0.663	0.631	0.599	0.663	SUBCLONAL	1	TRUE	0	0.870405684111288	1		706	576	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622188	162622188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1007797597	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	49	500	0	ENST00000366898.1:c.509G>A	p.Arg170Lys	p.R170K	ENST00000366898	NM_004562.2	170	aGg/aAg	4/12	1	2	FACETS	0.133	0.112	0.156	0.133	0.112	0.156	SUBCLONAL	1	TRUE	1	0.870405684111288	2		500	847	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971147	13971147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	249	487	0	ENST00000405192.2:c.782G>A	p.Arg261Lys	p.R261K	ENST00000405192	NM_001163147.1	261	aGa/aAa	8/12	1	2	FACETS	0.804	0.755	0.853	0.804	0.755	0.853	CLONAL	1	TRUE	1	0.870405684111288	2		487	712	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467717	50467717	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	192	566	0	ENST00000331340.3:c.952G>A	p.Ala318Thr	p.A318T	ENST00000331340	NM_006060.4	318	Gcc/Acc	8/8	1	2	FACETS	0.689	0.641	0.739	0.689	0.641	0.739	SUBCLONAL	1	TRUE	1	0.870405684111288	2		566	640	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335673	81335673	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	34	429	0	ENST00000222390.5:c.1687C>T	p.Gln563Ter	p.Q563*	ENST00000222390	NM_000601.4	563	Cag/Tag	15/18	0.642368331351559	1	FACETS	0.099	0.081	0.12	0.099	0.081	0.12	SUBCLONAL	1	TRUE	0	0.870405684111288	1		429	444	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124481033	124481033	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs776965979	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	159	288	0	ENST00000357628.3:c.1363A>G	p.Ile455Val	p.I455V	ENST00000357628	NM_015450.2	455	Ata/Gta	14/19	1	2	FACETS	0.951	0.883	1	0.951	0.883	1	CLONAL	1	TRUE	1	0.870405684111288	2		288	384	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534459	140534459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	47	468	0	ENST00000288602.6:c.454C>T	p.Pro152Ser	p.P152S	ENST00000288602	NM_004333.4	152	Cca/Tca	3/18	1	2	FACETS	0.148	0.124	0.174	0.148	0.124	0.174	SUBCLONAL	1	TRUE	1	0.870405684111288	2		468	732	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836281	151836281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	194	420	0	ENST00000262189.6:c.14524G>A	p.Gly4842Arg	p.G4842R	ENST00000262189	NM_170606.2	4842	Ggg/Agg	57/59	1	2	FACETS	0.737	0.686	0.789	0.737	0.686	0.789	SUBCLONAL	1	TRUE	1	0.870405684111288	2		420	605	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842299	151842299	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	289	559	0	ENST00000262189.6:c.14113C>T	p.Pro4705Ser	p.P4705S	ENST00000262189	NM_170606.2	4705	Ccc/Tcc	54/59	1	2	FACETS	0.726	0.684	0.768	0.726	0.684	0.768	SUBCLONAL	1	TRUE	1	0.870405684111288	2		559	915	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2101574	2101574	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	163	229	0	ENST00000349721.2:c.3083C>T	p.Ser1028Phe	p.S1028F	ENST00000349721	NM_003070.3	1028	tCc/tTc	22/34	1	2	FACETS	0.755	0.698	0.813	0.755	0.698	0.813	SUBCLONAL	1	TRUE	1	0.870405684111288	2		229	496	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126426	5126426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	194	405	0	ENST00000381652.3:c.3271C>T	p.Pro1091Ser	p.P1091S	ENST00000381652	NM_004972.3	1091	Cca/Tca	24/25	1	2	FACETS	0.72	0.67	0.772	0.72	0.67	0.772	SUBCLONAL	1	TRUE	1	0.870405684111288	2		405	619	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336426	80336426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	74	501	0	ENST00000286548.4:c.893C>T	p.Pro298Leu	p.P298L	ENST00000286548	NM_002072.3	298	cCc/cTc	7/7	1	2	FACETS	0.225	0.196	0.255	0.225	0.196	0.255	SUBCLONAL	1	TRUE	1	0.870405684111288	2		501	757	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482320	87482320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	268	502	0	ENST00000277120.3:c.1607C>T	p.Thr536Ile	p.T536I	ENST00000277120		536	aCc/aTc	14/19	1	2	FACETS	0.805	0.758	0.853	0.805	0.758	0.853	CLONAL	1	TRUE	1	0.870405684111288	2		502	765	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101909986	101909986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	77	400	0	ENST00000374994.4:c.1306C>T	p.Pro436Ser	p.P436S	ENST00000374994	NM_004612.2	436	Cca/Tca	8/9	1	2	FACETS	0.25	0.219	0.283	0.25	0.219	0.283	SUBCLONAL	1	TRUE	1	0.870405684111288	2		400	708	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133729597	133729597	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	196	436	1	ENST00000318560.5:c.226G>A	p.Gly76Arg	p.G76R	ENST00000318560	NM_005157.4	76	Gga/Aga	2/11	1	2	FACETS	0.716	0.666	0.767	0.716	0.666	0.767	SUBCLONAL	1	TRUE	1	0.870405684111288	2		437	629	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771752	135771752	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	232	622	0	ENST00000298552.3:c.3365G>A	p.Gly1122Asp	p.G1122D	ENST00000298552	NM_001162426.1	1122	gGc/gAc	23/23	1	2	FACETS	0.709	0.663	0.755	0.709	0.663	0.755	SUBCLONAL	1	TRUE	1	0.870405684111288	2		622	752	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412278	139412278	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622058	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	69	605	0	ENST00000277541.6:c.1367G>A	p.Cys456Tyr	p.C456Y	ENST00000277541	NM_017617.3	456	tGc/tAc	8/34	1	2	FACETS	0.244	0.212	0.278	0.244	0.212	0.278	SUBCLONAL	1	TRUE	1	0.870405684111288	2		605	651	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422716	47422716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1413219188	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	148	525	0	ENST00000377045.4:c.188G>A	p.Arg63Gln	p.R63Q	ENST00000377045	NM_001654.4	63	cGa/cAa	3/16	1	2	FACETS	0.537	0.492	0.584	0.537	0.492	0.584	SUBCLONAL	1	TRUE	1	0.870405684111288	2		525	633	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411671	63411671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	198	622	0	ENST00000330258.3:c.1496G>A	p.Ser499Asn	p.S499N	ENST00000330258	NM_152424.3	499	aGc/aAc	2/2	1	2	FACETS	0.659	0.613	0.707	0.659	0.613	0.707	SUBCLONAL	1	TRUE	1	0.870405684111288	2		622	690	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480590	123480590	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013678-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	174	500	0	ENST00000371139.4:c.98A>T	p.Asp33Val	p.D33V	ENST00000371139	NM_001114937.2	33	gAc/gTc	1/4	1	2	FACETS	0.727	0.674	0.782	0.727	0.674	0.782	SUBCLONAL	1	TRUE	1	0.870405684111288	2		500	550	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0014190-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	203	711	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.864	0.802	0.928	0.864	0.802	0.928	CLONAL	1	TRUE	1	0.53	2		711	887	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0014190-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	119	397	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.943	0.857	1	0.943	0.857	1	CLONAL	1	TRUE	1	0.53	2		397	476	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0014190-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	73	240	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.984	0.87	1	0.984	0.87	1	CLONAL	1	TRUE	1	0.53	2		240	280	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394805	45394805	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014190-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	111	430	0	ENST00000262160.6:c.544C>T	p.Arg182Ter	p.R182*	ENST00000262160	NM_005901.5	182	Cga/Tga	5/11	1	2	FACETS	0.815	0.736	0.898	0.815	0.736	0.898	CLONAL	1	TRUE	1	0.53	2		430	514	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395776	45395776	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014190-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	157	481	0	ENST00000262160.6:c.358C>T	p.Arg120Ter	p.R120*	ENST00000262160	NM_005901.5	120	Cga/Tga	4/11	1	2	FACETS	0.917	0.843	0.994	0.917	0.843	0.994	CLONAL	1	TRUE	1	0.53	2		481	646	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59793405	59793405	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014190-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	117	314	0	ENST00000259008.2:c.2399A>G	p.Tyr800Cys	p.Y800C	ENST00000259008	NM_032043.2	800	tAc/tGc	17/20	1	2	FACETS	0.981	0.891	1	0.981	0.891	1	CLONAL	1	TRUE	1	0.53	2		314	450	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593520	48593520	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014190-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	181	472	0	ENST00000342988.3:c.1271A>T	p.Asp424Val	p.D424V	ENST00000342988	NM_005359.5	424	gAt/gTt	10/12	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.53	2		472	667	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593532	48593533	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0014190-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	149	433	0	ENST00000342988.3:c.1284_1285del	p.Lys428AsnfsTer11	p.K428Nfs*11	ENST00000342988	NM_005359.5	428	aAG/a	10/12	1	2	FACETS	0.942	0.864	1	0.942	0.864	1	CLONAL	1	TRUE	1	0.53	2		433	597	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273230	198273230	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014190-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	187	504	0	ENST00000335508.6:c.980C>T	p.Pro327Leu	p.P327L	ENST00000335508	NM_012433.2	327	cCg/cTg	8/25	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.53	2		504	703	SUCCESS
APC	324	MSKCC	GRCh37	5	112173893	112173893	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014190-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	187	599	0	ENST00000257430.4:c.2602G>T	p.Glu868Ter	p.E868*	ENST00000257430	NM_000038.5	868	Gaa/Taa	16/16	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.53	2		599	682	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211685	36211685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1416954696	NA	P-0014190-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	104	685	0	ENST00000222270.7:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000222270	NM_014727.1	479	cGg/cAg	3/37	1	2	FACETS	0.764	0.686	0.845	0.764	0.686	0.845	SUBCLONAL	1	TRUE	1	0.53	2		685	514	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702654	52702654	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014190-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	103	281	0	ENST00000394830.3:c.244C>A	p.Pro82Thr	p.P82T	ENST00000394830	NM_018313.4	82	Cca/Aca	4/30	1	2	FACETS	0.792	0.712	0.876	0.792	0.712	0.876	SUBCLONAL	1	TRUE	1	0.53	2		281	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579395	7579395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016031-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	547	722	0	ENST00000269305.4:c.292C>T	p.Pro98Ser	p.P98S	ENST00000269305	NM_001126112.2	98	Cct/Tct	4/11	0.583811996471759	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.58393817364662	2		722	835	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160488	108160488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730881369	NA	P-0016031-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	173	450	0	ENST00000278616.4:c.4396C>T	p.Arg1466Ter	p.R1466*	ENST00000278616	NM_000051.3	1466	Cga/Tga	29/63	0.577790215437695	1	FACETS	0.978	0.91	1	0.978	0.91	1	CLONAL	1	TRUE	0	0.58393817364662	1		450	429	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976435	18976435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016031-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	397	598	0	ENST00000262803.5:c.3085G>A	p.Gly1029Arg	p.G1029R	ENST00000262803	NM_002911.3	1029	Gga/Aga	22/24	0.537675062775453	4	FACETS	0.95	0.904	0.996	0.95	0.904	0.996	CLONAL	2	TRUE	2	0.58393817364662	4		598	1134	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589845	212589845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016031-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	236	560	0	ENST00000342788.4:c.697G>A	p.Glu233Lys	p.E233K	ENST00000342788	NM_005235.2	233	Gaa/Aaa	6/28	0.537675062775453	4	FACETS	1	0.98	1	0.562	0.524	0.602	CLONAL	1	TRUE	2	0.58393817364662	4		560	1139	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285201	15285201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016031-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	202	666	1	ENST00000263388.2:c.4414G>A	p.Glu1472Lys	p.E1472K	ENST00000263388	NM_000435.2	1472	Gag/Aag	25/33	0.537675062775453	4	FACETS	1	0.93	1	0.502	0.465	0.541	CLONAL	1	TRUE	2	0.58393817364662	4		667	1091	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543800	212543800	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016031-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	200	549	0	ENST00000342788.4:c.1599A>G	p.Ile533Met	p.I533M	ENST00000342788	NM_005235.2	533	atA/atG	13/28	0.537675062775453	4	FACETS	0.974	0.901	1	0.487	0.45	0.525	CLONAL	1	TRUE	2	0.58393817364662	4		549	1114	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441407	149441408	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0016031-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	206	590	0	ENST00000286301.3:c.1631_1632delinsTT	p.Pro544Leu	p.P544L	ENST00000286301	NM_005211.3	544	cCC/cTT	12/22	0.273591502077765	3	FACETS	1	0.974	1	0.367	0.341	0.394	INDETERMINATE	1	TRUE	0	0.58393817364662	3		590	828	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636640	176636640	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1420606381	NA	P-0016031-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	102	518	0	ENST00000439151.2:c.1240C>T	p.Pro414Ser	p.P414S	ENST00000439151	NM_022455.4	414	Cct/Tct	5/23	0.247914511882597	5	FACETS	0.759	0.678	0.846	0.253	0.226	0.282	INDETERMINATE	1	TRUE	2	0.58393817364662	5		518	863	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686800	117686800	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016031-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	150	486	0	ENST00000368508.3:c.2917C>T	p.Pro973Ser	p.P973S	ENST00000368508	NM_002944.2	973	Cct/Tct	19/43	0.583811996471759	3	FACETS	0.931	0.853	1	0.465	0.426	0.507	CLONAL	1	TRUE	1	0.58393817364662	3		486	713	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0016244-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	142	812	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.355207654420311	2	FACETS	0.913	0.842	0.985	0.913	0.842	0.985	CLONAL	2	TRUE	0	0.415982851591636	2		812	374	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131787	2131787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1020561347	NA	P-0016244-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	250	531	0	ENST00000219476.3:c.3802C>T	p.Arg1268Cys	p.R1268C	ENST00000219476	NM_000548.3	1268	Cgc/Tgc	31/42	0.415982851591636	7	FACETS	0.97	0.914	1	0.97	0.914	1	CLONAL	4	TRUE	3	0.415982851591636	7		531	632	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256832	16256832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs887977680	NA	P-0016244-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	174	390	0	ENST00000375759.3:c.4097G>A	p.Arg1366Gln	p.R1366Q	ENST00000375759	NM_015001.2	1366	cGa/cAa	11/15	0.389643426402688	3	FACETS	0.92	0.861	0.98	1	0.99	1	CLONAL	3	TRUE	1	0.415982851591636	3		390	366	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1650196	1650196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199639167	NA	P-0016244-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	159	412	0	ENST00000344749.5:c.52G>A	p.Asp18Asn	p.D18N	ENST00000344749	NM_001136139.2	18	Gac/Aac	2/19	0.354124579881396	3	FACETS	0.882	0.821	0.943	0.882	0.821	0.943	CLONAL	3	TRUE	0	0.415982851591636	3		412	349	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294132	1294132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147056740	NA	P-0016244-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	106	515	0	ENST00000310581.5:c.869C>T	p.Ser290Phe	p.S290F	ENST00000310581	NM_198253.2	290	tCt/tTt	2/16	0.415982851591636	7	FACETS	1	0.979	1	0.279	0.25	0.31	CLONAL	1	TRUE	2	0.415982851591636	7		515	746	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509249	106509249	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016244-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	156	470	0	ENST00000359195.3:c.1243G>C	p.Glu415Gln	p.E415Q	ENST00000359195	NM_002649.2	415	Gag/Cag	2/11	0.354124579881396	3	FACETS	0.907	0.844	0.97	0.907	0.844	0.97	CLONAL	3	TRUE	0	0.415982851591636	3		470	333	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992734	68992734	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016244-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	254	373	0	ENST00000288368.4:c.1699G>A	p.Glu567Lys	p.E567K	ENST00000288368	NM_024870.2	567	Gag/Aag	16/40	0.415982851591636	9	FACETS	0.967	0.912	1	0.806	0.76	0.853	CLONAL	5	TRUE	3	0.415982851591636	9		373	620	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441113	149441113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200788902	NA	P-0016244-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	29	364	0	ENST00000286301.3:c.1799C>T	p.Thr600Met	p.T600M	ENST00000286301	NM_005211.3	600	aCg/aTg	13/22	0.421925773832748	4	FACETS	0.489	0.392	0.599	0.122	0.098	0.15	SUBCLONAL	1	TRUE	0	0.415982851591636	4		364	404	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115955	8115956	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0016627-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	117	564	0	ENST00000346208.3:c.1305dup	p.Ser436LeufsTer71	p.S436Lfs*71	ENST00000346208		434	cac/caCc	6/6	0.294700215816266	5	FACETS	1	0.982	1	0.355	0.32	0.392	CLONAL	1	TRUE	1	0.294700215816266	5		564	807	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530077	63530077	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016627-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3641	704	383	0	ENST00000307078.5:c.2358G>C	p.Leu786Phe	p.L786F	ENST00000307078	NM_004655.3	786	ttG/ttC	10/11	0.294700215816266	38	FACETS	0.99	0.95	1			1	CLONAL	7	TRUE	NA	0.294700215816266	38		383	4345	SUCCESS
BTK	695	MSKCC	GRCh37	X	100612524	100612524	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016627-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	123	451	0	ENST00000308731.7:c.1150G>A	p.Ala384Thr	p.A384T	ENST00000308731	NM_000061.2	384	Gca/Aca	13/19	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.294700215816266	2		451	581	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	184	304	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.18544850178662	6	FACETS	0.874	0.811	0.939	0.874	0.811	0.939	INDETERMINATE	3	TRUE	3	0.424967674995657	6		304	611	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0016837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	323	578	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.396662759298045	2	FACETS	0.82	0.776	0.864	0.82	0.776	0.864	CLONAL	2	TRUE	0	0.424967674995657	2		579	927	SUCCESS
YES1	7525	MSKCC	GRCh37	18	739784	739784	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	101	484	0	ENST00000314574.4:c.1088G>T	p.Gly363Val	p.G363V	ENST00000314574	NM_005433.3	363	gGa/gTa	9/12	0.294003283244987	5	FACETS	0.724	0.645	0.808			1	SUBCLONAL	1	TRUE	NA	0.424967674995657	5		484	1075	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228281	53228281	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	289	495	0	ENST00000375401.3:c.2121T>G	p.Cys707Trp	p.C707W	ENST00000375401	NM_004187.3	707	tgT/tgG	15/26	0.3881150090769	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.424967674995657	2		495	672	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048638	6048638	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs372539944	NA	P-0016837-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1309	172	836	0	ENST00000265849.7:c.13G>C	p.Glu5Gln	p.E5Q	ENST00000265849	NM_000535.5	5	Gag/Cag	1/15	0.51781671505723	5	FACETS	0.797	0.731	0.866	0.199	0.182	0.217	SUBCLONAL	1	TRUE	1	0.51781671505723	5		836	1481	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016837-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	80	304	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.215229458669634	5	FACETS	0.773	0.686	0.866	0.515	0.457	0.577	INDETERMINATE	2	TRUE	2	0.51781671505723	5		304	355	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0016837-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	262	578	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.354488109330985	2	FACETS	1	0.992	1	0.669	0.63	0.709	CLONAL	1	TRUE	0	0.51781671505723	2		579	756	SUCCESS
YES1	7525	MSKCC	GRCh37	18	739784	739784	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016837-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	46	484	0	ENST00000314574.4:c.1088G>T	p.Gly363Val	p.G363V	ENST00000314574	NM_005433.3	363	gGa/gTa	9/12	0.149325591440708	2	FACETS	0.581	0.491	0.678	0.29	0.245	0.339	INDETERMINATE	1	TRUE	0	0.51781671505723	2		484	306	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228281	53228281	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016837-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	288	495	0	ENST00000375401.3:c.2121T>G	p.Cys707Trp	p.C707W	ENST00000375401	NM_004187.3	707	tgT/tgG	15/26	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.51781671505723	2		495	793	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913355	NA	P-0016867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	91	460	0	ENST00000288602.6:c.1406G>T	p.Gly469Val	p.G469V	ENST00000288602	NM_004333.4	469	gGa/gTa	11/18	0.14618511433764	2	FACETS	0.758	0.674	0.847	0.758	0.674	0.847	SUBCLONAL	2	TRUE	0	0.2098716889351	2		460	572	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612062	189612062	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142981128	NA	P-0016867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	57	660	0	ENST00000264731.3:c.1814G>A	p.Arg605Gln	p.R605Q	ENST00000264731	NM_003722.4	605	cGg/cAg	14/14	1	2	FACETS	0.647	0.553	0.749	0.647	0.553	0.749	SUBCLONAL	1	TRUE	1	0.2098716889351	2		660	840	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221947	1221947	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	53	541	0	ENST00000326873.7:c.863-1G>T		p.X288_splice	ENST00000326873	NM_000455.4	288			1	2	FACETS	0.665	0.565	0.774	0.665	0.565	0.774	SUBCLONAL	1	TRUE	1	0.2098716889351	2		541	760	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578254	7578254	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551821	NA	P-0016867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	86	779	1	ENST00000269305.4:c.595G>T	p.Gly199Ter	p.G199*	ENST00000269305	NM_001126112.2	199	Gga/Tga	6/11	0.0667982406798129	3	FACETS	0.851	0.751	0.959			1	INDETERMINATE	1	TRUE	NA	0.2098716889351	3		780	1064	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900803	3900803	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs141982003	NA	P-0016867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	55	707	0	ENST00000262367.5:c.293G>T	p.Gly98Val	p.G98V	ENST00000262367	NM_004380.2	98	gGc/gTc	2/31	1	2	FACETS	0.584	0.498	0.679	0.584	0.498	0.679	SUBCLONAL	1	TRUE	1	0.2098716889351	2		707	897	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408882	41408882	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	104	517	0	ENST00000373198.4:c.544G>T	p.Val182Phe	p.V182F	ENST00000373198	NM_133170.3	182	Gtc/Ttc	4/32	0.2098716889351	0	FACETS	1	0.959	1			1	CLONAL	1	TRUE	0	0.2098716889351	0		517	688	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647607	3647607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483311055	NA	P-0016867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	68	734	0	ENST00000294008.3:c.1456C>T	p.Arg486Cys	p.R486C	ENST00000294008	NM_032444.2	486	Cgt/Tgt	7/15	1	2	FACETS	0.708	0.615	0.81	0.708	0.615	0.81	SUBCLONAL	1	TRUE	1	0.2098716889351	2		734	915	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933433	100933433	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	111	494	0	ENST00000325455.5:c.1957G>T	p.Ala653Ser	p.A653S	ENST00000325455	NM_001202474.3	653	Gct/Tct	4/8	NA	2	FACETS	0.776	0.698	0.857			1	INDETERMINATE	2	TRUE	NA	0.2098716889351	2		494	682	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419849	41419849	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	58	646	1	ENST00000373198.4:c.472C>A	p.Pro158Thr	p.P158T	ENST00000373198	NM_133170.3	158	Cca/Aca	3/32	0.2098716889351	0	FACETS	0.646	0.554	0.746			1	SUBCLONAL	1	TRUE	0	0.2098716889351	0		647	676	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207500	29207500	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs757228799	NA	P-0016867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	52	565	0	ENST00000240100.2:c.296C>G	p.Ser99Cys	p.S99C	ENST00000240100	NM_001394.6	99	tCc/tGc	1/4	0.2098716889351	1	FACETS	0.621	0.528	0.724	0.621	0.528	0.724	SUBCLONAL	1	TRUE	0	0.2098716889351	1		565	714	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105636	27105636	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200936451	NA	P-0016867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	78	716	0	ENST00000324856.7:c.5247G>T	p.Arg1749Ser	p.R1749S	ENST00000324856	NM_006015.4	1749	agG/agT	20/20	0.131195289402721	3	FACETS	0.732	0.641	0.83	0.366	0.32	0.415	SUBCLONAL	1	TRUE	1	0.2098716889351	3		716	1122	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731065	162731065	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	70	673	0	ENST00000367921.3:c.920G>C	p.Arg307Pro	p.R307P	ENST00000367921	NM_006182.2	307	cGc/cCc	9/18	1	2	FACETS	0.774	0.673	0.883	0.774	0.673	0.883	SUBCLONAL	1	TRUE	1	0.2098716889351	2		673	862	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248553	8248553	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs757437334	NA	P-0016867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	71	581	0	ENST00000335790.3:c.334G>C	p.Asp112His	p.D112H	ENST00000335790	NM_002315.2	112	Gac/Cac	3/4	0.2098716889351	1	FACETS	0.726	0.633	0.828	0.726	0.633	0.828	SUBCLONAL	1	TRUE	0	0.2098716889351	1		581	834	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456587	32456587	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1009810769	NA	P-0016867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	60	564	0	ENST00000332351.3:c.305G>T	p.Trp102Leu	p.W102L	ENST00000332351	NM_024426.4	102	tGg/tTg	1/10	0.2098716889351	1	FACETS	0.934	0.805	1	0.934	0.805	1	CLONAL	1	TRUE	0	0.2098716889351	1		564	548	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650587	18650587	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	80	409	0	ENST00000266497.5:c.2798T>A	p.Leu933Gln	p.L933Q	ENST00000266497		933	cTg/cAg	20/31	0.2098716889351	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.2098716889351	1		409	481	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427024	49427024	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	68	750	0	ENST00000301067.7:c.11464G>T	p.Gly3822Cys	p.G3822C	ENST00000301067	NM_003482.3	3822	Ggc/Tgc	39/54	0.152843064279243	4	FACETS	0.784	0.68	0.897	0.392	0.34	0.449	SUBCLONAL	1	TRUE	2	0.2098716889351	4		750	1000	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61305170	61305170	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	56	729	0	ENST00000341074.5:c.956G>T	p.Trp319Leu	p.W319L	ENST00000341074	NM_002974.2	319	tGg/tTg	8/8	0.2098716889351	1	FACETS	0.566	0.483	0.657	0.566	0.483	0.657	SUBCLONAL	1	TRUE	0	0.2098716889351	1		729	844	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144848	11144848	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	50	624	0	ENST00000358026.2:c.3923G>T	p.Arg1308Leu	p.R1308L	ENST00000358026	NM_001128849.1	1308	cGg/cTg	28/36	1	2	FACETS	0.548	0.463	0.641	0.548	0.463	0.641	SUBCLONAL	1	TRUE	1	0.2098716889351	2		624	870	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424990	47424990	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	92	632	0	ENST00000404338.3:c.3058G>T	p.Asp1020Tyr	p.D1020Y	ENST00000404338	NM_004491.4	1020	Gat/Tat	1/6	1	2	FACETS	0.934	0.828	1	0.934	0.828	1	CLONAL	1	TRUE	1	0.2098716889351	2		632	939	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812197	212812197	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	35	389	0	ENST00000342788.4:c.379G>T	p.Gly127Ter	p.G127*	ENST00000342788	NM_005235.2	127	Gga/Tga	3/28	NA	2	FACETS	0.654	0.535	0.788			1	INDETERMINATE	1	TRUE	NA	0.2098716889351	2		389	510	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933396	49933396	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	87	909	0	ENST00000296474.3:c.2794C>T	p.Gln932Ter	p.Q932*	ENST00000296474	NM_002447.2	932	Cag/Tag	11/20	1	2	FACETS	0.774	0.683	0.872	0.774	0.683	0.872	SUBCLONAL	1	TRUE	1	0.2098716889351	2		909	1071	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651394	52651394	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	69	496	0	ENST00000394830.3:c.1702T>G	p.Leu568Val	p.L568V	ENST00000394830	NM_018313.4	568	Ttg/Gtg	15/30	1	2	FACETS	0.896	0.779	1	0.896	0.779	1	CLONAL	1	TRUE	1	0.2098716889351	2		496	734	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911523	134911523	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	56	651	0	ENST00000398015.3:c.1990del	p.Asp664ThrfsTer3	p.D664Tfs*3	ENST00000398015	NM_004441.4	663	cGg/cg	11/16	1	2	FACETS	0.622	0.531	0.722	0.622	0.531	0.722	SUBCLONAL	1	TRUE	1	0.2098716889351	2		651	858	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539860	187539860	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374438707	NA	P-0016867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	73	717	0	ENST00000441802.2:c.7880C>T	p.Ser2627Phe	p.S2627F	ENST00000441802	NM_005245.3	2627	tCc/tTc	10/27	0.191491590766153	1	FACETS	0.717	0.625	0.815	0.717	0.625	0.815	SUBCLONAL	1	TRUE	0	0.2098716889351	1		717	869	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527342	137527342	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	31	337	0	ENST00000367739.4:c.304G>T	p.Val102Phe	p.V102F	ENST00000367739	NM_000416.2	102	Gtt/Ttt	3/7	1	2	FACETS	0.516	0.417	0.63	0.516	0.417	0.63	SUBCLONAL	1	TRUE	1	0.2098716889351	2		337	572	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336654	81336654	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0016867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	65	353	0	ENST00000222390.5:c.1568T>A	p.Leu523Ter	p.L523*	ENST00000222390	NM_000601.4	523	tTg/tAg	14/18	0.2098716889351	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.2098716889351	1		353	443	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392108	81392108	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	52	313	0	ENST00000222390.5:c.169C>A	p.Leu57Met	p.L57M	ENST00000222390	NM_000601.4	57	Ctg/Atg	2/18	0.2098716889351	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.2098716889351	1		313	364	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124532367	124532367	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1197625483	NA	P-0016867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	69	308	0	ENST00000357628.3:c.77A>G	p.Tyr26Cys	p.Y26C	ENST00000357628	NM_015450.2	26	tAt/tGt	6/19	0.14618511433764	2	FACETS	0.82	0.717	0.93	0.82	0.717	0.93	CLONAL	2	TRUE	0	0.2098716889351	2		308	401	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058587	69058587	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016867-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	32	256	0	ENST00000288368.4:c.4231G>A	p.Ala1411Thr	p.A1411T	ENST00000288368	NM_024870.2	1411	Gca/Aca	34/40	0.14618511433764	2	FACETS	0.824	0.67	0.998	0.412	0.335	0.499	CLONAL	1	TRUE	0	0.2098716889351	2		256	370	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	62	382	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.765	0.659	0.881	0.765	0.659	0.881	SUBCLONAL	1	TRUE	1	0.16	2		382	1013	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732969	30732969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893810	NA	P-0017171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	28	390	0	ENST00000295754.5:c.1582C>T	p.Arg528Cys	p.R528C	ENST00000295754	NM_003242.5	528	Cgt/Tgt	7/7	1	2	FACETS	0.941	0.752	1	0.941	0.752	1	CLONAL	1	TRUE	1	0.16	2		390	372	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs775623976	NA	P-0017171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	25	538	0	ENST00000335508.6:c.1873C>G	p.Arg625Gly	p.R625G	ENST00000335508	NM_012433.2	625	Cgt/Ggt	14/25	1	2	FACETS	0.488	0.383	0.609	0.488	0.383	0.609	SUBCLONAL	1	TRUE	1	0.16	2		538	641	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448393	56448393	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	67	709	0	ENST00000407977.2:c.254C>T	p.Ser85Phe	p.S85F	ENST00000407977		85	tCc/tTc	3/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.16	2		709	711	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018541-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	412	321	0				ENST00000310581	NM_198253.2	-/1132			0.536877990570238	7	FACETS	0.97	0.932	1	0.97	0.932	1	CLONAL	5	TRUE	2	0.536877990570238	7		321	741	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0018541-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	1370	700	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.536877990570238	9	FACETS	1	0.994	1			1	CLONAL	8	TRUE	NA	0.536877990570238	9		700	1799	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878061	48878062	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1131690852	NA	P-0018541-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	106	670	2	ENST00000267163.4:c.19dup	p.Arg7ProfsTer24	p.R7Pfs*24	ENST00000267163	NM_000321.2	5	acc/aCcc	1/27	0.536877990570238	3	FACETS	0.883	0.794	0.977	0.442	0.397	0.489	CLONAL	1	TRUE	1	0.536877990570238	3		672	567	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857925	9857925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs534440095	NA	P-0018541-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	319	688	1	ENST00000330684.3:c.3476G>A	p.Arg1159His	p.R1159H	ENST00000330684	NM_001134407.1	1159	cGc/cAc	13/13	0.535840736352414	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.536877990570238	3		689	729	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523588	41523588	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018541-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	148	553	0	ENST00000263253.7:c.1004G>A	p.Arg335His	p.R335H	ENST00000263253	NM_001429.3	335	cGc/cAc	4/31	0.535840736352414	3	FACETS	1	0.944	1	0.52	0.476	0.565	CLONAL	1	TRUE	1	0.536877990570238	3		553	673	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047305	77047305	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018541-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	146	509	0	ENST00000356341.3:c.1239G>C	p.Gln413His	p.Q413H	ENST00000356341	NM_002576.4	413	caG/caC	13/15	0.536877990570238	3	FACETS	1	0.932	1	0.51	0.467	0.556	CLONAL	1	TRUE	1	0.536877990570238	3		509	676	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879855	37879855	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018541-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	1644	778	1	ENST00000269571.5:c.2150A>T	p.Glu717Val	p.E717V	ENST00000269571		717	gAg/gTg	18/27	0.536877990570238	9	FACETS	1	0.997	1			1	CLONAL	8	TRUE	NA	0.536877990570238	9		779	2102	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47168147	47168147	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018541-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	212	287	0	ENST00000409792.3:c.78A>T	p.Glu26Asp	p.E26D	ENST00000409792	NM_014159.6	26	gaA/gaT	2/21	0.466255389151112	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.536877990570238	4		287	558	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652056	36652056	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018541-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	456	697	0	ENST00000244741.5:c.178G>T	p.Glu60Ter	p.E60*	ENST00000244741	NM_000389.4	60	Gag/Tag	2/3	0.536877990570238	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	1	0.536877990570238	4		697	860	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197077	26197077	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs373554594	NA	P-0018541-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	177	722	0	ENST00000356476.2:c.402G>C	p.Glu134Asp	p.E134D	ENST00000356476		134	gaG/gaC	1/1	0.536877990570238	4	FACETS	0.952	0.877	1	0.317	0.292	0.344	CLONAL	1	TRUE	1	0.536877990570238	4		722	1064	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	164	677	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.440389001553365	2		677	625	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435258	49435258	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1452715535	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	160	746	0	ENST00000301067.7:c.6295C>T	p.Arg2099Ter	p.R2099*	ENST00000301067	NM_003482.3	2099	Cga/Tga	31/54	1	2	FACETS	0.991	0.911	1	0.991	0.911	1	CLONAL	1	TRUE	1	0.440389001553365	2		746	733	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	120	620	6	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.739	0.668	0.815	0.739	0.668	0.815	SUBCLONAL	1	TRUE	1	0.440389001553365	2		626	737	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918596	44918597	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	140	307	0	ENST00000377967.4:c.1083_1084del	p.Tyr362Ter	p.Y362*	ENST00000377967	NM_021140.2	360	aCT/a	12/29	1	1	FACETS	0.895	0.832	0.958	1	0.992	1	CLONAL	2	TRUE	0	0.440389001553365	1		307	277	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	181	782	1	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.440389001553365	2		783	781	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	14	609	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.103	0.074	0.139	0.103	0.074	0.139	SUBCLONAL	1	TRUE	1	0.440389001553365	2		609	615	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539951	187539951	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs777631605	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	135	664	0	ENST00000441802.2:c.7789C>T	p.Arg2597Ter	p.R2597*	ENST00000441802	NM_005245.3	2597	Cga/Tga	10/27	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.440389001553365	2		664	575	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647757	2647757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201983709	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	176	612	0	ENST00000342085.4:c.1660G>A	p.Ala554Thr	p.A554T	ENST00000342085	NM_002613.4	554	Gct/Act	14/14	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.440389001553365	2		612	613	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546575	9546575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777430875	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	28	585	0	ENST00000353224.5:c.1447C>T	p.Arg483Trp	p.R483W	ENST00000353224	NM_177990.2	483	Cgg/Tgg	5/10	1	2	FACETS	0.26	0.207	0.32	0.26	0.207	0.32	SUBCLONAL	1	TRUE	1	0.440389001553365	2		585	490	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279935	18279935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	190	725	0	ENST00000222254.8:c.2018C>T	p.Thr673Met	p.T673M	ENST00000222254	NM_005027.3	673	aCg/aTg	16/16	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.440389001553365	2		725	637	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039372	47039372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	194	400	0	ENST00000377604.3:c.995G>A	p.Arg332His	p.R332H	ENST00000377604	NM_001204468.1	332	cGc/cAc	10/24	1	1	FACETS	0.926	0.871	0.98	1	0.994	1	CLONAL	2	TRUE	0	0.440389001553365	1		400	371	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070923	30070923	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145666157	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	151	583	0	ENST00000338641.4:c.1439C>T	p.Thr480Met	p.T480M	ENST00000338641	NM_000268.3	480	aCg/aTg	13/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.440389001553365	2		583	594	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842042	3842042	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783464	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	107	545	0	ENST00000262367.5:c.1270C>T	p.Arg424Ter	p.R424*	ENST00000262367	NM_004380.2	424	Cga/Tga	5/31	1	2	FACETS	0.97	0.874	1	0.97	0.874	1	CLONAL	1	TRUE	1	0.440389001553365	2		545	501	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609349	39609349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201418439	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	69	469	0	ENST00000262039.4:c.1651C>T	p.Arg551Trp	p.R551W	ENST00000262039	NM_002647.2	551	Cgg/Tgg	15/25	1	2	FACETS	0.654	0.571	0.744	0.654	0.571	0.744	SUBCLONAL	1	TRUE	1	0.440389001553365	2		469	479	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821918	72821918	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	150	766	0	ENST00000268489.5:c.10257del	p.Lys3420AsnfsTer65	p.K3420Nfs*65	ENST00000268489	NM_006885.3	3419	ccC/cc	10/10	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.440389001553365	2		766	667	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351595	89351595	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	126	688	1	ENST00000301030.4:c.1355del	p.Asn452IlefsTer3	p.N452Ifs*3	ENST00000301030	NM_001256183.1	452	aAt/at	9/13	1	2	FACETS	0.926	0.841	1	0.926	0.841	1	CLONAL	1	TRUE	1	0.440389001553365	2		689	618	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444932	49444933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767415197	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	157	868	0	ENST00000301067.7:c.2533dup	p.Arg845ProfsTer3	p.R845Pfs*3	ENST00000301067	NM_003482.3	845	cgg/cCgg	10/54	1	2	FACETS	0.893	0.819	0.971	0.893	0.819	0.971	CLONAL	1	TRUE	1	0.440389001553365	2		868	798	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948208	71948209	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs749079348	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	134	843	3	ENST00000298229.2:c.2927dup	p.Pro977ThrfsTer7	p.P977Tfs*7	ENST00000298229	NM_001567.3	974	gcc/gCcc	26/28	1	2	FACETS	0.797	0.724	0.872	0.797	0.724	0.872	SUBCLONAL	1	TRUE	1	0.440389001553365	2		846	764	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911638	114911638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1427214163	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	29	440	0	ENST00000543371.1:c.1156C>T	p.Arg386Trp	p.R386W	ENST00000543371	NM_001198531.1	386	Cgg/Tgg	10/14	1	2	FACETS	0.274	0.219	0.336	0.274	0.219	0.336	SUBCLONAL	1	TRUE	1	0.440389001553365	2		440	481	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924295	112924295	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1193000800	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	140	619	3	ENST00000351677.2:c.1241C>T	p.Thr414Met	p.T414M	ENST00000351677	NM_002834.3	414	aCg/aTg	11/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.440389001553365	2		622	577	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517412	157517412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138785718	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	114	513	0	ENST00000346085.5:c.3976C>T	p.Arg1326Cys	p.R1326C	ENST00000346085	NM_020732.3	1326	Cgc/Tgc	16/20	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.440389001553365	2		513	497	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026115	71026115	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs797045584	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	24	466	0	ENST00000318789.4:c.1507C>T	p.Arg503Ter	p.R503*	ENST00000318789	NM_032682.5	503	Cga/Tga	17/21	1	2	FACETS	0.236	0.184	0.296	0.236	0.184	0.296	SUBCLONAL	1	TRUE	1	0.440389001553365	2		466	462	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218425	36218425	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555730957	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	106	682	0	ENST00000222270.7:c.4204C>T	p.Arg1402Ter	p.R1402*	ENST00000222270	NM_014727.1	1402	Cga/Tga	16/37	1	2	FACETS	0.759	0.682	0.841	0.759	0.682	0.841	SUBCLONAL	1	TRUE	1	0.440389001553365	2		682	634	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272422	11272422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746532612	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	171	667	0	ENST00000361445.4:c.3508C>T	p.Arg1170Cys	p.R1170C	ENST00000361445	NM_004958.3	1170	Cgc/Tgc	23/58	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.440389001553365	2		667	626	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538991	187538991	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	144	752	0	ENST00000441802.2:c.8749C>T	p.Arg2917Ter	p.R2917*	ENST00000441802	NM_005245.3	2917	Cga/Tga	10/27	1	2	FACETS	0.893	0.816	0.974	0.893	0.816	0.974	CLONAL	1	TRUE	1	0.440389001553365	2		752	732	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738297	133738297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1394653602	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	188	732	0	ENST00000318560.5:c.697G>A	p.Asp233Asn	p.D233N	ENST00000318560	NM_005157.4	233	Gac/Aac	4/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.440389001553365	2		732	730	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504995	186504995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	27	528	0	ENST00000323963.5:c.851G>A	p.Arg284His	p.R284H	ENST00000323963		284	cGc/cAc	8/11	1	2	FACETS	0.246	0.195	0.305	0.246	0.195	0.305	SUBCLONAL	1	TRUE	1	0.440389001553365	2		528	498	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275708	41275708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886039332	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	136	667	0	ENST00000349496.5:c.1603C>T	p.Arg535Ter	p.R535*	ENST00000349496	NM_001904.3	535	Cga/Tga	10/15	1	2	FACETS	0.863	0.786	0.943	0.863	0.786	0.943	CLONAL	1	TRUE	1	0.440389001553365	2		667	716	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671680	67671680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201916739	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	152	373	2	ENST00000264010.4:c.2089G>A	p.Ala697Thr	p.A697T	ENST00000264010	NM_006565.3	697	Gca/Aca	12/12	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.440389001553365	2		375	654	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610103	10610103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	158	766	1	ENST00000171111.5:c.607G>A	p.Ala203Thr	p.A203T	ENST00000171111	NM_203500.1	203	Gcc/Acc	2/6	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.440389001553365	2		767	698	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942214	71942214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253875635	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	203	790	0	ENST00000298229.2:c.1478C>T	p.Thr493Met	p.T493M	ENST00000298229	NM_001567.3	493	aCg/aTg	12/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.440389001553365	2		790	791	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497892	25497892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398311586	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	158	678	0	ENST00000264709.3:c.557C>T	p.Pro186Leu	p.P186L	ENST00000264709	NM_175629.2	186	cCg/cTg	6/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.440389001553365	2		678	633	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784254	43784254	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	59	525	0	ENST00000382044.4:c.232C>T	p.Arg78Ter	p.R78*	ENST00000382044	NM_001141980.1	78	Cga/Tga	3/28	1	2	FACETS	0.582	0.502	0.67	0.582	0.502	0.67	SUBCLONAL	1	TRUE	1	0.440389001553365	2		525	460	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29442779	29442779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747273571	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	202	729	0	ENST00000544604.2:c.820C>T	p.Arg274Cys	p.R274C	ENST00000544604	NM_001206998.1	274	Cgc/Tgc	6/9	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.440389001553365	2		729	678	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510834	120510834	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	94	593	0	ENST00000256646.2:c.1130A>G	p.Asp377Gly	p.D377G	ENST00000256646	NM_024408.3	377	gAt/gGt	7/34	1	2	FACETS	0.798	0.712	0.889	0.798	0.712	0.889	SUBCLONAL	1	TRUE	1	0.440389001553365	2		593	535	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628119	90628121	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	189	934	0	ENST00000330062.3:c.1198_1200del	p.Lys400del	p.K400del	ENST00000330062	NM_002168.2	400	AAG/-	10/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.440389001553365	2		934	796	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37863389	37863389	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	150	800	0	ENST00000269571.5:c.220C>A	p.Leu74Met	p.L74M	ENST00000269571		74	Ctg/Atg	2/27	1	2	FACETS	0.908	0.831	0.989	0.908	0.831	0.989	CLONAL	1	TRUE	1	0.440389001553365	2		800	750	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184466	7184466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568470274	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	123	687	0	ENST00000302850.5:c.835C>T	p.Arg279Cys	p.R279C	ENST00000302850	NM_000208.2	279	Cgc/Tgc	3/22	1	2	FACETS	0.814	0.737	0.895	0.814	0.737	0.895	CLONAL	1	TRUE	1	0.440389001553365	2		687	686	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032425	11032425	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753002802	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	122	735	0	ENST00000327064.4:c.1819G>A	p.Gly607Arg	p.G607R	ENST00000327064	NM_199141.1	607	Ggg/Agg	16/16	1	2	FACETS	0.837	0.758	0.92	0.837	0.758	0.92	CLONAL	1	TRUE	1	0.440389001553365	2		735	662	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349652	15349652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs973091914	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	146	797	2	ENST00000263377.2:c.3922G>A	p.Ala1308Thr	p.A1308T	ENST00000263377	NM_058243.2	1308	Gcc/Acc	19/20	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.440389001553365	2		799	652	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425365	47425365	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	159	735	2	ENST00000404338.3:c.3433C>T	p.Arg1145Ter	p.R1145*	ENST00000404338	NM_004491.4	1145	Cga/Tga	1/6	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.440389001553365	2		737	692	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905986	50905986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1488821062	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	161	948	0	ENST00000440232.2:c.958G>A	p.Ala320Thr	p.A320T	ENST00000440232	NM_002691.3	320	Gcc/Acc	8/27	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.440389001553365	2		948	729	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21342386	21342386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200806641	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	107	576	0	ENST00000215739.8:c.488C>T	p.Thr163Met	p.T163M	ENST00000215739	NM_006767.3	163	aCg/aTg	5/21	1	2	FACETS	0.966	0.87	1	0.966	0.87	1	CLONAL	1	TRUE	1	0.440389001553365	2		576	503	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29445398	29445398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779789745	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	208	917	0	ENST00000544604.2:c.1229C>T	p.Pro410Leu	p.P410L	ENST00000544604	NM_001206998.1	410	cCg/cTg	8/9	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.440389001553365	2		917	833	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528546	89528546	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs376952059	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	65	336	0	ENST00000336596.2:c.2847-1G>A		p.X949_splice	ENST00000336596	NM_005233.5	949			1	2	FACETS	0.9	0.786	1	0.9	0.786	1	CLONAL	1	TRUE	1	0.440389001553365	2		336	328	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281489	142281489	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	21	503	0	ENST00000350721.4:c.755del	p.Leu252Ter	p.L252*	ENST00000350721	NM_001184.3	252	tTa/ta	4/47	1	2	FACETS	0.258	0.198	0.328	0.258	0.198	0.328	SUBCLONAL	1	TRUE	1	0.440389001553365	2		503	370	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188224	32188224	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141058087	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	164	916	0	ENST00000375023.3:c.1117C>T	p.Arg373Trp	p.R373W	ENST00000375023	NM_004557.3	373	Cgg/Tgg	6/30	1	2	FACETS	0.891	0.819	0.966	0.891	0.819	0.966	CLONAL	1	TRUE	1	0.440389001553365	2		916	836	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528595	157528595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781613431	NA	P-0019076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	163	748	0	ENST00000346085.5:c.6320G>A	p.Arg2107His	p.R2107H	ENST00000346085	NM_020732.3	2107	cGt/cAt	20/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.440389001553365	2		748	604	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0019303-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	108	579	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.254061405218838	5	FACETS	0.884	0.798	0.973	0.884	0.798	0.973	CLONAL	3	FALSE	2	0.254061405218838	5		579	443	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178646	56178646	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019303-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	11	479	0	ENST00000399503.3:c.3619C>T	p.Gln1207Ter	p.Q1207*	ENST00000399503	NM_005921.1	1207	Cag/Tag	14/20	0.254061405218838	1	FACETS	0.741	0.517	1	0.741	0.517	1	CLONAL	1	FALSE	0	0.254061405218838	1		479	102	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1555525429	NA	P-0019303-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	170	532	0	ENST00000269305.4:c.782+1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.240165912751018	3	FACETS	1	0.928	1	0.671	0.618	0.726	CLONAL	2	FALSE	0	0.254061405218838	3		532	749	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604749	48604749	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019303-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	26	538	0	ENST00000342988.3:c.1571G>A	p.Trp524Ter	p.W524*	ENST00000342988	NM_005359.5	524	tGg/tAg	12/12	0.254061405218838	2	FACETS	0.939	0.758	1	0.939	0.758	1	CLONAL	2	FALSE	0	0.254061405218838	2		538	109	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0023860-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	55	562	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	1	2	FACETS	0.83	0.71	0.961	0.83	0.71	0.961	CLONAL	1	TRUE	1	0.241972052290424	2		562	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs530941076	NA	P-0023860-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	102	923	0	ENST00000269305.4:c.658T>C	p.Tyr220His	p.Y220H	ENST00000269305	NM_001126112.2	220	Tat/Cat	6/11	0.241972052290424	1	FACETS	0.893	0.798	0.994	0.893	0.798	0.994	CLONAL	1	TRUE	0	0.241972052290424	1		923	830	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696658	47696658	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023860-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	71	698	0	ENST00000347630.2:c.290A>C	p.Glu97Ala	p.E97A	ENST00000347630	NM_001007230.1	97	gAa/gCa	5/11	0.238890868464151	3	FACETS	0.899	0.784	1	0.449	0.392	0.512	CLONAL	1	TRUE	1	0.241972052290424	3		698	732	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184785	32184785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11963697	NA	P-0023860-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	104	1016	0	ENST00000375023.3:c.1798G>A	p.Val600Ile	p.V600I	ENST00000375023	NM_004557.3	600	Gtt/Att	11/30	1	2	FACETS	0.883	0.789	0.982	0.883	0.789	0.982	CLONAL	1	TRUE	1	0.241972052290424	2		1016	974	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485900	8485900	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs201017248	NA	P-0023860-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	74	855	0	ENST00000356435.5:c.2917G>T	p.Val973Phe	p.V973F	ENST00000356435		973	Gtt/Ttt	17/35	1	2	FACETS	0.869	0.76	0.986	0.869	0.76	0.986	CLONAL	1	TRUE	1	0.241972052290424	2		855	704	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532622	46532622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	138	487	0	ENST00000262741.5:c.456del	p.Asp153MetfsTer2	p.D153Mfs*2	ENST00000262741	NM_003629.3	152	ctT/ct	4/10	NA	2	FACETS	0.617	0.562	0.675			1	INDETERMINATE	1	TRUE	NA	0.614923790153162	2		487	727	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612771	228612771	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	228	1043	0	ENST00000366696.1:c.256C>G	p.Gln86Glu	p.Q86E	ENST00000366696	NM_003493.2	86	Cag/Gag	1/1	1	2	FACETS	0.874	0.817	0.934	0.874	0.817	0.934	CLONAL	1	TRUE	1	0.614923790153162	2		1043	848	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948782	71948782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	301	897	0	ENST00000298229.2:c.3494C>T	p.Pro1165Leu	p.P1165L	ENST00000298229	NM_001567.3	1165	cCc/cTc	26/28	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.614923790153162	2		897	901	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782316	9782316	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	75	779	0	ENST00000377346.4:c.2249C>A	p.Thr750Asn	p.T750N	ENST00000377346	NM_005026.3	750	aCc/aAc	18/24	0.614923790153162	1	FACETS	0.301	0.264	0.341	0.301	0.264	0.341	SUBCLONAL	1	TRUE	0	0.614923790153162	1		779	561	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404952	404952	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	80	674	0	ENST00000399788.2:c.4242C>A	p.Ser1414Arg	p.S1414R	ENST00000399788	NM_001042603.1	1414	agC/agA	26/28	1	2	FACETS	0.267	0.234	0.302	0.267	0.234	0.302	SUBCLONAL	1	TRUE	1	0.614923790153162	2		674	976	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082286	16082286	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	118	849	0	ENST00000281043.3:c.100G>C	p.Asp34His	p.D34H	ENST00000281043	NM_005378.4	34	Gac/Cac	2/3	1	2	FACETS	0.377	0.34	0.417	0.377	0.34	0.417	SUBCLONAL	1	TRUE	1	0.614923790153162	2		849	1017	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532622	46532622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023957-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	50	487	0	ENST00000262741.5:c.456del	p.Asp153MetfsTer2	p.D153Mfs*2	ENST00000262741	NM_003629.3	152	ctT/ct	4/10	NA	2	FACETS	1	0.922	1			1	INDETERMINATE	1	TRUE	NA	0.802341029757558	2		487	116	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612771	228612771	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023957-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	39	1043	0	ENST00000366696.1:c.256C>G	p.Gln86Glu	p.Q86E	ENST00000366696	NM_003493.2	86	Cag/Gag	1/1	0.10085866471081	4	FACETS	0.826	0.705	0.953	0.826	0.705	0.953	INDETERMINATE	2	TRUE	2	0.802341029757558	4		1043	106	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948782	71948782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023957-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	77	897	0	ENST00000298229.2:c.3494C>T	p.Pro1165Leu	p.P1165L	ENST00000298229	NM_001567.3	1165	cCc/cTc	26/28	NA	2	FACETS	1	0.94	1			1	INDETERMINATE	1	TRUE	NA	0.802341029757558	2		897	180	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912616	32913011	+	inframe_deletion	In_Frame_Del	DEL	AGGGAAACACTCAGATTAAAGAAGATTTGTCAGATTTAACTTTTTTGGAAGTTGCGAAAGCTCAAGAAGCATGTCATGGTAATACTTCAAATAAAGAACAGTTAACTGCTACTAAAACGGAGCAAAATATAAAAGATTTTGAGACTTCTGATACATTTTTTCAGACTGCAAGTGGGAAAAATATTAGTGTCGCCAAAGAGTCATTTAATAAAATTGTAAATTTCTTTGATCAGAAACCAGAAGAATTGCATAACTTTTCCTTAAATTCTGAATTACATTCTGACATAAGAAAGAACAAAATGGACATTCTAAGTTATGAGGAAACAGACATAGTTAAACACAAAATACTGAAAGAAAGTGTCCCAGTTGGTACTGGAAATCAACTAGTGACCTTCC	AGGGAAACACTCAGATTAAAGAAGATTTGTCAGATTTAACTTTTTTGGAAGTTGCGAAAGCTCAAGAAGCATGTCATGGTAATACTTCAAATAAAGAACAGTTAACTGCTACTAAAACGGAGCAAAATATAAAAGATTTTGAGACTTCTGATACATTTTTTCAGACTGCAAGTGGGAAAAATATTAGTGTCGCCAAAGAGTCATTTAATAAAATTGTAAATTTCTTTGATCAGAAACCAGAAGAATTGCATAACTTTTCCTTAAATTCTGAATTACATTCTGACATAAGAAAGAACAAAATGGACATTCTAAGTTATGAGGAAACAGACATAGTTAAACACAAAATACTGAAAGAAAGTGTCCCAGTTGGTACTGGAAATCAACTAGTGACCTTCC	-	novel	NA	P-0023957-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	21	480	0	ENST00000380152.3:c.4129_4524del	p.Asn1377_Gly1508del	p.N1377_G1508del	ENST00000380152		1375	gAGGGAAACACTCAGATTAAAGAAGATTTGTCAGATTTAACTTTTTTGGAAGTTGCGAAAGCTCAAGAAGCATGTCATGGTAATACTTCAAATAAAGAACAGTTAACTGCTACTAAAACGGAGCAAAATATAAAAGATTTTGAGACTTCTGATACATTTTTTCAGACTGCAAGTGGGAAAAATATTAGTGTCGCCAAAGAGTCATTTAATAAAATTGTAAATTTCTTTGATCAGAAACCAGAAGAATTGCATAACTTTTCCTTAAATTCTGAATTACATTCTGACATAAGAAAGAACAAAATGGACATTCTAAGTTATGAGGAAACAGACATAGTTAAACACAAAATACTGAAAGAAAGTGTCCCAGTTGGTACTGGAAATCAACTAGTGACCTTCCag/gag	11/27	0.814040960600365	1	FACETS	0.825	0.682	0.964	0.825	0.682	0.964	CLONAL	1	TRUE	0	0.802341029757558	1		480	38	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169977829	169977829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023957-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	40	332	0	ENST00000295797.4:c.296C>T	p.Ser99Phe	p.S99F	ENST00000295797	NM_002740.5	99	tCt/tTt	3/18	0.395063410262049	4	FACETS	0.912	0.767	1			1	INDETERMINATE	1	TRUE	NA	0.802341029757558	4		332	197	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023957-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	71	692	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.814040960600365	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.802341029757558	1		692	101	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023957-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	11	706	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.814040960600365	1	FACETS	0.163	0.113	0.223	0.163	0.113	0.223	SUBCLONAL	1	TRUE	0	0.802341029757558	1		706	101	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045639	26045639	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs753541483	NA	P-0023957-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	16	609	0	ENST00000540144.1:c.1A>G	p.Met1?	p.M1?	ENST00000540144	NM_003531.2	1	Atg/Gtg	1/1	0.275204174953319	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.802341029757558	0		609	110	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532622	46532622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023957-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	282	487	0	ENST00000262741.5:c.456del	p.Asp153MetfsTer2	p.D153Mfs*2	ENST00000262741	NM_003629.3	152	ctT/ct	4/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.943264526313741	2		487	578	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612771	228612771	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023957-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	387	1043	0	ENST00000366696.1:c.256C>G	p.Gln86Glu	p.Q86E	ENST00000366696	NM_003493.2	86	Cag/Gag	1/1	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.943264526313741	2		1043	817	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948782	71948782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023957-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	499	897	0	ENST00000298229.2:c.3494C>T	p.Pro1165Leu	p.P1165L	ENST00000298229	NM_001567.3	1165	cCc/cTc	26/28	NA	2	FACETS	0.96	0.922	0.998			1	INDETERMINATE	1	TRUE	NA	0.943264526313741	2		897	1102	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912616	32913011	+	inframe_deletion	In_Frame_Del	DEL	AGGGAAACACTCAGATTAAAGAAGATTTGTCAGATTTAACTTTTTTGGAAGTTGCGAAAGCTCAAGAAGCATGTCATGGTAATACTTCAAATAAAGAACAGTTAACTGCTACTAAAACGGAGCAAAATATAAAAGATTTTGAGACTTCTGATACATTTTTTCAGACTGCAAGTGGGAAAAATATTAGTGTCGCCAAAGAGTCATTTAATAAAATTGTAAATTTCTTTGATCAGAAACCAGAAGAATTGCATAACTTTTCCTTAAATTCTGAATTACATTCTGACATAAGAAAGAACAAAATGGACATTCTAAGTTATGAGGAAACAGACATAGTTAAACACAAAATACTGAAAGAAAGTGTCCCAGTTGGTACTGGAAATCAACTAGTGACCTTCC	AGGGAAACACTCAGATTAAAGAAGATTTGTCAGATTTAACTTTTTTGGAAGTTGCGAAAGCTCAAGAAGCATGTCATGGTAATACTTCAAATAAAGAACAGTTAACTGCTACTAAAACGGAGCAAAATATAAAAGATTTTGAGACTTCTGATACATTTTTTCAGACTGCAAGTGGGAAAAATATTAGTGTCGCCAAAGAGTCATTTAATAAAATTGTAAATTTCTTTGATCAGAAACCAGAAGAATTGCATAACTTTTCCTTAAATTCTGAATTACATTCTGACATAAGAAAGAACAAAATGGACATTCTAAGTTATGAGGAAACAGACATAGTTAAACACAAAATACTGAAAGAAAGTGTCCCAGTTGGTACTGGAAATCAACTAGTGACCTTCC	-	novel	NA	P-0023957-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	90	480	0	ENST00000380152.3:c.4129_4524del	p.Asn1377_Gly1508del	p.N1377_G1508del	ENST00000380152		1375	gAGGGAAACACTCAGATTAAAGAAGATTTGTCAGATTTAACTTTTTTGGAAGTTGCGAAAGCTCAAGAAGCATGTCATGGTAATACTTCAAATAAAGAACAGTTAACTGCTACTAAAACGGAGCAAAATATAAAAGATTTTGAGACTTCTGATACATTTTTTCAGACTGCAAGTGGGAAAAATATTAGTGTCGCCAAAGAGTCATTTAATAAAATTGTAAATTTCTTTGATCAGAAACCAGAAGAATTGCATAACTTTTCCTTAAATTCTGAATTACATTCTGACATAAGAAAGAACAAAATGGACATTCTAAGTTATGAGGAAACAGACATAGTTAAACACAAAATACTGAAAGAAAGTGTCCCAGTTGGTACTGGAAATCAACTAGTGACCTTCCag/gag	11/27	0.943264526313741	1	FACETS	0.854	0.8	0.904	0.854	0.8	0.904	CLONAL	1	TRUE	0	0.943264526313741	1		480	118	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347199	73347827	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTAATGTTCAAGTTTAAAATGTGCTTCCAATATAATCTTTTCAAAATTTGTTGATTAGAATCTATATAGAACTCACTTTTCATAGTCATGATCAATAAAACTTATAGGTTTAAAAACTTACATAAAAGAGGCCAGGCACATTGGCTCATGCCTGTAATCTCAGCATTTTGGGAGGCTGAGGTGGGTGGATCACTTGAGGCCAGTTCAAGACCAGCCTGGCCAACACAGCGAAACCCTATGTCTACTAAAAATTAGCTGGGCACGGTAGTGCACGCCTGTAGTCCCAGCTAATCGGGAGGCTGAGACACAAGAATCGCTTGAACCTGGGAGGCTGAGGGTGCAGTGGGCCGAAATCACAGAACTGCACTCCAGCCGGGGCAACAGGGTGAGACTCTCTCTCAAAAAGAAGAAATTTACATAAAAGTAACCAAATGATTTACACTGGAATTTCATAAAATTAATTTTCAAAGTAGACATGCTACTTACCAGGTCACTTTGTGAAATATCTCTAAATTTCAGTACAAATTCTACATAAAAGTAGATTGTTTTTATTAAAAGCAGAAATACTATTCACAAAATTTTAATTAAACATCCCCACATAAAATTAATACTTTAAGCTTACATTTGG	ATTAATGTTCAAGTTTAAAATGTGCTTCCAATATAATCTTTTCAAAATTTGTTGATTAGAATCTATATAGAACTCACTTTTCATAGTCATGATCAATAAAACTTATAGGTTTAAAAACTTACATAAAAGAGGCCAGGCACATTGGCTCATGCCTGTAATCTCAGCATTTTGGGAGGCTGAGGTGGGTGGATCACTTGAGGCCAGTTCAAGACCAGCCTGGCCAACACAGCGAAACCCTATGTCTACTAAAAATTAGCTGGGCACGGTAGTGCACGCCTGTAGTCCCAGCTAATCGGGAGGCTGAGACACAAGAATCGCTTGAACCTGGGAGGCTGAGGGTGCAGTGGGCCGAAATCACAGAACTGCACTCCAGCCGGGGCAACAGGGTGAGACTCTCTCTCAAAAAGAAGAAATTTACATAAAAGTAACCAAATGATTTACACTGGAATTTCATAAAATTAATTTTCAAAGTAGACATGCTACTTACCAGGTCACTTTGTGAAATATCTCTAAATTTCAGTACAAATTCTACATAAAAGTAGATTGTTTTTATTAAAAGCAGAAATACTATTCACAAAATTTTAATTAAACATCCCCACATAAAATTAATACTTTAAGCTTACATTTGG	-	novel	NA	P-0023957-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	31	35	0	ENST00000377767.4:c.1234_1240-222del		p.X412_splice	ENST00000377767	NM_014953.3	412		8/21	0.943264526313741	3	FACETS	1	0.935	1	0.628	0.527	0.733	CLONAL	1	TRUE	1	0.943264526313741	3		35	77	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169977829	169977829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023957-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	182	332	0	ENST00000295797.4:c.296C>T	p.Ser99Phe	p.S99F	ENST00000295797	NM_002740.5	99	tCt/tTt	3/18	0.840980944725691	3	FACETS	0.723	0.669	0.78	0.362	0.334	0.39	SUBCLONAL	1	TRUE	1	0.943264526313741	3		332	785	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023957-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	267	692	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.943264526313741	1	FACETS	0.815	0.783	0.846	0.815	0.783	0.846	CLONAL	1	TRUE	0	0.943264526313741	1		692	367	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023957-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	69	706	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.943264526313741	1	FACETS	0.207	0.181	0.234	0.207	0.181	0.234	SUBCLONAL	1	TRUE	0	0.943264526313741	1		706	374	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653842	89653842	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1114167670	NA	P-0024129-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	197	302	0	ENST00000371953.3:c.141del	p.Asn48ThrfsTer6	p.N48Tfs*6	ENST00000371953	NM_000314.4	47	aGg/ag	2/9	0.849593499490111	2	FACETS	0.946	0.909	0.981	0.946	0.909	0.981	CLONAL	2	TRUE	0	0.849593499490111	2		302	245	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260316	149260316	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024129-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	370	510	0	ENST00000360632.3:c.577C>A	p.His193Asn	p.H193N	ENST00000360632	NM_015472.4	193	Cac/Aac	4/7	0.849593499490111	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.849593499490111	2		510	420	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0024129-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	355	485	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.849593499490111	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.849593499490111	2		485	414	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595519	55595519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913516	NA	P-0024129-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	163	461	0	ENST00000288135.5:c.2009C>T	p.Thr670Ile	p.T670I	ENST00000288135	NM_000222.2	670	aCa/aTa	14/21	0.849593499490111	2	FACETS	1	0.945	1	0.509	0.473	0.545	CLONAL	1	TRUE	0	0.849593499490111	2		461	377	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0025989-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	108	300	0	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	1	2	FACETS	0.867	0.783	0.954	0.867	0.783	0.954	CLONAL	1	TRUE	1	0.572719573817325	2		300	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578237	7578237	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025989-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	383	534	0	ENST00000269305.4:c.612G>C	p.Glu204Asp	p.E204D	ENST00000269305	NM_001126112.2	204	gaG/gaC	6/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.572719573817325	2		534	1290	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593594	55593647	+	inframe_deletion	In_Frame_Del	DEL	GAAGTACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATA	GAAGTACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATA	-	novel	NA	P-0025989-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	76	298	0	ENST00000288135.5:c.1662_1715del	p.Glu554_Ile571del	p.E554_I571del	ENST00000288135	NM_000222.2	554	GAAGTACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATA/-	11/21	1	2	FACETS	0.822	0.727	0.922	0.822	0.727	0.922	CLONAL	1	TRUE	1	0.572719573817325	2		298	323	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317321	87317321	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025989-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	77	371	0	ENST00000277120.3:c.346A>T	p.Asn116Tyr	p.N116Y	ENST00000277120		116	Aac/Tac	4/19	1	2	FACETS	0.741	0.655	0.832	0.741	0.655	0.832	SUBCLONAL	1	TRUE	1	0.572719573817325	2		371	363	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	116	321	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.91	2		321	231	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0026207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	52	544	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.411	0.352	0.474	0.411	0.352	0.474	SUBCLONAL	1	TRUE	1	0.91	2		544	278	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0026207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	155	277	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.987	0.918	1	0.987	0.918	1	CLONAL	1	TRUE	1	0.91	2		277	345	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981775	201981776	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	295	500	0	ENST00000359651.3:c.487dup	p.Ser163LysfsTer33	p.S163Kfs*33	ENST00000359651		162	-/A	4/8	1	2	FACETS	0.892	0.844	0.94	0.892	0.844	0.94	CLONAL	1	TRUE	1	0.91	2		500	727	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041016	42041016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1231328415	NA	P-0026207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	96	622	1	ENST00000219905.7:c.5394G>A	p.Met1798Ile	p.M1798I	ENST00000219905	NM_001164273.1	1798	atG/atA	16/24	1	2	FACETS	0.281	0.25	0.314	0.281	0.25	0.314	SUBCLONAL	1	TRUE	1	0.91	2		623	750	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720360	43720360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	304	465	0	ENST00000382044.4:c.3682G>A	p.Glu1228Lys	p.E1228K	ENST00000382044	NM_001141980.1	1228	Gaa/Aaa	18/28	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.91	2		465	668	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786652	3786652	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	353	442	0	ENST00000262367.5:c.4559A>T	p.Lys1520Met	p.K1520M	ENST00000262367	NM_004380.2	1520	aAg/aTg	27/31	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.91	2		442	750	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101091	26101091	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0026207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	226	351	0	ENST00000435504.4:c.1A>G	p.Met1?	p.M1?	ENST00000435504		1	Atg/Gtg	1/13	1	2	FACETS	0.937	0.881	0.994	0.937	0.881	0.994	CLONAL	1	TRUE	1	0.91	2		351	530	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44515577	44515577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	188	563	0	ENST00000291552.4:c.319G>A	p.Asp107Asn	p.D107N	ENST00000291552	NM_006758.2	107	Gac/Aac	5/8	1	2	FACETS	0.504	0.466	0.543	0.504	0.466	0.543	SUBCLONAL	1	TRUE	1	0.91	2		563	820	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568569	41568569	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	237	635	0	ENST00000263253.7:c.4519G>A	p.Asp1507Asn	p.D1507N	ENST00000263253	NM_001429.3	1507	Gat/Aat	28/31	1	2	FACETS	0.956	0.901	1	0.956	0.901	1	CLONAL	1	TRUE	1	0.91	2		635	545	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913381	NA	P-0026207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	163	167	0	ENST00000304494.5:c.322G>T	p.Asp108Tyr	p.D108Y	ENST00000304494	NM_000077.4	108	Gat/Tat	2/3	1	2	FACETS	0.995	0.927	1	0.995	0.927	1	CLONAL	1	TRUE	1	0.91	2		167	360	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942808	44942809	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0026207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	264	560	0	ENST00000377967.4:c.3388_3389insTT	p.Asn1130IlefsTer8	p.N1130Ifs*8	ENST00000377967	NM_021140.2	1130	aac/aTTac	23/29	1	2	FACETS	0.911	0.86	0.962	0.911	0.86	0.962	CLONAL	1	TRUE	1	0.91	2		560	637	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649623	48649623	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	68	636	0	ENST00000376670.3:c.107C>G	p.Ser36Cys	p.S36C	ENST00000376670	NM_002049.3	36	tCt/tGt	2/6	1	2	FACETS	0.17	0.147	0.195	0.17	0.147	0.195	SUBCLONAL	1	TRUE	1	0.91	2		636	880	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179031	123179037	+	frameshift_variant	Frame_Shift_Del	DEL	ACTTACC	ACTTACC	TAA	novel	NA	P-0026207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	91	564	1	ENST00000218089.9:c.480_486delinsTAA	p.Leu161LysfsTer21	p.L161Kfs*21	ENST00000218089	NM_001042749.1	160	ccACTTACC/ccTAA	8/35	1	2	FACETS	0.621	0.557	0.688	0.621	0.557	0.688	SUBCLONAL	1	TRUE	1	0.91	2		565	322	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0026685-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	94	377	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.600962511891386	4	FACETS	0.902	0.825	0.98	0.902	0.825	0.98	CLONAL	3	TRUE	1	0.600962511891386	4		377	185	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692941	89692941	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026685-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	129	620	0	ENST00000371953.3:c.428del	p.Gly143AlafsTer4	p.G143Afs*4	ENST00000371953	NM_000314.4	142	cGg/cg	5/9	0.600962511891386	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.600962511891386	3		620	236	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720822	89720822	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1554825602	NA	P-0026685-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	30	193	0	ENST00000371953.3:c.973del	p.Asp326ThrfsTer18	p.D326Tfs*18	ENST00000371953	NM_000314.4	325	Ctt/tt	8/9	0.600962511891386	3	FACETS	1	0.878	1	0.546	0.448	0.651	CLONAL	1	TRUE	1	0.600962511891386	3		193	119	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480583	123480583	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026685-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	44	579	0	ENST00000371139.4:c.91del	p.Leu31Ter	p.L31*	ENST00000371139	NM_001114937.2	31	Ctg/tg	1/4	0.455358264934723	1	FACETS	0.674	0.576	0.778	0.674	0.576	0.778	SUBCLONAL	1	TRUE	0	0.600962511891386	1		579	152	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0026685-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	111	377	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.509149595115022	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	FALSE	2	0.592660311562873	4		377	253	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692941	89692941	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026685-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	118	620	0	ENST00000371953.3:c.428del	p.Gly143AlafsTer4	p.G143Afs*4	ENST00000371953	NM_000314.4	142	cGg/cg	5/9	0.593561879214162	3	FACETS	0.935	0.859	1	0.935	0.859	1	CLONAL	2	FALSE	1	0.592660311562873	3		620	276	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720822	89720822	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1554825602	NA	P-0026685-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	17	193	0	ENST00000371953.3:c.973del	p.Asp326ThrfsTer18	p.D326Tfs*18	ENST00000371953	NM_000314.4	325	Ctt/tt	8/9	0.593561879214162	3	FACETS	0.8	0.607	1	0.4	0.303	0.51	CLONAL	1	FALSE	1	0.592660311562873	3		193	93	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480583	123480583	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026685-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	49	579	0	ENST00000371139.4:c.91del	p.Leu31Ter	p.L31*	ENST00000371139	NM_001114937.2	31	Ctg/tg	1/4	0.227382945334728	0	FACETS	0.335	0.287	0.386			1	INDETERMINATE	1	FALSE	0	0.592660311562873	0		579	201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0028963-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	234	458	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.812994759462609	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.812994759462609	1		458	325	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089782	5089782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028963-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	94	318	0	ENST00000381652.3:c.2680G>A	p.Asp894Asn	p.D894N	ENST00000381652	NM_004972.3	894	Gac/Aac	20/25	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.812994759462609	2		318	212	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541572	29541572	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1555612288	NA	P-0028963-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	33	162	0	ENST00000356175.3:c.1496T>G	p.Leu499Arg	p.L499R	ENST00000356175	NM_000267.3	499	cTa/cGa	13/57	0.812994759462609	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.812994759462609	1		162	42	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21350158	21350158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555928965	NA	P-0030387-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	129	528	0	ENST00000215739.8:c.2066C>T	p.Ser689Phe	p.S689F	ENST00000215739	NM_006767.3	689	tCc/tTc	17/21	0.359982708701147	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.359982708701147	1		528	547	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1555525429	NA	P-0031443-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	233	532	0	ENST00000269305.4:c.782+1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.746203919451655	1	FACETS	0.969	0.92	1	0.969	0.92	1	CLONAL	1	TRUE	0	0.746203919451655	1		532	404	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171714	36171714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031443-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	375	581	0	ENST00000300305.3:c.851C>T	p.Ser284Phe	p.S284F	ENST00000300305		284	tCc/tTc	7/8	0.396522851418308	3	FACETS	1	0.994	1	0.433	0.411	0.455	INDETERMINATE	1	TRUE	0	0.746203919451655	3		581	1063	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164757	47164757	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031443-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	152	484	0	ENST00000409792.3:c.1369G>A	p.Glu457Lys	p.E457K	ENST00000409792	NM_014159.6	457	Gag/Aag	3/21	1	2	FACETS	0.52	0.476	0.566	0.52	0.476	0.566	SUBCLONAL	1	TRUE	1	0.746203919451655	2		484	784	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970922	21971023	+	frameshift_variant	Frame_Shift_Del	DEL	CTATGCGGGCATGGTTACTGCCTCTGGTGCCCCCCGCAGCCGCGCGCAGGTACCGTGCGACATCGCGATGGCCCAGCTCCTCAGCCAGGTCCACGGGCAGAC	CTATGCGGGCATGGTTACTGCCTCTGGTGCCCCCCGCAGCCGCGCGCAGGTACCGTGCGACATCGCGATGGCCCAGCTCCTCAGCCAGGTCCACGGGCAGAC	AT	novel	NA	P-0031443-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	103	759	2	ENST00000304494.5:c.335_436delinsAT	p.Arg112HisfsTer48	p.R112Hfs*48	ENST00000304494	NM_000077.4	112	cGTCTGCCCGTGGACCTGGCTGAGGAGCTGGGCCATCGCGATGTCGCACGGTACCTGCGCGCGGCTGCGGGGGGCACCAGAGGCAGTAACCATGCCCGCATAGat/cATat	2/3	0.746203919451655	1	FACETS	0.558	0.506	0.612	0.558	0.506	0.612	SUBCLONAL	1	TRUE	0	0.746203919451655	1		761	310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0031710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	295	510	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.624076403681345	5	FACETS	0.926	0.895	0.957			1	CLONAL	5	TRUE	NA	0.660113154256122	5		510	384	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059246	27059246	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs927444249	NA	P-0031710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	210	280	0	ENST00000324856.7:c.1883T>C	p.Met628Thr	p.M628T	ENST00000324856	NM_006015.4	628	aTg/aCg	4/20	0.638500409461924	3	FACETS	0.922	0.879	0.963	0.922	0.879	0.963	CLONAL	3	TRUE	0	0.660113154256122	3		280	306	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059259	27059265	+	frameshift_variant	Frame_Shift_Del	DEL	TCAGTCA	TCAGTCA	-	novel	NA	P-0031710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	207	294	0	ENST00000324856.7:c.1896_1902del	p.Gln633AspfsTer12	p.Q633Dfs*12	ENST00000324856	NM_006015.4	632	ctTCAGTCA/ct	4/20	0.638500409461924	3	FACETS	0.906	0.862	0.948	0.906	0.862	0.948	CLONAL	3	TRUE	0	0.660113154256122	3		294	307	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986928	36986928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	49	414	0	ENST00000354822.5:c.761C>T	p.Ala254Val	p.A254V	ENST00000354822	NM_001079668.2	254	gCg/gTg	3/3	NA	2	FACETS	0.731	0.627	0.842			1	INDETERMINATE	1	TRUE	NA	0.660113154256122	2		414	203	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253427	226253427	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031710-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	28	49	0	ENST00000366813.1:c.201del	p.Phe68SerfsTer51	p.F68Sfs*51	ENST00000366813		67	Ccc/cc	2/3	0.660113154256122	4	FACETS	1	0.941	1	0.726	0.595	0.867	CLONAL	1	TRUE	2	0.660113154256122	4		49	97	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576880	7576883	+	frameshift_variant	Frame_Shift_Del	DEL	TGGT	TGGT	-	novel	NA	P-0031748-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	34	685	0	ENST00000269305.4:c.963_966del	p.Lys321AsnfsTer23	p.K321Nfs*23	ENST00000269305	NM_001126112.2	321	aaACCA/aa	9/11	1	2	FACETS	0.711	0.579	0.859	0.711	0.579	0.859	SUBCLONAL	1	TRUE	1	0.16	2		685	598	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772375	56772376	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0031748-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	49	529	0	ENST00000337432.4:c.229_230delinsTT	p.Gly77Phe	p.G77F	ENST00000337432	NM_058216.2	77	GGt/TTt	2/9	1	2	FACETS	0.988	0.836	1	0.988	0.836	1	CLONAL	1	TRUE	1	0.16	2		529	620	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625438	69625438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032111-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	58	810	0	ENST00000334134.2:c.355G>A	p.Glu119Lys	p.E119K	ENST00000334134	NM_005247.2	119	Gag/Aag	3/3	0.303596010722762	16	FACETS	1	0.947	1	0.088	0.075	0.102	CLONAL	1	TRUE	2	0.33	16		810	944	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934576	NA	P-0032111-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	114	797	0	ENST00000269305.4:c.818G>C	p.Arg273Pro	p.R273P	ENST00000269305	NM_001126112.2	273	cGt/cCt	8/11	0.286625912217711	4	FACETS	0.77	0.695	0.848	0.513	0.463	0.566	SUBCLONAL	2	TRUE	1	0.33	4		797	597	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89846317	89846317	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032111-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	34	770	0	ENST00000389301.3:c.1675G>C	p.Glu559Gln	p.E559Q	ENST00000389301	NM_000135.2	559	Gag/Cag	18/43	0.303596010722762	7	FACETS	0.669	0.546	0.809	0.167	0.136	0.203	SUBCLONAL	1	TRUE	3	0.33	7		770	562	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416500	49416500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032111-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	119	850	0	ENST00000301067.7:c.16211C>T	p.Ser5404Phe	p.S5404F	ENST00000301067	NM_003482.3	5404	tCc/tTc	51/54	0.303596010722762	12	FACETS	1	0.955	1	0.367	0.331	0.406	CLONAL	2	TRUE	6	0.33	12		850	867	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440058	49440058	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032111-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	95	902	0	ENST00000301067.7:c.4568G>A	p.Cys1523Tyr	p.C1523Y	ENST00000301067	NM_003482.3	1523	tGc/tAc	16/54	0.303596010722762	12	FACETS	1	0.951	1	0.373	0.332	0.417	CLONAL	2	TRUE	6	0.33	12		902	681	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857892	9857892	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032111-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	52	817	0	ENST00000330684.3:c.3509A>T	p.Asn1170Ile	p.N1170I	ENST00000330684	NM_001134407.1	1170	aAc/aTc	13/13	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.33	2		817	305	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096569	178096569	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032111-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	55	603	0	ENST00000397062.3:c.762C>A	p.Phe254Leu	p.F254L	ENST00000397062	NM_006164.4	254	ttC/ttA	5/5	0.246404220049916	1	FACETS	0.482	0.412	0.559	0.482	0.412	0.559	SUBCLONAL	1	TRUE	0	0.33	1		603	577	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129466	152129466	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032111-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	46	729	0	ENST00000206249.3:c.419C>G	p.Thr140Arg	p.T140R	ENST00000206249	NM_000125.3	140	aCg/aGg	1/8	0.303596010722762	3	FACETS	0.781	0.665	0.905	0.781	0.665	0.905	CLONAL	2	TRUE	1	0.33	3		729	208	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455642	189455642	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032111-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	17	487	0	ENST00000264731.3:c.176G>T	p.Trp59Leu	p.W59L	ENST00000264731	NM_003722.4	59	tGg/tTg	2/14	0.303596010722762	3	FACETS	0.504	0.377	0.655	0.252	0.188	0.328	SUBCLONAL	1	TRUE	1	0.33	3		487	238	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808931	3808936	+	frameshift_variant	Frame_Shift_Ins	INS	AGGGTT	AGGGTT	GTATCATGCCA	novel	NA	P-0032111-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	57	570	0	ENST00000262367.5:c.3288_3293delinsTGGCATGATAC	p.Thr1097GlyfsTer21	p.T1097Gfs*21	ENST00000262367	NM_004380.2	1096	ccAACCCTa/ccTGGCATGATACa	17/31	0.303596010722762	7	FACETS	1	0.955	1	0.323	0.277	0.373	CLONAL	1	TRUE	3	0.33	7		570	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934576	NA	P-0032111-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	39	797	0	ENST00000269305.4:c.818G>C	p.Arg273Pro	p.R273P	ENST00000269305	NM_001126112.2	273	cGt/cCt	8/11	0.448105236151671	3	FACETS	0.483	0.4	0.575	0.242	0.2	0.288	SUBCLONAL	1	FALSE	1	0.448105236151671	3		797	441	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89846317	89846317	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032111-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	21	770	0	ENST00000389301.3:c.1675G>C	p.Glu559Gln	p.E559Q	ENST00000389301	NM_000135.2	559	Gag/Cag	18/43	0.448105236151671	3	FACETS	0.365	0.281	0.464	0.183	0.14	0.232	SUBCLONAL	1	FALSE	1	0.448105236151671	3		770	314	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416500	49416500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032111-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	26	850	0	ENST00000301067.7:c.16211C>T	p.Ser5404Phe	p.S5404F	ENST00000301067	NM_003482.3	5404	tCc/tTc	51/54	0.448105236151671	6	FACETS	0.437	0.345	0.543	0.146	0.115	0.181	SUBCLONAL	1	FALSE	3	0.448105236151671	6		850	503	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440058	49440058	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032111-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	35	902	0	ENST00000301067.7:c.4568G>A	p.Cys1523Tyr	p.C1523Y	ENST00000301067	NM_003482.3	1523	tGc/tAc	16/54	0.448105236151671	6	FACETS	0.869	0.714	1	0.29	0.238	0.348	CLONAL	1	FALSE	3	0.448105236151671	6		902	341	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857892	9857892	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032111-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	15	817	0	ENST00000330684.3:c.3509A>T	p.Asn1170Ile	p.N1170I	ENST00000330684	NM_001134407.1	1170	aAc/aTc	13/13	0.448105236151671	3	FACETS	0.301	0.22	0.399	0.151	0.11	0.2	SUBCLONAL	1	FALSE	1	0.448105236151671	3		817	272	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096569	178096569	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032111-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	13	603	0	ENST00000397062.3:c.762C>A	p.Phe254Leu	p.F254L	ENST00000397062	NM_006164.4	254	ttC/ttA	5/5	1	2	FACETS	0.299	0.213	0.403	0.299	0.213	0.403	SUBCLONAL	1	FALSE	1	0.448105236151671	2		603	194	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129466	152129466	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032111-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	16	729	0	ENST00000206249.3:c.419C>G	p.Thr140Arg	p.T140R	ENST00000206249	NM_000125.3	140	aCg/aGg	1/8	0.312959343206435	3	FACETS	0.499	0.371	0.652	0.25	0.185	0.326	SUBCLONAL	1	FALSE	1	0.448105236151671	3		729	175	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808931	3808936	+	frameshift_variant	Frame_Shift_Ins	INS	AGGGTT	AGGGTT	GTATCATGCCA	novel	NA	P-0032111-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	22	570	0	ENST00000262367.5:c.3288_3293delinsTGGCATGATAC	p.Thr1097GlyfsTer21	p.T1097Gfs*21	ENST00000262367	NM_004380.2	1096	ccAACCCTa/ccTGGCATGATACa	17/31	0.448105236151671	3	FACETS	0.466	0.362	0.586	0.233	0.181	0.293	SUBCLONAL	1	FALSE	1	0.448105236151671	3		570	258	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0032683-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	202	416	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.248270022045459	3	FACETS	1	0.976	1	0.736	0.685	0.787	CLONAL	2	TRUE	0	0.324910190608134	3		416	655	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0033313-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	472	579	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.965958706743613	7	FACETS	1	0.993	1	0.886	0.861	0.91	CLONAL	5	TRUE	1	0.965958706743613	7		579	628	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0033313-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	295	819	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.649701561090143	3	FACETS	0.993	0.979	1			1	CLONAL	3	TRUE	NA	0.965958706743613	3		819	304	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976787	2976787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033313-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	66	709	0	ENST00000396946.4:c.1225G>A	p.Glu409Lys	p.E409K	ENST00000396946	NM_032415.4	409	Gag/Aag	9/25	0.965958706743613	8	FACETS	0.6	0.519	0.688	0.1	0.086	0.115	SUBCLONAL	1	TRUE	2	0.965958706743613	8		709	888	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261278	115261278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033767-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	279	542	0	ENST00000438362.2:c.2443C>T	p.Arg815Cys	p.R815C	ENST00000438362	NM_001242891.1	815	Cgc/Tgc	19/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.706739671744814	2		542	739	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89724870	89725106	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTTAAGAAGAGGGTCATTTAAAAGGCCTCTTAAAGATCATGTTTGTTACAGTGCTTAAAAATTAATATGTTCATCTGCAAAATGGAATAAAAAATCTGTTAAAAATATATTTCACTAAATAGTTTAAGATGAGTCATATTTGTGGGTTTTCATTTTAAATTTTCTTTCTCTAGGTGAAGCTGTACTTCACAAAAACAGTAGAGGAGCCGTCAAATCCAGAGGCTAGCAGTTCAACT	TCTTAAGAAGAGGGTCATTTAAAAGGCCTCTTAAAGATCATGTTTGTTACAGTGCTTAAAAATTAATATGTTCATCTGCAAAATGGAATAAAAAATCTGTTAAAAATATATTTCACTAAATAGTTTAAGATGAGTCATATTTGTGGGTTTTCATTTTAAATTTTCTTTCTCTAGGTGAAGCTGTACTTCACAAAAACAGTAGAGGAGCCGTCAAATCCAGAGGCTAGCAGTTCAACT	-	novel	NA	P-0033767-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	86	78	0	ENST00000371953.3:c.1027-171_1092del		p.X343_splice	ENST00000371953	NM_000314.4	343		9/9	0.705040666780544	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.706739671744814	2		78	112	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316349	14316350	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0033767-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	145	608	1	ENST00000256196.4:c.255_256delinsCT	p.Gly86Cys	p.G86C	ENST00000256196		85	acTGgc/acCTgc	3/6	0.705040666780544	3	FACETS	0.8	0.732	0.872	0.4	0.366	0.436	SUBCLONAL	1	TRUE	1	0.706739671744814	3		609	694	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798103	32798105	+	frameshift_variant	Frame_Shift_Del	DEL	GTC	GTC	TT	novel	NA	P-0033767-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	196	700	2	ENST00000374899.4:c.1574_1576delinsAA	p.Gly525GlufsTer36	p.G525Efs*36	ENST00000374899	NM_018833.2	525	gGACag/gAAag	9/12	0.705040666780544	3	FACETS	0.799	0.739	0.86	0.399	0.369	0.43	SUBCLONAL	1	TRUE	1	0.706739671744814	3		702	940	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48877946	48878238	+	splice_donor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	GTAACGGGAGTCGGGAGAGGACGGGGCGTGCCCCGACGTGCGCGCGCGTCGTCCTCCCCGGCGCTCCTCCACAGCTCGCTGGCTCCCGCCGCGGAAAGGCGTCATGCCGCCCAAAACCCCCCGAAAAACGGCCGCCACCGCCGCCGCTGCCGCCGCGGAACCCCCGGCACCGCCGCCGCCGCCCCCTCCTGAGGAGGACCCAGAGCAGGACAGCGGCCCGGAGGACCTGCCTCTCGTCAGGTGAGCGAGCAGAGCCGCCGTCGCCTCACGCGGGAAGGGCGCCCCGGGTGTGC	GTAACGGGAGTCGGGAGAGGACGGGGCGTGCCCCGACGTGCGCGCGCGTCGTCCTCCCCGGCGCTCCTCCACAGCTCGCTGGCTCCCGCCGCGGAAAGGCGTCATGCCGCCCAAAACCCCCCGAAAAACGGCCGCCACCGCCGCCGCTGCCGCCGCGGAACCCCCGGCACCGCCGCCGCCGCCCCCTCCTGAGGAGGACCCAGAGCAGGACAGCGGCCCGGAGGACCTGCCTCTCGTCAGGTGAGCGAGCAGAGCCGCCGTCGCCTCACGCGGGAAGGGCGCCCCGGGTGTGC	-	novel	NA	P-0033767-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	360	509	0	ENST00000267163.4:c.-100_137+56del		p.X34_splice	ENST00000267163	NM_000321.2	34		1/27	0.705040666780544	3	FACETS	0.872	0.841	0.903	0.872	0.841	0.903	CLONAL	3	TRUE	0	0.706739671744814	3		509	527	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422656	47422656	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033767-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	208	650	0	ENST00000404338.3:c.724A>C	p.Thr242Pro	p.T242P	ENST00000404338	NM_004491.4	242	Acc/Ccc	1/6	0.679632862614294	4	FACETS	0.923	0.856	0.992	0.308	0.285	0.331	CLONAL	1	TRUE	1	0.706739671744814	4		650	1089	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285164	198285164	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033767-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	256	583	0	ENST00000335508.6:c.403C>T	p.Pro135Ser	p.P135S	ENST00000335508	NM_012433.2	135	Cct/Tct	4/25	0.705040666780544	4	FACETS	1	0.97	1	0.532	0.497	0.567	CLONAL	1	TRUE	2	0.706739671744814	4		583	1163	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0033781-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	252	578	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.604000902537993	6	FACETS	0.973	0.936	1			1	CLONAL	5	TRUE	NA	0.836555162455489	6		578	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0033781-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	45	491	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.846968451634396	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.836555162455489	1		491	60	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615116	43615116	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377767424	NA	P-0033781-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	35	505	0	ENST00000355710.3:c.2530C>T	p.Arg844Trp	p.R844W	ENST00000355710	NM_020975.4	844	Cgg/Tgg	14/20	0.846968451634396	1	FACETS	0.468	0.394	0.546	0.468	0.394	0.546	SUBCLONAL	1	TRUE	0	0.836555162455489	1		505	104	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266711	198266711	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033781-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	78	303	0	ENST00000335508.6:c.2221A>G	p.Lys741Glu	p.K741E	ENST00000335508	NM_012433.2	741	Aag/Gag	15/25	0.19745104379944	2	FACETS	1	0.968	1	0.586	0.53	0.643	INDETERMINATE	1	TRUE	0	0.836555162455489	2		303	159	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627223	37627223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746609194	NA	P-0033781-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	28	370	0	ENST00000447079.4:c.1138C>T	p.Arg380Cys	p.R380C	ENST00000447079	NM_015083.1	380	Cgt/Tgt	2/14	0.590463834325708	4	FACETS	0.514	0.413	0.629	0.171	0.137	0.21	SUBCLONAL	1	TRUE	1	0.836555162455489	4		370	239	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873246	71873246	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033781-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	38	329	0	ENST00000357731.5:c.948T>G	p.Ser316Arg	p.S316R	ENST00000357731	NM_173808.2	316	agT/agG	7/7	0.409601021762029	3	FACETS	0.472	0.392	0.56	0.157	0.13	0.187	INDETERMINATE	1	TRUE	0	0.836555162455489	3		329	273	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897396	78897396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033781-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	24	565	0	ENST00000306801.3:c.2731C>T	p.Pro911Ser	p.P911S	ENST00000306801	NM_020761.2	911	Ccc/Tcc	23/34	0.543284715674917	4	FACETS	0.558	0.44	0.691	0.186	0.146	0.231	SUBCLONAL	1	TRUE	1	0.836555162455489	4		565	189	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422702	49422702	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035162-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	32	622	0	ENST00000301067.7:c.14291A>G	p.Glu4764Gly	p.E4764G	ENST00000301067	NM_003482.3	4764	gAg/gGg	45/54	0.559160206413054	3	FACETS	1	0.927	1	0.617	0.514	0.727	CLONAL	1	TRUE	1	0.672784517146541	3		622	103	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961011	15961011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142717545	NA	P-0035162-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	30	416	0	ENST00000268712.3:c.6209C>T	p.Ser2070Leu	p.S2070L	ENST00000268712	NM_006311.3	2070	tCg/tTg	40/46	1	2	FACETS	0.841	0.694	1	0.841	0.694	1	CLONAL	1	TRUE	1	0.672784517146541	2		416	106	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936268	78936268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035162-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	29	510	0	ENST00000306801.3:c.3700G>A	p.Gly1234Arg	p.G1234R	ENST00000306801	NM_020761.2	1234	Gga/Aga	32/34	0.672784517146541	5	FACETS	0.76	0.613	0.924	0.253	0.204	0.308	CLONAL	1	TRUE	2	0.672784517146541	5		510	228	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374341	138374341	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035162-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	34	458	0	ENST00000289153.2:c.3103G>A	p.Glu1035Lys	p.E1035K	ENST00000289153	NM_006219.2	1035	Gaa/Aaa	22/22	0.672784517146541	4	FACETS	0.983	0.813	1	0.491	0.406	0.585	CLONAL	1	TRUE	2	0.672784517146541	4		458	172	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120363	94120363	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035162-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	43	639	0	ENST00000369303.4:c.688G>T	p.Val230Phe	p.V230F	ENST00000369303	NM_004440.3	230	Gtt/Ttt	3/17	0.672784517146541	3	FACETS	1	0.919	1	0.562	0.479	0.65	CLONAL	1	TRUE	1	0.672784517146541	3		639	152	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411856	116411880	+	intron_variant	Intron	DEL	CCATGATAGCCGTCTTTAACAAGCT	CCATGATAGCCGTCTTTAACAAGCT	-	novel	NA	P-0035162-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	562	667	0	ENST00000397752.3:c.2888-46_2888-22del		p.*963*	ENST00000397752	NM_000245.2	-/1390			0.672784517146541	14	FACETS	0.989	0.974	1	0.989	0.974	1	CLONAL	14	TRUE	0	0.672784517146541	14		667	608	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423413	116423413	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035162-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	81	391	0	ENST00000397752.3:c.3688T>A	p.Tyr1230Asn	p.Y1230N	ENST00000397752	NM_000245.2	1230	Tat/Aat	19/21	0.672784517146541	14	FACETS	0.883	0.781	0.991	0.189	0.167	0.213	CLONAL	3	TRUE	0	0.672784517146541	14		391	458	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77937657	77937657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749634672	NA	P-0035162-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	26	443	0	ENST00000361507.4:c.1061G>A	p.Arg354His	p.R354H	ENST00000361507	NM_080491.2	354	cGc/cAc	4/10	0.672784517146541	5	FACETS	0.882	0.705	1	0.221	0.176	0.271	CLONAL	1	TRUE	1	0.672784517146541	5		443	176	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0035812-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	141	544	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.564456305307413	4	FACETS	1	0.985	1	0.452	0.415	0.491	CLONAL	1	TRUE	1	0.830228682212164	4		544	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578507	7578507	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519977	NA	P-0035812-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	696	824	0	ENST00000269305.4:c.423C>G	p.Cys141Trp	p.C141W	ENST00000269305	NM_001126112.2	141	tgC/tgG	5/11	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.830228682212164	2		824	805	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983130	201983130	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035812-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	965	478	0	ENST00000359651.3:c.979G>T	p.Glu327Ter	p.E327*	ENST00000359651		327	Gag/Tag	7/8	0.73845038504721	4	FACETS	0.977	0.955	0.999			1	CLONAL	3	TRUE	NA	0.830228682212164	4		478	1451	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226595615	226595615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035812-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	215	371	0	ENST00000366794.5:c.16G>A	p.Asp6Asn	p.D6N	ENST00000366794	NM_001618.3	6	Gat/Aat	1/23	NA	2	FACETS	0.927	0.868	0.986			1	INDETERMINATE	1	TRUE	NA	0.830228682212164	2		371	559	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271898	15271898	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035812-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2476	330	511	0	ENST00000263388.2:c.6541C>G	p.Pro2181Ala	p.P2181A	ENST00000263388	NM_000435.2	2181	Cca/Gca	33/33	0.830228682212164	7	FACETS	0.871	0.819	0.926			1	CLONAL	1	TRUE	NA	0.830228682212164	7		511	2806	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375412	15375412	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035812-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2312	332	519	0	ENST00000263377.2:c.1015C>T	p.Gln339Ter	p.Q339*	ENST00000263377	NM_058243.2	339	Cag/Tag	6/20	0.830228682212164	7	FACETS	0.93	0.875	0.988			1	CLONAL	1	TRUE	NA	0.830228682212164	7		519	2644	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221681	36221681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035812-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	315	465	0	ENST00000222270.7:c.5350C>T	p.Arg1784Trp	p.R1784W	ENST00000222270	NM_014727.1	1784	Cgg/Tgg	26/37	0.184522750813377	5	FACETS	0.772	0.729	0.817			1	INDETERMINATE	2	TRUE	NA	0.830228682212164	5		465	1103	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744954	39744954	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035812-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	261	374	0	ENST00000361337.2:c.1744G>C	p.Glu582Gln	p.E582Q	ENST00000361337	NM_003286.2	582	Gag/Cag	17/21	0.813334814998018	4	FACETS	0.935	0.875	0.997	0.312	0.291	0.333	CLONAL	1	TRUE	1	0.830228682212164	4		374	1231	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267844	46267844	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035812-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	285	456	0	ENST00000371998.3:c.2605C>G	p.Pro869Ala	p.P869A	ENST00000371998		869	Cca/Gca	14/23	0.813334814998018	4	FACETS	0.862	0.808	0.917	0.287	0.269	0.306	CLONAL	1	TRUE	1	0.830228682212164	4		456	1458	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26046008	26046008	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1373897096	NA	P-0035812-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	345	490	0	ENST00000540144.1:c.370G>A	p.Asp124Asn	p.D124N	ENST00000540144	NM_003531.2	124	Gat/Aat	1/1	0.832278012794436	3	FACETS	0.991	0.938	1	0.495	0.469	0.523	CLONAL	1	TRUE	1	0.830228682212164	3		490	1187	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197268	26197268	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035812-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1523	381	670	0	ENST00000356476.2:c.211C>G	p.Leu71Val	p.L71V	ENST00000356476		71	Cta/Gta	1/1	0.832278012794436	3	FACETS	0.682	0.645	0.72	0.341	0.322	0.36	SUBCLONAL	1	TRUE	1	0.830228682212164	3		670	1904	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729695	162729695	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035844-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	264	654	0	ENST00000367921.3:c.781A>G	p.Asn261Asp	p.N261D	ENST00000367921	NM_006182.2	261	Aac/Gac	8/18	0.92048716422117	3	FACETS	0.956	0.898	1	0.478	0.449	0.508	CLONAL	1	TRUE	1	0.925943331516001	3		654	873	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625224	69625225	+	missense_variant	Missense_Mutation	DNP	AT	AT	GC	novel	NA	P-0035844-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	275	658	0	ENST00000334134.2:c.568_569delinsGC	p.Met190Ala	p.M190A	ENST00000334134	NM_005247.2	190	ATg/GCg	3/3	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.925943331516001	2		658	580	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098369	108098369	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035844-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	129	347	0	ENST00000278616.4:c.18T>A	p.Asn6Lys	p.N6K	ENST00000278616	NM_000051.3	6	aaT/aaA	2/63	1	2	FACETS	0.908	0.836	0.98	0.908	0.836	0.98	CLONAL	1	TRUE	1	0.925943331516001	2		347	307	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0036450-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	337	415	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.660527921498389	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	2	0.721437068330522	4		421	791	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578217	7578217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036450-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	468	719	0	ENST00000269305.4:c.632C>T	p.Thr211Ile	p.T211I	ENST00000269305	NM_001126112.2	211	aCt/aTt	6/11	0.697421750315435	2	FACETS	0.987	0.958	1	0.987	0.958	1	CLONAL	2	TRUE	0	0.721437068330522	2		719	657	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0036450-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	136	377	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.345586148708181	4	FACETS	0.854	0.785	0.924			1	INDETERMINATE	2	TRUE	NA	0.721437068330522	4		377	380	SUCCESS
APC	324	MSKCC	GRCh37	5	112175346	112175356	+	frameshift_variant	Frame_Shift_Del	DEL	TTGAATTTTCT	TTGAATTTTCT	-	novel	NA	P-0036450-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	647	520	0	ENST00000257430.4:c.4056_4066del	p.Glu1353ArgfsTer18	p.E1353Rfs*18	ENST00000257430	NM_000038.5	1352	gTTGAATTTTCT/g	16/16	0.692977126545171	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	4	TRUE	0	0.721437068330522	4		520	768	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0036767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	56	176	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		176	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0036767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	103	465	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		465	833	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0036767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	27	160	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		160	397	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743943	40743943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763964405	NA	P-0036767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	50	271	0	ENST00000373198.4:c.3052C>T	p.Arg1018Ter	p.R1018*	ENST00000373198	NM_133170.3	1018	Cga/Tga	23/32	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		271	627	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519896	NA	P-0036767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	34	421	1	ENST00000281708.4:c.1514G>T	p.Arg505Leu	p.R505L	ENST00000281708	NM_033632.3	505	cGc/cTc	10/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		422	412	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652957	29652957	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs775874538	NA	P-0036767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	59	220	0	ENST00000356175.3:c.4892A>G	p.Asn1631Ser	p.N1631S	ENST00000356175	NM_000267.3	1631	aAt/aGt	36/57	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		220	666	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115724	8115743	+	frameshift_variant	Frame_Shift_Del	DEL	AGAAGGAAGGCATCCAGACC	AGAAGGAAGGCATCCAGACC	-	novel	NA	P-0036826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	52	303	0	ENST00000346208.3:c.1074_1093del	p.Glu359ProfsTer5	p.E359Pfs*5	ENST00000346208		357	aAGAAGGAAGGCATCCAGACC/a	6/6	1	2	FACETS	0.9	0.774	1	0.9	0.774	1	CLONAL	1	FALSE	1	0.491834947262388	2		303	235	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405224	70405224	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	53	413	1	ENST00000373644.4:c.2738C>A	p.Ser913Ter	p.S913*	ENST00000373644	NM_030625.2	913	tCa/tAa	4/12	1	2	FACETS	0.798	0.686	0.919	0.798	0.686	0.919	CLONAL	1	FALSE	1	0.491834947262388	2		414	270	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996789	73996789	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	82	298	1	ENST00000318443.5:c.1345G>T	p.Ala449Ser	p.A449S	ENST00000318443	NM_001024736.1	449	Gcg/Tcg	6/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.491834947262388	2		299	257	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4094479	4094479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768826287	NA	P-0036826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	218	672	1	ENST00000262948.5:c.1064C>T	p.Ala355Val	p.A355V	ENST00000262948	NM_030662.3	355	gCg/gTg	10/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.491834947262388	2		673	719	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543713	29543713	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	33	396	0	ENST00000389048.3:c.1450G>C	p.Asp484His	p.D484H	ENST00000389048	NM_004304.4	484	Gat/Cat	7/29	0.491834947262388	3	FACETS	0.262	0.213	0.318	0.131	0.106	0.159	SUBCLONAL	1	FALSE	1	0.491834947262388	3		396	638	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286788	212286788	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	21	423	0	ENST00000342788.4:c.2908C>G	p.Leu970Val	p.L970V	ENST00000342788	NM_005235.2	970	Ctg/Gtg	24/28	0.491834947262388	3	FACETS	0.272	0.209	0.346	0.136	0.104	0.173	SUBCLONAL	1	FALSE	1	0.491834947262388	3		423	391	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631310	117631320	+	frameshift_variant	Frame_Shift_Del	DEL	AGCAGGCCTTC	AGCAGGCCTTC	-	novel	NA	P-0036826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	81	356	0	ENST00000368508.3:c.6358_6368del	p.Glu2120ProfsTer20	p.E2120Pfs*20	ENST00000368508	NM_002944.2	2120	GAAGGCCTGCTc/c	40/43	1	2	FACETS	0.93	0.826	1	0.93	0.826	1	CLONAL	1	FALSE	1	0.491834947262388	2		356	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0037515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	172	608	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.243454956689455	3	FACETS	1	0.941	1	1	0.941	1	CLONAL	3	TRUE	0	0.273256247626611	3		610	470	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514471	148514471	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1454562282	NA	P-0037515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	33	328	0	ENST00000320356.2:c.1253G>A	p.Arg418Gln	p.R418Q	ENST00000320356	NM_004456.4	418	cGg/cAg	11/20	0.273256247626611	3	FACETS	0.827	0.675	0.997	0.276	0.225	0.333	CLONAL	1	TRUE	0	0.273256247626611	3		328	332	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501288	140501288	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507470	NA	P-0037515-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	56	333	0	ENST00000288602.6:c.784C>A	p.Gln262Lys	p.Q262K	ENST00000288602	NM_004333.4	262	Caa/Aaa	6/18	0.273256247626611	3	FACETS	1	0.96	1	0.448	0.385	0.515	CLONAL	1	TRUE	0	0.273256247626611	3		333	347	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0038126-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	66	575	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.895	0.793	1	0.895	0.793	1	CLONAL	1	TRUE	1	0.801221716683671	2		575	184	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858407	89858407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757760966	NA	P-0038126-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	196	710	0	ENST00000389301.3:c.1153C>T	p.His385Tyr	p.H385Y	ENST00000389301	NM_000135.2	385	Cac/Tac	13/43	0.801221716683671	1	FACETS	0.943	0.894	0.991	0.943	0.894	0.991	CLONAL	1	TRUE	0	0.801221716683671	1		710	311	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42002958	42002958	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038126-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	82	514	0	ENST00000219905.7:c.2498del	p.Asn833MetfsTer5	p.N833Mfs*5	ENST00000219905	NM_001164273.1	832	gAa/ga	8/24	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.801221716683671	2		514	188	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346743	89347692	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGTTGCTGAAGAAGGACTCCAGCCCGGAGGGAGGGGCGTAGGGAGCCGCCTCTGAGGTGGAGATGGCGGCGGGGACGGCGTCCACTCCGTCCTTGACGTCCTCCAGCCCCGGCTCAGCGACGGGCAGAGCGTACGGGGCAGGAGAGGCGGGAGGGGCGGGGTACGGCGCCTCCGAGGCGCTGAAGGGCCCTGGGGCGGCAGAGTGGAGGGGGTCCGCGGGGCAGAAACGCTTTGGGGACTCGGGGAATCTCTGTGGAGACTTCAGCAGGAGGTCCGAGCCCACAGGCCAGCTCACAGGGTTTTCAGAGGTGCCCCCGATCAGGCTAGAGGCAAGCGCCTGCTCGGAGGGGTGGGCCCACTCAACGGGCTCCTCGGTGATGACGGCGCTGAAGGGACCCTCGTCCAGCGGCTCCAGGTAGCTGGGCTCCGGGGGGATGATGGCGGCCGTCGCCTGCTGGTCCTCGGAGGTGTCCAGGTCCGGGGGAAGGGCCCCTTCGAGGGAAGGAACCAGCAGCTCGGCTCTGGGGGAAGGGGAAGGTTTTGCTTGTAAACTTGAGAAGACGCCCTCTGGAGACGGGGTGACAGTGACAACGGCAGCCGGTGGGCAGTGCAAAGCGTCGACTTTGGGCGACGGGAGGCCATAGTCTGGGGAGTAGTACCCTGGCGACAAGCAGGCAAACTTCTCCGCGGGAACCGGGGGCAGGGGCGCCCTGTCTTCCATCGAGGGTGGCATGGGAGAGTCGTAGCTGGAGGCAGCAGGAACGCTCTGCTGCCTGAAGAGCTTGTCTCCGACGCTGAATTCTTCCTCGGGGGTCCTCCTAATGTCGACAGAGACCGAGCGGTAAAGGTTTGTGGAGAGAGGCCTGGCAGGAGCCTGGCTGGCGTTTTCCGAAAGCCCACTTGAAGCCACGGAGAACCTGTCGAAAAAGGAGGGGGAGCAGGCGCTGG	GCAGTTGCTGAAGAAGGACTCCAGCCCGGAGGGAGGGGCGTAGGGAGCCGCCTCTGAGGTGGAGATGGCGGCGGGGACGGCGTCCACTCCGTCCTTGACGTCCTCCAGCCCCGGCTCAGCGACGGGCAGAGCGTACGGGGCAGGAGAGGCGGGAGGGGCGGGGTACGGCGCCTCCGAGGCGCTGAAGGGCCCTGGGGCGGCAGAGTGGAGGGGGTCCGCGGGGCAGAAACGCTTTGGGGACTCGGGGAATCTCTGTGGAGACTTCAGCAGGAGGTCCGAGCCCACAGGCCAGCTCACAGGGTTTTCAGAGGTGCCCCCGATCAGGCTAGAGGCAAGCGCCTGCTCGGAGGGGTGGGCCCACTCAACGGGCTCCTCGGTGATGACGGCGCTGAAGGGACCCTCGTCCAGCGGCTCCAGGTAGCTGGGCTCCGGGGGGATGATGGCGGCCGTCGCCTGCTGGTCCTCGGAGGTGTCCAGGTCCGGGGGAAGGGCCCCTTCGAGGGAAGGAACCAGCAGCTCGGCTCTGGGGGAAGGGGAAGGTTTTGCTTGTAAACTTGAGAAGACGCCCTCTGGAGACGGGGTGACAGTGACAACGGCAGCCGGTGGGCAGTGCAAAGCGTCGACTTTGGGCGACGGGAGGCCATAGTCTGGGGAGTAGTACCCTGGCGACAAGCAGGCAAACTTCTCCGCGGGAACCGGGGGCAGGGGCGCCCTGTCTTCCATCGAGGGTGGCATGGGAGAGTCGTAGCTGGAGGCAGCAGGAACGCTCTGCTGCCTGAAGAGCTTGTCTCCGACGCTGAATTCTTCCTCGGGGGTCCTCCTAATGTCGACAGAGACCGAGCGGTAAAGGTTTGTGGAGAGAGGCCTGGCAGGAGCCTGGCTGGCGTTTTCCGAAAGCCCACTTGAAGCCACGGAGAACCTGTCGAAAAAGGAGGGGGAGCAGGCGCTGG	-	novel	NA	P-0038126-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	159	764	0	ENST00000301030.4:c.5258_6207del	p.Thr1753LysfsTer32	p.T1753Kfs*32	ENST00000301030	NM_001256183.1	1753	aCCAGCGCCTGCTCCCCCTCCTTTTTCGACAGGTTCTCCGTGGCTTCAAGTGGGCTTTCGGAAAACGCCAGCCAGGCTCCTGCCAGGCCTCTCTCCACAAACCTTTACCGCTCGGTCTCTGTCGACATTAGGAGGACCCCCGAGGAAGAATTCAGCGTCGGAGACAAGCTCTTCAGGCAGCAGAGCGTTCCTGCTGCCTCCAGCTACGACTCTCCCATGCCACCCTCGATGGAAGACAGGGCGCCCCTGCCCCCGGTTCCCGCGGAGAAGTTTGCCTGCTTGTCGCCAGGGTACTACTCCCCAGACTATGGCCTCCCGTCGCCCAAAGTCGACGCTTTGCACTGCCCACCGGCTGCCGTTGTCACTGTCACCCCGTCTCCAGAGGGCGTCTTCTCAAGTTTACAAGCAAAACCTTCCCCTTCCCCCAGAGCCGAGCTGCTGGTTCCTTCCCTCGAAGGGGCCCTTCCCCCGGACCTGGACACCTCCGAGGACCAGCAGGCGACGGCCGCCATCATCCCCCCGGAGCCCAGCTACCTGGAGCCGCTGGACGAGGGTCCCTTCAGCGCCGTCATCACCGAGGAGCCCGTTGAGTGGGCCCACCCCTCCGAGCAGGCGCTTGCCTCTAGCCTGATCGGGGGCACCTCTGAAAACCCTGTGAGCTGGCCTGTGGGCTCGGACCTCCTGCTGAAGTCTCCACAGAGATTCCCCGAGTCCCCAAAGCGTTTCTGCCCCGCGGACCCCCTCCACTCTGCCGCCCCAGGGCCCTTCAGCGCCTCGGAGGCGCCGTACCCCGCCCCTCCCGCCTCTCCTGCCCCGTACGCTCTGCCCGTCGCTGAGCCGGGGCTGGAGGACGTCAAGGACGGAGTGGACGCCGTCCCCGCCGCCATCTCCACCTCAGAGGCGGCTCCCTACGCCCCTCCCTCCGGGCTGGAGTCCTTCTTCAGCAACTGC/a	9/13	0.801221716683671	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.801221716683671	1		764	232	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038202-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	87	382	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.294885460400799	2		382	510	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515240	103515240	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038202-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	62	707	0	ENST00000355739.4:c.1741G>T	p.Val581Phe	p.V581F	ENST00000355739	NM_000123.3	581	Gtc/Ttc	8/15	1	2	FACETS	0.407	0.351	0.47	0.407	0.351	0.47	SUBCLONAL	1	TRUE	1	0.294885460400799	2		707	1032	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544729	65544733	+	frameshift_variant	Frame_Shift_Del	DEL	TTGTC	TTGTC	-	novel	NA	P-0038202-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	130	700	0	ENST00000358664.4:c.193_197del	p.Asp65SerfsTer20	p.D65Sfs*20	ENST00000358664	NM_002382.4	65	GACAAa/a	4/5	0.2739367757196	1	FACETS	0.787	0.713	0.865	0.787	0.713	0.865	SUBCLONAL	1	TRUE	0	0.294885460400799	1		700	955	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082754	16082754	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs776717109	NA	P-0038202-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	49	584	0	ENST00000281043.3:c.568G>T	p.Ala190Ser	p.A190S	ENST00000281043	NM_005378.4	190	Gcc/Tcc	2/3	1	2	FACETS	0.368	0.31	0.432	0.368	0.31	0.432	SUBCLONAL	1	TRUE	1	0.294885460400799	2		584	903	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31369221	31369221	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0038202-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	147	649	0	ENST00000328111.2:c.204+1G>T		p.X68_splice	ENST00000328111	NM_006892.3	68			1	2	FACETS	0.945	0.862	1	0.945	0.862	1	CLONAL	1	TRUE	1	0.294885460400799	2		649	1055	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424711	47424711	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038202-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	167	783	0	ENST00000377045.4:c.519C>A	p.Asn173Lys	p.N173K	ENST00000377045	NM_001654.4	173	aaC/aaA	6/16	1	2	FACETS	0.862	0.79	0.938	0.862	0.79	0.938	CLONAL	1	TRUE	1	0.294885460400799	2		783	1314	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913492	NA	P-0038208-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	96	240	0	ENST00000286548.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000286548	NM_002072.3	209	cAa/cTa	5/7	1	2	FACETS	0.895	0.805	0.989	0.895	0.805	0.989	CLONAL	1	TRUE	1	0.625249285239351	2		240	343	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440888	52440903	+	protein_altering_variant	In_Frame_Del	DEL	CCTTGTCTGTCCACTC	CCTTGTCTGTCCACTC	G	novel	NA	P-0038208-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	171	505	0	ENST00000460680.1:c.601_616delinsC	p.Glu201_Ala206delinsPro	p.E201_A206delinsP	ENST00000460680	NM_004656.3	201	GAGTGGACAGACAAGGcc/Ccc	8/17	0.625249285239351	1	FACETS	0.919	0.856	0.983	0.919	0.856	0.983	CLONAL	1	TRUE	0	0.625249285239351	1		505	409	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798466	45798466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143353451	NA	P-0038580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	132	628	1	ENST00000450313.1:c.545G>A	p.Arg182His	p.R182H	ENST00000450313	NM_012222.2	182	cGt/cAt	7/16	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	FALSE	1	0.447947836902126	2		629	580	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175922	176175922	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	10	28	0	ENST00000367669.3:c.193G>C	p.Val65Leu	p.V65L	ENST00000367669	NM_022457.5	65	Gtg/Ctg	1/20	1	2	FACETS	0.519	0.356	0.719	0.519	0.356	0.719	SUBCLONAL	1	FALSE	1	0.447947836902126	2		28	86	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310884	123310884	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs200766273	NA	P-0038580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	109	451	0	ENST00000358487.5:c.544G>C	p.Gly182Arg	p.G182R	ENST00000358487	NM_000141.4	182	Ggg/Cgg	5/18	1	2	FACETS	0.932	0.841	1	0.932	0.841	1	CLONAL	1	FALSE	1	0.447947836902126	2		451	522	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188322	10188322	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs5030814	NA	P-0038580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	49	397	0	ENST00000256474.2:c.463+2T>C		p.X155_splice	ENST00000256474	NM_000551.3	155			0.447947836902126	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	FALSE	0	0.447947836902126	1		397	155	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436360	52436361	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	AA	novel	NA	P-0038580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	148	582	0	ENST00000460680.1:c.2133_2134delinsTT	p.Lys711_Gln712delinsAsnTer	p.K711_Q712delinsN*	ENST00000460680	NM_004656.3	711	aaGCag/aaTTag	17/17	0.447947836902126	1	FACETS	0.986	0.906	1	0.986	0.906	1	CLONAL	1	FALSE	0	0.447947836902126	1		582	520	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0038824-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	351	271	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.965	0.917	1	0.965	0.917	1	CLONAL	1	TRUE	1	0.778956948304685	2		272	934	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0038824-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	620	603	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.775738414048378	2	FACETS	0.988	0.964	1	0.988	0.964	1	CLONAL	2	TRUE	0	0.778956948304685	2		603	806	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412283	139412285	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	novel	NA	P-0038824-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	56	681	0	ENST00000277541.6:c.1360_1362del	p.Asn454del	p.N454del	ENST00000277541	NM_017617.3	454	AAC/-	8/34	1	2	FACETS	0.164	0.14	0.19	0.164	0.14	0.19	SUBCLONAL	1	TRUE	1	0.778956948304685	2		681	878	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918922	76918922	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0038824-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	303	259	0	ENST00000373344.5:c.4069A>T	p.Lys1357Ter	p.K1357*	ENST00000373344	NM_000489.3	1357	Aag/Tag	12/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.778956948304685	1		259	372	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0038984-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	73	397	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.275599955895474	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.275599955895474	1		397	372	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0038984-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	155	333	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.831	0.763	0.902	1	0.99	1	CLONAL	2	TRUE	1	0.275599955895474	2		333	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912660	NA	P-0038984-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	111	557	0	ENST00000269305.4:c.839G>T	p.Arg280Ile	p.R280I	ENST00000269305	NM_001126112.2	280	aGa/aTa	8/11	0.275599955895474	1	FACETS	0.917	0.825	1	0.917	0.825	1	CLONAL	1	TRUE	0	0.275599955895474	1		557	757	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939457	76939457	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038984-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	103	430	0	ENST00000373344.5:c.1291G>T	p.Glu431Ter	p.E431*	ENST00000373344	NM_000489.3	431	Gag/Tag	9/35	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.275599955895474	2		430	746	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948302	31948302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038984-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	81	438	0	ENST00000375333.2:c.890G>T	p.Arg297Ile	p.R297I	ENST00000375333	NM_032454.1	297	aGa/aTa	6/8	0.275599955895474	1	FACETS	0.93	0.821	1	0.93	0.821	1	CLONAL	1	TRUE	0	0.275599955895474	1		438	545	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264275	30264275	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038984-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	62	286	0	ENST00000322652.5:c.10C>G	p.Gln4Glu	p.Q4E	ENST00000322652	NM_015355.2	4	Cag/Gag	1/16	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.275599955895474	2		286	450	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352428	118352428	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0038984-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	81	362	0	ENST00000534358.1:c.3635-2A>T		p.X1212_splice	ENST00000534358	NM_005933.3	1212			1	2	FACETS	0.956	0.843	1	0.956	0.843	1	CLONAL	1	TRUE	1	0.275599955895474	2		362	615	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135320	30135320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038984-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	68	341	0	ENST00000331968.5:c.498G>T	p.Met166Ile	p.M166I	ENST00000331968	NM_002742.2	166	atG/atT	3/18	0.135602186072378	1	FACETS	0.828	0.721	0.942	0.828	0.721	0.942	INDETERMINATE	1	TRUE	0	0.275599955895474	1		341	514	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584409	39584409	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038984-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	89	405	0	ENST00000262039.4:c.1074G>T	p.Met358Ile	p.M358I	ENST00000262039	NM_002647.2	358	atG/atT	10/25	0.275599955895474	1	FACETS	0.934	0.83	1	0.934	0.83	1	CLONAL	1	TRUE	0	0.275599955895474	1		405	596	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615740	1615740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038984-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	142	636	0	ENST00000344749.5:c.1531G>A	p.Ala511Thr	p.A511T	ENST00000344749	NM_001136139.2	511	Gct/Act	17/19	0.275599955895474	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.275599955895474	1		636	839	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033768	48033768	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs756216566	NA	P-0038984-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	67	318	0	ENST00000234420.5:c.3979A>T	p.Asn1327Tyr	p.N1327Y	ENST00000234420	NM_000179.2	1327	Aat/Tat	9/10	0.135602186072378	1	FACETS	0.892	0.777	1	0.892	0.777	1	INDETERMINATE	1	TRUE	0	0.275599955895474	1		318	470	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156032	99156032	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038984-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	91	459	0	ENST00000074304.5:c.712A>T	p.Thr238Ser	p.T238S	ENST00000074304	NM_001134224.1	238	Act/Tct	10/26	0.135602186072378	1	FACETS	0.93	0.827	1	0.93	0.827	1	INDETERMINATE	1	TRUE	0	0.275599955895474	1		459	612	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495264	212495264	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038984-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	51	469	0	ENST00000342788.4:c.2002G>T	p.Gly668Cys	p.G668C	ENST00000342788	NM_005235.2	668	Ggt/Tgt	17/28	0.135602186072378	1	FACETS	0.564	0.479	0.657	0.564	0.479	0.657	INDETERMINATE	1	TRUE	0	0.275599955895474	1		469	566	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023778	31023778	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038984-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	120	568	0	ENST00000375687.4:c.3263A>T	p.Gln1088Leu	p.Q1088L	ENST00000375687	NM_015338.5	1088	cAg/cTg	13/13	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.275599955895474	2		568	840	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827970	40827970	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038984-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	121	551	0	ENST00000373198.4:c.2458G>T	p.Val820Leu	p.V820L	ENST00000373198	NM_133170.3	820	Gtg/Ttg	17/32	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.275599955895474	2		551	787	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445085	89445085	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038984-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	87	418	0	ENST00000336596.2:c.1405G>C	p.Asp469His	p.D469H	ENST00000336596	NM_005233.5	469	Gac/Cac	6/17	1	2	FACETS	0.967	0.857	1	0.967	0.857	1	CLONAL	1	TRUE	1	0.275599955895474	2		418	653	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670340	134670340	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038984-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	108	466	1	ENST00000398015.3:c.251G>T	p.Arg84Leu	p.R84L	ENST00000398015	NM_004441.4	84	cGc/cTc	3/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.275599955895474	2		467	673	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030346	180030346	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs185808242	NA	P-0038984-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	100	606	0	ENST00000261937.6:c.3938C>G	p.Pro1313Arg	p.P1313R	ENST00000261937	NM_182925.4	1313	cCt/cGt	30/30	1	2	FACETS	0.78	0.696	0.87	0.78	0.696	0.87	SUBCLONAL	1	TRUE	1	0.275599955895474	2		606	930	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686791	117686791	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs771176235	NA	P-0038984-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	80	362	0	ENST00000368508.3:c.2926G>T	p.Asp976Tyr	p.D976Y	ENST00000368508	NM_002944.2	976	Gac/Tac	19/43	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.275599955895474	2		362	527	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739969	41739969	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038984-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	106	456	0	ENST00000242208.4:c.4C>A	p.Pro2Thr	p.P2T	ENST00000242208	NM_002192.2	2	Ccc/Acc	2/3	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.275599955895474	2		456	680	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432863	432863	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038984-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	129	410	0	ENST00000399788.2:c.2053C>A	p.Leu685Ile	p.L685I	ENST00000399788	NM_001042603.1	685	Ctc/Atc	15/28	0.275599955895474	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.275599955895474	1		410	610	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432859	432859	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038984-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	134	412	0	ENST00000399788.2:c.2057C>G	p.Ser686Cys	p.S686C	ENST00000399788	NM_001042603.1	686	tCt/tGt	15/28	0.275599955895474	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.275599955895474	1		412	619	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437157	110437157	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038984-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	80	327	0	ENST00000375856.3:c.1244A>T	p.Lys415Met	p.K415M	ENST00000375856	NM_003749.2	415	aAg/aTg	1/2	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.275599955895474	2		327	510	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685544	29685544	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1567627751	NA	P-0038984-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	70	372	0	ENST00000356175.3:c.7954C>T	p.Gln2652Ter	p.Q2652*	ENST00000356175	NM_000267.3	2652	Caa/Taa	54/57	1	2	FACETS	0.983	0.858	1	0.983	0.858	1	CLONAL	1	TRUE	1	0.275599955895474	2		372	517	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971004	21971004	+	stop_lost	Nonstop_Mutation	SNP	A	A	C	novel	NA	P-0038984-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	106	659	0	ENST00000579755.1:c.397T>G	p.Ter133GlyextTer22	p.*133Gext*22	ENST00000579755		133	Tga/Gga	2/3	0.275599955895474	1	FACETS	0.78	0.699	0.867	0.78	0.699	0.867	SUBCLONAL	1	TRUE	0	0.275599955895474	1		659	850	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971018	21971018	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs104894104	NA	P-0038984-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	102	594	0	ENST00000304494.5:c.340C>A	p.Pro114Thr	p.P114T	ENST00000304494	NM_000077.4	114	Ccc/Acc	2/3	0.275599955895474	1	FACETS	0.794	0.71	0.883	0.794	0.71	0.883	SUBCLONAL	1	TRUE	0	0.275599955895474	1		594	804	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0039980-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	111	304	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.218357692102659	4	FACETS	0.995	0.893	1	0.498	0.446	0.552	CLONAL	1	TRUE	2	0.284222197637525	4		304	1008	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0039980-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	297	877	1	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.284222197637525	2	FACETS	0.99	0.933	1	0.99	0.933	1	CLONAL	2	TRUE	0	0.284222197637525	2		878	1055	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994847	73994847	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs7173476	NA	P-0039980-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	20	168	0	ENST00000318443.5:c.331C>T	p.Arg111Cys	p.R111C	ENST00000318443	NM_001024736.1	111	Cgc/Tgc	3/10	0.218357692102659	4	FACETS	0.741	0.568	0.942	0.37	0.284	0.471	CLONAL	1	TRUE	2	0.284222197637525	4		168	244	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439494	220439494	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764382434	NA	P-0039980-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	149	843	0	ENST00000243786.2:c.347G>A	p.Arg116Gln	p.R116Q	ENST00000243786	NM_002191.3	116	cGg/cAg	2/2	0.25852997945995	3	FACETS	1	0.945	1	0.525	0.478	0.574	CLONAL	1	TRUE	1	0.284222197637525	3		843	1141	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986820	36986821	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0039980-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	261	809	0	ENST00000354822.5:c.868dup	p.Val290GlyfsTer149	p.V290Gfs*149	ENST00000354822	NM_001079668.2	290	gtg/gGtg	3/3	NA	2	FACETS	1	0.95	1			1	INDETERMINATE	2	TRUE	NA	0.284222197637525	2		809	906	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652087	36652087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769049147	NA	P-0039980-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	144	877	0	ENST00000244741.5:c.209G>A	p.Gly70Asp	p.G70D	ENST00000244741	NM_000389.4	70	gGc/gAc	2/3	0.25852997945995	3	FACETS	0.99	0.901	1	0.495	0.45	0.542	CLONAL	1	TRUE	1	0.284222197637525	3		877	1169	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0039980-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	1125	355	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.284222197637525	18	FACETS	1	0.993	1	1	0.993	1	CLONAL	15	TRUE	3	0.284222197637525	18		355	1678	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935082	49935082	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039980-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	156	976	0	ENST00000296474.3:c.1917G>C	p.Glu639Asp	p.E639D	ENST00000296474	NM_002447.2	639	gaG/gaC	6/20	0.25852997945995	3	FACETS	0.938	0.857	1	0.469	0.428	0.512	CLONAL	1	TRUE	1	0.284222197637525	3		976	1336	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	118	456	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.941	0.849	1	0.941	0.849	1	CLONAL	1	TRUE	1	0.31	2		456	809	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	80	210	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.31	2		210	411	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	105	410	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.954	0.855	1	0.954	0.855	1	CLONAL	1	TRUE	1	0.31	2		412	710	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	112	363	5	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.31	2		368	708	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	65	272	0	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	1	2	FACETS	0.679	0.588	0.777	0.679	0.588	0.777	SUBCLONAL	1	TRUE	1	0.31	2		272	618	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544703	65544703	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs387906650	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	120	559	1	ENST00000358664.4:c.223C>T	p.Arg75Ter	p.R75*	ENST00000358664	NM_002382.4	75	Cga/Tga	4/5	1	2	FACETS	0.822	0.741	0.907	0.822	0.741	0.907	CLONAL	1	TRUE	1	0.31	2		560	942	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	78	385	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	0.792	0.697	0.895	0.792	0.697	0.895	SUBCLONAL	1	TRUE	1	0.31	2		385	635	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396382	396382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200741961	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	156	662	1	ENST00000262320.3:c.644C>T	p.Ser215Leu	p.S215L	ENST00000262320	NM_003502.3	215	tCg/tTg	2/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.31	2		663	957	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552152	29552152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199474738	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	56	256	0	ENST00000356175.3:c.1885G>A	p.Gly629Arg	p.G629R	ENST00000356175	NM_000267.3	629	Ggg/Agg	17/57	1	2	FACETS	0.969	0.833	1	0.969	0.833	1	CLONAL	1	TRUE	1	0.31	2		256	373	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	126	440	2	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.31	2		442	789	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	117	591	0	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	0.706	0.635	0.781	0.706	0.635	0.781	SUBCLONAL	1	TRUE	1	0.31	2		591	1069	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154887	2154887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1212009594	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	135	582	2	ENST00000434045.2:c.334G>A	p.Ala112Thr	p.A112T	ENST00000434045	NM_001127598.1	112	Gca/Aca	4/5	1	2	FACETS	0.901	0.818	0.988	0.901	0.818	0.988	CLONAL	1	TRUE	1	0.31	2		584	967	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	T	rs1023835002	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	109	389	0	ENST00000558401.1:c.1A>T	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Ttg	1/4	1	2	FACETS	0.986	0.886	1	0.986	0.886	1	CLONAL	1	TRUE	1	0.31	2		389	713	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109935	115109935	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	148	601	0	ENST00000257566.3:c.1943C>T	p.Pro648Leu	p.P648L	ENST00000257566	NM_016569.3	648	cCg/cTg	8/8	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.31	2		601	930	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523072	25523072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369618387	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	88	615	0	ENST00000264709.3:c.113G>A	p.Arg38His	p.R38H	ENST00000264709	NM_175629.2	38	cGc/cAc	3/23	1	2	FACETS	0.582	0.515	0.655	0.582	0.515	0.655	SUBCLONAL	1	TRUE	1	0.31	2		615	975	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1268701	1268701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748503447	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	181	743	0	ENST00000310581.5:c.2516C>T	p.Thr839Met	p.T839M	ENST00000310581	NM_198253.2	839	aCg/aTg	9/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.31	2		743	1073	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246488	46246488	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761166036	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	55	225	0	ENST00000334344.6:c.4582G>A	p.Ala1528Thr	p.A1528T	ENST00000334344	NM_152641.2	1528	Gca/Aca	15/21	1	2	FACETS	0.908	0.779	1	0.908	0.779	1	CLONAL	1	TRUE	1	0.31	2		225	391	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943789	71943789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773085707	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	156	652	2	ENST00000298229.2:c.1832G>A	p.Arg611His	p.R611H	ENST00000298229	NM_001567.3	611	cGc/cAc	15/28	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.31	2		654	982	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500450	149500450	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs112566969	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	110	453	1	ENST00000261799.4:c.2586+1G>A		p.X862_splice	ENST00000261799	NM_002609.3	862			1	2	FACETS	0.975	0.876	1	0.975	0.876	1	CLONAL	1	TRUE	1	0.31	2		454	728	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589609	67589610	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	58	139	0	ENST00000274335.5:c.1378dup	p.Ser460LysfsTer5	p.S460Kfs*5	ENST00000274335		458	gaa/gAaa	10/15	1	2	FACETS	0.917	0.791	1	0.917	0.791	1	CLONAL	1	TRUE	1	0.31	2		139	408	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864217	57864217	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	107	534	0	ENST00000228682.2:c.1694T>C	p.Phe565Ser	p.F565S	ENST00000228682	NM_005269.2	565	tTc/tCc	12/12	1	2	FACETS	0.869	0.78	0.965	0.869	0.78	0.965	CLONAL	1	TRUE	1	0.31	2		534	794	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233757	133233759	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1555225139	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	115	413	0	ENST00000320574.5:c.3545_3547del	p.Lys1182del	p.K1182del	ENST00000320574	NM_006231.2	1182	aAGAtc/atc	29/49	1	2	FACETS	0.951	0.857	1	0.951	0.857	1	CLONAL	1	TRUE	1	0.31	2		413	780	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15967457	15967457	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777612906	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	134	481	2	ENST00000268712.3:c.5146C>T	p.Arg1716Trp	p.R1716W	ENST00000268712	NM_006311.3	1716	Cgg/Tgg	35/46	1	2	FACETS	0.98	0.89	1	0.98	0.89	1	CLONAL	1	TRUE	1	0.31	2		483	882	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504391	149504391	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752228799	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	124	484	4	ENST00000261799.4:c.1811G>A	p.Arg604His	p.R604H	ENST00000261799	NM_002609.3	604	cGc/cAc	13/23	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.31	2		488	773	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097609	27097609	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	106	436	0	ENST00000324856.7:c.3199-1G>T		p.X1067_splice	ENST00000324856	NM_006015.4	1067			1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.31	2		436	684	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598251	28598251	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760115188	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	205	704	1	ENST00000253063.3:c.223C>T	p.Arg75Ter	p.R75*	ENST00000253063	NM_031459.4	75	Cga/Tga	3/10	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.31	2		705	1306	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841438	156841438	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1213292019	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	130	501	0	ENST00000524377.1:c.744del	p.Leu249Ter	p.L249*	ENST00000524377	NM_002529.3	247	ctG/ct	7/17	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.31	2		501	803	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746056	162746056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	103	335	0	ENST00000367921.3:c.2179G>A	p.Ala727Thr	p.A727T	ENST00000367921	NM_006182.2	727	Gct/Act	16/18	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.31	2		335	590	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114799802	114799802	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	113	430	0	ENST00000543371.1:c.469C>A	p.Pro157Thr	p.P157T	ENST00000543371	NM_001198531.1	157	Cca/Aca	5/14	1	2	FACETS	0.923	0.83	1	0.923	0.83	1	CLONAL	1	TRUE	1	0.31	2		430	790	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69458649	69458649	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	102	417	0	ENST00000227507.2:c.464T>C	p.Met155Thr	p.M155T	ENST00000227507	NM_053056.2	155	aTg/aCg	3/5	1	2	FACETS	0.911	0.815	1	0.911	0.815	1	CLONAL	1	TRUE	1	0.31	2		417	722	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431603	49431603	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	145	633	1	ENST00000301067.7:c.9536C>G	p.Thr3179Arg	p.T3179R	ENST00000301067	NM_003482.3	3179	aCa/aGa	34/54	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.31	2		634	924	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445472	49445472	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780891095	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	186	768	1	ENST00000301067.7:c.1994C>T	p.Pro665Leu	p.P665L	ENST00000301067	NM_003482.3	665	cCg/cTg	10/54	1	2	FACETS	0.956	0.881	1	0.956	0.881	1	CLONAL	1	TRUE	1	0.31	2		769	1255	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609330	81609330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121908882	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	62	226	0	ENST00000298171.2:c.928C>T	p.Arg310Cys	p.R310C	ENST00000298171	NM_000369.2	310	Cgc/Tgc	10/10	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.31	2		226	392	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820591	3820591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373284909	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	173	604	0	ENST00000262367.5:c.2860G>A	p.Ala954Thr	p.A954T	ENST00000262367	NM_004380.2	954	Gcc/Acc	14/31	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.31	2		604	1032	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900703	3900703	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	148	483	0	ENST00000262367.5:c.393del	p.Ser132AlafsTer20	p.S132Afs*20	ENST00000262367	NM_004380.2	131	ccC/cc	2/31	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.31	2		483	771	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133172	30133172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	103	383	0	ENST00000263025.4:c.326C>T	p.Ala109Val	p.A109V	ENST00000263025	NM_002746.2	109	gCg/gTg	2/9	1	2	FACETS	0.966	0.865	1	0.966	0.865	1	CLONAL	1	TRUE	1	0.31	2		383	688	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089881	16089881	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	70	290	0	ENST00000268712.3:c.229C>A	p.Pro77Thr	p.P77T	ENST00000268712	NM_006311.3	77	Cca/Aca	3/46	1	2	FACETS	0.841	0.734	0.956	0.841	0.734	0.956	CLONAL	1	TRUE	1	0.31	2		290	537	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602256	10602256	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	139	525	0	ENST00000171111.5:c.1322A>T	p.Glu441Val	p.E441V	ENST00000171111	NM_203500.1	441	gAg/gTg	3/6	1	2	FACETS	0.995	0.906	1	0.995	0.906	1	CLONAL	1	TRUE	1	0.31	2		525	901	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223199	36223199	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	186	848	0	ENST00000222270.7:c.5749A>C	p.Ser1917Arg	p.S1917R	ENST00000222270	NM_014727.1	1917	Agc/Cgc	28/37	1	2	FACETS	0.917	0.845	0.993	0.917	0.845	0.993	CLONAL	1	TRUE	1	0.31	2		848	1308	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702166	47702167	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	83	281	0	ENST00000233146.2:c.1763_1764del	p.Tyr588CysfsTer9	p.Y588Cfs*9	ENST00000233146	NM_000251.2	588	TAt/t	12/16	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.31	2		281	487	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713406	40713406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1270158620	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	140	590	2	ENST00000373198.4:c.4109G>A	p.Arg1370His	p.R1370H	ENST00000373198	NM_133170.3	1370	cGc/cAc	30/32	1	2	FACETS	0.894	0.813	0.979	0.894	0.813	0.979	CLONAL	1	TRUE	1	0.31	2		592	1010	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725012	49725012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145575614	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	114	522	0	ENST00000449682.2:c.332G>A	p.Arg111His	p.R111H	ENST00000449682	NM_020998.3	111	cGc/cAc	3/18	1	2	FACETS	0.867	0.78	0.959	0.867	0.78	0.959	CLONAL	1	TRUE	1	0.31	2		522	848	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467679	66467679	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	60	336	0	ENST00000273854.3:c.590C>T	p.Thr197Ile	p.T197I	ENST00000273854	NM_004439.5	197	aCa/aTa	3/18	1	2	FACETS	0.765	0.66	0.879	0.765	0.66	0.879	SUBCLONAL	1	TRUE	1	0.31	2		336	506	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183252	56183252	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	114	455	0	ENST00000399503.3:c.4162G>T	p.Asp1388Tyr	p.D1388Y	ENST00000399503	NM_005921.1	1388	Gat/Tat	18/20	1	2	FACETS	0.983	0.886	1	0.983	0.886	1	CLONAL	1	TRUE	1	0.31	2		455	748	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020315	123020315	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1431863732	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	124	483	0	ENST00000355640.3:c.803G>A	p.Arg268Gln	p.R268Q	ENST00000355640		268	cGg/cAg	2/7	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.31	2		483	786	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637540	52637540	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	37	213	0	ENST00000394830.3:c.2776del	p.Arg926GlufsTer82	p.R926Efs*82	ENST00000394830	NM_018313.4	926	Aga/ga	18/30	1	2	FACETS	0.422	0.347	0.506	0.422	0.347	0.506	SUBCLONAL	1	TRUE	1	0.31	2		213	566	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1977024	1977024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201530243	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	69	600	2	ENST00000382891.5:c.3518C>T	p.Thr1173Met	p.T1173M	ENST00000382891	NM_133335.3	1173	aCg/aTg	20/22	1	2	FACETS	0.465	0.404	0.532	0.465	0.404	0.532	SUBCLONAL	1	TRUE	1	0.31	2		602	957	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498145	498145	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	68	442	0	ENST00000399788.2:c.113G>A	p.Arg38His	p.R38H	ENST00000399788	NM_001042603.1	38	cGc/cAc	1/28	1	2	FACETS	0.643	0.559	0.734	0.643	0.559	0.734	SUBCLONAL	1	TRUE	1	0.31	2		442	682	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170554	7170554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	36	402	0	ENST00000302850.5:c.1477G>A	p.Ala493Thr	p.A493T	ENST00000302850	NM_000208.2	493	Gca/Aca	6/22	1	2	FACETS	0.33	0.271	0.398	0.33	0.271	0.398	SUBCLONAL	1	TRUE	1	0.31	2		402	703	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212482	36212482	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	133	681	0	ENST00000222270.7:c.2233C>T	p.Gln745Ter	p.Q745*	ENST00000222270	NM_014727.1	745	Caa/Taa	3/37	1	2	FACETS	0.757	0.686	0.832	0.757	0.686	0.832	SUBCLONAL	1	TRUE	1	0.31	2		681	1133	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99163081	99163081	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	71	432	0	ENST00000074304.5:c.1087C>A	p.Pro363Thr	p.P363T	ENST00000074304	NM_001134224.1	363	Cca/Aca	13/26	1	2	FACETS	0.67	0.584	0.762	0.67	0.584	0.762	SUBCLONAL	1	TRUE	1	0.31	2		432	684	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564656	86564656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	141	607	0	ENST00000274376.6:c.388C>T	p.Pro130Ser	p.P130S	ENST00000274376	NM_002890.2	130	Cca/Tca	1/25	1	2	FACETS	0.887	0.807	0.971	0.887	0.807	0.971	CLONAL	1	TRUE	1	0.31	2		607	1026	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94067982	94067982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	38	250	0	ENST00000369303.4:c.980C>T	p.Ala327Val	p.A327V	ENST00000369303	NM_004440.3	327	gCg/gTg	4/17	1	2	FACETS	0.7	0.58	0.834	0.7	0.58	0.834	SUBCLONAL	1	TRUE	1	0.31	2		250	350	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	157	456	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.31	2		456	997	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	29	210	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.767	0.618	0.934	0.767	0.618	0.934	CLONAL	1	TRUE	1	0.31	2		210	244	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	80	410	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.721	0.634	0.814	0.721	0.634	0.814	SUBCLONAL	1	TRUE	1	0.31	2		412	716	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991949	72991949	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs753977275	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	68	729	1	ENST00000268489.5:c.2096del	p.Gly699AlafsTer125	p.G699Afs*125	ENST00000268489	NM_006885.3	699	gGc/gc	2/10	1	2	FACETS	0.52	0.452	0.595	0.52	0.452	0.595	SUBCLONAL	1	TRUE	1	0.31	2		730	843	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	44	363	5	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	0.0851335310969118	0	FACETS	0.692	0.584	0.81			1	INDETERMINATE	1	TRUE	0	0.31	0		368	283	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	21	272	0	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	0.3	4	FACETS	0.616	0.475	0.781			1	SUBCLONAL	1	TRUE	NA	0.31	4		272	288	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544703	65544703	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs387906650	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	160	559	1	ENST00000358664.4:c.223C>T	p.Arg75Ter	p.R75*	ENST00000358664	NM_002382.4	75	Cga/Tga	4/5	1	2	FACETS	0.918	0.841	1	0.918	0.841	1	CLONAL	1	TRUE	1	0.31	2		560	1124	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	35	385	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	0.776	0.638	0.929	0.776	0.638	0.929	CLONAL	1	TRUE	1	0.31	2		385	291	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396382	396382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200741961	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	195	662	1	ENST00000262320.3:c.644C>T	p.Ser215Leu	p.S215L	ENST00000262320	NM_003502.3	215	tCg/tTg	2/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.31	2		663	1181	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552152	29552152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199474738	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	36	256	0	ENST00000356175.3:c.1885G>A	p.Gly629Arg	p.G629R	ENST00000356175	NM_000267.3	629	Ggg/Agg	17/57	1	2	FACETS	0.972	0.804	1	0.972	0.804	1	CLONAL	1	TRUE	1	0.31	2		256	239	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	113	440	2	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.31	2		442	717	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	176	591	0	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	0.852	0.783	0.925	0.852	0.783	0.925	CLONAL	1	TRUE	1	0.31	2		591	1332	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154887	2154887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1212009594	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	161	582	2	ENST00000434045.2:c.334G>A	p.Ala112Thr	p.A112T	ENST00000434045	NM_001127598.1	112	Gca/Aca	4/5	1	2	FACETS	0.902	0.825	0.982	0.902	0.825	0.982	CLONAL	1	TRUE	1	0.31	2		584	1152	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	T	rs1023835002	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	135	389	0	ENST00000558401.1:c.1A>T	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Ttg	1/4	1	2	FACETS	0.999	0.908	1	0.999	0.908	1	CLONAL	1	TRUE	1	0.31	2		389	872	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606273	93606273	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	117	847	4	ENST00000375746.1:c.98del	p.Gly33AlafsTer2	p.G33Afs*2	ENST00000375746	NM_001174167.1	31	caG/ca	2/14	1	2	FACETS	0.65	0.585	0.72	0.65	0.585	0.72	SUBCLONAL	1	TRUE	1	0.31	2		851	1161	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109935	115109935	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	126	601	0	ENST00000257566.3:c.1943C>T	p.Pro648Leu	p.P648L	ENST00000257566	NM_016569.3	648	cCg/cTg	8/8	1	2	FACETS	0.802	0.725	0.883	0.802	0.725	0.883	CLONAL	1	TRUE	1	0.31	2		601	1014	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523072	25523072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369618387	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	71	615	0	ENST00000264709.3:c.113G>A	p.Arg38His	p.R38H	ENST00000264709	NM_175629.2	38	cGc/cAc	3/23	1	2	FACETS	0.371	0.322	0.424	0.371	0.322	0.424	SUBCLONAL	1	TRUE	1	0.31	2		615	1236	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1268701	1268701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748503447	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1198	233	743	0	ENST00000310581.5:c.2516C>T	p.Thr839Met	p.T839M	ENST00000310581	NM_198253.2	839	aCg/aTg	9/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.31	2		743	1431	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246488	46246488	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761166036	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	54	225	0	ENST00000334344.6:c.4582G>A	p.Ala1528Thr	p.A1528T	ENST00000334344	NM_152641.2	1528	Gca/Aca	15/21	0.3	2	FACETS	0.976	0.837	1			1	CLONAL	1	TRUE	NA	0.31	2		225	357	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943789	71943789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773085707	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	187	652	2	ENST00000298229.2:c.1832G>A	p.Arg611His	p.R611H	ENST00000298229	NM_001567.3	611	cGc/cAc	15/28	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.31	2		654	1206	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500450	149500450	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs112566969	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	101	453	1	ENST00000261799.4:c.2586+1G>A		p.X862_splice	ENST00000261799	NM_002609.3	862			1	2	FACETS	0.748	0.668	0.834	0.748	0.668	0.834	SUBCLONAL	1	TRUE	1	0.31	2		454	871	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214398	36214398	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs868041281	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	90	543	0	ENST00000222270.7:c.3057del	p.Gly1020AlafsTer4	p.G1020Afs*4	ENST00000222270	NM_014727.1	1018	Aaa/aa	7/37	1	2	FACETS	0.581	0.514	0.652	0.581	0.514	0.652	SUBCLONAL	1	TRUE	1	0.31	2		543	1000	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589609	67589610	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	12	139	0	ENST00000274335.5:c.1378dup	p.Ser460LysfsTer5	p.S460Kfs*5	ENST00000274335		458	gaa/gAaa	10/15	1	2	FACETS	0.744	0.528	1	0.744	0.528	1	CLONAL	1	TRUE	1	0.31	2		139	104	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864217	57864217	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	157	534	0	ENST00000228682.2:c.1694T>C	p.Phe565Ser	p.F565S	ENST00000228682	NM_005269.2	565	tTc/tCc	12/12	1	2	FACETS	0.982	0.899	1	0.982	0.899	1	CLONAL	1	TRUE	1	0.31	2		534	1031	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233757	133233759	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1555225139	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	111	413	0	ENST00000320574.5:c.3545_3547del	p.Lys1182del	p.K1182del	ENST00000320574	NM_006231.2	1182	aAGAtc/atc	29/49	1	2	FACETS	0.782	0.702	0.867	0.782	0.702	0.867	SUBCLONAL	1	TRUE	1	0.31	2		413	916	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610572	52610573	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	31	142	0	ENST00000394830.3:c.3600dup	p.Met1201HisfsTer23	p.M1201Hfs*23	ENST00000394830	NM_018313.4	1200	-/C	23/30	1	2	FACETS	0.585	0.474	0.71	0.585	0.474	0.71	SUBCLONAL	1	TRUE	1	0.31	2		142	342	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15967457	15967457	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777612906	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	181	481	2	ENST00000268712.3:c.5146C>T	p.Arg1716Trp	p.R1716W	ENST00000268712	NM_006311.3	1716	Cgg/Tgg	35/46	0.3	4	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.31	4		483	1135	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504391	149504391	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752228799	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	163	484	4	ENST00000261799.4:c.1811G>A	p.Arg604His	p.R604H	ENST00000261799	NM_002609.3	604	cGc/cAc	13/23	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.31	2		488	962	SUCCESS
AR	367	MSKCC	GRCh37	X	66941674	66941674	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	65	299	1	ENST00000374690.3:c.2319-1G>T		p.X773_splice	ENST00000374690	NM_000044.3	773			1	2	FACETS	0.567	0.49	0.65	0.567	0.49	0.65	SUBCLONAL	1	TRUE	1	0.31	2		300	740	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2125862	2125862	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500975	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1282	169	1206	2	ENST00000219476.3:c.2608G>A	p.Ala870Thr	p.A870T	ENST00000219476	NM_000548.3	870	Gcc/Acc	23/42	1	2	FACETS	0.751	0.689	0.817	0.751	0.689	0.817	SUBCLONAL	1	TRUE	1	0.31	2		1208	1451	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097609	27097609	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	94	436	0	ENST00000324856.7:c.3199-1G>T		p.X1067_splice	ENST00000324856	NM_006015.4	1067			1	2	FACETS	0.815	0.725	0.911	0.815	0.725	0.911	CLONAL	1	TRUE	1	0.31	2		436	744	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598251	28598251	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760115188	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1255	199	704	1	ENST00000253063.3:c.223C>T	p.Arg75Ter	p.R75*	ENST00000253063	NM_031459.4	75	Cga/Tga	3/10	1	2	FACETS	0.883	0.816	0.953	0.883	0.816	0.953	CLONAL	1	TRUE	1	0.31	2		705	1454	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841438	156841438	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1213292019	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	127	501	0	ENST00000524377.1:c.744del	p.Leu249Ter	p.L249*	ENST00000524377	NM_002529.3	247	ctG/ct	7/17	1	2	FACETS	0.87	0.787	0.957	0.87	0.787	0.957	CLONAL	1	TRUE	1	0.31	2		501	942	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746056	162746056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	92	335	0	ENST00000367921.3:c.2179G>A	p.Ala727Thr	p.A727T	ENST00000367921	NM_006182.2	727	Gct/Act	16/18	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.31	2		335	528	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114799802	114799802	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	141	430	0	ENST00000543371.1:c.469C>A	p.Pro157Thr	p.P157T	ENST00000543371	NM_001198531.1	157	Cca/Aca	5/14	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.31	2		430	897	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69458649	69458649	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	119	417	0	ENST00000227507.2:c.464T>C	p.Met155Thr	p.M155T	ENST00000227507	NM_053056.2	155	aTg/aCg	3/5	1	2	FACETS	0.868	0.783	0.959	0.868	0.783	0.959	CLONAL	1	TRUE	1	0.31	2		417	884	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431603	49431603	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	141	633	1	ENST00000301067.7:c.9536C>G	p.Thr3179Arg	p.T3179R	ENST00000301067	NM_003482.3	3179	aCa/aGa	34/54	0.3	2	FACETS	0.862	0.784	0.944			1	CLONAL	1	TRUE	NA	0.31	2		634	1055	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445472	49445472	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780891095	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1387	215	768	1	ENST00000301067.7:c.1994C>T	p.Pro665Leu	p.P665L	ENST00000301067	NM_003482.3	665	cCg/cTg	10/54	0.3	2	FACETS	0.866	0.802	0.932			1	CLONAL	1	TRUE	NA	0.31	2		769	1602	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609330	81609330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121908882	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	63	226	0	ENST00000298171.2:c.928C>T	p.Arg310Cys	p.R310C	ENST00000298171	NM_000369.2	310	Cgc/Tgc	10/10	1	2	FACETS	0.972	0.844	1	0.972	0.844	1	CLONAL	1	TRUE	1	0.31	2		226	418	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820591	3820591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373284909	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	172	604	0	ENST00000262367.5:c.2860G>A	p.Ala954Thr	p.A954T	ENST00000262367	NM_004380.2	954	Gcc/Acc	14/31	1	2	FACETS	0.87	0.798	0.944	0.87	0.798	0.944	CLONAL	1	TRUE	1	0.31	2		604	1276	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900703	3900703	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	146	483	0	ENST00000262367.5:c.393del	p.Ser132AlafsTer20	p.S132Afs*20	ENST00000262367	NM_004380.2	131	ccC/cc	2/31	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.31	2		483	925	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133172	30133172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	126	383	0	ENST00000263025.4:c.326C>T	p.Ala109Val	p.A109V	ENST00000263025	NM_002746.2	109	gCg/gTg	2/9	1	2	FACETS	0.963	0.872	1	0.963	0.872	1	CLONAL	1	TRUE	1	0.31	2		383	844	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089881	16089881	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	79	290	0	ENST00000268712.3:c.229C>A	p.Pro77Thr	p.P77T	ENST00000268712	NM_006311.3	77	Cca/Aca	3/46	0.3	4	FACETS	1	0.961	1			1	CLONAL	1	TRUE	NA	0.31	4		290	548	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602256	10602256	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	146	525	0	ENST00000171111.5:c.1322A>T	p.Glu441Val	p.E441V	ENST00000171111	NM_203500.1	441	gAg/gTg	3/6	1	2	FACETS	0.838	0.763	0.917	0.838	0.763	0.917	CLONAL	1	TRUE	1	0.31	2		525	1124	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223199	36223199	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1506	248	848	0	ENST00000222270.7:c.5749A>C	p.Ser1917Arg	p.S1917R	ENST00000222270	NM_014727.1	1917	Agc/Cgc	28/37	1	2	FACETS	0.912	0.85	0.977	0.912	0.85	0.977	CLONAL	1	TRUE	1	0.31	2		848	1754	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702166	47702167	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	64	281	0	ENST00000233146.2:c.1763_1764del	p.Tyr588CysfsTer9	p.Y588Cfs*9	ENST00000233146	NM_000251.2	588	TAt/t	12/16	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.31	2		281	395	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713406	40713406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1270158620	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	193	590	2	ENST00000373198.4:c.4109G>A	p.Arg1370His	p.R1370H	ENST00000373198	NM_133170.3	1370	cGc/cAc	30/32	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.31	2		592	1147	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725012	49725012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145575614	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	191	522	0	ENST00000449682.2:c.332G>A	p.Arg111His	p.R111H	ENST00000449682	NM_020998.3	111	cGc/cAc	3/18	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.31	2		522	1059	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467679	66467679	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	46	336	0	ENST00000273854.3:c.590C>T	p.Thr197Ile	p.T197I	ENST00000273854	NM_004439.5	197	aCa/aTa	3/18	1	2	FACETS	0.771	0.651	0.903	0.771	0.651	0.903	CLONAL	1	TRUE	1	0.31	2		336	385	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183252	56183252	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	105	455	0	ENST00000399503.3:c.4162G>T	p.Asp1388Tyr	p.D1388Y	ENST00000399503	NM_005921.1	1388	Gat/Tat	18/20	1	2	FACETS	0.909	0.815	1	0.909	0.815	1	CLONAL	1	TRUE	1	0.31	2		455	745	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020315	123020315	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1431863732	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	57	483	0	ENST00000355640.3:c.803G>A	p.Arg268Gln	p.R268Q	ENST00000355640		268	cGg/cAg	2/7	0.182118126574606	0	FACETS	0.548	0.471	0.632			1	INDETERMINATE	1	TRUE	0	0.31	0		483	463	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363624	40363624	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	61	389	0	ENST00000397332.2:c.605T>G	p.Val202Gly	p.V202G	ENST00000397332	NM_001033082.2	202	gTt/gGt	3/3	1	2	FACETS	0.561	0.483	0.645	0.561	0.483	0.645	SUBCLONAL	1	TRUE	1	0.31	2		389	702	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161332149	161332149	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	12	62	0	ENST00000367975.2:c.439del	p.Gln147SerfsTer124	p.Q147Sfs*124	ENST00000367975	NM_003001.3	146	Ccc/cc	6/6	1	2	FACETS	0.469	0.33	0.639	0.469	0.33	0.639	SUBCLONAL	1	TRUE	1	0.31	2		62	165	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104269017	104269017	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	54	386	0	ENST00000369902.3:c.274A>C	p.Ser92Arg	p.S92R	ENST00000369902	NM_016169.3	92	Agc/Cgc	2/12	1	2	FACETS	0.324	0.275	0.378	0.324	0.275	0.378	SUBCLONAL	1	TRUE	1	0.31	2		386	1075	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210824	2210824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766521628	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	68	735	0	ENST00000398665.3:c.1321G>A	p.Val441Met	p.V441M	ENST00000398665	NM_032482.2	441	Gtg/Atg	14/28	0.0851335310969118	0	FACETS	0.363	0.315	0.416			1	INDETERMINATE	1	TRUE	0	0.31	0		735	833	SUCCESS
NF2	4771	MSKCC	GRCh37	22	29999997	29999997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	51	457	0	ENST00000338641.4:c.10G>A	p.Ala4Thr	p.A4T	ENST00000338641	NM_000268.3	4	Gcc/Acc	1/16	1	2	FACETS	0.621	0.528	0.723	0.621	0.528	0.723	SUBCLONAL	1	TRUE	1	0.31	2		457	530	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163118	47163118	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	22	98	0	ENST00000409792.3:c.3008G>A	p.Cys1003Tyr	p.C1003Y	ENST00000409792	NM_014159.6	1003	tGt/tAt	3/21	1	2	FACETS	0.54	0.419	0.679	0.54	0.419	0.679	SUBCLONAL	1	TRUE	1	0.31	2		98	263	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295229	1295229	+	upstream_gene_variant	5'Flank	SNP	G	G	T	rs1396158867	NA	P-0040250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	60	491	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.68	0.586	0.783	0.68	0.586	0.783	SUBCLONAL	1	TRUE	1	0.31	2		491	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0040751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	65	851	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.114038702896705	6	FACETS	0.882	0.785	0.98			1	INDETERMINATE	4	FALSE	NA	0.470961355165804	6		851	152	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0040751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	53	579	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.457600328114874	2	FACETS	0.81	0.708	0.915	0.81	0.708	0.915	CLONAL	2	FALSE	0	0.470961355165804	2		581	139	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440635	56440635	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0040751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	160	810	2	ENST00000407977.2:c.582+1G>A		p.X194_splice	ENST00000407977		194			0.470961355165804	3	FACETS	0.916	0.868	0.963	1	0.989	1	CLONAL	4	FALSE	0	0.470961355165804	3		812	229	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935789	15935789	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	48	501	1	ENST00000268712.3:c.7144C>A	p.Gln2382Lys	p.Q2382K	ENST00000268712	NM_006311.3	2382	Cag/Aag	46/46	0.37385606904734	1	FACETS	0.986	0.85	1	0.986	0.85	1	CLONAL	1	FALSE	0	0.470961355165804	1		502	158	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0040751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	203	851	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.325585796370008	0	FACETS	0.648	0.604	0.693			1	SUBCLONAL	1	TRUE	0	0.49757187484174	0		851	633	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0040751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	145	579	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.49757187484174	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.49757187484174	1		581	392	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440635	56440635	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0040751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	391	810	2	ENST00000407977.2:c.582+1G>A		p.X194_splice	ENST00000407977		194			0.49757187484174	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.49757187484174	2		812	716	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	204	544	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.98	1	1	0.996	1	CLONAL	4	FALSE	1	0.204104674254255	2		544	453	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321372	1321372	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1319865856	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	153	562	0	ENST00000400841.2:c.383C>T	p.Ser128Leu	p.S128L	ENST00000400841		128	tCg/tTg	4/6	0.212776157442256	1	FACETS	0.888	0.823	0.954	1	0.994	1	CLONAL	4	FALSE	0	0.204104674254255	1		562	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	308	578	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.159426590929326	3	FACETS	1	0.987	1	1	0.996	1	CLONAL	4	FALSE	1	0.204104674254255	3		579	744	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224208	53224208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	275	869	0	ENST00000375401.3:c.3343C>T	p.Arg1115Cys	p.R1115C	ENST00000375401	NM_004187.3	1115	Cgc/Tgc	22/26	0.212776157442256	1	FACETS	1	0.98	1	1	0.997	1	CLONAL	4	FALSE	0	0.204104674254255	1		869	567	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	111	467	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.13152571144952	0	FACETS	0.928	0.845	1			1	CLONAL	3	FALSE	0	0.204104674254255	0		467	311	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609918	81609918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762048531	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	82	404	0	ENST00000298171.2:c.1516G>A	p.Glu506Lys	p.E506K	ENST00000298171	NM_000369.2	506	Gag/Aag	10/10	1	2	FACETS	0.943	0.848	1	1	0.989	1	CLONAL	4	FALSE	1	0.204104674254255	2		404	213	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304233	65304233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1163790865	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	137	464	0	ENST00000342505.4:c.2882C>T	p.Ser961Leu	p.S961L	ENST00000342505	NM_002227.2	961	tCg/tTg	21/25	1	2	FACETS	0.956	0.881	1	1	0.993	1	CLONAL	4	FALSE	1	0.204104674254255	2		464	351	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	123	414	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	0.159426590929326	3	FACETS	1	0.962	1	1	0.992	1	CLONAL	5	FALSE	1	0.204104674254255	3		414	249	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	86	399	0	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	0.159426590929326	3	FACETS	1	0.901	1	1	0.987	1	CLONAL	4	FALSE	1	0.204104674254255	3		399	232	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	149	483	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	0.934	0.863	1	1	0.994	1	CLONAL	4	FALSE	1	0.204104674254255	2		483	391	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039374	49039374	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853293	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	182	687	1	ENST00000267163.4:c.2359C>T	p.Arg787Ter	p.R787*	ENST00000267163	NM_000321.2	787	Cga/Tga	23/27	1	2	FACETS	0.881	0.82	0.944	1	0.995	1	CLONAL	4	FALSE	1	0.204104674254255	2		688	506	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	164	463	1	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	0.999	0.929	1	1	0.994	1	CLONAL	4	FALSE	1	0.204104674254255	2		464	402	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777894	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	236	702	0	ENST00000361445.4:c.6644C>T	p.Ser2215Phe	p.S2215F	ENST00000361445	NM_004958.3	2215	tCt/tTt	47/58	NA	2	FACETS	1	0.957	1			1	INDETERMINATE	4	FALSE	NA	0.204104674254255	2		702	567	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424409	47424409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779648831	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	100	643	2	ENST00000377045.4:c.329C>T	p.Ala110Val	p.A110V	ENST00000377045	NM_001654.4	110	gCg/gTg	5/16	0.212776157442256	1	FACETS	0.932	0.837	1	1	0.986	1	CLONAL	2	FALSE	0	0.204104674254255	1		645	472	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238402	98238402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs575035810	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	162	504	1	ENST00000331920.6:c.1642G>A	p.Val548Met	p.V548M	ENST00000331920	NM_000264.3	548	Gtg/Atg	12/24	0.204104674254255	1	FACETS	0.998	0.924	1	1	0.994	1	CLONAL	3	FALSE	0	0.204104674254255	1		505	476	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	99	294	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.159426590929326	3	FACETS	1	0.939	1	1	0.989	1	CLONAL	4	FALSE	1	0.204104674254255	3		294	256	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670774	134670774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1435725610	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	127	540	0	ENST00000398015.3:c.685G>A	p.Ala229Thr	p.A229T	ENST00000398015	NM_004441.4	229	Gca/Aca	3/16	0.159426590929326	3	FACETS	0.919	0.842	0.999	1	0.99	1	CLONAL	4	FALSE	1	0.204104674254255	3		540	373	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97897778	97897778	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	113	364	0	ENST00000289081.3:c.693G>T	p.Lys231Asn	p.K231N	ENST00000289081	NM_000136.2	231	aaG/aaT	8/15	0.204104674254255	1	FACETS	0.931	0.853	1	1	0.992	1	CLONAL	4	FALSE	0	0.204104674254255	1		364	267	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	228	647	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	0.212629386467899	4	FACETS	1	0.944	1	1	0.995	1	CLONAL	5	FALSE	2	0.204104674254255	4		647	536	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916248	9916248	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397518472	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	104	555	0	ENST00000330684.3:c.2041C>T	p.Arg681Ter	p.R681*	ENST00000330684	NM_001134407.1	681	Cga/Tga	10/13	1	2	FACETS	1	0.931	1	1	0.992	1	CLONAL	4	FALSE	1	0.204104674254255	2		555	249	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210733	5210733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779302415	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	345	811	3	ENST00000357368.4:c.5318C>T	p.Ser1773Leu	p.S1773L	ENST00000357368	NM_002850.3	1773	tCg/tTg	34/38	0.212776157442256	3	FACETS	1	0.966	1	1	0.997	1	CLONAL	5	FALSE	1	0.204104674254255	3		814	733	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278106	41278106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	127	433	0	ENST00000349496.5:c.1982G>A	p.Arg661Gln	p.R661Q	ENST00000349496	NM_001904.3	661	cGa/cAa	13/15	0.159426590929326	3	FACETS	1	0.969	1	1	0.991	1	CLONAL	4	FALSE	1	0.204104674254255	3		433	309	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	433	644	1	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	0.204104674254255	5	FACETS	1	0.991	1	1	0.998	1	CLONAL	11	FALSE	2	0.204104674254255	5		645	493	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424958105	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	8	454	0	ENST00000334344.6:c.940C>T	p.Arg314Cys	p.R314C	ENST00000334344	NM_152641.2	314	Cgt/Tgt	8/21	0.212629386467899	4	FACETS	0.27	0.173	0.398	0.135	0.086	0.199	SUBCLONAL	1	FALSE	2	0.204104674254255	4		454	349	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274114	10274114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	147	729	0	ENST00000330684.3:c.155G>A	p.Arg52Gln	p.R52Q	ENST00000330684	NM_001134407.1	52	cGa/cAa	2/13	1	2	FACETS	0.973	0.9	1	1	0.994	1	CLONAL	4	FALSE	1	0.204104674254255	2		729	370	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335040	81335040	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751819844	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	119	389	0	ENST00000222390.5:c.1787C>T	p.Thr596Met	p.T596M	ENST00000222390	NM_000601.4	596	aCg/aTg	16/18	0.212629386467899	4	FACETS	1	0.946	1	1	0.99	1	CLONAL	4	FALSE	2	0.204104674254255	4		389	335	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48922000	48922000	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1566187856	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	79	304	0	ENST00000267163.4:c.539+1G>A		p.X180_splice	ENST00000267163	NM_000321.2	180			1	2	FACETS	0.942	0.838	1	1	0.987	1	CLONAL	3	FALSE	1	0.204104674254255	2		304	274	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976817	2976817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	197	867	0	ENST00000396946.4:c.1195G>A	p.Glu399Lys	p.E399K	ENST00000396946	NM_032415.4	399	Gaa/Aaa	9/25	0.17344438373444	0	FACETS	1	0.946	1			1	CLONAL	3	FALSE	0	0.204104674254255	0		867	505	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944623	38944623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	112	420	0	ENST00000357387.3:c.4838G>A	p.Arg1613His	p.R1613H	ENST00000357387	NM_152756.3	1613	cGc/cAc	36/38	1	2	FACETS	0.924	0.843	1	1	0.992	1	CLONAL	4	FALSE	1	0.204104674254255	2		420	297	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256623	133256623	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555230189	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	150	494	0	ENST00000320574.5:c.340C>T	p.Arg114Ter	p.R114*	ENST00000320574	NM_006231.2	114	Cga/Tga	5/49	0.212629386467899	4	FACETS	1	0.941	1	1	0.993	1	CLONAL	5	FALSE	2	0.204104674254255	4		494	348	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968610	55968610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374980446	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	183	761	1	ENST00000263923.4:c.2053G>A	p.Glu685Lys	p.E685K	ENST00000263923	NM_002253.2	685	Gaa/Aaa	14/30	0.212776157442256	0	FACETS	1	0.946	1			1	CLONAL	3	FALSE	0	0.204104674254255	0		762	468	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573436	55573436	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	74	460	0	ENST00000288135.5:c.1098G>T	p.Glu366Asp	p.E366D	ENST00000288135	NM_000222.2	366	gaG/gaT	6/21	0.212776157442256	0	FACETS	0.802	0.718	0.887			1	CLONAL	4	FALSE	0	0.204104674254255	0		460	180	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637141	176637141	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	193	633	2	ENST00000439151.2:c.1741G>T	p.Glu581Ter	p.E581*	ENST00000439151	NM_022455.4	581	Gaa/Taa	5/23	1	2	FACETS	1	0.981	1	1	0.995	1	CLONAL	4	FALSE	1	0.204104674254255	2		635	421	SUCCESS
AR	367	MSKCC	GRCh37	X	66766555	66766555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	187	779	0	ENST00000374690.3:c.1567G>A	p.Glu523Lys	p.E523K	ENST00000374690	NM_000044.3	523	Gaa/Aaa	1/8	0.212776157442256	1	FACETS	1	0.979	1	1	0.995	1	CLONAL	3	FALSE	0	0.204104674254255	1		779	489	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041074	42041074	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	268	752	0	ENST00000219905.7:c.5452C>T	p.Arg1818Ter	p.R1818*	ENST00000219905	NM_001164273.1	1818	Cga/Tga	16/24	1	2	FACETS	0.992	0.937	1	1	0.996	1	CLONAL	4	FALSE	1	0.204104674254255	2		752	662	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845890	156845890	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750477154	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	315	898	1	ENST00000524377.1:c.1520G>A	p.Arg507His	p.R507H	ENST00000524377	NM_002529.3	507	cGc/cAc	13/17	1	2	FACETS	1	0.981	1	1	0.997	1	CLONAL	4	FALSE	1	0.204104674254255	2		899	724	SUCCESS
APC	324	MSKCC	GRCh37	5	112178606	112178606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1311878041	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	95	392	0	ENST00000257430.4:c.7315C>T	p.Arg2439Cys	p.R2439C	ENST00000257430	NM_000038.5	2439	Cgc/Tgc	16/16	1	2	FACETS	0.942	0.854	1	1	0.991	1	CLONAL	4	FALSE	1	0.204104674254255	2		392	247	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347916	73347916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139907646	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	109	303	0	ENST00000377767.4:c.1145G>A	p.Arg382Gln	p.R382Q	ENST00000377767	NM_014953.3	382	cGa/cAa	8/21	1	2	FACETS	1	0.948	1	1	0.992	1	CLONAL	4	FALSE	1	0.204104674254255	2		303	254	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162904	47162904	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs757432733	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	148	460	0	ENST00000409792.3:c.3222G>T	p.Lys1074Asn	p.K1074N	ENST00000409792	NM_014159.6	1074	aaG/aaT	3/21	0.159426590929326	3	FACETS	0.957	0.888	1	1	0.993	1	CLONAL	5	FALSE	1	0.204104674254255	3		460	334	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346198	70346198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	93	667	1	ENST00000374080.3:c.2549G>A	p.Arg850Gln	p.R850Q	ENST00000374080		850	cGg/cAg	19/45	0.212776157442256	1	FACETS	0.901	0.805	1	1	0.985	1	CLONAL	2	FALSE	0	0.204104674254255	1		668	454	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467875	99467875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1469290616	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	155	424	0	ENST00000268035.6:c.2744C>T	p.Ser915Leu	p.S915L	ENST00000268035	NM_000875.3	915	tCg/tTg	13/21	1	2	FACETS	1	0.934	1	1	0.994	1	CLONAL	4	FALSE	1	0.204104674254255	2		424	377	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405122	70405122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771580099	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	224	603	1	ENST00000373644.4:c.2636C>T	p.Ser879Leu	p.S879L	ENST00000373644	NM_030625.2	879	tCg/tTg	4/12	1	2	FACETS	0.903	0.851	0.956	1	0.996	1	CLONAL	5	FALSE	1	0.204104674254255	2		604	486	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715847	117715847	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	98	397	0	ENST00000368508.3:c.911G>T	p.Arg304Ile	p.R304I	ENST00000368508	NM_002944.2	304	aGa/aTa	9/43	0.212776157442256	3	FACETS	0.935	0.846	1	1	0.987	1	CLONAL	4	FALSE	1	0.204104674254255	3		397	283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519996	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	420	881	0	ENST00000269305.4:c.395A>C	p.Lys132Thr	p.K132T	ENST00000269305	NM_001126112.2	132	aAg/aCg	5/11	0.159426590929326	3	FACETS	0.969	0.927	1	1	0.997	1	CLONAL	5	FALSE	1	0.204104674254255	3		881	936	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419049	419049	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	153	531	0	ENST00000399788.2:c.3298G>T	p.Glu1100Ter	p.E1100*	ENST00000399788	NM_001042603.1	1100	Gaa/Taa	22/28	0.204104674254255	5	FACETS	0.992	0.918	1	1	0.991	1	CLONAL	5	FALSE	2	0.204104674254255	5		531	395	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367325	50367325	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	30	476	0	ENST00000331340.3:c.132G>T	p.Gln44His	p.Q44H	ENST00000331340	NM_006060.4	44	caG/caT	3/8	0.17344438373444	0	FACETS	0.629	0.507	0.767			1	SUBCLONAL	1	FALSE	0	0.204104674254255	0		476	372	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045979	47045979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556782944	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	154	920	0	ENST00000377604.3:c.2774G>A	p.Arg925His	p.R925H	ENST00000377604	NM_001204468.1	925	cGc/cAc	24/24	0.212776157442256	1	FACETS	1	0.974	1	1	0.992	1	CLONAL	2	FALSE	0	0.204104674254255	1		920	595	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911140	29911140	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	226	814	0	ENST00000376809.5:c.439T>G	p.Tyr147Asp	p.Y147D	ENST00000376809	NM_002116.7	147	Tac/Gac	3/8	0.212776157442256	3	FACETS	1	0.969	1	1	0.995	1	CLONAL	4	FALSE	1	0.204104674254255	3		814	580	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212216	98212216	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	128	338	0	ENST00000331920.6:c.3456C>A	p.Phe1152Leu	p.F1152L	ENST00000331920	NM_000264.3	1152	ttC/ttA	21/24	0.204104674254255	1	FACETS	0.926	0.853	1	1	0.993	1	CLONAL	4	FALSE	0	0.204104674254255	1		338	304	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967173	134967173	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370164002	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	135	449	1	ENST00000398015.3:c.2512G>A	p.Glu838Lys	p.E838K	ENST00000398015	NM_004441.4	838	Gag/Aag	14/16	0.159426590929326	3	FACETS	0.917	0.846	0.988	1	0.992	1	CLONAL	5	FALSE	1	0.204104674254255	3		450	318	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929133	44929133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	151	631	0	ENST00000377967.4:c.2233G>A	p.Glu745Lys	p.E745K	ENST00000377967	NM_021140.2	745	Gag/Aag	17/29	0.212776157442256	1	FACETS	1	0.961	1	1	0.994	1	CLONAL	3	FALSE	0	0.204104674254255	1		631	417	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428244	47428244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	158	750	1	ENST00000377045.4:c.1204G>A	p.Asp402Asn	p.D402N	ENST00000377045	NM_001654.4	402	Gac/Aac	11/16	0.212776157442256	1	FACETS	0.858	0.791	0.927	1	0.993	1	CLONAL	3	FALSE	0	0.204104674254255	1		751	540	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937409	76937409	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	56	458	1	ENST00000373344.5:c.3339G>T	p.Glu1113Asp	p.E1113D	ENST00000373344	NM_000489.3	1113	gaG/gaT	9/35	0.212776157442256	1	FACETS	0.926	0.801	1	1	0.976	1	CLONAL	2	FALSE	0	0.204104674254255	1		459	266	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131972841	131972841	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	167	376	0	ENST00000265335.6:c.3424G>T	p.Glu1142Ter	p.E1142*	ENST00000265335		1142	Gaa/Taa	22/25	1	2	FACETS	1	0.961	1	1	0.995	1	CLONAL	4	FALSE	1	0.204104674254255	2		376	391	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356298	66356298	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	184	545	1	ENST00000273854.3:c.1199C>T	p.Ser400Phe	p.S400F	ENST00000273854	NM_004439.5	400	tCc/tTc	5/18	0.159426590929326	3	FACETS	0.998	0.935	1	1	0.994	1	CLONAL	5	FALSE	1	0.204104674254255	3		546	398	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981315	68981315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866864487	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	180	348	0	ENST00000288368.4:c.1387C>T	p.Arg463Cys	p.R463C	ENST00000288368	NM_024870.2	463	Cgc/Tgc	12/40	0.204104674254255	5	FACETS	0.98	0.92	1	1	0.993	1	CLONAL	7	FALSE	1	0.204104674254255	5		348	336	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045858	26045858	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs774188493	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	254	652	2	ENST00000540144.1:c.220G>T	p.Glu74Ter	p.E74*	ENST00000540144	NM_003531.2	74	Gaa/Taa	1/1	0.212776157442256	3	FACETS	1	0.984	1	1	0.995	1	CLONAL	4	FALSE	1	0.204104674254255	3		654	614	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001395	150001395	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	191	613	0	ENST00000253339.5:c.2209C>T	p.Arg737Ter	p.R737*	ENST00000253339		737	Cga/Tga	4/7	0.212776157442256	3	FACETS	0.978	0.916	1	1	0.995	1	CLONAL	5	FALSE	1	0.204104674254255	3		613	422	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809220	243809220	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	85	468	0	ENST00000263826.5:c.404C>T	p.Ala135Val	p.A135V	ENST00000263826	NM_005465.4	135	gCc/gTc	4/13	1	2	FACETS	1	0.927	1	1	0.989	1	CLONAL	3	FALSE	1	0.204104674254255	2		468	266	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317623	163317623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747173543	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	114	400	1	ENST00000271452.3:c.1019C>T	p.Ser340Leu	p.S340L	ENST00000271452	NM_145697.2	340	tCg/tTg	12/14	1	2	FACETS	0.99	0.906	1	1	0.992	1	CLONAL	4	FALSE	1	0.204104674254255	2		401	282	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561756	55561756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376469897	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	86	368	0	ENST00000288135.5:c.146G>A	p.Arg49His	p.R49H	ENST00000288135	NM_000222.2	49	cGc/cAc	2/21	0.212776157442256	0	FACETS	0.844	0.757	0.934			1	CLONAL	3	FALSE	0	0.204104674254255	0		368	265	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515335	103515335	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	80	339	0	ENST00000355739.4:c.1836G>T	p.Glu612Asp	p.E612D	ENST00000355739	NM_000123.3	612	gaG/gaT	8/15	1	2	FACETS	0.912	0.824	1	1	0.99	1	CLONAL	5	FALSE	1	0.204104674254255	2		339	172	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129833	55129833	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	72	429	2	ENST00000257290.5:c.368-1G>T		p.X123_splice	ENST00000257290	NM_006206.4	123			0.212776157442256	0	FACETS	0.918	0.816	1			1	CLONAL	3	FALSE	0	0.204104674254255	0		431	204	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206719	102206719	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	112	411	1	ENST00000263464.3:c.1347G>T	p.Lys449Asn	p.K449N	ENST00000263464	NM_001165.4	449	aaG/aaT	7/9	1	2	FACETS	0.994	0.909	1	1	0.992	1	CLONAL	4	FALSE	1	0.204104674254255	2		412	276	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875096	151875096	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	14	67	0	ENST00000262189.6:c.7443-1G>T		p.X2481_splice	ENST00000262189	NM_170606.2	2481			0.212629386467899	4	FACETS	0.898	0.675	1	1	0.915	1	CLONAL	4	FALSE	2	0.204104674254255	4		67	46	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436784	110436784	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	196	847	0	ENST00000375856.3:c.1617C>A	p.Phe539Leu	p.F539L	ENST00000375856	NM_003749.2	539	ttC/ttA	1/2	1	2	FACETS	0.943	0.881	1	1	0.995	1	CLONAL	4	FALSE	1	0.204104674254255	2		847	509	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098638	2098638	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	218	575	0	ENST00000219476.3:c.22G>T	p.Asp8Tyr	p.D8Y	ENST00000219476	NM_000548.3	8	Gat/Tat	2/42	1	2	FACETS	1	0.964	1	1	0.996	1	CLONAL	4	FALSE	1	0.204104674254255	2		575	515	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907720	76907720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	99	532	0	ENST00000373344.5:c.4441C>T	p.Arg1481Trp	p.R1481W	ENST00000373344	NM_000489.3	1481	Cgg/Tgg	15/35	0.212776157442256	1	FACETS	1	0.934	1	1	0.988	1	CLONAL	2	FALSE	0	0.204104674254255	1		532	414	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937356	76937356	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	58	435	0	ENST00000373344.5:c.3392G>T	p.Arg1131Ile	p.R1131I	ENST00000373344	NM_000489.3	1131	aGa/aTa	9/35	0.212776157442256	1	FACETS	1	0.872	1	1	0.979	1	CLONAL	2	FALSE	0	0.204104674254255	1		435	254	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845814	151845814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	194	715	2	ENST00000262189.6:c.13198C>T	p.Arg4400Trp	p.R4400W	ENST00000262189	NM_170606.2	4400	Cgg/Tgg	52/59	0.212629386467899	4	FACETS	0.946	0.884	1	1	0.994	1	CLONAL	5	FALSE	2	0.204104674254255	4		717	484	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125036	46125036	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	130	261	0	ENST00000334344.6:c.223G>T	p.Glu75Ter	p.E75*	ENST00000334344	NM_152641.2	75	Gag/Tag	3/21	0.212629386467899	4	FACETS	0.938	0.863	1	1	0.992	1	CLONAL	5	FALSE	2	0.204104674254255	4		261	327	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293070	91293070	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs569086568	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	131	510	0	ENST00000355112.3:c.572G>T	p.Arg191Ile	p.R191I	ENST00000355112	NM_000057.2	191	aGa/aTa	3/22	1	2	FACETS	0.972	0.895	1	1	0.993	1	CLONAL	4	FALSE	1	0.204104674254255	2		510	330	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934254	48934254	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1131690904	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	144	449	0	ENST00000267163.4:c.709G>T	p.Glu237Ter	p.E237*	ENST00000267163	NM_000321.2	237	Gaa/Taa	7/27	1	2	FACETS	1	0.965	1	1	0.993	1	CLONAL	3	FALSE	1	0.204104674254255	2		449	433	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164709	36164709	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1350744261	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	249	820	1	ENST00000300305.3:c.1166C>T	p.Ser389Leu	p.S389L	ENST00000300305		389	tCg/tTg	8/8	1	2	FACETS	0.997	0.939	1	1	0.996	1	CLONAL	4	FALSE	1	0.204104674254255	2		821	612	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192078	108192078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200431631	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	210	529	0	ENST00000278616.4:c.6503C>T	p.Ser2168Leu	p.S2168L	ENST00000278616	NM_000051.3	2168	tCg/tTg	45/63	1	2	FACETS	1	0.971	1	1	0.996	1	CLONAL	4	FALSE	1	0.204104674254255	2		529	487	SUCCESS
APC	324	MSKCC	GRCh37	5	112177377	112177377	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	83	357	0	ENST00000257430.4:c.6086C>A	p.Ser2029Tyr	p.S2029Y	ENST00000257430	NM_000038.5	2029	tCt/tAt	16/16	1	2	FACETS	1	0.913	1	1	0.99	1	CLONAL	5	FALSE	1	0.204104674254255	2		357	162	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800592	32800592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771425114	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	330	736	2	ENST00000374899.4:c.955C>T	p.Arg319Trp	p.R319W	ENST00000374899	NM_018833.2	319	Cgg/Tgg	6/12	0.212776157442256	3	FACETS	1	0.958	1	1	0.997	1	CLONAL	5	FALSE	1	0.204104674254255	3		738	708	SUCCESS
AR	367	MSKCC	GRCh37	X	66765677	66765677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1315081227	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	129	1063	1	ENST00000374690.3:c.689C>T	p.Ser230Leu	p.S230L	ENST00000374690	NM_000044.3	230	tCg/tTg	1/8	0.212776157442256	1	FACETS	1	0.975	1	1	0.991	1	CLONAL	2	FALSE	0	0.204104674254255	1		1064	479	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317915	8317915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748481193	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	88	452	0	ENST00000356435.5:c.5698G>A	p.Ala1900Thr	p.A1900T	ENST00000356435		1900	Gca/Aca	35/35	0.204104674254255	1	FACETS	1	0.916	1	1	0.989	1	CLONAL	3	FALSE	0	0.204104674254255	1		452	253	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877387	28877387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747687298	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	158	536	0	ENST00000282397.4:c.3934G>A	p.Ala1312Thr	p.A1312T	ENST00000282397	NM_002019.4	1312	Gct/Act	30/30	1	2	FACETS	0.882	0.816	0.949	1	0.994	1	CLONAL	4	FALSE	1	0.204104674254255	2		536	439	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771828	135771828	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	41	741	0	ENST00000298552.3:c.3289C>A	p.Arg1097Ser	p.R1097S	ENST00000298552	NM_001162426.1	1097	Cgt/Agt	23/23	0.204104674254255	1	FACETS	0.639	0.531	0.758	0.639	0.531	0.758	SUBCLONAL	1	FALSE	0	0.204104674254255	1		741	565	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236109	108236109	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	150	561	0	ENST00000278616.4:c.9045G>T	p.Glu3015Asp	p.E3015D	ENST00000278616	NM_000051.3	3015	gaG/gaT	63/63	1	2	FACETS	1	0.935	1	1	0.994	1	CLONAL	4	FALSE	1	0.204104674254255	2		561	364	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499355	89499355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758183213	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	221	403	0	ENST00000336596.2:c.2525G>A	p.Arg842Gln	p.R842Q	ENST00000336596	NM_005233.5	842	cGa/cAa	15/17	0.159426590929326	3	FACETS	1	0.946	1	1	0.995	1	CLONAL	5	FALSE	1	0.204104674254255	3		403	475	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90627542	90627542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1222149957	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	234	661	1	ENST00000330062.3:c.1315G>A	p.Asp439Asn	p.D439N	ENST00000330062	NM_002168.2	439	Gac/Aac	11/11	1	2	FACETS	1	0.949	1	1	0.996	1	CLONAL	4	FALSE	1	0.204104674254255	2		662	568	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216434	7216434	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs192050225	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	273	773	1	ENST00000380728.2:c.814C>T	p.Arg272Cys	p.R272C	ENST00000380728		272	Cgc/Tgc	10/11	0.159426590929326	3	FACETS	0.946	0.892	1	1	0.995	1	CLONAL	4	FALSE	1	0.204104674254255	3		774	779	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281838	39281838	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	164	581	1	ENST00000402219.2:c.637C>T	p.Arg213Ter	p.R213*	ENST00000402219	NM_005633.3	213	Cga/Tga	5/23	1	2	FACETS	0.99	0.919	1	1	0.994	1	CLONAL	4	FALSE	1	0.204104674254255	2		582	406	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635547	47635547	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	84	278	0	ENST00000233146.2:c.219G>T	p.Lys73Asn	p.K73N	ENST00000233146	NM_000251.2	73	aaG/aaT	2/16	1	2	FACETS	0.948	0.854	1	1	0.99	1	CLONAL	4	FALSE	1	0.204104674254255	2		278	217	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670680	86670680	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	78	242	0	ENST00000274376.6:c.1958G>T	p.Arg653Ile	p.R653I	ENST00000274376	NM_002890.2	653	aGa/aTa	15/25	1	2	FACETS	0.985	0.884	1	1	0.989	1	CLONAL	4	FALSE	1	0.204104674254255	2		242	194	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797005	42797005	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148703020	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	352	858	0	ENST00000575354.2:c.3463G>A	p.Ala1155Thr	p.A1155T	ENST00000575354	NM_015125.3	1155	Gcc/Acc	14/20	0.212776157442256	3	FACETS	0.948	0.903	0.993	1	0.997	1	CLONAL	5	FALSE	1	0.204104674254255	3		858	802	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257530	16257530	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	110	442	0	ENST00000375759.3:c.4795G>T	p.Glu1599Ter	p.E1599*	ENST00000375759	NM_015001.2	1599	Gaa/Taa	11/15	0.204104674254255	5	FACETS	0.985	0.898	1	1	0.987	1	CLONAL	5	FALSE	2	0.204104674254255	5		442	286	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528243	157528243	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs797045283	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	177	632	1	ENST00000346085.5:c.5968C>T	p.Arg1990Ter	p.R1990*	ENST00000346085	NM_020732.3	1990	Cga/Tga	20/20	0.212776157442256	3	FACETS	1	0.952	1	1	0.993	1	CLONAL	4	FALSE	1	0.204104674254255	3		633	464	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073845	8073845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	110	399	0	ENST00000377482.5:c.814G>A	p.Ala272Thr	p.A272T	ENST00000377482	NM_018948.3	272	Gct/Act	4/4	NA	2	FACETS	1	0.955	1			1	INDETERMINATE	4	FALSE	NA	0.204104674254255	2		399	253	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245910	41245910	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	188	621	0	ENST00000357654.3:c.1638G>T	p.Met546Ile	p.M546I	ENST00000357654	NM_007294.3	546	atG/atT	10/23	0.159426590929326	3	FACETS	0.923	0.863	0.984	1	0.994	1	CLONAL	5	FALSE	1	0.204104674254255	3		621	440	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131315	202131315	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	140	511	1	ENST00000358485.4:c.283G>T	p.Glu95Ter	p.E95*	ENST00000358485	NM_001080125.1	95	Gaa/Taa	2/9	1	2	FACETS	0.912	0.841	0.985	1	0.993	1	CLONAL	4	FALSE	1	0.204104674254255	2		512	376	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926518	59926518	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1330277587	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	217	578	0	ENST00000259008.2:c.479G>T	p.Arg160Ile	p.R160I	ENST00000259008	NM_032043.2	160	aGa/aTa	5/20	0.159426590929326	3	FACETS	1	0.976	1	1	0.995	1	CLONAL	4	FALSE	1	0.204104674254255	3		578	543	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542914	187542914	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	41	323	0	ENST00000441802.2:c.4826C>A	p.Ser1609Tyr	p.S1609Y	ENST00000441802	NM_005245.3	1609	tCt/tAt	10/27	0.159426590929326	3	FACETS	1	0.863	1	1	0.962	1	CLONAL	3	FALSE	1	0.204104674254255	3		323	145	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111886044	111886044	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769682050	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	219	655	0	ENST00000341259.2:c.1666G>A	p.Glu556Lys	p.E556K	ENST00000341259	NM_005475.2	556	Gaa/Aaa	8/8	0.212629386467899	4	FACETS	0.952	0.893	1	1	0.995	1	CLONAL	5	FALSE	2	0.204104674254255	4		655	543	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394441	162394441	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	89	382	0	ENST00000366898.1:c.627C>A	p.Phe209Leu	p.F209L	ENST00000366898	NM_004562.2	209	ttC/ttA	6/12	0.212776157442256	3	FACETS	1	0.945	1	1	0.988	1	CLONAL	4	FALSE	1	0.204104674254255	3		382	225	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467623	66467623	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	91	421	0	ENST00000273854.3:c.646G>T	p.Asp216Tyr	p.D216Y	ENST00000273854	NM_004439.5	216	Gat/Tat	3/18	0.159426590929326	3	FACETS	0.987	0.891	1	1	0.987	1	CLONAL	4	FALSE	1	0.204104674254255	3		421	249	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937769	76937769	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs371962239	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	171	544	0	ENST00000373344.5:c.2979G>T	p.Lys993Asn	p.K993N	ENST00000373344	NM_000489.3	993	aaG/aaT	9/35	0.212776157442256	1	FACETS	0.904	0.846	0.961	1	0.995	1	CLONAL	5	FALSE	0	0.204104674254255	1		544	333	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16248759	16248759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775761539	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	151	428	0	ENST00000375759.3:c.1765C>T	p.Arg589Trp	p.R589W	ENST00000375759	NM_015001.2	589	Cgg/Tgg	10/15	0.204104674254255	5	FACETS	1	0.971	1	1	0.992	1	CLONAL	5	FALSE	2	0.204104674254255	5		428	354	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106485	27106485	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	229	744	0	ENST00000324856.7:c.6096A>C	p.Glu2032Asp	p.E2032D	ENST00000324856	NM_006015.4	2032	gaA/gaC	20/20	0.204104674254255	5	FACETS	0.916	0.859	0.974	1	0.993	1	CLONAL	5	FALSE	2	0.204104674254255	5		744	640	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65300337	65300337	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	80	253	0	ENST00000342505.4:c.3373T>C	p.Tyr1125His	p.Y1125H	ENST00000342505	NM_002227.2	1125	Tat/Cat	25/25	1	2	FACETS	1	0.899	1	1	0.989	1	CLONAL	4	FALSE	1	0.204104674254255	2		253	196	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464428	120464428	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs747138507	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	100	450	0	ENST00000256646.2:c.5218C>A	p.Leu1740Ile	p.L1740I	ENST00000256646	NM_024408.3	1740	Ctc/Atc	29/34	1	2	FACETS	0.897	0.814	0.983	1	0.991	1	CLONAL	4	FALSE	1	0.204104674254255	2		450	273	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120502051	120502051	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	146	484	0	ENST00000256646.2:c.1990A>C	p.Asn664His	p.N664H	ENST00000256646	NM_024408.3	664	Aat/Cat	12/34	1	2	FACETS	0.903	0.838	0.968	1	0.994	1	CLONAL	5	FALSE	1	0.204104674254255	2		484	317	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551988	150551988	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	335	504	0	ENST00000369026.2:c.19A>C	p.Asn7His	p.N7H	ENST00000369026	NM_021960.4	7	Aac/Cac	1/3	1	2	FACETS	0.949	0.901	0.997	1	0.997	1	CLONAL	4	FALSE	1	0.204104674254255	2		504	865	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740150	162740150	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	198	546	0	ENST00000367921.3:c.1352C>A	p.Ser451Tyr	p.S451Y	ENST00000367921	NM_006182.2	451	tCt/tAt	12/18	1	2	FACETS	1	0.94	1	1	0.995	1	CLONAL	4	FALSE	1	0.204104674254255	2		546	483	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163310172	163310172	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	164	529	0	ENST00000271452.3:c.625A>C	p.Asn209His	p.N209H	ENST00000271452	NM_145697.2	209	Aat/Cat	9/14	1	2	FACETS	1	0.96	1	1	0.995	1	CLONAL	4	FALSE	1	0.204104674254255	2		529	384	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163313548	163313548	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	119	274	0	ENST00000271452.3:c.695C>A	p.Ser232Tyr	p.S232Y	ENST00000271452	NM_145697.2	232	tCt/tAt	10/14	1	2	FACETS	1	0.931	1	1	0.993	1	CLONAL	4	FALSE	1	0.204104674254255	2		274	287	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176105634	176105634	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	170	414	0	ENST00000367669.3:c.881A>C	p.Lys294Thr	p.K294T	ENST00000367669	NM_022457.5	294	aAg/aCg	7/20	1	2	FACETS	1	0.979	1	1	0.995	1	CLONAL	4	FALSE	1	0.204104674254255	2		414	371	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206661305	206661305	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	174	642	1	ENST00000367120.3:c.1671C>A	p.Phe557Leu	p.F557L	ENST00000367120	NM_014002.3	557	ttC/ttA	16/22	1	2	FACETS	0.929	0.863	0.995	1	0.995	1	CLONAL	4	FALSE	1	0.204104674254255	2		643	459	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727126	243727126	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	31	431	0	ENST00000263826.5:c.844G>T	p.Asp282Tyr	p.D282Y	ENST00000263826	NM_005465.4	282	Gat/Tat	9/13	1	2	FACETS	0.989	0.802	1	0.989	0.802	1	CLONAL	1	FALSE	1	0.204104674254255	2		431	307	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720853	89720853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1085308040	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	161	386	0	ENST00000371953.3:c.1004G>A	p.Arg335Gln	p.R335Q	ENST00000371953	NM_000314.4	335	cGa/cAa	8/9	1	2	FACETS	0.953	0.884	1	1	0.994	1	CLONAL	4	FALSE	1	0.204104674254255	2		386	414	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514203	69514203	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	180	782	0	ENST00000294312.3:c.478C>A	p.Leu160Ile	p.L160I	ENST00000294312	NM_005117.2	160	Ctt/Att	3/3	1	2	FACETS	1	0.981	1	1	0.995	1	CLONAL	3	FALSE	1	0.204104674254255	2		782	508	SUCCESS
EED	8726	MSKCC	GRCh37	11	85961451	85961451	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	122	291	0	ENST00000263360.6:c.228G>T	p.Lys76Asn	p.K76N	ENST00000263360	NM_003797.3	76	aaG/aaT	2/12	1	2	FACETS	1	0.961	1	1	0.993	1	CLONAL	4	FALSE	1	0.204104674254255	2		291	278	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375887	118375887	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	154	549	0	ENST00000534358.1:c.9280C>A	p.Leu3094Ile	p.L3094I	ENST00000534358	NM_005933.3	3094	Ctc/Atc	27/36	1	2	FACETS	0.904	0.84	0.967	1	0.994	1	CLONAL	5	FALSE	1	0.204104674254255	2		549	334	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142573	119142573	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	148	403	0	ENST00000264033.4:c.572G>T	p.Arg191Ile	p.R191I	ENST00000264033	NM_005188.3	191	aGa/aTa	3/16	1	2	FACETS	0.999	0.925	1	1	0.994	1	CLONAL	4	FALSE	1	0.204104674254255	2		403	363	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402022	402022	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	153	383	0	ENST00000399788.2:c.4769A>G	p.Asp1590Gly	p.D1590G	ENST00000399788	NM_001042603.1	1590	gAc/gGc	27/28	0.204104674254255	5	FACETS	0.943	0.876	1	1	0.992	1	CLONAL	6	FALSE	2	0.204104674254255	5		383	346	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656229	18656229	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	80	391	0	ENST00000266497.5:c.2908G>T	p.Val970Leu	p.V970L	ENST00000266497		970	Gta/Tta	21/31	0.212776157442256	0	FACETS	1	0.898	1			1	CLONAL	3	FALSE	0	0.204104674254255	0		391	208	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624446	21624446	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	196	593	0	ENST00000421138.2:c.1583G>T	p.Arg528Ile	p.R528I	ENST00000421138		528	aGa/aTa	14/16	0.212776157442256	0	FACETS	0.794	0.743	0.847			1	SUBCLONAL	4	FALSE	0	0.204104674254255	0		593	481	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420037	49420037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1175643324	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	287	648	0	ENST00000301067.7:c.15712C>T	p.Arg5238Trp	p.R5238W	ENST00000301067	NM_003482.3	5238	Cgg/Tgg	48/54	0.212629386467899	4	FACETS	1	0.955	1	1	0.996	1	CLONAL	5	FALSE	2	0.204104674254255	4		648	671	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426056	49426056	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	260	766	0	ENST00000301067.7:c.12432G>C	p.Gln4144His	p.Q4144H	ENST00000301067	NM_003482.3	4144	caG/caC	39/54	0.212629386467899	4	FACETS	0.974	0.919	1	1	0.996	1	CLONAL	5	FALSE	2	0.204104674254255	4		766	630	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858561	57858561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763470494	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	404	817	3	ENST00000228682.2:c.299G>A	p.Arg100His	p.R100H	ENST00000228682	NM_005269.2	100	cGc/cAc	4/12	0.212629386467899	4	FACETS	1	0.98	1	1	0.997	1	CLONAL	5	FALSE	2	0.204104674254255	4		820	915	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858584	57858584	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	354	816	0	ENST00000228682.2:c.322G>T	p.Ala108Ser	p.A108S	ENST00000228682	NM_005269.2	108	Gct/Tct	4/12	0.212629386467899	4	FACETS	0.998	0.95	1	1	0.997	1	CLONAL	5	FALSE	2	0.204104674254255	4		816	837	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910540	32910540	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	76	369	0	ENST00000380152.3:c.2048C>A	p.Ser683Tyr	p.S683Y	ENST00000380152		683	tCt/tAt	11/27	1	2	FACETS	1	0.91	1	1	0.987	1	CLONAL	3	FALSE	1	0.204104674254255	2		369	242	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912242	32912242	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	167	602	0	ENST00000380152.3:c.3750A>C	p.Glu1250Asp	p.E1250D	ENST00000380152		1250	gaA/gaC	11/27	1	2	FACETS	0.897	0.832	0.963	1	0.994	1	CLONAL	4	FALSE	1	0.204104674254255	2		602	456	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929164	32929164	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	167	575	0	ENST00000380152.3:c.7174A>C	p.Lys2392Gln	p.K2392Q	ENST00000380152		2392	Aaa/Caa	14/27	1	2	FACETS	1	0.962	1	1	0.995	1	CLONAL	4	FALSE	1	0.204104674254255	2		575	390	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953976	32953976	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587781497	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	136	460	0	ENST00000380152.3:c.9043A>G	p.Lys3015Glu	p.K3015E	ENST00000380152		3015	Aaa/Gaa	23/27	1	2	FACETS	1	0.961	1	1	0.994	1	CLONAL	4	FALSE	1	0.204104674254255	2		460	313	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133767	41133767	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	31	434	1	ENST00000379561.5:c.1861G>T	p.Asp621Tyr	p.D621Y	ENST00000379561	NM_002015.3	621	Gac/Tac	2/3	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	FALSE	1	0.204104674254255	2		435	217	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49280961	49280961	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	19	472	0	ENST00000282018.3:c.8G>T	p.Arg3Ile	p.R3I	ENST00000282018	NM_020377.2	3	aGa/aTa	1/1	1	2	FACETS	0.705	0.536	0.904	0.705	0.536	0.904	CLONAL	1	FALSE	1	0.204104674254255	2		472	264	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987193	36987193	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	185	798	0	ENST00000354822.5:c.496A>C	p.Asn166His	p.N166H	ENST00000354822	NM_001079668.2	166	Aac/Cac	3/3	1	2	FACETS	1	0.952	1	1	0.995	1	CLONAL	4	FALSE	1	0.204104674254255	2		798	443	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574308	95574308	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	85	357	0	ENST00000393063.1:c.2559A>G	p.Ile853Met	p.I853M	ENST00000393063	NM_030621.3	853	atA/atG	17/28	1	2	FACETS	0.992	0.895	1	1	0.99	1	CLONAL	4	FALSE	1	0.204104674254255	2		357	210	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005692	42005692	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	42	197	0	ENST00000219905.7:c.3428A>G	p.Tyr1143Cys	p.Y1143C	ENST00000219905	NM_001164273.1	1143	tAc/tGc	9/24	1	2	FACETS	0.999	0.861	1	1	0.98	1	CLONAL	4	FALSE	1	0.204104674254255	2		197	103	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028861	42028861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769019565	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	195	582	2	ENST00000219905.7:c.4399C>T	p.Arg1467Cys	p.R1467C	ENST00000219905	NM_001164273.1	1467	Cgt/Tgt	13/24	1	2	FACETS	0.938	0.876	1	1	0.995	1	CLONAL	4	FALSE	1	0.204104674254255	2		584	509	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748394	43748394	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	224	798	0	ENST00000382044.4:c.2412G>T	p.Glu804Asp	p.E804D	ENST00000382044	NM_001141980.1	804	gaG/gaT	12/28	1	2	FACETS	1	0.982	1	1	0.996	1	CLONAL	4	FALSE	1	0.204104674254255	2		798	495	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303967	91303967	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	161	624	0	ENST00000355112.3:c.1364T>G	p.Phe455Cys	p.F455C	ENST00000355112	NM_000057.2	455	tTt/tGt	7/22	1	2	FACETS	0.984	0.913	1	1	0.994	1	CLONAL	4	FALSE	1	0.204104674254255	2		624	401	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100477	2100477	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	237	459	0	ENST00000219476.3:c.215A>C	p.Lys72Thr	p.K72T	ENST00000219476	NM_000548.3	72	aAa/aCa	3/42	1	2	FACETS	1	0.971	1	1	0.996	1	CLONAL	4	FALSE	1	0.204104674254255	2		459	554	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647649	3647649	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	321	961	0	ENST00000294008.3:c.1414T>G	p.Leu472Val	p.L472V	ENST00000294008	NM_032444.2	472	Tta/Gta	7/15	1	2	FACETS	1	0.983	1	1	0.997	1	CLONAL	4	FALSE	1	0.204104674254255	2		961	730	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858619	9858619	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	100	508	0	ENST00000330684.3:c.2782G>T	p.Gly928Cys	p.G928C	ENST00000330684	NM_001134407.1	928	Ggt/Tgt	13/13	1	2	FACETS	1	0.947	1	1	0.991	1	CLONAL	4	FALSE	1	0.204104674254255	2		508	232	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916274	9916274	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	59	485	0	ENST00000330684.3:c.2015G>T	p.Arg672Ile	p.R672I	ENST00000330684	NM_001134407.1	672	aGa/aTa	10/13	1	2	FACETS	1	0.942	1	1	0.985	1	CLONAL	3	FALSE	1	0.204104674254255	2		485	171	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934881	9934881	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs752320310	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	91	550	2	ENST00000330684.3:c.1409C>A	p.Thr470Asn	p.T470N	ENST00000330684	NM_001134407.1	470	aCt/aAt	6/13	1	2	FACETS	0.982	0.889	1	1	0.99	1	CLONAL	4	FALSE	1	0.204104674254255	2		552	227	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042059	14042059	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	169	388	0	ENST00000311895.7:c.2606A>G	p.His869Arg	p.H869R	ENST00000311895	NM_005236.2	869	cAc/cGc	11/11	1	2	FACETS	1	0.971	1	1	0.995	1	CLONAL	4	FALSE	1	0.204104674254255	2		388	385	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829684	72829684	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	203	712	0	ENST00000268489.5:c.6897G>T	p.Lys2299Asn	p.K2299N	ENST00000268489	NM_006885.3	2299	aaG/aaT	9/10	1	2	FACETS	1	0.979	1	1	0.996	1	CLONAL	4	FALSE	1	0.204104674254255	2		712	452	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888055	81888055	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	61	371	0	ENST00000359376.3:c.200T>C	p.Ile67Thr	p.I67T	ENST00000359376	NM_002661.3	67	aTc/aCc	3/33	0.204104674254255	0	FACETS	0.991	0.875	1			1	CLONAL	3	FALSE	0	0.204104674254255	0		371	160	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81892762	81892762	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	65	359	0	ENST00000359376.3:c.473G>T	p.Arg158Ile	p.R158I	ENST00000359376	NM_002661.3	158	aGa/aTa	5/33	0.204104674254255	0	FACETS	0.934	0.826	1			1	CLONAL	3	FALSE	0	0.204104674254255	0		359	181	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350844	89350844	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	312	851	0	ENST00000301030.4:c.2106A>C	p.Lys702Asn	p.K702N	ENST00000301030	NM_001256183.1	702	aaA/aaC	9/13	0.212776157442256	4	FACETS	0.995	0.944	1			1	CLONAL	5	FALSE	NA	0.204104674254255	4		851	740	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7978965	7978965	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	238	559	0	ENST00000319144.4:c.1602G>T	p.Gln534His	p.Q534H	ENST00000319144	NM_001139.2	534	caG/caT	12/15	0.159426590929326	3	FACETS	1	0.974	1	1	0.996	1	CLONAL	5	FALSE	1	0.204104674254255	3		559	489	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556164	29556164	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs137854566	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	21	126	0	ENST00000356175.3:c.2531T>G	p.Leu844Arg	p.L844R	ENST00000356175	NM_000267.3	844	cTt/cGt	21/57	0.159426590929326	3	FACETS	1	0.851	1	1	0.951	1	CLONAL	4	FALSE	1	0.204104674254255	3		126	53	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811563	56811563	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	199	519	0	ENST00000337432.4:c.1111G>T	p.Asp371Tyr	p.D371Y	ENST00000337432	NM_058216.2	371	Gac/Tac	9/9	0.159426590929326	3	FACETS	0.97	0.91	1	1	0.995	1	CLONAL	5	FALSE	1	0.204104674254255	3		519	443	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763257	59763257	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	175	687	0	ENST00000259008.2:c.2845C>A	p.Pro949Thr	p.P949T	ENST00000259008	NM_032043.2	949	Cct/Act	19/20	0.159426590929326	3	FACETS	1	0.932	1	1	0.993	1	CLONAL	4	FALSE	1	0.204104674254255	3		687	471	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573551	48573551	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	85	294	0	ENST00000342988.3:c.135G>T	p.Lys45Asn	p.K45N	ENST00000342988	NM_005359.5	45	aaG/aaT	2/12	0.13152571144952	0	FACETS	0.825	0.745	0.906			1	CLONAL	4	FALSE	0	0.204104674254255	0		294	201	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117307	7117307	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	301	764	1	ENST00000302850.5:c.3909C>A	p.Phe1303Leu	p.F1303L	ENST00000302850	NM_000208.2	1303	ttC/ttA	22/22	0.212776157442256	3	FACETS	1	0.979	1	1	0.996	1	CLONAL	5	FALSE	1	0.204104674254255	3		765	618	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277050	18277050	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	290	644	0	ENST00000222254.8:c.1497G>T	p.Glu499Asp	p.E499D	ENST00000222254	NM_005027.3	499	gaG/gaT	12/16	0.212776157442256	3	FACETS	0.945	0.895	0.994	1	0.996	1	CLONAL	5	FALSE	1	0.204104674254255	3		644	663	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229290	36229290	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	270	742	0	ENST00000222270.7:c.7980C>A	p.Phe2660Leu	p.F2660L	ENST00000222270	NM_014727.1	2660	ttC/ttA	37/37	0.212776157442256	3	FACETS	1	0.983	1	1	0.996	1	CLONAL	4	FALSE	1	0.204104674254255	3		742	665	SUCCESS
ALK	238	MSKCC	GRCh37	2	29448332	29448332	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	245	1054	0	ENST00000389048.3:c.3167T>G	p.Met1056Arg	p.M1056R	ENST00000389048	NM_004304.4	1056	aTg/aGg	19/29	1	2	FACETS	0.945	0.889	1	1	0.996	1	CLONAL	4	FALSE	1	0.204104674254255	2		1054	635	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241979	39241979	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs727505093	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	106	321	0	ENST00000402219.2:c.1867T>G	p.Phe623Val	p.F623V	ENST00000402219	NM_005633.3	623	Ttt/Gtt	11/23	1	2	FACETS	0.889	0.809	0.972	1	0.991	1	CLONAL	4	FALSE	1	0.204104674254255	2		321	292	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606979	47606979	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	181	473	0	ENST00000263735.4:c.729T>G	p.Asp243Glu	p.D243E	ENST00000263735	NM_002354.2	243	gaT/gaG	7/9	1	2	FACETS	1	0.948	1	1	0.995	1	CLONAL	4	FALSE	1	0.204104674254255	2		473	435	SUCCESS
REL	5966	MSKCC	GRCh37	2	61148965	61148965	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	119	358	0	ENST00000295025.8:c.1155A>T	p.Glu385Asp	p.E385D	ENST00000295025	NM_002908.2	385	gaA/gaT	11/11	1	2	FACETS	0.946	0.867	1	1	0.992	1	CLONAL	4	FALSE	1	0.204104674254255	2		358	308	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715790	61715790	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	152	396	0	ENST00000401558.2:c.2139T>G	p.Ile713Met	p.I713M	ENST00000401558	NM_003400.3	713	atT/atG	18/25	1	2	FACETS	0.919	0.855	0.984	1	0.994	1	CLONAL	5	FALSE	1	0.204104674254255	2		396	324	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39745020	39745020	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	174	498	0	ENST00000361337.2:c.1810G>T	p.Glu604Ter	p.E604*	ENST00000361337	NM_003286.2	604	Gaa/Taa	17/21	1	2	FACETS	1	0.966	1	1	0.995	1	CLONAL	4	FALSE	1	0.204104674254255	2		498	403	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750337	39750337	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	41	335	0	ENST00000361337.2:c.1952T>C	p.Ile651Thr	p.I651T	ENST00000361337	NM_003286.2	651	aTt/aCt	19/21	1	2	FACETS	0.87	0.731	1	1	0.965	1	CLONAL	2	FALSE	1	0.204104674254255	2		335	231	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537219	41537219	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	247	570	0	ENST00000263253.7:c.2046G>T	p.Met682Ile	p.M682I	ENST00000263253	NM_001429.3	682	atG/atT	10/31	0.159426590929326	3	FACETS	1	0.981	1	1	0.995	1	CLONAL	4	FALSE	1	0.204104674254255	3		570	608	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713145	30713145	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	71	293	0	ENST00000295754.5:c.470A>C	p.Asn157Thr	p.N157T	ENST00000295754	NM_003242.5	157	aAt/aCt	4/7	0.159426590929326	3	FACETS	0.978	0.87	1	1	0.983	1	CLONAL	4	FALSE	1	0.204104674254255	3		293	196	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266472	41266472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	60	456	0	ENST00000349496.5:c.269G>A	p.Arg90Gln	p.R90Q	ENST00000349496	NM_001904.3	90	cGa/cAa	4/15	0.159426590929326	3	FACETS	0.97	0.841	1	0.97	0.841	1	CLONAL	2	FALSE	1	0.204104674254255	3		456	334	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268795	41268795	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	175	527	0	ENST00000349496.5:c.1033A>C	p.Lys345Gln	p.K345Q	ENST00000349496	NM_001904.3	345	Aag/Cag	7/15	0.159426590929326	3	FACETS	1	0.958	1	1	0.994	1	CLONAL	5	FALSE	1	0.204104674254255	3		527	366	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139559	47139559	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	123	322	0	ENST00000409792.3:c.5028G>T	p.Gln1676His	p.Q1676H	ENST00000409792	NM_014159.6	1676	caG/caT	9/21	0.159426590929326	3	FACETS	1	0.968	1	1	0.991	1	CLONAL	4	FALSE	1	0.204104674254255	3		322	299	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162745	47162745	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	162	418	0	ENST00000409792.3:c.3381A>C	p.Gln1127His	p.Q1127H	ENST00000409792	NM_014159.6	1127	caA/caC	3/21	0.159426590929326	3	FACETS	1	0.971	1	1	0.994	1	CLONAL	5	FALSE	1	0.204104674254255	3		418	326	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164316	47164316	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	105	373	0	ENST00000409792.3:c.1810A>C	p.Asn604His	p.N604H	ENST00000409792	NM_014159.6	604	Aat/Cat	3/21	0.159426590929326	3	FACETS	1	0.956	1	1	0.99	1	CLONAL	4	FALSE	1	0.204104674254255	3		373	262	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651490	52651490	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	246	546	0	ENST00000394830.3:c.1606C>A	p.Pro536Thr	p.P536T	ENST00000394830	NM_018313.4	536	Cca/Aca	15/30	0.159426590929326	3	FACETS	1	0.965	1	1	0.996	1	CLONAL	5	FALSE	1	0.204104674254255	3		546	517	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026848	71026848	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	89	291	0	ENST00000318789.4:c.1374T>G	p.Phe458Leu	p.F458L	ENST00000318789	NM_032682.5	458	ttT/ttG	16/21	0.159426590929326	3	FACETS	1	0.91	1	1	0.989	1	CLONAL	5	FALSE	1	0.204104674254255	3		291	192	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72861836	72861836	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	132	506	0	ENST00000325599.8:c.1046A>C	p.Lys349Thr	p.K349T	ENST00000325599	NM_018130.2	349	aAg/aCg	9/11	0.159426590929326	3	FACETS	0.914	0.843	0.986	1	0.992	1	CLONAL	5	FALSE	1	0.204104674254255	3		506	312	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119666136	119666136	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	156	448	0	ENST00000316626.5:c.345C>A	p.Phe115Leu	p.F115L	ENST00000316626		115	ttC/ttA	3/12	0.159426590929326	3	FACETS	0.944	0.877	1	1	0.993	1	CLONAL	5	FALSE	1	0.204104674254255	3		448	357	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880869	134880869	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	126	504	1	ENST00000398015.3:c.1432G>T	p.Glu478Ter	p.E478*	ENST00000398015	NM_004441.4	478	Gag/Tag	7/16	0.159426590929326	3	FACETS	0.958	0.883	1	1	0.992	1	CLONAL	5	FALSE	1	0.204104674254255	3		505	284	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433554	138433554	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	95	413	0	ENST00000289153.2:c.1058T>G	p.Val353Gly	p.V353G	ENST00000289153	NM_006219.2	353	gTc/gGc	7/22	0.159426590929326	3	FACETS	1	0.944	1	1	0.988	1	CLONAL	4	FALSE	1	0.204104674254255	3		413	242	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281786	142281786	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	185	591	0	ENST00000350721.4:c.458T>G	p.Phe153Cys	p.F153C	ENST00000350721	NM_001184.3	153	tTt/tGt	4/47	0.159426590929326	3	FACETS	0.977	0.914	1	1	0.994	1	CLONAL	5	FALSE	1	0.204104674254255	3		591	409	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165721	185165721	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	200	397	0	ENST00000265026.3:c.996A>C	p.Glu332Asp	p.E332D	ENST00000265026	NM_004721.4	332	gaA/gaC	5/14	0.159426590929326	3	FACETS	1	0.98	1	1	0.995	1	CLONAL	5	FALSE	1	0.204104674254255	3		397	394	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747846	41747846	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	165	492	0	ENST00000226382.2:c.923T>G	p.Leu308Ter	p.L308*	ENST00000226382	NM_003924.3	308	tTa/tGa	3/3	0.204104674254255	1	FACETS	0.896	0.833	0.96	1	0.994	1	CLONAL	4	FALSE	0	0.204104674254255	1		492	405	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956220	55956220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	127	503	0	ENST00000263923.4:c.3095G>T	p.Arg1032Leu	p.R1032L	ENST00000263923	NM_002253.2	1032	cGa/cTa	23/30	0.212776157442256	0	FACETS	0.781	0.718	0.845			1	SUBCLONAL	4	FALSE	0	0.204104674254255	0		503	317	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509140	66509140	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	98	321	0	ENST00000273854.3:c.187T>G	p.Leu63Val	p.L63V	ENST00000273854	NM_004439.5	63	Tta/Gta	2/18	0.159426590929326	3	FACETS	1	0.947	1	1	0.989	1	CLONAL	4	FALSE	1	0.204104674254255	3		321	249	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157123	106157123	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	135	523	0	ENST00000380013.4:c.2024C>A	p.Ser675Ter	p.S675*	ENST00000380013	NM_001127208.2	675	tCa/tAa	3/11	0.159426590929326	3	FACETS	1	0.949	1	1	0.992	1	CLONAL	4	FALSE	1	0.204104674254255	3		523	350	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158172	106158172	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	120	391	0	ENST00000380013.4:c.3073A>G	p.Ile1025Val	p.I1025V	ENST00000380013	NM_001127208.2	1025	Att/Gtt	3/11	0.159426590929326	3	FACETS	1	0.967	1	1	0.991	1	CLONAL	4	FALSE	1	0.204104674254255	3		391	293	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143129634	143129634	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	158	438	0	ENST00000262992.4:c.1016T>G	p.Phe339Cys	p.F339C	ENST00000262992	NM_001101669.1	339	tTt/tGt	12/24	0.159426590929326	3	FACETS	1	0.974	1	1	0.993	1	CLONAL	4	FALSE	1	0.204104674254255	3		438	386	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629183	187629183	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	125	573	0	ENST00000441802.2:c.1799A>C	p.Gln600Pro	p.Q600P	ENST00000441802	NM_005245.3	600	cAg/cCg	2/27	0.159426590929326	3	FACETS	1	0.962	1	1	0.991	1	CLONAL	4	FALSE	1	0.204104674254255	3		573	312	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876088	35876088	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	58	381	0	ENST00000303115.3:c.880T>G	p.Leu294Val	p.L294V	ENST00000303115	NM_002185.3	294	Tta/Gta	8/8	1	2	FACETS	1	0.935	1	1	0.984	1	CLONAL	3	FALSE	1	0.204104674254255	2		381	171	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947485	38947485	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs746262219	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	126	330	0	ENST00000357387.3:c.4195A>C	p.Asn1399His	p.N1399H	ENST00000357387	NM_152756.3	1399	Aat/Cat	32/38	1	2	FACETS	1	0.972	1	1	0.993	1	CLONAL	4	FALSE	1	0.204104674254255	2		330	276	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637739	176637739	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201327209	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	230	728	0	ENST00000439151.2:c.2339C>A	p.Ser780Ter	p.S780*	ENST00000439151	NM_022455.4	780	tCg/tAg	5/23	1	2	FACETS	0.947	0.889	1	1	0.996	1	CLONAL	4	FALSE	1	0.204104674254255	2		728	595	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675192	176675192	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	128	273	0	ENST00000439151.2:c.4508T>G	p.Met1503Arg	p.M1503R	ENST00000439151	NM_022455.4	1503	aTg/aGg	11/23	1	2	FACETS	0.999	0.919	1	1	0.993	1	CLONAL	4	FALSE	1	0.204104674254255	2		273	314	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687094	176687094	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	28	475	0	ENST00000439151.2:c.5071A>C	p.Asn1691His	p.N1691H	ENST00000439151	NM_022455.4	1691	Aat/Cat	14/23	1	2	FACETS	0.505	0.403	0.623	0.505	0.403	0.623	SUBCLONAL	1	FALSE	1	0.204104674254255	2		475	543	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681006	30681006	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	205	570	0	ENST00000376406.3:c.713G>T	p.Arg238Ile	p.R238I	ENST00000376406	NM_014641.2	238	aGa/aTa	5/15	0.212776157442256	3	FACETS	1	0.979	1	1	0.994	1	CLONAL	4	FALSE	1	0.204104674254255	3		570	501	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415040	109415040	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	210	662	0	ENST00000436639.2:c.237A>C	p.Lys79Asn	p.K79N	ENST00000436639	NM_014454.2	79	aaA/aaC	1/10	0.212776157442256	3	FACETS	1	0.972	1	1	0.994	1	CLONAL	4	FALSE	1	0.204104674254255	3		662	532	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015891	112015891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	118	406	0	ENST00000368678.4:c.1050C>A	p.Phe350Leu	p.F350L	ENST00000368678		350	ttC/ttA	10/13	0.212776157442256	3	FACETS	1	0.956	1	1	0.991	1	CLONAL	4	FALSE	1	0.204104674254255	3		406	298	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647523	117647523	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	110	544	0	ENST00000368508.3:c.5421T>G	p.Phe1807Leu	p.F1807L	ENST00000368508	NM_002944.2	1807	ttT/ttG	33/43	0.212776157442256	3	FACETS	1	0.957	1	1	0.99	1	CLONAL	4	FALSE	1	0.204104674254255	3		544	275	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662627	117662627	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	123	515	0	ENST00000368508.3:c.4838T>G	p.Phe1613Cys	p.F1613C	ENST00000368508	NM_002944.2	1613	tTt/tGt	29/43	0.212776157442256	3	FACETS	1	0.94	1	1	0.991	1	CLONAL	4	FALSE	1	0.204104674254255	3		515	322	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679163	117679163	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	68	333	1	ENST00000368508.3:c.3658G>T	p.Asp1220Tyr	p.D1220Y	ENST00000368508	NM_002944.2	1220	Gat/Tat	24/43	0.212776157442256	3	FACETS	1	0.94	1	1	0.984	1	CLONAL	4	FALSE	1	0.204104674254255	3		334	169	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704605	117704605	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	83	441	0	ENST00000368508.3:c.2371G>T	p.Asp791Tyr	p.D791Y	ENST00000368508	NM_002944.2	791	Gac/Tac	16/43	0.212776157442256	3	FACETS	0.962	0.863	1	1	0.986	1	CLONAL	4	FALSE	1	0.204104674254255	3		441	233	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419893	152419893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	147	529	0	ENST00000206249.3:c.1580G>A	p.Ser527Asn	p.S527N	ENST00000206249	NM_000125.3	527	aGc/aAc	8/8	0.212776157442256	3	FACETS	0.91	0.843	0.978	1	0.993	1	CLONAL	5	FALSE	1	0.204104674254255	3		529	349	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505364	157505364	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	148	435	1	ENST00000346085.5:c.3346-1G>A		p.X1116_splice	ENST00000346085	NM_020732.3	1116			0.212776157442256	3	FACETS	0.99	0.919	1	1	0.993	1	CLONAL	5	FALSE	1	0.204104674254255	3		436	323	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510782	157510782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1321954955	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	179	523	0	ENST00000346085.5:c.3557C>T	p.Ser1186Leu	p.S1186L	ENST00000346085	NM_020732.3	1186	tCg/tTg	14/20	0.212776157442256	3	FACETS	1	0.935	1	1	0.993	1	CLONAL	4	FALSE	1	0.204104674254255	3		523	481	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439740	140439740	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	155	601	0	ENST00000288602.6:c.1999T>G	p.Phe667Val	p.F667V	ENST00000288602	NM_004333.4	667	Ttt/Gtt	17/18	0.212629386467899	4	FACETS	0.955	0.885	1	1	0.993	1	CLONAL	5	FALSE	2	0.204104674254255	4		601	383	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453084	140453084	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	122	387	0	ENST00000288602.6:c.1851T>G	p.Ile617Met	p.I617M	ENST00000288602	NM_004333.4	617	atT/atG	15/18	0.212629386467899	4	FACETS	0.947	0.869	1	1	0.991	1	CLONAL	5	FALSE	2	0.204104674254255	4		387	304	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866696	117866696	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	47	447	0	ENST00000297338.2:c.949A>G	p.Lys317Glu	p.K317E	ENST00000297338	NM_006265.2	317	Aaa/Gaa	9/14	0.204104674254255	5	FACETS	1	0.943	1	0.317	0.268	0.372	CLONAL	1	FALSE	1	0.204104674254255	5		447	474	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090512	5090512	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	124	391	0	ENST00000381652.3:c.2828A>C	p.Lys943Thr	p.K943T	ENST00000381652	NM_004972.3	943	aAa/aCa	21/25	0.204104674254255	1	FACETS	0.947	0.872	1	1	0.993	1	CLONAL	4	FALSE	0	0.204104674254255	1		391	288	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126337	5126337	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	27	271	0	ENST00000381652.3:c.3182T>G	p.Phe1061Cys	p.F1061C	ENST00000381652	NM_004972.3	1061	tTt/tGt	24/25	0.204104674254255	1	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	FALSE	0	0.204104674254255	1		271	201	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484293	8484293	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	133	537	0	ENST00000356435.5:c.3239C>A	p.Ser1080Ter	p.S1080*	ENST00000356435		1080	tCa/tAa	19/35	0.204104674254255	1	FACETS	1	0.965	1	1	0.993	1	CLONAL	3	FALSE	0	0.204104674254255	1		537	358	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27218804	27218804	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	22	560	0	ENST00000380036.4:c.3092T>G	p.Ile1031Ser	p.I1031S	ENST00000380036	NM_000459.3	1031	aTt/aGt	20/23	0.204104674254255	1	FACETS	0.699	0.542	0.88	0.699	0.542	0.88	SUBCLONAL	1	FALSE	0	0.204104674254255	1		560	277	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342834	87342834	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	14	466	0	ENST00000277120.3:c.1119G>T	p.Gln373His	p.Q373H	ENST00000277120		373	caG/caT	9/19	0.204104674254255	1	FACETS	0.499	0.36	0.666	0.499	0.36	0.666	SUBCLONAL	1	FALSE	0	0.204104674254255	1		466	247	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98009776	98009776	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	109	329	0	ENST00000289081.3:c.188G>T	p.Arg63Ile	p.R63I	ENST00000289081	NM_000136.2	63	aGa/aTa	3/15	0.204104674254255	1	FACETS	1	0.967	1	1	0.992	1	CLONAL	3	FALSE	0	0.204104674254255	1		329	283	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911469	101911469	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	51	300	0	ENST00000374994.4:c.1394G>T	p.Arg465Ile	p.R465I	ENST00000374994	NM_004612.2	465	aGa/aTa	9/9	0.204104674254255	1	FACETS	1	0.894	1	1	0.982	1	CLONAL	3	FALSE	0	0.204104674254255	1		300	145	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412486	63412486	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	190	824	0	ENST00000330258.3:c.681A>C	p.Glu227Asp	p.E227D	ENST00000330258	NM_152424.3	227	gaA/gaC	2/2	0.212776157442256	1	FACETS	0.904	0.849	0.958	1	0.995	1	CLONAL	5	FALSE	0	0.204104674254255	1		824	370	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412493	63412493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	114	787	0	ENST00000330258.3:c.674G>T	p.Arg225Ile	p.R225I	ENST00000330258	NM_152424.3	225	aGa/aTa	2/2	0.212776157442256	1	FACETS	0.934	0.85	1	1	0.991	1	CLONAL	3	FALSE	0	0.204104674254255	1		787	358	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352807	70352807	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1463283108	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	122	724	1	ENST00000374080.3:c.4527+1G>A		p.X1509_splice	ENST00000374080		1509			0.212776157442256	1	FACETS	1	0.95	1	1	0.99	1	CLONAL	2	FALSE	0	0.204104674254255	1		725	502	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776306	76776306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	139	702	0	ENST00000373344.5:c.7160G>A	p.Arg2387Lys	p.R2387K	ENST00000373344	NM_000489.3	2387	aGa/aAa	34/35	0.212776157442256	1	FACETS	0.955	0.877	1	1	0.993	1	CLONAL	3	FALSE	0	0.204104674254255	1		702	427	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76777805	76777805	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	94	697	0	ENST00000373344.5:c.6911C>A	p.Ser2304Tyr	p.S2304Y	ENST00000373344	NM_000489.3	2304	tCt/tAt	32/35	0.212776157442256	1	FACETS	1	0.945	1	1	0.987	1	CLONAL	2	FALSE	0	0.204104674254255	1		697	382	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889176	76889176	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	159	457	0	ENST00000373344.5:c.4834C>A	p.Leu1612Ile	p.L1612I	ENST00000373344	NM_000489.3	1612	Ctt/Att	18/35	0.212776157442256	1	FACETS	0.958	0.897	1	1	0.995	1	CLONAL	5	FALSE	0	0.204104674254255	1		457	292	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937621	76937621	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	56	410	0	ENST00000373344.5:c.3127G>T	p.Glu1043Ter	p.E1043*	ENST00000373344	NM_000489.3	1043	Gaa/Taa	9/35	0.212776157442256	1	FACETS	0.972	0.849	1	1	0.983	1	CLONAL	3	FALSE	0	0.204104674254255	1		410	169	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938673	76938673	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	80	621	0	ENST00000373344.5:c.2075C>A	p.Ser692Ter	p.S692*	ENST00000373344	NM_000489.3	692	tCa/tAa	9/35	0.212776157442256	1	FACETS	0.98	0.869	1	1	0.984	1	CLONAL	2	FALSE	0	0.204104674254255	1		621	359	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939691	76939691	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	215	736	0	ENST00000373344.5:c.1057A>C	p.Ile353Leu	p.I353L	ENST00000373344	NM_000489.3	353	Att/Ctt	9/35	0.212776157442256	1	FACETS	0.968	0.915	1	1	0.996	1	CLONAL	5	FALSE	0	0.204104674254255	1		736	391	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019669	123019669	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	91	598	0	ENST00000355640.3:c.157C>A	p.Leu53Ile	p.L53I	ENST00000355640		53	Ctt/Att	2/7	0.212776157442256	1	FACETS	0.974	0.87	1	1	0.986	1	CLONAL	2	FALSE	0	0.204104674254255	1		598	411	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020002	123020002	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	87	739	0	ENST00000355640.3:c.490G>T	p.Glu164Ter	p.E164*	ENST00000355640		164	Gaa/Taa	2/7	0.212776157442256	1	FACETS	1	0.92	1	1	0.986	1	CLONAL	2	FALSE	0	0.204104674254255	1		739	369	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123041019	123041019	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	35	162	0	ENST00000355640.3:c.1482T>G	p.Ile494Met	p.I494M	ENST00000355640		494	atT/atG	7/7	0.212776157442256	1	FACETS	1	0.919	1	1	0.975	1	CLONAL	3	FALSE	0	0.204104674254255	1		162	90	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171450	123171450	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	84	461	0	ENST00000218089.9:c.362T>G	p.Phe121Cys	p.F121C	ENST00000218089	NM_001042749.1	121	tTt/tGt	6/35	0.212776157442256	1	FACETS	0.906	0.805	1	1	0.983	1	CLONAL	2	FALSE	0	0.204104674254255	1		461	408	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185026	123185026	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	93	449	0	ENST00000218089.9:c.1073A>C	p.Lys358Thr	p.K358T	ENST00000218089	NM_001042749.1	358	aAa/aCa	12/35	0.212776157442256	1	FACETS	1	0.942	1	1	0.987	1	CLONAL	2	FALSE	0	0.204104674254255	1		449	380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28934577	NA	P-0041461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	95	629	0	ENST00000269305.4:c.770T>C	p.Leu257Pro	p.L257P	ENST00000269305	NM_001126112.2	257	cTg/cCg	7/11	1	2	FACETS	0.934	0.829	1	0.934	0.829	1	CLONAL	1	TRUE	1	0.18	2		629	1130	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988452	41988453	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	69	524	0	ENST00000219905.7:c.1247dup	p.Asn416LysfsTer3	p.N416Kfs*3	ENST00000219905	NM_001164273.1	415	tca/tcAa	3/24	1	2	FACETS	0.786	0.683	0.899	0.786	0.683	0.899	SUBCLONAL	1	TRUE	1	0.18	2		524	975	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0041506-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	200	521	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.28989976463391	3	FACETS	0.878	0.823	0.933	1	0.985	1	CLONAL	4	TRUE	0	0.28989976463391	3		521	450	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589586	67589591	+	inframe_deletion	In_Frame_Del	DEL	ATGAAT	ATGAAT	-	novel	NA	P-0041506-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	117	287	0	ENST00000274335.5:c.1351_1356del	p.Glu451_Tyr452del	p.E451_Y452del	ENST00000274335		450	cATGAATat/cat	10/15	0.28989976463391	5	FACETS	1	0.943	1	1	0.943	1	CLONAL	3	TRUE	2	0.28989976463391	5		287	369	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457247	67457247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1566991387	NA	P-0041506-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	90	670	1	ENST00000327367.4:c.221G>A	p.Arg74Gln	p.R74Q	ENST00000327367	NM_005902.3	74	cGg/cAg	2/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.28989976463391	2		671	494	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89807255	89807259	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAA	AAGAA	-	novel	NA	P-0041506-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	200	404	0	ENST00000389301.3:c.3781_3785del	p.Phe1261LeufsTer15	p.F1261Lfs*15	ENST00000389301	NM_000135.2	1261	TTCTTc/c	38/43	0.28989976463391	3	FACETS	1	0.954	1	1	0.991	1	CLONAL	4	TRUE	0	0.28989976463391	3		404	389	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729844	41729844	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs908163566	NA	P-0041643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	69	422	0	ENST00000242208.4:c.685C>T	p.Arg229Trp	p.R229W	ENST00000242208	NM_002192.2	229	Cgg/Tgg	3/3	0.155693832860709	4	FACETS	0.932	0.81	1	0.466	0.405	0.532	CLONAL	1	TRUE	2	0.246965770624976	4		422	748	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579445	7579446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	157	766	0	ENST00000269305.4:c.241dup	p.Thr81AsnfsTer68	p.T81Nfs*68	ENST00000269305	NM_001126112.2	81	aca/aAca	4/11	0.182321126252416	2	FACETS	1	0.967	1	0.556	0.508	0.606	CLONAL	1	TRUE	0	0.246965770624976	2		766	1143	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042151	14042151	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	35	228	0	ENST00000311895.7:c.2698T>G	p.Phe900Val	p.F900V	ENST00000311895	NM_005236.2	900	Ttc/Gtc	11/11	1	2	FACETS	0.691	0.567	0.831	0.691	0.567	0.831	SUBCLONAL	1	TRUE	1	0.246965770624976	2		228	410	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628869	187628869	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200902471	NA	P-0041643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	82	494	0	ENST00000441802.2:c.2113G>A	p.Asp705Asn	p.D705N	ENST00000441802	NM_005245.3	705	Gat/Aat	2/27	0.0990782006771376	3	FACETS	0.928	0.817	1	0.464	0.408	0.524	INDETERMINATE	1	TRUE	1	0.246965770624976	3		494	804	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158186	26158420	+	coding_sequence_variant,5_prime_UTR_variant	Frame_Shift_Del	DEL	GGTACAAGTAAAGGAACGAAATAGCCAATGAAAAGGTAGACTTTTAAGTGTCGTTTACATTGGCATTTGTGACGACACTCTAAAATTAATCCAATCATAAACGAAATCTGATTAACCTCATTTGAATACCGCATCTATAAATGAACAGGGCCTCGGCGGGAGTGATTATTTTCTCAGGTGTTTGCAACAGTGTTCTAACTATTAACGCTACGATGCCTGAACCTACCAAGTCTGC	GGTACAAGTAAAGGAACGAAATAGCCAATGAAAAGGTAGACTTTTAAGTGTCGTTTACATTGGCATTTGTGACGACACTCTAAAATTAATCCAATCATAAACGAAATCTGATTAACCTCATTTGAATACCGCATCTATAAATGAACAGGGCCTCGGCGGGAGTGATTATTTTCTCAGGTGTTTGCAACAGTGTTCTAACTATTAACGCTACGATGCCTGAACCTACCAAGTCTGC	-	novel	NA	P-0041643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	34	65	0				ENST00000289316	NM_138720.2	?-8/126		1/2	0.155693832860709	4	FACETS	1	0.84	1	1	0.84	1	CLONAL	2	TRUE	2	0.246965770624976	4		65	169	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150022914	150022914	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0041643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	61	261	0	ENST00000253339.5:c.348+1G>A		p.X116_splice	ENST00000253339		116			0.217122767683721	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.246965770624976	1		261	395	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0041960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	87	377	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.227588791725855	4	FACETS	1	0.977	1	0.732	0.649	0.821	CLONAL	1	FALSE	2	0.227575881704506	4		377	641	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0041960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	37	420	0	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	1	2	FACETS	0.643	0.529	0.77	0.643	0.529	0.77	SUBCLONAL	1	FALSE	1	0.227575881704506	2		420	506	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561525	9561525	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs918236421	NA	P-0041960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	48	521	0	ENST00000353224.5:c.257T>C	p.Leu86Pro	p.L86P	ENST00000353224	NM_177990.2	86	cTa/cCa	4/10	0.169220067143541	0	FACETS	0.617	0.521	0.722			1	SUBCLONAL	1	FALSE	0	0.227575881704506	0		521	528	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798755	135798755	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	41	217	0	ENST00000298552.3:c.488C>A	p.Ser163Ter	p.S163*	ENST00000298552	NM_001162426.1	163	tCa/tAa	6/23	0.177879499344977	2	FACETS	1	0.937	1	0.632	0.529	0.745	CLONAL	1	FALSE	0	0.227575881704506	2		217	285	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719743	61719743	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	46	558	0	ENST00000401558.2:c.1525C>G	p.His509Asp	p.H509D	ENST00000401558	NM_003400.3	509	Cat/Gat	14/25	1	2	FACETS	0.588	0.494	0.693	0.588	0.494	0.693	SUBCLONAL	1	FALSE	1	0.227575881704506	2		558	687	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0042110-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	51	611	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.979	0.833	1	0.979	0.833	1	CLONAL	1	TRUE	1	0.229054259133418	2		611	455	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982356	25982356	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042110-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	53	359	0	ENST00000435504.4:c.934C>T	p.Arg312Ter	p.R312*	ENST00000435504		312	Cga/Tga	9/13	1	2	FACETS	0.883	0.753	1	0.883	0.753	1	CLONAL	1	TRUE	1	0.229054259133418	2		359	524	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0042110-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	62	590	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	0.803	0.693	0.923	0.803	0.693	0.923	CLONAL	1	TRUE	1	0.229054259133418	2		590	674	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913253	39913253	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042110-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	76	344	0	ENST00000378444.4:c.4862del	p.Pro1621GlnfsTer53	p.P1621Qfs*53	ENST00000378444	NM_001123385.1	1621	cCa/ca	14/15	1	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.229054259133418	1		344	395	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978935	25978935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042110-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	45	329	0	ENST00000435504.4:c.988G>A	p.Glu330Lys	p.E330K	ENST00000435504		330	Gaa/Aaa	10/13	1	2	FACETS	0.802	0.674	0.943	0.802	0.674	0.943	CLONAL	1	TRUE	1	0.229054259133418	2		329	490	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572350	41572350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042110-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	70	628	0	ENST00000263253.7:c.4879C>T	p.Arg1627Trp	p.R1627W	ENST00000263253	NM_001429.3	1627	Cgg/Tgg	30/31	1	2	FACETS	0.832	0.724	0.948	0.832	0.724	0.948	CLONAL	1	TRUE	1	0.229054259133418	2		628	735	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939825	71939825	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042110-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	288	742	0	ENST00000298229.2:c.452C>T	p.Ser151Phe	p.S151F	ENST00000298229	NM_001567.3	151	tCt/tTt	4/28	0.229054259133418	5	FACETS	1	0.973	1			1	CLONAL	3	TRUE	NA	0.229054259133418	5		742	1066	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636664	176636664	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042110-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	64	337	0	ENST00000439151.2:c.1264G>A	p.Glu422Lys	p.E422K	ENST00000439151	NM_022455.4	422	Gaa/Aaa	5/23	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.229054259133418	2		337	525	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32814981	32814981	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042110-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	61	494	0	ENST00000354258.4:c.2084A>G	p.Glu695Gly	p.E695G	ENST00000354258	NM_000593.5	695	gAg/gGg	10/11	1	2	FACETS	0.801	0.69	0.921	0.801	0.69	0.921	CLONAL	1	TRUE	1	0.229054259133418	2		494	665	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942853	44942853	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042110-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	34	132	0	ENST00000377967.4:c.3433G>C	p.Gly1145Arg	p.G1145R	ENST00000377967	NM_021140.2	1145	Ggt/Cgt	23/29	1	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.229054259133418	1		132	185	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778008	27778008	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042110-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	65	728	0	ENST00000369163.2:c.157C>T	p.Arg53Cys	p.R53C	ENST00000369163	NM_003536.2	53	Cgc/Tgc	1/1	1	2	FACETS	0.696	0.602	0.799	0.696	0.602	0.799	SUBCLONAL	1	TRUE	1	0.229054259133418	2		728	815	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0042157-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	550	851	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.824638286890902	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.82484460502544	2		851	631	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877133	89877133	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042157-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	239	342	0	ENST00000389301.3:c.504A>C	p.Gln168His	p.Q168H	ENST00000389301	NM_000135.2	168	caA/caC	5/43	0.824638286890902	3	FACETS	1	0.987	1	0.393	0.369	0.418	CLONAL	1	TRUE	0	0.82484460502544	3		342	694	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39745033	39745033	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0042157-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	261	361	0	ENST00000361337.2:c.1822+1G>C		p.X608_splice	ENST00000361337	NM_003286.2	608			0.328936805637182	6	FACETS	0.776	0.727	0.827	0.518	0.485	0.551	INDETERMINATE	2	TRUE	3	0.82484460502544	6		361	1080	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435300	110435302	+	inframe_deletion	In_Frame_Del	DEL	GGT	GGT	-	rs765493638	NA	P-0042164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	13	226	1	ENST00000375856.3:c.3099_3101del	p.Pro1036del	p.P1036del	ENST00000375856	NM_003749.2	1033	ccACCg/ccg	1/2	0.633150225102698	1	FACETS	0.206	0.148	0.277	0.206	0.148	0.277	SUBCLONAL	1	TRUE	0	0.633150225102698	1		227	136	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578453	7578453	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	259	865	0	ENST00000269305.4:c.477del	p.Met160TrpfsTer10	p.M160Wfs*10	ENST00000269305	NM_001126112.2	159	gcC/gc	5/11	0.633150225102698	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.633150225102698	1		865	543	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486027	29486027	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs1555605362	NA	P-0042164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	107	253	0	ENST00000356175.3:c.205-1G>C		p.X69_splice	ENST00000356175	NM_000267.3	69			0.633150225102698	1	FACETS	0.991	0.908	1	0.991	0.908	1	CLONAL	1	TRUE	0	0.633150225102698	1		253	233	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177641	56177641	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	143	459	0	ENST00000399503.3:c.2614G>T	p.Gly872Cys	p.G872C	ENST00000399503	NM_005921.1	872	Ggc/Tgc	14/20	0.633150225102698	1	FACETS	0.959	0.888	1	0.959	0.888	1	CLONAL	1	TRUE	0	0.633150225102698	1		459	322	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850813	128850813	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	225	654	0	ENST00000249373.3:c.1662del	p.Gln555ArgfsTer14	p.Q555Rfs*14	ENST00000249373	NM_005631.4	554	Ggg/gg	10/12	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.633150225102698	2		654	681	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624412	140624412	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397516906	NA	P-0042164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	48	177	0	ENST00000288602.6:c.92C>G	p.Ala31Gly	p.A31G	ENST00000288602	NM_004333.4	31	gCc/gGc	1/18	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.633150225102698	2		177	150	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128206856	128206856	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	85	432	0	ENST00000265960.3:c.1367C>G	p.Thr456Arg	p.T456R	ENST00000265960	NM_001006617.1	456	aCg/aGg	11/12	1	2	FACETS	0.579	0.513	0.648	0.579	0.513	0.648	SUBCLONAL	1	TRUE	1	0.633150225102698	2		432	464	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0042733-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	133	210	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.410945961166955	1	FACETS	0.364	0.332	0.397	0.364	0.332	0.397	INDETERMINATE	1	TRUE	0	0.789918835646817	1		210	560	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0042733-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	401	380	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.528799526948008	3	FACETS	0.948	0.909	0.986	0.948	0.909	0.986	CLONAL	2	TRUE	1	0.789918835646817	3		380	747	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0042733-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	399	465	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.789918835646817	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.789918835646817	2		465	497	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1687987	1687987	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042733-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	38	764	0	ENST00000378625.1:c.889G>T	p.Glu297Ter	p.E297*	ENST00000378625	NM_001198994.1	297	Gaa/Taa	7/14	0.355354014066716	1	FACETS	0.093	0.076	0.111	0.093	0.076	0.111	INDETERMINATE	1	TRUE	0	0.789918835646817	1		764	629	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88677059	88677059	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042733-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	166	325	0	ENST00000372037.3:c.844del	p.Leu282Ter	p.L282*	ENST00000372037	NM_004329.2	282	Cta/ta	9/13	0.410945961166955	1	FACETS	0.785	0.734	0.835	0.785	0.734	0.835	INDETERMINATE	1	TRUE	0	0.789918835646817	1		325	324	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505626	186505626	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042733-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	291	450	0	ENST00000323963.5:c.1034T>C	p.Val345Ala	p.V345A	ENST00000323963		345	gTt/gCt	10/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.789918835646817	2		450	696	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830052	72830052	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042811-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	44	496	0	ENST00000268489.5:c.6529G>A	p.Glu2177Lys	p.E2177K	ENST00000268489	NM_006885.3	2177	Gag/Aag	9/10	0.291585921993031	1	FACETS	0.988	0.834	1	0.988	0.834	1	CLONAL	1	TRUE	0	0.291585921993031	1		496	261	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555525585	NA	P-0042898-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	268	479	0	ENST00000269305.4:c.673-2A>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.302292125891263	3	FACETS	0.878	0.831	0.926	0.878	0.831	0.926	CLONAL	3	TRUE	0	0.41	3		479	598	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778944	9778944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042898-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	182	659	0	ENST00000377346.4:c.1213C>T	p.Arg405Cys	p.R405C	ENST00000377346	NM_005026.3	405	Cgc/Tgc	9/24	0.302292125891263	2	FACETS	1	0.99	1	0.713	0.66	0.766	CLONAL	1	TRUE	0	0.41	2		659	623	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755599	39755599	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042898-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	104	728	0	ENST00000288319.7:c.1166A>C	p.Lys389Thr	p.K389T	ENST00000288319	NM_182918.3	389	aAg/aCg	10/10	0.302292125891263	3	FACETS	0.708	0.634	0.788	0.354	0.317	0.394	SUBCLONAL	1	TRUE	1	0.41	3		728	863	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188384	32188384	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042898-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	98	800	0	ENST00000375023.3:c.957G>T	p.Glu319Asp	p.E319D	ENST00000375023	NM_004557.3	319	gaG/gaT	6/30	0.302292125891263	3	FACETS	0.732	0.653	0.816	0.244	0.217	0.272	SUBCLONAL	1	TRUE	0	0.41	3		800	787	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55270234	55270234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042898-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	48	725	0	ENST00000275493.2:c.3187G>A	p.Asp1063Asn	p.D1063N	ENST00000275493	NM_005228.3	1063	Gac/Aac	27/28	0.249613353460588	4	FACETS	0.392	0.33	0.461	0.196	0.165	0.231	SUBCLONAL	1	TRUE	2	0.41	4		725	842	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650343	48650343	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042898-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	62	775	0	ENST00000376670.3:c.313C>G	p.Pro105Ala	p.P105A	ENST00000376670	NM_002049.3	105	Cct/Gct	3/6	0.302292125891263	3	FACETS	0.41	0.353	0.472			1	SUBCLONAL	1	TRUE	NA	0.41	3		775	889	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926888	112926888	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507546	NA	P-0043067-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	141	506	0	ENST00000351677.2:c.1508G>T	p.Gly503Val	p.G503V	ENST00000351677	NM_002834.3	503	gGg/gTg	13/16	0.713680216799983	3	FACETS	0.793	0.733	0.854	0.793	0.733	0.854	SUBCLONAL	2	TRUE	1	0.713680216799983	3		506	338	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207089	1207090	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0043067-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	168	609	0	ENST00000326873.7:c.177_178del	p.Tyr60ArgfsTer102	p.Y60Rfs*102	ENST00000326873	NM_000455.4	59	tcTTac/tcac	1/10	0.713680216799983	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.713680216799983	1		609	274	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054827	5054828	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0043067-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	122	455	0	ENST00000381652.3:c.881dup	p.Gly295TrpfsTer10	p.G295Wfs*10	ENST00000381652	NM_004972.3	293	-/G	7/25	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.713680216799983	2		455	316	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0043397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	506	942	1	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.445907642314756	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.445907642314756	2		943	1104	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0043397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	199	612	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.445907642314756	3	FACETS	0.927	0.864	0.991	0.927	0.864	0.991	CLONAL	2	TRUE	1	0.445907642314756	3		612	589	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0043397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	83	266	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.244411567180121	3	FACETS	0.84	0.751	0.933	0.84	0.751	0.933	INDETERMINATE	2	TRUE	1	0.445907642314756	3		266	271	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0043397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	30	302	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.244411567180121	3	FACETS	0.677	0.548	0.822	0.339	0.274	0.411	INDETERMINATE	1	TRUE	1	0.445907642314756	3		303	243	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18972931	18972931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	179	747	1	ENST00000262803.5:c.2570G>A	p.Arg857Lys	p.R857K	ENST00000262803	NM_002911.3	857	aGg/aAg	18/24	0.445907642314756	3	FACETS	0.866	0.797	0.938	0.433	0.398	0.469	CLONAL	1	TRUE	1	0.445907642314756	3		748	1134	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	207	321	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.957	0.901	1	1	0.996	1	CLONAL	5	TRUE	1	0.209546211829739	2		321	413	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913920	32913920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358766	NA	P-0043579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	66	478	0	ENST00000380152.3:c.5428G>A	p.Val1810Ile	p.V1810I	ENST00000380152		1810	Gtt/Att	11/27	1	2	FACETS	1	0.946	1	1	0.986	1	CLONAL	3	TRUE	1	0.209546211829739	2		478	187	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579494	7579494	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1555526721	NA	P-0043789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	788	671	1	ENST00000269305.4:c.193A>T	p.Arg65Ter	p.R65*	ENST00000269305	NM_001126112.2	65	Aga/Tga	4/11	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.746385107551974	2		672	1018	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789661	3789661	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	303	535	0	ENST00000262367.5:c.4198G>C	p.Glu1400Gln	p.E1400Q	ENST00000262367	NM_004380.2	1400	Gag/Cag	25/31	0.746385107551974	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.746385107551974	1		535	508	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70411602	70411602	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0043789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	163	251	0	ENST00000373644.4:c.4277-1G>C		p.X1426_splice	ENST00000373644	NM_030625.2	1426			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.746385107551974	2		251	408	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880842	28880842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	299	522	0	ENST00000282397.4:c.3788G>A	p.Ser1263Asn	p.S1263N	ENST00000282397	NM_002019.4	1263	aGc/aAc	29/30	0.746385107551974	2	FACETS	0.977	0.924	1	0.489	0.462	0.516	CLONAL	1	TRUE	0	0.746385107551974	2		522	820	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2115571	2115606	+	inframe_deletion	In_Frame_Del	DEL	GCCGCATACTCGGCCTCCTTGGAGGATGTGAAGACA	GCCGCATACTCGGCCTCCTTGGAGGATGTGAAGACA	-	novel	NA	P-0043789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	342	554	0	ENST00000219476.3:c.1655_1690del	p.Ala552_Ala563del	p.A552_A563del	ENST00000219476	NM_000548.3	551	GCCGCATACTCGGCCTCCTTGGAGGATGTGAAGACA/-	16/42	0.746385107551974	1	FACETS	0.922	0.882	0.962	0.922	0.882	0.962	CLONAL	1	TRUE	0	0.746385107551974	1		554	623	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795331	39795331	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0043789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	248	446	0	ENST00000288319.7:c.388+1G>T		p.X130_splice	ENST00000288319	NM_182918.3	130			1	2	FACETS	0.979	0.92	1	0.979	0.92	1	CLONAL	1	TRUE	1	0.746385107551974	2		446	679	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0044098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	412	611	0				ENST00000310581	NM_198253.2	-/1132			0.469001201197455	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	2	0.629237811631985	4		611	934	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0044098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	654	529	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.602857401259839	3	FACETS	0.912	0.886	0.937	0.912	0.886	0.937	CLONAL	3	TRUE	0	0.629237811631985	3		529	999	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423632	88423632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1478926904	NA	P-0044098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	205	429	1	ENST00000360948.2:c.2203C>T	p.Arg735Cys	p.R735C	ENST00000360948	NM_001012338.2	735	Cgc/Tgc	18/19	NA	2	FACETS	0.807	0.75	0.866			1	INDETERMINATE	1	TRUE	NA	0.629237811631985	2		430	807	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579585	7579585	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	532	551	0	ENST00000269305.4:c.102del	p.Leu35CysfsTer9	p.L35Cfs*9	ENST00000269305	NM_001126112.2	34	ccC/cc	4/11	0.615209602100903	2	FACETS	0.977	0.946	1	0.977	0.946	1	CLONAL	2	TRUE	0	0.629237811631985	2		551	865	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290180	15290180	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371437217	NA	P-0044098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	336	887	0	ENST00000263388.2:c.3455C>T	p.Thr1152Met	p.T1152M	ENST00000263388	NM_000435.2	1152	aCg/aTg	21/33	0.629237811631985	3	FACETS	0.936	0.883	0.99	0.468	0.441	0.495	CLONAL	1	TRUE	1	0.629237811631985	3		887	1500	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934194	48934194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	27	178	0	ENST00000267163.4:c.649C>T	p.Gln217Ter	p.Q217*	ENST00000267163	NM_000321.2	217	Cag/Tag	7/27	0.629237811631985	1	FACETS	0.726	0.596	0.865	0.726	0.596	0.865	SUBCLONAL	1	TRUE	0	0.629237811631985	1		178	81	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289922	15289922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	324	738	0	ENST00000263388.2:c.3632C>T	p.Ser1211Leu	p.S1211L	ENST00000263388	NM_000435.2	1211	tCa/tTa	22/33	0.629237811631985	3	FACETS	0.99	0.933	1	0.495	0.466	0.524	CLONAL	1	TRUE	1	0.629237811631985	3		738	1368	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770612	40770612	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	195	458	0	ENST00000373198.4:c.2770G>T	p.Asp924Tyr	p.D924Y	ENST00000373198	NM_133170.3	924	Gac/Tac	19/32	NA	2	FACETS	0.733	0.679	0.788			1	INDETERMINATE	1	TRUE	NA	0.629237811631985	2		458	846	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289995	15289995	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	338	783	0	ENST00000263388.2:c.3559G>T	p.Gly1187Cys	p.G1187C	ENST00000263388	NM_000435.2	1187	Ggt/Tgt	22/33	0.629237811631985	3	FACETS	1	0.967	1	0.516	0.487	0.546	CLONAL	1	TRUE	1	0.629237811631985	3		783	1368	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290202	15290202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	324	848	0	ENST00000263388.2:c.3433C>T	p.Leu1145Phe	p.L1145F	ENST00000263388	NM_000435.2	1145	Ctc/Ttc	21/33	0.629237811631985	3	FACETS	0.912	0.86	0.966	0.456	0.43	0.483	CLONAL	1	TRUE	1	0.629237811631985	3		848	1484	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259791	142259791	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	559	430	0	ENST00000350721.4:c.3536G>C	p.Arg1179Thr	p.R1179T	ENST00000350721	NM_001184.3	1179	aGa/aCa	18/47	0.629237811631985	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	1	0.629237811631985	4		430	908	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940423	13940423	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	264	332	0	ENST00000405192.2:c.1083G>T	p.Met361Ile	p.M361I	ENST00000405192	NM_001163147.1	361	atG/atT	11/12	0.57537044227124	3	FACETS	0.875	0.827	0.925	0.875	0.827	0.925	CLONAL	2	TRUE	1	0.629237811631985	3		332	630	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965334	25965334	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	248	626	0	ENST00000435504.4:c.3872C>G	p.Ser1291Cys	p.S1291C	ENST00000435504		1291	tCt/tGt	13/13	0.469001201197455	4	FACETS	0.888	0.828	0.95	0.444	0.414	0.475	CLONAL	1	TRUE	2	0.629237811631985	4		626	1447	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612798	228612798	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1490	334	857	0	ENST00000366696.1:c.229C>G	p.Gln77Glu	p.Q77E	ENST00000366696	NM_003493.2	77	Cag/Gag	1/1	0.557907903316009	4	FACETS	0.948	0.893	1			1	CLONAL	1	TRUE	NA	0.629237811631985	4		857	1824	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77991939	77991939	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	196	457	0	ENST00000361507.4:c.84G>C	p.Lys28Asn	p.K28N	ENST00000361507	NM_080491.2	28	aaG/aaC	2/10	0.629237811631985	3	FACETS	0.875	0.81	0.942	0.437	0.405	0.471	CLONAL	1	TRUE	1	0.629237811631985	3		457	936	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514476	125514476	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	113	352	0	ENST00000428830.2:c.1171C>G	p.Gln391Glu	p.Q391E	ENST00000428830	NM_001114121.2	391	Caa/Gaa	11/14	0.559851254677726	4	FACETS	0.871	0.785	0.962	0.435	0.392	0.481	CLONAL	1	TRUE	2	0.629237811631985	4		352	672	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50488263	50488263	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	158	422	0	ENST00000394963.4:c.1177G>C	p.Asp393His	p.D393H	ENST00000394963	NM_003076.4	393	Gat/Cat	10/13	0.569002653134926	3	FACETS	0.814	0.747	0.884			1	CLONAL	1	TRUE	NA	0.629237811631985	3		422	811	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233180	69233180	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	198	508	0	ENST00000462284.1:c.1045G>C	p.Glu349Gln	p.E349Q	ENST00000462284	NM_002392.5	349	Gag/Cag	11/11	0.629237811631985	3	FACETS	0.985	0.914	1	0.492	0.457	0.53	CLONAL	1	TRUE	1	0.629237811631985	3		508	840	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929008	32929008	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	78	293	0	ENST00000380152.3:c.7018G>T	p.Glu2340Ter	p.E2340*	ENST00000380152		2340	Gaa/Taa	14/27	0.559554382546286	3	FACETS	0.834	0.737	0.936	0.417	0.368	0.468	CLONAL	1	TRUE	1	0.629237811631985	3		293	391	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988522	36988522	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	265	665	0	ENST00000354822.5:c.131C>G	p.Ser44Cys	p.S44C	ENST00000354822	NM_001079668.2	44	tCt/tGt	2/3	0.57537044227124	3	FACETS	1	0.971	1	0.529	0.496	0.563	CLONAL	1	TRUE	1	0.629237811631985	3		665	1046	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89869681	89869681	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201992220	NA	P-0044098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	125	375	0	ENST00000389301.3:c.778G>A	p.Glu260Lys	p.E260K	ENST00000389301	NM_000135.2	260	Gaa/Aaa	8/43	0.569002653134926	3	FACETS	0.83	0.753	0.911			1	CLONAL	1	TRUE	NA	0.629237811631985	3		375	629	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422923	47422923	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777460603	NA	P-0044098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1392	259	554	0	ENST00000404338.3:c.991G>A	p.Glu331Lys	p.E331K	ENST00000404338	NM_004491.4	331	Gag/Aag	1/6	0.629237811631985	5	FACETS	0.969	0.905	1	0.323	0.301	0.346	CLONAL	1	TRUE	2	0.629237811631985	5		554	1651	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965998	25965998	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	205	529	0	ENST00000435504.4:c.3208C>T	p.Leu1070Phe	p.L1070F	ENST00000435504		1070	Ctc/Ttc	13/13	0.469001201197455	4	FACETS	0.886	0.821	0.954	0.443	0.41	0.477	CLONAL	1	TRUE	2	0.629237811631985	4		529	1198	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919190	178919190	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	81	277	0	ENST00000263967.3:c.675C>G	p.Ile225Met	p.I225M	ENST00000263967	NM_006218.2	225	atC/atG	4/21	0.629237811631985	4	FACETS	0.728	0.642	0.82	0.243	0.214	0.274	SUBCLONAL	1	TRUE	1	0.629237811631985	4		277	576	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672681	30672681	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	633	713	0	ENST00000376406.3:c.4279G>C	p.Glu1427Gln	p.E1427Q	ENST00000376406	NM_014641.2	1427	Gag/Cag	10/15	0.629048876903004	4	FACETS	0.958	0.922	0.994	0.639	0.615	0.663	CLONAL	2	TRUE	1	0.629237811631985	4		713	1711	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346563	81346563	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	144	352	0	ENST00000222390.5:c.1390T>C	p.Cys464Arg	p.C464R	ENST00000222390	NM_000601.4	464	Tgc/Cgc	11/18	0.629237811631985	3	FACETS	0.988	0.905	1	0.494	0.452	0.538	CLONAL	1	TRUE	1	0.629237811631985	3		352	609	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950469	68950469	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1164719450	NA	P-0044098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	266	263	0	ENST00000288368.4:c.781C>G	p.Gln261Glu	p.Q261E	ENST00000288368	NM_024870.2	261	Caa/Gaa	7/40	0.402251518245522	6	FACETS	0.87	0.819	0.92	0.87	0.819	0.92	CLONAL	3	TRUE	3	0.629237811631985	6		263	732	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61305301	61305301	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044098-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	13	110	0	ENST00000341074.5:c.825G>T	p.Met275Ile	p.M275I	ENST00000341074	NM_002974.2	275	atG/atT	8/8	0.629237811631985	2	FACETS	0.372	0.268	0.497	0.186	0.134	0.249	SUBCLONAL	1	TRUE	0	0.629237811631985	2		110	111	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0044197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	222	302	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		302	548	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202738	16202738	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1362897593	NA	P-0044197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	76	465	0	ENST00000375759.3:c.446A>G	p.Tyr149Cys	p.Y149C	ENST00000375759	NM_015001.2	149	tAt/tGt	3/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		465	700	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158026	27158026	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	93	466	3	ENST00000380036.4:c.255del	p.Val86LeufsTer31	p.V86Lfs*31	ENST00000380036	NM_000459.3	84	Aaa/aa	2/23	1	2	FACETS	0.718	0.638	0.804	0.718	0.638	0.804	SUBCLONAL	1	TRUE	1	0.33	2		469	785	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	67	328	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.724	0.629	0.826	0.724	0.629	0.826	SUBCLONAL	1	TRUE	1	0.33	2		329	561	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	97	509	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.292673251079498	2	FACETS	0.802	0.715	0.895	0.401	0.357	0.448	CLONAL	1	TRUE	0	0.33	2		513	733	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	253	428	1	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	0.292673251079498	2	FACETS	0.933	0.875	0.991	0.933	0.875	0.991	CLONAL	2	TRUE	0	0.33	2		429	822	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	84	378	3	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	1	2	FACETS	0.72	0.636	0.81	0.72	0.636	0.81	SUBCLONAL	1	TRUE	1	0.33	2		381	707	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	104	463	4	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	0.292673251079498	2	FACETS	0.749	0.67	0.832	0.374	0.335	0.416	SUBCLONAL	1	TRUE	0	0.33	2		467	842	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671680	67671680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201916739	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	75	373	2	ENST00000264010.4:c.2089G>A	p.Ala697Thr	p.A697T	ENST00000264010	NM_006565.3	697	Gca/Aca	12/12	1	2	FACETS	0.756	0.663	0.856	0.756	0.663	0.856	SUBCLONAL	1	TRUE	1	0.33	2		375	601	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932085	39932085	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	57	233	0	ENST00000378444.4:c.2514del	p.Lys839SerfsTer17	p.K839Sfs*17	ENST00000378444	NM_001123385.1	838	ccC/cc	4/15	0.071756417227006	2	FACETS	0.802	0.689	0.923			1	INDETERMINATE	1	TRUE	NA	0.33	2		233	431	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732996	30732996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893809	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	80	301	0	ENST00000295754.5:c.1609C>T	p.Arg537Cys	p.R537C	ENST00000295754	NM_003242.5	537	Cgc/Tgc	7/7	1	2	FACETS	0.851	0.75	0.958	0.851	0.75	0.958	CLONAL	1	TRUE	1	0.33	2		301	570	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101267	27101268	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	68	423	0	ENST00000324856.7:c.4555dup	p.Gln1519ProfsTer13	p.Q1519Pfs*13	ENST00000324856	NM_006015.4	1517	gcc/gCcc	18/20	1	2	FACETS	0.662	0.575	0.755	0.662	0.575	0.755	SUBCLONAL	1	TRUE	1	0.33	2		423	623	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256769	19256769	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	56	334	3	ENST00000162023.5:c.944del	p.Pro315GlnfsTer?	p.P315Qfs*?	ENST00000162023		315	cCa/ca	13/13	1	2	FACETS	0.548	0.469	0.635	0.548	0.469	0.635	SUBCLONAL	1	TRUE	1	0.33	2		337	619	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	37	277	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.290630860457522	3	FACETS	0.67	0.553	0.8	0.335	0.276	0.4	SUBCLONAL	1	TRUE	1	0.33	3		277	390	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103755	47103756	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	90	384	1	ENST00000409792.3:c.6190_6191del	p.Asp2064ProfsTer8	p.D2064Pfs*8	ENST00000409792	NM_014159.6	2064	GAc/c	14/21	1	2	FACETS	0.76	0.674	0.851	0.76	0.674	0.851	SUBCLONAL	1	TRUE	1	0.33	2		385	718	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295801	212295801	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1423325504	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	65	336	0	ENST00000342788.4:c.2512C>T	p.Arg838Ter	p.R838*	ENST00000342788	NM_005235.2	838	Cga/Tga	21/28	1	2	FACETS	0.799	0.694	0.912	0.799	0.694	0.912	CLONAL	1	TRUE	1	0.33	2		336	493	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453398	40453399	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs759027671	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	64	532	2	ENST00000345506.4:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000345506	NM_003152.3	365	-/C	10/20	0.292673251079498	2	FACETS	0.477	0.412	0.548	0.239	0.206	0.274	SUBCLONAL	1	TRUE	0	0.33	2		534	813	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120115	70120115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	10	69	0	ENST00000245479.2:c.1121del	p.Pro374ArgfsTer9	p.P374Rfs*9	ENST00000245479	NM_000346.3	373	Ccc/cc	3/3	0.292673251079498	2	FACETS	0.588	0.402	0.819	0.294	0.201	0.41	SUBCLONAL	1	TRUE	0	0.33	2		69	103	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703538	47703538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63749932	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	83	364	0	ENST00000233146.2:c.2038C>T	p.Arg680Ter	p.R680*	ENST00000233146	NM_000251.2	680	Cga/Tga	13/16	1	2	FACETS	0.981	0.868	1	0.981	0.868	1	CLONAL	1	TRUE	1	0.33	2		364	513	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202351	138202351	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	52	373	0	ENST00000237289.4:c.2274del	p.Lys759SerfsTer57	p.K759Sfs*57	ENST00000237289	NM_001270507.1	756	gaC/ga	9/9	1	2	FACETS	0.511	0.434	0.595	0.511	0.434	0.595	SUBCLONAL	1	TRUE	1	0.33	2		373	617	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191049	185191049	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	66	446	1	ENST00000265026.3:c.1934del	p.Pro645LeufsTer19	p.P645Lfs*19	ENST00000265026	NM_004721.4	644	Ccc/cc	11/14	1	2	FACETS	0.522	0.452	0.598	0.522	0.452	0.598	SUBCLONAL	1	TRUE	1	0.33	2		447	766	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865540	57865540	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1295636010	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	189	446	1	ENST00000228682.2:c.3017G>A	p.Gly1006Asp	p.G1006D	ENST00000228682	NM_005269.2	1006	gGc/gAc	12/12	0.290630860457522	3	FACETS	0.878	0.813	0.945	0.878	0.813	0.945	CLONAL	2	TRUE	1	0.33	3		447	760	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955112	17955112	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755706305	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	43	487	2	ENST00000458235.1:c.115del	p.Gln39SerfsTer108	p.Q39Sfs*108	ENST00000458235	NM_000215.3	39	Cag/ag	2/24	1	2	FACETS	0.319	0.266	0.379	0.319	0.266	0.379	SUBCLONAL	1	TRUE	1	0.33	2		489	816	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434613	99434613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253103806	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	100	380	0	ENST00000268035.6:c.700G>A	p.Glu234Lys	p.E234K	ENST00000268035	NM_000875.3	234	Gag/Aag	3/21	1	2	FACETS	0.99	0.886	1	0.99	0.886	1	CLONAL	1	TRUE	1	0.33	2		380	612	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130337	11130337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs281875226	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	124	374	1	ENST00000358026.2:c.2576C>T	p.Thr859Met	p.T859M	ENST00000358026	NM_001128849.1	859	aCg/aTg	18/36	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.33	2		375	714	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801087	135801087	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs118203357	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	63	292	0	ENST00000298552.3:c.250G>A	p.Ala84Thr	p.A84T	ENST00000298552	NM_001162426.1	84	Gcc/Acc	5/23	1	2	FACETS	0.787	0.682	0.901	0.787	0.682	0.901	CLONAL	1	TRUE	1	0.33	2		292	485	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	122	501	0	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.838	0.757	0.924	0.838	0.757	0.924	CLONAL	1	TRUE	1	0.33	2		501	882	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427611	49427611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561903173	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	68	387	1	ENST00000301067.7:c.10877G>A	p.Arg3626Gln	p.R3626Q	ENST00000301067	NM_003482.3	3626	cGg/cAg	39/54	0.290630860457522	3	FACETS	0.785	0.683	0.895	0.392	0.341	0.448	SUBCLONAL	1	TRUE	1	0.33	3		388	612	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794440	42794440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776806622	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	134	579	1	ENST00000575354.2:c.1520G>A	p.Arg507His	p.R507H	ENST00000575354	NM_015125.3	507	cGc/cAc	10/20	1	2	FACETS	0.888	0.806	0.974	0.888	0.806	0.974	CLONAL	1	TRUE	1	0.33	2		580	915	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412242	139412242	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	83	441	0	ENST00000277541.6:c.1403T>C	p.Leu468Pro	p.L468P	ENST00000277541	NM_017617.3	468	cTg/cCg	8/34	1	2	FACETS	0.604	0.532	0.681	0.604	0.532	0.681	SUBCLONAL	1	TRUE	1	0.33	2		441	833	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936067	49936067	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201544530	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	87	470	0	ENST00000296474.3:c.1603C>T	p.Arg535Cys	p.R535C	ENST00000296474	NM_002447.2	535	Cgt/Tgt	4/20	1	2	FACETS	0.634	0.56	0.713	0.634	0.56	0.713	SUBCLONAL	1	TRUE	1	0.33	2		470	832	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952291	17952291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1376805771	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	42	472	0	ENST00000458235.1:c.1049G>A	p.Arg350Gln	p.R350Q	ENST00000458235	NM_000215.3	350	cGg/cAg	8/24	1	2	FACETS	0.31	0.258	0.368	0.31	0.258	0.368	SUBCLONAL	1	TRUE	1	0.33	2		472	821	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448517	49448517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763644658	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	91	322	0	ENST00000301067.7:c.194G>A	p.Arg65His	p.R65H	ENST00000301067	NM_003482.3	65	cGt/cAt	3/54	0.290630860457522	3	FACETS	0.865	0.768	0.969	0.432	0.384	0.485	CLONAL	1	TRUE	1	0.33	3		322	743	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155385	106155385	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1187881284	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	39	325	0	ENST00000380013.4:c.286C>T	p.Arg96Cys	p.R96C	ENST00000380013	NM_001127208.2	96	Cgc/Tgc	3/11	1	2	FACETS	0.443	0.367	0.529	0.443	0.367	0.529	SUBCLONAL	1	TRUE	1	0.33	2		325	533	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041882	14041882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	59	248	0	ENST00000311895.7:c.2429C>T	p.Ala810Val	p.A810V	ENST00000311895	NM_005236.2	810	gCg/gTg	11/11	1	2	FACETS	0.885	0.764	1	0.885	0.764	1	CLONAL	1	TRUE	1	0.33	2		248	404	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923700	39923700	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372187961	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	140	257	1	ENST00000378444.4:c.3391C>T	p.Arg1131Trp	p.R1131W	ENST00000378444	NM_001123385.1	1131	Cgg/Tgg	7/15	0.071756417227006	2	FACETS	1	0.936	1			1	INDETERMINATE	2	TRUE	NA	0.33	2		258	416	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291020	11291020	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	53	273	0	ENST00000361445.4:c.2741C>T	p.Ala914Val	p.A914V	ENST00000361445	NM_004958.3	914	gCt/gTt	18/58	1	2	FACETS	0.598	0.51	0.695	0.598	0.51	0.695	SUBCLONAL	1	TRUE	1	0.33	2		273	537	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254677	16254677	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	88	436	0	ENST00000375759.3:c.1942C>T	p.Arg648Trp	p.R648W	ENST00000375759	NM_015001.2	648	Cgg/Tgg	11/15	1	2	FACETS	0.826	0.732	0.926	0.826	0.732	0.926	CLONAL	1	TRUE	1	0.33	2		436	646	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937202	36937202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	78	450	1	ENST00000361632.4:c.1117G>A	p.Val373Ile	p.V373I	ENST00000361632		373	Gtt/Att	9/16	1	2	FACETS	0.605	0.53	0.684	0.605	0.53	0.684	SUBCLONAL	1	TRUE	1	0.33	2		451	782	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115272998	115272999	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	61	408	0	ENST00000438362.2:c.1374dup	p.Leu459ThrfsTer30	p.L459Tfs*30	ENST00000438362	NM_001242891.1	458	-/A	12/20	1	2	FACETS	0.661	0.571	0.76	0.661	0.571	0.76	SUBCLONAL	1	TRUE	1	0.33	2		408	559	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468184	120468185	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	87	415	1	ENST00000256646.2:c.4254dup	p.Ser1419GlnfsTer22	p.S1419Qfs*22	ENST00000256646	NM_024408.3	1418	-/C	25/34	1	2	FACETS	0.728	0.644	0.818	0.728	0.644	0.818	SUBCLONAL	1	TRUE	1	0.33	2		416	724	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226568856	226568856	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	70	377	0	ENST00000366794.5:c.1213A>G	p.Lys405Glu	p.K405E	ENST00000366794	NM_001618.3	405	Aag/Gag	9/23	1	2	FACETS	0.58	0.505	0.662	0.58	0.505	0.662	SUBCLONAL	1	TRUE	1	0.33	2		377	731	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851252	63851252	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	118	364	0	ENST00000279873.7:c.2030T>C	p.Leu677Pro	p.L677P	ENST00000279873	NM_032199.2	677	cTg/cCg	10/10	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.33	2		364	671	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910764	114910764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	84	347	0	ENST00000543371.1:c.886del	p.His296IlefsTer19	p.H296Ifs*19	ENST00000543371	NM_001198531.1	295	Ccc/cc	9/14	1	2	FACETS	0.8	0.707	0.9	0.8	0.707	0.9	SUBCLONAL	1	TRUE	1	0.33	2		347	636	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575445	64575446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	61	431	0	ENST00000312049.6:c.571dup	p.Glu191GlyfsTer5	p.E191Gfs*5	ENST00000312049	NM_130799.2	191	gag/gGag	3/10	1	2	FACETS	0.513	0.442	0.591	0.513	0.442	0.591	SUBCLONAL	1	TRUE	1	0.33	2		431	720	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244052	46244052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565622120	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	83	325	0	ENST00000334344.6:c.2146G>A	p.Ala716Thr	p.A716T	ENST00000334344	NM_152641.2	716	Gct/Act	15/21	0.290630860457522	3	FACETS	0.954	0.843	1	0.477	0.421	0.537	CLONAL	1	TRUE	1	0.33	3		325	614	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900365	3900365	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750411228	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	113	376	0	ENST00000262367.5:c.731C>T	p.Thr244Met	p.T244M	ENST00000262367	NM_004380.2	244	aCg/aTg	2/31	1	2	FACETS	0.949	0.854	1	0.949	0.854	1	CLONAL	1	TRUE	1	0.33	2		376	722	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56792497	56792497	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	30	284	0	ENST00000308159.5:c.227A>G	p.Gln76Arg	p.Q76R	ENST00000308159	NM_014669.4	76	cAg/cGg	3/22	1	2	FACETS	0.324	0.26	0.397	0.324	0.26	0.397	SUBCLONAL	1	TRUE	1	0.33	2		284	561	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89809229	89809231	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	117	366	0	ENST00000389301.3:c.3742_3744del	p.Lys1248del	p.K1248del	ENST00000389301	NM_000135.2	1248	AAG/-	37/43	1	2	FACETS	0.886	0.799	0.978	0.886	0.799	0.978	CLONAL	1	TRUE	1	0.33	2		366	800	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89833593	89833593	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs752160950	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	82	248	0	ENST00000389301.3:c.2557C>T	p.Arg853Ter	p.R853*	ENST00000389301	NM_000135.2	853	Cga/Tga	27/43	1	2	FACETS	0.988	0.874	1	0.988	0.874	1	CLONAL	1	TRUE	1	0.33	2		248	503	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663768	29663768	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs137854561	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	189	303	0	ENST00000356175.3:c.6200T>C	p.Leu2067Pro	p.L2067P	ENST00000356175	NM_000267.3	2067	cTg/cCg	41/57	0.292673251079498	2	FACETS	0.959	0.892	1	0.959	0.892	1	CLONAL	2	TRUE	0	0.33	2		303	597	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41242965	41242965	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507226	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	48	228	0	ENST00000357654.3:c.4181C>T	p.Thr1394Ile	p.T1394I	ENST00000357654	NM_007294.3	1394	aCt/aTt	11/23	0.292673251079498	2	FACETS	0.651	0.551	0.761	0.325	0.275	0.381	SUBCLONAL	1	TRUE	0	0.33	2		228	447	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745987	745987	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs774045264	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	32	279	0	ENST00000314574.4:c.535C>T	p.Arg179Ter	p.R179*	ENST00000314574	NM_005433.3	179	Cga/Tga	5/12	1	2	FACETS	0.526	0.427	0.637	0.526	0.427	0.637	SUBCLONAL	1	TRUE	1	0.33	2		279	369	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39573289	39573290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	68	224	0	ENST00000262039.4:c.775dup	p.Gln259ProfsTer9	p.Q259Pfs*9	ENST00000262039	NM_002647.2	257	gac/gaCc	7/25	1	2	FACETS	0.984	0.859	1	0.984	0.859	1	CLONAL	1	TRUE	1	0.33	2		224	419	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291474	10291474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753673660	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	42	387	2	ENST00000340748.4:c.205C>T	p.Arg69Cys	p.R69C	ENST00000340748		69	Cgt/Tgt	3/40	1	2	FACETS	0.382	0.318	0.453	0.382	0.318	0.453	SUBCLONAL	1	TRUE	1	0.33	2		389	667	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272507	15272507	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	65	297	0	ENST00000263388.2:c.5932C>A	p.Leu1978Met	p.L1978M	ENST00000263388	NM_000435.2	1978	Ctg/Atg	33/33	1	2	FACETS	0.619	0.537	0.709	0.619	0.537	0.709	SUBCLONAL	1	TRUE	1	0.33	2		297	636	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223430	36223430	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376111760	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	148	557	0	ENST00000222270.7:c.5980G>A	p.Ala1994Thr	p.A1994T	ENST00000222270	NM_014727.1	1994	Gcg/Acg	28/37	1	2	FACETS	0.954	0.871	1	0.954	0.871	1	CLONAL	1	TRUE	1	0.33	2		557	940	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224064	36224064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1185544469	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	175	513	1	ENST00000222270.7:c.6614C>T	p.Ala2205Val	p.A2205V	ENST00000222270	NM_014727.1	2205	gCt/gTt	28/37	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.33	2		514	946	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693838	47693838	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750780	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	44	206	0	ENST00000233146.2:c.1552C>T	p.Gln518Ter	p.Q518*	ENST00000233146	NM_000251.2	518	Cag/Tag	10/16	1	2	FACETS	0.762	0.641	0.895	0.762	0.641	0.895	SUBCLONAL	1	TRUE	1	0.33	2		206	350	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729879	30729879	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	37	193	0	ENST00000295754.5:c.1400T>C	p.Val467Ala	p.V467A	ENST00000295754	NM_003242.5	467	gTa/gCa	6/7	1	2	FACETS	0.587	0.484	0.701	0.587	0.484	0.701	SUBCLONAL	1	TRUE	1	0.33	2		193	382	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613085	52613085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1318993618	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	66	246	0	ENST00000394830.3:c.3443G>A	p.Arg1148His	p.R1148H	ENST00000394830	NM_018313.4	1148	cGt/cAt	22/30	1	2	FACETS	0.847	0.737	0.966	0.847	0.737	0.966	CLONAL	1	TRUE	1	0.33	2		246	472	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807782	1807782	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	62	398	0	ENST00000260795.2:c.1841T>C	p.Ile614Thr	p.I614T	ENST00000260795		614	aTc/aCc	13/17	1	2	FACETS	0.604	0.522	0.694	0.604	0.522	0.694	SUBCLONAL	1	TRUE	1	0.33	2		398	622	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247352	153247352	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	52	211	0	ENST00000281708.4:c.1450A>G	p.Arg484Gly	p.R484G	ENST00000281708	NM_033632.3	484	Agg/Ggg	10/12	1	2	FACETS	0.747	0.637	0.866	0.747	0.637	0.866	SUBCLONAL	1	TRUE	1	0.33	2		211	422	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753117	57753117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1185917187	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	56	277	0	ENST00000274289.3:c.899C>T	p.Pro300Leu	p.P300L	ENST00000274289	NM_006622.3	300	cCg/cTg	7/14	1	2	FACETS	0.842	0.724	0.971	0.842	0.724	0.971	CLONAL	1	TRUE	1	0.33	2		277	403	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80160688	80160688	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	76	403	0	ENST00000265081.6:c.3057A>T	p.Lys1019Asn	p.K1019N	ENST00000265081	NM_002439.4	1019	aaA/aaT	22/24	1	2	FACETS	0.842	0.74	0.952	0.842	0.74	0.952	CLONAL	1	TRUE	1	0.33	2		403	547	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910609	29910609	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	86	528	1	ENST00000376809.5:c.149G>T	p.Gly50Val	p.G50V	ENST00000376809	NM_002116.7	50	gGc/gTc	2/8	1	2	FACETS	0.619	0.547	0.697	0.619	0.547	0.697	SUBCLONAL	1	TRUE	1	0.33	2		529	842	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675696	30675696	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	110	566	0	ENST00000376406.3:c.2660G>A	p.Arg887Lys	p.R887K	ENST00000376406	NM_014641.2	887	aGg/aAg	8/15	1	2	FACETS	0.649	0.582	0.721	0.649	0.582	0.721	SUBCLONAL	1	TRUE	1	0.33	2		566	1027	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323312	31323312	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	23	168	0	ENST00000412585.2:c.677G>T	p.Arg226Met	p.R226M	ENST00000412585	NM_005514.6	226	aGg/aTg	4/8	1	2	FACETS	0.553	0.432	0.692	0.553	0.432	0.692	SUBCLONAL	1	TRUE	1	0.33	2		168	252	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324142	31324142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs281864617	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	36	377	0	ENST00000412585.2:c.421G>A	p.Ala141Thr	p.A141T	ENST00000412585	NM_005514.6	141	Gcc/Acc	3/8	1	2	FACETS	0.349	0.286	0.419	0.349	0.286	0.419	SUBCLONAL	1	TRUE	1	0.33	2		377	626	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878988	151878988	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138373177	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	73	337	0	ENST00000262189.6:c.5957G>A	p.Arg1986Gln	p.R1986Q	ENST00000262189	NM_170606.2	1986	cGg/cAg	36/59	1	2	FACETS	0.76	0.665	0.862	0.76	0.665	0.862	SUBCLONAL	1	TRUE	1	0.33	2		337	582	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345797	152345797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149186933	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	59	271	0	ENST00000359321.1:c.773G>A	p.Arg258His	p.R258H	ENST00000359321	NM_005431.1	258	cGt/cAt	3/3	1	2	FACETS	0.805	0.695	0.925	0.805	0.695	0.925	CLONAL	1	TRUE	1	0.33	2		271	444	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271232	38271232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781328162	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	101	514	0	ENST00000425967.3:c.2476G>A	p.Val826Ile	p.V826I	ENST00000425967	NM_001174067.1	826	Gtc/Atc	19/19	1	2	FACETS	0.73	0.651	0.813	0.73	0.651	0.813	SUBCLONAL	1	TRUE	1	0.33	2		514	839	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90995085	90995085	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs771475965	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	18	212	0	ENST00000265433.3:c.38-2A>G		p.X13_splice	ENST00000265433	NM_002485.4	13			1	2	FACETS	0.359	0.27	0.464	0.359	0.27	0.464	SUBCLONAL	1	TRUE	1	0.33	2		212	304	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595359	141595359	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs899336296	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	118	433	0	ENST00000220592.5:c.74C>A	p.Pro25His	p.P25H	ENST00000220592	NM_012154.3	25	cCt/cAt	2/19	1	2	FACETS	0.913	0.824	1	0.913	0.824	1	CLONAL	1	TRUE	1	0.33	2		433	783	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391910	139391910	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	89	501	0	ENST00000277541.6:c.6281A>G	p.Asp2094Gly	p.D2094G	ENST00000277541	NM_017617.3	2094	gAc/gGc	34/34	1	2	FACETS	0.617	0.546	0.693	0.617	0.546	0.693	SUBCLONAL	1	TRUE	1	0.33	2		501	874	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411825	139411825	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	76	433	0	ENST00000277541.6:c.1454T>C	p.Val485Ala	p.V485A	ENST00000277541	NM_017617.3	485	gTg/gCg	9/34	1	2	FACETS	0.552	0.483	0.626	0.552	0.483	0.626	SUBCLONAL	1	TRUE	1	0.33	2		433	835	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0044348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	183	544	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.814	0.755	0.875	0.814	0.755	0.875	CLONAL	1	TRUE	1	0.728495285532698	2		544	617	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398287	25398288	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTC	novel	NA	P-0044348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	111	398	0	ENST00000311936.3:c.29_31dup	p.Gly10dup	p.G10dup	ENST00000311936	NM_004985.3	10	gct/gGAGct	2/5	1	2	FACETS	0.667	0.603	0.734	0.667	0.603	0.734	SUBCLONAL	1	TRUE	1	0.728495285532698	2		398	457	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538990	187538990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755244994	NA	P-0044348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	197	479	0	ENST00000441802.2:c.8750G>A	p.Arg2917Gln	p.R2917Q	ENST00000441802	NM_005245.3	2917	cGa/cAa	10/27	1	2	FACETS	0.818	0.761	0.877	0.818	0.761	0.877	CLONAL	1	TRUE	1	0.728495285532698	2		479	661	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573127	64573127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs566593066	NA	P-0044348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	111	369	0	ENST00000312049.6:c.1165C>T	p.Arg389Trp	p.R389W	ENST00000312049	NM_130799.2	389	Cgg/Tgg	8/10	1	2	FACETS	0.808	0.733	0.886	0.808	0.733	0.886	CLONAL	1	TRUE	1	0.728495285532698	2		369	377	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163748	152163748	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs104893956	NA	P-0044348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	141	415	0	ENST00000206249.3:c.469C>T	p.Arg157Ter	p.R157*	ENST00000206249	NM_000125.3	157	Cga/Tga	2/8	1	2	FACETS	0.9	0.828	0.975	0.9	0.828	0.975	CLONAL	1	TRUE	1	0.728495285532698	2		415	430	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202605	108202605	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0044348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	91	280	0	ENST00000278616.4:c.7630-1G>A		p.X2544_splice	ENST00000278616	NM_000051.3	2544			1	2	FACETS	0.819	0.736	0.906	0.819	0.736	0.906	CLONAL	1	TRUE	1	0.728495285532698	2		280	305	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691208	18691208	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	114	322	0	ENST00000266497.5:c.3319A>G	p.Arg1107Gly	p.R1107G	ENST00000266497		1107	Aga/Gga	23/31	1	2	FACETS	0.862	0.784	0.943	0.862	0.784	0.943	CLONAL	1	TRUE	1	0.728495285532698	2		322	363	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628421	187628421	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1410329862	NA	P-0044348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	291	698	0	ENST00000441802.2:c.2561A>G	p.Asn854Ser	p.N854S	ENST00000441802	NM_005245.3	854	aAc/aGc	2/27	1	2	FACETS	0.927	0.875	0.98	0.927	0.875	0.98	CLONAL	1	TRUE	1	0.728495285532698	2		698	862	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163846	32163846	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	150	494	0	ENST00000375023.3:c.5380G>A	p.Glu1794Lys	p.E1794K	ENST00000375023	NM_004557.3	1794	Gag/Aag	30/30	1	2	FACETS	0.854	0.787	0.924	0.854	0.787	0.924	CLONAL	1	TRUE	1	0.728495285532698	2		494	482	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	124	321	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.400800818654542	2		321	464	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0044375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	50	380	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.84	0.717	0.973	0.84	0.717	0.973	CLONAL	1	TRUE	1	0.400800818654542	2		380	297	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204864	NA	P-0044465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	91	476	2	ENST00000371953.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000371953	NM_000314.4	171	Cag/Tag	6/9	0.25966683724116	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.25966683724116	1		478	571	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551682	150551682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	34	591	0	ENST00000369026.2:c.325G>A	p.Glu109Lys	p.E109K	ENST00000369026	NM_021960.4	109	Gag/Aag	1/3	0.25966683724116	3	FACETS	0.487	0.397	0.589	0.244	0.198	0.295	SUBCLONAL	1	TRUE	1	0.25966683724116	3		591	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573991	7573991	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567542019	NA	P-0044465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	127	1029	0	ENST00000269305.4:c.1036G>T	p.Glu346Ter	p.E346*	ENST00000269305	NM_001126112.2	346	Gag/Tag	10/11	0.25885030943586	1	FACETS	0.999	0.905	1	0.999	0.905	1	CLONAL	1	TRUE	0	0.25966683724116	1		1029	852	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056594	26056594	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	24	325	0	ENST00000343677.2:c.63G>T	p.Lys21Asn	p.K21N	ENST00000343677	NM_005319.3	21	aaG/aaT	1/1	1	2	FACETS	0.555	0.435	0.693	0.555	0.435	0.693	SUBCLONAL	1	TRUE	1	0.25966683724116	2		325	333	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988452	41988452	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0044465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	51	603	0	ENST00000219905.7:c.1244C>G	p.Ser415Ter	p.S415*	ENST00000219905	NM_001164273.1	415	tCa/tGa	3/24	1	2	FACETS	0.534	0.452	0.623	0.534	0.452	0.623	SUBCLONAL	1	TRUE	1	0.25966683724116	2		603	736	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366981	118366981	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	33	541	0	ENST00000534358.1:c.5563G>C	p.Asp1855His	p.D1855H	ENST00000534358	NM_005933.3	1855	Gat/Cat	20/36	1	2	FACETS	0.489	0.397	0.592	0.489	0.397	0.592	SUBCLONAL	1	TRUE	1	0.25966683724116	2		541	520	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512308	38512308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	114	1127	0	ENST00000254066.5:c.1219C>T	p.Pro407Ser	p.P407S	ENST00000254066	NM_000964.3	407	Ccg/Tcg	9/9	1	2	FACETS	0.955	0.859	1	0.955	0.859	1	CLONAL	1	TRUE	1	0.25966683724116	2		1127	919	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028656	12028656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	60	511	0	ENST00000353533.5:c.859C>T	p.Arg287Cys	p.R287C	ENST00000353533	NM_003010.3	287	Cgc/Tgc	8/11	0.25885030943586	1	FACETS	0.76	0.655	0.874	0.76	0.655	0.874	SUBCLONAL	1	TRUE	0	0.25966683724116	1		511	529	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982957	201982957	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs374568591	NA	P-0044465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	45	890	0	ENST00000359651.3:c.806C>T	p.Ala269Val	p.A269V	ENST00000359651		269	gCg/gTg	7/8	0.25966683724116	3	FACETS	0.462	0.387	0.546	0.231	0.193	0.273	SUBCLONAL	1	TRUE	1	0.25966683724116	3		890	847	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121069	3121069	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	89	1038	0	ENST00000078429.4:c.972C>G	p.Ile324Met	p.I324M	ENST00000078429	NM_002067.2	324	atC/atG	7/7	0.223508377487341	1	FACETS	0.725	0.642	0.814	0.725	0.642	0.814	SUBCLONAL	1	TRUE	0	0.25966683724116	1		1038	823	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11137003	11137013	+	frameshift_variant	Frame_Shift_Del	DEL	ACTGGCGGCAT	ACTGGCGGCAT	-	novel	NA	P-0044465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	78	872	1	ENST00000358026.2:c.3196_3206del	p.Thr1066CysfsTer12	p.T1066Cfs*12	ENST00000358026	NM_001128849.1	1066	ACTGGCGGCATt/t	23/36	0.256431323806929	2	FACETS	0.774	0.679	0.876	0.387	0.339	0.438	SUBCLONAL	1	TRUE	0	0.25966683724116	2		873	776	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439262	52439263	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTGGGATGGGGCT	novel	NA	P-0044465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	54	918	0	ENST00000460680.1:c.966_979dup	p.Ser327LysfsTer13	p.S327Kfs*13	ENST00000460680	NM_004656.3	327	agc/aAGCCCCATCCCACAgc	11/17	0.195229599295582	0	FACETS	0.441	0.375	0.512			1	SUBCLONAL	1	TRUE	0	0.25966683724116	0		918	699	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947127	178947127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	26	447	0	ENST00000263967.3:c.2563C>G	p.His855Asp	p.H855D	ENST00000263967	NM_006218.2	855	Cac/Gac	18/21	1	2	FACETS	0.399	0.315	0.496	0.399	0.315	0.496	SUBCLONAL	1	TRUE	1	0.25966683724116	2		447	502	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839836	27839836	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs963972613	NA	P-0044465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	78	835	0	ENST00000328488.2:c.258G>C	p.Gln86His	p.Q86H	ENST00000328488	NM_003533.2	86	caG/caC	1/1	1	2	FACETS	0.751	0.659	0.85	0.751	0.659	0.85	SUBCLONAL	1	TRUE	1	0.25966683724116	2		835	800	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	146	415	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.51	2		421	568	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	102	476	10	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.87	0.782	0.962	0.87	0.782	0.962	CLONAL	1	TRUE	1	0.51	2		486	460	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	66	397	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.2009402909681	0	FACETS	0.342	0.298	0.389			1	INDETERMINATE	1	TRUE	0	0.51	0		397	371	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349640	89349641	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs772267579	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	225	716	12	ENST00000301030.4:c.3309dup	p.Asp1104ArgfsTer2	p.D1104Rfs*2	ENST00000301030	NM_001256183.1	1103	-/A	9/13	1	2	FACETS	0.916	0.854	0.981	0.916	0.854	0.981	CLONAL	1	TRUE	1	0.51	2		728	963	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968660	55968660	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199774865	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	109	429	0	ENST00000263923.4:c.2003C>T	p.Thr668Met	p.T668M	ENST00000263923	NM_002253.2	668	aCg/aTg	14/30	1	2	FACETS	0.762	0.686	0.842	0.762	0.686	0.842	SUBCLONAL	1	TRUE	1	0.51	2		429	561	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817412	39817412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200306085	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	163	506	1	ENST00000288319.7:c.151G>A	p.Val51Ile	p.V51I	ENST00000288319	NM_182918.3	51	Gtc/Atc	2/10	0.2009402909681	0	FACETS	0.491	0.452	0.531			1	INDETERMINATE	1	TRUE	0	0.51	0		507	638	SUCCESS
APC	324	MSKCC	GRCh37	5	112111408	112111411	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	-	rs387906231	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	22	201	0	ENST00000257430.4:c.509_512del	p.Asp170ValfsTer4	p.D170Vfs*4	ENST00000257430	NM_000038.5	169	ATAGat/at	5/16	1	2	FACETS	0.784	0.618	0.97	0.784	0.618	0.97	CLONAL	1	TRUE	1	0.51	2		201	110	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662023	227662023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776903727	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	168	603	2	ENST00000305123.5:c.1432G>A	p.Ala478Thr	p.A478T	ENST00000305123	NM_005544.2	478	Gcc/Acc	1/2	1	2	FACETS	0.956	0.882	1	0.956	0.882	1	CLONAL	1	TRUE	1	0.51	2		605	689	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107096	27107096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	158	472	0	ENST00000324856.7:c.6707G>C	p.Arg2236Pro	p.R2236P	ENST00000324856	NM_006015.4	2236	cGc/cCc	20/20	1	2	FACETS	0.949	0.872	1	0.949	0.872	1	CLONAL	1	TRUE	1	0.51	2		472	653	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781375	3781375	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	292	732	0	ENST00000262367.5:c.4990C>T	p.Arg1664Cys	p.R1664C	ENST00000262367	NM_004380.2	1664	Cgc/Tgc	30/31	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.51	2		732	1120	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289952	15289952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778635935	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	305	815	1	ENST00000263388.2:c.3602G>A	p.Arg1201His	p.R1201H	ENST00000263388	NM_000435.2	1201	cGc/cAc	22/33	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.51	2		816	1153	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	135	509	1	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	0.821	0.748	0.897	0.821	0.748	0.897	CLONAL	1	TRUE	1	0.51	2		510	645	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027676	48027678	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs587782858	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	50	247	0	ENST00000234420.5:c.2561_2563del	p.Lys854del	p.K854del	ENST00000234420	NM_000179.2	852	AAG/-	4/10	1	2	FACETS	0.921	0.791	1	0.921	0.791	1	CLONAL	1	TRUE	1	0.51	2		247	213	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563461	87563461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1211018594	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	178	498	0	ENST00000277120.3:c.1849G>A	p.Val617Ile	p.V617I	ENST00000277120		617	Gtc/Atc	16/19	1	2	FACETS	0.937	0.866	1	0.937	0.866	1	CLONAL	1	TRUE	1	0.51	2		498	745	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435692	56435692	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	247	558	1	ENST00000407977.2:c.1445G>A	p.Cys482Tyr	p.C482Y	ENST00000407977		482	tGc/tAc	9/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.51	2		559	789	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	155	544	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	0.98	0.901	1	0.98	0.901	1	CLONAL	1	TRUE	1	0.51	2		544	620	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935635	49935635	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	254	604	0	ENST00000296474.3:c.1729del	p.His577ThrfsTer5	p.H577Tfs*5	ENST00000296474	NM_002447.2	577	Cac/ac	5/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.51	2		604	941	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926960	112926960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770363146	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	122	443	0	ENST00000351677.2:c.1580G>A	p.Arg527His	p.R527H	ENST00000351677	NM_002834.3	527	cGc/cAc	13/16	0.0899147548908582	0	FACETS	0.398	0.361	0.437			1	INDETERMINATE	1	TRUE	0	0.51	0		443	589	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204618	128204618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	264	732	0	ENST00000341105.2:c.823G>A	p.Ala275Thr	p.A275T	ENST00000341105	NM_032638.4	275	Gcc/Acc	3/6	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.51	2		732	979	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571498	95571498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	117	374	0	ENST00000393063.1:c.3179G>A	p.Arg1060His	p.R1060H	ENST00000393063	NM_030621.3	1060	cGc/cAc	21/28	1	2	FACETS	0.808	0.731	0.888	0.808	0.731	0.888	CLONAL	1	TRUE	1	0.51	2		374	568	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158637068	158637069	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CA	CA	-	rs141073095	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	66	554	2	ENST00000263640.3:c.111_112del	p.Cys37Ter	p.C37*	ENST00000263640	NM_001105.4	37	tgTGaa/tgaa	4/11	1	2	FACETS	0.337	0.292	0.386	0.337	0.292	0.386	SUBCLONAL	1	TRUE	1	0.51	2		556	768	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123752	11123752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568471266	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	209	546	0	ENST00000358026.2:c.2402G>A	p.Arg801His	p.R801H	ENST00000358026	NM_001128849.1	801	cGc/cAc	16/36	1	2	FACETS	0.967	0.899	1	0.967	0.899	1	CLONAL	1	TRUE	1	0.51	2		546	848	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779308	3779308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760771706	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	202	590	0	ENST00000262367.5:c.5740G>A	p.Val1914Met	p.V1914M	ENST00000262367	NM_004380.2	1914	Gtg/Atg	31/31	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.51	2		590	792	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911487	131911487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658808	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	47	244	0	ENST00000265335.6:c.232G>A	p.Val78Met	p.V78M	ENST00000265335		78	Gtg/Atg	3/25	1	2	FACETS	0.706	0.6	0.821	0.706	0.6	0.821	SUBCLONAL	1	TRUE	1	0.51	2		244	261	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198272802	198272802	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745511585	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	66	446	1	ENST00000335508.6:c.1159C>T	p.Arg387Trp	p.R387W	ENST00000335508	NM_012433.2	387	Cgg/Tgg	9/25	1	2	FACETS	0.609	0.53	0.694	0.609	0.53	0.694	SUBCLONAL	1	TRUE	1	0.51	2		447	425	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778909	9778909	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1048477125	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	256	661	0	ENST00000377346.4:c.1178C>T	p.Ala393Val	p.A393V	ENST00000377346	NM_005026.3	393	gCg/gTg	9/24	1	2	FACETS	0.929	0.869	0.99	0.929	0.869	0.99	CLONAL	1	TRUE	1	0.51	2		661	1081	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927393	245927393	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs778849787	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	34	446	1	ENST00000388985.4:c.1135C>G	p.Leu379Val	p.L379V	ENST00000388985		379	Ctg/Gtg	11/12	1	2	FACETS	0.216	0.175	0.261	0.216	0.175	0.261	SUBCLONAL	1	TRUE	1	0.51	2		447	618	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150333	108150333	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	22	227	0	ENST00000278616.4:c.3400A>G	p.Met1134Val	p.M1134V	ENST00000278616	NM_000051.3	1134	Atg/Gtg	23/63	1	2	FACETS	0.496	0.387	0.62	0.496	0.387	0.62	SUBCLONAL	1	TRUE	1	0.51	2		227	174	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	364671	364671	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	254	620	0	ENST00000262320.3:c.891G>A	p.Trp297Ter	p.W297*	ENST00000262320	NM_003502.3	297	tgG/tgA	3/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.51	2		620	891	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822111	72822111	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	114	489	0	ENST00000268489.5:c.10064T>C	p.Leu3355Pro	p.L3355P	ENST00000268489	NM_006885.3	3355	cTg/cCg	10/10	1	2	FACETS	0.746	0.674	0.823	0.746	0.674	0.823	SUBCLONAL	1	TRUE	1	0.51	2		489	599	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207046	1207046	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1198	65	761	1	ENST00000326873.7:c.134T>C	p.Leu45Pro	p.L45P	ENST00000326873	NM_000455.4	45	cTc/cCc	1/10	1	2	FACETS	0.202	0.174	0.232	0.202	0.174	0.232	SUBCLONAL	1	TRUE	1	0.51	2		762	1263	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7167988	7167988	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	166	479	0	ENST00000302850.5:c.1601A>G	p.Tyr534Cys	p.Y534C	ENST00000302850	NM_000208.2	534	tAc/tGc	7/22	1	2	FACETS	0.922	0.849	0.998	0.922	0.849	0.998	CLONAL	1	TRUE	1	0.51	2		479	706	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284996	15284996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1472208548	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	99	779	0	ENST00000263388.2:c.4619G>A	p.Arg1540His	p.R1540H	ENST00000263388	NM_000435.2	1540	cGc/cAc	25/33	1	2	FACETS	0.423	0.377	0.472	0.423	0.377	0.472	SUBCLONAL	1	TRUE	1	0.51	2		779	918	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881664	111881664	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	255	577	0	ENST00000393256.3:c.342del	p.Gln115LysfsTer20	p.Q115Kfs*20	ENST00000393256	NM_006538.4	114	acA/ac	2/4	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.51	2		577	994	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169981187	169981187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368704903	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	86	406	0	ENST00000295797.4:c.334C>T	p.Arg112Cys	p.R112C	ENST00000295797	NM_002740.5	112	Cgt/Tgt	4/18	1	2	FACETS	0.892	0.795	0.995	0.892	0.795	0.995	CLONAL	1	TRUE	1	0.51	2		406	378	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673517	30673517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1463478715	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	233	706	0	ENST00000376406.3:c.3443G>A	p.Ser1148Asn	p.S1148N	ENST00000376406	NM_014641.2	1148	aGc/aAc	10/15	1	2	FACETS	0.855	0.797	0.914	0.855	0.797	0.914	CLONAL	1	TRUE	1	0.51	2		706	1069	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322955	31322955	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	244	824	0	ENST00000412585.2:c.941G>A	p.Gly314Asp	p.G314D	ENST00000412585	NM_005514.6	314	gGc/gAc	5/8	1	2	FACETS	0.784	0.732	0.839	0.784	0.732	0.839	SUBCLONAL	1	TRUE	1	0.51	2		824	1220	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099301	157099301	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	202	380	0	ENST00000346085.5:c.241del	p.His81ThrfsTer30	p.H81Tfs*30	ENST00000346085	NM_020732.3	80	Ccc/cc	1/20	1	2	FACETS	0.906	0.841	0.974	0.906	0.841	0.974	CLONAL	1	TRUE	1	0.51	2		380	874	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515097	148515097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	165	416	0	ENST00000320356.2:c.1112G>A	p.Ser371Asn	p.S371N	ENST00000320356	NM_004456.4	371	aGc/aAc	10/20	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.51	2		416	624	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882024	36882024	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1323551948	NA	P-0044666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	278	725	0	ENST00000358127.4:c.989C>T	p.Pro330Leu	p.P330L	ENST00000358127	NM_001280556.1	330	cCg/cTg	8/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.51	2		725	1053	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	264	382	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.447063053862818	4	FACETS	0.986	0.933	1	0.986	0.933	1	CLONAL	3	TRUE	1	0.447063053862818	4		382	578	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056352	27056352	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1557591264	NA	P-0044750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	164	373	1	ENST00000324856.7:c.1348C>T	p.Gln450Ter	p.Q450*	ENST00000324856	NM_006015.4	450	Cag/Tag	2/20	0.447063053862818	3	FACETS	0.953	0.883	1	0.953	0.883	1	CLONAL	2	TRUE	1	0.447063053862818	3		374	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577495	7577507	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGACCTGGAGTCT	TGACCTGGAGTCT	-	novel	NA	P-0044750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	343	640	0	ENST00000269305.4:c.774_782+4del		p.X258_splice	ENST00000269305	NM_001126112.2	258		7/11	0.447063053862818	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.447063053862818	2		640	749	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457254	89457254	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	92	354	0	ENST00000336596.2:c.1735A>G	p.Lys579Glu	p.K579E	ENST00000336596	NM_005233.5	579	Aaa/Gaa	9/17	0.447063053862818	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.447063053862818	1		354	295	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525039	157525039	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0044750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	144	345	0	ENST00000346085.5:c.4934C>G	p.Ser1645Ter	p.S1645*	ENST00000346085	NM_020732.3	1645	tCa/tGa	19/20	0.447063053862818	2	FACETS	0.964	0.893	1	0.964	0.893	1	CLONAL	2	TRUE	0	0.447063053862818	2		345	334	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	198	321	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.68929177895412	2		321	485	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679366	29679366	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs866445127	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	186	507	0	ENST00000356175.3:c.7486C>T	p.Arg2496Ter	p.R2496*	ENST00000356175	NM_000267.3	2496	Cga/Tga	50/57	1	2	FACETS	0.923	0.857	0.99	0.923	0.857	0.99	CLONAL	1	TRUE	1	0.68929177895412	2		507	585	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	374	844	1	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	1	2	FACETS	0.989	0.94	1	0.989	0.94	1	CLONAL	1	TRUE	1	0.68929177895412	2		845	1097	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570058	212570058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1186772138	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	151	368	0	ENST00000342788.4:c.1183G>A	p.Val395Ile	p.V395I	ENST00000342788	NM_005235.2	395	Gtc/Atc	10/28	1	2	FACETS	0.892	0.822	0.965	0.892	0.822	0.965	CLONAL	1	TRUE	1	0.68929177895412	2		368	491	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056274	180056274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770915197	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	350	889	1	ENST00000261937.6:c.970G>A	p.Glu324Lys	p.E324K	ENST00000261937	NM_182925.4	324	Gag/Aag	7/30	1	2	FACETS	0.978	0.928	1	0.978	0.928	1	CLONAL	1	TRUE	1	0.68929177895412	2		890	1038	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245411	153245411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	208	513	0	ENST00000281708.4:c.1780C>T	p.Leu594Phe	p.L594F	ENST00000281708	NM_033632.3	594	Ctt/Ttt	11/12	1	2	FACETS	0.994	0.929	1	0.994	0.929	1	CLONAL	1	TRUE	1	0.68929177895412	2		513	607	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656262	18656262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774333984	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	179	430	0	ENST00000266497.5:c.2941C>T	p.Arg981Cys	p.R981C	ENST00000266497		981	Cgc/Tgc	21/31	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.68929177895412	2		430	461	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488718	212488718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267599191	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	184	513	0	ENST00000342788.4:c.2131C>T	p.Arg711Cys	p.R711C	ENST00000342788	NM_005235.2	711	Cgt/Tgt	18/28	1	2	FACETS	0.89	0.826	0.955	0.89	0.826	0.955	CLONAL	1	TRUE	1	0.68929177895412	2		513	600	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857020	9857020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555481892	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	90	201	0	ENST00000330684.3:c.4381G>A	p.Glu1461Lys	p.E1461K	ENST00000330684	NM_001134407.1	1461	Gaa/Aaa	13/13	1	2	FACETS	0.985	0.887	1	0.985	0.887	1	CLONAL	1	TRUE	1	0.68929177895412	2		201	265	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919595	28919595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs553261958	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	222	491	0	ENST00000282397.4:c.2342G>A	p.Arg781Gln	p.R781Q	ENST00000282397	NM_002019.4	781	cGa/cAa	16/30	1	2	FACETS	0.961	0.899	1	0.961	0.899	1	CLONAL	1	TRUE	1	0.68929177895412	2		491	670	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317539	1317539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	289	628	1	ENST00000400841.2:c.526G>A	p.Asp176Asn	p.D176N	ENST00000400841		176	Gat/Aat	5/6	1	2	FACETS	0.948	0.894	1	0.948	0.894	1	CLONAL	1	TRUE	1	0.68929177895412	2		629	885	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101176	41101176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370385649	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	245	657	0	ENST00000373198.4:c.1180G>A	p.Glu394Lys	p.E394K	ENST00000373198	NM_133170.3	394	Gaa/Aaa	8/32	1	2	FACETS	0.985	0.925	1	0.985	0.925	1	CLONAL	1	TRUE	1	0.68929177895412	2		657	722	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984919	9984919	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	248	581	0	ENST00000330684.3:c.1046C>T	p.Ser349Phe	p.S349F	ENST00000330684	NM_001134407.1	349	tCc/tTc	4/13	1	2	FACETS	0.983	0.923	1	0.983	0.923	1	CLONAL	1	TRUE	1	0.68929177895412	2		581	732	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627284	12627284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	177	386	0	ENST00000251849.4:c.1432G>A	p.Glu478Lys	p.E478K	ENST00000251849	NM_002880.3	478	Gaa/Aaa	14/17	1	2	FACETS	0.995	0.924	1	0.995	0.924	1	CLONAL	1	TRUE	1	0.68929177895412	2		386	516	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949089	71949089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	208	727	0	ENST00000298229.2:c.3556C>T	p.Pro1186Ser	p.P1186S	ENST00000298229	NM_001567.3	1186	Ccg/Tcg	27/28	0.645753316759123	4	FACETS	0.877	0.813	0.943			1	CLONAL	1	TRUE	NA	0.68929177895412	4		727	1163	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342592	87342592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1456574135	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	174	437	0	ENST00000277120.3:c.877G>A	p.Glu293Lys	p.E293K	ENST00000277120		293	Gaa/Aaa	9/19	1	2	FACETS	0.977	0.906	1	0.977	0.906	1	CLONAL	1	TRUE	1	0.68929177895412	2		437	517	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143350338	143350338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	70	124	0	ENST00000262992.4:c.124G>A	p.Glu42Lys	p.E42K	ENST00000262992	NM_001101669.1	42	Gaa/Aaa	3/24	1	2	FACETS	0.967	0.858	1	0.967	0.858	1	CLONAL	1	TRUE	1	0.68929177895412	2		124	210	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639878	3639878	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750580998	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	311	850	0	ENST00000294008.3:c.3761C>T	p.Ser1254Leu	p.S1254L	ENST00000294008	NM_032444.2	1254	tCg/tTg	12/15	1	2	FACETS	0.965	0.912	1	0.965	0.912	1	CLONAL	1	TRUE	1	0.68929177895412	2		850	935	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156150	106156150	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	130	332	0	ENST00000380013.4:c.1051G>T	p.Glu351Ter	p.E351*	ENST00000380013	NM_001127208.2	351	Gaa/Taa	3/11	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.68929177895412	2		332	372	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543557	9543557	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	206	456	0	ENST00000353224.5:c.1597G>A	p.Asp533Asn	p.D533N	ENST00000353224	NM_177990.2	533	Gac/Aac	6/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.68929177895412	2		456	584	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012402	29012402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	205	621	0	ENST00000282397.4:c.469C>T	p.Pro157Ser	p.P157S	ENST00000282397	NM_002019.4	157	Ccc/Tcc	4/30	1	2	FACETS	0.929	0.867	0.994	0.929	0.867	0.994	CLONAL	1	TRUE	1	0.68929177895412	2		621	640	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518013	176518013	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139464025	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	323	855	1	ENST00000292408.4:c.511C>T	p.Arg171Cys	p.R171C	ENST00000292408	NM_213647.1	171	Cgc/Tgc	5/18	1	2	FACETS	0.995	0.942	1	0.995	0.942	1	CLONAL	1	TRUE	1	0.68929177895412	2		856	942	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189349353	189349353	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200000559	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	122	325	0	ENST00000264731.3:c.49C>T	p.Pro17Ser	p.P17S	ENST00000264731	NM_003722.4	17	Cct/Tct	1/14	1	2	FACETS	0.967	0.884	1	0.967	0.884	1	CLONAL	1	TRUE	1	0.68929177895412	2		325	366	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226551693	226551693	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	252	518	0	ENST00000366794.5:c.2737G>T	p.Gly913Ter	p.G913*	ENST00000366794	NM_001618.3	913	Gga/Tga	20/23	1	2	FACETS	0.945	0.887	1	0.945	0.887	1	CLONAL	1	TRUE	1	0.68929177895412	2		518	774	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420993	49420993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	236	534	1	ENST00000301067.7:c.14756C>T	p.Ser4919Phe	p.S4919F	ENST00000301067	NM_003482.3	4919	tCc/tTc	48/54	0.155363023673924	3	FACETS	1	0.991	1	0.664	0.623	0.707	INDETERMINATE	1	TRUE	1	0.68929177895412	3		535	693	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347064	347065	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	314	766	1	ENST00000262320.3:c.1946_1947delinsTT	p.Thr649Ile	p.T649I	ENST00000262320	NM_003502.3	649	aCC/aTT	7/11	NA	2	FACETS	0.925	0.874	0.977			1	INDETERMINATE	1	TRUE	NA	0.68929177895412	2		767	985	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041591	14041591	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs757525012	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	191	509	0	ENST00000311895.7:c.2138T>C	p.Val713Ala	p.V713A	ENST00000311895	NM_005236.2	713	gTt/gCt	11/11	1	2	FACETS	0.991	0.923	1	0.991	0.923	1	CLONAL	1	TRUE	1	0.68929177895412	2		509	559	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877156	89877156	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	190	464	0	ENST00000389301.3:c.481T>A	p.Phe161Ile	p.F161I	ENST00000389301	NM_000135.2	161	Ttc/Atc	5/43	0.68929177895412	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.68929177895412	1		464	361	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585360	29585360	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	217	483	0	ENST00000356175.3:c.4111-2A>C		p.X1371_splice	ENST00000356175	NM_000267.3	1371			1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.68929177895412	2		483	624	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646886	37646886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	311	709	0	ENST00000447079.4:c.2008C>T	p.Pro670Ser	p.P670S	ENST00000447079	NM_015083.1	670	Cct/Tct	3/14	1	2	FACETS	0.936	0.885	0.988	0.936	0.885	0.988	CLONAL	1	TRUE	1	0.68929177895412	2		709	964	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621939	1621939	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs995251085	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	328	976	1	ENST00000344749.5:c.853G>A	p.Gly285Ser	p.G285S	ENST00000344749	NM_001136139.2	285	Ggt/Agt	11/19	1	2	FACETS	0.926	0.876	0.976	0.926	0.876	0.976	CLONAL	1	TRUE	1	0.68929177895412	2		977	1028	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226617	2226617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1332247019	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	345	924	0	ENST00000398665.3:c.4097C>T	p.Pro1366Leu	p.P1366L	ENST00000398665	NM_032482.2	1366	cCt/cTt	27/28	1	2	FACETS	0.963	0.913	1	0.963	0.913	1	CLONAL	1	TRUE	1	0.68929177895412	2		924	1039	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743981	41743981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	380	950	1	ENST00000301178.4:c.916C>T	p.His306Tyr	p.H306Y	ENST00000301178	NM_021913.4	306	Cac/Tac	7/20	1	2	FACETS	0.973	0.925	1	0.973	0.925	1	CLONAL	1	TRUE	1	0.68929177895412	2		951	1133	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551279	29551279	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	296	818	0	ENST00000389048.3:c.1351C>T	p.Leu451Phe	p.L451F	ENST00000389048	NM_004304.4	451	Ctt/Ttt	6/29	1	2	FACETS	0.975	0.921	1	0.975	0.921	1	CLONAL	1	TRUE	1	0.68929177895412	2		818	881	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520245	9520245	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	190	495	0	ENST00000353224.5:c.2024G>A	p.Gly675Glu	p.G675E	ENST00000353224	NM_177990.2	675	gGa/gAa	10/10	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.68929177895412	2		495	542	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546743	9546744	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	114	414	1	ENST00000353224.5:c.1278_1279delinsAA	p.Val427Met	p.V427M	ENST00000353224	NM_177990.2	426	agGGtg/agAAtg	5/10	1	2	FACETS	0.815	0.74	0.893	0.815	0.74	0.893	CLONAL	1	TRUE	1	0.68929177895412	2		415	406	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560919	9560919	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	191	494	0	ENST00000353224.5:c.863C>T	p.Ser288Leu	p.S288L	ENST00000353224	NM_177990.2	288	tCa/tTa	4/10	1	2	FACETS	0.922	0.858	0.988	0.922	0.858	0.988	CLONAL	1	TRUE	1	0.68929177895412	2		494	601	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39762943	39762943	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	154	340	0	ENST00000288319.7:c.893C>T	p.Pro298Leu	p.P298L	ENST00000288319	NM_182918.3	298	cCa/cTa	9/10	0.282257189297648	3	FACETS	1	0.983	1	0.618	0.57	0.668	INDETERMINATE	1	TRUE	1	0.68929177895412	3		340	486	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37038195	37038195	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs63750452	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	127	209	0	ENST00000231790.2:c.202A>G	p.Ile68Val	p.I68V	ENST00000231790	NM_000249.3	68	Atc/Gtc	2/19	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.68929177895412	2		209	323	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528642	89528642	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	97	234	0	ENST00000336596.2:c.2942T>C	p.Val981Ala	p.V981A	ENST00000336596	NM_005233.5	981	gTt/gCt	17/17	1	2	FACETS	0.948	0.856	1	0.948	0.856	1	CLONAL	1	TRUE	1	0.68929177895412	2		234	297	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521431	187521431	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	203	505	0	ENST00000441802.2:c.11724T>G	p.Asp3908Glu	p.D3908E	ENST00000441802	NM_005245.3	3908	gaT/gaG	22/27	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.68929177895412	2		505	568	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294978	1294978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	27	42	0	ENST00000310581.5:c.127G>A	p.Asp43Asn	p.D43N	ENST00000310581	NM_198253.2	43	Gac/Aac	1/16	1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	1	0.68929177895412	2		42	76	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497212	149497212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772895326	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	271	694	1	ENST00000261799.4:c.3106G>A	p.Gly1036Ser	p.G1036S	ENST00000261799	NM_002609.3	1036	Ggc/Agc	22/23	1	2	FACETS	0.912	0.858	0.967	0.912	0.858	0.967	CLONAL	1	TRUE	1	0.68929177895412	2		695	862	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500883	149500883	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	233	550	2	ENST00000261799.4:c.2347C>T	p.Pro783Ser	p.P783S	ENST00000261799	NM_002609.3	783	Cct/Tct	17/23	1	2	FACETS	0.973	0.912	1	0.973	0.912	1	CLONAL	1	TRUE	1	0.68929177895412	2		552	695	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637825	176637825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371421105	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	237	590	0	ENST00000439151.2:c.2425G>A	p.Glu809Lys	p.E809K	ENST00000439151	NM_022455.4	809	Gag/Aag	5/23	1	2	FACETS	0.937	0.878	0.997	0.937	0.878	0.997	CLONAL	1	TRUE	1	0.68929177895412	2		590	734	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172019	32172019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	268	667	0	ENST00000375023.3:c.3013G>A	p.Gly1005Arg	p.G1005R	ENST00000375023	NM_004557.3	1005	Gga/Aga	19/30	1	2	FACETS	0.968	0.912	1	0.968	0.912	1	CLONAL	1	TRUE	1	0.68929177895412	2		667	803	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068068	94068069	+	missense_variant	Missense_Mutation	DNP	AG	AG	GA	novel	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	122	342	0	ENST00000369303.4:c.893_894delinsTC	p.Thr298Ile	p.T298I	ENST00000369303	NM_004440.3	298	aCT/aTC	4/17	0.68929177895412	1	FACETS	0.892	0.823	0.962	0.892	0.823	0.962	CLONAL	1	TRUE	0	0.68929177895412	1		342	260	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001248	150001248	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	139	461	0	ENST00000253339.5:c.2356C>T	p.Pro786Ser	p.P786S	ENST00000253339		786	Cct/Tct	4/7	0.68929177895412	1	FACETS	0.593	0.544	0.643	0.593	0.544	0.643	SUBCLONAL	1	TRUE	0	0.68929177895412	1		461	446	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151855959	151855959	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	178	457	0	ENST00000262189.6:c.11659C>T	p.His3887Tyr	p.H3887Y	ENST00000262189	NM_170606.2	3887	Cac/Tac	44/59	0.68929177895412	3	FACETS	0.875	0.807	0.944	0.437	0.403	0.472	CLONAL	1	TRUE	1	0.68929177895412	3		457	794	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68999999	68999999	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	272	611	0	ENST00000288368.4:c.2068C>T	p.Gln690Ter	p.Q690*	ENST00000288368	NM_024870.2	690	Cag/Tag	19/40	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.68929177895412	2		611	784	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0044795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	166	380	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.972	0.898	1	0.972	0.898	1	CLONAL	1	TRUE	1	0.59	2		380	579	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056346	180056346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs186187161	NA	P-0044795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	57	818	0	ENST00000261937.6:c.898G>A	p.Val300Ile	p.V300I	ENST00000261937	NM_182925.4	300	Gtc/Atc	7/30	1	2	FACETS	0.21	0.179	0.244	0.21	0.179	0.244	SUBCLONAL	1	TRUE	1	0.59	2		818	920	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343593	343593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	118	890	0	ENST00000262320.3:c.2081C>T	p.Thr694Ile	p.T694I	ENST00000262320	NM_003502.3	694	aCc/aTc	8/11	0.498510359745157	2	FACETS	0.616	0.555	0.679	0.308	0.277	0.34	SUBCLONAL	1	TRUE	0	0.498510359745157	2		890	769	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196693	106196693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	102	554	0	ENST00000380013.4:c.5026C>T	p.His1676Tyr	p.H1676Y	ENST00000380013	NM_001127208.2	1676	Cat/Tat	11/11	1	2	FACETS	0.801	0.719	0.887	0.801	0.719	0.887	CLONAL	1	TRUE	1	0.498510359745157	2		554	511	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527281	137527281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	27	547	0	ENST00000367739.4:c.365G>A	p.Cys122Tyr	p.C122Y	ENST00000367739	NM_000416.2	122	tGc/tAc	3/7	0.498510359745157	2	FACETS	0.202	0.16	0.25	0.101	0.08	0.125	SUBCLONAL	1	TRUE	0	0.498510359745157	2		547	537	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	261	382	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.648837987695602	4	FACETS	0.99	0.937	1	0.99	0.937	1	CLONAL	2	TRUE	2	0.843712124431504	4		382	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0044847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	580	608	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.843712124431504	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.843712124431504	2		610	665	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0044847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	287	317	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.843712124431504	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.843712124431504	2		317	340	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519896	NA	P-0044847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	258	421	1	ENST00000281708.4:c.1514G>T	p.Arg505Leu	p.R505L	ENST00000281708	NM_033632.3	505	cGc/cTc	10/12	0.427522310488972	2	FACETS	0.753	0.719	0.787	0.753	0.719	0.787	INDETERMINATE	2	TRUE	0	0.843712124431504	2		422	406	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858821	78858821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768126116	NA	P-0044847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	467	807	1	ENST00000306801.3:c.1856C>T	p.Ala619Val	p.A619V	ENST00000306801	NM_020761.2	619	gCg/gTg	17/34	0.363560391437282	6	FACETS	1	0.993	1	0.593	0.567	0.619	INDETERMINATE	2	TRUE	2	0.843712124431504	6		808	1254	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685306	89685307	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0044847-T01-IM6	NA	A	A	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	105	136	0	ENST00000371953.3:c.202_203del	p.Tyr68GlnfsTer5	p.Y68Qfs*5	ENST00000371953	NM_000314.4	67	atATac/atac	3/9	0.843712124431504	2	FACETS	0.929	0.876	0.976	0.929	0.876	0.976	CLONAL	2	TRUE	0	0.843712124431504	2		136	134	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578507	7578507	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519977	NA	P-0044905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	493	824	0	ENST00000269305.4:c.423C>G	p.Cys141Trp	p.C141W	ENST00000269305	NM_001126112.2	141	tgC/tgG	5/11	0.526756332201543	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.526756332201543	1		824	1274	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431354	49431354	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	186	493	0	ENST00000301067.7:c.9785del	p.Lys3262ArgfsTer68	p.K3262Rfs*68	ENST00000301067	NM_003482.3	3262	aAg/ag	34/54	0.526756332201543	1	FACETS	0.792	0.734	0.851	0.792	0.734	0.851	SUBCLONAL	1	TRUE	0	0.526756332201543	1		493	657	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917778	29917778	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	389	677	0	ENST00000389048.3:c.890A>G	p.Glu297Gly	p.E297G	ENST00000389048	NM_004304.4	297	gAg/gGg	3/29	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.526756332201543	2		677	1390	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448576	89448576	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	197	477	1	ENST00000336596.2:c.1540G>T	p.Ala514Ser	p.A514S	ENST00000336596	NM_005233.5	514	Gcc/Tcc	7/17	1	2	FACETS	0.843	0.781	0.907	0.843	0.781	0.907	CLONAL	1	TRUE	1	0.526756332201543	2		478	887	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536223	106536223	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1431841112	NA	P-0044905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	216	445	0	ENST00000369096.4:c.190G>C	p.Asp64His	p.D64H	ENST00000369096	NM_001198.3	64	Gac/Cac	2/7	0.526756332201543	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.526756332201543	1		445	587	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975733	26975733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046176-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	378	705	0	ENST00000381527.3:c.1241G>A	p.Gly414Asp	p.G414D	ENST00000381527	NM_001260.1	414	gGt/gAt	12/13	0.810201137471483	1	FACETS	0.998	0.963	1	0.998	0.963	1	CLONAL	1	TRUE	0	0.810201137471483	1		705	556	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446916	187446916	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046176-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	166	933	0	ENST00000232014.4:c.1277A>T	p.Gln426Leu	p.Q426L	ENST00000232014	NM_001130845.1	426	cAg/cTg	5/10	1	2	FACETS	0.318	0.291	0.346	0.318	0.291	0.346	SUBCLONAL	1	TRUE	1	0.810201137471483	2		933	1290	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402558	139402558	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046176-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	98	856	0	ENST00000277541.6:c.3359G>T	p.Gly1120Val	p.G1120V	ENST00000277541	NM_017617.3	1120	gGg/gTg	21/34	1	2	FACETS	0.226	0.201	0.253	0.226	0.201	0.253	SUBCLONAL	1	TRUE	1	0.810201137471483	2		856	1071	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599026	28599026	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	197	365	1	ENST00000241453.7:c.2262del	p.Leu755PhefsTer26	p.L755Ffs*26	ENST00000241453	NM_004119.2	754	ggG/gg	18/24	0.607558151508033	4	FACETS	1	0.928	1	0.334	0.309	0.36	CLONAL	1	TRUE	1	0.607310424440387	4		366	1040	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046444-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	159	321	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.951	0.872	1	0.951	0.872	1	CLONAL	1	TRUE	1	0.37748841059539	2		321	886	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952006	178952006	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046444-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	30	571	0	ENST00000263967.3:c.3061T>C	p.Tyr1021His	p.Y1021H	ENST00000263967	NM_006218.2	1021	Tac/Cac	21/21	0.381203500556886	0	FACETS	0.811	0.666	0.969			1	CLONAL	1	TRUE	0	0.37748841059539	0		571	122	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0046444-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	94	436	0	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	1	2	FACETS	0.811	0.723	0.905	0.811	0.723	0.905	CLONAL	1	TRUE	1	0.37748841059539	2		436	614	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468063	50468063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046444-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1227	66	721	0	ENST00000331340.3:c.1298G>A	p.Arg433His	p.R433H	ENST00000331340	NM_006060.4	433	cGc/cAc	8/8	0.171789520755818	2	FACETS	0.27	0.233	0.311	0.135	0.116	0.156	INDETERMINATE	1	TRUE	0	0.37748841059539	2		721	1293	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345264	70345264	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046444-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	67	286	0	ENST00000374080.3:c.2290C>T	p.Arg764Ter	p.R764*	ENST00000374080		764	Cga/Tga	16/45	0.359550765963142	0	FACETS	0.583	0.509	0.662			1	SUBCLONAL	1	TRUE	NA	0.37748841059539	0		286	379	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106007	8106007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046444-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	64	660	0	ENST00000346208.3:c.827G>A	p.Arg276Gln	p.R276Q	ENST00000346208		276	cGa/cAa	4/6	1	2	FACETS	0.33	0.285	0.38	0.33	0.285	0.38	SUBCLONAL	1	TRUE	1	0.37748841059539	2		660	1026	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420109	49420109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123728	NA	P-0046444-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	79	657	0	ENST00000301067.7:c.15640C>T	p.Arg5214Cys	p.R5214C	ENST00000301067	NM_003482.3	5214	Cgc/Tgc	48/54	1	2	FACETS	0.376	0.329	0.426	0.376	0.329	0.426	SUBCLONAL	1	TRUE	1	0.37748841059539	2		657	1113	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115865	8115866	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0046444-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	113	834	0	ENST00000346208.3:c.1213dup	p.His405ProfsTer102	p.H405Pfs*102	ENST00000346208		404	agc/agCc	6/6	1	2	FACETS	0.488	0.438	0.542	0.488	0.438	0.542	SUBCLONAL	1	TRUE	1	0.37748841059539	2		834	1226	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981088	201981089	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTCT	novel	NA	P-0046444-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	147	548	0	ENST00000359651.3:c.167_168insTTCT	p.Lys56AsnfsTer37	p.K56Nfs*37	ENST00000359651		56	aag/aaTTCTg	2/8	0.340005093201915	2	FACETS	1	0.956	1	0.536	0.49	0.584	CLONAL	1	TRUE	0	0.37748841059539	2		548	727	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024024	27024024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046444-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	135	381	0	ENST00000324856.7:c.1133del	p.Pro378LeufsTer13	p.P378Lfs*13	ENST00000324856	NM_006015.4	377	aCc/ac	1/20	0.225108969530343	3	FACETS	1	0.978	1	0.617	0.562	0.675	INDETERMINATE	1	TRUE	1	0.37748841059539	3		381	689	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265455	198265455	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046444-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	42	410	0	ENST00000335508.6:c.2702A>G	p.Gln901Arg	p.Q901R	ENST00000335508	NM_012433.2	901	cAa/cGa	18/25	1	2	FACETS	0.959	0.823	1	1	0.972	1	CLONAL	2	TRUE	1	0.37748841059539	2		410	116	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938494	44938515	+	frameshift_variant	Frame_Shift_Del	DEL	CACTGGAACAAAGAAAATCTGG	CACTGGAACAAAGAAAATCTGG	-	novel	NA	P-0046444-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	80	225	0	ENST00000377967.4:c.3044_3065del	p.Thr1015IlefsTer26	p.T1015Ifs*26	ENST00000377967	NM_021140.2	1014	ccCACTGGAACAAAGAAAATCTGG/cc	20/29	1	1	FACETS	0.843	0.757	0.931	1	0.983	1	CLONAL	2	TRUE	0	0.37748841059539	1		225	204	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907705	76907705	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046444-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	17	245	0	ENST00000373344.5:c.4456G>C	p.Asp1486His	p.D1486H	ENST00000373344	NM_000489.3	1486	Gat/Cat	15/35	0.359550765963142	0	FACETS	0.234	0.174	0.304			1	SUBCLONAL	1	TRUE	NA	0.37748841059539	0		245	240	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150923439	150923439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046444-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	43	635	0	ENST00000271640.5:c.2086G>A	p.Glu696Lys	p.E696K	ENST00000271640	NM_001145415.1	696	Gag/Aag	13/22	0.152569029100174	3	FACETS	0.445	0.371	0.526	0.148	0.123	0.176	INDETERMINATE	1	TRUE	0	0.37748841059539	3		635	609	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150923034	150923034	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046444-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	66	588	0	ENST00000271640.5:c.1681G>A	p.Glu561Lys	p.E561K	ENST00000271640	NM_001145415.1	561	Gag/Aag	13/22	0.152569029100174	3	FACETS	0.404	0.349	0.464	0.135	0.116	0.155	INDETERMINATE	1	TRUE	0	0.37748841059539	3		588	1029	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912289	32912289	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046444-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	10	489	0	ENST00000380152.3:c.3797A>G	p.His1266Arg	p.H1266R	ENST00000380152		1266	cAt/cGt	11/27	0.246337344806155	3	FACETS	0.396	0.269	0.555	0.198	0.134	0.278	SUBCLONAL	1	TRUE	1	0.37748841059539	3		489	159	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044503	12044503	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046444-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	11	523	0	ENST00000353533.5:c.1126G>A	p.Glu376Lys	p.E376K	ENST00000353533	NM_003010.3	376	Gag/Aag	11/11	0.381203500556886	1	FACETS	0.415	0.288	0.569	0.415	0.288	0.569	SUBCLONAL	1	TRUE	0	0.37748841059539	1		523	114	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61708373	61708373	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1194653286	NA	P-0046444-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	21	388	0	ENST00000401558.2:c.3016C>G	p.Gln1006Glu	p.Q1006E	ENST00000401558	NM_003400.3	1006	Caa/Gaa	24/25	0.37748841059539	6	FACETS	0.479	0.368	0.608			1	SUBCLONAL	1	TRUE	NA	0.37748841059539	6		388	408	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96931053	96931053	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs749807415	NA	P-0046444-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	150	566	0	ENST00000258439.3:c.67C>A	p.Leu23Met	p.L23M	ENST00000258439	NM_001193304.2	23	Ctg/Atg	2/4	1	2	FACETS	0.831	0.759	0.907	0.831	0.759	0.907	CLONAL	1	TRUE	1	0.37748841059539	2		566	956	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250440	26250440	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046444-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	74	791	0	ENST00000446824.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000446824	NM_021018.2	132	Cgc/Ggc	1/1	0.381203500556886	3	FACETS	0.435	0.379	0.495	0.217	0.189	0.248	SUBCLONAL	1	TRUE	1	0.37748841059539	3		791	1072	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046690-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	31	321	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.528	0.426	0.643	0.528	0.426	0.643	SUBCLONAL	1	TRUE	1	0.254299877206357	2		321	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0046690-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	287	817	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.254299877206357	2	FACETS	0.894	0.843	0.945	1	0.992	1	CLONAL	3	TRUE	0	0.254299877206357	2		817	842	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879881	37879881	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046690-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	96	862	0	ENST00000269571.5:c.2176C>G	p.Leu726Val	p.L726V	ENST00000269571		726	Ctt/Gtt	18/27	0.254299877206357	1	FACETS	0.797	0.709	0.89	0.797	0.709	0.89	SUBCLONAL	1	TRUE	0	0.254299877206357	1		862	827	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853065	151853065	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046690-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	69	522	0	ENST00000262189.6:c.11890C>T	p.Gln3964Ter	p.Q3964*	ENST00000262189	NM_170606.2	3964	Cag/Tag	46/59	0.181392336650697	3	FACETS	0.781	0.679	0.892	0.391	0.339	0.446	SUBCLONAL	1	TRUE	1	0.254299877206357	3		522	783	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004226	150004226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046690-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	45	450	0	ENST00000253339.5:c.1999G>A	p.Glu667Lys	p.E667K	ENST00000253339		667	Gaa/Aaa	3/7	0.188882336247826	2	FACETS	1	0.915	1	0.565	0.477	0.662	CLONAL	1	TRUE	0	0.254299877206357	2		450	313	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257893	16257893	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046690-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	60	732	0	ENST00000375759.3:c.5158G>C	p.Glu1720Gln	p.E1720Q	ENST00000375759	NM_015001.2	1720	Gag/Cag	11/15	1	2	FACETS	0.573	0.493	0.662	0.573	0.493	0.662	SUBCLONAL	1	TRUE	1	0.254299877206357	2		732	823	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431975	49431975	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046690-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	51	737	0	ENST00000301067.7:c.9164del	p.Pro3055LeufsTer16	p.P3055Lfs*16	ENST00000301067	NM_003482.3	3055	cCt/ct	34/54	0.181392336650697	3	FACETS	0.59	0.5	0.689	0.295	0.25	0.345	SUBCLONAL	1	TRUE	1	0.254299877206357	3		737	766	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004295	150004295	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046690-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	33	523	0	ENST00000253339.5:c.1930G>C	p.Glu644Gln	p.E644Q	ENST00000253339		644	Gag/Cag	3/7	0.188882336247826	2	FACETS	0.754	0.615	0.91	0.377	0.307	0.455	CLONAL	1	TRUE	0	0.254299877206357	2		523	344	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004355	150004355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046690-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	39	574	0	ENST00000253339.5:c.1870G>A	p.Glu624Lys	p.E624K	ENST00000253339		624	Gaa/Aaa	3/7	0.188882336247826	2	FACETS	0.799	0.663	0.95	0.399	0.331	0.475	CLONAL	1	TRUE	0	0.254299877206357	2		574	384	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265438	152265438	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046690-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	60	593	0	ENST00000206249.3:c.891G>A	p.Met297Ile	p.M297I	ENST00000206249	NM_000125.3	297	atG/atA	4/8	0.188882336247826	2	FACETS	0.668	0.575	0.77	0.334	0.287	0.385	SUBCLONAL	1	TRUE	0	0.254299877206357	2		593	706	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099784	157099785	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046690-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	64	396	0	ENST00000346085.5:c.722dup	p.Ser241ArgfsTer13	p.S241Rfs*13	ENST00000346085	NM_020732.3	241	agc/aGgc	1/20	0.188882336247826	2	FACETS	0.758	0.661	0.862	0.758	0.661	0.862	SUBCLONAL	2	TRUE	0	0.254299877206357	2		396	332	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874686	151874686	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046690-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	151	737	0	ENST00000262189.6:c.7852C>T	p.Gln2618Ter	p.Q2618*	ENST00000262189	NM_170606.2	2618	Cag/Tag	38/59	0.181392336650697	3	FACETS	0.794	0.726	0.865	0.794	0.726	0.865	SUBCLONAL	2	TRUE	1	0.254299877206357	3		737	843	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359917	87359918	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046690-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	40	570	0	ENST00000277120.3:c.1226dup	p.Asp409GlufsTer7	p.D409Efs*7	ENST00000277120		409	gac/gAac	11/19	0.181392336650697	3	FACETS	0.468	0.388	0.559	0.234	0.194	0.28	SUBCLONAL	1	TRUE	1	0.254299877206357	3		570	757	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195119	123195126	+	frameshift_variant	Frame_Shift_Del	DEL	GCTACTGA	GCTACTGA	-	novel	NA	P-0046690-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	80	499	0	ENST00000218089.9:c.1465_1472del	p.Thr489AlafsTer9	p.T489Afs*9	ENST00000218089	NM_001042749.1	488	GCTACTGAg/g	16/35	0.1954500623697	2	FACETS	0.754	0.667	0.847	0.754	0.667	0.847	SUBCLONAL	2	TRUE	0	0.254299877206357	2		499	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046694-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	378	753	0	ENST00000269305.4:c.166G>T	p.Glu56Ter	p.E56*	ENST00000269305	NM_001126112.2	56	Gaa/Taa	4/11	0.78814152172262	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.78814152172262	1		753	571	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637555	52637555	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046694-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	110	184	0	ENST00000394830.3:c.2761C>T	p.Arg921Ter	p.R921*	ENST00000394830	NM_018313.4	921	Cga/Tga	18/30	0.78814152172262	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.78814152172262	1		184	168	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258970	153258970	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046694-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	128	280	0	ENST00000281708.4:c.845C>A	p.Ser282Ter	p.S282*	ENST00000281708	NM_033632.3	282	tCa/tAa	5/12	1	2	FACETS	0.841	0.77	0.915	0.841	0.77	0.915	CLONAL	1	TRUE	1	0.78814152172262	2		280	386	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149973	202149973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1272714323	NA	P-0046694-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	362	637	0	ENST00000358485.4:c.1414C>T	p.Arg472Ter	p.R472*	ENST00000358485	NM_001080125.1	472	Cga/Tga	8/9	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.78814152172262	2		637	843	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564671	86564671	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046694-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	405	842	0	ENST00000274376.6:c.407del	p.Pro136LeufsTer38	p.P136Lfs*38	ENST00000274376	NM_002890.2	135	Ccc/cc	1/25	0.78814152172262	1	FACETS	0.939	0.904	0.974	0.939	0.904	0.974	CLONAL	1	TRUE	0	0.78814152172262	1		842	663	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391458	139391458	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201613894	NA	P-0046694-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	394	865	0	ENST00000277541.6:c.6733G>A	p.Gly2245Arg	p.G2245R	ENST00000277541	NM_017617.3	2245	Ggg/Agg	34/34	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.78814152172262	2		865	946	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426700	49426700	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046694-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	362	775	0	ENST00000301067.7:c.11788C>T	p.Gln3930Ter	p.Q3930*	ENST00000301067	NM_003482.3	3930	Cag/Tag	39/54	1	2	FACETS	0.981	0.934	1	0.981	0.934	1	CLONAL	1	TRUE	1	0.78814152172262	2		775	936	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673717	176673717	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784117	NA	P-0046694-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	231	422	0	ENST00000439151.2:c.4417C>T	p.Arg1473Ter	p.R1473*	ENST00000439151	NM_022455.4	1473	Cga/Tga	10/23	0.78814152172262	1	FACETS	0.95	0.903	0.995	0.95	0.903	0.995	CLONAL	1	TRUE	0	0.78814152172262	1		422	374	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433632	49433633	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0046694-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	414	849	0	ENST00000301067.7:c.7920_7921del	p.Pro2641CysfsTer13	p.P2641Cfs*13	ENST00000301067	NM_003482.3	2640	tcTCct/tcct	31/54	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.78814152172262	2		849	990	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024706	11024706	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139789571	NA	P-0046694-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	306	611	0	ENST00000327064.4:c.823G>A	p.Ala275Thr	p.A275T	ENST00000327064	NM_199141.1	275	Gcc/Acc	6/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.78814152172262	2		611	722	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213908	36213909	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0046694-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	270	718	0	ENST00000222270.7:c.2735_2736del	p.Ala912ValfsTer4	p.A912Vfs*4	ENST00000222270	NM_014727.1	912	GCg/g	6/37	1	2	FACETS	0.852	0.802	0.903	0.852	0.802	0.903	CLONAL	1	TRUE	1	0.78814152172262	2		718	804	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61328312	61328312	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs2144498270	NA	P-0046694-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	213	406	0	ENST00000283752.5:c.139G>C	p.Asp47His	p.D47H	ENST00000283752	NM_006919.2	47	Gac/Cac	2/8	0.78814152172262	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.78814152172262	1		406	320	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0046936-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	421	608	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.467035934542178	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	4	TRUE	0	0.467035934542178	4		610	646	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238542	142238542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148064542	NA	P-0046936-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	108	231	0	ENST00000350721.4:c.4351C>T	p.Arg1451Trp	p.R1451W	ENST00000350721	NM_001184.3	1451	Cgg/Tgg	24/47	0.467035934542178	3	FACETS	1	0.971	1	0.602	0.543	0.664	CLONAL	1	TRUE	1	0.467035934542178	3		231	474	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566487	139566487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1050441878	NA	P-0046936-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	129	548	0	ENST00000308874.7:c.746G>A	p.Arg249His	p.R249H	ENST00000308874		249	cGc/cAc	9/10	0.462344215082549	4	FACETS	1	0.929	1	0.343	0.311	0.377	CLONAL	1	TRUE	1	0.467035934542178	4		548	788	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244781	46244781	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046936-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	116	576	0	ENST00000334344.6:c.2875A>G	p.Thr959Ala	p.T959A	ENST00000334344	NM_152641.2	959	Aca/Gca	15/21	0.467035934542178	3	FACETS	0.842	0.759	0.929	0.421	0.379	0.465	CLONAL	1	TRUE	1	0.467035934542178	3		576	728	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1956917	1956917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761204359	NA	P-0046936-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	248	480	0	ENST00000382891.5:c.2368G>A	p.Val790Ile	p.V790I	ENST00000382891	NM_133335.3	790	Gtt/Att	13/22	0.467035934542178	4	FACETS	0.997	0.936	1	0.499	0.468	0.53	CLONAL	2	TRUE	0	0.467035934542178	4		480	781	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0047288-T14-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	13	665	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.195	0.138	0.265	0.195	0.138	0.265	SUBCLONAL	1	TRUE	1	0.250292115325274	2		666	532	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988335	36988336	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0047288-T14-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	50	595	0	ENST00000354822.5:c.317_318insAC	p.Gln107ProfsTer19	p.Q107Pfs*19	ENST00000354822	NM_001079668.2	106	ccc/ccACc	2/3	0.250292115325274	1	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	0	0.250292115325274	1		595	336	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048225-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	41	321	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.854	0.719	0.999	0.854	0.719	0.999	CLONAL	1	TRUE	1	0.49	2		321	196	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0048225-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	85	329	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.911	0.81	1	0.911	0.81	1	CLONAL	1	TRUE	1	0.49	2		329	381	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0048225-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	78	277	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.765	0.676	0.861	0.765	0.676	0.861	SUBCLONAL	1	TRUE	1	0.49	2		277	416	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788617	3788617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519884	NA	P-0048225-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	44	315	0	ENST00000262367.5:c.4337G>A	p.Arg1446His	p.R1446H	ENST00000262367	NM_004380.2	1446	cGc/cAc	26/31	1	2	FACETS	0.791	0.67	0.923	0.791	0.67	0.923	CLONAL	1	TRUE	1	0.49	2		315	227	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425119	49425119	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048225-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	105	593	0	ENST00000301067.7:c.13369G>T	p.Glu4457Ter	p.E4457*	ENST00000301067	NM_003482.3	4457	Gaa/Taa	39/54	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.49	2		593	394	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988553	36988553	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048225-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	66	520	0	ENST00000354822.5:c.100A>T	p.Ser34Cys	p.S34C	ENST00000354822	NM_001079668.2	34	Agt/Tgt	2/3	1	2	FACETS	0.616	0.537	0.702	0.616	0.537	0.702	SUBCLONAL	1	TRUE	1	0.49	2		520	437	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482843	67482927	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	CCCCAAGCATCCGCTGTTCCAGTGTGTCTTAGAGACATCAAGTATGGTAGGGGAGGGCAGGCTTGGGGAAAATGGCCATGCAGGA	CCCCAAGCATCCGCTGTTCCAGTGTGTCTTAGAGACATCAAGTATGGTAGGGGAGGGCAGGCTTGGGGAAAATGGCCATGCAGGA	-	novel	NA	P-0048225-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	69	408	0	ENST00000327367.4:c.1247_*53del		p.*416*	ENST00000327367	NM_005902.3	416		9/9	1	2	FACETS	0.689	0.602	0.781	0.689	0.602	0.781	SUBCLONAL	1	TRUE	1	0.49	2		408	409	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860773	45860773	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048225-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	108	567	0	ENST00000391945.4:c.1336C>G	p.Pro446Ala	p.P446A	ENST00000391945	NM_000400.3	446	Ccc/Gcc	14/23	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.49	2		567	402	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945154	44945154	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048225-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	53	172	0	ENST00000377967.4:c.3478G>C	p.Gly1160Arg	p.G1160R	ENST00000377967	NM_021140.2	1160	Ggc/Cgc	24/29	0.3	2	FACETS	0.909	0.8	1	0.909	0.8	1	CLONAL	2	TRUE	0	0.49	2		172	119	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179163	123179187	+	frameshift_variant	Frame_Shift_Del	DEL	TACAGGATTGTCTGACTCACAAGTC	TACAGGATTGTCTGACTCACAAGTC	-	novel	NA	P-0048225-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	52	148	0	ENST00000218089.9:c.612_636del	p.Thr205GlufsTer12	p.T205Efs*12	ENST00000218089	NM_001042749.1	204	ctTACAGGATTGTCTGACTCACAAGTC/ct	8/35	0.3	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	2	TRUE	0	0.49	2		148	105	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47502632	47502632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1189080194	NA	P-0048225-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	63	309	0	ENST00000404338.3:c.4108G>A	p.Glu1370Lys	p.E1370K	ENST00000404338	NM_004491.4	1370	Gaa/Aaa	5/6	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.49	2		309	238	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0049278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	194	619	0	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	0.608006130336943	1	FACETS	0.635	0.591	0.68	0.635	0.591	0.68	SUBCLONAL	1	TRUE	0	0.676162168719656	1		619	598	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	225	589	0	ENST00000269305.4:c.398T>A	p.Met133Lys	p.M133K	ENST00000269305	NM_001126112.2	133	aTg/aAg	5/11	0.608006130336943	1	FACETS	0.892	0.84	0.944	0.892	0.84	0.944	CLONAL	1	TRUE	0	0.676162168719656	1		589	494	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680598	241680598	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778678782	NA	P-0049278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	99	360	0	ENST00000366560.3:c.151C>T	p.Arg51Trp	p.R51W	ENST00000366560	NM_000143.3	51	Cgg/Tgg	2/10	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.676162168719656	2		360	291	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624274	89624274	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs587782187	NA	P-0049278-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	165	294	0	ENST00000371953.3:c.48T>G	p.Tyr16Ter	p.Y16*	ENST00000371953	NM_000314.4	16	taT/taG	1/9	0.620049492037281	3	FACETS	0.77	0.715	0.826	0.77	0.715	0.826	SUBCLONAL	2	TRUE	1	0.676162168719656	3		294	424	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0049508-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	10	370	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.423584797670744	4	FACETS	1	0.816	1	0.598	0.431	0.777	CLONAL	2	TRUE	0	0.473875788455996	4		370	26	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	188	558	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	1	0.968	1	1	0.995	1	CLONAL	3	FALSE	1	0.216895506174608	2		558	541	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	243	503	0	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	1	0.98	1	1	0.996	1	CLONAL	3	FALSE	1	0.216895506174608	2		503	680	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510183	187510183	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765124620	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	202	719	3	ENST00000441802.2:c.13330G>A	p.Ala4444Thr	p.A4444T	ENST00000441802	NM_005245.3	4444	Gca/Aca	27/27	1	2	FACETS	1	0.972	1	1	0.995	1	CLONAL	3	FALSE	1	0.216895506174608	2		722	576	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	164	470	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	1	0.969	1	1	0.994	1	CLONAL	3	FALSE	1	0.216895506174608	2		470	465	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	188	695	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.961	0.893	1	1	0.994	1	CLONAL	3	FALSE	1	0.216895506174608	2		695	601	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	14	530	1	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	1	2	FACETS	0.279	0.2	0.375	0.279	0.2	0.375	SUBCLONAL	1	FALSE	1	0.216895506174608	2		531	463	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	137	497	4	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	1	2	FACETS	1	0.958	1	1	0.993	1	CLONAL	3	FALSE	1	0.216895506174608	2		501	395	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106861	27106861	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	211	749	0	ENST00000324856.7:c.6472C>T	p.Arg2158Ter	p.R2158*	ENST00000324856	NM_006015.4	2158	Cga/Tga	20/20	1	2	FACETS	0.983	0.917	1	1	0.995	1	CLONAL	3	FALSE	1	0.216895506174608	2		749	660	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890149	76890150	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	153	227	0	ENST00000373344.5:c.4744dup	p.Thr1582AsnfsTer19	p.T1582Nfs*19	ENST00000373344	NM_000489.3	1582	aca/aAca	17/35	1	2	FACETS	0.843	0.775	0.913	1	0.993	1	CLONAL	3	FALSE	1	0.216895506174608	2		227	558	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251976	8251976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371807297	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	242	761	1	ENST00000335790.3:c.101G>A	p.Arg34His	p.R34H	ENST00000335790	NM_002315.2	34	cGc/cAc	2/4	1	2	FACETS	1	0.983	1	1	0.996	1	CLONAL	3	FALSE	1	0.216895506174608	2		762	663	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	142	415	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.927	1	1	0.993	1	CLONAL	3	FALSE	1	0.216895506174608	2		421	433	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444659	78444659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs908264837	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	211	553	0	ENST00000370768.2:c.30del	p.Ser11LeufsTer43	p.S11Lfs*43	ENST00000370768	NM_003902.3	10	ccC/cc	1/20	1	2	FACETS	0.977	0.912	1	1	0.995	1	CLONAL	3	FALSE	1	0.216895506174608	2		553	664	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	53	800	1	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.677	0.576	0.788	0.677	0.576	0.788	SUBCLONAL	1	FALSE	1	0.216895506174608	2		801	722	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755478	133755478	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355584861	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	187	656	1	ENST00000318560.5:c.1447C>T	p.Arg483Trp	p.R483W	ENST00000318560	NM_005157.4	483	Cgg/Tgg	9/11	1	2	FACETS	1	0.963	1	1	0.995	1	CLONAL	3	FALSE	1	0.216895506174608	2		657	546	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053310	37053310	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs587779022	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	229	586	0	ENST00000231790.2:c.546-1G>A		p.X182_splice	ENST00000231790	NM_000249.3	182			1	2	FACETS	1	0.983	1	1	0.996	1	CLONAL	3	FALSE	1	0.216895506174608	2		586	620	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450145	32450145	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1193052708	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	182	654	1	ENST00000332351.3:c.667G>A	p.Asp223Asn	p.D223N	ENST00000332351	NM_024426.4	223	Gac/Aac	2/10	1	2	FACETS	1	0.939	1	1	0.994	1	CLONAL	3	FALSE	1	0.216895506174608	2		655	553	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042540	37042540	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267607727	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	179	509	0	ENST00000231790.2:c.302G>A	p.Gly101Asp	p.G101D	ENST00000231790	NM_000249.3	101	gGt/gAt	3/19	1	2	FACETS	0.878	0.817	0.94	1	0.995	1	CLONAL	4	FALSE	1	0.216895506174608	2		509	470	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129454	30129454	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1284498604	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	168	624	0	ENST00000263025.4:c.574G>A	p.Asp192Asn	p.D192N	ENST00000263025	NM_002746.2	192	Gat/Aat	4/9	1	2	FACETS	0.991	0.918	1	1	0.994	1	CLONAL	3	FALSE	1	0.216895506174608	2		624	521	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434959	49434959	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555192751	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	161	771	0	ENST00000301067.7:c.6594del	p.Tyr2199IlefsTer65	p.Y2199Ifs*65	ENST00000301067	NM_003482.3	2198	ccC/cc	31/54	1	2	FACETS	1	0.951	1	1	0.994	1	CLONAL	3	FALSE	1	0.216895506174608	2		771	477	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158026	27158026	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	229	466	3	ENST00000380036.4:c.255del	p.Val86LeufsTer31	p.V86Lfs*31	ENST00000380036	NM_000459.3	84	Aaa/aa	2/23	1	2	FACETS	1	0.978	1	1	0.996	1	CLONAL	3	FALSE	1	0.216895506174608	2		469	646	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437711	49437713	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs886049482	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	196	734	0	ENST00000301067.7:c.5257_5259del	p.Lys1753del	p.K1753del	ENST00000301067	NM_003482.3	1753	AAG/-	22/54	1	2	FACETS	0.898	0.835	0.963	1	0.995	1	CLONAL	3	FALSE	1	0.216895506174608	2		734	671	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740749	58740749	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs779070661	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	239	784	0	ENST00000305921.3:c.1654C>T	p.Arg552Ter	p.R552*	ENST00000305921	NM_003620.3	552	Cga/Tga	6/6	1	2	FACETS	1	0.976	1	1	0.996	1	CLONAL	3	FALSE	1	0.216895506174608	2		784	682	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800903	120800903	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748469666	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	192	616	0	ENST00000257552.2:c.345del	p.Leu116CysfsTer3	p.L116Cfs*3	ENST00000257552	NM_002442.3	115	ggG/gg	6/15	1	2	FACETS	0.946	0.879	1	1	0.995	1	CLONAL	3	FALSE	1	0.216895506174608	2		616	624	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309058	137309058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139536056	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	169	672	0	ENST00000481739.1:c.665C>T	p.Ser222Leu	p.S222L	ENST00000481739	NM_002957.4	222	tCg/tTg	5/10	1	2	FACETS	0.951	0.88	1	1	0.994	1	CLONAL	3	FALSE	1	0.216895506174608	2		672	546	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789627	3789627	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	200	656	0	ENST00000262367.5:c.4232G>T	p.Gly1411Val	p.G1411V	ENST00000262367	NM_004380.2	1411	gGa/gTa	25/31	1	2	FACETS	1	0.972	1	1	0.995	1	CLONAL	3	FALSE	1	0.216895506174608	2		656	571	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21341825	21341825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769001939	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	202	718	0	ENST00000215739.8:c.353G>A	p.Arg118His	p.R118H	ENST00000215739	NM_006767.3	118	cGt/cAt	4/21	1	2	FACETS	1	0.967	1	1	0.995	1	CLONAL	3	FALSE	1	0.216895506174608	2		718	587	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105932	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	216	817	0	ENST00000324856.7:c.5542_5543insT	p.Gly1848ValfsTer6	p.G1848Vfs*6	ENST00000324856	NM_006015.4	1848	ggg/gTgg	20/20	1	2	FACETS	1	0.961	1	1	0.995	1	CLONAL	3	FALSE	1	0.216895506174608	2		817	639	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36826891	36826891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	195	654	1	ENST00000373129.3:c.43G>A	p.Ala15Thr	p.A15T	ENST00000373129	NM_032017.1	15	Gcc/Acc	3/12	1	2	FACETS	1	0.977	1	1	0.995	1	CLONAL	3	FALSE	1	0.216895506174608	2		655	543	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230492905	230492905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs534656022	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	189	723	0	ENST00000391860.1:c.149C>T	p.Thr50Met	p.T50M	ENST00000391860	NM_001258311.1	50	aCg/aTg	2/7	1	2	FACETS	1	0.973	1	1	0.995	1	CLONAL	3	FALSE	1	0.216895506174608	2		723	534	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619891	21619891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	175	626	0	ENST00000382592.4:c.275G>A	p.Gly92Asp	p.G92D	ENST00000382592	NM_014572.2	92	gGc/gAc	2/8	1	2	FACETS	1	0.955	1	1	0.994	1	CLONAL	3	FALSE	1	0.216895506174608	2		626	518	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436309	110436309	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766098208	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	159	876	0	ENST00000375856.3:c.2092G>A	p.Ala698Thr	p.A698T	ENST00000375856	NM_003749.2	698	Gcc/Acc	1/2	1	2	FACETS	0.837	0.771	0.905	1	0.993	1	CLONAL	3	FALSE	1	0.216895506174608	2		876	584	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288690	15288690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	84	340	0	ENST00000263388.2:c.4049G>A	p.Cys1350Tyr	p.C1350Y	ENST00000263388	NM_000435.2	1350	tGc/tAc	24/33	1	2	FACETS	1	0.951	1	1	0.989	1	CLONAL	3	FALSE	1	0.216895506174608	2		340	235	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258515	19258515	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146991038	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	198	780	0	ENST00000162023.5:c.385C>T	p.Arg129Trp	p.R129W	ENST00000162023		129	Cgg/Tgg	8/13	1	2	FACETS	1	0.974	1	1	0.995	1	CLONAL	3	FALSE	1	0.216895506174608	2		780	560	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21347104	21347104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	184	639	0	ENST00000215739.8:c.1171C>T	p.His391Tyr	p.H391Y	ENST00000215739	NM_006767.3	391	Cac/Tac	11/21	1	2	FACETS	1	0.97	1	1	0.995	1	CLONAL	3	FALSE	1	0.216895506174608	2		639	524	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31239468	31239469	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	216	888	0	ENST00000376228.5:c.250dup	p.Trp84LeufsTer15	p.W84Lfs*15	ENST00000376228	NM_002117.5	84	tgg/tTgg	2/8	1	2	FACETS	1	0.968	1	1	0.995	1	CLONAL	3	FALSE	1	0.216895506174608	2		888	629	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482317	87482317	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1201764479	NA	P-0049688-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	159	666	0	ENST00000277120.3:c.1604T>C	p.Ile535Thr	p.I535T	ENST00000277120		535	aTc/aCc	14/19	1	2	FACETS	0.989	0.914	1	1	0.994	1	CLONAL	3	FALSE	1	0.216895506174608	2		666	494	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10800510	10800510	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	30	465	0	ENST00000361367.2:c.3380G>A	p.Ser1127Asn	p.S1127N	ENST00000361367	NM_014633.3	1127	aGt/aAt	25/25	0.643213026183681	1	FACETS	0.167	0.135	0.205	0.167	0.135	0.205	SUBCLONAL	1	TRUE	0	0.643213026183681	1		465	378	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136196	64136196	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398172112	NA	P-0050403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	232	529	0	ENST00000334205.4:c.1355G>A	p.Arg452His	p.R452H	ENST00000334205	NM_003942.2	452	cGc/cAc	12/17	0.643213026183681	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.643213026183681	1		529	471	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0050403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	211	576	5	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	0.643213026183681	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.643213026183681	1		581	435	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0050403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	257	602	3	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	0.643213026183681	1	FACETS	0.953	0.901	1	0.953	0.901	1	CLONAL	1	TRUE	0	0.643213026183681	1		605	569	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475209	475209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	286	409	0	ENST00000399788.2:c.428G>A	p.Gly143Asp	p.G143D	ENST00000399788	NM_001042603.1	143	gGt/gAt	4/28	0.584941351625046	2	FACETS	0.896	0.855	0.937	0.896	0.855	0.937	CLONAL	2	TRUE	0	0.643213026183681	2		409	496	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50786334	50786334	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	29	343	0	ENST00000307179.4:c.2515A>G	p.Thr839Ala	p.T839A	ENST00000307179		839	Aca/Gca	16/20	1	2	FACETS	0.19	0.152	0.233	0.19	0.152	0.233	SUBCLONAL	1	TRUE	1	0.643213026183681	2		343	475	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396792	396792	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	209	536	0	ENST00000262320.3:c.234del	p.Thr79ProfsTer5	p.T79Pfs*5	ENST00000262320	NM_003502.3	78	ccC/cc	2/11	0.643213026183681	1	FACETS	0.952	0.894	1	0.952	0.894	1	CLONAL	1	TRUE	0	0.643213026183681	1		536	463	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126104	2126104	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	40	492	0	ENST00000219476.3:c.2675T>A	p.Val892Asp	p.V892D	ENST00000219476	NM_000548.3	892	gTc/gAc	24/42	0.643213026183681	1	FACETS	0.207	0.172	0.246	0.207	0.172	0.246	SUBCLONAL	1	TRUE	0	0.643213026183681	1		492	408	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847399	68847399	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0050403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	179	388	0	ENST00000261769.5:c.1320+1G>T		p.X440_splice	ENST00000261769	NM_004360.3	440			0.643213026183681	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.643213026183681	1		388	341	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822586	72822586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	214	589	1	ENST00000268489.5:c.9589del	p.Gln3197SerfsTer44	p.Q3197Sfs*44	ENST00000268489	NM_006885.3	3197	Cag/ag	10/10	0.643213026183681	1	FACETS	0.88	0.826	0.935	0.88	0.826	0.935	CLONAL	1	TRUE	0	0.643213026183681	1		590	513	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131231	17131231	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	239	535	0	ENST00000285071.4:c.221C>A	p.Pro74Gln	p.P74Q	ENST00000285071	NM_144997.5	74	cCg/cAg	4/14	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.643213026183681	2		535	695	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219387	1219387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748464757	NA	P-0050403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	111	422	0	ENST00000326873.7:c.439C>T	p.Arg147Cys	p.R147C	ENST00000326873	NM_000455.4	147	Cgt/Tgt	3/10	1	2	FACETS	0.639	0.577	0.705	0.639	0.577	0.705	SUBCLONAL	1	TRUE	1	0.643213026183681	2		422	540	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122772	7122772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767224035	NA	P-0050403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	190	491	0	ENST00000302850.5:c.3382C>T	p.Arg1128Cys	p.R1128C	ENST00000302850	NM_000208.2	1128	Cgc/Tgc	19/22	1	2	FACETS	0.941	0.874	1	0.941	0.874	1	CLONAL	1	TRUE	1	0.643213026183681	2		491	628	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656913	47656913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139652783	NA	P-0050403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	53	231	0	ENST00000233146.2:c.1109C>T	p.Ala370Val	p.A370V	ENST00000233146	NM_000251.2	370	gCa/gTa	7/16	1	2	FACETS	0.41	0.35	0.475	0.41	0.35	0.475	SUBCLONAL	1	TRUE	1	0.643213026183681	2		231	402	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383233	31383233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771192296	NA	P-0050403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	201	506	0	ENST00000328111.2:c.1145G>A	p.Arg382His	p.R382H	ENST00000328111	NM_006892.3	382	cGc/cAc	11/23	1	2	FACETS	0.943	0.878	1	0.943	0.878	1	CLONAL	1	TRUE	1	0.643213026183681	2		506	663	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29439408	29439408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368142754	NA	P-0050403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	29	409	0	ENST00000544604.2:c.623G>A	p.Arg208His	p.R208H	ENST00000544604	NM_001206998.1	208	cGc/cAc	4/9	1	2	FACETS	0.155	0.124	0.191	0.155	0.124	0.191	SUBCLONAL	1	TRUE	1	0.643213026183681	2		409	580	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37038135	37038135	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778913	NA	P-0050403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	149	298	0	ENST00000231790.2:c.142C>T	p.Gln48Ter	p.Q48*	ENST00000231790	NM_000249.3	48	Caa/Taa	2/19	0.643213026183681	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.643213026183681	1		298	313	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125772	47125772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	30	335	0	ENST00000409792.3:c.5498C>T	p.Ala1833Val	p.A1833V	ENST00000409792	NM_014159.6	1833	gCt/gTt	12/21	0.643213026183681	1	FACETS	0.167	0.135	0.205	0.167	0.135	0.205	SUBCLONAL	1	TRUE	0	0.643213026183681	1		335	378	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664844	138664844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	26	360	0	ENST00000330315.3:c.721G>A	p.Ala241Thr	p.A241T	ENST00000330315	NM_023067.3	241	Gcg/Acg	1/1	0.643213026183681	1	FACETS	0.214	0.17	0.265	0.214	0.17	0.265	SUBCLONAL	1	TRUE	0	0.643213026183681	1		360	256	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807109	1807109	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200780581	NA	P-0050403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	48	532	0	ENST00000260795.2:c.1440G>T	p.Glu480Asp	p.E480D	ENST00000260795		480	gaG/gaT	10/17	0.643213026183681	1	FACETS	0.256	0.216	0.299	0.256	0.216	0.299	SUBCLONAL	1	TRUE	0	0.643213026183681	1		532	396	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955965	55955965	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754208569	NA	P-0050403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	29	370	0	ENST00000263923.4:c.3197G>A	p.Arg1066His	p.R1066H	ENST00000263923	NM_002253.2	1066	cGc/cAc	24/30	0.643213026183681	1	FACETS	0.199	0.159	0.243	0.199	0.159	0.243	SUBCLONAL	1	TRUE	0	0.643213026183681	1		370	308	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971292	13971292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772105404	NA	P-0050403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	202	449	0	ENST00000405192.2:c.637C>T	p.Arg213Cys	p.R213C	ENST00000405192	NM_001163147.1	213	Cgc/Tgc	8/12	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.643213026183681	2		449	620	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259437	55259437	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772091823	NA	P-0050403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	23	367	0	ENST00000275493.2:c.2495G>A	p.Arg832His	p.R832H	ENST00000275493	NM_005228.3	832	cGc/cAc	21/28	1	2	FACETS	0.158	0.122	0.199	0.158	0.122	0.199	SUBCLONAL	1	TRUE	1	0.643213026183681	2		367	453	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879375	151879377	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0050403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	38	561	0	ENST00000262189.6:c.5568_5570del	p.Pro1857del	p.P1857del	ENST00000262189	NM_170606.2	1856	ccTCCa/cca	36/59	1	2	FACETS	0.162	0.133	0.194	0.162	0.133	0.194	SUBCLONAL	1	TRUE	1	0.643213026183681	2		561	730	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006024	22006024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	257	601	0	ENST00000276925.6:c.379G>A	p.Asp127Asn	p.D127N	ENST00000276925	NM_004936.3	127	Gac/Aac	2/2	0.643213026183681	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.643213026183681	1		601	530	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650067	93650067	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774431067	NA	P-0050403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	45	351	0	ENST00000375746.1:c.1618G>A	p.Ala540Thr	p.A540T	ENST00000375746	NM_001174167.1	540	Gct/Act	12/14	0.643213026183681	1	FACETS	0.264	0.223	0.31	0.264	0.223	0.31	SUBCLONAL	1	TRUE	0	0.643213026183681	1		351	359	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405641	139405642	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0050403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	194	448	0	ENST00000277541.6:c.2549_2550del	p.Tyr850Ter	p.Y850*	ENST00000277541	NM_017617.3	850	tAT/t	16/34	0.643213026183681	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.643213026183681	1		448	393	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	208	637	0	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	2	FACETS	0.838	0.78	0.898	0.838	0.78	0.898	CLONAL	1	TRUE	1	0.643213026183681	2		637	772	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430750	47430750	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1488217404	NA	P-0050403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	34	542	1	ENST00000377045.4:c.1715G>A	p.Arg572Gln	p.R572Q	ENST00000377045	NM_001654.4	572	cGg/cAg	16/16	1	2	FACETS	0.156	0.127	0.189	0.156	0.127	0.189	SUBCLONAL	1	TRUE	1	0.643213026183681	2		543	677	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222168	53222168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556831986	NA	P-0050403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	50	479	0	ENST00000375401.3:c.4664C>T	p.Pro1555Leu	p.P1555L	ENST00000375401	NM_004187.3	1555	cCg/cTg	26/26	1	2	FACETS	0.252	0.214	0.295	0.252	0.214	0.295	SUBCLONAL	1	TRUE	1	0.643213026183681	2		479	616	SUCCESS
BTK	695	MSKCC	GRCh37	X	100604932	100604932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050403-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	132	250	1	ENST00000308731.7:c.1921C>T	p.Arg641Cys	p.R641C	ENST00000308731	NM_000061.2	641	Cgt/Tgt	19/19	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.643213026183681	2		251	410	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14303239	14303242	+	frameshift_variant	Frame_Shift_Del	DEL	CTAA	CTAA	-	novel	NA	P-0050988-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	31	323	0	ENST00000256196.4:c.433_436del	p.Leu145HisfsTer6	p.L145Hfs*6	ENST00000256196		145	TTAGca/ca	5/6	1	2	FACETS	0.717	0.58	0.873	0.717	0.58	0.873	SUBCLONAL	1	TRUE	1	0.192944607634811	2		323	448	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120662	115120662	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050988-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	34	589	0	ENST00000257566.3:c.344A>T	p.Gln115Leu	p.Q115L	ENST00000257566	NM_016569.3	115	cAg/cTg	1/8	1	2	FACETS	0.566	0.461	0.684	0.566	0.461	0.684	SUBCLONAL	1	TRUE	1	0.192944607634811	2		589	623	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665824	29665824	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1060500355	NA	P-0050988-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	33	190	0	ENST00000356175.3:c.6858+1G>T		p.X2286_splice	ENST00000356175	NM_000267.3	2286			1	2	FACETS	0.972	0.793	1	0.972	0.793	1	CLONAL	1	TRUE	1	0.192944607634811	2		190	352	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652377	48652377	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1557020602	NA	P-0050988-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	40	608	0	ENST00000376670.3:c.1048G>A	p.Ala350Thr	p.A350T	ENST00000376670	NM_002049.3	350	Gct/Act	6/6	1	2	FACETS	0.779	0.647	0.927	0.779	0.647	0.927	CLONAL	1	TRUE	1	0.192944607634811	2		608	532	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069284	30069284	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	216	597	0	ENST00000338641.4:c.1149del	p.Leu384TrpfsTer42	p.L384Wfs*42	ENST00000338641	NM_000268.3	383	ctG/ct	12/16	0.3	0	FACETS		NA	1			1	INDETERMINATE	2	TRUE	0	0.61	0		597	277	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069284	30069284	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051390-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	398	597	0	ENST00000338641.4:c.1149del	p.Leu384TrpfsTer42	p.L384Wfs*42	ENST00000338641	NM_000268.3	383	ctG/ct	12/16	0.812888262442807	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	FALSE	0	0.812888262442807	1		597	511	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069284	30069284	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051390-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	264	597	0	ENST00000338641.4:c.1149del	p.Leu384TrpfsTer42	p.L384Wfs*42	ENST00000338641	NM_000268.3	383	ctG/ct	12/16	0.745767052299382	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		597	399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0051676-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	46	499	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.754	0.634	0.886	0.754	0.634	0.886	SUBCLONAL	1	TRUE	1	0.220313441266768	2		500	554	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051676-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	28	470	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	1	2	FACETS	0.47	0.374	0.579	0.47	0.374	0.579	SUBCLONAL	1	TRUE	1	0.220313441266768	2		470	541	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933781	39933781	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051676-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	63	298	0	ENST00000378444.4:c.818C>T	p.Ser273Phe	p.S273F	ENST00000378444	NM_001123385.1	273	tCc/tTc	4/15	0.220313441266768	2	FACETS	0.883	0.769	1			1	CLONAL	2	TRUE	NA	0.220313441266768	2		298	324	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983275	149983275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051676-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	108	410	2	ENST00000253339.5:c.2983C>T	p.Arg995Cys	p.R995C	ENST00000253339		995	Cgc/Tgc	7/7	0.204618217346019	2	FACETS	0.866	0.78	0.957	0.866	0.78	0.957	CLONAL	2	TRUE	0	0.220313441266768	2		412	566	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0051676-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	28	417	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	1	2	FACETS	0.637	0.509	0.783	0.637	0.509	0.783	SUBCLONAL	1	TRUE	1	0.220313441266768	2		417	399	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295434	1295435	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0051676-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	40	518	0				ENST00000310581	NM_198253.2	-/1132			0.220313441266768	0	FACETS	0.993	0.83	1			1	CLONAL	1	TRUE	0	0.220313441266768	0		518	285	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264129	16264129	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1309232938	NA	P-0051676-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	51	515	0	ENST00000375759.3:c.10498C>G	p.Gln3500Glu	p.Q3500E	ENST00000375759	NM_015001.2	3500	Caa/Gaa	12/15	0.204618217346019	2	FACETS	0.93	0.791	1	0.465	0.395	0.541	CLONAL	1	TRUE	0	0.220313441266768	2		515	498	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287503	46287503	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0051676-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	102	306	0	ENST00000334344.6:c.5362A>T	p.Arg1788Ter	p.R1788*	ENST00000334344	NM_152641.2	1788	Aga/Tga	20/21	0.170955703973865	3	FACETS	1	0.966	1	0.782	0.704	0.865	CLONAL	2	TRUE	0	0.220313441266768	3		306	438	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448521	49448521	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761525910	NA	P-0051676-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	50	516	1	ENST00000301067.7:c.190C>T	p.Arg64Trp	p.R64W	ENST00000301067	NM_003482.3	64	Cgg/Tgg	3/54	0.170955703973865	3	FACETS	0.8	0.678	0.934	0.267	0.226	0.312	CLONAL	1	TRUE	0	0.220313441266768	3		517	630	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028714	42028714	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1029483306	NA	P-0051676-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	45	432	0	ENST00000219905.7:c.4252G>C	p.Asp1418His	p.D1418H	ENST00000219905	NM_001164273.1	1418	Gat/Cat	13/24	1	2	FACETS	0.834	0.701	0.981	0.834	0.701	0.981	CLONAL	1	TRUE	1	0.220313441266768	2		432	490	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006624	62006624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051676-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	39	460	0	ENST00000392795.3:c.655G>A	p.Val219Met	p.V219M	ENST00000392795	NM_001039933.1	219	Gtg/Atg	6/6	1	2	FACETS	0.831	0.689	0.989	0.831	0.689	0.989	CLONAL	1	TRUE	1	0.220313441266768	2		460	426	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403191	213403191	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051676-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	32	357	0	ENST00000342788.4:c.64C>A	p.Pro22Thr	p.P22T	ENST00000342788	NM_005235.2	22	Ccc/Acc	1/28	0.204618217346019	2	FACETS	0.888	0.723	1	0.444	0.361	0.538	CLONAL	1	TRUE	0	0.220313441266768	2		357	327	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266530	41266531	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0051676-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	59	400	0	ENST00000349496.5:c.327_328delinsTT	p.Pro110Ser	p.P110S	ENST00000349496	NM_001904.3	109	atCCca/atTTca	4/15	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.220313441266768	2		400	530	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413710	138413711	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0051676-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	50	359	0	ENST00000289153.2:c.1809_1810delinsTT	p.Arg604Trp	p.R604W	ENST00000289153	NM_006219.2	603	ccCCgg/ccTTgg	12/22	1	2	FACETS	0.95	0.806	1	0.95	0.806	1	CLONAL	1	TRUE	1	0.220313441266768	2		359	478	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271239	153271239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265788422	NA	P-0051676-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	68	282	0	ENST00000281708.4:c.539C>T	p.Ser180Phe	p.S180F	ENST00000281708	NM_033632.3	180	tCt/tTt	3/12	0.204618217346019	2	FACETS	0.764	0.668	0.867	0.764	0.668	0.867	SUBCLONAL	2	TRUE	0	0.220313441266768	2		282	404	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521112	187521113	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0051676-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	51	421	1	ENST00000441802.2:c.12042_12043delinsAA	p.Glu4015Lys	p.E4015K	ENST00000441802	NM_005245.3	4014	acGGaa/acAAaa	22/27	0.220313441266768	1	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	0	0.220313441266768	1		422	385	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630913	187630914	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0051676-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	76	437	0	ENST00000441802.2:c.68dup	p.Ser24GlnfsTer5	p.S24Qfs*5	ENST00000441802	NM_005245.3	23	ggc/ggGc	2/27	0.220313441266768	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.220313441266768	1		437	503	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405823	157405823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051676-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	59	477	0	ENST00000346085.5:c.2065C>T	p.Pro689Ser	p.P689S	ENST00000346085	NM_020732.3	689	Ccc/Tcc	6/20	0.204618217346019	2	FACETS	0.941	0.81	1	0.471	0.405	0.542	CLONAL	1	TRUE	0	0.220313441266768	2		477	569	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412358	139412358	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051676-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	204	443	0	ENST00000277541.6:c.1287C>G	p.Cys429Trp	p.C429W	ENST00000277541	NM_017617.3	429	tgC/tgG	8/34	0.220313441266768	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.220313441266768	3		443	592	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356431	70356431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051676-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	90	241	0	ENST00000374080.3:c.5326C>T	p.Pro1776Ser	p.P1776S	ENST00000374080		1776	Cca/Tca	37/45	0.220313441266768	2	FACETS	0.939	0.844	1			1	CLONAL	3	TRUE	NA	0.220313441266768	2		241	290	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067450	37067450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051676-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	53	467	0	ENST00000231790.2:c.1361G>A	p.Gly454Glu	p.G454E	ENST00000231790	NM_000249.3	454	gGg/gAg	12/19	1	2	FACETS	0.884	0.754	1	0.884	0.754	1	CLONAL	1	TRUE	1	0.220313441266768	2		467	544	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023049	150023049	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051676-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	40	477	0	ENST00000253339.5:c.214G>T	p.Gly72Trp	p.G72W	ENST00000253339		72	Ggg/Tgg	1/7	0.204618217346019	2	FACETS	0.776	0.645	0.922	0.388	0.322	0.461	CLONAL	1	TRUE	0	0.220313441266768	2		477	468	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0052010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	115	465	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.203143128392394	2	FACETS	0.837	0.756	0.922	0.837	0.756	0.922	CLONAL	2	TRUE	0	0.229739464586159	2		465	598	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0052010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	95	382	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.183692467893394	3	FACETS	1	0.954	1	0.746	0.668	0.827	CLONAL	2	TRUE	0	0.229739464586159	3		382	412	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681757	30681757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779352833	NA	P-0052010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	69	598	0	ENST00000376406.3:c.340C>T	p.Arg114Cys	p.R114C	ENST00000376406	NM_014641.2	114	Cgt/Tgt	3/15	1	2	FACETS	0.876	0.762	0.999	0.876	0.762	0.999	CLONAL	1	TRUE	1	0.229739464586159	2		598	686	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405929	49405929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052010-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	37	390	0	ENST00000418115.1:c.209G>A	p.Arg70Lys	p.R70K	ENST00000418115	NM_001664.2	70	aGg/aAg	3/5	1	2	FACETS	0.515	0.423	0.617	0.515	0.423	0.617	SUBCLONAL	1	TRUE	1	0.229739464586159	2		390	626	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	115	189	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	0.100712122437029	2	FACETS	0.828	0.751	0.907			1	INDETERMINATE	2	TRUE	NA	0.332417634139354	2		189	418	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0054099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	71	611	0				ENST00000310581	NM_198253.2	-/1132			0.251669577427266	1	FACETS	0.666	0.582	0.756	0.666	0.582	0.756	SUBCLONAL	1	TRUE	0	0.332417634139354	1		611	535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0054099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	315	769	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.332417634139354	4	FACETS	1	0.991	1	0.828	0.783	0.875	CLONAL	2	TRUE	1	0.332417634139354	4		770	1016	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397738	49397738	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	173	566	0	ENST00000418115.1:c.486G>C	p.Lys162Asn	p.K162N	ENST00000418115	NM_001664.2	162	aaG/aaC	5/5	0.332417634139354	3	FACETS	1	0.988	1	0.695	0.64	0.753	CLONAL	1	TRUE	1	0.332417634139354	3		566	873	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120523	2120523	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45517199	NA	P-0054099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	122	732	0	ENST00000219476.3:c.1783C>T	p.Gln595Ter	p.Q595*	ENST00000219476	NM_000548.3	595	Cag/Tag	17/42	0.314382582550399	1	FACETS	0.826	0.747	0.909	0.826	0.747	0.909	CLONAL	1	TRUE	0	0.332417634139354	1		732	741	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333944	70333944	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	50	630	0	ENST00000373644.4:c.1849C>T	p.Gln617Ter	p.Q617*	ENST00000373644	NM_030625.2	617	Cag/Tag	2/12	1	2	FACETS	0.561	0.476	0.655	0.561	0.476	0.655	SUBCLONAL	1	TRUE	1	0.332417634139354	2		630	536	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100988	27100988	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	122	690	0	ENST00000324856.7:c.4270C>T	p.Gln1424Ter	p.Q1424*	ENST00000324856	NM_006015.4	1424	Cag/Tag	18/20	1	2	FACETS	0.858	0.776	0.946	0.858	0.776	0.946	CLONAL	1	TRUE	1	0.332417634139354	2		690	855	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034868	42034868	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	107	685	0	ENST00000219905.7:c.4710C>G	p.Ile1570Met	p.I1570M	ENST00000219905	NM_001164273.1	1570	atC/atG	15/24	1	2	FACETS	0.914	0.821	1	0.914	0.821	1	CLONAL	1	TRUE	1	0.332417634139354	2		685	704	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006363	12006363	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	61	523	0	ENST00000396373.4:c.331G>A	p.Asp111Asn	p.D111N	ENST00000396373	NM_001987.4	111	Gat/Aat	4/8	0.188939316917985	3	FACETS	0.844	0.729	0.969	0.422	0.364	0.485	INDETERMINATE	1	TRUE	1	0.332417634139354	3		523	507	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101195	27101195	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	109	773	0	ENST00000324856.7:c.4477C>G	p.Gln1493Glu	p.Q1493E	ENST00000324856	NM_006015.4	1493	Cag/Gag	18/20	1	2	FACETS	0.695	0.623	0.772	0.695	0.623	0.772	SUBCLONAL	1	TRUE	1	0.332417634139354	2		773	943	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142479	119142479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	27	508	0	ENST00000264033.4:c.478C>T	p.His160Tyr	p.H160Y	ENST00000264033	NM_005188.3	160	Cac/Tac	3/16	1	2	FACETS	0.516	0.411	0.635	0.516	0.411	0.635	SUBCLONAL	1	TRUE	1	0.332417634139354	2		508	315	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418594	49418594	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0054099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	101	754	0	ENST00000301067.7:c.15920C>G	p.Ser5307Ter	p.S5307*	ENST00000301067	NM_003482.3	5307	tCa/tGa	49/54	0.188939316917985	3	FACETS	0.757	0.676	0.844	0.379	0.338	0.422	INDETERMINATE	1	TRUE	1	0.332417634139354	3		754	936	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444136	49444136	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	110	771	0	ENST00000301067.7:c.3235del	p.Ser1079GlnfsTer40	p.S1079Qfs*40	ENST00000301067	NM_003482.3	1079	Tca/ca	11/54	0.188939316917985	3	FACETS	0.933	0.838	1	0.467	0.419	0.517	INDETERMINATE	1	TRUE	1	0.332417634139354	3		771	827	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133854	2134800	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGGGGCTCCTTAGGGGAGGCAGGGCTCTGCGTGGGTGTGCCTGCACCCTGGGAACTGGCTCTGAACTTGGGGGAGATGTTCTTCCACATCCCTCGTGCACAGACGGTCTGCACTTTGCAGCCATCCACCTGGGCCGGCCCTGGCTGCTGGGCAGCCTGTGGTCTCAGGGGATGCTGATACCTCTGCTCACGCAGTGTGGGGCACAGCTGGTGGCAGTGCTGCTGCGTCAACGGGCGGGGGCCGTAGCCTGGTGCTCGGGCTGGTCTGTGGCCCTGGGATGGAGGACAGATAGGGCCTCACCACCTCCAGGTCAACCCCAGGTGGGCTCGAGGGTGCCTGCTGACAGGGGTTCTCTTTGGGATGGTCCTTTCTAGTCGTCCTCAGTCTCCAGCCAGGAGGAGAAGTCGCTCCACGCGGAGGAGCTGGTTGGCAGGGGCATCCCCATCGAGCGAGTCGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCTTCCAGCCCTCGCAGCCCCTGAGCAAGTCCAGCTCCTCTCCCGAGCTGCAGACTCTGCAGGACATCCTCGGGGACCCTGGGGACAAGGCCGACGTGGGCCGGCTGAGCCCTGAGGTTAAGGCCCGGTCACAGTCAGGGACCCTGGACGGGGAAAGTGCTGCCTGGTCGGCCTCGGGCGAAGACAGTCGGGGCCAGCCCGAGGGTCCCTTGCCTTCCAGCTCCCCCCGCTCGCCCAGTGGCCTCCGGCCCCGAGGTTACACCATCTCCGACTCGGCCCCATCACGCAGGGGCAAGAGAGTAGAGAGGGACGCCTTAAAGAGCAGAGCCACAGCCTCCAATGCAGAGAAAGTGCCAGGCATCAACCCCAGGTGGGCCTCTTGCTTCCGGGCGGGGCTCCTGACACCTCTCCTGCGGGAACCTGGTGCCTCACTTGCCCCAGGCCGAGCGGGCTG	GGGGGGCTCCTTAGGGGAGGCAGGGCTCTGCGTGGGTGTGCCTGCACCCTGGGAACTGGCTCTGAACTTGGGGGAGATGTTCTTCCACATCCCTCGTGCACAGACGGTCTGCACTTTGCAGCCATCCACCTGGGCCGGCCCTGGCTGCTGGGCAGCCTGTGGTCTCAGGGGATGCTGATACCTCTGCTCACGCAGTGTGGGGCACAGCTGGTGGCAGTGCTGCTGCGTCAACGGGCGGGGGCCGTAGCCTGGTGCTCGGGCTGGTCTGTGGCCCTGGGATGGAGGACAGATAGGGCCTCACCACCTCCAGGTCAACCCCAGGTGGGCTCGAGGGTGCCTGCTGACAGGGGTTCTCTTTGGGATGGTCCTTTCTAGTCGTCCTCAGTCTCCAGCCAGGAGGAGAAGTCGCTCCACGCGGAGGAGCTGGTTGGCAGGGGCATCCCCATCGAGCGAGTCGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCTTCCAGCCCTCGCAGCCCCTGAGCAAGTCCAGCTCCTCTCCCGAGCTGCAGACTCTGCAGGACATCCTCGGGGACCCTGGGGACAAGGCCGACGTGGGCCGGCTGAGCCCTGAGGTTAAGGCCCGGTCACAGTCAGGGACCCTGGACGGGGAAAGTGCTGCCTGGTCGGCCTCGGGCGAAGACAGTCGGGGCCAGCCCGAGGGTCCCTTGCCTTCCAGCTCCCCCCGCTCGCCCAGTGGCCTCCGGCCCCGAGGTTACACCATCTCCGACTCGGCCCCATCACGCAGGGGCAAGAGAGTAGAGAGGGACGCCTTAAAGAGCAGAGCCACAGCCTCCAATGCAGAGAAAGTGCCAGGCATCAACCCCAGGTGGGCCTCTTGCTTCCGGGCGGGGCTCCTGACACCTCTCCTGCGGGAACCTGGTGCCTCACTTGCCCCAGGCCGAGCGGGCTG	-	novel	NA	P-0054099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	95	585	0	ENST00000219476.3:c.4005+40_4493+87del		p.X1335_splice	ENST00000219476	NM_000548.3	1335		34/42	0.314382582550399	1	FACETS	0.79	0.705	0.881	0.79	0.705	0.881	SUBCLONAL	1	TRUE	0	0.332417634139354	1		585	603	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974821	15974821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	90	540	0	ENST00000268712.3:c.4054C>T	p.His1352Tyr	p.H1352Y	ENST00000268712	NM_006311.3	1352	Cat/Tat	30/46	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.332417634139354	2		540	469	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2208937	2208937	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	39	318	0	ENST00000398665.3:c.967G>C	p.Glu323Gln	p.E323Q	ENST00000398665	NM_032482.2	323	Gaa/Caa	12/28	1	2	FACETS	0.639	0.531	0.76	0.639	0.531	0.76	SUBCLONAL	1	TRUE	1	0.332417634139354	2		318	367	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907686	111907686	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	103	566	0	ENST00000393256.3:c.460C>G	p.Arg154Gly	p.R154G	ENST00000393256	NM_006538.4	154	Cgt/Ggt	3/4	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.332417634139354	2		566	610	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645784	12645784	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	134	477	0	ENST00000251849.4:c.685C>T	p.Gln229Ter	p.Q229*	ENST00000251849	NM_002880.3	229	Cag/Tag	7/17	0.332417634139354	3	FACETS	0.769	0.701	0.841	0.769	0.701	0.841	SUBCLONAL	2	TRUE	1	0.332417634139354	3		477	611	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675202	30675202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	127	733	0	ENST00000376406.3:c.3043G>A	p.Glu1015Lys	p.E1015K	ENST00000376406	NM_014641.2	1015	Gag/Aag	9/15	0.188939316917985	3	FACETS	0.985	0.891	1	0.492	0.445	0.542	INDETERMINATE	1	TRUE	1	0.332417634139354	3		733	905	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679876	30679876	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	138	803	0	ENST00000376406.3:c.1843C>G	p.Leu615Val	p.L615V	ENST00000376406	NM_014641.2	615	Ctt/Gtt	5/15	0.188939316917985	3	FACETS	0.966	0.878	1	0.483	0.439	0.53	INDETERMINATE	1	TRUE	1	0.332417634139354	3		803	1002	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2969666	2969666	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747866557	NA	P-0054099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	88	691	0	ENST00000396946.4:c.1613C>G	p.Ser538Cys	p.S538C	ENST00000396946	NM_032415.4	538	tCc/tGc	12/25	1	2	FACETS	0.715	0.634	0.803	0.715	0.634	0.803	SUBCLONAL	1	TRUE	1	0.332417634139354	2		691	740	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409014	139409014	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	103	841	0	ENST00000277541.6:c.2155G>A	p.Glu719Lys	p.E719K	ENST00000277541	NM_017617.3	719	Gag/Aag	13/34	1	2	FACETS	0.708	0.633	0.788	0.708	0.633	0.788	SUBCLONAL	1	TRUE	1	0.332417634139354	2		841	875	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820205	139820205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	110	735	0	ENST00000247668.2:c.1358C>T	p.Ser453Leu	p.S453L	ENST00000247668	NM_021138.3	453	tCa/tTa	11/11	1	2	FACETS	0.762	0.684	0.845	0.762	0.684	0.845	SUBCLONAL	1	TRUE	1	0.332417634139354	2		735	868	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358497	67358497	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	117	638	0	ENST00000327367.4:c.5C>T	p.Ser2Leu	p.S2L	ENST00000327367	NM_005902.3	2	tCg/tTg	1/9	1	2	FACETS	0.762	0.686	0.842	0.762	0.686	0.842	SUBCLONAL	1	TRUE	1	0.332417634139354	2		638	924	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7293826	7293826	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1201722489	NA	P-0054099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	151	1286	1	ENST00000302850.5:c.77C>A	p.Ala26Glu	p.A26E	ENST00000302850	NM_000208.2	26	gCg/gAg	1/22	1	2	FACETS	0.841	0.768	0.918	0.841	0.768	0.918	CLONAL	1	TRUE	1	0.332417634139354	2		1287	1080	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775501	39775501	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	105	753	0	ENST00000288319.7:c.519G>C	p.Lys173Asn	p.K173N	ENST00000288319	NM_182918.3	173	aaG/aaC	4/10	1	2	FACETS	0.814	0.729	0.904	0.814	0.729	0.904	CLONAL	1	TRUE	1	0.332417634139354	2		753	776	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573700	41573700	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	112	843	0	ENST00000263253.7:c.5985G>T	p.Trp1995Cys	p.W1995C	ENST00000263253	NM_001429.3	1995	tgG/tgT	31/31	1	2	FACETS	0.757	0.68	0.839	0.757	0.68	0.839	SUBCLONAL	1	TRUE	1	0.332417634139354	2		843	890	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	176	456	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.887	0.817	0.96	0.887	0.817	0.96	CLONAL	1	TRUE	1	0.42	2		456	945	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	42	210	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.791	0.665	0.928	0.791	0.665	0.928	CLONAL	1	TRUE	1	0.42	2		210	253	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991949	72991949	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs753977275	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	176	729	1	ENST00000268489.5:c.2096del	p.Gly699AlafsTer125	p.G699Afs*125	ENST00000268489	NM_006885.3	699	gGc/gc	2/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.42	2		730	755	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	42	476	10	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.897	0.756	1	0.897	0.756	1	CLONAL	1	TRUE	1	0.42	2		486	223	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863054	56863054	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1266824391	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	25	468	1	ENST00000519728.1:c.327del	p.Glu110LysfsTer15	p.E110Kfs*15	ENST00000519728	NM_002350.3	107	acA/ac	5/13	1	2	FACETS	0.401	0.316	0.498	0.401	0.316	0.498	SUBCLONAL	1	TRUE	1	0.42	2		469	297	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	79	1069	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	0.11167184242444	3	FACETS	0.511	0.448	0.578	0.255	0.224	0.289	INDETERMINATE	1	TRUE	1	0.42	3		1071	891	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351595	89351595	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	151	688	1	ENST00000301030.4:c.1355del	p.Asn452IlefsTer3	p.N452Ifs*3	ENST00000301030	NM_001256183.1	452	aAt/at	9/13	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.42	2		689	648	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294665	1294665	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	126	853	4	ENST00000310581.5:c.336del	p.Glu113ArgfsTer15	p.E113Rfs*15	ENST00000310581	NM_198253.2	112	ccC/cc	2/16	1	2	FACETS	0.849	0.769	0.932	0.849	0.769	0.932	CLONAL	1	TRUE	1	0.42	2		857	707	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	201	737	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.42	2		737	941	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250883	153250883	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	32	444	0	ENST00000281708.4:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000281708	NM_033632.3	393	Cga/Tga	8/12	1	2	FACETS	0.871	0.715	1	0.871	0.715	1	CLONAL	1	TRUE	1	0.42	2		444	175	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	157	843	5	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			0.11167184242444	3	FACETS	1	0.966	1	0.551	0.505	0.599	INDETERMINATE	1	TRUE	1	0.42	3		848	821	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932085	39932085	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	210	233	0	ENST00000378444.4:c.2514del	p.Lys839SerfsTer17	p.K839Sfs*17	ENST00000378444	NM_001123385.1	838	ccC/cc	4/15	0.11167184242444	0	FACETS	0.591	0.548	0.634			1	INDETERMINATE	1	TRUE	0	0.42	0		233	982	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843724	156843724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	232	1045	0	ENST00000524377.1:c.1150G>A	p.Glu384Lys	p.E384K	ENST00000524377	NM_002529.3	384	Gag/Aag	8/17	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.42	2		1045	1023	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693887	47693887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778523	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	16	331	0	ENST00000233146.2:c.1601G>A	p.Arg534His	p.R534H	ENST00000233146	NM_000251.2	534	cGt/cAt	10/16	1	2	FACETS	0.699	0.523	0.903	0.699	0.523	0.903	SUBCLONAL	1	TRUE	1	0.42	2		331	109	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999006	100999006	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1333528332	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	161	884	0	ENST00000325455.5:c.796G>A	p.Ala266Thr	p.A266T	ENST00000325455	NM_001202474.3	266	Gcc/Acc	1/8	0.11167184242444	0	FACETS	0.6	0.551	0.651			1	INDETERMINATE	1	TRUE	0	0.42	0		884	741	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263974	104263974	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776579	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	128	638	5	ENST00000369902.3:c.71del	p.Pro24ArgfsTer72	p.P24Rfs*72	ENST00000369902	NM_016169.3	22	gCc/gc	1/12	1	2	FACETS	0.98	0.891	1	0.98	0.891	1	CLONAL	1	TRUE	1	0.42	2		643	622	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399876	139399876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369915496	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	173	830	0	ENST00000277541.6:c.4472C>T	p.Thr1491Met	p.T1491M	ENST00000277541	NM_017617.3	1491	aCg/aTg	25/34	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.42	2		830	814	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	158	558	4	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	0.11167184242444	3	FACETS	0.956	0.876	1	0.478	0.438	0.52	INDETERMINATE	1	TRUE	1	0.42	3		562	952	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341261	8341261	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759691127	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	43	579	0	ENST00000356435.5:c.4955C>T	p.Ala1652Val	p.A1652V	ENST00000356435		1652	gCc/gTc	30/35	1	2	FACETS	0.785	0.661	0.919	0.785	0.661	0.919	CLONAL	1	TRUE	1	0.42	2		579	261	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180049755	180049755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776380290	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	39	624	0	ENST00000261937.6:c.1633C>T	p.Arg545Trp	p.R545W	ENST00000261937	NM_182925.4	545	Cgg/Tgg	12/30	1	2	FACETS	0.26	0.215	0.311	0.26	0.215	0.311	SUBCLONAL	1	TRUE	1	0.42	2		624	714	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120100	70120100	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	180	816	0	ENST00000245479.2:c.1102C>T	p.Gln368Ter	p.Q368*	ENST00000245479	NM_000346.3	368	Cag/Tag	3/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.42	2		816	759	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150001	202150001	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	161	795	0	ENST00000358485.4:c.1442T>C	p.Ile481Thr	p.I481T	ENST00000358485	NM_001080125.1	481	aTc/aCc	8/9	1	2	FACETS	0.876	0.804	0.952	0.876	0.804	0.952	CLONAL	1	TRUE	1	0.42	2		795	875	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258735	16258735	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	209	980	1	ENST00000375759.3:c.6005del	p.Asn2002MetfsTer20	p.N2002Mfs*20	ENST00000375759	NM_015001.2	2000	ggA/gg	11/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.42	2		981	956	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905432	11905432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34966596	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	42	531	0	ENST00000396373.4:c.82G>A	p.Ala28Thr	p.A28T	ENST00000396373	NM_001987.4	28	Gct/Act	2/8	0.11167184242444	3	FACETS	0.349	0.291	0.415	0.175	0.145	0.208	INDETERMINATE	1	TRUE	1	0.42	3		531	693	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057933	27057933	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	101	929	0	ENST00000324856.7:c.1641C>A	p.Ser547Arg	p.S547R	ENST00000324856	NM_006015.4	547	agC/agA	3/20	1	2	FACETS	0.464	0.413	0.518	0.464	0.413	0.518	SUBCLONAL	1	TRUE	1	0.42	2		929	1037	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984451	201984451	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	rs1314587735	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	120	710	0	ENST00000359651.3:c.1116A>G	p.Ter372TrpextTer43	p.*372Wext*43	ENST00000359651		372	tgA/tgG	8/8	1	2	FACETS	0.67	0.605	0.739	0.67	0.605	0.739	SUBCLONAL	1	TRUE	1	0.42	2		710	853	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206942003	206942003	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	36	478	0	ENST00000423557.1:c.515T>C	p.Met172Thr	p.M172T	ENST00000423557	NM_000572.2	172	aTg/aCg	5/5	1	2	FACETS	0.43	0.353	0.515	0.43	0.353	0.515	SUBCLONAL	1	TRUE	1	0.42	2		478	399	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69456148	69456148	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753863475	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	80	872	0	ENST00000227507.2:c.67C>T	p.Leu23Phe	p.L23F	ENST00000227507	NM_053056.2	23	Ctc/Ttc	1/5	0.11167184242444	3	FACETS	0.504	0.442	0.57	0.252	0.221	0.285	INDETERMINATE	1	TRUE	1	0.42	3		872	915	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643756	38643756	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	163	654	0	ENST00000299084.4:c.1226C>A	p.Ala409Asp	p.A409D	ENST00000299084	NM_152594.2	409	gCt/gAt	7/7	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.42	2		654	744	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456477	99456477	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	164	701	0	ENST00000268035.6:c.1794G>T	p.Lys598Asn	p.K598N	ENST00000268035	NM_000875.3	598	aaG/aaT	8/21	1	2	FACETS	0.995	0.915	1	0.995	0.915	1	CLONAL	1	TRUE	1	0.42	2		701	785	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984272	7984272	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	185	772	1	ENST00000319144.4:c.457C>A	p.Leu153Met	p.L153M	ENST00000319144	NM_001139.2	153	Ctg/Atg	4/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.42	2		773	839	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38788581	38788581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753397709	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	141	530	0	ENST00000348513.6:c.580G>A	p.Ala194Thr	p.A194T	ENST00000348513	NM_003079.4	194	Gcc/Acc	8/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.42	2		530	603	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441475	40441475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	194	636	0	ENST00000345506.4:c.46C>T	p.Arg16Cys	p.R16C	ENST00000345506	NM_003152.3	16	Cgc/Tgc	3/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.42	2		636	798	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609397	39609397	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	95	441	0	ENST00000262039.4:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000262039	NM_002647.2	567	Aag/Gag	15/25	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.42	2		441	398	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271817	15271817	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1222453157	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	204	1079	0	ENST00000263388.2:c.6622C>T	p.Pro2208Ser	p.P2208S	ENST00000263388	NM_000435.2	2208	Ccc/Tcc	33/33	0.11167184242444	3	FACETS	1	0.984	1	0.604	0.56	0.65	INDETERMINATE	1	TRUE	1	0.42	3		1079	973	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47601043	47601043	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	55	608	0	ENST00000263735.4:c.281T>G	p.Leu94Arg	p.L94R	ENST00000263735	NM_002354.2	94	cTt/cGt	3/9	1	2	FACETS	0.349	0.297	0.405	0.349	0.297	0.405	SUBCLONAL	1	TRUE	1	0.42	2		608	751	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286823	212286823	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	23	467	0	ENST00000342788.4:c.2873T>G	p.Met958Arg	p.M958R	ENST00000342788	NM_005235.2	958	aTg/aGg	24/28	1	2	FACETS	0.622	0.489	0.774	0.622	0.489	0.774	SUBCLONAL	1	TRUE	1	0.42	2		467	176	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368136	31368136	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568830313	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	152	862	0	ENST00000328111.2:c.7G>A	p.Gly3Arg	p.G3R	ENST00000328111	NM_006892.3	3	Gga/Aga	2/23	1	2	FACETS	0.901	0.825	0.981	0.901	0.825	0.981	CLONAL	1	TRUE	1	0.42	2		862	803	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138407782	138407782	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	103	512	0	ENST00000289153.2:c.2071T>A	p.Phe691Ile	p.F691I	ENST00000289153	NM_006219.2	691	Ttt/Att	14/22	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.42	2		512	439	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149238663	149238663	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	131	601	1	ENST00000360632.3:c.1132G>T	p.Asp378Tyr	p.D378Y	ENST00000360632	NM_015472.4	378	Gac/Tac	7/7	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.42	2		602	533	SUCCESS
ALB	213	MSKCC	GRCh37	4	74279161	74279162	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs77449454	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	75	559	0	ENST00000295897.4:c.872dup	p.Asn291LysfsTer8	p.N291Kfs*8	ENST00000295897	NM_000477.5	290	gaa/gAaa	8/15	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.42	2		559	348	SUCCESS
APC	324	MSKCC	GRCh37	5	112175022	112175022	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	83	493	0	ENST00000257430.4:c.3734del	p.Lys1245ArgfsTer20	p.K1245Rfs*20	ENST00000257430	NM_000038.5	1244	cAa/ca	16/16	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.42	2		493	373	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180076530	180076530	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1356792862	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	90	1237	0	ENST00000261937.6:c.16G>A	p.Ala6Thr	p.A6T	ENST00000261937	NM_182925.4	6	Gcg/Acg	1/30	1	2	FACETS	0.475	0.421	0.534	0.475	0.421	0.534	SUBCLONAL	1	TRUE	1	0.42	2		1237	902	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797759	32797759	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	60	748	0	ENST00000374899.4:c.1743G>T	p.Gln581His	p.Q581H	ENST00000374899	NM_018833.2	581	caG/caT	10/12	1	2	FACETS	0.352	0.302	0.406	0.352	0.302	0.406	SUBCLONAL	1	TRUE	1	0.42	2		748	812	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38173510	38173510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752707421	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	75	533	0	ENST00000317025.8:c.1906G>A	p.Ala636Thr	p.A636T	ENST00000317025	NM_023034.1	636	Gcc/Acc	10/24	1	2	FACETS	0.891	0.784	1	0.891	0.784	1	CLONAL	1	TRUE	1	0.42	2		533	401	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967683	90967683	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	18	413	0	ENST00000265433.3:c.1225del	p.Thr409GlnfsTer16	p.T409Qfs*16	ENST00000265433	NM_002485.4	409	Aca/ca	10/16	1	2	FACETS	0.501	0.379	0.643	0.501	0.379	0.643	SUBCLONAL	1	TRUE	1	0.42	2		413	171	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317093	87317093	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	49	545	0	ENST00000277120.3:c.232A>G	p.Arg78Gly	p.R78G	ENST00000277120		78	Agg/Ggg	3/19	1	2	FACETS	0.476	0.403	0.556	0.476	0.403	0.556	SUBCLONAL	1	TRUE	1	0.42	2		545	490	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404325	139404325	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	190	973	0	ENST00000277541.6:c.2829G>T	p.Glu943Asp	p.E943D	ENST00000277541	NM_017617.3	943	gaG/gaT	18/34	1	2	FACETS	0.992	0.918	1	0.992	0.918	1	CLONAL	1	TRUE	1	0.42	2		973	912	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649611	48649611	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	155	754	0	ENST00000376670.3:c.95T>C	p.Val32Ala	p.V32A	ENST00000376670	NM_002049.3	32	gTt/gCt	2/6	0.11167184242444	0	FACETS	0.579	0.53	0.629			1	INDETERMINATE	1	TRUE	0	0.42	0		754	740	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608957	100608957	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054381-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	42	530	0	ENST00000308731.7:c.1651T>C	p.Tyr551His	p.Y551H	ENST00000308731	NM_000061.2	551	Tac/Cac	17/19	0.11167184242444	0	FACETS	0.221	0.184	0.262			1	INDETERMINATE	1	TRUE	0	0.42	0		530	526	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054800-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	428	377	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.594024660299496	4	FACETS	0.992	0.954	1			1	CLONAL	3	TRUE	NA	0.594024660299496	4		377	772	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577569	7577569	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519981	NA	P-0054800-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	427	461	0	ENST00000269305.4:c.712T>C	p.Cys238Arg	p.C238R	ENST00000269305	NM_001126112.2	238	Tgt/Cgt	7/11	0.594024660299496	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.594024660299496	2		461	707	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0055049-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	231	684	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	0.205575623652062	3	FACETS	1	0.976	1	0.726	0.679	0.775	CLONAL	2	FALSE	0	0.3	3		684	813	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579327	7579328	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055049-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	332	672	0	ENST00000269305.4:c.359dup	p.Ser121ValfsTer28	p.S121Vfs*28	ENST00000269305	NM_001126112.2	120	aag/aaAg	4/11	0.3	3	FACETS	0.848	0.803	0.893	0.848	0.803	0.893	CLONAL	3	FALSE	0	0.3	3		672	1001	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055128-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	81	321	0				ENST00000310581	NM_198253.2	-/1132			0.175348522303522	0	FACETS	0.547	0.483	0.614			1	INDETERMINATE	1	TRUE	0	0.38777132205666	0		321	468	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0055128-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	122	382	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.254830804339628	3	FACETS	0.779	0.708	0.853	0.779	0.708	0.853	SUBCLONAL	2	TRUE	1	0.38777132205666	3		382	482	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983060	201983060	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055128-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	146	488	0	ENST00000359651.3:c.909C>A	p.Phe303Leu	p.F303L	ENST00000359651		303	ttC/ttA	7/8	1	2	FACETS	0.884	0.807	0.965	0.884	0.807	0.965	CLONAL	1	TRUE	1	0.38777132205666	2		488	852	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849146	156849146	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055128-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	54	442	0	ENST00000524377.1:c.2038T>A	p.Tyr680Asn	p.Y680N	ENST00000524377	NM_002529.3	680	Tat/Aat	15/17	1	2	FACETS	0.332	0.282	0.386	0.332	0.282	0.386	SUBCLONAL	1	TRUE	1	0.38777132205666	2		442	839	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981109	201981110	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0055128-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	124	437	0	ENST00000359651.3:c.189dup	p.Pro64AlafsTer28	p.P64Afs*28	ENST00000359651		63	cag/caGg	2/8	1	2	FACETS	0.89	0.806	0.978	0.89	0.806	0.978	CLONAL	1	TRUE	1	0.38777132205666	2		437	719	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657671	37657671	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055128-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	115	303	0	ENST00000447079.4:c.2588C>G	p.Ser863Cys	p.S863C	ENST00000447079	NM_015083.1	863	tCt/tGt	6/14	0.38777132205666	3	FACETS	0.984	0.887	1	0.492	0.443	0.543	CLONAL	1	TRUE	1	0.38777132205666	3		303	720	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440766	56440766	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055128-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	81	492	0	ENST00000407977.2:c.452T>G	p.Leu151Arg	p.L151R	ENST00000407977		151	cTg/cGg	5/10	0.38777132205666	3	FACETS	0.473	0.416	0.535	0.237	0.208	0.268	SUBCLONAL	1	TRUE	1	0.38777132205666	3		492	1054	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302993	15302993	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs797045014	NA	P-0055128-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	82	596	0	ENST00000263388.2:c.457C>T	p.Arg153Cys	p.R153C	ENST00000263388	NM_000435.2	153	Cgc/Tgc	4/33	1	2	FACETS	0.47	0.413	0.531	0.47	0.413	0.531	SUBCLONAL	1	TRUE	1	0.38777132205666	2		596	900	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070887	30070887	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055128-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	53	401	2	ENST00000338641.4:c.1403C>A	p.Ala468Asp	p.A468D	ENST00000338641	NM_000268.3	468	gCc/gAc	13/16	1	2	FACETS	0.431	0.367	0.502	0.431	0.367	0.502	SUBCLONAL	1	TRUE	1	0.38777132205666	2		403	634	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169540	27169540	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055128-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	50	420	1	ENST00000380036.4:c.541G>A	p.Ala181Thr	p.A181T	ENST00000380036	NM_000459.3	181	Gct/Act	4/23	0.38777132205666	1	FACETS	0.338	0.286	0.395	0.338	0.286	0.395	SUBCLONAL	1	TRUE	0	0.38777132205666	1		421	615	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101890460	101891313	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGCCAGTCATTTCTGTAGTTAGGTTGCCTATGTGGTTGGAGCATGTATGTATTGTTACAGGTGTAGTCTGCTTGGCTTCCCTAAGAGAATGCCCCAGTCCTGGCCAGAATATACATGTCTTTTTTAGGGTTTGCACCAAGGGGAATAGAGAGTGTCTGGCTCAGTACAAATCTGTTTCCGTTACTCCATTATCCAGAAAGCCACTGAAATGGCATTAGCCTACACTTAATGGGTGGTAGTGTTTTCACACATTGCTTCTCAAAGGAGGAGTATGTGAATGTTTAGTTTGGGCCTGGTAAAAAAAAAAAAAAAAAAAAAAAAGTATAACCATTACAAATTTAAATGTACTTTGTTTCTAATGGGAAGGCAAATGCTTGCCTTGCTTTGATGAAATTGAACATAACAAAATTTTTCTATACTTGGAAGCAAAAAACTTCAGGAAAAAACCTGGGTCCAAATGTTGCTACATTTCCTTGGGCTTCCACGTGTATGTGGTTCTTAATATAATTTGAAACTTCTAAGAGCAACAAATAGTTGTTTTTTGCTTCTAAGAGCAACAAACAGTGCATAGAAATTGTGTGATAATAGGATCAAGAATGTATTATTAGAGTGAATATTGGATAATTTCAAACTGTTAACCTTGAGATTTTTTCTAAGAATCTTTCTCTTTTTCCAGCGTTACAGTGTTTCTGCCACCTCTGTACAAAAGACAATTTTACTTGTGTGACAGATGGGCTCTGCTTTGTCTCTGTCACAGAGACCACAGACAAAGTTATACACAACAGCATGTGTATAGCTGAAATTGACTTAATTCCTCGAGATAGGCCGTTTGTATGTGCACCCTCTTCAAAAA	CTGCCAGTCATTTCTGTAGTTAGGTTGCCTATGTGGTTGGAGCATGTATGTATTGTTACAGGTGTAGTCTGCTTGGCTTCCCTAAGAGAATGCCCCAGTCCTGGCCAGAATATACATGTCTTTTTTAGGGTTTGCACCAAGGGGAATAGAGAGTGTCTGGCTCAGTACAAATCTGTTTCCGTTACTCCATTATCCAGAAAGCCACTGAAATGGCATTAGCCTACACTTAATGGGTGGTAGTGTTTTCACACATTGCTTCTCAAAGGAGGAGTATGTGAATGTTTAGTTTGGGCCTGGTAAAAAAAAAAAAAAAAAAAAAAAAGTATAACCATTACAAATTTAAATGTACTTTGTTTCTAATGGGAAGGCAAATGCTTGCCTTGCTTTGATGAAATTGAACATAACAAAATTTTTCTATACTTGGAAGCAAAAAACTTCAGGAAAAAACCTGGGTCCAAATGTTGCTACATTTCCTTGGGCTTCCACGTGTATGTGGTTCTTAATATAATTTGAAACTTCTAAGAGCAACAAATAGTTGTTTTTTGCTTCTAAGAGCAACAAACAGTGCATAGAAATTGTGTGATAATAGGATCAAGAATGTATTATTAGAGTGAATATTGGATAATTTCAAACTGTTAACCTTGAGATTTTTTCTAAGAATCTTTCTCTTTTTCCAGCGTTACAGTGTTTCTGCCACCTCTGTACAAAAGACAATTTTACTTGTGTGACAGATGGGCTCTGCTTTGTCTCTGTCACAGAGACCACAGACAAAGTTATACACAACAGCATGTGTATAGCTGAAATTGACTTAATTCCTCGAGATAGGCCGTTTGTATGTGCACCCTCTTCAAAAA	-	novel	NA	P-0055128-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1	64	0	0	ENST00000374994.4:c.98-674_277del		p.X33_splice	ENST00000374994	NM_004612.2	33		2/9	0.38777132205666	1	FACETS	1	0.983	1	1	0.989	1	CLONAL	4	TRUE	0	0.38777132205666	1		0	65	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579487	7579487	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	221	1115	0	ENST00000269305.4:c.200del	p.Pro67GlnfsTer56	p.P67Qfs*56	ENST00000269305	NM_001126112.2	67	cCa/ca	4/11	0.224873186515534	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	0	0.224873186515534	2		1115	975	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112022	115112022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773504740	NA	P-0055263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	187	1086	1	ENST00000257566.3:c.1718C>T	p.Ala573Val	p.A573V	ENST00000257566	NM_016569.3	573	gCg/gTg	7/8	0.205500075913976	4	FACETS	0.957	0.884	1	0.957	0.884	1	CLONAL	2	TRUE	2	0.224873186515534	4		1087	1064	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056238	27056238	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	64	886	0	ENST00000324856.7:c.1234C>T	p.Gln412Ter	p.Q412*	ENST00000324856	NM_006015.4	412	Cag/Tag	2/20	0.169259842736601	1	FACETS	0.742	0.642	0.851	0.742	0.642	0.851	SUBCLONAL	1	TRUE	0	0.224873186515534	1		886	681	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372419	118372419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555045700	NA	P-0055263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	54	639	1	ENST00000534358.1:c.6352G>A	p.Glu2118Lys	p.E2118K	ENST00000534358	NM_005933.3	2118	Gaa/Aaa	26/36	0.205500075913976	4	FACETS	0.818	0.698	0.951	0.409	0.349	0.476	CLONAL	1	TRUE	2	0.224873186515534	4		640	719	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637652	23637652	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	73	742	0	ENST00000261584.4:c.2653C>T	p.Pro885Ser	p.P885S	ENST00000261584	NM_024675.3	885	Cca/Tca	7/13	0.205500075913976	4	FACETS	1	0.887	1	0.508	0.444	0.578	CLONAL	1	TRUE	2	0.224873186515534	4		742	782	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845612	68845632	+	inframe_deletion	In_Frame_Del	DEL	CACAGACGCGGACGATGATGT	CACAGACGCGGACGATGATGT	-	novel	NA	P-0055263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	153	667	0	ENST00000261769.5:c.858_878del	p.Thr287_Val293del	p.T287_V293del	ENST00000261769	NM_004360.3	286	gcCACAGACGCGGACGATGATGTg/gcg	7/16	0.205500075913976	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	2	0.224873186515534	4		667	784	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176516691	176516692	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	67	810	0	ENST00000292408.4:c.90dup	p.Glu31Ter	p.E31*	ENST00000292408	NM_213647.1	30	ctt/cTtt	2/18	0.224873186515534	4	FACETS	0.822	0.713	0.941	0.274	0.237	0.314	CLONAL	1	TRUE	1	0.224873186515534	4		810	888	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974721	21974722	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	146	611	0	ENST00000304494.5:c.105_106insA	p.Ala36SerfsTer8	p.A36Sfs*8	ENST00000304494	NM_000077.4	35	-/A	1/3	0.224873186515534	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.224873186515534	2		611	547	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0055279-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	236	377	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.685563864509011	5	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	TRUE	2	0.685563864509011	5		377	442	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790930	89790930	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055279-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	211	715	0	ENST00000336032.3:c.317C>T	p.Pro106Leu	p.P106L	ENST00000336032	NM_006813.2	106	cCc/cTc	1/2	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.685563864509011	2		715	553	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0055449-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	291	544	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.528565994961888	7	FACETS	0.936	0.897	0.975	1	0.99	1	CLONAL	6	FALSE	2	0.528565994961888	7		544	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0055449-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	469	593	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.52547494624411	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	FALSE	0	0.528565994961888	3		593	746	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022913	27022938	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGCCGCCGCCAGCAGCCTGGGCAA	CCCGCCGCCGCCAGCAGCCTGGGCAA	-	rs797045262	NA	P-0055449-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	161	499	0	ENST00000324856.7:c.31_56del	p.Ser11AlafsTer91	p.S11Afs*91	ENST00000324856	NM_006015.4	7	CCCGCCGCCGCCAGCAGCCTGGGCAAc/c	1/20	0.527848128152842	2	FACETS	1	0.989	1	0.713	0.661	0.767	CLONAL	1	FALSE	0	0.528565994961888	2		499	427	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391075	89391075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs995238704	NA	P-0055449-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	265	504	0	ENST00000336596.2:c.1141C>T	p.Arg381Cys	p.R381C	ENST00000336596	NM_005233.5	381	Cgc/Tgc	5/17	0.527848128152842	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	FALSE	0	0.528565994961888	2		504	499	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231410	46231410	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0055449-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	123	461	0	ENST00000334344.6:c.1250C>G	p.Ser417Ter	p.S417*	ENST00000334344	NM_152641.2	417	tCa/tGa	10/21	0.509478011146691	4	FACETS	1	0.949	1			1	CLONAL	1	FALSE	NA	0.528565994961888	4		461	664	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481793	40481793	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055449-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	119	345	0	ENST00000264657.5:c.1111G>A	p.Asp371Asn	p.D371N	ENST00000264657	NM_139276.2	371	Gac/Aac	12/24	0.527848128152842	2	FACETS	1	0.971	1	0.579	0.527	0.632	CLONAL	1	FALSE	0	0.528565994961888	2		345	389	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1331520	1331520	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055449-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	120	394	0	ENST00000400841.2:c.8G>C	p.Arg3Pro	p.R3P	ENST00000400841		3	cGg/cCg	1/6	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	1	0.528565994961888	2		394	435	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975358	13975358	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055449-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	145	462	0	ENST00000405192.2:c.529G>C	p.Asp177His	p.D177H	ENST00000405192	NM_001163147.1	177	Gat/Cat	7/12	0.494650990843291	4	FACETS	1	0.963	1	0.55	0.502	0.6	CLONAL	1	FALSE	2	0.528565994961888	4		462	763	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459531	50459531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055475-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	13	527	0	ENST00000331340.3:c.820C>T	p.Arg274Cys	p.R274C	ENST00000331340	NM_006060.4	274	Cgt/Tgt	7/8	0.227532603551559	4	FACETS	0.858	0.623	1	0.858	0.623	1	CLONAL	2	TRUE	2	0.253341796371006	4		527	75	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375142	31375142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537913125	NA	P-0055475-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	19	810	0	ENST00000328111.2:c.539C>T	p.Thr180Met	p.T180M	ENST00000328111	NM_006892.3	180	aCg/aTg	6/23	0.205787470093556	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	0	0.253341796371006	1		810	94	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551418	141551418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055475-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	15	603	0	ENST00000220592.5:c.1879G>A	p.Ala627Thr	p.A627T	ENST00000220592	NM_012154.3	627	Gcc/Acc	15/19	0.141336113131357	4	FACETS	1	0.762	1	0.519	0.382	0.681	INDETERMINATE	1	TRUE	2	0.253341796371006	4		603	143	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120430	70120431	+	frameshift_variant	Frame_Shift_Ins	INS	AC	AC	GTA	novel	NA	P-0055475-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	25	803	0	ENST00000245479.2:c.1432_1433delinsGTA	p.Thr478ValfsTer100	p.T478Vfs*100	ENST00000245479	NM_000346.3	478	ACc/GTAc	3/3	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.253341796371006	2		803	166	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21349286	21349286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055475-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	26	802	1	ENST00000215739.8:c.1913G>A	p.Arg638His	p.R638H	ENST00000215739	NM_006767.3	638	cGc/cAc	16/21	0.151592439760048	0	FACETS	0.672	0.535	0.828			1	INDETERMINATE	1	TRUE	0	0.253341796371006	0		803	228	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026096	71026096	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	158	228	0	ENST00000318789.4:c.1526G>A	p.Trp509Ter	p.W509*	ENST00000318789	NM_032682.5	509	tGg/tAg	17/21	1	2	FACETS	0.915	0.846	0.985	1	0.994	1	CLONAL	3	TRUE	1	0.259969555598515	2		228	443	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913517	NA	P-0056963-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	265	466	0	ENST00000288135.5:c.1676T>A	p.Val559Asp	p.V559D	ENST00000288135	NM_000222.2	559	gTt/gAt	11/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		466	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0057275-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	335	621	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.591175422511576	2	FACETS	0.979	0.937	1	0.979	0.937	1	CLONAL	2	TRUE	0	0.591175422511576	2		621	579	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953760	48953760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913302	NA	P-0057275-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	172	165	0	ENST00000267163.4:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000267163	NM_000321.2	455	Cga/Tga	14/27	0.587974818919538	4	FACETS	0.901	0.853	0.947	0.901	0.853	0.947	CLONAL	4	TRUE	0	0.591175422511576	4		165	257	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450048	32450048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444869026	NA	P-0057275-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	262	525	0	ENST00000332351.3:c.764C>T	p.Ser255Leu	p.S255L	ENST00000332351	NM_024426.4	255	tCg/tTg	2/10	0.568962321431775	3	FACETS	0.843	0.795	0.892	0.843	0.795	0.892	CLONAL	2	TRUE	1	0.591175422511576	3		525	681	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295241	1295241	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0057275-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	142	632	0				ENST00000310581	NM_198253.2	-/1132			0.544810502171829	4	FACETS	1	0.952	1	0.355	0.324	0.387	CLONAL	1	TRUE	1	0.591175422511576	4		632	718	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410043	63410043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1486040300	NA	P-0057275-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	141	724	0	ENST00000330258.3:c.3124C>A	p.Gln1042Lys	p.Q1042K	ENST00000330258	NM_152424.3	1042	Cag/Aag	2/2	0.591338399408041	3	FACETS	0.801	0.73	0.874	0.4	0.365	0.437	CLONAL	1	TRUE	1	0.591175422511576	3		724	772	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18576952	18576952	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057275-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	191	406	0	ENST00000266497.5:c.2360A>T	p.Gln787Leu	p.Q787L	ENST00000266497		787	cAg/cTg	16/31	0.591338399408041	4	FACETS	0.983	0.916	1	0.491	0.458	0.526	CLONAL	2	TRUE	0	0.591175422511576	4		406	523	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132940	30132940	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057275-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	113	422	0	ENST00000331968.5:c.661G>C	p.Glu221Gln	p.E221Q	ENST00000331968	NM_002742.2	221	Gaa/Caa	4/18	0.492910135894489	4	FACETS	0.755	0.679	0.835			1	SUBCLONAL	1	TRUE	NA	0.591175422511576	4		422	806	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687249	37687249	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057275-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	344	692	0	ENST00000447079.4:c.4153G>A	p.Glu1385Lys	p.E1385K	ENST00000447079	NM_015083.1	1385	Gag/Aag	14/14	0.591338399408041	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	2	0.591175422511576	4		692	921	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291916	15291916	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057275-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	1017	658	0	ENST00000263388.2:c.2850C>G	p.Cys950Trp	p.C950W	ENST00000263388	NM_000435.2	950	tgC/tgG	18/33	0.591175422511576	7	FACETS	1	0.994	1			1	CLONAL	5	TRUE	NA	0.591175422511576	7		658	1620	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223681	36223681	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057275-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	444	809	0	ENST00000222270.7:c.6231G>C	p.Gln2077His	p.Q2077H	ENST00000222270	NM_014727.1	2077	caG/caC	28/37	0.541809002578213	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.591175422511576	4		809	1120	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637344	176637344	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057275-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	236	529	1	ENST00000439151.2:c.1944C>G	p.Asp648Glu	p.D648E	ENST00000439151	NM_022455.4	648	gaC/gaG	5/23	NA	2	FACETS	1	0.955	1			1	INDETERMINATE	2	TRUE	NA	0.591175422511576	2		530	397	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761069	59761069	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057275-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	71	341	0	ENST00000259008.2:c.3338A>C	p.Lys1113Thr	p.K1113T	ENST00000259008	NM_032043.2	1113	aAa/aCa	20/20	0.591338399408041	4	FACETS	0.865	0.757	0.98	0.432	0.378	0.49	CLONAL	1	TRUE	2	0.591175422511576	4		341	442	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096012	11096012	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057275-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	181	601	0	ENST00000358026.2:c.286A>G	p.Met96Val	p.M96V	ENST00000358026	NM_001128849.1	96	Atg/Gtg	3/36	0.582584815864859	3	FACETS	1	0.976	1	0.563	0.521	0.607	CLONAL	1	TRUE	1	0.591175422511576	3		601	704	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1296205	1296205	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0057275-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	486	642	0				ENST00000310581	NM_198253.2	-/1132			0.544810502171829	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	1	0.591175422511576	4		642	847	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163384	32163384	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057275-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	521	672	0	ENST00000375023.3:c.5842G>C	p.Asp1948His	p.D1948H	ENST00000375023	NM_004557.3	1948	Gac/Cac	30/30	0.591338399408041	4	FACETS	0.993	0.952	1	0.993	0.952	1	CLONAL	2	TRUE	2	0.591175422511576	4		672	1412	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525569	137525569	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906572	NA	P-0057275-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	62	386	0	ENST00000367739.4:c.446C>T	p.Ser149Leu	p.S149L	ENST00000367739	NM_000416.2	149	tCa/tTa	4/7	0.541809002578213	4	FACETS	0.828	0.718	0.947	0.414	0.359	0.474	CLONAL	1	TRUE	2	0.591175422511576	4		386	403	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332872	152332872	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057275-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	110	412	0	ENST00000206249.3:c.1178G>T	p.Trp393Leu	p.W393L	ENST00000206249	NM_000125.3	393	tGg/tTg	5/8	0.541809002578213	4	FACETS	0.931	0.838	1	0.466	0.419	0.515	CLONAL	1	TRUE	2	0.591175422511576	4		412	636	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859253	151859253	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057275-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	193	338	0	ENST00000262189.6:c.11409C>G	p.Asp3803Glu	p.D3803E	ENST00000262189	NM_170606.2	3803	gaC/gaG	43/59	0.591175422511576	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.591175422511576	2		338	299	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	70	415	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.539	0.472	0.611	0.539	0.472	0.611	SUBCLONAL	1	TRUE	1	0.63	2		421	412	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	119	591	9	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.58	0.525	0.639	0.58	0.525	0.639	SUBCLONAL	1	TRUE	1	0.63	2		600	651	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	233	509	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.984	0.921	1	0.984	0.921	1	CLONAL	1	TRUE	1	0.63	2		513	752	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	23	282	0	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	1	FACETS	0.255	0.2	0.318	0.255	0.2	0.318	SUBCLONAL	1	TRUE	0	0.63	1		282	196	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948284	71948284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs569099732	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	108	615	0	ENST00000298229.2:c.2996C>T	p.Pro999Leu	p.P999L	ENST00000298229	NM_001567.3	999	cCg/cTg	26/28	1	2	FACETS	0.495	0.444	0.548	0.495	0.444	0.548	SUBCLONAL	1	TRUE	1	0.63	2		615	693	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284979	15284979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774475688	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	67	511	0	ENST00000263388.2:c.4636C>T	p.Arg1546Cys	p.R1546C	ENST00000263388	NM_000435.2	1546	Cgc/Tgc	25/33	1	2	FACETS	0.413	0.359	0.471	0.413	0.359	0.471	SUBCLONAL	1	TRUE	1	0.63	2		511	515	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	98	602	3	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.481	0.429	0.536	0.481	0.429	0.536	SUBCLONAL	1	TRUE	1	0.63	2		605	647	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262039	16262039	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs779284390	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	114	584	0	ENST00000375759.3:c.9304A>G	p.Thr3102Ala	p.T3102A	ENST00000375759	NM_015001.2	3102	Act/Gct	11/15	1	2	FACETS	0.574	0.517	0.633	0.574	0.517	0.633	SUBCLONAL	1	TRUE	1	0.63	2		584	631	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464944	120464945	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	81	436	0	ENST00000256646.2:c.5127_5128del	p.Trp1710AlafsTer3	p.W1710Afs*3	ENST00000256646	NM_024408.3	1709	ctCTgg/ctgg	28/34	1	2	FACETS	0.51	0.451	0.574	0.51	0.451	0.574	SUBCLONAL	1	TRUE	1	0.63	2		436	504	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480090	120480090	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	107	403	0	ENST00000256646.2:c.3338-1G>T		p.X1113_splice	ENST00000256646	NM_024408.3	1113			1	2	FACETS	0.614	0.553	0.679	0.614	0.553	0.679	SUBCLONAL	1	TRUE	1	0.63	2		403	553	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843719	156843719	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763940977	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	110	664	0	ENST00000524377.1:c.1145C>A	p.Pro382His	p.P382H	ENST00000524377	NM_002529.3	382	cCt/cAt	8/17	1	2	FACETS	0.481	0.432	0.533	0.481	0.432	0.533	SUBCLONAL	1	TRUE	1	0.63	2		664	726	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851324	156851324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759637817	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	47	474	0	ENST00000524377.1:c.2281C>T	p.Arg761Trp	p.R761W	ENST00000524377	NM_002529.3	761	Cgg/Tgg	17/17	1	2	FACETS	0.269	0.226	0.316	0.269	0.226	0.316	SUBCLONAL	1	TRUE	1	0.63	2		474	555	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102196013	102196013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	76	442	0	ENST00000263464.3:c.773G>A	p.Arg258His	p.R258H	ENST00000263464	NM_001165.4	258	cGc/cAc	2/9	1	2	FACETS	0.447	0.392	0.505	0.447	0.392	0.505	SUBCLONAL	1	TRUE	1	0.63	2		442	540	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417050	417050	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199716528	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	115	549	0	ENST00000399788.2:c.3500G>A	p.Arg1167His	p.R1167H	ENST00000399788	NM_001042603.1	1167	cGc/cAc	23/28	1	2	FACETS	0.595	0.537	0.655	0.595	0.537	0.655	SUBCLONAL	1	TRUE	1	0.63	2		549	614	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491390	18491390	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1377942847	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	56	264	2	ENST00000266497.5:c.1309del	p.Ile437TyrfsTer5	p.I437Yfs*5	ENST00000266497		435	Aaa/aa	8/31	1	2	FACETS	0.517	0.445	0.595	0.517	0.445	0.595	SUBCLONAL	1	TRUE	1	0.63	2		266	344	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287447	46287447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	50	307	0	ENST00000334344.6:c.5306G>A	p.Arg1769Gln	p.R1769Q	ENST00000334344	NM_152641.2	1769	cGa/cAa	20/21	1	2	FACETS	0.391	0.332	0.455	0.391	0.332	0.455	SUBCLONAL	1	TRUE	1	0.63	2		307	406	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438211	49438211	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	84	383	0	ENST00000301067.7:c.5058del	p.Lys1686AsnfsTer36	p.K1686Nfs*36	ENST00000301067	NM_003482.3	1686	aaA/aa	20/54	1	2	FACETS	0.59	0.523	0.661	0.59	0.523	0.661	SUBCLONAL	1	TRUE	1	0.63	2		383	452	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562455	95562455	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	114	538	1	ENST00000393063.1:c.4802del	p.Lys1601ArgfsTer19	p.K1601Rfs*19	ENST00000393063	NM_030621.3	1601	aAg/ag	24/28	1	2	FACETS	0.56	0.505	0.618	0.56	0.505	0.618	SUBCLONAL	1	TRUE	1	0.63	2		539	646	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95583999	95583999	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1006363970	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	50	318	0	ENST00000393063.1:c.1469G>A	p.Arg490His	p.R490H	ENST00000393063	NM_030621.3	490	cGc/cAc	10/28	1	2	FACETS	0.368	0.313	0.429	0.368	0.313	0.429	SUBCLONAL	1	TRUE	1	0.63	2		318	431	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50782604	50782604	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs78727795	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	110	485	1	ENST00000307179.4:c.2116C>T	p.Arg706Trp	p.R706W	ENST00000307179		706	Cgg/Tgg	14/20	1	2	FACETS	0.565	0.509	0.625	0.565	0.509	0.625	SUBCLONAL	1	TRUE	1	0.63	2		486	618	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467855	99467856	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	81	460	0	ENST00000268035.6:c.2732_2733dup	p.Gly912LeufsTer26	p.G912Lfs*26	ENST00000268035	NM_000875.3	908	-/TC	13/21	1	2	FACETS	0.422	0.371	0.475	0.422	0.371	0.475	SUBCLONAL	1	TRUE	1	0.63	2		460	610	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339552	339552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777185421	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	49	409	0	ENST00000262320.3:c.2350G>A	p.Val784Ile	p.V784I	ENST00000262320	NM_003502.3	784	Gtt/Att	10/11	1	2	FACETS	0.335	0.284	0.392	0.335	0.284	0.392	SUBCLONAL	1	TRUE	1	0.63	2		409	464	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122296	2122296	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182538665	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	109	491	1	ENST00000219476.3:c.2152C>T	p.Arg718Cys	p.R718C	ENST00000219476	NM_000548.3	718	Cgc/Tgc	20/42	1	2	FACETS	0.605	0.545	0.668	0.605	0.545	0.668	SUBCLONAL	1	TRUE	1	0.63	2		492	572	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126498	2126498	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781587135	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	73	473	0	ENST00000219476.3:c.2749C>T	p.Arg917Trp	p.R917W	ENST00000219476	NM_000548.3	917	Cgg/Tgg	25/42	1	2	FACETS	0.513	0.45	0.58	0.513	0.45	0.58	SUBCLONAL	1	TRUE	1	0.63	2		473	452	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041981	14041981	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	99	460	0	ENST00000311895.7:c.2528A>G	p.Lys843Arg	p.K843R	ENST00000311895	NM_005236.2	843	aAg/aGg	11/11	1	2	FACETS	0.563	0.504	0.626	0.563	0.504	0.626	SUBCLONAL	1	TRUE	1	0.63	2		460	558	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063359	67063359	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	80	420	0	ENST00000412916.2:c.54del	p.Phe18LeufsTer4	p.F18Lfs*4	ENST00000412916		17	Ttt/tt	1/6	1	2	FACETS	0.481	0.424	0.542	0.481	0.424	0.542	SUBCLONAL	1	TRUE	1	0.63	2		420	528	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819713	81819713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1347311494	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	74	487	0	ENST00000359376.3:c.119G>A	p.Arg40Gln	p.R40Q	ENST00000359376	NM_002661.3	40	cGg/cAg	2/33	1	2	FACETS	0.422	0.369	0.478	0.422	0.369	0.478	SUBCLONAL	1	TRUE	1	0.63	2		487	557	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346256	89346256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760007187	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	92	603	0	ENST00000301030.4:c.6694C>T	p.Arg2232Cys	p.R2232C	ENST00000301030	NM_001256183.1	2232	Cgt/Tgt	9/13	1	2	FACETS	0.543	0.484	0.606	0.543	0.484	0.606	SUBCLONAL	1	TRUE	1	0.63	2		603	538	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264354	30264354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1284405136	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	88	398	1	ENST00000322652.5:c.89C>T	p.Ala30Val	p.A30V	ENST00000322652	NM_015355.2	30	gCg/gTg	1/16	1	2	FACETS	0.615	0.548	0.687	0.615	0.548	0.687	SUBCLONAL	1	TRUE	1	0.63	2		399	454	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554687	63554687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	130	601	0	ENST00000307078.5:c.52C>T	p.Arg18Cys	p.R18C	ENST00000307078	NM_004655.3	18	Cgt/Tgt	2/11	1	2	FACETS	0.595	0.54	0.652	0.595	0.54	0.652	SUBCLONAL	1	TRUE	1	0.63	2		601	694	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511665	66511665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746486900	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	77	394	0	ENST00000358598.2:c.125G>A	p.Arg42Gln	p.R42Q	ENST00000358598	NM_212471.2	42	cGa/cAa	2/11	1	2	FACETS	0.491	0.432	0.554	0.491	0.432	0.554	SUBCLONAL	1	TRUE	1	0.63	2		394	498	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612347	1612347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200962332	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	104	536	2	ENST00000344749.5:c.1672C>T	p.Arg558Cys	p.R558C	ENST00000344749	NM_001136139.2	558	Cgc/Tgc	18/19	1	2	FACETS	0.575	0.516	0.637	0.575	0.516	0.637	SUBCLONAL	1	TRUE	1	0.63	2		538	574	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	21	172	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.39	0.302	0.491	0.39	0.302	0.491	SUBCLONAL	1	TRUE	1	0.63	2		172	171	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7293878	7293878	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	102	832	0	ENST00000302850.5:c.25del	p.Ala9ArgfsTer56	p.A9Rfs*56	ENST00000302850	NM_000208.2	9	Gcg/cg	1/22	1	2	FACETS	0.446	0.399	0.496	0.446	0.399	0.496	SUBCLONAL	1	TRUE	1	0.63	2		832	726	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602473	10602473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	97	671	1	ENST00000171111.5:c.1105G>A	p.Val369Met	p.V369M	ENST00000171111	NM_203500.1	369	Gtg/Atg	3/6	1	2	FACETS	0.422	0.376	0.471	0.422	0.376	0.471	SUBCLONAL	1	TRUE	1	0.63	2		672	729	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123721	11123721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	86	483	0	ENST00000358026.2:c.2371G>A	p.Ala791Thr	p.A791T	ENST00000358026	NM_001128849.1	791	Gcg/Acg	16/36	1	2	FACETS	0.522	0.463	0.585	0.522	0.463	0.585	SUBCLONAL	1	TRUE	1	0.63	2		483	523	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298137	15298137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200317373	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	71	368	0	ENST00000263388.2:c.1619C>T	p.Thr540Met	p.T540M	ENST00000263388	NM_000435.2	540	aCg/aTg	11/33	1	2	FACETS	0.5	0.437	0.567	0.5	0.437	0.567	SUBCLONAL	1	TRUE	1	0.63	2		368	451	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302906	15302906	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28933697	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	77	661	0	ENST00000263388.2:c.544C>T	p.Arg182Cys	p.R182C	ENST00000263388	NM_000435.2	182	Cgc/Tgc	4/33	1	2	FACETS	0.42	0.369	0.475	0.42	0.369	0.475	SUBCLONAL	1	TRUE	1	0.63	2		661	582	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355251	15355251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201388205	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	46	354	0	ENST00000263377.2:c.2372C>T	p.Pro791Leu	p.P791L	ENST00000263377	NM_058243.2	791	cCg/cTg	13/20	1	2	FACETS	0.449	0.38	0.525	0.449	0.38	0.525	SUBCLONAL	1	TRUE	1	0.63	2		354	325	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966871	18966871	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1206061112	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	89	534	1	ENST00000262803.5:c.1682T>C	p.Leu561Pro	p.L561P	ENST00000262803	NM_002911.3	561	cTg/cCg	12/24	1	2	FACETS	0.485	0.43	0.543	0.485	0.43	0.543	SUBCLONAL	1	TRUE	1	0.63	2		535	583	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212537	36212537	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370359238	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	308	622	0	ENST00000222270.7:c.2288C>T	p.Pro763Leu	p.P763L	ENST00000222270	NM_014727.1	763	cCg/cTg	3/37	0.3	4	FACETS	0.951	0.9	1	0.634	0.6	0.669	INDETERMINATE	2	TRUE	1	0.63	4		622	838	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224199	36224199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775887663	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	161	334	0	ENST00000222270.7:c.6749G>A	p.Arg2250His	p.R2250H	ENST00000222270	NM_014727.1	2250	cGc/cAc	28/37	0.3	4	FACETS	0.922	0.853	0.991	0.614	0.569	0.661	INDETERMINATE	2	TRUE	1	0.63	4		334	452	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793238	42793238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763699553	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	345	650	0	ENST00000575354.2:c.1130C>T	p.Thr377Met	p.T377M	ENST00000575354	NM_015125.3	377	aCg/aTg	7/20	0.3	4	FACETS	0.935	0.887	0.983	0.623	0.591	0.655	INDETERMINATE	2	TRUE	1	0.63	4		650	955	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794718	42794718	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1296019502	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	89	529	0	ENST00000575354.2:c.1798C>T	p.Arg600Cys	p.R600C	ENST00000575354	NM_015125.3	600	Cgc/Tgc	10/20	0.3	4	FACETS	0.598	0.53	0.671	0.199	0.176	0.224	INDETERMINATE	1	TRUE	1	0.63	4		529	770	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872187	45872187	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1238502237	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	56	547	0	ENST00000391945.4:c.246+1G>T		p.X82_splice	ENST00000391945	NM_000400.3	82			0.3	4	FACETS	0.386	0.33	0.448	0.129	0.11	0.15	INDETERMINATE	1	TRUE	1	0.63	4		547	750	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424279	47424279	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	290	456	0	ENST00000404338.3:c.2347C>T	p.Arg783Ter	p.R783*	ENST00000404338	NM_004491.4	783	Cga/Tga	1/6	0.3	4	FACETS	1	0.959	1	0.678	0.641	0.715	INDETERMINATE	2	TRUE	1	0.63	4		456	738	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424841	47424841	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	105	560	0	ENST00000404338.3:c.2914del	p.Arg972GlyfsTer55	p.R972Gfs*55	ENST00000404338	NM_004491.4	970	tCc/tc	1/6	0.3	4	FACETS	0.604	0.54	0.671	0.201	0.18	0.224	INDETERMINATE	1	TRUE	1	0.63	4		560	900	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909472	50909472	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501840	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	78	509	0	ENST00000440232.2:c.1276G>A	p.Gly426Ser	p.G426S	ENST00000440232	NM_002691.3	426	Ggc/Agc	11/27	0.3	4	FACETS	0.503	0.441	0.569	0.168	0.147	0.19	INDETERMINATE	1	TRUE	1	0.63	4		509	803	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982503	25982503	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	43	343	0	ENST00000435504.4:c.787del	p.Arg263GlufsTer24	p.R263Efs*24	ENST00000435504		263	Aga/ga	9/13	1	2	FACETS	0.3	0.251	0.354	0.3	0.251	0.354	SUBCLONAL	1	TRUE	1	0.63	2		343	455	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449893	29449893	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	89	610	0	ENST00000389048.3:c.2962A>C	p.Ser988Arg	p.S988R	ENST00000389048	NM_004304.4	988	Agt/Cgt	18/29	1	2	FACETS	0.452	0.401	0.506	0.452	0.401	0.506	SUBCLONAL	1	TRUE	1	0.63	2		610	625	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451841	29451841	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	40	391	0	ENST00000389048.3:c.2724G>T	p.Gln908His	p.Q908H	ENST00000389048	NM_004304.4	908	caG/caT	16/29	1	2	FACETS	0.401	0.334	0.474	0.401	0.334	0.474	SUBCLONAL	1	TRUE	1	0.63	2		391	317	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607547	46607547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375648855	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	113	605	0	ENST00000263734.3:c.1736C>T	p.Pro579Leu	p.P579L	ENST00000263734	NM_001430.4	579	cCg/cTg	12/16	0.3	1	FACETS	0.476	0.43	0.524	0.476	0.43	0.524	INDETERMINATE	1	TRUE	0	0.63	1		605	516	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253829	30253829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759194807	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	84	476	0	ENST00000307677.4:c.625C>T	p.Arg209Cys	p.R209C	ENST00000307677	NM_138578.1	209	Cgc/Tgc	3/3	1	2	FACETS	0.483	0.427	0.543	0.483	0.427	0.543	SUBCLONAL	1	TRUE	1	0.63	2		476	552	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710554	40710554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746059787	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	62	445	0	ENST00000373198.4:c.4297C>T	p.Arg1433Cys	p.R1433C	ENST00000373198	NM_133170.3	1433	Cgt/Tgt	31/32	1	2	FACETS	0.463	0.401	0.53	0.463	0.401	0.53	SUBCLONAL	1	TRUE	1	0.63	2		445	425	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076932	41076932	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	62	348	0	ENST00000373198.4:c.1488del	p.Phe498LeufsTer103	p.F498Lfs*103	ENST00000373198	NM_133170.3	496	ggG/gg	9/32	1	2	FACETS	0.478	0.414	0.547	0.478	0.414	0.547	SUBCLONAL	1	TRUE	1	0.63	2		348	412	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755518	39755518	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760527652	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	88	618	0	ENST00000288319.7:c.1247C>T	p.Pro416Leu	p.P416L	ENST00000288319	NM_182918.3	416	cCg/cTg	10/10	1	2	FACETS	0.4	0.354	0.449	0.4	0.354	0.449	SUBCLONAL	1	TRUE	1	0.63	2		618	698	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566475	41566475	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	66	347	0	ENST00000263253.7:c.4352A>G	p.His1451Arg	p.H1451R	ENST00000263253	NM_001429.3	1451	cAt/cGt	27/31	1	2	FACETS	0.4	0.347	0.457	0.4	0.347	0.457	SUBCLONAL	1	TRUE	1	0.63	2		347	524	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574607	41574607	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	100	525	0	ENST00000263253.7:c.6892C>T	p.Gln2298Ter	p.Q2298*	ENST00000263253	NM_001429.3	2298	Cag/Tag	31/31	1	2	FACETS	0.461	0.412	0.513	0.461	0.412	0.513	SUBCLONAL	1	TRUE	1	0.63	2		525	689	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162540	47162540	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs770731608	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	75	387	0	ENST00000409792.3:c.3586T>C	p.Ser1196Pro	p.S1196P	ENST00000409792	NM_014159.6	1196	Tct/Cct	3/21	1	2	FACETS	0.473	0.416	0.535	0.473	0.416	0.535	SUBCLONAL	1	TRUE	1	0.63	2		387	503	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413010	49413010	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519952	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	86	392	0	ENST00000418115.1:c.13C>T	p.Arg5Trp	p.R5W	ENST00000418115	NM_001664.2	5	Cgg/Tgg	2/5	1	2	FACETS	0.548	0.486	0.614	0.548	0.486	0.614	SUBCLONAL	1	TRUE	1	0.63	2		392	498	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623187	52623187	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	50	416	0	ENST00000394830.3:c.2864del	p.Asn955ThrfsTer53	p.N955Tfs*53	ENST00000394830	NM_018313.4	955	aAc/ac	19/30	1	2	FACETS	0.275	0.233	0.321	0.275	0.233	0.321	SUBCLONAL	1	TRUE	1	0.63	2		416	577	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662965	52662965	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754097433	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	69	318	0	ENST00000394830.3:c.1388A>G	p.Asn463Ser	p.N463S	ENST00000394830	NM_018313.4	463	aAt/aGt	13/30	1	2	FACETS	0.563	0.493	0.638	0.563	0.493	0.638	SUBCLONAL	1	TRUE	1	0.63	2		318	389	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204842	128204842	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs768767517	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	86	587	1	ENST00000341105.2:c.599del	p.Gly200ValfsTer18	p.G200Vfs*18	ENST00000341105	NM_032638.4	200	gGt/gt	3/6	1	2	FACETS	0.458	0.406	0.514	0.458	0.406	0.514	SUBCLONAL	1	TRUE	1	0.63	2		588	596	SUCCESS
ATR	545	MSKCC	GRCh37	3	142254993	142254993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	39	213	0	ENST00000350721.4:c.3776C>T	p.Pro1259Leu	p.P1259L	ENST00000350721	NM_001184.3	1259	cCa/cTa	20/47	0.250361297520716	3	FACETS	0.651	0.543	0.77	0.326	0.271	0.385	INDETERMINATE	1	TRUE	1	0.63	3		213	250	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	76	399	0	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	0.250361297520716	3	FACETS	0.783	0.691	0.882	0.392	0.345	0.441	INDETERMINATE	1	TRUE	1	0.63	3		399	405	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198255	185198255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759993681	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	134	459	0	ENST00000265026.3:c.2737G>A	p.Val913Met	p.V913M	ENST00000265026	NM_004721.4	913	Gtg/Atg	13/14	1	2	FACETS	0.633	0.576	0.692	0.633	0.576	0.692	SUBCLONAL	1	TRUE	1	0.63	2		459	672	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158447	106158447	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	54	379	0	ENST00000380013.4:c.3353del	p.Asn1118IlefsTer19	p.N1118Ifs*19	ENST00000380013	NM_001127208.2	1116	atA/at	3/11	1	2	FACETS	0.398	0.34	0.46	0.398	0.34	0.46	SUBCLONAL	1	TRUE	1	0.63	2		379	431	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224529	224529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370481102	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	43	200	0	ENST00000264932.6:c.205G>A	p.Ala69Thr	p.A69T	ENST00000264932	NM_004168.2	69	Gct/Act	3/15	1	2	FACETS	0.533	0.449	0.625	0.533	0.449	0.625	SUBCLONAL	1	TRUE	1	0.63	2		200	256	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681924	30681924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754781804	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	96	498	0	ENST00000376406.3:c.173G>A	p.Arg58Gln	p.R58Q	ENST00000376406	NM_014641.2	58	cGa/cAa	3/15	1	2	FACETS	0.551	0.492	0.614	0.551	0.492	0.614	SUBCLONAL	1	TRUE	1	0.63	2		498	553	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64288882	64288882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773307144	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	66	288	0	ENST00000370651.3:c.278G>A	p.Arg93His	p.R93H	ENST00000370651	NM_003463.4	93	cGt/cAt	4/6	1	2	FACETS	0.529	0.461	0.602	0.529	0.461	0.602	SUBCLONAL	1	TRUE	1	0.63	2		288	396	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983042	111983042	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	98	568	1	ENST00000368678.4:c.1505del	p.Lys502ArgfsTer53	p.K502Rfs*53	ENST00000368678		502	aAg/ag	13/13	1	2	FACETS	0.503	0.449	0.56	0.503	0.449	0.56	SUBCLONAL	1	TRUE	1	0.63	2		569	619	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771163	161771163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755627153	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	80	425	0	ENST00000366898.1:c.1366G>A	p.Val456Ile	p.V456I	ENST00000366898	NM_004562.2	456	Gtc/Atc	12/12	1	2	FACETS	0.525	0.463	0.59	0.525	0.463	0.59	SUBCLONAL	1	TRUE	1	0.63	2		425	484	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983995	2983995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	69	463	0	ENST00000396946.4:c.535C>T	p.Arg179Trp	p.R179W	ENST00000396946	NM_032415.4	179	Cgg/Tgg	5/25	1	2	FACETS	0.431	0.376	0.491	0.431	0.376	0.491	SUBCLONAL	1	TRUE	1	0.63	2		463	508	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043349	6043349	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781716	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	15	98	1	ENST00000265849.7:c.325del	p.Glu109LysfsTer3	p.E109Kfs*3	ENST00000265849	NM_000535.5	109	Gaa/aa	4/15	1	2	FACETS	0.421	0.311	0.551	0.421	0.311	0.551	SUBCLONAL	1	TRUE	1	0.63	2		99	113	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	85	567	2	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.509	0.451	0.571	0.509	0.451	0.571	SUBCLONAL	1	TRUE	1	0.63	2		569	530	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845702	151845702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771018478	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	98	497	0	ENST00000262189.6:c.13310C>T	p.Thr4437Met	p.T4437M	ENST00000262189	NM_170606.2	4437	aCg/aTg	52/59	1	2	FACETS	0.517	0.462	0.575	0.517	0.462	0.575	SUBCLONAL	1	TRUE	1	0.63	2		497	602	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2161842	2161842	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1563814671	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	173	462	0	ENST00000349721.2:c.4143del	p.Lys1382AsnfsTer2	p.K1382Nfs*2	ENST00000349721	NM_003070.3	1380	Ccc/cc	28/34	0.250361297520716	3	FACETS	1	0.927	1	0.502	0.463	0.543	INDETERMINATE	1	TRUE	1	0.63	3		462	719	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212851	27212851	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760084463	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	56	490	0	ENST00000380036.4:c.2833G>A	p.Ala945Thr	p.A945T	ENST00000380036	NM_000459.3	945	Gct/Act	17/23	0.250361297520716	3	FACETS	0.364	0.311	0.422	0.182	0.155	0.211	INDETERMINATE	1	TRUE	1	0.63	3		490	642	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840626	36840626	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	68	475	0	ENST00000358127.4:c.1107del	p.Tyr370ThrfsTer33	p.Y370Tfs*33	ENST00000358127	NM_001280556.1	369	ccC/cc	10/10	0.250361297520716	3	FACETS	0.551	0.48	0.628	0.276	0.24	0.314	INDETERMINATE	1	TRUE	1	0.63	3		475	515	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570325	87570325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	183	584	0	ENST00000277120.3:c.2065G>A	p.Val689Met	p.V689M	ENST00000277120		689	Gtg/Atg	17/19	0.250361297520716	3	FACETS	1	0.975	1	0.558	0.516	0.6	INDETERMINATE	1	TRUE	1	0.63	3		584	685	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209593	98209593	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	152	512	0	ENST00000331920.6:c.3945del	p.Tyr1316ThrfsTer56	p.Y1316Tfs*56	ENST00000331920	NM_000264.3	1315	ccC/cc	23/24	0.250361297520716	3	FACETS	0.982	0.901	1	0.491	0.45	0.533	INDETERMINATE	1	TRUE	1	0.63	3		512	646	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412318	139412318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057315-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	155	553	0	ENST00000277541.6:c.1327G>A	p.Gly443Ser	p.G443S	ENST00000277541	NM_017617.3	443	Ggc/Agc	8/34	0.250361297520716	3	FACETS	0.947	0.87	1	0.474	0.435	0.514	INDETERMINATE	1	TRUE	1	0.63	3		553	683	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057491-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	117	321	0				ENST00000310581	NM_198253.2	-/1132			0.300265951106813	6	FACETS	0.908	0.826	0.993	0.681	0.619	0.745	CLONAL	3	TRUE	2	0.37	6		321	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057491-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	217	470	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.251712915523847	3	FACETS	1	0.984	1	0.773	0.724	0.824	CLONAL	2	TRUE	0	0.37	3		470	599	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535283	66535283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs547670481	NA	P-0057491-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	60	437	0	ENST00000273854.3:c.178G>A	p.Glu60Lys	p.E60K	ENST00000273854	NM_004439.5	60	Gaa/Aaa	1/18	0.300265951106813	5	FACETS	0.922	0.795	1	0.23	0.198	0.265	CLONAL	1	TRUE	1	0.37	5		437	547	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983018	201983019	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0057491-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	173	531	0	ENST00000359651.3:c.869_870dup	p.Gly291ArgfsTer4	p.G291Rfs*4	ENST00000359651		289	-/GA	7/8	0.272994038106105	3	FACETS	0.901	0.833	0.971	0.901	0.833	0.971	CLONAL	2	TRUE	1	0.37	3		531	615	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023002	33023002	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057491-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	116	453	0	ENST00000300177.4:c.111C>G	p.Asp37Glu	p.D37E	ENST00000300177	NM_001191322.1	37	gaC/gaG	2/2	0.0909282632881752	4	FACETS	0.8	0.724	0.88	0.8	0.724	0.88	INDETERMINATE	2	TRUE	2	0.37	4		453	537	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18960921	18960921	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057491-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	46	373	0	ENST00000262803.5:c.499G>T	p.Glu167Ter	p.E167*	ENST00000262803	NM_002911.3	167	Gag/Tag	4/24	0.300265951106813	7	FACETS	0.696	0.585	0.819	0.139	0.117	0.164	SUBCLONAL	1	TRUE	2	0.37	7		373	688	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47087991	47087991	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057491-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	72	345	0	ENST00000409792.3:c.7084C>A	p.Gln2362Lys	p.Q2362K	ENST00000409792	NM_014159.6	2362	Cag/Aag	16/21	0.231640814217056	3	FACETS	0.734	0.642	0.834	0.367	0.321	0.417	SUBCLONAL	1	TRUE	1	0.37	3		345	628	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779038	135779038	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057491-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	205	367	0	ENST00000298552.3:c.2208G>A	p.Met736Ile	p.M736I	ENST00000298552	NM_001162426.1	736	atG/atA	17/23	0.300265951106813	3	FACETS	0.945	0.887	1	0.945	0.887	1	CLONAL	3	TRUE	0	0.37	3		367	463	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363243	40363243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057491-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	157	502	0	ENST00000397332.2:c.986C>T	p.Ser329Leu	p.S329L	ENST00000397332	NM_001033082.2	329	tCg/tTg	3/3	0.138621930702903	5	FACETS	1	0.926	1	0.672	0.617	0.728	INDETERMINATE	2	TRUE	2	0.37	5		502	655	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61306439	61306439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868227362	NA	P-0057491-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	24	323	0	ENST00000341074.5:c.748G>A	p.Glu250Lys	p.E250K	ENST00000341074	NM_002974.2	250	Gaa/Aaa	7/8	0.300265951106813	5	FACETS	0.44	0.344	0.552	0.11	0.086	0.138	SUBCLONAL	1	TRUE	1	0.37	5		323	458	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551522	150551522	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057571-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	120	623	0	ENST00000369026.2:c.485C>G	p.Ser162Trp	p.S162W	ENST00000369026	NM_021960.4	162	tCg/tGg	1/3	1	2	FACETS	0.351	0.316	0.388	0.351	0.316	0.388	SUBCLONAL	1	TRUE	1	0.672199298871175	2		623	1016	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873554	151873554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057571-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	64	537	0	ENST00000262189.6:c.8984C>T	p.Pro2995Leu	p.P2995L	ENST00000262189	NM_170606.2	2995	cCa/cTa	38/59	0.462388505812704	2	FACETS	0.164	0.141	0.189	0.082	0.07	0.095	SUBCLONAL	1	TRUE	0	0.672199298871175	2		537	1159	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748114	43748114	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057571-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	252	463	0	ENST00000382044.4:c.2692C>A	p.Gln898Lys	p.Q898K	ENST00000382044	NM_001141980.1	898	Caa/Aaa	12/28	0.160103470761466	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.672199298871175	0		463	713	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59871083	59871083	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057571-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	52	212	0	ENST00000259008.2:c.1348G>C	p.Glu450Gln	p.E450Q	ENST00000259008	NM_032043.2	450	Gaa/Caa	10/20	1	2	FACETS	0.217	0.184	0.253	0.217	0.184	0.253	SUBCLONAL	1	TRUE	1	0.672199298871175	2		212	713	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456585	32456585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057858-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	39	409	0	ENST00000332351.3:c.307del	p.Ala103ArgfsTer55	p.A103Rfs*55	ENST00000332351	NM_024426.4	103	Gcg/cg	1/10	1	2	FACETS	0.849	0.705	1	0.849	0.705	1	CLONAL	1	TRUE	1	0.240447161079421	2		409	382	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912933	32912942	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGAAACAG	GAGGAAACAG	-	novel	NA	P-0057858-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	76	488	0	ENST00000380152.3:c.4441_4450del	p.Glu1481ThrfsTer2	p.E1481Tfs*2	ENST00000380152		1481	GAGGAAACAGac/ac	11/27	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.240447161079421	2		488	485	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778582	3778582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057858-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	71	550	0	ENST00000262367.5:c.6466C>T	p.Pro2156Ser	p.P2156S	ENST00000262367	NM_004380.2	2156	Cca/Tca	31/31	1	2	FACETS	0.906	0.79	1	0.906	0.79	1	CLONAL	1	TRUE	1	0.240447161079421	2		550	652	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821392	72821392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057858-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	45	423	2	ENST00000268489.5:c.10783G>A	p.Asp3595Asn	p.D3595N	ENST00000268489	NM_006885.3	3595	Gac/Aac	10/10	1	2	FACETS	0.725	0.609	0.854	0.725	0.609	0.854	SUBCLONAL	1	TRUE	1	0.240447161079421	2		425	516	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200076	128200076	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057858-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	77	561	0	ENST00000341105.2:c.1229G>T	p.Gly410Val	p.G410V	ENST00000341105	NM_032638.4	410	gGg/gTg	6/6	1	2	FACETS	0.812	0.712	0.92	0.812	0.712	0.92	CLONAL	1	TRUE	1	0.240447161079421	2		561	789	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156982	106156982	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057858-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	90	614	1	ENST00000380013.4:c.1883A>G	p.Glu628Gly	p.E628G	ENST00000380013	NM_001127208.2	628	gAg/gGg	3/11	1	2	FACETS	0.948	0.84	1	0.948	0.84	1	CLONAL	1	TRUE	1	0.240447161079421	2		615	790	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578474	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057884-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	195	611	0	ENST00000269305.4:c.456del	p.Gly154AlafsTer16	p.G154Afs*16	ENST00000269305	NM_001126112.2	152	ccG/cc	5/11	0.20718878471548	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.219419341962382	2		611	862	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741664	17741664	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057884-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	136	508	0	ENST00000250003.3:c.335A>G	p.Lys112Arg	p.K112R	ENST00000250003	NM_002478.4	112	aAg/aGg	1/3	1	2	FACETS	0.872	0.794	0.953	1	0.989	1	CLONAL	2	TRUE	1	0.219419341962382	2		508	711	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201933	102201934	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057884-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	47	389	0	ENST00000263464.3:c.1287dup	p.Glu430ArgfsTer8	p.E430Rfs*8	ENST00000263464	NM_001165.4	429	gaa/gAaa	6/9	1	2	FACETS	0.735	0.619	0.862	0.735	0.619	0.862	SUBCLONAL	1	TRUE	1	0.219419341962382	2		389	583	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762393	41762393	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057884-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	112	465	0	ENST00000301178.4:c.2073C>A	p.Phe691Leu	p.F691L	ENST00000301178	NM_021913.4	691	ttC/ttA	18/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.219419341962382	2		465	731	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368530	225368530	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057884-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	34	303	0	ENST00000264414.4:c.1216C>T	p.Gln406Ter	p.Q406*	ENST00000264414	NM_003590.4	406	Caa/Taa	9/16	1	2	FACETS	0.678	0.554	0.818	0.678	0.554	0.818	SUBCLONAL	1	TRUE	1	0.219419341962382	2		303	457	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175769	24175769	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057884-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	40	558	0	ENST00000263121.7:c.997C>G	p.Leu333Val	p.L333V	ENST00000263121	NM_003073.3	333	Ctg/Gtg	8/9	0.119338081894902	3	FACETS	0.516	0.427	0.616	0.258	0.213	0.308	INDETERMINATE	1	TRUE	1	0.219419341962382	3		558	784	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462416	89462416	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057884-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	53	352	0	ENST00000336596.2:c.1888G>T	p.Gly630Cys	p.G630C	ENST00000336596	NM_005233.5	630	Ggt/Tgt	10/17	0.219419341962382	1	FACETS	0.937	0.8	1	0.937	0.8	1	CLONAL	1	TRUE	0	0.219419341962382	1		352	459	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55569894	55569894	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057884-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	38	242	0	ENST00000288135.5:c.761A>T	p.Lys254Ile	p.K254I	ENST00000288135	NM_000222.2	254	aAa/aTa	5/21	0.206494633263038	3	FACETS	1	0.896	1	0.559	0.463	0.665	CLONAL	1	TRUE	1	0.219419341962382	3		242	344	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201815	66201815	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057884-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	65	363	0	ENST00000273854.3:c.2687G>C	p.Arg896Pro	p.R896P	ENST00000273854	NM_004439.5	896	cGt/cCt	16/18	1	2	FACETS	0.967	0.838	1	0.967	0.838	1	CLONAL	1	TRUE	1	0.219419341962382	2		363	613	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38949971	38949971	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057884-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	93	429	0	ENST00000357387.3:c.3979G>A	p.Ala1327Thr	p.A1327T	ENST00000357387	NM_152756.3	1327	Gct/Act	31/38	0.197890493367685	5	FACETS	1	0.974	1	0.334	0.296	0.374	CLONAL	1	TRUE	1	0.219419341962382	5		429	844	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341147	8341147	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057884-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	50	392	0	ENST00000356435.5:c.5069C>A	p.Pro1690His	p.P1690H	ENST00000356435		1690	cCt/cAt	30/35	1	2	FACETS	0.807	0.684	0.941	0.807	0.684	0.941	CLONAL	1	TRUE	1	0.219419341962382	2		392	565	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057998-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	38	321	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	0.603	0.498	0.719	0.603	0.498	0.719	SUBCLONAL	1	TRUE	0	0.26	1		321	422	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0057998-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	17	534	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.21	0.155	0.275	0.21	0.155	0.275	SUBCLONAL	1	TRUE	1	0.26	2		534	624	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519985	NA	P-0057998-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	68	461	0	ENST00000269305.4:c.857A>G	p.Glu286Gly	p.E286G	ENST00000269305	NM_001126112.2	286	gAa/gGa	8/11	1	2	FACETS	0.822	0.715	0.938	0.822	0.715	0.938	CLONAL	1	TRUE	1	0.26	2		461	636	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004630	16004630	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0057998-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	35	675	0	ENST00000268712.3:c.2624C>G	p.Ser875Ter	p.S875*	ENST00000268712	NM_006311.3	875	tCa/tGa	20/46	1	2	FACETS	0.423	0.346	0.511	0.423	0.346	0.511	SUBCLONAL	1	TRUE	1	0.26	2		675	636	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069466	30069466	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0057998-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	82	399	0	ENST00000338641.4:c.1331C>G	p.Ser444Ter	p.S444*	ENST00000338641	NM_000268.3	444	tCa/tGa	12/16	0.3	1	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	0	0.26	1		399	543	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102071	27102071	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057998-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	52	371	0	ENST00000324856.7:c.5000del	p.Pro1667ArgfsTer6	p.P1667Rfs*6	ENST00000324856	NM_006015.4	1666	aCc/ac	19/20	0.3	1	FACETS	0.525	0.446	0.612	0.525	0.446	0.612	SUBCLONAL	1	TRUE	0	0.26	1		371	663	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230561658	230561658	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0057998-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	54	273	0				ENST00000391860	NM_001258311.1	-/409			1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.26	2		273	413	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36653541	36653542	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057998-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	44	314	0	ENST00000244741.5:c.462dup	p.Arg155ThrfsTer42	p.R155Tfs*42	ENST00000244741	NM_000389.4	153	-/A	3/3	1	2	FACETS	0.609	0.51	0.718	0.609	0.51	0.718	SUBCLONAL	1	TRUE	1	0.26	2		314	556	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	36	321	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.933	0.768	1	0.933	0.768	1	CLONAL	1	TRUE	1	0.19	2		321	406	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132542	11132542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	50	580	0	ENST00000358026.2:c.2758G>A	p.Glu920Lys	p.E920K	ENST00000358026	NM_001128849.1	920	Gag/Aag	19/36	1	2	FACETS	0.647	0.548	0.758	0.647	0.548	0.758	SUBCLONAL	1	TRUE	1	0.19	2		580	813	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555526101	NA	P-0058014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	74	631	0	ENST00000269305.4:c.497C>G	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tGa	5/11	1	2	FACETS	0.921	0.805	1	0.921	0.805	1	CLONAL	1	TRUE	1	0.19	2		631	846	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104759	69104759	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs139672596	NA	P-0058014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	67	475	0	ENST00000288368.4:c.4603C>T	p.Arg1535Trp	p.R1535W	ENST00000288368	NM_024870.2	1535	Cgg/Tgg	37/40	1	2	FACETS	0.938	0.814	1	0.938	0.814	1	CLONAL	1	TRUE	1	0.19	2		475	752	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022540	12022540	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	65	717	0	ENST00000396373.4:c.646G>A	p.Glu216Lys	p.E216K	ENST00000396373	NM_001987.4	216	Gag/Aag	5/8	1	2	FACETS	0.733	0.634	0.842	0.733	0.634	0.842	SUBCLONAL	1	TRUE	1	0.19	2		717	933	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404508	70404508	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	51	534	0	ENST00000373644.4:c.2022C>A	p.Tyr674Ter	p.Y674*	ENST00000373644	NM_030625.2	674	taC/taA	4/12	1	2	FACETS	0.874	0.742	1	0.874	0.742	1	CLONAL	1	TRUE	1	0.19	2		534	614	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413607	32413607	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	43	412	0	ENST00000332351.3:c.1343T>A	p.Val448Glu	p.V448E	ENST00000332351	NM_024426.4	448	gTg/gAg	9/10	1	2	FACETS	0.779	0.651	0.921	0.779	0.651	0.921	CLONAL	1	TRUE	1	0.19	2		412	581	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441791	49441791	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	82	456	0	ENST00000301067.7:c.4193C>A	p.Ser1398Ter	p.S1398*	ENST00000301067	NM_003482.3	1398	tCg/tAg	14/54	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.19	2		456	653	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673725	37673725	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	126	541	0	ENST00000447079.4:c.2879G>T	p.Trp960Leu	p.W960L	ENST00000447079	NM_015083.1	960	tGg/tTg	10/14	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.19	2		541	936	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749373	41749373	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	32	341	0	ENST00000226382.2:c.422G>C	p.Arg141Pro	p.R141P	ENST00000226382	NM_003924.3	141	cGa/cCa	2/3	1	2	FACETS	0.812	0.659	0.984	0.812	0.659	0.984	CLONAL	1	TRUE	1	0.19	2		341	415	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038486	47038505	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCCTGTGCCTCACAGTGTG	GGCCTGTGCCTCACAGTGTG	-	novel	NA	P-0058014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	46	218	0	ENST00000377604.3:c.664-15_668del		p.X222_splice	ENST00000377604	NM_001204468.1	222		8/24	1	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.19	1		218	338	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242753	16242753	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	34	527	0	ENST00000375759.3:c.1374C>A	p.Phe458Leu	p.F458L	ENST00000375759	NM_015001.2	458	ttC/ttA	6/15	1	2	FACETS	0.53	0.432	0.642	0.53	0.432	0.642	SUBCLONAL	1	TRUE	1	0.19	2		527	675	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294704	1294704	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	37	518	0	ENST00000310581.5:c.297C>A	p.Phe99Leu	p.F99L	ENST00000310581	NM_198253.2	99	ttC/ttA	2/16	1	2	FACETS	0.7	0.577	0.84	0.7	0.577	0.84	SUBCLONAL	1	TRUE	1	0.19	2		518	556	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79974845	79974845	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058014-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	41	469	0	ENST00000265081.6:c.1273G>C	p.Glu425Gln	p.E425Q	ENST00000265081	NM_002439.4	425	Gag/Cag	8/24	1	2	FACETS	0.569	0.473	0.677	0.569	0.473	0.677	SUBCLONAL	1	TRUE	1	0.19	2		469	758	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591888	48591888	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519739	NA	P-0058080-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	60	457	0	ENST00000342988.3:c.1051G>C	p.Asp351His	p.D351H	ENST00000342988	NM_005359.5	351	Gat/Cat	9/12	0.340128371452347	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	0	0.340128371452347	2		457	158	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0058080-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	192	817	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.338769759329136	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	3	TRUE	0	0.340128371452347	3		817	423	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0058080-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	53	612	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.220172194551265	4	FACETS	1	0.868	1	1	0.868	1	CLONAL	2	TRUE	2	0.340128371452347	4		612	208	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430368	181430368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058080-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	97	409	0	ENST00000325404.1:c.220C>T	p.Arg74Cys	p.R74C	ENST00000325404	NM_003106.3	74	Cgc/Tgc	1/1	0.215580314465484	5	FACETS	1	0.948	1	0.727	0.653	0.805	CLONAL	2	TRUE	2	0.340128371452347	5		409	395	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851696	134851696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576710309	NA	P-0058080-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	140	574	0	ENST00000398015.3:c.1102C>T	p.Arg368Trp	p.R368W	ENST00000398015	NM_004441.4	368	Cgg/Tgg	5/16	0.215580314465484	5	FACETS	0.935	0.859	1	0.935	0.859	1	CLONAL	3	TRUE	2	0.340128371452347	5		574	443	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779128	3779128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395505964	NA	P-0058080-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	65	563	0	ENST00000262367.5:c.5920C>T	p.Arg1974Trp	p.R1974W	ENST00000262367	NM_004380.2	1974	Cgg/Tgg	31/31	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.340128371452347	2		563	356	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612245	1612245	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058080-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	109	505	0	ENST00000344749.5:c.1774G>C	p.Ala592Pro	p.A592P	ENST00000344749	NM_001136139.2	592	Gcc/Ccc	18/19	0.30757062115824	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	1	0.340128371452347	3		505	349	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257667	19257667	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058080-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	113	630	0	ENST00000162023.5:c.559T>C	p.Phe187Leu	p.F187L	ENST00000162023		187	Ttc/Ctc	10/13	0.30757062115824	3	FACETS	0.805	0.728	0.885	0.805	0.728	0.885	CLONAL	2	TRUE	1	0.340128371452347	3		630	483	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786859	135786859	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058080-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	64	390	0	ENST00000298552.3:c.1010T>C	p.Leu337Pro	p.L337P	ENST00000298552	NM_001162426.1	337	cTg/cCg	10/23	0.340128371452347	5	FACETS	0.95	0.83	1	0.634	0.553	0.719	CLONAL	2	TRUE	2	0.340128371452347	5		390	299	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285799	46285799	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058080-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	29	446	0	ENST00000334344.6:c.5067G>C	p.Lys1689Asn	p.K1689N	ENST00000334344	NM_152641.2	1689	aaG/aaC	18/21	0.340128371452347	5	FACETS	0.805	0.647	0.984	0.268	0.215	0.328	CLONAL	1	TRUE	2	0.340128371452347	5		446	320	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0058179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	47	611	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.833	0.714	0.959	1	0.97	1	CLONAL	2	TRUE	1	0.33	2		611	171	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0058179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	57	877	1	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.27587778207213	2	FACETS	0.834	0.726	0.949	0.834	0.726	0.949	CLONAL	2	TRUE	0	0.33	2		878	207	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100093	157100117	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCGGCGGCGGCAGCAGCAGGAG	GCGGCGGCGGCGGCAGCAGCAGGAG	-	novel	NA	P-0058179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	81	563	0	ENST00000346085.5:c.1044_1068del	p.Ala350MetfsTer11	p.A350Mfs*11	ENST00000346085	NM_020732.3	344	GCGGCGGCGGCGGCAGCAGCAGGAGgc/gc	1/20	0.3	3	FACETS	0.885	0.787	0.988	0.59	0.525	0.659	CLONAL	2	TRUE	0	0.33	3		563	323	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879854	37879854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	81	642	0	ENST00000269571.5:c.2149G>C	p.Glu717Gln	p.E717Q	ENST00000269571		717	Gag/Cag	18/27	0.218944851368413	4	FACETS	0.93	0.826	1	0.93	0.826	1	CLONAL	2	TRUE	2	0.33	4		642	351	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426813	212426813	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	32	330	0	ENST00000342788.4:c.2302G>A	p.Glu768Lys	p.E768K	ENST00000342788	NM_005235.2	768	Gaa/Aaa	20/28	1	2	FACETS	0.946	0.774	1	0.946	0.774	1	CLONAL	1	TRUE	1	0.33	2		330	205	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436403	52436403	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	47	537	0	ENST00000460680.1:c.2091del	p.Val698CysfsTer38	p.V698Cfs*38	ENST00000460680	NM_004656.3	697	tcC/tc	17/17	0.157738160463604	4	FACETS	1	0.948	1	0.644	0.547	0.75	INDETERMINATE	1	TRUE	2	0.33	4		537	294	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629376	187629376	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs888101917	NA	P-0058179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	46	490	0	ENST00000441802.2:c.1606C>G	p.Leu536Val	p.L536V	ENST00000441802	NM_005245.3	536	Ctg/Gtg	2/27	0.157738160463604	4	FACETS	1	0.948	1	0.648	0.549	0.756	INDETERMINATE	1	TRUE	2	0.33	4		490	286	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711025	114711025	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	19	162	0	ENST00000543371.1:c.249G>C	p.Leu83Phe	p.L83F	ENST00000543371	NM_001198531.1	83	ttG/ttC	2/14	0.25062070963662	2	FACETS	0.702	0.537	0.894	0.351	0.268	0.447	SUBCLONAL	1	TRUE	0	0.33	2		162	164	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434760	49434760	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	68	694	0	ENST00000301067.7:c.6793G>T	p.Gly2265Ter	p.G2265*	ENST00000301067	NM_003482.3	2265	Gga/Tga	31/54	0.250783270245026	5	FACETS	1	0.97	1	0.47	0.41	0.534	CLONAL	1	TRUE	2	0.33	5		694	437	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254566	10254577	+	inframe_deletion	In_Frame_Del	DEL	CTTTGATGTAGT	CTTTGATGTAGT	-	novel	NA	P-0058179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	26	439	0	ENST00000340748.4:c.2933_2944del	p.Asp978_Lys981del	p.D978_K981del	ENST00000340748		978	gACTACATCAAAGgc/ggc	28/40	0.20405119703055	3	FACETS	0.712	0.565	0.878	0.356	0.282	0.439	SUBCLONAL	1	TRUE	1	0.33	3		439	258	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911176	29911176	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs76385482	NA	P-0058179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	15	240	0	ENST00000376809.5:c.475G>A	p.Ala159Thr	p.A159T	ENST00000376809	NM_002116.7	159	Gcg/Acg	3/8	0.3	3	FACETS	1	0.774	1	0.35	0.259	0.455	CLONAL	1	TRUE	0	0.33	3		240	101	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90992974	90992974	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	30	310	0	ENST00000265433.3:c.468A>T	p.Lys156Asn	p.K156N	ENST00000265433	NM_002485.4	156	aaA/aaT	4/16	0.3	5	FACETS	0.871	0.711	1	0.348	0.284	0.419	CLONAL	2	TRUE	0	0.33	5		310	156	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427423	49427423	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058232-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	91	573	0	ENST00000301067.7:c.11065del	p.Ala3689LeufsTer60	p.A3689Lfs*60	ENST00000301067	NM_003482.3	3689	Gct/ct	39/54	0.27379903489864	5	FACETS	0.854	0.763	0.95	0.57	0.509	0.633	CLONAL	2	TRUE	2	0.432650705534525	5		573	406	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828146	72828146	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058232-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	41	477	0	ENST00000268489.5:c.8435del	p.Asp2812AlafsTer12	p.D2812Afs*12	ENST00000268489	NM_006885.3	2812	gAc/gc	9/10	0.245262751391582	3	FACETS	1	0.846	1	0.503	0.423	0.591	INDETERMINATE	1	TRUE	1	0.432650705534525	3		477	229	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598137	52598137	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058232-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	47	410	0	ENST00000394830.3:c.3729del	p.Met1243IlefsTer7	p.M1243Ifs*7	ENST00000394830	NM_018313.4	1243	atG/at	24/30	1	2	FACETS	0.992	0.846	1	0.992	0.846	1	CLONAL	1	TRUE	1	0.432650705534525	2		410	219	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794419	242794419	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058379-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	135	467	0	ENST00000334409.5:c.523G>T	p.Gly175Cys	p.G175C	ENST00000334409	NM_005018.2	175	Ggc/Tgc	3/5	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.472705804878697	2		467	464	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623085	52623085	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0058379-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	108	332	0	ENST00000394830.3:c.2965+1G>A		p.X989_splice	ENST00000394830	NM_018313.4	989			0.472705804878697	1	FACETS	0.892	0.808	0.981	0.892	0.808	0.981	CLONAL	1	TRUE	0	0.472705804878697	1		332	391	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	89	321	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		321	272	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	492	189	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		189	594	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0058881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	456	385	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		385	663	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0058881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	394	392	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		392	1159	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027160	49027160	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0058881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	132	120	0	ENST00000267163.4:c.1727C>G	p.Ser576Ter	p.S576*	ENST00000267163	NM_000321.2	576	tCa/tGa	18/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		120	231	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085824	16085824	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	756	258	0	ENST00000281043.3:c.1000G>T	p.Ala334Ser	p.A334S	ENST00000281043	NM_005378.4	334	Gcc/Tcc	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		258	930	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024636	31024637	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1555912897	NA	P-0058881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	223	324	0	ENST00000375687.4:c.4127dup	p.Pro1377SerfsTer3	p.P1377Sfs*3	ENST00000375687	NM_015338.5	1374	gtg/gtGg	13/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		324	1339	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215302	123215302	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	149	43	0	ENST00000218089.9:c.2848G>T	p.Glu950Ter	p.E950*	ENST00000218089	NM_001042749.1	950	Gaa/Taa	28/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		43	178	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790158	40790158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781621750	NA	P-0058881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	326	277	0	ENST00000373198.4:c.2573C>T	p.Ser858Phe	p.S858F	ENST00000373198	NM_133170.3	858	tCc/tTc	18/32	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		277	859	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259138	36259138	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0058881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	394	239	0	ENST00000300305.3:c.351+2T>C		p.X117_splice	ENST00000300305		117			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		239	1227	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155120	108155120	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	279	109	0	ENST00000278616.4:c.3913G>C	p.Asp1305His	p.D1305H	ENST00000278616	NM_000051.3	1305	Gac/Cac	26/63	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		109	521	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422861	49422909	+	frameshift_variant	Frame_Shift_Del	DEL	GGAATGAGGGGGATGACAGGGGAGAGGGCCCGGTCCTCTTGCTCCCACC	GGAATGAGGGGGATGACAGGGGAGAGGGCCCGGTCCTCTTGCTCCCACC	-	novel	NA	P-0058881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	360	356	0	ENST00000301067.7:c.14186_14234del	p.Arg4729LeufsTer52	p.R4729Lfs*52	ENST00000301067	NM_003482.3	4729	cGGTGGGAGCAAGAGGACCGGGCCCTCTCCCCTGTCATCCCCCTCATTCCt/ct	44/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		356	1154	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33689760	33689760	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1442895068	NA	P-0058881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	431	264	0	ENST00000308377.4:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000308377	NM_152270.3	356	cCa/cTa	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		264	995	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247173	153247198	+	frameshift_variant	Frame_Shift_Del	DEL	TCTATTAGTATGCCCCTGCAACGTGT	TCTATTAGTATGCCCCTGCAACGTGT	-	novel	NA	P-0058881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	329	199	0	ENST00000281708.4:c.1604_1629del	p.His535ArgfsTer7	p.H535Rfs*7	ENST00000281708	NM_033632.3	535	cACACGTTGCAGGGGCATACTAATAGA/c	10/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		199	739	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629999	187629999	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	553	295	0	ENST00000441802.2:c.983A>G	p.His328Arg	p.H328R	ENST00000441802	NM_005245.3	328	cAt/cGt	2/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		295	1143	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1266639	1266639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918666	NA	P-0058881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	184	222	0	ENST00000310581.5:c.2594G>A	p.Arg865His	p.R865H	ENST00000310581	NM_198253.2	865	cGt/cAt	10/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		222	468	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964406	70964406	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	300	257	0	ENST00000276594.2:c.1622A>T	p.Lys541Met	p.K541M	ENST00000276594	NM_024504.3	541	aAg/aTg	8/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		257	780	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165663	118165663	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776281952	NA	P-0058881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	231	421	1	ENST00000369448.3:c.173G>A	p.Arg58Gln	p.R58Q	ENST00000369448	NM_017709.3	58	cGg/cAg	2/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		422	1082	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152074	11152074	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	217	382	0	ENST00000358026.2:c.4358C>G	p.Ser1453Cys	p.S1453C	ENST00000358026	NM_001128849.1	1453	tCc/tGc	31/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		382	949	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051636	128051636	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	441	173	0	ENST00000285398.2:c.22G>C	p.Asp8His	p.D8H	ENST00000285398	NM_000122.1	8	Gac/Cac	1/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		173	740	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324565	62324565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369716125	NA	P-0058881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	565	298	1	ENST00000360203.5:c.2921G>A	p.Arg974Gln	p.R974Q	ENST00000360203	NM_001283009.1	974	cGa/cAa	30/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		299	1123	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0058883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	64	382	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.380557013042143	2		382	326	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913273	NA	P-0058883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	39	184	0	ENST00000263967.3:c.1624G>C	p.Glu542Gln	p.E542Q	ENST00000263967	NM_006218.2	542	Gaa/Caa	10/21	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.380557013042143	2		184	182	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442820	99442820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148662051	NA	P-0058883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	117	517	0	ENST00000268035.6:c.1217G>A	p.Arg406His	p.R406H	ENST00000268035	NM_000875.3	406	cGc/cAc	5/21	1	2	FACETS	0.997	0.901	1	0.997	0.901	1	CLONAL	1	TRUE	1	0.380557013042143	2		517	617	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586250	48586250	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	72	294	0	ENST00000342988.3:c.919G>T	p.Glu307Ter	p.E307*	ENST00000342988	NM_005359.5	307	Gag/Tag	8/12	0.380557013042143	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.380557013042143	1		294	285	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249356	110249356	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201645553	NA	P-0058883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	141	595	0	ENST00000374672.4:c.1217C>T	p.Thr406Ile	p.T406I	ENST00000374672	NM_004235.4	406	aCc/aTc	4/5	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.380557013042143	2		595	706	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007731	45007731	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058883-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	101	439	0	ENST00000558401.1:c.178del	p.Leu60Ter	p.L60*	ENST00000558401	NM_004048.2	60	Ctg/tg	2/4	1	2	FACETS	0.931	0.835	1	0.931	0.835	1	CLONAL	1	TRUE	1	0.380557013042143	2		439	570	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455144	50455144	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058925-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	39	510	0	ENST00000331340.3:c.691G>A	p.Gly231Ser	p.G231S	ENST00000331340	NM_006060.4	231	Ggc/Agc	6/8	1	2	FACETS	0.974	0.807	1	0.974	0.807	1	CLONAL	1	TRUE	1	0.17	2		510	471	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682400	52682400	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058925-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	21	392	1	ENST00000394830.3:c.773del	p.Asn258MetfsTer25	p.N258Mfs*25	ENST00000394830	NM_018313.4	258	aAt/at	8/30	1	2	FACETS	0.774	0.596	0.982	0.774	0.596	0.982	CLONAL	1	TRUE	1	0.17	2		393	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520008	NA	P-0058925-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	88	707	0	ENST00000269305.4:c.613T>G	p.Tyr205Asp	p.Y205D	ENST00000269305	NM_001126112.2	205	Tat/Gat	6/11	0.289166646483753	3	FACETS	1	0.975	1	0.704	0.623	0.791	CLONAL	1	TRUE	1	0.17	3		707	798	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146538	55146538	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058925-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	28	498	0	ENST00000257290.5:c.2212G>A	p.Asp738Asn	p.D738N	ENST00000257290	NM_006206.4	738	Gat/Aat	16/23	1	2	FACETS	0.631	0.503	0.778	0.631	0.503	0.778	SUBCLONAL	1	TRUE	1	0.17	2		498	522	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024426	31024426	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058925-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	35	649	0	ENST00000375687.4:c.3915del	p.Phe1305LeufsTer145	p.F1305Lfs*145	ENST00000375687	NM_015338.5	1304	cTt/ct	13/13	1	2	FACETS	0.631	0.515	0.761	0.631	0.515	0.761	SUBCLONAL	1	TRUE	1	0.17	2		649	653	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050680	30050680	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058925-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	59	521	0	ENST00000338641.4:c.482G>T	p.Gly161Val	p.G161V	ENST00000338641	NM_000268.3	161	gGa/gTa	5/16	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.17	2		521	629	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672384	86672384	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0058925-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	24	336	0	ENST00000274376.6:c.2184+2T>C		p.X728_splice	ENST00000274376	NM_002890.2	728			1	2	FACETS	0.911	0.715	1	0.911	0.715	1	CLONAL	1	TRUE	1	0.17	2		336	310	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026753	48026753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058925-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	46	627	0	ENST00000234420.5:c.1635del	p.Glu546ArgfsTer25	p.E546Rfs*25	ENST00000234420	NM_000179.2	544	gAa/ga	4/10	1	2	FACETS	0.815	0.685	0.959	0.815	0.685	0.959	CLONAL	1	TRUE	1	0.17	2		627	664	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798962	45798962	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058925-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	85	798	0	ENST00000450313.1:c.383A>T	p.Tyr128Phe	p.Y128F	ENST00000450313	NM_012222.2	128	tAt/tTt	4/16	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.17	2		798	838	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230486754	230486754	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058925-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	43	610	1	ENST00000391860.1:c.499A>G	p.Lys167Glu	p.K167E	ENST00000391860	NM_001258311.1	167	Aaa/Gaa	3/7	1	2	FACETS	0.889	0.743	1	0.889	0.743	1	CLONAL	1	TRUE	1	0.17	2		611	569	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136195	64136195	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1170953272	NA	P-0058925-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	49	748	0	ENST00000334205.4:c.1354C>T	p.Arg452Cys	p.R452C	ENST00000334205	NM_003942.2	452	Cgc/Tgc	12/17	1	2	FACETS	0.927	0.784	1	0.927	0.784	1	CLONAL	1	TRUE	1	0.17	2		748	622	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605185	46605185	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058925-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	32	612	0	ENST00000263734.3:c.1402A>G	p.Thr468Ala	p.T468A	ENST00000263734	NM_001430.4	468	Acc/Gcc	10/16	1	2	FACETS	0.609	0.493	0.741	0.609	0.493	0.741	SUBCLONAL	1	TRUE	1	0.17	2		612	618	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251137	251137	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058925-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	23	262	0	ENST00000264932.6:c.1582G>T	p.Val528Leu	p.V528L	ENST00000264932	NM_004168.2	528	Gtg/Ttg	12/15	0.244958536292021	1	FACETS	0.878	0.686	1	0.878	0.686	1	CLONAL	1	TRUE	0	0.17	1		262	282	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248087	110248087	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058925-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	36	523	0	ENST00000374672.4:c.1385A>T	p.Asp462Val	p.D462V	ENST00000374672	NM_004235.4	462	gAc/gTc	5/5	1	2	FACETS	0.759	0.623	0.912	0.759	0.623	0.912	CLONAL	1	TRUE	1	0.17	2		523	558	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410312	63410312	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058925-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	42	784	0	ENST00000330258.3:c.2855C>G	p.Pro952Arg	p.P952R	ENST00000330258	NM_152424.3	952	cCc/cGc	2/2	1	2	FACETS	0.691	0.575	0.82	0.691	0.575	0.82	SUBCLONAL	1	TRUE	1	0.17	2		784	715	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	188	550	2	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.897	0.833	0.964	0.897	0.833	0.964	CLONAL	1	TRUE	1	0.644569699266984	2		552	650	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	250	620	6	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.822	0.769	0.875	0.822	0.769	0.875	CLONAL	1	TRUE	1	0.644569699266984	2		626	944	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	733	666	1	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	1	0.996	1	1	0.998	1	CLONAL	2	TRUE	1	0.644569699266984	2		667	1040	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882019	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	641	645	1	ENST00000269305.4:c.455del	p.Pro152ArgfsTer18	p.P152Rfs*18	ENST00000269305	NM_001126112.2	152	cCg/cg	5/11	0.644569699266984	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	1	0.644569699266984	3		646	1190	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955165	17955165	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752820429	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	318	517	0	ENST00000458235.1:c.62C>T	p.Thr21Met	p.T21M	ENST00000458235	NM_000215.3	21	aCg/aTg	2/24	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.644569699266984	2		517	816	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129329	152129329	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	272	544	4	ENST00000206249.3:c.287del	p.Gly96ValfsTer13	p.G96Vfs*13	ENST00000206249	NM_000125.3	94	ctG/ct	1/8	1	2	FACETS	0.987	0.929	1	0.987	0.929	1	CLONAL	1	TRUE	1	0.644569699266984	2		548	855	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	336	600	2	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.644569699266984	2		602	1036	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	273	440	0	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.644569699266984	2		440	771	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44894229	44894232	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	AAGT	AAGT	-	novel	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	50	146	0	ENST00000377967.4:c.619+4_619+7del		p.X207_splice	ENST00000377967	NM_021140.2	207		7/29	0.604605867106095	2	FACETS	0.808	0.714	0.901			1	CLONAL	2	TRUE	NA	0.644569699266984	2		146	96	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370236	40370236	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs761761205	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	402	535	4	ENST00000293328.3:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000293328	NM_012448.3	368	Cag/ag	9/19	0.644569699266984	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.644569699266984	3		539	752	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255472	16255472	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	205	492	0	ENST00000375759.3:c.2737C>A	p.Leu913Met	p.L913M	ENST00000375759	NM_015001.2	913	Ctg/Atg	11/15	1	2	FACETS	0.997	0.93	1	0.997	0.93	1	CLONAL	1	TRUE	1	0.644569699266984	2		492	638	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182709	38182709	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370623345	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	317	512	0	ENST00000396334.3:c.862G>A	p.Asp288Asn	p.D288N	ENST00000396334	NM_002468.4	288	Gac/Aac	5/5	0.644569699266984	3	FACETS	1	0.99	1	0.601	0.567	0.635	CLONAL	1	TRUE	1	0.644569699266984	3		512	1082	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	124	493	7	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.903	0.824	0.985	0.903	0.824	0.985	CLONAL	1	TRUE	1	0.644569699266984	2		500	426	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266898	41266898	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1172941347	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	413	491	0	ENST00000349496.5:c.569G>A	p.Arg190His	p.R190H	ENST00000349496	NM_001904.3	190	cGt/cAt	5/15	0.644569699266984	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.644569699266984	3		491	825	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912664	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	205	459	1	ENST00000269305.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000269305	NM_001126112.2	337	cGc/cAc	10/11	0.644569699266984	3	FACETS	0.983	0.913	1	0.491	0.456	0.528	CLONAL	1	TRUE	1	0.644569699266984	3		460	856	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729394	41729394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	284	513	0	ENST00000242208.4:c.1135C>T	p.Arg379Trp	p.R379W	ENST00000242208	NM_002192.2	379	Cgg/Tgg	3/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.644569699266984	2		513	811	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797778	42797778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778127638	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	345	606	1	ENST00000575354.2:c.3830G>A	p.Arg1277His	p.R1277H	ENST00000575354	NM_015125.3	1277	cGc/cAc	16/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.644569699266984	2		607	958	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372071	55372071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	318	587	0	ENST00000297316.4:c.761C>T	p.Ala254Val	p.A254V	ENST00000297316	NM_022454.3	254	gCg/gTg	2/2	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.644569699266984	2		587	885	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432117	121432118	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776825	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	501	563	10	ENST00000257555.6:c.872dup	p.Gly292ArgfsTer25	p.G292Rfs*25	ENST00000257555		288	-/C	4/10	0.644569699266984	3	FACETS	0.86	0.825	0.895	0.86	0.825	0.895	CLONAL	2	TRUE	1	0.644569699266984	3		573	1195	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448601	89448601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775665893	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	427	474	3	ENST00000336596.2:c.1565G>A	p.Arg522His	p.R522H	ENST00000336596	NM_005233.5	522	cGc/cAc	7/17	0.644569699266984	3	FACETS	0.963	0.922	1	0.963	0.922	1	CLONAL	2	TRUE	1	0.644569699266984	3		477	910	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413710	138413710	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	448	407	0	ENST00000289153.2:c.1810del	p.Arg604GlyfsTer4	p.R604Gfs*4	ENST00000289153	NM_006219.2	604	Cgg/gg	12/22	0.644569699266984	3	FACETS	0.965	0.926	1	0.965	0.926	1	CLONAL	2	TRUE	1	0.644569699266984	3		407	952	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349640	89349641	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs772267579	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	125	716	12	ENST00000301030.4:c.3309dup	p.Asp1104ArgfsTer2	p.D1104Rfs*2	ENST00000301030	NM_001256183.1	1103	-/A	9/13	1	2	FACETS	0.817	0.744	0.892	0.817	0.744	0.892	CLONAL	1	TRUE	1	0.644569699266984	2		728	475	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733512	85733513	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs387906350	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	134	517	0	ENST00000370580.1:c.499dup	p.Ser167PhefsTer3	p.S167Ffs*3	ENST00000370580	NM_003921.4	167	tct/tTct	3/3	1	2	FACETS	0.875	0.801	0.953	0.875	0.801	0.953	CLONAL	1	TRUE	1	0.644569699266984	2		517	475	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405141	139405141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1448345366	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	329	599	0	ENST00000277541.6:c.2704C>T	p.Arg902Cys	p.R902C	ENST00000277541	NM_017617.3	902	Cgc/Tgc	17/34	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.644569699266984	2		599	914	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337683	73337684	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	80	380	0	ENST00000377767.4:c.2032dup	p.Ile678AsnfsTer3	p.I678Nfs*3	ENST00000377767	NM_014953.3	678	att/aAtt	16/21	1	2	FACETS	0.862	0.767	0.961	0.862	0.767	0.961	CLONAL	1	TRUE	1	0.644569699266984	2		380	288	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	172	405	16	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	1	2	FACETS	0.783	0.733	0.832	1	0.992	1	SUBCLONAL	2	TRUE	1	0.644569699266984	2		421	341	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095826	178095826	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1434375367	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	110	524	0	ENST00000397062.3:c.1505G>A	p.Arg502His	p.R502H	ENST00000397062	NM_006164.4	502	cGt/cAt	5/5	1	2	FACETS	0.76	0.687	0.836	0.76	0.687	0.836	SUBCLONAL	1	TRUE	1	0.644569699266984	2		524	449	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749148	43749148	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758857922	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	108	468	0	ENST00000382044.4:c.1658C>T	p.Thr553Met	p.T553M	ENST00000382044	NM_001141980.1	553	aCg/aTg	12/28	1	2	FACETS	0.857	0.776	0.942	0.857	0.776	0.942	CLONAL	1	TRUE	1	0.644569699266984	2		468	391	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300386	11300386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767105252	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	252	460	2	ENST00000361445.4:c.1760G>A	p.Arg587Gln	p.R587Q	ENST00000361445	NM_004958.3	587	cGa/cAa	11/58	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.644569699266984	2		462	691	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218098	36218098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	222	410	0	ENST00000222270.7:c.4045G>A	p.Asp1349Asn	p.D1349N	ENST00000222270	NM_014727.1	1349	Gac/Aac	15/37	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.644569699266984	2		410	629	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448479	49448479	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs941339684	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	299	541	0	ENST00000301067.7:c.232G>A	p.Gly78Arg	p.G78R	ENST00000301067	NM_003482.3	78	Ggg/Agg	3/54	0.644569699266984	3	FACETS	1	0.959	1	0.512	0.482	0.543	CLONAL	1	TRUE	1	0.644569699266984	3		541	1198	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218359	133218359	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	255	463	0	ENST00000320574.5:c.5252C>G	p.Ala1751Gly	p.A1751G	ENST00000320574	NM_006231.2	1751	gCc/gGc	39/49	0.644569699266984	3	FACETS	1	0.962	1	0.519	0.486	0.553	CLONAL	1	TRUE	1	0.644569699266984	3		463	1008	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026605	48026605	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779212	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	39	482	0	ENST00000234420.5:c.1483C>T	p.Arg495Ter	p.R495*	ENST00000234420	NM_000179.2	495	Cga/Tga	4/10	0.644569699266984	1	FACETS	0.216	0.179	0.257	0.216	0.179	0.257	SUBCLONAL	1	TRUE	0	0.644569699266984	1		482	380	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966987	25966987	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	313	559	2	ENST00000435504.4:c.2219C>T	p.Thr740Met	p.T740M	ENST00000435504		740	aCg/aTg	13/13	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.644569699266984	2		561	827	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807357	1807357	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	362	639	0	ENST00000260795.2:c.1610del	p.Asn537ThrfsTer89	p.N537Tfs*89	ENST00000260795		536	Aaa/aa	11/17	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.644569699266984	2		639	1001	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870236	44870236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768230343	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	74	124	0	ENST00000377967.4:c.415G>A	p.Val139Ile	p.V139I	ENST00000377967	NM_021140.2	139	Gtc/Atc	5/29	0.604605867106095	2	FACETS	1	0.957	1			1	CLONAL	2	TRUE	NA	0.644569699266984	2		124	108	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776550	9776550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	278	485	0	ENST00000377346.4:c.653C>T	p.Ala218Val	p.A218V	ENST00000377346	NM_005026.3	218	gCc/gTc	6/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.644569699266984	2		485	771	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200823	67200823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750710697	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	265	618	2	ENST00000312629.5:c.811G>A	p.Ala271Thr	p.A271T	ENST00000312629	NM_003952.2	271	Gca/Aca	10/15	1	2	FACETS	0.989	0.931	1	0.989	0.931	1	CLONAL	1	TRUE	1	0.644569699266984	2		620	831	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56402534	56402534	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	53	276	0	ENST00000348428.3:c.1576A>G	p.Thr526Ala	p.T526A	ENST00000348428	NM_006785.3	526	Act/Gct	13/17	1	2	FACETS	0.709	0.611	0.813	0.709	0.611	0.813	SUBCLONAL	1	TRUE	1	0.644569699266984	2		276	232	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10271075	10271075	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773301158	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	122	348	0	ENST00000340748.4:c.980C>T	p.Thr327Met	p.T327M	ENST00000340748		327	aCg/aTg	13/40	1	2	FACETS	0.981	0.895	1	0.981	0.895	1	CLONAL	1	TRUE	1	0.644569699266984	2		348	386	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791375	42791375	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	342	673	0	ENST00000575354.2:c.435G>T	p.Glu145Asp	p.E145D	ENST00000575354	NM_015125.3	145	gaG/gaT	3/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.644569699266984	2		673	1000	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797366	42797366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	362	583	0	ENST00000575354.2:c.3728C>T	p.Ala1243Val	p.A1243V	ENST00000575354	NM_015125.3	1243	gCc/gTc	15/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.644569699266984	2		583	1042	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169988314	169988314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1329586167	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	178	356	0	ENST00000295797.4:c.556G>A	p.Val186Ile	p.V186I	ENST00000295797	NM_002740.5	186	Gtc/Atc	6/18	0.644569699266984	3	FACETS	0.779	0.724	0.834	0.779	0.724	0.834	SUBCLONAL	2	TRUE	1	0.644569699266984	3		356	469	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845180	128845180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	83	538	0	ENST00000249373.3:c.674C>T	p.Ala225Val	p.A225V	ENST00000249373	NM_005631.4	225	gCt/gTt	3/12	1	2	FACETS	0.284	0.25	0.321	0.284	0.25	0.321	SUBCLONAL	1	TRUE	1	0.644569699266984	2		538	906	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194647	29194647	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	273	560	1	ENST00000240100.2:c.1081A>G	p.Thr361Ala	p.T361A	ENST00000240100	NM_001394.6	361	Acc/Gcc	4/4	0.644569699266984	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.644569699266984	1		561	499	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752732	128752734	+	inframe_deletion	In_Frame_Del	DEL	CTG	CTG	-	novel	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	278	503	0	ENST00000377970.2:c.896_898del	p.Ala299del	p.A299del	ENST00000377970	NM_002467.4	298	tCTGct/tct	3/3	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.644569699266984	2		503	782	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206613	27206613	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058939-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	131	393	0	ENST00000380036.4:c.2398A>G	p.Thr800Ala	p.T800A	ENST00000380036	NM_000459.3	800	Act/Gct	15/23	1	2	FACETS	0.952	0.871	1	0.952	0.871	1	CLONAL	1	TRUE	1	0.644569699266984	2		393	427	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528073	157528073	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs774896570	NA	P-0058980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	75	473	0	ENST00000346085.5:c.5798C>G	p.Thr1933Ser	p.T1933S	ENST00000346085	NM_020732.3	1933	aCc/aGc	20/20	1	2	FACETS	0.606	0.531	0.687	0.606	0.531	0.687	SUBCLONAL	1	TRUE	1	0.361368267027977	2		473	685	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929583	44929583	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	49	154	0	ENST00000377967.4:c.2683del	p.Glu895LysfsTer3	p.E895Kfs*3	ENST00000377967	NM_021140.2	895	Gaa/aa	17/29	1	1	FACETS	0.922	0.788	1	0.922	0.788	1	CLONAL	1	TRUE	0	0.361368267027977	1		154	241	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	361	843	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.289937020321891	3	FACETS	1	0.955	1			1	CLONAL	3	TRUE	NA	0.289937020321891	3		843	946	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343685	343685	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs750092964	NA	P-0059013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	123	612	0	ENST00000262320.3:c.1989G>T	p.Glu663Asp	p.E663D	ENST00000262320	NM_003502.3	663	gaG/gaT	8/11	0.289937020321891	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.289937020321891	1		612	593	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954299	48954299	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0059013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	54	183	0	ENST00000267163.4:c.1422-2A>G		p.X474_splice	ENST00000267163	NM_000321.2	474			0.27714471185325	2	FACETS	0.793	0.684	0.908	0.793	0.684	0.908	CLONAL	2	TRUE	0	0.289937020321891	2		183	235	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215923	36215923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	215	616	0	ENST00000222270.7:c.3463C>T	p.Pro1155Ser	p.P1155S	ENST00000222270	NM_014727.1	1155	Ccc/Tcc	10/37	0.230169291746825	4	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	2	0.289937020321891	4		616	929	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602942	55602942	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs374440815	NA	P-0059013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	66	464	0	ENST00000288135.5:c.2652G>T	p.Lys884Asn	p.K884N	ENST00000288135	NM_000222.2	884	aaG/aaT	19/21	1	2	FACETS	0.823	0.715	0.94	0.823	0.715	0.94	CLONAL	1	TRUE	1	0.289937020321891	2		464	553	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472661	88472662	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0059013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	80	557	1	ENST00000360948.2:c.1893_1894delinsAA	p.His632Asn	p.H632N	ENST00000360948	NM_001012338.2	631	gcCCat/gcAAat	16/19	0.289937020321891	3	FACETS	0.881	0.775	0.995	0.441	0.387	0.498	CLONAL	1	TRUE	1	0.289937020321891	3		558	717	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602445	10602445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1244523465	NA	P-0059013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	317	786	0	ENST00000171111.5:c.1133G>A	p.Gly378Asp	p.G378D	ENST00000171111	NM_203500.1	378	gGc/gAc	3/6	0.27714471185325	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.289937020321891	2		786	994	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956114	175956114	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	98	366	0	ENST00000367669.3:c.2098G>C	p.Val700Leu	p.V700L	ENST00000367669	NM_022457.5	700	Gtt/Ctt	18/20	0.26618265380301	5	FACETS	0.931	0.833	1	0.621	0.555	0.689	CLONAL	2	TRUE	2	0.289937020321891	5		366	521	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206665040	206665040	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1572266402	NA	P-0059013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	248	551	0	ENST00000367120.3:c.1793A>G	p.Gln598Arg	p.Q598R	ENST00000367120	NM_014002.3	598	cAg/cGg	18/22	0.26618265380301	5	FACETS	0.914	0.856	0.974	0.914	0.856	0.974	CLONAL	3	TRUE	2	0.289937020321891	5		551	895	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549764	226549764	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	185	419	0	ENST00000366794.5:c.2869G>T	p.Asp957Tyr	p.D957Y	ENST00000366794	NM_001618.3	957	Gat/Tat	22/23	0.26618265380301	5	FACETS	0.876	0.811	0.942	0.876	0.811	0.942	CLONAL	3	TRUE	2	0.289937020321891	5		419	697	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118925	115118929	+	frameshift_variant	Frame_Shift_Del	DEL	CTCAC	CTCAC	-	novel	NA	P-0059013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	88	383	0	ENST00000257566.3:c.412_416del	p.Val138MetfsTer6	p.V138Mfs*6	ENST00000257566	NM_016569.3	138	GTGAGa/a	2/8	0.289937020321891	3	FACETS	1	0.969	1	0.632	0.561	0.707	CLONAL	1	TRUE	1	0.289937020321891	3		383	550	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041732	42041733	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0059013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	166	609	0	ENST00000219905.7:c.5927_5928del	p.Asp1976AlafsTer4	p.D1976Afs*4	ENST00000219905	NM_001164273.1	1976	gAC/g	17/24	0.289937020321891	3	FACETS	0.91	0.838	0.985	0.91	0.838	0.985	CLONAL	2	TRUE	1	0.289937020321891	3		609	720	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30323859	30323859	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	90	233	0	ENST00000322652.5:c.1837G>T	p.Val613Leu	p.V613L	ENST00000322652	NM_015355.2	613	Gtg/Ttg	15/16	0.289937020321891	3	FACETS	0.971	0.869	1	0.971	0.869	1	CLONAL	2	TRUE	1	0.289937020321891	3		233	366	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435276	56435276	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	122	806	0	ENST00000407977.2:c.1861G>T	p.Glu621Ter	p.E621*	ENST00000407977		621	Gag/Tag	9/10	0.289937020321891	3	FACETS	0.937	0.846	1	0.469	0.423	0.517	CLONAL	1	TRUE	1	0.289937020321891	3		806	1028	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435295	56435295	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	135	775	0	ENST00000407977.2:c.1842G>T	p.Gln614His	p.Q614H	ENST00000407977		614	caG/caT	9/10	0.289937020321891	3	FACETS	1	0.947	1	0.532	0.482	0.583	CLONAL	1	TRUE	1	0.289937020321891	3		775	1003	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762867	40762867	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	197	608	0	ENST00000392038.2:c.141G>T	p.Gln47His	p.Q47H	ENST00000392038	NM_001626.4	47	caG/caT	3/14	0.230169291746825	4	FACETS	0.977	0.905	1	0.977	0.905	1	CLONAL	2	TRUE	2	0.289937020321891	4		608	897	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793087	42793087	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	112	608	0	ENST00000575354.2:c.979G>A	p.Asp327Asn	p.D327N	ENST00000575354	NM_015125.3	327	Gac/Aac	7/20	0.230169291746825	4	FACETS	1	0.951	1	0.548	0.492	0.607	CLONAL	1	TRUE	2	0.289937020321891	4		608	909	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424520	47424520	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	202	571	0	ENST00000404338.3:c.2588G>T	p.Arg863Leu	p.R863L	ENST00000404338	NM_004491.4	863	cGt/cTt	1/6	0.27714471185325	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	0	0.289937020321891	2		571	691	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160381	99160381	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	112	643	0	ENST00000074304.5:c.860G>T	p.Trp287Leu	p.W287L	ENST00000074304	NM_001134224.1	287	tGg/tTg	11/26	0.289937020321891	3	FACETS	1	0.938	1	0.53	0.476	0.587	CLONAL	1	TRUE	1	0.289937020321891	3		643	835	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790100	40790100	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	130	585	0	ENST00000373198.4:c.2631G>T	p.Met877Ile	p.M877I	ENST00000373198	NM_133170.3	877	atG/atT	18/32	0.289937020321891	3	FACETS	1	0.978	1	0.628	0.57	0.69	CLONAL	1	TRUE	1	0.289937020321891	3		585	817	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242742	66242742	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	86	538	0	ENST00000273854.3:c.1830C>G	p.Cys610Trp	p.C610W	ENST00000273854	NM_004439.5	610	tgC/tgG	9/18	1	2	FACETS	0.948	0.839	1	0.948	0.839	1	CLONAL	1	TRUE	1	0.289937020321891	2		538	626	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143326407	143326407	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	66	483	0	ENST00000262992.4:c.207C>A	p.His69Gln	p.H69Q	ENST00000262992	NM_001101669.1	69	caC/caA	4/24	1	2	FACETS	0.838	0.729	0.957	0.838	0.729	0.957	CLONAL	1	TRUE	1	0.289937020321891	2		483	543	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144359244	144359244	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1272716603	NA	P-0059013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	85	478	0	ENST00000262995.4:c.686A>T	p.Lys229Ile	p.K229I	ENST00000262995	NM_207123.2	229	aAa/aTa	4/11	1	2	FACETS	0.985	0.872	1	0.985	0.872	1	CLONAL	1	TRUE	1	0.289937020321891	2		478	595	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521072	187521072	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	80	588	0	ENST00000441802.2:c.12083G>C	p.Cys4028Ser	p.C4028S	ENST00000441802	NM_005245.3	4028	tGc/tCc	22/27	1	2	FACETS	0.795	0.7	0.898	0.795	0.7	0.898	SUBCLONAL	1	TRUE	1	0.289937020321891	2		588	694	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557340	187557340	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	106	544	0	ENST00000441802.2:c.4022T>C	p.Leu1341Pro	p.L1341P	ENST00000441802	NM_005245.3	1341	cTc/cCc	6/27	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.289937020321891	2		544	635	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629347	187629347	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	97	576	0	ENST00000441802.2:c.1635G>T	p.Leu545Phe	p.L545F	ENST00000441802	NM_005245.3	545	ttG/ttT	2/27	1	2	FACETS	0.952	0.849	1	0.952	0.849	1	CLONAL	1	TRUE	1	0.289937020321891	2		576	703	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31407035	31407035	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	167	420	0	ENST00000344624.3:c.3872G>T	p.Gly1291Val	p.G1291V	ENST00000344624		1291	gGc/gTc	31/33	0.276789186595828	5	FACETS	1	0.978	1	0.586	0.54	0.634	CLONAL	2	TRUE	1	0.289937020321891	5		420	705	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20486942	20486942	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	43	268	0	ENST00000346618.3:c.907G>T	p.Asp303Tyr	p.D303Y	ENST00000346618	NM_001949.4	303	Gat/Tat	5/7	1	2	FACETS	0.781	0.655	0.919	0.781	0.655	0.919	CLONAL	1	TRUE	1	0.289937020321891	2		268	380	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056026	26056026	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	137	543	0	ENST00000343677.2:c.631A>G	p.Lys211Glu	p.K211E	ENST00000343677	NM_005319.3	211	Aag/Gag	1/1	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.289937020321891	2		543	772	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124532364	124532364	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	83	322	0	ENST00000357628.3:c.80G>T	p.Gly27Val	p.G27V	ENST00000357628	NM_015450.2	27	gGt/gTt	6/19	0.289937020321891	3	FACETS	0.921	0.819	1	0.921	0.819	1	CLONAL	2	TRUE	1	0.289937020321891	3		322	356	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486045	8486045	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	185	638	0	ENST00000356435.5:c.2772C>A	p.Asn924Lys	p.N924K	ENST00000356435		924	aaC/aaA	17/35	0.27714471185325	2	FACETS	0.926	0.858	0.996	0.926	0.858	0.996	CLONAL	2	TRUE	0	0.289937020321891	2		638	689	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518069	8518069	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	150	451	0	ENST00000356435.5:c.1322C>A	p.Pro441His	p.P441H	ENST00000356435		441	cCt/cAt	10/35	0.27714471185325	2	FACETS	0.887	0.815	0.963	0.887	0.815	0.963	CLONAL	2	TRUE	0	0.289937020321891	2		451	583	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247529	53247529	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059013-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	104	282	0	ENST00000375401.3:c.280G>C	p.Glu94Gln	p.E94Q	ENST00000375401	NM_004187.3	94	Gaa/Caa	3/26	1	1	FACETS	0.876	0.793	0.963	1	0.987	1	CLONAL	2	TRUE	0	0.289937020321891	1		282	350	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226595569	226595569	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059067-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	26	315	0	ENST00000366794.5:c.62del	p.Cys21SerfsTer74	p.C21Sfs*74	ENST00000366794	NM_001618.3	21	tGc/tc	1/23	0.546953964296784	5	FACETS	0.36	0.285	0.447	0.12	0.095	0.149	SUBCLONAL	1	TRUE	2	0.597813054625349	5		315	458	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443864	52443864	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059238-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	211	610	0	ENST00000460680.1:c.31G>T	p.Asp11Tyr	p.D11Y	ENST00000460680	NM_004656.3	11	Gac/Tac	1/17	0.494374353378289	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.494374353378289	2		610	413	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0059256-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	3928	578	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.53736073217371	41	FACETS	0.988	0.983	0.994	1	0.998	1	CLONAL	40	TRUE	2	0.53736073217371	41		578	4245	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126730	5126730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1437629509	NA	P-0059256-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	57	360	0	ENST00000381652.3:c.3338G>A	p.Arg1113His	p.R1113H	ENST00000381652	NM_004972.3	1113	cGc/cAc	25/25	0.520688657869988	3	FACETS	0.863	0.745	0.989	0.288	0.248	0.33	CLONAL	1	TRUE	0	0.53736073217371	3		360	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0059256-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	406	666	3	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.5233446684026	4	FACETS	0.962	0.929	0.994	0.962	0.929	0.994	CLONAL	4	TRUE	0	0.53736073217371	4		669	604	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268969	55268969	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059256-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	5128	563	41	ENST00000275493.2:c.3035A>T	p.Asp1012Val	p.D1012V	ENST00000275493	NM_005228.3	1012	gAt/gTt	25/28	0.53736073217371	41	FACETS	0.994	0.989	0.999	1	0.999	1	CLONAL	40	TRUE	2	0.53736073217371	41		604	5510	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475456	12475456	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059256-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	87	460	2	ENST00000287820.6:c.1330G>T	p.Ala444Ser	p.A444S	ENST00000287820	NM_015869.4	444	Gcc/Tcc	7/7	1	2	FACETS	0.955	0.853	1	0.955	0.853	1	CLONAL	1	TRUE	1	0.53736073217371	2		462	339	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778149	27778149	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059256-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	163	757	1	ENST00000369163.2:c.298T>A	p.Tyr100Asn	p.Y100N	ENST00000369163	NM_003536.2	100	Tac/Aac	1/1	0.536672704989634	4	FACETS	0.977	0.896	1	0.326	0.298	0.354	CLONAL	1	TRUE	1	0.53736073217371	4		758	955	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649054	86649054	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0059256-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	61	302	0	ENST00000274376.6:c.1332+2T>G		p.X444_splice	ENST00000274376	NM_002890.2	444			0.536672704989634	3	FACETS	1	0.898	1	0.518	0.451	0.59	CLONAL	1	TRUE	1	0.53736073217371	3		302	278	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059470-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	32	377	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.887	0.719	1	0.887	0.719	1	CLONAL	1	TRUE	1	0.16	2		377	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0059470-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	56	453	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.16	2		453	659	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842732	68842732	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059500-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	187	300	0	ENST00000261769.5:c.668A>C	p.Glu223Ala	p.E223A	ENST00000261769	NM_004360.3	223	gAa/gCa	5/16	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.339553629652126	2		300	746	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579310	7579310	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1555526469	NA	P-0059500-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	29	366	0	ENST00000269305.4:c.375+2T>C		p.X125_splice	ENST00000269305	NM_001126112.2	125			1	2	FACETS	0.303	0.243	0.373	0.303	0.243	0.373	SUBCLONAL	1	TRUE	1	0.339553629652126	2		366	563	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007156	62007156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148032848	NA	P-0059500-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	48	361	0	ENST00000392795.3:c.526G>A	p.Val176Met	p.V176M	ENST00000392795	NM_001039933.1	176	Gtg/Atg	4/6	1	2	FACETS	0.397	0.335	0.466	0.397	0.335	0.466	SUBCLONAL	1	TRUE	1	0.339553629652126	2		361	712	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513321	44513321	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059500-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	44	438	0	ENST00000291552.4:c.614G>T	p.Arg205Leu	p.R205L	ENST00000291552	NM_006758.2	205	cGg/cTg	8/8	1	2	FACETS	0.343	0.286	0.406	0.343	0.286	0.406	SUBCLONAL	1	TRUE	1	0.339553629652126	2		438	756	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578184	7578184	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567551073	NA	P-0059521-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	343	616	0	ENST00000269305.4:c.665del	p.Pro222ArgfsTer25	p.P222Rfs*25	ENST00000269305	NM_001126112.2	222	cCg/cg	6/11	0.230243738812768	5	FACETS	1	0.978	1	0.838	0.797	0.879	CLONAL	4	TRUE	0	0.291059462985617	5		616	808	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829806	76829806	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059521-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	41	354	0	ENST00000373344.5:c.6235C>T	p.Arg2079Ter	p.R2079*	ENST00000373344	NM_000489.3	2079	Cga/Tga	28/35	0.40392648725294	1	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	0	0.291059462985617	1		354	234	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218486	1218486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1316669124	NA	P-0059521-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	53	453	0	ENST00000326873.7:c.361G>A	p.Glu121Lys	p.E121K	ENST00000326873	NM_000455.4	121	Gag/Aag	2/10	0.40392648725294	3	FACETS	0.724	0.617	0.842	0.362	0.308	0.421	SUBCLONAL	1	TRUE	1	0.291059462985617	3		453	576	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955490	48955494	+	frameshift_variant	Frame_Shift_Del	DEL	ATCAA	ATCAA	-	novel	NA	P-0059521-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	166	359	0	ENST00000267163.4:c.1607_1611del	p.Ile536SerfsTer17	p.I536Sfs*17	ENST00000267163	NM_000321.2	536	ATCAAa/a	17/27	0.295287262408151	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	3	TRUE	0	0.291059462985617	3		359	425	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262355	39262355	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0059521-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	62	367	0	ENST00000402219.2:c.1072A>T	p.Lys358Ter	p.K358*	ENST00000402219	NM_005633.3	358	Aag/Tag	8/23	0.109504231740212	6	FACETS	0.784	0.679	0.897	0.523	0.453	0.598	INDETERMINATE	2	TRUE	3	0.291059462985617	6		367	430	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962600	38962600	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059521-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	684	345	0	ENST00000357387.3:c.1655G>T	p.Gly552Val	p.G552V	ENST00000357387	NM_152756.3	552	gGg/gTg	18/38	0.291059462985617	20	FACETS	1	0.985	1	1	0.985	1	CLONAL	18	TRUE	2	0.291059462985617	20		345	934	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059525-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	22	321	0				ENST00000310581	NM_198253.2	-/1132			0.232390180428578	1	FACETS	0.565	0.438	0.712	0.565	0.438	0.712	SUBCLONAL	1	FALSE	0	0.232390180428578	1		321	296	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059525-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	15	545	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	0.123932393612969	4	FACETS	0.441	0.321	0.585	0.22	0.16	0.293	INDETERMINATE	1	FALSE	2	0.232390180428578	4		545	361	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534287	534288	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0059525-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	20	720	0	ENST00000451590.1:c.35_36delinsTT	p.Gly12Val	p.G12V	ENST00000451590	NM_001130442.1	12	gGC/gTT	2/5	0.197829241149878	0	FACETS	0.212	0.161	0.272			1	SUBCLONAL	1	FALSE	0	0.232390180428578	0		720	624	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707902	43707903	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0059525-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	39	731	0	ENST00000382044.4:c.4978_4979del	p.Glu1660LysfsTer19	p.E1660Kfs*19	ENST00000382044	NM_001141980.1	1660	GAa/a	23/28	1	2	FACETS	0.543	0.449	0.648	0.543	0.449	0.648	SUBCLONAL	1	FALSE	1	0.232390180428578	2		731	618	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727505	88727505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059537-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	61	545	0	ENST00000360948.2:c.274C>T	p.His92Tyr	p.H92Y	ENST00000360948	NM_001012338.2	92	Cac/Tac	3/19	1	2	FACETS	0.827	0.713	0.951	0.827	0.713	0.951	CLONAL	1	TRUE	1	0.229058715405	2		545	644	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911247	32911247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs431825298	NA	P-0059537-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	83	481	0	ENST00000380152.3:c.2755G>A	p.Glu919Lys	p.E919K	ENST00000380152		919	Gaa/Aaa	11/27	0.229058715405	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.229058715405	1		481	475	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10785066	10785066	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059537-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	61	401	0	ENST00000361367.2:c.938C>G	p.Ala313Gly	p.A313G	ENST00000361367	NM_014633.3	313	gCt/gGt	8/25	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.229058715405	2		401	487	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120890	115120897	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCTG	GGCGGCTG	-	novel	NA	P-0059537-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	61	571	1	ENST00000257566.3:c.109_116del	p.Gln37ValfsTer71	p.Q37Vfs*71	ENST00000257566	NM_016569.3	37	CAGCCGCCg/g	1/8	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.229058715405	2		572	481	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348701	11348701	+	stop_lost	Nonstop_Mutation	SNP	C	C	A	novel	NA	P-0059537-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	50	472	0	ENST00000332029.2:c.635G>T	p.Ter212LeuextTer60	p.*212Lext*60	ENST00000332029	NM_003745.1	212	tGa/tTa	2/2	1	2	FACETS	0.886	0.752	1	0.886	0.752	1	CLONAL	1	TRUE	1	0.229058715405	2		472	493	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857377	68857378	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0059537-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	70	467	0	ENST00000261769.5:c.2013_2014del	p.Asp671GlufsTer4	p.D671Efs*4	ENST00000261769	NM_004360.3	671	gAT/g	13/16	0.229058715405	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	0	0.229058715405	1		467	515	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0059594-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	122	382	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.789	0.72	0.861	0.789	0.72	0.861	SUBCLONAL	1	TRUE	1	0.76704460781523	2		382	403	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254962	16254962	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059594-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	317	613	0	ENST00000375759.3:c.2227C>T	p.Gln743Ter	p.Q743*	ENST00000375759	NM_015001.2	743	Cag/Tag	11/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.76704460781523	2		613	800	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094488	27094488	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059594-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	294	597	0	ENST00000324856.7:c.3196C>T	p.Gln1066Ter	p.Q1066*	ENST00000324856	NM_006015.4	1066	Cag/Tag	11/20	0.76704460781523	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.76704460781523	1		597	456	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255515	16255515	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1271316907	NA	P-0059594-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	277	605	0	ENST00000375759.3:c.2780C>A	p.Ser927Tyr	p.S927Y	ENST00000375759	NM_015001.2	927	tCt/tAt	11/15	1	2	FACETS	0.988	0.933	1	0.988	0.933	1	CLONAL	1	TRUE	1	0.76704460781523	2		605	731	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265255	16265255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749521610	NA	P-0059594-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	264	561	0	ENST00000375759.3:c.10747C>T	p.Arg3583Cys	p.R3583C	ENST00000375759	NM_015001.2	3583	Cgt/Tgt	14/15	1	2	FACETS	0.99	0.934	1	0.99	0.934	1	CLONAL	1	TRUE	1	0.76704460781523	2		561	695	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739044	46739044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059594-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	248	483	0	ENST00000371975.4:c.1393G>A	p.Asp465Asn	p.D465N	ENST00000371975	NM_003579.3	465	Gat/Aat	13/18	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.76704460781523	2		483	597	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123888159	123888159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059594-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	209	390	0	ENST00000330479.4:c.637G>A	p.Gly213Arg	p.G213R	ENST00000330479	NM_020382.3	213	Ggg/Agg	6/9	1	2	FACETS	0.89	0.832	0.95	0.89	0.832	0.95	CLONAL	1	TRUE	1	0.76704460781523	2		390	612	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169350	99169350	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059594-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	321	569	0	ENST00000074304.5:c.1280A>T	p.Tyr427Phe	p.Y427F	ENST00000074304	NM_001134224.1	427	tAc/tTc	15/26	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.76704460781523	2		569	772	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138376638	138376638	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059594-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	159	319	1	ENST00000289153.2:c.2836A>G	p.Lys946Glu	p.K946E	ENST00000289153	NM_006219.2	946	Aaa/Gaa	20/22	1	2	FACETS	0.978	0.906	1	0.978	0.906	1	CLONAL	1	TRUE	1	0.76704460781523	2		320	424	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665461	176665461	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059594-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	314	581	0	ENST00000439151.2:c.4145C>G	p.Ser1382Cys	p.S1382C	ENST00000439151	NM_022455.4	1382	tCt/tGt	7/23	1	2	FACETS	0.974	0.922	1	0.974	0.922	1	CLONAL	1	TRUE	1	0.76704460781523	2		581	841	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469979	157469979	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554226097	NA	P-0059594-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	455	725	0	ENST00000346085.5:c.2773C>T	p.Gln925Ter	p.Q925*	ENST00000346085	NM_020732.3	925	Cag/Tag	9/20	0.373968687016979	3	FACETS	0.839	0.805	0.874	0.839	0.805	0.874	INDETERMINATE	2	TRUE	1	0.76704460781523	3		725	978	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913315	NA	P-0059662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	191	621	1	ENST00000326873.7:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000326873	NM_000455.4	194	Gac/Tac	4/10	0.285853929666771	2	FACETS	0.892	0.827	0.959	0.892	0.827	0.959	CLONAL	2	TRUE	0	0.285853929666771	2		622	749	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916932	178916932	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	149	456	0	ENST00000263967.3:c.319A>T	p.Asn107Tyr	p.N107Y	ENST00000263967	NM_006218.2	107	Aac/Tac	2/21	0.271511316482123	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.285853929666771	3		456	538	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50741616	50741616	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	46	291	0	ENST00000307179.4:c.269T>C	p.Leu90Pro	p.L90P	ENST00000307179		90	cTt/cCt	4/20	0.285853929666771	2	FACETS	0.912	0.77	1	0.456	0.385	0.534	CLONAL	1	TRUE	0	0.285853929666771	2		291	353	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817781	3817781	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	93	468	0	ENST00000262367.5:c.3190G>C	p.Glu1064Gln	p.E1064Q	ENST00000262367	NM_004380.2	1064	Gag/Cag	16/31	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.285853929666771	2		468	642	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554109	63554109	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs756185275	NA	P-0059662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	118	596	0	ENST00000307078.5:c.630G>C	p.Met210Ile	p.M210I	ENST00000307078	NM_004655.3	210	atG/atC	2/11	0.285853929666771	2	FACETS	1	0.918	1	0.51	0.459	0.563	CLONAL	1	TRUE	0	0.285853929666771	2		596	810	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024589	11024589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201607510	NA	P-0059662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	236	534	0	ENST00000327064.4:c.706G>A	p.Val236Met	p.V236M	ENST00000327064	NM_199141.1	236	Gtg/Atg	6/16	0.285853929666771	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.285853929666771	2		534	719	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945147	38945147	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	62	399	0	ENST00000357387.3:c.4657G>C	p.Asp1553His	p.D1553H	ENST00000357387	NM_152756.3	1553	Gat/Cat	35/38	1	2	FACETS	0.882	0.763	1	0.882	0.763	1	CLONAL	1	TRUE	1	0.285853929666771	2		399	492	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569293	67569293	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	76	454	0	ENST00000274335.5:c.410A>G	p.Glu137Gly	p.E137G	ENST00000274335		137	gAa/gGa	2/15	1	2	FACETS	0.869	0.763	0.983	0.869	0.763	0.983	CLONAL	1	TRUE	1	0.285853929666771	2		454	612	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6045629	6045629	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	24	136	0	ENST00000265849.7:c.57T>A	p.Asp19Glu	p.D19E	ENST00000265849	NM_000535.5	19	gaT/gaA	2/15	1	2	FACETS	0.971	0.767	1	0.971	0.767	1	CLONAL	1	TRUE	1	0.285853929666771	2		136	173	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466578	120466578	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs893877808	NA	P-0059685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	64	493	0	ENST00000256646.2:c.4541A>G	p.Lys1514Arg	p.K1514R	ENST00000256646	NM_024408.3	1514	aAa/aGa	26/34	1	2	FACETS	0.52	0.451	0.594	0.52	0.451	0.594	SUBCLONAL	1	TRUE	1	0.544700220372019	2		493	452	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508373	106508373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	95	541	0	ENST00000359195.3:c.367C>T	p.Arg123Cys	p.R123C	ENST00000359195	NM_002649.2	123	Cgc/Tgc	2/11	0.211379889056521	4	FACETS	0.931	0.83	1	0.465	0.415	0.519	INDETERMINATE	1	TRUE	2	0.544700220372019	4		541	579	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288370	15288370	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	96	571	0	ENST00000263388.2:c.4369G>C	p.Asp1457His	p.D1457H	ENST00000263388	NM_000435.2	1457	Gac/Cac	24/33	0.339473845413842	3	FACETS	0.902	0.807	1			1	CLONAL	1	TRUE	NA	0.544700220372019	3		571	497	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059781-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	124	321	0				ENST00000310581	NM_198253.2	-/1132			0.371125545827537	5	FACETS	1	0.978	1	0.82	0.748	0.894	CLONAL	2	TRUE	2	0.371125545827537	5		321	423	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955538	48955538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913303	NA	P-0059781-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	142	233	0	ENST00000267163.4:c.1654C>T	p.Arg552Ter	p.R552*	ENST00000267163	NM_000321.2	552	Cga/Tga	17/27	0.218031630282154	4	FACETS	0.961	0.88	1	0.961	0.88	1	INDETERMINATE	2	TRUE	2	0.371125545827537	4		233	546	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456898	149456898	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059781-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	301	696	0	ENST00000286301.3:c.830C>G	p.Ser277Cys	p.S277C	ENST00000286301	NM_005211.3	277	tCc/tGc	6/22	0.371125545827537	3	FACETS	1	0.983	1	0.73	0.69	0.771	CLONAL	2	TRUE	0	0.371125545827537	3		696	878	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463566	25463566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059781-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	126	575	0	ENST00000264709.3:c.2116G>A	p.Gly706Arg	p.G706R	ENST00000264709	NM_175629.2	706	Ggg/Agg	18/23	0.371125545827537	2	FACETS	1	0.965	1	0.564	0.512	0.618	CLONAL	1	TRUE	0	0.371125545827537	2		575	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0059781-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	291	516	0	ENST00000269305.4:c.375+1G>T		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.371125545827537	3	FACETS	0.976	0.926	1	0.976	0.926	1	CLONAL	3	TRUE	0	0.371125545827537	3		516	635	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929191	44929191	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs772552174	NA	P-0059781-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	180	257	1	ENST00000377967.4:c.2291A>G	p.His764Arg	p.H764R	ENST00000377967	NM_021140.2	764	cAt/cGt	17/29	0.264505783658699	2	FACETS	0.977	0.918	1			1	CLONAL	3	TRUE	NA	0.371125545827537	2		258	331	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844408	156844408	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059781-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1361	324	934	0	ENST00000524377.1:c.1241C>A	p.Thr414Lys	p.T414K	ENST00000524377	NM_002529.3	414	aCa/aAa	10/17	0.371125545827537	7	FACETS	0.999	0.94	1	0.4	0.376	0.424	CLONAL	2	TRUE	2	0.371125545827537	7		934	1685	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953742	48953742	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059781-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	121	264	0	ENST00000267163.4:c.1345G>C	p.Gly449Arg	p.G449R	ENST00000267163	NM_000321.2	449	Gga/Cga	14/27	0.218031630282154	4	FACETS	0.88	0.799	0.964	0.88	0.799	0.964	INDETERMINATE	2	TRUE	2	0.371125545827537	4		264	508	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484844	57484844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059781-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	41	667	0	ENST00000371085.3:c.824G>A	p.Ser275Asn	p.S275N	ENST00000371085	NM_000516.4	275	aGc/aAc	10/13	0.249303422935929	3	FACETS	0.36	0.299	0.428	0.18	0.149	0.214	SUBCLONAL	1	TRUE	1	0.371125545827537	3		667	728	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200151	128200151	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059781-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	82	529	0	ENST00000341105.2:c.1154C>A	p.Pro385Gln	p.P385Q	ENST00000341105	NM_032638.4	385	cCa/cAa	6/6	1	2	FACETS	0.863	0.763	0.97	0.863	0.763	0.97	CLONAL	1	TRUE	1	0.371125545827537	2		529	512	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209331	98209331	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059781-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	105	553	0	ENST00000331920.6:c.4207G>T	p.Glu1403Ter	p.E1403*	ENST00000331920	NM_000264.3	1403	Gag/Tag	23/24	0.371125545827537	4	FACETS	0.987	0.884	1	0.329	0.294	0.366	CLONAL	1	TRUE	1	0.371125545827537	4		553	786	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456495	189456495	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	GT	novel	NA	P-0059791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	201	578	0	ENST00000264731.3:c.256delinsGT	p.Thr86ValfsTer5	p.T86Vfs*5	ENST00000264731	NM_003722.4	86	Aca/GTca	3/14	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.569426018718993	2		578	678	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059807-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	33	321	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.839	0.686	1	0.839	0.686	1	CLONAL	1	TRUE	1	0.273073300866232	2		321	288	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0059807-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	134	665	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.260332816975823	2	FACETS	0.96	0.878	1	0.96	0.878	1	CLONAL	2	TRUE	0	0.273073300866232	2		666	511	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510219	187510219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276553545	NA	P-0059807-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	72	451	0	ENST00000441802.2:c.13294G>A	p.Glu4432Lys	p.E4432K	ENST00000441802	NM_005245.3	4432	Gaa/Aaa	27/27	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.273073300866232	2		451	480	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591145	67591145	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059807-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	55	415	0	ENST00000274335.5:c.1738T>G	p.Tyr580Asp	p.Y580D	ENST00000274335		580	Tac/Gac	12/15	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.273073300866232	2		415	302	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033826	49033827	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0059807-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	31	289	0	ENST00000267163.4:c.1964_1965del	p.Tyr655SerfsTer12	p.Y655Sfs*12	ENST00000267163	NM_000321.2	655	TAt/t	20/27	0.273073300866232	1	FACETS	0.734	0.596	0.889	0.734	0.596	0.889	SUBCLONAL	1	TRUE	0	0.273073300866232	1		289	267	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0059822-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	686	608	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.87128050337122	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.88715998685373	3		610	742	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50490725	50490725	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059822-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	155	421	0	ENST00000394963.4:c.1362C>G	p.Asp454Glu	p.D454E	ENST00000394963	NM_003076.4	454	gaC/gaG	11/13	0.464662725905383	1	FACETS	0.403	0.372	0.436	0.403	0.372	0.436	INDETERMINATE	1	TRUE	0	0.88715998685373	1		421	482	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504609	103504609	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059822-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	72	386	0	ENST00000355739.4:c.230A>G	p.Asp77Gly	p.D77G	ENST00000355739	NM_000123.3	77	gAt/gGt	2/15	0.702319211146457	3	FACETS	0.329	0.287	0.374	0.164	0.143	0.187	SUBCLONAL	1	TRUE	1	0.88715998685373	3		386	713	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007680	45007680	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059822-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	45	529	0	ENST00000558401.1:c.127C>G	p.Leu43Val	p.L43V	ENST00000558401	NM_004048.2	43	Ctg/Gtg	2/4	1	2	FACETS	0.173	0.145	0.205	0.173	0.145	0.205	SUBCLONAL	1	TRUE	1	0.88715998685373	2		529	585	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023806	31023835	+	inframe_deletion	In_Frame_Del	DEL	TGGGTCCTCAGTGGAGGCCACTAACCCACT	TGGGTCCTCAGTGGAGGCCACTAACCCACT	-	novel	NA	P-0059822-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	390	700	3	ENST00000375687.4:c.3293_3322del	p.Gly1098_Leu1107del	p.G1098_L1107del	ENST00000375687	NM_015338.5	1097	ccTGGGTCCTCAGTGGAGGCCACTAACCCACTt/cct	13/13	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.88715998685373	2		703	771	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24134061	24134103	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAACAAAACCTAACACTAAGGGTGCGTCTTCACGAGGGTTTGT	AAACAAAACCTAACACTAAGGGTGCGTCTTCACGAGGGTTTGT	-	novel	NA	P-0059822-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	189	558	0	ENST00000263121.7:c.216_232+26del		p.X72_splice	ENST00000263121	NM_003073.3	72		2/9	1	2	FACETS	0.789	0.735	0.845	0.789	0.735	0.845	SUBCLONAL	1	TRUE	1	0.88715998685373	2		558	540	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169061	32169061	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059822-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	334	790	2	ENST00000375023.3:c.3972G>C	p.Arg1324Ser	p.R1324S	ENST00000375023	NM_004557.3	1324	agG/agC	22/30	0.88715998685373	2	FACETS	1	0.985	1	0.539	0.514	0.565	CLONAL	1	TRUE	0	0.88715998685373	2		792	698	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696432	47696432	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519968	NA	P-0059853-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	126	406	0	ENST00000347630.2:c.391T>G	p.Trp131Gly	p.W131G	ENST00000347630	NM_001007230.1	131	Tgg/Ggg	6/11	1	2	FACETS	0.91	0.826	0.999	0.91	0.826	0.999	CLONAL	1	TRUE	1	0.41141106270247	2		406	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578412	7578412	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519747	NA	P-0059853-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	167	620	0	ENST00000269305.4:c.518T>C	p.Val173Ala	p.V173A	ENST00000269305	NM_001126112.2	173	gTg/gCg	5/11	0.41141106270247	1	FACETS	0.976	0.9	1	0.976	0.9	1	CLONAL	1	TRUE	0	0.41141106270247	1		620	661	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211151	2211151	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777324633	NA	P-0059853-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	151	593	0	ENST00000398665.3:c.1405C>T	p.Arg469Trp	p.R469W	ENST00000398665	NM_032482.2	469	Cgg/Tgg	15/28	0.251834973843213	1	FACETS	0.832	0.762	0.904	0.832	0.762	0.904	CLONAL	1	TRUE	0	0.41141106270247	1		593	701	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974792	21974792	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs141798398	NA	P-0059857-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	134	536	0	ENST00000304494.5:c.35C>A	p.Ser12Ter	p.S12*	ENST00000304494	NM_000077.4	12	tCg/tAg	1/3	0.242407798081017	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.242407798081017	1		536	727	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587781845	NA	P-0059857-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	130	596	0	ENST00000269305.4:c.511G>T	p.Glu171Ter	p.E171*	ENST00000269305	NM_001126112.2	171	Gag/Tag	5/11	0.242407798081017	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.242407798081017	1		596	808	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527318	137527318	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059857-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	62	379	0	ENST00000367739.4:c.328G>T	p.Glu110Ter	p.E110*	ENST00000367739	NM_000416.2	110	Gaa/Taa	3/7	0.242407798081017	1	FACETS	0.756	0.653	0.867	0.756	0.653	0.867	SUBCLONAL	1	TRUE	0	0.242407798081017	1		379	595	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813715	50813715	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059857-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	90	474	0	ENST00000398568.2:c.1269G>T	p.Met423Ile	p.M423I	ENST00000398568	NM_001042412.1	423	atG/atT	8/18	0.242407798081017	1	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	0	0.242407798081017	1		474	637	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117581	4117581	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059857-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	64	309	0	ENST00000262948.5:c.139G>T	p.Asp47Tyr	p.D47Y	ENST00000262948	NM_030662.3	47	Gac/Tac	2/11	0.242407798081017	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.242407798081017	1		309	425	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098452	11098452	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059857-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	72	484	0	ENST00000358026.2:c.972del	p.Val325Ter	p.V325*	ENST00000358026	NM_001128849.1	324	Ccc/cc	6/36	0.242407798081017	1	FACETS	0.834	0.729	0.947	0.834	0.729	0.947	CLONAL	1	TRUE	0	0.242407798081017	1		484	626	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392189	81392189	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0059857-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	58	232	0	ENST00000222390.5:c.89-1G>T		p.X30_splice	ENST00000222390	NM_000601.4	30			0.242407798081017	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.242407798081017	1		232	389	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523568	148523568	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059857-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	68	386	0	ENST00000320356.2:c.885C>A	p.Phe295Leu	p.F295L	ENST00000320356	NM_004456.4	295	ttC/ttA	8/20	0.242407798081017	3	FACETS	0.894	0.777	1	0.447	0.388	0.51	CLONAL	1	TRUE	1	0.242407798081017	3		386	704	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549589	5549589	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059857-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	96	458	0	ENST00000397747.3:c.616A>G	p.Ser206Gly	p.S206G	ENST00000397747	NM_025239.3	206	Agc/Ggc	4/7	0.242407798081017	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.242407798081017	1		458	616	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169551	27169551	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059857-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	112	500	0	ENST00000380036.4:c.552G>T	p.Gln184His	p.Q184H	ENST00000380036	NM_000459.3	184	caG/caT	4/23	0.242407798081017	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.242407798081017	1		500	683	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98011503	98011503	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059857-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	80	455	0	ENST00000289081.3:c.71A>T	p.Gln24Leu	p.Q24L	ENST00000289081	NM_000136.2	24	cAg/cTg	2/15	1	2	FACETS	0.979	0.862	1	0.979	0.862	1	CLONAL	1	TRUE	1	0.242407798081017	2		455	674	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059973-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	50	321	0				ENST00000310581	NM_198253.2	-/1132			0.142701843298696	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.763340296121501	0		321	168	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0059973-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	293	504	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	0.359900252139655	3	FACETS	0.79	0.749	0.832	0.79	0.749	0.832	INDETERMINATE	2	TRUE	1	0.763340296121501	3		504	671	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855984	68855984	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121964877	NA	P-0059973-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	207	528	0	ENST00000261769.5:c.1792C>T	p.Arg598Ter	p.R598*	ENST00000261769	NM_004360.3	598	Cga/Tga	12/16	0.763340296121501	1	FACETS	0.975	0.924	1	0.975	0.924	1	CLONAL	1	TRUE	0	0.763340296121501	1		528	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0059973-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	43	640	1	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	0.763340296121501	1	FACETS	0.203	0.17	0.239	0.203	0.17	0.239	SUBCLONAL	1	TRUE	0	0.763340296121501	1		641	343	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150436	157150436	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554256703	NA	P-0059973-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	216	571	0	ENST00000346085.5:c.1618C>T	p.Gln540Ter	p.Q540*	ENST00000346085	NM_020732.3	540	Cag/Tag	2/20	1	2	FACETS	0.935	0.875	0.997	0.935	0.875	0.997	CLONAL	1	TRUE	1	0.763340296121501	2		571	605	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967042	25967042	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059973-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	148	595	0	ENST00000435504.4:c.2164G>A	p.Glu722Lys	p.E722K	ENST00000435504		722	Gaa/Aaa	13/13	1	2	FACETS	0.898	0.828	0.969	0.898	0.828	0.969	CLONAL	1	TRUE	1	0.763340296121501	2		595	432	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100198	27100198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059973-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	228	630	0	ENST00000324856.7:c.3994C>T	p.Gln1332Ter	p.Q1332*	ENST00000324856	NM_006015.4	1332	Cag/Tag	16/20	1	2	FACETS	0.944	0.885	1	0.944	0.885	1	CLONAL	1	TRUE	1	0.763340296121501	2		630	633	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248409	59248409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184098204	NA	P-0059973-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	184	649	0	ENST00000371222.2:c.334G>A	p.Glu112Lys	p.E112K	ENST00000371222	NM_002228.3	112	Gag/Aag	1/1	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.763340296121501	2		649	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0059973-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	9	391	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.763340296121501	1	FACETS	0.062	0.04	0.089	0.062	0.04	0.089	SUBCLONAL	1	TRUE	0	0.763340296121501	1		391	237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578188	7578188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201592	NA	P-0059973-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	48	636	0	ENST00000269305.4:c.661G>A	p.Glu221Lys	p.E221K	ENST00000269305	NM_001126112.2	221	Gag/Aag	6/11	0.763340296121501	1	FACETS	0.222	0.188	0.259	0.222	0.188	0.259	SUBCLONAL	1	TRUE	0	0.763340296121501	1		636	350	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437151	49437152	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0059973-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	203	467	2	ENST00000301067.7:c.5527dup	p.Thr1843AsnfsTer5	p.T1843Nfs*5	ENST00000301067	NM_003482.3	1843	aca/aAca	24/54	0.201109561465639	4	FACETS	0.965	0.904	1	0.965	0.904	1	INDETERMINATE	2	TRUE	2	0.763340296121501	4		469	486	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059213	27059213	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0059973-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	156	396	0	ENST00000324856.7:c.1850C>G	p.Ser617Ter	p.S617*	ENST00000324856	NM_006015.4	617	tCa/tGa	4/20	1	2	FACETS	0.892	0.824	0.962	0.892	0.824	0.962	CLONAL	1	TRUE	1	0.763340296121501	2		396	458	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748320	43748321	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0059973-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	193	613	0	ENST00000382044.4:c.2485_2486del	p.Glu829ThrfsTer18	p.E829Tfs*18	ENST00000382044	NM_001141980.1	829	GAa/a	12/28	1	2	FACETS	0.893	0.832	0.956	0.893	0.832	0.956	CLONAL	1	TRUE	1	0.763340296121501	2		613	566	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216690	2216690	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059973-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	189	672	0	ENST00000398665.3:c.2334G>C	p.Lys778Asn	p.K778N	ENST00000398665	NM_032482.2	778	aaG/aaC	20/28	0.172461614406092	1	FACETS	0.658	0.615	0.703	0.658	0.615	0.703	INDETERMINATE	1	TRUE	0	0.763340296121501	1		672	465	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275023	41275023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059973-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	306	634	0	ENST00000349496.5:c.1189G>A	p.Gly397Arg	p.G397R	ENST00000349496	NM_001904.3	397	Ggg/Agg	9/15	0.359900252139655	3	FACETS	0.856	0.814	0.898	0.856	0.814	0.898	INDETERMINATE	2	TRUE	1	0.763340296121501	3		634	647	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670264	134670264	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059973-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	200	523	0	ENST00000398015.3:c.175C>G	p.Gln59Glu	p.Q59E	ENST00000398015	NM_004441.4	59	Cag/Gag	3/16	0.763340296121501	1	FACETS	0.706	0.662	0.751	0.706	0.662	0.751	SUBCLONAL	1	TRUE	0	0.763340296121501	1		523	459	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403449	139403449	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059973-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	187	543	0	ENST00000277541.6:c.3044G>A	p.Gly1015Asp	p.G1015D	ENST00000277541	NM_017617.3	1015	gGc/gAc	19/34	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.763340296121501	2		543	429	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0060070-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	85	768	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	0.176880969512977	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		768	517	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020447	69020447	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060070-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	84	424	0	ENST00000288368.4:c.2819T>C	p.Val940Ala	p.V940A	ENST00000288368	NM_024870.2	940	gTc/gCc	24/40	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		424	609	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0060073-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	201	589	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.968	0.9	1	0.968	0.9	1	CLONAL	1	TRUE	1	0.55883160642708	2		589	743	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023848	27023849	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGGCCCCAGGACGGGGGCGCCGGCAA	novel	NA	P-0060073-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	188	396	1	ENST00000324856.7:c.961_986dup	p.Ala330ArgfsTer42	p.A330Rfs*42	ENST00000324856	NM_006015.4	318	-/GGGCCCCAGGACGGGGGCGCCGGCAA	1/20	0.55883160642708	1	FACETS	0.635	0.588	0.684	0.635	0.588	0.684	SUBCLONAL	1	TRUE	0	0.55883160642708	1		397	763	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687060	37687060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060073-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	75	393	0	ENST00000447079.4:c.3964G>A	p.Ala1322Thr	p.A1322T	ENST00000447079	NM_015083.1	1322	Gcc/Acc	14/14	1	2	FACETS	0.313	0.273	0.356	0.313	0.273	0.356	SUBCLONAL	1	TRUE	1	0.55883160642708	2		393	858	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591151	67591151	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060073-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	171	284	0	ENST00000274335.5:c.1744A>C	p.Met582Leu	p.M582L	ENST00000274335		582	Atg/Ctg	12/15	1	2	FACETS	0.863	0.796	0.933	0.863	0.796	0.933	CLONAL	1	TRUE	1	0.55883160642708	2		284	709	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687060	37687060	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060073-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	56	393	0	ENST00000447079.4:c.3964G>T	p.Ala1322Ser	p.A1322S	ENST00000447079	NM_015083.1	1322	Gcc/Tcc	14/14	1	2	FACETS	0.234	0.199	0.271	0.234	0.199	0.271	SUBCLONAL	1	TRUE	1	0.55883160642708	2		393	858	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060093-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	16	321	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.347	0.256	0.456	0.347	0.256	0.456	SUBCLONAL	1	TRUE	1	0.290733844501262	2		321	317	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578513	7578513	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567554121	NA	P-0060093-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	45	542	0	ENST00000269305.4:c.417G>T	p.Lys139Asn	p.K139N	ENST00000269305	NM_001126112.2	139	aaG/aaT	5/11	1	2	FACETS	0.478	0.401	0.564	0.478	0.401	0.564	SUBCLONAL	1	TRUE	1	0.290733844501262	2		542	647	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233813	133233813	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060093-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	91	509	0	ENST00000320574.5:c.3491C>T	p.Pro1164Leu	p.P1164L	ENST00000320574	NM_006231.2	1164	cCc/cTc	29/49	1	2	FACETS	0.929	0.825	1	0.929	0.825	1	CLONAL	1	TRUE	1	0.290733844501262	2		509	674	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632355	1632355	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060093-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	31	450	0	ENST00000344749.5:c.195del	p.Ser65ArgfsTer56	p.S65Rfs*56	ENST00000344749	NM_001136139.2	65	agC/ag	4/19	1	2	FACETS	0.389	0.314	0.475	0.389	0.314	0.475	SUBCLONAL	1	TRUE	1	0.290733844501262	2		450	548	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077442	30077443	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0060093-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	51	373	0	ENST00000338641.4:c.1591_1592del	p.Lys531GlufsTer10	p.K531Efs*10	ENST00000338641	NM_000268.3	530	gAA/g	15/16	1	2	FACETS	0.607	0.515	0.708	0.607	0.515	0.708	SUBCLONAL	1	TRUE	1	0.290733844501262	2		373	578	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437294	52437295	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGAGGAA	novel	NA	P-0060093-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	54	503	0	ENST00000460680.1:c.1743_1749dup	p.Pro584PhefsTer61	p.P584Ffs*61	ENST00000460680	NM_004656.3	583	-/TTCCTCG	14/17	0.290733844501262	1	FACETS	0.702	0.601	0.813	0.702	0.601	0.813	SUBCLONAL	1	TRUE	0	0.290733844501262	1		503	452	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713696	52713696	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060093-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	69	396	0	ENST00000394830.3:c.32del	p.Pro11LeufsTer34	p.P11Lfs*34	ENST00000394830	NM_018313.4	11	cCt/ct	2/30	0.290733844501262	1	FACETS	0.789	0.689	0.898	0.789	0.689	0.898	SUBCLONAL	1	TRUE	0	0.290733844501262	1		396	514	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771171	161771171	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060093-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	28	355	0	ENST00000366898.1:c.1358G>C	p.Trp453Ser	p.W453S	ENST00000366898	NM_004562.2	453	tGg/tCg	12/12	0.244186575743386	2	FACETS	0.355	0.283	0.437	0.177	0.141	0.219	SUBCLONAL	1	TRUE	0	0.290733844501262	2		355	543	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0060182-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	427	299	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.590041413439085	7	FACETS	0.917	0.886	0.948	0.917	0.886	0.948	CLONAL	6	TRUE	1	0.590041413439085	7		299	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0060182-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	117	460	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.590041413439085	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.590041413439085	1		460	277	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020874	112020874	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0060182-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	15	297	0	ENST00000368678.4:c.698-1G>C		p.X233_splice	ENST00000368678		233			0.395217271755854	1	FACETS	0.132	0.096	0.175	0.132	0.096	0.175	SUBCLONAL	1	TRUE	0	0.590041413439085	1		297	272	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557629	95557629	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060314-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	207	470	0	ENST00000393063.1:c.5438A>C	p.Glu1813Ala	p.E1813A	ENST00000393063	NM_030621.3	1813	gAg/gCg	26/28	0.325805154119515	2	FACETS	0.923	0.86	0.987	0.923	0.86	0.987	CLONAL	2	TRUE	0	0.331290840779748	2		470	677	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060326-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	267	758	0	ENST00000326873.7:c.667G>T	p.Glu223Ter	p.E223*	ENST00000326873	NM_000455.4	223	Gag/Tag	5/10	0.313153314310825	2	FACETS	0.952	0.896	1	0.952	0.896	1	CLONAL	2	TRUE	0	0.349666663487985	2		758	802	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259364	36259364	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555899881	NA	P-0060326-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	219	506	0	ENST00000300305.3:c.127C>T	p.Pro43Ser	p.P43S	ENST00000300305		43	Cct/Tct	3/8	0.285947487345031	3	FACETS	0.879	0.819	0.941	0.879	0.819	0.941	CLONAL	2	TRUE	1	0.349666663487985	3		506	837	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70971059	70971059	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060326-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	402	364	0	ENST00000276594.2:c.1202G>T	p.Arg401Ile	p.R401I	ENST00000276594	NM_024504.3	401	aGa/aTa	6/8	0.349666663487985	5	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	2	0.349666663487985	5		364	1021	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243362	46243362	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0060326-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	138	350	0	ENST00000334344.6:c.1716-1G>T		p.X572_splice	ENST00000334344	NM_152641.2	572			0.235365847052955	4	FACETS	0.886	0.809	0.966	0.886	0.809	0.966	CLONAL	2	TRUE	2	0.349666663487985	4		350	601	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657053	47657053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060326-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	131	294	0	ENST00000233146.2:c.1249G>A	p.Val417Ile	p.V417I	ENST00000233146	NM_000251.2	417	Gtt/Att	7/16	0.194172702076184	4	FACETS	0.833	0.758	0.911	0.833	0.758	0.911	INDETERMINATE	2	TRUE	2	0.349666663487985	4		294	607	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729865	41729865	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060326-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	114	497	0	ENST00000242208.4:c.664C>A	p.Pro222Thr	p.P222T	ENST00000242208	NM_002192.2	222	Cct/Act	3/3	0.285947487345031	3	FACETS	0.932	0.839	1	0.466	0.419	0.516	CLONAL	1	TRUE	1	0.349666663487985	3		497	822	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610419	10610419	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060326-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	320	551	0	ENST00000171111.5:c.291G>T	p.Lys97Asn	p.K97N	ENST00000171111	NM_203500.1	97	aaG/aaT	2/6	0.313153314310825	2	FACETS	0.994	0.941	1	0.994	0.941	1	CLONAL	2	TRUE	0	0.349666663487985	2		551	921	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273398	38273398	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060326-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	231	534	0	ENST00000425967.3:c.1937C>A	p.Ala646Asp	p.A646D	ENST00000425967	NM_001174067.1	646	gCc/gAc	14/19	0.313153314310825	2	FACETS	0.848	0.793	0.904	0.848	0.793	0.904	CLONAL	2	TRUE	0	0.349666663487985	2		534	779	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578515	7578517	+	stop_gained	Nonsense_Mutation	TNP	TGG	TGG	AGA	novel	NA	P-0060326-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	304	557	0	ENST00000269305.4:c.413_415delinsTCT	p.Ala138_Lys139delinsValTer	p.A138_K139delinsV*	ENST00000269305	NM_001126112.2	138	gCCAag/gTCTag	5/11	0.313153314310825	2	FACETS	0.923	0.872	0.975	0.923	0.872	0.975	CLONAL	2	TRUE	0	0.349666663487985	2		557	942	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578315	226578315	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060326-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	151	483	0	ENST00000366794.5:c.413G>C	p.Arg138Pro	p.R138P	ENST00000366794	NM_001618.3	138	cGc/cCc	4/23	0.208525894592001	3	FACETS	1	0.976	1	0.59	0.539	0.643	INDETERMINATE	1	TRUE	1	0.349666663487985	3		483	860	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18439799	18439799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060326-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	64	266	0	ENST00000266497.5:c.697C>A	p.Gln233Lys	p.Q233K	ENST00000266497		233	Cag/Aag	2/31	0.313153314310825	2	FACETS	1	0.965	1	0.658	0.576	0.746	CLONAL	1	TRUE	0	0.349666663487985	2		266	278	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246378	46246378	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0060326-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	255	508	0	ENST00000334344.6:c.4472C>G	p.Ser1491Ter	p.S1491*	ENST00000334344	NM_152641.2	1491	tCa/tGa	15/21	0.235365847052955	4	FACETS	0.945	0.884	1	0.945	0.884	1	CLONAL	2	TRUE	2	0.349666663487985	4		508	1042	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679131	88679131	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060326-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	90	424	0	ENST00000360948.2:c.906C>A	p.Tyr302Ter	p.Y302*	ENST00000360948	NM_001012338.2	302	taC/taA	8/19	0.349666663487985	5	FACETS	0.859	0.76	0.964	0.215	0.19	0.241	CLONAL	1	TRUE	1	0.349666663487985	5		424	914	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094710	2094710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150437839	NA	P-0060326-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	223	476	1	ENST00000219066.1:c.470G>A	p.Arg157Gln	p.R157Q	ENST00000219066	NM_002528.5	157	cGg/cAg	3/6	0.285947487345031	3	FACETS	0.916	0.855	0.979	0.916	0.855	0.979	CLONAL	2	TRUE	1	0.349666663487985	3		477	818	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936764	78936764	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060326-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	268	567	0	ENST00000306801.3:c.3846C>A	p.Ser1282Arg	p.S1282R	ENST00000306801	NM_020761.2	1282	agC/agA	33/34	0.269136434025665	3	FACETS	0.864	0.811	0.919	0.864	0.811	0.919	CLONAL	2	TRUE	1	0.349666663487985	3		567	1042	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607650	46607650	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs777399123	NA	P-0060326-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	262	576	0	ENST00000263734.3:c.1839C>G	p.Ser613Arg	p.S613R	ENST00000263734	NM_001430.4	613	agC/agG	12/16	0.194172702076184	4	FACETS	0.979	0.918	1	0.979	0.918	1	INDETERMINATE	2	TRUE	2	0.349666663487985	4		576	1033	SUCCESS
ALB	213	MSKCC	GRCh37	4	74283891	74283891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060326-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	107	422	0	ENST00000295897.4:c.1515G>T	p.Leu505Phe	p.L505F	ENST00000295897	NM_000477.5	505	ttG/ttT	12/15	0.285947487345031	3	FACETS	1	0.899	1	0.501	0.449	0.555	CLONAL	1	TRUE	1	0.349666663487985	3		422	718	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31511199	31511199	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060326-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	107	346	0	ENST00000344624.3:c.1375G>C	p.Ala459Pro	p.A459P	ENST00000344624		459	Gcc/Ccc	6/33	1	2	FACETS	0.924	0.83	1	0.924	0.83	1	CLONAL	1	TRUE	1	0.349666663487985	2		346	662	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31947309	31947309	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060326-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	116	473	0	ENST00000375333.2:c.794G>T	p.Gly265Val	p.G265V	ENST00000375333	NM_032454.1	265	gGc/gTc	5/8	0.349666663487985	4	FACETS	0.805	0.724	0.892	0.268	0.241	0.298	CLONAL	1	TRUE	1	0.349666663487985	4		473	1112	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289017	33289017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374371492	NA	P-0060326-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	448	580	0	ENST00000374542.5:c.535C>T	p.Pro179Ser	p.P179S	ENST00000374542	NM_001141970.1	179	Cca/Tca	3/8	0.349666663487985	4	FACETS	0.966	0.923	1	0.966	0.923	1	CLONAL	3	TRUE	1	0.349666663487985	4		580	1194	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009334	69009335	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AT	novel	NA	P-0060326-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	241	358	0	ENST00000288368.4:c.2451_2452delinsAT	p.Glu818Ter	p.E818*	ENST00000288368	NM_024870.2	817	ctGGaa/ctATaa	22/40	0.349666663487985	5	FACETS	0.863	0.808	0.919	0.863	0.808	0.919	CLONAL	3	TRUE	2	0.349666663487985	5		358	812	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524949	8524949	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs771217760	NA	P-0060326-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	146	320	0	ENST00000356435.5:c.655G>T	p.Ala219Ser	p.A219S	ENST00000356435		219	Gct/Tct	7/35	0.313153314310825	2	FACETS	0.859	0.79	0.931	0.859	0.79	0.931	CLONAL	2	TRUE	0	0.349666663487985	2		320	486	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428430	47428430	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060326-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	202	472	0	ENST00000377045.4:c.1298A>G	p.Asn433Ser	p.N433S	ENST00000377045	NM_001654.4	433	aAc/aGc	12/16	0.194172702076184	4	FACETS	0.847	0.786	0.911	0.847	0.786	0.911	INDETERMINATE	2	TRUE	2	0.349666663487985	4		472	920	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256120	16256121	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0060336-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	496	477	0	ENST00000375759.3:c.3385_3386del	p.Val1129Ter	p.V1129*	ENST00000375759	NM_015001.2	1129	GTt/t	11/15	0.746133362236327	3	FACETS	0.972	0.936	1	0.972	0.936	1	CLONAL	2	TRUE	1	0.746133362236327	3		477	939	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578582	7579480	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAAAGTCAGGGCACAAGTGAACAGATAAAGCAACTGGAAGACGGCAGCAAAGAAACAAACATGCGTAAGCACCTCCTGCAACCCACTAGCGAGCTAGAGAGAGTTGGCGTCTACACCTCAGGAGCTTTTCTTTTTTTTTTTTTTTTTTGAGATAGGGTCTTGCTCTGTCACTCAGGCTGGAGCACAGTGGTGTGATCACAGCTCACTGCAGCCTCCATCTCCTGGCCTCAAGTGATCTTCCCACCTCAGCCTCCTAAGTGGCTGGGACTATAGGTGTGCACCACCATGCCTGGCTAATTTTTTGTATTTTTTTGTAGAGACGAGGTTTCATCATGTTACCCAGGCTGGTCTTGAACTCCTGGGCTCAGGTGATCTGCCTGCCTTGGCCTCTTTGAGAGTGCTGGGATTGCAGGTGTGAGCCACCAAGCCTGGTCAGGAGCTTATTTTCAAAAGCCAAGGAATACACGTGGATGAAGAAAAAGAAAAGTTCTGCATCCCCAGGAGAGATGCTGAGGGTGTGATGGGATGGATAAAAGCCCAAATTCAAGGGGGGAATATTCAACTTTGGGACAGGAGTCAGAGATCACACATTAAGTGGGTAAACTATAAAAAAACACTGACAGGAAGCCAAAGGGTGAAGAGGAATCCCAAAGTTCCAAACAAAAGAAATGCAGGGGGATACGGCCAGGCATTGAAGTCTCATGGAAGCCAGCCCCTCAGGGCAACTGACCGTGCAAGTCACAGACTTGGCTGTCCCAGAATGCAAGAAGCCCAGACGGAAACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGGACAGAAGATGACAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTGCAGGGGCCACGGGGGGAGCA	GAAAGTCAGGGCACAAGTGAACAGATAAAGCAACTGGAAGACGGCAGCAAAGAAACAAACATGCGTAAGCACCTCCTGCAACCCACTAGCGAGCTAGAGAGAGTTGGCGTCTACACCTCAGGAGCTTTTCTTTTTTTTTTTTTTTTTTGAGATAGGGTCTTGCTCTGTCACTCAGGCTGGAGCACAGTGGTGTGATCACAGCTCACTGCAGCCTCCATCTCCTGGCCTCAAGTGATCTTCCCACCTCAGCCTCCTAAGTGGCTGGGACTATAGGTGTGCACCACCATGCCTGGCTAATTTTTTGTATTTTTTTGTAGAGACGAGGTTTCATCATGTTACCCAGGCTGGTCTTGAACTCCTGGGCTCAGGTGATCTGCCTGCCTTGGCCTCTTTGAGAGTGCTGGGATTGCAGGTGTGAGCCACCAAGCCTGGTCAGGAGCTTATTTTCAAAAGCCAAGGAATACACGTGGATGAAGAAAAAGAAAAGTTCTGCATCCCCAGGAGAGATGCTGAGGGTGTGATGGGATGGATAAAAGCCCAAATTCAAGGGGGGAATATTCAACTTTGGGACAGGAGTCAGAGATCACACATTAAGTGGGTAAACTATAAAAAAACACTGACAGGAAGCCAAAGGGTGAAGAGGAATCCCAAAGTTCCAAACAAAAGAAATGCAGGGGGATACGGCCAGGCATTGAAGTCTCATGGAAGCCAGCCCCTCAGGGCAACTGACCGTGCAAGTCACAGACTTGGCTGTCCCAGAATGCAAGAAGCCCAGACGGAAACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGGACAGAAGATGACAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTGCAGGGGCCACGGGGGGAGCA	-	novel	NA	P-0060342-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	139	385	0	ENST00000269305.4:c.207_376-28del		p.X69_splice	ENST00000269305	NM_001126112.2	69		4/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		385	419	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0060417-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	297	380	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.28093818603686	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	2	0.4263709053745	4		380	821	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0060464-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	369	771	0	ENST00000346208.3:c.1220_1221insA	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcAg	6/6	1	2	FACETS	0.958	0.911	1	0.958	0.911	1	CLONAL	1	TRUE	1	0.781518415440049	2		771	986	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0060473-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	156	382	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.153736245705363	3	FACETS	0.845	0.78	0.912	0.845	0.78	0.912	INDETERMINATE	2	TRUE	1	0.473564513160306	3		382	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0060473-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	214	510	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.470180219074054	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.473564513160306	1		510	672	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175883	24175883	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060473-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	118	505	1	ENST00000263121.7:c.1111A>T	p.Asn371Tyr	p.N371Y	ENST00000263121	NM_003073.3	371	Aac/Tac	8/9	NA	2	FACETS	0.767	0.693	0.844			1	INDETERMINATE	1	TRUE	NA	0.473564513160306	2		506	650	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607157	189607157	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060474-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	410	886	0	ENST00000264731.3:c.1536G>A	p.Met512Ile	p.M512I	ENST00000264731	NM_003722.4	512	atG/atA	12/14	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.703036004696907	2		886	1150	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156711	20156716	+	inframe_deletion	In_Frame_Del	DEL	TACCCC	TACCCC	-	novel	NA	P-0060474-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	129	316	1	ENST00000379607.5:c.41_46del	p.Arg14_Gly15del	p.R14_G15del	ENST00000379607	NM_001412.3	14	aGGGGTAag/aag	2/7	1	2	FACETS	0.603	0.548	0.66	0.603	0.548	0.66	SUBCLONAL	1	TRUE	1	0.703036004696907	2		317	609	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448178	49448178	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060474-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	422	692	0	ENST00000301067.7:c.422G>A	p.Trp141Ter	p.W141*	ENST00000301067	NM_003482.3	141	tGg/tAg	4/54	1	2	FACETS	0.984	0.938	1	0.984	0.938	1	CLONAL	1	TRUE	1	0.703036004696907	2		692	1220	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0060476-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	376	1000	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.582213291687947	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.582213291687947	1		1000	864	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717778	89717778	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0060476-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	39	322	0	ENST00000371953.3:c.801+2T>G		p.X267_splice	ENST00000371953	NM_000314.4	267			0.304984653037004	0	FACETS	0.331	0.278	0.388			1	INDETERMINATE	1	TRUE	0	0.582213291687947	0		322	169	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519895	NA	P-0060476-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	202	567	0	ENST00000281708.4:c.1394G>T	p.Arg465Leu	p.R465L	ENST00000281708	NM_033632.3	465	cGt/cTt	9/12	0.582213291687947	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.582213291687947	1		567	431	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445178	49445178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771291128	NA	P-0060476-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	388	1226	0	ENST00000301067.7:c.2288C>T	p.Pro763Leu	p.P763L	ENST00000301067	NM_003482.3	763	cCg/cTg	10/54	1	2	FACETS	0.949	0.901	0.999	0.949	0.901	0.999	CLONAL	1	TRUE	1	0.582213291687947	2		1226	1404	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602645	10602645	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060476-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	392	983	0	ENST00000171111.5:c.933C>G	p.His311Gln	p.H311Q	ENST00000171111	NM_203500.1	311	caC/caG	3/6	0.582213291687947	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.582213291687947	1		983	949	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954346	48954346	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060476-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	41	371	0	ENST00000267163.4:c.1467C>A	p.Cys489Ter	p.C489*	ENST00000267163	NM_000321.2	489	tgC/tgA	16/27	0.582213291687947	1	FACETS	0.523	0.441	0.612	0.523	0.441	0.612	SUBCLONAL	1	TRUE	0	0.582213291687947	1		371	191	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731157	162731157	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060476-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	327	984	0	ENST00000367921.3:c.1012C>G	p.Leu338Val	p.L338V	ENST00000367921	NM_006182.2	338	Ctc/Gtc	9/18	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.582213291687947	2		984	1122	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541638	120541638	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060476-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	292	939	0	ENST00000229340.5:c.219C>G	p.Ile73Met	p.I73M	ENST00000229340	NM_006861.6	73	atC/atG	3/6	0.423918618109995	3	FACETS	0.926	0.869	0.984	0.463	0.434	0.492	CLONAL	1	TRUE	1	0.582213291687947	3		939	1399	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993666	72993666	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060476-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	451	1081	0	ENST00000268489.5:c.379G>T	p.Glu127Ter	p.E127*	ENST00000268489	NM_006885.3	127	Gag/Tag	2/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.582213291687947	2		1081	1370	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528167	29528167	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060476-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	108	532	0	ENST00000356175.3:c.1175A>C	p.Gln392Pro	p.Q392P	ENST00000356175	NM_000267.3	392	cAa/cCa	10/57	1	2	FACETS	0.954	0.863	1	0.954	0.863	1	CLONAL	1	TRUE	1	0.582213291687947	2		532	389	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383088	42383088	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060476-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	178	516	0	ENST00000221972.3:c.108C>A	p.His36Gln	p.H36Q	ENST00000221972	NM_021601.3	36	caC/caA	2/5	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.582213291687947	2		516	583	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402493	20402493	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060476-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	225	760	0	ENST00000346618.3:c.30G>T	p.Glu10Asp	p.E10D	ENST00000346618	NM_001949.4	10	gaG/gaT	1/7	1	2	FACETS	0.814	0.758	0.871	0.814	0.758	0.871	CLONAL	1	TRUE	1	0.582213291687947	2		760	950	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060495-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	393	922	0	ENST00000269305.4:c.472C>G	p.Arg158Gly	p.R158G	ENST00000269305	NM_001126112.2	158	Cgc/Ggc	5/11	0.500221909859835	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.500272995074176	2		922	733	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105565	27105565	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060495-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	249	569	0	ENST00000324856.7:c.5176G>T	p.Glu1726Ter	p.E1726*	ENST00000324856	NM_006015.4	1726	Gag/Tag	20/20	0.500221909859835	3	FACETS	0.947	0.891	1	0.947	0.891	1	CLONAL	2	TRUE	1	0.500272995074176	3		569	657	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259610	89259610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194420863	NA	P-0060495-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	132	469	0	ENST00000336596.2:c.754G>A	p.Val252Ile	p.V252I	ENST00000336596	NM_005233.5	252	Gta/Ata	3/17	0.500221909859835	3	FACETS	0.989	0.9	1	0.495	0.45	0.541	CLONAL	1	TRUE	1	0.500272995074176	3		469	667	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363231	40363231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768216635	NA	P-0060495-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	178	726	2	ENST00000397332.2:c.998C>T	p.Ala333Val	p.A333V	ENST00000397332	NM_001033082.2	333	gCg/gTg	3/3	0.479635437979874	5	FACETS	1	0.973	1	0.282	0.259	0.305	CLONAL	1	TRUE	1	0.500272995074176	5		728	1106	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644489	3644489	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151026877	NA	P-0060495-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	176	862	0	ENST00000294008.3:c.2125G>A	p.Val709Met	p.V709M	ENST00000294008	NM_032444.2	709	Gtg/Atg	10/15	0.500221909859835	3	FACETS	1	0.978	1	0.386	0.356	0.417	CLONAL	1	TRUE	0	0.500272995074176	3		862	759	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349567	15349567	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060495-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	78	756	0	ENST00000263377.2:c.4007G>T	p.Arg1336Ile	p.R1336I	ENST00000263377	NM_058243.2	1336	aGa/aTa	19/20	0.480818568292129	4	FACETS	0.644	0.565	0.728	0.322	0.282	0.364	SUBCLONAL	1	TRUE	2	0.500272995074176	4		756	727	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220890	36220890	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060495-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	131	699	0	ENST00000222270.7:c.4940C>G	p.Pro1647Arg	p.P1647R	ENST00000222270	NM_014727.1	1647	cCt/cGt	23/37	0.480818568292129	4	FACETS	0.985	0.894	1	0.492	0.447	0.54	CLONAL	1	TRUE	2	0.500272995074176	4		699	798	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577576	7577584	+	protein_altering_variant	In_Frame_Del	DEL	GTTGTAGTG	GTTGTAGTG	ACA	novel	NA	P-0060495-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	116	635	1	ENST00000269305.4:c.697_705delinsTGT	p.His233_Asn235delinsCys	p.H233_N235delinsC	ENST00000269305	NM_001126112.2	233	CACTACAAC/TGT	7/11	0.500221909859835	2	FACETS	0.875	0.792	0.962	0.437	0.396	0.481	CLONAL	1	TRUE	0	0.500272995074176	2		636	530	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0060496-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	44	176	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.190146223300652	1	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	FALSE	0	0.218964545764964	1		176	325	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222964	5222964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060496-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	86	822	0	ENST00000357368.4:c.2839C>T	p.Leu947Phe	p.L947F	ENST00000357368	NM_002850.3	947	Ctt/Ttt	18/38	0.123643624612791	4	FACETS	1	0.971	1	0.663	0.586	0.745	INDETERMINATE	1	FALSE	2	0.218964545764964	4		822	722	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112323	115112324	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	rs1381943852	NA	P-0060496-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	49	702	0	ENST00000257566.3:c.1416_1417del	p.Leu473ProfsTer218	p.L473Pfs*218	ENST00000257566	NM_016569.3	472	gcGCtc/gctc	7/8	0.182292655935863	3	FACETS	0.844	0.715	0.988	0.422	0.357	0.494	CLONAL	1	FALSE	1	0.218964545764964	3		702	588	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120971	115120971	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060496-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	87	680	0	ENST00000257566.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000257566	NM_016569.3	12	gGg/gTg	1/8	0.182292655935863	3	FACETS	1	0.959	1	0.593	0.524	0.666	CLONAL	1	FALSE	1	0.218964545764964	3		680	744	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115603	108115604	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	rs876659003	NA	P-0060496-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	47	438	0	ENST00000278616.4:c.756_757del	p.Cys252Ter	p.C252*	ENST00000278616	NM_000051.3	251	GTg/g	7/63	0.221259918170903	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	0	0.218964545764964	1		438	323	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423730	47423730	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060496-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	88	600	0	ENST00000404338.3:c.1798T>G	p.Leu600Val	p.L600V	ENST00000404338	NM_004491.4	600	Ttg/Gtg	1/6	0.192210525036265	3	FACETS	1	0.965	1	0.618	0.548	0.694	CLONAL	1	FALSE	1	0.218964545764964	3		600	721	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400112	41400112	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060496-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	71	473	0	ENST00000373198.4:c.647G>T	p.Gly216Val	p.G216V	ENST00000373198	NM_133170.3	216	gGt/gTt	5/32	0.182292655935863	3	FACETS	1	0.941	1	0.568	0.496	0.647	CLONAL	1	FALSE	1	0.218964545764964	3		473	633	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449550	149449550	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060496-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	85	746	0	ENST00000286301.3:c.1396G>T	p.Val466Leu	p.V466L	ENST00000286301	NM_005211.3	466	Gtg/Ttg	10/22	0.183570962217192	1	FACETS	0.851	0.752	0.958	0.851	0.752	0.958	CLONAL	1	FALSE	0	0.218964545764964	1		746	812	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161970032	161970032	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060496-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	65	484	0	ENST00000366898.1:c.937A>C	p.Asn313His	p.N313H	ENST00000366898	NM_004562.2	313	Aac/Cac	9/12	0.206817834625769	3	FACETS	1	0.961	1			1	CLONAL	1	FALSE	NA	0.218964545764964	3		484	507	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966557	36966557	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0060496-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	84	631	0	ENST00000358127.4:c.769A>T	p.Lys257Ter	p.K257*	ENST00000358127	NM_001280556.1	257	Aag/Tag	6/10	0.192210525036265	3	FACETS	1	0.96	1	0.603	0.532	0.679	CLONAL	1	FALSE	1	0.218964545764964	3		631	706	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040724	47040741	+	inframe_deletion	In_Frame_Del	DEL	CCTCTATGCCCATGGCTA	CCTCTATGCCCATGGCTA	-	novel	NA	P-0060496-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	62	641	0	ENST00000377604.3:c.1363_1380del	p.Tyr455_Leu460del	p.Y455_L460del	ENST00000377604	NM_001204468.1	453	tcCCTCTATGCCCATGGCTAc/tcc	13/24	0.11640711961662	3	FACETS	0.945	0.816	1			1	INDETERMINATE	1	FALSE	NA	0.218964545764964	3		641	665	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106159	27106159	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060497-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	69	729	0	ENST00000324856.7:c.5770G>T	p.Glu1924Ter	p.E1924*	ENST00000324856	NM_006015.4	1924	Gag/Tag	20/20	0.18738357790612	1	FACETS	0.743	0.648	0.847	0.743	0.648	0.847	SUBCLONAL	1	TRUE	0	0.271054527394498	1		729	592	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216590	108216590	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060497-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	55	515	0	ENST00000278616.4:c.8539G>C	p.Glu2847Gln	p.E2847Q	ENST00000278616	NM_000051.3	2847	Gag/Cag	58/63	0.271054527394498	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.271054527394498	1		515	251	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207093	1207093	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060497-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	113	713	0	ENST00000326873.7:c.181G>C	p.Gly61Arg	p.G61R	ENST00000326873	NM_000455.4	61	Ggc/Cgc	1/10	0.217441998696799	2	FACETS	0.765	0.691	0.843	0.765	0.691	0.843	SUBCLONAL	2	TRUE	0	0.271054527394498	2		713	545	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178197	56178198	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0060497-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	35	637	0	ENST00000399503.3:c.3171dup	p.His1058ThrfsTer7	p.H1058Tfs*7	ENST00000399503	NM_005921.1	1057	ata/atAa	14/20	1	2	FACETS	0.455	0.372	0.548	0.455	0.372	0.548	SUBCLONAL	1	TRUE	1	0.271054527394498	2		637	568	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211612	36211612	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060497-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	80	567	0	ENST00000222270.7:c.1363G>T	p.Glu455Ter	p.E455*	ENST00000222270	NM_014727.1	455	Gaa/Taa	3/37	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.271054527394498	2		567	528	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153562	108153564	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0060497-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	59	356	0	ENST00000278616.4:c.3703_3705del	p.Pro1235del	p.P1235del	ENST00000278616	NM_000051.3	1234	ttTCCt/ttt	25/63	0.271054527394498	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.271054527394498	1		356	292	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398280	25398281	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0060497-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	48	389	0	ENST00000311936.3:c.38_39delinsTT	p.Gly13Val	p.G13V	ENST00000311936	NM_004985.3	13	gGC/gTT	2/5	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.271054527394498	2		389	320	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519797	29519797	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060497-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	94	593	0	ENST00000389048.3:c.1774C>A	p.Leu592Met	p.L592M	ENST00000389048	NM_004304.4	592	Ctg/Atg	9/29	0.271054527394498	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.271054527394498	1		593	529	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281488	198281489	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060497-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	36	635	0	ENST00000335508.6:c.642dup	p.Leu215ThrfsTer20	p.L215Tfs*20	ENST00000335508	NM_012433.2	214	-/A	6/25	1	2	FACETS	0.471	0.386	0.566	0.471	0.386	0.566	SUBCLONAL	1	TRUE	1	0.271054527394498	2		635	564	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747138	40747138	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060497-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	55	469	0	ENST00000373198.4:c.2944C>A	p.Pro982Thr	p.P982T	ENST00000373198	NM_133170.3	982	Ccg/Acg	22/32	1	2	FACETS	0.849	0.727	0.982	0.849	0.727	0.982	CLONAL	1	TRUE	1	0.271054527394498	2		469	478	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980820	40980820	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060497-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	86	597	0	ENST00000373198.4:c.1666C>A	p.Leu556Met	p.L556M	ENST00000373198	NM_133170.3	556	Ctg/Atg	10/32	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.271054527394498	2		597	527	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270188	66270188	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060497-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	27	501	0	ENST00000273854.3:c.1694C>A	p.Ala565Glu	p.A565E	ENST00000273854	NM_004439.5	565	gCa/gAa	8/18	0.18738357790612	1	FACETS	0.434	0.345	0.536	0.434	0.345	0.536	SUBCLONAL	1	TRUE	0	0.271054527394498	1		501	397	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314937	1314937	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1233819869	NA	P-0060497-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	73	573	0	ENST00000400841.2:c.724C>A	p.Leu242Met	p.L242M	ENST00000400841		242	Ctg/Atg	6/6	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.271054527394498	2		573	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0060514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	86	499	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.247954804089701	3	FACETS	0.862	0.774	0.952	0.862	0.774	0.952	CLONAL	3	FALSE	0	0.307022427665506	3		500	250	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0060514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	165	905	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.307022427665506	5	FACETS	1	0.971	1	0.743	0.684	0.804	CLONAL	2	FALSE	2	0.307022427665506	5		905	704	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338671	70338671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	145	339	0	ENST00000374080.3:c.67G>T	p.Asp23Tyr	p.D23Y	ENST00000374080		23	Gat/Tat	1/45	0.307058515589976	4	FACETS	0.896	0.819	0.976	0.597	0.546	0.651	CLONAL	2	FALSE	1	0.307022427665506	4		339	689	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041927	14041927	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765253522	NA	P-0060514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	94	838	0	ENST00000311895.7:c.2474C>T	p.Ala825Val	p.A825V	ENST00000311895	NM_005236.2	825	gCg/gTg	11/11	0.307058515589976	4	FACETS	1	0.957	1	0.751	0.675	0.832	CLONAL	2	FALSE	1	0.307022427665506	4		838	355	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101252	27101252	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	132	991	0	ENST00000324856.7:c.4534del	p.Gln1512ArgfsTer15	p.Q1512Rfs*15	ENST00000324856	NM_006015.4	1512	Cag/ag	18/20	0.243337953008685	5	FACETS	0.889	0.812	0.968	0.889	0.812	0.968	CLONAL	3	FALSE	2	0.307022427665506	5		991	471	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467828	50467828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1040607869	NA	P-0060516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1869	955	634	6	ENST00000331340.3:c.1063G>A	p.Ala355Thr	p.A355T	ENST00000331340	NM_006060.4	355	Gcg/Acg	8/8	0.599513059511813	3	FACETS	1	0.996	1	0.584	0.565	0.603	CLONAL	1	TRUE	1	0.815292576715082	3		640	2824	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578217	7578217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	494	719	0	ENST00000269305.4:c.632C>T	p.Thr211Ile	p.T211I	ENST00000269305	NM_001126112.2	211	aCt/aTt	6/11	0.815292576715082	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.815292576715082	1		719	660	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602973	55602973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774405431	NA	P-0060516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	29	342	0	ENST00000288135.5:c.2683G>A	p.Ala895Thr	p.A895T	ENST00000288135	NM_000222.2	895	Gca/Aca	19/21	0.815292576715082	1	FACETS	0.354	0.289	0.425	0.354	0.289	0.425	SUBCLONAL	1	TRUE	0	0.815292576715082	1		342	119	SUCCESS
APC	324	MSKCC	GRCh37	5	112175466	112175466	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786204170	NA	P-0060516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	115	403	2	ENST00000257430.4:c.4175C>A	p.Ser1392Ter	p.S1392*	ENST00000257430	NM_000038.5	1392	tCa/tAa	16/16	0.815292576715082	1	FACETS	0.934	0.871	0.994	0.934	0.871	0.994	CLONAL	1	TRUE	0	0.815292576715082	1		405	179	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374979	45374980	+	stop_gained,inframe_insertion	Nonsense_Mutation	INS	-	-	TAC	novel	NA	P-0060516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	10	275	0	ENST00000262160.6:c.863_864insGTA	p.Glu288_Thr289insTer	p.E288_T289ins*	ENST00000262160	NM_005901.5	288	gaa/gaGTAa	8/11	0.815292576715082	1	FACETS	0.133	0.091	0.186	0.133	0.091	0.186	SUBCLONAL	1	TRUE	0	0.815292576715082	1		275	109	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920444	114920444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1219807932	NA	P-0060516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	60	347	1	ENST00000543371.1:c.1385C>T	p.Pro462Leu	p.P462L	ENST00000543371	NM_001198531.1	462	cCg/cTg	13/14	0.4329434828162	1	FACETS	0.325	0.283	0.371	0.325	0.283	0.371	INDETERMINATE	1	TRUE	0	0.815292576715082	1		348	268	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122613	108122613	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	19	240	1	ENST00000278616.4:c.1657G>A	p.Gly553Arg	p.G553R	ENST00000278616	NM_000051.3	553	Gga/Aga	11/63	0.461020657420855	1	FACETS	0.46	0.362	0.567	0.46	0.362	0.567	INDETERMINATE	1	TRUE	0	0.815292576715082	1		241	60	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533716	63533716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1851	1286	836	5	ENST00000307078.5:c.1438del	p.Leu480CysfsTer27	p.L480Cfs*27	ENST00000307078	NM_004655.3	480	Ctg/tg	6/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.815292576715082	2		841	3137	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219960	5219960	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	218	555	0	ENST00000357368.4:c.3755A>T	p.Lys1252Met	p.K1252M	ENST00000357368	NM_002850.3	1252	aAg/aTg	22/38	0.420248970507831	1	FACETS	0.249	0.231	0.268	0.249	0.231	0.268	INDETERMINATE	1	TRUE	0	0.815292576715082	1		555	1270	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2039776	2039777	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCAG	rs113070757	NA	P-0060516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1755	489	733	1	ENST00000349721.2:c.702_707dup	p.Gln237_Gln238dup	p.Q237_Q238dup	ENST00000349721	NM_003070.3	237	-/CAGCAG	4/34	0.420248970507831	1	FACETS	0.317	0.301	0.332	0.317	0.301	0.332	INDETERMINATE	1	TRUE	0	0.815292576715082	1		734	2244	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856655	111856655	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1014425313	NA	P-0060520-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	215	494	0	ENST00000341259.2:c.706G>A	p.Val236Met	p.V236M	ENST00000341259	NM_005475.2	236	Gtg/Atg	2/8	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.692485295035026	2		494	604	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186639	108186639	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0060520-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	157	401	0	ENST00000278616.4:c.6095+1G>T		p.X2032_splice	ENST00000278616	NM_000051.3	2032			1	2	FACETS	0.821	0.757	0.888	0.821	0.757	0.888	CLONAL	1	TRUE	1	0.692485295035026	2		401	552	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561890	55561890	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs146081659	NA	P-0060520-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	216	458	0	ENST00000288135.5:c.280A>G	p.Lys94Glu	p.K94E	ENST00000288135	NM_000222.2	94	Aaa/Gaa	2/21	0.216966654312732	3	FACETS	1	0.987	1	0.615	0.574	0.657	INDETERMINATE	1	TRUE	1	0.692485295035026	3		458	683	SUCCESS
APC	324	MSKCC	GRCh37	5	112175834	112175835	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0060520-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	61	537	0	ENST00000257430.4:c.4544_4545del	p.Phe1515TyrfsTer17	p.F1515Yfs*17	ENST00000257430	NM_000038.5	1515	TTt/t	16/16	0.692485295035026	1	FACETS	0.291	0.252	0.333	0.291	0.252	0.333	SUBCLONAL	1	TRUE	0	0.692485295035026	1		537	396	SUCCESS
APC	324	MSKCC	GRCh37	5	112176688	112176688	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060520-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	42	493	0	ENST00000257430.4:c.5399del	p.Asn1800MetfsTer17	p.N1800Mfs*17	ENST00000257430	NM_000038.5	1799	ttA/tt	16/16	0.692485295035026	1	FACETS	0.222	0.185	0.262	0.222	0.185	0.262	SUBCLONAL	1	TRUE	0	0.692485295035026	1		493	358	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801124	135801124	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs765578482	NA	P-0060520-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	160	364	0	ENST00000298552.3:c.213C>A	p.His71Gln	p.H71Q	ENST00000298552	NM_001162426.1	71	caC/caA	5/23	0.578998589928692	1	FACETS	0.716	0.663	0.769	0.716	0.663	0.769	SUBCLONAL	1	TRUE	0	0.692485295035026	1		364	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0060556-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	107	608	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.318429788606497	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.318429788606497	1		610	543	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0060556-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	113	660	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.988	0.89	1	0.988	0.89	1	CLONAL	1	TRUE	1	0.318429788606497	2		660	718	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928226	178928226	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519872	NA	P-0060556-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	175	440	0	ENST00000263967.3:c.1412C>T	p.Pro471Leu	p.P471L	ENST00000263967	NM_006218.2	471	cCa/cTa	9/21	0.318429788606497	3	FACETS	0.955	0.883	1	0.955	0.883	1	CLONAL	2	TRUE	1	0.318429788606497	3		440	667	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519451	137519451	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747769538	NA	P-0060556-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	100	482	0	ENST00000367739.4:c.1187C>T	p.Ser396Leu	p.S396L	ENST00000367739	NM_000416.2	396	tCg/tTg	7/7	1	2	FACETS	0.752	0.671	0.838	0.752	0.671	0.838	SUBCLONAL	1	TRUE	1	0.318429788606497	2		482	835	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807471	36807471	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060556-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	54	492	0	ENST00000373129.3:c.1193G>C	p.Trp398Ser	p.W398S	ENST00000373129	NM_032017.1	398	tGg/tCg	12/12	0.296156765844116	2	FACETS	0.527	0.449	0.612	0.263	0.224	0.306	SUBCLONAL	1	TRUE	0	0.318429788606497	2		492	644	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78931457	78931457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060556-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	123	479	0	ENST00000306801.3:c.3404C>T	p.Thr1135Ile	p.T1135I	ENST00000306801	NM_020761.2	1135	aCc/aTc	29/34	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.318429788606497	2		479	674	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060581-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	31	321	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		321	359	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0060583-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	153	453	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.548314927954035	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	0	0.548314927954035	2		453	279	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160702	56160702	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060583-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	78	473	0	ENST00000399503.3:c.976T>C	p.Ser326Pro	p.S326P	ENST00000399503	NM_005921.1	326	Tct/Cct	4/20	1	2	FACETS	0.942	0.836	1	0.942	0.836	1	CLONAL	1	TRUE	1	0.548314927954035	2		473	302	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056170	26056170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257086752	NA	P-0060583-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	125	557	0	ENST00000343677.2:c.487G>A	p.Ala163Thr	p.A163T	ENST00000343677	NM_005319.3	163	Gcg/Acg	1/1	0.548314927954035	4	FACETS	1	0.957	1	0.364	0.33	0.4	CLONAL	1	TRUE	1	0.548314927954035	4		557	646	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023722	27023756	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCGGCCCCTCCGCGGCCGGCGGGGGAACTCCCC	AGGCGGCCCCTCCGCGGCCGGCGGGGGAACTCCCC	-	novel	NA	P-0060651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	161	684	0	ENST00000324856.7:c.830_864del	p.Gly277AlafsTer111	p.G277Afs*111	ENST00000324856	NM_006015.4	276	ggAGGCGGCCCCTCCGCGGCCGGCGGGGGAACTCCCCag/ggag	1/20	0.79585347933265	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.79585347933265	1		684	230	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101193	27101193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	202	766	0	ENST00000324856.7:c.4475C>T	p.Ala1492Val	p.A1492V	ENST00000324856	NM_006015.4	1492	gCt/gTt	18/20	0.79585347933265	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.79585347933265	1		766	287	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750600586	NA	P-0060656-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	431	561	0	ENST00000269305.4:c.413C>T	p.Ala138Val	p.A138V	ENST00000269305	NM_001126112.2	138	gCc/gTc	5/11	0.313448584125453	3	FACETS	1	0.992	1	0.755	0.725	0.786	INDETERMINATE	2	TRUE	0	0.581793521819591	3		561	844	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916948	178916950	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0060656-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	144	394	0	ENST00000263967.3:c.337_339del	p.Leu113del	p.L113del	ENST00000263967	NM_006218.2	112	aTCCtc/atc	2/21	0.577349647783535	3	FACETS	1	0.988	1	0.736	0.677	0.796	CLONAL	1	TRUE	1	0.581793521819591	3		394	434	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610086	43610086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs184498773	NA	P-0060656-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	241	706	0	ENST00000355710.3:c.2038G>A	p.Ala680Thr	p.A680T	ENST00000355710	NM_020975.4	680	Gcc/Acc	11/20	1	2	FACETS	0.959	0.897	1	0.959	0.897	1	CLONAL	1	TRUE	1	0.581793521819591	2		706	864	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350753	15350753	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060656-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	234	538	0	ENST00000263377.2:c.3250C>G	p.Pro1084Ala	p.P1084A	ENST00000263377	NM_058243.2	1084	Cca/Gca	15/20	1	2	FACETS	0.975	0.912	1	0.975	0.912	1	CLONAL	1	TRUE	1	0.581793521819591	2		538	825	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	279	611	0				ENST00000310581	NM_198253.2	-/1132			0.697225310629724	4	FACETS	1	0.993	1	0.475	0.448	0.503	CLONAL	1	TRUE	1	0.897034852102347	4		611	828	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607157	189607157	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	376	886	0	ENST00000264731.3:c.1536G>A	p.Met512Ile	p.M512I	ENST00000264731	NM_003722.4	512	atG/atA	12/14	0.840422818969209	3	FACETS	0.951	0.902	1	0.475	0.451	0.5	CLONAL	1	TRUE	1	0.897034852102347	3		886	1277	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115272956	115272956	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	660	656	0	ENST00000438362.2:c.1417C>G	p.Arg473Gly	p.R473G	ENST00000438362	NM_001242891.1	473	Cgt/Ggt	12/20	0.850976932024877	4	FACETS	0.987	0.974	0.999	0.987	0.974	0.999	CLONAL	4	TRUE	0	0.897034852102347	4		656	707	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518431	204518431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	857	716	0	ENST00000367182.3:c.1094C>T	p.Thr365Ile	p.T365I	ENST00000367182	NM_001278516.1	365	aCc/aTc	11/11	0.897034852102347	3	FACETS	0.981	0.969	0.993	0.981	0.969	0.993	CLONAL	3	TRUE	0	0.897034852102347	3		716	940	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343318	118343318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	314	760	0	ENST00000534358.1:c.1444C>T	p.Pro482Ser	p.P482S	ENST00000534358	NM_005933.3	482	Ccc/Tcc	3/36	1	2	FACETS	0.9	0.853	0.947	0.9	0.853	0.947	CLONAL	1	TRUE	1	0.897034852102347	2		760	778	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699269	18699269	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	201	606	0	ENST00000266497.5:c.3370G>A	p.Gly1124Arg	p.G1124R	ENST00000266497		1124	Gga/Aga	24/31	0.40522469305568	3	FACETS	1	0.939	1	0.336	0.313	0.36	INDETERMINATE	1	TRUE	0	0.897034852102347	3		606	644	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793432	18793432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187869576	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	111	515	0	ENST00000266497.5:c.4129C>T	p.Arg1377Cys	p.R1377C	ENST00000266497		1377	Cgt/Tgt	30/31	0.40522469305568	3	FACETS	0.87	0.788	0.955	0.29	0.262	0.319	INDETERMINATE	1	TRUE	0	0.897034852102347	3		515	412	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944785	31944785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	408	456	0	ENST00000340398.3:c.316G>A	p.Asp106Asn	p.D106N	ENST00000340398	NM_001013699.2	106	Gat/Aat	1/1	0.40522469305568	3	FACETS	0.949	0.913	0.985	0.633	0.609	0.657	INDETERMINATE	2	TRUE	0	0.897034852102347	3		456	694	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519021	103519021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775080842	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	271	641	0	ENST00000355739.4:c.2359C>T	p.Pro787Ser	p.P787S	ENST00000355739	NM_000123.3	787	Ccc/Tcc	11/15	0.897034852102347	3	FACETS	0.925	0.869	0.982	0.463	0.434	0.491	CLONAL	1	TRUE	1	0.897034852102347	3		641	946	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609918	81609918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762048531	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	374	404	0	ENST00000298171.2:c.1516G>A	p.Glu506Lys	p.E506K	ENST00000298171	NM_000369.2	506	Gag/Aag	10/10	0.888780640412506	3	FACETS	1	0.949	1	0.5	0.474	0.526	CLONAL	1	TRUE	1	0.897034852102347	3		404	1208	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582936	95582936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1007754435	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	167	593	0	ENST00000393063.1:c.1606C>T	p.Arg536Cys	p.R536C	ENST00000393063	NM_030621.3	536	Cgt/Tgt	11/28	0.888780640412506	3	FACETS	1	0.934	1	0.505	0.467	0.544	CLONAL	1	TRUE	1	0.897034852102347	3		593	534	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40998457	40998457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	420	535	0	ENST00000267868.3:c.308C>T	p.Thr103Ile	p.T103I	ENST00000267868	NM_002875.4	103	aCt/aTt	4/10	0.869179080930452	2	FACETS	0.99	0.969	1	0.99	0.969	1	CLONAL	2	TRUE	0	0.897034852102347	2		535	473	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472442	88472442	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	287	682	0	ENST00000360948.2:c.2113T>A	p.Tyr705Asn	p.Y705N	ENST00000360948	NM_001012338.2	705	Tac/Aac	16/19	0.897034852102347	4	FACETS	0.878	0.824	0.934	0.439	0.412	0.467	CLONAL	1	TRUE	2	0.897034852102347	4		682	1382	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779058	3779058	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758101123	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	721	959	0	ENST00000262367.5:c.5990C>T	p.Pro1997Leu	p.P1997L	ENST00000262367	NM_004380.2	1997	cCc/cTc	31/31	0.871140307233308	3	FACETS	0.955	0.94	0.969	0.955	0.94	0.969	CLONAL	3	TRUE	0	0.897034852102347	3		959	813	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892299	9892299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs796052549	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	311	739	0	ENST00000330684.3:c.2191G>A	p.Asp731Asn	p.D731N	ENST00000330684	NM_001134407.1	731	Gat/Aat	11/13	0.218311210715444	3	FACETS	1	0.994	1	0.68	0.645	0.715	INDETERMINATE	1	TRUE	1	0.897034852102347	3		739	739	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973739	15973739	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	339	781	0	ENST00000268712.3:c.4253C>G	p.Pro1418Arg	p.P1418R	ENST00000268712	NM_006311.3	1418	cCt/cGt	31/46	0.5902972279924	4	FACETS	1	0.992	1	0.423	0.4	0.446	CLONAL	1	TRUE	1	0.897034852102347	4		781	1130	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61305302	61305302	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	41	157	0	ENST00000341074.5:c.824T>C	p.Met275Thr	p.M275T	ENST00000341074	NM_002974.2	275	aTg/aCg	8/8	0.461133823669101	5	FACETS	1	0.942	1	0.423	0.357	0.493	INDETERMINATE	1	TRUE	2	0.897034852102347	5		157	169	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61305324	61305324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	52	63	0	ENST00000341074.5:c.802G>A	p.Glu268Lys	p.E268K	ENST00000341074	NM_002974.2	268	Gaa/Aaa	8/8	0.461133823669101	5	FACETS	0.922	0.863	0.968	1	0.983	1	INDETERMINATE	5	TRUE	2	0.897034852102347	5		63	59	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61328048	61328048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	127	150	0	ENST00000283752.5:c.208G>A	p.Ala70Thr	p.A70T	ENST00000283752	NM_006919.2	70	Gct/Act	3/8	0.461133823669101	5	FACETS	1	0.978	1	0.785	0.724	0.847	INDETERMINATE	2	TRUE	2	0.897034852102347	5		150	282	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7126603	7126603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	280	663	0	ENST00000302850.5:c.3005C>T	p.Ala1002Val	p.A1002V	ENST00000302850	NM_000208.2	1002	gCc/gTc	16/22	0.199364916581098	4	FACETS	0.914	0.865	0.963	0.914	0.865	0.963	INDETERMINATE	2	TRUE	2	0.897034852102347	4		663	648	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670708	134670708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	607	783	0	ENST00000398015.3:c.619C>T	p.Pro207Ser	p.P207S	ENST00000398015	NM_004441.4	207	Cca/Tca	3/16	0.526881259232082	4	FACETS	1	0.996	1	0.82	0.794	0.845	INDETERMINATE	2	TRUE	1	0.897034852102347	4		783	1044	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748171	41748171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	674	731	0	ENST00000226382.2:c.598C>T	p.Pro200Ser	p.P200S	ENST00000226382	NM_003924.3	200	Ccc/Tcc	3/3	0.40522469305568	3	FACETS	1	0.988	1	0.686	0.666	0.705	INDETERMINATE	2	TRUE	0	0.897034852102347	3		731	1058	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193889	106193889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395976555	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	623	651	1	ENST00000380013.4:c.4351C>T	p.Arg1451Trp	p.R1451W	ENST00000380013	NM_001127208.2	1451	Cgg/Tgg	10/11	0.897034852102347	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.897034852102347	3		652	990	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557220	187557220	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	667	779	0	ENST00000441802.2:c.4142C>T	p.Ser1381Phe	p.S1381F	ENST00000441802	NM_005245.3	1381	tCt/tTt	6/27	0.792530099546373	4	FACETS	0.889	0.864	0.914			1	CLONAL	3	TRUE	NA	0.897034852102347	4		779	1058	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295230	+	upstream_gene_variant	5'Flank	TNP	GGG	GGG	AGA	novel	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	200	681	0				ENST00000310581	NM_198253.2	-/1132			0.697225310629724	4	FACETS	1	0.982	1	0.388	0.36	0.416	CLONAL	1	TRUE	1	0.897034852102347	4		681	727	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449475	31449475	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	450	608	0	ENST00000344624.3:c.2734C>T	p.His912Tyr	p.H912Y	ENST00000344624		912	Cat/Tat	19/33	0.888780640412506	3	FACETS	0.949	0.914	0.983	0.949	0.914	0.983	CLONAL	2	TRUE	1	0.897034852102347	3		608	766	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31472215	31472215	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	623	688	0	ENST00000344624.3:c.2196A>T	p.Lys732Asn	p.K732N	ENST00000344624		732	aaA/aaT	14/33	0.888780640412506	3	FACETS	0.98	0.95	1	0.98	0.95	1	CLONAL	2	TRUE	1	0.897034852102347	3		688	1027	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967910	93967910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	190	559	0	ENST00000369303.4:c.2017G>A	p.Glu673Lys	p.E673K	ENST00000369303	NM_004440.3	673	Gaa/Aaa	11/17	0.88314152374173	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.897034852102347	1		559	220	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679122	117679122	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	126	532	0	ENST00000368508.3:c.3699G>A	p.Trp1233Ter	p.W1233*	ENST00000368508	NM_002944.2	1233	tgG/tgA	24/43	0.88314152374173	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.897034852102347	1		532	151	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	1146	410	1	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.897034852102347	10	FACETS	0.964	0.95	0.977			1	CLONAL	9	TRUE	NA	0.897034852102347	10		411	1351	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845357	151845357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1223	414	821	0	ENST00000262189.6:c.13655G>A	p.Ser4552Asn	p.S4552N	ENST00000262189	NM_170606.2	4552	aGc/aAc	52/59	0.675263388355262	5	FACETS	1	0.994	1	0.331	0.314	0.348	CLONAL	1	TRUE	1	0.897034852102347	5		821	1637	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845894	151845894	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	793	693	0	ENST00000262189.6:c.13118C>A	p.Pro4373Gln	p.P4373Q	ENST00000262189	NM_170606.2	4373	cCa/cAa	52/59	0.675263388355262	5	FACETS	0.927	0.906	0.949	0.927	0.906	0.949	CLONAL	4	TRUE	1	0.897034852102347	5		693	1118	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874176	151874176	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	172	519	0	ENST00000262189.6:c.8362C>T	p.Gln2788Ter	p.Q2788*	ENST00000262189	NM_170606.2	2788	Cag/Tag	38/59	0.675263388355262	5	FACETS	1	0.981	1	0.301	0.278	0.326	CLONAL	1	TRUE	1	0.897034852102347	5		519	746	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372155	55372155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1219111000	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	698	937	0	ENST00000297316.4:c.845C>T	p.Ser282Leu	p.S282L	ENST00000297316	NM_022454.3	282	tCg/tTg	2/2	0.402238046436066	6	FACETS	0.96	0.928	0.992	0.96	0.928	0.992	INDETERMINATE	3	TRUE	3	0.897034852102347	6		937	1510	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68982094	68982094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	53	243	0	ENST00000288368.4:c.1468C>T	p.His490Tyr	p.H490Y	ENST00000288368	NM_024870.2	490	Cat/Tat	13/40	0.402238046436066	6	FACETS	0.821	0.71	0.939	0.548	0.473	0.626	INDETERMINATE	2	TRUE	3	0.897034852102347	6		243	201	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341129	8341129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	237	612	0	ENST00000356435.5:c.5087G>A	p.Gly1696Glu	p.G1696E	ENST00000356435		1696	gGa/gAa	30/35	0.461133823669101	5	FACETS	0.985	0.926	1	0.657	0.617	0.697	INDETERMINATE	2	TRUE	2	0.897034852102347	5		612	629	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471030	8471030	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	352	548	0	ENST00000356435.5:c.3469C>T	p.Pro1157Ser	p.P1157S	ENST00000356435		1157	Cca/Tca	20/35	0.461133823669101	5	FACETS	0.863	0.824	0.902	0.863	0.824	0.902	INDETERMINATE	3	TRUE	2	0.897034852102347	5		548	711	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285829	87285829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	527	894	0	ENST00000277120.3:c.166C>T	p.Pro56Ser	p.P56S	ENST00000277120		56	Ccg/Tcg	2/19	0.461133823669101	5	FACETS	1	0.98	1	0.69	0.662	0.718	INDETERMINATE	2	TRUE	2	0.897034852102347	5		894	1332	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93607788	93607788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867869952	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	615	670	0	ENST00000375746.1:c.490G>A	p.Glu164Lys	p.E164K	ENST00000375746	NM_001174167.1	164	Gaa/Aaa	3/14	0.871140307233308	3	FACETS	0.934	0.917	0.95	0.934	0.917	0.95	CLONAL	3	TRUE	0	0.897034852102347	3		670	709	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915831	127915831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	437	506	0	ENST00000373547.4:c.650G>A	p.Gly217Glu	p.G217E	ENST00000373547	NM_002721.4	217	gGa/gAa	6/7	0.509935066959573	5	FACETS	0.856	0.821	0.891	0.856	0.821	0.891	INDETERMINATE	3	TRUE	2	0.897034852102347	5		506	890	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2029083	2029084	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	G	novel	NA	P-0060669-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	705	923	0	ENST00000349721.2:c.61_62delinsG	p.Pro21ValfsTer23	p.P21Vfs*23	ENST00000349721	NM_003070.3	21	CCt/Gt	2/34	0.461133823669101	5	FACETS	1	0.996	1	0.811	0.784	0.837	INDETERMINATE	2	TRUE	2	0.897034852102347	5		923	1516	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193181224	193181224	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0060676-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	39	284	1	ENST00000367435.3:c.1060A>T	p.Lys354Ter	p.K354*	ENST00000367435	NM_024529.4	354	Aag/Tag	12/17	0.323508370233824	5	FACETS	0.859	0.712	1	0.215	0.178	0.256	CLONAL	1	TRUE	1	0.323508370233824	5		285	417	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333591	70333591	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060676-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	124	492	0	ENST00000373644.4:c.1496A>G	p.Asn499Ser	p.N499S	ENST00000373644	NM_030625.2	499	aAt/aGt	2/12	NA	2	FACETS	0.804	0.731	0.879			1	INDETERMINATE	2	TRUE	NA	0.323508370233824	2		492	477	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400719	56400719	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060676-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	36	370	0	ENST00000348428.3:c.1313A>G	p.Asn438Ser	p.N438S	ENST00000348428	NM_006785.3	438	aAt/aGt	11/17	0.141672115072874	3	FACETS	0.763	0.628	0.912	0.381	0.314	0.456	INDETERMINATE	1	TRUE	1	0.323508370233824	3		370	339	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0060677-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	71	380	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.330407014313246	2		380	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0060677-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	122	465	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.22669793598071	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.330407014313246	1		465	449	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215595163	215595163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377227840	NA	P-0060677-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	89	422	0	ENST00000260947.4:c.1973G>A	p.Arg658His	p.R658H	ENST00000260947	NM_000465.2	658	cGc/cAc	10/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.330407014313246	2		422	397	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183567	185183567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199572011	NA	P-0060677-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	89	442	0	ENST00000265026.3:c.1421G>A	p.Arg474Gln	p.R474Q	ENST00000265026	NM_004721.4	474	cGg/cAg	9/14	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.330407014313246	2		442	527	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087555	27087555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1171422700	NA	P-0060677-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	62	603	0	ENST00000324856.7:c.2129G>A	p.Arg710His	p.R710H	ENST00000324856	NM_006015.4	710	cGc/cAc	5/20	0.153941925539995	0	FACETS	0.433	0.374	0.498			1	INDETERMINATE	1	TRUE	0	0.330407014313246	0		603	580	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0060678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	45	436	0	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.521391430680348	2		436	167	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0060678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	93	646	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.894	0.8	0.992	0.894	0.8	0.992	CLONAL	1	TRUE	1	0.521391430680348	2		646	399	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0060678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	44	176	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.521391430680348	2		176	146	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0060678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	50	160	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.521391430680348	2		160	187	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0060678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	25	533	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.761	0.609	0.93	0.761	0.609	0.93	CLONAL	1	TRUE	1	0.521391430680348	2		533	126	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241924	72241924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs552625764	NA	P-0060678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	38	521	0	ENST00000357731.5:c.466G>A	p.Val156Ile	p.V156I	ENST00000357731	NM_173808.2	156	Gtc/Atc	3/7	1	2	FACETS	0.751	0.628	0.886	0.751	0.628	0.886	SUBCLONAL	1	TRUE	1	0.521391430680348	2		521	194	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576845	7576871	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTAGTACCTGAAGGGTGAAATATTCT	CTTAGTACCTGAAGGGTGAAATATTCT	-	novel	NA	P-0060678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	38	597	0	ENST00000269305.4:c.975_993+8del		p.X325_splice	ENST00000269305	NM_001126112.2	325		9/11	1	2	FACETS	0.923	0.775	1	0.923	0.775	1	CLONAL	1	TRUE	1	0.521391430680348	2		597	158	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0060679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	32	245	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.16	2		245	335	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0060679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	13	370	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.342	0.243	0.464	0.342	0.243	0.464	SUBCLONAL	1	TRUE	1	0.16	2		370	475	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107135	27107135	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0060679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	33	487	0	ENST00000324856.7:c.6746C>G	p.Ser2249Ter	p.S2249*	ENST00000324856	NM_006015.4	2249	tCa/tGa	20/20	1	2	FACETS	0.627	0.509	0.761	0.627	0.509	0.761	SUBCLONAL	1	TRUE	1	0.16	2		487	658	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670957	30670957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868678495	NA	P-0060679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	47	462	0	ENST00000376406.3:c.5789G>A	p.Arg1930His	p.R1930H	ENST00000376406	NM_014641.2	1930	cGc/cAc	12/15	1	2	FACETS	0.925	0.78	1	0.925	0.78	1	CLONAL	1	TRUE	1	0.16	2		462	635	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907037	101907037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	26	299	0	ENST00000374994.4:c.997G>A	p.Asp333Asn	p.D333N	ENST00000374994	NM_004612.2	333	Gat/Aat	6/9	1	2	FACETS	0.991	0.786	1	0.991	0.786	1	CLONAL	1	TRUE	1	0.16	2		299	328	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976801	2976801	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	29	459	0	ENST00000396946.4:c.1211G>A	p.Arg404Lys	p.R404K	ENST00000396946	NM_032415.4	404	aGg/aAg	9/25	1	2	FACETS	0.645	0.516	0.792	0.645	0.516	0.792	SUBCLONAL	1	TRUE	1	0.16	2		459	562	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0060680-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	23	534	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.644	0.5	0.812	0.644	0.5	0.812	SUBCLONAL	1	TRUE	1	0.11	2		534	649	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0060680-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	27	608	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.0808975775045723	0	FACETS	0.799	0.634	0.988			1	CLONAL	1	TRUE	0	0.11	0		610	547	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0060680-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	8	240	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.127681120651991	3	FACETS	0.462	0.296	0.679	0.231	0.148	0.34	SUBCLONAL	1	TRUE	1	0.11	3		240	332	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740603	58740603	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs375618423	NA	P-0060680-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	38	592	0	ENST00000305921.3:c.1508C>G	p.Ser503Ter	p.S503*	ENST00000305921	NM_003620.3	503	tCa/tGa	6/6	0.0808975775045723	0	FACETS	0.889	0.733	1			1	CLONAL	1	TRUE	0	0.11	0		592	692	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857992	9857992	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1372666082	NA	P-0060680-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	31	598	0	ENST00000330684.3:c.3409G>C	p.Glu1137Gln	p.E1137Q	ENST00000330684	NM_001134407.1	1137	Gaa/Caa	13/13	0.0808975775045723	0	FACETS	0.856	0.691	1			1	CLONAL	1	TRUE	0	0.11	0		598	586	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0060681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	301	453	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.258263324408719	3	FACETS	0.85	0.809	0.891	0.85	0.809	0.891	INDETERMINATE	3	TRUE	0	0.498839679970796	3		453	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0060681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	96	812	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.258263324408719	3	FACETS	0.667	0.594	0.744	0.222	0.198	0.248	INDETERMINATE	1	TRUE	0	0.498839679970796	3		812	721	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073938	8073938	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	46	637	0	ENST00000377482.5:c.721C>G	p.Gln241Glu	p.Q241E	ENST00000377482	NM_018948.3	241	Cag/Gag	4/4	1	2	FACETS	0.328	0.275	0.385	0.328	0.275	0.385	SUBCLONAL	1	TRUE	1	0.498839679970796	2		637	563	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150921998	150921998	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	200	560	0	ENST00000271640.5:c.1577A>G	p.Tyr526Cys	p.Y526C	ENST00000271640	NM_001145415.1	526	tAt/tGt	12/22	0.279231712870039	4	FACETS	0.987	0.92	1	0.987	0.92	1	INDETERMINATE	2	TRUE	2	0.498839679970796	4		560	609	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934177	48934178	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCTG	novel	NA	P-0060681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	53	420	0	ENST00000267163.4:c.633_636dup	p.Val213SerfsTer13	p.V213Sfs*13	ENST00000267163	NM_000321.2	211	gat/gaTCTGt	7/27	0.156173223106903	3	FACETS	0.955	0.821	1	0.478	0.41	0.55	INDETERMINATE	1	TRUE	1	0.498839679970796	3		420	278	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671644	67671644	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1406881801	NA	P-0060681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	132	507	0	ENST00000264010.4:c.2053A>G	p.Ile685Val	p.I685V	ENST00000264010	NM_006565.3	685	Ata/Gta	12/12	0.153938672410149	5	FACETS	0.796	0.726	0.87	0.531	0.484	0.58	INDETERMINATE	2	TRUE	2	0.498839679970796	5		507	581	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098807	178098807	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	78	545	0	ENST00000397062.3:c.238A>G	p.Thr80Ala	p.T80A	ENST00000397062	NM_006164.4	80	Aca/Gca	2/5	1	2	FACETS	0.488	0.429	0.551	0.488	0.429	0.551	SUBCLONAL	1	TRUE	1	0.498839679970796	2		545	641	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026132	71026132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751543308	NA	P-0060681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	75	414	0	ENST00000318789.4:c.1490G>A	p.Arg497Gln	p.R497Q	ENST00000318789	NM_032682.5	497	cGa/cAa	17/21	0.498839679970796	2	FACETS	0.808	0.713	0.91	0.404	0.356	0.455	CLONAL	1	TRUE	0	0.498839679970796	2		414	372	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27217702	27217702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773518368	NA	P-0060681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	27	429	1	ENST00000380036.4:c.3008G>A	p.Arg1003His	p.R1003H	ENST00000380036	NM_000459.3	1003	cGc/cAc	19/23	0.183859972708484	3	FACETS	0.301	0.239	0.372	0.1	0.079	0.124	INDETERMINATE	1	TRUE	0	0.498839679970796	3		430	450	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444659	78444659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs908264837	NA	P-0060682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	109	553	0	ENST00000370768.2:c.30del	p.Ser11LeufsTer43	p.S11Lfs*43	ENST00000370768	NM_003902.3	10	ccC/cc	1/20	1	2	FACETS	0.576	0.517	0.638	0.576	0.517	0.638	SUBCLONAL	1	TRUE	1	0.520969554371177	2		553	727	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	48	328	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.259	0.218	0.304	0.259	0.218	0.304	SUBCLONAL	1	TRUE	1	0.520969554371177	2		329	711	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0060682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	201	591	9	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.520969554371177	2		600	730	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0060682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	213	509	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.919	0.855	0.985	0.919	0.855	0.985	CLONAL	1	TRUE	1	0.520969554371177	2		513	890	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0060682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	13	241	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.349	0.25	0.468	0.349	0.25	0.468	SUBCLONAL	1	TRUE	1	0.520969554371177	2		241	143	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	168	378	3	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	1	2	FACETS	0.948	0.875	1	0.948	0.875	1	CLONAL	1	TRUE	1	0.520969554371177	2		381	680	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	176	558	4	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	1	2	FACETS	0.949	0.877	1	0.949	0.877	1	CLONAL	1	TRUE	1	0.520969554371177	2		562	712	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692922	89692922	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201044	NA	P-0060682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	86	396	0	ENST00000371953.3:c.406T>C	p.Cys136Arg	p.C136R	ENST00000371953	NM_000314.4	136	Tgt/Cgt	5/9	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.520969554371177	2		396	267	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175857	24175859	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs875989800	NA	P-0060682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	41	454	0	ENST00000263121.7:c.1091_1093del	p.Lys364del	p.K364del	ENST00000263121	NM_003073.3	362	gAGAag/gag	8/9	0.520969554371177	2	FACETS	0.248	0.206	0.295	0.124	0.103	0.148	SUBCLONAL	1	TRUE	0	0.520969554371177	2		454	635	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007332	143007332	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	76	285	0	ENST00000262992.4:c.2452del	p.Arg818GlufsTer4	p.R818Efs*4	ENST00000262992	NM_001101669.1	818	Aga/ga	22/24	1	2	FACETS	0.976	0.865	1	0.976	0.865	1	CLONAL	1	TRUE	1	0.520969554371177	2		285	299	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693002	89693003	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0060682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	63	327	0	ENST00000371953.3:c.491dup	p.Val166SerfsTer14	p.V166Sfs*14	ENST00000371953	NM_000314.4	162	-/A	5/9	1	2	FACETS	0.945	0.826	1	0.945	0.826	1	CLONAL	1	TRUE	1	0.520969554371177	2		327	256	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346158	89346158	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs878855327	NA	P-0060682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	16	570	0	ENST00000301030.4:c.6792del	p.Ala2265ProfsTer72	p.A2265Pfs*72	ENST00000301030	NM_001256183.1	2264	ccC/cc	9/13	1	2	FACETS	0.1	0.073	0.132	0.1	0.073	0.132	SUBCLONAL	1	TRUE	1	0.520969554371177	2		570	615	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958090	54958090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370497957	NA	P-0060682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	29	418	1	ENST00000312783.6:c.517G>A	p.Gly173Arg	p.G173R	ENST00000312783	NM_198436.1	173	Gga/Aga	6/10	1	2	FACETS	0.246	0.197	0.302	0.246	0.197	0.302	SUBCLONAL	1	TRUE	1	0.520969554371177	2		419	453	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183755	10183757	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs5030648	NA	P-0060682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	14	487	0	ENST00000256474.2:c.227_229del	p.Phe76del	p.F76del	ENST00000256474	NM_000551.3	75	aTCTtc/atc	1/3	1	2	FACETS	0.1	0.072	0.135	0.1	0.072	0.135	SUBCLONAL	1	TRUE	1	0.520969554371177	2		487	535	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416473	29416473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199940609	NA	P-0060682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	197	572	0	ENST00000389048.3:c.4480G>A	p.Gly1494Arg	p.G1494R	ENST00000389048	NM_004304.4	1494	Gga/Aga	29/29	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.520969554371177	2		572	754	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993366	72993366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140855443	NA	P-0060682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	159	560	0	ENST00000268489.5:c.679G>A	p.Val227Ile	p.V227I	ENST00000268489	NM_006885.3	227	Gtc/Atc	2/10	1	2	FACETS	0.836	0.768	0.907	0.836	0.768	0.907	CLONAL	1	TRUE	1	0.520969554371177	2		560	730	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214734	36214734	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	81	482	1	ENST00000222270.7:c.3163del	p.Arg1055GlyfsTer127	p.R1055Gfs*127	ENST00000222270	NM_014727.1	1054	Ccc/cc	8/37	1	2	FACETS	0.523	0.461	0.589	0.523	0.461	0.589	SUBCLONAL	1	TRUE	1	0.520969554371177	2		483	595	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505386	157505386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs960166468	NA	P-0060682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	34	378	0	ENST00000346085.5:c.3367C>T	p.Arg1123Cys	p.R1123C	ENST00000346085	NM_020732.3	1123	Cgt/Tgt	13/20	1	2	FACETS	0.248	0.202	0.3	0.248	0.202	0.3	SUBCLONAL	1	TRUE	1	0.520969554371177	2		378	526	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552144	29552144	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	76	375	0	ENST00000356175.3:c.1882del	p.Tyr628ThrfsTer3	p.Y628Tfs*3	ENST00000356175	NM_000267.3	626	cTt/ct	17/57	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.520969554371177	2		375	267	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165630	118165631	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0060682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	159	586	0	ENST00000369448.3:c.142_143del	p.Leu48GlufsTer61	p.L48Efs*61	ENST00000369448	NM_017709.3	47	aCT/a	2/2	1	2	FACETS	0.773	0.709	0.839	0.773	0.709	0.839	SUBCLONAL	1	TRUE	1	0.520969554371177	2		586	790	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156848968	156848968	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	108	596	0	ENST00000524377.1:c.1864del	p.Leu622TrpfsTer36	p.L622Wfs*36	ENST00000524377	NM_002529.3	620	ggC/gg	15/17	0.520969554371177	3	FACETS	0.564	0.506	0.627	0.282	0.253	0.314	SUBCLONAL	1	TRUE	1	0.520969554371177	3		596	926	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10792121	10792122	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0060682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	55	407	0	ENST00000361367.2:c.2320dup	p.Ser774LysfsTer2	p.S774Kfs*2	ENST00000361367	NM_014633.3	772	gaa/gAaa	18/25	1	2	FACETS	0.634	0.545	0.73	0.634	0.545	0.73	SUBCLONAL	1	TRUE	1	0.520969554371177	2		407	333	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420841	49420841	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	186	551	0	ENST00000301067.7:c.14908G>T	p.Glu4970Ter	p.E4970*	ENST00000301067	NM_003482.3	4970	Gaa/Taa	48/54	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.520969554371177	2		551	688	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900431	3900431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	122	520	0	ENST00000262367.5:c.665C>T	p.Ala222Val	p.A222V	ENST00000262367	NM_004380.2	222	gCt/gTt	2/31	1	2	FACETS	0.73	0.661	0.802	0.73	0.661	0.802	SUBCLONAL	1	TRUE	1	0.520969554371177	2		520	642	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544687	86544687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	45	590	0	ENST00000262426.4:c.512G>A	p.Gly171Asp	p.G171D	ENST00000262426	NM_001451.2	171	gGc/gAc	1/2	1	2	FACETS	0.285	0.239	0.336	0.285	0.239	0.336	SUBCLONAL	1	TRUE	1	0.520969554371177	2		590	606	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559901	29559901	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0060682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	126	473	0	ENST00000356175.3:c.3496+2T>C		p.X1166_splice	ENST00000356175	NM_000267.3	1166			1	2	FACETS	0.943	0.858	1	0.943	0.858	1	CLONAL	1	TRUE	1	0.520969554371177	2		473	513	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221657	36221657	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1599690765	NA	P-0060682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	170	610	0	ENST00000222270.7:c.5326T>G	p.Tyr1776Asp	p.Y1776D	ENST00000222270	NM_014727.1	1776	Tat/Gat	26/37	1	2	FACETS	0.964	0.89	1	0.964	0.89	1	CLONAL	1	TRUE	1	0.520969554371177	2		610	677	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180425	38180425	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	55	585	0	ENST00000396334.3:c.273G>A	p.Trp91Ter	p.W91*	ENST00000396334	NM_002468.4	91	tgG/tgA	1/5	1	2	FACETS	0.319	0.273	0.371	0.319	0.273	0.371	SUBCLONAL	1	TRUE	1	0.520969554371177	2		585	661	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665409	182665409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	12	199	0	ENST00000292782.4:c.532G>A	p.Ala178Thr	p.A178T	ENST00000292782	NM_020640.2	178	Gcc/Acc	5/7	1	2	FACETS	0.366	0.258	0.496	0.366	0.258	0.496	SUBCLONAL	1	TRUE	1	0.520969554371177	2		199	126	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798429	32798429	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	106	534	0	ENST00000374899.4:c.1427C>T	p.Ala476Val	p.A476V	ENST00000374899	NM_018833.2	476	gCa/gTa	8/12	1	2	FACETS	0.599	0.538	0.665	0.599	0.538	0.665	SUBCLONAL	1	TRUE	1	0.520969554371177	2		534	679	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0060683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	106	385	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.350947639766132	3	FACETS	1	0.956	1	0.558	0.501	0.619	CLONAL	1	TRUE	1	0.350947639766132	3		385	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs886039483	NA	P-0060683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	210	484	0	ENST00000269305.4:c.376T>G	p.Tyr126Asp	p.Y126D	ENST00000269305	NM_001126112.2	126	Tac/Gac	5/11	0.350947639766132	3	FACETS	0.984	0.917	1	0.984	0.917	1	CLONAL	2	TRUE	1	0.350947639766132	3		484	715	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733231	74733360	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	GCCGTAGCTCATAGCTCTGAGTGGCGGCCCGGAGCCCCGCGAACTGGCGCCGGCTTCCTCAGCTCTGGGCGGTGCGACGCCGCGCCTCTCAGGCAGTTGCCTTCCGCGTGGGGACACTGGGAAAGGCCTT	GCCGTAGCTCATAGCTCTGAGTGGCGGCCCGGAGCCCCGCGAACTGGCGCCGGCTTCCTCAGCTCTGGGCGGTGCGACGCCGCGCCTCTCAGGCAGTTGCCTTCCGCGTGGGGACACTGGGAAAGGCCTT	-	novel	NA	P-0060684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	55	551	0	ENST00000359995.5:c.-118_12del		p.*40*	ENST00000359995	NM_001195427.1	?-4/221		1/3	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		551	334	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	207	321	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.943	0.885	1	0.943	0.885	1	CLONAL	1	TRUE	1	0.920276078441754	2		321	477	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0060685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	854	277	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.820906543690709	3	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.920276078441754	3		277	1335	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144113	11144113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	367	650	1	ENST00000358026.2:c.3694G>A	p.Gly1232Ser	p.G1232S	ENST00000358026	NM_001128849.1	1232	Ggc/Agc	26/36	1	2	FACETS	0.994	0.949	1	0.994	0.949	1	CLONAL	1	TRUE	1	0.920276078441754	2		651	802	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041606	47041606	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	400	306	0	ENST00000377604.3:c.1831G>T	p.Glu611Ter	p.E611*	ENST00000377604	NM_001204468.1	611	Gag/Tag	17/24	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.920276078441754	1		306	421	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966766	44966766	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	186	210	0	ENST00000377967.4:c.3990C>A	p.Tyr1330Ter	p.Y1330*	ENST00000377967	NM_021140.2	1330	taC/taA	27/29	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.920276078441754	1		210	206	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828057	3828057	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	354	485	0	ENST00000262367.5:c.2068del	p.Ala690LeufsTer5	p.A690Lfs*5	ENST00000262367	NM_004380.2	690	Gct/ct	10/31	0.920276078441754	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.920276078441754	1		485	405	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980291	201980292	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0060685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	412	534	0	ENST00000359651.3:c.28_29dup	p.Ser12LeufsTer32	p.S12Lfs*32	ENST00000359651		9	-/AT	1/8	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.920276078441754	2		534	869	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231489066	231489066	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	297	450	0	ENST00000295050.7:c.1429G>C	p.Glu477Gln	p.E477Q	ENST00000295050	NM_032018.5	477	Gaa/Caa	5/5	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.920276078441754	2		450	640	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115749	8115750	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGAAAAATGTCTAGCAAAT	novel	NA	P-0060685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	174	506	0	ENST00000346208.3:c.1097_1115dup	p.Lys374AsnfsTer3	p.K374Nfs*3	ENST00000346208		365	-/CGAAAAATGTCTAGCAAAT	6/6	1	2	FACETS	0.589	0.544	0.635	0.589	0.544	0.635	SUBCLONAL	1	TRUE	1	0.920276078441754	2		506	642	SUCCESS
BLM	641	MSKCC	GRCh37	15	91334000	91334000	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	260	382	0	ENST00000355112.3:c.2945G>T	p.Arg982Ile	p.R982I	ENST00000355112	NM_000057.2	982	aGa/aTa	15/22	1	2	FACETS	0.937	0.885	0.989	0.937	0.885	0.989	CLONAL	1	TRUE	1	0.920276078441754	2		382	603	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7977069	7977069	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	282	307	0	ENST00000319144.4:c.1661C>A	p.Pro554His	p.P554H	ENST00000319144	NM_001139.2	554	cCt/cAt	13/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.920276078441754	2		307	558	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250281	39250281	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	190	426	0	ENST00000402219.2:c.1288G>C	p.Asp430His	p.D430H	ENST00000402219	NM_005633.3	430	Gat/Cat	10/23	1	2	FACETS	0.916	0.856	0.976	0.916	0.856	0.976	CLONAL	1	TRUE	1	0.920276078441754	2		426	451	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162186	47162186	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	382	528	0	ENST00000409792.3:c.3940C>A	p.Pro1314Thr	p.P1314T	ENST00000409792	NM_014159.6	1314	Cct/Act	3/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.920276078441754	2		528	797	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109311862	109311862	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	158	355	0	ENST00000436639.2:c.1410C>A	p.Cys470Ter	p.C470*	ENST00000436639	NM_014454.2	470	tgC/tgA	8/10	1	2	FACETS	0.921	0.855	0.987	0.921	0.855	0.987	CLONAL	1	TRUE	1	0.920276078441754	2		355	373	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001039	150001040	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0060685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	134	417	0	ENST00000253339.5:c.2564_2565delinsTT	p.Trp855Phe	p.W855F	ENST00000253339		855	tGG/tTT	4/7	1	2	FACETS	0.872	0.803	0.942	0.872	0.803	0.942	CLONAL	1	TRUE	1	0.920276078441754	2		417	334	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0060686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	10	286	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.244378032653272	3	FACETS	1	0.781	1	0.765	0.537	1	CLONAL	2	FALSE	0	0.244378032653272	3		286	40	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577157	7577157	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0060686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	17	443	0	ENST00000269305.4:c.783-2A>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.225091889666849	3	FACETS	1	0.87	1	0.813	0.625	1	CLONAL	2	FALSE	0	0.244378032653272	3		443	64	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963922	2963922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	20	610	0	ENST00000396946.4:c.1885G>A	p.Asp629Asn	p.D629N	ENST00000396946	NM_032415.4	629	Gat/Aat	15/25	0.244378032653272	5	FACETS	1	0.869	1	1	0.869	1	CLONAL	2	FALSE	3	0.244378032653272	5		610	95	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222490	2222490	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs995952663	NA	P-0060686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	35	494	0	ENST00000398665.3:c.3322C>T	p.Arg1108Ter	p.R1108*	ENST00000398665	NM_032482.2	1108	Cga/Tga	24/28	0.244378032653272	3	FACETS	1	0.901	1	1	0.901	1	CLONAL	3	FALSE	0	0.244378032653272	3		494	98	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63898396	63898396	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1447735583	NA	P-0060686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	10	468	0	ENST00000398590.3:c.122C>A	p.Pro41Gln	p.P41Q	ENST00000398590	NM_001177387.1	41	cCg/cAg	3/14	0.244378032653272	3	FACETS	1	0.769	1	1	0.769	1	CLONAL	2	FALSE	1	0.244378032653272	3		468	41	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0060699-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	379	665	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.574398820944977	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.574398820944977	1		666	783	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426690	212426690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060699-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	146	655	0	ENST00000342788.4:c.2425C>T	p.His809Tyr	p.H809Y	ENST00000342788	NM_005235.2	809	Cac/Tac	20/28	1	2	FACETS	0.588	0.536	0.642	0.588	0.536	0.642	SUBCLONAL	1	TRUE	1	0.574398820944977	2		655	865	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593271	67593349	+	frameshift_variant	Frame_Shift_Del	DEL	AACAAAACAGCAACTGGCTATGGCTTTGCCGAGCCCTATAACTTGTACAGCTCTCTGAAAGAACTGGTGCTACATTACC	AACAAAACAGCAACTGGCTATGGCTTTGCCGAGCCCTATAACTTGTACAGCTCTCTGAAAGAACTGGTGCTACATTACC	-	novel	NA	P-0060699-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	277	631	0	ENST00000274335.5:c.2021_2099del	p.Lys674ThrfsTer15	p.K674Tfs*15	ENST00000274335		673	AACAAAACAGCAACTGGCTATGGCTTTGCCGAGCCCTATAACTTGTACAGCTCTCTGAAAGAACTGGTGCTACATTACCaa/aa	15/15	0.574398820944977	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.574398820944977	1		631	677	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602806	10602806	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060703-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	647	639	0	ENST00000171111.5:c.772G>T	p.Glu258Ter	p.E258*	ENST00000171111	NM_203500.1	258	Gaa/Taa	3/6	0.59244425253612	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.597901003935448	2		639	1062	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604750	48604750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060703-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	250	469	0	ENST00000342988.3:c.1572G>T	p.Trp524Cys	p.W524C	ENST00000342988	NM_005359.5	524	tgG/tgT	12/12	0.597901003935448	1	FACETS	0.932	0.878	0.987	0.932	0.878	0.987	CLONAL	1	TRUE	0	0.597901003935448	1		469	629	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218446	1218447	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0060703-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	189	406	0	ENST00000326873.7:c.326dup	p.Asn109LysfsTer54	p.N109Kfs*54	ENST00000326873	NM_000455.4	107	-/A	2/10	0.597901003935448	1	FACETS	0.916	0.855	0.978	0.916	0.855	0.978	CLONAL	1	TRUE	0	0.597901003935448	1		406	484	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508239	106508239	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060703-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	239	538	1	ENST00000359195.3:c.233C>A	p.Ala78Glu	p.A78E	ENST00000359195	NM_002649.2	78	gCg/gAg	2/11	1	2	FACETS	0.851	0.796	0.909	0.851	0.796	0.909	CLONAL	1	TRUE	1	0.597901003935448	2		539	939	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99192838	99192838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs530243293	NA	P-0060703-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	186	320	0	ENST00000268035.6:c.28C>T	p.Pro10Ser	p.P10S	ENST00000268035	NM_000875.3	10	Ccg/Tcg	1/21	1	2	FACETS	0.969	0.899	1	0.969	0.899	1	CLONAL	1	TRUE	1	0.597901003935448	2		320	642	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266107	41266108	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0060703-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	250	463	0	ENST00000349496.5:c.104_105delinsAA	p.Ile35Lys	p.I35K	ENST00000349496	NM_001904.3	35	aTC/aAA	3/15	0.597901003935448	1	FACETS	0.953	0.898	1	0.953	0.898	1	CLONAL	1	TRUE	0	0.597901003935448	1		463	615	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21345963	21345963	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1419091884	NA	P-0060703-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	237	529	0	ENST00000215739.8:c.842del	p.Pro281ArgfsTer70	p.P281Rfs*70	ENST00000215739	NM_006767.3	280	Ccc/cc	9/21	0.597901003935448	1	FACETS	0.934	0.879	0.99	0.934	0.879	0.99	CLONAL	1	TRUE	0	0.597901003935448	1		529	595	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976840	55976840	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060703-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	225	381	0	ENST00000263923.4:c.1072C>A	p.Pro358Thr	p.P358T	ENST00000263923	NM_002253.2	358	Cca/Aca	8/30	0.329255632842822	1	FACETS	0.852	0.799	0.907	0.852	0.799	0.907	INDETERMINATE	1	TRUE	0	0.597901003935448	1		381	619	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862942	117862942	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060703-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	56	242	0	ENST00000297338.2:c.1535T>C	p.Ile512Thr	p.I512T	ENST00000297338	NM_006265.2	512	aTc/aCc	12/14	0.329255632842822	1	FACETS	0.471	0.406	0.54	0.471	0.406	0.54	INDETERMINATE	1	TRUE	0	0.597901003935448	1		242	279	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0060704-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	341	646	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.482214014877461	2	FACETS	0.819	0.782	0.857	0.819	0.782	0.857	CLONAL	2	TRUE	0	0.61930316829698	2		646	672	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0060704-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	406	579	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.61930316829698	6	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	3	0.61930316829698	6		579	904	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37865577	37865577	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060704-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	717	488	0	ENST00000269571.5:c.446T>G	p.Leu149Trp	p.L149W	ENST00000269571		149	tTg/tGg	4/27	0.61930316829698	3	FACETS	0.977	0.952	1	0.977	0.952	1	CLONAL	3	TRUE	0	0.61930316829698	3		488	1035	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39774477	39774477	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0060704-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	207	440	0	ENST00000288319.7:c.673+2T>C		p.X225_splice	ENST00000288319	NM_182918.3	225			0.589099170578305	4	FACETS	1	0.99	1	0.344	0.32	0.369	CLONAL	1	TRUE	0	0.61930316829698	4		440	786	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713691	30713691	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs727503473	NA	P-0060704-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	431	664	0	ENST00000295754.5:c.1016G>T	p.Arg339Leu	p.R339L	ENST00000295754	NM_003242.5	339	cGg/cTg	4/7	0.61930316829698	4	FACETS	1	0.984	1	0.53	0.507	0.554	CLONAL	2	TRUE	0	0.61930316829698	4		664	1063	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37038114	37038114	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs267607713	NA	P-0060704-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	90	278	0	ENST00000231790.2:c.121G>C	p.Asp41His	p.D41H	ENST00000231790	NM_000249.3	41	Gat/Cat	2/19	0.61930316829698	4	FACETS	0.856	0.761	0.956	0.214	0.19	0.239	CLONAL	1	TRUE	0	0.61930316829698	4		278	550	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169999044	169999044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060704-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	350	315	0	ENST00000295797.4:c.973G>A	p.Glu325Lys	p.E325K	ENST00000295797	NM_002740.5	325	Gaa/Aaa	10/18	0.590642257959789	5	FACETS	1	0.983	1	0.636	0.607	0.664	CLONAL	3	TRUE	0	0.61930316829698	5		315	686	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564471	55564471	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060704-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	329	452	0	ENST00000288135.5:c.359T>C	p.Val120Ala	p.V120A	ENST00000288135	NM_000222.2	120	gTt/gCt	3/21	0.486008114082738	3	FACETS	1	0.992	1	0.777	0.743	0.811	CLONAL	2	TRUE	0	0.61930316829698	3		452	597	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681114	117681114	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs769432383	NA	P-0060704-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	112	391	0	ENST00000368508.3:c.3506T>C	p.Met1169Thr	p.M1169T	ENST00000368508	NM_002944.2	1169	aTg/aCg	23/43	1	2	FACETS	0.749	0.677	0.824	0.749	0.677	0.824	SUBCLONAL	1	TRUE	1	0.61930316829698	2		391	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0060705-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	437	1000	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.799023358920567	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.799023358920567	1		1000	592	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954221	48954221	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0060705-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	264	231	0	ENST00000267163.4:c.1421+1G>T		p.X474_splice	ENST00000267163	NM_000321.2	474			0.799023358920567	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.799023358920567	2		231	321	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881114	37881114	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368094521	NA	P-0060705-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1240	391	694	1	ENST00000269571.5:c.2443G>A	p.Gly815Arg	p.G815R	ENST00000269571		815	Gga/Aga	20/27	0.789180375126211	4	FACETS	1	0.983	1	0.36	0.341	0.379	CLONAL	1	TRUE	1	0.799023358920567	4		695	1631	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898819	134898819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060705-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	287	500	0	ENST00000398015.3:c.1877G>A	p.Gly626Glu	p.G626E	ENST00000398015	NM_004441.4	626	gGa/gAa	10/16	0.799023358920567	2	FACETS	1	0.97	1	0.518	0.49	0.546	CLONAL	1	TRUE	0	0.799023358920567	2		500	694	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660274	227660274	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1174574402	NA	P-0060705-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	730	706	0	ENST00000305123.5:c.3181G>T	p.Gly1061Trp	p.G1061W	ENST00000305123	NM_005544.2	1061	Ggg/Tgg	1/2	0.799023358920567	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.799023358920567	3		706	1228	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602686	10602686	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0060705-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	1108	707	2	ENST00000171111.5:c.892A>T	p.Lys298Ter	p.K298*	ENST00000171111	NM_203500.1	298	Aag/Tag	3/6	0.799023358920567	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.799023358920567	3		709	1281	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18762564	18762564	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0060705-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	401	338	0	ENST00000266497.5:c.4059+1G>C		p.X1353_splice	ENST00000266497		1353			0.799023358920567	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.799023358920567	3		338	464	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437269	110437269	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060705-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	186	190	0	ENST00000375856.3:c.1132G>C	p.Ala378Pro	p.A378P	ENST00000375856	NM_003749.2	378	Gcg/Ccg	1/2	0.799023358920567	5	FACETS	1	0.985	1	0.253	0.234	0.273	CLONAL	1	TRUE	0	0.799023358920567	5		190	809	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733122	74733122	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060705-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1328	407	627	0	ENST00000359995.5:c.121G>A	p.Gly41Ser	p.G41S	ENST00000359995	NM_001195427.1	41	Ggc/Agc	1/3	0.789180375126211	4	FACETS	1	0.979	1	0.352	0.334	0.371	CLONAL	1	TRUE	1	0.799023358920567	4		627	1735	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61305258	61305258	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060705-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	46	263	1	ENST00000341074.5:c.868G>T	p.Glu290Ter	p.E290*	ENST00000341074	NM_002974.2	290	Gaa/Taa	8/8	0.422361776435382	3	FACETS	0.39	0.329	0.458	0.13	0.109	0.153	INDETERMINATE	1	TRUE	0	0.799023358920567	3		264	413	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251818	212251818	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060705-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	750	595	1	ENST00000342788.4:c.3241T>C	p.Tyr1081His	p.Y1081H	ENST00000342788	NM_005235.2	1081	Tac/Cac	27/28	0.799023358920567	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.799023358920567	3		596	1264	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980926	40980926	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0060705-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	244	575	2	ENST00000373198.4:c.1561-1G>T		p.X521_splice	ENST00000373198	NM_133170.3	521			0.360979506237472	5	FACETS	1	0.982	1	0.382	0.357	0.409	INDETERMINATE	1	TRUE	2	0.799023358920567	5		577	1171	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564672	86564672	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060705-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	452	699	0	ENST00000274376.6:c.404C>A	p.Pro135His	p.P135H	ENST00000274376	NM_002890.2	135	cCc/cAc	1/25	0.772362829664356	3	FACETS	1	0.986	1	0.54	0.515	0.566	CLONAL	1	TRUE	1	0.799023358920567	3		699	1465	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172082	32172082	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060705-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	314	636	0	ENST00000375023.3:c.2950A>C	p.Thr984Pro	p.T984P	ENST00000375023	NM_004557.3	984	Act/Cct	19/30	0.799023358920567	3	FACETS	0.962	0.908	1	0.481	0.454	0.509	CLONAL	1	TRUE	1	0.799023358920567	3		636	1143	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979424	2979424	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060705-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	244	501	0	ENST00000396946.4:c.823del	p.Met275CysfsTer2	p.M275Cfs*2	ENST00000396946	NM_032415.4	275	Atg/tg	6/25	0.772362829664356	3	FACETS	0.888	0.83	0.947	0.444	0.415	0.474	CLONAL	1	TRUE	1	0.799023358920567	3		501	963	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737777	145737777	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060705-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	1006	786	1	ENST00000428558.2:c.3053C>G	p.Thr1018Arg	p.T1018R	ENST00000428558	NM_004260.3	1018	aCa/aGa	18/22	0.579646580568949	5	FACETS	0.875	0.851	0.899	0.875	0.851	0.899	CLONAL	3	TRUE	2	0.799023358920567	5		787	2110	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449832	8449832	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060705-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	486	481	1	ENST00000356435.5:c.3881G>T	p.Arg1294Met	p.R1294M	ENST00000356435		1294	aGg/aTg	23/35	0.590888555260894	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.799023358920567	4		482	1049	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0060711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	21	382	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.250759638654763	5	FACETS	1	0.838	1	0.37	0.285	0.468	CLONAL	1	TRUE	2	0.21	5		382	237	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208036	5208036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772956659	NA	P-0060711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	44	658	0	ENST00000357368.4:c.5675C>T	p.Thr1892Met	p.T1892M	ENST00000357368	NM_002850.3	1892	aCg/aTg	37/38	0.305799400551851	3	FACETS	0.776	0.65	0.916	0.388	0.325	0.458	CLONAL	1	TRUE	1	0.21	3		658	597	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149940	202149940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	63	743	0	ENST00000358485.4:c.1381G>A	p.Gly461Arg	p.G461R	ENST00000358485	NM_001080125.1	461	Ggg/Agg	8/9	0.250759638654763	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	0	0.21	1		743	509	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992152	11992161	+	frameshift_variant	Frame_Shift_Del	DEL	CAATTGACAG	CAATTGACAG	-	novel	NA	P-0060711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	44	483	0	ENST00000396373.4:c.245_254del	p.Ile82ThrfsTer5	p.I82Tfs*5	ENST00000396373	NM_001987.4	81	cCAATTGACAGc/cc	3/8	0.250759638654763	5	FACETS	1	0.928	1	0.4	0.336	0.472	CLONAL	1	TRUE	2	0.21	5		483	459	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435900	56435901	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0060711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	71	731	0	ENST00000407977.2:c.1235_1236dup	p.Ala413MetfsTer7	p.A413Mfs*7	ENST00000407977		412	-/AT	9/10	0.162106859591344	3	FACETS	1	0.962	1	0.641	0.56	0.728	CLONAL	1	TRUE	1	0.21	3		731	583	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981810	63981810	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372175214	NA	P-0060711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	62	666	0	ENST00000398590.3:c.2312G>A	p.Arg771Gln	p.R771Q	ENST00000398590	NM_001177387.1	771	cGg/cAg	12/14	1	2	FACETS	0.852	0.735	0.979	0.852	0.735	0.979	CLONAL	1	TRUE	1	0.21	2		666	693	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043460	180043460	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	30	670	0	ENST00000261937.6:c.3126C>A	p.Asn1042Lys	p.N1042K	ENST00000261937	NM_182925.4	1042	aaC/aaA	23/30	0.250759638654763	1	FACETS	0.473	0.38	0.578	0.473	0.38	0.578	SUBCLONAL	1	TRUE	0	0.21	1		670	541	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412813	63412813	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	42	572	0	ENST00000330258.3:c.354del	p.Pro119LeufsTer51	p.P119Lfs*51	ENST00000330258	NM_152424.3	118	ctG/ct	2/2	0.162106859591344	3	FACETS	0.815	0.68	0.966	0.408	0.34	0.483	CLONAL	1	TRUE	1	0.21	3		572	542	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	46	321	0				ENST00000310581	NM_198253.2	-/1132			0.183284561685161	1	FACETS	0.42	0.352	0.495	0.42	0.352	0.495	SUBCLONAL	1	TRUE	0	0.247699254535155	1		321	775	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0060714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	29	544	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.188862550586029	3	FACETS	0.964	0.776	1	0.482	0.388	0.588	CLONAL	1	TRUE	1	0.247699254535155	3		544	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0060714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	66	642	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.203146596406272	1	FACETS	0.54	0.467	0.619	0.54	0.467	0.619	SUBCLONAL	1	TRUE	0	0.247699254535155	1		642	865	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577077	7577077	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs748891343	NA	P-0060714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	65	650	0	ENST00000269305.4:c.861G>C	p.Glu287Asp	p.E287D	ENST00000269305	NM_001126112.2	287	gaG/gaC	8/11	0.203146596406272	1	FACETS	0.503	0.435	0.577	0.503	0.435	0.577	SUBCLONAL	1	TRUE	0	0.247699254535155	1		650	914	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700235	117700235	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	34	466	0	ENST00000368508.3:c.2584C>T	p.Leu862Phe	p.L862F	ENST00000368508	NM_002944.2	862	Ctt/Ttt	17/43	1	2	FACETS	0.539	0.44	0.651	0.539	0.44	0.651	SUBCLONAL	1	TRUE	1	0.247699254535155	2		466	509	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059242	27059242	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	67	521	0	ENST00000324856.7:c.1879G>A	p.Asp627Asn	p.D627N	ENST00000324856	NM_006015.4	627	Gat/Aat	4/20	1	2	FACETS	0.771	0.669	0.881	0.771	0.669	0.881	SUBCLONAL	1	TRUE	1	0.247699254535155	2		521	702	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373751	118373751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs387907275	NA	P-0060714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	101	688	1	ENST00000534358.1:c.7144C>T	p.Arg2382Ter	p.R2382*	ENST00000534358	NM_005933.3	2382	Cga/Tga	27/36	1	2	FACETS	0.99	0.884	1	0.99	0.884	1	CLONAL	1	TRUE	1	0.247699254535155	2		689	824	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073754	8073754	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	72	727	0	ENST00000377482.5:c.905C>A	p.Ser302Ter	p.S302*	ENST00000377482	NM_018948.3	302	tCa/tAa	4/4	1	2	FACETS	0.548	0.478	0.625	0.548	0.478	0.625	SUBCLONAL	1	TRUE	1	0.247699254535155	2		727	1060	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820876	36820876	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	91	730	0	ENST00000373129.3:c.501G>C	p.Lys167Asn	p.K167N	ENST00000373129	NM_032017.1	167	aaG/aaC	6/12	1	2	FACETS	0.757	0.67	0.849	0.757	0.67	0.849	SUBCLONAL	1	TRUE	1	0.247699254535155	2		730	971	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438242	49438254	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTCCACATCAG	GGCTCCACATCAG	-	novel	NA	P-0060714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	171	673	0	ENST00000301067.7:c.5015_5027del	p.Pro1672LeufsTer46	p.P1672Lfs*46	ENST00000301067	NM_003482.3	1672	cCTGATGTGGAGCCt/ct	20/54	0.247699254535155	3	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.247699254535155	3		673	1152	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518159	103518159	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	166	666	0	ENST00000355739.4:c.2097C>A	p.Ser699Arg	p.S699R	ENST00000355739	NM_000123.3	699	agC/agA	9/15	0.156532355837473	2	FACETS	0.784	0.72	0.85	0.784	0.72	0.85	SUBCLONAL	2	TRUE	0	0.247699254535155	2		666	855	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590714	95590714	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	49	521	0	ENST00000393063.1:c.1195G>C	p.Glu399Gln	p.E399Q	ENST00000393063	NM_030621.3	399	Gag/Cag	9/28	1	2	FACETS	0.604	0.511	0.707	0.604	0.511	0.707	SUBCLONAL	1	TRUE	1	0.247699254535155	2		521	655	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026147	71026147	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	80	426	0	ENST00000318789.4:c.1475A>G	p.Tyr492Cys	p.Y492C	ENST00000318789	NM_032682.5	492	tAt/tGt	17/21	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.247699254535155	2		426	642	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740615	145740615	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	234	809	0	ENST00000428558.2:c.1402G>T	p.Glu468Ter	p.E468*	ENST00000428558	NM_004260.3	468	Gag/Tag	8/22	0.188862550586029	3	FACETS	0.763	0.71	0.818	0.763	0.71	0.818	SUBCLONAL	2	TRUE	1	0.247699254535155	3		809	1392	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922753	44922775	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTGGCCAGCAGCCACAGCTTG	CTCTGGCCAGCAGCCACAGCTTG	-	novel	NA	P-0060714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	116	302	0	ENST00000377967.4:c.1619_1641del	p.Gly540AspfsTer5	p.G540Dfs*5	ENST00000377967	NM_021140.2	538	gtCTCTGGCCAGCAGCCACAGCTTGct/gtct	16/29	0.247699254535155	2	FACETS	1	0.932	1			1	CLONAL	2	TRUE	NA	0.247699254535155	2		302	453	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928834	44928834	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	33	188	0	ENST00000377967.4:c.1934A>T	p.Lys645Ile	p.K645I	ENST00000377967	NM_021140.2	645	aAa/aTa	17/29	0.247699254535155	2	FACETS	0.777	0.634	0.937			1	CLONAL	1	TRUE	NA	0.247699254535155	2		188	343	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0060724-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	165	377	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.273191567842621	3	FACETS	0.942	0.869	1	0.942	0.869	1	CLONAL	2	TRUE	1	0.332756372526153	3		377	614	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0060725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	69	377	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.989	0.865	1	0.989	0.865	1	CLONAL	1	TRUE	1	0.322251758979713	2		377	433	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505342	186505342	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0060725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	89	602	0	ENST00000323963.5:c.968C>G	p.Ser323Ter	p.S323*	ENST00000323963		323	tCa/tGa	9/11	1	2	FACETS	0.837	0.742	0.938	0.837	0.742	0.938	CLONAL	1	TRUE	1	0.322251758979713	2		602	660	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647508	23647508	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	94	516	0	ENST00000261584.4:c.359G>T	p.Arg120Ile	p.R120I	ENST00000261584	NM_024675.3	120	aGa/aTa	4/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.322251758979713	2		516	489	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106731	27106731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	110	827	0	ENST00000324856.7:c.6342del	p.Gln2115ArgfsTer20	p.Q2115Rfs*20	ENST00000324856	NM_006015.4	2114	ccG/cc	20/20	1	2	FACETS	0.876	0.787	0.971	0.876	0.787	0.971	CLONAL	1	TRUE	1	0.322251758979713	2		827	779	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915247	32915247	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs876658504	NA	P-0060725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	69	629	0	ENST00000380152.3:c.6755C>G	p.Ser2252Cys	p.S2252C	ENST00000380152		2252	tCt/tGt	11/27	1	2	FACETS	0.681	0.593	0.776	0.681	0.593	0.776	SUBCLONAL	1	TRUE	1	0.322251758979713	2		629	629	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426794	212426794	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	75	556	0	ENST00000342788.4:c.2321G>T	p.Ser774Ile	p.S774I	ENST00000342788	NM_005235.2	774	aGt/aTt	20/28	1	2	FACETS	0.801	0.703	0.907	0.801	0.703	0.907	CLONAL	1	TRUE	1	0.322251758979713	2		556	581	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169002	32169002	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	115	811	0	ENST00000375023.3:c.4031G>C	p.Gly1344Ala	p.G1344A	ENST00000375023	NM_004557.3	1344	gGg/gCg	22/30	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.322251758979713	2		811	648	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959091	2959092	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0060725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	78	713	0	ENST00000396946.4:c.2424_2425delinsAA	p.Tyr808_Gln809delinsTer	p.Y808_Q809delins*	ENST00000396946	NM_032415.4	808	taCCag/taAAag	18/25	1	2	FACETS	0.857	0.754	0.967	0.857	0.754	0.967	CLONAL	1	TRUE	1	0.322251758979713	2		713	565	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779081	135779081	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	106	649	0	ENST00000298552.3:c.2165A>C	p.Lys722Thr	p.K722T	ENST00000298552	NM_001162426.1	722	aAg/aCg	17/23	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.322251758979713	2		649	626	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045525	47045526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGAGCCCAAGAGG	novel	NA	P-0060725-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	82	856	0	ENST00000377604.3:c.2495_2507dup	p.Lys837AlafsTer27	p.K837Afs*27	ENST00000377604	NM_001204468.1	831	cca/ccAGAGCCCAAGAGGa	22/24	1	2	FACETS	0.704	0.62	0.794	0.704	0.62	0.794	SUBCLONAL	1	TRUE	1	0.322251758979713	2		856	723	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	46	321	0				ENST00000310581	NM_198253.2	-/1132			0.205304545478989	2	FACETS	1	0.95	1	0.661	0.56	0.773	CLONAL	1	TRUE	0	0.217999424613846	2		321	319	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226309	2226309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	41	790	0	ENST00000326181.6:c.1922G>A	p.Arg641His	p.R641H	ENST00000326181	NM_032271.2	641	cGt/cAt	20/21	1	2	FACETS	0.57	0.474	0.678	0.57	0.474	0.678	SUBCLONAL	1	TRUE	1	0.217999424613846	2		790	660	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443481	49443481	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781156556	NA	P-0060726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	82	717	0	ENST00000301067.7:c.3890G>A	p.Arg1297His	p.R1297H	ENST00000301067	NM_003482.3	1297	cGt/cAt	11/54	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.217999424613846	2		717	636	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998462	100998462	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0060726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	34	657	0	ENST00000325455.5:c.1340C>G	p.Ser447Ter	p.S447*	ENST00000325455	NM_001202474.3	447	tCa/tGa	1/8	1	2	FACETS	0.664	0.542	0.801	0.664	0.542	0.801	SUBCLONAL	1	TRUE	1	0.217999424613846	2		657	470	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871802	12871803	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0060726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	41	541	0	ENST00000228872.4:c.520_521del	p.Val174PhefsTer30	p.V174Ffs*30	ENST00000228872	NM_004064.3	173	aaTGtt/aatt	2/3	1	2	FACETS	0.476	0.395	0.567	0.476	0.395	0.567	SUBCLONAL	1	TRUE	1	0.217999424613846	2		541	790	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434787	110434787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060726-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	66	725	0	ENST00000375856.3:c.3614G>A	p.Arg1205Gln	p.R1205Q	ENST00000375856	NM_003749.2	1205	cGa/cAa	1/2	1	2	FACETS	0.908	0.788	1	0.908	0.788	1	CLONAL	1	TRUE	1	0.217999424613846	2		725	667	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11168269	11168269	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060729-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	148	623	0	ENST00000361445.4:c.7603C>T	p.His2535Tyr	p.H2535Y	ENST00000361445	NM_004958.3	2535	Cat/Tat	57/58	0.654930022979424	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	FALSE	0	0.654930022979424	1		623	300	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455091	50455091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1422790468	NA	P-0060748-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	66	417	0	ENST00000331340.3:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000331340	NM_006060.4	213	cGa/cAa	6/8	1	2	FACETS	0.948	0.821	1	0.948	0.821	1	CLONAL	1	TRUE	1	0.175582294892618	2		417	793	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600386	10600386	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060748-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	98	621	0	ENST00000171111.5:c.1469A>G	p.Tyr490Cys	p.Y490C	ENST00000171111	NM_203500.1	490	tAc/tGc	4/6	0.175582294892618	1	FACETS	0.946	0.842	1	0.946	0.842	1	CLONAL	1	TRUE	0	0.175582294892618	1		621	1076	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0060757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	89	382	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.170744117281571	3	FACETS	0.995	0.889	1	0.664	0.592	0.739	CLONAL	2	TRUE	0	0.26427866448997	3		382	383	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	113	758	0	ENST00000326873.7:c.667G>T	p.Glu223Ter	p.E223*	ENST00000326873	NM_000455.4	223	Gag/Tag	5/10	1	2	FACETS	0.991	0.891	1	0.991	0.891	1	CLONAL	1	TRUE	1	0.26427866448997	2		758	863	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0060757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	119	840	0	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	1	2	FACETS	0.937	0.845	1	0.937	0.845	1	CLONAL	1	TRUE	1	0.26427866448997	2		840	961	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599867	10599867	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0060757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	82	574	0	ENST00000171111.5:c.1708+1G>T		p.X570_splice	ENST00000171111	NM_203500.1	570			1	2	FACETS	0.936	0.826	1	0.936	0.826	1	CLONAL	1	TRUE	1	0.26427866448997	2		574	663	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541874	187541874	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs549753426	NA	P-0060765-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	245	604	0	ENST00000441802.2:c.5866G>A	p.Asp1956Asn	p.D1956N	ENST00000441802	NM_005245.3	1956	Gat/Aat	10/27	0.184726056387189	1	FACETS	0.711	0.668	0.754	0.711	0.668	0.754	INDETERMINATE	1	FALSE	0	0.67556284248498	1		604	676	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169940551	169940551	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060765-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	294	446	0	ENST00000295797.4:c.94T>C	p.Tyr32His	p.Y32H	ENST00000295797	NM_002740.5	32	Tac/Cac	1/18	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.67556284248498	2		446	783	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890149	76890150	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060767-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	244	227	0	ENST00000373344.5:c.4744dup	p.Thr1582AsnfsTer19	p.T1582Nfs*19	ENST00000373344	NM_000489.3	1582	aca/aAca	17/35	1	1	FACETS	0.905	0.869	0.94	0.905	0.869	0.94	CLONAL	1	TRUE	0	0.893129011183928	1		227	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0060767-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	792	817	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.893129011183928	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.893129011183928	1		817	941	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0060767-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	263	342	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.893129011183928	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.893129011183928	1		342	324	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881489	48881492	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	novel	NA	P-0060767-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	172	242	0	ENST00000267163.4:c.217_220del	p.Arg73LeufsTer3	p.R73Lfs*3	ENST00000267163	NM_000321.2	71	AGAGag/ag	2/27	0.893129011183928	1	FACETS	0.931	0.887	0.972	0.931	0.887	0.972	CLONAL	1	TRUE	0	0.893129011183928	1		242	229	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876545	59876545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748105919	NA	P-0060767-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	349	435	0	ENST00000259008.2:c.1256G>A	p.Arg419Gln	p.R419Q	ENST00000259008	NM_032043.2	419	cGg/cAg	9/20	0.893129011183928	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.893129011183928	1		435	427	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134496	2134496	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060767-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	771	962	0	ENST00000219476.3:c.4276del	p.Glu1426LysfsTer50	p.E1426Kfs*50	ENST00000219476	NM_000548.3	1425	Ggg/gg	34/42	0.893129011183928	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.893129011183928	1		962	945	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602713	10602713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1213490014	NA	P-0060767-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	730	883	0	ENST00000171111.5:c.865G>A	p.Glu289Lys	p.E289K	ENST00000171111	NM_203500.1	289	Gag/Aag	3/6	0.893129011183928	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.893129011183928	1		883	889	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026728	48026731	+	frameshift_variant	Frame_Shift_Del	DEL	AGTA	AGTA	-	rs863224829	NA	P-0060767-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	473	605	0	ENST00000234420.5:c.1610_1613del	p.Lys537IlefsTer33	p.K537Ifs*33	ENST00000234420	NM_000179.2	536	AGTAag/ag	4/10	0.893129011183928	1	FACETS	0.952	0.926	0.976	0.952	0.926	0.976	CLONAL	1	TRUE	0	0.893129011183928	1		605	616	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67632191	67632191	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0060767-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	250	359	0	ENST00000272342.5:c.2377A>T	p.Lys793Ter	p.K793*	ENST00000272342	NM_019002.3	793	Aaa/Taa	5/6	0.893129011183928	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.893129011183928	1		359	303	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796546	57796546	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1578513720	NA	P-0060767-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	422	514	0	ENST00000309042.7:c.1522A>G	p.Ser508Gly	p.S508G	ENST00000309042	NM_005612.4	508	Agc/Ggc	4/4	0.893129011183928	1	FACETS	0.987	0.96	1	0.987	0.96	1	CLONAL	1	TRUE	0	0.893129011183928	1		514	530	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427744	49427744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	69	778	0	ENST00000301067.7:c.10744C>T	p.Arg3582Trp	p.R3582W	ENST00000301067	NM_003482.3	3582	Cgg/Tgg	39/54	0.360740504160229	3	FACETS	0.987	0.865	1	0.494	0.432	0.56	CLONAL	1	TRUE	1	0.45062647242019	3		778	380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs587781702	NA	P-0060791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	123	866	0	ENST00000269305.4:c.920-1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.45062647242019	3	FACETS	0.984	0.901	1	0.656	0.6	0.713	CLONAL	2	TRUE	0	0.45062647242019	3		866	340	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40500480	40500480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	133	496	0	ENST00000264657.5:c.55C>T	p.His19Tyr	p.H19Y	ENST00000264657	NM_139276.2	19	Cat/Tat	2/24	0.333965024140093	2	FACETS	1	0.987	1	0.732	0.672	0.795	CLONAL	1	TRUE	0	0.45062647242019	2		496	403	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222488	2222488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	79	777	0	ENST00000398665.3:c.3320G>A	p.Arg1107His	p.R1107H	ENST00000398665	NM_032482.2	1107	cGc/cAc	24/28	1	2	FACETS	0.906	0.802	1	0.906	0.802	1	CLONAL	1	TRUE	1	0.45062647242019	2		777	387	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226266	2226266	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060791-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	65	895	0	ENST00000398665.3:c.3746C>G	p.Ser1249Cys	p.S1249C	ENST00000398665	NM_032482.2	1249	tCc/tGc	27/28	1	2	FACETS	0.609	0.529	0.695	0.609	0.529	0.695	SUBCLONAL	1	TRUE	1	0.45062647242019	2		895	474	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0060792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	220	863	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.264053051784443	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.348216576720562	1		863	996	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347108	89347108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs907255990	NA	P-0060792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	181	907	0	ENST00000301030.4:c.5842G>A	p.Val1948Ile	p.V1948I	ENST00000301030	NM_001256183.1	1948	Gtt/Att	9/13	0.118314974051423	0	FACETS	0.625	0.575	0.676			1	INDETERMINATE	1	TRUE	0	0.348216576720562	0		907	1085	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575677	48575677	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs377767329	NA	P-0060792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	17	169	0	ENST00000342988.3:c.437T>G	p.Leu146Ter	p.L146*	ENST00000342988	NM_005359.5	146	tTa/tGa	4/12	0.348216576720562	1	FACETS	0.938	0.713	1	0.938	0.713	1	CLONAL	1	TRUE	0	0.348216576720562	1		169	86	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212459	5212459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs182037655	NA	P-0060792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	97	733	1	ENST00000357368.4:c.4658C>T	p.Thr1553Met	p.T1553M	ENST00000357368	NM_002850.3	1553	aCg/aTg	31/38	0.348216576720562	1	FACETS	0.495	0.44	0.553	0.495	0.44	0.553	SUBCLONAL	1	TRUE	0	0.348216576720562	1		734	930	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380276	+	missense_variant	Missense_Mutation	DNP	TT	TT	CA	novel	NA	P-0060792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	99	405	1	ENST00000311936.3:c.182_183delinsTG	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAA/cTG	3/5	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.348216576720562	NA		406	541	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476399	88476399	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	92	518	0	ENST00000360948.2:c.1733C>A	p.Thr578Asn	p.T578N	ENST00000360948	NM_001012338.2	578	aCc/aAc	15/19	0.293292795344813	0	FACETS	0.546	0.485	0.61			1	SUBCLONAL	1	TRUE	0	0.348216576720562	0		518	631	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732996	30732996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893809	NA	P-0060792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	183	301	0	ENST00000295754.5:c.1609C>T	p.Arg537Cys	p.R537C	ENST00000295754	NM_003242.5	537	Cgc/Tgc	7/7	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.348216576720562	2		301	1028	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631356	117631356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	73	437	0	ENST00000368508.3:c.6322G>A	p.Asp2108Asn	p.D2108N	ENST00000368508	NM_002944.2	2108	Gac/Aac	40/43	0.348216576720562	1	FACETS	0.815	0.716	0.921	0.815	0.716	0.921	CLONAL	1	TRUE	0	0.348216576720562	1		437	425	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503838	149503838	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs864309711	NA	P-0060793-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	190	711	0	ENST00000261799.4:c.1998C>A	p.Asn666Lys	p.N666K	ENST00000261799	NM_002609.3	666	aaC/aaA	14/23	0.658983858266277	3	FACETS	1	0.932	1	0.503	0.466	0.541	CLONAL	1	TRUE	1	0.658983858266277	3		711	762	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505050	149505051	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGCAGCTGCAT	novel	NA	P-0060793-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	293	752	0	ENST00000261799.4:c.1753_1764dup	p.Met585_Pro588dup	p.M585_P588dup	ENST00000261799	NM_002609.3	585	-/ATGCAGCTGCCC	12/23	0.658983858266277	3	FACETS	1	0.994	1	0.723	0.683	0.763	CLONAL	1	TRUE	1	0.658983858266277	3		752	818	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	126	321	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.899	0.825	0.974	0.899	0.825	0.974	CLONAL	1	TRUE	1	0.849644601223934	2		321	330	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0060794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6084	929	565	0	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.849644601223934	33	FACETS	1	0.993	1	0.138	0.133	0.144	CLONAL	4	TRUE	1	0.849644601223934	33		565	7013	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913250	NA	P-0060795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	169	399	0	ENST00000369535.4:c.34G>C	p.Gly12Arg	p.G12R	ENST00000369535	NM_002524.4	12	Ggt/Cgt	2/7	1	2	FACETS	0.969	0.9	1	0.969	0.9	1	CLONAL	1	TRUE	1	0.79823908491048	2		399	437	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598160	55598160	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	147	356	0	ENST00000288135.5:c.2357A>G	p.Lys786Arg	p.K786R	ENST00000288135	NM_000222.2	786	aAg/aGg	16/21	0.797334401122585	3	FACETS	0.946	0.868	1	0.473	0.434	0.513	CLONAL	1	TRUE	1	0.79823908491048	3		356	545	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289259	33289260	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0060795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	97	550	0	ENST00000374542.5:c.292_293del	p.Leu98ValfsTer13	p.L98Vfs*13	ENST00000374542	NM_001141970.1	98	CTg/g	3/8	0.635822069827632	4	FACETS	0.433	0.385	0.485	0.217	0.192	0.243	SUBCLONAL	1	TRUE	2	0.79823908491048	4		550	1009	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	270	321	0				ENST00000310581	NM_198253.2	-/1132			0.3	6	FACETS	0.907	0.86	0.954	0.907	0.86	0.954	CLONAL	5	TRUE	1	0.37	6		321	560	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0060803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	547	428	0	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	0.3	7	FACETS	1	0.979	1	1	0.979	1	CLONAL	6	TRUE	1	0.37	7		428	933	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050906	49050906	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	50	364	0	ENST00000267163.4:c.2590G>T	p.Glu864Ter	p.E864*	ENST00000267163	NM_000321.2	864	Gaa/Taa	25/27	0.3	0	FACETS	0.695	0.595	0.802			1	SUBCLONAL	1	TRUE	0	0.37	0		364	245	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412639	139412639	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1037236860	NA	P-0060803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	53	636	0	ENST00000277541.6:c.1205C>T	p.Ser402Leu	p.S402L	ENST00000277541	NM_017617.3	402	tCg/tTg	7/34	1	2	FACETS	0.362	0.307	0.421	0.362	0.307	0.421	SUBCLONAL	1	TRUE	1	0.37	2		636	792	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867571	45867571	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	254	792	1	ENST00000391945.4:c.737C>A	p.Ser246Tyr	p.S246Y	ENST00000391945	NM_000400.3	246	tCc/tAc	9/23	1	2	FACETS	0.942	0.886	0.999	1	0.995	1	CLONAL	2	TRUE	1	0.37	2		793	729	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935554	49935554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	102	637	0	ENST00000296474.3:c.1810G>A	p.Glu604Lys	p.E604K	ENST00000296474	NM_002447.2	604	Gag/Aag	5/20	0.203844179442472	2	FACETS	0.782	0.7	0.869	0.391	0.35	0.435	INDETERMINATE	1	TRUE	0	0.37	2		637	705	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305439	65305439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	78	519	0	ENST00000342505.4:c.2689G>A	p.Glu897Lys	p.E897K	ENST00000342505	NM_002227.2	897	Gaa/Aaa	20/25	1	2	FACETS	0.614	0.539	0.694	0.614	0.539	0.694	SUBCLONAL	1	TRUE	1	0.37	2		519	687	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780661	56780661	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	58	326	0	ENST00000337432.4:c.676C>T	p.Leu226Phe	p.L226F	ENST00000337432	NM_058216.2	226	Ctt/Ttt	4/9	0.3	4	FACETS	1	0.96	1	0.441	0.381	0.505	CLONAL	1	TRUE	1	0.37	4		326	325	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281275	46281275	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	43	443	0	ENST00000371998.3:c.4072C>G	p.Gln1358Glu	p.Q1358E	ENST00000371998		1358	Cag/Gag	21/23	1	2	FACETS	0.38	0.317	0.45	0.38	0.317	0.45	SUBCLONAL	1	TRUE	1	0.37	2		443	612	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578403	+	inframe_deletion	In_Frame_Del	DEL	GGGGGC	GGGGGC	-	novel	NA	P-0060803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	375	660	0	ENST00000269305.4:c.527_532del	p.Cys176_His178delinsTyr	p.C176_H178delinsY	ENST00000269305	NM_001126112.2	176	tGCCCCCac/tac	5/11	0.3	1	FACETS	1	0.99	1	1	0.997	1	CLONAL	2	TRUE	0	0.37	1		660	744	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247902	59247902	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	214	652	0	ENST00000371222.2:c.841G>C	p.Glu281Gln	p.E281Q	ENST00000371222	NM_002228.3	281	Gag/Cag	1/1	0.0242463723707682	3	FACETS	0.835	0.777	0.894	0.835	0.777	0.894	INDETERMINATE	2	TRUE	1	0.37	3		652	821	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915301	32915301	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	27	351	0	ENST00000380152.3:c.6809G>C	p.Gly2270Ala	p.G2270A	ENST00000380152		2270	gGa/gCa	11/27	0.3	1	FACETS	0.466	0.372	0.573	0.466	0.372	0.573	SUBCLONAL	1	TRUE	0	0.37	1		351	255	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107971	30107971	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	186	453	0	ENST00000331968.5:c.836C>G	p.Thr279Ser	p.T279S	ENST00000331968	NM_002742.2	279	aCc/aGc	5/18	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.37	2		453	673	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383882	15383882	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	53	508	0	ENST00000263377.2:c.29G>C	p.Arg10Thr	p.R10T	ENST00000263377	NM_058243.2	10	aGa/aCa	2/20	1	2	FACETS	0.513	0.438	0.597	0.513	0.438	0.597	SUBCLONAL	1	TRUE	1	0.37	2		508	558	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149862	202149862	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	172	585	0	ENST00000358485.4:c.1303G>A	p.Glu435Lys	p.E435K	ENST00000358485	NM_001080125.1	435	Gag/Aag	8/9	0.3	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.37	1		585	521	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49724643	49724643	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	93	437	0	ENST00000449682.2:c.546G>C	p.Trp182Cys	p.W182C	ENST00000449682	NM_020998.3	182	tgG/tgC	5/18	0.203844179442472	2	FACETS	0.974	0.869	1	0.487	0.434	0.543	INDETERMINATE	1	TRUE	0	0.37	2		437	516	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226948	142226948	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	26	230	0	ENST00000350721.4:c.4856C>G	p.Ser1619Cys	p.S1619C	ENST00000350721	NM_001184.3	1619	tCt/tGt	28/47	0.260316453360851	3	FACETS	0.793	0.632	0.975	0.397	0.316	0.488	CLONAL	1	TRUE	1	0.37	3		230	210	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131951752	131951752	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	22	119	0	ENST00000265335.6:c.3094A>G	p.Lys1032Glu	p.K1032E	ENST00000265335		1032	Aaa/Gaa	20/25	0.3	1	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	0	0.37	1		119	82	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275484	38275484	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	54	547	0	ENST00000425967.3:c.1549G>A	p.Glu517Lys	p.E517K	ENST00000425967	NM_001174067.1	517	Gag/Aag	12/19	0.3	1	FACETS	0.394	0.336	0.457	0.394	0.336	0.457	SUBCLONAL	1	TRUE	0	0.37	1		547	604	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0060804-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	196	508	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.880156199460587	2		508	439	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150933039	150933039	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060804-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	202	468	0	ENST00000271640.5:c.2501G>A	p.Gly834Asp	p.G834D	ENST00000271640	NM_001145415.1	834	gGc/gAc	16/22	1	2	FACETS	0.935	0.875	0.995	0.935	0.875	0.995	CLONAL	1	TRUE	1	0.880156199460587	2		468	491	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913162	32913162	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs80358698	NA	P-0060804-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	69	496	0	ENST00000380152.3:c.4670C>G	p.Thr1557Ser	p.T1557S	ENST00000380152		1557	aCc/aGc	11/27	1	2	FACETS	0.305	0.266	0.347	0.305	0.266	0.347	SUBCLONAL	1	TRUE	1	0.880156199460587	2		496	514	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652078	36652078	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs45548832	NA	P-0060804-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	302	851	0	ENST00000244741.5:c.200G>T	p.Arg67Leu	p.R67L	ENST00000244741	NM_000389.4	67	cGt/cTt	2/3	1	2	FACETS	0.927	0.879	0.976	0.927	0.879	0.976	CLONAL	1	TRUE	1	0.880156199460587	2		851	740	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207528	29207528	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060804-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	223	587	0	ENST00000240100.2:c.268G>A	p.Glu90Lys	p.E90K	ENST00000240100	NM_001394.6	90	Gag/Aag	1/4	1	2	FACETS	0.926	0.87	0.983	0.926	0.87	0.983	CLONAL	1	TRUE	1	0.880156199460587	2		587	547	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207605	29207605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060804-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	246	635	0	ENST00000240100.2:c.191C>T	p.Ser64Leu	p.S64L	ENST00000240100	NM_001394.6	64	tCg/tTg	1/4	1	2	FACETS	0.952	0.898	1	0.952	0.898	1	CLONAL	1	TRUE	1	0.880156199460587	2		635	587	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549391	5549391	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060804-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	231	573	0	ENST00000397747.3:c.418G>C	p.Glu140Gln	p.E140Q	ENST00000397747	NM_025239.3	140	Gag/Cag	4/7	1	2	FACETS	0.968	0.911	1	0.968	0.911	1	CLONAL	1	TRUE	1	0.880156199460587	2		573	542	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633430	8633430	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0060804-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	163	442	0	ENST00000356435.5:c.239C>G	p.Ser80Ter	p.S80*	ENST00000356435		80	tCa/tGa	3/35	1	2	FACETS	0.955	0.888	1	0.955	0.888	1	CLONAL	1	TRUE	1	0.880156199460587	2		442	388	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185046	123185046	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060804-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	87	160	0	ENST00000218089.9:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000218089	NM_001042749.1	365	Gaa/Aaa	12/35	1	2	FACETS	0.998	0.904	1	0.998	0.904	1	CLONAL	1	TRUE	1	0.880156199460587	2		160	198	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0060805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	274	499	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.577195741303006	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.577195741303006	1		500	663	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144113	11144113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	444	650	1	ENST00000358026.2:c.3694G>A	p.Gly1232Ser	p.G1232S	ENST00000358026	NM_001128849.1	1232	Ggc/Agc	26/36	0.231367715677433	3	FACETS	0.908	0.868	0.947	0.908	0.868	0.947	INDETERMINATE	2	TRUE	1	0.577195741303006	3		651	1092	SUCCESS
APC	324	MSKCC	GRCh37	5	112164671	112164671	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0060805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	44	261	0	ENST00000257430.4:c.1743+2T>C		p.X581_splice	ENST00000257430	NM_000038.5	581			0.577195741303006	1	FACETS	0.486	0.412	0.567	0.486	0.412	0.567	SUBCLONAL	1	TRUE	0	0.577195741303006	1		261	223	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971117	55971117	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	173	438	1	ENST00000263923.4:c.1680G>T	p.Gln560His	p.Q560H	ENST00000263923	NM_002253.2	560	caG/caT	13/30	0.577195741303006	3	FACETS	0.835	0.769	0.904	0.418	0.384	0.452	CLONAL	1	TRUE	1	0.577195741303006	3		439	925	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098756	2098756	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs137854226	NA	P-0060805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	141	453	1	ENST00000219476.3:c.138+2T>C		p.X46_splice	ENST00000219476	NM_000548.3	46			0.577195741303006	1	FACETS	0.667	0.611	0.725	0.667	0.611	0.725	SUBCLONAL	1	TRUE	0	0.577195741303006	1		454	521	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162375	47162375	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	146	659	0	ENST00000409792.3:c.3751T>G	p.Ser1251Ala	p.S1251A	ENST00000409792	NM_014159.6	1251	Tca/Gca	3/21	0.554304243594699	3	FACETS	0.685	0.625	0.749			1	SUBCLONAL	1	TRUE	NA	0.577195741303006	3		659	951	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721685	176721685	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	130	768	0	ENST00000439151.2:c.7316T>G	p.Leu2439Arg	p.L2439R	ENST00000439151	NM_022455.4	2439	cTg/cGg	23/23	0.577195741303006	1	FACETS	0.509	0.462	0.557	0.509	0.462	0.557	SUBCLONAL	1	TRUE	0	0.577195741303006	1		768	630	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	61	321	0				ENST00000310581	NM_198253.2	-/1132			0.333452116845536	1	FACETS	0.658	0.577	0.743	0.658	0.577	0.743	INDETERMINATE	1	TRUE	0	0.63575895591317	1		321	199	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259521	89259521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1282065699	NA	P-0060806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	25	815	0	ENST00000336596.2:c.665C>T	p.Ser222Phe	p.S222F	ENST00000336596	NM_005233.5	222	tCc/tTc	3/17	0.333452116845536	1	FACETS	0.298	0.236	0.368	0.298	0.236	0.368	INDETERMINATE	1	TRUE	0	0.63575895591317	1		815	180	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10794701	10794701	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	27	545	0	ENST00000361367.2:c.2608G>C	p.Glu870Gln	p.E870Q	ENST00000361367	NM_014633.3	870	Gag/Cag	21/25	0.63575895591317	1	FACETS	0.491	0.398	0.594	0.491	0.398	0.594	SUBCLONAL	1	TRUE	0	0.63575895591317	1		545	118	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445175	49445175	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	232	1238	1	ENST00000301067.7:c.2291del	p.Gln764ArgfsTer166	p.Q764Rfs*166	ENST00000301067	NM_003482.3	764	cAg/cg	10/54	0.179924910283956	4	FACETS	0.902	0.846	0.959	0.902	0.846	0.959	INDETERMINATE	2	TRUE	2	0.63575895591317	4		1239	662	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61304969	61304969	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	17	370	0	ENST00000341074.5:c.1157G>C	p.Arg386Thr	p.R386T	ENST00000341074	NM_002974.2	386	aGa/aCa	8/8	0.467598933941163	1	FACETS	0.405	0.308	0.517	0.405	0.308	0.517	SUBCLONAL	1	TRUE	0	0.63575895591317	1		370	90	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518327	204518327	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060807-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	150	439	0	ENST00000367182.3:c.990G>T	p.Trp330Cys	p.W330C	ENST00000367182	NM_001278516.1	330	tgG/tgT	11/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.507400922300111	2		439	571	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40461091	40461091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060807-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	143	292	0	ENST00000345506.4:c.2089C>T	p.Pro697Ser	p.P697S	ENST00000345506	NM_003152.3	697	Cca/Tca	18/20	0.509612311145669	3	FACETS	0.963	0.879	1	0.481	0.439	0.525	CLONAL	1	TRUE	1	0.507400922300111	3		292	734	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161282	185161282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060807-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	130	361	0	ENST00000265026.3:c.709G>A	p.Ala237Thr	p.A237T	ENST00000265026	NM_004721.4	237	Gcc/Acc	4/14	0.509612311145669	3	FACETS	1	0.962	1	0.552	0.502	0.604	CLONAL	1	TRUE	1	0.507400922300111	3		361	582	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979500	55979500	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060807-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	119	365	0	ENST00000263923.4:c.947A>T	p.Lys316Met	p.K316M	ENST00000263923	NM_002253.2	316	aAg/aTg	7/30	0.507400922300111	5	FACETS	0.83	0.748	0.917	0.277	0.249	0.306	CLONAL	1	TRUE	2	0.507400922300111	5		365	995	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405899	70405899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	27	594	0	ENST00000373644.4:c.3413C>T	p.Ser1138Leu	p.S1138L	ENST00000373644	NM_030625.2	1138	tCa/tTa	4/12	1	2	FACETS	0.25	0.198	0.309	0.25	0.198	0.309	SUBCLONAL	1	TRUE	1	0.5312859122176	2		594	407	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497215	149497215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748918501	NA	P-0060808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	64	639	0	ENST00000261799.4:c.3103G>A	p.Glu1035Lys	p.E1035K	ENST00000261799	NM_002609.3	1035	Gag/Aag	22/23	0.413266050316358	1	FACETS	0.35	0.303	0.4	0.35	0.303	0.4	SUBCLONAL	1	TRUE	0	0.5312859122176	1		639	506	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78933909	78933909	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1342049284	NA	P-0060808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	68	695	0	ENST00000306801.3:c.3509C>T	p.Thr1170Met	p.T1170M	ENST00000306801	NM_020761.2	1170	aCg/aTg	30/34	0.505276562491635	2	FACETS	0.489	0.425	0.557	0.244	0.212	0.279	SUBCLONAL	1	TRUE	0	0.5312859122176	2		695	524	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247384	153247384	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0060808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	133	532	0	ENST00000281708.4:c.1419-1G>A		p.X473_splice	ENST00000281708	NM_033632.3	473			0.33867993199672	1	FACETS	0.71	0.648	0.774	0.71	0.648	0.774	SUBCLONAL	1	TRUE	0	0.5312859122176	1		532	518	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288635	33288635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138014437	NA	P-0060808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	91	697	1	ENST00000374542.5:c.917G>A	p.Arg306Gln	p.R306Q	ENST00000374542	NM_001141970.1	306	cGa/cAa	3/8	0.5312859122176	3	FACETS	0.427	0.378	0.479	0.142	0.126	0.16	SUBCLONAL	1	TRUE	0	0.5312859122176	3		698	1016	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094895	11094895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	48	677	0	ENST00000358026.2:c.68C>T	p.Ser23Phe	p.S23F	ENST00000358026	NM_001128849.1	23	tCc/tTc	2/36	0.506553771208338	1	FACETS	0.282	0.238	0.33	0.282	0.238	0.33	SUBCLONAL	1	TRUE	0	0.5312859122176	1		677	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0060809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	663	512	0	ENST00000269305.4:c.673-2A>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.751322722139474	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.751322722139474	2		512	792	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426973	49426973	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555188653	NA	P-0060809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	481	827	0	ENST00000301067.7:c.11515C>T	p.Gln3839Ter	p.Q3839*	ENST00000301067	NM_003482.3	3839	Cag/Tag	39/54	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	1	TRUE	NA	0.751322722139474	2		827	1042	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443819	49443821	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0060809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	338	836	0	ENST00000301067.7:c.3550_3552del	p.Glu1184del	p.E1184del	ENST00000301067	NM_003482.3	1184	GAA/-	11/54	NA	2	FACETS	0.735	0.695	0.776			1	INDETERMINATE	1	TRUE	NA	0.751322722139474	2		836	1224	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828517	72828517	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	174	681	0	ENST00000268489.5:c.8064G>C	p.Trp2688Cys	p.W2688C	ENST00000268489	NM_006885.3	2688	tgG/tgC	9/10	0.751322722139474	1	FACETS	0.499	0.462	0.538	0.499	0.462	0.538	SUBCLONAL	1	TRUE	0	0.751322722139474	1		681	579	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0060812-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	210	286	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.533387051926684	5	FACETS	1	0.964	1	1	0.964	1	CLONAL	4	TRUE	1	0.533387051926684	5		286	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579372	7579372	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060812-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	296	555	0	ENST00000269305.4:c.315del	p.Ser106AlafsTer17	p.S106Afs*17	ENST00000269305	NM_001126112.2	105	ggC/gg	4/11	0.533387051926684	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.533387051926684	2		555	534	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	174	544	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.967	1	1	0.993	1	CLONAL	2	TRUE	1	0.284007660465442	2		544	569	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420289	49420289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768551828	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	278	415	0	ENST00000301067.7:c.15460C>T	p.Arg5154Trp	p.R5154W	ENST00000301067	NM_003482.3	5154	Cgg/Tgg	48/54	1	2	FACETS	1	0.984	1	1	0.996	1	CLONAL	2	TRUE	1	0.284007660465442	2		415	876	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	71	282	0	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	0.284007660465442	0	FACETS	0.755	0.669	0.846			1	SUBCLONAL	2	TRUE	0	0.284007660465442	0		282	237	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	346	490	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	1	0.991	1	1	0.997	1	CLONAL	2	TRUE	1	0.284007660465442	2		490	1018	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	223	356	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	1	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	2	TRUE	1	0.284007660465442	2		356	671	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	181	305	0	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.865	0.8	0.932	1	0.992	1	CLONAL	2	TRUE	1	0.284007660465442	2		305	737	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685281	89685281	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060500116	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	128	245	0	ENST00000371953.3:c.176C>G	p.Ser59Ter	p.S59*	ENST00000371953	NM_000314.4	59	tCa/tGa	3/9	1	2	FACETS	1	0.972	1	1	0.991	1	CLONAL	2	TRUE	1	0.284007660465442	2		245	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	40	355	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	1	2	FACETS	0.393	0.326	0.469	0.393	0.326	0.469	SUBCLONAL	1	TRUE	1	0.284007660465442	2		355	716	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097751	27097751	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	227	411	4	ENST00000324856.7:c.3344del	p.Pro1115GlnfsTer46	p.P1115Qfs*46	ENST00000324856	NM_006015.4	1114	Ccc/cc	12/20	1	2	FACETS	1	0.977	1	1	0.995	1	CLONAL	2	TRUE	1	0.284007660465442	2		415	732	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	298	477	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.284007660465442	2		477	889	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057936	27057937	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1415146710	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	262	422	0	ENST00000324856.7:c.1650dup	p.Tyr551LeufsTer72	p.Y551Lfs*72	ENST00000324856	NM_006015.4	548	-/C	3/20	1	2	FACETS	1	0.954	1	1	0.995	1	CLONAL	2	TRUE	1	0.284007660465442	2		422	905	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216477	108216477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587782558	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	132	222	2	ENST00000278616.4:c.8432del	p.Lys2811SerfsTer46	p.K2811Sfs*46	ENST00000278616	NM_000051.3	2809	cAa/ca	58/63	1	2	FACETS	1	0.966	1	1	0.991	1	CLONAL	2	TRUE	1	0.284007660465442	2		224	420	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	154	326	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	0.991	0.912	1	1	0.992	1	CLONAL	2	TRUE	1	0.284007660465442	2		326	547	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027886	48027886	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779246	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	226	370	0	ENST00000234420.5:c.2764C>T	p.Arg922Ter	p.R922*	ENST00000234420	NM_000179.2	922	Cga/Tga	4/10	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.284007660465442	2		370	672	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913027	32913027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358685	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	240	416	0	ENST00000380152.3:c.4535G>A	p.Arg1512His	p.R1512H	ENST00000380152		1512	cGt/cAt	11/27	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.284007660465442	2		416	741	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	226	373	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.284007660465442	2		373	676	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161221	56161221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781300314	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	174	316	0	ENST00000399503.3:c.1090C>T	p.Arg364Trp	p.R364W	ENST00000399503	NM_005921.1	364	Cgg/Tgg	5/20	1	2	FACETS	1	0.941	1	1	0.993	1	CLONAL	2	TRUE	1	0.284007660465442	2		316	601	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346627	89346627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201509886	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	589	426	3	ENST00000301030.4:c.6323G>A	p.Gly2108Asp	p.G2108D	ENST00000301030	NM_001256183.1	2108	gGc/gAc	9/13	0.284007660465442	2	FACETS	0.973	0.945	0.999	1	0.998	1	CLONAL	5	TRUE	0	0.284007660465442	2		429	853	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046958	128046958	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs772883177	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	267	369	2	ENST00000285398.2:c.777A>T	p.Glu259Asp	p.E259D	ENST00000285398	NM_000122.1	259	gaA/gaT	6/15	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.284007660465442	2		371	772	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419956	152419956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775806382	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	219	472	1	ENST00000206249.3:c.1643G>A	p.Arg548His	p.R548H	ENST00000206249	NM_000125.3	548	cGc/cAc	8/8	1	2	FACETS	0.963	0.898	1	1	0.994	1	CLONAL	2	TRUE	1	0.284007660465442	2		473	801	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574679	41574679	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	321	539	3	ENST00000263253.7:c.6970del	p.His2324ThrfsTer29	p.H2324Tfs*29	ENST00000263253	NM_001429.3	2322	Ccc/cc	31/31	1	2	FACETS	1	0.98	1	1	0.996	1	CLONAL	2	TRUE	1	0.284007660465442	2		542	1052	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	240	476	1	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.947	0.886	1	1	0.994	1	CLONAL	2	TRUE	1	0.284007660465442	2		477	892	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523088	25523088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758534627	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	307	399	1	ENST00000264709.3:c.97C>T	p.Arg33Cys	p.R33C	ENST00000264709	NM_175629.2	33	Cgt/Tgt	3/23	1	2	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	TRUE	1	0.284007660465442	2		400	873	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431874	49431874	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	283	530	1	ENST00000301067.7:c.9265del	p.Val3089TrpfsTer30	p.V3089Wfs*30	ENST00000301067	NM_003482.3	3089	Gtg/tg	34/54	1	2	FACETS	1	0.968	1	1	0.995	1	CLONAL	2	TRUE	1	0.284007660465442	2		531	956	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295827	15295827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs75291244	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	278	339	0	ENST00000263388.2:c.2300G>A	p.Arg767His	p.R767H	ENST00000263388	NM_000435.2	767	cGt/cAt	15/33	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.284007660465442	2		339	790	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780828	9780828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1441813233	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	246	402	0	ENST00000377346.4:c.1550G>A	p.Arg517Gln	p.R517Q	ENST00000377346	NM_005026.3	517	cGg/cAg	13/24	1	2	FACETS	1	0.969	1	1	0.995	1	CLONAL	2	TRUE	1	0.284007660465442	2		402	823	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220868	36220868	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	228	380	1	ENST00000222270.7:c.4918C>T	p.Arg1640Cys	p.R1640C	ENST00000222270	NM_014727.1	1640	Cgc/Tgc	23/37	1	2	FACETS	1	0.956	1	1	0.994	1	CLONAL	2	TRUE	1	0.284007660465442	2		381	780	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846107	151846107	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	292	489	2	ENST00000262189.6:c.12905del	p.Pro4302LeufsTer24	p.P4302Lfs*24	ENST00000262189	NM_170606.2	4302	cCt/ct	52/59	1	2	FACETS	1	0.979	1	1	0.996	1	CLONAL	2	TRUE	1	0.284007660465442	2		491	953	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17941419	17941419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	266	364	2	ENST00000458235.1:c.2989G>A	p.Glu997Lys	p.E997K	ENST00000458235	NM_000215.3	997	Gaa/Aaa	22/24	1	2	FACETS	1	0.985	1	1	0.996	1	CLONAL	2	TRUE	1	0.284007660465442	2		366	825	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006636	62006636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369201285	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	300	397	2	ENST00000392795.3:c.643C>T	p.Arg215Trp	p.R215W	ENST00000392795	NM_001039933.1	215	Cgg/Tgg	6/6	1	2	FACETS	1	0.987	1	1	0.996	1	CLONAL	2	TRUE	1	0.284007660465442	2		399	923	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52722992	52722992	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1362406458	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	216	377	2	ENST00000322088.6:c.1177G>A	p.Glu393Lys	p.E393K	ENST00000322088	NM_014225.5	393	Gag/Aag	10/15	1	2	FACETS	1	0.966	1	1	0.994	1	CLONAL	2	TRUE	1	0.284007660465442	2		379	721	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270389	10270389	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	289	393	1	ENST00000340748.4:c.1177G>A	p.Glu393Lys	p.E393K	ENST00000340748		393	Gag/Aag	16/40	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.284007660465442	2		394	870	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202759	16202759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375675403	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	272	377	0	ENST00000375759.3:c.467C>T	p.Thr156Met	p.T156M	ENST00000375759	NM_015001.2	156	aCg/aTg	3/15	1	2	FACETS	1	0.985	1	1	0.996	1	CLONAL	2	TRUE	1	0.284007660465442	2		377	840	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546931	9546931	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	255	471	2	ENST00000353224.5:c.1091C>A	p.Ser364Ter	p.S364*	ENST00000353224	NM_177990.2	364	tCg/tAg	5/10	1	2	FACETS	1	0.947	1	1	0.995	1	CLONAL	2	TRUE	1	0.284007660465442	2		473	889	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720297	43720297	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	212	329	0	ENST00000382044.4:c.3745C>T	p.Arg1249Trp	p.R1249W	ENST00000382044	NM_001141980.1	1249	Cgg/Tgg	18/28	1	2	FACETS	1	0.954	1	1	0.994	1	CLONAL	2	TRUE	1	0.284007660465442	2		329	725	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705410	43705410	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764425387	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	261	427	2	ENST00000382044.4:c.5212G>A	p.Ala1738Thr	p.A1738T	ENST00000382044	NM_001141980.1	1738	Gca/Aca	24/28	1	2	FACETS	1	0.983	1	1	0.995	1	CLONAL	2	TRUE	1	0.284007660465442	2		429	821	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066912	30066912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752897300	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	212	299	0	ENST00000331968.5:c.2219G>A	p.Arg740Gln	p.R740Q	ENST00000331968	NM_002742.2	740	cGg/cAg	16/18	1	2	FACETS	0.849	0.794	0.905	1	0.995	1	CLONAL	3	TRUE	1	0.284007660465442	2		299	586	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851816	63851816	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200382682	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	196	461	4	ENST00000279873.7:c.2594C>T	p.Ser865Leu	p.S865L	ENST00000279873	NM_032199.2	865	tCg/tTg	10/10	1	2	FACETS	0.881	0.818	0.947	1	0.993	1	CLONAL	2	TRUE	1	0.284007660465442	2		465	783	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430826	78430826	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1557452212	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	251	401	0	ENST00000370768.2:c.563A>C	p.Gln188Pro	p.Q188P	ENST00000370768	NM_003902.3	188	cAa/cCa	8/20	1	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	2	TRUE	1	0.284007660465442	2		401	770	SUCCESS
FH	2271	MSKCC	GRCh37	1	241661251	241661251	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	175	277	0	ENST00000366560.3:c.1410G>T	p.Lys470Asn	p.K470N	ENST00000366560	NM_000143.3	470	aaG/aaT	10/10	0.284007660465442	4	FACETS	1	0.979	1	0.776	0.717	0.837	CLONAL	2	TRUE	1	0.284007660465442	4		277	680	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129712	108129712	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	161	254	0	ENST00000278616.4:c.2377-1G>A		p.X793_splice	ENST00000278616	NM_000051.3	793			1	2	FACETS	1	0.978	1	1	0.993	1	CLONAL	2	TRUE	1	0.284007660465442	2		254	492	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487178	56487178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	81	359	1	ENST00000267101.3:c.1324G>A	p.Gly442Ser	p.G442S	ENST00000267101	NM_001982.3	442	Ggc/Agc	12/28	1	2	FACETS	0.849	0.748	0.957	0.849	0.748	0.957	CLONAL	1	TRUE	1	0.284007660465442	2		360	672	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30047515	30047515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	111	266	4	ENST00000331968.5:c.2486G>A	p.Ser829Asn	p.S829N	ENST00000331968	NM_002742.2	829	aGt/aAt	17/18	1	2	FACETS	1	0.931	1	1	0.989	1	CLONAL	2	TRUE	1	0.284007660465442	2		270	379	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239350	105239350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1219649544	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	400	478	0	ENST00000349310.3:c.1037G>A	p.Arg346His	p.R346H	ENST00000349310	NM_001014432.1	346	cGc/cAc	12/15	0.160267627449331	3	FACETS	1	0.97	1			1	INDETERMINATE	3	TRUE	NA	0.284007660465442	3		478	1049	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292752	91292752	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	262	406	1	ENST00000355112.3:c.254G>T	p.Arg85Met	p.R85M	ENST00000355112	NM_000057.2	85	aGg/aTg	3/22	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.284007660465442	2		407	818	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679688	33679688	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761087261	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	270	448	2	ENST00000308377.4:c.2393G>A	p.Arg798His	p.R798H	ENST00000308377	NM_152270.3	798	cGc/cAc	5/5	1	2	FACETS	1	0.985	1	1	0.996	1	CLONAL	2	TRUE	1	0.284007660465442	2		450	833	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4123869	4123869	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	112	259	0	ENST00000262948.5:c.4C>A	p.Leu2Met	p.L2M	ENST00000262948	NM_030662.3	2	Ctg/Atg	1/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.284007660465442	2		259	595	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6230661	6230661	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767911025	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	250	427	2	ENST00000252674.7:c.340G>A	p.Val114Met	p.V114M	ENST00000252674	NM_005934.3	114	Gtg/Atg	4/12	1	2	FACETS	1	0.978	1	1	0.995	1	CLONAL	2	TRUE	1	0.284007660465442	2		429	809	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291154	10291154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751662619	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	436	624	2	ENST00000340748.4:c.317G>A	p.Arg106His	p.R106H	ENST00000340748		106	cGt/cAt	4/40	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	1	0.284007660465442	2		626	1295	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144509	11144509	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778685	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	198	331	0	ENST00000358026.2:c.3841G>A	p.Val1281Ile	p.V1281I	ENST00000358026	NM_001128849.1	1281	Gtc/Atc	27/36	1	2	FACETS	1	0.983	1	1	0.994	1	CLONAL	2	TRUE	1	0.284007660465442	2		331	599	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867345	45867345	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	296	413	0	ENST00000391945.4:c.848A>G	p.Asp283Gly	p.D283G	ENST00000391945	NM_000400.3	283	gAc/gGc	10/23	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.284007660465442	2		413	885	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423760	47423760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	248	414	3	ENST00000404338.3:c.1828C>T	p.Arg610Ter	p.R610*	ENST00000404338	NM_004491.4	610	Cga/Tga	1/6	1	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	2	TRUE	1	0.284007660465442	2		417	759	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46608746	46608746	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1344802648	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	103	435	1	ENST00000263734.3:c.2057G>A	p.Gly686Asp	p.G686D	ENST00000263734	NM_001430.4	686	gGt/gAt	13/16	1	2	FACETS	0.947	0.847	1	0.947	0.847	1	CLONAL	1	TRUE	1	0.284007660465442	2		436	766	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162384	47162384	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	229	453	4	ENST00000409792.3:c.3742G>T	p.Gly1248Cys	p.G1248C	ENST00000409792	NM_014159.6	1248	Ggc/Tgc	3/21	1	2	FACETS	0.992	0.927	1	1	0.994	1	CLONAL	2	TRUE	1	0.284007660465442	2		457	813	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924838	49924838	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	295	481	2	ENST00000296474.3:c.4105C>T	p.His1369Tyr	p.H1369Y	ENST00000296474	NM_002447.2	1369	Cat/Tat	20/20	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.284007660465442	2		483	892	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446959	187446959	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239334107	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	331	526	4	ENST00000232014.4:c.1234C>T	p.Pro412Ser	p.P412S	ENST00000232014	NM_001130845.1	412	Cct/Tct	5/10	1	2	FACETS	1	0.987	1	1	0.996	1	CLONAL	2	TRUE	1	0.284007660465442	2		530	1034	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139202	37139202	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	240	514	0	ENST00000373509.5:c.542A>C	p.Glu181Ala	p.E181A	ENST00000373509	NM_002648.3	181	gAg/gCg	4/6	1	2	FACETS	1	0.973	1	1	0.995	1	CLONAL	2	TRUE	1	0.284007660465442	2		514	789	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137528169	137528169	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	142	330	4	ENST00000367739.4:c.131C>A	p.Pro44His	p.P44H	ENST00000367739	NM_000416.2	44	cCt/cAt	2/7	1	2	FACETS	0.943	0.865	1	1	0.991	1	CLONAL	2	TRUE	1	0.284007660465442	2		334	530	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268909	55268909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	273	444	2	ENST00000275493.2:c.2975C>A	p.Pro992His	p.P992H	ENST00000275493	NM_005228.3	992	cCt/cAt	25/28	1	2	FACETS	1	0.984	1	1	0.996	1	CLONAL	2	TRUE	1	0.284007660465442	2		446	857	SUCCESS
MET	4233	MSKCC	GRCh37	7	116414999	116414999	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	246	443	0	ENST00000397752.3:c.3093G>A	p.Met1031Ile	p.M1031I	ENST00000397752	NM_000245.2	1031	atG/atA	15/21	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.284007660465442	2		443	761	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772008	135772012	+	missense_variant	Missense_Mutation	ONP	CTCCA	CTCCA	TGCCT	novel	NA	P-0060814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	56	459	2	ENST00000298552.3:c.3105_3109delinsAGGCA	p.Gly1037Ser	p.G1037S	ENST00000298552	NM_001162426.1	1035	ggTGGAGgc/ggAGGCAgc	23/23	0.284007660465442	1	FACETS	0.513	0.439	0.595	0.513	0.439	0.595	SUBCLONAL	1	TRUE	0	0.284007660465442	1		461	659	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061138	38061138	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs770099992	NA	P-0060815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	27	460	0	ENST00000250448.2:c.851del	p.Gly284AlafsTer37	p.G284Afs*37	ENST00000250448	NM_004496.3	284	gGc/gc	2/2	1	2	FACETS	0.482	0.381	0.597	0.482	0.381	0.597	SUBCLONAL	1	TRUE	1	0.14	2		460	801	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061189	38061198	+	frameshift_variant	Frame_Shift_Del	DEL	TTGAAGCGCT	TTGAAGCGCT	-	novel	NA	P-0060815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	54	420	0	ENST00000250448.2:c.791_800del	p.Lys264SerfsTer54	p.K264Sfs*54	ENST00000250448	NM_004496.3	264	aAGCGCTTCAAg/ag	2/2	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.14	2		420	733	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0060837-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	35	341	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.868	0.714	1	0.868	0.714	1	CLONAL	1	FALSE	1	0.268698278776317	2		341	300	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060837-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	26	375	0	ENST00000263967.3:c.3012G>A	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atA	21/21	1	2	FACETS	0.628	0.498	0.777	0.628	0.498	0.777	SUBCLONAL	1	FALSE	1	0.268698278776317	2		375	308	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519927	NA	P-0060837-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	29	163	0	ENST00000263967.3:c.1625A>T	p.Glu542Val	p.E542V	ENST00000263967	NM_006218.2	542	gAa/gTa	10/21	1	2	FACETS	0.926	0.748	1	0.926	0.748	1	CLONAL	1	FALSE	1	0.268698278776317	2		163	233	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119971	70119971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060837-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	49	461	0	ENST00000245479.2:c.973G>A	p.Ala325Thr	p.A325T	ENST00000245479	NM_000346.3	325	Gcg/Acg	3/3	1	2	FACETS	0.76	0.644	0.887	0.76	0.644	0.887	SUBCLONAL	1	FALSE	1	0.268698278776317	2		461	480	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712018	89712018	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs727504114	NA	P-0060837-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	34	298	0	ENST00000371953.3:c.634+2T>C		p.X212_splice	ENST00000371953	NM_000314.4	212			1	2	FACETS	0.832	0.682	1	0.832	0.682	1	CLONAL	1	FALSE	1	0.268698278776317	2		298	304	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845622	63845622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060837-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	74	477	0	ENST00000279873.7:c.1365del	p.Glu456LysfsTer23	p.E456Kfs*23	ENST00000279873	NM_032199.2	454	gAa/ga	9/10	1	2	FACETS	0.855	0.749	0.97	0.855	0.749	0.97	CLONAL	1	FALSE	1	0.268698278776317	2		477	644	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023655	27023673	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCCAGCGCCTCCGCCTC	CCTCCAGCGCCTCCGCCTC	-	novel	NA	P-0060837-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	36	487	0	ENST00000324856.7:c.762_780del	p.Ser255ArgfsTer102	p.S255Rfs*102	ENST00000324856	NM_006015.4	254	tCCTCCAGCGCCTCCGCCTCc/tc	1/20	1	2	FACETS	0.705	0.58	0.845	0.705	0.58	0.845	SUBCLONAL	1	FALSE	1	0.268698278776317	2		487	380	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2137903	2137904	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACT	novel	NA	P-0060837-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	117	506	0	ENST00000219476.3:c.5032_5034dup	p.Tyr1678dup	p.Y1678dup	ENST00000219476	NM_000548.3	1678	gac/gACTac	39/42	0.17479311510527	2	FACETS	0.757	0.685	0.833	0.757	0.685	0.833	SUBCLONAL	2	FALSE	0	0.268698278776317	2		506	575	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0060856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	27	286	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.173830719911842	4	FACETS	0.831	0.66	1	0.415	0.33	0.513	CLONAL	1	TRUE	2	0.173830719911842	4		286	439	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484597	57484597	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs137854533	NA	P-0060856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	37	608	0	ENST00000371085.3:c.681G>C	p.Gln227His	p.Q227H	ENST00000371085	NM_000516.4	227	caG/caC	9/13	1	2	FACETS	0.948	0.782	1	0.948	0.782	1	CLONAL	1	TRUE	1	0.173830719911842	2		608	449	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057848	27057848	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	62	708	0	ENST00000324856.7:c.1556C>G	p.Ser519Cys	p.S519C	ENST00000324856	NM_006015.4	519	tCc/tGc	3/20	0.173830719911842	4	FACETS	1	0.958	1	0.433	0.374	0.498	CLONAL	1	TRUE	1	0.173830719911842	4		708	644	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644570	3644570	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	26	516	0	ENST00000294008.3:c.2044G>T	p.Gly682Cys	p.G682C	ENST00000294008	NM_032444.2	682	Ggc/Tgc	10/15	0.173830719911842	4	FACETS	0.949	0.752	1	0.475	0.376	0.588	CLONAL	1	TRUE	2	0.173830719911842	4		516	370	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22143098	22143098	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0060856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	24	343	0	ENST00000215832.6:c.610-1G>T		p.X204_splice	ENST00000215832	NM_002745.4	204			1	2	FACETS	0.832	0.652	1	0.832	0.652	1	CLONAL	1	TRUE	1	0.173830719911842	2		343	332	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278806	1278806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1321220917	NA	P-0060856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	44	508	0	ENST00000310581.5:c.2236G>A	p.Val746Met	p.V746M	ENST00000310581	NM_198253.2	746	Gtg/Atg	6/16	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.173830719911842	2		508	421	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0060860-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	51	222	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.878	0.753	1	0.878	0.753	1	CLONAL	1	TRUE	1	0.452095697970733	2		222	257	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856113	68856113	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782750	NA	P-0060860-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	158	484	0	ENST00000261769.5:c.1921C>T	p.Gln641Ter	p.Q641*	ENST00000261769	NM_004360.3	641	Cag/Tag	12/16	0.452095697970733	1	FACETS	0.941	0.867	1	0.941	0.867	1	CLONAL	1	TRUE	0	0.452095697970733	1		484	575	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089676	27089676	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060860-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	429	733	0	ENST00000324856.7:c.2632C>T	p.Gln878Ter	p.Q878*	ENST00000324856	NM_006015.4	878	Cag/Tag	8/20	0.452095697970733	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.452095697970733	2		733	918	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334776	81334776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1267493094	NA	P-0060860-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	129	424	0	ENST00000222390.5:c.1940G>A	p.Arg647Gln	p.R647Q	ENST00000222390	NM_000601.4	647	cGa/cAa	17/18	0.452095697970733	2	FACETS	1	0.915	1	0.502	0.457	0.55	CLONAL	1	TRUE	0	0.452095697970733	2		424	568	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938337	76938337	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060860-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	99	374	0	ENST00000373344.5:c.2411C>A	p.Ser804Tyr	p.S804Y	ENST00000373344	NM_000489.3	804	tCt/tAt	9/35	0.38451809971898	3	FACETS	0.978	0.876	1	0.489	0.438	0.543	CLONAL	1	TRUE	1	0.452095697970733	3		374	549	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731036	162731036	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060860-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	182	541	0	ENST00000367921.3:c.891G>C	p.Lys297Asn	p.K297N	ENST00000367921	NM_006182.2	297	aaG/aaC	9/18	0.452095697970733	4	FACETS	1	0.961	1	0.357	0.328	0.386	CLONAL	1	TRUE	1	0.452095697970733	4		541	1093	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572938	7572938	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060860-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	174	526	0	ENST00000269305.4:c.1171G>C	p.Asp391His	p.D391H	ENST00000269305	NM_001126112.2	391	Gac/Cac	11/11	1	2	FACETS	0.969	0.894	1	0.969	0.894	1	CLONAL	1	TRUE	1	0.452095697970733	2		526	794	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075305	16075305	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060860-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	118	338	0	ENST00000268712.3:c.247C>G	p.Gln83Glu	p.Q83E	ENST00000268712	NM_006311.3	83	Caa/Gaa	4/46	1	2	FACETS	0.857	0.775	0.943	0.857	0.775	0.943	CLONAL	1	TRUE	1	0.452095697970733	2		338	609	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178941917	178941917	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060860-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	122	355	0	ENST00000263967.3:c.2236G>A	p.Asp746Asn	p.D746N	ENST00000263967	NM_006218.2	746	Gat/Aat	15/21	1	2	FACETS	0.96	0.871	1	0.96	0.871	1	CLONAL	1	TRUE	1	0.452095697970733	2		355	562	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106543568	106543568	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060860-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	118	368	0	ENST00000369096.4:c.370G>C	p.Asp124His	p.D124H	ENST00000369096	NM_001198.3	124	Gac/Cac	3/7	1	2	FACETS	0.919	0.832	1	0.919	0.832	1	CLONAL	1	TRUE	1	0.452095697970733	2		368	568	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863308	56863308	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060860-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	32	327	0	ENST00000519728.1:c.452G>C	p.Gly151Ala	p.G151A	ENST00000519728	NM_002350.3	151	gGa/gCa	6/13	1	2	FACETS	0.278	0.225	0.338	0.278	0.225	0.338	SUBCLONAL	1	TRUE	1	0.452095697970733	2		327	510	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0060864-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	105	567	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	0.30810789010421	1	FACETS	0.859	0.771	0.953	0.859	0.771	0.953	CLONAL	1	TRUE	0	0.30810789010421	1		567	671	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849054	156849054	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786205449	NA	P-0060864-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	219	763	1	ENST00000524377.1:c.1946G>A	p.Arg649Gln	p.R649Q	ENST00000524377	NM_002529.3	649	cGg/cAg	15/17	0.30810789010421	4	FACETS	0.782	0.726	0.84	0.521	0.484	0.56	SUBCLONAL	2	TRUE	1	0.30810789010421	4		764	1189	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972324	32972324	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060864-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	70	317	0	ENST00000380152.3:c.9674A>G	p.Tyr3225Cys	p.Y3225C	ENST00000380152		3225	tAt/tGt	27/27	0.30810789010421	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.30810789010421	1		317	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579312	7579312	+	splice_region_variant,synonymous_variant	Splice_Region	SNP	C	C	T	rs55863639	NA	P-0060872-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	243	1056	1	ENST00000269305.4:c.375G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125	acG/acA	4/11	0.432024067765652	1	FACETS	1	0.993	1	1	0.993	1	INDETERMINATE	1	TRUE	0	0.823655411082367	1		1057	302	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0060872-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	42	109	0	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	0.823655411082367	2	FACETS	0.864	0.776	0.945	0.864	0.776	0.945	CLONAL	2	TRUE	0	0.823655411082367	2		109	59	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048166	180048166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369049878	NA	P-0060872-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	421	1794	1	ENST00000261937.6:c.2107G>A	p.Gly703Arg	p.G703R	ENST00000261937	NM_182925.4	703	Gga/Aga	14/30	0.800198056513887	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.823655411082367	4		1795	879	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749443	41749443	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060872-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	190	900	1	ENST00000226382.2:c.352G>A	p.Ala118Thr	p.A118T	ENST00000226382	NM_003924.3	118	Gcg/Acg	2/3	0.294211734465649	6	FACETS	1	0.982	1	0.58	0.541	0.621	INDETERMINATE	2	TRUE	2	0.823655411082367	6		901	526	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	97	380	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.43	2		380	441	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	147	711	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.43	2		711	677	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	68	476	10	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.85	0.744	0.964	0.85	0.744	0.964	CLONAL	1	TRUE	1	0.43	2		486	372	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451841	29451841	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	66	391	0	ENST00000389048.3:c.2724G>T	p.Gln908His	p.Q908H	ENST00000389048	NM_004304.4	908	caG/caT	16/29	0.3	0	FACETS	0.745	0.655	0.839			1	SUBCLONAL	1	TRUE	0	0.43	0		391	235	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	17	594	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	0.146	0.108	0.191	0.146	0.108	0.191	SUBCLONAL	1	TRUE	1	0.43	2		594	543	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743932	41743933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs778012871	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	88	776	0	ENST00000301178.4:c.874dup	p.His292ProfsTer47	p.H292Pfs*47	ENST00000301178	NM_021913.4	289	-/C	7/20	1	2	FACETS	0.84	0.747	0.939	0.84	0.747	0.939	CLONAL	1	TRUE	1	0.43	2		776	487	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755128667	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	267	953	0	ENST00000407977.2:c.1976dup	p.Pro660SerfsTer87	p.P660Sfs*87	ENST00000407977		659	ggt/ggGt	9/10	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.43	2		953	885	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405045	405045	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377483798	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	267	543	0	ENST00000380956.4:c.1127G>A	p.Arg376His	p.R376H	ENST00000380956	NM_001195286.1	376	cGc/cAc	8/9	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.43	2		543	521	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255883	16255883	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	144	718	0	ENST00000375759.3:c.3154del	p.Ile1052SerfsTer40	p.I1052Sfs*40	ENST00000375759	NM_015001.2	1050	Aaa/aa	11/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.43	2		718	591	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129338	152129338	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1361952517	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	145	782	0	ENST00000206249.3:c.296del	p.Pro99HisfsTer10	p.P99Hfs*10	ENST00000206249	NM_000125.3	97	ttC/tt	1/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.43	2		782	578	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56792470	56792470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	132	593	0	ENST00000308159.5:c.200G>A	p.Arg67Gln	p.R67Q	ENST00000308159	NM_014669.4	67	cGg/cAg	3/22	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.43	2		593	527	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241276	105241276	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	102	774	0	ENST00000349310.3:c.632C>T	p.Thr211Ile	p.T211I	ENST00000349310	NM_001014432.1	211	aCa/aTa	8/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.43	2		774	403	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061725	38061726	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs766493600	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	26	940	1	ENST00000250448.2:c.263dup	p.Ser89LeufsTer138	p.S89Lfs*138	ENST00000250448	NM_004496.3	88	ggc/ggGc	2/2	1	2	FACETS	0.192	0.151	0.239	0.192	0.151	0.239	SUBCLONAL	1	TRUE	1	0.43	2		941	629	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030467	47030469	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs781998738	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	117	683	12	ENST00000377604.3:c.254_256del	p.Arg85del	p.R85del	ENST00000377604	NM_001204468.1	81	aGGCgg/agg	4/24	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.43	2		695	461	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821048	32821048	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	276	924	2	ENST00000354258.4:c.546del	p.Ser184ProfsTer54	p.S184Pfs*54	ENST00000354258	NM_000593.5	182	ccC/cc	1/11	0.3	4	FACETS	0.865	0.817	0.914	0.649	0.613	0.686	CLONAL	3	TRUE	0	0.43	4		926	707	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099403	157099408	+	inframe_deletion	In_Frame_Del	DEL	CAGCAG	CAGCAG	-	rs587779743	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	83	948	0	ENST00000346085.5:c.357_362del	p.Gln130_Gln131del	p.Q130_Q131del	ENST00000346085	NM_020732.3	114	CAGCAG/-	1/20	1	2	FACETS	0.465	0.409	0.524	0.465	0.409	0.524	SUBCLONAL	1	TRUE	1	0.43	2		948	831	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022502	12022502	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1232497641	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	255	951	0	ENST00000396373.4:c.613del	p.Leu205TrpfsTer4	p.L205Wfs*4	ENST00000396373	NM_001987.4	203	tCc/tc	5/8	0.3	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	2	0.43	4		951	830	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8111056	8111056	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs548042738	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	160	697	0	ENST00000585124.1:c.151G>T	p.Ala51Ser	p.A51S	ENST00000585124	NM_004217.3	51	Gct/Tct	3/9	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.43	2		697	732	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214713	36214714	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	52	777	1	ENST00000222270.7:c.3145dup	p.Ala1049GlyfsTer39	p.A1049Gfs*39	ENST00000222270	NM_014727.1	1047	cgg/cGgg	8/37	1	2	FACETS	0.597	0.51	0.693	0.597	0.51	0.693	SUBCLONAL	1	TRUE	1	0.43	2		778	405	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119717	70119717	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	167	465	1	ENST00000245479.2:c.723del	p.Thr243ProfsTer10	p.T243Pfs*10	ENST00000245479	NM_000346.3	240	aCc/ac	3/3	1	2	FACETS	0.969	0.901	1	1	0.993	1	CLONAL	2	TRUE	1	0.43	2		466	401	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598252	28598252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs994631336	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	181	743	0	ENST00000253063.3:c.224G>A	p.Arg75Gln	p.R75Q	ENST00000253063	NM_031459.4	75	cGa/cAa	3/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.43	2		743	582	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047665	180047665	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757057248	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	131	825	0	ENST00000261937.6:c.2350G>A	p.Val784Ile	p.V784I	ENST00000261937	NM_182925.4	784	Gtc/Atc	16/30	0.3	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.43	1		825	458	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605215	46605215	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1407435090	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	127	636	9	ENST00000263734.3:c.1432A>T	p.Ser478Cys	p.S478C	ENST00000263734	NM_001430.4	478	Agc/Tgc	10/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.43	2		645	457	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213019	39213020	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	139	753	0	ENST00000402219.2:c.3947_3948del	p.His1316ProfsTer29	p.H1316Pfs*29	ENST00000402219	NM_005633.3	1316	cAC/c	23/23	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.43	2		753	629	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130433	29130434	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs876661156	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	111	832	0	ENST00000328354.6:c.276dup	p.Trp93LeufsTer15	p.W93Lfs*15	ENST00000328354	NM_007194.3	92	-/C	2/15	0.3	1	FACETS	0.736	0.663	0.811	0.736	0.663	0.811	SUBCLONAL	1	TRUE	0	0.43	1		832	551	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899174	78899174	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199756138	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	150	650	0	ENST00000306801.3:c.2813C>T	p.Ala938Val	p.A938V	ENST00000306801	NM_020761.2	938	gCg/gTg	24/34	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.43	2		650	488	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99472846	99472846	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778465734	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	131	596	0	ENST00000268035.6:c.2842G>A	p.Val948Met	p.V948M	ENST00000268035	NM_000875.3	948	Gtg/Atg	14/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.43	2		596	545	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713238	43713238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1273385388	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	137	718	0	ENST00000382044.4:c.4235G>A	p.Arg1412Gln	p.R1412Q	ENST00000382044	NM_001141980.1	1412	cGg/cAg	20/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.43	2		718	506	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215617262	215617262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753479021	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	95	388	0	ENST00000260947.4:c.1586G>A	p.Arg529Gln	p.R529Q	ENST00000260947	NM_000465.2	529	cGg/cAg	7/11	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.43	2		388	434	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190884	106190884	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	169	547	0	ENST00000380013.4:c.4162A>G	p.Met1388Val	p.M1388V	ENST00000380013	NM_001127208.2	1388	Atg/Gtg	9/11	0.0806996691323385	3	FACETS	0.77	0.711	0.831	0.77	0.711	0.831	INDETERMINATE	2	TRUE	1	0.43	3		547	620	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372392	55372392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	100	892	0	ENST00000297316.4:c.1082C>T	p.Thr361Met	p.T361M	ENST00000297316	NM_022454.3	361	aCg/aTg	2/2	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.43	2		892	440	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44911007	44911010	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	59	691	0	ENST00000377967.4:c.711_714del	p.Ser238HisfsTer3	p.S238Hfs*3	ENST00000377967	NM_021140.2	236	aaTCTT/aa	9/29	1	2	FACETS	0.537	0.462	0.618	0.537	0.462	0.618	SUBCLONAL	1	TRUE	1	0.43	2		691	511	SUCCESS
APC	324	MSKCC	GRCh37	5	112170862	112170862	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1060503318	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	82	395	0	ENST00000257430.4:c.1958G>T	p.Arg653Met	p.R653M	ENST00000257430	NM_000038.5	653	aGg/aTg	15/16	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.43	2		395	362	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351844	89351844	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	163	670	0	ENST00000301030.4:c.1106del	p.Lys369ArgfsTer58	p.K369Rfs*58	ENST00000301030	NM_001256183.1	369	aAg/ag	9/13	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.43	2		670	509	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163325177	163325177	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	77	385	0	ENST00000271452.3:c.1316del	p.Lys439ArgfsTer10	p.K439Rfs*10	ENST00000271452	NM_145697.2	438	gAa/ga	14/14	1	2	FACETS	0.895	0.79	1	0.895	0.79	1	CLONAL	1	TRUE	1	0.43	2		385	400	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047187	77047187	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	143	742	0	ENST00000356341.3:c.1357A>G	p.Met453Val	p.M453V	ENST00000356341	NM_002576.4	453	Atg/Gtg	13/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.43	2		742	551	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383229	4383229	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	49	768	2	ENST00000261254.3:c.23T>C	p.Val8Ala	p.V8A	ENST00000261254	NM_001759.3	8	gTg/gCg	1/5	0.3	1	FACETS	0.33	0.279	0.386	0.33	0.279	0.386	SUBCLONAL	1	TRUE	0	0.43	1		770	542	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245464	46245465	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	164	709	0	ENST00000334344.6:c.3560_3561del	p.Val1187GlufsTer53	p.V1187Efs*53	ENST00000334344	NM_152641.2	1186	acTGtg/actg	15/21	0.0806996691323385	3	FACETS	1	0.988	1	0.717	0.661	0.776	INDETERMINATE	1	TRUE	1	0.43	3		709	646	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986740	36986740	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	24	855	0	ENST00000354822.5:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000354822	NM_001079668.2	317	Cag/Tag	3/3	1	2	FACETS	0.282	0.22	0.353	0.282	0.22	0.353	SUBCLONAL	1	TRUE	1	0.43	2		855	396	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724872	43724872	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	124	653	0	ENST00000382044.4:c.3195del	p.Asn1066ThrfsTer30	p.N1066Tfs*30	ENST00000382044	NM_001141980.1	1065	ggG/gg	17/28	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.43	2		653	512	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786696	3786697	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	142	669	0	ENST00000262367.5:c.4514dup	p.Met1506AspfsTer13	p.M1506Dfs*13	ENST00000262367	NM_004380.2	1505	aag/aaAg	27/31	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.43	2		669	532	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845574	72845574	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	61	802	1	ENST00000268489.5:c.3766del	p.Leu1256CysfsTer32	p.L1256Cfs*32	ENST00000268489	NM_006885.3	1256	Ctg/tg	7/10	1	2	FACETS	0.521	0.449	0.598	0.521	0.449	0.598	SUBCLONAL	1	TRUE	1	0.43	2		803	545	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661917	29661917	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	78	504	0	ENST00000356175.3:c.5815del	p.Cys1939AlafsTer19	p.C1939Afs*19	ENST00000356175	NM_000267.3	1937	cgT/cg	39/57	1	2	FACETS	0.813	0.718	0.916	0.813	0.718	0.916	CLONAL	1	TRUE	1	0.43	2		504	446	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272435	15272435	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752977489	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	130	790	0	ENST00000263388.2:c.6004G>A	p.Asp2002Asn	p.D2002N	ENST00000263388	NM_000435.2	2002	Gac/Aac	33/33	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.43	2		790	433	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607508	46607508	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	151	814	0	ENST00000263734.3:c.1698del	p.Met567Ter	p.M567*	ENST00000263734	NM_001430.4	566	gCc/gc	12/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.43	2		814	577	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225365143	225365143	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	182	557	0	ENST00000264414.4:c.1547A>C	p.Gln516Pro	p.Q516P	ENST00000264414	NM_003590.4	516	cAg/cCg	11/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.43	2		557	700	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561319	9561319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753315436	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	175	619	0	ENST00000353224.5:c.463G>A	p.Asp155Asn	p.D155N	ENST00000353224	NM_177990.2	155	Gat/Aat	4/10	0.3	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.43	1		619	559	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280730	41280730	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	135	741	0	ENST00000349496.5:c.2243A>G	p.Tyr748Cys	p.Y748C	ENST00000349496	NM_001904.3	748	tAt/tGt	15/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.43	2		741	541	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200024	128200024	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	130	957	0	ENST00000341105.2:c.1281del	p.Phe428SerfsTer49	p.F428Sfs*49	ENST00000341105	NM_032638.4	427	ccC/cc	6/6	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.43	2		957	530	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589801	55589801	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	122	504	0	ENST00000288135.5:c.1283G>A	p.Cys428Tyr	p.C428Y	ENST00000288135	NM_000222.2	428	tGt/tAt	8/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.43	2		504	527	SUCCESS
ALB	213	MSKCC	GRCh37	4	74272414	74272414	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	96	449	0	ENST00000295897.4:c.206A>G	p.Glu69Gly	p.E69G	ENST00000295897	NM_000477.5	69	gAa/gGa	3/15	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.43	2		449	395	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549499	187549499	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	145	698	0	ENST00000441802.2:c.4619C>A	p.Pro1540His	p.P1540H	ENST00000441802	NM_005245.3	1540	cCt/cAt	9/27	0.0806996691323385	3	FACETS	1	0.988	1	0.738	0.677	0.802	INDETERMINATE	1	TRUE	1	0.43	3		698	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0060881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	50	454	0	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	1	2	FACETS	0.64	0.541	0.748	0.64	0.541	0.748	SUBCLONAL	1	TRUE	1	0.19	2		454	823	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685281	89685281	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060500116	NA	P-0060881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	26	245	0	ENST00000371953.3:c.176C>G	p.Ser59Ter	p.S59*	ENST00000371953	NM_000314.4	59	tCa/tGa	3/9	1	2	FACETS	0.883	0.7	1	0.883	0.7	1	CLONAL	1	TRUE	1	0.19	2		245	310	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220604	1220604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555738372	NA	P-0060881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	57	662	0	ENST00000326873.7:c.622G>A	p.Asp208Asn	p.D208N	ENST00000326873	NM_000455.4	208	Gac/Aac	5/10	1	2	FACETS	0.633	0.541	0.734	0.633	0.541	0.734	SUBCLONAL	1	TRUE	1	0.19	2		662	948	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10800327	10800327	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	68	621	0	ENST00000361367.2:c.3197C>G	p.Ser1066Cys	p.S1066C	ENST00000361367	NM_014633.3	1066	tCt/tGt	25/25	1	2	FACETS	0.77	0.669	0.881	0.77	0.669	0.881	SUBCLONAL	1	TRUE	1	0.19	2		621	929	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0060881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	367	1000	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.514170623644458	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	FALSE	0	0.507969804099779	2		1000	647	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150933419	150933419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1258	75	639	0	ENST00000271640.5:c.2881C>T	p.Pro961Ser	p.P961S	ENST00000271640	NM_001145415.1	961	Ccc/Tcc	16/22	0.507969804099779	6	FACETS	0.447	0.39	0.509			1	SUBCLONAL	1	FALSE	NA	0.507969804099779	6		639	1333	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934555	9934555	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	156	488	0	ENST00000330684.3:c.1600A>G	p.Ser534Gly	p.S534G	ENST00000330684	NM_001134407.1	534	Agt/Ggt	7/13	0.517782107908032	3	FACETS	1	0.969	1	0.557	0.512	0.605	CLONAL	1	FALSE	1	0.507969804099779	3		488	691	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348467	89348467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	62	699	0	ENST00000301030.4:c.4483C>T	p.His1495Tyr	p.H1495Y	ENST00000301030	NM_001256183.1	1495	Cat/Tat	9/13	0.510658546348625	4	FACETS	0.307	0.264	0.354	0.077	0.066	0.089	SUBCLONAL	1	FALSE	0	0.507969804099779	4		699	1199	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519920	NA	P-0060881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	310	445	0	ENST00000397062.3:c.85G>T	p.Asp29Tyr	p.D29Y	ENST00000397062	NM_006164.4	29	Gat/Tat	2/5	0.517782107908032	4	FACETS	1	0.947	1			1	CLONAL	2	FALSE	NA	0.507969804099779	4		445	919	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259241	89259241	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1844	100	462	0	ENST00000336596.2:c.385G>T	p.Asp129Tyr	p.D129Y	ENST00000336596	NM_005233.5	129	Gat/Tat	3/17	0.20952559703546	5	FACETS	0.357	0.317	0.4	0.119	0.105	0.134	INDETERMINATE	1	FALSE	2	0.507969804099779	5		462	1944	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031895	26031895	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	75	670	0	ENST00000244661.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000244661	NM_003537.3	132	Cgc/Ggc	1/1	0.282334700887109	3	FACETS	0.377	0.33	0.429	0.189	0.165	0.215	INDETERMINATE	1	FALSE	1	0.507969804099779	3		670	981	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528511	157528511	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	253	635	0	ENST00000346085.5:c.6236A>C	p.Gln2079Pro	p.Q2079P	ENST00000346085	NM_020732.3	2079	cAg/cCg	20/20	0.389760638806275	3	FACETS	0.808	0.759	0.858	0.808	0.759	0.858	CLONAL	2	FALSE	1	0.507969804099779	3		635	773	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971146	21971146	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	266	707	0	ENST00000304494.5:c.212A>T	p.Asn71Ile	p.N71I	ENST00000304494	NM_000077.4	71	aAc/aTc	2/3	0.490027452234608	2	FACETS	0.901	0.853	0.95	0.901	0.853	0.95	CLONAL	2	FALSE	0	0.507969804099779	2		707	581	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923206	39923206	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0060881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	37	364	0	ENST00000378444.4:c.3503-1G>A		p.X1168_splice	ENST00000378444	NM_001123385.1	1168			0.327425521236026	3	FACETS	0.395	0.326	0.473	0.132	0.108	0.158	SUBCLONAL	1	FALSE	0	0.507969804099779	3		364	462	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938569	76938569	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060881-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	68	410	0	ENST00000373344.5:c.2179C>A	p.Gln727Lys	p.Q727K	ENST00000373344	NM_000489.3	727	Caa/Aaa	9/35	0.319071953092601	2	FACETS	0.485	0.422	0.553	0.243	0.211	0.277	SUBCLONAL	1	FALSE	0	0.507969804099779	2		410	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0060881-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	253	1031	0	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.635058413062301	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.635058413062301	1		1031	517	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919223	48919223	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1566186840	NA	P-0060881-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	22	232	0	ENST00000267163.4:c.388A>T	p.Lys130Ter	p.K130*	ENST00000267163	NM_000321.2	130	Aaa/Taa	4/27	0.635058413062301	1	FACETS	0.965	0.788	1	0.965	0.788	1	CLONAL	1	TRUE	0	0.635058413062301	1		232	49	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77937768	77937768	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060881-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	200	983	1	ENST00000361507.4:c.950C>A	p.Pro317Gln	p.P317Q	ENST00000361507	NM_080491.2	317	cCg/cAg	4/10	0.635058413062301	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.635058413062301	1		984	401	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246456	46246456	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060881-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	138	856	0	ENST00000334344.6:c.4550G>T	p.Arg1517Met	p.R1517M	ENST00000334344	NM_152641.2	1517	aGg/aTg	15/21	0.48971131207453	1	FACETS	0.546	0.499	0.595	0.546	0.499	0.595	SUBCLONAL	1	TRUE	0	0.635058413062301	1		856	543	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993070	72993070	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060881-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	148	899	0	ENST00000268489.5:c.975C>G	p.Ile325Met	p.I325M	ENST00000268489	NM_006885.3	325	atC/atG	2/10	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.635058413062301	2		899	443	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259280	89259280	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0060881-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	18	754	0	ENST00000336596.2:c.424A>T	p.Lys142Ter	p.K142*	ENST00000336596	NM_005233.5	142	Aag/Tag	3/17	0.635058413062301	1	FACETS	0.13	0.098	0.169	0.13	0.098	0.169	SUBCLONAL	1	TRUE	0	0.635058413062301	1		754	297	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200771	128200771	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060881-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	171	667	0	ENST00000341105.2:c.1034C>A	p.Ala345Asp	p.A345D	ENST00000341105	NM_032638.4	345	gCc/gAc	5/6	0.586941319137116	4	FACETS	1	0.987	1	0.443	0.409	0.479	CLONAL	1	TRUE	1	0.635058413062301	4		667	662	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197145	26197145	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772873150	NA	P-0060881-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	284	1139	0	ENST00000356476.2:c.334G>A	p.Ala112Thr	p.A112T	ENST00000356476		112	Gcc/Acc	1/1	0.504770174573167	1	FACETS	0.806	0.762	0.852	0.806	0.762	0.852	CLONAL	1	TRUE	0	0.635058413062301	1		1139	757	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958417	90958417	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1563513080	NA	P-0060881-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	68	427	0	ENST00000265433.3:c.2021G>T	p.Gly674Val	p.G674V	ENST00000265433	NM_002485.4	674	gGc/gTc	13/16	0.31703946321002	2	FACETS	1	0.96	1	0.595	0.528	0.663	INDETERMINATE	1	TRUE	0	0.635058413062301	2		427	180	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0060881-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	59	367	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	0.48045114492912	4	FACETS	0.874	0.764	0.989	0.874	0.764	0.989	CLONAL	2	TRUE	2	0.521218898143306	4		367	197	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577595	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0060881-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	160	355	0	ENST00000269305.4:c.686_687del	p.Cys229TyrfsTer10	p.C229Yfs*10	ENST00000269305	NM_001126112.2	229	tGT/t	7/11	0.510962840542969	5	FACETS	1	0.966	1	0.832	0.782	0.88	CLONAL	4	TRUE	0	0.521218898143306	5		355	263	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524452	187524452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060881-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	72	351	0	ENST00000441802.2:c.11228G>A	p.Cys3743Tyr	p.C3743Y	ENST00000441802	NM_005245.3	3743	tGc/tAc	19/27	0.521218898143306	2	FACETS	0.966	0.871	1	0.966	0.871	1	CLONAL	2	TRUE	0	0.521218898143306	2		351	143	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415874	49415875	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0060881-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	84	423	0	ENST00000301067.7:c.16472_16473del	p.Glu5491GlyfsTer20	p.E5491Gfs*20	ENST00000301067	NM_003482.3	5491	gAG/g	53/54	0.521218898143306	4	FACETS	0.908	0.813	1	0.908	0.813	1	CLONAL	2	TRUE	2	0.521218898143306	4		423	270	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443002	49443002	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0060881-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	191	346	0	ENST00000301067.7:c.3907-1G>C		p.X1303_splice	ENST00000301067	NM_003482.3	1303			0.521218898143306	4	FACETS	0.876	0.821	0.933	1	0.99	1	CLONAL	3	TRUE	2	0.521218898143306	4		346	424	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858560	9858560	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060881-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	51	454	0	ENST00000330684.3:c.2841G>C	p.Arg947Ser	p.R947S	ENST00000330684	NM_001134407.1	947	agG/agC	13/13	0.48045114492912	4	FACETS	1	0.89	1	1	0.89	1	CLONAL	2	TRUE	2	0.521218898143306	4		454	145	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533274	29533274	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060881-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	51	306	0	ENST00000356175.3:c.1278del	p.Trp426CysfsTer47	p.W426Cfs*47	ENST00000356175	NM_000267.3	426	tGg/tg	12/57	0.494350463761653	2	FACETS	0.844	0.74	0.949	0.844	0.74	0.949	CLONAL	2	TRUE	0	0.521218898143306	2		306	116	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957516	1957516	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060881-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	124	337	0	ENST00000382891.5:c.2615G>T	p.Cys872Phe	p.C872F	ENST00000382891	NM_133335.3	872	tGc/tTc	14/22	0.521218898143306	2	FACETS	0.839	0.786	0.891	1	0.987	1	CLONAL	3	TRUE	0	0.521218898143306	2		337	189	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592056	67592056	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060881-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	86	316	0	ENST00000274335.5:c.1872G>C	p.Trp624Cys	p.W624C	ENST00000274335		624	tgG/tgC	14/15	0.521218898143306	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	0	0.521218898143306	2		316	159	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033216	69033216	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060881-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	40	263	0	ENST00000288368.4:c.3656A>T	p.Lys1219Met	p.K1219M	ENST00000288368	NM_024870.2	1219	aAg/aTg	30/40	0.521218898143306	4	FACETS	0.965	0.822	1	0.965	0.822	1	CLONAL	2	TRUE	2	0.521218898143306	4		263	121	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411041	63411041	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060881-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	51	464	0	ENST00000330258.3:c.2126G>C	p.Cys709Ser	p.C709S	ENST00000330258	NM_152424.3	709	tGc/tCc	2/2	0.281234881233657	5	FACETS	0.872	0.751	1	0.581	0.501	0.667	INDETERMINATE	2	TRUE	2	0.521218898143306	5		464	200	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0060882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	217	382	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.340835847802001	7	FACETS	0.934	0.877	0.991	0.934	0.877	0.991	CLONAL	5	TRUE	2	0.340835847802001	7		382	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0060882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	224	385	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	0.111482372689108	5	FACETS	0.946	0.885	1			1	INDETERMINATE	3	TRUE	NA	0.340835847802001	5		385	700	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021440	42021440	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	96	644	0	ENST00000219905.7:c.3736C>T	p.Arg1246Ter	p.R1246*	ENST00000219905	NM_001164273.1	1246	Cga/Tga	11/24	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.340835847802001	2		644	502	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911494	114911495	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	86	538	0	ENST00000543371.1:c.1012_1013insT	p.Asp338ValfsTer18	p.D338Vfs*18	ENST00000543371	NM_001198531.1	338	gac/gTac	10/14	1	2	FACETS	0.923	0.818	1	0.923	0.818	1	CLONAL	1	TRUE	1	0.340835847802001	2		538	547	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625410	69625410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782768201	NA	P-0060882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	106	699	0	ENST00000334134.2:c.383C>T	p.Thr128Met	p.T128M	ENST00000334134	NM_005247.2	128	aCg/aTg	3/3	NA	2	FACETS	0.844	0.757	0.936			1	INDETERMINATE	1	TRUE	NA	0.340835847802001	2		699	737	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640625	3640625	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	114	824	0	ENST00000294008.3:c.3014A>G	p.Glu1005Gly	p.E1005G	ENST00000294008	NM_032444.2	1005	gAg/gGg	12/15	0.263722535412111	4	FACETS	0.862	0.774	0.954	0.431	0.387	0.477	CLONAL	1	TRUE	2	0.340835847802001	4		824	1041	SUCCESS
APC	324	MSKCC	GRCh37	5	112175530	112175534	+	frameshift_variant	Frame_Shift_Del	DEL	GGTAA	GGTAA	-	novel	NA	P-0060882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	214	662	0	ENST00000257430.4:c.4240_4244del	p.Val1414TrpfsTer7	p.V1414Wfs*7	ENST00000257430	NM_000038.5	1413	atGGTAAgt/atgt	16/16	0.337704889969036	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	0	0.340835847802001	2		662	626	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631255	176631255	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0060882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	67	612	0	ENST00000439151.2:c.1198A>T	p.Arg400Ter	p.R400*	ENST00000439151	NM_022455.4	400	Aga/Tga	4/23	0.337704889969036	2	FACETS	0.696	0.605	0.794	0.348	0.302	0.397	SUBCLONAL	1	TRUE	0	0.340835847802001	2		612	565	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0060883-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	74	768	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	0.162887246745087	1	FACETS	0.911	0.798	1	0.911	0.798	1	CLONAL	1	TRUE	0	0.23	1		768	625	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0060883-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	39	589	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.897	0.745	1	0.897	0.745	1	CLONAL	1	TRUE	1	0.23	2		589	378	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0060883-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	50	612	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.23	2		612	347	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201099	108201099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759728261	NA	P-0060883-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	35	597	0	ENST00000278616.4:c.7466C>T	p.Ser2489Phe	p.S2489F	ENST00000278616	NM_000051.3	2489	tCc/tTc	50/63	1	2	FACETS	0.805	0.661	0.967	0.805	0.661	0.967	CLONAL	1	TRUE	1	0.23	2		597	378	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0060883-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	29	689	0				ENST00000310581	NM_198253.2	-/1132			0.162887246745087	1	FACETS	0.629	0.505	0.769	0.629	0.505	0.769	SUBCLONAL	1	TRUE	0	0.23	1		689	355	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578247	7578247	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0060883-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	88	867	0	ENST00000269305.4:c.602T>A	p.Leu201Ter	p.L201*	ENST00000269305	NM_001126112.2	201	tTg/tAg	6/11	0.201448638782564	1	FACETS	0.913	0.808	1	0.913	0.808	1	CLONAL	1	TRUE	0	0.23	1		867	742	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350062	81350062	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs759145490	NA	P-0060883-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	10	392	0	ENST00000222390.5:c.1270C>T	p.Arg424Cys	p.R424C	ENST00000222390	NM_000601.4	424	Cgt/Tgt	10/18	1	2	FACETS	0.46	0.312	0.646	0.46	0.312	0.646	SUBCLONAL	1	TRUE	1	0.23	2		392	189	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553441	106553441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746535819	NA	P-0060883-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	67	770	0	ENST00000369096.4:c.1406C>T	p.Ser469Leu	p.S469L	ENST00000369096	NM_001198.3	469	tCg/tTg	5/7	1	2	FACETS	0.91	0.791	1	0.91	0.791	1	CLONAL	1	TRUE	1	0.23	2		770	640	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790129	40790129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060883-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	99	771	0	ENST00000373198.4:c.2602C>T	p.Pro868Ser	p.P868S	ENST00000373198	NM_133170.3	868	Ccc/Tcc	18/32	1	2	FACETS	0.983	0.876	1	0.983	0.876	1	CLONAL	1	TRUE	1	0.23	2		771	876	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99204042	99204042	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529481819	NA	P-0060883-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	42	508	0	ENST00000074304.5:c.2905G>A	p.Glu969Lys	p.E969K	ENST00000074304	NM_001134224.1	969	Gaa/Aaa	26/26	1	2	FACETS	0.893	0.747	1	0.893	0.747	1	CLONAL	1	TRUE	1	0.23	2		508	409	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864126	57864126	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144673003	NA	P-0060883-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	71	825	0	ENST00000228682.2:c.1603C>T	p.Pro535Ser	p.P535S	ENST00000228682	NM_005269.2	535	Ccc/Tcc	12/12	1	2	FACETS	0.696	0.606	0.794	0.696	0.606	0.794	SUBCLONAL	1	TRUE	1	0.23	2		825	887	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645688	12645688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121434594	NA	P-0060883-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	45	630	0	ENST00000251849.4:c.781C>T	p.Pro261Ser	p.P261S	ENST00000251849	NM_002880.3	261	Cct/Tct	7/17	1	2	FACETS	0.572	0.48	0.675	0.572	0.48	0.675	SUBCLONAL	1	TRUE	1	0.23	2		630	684	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251206	115251206	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060883-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	19	552	0	ENST00000369535.4:c.520A>G	p.Ser174Gly	p.S174G	ENST00000369535	NM_002524.4	174	Agt/Ggt	5/7	1	2	FACETS	0.472	0.358	0.607	0.472	0.358	0.607	SUBCLONAL	1	TRUE	1	0.23	2		552	350	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38787097	38787097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060883-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	71	614	0	ENST00000348513.6:c.896G>A	p.Arg299Lys	p.R299K	ENST00000348513	NM_003079.4	299	aGg/aAg	10/11	0.201448638782564	1	FACETS	0.746	0.651	0.85	0.746	0.651	0.85	SUBCLONAL	1	TRUE	0	0.23	1		614	732	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244205	5244206	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0060883-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	41	818	0	ENST00000357368.4:c.1276_1277delinsTT	p.Pro426Leu	p.P426L	ENST00000357368	NM_002850.3	426	CCg/TTg	11/38	1	2	FACETS	0.528	0.439	0.628	0.528	0.439	0.628	SUBCLONAL	1	TRUE	1	0.23	2		818	675	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422555	225422555	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060883-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	16	363	0	ENST00000264414.4:c.85T>G	p.Tyr29Asp	p.Y29D	ENST00000264414	NM_003590.4	29	Tat/Gat	2/16	1	2	FACETS	0.659	0.488	0.863	0.659	0.488	0.863	SUBCLONAL	1	TRUE	1	0.23	2		363	211	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008919	152008919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060883-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	42	546	1	ENST00000262189.6:c.703G>A	p.Asp235Asn	p.D235N	ENST00000262189	NM_170606.2	235	Gat/Aat	5/59	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.23	2		547	347	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0060890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	90	382	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.155105738826823	5	FACETS	1	0.962	1	0.78	0.698	0.867	INDETERMINATE	2	TRUE	2	0.311737714766083	5		382	362	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851286	156851286	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745776726	NA	P-0060890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	76	478	0	ENST00000524377.1:c.2243G>A	p.Arg748Gln	p.R748Q	ENST00000524377	NM_002529.3	748	cGg/cAg	17/17	0.202394252351523	4	FACETS	0.941	0.825	1	0.47	0.412	0.533	CLONAL	1	TRUE	2	0.311737714766083	4		478	680	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0060890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	142	416	0	ENST00000257430.4:c.3919dup	p.Ile1307AsnfsTer8	p.I1307Nfs*8	ENST00000257430	NM_000038.5	1306	gaa/gAaa	16/16	0.311737714766083	3	FACETS	0.908	0.831	0.988	0.908	0.831	0.988	CLONAL	2	TRUE	1	0.311737714766083	3		416	580	SUCCESS
APC	324	MSKCC	GRCh37	5	112175322	112175322	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1114167578	NA	P-0060890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	99	448	0	ENST00000257430.4:c.4031C>G	p.Ser1344Ter	p.S1344*	ENST00000257430	NM_000038.5	1344	tCa/tGa	16/16	0.311737714766083	3	FACETS	1	0.959	1	0.574	0.513	0.638	CLONAL	1	TRUE	1	0.311737714766083	3		448	640	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912188	114912188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	150	331	0	ENST00000543371.1:c.1258C>T	p.Arg420Trp	p.R420W	ENST00000543371	NM_001198531.1	420	Cgg/Tgg	11/14	0.202394252351523	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.311737714766083	4		331	556	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554409	63554409	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	168	537	0	ENST00000307078.5:c.330C>G	p.Phe110Leu	p.F110L	ENST00000307078	NM_004655.3	110	ttC/ttG	2/11	0.112902038022516	5	FACETS	0.92	0.851	0.992	0.69	0.638	0.744	INDETERMINATE	3	TRUE	1	0.311737714766083	5		537	573	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953283	17953283	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	61	511	0	ENST00000458235.1:c.703A>C	p.Met235Leu	p.M235L	ENST00000458235	NM_000215.3	235	Atg/Ctg	6/24	0.311737714766083	3	FACETS	0.878	0.759	1	0.293	0.253	0.336	CLONAL	1	TRUE	0	0.311737714766083	3		511	515	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644703	134644703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536029159	NA	P-0060891-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	52	484	2	ENST00000398015.3:c.104C>T	p.Thr35Met	p.T35M	ENST00000398015	NM_004441.4	35	aCg/aTg	2/16	0.314935244638844	3	FACETS	0.434	0.369	0.505	0.145	0.123	0.169	SUBCLONAL	1	TRUE	0	0.505207336971328	3		486	594	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148529772	148529772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060891-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	173	241	0	ENST00000320356.2:c.317C>T	p.Ser106Leu	p.S106L	ENST00000320356	NM_004456.4	106	tCa/tTa	4/20	0.505876922530962	4	FACETS	0.919	0.851	0.989			1	CLONAL	2	TRUE	NA	0.505207336971328	4		241	561	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630400	47630400	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779976	NA	P-0060891-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	265	578	0	ENST00000233146.2:c.70C>T	p.Gln24Ter	p.Q24*	ENST00000233146	NM_000251.2	24	Cag/Tag	1/16	0.505876922530962	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.505207336971328	3		578	608	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25462069	25462070	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0060891-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	86	468	1	ENST00000264709.3:c.2337_2338delinsTT	p.Met779_Ile780delinsIlePhe	p.M779_I780delinsIF	ENST00000264709	NM_175629.2	779	atGAtt/atTTtt	20/23	0.505876922530962	4	FACETS	0.603	0.532	0.679	0.201	0.177	0.227	SUBCLONAL	1	TRUE	1	0.505207336971328	4		469	850	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149637	202149637	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060891-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	129	476	0	ENST00000358485.4:c.1078C>G	p.Leu360Val	p.L360V	ENST00000358485	NM_001080125.1	360	Ctc/Gtc	8/9	0.505876922530962	3	FACETS	0.923	0.838	1	0.462	0.419	0.506	CLONAL	1	TRUE	1	0.505207336971328	3		476	693	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190334	32190334	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060891-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	150	525	0	ENST00000375023.3:c.405C>G	p.Ile135Met	p.I135M	ENST00000375023	NM_004557.3	135	atC/atG	3/30	0.505876922530962	3	FACETS	0.919	0.841	1	0.46	0.42	0.501	CLONAL	1	TRUE	1	0.505207336971328	3		525	809	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190498	32190498	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060891-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	161	645	0	ENST00000375023.3:c.241C>A	p.Gln81Lys	p.Q81K	ENST00000375023	NM_004557.3	81	Caa/Aaa	3/30	0.505876922530962	3	FACETS	0.928	0.852	1	0.464	0.426	0.504	CLONAL	1	TRUE	1	0.505207336971328	3		645	860	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190516	32190516	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060891-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	157	617	0	ENST00000375023.3:c.223C>A	p.Gln75Lys	p.Q75K	ENST00000375023	NM_004557.3	75	Caa/Aaa	3/30	0.505876922530962	3	FACETS	0.915	0.838	0.995	0.457	0.419	0.498	CLONAL	1	TRUE	1	0.505207336971328	3		617	851	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	260	321	0				ENST00000310581	NM_198253.2	-/1132			0.291103738881983	8	FACETS	0.921	0.867	0.975	0.921	0.867	0.975	CLONAL	5	FALSE	3	0.291103738881983	8		321	727	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0060905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	96	501	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.291103738881983	5	FACETS	1	0.98	1	0.499	0.445	0.556	CLONAL	1	FALSE	2	0.291103738881983	5		501	633	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0060905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	121	613	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.291103738881983	5	FACETS	0.879	0.796	0.967	0.586	0.53	0.645	CLONAL	2	FALSE	2	0.291103738881983	5		613	679	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0060905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	198	765	0	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.291103738881983	5	FACETS	1	0.982	1	0.786	0.729	0.845	CLONAL	2	FALSE	2	0.291103738881983	5		765	829	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519361	176519361	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs938855503	NA	P-0060905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	109	676	0	ENST00000292408.4:c.767C>T	p.Pro256Leu	p.P256L	ENST00000292408	NM_213647.1	256	cCg/cTg	7/18	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.291103738881983	2		676	567	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199603	16199603	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	58	559	0	ENST00000375759.3:c.376G>C	p.Glu126Gln	p.E126Q	ENST00000375759	NM_015001.2	126	Gaa/Caa	2/15	0.291103738881983	5	FACETS	0.775	0.664	0.895	0.258	0.221	0.299	SUBCLONAL	1	FALSE	2	0.291103738881983	5		559	739	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18473916	18473916	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	88	300	0	ENST00000266497.5:c.1158G>T	p.Gln386His	p.Q386H	ENST00000266497		386	caG/caT	6/31	0.291103738881983	3	FACETS	1	0.907	1	0.677	0.605	0.752	CLONAL	2	FALSE	0	0.291103738881983	3		300	341	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134301	41134301	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	39	531	0	ENST00000379561.5:c.1327C>G	p.Gln443Glu	p.Q443E	ENST00000379561	NM_002015.3	443	Cag/Gag	2/3	0.211908145690826	5	FACETS	0.57	0.471	0.681	0.19	0.157	0.227	SUBCLONAL	1	FALSE	2	0.291103738881983	5		531	675	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1296261	1296261	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0060905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	222	705	1				ENST00000310581	NM_198253.2	-/1132			0.291103738881983	8	FACETS	1	0.957	1	0.621	0.579	0.665	CLONAL	3	FALSE	3	0.291103738881983	8		706	920	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0060912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	395	377	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.284125251529979	8	FACETS	1	0.971	1	1	0.971	1	CLONAL	6	TRUE	2	0.284125251529979	8		377	842	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578242	7578242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882003	NA	P-0060912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	246	594	0	ENST00000269305.4:c.607G>A	p.Val203Met	p.V203M	ENST00000269305	NM_001126112.2	203	Gtg/Atg	6/11	0.265824753030859	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.284125251529979	2		594	825	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579584	7579585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0060926-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	164	639	0	ENST00000269305.4:c.102dup	p.Pro36AlafsTer7	p.P36Afs*7	ENST00000269305	NM_001126112.2	34	-/C	4/11	0.346992898602329	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.346992898602329	1		639	699	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653790	89653790	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs794727243	NA	P-0060926-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	22	168	0	ENST00000371953.3:c.88C>A	p.Pro30Thr	p.P30T	ENST00000371953	NM_000314.4	30	Cca/Aca	2/9	1	2	FACETS	0.593	0.461	0.744	0.593	0.461	0.744	SUBCLONAL	1	TRUE	1	0.346992898602329	2		168	214	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434645	110434645	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1036462353	NA	P-0060926-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	181	765	0	ENST00000375856.3:c.3756C>G	p.Asn1252Lys	p.N1252K	ENST00000375856	NM_003749.2	1252	aaC/aaG	1/2	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.346992898602329	2		765	822	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0060927-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	230	304	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.891764584763537	2		304	505	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0060927-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	161	380	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.891764584763537	1	FACETS	0.962	0.918	1	0.962	0.918	1	CLONAL	1	TRUE	0	0.891764584763537	1		380	208	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0060927-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	264	851	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.891764584763537	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.891764584763537	1		851	312	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0060927-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	173	424	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.951	0.886	1	0.951	0.886	1	CLONAL	1	TRUE	1	0.891764584763537	2		424	408	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933593	39933594	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0060927-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	193	374	0	ENST00000378444.4:c.1005dup	p.Ser336LeufsTer45	p.S336Lfs*45	ENST00000378444	NM_001123385.1	335	-/C	4/15	0.461213745466902	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	NA	0.891764584763537	0		374	271	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593466	48593466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064796102	NA	P-0060927-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	312	462	0	ENST00000342988.3:c.1217C>T	p.Ala406Val	p.A406V	ENST00000342988	NM_005359.5	406	gCg/gTg	10/12	0.891764584763537	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.891764584763537	1		462	376	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060927-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	245	648	0	ENST00000261937.6:c.89C>T	p.Pro30Leu	p.P30L	ENST00000261937	NM_182925.4	30	cCg/cTg	2/30	NA	2	FACETS	0.992	0.936	1			1	INDETERMINATE	1	TRUE	NA	0.891764584763537	2		648	554	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884785	111884785	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751330475	NA	P-0060927-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	327	666	0	ENST00000341259.2:c.874G>A	p.Glu292Lys	p.E292K	ENST00000341259	NM_005475.2	292	Gag/Aag	4/8	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.891764584763537	2		666	716	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649978	88649978	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786201792	NA	P-0060927-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	298	374	0	ENST00000372037.3:c.227G>A	p.Cys76Tyr	p.C76Y	ENST00000372037	NM_004329.2	76	tGc/tAc	4/13	0.891764584763537	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.891764584763537	2		374	330	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606833	43606833	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060927-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	108	816	0	ENST00000355710.3:c.1442T>G	p.Leu481Arg	p.L481R	ENST00000355710	NM_020975.4	481	cTt/cGt	7/20	1	2	FACETS	0.307	0.275	0.34	0.307	0.275	0.34	SUBCLONAL	1	TRUE	1	0.891764584763537	2		816	790	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609500	81609500	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060927-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	204	552	2	ENST00000298171.2:c.1098T>G	p.Phe366Leu	p.F366L	ENST00000298171	NM_000369.2	366	ttT/ttG	10/10	0.223129165469649	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.891764584763537	0		554	471	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647082	23647082	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1060502732	NA	P-0060927-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	71	590	0	ENST00000261584.4:c.785T>G	p.Leu262Arg	p.L262R	ENST00000261584	NM_024675.3	262	cTt/cGt	4/13	0.425121125089619	1	FACETS	0.227	0.199	0.257	0.227	0.199	0.257	INDETERMINATE	1	TRUE	0	0.891764584763537	1		590	389	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163858	152163859	+	missense_variant	Missense_Mutation	DNP	AG	AG	GT	novel	NA	P-0060927-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	74	500	0	ENST00000206249.3:c.579_580delinsGT	p.Gly194Cys	p.G194C	ENST00000206249	NM_000125.3	193	tcAGgc/tcGTgc	2/8	1	2	FACETS	0.29	0.253	0.328	0.29	0.253	0.328	SUBCLONAL	1	TRUE	1	0.891764584763537	2		500	573	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0060928-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	815	277	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.15010034881567	5	FACETS	1	0.977	1			1	INDETERMINATE	3	TRUE	NA	0.628857416671954	5		277	1666	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437782	52437782	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0060928-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	363	656	0	ENST00000460680.1:c.1379C>G	p.Ser460Ter	p.S460*	ENST00000460680	NM_004656.3	460	tCa/tGa	13/17	0.628857416671954	1	FACETS	0.991	0.945	1	0.991	0.945	1	CLONAL	1	TRUE	0	0.628857416671954	1		656	799	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923257	131923257	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs555367432	NA	P-0060928-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	60	141	0	ENST00000265335.6:c.760C>T	p.Arg254Cys	p.R254C	ENST00000265335		254	Cgt/Tgt	6/25	1	2	FACETS	0.94	0.823	1	0.94	0.823	1	CLONAL	1	TRUE	1	0.628857416671954	2		141	203	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012365	176012365	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060928-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	111	342	0	ENST00000367669.3:c.1569G>C	p.Leu523Phe	p.L523F	ENST00000367669	NM_022457.5	523	ttG/ttC	14/20	0.34035900912713	6	FACETS	0.717	0.643	0.796			1	INDETERMINATE	1	TRUE	NA	0.628857416671954	6		342	1111	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489549	56489549	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060928-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	399	624	0	ENST00000267101.3:c.2014C>G	p.Gln672Glu	p.Q672E	ENST00000267101	NM_001982.3	672	Cag/Gag	17/28	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.628857416671954	2		624	1246	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211441	36211441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060928-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	368	817	0	ENST00000222270.7:c.1192G>A	p.Glu398Lys	p.E398K	ENST00000222270	NM_014727.1	398	Gag/Aag	3/37	1	2	FACETS	0.954	0.905	1	0.954	0.905	1	CLONAL	1	TRUE	1	0.628857416671954	2		817	1227	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67626340	67626340	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0060928-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	269	237	0	ENST00000272342.5:c.263C>G	p.Ser88Ter	p.S88*	ENST00000272342	NM_019002.3	88	tCa/tGa	2/6	0.628857416671954	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.628857416671954	2		237	426	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101188	41101188	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060928-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	303	573	0	ENST00000373198.4:c.1168C>T	p.Pro390Ser	p.P390S	ENST00000373198	NM_133170.3	390	Cca/Tca	8/32	NA	2	FACETS	0.938	0.885	0.993			1	INDETERMINATE	1	TRUE	NA	0.628857416671954	2		573	1027	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0060929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	102	304	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.579935684841463	2		304	317	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	276	887	0	ENST00000227507.2:c.859C>T	p.Pro287Ser	p.P287S	ENST00000227507	NM_053056.2	287	Ccc/Tcc	5/5	1	2	FACETS	0.995	0.935	1	0.995	0.935	1	CLONAL	1	TRUE	1	0.579935684841463	2		887	957	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0060929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	187	591	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.992	0.921	1	0.992	0.921	1	CLONAL	1	TRUE	1	0.579935684841463	2		591	650	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059176	27059176	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	184	368	0	ENST00000324856.7:c.1813C>T	p.Gln605Ter	p.Q605*	ENST00000324856	NM_006015.4	605	Caa/Taa	4/20	0.549773951214159	2	FACETS	0.967	0.911	1	0.967	0.911	1	CLONAL	2	TRUE	0	0.579935684841463	2		368	328	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278343	39278343	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	63	235	0	ENST00000402219.2:c.806T>A	p.Met269Lys	p.M269K	ENST00000402219	NM_005633.3	269	aTg/aAg	6/23	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.579935684841463	2		235	191	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525654	187525654	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1408225595	NA	P-0060929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	109	566	0	ENST00000441802.2:c.10425del	p.Phe3476SerfsTer6	p.F3476Sfs*6	ENST00000441802	NM_005245.3	3475	ccC/cc	18/27	1	2	FACETS	0.828	0.748	0.912	0.828	0.748	0.912	CLONAL	1	TRUE	1	0.579935684841463	2		566	454	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875635	56875635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	192	542	0	ENST00000308159.5:c.2239G>A	p.Glu747Lys	p.E747K	ENST00000308159	NM_014669.4	747	Gaa/Aaa	21/22	1	2	FACETS	0.996	0.925	1	0.996	0.925	1	CLONAL	1	TRUE	1	0.579935684841463	2		542	665	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0060930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	337	674	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.529731838882194	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.525462331286396	2		674	609	SUCCESS
APC	324	MSKCC	GRCh37	5	112174096	112174096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs137854575	NA	P-0060930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	94	280	0	ENST00000257430.4:c.2805C>A	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	taC/taA	16/16	0.382379749751513	4	FACETS	1	0.971	1	0.627	0.561	0.697	CLONAL	1	TRUE	2	0.525462331286396	4		280	435	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200113	128200113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906629	NA	P-0060930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	195	685	0	ENST00000341105.2:c.1192C>T	p.Arg398Trp	p.R398W	ENST00000341105	NM_032638.4	398	Cgg/Tgg	6/6	0.301887938036648	4	FACETS	0.785	0.729	0.843	0.785	0.729	0.843	INDETERMINATE	2	TRUE	2	0.525462331286396	4		685	721	SUCCESS
APC	324	MSKCC	GRCh37	5	112175577	112175577	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	328	447	0	ENST00000257430.4:c.4288del	p.Thr1430ProfsTer43	p.T1430Pfs*43	ENST00000257430	NM_000038.5	1429	cAa/ca	16/16	0.382379749751513	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	2	0.525462331286396	4		447	810	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435948	110435948	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs754539856	NA	P-0060930-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1259	74	767	0	ENST00000375856.3:c.2453G>T	p.Gly818Val	p.G818V	ENST00000375856	NM_003749.2	818	gGg/gTg	1/2	0.525462331286396	7	FACETS	0.489	0.426	0.557	0.081	0.071	0.093	SUBCLONAL	1	TRUE	1	0.525462331286396	7		767	1333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0060931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	364	758	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.566851618874648	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.565174095587668	2		758	535	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849452	68849452	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	17	574	0	ENST00000261769.5:c.1355T>C	p.Leu452Pro	p.L452P	ENST00000261769	NM_004360.3	452	cTa/cCa	10/16	0.566851618874648	1	FACETS	0.132	0.098	0.172	0.132	0.098	0.172	SUBCLONAL	1	TRUE	0	0.565174095587668	1		574	327	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36814356	36814356	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	67	663	1	ENST00000373129.3:c.684C>A	p.Asp228Glu	p.D228E	ENST00000373129	NM_032017.1	228	gaC/gaA	8/12	0.431951173323624	5	FACETS	0.506	0.438	0.579	0.169	0.146	0.193	SUBCLONAL	1	TRUE	2	0.565174095587668	5		664	866	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054557	42054557	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	26	354	0	ENST00000219905.7:c.7741A>C	p.Thr2581Pro	p.T2581P	ENST00000219905	NM_001164273.1	2581	Aca/Cca	22/24	1	2	FACETS	0.325	0.258	0.402	0.325	0.258	0.402	SUBCLONAL	1	TRUE	1	0.565174095587668	2		354	283	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347342	89347342	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	96	743	0	ENST00000301030.4:c.5608G>T	p.Ala1870Ser	p.A1870S	ENST00000301030	NM_001256183.1	1870	Gct/Tct	9/13	0.361474091140078	3	FACETS	0.75	0.67	0.835	0.25	0.223	0.279	SUBCLONAL	1	TRUE	0	0.565174095587668	3		743	581	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367949	15367949	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs200046003	NA	P-0060931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	53	590	0	ENST00000263377.2:c.1377C>G	p.Asp459Glu	p.D459E	ENST00000263377	NM_058243.2	459	gaC/gaG	8/20	0.566851618874648	3	FACETS	0.424	0.361	0.492	0.212	0.18	0.246	SUBCLONAL	1	TRUE	1	0.565174095587668	3		590	568	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803004	32803037	+	frameshift_variant	Frame_Shift_Del	DEL	CGAGGCGATATGCTGAGCATGAAGCCATACAGCC	CGAGGCGATATGCTGAGCATGAAGCCATACAGCC	-	novel	NA	P-0060931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	54	631	0	ENST00000374899.4:c.839_872del	p.Gly280AspfsTer14	p.G280Dfs*14	ENST00000374899	NM_018833.2	280	gGGCTGTATGGCTTCATGCTCAGCATATCGCCTCGa/ga	5/12	1	2	FACETS	0.361	0.308	0.419	0.361	0.308	0.419	SUBCLONAL	1	TRUE	1	0.565174095587668	2		631	529	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187314	38187314	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs769379117	NA	P-0060931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	45	432	0	ENST00000317025.8:c.1163A>G	p.Glu388Gly	p.E388G	ENST00000317025	NM_023034.1	388	gAa/gGa	6/24	1	2	FACETS	0.38	0.32	0.447	0.38	0.32	0.447	SUBCLONAL	1	TRUE	1	0.565174095587668	2		432	419	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750474	128750600	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTTGTGTGCCCCGCTCCAGCAGCCTCCCGCGACGATGCCCCTCAACGTTAGCTTCACCAACAGGAACTATGACCTCGACTACGACTCGGTGCAGCCGTATTTCTACTGCGACGAGGAGGAGAACTT	CTTTGTGTGCCCCGCTCCAGCAGCCTCCCGCGACGATGCCCCTCAACGTTAGCTTCACCAACAGGAACTATGACCTCGACTACGACTCGGTGCAGCCGTATTTCTACTGCGACGAGGAGGAGAACTT	-	novel	NA	P-0060931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	108	618	0	ENST00000377970.2:c.31-18_139del		p.X11_splice	ENST00000377970	NM_002467.4	11		2/3	0.565174095587668	8	FACETS	0.982	0.88	1	0.196	0.176	0.219	CLONAL	1	TRUE	3	0.565174095587668	8		618	1049	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356428	70356428	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1271902285	NA	P-0060931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	70	745	0	ENST00000374080.3:c.5323G>T	p.Ala1775Ser	p.A1775S	ENST00000374080		1775	Gct/Tct	37/45	NA	2	FACETS	0.56	0.49	0.636			1	INDETERMINATE	1	TRUE	NA	0.565174095587668	2		745	442	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284979	15284979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774475688	NA	P-0060932-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	61	511	0	ENST00000263388.2:c.4636C>T	p.Arg1546Cys	p.R1546C	ENST00000263388	NM_000435.2	1546	Cgc/Tgc	25/33	0.571017300190074	4	FACETS	0.236	0.203	0.273	0.079	0.067	0.091	SUBCLONAL	1	TRUE	1	0.809724092910509	4		511	1153	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739033	40739033	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060932-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	73	822	0	ENST00000373198.4:c.3251T>C	p.Phe1084Ser	p.F1084S	ENST00000373198	NM_133170.3	1084	tTc/tCc	24/32	0.245218832217589	3	FACETS	0.264	0.23	0.3	0.088	0.076	0.1	INDETERMINATE	1	TRUE	0	0.809724092910509	3		822	961	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0060933-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	548	817	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.760992103425007	2	FACETS	0.997	0.972	1	0.997	0.972	1	CLONAL	2	TRUE	0	0.760992103425007	2		817	722	SUCCESS
APC	324	MSKCC	GRCh37	5	112151291	112151291	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs876660765	NA	P-0060933-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	122	323	0	ENST00000257430.4:c.933+1G>A		p.X311_splice	ENST00000257430	NM_000038.5	311			1	2	FACETS	0.844	0.77	0.919	0.844	0.77	0.919	CLONAL	1	TRUE	1	0.760992103425007	2		323	380	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218452	5218452	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753143589	NA	P-0060933-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	413	566	0	ENST00000357368.4:c.4027C>T	p.Arg1343Cys	p.R1343C	ENST00000357368	NM_002850.3	1343	Cgc/Tgc	25/38	0.730668269215776	3	FACETS	0.973	0.934	1	0.973	0.934	1	CLONAL	2	TRUE	1	0.760992103425007	3		566	770	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925327	114925327	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060933-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	334	518	0	ENST00000543371.1:c.1405T>C	p.Cys469Arg	p.C469R	ENST00000543371	NM_001198531.1	469	Tgc/Cgc	14/14	0.499563922904	3	FACETS	0.954	0.911	0.997	0.954	0.911	0.997	CLONAL	2	TRUE	1	0.760992103425007	3		518	635	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422821	47422821	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060933-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	165	508	0	ENST00000404338.3:c.889C>T	p.Arg297Ter	p.R297*	ENST00000404338	NM_004491.4	297	Cga/Tga	1/6	0.730668269215776	3	FACETS	0.84	0.773	0.909	0.42	0.386	0.455	CLONAL	1	TRUE	1	0.760992103425007	3		508	713	SUCCESS
APC	324	MSKCC	GRCh37	5	112170801	112170801	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060933-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	157	329	0	ENST00000257430.4:c.1897G>T	p.Glu633Ter	p.E633*	ENST00000257430	NM_000038.5	633	Gaa/Taa	15/16	1	2	FACETS	0.903	0.835	0.973	0.903	0.835	0.973	CLONAL	1	TRUE	1	0.760992103425007	2		329	457	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0060934-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	117	544	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.218241224665821	3	FACETS	0.971	0.885	1	0.971	0.885	1	INDETERMINATE	2	TRUE	1	0.399264940969611	3		544	362	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0060934-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	237	355	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.399264940969611	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.399264940969611	3		355	690	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0060934-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	345	160	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	0.386910133284603	3	FACETS	0.945	0.895	0.995	0.945	0.895	0.995	CLONAL	2	TRUE	1	0.399264940969611	3		160	1097	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163398	108163400	+	inframe_deletion	In_Frame_Del	DEL	TTA	TTA	-	rs1555099818	NA	P-0060934-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	98	483	0	ENST00000278616.4:c.4492_4494del	p.Leu1498del	p.L1498del	ENST00000278616	NM_000051.3	1497	TTA/-	30/63	1	2	FACETS	0.776	0.693	0.863	0.776	0.693	0.863	SUBCLONAL	1	TRUE	1	0.399264940969611	2		483	633	SUCCESS
APC	324	MSKCC	GRCh37	5	112174286	112174286	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs75239284	NA	P-0060934-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	198	545	1	ENST00000257430.4:c.2995C>T	p.Gln999Ter	p.Q999*	ENST00000257430	NM_000038.5	999	Caa/Taa	16/16	0.386910133284603	3	FACETS	1	0.978	1	0.574	0.531	0.618	CLONAL	1	TRUE	1	0.399264940969611	3		546	1037	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808636	1808636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762888506	NA	P-0060934-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	226	910	0	ENST00000260795.2:c.2249G>A	p.Arg750His	p.R750H	ENST00000260795		750	cGt/cAt	16/17	1	2	FACETS	0.894	0.831	0.959	0.894	0.831	0.959	CLONAL	1	TRUE	1	0.399264940969611	2		910	1266	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142105	108142105	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730881388	NA	P-0060934-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	140	482	0	ENST00000278616.4:c.3049C>T	p.Gln1017Ter	p.Q1017*	ENST00000278616	NM_000051.3	1017	Cag/Tag	20/63	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.399264940969611	2		482	621	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659648	88659648	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0060934-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	165	457	0	ENST00000372037.3:c.430+1G>A		p.X144_splice	ENST00000372037	NM_004329.2	144			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.399264940969611	2		457	789	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060935-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	121	321	0				ENST00000310581	NM_198253.2	-/1132			0.342695837168325	6	FACETS	1	0.966	1	0.232	0.209	0.256	CLONAL	1	FALSE	1	0.342695837168325	6		321	1027	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587781702	NA	P-0060935-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	468	727	1	ENST00000269305.4:c.920-1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.311276661289652	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	FALSE	1	0.342695837168325	4		728	1186	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023676	27023676	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs867647567	NA	P-0060935-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	206	687	0	ENST00000324856.7:c.782C>A	p.Ser261Ter	p.S261*	ENST00000324856	NM_006015.4	261	tCg/tAg	1/20	0.154397602764559	4	FACETS	0.923	0.858	0.991	0.923	0.858	0.991	INDETERMINATE	2	FALSE	2	0.342695837168325	4		687	874	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28601408	28601408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060935-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	88	627	0	ENST00000253063.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000253063	NM_031459.4	365	Gag/Aag	8/10	0.154397602764559	4	FACETS	0.692	0.611	0.778	0.346	0.305	0.389	INDETERMINATE	1	FALSE	2	0.342695837168325	4		627	997	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060935-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	358	603	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	0.303887109389858	3	FACETS	0.965	0.92	1	0.965	0.92	1	CLONAL	3	FALSE	0	0.342695837168325	3		603	845	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237622	133237622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs989886155	NA	P-0060935-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	340	582	0	ENST00000320574.5:c.2993C>T	p.Thr998Met	p.T998M	ENST00000320574	NM_006231.2	998	aCg/aTg	25/49	0.303887109389858	3	FACETS	0.943	0.896	0.989	0.943	0.896	0.989	CLONAL	3	FALSE	0	0.342695837168325	3		582	822	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576243	88576243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060935-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	171	557	0	ENST00000360948.2:c.1430C>T	p.Ser477Leu	p.S477L	ENST00000360948	NM_001012338.2	477	tCa/tTa	13/19	0.241307311408097	3	FACETS	1	0.988	1	0.712	0.656	0.771	CLONAL	1	FALSE	1	0.342695837168325	3		557	821	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916218	9916218	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060935-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	39	540	0	ENST00000330684.3:c.2071G>C	p.Glu691Gln	p.E691Q	ENST00000330684	NM_001134407.1	691	Gag/Cag	10/13	1	2	FACETS	0.299	0.246	0.357	0.299	0.246	0.357	SUBCLONAL	1	FALSE	1	0.342695837168325	2		540	762	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577543	7577543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1019340046	NA	P-0060935-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	114	584	0	ENST00000269305.4:c.738G>A	p.Met246Ile	p.M246I	ENST00000269305	NM_001126112.2	246	atG/atA	7/11	0.311276661289652	4	FACETS	0.978	0.88	1	0.326	0.293	0.361	CLONAL	1	FALSE	1	0.342695837168325	4		584	913	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117540	4117540	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060935-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	15	194	0	ENST00000262948.5:c.180G>T	p.Gln60His	p.Q60H	ENST00000262948	NM_030662.3	60	caG/caT	2/11	1	2	FACETS	0.304	0.222	0.403	0.304	0.222	0.403	SUBCLONAL	1	FALSE	1	0.342695837168325	2		194	288	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044381	128044381	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060935-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	81	643	0	ENST00000285398.2:c.1240G>A	p.Gly414Ser	p.G414S	ENST00000285398	NM_000122.1	414	Ggc/Agc	8/15	0.342695837168325	3	FACETS	0.517	0.454	0.586	0.259	0.227	0.293	SUBCLONAL	1	FALSE	1	0.342695837168325	3		643	1070	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556672	41556672	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs779792116	NA	P-0060935-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	175	523	0	ENST00000263253.7:c.3617A>G	p.Asn1206Ser	p.N1206S	ENST00000263253	NM_001429.3	1206	aAt/aGt	20/31	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.342695837168325	2		523	780	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138400828	138400828	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060935-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	30	249	0	ENST00000289153.2:c.2485G>A	p.Glu829Lys	p.E829K	ENST00000289153	NM_006219.2	829	Gaa/Aaa	17/22	0.333307467706622	4	FACETS	0.517	0.416	0.631	0.258	0.208	0.316	SUBCLONAL	1	FALSE	2	0.342695837168325	4		249	455	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916728	178916728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060935-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	160	300	0	ENST00000263967.3:c.115G>A	p.Glu39Lys	p.E39K	ENST00000263967	NM_006218.2	39	Gag/Aag	2/21	0.333307467706622	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	FALSE	2	0.342695837168325	4		300	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0060937-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	223	712	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.292182608252308	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.292182608252308	2		712	711	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0060937-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	197	660	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.245855179058715	3	FACETS	0.891	0.826	0.959	0.891	0.826	0.959	CLONAL	2	TRUE	1	0.292182608252308	3		660	867	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0060937-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	175	356	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	0.173910422794954	3	FACETS	0.892	0.828	0.958	0.892	0.828	0.958	INDETERMINATE	3	TRUE	0	0.292182608252308	3		356	513	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863213	57863213	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0060937-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	91	545	0	ENST00000228682.2:c.1309-1G>A		p.X437_splice	ENST00000228682	NM_005269.2	437			0.226099641779491	3	FACETS	1	0.971	1	0.642	0.571	0.717	CLONAL	1	TRUE	1	0.292182608252308	3		545	556	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145445	58145445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060937-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	138	658	0	ENST00000257904.6:c.56C>T	p.Thr19Ile	p.T19I	ENST00000257904	NM_000075.3	19	aCa/aTa	2/8	0.26833056726216	2	FACETS	0.848	0.775	0.924	0.848	0.775	0.924	CLONAL	2	TRUE	0	0.292182608252308	2		658	557	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845809	72845809	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060937-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	37	702	0	ENST00000268489.5:c.3658G>A	p.Glu1220Lys	p.E1220K	ENST00000268489	NM_006885.3	1220	Gag/Aag	6/10	0.128143306171638	4	FACETS	0.456	0.374	0.547	0.152	0.124	0.183	INDETERMINATE	1	TRUE	1	0.292182608252308	4		702	718	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099846	27099848	+	frameshift_variant	Frame_Shift_Del	DEL	GTG	GTG	A	novel	NA	P-0060937-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	115	580	0	ENST00000324856.7:c.3725_3727delinsA	p.Ser1242LysfsTer16	p.S1242Kfs*16	ENST00000324856	NM_006015.4	1242	aGTGat/aAat	15/20	1	2	FACETS	0.761	0.689	0.837	1	0.985	1	SUBCLONAL	2	TRUE	1	0.292182608252308	2		580	517	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0060938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	38	382	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		382	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0060938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	169	705	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		705	1188	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845534	151845534	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	90	610	0	ENST00000262189.6:c.13478G>A	p.Cys4493Tyr	p.C4493Y	ENST00000262189	NM_170606.2	4493	tGc/tAc	52/59	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		610	1011	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	352	321	0				ENST00000310581	NM_198253.2	-/1132			0.682189820372211	10	FACETS	0.996	0.957	1	0.871	0.838	0.904	CLONAL	7	FALSE	2	0.682189820372211	10		321	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	389	473	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.693992712517605	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	4	FALSE	0	0.682189820372211	4		473	446	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191099	2191099	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	263	556	0	ENST00000398665.3:c.353C>T	p.Ser118Leu	p.S118L	ENST00000398665	NM_032482.2	118	tCg/tTg	5/28	0.421278582607693	5	FACETS	0.906	0.857	0.955	0.906	0.857	0.955	CLONAL	3	FALSE	2	0.682189820372211	5		556	574	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948136	178948136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	144	431	0	ENST00000263967.3:c.2908G>A	p.Glu970Lys	p.E970K	ENST00000263967	NM_006218.2	970	Gaa/Aaa	20/21	0.560466671955475	5	FACETS	0.98	0.902	1	0.653	0.601	0.707	CLONAL	2	FALSE	2	0.682189820372211	5		431	436	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793483	18793483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603405	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	121	303	0	ENST00000266497.5:c.4180G>A	p.Glu1394Lys	p.E1394K	ENST00000266497		1394	Gaa/Aaa	30/31	0.465726929202676	6	FACETS	0.908	0.84	0.975	0.908	0.84	0.975	CLONAL	4	FALSE	2	0.682189820372211	6		303	231	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239420	105239420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	270	765	0	ENST00000349310.3:c.967G>A	p.Asp323Asn	p.D323N	ENST00000349310	NM_001014432.1	323	Gac/Aac	12/15	0.378164097124788	4	FACETS	1	0.981	1	0.785	0.75	0.819	INDETERMINATE	3	FALSE	0	0.682189820372211	4		765	424	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146647	185146647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	121	472	0	ENST00000265026.3:c.278C>T	p.Ser93Leu	p.S93L	ENST00000265026	NM_004721.4	93	tCa/tTa	2/14	0.560466671955475	5	FACETS	1	0.984	1	0.475	0.431	0.52	CLONAL	1	FALSE	2	0.682189820372211	5		472	504	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028037	69028037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	372	400	0	ENST00000288368.4:c.3196G>A	p.Glu1066Lys	p.E1066K	ENST00000288368	NM_024870.2	1066	Gag/Aag	26/40	0.682189820372211	8	FACETS	0.975	0.939	1	0.975	0.939	1	CLONAL	6	FALSE	2	0.682189820372211	8		400	568	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99192845	99192845	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs774479139	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	29	420	0	ENST00000268035.6:c.35C>G	p.Ser12Trp	p.S12W	ENST00000268035	NM_000875.3	12	tCg/tGg	1/21	0.462156024426029	3	FACETS	0.477	0.385	0.581	0.239	0.192	0.291	SUBCLONAL	1	FALSE	1	0.682189820372211	3		420	239	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188794	32188794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	286	736	0	ENST00000375023.3:c.760G>A	p.Glu254Lys	p.E254K	ENST00000375023	NM_004557.3	254	Gag/Aag	4/30	0.295306004966308	4	FACETS	1	0.956	1	0.75	0.717	0.783	INDETERMINATE	3	FALSE	0	0.682189820372211	4		736	470	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424086	49424086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218766571	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	215	465	0	ENST00000301067.7:c.13976G>A	p.Arg4659Gln	p.R4659Q	ENST00000301067	NM_003482.3	4659	cGg/cAg	42/54	0.693992712517605	3	FACETS	0.87	0.828	0.91	1	0.993	1	CLONAL	3	FALSE	1	0.682189820372211	3		465	324	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229363	36229363	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	225	649	0	ENST00000222270.7:c.8053G>C	p.Glu2685Gln	p.E2685Q	ENST00000222270	NM_014727.1	2685	Gag/Cag	37/37	0.693992712517605	4	FACETS	0.972	0.912	1	0.972	0.912	1	CLONAL	2	FALSE	2	0.682189820372211	4		649	571	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261743	16261743	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1386910185	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	148	661	0	ENST00000375759.3:c.9008C>T	p.Ser3003Leu	p.S3003L	ENST00000375759	NM_015001.2	3003	tCg/tTg	11/15	0.693992712517605	3	FACETS	1	0.98	1	0.601	0.553	0.651	CLONAL	1	FALSE	1	0.682189820372211	3		661	484	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4387983	4387983	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	257	545	0	ENST00000261254.3:c.469C>T	p.His157Tyr	p.H157Y	ENST00000261254	NM_001759.3	157	Cat/Tat	3/5	0.465726929202676	6	FACETS	1	0.964	1	1	0.964	1	CLONAL	4	FALSE	2	0.682189820372211	6		545	439	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436082	49436082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886042896	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	215	496	0	ENST00000301067.7:c.5899G>A	p.Gly1967Ser	p.G1967S	ENST00000301067	NM_003482.3	1967	Ggt/Agt	28/54	0.693992712517605	3	FACETS	0.839	0.797	0.879	1	0.992	1	CLONAL	3	FALSE	1	0.682189820372211	3		496	336	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445644	49445644	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	85	870	0	ENST00000301067.7:c.1822C>G	p.Leu608Val	p.L608V	ENST00000301067	NM_003482.3	608	Ctg/Gtg	10/54	0.693992712517605	3	FACETS	0.579	0.513	0.65	0.29	0.256	0.325	SUBCLONAL	1	FALSE	1	0.682189820372211	3		870	577	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120783427	120783427	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	124	498	0	ENST00000257552.2:c.1056G>C	p.Leu352Phe	p.L352F	ENST00000257552	NM_002442.3	352	ttG/ttC	14/15	0.693992712517605	3	FACETS	1	0.972	1	0.58	0.529	0.633	CLONAL	1	FALSE	1	0.682189820372211	3		498	420	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050845	49050845	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	117	292	1	ENST00000267163.4:c.2529G>C	p.Glu843Asp	p.E843D	ENST00000267163	NM_000321.2	843	gaG/gaC	25/27	0.31403464570214	5	FACETS	0.88	0.808	0.952	0.88	0.808	0.952	INDETERMINATE	3	FALSE	2	0.682189820372211	5		293	263	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569702	95569702	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	66	549	0	ENST00000393063.1:c.4031C>T	p.Ser1344Leu	p.S1344L	ENST00000393063	NM_030621.3	1344	tCa/tTa	22/28	0.378164097124788	4	FACETS	0.835	0.728	0.949	0.209	0.182	0.238	INDETERMINATE	1	FALSE	0	0.682189820372211	4		549	390	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459328	99459328	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	129	429	0	ENST00000268035.6:c.1964G>C	p.Gly655Ala	p.G655A	ENST00000268035	NM_000875.3	655	gGc/gCc	9/21	0.462156024426029	3	FACETS	1	0.986	1	0.712	0.654	0.772	CLONAL	1	FALSE	1	0.682189820372211	3		429	356	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81954819	81954819	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs374154653	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	84	416	0	ENST00000359376.3:c.2252C>G	p.Ser751Cys	p.S751C	ENST00000359376	NM_002661.3	751	tCc/tGc	21/33	0.693992712517605	3	FACETS	0.936	0.833	1	0.468	0.416	0.522	CLONAL	1	FALSE	1	0.682189820372211	3		416	353	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89869741	89869741	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	145	336	0	ENST00000389301.3:c.718C>G	p.Gln240Glu	p.Q240E	ENST00000389301	NM_000135.2	240	Caa/Gaa	8/43	0.202463687635195	2	FACETS	0.854	0.799	0.908	0.854	0.799	0.908	INDETERMINATE	2	FALSE	0	0.682189820372211	2		336	249	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743026	743026	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	228	354	0	ENST00000314574.4:c.952del	p.Leu318PhefsTer6	p.L318Ffs*6	ENST00000314574	NM_005433.3	318	Ctt/tt	8/12	0.693992712517605	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	FALSE	0	0.682189820372211	3		354	266	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279592	18279592	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	124	627	0	ENST00000222254.8:c.1865G>C	p.Trp622Ser	p.W622S	ENST00000222254	NM_005027.3	622	tGg/tCg	15/16	0.693992712517605	4	FACETS	1	0.96	1	0.551	0.5	0.604	CLONAL	1	FALSE	2	0.682189820372211	4		627	555	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279624	18279624	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	138	645	0	ENST00000222254.8:c.1897G>A	p.Glu633Lys	p.E633K	ENST00000222254	NM_005027.3	633	Gag/Aag	15/16	0.693992712517605	4	FACETS	1	0.969	1	0.567	0.518	0.619	CLONAL	1	FALSE	2	0.682189820372211	4		645	600	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976405	25976405	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	135	294	0	ENST00000435504.4:c.1140G>C	p.Gln380His	p.Q380H	ENST00000435504		380	caG/caC	11/13	0.560466671955475	5	FACETS	0.957	0.887	1	0.957	0.887	1	CLONAL	3	FALSE	2	0.682189820372211	5		294	279	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044321	128044321	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1434876636	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	81	548	0	ENST00000285398.2:c.1300G>T	p.Glu434Ter	p.E434*	ENST00000285398	NM_000122.1	434	Gag/Tag	8/15	0.693992712517605	3	FACETS	0.716	0.633	0.803	0.358	0.316	0.402	SUBCLONAL	1	FALSE	1	0.682189820372211	3		548	445	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022748	31022748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	411	668	0	ENST00000375687.4:c.2233G>A	p.Asp745Asn	p.D745N	ENST00000375687	NM_015338.5	745	Gat/Aat	13/13	0.693992712517605	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	FALSE	1	0.682189820372211	4		668	615	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324308	62324308	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	134	640	0	ENST00000360203.5:c.2803C>G	p.Leu935Val	p.L935V	ENST00000360203	NM_001283009.1	935	Ctc/Gtc	29/35	0.693992712517605	4	FACETS	1	0.921	1	0.337	0.307	0.369	CLONAL	1	FALSE	1	0.682189820372211	4		640	653	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274916	41274916	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	209	538	0	ENST00000349496.5:c.1166C>T	p.Ser389Leu	p.S389L	ENST00000349496	NM_001904.3	389	tCa/tTa	8/15	0.682189820372211	5	FACETS	0.995	0.929	1	0.663	0.619	0.708	CLONAL	2	FALSE	2	0.682189820372211	5		538	623	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940389	49940389	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	402	686	0	ENST00000296474.3:c.654C>G	p.Ile218Met	p.I218M	ENST00000296474	NM_002447.2	218	atC/atG	1/20	0.682189820372211	5	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	FALSE	2	0.682189820372211	5		686	688	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102894	71102894	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	191	490	0	ENST00000318789.4:c.313C>T	p.Gln105Ter	p.Q105*	ENST00000318789	NM_032682.5	105	Caa/Taa	8/21	0.682189820372211	5	FACETS	1	0.968	1	0.71	0.661	0.759	CLONAL	2	FALSE	2	0.682189820372211	5		490	532	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474738	138474738	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	125	369	0	ENST00000289153.2:c.255G>C	p.Gln85His	p.Q85H	ENST00000289153	NM_006219.2	85	caG/caC	2/22	0.560466671955475	5	FACETS	1	0.958	1	0.716	0.656	0.778	CLONAL	2	FALSE	2	0.682189820372211	5		369	345	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196663	106196663	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs901770487	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	261	586	0	ENST00000380013.4:c.4996C>A	p.Pro1666Thr	p.P1666T	ENST00000380013	NM_001127208.2	1666	Cct/Act	11/11	0.693992712517605	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	FALSE	0	0.682189820372211	3		586	336	SUCCESS
APC	324	MSKCC	GRCh37	5	112174847	112174847	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	196	429	0	ENST00000257430.4:c.3556G>C	p.Asp1186His	p.D1186H	ENST00000257430	NM_000038.5	1186	Gat/Cat	16/16	0.462002886434296	3	FACETS	1	0.989	1	0.8	0.757	0.842	CLONAL	2	FALSE	0	0.682189820372211	3		429	321	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197235	26197235	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	94	858	0	ENST00000356476.2:c.244G>A	p.Asp82Asn	p.D82N	ENST00000356476		82	Gat/Aat	1/1	0.421278582607693	5	FACETS	0.763	0.679	0.853	0.254	0.226	0.285	SUBCLONAL	1	FALSE	2	0.682189820372211	5		858	731	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124464054	124464054	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	33	324	0	ENST00000357628.3:c.1867C>G	p.Gln623Glu	p.Q623E	ENST00000357628	NM_015450.2	623	Cag/Gag	19/19	0.693992712517605	3	FACETS	0.649	0.533	0.777	0.324	0.266	0.389	SUBCLONAL	1	FALSE	1	0.682189820372211	3		324	200	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172971	38172971	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	147	471	0	ENST00000317025.8:c.2078G>C	p.Arg693Thr	p.R693T	ENST00000317025	NM_023034.1	693	aGa/aCa	11/24	0.538547634889061	6	FACETS	0.923	0.847	1			1	CLONAL	2	FALSE	NA	0.682189820372211	6		471	552	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285462	38285462	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	244	556	0	ENST00000425967.3:c.691G>C	p.Asp231His	p.D231H	ENST00000425967	NM_001174067.1	231	Gac/Cac	6/19	0.538547634889061	6	FACETS	0.94	0.885	0.995			1	CLONAL	3	FALSE	NA	0.682189820372211	6		556	600	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980570	70980570	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	249	596	0	ENST00000276594.2:c.807C>G	p.Phe269Leu	p.F269L	ENST00000276594	NM_024504.3	269	ttC/ttG	4/8	0.682189820372211	8	FACETS	1	0.987	1	0.402	0.376	0.428	CLONAL	2	FALSE	2	0.682189820372211	8		596	923	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955548	90955548	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs730881857	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	119	377	0	ENST00000265433.3:c.2117C>G	p.Ser706Ter	p.S706*	ENST00000265433	NM_002485.4	706	tCa/tGa	14/16	0.682189820372211	8	FACETS	0.854	0.773	0.94	0.285	0.257	0.314	CLONAL	2	FALSE	2	0.682189820372211	8		377	622	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802646	139802646	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767764133	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	317	494	0	ENST00000247668.2:c.491G>A	p.Arg164Gln	p.R164Q	ENST00000247668	NM_021138.3	164	cGg/cAg	5/11	0.693992712517605	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	FALSE	0	0.682189820372211	3		494	375	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870246	44870246	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	86	147	0	ENST00000377967.4:c.425A>C	p.His142Pro	p.H142P	ENST00000377967	NM_021140.2	142	cAt/cCt	5/29	0.693992712517605	2	FACETS	1	0.985	1			1	CLONAL	2	FALSE	NA	0.682189820372211	2		147	105	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342170	70342170	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	249	325	0	ENST00000374080.3:c.1222G>A	p.Glu408Lys	p.E408K	ENST00000374080		408	Gag/Aag	8/45	0.693992712517605	2	FACETS	1	0.995	1			1	CLONAL	2	FALSE	NA	0.682189820372211	2		325	300	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940015	76940015	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	203	199	0	ENST00000373344.5:c.733C>G	p.Leu245Val	p.L245V	ENST00000373344	NM_000489.3	245	Cta/Gta	9/35	0.693992712517605	2	FACETS	1	0.994	1			1	CLONAL	2	FALSE	NA	0.682189820372211	2		199	244	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183763	10183763	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs869025621	NA	P-0060940-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	87	528	0	ENST00000256474.2:c.232A>T	p.Asn78Tyr	p.N78Y	ENST00000256474	NM_000551.3	78	Aat/Tat	1/3	0.300518108452448	1	FACETS	0.972	0.865	1	0.972	0.865	1	CLONAL	1	TRUE	0	0.35	1		528	422	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554239	29554239	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060940-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	63	323	0	ENST00000356175.3:c.2255G>C	p.Arg752Thr	p.R752T	ENST00000356175	NM_000267.3	752	aGa/aCa	19/57	1	2	FACETS	0.786	0.681	0.899	0.786	0.681	0.899	SUBCLONAL	1	TRUE	1	0.35	2		323	458	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099161	157099161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1325414473	NA	P-0060940-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	84	437	0	ENST00000346085.5:c.98C>T	p.Ala33Val	p.A33V	ENST00000346085	NM_020732.3	33	gCg/gTg	1/20	1	2	FACETS	0.964	0.854	1	0.964	0.854	1	CLONAL	1	TRUE	1	0.35	2		437	498	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0060940-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	149	380	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.266540870653554	3	FACETS	1	0.989	1	0.748	0.689	0.808	INDETERMINATE	1	TRUE	1	0.565208920127896	3		380	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0060940-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	353	417	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.565208920127896	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.565208920127896	2		417	599	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132955	30132955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145651161	NA	P-0060940-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	249	417	0	ENST00000331968.5:c.646C>T	p.Arg216Cys	p.R216C	ENST00000331968	NM_002742.2	216	Cgc/Tgc	4/18	0.55492791778108	2	FACETS	0.914	0.866	0.962	0.914	0.866	0.962	CLONAL	2	TRUE	0	0.565208920127896	2		417	482	SUCCESS
H3C13	653604	MSKCC	GRCh37	1	149784840	149784840	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060940-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	36	396	0	ENST00000331491.1:c.397G>A	p.Gly133Arg	p.G133R	ENST00000331491	NM_001123375.2	133	Ggg/Agg	1/1	0.494357341317767	4	FACETS	0.314	0.257	0.377	0.078	0.064	0.095	SUBCLONAL	1	TRUE	0	0.565208920127896	4		396	636	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984951	101984951	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs759363788	NA	P-0060940-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	29	218	0	ENST00000282441.5:c.398A>C	p.Gln133Pro	p.Q133P	ENST00000282441	NM_001130145.2	133	cAg/cCg	2/9	0.355492746218302	2	FACETS	0.372	0.299	0.454	0.186	0.149	0.227	SUBCLONAL	1	TRUE	0	0.565208920127896	2		218	276	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144666	55144666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060940-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	71	382	0	ENST00000257290.5:c.2140G>A	p.Asp714Asn	p.D714N	ENST00000257290	NM_006206.4	714	Gat/Aat	15/23	NA	2	FACETS	0.428	0.374	0.487			1	INDETERMINATE	1	TRUE	NA	0.565208920127896	2		382	587	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	75	321	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.855	0.752	0.966	0.855	0.752	0.966	CLONAL	1	TRUE	1	0.363789320831002	2		321	482	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	148	189	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	1	1	FACETS	0.791	0.729	0.853	1	0.99	1	SUBCLONAL	2	TRUE	0	0.363789320831002	1		189	421	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0060947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	241	277	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.213786646464871	3	FACETS	0.854	0.799	0.911	0.854	0.799	0.911	INDETERMINATE	2	TRUE	1	0.363789320831002	3		277	917	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584560	48584560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	148	626	0	ENST00000342988.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000342988	NM_005359.5	245	Cag/Tag	6/12	0.355006420630997	1	FACETS	0.935	0.856	1	0.935	0.856	1	CLONAL	1	TRUE	0	0.363789320831002	1		626	712	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587778720	NA	P-0060947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	139	720	0	ENST00000269305.4:c.638G>C	p.Arg213Pro	p.R213P	ENST00000269305	NM_001126112.2	213	cGa/cCa	6/11	0.355006420630997	1	FACETS	0.852	0.776	0.931	0.852	0.776	0.931	CLONAL	1	TRUE	0	0.363789320831002	1		720	734	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0060947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	131	529	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.363789320831002	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.363789320831002	1		529	570	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236152	108236152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879254215	NA	P-0060947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	132	617	0	ENST00000278616.4:c.9088G>A	p.Gly3030Arg	p.G3030R	ENST00000278616	NM_000051.3	3030	Gga/Aga	63/63	1	2	FACETS	0.987	0.897	1	0.987	0.897	1	CLONAL	1	TRUE	1	0.363789320831002	2		617	735	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36823984	36823984	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0060947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	113	539	0	ENST00000373129.3:c.199-1G>T		p.X67_splice	ENST00000373129	NM_032017.1	67			1	2	FACETS	0.953	0.859	1	0.953	0.859	1	CLONAL	1	TRUE	1	0.363789320831002	2		539	652	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982425	201982426	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0060947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	162	663	0	ENST00000359651.3:c.805_805+1dup		p.-268fs	ENST00000359651		268	-/GG	6/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.363789320831002	2		663	842	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178640	108178640	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	74	459	0	ENST00000278616.4:c.5691C>G	p.Phe1897Leu	p.F1897L	ENST00000278616	NM_000051.3	1897	ttC/ttG	38/63	1	2	FACETS	0.933	0.82	1	0.933	0.82	1	CLONAL	1	TRUE	1	0.363789320831002	2		459	436	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39593545	39593545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1262517095	NA	P-0060947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	35	297	0	ENST00000262039.4:c.1310C>T	p.Ser437Phe	p.S437F	ENST00000262039	NM_002647.2	437	tCt/tTt	11/25	0.355006420630997	1	FACETS	0.697	0.575	0.831	0.697	0.575	0.831	SUBCLONAL	1	TRUE	0	0.363789320831002	1		297	226	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098906	178098906	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	110	487	0	ENST00000397062.3:c.139G>C	p.Glu47Gln	p.E47Q	ENST00000397062	NM_006164.4	47	Gag/Cag	2/5	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.363789320831002	2		487	600	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63898320	63898320	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	130	551	0	ENST00000398590.3:c.46G>A	p.Ala16Thr	p.A16T	ENST00000398590	NM_001177387.1	16	Gcg/Acg	3/14	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.363789320831002	2		551	580	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777935	27777935	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	199	873	0	ENST00000369163.2:c.84G>C	p.Lys28Asn	p.K28N	ENST00000369163	NM_003536.2	28	aaG/aaC	1/1	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.363789320831002	2		873	1042	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149982964	149982964	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	84	441	0	ENST00000253339.5:c.3294A>T	p.Glu1098Asp	p.E1098D	ENST00000253339		1098	gaA/gaT	7/7	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.363789320831002	2		441	408	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060948-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	61	321	0				ENST00000310581	NM_198253.2	-/1132			0.295663983739442	4	FACETS	0.983	0.849	1	0.328	0.283	0.376	CLONAL	1	TRUE	1	0.344959954788672	4		321	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0060948-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	256	769	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.313639404225304	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.344959954788672	2		770	715	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89865593	89865593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200220791	NA	P-0060948-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	110	649	0	ENST00000389301.3:c.874C>T	p.His292Tyr	p.H292Y	ENST00000389301	NM_000135.2	292	Cac/Tac	10/43	0.322742484599957	5	FACETS	0.972	0.871	1	0.243	0.217	0.27	CLONAL	1	TRUE	1	0.344959954788672	5		649	996	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420606	49420606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886041404	NA	P-0060948-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	109	737	1	ENST00000301067.7:c.15143G>A	p.Arg5048His	p.R5048H	ENST00000301067	NM_003482.3	5048	cGt/cAt	48/54	0.306439535943308	3	FACETS	1	0.909	1	0.506	0.454	0.561	CLONAL	1	TRUE	1	0.344959954788672	3		738	732	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950699	38950699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060948-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	56	407	0	ENST00000357387.3:c.3251C>T	p.Ser1084Leu	p.S1084L	ENST00000357387	NM_152756.3	1084	tCa/tTa	31/38	0.295663983739442	4	FACETS	0.827	0.709	0.956	0.276	0.236	0.319	CLONAL	1	TRUE	1	0.344959954788672	4		407	528	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602918	10602918	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060948-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	84	599	0	ENST00000171111.5:c.660C>G	p.Phe220Leu	p.F220L	ENST00000171111	NM_203500.1	220	ttC/ttG	3/6	0.221597978274455	5	FACETS	0.879	0.775	0.99	0.293	0.258	0.33	CLONAL	1	TRUE	2	0.344959954788672	5		599	841	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212908	94212908	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060948-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	47	387	0	ENST00000323929.3:c.334C>G	p.Gln112Glu	p.Q112E	ENST00000323929	NM_005591.3	112	Caa/Gaa	5/20	0.306439535943308	3	FACETS	0.789	0.667	0.923	0.394	0.333	0.462	CLONAL	1	TRUE	1	0.344959954788672	3		387	405	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641513	18641513	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060948-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	56	405	0	ENST00000266497.5:c.2512C>G	p.Leu838Val	p.L838V	ENST00000266497		838	Ctg/Gtg	17/31	0.306439535943308	3	FACETS	0.79	0.677	0.912	0.395	0.338	0.456	CLONAL	1	TRUE	1	0.344959954788672	3		405	482	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346185	89346185	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060948-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	98	807	0	ENST00000301030.4:c.6765C>A	p.Asp2255Glu	p.D2255E	ENST00000301030	NM_001256183.1	2255	gaC/gaA	9/13	0.322742484599957	5	FACETS	0.944	0.841	1	0.236	0.21	0.264	CLONAL	1	TRUE	1	0.344959954788672	5		807	913	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968801	15968801	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060948-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	104	424	0	ENST00000268712.3:c.4949G>C	p.Arg1650Thr	p.R1650T	ENST00000268712	NM_006311.3	1650	aGa/aCa	33/46	0.313639404225304	2	FACETS	1	0.943	1	0.536	0.482	0.594	CLONAL	1	TRUE	0	0.344959954788672	2		424	562	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542654	187542655	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0060948-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	71	488	0	ENST00000441802.2:c.5085_5086del	p.Val1697GlyfsTer3	p.V1697Gfs*3	ENST00000441802	NM_005245.3	1695	tcATca/tcca	10/27	0.295663983739442	4	FACETS	0.932	0.814	1	0.311	0.271	0.353	CLONAL	1	TRUE	1	0.344959954788672	4		488	594	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939611	131939611	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0060948-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	32	178	0	ENST00000265335.6:c.2398-1G>C		p.X800_splice	ENST00000265335		800			1	2	FACETS	0.928	0.759	1	0.928	0.759	1	CLONAL	1	TRUE	1	0.344959954788672	2		178	200	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045930	26045930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060948-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	128	793	0	ENST00000540144.1:c.292G>A	p.Glu98Lys	p.E98K	ENST00000540144	NM_003531.2	98	Gag/Aag	1/1	1	2	FACETS	0.877	0.795	0.964	0.877	0.795	0.964	CLONAL	1	TRUE	1	0.344959954788672	2		793	846	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0060950-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	423	817	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.647570785825003	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.647570785825003	1		817	668	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0060950-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	176	497	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	1	2	FACETS	0.972	0.901	1	0.972	0.901	1	CLONAL	1	TRUE	1	0.647570785825003	2		497	559	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0060950-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	101	397	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.647570785825003	2		397	307	SUCCESS
APC	324	MSKCC	GRCh37	5	112175171	112175171	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085373	NA	P-0060950-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	148	456	0	ENST00000257430.4:c.3880C>T	p.Gln1294Ter	p.Q1294*	ENST00000257430	NM_000038.5	1294	Cag/Tag	16/16	1	2	FACETS	0.874	0.803	0.947	0.874	0.803	0.947	CLONAL	1	TRUE	1	0.647570785825003	2		456	523	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119762	70119763	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0060950-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	244	399	0	ENST00000245479.2:c.768dup	p.Arg257AlafsTer39	p.R257Afs*39	ENST00000245479	NM_000346.3	255	gag/gaGg	3/3	0.325374798783772	2	FACETS	1	0.993	1	0.704	0.665	0.744	INDETERMINATE	1	TRUE	0	0.647570785825003	2		399	535	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919304	48919304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060950-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	24	206	0	ENST00000267163.4:c.469G>A	p.Val157Ile	p.V157I	ENST00000267163	NM_000321.2	157	Gta/Ata	4/27	0.461393483020793	1	FACETS	0.302	0.239	0.374	0.302	0.239	0.374	SUBCLONAL	1	TRUE	0	0.647570785825003	1		206	166	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127460	55127460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779332376	NA	P-0060951-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	129	463	3	ENST00000257290.5:c.248C>T	p.Thr83Met	p.T83M	ENST00000257290	NM_006206.4	83	aCg/aTg	3/23	0.564884120004926	3	FACETS	0.888	0.808	0.973	0.444	0.404	0.487	CLONAL	1	TRUE	1	0.586886236662114	3		466	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578232	7578232	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0060951-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	532	611	0	ENST00000269305.4:c.617T>A	p.Leu206Ter	p.L206*	ENST00000269305	NM_001126112.2	206	tTg/tAg	6/11	0.586886236662114	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.586886236662114	3		611	740	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026152	36026152	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060951-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	246	587	0	ENST00000358208.4:c.754A>C	p.Lys252Gln	p.K252Q	ENST00000358208		252	Aag/Cag	7/12	0.586886236662114	6	FACETS	0.915	0.856	0.976	0.457	0.428	0.488	CLONAL	2	TRUE	2	0.586886236662114	6		587	996	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679542	86679542	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060951-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	80	203	0	ENST00000274376.6:c.2703T>A	p.Phe901Leu	p.F901L	ENST00000274376	NM_002890.2	901	ttT/ttA	21/25	0.574002732543043	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	0	0.586886236662114	2		203	132	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858047	152858047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1432027234	NA	P-0060951-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	181	590	0	ENST00000406277.2:c.568G>A	p.Ala190Thr	p.A190T	ENST00000406277	NM_152274.4	190	Gcc/Acc	6/7	0.586886236662114	6	FACETS	1	0.989	1	0.364	0.335	0.394	CLONAL	1	TRUE	2	0.586886236662114	6		590	921	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910860	32910860	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs398122746	NA	P-0060952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	118	436	5	ENST00000380152.3:c.2368G>T	p.Glu790Ter	p.E790*	ENST00000380152		790	Gaa/Taa	11/27	0.654692171407739	1	FACETS	0.905	0.831	0.979	0.905	0.831	0.979	CLONAL	1	TRUE	0	0.654692171407739	1		441	268	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030451	49030484	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GAAATCTACCTCTCTTTCACTGTTTTATAAAAAA	GAAATCTACCTCTCTTTCACTGTTTTATAAAAAA	-	novel	NA	P-0060952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	133	361	1	ENST00000267163.4:c.1927_1960del	p.Lys643CysfsTer4	p.K643Cfs*4	ENST00000267163	NM_000321.2	642	ttGAAATCTACCTCTCTTTCACTGTTTTATAAAAAA/tt	19/27	0.654692171407739	1	FACETS	0.908	0.839	0.978	0.908	0.839	0.978	CLONAL	1	TRUE	0	0.654692171407739	1		362	301	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	231076	231076	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	241	595	3	ENST00000264932.6:c.856C>A	p.Pro286Thr	p.P286T	ENST00000264932	NM_004168.2	286	Cct/Act	7/15	1	2	FACETS	0.97	0.909	1	0.97	0.909	1	CLONAL	1	TRUE	1	0.654692171407739	2		598	759	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0060953-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	196	608	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.319497581373537	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.319497581373537	1		610	859	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074328	8074336	+	inframe_deletion	In_Frame_Del	DEL	CTTGATCCT	CTTGATCCT	-	novel	NA	P-0060953-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	90	545	0	ENST00000377482.5:c.323_331del	p.Glu108_Gln110del	p.E108_Q110del	ENST00000377482	NM_018948.3	108	gAGGATCAAGtt/gtt	4/4	1	2	FACETS	0.579	0.512	0.65	0.579	0.512	0.65	SUBCLONAL	1	TRUE	1	0.319497581373537	2		545	973	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30099976	30099993	+	inframe_deletion	In_Frame_Del	DEL	GGAGCCCTTGGGAATGAC	GGAGCCCTTGGGAATGAC	-	novel	NA	P-0060953-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	169	518	1	ENST00000331968.5:c.1627_1644del	p.Val543_Ser548del	p.V543_S548del	ENST00000331968	NM_002742.2	543	GTCATTCCCAAGGGCTCC/-	10/18	0.286790718351969	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.319497581373537	1		519	837	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712668	43712668	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060953-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	105	623	0	ENST00000382044.4:c.4516T>G	p.Phe1506Val	p.F1506V	ENST00000382044	NM_001141980.1	1506	Ttt/Gtt	21/28	0.319497581373537	1	FACETS	0.566	0.506	0.63	0.566	0.506	0.63	SUBCLONAL	1	TRUE	0	0.319497581373537	1		623	976	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878108	151878109	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0060953-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	398	647	0	ENST00000262189.6:c.6836dup	p.Gly2280TrpfsTer9	p.G2280Wfs*9	ENST00000262189	NM_170606.2	2279	cct/ccCt	36/59	0.319497581373537	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.319497581373537	2		647	1212	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239114	98239114	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060953-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	57	540	0	ENST00000331920.6:c.1529T>C	p.Val510Ala	p.V510A	ENST00000331920	NM_000264.3	510	gTt/gCt	11/24	1	2	FACETS	0.382	0.327	0.443	0.382	0.327	0.443	SUBCLONAL	1	TRUE	1	0.319497581373537	2		540	933	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0060954-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	23	646	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.638	0.495	0.803	0.638	0.495	0.803	SUBCLONAL	1	TRUE	1	0.13	2		646	555	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0060954-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	29	382	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.13	2		382	314	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971135	21971136	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0060954-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	37	701	0	ENST00000304494.5:c.221_222dup	p.Pro75ThrfsTer72	p.P75Tfs*72	ENST00000304494	NM_000077.4	74	-/AC	2/3	1	2	FACETS	0.861	0.708	1	0.861	0.708	1	CLONAL	1	TRUE	1	0.13	2		701	661	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0060955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	22	304	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.203	0.156	0.257	0.203	0.156	0.257	SUBCLONAL	1	TRUE	1	0.411380127817345	2		304	528	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0060958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	184	578	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.41711147907587	4	FACETS	0.997	0.93	1	0.997	0.93	1	CLONAL	2	TRUE	2	0.692603449031535	4		578	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0060958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	209	665	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.692603449031535	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.692603449031535	2		666	285	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944986	31944986	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	48	814	0	ENST00000340398.3:c.115C>G	p.His39Asp	p.H39D	ENST00000340398	NM_001013699.2	39	Cat/Gat	1/1	0.216035209508523	3	FACETS	0.477	0.404	0.557	0.159	0.134	0.186	INDETERMINATE	1	TRUE	0	0.692603449031535	3		814	391	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100030	11100030	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	113	677	0	ENST00000358026.2:c.1156G>T	p.Glu386Ter	p.E386*	ENST00000358026	NM_001128849.1	386	Gaa/Taa	7/36	0.535361561109576	1	FACETS	0.931	0.858	1	0.931	0.858	1	CLONAL	1	TRUE	0	0.692603449031535	1		677	229	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791161	42791161	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	63	816	0	ENST00000575354.2:c.221C>T	p.Pro74Leu	p.P74L	ENST00000575354	NM_015125.3	74	cCt/cTt	3/20	1	2	FACETS	0.444	0.385	0.507	0.444	0.385	0.507	SUBCLONAL	1	TRUE	1	0.692603449031535	2		816	410	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170011177	170011177	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	28	471	0	ENST00000295797.4:c.1298G>C	p.Ser433Thr	p.S433T	ENST00000295797	NM_002740.5	433	aGt/aCt	14/18	0.692603449031535	1	FACETS	0.426	0.346	0.514	0.426	0.346	0.514	SUBCLONAL	1	TRUE	0	0.692603449031535	1		471	124	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578441	7578441	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	262	1550	0	ENST00000269305.4:c.489C>A	p.Tyr163Ter	p.Y163*	ENST00000269305	NM_001126112.2	163	taC/taA	5/11	0.8217525721754	1	FACETS	0.952	0.912	0.991	0.952	0.912	0.991	CLONAL	1	TRUE	0	0.833649755587037	1		1550	385	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100148	157100148	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1380676072	NA	P-0060959-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	181	1682	0	ENST00000346085.5:c.1085C>T	p.Ser362Phe	p.S362F	ENST00000346085	NM_020732.3	362	tCc/tTc	1/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.833649755587037	2		1682	413	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0060960-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	219	665	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.401378437283583	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.401378437283583	3		666	639	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060960-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	166	414	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	0.350140824439055	4	FACETS	0.963	0.903	1	0.963	0.903	1	CLONAL	4	TRUE	0	0.401378437283583	4		414	301	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778785	76778787	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1557042392	NA	P-0060960-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	32	402	1	ENST00000373344.5:c.6792_6794del	p.Glu2265del	p.E2265del	ENST00000373344	NM_000489.3	2264	gaAGAg/gag	31/35	0.203023978483229	2	FACETS	0.789	0.646	0.948	0.395	0.323	0.474	INDETERMINATE	1	TRUE	0	0.401378437283583	2		403	202	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278114	41278114	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060960-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	60	437	0	ENST00000349496.5:c.1990G>A	p.Glu664Lys	p.E664K	ENST00000349496	NM_001904.3	664	Gag/Aag	13/15	0.188865694467597	3	FACETS	0.9	0.778	1	0.3	0.259	0.344	INDETERMINATE	1	TRUE	0	0.401378437283583	3		437	399	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63898395	63898395	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060960-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	108	481	0	ENST00000398590.3:c.121C>A	p.Pro41Thr	p.P41T	ENST00000398590	NM_001177387.1	41	Ccg/Acg	3/14	0.188865694467597	3	FACETS	0.877	0.787	0.972	0.292	0.262	0.324	INDETERMINATE	1	TRUE	0	0.401378437283583	3		481	737	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575476	64575476	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060960-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	107	624	0	ENST00000312049.6:c.541C>G	p.His181Asp	p.H181D	ENST00000312049	NM_130799.2	181	Cat/Gat	3/10	0.401378437283583	3	FACETS	0.801	0.718	0.889	0.401	0.359	0.445	CLONAL	1	TRUE	1	0.401378437283583	3		624	799	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608092	28608092	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060960-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	38	419	0	ENST00000241453.7:c.1874T>A	p.Met625Lys	p.M625K	ENST00000241453	NM_004119.2	625	aTg/aAg	15/24	0.154327062616338	4	FACETS	0.679	0.562	0.809	0.339	0.281	0.405	INDETERMINATE	1	TRUE	2	0.401378437283583	4		419	391	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919200	178919200	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060960-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	22	322	0	ENST00000263967.3:c.685A>C	p.Thr229Pro	p.T229P	ENST00000263967	NM_006218.2	229	Act/Cct	4/21	0.350140824439055	4	FACETS	0.582	0.452	0.732	0.145	0.113	0.183	SUBCLONAL	1	TRUE	0	0.401378437283583	4		322	264	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459438	50459438	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060960-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	28	351	0	ENST00000331340.3:c.727G>C	p.Glu243Gln	p.E243Q	ENST00000331340	NM_006060.4	243	Gaa/Caa	7/8	0.237866602364415	3	FACETS	0.5	0.4	0.614	0.25	0.2	0.307	INDETERMINATE	1	TRUE	1	0.401378437283583	3		351	335	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0060961-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	285	382	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.594814894126455	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.594814894126455	3		382	617	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0060962-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	232	380	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.687059884171679	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.687059884171679	3		380	421	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295346	1295346	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0060962-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	416	843	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.687059884171679	NA		843	802	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295242	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0060962-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	269	635	0				ENST00000310581	NM_198253.2	-/1132			0.641155317786298	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.687059884171679	3		635	502	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295178	1295178	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1027528638	NA	P-0060962-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	269	686	0				ENST00000310581	NM_198253.2	-/1132			0.641155317786298	3	FACETS	0.991	0.94	1	0.991	0.94	1	CLONAL	2	TRUE	1	0.687059884171679	3		686	531	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93657859	93657859	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060962-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	158	586	0	ENST00000375746.1:c.1885T>C	p.Tyr629His	p.Y629H	ENST00000375746	NM_001174167.1	629	Tac/Cac	14/14	0.641155317786298	3	FACETS	1	0.952	1	0.524	0.482	0.567	CLONAL	1	TRUE	1	0.687059884171679	3		586	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0060963-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	300	665	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.502318125067389	2		666	1150	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098965	178098965	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060963-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	238	180	0	ENST00000397062.3:c.80A>G	p.Asp27Gly	p.D27G	ENST00000397062	NM_006164.4	27	gAt/gGt	2/5	1	2	FACETS	0.988	0.923	1	0.988	0.923	1	CLONAL	1	FALSE	1	0.502318125067389	2		180	959	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030409	49030410	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0060963-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	244	211	0	ENST00000267163.4:c.1887_1888del	p.Glu629AspfsTer23	p.E629Dfs*23	ENST00000267163	NM_000321.2	628	gcAGag/gcag	19/27	0.502318125067389	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	0	0.502318125067389	1		211	711	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060963-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	333	585	0	ENST00000269305.4:c.398del	p.Met133SerfsTer37	p.M133Sfs*37	ENST00000269305	NM_001126112.2	133	aTg/ag	5/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.502318125067389	2		585	1165	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10244378	10244892	+	splice_donor_variant,splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTGAAGGGAAATAAAAGGAAAAGTCACTCTGGGGAACACGCCCGGTGTCACGCCACTTGACAGGCGAGTAACAGACATGGACCATCAGGAAACATTAACGTACTGATGTTAACAGCTGACCCAATAAGTGGCAGAGTGCTAAGGGAACGTTCACGGAGACTGAACACTCCTCAAACGGTCCCCAGAGGGTTCTAGACCCAGAGGCTCAAGTGAGCAGCTGAGGCAGGTGCCTGCTGAGCCAAATTCACCGAGCAGGAGTGAGGGAAACGGCCCCAGGGCCAGCCCAGCAGCCAACCTGACCAAAGGCCTGCTGTGTGCAGCACGCCTGCTCTAAGCACTTGACACGTGCAACTCACTCAATCCTCACAGCAGCCCCTTGAGAAAGATGGGGCCACGAACGTGGGTAGGTGACCCGCCTGAGTCCCAGAGCCCAAAACGGTGGCCAGCAACTGCCCCCACATGTACCCCCAGAGGGCAGTCAGGCCCCAGAGGAAGCCTGGCCCACCCCACCATAC	CTGAAGGGAAATAAAAGGAAAAGTCACTCTGGGGAACACGCCCGGTGTCACGCCACTTGACAGGCGAGTAACAGACATGGACCATCAGGAAACATTAACGTACTGATGTTAACAGCTGACCCAATAAGTGGCAGAGTGCTAAGGGAACGTTCACGGAGACTGAACACTCCTCAAACGGTCCCCAGAGGGTTCTAGACCCAGAGGCTCAAGTGAGCAGCTGAGGCAGGTGCCTGCTGAGCCAAATTCACCGAGCAGGAGTGAGGGAAACGGCCCCAGGGCCAGCCCAGCAGCCAACCTGACCAAAGGCCTGCTGTGTGCAGCACGCCTGCTCTAAGCACTTGACACGTGCAACTCACTCAATCCTCACAGCAGCCCCTTGAGAAAGATGGGGCCACGAACGTGGGTAGGTGACCCGCCTGAGTCCCAGAGCCCAAAACGGTGGCCAGCAACTGCCCCCACATGTACCCCCAGAGGGCAGTCAGGCCCCAGAGGAAGCCTGGCCCACCCCACCATAC	-	novel	NA	P-0060963-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	46	267	0	ENST00000340748.4:c.4816+1_4817-1del		p.X1606_splice	ENST00000340748		1606			1	2	FACETS	0.235	0.197	0.277	0.235	0.197	0.277	SUBCLONAL	1	FALSE	1	0.502318125067389	2		267	779	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561821	55561821	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060963-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	233	272	0	ENST00000288135.5:c.211C>G	p.Leu71Val	p.L71V	ENST00000288135	NM_000222.2	71	Ctg/Gtg	2/21	0.502318125067389	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	0	0.502318125067389	1		272	693	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521158	187521159	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0060963-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	275	464	0	ENST00000441802.2:c.11996dup	p.Glu4000ArgfsTer51	p.E4000Rfs*51	ENST00000441802	NM_005245.3	3999	atc/atTc	22/27	0.502318125067389	1	FACETS	0.978	0.922	1	0.978	0.922	1	CLONAL	1	FALSE	0	0.502318125067389	1		464	838	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0060964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	229	271	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.68	2		272	626	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0060964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	493	510	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.681479825941641	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.68	2		510	638	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854962	76854962	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	195	199	0	ENST00000373344.5:c.5874G>A	p.Trp1958Ter	p.W1958*	ENST00000373344	NM_000489.3	1958	tgG/tgA	25/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.68	1		199	266	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851339	156851339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760974854	NA	P-0060964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	84	467	0	ENST00000524377.1:c.2296C>T	p.Arg766Trp	p.R766W	ENST00000524377	NM_002529.3	766	Cgg/Tgg	17/17	1	2	FACETS	0.418	0.369	0.47	0.418	0.369	0.47	SUBCLONAL	1	TRUE	1	0.68	2		467	591	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662395	227662395	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	41	496	0	ENST00000305123.5:c.1060A>G	p.Thr354Ala	p.T354A	ENST00000305123	NM_005544.2	354	Acc/Gcc	1/2	1	2	FACETS	0.168	0.139	0.2	0.168	0.139	0.2	SUBCLONAL	1	TRUE	1	0.68	2		496	717	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245080	53245080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1428740468	NA	P-0060965-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	41	482	0	ENST00000375401.3:c.860C>T	p.Ser287Leu	p.S287L	ENST00000375401	NM_004187.3	287	tCg/tTg	7/26	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		482	723	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800924	243800924	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060965-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	25	176	0	ENST00000263826.5:c.550A>T	p.Ile184Phe	p.I184F	ENST00000263826	NM_005465.4	184	Att/Ttt	5/13	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		176	287	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0060966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	20	608	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.195	0.148	0.251	0.195	0.148	0.251	SUBCLONAL	1	TRUE	1	0.24	2		610	853	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	17	311	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	1	2	FACETS	0.19	0.141	0.25	0.19	0.141	0.25	SUBCLONAL	1	TRUE	1	0.24	2		311	744	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952967	2952967	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	193	487	0	ENST00000396946.4:c.2973G>T	p.Arg991Ser	p.R991S	ENST00000396946	NM_032415.4	991	agG/agT	22/25	1	2	FACETS	0.994	0.92	1	0.994	0.92	1	CLONAL	1	TRUE	1	0.409473250934299	2		487	948	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	93	321	0				ENST00000310581	NM_198253.2	-/1132			0.397258925502829	1	FACETS	0.495	0.441	0.551	0.495	0.441	0.551	SUBCLONAL	1	TRUE	0	0.557899001615317	1		321	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0060968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	374	584	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.557899001615317	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.557899001615317	1		584	774	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129169	64129169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746466314	NA	P-0060968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	242	524	0	ENST00000334205.4:c.707C>T	p.Ser236Leu	p.S236L	ENST00000334205	NM_003942.2	236	tCg/tTg	7/17	0.557899001615317	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.557899001615317	1		524	610	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278865	1278865	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149566858	NA	P-0060968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	170	488	0	ENST00000310581.5:c.2177C>T	p.Thr726Met	p.T726M	ENST00000310581	NM_198253.2	726	aCg/aTg	6/16	0.397258925502829	1	FACETS	0.7	0.646	0.755	0.7	0.646	0.755	SUBCLONAL	1	TRUE	0	0.557899001615317	1		488	628	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982965	201982966	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0060968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	168	527	0	ENST00000359651.3:c.815_816dup	p.Thr273AlafsTer22	p.T273Afs*22	ENST00000359651		272	ggc/gGCgc	7/8	0.218331116623723	2	FACETS	0.895	0.825	0.967	0.447	0.412	0.484	INDETERMINATE	1	TRUE	0	0.557899001615317	2		527	673	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22404977	22404977	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	10	66	0	ENST00000344548.3:c.6G>T	p.Gln2His	p.Q2H	ENST00000344548	NM_001039802.1	2	caG/caT	3/7	1	2	FACETS	0.314	0.214	0.439	0.314	0.214	0.439	SUBCLONAL	1	TRUE	1	0.557899001615317	2		66	114	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089618	27089618	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	66	613	0	ENST00000324856.7:c.2574G>C	p.Met858Ile	p.M858I	ENST00000324856	NM_006015.4	858	atG/atC	8/20	1	2	FACETS	0.266	0.23	0.305	0.266	0.23	0.305	SUBCLONAL	1	TRUE	1	0.557899001615317	2		613	891	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332900	70332900	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	54	486	0	ENST00000373644.4:c.805C>T	p.Gln269Ter	p.Q269*	ENST00000373644	NM_030625.2	269	Cag/Tag	2/12	NA	2	FACETS	0.318	0.271	0.37			1	INDETERMINATE	1	TRUE	NA	0.557899001615317	2		486	608	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859009	57859009	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	78	454	0	ENST00000228682.2:c.505C>G	p.Gln169Glu	p.Q169E	ENST00000228682	NM_005269.2	169	Cag/Gag	5/12	1	2	FACETS	0.363	0.318	0.411	0.363	0.318	0.411	SUBCLONAL	1	TRUE	1	0.557899001615317	2		454	771	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120770	115120770	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	73	631	0	ENST00000257566.3:c.236C>G	p.Ser79Cys	p.S79C	ENST00000257566	NM_016569.3	79	tCc/tGc	1/8	0.316135769467655	1	FACETS	0.269	0.235	0.306	0.269	0.235	0.306	INDETERMINATE	1	TRUE	0	0.557899001615317	1		631	701	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120778	115120778	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	75	642	0	ENST00000257566.3:c.228C>G	p.Ile76Met	p.I76M	ENST00000257566	NM_016569.3	76	atC/atG	1/8	0.316135769467655	1	FACETS	0.274	0.239	0.311	0.274	0.239	0.311	INDETERMINATE	1	TRUE	0	0.557899001615317	1		642	708	SUCCESS
BLM	641	MSKCC	GRCh37	15	91298125	91298125	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	47	364	0	ENST00000355112.3:c.1044G>C	p.Met348Ile	p.M348I	ENST00000355112	NM_000057.2	348	atG/atC	5/22	0.397258925502829	1	FACETS	0.228	0.192	0.268	0.228	0.192	0.268	SUBCLONAL	1	TRUE	0	0.557899001615317	1		364	533	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831954	72831954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	101	496	0	ENST00000268489.5:c.4627C>T	p.Arg1543Cys	p.R1543C	ENST00000268489	NM_006885.3	1543	Cgc/Tgc	9/10	0.316135769467655	1	FACETS	0.405	0.363	0.451	0.405	0.363	0.451	INDETERMINATE	1	TRUE	0	0.557899001615317	1		496	644	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832449	72832449	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	123	473	0	ENST00000268489.5:c.4132C>G	p.Gln1378Glu	p.Q1378E	ENST00000268489	NM_006885.3	1378	Cag/Gag	9/10	0.316135769467655	1	FACETS	0.458	0.415	0.504	0.458	0.415	0.504	INDETERMINATE	1	TRUE	0	0.557899001615317	1		473	694	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222829	5222829	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	191	594	0	ENST00000357368.4:c.2974G>C	p.Glu992Gln	p.E992Q	ENST00000357368	NM_002850.3	992	Gag/Cag	18/38	1	2	FACETS	0.932	0.864	1	0.932	0.864	1	CLONAL	1	TRUE	1	0.557899001615317	2		594	735	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160363	99160363	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	77	502	0	ENST00000074304.5:c.842G>C	p.Gly281Ala	p.G281A	ENST00000074304	NM_001134224.1	281	gGa/gCa	11/26	0.223349368855162	2	FACETS	0.337	0.295	0.382	0.169	0.147	0.191	INDETERMINATE	1	TRUE	0	0.557899001615317	2		502	819	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627388	37627388	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	54	498	0	ENST00000249071.6:c.331A>G	p.Ile111Val	p.I111V	ENST00000249071	NM_002872.4	111	Atc/Gtc	5/7	0.439207888875957	1	FACETS	0.193	0.164	0.225	0.193	0.164	0.225	SUBCLONAL	1	TRUE	0	0.557899001615317	1		498	723	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144381570	144381570	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0060968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	97	418	0	ENST00000262995.4:c.1823C>G	p.Ser608Ter	p.S608*	ENST00000262995	NM_207123.2	608	tCa/tGa	9/11	1	2	FACETS	0.467	0.416	0.521	0.467	0.416	0.521	SUBCLONAL	1	TRUE	1	0.557899001615317	2		418	745	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31472241	31472241	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	57	467	0	ENST00000344624.3:c.2170C>T	p.Gln724Ter	p.Q724*	ENST00000344624		724	Cag/Tag	14/33	0.22019667940663	0	FACETS	0.145	0.124	0.168			1	INDETERMINATE	1	TRUE	0	0.557899001615317	0		467	622	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983114	111983114	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	54	504	0	ENST00000368678.4:c.1433G>T	p.Arg478Leu	p.R478L	ENST00000368678		478	cGa/cTa	13/13	0.439207888875957	1	FACETS	0.227	0.193	0.263	0.227	0.193	0.263	SUBCLONAL	1	TRUE	0	0.557899001615317	1		504	616	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419980	152419980	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	224	533	0	ENST00000206249.3:c.1667G>C	p.Gly556Ala	p.G556A	ENST00000206249	NM_000125.3	556	gGa/gCa	8/8	0.439207888875957	1	FACETS	0.86	0.805	0.917	0.86	0.805	0.917	CLONAL	1	TRUE	0	0.557899001615317	1		533	673	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683683	162683683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377591051	NA	P-0060968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	88	457	0	ENST00000366898.1:c.286G>A	p.Glu96Lys	p.E96K	ENST00000366898	NM_004562.2	96	Gag/Aag	3/12	0.557899001615317	1	FACETS	0.46	0.409	0.515	0.46	0.409	0.515	SUBCLONAL	1	TRUE	0	0.557899001615317	1		457	494	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859468	151859468	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	58	533	0	ENST00000262189.6:c.11194G>C	p.Glu3732Gln	p.E3732Q	ENST00000262189	NM_170606.2	3732	Gag/Cag	43/59	NA	2	FACETS	0.255	0.218	0.295			1	INDETERMINATE	1	TRUE	NA	0.557899001615317	2		533	815	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931904	39931904	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	55	535	0	ENST00000378444.4:c.2695C>G	p.Pro899Ala	p.P899A	ENST00000378444	NM_001123385.1	899	Cca/Gca	4/15	0.439207888875957	1	FACETS	0.24	0.205	0.279	0.24	0.205	0.279	SUBCLONAL	1	TRUE	0	0.557899001615317	1		535	592	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411276	63411276	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	170	975	0	ENST00000330258.3:c.1891C>T	p.Arg631Ter	p.R631*	ENST00000330258	NM_152424.3	631	Cga/Tga	2/2	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.345830485553609	2		975	963	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852243	128852243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149170801	NA	P-0060976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	163	780	0	ENST00000249373.3:c.2315G>A	p.Arg772His	p.R772H	ENST00000249373	NM_005631.4	772	cGc/cAc	12/12	0.345830485553609	3	FACETS	1	0.964	1	0.547	0.501	0.595	CLONAL	1	TRUE	1	0.345830485553609	3		780	1011	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825359	134825359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761687482	NA	P-0060976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	137	711	0	ENST00000398015.3:c.875G>A	p.Arg292His	p.R292H	ENST00000398015	NM_004441.4	292	cGc/cAc	4/16	1	2	FACETS	0.977	0.889	1	0.977	0.889	1	CLONAL	1	TRUE	1	0.345830485553609	2		711	811	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0060976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	119	422	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.345830485553609	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.345830485553609	1		422	540	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117912	70117912	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	171	833	0	ENST00000245479.2:c.380A>G	p.Tyr127Cys	p.Y127C	ENST00000245479	NM_000346.3	127	tAc/tGc	1/3	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.345830485553609	2		833	862	SUCCESS
APC	324	MSKCC	GRCh37	5	112154977	112154977	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	132	569	0	ENST00000257430.4:c.1248C>A	p.Tyr416Ter	p.Y416*	ENST00000257430	NM_000038.5	416	taC/taA	10/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.345830485553609	2		569	594	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772703	135772703	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs989183765	NA	P-0060976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	174	688	0	ENST00000298552.3:c.2843A>G	p.Tyr948Cys	p.Y948C	ENST00000298552	NM_001162426.1	948	tAt/tGt	22/23	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.345830485553609	2		688	948	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551085	41551085	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	113	421	0	ENST00000263253.7:c.3229C>A	p.Gln1077Lys	p.Q1077K	ENST00000263253	NM_001429.3	1077	Caa/Aaa	17/31	0.368059013176263	1	FACETS	0.664	0.601	0.731	0.664	0.601	0.731	SUBCLONAL	1	TRUE	0	0.497200868932299	1		421	514	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597816	43597816	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	91	697	0	ENST00000355710.3:c.364T>C	p.Tyr122His	p.Y122H	ENST00000355710	NM_020975.4	122	Tac/Cac	3/20	1	2	FACETS	0.715	0.637	0.798	0.715	0.637	0.798	SUBCLONAL	1	TRUE	1	0.497200868932299	2		697	512	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033970	49033970	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0060978-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	267	487	0	ENST00000267163.4:c.2106+1G>C		p.X702_splice	ENST00000267163	NM_000321.2	702			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		487	363	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0060979-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	75	510	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.836	0.731	0.95	0.836	0.731	0.95	CLONAL	1	TRUE	1	0.19	2		510	944	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060979-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	93	403	0	ENST00000267101.3:c.273G>T	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atT	3/28	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.19	2		403	904	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041657	47041657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060979-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	32	269	0	ENST00000377604.3:c.1882G>T	p.Glu628Ter	p.E628*	ENST00000377604	NM_001204468.1	628	Gag/Tag	17/24	1	1	FACETS	0.533	0.431	0.648	0.533	0.431	0.648	SUBCLONAL	1	TRUE	0	0.19	1		269	572	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801127	135801127	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs118203353	NA	P-0060979-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	71	310	2	ENST00000298552.3:c.211-1G>A		p.X71_splice	ENST00000298552	NM_001162426.1	71			1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.19	2		312	730	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11301702	11301702	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060979-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	60	450	0	ENST00000361445.4:c.1449C>G	p.Phe483Leu	p.F483L	ENST00000361445	NM_004958.3	483	ttC/ttG	10/58	1	2	FACETS	0.718	0.617	0.828	0.718	0.617	0.828	SUBCLONAL	1	TRUE	1	0.19	2		450	880	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212607	133212607	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060979-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	81	377	0	ENST00000320574.5:c.5682C>G	p.Ile1894Met	p.I1894M	ENST00000320574	NM_006231.2	1894	atC/atG	42/49	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.19	2		377	835	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553389	41553390	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060979-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	74	433	0	ENST00000263253.7:c.3480dup	p.Gly1161TrpfsTer28	p.G1161Wfs*28	ENST00000263253	NM_001429.3	1160	ctt/cTtt	18/31	1	2	FACETS	0.92	0.804	1	0.92	0.804	1	CLONAL	1	TRUE	1	0.19	2		433	847	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2181638	2181638	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060979-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	29	256	0	ENST00000349721.2:c.4321G>C	p.Glu1441Gln	p.E1441Q	ENST00000349721	NM_003070.3	1441	Gaa/Caa	30/34	1	2	FACETS	0.57	0.456	0.699	0.57	0.456	0.699	SUBCLONAL	1	TRUE	1	0.19	2		256	536	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	117	321	0				ENST00000310581	NM_198253.2	-/1132			0.575572773674983	4	FACETS	0.8	0.721	0.883	0.267	0.24	0.295	SUBCLONAL	1	TRUE	1	0.575572773674983	4		321	801	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	65	544	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.241465086893094	3	FACETS	1	0.939	1	0.559	0.49	0.632	INDETERMINATE	1	TRUE	1	0.575572773674983	3		544	260	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	437	518	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.572222712729646	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.575572773674983	2		518	740	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030426	49030426	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	265	406	0	ENST00000267163.4:c.1901C>G	p.Ser634Ter	p.S634*	ENST00000267163	NM_000321.2	634	tCa/tGa	19/27	0.414366297700177	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.575572773674983	1		406	528	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372320	55372320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	120	769	0	ENST00000297316.4:c.1010C>T	p.Pro337Leu	p.P337L	ENST00000297316	NM_022454.3	337	cCg/cTg	2/2	0.282753475558428	2	FACETS	0.485	0.437	0.535	0.242	0.218	0.268	INDETERMINATE	1	TRUE	0	0.575572773674983	2		769	860	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874290	155874290	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs869025192	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	492	474	0	ENST00000368323.3:c.241G>C	p.Glu81Gln	p.E81Q	ENST00000368323	NM_006912.5	81	Gag/Cag	5/6	0.575572773674983	6	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.575572773674983	6		474	1616	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057835	27057835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	308	803	0	ENST00000324856.7:c.1543C>T	p.Gln515Ter	p.Q515*	ENST00000324856	NM_006015.4	515	Cag/Tag	3/20	NA	2	FACETS	1	0.957	1			1	INDETERMINATE	1	TRUE	NA	0.575572773674983	2		803	1053	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737690	145737690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	157	858	0	ENST00000428558.2:c.3073G>A	p.Gly1025Arg	p.G1025R	ENST00000428558	NM_004260.3	1025	Ggg/Agg	19/22	0.282753475558428	2	FACETS	0.495	0.453	0.54	0.248	0.226	0.27	INDETERMINATE	1	TRUE	0	0.575572773674983	2		858	1102	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393194	393194	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	96	579	0	ENST00000380956.4:c.42G>C	p.Met14Ile	p.M14I	ENST00000380956	NM_001195286.1	14	atG/atC	2/9	NA	2	FACETS	0.451	0.402	0.504			1	INDETERMINATE	1	TRUE	NA	0.575572773674983	2		579	739	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606119	47606119	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs770760223	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	31	221	0	ENST00000263735.4:c.583C>G	p.Leu195Val	p.L195V	ENST00000263735	NM_002354.2	195	Ctg/Gtg	6/9	1	2	FACETS	0.511	0.416	0.616	0.511	0.416	0.616	SUBCLONAL	1	TRUE	1	0.575572773674983	2		221	211	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401847	139401847	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs548083258	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	109	612	0	ENST00000277541.6:c.3553G>A	p.Asp1185Asn	p.D1185N	ENST00000277541	NM_017617.3	1185	Gac/Aac	22/34	0.575572773674983	2	FACETS	0.415	0.372	0.461	0.207	0.186	0.231	SUBCLONAL	1	TRUE	0	0.575572773674983	2		612	913	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46597045	46597045	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777687956	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	73	398	0	ENST00000263734.3:c.859G>A	p.Glu287Lys	p.E287K	ENST00000263734	NM_001430.4	287	Gag/Aag	7/16	1	2	FACETS	0.408	0.357	0.463	0.408	0.357	0.463	SUBCLONAL	1	TRUE	1	0.575572773674983	2		398	622	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564765	41564765	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	196	525	0	ENST00000263253.7:c.4066C>T	p.Arg1356Ter	p.R1356*	ENST00000263253	NM_001429.3	1356	Cga/Tga	25/31	0.3725067060081	1	FACETS	0.842	0.785	0.901	0.842	0.785	0.901	CLONAL	1	TRUE	0	0.575572773674983	1		525	576	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738456	145738456	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	115	635	0	ENST00000428558.2:c.2529G>C	p.Lys843Asn	p.K843N	ENST00000428558	NM_004260.3	843	aaG/aaC	16/22	0.282753475558428	2	FACETS	0.505	0.455	0.558	0.253	0.227	0.279	INDETERMINATE	1	TRUE	0	0.575572773674983	2		635	791	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443617	49443617	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	139	644	0	ENST00000301067.7:c.3754C>G	p.Arg1252Gly	p.R1252G	ENST00000301067	NM_003482.3	1252	Cga/Gga	11/54	0.332548116612735	1	FACETS	0.529	0.483	0.578	0.529	0.483	0.578	INDETERMINATE	1	TRUE	0	0.575572773674983	1		644	650	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872049	37872049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	120	724	0	ENST00000269571.5:c.1370C>T	p.Ser457Leu	p.S457L	ENST00000269571		457	tCa/tTa	12/27	1	2	FACETS	0.444	0.4	0.49	0.444	0.4	0.49	SUBCLONAL	1	TRUE	1	0.575572773674983	2		724	940	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819936	170819936	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	35	360	0	ENST00000296930.5:c.478G>T	p.Ala160Ser	p.A160S	ENST00000296930	NM_002520.6	160	Gct/Tct	6/11	0.3725067060081	1	FACETS	0.299	0.245	0.358	0.299	0.245	0.358	SUBCLONAL	1	TRUE	0	0.575572773674983	1		360	290	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754908	29754908	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	87	600	0	ENST00000389048.3:c.1027G>A	p.Glu343Lys	p.E343K	ENST00000389048	NM_004304.4	343	Gag/Aag	4/29	1	2	FACETS	0.399	0.353	0.448	0.399	0.353	0.448	SUBCLONAL	1	TRUE	1	0.575572773674983	2		600	758	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115725	8115725	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	111	452	0	ENST00000346208.3:c.1071G>C	p.Lys357Asn	p.K357N	ENST00000346208		357	aaG/aaC	6/6	0.496792629064073	3	FACETS	0.683	0.614	0.756	0.342	0.307	0.378	SUBCLONAL	1	TRUE	1	0.575572773674983	3		452	727	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288960	11288960	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	173	513	0	ENST00000361445.4:c.2795G>C	p.Ser932Thr	p.S932T	ENST00000361445	NM_004958.3	932	aGt/aCt	19/58	0.332548116612735	1	FACETS	0.776	0.718	0.834	0.776	0.718	0.834	INDETERMINATE	1	TRUE	0	0.575572773674983	1		513	552	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057721	27057721	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	267	725	0	ENST00000324856.7:c.1429C>T	p.His477Tyr	p.H477Y	ENST00000324856	NM_006015.4	477	Cac/Tac	3/20	NA	2	FACETS	0.997	0.936	1			1	INDETERMINATE	1	TRUE	NA	0.575572773674983	2		725	931	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175846	176175846	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	210	558	0	ENST00000367669.3:c.269G>A	p.Ser90Asn	p.S90N	ENST00000367669	NM_022457.5	90	aGc/aAc	1/20	0.252641633811728	6	FACETS	1	0.991	1	0.247	0.229	0.266	INDETERMINATE	1	TRUE	0	0.575572773674983	6		558	1058	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419049	419049	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	87	461	0	ENST00000399788.2:c.3298G>C	p.Glu1100Gln	p.E1100Q	ENST00000399788	NM_001042603.1	1100	Gaa/Caa	22/28	0.332548116612735	1	FACETS	0.358	0.317	0.401	0.358	0.317	0.401	INDETERMINATE	1	TRUE	0	0.575572773674983	1		461	602	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21630884	21630884	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	85	414	0	ENST00000421138.2:c.720C>G	p.Ile240Met	p.I240M	ENST00000421138		240	atC/atG	8/16	0.332548116612735	1	FACETS	0.405	0.358	0.454	0.405	0.358	0.454	INDETERMINATE	1	TRUE	0	0.575572773674983	1		414	520	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231196	46231196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	33	293	0	ENST00000334344.6:c.1116G>A	p.Met372Ile	p.M372I	ENST00000334344	NM_152641.2	372	atG/atA	9/21	0.332548116612735	1	FACETS	0.402	0.33	0.482	0.402	0.33	0.482	INDETERMINATE	1	TRUE	0	0.575572773674983	1		293	203	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421801	49421801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770536689	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	139	716	0	ENST00000301067.7:c.14506G>A	p.Glu4836Lys	p.E4836K	ENST00000301067	NM_003482.3	4836	Gag/Aag	46/54	0.332548116612735	1	FACETS	0.398	0.362	0.435	0.398	0.362	0.435	INDETERMINATE	1	TRUE	0	0.575572773674983	1		716	865	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117407	115117407	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	109	506	0	ENST00000257566.3:c.767G>C	p.Arg256Thr	p.R256T	ENST00000257566	NM_016569.3	256	aGa/aCa	4/8	0.332548116612735	1	FACETS	0.401	0.361	0.444	0.401	0.361	0.444	INDETERMINATE	1	TRUE	0	0.575572773674983	1		506	672	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578303	28578303	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	75	412	0	ENST00000241453.7:c.2868G>C	p.Gln956His	p.Q956H	ENST00000241453	NM_004119.2	956	caG/caC	24/24	0.300706861092698	5	FACETS	0.648	0.567	0.736	0.216	0.189	0.246	INDETERMINATE	1	TRUE	2	0.575572773674983	5		412	749	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336244	73336244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs889041109	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	79	393	0	ENST00000377767.4:c.2159C>T	p.Ser720Phe	p.S720F	ENST00000377767	NM_014953.3	720	tCt/tTt	17/21	0.264369766007316	4	FACETS	0.687	0.604	0.775	0.343	0.302	0.388	INDETERMINATE	1	TRUE	2	0.575572773674983	4		393	630	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435591	110435591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1304221019	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	264	566	0	ENST00000375856.3:c.2810C>T	p.Pro937Leu	p.P937L	ENST00000375856	NM_003749.2	937	cCc/cTc	1/2	0.264369766007316	4	FACETS	0.901	0.848	0.956	0.901	0.848	0.956	INDETERMINATE	2	TRUE	2	0.575572773674983	4		566	802	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988723	41988723	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	89	463	0	ENST00000219905.7:c.1515G>C	p.Leu505Phe	p.L505F	ENST00000219905	NM_001164273.1	505	ttG/ttC	3/24	1	2	FACETS	0.558	0.496	0.624	0.558	0.496	0.624	SUBCLONAL	1	TRUE	1	0.575572773674983	2		463	554	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50769556	50769556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	81	376	0	ENST00000307179.4:c.1078G>A	p.Glu360Lys	p.E360K	ENST00000307179		360	Gaa/Aaa	10/20	1	2	FACETS	0.553	0.488	0.622	0.553	0.488	0.622	SUBCLONAL	1	TRUE	1	0.575572773674983	2		376	509	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50773990	50773990	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs778969876	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	57	597	0	ENST00000307179.4:c.1531G>C	p.Glu511Gln	p.E511Q	ENST00000307179		511	Gaa/Caa	11/20	1	2	FACETS	0.348	0.298	0.402	0.348	0.298	0.402	SUBCLONAL	1	TRUE	1	0.575572773674983	2		597	569	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923732	72923732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750992243	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	98	621	0	ENST00000268489.5:c.3346G>A	p.Glu1116Lys	p.E1116K	ENST00000268489	NM_006885.3	1116	Gag/Aag	4/10	NA	2	FACETS	0.457	0.408	0.51			1	INDETERMINATE	1	TRUE	NA	0.575572773674983	2		621	745	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55334460	55334460	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	125	288	0	ENST00000284073.2:c.64A>G	p.Lys22Glu	p.K22E	ENST00000284073	NM_138962.2	22	Aaa/Gaa	2/14	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.575572773674983	2		288	407	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422987	47422987	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	215	552	0	ENST00000404338.3:c.1055T>G	p.Ile352Arg	p.I352R	ENST00000404338	NM_004491.4	352	aTa/aGa	1/6	0.241465086893094	3	FACETS	1	0.983	1	0.584	0.544	0.626	INDETERMINATE	1	TRUE	1	0.575572773674983	3		552	823	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026375	48026375	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	93	552	0	ENST00000234420.5:c.1253C>T	p.Ser418Phe	p.S418F	ENST00000234420	NM_000179.2	418	tCt/tTt	4/10	1	2	FACETS	0.482	0.429	0.539	0.482	0.429	0.539	SUBCLONAL	1	TRUE	1	0.575572773674983	2		552	670	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566760	212566760	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	85	527	0	ENST00000342788.4:c.1421G>C	p.Trp474Ser	p.W474S	ENST00000342788	NM_005235.2	474	tGg/tCg	12/28	1	2	FACETS	0.429	0.379	0.483	0.429	0.379	0.483	SUBCLONAL	1	TRUE	1	0.575572773674983	2		527	688	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346795	225346795	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	49	305	0	ENST00000264414.4:c.1843G>A	p.Glu615Lys	p.E615K	ENST00000264414	NM_003590.4	615	Gaa/Aaa	14/16	1	2	FACETS	0.489	0.416	0.569	0.489	0.416	0.569	SUBCLONAL	1	TRUE	1	0.575572773674983	2		305	348	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62312017	62312017	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	61	429	0	ENST00000360203.5:c.1136G>C	p.Arg379Pro	p.R379P	ENST00000360203	NM_001283009.1	379	cGt/cCt	14/35	0.496792629064073	3	FACETS	0.456	0.394	0.525	0.228	0.197	0.263	SUBCLONAL	1	TRUE	1	0.575572773674983	3		429	598	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21345955	21345955	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	102	692	0	ENST00000215739.8:c.830C>T	p.Ser277Phe	p.S277F	ENST00000215739	NM_006767.3	277	tCc/tTc	9/21	0.339620017088685	0	FACETS	0.241	0.215	0.268			1	INDETERMINATE	1	TRUE	0	0.575572773674983	0		692	625	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430380	181430380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	61	502	0	ENST00000325404.1:c.232G>A	p.Glu78Lys	p.E78K	ENST00000325404	NM_003106.3	78	Gag/Aag	1/1	0.241465086893094	3	FACETS	0.346	0.298	0.399	0.173	0.149	0.2	INDETERMINATE	1	TRUE	1	0.575572773674983	3		502	789	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1962820	1962820	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	102	552	0	ENST00000382891.5:c.3314G>A	p.Arg1105Lys	p.R1105K	ENST00000382891	NM_133335.3	1105	aGa/aAa	18/22	0.282753475558428	2	FACETS	0.515	0.461	0.573	0.258	0.23	0.287	INDETERMINATE	1	TRUE	0	0.575572773674983	2		552	688	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796858	57796858	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1363425700	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	102	666	0	ENST00000309042.7:c.1834C>T	p.Gln612Ter	p.Q612*	ENST00000309042	NM_005612.4	612	Cag/Tag	4/4	0.282753475558428	2	FACETS	0.43	0.384	0.478	0.215	0.192	0.239	INDETERMINATE	1	TRUE	0	0.575572773674983	2		666	825	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287511	33287511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1406104161	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	95	627	0	ENST00000374542.5:c.1586C>T	p.Ser529Leu	p.S529L	ENST00000374542	NM_001141970.1	529	tCa/tTa	6/8	0.282753475558428	2	FACETS	0.396	0.352	0.443	0.198	0.176	0.222	INDETERMINATE	1	TRUE	0	0.575572773674983	2		627	833	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020865	112020865	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	71	338	0	ENST00000368678.4:c.706G>T	p.Asp236Tyr	p.D236Y	ENST00000368678		236	Gat/Tat	8/13	0.515114890990082	2	FACETS	0.629	0.552	0.712	0.315	0.276	0.356	SUBCLONAL	1	TRUE	0	0.575572773674983	2		338	392	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704490	117704490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	64	387	0	ENST00000368508.3:c.2486C>T	p.Ser829Phe	p.S829F	ENST00000368508	NM_002944.2	829	tCt/tTt	16/43	0.515114890990082	2	FACETS	0.535	0.464	0.61	0.267	0.232	0.305	SUBCLONAL	1	TRUE	0	0.575572773674983	2		387	416	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526650	106526650	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	64	423	0	ENST00000359195.3:c.2943G>C	p.Glu981Asp	p.E981D	ENST00000359195	NM_002649.2	981	gaG/gaC	10/11	0.241465086893094	3	FACETS	0.478	0.414	0.548	0.239	0.207	0.274	INDETERMINATE	1	TRUE	1	0.575572773674983	3		423	599	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880148	151880148	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	84	418	0	ENST00000262189.6:c.5176G>C	p.Asp1726His	p.D1726H	ENST00000262189	NM_170606.2	1726	Gat/Cat	35/59	0.241465086893094	3	FACETS	0.639	0.565	0.718	0.32	0.282	0.359	INDETERMINATE	1	TRUE	1	0.575572773674983	3		418	588	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271258	38271258	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs775161322	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	80	614	0	ENST00000425967.3:c.2450C>G	p.Ser817Cys	p.S817C	ENST00000425967	NM_001174067.1	817	tCt/tGt	19/19	0.282753475558428	2	FACETS	0.406	0.357	0.458	0.203	0.178	0.229	INDETERMINATE	1	TRUE	0	0.575572773674983	2		614	685	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2060828	2060828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	64	447	0	ENST00000349721.2:c.1534G>A	p.Glu512Lys	p.E512K	ENST00000349721	NM_003070.3	512	Gag/Aag	9/34	0.274055454431493	3	FACETS	0.405	0.35	0.464	0.135	0.116	0.155	INDETERMINATE	1	TRUE	0	0.575572773674983	3		447	708	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128268631	128268631	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060980-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	171	432	0	ENST00000265960.3:c.1024G>T	p.Glu342Ter	p.E342*	ENST00000265960	NM_001006617.1	342	Gag/Tag	8/12	0.575572773674983	2	FACETS	0.84	0.775	0.908	0.42	0.387	0.454	CLONAL	1	TRUE	0	0.575572773674983	2		432	707	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0060981-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	10	544	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.988	0.67	1	0.988	0.67	1	CLONAL	1	TRUE	1	0.11	2		544	184	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0060981-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	18	304	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.613	0.46	0.795	0.613	0.46	0.795	SUBCLONAL	1	TRUE	1	0.11	2		304	534	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0060981-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	20	410	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	1	2	FACETS	0.685	0.522	0.877	0.685	0.522	0.877	SUBCLONAL	1	TRUE	1	0.11	2		410	531	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0060981-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	41	730	0	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	1	2	FACETS	0.881	0.731	1	0.881	0.731	1	CLONAL	1	TRUE	1	0.11	2		730	846	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29445779	29445779	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060981-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	43	603	0	ENST00000544604.2:c.1610C>A	p.Ser537Ter	p.S537*	ENST00000544604	NM_001206998.1	537	tCg/tAg	8/9	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.11	2		603	583	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181765	56181765	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060981-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	10	311	0	ENST00000399503.3:c.3989C>A	p.Ser1330Ter	p.S1330*	ENST00000399503	NM_005921.1	1330	tCg/tAg	17/20	1	2	FACETS	0.501	0.338	0.708	0.501	0.338	0.708	SUBCLONAL	1	TRUE	1	0.11	2		311	363	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0060998-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	2157	578	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.604260182010332	10	FACETS	1	0.997	1	0.918	0.905	0.93	CLONAL	8	TRUE	1	0.604260182010332	10		578	2954	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439848	51439848	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060998-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	181	522	0	ENST00000262662.1:c.413A>G	p.Asp138Gly	p.D138G	ENST00000262662		138	gAc/gGc	4/4	0.560084532369562	2	FACETS	0.653	0.603	0.706	0.327	0.301	0.353	SUBCLONAL	1	TRUE	0	0.604260182010332	2		522	917	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579491	7579492	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0060998-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	551	609	0	ENST00000269305.4:c.194_195dup	p.Met66GlufsTer58	p.M66Efs*58	ENST00000269305	NM_001126112.2	65	-/GA	4/11	0.560084532369562	2	FACETS	0.845	0.815	0.875	0.845	0.815	0.875	CLONAL	2	TRUE	0	0.604260182010332	2		609	1079	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16001732	16001732	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060998-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	81	425	0	ENST00000268712.3:c.2769T>A	p.Asn923Lys	p.N923K	ENST00000268712	NM_006311.3	923	aaT/aaA	21/46	1	2	FACETS	0.52	0.459	0.584	0.52	0.459	0.584	SUBCLONAL	1	TRUE	1	0.604260182010332	2		425	516	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900071	151900071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060998-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	28	398	0	ENST00000262189.6:c.4040G>A	p.Arg1347Lys	p.R1347K	ENST00000262189	NM_170606.2	1347	aGa/aAa	26/59	0.604260182010332	3	FACETS	0.408	0.326	0.5	0.204	0.163	0.25	SUBCLONAL	1	TRUE	1	0.604260182010332	3		398	296	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061000-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	470	321	0				ENST00000310581	NM_198253.2	-/1132			0.300635922375241	4	FACETS	0.936	0.895	0.977	0.936	0.895	0.977	CLONAL	3	TRUE	1	0.35	4		321	1291	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0061000-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	231	501	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.242096238504988	2	FACETS	1	0.99	1	0.663	0.619	0.71	CLONAL	1	TRUE	0	0.35	2		501	995	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163720	32163720	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061000-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	176	694	0	ENST00000375023.3:c.5506G>C	p.Glu1836Gln	p.E1836Q	ENST00000375023	NM_004557.3	1836	Gag/Cag	30/30	1	2	FACETS	0.848	0.78	0.919	0.848	0.78	0.919	CLONAL	1	TRUE	1	0.35	2		694	1186	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796754	135796754	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203434	NA	P-0061000-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	214	460	0	ENST00000298552.3:c.733C>T	p.Arg245Ter	p.R245*	ENST00000298552	NM_001162426.1	245	Cga/Tga	8/23	0.300635922375241	2	FACETS	0.79	0.736	0.845	0.79	0.736	0.845	SUBCLONAL	2	TRUE	0	0.35	2		460	774	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459188	120459188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772005110	NA	P-0061000-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1436	77	855	0	ENST00000256646.2:c.6157C>T	p.Arg2053Cys	p.R2053C	ENST00000256646	NM_024408.3	2053	Cgc/Tgc	34/34	0.213412275566557	2	FACETS	0.291	0.254	0.331	0.145	0.127	0.166	SUBCLONAL	1	TRUE	0	0.35	2		855	1513	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918259	44918259	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0061000-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	79	149	0	ENST00000377967.4:c.884C>G	p.Ser295Ter	p.S295*	ENST00000377967	NM_021140.2	295	tCa/tGa	11/29	0.300635922375241	2	FACETS	0.833	0.742	0.928			1	CLONAL	2	TRUE	NA	0.35	2		149	271	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088795	27088795	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061000-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	221	693	1	ENST00000324856.7:c.2404C>T	p.Gln802Ter	p.Q802*	ENST00000324856	NM_006015.4	802	Cag/Tag	7/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.35	2		694	1111	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351902	89351902	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061000-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1421	79	843	0	ENST00000301030.4:c.1048G>C	p.Asp350His	p.D350H	ENST00000301030	NM_001256183.1	350	Gat/Cat	9/13	0.164495484507654	3	FACETS	0.354	0.309	0.402	0.118	0.103	0.134	INDETERMINATE	1	TRUE	0	0.35	3		843	1500	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369223	118369223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061000-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	283	565	0	ENST00000534358.1:c.5941C>T	p.Arg1981Trp	p.R1981W	ENST00000534358	NM_005933.3	1981	Cgg/Tgg	22/36	0.281290650372928	3	FACETS	0.855	0.804	0.908	0.855	0.804	0.908	CLONAL	2	TRUE	1	0.35	3		565	1111	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752724	42752724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764618715	NA	P-0061000-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	62	767	0	ENST00000222329.4:c.1540C>T	p.Arg514Cys	p.R514C	ENST00000222329	NM_006494.2	514	Cgt/Tgt	4/4	1	2	FACETS	0.295	0.253	0.34	0.295	0.253	0.34	SUBCLONAL	1	TRUE	1	0.35	2		767	1202	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185195165	185195165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061000-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	305	491	0	ENST00000265026.3:c.2482G>A	p.Glu828Lys	p.E828K	ENST00000265026	NM_004721.4	828	Gaa/Aaa	12/14	0.300635922375241	3	FACETS	0.996	0.94	1	0.996	0.94	1	CLONAL	2	TRUE	1	0.35	3		491	1028	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292577	15292577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061000-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	76	789	0	ENST00000263388.2:c.2602G>A	p.Val868Met	p.V868M	ENST00000263388	NM_000435.2	868	Gtg/Atg	17/33	1	2	FACETS	0.35	0.306	0.398	0.35	0.306	0.398	SUBCLONAL	1	TRUE	1	0.35	2		789	1241	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998910	100998910	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061000-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1375	104	795	0	ENST00000325455.5:c.892A>G	p.Thr298Ala	p.T298A	ENST00000325455	NM_001202474.3	298	Acc/Gcc	1/8	0.281290650372928	3	FACETS	0.472	0.421	0.527	0.236	0.21	0.264	SUBCLONAL	1	TRUE	1	0.35	3		795	1479	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372438	118372438	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061000-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	275	694	0	ENST00000534358.1:c.6371C>A	p.Ser2124Ter	p.S2124*	ENST00000534358	NM_005933.3	2124	tCa/tAa	26/36	0.281290650372928	3	FACETS	1	0.993	1	0.724	0.678	0.77	CLONAL	1	TRUE	1	0.35	3		694	1276	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95556846	95556846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061000-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	85	384	0	ENST00000393063.1:c.5758C>T	p.Pro1920Ser	p.P1920S	ENST00000393063	NM_030621.3	1920	Ccc/Tcc	28/28	0.242633246704217	3	FACETS	0.797	0.704	0.896	0.399	0.352	0.448	SUBCLONAL	1	TRUE	1	0.35	3		384	716	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988821	41988821	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061000-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	310	609	0	ENST00000219905.7:c.1613G>C	p.Arg538Thr	p.R538T	ENST00000219905	NM_001164273.1	538	aGa/aCa	3/24	0.300635922375241	2	FACETS	0.871	0.822	0.92	0.871	0.822	0.92	CLONAL	2	TRUE	0	0.35	2		609	1017	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351835	89351835	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061000-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1162	71	694	0	ENST00000301030.4:c.1115G>C	p.Arg372Thr	p.R372T	ENST00000301030	NM_001256183.1	372	aGa/aCa	9/13	0.164495484507654	3	FACETS	0.387	0.336	0.442	0.129	0.112	0.148	INDETERMINATE	1	TRUE	0	0.35	3		694	1233	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660138	227660138	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061000-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1244	269	870	0	ENST00000305123.5:c.3317C>A	p.Ser1106Ter	p.S1106*	ENST00000305123	NM_005544.2	1106	tCa/tAa	1/2	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.35	2		870	1513	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663313	227663313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1427330157	NA	P-0061000-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	212	677	0	ENST00000305123.5:c.142G>A	p.Glu48Lys	p.E48K	ENST00000305123	NM_005544.2	48	Gag/Aag	1/2	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.35	2		677	1053	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39021181	39021181	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0061000-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	50	391	0	ENST00000357387.3:c.155C>G	p.Ser52Ter	p.S52*	ENST00000357387	NM_152756.3	52	tCa/tGa	3/38	0.300635922375241	4	FACETS	0.526	0.445	0.616	0.175	0.148	0.206	SUBCLONAL	1	TRUE	1	0.35	4		391	733	SUCCESS
APC	324	MSKCC	GRCh37	5	112090669	112090669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061000-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	66	333	0	ENST00000257430.4:c.82G>A	p.Glu28Lys	p.E28K	ENST00000257430	NM_000038.5	28	Gaa/Aaa	2/16	1	2	FACETS	0.614	0.533	0.702	0.614	0.533	0.702	SUBCLONAL	1	TRUE	1	0.35	2		333	614	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637369	176637369	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs944488573	NA	P-0061000-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	62	710	0	ENST00000439151.2:c.1969G>C	p.Glu657Gln	p.E657Q	ENST00000439151	NM_022455.4	657	Gag/Cag	5/23	1	2	FACETS	0.335	0.288	0.386	0.335	0.288	0.386	SUBCLONAL	1	TRUE	1	0.35	2		710	1058	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325410	1325410	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061000-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	156	695	0	ENST00000400841.2:c.265G>C	p.Glu89Gln	p.E89Q	ENST00000400841		89	Gag/Cag	3/6	0.300635922375241	0	FACETS	0.64	0.586	0.697			1	SUBCLONAL	1	TRUE	NA	0.35	0		695	905	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76953092	76953092	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0061000-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	92	157	0	ENST00000373344.5:c.221C>G	p.Ser74Ter	p.S74*	ENST00000373344	NM_000489.3	74	tCa/tGa	4/35	0.220174127934723	2	FACETS	0.897	0.807	0.99			1	CLONAL	2	TRUE	NA	0.35	2		157	293	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061032-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	197	321	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		321	992	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0061032-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	152	380	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		380	747	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121448	108121450	+	inframe_deletion	In_Frame_Del	DEL	TAA	TAA	-	novel	NA	P-0061032-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	131	298	0	ENST00000278616.4:c.1258_1260del	p.Ile420del	p.I420del	ENST00000278616	NM_000051.3	419	tTAAta/tta	10/63	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		298	705	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913355	NA	P-0061045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	36	460	0	ENST00000288602.6:c.1406G>T	p.Gly469Val	p.G469V	ENST00000288602	NM_004333.4	469	gGa/gTa	11/18	1	2	FACETS	0.729	0.603	0.868	0.729	0.603	0.868	SUBCLONAL	1	TRUE	1	0.413283642253032	2		460	239	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0061045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	41	529	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.413283642253032	1	FACETS	0.601	0.504	0.707	0.601	0.504	0.707	SUBCLONAL	1	TRUE	0	0.413283642253032	1		529	262	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981167	201981168	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	72	744	0	ENST00000359651.3:c.248dup	p.Asn83LysfsTer9	p.N83Kfs*9	ENST00000359651		82	-/A	2/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.413283642253032	2		744	258	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105551	27105551	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	46	702	0	ENST00000324856.7:c.5162G>C	p.Arg1721Pro	p.R1721P	ENST00000324856	NM_006015.4	1721	cGa/cCa	20/20	1	2	FACETS	0.776	0.657	0.905	0.776	0.657	0.905	CLONAL	1	TRUE	1	0.413283642253032	2		702	287	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651956	36651957	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	139	789	0	ENST00000244741.5:c.79dup	p.Ser27LysfsTer9	p.S27Kfs*9	ENST00000244741	NM_000389.4	26	-/A	2/3	0.334419832382512	2	FACETS	0.837	0.769	0.906	0.837	0.769	0.906	CLONAL	2	TRUE	0	0.413283642253032	2		789	402	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105721	27105721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	50	740	1	ENST00000324856.7:c.5332G>A	p.Glu1778Lys	p.E1778K	ENST00000324856	NM_006015.4	1778	Gaa/Aaa	20/20	1	2	FACETS	0.823	0.703	0.953	0.823	0.703	0.953	CLONAL	1	TRUE	1	0.413283642253032	2		741	294	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101637	27101637	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	80	978	0	ENST00000324856.7:c.4919C>G	p.Thr1640Ser	p.T1640S	ENST00000324856	NM_006015.4	1640	aCc/aGc	18/20	1	2	FACETS	0.815	0.72	0.916	0.815	0.72	0.916	CLONAL	1	TRUE	1	0.413283642253032	2		978	475	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106288	27106288	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	69	907	0	ENST00000324856.7:c.5899C>A	p.Leu1967Met	p.L1967M	ENST00000324856	NM_006015.4	1967	Ctg/Atg	20/20	1	2	FACETS	0.854	0.747	0.968	0.854	0.747	0.968	CLONAL	1	TRUE	1	0.413283642253032	2		907	391	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106483	27106483	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	80	930	0	ENST00000324856.7:c.6094G>C	p.Glu2032Gln	p.E2032Q	ENST00000324856	NM_006015.4	2032	Gaa/Caa	20/20	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.413283642253032	2		930	386	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733028	74733029	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TAGC	novel	NA	P-0061045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	70	775	0	ENST00000359995.5:c.211_214dup	p.Met72SerfsTer53	p.M72Sfs*53	ENST00000359995	NM_001195427.1	72	atg/aGCTAtg	1/3	1	2	FACETS	0.931	0.816	1	0.931	0.816	1	CLONAL	1	TRUE	1	0.413283642253032	2		775	364	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170522	11170522	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	64	872	0	ENST00000358026.2:c.4825G>C	p.Glu1609Gln	p.E1609Q	ENST00000358026	NM_001128849.1	1609	Gag/Cag	34/36	0.240456383468432	2	FACETS	0.839	0.731	0.956	0.42	0.365	0.478	INDETERMINATE	1	TRUE	0	0.413283642253032	2		872	369	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525101	187525101	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	87	543	0	ENST00000441802.2:c.10579T>C	p.Ser3527Pro	p.S3527P	ENST00000441802	NM_005245.3	3527	Tct/Cct	19/27	0.34011192301874	2	FACETS	0.842	0.757	0.93	0.842	0.757	0.93	CLONAL	2	TRUE	0	0.413283642253032	2		543	250	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061046-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	142	377	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.152028720901975	4	FACETS	0.955	0.874	1	0.955	0.874	1	INDETERMINATE	2	TRUE	2	0.34	4		377	586	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0061046-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	131	210	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.281683736247491	0	FACETS	0.942	0.859	1			1	CLONAL	1	TRUE	0	0.34	0		210	540	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0061046-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	62	682	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.407	0.351	0.469	0.407	0.351	0.469	SUBCLONAL	1	TRUE	1	0.34	2		683	895	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276860	15276861	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs753725730	NA	P-0061046-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	180	764	3	ENST00000263388.2:c.5404dup	p.Ala1802GlyfsTer8	p.A1802Gfs*8	ENST00000263388	NM_000435.2	1802	gct/gGct	30/33	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.34	2		767	979	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374944	45374944	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061046-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	59	566	0	ENST00000262160.6:c.899A>G	p.Asp300Gly	p.D300G	ENST00000262160	NM_005901.5	300	gAt/gGt	8/11	1	2	FACETS	0.459	0.394	0.53	0.459	0.394	0.53	SUBCLONAL	1	TRUE	1	0.34	2		566	756	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912149	114912149	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061046-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	81	559	0	ENST00000543371.1:c.1219C>T	p.Arg407Ter	p.R407*	ENST00000543371	NM_001198531.1	407	Cga/Tga	11/14	1	2	FACETS	0.672	0.592	0.758	0.672	0.592	0.758	SUBCLONAL	1	TRUE	1	0.34	2		559	709	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338701	70338701	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061046-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	121	478	0	ENST00000374080.3:c.97G>C	p.Glu33Gln	p.E33Q	ENST00000374080		33	Gag/Cag	1/45	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.34	2		478	697	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100227	30100227	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061046-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	58	312	0	ENST00000331968.5:c.1393G>T	p.Glu465Ter	p.E465*	ENST00000331968	NM_002742.2	465	Gaa/Taa	10/18	1	2	FACETS	0.895	0.773	1	0.895	0.773	1	CLONAL	1	TRUE	1	0.34	2		312	381	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2090028	2090028	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs149287105	NA	P-0061046-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	118	795	0	ENST00000219066.1:c.836A>G	p.Asn279Ser	p.N279S	ENST00000219066	NM_002528.5	279	aAt/aGt	6/6	1	2	FACETS	0.671	0.604	0.742	0.671	0.604	0.742	SUBCLONAL	1	TRUE	1	0.34	2		795	1034	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660171	227660171	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061046-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	177	777	0	ENST00000305123.5:c.3284G>T	p.Cys1095Phe	p.C1095F	ENST00000305123	NM_005544.2	1095	tGc/tTc	1/2	1	2	FACETS	0.988	0.909	1	0.988	0.909	1	CLONAL	1	TRUE	1	0.34	2		777	1054	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721964	176721964	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061046-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	403	929	0	ENST00000439151.2:c.7595C>A	p.Ser2532Ter	p.S2532*	ENST00000439151	NM_022455.4	2532	tCa/tAa	23/23	0.3	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.34	3		929	1329	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349048	70349048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061046-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	179	723	0	ENST00000374080.3:c.3560C>T	p.Pro1187Leu	p.P1187L	ENST00000374080		1187	cCt/cTt	25/45	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.34	2		723	945	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0061047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	193	271	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.528873979055858	2	FACETS	0.473	0.437	0.509	0.236	0.218	0.255	INDETERMINATE	1	TRUE	0	0.947671169665577	2		272	862	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0061047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	1417	819	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.947671169665577	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.947671169665577	2		819	1462	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100414	157100414	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1438676618	NA	P-0061047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	12	331	2	ENST00000346085.5:c.1351T>C	p.Ser451Pro	p.S451P	ENST00000346085	NM_020732.3	451	Tcg/Ccg	1/20	0.947671169665577	1	FACETS	0.064	0.045	0.088	0.064	0.045	0.088	SUBCLONAL	1	TRUE	0	0.947671169665577	1		333	208	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867391	68867391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34507583	NA	P-0061047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	491	724	0	ENST00000261769.5:c.2638G>A	p.Glu880Lys	p.E880K	ENST00000261769	NM_004360.3	880	Gag/Aag	16/16	1	2	FACETS	0.926	0.889	0.963	0.926	0.889	0.963	CLONAL	1	TRUE	1	0.947671169665577	2		724	1119	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937770	76937770	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	246	514	0	ENST00000373344.5:c.2978del	p.Lys993ArgfsTer10	p.K993Rfs*10	ENST00000373344	NM_000489.3	993	aAg/ag	9/35	0.628714444593246	1	FACETS	0.624	0.592	0.655	0.624	0.592	0.655	SUBCLONAL	1	TRUE	0	0.947671169665577	1		514	438	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs763804037	NA	P-0061047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	1195	890	0	ENST00000304494.5:c.143C>G	p.Pro48Arg	p.P48R	ENST00000304494	NM_000077.4	48	cCg/cGg	1/3	0.947671169665577	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.947671169665577	2		890	1234	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257281	16257283	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	rs1557759482	NA	P-0061047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	382	737	0	ENST00000375759.3:c.4546_4548del	p.Lys1516del	p.K1516del	ENST00000375759	NM_015001.2	1516	AAA/-	11/15	0.139304032573495	3	FACETS	1	0.992	1	0.399	0.38	0.418	INDETERMINATE	1	TRUE	0	0.947671169665577	3		737	993	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50774006	50774006	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	185	593	0	ENST00000307179.4:c.1547A>C	p.Glu516Ala	p.E516A	ENST00000307179		516	gAg/gCg	11/20	0.393154678228355	2	FACETS	0.571	0.529	0.614	0.285	0.264	0.307	INDETERMINATE	1	TRUE	0	0.947671169665577	2		593	684	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349169	11349169	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	181	825	3	ENST00000332029.2:c.167G>A	p.Arg56His	p.R56H	ENST00000332029	NM_003745.1	56	cGc/cAc	2/2	1	2	FACETS	0.325	0.299	0.353	0.325	0.299	0.353	SUBCLONAL	1	TRUE	1	0.947671169665577	2		828	1174	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81973631	81973631	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	81	683	0	ENST00000359376.3:c.3448C>A	p.His1150Asn	p.H1150N	ENST00000359376	NM_002661.3	1150	Cat/Aat	30/33	0.947671169665577	1	FACETS	0.191	0.168	0.215	0.191	0.168	0.215	SUBCLONAL	1	TRUE	0	0.947671169665577	1		683	471	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232196	98232198	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0061047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1440	129	666	0	ENST00000331920.6:c.1744_1746del	p.Val582del	p.V582del	ENST00000331920	NM_000264.3	582	GTG/-	13/24	0.310797581123568	5	FACETS	0.42	0.379	0.464	0.084	0.075	0.093	INDETERMINATE	1	TRUE	0	0.947671169665577	5		666	1569	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968215	18968215	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061048-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	190	614	0	ENST00000262803.5:c.2055C>G	p.Phe685Leu	p.F685L	ENST00000262803	NM_002911.3	685	ttC/ttG	15/24	0.136755876287767	4	FACETS	0.751	0.696	0.809	0.751	0.696	0.809	INDETERMINATE	2	TRUE	2	0.48799812306285	4		614	771	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794874	242794874	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061048-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	204	790	0	ENST00000334409.5:c.335G>T	p.Arg112Met	p.R112M	ENST00000334409	NM_005018.2	112	aGg/aTg	2/5	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.48799812306285	2		790	832	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31390266	31390266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769823434	NA	P-0061048-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	184	622	0	ENST00000328111.2:c.2221G>A	p.Gly741Arg	p.G741R	ENST00000328111	NM_006892.3	741	Ggg/Agg	20/23	1	2	FACETS	0.883	0.816	0.953	0.883	0.816	0.953	CLONAL	1	TRUE	1	0.48799812306285	2		622	854	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651282	52651282	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061048-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	174	634	0	ENST00000394830.3:c.1814C>G	p.Ser605Cys	p.S605C	ENST00000394830	NM_018313.4	605	tCc/tGc	15/30	0.445209106015404	1	FACETS	0.799	0.738	0.862	0.799	0.738	0.862	SUBCLONAL	1	TRUE	0	0.48799812306285	1		634	675	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	28	321	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.858	0.688	1	0.858	0.688	1	CLONAL	1	TRUE	1	0.25	2		321	261	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0061049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	54	684	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.25	2		684	430	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441213	52441213	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	38	530	0	ENST00000460680.1:c.557T>A	p.Leu186Gln	p.L186Q	ENST00000460680	NM_004656.3	186	cTg/cAg	7/17	0.3	1	FACETS	0.758	0.628	0.902	0.758	0.628	0.902	CLONAL	1	TRUE	0	0.25	1		530	351	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30323873	30323873	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	19	269	0	ENST00000322652.5:c.1851G>T	p.Trp617Cys	p.W617C	ENST00000322652	NM_015355.2	617	tgG/tgT	15/16	1	2	FACETS	0.813	0.62	1	0.813	0.62	1	CLONAL	1	TRUE	1	0.25	2		269	187	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799110	42799110	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	41	436	0	ENST00000575354.2:c.4594G>T	p.Glu1532Ter	p.E1532*	ENST00000575354	NM_015125.3	1532	Gag/Tag	20/20	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.25	2		436	306	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250495	26250495	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	49	736	0	ENST00000446824.2:c.339C>G	p.Ile113Met	p.I113M	ENST00000446824	NM_021018.2	113	atC/atG	1/1	1	2	FACETS	0.936	0.794	1	0.936	0.794	1	CLONAL	1	TRUE	1	0.25	2		736	419	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873977	151873977	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	49	432	0	ENST00000262189.6:c.8561C>T	p.Ser2854Leu	p.S2854L	ENST00000262189	NM_170606.2	2854	tCa/tTa	38/59	0.0910999107112282	3	FACETS	1	0.923	1	0.571	0.485	0.666	INDETERMINATE	1	TRUE	1	0.25	3		432	386	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22008926	22008927	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0061049-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	26	780	0	ENST00000276925.6:c.26_27del	p.Pro9GlnfsTer7	p.P9Qfs*7	ENST00000276925	NM_004936.3	9	cCC/c	1/2	0.3	1	FACETS	0.523	0.414	0.648	0.523	0.414	0.648	SUBCLONAL	1	TRUE	0	0.25	1		780	348	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061049-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	28	321	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	FALSE	1	0.209380550980741	2		321	217	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0061049-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	62	684	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	0.9	0.777	1	0.9	0.777	1	CLONAL	1	FALSE	1	0.209380550980741	2		684	658	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441213	52441213	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061049-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	52	530	0	ENST00000460680.1:c.557T>A	p.Leu186Gln	p.L186Q	ENST00000460680	NM_004656.3	186	cTg/cAg	7/17	0.209380550980741	1	FACETS	0.884	0.753	1	0.884	0.753	1	CLONAL	1	FALSE	0	0.209380550980741	1		530	503	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30323873	30323873	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061049-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	46	269	0	ENST00000322652.5:c.1851G>T	p.Trp617Cys	p.W617C	ENST00000322652	NM_015355.2	617	tgG/tgT	15/16	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	FALSE	1	0.209380550980741	2		269	386	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799110	42799110	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061049-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	27	436	0	ENST00000575354.2:c.4594G>T	p.Glu1532Ter	p.E1532*	ENST00000575354	NM_015125.3	1532	Gag/Tag	20/20	1	2	FACETS	0.835	0.665	1	0.835	0.665	1	CLONAL	1	FALSE	1	0.209380550980741	2		436	309	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250495	26250495	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061049-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	99	736	0	ENST00000446824.2:c.339C>G	p.Ile113Met	p.I113M	ENST00000446824	NM_021018.2	113	atC/atG	1/1	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.209380550980741	2		736	782	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873977	151873977	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061049-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	48	432	0	ENST00000262189.6:c.8561C>T	p.Ser2854Leu	p.S2854L	ENST00000262189	NM_170606.2	2854	tCa/tTa	38/59	1	2	FACETS	0.747	0.63	0.875	0.747	0.63	0.875	SUBCLONAL	1	FALSE	1	0.209380550980741	2		432	614	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0061050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	289	578	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.152100320058494	5	FACETS	0.922	0.867	0.978	0.691	0.65	0.734	CLONAL	3	FALSE	1	0.248176382730703	5		578	1156	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863224683	NA	P-0061050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	111	710	0	ENST00000269305.4:c.388C>G	p.Leu130Val	p.L130V	ENST00000269305	NM_001126112.2	130	Ctc/Gtc	5/11	1	2	FACETS	0.802	0.719	0.891	0.802	0.719	0.891	CLONAL	1	FALSE	1	0.248176382730703	2		710	1115	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0061051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	152	578	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.110126426612428	4	FACETS	0.921	0.842	1	0.921	0.842	1	INDETERMINATE	2	TRUE	2	0.212048201349275	4		578	943	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0061051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	90	302	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.212048201349275	2		302	825	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916924	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	14	440	0	ENST00000263967.3:c.311C>A	p.Pro104Gln	p.P104Q	ENST00000263967	NM_006218.2	104	cCa/cAa	2/21	1	2	FACETS	0.196	0.14	0.263	0.196	0.14	0.263	SUBCLONAL	1	TRUE	1	0.212048201349275	2		440	675	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443695	29443695	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863225281	NA	P-0061054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	37	599	0	ENST00000389048.3:c.3522C>G	p.Phe1174Leu	p.F1174L	ENST00000389048	NM_004304.4	1174	ttC/ttG	23/29	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		599	669	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954272	32954273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359752	NA	P-0061055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	10	319	2	ENST00000380152.3:c.9253dup	p.Thr3085AsnfsTer26	p.T3085Nfs*26	ENST00000380152		3082	-/A	24/27	1	2	FACETS	0.551	0.373	0.774	0.551	0.373	0.774	SUBCLONAL	1	TRUE	1	0.200543380314238	2		321	181	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499772	8499772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773166856	NA	P-0061055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	42	525	0	ENST00000356435.5:c.2197C>T	p.Arg733Cys	p.R733C	ENST00000356435		733	Cgc/Tgc	14/35	0.200543380314238	1	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	0	0.200543380314238	1		525	349	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11022914	11022914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	23	506	0	ENST00000327064.4:c.613G>A	p.Ala205Thr	p.A205T	ENST00000327064	NM_199141.1	205	Gct/Act	5/16	1	2	FACETS	0.76	0.593	0.952	0.76	0.593	0.952	CLONAL	1	TRUE	1	0.200543380314238	2		506	302	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0061056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	39	611	0				ENST00000310581	NM_198253.2	-/1132			0.273302325449645	1	FACETS	0.94	0.784	1	0.94	0.784	1	CLONAL	1	TRUE	0	0.273302325449645	1		611	262	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0061056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	118	608	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.238102415449403	2	FACETS	0.896	0.813	0.982	0.896	0.813	0.982	CLONAL	2	TRUE	0	0.273302325449645	2		610	482	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258775	115258775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	60	436	0	ENST00000369535.4:c.7G>A	p.Glu3Lys	p.E3K	ENST00000369535	NM_002524.4	3	Gag/Aag	2/7	1	2	FACETS	0.851	0.734	0.978	0.851	0.734	0.978	CLONAL	1	TRUE	1	0.273302325449645	2		436	516	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342782	118342782	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	67	566	0	ENST00000534358.1:c.908G>C	p.Arg303Thr	p.R303T	ENST00000534358	NM_005933.3	303	aGa/aCa	3/36	0.0739857351571929	3	FACETS	0.949	0.825	1	0.475	0.412	0.542	INDETERMINATE	1	TRUE	1	0.273302325449645	3		566	587	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427168	49427168	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	287	871	0	ENST00000301067.7:c.11320C>T	p.Gln3774Ter	p.Q3774*	ENST00000301067	NM_003482.3	3774	Cag/Tag	39/54	0.273302325449645	6	FACETS	1	0.978	1	1	0.978	1	CLONAL	4	TRUE	2	0.273302325449645	6		871	763	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482550	56482550	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	157	647	0	ENST00000267101.3:c.1007C>A	p.Ser336Tyr	p.S336Y	ENST00000267101	NM_001982.3	336	tCt/tAt	9/28	0.0137228541472991	3	FACETS	1	0.966	1			1	INDETERMINATE	2	TRUE	NA	0.273302325449645	3		647	598	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350791	89350791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	62	439	0	ENST00000301030.4:c.2159G>A	p.Arg720Lys	p.R720K	ENST00000301030	NM_001256183.1	720	aGa/aAa	9/13	0.273302325449645	1	FACETS	0.97	0.841	1	0.97	0.841	1	CLONAL	1	TRUE	0	0.273302325449645	1		439	404	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223256	41223256	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs80358008	NA	P-0061056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	66	486	0	ENST00000357654.3:c.4676-1G>A		p.X1559_splice	ENST00000357654	NM_007294.3	1559			0.257573348900118	3	FACETS	0.98	0.852	1	0.49	0.426	0.56	CLONAL	1	TRUE	1	0.273302325449645	3		486	560	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534347	63534347	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	156	871	0	ENST00000307078.5:c.1174G>C	p.Glu392Gln	p.E392Q	ENST00000307078	NM_004655.3	392	Gag/Cag	5/11	0.25599798763711	4	FACETS	0.911	0.835	0.99	0.607	0.556	0.66	CLONAL	2	TRUE	1	0.273302325449645	4		871	798	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412884	49412884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	58	549	0	ENST00000418115.1:c.139G>A	p.Glu47Lys	p.E47K	ENST00000418115	NM_001664.2	47	Gag/Aag	2/5	0.260869772871624	3	FACETS	0.809	0.695	0.934	0.27	0.231	0.312	CLONAL	1	TRUE	0	0.273302325449645	3		549	596	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114712	73114712	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	46	320	0	ENST00000356692.5:c.1093G>T	p.Glu365Ter	p.E365*	ENST00000356692		365	Gaa/Taa	9/9	0.260869772871624	3	FACETS	1	0.897	1	0.36	0.304	0.422	CLONAL	1	TRUE	0	0.273302325449645	3		320	354	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447721	187447721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746850741	NA	P-0061056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	290	752	0	ENST00000232014.4:c.472C>T	p.Arg158Trp	p.R158W	ENST00000232014	NM_001130845.1	158	Cgg/Tgg	5/10	0.273302325449645	5	FACETS	1	0.975	1	0.795	0.749	0.842	CLONAL	3	TRUE	1	0.273302325449645	5		752	941	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332949	153332949	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	108	494	0	ENST00000281708.4:c.7C>T	p.Gln3Ter	p.Q3*	ENST00000281708	NM_033632.3	3	Cag/Tag	2/12	0.127156537824801	4	FACETS	1	0.976	1	0.436	0.391	0.483	INDETERMINATE	1	TRUE	1	0.273302325449645	4		494	770	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671418	30671418	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	67	712	0	ENST00000376406.3:c.5542G>T	p.Glu1848Ter	p.E1848*	ENST00000376406	NM_014641.2	1848	Gag/Tag	10/15	0.257573348900118	3	FACETS	0.8	0.694	0.914	0.4	0.347	0.457	CLONAL	1	TRUE	1	0.273302325449645	3		712	697	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942843	44942843	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	88	172	0	ENST00000377967.4:c.3423C>A	p.Ser1141Arg	p.S1141R	ENST00000377967	NM_021140.2	1141	agC/agA	23/29	0.273302325449645	2	FACETS	1	0.956	1			1	CLONAL	2	TRUE	NA	0.273302325449645	2		172	287	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039297	47039297	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	194	341	0	ENST00000377604.3:c.920T>C	p.Leu307Pro	p.L307P	ENST00000377604	NM_001204468.1	307	cTg/cCg	10/24	0.273302325449645	2	FACETS	1	0.98	1			1	CLONAL	3	TRUE	NA	0.273302325449645	2		341	425	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061057-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	268	377	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.61798415801922	3	FACETS	0.902	0.853	0.952	0.902	0.853	0.952	CLONAL	2	TRUE	1	0.625085329880699	3		377	624	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056307	27056307	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061057-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	230	741	0	ENST00000324856.7:c.1303C>T	p.Gln435Ter	p.Q435*	ENST00000324856	NM_006015.4	435	Cag/Tag	2/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.625085329880699	2		741	713	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819733	81819733	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061057-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	208	636	2	ENST00000359376.3:c.139A>G	p.Met47Val	p.M47V	ENST00000359376	NM_002661.3	47	Atg/Gtg	2/33	0.61798415801922	3	FACETS	0.927	0.861	0.996	0.464	0.43	0.498	CLONAL	1	TRUE	1	0.625085329880699	3		638	942	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572988	41572988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061057-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	228	723	0	ENST00000263253.7:c.5273G>A	p.Cys1758Tyr	p.C1758Y	ENST00000263253	NM_001429.3	1758	tGc/tAc	31/31	1	2	FACETS	0.915	0.855	0.977	0.915	0.855	0.977	CLONAL	1	TRUE	1	0.625085329880699	2		723	797	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0061057-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	156	356	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	1	2	FACETS	0.949	0.875	1	0.949	0.875	1	CLONAL	1	TRUE	1	0.625085329880699	2		356	526	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130095	143130095	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061057-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	98	343	0	ENST00000262992.4:c.921G>A	p.Met307Ile	p.M307I	ENST00000262992	NM_001101669.1	307	atG/atA	11/24	1	2	FACETS	0.802	0.721	0.887	0.802	0.721	0.887	CLONAL	1	TRUE	1	0.625085329880699	2		343	391	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	189	321	0				ENST00000310581	NM_198253.2	-/1132			0.35244469214057	3	FACETS	0.902	0.838	0.969	0.902	0.838	0.969	CLONAL	2	TRUE	1	0.391312703697385	3		321	640	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729163	66729163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516792	NA	P-0061058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	204	534	0	ENST00000307102.5:c.371C>T	p.Pro124Leu	p.P124L	ENST00000307102	NM_002755.3	124	cCg/cTg	3/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.391312703697385	2		534	1021	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0061058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	296	508	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.34532132838088	3	FACETS	0.986	0.931	1	0.986	0.931	1	CLONAL	2	TRUE	1	0.391312703697385	3		508	917	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709162	117709162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867987684	NA	P-0061058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	150	474	0	ENST00000368508.3:c.1795G>A	p.Glu599Lys	p.E599K	ENST00000368508	NM_002944.2	599	Gaa/Aaa	13/43	1	2	FACETS	0.984	0.901	1	0.984	0.901	1	CLONAL	1	TRUE	1	0.391312703697385	2		474	779	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905490	11905490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745855585	NA	P-0061058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	167	504	0	ENST00000396373.4:c.140C>T	p.Ser47Leu	p.S47L	ENST00000396373	NM_001987.4	47	tCg/tTg	2/8	1	2	FACETS	0.96	0.882	1	0.96	0.882	1	CLONAL	1	TRUE	1	0.391312703697385	2		504	889	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394848	394848	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1302327519	NA	P-0061058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	199	578	0	ENST00000380956.4:c.244C>T	p.Arg82Ter	p.R82*	ENST00000380956	NM_001195286.1	82	Cga/Tga	3/9	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.391312703697385	2		578	997	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109770	115109770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	194	681	0	ENST00000257566.3:c.2108C>T	p.Ser703Phe	p.S703F	ENST00000257566	NM_016569.3	703	tCc/tTc	8/8	1	2	FACETS	0.992	0.917	1	0.992	0.917	1	CLONAL	1	TRUE	1	0.391312703697385	2		681	1000	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561090	9561090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	160	519	0	ENST00000353224.5:c.692C>T	p.Ser231Leu	p.S231L	ENST00000353224	NM_177990.2	231	tCa/tTa	4/10	1	2	FACETS	0.909	0.833	0.987	0.909	0.833	0.987	CLONAL	1	TRUE	1	0.391312703697385	2		519	900	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970884	55970884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	156	504	0	ENST00000263923.4:c.1913G>A	p.Gly638Glu	p.G638E	ENST00000263923	NM_002253.2	638	gGa/gAa	13/30	1	2	FACETS	0.95	0.871	1	0.95	0.871	1	CLONAL	1	TRUE	1	0.391312703697385	2		504	839	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636826	8636826	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1353675904	NA	P-0061058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	153	472	0	ENST00000356435.5:c.83G>A	p.Arg28Gln	p.R28Q	ENST00000356435		28	cGa/cAa	2/35	0.391312703697385	1	FACETS	0.853	0.782	0.928	0.853	0.782	0.928	CLONAL	1	TRUE	0	0.391312703697385	1		472	737	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060983	38060983	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	129	706	0	ENST00000250448.2:c.1006G>A	p.Asp336Asn	p.D336N	ENST00000250448	NM_004496.3	336	Gac/Aac	2/2	1	2	FACETS	0.849	0.77	0.931	0.849	0.77	0.931	CLONAL	1	TRUE	1	0.391312703697385	2		706	777	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526111	189526111	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs779179533	NA	P-0061058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	223	697	0	ENST00000264731.3:c.375G>C	p.Gln125His	p.Q125H	ENST00000264731	NM_003722.4	125	caG/caC	4/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.391312703697385	2		697	1008	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259220	16259220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	198	754	0	ENST00000375759.3:c.6485C>T	p.Ala2162Val	p.A2162V	ENST00000375759	NM_015001.2	2162	gCc/gTc	11/15	0.35244469214057	3	FACETS	0.95	0.878	1	0.475	0.439	0.513	CLONAL	1	TRUE	1	0.391312703697385	3		754	1274	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724554	162724554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	226	660	0	ENST00000367921.3:c.326G>A	p.Gly109Asp	p.G109D	ENST00000367921	NM_006182.2	109	gGt/gAt	5/18	0.34532132838088	3	FACETS	1	0.966	1	0.532	0.494	0.571	CLONAL	1	TRUE	1	0.391312703697385	3		660	1298	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685312	89685312	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	23	141	0	ENST00000371953.3:c.207T>G	p.Asn69Lys	p.N69K	ENST00000371953	NM_000314.4	69	aaT/aaG	3/9	0.391312703697385	1	FACETS	0.374	0.292	0.468	0.374	0.292	0.468	SUBCLONAL	1	TRUE	0	0.391312703697385	1		141	253	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003368	57003369	+	missense_variant,NMD_transcript_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0061058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	185	698	0	ENST00000257254.3:c.1110_1111delinsTT	p.Pro371Ser	p.P371S	ENST00000257254		370	atCCcc/atTTcc	1/2	1	2	FACETS	0.938	0.866	1	0.938	0.866	1	CLONAL	1	TRUE	1	0.391312703697385	2		698	1008	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292666	91292666	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	122	371	0	ENST00000355112.3:c.168A>T	p.Lys56Asn	p.K56N	ENST00000355112	NM_000057.2	56	aaA/aaT	3/22	1	2	FACETS	0.913	0.826	1	0.913	0.826	1	CLONAL	1	TRUE	1	0.391312703697385	2		371	683	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995204	15995204	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	157	496	2	ENST00000268712.3:c.2989T>C	p.Ser997Pro	p.S997P	ENST00000268712	NM_006311.3	997	Tcc/Ccc	22/46	1	2	FACETS	0.945	0.866	1	0.945	0.866	1	CLONAL	1	TRUE	1	0.391312703697385	2		498	849	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33680001	33680001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	132	544	0	ENST00000308377.4:c.2080G>A	p.Gly694Ser	p.G694S	ENST00000308377	NM_152270.3	694	Ggc/Agc	5/5	1	2	FACETS	0.762	0.692	0.837	0.762	0.692	0.837	SUBCLONAL	1	TRUE	1	0.391312703697385	2		544	885	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573634	48573634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	134	438	0	ENST00000342988.3:c.218C>T	p.Thr73Ile	p.T73I	ENST00000342988	NM_005359.5	73	aCc/aTc	2/12	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.391312703697385	2		438	650	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47502656	47502656	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	98	338	0	ENST00000404338.3:c.4132C>A	p.His1378Asn	p.H1378N	ENST00000404338	NM_004491.4	1378	Cac/Aac	5/6	1	2	FACETS	0.85	0.76	0.946	0.85	0.76	0.946	CLONAL	1	TRUE	1	0.391312703697385	2		338	589	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47600972	47600973	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0061058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	115	455	0	ENST00000263735.4:c.210_211delinsAA	p.Ala71Thr	p.A71T	ENST00000263735	NM_002354.2	70	aaGGca/aaAAca	3/9	1	2	FACETS	0.785	0.707	0.867	0.785	0.707	0.867	SUBCLONAL	1	TRUE	1	0.391312703697385	2		455	749	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827994	40827994	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	186	568	0	ENST00000373198.4:c.2434G>A	p.Gly812Arg	p.G812R	ENST00000373198	NM_133170.3	812	Gga/Aga	17/32	1	2	FACETS	0.996	0.92	1	0.996	0.92	1	CLONAL	1	TRUE	1	0.391312703697385	2		568	954	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468472	89468472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	149	456	0	ENST00000336596.2:c.2006G>A	p.Gly669Glu	p.G669E	ENST00000336596	NM_005233.5	669	gGa/gAa	11/17	1	2	FACETS	0.854	0.78	0.931	0.854	0.78	0.931	CLONAL	1	TRUE	1	0.391312703697385	2		456	892	SUCCESS
REST	5978	MSKCC	GRCh37	4	57797389	57797389	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	222	816	2	ENST00000309042.7:c.2365C>T	p.Gln789Ter	p.Q789*	ENST00000309042	NM_005612.4	789	Cag/Tag	4/4	1	2	FACETS	0.982	0.913	1	0.982	0.913	1	CLONAL	1	TRUE	1	0.391312703697385	2		818	1156	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057708	180057708	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	203	616	0	ENST00000261937.6:c.247G>C	p.Asp83His	p.D83H	ENST00000261937	NM_182925.4	83	Gac/Cac	3/30	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.391312703697385	2		616	934	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93953257	93953258	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0061058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	85	321	0	ENST00000369303.4:c.2883_2884delinsAA	p.Asp962Asn	p.D962N	ENST00000369303	NM_004440.3	961	gaGGat/gaAAat	17/17	1	2	FACETS	0.779	0.689	0.874	0.779	0.689	0.874	SUBCLONAL	1	TRUE	1	0.391312703697385	2		321	558	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739490	145739490	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	175	667	0	ENST00000428558.2:c.1880T>A	p.Val627Glu	p.V627E	ENST00000428558	NM_004260.3	627	gTg/gAg	12/22	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.391312703697385	2		667	871	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229692	98229693	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0061058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	131	422	0	ENST00000331920.6:c.2265_2266delinsTT	p.Leu756Phe	p.L756F	ENST00000331920	NM_000264.3	755	ttCCtt/ttTTtt	15/24	1	2	FACETS	0.864	0.784	0.947	0.864	0.784	0.947	CLONAL	1	TRUE	1	0.391312703697385	2		422	775	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246267	46246267	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061060-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	153	655	1	ENST00000334344.6:c.4361C>T	p.Ser1454Leu	p.S1454L	ENST00000334344	NM_152641.2	1454	tCa/tTa	15/21	1	2	FACETS	0.764	0.698	0.833	0.764	0.698	0.833	SUBCLONAL	1	TRUE	1	0.398439882399506	2		656	1005	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618851	37618866	+	protein_altering_variant	In_Frame_Del	DEL	CATCCAAGCTCCACAA	CATCCAAGCTCCACAA	G	novel	NA	P-0061060-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1237	605	832	3	ENST00000447079.4:c.527_542delinsG	p.Ser176_Lys181delinsTrp	p.S176_K181delinsW	ENST00000447079	NM_015083.1	176	tCATCCAAGCTCCACAAg/tGg	1/14	0.349445176274302	3	FACETS	0.989	0.95	1	0.989	0.95	1	CLONAL	2	TRUE	1	0.398439882399506	3		835	1842	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604778	48604778	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767383	NA	P-0061061-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	123	671	0	ENST00000342988.3:c.1600C>T	p.Gln534Ter	p.Q534*	ENST00000342988	NM_005359.5	534	Cag/Tag	12/12	0.244254882791545	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.244254882791545	1		671	829	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0061061-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	41	370	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.671	0.559	0.797	0.671	0.559	0.797	SUBCLONAL	1	TRUE	1	0.244254882791545	2		370	500	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687558	37687558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749610847	NA	P-0061061-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	86	574	0	ENST00000447079.4:c.4462G>A	p.Val1488Ile	p.V1488I	ENST00000447079	NM_015083.1	1488	Gtt/Att	14/14	1	2	FACETS	0.874	0.772	0.983	0.874	0.772	0.983	CLONAL	1	TRUE	1	0.244254882791545	2		574	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0061062-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	360	465	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.439686805349688	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	0	0.439647494646614	3		465	629	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082191	16082191	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs370558211	NA	P-0061062-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	84	530	0	ENST00000281043.3:c.5C>G	p.Pro2Arg	p.P2R	ENST00000281043	NM_005378.4	2	cCg/cGg	2/3	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.439647494646614	2		530	361	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066811	77066811	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061062-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	92	565	0	ENST00000356341.3:c.674C>T	p.Thr225Ile	p.T225I	ENST00000356341	NM_002576.4	225	aCt/aTt	7/15	1	2	FACETS	0.677	0.602	0.757	0.677	0.602	0.757	SUBCLONAL	1	TRUE	1	0.439647494646614	2		565	618	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817877	3817877	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061062-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	105	475	0	ENST00000262367.5:c.3094del	p.Val1032LeufsTer7	p.V1032Lfs*7	ENST00000262367	NM_004380.2	1032	Gtt/tt	16/31	1	2	FACETS	0.959	0.863	1	0.959	0.863	1	CLONAL	1	TRUE	1	0.439647494646614	2		475	498	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41197730	41197982	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTGTCCAGCTCCTGGCACTGGTAGAGTGCTACACTGTCCAACACCCACTCTCGGGTCACCACAGGTGCCTCACACATCTGCCCAATTGCTGGAGACAGAGAACACAAGCAGAGATTAGTGTCAATTCATTCTCCTGGACTAGGCTCTAATCAATCGACTCCAGGGTCCTGGTTGTATGAGTTCTTAGGATTAATGAGGTAGAAGCTAATTTTTTTTTTTTTTTTTTGAGACGGAGTCTTGCTCTGTCGCCG	AGGTGTCCAGCTCCTGGCACTGGTAGAGTGCTACACTGTCCAACACCCACTCTCGGGTCACCACAGGTGCCTCACACATCTGCCCAATTGCTGGAGACAGAGAACACAAGCAGAGATTAGTGTCAATTCATTCTCCTGGACTAGGCTCTAATCAATCGACTCCAGGGTCCTGGTTGTATGAGTTCTTAGGATTAATGAGGTAGAAGCTAATTTTTTTTTTTTTTTTTTGAGACGGAGTCTTGCTCTGTCGCCG	-	novel	NA	P-0061062-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	100	658	0	ENST00000357654.3:c.5468-163_5557del		p.X1823_splice	ENST00000357654	NM_007294.3	1823		23/23	0.439686805349688	4	FACETS	0.807	0.72	0.899	0.202	0.18	0.225	CLONAL	1	TRUE	0	0.439647494646614	4		658	812	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661287	227661287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061062-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	48	729	1	ENST00000305123.5:c.2168G>A	p.Gly723Asp	p.G723D	ENST00000305123	NM_005544.2	723	gGt/gAt	1/2	0.438829769304058	4	FACETS	0.443	0.373	0.52	0.148	0.124	0.174	SUBCLONAL	1	TRUE	1	0.439647494646614	4		730	710	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62298830	62298830	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061062-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	167	579	0	ENST00000360203.5:c.623C>G	p.Pro208Arg	p.P208R	ENST00000360203	NM_001283009.1	208	cCt/cGt	8/35	0.439686805349688	3	FACETS	0.863	0.798	0.929	0.863	0.798	0.929	CLONAL	2	TRUE	1	0.439647494646614	3		579	537	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24135876	24135876	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0061062-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	63	630	0	ENST00000263121.7:c.362+1G>C		p.X121_splice	ENST00000263121	NM_003073.3	121			0.439686805349688	2	FACETS	0.459	0.396	0.526	0.229	0.198	0.263	SUBCLONAL	1	TRUE	0	0.439647494646614	2		630	625	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911659	134911659	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061062-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	90	521	0	ENST00000398015.3:c.2124C>A	p.Phe708Leu	p.F708L	ENST00000398015	NM_004441.4	708	ttC/ttA	11/16	0.439686805349688	3	FACETS	0.983	0.875	1	0.492	0.437	0.549	CLONAL	1	TRUE	1	0.439647494646614	3		521	508	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020809	26020809	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061062-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	294	819	2	ENST00000357647.3:c.92C>A	p.Pro31Gln	p.P31Q	ENST00000357647	NM_003529.2	31	cCg/cAg	1/1	0.439686805349688	3	FACETS	0.978	0.924	1	0.978	0.924	1	CLONAL	2	TRUE	1	0.439647494646614	3		821	834	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858455	27858455	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061062-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	62	777	0	ENST00000359303.2:c.116C>T	p.Pro39Leu	p.P39L	ENST00000359303	NM_003535.2	39	cCc/cTc	1/1	0.439686805349688	3	FACETS	0.447	0.385	0.514	0.223	0.192	0.257	SUBCLONAL	1	TRUE	1	0.439647494646614	3		777	770	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331985	81331985	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061062-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	67	426	0	ENST00000222390.5:c.2099C>A	p.Pro700Gln	p.P700Q	ENST00000222390	NM_000601.4	700	cCa/cAa	18/18	1	2	FACETS	0.849	0.742	0.963	0.849	0.742	0.963	CLONAL	1	TRUE	1	0.439647494646614	2		426	359	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922694	44922694	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs397514628	NA	P-0061062-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	85	441	0	ENST00000377967.4:c.1555C>G	p.Arg519Gly	p.R519G	ENST00000377967	NM_021140.2	519	Cga/Gga	16/29	0.439686805349688	2	FACETS	0.823	0.73	0.921	0.411	0.365	0.461	CLONAL	1	TRUE	0	0.439647494646614	2		441	470	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114905777	114905777	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061063-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	257	437	0	ENST00000543371.1:c.796C>T	p.Gln266Ter	p.Q266*	ENST00000543371	NM_001198531.1	266	Caa/Taa	8/14	0.599077048510468	2	FACETS	0.951	0.905	0.997	0.951	0.905	0.997	CLONAL	2	TRUE	0	0.599077048510468	2		437	451	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636839	73636839	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061063-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	701	537	0	ENST00000377687.4:c.1102G>C	p.Glu368Gln	p.E368Q	ENST00000377687	NM_001730.3	368	Gag/Cag	2/4	0.597834156997893	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.599077048510468	3		537	993	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224220	53224220	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061063-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	384	641	0	ENST00000375401.3:c.3331G>C	p.Asp1111His	p.D1111H	ENST00000375401	NM_004187.3	1111	Gac/Cac	22/26	0.517320044284827	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.599077048510468	4		641	1004	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114905777	114905777	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061063-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	76	437	0	ENST00000543371.1:c.796C>T	p.Gln266Ter	p.Q266*	ENST00000543371	NM_001198531.1	266	Caa/Taa	8/14	0.532782017313012	3	FACETS	0.974	0.874	1	0.974	0.874	1	CLONAL	2	TRUE	1	0.538162303564591	3		437	184	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636839	73636839	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061063-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	893	537	0	ENST00000377687.4:c.1102G>C	p.Glu368Gln	p.E368Q	ENST00000377687	NM_001730.3	368	Gag/Cag	2/4	0.538162303564591	8	FACETS	0.959	0.946	0.972			1	CLONAL	9	TRUE	NA	0.538162303564591	8		537	1005	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224220	53224220	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061063-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	55	641	0	ENST00000375401.3:c.3331G>C	p.Asp1111His	p.D1111H	ENST00000375401	NM_004187.3	1111	Gac/Cac	22/26	0.542610696651929	0	FACETS	0.774	0.683	0.866			1	SUBCLONAL	1	TRUE	0	0.538162303564591	0		641	122	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575080	48575080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061063-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	24	516	0	ENST00000342988.3:c.274C>T	p.His92Tyr	p.H92Y	ENST00000342988	NM_005359.5	92	Cat/Tat	3/12	0.542610696651929	1	FACETS	0.31	0.244	0.386	0.31	0.244	0.386	SUBCLONAL	1	TRUE	0	0.538162303564591	1		516	210	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0061064-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	191	341	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.774968168478479	3	FACETS	0.979	0.909	1	0.49	0.454	0.526	CLONAL	1	TRUE	1	0.783492119863885	3		341	693	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0061064-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	195	370	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.774968168478479	3	FACETS	0.914	0.848	0.982	0.457	0.424	0.491	CLONAL	1	TRUE	1	0.783492119863885	3		370	758	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0061064-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	108	591	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.321	0.287	0.356	0.321	0.287	0.356	SUBCLONAL	1	TRUE	1	0.783492119863885	2		591	859	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274897	41274897	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061064-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	269	652	0	ENST00000349496.5:c.1147T>C	p.Trp383Arg	p.W383R	ENST00000349496	NM_001904.3	383	Tgg/Cgg	8/15	1	2	FACETS	0.884	0.832	0.936	0.884	0.832	0.936	CLONAL	1	TRUE	1	0.783492119863885	2		652	777	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107152	27107152	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061064-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	333	831	0	ENST00000324856.7:c.6763G>T	p.Glu2255Ter	p.E2255*	ENST00000324856	NM_006015.4	2255	Gaa/Taa	20/20	1	2	FACETS	0.928	0.88	0.977	0.928	0.88	0.977	CLONAL	1	TRUE	1	0.783492119863885	2		831	916	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720663	89720663	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061064-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	94	108	0	ENST00000371953.3:c.814del	p.His272ThrfsTer4	p.H272Tfs*4	ENST00000371953	NM_000314.4	272	Cac/ac	8/9	0.774968168478479	3	FACETS	0.971	0.891	1	0.971	0.891	1	CLONAL	2	TRUE	1	0.783492119863885	3		108	172	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786707	3786707	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061064-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	339	625	0	ENST00000262367.5:c.4504T>C	p.Trp1502Arg	p.W1502R	ENST00000262367	NM_004380.2	1502	Tgg/Cgg	27/31	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.783492119863885	2		625	837	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562851	95562852	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1064795904	NA	P-0061064-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	200	585	0	ENST00000393063.1:c.4405_4406del	p.Leu1469PhefsTer7	p.L1469Ffs*7	ENST00000393063	NM_030621.3	1469	CTt/t	24/28	1	2	FACETS	0.838	0.781	0.897	0.838	0.781	0.897	CLONAL	1	TRUE	1	0.783492119863885	2		585	609	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233126	66233126	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061064-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	230	432	0	ENST00000273854.3:c.1873A>C	p.Lys625Gln	p.K625Q	ENST00000273854	NM_004439.5	625	Aaa/Caa	10/18	1	2	FACETS	0.95	0.892	1	0.95	0.892	1	CLONAL	1	TRUE	1	0.783492119863885	2		432	618	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591085	67591085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061064-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	263	479	0	ENST00000274335.5:c.1678G>A	p.Asp560Asn	p.D560N	ENST00000274335		560	Gac/Aac	12/15	1	2	FACETS	0.969	0.913	1	0.969	0.913	1	CLONAL	1	TRUE	1	0.783492119863885	2		479	693	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591260	67591303	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAGGTGTTCGGCAAAAGAAGTTGAACGAGTGGTTGGGCAATG	AAAAGGTGTTCGGCAAAAGAAGTTGAACGAGTGGTTGGGCAATG	-	novel	NA	P-0061064-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	154	532	0	ENST00000274335.5:c.1762_1805del	p.Gly588HisfsTer2	p.G588Hfs*2	ENST00000274335		586	caAAAAGGTGTTCGGCAAAAGAAGTTGAACGAGTGGTTGGGCAATGaa/caaa	13/15	1	2	FACETS	0.561	0.514	0.609	0.561	0.514	0.609	SUBCLONAL	1	TRUE	1	0.783492119863885	2		532	701	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406383	70406383	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149145995	NA	P-0061065-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	337	741	0	ENST00000373644.4:c.3897G>C	p.Leu1299Phe	p.L1299F	ENST00000373644	NM_030625.2	1299	ttG/ttC	4/12	1	2	FACETS	0.889	0.843	0.935	1	0.997	1	CLONAL	3	TRUE	1	0.274115738683099	2		741	922	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492324	56492324	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061065-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	2756	629	0	ENST00000267101.3:c.2657G>A	p.Gly886Glu	p.G886E	ENST00000267101	NM_001982.3	886	gGg/gAg	22/28	0.274115738683099	21	FACETS	0.987	0.976	0.997			1	CLONAL	21	TRUE	NA	0.274115738683099	21		629	3497	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0061066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	520	544	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.608744608775988	8	FACETS	0.959	0.928	0.99	0.959	0.928	0.99	CLONAL	6	TRUE	2	0.608744608775988	8		544	839	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945379	71945381	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	novel	NA	P-0061066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	197	661	0	ENST00000298229.2:c.2268_2270del	p.Ile756_Val757delinsMet	p.I756_V757delinsM	ENST00000298229	NM_001567.3	756	aTTGtg/atg	20/28	1	2	FACETS	0.96	0.893	1	0.96	0.893	1	CLONAL	1	TRUE	1	0.608744608775988	2		661	674	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431850	49431850	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	277	974	0	ENST00000301067.7:c.9289G>C	p.Glu3097Gln	p.E3097Q	ENST00000301067	NM_003482.3	3097	Gag/Cag	34/54	0.423545438691128	4	FACETS	1	0.987	1	0.595	0.558	0.633	CLONAL	1	TRUE	2	0.608744608775988	4		974	1230	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431898	49431898	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	283	966	0	ENST00000301067.7:c.9241G>C	p.Glu3081Gln	p.E3081Q	ENST00000301067	NM_003482.3	3081	Gaa/Caa	34/54	0.423545438691128	4	FACETS	1	0.985	1	0.572	0.536	0.608	CLONAL	1	TRUE	2	0.608744608775988	4		966	1308	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40364181	40364181	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0061066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	157	434	0	ENST00000293328.3:c.1501A>T	p.Lys501Ter	p.K501*	ENST00000293328	NM_012448.3	501	Aaa/Taa	13/19	0.105779159802638	6	FACETS	0.832	0.765	0.903	0.555	0.51	0.602	INDETERMINATE	2	TRUE	3	0.608744608775988	6		434	687	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031973	26031973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	285	808	0	ENST00000244661.2:c.316G>C	p.Glu106Gln	p.E106Q	ENST00000244661	NM_003537.3	106	Gag/Cag	1/1	0.586448763244589	2	FACETS	1	0.972	1	0.525	0.495	0.556	CLONAL	1	TRUE	0	0.608744608775988	2		808	891	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056515	26056515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs902939492	NA	P-0061066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	84	717	0	ENST00000343677.2:c.142G>A	p.Val48Met	p.V48M	ENST00000343677	NM_005319.3	48	Gtg/Atg	1/1	0.586448763244589	2	FACETS	0.356	0.314	0.401	0.178	0.157	0.201	SUBCLONAL	1	TRUE	0	0.608744608775988	2		717	776	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522536	157522536	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	274	863	0	ENST00000346085.5:c.4808G>C	p.Arg1603Thr	p.R1603T	ENST00000346085	NM_020732.3	1603	aGa/aCa	18/20	0.608744608775988	2	FACETS	1	0.947	1	0.503	0.473	0.534	CLONAL	1	TRUE	0	0.608744608775988	2		863	894	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864642	56864642	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061066-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	217	475	0	ENST00000519728.1:c.605C>A	p.Pro202His	p.P202H	ENST00000519728	NM_002350.3	202	cCc/cAc	7/13	0.57721307381079	3	FACETS	1	0.988	1	0.627	0.585	0.67	CLONAL	1	TRUE	1	0.608744608775988	3		475	742	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741796	40741796	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0061067-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	61	981	0	ENST00000392038.2:c.1175+1G>A		p.X392_splice	ENST00000392038	NM_001626.4	392			0.27950419554466	5	FACETS	0.843	0.728	0.967	0.281	0.242	0.323	INDETERMINATE	1	TRUE	2	0.532669002305147	5		981	489	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932819	39932819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764515953	NA	P-0061067-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	110	1248	0	ENST00000378444.4:c.1780G>A	p.Val594Ile	p.V594I	ENST00000378444	NM_001123385.1	594	Gtt/Att	4/15	0.31664172563054	4	FACETS	1	0.969	1	0.594	0.535	0.655	INDETERMINATE	1	TRUE	2	0.532669002305147	4		1248	533	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828126	243828126	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061068-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	118	262	0	ENST00000263826.5:c.232C>A	p.Gln78Lys	p.Q78K	ENST00000263826	NM_005465.4	78	Cag/Aag	3/13	NA	2	FACETS	0.511	0.463	0.561			1	INDETERMINATE	1	TRUE	NA	0.8911663427511	2		262	518	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696688	47696688	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519971	NA	P-0061068-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	771	605	0	ENST00000347630.2:c.260A>G	p.Tyr87Cys	p.Y87C	ENST00000347630	NM_001007230.1	87	tAc/tGc	5/11	0.8911663427511	3	FACETS	0.977	0.95	1	0.977	0.95	1	CLONAL	2	TRUE	1	0.8911663427511	3		605	1280	SUCCESS
APC	324	MSKCC	GRCh37	5	112111357	112111358	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061068-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	97	212	0	ENST00000257430.4:c.458dup	p.Glu154GlyfsTer14	p.E154Gfs*14	ENST00000257430	NM_000038.5	152	gaa/gAaa	5/16	0.8911663427511	1	FACETS	0.928	0.87	0.983	0.928	0.87	0.983	CLONAL	1	TRUE	0	0.8911663427511	1		212	130	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151776	108151777	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	C	novel	NA	P-0061068-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	233	324	0	ENST00000278616.4:c.3457_3458delinsC	p.Val1153LeufsTer3	p.V1153Lfs*3	ENST00000278616	NM_000051.3	1153	GTt/Ct	24/63	1	2	FACETS	0.916	0.861	0.971	0.916	0.861	0.971	CLONAL	1	TRUE	1	0.8911663427511	2		324	571	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1688724	1688724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1335212018	NA	P-0061071-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	27	462	0	ENST00000378625.1:c.601C>T	p.Arg201Trp	p.R201W	ENST00000378625	NM_001198994.1	201	Cgg/Tgg	6/14	1	2	FACETS	0.35	0.278	0.433	0.35	0.278	0.433	SUBCLONAL	1	TRUE	1	0.36	2		462	428	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579524	7579531	+	frameshift_variant	Frame_Shift_Del	DEL	TGAACCAT	TGAACCAT	-	novel	NA	P-0061071-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	154	630	0	ENST00000269305.4:c.156_163del	p.Gln52HisfsTer2	p.Q52Hfs*2	ENST00000269305	NM_001126112.2	52	caATGGTTCAct/cact	4/11	0.146051899788438	4	FACETS	0.998	0.918	1			1	INDETERMINATE	2	TRUE	NA	0.36	4		630	583	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186501416	186501416	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061071-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	19	346	0	ENST00000323963.5:c.17C>A	p.Ala6Glu	p.A6E	ENST00000323963		6	gCg/gAg	1/11	0.104356084161245	3	FACETS	0.341	0.258	0.439	0.171	0.129	0.22	INDETERMINATE	1	TRUE	1	0.36	3		346	365	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	8	321	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.472	0.305	0.685	0.472	0.305	0.685	SUBCLONAL	1	TRUE	1	0.29	2		321	117	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0061083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	7	0	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.3	3	FACETS	0.398	0.248	0.594	0.199	0.124	0.297	SUBCLONAL	1	TRUE	1	0.29	3		0	139	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549353	21549353	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753092502	NA	P-0061083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	38	558	1	ENST00000382592.4:c.2923G>A	p.Ala975Thr	p.A975T	ENST00000382592	NM_014572.2	975	Gcc/Acc	8/8	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.29	2		559	256	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692971	89692971	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1554898197	NA	P-0061083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	14	333	0	ENST00000371953.3:c.455T>C	p.Leu152Pro	p.L152P	ENST00000371953	NM_000314.4	152	cTa/cCa	5/9	0.3	1	FACETS	1	0.758	1	1	0.758	1	CLONAL	1	TRUE	0	0.29	1		333	80	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259588	16259588	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	35	536	0	ENST00000375759.3:c.6853C>G	p.Pro2285Ala	p.P2285A	ENST00000375759	NM_015001.2	2285	Cca/Gca	11/15	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.29	2		536	216	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562957	29562957	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	5	0	0	ENST00000356175.3:c.3892C>T	p.Gln1298Ter	p.Q1298*	ENST00000356175	NM_000267.3	1298	Caa/Taa	29/57	0.244275453793001	1	FACETS	0.339	0.192	0.541	0.339	0.192	0.541	SUBCLONAL	1	TRUE	0	0.29	1		0	87	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061083-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	57	321	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.912	0.792	1	0.912	0.792	1	CLONAL	1	TRUE	1	0.529513372484761	2		321	236	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0061083-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	47	0	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.529513372484761	3	FACETS	0.796	0.676	0.927	0.398	0.338	0.464	CLONAL	1	TRUE	1	0.529513372484761	3		0	282	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549353	21549353	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753092502	NA	P-0061083-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	117	558	1	ENST00000382592.4:c.2923G>A	p.Ala975Thr	p.A975T	ENST00000382592	NM_014572.2	975	Gcc/Acc	8/8	1	2	FACETS	0.94	0.853	1	0.94	0.853	1	CLONAL	1	TRUE	1	0.529513372484761	2		559	470	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692971	89692971	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1554898197	NA	P-0061083-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	59	333	0	ENST00000371953.3:c.455T>C	p.Leu152Pro	p.L152P	ENST00000371953	NM_000314.4	152	cTa/cCa	5/9	0.529513372484761	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.529513372484761	1		333	137	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259588	16259588	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061083-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	129	536	0	ENST00000375759.3:c.6853C>G	p.Pro2285Ala	p.P2285A	ENST00000375759	NM_015001.2	2285	Cca/Gca	11/15	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.529513372484761	2		536	476	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562957	29562957	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061083-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	48	0	0	ENST00000356175.3:c.3892C>T	p.Gln1298Ter	p.Q1298*	ENST00000356175	NM_000267.3	1298	Caa/Taa	29/57	0.529513372484761	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.529513372484761	1		0	125	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0061084-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	60	382	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.858	0.743	0.981	0.858	0.743	0.981	CLONAL	1	TRUE	1	0.399825356075269	2		382	350	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436026	56436026	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771831816	NA	P-0061084-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	137	626	0	ENST00000407977.2:c.1111C>T	p.Arg371Ter	p.R371*	ENST00000407977		371	Cga/Tga	9/10	0.199078741824151	2	FACETS	1	0.981	1	0.636	0.581	0.692	INDETERMINATE	1	TRUE	0	0.399825356075269	2		626	539	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840613	36840613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756710542	NA	P-0061084-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	47	421	0	ENST00000358127.4:c.1120G>A	p.Ala374Thr	p.A374T	ENST00000358127	NM_001280556.1	374	Gct/Act	10/10	1	2	FACETS	0.6	0.507	0.701	0.6	0.507	0.701	SUBCLONAL	1	TRUE	1	0.399825356075269	2		421	392	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415162	109415162	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768980649	NA	P-0061085-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	43	374	0	ENST00000436639.2:c.115C>T	p.Leu39Phe	p.L39F	ENST00000436639	NM_014454.2	39	Ctt/Ttt	1/10	1	2	FACETS	0.92	0.768	1	0.92	0.768	1	CLONAL	1	TRUE	1	0.14	2		374	668	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955538	48955538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913303	NA	P-0061086-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	174	233	0	ENST00000267163.4:c.1654C>T	p.Arg552Ter	p.R552*	ENST00000267163	NM_000321.2	552	Cga/Tga	17/27	0.448222400112198	3	FACETS	0.852	0.791	0.915	0.852	0.791	0.915	CLONAL	2	TRUE	1	0.509391321237688	3		233	503	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044416	5044416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147483622	NA	P-0061086-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	36	232	0	ENST00000381652.3:c.364C>T	p.Arg122Cys	p.R122C	ENST00000381652	NM_004972.3	122	Cgt/Tgt	5/25	0.240446183722475	5	FACETS	0.449	0.369	0.54	0.15	0.123	0.18	INDETERMINATE	1	TRUE	2	0.509391321237688	5		232	555	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061088-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	264	321	0				ENST00000310581	NM_198253.2	-/1132			0.767645841767125	5	FACETS	0.911	0.871	0.95	0.911	0.871	0.95	CLONAL	4	TRUE	1	0.767645841767125	5		321	406	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0061088-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	275	436	0	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	0.767645841767125	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.767645841767125	3		436	461	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133761036	133761036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1456042173	NA	P-0061088-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	131	583	0	ENST00000318560.5:c.3359C>T	p.Ser1120Leu	p.S1120L	ENST00000318560	NM_005157.4	1120	tCg/tTg	11/11	0.675914257975598	4	FACETS	0.975	0.887	1	0.487	0.443	0.533	CLONAL	1	TRUE	2	0.767645841767125	4		583	619	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332699	153332699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780061054	NA	P-0061088-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	500	579	0	ENST00000281708.4:c.257C>T	p.Ser86Leu	p.S86L	ENST00000281708	NM_033632.3	86	tCg/tTg	2/12	0.754201742341001	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	1	0.767645841767125	4		579	763	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030426	49030426	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061088-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	459	437	0	ENST00000267163.4:c.1901C>A	p.Ser634Ter	p.S634*	ENST00000267163	NM_000321.2	634	tCa/tAa	19/27	0.672301488329916	3	FACETS	1	0.993	1			1	CLONAL	3	TRUE	NA	0.767645841767125	3		437	530	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39708741	39708741	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061088-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	149	351	0	ENST00000361337.2:c.352G>C	p.Asp118His	p.D118H	ENST00000361337	NM_003286.2	118	Gat/Cat	6/21	0.675914257975598	4	FACETS	1	0.982	1	0.626	0.575	0.679	CLONAL	1	TRUE	2	0.767645841767125	4		351	548	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480341	56480341	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061088-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	275	443	0	ENST00000267101.3:c.448G>C	p.Glu150Gln	p.E150Q	ENST00000267101	NM_001982.3	150	Gag/Cag	4/28	0.767645841767125	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.767645841767125	3		443	457	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984408	201984408	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0061088-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	930	526	0	ENST00000359651.3:c.1073C>G	p.Ser358Ter	p.S358*	ENST00000359651		358	tCa/tGa	8/8	0.767645841767125	5	FACETS	1	0.998	1	1	0.998	1	CLONAL	5	TRUE	0	0.767645841767125	5		526	996	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026622	6026622	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061088-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	180	537	0	ENST00000265849.7:c.1774C>G	p.Gln592Glu	p.Q592E	ENST00000265849	NM_000535.5	592	Caa/Gaa	11/15	0.751909868719697	3	FACETS	0.976	0.903	1	0.488	0.451	0.526	CLONAL	1	TRUE	1	0.767645841767125	3		537	665	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132787	152132787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061088-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	98	419	0	ENST00000262189.6:c.85C>T	p.Pro29Ser	p.P29S	ENST00000262189	NM_170606.2	29	Ccc/Tcc	1/59	0.751909868719697	3	FACETS	1	0.906	1	0.503	0.453	0.556	CLONAL	1	TRUE	1	0.767645841767125	3		419	351	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039462	49039462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061088-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	420	460	0	ENST00000267163.4:c.2447C>T	p.Ser816Leu	p.S816L	ENST00000267163	NM_000321.2	816	tCa/tTa	23/27	0.672301488329916	3	FACETS	0.984	0.959	1			1	CLONAL	3	TRUE	NA	0.767645841767125	3		460	513	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366970	40366970	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369326949	NA	P-0061088-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	135	763	0	ENST00000397332.2:c.227G>A	p.Gly76Asp	p.G76D	ENST00000397332	NM_001033082.2	76	gGc/gAc	2/3	0.571043359156096	6	FACETS	0.823	0.747	0.904			1	CLONAL	1	TRUE	NA	0.767645841767125	6		763	1083	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223125	5223125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748343733	NA	P-0061088-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	158	743	0	ENST00000357368.4:c.2678C>T	p.Ser893Leu	p.S893L	ENST00000357368	NM_002850.3	893	tCa/tTa	18/38	0.767645841767125	3	FACETS	1	0.97	1	0.551	0.508	0.595	CLONAL	1	TRUE	1	0.767645841767125	3		743	517	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92252372	92252372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061088-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	96	304	0	ENST00000265734.4:c.676G>A	p.Asp226Asn	p.D226N	ENST00000265734	NM_001259.6	226	Gat/Aat	6/8	0.751909868719697	3	FACETS	0.983	0.884	1	0.492	0.442	0.544	CLONAL	1	TRUE	1	0.767645841767125	3		304	352	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	84	321	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.968	0.87	1	0.968	0.87	1	CLONAL	1	TRUE	1	0.761186128928628	2		321	228	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0061089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	336	677	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.682785548110325	4	FACETS	0.979	0.931	1	0.653	0.621	0.685	CLONAL	2	TRUE	1	0.761186128928628	4		677	794	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0061089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	113	476	10	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.958	0.874	1	0.958	0.874	1	CLONAL	1	TRUE	1	0.761186128928628	2		486	310	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0061089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	157	305	0	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.927	0.857	0.998	0.927	0.857	0.998	CLONAL	1	TRUE	1	0.761186128928628	2		305	445	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781419	135781419	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	168	546	0	ENST00000298552.3:c.1546C>T	p.Gln516Ter	p.Q516*	ENST00000298552	NM_001162426.1	516	Cag/Tag	15/23	0.761186128928628	1	FACETS	0.97	0.913	1	0.97	0.913	1	CLONAL	1	TRUE	0	0.761186128928628	1		546	282	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308382	15308383	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs749829137	NA	P-0061089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	132	635	2	ENST00000263388.2:c.125dup	p.Cys43LeufsTer32	p.C43Lfs*32	ENST00000263388	NM_000435.2	42	cct/ccCt	2/33	1	2	FACETS	0.704	0.642	0.767	0.704	0.642	0.767	SUBCLONAL	1	TRUE	1	0.761186128928628	2		637	493	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484345	8484347	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1282828198	NA	P-0061089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	88	369	0	ENST00000356435.5:c.3185_3187del	p.Glu1062del	p.E1062del	ENST00000356435		1062	gAAGtg/gtg	19/35	0.761186128928628	1	FACETS	0.89	0.814	0.965	0.89	0.814	0.965	CLONAL	1	TRUE	0	0.761186128928628	1		369	161	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402737	20402737	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	138	585	0	ENST00000346618.3:c.274G>C	p.Glu92Gln	p.E92Q	ENST00000346618	NM_001949.4	92	Gag/Cag	1/7	1	2	FACETS	0.944	0.869	1	0.944	0.869	1	CLONAL	1	TRUE	1	0.761186128928628	2		585	384	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262117	10262119	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0061089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	179	556	1	ENST00000340748.4:c.2172_2174del	p.Lys725del	p.K725del	ENST00000340748		724	aaGAAa/aaa	23/40	1	2	FACETS	0.994	0.926	1	0.994	0.926	1	CLONAL	1	TRUE	1	0.761186128928628	2		557	473	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78931424	78931424	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	229	542	0	ENST00000306801.3:c.3371G>C	p.Gly1124Ala	p.G1124A	ENST00000306801	NM_020761.2	1124	gGa/gCa	29/34	0.539760604654502	4	FACETS	0.788	0.739	0.839	0.526	0.492	0.56	SUBCLONAL	2	TRUE	1	0.761186128928628	4		542	672	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572904	41572904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	219	625	0	ENST00000263253.7:c.5189C>T	p.Ser1730Phe	p.S1730F	ENST00000263253	NM_001429.3	1730	tCt/tTt	31/31	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.761186128928628	2		625	540	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37091976	37091976	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0061089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	148	428	0	ENST00000231790.2:c.2104-1G>C		p.X702_splice	ENST00000231790	NM_000249.3	702			0.761186128928628	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.761186128928628	1		428	224	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469956	157469956	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	165	642	0	ENST00000346085.5:c.2754del	p.Ser919ValfsTer20	p.S919Vfs*20	ENST00000346085	NM_020732.3	917	aCc/ac	9/20	1	2	FACETS	0.888	0.822	0.956	0.888	0.822	0.956	CLONAL	1	TRUE	1	0.761186128928628	2		642	488	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741780	17741780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	124	566	0	ENST00000250003.3:c.451C>T	p.Arg151Cys	p.R151C	ENST00000250003	NM_002478.4	151	Cgc/Tgc	1/3	0.761186128928628	1	FACETS	0.97	0.904	1	0.97	0.904	1	CLONAL	1	TRUE	0	0.761186128928628	1		566	208	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786206	3786206	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0061089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	133	420	0	ENST00000262367.5:c.4561-2A>G		p.X1521_splice	ENST00000262367	NM_004380.2	1521			1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.761186128928628	2		420	344	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129350	64129350	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	85	599	0	ENST00000334205.4:c.782T>C	p.Phe261Ser	p.F261S	ENST00000334205	NM_003942.2	261	tTc/tCc	8/17	1	2	FACETS	0.604	0.537	0.673	0.604	0.537	0.673	SUBCLONAL	1	TRUE	1	0.761186128928628	2		599	370	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955118	17955118	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs955716335	NA	P-0061089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	136	520	0	ENST00000458235.1:c.109C>G	p.Pro37Ala	p.P37A	ENST00000458235	NM_000215.3	37	Ccc/Gcc	2/24	1	2	FACETS	0.945	0.869	1	0.945	0.869	1	CLONAL	1	TRUE	1	0.761186128928628	2		520	378	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124454	94124457	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	novel	NA	P-0061089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	59	362	0	ENST00000369303.4:c.126_129del	p.Thr43SerfsTer57	p.T43Sfs*57	ENST00000369303	NM_004440.3	42	caAACA/ca	2/17	1	2	FACETS	0.825	0.722	0.932	0.825	0.722	0.932	CLONAL	1	TRUE	1	0.761186128928628	2		362	188	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136346	202136346	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1244888701	NA	P-0061089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	203	402	0	ENST00000358485.4:c.588+2T>C		p.X196_splice	ENST00000358485	NM_001080125.1	196			1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.761186128928628	2		402	430	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162722980	162722980	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	131	434	0	ENST00000367921.3:c.178T>C	p.Tyr60His	p.Y60H	ENST00000367921	NM_006182.2	60	Tat/Cat	4/18	1	2	FACETS	0.97	0.891	1	0.97	0.891	1	CLONAL	1	TRUE	1	0.761186128928628	2		434	355	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607648	43607648	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	259	1043	1	ENST00000355710.3:c.1624G>C	p.Glu542Gln	p.E542Q	ENST00000355710	NM_020975.4	542	Gag/Cag	8/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.761186128928628	2		1044	634	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10789540	10789540	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0061089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	186	510	0	ENST00000361367.2:c.1872+2T>C		p.X624_splice	ENST00000361367	NM_014633.3	624			0.761186128928628	1	FACETS	0.999	0.944	1	0.999	0.944	1	CLONAL	1	TRUE	0	0.761186128928628	1		510	303	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885611	111885611	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	172	565	0	ENST00000341259.2:c.1388T>C	p.Val463Ala	p.V463A	ENST00000341259	NM_005475.2	463	gTa/gCa	7/8	0.761186128928628	2	FACETS	0.945	0.878	1	0.473	0.439	0.508	CLONAL	1	TRUE	0	0.761186128928628	2		565	478	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911357	32911358	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	128	440	0	ENST00000380152.3:c.2870dup	p.Asn957LysfsTer2	p.N957Kfs*2	ENST00000380152		955	-/A	11/27	1	2	FACETS	0.929	0.852	1	0.929	0.852	1	CLONAL	1	TRUE	1	0.761186128928628	2		440	362	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33430338	33430338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28363282	NA	P-0061089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	166	639	0	ENST00000345365.6:c.673G>A	p.Ala225Thr	p.A225T	ENST00000345365	NM_002878.3	225	Gcc/Acc	8/10	1	2	FACETS	0.885	0.819	0.952	0.885	0.819	0.952	CLONAL	1	TRUE	1	0.761186128928628	2		639	493	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876495	59876495	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	146	390	0	ENST00000259008.2:c.1306G>C	p.Glu436Gln	p.E436Q	ENST00000259008	NM_032043.2	436	Gaa/Caa	9/20	0.539760604654502	4	FACETS	1	0.975	1	0.389	0.356	0.423	CLONAL	1	TRUE	1	0.761186128928628	4		390	579	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621869	1621869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1477354195	NA	P-0061089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	167	628	0	ENST00000344749.5:c.923C>T	p.Thr308Met	p.T308M	ENST00000344749	NM_001136139.2	308	aCg/aTg	11/19	1	2	FACETS	0.99	0.919	1	0.99	0.919	1	CLONAL	1	TRUE	1	0.761186128928628	2		628	443	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244296	5244296	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	163	721	0	ENST00000357368.4:c.1186T>C	p.Ser396Pro	p.S396P	ENST00000357368	NM_002850.3	396	Tcg/Ccg	11/38	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.761186128928628	2		721	408	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732741	204732741	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	36	459	0	ENST00000302823.3:c.81del	p.Leu28PhefsTer44	p.L28Ffs*44	ENST00000302823	NM_005214.4	26	Ttt/tt	1/4	1	2	FACETS	0.172	0.141	0.207	0.172	0.141	0.207	SUBCLONAL	1	TRUE	1	0.761186128928628	2		459	551	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572294	41572294	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	139	578	0	ENST00000263253.7:c.4823C>A	p.Ser1608Tyr	p.S1608Y	ENST00000263253	NM_001429.3	1608	tCc/tAc	30/31	1	2	FACETS	0.845	0.776	0.916	0.845	0.776	0.916	CLONAL	1	TRUE	1	0.761186128928628	2		578	432	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572976	41572976	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	169	659	0	ENST00000263253.7:c.5261C>T	p.Ser1754Leu	p.S1754L	ENST00000263253	NM_001429.3	1754	tCa/tTa	31/31	1	2	FACETS	0.904	0.838	0.972	0.904	0.838	0.972	CLONAL	1	TRUE	1	0.761186128928628	2		659	491	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545716	106545716	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	74	481	0	ENST00000359195.3:c.3197del	p.Lys1066SerfsTer42	p.K1066Sfs*42	ENST00000359195	NM_002649.2	1065	Aaa/aa	11/11	1	2	FACETS	0.567	0.5	0.638	0.567	0.5	0.638	SUBCLONAL	1	TRUE	1	0.761186128928628	2		481	343	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061090-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	121	321	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.771	0.7	0.844	0.771	0.7	0.844	SUBCLONAL	1	TRUE	1	0.651481502130025	2		321	482	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0061090-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	58	544	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.813	0.708	0.924	0.813	0.708	0.924	CLONAL	1	TRUE	1	0.651481502130025	2		544	219	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098957	178098957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061090-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	9	368	0	ENST00000397062.3:c.88C>T	p.Leu30Phe	p.L30F	ENST00000397062	NM_006164.4	30	Ctt/Ttt	2/5	1	2	FACETS	0.065	0.043	0.094	0.065	0.043	0.094	SUBCLONAL	1	TRUE	1	0.651481502130025	2		368	423	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336064	73336064	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061090-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	135	406	0	ENST00000377767.4:c.2339G>C	p.Arg780Thr	p.R780T	ENST00000377767	NM_014953.3	780	aGa/aCa	17/21	1	2	FACETS	0.975	0.894	1	0.975	0.894	1	CLONAL	1	TRUE	1	0.651481502130025	2		406	425	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149961	202149962	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs587776665	NA	P-0061090-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	228	533	0	ENST00000358485.4:c.1405_1406del	p.Val469PhefsTer28	p.V469Ffs*28	ENST00000358485	NM_001080125.1	468	TGt/t	8/9	1	2	FACETS	0.996	0.932	1	0.996	0.932	1	CLONAL	1	TRUE	1	0.651481502130025	2		533	703	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413070	63413070	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061090-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	194	504	0	ENST00000330258.3:c.97G>A	p.Ala33Thr	p.A33T	ENST00000330258	NM_152424.3	33	Gca/Aca	2/2	1	2	FACETS	0.916	0.852	0.982	0.916	0.852	0.982	CLONAL	1	TRUE	1	0.651481502130025	2		504	650	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413009	49413009	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519953	NA	P-0061090-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	131	384	0	ENST00000418115.1:c.14G>T	p.Arg5Leu	p.R5L	ENST00000418115	NM_001664.2	5	cGg/cTg	2/5	1	2	FACETS	0.908	0.83	0.988	0.908	0.83	0.988	CLONAL	1	TRUE	1	0.651481502130025	2		384	443	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323253	31323253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45445194	NA	P-0061090-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	176	345	0	ENST00000412585.2:c.736G>A	p.Glu246Lys	p.E246K	ENST00000412585	NM_005514.6	246	Gag/Aag	4/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.651481502130025	2		345	496	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894230	NA	P-0061090-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	225	452	0	ENST00000451590.1:c.35G>A	p.Gly12Asp	p.G12D	ENST00000451590	NM_001130442.1	12	gGc/gAc	2/5	1	2	FACETS	0.978	0.915	1	0.978	0.915	1	CLONAL	1	TRUE	1	0.651481502130025	2		452	706	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462205	120462211	+	frameshift_variant	Frame_Shift_Del	DEL	GAGAGAA	GAGAGAA	-	novel	NA	P-0061090-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	172	461	0	ENST00000256646.2:c.5505_5511del	p.Ser1836GlufsTer7	p.S1836Efs*7	ENST00000256646	NM_024408.3	1835	gcTTCTCTC/gc	31/34	1	2	FACETS	0.901	0.834	0.971	0.901	0.834	0.971	CLONAL	1	TRUE	1	0.651481502130025	2		461	586	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120469225	120469225	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061090-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	172	412	0	ENST00000256646.2:c.3902G>T	p.Cys1301Phe	p.C1301F	ENST00000256646	NM_024408.3	1301	tGt/tTt	24/34	1	2	FACETS	0.833	0.77	0.898	0.833	0.77	0.898	CLONAL	1	TRUE	1	0.651481502130025	2		412	634	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924376	112924376	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061090-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	69	433	0	ENST00000351677.2:c.1322A>T	p.Glu441Val	p.E441V	ENST00000351677	NM_002834.3	441	gAg/gTg	11/16	1	2	FACETS	0.311	0.27	0.354	0.311	0.27	0.354	SUBCLONAL	1	TRUE	1	0.651481502130025	2		433	682	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918698	32918698	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061090-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	10	208	0	ENST00000380152.3:c.6845A>G	p.Glu2282Gly	p.E2282G	ENST00000380152		2282	gAa/gGa	12/27	1	2	FACETS	0.176	0.119	0.248	0.176	0.119	0.248	SUBCLONAL	1	TRUE	1	0.651481502130025	2		208	174	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525110	187525110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061090-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	119	364	0	ENST00000441802.2:c.10570C>T	p.Gln3524Ter	p.Q3524*	ENST00000441802	NM_005245.3	3524	Cag/Tag	19/27	1	2	FACETS	0.81	0.736	0.887	0.81	0.736	0.887	CLONAL	1	TRUE	1	0.651481502130025	2		364	451	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323238	31323238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061090-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	211	436	0	ENST00000412585.2:c.751G>A	p.Asp251Asn	p.D251N	ENST00000412585	NM_005514.6	251	Gac/Aac	4/8	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.651481502130025	2		436	622	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061101-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	95	377	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.254279220243521	4	FACETS	1	0.972	1			1	CLONAL	1	TRUE	NA	0.29	4		377	657	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534226	534226	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061103-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	57	522	0	ENST00000451590.1:c.97G>T	p.Asp33Tyr	p.D33Y	ENST00000451590	NM_001130442.1	33	Gac/Tac	2/5	1	2	FACETS	0.86	0.744	0.985	0.86	0.744	0.985	CLONAL	1	TRUE	1	0.463515170055561	2		522	286	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56787276	56787276	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061103-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	67	354	0	ENST00000337432.4:c.762C>G	p.Asp254Glu	p.D254E	ENST00000337432	NM_058216.2	254	gaC/gaG	5/9	0.457625998213257	3	FACETS	1	0.91	1	0.525	0.459	0.596	CLONAL	1	TRUE	1	0.463515170055561	3		354	339	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144380555	144380555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061103-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	52	373	0	ENST00000262995.4:c.1693G>A	p.Glu565Lys	p.E565K	ENST00000262995	NM_207123.2	565	Gaa/Aaa	8/11	1	2	FACETS	0.87	0.747	1	0.87	0.747	1	CLONAL	1	TRUE	1	0.463515170055561	2		373	258	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0061104-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	28	286	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.973	0.777	1	0.973	0.777	1	CLONAL	1	TRUE	1	0.14	2		286	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579399	+	frameshift_variant	Frame_Shift_Del	DEL	GGAAACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGGACA	GGAAACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGGACA	-	novel	NA	P-0061104-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	42	632	0	ENST00000269305.4:c.288_328del	p.Val97SerfsTer38	p.V97Sfs*38	ENST00000269305	NM_001126112.2	96	tcTGTCCCTTCCCAGAAAACCTACCAGGGCAGCTACGGTTTCCgt/tcgt	4/11	1	2	FACETS	0.717	0.596	0.851	0.717	0.596	0.851	SUBCLONAL	1	TRUE	1	0.14	2		632	837	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0061105-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	490	769	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.909376462292212	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.909376462292212	1		770	566	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572311	41572311	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061105-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	419	624	0	ENST00000263253.7:c.4840G>A	p.Asp1614Asn	p.D1614N	ENST00000263253	NM_001429.3	1614	Gat/Aat	30/31	1	2	FACETS	0.928	0.887	0.969	0.928	0.887	0.969	CLONAL	1	TRUE	1	0.909376462292212	2		624	993	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0061105-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	112	240	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.29457718214089	6	FACETS	1	0.976	1	0.212	0.191	0.234	INDETERMINATE	1	TRUE	0	0.909376462292212	6		240	546	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739909	41739909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061105-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	440	470	0	ENST00000242208.4:c.64C>T	p.Pro22Ser	p.P22S	ENST00000242208	NM_002192.2	22	Ccc/Tcc	2/3	0.526442560889538	3	FACETS	1	0.994	1	0.628	0.601	0.657	INDETERMINATE	1	TRUE	1	0.909376462292212	3		470	1120	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352342	73352342	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061105-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	315	388	0	ENST00000377767.4:c.563G>T	p.Gly188Val	p.G188V	ENST00000377767	NM_014953.3	188	gGa/gTa	3/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.909376462292212	2		388	679	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495050	56495050	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758743468	NA	P-0061105-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	544	645	0	ENST00000267101.3:c.3407G>A	p.Arg1136His	p.R1136H	ENST00000267101	NM_001982.3	1136	cGc/cAc	27/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.909376462292212	2		645	1165	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214792	36214792	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061105-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	403	503	0	ENST00000222270.7:c.3218G>A	p.Arg1073His	p.R1073H	ENST00000222270	NM_014727.1	1073	cGc/cAc	8/37	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.909376462292212	2		503	855	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948284	71948284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs569099732	NA	P-0061105-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	225	615	0	ENST00000298229.2:c.2996C>T	p.Pro999Leu	p.P999L	ENST00000298229	NM_001567.3	999	cCg/cTg	26/28	0.518773186430641	1	FACETS	0.322	0.3	0.344	0.322	0.3	0.344	INDETERMINATE	1	TRUE	0	0.909376462292212	1		615	839	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860377	42860377	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061105-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	439	487	1	ENST00000398585.3:c.500C>G	p.Ser167Cys	p.S167C	ENST00000398585	NM_001135099.1	167	tCt/tGt	5/14	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.909376462292212	2		488	923	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209101872	209101872	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061105-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	277	369	0	ENST00000345146.2:c.1176G>C	p.Leu392Phe	p.L392F	ENST00000345146	NM_005896.2	392	ttG/ttC	10/10	1	2	FACETS	0.953	0.902	1	0.953	0.902	1	CLONAL	1	TRUE	1	0.909376462292212	2		369	639	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261277	16261277	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061105-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	432	642	0	ENST00000375759.3:c.8542C>T	p.Gln2848Ter	p.Q2848*	ENST00000375759	NM_015001.2	2848	Cag/Tag	11/15	0.863596471483515	3	FACETS	0.906	0.863	0.951	0.453	0.431	0.476	CLONAL	1	TRUE	1	0.909376462292212	3		642	1525	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097729	27097729	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061105-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	486	523	0	ENST00000324856.7:c.3318G>C	p.Lys1106Asn	p.K1106N	ENST00000324856	NM_006015.4	1106	aaG/aaC	12/20	0.863596471483515	3	FACETS	1	0.988	1	0.545	0.521	0.569	CLONAL	1	TRUE	1	0.909376462292212	3		523	1426	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230492944	230492944	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769792238	NA	P-0061105-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	468	583	0	ENST00000391860.1:c.110G>A	p.Arg37Gln	p.R37Q	ENST00000391860	NM_001258311.1	37	cGg/cAg	2/7	0.863596471483515	3	FACETS	1	0.982	1	0.525	0.502	0.549	CLONAL	1	TRUE	1	0.909376462292212	3		583	1425	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977167	85977167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061105-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	189	223	0	ENST00000263360.6:c.769G>A	p.Asp257Asn	p.D257N	ENST00000263360	NM_003797.3	257	Gat/Aat	8/12	0.909376462292212	1	FACETS	0.999	0.961	1	0.999	0.961	1	CLONAL	1	TRUE	0	0.909376462292212	1		223	227	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40998477	40998477	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061105-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	261	284	0	ENST00000267868.3:c.328G>C	p.Asp110His	p.D110H	ENST00000267868	NM_002875.4	110	Gac/Cac	4/10	1	2	FACETS	0.98	0.926	1	0.98	0.926	1	CLONAL	1	TRUE	1	0.909376462292212	2		284	586	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003132	42003132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061105-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	403	507	0	ENST00000219905.7:c.2669C>T	p.Ser890Phe	p.S890F	ENST00000219905	NM_001164273.1	890	tCt/tTt	8/24	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.909376462292212	2		507	826	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250964	99250964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061105-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	940	574	1	ENST00000268035.6:c.268G>A	p.Val90Met	p.V90M	ENST00000268035	NM_000875.3	90	Gtg/Atg	2/21	0.863596471483515	3	FACETS	0.994	0.97	1	0.994	0.97	1	CLONAL	2	TRUE	1	0.909376462292212	3		575	1512	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654692	67654692	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061105-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	365	422	0	ENST00000264010.4:c.1179G>C	p.Lys393Asn	p.K393N	ENST00000264010	NM_006565.3	393	aaG/aaC	6/12	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.909376462292212	2		422	777	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862145	68862145	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061105-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	438	498	0	ENST00000261769.5:c.2233G>T	p.Glu745Ter	p.E745*	ENST00000261769	NM_004360.3	745	Gag/Tag	14/16	1	2	FACETS	0.987	0.945	1	0.987	0.945	1	CLONAL	1	TRUE	1	0.909376462292212	2		498	976	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10284551	10284551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061105-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	236	300	0	ENST00000340748.4:c.631G>A	p.Glu211Lys	p.E211K	ENST00000340748		211	Gaa/Aaa	7/40	1	2	FACETS	0.944	0.889	0.999	0.944	0.889	0.999	CLONAL	1	TRUE	1	0.909376462292212	2		300	550	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141463	11141463	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061105-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	479	623	0	ENST00000358026.2:c.3440C>G	p.Ser1147Cys	p.S1147C	ENST00000358026	NM_001128849.1	1147	tCt/tGt	25/36	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.909376462292212	2		623	1007	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39239409	39239409	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061105-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	271	338	0	ENST00000402219.2:c.2248C>T	p.His750Tyr	p.H750Y	ENST00000402219	NM_005633.3	750	Cat/Tat	14/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.909376462292212	2		338	574	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662261	227662269	+	inframe_deletion	In_Frame_Del	DEL	ACTGGTGCT	ACTGGTGCT	-	novel	NA	P-0061105-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	473	723	0	ENST00000305123.5:c.1186_1194del	p.Ser396_Ser398del	p.S396_S398del	ENST00000305123	NM_005544.2	396	AGCACCAGT/-	1/2	1	2	FACETS	0.926	0.887	0.964	0.926	0.887	0.964	CLONAL	1	TRUE	1	0.909376462292212	2		723	1124	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205871	128205871	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061105-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	179	501	0	ENST00000341105.2:c.4G>C	p.Glu2Gln	p.E2Q	ENST00000341105	NM_032638.4	2	Gag/Cag	2/6	0.409096318577862	3	FACETS	0.624	0.575	0.675	0.208	0.191	0.225	INDETERMINATE	1	TRUE	0	0.909376462292212	3		501	918	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2972215	2972215	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061105-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	332	346	0	ENST00000396946.4:c.1524G>C	p.Gln508His	p.Q508H	ENST00000396946	NM_032415.4	508	caG/caC	11/25	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.909376462292212	2		346	690	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945406	151945406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061105-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	245	290	0	ENST00000262189.6:c.2113G>A	p.Glu705Lys	p.E705K	ENST00000262189	NM_170606.2	705	Gaa/Aaa	14/59	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.909376462292212	2		290	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0061106-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	478	817	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.689262498843343	6	FACETS	1	0.996	1			1	CLONAL	5	TRUE	NA	0.849923858397495	6		817	553	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2180724	2180724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061106-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	137	231	0	ENST00000398665.3:c.94G>A	p.Asp32Asn	p.D32N	ENST00000398665	NM_032482.2	32	Gat/Aat	2/28	0.51419547922473	4	FACETS	0.842	0.776	0.91			1	CLONAL	2	TRUE	NA	0.849923858397495	4		231	354	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446250	29446250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061106-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	137	570	1	ENST00000389048.3:c.3317G>A	p.Ser1106Asn	p.S1106N	ENST00000389048	NM_004304.4	1106	aGt/aAt	20/29	0.541259370182872	2	FACETS	1	0.98	1	0.584	0.542	0.626	CLONAL	1	TRUE	0	0.849923858397495	2		571	276	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	142	377	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.171793633606895	3	FACETS	0.805	0.74	0.872	0.537	0.493	0.582	INDETERMINATE	2	TRUE	0	0.495718845589286	3		377	444	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0061107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	191	304	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.495718845589286	2		304	748	SUCCESS
APC	324	MSKCC	GRCh37	5	112174096	112174096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs137854575	NA	P-0061107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	148	280	0	ENST00000257430.4:c.2805C>A	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	taC/taA	16/16	0.495718845589286	3	FACETS	0.973	0.89	1	0.486	0.445	0.53	CLONAL	1	TRUE	1	0.495718845589286	3		280	766	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587777893	NA	P-0061107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	259	571	0	ENST00000361445.4:c.5930C>A	p.Thr1977Lys	p.T1977K	ENST00000361445	NM_004958.3	1977	aCa/aAa	43/58	0.495718845589286	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.495718845589286	1		571	725	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375038	45375041	+	frameshift_variant	Frame_Shift_Del	DEL	AGTA	AGTA	-	novel	NA	P-0061107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	138	442	0	ENST00000262160.6:c.802_805del	p.Tyr268GlnfsTer9	p.Y268Qfs*9	ENST00000262160	NM_005901.5	268	TACTca/ca	8/11	0.495718845589286	1	FACETS	0.876	0.803	0.952	0.876	0.803	0.952	CLONAL	1	TRUE	0	0.495718845589286	1		442	478	SUCCESS
APC	324	MSKCC	GRCh37	5	112175776	112175776	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	420	544	0	ENST00000257430.4:c.4485del	p.Ser1495ArgfsTer12	p.S1495Rfs*12	ENST00000257430	NM_000038.5	1495	agT/ag	16/16	0.495718845589286	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.495718845589286	3		544	1049	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729864	41729864	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	209	629	0	ENST00000242208.4:c.665C>T	p.Pro222Leu	p.P222L	ENST00000242208	NM_002192.2	222	cCt/cTt	3/3	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.495718845589286	2		629	800	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	122	544	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.891647024086702	3	FACETS	1	0.942	1	0.521	0.475	0.567	CLONAL	1	TRUE	1	0.891647024086702	3		544	380	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	299	399	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	0.876058275572353	2	FACETS	0.803	0.759	0.848	0.402	0.379	0.424	CLONAL	1	TRUE	0	0.891647024086702	2		399	835	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319420	11319420	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	470	646	0	ENST00000361445.4:c.47C>G	p.Ser16Cys	p.S16C	ENST00000361445	NM_004958.3	16	tCt/tGt	2/58	0.828547844113382	3	FACETS	0.971	0.927	1	0.486	0.463	0.508	CLONAL	1	TRUE	1	0.891647024086702	3		646	1569	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094480	27094480	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	388	602	0	ENST00000324856.7:c.3188G>C	p.Gly1063Ala	p.G1063A	ENST00000324856	NM_006015.4	1063	gGa/gCa	11/20	0.891647024086702	3	FACETS	0.991	0.941	1	0.495	0.47	0.521	CLONAL	1	TRUE	1	0.891647024086702	3		602	1270	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36826858	36826858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	341	515	0	ENST00000373129.3:c.76G>A	p.Gly26Arg	p.G26R	ENST00000373129	NM_032017.1	26	Gga/Aga	3/12	1	2	FACETS	0.932	0.886	0.978	0.932	0.886	0.978	CLONAL	1	TRUE	1	0.891647024086702	2		515	821	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162688904	162688904	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	252	385	0	ENST00000367921.3:c.51C>G	p.Ile17Met	p.I17M	ENST00000367921	NM_006182.2	17	atC/atG	3/18	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.891647024086702	2		385	539	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021924	246021924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	301	458	0	ENST00000388985.4:c.950C>T	p.Ser317Phe	p.S317F	ENST00000388985		317	tCt/tTt	10/12	1	2	FACETS	0.973	0.923	1	0.973	0.923	1	CLONAL	1	TRUE	1	0.891647024086702	2		458	694	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450742	70450742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	466	700	0	ENST00000373644.4:c.5582C>T	p.Pro1861Leu	p.P1861L	ENST00000373644	NM_030625.2	1861	cCa/cTa	12/12	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.891647024086702	2		700	1039	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514125	69514125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	60	688	0	ENST00000294312.3:c.556G>A	p.Asp186Asn	p.D186N	ENST00000294312	NM_005117.2	186	Gac/Aac	3/3	1	2	FACETS	0.157	0.135	0.182	0.157	0.135	0.182	SUBCLONAL	1	TRUE	1	0.891647024086702	2		688	856	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77048410	77048410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	238	474	0	ENST00000356341.3:c.1175G>A	p.Ser392Asn	p.S392N	ENST00000356341	NM_002576.4	392	aGt/aAt	12/15	1	2	FACETS	0.885	0.833	0.939	0.885	0.833	0.939	CLONAL	1	TRUE	1	0.891647024086702	2		474	603	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375734	118375735	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	399	715	0	ENST00000534358.1:c.9127_9128delinsTT	p.Pro3043Phe	p.P3043F	ENST00000534358	NM_005933.3	3043	CCc/TTc	27/36	1	2	FACETS	0.973	0.929	1	0.973	0.929	1	CLONAL	1	TRUE	1	0.891647024086702	2		715	920	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156272	119156272	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	267	451	0	ENST00000264033.4:c.1937C>T	p.Ser646Phe	p.S646F	ENST00000264033	NM_005188.3	646	tCc/tTc	11/16	1	2	FACETS	0.852	0.803	0.901	0.852	0.803	0.901	CLONAL	1	TRUE	1	0.891647024086702	2		451	703	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231490	46231491	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	156	373	0	ENST00000334344.6:c.1330_1330+1delinsAA		p.X444_splice	ENST00000334344	NM_152641.2	444		10/21	1	2	FACETS	0.862	0.798	0.927	0.862	0.798	0.927	CLONAL	1	TRUE	1	0.891647024086702	2		373	406	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490543	56490544	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	283	506	0	ENST00000267101.3:c.2187_2188delinsTT	p.Pro730Ser	p.P730S	ENST00000267101	NM_001982.3	729	atCCct/atTTct	19/28	1	2	FACETS	0.953	0.902	1	0.953	0.902	1	CLONAL	1	TRUE	1	0.891647024086702	2		506	666	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864841	57864841	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	404	806	0	ENST00000228682.2:c.2318C>T	p.Pro773Leu	p.P773L	ENST00000228682	NM_005269.2	773	cCt/cTt	12/12	1	2	FACETS	0.93	0.888	0.973	0.93	0.888	0.973	CLONAL	1	TRUE	1	0.891647024086702	2		806	974	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222628	69222628	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763423670	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	210	477	0	ENST00000462284.1:c.601G>A	p.Glu201Lys	p.E201K	ENST00000462284	NM_002392.5	201	Gaa/Aaa	8/11	1	2	FACETS	0.892	0.836	0.949	0.892	0.836	0.949	CLONAL	1	TRUE	1	0.891647024086702	2		477	528	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256560	133256560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500817	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	278	512	0	ENST00000320574.5:c.403C>T	p.Pro135Ser	p.P135S	ENST00000320574	NM_006231.2	135	Ccc/Tcc	5/49	1	2	FACETS	0.936	0.886	0.987	0.936	0.886	0.987	CLONAL	1	TRUE	1	0.891647024086702	2		512	666	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953629	32953629	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	168	463	0	ENST00000380152.3:c.8930A>G	p.Tyr2977Cys	p.Y2977C	ENST00000380152		2977	tAt/tGt	22/27	1	2	FACETS	0.883	0.82	0.946	0.883	0.82	0.946	CLONAL	1	TRUE	1	0.891647024086702	2		463	427	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954326	48954326	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	124	243	0	ENST00000267163.4:c.1447C>T	p.His483Tyr	p.H483Y	ENST00000267163	NM_000321.2	483	Cat/Tat	16/27	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.891647024086702	2		243	276	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030485	49030486	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	169	317	0	ENST00000267163.4:c.1960_1960+1delinsAA		p.X654_splice	ENST00000267163	NM_000321.2	654		19/27	1	2	FACETS	0.916	0.852	0.98	0.916	0.852	0.98	CLONAL	1	TRUE	1	0.891647024086702	2		317	414	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066787	30066787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	233	474	1	ENST00000331968.5:c.2344C>T	p.Pro782Ser	p.P782S	ENST00000331968	NM_002742.2	782	Cca/Tca	16/18	1	2	FACETS	0.945	0.889	1	0.945	0.889	1	CLONAL	1	TRUE	1	0.891647024086702	2		475	553	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061406	38061406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	385	606	0	ENST00000250448.2:c.583G>A	p.Glu195Lys	p.E195K	ENST00000250448	NM_004496.3	195	Gag/Aag	2/2	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.891647024086702	2		606	781	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061532	38061532	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	313	687	0	ENST00000250448.2:c.457G>T	p.Ala153Ser	p.A153S	ENST00000250448	NM_004496.3	153	Gcg/Tcg	2/2	1	2	FACETS	0.989	0.939	1	0.989	0.939	1	CLONAL	1	TRUE	1	0.891647024086702	2		687	710	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028816	42028816	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	332	657	0	ENST00000219905.7:c.4354T>G	p.Phe1452Val	p.F1452V	ENST00000219905	NM_001164273.1	1452	Ttt/Gtt	13/24	0.891647024086702	1	FACETS	0.923	0.892	0.953	0.923	0.892	0.953	CLONAL	1	TRUE	0	0.891647024086702	1		657	447	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003747	45003747	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs1057519877	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	276	587	0	ENST00000558401.1:c.3G>A	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	atG/atA	1/4	0.891647024086702	1	FACETS	0.764	0.73	0.798	0.764	0.73	0.798	SUBCLONAL	1	TRUE	0	0.891647024086702	1		587	449	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007645	45007645	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	32	503	0	ENST00000558401.1:c.92C>G	p.Ser31Ter	p.S31*	ENST00000558401	NM_004048.2	31	tCa/tGa	2/4	0.891647024086702	1	FACETS	0.143	0.116	0.173	0.143	0.116	0.173	SUBCLONAL	1	TRUE	0	0.891647024086702	1		503	278	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130303	2130303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45483391	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	479	788	0	ENST00000219476.3:c.3535G>A	p.Glu1179Lys	p.E1179K	ENST00000219476	NM_000548.3	1179	Gag/Aag	30/42	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.891647024086702	2		788	1073	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129707	30129707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	340	573	0	ENST00000263025.4:c.506C>T	p.Pro169Leu	p.P169L	ENST00000263025	NM_002746.2	169	cCc/cTc	3/9	1	2	FACETS	0.984	0.937	1	0.984	0.937	1	CLONAL	1	TRUE	1	0.891647024086702	2		573	775	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578264	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	350	708	1	ENST00000269305.4:c.585_586delinsTT	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	195	atCCga/atTTga	6/11	0.891647024086702	1	FACETS	0.958	0.928	0.987	0.958	0.928	0.987	CLONAL	1	TRUE	0	0.891647024086702	1		709	454	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089980	16089980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1431286801	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	296	369	0	ENST00000268712.3:c.130C>T	p.Arg44Cys	p.R44C	ENST00000268712	NM_006311.3	44	Cgt/Tgt	3/46	0.891647024086702	1	FACETS	0.956	0.923	0.987	0.956	0.923	0.987	CLONAL	1	TRUE	0	0.891647024086702	1		369	385	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533791	63533791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779863826	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	448	747	0	ENST00000307078.5:c.1363C>T	p.Pro455Ser	p.P455S	ENST00000307078	NM_004655.3	455	Cca/Tca	6/11	0.876058275572353	2	FACETS	1	0.966	1	0.504	0.483	0.526	CLONAL	1	TRUE	0	0.891647024086702	2		747	996	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775164	73775164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867543814	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	537	914	0	ENST00000254810.4:c.92C>T	p.Pro31Leu	p.P31L	ENST00000254810	NM_005324.3	31	cCc/cTc	2/4	0.876058275572353	2	FACETS	1	0.983	1	0.519	0.499	0.539	CLONAL	1	TRUE	0	0.891647024086702	2		914	1161	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299893	15299893	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	459	733	0	ENST00000263388.2:c.1285G>A	p.Glu429Lys	p.E429K	ENST00000263388	NM_000435.2	429	Gag/Aag	8/33	1	2	FACETS	0.979	0.938	1	0.979	0.938	1	CLONAL	1	TRUE	1	0.891647024086702	2		733	1052	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224342	36224343	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	375	842	0	ENST00000222270.7:c.6892_6893delinsTT	p.Pro2298Phe	p.P2298F	ENST00000222270	NM_014727.1	2298	CCc/TTc	28/37	1	2	FACETS	0.917	0.874	0.961	0.917	0.874	0.961	CLONAL	1	TRUE	1	0.891647024086702	2		842	917	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224516	36224516	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	349	834	0	ENST00000222270.7:c.6978G>A	p.Met2326Ile	p.M2326I	ENST00000222270	NM_014727.1	2326	atG/atA	29/37	1	2	FACETS	0.839	0.797	0.882	0.839	0.797	0.882	CLONAL	1	TRUE	1	0.891647024086702	2		834	933	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765760	41765760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	754	699	0	ENST00000301178.4:c.2636C>T	p.Pro879Leu	p.P879L	ENST00000301178	NM_021913.4	879	cCt/cTt	20/20	0.66915454954529	3	FACETS	0.985	0.958	1			1	CLONAL	2	TRUE	NA	0.891647024086702	3		699	1241	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794685	42794685	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767618694	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	340	702	0	ENST00000575354.2:c.1765C>T	p.Arg589Trp	p.R589W	ENST00000575354	NM_015125.3	589	Cgg/Tgg	10/20	0.66915454954529	3	FACETS	0.968	0.916	1			1	CLONAL	1	TRUE	NA	0.891647024086702	3		702	1139	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015063	27015063	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	324	492	0	ENST00000335756.4:c.165G>C	p.Gln55His	p.Q55H	ENST00000335756	NM_001809.3	55	caG/caC	2/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.891647024086702	2		492	683	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690287	47690287	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	37	449	0	ENST00000233146.2:c.1504G>C	p.Asp502His	p.D502H	ENST00000233146	NM_000251.2	502	Gat/Cat	9/16	1	2	FACETS	0.189	0.156	0.227	0.189	0.156	0.227	SUBCLONAL	1	TRUE	1	0.891647024086702	2		449	438	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61708373	61708373	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	150	332	0	ENST00000401558.2:c.3016C>T	p.Gln1006Ter	p.Q1006*	ENST00000401558	NM_003400.3	1006	Caa/Taa	24/25	1	2	FACETS	0.897	0.831	0.965	0.897	0.831	0.965	CLONAL	1	TRUE	1	0.891647024086702	2		332	375	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872786	136872787	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	353	690	0	ENST00000241393.3:c.711_712delinsTT	p.Leu238Phe	p.L238F	ENST00000241393	NM_003467.2	237	gcCCtc/gcTTtc	2/2	1	2	FACETS	0.936	0.891	0.981	0.936	0.891	0.981	CLONAL	1	TRUE	1	0.891647024086702	2		690	846	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248443	212248443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141902440	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	403	703	0	ENST00000342788.4:c.3824G>A	p.Arg1275Gln	p.R1275Q	ENST00000342788	NM_005235.2	1275	cGg/cAg	28/28	1	2	FACETS	0.967	0.924	1	0.967	0.924	1	CLONAL	1	TRUE	1	0.891647024086702	2		703	935	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795129	242795129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	717	702	0	ENST00000334409.5:c.80C>T	p.Ser27Phe	p.S27F	ENST00000334409	NM_005018.2	27	tCc/tTc	2/5	1	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	1	0.891647024086702	2		702	1177	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306556	41306556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	253	528	0	ENST00000373198.4:c.1103G>A	p.Gly368Glu	p.G368E	ENST00000373198	NM_133170.3	368	gGg/gAg	7/32	0.826536740026005	3	FACETS	0.894	0.838	0.951	0.447	0.419	0.476	CLONAL	1	TRUE	1	0.891647024086702	3		528	918	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262931	46262932	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	167	425	0	ENST00000371998.3:c.1104_1105delinsTT	p.Leu369Phe	p.L369F	ENST00000371998		368	ttCCtt/ttTTtt	10/23	0.365410800237969	3	FACETS	0.971	0.897	1	0.485	0.448	0.523	INDETERMINATE	1	TRUE	1	0.891647024086702	3		425	558	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498474	89498474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	246	478	0	ENST00000336596.2:c.2446G>A	p.Glu816Lys	p.E816K	ENST00000336596	NM_005233.5	816	Gag/Aag	14/17	0.891647024086702	1	FACETS	0.932	0.896	0.967	0.932	0.896	0.967	CLONAL	1	TRUE	0	0.891647024086702	1		478	328	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200131	128200131	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777230453	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	358	616	0	ENST00000341105.2:c.1174G>A	p.Gly392Arg	p.G392R	ENST00000341105	NM_032638.4	392	Ggg/Agg	6/6	0.891647024086702	3	FACETS	0.92	0.872	0.969	0.46	0.436	0.485	CLONAL	1	TRUE	1	0.891647024086702	3		616	1262	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670813	134670813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765851482	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	321	653	0	ENST00000398015.3:c.724G>A	p.Gly242Arg	p.G242R	ENST00000398015	NM_004441.4	242	Ggg/Agg	3/16	0.891647024086702	3	FACETS	0.887	0.838	0.938	0.444	0.419	0.469	CLONAL	1	TRUE	1	0.891647024086702	3		653	1173	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170002286	170002286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	67	192	0	ENST00000295797.4:c.1105C>T	p.Leu369Phe	p.L369F	ENST00000295797	NM_002740.5	369	Ctt/Ttt	12/18	0.891647024086702	3	FACETS	0.826	0.726	0.932	0.413	0.363	0.466	CLONAL	1	TRUE	1	0.891647024086702	3		192	263	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519925	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	183	424	0	ENST00000263967.3:c.1357G>C	p.Glu453Gln	p.E453Q	ENST00000263967	NM_006218.2	453	Gaa/Caa	8/21	0.891647024086702	3	FACETS	0.945	0.876	1	0.473	0.438	0.508	CLONAL	1	TRUE	1	0.891647024086702	3		424	628	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803100	1803101	+	missense_variant	Missense_Mutation	DNP	CT	CT	TA	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	244	676	0	ENST00000260795.2:c.452_453delinsTA	p.Pro151Leu	p.P151L	ENST00000260795		151	cCT/cTA	4/17	0.891647024086702	3	FACETS	0.734	0.686	0.784	0.367	0.343	0.392	SUBCLONAL	1	TRUE	1	0.891647024086702	3		676	1078	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161408	55161408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	38	529	0	ENST00000257290.5:c.3239C>T	p.Ser1080Phe	p.S1080F	ENST00000257290	NM_006206.4	1080	tCt/tTt	23/23	1	2	FACETS	0.126	0.103	0.151	0.126	0.103	0.151	SUBCLONAL	1	TRUE	1	0.891647024086702	2		529	679	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972108	55972108	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	258	425	0	ENST00000263923.4:c.1537-1G>A		p.X513_splice	ENST00000263923	NM_002253.2	513			1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.891647024086702	2		425	566	SUCCESS
ALB	213	MSKCC	GRCh37	4	74283931	74283931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	246	441	0	ENST00000295897.4:c.1555G>A	p.Glu519Lys	p.E519K	ENST00000295897	NM_000477.5	519	Gaa/Aaa	12/15	1	2	FACETS	0.923	0.869	0.977	0.923	0.869	0.977	CLONAL	1	TRUE	1	0.891647024086702	2		441	598	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144336882	144336882	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201202756	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	175	427	0	ENST00000262995.4:c.325C>T	p.Arg109Cys	p.R109C	ENST00000262995	NM_207123.2	109	Cgt/Tgt	2/11	1	2	FACETS	0.984	0.918	1	0.984	0.918	1	CLONAL	1	TRUE	1	0.891647024086702	2		427	399	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510373	187510374	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	167	414	0	ENST00000441802.2:c.13139_13140delinsAA	p.Gly4380Glu	p.G4380E	ENST00000441802	NM_005245.3	4380	gGG/gAA	27/27	1	2	FACETS	0.886	0.823	0.949	0.886	0.823	0.949	CLONAL	1	TRUE	1	0.891647024086702	2		414	423	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538904	187538904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	227	556	0	ENST00000441802.2:c.8836G>A	p.Asp2946Asn	p.D2946N	ENST00000441802	NM_005245.3	2946	Gat/Aat	10/27	1	2	FACETS	0.929	0.873	0.986	0.929	0.873	0.986	CLONAL	1	TRUE	1	0.891647024086702	2		556	548	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	916060	916060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2150692880	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	304	594	0	ENST00000166345.3:c.1175C>T	p.Pro392Leu	p.P392L	ENST00000166345	NM_004237.3	392	cCc/cTc	12/13	1	2	FACETS	0.851	0.806	0.897	0.851	0.806	0.897	CLONAL	1	TRUE	1	0.891647024086702	2		594	801	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295230	1295230	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs796516131	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	265	572	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.996	0.942	1	0.996	0.942	1	CLONAL	1	TRUE	1	0.891647024086702	2		572	597	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80074654	80074654	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs1386308078	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	221	359	0	ENST00000265081.6:c.2434G>C	p.Glu812Gln	p.E812Q	ENST00000265081	NM_002439.4	812	Gag/Cag	17/24	1	2	FACETS	0.976	0.918	1	0.976	0.918	1	CLONAL	1	TRUE	1	0.891647024086702	2		359	508	SUCCESS
APC	324	MSKCC	GRCh37	5	112154789	112154789	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs556566281	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	277	558	0	ENST00000257430.4:c.1060C>T	p.Pro354Ser	p.P354S	ENST00000257430	NM_000038.5	354	Cct/Tct	10/16	1	2	FACETS	0.884	0.835	0.933	0.884	0.835	0.933	CLONAL	1	TRUE	1	0.891647024086702	2		558	703	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915639	131915639	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	151	268	0	ENST00000265335.6:c.637C>G	p.Leu213Val	p.L213V	ENST00000265335		213	Ctg/Gtg	5/25	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.891647024086702	2		268	329	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638258	176638258	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	368	612	0	ENST00000439151.2:c.2858C>G	p.Ser953Cys	p.S953C	ENST00000439151	NM_022455.4	953	tCt/tGt	5/23	1	2	FACETS	0.998	0.952	1	0.998	0.952	1	CLONAL	1	TRUE	1	0.891647024086702	2		612	827	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056443	26056443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1252419231	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	369	606	0	ENST00000343677.2:c.214G>A	p.Asp72Asn	p.D72N	ENST00000343677	NM_005319.3	72	Gat/Aat	1/1	1	2	FACETS	0.964	0.919	1	0.964	0.919	1	CLONAL	1	TRUE	1	0.891647024086702	2		606	859	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940120	31940120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	410	845	0	ENST00000375333.2:c.262G>A	p.Glu88Lys	p.E88K	ENST00000375333	NM_032454.1	88	Gaa/Aaa	2/8	1	2	FACETS	0.958	0.915	1	0.958	0.915	1	CLONAL	1	TRUE	1	0.891647024086702	2		845	960	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946355	2946355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372251654	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	283	619	0	ENST00000396946.4:c.3382G>A	p.Val1128Ile	p.V1128I	ENST00000396946	NM_032415.4	1128	Gta/Ata	25/25	1	2	FACETS	0.79	0.745	0.835	0.79	0.745	0.835	SUBCLONAL	1	TRUE	1	0.891647024086702	2		619	804	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268918	55268918	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs940489358	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	414	651	0	ENST00000275493.2:c.2984C>G	p.Ser995Cys	p.S995C	ENST00000275493	NM_005228.3	995	tCc/tGc	25/28	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.891647024086702	2		651	896	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151893077	151893077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	159	317	0	ENST00000262189.6:c.4293A>T	p.Leu1431Phe	p.L1431F	ENST00000262189	NM_170606.2	1431	ttA/ttT	28/59	0.600671668961356	3	FACETS	1	0.976	1	0.565	0.523	0.609	CLONAL	1	TRUE	1	0.891647024086702	3		317	456	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74858890	74858890	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	250	426	0	ENST00000284811.8:c.314T>G	p.Met105Arg	p.M105R	ENST00000284811		105	aTg/aGg	4/4	1	2	FACETS	0.949	0.895	1	0.949	0.895	1	CLONAL	1	TRUE	1	0.891647024086702	2		426	591	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2077700	2077700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	327	594	0	ENST00000349721.2:c.2108C>T	p.Thr703Ile	p.T703I	ENST00000349721	NM_003070.3	703	aCc/aTc	14/34	1	2	FACETS	0.95	0.903	0.998	0.95	0.903	0.998	CLONAL	1	TRUE	1	0.891647024086702	2		594	772	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485912	8485913	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	305	623	0	ENST00000356435.5:c.2904_2905delinsAA	p.Met968_Glu969delinsIleLys	p.M968_E969delinsIK	ENST00000356435		968	atGGag/atAAag	17/35	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.891647024086702	2		623	676	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270636	98270636	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	190	447	0	ENST00000331920.6:c.8C>A	p.Ser3Ter	p.S3*	ENST00000331920	NM_000264.3	3	tCg/tAg	1/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.891647024086702	2		447	390	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779102	135779102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs986350787	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	345	646	0	ENST00000298552.3:c.2144G>A	p.Arg715Gln	p.R715Q	ENST00000298552	NM_001162426.1	715	cGg/cAg	17/23	1	2	FACETS	0.947	0.901	0.993	0.947	0.901	0.993	CLONAL	1	TRUE	1	0.891647024086702	2		646	817	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139818373	139818373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754210099	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	346	483	0	ENST00000247668.2:c.1208G>A	p.Arg403Gln	p.R403Q	ENST00000247668	NM_021138.3	403	cGa/cAa	10/11	1	2	FACETS	0.998	0.95	1	0.998	0.95	1	CLONAL	1	TRUE	1	0.891647024086702	2		483	778	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321372	1321372	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1319865856	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	291	562	0	ENST00000400841.2:c.383C>T	p.Ser128Leu	p.S128L	ENST00000400841		128	tCg/tTg	4/6	1	2	FACETS	0.828	0.783	0.875	0.828	0.783	0.875	CLONAL	1	TRUE	1	0.891647024086702	2		562	788	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911436	39911436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437936868	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	315	547	0	ENST00000378444.4:c.5194G>A	p.Glu1732Lys	p.E1732K	ENST00000378444	NM_001123385.1	1732	Gaa/Aaa	15/15	1	2	FACETS	0.897	0.85	0.943	0.897	0.85	0.943	CLONAL	1	TRUE	1	0.891647024086702	2		547	788	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231037	53231037	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	360	664	0	ENST00000375401.3:c.1865G>T	p.Trp622Leu	p.W622L	ENST00000375401	NM_004187.3	622	tGg/tTg	13/26	1	2	FACETS	0.897	0.854	0.941	0.897	0.854	0.941	CLONAL	1	TRUE	1	0.891647024086702	2		664	900	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626652	100626652	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	194	405	0	ENST00000308731.7:c.278C>T	p.Ser93Leu	p.S93L	ENST00000308731	NM_000061.2	93	tCa/tTa	4/19	1	2	FACETS	0.967	0.905	1	0.967	0.905	1	CLONAL	1	TRUE	1	0.891647024086702	2		405	450	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664899	138664914	+	protein_altering_variant	In_Frame_Del	DEL	TGCCGCCATCTGGCAG	TGCCGCCATCTGGCAG	A	novel	NA	P-0061108-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	29	356	0	ENST00000330315.3:c.651_666delinsT	p.Cys218_Ala222del	p.C218_A222del	ENST00000330315	NM_023067.3	217	tcCTGCCAGATGGCGGCA/tcT	1/1	0.464055224616345	1	FACETS	0.346	0.279	0.422	0.346	0.279	0.422	SUBCLONAL	1	TRUE	0	0.495836111456161	1		356	254	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249007	+	missense_variant	Missense_Mutation	TNP	GCG	GCG	TCT	novel	NA	P-0061127-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	73	355	0	ENST00000275493.2:c.2303_2305delinsTCT	p.Ser768_Val769delinsIleLeu	p.S768_V769delinsIL	ENST00000275493	NM_005228.3	768	aGCGtg/aTCTtg	20/28	1	2	FACETS	0.935	0.82	1	0.935	0.82	1	CLONAL	1	TRUE	1	0.350284536086085	2		355	446	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519337	176519337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758837002	NA	P-0061127-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	75	415	0	ENST00000292408.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000292408	NM_213647.1	248	cGg/cAg	7/18	0.325998410469545	3	FACETS	1	0.913	1	0.524	0.46	0.592	CLONAL	1	TRUE	1	0.350284536086085	3		415	480	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041857	42041857	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061127-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	59	441	0	ENST00000219905.7:c.6052G>T	p.Glu2018Ter	p.E2018*	ENST00000219905	NM_001164273.1	2018	Gaa/Taa	17/24	1	2	FACETS	0.718	0.619	0.826	0.718	0.619	0.826	SUBCLONAL	1	TRUE	1	0.350284536086085	2		441	469	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528590	8528590	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0061127-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	54	324	1	ENST00000356435.5:c.541+1G>T		p.X181_splice	ENST00000356435		181			1	2	FACETS	0.761	0.652	0.88	0.761	0.652	0.88	SUBCLONAL	1	TRUE	1	0.350284536086085	2		325	405	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506391	120506391	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061127-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	91	377	0	ENST00000256646.2:c.1721G>T	p.Cys574Phe	p.C574F	ENST00000256646	NM_024408.3	574	tGt/tTt	11/34	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.350284536086085	2		377	488	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86545017	86545017	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs778302454	NA	P-0061127-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	53	374	0	ENST00000262426.4:c.842G>T	p.Gly281Val	p.G281V	ENST00000262426	NM_001451.2	281	gGc/gTc	1/2	1	2	FACETS	0.909	0.779	1	0.909	0.779	1	CLONAL	1	TRUE	1	0.350284536086085	2		374	333	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433946	149433946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061127-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	132	428	0	ENST00000286301.3:c.2702C>A	p.Pro901His	p.P901H	ENST00000286301	NM_005211.3	901	cCc/cAc	21/22	0.325998410469545	3	FACETS	0.942	0.861	1	0.942	0.861	1	CLONAL	2	TRUE	1	0.350284536086085	3		428	470	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434542	140434542	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs368528867	NA	P-0061127-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	75	281	0	ENST00000288602.6:c.2156G>T	p.Arg719Leu	p.R719L	ENST00000288602	NM_004333.4	719	cGc/cTc	18/18	1	2	FACETS	0.987	0.868	1	0.987	0.868	1	CLONAL	1	TRUE	1	0.350284536086085	2		281	434	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028773	47028775	+	frameshift_variant	Frame_Shift_Del	DEL	GTG	GTG	TT	novel	NA	P-0061127-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	84	455	0	ENST00000377604.3:c.77_79delinsTT	p.Gly26ValfsTer108	p.G26Vfs*108	ENST00000377604	NM_001204468.1	26	gGTGgg/gTTgg	3/24	1	2	FACETS	0.955	0.846	1	0.955	0.846	1	CLONAL	1	TRUE	1	0.350284536086085	2		455	502	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	138	321	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.363223201927743	2		321	511	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0061128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	32	544	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.259912021934483	4	FACETS	0.66	0.536	0.799	0.33	0.268	0.4	SUBCLONAL	1	TRUE	2	0.363223201927743	4		544	364	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305348	39305348	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	215	314	0	ENST00000373001.3:c.1077C>A	p.Phe359Leu	p.F359L	ENST00000373001	NM_022157.3	359	ttC/ttA	7/7	0.363223201927743	3	FACETS	1	0.991	1	0.742	0.69	0.796	CLONAL	1	TRUE	1	0.363223201927743	3		314	942	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304233	65304233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1163790865	NA	P-0061128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	153	464	0	ENST00000342505.4:c.2882C>T	p.Ser961Leu	p.S961L	ENST00000342505	NM_002227.2	961	tCg/tTg	21/25	0.363223201927743	2	FACETS	1	0.986	1	0.685	0.629	0.743	CLONAL	1	TRUE	0	0.363223201927743	2		464	615	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845501	63845501	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	184	324	0	ENST00000279873.7:c.1240G>T	p.Asp414Tyr	p.D414Y	ENST00000279873	NM_032199.2	414	Gat/Tat	9/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.363223201927743	2		324	685	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428019	49428019	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	210	393	0	ENST00000301067.7:c.10571A>T	p.Gln3524Leu	p.Q3524L	ENST00000301067	NM_003482.3	3524	cAg/cTg	38/54	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.363223201927743	2		393	802	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39216450	39216450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	114	210	0	ENST00000402219.2:c.3352G>A	p.Asp1118Asn	p.D1118N	ENST00000402219	NM_005633.3	1118	Gat/Aat	21/23	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.363223201927743	2		210	423	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0061128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	32	240	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.259912021934483	4	FACETS	0.767	0.624	0.928	0.384	0.312	0.464	CLONAL	1	TRUE	2	0.363223201927743	4		240	313	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0061128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	17	317	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.259912021934483	4	FACETS	0.321	0.238	0.419	0.16	0.119	0.21	SUBCLONAL	1	TRUE	2	0.363223201927743	4		317	398	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146724	185146724	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	138	383	0	ENST00000265026.3:c.355C>T	p.Gln119Ter	p.Q119*	ENST00000265026	NM_004721.4	119	Cag/Tag	2/14	0.259912021934483	4	FACETS	0.996	0.905	1	0.498	0.452	0.546	CLONAL	1	TRUE	2	0.363223201927743	4		383	1040	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505336	186505336	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0061128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	81	322	0	ENST00000323963.5:c.962C>G	p.Ser321Ter	p.S321*	ENST00000323963		321	tCa/tGa	9/11	0.259912021934483	4	FACETS	0.683	0.601	0.772	0.342	0.3	0.386	SUBCLONAL	1	TRUE	2	0.363223201927743	4		322	890	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415155	109415155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	202	336	0	ENST00000436639.2:c.122C>T	p.Ser41Leu	p.S41L	ENST00000436639	NM_014454.2	41	tCg/tTg	1/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.363223201927743	2		336	783	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856070	151856070	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	248	369	0	ENST00000262189.6:c.11548C>T	p.Arg3850Ter	p.R3850*	ENST00000262189	NM_170606.2	3850	Cga/Tga	44/59	1	2	FACETS	0.837	0.785	0.89	1	0.994	1	CLONAL	2	TRUE	1	0.363223201927743	2		369	816	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878763	151878763	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0061128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	204	402	0	ENST00000262189.6:c.6182C>G	p.Ser2061Ter	p.S2061*	ENST00000262189	NM_170606.2	2061	tCa/tGa	36/59	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.363223201927743	2		402	857	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080560	5080560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	136	268	0	ENST00000381652.3:c.2311C>T	p.Gln771Ter	p.Q771*	ENST00000381652	NM_004972.3	771	Cag/Tag	18/25	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.363223201927743	2		268	529	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090794	5090794	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	140	319	0	ENST00000381652.3:c.2942A>G	p.Asn981Ser	p.N981S	ENST00000381652	NM_004972.3	981	aAt/aGt	22/25	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.363223201927743	2		319	563	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123048	5123048	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0061128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	174	310	0	ENST00000381652.3:c.3104C>G	p.Ser1035Ter	p.S1035*	ENST00000381652	NM_004972.3	1035	tCa/tGa	23/25	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.363223201927743	2		310	696	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760625	133760625	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	224	462	0	ENST00000318560.5:c.2948C>G	p.Ser983Cys	p.S983C	ENST00000318560	NM_005157.4	983	tCc/tGc	11/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.363223201927743	2		462	923	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293682	137293682	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568762857	NA	P-0061128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	160	466	0	ENST00000481739.1:c.233C>T	p.Ser78Leu	p.S78L	ENST00000481739	NM_002957.4	78	tCg/tTg	2/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.363223201927743	2		466	727	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061129-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	237	321	0				ENST00000310581	NM_198253.2	-/1132			0.386418475912675	5	FACETS	0.891	0.841	0.941	0.891	0.841	0.941	CLONAL	4	TRUE	1	0.428506768210257	5		321	510	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0061129-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	32	282	0	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	0.350363347749417	2	FACETS	0.688	0.563	0.828			1	SUBCLONAL	1	TRUE	NA	0.428506768210257	2		282	217	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519927	NA	P-0061129-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	108	163	0	ENST00000263967.3:c.1625A>T	p.Glu542Val	p.E542V	ENST00000263967	NM_006218.2	542	gAa/gTa	10/21	0.284358775100194	5	FACETS	1	0.969	1	0.775	0.703	0.85	CLONAL	2	TRUE	2	0.428506768210257	5		163	356	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061129-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	337	428	0	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	0.428506768210257	5	FACETS	0.974	0.925	1	0.974	0.925	1	CLONAL	3	TRUE	2	0.428506768210257	5		428	884	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545855	41545855	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867077693	NA	P-0061129-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	137	394	0	ENST00000263253.7:c.2470C>T	p.Gln824Ter	p.Q824*	ENST00000263253	NM_001429.3	824	Caa/Taa	14/31	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.428506768210257	2		394	621	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47735825	47735825	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061129-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	126	331	0	ENST00000449228.1:c.35C>T	p.Pro12Leu	p.P12L	ENST00000449228	NM_001127240.2	12	cCa/cTa	1/4	0.428506768210257	5	FACETS	1	0.969	1	0.388	0.351	0.426	CLONAL	1	TRUE	2	0.428506768210257	5		331	831	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778096	135778096	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203671	NA	P-0061129-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	208	282	0	ENST00000298552.3:c.2287C>T	p.Gln763Ter	p.Q763*	ENST00000298552	NM_001162426.1	763	Cag/Tag	18/23	0.428506768210257	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.428506768210257	2		282	461	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386512	81386512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061129-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	42	239	0	ENST00000222390.5:c.475G>A	p.Glu159Lys	p.E159K	ENST00000222390	NM_000601.4	159	Gaa/Aaa	4/18	0.428506768210257	5	FACETS	0.55	0.459	0.653	0.183	0.153	0.218	SUBCLONAL	1	TRUE	2	0.428506768210257	5		239	585	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184733	185184733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061129-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	127	306	0	ENST00000265026.3:c.1625C>T	p.Ser542Phe	p.S542F	ENST00000265026	NM_004721.4	542	tCt/tTt	10/14	0.284358775100194	5	FACETS	1	0.977	1	0.419	0.379	0.46	CLONAL	1	TRUE	2	0.428506768210257	5		306	775	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211212	2211212	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0061129-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	99	321	0	ENST00000398665.3:c.1465+1G>T		p.X489_splice	ENST00000398665	NM_032482.2	489			0.147019918923134	5	FACETS	1	0.98	1	0.357	0.319	0.396	INDETERMINATE	1	TRUE	1	0.428506768210257	5		321	532	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426589	49426589	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061129-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	1997	540	0	ENST00000301067.7:c.11899C>T	p.Gln3967Ter	p.Q3967*	ENST00000301067	NM_003482.3	3967	Caa/Taa	39/54	0.428506768210257	12	FACETS	1	0.997	1			1	CLONAL	11	TRUE	NA	0.428506768210257	12		540	2553	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437968	110437968	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061129-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	104	197	0	ENST00000375856.3:c.433G>C	p.Glu145Gln	p.E145Q	ENST00000375856	NM_003749.2	145	Gag/Cag	1/2	0.200744227894248	3	FACETS	0.918	0.832	1	0.918	0.832	1	INDETERMINATE	2	TRUE	1	0.428506768210257	3		197	321	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43772132	43772132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1430354090	NA	P-0061129-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	91	312	0	ENST00000382044.4:c.583G>A	p.Val195Met	p.V195M	ENST00000382044	NM_001141980.1	195	Gtg/Atg	6/28	1	2	FACETS	0.892	0.796	0.995	0.892	0.796	0.995	CLONAL	1	TRUE	1	0.428506768210257	2		312	476	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772254	68772254	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061129-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	101	313	0	ENST00000261769.5:c.103G>A	p.Glu35Lys	p.E35K	ENST00000261769	NM_004360.3	35	Gag/Aag	2/16	0.428506768210257	4	FACETS	1	0.916	1	0.342	0.306	0.381	CLONAL	1	TRUE	1	0.428506768210257	4		313	656	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578548	7578563	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGAGTACTGTAGGAA	GGGAGTACTGTAGGAA	-	novel	NA	P-0061129-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	224	380	0	ENST00000269305.4:c.376-9_382del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	0.428506768210257	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.428506768210257	2		380	491	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424011	47424011	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061129-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	345	374	0	ENST00000404338.3:c.2079A>T	p.Leu693Phe	p.L693F	ENST00000404338	NM_004491.4	693	ttA/ttT	1/6	0.428506768210257	5	FACETS	0.931	0.884	0.979	0.931	0.884	0.979	CLONAL	3	TRUE	2	0.428506768210257	5		374	947	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525716	187525724	+	inframe_deletion	In_Frame_Del	DEL	CTGGCTTAT	CTGGCTTAT	-	novel	NA	P-0061129-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	104	309	0	ENST00000441802.2:c.10355_10363del	p.Asn3452_Val3455delinsMet	p.N3452_V3455delinsM	ENST00000441802	NM_005245.3	3452	aATAAGCCAGtg/atg	18/27	0.428506768210257	3	FACETS	1	0.924	1	0.517	0.464	0.573	CLONAL	1	TRUE	1	0.428506768210257	3		309	570	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911180	29911180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs78923580	NA	P-0061129-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	90	149	0	ENST00000376809.5:c.479C>T	p.Ala160Val	p.A160V	ENST00000376809	NM_002116.7	160	gCg/gTg	3/8	0.147019918923134	5	FACETS	0.833	0.75	0.92	0.625	0.562	0.69	INDETERMINATE	3	TRUE	1	0.428506768210257	5		149	276	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912377	29912377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061129-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	96	344	0	ENST00000376809.5:c.996G>A	p.Trp332Ter	p.W332*	ENST00000376809	NM_002116.7	332	tgG/tgA	5/8	0.147019918923134	5	FACETS	1	0.974	1	0.327	0.292	0.365	INDETERMINATE	1	TRUE	1	0.428506768210257	5		344	562	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242266	98242266	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061129-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	210	299	0	ENST00000331920.6:c.1052C>T	p.Thr351Ile	p.T351I	ENST00000331920	NM_000264.3	351	aCt/aTt	7/24	0.428506768210257	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	0	0.428506768210257	2		299	489	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870202	44870209	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACAGAATG	ACAGAATG	-	novel	NA	P-0061129-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	105	93	0	ENST00000377967.4:c.385-4_388del		p.X129_splice	ENST00000377967	NM_021140.2	129		5/29	0.350363347749417	2	FACETS	0.86	0.793	0.926			1	CLONAL	3	TRUE	NA	0.428506768210257	2		93	190	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588793	69588793	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	35	326	0	ENST00000168712.1:c.443C>T	p.Ser148Leu	p.S148L	ENST00000168712	NM_002007.2	148	tCg/tTg	2/3	0.151265322426224	6	FACETS	1	0.838	1	0.34	0.279	0.407	INDETERMINATE	1	TRUE	3	0.495857751669266	6		326	276	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183794	10183794	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	164	455	0	ENST00000256474.2:c.263G>T	p.Trp88Leu	p.W88L	ENST00000256474	NM_000551.3	88	tGg/tTg	1/3	0.495857751669266	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.495857751669266	2		455	295	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11276237	11276237	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	65	368	0	ENST00000361445.4:c.3085C>A	p.Pro1029Thr	p.P1029T	ENST00000361445	NM_004958.3	1029	Cct/Act	20/58	0.434383723423711	3	FACETS	1	0.904	1	0.521	0.455	0.591	CLONAL	1	TRUE	1	0.495857751669266	3		368	314	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285215	198285215	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	159	376	0	ENST00000335508.6:c.352G>A	p.Glu118Lys	p.E118K	ENST00000335508	NM_012433.2	118	Gaa/Aaa	4/25	0.438192625523476	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.495857751669266	3		376	337	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651499	52651500	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	148	418	0	ENST00000394830.3:c.1596dup	p.Ala533SerfsTer12	p.A533Sfs*12	ENST00000394830	NM_018313.4	532	-/A	15/30	0.495857751669266	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.495857751669266	2		418	284	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205673	128205673	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs534541303	NA	P-0061130-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	156	392	0	ENST00000341105.2:c.202G>T	p.Ala68Ser	p.A68S	ENST00000341105	NM_032638.4	68	Gcg/Tcg	2/6	0.151265322426224	6	FACETS	1	0.96	1	1	0.96	1	INDETERMINATE	3	TRUE	3	0.495857751669266	6		392	396	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0061131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	221	242	0	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.718194640744608	1		242	315	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0061131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	188	478	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.718194640744608	2		478	516	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870675	12870897	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	CTTCCGAGAGGGGTTCGGGCTGCGTAGGGGCGCTTTGTTTTGTTCGGTTTTGTTTTTTTGAGAGTGCGAGAGAGGCGGTCGTGCAGACCCGGGAGAAAGATGTCAAACGTGCGAGTGTCTAACGGGAGCCCTAGCCTGGAGCGGATGGACGCCAGGCAGGCGGAGCACCCCAAGCCCTCGGCCTGCAGGAACCTCTTCGGCCCGGTGGACCACGAAGAGTTAA	CTTCCGAGAGGGGTTCGGGCTGCGTAGGGGCGCTTTGTTTTGTTCGGTTTTGTTTTTTTGAGAGTGCGAGAGAGGCGGTCGTGCAGACCCGGGAGAAAGATGTCAAACGTGCGAGTGTCTAACGGGAGCCCTAGCCTGGAGCGGATGGACGCCAGGCAGGCGGAGCACCCCAAGCCCTCGGCCTGCAGGAACCTCTTCGGCCCGGTGGACCACGAAGAGTTAA	-	novel	NA	P-0061131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	154	181	0	ENST00000228872.4:c.-98_125del		p.*33*	ENST00000228872	NM_004064.3	?-42/198		1/3	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.718194640744608	2		181	324	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857804	9857805	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0061131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	246	644	0	ENST00000330684.3:c.3596dup	p.His1200AlafsTer3	p.H1200Afs*3	ENST00000330684	NM_001134407.1	1199	ccg/ccCg	13/13	1	2	FACETS	0.917	0.861	0.975	0.917	0.861	0.975	CLONAL	1	TRUE	1	0.718194640744608	2		644	747	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933460	39933463	+	frameshift_variant	Frame_Shift_Del	DEL	CTAA	CTAA	-	rs864309702	NA	P-0061141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	85	268	0	ENST00000378444.4:c.1136_1139del	p.Val379AlafsTer62	p.V379Afs*62	ENST00000378444	NM_001123385.1	379	gTTAGc/gc	4/15	0.3	2	FACETS	0.888	0.807	0.968			1	INDETERMINATE	2	TRUE	NA	0.56	2		268	171	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193519	99193519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	44	528	0	ENST00000074304.5:c.2714C>T	p.Ser905Leu	p.S905L	ENST00000074304	NM_001134224.1	905	tCg/tTg	25/26	1	2	FACETS	0.616	0.521	0.72	0.616	0.521	0.72	SUBCLONAL	1	TRUE	1	0.56	2		528	255	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262316	115262317	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	49	409	0	ENST00000438362.2:c.2237dup	p.His747ProfsTer10	p.H747Pfs*10	ENST00000438362	NM_001242891.1	746	ttc/ttTc	18/20	1	2	FACETS	0.806	0.691	0.93	0.806	0.691	0.93	CLONAL	1	TRUE	1	0.56	2		409	217	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906769	50906769	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	69	451	0	ENST00000440232.2:c.1157G>T	p.Arg386Leu	p.R386L	ENST00000440232	NM_002691.3	386	cGt/cTt	10/27	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.56	2		451	236	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	393	509	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.981	0.944	1	1	0.997	1	CLONAL	2	TRUE	1	0.626839400974417	2		513	639	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	118	553	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.884	0.803	0.967	0.884	0.803	0.967	CLONAL	1	TRUE	1	0.626839400974417	2		553	426	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	136	525	3	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.851	0.778	0.926	0.851	0.778	0.926	CLONAL	1	TRUE	1	0.626839400974417	2		528	510	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606272	93606273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1182878074	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	158	494	0	ENST00000375746.1:c.98dup	p.Met34HisfsTer3	p.M34Hfs*3	ENST00000375746	NM_001174167.1	31	cag/caGg	2/14	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.626839400974417	2		494	471	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	139	390	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	1	2	FACETS	0.981	0.9	1	0.981	0.9	1	CLONAL	1	TRUE	1	0.626839400974417	2		390	452	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	57	151	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.626839400974417	2		151	174	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	197	749	15	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.626839400974417	2		764	587	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066611	94066611	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	187	557	0	ENST00000369303.4:c.1148G>T	p.Gly383Val	p.G383V	ENST00000369303	NM_004440.3	383	gGg/gTg	5/17	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.626839400974417	2		557	545	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	147	378	3	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	1	2	FACETS	0.89	0.817	0.965	0.89	0.817	0.965	CLONAL	1	TRUE	1	0.626839400974417	2		381	527	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222475	2222475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200919682	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	177	506	3	ENST00000398665.3:c.3307G>A	p.Val1103Met	p.V1103M	ENST00000398665	NM_032482.2	1103	Gtg/Atg	24/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.626839400974417	2		509	494	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619228	23619228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201657283	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	171	405	0	ENST00000261584.4:c.3307G>A	p.Val1103Met	p.V1103M	ENST00000261584	NM_024675.3	1103	Gtg/Atg	12/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.626839400974417	2		405	496	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720803	89720804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs786204892	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	37	154	0	ENST00000371953.3:c.955dup	p.Thr319AsnfsTer6	p.T319Nfs*6	ENST00000371953	NM_000314.4	318	-/A	8/9	1	2	FACETS	0.843	0.708	0.988	0.843	0.708	0.988	CLONAL	1	TRUE	1	0.626839400974417	2		154	140	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793431	242793431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376257658	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	144	514	0	ENST00000334409.5:c.646G>A	p.Val216Met	p.V216M	ENST00000334409	NM_005018.2	216	Gtg/Atg	5/5	1	2	FACETS	0.943	0.867	1	0.943	0.867	1	CLONAL	1	TRUE	1	0.626839400974417	2		514	487	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105676	27105678	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs753766136	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	185	518	4	ENST00000324856.7:c.5299_5301del	p.Glu1767del	p.E1767del	ENST00000324856	NM_006015.4	1763	GAA/-	20/20	1	2	FACETS	0.969	0.9	1	0.969	0.9	1	CLONAL	1	TRUE	1	0.626839400974417	2		522	609	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	173	1069	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.626839400974417	2		1071	500	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453399	40453399	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs759027671	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	200	450	4	ENST00000345506.4:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000345506	NM_003152.3	366	Ccc/cc	10/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.626839400974417	2		454	588	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421833	49421833	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	216	645	0	ENST00000301067.7:c.14474G>T	p.Arg4825Leu	p.R4825L	ENST00000301067	NM_003482.3	4825	cGg/cTg	46/54	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.626839400974417	2		645	625	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328378	137328380	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs763369916	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	138	604	0	ENST00000481739.1:c.1315_1317del	p.Phe439del	p.F439del	ENST00000481739	NM_002957.4	436	cTCTtc/ctc	10/10	1	2	FACETS	0.881	0.806	0.957	0.881	0.806	0.957	CLONAL	1	TRUE	1	0.626839400974417	2		604	500	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827723	72827723	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	162	538	0	ENST00000268489.5:c.8858T>C	p.Met2953Thr	p.M2953T	ENST00000268489	NM_006885.3	2953	aTg/aCg	9/10	1	2	FACETS	0.977	0.902	1	0.977	0.902	1	CLONAL	1	TRUE	1	0.626839400974417	2		538	529	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251934	8251934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	202	646	0	ENST00000335790.3:c.143G>A	p.Cys48Tyr	p.C48Y	ENST00000335790	NM_002315.2	48	tGc/tAc	2/4	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.626839400974417	2		646	592	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945655	71945655	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	132	456	0	ENST00000298229.2:c.2411C>A	p.Pro804His	p.P804H	ENST00000298229	NM_001567.3	804	cCc/cAc	21/28	1	2	FACETS	0.959	0.878	1	0.959	0.878	1	CLONAL	1	TRUE	1	0.626839400974417	2		456	439	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678622	88678622	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	117	414	1	ENST00000360948.2:c.914del	p.Pro305HisfsTer4	p.P305Hfs*4	ENST00000360948	NM_001012338.2	305	cCa/ca	9/19	1	2	FACETS	0.835	0.758	0.915	0.835	0.758	0.915	CLONAL	1	TRUE	1	0.626839400974417	2		415	447	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490330	29490330	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555606096	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	173	347	0	ENST00000356175.3:c.415T>C	p.Ser139Pro	p.S139P	ENST00000356175	NM_000267.3	139	Tct/Cct	4/57	1	2	FACETS	0.996	0.923	1	0.996	0.923	1	CLONAL	1	TRUE	1	0.626839400974417	2		347	554	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38792704	38792704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	155	268	0	ENST00000348513.6:c.312G>A	p.Trp104Ter	p.W104*	ENST00000348513	NM_003079.4	104	tgG/tgA	6/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.626839400974417	2		268	407	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099318	4099318	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	99	571	0	ENST00000262948.5:c.800T>C	p.Ile267Thr	p.I267T	ENST00000262948	NM_030662.3	267	aTc/aCc	7/11	1	2	FACETS	0.782	0.703	0.865	0.782	0.703	0.865	SUBCLONAL	1	TRUE	1	0.626839400974417	2		571	404	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385058	31385058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	165	454	0	ENST00000328111.2:c.1443C>A	p.Cys481Ter	p.C481*	ENST00000328111	NM_006892.3	481	tgC/tgA	14/23	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.626839400974417	2		454	520	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29442796	29442797	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	200	498	0	ENST00000544604.2:c.841dup	p.Ala281GlyfsTer22	p.A281Gfs*22	ENST00000544604	NM_001206998.1	279	-/G	6/9	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.626839400974417	2		498	592	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266573	41266573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751808983	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	178	486	0	ENST00000349496.5:c.370C>T	p.Arg124Cys	p.R124C	ENST00000349496	NM_001904.3	124	Cgt/Tgt	4/15	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.626839400974417	2		486	513	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259307	89259307	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	161	476	0	ENST00000336596.2:c.451A>G	p.Ser151Gly	p.S151G	ENST00000336596	NM_005233.5	151	Agt/Ggt	3/17	1	2	FACETS	0.99	0.914	1	0.99	0.914	1	CLONAL	1	TRUE	1	0.626839400974417	2		476	519	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281775	142281775	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	136	474	0	ENST00000350721.4:c.469G>C	p.Val157Leu	p.V157L	ENST00000350721	NM_001184.3	157	Gtt/Ctt	4/47	1	2	FACETS	0.988	0.906	1	0.988	0.906	1	CLONAL	1	TRUE	1	0.626839400974417	2		474	439	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522555	67522556	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	170	392	0	ENST00000274335.5:c.55_56del	p.Glu19ArgfsTer4	p.E19Rfs*4	ENST00000274335		18	AGa/a	1/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.626839400974417	2		392	512	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588143	67588143	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	135	396	0	ENST00000274335.5:c.974del	p.Asn325IlefsTer19	p.N325Ifs*19	ENST00000274335		325	Aat/at	7/15	1	2	FACETS	0.97	0.889	1	0.97	0.889	1	CLONAL	1	TRUE	1	0.626839400974417	2		396	444	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710863	117710863	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	134	538	0	ENST00000368508.3:c.1409T>G	p.Phe470Cys	p.F470C	ENST00000368508	NM_002944.2	470	tTc/tGc	12/43	1	2	FACETS	0.938	0.858	1	0.938	0.858	1	CLONAL	1	TRUE	1	0.626839400974417	2		538	456	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370771	55370771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	145	549	0	ENST00000297316.4:c.73G>A	p.Ala25Thr	p.A25T	ENST00000297316	NM_022454.3	25	Gcc/Acc	1/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.626839400974417	2		549	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578250	7578250	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1131691011	NA	P-0061144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	120	473	0	ENST00000269305.4:c.599del	p.Asn200IlefsTer47	p.N200Ifs*47	ENST00000269305	NM_001126112.2	200	aAt/at	6/11	0.202321643727601	3	FACETS	0.942	0.852	1	0.942	0.852	1	CLONAL	2	TRUE	1	0.202321643727601	3		473	693	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061012	38061033	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGCCGGCGCGCCCTCTAGCT	GGGGCCGGCGCGCCCTCTAGCT	-	novel	NA	P-0061144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	147	541	0	ENST00000250448.2:c.956_977del	p.Gln319ProfsTer24	p.Q319Pfs*24	ENST00000250448	NM_004496.3	319	cAGCTAGAGGGCGCGCCGGCCCCc/cc	2/2	0.200924260966266	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.202321643727601	4		541	748	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	22	321	0				ENST00000310581	NM_198253.2	-/1132			0.190420252157083	3	FACETS	1	0.821	1	0.532	0.414	0.668	CLONAL	1	TRUE	1	0.209608140134718	3		321	218	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0061145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	9	375	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	0.209608140134718	2	FACETS	0.247	0.162	0.355	0.123	0.081	0.178	SUBCLONAL	1	TRUE	0	0.209608140134718	2		375	348	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0061145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	28	240	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.0472697960704695	4	FACETS	0.945	0.763	1	0.945	0.763	1	INDETERMINATE	2	TRUE	2	0.209608140134718	4		240	171	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971003	21971003	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	37	613	0	ENST00000304494.5:c.355G>T	p.Glu119Ter	p.E119*	ENST00000304494	NM_000077.4	119	Gag/Tag	2/3	0.209608140134718	0	FACETS	0.773	0.638	0.923			1	CLONAL	1	TRUE	0	0.209608140134718	0		613	361	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524489	44524489	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	29	334	0	ENST00000291552.4:c.68A>G	p.Lys23Arg	p.K23R	ENST00000291552	NM_006758.2	23	aAa/aGa	2/8	0.190420252157083	3	FACETS	0.828	0.665	1	0.414	0.332	0.507	CLONAL	1	TRUE	1	0.209608140134718	3		334	369	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969884	81969884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199840870	NA	P-0061145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	39	499	0	ENST00000359376.3:c.2953G>A	p.Val985Ile	p.V985I	ENST00000359376	NM_002661.3	985	Gtc/Atc	27/33	0.209608140134718	4	FACETS	0.924	0.766	1	0.308	0.255	0.367	CLONAL	1	TRUE	1	0.209608140134718	4		499	487	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061532	38061532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781269308	NA	P-0061145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	57	523	0	ENST00000250448.2:c.457G>A	p.Ala153Thr	p.A153T	ENST00000250448	NM_004496.3	153	Gcg/Acg	2/2	0.147371881831448	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	2	TRUE	0	0.209608140134718	2		523	272	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111855978	111855978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1484288251	NA	P-0061145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	32	490	0	ENST00000341259.2:c.29C>T	p.Ser10Leu	p.S10L	ENST00000341259	NM_005475.2	10	tCg/tTg	2/8	0.0472697960704695	4	FACETS	0.873	0.709	1	0.437	0.354	0.53	INDETERMINATE	1	TRUE	2	0.209608140134718	4		490	423	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487153	56487153	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	70	399	0	ENST00000267101.3:c.1299G>C	p.Met433Ile	p.M433I	ENST00000267101	NM_001982.3	433	atG/atC	12/28	0.209608140134718	6	FACETS	0.913	0.802	1	0.685	0.601	0.774	CLONAL	3	TRUE	2	0.209608140134718	6		399	346	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749515	41749515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	34	419	0	ENST00000226382.2:c.280G>A	p.Glu94Lys	p.E94K	ENST00000226382	NM_003924.3	94	Gag/Aag	2/3	1	2	FACETS	0.992	0.813	1	0.992	0.813	1	CLONAL	1	TRUE	1	0.209608140134718	2		419	327	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942795	44942796	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	53	196	0	ENST00000377967.4:c.3376dup	p.Ile1126AsnfsTer25	p.I1126Nfs*25	ENST00000377967	NM_021140.2	1125	-/A	23/29	0.209608140134718	3	FACETS	0.922	0.797	1			1	CLONAL	3	TRUE	NA	0.209608140134718	3		196	202	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577103	7577103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555525248	NA	P-0061145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	93	535	0	ENST00000269305.4:c.835G>A	p.Gly279Arg	p.G279R	ENST00000269305	NM_001126112.2	279	Ggg/Agg	8/11	0.209608140134718	2	FACETS	0.969	0.866	1	0.969	0.866	1	CLONAL	2	TRUE	0	0.209608140134718	2		535	458	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118354898	118354898	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	34	394	0	ENST00000534358.1:c.4087G>T	p.Glu1363Ter	p.E1363*	ENST00000534358	NM_005933.3	1363	Gaa/Taa	9/36	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.209608140134718	2		394	294	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290277	15290277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	53	638	0	ENST00000263388.2:c.3358G>A	p.Glu1120Lys	p.E1120K	ENST00000263388	NM_000435.2	1120	Gag/Aag	21/33	0.209608140134718	3	FACETS	1	0.905	1	0.541	0.462	0.629	CLONAL	1	TRUE	1	0.209608140134718	3		638	516	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637552	52637552	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	23	377	0	ENST00000394830.3:c.2764G>C	p.Glu922Gln	p.E922Q	ENST00000394830	NM_018313.4	922	Gaa/Caa	18/30	0.0472697960704695	4	FACETS	0.654	0.509	0.822	0.327	0.254	0.411	INDETERMINATE	1	TRUE	2	0.209608140134718	4		377	406	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637717	52637717	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	34	363	0	ENST00000394830.3:c.2599G>C	p.Glu867Gln	p.E867Q	ENST00000394830	NM_018313.4	867	Gaa/Caa	18/30	0.0472697960704695	4	FACETS	1	0.911	1	0.598	0.49	0.719	INDETERMINATE	1	TRUE	2	0.209608140134718	4		363	328	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637726	52637726	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	31	352	0	ENST00000394830.3:c.2590G>C	p.Asp864His	p.D864H	ENST00000394830	NM_018313.4	864	Gat/Cat	18/30	0.0472697960704695	4	FACETS	1	0.892	1	0.577	0.468	0.7	INDETERMINATE	1	TRUE	2	0.209608140134718	4		352	310	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179218	123179218	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	33	171	0	ENST00000218089.9:c.667G>T	p.Ala223Ser	p.A223S	ENST00000218089	NM_001042749.1	223	Gct/Tct	8/35	0.0961264919051574	2	FACETS	1	0.892	1			1	INDETERMINATE	2	TRUE	NA	0.209608140134718	2		171	142	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0061147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	46	382	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.902	0.763	1	0.902	0.763	1	CLONAL	1	TRUE	1	0.31	2		382	329	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28963995	28963995	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061148-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	57	411	0	ENST00000282397.4:c.1907G>T	p.Cys636Phe	p.C636F	ENST00000282397	NM_002019.4	636	tGc/tTc	13/30	1	2	FACETS	0.775	0.666	0.895	0.775	0.666	0.895	SUBCLONAL	1	TRUE	1	0.272752447147092	2		411	539	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962298	2962298	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769577430	NA	P-0061148-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	79	385	1	ENST00000396946.4:c.2239G>A	p.Val747Ile	p.V747I	ENST00000396946	NM_032415.4	747	Gtc/Atc	17/25	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.272752447147092	2		386	440	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163774	72163774	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061148-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	65	382	0	ENST00000357731.5:c.584G>T	p.Arg195Met	p.R195M	ENST00000357731	NM_173808.2	195	aGg/aTg	4/7	1	2	FACETS	0.953	0.828	1	0.953	0.828	1	CLONAL	1	TRUE	1	0.272752447147092	2		382	500	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121799	108121800	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0061148-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	82	423	0	ENST00000278616.4:c.1607_1607+1delinsTT		p.X536_splice	ENST00000278616	NM_000051.3	536		10/63	0.272752447147092	1	FACETS	0.892	0.788	1	0.892	0.788	1	CLONAL	1	TRUE	0	0.272752447147092	1		423	582	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398133	4398133	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061148-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	50	408	0	ENST00000261254.3:c.697G>T	p.Ala233Ser	p.A233S	ENST00000261254	NM_001759.3	233	Gct/Tct	4/5	1	2	FACETS	0.787	0.668	0.917	0.787	0.668	0.917	CLONAL	1	TRUE	1	0.272752447147092	2		408	466	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435523	18435523	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061148-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	81	428	0	ENST00000266497.5:c.509del	p.Gly170AspfsTer29	p.G170Dfs*29	ENST00000266497		170	Gga/ga	1/31	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.272752447147092	2		428	528	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991088	41991088	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061148-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	79	341	0	ENST00000219905.7:c.2043del	p.Thr682GlnfsTer29	p.T682Qfs*29	ENST00000219905	NM_001164273.1	681	Ggg/gg	4/24	1	2	FACETS	0.939	0.826	1	0.939	0.826	1	CLONAL	1	TRUE	1	0.272752447147092	2		341	617	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000056	42000057	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0061148-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	84	433	0	ENST00000219905.7:c.2320_2320+1dup		p.-773fs	ENST00000219905	NM_001164273.1	773	-/GG	6/24	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.272752447147092	2		433	571	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351302	89351302	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061148-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	80	602	0	ENST00000301030.4:c.1648A>T	p.Asn550Tyr	p.N550Y	ENST00000301030	NM_001256183.1	550	Aat/Tat	9/13	0.272752447147092	1	FACETS	0.795	0.7	0.897	0.795	0.7	0.897	SUBCLONAL	1	TRUE	0	0.272752447147092	1		602	637	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562746	29562746	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs199474742	NA	P-0061148-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	93	406	0	ENST00000356175.3:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000356175	NM_000267.3	1276	Cga/Tga	28/57	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.272752447147092	2		406	532	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663807	29663807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756746198	NA	P-0061148-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	110	389	0	ENST00000356175.3:c.6239C>T	p.Pro2080Leu	p.P2080L	ENST00000356175	NM_000267.3	2080	cCc/cTc	41/57	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.272752447147092	2		389	652	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58701013	58701013	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061148-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	98	424	0	ENST00000305921.3:c.604G>C	p.Asp202His	p.D202H	ENST00000305921	NM_003620.3	202	Gac/Cac	2/6	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.272752447147092	2		424	664	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498477	89498477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753130827	NA	P-0061148-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	68	378	0	ENST00000336596.2:c.2449G>A	p.Val817Met	p.V817M	ENST00000336596	NM_005233.5	817	Gtg/Atg	14/17	1	2	FACETS	0.895	0.78	1	0.895	0.78	1	CLONAL	1	TRUE	1	0.272752447147092	2		378	557	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528604	89528604	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061148-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	99	378	0	ENST00000336596.2:c.2904C>G	p.Ser968Arg	p.S968R	ENST00000336596	NM_005233.5	968	agC/agG	17/17	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.272752447147092	2		378	555	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750589	57750589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1414255106	NA	P-0061148-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	75	391	0	ENST00000274289.3:c.1879C>T	p.His627Tyr	p.H627Y	ENST00000274289	NM_006622.3	627	Cat/Tat	14/14	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.272752447147092	2		391	547	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117632231	117632231	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061148-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	80	335	0	ENST00000368508.3:c.6185A>C	p.Asp2062Ala	p.D2062A	ENST00000368508	NM_002944.2	2062	gAt/gCt	39/43	0.272752447147092	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.272752447147092	1		335	415	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940465	13940465	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0061148-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	76	315	0	ENST00000405192.2:c.1042-1G>T		p.X348_splice	ENST00000405192	NM_001163147.1	348			1	2	FACETS	0.945	0.829	1	0.945	0.829	1	CLONAL	1	TRUE	1	0.272752447147092	2		315	590	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319965	8319965	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061148-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	82	385	0	ENST00000356435.5:c.5536G>C	p.Ala1846Pro	p.A1846P	ENST00000356435		1846	Gcg/Ccg	34/35	0.272752447147092	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	0	0.272752447147092	1		385	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691039	NA	P-0061149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	324	581	0	ENST00000269305.4:c.919+1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.345995534934719	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.359410574618306	2		581	848	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0061149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	188	448	0	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	0.190411145626476	5	FACETS	0.976	0.903	1	0.651	0.602	0.701	INDETERMINATE	2	TRUE	2	0.359410574618306	5		448	825	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541789	187541789	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1444904972	NA	P-0061149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	249	538	0	ENST00000441802.2:c.5951A>G	p.Tyr1984Cys	p.Y1984C	ENST00000441802	NM_005245.3	1984	tAc/tGc	10/27	0.218912839508994	3	FACETS	0.948	0.889	1			1	CLONAL	2	TRUE	NA	0.359410574618306	3		538	862	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	117	611	0				ENST00000310581	NM_198253.2	-/1132			0.297130238056647	3	FACETS	1	0.984	1	0.727	0.66	0.796	CLONAL	1	TRUE	1	0.446624547971079	3		611	441	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	174	539	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.326136263252511	3	FACETS	0.819	0.758	0.881	0.819	0.758	0.881	CLONAL	2	TRUE	1	0.446624547971079	3		539	582	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	136	393	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.297130238056647	3	FACETS	1	0.986	1	0.71	0.649	0.773	CLONAL	1	TRUE	1	0.446624547971079	3		393	525	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	188	942	1	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.299943694042235	2	FACETS	1	0.989	1	0.68	0.631	0.73	CLONAL	1	TRUE	0	0.446624547971079	2		943	619	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913385	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	72	539	0	ENST00000304494.5:c.247C>G	p.His83Asp	p.H83D	ENST00000304494	NM_000077.4	83	Cac/Gac	2/3	0.326136263252511	3	FACETS	0.678	0.592	0.769	0.339	0.296	0.385	SUBCLONAL	1	TRUE	1	0.446624547971079	3		539	582	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136799	2136799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137854153	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	199	553	1	ENST00000219476.3:c.4916G>A	p.Arg1639His	p.R1639H	ENST00000219476	NM_000548.3	1639	cGc/cAc	38/42	0.297130238056647	3	FACETS	0.837	0.779	0.897	0.837	0.779	0.897	CLONAL	2	TRUE	1	0.446624547971079	3		554	651	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259262	89259262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770780950	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	154	419	0	ENST00000336596.2:c.406C>T	p.Arg136Ter	p.R136*	ENST00000336596	NM_005233.5	136	Cga/Tga	3/17	0.296042579324744	4	FACETS	0.823	0.756	0.892	0.823	0.756	0.892	CLONAL	2	TRUE	2	0.446624547971079	4		419	606	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857524	9857524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778230379	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	62	476	0	ENST00000330684.3:c.3877G>A	p.Asp1293Asn	p.D1293N	ENST00000330684	NM_001134407.1	1293	Gat/Aat	13/13	0.297130238056647	3	FACETS	0.657	0.568	0.753	0.328	0.284	0.377	SUBCLONAL	1	TRUE	1	0.446624547971079	3		476	517	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42842607	42842607	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	78	461	0	ENST00000398585.3:c.1250G>A	p.Trp417Ter	p.W417*	ENST00000398585	NM_001135099.1	417	tGg/tAg	11/14	0.326136263252511	3	FACETS	0.748	0.658	0.845	0.374	0.329	0.423	SUBCLONAL	1	TRUE	1	0.446624547971079	3		461	571	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574362	41574362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	144	552	0	ENST00000263253.7:c.6647G>A	p.Gly2216Glu	p.G2216E	ENST00000263253	NM_001429.3	2216	gGa/gAa	31/31	0.296042579324744	4	FACETS	1	0.986	1	0.705	0.644	0.767	CLONAL	1	TRUE	2	0.446624547971079	4		552	662	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587161	189587161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173679499	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	114	349	0	ENST00000264731.3:c.1178G>A	p.Arg393Gln	p.R393Q	ENST00000264731	NM_003722.4	393	cGa/cAa	9/14	0.296042579324744	4	FACETS	0.751	0.679	0.825	0.751	0.679	0.825	SUBCLONAL	2	TRUE	2	0.446624547971079	4		349	492	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508059	106508059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142380460	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	159	394	0	ENST00000359195.3:c.53G>A	p.Arg18Gln	p.R18Q	ENST00000359195	NM_002649.2	18	cGa/cAa	2/11	0.297130238056647	3	FACETS	0.873	0.806	0.941	0.873	0.806	0.941	CLONAL	2	TRUE	1	0.446624547971079	3		394	499	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518175	8518175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1354824749	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	101	415	0	ENST00000356435.5:c.1216G>A	p.Glu406Lys	p.E406K	ENST00000356435		406	Gaa/Aaa	10/35	0.326136263252511	3	FACETS	1	0.955	1	0.558	0.5	0.618	CLONAL	1	TRUE	1	0.446624547971079	3		415	496	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858706	9858706	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs796052553	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	146	468	0	ENST00000330684.3:c.2695C>T	p.Arg899Trp	p.R899W	ENST00000330684	NM_001134407.1	899	Cgg/Tgg	13/13	0.297130238056647	3	FACETS	0.759	0.697	0.823	0.759	0.697	0.823	SUBCLONAL	2	TRUE	1	0.446624547971079	3		468	527	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799632	3799632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267606752	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	74	219	0	ENST00000262367.5:c.3832G>A	p.Glu1278Lys	p.E1278K	ENST00000262367	NM_004380.2	1278	Gaa/Aaa	21/31	0.297130238056647	3	FACETS	1	0.966	1	0.633	0.559	0.712	CLONAL	1	TRUE	1	0.446624547971079	3		219	320	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923440	9923440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	62	427	0	ENST00000330684.3:c.1847C>T	p.Ser616Phe	p.S616F	ENST00000330684	NM_001134407.1	616	tCc/tTc	9/13	0.297130238056647	3	FACETS	0.659	0.57	0.756	0.33	0.285	0.378	SUBCLONAL	1	TRUE	1	0.446624547971079	3		427	515	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940079	31940079	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	181	643	0	ENST00000375333.2:c.221G>A	p.Gly74Glu	p.G74E	ENST00000375333	NM_032454.1	74	gGa/gAa	2/8	0.268084670135634	4	FACETS	1	0.988	1	0.68	0.628	0.735	CLONAL	1	TRUE	2	0.446624547971079	4		643	862	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057081	180057081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139378654	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	70	538	0	ENST00000261937.6:c.538G>A	p.Gly180Arg	p.G180R	ENST00000261937	NM_182925.4	180	Ggg/Agg	5/30	1	2	FACETS	0.683	0.597	0.775	0.683	0.597	0.775	SUBCLONAL	1	TRUE	1	0.446624547971079	2		538	459	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949069	151949069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776295921	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	64	344	1	ENST00000262189.6:c.1576C>T	p.Arg526Cys	p.R526C	ENST00000262189	NM_170606.2	526	Cgt/Tgt	11/59	0.297130238056647	3	FACETS	0.751	0.652	0.858	0.375	0.326	0.429	SUBCLONAL	1	TRUE	1	0.446624547971079	3		345	467	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265697	10265697	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	156	440	1	ENST00000340748.4:c.1480G>A	p.Glu494Lys	p.E494K	ENST00000340748		494	Gag/Aag	19/40	0.223338336546523	4	FACETS	0.919	0.846	0.994	0.919	0.846	0.994	INDETERMINATE	2	TRUE	2	0.446624547971079	4		441	550	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643794	38643794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	88	445	0	ENST00000299084.4:c.1264C>T	p.Pro422Ser	p.P422S	ENST00000299084	NM_152594.2	422	Cct/Tct	7/7	0.326136263252511	3	FACETS	0.846	0.751	0.947	0.423	0.375	0.474	CLONAL	1	TRUE	1	0.446624547971079	3		445	570	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641159	117641159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	171	545	0	ENST00000368508.3:c.5812C>T	p.Pro1938Ser	p.P1938S	ENST00000368508	NM_002944.2	1938	Cct/Tct	36/43	0.299943694042235	2	FACETS	1	0.99	1	0.725	0.672	0.78	CLONAL	1	TRUE	0	0.446624547971079	2		545	528	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400336	225400336	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	201	300	1	ENST00000264414.4:c.287C>T	p.Ser96Leu	p.S96L	ENST00000264414	NM_003590.4	96	tCa/tTa	3/16	0.301375079744734	6	FACETS	1	0.972	1	0.804	0.751	0.857	CLONAL	3	TRUE	2	0.446624547971079	6		301	530	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044581	128044581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	137	404	0	ENST00000285398.2:c.1040C>T	p.Ser347Phe	p.S347F	ENST00000285398	NM_000122.1	347	tCc/tTc	8/15	0.176247322992263	5	FACETS	0.851	0.777	0.928	0.567	0.518	0.619	INDETERMINATE	2	TRUE	2	0.446624547971079	5		404	602	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797202	45797202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908382	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	84	599	0	ENST00000450313.1:c.1213C>T	p.Pro405Ser	p.P405S	ENST00000450313	NM_012222.2	405	Ccg/Tcg	13/16	0.297130238056647	3	FACETS	0.732	0.647	0.822	0.366	0.323	0.411	SUBCLONAL	1	TRUE	1	0.446624547971079	3		599	629	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551606	150551606	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	442	498	0	ENST00000369026.2:c.401del	p.Leu134ProfsTer110	p.L134Pfs*110	ENST00000369026	NM_021960.4	134	cTc/cc	1/3	0.446624547971079	6	FACETS	0.88	0.842	0.918	0.88	0.842	0.918	CLONAL	4	TRUE	2	0.446624547971079	6		498	1065	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162688912	162688912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	122	329	0	ENST00000367921.3:c.59C>T	p.Ser20Phe	p.S20F	ENST00000367921	NM_006182.2	20	tCt/tTt	3/18	0.446624547971079	6	FACETS	0.856	0.776	0.94	0.428	0.388	0.47	CLONAL	2	TRUE	2	0.446624547971079	6		329	604	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609931	43609931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs905507912	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	68	649	0	ENST00000355710.3:c.1883C>T	p.Pro628Leu	p.P628L	ENST00000355710	NM_020975.4	628	cCa/cTa	11/20	0.297130238056647	3	FACETS	0.501	0.435	0.573	0.251	0.217	0.287	SUBCLONAL	1	TRUE	1	0.446624547971079	3		649	743	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132924	64132924	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	134	522	0	ENST00000334205.4:c.1058C>T	p.Pro353Leu	p.P353L	ENST00000334205	NM_003942.2	353	cCc/cTc	9/17	0.296042579324744	4	FACETS	1	0.983	1	0.669	0.609	0.731	CLONAL	1	TRUE	2	0.446624547971079	4		522	649	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424788	49424796	+	inframe_deletion	In_Frame_Del	DEL	GGTGTCAAA	GGTGTCAAA	-	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	130	541	0	ENST00000301067.7:c.13551_13559del	p.Leu4518_Pro4520del	p.L4518_P4520del	ENST00000301067	NM_003482.3	4517	ccTTTGACACCg/ccg	40/54	0.297130238056647	3	FACETS	1	0.978	1	0.616	0.561	0.674	CLONAL	1	TRUE	1	0.446624547971079	3		541	578	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51504572	51504572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	143	437	0	ENST00000260433.2:c.1208G>A	p.Arg403Lys	p.R403K	ENST00000260433		403	aGa/aAa	9/10	0.326136263252511	3	FACETS	0.755	0.692	0.819	0.755	0.692	0.819	SUBCLONAL	2	TRUE	1	0.446624547971079	3		437	519	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862733	9862733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	115	418	0	ENST00000330684.3:c.2570C>T	p.Pro857Leu	p.P857L	ENST00000330684	NM_001134407.1	857	cCt/cTt	12/13	0.297130238056647	3	FACETS	1	0.977	1	0.635	0.575	0.698	CLONAL	1	TRUE	1	0.446624547971079	3		418	496	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944228	81944228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	68	405	0	ENST00000359376.3:c.1837C>T	p.Leu613Phe	p.L613F	ENST00000359376	NM_002661.3	613	Ctc/Ttc	18/33	0.297130238056647	3	FACETS	0.796	0.694	0.905	0.398	0.347	0.453	CLONAL	1	TRUE	1	0.446624547971079	3		405	468	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544236	86544237	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	124	565	0	ENST00000262426.4:c.61_62delinsAT	p.Gly21Ile	p.G21I	ENST00000262426	NM_001451.2	21	GGa/ATa	1/2	0.297130238056647	3	FACETS	1	0.98	1	0.648	0.589	0.71	CLONAL	1	TRUE	1	0.446624547971079	3		565	524	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667834	37667834	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	120	360	0	ENST00000447079.4:c.2719del	p.Leu907CysfsTer2	p.L907Cfs*2	ENST00000447079	NM_015083.1	907	Ctg/tg	8/14	0.296042579324744	4	FACETS	1	0.984	1	0.731	0.663	0.802	CLONAL	1	TRUE	2	0.446624547971079	4		360	532	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354406	40354406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	187	703	0	ENST00000293328.3:c.2189C>T	p.Pro730Leu	p.P730L	ENST00000293328	NM_012448.3	730	cCc/cTc	18/19	0.296042579324744	4	FACETS	1	0.99	1	0.735	0.68	0.792	CLONAL	1	TRUE	2	0.446624547971079	4		703	824	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118893	70118894	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	159	617	0	ENST00000245479.2:c.465_466delinsAA	p.Glu156Lys	p.E156K	ENST00000245479	NM_000346.3	155	gtGGag/gtAAag	2/3	0.297130238056647	3	FACETS	1	0.987	1	0.686	0.631	0.743	CLONAL	1	TRUE	1	0.446624547971079	3		617	635	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796095	78796095	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	71	459	0	ENST00000306801.3:c.985C>T	p.Pro329Ser	p.P329S	ENST00000306801	NM_020761.2	329	Ccc/Tcc	8/34	0.297130238056647	3	FACETS	0.696	0.608	0.79	0.348	0.304	0.395	SUBCLONAL	1	TRUE	1	0.446624547971079	3		459	559	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61306458	61306458	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	54	324	0	ENST00000341074.5:c.729G>A	p.Met243Ile	p.M243I	ENST00000341074	NM_002974.2	243	atG/atA	7/8	0.297130238056647	3	FACETS	0.774	0.664	0.895	0.387	0.332	0.448	SUBCLONAL	1	TRUE	1	0.446624547971079	3		324	382	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61307011	61307011	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	37	210	0	ENST00000341074.5:c.470-1G>A		p.X157_splice	ENST00000341074	NM_002974.2	157			0.297130238056647	3	FACETS	0.714	0.591	0.85	0.357	0.295	0.425	SUBCLONAL	1	TRUE	1	0.446624547971079	3		210	284	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149861	99149861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	132	372	0	ENST00000074304.5:c.173C>T	p.Pro58Leu	p.P58L	ENST00000074304	NM_001134224.1	58	cCa/cTa	5/26	0.176247322992263	5	FACETS	0.872	0.795	0.952	0.581	0.53	0.635	INDETERMINATE	2	TRUE	2	0.446624547971079	5		372	566	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095763	178095763	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	139	452	0	ENST00000397062.3:c.1568T>C	p.Val523Ala	p.V523A	ENST00000397062	NM_006164.4	523	gTa/gCa	5/5	0.176247322992263	5	FACETS	0.964	0.882	1	0.643	0.588	0.7	INDETERMINATE	2	TRUE	2	0.446624547971079	5		452	539	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560791	9560791	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	139	482	0	ENST00000353224.5:c.990+1G>A		p.X330_splice	ENST00000353224	NM_177990.2	330			0.176247322992263	5	FACETS	0.869	0.794	0.947	0.579	0.529	0.632	INDETERMINATE	2	TRUE	2	0.446624547971079	5		482	598	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655442	45655442	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	66	476	0	ENST00000407780.3:c.410A>T	p.Asn137Ile	p.N137I	ENST00000407780	NM_001283052.1	137	aAc/aTc	4/7	0.326136263252511	3	FACETS	0.753	0.655	0.859	0.377	0.327	0.43	SUBCLONAL	1	TRUE	1	0.446624547971079	3		476	480	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050390	37050390	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs63750102	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	110	297	0	ENST00000231790.2:c.539T>C	p.Val180Ala	p.V180A	ENST00000231790	NM_000249.3	180	gTt/gCt	6/19	0.296042579324744	4	FACETS	0.756	0.683	0.833	0.756	0.683	0.833	SUBCLONAL	2	TRUE	2	0.446624547971079	4		297	471	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277853	41277853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1306221365	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	129	413	0	ENST00000349496.5:c.1817C>T	p.Pro606Leu	p.P606L	ENST00000349496	NM_001904.3	606	cCc/cTc	12/15	0.296042579324744	4	FACETS	1	0.984	1	0.692	0.629	0.757	CLONAL	1	TRUE	2	0.446624547971079	4		413	604	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990455	69990455	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	111	309	0	ENST00000394351.3:c.414G>A	p.Met138Ile	p.M138I	ENST00000394351	NM_000248.3	138	atG/atA	4/9	0.296042579324744	4	FACETS	0.772	0.697	0.849	0.772	0.697	0.849	SUBCLONAL	2	TRUE	2	0.446624547971079	4		309	466	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131976363	131976364	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	70	393	0	ENST00000265335.6:c.3619-1_3619delinsAA		p.X1207_splice	ENST00000265335		1207		24/25	1	2	FACETS	0.646	0.565	0.734	0.646	0.565	0.734	SUBCLONAL	1	TRUE	1	0.446624547971079	2		393	485	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166428	32166428	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs1174632202	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	163	495	0	ENST00000375023.3:c.4615C>T	p.Gln1539Ter	p.Q1539*	ENST00000375023	NM_004557.3	1539	Cag/Tag	25/30	0.268084670135634	4	FACETS	0.78	0.718	0.844	0.78	0.718	0.844	SUBCLONAL	2	TRUE	2	0.446624547971079	4		495	677	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289251	33289252	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	128	452	2	ENST00000374542.5:c.300_301delinsAA	p.Ala101Thr	p.A101T	ENST00000374542	NM_001141970.1	100	ttGGcc/ttAAcc	3/8	0.268084670135634	4	FACETS	1	0.984	1	0.711	0.647	0.778	CLONAL	1	TRUE	2	0.446624547971079	4		454	583	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553155	106553155	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	139	547	0	ENST00000369096.4:c.1120T>G	p.Tyr374Asp	p.Y374D	ENST00000369096	NM_001198.3	374	Tac/Gac	5/7	0.299943694042235	2	FACETS	1	0.977	1	0.596	0.546	0.649	CLONAL	1	TRUE	0	0.446624547971079	2		547	522	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69027999	69027999	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	79	330	0	ENST00000288368.4:c.3158C>T	p.Ser1053Leu	p.S1053L	ENST00000288368	NM_024870.2	1053	tCa/tTa	26/40	0.296042579324744	4	FACETS	1	0.968	1	0.638	0.564	0.717	CLONAL	1	TRUE	2	0.446624547971079	4		330	401	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534921	5534922	+	missense_variant	Missense_Mutation	DNP	GA	GA	AC	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	147	530	1	ENST00000397747.3:c.232_233delinsAC	p.Glu78Thr	p.E78T	ENST00000397747	NM_025239.3	78	GAg/ACg	3/7	0.326136263252511	3	FACETS	1	0.986	1	0.691	0.633	0.75	CLONAL	1	TRUE	1	0.446624547971079	3		531	583	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8527350	8527350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	45	173	0	ENST00000356435.5:c.545C>T	p.Ser182Phe	p.S182F	ENST00000356435		182	tCt/tTt	5/35	0.326136263252511	3	FACETS	1	0.933	1	0.593	0.504	0.688	CLONAL	1	TRUE	1	0.446624547971079	3		173	208	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608256	100608256	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061150-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	61	222	0	ENST00000308731.7:c.1834C>T	p.Gln612Ter	p.Q612*	ENST00000308731	NM_000061.2	612	Caa/Taa	18/19	1	1	FACETS	0.956	0.836	1	0.956	0.836	1	CLONAL	1	TRUE	0	0.446624547971079	1		222	222	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0061151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	119	304	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.502	0.455	0.551	0.502	0.455	0.551	SUBCLONAL	1	TRUE	1	0.855978978081147	2		304	554	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554225	63554225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	131	633	0	ENST00000307078.5:c.514G>A	p.Asp172Asn	p.D172N	ENST00000307078	NM_004655.3	172	Gac/Aac	2/11	1	2	FACETS	0.496	0.451	0.543	0.496	0.451	0.543	SUBCLONAL	1	TRUE	1	0.855978978081147	2		633	617	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874334	151874334	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0061151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	137	465	0	ENST00000262189.6:c.8204T>G	p.Leu2735Ter	p.L2735*	ENST00000262189	NM_170606.2	2735	tTa/tGa	38/59	1	2	FACETS	0.517	0.472	0.564	0.517	0.472	0.564	SUBCLONAL	1	TRUE	1	0.855978978081147	2		465	619	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015628	27015656	+	protein_altering_variant	In_Frame_Del	DEL	GAGAAATATGTGTTAAATTCACTCGTGGT	GAGAAATATGTGTTAAATTCACTCGTGGT	CA	novel	NA	P-0061151-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	107	497	2	ENST00000335756.4:c.215_243delinsCA	p.Arg72_Gly81delinsThr	p.R72_G81delinsT	ENST00000335756	NM_001809.3	72	aGAGAAATATGTGTTAAATTCACTCGTGGT/aCA	3/5	1	2	FACETS	0.443	0.399	0.49	0.443	0.399	0.49	SUBCLONAL	1	TRUE	1	0.855978978081147	2		499	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579580	7579580	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781866	NA	P-0061153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	142	710	0	ENST00000269305.4:c.107C>T	p.Pro36Leu	p.P36L	ENST00000269305	NM_001126112.2	36	cCg/cTg	4/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.396032273330373	2		710	567	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1956932	1956932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1190376594	NA	P-0061153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	134	628	0	ENST00000382891.5:c.2383G>A	p.Gly795Arg	p.G795R	ENST00000382891	NM_133335.3	795	Ggg/Agg	13/22	1	2	FACETS	0.968	0.881	1	0.968	0.881	1	CLONAL	1	TRUE	1	0.396032273330373	2		628	699	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572311	41572311	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	65	624	0	ENST00000263253.7:c.4840G>A	p.Asp1614Asn	p.D1614N	ENST00000263253	NM_001429.3	1614	Gat/Aat	30/31	1	2	FACETS	0.565	0.49	0.646	0.565	0.49	0.646	SUBCLONAL	1	TRUE	1	0.396032273330373	2		624	581	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591895	48591895	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs377767346	NA	P-0061153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	67	621	0	ENST00000342988.3:c.1058A>C	p.Tyr353Ser	p.Y353S	ENST00000342988	NM_005359.5	353	tAc/tCc	9/12	0.359410553864595	1	FACETS	0.525	0.457	0.598	0.525	0.457	0.598	SUBCLONAL	1	TRUE	0	0.396032273330373	1		621	517	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591943	48591943	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	67	532	0	ENST00000342988.3:c.1106A>T	p.Asn369Ile	p.N369I	ENST00000342988	NM_005359.5	369	aAt/aTt	9/12	0.359410553864595	1	FACETS	0.547	0.476	0.624	0.547	0.476	0.624	SUBCLONAL	1	TRUE	0	0.396032273330373	1		532	496	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84393415	84393415	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	40	318	0	ENST00000321945.7:c.242A>C	p.Asn81Thr	p.N81T	ENST00000321945	NM_139076.2	81	aAt/aCt	4/9	1	2	FACETS	0.645	0.538	0.764	0.645	0.538	0.764	SUBCLONAL	1	TRUE	1	0.396032273330373	2		318	313	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0061154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	107	592	0	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.140019270894409	3	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.21	3		592	771	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	112	328	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.21	2		329	931	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0061154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	120	780	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.21	2		780	914	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936768	78936768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs987417975	NA	P-0061154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	87	654	0	ENST00000306801.3:c.3850G>A	p.Gly1284Arg	p.G1284R	ENST00000306801	NM_020761.2	1284	Gga/Aga	33/34	1	2	FACETS	0.927	0.819	1	0.927	0.819	1	CLONAL	1	TRUE	1	0.21	2		654	894	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446270	187446270	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	100	532	3	ENST00000232014.4:c.1418del	p.Pro473ArgfsTer117	p.P473Rfs*117	ENST00000232014	NM_001130845.1	473	cCg/cg	6/10	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.21	2		535	885	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610695	52610695	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	94	468	0	ENST00000394830.3:c.3478C>T	p.Arg1160Ter	p.R1160*	ENST00000394830	NM_018313.4	1160	Cga/Tga	23/30	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.21	2		468	606	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641214	3641214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs546657275	NA	P-0061154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	64	572	0	ENST00000294008.3:c.2425G>A	p.Glu809Lys	p.E809K	ENST00000294008	NM_032444.2	809	Gaa/Aaa	12/15	1	2	FACETS	0.805	0.696	0.924	0.805	0.696	0.924	CLONAL	1	TRUE	1	0.21	2		572	757	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863054	56863054	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1266824391	NA	P-0061154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	38	468	1	ENST00000519728.1:c.327del	p.Glu110LysfsTer15	p.E110Kfs*15	ENST00000519728	NM_002350.3	107	acA/ac	5/13	1	2	FACETS	0.548	0.452	0.656	0.548	0.452	0.656	SUBCLONAL	1	TRUE	1	0.21	2		469	660	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652243	48652243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	312	573	1	ENST00000376670.3:c.914G>A	p.Arg305Gln	p.R305Q	ENST00000376670	NM_002049.3	305	cGa/cAa	6/6	0.255304339409572	4	FACETS	0.939	0.888	0.992			1	CLONAL	4	TRUE	NA	0.21	4		574	957	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247573	53247573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	65	532	0	ENST00000375401.3:c.236C>T	p.Thr79Met	p.T79M	ENST00000375401	NM_004187.3	79	aCg/aTg	3/26	1	2	FACETS	0.826	0.716	0.947	0.826	0.716	0.947	CLONAL	1	TRUE	1	0.21	2		532	749	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446922	18446922	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	48	287	0	ENST00000266497.5:c.1007T>C	p.Val336Ala	p.V336A	ENST00000266497		336	gTa/gCa	4/31	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.21	2		287	418	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849011	156849011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749869863	NA	P-0061154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	62	638	0	ENST00000524377.1:c.1903G>A	p.Ala635Thr	p.A635T	ENST00000524377	NM_002529.3	635	Gct/Act	15/17	1	2	FACETS	0.707	0.609	0.814	0.707	0.609	0.814	SUBCLONAL	1	TRUE	1	0.21	2		638	835	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112489	115112490	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	80	571	0	ENST00000257566.3:c.1250dup	p.Ala418ArgfsTer3	p.A418Rfs*3	ENST00000257566	NM_016569.3	417	ttc/ttTc	7/8	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.21	2		571	740	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442837	99442837	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	51	463	0	ENST00000268035.6:c.1234G>C	p.Glu412Gln	p.E412Q	ENST00000268035	NM_000875.3	412	Gag/Cag	5/21	1	2	FACETS	0.728	0.618	0.85	0.728	0.618	0.85	SUBCLONAL	1	TRUE	1	0.21	2		463	667	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732927	30732927	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs193922664	NA	P-0061154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	72	525	0	ENST00000295754.5:c.1540T>C	p.Cys514Arg	p.C514R	ENST00000295754	NM_003242.5	514	Tgt/Cgt	7/7	NA	2	FACETS	1	0.905	1			1	INDETERMINATE	1	TRUE	NA	0.21	2		525	657	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72897416	72897416	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	41	539	0	ENST00000325599.8:c.76G>A	p.Val26Ile	p.V26I	ENST00000325599	NM_018130.2	26	Gtc/Atc	1/11	1	2	FACETS	0.566	0.47	0.673	0.566	0.47	0.673	SUBCLONAL	1	TRUE	1	0.21	2		539	690	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752781	42752781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772231752	NA	P-0061155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	48	562	0	ENST00000222329.4:c.1483G>A	p.Glu495Lys	p.E495K	ENST00000222329	NM_006494.2	495	Gaa/Aaa	4/4	1	2	FACETS	0.875	0.737	1	0.875	0.737	1	CLONAL	1	TRUE	1	0.14	2		562	784	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980352	201980352	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	55	634	0	ENST00000359651.3:c.92del	p.Pro31LeufsTer12	p.P31Lfs*12	ENST00000359651		30	Ccc/cc	1/8	1	2	FACETS	0.865	0.738	1	0.865	0.738	1	CLONAL	1	TRUE	1	0.14	2		634	908	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253376	226253376	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	19	230	0	ENST00000366813.1:c.148C>A	p.Arg50Ser	p.R50S	ENST00000366813		50	Cgt/Agt	2/3	1	2	FACETS	0.805	0.611	1	0.805	0.611	1	CLONAL	1	TRUE	1	0.14	2		230	337	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281814	39281814	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1007628403	NA	P-0061155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	30	278	0	ENST00000402219.2:c.661C>G	p.Leu221Val	p.L221V	ENST00000402219	NM_005633.3	221	Cta/Gta	5/23	1	2	FACETS	0.997	0.803	1	0.997	0.803	1	CLONAL	1	TRUE	1	0.14	2		278	430	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	88	382	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.954	1	1	0.987	1	CLONAL	2	TRUE	1	0.21	2		382	371	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	159	498	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.979	1	1	0.993	1	CLONAL	2	TRUE	1	0.21	2		498	637	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	183	509	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.944	1	1	0.993	1	CLONAL	2	TRUE	1	0.21	2		513	849	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	94	476	10	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.956	0.855	1	1	0.986	1	CLONAL	2	TRUE	1	0.21	2		486	468	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	126	539	1	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	1	0.932	1	1	0.99	1	CLONAL	2	TRUE	1	0.21	2		540	582	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	181	428	1	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	1	2	FACETS	1	0.973	1	1	0.993	1	CLONAL	2	TRUE	1	0.21	2		429	773	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	118	525	3	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.816	0.737	0.899	1	0.986	1	CLONAL	2	TRUE	1	0.21	2		528	689	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	205	622	0	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	1	0.98	1	1	0.994	1	CLONAL	2	TRUE	1	0.21	2		622	852	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306996	65306997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	141	490	4	ENST00000342505.4:c.2580dup	p.Pro861ThrfsTer4	p.P861Tfs*4	ENST00000342505	NM_002227.2	860	-/A	19/25	1	2	FACETS	1	0.967	1	1	0.992	1	CLONAL	2	TRUE	1	0.21	2		494	602	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61729435	61729435	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	29	245	0	ENST00000401558.2:c.312del	p.Lys104AsnfsTer17	p.K104Nfs*17	ENST00000401558	NM_003400.3	104	aaA/aa	5/25	1	2	FACETS	0.719	0.577	0.881	0.719	0.577	0.881	SUBCLONAL	1	TRUE	1	0.21	2		245	384	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271331	18271331	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	199	589	1	ENST00000222254.8:c.377del	p.Pro126LeufsTer4	p.P126Lfs*4	ENST00000222254	NM_005027.3	125	Ccc/cc	3/16	1	2	FACETS	1	0.967	1	1	0.994	1	CLONAL	2	TRUE	1	0.21	2		590	883	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273806	18273806	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	204	581	0	ENST00000222254.8:c.1139T>A	p.Val380Asp	p.V380D	ENST00000222254	NM_005027.3	380	gTc/gAc	10/16	1	2	FACETS	1	0.982	1	1	0.994	1	CLONAL	2	TRUE	1	0.21	2		581	835	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390072	89390072	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765502894	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	119	355	0	ENST00000336596.2:c.821G>A	p.Arg274Gln	p.R274Q	ENST00000336596	NM_005233.5	274	cGa/cAa	4/17	1	2	FACETS	0.863	0.784	0.944	1	0.991	1	CLONAL	3	TRUE	1	0.21	2		355	438	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256409	46256409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754382773	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	123	437	0	ENST00000371998.3:c.637G>A	p.Ala213Thr	p.A213T	ENST00000371998		213	Gcc/Acc	7/23	1	2	FACETS	0.85	0.77	0.934	1	0.987	1	CLONAL	2	TRUE	1	0.21	2		437	689	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214821	36214821	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	119	489	0	ENST00000222270.7:c.3247C>T	p.Arg1083Ter	p.R1083*	ENST00000222270	NM_014727.1	1083	Cga/Tga	8/37	1	2	FACETS	1	0.943	1	1	0.99	1	CLONAL	2	TRUE	1	0.21	2		489	537	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528554	89528554	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	65	336	0	ENST00000336596.2:c.2858del	p.Lys953ArgfsTer20	p.K953Rfs*20	ENST00000336596	NM_005233.5	952	Aaa/aa	17/17	1	2	FACETS	0.792	0.689	0.901	1	0.974	1	CLONAL	2	TRUE	1	0.21	2		336	391	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022989	33022990	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	166	520	0	ENST00000300177.4:c.104dup	p.Pro36AlafsTer8	p.P36Afs*8	ENST00000300177	NM_001191322.1	33	atc/atCc	2/2	1	2	FACETS	1	0.976	1	1	0.993	1	CLONAL	2	TRUE	1	0.21	2		520	686	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450154	32450154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	44	534	0	ENST00000332351.3:c.658G>A	p.Val220Ile	p.V220I	ENST00000332351	NM_024426.4	220	Gtc/Atc	2/10	1	2	FACETS	0.773	0.648	0.912	0.773	0.648	0.912	CLONAL	1	TRUE	1	0.21	2		534	542	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910627	50910627	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1181610918	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	171	525	0	ENST00000440232.2:c.1730G>A	p.Gly577Asp	p.G577D	ENST00000440232	NM_002691.3	577	gGc/gAc	14/27	1	2	FACETS	0.84	0.776	0.907	1	0.994	1	CLONAL	3	TRUE	1	0.21	2		525	646	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524364	176524364	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759042869	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	131	582	0	ENST00000292408.4:c.2225C>T	p.Ala742Val	p.A742V	ENST00000292408	NM_213647.1	742	gCg/gTg	17/18	1	2	FACETS	0.932	0.848	1	1	0.989	1	CLONAL	2	TRUE	1	0.21	2		582	669	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438206	110438206	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	98	404	2	ENST00000375856.3:c.195del	p.Ser66ArgfsTer27	p.S66Rfs*27	ENST00000375856	NM_003749.2	65	ggG/gg	1/2	1	2	FACETS	0.92	0.824	1	1	0.986	1	CLONAL	2	TRUE	1	0.21	2		406	507	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605204	46605204	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1459319402	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	132	421	8	ENST00000263734.3:c.1421G>C	p.Ser474Thr	p.S474T	ENST00000263734	NM_001430.4	474	aGc/aCc	10/16	1	2	FACETS	1	0.98	1	1	0.992	1	CLONAL	2	TRUE	1	0.21	2		429	504	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602679	10602679	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	183	607	0	ENST00000171111.5:c.899A>G	p.Tyr300Cys	p.Y300C	ENST00000171111	NM_203500.1	300	tAc/tGc	3/6	1	2	FACETS	1	0.972	1	1	0.993	1	CLONAL	2	TRUE	1	0.21	2		607	790	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750683	128750683	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121918685	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	176	580	0	ENST00000377970.2:c.220C>G	p.Pro74Ala	p.P74A	ENST00000377970	NM_002467.4	74	Ccg/Gcg	2/3	1	2	FACETS	1	0.981	1	1	0.993	1	CLONAL	2	TRUE	1	0.21	2		580	706	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107996	30107996	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1165306493	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	34	403	0	ENST00000331968.5:c.811C>T	p.His271Tyr	p.H271Y	ENST00000331968	NM_002742.2	271	Cac/Tac	5/18	1	2	FACETS	0.51	0.415	0.617	0.51	0.415	0.617	SUBCLONAL	1	TRUE	1	0.21	2		403	635	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597451	10597451	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	130	450	0	ENST00000171111.5:c.1752C>A	p.Tyr584Ter	p.Y584*	ENST00000171111	NM_203500.1	584	taC/taA	6/6	1	2	FACETS	1	0.932	1	1	0.99	1	CLONAL	2	TRUE	1	0.21	2		450	602	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47503744	47503746	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1387779417	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	162	600	1	ENST00000404338.3:c.4307_4309del	p.Phe1436del	p.F1436del	ENST00000404338	NM_004491.4	1433	ccCTTc/ccc	6/6	0.206553345652386	3	FACETS	1	0.968	1			1	CLONAL	2	TRUE	NA	0.21	3		601	773	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099718	157099718	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	67	331	0	ENST00000346085.5:c.659del	p.Gly220AlafsTer46	p.G220Afs*46	ENST00000346085	NM_020732.3	219	Ggg/gg	1/20	1	2	FACETS	0.909	0.795	1	1	0.979	1	CLONAL	2	TRUE	1	0.21	2		331	351	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679887	33679887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200734680	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	121	512	0	ENST00000308377.4:c.2194C>T	p.Arg732Cys	p.R732C	ENST00000308377	NM_152270.3	732	Cgc/Tgc	5/5	1	2	FACETS	0.92	0.834	1	1	0.988	1	CLONAL	2	TRUE	1	0.21	2		512	626	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313214	65313214	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	36	449	0	ENST00000342505.4:c.1899+1G>A		p.X633_splice	ENST00000342505	NM_002227.2	633			1	2	FACETS	0.606	0.497	0.728	0.606	0.497	0.728	SUBCLONAL	1	TRUE	1	0.21	2		449	566	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65316550	65316550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	114	438	0	ENST00000342505.4:c.1692G>A	p.Trp564Ter	p.W564*	ENST00000342505	NM_002227.2	564	tgG/tgA	12/25	1	2	FACETS	0.966	0.873	1	1	0.988	1	CLONAL	2	TRUE	1	0.21	2		438	562	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624297	89624297	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	109	309	0	ENST00000371953.3:c.71A>C	p.Asp24Ala	p.D24A	ENST00000371953	NM_000314.4	24	gAc/gCc	1/9	1	2	FACETS	0.972	0.876	1	1	0.988	1	CLONAL	2	TRUE	1	0.21	2		309	534	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948587	71948587	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	161	678	2	ENST00000298229.2:c.3299C>A	p.Pro1100His	p.P1100H	ENST00000298229	NM_001567.3	1100	cCc/cAc	26/28	1	2	FACETS	1	0.921	1	1	0.992	1	CLONAL	2	TRUE	1	0.21	2		680	765	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114695	108114695	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060501616	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	91	262	0	ENST00000278616.4:c.512A>G	p.Tyr171Cys	p.Y171C	ENST00000278616	NM_000051.3	171	tAc/tGc	6/63	1	2	FACETS	1	0.941	1	1	0.987	1	CLONAL	2	TRUE	1	0.21	2		262	402	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375875	118375875	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	174	574	1	ENST00000534358.1:c.9268C>T	p.Pro3090Ser	p.P3090S	ENST00000534358	NM_005933.3	3090	Cca/Tca	27/36	1	2	FACETS	1	0.965	1	1	0.993	1	CLONAL	2	TRUE	1	0.21	2		575	766	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434164	121434164	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	180	571	0	ENST00000257555.6:c.1059del	p.Thr354ArgfsTer10	p.T354Rfs*10	ENST00000257555		352	tCc/tc	5/10	1	2	FACETS	1	0.974	1	1	0.993	1	CLONAL	2	TRUE	1	0.21	2		571	764	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346444	89346444	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	163	520	0	ENST00000301030.4:c.6506G>T	p.Gly2169Val	p.G2169V	ENST00000301030	NM_001256183.1	2169	gGg/gTg	9/13	1	2	FACETS	1	0.981	1	1	0.993	1	CLONAL	2	TRUE	1	0.21	2		520	642	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223350	2223350	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	178	558	0	ENST00000398665.3:c.3461C>A	p.Pro1154His	p.P1154H	ENST00000398665	NM_032482.2	1154	cCt/cAt	25/28	1	2	FACETS	1	0.981	1	1	0.993	1	CLONAL	2	TRUE	1	0.21	2		558	718	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765756	41765756	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	177	563	0	ENST00000301178.4:c.2632C>A	p.Gln878Lys	p.Q878K	ENST00000301178	NM_021913.4	878	Cag/Aag	20/20	1	2	FACETS	1	0.965	1	1	0.993	1	CLONAL	2	TRUE	1	0.21	2		563	782	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309634	30309634	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	200	658	0	ENST00000307677.4:c.388C>A	p.Leu130Ile	p.L130I	ENST00000307677	NM_138578.1	130	Ctc/Atc	2/3	1	2	FACETS	1	0.965	1	1	0.994	1	CLONAL	2	TRUE	1	0.21	2		658	893	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29279846	29279846	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	54	183	0	ENST00000544604.2:c.92del	p.Leu31ArgfsTer91	p.L31Rfs*91	ENST00000544604	NM_001206998.1	31	cTg/cg	1/9	1	2	FACETS	1	0.873	1	1	0.977	1	CLONAL	2	TRUE	1	0.21	2		183	254	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29438529	29438529	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	120	338	0	ENST00000544604.2:c.473T>G	p.Val158Gly	p.V158G	ENST00000544604	NM_001206998.1	158	gTg/gGg	3/9	1	2	FACETS	1	0.92	1	1	0.989	1	CLONAL	2	TRUE	1	0.21	2		338	562	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070301	37070301	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	135	476	0	ENST00000231790.2:c.1436T>C	p.Val479Ala	p.V479A	ENST00000231790	NM_000249.3	479	gTg/gCg	13/19	1	2	FACETS	1	0.963	1	1	0.991	1	CLONAL	2	TRUE	1	0.21	2		476	582	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436644	52436644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	170	577	0	ENST00000460680.1:c.2030C>T	p.Thr677Ile	p.T677I	ENST00000460680	NM_004656.3	677	aCc/aTc	16/17	1	2	FACETS	1	0.976	1	1	0.993	1	CLONAL	2	TRUE	1	0.21	2		577	708	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593289	67593289	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	168	458	0	ENST00000274335.5:c.2035T>G	p.Tyr679Asp	p.Y679D	ENST00000274335		679	Tat/Gat	15/15	1	2	FACETS	0.839	0.774	0.905	1	0.993	1	CLONAL	3	TRUE	1	0.21	2		458	636	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818896	32818896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs545594615	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	139	447	1	ENST00000354258.4:c.1055C>T	p.Thr352Met	p.T352M	ENST00000354258	NM_000593.5	352	aCg/aTg	4/11	1	2	FACETS	1	0.961	1	1	0.991	1	CLONAL	2	TRUE	1	0.21	2		448	606	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436038	116436038	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	172	509	0	ENST00000397752.3:c.4033A>G	p.Ile1345Val	p.I1345V	ENST00000397752	NM_000245.2	1345	Att/Gtt	21/21	1	2	FACETS	1	0.98	1	1	0.993	1	CLONAL	2	TRUE	1	0.21	2		509	693	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157956	27157957	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	50	548	0	ENST00000380036.4:c.183dup	p.Glu62Ter	p.E62*	ENST00000380036	NM_000459.3	60	-/T	2/23	1	2	FACETS	0.645	0.546	0.755	0.645	0.546	0.755	SUBCLONAL	1	TRUE	1	0.21	2		548	738	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185589	27185589	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1489568835	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	40	465	0	ENST00000380036.4:c.1289C>T	p.Ala430Val	p.A430V	ENST00000380036	NM_000459.3	430	gCt/gTt	9/23	1	2	FACETS	0.573	0.475	0.683	0.573	0.475	0.683	SUBCLONAL	1	TRUE	1	0.21	2		465	665	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44911033	44911033	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	58	666	0	ENST00000377967.4:c.734T>C	p.Val245Ala	p.V245A	ENST00000377967	NM_021140.2	245	gTc/gCc	9/29	1	2	FACETS	0.749	0.643	0.866	0.749	0.643	0.866	SUBCLONAL	1	TRUE	1	0.21	2		666	737	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890149	76890150	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	49	227	0	ENST00000373344.5:c.4744dup	p.Thr1582AsnfsTer19	p.T1582Nfs*19	ENST00000373344	NM_000489.3	1582	aca/aAca	17/35	1	2	FACETS	0.883	0.75	1	0.883	0.75	1	CLONAL	1	TRUE	1	0.266016672331961	2		227	417	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	33	372	1	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.889	0.727	1	0.889	0.727	1	CLONAL	1	TRUE	1	0.266016672331961	2		373	279	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	230	509	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.97	1	1	0.995	1	CLONAL	2	TRUE	1	0.266016672331961	2		513	813	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101402	27101402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	21	576	0	ENST00000324856.7:c.4689del	p.Met1564Ter	p.M1564*	ENST00000324856	NM_006015.4	1562	Ccc/cc	18/20	1	2	FACETS	0.484	0.373	0.614	0.484	0.373	0.614	SUBCLONAL	1	TRUE	1	0.266016672331961	2		576	326	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	78	539	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.266016672331961	2		539	565	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	111	778	0	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.266016672331961	2		778	768	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443613	52443613	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	39	688	0	ENST00000460680.1:c.79del	p.Val27CysfsTer45	p.V27Cfs*45	ENST00000460680	NM_004656.3	27	Gtg/tg	3/17	1	2	FACETS	0.381	0.314	0.455	0.381	0.314	0.455	SUBCLONAL	1	TRUE	1	0.266016672331961	2		688	770	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	49	521	3	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	0.266016672331961	3	FACETS	0.674	0.57	0.789	0.337	0.285	0.395	SUBCLONAL	1	TRUE	1	0.266016672331961	3		524	619	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332109	70332109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777837034	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	64	450	0	ENST00000373644.4:c.14G>A	p.Arg5His	p.R5H	ENST00000373644	NM_030625.2	5	cGc/cAc	2/12	1	2	FACETS	0.97	0.842	1	0.97	0.842	1	CLONAL	1	TRUE	1	0.266016672331961	2		450	496	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372092	55372093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	54	687	2	ENST00000297316.4:c.788dup	p.Glu264GlyfsTer101	p.E264Gfs*101	ENST00000297316	NM_022454.3	261	ggc/ggCc	2/2	0.266016672331961	3	FACETS	0.763	0.651	0.885	0.381	0.325	0.443	SUBCLONAL	1	TRUE	1	0.266016672331961	3		689	603	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437494	110437494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	73	562	0	ENST00000375856.3:c.907C>T	p.Arg303Cys	p.R303C	ENST00000375856	NM_003749.2	303	Cgc/Tgc	1/2	0.266016672331961	3	FACETS	0.992	0.868	1	0.496	0.434	0.563	CLONAL	1	TRUE	1	0.266016672331961	3		562	627	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107008	27107008	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	60	771	0	ENST00000324856.7:c.6619C>T	p.Gln2207Ter	p.Q2207*	ENST00000324856	NM_006015.4	2207	Cag/Tag	20/20	1	2	FACETS	0.538	0.462	0.62	0.538	0.462	0.62	SUBCLONAL	1	TRUE	1	0.266016672331961	2		771	839	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760559	133760559	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs557879885	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	118	674	2	ENST00000318560.5:c.2882C>T	p.Pro961Leu	p.P961L	ENST00000318560	NM_005157.4	961	cCg/cTg	11/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.266016672331961	2		676	715	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829075	128829075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1247591045	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	50	441	1	ENST00000249373.3:c.88del	p.Ala30ArgfsTer25	p.A30Rfs*25	ENST00000249373	NM_005631.4	28	cGg/cg	1/12	0.266016672331961	3	FACETS	0.84	0.713	0.98	0.42	0.356	0.49	CLONAL	1	TRUE	1	0.266016672331961	3		442	507	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825519	50825519	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	15	395	3	ENST00000398568.2:c.2156del	p.Asn719MetfsTer13	p.N719Mfs*13	ENST00000398568	NM_001042412.1	717	gAa/ga	14/18	1	2	FACETS	0.453	0.331	0.599	0.453	0.331	0.599	SUBCLONAL	1	TRUE	1	0.266016672331961	2		398	249	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163376	47163377	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	58	500	1	ENST00000409792.3:c.2749dup	p.Ser917LysfsTer18	p.S917Kfs*18	ENST00000409792	NM_014159.6	917	agt/aAgt	3/21	1	2	FACETS	0.978	0.842	1	0.978	0.842	1	CLONAL	1	TRUE	1	0.266016672331961	2		501	446	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	110	827	0	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.266016672331961	2		827	820	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350438	89350438	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	64	530	0	ENST00000301030.4:c.2512C>T	p.Arg838Ter	p.R838*	ENST00000301030	NM_001256183.1	838	Cga/Tga	9/13	1	2	FACETS	0.888	0.769	1	0.888	0.769	1	CLONAL	1	TRUE	1	0.266016672331961	2		530	542	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350105	89350105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368593056	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	119	785	2	ENST00000301030.4:c.2845C>T	p.Arg949Trp	p.R949W	ENST00000301030	NM_001256183.1	949	Cgg/Tgg	9/13	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.266016672331961	2		787	814	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216189	36216189	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	103	693	2	ENST00000222270.7:c.3602del	p.Pro1201ArgfsTer154	p.P1201Rfs*154	ENST00000222270	NM_014727.1	1199	ggC/gg	11/37	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.266016672331961	2		695	700	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874149	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	57	517	3	ENST00000262189.6:c.8389_8390del	p.Lys2797GlyfsTer11	p.K2797Gfs*11	ENST00000262189	NM_170606.2	2797	AAg/g	38/59	0.266016672331961	3	FACETS	0.896	0.769	1	0.448	0.384	0.517	CLONAL	1	TRUE	1	0.266016672331961	3		520	542	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445271	49445271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200451733	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	104	930	1	ENST00000301067.7:c.2195C>T	p.Pro732Leu	p.P732L	ENST00000301067	NM_003482.3	732	cCg/cTg	10/54	1	2	FACETS	0.842	0.753	0.937	0.842	0.753	0.937	CLONAL	1	TRUE	1	0.266016672331961	2		931	929	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900080	151900081	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	21	390	0	ENST00000262189.6:c.4030dup	p.Ile1344AsnfsTer11	p.I1344Nfs*11	ENST00000262189	NM_170606.2	1344	ata/aAta	26/59	0.266016672331961	3	FACETS	0.579	0.446	0.734	0.289	0.223	0.367	SUBCLONAL	1	TRUE	1	0.266016672331961	3		390	309	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099445	157099450	+	inframe_deletion	In_Frame_Del	DEL	CAGCAA	CAGCAA	-	novel	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	74	800	0	ENST00000346085.5:c.390_395del	p.Gln130_Gln131del	p.Q130_Q131del	ENST00000346085	NM_020732.3	128	CAGCAA/-	1/20	1	2	FACETS	0.627	0.547	0.712	0.627	0.547	0.712	SUBCLONAL	1	TRUE	1	0.266016672331961	2		800	888	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879229	151879229	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763438739	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	75	680	0	ENST00000262189.6:c.5716C>T	p.Arg1906Ter	p.R1906*	ENST00000262189	NM_170606.2	1906	Cga/Tga	36/59	0.266016672331961	3	FACETS	0.882	0.773	1	0.441	0.386	0.501	CLONAL	1	TRUE	1	0.266016672331961	3		680	724	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791587	42791587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767502801	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	103	709	0	ENST00000575354.2:c.568C>T	p.Arg190Cys	p.R190C	ENST00000575354	NM_015125.3	190	Cgc/Tgc	4/20	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.266016672331961	2		709	739	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234450	41234450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs4986849	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	91	548	0	ENST00000357654.3:c.4328G>A	p.Arg1443Gln	p.R1443Q	ENST00000357654	NM_007294.3	1443	cGa/cAa	12/23	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.266016672331961	2		548	638	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221276	36221276	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	91	708	0	ENST00000222270.7:c.5110C>T	p.Arg1704Cys	p.R1704C	ENST00000222270	NM_014727.1	1704	Cgc/Tgc	24/37	1	2	FACETS	0.948	0.841	1	0.948	0.841	1	CLONAL	1	TRUE	1	0.266016672331961	2		708	722	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811652	102811652	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	54	664	0	ENST00000307046.8:c.532C>T	p.Gln178Ter	p.Q178*	ENST00000307046	NM_001111285.1	178	Cag/Tag	4/4	1	2	FACETS	0.637	0.544	0.74	0.637	0.544	0.74	SUBCLONAL	1	TRUE	1	0.266016672331961	2		664	637	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355060	15355060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199540579	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	84	588	0	ENST00000263377.2:c.2563G>A	p.Ala855Thr	p.A855T	ENST00000263377	NM_058243.2	855	Gca/Aca	13/20	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.266016672331961	2		588	589	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431834	49431834	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	118	793	0	ENST00000301067.7:c.9305del	p.Pro3102LeufsTer17	p.P3102Lfs*17	ENST00000301067	NM_003482.3	3102	cCt/ct	34/54	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.266016672331961	2		793	764	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438129	438129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	87	564	0	ENST00000399788.2:c.1840G>A	p.Glu614Lys	p.E614K	ENST00000399788	NM_001042603.1	614	Gag/Aag	14/28	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.266016672331961	2		564	620	SUCCESS
PHF6	84295	MSKCC	GRCh37	X	133511691	133511691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1302895379	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	30	359	0	ENST00000332070.3:c.44G>A	p.Arg15His	p.R15H	ENST00000332070	NM_032458.2	15	cGc/cAc	2/10	1	2	FACETS	0.73	0.589	0.889	0.73	0.589	0.889	SUBCLONAL	1	TRUE	1	0.266016672331961	2		359	309	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274097	10274097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143833346	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	91	649	0	ENST00000330684.3:c.172G>A	p.Glu58Lys	p.E58K	ENST00000330684	NM_001134407.1	58	Gag/Aag	2/13	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.266016672331961	2		649	576	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184640	11184640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	78	467	0	ENST00000361445.4:c.6577C>T	p.Arg2193Cys	p.R2193C	ENST00000361445	NM_004958.3	2193	Cgc/Tgc	47/58	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.266016672331961	2		467	528	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911285	29911285	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	27	530	0	ENST00000376809.5:c.584A>G	p.Tyr195Cys	p.Y195C	ENST00000376809	NM_002116.7	195	tAc/tGc	3/8	1	2	FACETS	0.381	0.302	0.471	0.381	0.302	0.471	SUBCLONAL	1	TRUE	1	0.266016672331961	2		530	533	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214651	36214651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752780080	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	90	561	0	ENST00000222270.7:c.3077C>T	p.Thr1026Met	p.T1026M	ENST00000222270	NM_014727.1	1026	aCg/aTg	8/37	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.266016672331961	2		561	540	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	21	315	4	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	0.58	0.447	0.735	0.58	0.447	0.735	SUBCLONAL	1	TRUE	1	0.266016672331961	2		319	272	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226551	2226551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	99	739	1	ENST00000398665.3:c.4031C>T	p.Ala1344Val	p.A1344V	ENST00000398665	NM_032482.2	1344	gCg/gTg	27/28	1	2	FACETS	0.974	0.87	1	0.974	0.87	1	CLONAL	1	TRUE	1	0.266016672331961	2		740	764	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205275	46205276	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACAG	novel	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	64	422	0	ENST00000334344.6:c.360_363dup	p.Leu122ThrfsTer33	p.L122Tfs*33	ENST00000334344	NM_152641.2	120	cca/ccACAGa	4/21	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.266016672331961	2		422	473	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422667	49422667	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	88	656	0	ENST00000301067.7:c.14326A>G	p.Lys4776Glu	p.K4776E	ENST00000301067	NM_003482.3	4776	Aag/Gag	45/54	1	2	FACETS	0.993	0.881	1	0.993	0.881	1	CLONAL	1	TRUE	1	0.266016672331961	2		656	666	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431855	49431855	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	120	807	0	ENST00000301067.7:c.9284G>C	p.Gly3095Ala	p.G3095A	ENST00000301067	NM_003482.3	3095	gGc/gCc	34/54	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.266016672331961	2		807	796	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435747	110435747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	139	644	0	ENST00000375856.3:c.2654G>A	p.Gly885Asp	p.G885D	ENST00000375856	NM_003749.2	885	gGc/gAc	1/2	0.266016672331961	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.266016672331961	3		644	532	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302247	15302247	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs373870097	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	100	532	0	ENST00000263388.2:c.1024A>G	p.Met342Val	p.M342V	ENST00000263388	NM_000435.2	342	Atg/Gtg	6/33	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.266016672331961	2		532	600	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044438	128044438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	106	564	0	ENST00000285398.2:c.1183G>A	p.Asp395Asn	p.D395N	ENST00000285398	NM_000122.1	395	Gat/Aat	8/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.266016672331961	2		564	710	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021572	31021572	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	107	629	0	ENST00000375687.4:c.1571G>T	p.Arg524Met	p.R524M	ENST00000375687	NM_015338.5	524	aGg/aTg	12/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.266016672331961	2		629	681	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546159	41546159	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	84	558	1	ENST00000263253.7:c.2774C>A	p.Pro925His	p.P925H	ENST00000263253	NM_001429.3	925	cCt/cAt	14/31	1	2	FACETS	0.921	0.813	1	0.921	0.813	1	CLONAL	1	TRUE	1	0.266016672331961	2		559	686	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566469	41566469	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	77	524	0	ENST00000263253.7:c.4346A>G	p.His1449Arg	p.H1449R	ENST00000263253	NM_001429.3	1449	cAt/cGt	27/31	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.266016672331961	2		524	522	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440293	187440293	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755174150	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	37	549	0	ENST00000232014.4:c.2074C>T	p.Arg692Cys	p.R692C	ENST00000232014	NM_001130845.1	692	Cgc/Tgc	10/10	1	2	FACETS	0.439	0.361	0.527	0.439	0.361	0.527	SUBCLONAL	1	TRUE	1	0.266016672331961	2		549	633	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250705	26250705	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	195	775	1	ENST00000446824.2:c.129G>C	p.Arg43Ser	p.R43S	ENST00000446824	NM_021018.2	43	agG/agC	1/1	1	2	FACETS	0.821	0.76	0.884	1	0.992	1	CLONAL	2	TRUE	1	0.266016672331961	2		776	893	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166783	32166784	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	56	636	0	ENST00000375023.3:c.4454dup	p.Gly1486TrpfsTer36	p.G1486Wfs*36	ENST00000375023	NM_004557.3	1485	cct/ccCt	24/30	1	2	FACETS	0.551	0.471	0.639	0.551	0.471	0.639	SUBCLONAL	1	TRUE	1	0.266016672331961	2		636	764	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509460	106509460	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	93	636	0	ENST00000359195.3:c.1454G>T	p.Trp485Leu	p.W485L	ENST00000359195	NM_002649.2	485	tGg/tTg	2/11	0.266016672331961	3	FACETS	1	0.907	1	0.511	0.454	0.572	CLONAL	1	TRUE	1	0.266016672331961	3		636	775	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215821	98215821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766037357	NA	P-0061157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	69	526	1	ENST00000331920.6:c.3388G>A	p.Ala1130Thr	p.A1130T	ENST00000331920	NM_000264.3	1130	Gcc/Acc	20/24	1	2	FACETS	0.936	0.816	1	0.936	0.816	1	CLONAL	1	TRUE	1	0.266016672331961	2		527	554	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0061158-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	269	329	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.295867063436883	4	FACETS	1	0.963	1			1	CLONAL	3	TRUE	NA	0.364531588003911	4		329	655	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0061158-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	106	498	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.364531588003911	2		498	474	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0061158-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	100	548	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	1	2	FACETS	0.904	0.809	1	0.904	0.809	1	CLONAL	1	TRUE	1	0.364531588003911	2		548	607	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266112	41266112	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913228	NA	P-0061158-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	119	444	0	ENST00000349496.5:c.109T>G	p.Ser37Ala	p.S37A	ENST00000349496	NM_001904.3	37	Tct/Gct	3/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.364531588003911	2		444	586	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321621	30321622	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0061158-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	73	324	0	ENST00000322652.5:c.1476_1477del	p.Asn492LysfsTer4	p.N492Kfs*4	ENST00000322652	NM_015355.2	492	aaTGag/aaag	13/16	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.364531588003911	2		324	396	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106364	27106364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	224	686	0	ENST00000324856.7:c.5975C>T	p.Ser1992Leu	p.S1992L	ENST00000324856	NM_006015.4	1992	tCa/tTa	20/20	1	2	FACETS	0.913	0.857	0.971	0.913	0.857	0.971	CLONAL	1	TRUE	1	0.83	2		686	591	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	127	321	0				ENST00000310581	NM_198253.2	-/1132			0.363093222785558	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.363093222785558	3		321	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514495	NA	P-0061160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	249	705	0	ENST00000269305.4:c.542G>A	p.Arg181His	p.R181H	ENST00000269305	NM_001126112.2	181	cGc/cAc	5/11	0.338334875461973	2	FACETS	0.978	0.92	1	0.978	0.92	1	CLONAL	2	TRUE	0	0.363093222785558	2		705	701	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069931	5069931	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0061160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	44	430	0	ENST00000381652.3:c.1520C>G	p.Ser507Ter	p.S507*	ENST00000381652	NM_004972.3	507	tCa/tGa	12/25	0.363093222785558	1	FACETS	0.743	0.627	0.869	0.743	0.627	0.869	SUBCLONAL	1	TRUE	0	0.363093222785558	1		430	267	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983114	111983114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	59	614	0	ENST00000368678.4:c.1433G>A	p.Arg478Gln	p.R478Q	ENST00000368678		478	cGa/cAa	13/13	0.320323117208285	2	FACETS	0.499	0.429	0.576	0.25	0.214	0.288	SUBCLONAL	1	TRUE	0	0.363093222785558	2		614	651	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733044	74733044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	41	486	0	ENST00000359995.5:c.199G>A	p.Asp67Asn	p.D67N	ENST00000359995	NM_001195427.1	67	Gac/Aac	1/3	0.363093222785558	3	FACETS	0.522	0.435	0.62	0.261	0.217	0.31	SUBCLONAL	1	TRUE	1	0.363093222785558	3		486	511	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371641	225371641	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	62	490	0	ENST00000264414.4:c.963G>C	p.Leu321Phe	p.L321F	ENST00000264414	NM_003590.4	321	ttG/ttC	7/16	1	2	FACETS	0.865	0.75	0.988	0.865	0.75	0.988	CLONAL	1	TRUE	1	0.363093222785558	2		490	395	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058461	69058461	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	58	406	0	ENST00000288368.4:c.4105C>T	p.Gln1369Ter	p.Q1369*	ENST00000288368	NM_024870.2	1369	Caa/Taa	34/40	0.338334875461973	2	FACETS	0.905	0.782	1	0.453	0.391	0.519	CLONAL	1	TRUE	0	0.363093222785558	2		406	353	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38949911	38949911	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	61	630	0	ENST00000357387.3:c.4039C>T	p.His1347Tyr	p.H1347Y	ENST00000357387	NM_152756.3	1347	Cac/Tac	31/38	0.363093222785558	3	FACETS	0.698	0.602	0.802	0.349	0.301	0.401	SUBCLONAL	1	TRUE	1	0.363093222785558	3		630	569	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774181	56774181	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555594861	NA	P-0061160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	61	583	0	ENST00000337432.4:c.532C>T	p.Gln178Ter	p.Q178*	ENST00000337432	NM_058216.2	178	Cag/Tag	3/9	0.363093222785558	3	FACETS	0.633	0.546	0.728	0.317	0.273	0.364	SUBCLONAL	1	TRUE	1	0.363093222785558	3		583	627	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222034	2222034	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	74	608	0	ENST00000398665.3:c.2866C>G	p.Leu956Val	p.L956V	ENST00000398665	NM_032482.2	956	Ctc/Gtc	24/28	0.280629727032953	3	FACETS	0.786	0.688	0.891	0.262	0.229	0.297	SUBCLONAL	1	TRUE	0	0.363093222785558	3		608	613	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223667	36223667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	110	747	0	ENST00000222270.7:c.6217G>A	p.Glu2073Lys	p.E2073K	ENST00000222270	NM_014727.1	2073	Gag/Aag	28/37	0.363093222785558	5	FACETS	1	0.921	1	0.344	0.308	0.381	CLONAL	1	TRUE	2	0.363093222785558	5		747	908	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536166	106536166	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	56	574	0	ENST00000369096.4:c.133G>A	p.Asp45Asn	p.D45N	ENST00000369096	NM_001198.3	45	Gat/Aat	2/7	0.320323117208285	2	FACETS	0.431	0.368	0.499	0.215	0.184	0.25	SUBCLONAL	1	TRUE	0	0.363093222785558	2		574	716	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247165	153247165	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0061160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	47	439	0	ENST00000281708.4:c.1637C>G	p.Ser546Ter	p.S546*	ENST00000281708	NM_033632.3	546	tCa/tGa	10/12	1	2	FACETS	0.559	0.472	0.655	0.559	0.472	0.655	SUBCLONAL	1	TRUE	1	0.363093222785558	2		439	463	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107174	27107174	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	141	605	0	ENST00000324856.7:c.6785C>A	p.Ser2262Ter	p.S2262*	ENST00000324856	NM_006015.4	2262	tCg/tAg	20/20	0.358295007072504	3	FACETS	1	0.986	1	0.708	0.647	0.772	CLONAL	1	TRUE	1	0.363093222785558	3		605	648	SUCCESS
H3C13	653604	MSKCC	GRCh37	1	149784837	149784837	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	85	422	0	ENST00000331491.1:c.400G>C	p.Glu134Gln	p.E134Q	ENST00000331491	NM_001123375.2	134	Gag/Cag	1/1	0.358295007072504	3	FACETS	1	0.907	1	0.513	0.454	0.576	CLONAL	1	TRUE	1	0.363093222785558	3		422	539	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435871	49435871	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0061160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	102	681	0	ENST00000301067.7:c.6109+1G>T		p.X2037_splice	ENST00000301067	NM_003482.3	2037			0.358295007072504	3	FACETS	0.935	0.837	1	0.467	0.418	0.52	CLONAL	1	TRUE	1	0.363093222785558	3		681	710	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864639	57864639	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	62	623	0	ENST00000228682.2:c.2116G>C	p.Glu706Gln	p.E706Q	ENST00000228682	NM_005269.2	706	Gag/Cag	12/12	0.358295007072504	3	FACETS	0.572	0.494	0.658	0.286	0.247	0.329	SUBCLONAL	1	TRUE	1	0.363093222785558	3		623	705	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934521	9934521	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	57	502	0	ENST00000330684.3:c.1634C>A	p.Ser545Ter	p.S545*	ENST00000330684	NM_001134407.1	545	tCa/tAa	7/13	0.363093222785558	3	FACETS	0.578	0.495	0.668	0.289	0.247	0.334	SUBCLONAL	1	TRUE	1	0.363093222785558	3		502	642	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33430304	33430304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	115	701	0	ENST00000345365.6:c.707C>T	p.Thr236Ile	p.T236I	ENST00000345365	NM_002878.3	236	aCc/aTc	8/10	0.363093222785558	3	FACETS	0.832	0.748	0.92	0.416	0.374	0.46	CLONAL	1	TRUE	1	0.363093222785558	3		701	900	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38788493	38788493	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	54	479	0	ENST00000348513.6:c.668G>C	p.Arg223Thr	p.R223T	ENST00000348513	NM_003079.4	223	aGa/aCa	8/11	0.363093222785558	3	FACETS	0.519	0.443	0.603	0.26	0.221	0.302	SUBCLONAL	1	TRUE	1	0.363093222785558	3		479	677	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221336	36221336	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	136	821	0	ENST00000222270.7:c.5170G>A	p.Glu1724Lys	p.E1724K	ENST00000222270	NM_014727.1	1724	Gaa/Aaa	24/37	0.363093222785558	5	FACETS	1	0.957	1	0.364	0.33	0.4	CLONAL	1	TRUE	2	0.363093222785558	5		821	1060	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229213	36229213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	103	685	0	ENST00000222270.7:c.7903G>A	p.Asp2635Asn	p.D2635N	ENST00000222270	NM_014727.1	2635	Gac/Aac	37/37	0.363093222785558	5	FACETS	0.923	0.825	1	0.308	0.275	0.343	CLONAL	1	TRUE	2	0.363093222785558	5		685	949	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982379	25982491	+	frameshift_variant	Frame_Shift_Del	DEL	AGCAGTCGTTGCTGGCAATCTCCAGGAAGGACTGAAAATGTGTGCTTGTTGATCAGTGCTCGCAGATTTGTATTAACCAGAATGGAGTCCGGTGTCTCAACGTCAATGTCAGC	AGCAGTCGTTGCTGGCAATCTCCAGGAAGGACTGAAAATGTGTGCTTGTTGATCAGTGCTCGCAGATTTGTATTAACCAGAATGGAGTCCGGTGTCTCAACGTCAATGTCAGC	-	novel	NA	P-0061160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	39	455	0	ENST00000435504.4:c.799_911del	p.Ala267PhefsTer24	p.A267Ffs*24	ENST00000435504		267	GCTGACATTGACGTTGAGACACCGGACTCCATTCTGGTTAATACAAATCTGCGAGCACTGATCAACAAGCACACATTTTCAGTCCTTCCTGGAGATTGCCAGCAACGACTGCTt/t	9/13	0.363093222785558	3	FACETS	0.359	0.296	0.429	0.18	0.148	0.215	SUBCLONAL	1	TRUE	1	0.363093222785558	3		455	707	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152300	99152300	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1247867306	NA	P-0061160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	59	469	0	ENST00000074304.5:c.379C>T	p.Gln127Ter	p.Q127*	ENST00000074304	NM_001134224.1	127	Cag/Tag	6/26	0.358295007072504	3	FACETS	0.766	0.66	0.882	0.383	0.33	0.441	SUBCLONAL	1	TRUE	1	0.363093222785558	3		469	501	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622553	158622553	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	87	496	0	ENST00000263640.3:c.946C>G	p.Leu316Val	p.L316V	ENST00000263640	NM_001105.4	316	Ctt/Gtt	8/11	1	2	FACETS	0.823	0.73	0.923	0.823	0.73	0.923	CLONAL	1	TRUE	1	0.363093222785558	2		496	582	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190742071	190742071	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	56	439	1	ENST00000441310.2:c.2708G>A	p.Arg903Lys	p.R903K	ENST00000441310	NM_000534.4	903	aGa/aAa	13/13	0.363093222785558	4	FACETS	0.796	0.683	0.92	0.265	0.227	0.307	CLONAL	1	TRUE	1	0.363093222785558	4		440	528	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39706225	39706225	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	93	357	0	ENST00000361337.2:c.283C>G	p.Arg95Gly	p.R95G	ENST00000361337	NM_003286.2	95	Cga/Gga	5/21	0.363093222785558	3	FACETS	1	0.928	1	0.527	0.47	0.588	CLONAL	1	TRUE	1	0.363093222785558	3		357	574	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138423314	138423314	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs780707259	NA	P-0061160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	71	372	0	ENST00000289153.2:c.1552A>G	p.Ile518Val	p.I518V	ENST00000289153	NM_006219.2	518	Att/Gtt	10/22	0.359322503362588	2	FACETS	1	0.898	1	0.513	0.45	0.58	CLONAL	1	TRUE	0	0.363093222785558	2		372	381	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967218	93967218	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	64	451	1	ENST00000369303.4:c.2134G>A	p.Glu712Lys	p.E712K	ENST00000369303	NM_004440.3	712	Gag/Aag	12/17	0.363093222785558	6	FACETS	0.939	0.813	1	0.235	0.203	0.269	CLONAL	1	TRUE	2	0.363093222785558	6		452	648	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099643	157099643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1373786950	NA	P-0061160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	46	344	0	ENST00000346085.5:c.580G>A	p.Glu194Lys	p.E194K	ENST00000346085	NM_020732.3	194	Gag/Aag	1/20	0.320323117208285	2	FACETS	0.908	0.77	1	0.454	0.385	0.53	CLONAL	1	TRUE	0	0.363093222785558	2		344	279	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739392	145739392	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	76	511	0	ENST00000428558.2:c.1978G>T	p.Glu660Ter	p.E660*	ENST00000428558	NM_004260.3	660	Gaa/Taa	12/22	0.363093222785558	3	FACETS	0.931	0.819	1	0.31	0.273	0.351	CLONAL	1	TRUE	0	0.363093222785558	3		511	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0061161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	81	608	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.303052987752746	1	FACETS	0.834	0.737	0.938	0.834	0.737	0.938	CLONAL	1	TRUE	0	0.32	1		610	510	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225591	26225591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	148	639	0	ENST00000360408.1:c.209G>A	p.Arg70His	p.R70H	ENST00000360408	NM_003532.2	70	cGc/cAc	1/1	0.303052987752746	1	FACETS	0.916	0.837	0.999	0.916	0.837	0.999	CLONAL	1	TRUE	0	0.32	1		639	848	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578440	7578440	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs879254249	NA	P-0061162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	228	634	0	ENST00000269305.4:c.490A>G	p.Lys164Glu	p.K164E	ENST00000269305	NM_001126112.2	164	Aag/Gag	5/11	0.632718628322792	1	FACETS	0.997	0.94	1	0.997	0.94	1	CLONAL	1	TRUE	0	0.632718628322792	1		634	494	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715299	61715299	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0061162-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	113	389	0	ENST00000401558.2:c.2313+1G>T		p.X771_splice	ENST00000401558	NM_003400.3	771			0.154214849262576	6	FACETS	0.848	0.768	0.933			1	INDETERMINATE	2	TRUE	NA	0.632718628322792	6		389	477	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0061163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	19	544	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.430235860783138	1	FACETS	0.978	0.768	1	0.978	0.768	1	CLONAL	1	TRUE	0	0.476994119480262	1		544	62	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257434	16257434	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	11	612	0	ENST00000375759.3:c.4699G>C	p.Glu1567Gln	p.E1567Q	ENST00000375759	NM_015001.2	1567	Gag/Cag	11/15	0.476980351221087	1	FACETS	0.244	0.169	0.336	0.244	0.169	0.336	SUBCLONAL	1	TRUE	0	0.476994119480262	1		612	144	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115742	8115742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	51	533	0	ENST00000346208.3:c.1088C>T	p.Thr363Ile	p.T363I	ENST00000346208		363	aCc/aTc	6/6	0.224767436316555	1	FACETS	0.517	0.442	0.599	0.517	0.442	0.599	INDETERMINATE	1	TRUE	0	0.476994119480262	1		533	315	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948044	178948044	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	42	459	0	ENST00000263967.3:c.2816A>G	p.Asp939Gly	p.D939G	ENST00000263967	NM_006218.2	939	gAt/gGt	20/21	0.430235860783138	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.476994119480262	1		459	113	SUCCESS
APC	324	MSKCC	GRCh37	5	112178503	112178503	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	10	510	0	ENST00000257430.4:c.7212G>C	p.Met2404Ile	p.M2404I	ENST00000257430	NM_000038.5	2404	atG/atC	16/16	0.224767436316555	1	FACETS	0.264	0.179	0.369	0.264	0.179	0.369	INDETERMINATE	1	TRUE	0	0.476994119480262	1		510	121	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611865	100611865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1305768982	NA	P-0061163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	26	509	0	ENST00000308731.7:c.1256G>A	p.Gly419Glu	p.G419E	ENST00000308731	NM_000061.2	419	gGg/gAg	14/19	0.476994119480262	1	FACETS	0.296	0.235	0.366	0.296	0.235	0.366	SUBCLONAL	1	TRUE	0	0.476994119480262	1		509	280	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968251	134968251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373797543	NA	P-0061164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	147	535	0	ENST00000398015.3:c.2764G>A	p.Ala922Thr	p.A922T	ENST00000398015	NM_004441.4	922	Gcc/Acc	15/16	1	2	FACETS	0.977	0.906	1	0.977	0.906	1	CLONAL	1	TRUE	1	0.89	2		535	338	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0061165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	164	646	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.475182802884623	0	FACETS	0.657	0.607	0.709			1	SUBCLONAL	1	FALSE	0	0.475182802884623	0		646	551	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651643	48651643	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	23	290	2	ENST00000376670.3:c.809G>A	p.Arg270Gln	p.R270Q	ENST00000376670	NM_002049.3	270	cGg/cAg	5/6	1	1	FACETS	0.18	0.14	0.227	0.18	0.14	0.227	SUBCLONAL	1	FALSE	0	0.475182802884623	1		292	409	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	38	341	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.854	1	1	0.975	1	CLONAL	3	FALSE	1	0.149716163030823	2		341	166	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	47	540	2	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.781	0.66	0.913	1	0.963	1	CLONAL	2	FALSE	1	0.149716163030823	2		542	402	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	80	509	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.149716163030823	3	FACETS	0.936	0.829	1	1	0.975	1	CLONAL	3	FALSE	1	0.149716163030823	3		513	409	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	46	512	6	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.906	0.771	1	1	0.978	1	CLONAL	3	FALSE	1	0.149716163030823	2		518	226	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	77	550	2	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	1	0.897	1	1	0.987	1	CLONAL	3	FALSE	1	0.149716163030823	2		552	338	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440912	52440912	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1205668341	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	96	451	3	ENST00000460680.1:c.592del	p.Glu198ArgfsTer33	p.E198Rfs*33	ENST00000460680	NM_004656.3	198	Gag/ag	8/17	1	2	FACETS	0.904	0.809	1	1	0.989	1	CLONAL	3	FALSE	1	0.149716163030823	2		454	473	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986991	36986991	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	48	368	0	ENST00000354822.5:c.698C>T	p.Thr233Met	p.T233M	ENST00000354822	NM_001079668.2	233	aCg/aTg	3/3	1	2	FACETS	1	0.904	1	1	0.982	1	CLONAL	4	FALSE	1	0.149716163030823	2		368	151	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149728	202149728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	59	577	0	ENST00000358485.4:c.1173del	p.Ile392SerfsTer4	p.I392Sfs*4	ENST00000358485	NM_001080125.1	390	gCc/gc	8/9	1	2	FACETS	1	0.875	1	1	0.983	1	CLONAL	3	FALSE	1	0.149716163030823	2		577	261	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741915	17741915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	63	368	0	ENST00000250003.3:c.586G>A	p.Asp196Asn	p.D196N	ENST00000250003	NM_002478.4	196	Gac/Aac	1/3	1	2	FACETS	0.956	0.839	1	1	0.986	1	CLONAL	4	FALSE	1	0.149716163030823	2		368	220	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	37	369	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	1	0.915	1	1	0.97	1	CLONAL	2	FALSE	1	0.149716163030823	2		369	211	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437173	220437173	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746580263	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	96	431	0	ENST00000243786.2:c.77G>A	p.Arg26Gln	p.R26Q	ENST00000243786	NM_002191.3	26	cGg/cAg	1/2	1	2	FACETS	0.943	0.849	1	1	0.99	1	CLONAL	4	FALSE	1	0.149716163030823	2		431	340	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070411	37070411	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1553653195	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	65	424	0	ENST00000231790.2:c.1546C>T	p.Gln516Ter	p.Q516*	ENST00000231790	NM_000249.3	516	Cag/Tag	13/19	1	2	FACETS	1	0.885	1	1	0.985	1	CLONAL	3	FALSE	1	0.149716163030823	2		424	286	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934243	49934243	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1407832113	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	95	483	8	ENST00000296474.3:c.2264del	p.Gly755ValfsTer19	p.G755Vfs*19	ENST00000296474	NM_002447.2	755	gGt/gt	8/20	1	2	FACETS	1	0.941	1	1	0.99	1	CLONAL	3	FALSE	1	0.149716163030823	2		491	395	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101612	27101612	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	120	503	0	ENST00000324856.7:c.4899del	p.Met1634Ter	p.M1634*	ENST00000324856	NM_006015.4	1632	Ccc/cc	18/20	1	2	FACETS	1	0.962	1	1	0.992	1	CLONAL	3	FALSE	1	0.149716163030823	2		503	481	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101116	27101117	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	68	488	0	ENST00000324856.7:c.4403dup	p.Gly1469TrpfsTer22	p.G1469Wfs*22	ENST00000324856	NM_006015.4	1466	-/C	18/20	1	2	FACETS	0.851	0.744	0.964	1	0.984	1	CLONAL	3	FALSE	1	0.149716163030823	2		488	356	SUCCESS
PHF6	84295	MSKCC	GRCh37	X	133549136	133549136	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1556019107	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	27	333	0	ENST00000332070.3:c.820C>T	p.Arg274Ter	p.R274*	ENST00000332070	NM_032458.2	274	Cga/Tga	8/10	0.149716163030823	1	FACETS	1	0.848	1	1	0.966	1	CLONAL	3	FALSE	0	0.149716163030823	1		333	106	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143052	30143052	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1244823020	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	115	577	0	ENST00000389048.3:c.474del	p.Glu160ArgfsTer26	p.E160Rfs*26	ENST00000389048	NM_004304.4	158	ccC/cc	1/29	1	2	FACETS	0.948	0.861	1	1	0.992	1	CLONAL	4	FALSE	1	0.149716163030823	2		577	405	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464463	25464463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758490363	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	93	420	1	ENST00000264709.3:c.2050G>A	p.Val684Ile	p.V684I	ENST00000264709	NM_175629.2	684	Gtc/Atc	17/23	1	2	FACETS	1	0.959	1	1	0.99	1	CLONAL	3	FALSE	1	0.149716163030823	2		421	364	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980558	1980559	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs752037034	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	128	539	12	ENST00000382891.5:c.4028dup	p.Glu1344ArgfsTer91	p.E1344Rfs*91	ENST00000382891	NM_133335.3	1340	-/C	22/22	1	2	FACETS	0.967	0.883	1	1	0.993	1	CLONAL	4	FALSE	1	0.149716163030823	2		551	442	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527727	157527727	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	123	509	0	ENST00000346085.5:c.5452C>T	p.His1818Tyr	p.H1818Y	ENST00000346085	NM_020732.3	1818	Cac/Tac	20/20	1	2	FACETS	1	0.96	1	1	0.992	1	CLONAL	3	FALSE	1	0.149716163030823	2		509	497	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	72	451	1	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	0.149716163030823	3	FACETS	0.879	0.772	0.993	1	0.967	1	CLONAL	3	FALSE	1	0.149716163030823	3		452	392	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696740	47696740	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	17	416	1	ENST00000347630.2:c.208C>T	p.Arg70Ter	p.R70*	ENST00000347630	NM_001007230.1	70	Cga/Tga	5/11	0.149716163030823	3	FACETS	1	0.822	1	0.565	0.423	0.733	CLONAL	1	FALSE	1	0.149716163030823	3		417	216	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785984	135785984	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	90	473	0	ENST00000298552.3:c.1237del	p.Gln413ArgfsTer27	p.Q413Rfs*27	ENST00000298552	NM_001162426.1	413	Cag/ag	12/23	1	2	FACETS	0.985	0.879	1	1	0.989	1	CLONAL	3	FALSE	1	0.149716163030823	2		473	407	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500476	99500476	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	119	492	0	ENST00000268035.6:c.3913del	p.Leu1305TrpfsTer45	p.L1305Wfs*45	ENST00000268035	NM_000875.3	1303	gtC/gt	21/21	1	2	FACETS	0.879	0.799	0.963	1	0.992	1	CLONAL	4	FALSE	1	0.149716163030823	2		492	452	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465976	69465976	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	116	523	0	ENST00000227507.2:c.814G>T	p.Glu272Ter	p.E272*	ENST00000227507	NM_053056.2	272	Gag/Tag	5/5	1	2	FACETS	0.886	0.805	0.972	1	0.992	1	CLONAL	4	FALSE	1	0.149716163030823	2		523	437	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946831	17946831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	109	458	0	ENST00000458235.1:c.1816G>A	p.Gly606Arg	p.G606R	ENST00000458235	NM_000215.3	606	Ggg/Agg	14/24	0.149716163030823	3	FACETS	1	0.921	1	1	0.989	1	CLONAL	4	FALSE	1	0.149716163030823	3		458	384	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692885	89692885	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	28	233	0	ENST00000371953.3:c.369C>A	p.His123Gln	p.H123Q	ENST00000371953	NM_000314.4	123	caC/caA	5/9	1	2	FACETS	1	0.836	1	1	0.966	1	CLONAL	3	FALSE	1	0.149716163030823	2		233	121	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478122	99478122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1470161328	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	98	469	0	ENST00000268035.6:c.3026C>T	p.Ser1009Leu	p.S1009L	ENST00000268035	NM_000875.3	1009	tCg/tTg	16/21	1	2	FACETS	1	0.956	1	1	0.99	1	CLONAL	3	FALSE	1	0.149716163030823	2		469	391	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50821755	50821755	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	15	255	0	ENST00000398568.2:c.2095del	p.Ile699Ter	p.I699*	ENST00000398568	NM_001042412.1	697	ctA/ct	13/18	1	2	FACETS	1	0.791	1	1	0.925	1	CLONAL	2	FALSE	1	0.149716163030823	2		255	93	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851177	151851177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141966811	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	57	463	0	ENST00000262189.6:c.12194C>T	p.Ala4065Val	p.A4065V	ENST00000262189	NM_170606.2	4065	gCg/gTg	48/59	1	2	FACETS	1	0.891	1	1	0.985	1	CLONAL	4	FALSE	1	0.149716163030823	2		463	186	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912404	50912405	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	80	428	0	ENST00000440232.2:c.1923dup	p.Thr642HisfsTer97	p.T642Hfs*97	ENST00000440232	NM_002691.3	640	acc/aCcc	16/27	0.149716163030823	3	FACETS	0.983	0.875	1	1	0.985	1	CLONAL	4	FALSE	1	0.149716163030823	3		428	292	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843774	151843775	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	72	427	0	ENST00000262189.6:c.13940dup	p.Ser4648ValfsTer2	p.S4648Vfs*2	ENST00000262189	NM_170606.2	4647	aag/aaAg	53/59	1	2	FACETS	1	0.954	1	1	0.987	1	CLONAL	3	FALSE	1	0.149716163030823	2		427	275	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354155	15354155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1477636105	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	61	369	0	ENST00000263377.2:c.2725C>T	p.Pro909Ser	p.P909S	ENST00000263377	NM_058243.2	909	Ccc/Tcc	14/20	0.149716163030823	3	FACETS	1	0.935	1	1	0.976	1	CLONAL	3	FALSE	1	0.149716163030823	3		369	261	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344119	70344119	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	49	430	0	ENST00000374080.3:c.1855A>G	p.Ile619Val	p.I619V	ENST00000374080		619	Atc/Gtc	13/45	0.149716163030823	1	FACETS	1	0.92	1	1	0.976	1	CLONAL	2	FALSE	0	0.149716163030823	1		430	270	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50784990	50784990	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs146125856	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	18	250	2	ENST00000307179.4:c.2327T>C	p.Leu776Pro	p.L776P	ENST00000307179		776	cTt/cCt	15/20	1	2	FACETS	0.904	0.687	1	1	0.926	1	CLONAL	2	FALSE	1	0.149716163030823	2		252	133	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422257	47422257	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1324454897	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	85	461	0	ENST00000404338.3:c.325C>T	p.Arg109Ter	p.R109*	ENST00000404338	NM_004491.4	109	Cga/Tga	1/6	0.149716163030823	3	FACETS	1	0.957	1	1	0.983	1	CLONAL	3	FALSE	1	0.149716163030823	3		461	354	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63898390	63898390	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs868854400	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	55	297	2	ENST00000398590.3:c.116A>C	p.Gln39Pro	p.Q39P	ENST00000398590	NM_001177387.1	39	cAg/cCg	3/14	1	2	FACETS	1	0.949	1	1	0.98	1	CLONAL	2	FALSE	1	0.149716163030823	2		299	299	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1685602	1685602	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	110	482	0	ENST00000378625.1:c.1424C>G	p.Ala475Gly	p.A475G	ENST00000378625	NM_001198994.1	475	gCg/gGg	12/14	1	2	FACETS	1	0.968	1	1	0.991	1	CLONAL	3	FALSE	1	0.149716163030823	2		482	422	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106757	27106757	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	131	555	0	ENST00000324856.7:c.6368G>T	p.Ser2123Ile	p.S2123I	ENST00000324856	NM_006015.4	2123	aGc/aTc	20/20	1	2	FACETS	1	0.968	1	1	0.993	1	CLONAL	3	FALSE	1	0.149716163030823	2		555	515	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682997	241682997	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs766915154	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	97	396	0	ENST00000366560.3:c.26C>G	p.Ala9Gly	p.A9G	ENST00000366560	NM_000143.3	9	gCg/gGg	1/10	1	2	FACETS	0.915	0.823	1	1	0.99	1	CLONAL	4	FALSE	1	0.149716163030823	2		396	354	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622167	43622167	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs138010639	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	51	462	0	ENST00000355710.3:c.3184T>C	p.Tyr1062His	p.Y1062H	ENST00000355710	NM_020975.4	1062	Tat/Cat	19/20	1	2	FACETS	0.966	0.83	1	1	0.981	1	CLONAL	3	FALSE	1	0.149716163030823	2		462	235	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533873	533873	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913496	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	123	505	0	ENST00000451590.1:c.183G>T	p.Gln61His	p.Q61H	ENST00000451590	NM_001130442.1	61	caG/caT	3/5	1	2	FACETS	1	0.945	1	1	0.992	1	CLONAL	3	FALSE	1	0.149716163030823	2		505	519	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913368	28913368	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	58	365	0	ENST00000282397.4:c.2425C>T	p.Gln809Ter	p.Q809*	ENST00000282397	NM_002019.4	809	Cag/Tag	17/30	0.149716163030823	0	FACETS	0.972	0.846	1			1	CLONAL	3	FALSE	0	0.149716163030823	0		365	226	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931801	28931801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1233164771	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	21	449	0	ENST00000282397.4:c.2138G>A	p.Ser713Asn	p.S713N	ENST00000282397	NM_002019.4	713	aGc/aAc	15/30	0.149716163030823	0	FACETS	1	0.864	1			1	CLONAL	1	FALSE	0	0.149716163030823	0		449	203	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434412	110434412	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	88	380	0	ENST00000375856.3:c.3989T>C	p.Leu1330Ser	p.L1330S	ENST00000375856	NM_003749.2	1330	tTg/tCg	1/2	1	2	FACETS	1	0.914	1	1	0.99	1	CLONAL	4	FALSE	1	0.149716163030823	2		380	288	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435377	110435377	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	113	440	0	ENST00000375856.3:c.3024del	p.Glu1009ArgfsTer97	p.E1009Rfs*97	ENST00000375856	NM_003749.2	1008	ccC/cc	1/2	1	2	FACETS	1	0.946	1	1	0.991	1	CLONAL	3	FALSE	1	0.149716163030823	2		440	472	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562799	95562799	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	29	499	0	ENST00000393063.1:c.4458del	p.Lys1486AsnfsTer4	p.K1486Nfs*4	ENST00000393063	NM_030621.3	1486	aaA/aa	24/28	1	2	FACETS	0.857	0.692	1	1	0.949	1	CLONAL	2	FALSE	1	0.149716163030823	2		499	226	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028566	42028566	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	68	506	0	ENST00000219905.7:c.4104G>T	p.Lys1368Asn	p.K1368N	ENST00000219905	NM_001164273.1	1368	aaG/aaT	13/24	1	2	FACETS	1	0.924	1	1	0.986	1	CLONAL	3	FALSE	1	0.149716163030823	2		506	283	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347446	91347446	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	36	397	0	ENST00000355112.3:c.3608C>A	p.Ala1203Glu	p.A1203E	ENST00000355112	NM_000057.2	1203	gCg/gAg	19/22	1	2	FACETS	1	0.917	1	1	0.969	1	CLONAL	2	FALSE	1	0.149716163030823	2		397	203	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655371	67655371	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	52	435	0	ENST00000264010.4:c.1234T>C	p.Cys412Arg	p.C412R	ENST00000264010	NM_006565.3	412	Tgt/Cgt	7/12	1	2	FACETS	1	0.867	1	1	0.981	1	CLONAL	3	FALSE	1	0.149716163030823	2		435	230	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822219	72822219	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	79	572	1	ENST00000268489.5:c.9956A>G	p.Tyr3319Cys	p.Y3319C	ENST00000268489	NM_006885.3	3319	tAt/tGt	10/10	1	2	FACETS	1	0.947	1	1	0.988	1	CLONAL	3	FALSE	1	0.149716163030823	2		573	315	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993522	72993522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1004079875	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	115	541	0	ENST00000268489.5:c.523C>T	p.Pro175Ser	p.P175S	ENST00000268489	NM_006885.3	175	Cct/Tct	2/10	1	2	FACETS	1	0.963	1	1	0.992	1	CLONAL	4	FALSE	1	0.149716163030823	2		541	347	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075157	16075157	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs190110703	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	122	469	0	ENST00000268712.3:c.395C>T	p.Pro132Leu	p.P132L	ENST00000268712	NM_006311.3	132	cCg/cTg	4/46	0.149716163030823	3	FACETS	0.94	0.855	1	1	0.989	1	CLONAL	4	FALSE	1	0.149716163030823	3		469	466	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290984	15290984	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	101	513	0	ENST00000263388.2:c.3226C>A	p.Arg1076Ser	p.R1076S	ENST00000263388	NM_000435.2	1076	Cgt/Agt	20/33	0.149716163030823	3	FACETS	1	0.903	1	1	0.988	1	CLONAL	4	FALSE	1	0.149716163030823	3		513	362	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229376	36229378	+	inframe_deletion	In_Frame_Del	DEL	ACT	ACT	-	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	102	507	0	ENST00000222270.7:c.8068_8070del	p.Tyr2690del	p.Y2690del	ENST00000222270	NM_014727.1	2689	gACTac/gac	37/37	0.149716163030823	3	FACETS	1	0.946	1	1	0.984	1	CLONAL	3	FALSE	1	0.149716163030823	3		507	452	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257757	198257757	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	41	446	0	ENST00000335508.6:c.3695G>C	p.Gly1232Ala	p.G1232A	ENST00000335508	NM_012433.2	1232	gGa/gCa	24/25	1	2	FACETS	0.946	0.797	1	1	0.976	1	CLONAL	3	FALSE	1	0.149716163030823	2		446	193	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022262	31022262	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	75	438	0	ENST00000375687.4:c.1747T>C	p.Trp583Arg	p.W583R	ENST00000375687	NM_015338.5	583	Tgg/Cgg	13/13	1	2	FACETS	1	0.93	1	1	0.988	1	CLONAL	4	FALSE	1	0.149716163030823	2		438	236	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266210	41266211	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	62	436	0	ENST00000349496.5:c.211dup	p.Ser71PhefsTer11	p.S71Ffs*11	ENST00000349496	NM_001904.3	69	-/T	3/15	1	2	FACETS	1	0.936	1	1	0.985	1	CLONAL	3	FALSE	1	0.149716163030823	2		436	247	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1959663	1959663	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	57	288	2	ENST00000382891.5:c.2885T>C	p.Leu962Pro	p.L962P	ENST00000382891	NM_133335.3	962	cTg/cCg	16/22	1	2	FACETS	0.929	0.809	1	1	0.984	1	CLONAL	4	FALSE	1	0.149716163030823	2		290	205	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564678	55564678	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	22	362	0	ENST00000288135.5:c.566A>G	p.Asp189Gly	p.D189G	ENST00000288135	NM_000222.2	189	gAc/gGc	3/21	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	FALSE	1	0.149716163030823	2		362	200	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356280	66356281	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	72	487	0	ENST00000273854.3:c.1215_1216dup	p.Glu406ValfsTer17	p.E406Vfs*17	ENST00000273854	NM_004439.5	406	gag/gTGag	5/18	1	2	FACETS	0.929	0.818	1	1	0.986	1	CLONAL	3	FALSE	1	0.149716163030823	2		487	345	SUCCESS
ALB	213	MSKCC	GRCh37	4	74275083	74275083	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	28	312	0	ENST00000295897.4:c.494A>T	p.Glu165Val	p.E165V	ENST00000295897	NM_000477.5	165	gAa/gTa	5/15	1	2	FACETS	0.937	0.761	1	1	0.965	1	CLONAL	3	FALSE	1	0.149716163030823	2		312	133	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157539	106157539	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	43	469	0	ENST00000380013.4:c.2440C>G	p.Arg814Gly	p.R814G	ENST00000380013	NM_001127208.2	814	Cgt/Ggt	3/11	1	2	FACETS	0.934	0.79	1	1	0.977	1	CLONAL	3	FALSE	1	0.149716163030823	2		469	205	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295365	1295365	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	16	544	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.694	0.512	0.911	0.694	0.512	0.911	SUBCLONAL	1	FALSE	1	0.149716163030823	2		545	308	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637859	176637859	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	51	409	0	ENST00000439151.2:c.2459A>C	p.Lys820Thr	p.K820T	ENST00000439151	NM_022455.4	820	aAa/aCa	5/23	1	2	FACETS	1	0.938	1	1	0.982	1	CLONAL	3	FALSE	1	0.149716163030823	2		409	195	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120512	94120512	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	41	434	0	ENST00000369303.4:c.539A>T	p.Lys180Met	p.K180M	ENST00000369303	NM_004440.3	180	aAg/aTg	3/17	1	2	FACETS	1	0.925	1	1	0.978	1	CLONAL	3	FALSE	1	0.149716163030823	2		434	157	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015578	112015578	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	89	394	0	ENST00000368678.4:c.1264G>T	p.Gly422Cys	p.G422C	ENST00000368678		422	Ggt/Tgt	11/13	1	2	FACETS	0.926	0.829	1	1	0.99	1	CLONAL	4	FALSE	1	0.149716163030823	2		394	321	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189039	38189039	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	33	376	0	ENST00000317025.8:c.975del	p.Lys325AsnfsTer55	p.K325Nfs*55	ENST00000317025	NM_023034.1	325	aaA/aa	5/24	0.149716163030823	3	FACETS	0.855	0.699	1	0.855	0.699	1	CLONAL	2	FALSE	1	0.149716163030823	3		376	277	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869515	117869515	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	44	407	0	ENST00000297338.2:c.679G>T	p.Gly227Ter	p.G227*	ENST00000297338	NM_006265.2	227	Gga/Tga	6/14	0.149716163030823	3	FACETS	1	0.895	1	1	0.965	1	CLONAL	3	FALSE	1	0.149716163030823	3		407	197	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2060826	2060826	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	40	410	0	ENST00000349721.2:c.1532A>G	p.Glu511Gly	p.E511G	ENST00000349721	NM_003070.3	511	gAg/gGg	9/34	1	2	FACETS	0.852	0.715	1	1	0.974	1	CLONAL	3	FALSE	1	0.149716163030823	2		410	209	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239830	98239830	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs863225054	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	45	363	0	ENST00000331920.6:c.1502A>G	p.Gln501Arg	p.Q501R	ENST00000331920	NM_000264.3	501	cAg/cGg	10/24	1	2	FACETS	0.875	0.742	1	1	0.977	1	CLONAL	3	FALSE	1	0.149716163030823	2		363	229	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399281	139399281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	97	457	0	ENST00000277541.6:c.4862G>A	p.Gly1621Asp	p.G1621D	ENST00000277541	NM_017617.3	1621	gGc/gAc	26/34	1	2	FACETS	0.888	0.798	0.981	1	0.99	1	CLONAL	4	FALSE	1	0.149716163030823	2		457	365	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404216	139404216	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	47	461	0	ENST00000277541.6:c.2938T>C	p.Cys980Arg	p.C980R	ENST00000277541	NM_017617.3	980	Tgt/Cgt	18/34	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.149716163030823	2		461	453	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348472	70348472	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	33	453	0	ENST00000374080.3:c.3379T>C	p.Ser1127Pro	p.S1127P	ENST00000374080		1127	Tcg/Ccg	24/45	0.149716163030823	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	0	0.149716163030823	1		453	277	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349012	70349012	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	59	486	0	ENST00000374080.3:c.3524T>C	p.Ile1175Thr	p.I1175T	ENST00000374080		1175	aTc/aCc	25/45	0.149716163030823	1	FACETS	1	0.871	1	1	0.978	1	CLONAL	2	FALSE	0	0.149716163030823	1		486	362	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0061173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	119	499	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.354300529351155	1	FACETS	0.918	0.832	1	0.918	0.832	1	CLONAL	1	TRUE	0	0.380994328302287	1		500	551	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0061173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	49	372	1	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.380994328302287	2		373	248	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357196	70357196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200663107	NA	P-0061173-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	47	647	1	ENST00000374080.3:c.5711C>T	p.Ala1904Val	p.A1904V	ENST00000374080		1904	gCg/gTg	39/45	1	2	FACETS	0.425	0.358	0.499	0.425	0.358	0.499	SUBCLONAL	1	TRUE	1	0.380994328302287	2		648	580	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591888	48591888	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	123	434	0	ENST00000342988.3:c.1051G>T	p.Asp351Tyr	p.D351Y	ENST00000342988	NM_005359.5	351	Gat/Tat	9/12	0.68311046894359	1	FACETS	0.841	0.774	0.909	0.841	0.774	0.909	CLONAL	1	TRUE	0	0.68311046894359	1		434	282	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0061174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	170	711	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.813	0.751	0.877	0.813	0.751	0.877	CLONAL	1	TRUE	1	0.68311046894359	2		711	612	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163749	152163749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1207112399	NA	P-0061174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	144	444	0	ENST00000206249.3:c.470G>A	p.Arg157Gln	p.R157Q	ENST00000206249	NM_000125.3	157	cGa/cAa	2/8	1	2	FACETS	0.956	0.88	1	0.956	0.88	1	CLONAL	1	TRUE	1	0.68311046894359	2		444	441	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453145	140453145	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913366	NA	P-0061174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	198	320	0	ENST00000288602.6:c.1790T>G	p.Leu597Arg	p.L597R	ENST00000288602	NM_004333.4	597	cTa/cGa	15/18	0.566499666712042	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.68311046894359	4		320	467	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831446	72831446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143025874	NA	P-0061174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	163	544	0	ENST00000268489.5:c.5135G>A	p.Arg1712Gln	p.R1712Q	ENST00000268489	NM_006885.3	1712	cGg/cAg	9/10	0.642156063500574	2	FACETS	0.858	0.792	0.926	0.429	0.396	0.463	CLONAL	1	TRUE	0	0.68311046894359	2		544	556	SUCCESS
APC	324	MSKCC	GRCh37	5	112175069	112175069	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	95	336	0	ENST00000257430.4:c.3778C>T	p.Gln1260Ter	p.Q1260*	ENST00000257430	NM_000038.5	1260	Cag/Tag	16/16	1	2	FACETS	0.927	0.836	1	0.927	0.836	1	CLONAL	1	TRUE	1	0.68311046894359	2		336	300	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584713	48584713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	172	465	0	ENST00000342988.3:c.791G>A	p.Ser264Asn	p.S264N	ENST00000342988	NM_005359.5	264	aGc/aAc	7/12	0.68311046894359	1	FACETS	0.877	0.819	0.936	0.877	0.819	0.936	CLONAL	1	TRUE	0	0.68311046894359	1		465	378	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981169	201981170	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0061174-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	412	552	0	ENST00000359651.3:c.249dup	p.Lys84GlnfsTer8	p.K84Qfs*8	ENST00000359651		83	aac/aaCc	2/8	0.657647538096116	3	FACETS	0.93	0.89	0.97	0.93	0.89	0.97	CLONAL	2	TRUE	1	0.68311046894359	3		552	870	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134526	2134526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1441136255	NA	P-0061175-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	56	753	0	ENST00000219476.3:c.4303G>A	p.Glu1435Lys	p.E1435K	ENST00000219476	NM_000548.3	1435	Gaa/Aaa	34/42	1	2	FACETS	0.318	0.272	0.37	0.318	0.272	0.37	SUBCLONAL	1	TRUE	1	0.385467547548023	2		753	913	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0061176-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	70	382	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.777	0.681	0.88	1	0.976	1	SUBCLONAL	2	TRUE	1	0.230443546414915	2		382	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0061176-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	40	339	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	1	2	FACETS	0.627	0.52	0.746	0.627	0.52	0.746	SUBCLONAL	1	TRUE	1	0.230443546414915	2		339	554	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356238	70356238	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061176-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	33	454	0	ENST00000374080.3:c.5133C>A	p.Asp1711Glu	p.D1711E	ENST00000374080		1711	gaC/gaA	37/45	1	2	FACETS	0.438	0.355	0.531	0.438	0.355	0.531	SUBCLONAL	1	TRUE	1	0.230443546414915	2		454	654	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593621	55593662	+	inframe_deletion	In_Frame_Del	DEL	ATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTT	ATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTT	-	novel	NA	P-0061177-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	222	404	0	ENST00000288135.5:c.1687_1728del	p.Ile563_Leu576del	p.I563_L576del	ENST00000288135	NM_000222.2	563	ATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTT/-	11/21	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.740096601982451	2		404	588	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061178-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	335	321	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.884	0.838	0.931	0.884	0.838	0.931	CLONAL	1	TRUE	1	0.76682063140491	2		321	988	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954300	48954300	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1461382798	NA	P-0061178-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	92	177	0	ENST00000267163.4:c.1422-1G>A		p.X474_splice	ENST00000267163	NM_000321.2	474			0.76682063140491	1	FACETS	0.902	0.828	0.975	0.902	0.828	0.975	CLONAL	1	TRUE	0	0.76682063140491	1		177	164	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0061178-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	825	473	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.76682063140491	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.76682063140491	2		473	1060	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720876	89720876	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs786201041	NA	P-0061178-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	55	100	0	ENST00000371953.3:c.1026+1G>A		p.X342_splice	ENST00000371953	NM_000314.4	342			0.76682063140491	1	FACETS	0.983	0.884	1	0.983	0.884	1	CLONAL	1	TRUE	0	0.76682063140491	1		100	90	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0061179-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	211	526	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	1	2	FACETS	0.788	0.732	0.847	0.788	0.732	0.847	SUBCLONAL	1	TRUE	1	0.508894197607686	2		526	1052	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099989	27099989	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0061179-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	543	577	0	ENST00000324856.7:c.3866+2T>A		p.X1289_splice	ENST00000324856	NM_006015.4	1289			0.307154128367488	2	FACETS	0.897	0.864	0.931	0.897	0.864	0.931	CLONAL	2	TRUE	0	0.508894197607686	2		577	1189	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519958	NA	P-0061179-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	218	426	0	ENST00000481739.1:c.1280C>A	p.Ser427Tyr	p.S427Y	ENST00000481739	NM_002957.4	427	tCc/tAc	10/10	1	2	FACETS	0.983	0.915	1	0.983	0.915	1	CLONAL	1	TRUE	1	0.508894197607686	2		426	872	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427930	49427930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061179-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	230	481	0	ENST00000301067.7:c.10660C>T	p.Arg3554Cys	p.R3554C	ENST00000301067	NM_003482.3	3554	Cgt/Tgt	38/54	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.508894197607686	2		481	891	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66520197	66520197	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061179-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	252	368	0	ENST00000358598.2:c.481G>T	p.Gly161Ter	p.G161*	ENST00000358598	NM_212471.2	161	Gga/Tga	5/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.508894197607686	2		368	917	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628127	187628128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0061179-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	244	449	0	ENST00000441802.2:c.2854dup	p.His952ProfsTer4	p.H952Pfs*4	ENST00000441802	NM_005245.3	952	cac/cCac	2/27	1	2	FACETS	0.991	0.927	1	0.991	0.927	1	CLONAL	1	TRUE	1	0.508894197607686	2		449	968	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805749	32805749	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061179-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	302	623	0	ENST00000374899.4:c.262C>G	p.Arg88Gly	p.R88G	ENST00000374899	NM_018833.2	88	Cgt/Ggt	2/12	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.508894197607686	2		623	1151	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060599	38060600	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0061179-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	138	593	0	ENST00000250448.2:c.1389_1390del	p.Tyr464PhefsTer93	p.Y464Ffs*93	ENST00000250448	NM_004496.3	463	gtGTat/gtat	2/2	1	2	FACETS	0.423	0.383	0.464	0.423	0.383	0.464	SUBCLONAL	1	TRUE	1	0.508894197607686	2		593	1283	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33680060	33680060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202123744	NA	P-0061179-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	153	0	0	ENST00000308377.4:c.2021G>A	p.Arg674His	p.R674H	ENST00000308377	NM_152270.3	674	cGt/cAt	5/5	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.508894197607686	2		0	542	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0061179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	48	526	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.183723362637519	3	FACETS	0.65	0.547	0.764	0.325	0.273	0.382	SUBCLONAL	1	TRUE	1	0.15	3		526	1058	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099989	27099989	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0061179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	110	577	0	ENST00000324856.7:c.3866+2T>A		p.X1289_splice	ENST00000324856	NM_006015.4	1289			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.15	2		577	1215	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519958	NA	P-0061179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	29	426	0	ENST00000481739.1:c.1280C>A	p.Ser427Tyr	p.S427Y	ENST00000481739	NM_002957.4	427	tCc/tAc	10/10	1	2	FACETS	0.487	0.389	0.599	0.487	0.389	0.599	SUBCLONAL	1	TRUE	1	0.15	2		426	794	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427930	49427930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	45	481	0	ENST00000301067.7:c.10660C>T	p.Arg3554Cys	p.R3554C	ENST00000301067	NM_003482.3	3554	Cgt/Tgt	38/54	0.183723362637519	3	FACETS	0.769	0.644	0.908	0.384	0.322	0.454	CLONAL	1	TRUE	1	0.15	3		481	839	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66520197	66520197	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	42	368	0	ENST00000358598.2:c.481G>T	p.Gly161Ter	p.G161*	ENST00000358598	NM_212471.2	161	Gga/Tga	5/11	0.183723362637519	3	FACETS	0.736	0.612	0.874	0.368	0.306	0.437	SUBCLONAL	1	TRUE	1	0.15	3		368	818	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628127	187628128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0061179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	36	449	0	ENST00000441802.2:c.2854dup	p.His952ProfsTer4	p.H952Pfs*4	ENST00000441802	NM_005245.3	952	cac/cCac	2/27	0.176978009221507	0	FACETS	0.597	0.49	0.719			1	SUBCLONAL	1	TRUE	0	0.15	0		449	683	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805749	32805749	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1292	77	623	0	ENST00000374899.4:c.262C>G	p.Arg88Gly	p.R88G	ENST00000374899	NM_018833.2	88	Cgt/Ggt	2/12	0.3	5	FACETS	0.919	0.803	1	0.459	0.401	0.522	CLONAL	1	TRUE	3	0.15	5		623	1369	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33680060	33680060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202123744	NA	P-0061179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	18	0	0	ENST00000308377.4:c.2021G>A	p.Arg674His	p.R674H	ENST00000308377	NM_152270.3	674	cGt/cAt	5/5	0.183723362637519	3	FACETS	0.466	0.349	0.605	0.233	0.174	0.303	SUBCLONAL	1	TRUE	1	0.15	3		0	554	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414399	6414399	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	68	263	0	ENST00000356142.4:c.33C>A	p.Asp11Glu	p.D11E	ENST00000356142	NM_018890.3	11	gaC/gaA	1/7	0.265348788476044	4	FACETS	1	0.969	1			1	CLONAL	1	TRUE	NA	0.15	4		263	732	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657502	29657502	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	30	237	0	ENST00000356175.3:c.5735G>C	p.Gly1912Ala	p.G1912A	ENST00000356175	NM_000267.3	1912	gGa/gCa	38/57	0.183723362637519	3	FACETS	1	0.845	1	0.528	0.425	0.645	CLONAL	1	TRUE	1	0.15	3		237	407	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	123	321	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.437507676028905	2		321	423	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0061180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	104	380	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.437507676028905	2		380	348	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061181-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	345	377	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.371527755893006	8	FACETS	0.942	0.899	0.985	0.942	0.899	0.985	CLONAL	6	TRUE	2	0.371527755893006	8		377	695	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0061181-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	262	769	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.338350949461398	3	FACETS	0.906	0.856	0.957	0.906	0.856	0.957	CLONAL	3	TRUE	0	0.371527755893006	3		770	615	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023144	27023145	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCGGCGGCGGAGCCGGCA	rs749452696	NA	P-0061181-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	77	443	0	ENST00000324856.7:c.261_278dup	p.Ala88_Gly93dup	p.A88_G93dup	ENST00000324856	NM_006015.4	88	ggc/gGCGGCGGCGGAGCCGGCAgc	1/20	0.348781424554185	3	FACETS	0.853	0.75	0.964	0.427	0.375	0.482	CLONAL	1	TRUE	1	0.371527755893006	3		443	576	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199704	138199704	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061181-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	231	352	0	ENST00000237289.4:c.1122A>C	p.Glu374Asp	p.E374D	ENST00000237289	NM_001270507.1	374	gaA/gaC	7/9	0.217002197781107	5	FACETS	1	0.984	1	0.771	0.721	0.823	INDETERMINATE	2	TRUE	2	0.371527755893006	5		352	837	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0061182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	360	817	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.584369400952781	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.584369400952781	1		817	812	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0061182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	338	497	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.584369400952781	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.584369400952781	1		497	665	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857727	9857727	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0061182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	205	573	0	ENST00000330684.3:c.3674C>G	p.Ser1225Ter	p.S1225*	ENST00000330684	NM_001134407.1	1225	tCa/tGa	13/13	1	2	FACETS	0.549	0.508	0.592	0.549	0.508	0.592	SUBCLONAL	1	TRUE	1	0.584369400952781	2		573	1278	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974372	93974372	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	29	252	0	ENST00000369303.4:c.1682T>A	p.Val561Asp	p.V561D	ENST00000369303	NM_004440.3	561	gTt/gAt	8/17	1	2	FACETS	0.212	0.169	0.26	0.212	0.169	0.26	SUBCLONAL	1	TRUE	1	0.584369400952781	2		252	469	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099315	157099315	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs372726215	NA	P-0061182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	170	557	1	ENST00000346085.5:c.252C>G	p.His84Gln	p.H84Q	ENST00000346085	NM_020732.3	84	caC/caG	1/20	1	2	FACETS	0.573	0.526	0.621	0.573	0.526	0.621	SUBCLONAL	1	TRUE	1	0.584369400952781	2		558	1016	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0061182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	190	296	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	0.335309135679534	1	FACETS	0.825	0.768	0.883	0.825	0.768	0.883	INDETERMINATE	1	TRUE	0	0.584369400952781	1		296	558	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982101	201982102	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0061182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	157	564	0	ENST00000359651.3:c.627dup	p.Ser210LeufsTer7	p.S210Lfs*7	ENST00000359651		209	tcc/tCcc	5/8	0.345198238742336	1	FACETS	0.411	0.376	0.448	0.411	0.376	0.448	INDETERMINATE	1	TRUE	0	0.584369400952781	1		564	925	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63938116	63938116	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	94	340	0	ENST00000398590.3:c.456C>G	p.Asp152Glu	p.D152E	ENST00000398590	NM_001177387.1	152	gaC/gaG	5/14	1	2	FACETS	0.507	0.452	0.567	0.507	0.452	0.567	SUBCLONAL	1	TRUE	1	0.584369400952781	2		340	634	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628434	187628434	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs757406003	NA	P-0061182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	108	560	0	ENST00000441802.2:c.2548G>C	p.Asp850His	p.D850H	ENST00000441802	NM_005245.3	850	Gac/Cac	2/27	1	2	FACETS	0.356	0.319	0.396	0.356	0.319	0.396	SUBCLONAL	1	TRUE	1	0.584369400952781	2		560	1038	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876439	35876439	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	153	503	0	ENST00000303115.3:c.1231A>T	p.Thr411Ser	p.T411S	ENST00000303115	NM_002185.3	411	Aca/Tca	8/8	0.391512699295651	1	FACETS	0.434	0.397	0.473	0.434	0.397	0.473	SUBCLONAL	1	TRUE	0	0.584369400952781	1		503	854	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126715	5126715	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	44	300	0	ENST00000381652.3:c.3323A>C	p.Asn1108Thr	p.N1108T	ENST00000381652	NM_004972.3	1108	aAt/aCt	25/25	1	2	FACETS	0.3	0.251	0.354	0.3	0.251	0.354	SUBCLONAL	1	TRUE	1	0.584369400952781	2		300	502	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855241	76855241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	54	252	0	ENST00000373344.5:c.5746G>A	p.Asp1916Asn	p.D1916N	ENST00000373344	NM_000489.3	1916	Gat/Aat	24/35	0.345198238742336	1	FACETS	0.328	0.281	0.379	0.328	0.281	0.379	INDETERMINATE	1	TRUE	0	0.584369400952781	1		252	399	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061183-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	101	321	0				ENST00000310581	NM_198253.2	-/1132			0.720976708338346	3	FACETS	1	0.969	1	0.588	0.532	0.647	CLONAL	1	TRUE	1	0.720976708338346	3		321	324	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662909	52662909	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0061183-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	202	417	0	ENST00000394830.3:c.1443+1G>C		p.X481_splice	ENST00000394830	NM_018313.4	481			0.720976708338346	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.720976708338346	2		417	247	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343587	343587	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061183-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	282	780	0	ENST00000262320.3:c.2087del	p.Pro696HisfsTer9	p.P696Hfs*9	ENST00000262320	NM_003502.3	696	cCa/ca	8/11	0.720976708338346	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.720976708338346	2		780	359	SUCCESS
APC	324	MSKCC	GRCh37	5	112154804	112154804	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061183-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	123	575	2	ENST00000257430.4:c.1075C>T	p.Leu359Phe	p.L359F	ENST00000257430	NM_000038.5	359	Ctt/Ttt	10/16	0.720976708338346	3	FACETS	1	0.971	1	0.575	0.524	0.627	CLONAL	1	TRUE	1	0.720976708338346	3		577	404	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403322	116403322	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061183-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	152	425	0	ENST00000397752.3:c.2583G>C	p.Lys861Asn	p.K861N	ENST00000397752	NM_000245.2	861	aaG/aaC	11/21	0.565760777985124	4	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	2	0.720976708338346	4		425	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0061184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	366	851	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.638133373224823	2	FACETS	0.99	0.953	1	0.99	0.953	1	CLONAL	2	TRUE	0	0.651743777595406	2		851	567	SUCCESS
APC	324	MSKCC	GRCh37	5	112175358	112175358	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1554085480	NA	P-0061184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	315	506	0	ENST00000257430.4:c.4067C>G	p.Ser1356Ter	p.S1356*	ENST00000257430	NM_000038.5	1356	tCa/tGa	16/16	0.651743777595406	2	FACETS	0.908	0.869	0.947	0.908	0.869	0.947	CLONAL	2	TRUE	0	0.651743777595406	2		506	532	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095537	178095540	+	frameshift_variant	Frame_Shift_Del	DEL	CTTA	CTTA	-	rs748937667	NA	P-0061184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	73	380	0	ENST00000397062.3:c.1791_1794del	p.Ser597ArgfsTer14	p.S597Rfs*14	ENST00000397062	NM_006164.4	597	agTAAG/ag	5/5	0.651743777595406	3	FACETS	1	0.928	1	0.534	0.472	0.599	CLONAL	1	TRUE	1	0.651743777595406	3		380	278	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879348	56879348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	173	491	0	ENST00000519728.1:c.865G>A	p.Glu289Lys	p.E289K	ENST00000519728	NM_002350.3	289	Gaa/Aaa	9/13	0.637374261658011	6	FACETS	0.879	0.806	0.954	0.176	0.161	0.191	CLONAL	1	TRUE	1	0.651743777595406	6		491	1392	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95556938	95556938	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	138	438	0	ENST00000393063.1:c.5666A>T	p.Lys1889Ile	p.K1889I	ENST00000393063	NM_030621.3	1889	aAa/aTa	28/28	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.651743777595406	2		438	423	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508755	106508755	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061184-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	625	614	0	ENST00000359195.3:c.749C>T	p.Thr250Ile	p.T250I	ENST00000359195	NM_002649.2	250	aCc/aTc	2/11	0.651743777595406	5	FACETS	0.981	0.947	1	0.981	0.947	1	CLONAL	3	TRUE	2	0.651743777595406	5		614	1289	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0061185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	280	537	0	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.894187080132124	1	FACETS	0.941	0.907	0.973	0.941	0.907	0.973	CLONAL	1	TRUE	0	0.894187080132124	1		537	368	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118365458	118365458	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061185-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	24	359	0	ENST00000534358.1:c.5339G>C	p.Trp1780Ser	p.W1780S	ENST00000534358	NM_005933.3	1780	tGg/tCg	18/36	1	2	FACETS	0.137	0.107	0.172	0.137	0.107	0.172	SUBCLONAL	1	TRUE	1	0.894187080132124	2		359	392	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457758	149457758	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs758322216	NA	P-0061186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	112	585	0	ENST00000286301.3:c.646C>T	p.Arg216Ter	p.R216*	ENST00000286301	NM_005211.3	216	Cga/Tga	5/22	1	2	FACETS	0.483	0.434	0.536	0.483	0.434	0.536	SUBCLONAL	1	TRUE	1	0.480118137916406	2		585	965	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926888	112926888	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507546	NA	P-0061186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	66	506	0	ENST00000351677.2:c.1508G>T	p.Gly503Val	p.G503V	ENST00000351677	NM_002834.3	503	gGg/gTg	13/16	0.267041082410324	1	FACETS	0.303	0.262	0.347	0.303	0.262	0.347	INDETERMINATE	1	TRUE	0	0.480118137916406	1		506	690	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409102	4409102	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778716956	NA	P-0061186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	134	520	0	ENST00000261254.3:c.797G>A	p.Arg266His	p.R266H	ENST00000261254	NM_001759.3	266	cGt/cAt	5/5	0.267041082410324	1	FACETS	0.5	0.454	0.549	0.5	0.454	0.549	INDETERMINATE	1	TRUE	0	0.480118137916406	1		520	848	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089686	27089686	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0061186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	294	713	0	ENST00000324856.7:c.2642C>G	p.Ser881Ter	p.S881*	ENST00000324856	NM_006015.4	881	tCa/tGa	8/20	0.480118137916406	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.480118137916406	1		713	892	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272789	18272789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	251	683	0	ENST00000222254.8:c.829C>T	p.Pro277Ser	p.P277S	ENST00000222254	NM_005027.3	277	Cct/Tct	7/16	1	2	FACETS	0.918	0.858	0.98	0.918	0.858	0.98	CLONAL	1	TRUE	1	0.480118137916406	2		683	1139	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878235	151878235	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	147	657	1	ENST00000262189.6:c.6710C>A	p.Ser2237Ter	p.S2237*	ENST00000262189	NM_170606.2	2237	tCa/tAa	36/59	1	2	FACETS	0.527	0.48	0.577	0.527	0.48	0.577	SUBCLONAL	1	TRUE	1	0.480118137916406	2		658	1162	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981937	70981937	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	114	697	0	ENST00000276594.2:c.159C>G	p.Phe53Leu	p.F53L	ENST00000276594	NM_024504.3	53	ttC/ttG	2/8	0.251638939509123	0	FACETS	0.3	0.269	0.332			1	INDETERMINATE	1	TRUE	0	0.480118137916406	0		697	824	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0061187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	272	851	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.19740361592577	2	FACETS	1	0.993	1	0.669	0.633	0.706	INDETERMINATE	1	TRUE	0	0.629215445609651	2		851	646	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0061187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	213	492	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.629215445609651	2		492	636	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052629	42052629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	207	544	0	ENST00000219905.7:c.7300C>T	p.Arg2434Trp	p.R2434W	ENST00000219905	NM_001164273.1	2434	Cgg/Tgg	20/24	1	2	FACETS	0.933	0.869	0.999	0.933	0.869	0.999	CLONAL	1	TRUE	1	0.629215445609651	2		544	705	SUCCESS
APC	324	MSKCC	GRCh37	5	112175890	112175890	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	164	480	0	ENST00000257430.4:c.4599del	p.Asn1533LysfsTer32	p.N1533Kfs*32	ENST00000257430	NM_000038.5	1533	aaT/aa	16/16	0.610168204527688	1	FACETS	0.851	0.79	0.913	0.851	0.79	0.913	CLONAL	1	TRUE	0	0.629215445609651	1		480	420	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720869	89720869	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1564568689	NA	P-0061187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	142	181	0	ENST00000371953.3:c.1023del	p.Phe341LeufsTer3	p.F341Lfs*3	ENST00000371953	NM_000314.4	340	aaT/aa	8/9	0.629215445609651	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.629215445609651	2		181	218	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059145	47059145	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	213	469	0	ENST00000409792.3:c.7516A>G	p.Lys2506Glu	p.K2506E	ENST00000409792	NM_014159.6	2506	Aaa/Gaa	20/21	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.629215445609651	2		469	632	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200778	128200778	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	378	469	0	ENST00000341105.2:c.1027A>G	p.Arg343Gly	p.R343G	ENST00000341105	NM_032638.4	343	Aga/Gga	5/6	0.629215445609651	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.629215445609651	3		469	786	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531143	187531143	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	180	448	0	ENST00000441802.2:c.9880G>T	p.Asp3294Tyr	p.D3294Y	ENST00000441802	NM_005245.3	3294	Gat/Tat	15/27	1	2	FACETS	0.992	0.92	1	0.992	0.92	1	CLONAL	1	TRUE	1	0.629215445609651	2		448	577	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589522	67589552	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTAATCTTTCTAGGATCAAGTTGTCAAAG	TTTTAATCTTTCTAGGATCAAGTTGTCAAAG	AAAAT	novel	NA	P-0061187-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	51	167	0	ENST00000274335.5:c.1300-15_1315delinsAAAAT		p.X434_splice	ENST00000274335		434		10/15	1	2	FACETS	0.811	0.698	0.93	0.811	0.698	0.93	CLONAL	1	TRUE	1	0.629215445609651	2		167	200	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412899	49412899	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061188-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	27	463	0	ENST00000418115.1:c.124T>C	p.Tyr42His	p.Y42H	ENST00000418115	NM_001664.2	42	Tat/Cat	2/5	1	2	FACETS	0.427	0.338	0.53	0.427	0.338	0.53	SUBCLONAL	1	TRUE	1	0.15	2		463	843	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61305233	61305233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367838172	NA	P-0061188-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	29	347	1	ENST00000341074.5:c.893C>T	p.Thr298Met	p.T298M	ENST00000341074	NM_002974.2	298	aCg/aTg	8/8	1	2	FACETS	0.773	0.62	0.949	0.773	0.62	0.949	CLONAL	1	TRUE	1	0.15	2		348	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0061190-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	570	712	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.564573708873671	2	FACETS	0.988	0.955	1	0.988	0.955	1	CLONAL	2	TRUE	0	0.564573708873671	2		712	1022	SUCCESS
AR	367	MSKCC	GRCh37	X	66765159	66765185	+	inframe_deletion	In_Frame_Del	DEL	GCAGCAGCAGCAGCAGCAGCAGCAGCA	GCAGCAGCAGCAGCAGCAGCAGCAGCA	-	rs3032358	NA	P-0061190-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	48	191	0	ENST00000374690.3:c.213_239del	p.Gln72_Gln80del	p.Q72_Q80del	ENST00000374690	NM_000044.3	57	ctGCAGCAGCAGCAGCAGCAGCAGCAGCAg/ctg	1/8	1	1	FACETS	0.479	0.408	0.555	0.479	0.408	0.555	SUBCLONAL	1	TRUE	0	0.564573708873671	1		191	255	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28971153	28971153	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061190-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	276	467	0	ENST00000282397.4:c.1604G>A	p.Cys535Tyr	p.C535Y	ENST00000282397	NM_002019.4	535	tGc/tAc	12/30	0.564573708873671	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.564573708873671	1		467	545	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412046	116412046	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	G	novel	NA	P-0061190-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	1236	495	0	ENST00000397752.3:c.3028+3A>G		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.564573708873671	6	FACETS	1	0.984	1	1	0.984	1	CLONAL	6	TRUE	0	0.564573708873671	6		495	1554	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124511006	124511006	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061190-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	494	295	0	ENST00000357628.3:c.214A>T	p.Ile72Phe	p.I72F	ENST00000357628	NM_015450.2	72	Att/Ttt	7/19	0.564573708873671	5	FACETS	0.985	0.958	1	0.985	0.958	1	CLONAL	5	TRUE	0	0.564573708873671	5		295	656	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	104	377	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.921	0.829	1	0.921	0.829	1	CLONAL	1	TRUE	1	0.461634416900632	2		377	489	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0061191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	235	817	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.411397614360967	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.461634416900632	1		817	748	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0061191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	264	622	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.195574939789422	3	FACETS	1	0.993	1	0.745	0.699	0.792	INDETERMINATE	1	TRUE	1	0.461634416900632	3		622	945	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs377767347	NA	P-0061191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	186	566	0	ENST00000342988.3:c.1082G>T	p.Arg361Leu	p.R361L	ENST00000342988	NM_005359.5	361	cGc/cTc	9/12	0.461634416900632	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.461634416900632	1		566	615	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412095	63412095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852217	NA	P-0061191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	280	366	0	ENST00000330258.3:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000330258	NM_152424.3	358	Cga/Tga	2/2	1	1	FACETS	0.875	0.832	0.918	1	0.995	1	CLONAL	2	TRUE	0	0.461634416900632	1		366	533	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107230	193107230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	104	455	0	ENST00000367435.3:c.439C>T	p.Arg147Cys	p.R147C	ENST00000367435	NM_024529.4	147	Cgc/Tgc	6/17	1	2	FACETS	0.806	0.724	0.893	0.806	0.724	0.893	CLONAL	1	TRUE	1	0.461634416900632	2		455	559	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047957	180047957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1460398148	NA	P-0061191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	216	795	0	ENST00000261937.6:c.2218G>A	p.Glu740Lys	p.E740K	ENST00000261937	NM_182925.4	740	Gag/Aag	15/30	1	2	FACETS	0.912	0.848	0.979	0.912	0.848	0.979	CLONAL	1	TRUE	1	0.461634416900632	2		795	1026	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3645686	3645686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769084265	NA	P-0061191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	53	628	0	ENST00000294008.3:c.1933G>A	p.Val645Met	p.V645M	ENST00000294008	NM_032444.2	645	Gtg/Atg	9/15	1	2	FACETS	0.247	0.21	0.288	0.247	0.21	0.288	SUBCLONAL	1	TRUE	1	0.461634416900632	2		628	929	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163313571	163313571	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	21	197	0	ENST00000271452.3:c.718T>G	p.Leu240Val	p.L240V	ENST00000271452	NM_145697.2	240	Ttg/Gtg	10/14	1	2	FACETS	0.283	0.218	0.36	0.283	0.218	0.36	SUBCLONAL	1	TRUE	1	0.461634416900632	2		197	321	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827351	72827351	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	47	568	0	ENST00000268489.5:c.9230C>G	p.Ala3077Gly	p.A3077G	ENST00000268489	NM_006885.3	3077	gCt/gGt	9/10	0.195574939789422	3	FACETS	0.295	0.248	0.347	0.147	0.124	0.174	INDETERMINATE	1	TRUE	1	0.461634416900632	3		568	850	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120021	70120755	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	GCCGCCGCCACCCCCGCAGCAGCCCCCACAGGCCCCGCCGGCCCCGCAGGCGCCCCCGCAGCCGCAGGCGGCGCCCCCACAGCAGCCGGCGGCACCCCCGCAGCAGCCACAGGCGCACACGCTGACCACGCTGAGCAGCGAGCCGGGCCAGTCCCAGCGAACGCACATCAAGACGGAGCAGCTGAGCCCCAGCCACTACAGCGAGCAGCAGCAGCACTCGCCCCAACAGATCGCCTACAGCCCCTTCAACCTCCCACACTACAGCCCCTCCTACCCGCCCATCACCCGCTCACAGTACGACTACACCGACCACCAGAACTCCAGCTCCTACTACAGCCACGCGGCAGGCCAGGGCACCGGCCTCTACTCCACCTTCACCTACATGAACCCCGCTCAGCGCCCCATGTACACCCCCATCGCCGACACCTCTGGGGTCCCTTCCATCCCGCAGACCCACAGCCCCCAGCACTGGGAACAACCCGTCTACACACAGCTCACTCGACCTTGAGGAGGCCTCCCACGAAGGGCGAAGATGGCCGAGATGATCCTAAAAATAACCGAAGAAAGAGAGGACCAACCAGAATTCCCTTTGGACATTTGTGTTTTTTTGTTTTTTTATTTTGTTTTGTTTTTTCTTCTTCTTCTTCTTCCTTAAAGACATTTAAGCTAAAGGCAACTCGTACCCAAATTTCCAAGACACAAACATGACCTATCCAAGCGCATTACCCACTTGTG	GCCGCCGCCACCCCCGCAGCAGCCCCCACAGGCCCCGCCGGCCCCGCAGGCGCCCCCGCAGCCGCAGGCGGCGCCCCCACAGCAGCCGGCGGCACCCCCGCAGCAGCCACAGGCGCACACGCTGACCACGCTGAGCAGCGAGCCGGGCCAGTCCCAGCGAACGCACATCAAGACGGAGCAGCTGAGCCCCAGCCACTACAGCGAGCAGCAGCAGCACTCGCCCCAACAGATCGCCTACAGCCCCTTCAACCTCCCACACTACAGCCCCTCCTACCCGCCCATCACCCGCTCACAGTACGACTACACCGACCACCAGAACTCCAGCTCCTACTACAGCCACGCGGCAGGCCAGGGCACCGGCCTCTACTCCACCTTCACCTACATGAACCCCGCTCAGCGCCCCATGTACACCCCCATCGCCGACACCTCTGGGGTCCCTTCCATCCCGCAGACCCACAGCCCCCAGCACTGGGAACAACCCGTCTACACACAGCTCACTCGACCTTGAGGAGGCCTCCCACGAAGGGCGAAGATGGCCGAGATGATCCTAAAAATAACCGAAGAAAGAGAGGACCAACCAGAATTCCCTTTGGACATTTGTGTTTTTTTGTTTTTTTATTTTGTTTTGTTTTTTCTTCTTCTTCTTCTTCCTTAAAGACATTTAAGCTAAAGGCAACTCGTACCCAAATTTCCAAGACACAAACATGACCTATCCAAGCGCATTACCCACTTGTG	-	novel	NA	P-0061191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	61	625	0	ENST00000245479.2:c.1026_*230del		p.*342*	ENST00000245479	NM_000346.3	341		3/3	1	2	FACETS	0.335	0.288	0.386	0.335	0.288	0.386	SUBCLONAL	1	TRUE	1	0.461634416900632	2		625	789	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793083	33793083	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	45	555	0	ENST00000498907.2:c.238G>T	p.Asp80Tyr	p.D80Y	ENST00000498907	NM_004364.3	80	Gac/Tac	1/1	1	2	FACETS	0.254	0.213	0.3	0.254	0.213	0.3	SUBCLONAL	1	TRUE	1	0.461634416900632	2		555	767	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021795	69021795	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	149	488	0	ENST00000288368.4:c.3083A>T	p.Lys1028Ile	p.K1028I	ENST00000288368	NM_024870.2	1028	aAa/aTa	25/40	0.143253791336418	0	FACETS	0.516	0.472	0.561			1	INDETERMINATE	1	TRUE	0	0.461634416900632	0		488	674	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579575	7579575	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	535	691	0	ENST00000269305.4:c.112C>T	p.Gln38Ter	p.Q38*	ENST00000269305	NM_001126112.2	38	Caa/Taa	4/11	0.852517838959711	2	FACETS	0.986	0.965	1	0.986	0.965	1	CLONAL	2	TRUE	0	0.862841419924778	2		691	629	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624526	93624526	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	277	572	0	ENST00000375746.1:c.617G>T	p.Cys206Phe	p.C206F	ENST00000375746	NM_001174167.1	206	tGc/tTc	4/14	1	2	FACETS	0.98	0.927	1	0.98	0.927	1	CLONAL	1	TRUE	1	0.862841419924778	2		572	655	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068433	26068433	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0061192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	119	150	0	ENST00000435504.4:c.58-1G>A		p.X20_splice	ENST00000435504		20			0.835719547771677	3	FACETS	0.968	0.928	1	0.968	0.928	1	CLONAL	3	TRUE	0	0.862841419924778	3		150	136	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179075	123179075	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	235	414	0	ENST00000218089.9:c.524T>A	p.Phe175Tyr	p.F175Y	ENST00000218089	NM_001042749.1	175	tTt/tAt	8/35	0.494161024372795	5	FACETS	0.953	0.894	1	0.635	0.596	0.675	INDETERMINATE	2	TRUE	2	0.862841419924778	5		414	656	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477837	140477851	+	inframe_deletion	In_Frame_Del	DEL	TAGGTGCTGTCACAT	TAGGTGCTGTCACAT	-	novel	NA	P-0061194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	31	360	0	ENST00000288602.6:c.1457_1471del	p.Asn486_Pro490del	p.N486_P490del	ENST00000288602	NM_004333.4	486	aATGTGACAGCACCTAca/aca	12/18	0.614203751393843	3	FACETS	0.58	0.472	0.701	0.29	0.236	0.351	SUBCLONAL	1	TRUE	1	0.626579527872806	3		360	224	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591933	48591933	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060500733	NA	P-0061194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	85	453	0	ENST00000342988.3:c.1096C>T	p.Gln366Ter	p.Q366*	ENST00000342988	NM_005359.5	366	Caa/Taa	9/12	0.626579527872806	1	FACETS	0.839	0.756	0.925	0.839	0.756	0.925	CLONAL	1	TRUE	0	0.626579527872806	1		453	222	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	118	551	0	ENST00000269305.4:c.991del	p.Gln331ArgfsTer14	p.Q331Rfs*14	ENST00000269305	NM_001126112.2	331	Cag/ag	9/11	0.614316209165138	1	FACETS	0.924	0.848	1	0.924	0.848	1	CLONAL	1	TRUE	0	0.626579527872806	1		551	280	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348272	89348272	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	176	576	0	ENST00000301030.4:c.4678G>T	p.Asp1560Tyr	p.D1560Y	ENST00000301030	NM_001256183.1	1560	Gac/Tac	9/13	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.626579527872806	2		576	500	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	200	321	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		321	844	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994137	21994137	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1060501262	NA	P-0061195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	261	601	0	ENST00000579755.1:c.193+1G>A		p.X65_splice	ENST00000579755		65			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		601	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0061196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	147	578	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.489115978171379	1	FACETS	0.953	0.879	1	0.953	0.879	1	CLONAL	1	TRUE	0	0.535358016512986	1		579	422	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434748	99434748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567180721	NA	P-0061196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	42	610	1	ENST00000268035.6:c.835C>T	p.Arg279Cys	p.R279C	ENST00000268035	NM_000875.3	279	Cgt/Tgt	3/21	1	2	FACETS	0.284	0.236	0.336	0.284	0.236	0.336	SUBCLONAL	1	TRUE	1	0.535358016512986	2		611	553	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956723	68956723	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs750933833	NA	P-0061196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	26	298	0	ENST00000288368.4:c.841C>T	p.Arg281Trp	p.R281W	ENST00000288368	NM_024870.2	281	Cgg/Tgg	8/40	0.535358016512986	5	FACETS	0.651	0.517	0.804	0.163	0.129	0.201	SUBCLONAL	1	TRUE	1	0.535358016512986	5		298	269	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603057	48603076	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCACAAGCTGCAGCAGCT	CTGCACAAGCTGCAGCAGCT	-	novel	NA	P-0061196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	119	455	0	ENST00000342988.3:c.1358_1377del	p.Thr453SerfsTer34	p.T453Sfs*34	ENST00000342988	NM_005359.5	453	aCTGCACAAGCTGCAGCAGCT/a	11/12	0.535358016512986	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.535358016512986	1		455	321	SUCCESS
APC	324	MSKCC	GRCh37	5	112175698	112175722	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTGCAGTAAATGCTGCAGTTCAG	AGCTGCAGTAAATGCTGCAGTTCAG	-	novel	NA	P-0061196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	114	599	0	ENST00000257430.4:c.4409_4433del	p.Ala1470GlyfsTer29	p.A1470Gfs*29	ENST00000257430	NM_000038.5	1469	caAGCTGCAGTAAATGCTGCAGTTCAG/ca	16/16	0.515202077246235	2	FACETS	0.852	0.782	0.922	0.852	0.782	0.922	CLONAL	2	TRUE	0	0.535358016512986	2		599	250	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231123	53231123	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	96	553	0	ENST00000375401.3:c.1779T>A	p.Phe593Leu	p.F593L	ENST00000375401	NM_004187.3	593	ttT/ttA	13/26	0.487219794057867	3	FACETS	0.924	0.827	1	0.462	0.413	0.514	CLONAL	1	TRUE	1	0.535358016512986	3		553	492	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0061197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	49	382	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.18	2		382	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577034	7577035	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	54	556	0	ENST00000269305.4:c.903dup	p.Gly302ArgfsTer4	p.G302Rfs*4	ENST00000269305	NM_001126112.2	301	-/A	8/11	1	2	FACETS	0.969	0.827	1	0.969	0.827	1	CLONAL	1	TRUE	1	0.18	2		556	619	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660079	227660079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	50	589	0	ENST00000305123.5:c.3376G>A	p.Gly1126Arg	p.G1126R	ENST00000305123	NM_005544.2	1126	Ggg/Agg	1/2	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.18	2		589	545	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913499	NA	P-0061198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	101	472	0	ENST00000345146.2:c.394C>A	p.Arg132Ser	p.R132S	ENST00000345146	NM_005896.2	132	Cgt/Agt	4/10	1	2	FACETS	0.823	0.737	0.914	0.823	0.737	0.914	CLONAL	1	TRUE	1	0.399086695045559	2		472	615	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077591	30077591	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0061198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	105	473	0	ENST00000338641.4:c.1737+1G>A		p.X579_splice	ENST00000338641	NM_000268.3	579			0.399086695045559	1	FACETS	0.964	0.869	1	0.964	0.869	1	CLONAL	1	TRUE	0	0.399086695045559	1		473	437	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375329	118375329	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	135	598	0	ENST00000534358.1:c.8722G>T	p.Glu2908Ter	p.E2908*	ENST00000534358	NM_005933.3	2908	Gaa/Taa	27/36	0.315555166666294	1	FACETS	0.921	0.84	1	0.921	0.84	1	CLONAL	1	TRUE	0	0.399086695045559	1		598	588	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472231	472231	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	93	439	0	ENST00000399788.2:c.570A>T	p.Glu190Asp	p.E190D	ENST00000399788	NM_001042603.1	190	gaA/gaT	5/28	1	2	FACETS	0.804	0.716	0.897	0.804	0.716	0.897	CLONAL	1	TRUE	1	0.399086695045559	2		439	580	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753545	42753545	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061198-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	69	816	0	ENST00000222329.4:c.719G>C	p.Gly240Ala	p.G240A	ENST00000222329	NM_006494.2	240	gGt/gCt	4/4	1	2	FACETS	0.402	0.349	0.459	0.402	0.349	0.459	SUBCLONAL	1	TRUE	1	0.399086695045559	2		816	860	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928060	178928086	+	inframe_deletion	In_Frame_Del	DEL	GCCAGTACCTCATGGATTAGAAGATTT	GCCAGTACCTCATGGATTAGAAGATTT	-	novel	NA	P-0061199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	81	336	0	ENST00000263967.3:c.1340_1366del	p.Pro447_Leu455del	p.P447_L455del	ENST00000263967	NM_006218.2	446	tgGCCAGTACCTCATGGATTAGAAGATTTg/tgg	8/21	1	2	FACETS	0.941	0.832	1	0.941	0.832	1	CLONAL	1	TRUE	1	0.366918781037586	2		336	469	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060782	38060784	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0061199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	96	567	0	ENST00000250448.2:c.1205_1207del	p.Ile402del	p.I402del	ENST00000250448	NM_004496.3	402	aTCAac/aac	2/2	1	2	FACETS	0.926	0.827	1	0.926	0.827	1	CLONAL	1	TRUE	1	0.366918781037586	2		567	565	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0061199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	224	396	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	0.861	0.805	0.918	1	0.994	1	CLONAL	2	TRUE	1	0.366918781037586	2		396	709	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226355	133226355	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061199-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	44	468	0	ENST00000320574.5:c.3703C>A	p.Leu1235Ile	p.L1235I	ENST00000320574	NM_006231.2	1235	Ctt/Att	30/49	1	2	FACETS	0.479	0.401	0.565	0.479	0.401	0.565	SUBCLONAL	1	TRUE	1	0.366918781037586	2		468	501	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0061200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	128	611	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.600161385959227	2		611	343	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587777894	NA	P-0061200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	163	400	0	ENST00000361445.4:c.6644C>A	p.Ser2215Tyr	p.S2215Y	ENST00000361445	NM_004958.3	2215	tCt/tAt	47/58	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.600161385959227	2		400	523	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254708	16254708	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	174	464	0	ENST00000375759.3:c.1973A>G	p.Tyr658Cys	p.Y658C	ENST00000375759	NM_015001.2	658	tAt/tGt	11/15	1	2	FACETS	0.981	0.908	1	0.981	0.908	1	CLONAL	1	TRUE	1	0.600161385959227	2		464	591	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108110	30108110	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	94	255	0	ENST00000331968.5:c.697C>T	p.Gln233Ter	p.Q233*	ENST00000331968	NM_002742.2	233	Caa/Taa	5/18	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.600161385959227	2		255	307	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191470	10191470	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs5030817	NA	P-0061200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	122	356	0	ENST00000256474.2:c.464-1G>C		p.X155_splice	ENST00000256474	NM_000551.3	155			NA	2	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.600161385959227	2		356	336	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441307	52441307	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061200-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	109	640	1	ENST00000460680.1:c.463A>G	p.Lys155Glu	p.K155E	ENST00000460680	NM_004656.3	155	Aag/Gag	7/17	0.600161385959227	1	FACETS	0.456	0.411	0.504	0.456	0.411	0.504	SUBCLONAL	1	TRUE	0	0.600161385959227	1		641	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0061201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	23	817	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.565	0.439	0.711	0.565	0.439	0.711	SUBCLONAL	1	TRUE	1	0.14	2		817	582	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440963	56440963	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0061201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	51	525	0	ENST00000407977.2:c.376-2A>G		p.X126_splice	ENST00000407977		126			1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.14	2		525	592	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0061201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	53	286	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.22273243797709	3	FACETS	0.797	0.68	0.925	0.797	0.68	0.925	CLONAL	2	TRUE	1	0.14	3		286	508	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591818	48591818	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061201-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	33	501	0	ENST00000342988.3:c.982del	p.Tyr328ThrfsTer8	p.Y328Tfs*8	ENST00000342988	NM_005359.5	327	gcT/gc	9/12	1	2	FACETS	0.698	0.567	0.847	0.698	0.567	0.847	SUBCLONAL	1	TRUE	1	0.14	2		501	675	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	22	377	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.240093622089121	3	FACETS	1	0.852	1	0.558	0.437	0.695	CLONAL	1	FALSE	1	0.327861465613538	3		377	140	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0061202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	89	416	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.320931539806394	4	FACETS	0.964	0.861	1			1	CLONAL	2	FALSE	NA	0.327861465613538	4		416	374	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	38	484	0	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	0.327861465613538	1	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	FALSE	0	0.327861465613538	1		484	193	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306602	41306602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1419824411	NA	P-0061202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	49	350	0	ENST00000373198.4:c.1057G>A	p.Asp353Asn	p.D353N	ENST00000373198	NM_133170.3	353	Gat/Aat	7/32	0.188310574358455	4	FACETS	0.945	0.81	1	0.945	0.81	1	INDETERMINATE	2	FALSE	2	0.327861465613538	4		350	210	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859598	57859598	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1215799189	NA	P-0061202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	77	576	0	ENST00000228682.2:c.652C>T	p.Arg218Trp	p.R218W	ENST00000228682	NM_005269.2	218	Cgg/Tgg	7/12	0.240093622089121	3	FACETS	1	0.945	1	0.565	0.497	0.637	CLONAL	1	FALSE	1	0.327861465613538	3		576	484	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420289	49420289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768551828	NA	P-0061202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	51	415	0	ENST00000301067.7:c.15460C>T	p.Arg5154Trp	p.R5154W	ENST00000301067	NM_003482.3	5154	Cgg/Tgg	48/54	0.240093622089121	3	FACETS	0.798	0.679	0.928	0.399	0.339	0.464	CLONAL	1	FALSE	1	0.327861465613538	3		415	454	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052552	42052565	+	frameshift_variant	Frame_Shift_Del	DEL	ATTACTGGAGTGAC	ATTACTGGAGTGAC	-	novel	NA	P-0061202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	53	425	0	ENST00000219905.7:c.7224_7237del	p.Asp2408GlufsTer20	p.D2408Efs*20	ENST00000219905	NM_001164273.1	2408	gATTACTGGAGTGAC/g	20/24	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	FALSE	1	0.327861465613538	2		425	271	SUCCESS
APC	324	MSKCC	GRCh37	5	112173905	112173906	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0061202-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	39	461	0	ENST00000257430.4:c.2614_2615del	p.Thr872PhefsTer39	p.T872Ffs*39	ENST00000257430	NM_000038.5	872	ACt/t	16/16	0.158438432437644	2	FACETS	0.991	0.828	1	0.496	0.414	0.586	INDETERMINATE	1	FALSE	0	0.327861465613538	2		461	240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0061203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	77	453	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.472547013499888	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.472089193641023	1		453	187	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0061203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	135	682	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.264771027127002	4	FACETS	0.929	0.851	1	0.929	0.851	1	INDETERMINATE	2	TRUE	2	0.472089193641023	4		683	453	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508328	106508328	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769318398	NA	P-0061203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	25	532	0	ENST00000359195.3:c.322G>A	p.Glu108Lys	p.E108K	ENST00000359195	NM_002649.2	108	Gag/Aag	2/11	0.472547013499888	4	FACETS	0.448	0.353	0.557	0.149	0.117	0.186	SUBCLONAL	1	TRUE	1	0.472089193641023	4		532	348	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511655	38511655	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061203-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	28	565	0	ENST00000254066.5:c.1153C>T	p.Arg385Ter	p.R385*	ENST00000254066	NM_000964.3	385	Cga/Tga	8/9	0.252247889568557	2	FACETS	0.587	0.473	0.716	0.294	0.236	0.358	INDETERMINATE	1	TRUE	0	0.472089193641023	2		565	202	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	71	503	0	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.417	0.364	0.475	0.417	0.364	0.475	SUBCLONAL	1	TRUE	1	0.514443699771394	2		503	662	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	41	544	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.625	0.524	0.736	0.625	0.524	0.736	SUBCLONAL	1	TRUE	1	0.514443699771394	2		544	255	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	165	410	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.514443699771394	2		412	617	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	135	380	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.514443699771394	2		380	511	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784041	9784041	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752328071	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	142	458	0	ENST00000377346.4:c.2609G>A	p.Arg870Gln	p.R870Q	ENST00000377346	NM_005026.3	870	cGa/cAa	21/24	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.514443699771394	2		458	478	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257525	16257525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	62	518	0	ENST00000375759.3:c.4794del	p.Glu1599LysfsTer33	p.E1599Kfs*33	ENST00000375759	NM_015001.2	1597	gAa/ga	11/15	1	2	FACETS	0.337	0.29	0.387	0.337	0.29	0.387	SUBCLONAL	1	TRUE	1	0.514443699771394	2		518	716	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	57	328	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.35	0.299	0.404	0.35	0.299	0.404	SUBCLONAL	1	TRUE	1	0.514443699771394	2		329	634	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106506	27106507	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	47	589	0	ENST00000324856.7:c.6121dup	p.Val2041GlyfsTer58	p.V2041Gfs*58	ENST00000324856	NM_006015.4	2039	-/G	20/20	1	2	FACETS	0.235	0.197	0.276	0.235	0.197	0.276	SUBCLONAL	1	TRUE	1	0.514443699771394	2		589	779	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	98	665	0	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	1	2	FACETS	0.663	0.592	0.737	0.663	0.592	0.737	SUBCLONAL	1	TRUE	1	0.514443699771394	2		665	575	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339128	65339129	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	200	495	0	ENST00000342505.4:c.407dup	p.Asn136LysfsTer16	p.N136Kfs*16	ENST00000342505	NM_002227.2	136	aat/aaAt	5/25	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.514443699771394	2		495	687	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058517	72058517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372023233	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	175	405	2	ENST00000357731.5:c.923C>T	p.Ala308Val	p.A308V	ENST00000357731	NM_173808.2	308	gCg/gTg	6/7	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.514443699771394	2		407	586	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838380	156838380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202030811	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	184	563	0	ENST00000524377.1:c.658C>T	p.Arg220Trp	p.R220W	ENST00000524377	NM_002529.3	220	Cgg/Tgg	6/17	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.514443699771394	2		563	649	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604668	43604668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371731991	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	141	474	0	ENST00000355710.3:c.1253G>A	p.Arg418Gln	p.R418Q	ENST00000355710	NM_020975.4	418	cGa/cAa	6/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.514443699771394	2		474	530	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759868	63759868	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766186442	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	134	435	0	ENST00000279873.7:c.521C>T	p.Thr174Met	p.T174M	ENST00000279873	NM_032199.2	174	aCg/aTg	4/10	1	2	FACETS	0.979	0.894	1	0.979	0.894	1	CLONAL	1	TRUE	1	0.514443699771394	2		435	532	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405959	70405959	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200333871	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	207	464	0	ENST00000373644.4:c.3473G>A	p.Arg1158Gln	p.R1158Q	ENST00000373644	NM_030625.2	1158	cGg/cAg	4/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.514443699771394	2		464	716	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724426	112724426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	172	467	1	ENST00000369452.4:c.310C>T	p.Arg104Cys	p.R104C	ENST00000369452	NM_007373.3	104	Cgt/Tgt	2/9	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.514443699771394	2		468	619	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154241	2154242	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755455183	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	121	549	1	ENST00000434045.2:c.686dup	p.Glu230ArgfsTer50	p.E230Rfs*50	ENST00000434045	NM_001127598.1	229	cca/ccCa	5/5	1	2	FACETS	0.878	0.796	0.963	0.878	0.796	0.963	CLONAL	1	TRUE	1	0.514443699771394	2		550	536	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942228	71942228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746333764	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	57	416	0	ENST00000298229.2:c.1492C>T	p.Arg498Cys	p.R498C	ENST00000298229	NM_001567.3	498	Cgc/Tgc	12/28	1	2	FACETS	0.438	0.376	0.506	0.438	0.376	0.506	SUBCLONAL	1	TRUE	1	0.514443699771394	2		416	506	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307394	118307394	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	26	237	3	ENST00000534358.1:c.173del	p.Pro58ArgfsTer92	p.P58Rfs*92	ENST00000534358	NM_005933.3	56	tCc/tc	1/36	1	2	FACETS	0.732	0.588	0.893	0.732	0.588	0.893	SUBCLONAL	1	TRUE	1	0.514443699771394	2		240	138	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427665	49427667	+	inframe_deletion	In_Frame_Del	DEL	TGC	TGC	-	rs747016071	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	174	557	8	ENST00000301067.7:c.10821_10823del	p.Gln3612del	p.Q3612del	ENST00000301067	NM_003482.3	3607	caGCAa/caa	39/54	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.514443699771394	2		565	593	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435258	49435258	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1452715535	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	77	746	0	ENST00000301067.7:c.6295C>T	p.Arg2099Ter	p.R2099*	ENST00000301067	NM_003482.3	2099	Cga/Tga	31/54	1	2	FACETS	0.612	0.539	0.691	0.612	0.539	0.691	SUBCLONAL	1	TRUE	1	0.514443699771394	2		746	489	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109903	115109903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1182290035	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	93	509	0	ENST00000257566.3:c.1975G>A	p.Ala659Thr	p.A659T	ENST00000257566	NM_016569.3	659	Gcc/Acc	8/8	1	2	FACETS	0.818	0.731	0.91	0.818	0.731	0.91	CLONAL	1	TRUE	1	0.514443699771394	2		509	442	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	149	591	9	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.514443699771394	2		600	519	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626775	28626775	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	59	335	0	ENST00000241453.7:c.521G>C	p.Arg174Thr	p.R174T	ENST00000241453	NM_004119.2	174	aGa/aCa	5/24	1	2	FACETS	0.434	0.374	0.5	0.434	0.374	0.5	SUBCLONAL	1	TRUE	1	0.514443699771394	2		335	528	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008324	29008324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770377283	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	79	421	0	ENST00000282397.4:c.547C>T	p.Arg183Cys	p.R183C	ENST00000282397	NM_002019.4	183	Cgc/Tgc	5/30	1	2	FACETS	0.602	0.531	0.678	0.602	0.531	0.678	SUBCLONAL	1	TRUE	1	0.514443699771394	2		421	510	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	136	363	5	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.514443699771394	2		368	493	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240075	41240075	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs914847913	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	53	224	0	ENST00000379561.5:c.275C>T	p.Ala92Val	p.A92V	ENST00000379561	NM_002015.3	92	gCg/gTg	1/3	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.514443699771394	2		224	181	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524611	103524612	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs752661599	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	161	383	6	ENST00000355739.4:c.2751dup	p.Leu918IlefsTer12	p.L918Ifs*12	ENST00000355739	NM_000123.3	914	-/A	13/15	1	2	FACETS	0.998	0.919	1	0.998	0.919	1	CLONAL	1	TRUE	1	0.514443699771394	2		389	627	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81563000	81563000	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	139	370	0	ENST00000298171.2:c.563G>A	p.Gly188Asp	p.G188D	ENST00000298171	NM_000369.2	188	gGc/gAc	7/10	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.514443699771394	2		370	538	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51504528	51504528	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs775998808	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	56	336	0	ENST00000260433.2:c.1252T>G	p.Phe418Val	p.F418V	ENST00000260433		418	Ttt/Gtt	9/10	1	2	FACETS	0.415	0.355	0.48	0.415	0.355	0.48	SUBCLONAL	1	TRUE	1	0.514443699771394	2		336	525	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223295	2223295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376570339	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	164	546	1	ENST00000326181.6:c.907G>A	p.Val303Met	p.V303M	ENST00000326181	NM_032271.2	303	Gtg/Atg	10/21	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.514443699771394	2		547	621	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858232	9858232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1187237144	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	176	511	0	ENST00000330684.3:c.3169G>A	p.Ala1057Thr	p.A1057T	ENST00000330684	NM_001134407.1	1057	Gcc/Acc	13/13	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.514443699771394	2		511	648	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56839518	56839518	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1389829048	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	66	395	0	ENST00000308159.5:c.463G>A	p.Ala155Thr	p.A155T	ENST00000308159	NM_014669.4	155	Gcc/Acc	5/22	1	2	FACETS	0.465	0.404	0.531	0.465	0.404	0.531	SUBCLONAL	1	TRUE	1	0.514443699771394	2		395	552	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842650	68842650	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	47	520	0	ENST00000261769.5:c.586G>A	p.Gly196Arg	p.G196R	ENST00000261769	NM_004360.3	196	Gga/Aga	5/16	1	2	FACETS	0.257	0.216	0.303	0.257	0.216	0.303	SUBCLONAL	1	TRUE	1	0.514443699771394	2		520	710	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888105	81888105	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	186	421	1	ENST00000359376.3:c.250C>T	p.Arg84Ter	p.R84*	ENST00000359376	NM_002661.3	84	Cga/Tga	3/33	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.514443699771394	2		422	555	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544772	86544772	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	113	414	0	ENST00000262426.4:c.597G>T	p.Leu199Phe	p.L199F	ENST00000262426	NM_001451.2	199	ttG/ttT	1/2	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.514443699771394	2		414	414	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347776	89347776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764002055	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	144	517	0	ENST00000301030.4:c.5174C>T	p.Pro1725Leu	p.P1725L	ENST00000301030	NM_001256183.1	1725	cCg/cTg	9/13	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.514443699771394	2		517	554	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8109941	8109941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	145	457	0	ENST00000585124.1:c.554C>T	p.Ala185Val	p.A185V	ENST00000585124	NM_004217.3	185	gCa/gTa	7/9	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.514443699771394	2		457	528	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	117	450	3	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.847	0.767	0.931	0.847	0.767	0.931	CLONAL	1	TRUE	1	0.514443699771394	2		453	537	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627730	37627730	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	168	459	0	ENST00000447079.4:c.1649del	p.Pro550LeufsTer60	p.P550Lfs*60	ENST00000447079	NM_015083.1	549	Ccc/cc	2/14	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.514443699771394	2		459	564	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511592	38511592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758706699	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	136	461	0	ENST00000254066.5:c.1090C>T	p.Arg364Trp	p.R364W	ENST00000254066	NM_000964.3	364	Cgg/Tgg	8/9	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.514443699771394	2		461	519	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47679303	47679303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	51	382	0	ENST00000347630.2:c.904G>A	p.Ala302Thr	p.A302T	ENST00000347630	NM_001007230.1	302	Gct/Act	10/11	1	2	FACETS	0.375	0.318	0.437	0.375	0.318	0.437	SUBCLONAL	1	TRUE	1	0.514443699771394	2		382	529	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	314	509	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.929	0.884	0.974	1	0.996	1	CLONAL	2	TRUE	1	0.514443699771394	2		513	657	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532501	63532501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755519590	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	56	519	0	ENST00000307078.5:c.2078C>T	p.Thr693Met	p.T693M	ENST00000307078	NM_004655.3	693	aCg/aTg	8/11	1	2	FACETS	0.342	0.292	0.396	0.342	0.292	0.396	SUBCLONAL	1	TRUE	1	0.514443699771394	2		519	637	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733194	74733194	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	47	474	0	ENST00000359995.5:c.49A>G	p.Lys17Glu	p.K17E	ENST00000359995	NM_001195427.1	17	Aag/Gag	1/3	1	2	FACETS	0.459	0.388	0.537	0.459	0.388	0.537	SUBCLONAL	1	TRUE	1	0.514443699771394	2		474	398	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897352	78897352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	163	634	0	ENST00000306801.3:c.2687C>T	p.Pro896Leu	p.P896L	ENST00000306801	NM_020761.2	896	cCg/cTg	23/34	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.514443699771394	2		634	609	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936356	78936356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	46	492	0	ENST00000306801.3:c.3788C>T	p.Pro1263Leu	p.P1263L	ENST00000306801	NM_020761.2	1263	cCc/cTc	32/34	1	2	FACETS	0.343	0.289	0.403	0.343	0.289	0.403	SUBCLONAL	1	TRUE	1	0.514443699771394	2		492	521	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599916	10599916	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs946921406	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	190	440	0	ENST00000171111.5:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000171111	NM_203500.1	554	Cga/Tga	5/6	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.514443699771394	2		440	634	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143994	11143994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	100	460	0	ENST00000358026.2:c.3575G>A	p.Arg1192His	p.R1192H	ENST00000358026	NM_001128849.1	1192	cGc/cAc	26/36	1	2	FACETS	0.782	0.702	0.867	0.782	0.702	0.867	SUBCLONAL	1	TRUE	1	0.514443699771394	2		460	497	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11150180	11150180	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779801126	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	140	341	1	ENST00000358026.2:c.4217G>A	p.Arg1406His	p.R1406H	ENST00000358026	NM_001128849.1	1406	cGt/cAt	30/36	1	2	FACETS	0.926	0.846	1	0.926	0.846	1	CLONAL	1	TRUE	1	0.514443699771394	2		342	588	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170724	11170724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356932636	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	138	481	0	ENST00000358026.2:c.4868G>A	p.Arg1623Gln	p.R1623Q	ENST00000358026	NM_001128849.1	1623	cGg/cAg	35/36	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.514443699771394	2		481	477	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272094	15272095	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	135	572	0	ENST00000263388.2:c.6344dup	p.Ala2116CysfsTer9	p.A2116Cfs*9	ENST00000263388	NM_000435.2	2115	cct/ccCt	33/33	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.514443699771394	2		572	455	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366911	15366911	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	147	448	0	ENST00000263377.2:c.1715del	p.Lys572ArgfsTer12	p.K572Rfs*12	ENST00000263377	NM_058243.2	572	aAg/ag	9/20	1	2	FACETS	0.979	0.897	1	0.979	0.897	1	CLONAL	1	TRUE	1	0.514443699771394	2		448	584	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214094	36214094	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253599925	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	175	527	0	ENST00000222270.7:c.2920C>T	p.Arg974Cys	p.R974C	ENST00000222270	NM_014727.1	974	Cgt/Tgt	6/37	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.514443699771394	2		527	614	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224339	36224340	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	70	629	0	ENST00000222270.7:c.6895dup	p.Arg2299ProfsTer4	p.R2299Pfs*4	ENST00000222270	NM_014727.1	2297	gcc/gCcc	28/37	1	2	FACETS	0.46	0.401	0.523	0.46	0.401	0.523	SUBCLONAL	1	TRUE	1	0.514443699771394	2		629	592	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905034	50905034	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	19	339	0	ENST00000440232.2:c.317-1G>A		p.X106_splice	ENST00000440232	NM_002691.3	106			1	2	FACETS	0.221	0.167	0.284	0.221	0.167	0.284	SUBCLONAL	1	TRUE	1	0.514443699771394	2		339	334	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917041	50917041	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759190487	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	159	579	0	ENST00000440232.2:c.2293G>A	p.Val765Met	p.V765M	ENST00000440232	NM_002691.3	765	Gtg/Atg	19/27	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.514443699771394	2		579	567	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082313	16082314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs780080562	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	118	484	0	ENST00000281043.3:c.134dup	p.Glu47GlyfsTer8	p.E47Gfs*8	ENST00000281043	NM_005378.4	43	acc/aCcc	2/3	1	2	FACETS	0.9	0.815	0.987	0.9	0.815	0.987	CLONAL	1	TRUE	1	0.514443699771394	2		484	510	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085680	16085680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776847158	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	109	437	0	ENST00000281043.3:c.856C>T	p.Arg286Cys	p.R286C	ENST00000281043	NM_005378.4	286	Cgt/Tgt	3/3	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.514443699771394	2		437	422	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966873	25966873	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1271466699	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	170	578	6	ENST00000435504.4:c.2333del	p.Pro778GlnfsTer21	p.P778Qfs*21	ENST00000435504		778	cCa/ca	13/13	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.514443699771394	2		584	661	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47710016	47710016	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	109	302	0	ENST00000233146.2:c.2736del	p.Ala913LeufsTer3	p.A913Lfs*3	ENST00000233146	NM_000251.2	911	ctA/ct	16/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.514443699771394	2		302	367	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873022	136873022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	31	534	0	ENST00000241393.3:c.476G>A	p.Gly159Asp	p.G159D	ENST00000241393	NM_003467.2	159	gGc/gAc	2/2	1	2	FACETS	0.202	0.162	0.247	0.202	0.162	0.247	SUBCLONAL	1	TRUE	1	0.514443699771394	2		534	597	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736166	204736166	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	122	382	0	ENST00000302823.3:c.529del	p.Tyr177IlefsTer10	p.Y177Ifs*10	ENST00000302823	NM_005214.4	175	Ttt/tt	3/4	1	2	FACETS	0.834	0.756	0.915	0.834	0.756	0.915	CLONAL	1	TRUE	1	0.514443699771394	2		382	569	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661664	227661664	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs761880048	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	123	526	15	ENST00000305123.5:c.1791del	p.His598ThrfsTer38	p.H598Tfs*38	ENST00000305123	NM_005544.2	597	ggG/gg	1/2	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.514443699771394	2		541	467	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663299	227663301	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs753296153	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	85	427	0	ENST00000305123.5:c.154_156del	p.Lys52del	p.K52del	ENST00000305123	NM_005544.2	52	AAG/-	1/2	1	2	FACETS	0.877	0.78	0.978	0.877	0.78	0.978	CLONAL	1	TRUE	1	0.514443699771394	2		427	377	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024960	31024960	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779918659	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	65	471	1	ENST00000375687.4:c.4445C>T	p.Ala1482Val	p.A1482V	ENST00000375687	NM_015338.5	1482	gCg/gTg	13/13	0.514443699771394	3	FACETS	0.332	0.287	0.382	0.166	0.143	0.191	SUBCLONAL	1	TRUE	1	0.514443699771394	3		472	956	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031696	36031696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1305388441	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	131	596	0	ENST00000358208.4:c.1525C>T	p.Arg509Trp	p.R509W	ENST00000358208		509	Cgg/Tgg	12/12	0.514443699771394	3	FACETS	0.875	0.795	0.959	0.437	0.397	0.48	CLONAL	1	TRUE	1	0.514443699771394	3		596	732	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744069	39744070	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	156	361	0	ENST00000361337.2:c.1698_1699del	p.Asp566GlufsTer9	p.D566Efs*9	ENST00000361337	NM_003286.2	566	gAT/g	16/21	0.514443699771394	3	FACETS	1	0.981	1	0.615	0.565	0.666	CLONAL	1	TRUE	1	0.514443699771394	3		361	620	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714426	40714426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	56	429	0	ENST00000373198.4:c.3971C>T	p.Ser1324Phe	p.S1324F	ENST00000373198	NM_133170.3	1324	tCc/tTc	29/32	0.514443699771394	3	FACETS	0.372	0.318	0.431	0.186	0.159	0.216	SUBCLONAL	1	TRUE	1	0.514443699771394	3		429	736	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385198	41385198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	229	427	1	ENST00000373198.4:c.763G>A	p.Ala255Thr	p.A255T	ENST00000373198	NM_133170.3	255	Gca/Aca	6/32	0.514443699771394	3	FACETS	0.975	0.916	1	0.975	0.916	1	CLONAL	2	TRUE	1	0.514443699771394	3		428	574	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279837	46279842	+	inframe_deletion	In_Frame_Del	DEL	CAGCAG	CAGCAG	-	rs3830809	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	171	419	4	ENST00000371998.3:c.3786_3791del	p.Gln1275_Gln1276del	p.Q1275_Q1276del	ENST00000371998		1255	CAGCAG/-	20/23	0.514443699771394	3	FACETS	1	0.98	1	0.593	0.547	0.641	CLONAL	1	TRUE	1	0.514443699771394	3		423	705	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755663	39755663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	51	495	0	ENST00000288319.7:c.1102G>A	p.Ala368Thr	p.A368T	ENST00000288319	NM_182918.3	368	Gcc/Acc	10/10	1	2	FACETS	0.434	0.369	0.505	0.434	0.369	0.505	SUBCLONAL	1	TRUE	1	0.514443699771394	2		495	457	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513282	44513287	+	inframe_deletion	In_Frame_Del	DEL	CCACCG	CCACCG	-	rs745888281	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	15	477	1	ENST00000291552.4:c.648_653del	p.Gly222_Gly223del	p.G222_G223del	ENST00000291552	NM_006758.2	216	ggCGGTGGt/ggt	8/8	1	2	FACETS	0.081	0.058	0.108	0.081	0.058	0.108	SUBCLONAL	1	TRUE	1	0.514443699771394	2		478	720	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121082	29121082	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs781254437	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	73	364	0	ENST00000328354.6:c.475T>C	p.Tyr159His	p.Y159H	ENST00000328354	NM_007194.3	159	Tac/Cac	4/15	1	2	FACETS	0.702	0.617	0.793	0.702	0.617	0.793	SUBCLONAL	1	TRUE	1	0.514443699771394	2		364	404	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	172	453	1	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.514443699771394	2		454	594	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932713	49932713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1156805771	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	173	540	0	ENST00000296474.3:c.3158G>A	p.Arg1053Gln	p.R1053Q	ENST00000296474	NM_002447.2	1053	cGg/cAg	14/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.514443699771394	2		540	583	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63967897	63967897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777248770	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	73	421	0	ENST00000398590.3:c.788C>T	p.Pro263Leu	p.P263L	ENST00000398590	NM_001177387.1	263	cCg/cTg	7/14	1	2	FACETS	0.488	0.427	0.553	0.488	0.427	0.553	SUBCLONAL	1	TRUE	1	0.514443699771394	2		421	582	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884875	134884875	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368240835	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	119	344	0	ENST00000398015.3:c.1651G>A	p.Val551Met	p.V551M	ENST00000398015	NM_004441.4	551	Gtg/Atg	8/16	1	2	FACETS	0.942	0.855	1	0.942	0.855	1	CLONAL	1	TRUE	1	0.514443699771394	2		344	491	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138382792	138382792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	150	368	0	ENST00000289153.2:c.2752G>A	p.Gly918Ser	p.G918S	ENST00000289153	NM_006219.2	918	Ggt/Agt	19/22	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.514443699771394	2		368	483	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540064	187540064	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	35	444	0	ENST00000441802.2:c.7676C>A	p.Pro2559Gln	p.P2559Q	ENST00000441802	NM_005245.3	2559	cCg/cAg	10/27	1	2	FACETS	0.203	0.166	0.245	0.203	0.166	0.245	SUBCLONAL	1	TRUE	1	0.514443699771394	2		444	670	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629337	187629337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376582889	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	184	471	2	ENST00000441802.2:c.1645C>T	p.Arg549Trp	p.R549W	ENST00000441802	NM_005245.3	549	Cgg/Tgg	2/27	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.514443699771394	2		473	685	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251506	251506	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	39	168	0	ENST00000264932.6:c.1717C>A	p.Leu573Met	p.L573M	ENST00000264932	NM_004168.2	573	Ctg/Atg	13/15	1	2	FACETS	0.689	0.576	0.813	0.689	0.576	0.813	SUBCLONAL	1	TRUE	1	0.514443699771394	2		168	220	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	183	512	6	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.514443699771394	2		518	665	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	223	476	10	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.918	0.865	0.972	1	0.994	1	CLONAL	2	TRUE	1	0.514443699771394	2		486	472	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518067	176518067	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	143	523	0	ENST00000292408.4:c.565C>T	p.Gln189Ter	p.Q189*	ENST00000292408	NM_213647.1	189	Cag/Tag	5/18	1	2	FACETS	0.919	0.841	1	0.919	0.841	1	CLONAL	1	TRUE	1	0.514443699771394	2		523	605	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31236946	31236946	+	stop_lost	Nonstop_Mutation	SNP	T	T	G	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	40	304	0	ENST00000376228.5:c.1101A>C	p.Ter367CysextTer41	p.*367Cext*41	ENST00000376228	NM_002117.5	367	tgA/tgC	8/8	1	2	FACETS	0.416	0.346	0.493	0.416	0.346	0.493	SUBCLONAL	1	TRUE	1	0.514443699771394	2		304	374	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	93	336	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	0.895	0.801	0.994	0.895	0.801	0.994	CLONAL	1	TRUE	1	0.514443699771394	2		336	404	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940500	31940500	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	129	457	0	ENST00000375333.2:c.533T>G	p.Leu178Arg	p.L178R	ENST00000375333	NM_032454.1	178	cTt/cGt	3/8	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.514443699771394	2		457	474	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651973	36651973	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	154	492	1	ENST00000244741.5:c.95G>A	p.Arg32His	p.R32H	ENST00000244741	NM_000389.4	32	cGc/cAc	2/3	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.514443699771394	2		493	569	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509191	106509191	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	184	520	0	ENST00000359195.3:c.1185C>A	p.Cys395Ter	p.C395*	ENST00000359195	NM_002649.2	395	tgC/tgA	2/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.514443699771394	2		520	604	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38139019	38139019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	238	345	0	ENST00000317025.8:c.3584G>A	p.Ser1195Asn	p.S1195N	ENST00000317025	NM_023034.1	1195	aGt/aAt	20/24	0.514443699771394	3	FACETS	0.917	0.862	0.974	0.917	0.862	0.974	CLONAL	2	TRUE	1	0.514443699771394	3		345	634	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981892	70981892	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	56	568	0	ENST00000276594.2:c.204del	p.Phe69SerfsTer10	p.F69Sfs*10	ENST00000276594	NM_024504.3	68	ccC/cc	2/8	0.514443699771394	3	FACETS	0.4	0.342	0.464	0.2	0.171	0.232	SUBCLONAL	1	TRUE	1	0.514443699771394	3		568	684	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5065031	5065031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868456341	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	24	310	0	ENST00000381652.3:c.1205G>A	p.Gly402Asp	p.G402D	ENST00000381652	NM_004972.3	402	gGc/gAc	9/25	1	2	FACETS	0.196	0.153	0.246	0.196	0.153	0.246	SUBCLONAL	1	TRUE	1	0.514443699771394	2		310	475	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006101	22006101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1425823622	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	165	544	0	ENST00000276925.6:c.302G>A	p.Arg101Gln	p.R101Q	ENST00000276925	NM_004936.3	101	cGg/cAg	2/2	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.514443699771394	2		544	553	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	121	553	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.514443699771394	2		553	456	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396836	139396836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777859108	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	150	420	0	ENST00000277541.6:c.5272C>T	p.Arg1758Cys	p.R1758C	ENST00000277541	NM_017617.3	1758	Cgc/Tgc	28/34	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.514443699771394	2		420	437	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224208	53224208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	166	869	0	ENST00000375401.3:c.3343C>T	p.Arg1115Cys	p.R1115C	ENST00000375401	NM_004187.3	1115	Cgc/Tgc	22/26	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.514443699771394	2		869	592	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	80	428	0	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	1	2	FACETS	0.611	0.539	0.688	0.611	0.539	0.688	SUBCLONAL	1	TRUE	1	0.514443699771394	2		428	509	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412694	63412694	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	83	440	0	ENST00000330258.3:c.473A>C	p.Lys158Thr	p.K158T	ENST00000330258	NM_152424.3	158	aAg/aCg	2/2	1	2	FACETS	0.7	0.62	0.785	0.7	0.62	0.785	SUBCLONAL	1	TRUE	1	0.514443699771394	2		440	461	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	9	282	0	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	2	FACETS	0.108	0.071	0.156	0.108	0.071	0.156	SUBCLONAL	1	TRUE	1	0.514443699771394	2		282	324	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438317	110438322	+	inframe_deletion	In_Frame_Del	DEL	GTTGTT	GTTGTT	-	rs532810290	NA	P-0061204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	63	357	0	ENST00000375856.3:c.79_84del	p.Asn27_Asn28del	p.N27_N28del	ENST00000375856	NM_003749.2	27	AACAAC/-	1/2	1	2	FACETS	0.645	0.56	0.735	0.645	0.56	0.735	SUBCLONAL	1	TRUE	1	0.514443699771394	2		357	380	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0061205-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	321	329	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.547548418915899	7	FACETS	1	0.979	1			1	CLONAL	4	TRUE	NA	0.547548418915899	7		329	661	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439839	220439839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761479412	NA	P-0061205-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	143	670	0	ENST00000243786.2:c.692G>A	p.Arg231Gln	p.R231Q	ENST00000243786	NM_002191.3	231	cGa/cAa	2/2	0.20566199812908	2	FACETS	0.95	0.884	1	0.95	0.884	1	INDETERMINATE	2	TRUE	0	0.547548418915899	2		670	275	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88635839	88635839	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554886821	NA	P-0061205-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	46	306	0	ENST00000372037.3:c.64C>T	p.Gln22Ter	p.Q22*	ENST00000372037	NM_004329.2	22	Caa/Taa	3/13	0.235002963567112	2	FACETS	0.771	0.656	0.894	0.385	0.328	0.447	INDETERMINATE	1	TRUE	0	0.547548418915899	2		306	218	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376874	118376874	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1443235781	NA	P-0061205-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	229	633	0	ENST00000534358.1:c.10267A>G	p.Ile3423Val	p.I3423V	ENST00000534358	NM_005933.3	3423	Ata/Gta	27/36	0.553257342493156	3	FACETS	1	0.985	1			1	CLONAL	2	TRUE	NA	0.547548418915899	3		633	472	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914853	32914853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782183	NA	P-0061205-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	245	539	0	ENST00000380152.3:c.6361G>A	p.Glu2121Lys	p.E2121K	ENST00000380152		2121	Gaa/Aaa	11/27	0.553257342493156	3	FACETS	0.878	0.833	0.921	1	0.993	1	CLONAL	3	TRUE	1	0.547548418915899	3		539	433	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412958	49412958	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061205-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	293	554	0	ENST00000418115.1:c.65T>A	p.Leu22His	p.L22H	ENST00000418115	NM_001664.2	22	cTc/cAc	2/5	0.553257342493156	2	FACETS	0.877	0.844	0.908	1	0.995	1	CLONAL	3	TRUE	0	0.547548418915899	2		554	407	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969160	93969160	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061205-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	376	462	0	ENST00000369303.4:c.1836A>T	p.Glu612Asp	p.E612D	ENST00000369303	NM_004440.3	612	gaA/gaT	10/17	0.24623318428322	6	FACETS	0.951	0.915	0.987	0.793	0.762	0.823	INDETERMINATE	5	TRUE	0	0.547548418915899	6		462	605	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057304	180057304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140347743	NA	P-0061206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	259	531	0	ENST00000261937.6:c.434C>T	p.Thr145Met	p.T145M	ENST00000261937	NM_182925.4	145	aCg/aTg	4/30	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.897453690935074	2		531	577	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432128	121432128	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	442	534	0	ENST00000257555.6:c.875G>T	p.Gly292Val	p.G292V	ENST00000257555		292	gGg/gTg	4/10	0.897453690935074	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.897453690935074	2		534	484	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29497003	29497003	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397514641	NA	P-0061206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	157	288	0	ENST00000356175.3:c.574C>T	p.Arg192Ter	p.R192*	ENST00000356175	NM_000267.3	192	Cga/Tga	5/57	0.897453690935074	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.897453690935074	1		288	191	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055677	152055677	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	250	387	0	ENST00000262189.6:c.245A>G	p.Glu82Gly	p.E82G	ENST00000262189	NM_170606.2	82	gAa/gGa	2/59	0.50015386791184	4	FACETS	1	0.992	1	0.454	0.426	0.482	INDETERMINATE	1	TRUE	1	0.897453690935074	4		387	777	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0061207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	264	473	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.873433221703329	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.873433221703329	1		473	339	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617419	43617419	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	212	522	0	ENST00000355710.3:c.2756C>A	p.Ala919Glu	p.A919E	ENST00000355710	NM_020975.4	919	gCa/gAa	16/20	1	2	FACETS	0.914	0.857	0.972	0.914	0.857	0.972	CLONAL	1	TRUE	1	0.873433221703329	2		522	531	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543638	29543657	+	frameshift_variant	Frame_Shift_Del	DEL	CATCCTTTAGGGTCCTGACC	CATCCTTTAGGGTCCTGACC	AGTGACAGTG	novel	NA	P-0061207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	274	626	0	ENST00000389048.3:c.1506_1525delinsCACTGTCACT	p.Gln502HisfsTer30	p.Q502Hfs*30	ENST00000389048	NM_004304.4	502	caGGTCAGGACCCTAAAGGATGcc/caCACTGTCACTcc	7/29	1	2	FACETS	0.952	0.9	1	0.952	0.9	1	CLONAL	1	TRUE	1	0.873433221703329	2		626	659	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	8	329	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.102	0.065	0.15	0.102	0.065	0.15	SUBCLONAL	1	TRUE	1	0.41	2		329	383	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	27	665	0	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	1	2	FACETS	0.266	0.211	0.329	0.266	0.211	0.329	SUBCLONAL	1	TRUE	1	0.41	2		665	495	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	60	620	6	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.71	0.614	0.815	0.71	0.614	0.815	SUBCLONAL	1	TRUE	1	0.41	2		626	412	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053022	180053023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750808726	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	26	826	0	ENST00000261937.6:c.1267dup	p.Gln423ProfsTer4	p.Q423Pfs*4	ENST00000261937	NM_182925.4	423	cag/cCag	10/30	1	2	FACETS	0.294	0.232	0.364	0.294	0.232	0.364	SUBCLONAL	1	TRUE	1	0.41	2		826	432	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77069992	77069992	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	39	696	0	ENST00000356341.3:c.548A>C	p.Asp183Ala	p.D183A	ENST00000356341	NM_002576.4	183	gAt/gCt	6/15	1	2	FACETS	0.35	0.29	0.418	0.35	0.29	0.418	SUBCLONAL	1	TRUE	1	0.41	2		696	543	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	83	463	4	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.98	0.87	1	0.98	0.87	1	CLONAL	1	TRUE	1	0.41	2		467	413	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108788	2108788	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	99	635	1	ENST00000219476.3:c.894del	p.Phe298LeufsTer65	p.F298Lfs*65	ENST00000219476	NM_000548.3	297	Ttt/tt	10/42	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.41	2		636	483	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043355	6043355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188006077	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	22	109	0	ENST00000265849.7:c.319C>T	p.Arg107Trp	p.R107W	ENST00000265849	NM_000535.5	107	Cgg/Tgg	4/15	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.41	2		109	87	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760024	133760024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	76	556	1	ENST00000318560.5:c.2352del	p.Arg785GlyfsTer3	p.R785Gfs*3	ENST00000318560	NM_005157.4	783	Ccc/cc	11/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.41	2		557	321	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	98	701	3	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.41	2		704	429	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265061	198265061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	83	565	0	ENST00000335508.6:c.2816G>A	p.Arg939His	p.R939H	ENST00000335508	NM_012433.2	939	cGt/cAt	19/25	1	2	FACETS	0.84	0.744	0.942	0.84	0.744	0.942	CLONAL	1	TRUE	1	0.41	2		565	482	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857196	9857196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs74935155	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	101	723	0	ENST00000330684.3:c.4205G>A	p.Arg1402Gln	p.R1402Q	ENST00000330684	NM_001134407.1	1402	cGg/cAg	13/13	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.41	2		723	475	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692929	89692929	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1554898159	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	52	629	0	ENST00000371953.3:c.413A>G	p.Tyr138Cys	p.Y138C	ENST00000371953	NM_000314.4	138	tAt/tGt	5/9	1	2	FACETS	0.673	0.575	0.78	0.673	0.575	0.78	SUBCLONAL	1	TRUE	1	0.41	2		629	377	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164838	36164839	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	28	719	0	ENST00000300305.3:c.1036dup	p.Arg346ProfsTer254	p.R346Pfs*254	ENST00000300305		346	cgc/cCgc	8/8	1	2	FACETS	0.285	0.227	0.351	0.285	0.227	0.351	SUBCLONAL	1	TRUE	1	0.41	2		719	479	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211580	98211580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762040036	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	86	568	0	ENST00000331920.6:c.3575G>A	p.Arg1192His	p.R1192H	ENST00000331920	NM_000264.3	1192	cGc/cAc	22/24	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.41	2		568	406	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	39	666	1	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.369	0.305	0.44	0.369	0.305	0.44	SUBCLONAL	1	TRUE	1	0.41	2		667	516	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636997	176636997	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	77	717	0	ENST00000439151.2:c.1597C>A	p.Leu533Ile	p.L533I	ENST00000439151	NM_022455.4	533	Ctt/Att	5/23	1	2	FACETS	0.871	0.768	0.981	0.871	0.768	0.981	CLONAL	1	TRUE	1	0.41	2		717	431	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845292	42845294	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	67	627	0	ENST00000398585.3:c.968_970del	p.Ile323del	p.I323del	ENST00000398585	NM_001135099.1	323	aTCAcc/acc	9/14	1	2	FACETS	0.879	0.768	0.997	0.879	0.768	0.997	CLONAL	1	TRUE	1	0.41	2		627	372	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248737	212248737	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	21	648	0	ENST00000342788.4:c.3530del	p.Asn1177MetfsTer27	p.N1177Mfs*27	ENST00000342788	NM_005235.2	1177	aAt/at	28/28	1	2	FACETS	0.275	0.211	0.349	0.275	0.211	0.349	SUBCLONAL	1	TRUE	1	0.41	2		648	373	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258943	16258944	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	130	808	0	ENST00000375759.3:c.6215dup	p.Asn2072LysfsTer51	p.N2072Kfs*51	ENST00000375759	NM_015001.2	2070	gaa/gAaa	11/15	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.41	2		808	624	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133756012	133756012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs574660646	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	81	636	0	ENST00000318560.5:c.1639G>A	p.Val547Met	p.V547M	ENST00000318560	NM_005157.4	547	Gtg/Atg	10/11	1	2	FACETS	0.95	0.841	1	0.95	0.841	1	CLONAL	1	TRUE	1	0.41	2		636	416	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273026	18273026	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	26	651	3	ENST00000222254.8:c.921del	p.Lys308ArgfsTer33	p.K308Rfs*33	ENST00000222254	NM_005027.3	306	Ccc/cc	8/16	1	2	FACETS	0.298	0.236	0.37	0.298	0.236	0.37	SUBCLONAL	1	TRUE	1	0.41	2		654	425	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551412	141551412	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	28	532	0	ENST00000220592.5:c.1885G>A	p.Val629Met	p.V629M	ENST00000220592	NM_012154.3	629	Gtg/Atg	15/19	1	2	FACETS	0.373	0.298	0.459	0.373	0.298	0.459	SUBCLONAL	1	TRUE	1	0.41	2		532	366	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252024	133252024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	93	646	1	ENST00000320574.5:c.1186del	p.Glu396SerfsTer16	p.E396Sfs*16	ENST00000320574	NM_006231.2	396	Gag/ag	12/49	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.41	2		647	404	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467614	50467614	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	22	479	0	ENST00000331340.3:c.851-2A>G		p.X284_splice	ENST00000331340	NM_006060.4	284			1	2	FACETS	0.346	0.268	0.437	0.346	0.268	0.437	SUBCLONAL	1	TRUE	1	0.41	2		479	310	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878058	48878058	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1226865525	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	51	594	1	ENST00000267163.4:c.13del	p.Thr5ProfsTer60	p.T5Pfs*60	ENST00000267163	NM_000321.2	4	Aaa/aa	1/27	1	2	FACETS	0.898	0.769	1	0.898	0.769	1	CLONAL	1	TRUE	1	0.41	2		595	277	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981613	101981614	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	31	695	0	ENST00000282441.5:c.40dup	p.Gln14ProfsTer98	p.Q14Pfs*98	ENST00000282441	NM_001130145.2	12	gcc/gCcc	1/9	1	2	FACETS	0.66	0.537	0.798	0.66	0.537	0.798	SUBCLONAL	1	TRUE	1	0.41	2		695	229	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73342975	73342975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757306363	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	21	429	0	ENST00000377767.4:c.1831C>T	p.Arg611Cys	p.R611C	ENST00000377767	NM_014953.3	611	Cgt/Tgt	14/21	1	2	FACETS	0.339	0.261	0.43	0.339	0.261	0.43	SUBCLONAL	1	TRUE	1	0.41	2		429	302	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17125885	17125885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257705335	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	39	630	0	ENST00000285071.4:c.709G>A	p.Ala237Thr	p.A237T	ENST00000285071	NM_144997.5	237	Gcc/Acc	7/14	1	2	FACETS	0.367	0.304	0.438	0.367	0.304	0.438	SUBCLONAL	1	TRUE	1	0.41	2		630	518	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510194	120510194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199565938	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	97	614	0	ENST00000256646.2:c.1315G>A	p.Ala439Thr	p.A439T	ENST00000256646	NM_024408.3	439	Gcc/Acc	8/34	1	2	FACETS	0.933	0.835	1	0.933	0.835	1	CLONAL	1	TRUE	1	0.41	2		614	507	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226704	2226704	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750419812	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	89	823	0	ENST00000398665.3:c.4184C>T	p.Pro1395Leu	p.P1395L	ENST00000398665	NM_032482.2	1395	cCg/cTg	27/28	1	2	FACETS	0.932	0.83	1	0.932	0.83	1	CLONAL	1	TRUE	1	0.41	2		823	466	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211753	36211753	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374554860	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	28	767	2	ENST00000222270.7:c.1504G>A	p.Ala502Thr	p.A502T	ENST00000222270	NM_014727.1	502	Gcc/Acc	3/37	1	2	FACETS	0.285	0.227	0.351	0.285	0.227	0.351	SUBCLONAL	1	TRUE	1	0.41	2		769	479	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416795	416795	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	26	702	0	ENST00000399788.2:c.3755G>A	p.Arg1252His	p.R1252H	ENST00000399788	NM_001042603.1	1252	cGt/cAt	23/28	1	2	FACETS	0.248	0.196	0.309	0.248	0.196	0.309	SUBCLONAL	1	TRUE	1	0.41	2		702	511	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181290	123181290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	52	252	0	ENST00000218089.9:c.754C>T	p.Arg252Trp	p.R252W	ENST00000218089	NM_001042749.1	252	Cgg/Tgg	9/35	1	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.41	1		252	139	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831029	72831029	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	95	693	1	ENST00000268489.5:c.5552C>A	p.Pro1851Gln	p.P1851Q	ENST00000268489	NM_006885.3	1851	cCg/cAg	9/10	1	2	FACETS	0.99	0.886	1	0.99	0.886	1	CLONAL	1	TRUE	1	0.41	2		694	468	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624244	89624245	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs786204881	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	20	201	0	ENST00000371953.3:c.21_22del	p.Glu7AspfsTer3	p.E7Dfs*3	ENST00000371953	NM_000314.4	6	aaAGag/aaag	1/9	1	2	FACETS	0.75	0.58	0.944	0.75	0.58	0.944	CLONAL	1	TRUE	1	0.41	2		201	130	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649530	206649530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	131	676	1	ENST00000367120.3:c.365G>A	p.Gly122Asp	p.G122D	ENST00000367120	NM_014002.3	122	gGc/gAc	6/22	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.41	2		677	505	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164151	108164151	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1408892416	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	71	511	0	ENST00000278616.4:c.4723C>T	p.Arg1575Cys	p.R1575C	ENST00000278616	NM_000051.3	1575	Cgt/Tgt	31/63	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.41	2		511	333	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16052794	16052795	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	17	305	0	ENST00000268712.3:c.879dup	p.Lys294Ter	p.K294*	ENST00000268712	NM_006311.3	293	-/T	9/46	1	2	FACETS	0.334	0.25	0.435	0.334	0.25	0.435	SUBCLONAL	1	TRUE	1	0.41	2		305	248	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1687996	1687996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200152611	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	110	718	0	ENST00000378625.1:c.880G>A	p.Ala294Thr	p.A294T	ENST00000378625	NM_001198994.1	294	Gcc/Acc	7/14	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.41	2		718	476	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257034	16257035	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	85	688	0	ENST00000375759.3:c.4301_4302del	p.Phe1434CysfsTer4	p.F1434Cfs*4	ENST00000375759	NM_015001.2	1433	tcTTtt/tctt	11/15	1	2	FACETS	0.909	0.807	1	0.909	0.807	1	CLONAL	1	TRUE	1	0.41	2		688	456	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834186	156834186	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543320028	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	49	679	0	ENST00000524377.1:c.253C>T	p.Arg85Cys	p.R85C	ENST00000524377	NM_002529.3	85	Cgt/Tgt	2/17	1	2	FACETS	0.58	0.492	0.676	0.58	0.492	0.676	SUBCLONAL	1	TRUE	1	0.41	2		679	412	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852351	63852351	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	29	736	0	ENST00000279873.7:c.3129G>T	p.Lys1043Asn	p.K1043N	ENST00000279873	NM_032199.2	1043	aaG/aaT	10/10	1	2	FACETS	0.323	0.259	0.396	0.323	0.259	0.396	SUBCLONAL	1	TRUE	1	0.41	2		736	438	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710617	114710619	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	89	603	0	ENST00000543371.1:c.105_107del	p.Ser36del	p.S36del	ENST00000543371	NM_001198531.1	34	aaCTCc/aac	1/14	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.41	2		603	432	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988147	85988147	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	69	575	0	ENST00000263360.6:c.1092G>A	p.Trp364Ter	p.W364*	ENST00000263360	NM_003797.3	364	tgG/tgA	10/12	1	2	FACETS	0.874	0.765	0.991	0.874	0.765	0.991	CLONAL	1	TRUE	1	0.41	2		575	385	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536832	120536832	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	22	556	0	ENST00000229340.5:c.352+2T>C		p.X118_splice	ENST00000229340	NM_006861.6	118			1	2	FACETS	0.319	0.247	0.403	0.319	0.247	0.403	SUBCLONAL	1	TRUE	1	0.41	2		556	336	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515139	103515139	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1381013306	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	49	718	1	ENST00000355739.4:c.1640A>G	p.Asn547Ser	p.N547S	ENST00000355739	NM_000123.3	547	aAc/aGc	8/15	1	2	FACETS	0.494	0.418	0.577	0.494	0.418	0.577	SUBCLONAL	1	TRUE	1	0.41	2		719	484	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435931	110435931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	83	706	0	ENST00000375856.3:c.2470G>A	p.Val824Met	p.V824M	ENST00000375856	NM_003749.2	824	Gtg/Atg	1/2	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.41	2		706	348	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832450	72832450	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	124	673	0	ENST00000268489.5:c.4131del	p.Gln1378ArgfsTer47	p.Q1378Rfs*47	ENST00000268489	NM_006885.3	1377	ctT/ct	9/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.41	2		673	543	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7141774	7141774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200110540	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	91	567	0	ENST00000302850.5:c.2596G>A	p.Val866Ile	p.V866I	ENST00000302850	NM_000208.2	866	Gtc/Atc	13/22	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.41	2		567	431	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265340	10265341	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	33	746	0	ENST00000340748.4:c.1705dup	p.Asp569GlyfsTer3	p.D569Gfs*3	ENST00000340748		569	gac/gGac	20/40	1	2	FACETS	0.347	0.282	0.42	0.347	0.282	0.42	SUBCLONAL	1	TRUE	1	0.41	2		746	464	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794626	42794627	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	31	650	0	ENST00000575354.2:c.1711dup	p.Leu571ProfsTer119	p.L571Pfs*119	ENST00000575354	NM_015125.3	569	ggc/ggCc	10/20	1	2	FACETS	0.483	0.391	0.586	0.483	0.391	0.586	SUBCLONAL	1	TRUE	1	0.41	2		650	313	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797776	42797777	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	81	702	0	ENST00000575354.2:c.3831_3832del	p.Val1278ProfsTer65	p.V1278Pfs*65	ENST00000575354	NM_015125.3	1276	tgGCgc/tggc	16/20	1	2	FACETS	0.985	0.873	1	0.985	0.873	1	CLONAL	1	TRUE	1	0.41	2		702	401	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726012	61726013	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	59	457	0	ENST00000401558.2:c.626_627del	p.Cys209SerfsTer34	p.C209Sfs*34	ENST00000401558	NM_003400.3	209	tGT/t	8/25	1	2	FACETS	0.934	0.81	1	0.934	0.81	1	CLONAL	1	TRUE	1	0.41	2		457	308	SUCCESS
REST	5978	MSKCC	GRCh37	4	57776808	57776808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	86	575	1	ENST00000309042.7:c.4G>A	p.Ala2Thr	p.A2T	ENST00000309042	NM_005612.4	2	Gcc/Acc	2/4	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.41	2		576	394	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295960	1295960	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	62	839	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.659	0.57	0.755	0.659	0.57	0.755	SUBCLONAL	1	TRUE	1	0.41	2		839	459	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170334	32170334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761986491	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	72	660	0	ENST00000375023.3:c.3274G>A	p.Gly1092Ser	p.G1092S	ENST00000375023	NM_004557.3	1092	Ggc/Agc	21/30	1	2	FACETS	0.791	0.694	0.895	0.791	0.694	0.895	SUBCLONAL	1	TRUE	1	0.41	2		660	444	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508306	106508306	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	87	675	0	ENST00000359195.3:c.300T>A	p.Tyr100Ter	p.Y100*	ENST00000359195	NM_002649.2	100	taT/taA	2/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.41	2		675	368	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29195838	29195838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764888128	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	93	657	0	ENST00000240100.2:c.760G>A	p.Asp254Asn	p.D254N	ENST00000240100	NM_001394.6	254	Gac/Aac	3/4	1	2	FACETS	0.945	0.844	1	0.945	0.844	1	CLONAL	1	TRUE	1	0.41	2		657	480	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549200	87549200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	51	508	0	ENST00000277120.3:c.1757C>T	p.Ala586Val	p.A586V	ENST00000277120		586	gCa/gTa	15/19	1	2	FACETS	0.876	0.75	1	0.876	0.75	1	CLONAL	1	TRUE	1	0.41	2		508	284	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636261	87636261	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	32	664	0	ENST00000277120.3:c.2426A>G	p.Glu809Gly	p.E809G	ENST00000277120		809	gAg/gGg	19/19	1	2	FACETS	0.332	0.269	0.404	0.332	0.269	0.404	SUBCLONAL	1	TRUE	1	0.41	2		664	470	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	202	321	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.862905783272674	2		321	454	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152108	55152112	+	missense_variant	Missense_Mutation	ONP	CGAAC	CGAAC	TGAAA	novel	NA	P-0061210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	3795	529	0	ENST00000257290.5:c.2540_2544delinsTGAAA	p.Ser847_Asn848delinsLeuLys	p.S847_N848delinsLK	ENST00000257290	NM_006206.4	847	tCGAAC/tTGAAA	18/23	0.862905783272674	12	FACETS	1	0.999	1	0.947	0.939	0.955	CLONAL	10	TRUE	1	0.862905783272674	12		529	4487	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959462	26959462	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	116	423	0	ENST00000381527.3:c.629A>G	p.His210Arg	p.H210R	ENST00000381527	NM_001260.1	210	cAt/cGt	6/13	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.440310613474599	2		423	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0061212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	109	391	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.264776646285585	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.392137187558641	1		391	412	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248872	133248872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	104	515	0	ENST00000320574.5:c.1723G>A	p.Glu575Lys	p.E575K	ENST00000320574	NM_006231.2	575	Gag/Aag	16/49	0.392137187558641	1	FACETS	0.877	0.789	0.97	0.877	0.789	0.97	CLONAL	1	TRUE	0	0.392137187558641	1		515	486	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157812	106157812	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	77	517	0	ENST00000380013.4:c.2713G>C	p.Asp905His	p.D905H	ENST00000380013	NM_001127208.2	905	Gat/Cat	3/11	0.392137187558641	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.392137187558641	1		517	287	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776904	76776904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	24	221	0	ENST00000373344.5:c.7048C>T	p.Leu2350Phe	p.L2350F	ENST00000373344	NM_000489.3	2350	Ctt/Ttt	33/35	1	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.392137187558641	1		221	66	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264754	11264754	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	84	456	0	ENST00000361445.4:c.3808G>T	p.Gly1270Cys	p.G1270C	ENST00000361445	NM_004958.3	1270	Ggc/Tgc	26/58	1	2	FACETS	0.935	0.83	1	0.935	0.83	1	CLONAL	1	TRUE	1	0.392137187558641	2		456	458	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054983	176054983	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	41	411	0	ENST00000367669.3:c.1070G>T	p.Arg357Leu	p.R357L	ENST00000367669	NM_022457.5	357	cGa/cTa	10/20	0.392137187558641	3	FACETS	1	0.939	1	0.628	0.529	0.736	CLONAL	1	TRUE	1	0.392137187558641	3		411	199	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572938	7572938	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	129	548	0	ENST00000269305.4:c.1171G>A	p.Asp391Asn	p.D391N	ENST00000269305	NM_001126112.2	391	Gac/Aac	11/11	0.264776646285585	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.392137187558641	1		548	474	SUCCESS
REL	5966	MSKCC	GRCh37	2	61148957	61148957	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs763163128	NA	P-0061212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	77	504	0	ENST00000295025.8:c.1147C>G	p.Gln383Glu	p.Q383E	ENST00000295025	NM_002908.2	383	Caa/Gaa	11/11	1	2	FACETS	0.843	0.742	0.95	0.843	0.742	0.95	CLONAL	1	TRUE	1	0.392137187558641	2		504	466	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007053	152007053	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	43	363	0	ENST00000262189.6:c.847G>A	p.Glu283Lys	p.E283K	ENST00000262189	NM_170606.2	283	Gaa/Aaa	6/59	1	2	FACETS	0.736	0.619	0.864	0.736	0.619	0.864	SUBCLONAL	1	TRUE	1	0.392137187558641	2		363	298	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0061213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	46	552	1	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	1	2	FACETS	0.614	0.517	0.722	0.614	0.517	0.722	SUBCLONAL	1	TRUE	1	0.27	2		553	555	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432563	49432563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	58	600	0	ENST00000301067.7:c.8576C>T	p.Thr2859Ile	p.T2859I	ENST00000301067	NM_003482.3	2859	aCc/aTc	34/54	1	2	FACETS	0.696	0.598	0.804	0.696	0.598	0.804	SUBCLONAL	1	TRUE	1	0.27	2		600	617	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	74	377	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.286699281716251	1	FACETS	0.847	0.743	0.959	0.847	0.743	0.959	CLONAL	1	TRUE	0	0.286699281716251	1		377	522	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603044	48603044	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781359	NA	P-0061214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	95	342	0	ENST00000342988.3:c.1345C>T	p.Gln449Ter	p.Q449*	ENST00000342988	NM_005359.5	449	Cag/Tag	11/12	0.286699281716251	1	FACETS	0.879	0.783	0.98	0.879	0.783	0.98	CLONAL	1	TRUE	0	0.286699281716251	1		342	646	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971035	21971035	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	120	593	0	ENST00000304494.5:c.323A>G	p.Asp108Gly	p.D108G	ENST00000304494	NM_000077.4	108	gAt/gGt	2/3	0.286699281716251	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.286699281716251	1		593	588	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440011	56440011	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0061214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	84	456	0	ENST00000407977.2:c.583-2A>T		p.X195_splice	ENST00000407977		195			0.286699281716251	1	FACETS	0.965	0.855	1	0.965	0.855	1	CLONAL	1	TRUE	0	0.286699281716251	1		456	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576899	7576900	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	C	novel	NA	P-0061214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	114	643	0	ENST00000269305.4:c.946_947delinsG	p.Pro316AlafsTer29	p.P316Afs*29	ENST00000269305	NM_001126112.2	316	CCc/Gc	9/11	0.286699281716251	1	FACETS	0.969	0.873	1	0.969	0.873	1	CLONAL	1	TRUE	0	0.286699281716251	1		643	703	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0061215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	77	611	0				ENST00000310581	NM_198253.2	-/1132			0.482711615591765	3	FACETS	0.825	0.727	0.93	0.413	0.363	0.465	CLONAL	1	TRUE	1	0.482711615591765	3		611	480	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205768	108205768	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1555127166	NA	P-0061215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	93	395	0	ENST00000278616.4:c.8083G>T	p.Gly2695Cys	p.G2695C	ENST00000278616	NM_000051.3	2695	Ggt/Tgt	55/63	0.350366458224568	3	FACETS	0.72	0.641	0.805	0.36	0.32	0.403	SUBCLONAL	1	TRUE	1	0.482711615591765	3		395	664	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432347	49432347	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	137	668	0	ENST00000301067.7:c.8792del	p.Pro2931HisfsTer12	p.P2931Hfs*12	ENST00000301067	NM_003482.3	2931	cCa/ca	34/54	1	2	FACETS	0.737	0.671	0.806	0.737	0.671	0.806	SUBCLONAL	1	TRUE	1	0.482711615591765	2		668	770	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954300	48954300	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0061215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	81	261	0	ENST00000267163.4:c.1422-1G>C		p.X474_splice	ENST00000267163	NM_000321.2	474			0.375300577198157	1	FACETS	0.875	0.78	0.975	0.875	0.78	0.975	CLONAL	1	TRUE	0	0.482711615591765	1		261	291	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094360	27094360	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061215-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	349	633	0	ENST00000324856.7:c.3068G>C	p.Trp1023Ser	p.W1023S	ENST00000324856	NM_006015.4	1023	tGg/tCg	11/20	0.482711615591765	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.482711615591765	3		633	887	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0061216-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	43	470	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.858	0.723	1	0.858	0.723	1	CLONAL	1	TRUE	1	0.372592456410114	2		470	269	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0061216-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	90	453	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.372592456410114	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.372592456410114	1		453	384	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593504	48593504	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061216-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	104	461	0	ENST00000342988.3:c.1255G>T	p.Gly419Trp	p.G419W	ENST00000342988	NM_005359.5	419	Ggg/Tgg	10/12	0.372592456410114	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.372592456410114	1		461	388	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0061216-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	59	516	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.951	0.823	1	0.951	0.823	1	CLONAL	1	TRUE	1	0.372592456410114	2		516	333	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043464	180043464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061216-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	146	562	0	ENST00000261937.6:c.3122G>A	p.Arg1041Gln	p.R1041Q	ENST00000261937	NM_182925.4	1041	cGg/cAg	23/30	0.222964480780388	1	FACETS	0.815	0.753	0.879	1	0.99	1	INDETERMINATE	2	TRUE	0	0.372592456410114	1		562	391	SUCCESS
APC	324	MSKCC	GRCh37	5	112175533	112175533	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061216-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	189	629	0	ENST00000257430.4:c.4243del	p.Ser1415ValfsTer4	p.S1415Vfs*4	ENST00000257430	NM_000038.5	1414	gtA/gt	16/16	0.372592456410114	2	FACETS	0.964	0.898	1	0.964	0.898	1	CLONAL	2	TRUE	0	0.372592456410114	2		629	526	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032523	12032523	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061216-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	42	318	0	ENST00000353533.5:c.959T>C	p.Val320Ala	p.V320A	ENST00000353533	NM_003010.3	320	gTc/gCc	9/11	0.372592456410114	1	FACETS	0.951	0.803	1	0.951	0.803	1	CLONAL	1	TRUE	0	0.372592456410114	1		318	193	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99154381	99154381	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061216-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	115	548	0	ENST00000074304.5:c.523G>A	p.Glu175Lys	p.E175K	ENST00000074304	NM_001134224.1	175	Gag/Aag	8/26	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.372592456410114	2		548	515	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719769	190719769	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061216-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	73	512	0	ENST00000441310.2:c.1771A>C	p.Ile591Leu	p.I591L	ENST00000441310	NM_000534.4	591	Ata/Cta	9/13	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.372592456410114	2		512	351	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262804	46262804	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061216-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	53	538	0	ENST00000371998.3:c.977G>A	p.Gly326Asp	p.G326D	ENST00000371998		326	gGc/gAc	10/23	1	2	FACETS	0.865	0.741	0.998	0.865	0.741	0.998	CLONAL	1	TRUE	1	0.372592456410114	2		538	329	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249465	153249465	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061216-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	87	513	0	ENST00000281708.4:c.1313C>T	p.Ser438Phe	p.S438F	ENST00000281708	NM_033632.3	438	tCt/tTt	9/12	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.372592456410114	2		513	340	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0061217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	146	390	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.489939614181156	2		390	498	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207064	1207065	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1131690917	NA	P-0061217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	91	506	0	ENST00000326873.7:c.157dup	p.Asp53GlyfsTer110	p.D53Gfs*110	ENST00000326873	NM_000455.4	51	atg/atGg	1/10	0.382339210280964	1	FACETS	0.781	0.699	0.867	0.781	0.699	0.867	SUBCLONAL	1	TRUE	0	0.489939614181156	1		506	359	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040794	47040794	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	139	651	0	ENST00000377604.3:c.1429G>T	p.Gly477Ter	p.G477*	ENST00000377604	NM_001204468.1	477	Gga/Tga	13/24	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.489939614181156	2		651	492	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742522	17742522	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	88	416	0	ENST00000250003.3:c.704C>A	p.Pro235His	p.P235H	ENST00000250003	NM_002478.4	235	cCc/cAc	2/3	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.489939614181156	2		416	353	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670620	67670620	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	122	486	0	ENST00000264010.4:c.1865A>T	p.Asn622Ile	p.N622I	ENST00000264010	NM_006565.3	622	aAt/aTt	11/12	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.489939614181156	2		486	493	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63531840	63531840	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0061217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	125	479	0	ENST00000307078.5:c.2142-1G>T		p.X714_splice	ENST00000307078	NM_004655.3	714			1	2	FACETS	0.981	0.893	1	0.981	0.893	1	CLONAL	1	TRUE	1	0.489939614181156	2		479	520	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409802	63409802	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	107	574	0	ENST00000330258.3:c.3365C>A	p.Thr1122Asn	p.T1122N	ENST00000330258	NM_152424.3	1122	aCc/aAc	2/2	1	2	FACETS	0.977	0.882	1	0.977	0.882	1	CLONAL	1	TRUE	1	0.489939614181156	2		574	447	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796387	57796388	+	frameshift_variant	Frame_Shift_Ins	INS	GG	GG	TGT	novel	NA	P-0061217-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	152	478	0	ENST00000309042.7:c.1363_1364delinsTGT	p.Gly455CysfsTer9	p.G455Cfs*9	ENST00000309042	NM_005612.4	455	GGg/TGTg	4/4	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.489939614181156	2		478	607	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371708	225371708	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	88	461	0	ENST00000264414.4:c.896T>G	p.Met299Arg	p.M299R	ENST00000264414	NM_003590.4	299	aTg/aGg	7/16	1	2	FACETS	0.988	0.892	1	0.988	0.892	1	CLONAL	1	TRUE	1	0.784938389684999	2		461	227	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448518	49448518	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1189364625	NA	P-0061224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	44	734	0	ENST00000301067.7:c.193C>T	p.Arg65Cys	p.R65C	ENST00000301067	NM_003482.3	65	Cgt/Tgt	3/54	1	2	FACETS	0.135	0.113	0.16	0.135	0.113	0.16	SUBCLONAL	1	TRUE	1	0.784938389684999	2		734	830	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44515842	44515842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	73	452	0	ENST00000291552.4:c.211G>A	p.Asp71Asn	p.D71N	ENST00000291552	NM_006758.2	71	Gat/Aat	4/8	1	2	FACETS	0.361	0.316	0.409	0.361	0.316	0.409	SUBCLONAL	1	TRUE	1	0.784938389684999	2		452	515	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285677	46285678	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0061224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	192	509	0	ENST00000334344.6:c.5040_5041dup	p.Ser1681PhefsTer21	p.S1681Ffs*21	ENST00000334344	NM_152641.2	1679	-/TT	17/21	1	2	FACETS	0.935	0.872	1	0.935	0.872	1	CLONAL	1	TRUE	1	0.784938389684999	2		509	523	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486027	29486027	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0061224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	54	254	0	ENST00000356175.3:c.205-1G>A		p.X69_splice	ENST00000356175	NM_000267.3	69			0.784938389684999	1	FACETS	0.88	0.786	0.972	0.88	0.786	0.972	CLONAL	1	TRUE	0	0.784938389684999	1		254	95	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182905	123182907	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0061224-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	118	128	0	ENST00000218089.9:c.872_874del	p.Gly291del	p.G291del	ENST00000218089	NM_001042749.1	290	aaAGGa/aaa	10/35	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.784938389684999	1		128	152	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991910	72991910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779741152	NA	P-0061225-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	39	618	0	ENST00000268489.5:c.2135G>A	p.Arg712Gln	p.R712Q	ENST00000268489	NM_006885.3	712	cGg/cAg	2/10	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.400975918028857	2		618	171	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0061226-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	39	611	0				ENST00000310581	NM_198253.2	-/1132			0.397654450327071	1	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	0	0.397654450327071	1		611	157	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0061226-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	117	380	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.152089200519508	3	FACETS	0.832	0.756	0.911	0.832	0.756	0.911	INDETERMINATE	2	TRUE	1	0.397654450327071	3		380	424	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0061226-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	66	589	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.808	0.704	0.919	0.808	0.704	0.919	CLONAL	1	TRUE	1	0.397654450327071	2		589	411	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259184	89259184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061226-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	66	316	0	ENST00000336596.2:c.328C>T	p.Pro110Ser	p.P110S	ENST00000336596	NM_005233.5	110	Cca/Tca	3/17	0.112716727257786	3	FACETS	1	0.878	1	0.504	0.439	0.573	INDETERMINATE	1	TRUE	1	0.397654450327071	3		316	395	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169254	99169254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061226-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	81	341	0	ENST00000074304.5:c.1184C>T	p.Ser395Leu	p.S395L	ENST00000074304	NM_001134224.1	395	tCa/tTa	15/26	0.397654450327071	1	FACETS	0.949	0.843	1	0.949	0.843	1	CLONAL	1	TRUE	0	0.397654450327071	1		341	344	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692836	89692836	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs786204858	NA	P-0061226-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	23	42	0	ENST00000371953.3:c.320A>T	p.Asp107Val	p.D107V	ENST00000371953	NM_000314.4	107	gAt/gTt	5/9	0.397654450327071	1	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	0	0.397654450327071	1		42	81	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486344	8486344	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061226-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	91	315	0	ENST00000356435.5:c.2473G>A	p.Gly825Arg	p.G825R	ENST00000356435		825	Ggg/Agg	17/35	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.397654450327071	2		315	347	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715752	18715752	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061226-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	57	261	0	ENST00000266497.5:c.3583G>T	p.Glu1195Ter	p.E1195*	ENST00000266497		1195	Gaa/Taa	25/31	NA	2	FACETS	0.805	0.694	0.925			1	INDETERMINATE	1	TRUE	NA	0.397654450327071	2		261	356	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984387	72984387	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061226-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	81	537	1	ENST00000268489.5:c.3197C>T	p.Ala1066Val	p.A1066V	ENST00000268489	NM_006885.3	1066	gCc/gTc	3/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.397654450327071	2		538	360	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124503592	124503592	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061227-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	135	562	0	ENST00000357628.3:c.358A>G	p.Ser120Gly	p.S120G	ENST00000357628	NM_015450.2	120	Agc/Ggc	8/19	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.284505196808745	2		562	733	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72994002	72994002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061228-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	174	500	0	ENST00000268489.5:c.43G>A	p.Gly15Arg	p.G15R	ENST00000268489	NM_006885.3	15	Ggg/Agg	2/10	1	2	FACETS	1	0.983	1	1	0.994	1	CLONAL	2	FALSE	1	0.3	2		500	488	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0061229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	397	804	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	0.274384917430781	5	FACETS	0.969	0.925	1	0.969	0.925	1	INDETERMINATE	3	TRUE	2	0.536752015030259	5		804	919	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1720607	1720619	+	frameshift_variant	Frame_Shift_Del	DEL	GTCATGGGAGTAA	GTCATGGGAGTAA	-	novel	NA	P-0061229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	98	639	0	ENST00000378609.4:c.789_801del	p.Tyr264ThrfsTer53	p.Y264Tfs*53	ENST00000378609	NM_002074.3	263	acTTACTCCCATGAC/ac	10/12	0.461108823568479	4	FACETS	1	0.955	1			1	CLONAL	1	TRUE	NA	0.536752015030259	4		639	501	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11150206	11150206	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	105	485	0	ENST00000358026.2:c.4243C>T	p.Gln1415Ter	p.Q1415*	ENST00000358026	NM_001128849.1	1415	Cag/Tag	30/36	0.541352429669234	3	FACETS	0.911	0.819	1	0.455	0.409	0.504	CLONAL	1	TRUE	1	0.536752015030259	3		485	545	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465561	8465561	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	63	614	0	ENST00000356435.5:c.3619del	p.Asp1207MetfsTer24	p.D1207Mfs*24	ENST00000356435		1207	Gat/at	21/35	0.391248659900256	3	FACETS	0.75	0.651	0.856	0.375	0.325	0.428	SUBCLONAL	1	TRUE	1	0.536752015030259	3		614	397	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061231-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	81	377	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.25924784189975	4	FACETS	0.901	0.8	1	0.901	0.8	1	CLONAL	2	TRUE	2	0.359437133296615	4		377	340	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0061231-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	85	577	0	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	0.351108251927309	3	FACETS	0.959	0.849	1	0.479	0.424	0.538	CLONAL	1	TRUE	1	0.359437133296615	3		577	582	SUCCESS
APC	324	MSKCC	GRCh37	5	112175096	112175097	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs786203760	NA	P-0061231-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	130	477	0	ENST00000257430.4:c.3807_3808del	p.Ile1269MetfsTer6	p.I1269Mfs*6	ENST00000257430	NM_000038.5	1269	ATa/a	16/16	0.351108251927309	3	FACETS	0.968	0.885	1	0.968	0.885	1	CLONAL	2	TRUE	1	0.359437133296615	3		477	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1555525367	NA	P-0061231-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	175	492	0	ENST00000269305.4:c.783-1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.359437133296615	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	2	TRUE	0	0.359437133296615	2		492	485	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427464	49427465	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061241-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	103	496	0	ENST00000301067.7:c.11023dup	p.Thr3675AsnfsTer38	p.T3675Nfs*38	ENST00000301067	NM_003482.3	3675	aca/aAca	39/54	0.182339160055938	4	FACETS	0.918	0.836	1	0.918	0.836	1	INDETERMINATE	2	TRUE	2	0.769161229241921	4		496	258	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0061242-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	97	382	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.466318263056395	3	FACETS	0.987	0.898	1	0.987	0.898	1	CLONAL	2	TRUE	1	0.543161991526992	3		382	230	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0061242-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	83	608	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.543161991526992	1	FACETS	0.994	0.893	1	0.994	0.893	1	CLONAL	1	TRUE	0	0.543161991526992	1		610	224	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652419	206652419	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061242-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	73	513	0	ENST00000367120.3:c.1126A>G	p.Ser376Gly	p.S376G	ENST00000367120	NM_014002.3	376	Agc/Ggc	10/22	1	2	FACETS	0.745	0.655	0.839	0.745	0.655	0.839	SUBCLONAL	1	TRUE	1	0.543161991526992	2		513	361	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485810	8485810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159859	NA	P-0061242-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	84	369	2	ENST00000356435.5:c.3007G>A	p.Gly1003Arg	p.G1003R	ENST00000356435		1003	Ggg/Agg	17/35	0.543161991526992	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.543161991526992	1		371	179	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061243-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	76	321	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.835	0.738	0.939	0.835	0.738	0.939	CLONAL	1	TRUE	1	0.499874258655547	2		321	364	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0061243-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	96	544	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.499874258655547	2		544	355	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220274	55220274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061243-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3138	1973	272	0	ENST00000275493.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000275493	NM_005228.3	222	Cgc/Tgc	6/28	0.499874258655547	40	FACETS	1	0.988	1	0.405	0.396	0.414	CLONAL	16	TRUE	0	0.499874258655547	40		272	5111	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381529	81381529	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061243-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	156	294	0	ENST00000222390.5:c.532C>T	p.Arg178Ter	p.R178*	ENST00000222390	NM_000601.4	178	Cga/Tga	5/18	0.415713799107522	3	FACETS	1	0.939	1	0.514	0.471	0.559	CLONAL	1	TRUE	1	0.499874258655547	3		294	759	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418969	116418969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061243-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	84	368	0	ENST00000397752.3:c.3480G>A	p.Met1160Ile	p.M1160I	ENST00000397752	NM_000245.2	1160	atG/atA	17/21	0.415713799107522	3	FACETS	0.566	0.5	0.638	0.283	0.25	0.319	SUBCLONAL	1	TRUE	1	0.499874258655547	3		368	742	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753149	42753151	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs199960550	NA	P-0061245-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	126	600	7	ENST00000222329.4:c.1113_1115del	p.Ser373del	p.S373del	ENST00000222329	NM_006494.2	371	tcTTCc/tcc	4/4	0.361980924902422	2	FACETS	1	0.954	1	0.541	0.49	0.593	CLONAL	1	TRUE	0	0.361980924902422	2		607	644	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287487	46287487	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061245-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	117	333	0	ENST00000334344.6:c.5347del	p.Ser1783GlnfsTer8	p.S1783Qfs*8	ENST00000334344	NM_152641.2	1782	taT/ta	20/21	0.327203989320869	2	FACETS	0.926	0.845	1	0.926	0.845	1	CLONAL	2	TRUE	0	0.361980924902422	2		333	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0061245-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	226	435	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.272566139631264	3	FACETS	0.842	0.79	0.894	0.842	0.79	0.894	CLONAL	3	TRUE	0	0.361980924902422	3		435	584	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268766	41268766	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061245-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	159	406	0	ENST00000349496.5:c.1004A>T	p.Lys335Ile	p.K335I	ENST00000349496	NM_001904.3	335	aAa/aTa	7/15	0.272566139631264	3	FACETS	1	0.978	1	0.767	0.709	0.826	CLONAL	2	TRUE	0	0.361980924902422	3		406	451	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124491965	124491965	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061245-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	53	290	0	ENST00000357628.3:c.910G>C	p.Asp304His	p.D304H	ENST00000357628	NM_015450.2	304	Gat/Cat	11/19	0.361980924902422	3	FACETS	1	0.89	1	0.522	0.448	0.603	CLONAL	1	TRUE	1	0.361980924902422	3		290	331	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0061246-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	191	380	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.445464688123194	4	FACETS	0.832	0.773	0.893	0.832	0.773	0.893	CLONAL	2	TRUE	2	0.54607762473995	4		380	650	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372022	55372022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061246-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	216	450	0	ENST00000297316.4:c.712G>A	p.Ala238Thr	p.A238T	ENST00000297316	NM_022454.3	238	Gcc/Acc	2/2	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.54607762473995	2		450	740	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576883	7576883	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061246-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	509	596	0	ENST00000269305.4:c.963del	p.Lys321AsnfsTer24	p.K321Nfs*24	ENST00000269305	NM_001126112.2	321	aaA/aa	9/11	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	2	TRUE	NA	0.54607762473995	2		596	930	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061246-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	159	333	2	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	1	2	FACETS	0.952	0.876	1	0.952	0.876	1	CLONAL	1	TRUE	1	0.54607762473995	2		335	612	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702391	47702391	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs752241362	NA	P-0061246-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	119	272	0	ENST00000233146.2:c.1987A>T	p.Met663Leu	p.M663L	ENST00000233146	NM_000251.2	663	Atg/Ttg	12/16	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.54607762473995	2		272	422	SUCCESS
AR	367	MSKCC	GRCh37	X	66863125	66863125	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139524801	NA	P-0061246-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	202	383	0	ENST00000374690.3:c.1644G>T	p.Leu548Phe	p.L548F	ENST00000374690	NM_000044.3	548	ttG/ttT	2/8	1	2	FACETS	0.966	0.898	1	0.966	0.898	1	CLONAL	1	TRUE	1	0.54607762473995	2		383	766	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129903	69129903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752113779	NA	P-0061246-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	223	406	0	ENST00000288368.4:c.4657G>A	p.Gly1553Arg	p.G1553R	ENST00000288368	NM_024870.2	1553	Gga/Aga	38/40	1	2	FACETS	0.941	0.877	1	0.941	0.877	1	CLONAL	1	TRUE	1	0.54607762473995	2		406	868	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440742	56440742	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061246-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	252	480	0	ENST00000407977.2:c.476G>A	p.Trp159Ter	p.W159*	ENST00000407977		159	tGg/tAg	5/10	0.54607762473995	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.54607762473995	1		480	598	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0061247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	184	371	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.806	0.75	0.862	1	0.992	1	CLONAL	2	TRUE	1	0.47	2		371	486	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295397	1295397	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0061247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	27	437	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.383	0.305	0.472	0.383	0.305	0.472	SUBCLONAL	1	TRUE	1	0.47	2		437	300	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0061248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	77	498	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.446158929631691	1		498	207	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0061248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	83	299	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.446158929631691	2		299	369	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133785	2133785	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	106	428	0	ENST00000219476.3:c.3973G>C	p.Gly1325Arg	p.G1325R	ENST00000219476	NM_000548.3	1325	Ggc/Cgc	33/42	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.446158929631691	2		428	426	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714421	40714421	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1447304698	NA	P-0061248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	117	375	0	ENST00000373198.4:c.3976G>C	p.Asp1326His	p.D1326H	ENST00000373198	NM_133170.3	1326	Gac/Cac	29/32	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.446158929631691	2		375	521	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858139	152858139	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	198	202	0	ENST00000406277.2:c.476G>A	p.Trp159Ter	p.W159*	ENST00000406277	NM_152274.4	159	tGg/tAg	6/7	0.368563775470626	2	FACETS	0.897	0.848	0.944			1	CLONAL	3	TRUE	NA	0.446158929631691	2		202	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577123	7577123	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876660333	NA	P-0061252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	81	538	0	ENST00000269305.4:c.815T>A	p.Val272Glu	p.V272E	ENST00000269305	NM_001126112.2	272	gTg/gAg	8/11	0.294927086531667	1	FACETS	0.938	0.83	1	0.938	0.83	1	CLONAL	1	TRUE	0	0.316572657622478	1		538	459	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992339	72992339	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs372337934	NA	P-0061252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	74	608	0	ENST00000268489.5:c.1706G>C	p.Arg569Pro	p.R569P	ENST00000268489	NM_006885.3	569	cGt/cCt	2/10	1	2	FACETS	0.894	0.784	1	0.894	0.784	1	CLONAL	1	TRUE	1	0.316572657622478	2		608	523	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591311	67591312	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0061252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	73	379	0	ENST00000274335.5:c.1809_1810del	p.Glu604ArgfsTer9	p.E604Rfs*9	ENST00000274335		603	acTGaa/acaa	13/15	1	2	FACETS	0.943	0.827	1	0.943	0.827	1	CLONAL	1	TRUE	1	0.316572657622478	2		379	489	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061253-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	86	377	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.3	5	FACETS	1	0.923	1			1	CLONAL	3	TRUE	NA	0.2	5		377	357	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0061253-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	64	665	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.2	2		665	560	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971170	21971170	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061253-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	37	589	0	ENST00000304494.5:c.188T>A	p.Leu63Gln	p.L63Q	ENST00000304494	NM_000077.4	63	cTg/cAg	2/3	0.3	1	FACETS	0.713	0.588	0.853	0.713	0.588	0.853	SUBCLONAL	1	TRUE	0	0.2	1		589	467	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672773	30672773	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1342894416	NA	P-0061253-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	50	790	0	ENST00000376406.3:c.4187A>C	p.Lys1396Thr	p.K1396T	ENST00000376406	NM_014641.2	1396	aAa/aCa	10/15	1	2	FACETS	0.641	0.542	0.75	0.641	0.542	0.75	SUBCLONAL	1	TRUE	1	0.2	2		790	780	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	152	377	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.299631030080549	3	FACETS	1	0.985	1	0.792	0.741	0.843	INDETERMINATE	2	TRUE	0	0.60930970543246	3		377	274	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	134	367	1	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.60930970543246	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.60930970543246	1		368	232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0061254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	289	740	2	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	0.60930970543246	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.60930970543246	1		742	539	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971068	21971068	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	147	573	0	ENST00000304494.5:c.290T>C	p.Leu97Pro	p.L97P	ENST00000304494	NM_000077.4	97	cTg/cCg	2/3	0.423066290007633	1	FACETS	0.837	0.772	0.903	0.837	0.772	0.903	CLONAL	1	TRUE	0	0.60930970543246	1		573	401	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845415	151845415	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	204	594	1	ENST00000262189.6:c.13597C>T	p.Arg4533Ter	p.R4533*	ENST00000262189	NM_170606.2	4533	Cga/Tga	52/59	0.297036495347502	3	FACETS	0.838	0.784	0.893	0.838	0.784	0.893	INDETERMINATE	2	TRUE	1	0.60930970543246	3		595	521	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135357	30135357	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	49	499	0	ENST00000331968.5:c.461A>G	p.Tyr154Cys	p.Y154C	ENST00000331968	NM_002742.2	154	tAc/tGc	3/18	1	2	FACETS	0.47	0.4	0.547	0.47	0.4	0.547	SUBCLONAL	1	TRUE	1	0.60930970543246	2		499	342	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970984	21970993	+	frameshift_variant	Frame_Shift_Del	DEL	TCGCGATGGC	TCGCGATGGC	-	novel	NA	P-0061254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	80	690	1	ENST00000304494.5:c.365_374del	p.Gly122ValfsTer21	p.G122Vfs*21	ENST00000304494	NM_000077.4	122	gGCCATCGCGAt/gt	2/3	0.423066290007633	1	FACETS	0.37	0.327	0.417	0.37	0.327	0.417	SUBCLONAL	1	TRUE	0	0.60930970543246	1		691	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0061255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	177	665	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.810374160761183	4	FACETS	1	0.98	1			1	CLONAL	2	TRUE	NA	0.847979550915504	4		666	347	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252155	226252155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553260624	NA	P-0061255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	68	196	0	ENST00000366813.1:c.103G>A	p.Gly35Arg	p.G35R	ENST00000366813		35	Ggg/Agg	1/3	0.299455994070245	1	FACETS	0.651	0.583	0.718	0.651	0.583	0.718	INDETERMINATE	1	TRUE	0	0.847979550915504	1		196	142	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937744	76937744	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	44	488	0	ENST00000373344.5:c.3004del	p.Val1002Ter	p.V1002*	ENST00000373344	NM_000489.3	1002	Gta/ta	9/35	0.847979550915504	1	FACETS	0.949	0.852	1	0.949	0.852	1	CLONAL	1	TRUE	0	0.847979550915504	1		488	63	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390994	89390994	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779599137	NA	P-0061256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	84	328	0	ENST00000336596.2:c.1060C>T	p.Arg354Trp	p.R354W	ENST00000336596	NM_005233.5	354	Cgg/Tgg	5/17	1	2	FACETS	0.642	0.569	0.72	0.642	0.569	0.72	SUBCLONAL	1	TRUE	1	0.541760620299841	2		328	483	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038891	12038891	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	79	379	0	ENST00000396373.4:c.1184C>A	p.Ser395Tyr	p.S395Y	ENST00000396373	NM_001987.4	395	tCc/tAc	7/8	1	2	FACETS	0.443	0.389	0.5	0.443	0.389	0.5	SUBCLONAL	1	TRUE	1	0.541760620299841	2		379	659	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829665	72829666	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	154	366	0	ENST00000268489.5:c.6915dup	p.Glu2306ArgfsTer9	p.E2306Rfs*9	ENST00000268489	NM_006885.3	2305	-/A	9/10	1	2	FACETS	0.97	0.892	1	0.97	0.892	1	CLONAL	1	TRUE	1	0.541760620299841	2		366	586	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191306	185191306	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0061256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	104	452	0	ENST00000265026.3:c.2187T>A	p.Tyr729Ter	p.Y729*	ENST00000265026	NM_004721.4	729	taT/taA	11/14	1	2	FACETS	0.733	0.658	0.811	0.733	0.658	0.811	SUBCLONAL	1	TRUE	1	0.541760620299841	2		452	524	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754079	42754080	+	missense_variant	Missense_Mutation	DNP	CT	CT	AA	novel	NA	P-0061257-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	51	533	1	ENST00000222329.4:c.272_273delinsTT	p.Lys91Ile	p.K91I	ENST00000222329	NM_006494.2	91	aAG/aTT	3/4	1	2	FACETS	0.932	0.794	1	0.932	0.794	1	CLONAL	1	FALSE	1	0.255653925194591	2		534	428	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247024	53247024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061257-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	63	251	1	ENST00000375401.3:c.476G>A	p.Arg159His	p.R159H	ENST00000375401	NM_004187.3	159	cGc/cAc	4/26	1	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	0	0.255653925194591	1		252	294	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584513	48584514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs377767334	NA	P-0061258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	49	431	0	ENST00000342988.3:c.692dup	p.Ser232GlnfsTer3	p.S232Qfs*3	ENST00000342988	NM_005359.5	229	ctg/ctGg	6/12	1	2	FACETS	0.889	0.754	1	0.889	0.754	1	CLONAL	1	TRUE	1	0.26	2		431	424	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519919	29519919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374136388	NA	P-0061258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	40	431	0	ENST00000389048.3:c.1652G>A	p.Arg551Gln	p.R551Q	ENST00000389048	NM_004304.4	551	cGa/cAa	9/29	1	2	FACETS	0.864	0.72	1	0.864	0.72	1	CLONAL	1	TRUE	1	0.26	2		431	356	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162077	47162078	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	30	449	0	ENST00000409792.3:c.4048dup	p.Ser1350PhefsTer6	p.S1350Ffs*6	ENST00000409792	NM_014159.6	1350	tca/tTca	3/21	1	2	FACETS	0.443	0.356	0.542	0.443	0.356	0.542	SUBCLONAL	1	TRUE	1	0.26	2		449	521	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942035	44942036	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0061258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	57	174	0	ENST00000377967.4:c.3284+2dup		p.X1095_splice	ENST00000377967	NM_021140.2	1095			1	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.26	1		174	269	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087955	27087955	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	29	459	0	ENST00000324856.7:c.2242C>T	p.Gln748Ter	p.Q748*	ENST00000324856	NM_006015.4	748	Caa/Taa	6/20	1	2	FACETS	0.446	0.357	0.548	0.446	0.357	0.548	SUBCLONAL	1	TRUE	1	0.26	2		459	500	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0061258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	22	176	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.414	0.32	0.523	0.414	0.32	0.523	SUBCLONAL	1	TRUE	1	0.26	2		176	409	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120039	70120040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0061258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	29	437	0	ENST00000245479.2:c.1042_1043dup	p.Gln348HisfsTer36	p.Q348Hfs*36	ENST00000245479	NM_000346.3	347	-/CA	3/3	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.26	2		437	196	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	101	377	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.717307056218881	5	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	TRUE	2	0.717307056218881	5		377	170	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0061263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	35	579	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.717307056218881	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.717307056218881	1		581	53	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0061263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	80	674	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.598252892744024	3	FACETS	0.886	0.82	0.948	0.886	0.82	0.948	CLONAL	3	TRUE	0	0.717307056218881	3		674	114	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981891	63981891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	32	594	1	ENST00000398590.3:c.2393G>A	p.Ser798Asn	p.S798N	ENST00000398590	NM_001177387.1	798	aGt/aAt	12/14	0.300143670172851	3	FACETS	1	0.867	1	0.351	0.291	0.416	INDETERMINATE	1	TRUE	0	0.717307056218881	3		595	115	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0061264-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	244	210	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.64613157531407	1	FACETS	0.931	0.879	0.984	0.931	0.879	0.984	CLONAL	1	TRUE	0	0.64613157531407	1		210	549	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0061264-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	149	544	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.887	0.815	0.961	0.887	0.815	0.961	CLONAL	1	TRUE	1	0.64613157531407	2		544	520	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0061264-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	99	241	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	0.64613157531407	3	FACETS	1	0.937	1	0.528	0.475	0.583	CLONAL	1	TRUE	1	0.64613157531407	3		241	384	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18960982	18960982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061264-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	294	511	0	ENST00000262803.5:c.560G>A	p.Gly187Asp	p.G187D	ENST00000262803	NM_002911.3	187	gGc/gAc	4/24	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.64613157531407	2		511	840	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0061266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	141	456	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.795	0.723	0.871	1	0.988	1	SUBCLONAL	2	TRUE	1	0.171957593525774	2		456	1031	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777673	9777673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	303	635	0	ENST00000377346.4:c.1009G>A	p.Glu337Lys	p.E337K	ENST00000377346	NM_005026.3	337	Gag/Aag	8/24	0.171957593525774	5	FACETS	1	0.962	1	0.773	0.727	0.821	CLONAL	3	TRUE	1	0.171957593525774	5		635	1433	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11301688	11301688	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	60	518	0	ENST00000361445.4:c.1463T>C	p.Met488Thr	p.M488T	ENST00000361445	NM_004958.3	488	aTg/aCg	10/58	0.171957593525774	5	FACETS	0.804	0.69	0.929	0.201	0.172	0.233	CLONAL	1	TRUE	1	0.171957593525774	5		518	1092	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22405023	22405023	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	20	129	0	ENST00000344548.3:c.52T>C	p.Cys18Arg	p.C18R	ENST00000344548	NM_001039802.1	18	Tgt/Cgt	3/7	1	2	FACETS	0.909	0.696	1	0.909	0.696	1	CLONAL	1	TRUE	1	0.171957593525774	2		129	256	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092947	27092947	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0061266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	62	587	0	ENST00000324856.7:c.2879-1G>A		p.X960_splice	ENST00000324856	NM_006015.4	960			1	2	FACETS	0.706	0.608	0.814	0.706	0.608	0.814	SUBCLONAL	1	TRUE	1	0.171957593525774	2		587	1021	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426850	49426865	+	frameshift_variant	Frame_Shift_Del	DEL	GACTCTGCTGAAGATG	GACTCTGCTGAAGATG	-	novel	NA	P-0061266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	73	645	0	ENST00000301067.7:c.11623_11638del	p.His3875Ter	p.H3875*	ENST00000301067	NM_003482.3	3875	CATCTTCAGCAGAGTCtg/tg	39/54	1	2	FACETS	0.804	0.701	0.916	0.804	0.701	0.916	CLONAL	1	TRUE	1	0.171957593525774	2		645	1056	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69203035	69203035	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	75	488	0	ENST00000462284.1:c.62C>G	p.Thr21Ser	p.T21S	ENST00000462284	NM_002392.5	21	aCc/aGc	2/11	1	2	FACETS	0.806	0.704	0.917	0.806	0.704	0.917	CLONAL	1	TRUE	1	0.171957593525774	2		488	1082	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578175	7578175	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0061266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	50	657	1	ENST00000269305.4:c.672+2T>C		p.X224_splice	ENST00000269305	NM_001126112.2	224			1	2	FACETS	0.531	0.448	0.622	0.531	0.448	0.622	SUBCLONAL	1	TRUE	1	0.171957593525774	2		658	1096	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418435	49418436	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	C	novel	NA	P-0061266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	75	644	0	ENST00000301067.7:c.15977_15978delinsG	p.Leu5326ArgfsTer7	p.L5326Rfs*7	ENST00000301067	NM_003482.3	5326	cTT/cG	50/54	1	2	FACETS	0.825	0.721	0.938	0.825	0.721	0.938	CLONAL	1	TRUE	1	0.171957593525774	2		644	1057	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0061268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	148	382	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.513189655047643	2		382	506	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0061269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	299	210	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.606286394891454	2	FACETS	0.898	0.856	0.94	0.898	0.856	0.94	CLONAL	2	TRUE	0	0.606286394891454	2		210	549	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0061269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	178	176	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.606286394891454	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.606286394891454	2		176	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0061269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	379	699	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.606286394891454	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.606286394891454	2		699	608	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593504	48593504	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	159	461	0	ENST00000342988.3:c.1255G>T	p.Gly419Trp	p.G419W	ENST00000342988	NM_005359.5	419	Ggg/Tgg	10/12	0.606286394891454	1	FACETS	0.909	0.843	0.976	0.909	0.843	0.976	CLONAL	1	TRUE	0	0.606286394891454	1		461	402	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120717	115120717	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	351	655	0	ENST00000257566.3:c.289G>T	p.Glu97Ter	p.E97*	ENST00000257566	NM_016569.3	97	Gaa/Taa	1/8	0.606286394891454	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.606286394891454	2		655	565	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445202	49445202	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776110112	NA	P-0061269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	316	879	0	ENST00000301067.7:c.2264G>A	p.Arg755Gln	p.R755Q	ENST00000301067	NM_003482.3	755	cGg/cAg	10/54	0.606286394891454	2	FACETS	0.886	0.846	0.927	0.886	0.846	0.927	CLONAL	2	TRUE	0	0.606286394891454	2		879	588	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412011	63412011	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	321	474	0	ENST00000330258.3:c.1156G>T	p.Glu386Ter	p.E386*	ENST00000330258	NM_152424.3	386	Gaa/Taa	2/2	0.529620191021442	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.606286394891454	2		474	435	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151624	55151624	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1242960071	NA	P-0061269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	109	419	0	ENST00000257290.5:c.2410C>T	p.Arg804Ter	p.R804*	ENST00000257290	NM_006206.4	804	Cga/Tga	17/23	1	2	FACETS	0.996	0.903	1	0.996	0.903	1	CLONAL	1	TRUE	1	0.606286394891454	2		419	361	SUCCESS
APC	324	MSKCC	GRCh37	5	112164650	112164650	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	239	408	0	ENST00000257430.4:c.1724G>T	p.Cys575Phe	p.C575F	ENST00000257430	NM_000038.5	575	tGt/tTt	14/16	0.606286394891454	2	FACETS	0.986	0.937	1	0.986	0.937	1	CLONAL	2	TRUE	0	0.606286394891454	2		408	400	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0061270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	161	400	0	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.516763225790845	2		400	574	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0061270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	200	550	2	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.943	0.875	1	0.943	0.875	1	CLONAL	1	TRUE	1	0.516763225790845	2		552	821	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231771	36231800	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TTCGAGGTTCTCGGGGCCCATCCACTGTGA	TTCGAGGTTCTCGGGGCCCATCCACTGTGA	-	novel	NA	P-0061270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	214	593	0	ENST00000300305.3:c.584_613del	p.Ile195_Arg204del	p.I195_R204del	ENST00000300305		195	aTCACAGTGGATGGGCCCCGAGAACCTCGAAga/aga	5/8	1	2	FACETS	0.999	0.93	1	0.999	0.93	1	CLONAL	1	TRUE	1	0.516763225790845	2		593	829	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390212	89390212	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061270-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	154	418	0	ENST00000336596.2:c.961G>T	p.Ala321Ser	p.A321S	ENST00000336596	NM_005233.5	321	Gct/Tct	4/17	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.516763225790845	2		418	560	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0061271-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	11	357	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	0.478206922908183	3	FACETS	0.101	0.069	0.14	0.05	0.034	0.07	SUBCLONAL	1	TRUE	1	0.608317712176173	3		357	469	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0061272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	230	490	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.600308017988697	6	FACETS	0.927	0.865	0.99	0.463	0.432	0.495	CLONAL	2	TRUE	2	0.600308017988697	6		490	910	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0061272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	241	580	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.600308017988697	3	FACETS	0.836	0.795	0.878	0.836	0.795	0.878	CLONAL	3	TRUE	0	0.600308017988697	3		580	416	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134598	2134598	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45517340	NA	P-0061272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	225	862	1	ENST00000219476.3:c.4375C>T	p.Arg1459Ter	p.R1459*	ENST00000219476	NM_000548.3	1459	Cga/Tga	34/42	0.51788726835829	2	FACETS	0.901	0.852	0.949	0.901	0.852	0.949	CLONAL	2	TRUE	0	0.600308017988697	2		863	416	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141874	108141874	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587781558	NA	P-0061272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	124	427	1	ENST00000278616.4:c.2921+1G>A		p.X974_splice	ENST00000278616	NM_000051.3	974			0.600308017988697	3	FACETS	1	0.976	1	0.604	0.55	0.659	CLONAL	1	TRUE	1	0.600308017988697	3		428	445	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028137	69028137	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	129	555	0	ENST00000288368.4:c.3296A>T	p.His1099Leu	p.H1099L	ENST00000288368	NM_024870.2	1099	cAt/cTt	26/40	0.297437356942035	3	FACETS	0.789	0.724	0.856	0.789	0.724	0.856	INDETERMINATE	2	TRUE	1	0.600308017988697	3		555	354	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0061272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	219	397	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.600308017988697	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.600308017988697	3		397	446	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186737	108186737	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0061272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	151	529	0	ENST00000278616.4:c.6096-1G>C		p.X2032_splice	ENST00000278616	NM_000051.3	2032			0.600308017988697	3	FACETS	1	0.988	1	0.724	0.667	0.781	CLONAL	1	TRUE	1	0.600308017988697	3		529	452	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267823	7267823	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1388989393	NA	P-0061272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	51	616	0	ENST00000302850.5:c.185T>C	p.Ile62Thr	p.I62T	ENST00000302850	NM_000208.2	62	aTa/aCa	2/22	0.356860253149458	2	FACETS	0.439	0.374	0.51	0.22	0.187	0.255	INDETERMINATE	1	TRUE	0	0.600308017988697	2		616	387	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396225	139396225	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	54	625	0	ENST00000277541.6:c.5613C>G	p.Cys1871Trp	p.C1871W	ENST00000277541	NM_017617.3	1871	tgC/tgG	30/34	0.387931115175528	4	FACETS	0.571	0.488	0.662	0.286	0.244	0.331	SUBCLONAL	1	TRUE	2	0.600308017988697	4		625	504	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	88	377	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.201429961667049	2		377	631	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0061273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	70	467	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.201429961667049	1	FACETS	0.681	0.592	0.777	0.681	0.592	0.777	SUBCLONAL	1	TRUE	0	0.201429961667049	1		467	918	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0061273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	85	705	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	0.832	0.734	0.938	0.832	0.734	0.938	CLONAL	1	TRUE	1	0.201429961667049	2		705	1014	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265336	152265336	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	256	505	0	ENST00000206249.3:c.790del	p.Met264CysfsTer2	p.M264Cfs*2	ENST00000206249	NM_000125.3	263	agA/ag	4/8	1	2	FACETS	0.95	0.893	1	0.95	0.893	1	CLONAL	1	TRUE	1	0.719682113146571	2		505	749	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0061284-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	201	286	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.521992050992135	2		286	700	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937164	39937164	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061284-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	190	322	0	ENST00000378444.4:c.19del	p.Leu7CysfsTer9	p.L7Cfs*9	ENST00000378444	NM_001123385.1	7	Ctg/tg	2/15	1	2	FACETS	0.957	0.887	1	0.957	0.887	1	CLONAL	1	TRUE	1	0.521992050992135	2		322	761	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440379	52440379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061284-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	205	436	1	ENST00000460680.1:c.673G>A	p.Asp225Asn	p.D225N	ENST00000460680	NM_004656.3	225	Gac/Aac	9/17	1	2	FACETS	0.944	0.877	1	0.944	0.877	1	CLONAL	1	TRUE	1	0.521992050992135	2		437	832	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579559	7579559	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061284-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	236	471	0	ENST00000269305.4:c.128del	p.Leu43Ter	p.L43*	ENST00000269305	NM_001126112.2	43	tTg/tg	4/11	0.521992050992135	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.521992050992135	1		471	614	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295346	1295346	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0061284-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	166	843	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.521992050992135	2		843	610	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971203	21971219	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATGACCTGCCAGAGAGA	ATGACCTGCCAGAGAGA	-	novel	NA	P-0061284-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	173	411	0	ENST00000304494.5:c.151-12_155del		p.X51_splice	ENST00000304494	NM_000077.4	51		2/3	0.521992050992135	1	FACETS	0.881	0.816	0.948	0.881	0.816	0.948	CLONAL	1	TRUE	0	0.521992050992135	1		411	556	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603070	48603085	+	frameshift_variant	Frame_Shift_Del	DEL	AGCAGCTGCCCAGGCA	AGCAGCTGCCCAGGCA	GC	novel	NA	P-0061284-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	319	313	1	ENST00000342988.3:c.1371_1386delinsGC	p.Ala458ArgfsTer31	p.A458Rfs*31	ENST00000342988	NM_005359.5	457	gcAGCAGCTGCCCAGGCA/gcGC	11/12	0.521992050992135	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.521992050992135	1		314	766	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521315	187521315	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	87	435	0	ENST00000441802.2:c.11840del	p.Asp3947ValfsTer36	p.D3947Vfs*36	ENST00000441802	NM_005245.3	3947	gAt/gt	22/27	0.256903637326256	4	FACETS	1	0.98	1	0.749	0.669	0.832	INDETERMINATE	1	TRUE	2	0.556575698483732	4		435	325	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271274	38271274	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	142	528	0	ENST00000425967.3:c.2434C>T	p.Pro812Ser	p.P812S	ENST00000425967	NM_001174067.1	812	Ccc/Tcc	19/19	0.556575698483732	8	FACETS	1	0.932	1	0.508	0.467	0.55	CLONAL	3	TRUE	2	0.556575698483732	8		528	447	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741988	162741988	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	156	494	0	ENST00000367921.3:c.1679G>C	p.Arg560Thr	p.R560T	ENST00000367921	NM_006182.2	560	aGg/aCg	13/18	0.520222806788309	5	FACETS	0.96	0.892	1	0.96	0.892	1	CLONAL	3	TRUE	2	0.556575698483732	5		494	357	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427981	49427982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCG	novel	NA	P-0061285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	160	467	0	ENST00000301067.7:c.10606_10608dup	p.Arg3536dup	p.R3536dup	ENST00000301067	NM_003482.3	3536	-/CGC	38/54	0.524189129256377	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.556575698483732	3		467	326	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61323047	61323047	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	10	557	0	ENST00000283752.5:c.1017G>T	p.Glu339Asp	p.E339D	ENST00000283752	NM_006919.2	339	gaG/gaT	8/8	0.556575698483732	1	FACETS	0.151	0.102	0.212	0.151	0.102	0.212	SUBCLONAL	1	TRUE	0	0.556575698483732	1		557	172	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2033013	2033013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	27	367	0	ENST00000349721.2:c.287G>A	p.Gly96Asp	p.G96D	ENST00000349721	NM_003070.3	96	gGc/gAc	3/34	0.520222806788309	5	FACETS	0.467	0.372	0.577	0.156	0.124	0.193	SUBCLONAL	1	TRUE	2	0.556575698483732	5		367	381	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223355	53223355	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	10	205	0	ENST00000375401.3:c.4004C>A	p.Pro1335His	p.P1335H	ENST00000375401	NM_004187.3	1335	cCc/cAc	23/26	0.556575698483732	3	FACETS	0.231	0.156	0.325			1	SUBCLONAL	1	TRUE	NA	0.556575698483732	3		205	199	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041895	42041900	+	frameshift_variant	Frame_Shift_Del	DEL	TCATTT	TCATTT	A	novel	NA	P-0061285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	108	441	0	ENST00000219905.7:c.6090_6095delinsA	p.Asp2030GlufsTer3	p.D2030Efs*3	ENST00000219905	NM_001164273.1	2030	gaTCATTTg/gaAg	17/24	0.556575698483732	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.556575698483732	2		441	189	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0061287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	83	304	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.347	0.307	0.391	0.347	0.307	0.391	SUBCLONAL	1	TRUE	1	0.82	2		304	583	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0061287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	171	399	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.561	0.517	0.606	0.561	0.517	0.606	SUBCLONAL	1	TRUE	1	0.82	2		399	744	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711875	89711875	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587782603	NA	P-0061287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	85	249	0	ENST00000371953.3:c.493G>A	p.Gly165Arg	p.G165R	ENST00000371953	NM_000314.4	165	Gga/Aga	6/9	1	2	FACETS	0.436	0.386	0.488	0.436	0.386	0.488	SUBCLONAL	1	TRUE	1	0.82	2		249	476	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589592	67589593	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	40	316	0	ENST00000274335.5:c.1356dup	p.Asn453Ter	p.N453*	ENST00000274335		452	tat/taTt	10/15	1	2	FACETS	0.245	0.204	0.291	0.245	0.204	0.291	SUBCLONAL	1	TRUE	1	0.82	2		316	398	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059206	27059207	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0061287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	94	300	0	ENST00000324856.7:c.1847_1848dup	p.Ser617ProfsTer3	p.S617Pfs*3	ENST00000324856	NM_006015.4	615	gcc/gCCcc	4/20	1	2	FACETS	0.474	0.423	0.527	0.474	0.423	0.527	SUBCLONAL	1	TRUE	1	0.82	2		300	484	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717695	89717711	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTGAGTTCCCTCAGC	CTTTGAGTTCCCTCAGC	-	novel	NA	P-0061287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	101	289	0	ENST00000371953.3:c.721_737del	p.Phe241ValfsTer6	p.F241Vfs*6	ENST00000371953	NM_000314.4	240	taCTTTGAGTTCCCTCAGCcg/tacg	7/9	1	2	FACETS	0.496	0.445	0.549	0.496	0.445	0.549	SUBCLONAL	1	TRUE	1	0.82	2		289	497	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954378	48954378	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1131690909	NA	P-0061287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	51	268	0	ENST00000267163.4:c.1498+1G>A		p.X500_splice	ENST00000267163	NM_000321.2	500			0.816347035459569	1	FACETS	0.22	0.187	0.255	0.22	0.187	0.255	SUBCLONAL	1	TRUE	0	0.82	1		268	334	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38785169	38785169	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	55	363	0	ENST00000348513.6:c.1104G>C	p.Glu368Asp	p.E368D	ENST00000348513	NM_003079.4	368	gaG/gaC	11/11	1	2	FACETS	0.217	0.185	0.252	0.217	0.185	0.252	SUBCLONAL	1	TRUE	1	0.82	2		363	617	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119019	70119019	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	88	532	0	ENST00000245479.2:c.591del	p.His197GlnfsTer22	p.H197Qfs*22	ENST00000245479	NM_000346.3	197	caC/ca	2/3	1	2	FACETS	0.333	0.295	0.374	0.333	0.295	0.374	SUBCLONAL	1	TRUE	1	0.82	2		532	644	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21344759	21344759	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	131	410	0	ENST00000215739.8:c.736C>A	p.Gln246Lys	p.Q246K	ENST00000215739	NM_006767.3	246	Caa/Aaa	8/21	1	2	FACETS	0.491	0.446	0.537	0.491	0.446	0.537	SUBCLONAL	1	TRUE	1	0.82	2		410	651	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589426	67589851	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCGTAATTACATAATTGCAATTTTAAAGATGTTTCCATGTCAGCTATTTTGTTAAACAATTGTTATTTGATTAAATACCTTATCCATTGAATTTATTTTAATCTTTCTAGGATCAAGTTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACACTCAGTTTCAAGAAAAAAGTCGAGAATATGATAGATTATATGAAGAATATACCCGCACATCCCAGGTGAGTTTTCTATGAAAATCAGATTAAAAAATAAGAGTTCTAAACTTTTAAAGACTAACATGGAAAAAAGAATTTAAAAGGTTGAGTTTTTACGAATGAGGTGGGGGTGAGAGCATTTATTTGTGAATCATTGTTGATTATTCTAGTGTAATATCTCTAAAGCTTTAAACCAAAAATTTTAAGTATCAG	CTCGTAATTACATAATTGCAATTTTAAAGATGTTTCCATGTCAGCTATTTTGTTAAACAATTGTTATTTGATTAAATACCTTATCCATTGAATTTATTTTAATCTTTCTAGGATCAAGTTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACACTCAGTTTCAAGAAAAAAGTCGAGAATATGATAGATTATATGAAGAATATACCCGCACATCCCAGGTGAGTTTTCTATGAAAATCAGATTAAAAAATAAGAGTTCTAAACTTTTAAAGACTAACATGGAAAAAAGAATTTAAAAGGTTGAGTTTTTACGAATGAGGTGGGGGTGAGAGCATTTATTTGTGAATCATTGTTGATTATTCTAGTGTAATATCTCTAAAGCTTTAAACCAAAAATTTTAAGTATCAG	-	novel	NA	P-0061287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	18	202	0	ENST00000274335.5:c.1300-111_1425+189del		p.X434_splice	ENST00000274335		434		10/15	1	2	FACETS	0.178	0.134	0.231	0.178	0.134	0.231	SUBCLONAL	1	TRUE	1	0.82	2		202	246	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	38	377	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.399	0.329	0.476	0.399	0.329	0.476	SUBCLONAL	1	TRUE	1	0.402893583515494	2		377	473	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346338	73346338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	48	391	0	ENST00000377767.4:c.1462G>A	p.Asp488Asn	p.D488N	ENST00000377767	NM_014953.3	488	Gat/Aat	10/21	1	2	FACETS	0.439	0.371	0.514	0.439	0.371	0.514	SUBCLONAL	1	TRUE	1	0.402893583515494	2		391	543	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023741	27023744	+	frameshift_variant	Frame_Shift_Del	DEL	GGCG	GGCG	-	novel	NA	P-0061288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	76	503	0	ENST00000324856.7:c.849_852del	p.Gly284GlufsTer78	p.G284Efs*78	ENST00000324856	NM_006015.4	283	GGCGgg/gg	1/20	1	2	FACETS	0.733	0.644	0.828	0.733	0.644	0.828	SUBCLONAL	1	TRUE	1	0.402893583515494	2		503	515	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106240	27106244	+	frameshift_variant	Frame_Shift_Del	DEL	AACAT	AACAT	-	novel	NA	P-0061288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	50	535	0	ENST00000324856.7:c.5851_5855del	p.Asn1951GlnfsTer10	p.N1951Qfs*10	ENST00000324856	NM_006015.4	1951	AACATc/c	20/20	1	2	FACETS	0.33	0.279	0.386	0.33	0.279	0.386	SUBCLONAL	1	TRUE	1	0.402893583515494	2		535	753	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573196	64573196	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	177	551	0	ENST00000312049.6:c.1096G>T	p.Glu366Ter	p.E366*	ENST00000312049	NM_130799.2	366	Gaa/Taa	8/10	0.745998823010102	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.745998823010102	1		551	287	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	118	321	0				ENST00000310581	NM_198253.2	-/1132			0.224139032776341	3	FACETS	0.928	0.841	1	0.928	0.841	1	CLONAL	2	TRUE	1	0.278501376187507	3		321	520	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0061290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	205	302	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.845	0.785	0.907	1	0.992	1	CLONAL	2	TRUE	1	0.278501376187507	2		302	871	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs371769427	NA	P-0061290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	60	298	0	ENST00000291552.4:c.101C>A	p.Ser34Tyr	p.S34Y	ENST00000291552	NM_006758.2	34	tCt/tAt	2/8	1	2	FACETS	0.713	0.614	0.821	0.713	0.614	0.821	SUBCLONAL	1	TRUE	1	0.278501376187507	2		298	604	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804382	43804382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201101813	NA	P-0061290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	84	367	0	ENST00000372470.3:c.382G>A	p.Asp128Asn	p.D128N	ENST00000372470	NM_005373.2	128	Gac/Aac	3/12	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.278501376187507	2		367	594	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028717	42028717	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	76	510	0	ENST00000219905.7:c.4255G>T	p.Gly1419Cys	p.G1419C	ENST00000219905	NM_001164273.1	1419	Ggt/Tgt	13/24	1	2	FACETS	0.74	0.648	0.838	0.74	0.648	0.838	SUBCLONAL	1	TRUE	1	0.278501376187507	2		510	738	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129142	2129142	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	85	475	0	ENST00000219476.3:c.3076T>A	p.Cys1026Ser	p.C1026S	ENST00000219476	NM_000548.3	1026	Tgt/Agt	27/42	1	2	FACETS	0.837	0.74	0.942	0.837	0.74	0.942	CLONAL	1	TRUE	1	0.278501376187507	2		475	729	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41197740	41197740	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	126	508	0	ENST00000357654.3:c.5547G>T	p.Glu1849Asp	p.E1849D	ENST00000357654	NM_007294.3	1849	gaG/gaT	23/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.278501376187507	2		508	816	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0061291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	22	665	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.247	0.191	0.313	0.247	0.191	0.313	SUBCLONAL	1	TRUE	1	0.32	2		666	556	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217852	7217855	+	frameshift_variant	Frame_Shift_Del	DEL	TTTC	TTTC	-	novel	NA	P-0061291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	41	480	0	ENST00000380728.2:c.156_159del	p.Lys53ArgfsTer9	p.K53Rfs*9	ENST00000380728		52	aaGAAA/aa	3/11	1	2	FACETS	0.345	0.286	0.411	0.345	0.286	0.411	SUBCLONAL	1	TRUE	1	0.32	2		480	743	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927381	49927381	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	38	495	0	ENST00000296474.3:c.3923A>T	p.Gln1308Leu	p.Q1308L	ENST00000296474	NM_002447.2	1308	cAg/cTg	19/20	0.114056811205478	3	FACETS	0.457	0.377	0.547	0.228	0.188	0.274	INDETERMINATE	1	TRUE	1	0.32	3		495	603	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006884	47006884	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	28	213	0	ENST00000377604.3:c.4G>A	p.Glu2Lys	p.E2K	ENST00000377604	NM_001204468.1	2	Gag/Aag	2/24	0.104622239620302	2	FACETS	0.554	0.443	0.679			1	INDETERMINATE	1	TRUE	NA	0.32	2		213	316	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0061292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	370	660	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.56976485954154	4	FACETS	0.996	0.955	1	0.996	0.955	1	CLONAL	3	TRUE	1	0.56976485954154	4		660	682	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577095	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519984	NA	P-0061292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	288	423	0	ENST00000269305.4:c.843C>G	p.Asp281Glu	p.D281E	ENST00000269305	NM_001126112.2	281	gaC/gaG	8/11	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	2	TRUE	NA	0.56976485954154	2		423	475	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514608	103514608	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370885325	NA	P-0061292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	118	446	0	ENST00000355739.4:c.1109G>A	p.Arg370His	p.R370H	ENST00000355739	NM_000123.3	370	cGt/cAt	8/15	0.56976485954154	2	FACETS	0.822	0.745	0.902	0.411	0.372	0.451	CLONAL	1	TRUE	0	0.56976485954154	2		446	504	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423667	47423668	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCCGGCCG	novel	NA	P-0061292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	140	403	0	ENST00000404338.3:c.1738_1745dup	p.Asp583GlyfsTer48	p.D583Gfs*48	ENST00000404338	NM_004491.4	579	atc/aTCCGGCCGtc	1/6	0.56976485954154	4	FACETS	0.981	0.895	1	0.327	0.298	0.358	CLONAL	1	TRUE	1	0.56976485954154	4		403	786	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061293-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	47	321	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.898	0.764	1	0.898	0.764	1	CLONAL	1	TRUE	1	0.422234465338006	2		321	248	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0061293-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	117	769	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.422234465338006	1	FACETS	0.972	0.882	1	0.972	0.882	1	CLONAL	1	TRUE	0	0.422234465338006	1		770	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061293-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	114	552	0	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	0.422234465338006	1	FACETS	0.993	0.901	1	0.993	0.901	1	CLONAL	1	TRUE	0	0.422234465338006	1		552	429	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338701	70338701	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs769202858	NA	P-0061293-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	55	184	0	ENST00000374080.3:c.97G>A	p.Glu33Lys	p.E33K	ENST00000374080		33	Gag/Aag	1/45	1	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.422234465338006	1		184	161	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426235	49426235	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061293-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	128	594	0	ENST00000301067.7:c.12253C>T	p.Gln4085Ter	p.Q4085*	ENST00000301067	NM_003482.3	4085	Cag/Tag	39/54	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.422234465338006	2		594	568	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426916	49426916	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061293-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	110	585	0	ENST00000301067.7:c.11572C>T	p.Gln3858Ter	p.Q3858*	ENST00000301067	NM_003482.3	3858	Cag/Tag	39/54	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.422234465338006	2		585	459	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56363673	56363673	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061293-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	93	336	0	ENST00000348428.3:c.452C>G	p.Thr151Ser	p.T151S	ENST00000348428	NM_006785.3	151	aCt/aGt	3/17	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.422234465338006	2		336	427	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446208	29446208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061293-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	72	549	0	ENST00000544604.2:c.2039G>A	p.Ser680Asn	p.S680N	ENST00000544604	NM_001206998.1	680	aGc/aAc	8/9	0.422234465338006	1	FACETS	0.767	0.674	0.865	0.767	0.674	0.865	SUBCLONAL	1	TRUE	0	0.422234465338006	1		549	351	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	240569	240569	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061293-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	13	51	0	ENST00000264932.6:c.1529A>G	p.Glu510Gly	p.E510G	ENST00000264932	NM_004168.2	510	gAa/gGa	11/15	1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	1	0.422234465338006	2		51	48	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577077	7577079	+	missense_variant	Missense_Mutation	TNP	CTC	CTC	TTT	novel	NA	P-0061293-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	115	583	0	ENST00000269305.4:c.859_861delinsAAA	p.Glu287Lys	p.E287K	ENST00000269305	NM_001126112.2	287	GAG/AAA	8/11	0.422234465338006	1	FACETS	0.957	0.868	1	0.957	0.868	1	CLONAL	1	TRUE	0	0.422234465338006	1		583	449	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	165	321	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.839	0.776	0.905	0.839	0.776	0.905	CLONAL	1	TRUE	1	0.729374209240446	2		321	539	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0061293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	303	769	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.729374209240446	1	FACETS	0.996	0.951	1	0.996	0.951	1	CLONAL	1	TRUE	0	0.729374209240446	1		770	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	288	552	0	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	0.729374209240446	1	FACETS	0.995	0.95	1	0.995	0.95	1	CLONAL	1	TRUE	0	0.729374209240446	1		552	504	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338701	70338701	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs769202858	NA	P-0061293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	232	184	0	ENST00000374080.3:c.97G>A	p.Glu33Lys	p.E33K	ENST00000374080		33	Gag/Aag	1/45	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.729374209240446	1		184	321	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426235	49426235	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	338	594	0	ENST00000301067.7:c.12253C>T	p.Gln4085Ter	p.Q4085*	ENST00000301067	NM_003482.3	4085	Cag/Tag	39/54	1	2	FACETS	0.936	0.887	0.986	0.936	0.887	0.986	CLONAL	1	TRUE	1	0.729374209240446	2		594	990	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426916	49426916	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	370	585	0	ENST00000301067.7:c.11572C>T	p.Gln3858Ter	p.Q3858*	ENST00000301067	NM_003482.3	3858	Cag/Tag	39/54	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.729374209240446	2		585	991	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56363673	56363673	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	158	336	0	ENST00000348428.3:c.452C>G	p.Thr151Ser	p.T151S	ENST00000348428	NM_006785.3	151	aCt/aGt	3/17	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.729374209240446	2		336	356	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446208	29446208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	272	549	0	ENST00000544604.2:c.2039G>A	p.Ser680Asn	p.S680N	ENST00000544604	NM_001206998.1	680	aGc/aAc	8/9	0.208387537092105	1	FACETS	0.673	0.635	0.711	0.673	0.635	0.711	INDETERMINATE	1	TRUE	0	0.729374209240446	1		549	704	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	240569	240569	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	32	51	0	ENST00000264932.6:c.1529A>G	p.Glu510Gly	p.E510G	ENST00000264932	NM_004168.2	510	gAa/gGa	11/15	1	2	FACETS	0.836	0.695	0.985	0.836	0.695	0.985	CLONAL	1	TRUE	1	0.729374209240446	2		51	105	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577077	7577079	+	missense_variant	Missense_Mutation	TNP	CTC	CTC	TTT	novel	NA	P-0061293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	292	583	0	ENST00000269305.4:c.859_861delinsAAA	p.Glu287Lys	p.E287K	ENST00000269305	NM_001126112.2	287	GAG/AAA	8/11	0.729374209240446	1	FACETS	0.949	0.904	0.993	0.949	0.904	0.993	CLONAL	1	TRUE	0	0.729374209240446	1		583	536	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0061294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	58	176	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.896	0.771	1	0.896	0.771	1	CLONAL	1	TRUE	1	0.276062031021113	2		176	469	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261121	16261121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202070337	NA	P-0061294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	75	487	0	ENST00000375759.3:c.8386C>T	p.Arg2796Cys	p.R2796C	ENST00000375759	NM_015001.2	2796	Cgt/Tgt	11/15	1	2	FACETS	0.875	0.767	0.991	0.875	0.767	0.991	CLONAL	1	TRUE	1	0.276062031021113	2		487	621	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986542	36986543	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0061294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	68	483	0	ENST00000354822.5:c.1146dup	p.Ser383LeufsTer56	p.S383Lfs*56	ENST00000354822	NM_001079668.2	382	-/C	3/3	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.276062031021113	2		483	490	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964348	55964348	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	54	301	0	ENST00000263923.4:c.2465A>G	p.Tyr822Cys	p.Y822C	ENST00000263923	NM_002253.2	822	tAt/tGt	17/30	1	2	FACETS	0.786	0.672	0.91	0.786	0.672	0.91	CLONAL	1	TRUE	1	0.276062031021113	2		301	498	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430757	47430758	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0061294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	64	422	0	ENST00000377045.4:c.1722_1723delinsAA	p.Pro575Thr	p.P575T	ENST00000377045	NM_001654.4	574	ctCCcc/ctAAcc	16/16	1	2	FACETS	0.885	0.767	1	0.885	0.767	1	CLONAL	1	TRUE	1	0.276062031021113	2		422	524	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937455	76937456	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0061294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	78	387	0	ENST00000373344.5:c.3292_3293delinsCT	p.Gly1098Leu	p.G1098L	ENST00000373344	NM_000489.3	1098	GGa/CTa	9/35	1	2	FACETS	0.864	0.759	0.977	0.864	0.759	0.977	CLONAL	1	TRUE	1	0.276062031021113	2		387	654	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480538	123480538	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	62	375	0	ENST00000371139.4:c.46G>T	p.Gly16Cys	p.G16C	ENST00000371139	NM_001114937.2	16	Ggc/Tgc	1/4	1	2	FACETS	0.897	0.776	1	0.897	0.776	1	CLONAL	1	TRUE	1	0.276062031021113	2		375	501	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987030	36987031	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	G	novel	NA	P-0061294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	32	315	0	ENST00000354822.5:c.658_659delinsC	p.Glu220ArgfsTer8	p.E220Rfs*8	ENST00000354822	NM_001079668.2	220	GAg/Cg	3/3	1	2	FACETS	0.696	0.566	0.843	0.696	0.566	0.843	SUBCLONAL	1	TRUE	1	0.276062031021113	2		315	333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0061325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	57	453	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.831	0.717	0.954	1	0.973	1	CLONAL	2	TRUE	1	0.2	2		453	343	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0061325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	124	407	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.229784432142581	3	FACETS	0.963	0.877	1	1	0.985	1	CLONAL	3	TRUE	1	0.2	3		407	472	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0061325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	35	245	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	0.119778901847287	4	FACETS	1	0.924	1	0.418	0.343	0.501	INDETERMINATE	1	TRUE	1	0.2	4		245	335	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885238	111885238	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	30	623	0	ENST00000341259.2:c.1126C>T	p.Gln376Ter	p.Q376*	ENST00000341259	NM_005475.2	376	Cag/Tag	6/8	1	2	FACETS	0.719	0.579	0.878	0.719	0.579	0.878	SUBCLONAL	1	TRUE	1	0.2	2		623	417	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572198	64572198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	24	665	1	ENST00000312049.6:c.1441C>T	p.Arg481Trp	p.R481W	ENST00000312049	NM_130799.2	481	Cgg/Tgg	10/10	1	2	FACETS	0.633	0.496	0.792	0.633	0.496	0.792	SUBCLONAL	1	TRUE	1	0.2	2		666	379	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620466	52620466	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	35	449	0	ENST00000394830.3:c.3287C>G	p.Ala1096Gly	p.A1096G	ENST00000394830	NM_018313.4	1096	gCt/gGt	21/30	1	2	FACETS	0.808	0.663	0.972	0.808	0.663	0.972	CLONAL	1	TRUE	1	0.2	2		449	433	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0061326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	38	544	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.267940598798996	4	FACETS	0.949	0.786	1	0.316	0.262	0.377	CLONAL	1	TRUE	1	0.267940598798996	4		544	379	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0061326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	68	363	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.267940598798996	2		363	499	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639767	3639767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754761366	NA	P-0061326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	84	604	0	ENST00000294008.3:c.3872C>T	p.Thr1291Met	p.T1291M	ENST00000294008	NM_032444.2	1291	aCg/aTg	12/15	1	2	FACETS	0.887	0.783	0.998	0.887	0.783	0.998	CLONAL	1	TRUE	1	0.267940598798996	2		604	707	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97873833	97873833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200719554	NA	P-0061326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	117	580	3	ENST00000289081.3:c.1241C>T	p.Ser414Leu	p.S414L	ENST00000289081	NM_000136.2	414	tCg/tTg	13/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.267940598798996	2		583	682	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489589	40489664	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTCACTCACGATGCTCTGGTTGGAAACCAAAACAAAGTCAGAAAACATTTCCTCAGACTGTCTCTAACCACATTC	GCTCACTCACGATGCTCTGGTTGGAAACCAAAACAAAGTCAGAAAACATTTCCTCAGACTGTCTCTAACCACATTC	-	novel	NA	P-0061326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	80	508	0	ENST00000264657.5:c.646-60_661del		p.X216_splice	ENST00000264657	NM_139276.2	216		8/24	1	2	FACETS	0.979	0.863	1	0.979	0.863	1	CLONAL	1	TRUE	1	0.267940598798996	2		508	610	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176563009	176563009	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1159878880	NA	P-0061326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	74	398	0	ENST00000439151.2:c.905C>G	p.Ser302Cys	p.S302C	ENST00000439151	NM_022455.4	302	tCt/tGt	2/23	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.267940598798996	2		398	535	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072547	5072547	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	58	410	0	ENST00000381652.3:c.1697A>G	p.Glu566Gly	p.E566G	ENST00000381652	NM_004972.3	566	gAa/gGa	13/25	1	2	FACETS	0.739	0.635	0.852	0.739	0.635	0.852	SUBCLONAL	1	TRUE	1	0.267940598798996	2		410	586	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	262	321	0				ENST00000310581	NM_198253.2	-/1132			0.669249348062978	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.689002901227323	4		321	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0061327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	539	817	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.689002901227323	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.689002901227323	3		817	676	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0061327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	208	441	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.689002901227323	3	FACETS	1	0.982	1	0.577	0.537	0.617	CLONAL	1	TRUE	1	0.689002901227323	3		441	704	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729163	66729163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516792	NA	P-0061327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	319	534	0	ENST00000307102.5:c.371C>T	p.Pro124Leu	p.P124L	ENST00000307102	NM_002755.3	124	cCg/cTg	3/11	0.689002901227323	3	FACETS	0.98	0.934	1	0.98	0.934	1	CLONAL	2	TRUE	1	0.689002901227323	3		534	635	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814713	139814713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753016580	NA	P-0061327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	350	475	1	ENST00000247668.2:c.706G>A	p.Glu236Lys	p.E236K	ENST00000247668	NM_021138.3	236	Gag/Aag	8/11	0.689002901227323	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.689002901227323	2		476	467	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121873	2121873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746315218	NA	P-0061327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	156	450	0	ENST00000219476.3:c.2035G>A	p.Val679Met	p.V679M	ENST00000219476	NM_000548.3	679	Gtg/Atg	19/42	0.676453497777993	4	FACETS	1	0.976	1	0.388	0.356	0.421	CLONAL	1	TRUE	1	0.689002901227323	4		450	657	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856313	111856313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747913408	NA	P-0061327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	132	478	0	ENST00000341259.2:c.364G>A	p.Glu122Lys	p.E122K	ENST00000341259	NM_005475.2	122	Gag/Aag	2/8	0.689002901227323	3	FACETS	1	0.939	1	0.517	0.472	0.564	CLONAL	1	TRUE	1	0.689002901227323	3		478	498	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023733	27023733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	356	504	0	ENST00000324856.7:c.839C>T	p.Ser280Phe	p.S280F	ENST00000324856	NM_006015.4	280	tCc/tTc	1/20	0.689002901227323	3	FACETS	0.969	0.926	1	0.969	0.926	1	CLONAL	2	TRUE	1	0.689002901227323	3		504	717	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56477631	56477631	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	338	395	0	ENST00000267101.3:c.179T>G	p.Met60Arg	p.M60R	ENST00000267101	NM_001982.3	60	aTg/aGg	2/28	0.689002901227323	3	FACETS	0.981	0.937	1	0.981	0.937	1	CLONAL	2	TRUE	1	0.689002901227323	3		395	672	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971099	21971099	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	311	492	0	ENST00000304494.5:c.259del	p.Arg87GlyfsTer59	p.R87Gfs*59	ENST00000304494	NM_000077.4	87	Cgg/gg	2/3	0.689002901227323	2	FACETS	0.992	0.954	1	0.992	0.954	1	CLONAL	2	TRUE	0	0.689002901227323	2		492	455	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035075	37035075	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs587779008	NA	P-0061327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	380	456	0	ENST00000231790.2:c.37G>T	p.Glu13Ter	p.E13*	ENST00000231790	NM_000249.3	13	Gag/Tag	1/19	0.689002901227323	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.689002901227323	3		456	736	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13949314	13949314	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	218	315	0	ENST00000405192.2:c.814G>C	p.Glu272Gln	p.E272Q	ENST00000405192	NM_001163147.1	272	Gaa/Caa	9/12	0.669249348062978	4	FACETS	0.851	0.796	0.907	0.851	0.796	0.907	CLONAL	2	TRUE	2	0.689002901227323	4		315	628	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162774	47162774	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061331-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	57	414	0	ENST00000409792.3:c.3352G>T	p.Glu1118Ter	p.E1118*	ENST00000409792	NM_014159.6	1118	Gaa/Taa	3/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.14	2		414	674	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713211	30713223	+	protein_altering_variant	In_Frame_Del	DEL	CCATATCTGTCAT	CCATATCTGTCAT	A	novel	NA	P-0061331-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	41	539	0	ENST00000295754.5:c.536_548delinsA	p.Ala179_Ile183delinsAsp	p.A179_I183delinsD	ENST00000295754	NM_003242.5	179	gCCATATCTGTCATc/gAc	4/7	1	2	FACETS	0.811	0.674	0.965	0.811	0.674	0.965	CLONAL	1	TRUE	1	0.14	2		539	722	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587781702	NA	P-0061334-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	173	727	1	ENST00000269305.4:c.920-1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.294135789011506	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.29	2		728	572	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733560	85733560	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061334-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	40	302	0	ENST00000370580.1:c.452C>G	p.Thr151Ser	p.T151S	ENST00000370580	NM_003921.4	151	aCt/aGt	3/3	0.233261197799225	4	FACETS	0.634	0.526	0.755	0.211	0.175	0.252	SUBCLONAL	1	TRUE	1	0.29	4		302	561	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163325200	163325200	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061334-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	23	218	0	ENST00000271452.3:c.1336G>T	p.Ala446Ser	p.A446S	ENST00000271452	NM_145697.2	446	Gct/Tct	14/14	0.276422036298674	3	FACETS	0.599	0.468	0.752	0.3	0.234	0.376	SUBCLONAL	1	TRUE	1	0.29	3		218	303	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332756	70332756	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061334-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	70	272	0	ENST00000373644.4:c.661A>G	p.Thr221Ala	p.T221A	ENST00000373644	NM_030625.2	221	Aca/Gca	2/12	0.29516241264718	2	FACETS	1	0.934	1	0.552	0.483	0.627	CLONAL	1	TRUE	0	0.29	2		272	437	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857101	9857101	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061334-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	86	318	0	ENST00000330684.3:c.4300A>G	p.Asn1434Asp	p.N1434D	ENST00000330684	NM_001134407.1	1434	Aat/Gat	13/13	0.29516241264718	3	FACETS	1	0.973	1	0.667	0.592	0.747	CLONAL	1	TRUE	1	0.29	3		318	509	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857268	9857268	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061334-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	49	398	0	ENST00000330684.3:c.4133T>G	p.Val1378Gly	p.V1378G	ENST00000330684	NM_001134407.1	1378	gTt/gGt	13/13	0.29516241264718	3	FACETS	0.66	0.559	0.772	0.33	0.279	0.386	SUBCLONAL	1	TRUE	1	0.29	3		398	586	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117632246	117632246	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061334-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	36	231	0	ENST00000368508.3:c.6170T>G	p.Val2057Gly	p.V2057G	ENST00000368508	NM_002944.2	2057	gTa/gGa	39/43	1	2	FACETS	0.686	0.565	0.821	0.686	0.565	0.821	SUBCLONAL	1	TRUE	1	0.29	2		231	362	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513316	106513317	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061334-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	30	270	0	ENST00000359195.3:c.2221dup	p.Met741AsnfsTer8	p.M741Nfs*8	ENST00000359195	NM_002649.2	740	-/A	4/11	0.192258359747121	5	FACETS	0.505	0.406	0.618	0.168	0.135	0.206	SUBCLONAL	1	TRUE	2	0.29	5		270	588	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27192582	27192609	+	frameshift_variant	Frame_Shift_Del	DEL	CATCCTGGACCTGTGAGACGCTTCACAA	CATCCTGGACCTGTGAGACGCTTCACAA	-	novel	NA	P-0061334-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	48	268	0	ENST00000380036.4:c.1587_1614del	p.His529GlnfsTer12	p.H529Qfs*12	ENST00000380036	NM_000459.3	529	CATCCTGGACCTGTGAGACGCTTCACAAca/ca	11/23	1	2	FACETS	0.709	0.6	0.829	0.709	0.6	0.829	SUBCLONAL	1	TRUE	1	0.29	2		268	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579366	7579366	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs770776262	NA	P-0061335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	360	456	0	ENST00000269305.4:c.321C>A	p.Tyr107Ter	p.Y107*	ENST00000269305	NM_001126112.2	107	taC/taA	4/11	0.734060226890009	1	FACETS	0.987	0.949	1	0.987	0.949	1	CLONAL	1	TRUE	0	0.764634234734028	1		456	589	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098816	178098816	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	342	366	0	ENST00000397062.3:c.229G>C	p.Asp77His	p.D77H	ENST00000397062	NM_006164.4	77	Gat/Cat	2/5	0.301928269087294	1	FACETS	0.719	0.685	0.754	0.719	0.685	0.754	INDETERMINATE	1	TRUE	0	0.764634234734028	1		366	768	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435625	110435625	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	263	402	0	ENST00000375856.3:c.2776G>T	p.Glu926Ter	p.E926*	ENST00000375856	NM_003749.2	926	Gag/Tag	1/2	0.764634234734028	1	FACETS	0.926	0.881	0.97	0.926	0.881	0.97	CLONAL	1	TRUE	0	0.764634234734028	1		402	459	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845640	72845640	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148354034	NA	P-0061335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	313	436	0	ENST00000268489.5:c.3700G>A	p.Asp1234Asn	p.D1234N	ENST00000268489	NM_006885.3	1234	Gat/Aat	7/10	1	2	FACETS	0.944	0.894	0.995	0.944	0.894	0.995	CLONAL	1	TRUE	1	0.764634234734028	2		436	867	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466522	120466522	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	289	413	0	ENST00000256646.2:c.4597G>T	p.Asp1533Tyr	p.D1533Y	ENST00000256646	NM_024408.3	1533	Gac/Tac	26/34	1	2	FACETS	0.905	0.855	0.957	0.905	0.855	0.957	CLONAL	1	TRUE	1	0.764634234734028	2		413	835	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433896	49433896	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	403	572	0	ENST00000301067.7:c.7657C>T	p.Gln2553Ter	p.Q2553*	ENST00000301067	NM_003482.3	2553	Cag/Tag	31/54	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.764634234734028	2		572	1004	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196433	106196433	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs368705448	NA	P-0061335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	316	404	0	ENST00000380013.4:c.4766A>G	p.Tyr1589Cys	p.Y1589C	ENST00000380013	NM_001127208.2	1589	tAt/tGt	11/11	0.764634234734028	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.764634234734028	1		404	493	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361126	66361126	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	134	322	0	ENST00000273854.3:c.1046del	p.Pro349HisfsTer73	p.P349Hfs*73	ENST00000273854	NM_004439.5	349	cCa/ca	4/18	0.301928269087294	1	FACETS	0.489	0.447	0.531	0.489	0.447	0.531	INDETERMINATE	1	TRUE	0	0.764634234734028	1		322	443	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192445	138192445	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	305	349	0	ENST00000237289.4:c.81A>T	p.Glu27Asp	p.E27D	ENST00000237289	NM_001270507.1	27	gaA/gaT	2/9	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.764634234734028	2		349	728	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911588	39911588	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	230	360	0	ENST00000378444.4:c.5042G>C	p.Arg1681Pro	p.R1681P	ENST00000378444	NM_001123385.1	1681	cGc/cCc	15/15	1	2	FACETS	0.836	0.782	0.89	0.836	0.782	0.89	CLONAL	1	TRUE	1	0.764634234734028	2		360	720	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429330	47429330	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	234	452	0	ENST00000377045.4:c.1458C>A	p.Tyr486Ter	p.Y486*	ENST00000377045	NM_001654.4	486	taC/taA	14/16	1	2	FACETS	0.832	0.779	0.886	0.832	0.779	0.886	CLONAL	1	TRUE	1	0.764634234734028	2		452	736	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181324	123181324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1396727782	NA	P-0061335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	46	225	0	ENST00000218089.9:c.788G>A	p.Arg263Lys	p.R263K	ENST00000218089	NM_001042749.1	263	aGg/aAg	9/35	0.391727679748725	1	FACETS	0.387	0.33	0.448	0.387	0.33	0.448	INDETERMINATE	1	TRUE	0	0.764634234734028	1		225	192	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258323	16258323	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	323	419	0	ENST00000375759.3:c.5588A>G	p.Gln1863Arg	p.Q1863R	ENST00000375759	NM_015001.2	1863	cAg/cGg	11/15	0.290459791540224	2	FACETS	0.922	0.875	0.97	1	0.994	1	CLONAL	3	TRUE	0	0.290459791540224	2		419	804	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258944	16258944	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	205	524	0	ENST00000375759.3:c.6215del	p.Asn2072ThrfsTer14	p.N2072Tfs*14	ENST00000375759	NM_015001.2	2070	gAa/ga	11/15	0.290459791540224	2	FACETS	0.769	0.714	0.826	0.769	0.714	0.826	SUBCLONAL	2	TRUE	0	0.290459791540224	2		524	918	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023530	27023530	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	570	385	0	ENST00000324856.7:c.636C>A	p.Tyr212Ter	p.Y212*	ENST00000324856	NM_006015.4	212	taC/taA	1/20	0.290459791540224	2	FACETS	0.992	0.966	1	1	0.998	1	CLONAL	5	TRUE	0	0.290459791540224	2		385	791	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28595739	28595739	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1038449460	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	321	408	2	ENST00000253063.3:c.136G>A	p.Ala46Thr	p.A46T	ENST00000253063	NM_031459.4	46	Gcc/Acc	2/10	0.290459791540224	2	FACETS	0.866	0.821	0.911	1	0.993	1	CLONAL	3	TRUE	0	0.290459791540224	2		410	851	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263192	115263192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	271	329	0	ENST00000438362.2:c.2158C>T	p.Arg720Cys	p.R720C	ENST00000438362	NM_001242891.1	720	Cgc/Tgc	17/20	0.290459791540224	2	FACETS	0.87	0.821	0.92	1	0.992	1	CLONAL	3	TRUE	0	0.290459791540224	2		329	715	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	132	342	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	1	0.979	1	1	0.992	1	CLONAL	2	TRUE	1	0.290459791540224	2		342	376	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720649	89720649	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs587782455	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	55	137	0	ENST00000371953.3:c.802-2A>G		p.X268_splice	ENST00000371953	NM_000314.4	268			1	2	FACETS	1	0.937	1	1	0.98	1	CLONAL	2	TRUE	1	0.290459791540224	2		137	168	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380338	14380339	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCCCACGCC	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	472	422	0	ENST00000256196.4:c.70_78dup	p.Gly24_Gly26dup	p.G24_G26dup	ENST00000256196		24	-/GGCGTGGGC	1/6	0.290459791540224	2	FACETS	1	0.988	1	1	0.998	1	CLONAL	4	TRUE	0	0.290459791540224	2		422	775	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	333	887	0	ENST00000227507.2:c.859C>T	p.Pro287Ser	p.P287S	ENST00000227507	NM_053056.2	287	Ccc/Tcc	5/5	1	2	FACETS	0.914	0.868	0.961	1	0.997	1	CLONAL	3	TRUE	1	0.290459791540224	2		887	836	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77930402	77930404	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	45	407	0	ENST00000361507.4:c.1945_1947del	p.Glu649del	p.E649del	ENST00000361507	NM_080491.2	649	GAG/-	10/10	1	2	FACETS	0.422	0.353	0.498	0.422	0.353	0.498	SUBCLONAL	1	TRUE	1	0.290459791540224	2		407	735	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196880	108196880	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	36	292	0	ENST00000278616.4:c.6908del	p.Lys2303ArgfsTer7	p.K2303Rfs*7	ENST00000278616	NM_000051.3	2301	gcA/gc	47/63	1	2	FACETS	0.462	0.379	0.555	0.462	0.379	0.555	SUBCLONAL	1	TRUE	1	0.290459791540224	2		292	537	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374217	118374217	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	196	413	0	ENST00000534358.1:c.7610A>G	p.Gln2537Arg	p.Q2537R	ENST00000534358	NM_005933.3	2537	cAa/cGa	27/36	1	2	FACETS	0.803	0.745	0.864	1	0.992	1	CLONAL	2	TRUE	1	0.290459791540224	2		413	840	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	218	434	1	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	0.928	0.865	0.992	1	0.994	1	CLONAL	2	TRUE	1	0.290459791540224	2		435	809	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022882	12022882	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	51	608	0	ENST00000396373.4:c.988A>G	p.Met330Val	p.M330V	ENST00000396373	NM_001987.4	330	Atg/Gtg	5/8	1	2	FACETS	0.354	0.3	0.415	0.354	0.3	0.415	SUBCLONAL	1	TRUE	1	0.290459791540224	2		608	991	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434982	49434983	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	275	497	0	ENST00000301067.7:c.6570dup	p.Thr2191HisfsTer11	p.T2191Hfs*11	ENST00000301067	NM_003482.3	2190	-/C	31/54	0.136843381332168	3	FACETS	0.862	0.811	0.913	1	0.991	1	INDETERMINATE	3	TRUE	1	0.290459791540224	3		497	839	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445437	49445438	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	423	584	0	ENST00000301067.7:c.2027_2028dup	p.Glu677ArgfsTer254	p.E677Rfs*254	ENST00000301067	NM_003482.3	676	-/AG	10/54	0.136843381332168	3	FACETS	0.956	0.912	1	1	0.995	1	INDETERMINATE	3	TRUE	1	0.290459791540224	3		584	1163	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115425	115115425	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	55	337	0	ENST00000257566.3:c.901A>G	p.Lys301Glu	p.K301E	ENST00000257566	NM_016569.3	301	Aaa/Gaa	5/8	1	2	FACETS	0.75	0.642	0.868	0.75	0.642	0.868	SUBCLONAL	1	TRUE	1	0.290459791540224	2		337	505	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893614	28893614	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs895427992	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	39	304	0	ENST00000282397.4:c.3232A>G	p.Thr1078Ala	p.T1078A	ENST00000282397	NM_002019.4	1078	Acc/Gcc	24/30	1	2	FACETS	0.527	0.436	0.628	0.527	0.436	0.628	SUBCLONAL	1	TRUE	1	0.290459791540224	2		304	510	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28979919	28979919	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	20	235	0	ENST00000282397.4:c.1549A>G	p.Lys517Glu	p.K517E	ENST00000282397	NM_002019.4	517	Aag/Gag	11/30	1	2	FACETS	0.437	0.334	0.558	0.437	0.334	0.558	SUBCLONAL	1	TRUE	1	0.290459791540224	2		235	315	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281951	49281951	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	28	405	0	ENST00000282018.3:c.1001del	p.Phe334SerfsTer7	p.F334Sfs*7	ENST00000282018	NM_020377.2	333	gTt/gt	1/1	1	2	FACETS	0.344	0.274	0.425	0.344	0.274	0.425	SUBCLONAL	1	TRUE	1	0.290459791540224	2		405	560	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590575	95590575	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	183	293	0	ENST00000393063.1:c.1334T>A	p.Ile445Asn	p.I445N	ENST00000393063	NM_030621.3	445	aTt/aAt	9/28	1	2	FACETS	0.884	0.824	0.946	1	0.994	1	CLONAL	3	TRUE	1	0.290459791540224	2		293	475	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007619	45007619	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs111482205	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	25	341	0	ENST00000558401.1:c.68-2A>G		p.X23_splice	ENST00000558401	NM_004048.2	23			1	2	FACETS	0.26	0.204	0.325	0.26	0.204	0.325	SUBCLONAL	1	TRUE	1	0.290459791540224	2		341	662	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	338189	338189	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs34015754	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	290	439	0	ENST00000262320.3:c.2522G>A	p.Arg841Gln	p.R841Q	ENST00000262320	NM_003502.3	841	cGa/cAa	11/11	1	2	FACETS	0.866	0.818	0.914	1	0.996	1	CLONAL	3	TRUE	1	0.290459791540224	2		439	769	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226155	2226155	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	112	447	0	ENST00000326181.6:c.1852A>C	p.Ser618Arg	p.S618R	ENST00000326181	NM_032271.2	618	Agt/Cgt	19/21	1	2	FACETS	0.947	0.852	1	0.947	0.852	1	CLONAL	1	TRUE	1	0.290459791540224	2		447	814	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656674	3656674	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778738306	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	45	382	0	ENST00000294008.3:c.561G>T	p.Gln187His	p.Q187H	ENST00000294008	NM_032444.2	187	caG/caT	3/15	1	2	FACETS	0.417	0.349	0.492	0.417	0.349	0.492	SUBCLONAL	1	TRUE	1	0.290459791540224	2		382	743	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829773	72829773	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	61	372	0	ENST00000268489.5:c.6808G>A	p.Asp2270Asn	p.D2270N	ENST00000268489	NM_006885.3	2270	Gat/Aat	9/10	1	2	FACETS	0.612	0.527	0.705	0.612	0.527	0.705	SUBCLONAL	1	TRUE	1	0.290459791540224	2		372	686	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831357	72831358	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTG	rs34918837	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	171	462	1	ENST00000268489.5:c.5221_5223dup	p.Gln1741dup	p.Q1741dup	ENST00000268489	NM_006885.3	1741	-/CAA	9/10	1	2	FACETS	0.794	0.732	0.859	1	0.99	1	SUBCLONAL	2	TRUE	1	0.290459791540224	2		463	741	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	60	540	2	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.487	0.418	0.562	0.487	0.418	0.562	SUBCLONAL	1	TRUE	1	0.290459791540224	2		542	849	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979987	7979987	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746723399	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	70	416	2	ENST00000319144.4:c.1350del	p.Leu451SerfsTer16	p.L451Sfs*16	ENST00000319144	NM_001139.2	450	ggG/gg	10/15	1	2	FACETS	0.61	0.531	0.696	0.61	0.531	0.696	SUBCLONAL	1	TRUE	1	0.290459791540224	2		418	790	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243549	41243549	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397509125	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	268	394	0	ENST00000357654.3:c.3999del	p.Gly1334ValfsTer2	p.G1334Vfs*2	ENST00000357654	NM_007294.3	1333	gtT/gt	10/23	1	2	FACETS	0.856	0.807	0.905	1	0.996	1	CLONAL	3	TRUE	1	0.290459791540224	2		394	719	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	308	432	0	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	0.966	0.916	1	1	0.997	1	CLONAL	3	TRUE	1	0.290459791540224	2		432	732	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222906	5222906	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs915133073	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	416	457	1	ENST00000357368.4:c.2897C>T	p.Thr966Met	p.T966M	ENST00000357368	NM_002850.3	966	aCg/aTg	18/38	0.290459791540224	2	FACETS	0.915	0.884	0.946	1	0.997	1	CLONAL	5	TRUE	0	0.290459791540224	2		458	626	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229037	36229037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	326	504	2	ENST00000222270.7:c.7817G>A	p.Gly2606Asp	p.G2606D	ENST00000222270	NM_014727.1	2606	gGc/gAc	36/37	1	2	FACETS	0.851	0.807	0.896	1	0.997	1	CLONAL	3	TRUE	1	0.290459791540224	2		506	879	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753149	42753151	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs199960550	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	328	600	7	ENST00000222329.4:c.1113_1115del	p.Ser373del	p.S373del	ENST00000222329	NM_006494.2	371	tcTTCc/tcc	4/4	1	2	FACETS	1	0.98	1	1	0.996	1	CLONAL	2	TRUE	1	0.290459791540224	2		607	1054	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46588037	46588037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780349023	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	61	434	1	ENST00000263734.3:c.587C>T	p.Thr196Met	p.T196M	ENST00000263734	NM_001430.4	196	aCg/aTg	6/16	1	2	FACETS	0.478	0.411	0.552	0.478	0.411	0.552	SUBCLONAL	1	TRUE	1	0.290459791540224	2		435	878	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	273	473	1	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	1	2	FACETS	1	0.985	1	1	0.996	1	CLONAL	2	TRUE	1	0.290459791540224	2		474	832	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523277	9523277	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	48	345	0	ENST00000353224.5:c.1960A>G	p.Arg654Gly	p.R654G	ENST00000353224	NM_177990.2	654	Agg/Ggg	9/10	1	2	FACETS	0.49	0.414	0.575	0.49	0.414	0.575	SUBCLONAL	1	TRUE	1	0.290459791540224	2		345	674	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742632	39742632	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	88	332	0	ENST00000361337.2:c.1478del	p.Lys493ArgfsTer33	p.K493Rfs*33	ENST00000361337	NM_003286.2	492	gAa/ga	15/21	1	2	FACETS	0.906	0.803	1	0.906	0.803	1	CLONAL	1	TRUE	1	0.290459791540224	2		332	669	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29115401	29115401	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs775134484	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	32	187	0	ENST00000328354.6:c.665T>C	p.Met222Thr	p.M222T	ENST00000328354	NM_007194.3	222	aTg/aCg	5/15	1	2	FACETS	0.571	0.463	0.692	0.571	0.463	0.692	SUBCLONAL	1	TRUE	1	0.290459791540224	2		187	386	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566522	41566522	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	51	301	0	ENST00000263253.7:c.4399T>C	p.Tyr1467His	p.Y1467H	ENST00000263253	NM_001429.3	1467	Tac/Cac	27/31	1	2	FACETS	0.516	0.438	0.603	0.516	0.438	0.603	SUBCLONAL	1	TRUE	1	0.290459791540224	2		301	680	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442032	52442032	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	83	378	0	ENST00000460680.1:c.317T>C	p.Val106Ala	p.V106A	ENST00000460680	NM_004656.3	106	gTg/gCg	5/17	0.136843381332168	3	FACETS	0.8	0.705	0.902	0.4	0.352	0.451	INDETERMINATE	1	TRUE	1	0.290459791540224	3		378	818	SUCCESS
ALB	213	MSKCC	GRCh37	4	74280835	74280835	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	225	350	0	ENST00000295897.4:c.1142T>C	p.Leu381Pro	p.L381P	ENST00000295897	NM_000477.5	381	cTa/cCa	9/15	1	2	FACETS	0.937	0.881	0.995	1	0.995	1	CLONAL	3	TRUE	1	0.290459791540224	2		350	551	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950613	38950613	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	32	384	0	ENST00000357387.3:c.3337A>G	p.Ser1113Gly	p.S1113G	ENST00000357387	NM_152756.3	1113	Agt/Ggt	31/38	1	2	FACETS	0.472	0.382	0.573	0.472	0.382	0.573	SUBCLONAL	1	TRUE	1	0.290459791540224	2		384	467	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170949	56170949	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	314	433	0	ENST00000399503.3:c.1780del	p.Ala594ProfsTer62	p.A594Pfs*62	ENST00000399503	NM_005921.1	593	Ggg/gg	10/20	1	2	FACETS	1	0.987	1	1	0.996	1	CLONAL	2	TRUE	1	0.290459791540224	2		433	947	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589312	67589312	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	90	250	2	ENST00000274335.5:c.1299+1G>A		p.X433_splice	ENST00000274335		433			1	2	FACETS	1	0.968	1	1	0.988	1	CLONAL	2	TRUE	1	0.290459791540224	2		252	261	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589584	67589586	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	77	184	0	ENST00000274335.5:c.1347_1349del	p.Leu449_His450delinsPhe	p.L449_H450delinsF	ENST00000274335		449	ttACAt/ttt	10/15	1	2	FACETS	1	0.954	1	1	0.986	1	CLONAL	2	TRUE	1	0.290459791540224	2		184	234	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041140	180041140	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	314	466	0	ENST00000261937.6:c.3259T>G	p.Phe1087Val	p.F1087V	ENST00000261937	NM_182925.4	1087	Ttc/Gtc	24/30	1	2	FACETS	0.907	0.859	0.954	1	0.997	1	CLONAL	3	TRUE	1	0.290459791540224	2		466	795	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536133	106536133	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs923684599	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	295	404	0	ENST00000369096.4:c.100A>G	p.Lys34Glu	p.K34E	ENST00000369096	NM_001198.3	34	Aag/Gag	2/7	0.104516965613386	3	FACETS	0.89	0.841	0.941			1	INDETERMINATE	3	TRUE	NA	0.290459791540224	3		404	871	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553665	106553665	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	257	428	0	ENST00000369096.4:c.1630G>A	p.Asp544Asn	p.D544N	ENST00000369096	NM_001198.3	544	Gac/Aac	5/7	0.104516965613386	3	FACETS	0.942	0.887	0.999			1	INDETERMINATE	3	TRUE	NA	0.290459791540224	3		428	717	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334846	81334846	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	186	322	0	ENST00000222390.5:c.1870A>G	p.Asn624Asp	p.N624D	ENST00000222390	NM_000601.4	624	Aac/Gac	17/18	1	2	FACETS	0.857	0.799	0.917	1	0.994	1	CLONAL	3	TRUE	1	0.290459791540224	2		322	498	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380055	116380055	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863224694	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	213	355	0	ENST00000397752.3:c.1444G>A	p.Asp482Asn	p.D482N	ENST00000397752	NM_000245.2	482	Gac/Aac	4/21	1	2	FACETS	0.878	0.822	0.934	1	0.995	1	CLONAL	3	TRUE	1	0.290459791540224	2		355	557	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370788	55370788	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	282	405	0	ENST00000297316.4:c.93del	p.Trp32GlyfsTer5	p.W32Gfs*5	ENST00000297316	NM_022454.3	30	tgC/tg	1/2	1	2	FACETS	0.887	0.838	0.936	1	0.996	1	CLONAL	3	TRUE	1	0.290459791540224	2		405	730	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956760	68956760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745582647	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	181	281	0	ENST00000288368.4:c.878G>A	p.Arg293Gln	p.R293Q	ENST00000288368	NM_024870.2	293	cGg/cAg	8/40	1	2	FACETS	0.905	0.843	0.968	1	0.994	1	CLONAL	3	TRUE	1	0.290459791540224	2		281	459	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978659	70978659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370561462	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	261	382	0	ENST00000276594.2:c.994C>T	p.Arg332Cys	p.R332C	ENST00000276594	NM_024504.3	332	Cgc/Tgc	5/8	1	2	FACETS	0.875	0.824	0.926	1	0.996	1	CLONAL	3	TRUE	1	0.290459791540224	2		382	685	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750687	128750687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	365	446	0	ENST00000377970.2:c.224C>T	p.Pro75Leu	p.P75L	ENST00000377970	NM_002467.4	75	cCc/cTc	2/3	1	2	FACETS	0.993	0.946	1	1	0.997	1	CLONAL	3	TRUE	1	0.290459791540224	2		446	844	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268792	98268793	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	263	430	0	ENST00000331920.6:c.290dup	p.Asn97LysfsTer43	p.N97Kfs*43	ENST00000331920	NM_000264.3	97	aac/aaAc	2/24	1	2	FACETS	1	0.986	1	1	0.996	1	CLONAL	2	TRUE	1	0.290459791540224	2		430	783	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785964	135785964	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs118203506	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	582	369	1	ENST00000298552.3:c.1257del	p.Arg420GlyfsTer20	p.R420Gfs*20	ENST00000298552	NM_001162426.1	419	ccC/cc	12/23	1	2	FACETS	1	0.989	1	1	0.998	1	CLONAL	5	TRUE	1	0.290459791540224	2		370	781	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135804221	135804221	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	214	454	0	ENST00000298552.3:c.39G>A	p.Met13Ile	p.M13I	ENST00000298552	NM_001162426.1	13	atG/atA	3/23	1	2	FACETS	0.872	0.812	0.934	1	0.993	1	CLONAL	2	TRUE	1	0.290459791540224	2		454	845	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15821895	15821896	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	148	250	0	ENST00000307771.7:c.294dup	p.Arg99ThrfsTer46	p.R99Tfs*46	ENST00000307771	NM_005089.3	96	-/A	4/11	0.224217026770921	1	FACETS	0.907	0.835	0.982	1	0.991	1	CLONAL	2	TRUE	0	0.290459791540224	1		250	480	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	270	498	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.224217026770921	1	FACETS	0.842	0.796	0.888	1	0.996	1	CLONAL	3	TRUE	0	0.290459791540224	1		498	629	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230796	53230796	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061342-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	50	410	0	ENST00000375401.3:c.1997T>C	p.Val666Ala	p.V666A	ENST00000375401	NM_004187.3	666	gTg/gCg	14/26	0.290459791540224	1	FACETS	0.438	0.371	0.512	0.438	0.371	0.512	SUBCLONAL	1	TRUE	0	0.290459791540224	1		410	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577548	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0061347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	80	352	1	ENST00000269305.4:c.733_734delinsTT	p.Gly245Phe	p.G245F	ENST00000269305	NM_001126112.2	245	GGc/TTc	7/11	0.18489687237468	2	FACETS	1	0.963	1	0.618	0.545	0.697	CLONAL	1	TRUE	0	0.21315438995468	2		353	607	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858038	40858038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748173627	NA	P-0061347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	93	375	0	ENST00000428826.2:c.1826G>A	p.Arg609His	p.R609H	ENST00000428826		609	cGt/cAt	16/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.21315438995468	2		375	708	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615548	43615548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	55	522	0	ENST00000355710.3:c.2627C>T	p.Ala876Val	p.A876V	ENST00000355710	NM_020975.4	876	gCa/gTa	15/20	0.191556847144933	3	FACETS	0.674	0.575	0.783	0.337	0.287	0.392	SUBCLONAL	1	TRUE	1	0.21315438995468	3		522	847	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458983	120458983	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	66	501	0	ENST00000256646.2:c.6362A>C	p.Lys2121Thr	p.K2121T	ENST00000256646	NM_024408.3	2121	aAg/aCg	34/34	0.21315438995468	3	FACETS	0.712	0.616	0.817	0.356	0.308	0.409	SUBCLONAL	1	TRUE	1	0.21315438995468	3		501	962	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129095	2129095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1194695685	NA	P-0061347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	62	538	1	ENST00000219476.3:c.3029A>G	p.Gln1010Arg	p.Q1010R	ENST00000219476	NM_000548.3	1010	cAg/cGg	27/42	0.183839342582383	4	FACETS	0.742	0.639	0.855	0.371	0.319	0.428	SUBCLONAL	1	TRUE	2	0.21315438995468	4		539	951	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842678	68842678	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1567504835	NA	P-0061347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	190	436	0	ENST00000261769.5:c.614T>C	p.Phe205Ser	p.F205S	ENST00000261769	NM_004360.3	205	tTt/tCt	5/16	0.21315438995468	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.21315438995468	2		436	743	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264808	46264808	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061347-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	65	367	0	ENST00000371998.3:c.1678A>G	p.Ser560Gly	p.S560G	ENST00000371998		560	Agt/Ggt	12/23	0.183839342582383	4	FACETS	0.86	0.744	0.987	0.43	0.372	0.494	CLONAL	1	TRUE	2	0.21315438995468	4		367	860	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518944	187518944	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061348-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	90	374	1	ENST00000441802.2:c.12260G>A	p.Cys4087Tyr	p.C4087Y	ENST00000441802	NM_005245.3	4087	tGt/tAt	24/27	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.31	2		375	576	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534321	187534321	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061348-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	110	478	0	ENST00000441802.2:c.9405del	p.Phe3135LeufsTer10	p.F3135Lfs*10	ENST00000441802	NM_005245.3	3135	ttT/tt	13/27	1	2	FACETS	0.978	0.879	1	0.978	0.879	1	CLONAL	1	TRUE	1	0.31	2		478	726	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417515	139417515	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0061348-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	146	559	0	ENST00000277541.6:c.529C>T	p.Gln177Ter	p.Q177*	ENST00000277541	NM_017617.3	177	Cag/Tag	4/34	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.31	2		559	823	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418256	139418256	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061348-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	85	549	0	ENST00000277541.6:c.316T>A	p.Cys106Ser	p.C106S	ENST00000277541	NM_017617.3	106	Tgc/Agc	3/34	1	2	FACETS	0.686	0.606	0.773	0.686	0.606	0.773	SUBCLONAL	1	TRUE	1	0.31	2		549	799	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	197	321	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.887	0.829	0.947	0.887	0.829	0.947	CLONAL	1	TRUE	1	0.845642916755514	2		321	525	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0061351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	272	768	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	1	2	FACETS	0.911	0.86	0.963	0.911	0.86	0.963	CLONAL	1	TRUE	1	0.845642916755514	2		768	706	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0061351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	271	471	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	0.92	0.868	0.972	0.92	0.868	0.972	CLONAL	1	TRUE	1	0.845642916755514	2		471	697	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300125	15300125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201917592	NA	P-0061351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	302	660	0	ENST00000263388.2:c.1151C>T	p.Thr384Met	p.T384M	ENST00000263388	NM_000435.2	384	aCg/aTg	7/33	1	2	FACETS	0.954	0.903	1	0.954	0.903	1	CLONAL	1	TRUE	1	0.845642916755514	2		660	749	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221463	36221463	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	341	655	0	ENST00000222270.7:c.5222G>T	p.Gly1741Val	p.G1741V	ENST00000222270	NM_014727.1	1741	gGt/gTt	25/37	1	2	FACETS	0.879	0.835	0.925	0.879	0.835	0.925	CLONAL	1	TRUE	1	0.845642916755514	2		655	917	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170372	119170372	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	328	569	0	ENST00000264033.4:c.2602G>T	p.Gly868Trp	p.G868W	ENST00000264033	NM_005188.3	868	Ggg/Tgg	16/16	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.845642916755514	2		569	709	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978516	70978516	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	256	497	0	ENST00000276594.2:c.1137C>A	p.Ser379Arg	p.S379R	ENST00000276594	NM_024504.3	379	agC/agA	5/8	1	2	FACETS	0.983	0.927	1	0.983	0.927	1	CLONAL	1	TRUE	1	0.845642916755514	2		497	616	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144113	11144113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	272	650	1	ENST00000358026.2:c.3694G>A	p.Gly1232Ser	p.G1232S	ENST00000358026	NM_001128849.1	1232	Ggc/Agc	26/36	1	2	FACETS	0.885	0.835	0.936	0.885	0.835	0.936	CLONAL	1	TRUE	1	0.845642916755514	2		651	727	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491138	120491138	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	293	542	0	ENST00000256646.2:c.2651A>T	p.Asn884Ile	p.N884I	ENST00000256646	NM_024408.3	884	aAc/aTc	17/34	1	2	FACETS	0.977	0.926	1	0.977	0.926	1	CLONAL	1	TRUE	1	0.845642916755514	2		542	709	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981486	201981486	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	239	528	0	ENST00000359651.3:c.400G>C	p.Asp134His	p.D134H	ENST00000359651		134	Gat/Cat	3/8	1	2	FACETS	0.952	0.895	1	0.952	0.895	1	CLONAL	1	TRUE	1	0.845642916755514	2		528	594	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984362	201984380	+	frameshift_variant	Frame_Shift_Del	DEL	GAACGGGTGGATGGCCGGC	GAACGGGTGGATGGCCGGC	-	novel	NA	P-0061351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	256	478	0	ENST00000359651.3:c.1029_1047del	p.Glu343AspfsTer98	p.E343Dfs*98	ENST00000359651		343	GAACGGGTGGATGGCCGGCga/ga	8/8	1	2	FACETS	0.912	0.859	0.965	0.912	0.859	0.965	CLONAL	1	TRUE	1	0.845642916755514	2		478	664	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244572	46244572	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0061351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	307	614	0	ENST00000334344.6:c.2666C>G	p.Ser889Ter	p.S889*	ENST00000334344	NM_152641.2	889	tCa/tGa	15/21	1	2	FACETS	0.991	0.94	1	0.991	0.94	1	CLONAL	1	TRUE	1	0.845642916755514	2		614	733	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032304	12032537	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGATTCTGAAGATTCCTCCCCAAGCTAACCTGTGTTTAATTCAAGGCTTTACTAGAGTTTTGCTTGTAGTTTAGATTTTTTTGTGGCCCTTCCAGTGGGGAGTAGTAAATGATGCCTGGTGTATTTTGCTCTTTCCTCTTTGTTCTCTTTAGTATGAGTTGGCCACAGGCCGATTTCCTTATCCAAAGTGGAATAGTGTATTTGATCAACTAACACAAGTCGTGAAAGGAGATC	TGATTCTGAAGATTCCTCCCCAAGCTAACCTGTGTTTAATTCAAGGCTTTACTAGAGTTTTGCTTGTAGTTTAGATTTTTTTGTGGCCCTTCCAGTGGGGAGTAGTAAATGATGCCTGGTGTATTTTGCTCTTTCCTCTTTGTTCTCTTTAGTATGAGTTGGCCACAGGCCGATTTCCTTATCCAAAGTGGAATAGTGTATTTGATCAACTAACACAAGTCGTGAAAGGAGATC	-	novel	NA	P-0061351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	48	110	0	ENST00000353533.5:c.892-152_973del		p.X298_splice	ENST00000353533	NM_003010.3	298		9/11	0.816437616376774	1	FACETS	0.964	0.871	1	0.964	0.871	1	CLONAL	1	TRUE	0	0.845642916755514	1		110	68	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032603	12033625	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGTGAGTACCTGATTTATGAATGGTCGAACACGCATGGCGAGAATAGTGAGATTTACTTGGTCTTAGCAGCATTGGTACTTTACATGGAGGAAGGGGACCCTTGGTCACATCACCCTACTTTTCAAGCTGGGACTCTGGATCACTGTGGCTGTATGGAAGGTTACAGCTAGCTGGGAGAGGCATCACCTTCTTATTCTGCTACTCAGGTATTGGTGAAAAACAGCCATGAGTGGTGGAGAGGCTGCTGTCTCCAGACTTCCAGTACCTGGTACAAGAAATACCAGGTTAAACTTCTAGGTGAGACTGATCATCTTACTCTAATGTGGTTCTCACAATGCAATTGCACCAAAATCACCTGGAAGCATTTACTGAATCAAGAGCTTGCCAGATCAGACTTTCAGGGTTGGATCTCTGTTCTGACATAACATAGAAAACAGTTGGTTATATGTAGTAGGGTCACATCCACACGCAAAGTGTAGTTGGTAGAACTGTATATCTTTGCTCTCTGAAACCTTACTCCAAGGAAGATGTGAACCCCACACCTGTTGTTGTTTGTCTACCTTTTTAATAGTTTGTTGTGTGTTTGTGTATATGTAGCACCTAAGAATAAACATATGCAGATATGGCAGTAATATAATCATGCTTTATACTGTTTTAGGCTCTTTTAAATAAAATCTTTTTGTGTTATCATTTGGATATTTTTGACATTTATTTTGTTTATCCAACATGATTTAAATATAAGACATGCTATGAACAAAAAGCCTCAGAGCATTTTGTGTATCTTCTGTTTATTCCTGAAAATACCTTTTGGTTTCTCATAATTTTTTCCTGCTAAGAATGCGGTTTCTCCTCATTTTAGGTCTTATAGACTTAAATCAGGGTCTAACATTGCCCTCCTTTGTATGAAAAATTTAAAAATATTTGTTTGACTATAGTTTTTAAGTCTCTTTCATCTTCTGTAACCAAATTCTACTTTTGTGTTGGTTTTTCAGAGGGGAGAGGAATACTTCAAGATTTTCTA	TGGTGAGTACCTGATTTATGAATGGTCGAACACGCATGGCGAGAATAGTGAGATTTACTTGGTCTTAGCAGCATTGGTACTTTACATGGAGGAAGGGGACCCTTGGTCACATCACCCTACTTTTCAAGCTGGGACTCTGGATCACTGTGGCTGTATGGAAGGTTACAGCTAGCTGGGAGAGGCATCACCTTCTTATTCTGCTACTCAGGTATTGGTGAAAAACAGCCATGAGTGGTGGAGAGGCTGCTGTCTCCAGACTTCCAGTACCTGGTACAAGAAATACCAGGTTAAACTTCTAGGTGAGACTGATCATCTTACTCTAATGTGGTTCTCACAATGCAATTGCACCAAAATCACCTGGAAGCATTTACTGAATCAAGAGCTTGCCAGATCAGACTTTCAGGGTTGGATCTCTGTTCTGACATAACATAGAAAACAGTTGGTTATATGTAGTAGGGTCACATCCACACGCAAAGTGTAGTTGGTAGAACTGTATATCTTTGCTCTCTGAAACCTTACTCCAAGGAAGATGTGAACCCCACACCTGTTGTTGTTTGTCTACCTTTTTAATAGTTTGTTGTGTGTTTGTGTATATGTAGCACCTAAGAATAAACATATGCAGATATGGCAGTAATATAATCATGCTTTATACTGTTTTAGGCTCTTTTAAATAAAATCTTTTTGTGTTATCATTTGGATATTTTTGACATTTATTTTGTTTATCCAACATGATTTAAATATAAGACATGCTATGAACAAAAAGCCTCAGAGCATTTTGTGTATCTTCTGTTTATTCCTGAAAATACCTTTTGGTTTCTCATAATTTTTTCCTGCTAAGAATGCGGTTTCTCCTCATTTTAGGTCTTATAGACTTAAATCAGGGTCTAACATTGCCCTCCTTTGTATGAAAAATTTAAAAATATTTGTTTGACTATAGTTTTTAAGTCTCTTTCATCTTCTGTAACCAAATTCTACTTTTGTGTTGGTTTTTCAGAGGGGAGAGGAATACTTCAAGATTTTCTA	-	novel	NA	P-0061351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	64	447	0	ENST00000353533.5:c.1039_1040+1021del		p.X347_splice	ENST00000353533	NM_003010.3	347		9/11	0.816437616376774	1	FACETS	0.403	0.354	0.454	0.403	0.354	0.454	SUBCLONAL	1	TRUE	0	0.845642916755514	1		447	217	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38785246	38785246	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0061351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	195	424	0	ENST00000348513.6:c.1028-1G>T		p.X343_splice	ENST00000348513	NM_003079.4	343			0.845642916755514	3	FACETS	0.946	0.878	1	0.473	0.439	0.508	CLONAL	1	TRUE	1	0.845642916755514	3		424	694	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475329	40475329	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	533	524	0	ENST00000264657.5:c.1697A>T	p.Asp566Val	p.D566V	ENST00000264657	NM_139276.2	566	gAc/gTc	19/24	0.845642916755514	3	FACETS	0.921	0.889	0.953	0.921	0.889	0.953	CLONAL	2	TRUE	1	0.845642916755514	3		524	974	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7128948	7128948	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	266	434	0	ENST00000302850.5:c.2860A>G	p.Ile954Val	p.I954V	ENST00000302850	NM_000208.2	954	Att/Gtt	15/22	1	2	FACETS	0.983	0.929	1	0.983	0.929	1	CLONAL	1	TRUE	1	0.845642916755514	2		434	640	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050957	13050957	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	344	617	0	ENST00000316448.5:c.488G>T	p.Cys163Phe	p.C163F	ENST00000316448	NM_004343.3	163	tGc/tTc	4/9	1	2	FACETS	0.952	0.905	0.999	0.952	0.905	0.999	CLONAL	1	TRUE	1	0.845642916755514	2		617	855	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798832	42798832	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	45	602	0	ENST00000575354.2:c.4404C>A	p.Asp1468Glu	p.D1468E	ENST00000575354	NM_015125.3	1468	gaC/gaA	19/20	1	2	FACETS	0.151	0.126	0.179	0.151	0.126	0.179	SUBCLONAL	1	TRUE	1	0.845642916755514	2		602	704	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205768	128205768	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	266	621	0	ENST00000341105.2:c.107C>A	p.Pro36His	p.P36H	ENST00000341105	NM_032638.4	36	cCc/cAc	2/6	1	2	FACETS	0.927	0.874	0.98	0.927	0.874	0.98	CLONAL	1	TRUE	1	0.845642916755514	2		621	679	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274868	142274868	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	210	402	0	ENST00000350721.4:c.2192C>G	p.Pro731Arg	p.P731R	ENST00000350721	NM_001184.3	731	cCt/cGt	10/47	1	2	FACETS	0.972	0.911	1	0.972	0.911	1	CLONAL	1	TRUE	1	0.845642916755514	2		402	511	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231679	66231679	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	157	401	0	ENST00000273854.3:c.2021G>T	p.Cys674Phe	p.C674F	ENST00000273854	NM_004439.5	674	tGt/tTt	11/18	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.845642916755514	2		401	364	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143324117	143324117	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	169	350	0	ENST00000262992.4:c.346G>T	p.Asp116Tyr	p.D116Y	ENST00000262992	NM_001101669.1	116	Gat/Tat	5/24	1	2	FACETS	0.858	0.796	0.921	0.858	0.796	0.921	CLONAL	1	TRUE	1	0.845642916755514	2		350	466	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341089	8341089	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0061351-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	180	391	0	ENST00000356435.5:c.5126+1G>A		p.X1709_splice	ENST00000356435		1709			1	2	FACETS	0.86	0.8	0.921	0.86	0.8	0.921	CLONAL	1	TRUE	1	0.845642916755514	2		391	495	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061352-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	96	377	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.176201030313962	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	3	TRUE	0	0.188761085685012	3		377	331	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602719	55602719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752695117	NA	P-0061352-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	38	254	0	ENST00000288135.5:c.2540C>T	p.Thr847Met	p.T847M	ENST00000288135	NM_000222.2	847	aCg/aTg	18/21	1	2	FACETS	0.917	0.758	1	0.917	0.758	1	CLONAL	1	TRUE	1	0.188761085685012	2		254	439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0061352-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	44	468	0	ENST00000269305.4:c.560-1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			1	2	FACETS	0.873	0.732	1	0.873	0.732	1	CLONAL	1	TRUE	1	0.188761085685012	2		468	534	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413610	32413610	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061352-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	23	267	0	ENST00000332351.3:c.1340G>T	p.Gly447Val	p.G447V	ENST00000332351	NM_024426.4	447	gGt/gTt	9/10	1	2	FACETS	0.571	0.444	0.718	0.571	0.444	0.718	SUBCLONAL	1	TRUE	1	0.188761085685012	2		267	427	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339492	81339492	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061352-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	38	247	0	ENST00000222390.5:c.1512C>A	p.Asn504Lys	p.N504K	ENST00000222390	NM_000601.4	504	aaC/aaA	13/18	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.188761085685012	2		247	378	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325056	123325056	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061352-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	63	395	0	ENST00000358487.5:c.272A>G	p.Tyr91Cys	p.Y91C	ENST00000358487	NM_000141.4	91	tAc/tGc	3/18	0.188761085685012	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.188761085685012	1		395	530	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398082	4398082	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061352-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	110	308	0	ENST00000261254.3:c.646C>G	p.Gln216Glu	p.Q216E	ENST00000261254	NM_001759.3	216	Cag/Gag	4/5	0.176201030313962	3	FACETS	0.878	0.793	0.968	0.878	0.793	0.968	CLONAL	3	TRUE	0	0.188761085685012	3		308	484	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202806	133202806	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061352-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	51	439	0	ENST00000320574.5:c.6428A>T	p.Gln2143Leu	p.Q2143L	ENST00000320574	NM_006231.2	2143	cAg/cTg	46/49	0.188761085685012	1	FACETS	0.965	0.821	1	0.965	0.821	1	CLONAL	1	TRUE	0	0.188761085685012	1		439	507	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678344	88678344	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061352-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	32	332	0	ENST00000360948.2:c.1192G>T	p.Glu398Ter	p.E398*	ENST00000360948	NM_001012338.2	398	Gag/Tag	9/19	1	2	FACETS	0.904	0.734	1	0.904	0.734	1	CLONAL	1	TRUE	1	0.188761085685012	2		332	375	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872023	37872024	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0061352-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	45	469	1	ENST00000269571.5:c.1344_1345delinsTT	p.Gly449Cys	p.G449C	ENST00000269571		448	ctGGgc/ctTTgc	12/27	1	2	FACETS	0.908	0.763	1	0.908	0.763	1	CLONAL	1	TRUE	1	0.188761085685012	2		470	525	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007580	62007580	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061352-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	40	400	0	ENST00000392795.3:c.287G>T	p.Arg96Leu	p.R96L	ENST00000392795	NM_001039933.1	96	cGc/cTc	3/6	1	2	FACETS	0.788	0.654	0.937	0.788	0.654	0.937	CLONAL	1	TRUE	1	0.188761085685012	2		400	538	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467383	66467383	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061352-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	49	343	0	ENST00000273854.3:c.886G>C	p.Glu296Gln	p.E296Q	ENST00000273854	NM_004439.5	296	Gaa/Caa	3/18	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.188761085685012	2		343	441	SUCCESS
APC	324	MSKCC	GRCh37	5	112111342	112111342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061352-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	18	172	0	ENST00000257430.4:c.439G>A	p.Asp147Asn	p.D147N	ENST00000257430	NM_000038.5	147	Gat/Aat	5/16	1	2	FACETS	0.669	0.504	0.865	0.669	0.504	0.865	SUBCLONAL	1	TRUE	1	0.188761085685012	2		172	285	SUCCESS
APC	324	MSKCC	GRCh37	5	112111369	112111369	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1554071538	NA	P-0061352-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	20	175	0	ENST00000257430.4:c.466G>C	p.Asp156His	p.D156H	ENST00000257430	NM_000038.5	156	Gac/Cac	5/16	1	2	FACETS	0.723	0.553	0.922	0.723	0.553	0.922	CLONAL	1	TRUE	1	0.188761085685012	2		175	293	SUCCESS
APC	324	MSKCC	GRCh37	5	112111392	112111392	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876660717	NA	P-0061352-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	24	188	0	ENST00000257430.4:c.489G>C	p.Gln163His	p.Q163H	ENST00000257430	NM_000038.5	163	caG/caC	5/16	1	2	FACETS	0.915	0.719	1	0.915	0.719	1	CLONAL	1	TRUE	1	0.188761085685012	2		188	278	SUCCESS
APC	324	MSKCC	GRCh37	5	112111411	112111411	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061352-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	24	191	0	ENST00000257430.4:c.508G>C	p.Asp170His	p.D170H	ENST00000257430	NM_000038.5	170	Gat/Cat	5/16	1	2	FACETS	0.902	0.708	1	0.902	0.708	1	CLONAL	1	TRUE	1	0.188761085685012	2		191	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0061362-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	331	665	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.618097293647769	2	FACETS	0.975	0.935	1	0.975	0.935	1	CLONAL	2	TRUE	0	0.642076991541236	2		666	529	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623912	28623912	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0061362-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	231	337	0	ENST00000241453.7:c.743-1G>T		p.X248_splice	ENST00000241453	NM_004119.2	248			0.619221421838383	5	FACETS	1	0.969	1	0.702	0.658	0.747	CLONAL	2	TRUE	2	0.642076991541236	5		337	671	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266015	41266600	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGA	AGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGA	-	novel	NA	P-0061362-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	130	362	0	ENST00000349496.5:c.14-1_398del		p.X5_splice	ENST00000349496	NM_001904.3	5		3-4/15	0.619863668624478	3	FACETS	1	0.987	1	0.743	0.682	0.805	CLONAL	1	TRUE	1	0.642076991541236	3		362	360	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0061363-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	39	544	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.474	0.394	0.562	0.474	0.394	0.562	SUBCLONAL	1	TRUE	1	0.533980008640991	2		544	308	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971029	21971029	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519852	NA	P-0061364-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	138	468	0	ENST00000304494.5:c.329G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tGg/tAg	2/3	0.229311389805536	0	FACETS	1	0.975	1			1	CLONAL	1	TRUE	0	0.269028845136865	0		468	635	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105788	27105789	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0061364-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	337	481	0	ENST00000324856.7:c.5400_5401del	p.Asn1800LysfsTer2	p.N1800Kfs*2	ENST00000324856	NM_006015.4	1800	aAT/a	20/20	0.269028845136865	2	FACETS	0.953	0.91	0.996	1	0.996	1	CLONAL	4	TRUE	0	0.269028845136865	2		481	657	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231483634	231483634	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061364-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	198	322	0	ENST00000295050.7:c.413T>C	p.Met138Thr	p.M138T	ENST00000295050	NM_032018.5	138	aTg/aCg	3/5	1	2	FACETS	1	0.986	1	1	0.994	1	CLONAL	2	TRUE	1	0.269028845136865	2		322	603	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420173	88420173	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061364-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	167	350	0	ENST00000360948.2:c.2513T>C	p.Leu838Pro	p.L838P	ENST00000360948	NM_001012338.2	838	cTt/cCt	19/19	0.168653182197032	3	FACETS	1	0.951	1	0.695	0.64	0.751	CLONAL	2	TRUE	0	0.269028845136865	3		350	676	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827942	40827942	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061364-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	394	479	0	ENST00000373198.4:c.2486A>C	p.Lys829Thr	p.K829T	ENST00000373198	NM_133170.3	829	aAg/aCg	17/32	0.269028845136865	4	FACETS	1	0.989	1	1	0.996	1	CLONAL	4	TRUE	1	0.269028845136865	4		479	847	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259293	36259320	+	frameshift_variant	Frame_Shift_Del	DEL	GGCAGCGCCGGCGTCCGGGGCGCCCAGC	GGCAGCGCCGGCGTCCGGGGCGCCCAGC	-	novel	NA	P-0061364-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	115	416	0	ENST00000300305.3:c.171_198del	p.Leu58TrpfsTer5	p.L58Wfs*5	ENST00000300305		57	ccGCTGGGCGCCCCGGACGCCGGCGCTGCC/cc	3/8	0.269028845136865	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.269028845136865	1		416	515	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80109463	80109463	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs767359174	NA	P-0061364-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	81	342	0	ENST00000265081.6:c.2716A>G	p.Ile906Val	p.I906V	ENST00000265081	NM_002439.4	906	Ata/Gta	20/24	0.269028845136865	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.269028845136865	1		342	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578512	7578513	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0061364-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	408	434	0	ENST00000269305.4:c.417_418insCA	p.Thr140GlnfsTer31	p.T140Qfs*31	ENST00000269305	NM_001126112.2	139	-/CA	5/11	0.188713893476834	3	FACETS	0.992	0.954	1			1	CLONAL	5	TRUE	NA	0.269028845136865	3		434	694	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0061365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	16	341	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.374	0.276	0.491	0.374	0.276	0.491	SUBCLONAL	1	TRUE	1	0.314708536277211	2		341	272	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589610	67589612	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	novel	NA	P-0061365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	9	188	0	ENST00000274335.5:c.1376_1378del	p.Lys459del	p.K459del	ENST00000274335		458	gAAAaa/gaa	10/15	1	2	FACETS	0.433	0.288	0.617	0.433	0.288	0.617	SUBCLONAL	1	TRUE	1	0.314708536277211	2		188	132	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578476	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTGCCGGGCGG	GGGTGCCGGGCGG	-	rs876659215	NA	P-0061365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	22	593	0	ENST00000269305.4:c.454_466del	p.Pro152AlafsTer14	p.P152Afs*14	ENST00000269305	NM_001126112.2	152	CCGCCCGGCACCCgc/gc	5/11	1	2	FACETS	0.242	0.187	0.307	0.242	0.187	0.307	SUBCLONAL	1	TRUE	1	0.314708536277211	2		593	577	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874263	155874263	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1557960039	NA	P-0061365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	24	408	0	ENST00000368323.3:c.268A>G	p.Met90Val	p.M90V	ENST00000368323	NM_006912.5	90	Atg/Gtg	5/6	1	2	FACETS	0.327	0.256	0.41	0.327	0.256	0.41	SUBCLONAL	1	TRUE	1	0.314708536277211	2		408	466	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590990	67590992	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	novel	NA	P-0061365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	13	225	0	ENST00000274335.5:c.1585_1587del	p.Asp529del	p.D529del	ENST00000274335		528	tATGat/tat	12/15	1	2	FACETS	0.362	0.258	0.489	0.362	0.258	0.489	SUBCLONAL	1	TRUE	1	0.314708536277211	2		225	228	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717683	89717684	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAGT	novel	NA	P-0061365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	19	306	0	ENST00000371953.3:c.709_712dup	p.Phe238Ter	p.F238*	ENST00000371953	NM_000314.4	236	-/AAGT	7/9	1	2	FACETS	0.342	0.259	0.44	0.342	0.259	0.44	SUBCLONAL	1	TRUE	1	0.314708536277211	2		306	353	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271413	38271438	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCTCTGGCACGGGCAGCCTTACCTG	GGCTCTGGCACGGGCAGCCTTACCTG	-	novel	NA	P-0061365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	20	465	0	ENST00000425967.3:c.2383_2385+23del		p.X795_splice	ENST00000425967	NM_001174067.1	795		18/19	1	2	FACETS	0.326	0.249	0.417	0.326	0.249	0.417	SUBCLONAL	1	TRUE	1	0.314708536277211	2		465	390	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3094727	3094728	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAGC	novel	NA	P-0061367-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	126	387	0	ENST00000078429.4:c.80_83dup	p.Leu29AlafsTer138	p.L29Afs*138	ENST00000078429	NM_002067.2	26	-/AAGC	1/7	0.436015650681288	2	FACETS	0.815	0.747	0.884	0.815	0.747	0.884	CLONAL	2	TRUE	0	0.444385069996678	2		387	348	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752949	42752949	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061367-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	30	555	0	ENST00000222329.4:c.1315G>A	p.Glu439Lys	p.E439K	ENST00000222329	NM_006494.2	439	Gag/Aag	4/4	0.347592309148493	4	FACETS	0.342	0.274	0.418	0.171	0.137	0.209	SUBCLONAL	1	TRUE	2	0.444385069996678	4		555	571	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221717	22221742	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	GCCGCCGCCGCCATGTTGGCTGCCGG	GCCGCCGCCGCCATGTTGGCTGCCGG	-	novel	NA	P-0061367-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	104	408	0	ENST00000215832.6:c.-12_14del		p.*4*	ENST00000215832	NM_002745.4	?-5/360		1/9	0.146313424488189	6	FACETS	1	0.939	1			1	INDETERMINATE	2	TRUE	NA	0.444385069996678	6		408	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0061368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	496	665	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.758142418623709	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.759344760262143	2		666	638	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0061368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	267	863	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.758142418623709	1	FACETS	0.963	0.918	1	0.963	0.918	1	CLONAL	1	TRUE	0	0.759344760262143	1		863	453	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TC	novel	NA	P-0061368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	275	340	0	ENST00000311936.3:c.180_181inv	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggGAaa	3/5	0.758142418623709	4	FACETS	0.874	0.825	0.924	0.874	0.825	0.924	CLONAL	2	TRUE	2	0.759344760262143	4		340	729	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	91	382	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.463729528148133	2		382	313	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	130	410	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.811	0.737	0.889	0.811	0.737	0.889	CLONAL	1	TRUE	1	0.463729528148133	2		412	691	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	119	304	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.463729528148133	2		304	500	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	153	431	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.463729528148133	2		432	660	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696802	176696802	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	130	348	0	ENST00000439151.2:c.5508del	p.Ala1837LeufsTer12	p.A1837Lfs*12	ENST00000439151	NM_022455.4	1835	Aaa/aa	16/23	1	2	FACETS	0.968	0.882	1	0.968	0.882	1	CLONAL	1	TRUE	1	0.463729528148133	2		348	579	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	150	544	0	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	1	2	FACETS	0.967	0.886	1	0.967	0.886	1	CLONAL	1	TRUE	1	0.463729528148133	2		544	669	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165213	47165213	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	92	315	0	ENST00000409792.3:c.913del	p.Thr305GlnfsTer35	p.T305Qfs*35	ENST00000409792	NM_014159.6	305	Aca/ca	3/21	1	2	FACETS	0.821	0.733	0.915	0.821	0.733	0.915	CLONAL	1	TRUE	1	0.463729528148133	2		315	483	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	95	328	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.463729528148133	2		328	389	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681119	117681120	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs748436511	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	23	337	0	ENST00000368508.3:c.3500dup	p.Leu1167PhefsTer26	p.L1167Ffs*26	ENST00000368508	NM_002944.2	1167	tta/ttTa	23/43	1	2	FACETS	0.243	0.189	0.306	0.243	0.189	0.306	SUBCLONAL	1	TRUE	1	0.463729528148133	2		337	408	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830441	72830441	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	72	262	0	ENST00000268489.5:c.6140del	p.Pro2047LeufsTer54	p.P2047Lfs*54	ENST00000268489	NM_006885.3	2047	cCt/ct	9/10	1	2	FACETS	0.933	0.821	1	0.933	0.821	1	CLONAL	1	TRUE	1	0.463729528148133	2		262	333	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446310	29446310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138589984	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	140	491	0	ENST00000389048.3:c.3257C>T	p.Ser1086Leu	p.S1086L	ENST00000389048	NM_004304.4	1086	tCg/tTg	20/29	1	2	FACETS	0.913	0.834	0.996	0.913	0.834	0.996	CLONAL	1	TRUE	1	0.463729528148133	2		491	661	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070869	30070869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373650983	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	115	378	0	ENST00000338641.4:c.1385G>A	p.Arg462His	p.R462H	ENST00000338641	NM_000268.3	462	cGc/cAc	13/16	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.463729528148133	2		378	472	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778858	76778858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	92	303	0	ENST00000373344.5:c.6721C>T	p.Leu2241Phe	p.L2241F	ENST00000373344	NM_000489.3	2241	Ctt/Ttt	31/35	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.463729528148133	2		303	363	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673759	176673759	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	122	317	0	ENST00000439151.2:c.4463del	p.Asn1488MetfsTer15	p.N1488Mfs*15	ENST00000439151	NM_022455.4	1487	Aaa/aa	10/23	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.463729528148133	2		317	495	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991949	72991949	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs753977275	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	120	729	1	ENST00000268489.5:c.2096del	p.Gly699AlafsTer125	p.G699Afs*125	ENST00000268489	NM_006885.3	699	gGc/gc	2/10	1	2	FACETS	0.877	0.795	0.964	0.877	0.795	0.964	CLONAL	1	TRUE	1	0.463729528148133	2		730	590	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125832	47125832	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	84	285	1	ENST00000409792.3:c.5438del	p.Asn1813IlefsTer25	p.N1813Ifs*25	ENST00000409792	NM_014159.6	1813	aAt/at	12/21	1	2	FACETS	0.886	0.787	0.991	0.886	0.787	0.991	CLONAL	1	TRUE	1	0.463729528148133	2		286	409	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256430	16256430	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760748544	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	36	498	0	ENST00000375759.3:c.3695A>G	p.His1232Arg	p.H1232R	ENST00000375759	NM_015001.2	1232	cAt/cGt	11/15	1	2	FACETS	0.216	0.177	0.26	0.216	0.177	0.26	SUBCLONAL	1	TRUE	1	0.463729528148133	2		498	719	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220069	36220069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1239076295	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	178	564	0	ENST00000222270.7:c.4789C>T	p.Arg1597Trp	p.R1597W	ENST00000222270	NM_014727.1	1597	Cgg/Tgg	22/37	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.463729528148133	2		564	742	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646980	23646981	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	110	340	1	ENST00000261584.4:c.886dup	p.Met296AsnfsTer7	p.M296Nfs*7	ENST00000261584	NM_024675.3	296	atg/aAtg	4/13	1	2	FACETS	0.843	0.759	0.93	0.843	0.759	0.93	CLONAL	1	TRUE	1	0.463729528148133	2		341	563	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857379	9857380	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	72	490	0	ENST00000330684.3:c.4021dup	p.Ser1341LysfsTer25	p.S1341Kfs*25	ENST00000330684	NM_001134407.1	1341	agc/aAgc	13/13	1	2	FACETS	0.506	0.442	0.575	0.506	0.442	0.575	SUBCLONAL	1	TRUE	1	0.463729528148133	2		490	614	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946436	2946436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761965340	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	116	423	0	ENST00000396946.4:c.3301C>T	p.Arg1101Cys	p.R1101C	ENST00000396946	NM_032415.4	1101	Cgc/Tgc	25/25	1	2	FACETS	0.895	0.81	0.985	0.895	0.81	0.985	CLONAL	1	TRUE	1	0.463729528148133	2		423	559	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553699	106553699	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	65	410	0	ENST00000369096.4:c.1664A>G	p.Asn555Ser	p.N555S	ENST00000369096	NM_001198.3	555	aAc/aGc	5/7	1	2	FACETS	0.444	0.385	0.509	0.444	0.385	0.509	SUBCLONAL	1	TRUE	1	0.463729528148133	2		410	631	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528201	157528201	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	157	513	0	ENST00000346085.5:c.5926G>T	p.Gly1976Trp	p.G1976W	ENST00000346085	NM_020732.3	1976	Ggg/Tgg	20/20	1	2	FACETS	0.971	0.892	1	0.971	0.892	1	CLONAL	1	TRUE	1	0.463729528148133	2		513	697	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356303	66356303	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	144	424	0	ENST00000273854.3:c.1194C>A	p.Cys398Ter	p.C398*	ENST00000273854	NM_004439.5	398	tgC/tgA	5/18	1	2	FACETS	0.907	0.829	0.988	0.907	0.829	0.988	CLONAL	1	TRUE	1	0.463729528148133	2		424	685	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944890	131944890	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748452537	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	37	173	0	ENST00000265335.6:c.2911G>A	p.Asp971Asn	p.D971N	ENST00000265335		971	Gac/Aac	18/25	1	2	FACETS	0.659	0.547	0.783	0.659	0.547	0.783	SUBCLONAL	1	TRUE	1	0.463729528148133	2		173	242	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51535061	51535061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200111039	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	146	392	0	ENST00000260433.2:c.49G>A	p.Val17Met	p.V17M	ENST00000260433		17	Gtg/Atg	2/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.463729528148133	2		392	564	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176104176	176104176	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	67	285	0	ENST00000367669.3:c.938C>G	p.Pro313Arg	p.P313R	ENST00000367669	NM_022457.5	313	cCt/cGt	8/20	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.463729528148133	2		285	287	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720660	89720660	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167634	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	36	84	0	ENST00000371953.3:c.813del	p.His272ThrfsTer4	p.H272Tfs*4	ENST00000371953	NM_000314.4	271	Ttt/tt	8/9	1	2	FACETS	0.93	0.775	1	0.93	0.775	1	CLONAL	1	TRUE	1	0.463729528148133	2		84	167	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490289	29490289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149003051	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	132	365	0	ENST00000356175.3:c.374G>A	p.Arg125His	p.R125H	ENST00000356175	NM_000267.3	125	cGt/cAt	4/57	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.463729528148133	2		365	526	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117957	70117957	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	152	473	0	ENST00000245479.2:c.425T>C	p.Leu142Pro	p.L142P	ENST00000245479	NM_000346.3	142	cTc/cCc	1/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.463729528148133	2		473	542	SUCCESS
ALK	238	MSKCC	GRCh37	2	29430082	29430082	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	103	318	0	ENST00000389048.3:c.3893del	p.Pro1298GlnfsTer64	p.P1298Qfs*64	ENST00000389048	NM_004304.4	1298	cCa/ca	26/29	1	2	FACETS	0.943	0.848	1	0.943	0.848	1	CLONAL	1	TRUE	1	0.463729528148133	2		318	471	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989491	212989491	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1201600413	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	139	354	0	ENST00000342788.4:c.220C>A	p.Leu74Ile	p.L74I	ENST00000342788	NM_005235.2	74	Ctc/Atc	2/28	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.463729528148133	2		354	543	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760472	133760473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	111	491	0	ENST00000318560.5:c.2799dup	p.Ala934SerfsTer6	p.A934Sfs*6	ENST00000318560	NM_005157.4	932	aca/acAa	11/11	1	2	FACETS	0.896	0.809	0.988	0.896	0.809	0.988	CLONAL	1	TRUE	1	0.463729528148133	2		491	534	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860130	152860130	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	126	300	0	ENST00000406277.2:c.298A>T	p.Asn100Tyr	p.N100Y	ENST00000406277	NM_152274.4	100	Aac/Tac	5/7	1		FACETS		0.961	1				CLONAL	1	TRUE	1	0.463729528148133	2		300	494	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521694	89521694	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs150555764	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	126	352	0	ENST00000336596.2:c.2771G>A	p.Trp924Ter	p.W924*	ENST00000336596	NM_005233.5	924	tGg/tAg	16/17	1	2	FACETS	0.937	0.851	1	0.937	0.851	1	CLONAL	1	TRUE	1	0.463729528148133	2		352	580	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045928	26045928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	174	574	0	ENST00000540144.1:c.290G>A	p.Cys97Tyr	p.C97Y	ENST00000540144	NM_003531.2	97	tGt/tAt	1/1	1	2	FACETS	0.955	0.88	1	0.955	0.88	1	CLONAL	1	TRUE	1	0.463729528148133	2		574	786	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338671	70338671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	143	339	0	ENST00000374080.3:c.67G>T	p.Asp23Tyr	p.D23Y	ENST00000374080		23	Gat/Tat	1/45	0.506107534299722	1	FACETS	0.775	0.723	0.826	0.775	0.723	0.826	SUBCLONAL	1	TRUE	0	0.824801168317243	1		339	263	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0061371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	211	399	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.824801168317243	2		399	426	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	176	400	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.824801168317243	2		400	370	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40500444	40500444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	18	250	0	ENST00000264657.5:c.91C>T	p.Arg31Trp	p.R31W	ENST00000264657	NM_139276.2	31	Cgg/Tgg	2/24	0.824801168317243	1	FACETS	0.136	0.103	0.176	0.136	0.103	0.176	SUBCLONAL	1	TRUE	0	0.824801168317243	1		250	188	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693010	89693010	+	splice_donor_variant	Splice_Site	DEL	T	T	-	rs1060500124	NA	P-0061371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	295	164	0	ENST00000371953.3:c.492+2del		p.X164_splice	ENST00000371953	NM_000314.4	164			0.824801168317243	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.824801168317243	3		164	322	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100161	27100161	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0061371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	228	566	0	ENST00000324856.7:c.3957T>G	p.Tyr1319Ter	p.Y1319*	ENST00000324856	NM_006015.4	1319	taT/taG	16/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.824801168317243	2		566	470	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182601	99182601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	463	436	0	ENST00000074304.5:c.2404G>A	p.Gly802Ser	p.G802S	ENST00000074304	NM_001134224.1	802	Ggc/Agc	22/26	0.183462962785016	3	FACETS	1	0.997	1	1	0.997	1	INDETERMINATE	3	TRUE	0	0.824801168317243	3		436	481	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061372-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	43	377	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.192692672589563	3	FACETS	1	0.94	1	0.637	0.535	0.75	CLONAL	1	FALSE	1	0.21474213626177	3		377	348	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216546	108216546	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs529296539	NA	P-0061372-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	13	298	0	ENST00000278616.4:c.8495G>C	p.Arg2832Pro	p.R2832P	ENST00000278616	NM_000051.3	2832	cGt/cCt	58/63	1	2	FACETS	0.316	0.224	0.429	0.316	0.224	0.429	SUBCLONAL	1	FALSE	1	0.21474213626177	2		298	383	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781314	3781314	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061372-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	32	571	0	ENST00000262367.5:c.5051C>T	p.Ser1684Phe	p.S1684F	ENST00000262367	NM_004380.2	1684	tCc/tTc	30/31	1	2	FACETS	0.469	0.379	0.57	0.469	0.379	0.57	SUBCLONAL	1	FALSE	1	0.21474213626177	2		571	636	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25458657	25458657	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061372-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	30	399	0	ENST00000264709.3:c.2516C>A	p.Ser839Tyr	p.S839Y	ENST00000264709	NM_175629.2	839	tCc/tAc	22/23	1	2	FACETS	0.507	0.407	0.621	0.507	0.407	0.621	SUBCLONAL	1	FALSE	1	0.21474213626177	2		399	551	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467926	66467926	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061372-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	29	347	0	ENST00000273854.3:c.343A>T	p.Thr115Ser	p.T115S	ENST00000273854	NM_004439.5	115	Acc/Tcc	3/18	1	2	FACETS	0.621	0.498	0.761	0.621	0.498	0.761	SUBCLONAL	1	FALSE	1	0.21474213626177	2		347	435	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032573	47032573	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061372-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	22	204	0	ENST00000377604.3:c.479G>T	p.Arg160Leu	p.R160L	ENST00000377604	NM_001204468.1	160	cGg/cTg	5/24	1	1	FACETS	0.644	0.5	0.811	0.644	0.5	0.811	SUBCLONAL	1	FALSE	0	0.21474213626177	1		204	284	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0061373-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	15	407	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.581	0.424	0.771	0.581	0.424	0.771	SUBCLONAL	1	TRUE	1	0.15	2		407	344	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs121913292	NA	P-0061373-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	29	293	0	ENST00000371953.3:c.389del	p.Arg130GlnfsTer4	p.R130Qfs*4	ENST00000371953	NM_000314.4	130	cGa/ca	5/9	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.15	2		293	299	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220473	123220474	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0061373-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	30	326	0	ENST00000218089.9:c.3131dup	p.Tyr1044Ter	p.Y1044*	ENST00000218089	NM_001042749.1	1044	tac/tAac	30/35	1	2	FACETS	0.891	0.717	1	0.891	0.717	1	CLONAL	1	TRUE	1	0.15	2		326	449	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683478	29683478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061373-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	14	238	0	ENST00000356175.3:c.7553G>A	p.Gly2518Glu	p.G2518E	ENST00000356175	NM_000267.3	2518	gGa/gAa	51/57	1	2	FACETS	0.815	0.589	1	0.815	0.589	1	CLONAL	1	TRUE	1	0.15	2		238	229	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664711	138664711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061373-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	29	366	0	ENST00000330315.3:c.854C>T	p.Pro285Leu	p.P285L	ENST00000330315	NM_023067.3	285	cCg/cTg	1/1	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.15	2		366	343	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101115	27101127	+	frameshift_variant	Frame_Shift_Del	DEL	CACCCCCTGGCAC	CACCCCCTGGCAC	GG	novel	NA	P-0061373-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	30	485	1	ENST00000324856.7:c.4397_4409delinsGG	p.Ala1466GlyfsTer21	p.A1466Gfs*21	ENST00000324856	NM_006015.4	1466	gCACCCCCTGGCACc/gGGc	18/20	1	2	FACETS	0.755	0.607	0.923	0.755	0.607	0.923	CLONAL	1	TRUE	1	0.15	2		486	530	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589589	67589595	+	protein_altering_variant	In_Frame_Del	DEL	AATATAA	AATATAA	C	novel	NA	P-0061373-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	12	190	0	ENST00000274335.5:c.1352_1358delinsC	p.Glu451_Asn453delinsAla	p.E451_N453delinsA	ENST00000274335		451	gAATATAAc/gCc	10/15	1	2	FACETS	0.93	0.655	1	0.93	0.655	1	CLONAL	1	TRUE	1	0.15	2		190	172	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106648	27106648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553153748	NA	P-0061374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	18	513	0	ENST00000324856.7:c.6259G>A	p.Gly2087Arg	p.G2087R	ENST00000324856	NM_006015.4	2087	Gga/Aga	20/20	1	2	FACETS	0.14	0.104	0.182	0.14	0.104	0.182	SUBCLONAL	1	TRUE	1	0.4	2		513	645	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0061374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	253	544	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.3	2	FACETS	1	0.989	1	1	0.995	1	CLONAL	3	TRUE	0	0.4	2		544	379	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0061374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	206	504	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.772	0.72	0.826	1	0.992	1	SUBCLONAL	2	TRUE	1	0.4	2		504	667	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346338	73346338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	17	391	0	ENST00000377767.4:c.1462G>A	p.Asp488Asn	p.D488N	ENST00000377767	NM_014953.3	488	Gat/Aat	10/21	1	2	FACETS	0.193	0.143	0.252	0.193	0.143	0.252	SUBCLONAL	1	TRUE	1	0.4	2		391	441	SUCCESS
APC	324	MSKCC	GRCh37	5	112178607	112178607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1221895599	NA	P-0061374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	104	334	0	ENST00000257430.4:c.7316G>A	p.Arg2439His	p.R2439H	ENST00000257430	NM_000038.5	2439	cGc/cAc	16/16	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.4	2		334	518	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591892	48591892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767345	NA	P-0061385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	35	510	2	ENST00000342988.3:c.1055G>A	p.Gly352Glu	p.G352E	ENST00000342988	NM_005359.5	352	gGa/gAa	9/12	1	2	FACETS	0.453	0.37	0.546	0.453	0.37	0.546	SUBCLONAL	1	FALSE	1	0.255927887551362	2		512	604	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0061385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	44	465	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.519	0.434	0.613	0.519	0.434	0.613	SUBCLONAL	1	FALSE	1	0.255927887551362	2		465	663	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448271	56448271	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0061385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	84	535	0	ENST00000407977.2:c.375+1G>A		p.X125_splice	ENST00000407977		125			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	1	0.255927887551362	2		535	590	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	95	377	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.153356312996298	3	FACETS	0.765	0.683	0.852	0.765	0.683	0.852	INDETERMINATE	2	FALSE	1	0.255927887551362	3		377	547	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911586	32911586	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0061385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	30	342	0	ENST00000380152.3:c.3094A>C	p.Lys1032Gln	p.K1032Q	ENST00000380152		1032	Aaa/Caa	11/27	1	2	FACETS	0.442	0.355	0.54	0.442	0.355	0.54	SUBCLONAL	1	FALSE	1	0.255927887551362	2		342	531	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713263	30713263	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	50	565	0	ENST00000295754.5:c.588G>C	p.Lys196Asn	p.K196N	ENST00000295754	NM_003242.5	196	aaG/aaC	4/7	1	2	FACETS	0.581	0.492	0.68	0.581	0.492	0.68	SUBCLONAL	1	FALSE	1	0.255927887551362	2		565	672	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955022	93955022	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	24	287	0	ENST00000369303.4:c.2876C>G	p.Thr959Ser	p.T959S	ENST00000369303	NM_004440.3	959	aCt/aGt	16/17	1	2	FACETS	0.491	0.384	0.614	0.491	0.384	0.614	SUBCLONAL	1	FALSE	1	0.255927887551362	2		287	382	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412252	139412252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057523819	NA	P-0061386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	80	485	0	ENST00000277541.6:c.1393G>A	p.Ala465Thr	p.A465T	ENST00000277541	NM_017617.3	465	Gcc/Acc	8/34	1	2	FACETS	0.806	0.71	0.907	0.806	0.71	0.907	CLONAL	1	TRUE	1	0.359839789359962	2		485	552	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278070	18278070	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs886041602	NA	P-0061386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	59	451	0	ENST00000222254.8:c.1690A>G	p.Lys564Glu	p.K564E	ENST00000222254	NM_005027.3	564	Aag/Gag	13/16	1	2	FACETS	0.558	0.48	0.643	0.558	0.48	0.643	SUBCLONAL	1	TRUE	1	0.359839789359962	2		451	588	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060835	38060889	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGACTCGTGGGGTGCCAAGCCGTGTGCCGGGTGAGAGGCGGGCACAGAGGCCA	TGGGACTCGTGGGGTGCCAAGCCGTGTGCCGGGTGAGAGGCGGGCACAGAGGCCA	-	novel	NA	P-0061386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	99	621	1	ENST00000250448.2:c.1100_1154del	p.Leu367ArgfsTer4	p.L367Rfs*4	ENST00000250448	NM_004496.3	367	cTGGCCTCTGTGCCCGCCTCTCACCCGGCACACGGCTTGGCACCCCACGAGTCCCAg/cg	2/2	1	2	FACETS	0.721	0.644	0.804	0.721	0.644	0.804	SUBCLONAL	1	TRUE	1	0.359839789359962	2		622	763	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577563	7577573	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	TGTTACACATG	TGTTACACATG	-	novel	NA	P-0061386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	101	398	0	ENST00000269305.4:c.708_718del	p.Tyr236Ter	p.Y236*	ENST00000269305	NM_001126112.2	236	taCATGTGTAACAgt/tagt	7/11	0.359839789359962	1	FACETS	0.913	0.82	1	0.913	0.82	1	CLONAL	1	TRUE	0	0.359839789359962	1		398	504	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956595	93956595	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	95	390	0	ENST00000369303.4:c.2641C>G	p.Pro881Ala	p.P881A	ENST00000369303	NM_004440.3	881	Cca/Gca	15/17	1	2	FACETS	0.946	0.845	1	0.946	0.845	1	CLONAL	1	TRUE	1	0.359839789359962	2		390	558	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0061388-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	69	321	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.889	0.777	1	0.889	0.777	1	CLONAL	1	TRUE	1	0.369719521139829	2		321	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0061388-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	116	665	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.369719521139829	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.369719521139829	1		666	501	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172449	108172449	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061388-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	57	426	0	ENST00000278616.4:c.5252del	p.Glu1751GlyfsTer5	p.E1751Gfs*5	ENST00000278616	NM_000051.3	1751	gAg/gg	35/63	1	2	FACETS	0.918	0.792	1	0.918	0.792	1	CLONAL	1	TRUE	1	0.369719521139829	2		426	336	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560460	65560461	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AACTGTG	novel	NA	P-0061388-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	71	409	0	ENST00000358664.4:c.130_136dup	p.Leu46SerfsTer43	p.L46Sfs*43	ENST00000358664	NM_002382.4	46	ttg/tCACAGTTtg	3/5	0.369719521139829	1	FACETS	0.704	0.616	0.797	0.704	0.616	0.797	SUBCLONAL	1	TRUE	0	0.369719521139829	1		409	445	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821581	72821581	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061388-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	95	578	0	ENST00000268489.5:c.10594del	p.Leu3532TrpfsTer13	p.L3532Wfs*13	ENST00000268489	NM_006885.3	3532	Ctg/tg	10/10	1	2	FACETS	0.822	0.733	0.917	0.822	0.733	0.917	CLONAL	1	TRUE	1	0.369719521139829	2		578	625	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023366	31023366	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1021817273	NA	P-0061388-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	95	400	0	ENST00000375687.4:c.2851G>A	p.Asp951Asn	p.D951N	ENST00000375687	NM_015338.5	951	Gat/Aat	13/13	0.152898139223706	3	FACETS	0.99	0.883	1	0.495	0.441	0.552	INDETERMINATE	1	TRUE	1	0.369719521139829	3		400	615	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186501403	186501403	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061388-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	78	355	0	ENST00000323963.5:c.4T>G	p.Ser2Ala	p.S2A	ENST00000323963		2	Tct/Gct	1/11	1	2	FACETS	0.837	0.738	0.944	0.837	0.738	0.944	CLONAL	1	TRUE	1	0.369719521139829	2		355	504	SUCCESS
ALB	213	MSKCC	GRCh37	4	74276076	74276077	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0061388-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	66	337	0	ENST00000295897.4:c.665_666dup	p.Lys223SerfsTer19	p.K223Sfs*19	ENST00000295897	NM_000477.5	221	-/CT	6/15	0.369719521139829	1	FACETS	0.951	0.832	1	0.951	0.832	1	CLONAL	1	TRUE	0	0.369719521139829	1		337	306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0061389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	316	646	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.604645341451969	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.604645341451969	1		646	712	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0061389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	145	456	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.604645341451969	1	FACETS	0.435	0.397	0.475	0.435	0.397	0.475	SUBCLONAL	1	TRUE	0	0.604645341451969	1		456	769	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591888	48591888	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519739	NA	P-0061389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	12	457	0	ENST00000342988.3:c.1051G>C	p.Asp351His	p.D351H	ENST00000342988	NM_005359.5	351	Gat/Cat	9/12	0.604645341451969	1	FACETS	0.065	0.045	0.089	0.065	0.045	0.089	SUBCLONAL	1	TRUE	0	0.604645341451969	1		457	429	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732617	190732617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375020232	NA	P-0061389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	231	402	0	ENST00000441310.2:c.2435G>A	p.Arg812His	p.R812H	ENST00000441310	NM_000534.4	812	cGt/cAt	11/13	0.602023626483077	2	FACETS	0.982	0.933	1	0.982	0.933	1	CLONAL	2	TRUE	0	0.604645341451969	2		402	389	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355206	81355206	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	203	391	0	ENST00000222390.5:c.1168G>T	p.Asp390Tyr	p.D390Y	ENST00000222390	NM_000601.4	390	Gat/Tat	9/18	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.604645341451969	2		391	639	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221699	36221699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	206	629	0	ENST00000222270.7:c.5368G>A	p.Glu1790Lys	p.E1790K	ENST00000222270	NM_014727.1	1790	Gaa/Aaa	26/37	0.288886892300118	1	FACETS	0.468	0.434	0.503	0.468	0.434	0.503	INDETERMINATE	1	TRUE	0	0.604645341451969	1		629	1016	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138087	2138087	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	399	681	0	ENST00000219476.3:c.5107G>A	p.Val1703Met	p.V1703M	ENST00000219476	NM_000548.3	1703	Gtg/Atg	40/42	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.604645341451969	2		681	1255	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970918	70970918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1211840014	NA	P-0061389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	148	522	0	ENST00000276594.2:c.1343G>A	p.Arg448Gln	p.R448Q	ENST00000276594	NM_024504.3	448	cGg/cAg	6/8	0.288886892300118	1	FACETS	0.444	0.406	0.484	0.444	0.406	0.484	INDETERMINATE	1	TRUE	0	0.604645341451969	1		522	769	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0061389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	114	382	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.137641616314178	6	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.604645341451969	6		382	577	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435285	49435285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs758283638	NA	P-0061389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	295	635	0	ENST00000301067.7:c.6268G>T	p.Val2090Leu	p.V2090L	ENST00000301067	NM_003482.3	2090	Gtg/Ttg	31/54	NA	2	FACETS	0.934	0.88	0.989			1	INDETERMINATE	1	TRUE	NA	0.604645341451969	2		635	1045	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007419	45007818	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGATACCAAGTCACGGTTTATTCTTCAAAATGGAGGTGGCTTGTTGGGAAGGTGGAAGCTCATTTGGCCAGAGTGGAAATGGAATTGGGAGAAATCGATGACCAAATGTAAACACTTGGTGCCTGATATAGCTTGACACCAAGTTAGCCCCAAGTGAAATACCCTGGCAATATTAATGTGTCTTTTCCCGATATTCCTCAGGTACTCCAAAGATTCAGGTTTACTCACGTCATCCAGCAGAGAATGGAAAGTCAAATTTCCTGAATTGCTATGTGTCTGGGTTTCATCCATCCGACATTGAAGTTGACTTACTGAAGAATGGAGAGAGAATTGAAAAAGTGGAGCATTCAGACTTGTCTTTCAGCAAGGACTGGTCTTTCTATCTCTTGTACTACACTG	AAGATACCAAGTCACGGTTTATTCTTCAAAATGGAGGTGGCTTGTTGGGAAGGTGGAAGCTCATTTGGCCAGAGTGGAAATGGAATTGGGAGAAATCGATGACCAAATGTAAACACTTGGTGCCTGATATAGCTTGACACCAAGTTAGCCCCAAGTGAAATACCCTGGCAATATTAATGTGTCTTTTCCCGATATTCCTCAGGTACTCCAAAGATTCAGGTTTACTCACGTCATCCAGCAGAGAATGGAAAGTCAAATTTCCTGAATTGCTATGTGTCTGGGTTTCATCCATCCGACATTGAAGTTGACTTACTGAAGAATGGAGAGAGAATTGAAAAAGTGGAGCATTCAGACTTGTCTTTCAGCAAGGACTGGTCTTTCTATCTCTTGTACTACACTG	-	novel	NA	P-0061389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	86	64	0	ENST00000558401.1:c.68-200_267del		p.X23_splice	ENST00000558401	NM_004048.2	23		2/4	0.604645341451969	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.604645341451969	1		64	162	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989526	212989526	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	500	507	0	ENST00000342788.4:c.185A>T	p.Asn62Ile	p.N62I	ENST00000342788	NM_005235.2	62	aAc/aTc	2/28	0.602023626483077	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.604645341451969	2		507	814	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306622	41306622	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	162	438	0	ENST00000373198.4:c.1037A>C	p.Lys346Thr	p.K346T	ENST00000373198	NM_133170.3	346	aAg/aCg	7/32	1	2	FACETS	0.74	0.68	0.802	0.74	0.68	0.802	SUBCLONAL	1	TRUE	1	0.604645341451969	2		438	724	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266150	41266156	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCAAT	AGGCAAT	-	novel	NA	P-0061389-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	120	545	0	ENST00000349496.5:c.147_153del	p.Lys49AsnfsTer29	p.K49Nfs*29	ENST00000349496	NM_001904.3	49	aaAGGCAAT/aa	3/15	0.204416327664852	2	FACETS	0.534	0.483	0.589	0.267	0.241	0.295	INDETERMINATE	1	TRUE	0	0.604645341451969	2		545	743	SUCCESS
ATM	472	MSKCC	GRCh37	11	108126969	108126969	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061390-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	18	277	0	ENST00000278616.4:c.2152del	p.Cys718ValfsTer17	p.C718Vfs*17	ENST00000278616	NM_000051.3	718	Tgt/gt	14/63	1	2	FACETS	0.551	0.415	0.712	0.551	0.415	0.712	SUBCLONAL	1	FALSE	1	0.239318805769981	2		277	273	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100109	30100109	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061390-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	32	441	0	ENST00000331968.5:c.1511G>C	p.Gly504Ala	p.G504A	ENST00000331968	NM_002742.2	504	gGa/gCa	10/18	0.239318805769981	1	FACETS	0.54	0.438	0.655	0.54	0.438	0.655	SUBCLONAL	1	FALSE	0	0.239318805769981	1		441	436	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0061391-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	63	377	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.892	0.774	1	0.892	0.774	1	CLONAL	1	TRUE	1	0.338721148922101	2		377	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0061391-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	139	621	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.326742657183071	1	FACETS	0.974	0.888	1	0.974	0.888	1	CLONAL	1	TRUE	0	0.338721148922101	1		621	700	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222730	5222731	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs756013055	NA	P-0061391-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	89	426	0	ENST00000357368.4:c.3072dup	p.Val1025ArgfsTer34	p.V1025Rfs*34	ENST00000357368	NM_002850.3	1024	-/C	18/38	0.338721148922101	3	FACETS	0.882	0.782	0.988	0.441	0.391	0.494	CLONAL	1	TRUE	1	0.338721148922101	3		426	697	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89880959	89880959	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061391-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	64	303	0	ENST00000389301.3:c.252G>T	p.Glu84Asp	p.E84D	ENST00000389301	NM_000135.2	84	gaG/gaT	3/43	1	2	FACETS	0.727	0.63	0.831	0.727	0.63	0.831	SUBCLONAL	1	TRUE	1	0.338721148922101	2		303	520	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591936	48591941	+	inframe_deletion	In_Frame_Del	DEL	CTCTCC	CTCTCC	-	novel	NA	P-0061391-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	97	438	0	ENST00000342988.3:c.1099_1104del	p.Leu367_Ser368del	p.L367_S368del	ENST00000342988	NM_005359.5	367	CTCTCC/-	9/12	0.326742657183071	1	FACETS	0.859	0.768	0.955	0.859	0.768	0.955	CLONAL	1	TRUE	0	0.338721148922101	1		438	554	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662448	117662448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1260462127	NA	P-0061391-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	112	405	0	ENST00000368508.3:c.4929G>A	p.Met1643Ile	p.M1643I	ENST00000368508	NM_002944.2	1643	atG/atA	30/43	0.326742657183071	1	FACETS	0.96	0.866	1	0.96	0.866	1	CLONAL	1	TRUE	0	0.338721148922101	1		405	572	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974738	21974742	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCG	GCCCG	-	novel	NA	P-0061391-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	147	532	0	ENST00000304494.5:c.85_89del	p.Arg29AlafsTer13	p.R29Afs*13	ENST00000304494	NM_000077.4	29	CGGGCg/g	1/3	0.326742657183071	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.338721148922101	1		532	670	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593589	55593594	+	inframe_deletion	In_Frame_Del	DEL	TGTATG	TGTATG	-	novel	NA	P-0061392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	102	355	0	ENST00000288135.5:c.1655_1660del	p.Met552_Glu554delinsLys	p.M552_E554delinsK	ENST00000288135	NM_000222.2	552	aTGTATGaa/aaa	11/21	1	2	FACETS	0.969	0.87	1	0.969	0.87	1	CLONAL	1	TRUE	1	0.427114577583671	2		355	493	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0061393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	60	544	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.344672093993647	2	FACETS	0.762	0.667	0.862	0.381	0.333	0.431	INDETERMINATE	1	TRUE	0	0.7870333803012	2		544	200	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0061393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	156	271	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.372879792047378	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.7870333803012	0		272	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0061393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	536	589	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.775823712078592	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.7870333803012	2		589	664	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020754	37020754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	98	468	0	ENST00000358127.4:c.91C>T	p.Arg31Trp	p.R31W	ENST00000358127	NM_001280556.1	31	Cgg/Tgg	2/10	1	2	FACETS	0.506	0.453	0.562	0.506	0.453	0.562	SUBCLONAL	1	TRUE	1	0.7870333803012	2		468	492	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907602	76907602	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0061393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	132	351	0	ENST00000373344.5:c.4557+2T>G		p.X1519_splice	ENST00000373344	NM_000489.3	1519			0.29099433936854	1	FACETS	0.683	0.63	0.736	0.683	0.63	0.736	INDETERMINATE	1	TRUE	0	0.7870333803012	1		351	298	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554300	106554300	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	238	520	3	ENST00000369096.4:c.1828A>G	p.Lys610Glu	p.K610E	ENST00000369096	NM_001198.3	610	Aag/Gag	6/7	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.7870333803012	2		523	601	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974715	21974715	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	75	611	0	ENST00000304494.5:c.112C>A	p.Pro38Thr	p.P38T	ENST00000304494	NM_000077.4	38	Ccc/Acc	1/3	0.388326160565373	3	FACETS	0.35	0.306	0.397	0.175	0.153	0.199	INDETERMINATE	1	TRUE	1	0.7870333803012	3		611	759	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210201	123210201	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	46	378	0	ENST00000218089.9:c.2553A>T	p.Glu851Asp	p.E851D	ENST00000218089	NM_001042749.1	851	gaA/gaT	26/35	0.29099433936854	1	FACETS	0.201	0.169	0.235	0.201	0.169	0.235	INDETERMINATE	1	TRUE	0	0.7870333803012	1		378	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578528	7578528	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	167	483	0	ENST00000269305.4:c.402T>A	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	ttT/ttA	5/11	0.642655457576588	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.642655457576588	1		483	317	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442575	52442575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	126	442	1	ENST00000460680.1:c.170G>A	p.Arg57Gln	p.R57Q	ENST00000460680	NM_004656.3	57	cGg/cAg	4/17	0.642655457576588	1	FACETS	0.774	0.709	0.839	0.774	0.709	0.839	SUBCLONAL	1	TRUE	0	0.642655457576588	1		443	344	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675082	40675082	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1307486609	NA	P-0061394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	120	408	0	ENST00000249776.8:c.46A>C	p.Thr16Pro	p.T16P	ENST00000249776	NM_033286.3	16	Aca/Cca	1/9	0.642655457576588	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.642655457576588	1		408	249	SUCCESS
BLM	641	MSKCC	GRCh37	15	91334015	91334015	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555423111	NA	P-0061394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	114	335	0	ENST00000355112.3:c.2960C>G	p.Ser987Cys	p.S987C	ENST00000355112	NM_000057.2	987	tCt/tGt	15/22	0.642655457576588	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.642655457576588	1		335	218	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091850	29091850	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	34	83	0	ENST00000328354.6:c.1107del	p.Phe369LeufsTer13	p.F369Lfs*13	ENST00000328354	NM_007194.3	369	ttT/tt	11/15	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.642655457576588	2		83	88	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008909	152008909	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	174	338	0	ENST00000262189.6:c.713A>T	p.Asp238Val	p.D238V	ENST00000262189	NM_170606.2	238	gAt/gTt	5/59	0.183442715493122	1	FACETS	0.883	0.823	0.944	0.883	0.823	0.944	INDETERMINATE	1	TRUE	0	0.642655457576588	1		338	416	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	14	596	0	ENST00000397752.3:c.3028G>A	p.Asp1010Asn	p.D1010N	ENST00000397752	NM_000245.2	1010	Gat/Aat	14/21	0.247724420612301	1	FACETS	0.583	0.422	0.775	0.583	0.422	0.775	SUBCLONAL	1	TRUE	0	0.247724420612301	1		596	170	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185200218	185200218	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	16	405	0	ENST00000265026.3:c.2877del	p.Lys959AsnfsTer19	p.K959Nfs*19	ENST00000265026	NM_004721.4	959	Aaa/aa	14/14	1	2	FACETS	0.609	0.451	0.797	0.609	0.451	0.797	SUBCLONAL	1	TRUE	1	0.247724420612301	2		405	212	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691003	NA	P-0061461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	143	429	0	ENST00000269305.4:c.96+1G>T		p.X32_splice	ENST00000269305	NM_001126112.2	32			0.543002550589431	3	FACETS	0.993	0.933	1	0.993	0.933	1	CLONAL	3	TRUE	0	0.548525648088803	3		429	223	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741910	162741910	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	107	536	0	ENST00000367921.3:c.1601G>T	p.Gly534Val	p.G534V	ENST00000367921	NM_006182.2	534	gGa/gTa	13/18	0.549734166683484	5	FACETS	0.982	0.89	1	0.655	0.593	0.719	CLONAL	2	TRUE	2	0.548525648088803	5		536	362	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438084	438084	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs758504046	NA	P-0061461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	98	505	0	ENST00000399788.2:c.1885G>T	p.Val629Leu	p.V629L	ENST00000399788	NM_001042603.1	629	Gtg/Ttg	14/28	0.551110592740183	5	FACETS	1	0.904	1	0.668	0.602	0.736	CLONAL	2	TRUE	2	0.548525648088803	5		505	325	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948000	17948000	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	67	429	0	ENST00000458235.1:c.1724T>C	p.Leu575Ser	p.L575S	ENST00000458235	NM_000215.3	575	tTg/tCg	13/24	0.551110592740183	3	FACETS	1	0.96	1	0.615	0.541	0.693	CLONAL	1	TRUE	1	0.548525648088803	3		429	253	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425088	47425088	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0061461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	120	556	0	ENST00000404338.3:c.3158del	p.Lys1053ArgfsTer7	p.K1053Rfs*7	ENST00000404338	NM_004491.4	1052	acA/ac	1/6	0.471985299439589	4	FACETS	0.988	0.903	1	0.988	0.903	1	CLONAL	2	TRUE	2	0.548525648088803	4		556	343	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400011	49400011	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0061461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	129	472	0	ENST00000418115.1:c.326A>G	p.Asn109Ser	p.N109S	ENST00000418115	NM_001664.2	109	aAc/aGc	4/5	0.551110592740183	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.548525648088803	2		472	201	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867494	35867494	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	159	447	0	ENST00000303115.3:c.308G>T	p.Gly103Val	p.G103V	ENST00000303115	NM_002185.3	103	gGa/gTa	3/8	0.548525648088803	7	FACETS	0.93	0.859	1	0.558	0.515	0.602	CLONAL	3	TRUE	2	0.548525648088803	7		447	493	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851393	151851393	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776094080	NA	P-0061461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	58	510	0	ENST00000262189.6:c.12098C>T	p.Pro4033Leu	p.P4033L	ENST00000262189	NM_170606.2	4033	cCg/cTg	47/59	0.548525648088803	7	FACETS	0.913	0.785	1			1	CLONAL	1	TRUE	NA	0.548525648088803	7		510	549	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898755	134898755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs546798910	NA	P-0061462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	115	520	0	ENST00000398015.3:c.1813G>A	p.Glu605Lys	p.E605K	ENST00000398015	NM_004441.4	605	Gaa/Aaa	10/16	1	2	FACETS	0.984	0.889	1	0.984	0.889	1	CLONAL	1	TRUE	1	0.410166716977359	2		520	570	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322719	30322719	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	92	415	0	ENST00000322652.5:c.1732G>T	p.Glu578Ter	p.E578*	ENST00000322652	NM_015355.2	578	Gaa/Taa	14/16	0.410231493780966	1	FACETS	0.898	0.804	0.998	0.898	0.804	0.998	CLONAL	1	TRUE	0	0.410166716977359	1		415	397	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610499	10610499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs541663797	NA	P-0061462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	140	463	0	ENST00000171111.5:c.211C>T	p.Arg71Trp	p.R71W	ENST00000171111	NM_203500.1	71	Cgg/Tgg	2/6	0.410231493780966	1	FACETS	0.999	0.915	1	0.999	0.915	1	CLONAL	1	TRUE	0	0.410166716977359	1		463	543	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861964	57861964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	300	524	0	ENST00000228682.2:c.1265C>T	p.Pro422Leu	p.P422L	ENST00000228682	NM_005269.2	422	cCc/cTc	10/12	0.410166716977359	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.410166716977359	2		524	678	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2202697	2202697	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0061462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	102	472	0	ENST00000398665.3:c.708-2A>T		p.X236_splice	ENST00000398665	NM_032482.2	236			0.410231493780966	1	FACETS	0.915	0.824	1	0.915	0.824	1	CLONAL	1	TRUE	0	0.410166716977359	1		472	432	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134484	30134484	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	113	330	0	ENST00000263025.4:c.47G>C	p.Arg16Thr	p.R16T	ENST00000263025	NM_002746.2	16	aGa/aCa	1/9	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.410166716977359	2		330	460	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483100	29483100	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1060500330	NA	P-0061462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	79	364	0	ENST00000356175.3:c.160G>T	p.Val54Phe	p.V54F	ENST00000356175	NM_000267.3	54	Gtt/Ttt	2/57	0.410231493780966	1	FACETS	0.991	0.88	1	0.991	0.88	1	CLONAL	1	TRUE	0	0.410166716977359	1		364	309	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095002	11095002	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1315494799	NA	P-0061462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	125	548	0	ENST00000358026.2:c.175C>T	p.Gln59Ter	p.Q59*	ENST00000358026	NM_001128849.1	59	Cag/Tag	2/36	0.410231493780966	1	FACETS	0.989	0.9	1	0.989	0.9	1	CLONAL	1	TRUE	0	0.410166716977359	1		548	490	SUCCESS
AXL	558	MSKCC	GRCh37	19	41759516	41759516	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1568418105	NA	P-0061462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	119	504	0	ENST00000301178.4:c.1939C>G	p.Gln647Glu	p.Q647E	ENST00000301178	NM_021913.4	647	Cag/Gag	17/20	1	2	FACETS	0.943	0.854	1	0.943	0.854	1	CLONAL	1	TRUE	1	0.410166716977359	2		504	615	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149787	202149792	+	inframe_deletion	In_Frame_Del	DEL	AAACCC	AAACCC	-	novel	NA	P-0061462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	128	595	0	ENST00000358485.4:c.1231_1236del	p.Pro411_Lys412del	p.P411_K412del	ENST00000358485	NM_001080125.1	410	AAACCC/-	8/9	1	2	FACETS	0.893	0.81	0.979	0.893	0.81	0.979	CLONAL	1	TRUE	1	0.410166716977359	2		595	699	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514820	44514820	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	158	573	0	ENST00000291552.4:c.427G>T	p.Glu143Ter	p.E143*	ENST00000291552	NM_006758.2	143	Gag/Tag	6/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.410166716977359	2		573	671	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236600	236600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	31	152	0	ENST00000264932.6:c.1318G>A	p.Glu440Lys	p.E440K	ENST00000264932	NM_004168.2	440	Gag/Aag	10/15	0.410166716977359	5	FACETS	0.727	0.589	0.882	0.182	0.147	0.221	SUBCLONAL	1	TRUE	1	0.410166716977359	5		152	336	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859846	151859846	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0061462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	130	563	0	ENST00000262189.6:c.10816del	p.Arg3606GlufsTer24	p.R3606Efs*24	ENST00000262189	NM_170606.2	3606	Aga/ga	43/59	1	2	FACETS	0.873	0.793	0.957	0.873	0.793	0.957	CLONAL	1	TRUE	1	0.410166716977359	2		563	726	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184087	123184087	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061462-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	100	438	0	ENST00000218089.9:c.945G>C	p.Trp315Cys	p.W315C	ENST00000218089	NM_001042749.1	315	tgG/tgC	11/35	0.410231493780966	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.410166716977359	1		438	363	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1023835002	NA	P-0061463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	197	485	0	ENST00000558401.1:c.1A>G	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Gtg	1/4	0.576825605430817	1	FACETS	0.833	0.778	0.89	0.833	0.778	0.89	CLONAL	1	TRUE	0	0.60744895073108	1		485	542	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0061463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	169	375	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	0.605266350673045	1	FACETS	0.877	0.814	0.94	0.877	0.814	0.94	CLONAL	1	TRUE	0	0.60744895073108	1		375	442	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874261	155874261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352822	NA	P-0061463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	249	512	0	ENST00000368323.3:c.270G>A	p.Met90Ile	p.M90I	ENST00000368323	NM_006912.5	90	atG/atA	5/6	0.2613126667781	3	FACETS	1	0.978	1	0.548	0.513	0.584	INDETERMINATE	1	TRUE	1	0.60744895073108	3		512	975	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250978	99250978	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	249	571	0	ENST00000268035.6:c.282G>C	p.Glu94Asp	p.E94D	ENST00000268035	NM_000875.3	94	gaG/gaC	2/21	0.576825605430817	1	FACETS	0.924	0.87	0.978	0.924	0.87	0.978	CLONAL	1	TRUE	0	0.60744895073108	1		571	618	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189912	66189912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	161	410	0	ENST00000273854.3:c.3034C>T	p.Leu1012Phe	p.L1012F	ENST00000273854	NM_004439.5	1012	Ctt/Ttt	18/18	1	2	FACETS	0.974	0.899	1	0.974	0.899	1	CLONAL	1	TRUE	1	0.60744895073108	2		410	544	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220707	1220707	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	226	397	0	ENST00000326873.7:c.725G>T	p.Gly242Val	p.G242V	ENST00000326873	NM_000455.4	242	gGg/gTg	5/10	0.576825605430817	1	FACETS	0.928	0.872	0.985	0.928	0.872	0.985	CLONAL	1	TRUE	0	0.60744895073108	1		397	558	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602822	10602822	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	295	562	0	ENST00000171111.5:c.756G>T	p.Trp252Cys	p.W252C	ENST00000171111	NM_203500.1	252	tgG/tgT	3/6	0.576825605430817	1	FACETS	0.963	0.913	1	0.963	0.913	1	CLONAL	1	TRUE	0	0.60744895073108	1		562	702	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048638	6048638	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs372539944	NA	P-0061463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	290	836	0	ENST00000265849.7:c.13G>C	p.Glu5Gln	p.E5Q	ENST00000265849	NM_000535.5	5	Gag/Cag	1/15	1	2	FACETS	0.897	0.844	0.951	0.897	0.844	0.951	CLONAL	1	TRUE	1	0.60744895073108	2		836	1065	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158205	106158205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1383701111	NA	P-0061463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	262	519	0	ENST00000380013.4:c.3106C>T	p.His1036Tyr	p.H1036Y	ENST00000380013	NM_001127208.2	1036	Cac/Tac	3/11	1	2	FACETS	0.965	0.906	1	0.965	0.906	1	CLONAL	1	TRUE	1	0.60744895073108	2		519	894	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437376	110437376	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776945626	NA	P-0061463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	172	293	0	ENST00000375856.3:c.1025C>T	p.Ser342Leu	p.S342L	ENST00000375856	NM_003749.2	342	tCg/tTg	1/2	0.381180407487938	1	FACETS	0.9	0.837	0.964	0.9	0.837	0.964	CLONAL	1	TRUE	0	0.60744895073108	1		293	438	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965421	18965421	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	140	333	0	ENST00000262803.5:c.1168G>C	p.Glu390Gln	p.E390Q	ENST00000262803	NM_002911.3	390	Gag/Cag	9/24	NA	2	FACETS	0.807	0.738	0.879			1	INDETERMINATE	1	TRUE	NA	0.60744895073108	2		333	571	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876536	35876536	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0061463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	109	528	0	ENST00000303115.3:c.1328C>G	p.Ser443Ter	p.S443*	ENST00000303115	NM_002185.3	443	tCa/tGa	8/8	0.332273482298215	1	FACETS	0.385	0.346	0.426	0.385	0.346	0.426	INDETERMINATE	1	TRUE	0	0.60744895073108	1		528	649	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553172	41553172	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0061463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	160	411	0	ENST00000263253.7:c.3262-1G>C		p.X1088_splice	ENST00000263253	NM_001429.3	1088			1	2	FACETS	0.929	0.857	1	0.929	0.857	1	CLONAL	1	TRUE	1	0.60744895073108	2		411	567	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874221	155874221	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	256	516	0	ENST00000368323.3:c.310G>C	p.Asp104His	p.D104H	ENST00000368323	NM_006912.5	104	Gat/Cat	5/6	0.2613126667781	3	FACETS	1	0.979	1	0.549	0.514	0.585	INDETERMINATE	1	TRUE	1	0.60744895073108	3		516	1001	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64126729	64126729	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	172	366	0	ENST00000334205.4:c.22G>A	p.Glu8Lys	p.E8K	ENST00000334205	NM_003942.2	8	Gag/Aag	1/17	1	2	FACETS	0.849	0.784	0.916	0.849	0.784	0.916	CLONAL	1	TRUE	1	0.60744895073108	2		366	667	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127775	64127775	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs905329669	NA	P-0061463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	204	428	0	ENST00000334205.4:c.268G>T	p.Glu90Ter	p.E90*	ENST00000334205	NM_003942.2	90	Gag/Tag	3/17	1	2	FACETS	0.937	0.872	1	0.937	0.872	1	CLONAL	1	TRUE	1	0.60744895073108	2		428	717	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514274	69514274	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	248	550	0	ENST00000294312.3:c.407C>A	p.Ser136Tyr	p.S136Y	ENST00000294312	NM_005117.2	136	tCc/tAc	3/3	1	2	FACETS	0.974	0.914	1	0.974	0.914	1	CLONAL	1	TRUE	1	0.60744895073108	2		550	838	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630756	90630756	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs780131378	NA	P-0061463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	272	547	0	ENST00000330062.3:c.730T>C	p.Trp244Arg	p.W244R	ENST00000330062	NM_002168.2	244	Tgg/Cgg	6/11	0.576825605430817	1	FACETS	0.901	0.851	0.952	0.901	0.851	0.952	CLONAL	1	TRUE	0	0.60744895073108	1		547	692	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556931	29556931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	34	134	0	ENST00000356175.3:c.2929G>A	p.Glu977Lys	p.E977K	ENST00000356175	NM_000267.3	977	Gaa/Aaa	22/57	1	2	FACETS	0.788	0.655	0.933	0.788	0.655	0.933	CLONAL	1	TRUE	1	0.60744895073108	2		134	142	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775238	73775238	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	292	592	0	ENST00000254810.4:c.18G>C	p.Gln6His	p.Q6H	ENST00000254810	NM_005324.3	6	caG/caC	2/4	1	2	FACETS	0.976	0.92	1	0.976	0.92	1	CLONAL	1	TRUE	1	0.60744895073108	2		592	985	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758844	41758844	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0061463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	242	518	0	ENST00000301178.4:c.1898T>A	p.Leu633His	p.L633H	ENST00000301178	NM_021913.4	633	cTc/cAc	16/20	1	2	FACETS	0.944	0.884	1	0.944	0.884	1	CLONAL	1	TRUE	1	0.60744895073108	2		518	844	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160245	22160245	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	224	518	0	ENST00000215832.6:c.386T>C	p.Phe129Ser	p.F129S	ENST00000215832	NM_002745.4	129	tTt/tCt	3/9	1	2	FACETS	0.876	0.817	0.936	0.876	0.817	0.936	CLONAL	1	TRUE	1	0.60744895073108	2		518	842	SUCCESS
ALB	213	MSKCC	GRCh37	4	74274368	74274368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	182	467	0	ENST00000295897.4:c.328G>A	p.Glu110Lys	p.E110K	ENST00000295897	NM_000477.5	110	Gaa/Aaa	4/15	1	2	FACETS	0.877	0.812	0.944	0.877	0.812	0.944	CLONAL	1	TRUE	1	0.60744895073108	2		467	683	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158199	106158199	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1405763806	NA	P-0061463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	270	525	0	ENST00000380013.4:c.3100C>T	p.Gln1034Ter	p.Q1034*	ENST00000380013	NM_001127208.2	1034	Cag/Tag	3/11	1	2	FACETS	0.975	0.916	1	0.975	0.916	1	CLONAL	1	TRUE	1	0.60744895073108	2		525	912	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163297	32163297	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	270	580	0	ENST00000375023.3:c.5929G>T	p.Glu1977Ter	p.E1977*	ENST00000375023	NM_004557.3	1977	Gag/Tag	30/30	1	2	FACETS	0.922	0.866	0.979	0.922	0.866	0.979	CLONAL	1	TRUE	1	0.60744895073108	2		580	964	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117874120	117874120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	184	355	0	ENST00000297338.2:c.334G>A	p.Glu112Lys	p.E112K	ENST00000297338	NM_006265.2	112	Gaa/Aaa	4/14	0.530043098688884	4	FACETS	0.893	0.831	0.958	0.596	0.554	0.639	CLONAL	2	TRUE	1	0.60744895073108	4		355	545	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137325947	137325947	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0061463-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	233	366	0	ENST00000481739.1:c.1136-1G>T		p.X379_splice	ENST00000481739	NM_002957.4	379			0.576825605430817	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.60744895073108	1		366	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0061465-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	206	453	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.63998307765389	1	FACETS	0.975	0.916	1	0.975	0.916	1	CLONAL	1	TRUE	0	0.63998307765389	1		453	449	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0061465-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	15	318	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.363628769978751	1	FACETS	0.08	0.058	0.106	0.08	0.058	0.106	INDETERMINATE	1	TRUE	0	0.63998307765389	1		318	400	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0061465-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	244	210	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.63998307765389	1	FACETS	0.921	0.869	0.974	0.921	0.869	0.974	CLONAL	1	TRUE	0	0.63998307765389	1		210	563	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303220	15303220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs932099250	NA	P-0061465-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	227	532	0	ENST00000263388.2:c.308G>A	p.Arg103Gln	p.R103Q	ENST00000263388	NM_000435.2	103	cGa/cAa	3/33	0.63998307765389	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.63998307765389	1		532	480	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244034	153244034	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0061465-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	400	481	0	ENST00000281708.4:c.2123G>C	p.Ter708SerextTer53	p.*708Sext*53	ENST00000281708	NM_033632.3	708	tGa/tCa	12/12	0.58918388416813	2	FACETS	0.951	0.916	0.987	0.951	0.916	0.987	CLONAL	2	TRUE	0	0.63998307765389	2		481	657	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121912651	NA	P-0061466-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	404	431	0	ENST00000269305.4:c.742C>G	p.Arg248Gly	p.R248G	ENST00000269305	NM_001126112.2	248	Cgg/Ggg	7/11	0.525311093308418	2	FACETS	0.96	0.923	0.997	0.96	0.923	0.997	CLONAL	2	TRUE	0	0.598724133804189	2		431	703	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936766	78936766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061466-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	361	595	0	ENST00000306801.3:c.3848G>A	p.Ser1283Asn	p.S1283N	ENST00000306801	NM_020761.2	1283	aGc/aAc	33/34	0.598724133804189	3	FACETS	0.917	0.874	0.961	0.917	0.874	0.961	CLONAL	2	TRUE	1	0.598724133804189	3		595	854	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004255	150004255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1314146200	NA	P-0061468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	106	426	0	ENST00000253339.5:c.1970G>A	p.Arg657His	p.R657H	ENST00000253339		657	cGt/cAt	3/7	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.435082227640194	2		426	452	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257173	16257176	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	novel	NA	P-0061468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	134	509	0	ENST00000375759.3:c.4441_4444del	p.Glu1481ArgfsTer14	p.E1481Rfs*14	ENST00000375759	NM_015001.2	1480	AAAGaa/aa	11/15	1	2	FACETS	0.871	0.793	0.953	0.871	0.793	0.953	CLONAL	1	TRUE	1	0.435082227640194	2		509	707	SUCCESS
ATM	472	MSKCC	GRCh37	11	108183151	108183151	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	151	369	0	ENST00000278616.4:c.5932G>C	p.Glu1978Gln	p.E1978Q	ENST00000278616	NM_000051.3	1978	Gaa/Caa	40/63	0.400048778985897	3	FACETS	0.882	0.813	0.954	0.882	0.813	0.954	CLONAL	2	TRUE	1	0.435082227640194	3		369	479	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061010	38061011	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0061468-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	129	525	0	ENST00000250448.2:c.977_978dup	p.Gly327ProfsTer24	p.G327Pfs*24	ENST00000250448	NM_004496.3	326	-/CC	2/2	1	2	FACETS	0.922	0.838	1	0.922	0.838	1	CLONAL	1	TRUE	1	0.435082227640194	2		525	643	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0061469-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	34	677	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.148737435519495	3	FACETS	0.636	0.518	0.77	0.318	0.259	0.385	SUBCLONAL	1	TRUE	1	0.17	3		677	682	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0061469-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	66	189	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	0.3	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	2	TRUE	0	0.17	2		189	367	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0061469-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	36	611	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.833	1	1	0.833	1	CLONAL	1	TRUE	1	0.17	2		611	418	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732533	74732533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061469-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	45	444	0	ENST00000359995.5:c.376C>T	p.Arg126Cys	p.R126C	ENST00000359995	NM_001195427.1	126	Cgc/Tgc	2/3	1	2	FACETS	0.935	0.785	1	0.935	0.785	1	CLONAL	1	TRUE	1	0.17	2		444	566	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63531751	63531751	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1314547209	NA	P-0061469-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	37	377	1	ENST00000307078.5:c.2230C>T	p.Pro744Ser	p.P744S	ENST00000307078	NM_004655.3	744	Cca/Tca	9/11	1	2	FACETS	0.821	0.676	0.984	0.821	0.676	0.984	CLONAL	1	TRUE	1	0.17	2		378	530	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021740	71021740	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061469-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	80	436	0	ENST00000318789.4:c.1618G>T	p.Glu540Ter	p.E540*	ENST00000318789	NM_032682.5	540	Gaa/Taa	18/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.17	2		436	732	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295606	1295606	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0061469-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	40	553	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.758	0.628	0.902	0.758	0.628	0.902	CLONAL	1	TRUE	1	0.17	2		553	621	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851866	128851867	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0061469-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	28	467	0	ENST00000249373.3:c.1943dup	p.Glu649ArgfsTer10	p.E649Rfs*10	ENST00000249373	NM_005631.4	646	-/C	12/12	1	2	FACETS	0.647	0.516	0.797	0.647	0.516	0.797	SUBCLONAL	1	TRUE	1	0.17	2		467	509	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399816	139399816	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061469-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	44	482	0	ENST00000277541.6:c.4532C>T	p.Ser1511Leu	p.S1511L	ENST00000277541	NM_017617.3	1511	tCa/tTa	25/34	1	2	FACETS	0.79	0.661	0.933	0.79	0.661	0.933	CLONAL	1	TRUE	1	0.17	2		482	655	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0061470-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	137	453	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.80075492827414	2	FACETS	0.98	0.935	1	0.98	0.935	1	CLONAL	2	TRUE	0	0.831993011700717	2		453	168	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123836	46123837	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0061470-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	194	406	0	ENST00000334344.6:c.109dup	p.Ile37AsnfsTer29	p.I37Nfs*29	ENST00000334344	NM_152641.2	34	-/A	2/21	0.831993011700717	3	FACETS	0.885	0.833	0.937	0.885	0.833	0.937	CLONAL	2	TRUE	1	0.831993011700717	3		406	373	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287446	46287446	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs774801990	NA	P-0061470-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	56	355	0	ENST00000334344.6:c.5305C>T	p.Arg1769Ter	p.R1769*	ENST00000334344	NM_152641.2	1769	Cga/Tga	20/21	0.831993011700717	3	FACETS	0.934	0.812	1	0.467	0.406	0.532	CLONAL	1	TRUE	1	0.831993011700717	3		355	204	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120652	115120652	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061470-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	112	437	0	ENST00000257566.3:c.354G>T	p.Lys118Asn	p.K118N	ENST00000257566	NM_016569.3	118	aaG/aaT	1/8	0.831993011700717	3	FACETS	1	0.976	1	0.605	0.551	0.66	CLONAL	1	TRUE	1	0.831993011700717	3		437	315	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280028	66280028	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1276862103	NA	P-0061470-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	61	316	1	ENST00000273854.3:c.1661G>T	p.Arg554Ile	p.R554I	ENST00000273854	NM_004439.5	554	aGa/aTa	7/18	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.831993011700717	2		317	135	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0061471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	186	592	0	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.251212932264342	2	FACETS	0.849	0.785	0.916	0.849	0.785	0.916	CLONAL	2	TRUE	0	0.251212932264342	2		592	872	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574005	7574005	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	163	356	0	ENST00000269305.4:c.1022T>C	p.Phe341Ser	p.F341S	ENST00000269305	NM_001126112.2	341	tTc/tCc	10/11	0.141196615707159	3	FACETS	1	0.978	1	0.778	0.717	0.841	INDETERMINATE	2	TRUE	0	0.251212932264342	3		356	626	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2208944	2208944	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0061471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	127	284	0	ENST00000398665.3:c.974A>G	p.Tyr325Cys	p.Y325C	ENST00000398665	NM_032482.2	325	tAt/tGt	12/28	0.251212932264342	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.251212932264342	2		284	447	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426127	47426127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0061471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	193	498	0	ENST00000377045.4:c.647C>G	p.Pro216Arg	p.P216R	ENST00000377045	NM_001654.4	216	cCc/cGc	7/16	0.251212932264342	3	FACETS	0.923	0.854	0.994	0.923	0.854	0.994	CLONAL	2	TRUE	1	0.251212932264342	3		498	937	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047494	49047494	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0061471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	58	285	0	ENST00000267163.4:c.2490-2A>T		p.X830_splice	ENST00000267163	NM_000321.2	830			0.251119358485124	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.251212932264342	2		285	191	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414266	32414266	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	150	369	0	ENST00000332351.3:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000332351	NM_024426.4	429	Gaa/Taa	8/10	0.251212932264342	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.251212932264342	2		369	548	SUCCESS
MAD2L2	10459	MSKCC	GRCh37	1	11740433	11740433	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0061471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	175	391	0	ENST00000235310.3:c.136A>C	p.Lys46Gln	p.K46Q	ENST00000235310		46	Aag/Cag	5/11	0.251212932264342	3	FACETS	0.929	0.856	1	0.929	0.856	1	CLONAL	2	TRUE	1	0.251212932264342	3		391	844	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429829	78429830	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0061471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	118	431	0	ENST00000370768.2:c.958_959del	p.Glu320LysfsTer30	p.E320Kfs*30	ENST00000370768	NM_003902.3	320	GAa/a	12/20	0.251212932264342	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.251212932264342	3		431	456	SUCCESS
H3C13	653604	MSKCC	GRCh37	1	149784837	149784837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	58	328	0	ENST00000331491.1:c.400G>A	p.Glu134Lys	p.E134K	ENST00000331491	NM_001123375.2	134	Gag/Aag	1/1	0.251212932264342	5	FACETS	1	0.868	1	0.253	0.217	0.292	CLONAL	1	TRUE	1	0.251212932264342	5		328	629	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163298057	163298057	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0061471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	47	360	0	ENST00000271452.3:c.238G>T	p.Glu80Ter	p.E80*	ENST00000271452	NM_145697.2	80	Gaa/Taa	4/14	0.251212932264342	5	FACETS	1	0.96	1	0.368	0.311	0.43	CLONAL	1	TRUE	1	0.251212932264342	5		360	350	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223046	1223046	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1405959130	NA	P-0061471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	211	492	0	ENST00000326873.7:c.983C>G	p.Thr328Ser	p.T328S	ENST00000326873	NM_000455.4	328	aCc/aGc	8/10	0.251212932264342	2	FACETS	0.946	0.88	1	0.946	0.88	1	CLONAL	2	TRUE	0	0.251212932264342	2		492	888	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498383	89498383	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	89	362	0	ENST00000336596.2:c.2355G>T	p.Lys785Asn	p.K785N	ENST00000336596	NM_005233.5	785	aaG/aaT	14/17	0.251212932264342	2	FACETS	0.911	0.813	1	0.911	0.813	1	CLONAL	2	TRUE	0	0.251212932264342	2		362	389	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048885	180048886	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0061471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	167	498	1	ENST00000261937.6:c.1676_1677delinsAA	p.Thr559Lys	p.T559K	ENST00000261937	NM_182925.4	559	aCC/aAA	13/30	0.141490774633692	4	FACETS	0.951	0.874	1	0.951	0.874	1	INDETERMINATE	2	TRUE	2	0.251212932264342	4		499	875	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965330	68965330	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0061471-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	52	317	0	ENST00000288368.4:c.944-2A>T		p.X315_splice	ENST00000288368	NM_024870.2	315			0.141490774633692	4	FACETS	0.83	0.711	0.959	0.83	0.711	0.959	INDETERMINATE	2	TRUE	2	0.251212932264342	4		317	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203436	NA	P-0061472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	50	556	0	ENST00000269305.4:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269305	NM_001126112.2	163	Tac/Cac	5/11	1	2	FACETS	0.393	0.333	0.46	0.393	0.333	0.46	SUBCLONAL	1	TRUE	1	0.36	2		556	706	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946137	55946137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	35	472	0	ENST00000263923.4:c.4042G>A	p.Gly1348Arg	p.G1348R	ENST00000263923	NM_002253.2	1348	Ggg/Agg	30/30	1	2	FACETS	0.322	0.263	0.388	0.322	0.263	0.388	SUBCLONAL	1	TRUE	1	0.36	2		472	604	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136880	55136880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514549	NA	P-0061472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	21	300	0	ENST00000257290.5:c.1202C>T	p.Ala401Val	p.A401V	ENST00000257290	NM_006206.4	401	gCt/gTt	8/23	1	2	FACETS	0.326	0.25	0.414	0.326	0.25	0.414	SUBCLONAL	1	TRUE	1	0.36	2		300	358	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409083	4409083	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1445439577	NA	P-0061472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	35	436	0	ENST00000261254.3:c.778C>A	p.Gln260Lys	p.Q260K	ENST00000261254	NM_001759.3	260	Cag/Aag	5/5	1	2	FACETS	0.288	0.235	0.347	0.288	0.235	0.347	SUBCLONAL	1	TRUE	1	0.36	2		436	676	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141550	11141550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0061472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	38	544	0	ENST00000358026.2:c.3527G>T	p.Ser1176Ile	p.S1176I	ENST00000358026	NM_001128849.1	1176	aGc/aTc	25/36	1	2	FACETS	0.343	0.283	0.411	0.343	0.283	0.411	SUBCLONAL	1	TRUE	1	0.36	2		544	615	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186892	142186892	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	27	372	0	ENST00000350721.4:c.6571G>T	p.Val2191Leu	p.V2191L	ENST00000350721	NM_001184.3	2191	Gtg/Ttg	39/47	1	2	FACETS	0.412	0.328	0.508	0.412	0.328	0.508	SUBCLONAL	1	TRUE	1	0.36	2		372	364	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286220	66286220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	24	435	0	ENST00000273854.3:c.1466G>T	p.Trp489Leu	p.W489L	ENST00000273854	NM_004439.5	489	tGg/tTg	6/18	1	2	FACETS	0.367	0.288	0.459	0.367	0.288	0.459	SUBCLONAL	1	TRUE	1	0.36	2		435	363	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531127	187531128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0061472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	36	429	0	ENST00000441802.2:c.9895dup	p.His3299ProfsTer2	p.H3299Pfs*2	ENST00000441802	NM_005245.3	3299	cat/cCat	15/27	1	2	FACETS	0.355	0.291	0.427	0.355	0.291	0.427	SUBCLONAL	1	TRUE	1	0.36	2		429	563	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707702	176707702	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	36	548	0	ENST00000439151.2:c.5759G>C	p.Cys1920Ser	p.C1920S	ENST00000439151	NM_022455.4	1920	tGc/tCc	18/23	1	2	FACETS	0.282	0.231	0.339	0.282	0.231	0.339	SUBCLONAL	1	TRUE	1	0.36	2		548	710	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402492	139402492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0061472-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	30	482	2	ENST00000277541.6:c.3425G>A	p.Cys1142Tyr	p.C1142Y	ENST00000277541	NM_017617.3	1142	tGt/tAt	21/34	1	2	FACETS	0.288	0.231	0.353	0.288	0.231	0.353	SUBCLONAL	1	TRUE	1	0.36	2		484	578	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875627	35875627	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369971728	NA	P-0061474-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	36	412	0	ENST00000303115.3:c.814G>A	p.Val272Ile	p.V272I	ENST00000303115	NM_002185.3	272	Gta/Ata	7/8	1	2	FACETS	0.622	0.511	0.747	0.622	0.511	0.747	SUBCLONAL	1	TRUE	1	0.251067972864248	2		412	461	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417398	139417398	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0061474-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	104	568	0	ENST00000277541.6:c.646G>T	p.Glu216Ter	p.E216*	ENST00000277541	NM_017617.3	216	Gag/Tag	4/34	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.251067972864248	2		568	724	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175996814	175996814	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0061474-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	81	371	0	ENST00000367669.3:c.1623G>T	p.Trp541Cys	p.W541C	ENST00000367669	NM_022457.5	541	tgG/tgT	15/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.251067972864248	2		371	552	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180397	94180397	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0061474-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	37	396	0	ENST00000323929.3:c.1771C>G	p.Gln591Glu	p.Q591E	ENST00000323929	NM_005591.3	591	Caa/Gaa	15/20	1	2	FACETS	0.606	0.5	0.726	0.606	0.5	0.726	SUBCLONAL	1	TRUE	1	0.251067972864248	2		396	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577516	7577516	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0061474-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	81	431	0	ENST00000269305.4:c.765del	p.Thr256HisfsTer89	p.T256Hfs*89	ENST00000269305	NM_001126112.2	255	atC/at	7/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.251067972864248	2		431	560	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033210	69033210	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0061474-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	78	369	0	ENST00000288368.4:c.3650A>T	p.His1217Leu	p.H1217L	ENST00000288368	NM_024870.2	1217	cAt/cTt	30/40	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.251067972864248	2		369	571	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0061476-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	81	579	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.283937893555188	3	FACETS	0.895	0.795	1	0.895	0.795	1	CLONAL	2	TRUE	1	0.305961361885994	3		579	341	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519731	176519731	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1348650129	NA	P-0061476-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	76	443	0	ENST00000292408.4:c.1003G>A	p.Ala335Thr	p.A335T	ENST00000292408	NM_213647.1	335	Gca/Aca	8/18	0.283937893555188	3	FACETS	0.895	0.792	1	0.895	0.792	1	CLONAL	2	TRUE	1	0.305961361885994	3		443	320	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281908	49281908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0061476-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	21	395	0	ENST00000282018.3:c.955G>A	p.Ala319Thr	p.A319T	ENST00000282018	NM_020377.2	319	Gca/Aca	1/1	0.283937893555188	3	FACETS	0.423	0.325	0.538	0.212	0.162	0.269	SUBCLONAL	1	TRUE	1	0.305961361885994	3		395	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0000196-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	187	932	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.282773701402504	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	0	0.282773701402504	2		932	655	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0000196-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	543	542	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.282773701402504	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	4	TRUE	0	0.282773701402504	4		542	1172	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161222	56161222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000196-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	274	759	0	ENST00000399503.3:c.1091G>A	p.Arg364Gln	p.R364Q	ENST00000399503	NM_005921.1	364	cGg/cAg	5/20	0.282773701402504	4	FACETS	0.947	0.888	1	0.947	0.888	1	CLONAL	2	TRUE	2	0.282773701402504	4		759	1312	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161259	56161259	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000196-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	242	659	0	ENST00000399503.3:c.1128G>A	p.Trp376Ter	p.W376*	ENST00000399503	NM_005921.1	376	tgG/tgA	5/20	0.282773701402504	4	FACETS	0.986	0.921	1	0.986	0.921	1	CLONAL	2	TRUE	2	0.282773701402504	4		659	1113	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32903618	32903618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660484	NA	P-0000196-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	70	739	0	ENST00000380152.3:c.670G>A	p.Asp224Asn	p.D224N	ENST00000380152		224	Gat/Aat	8/27	0.254506116204709	4	FACETS	0.561	0.487	0.641	0.14	0.121	0.161	SUBCLONAL	1	TRUE	0	0.282773701402504	4		739	1133	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619282	37619283	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0000196-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	115	311	0	ENST00000447079.4:c.959dup	p.Ser320ArgfsTer31	p.S320Rfs*31	ENST00000447079	NM_015083.1	320	agc/aGgc	1/14	0.282773701402504	2	FACETS	0.904	0.819	0.992	0.904	0.819	0.992	CLONAL	2	TRUE	0	0.282773701402504	2		311	450	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252988	36252988	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000196-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	164	360	0	ENST00000300305.3:c.374del	p.Pro125GlnfsTer8	p.P125Qfs*8	ENST00000300305		125	cCa/ca	4/8	0.282773701402504	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.282773701402504	3		360	621	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696449	47696449	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	235	551	0	ENST00000347630.2:c.374T>G	p.Phe125Cys	p.F125C	ENST00000347630	NM_001007230.1	125	tTt/tGt	6/11	0.654233849603122	2	FACETS	1	0.984	1	0.566	0.531	0.601	CLONAL	1	TRUE	0	0.664820781547621	2		551	625	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400279	225400279	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	118	297	0	ENST00000264414.4:c.344C>G	p.Ala115Gly	p.A115G	ENST00000264414	NM_003590.4	115	gCt/gGt	3/16	1	2	FACETS	0.913	0.831	0.997	0.913	0.831	0.997	CLONAL	1	TRUE	1	0.664820781547621	2		297	389	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177822	142177822	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	130	279	0	ENST00000350721.4:c.7481A>C	p.Asp2494Ala	p.D2494A	ENST00000350721	NM_001184.3	2494	gAt/gCt	44/47	0.664820781547621	3	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.664820781547621	3		279	443	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627337	37627340	+	frameshift_variant	Frame_Shift_Del	DEL	AAGG	AAGG	-	novel	NA	P-0000505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	517	536	0	ENST00000447079.4:c.1253_1256del	p.Lys418SerfsTer17	p.K418Sfs*17	ENST00000447079	NM_015083.1	418	AAGGag/ag	2/14	0.172033561681562	5	FACETS	0.997	0.966	1			1	INDETERMINATE	4	TRUE	NA	0.664820781547621	5		536	779	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552648	18552648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	122	672	0	ENST00000266497.5:c.2059G>A	p.Glu687Lys	p.E687K	ENST00000266497		687	Gaa/Aaa	14/31	1	2	FACETS	0.464	0.419	0.511	0.464	0.419	0.511	SUBCLONAL	1	TRUE	1	0.664820781547621	2		672	791	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023196	33023196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	82	496	0	ENST00000300177.4:c.305C>T	p.Thr102Ile	p.T102I	ENST00000300177	NM_001191322.1	102	aCc/aTc	2/2	NA	2	FACETS	0.442	0.39	0.497			1	INDETERMINATE	1	TRUE	NA	0.664820781547621	2		496	558	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923265	78923265	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	229	547	0	ENST00000306801.3:c.3288G>A	p.Trp1096Ter	p.W1096*	ENST00000306801	NM_020761.2	1096	tgG/tgA	28/34	0.661943952660893	2	FACETS	0.939	0.878	1	0.469	0.439	0.5	CLONAL	1	TRUE	0	0.664820781547621	2		547	734	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000514-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	15	243	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.896	0.664	1	0.896	0.664	1	CLONAL	1	TRUE	1	0.331602060574674	2		243	101	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0000514-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	21	342	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.331602060574674	2		342	113	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771321	68771321	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs878854691	NA	P-0000514-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	12	270	0	ENST00000261769.5:c.3G>A	p.Met1?	p.M1?	ENST00000261769	NM_004360.3	1	atG/atA	1/16	0.331602060574674	1	FACETS	0.99	0.712	1	0.99	0.712	1	CLONAL	1	TRUE	0	0.331602060574674	1		270	61	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692896	89692896	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs398123322	NA	P-0000648-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	121	355	0	ENST00000371953.3:c.380G>T	p.Gly127Val	p.G127V	ENST00000371953	NM_000314.4	127	gGa/gTa	5/9	1	2	FACETS	0.958	0.866	1	1	0.989	1	CLONAL	2	TRUE	1	0.18	2		355	702	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781504	NA	P-0000648-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	62	406	0	ENST00000269305.4:c.314G>T	p.Gly105Val	p.G105V	ENST00000269305	NM_001126112.2	105	gGc/gTc	4/11	0.3	1	FACETS	0.848	0.732	0.975	0.848	0.732	0.975	CLONAL	1	TRUE	0	0.18	1		406	739	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001396-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	81	243	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.298297375710467	3	FACETS	0.967	0.853	1	0.484	0.426	0.545	CLONAL	1	TRUE	1	0.31	3		243	624	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577524	7577524	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001396-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	159	464	0	ENST00000269305.4:c.757A>C	p.Thr253Pro	p.T253P	ENST00000269305	NM_001126112.2	253	Acc/Ccc	7/11	0.298297375710467	2	FACETS	0.964	0.889	1	0.964	0.889	1	CLONAL	2	TRUE	0	0.31	2		464	532	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687586	29687586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001396-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	109	522	0	ENST00000356175.3:c.8179G>A	p.Glu2727Lys	p.E2727K	ENST00000356175	NM_000267.3	2727	Gaa/Aaa	56/57	0.298297375710467	4	FACETS	0.958	0.859	1	0.319	0.286	0.355	CLONAL	1	TRUE	1	0.31	4		522	962	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691950	30691950	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001396-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	48	249	0	ENST00000295754.5:c.453del	p.Glu152AsnfsTer11	p.E152Nfs*11	ENST00000295754	NM_003242.5	151	gAa/ga	3/7	1	2	FACETS	0.691	0.585	0.808	0.691	0.585	0.808	SUBCLONAL	1	TRUE	1	0.31	2		249	448	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40478169	40478169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1288968449	NA	P-0001396-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	103	479	0	ENST00000264657.5:c.1330G>A	p.Glu444Lys	p.E444K	ENST00000264657	NM_139276.2	444	Gag/Aag	15/24	0.287402055730053	3	FACETS	0.909	0.813	1	0.455	0.406	0.506	CLONAL	1	TRUE	1	0.31	3		479	844	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419932	152419932	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001504-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	44	548	0	ENST00000206249.3:c.1619T>A	p.Leu540Gln	p.L540Q	ENST00000206249	NM_000125.3	540	cTg/cAg	8/8	0.531501292398223	1	FACETS	0.215	0.18	0.254	0.215	0.18	0.254	SUBCLONAL	1	TRUE	0	0.531501292398223	1		548	565	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196056	67196056	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334740541	NA	P-0001504-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1249	102	1008	2	ENST00000312629.5:c.40G>A	p.Gly14Ser	p.G14S	ENST00000312629	NM_003952.2	14	Ggc/Agc	1/15	0.531501292398223	5	FACETS	0.511	0.455	0.57			1	SUBCLONAL	1	TRUE	NA	0.531501292398223	5		1010	1351	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196056	67196056	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334740541	NA	P-0001504-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1525	136	1008	2	ENST00000312629.5:c.40G>A	p.Gly14Ser	p.G14S	ENST00000312629	NM_003952.2	14	Ggc/Agc	1/15	0.530842087899696	8	FACETS	0.8	0.724	0.88	0.133	0.12	0.147	SUBCLONAL	1	TRUE	2	0.530842087899696	8		1010	1661	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0001939-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	93	304	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.258590544557326	1	FACETS	0.715	0.639	0.795	0.715	0.639	0.795	INDETERMINATE	1	TRUE	0	0.470323596589147	1		304	423	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193995	106193995	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1376289450	NA	P-0001939-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	86	344	0	ENST00000380013.4:c.4457C>G	p.Ser1486Ter	p.S1486*	ENST00000380013	NM_001127208.2	1486	tCa/tGa	10/11	1	2	FACETS	0.355	0.313	0.4	0.355	0.313	0.4	SUBCLONAL	1	TRUE	1	0.470323596589147	2		344	1030	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121074	3121074	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0001939-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	174	532	0	ENST00000078429.4:c.977C>G	p.Ser326Ter	p.S326*	ENST00000078429	NM_002067.2	326	tCa/tGa	7/7	1	2	FACETS	0.563	0.516	0.611	0.563	0.516	0.611	SUBCLONAL	1	TRUE	1	0.470323596589147	2		532	1315	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40739804	40739804	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001939-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	176	402	0	ENST00000392038.2:c.1421C>G	p.Ser474Cys	p.S474C	ENST00000392038	NM_001626.4	474	tCc/tGc	14/14	0.258590544557326	1	FACETS	0.578	0.532	0.626	0.578	0.532	0.626	INDETERMINATE	1	TRUE	0	0.470323596589147	1		402	991	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979361	40979361	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001939-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	87	221	0	ENST00000373198.4:c.1772T>A	p.Met591Lys	p.M591K	ENST00000373198	NM_133170.3	591	aTg/aAg	11/32	0.184136419933664	3	FACETS	0.57	0.504	0.641	0.285	0.252	0.321	INDETERMINATE	1	TRUE	1	0.470323596589147	3		221	802	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023565	31023565	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	174	404	0	ENST00000375687.4:c.3050A>G	p.Asp1017Gly	p.D1017G	ENST00000375687	NM_015338.5	1017	gAc/gGc	13/13	1	2	FACETS	0.911	0.847	0.976	0.911	0.847	0.976	CLONAL	1	TRUE	1	0.826772281820428	2		404	462	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937111	76937111	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004269-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	204	680	0	ENST00000373344.5:c.3637C>T	p.Gln1213Ter	p.Q1213*	ENST00000373344	NM_000489.3	1213	Cag/Tag	9/35	NA	2	FACETS	0.684	0.637	0.733			1	INDETERMINATE	1	TRUE	NA	0.826772281820428	2		680	721	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0004313-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	41	327	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.758	0.634	0.895	0.758	0.634	0.895	SUBCLONAL	1	TRUE	1	0.347716758723256	2		327	311	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0004313-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	44	476	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.727	0.612	0.854	0.727	0.612	0.854	SUBCLONAL	1	TRUE	1	0.347716758723256	2		476	348	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004322-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	26	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		334	678	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0004322-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	25	821	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		822	679	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0004697-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	278	395	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.653359780915453	3	FACETS	0.968	0.921	1	0.968	0.921	1	CLONAL	2	TRUE	1	0.760526457513466	3		395	521	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0004697-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	196	937	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	0.674576825072664	3	FACETS	0.977	0.908	1	0.489	0.454	0.525	CLONAL	1	TRUE	1	0.760526457513466	3		937	728	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419986	41419986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372989163	NA	P-0004697-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	578	967	0	ENST00000373198.4:c.335G>A	p.Arg112His	p.R112H	ENST00000373198	NM_133170.3	112	cGt/cAt	3/32	0.624599610568588	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	2	0.760526457513466	4		967	1245	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0004697-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	571	659	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.737887263638706	2	FACETS	0.976	0.951	1	0.976	0.951	1	CLONAL	2	TRUE	0	0.760526457513466	2		659	769	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381529	81381529	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004697-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	469	1086	0	ENST00000222390.5:c.532C>T	p.Arg178Ter	p.R178*	ENST00000222390	NM_000601.4	178	Cga/Tga	5/18	0.760526457513466	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	1	0.760526457513466	4		1086	709	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052629	42052629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004697-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	476	1247	1	ENST00000219905.7:c.7300C>T	p.Arg2434Trp	p.R2434W	ENST00000219905	NM_001164273.1	2434	Cgg/Tgg	20/24	0.759837078915729	2	FACETS	0.964	0.937	0.991	0.964	0.937	0.991	CLONAL	2	TRUE	0	0.760526457513466	2		1248	649	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131418	17131418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751171641	NA	P-0004697-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	310	642	0	ENST00000285071.4:c.34G>A	p.Glu12Lys	p.E12K	ENST00000285071	NM_144997.5	12	Gag/Aag	4/14	0.737887263638706	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.760526457513466	2		642	406	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593505	48593505	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004697-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	274	573	1	ENST00000342988.3:c.1256G>T	p.Gly419Val	p.G419V	ENST00000342988	NM_005359.5	419	gGg/gTg	10/12	0.759837078915729	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.760526457513466	2		574	338	SUCCESS
APC	324	MSKCC	GRCh37	5	112173639	112173652	+	frameshift_variant	Frame_Shift_Del	DEL	CATCTCATCGTAGT	CATCTCATCGTAGT	-	novel	NA	P-0004697-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	306	837	0	ENST00000257430.4:c.2348_2361del	p.Ala783GlufsTer11	p.A783Efs*11	ENST00000257430	NM_000038.5	783	gCATCTCATCGTAGT/g	16/16	0.674576825072664	3	FACETS	0.929	0.884	0.973	0.929	0.884	0.973	CLONAL	2	TRUE	1	0.760526457513466	3		837	598	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0004840-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	424	395	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.614475756027237	6	FACETS	0.977	0.939	1			1	CLONAL	4	TRUE	NA	0.614475756027237	6		395	787	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622169	162622169	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004840-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	60	317	0	ENST00000366898.1:c.528G>C	p.Leu176Phe	p.L176F	ENST00000366898	NM_004562.2	176	ttG/ttC	4/12	0.504785547445578	3	FACETS	0.749	0.649	0.856	0.374	0.324	0.428	SUBCLONAL	1	TRUE	1	0.614475756027237	3		317	341	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690846	89690846	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004840-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	171	230	0	ENST00000371953.3:c.253G>T	p.Val85Phe	p.V85F	ENST00000371953	NM_000314.4	85	Gtt/Ttt	4/9	0.499982148909063	2	FACETS	0.833	0.78	0.886	0.833	0.78	0.886	CLONAL	2	TRUE	0	0.614475756027237	2		230	334	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845934	72845934	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005078-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	50	544	0	ENST00000268489.5:c.3533C>A	p.Ser1178Ter	p.S1178*	ENST00000268489	NM_006885.3	1178	tCg/tAg	6/10	1	2	FACETS	0.393	0.332	0.459	0.393	0.332	0.459	SUBCLONAL	1	TRUE	1	0.34	2		544	749	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428569	72428569	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005078-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	35	470	0	ENST00000477973.2:c.433del	p.Ile146SerfsTer62	p.I146Sfs*62	ENST00000477973	NM_012234.5	145	cgG/cg	2/4	1	2	FACETS	0.339	0.277	0.409	0.339	0.277	0.409	SUBCLONAL	1	TRUE	1	0.34	2		470	608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0005132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	183	919	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.859	0.792	0.928	0.859	0.792	0.928	CLONAL	1	TRUE	1	0.416289915469886	2		919	1024	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0005132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	258	462	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.374488155990151	3	FACETS	0.899	0.844	0.955	0.899	0.844	0.955	CLONAL	2	TRUE	1	0.416289915469886	3		462	833	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90949272	90949272	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	382	398	0	ENST00000265433.3:c.2216T>C	p.Leu739Pro	p.L739P	ENST00000265433	NM_002485.4	739	cTt/cCt	15/16	0.380740917627185	4	FACETS	0.854	0.813	0.895	0.854	0.813	0.895	CLONAL	3	TRUE	1	0.416289915469886	4		398	1015	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479829	67479829	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	343	507	0	ENST00000327367.4:c.1136G>A	p.Gly379Asp	p.G379D	ENST00000327367	NM_005902.3	379	gGc/gAc	8/9	0.416289915469886	2	FACETS	0.93	0.883	0.977	0.93	0.883	0.977	CLONAL	2	TRUE	0	0.416289915469886	2		507	886	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0005132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	170	536	0	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.416289915469886	2		536	802	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593504	48593504	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	110	374	1	ENST00000342988.3:c.1255G>T	p.Gly419Trp	p.G419W	ENST00000342988	NM_005359.5	419	Ggg/Tgg	10/12	0.371588790717303	1	FACETS	0.764	0.688	0.843	0.764	0.688	0.843	SUBCLONAL	1	TRUE	0	0.416289915469886	1		375	548	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426120	47426120	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005132-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	390	971	0	ENST00000377045.4:c.640T>C	p.Ser214Pro	p.S214P	ENST00000377045	NM_001654.4	214	Tcc/Ccc	7/16	0.370769832322663	2	FACETS	0.871	0.835	0.907			1	CLONAL	3	TRUE	NA	0.416289915469886	2		971	717	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370815	225370815	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	233	227	0	ENST00000264414.4:c.1064T>C	p.Phe355Ser	p.F355S	ENST00000264414	NM_003590.4	355	tTc/tCc	8/16	0.159464682239231	3	FACETS	0.829	0.773	0.885	0.829	0.773	0.885	INDETERMINATE	2	TRUE	1	0.35	3		227	944	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170363	119170363	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	59	262	0	ENST00000264033.4:c.2593A>G	p.Met865Val	p.M865V	ENST00000264033	NM_005188.3	865	Atg/Gtg	16/16	0.251989083116423	1	FACETS	0.415	0.357	0.479	0.415	0.357	0.479	SUBCLONAL	1	TRUE	0	0.35	1		262	670	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720779	89720780	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	23	66	0	ENST00000371953.3:c.932dup	p.Asn311LysfsTer2	p.N311Kfs*2	ENST00000371953	NM_000314.4	310	-/A	8/9	1	2	FACETS	0.703	0.551	0.875	0.703	0.551	0.875	SUBCLONAL	1	TRUE	1	0.35	2		66	187	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115712	8115875	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGGCCGCCCTCTCCAGACACATGTCCTCCCTGAGCCACATCTCG	CCCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGGCCGCCCTCTCCAGACACATGTCCTCCCTGAGCCACATCTCG	-	novel	NA	P-0006847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	75	251	0	ENST00000346208.3:c.1062_1225del	p.Thr355GlnfsTer97	p.T355Qfs*97	ENST00000346208		353	cCCCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCATGACTCACTGGAGGACTTCCCCAAGAACAGCTCGTTTAACCCGGCCGCCCTCTCCAGACACATGTCCTCCCTGAGCCACATCTCG/c	6/6	1	2	FACETS	0.873	0.771	0.98	0.873	0.771	0.98	CLONAL	1	TRUE	1	0.527336568493503	2		251	326	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349999	15349999	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	209	691	0	ENST00000263377.2:c.3653A>C	p.Lys1218Thr	p.K1218T	ENST00000263377	NM_058243.2	1218	aAg/aCg	18/20	1	2	FACETS	0.955	0.888	1	0.955	0.888	1	CLONAL	1	TRUE	1	0.527336568493503	2		691	830	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274827	38274827	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	755	339	0	ENST00000425967.3:c.1753G>C	p.Asp585His	p.D585H	ENST00000425967	NM_001174067.1	585	Gat/Cat	13/19	0.527336568493503	7	FACETS	1	0.993	1			1	CLONAL	6	TRUE	NA	0.527336568493503	7		339	1060	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057999	27058000	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCTCGACGCTCTC	novel	NA	P-0006847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	121	479	0	ENST00000324856.7:c.1710_1723dup	p.Gln575ProfsTer49	p.Q575Pfs*49	ENST00000324856	NM_006015.4	569	-/CCCTCGACGCTCTC	3/20	1	2	FACETS	0.724	0.655	0.796	0.724	0.655	0.796	SUBCLONAL	1	TRUE	1	0.527336568493503	2		479	634	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073811	8073811	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	95	328	0	ENST00000377482.5:c.848T>A	p.Val283Asp	p.V283D	ENST00000377482	NM_018948.3	283	gTt/gAt	4/4	1	2	FACETS	0.917	0.822	1	0.917	0.822	1	CLONAL	1	TRUE	1	0.527336568493503	2		328	393	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248411	59248412	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGAAGC	novel	NA	P-0006847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	112	337	0	ENST00000371222.2:c.326_331dup	p.Gly109_Phe110dup	p.G109_F110dup	ENST00000371222	NM_002228.3	109	gcc/gGCTTCGcc	1/1	1	2	FACETS	0.986	0.893	1	0.986	0.893	1	CLONAL	1	TRUE	1	0.527336568493503	2		337	431	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628105	90628105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006847-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	225	628	3	ENST00000330062.3:c.1214C>T	p.Thr405Met	p.T405M	ENST00000330062	NM_002168.2	405	aCg/aTg	10/11	0.524774872171471	3	FACETS	1	0.934	1	0.502	0.467	0.538	CLONAL	1	TRUE	1	0.527336568493503	3		631	1075	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0007135-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	215	418	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.53868912710663	4	FACETS	0.973	0.91	1	0.973	0.91	1	CLONAL	2	TRUE	2	0.53868912710663	4		418	631	SUCCESS
APC	324	MSKCC	GRCh37	5	112175746	112175746	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007135-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	242	360	0	ENST00000257430.4:c.4455del	p.Asp1486IlefsTer21	p.D1486Ifs*21	ENST00000257430	NM_000038.5	1485	gcT/gc	16/16	0.502178838232582	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	4	TRUE	0	0.53868912710663	4		360	340	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21565425	21565425	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007135-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	103	848	0	ENST00000382592.4:c.461A>C	p.Lys154Thr	p.K154T	ENST00000382592	NM_014572.2	154	aAg/aCg	3/8	0.53868912710663	5	FACETS	0.869	0.777	0.966	0.217	0.194	0.242	CLONAL	1	TRUE	1	0.53868912710663	5		848	796	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198283245	198283245	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007135-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	176	678	0	ENST00000335508.6:c.483G>C	p.Leu161Phe	p.L161F	ENST00000335508	NM_012433.2	161	ttG/ttC	5/25	0.53868912710663	4	FACETS	1	0.99	1	0.37	0.341	0.399	CLONAL	1	TRUE	0	0.53868912710663	4		678	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587781702	NA	P-0007135-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	177	482	0	ENST00000269305.4:c.920-1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.477601834180771	2	FACETS	0.939	0.88	0.998	0.939	0.88	0.998	CLONAL	2	TRUE	0	0.53868912710663	2		482	350	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266217	18266859	+	splice_acceptor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	GGGTGAGAGGAGTTGGCCTGGCTAACGCTGCCCTATCCCTGTCTCCCTAGGTCGGCGTCCTCAGCTGGCCGAGCATGGTGGCAGCCTGCACCCTTGGCTCCCTTGTCTGGTGCAGCCAGCAGAGCCGCCAGCCTTGGGCGCCCATGGCCCTCCGTGTGAGGGCGTGAGCGGCCTGCCCCAGCCTCACCTGCTGATGGAGGACTCAATGGCCCAGTGACCTGACACCACACCACCAACTCCCTCCCACCAGCTGACGAATGGTGGACCCAGTGACGAGTGGCCCTTGTAAGGGTCATGGAATAATTTGAAGCGAGGCATGAGCGGCCCCTGTGGTCGCCTGTGACTGCTGGAGATAGAGGTCCCAGCACCCCAAGCCAACCCAGCGGACCCTCCCAGCCCTGCTTCAACCAATGGGGCCAGTGGGGCTCCAAGCAGCCACCTAACCATCCAGACCCCACCCCACTCACGCGGCCATGGCGGGCCCTGAGGGCTTCCAGTACCGCGCTCTGTACCCGTTCCGCCGGGAGCGGCCGGAGGACCTGGAGCTGCTGCCCGGCGACGTGCTGGTAGTGAGCCGGGCGGCCTTGCAGGCGCTGGGCGTGGCCGAGGGTGGCGAGCGCTGCCCACAGAGCGTGGGCTGGAT	GGGTGAGAGGAGTTGGCCTGGCTAACGCTGCCCTATCCCTGTCTCCCTAGGTCGGCGTCCTCAGCTGGCCGAGCATGGTGGCAGCCTGCACCCTTGGCTCCCTTGTCTGGTGCAGCCAGCAGAGCCGCCAGCCTTGGGCGCCCATGGCCCTCCGTGTGAGGGCGTGAGCGGCCTGCCCCAGCCTCACCTGCTGATGGAGGACTCAATGGCCCAGTGACCTGACACCACACCACCAACTCCCTCCCACCAGCTGACGAATGGTGGACCCAGTGACGAGTGGCCCTTGTAAGGGTCATGGAATAATTTGAAGCGAGGCATGAGCGGCCCCTGTGGTCGCCTGTGACTGCTGGAGATAGAGGTCCCAGCACCCCAAGCCAACCCAGCGGACCCTCCCAGCCCTGCTTCAACCAATGGGGCCAGTGGGGCTCCAAGCAGCCACCTAACCATCCAGACCCCACCCCACTCACGCGGCCATGGCGGGCCCTGAGGGCTTCCAGTACCGCGCTCTGTACCCGTTCCGCCGGGAGCGGCCGGAGGACCTGGAGCTGCTGCCCGGCGACGTGCTGGTAGTGAGCCGGGCGGCCTTGCAGGCGCTGGGCGTGGCCGAGGGTGGCGAGCGCTGCCCACAGAGCGTGGGCTGGAT	-	novel	NA	P-0007135-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	150	0	0	ENST00000222254.8:c.-423-49_171del		p.X141_splice	ENST00000222254	NM_005027.3	141		2/16	0.31049226829312	4	FACETS	1	0.947	1	1	0.947	1	INDETERMINATE	2	TRUE	2	0.53868912710663	4		0	415	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211511	36211511	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753305236	NA	P-0007135-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	134	715	3	ENST00000222270.7:c.1262C>T	p.Ser421Leu	p.S421L	ENST00000222270	NM_014727.1	421	tCg/tTg	3/37	0.395872021360057	4	FACETS	0.767	0.701	0.835	0.767	0.701	0.835	SUBCLONAL	2	TRUE	2	0.53868912710663	4		718	499	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017222	31017222	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007135-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	101	437	0	ENST00000375687.4:c.553G>C	p.Glu185Gln	p.E185Q	ENST00000375687	NM_015338.5	185	Gaa/Caa	7/13	0.53868912710663	8	FACETS	0.822	0.736	0.912	0.329	0.294	0.365	CLONAL	2	TRUE	3	0.53868912710663	8		437	597	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0008027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	158	389	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.974	0.901	1	0.974	0.901	1	CLONAL	1	TRUE	1	0.723846477529902	2		389	448	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775025	73775025	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	33	203	0	ENST00000254810.4:c.148C>T	p.Arg50Ter	p.R50*	ENST00000254810	NM_005324.3	50	Cga/Tga	3/4	1	2	FACETS	0.413	0.338	0.495	0.413	0.338	0.495	SUBCLONAL	1	TRUE	1	0.723846477529902	2		203	221	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061213	38061213	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008027-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	55	228	0	ENST00000250448.2:c.776A>G	p.Tyr259Cys	p.Y259C	ENST00000250448	NM_004496.3	259	tAc/tGc	2/2	1	2	FACETS	0.962	0.841	1	0.962	0.841	1	CLONAL	1	TRUE	1	0.723846477529902	2		228	158	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0008099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	119	395	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.676	0.609	0.747	0.676	0.609	0.747	SUBCLONAL	1	TRUE	1	0.33	2		395	1067	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020377	123020377	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	50	374	0	ENST00000355640.3:c.865T>C	p.Phe289Leu	p.F289L	ENST00000355640		289	Ttt/Ctt	2/7	0.285902312678487	1	FACETS	0.453	0.384	0.528	0.453	0.384	0.528	SUBCLONAL	1	TRUE	0	0.33	1		374	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576916	7576917	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0008099-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	50	478	0	ENST00000269305.4:c.929_930insG	p.Asn310LysfsTer27	p.N310Kfs*27	ENST00000269305	NM_001126112.2	310	aac/aaGc	9/11	1	2	FACETS	0.378	0.32	0.443	0.378	0.32	0.443	SUBCLONAL	1	TRUE	1	0.33	2		478	801	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578463	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371524413	NA	P-0008404-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	359	368	0	ENST00000269305.4:c.467G>C	p.Arg156Pro	p.R156P	ENST00000269305	NM_001126112.2	156	cGc/cCc	5/11	0.839149455564474	1	FACETS	0.934	0.9	0.967	0.934	0.9	0.967	CLONAL	1	TRUE	0	0.839149455564474	1		368	532	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007635	45007635	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008404-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	308	325	0	ENST00000558401.1:c.82C>T	p.Gln28Ter	p.Q28*	ENST00000558401	NM_004048.2	28	Cag/Tag	2/4	0.839149455564474	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.839149455564474	1		325	424	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs869025608	NA	P-0008404-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	452	486	0	ENST00000307102.5:c.171G>T	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaT	2/11	1	2	FACETS	0.937	0.896	0.978	0.937	0.896	0.978	CLONAL	1	TRUE	1	0.839149455564474	2		486	1150	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921551	178921551	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008404-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	512	393	0	ENST00000263967.3:c.1033A>T	p.Asn345Tyr	p.N345Y	ENST00000263967	NM_006218.2	345	Aat/Tat	5/21	0.826896700919496	3	FACETS	0.867	0.835	0.899	0.867	0.835	0.899	CLONAL	2	TRUE	1	0.839149455564474	3		393	999	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449671	187449671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008404-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	867	461	0	ENST00000232014.4:c.209G>A	p.Ser70Asn	p.S70N	ENST00000232014	NM_001130845.1	70	aGt/aAt	4/10	0.826896700919496	3	FACETS	0.959	0.933	0.985	0.959	0.933	0.985	CLONAL	2	TRUE	1	0.839149455564474	3		461	1529	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202292	138202292	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008404-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	365	364	0	ENST00000237289.4:c.2209C>T	p.Gln737Ter	p.Q737*	ENST00000237289	NM_001270507.1	737	Cag/Tag	9/9	0.837293817446938	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.839149455564474	1		364	502	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271208	38271208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765900637	NA	P-0008404-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	233	235	1	ENST00000425967.3:c.2500G>A	p.Glu834Lys	p.E834K	ENST00000425967	NM_001174067.1	834	Gag/Aag	19/19	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.839149455564474	2		236	545	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499623	18499623	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008404-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	519	589	2	ENST00000266497.5:c.1478T>A	p.Leu493Gln	p.L493Q	ENST00000266497		493	cTa/cAa	10/31	1	2	FACETS	0.935	0.897	0.973	0.935	0.897	0.973	CLONAL	1	TRUE	1	0.839149455564474	2		591	1323	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202293	133202293	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1220509815	NA	P-0008404-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	470	381	0	ENST00000320574.5:c.6595A>T	p.Ile2199Phe	p.I2199F	ENST00000320574	NM_006231.2	2199	Atc/Ttc	47/49	0.839149455564474	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.839149455564474	1		381	603	SUCCESS
BLM	641	MSKCC	GRCh37	15	91337474	91337474	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008404-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	400	541	0	ENST00000355112.3:c.3097A>G	p.Ile1033Val	p.I1033V	ENST00000355112	NM_000057.2	1033	Ata/Gta	16/22	0.839149455564474	3	FACETS	0.935	0.888	0.983			1	CLONAL	1	TRUE	NA	0.839149455564474	3		541	1447	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314616	30314616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008404-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	478	506	0	ENST00000262643.3:c.1165C>T	p.Leu389Phe	p.L389F	ENST00000262643	NM_001238.2	389	Ctc/Ttc	12/12	0.839149455564474	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.839149455564474	1		506	646	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602571	10602583	+	frameshift_variant	Frame_Shift_Del	DEL	CGGAAGTAGCCGC	CGGAAGTAGCCGC	-	novel	NA	P-0008404-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	200	330	0	ENST00000171111.5:c.995_1007del	p.Gly332AspfsTer64	p.G332Dfs*64	ENST00000171111	NM_203500.1	332	gGCGGCTACTTCCGa/ga	3/6	0.839149455564474	1	FACETS	0.625	0.586	0.664	0.625	0.586	0.664	SUBCLONAL	1	TRUE	0	0.839149455564474	1		330	443	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220394	1220394	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008404-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	407	439	0	ENST00000326873.7:c.488del	p.Gly163AlafsTer124	p.G163Afs*124	ENST00000326873	NM_000455.4	163	Ggc/gc	4/10	0.839149455564474	1	FACETS	0.964	0.932	0.995	0.964	0.932	0.995	CLONAL	1	TRUE	0	0.839149455564474	1		439	584	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	75	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.499582568298972	2	FACETS	0.348	0.304	0.396	0.174	0.152	0.198	SUBCLONAL	1	FALSE	0	0.499582568298972	2		334	862	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0008527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	97	534	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.321308463320205	2	FACETS	0.479	0.426	0.535	0.239	0.213	0.268	SUBCLONAL	1	FALSE	0	0.499582568298972	2		535	811	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647056	23647056	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	82	595	0	ENST00000261584.4:c.811A>C	p.Ser271Arg	p.S271R	ENST00000261584	NM_024675.3	271	Agt/Cgt	4/13	0.292059788991687	2	FACETS	0.346	0.304	0.391	0.173	0.152	0.196	INDETERMINATE	1	FALSE	0	0.499582568298972	2		595	948	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971202	21971203	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0008527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	27	107	0	ENST00000304494.5:c.155dup	p.Met52IlefsTer68	p.M52Ifs*68	ENST00000304494	NM_000077.4	52	atg/atTg	2/3	0.265703470319471	3	FACETS	0.587	0.47	0.72	0.196	0.156	0.24	INDETERMINATE	1	FALSE	0	0.499582568298972	3		107	230	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	515	205	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.686216368110647	9	FACETS	1	0.975	1			1	CLONAL	4	FALSE	NA	0.686216368110647	9		205	1250	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056026	26056026	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs928708568	NA	P-0008574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	363	135	0	ENST00000343677.2:c.631A>C	p.Lys211Gln	p.K211Q	ENST00000343677	NM_005319.3	211	Aag/Cag	1/1	0.686216368110647	6	FACETS	0.927	0.887	0.966			1	CLONAL	4	FALSE	NA	0.686216368110647	6		135	677	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325595	87325595	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	41	394	0	ENST00000277120.3:c.472T>C	p.Trp158Arg	p.W158R	ENST00000277120		158	Tgg/Cgg	6/19	0.65189892460985	3	FACETS	0.196	0.162	0.234			1	SUBCLONAL	1	FALSE	NA	0.686216368110647	3		394	819	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609685	81609685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	392	504	0	ENST00000298171.2:c.1283C>T	p.Ala428Val	p.A428V	ENST00000298171	NM_000369.2	428	gCt/gTt	10/10	0.698040343677718	4	FACETS	1	0.995	1	0.719	0.683	0.756	CLONAL	1	FALSE	2	0.686216368110647	4		504	1340	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0009219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	273	327	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.984	0.927	1	0.984	0.927	1	CLONAL	1	TRUE	1	0.704348876592824	2		327	788	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0009219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	173	476	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.948	0.879	1	0.948	0.879	1	CLONAL	1	TRUE	1	0.704348876592824	2		476	518	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321351	1321351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763354527	NA	P-0009219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	257	398	1	ENST00000400841.2:c.404C>T	p.Thr135Met	p.T135M	ENST00000400841		135	aCg/aTg	4/6	1	2	FACETS	0.877	0.824	0.932	0.877	0.824	0.932	CLONAL	1	TRUE	1	0.704348876592824	2		399	832	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798371	42798372	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0009219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	28	404	2	ENST00000575354.2:c.4244_4245del	p.Arg1415LysfsTer25	p.R1415Kfs*25	ENST00000575354	NM_015125.3	1414	atGAga/atga	18/20	0.704348876592824	1	FACETS	0.105	0.083	0.13	0.105	0.083	0.13	SUBCLONAL	1	TRUE	0	0.704348876592824	1		406	490	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798411	42798412	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0009219-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	80	422	0	ENST00000575354.2:c.4282_4283del	p.Lys1428GlufsTer12	p.K1428Efs*12	ENST00000575354	NM_015125.3	1428	AAg/g	18/20	0.704348876592824	1	FACETS	0.316	0.279	0.355	0.316	0.279	0.355	SUBCLONAL	1	TRUE	0	0.704348876592824	1		422	466	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609942	43609947	+	inframe_deletion	In_Frame_Del	DEL	GAGCTG	GAGCTG	-	rs121913312	NA	P-0010017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	819	848	0	ENST00000355710.3:c.1894_1899del	p.Glu632_Leu633del	p.E632_L633del	ENST00000355710	NM_020975.4	632	GAGCTG/-	11/20	0.63775687247015	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.641543487390867	2		848	1231	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0010620-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	166	910	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.726	0.667	0.787	0.726	0.667	0.787	SUBCLONAL	1	TRUE	1	0.522673790394738	2		910	875	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0010620-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	131	583	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.506927157124754	3	FACETS	0.865	0.786	0.948	0.432	0.393	0.474	CLONAL	1	TRUE	1	0.522673790394738	3		583	731	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0010620-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	113	317	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.669	0.603	0.739	0.669	0.603	0.739	SUBCLONAL	1	TRUE	1	0.522673790394738	2		317	646	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426121	47426121	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010620-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	218	1028	0	ENST00000377045.4:c.641C>A	p.Ser214Tyr	p.S214Y	ENST00000377045	NM_001654.4	214	tCc/tAc	7/16	1	2	FACETS	0.788	0.733	0.846	0.788	0.733	0.846	SUBCLONAL	1	TRUE	1	0.522673790394738	2		1028	1058	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0010620-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	53	355	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	1	2	FACETS	0.748	0.643	0.861	0.748	0.643	0.861	SUBCLONAL	1	TRUE	1	0.522673790394738	2		355	271	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338671	70338671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010620-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	141	838	0	ENST00000374080.3:c.67G>T	p.Asp23Tyr	p.D23Y	ENST00000374080		23	Gat/Tat	1/45	1	2	FACETS	0.634	0.577	0.693	0.634	0.577	0.693	SUBCLONAL	1	TRUE	1	0.522673790394738	2		838	851	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692780	89692780	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1554898056	NA	P-0010620-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	180	443	0	ENST00000371953.3:c.264T>A	p.Tyr88Ter	p.Y88*	ENST00000371953	NM_000314.4	88	taT/taA	5/9	0.506927157124754	3	FACETS	1	0.99	1	0.725	0.672	0.78	CLONAL	1	TRUE	1	0.522673790394738	3		443	599	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023349	27023349	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010620-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	67	339	0	ENST00000324856.7:c.456del	p.Gln152HisfsTer80	p.Q152Hfs*80	ENST00000324856	NM_006015.4	152	cAa/ca	1/20	1	2	FACETS	0.675	0.589	0.766	0.675	0.589	0.766	SUBCLONAL	1	TRUE	1	0.522673790394738	2		339	380	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591135	67591136	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGA	novel	NA	P-0010620-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	86	495	0	ENST00000274335.5:c.1729_1731dup	p.Arg577dup	p.R577dup	ENST00000274335		577	-/AGA	12/15	1	2	FACETS	0.652	0.578	0.73	0.652	0.578	0.73	SUBCLONAL	1	TRUE	1	0.522673790394738	2		495	505	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0010935-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	246	622	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	0.44320810211311	4	FACETS	1	0.965	1	1	0.994	1	CLONAL	3	TRUE	2	0.453400841681738	4		622	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519992	NA	P-0012114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	50	693	1	ENST00000269305.4:c.641A>T	p.His214Leu	p.H214L	ENST00000269305	NM_001126112.2	214	cAt/cTt	6/11	1	2	FACETS	0.435	0.368	0.509	0.435	0.368	0.509	SUBCLONAL	1	TRUE	1	0.27	2		694	852	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0012335-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	2	476	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.262	0.101	0.532	0.262	0.101	0.532	SUBCLONAL	1	TRUE	1	0.324872071584062	2		476	47	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0012335-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	11	500	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	0.24422784514166	4	FACETS	0.846	0.6	1	0.846	0.6	1	CLONAL	2	TRUE	2	0.324872071584062	4		500	53	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0012335-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	6	0	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	0.754	0.458	1	0.754	0.458	1	CLONAL	1	TRUE	1	0.324872071584062	2		0	49	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755612	39755612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776452839	NA	P-0012335-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	4	0	0	ENST00000288319.7:c.1153C>T	p.Arg385Cys	p.R385C	ENST00000288319	NM_182918.3	385	Cgc/Tgc	10/10	0.135086393682204	4	FACETS	0.796	0.424	1	0.398	0.212	0.657	INDETERMINATE	1	TRUE	2	0.324872071584062	4		0	41	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131142	55131142	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012335-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	203	439	0	ENST00000257290.5:c.685G>A	p.Glu229Lys	p.E229K	ENST00000257290	NM_006206.4	229	Gaa/Aaa	5/23	0.324872071584062	20	FACETS	1	0.968	1	1	0.968	1	CLONAL	19	TRUE	1	0.324872071584062	20		439	256	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033352	48033352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750949	NA	P-0012335-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	8	401	0	ENST00000234420.5:c.3656C>T	p.Thr1219Ile	p.T1219I	ENST00000234420	NM_000179.2	1219	aCt/aTt	8/10	1	2	FACETS	0.985	0.649	1	0.985	0.649	1	CLONAL	1	TRUE	1	0.324872071584062	2		401	50	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877484	28877484	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012335-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	10	471	0	ENST00000282397.4:c.3837T>G	p.Ser1279Arg	p.S1279R	ENST00000282397	NM_002019.4	1279	agT/agG	30/30	1	2	FACETS	1	0.77	1	1	0.77	1	CLONAL	1	TRUE	1	0.324872071584062	2		471	54	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757396	40757396	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1374515118	NA	P-0012335-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	8	574	1	ENST00000373198.4:c.2902G>A	p.Asp968Asn	p.D968N	ENST00000373198	NM_133170.3	968	Gac/Aac	20/32	0.324872071584062	1	FACETS	0.724	0.475	1	0.724	0.475	1	CLONAL	1	TRUE	0	0.324872071584062	1		575	57	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077580	30077580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012335-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	9	0	0	ENST00000338641.4:c.1727C>T	p.Thr576Ile	p.T576I	ENST00000338641	NM_000268.3	576	aCc/aTc	15/16	1	2	FACETS	0.676	0.452	0.953	0.676	0.452	0.953	SUBCLONAL	1	TRUE	1	0.324872071584062	2		0	82	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934069	39934070	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0012335-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	14	615	0	ENST00000378444.4:c.529_530del	p.Ser177ProfsTer8	p.S177Pfs*8	ENST00000378444	NM_001123385.1	177	AGc/c	4/15	0.24422784514166	4	FACETS	1	0.874	1	0.696	0.512	0.911	CLONAL	1	TRUE	2	0.324872071584062	4		615	82	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503908	149503908	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012335-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	17	553	0	ENST00000261799.4:c.1928G>A	p.Ser643Asn	p.S643N	ENST00000261799	NM_002609.3	643	aGt/aAt	14/23	0.244237014225452	1	FACETS	0.923	0.7	1	0.923	0.7	1	CLONAL	1	TRUE	0	0.324872071584062	1		553	95	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0012671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	413	327	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.978	0.933	1	0.978	0.933	1	CLONAL	1	TRUE	1	0.823569224680166	2		327	1026	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	rs786202799	NA	P-0012671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	717	340	0	ENST00000269305.4:c.376-2A>C		p.X126_splice	ENST00000269305	NM_001126112.2	126			NA	2	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.823569224680166	2		340	853	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939473	76939474	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0012671-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	459	480	0	ENST00000373344.5:c.1274_1275del	p.Lys425ArgfsTer8	p.K425Rfs*8	ENST00000373344	NM_000489.3	425	aAA/a	9/35	0.823569224680166	1	FACETS	0.97	0.939	1	0.97	0.939	1	CLONAL	1	TRUE	0	0.823569224680166	1		480	676	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0012757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	77	810	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.299493170594834	1	FACETS	0.808	0.711	0.912	0.808	0.711	0.912	CLONAL	1	TRUE	0	0.3	1		810	540	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909306	41909327	+	frameshift_variant	Frame_Shift_Del	DEL	GGACACGCTGGTCCCCCAGCAG	GGACACGCTGGTCCCCCAGCAG	-	novel	NA	P-0012757-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	62	314	0	ENST00000372991.4:c.61_82del	p.Leu21CysfsTer55	p.L21Cfs*55	ENST00000372991	NM_001760.3	21	CTGCTGGGGGACCAGCGTGTCCtg/tg	1/5	1	2	FACETS	0.927	0.803	1	0.927	0.803	1	CLONAL	1	TRUE	1	0.3	2		314	446	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	97	759	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.866	0.78	0.956	0.866	0.78	0.956	CLONAL	1	TRUE	1	0.652833778416055	2		760	343	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0013048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	188	327	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.962	0.894	1	0.962	0.894	1	CLONAL	1	TRUE	1	0.652833778416055	2		327	599	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0013048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	209	243	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.652833778416055	2		243	575	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842344	151842344	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs749571160	NA	P-0013048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	78	491	0	ENST00000262189.6:c.14068C>T	p.Arg4690Ter	p.R4690*	ENST00000262189	NM_170606.2	4690	Cga/Tga	54/59	1	2	FACETS	0.378	0.332	0.427	0.378	0.332	0.427	SUBCLONAL	1	TRUE	1	0.652833778416055	2		491	633	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193219829	193219829	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	24	276	0	ENST00000367435.3:c.1583A>C	p.His528Pro	p.H528P	ENST00000367435	NM_024529.4	528	cAc/cCc	17/17	1	2	FACETS	0.163	0.127	0.205	0.163	0.127	0.205	SUBCLONAL	1	TRUE	1	0.652833778416055	2		276	450	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358478	91358478	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1022266595	NA	P-0013048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	55	656	0	ENST00000355112.3:c.4223C>T	p.Pro1408Leu	p.P1408L	ENST00000355112	NM_000057.2	1408	cCg/cTg	22/22	1	2	FACETS	0.225	0.192	0.261	0.225	0.192	0.261	SUBCLONAL	1	TRUE	1	0.652833778416055	2		656	749	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791728	42791728	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	38	560	0	ENST00000575354.2:c.614A>T	p.Asn205Ile	p.N205I	ENST00000575354	NM_015125.3	205	aAt/aTt	5/20	0.652833778416055	1	FACETS	0.191	0.158	0.228	0.191	0.158	0.228	SUBCLONAL	1	TRUE	0	0.652833778416055	1		560	410	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795757	42795757	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	48	766	1	ENST00000575354.2:c.2746C>T	p.Gln916Ter	p.Q916*	ENST00000575354	NM_015125.3	916	Cag/Tag	11/20	0.652833778416055	1	FACETS	0.182	0.153	0.214	0.182	0.153	0.214	SUBCLONAL	1	TRUE	0	0.652833778416055	1		767	544	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0013580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10538	308	907	3	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.597493735302315	27	FACETS	0.805	0.752	0.86			1	CLONAL	1	TRUE	NA	0.597493735302315	27		910	10846	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692986	89692989	+	frameshift_variant	Frame_Shift_Del	DEL	AAGT	AAGT	-	novel	NA	P-0013580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	150	303	0	ENST00000371953.3:c.473_476del	p.Val158GlyfsTer8	p.V158Gfs*8	ENST00000371953	NM_000314.4	157	gAAGTa/ga	5/9	0.597493735302315	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.597493735302315	1		303	327	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427453	427453	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780617531	NA	P-0013580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	99	639	0	ENST00000399788.2:c.2716G>A	p.Glu906Lys	p.E906K	ENST00000399788	NM_001042603.1	906	Gaa/Aaa	19/28	1	2	FACETS	0.369	0.329	0.412	0.369	0.329	0.412	SUBCLONAL	1	TRUE	1	0.597493735302315	2		639	898	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456460	89456460	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1221318412	NA	P-0013580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	338	691	3	ENST00000336596.2:c.1636G>A	p.Ala546Thr	p.A546T	ENST00000336596	NM_005233.5	546	Gcc/Acc	8/17	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.597493735302315	2		694	1076	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981069	55981069	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1259259717	NA	P-0013580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	47	442	0	ENST00000263923.4:c.630G>C	p.Gln210His	p.Q210H	ENST00000263923	NM_002253.2	210	caG/caC	5/30	1	2	FACETS	0.27	0.228	0.318	0.27	0.228	0.318	SUBCLONAL	1	TRUE	1	0.597493735302315	2		442	582	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0013734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	54	761	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.812	0.691	0.945	0.812	0.691	0.945	CLONAL	1	TRUE	1	0.14	2		764	950	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0013734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	28	389	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.815	0.65	1	0.815	0.65	1	CLONAL	1	TRUE	1	0.14	2		389	491	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120642	115120642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1375	158	753	1	ENST00000257566.3:c.364G>A	p.Glu122Lys	p.E122K	ENST00000257566	NM_016569.3	122	Gag/Aag	1/8	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.14	2		754	1533	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138111	2138111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139779505	NA	P-0013734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	65	539	1	ENST00000219476.3:c.5131G>A	p.Val1711Met	p.V1711M	ENST00000219476	NM_000548.3	1711	Gtg/Atg	40/42	1	2	FACETS	0.878	0.758	1	0.878	0.758	1	CLONAL	1	TRUE	1	0.14	2		540	1058	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683807	117683807	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013734-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	42	407	0	ENST00000368508.3:c.3340C>G	p.Gln1114Glu	p.Q1114E	ENST00000368508	NM_002944.2	1114	Caa/Gaa	21/43	0.3	1	FACETS	0.794	0.661	0.942	0.794	0.661	0.942	CLONAL	1	TRUE	0	0.14	1		407	703	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21341837	21341837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587777177	NA	P-0013949-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	121	765	0	ENST00000215739.8:c.365C>T	p.Ser122Leu	p.S122L	ENST00000215739	NM_006767.3	122	tCg/tTg	4/21	1	2	FACETS	0.958	0.866	1	0.958	0.866	1	CLONAL	1	TRUE	1	0.347063554369484	2		765	728	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398286	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0013978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	70	483	1	ENST00000311936.3:c.33_34delinsCT	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	11	gcTGgt/gcCTgt	2/5	1	2	FACETS	0.88	0.767	1	0.88	0.767	1	CLONAL	1	TRUE	1	0.23532299746497	2		484	676	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057002	180057002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	69	736	2	ENST00000261937.6:c.617G>A	p.Cys206Tyr	p.C206Y	ENST00000261937	NM_182925.4	206	tGc/tAc	5/30	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.23532299746497	2		738	537	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226899	2226899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762029066	NA	P-0013978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	44	267	1	ENST00000398665.3:c.4379C>T	p.Thr1460Met	p.T1460M	ENST00000398665	NM_032482.2	1460	aCg/aTg	27/28	0.216283886174071	0	FACETS	1	0.903	1			1	CLONAL	1	TRUE	0	0.23532299746497	0		268	261	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73096464	73096464	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	35	236	1	ENST00000356692.5:c.244G>T	p.Glu82Ter	p.E82*	ENST00000356692		82	Gaa/Taa	3/9	0.133374541200613	4	FACETS	1	0.93	1	0.645	0.53	0.772	INDETERMINATE	1	TRUE	2	0.23532299746497	4		237	285	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911555	134911555	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	82	575	0	ENST00000398015.3:c.2020C>A	p.Gln674Lys	p.Q674K	ENST00000398015	NM_004441.4	674	Cag/Aag	11/16	0.23532299746497	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.23532299746497	1		575	569	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964909	55964909	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	82	519	0	ENST00000263923.4:c.2328G>C	p.Met776Ile	p.M776I	ENST00000263923	NM_002253.2	776	atG/atC	16/30	1	2	FACETS	0.994	0.877	1	0.994	0.877	1	CLONAL	1	TRUE	1	0.23532299746497	2		519	701	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508546	106508546	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	32	262	0	ENST00000359195.3:c.540G>C	p.Leu180Phe	p.L180F	ENST00000359195	NM_002649.2	180	ttG/ttC	2/11	0.133374541200613	4	FACETS	1	0.905	1	0.594	0.483	0.717	INDETERMINATE	1	TRUE	2	0.23532299746497	4		262	283	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98009745	98009745	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013978-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	62	431	0	ENST00000289081.3:c.219A>C	p.Lys73Asn	p.K73N	ENST00000289081	NM_000136.2	73	aaA/aaC	3/15	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.23532299746497	2		431	496	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593618	55593662	+	inframe_deletion	In_Frame_Del	DEL	GAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTT	GAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTT	-	novel	NA	P-0014184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	179	838	0	ENST00000288135.5:c.1684_1728del	p.Glu562_Leu576del	p.E562_L576del	ENST00000288135	NM_000222.2	562	GAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTT/-	11/21	1	2	FACETS	0.783	0.725	0.844	0.783	0.725	0.844	SUBCLONAL	1	TRUE	1	0.674091162029611	2		838	678	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0014338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	171	665	2	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.289809230411403	4	FACETS	1	0.987	1	0.466	0.428	0.506	CLONAL	1	TRUE	1	0.289809230411403	4		667	1088	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0014338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	84	556	0	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	0.289809230411403	4	FACETS	0.849	0.748	0.957	0.283	0.249	0.319	CLONAL	1	TRUE	1	0.289809230411403	4		556	881	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0014338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	88	631	1	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.289809230411403	2		632	607	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3841980	3841980	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0014338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	67	366	0	ENST00000262367.5:c.1330+2T>C		p.X444_splice	ENST00000262367	NM_004380.2	444			0.26313335075114	3	FACETS	0.939	0.816	1	0.469	0.408	0.536	CLONAL	1	TRUE	1	0.289809230411403	3		366	564	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0014490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	216	558	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.946	0.879	1	0.946	0.879	1	CLONAL	1	TRUE	1	0.431443718712387	2		558	1059	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971053	21971053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137854598	NA	P-0014490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	155	326	0	ENST00000304494.5:c.305C>T	p.Ala102Val	p.A102V	ENST00000304494	NM_000077.4	102	gCg/gTg	2/3	0.23639270552729	1	FACETS	0.944	0.868	1	0.944	0.868	1	INDETERMINATE	1	TRUE	0	0.431443718712387	1		326	597	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862159	68862163	+	frameshift_variant	Frame_Shift_Del	DEL	GGACA	GGACA	-	novel	NA	P-0014490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	184	384	0	ENST00000261769.5:c.2247_2251del	p.Asp750ArgfsTer5	p.D750Rfs*5	ENST00000261769	NM_004360.3	749	cgGGACAac/cgac	14/16	0.431443718712387	1	FACETS	0.968	0.897	1	0.968	0.897	1	CLONAL	1	TRUE	0	0.431443718712387	1		384	691	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160661	56160681	+	inframe_deletion	In_Frame_Del	DEL	TGCGGGCCAGACTGTACTTAC	TGCGGGCCAGACTGTACTTAC	-	novel	NA	P-0014955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	147	556	0	ENST00000399503.3:c.938_958del	p.Arg313_Leu319del	p.R313_L319del	ENST00000399503	NM_005921.1	312	aTGCGGGCCAGACTGTACTTACtg/atg	4/20	1	2	FACETS	0.654	0.598	0.712	0.654	0.598	0.712	SUBCLONAL	1	TRUE	1	0.612009583383115	2		556	735	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183249	56183249	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	182	565	0	ENST00000399503.3:c.4159G>C	p.Ala1387Pro	p.A1387P	ENST00000399503	NM_005921.1	1387	Gca/Cca	18/20	1	2	FACETS	0.803	0.742	0.865	0.803	0.742	0.865	CLONAL	1	TRUE	1	0.612009583383115	2		565	741	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0015298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	163	395	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.892	0.819	0.967	0.892	0.819	0.967	CLONAL	1	TRUE	1	0.462235217003903	2		395	791	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247810	59247811	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0015298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	338	666	0	ENST00000371222.2:c.932_933del	p.Lys311SerfsTer6	p.K311Sfs*6	ENST00000371222	NM_002228.3	311	aAA/a	1/1	0.462235217003903	1	FACETS	0.955	0.903	1	0.955	0.903	1	CLONAL	1	TRUE	0	0.462235217003903	1		666	1178	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196143	108196143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564652222	NA	P-0015298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	199	490	1	ENST00000278616.4:c.6679C>T	p.Arg2227Cys	p.R2227C	ENST00000278616	NM_000051.3	2227	Cgc/Tgc	46/63	0.462235217003903	1	FACETS	0.946	0.879	1	0.946	0.879	1	CLONAL	1	TRUE	0	0.462235217003903	1		491	700	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790512	3790512	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	272	537	0	ENST00000262367.5:c.4021C>T	p.Arg1341Ter	p.R1341*	ENST00000262367	NM_004380.2	1341	Cga/Tga	24/31	1	2	FACETS	0.896	0.84	0.955	0.896	0.84	0.955	CLONAL	1	TRUE	1	0.462235217003903	2		537	1313	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051469	13051469	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	144	395	0	ENST00000316448.5:c.816+1G>A		p.X272_splice	ENST00000316448	NM_004343.3	272			0.462235217003903	1	FACETS	0.765	0.7	0.833	0.765	0.7	0.833	SUBCLONAL	1	TRUE	0	0.462235217003903	1		395	626	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686326	30686326	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	123	367	0	ENST00000295754.5:c.182G>T	p.Cys61Phe	p.C61F	ENST00000295754	NM_003242.5	61	tGt/tTt	2/7	0.462235217003903	1	FACETS	0.582	0.527	0.64	0.582	0.527	0.64	SUBCLONAL	1	TRUE	0	0.462235217003903	1		367	703	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391168	89391168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772463834	NA	P-0015298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	205	392	0	ENST00000336596.2:c.1234G>A	p.Val412Ile	p.V412I	ENST00000336596	NM_005233.5	412	Gtt/Att	5/17	1	2	FACETS	0.939	0.871	1	0.939	0.871	1	CLONAL	1	TRUE	1	0.462235217003903	2		392	945	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589251	67589452	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGCTCAGTATAATCCCAAATTGGATGTGAAATTACTTTATCCAGTATCCAAATACCAACAGGTAATAAAAACTGAATGAATTATCCAGTTACGATGTTTAGACAAGATCCTTTTAATACTTAGAAAACATTTGAAGCAGATGAATTACATGTAATCAAGTCTAAAAAACTTGACACTCGTAATTACATAATTGCAATTTTAA	AGCTCAGTATAATCCCAAATTGGATGTGAAATTACTTTATCCAGTATCCAAATACCAACAGGTAATAAAAACTGAATGAATTATCCAGTTACGATGTTTAGACAAGATCCTTTTAATACTTAGAAAACATTTGAAGCAGATGAATTACATGTAATCAAGTCTAAAAAACTTGACACTCGTAATTACATAATTGCAATTTTAA	-	novel	NA	P-0015298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	90	362	0	ENST00000274335.5:c.1241_1300-83del		p.X414_splice	ENST00000274335		414		9/15	0.462235217003903	1	FACETS	0.679	0.605	0.757	0.679	0.605	0.757	SUBCLONAL	1	TRUE	0	0.462235217003903	1		362	441	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0015298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	172	383	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.922	0.85	0.998	0.922	0.85	0.998	CLONAL	1	TRUE	1	0.462235217003903	2		384	807	SUCCESS
APC	324	MSKCC	GRCh37	5	112175789	112175789	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	134	289	0	ENST00000257430.4:c.4501del	p.Ser1501LeufsTer6	p.S1501Lfs*6	ENST00000257430	NM_000038.5	1500	Ttt/tt	16/16	1	2	FACETS	0.957	0.872	1	0.957	0.872	1	CLONAL	1	TRUE	1	0.462235217003903	2		289	606	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508425	106508425	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754761135	NA	P-0015298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	103	194	0	ENST00000359195.3:c.419G>A	p.Arg140Gln	p.R140Q	ENST00000359195	NM_002649.2	140	cGg/cAg	2/11	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.462235217003903	2		194	416	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501350	140501350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906660	NA	P-0015298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	103	330	0	ENST00000288602.6:c.722C>T	p.Thr241Met	p.T241M	ENST00000288602	NM_004333.4	241	aCg/aTg	6/18	1	2	FACETS	0.713	0.639	0.791	0.713	0.639	0.791	SUBCLONAL	1	TRUE	1	0.462235217003903	2		330	625	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0016848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	230	795	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	0.814	0.759	0.87	0.814	0.759	0.87	CLONAL	1	TRUE	1	0.576782404919254	2		795	980	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	31	395	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.544	0.438	0.665	0.544	0.438	0.665	SUBCLONAL	1	TRUE	1	0.12	2		395	950	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017558-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	52	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.157270007136811	3	FACETS	1	0.964	1	0.728	0.623	0.841	CLONAL	1	FALSE	1	0.248767643603877	3		334	323	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0017558-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	34	443	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	0.546	0.445	0.659	0.546	0.445	0.659	SUBCLONAL	1	FALSE	1	0.248767643603877	2		443	501	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376176	225376176	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs748814630	NA	P-0017558-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	40	365	0	ENST00000264414.4:c.778A>G	p.Ile260Val	p.I260V	ENST00000264414	NM_003590.4	260	Att/Gtt	6/16	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	FALSE	1	0.248767643603877	2		365	286	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405931	157405932	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	rs1554294665	NA	P-0017558-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	55	479	0	ENST00000346085.5:c.2176_2177dup	p.His727LeufsTer19	p.H727Lfs*19	ENST00000346085	NM_020732.3	725	tcc/tCCcc	6/20	0.189428675214339	1	FACETS	0.656	0.561	0.76	0.656	0.561	0.76	SUBCLONAL	1	FALSE	0	0.248767643603877	1		479	590	SUCCESS
APC	324	MSKCC	GRCh37	5	112176363	112176427	+	frameshift_variant	Frame_Shift_Del	DEL	CTACAGAAGGCAGAAGTACAGATGAGGCTCAAGGAGGAAAAACCTCATCTGTAACCATACCTGAA	CTACAGAAGGCAGAAGTACAGATGAGGCTCAAGGAGGAAAAACCTCATCTGTAACCATACCTGAA	TGG	novel	NA	P-0017558-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	44	429	1	ENST00000257430.4:c.5072_5136delinsTGG	p.Pro1691LeufsTer4	p.P1691Lfs*4	ENST00000257430	NM_000038.5	1691	cCTACAGAAGGCAGAAGTACAGATGAGGCTCAAGGAGGAAAAACCTCATCTGTAACCATACCTGAA/cTGG	16/16	0.189428675214339	1	FACETS	0.607	0.509	0.716	0.607	0.509	0.716	SUBCLONAL	1	FALSE	0	0.248767643603877	1		430	510	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0017934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	368	395	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.874	0.831	0.918	1	0.996	1	CLONAL	2	TRUE	1	0.406680417752194	2		395	1035	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0017934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	51	761	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.336383746961366	0	FACETS	0.281	0.238	0.327			1	SUBCLONAL	1	TRUE	0	0.406680417752194	0		764	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0017934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	41	652	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.336383746961366	0	FACETS	0.139	0.115	0.166			1	SUBCLONAL	1	TRUE	0	0.406680417752194	0		653	862	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0017934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	316	450	0	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	1	2	FACETS	0.958	0.908	1	1	0.996	1	CLONAL	2	TRUE	1	0.406680417752194	2		450	811	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0017934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	444	543	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.371657439715888	2	FACETS	0.84	0.807	0.874	1	0.995	1	CLONAL	3	TRUE	0	0.406680417752194	2		545	866	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0017934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	23	502	1	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	0.336383746961366	0	FACETS	0.141	0.109	0.178			1	SUBCLONAL	1	TRUE	0	0.406680417752194	0		503	476	SUCCESS
APC	324	MSKCC	GRCh37	5	112175438	112175439	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0017934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	139	267	0	ENST00000257430.4:c.4147_4148del	p.Met1383ValfsTer2	p.M1383Vfs*2	ENST00000257430	NM_000038.5	1383	ATg/g	16/16	1	2	FACETS	0.828	0.761	0.896	1	0.99	1	CLONAL	2	TRUE	1	0.406680417752194	2		267	413	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023447	27023447	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	335	547	1	ENST00000324856.7:c.553C>T	p.Gln185Ter	p.Q185*	ENST00000324856	NM_006015.4	185	Cag/Tag	1/20	1	2	FACETS	1	0.963	1	1	0.996	1	CLONAL	2	TRUE	1	0.406680417752194	2		548	811	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577519	7577519	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	131	531	0	ENST00000269305.4:c.762del	p.Ile255SerfsTer90	p.I255Sfs*90	ENST00000269305	NM_001126112.2	254	atC/at	7/11	0.336383746961366	0	FACETS	0.764	0.698	0.834			1	SUBCLONAL	1	TRUE	0	0.406680417752194	0		531	500	SUCCESS
APC	324	MSKCC	GRCh37	5	112155042	112155042	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0017934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	228	326	0	ENST00000257430.4:c.1312+1G>T		p.X438_splice	ENST00000257430	NM_000038.5	438			1	2	FACETS	0.957	0.898	1	1	0.994	1	CLONAL	2	TRUE	1	0.406680417752194	2		326	586	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151871297	151871297	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	661	469	0	ENST00000262189.6:c.9293A>C	p.Lys3098Thr	p.K3098T	ENST00000262189	NM_170606.2	3098	aAa/aCa	39/59	0.361239517188005	4	FACETS	0.966	0.936	0.995	1	0.997	1	CLONAL	4	TRUE	1	0.406680417752194	4		469	1184	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	168	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.177780701342327	3	FACETS	0.936	0.859	1	0.936	0.859	1	CLONAL	2	FALSE	1	0.177780701342327	3		334	1099	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0018293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	168	729	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.852	0.782	0.926	1	0.99	1	CLONAL	2	FALSE	1	0.177780701342327	2		729	1109	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101608	27101609	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGC	novel	NA	P-0018293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	129	536	0	ENST00000324856.7:c.4892_4895dup	p.Pro1633AlafsTer16	p.P1633Afs*16	ENST00000324856	NM_006015.4	1630	-/CAGC	18/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.177780701342327	2		536	1129	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575169	48575169	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	51	206	1	ENST00000342988.3:c.366del	p.Lys122AsnfsTer7	p.K122Nfs*7	ENST00000342988	NM_005359.5	121	ttA/tt	3/12	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	FALSE	1	0.177780701342327	2		207	511	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068123	94068123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778426683	NA	P-0018293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	56	253	0	ENST00000369303.4:c.839G>A	p.Gly280Asp	p.G280D	ENST00000369303	NM_004440.3	280	gGc/gAc	4/17	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	FALSE	1	0.177780701342327	2		253	577	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681074	117681077	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	rs779372215	NA	P-0018293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	113	422	0	ENST00000368508.3:c.3543_3546del	p.Arg1182LeufsTer60	p.R1182Lfs*60	ENST00000368508	NM_002944.2	1181	gaAAGA/ga	23/43	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.177780701342327	2		422	1040	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971089	21971089	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	104	338	0	ENST00000304494.5:c.269del	p.Phe90SerfsTer56	p.F90Sfs*56	ENST00000304494	NM_000077.4	90	tTc/tc	2/3	0.177780701342327	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	2	FALSE	0	0.177780701342327	2		338	582	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149440515	149440515	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs943493417	NA	P-0019581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	80	596	0	ENST00000286301.3:c.1879A>G	p.Lys627Glu	p.K627E	ENST00000286301	NM_005211.3	627	Aag/Gag	14/22	1	2	FACETS	0.468	0.411	0.53	0.468	0.411	0.53	SUBCLONAL	1	TRUE	1	0.382869694714572	2		596	892	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965555	93965555	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0019581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	55	402	0	ENST00000369303.4:c.2373T>G	p.Tyr791Ter	p.Y791*	ENST00000369303	NM_004440.3	791	taT/taG	13/17	1	2	FACETS	0.409	0.349	0.475	0.409	0.349	0.475	SUBCLONAL	1	TRUE	1	0.382869694714572	2		402	702	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0020245-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	362	810	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.711871589089164	4	FACETS	0.848	0.814	0.882	0.848	0.814	0.882	CLONAL	3	TRUE	1	0.866235239557134	4		810	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0020245-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	597	534	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.862283078997762	2	FACETS	0.968	0.948	0.987	0.968	0.948	0.987	CLONAL	2	TRUE	0	0.866235239557134	2		535	712	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779271	3779271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370704436	NA	P-0020245-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	287	722	0	ENST00000262367.5:c.5777G>A	p.Arg1926Gln	p.R1926Q	ENST00000262367	NM_004380.2	1926	cGg/cAg	31/31	0.866631833062187	5	FACETS	1	0.992	1	0.45	0.423	0.478	CLONAL	1	TRUE	2	0.866235239557134	5		722	1129	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486247	8486247	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139171396	NA	P-0020245-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	259	683	0	ENST00000356435.5:c.2570G>A	p.Arg857His	p.R857H	ENST00000356435		857	cGt/cAt	17/35	1	2	FACETS	0.882	0.831	0.934	0.882	0.831	0.934	CLONAL	1	TRUE	1	0.866235239557134	2		683	678	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520761	176520761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141530067	NA	P-0020245-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	198	396	1	ENST00000292408.4:c.1504G>A	p.Val502Ile	p.V502I	ENST00000292408	NM_213647.1	502	Gtc/Atc	11/18	1	2	FACETS	0.99	0.927	1	0.99	0.927	1	CLONAL	1	TRUE	1	0.866235239557134	2		397	462	SUCCESS
APC	324	MSKCC	GRCh37	5	112175608	112175608	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020245-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	341	744	0	ENST00000257430.4:c.4317del	p.Pro1440HisfsTer33	p.P1440Hfs*33	ENST00000257430	NM_000038.5	1439	ccT/cc	16/16	0.866631833062187	1	FACETS	0.962	0.929	0.993	0.962	0.929	0.993	CLONAL	1	TRUE	0	0.866235239557134	1		744	464	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43817918	43817918	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020245-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	396	768	0	ENST00000372470.3:c.1597C>T	p.Pro533Ser	p.P533S	ENST00000372470	NM_005373.2	533	Cca/Tca	11/12	0.862283078997762	2	FACETS	1	0.977	1	0.517	0.494	0.54	CLONAL	1	TRUE	0	0.866235239557134	2		768	884	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851321	156851321	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020450-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	66	819	0	ENST00000524377.1:c.2278A>C	p.Met760Leu	p.M760L	ENST00000524377	NM_002529.3	760	Atg/Ctg	17/17	0.276463618035343	1	FACETS	0.51	0.442	0.584	0.51	0.442	0.584	SUBCLONAL	1	TRUE	0	0.276463618035343	1		819	807	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087536	27087536	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760364683	NA	P-0020450-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	70	708	2	ENST00000324856.7:c.2110G>A	p.Ala704Thr	p.A704T	ENST00000324856	NM_006015.4	704	Gcc/Acc	5/20	1	2	FACETS	0.62	0.539	0.707	0.62	0.539	0.707	SUBCLONAL	1	TRUE	1	0.276463618035343	2		710	817	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572625	64572625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757179911	NA	P-0020450-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	69	746	3	ENST00000312049.6:c.1231G>A	p.Ala411Thr	p.A411T	ENST00000312049	NM_130799.2	411	Gcc/Acc	9/10	1	2	FACETS	0.507	0.44	0.579	0.507	0.44	0.579	SUBCLONAL	1	TRUE	1	0.276463618035343	2		749	985	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0020771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	519	919	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.496936271666028	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.496936271666028	2		919	971	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0020771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	254	410	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.496936271666028	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.496936271666028	3		410	540	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052632	42052632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779811318	NA	P-0020771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	178	675	0	ENST00000219905.7:c.7303C>T	p.Arg2435Trp	p.R2435W	ENST00000219905	NM_001164273.1	2435	Cgg/Tgg	20/24	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.496936271666028	2		675	648	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609732	81609732	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754118014	NA	P-0020771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	271	632	2	ENST00000298171.2:c.1330T>C	p.Tyr444His	p.Y444H	ENST00000298171	NM_000369.2	444	Tac/Cac	10/10	0.170069686398869	6	FACETS	0.883	0.831	0.936	0.883	0.831	0.936	INDETERMINATE	3	TRUE	3	0.496936271666028	6		634	821	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435634	149435634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	95	848	0	ENST00000286301.3:c.2509G>A	p.Asp837Asn	p.D837N	ENST00000286301	NM_005211.3	837	Gac/Aac	19/22	1	2	FACETS	0.503	0.448	0.562	0.503	0.448	0.562	SUBCLONAL	1	TRUE	1	0.496936271666028	2		848	760	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961055	55961055	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1229432573	NA	P-0020771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	56	1013	1	ENST00000263923.4:c.2885G>A	p.Arg962His	p.R962H	ENST00000263923	NM_002253.2	962	cGc/cAc	21/30	0.496936271666028	2	FACETS	0.254	0.217	0.295	0.127	0.108	0.148	SUBCLONAL	1	TRUE	0	0.496936271666028	2		1014	887	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36945037	36945037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200059719	NA	P-0020771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	430	911	2	ENST00000361632.4:c.61G>A	p.Gly21Arg	p.G21R	ENST00000361632		21	Gga/Aga	2/16	0.317407543131326	3	FACETS	1	0.992	1	0.769	0.737	0.802	CLONAL	2	TRUE	0	0.496936271666028	3		913	936	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374942	45374942	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	321	702	1	ENST00000262160.6:c.901G>T	p.Gly301Cys	p.G301C	ENST00000262160	NM_005901.5	301	Ggc/Tgc	8/11	0.496936271666028	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.496936271666028	2		703	591	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456596	138456596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774144681	NA	P-0020771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	238	749	0	ENST00000289153.2:c.754G>A	p.Gly252Arg	p.G252R	ENST00000289153	NM_006219.2	252	Ggg/Agg	4/22	0.456095069968904	3	FACETS	0.902	0.847	0.958	0.902	0.847	0.958	CLONAL	2	TRUE	1	0.496936271666028	3		749	663	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002939	69002939	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773432628	NA	P-0020771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	163	324	0	ENST00000288368.4:c.2239C>T	p.Arg747Trp	p.R747W	ENST00000288368	NM_024870.2	747	Cgg/Tgg	20/40	0.170069686398869	6	FACETS	0.914	0.846	0.984	0.914	0.846	0.984	INDETERMINATE	3	TRUE	3	0.496936271666028	6		324	477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020798-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	181	628	0	ENST00000269305.4:c.383del	p.Pro128LeufsTer42	p.P128Lfs*42	ENST00000269305	NM_001126112.2	128	cCt/ct	5/11	0.274145241618348	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.274145241618348	2		628	644	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024682	11024682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020798-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	124	503	1	ENST00000327064.4:c.799C>T	p.Arg267Cys	p.R267C	ENST00000327064	NM_199141.1	267	Cgc/Tgc	6/16	0.274145241618348	7	FACETS	1	0.976	1	0.493	0.447	0.541	CLONAL	2	TRUE	2	0.274145241618348	7		504	619	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210442	2210442	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020798-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	51	714	0	ENST00000398665.3:c.1049A>T	p.Lys350Met	p.K350M	ENST00000398665	NM_032482.2	350	aAg/aTg	13/28	0.274145241618348	2	FACETS	0.681	0.579	0.794	0.341	0.289	0.397	SUBCLONAL	1	TRUE	0	0.274145241618348	2		714	546	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196440	106196440	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020798-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	31	544	0	ENST00000380013.4:c.4773C>G	p.Ser1591Arg	p.S1591R	ENST00000380013	NM_001127208.2	1591	agC/agG	11/11	0.166716653973079	4	FACETS	0.611	0.493	0.744	0.305	0.246	0.372	SUBCLONAL	1	TRUE	2	0.274145241618348	4		544	472	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0021029-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	83	395	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.156486923015209	3	FACETS	0.877	0.776	0.984	0.877	0.776	0.984	CLONAL	2	TRUE	1	0.205108100699669	3		395	509	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1691262	1691262	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021029-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	66	699	0	ENST00000378625.1:c.343C>T	p.Gln115Ter	p.Q115*	ENST00000378625	NM_001198994.1	115	Cag/Tag	4/14	1	2	FACETS	0.889	0.771	1	0.889	0.771	1	CLONAL	1	TRUE	1	0.205108100699669	2		699	724	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552816	226552816	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021029-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	96	691	0	ENST00000366794.5:c.2545A>C	p.Lys849Gln	p.K849Q	ENST00000366794	NM_001618.3	849	Aag/Cag	19/23	0.20170051886441	3	FACETS	1	0.95	1	0.56	0.498	0.626	CLONAL	1	TRUE	1	0.205108100699669	3		691	922	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281743	49281743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021029-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	40	659	0	ENST00000282018.3:c.790C>T	p.His264Tyr	p.H264Y	ENST00000282018	NM_020377.2	264	Cac/Tac	1/1	1	2	FACETS	0.546	0.453	0.651	0.546	0.453	0.651	SUBCLONAL	1	TRUE	1	0.205108100699669	2		659	714	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293169	91293169	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs770111029	NA	P-0021029-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	103	619	0	ENST00000355112.3:c.671A>G	p.Gln224Arg	p.Q224R	ENST00000355112	NM_000057.2	224	cAg/cGg	3/22	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.205108100699669	2		619	747	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921798	111921798	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021029-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	66	487	0	ENST00000393256.3:c.587G>A	p.Arg196Lys	p.R196K	ENST00000393256	NM_006538.4	196	aGa/aAa	4/4	0.20170051886441	3	FACETS	0.958	0.83	1	0.479	0.415	0.548	CLONAL	1	TRUE	1	0.205108100699669	3		487	741	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458322	12458322	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021029-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	93	639	0	ENST00000287820.6:c.939C>G	p.Cys313Trp	p.C313W	ENST00000287820	NM_015869.4	313	tgC/tgG	6/7	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.205108100699669	2		639	766	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55597538	55597538	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021029-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	29	425	0	ENST00000288135.5:c.2186C>G	p.Ser729Cys	p.S729C	ENST00000288135	NM_000222.2	729	tCt/tGt	15/21	1	2	FACETS	0.55	0.441	0.675	0.55	0.441	0.675	SUBCLONAL	1	TRUE	1	0.205108100699669	2		425	514	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540885	187540885	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021029-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	82	706	0	ENST00000441802.2:c.6855G>T	p.Gln2285His	p.Q2285H	ENST00000441802	NM_005245.3	2285	caG/caT	10/27	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.205108100699669	2		706	775	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845590	128845590	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs772693769	NA	P-0021029-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	160	615	0	ENST00000249373.3:c.887G>T	p.Arg296Leu	p.R296L	ENST00000249373	NM_005631.4	296	cGt/cTt	4/12	0.20170051886441	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.205108100699669	3		615	756	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346158	152346158	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021029-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	85	624	0	ENST00000359321.1:c.412T>C	p.Cys138Arg	p.C138R	ENST00000359321	NM_005431.1	138	Tgt/Cgt	3/3	0.20170051886441	3	FACETS	1	0.946	1	0.562	0.496	0.633	CLONAL	1	TRUE	1	0.205108100699669	3		624	813	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859878	117859878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780692465	NA	P-0021029-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	59	487	0	ENST00000297338.2:c.1757G>A	p.Arg586Gln	p.R586Q	ENST00000297338	NM_006265.2	586	cGa/cAa	14/14	0.0801033887117759	4	FACETS	0.864	0.742	0.998	0.432	0.371	0.499	INDETERMINATE	1	TRUE	2	0.205108100699669	4		487	802	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815640	139815640	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021029-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	55	606	0	ENST00000247668.2:c.1111G>T	p.Gly371Cys	p.G371C	ENST00000247668	NM_021138.3	371	Ggc/Tgc	9/11	1	2	FACETS	0.805	0.688	0.934	0.805	0.688	0.934	CLONAL	1	TRUE	1	0.205108100699669	2		606	666	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	33	418	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.241005827531155	2		418	200	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610033	43610033	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	51	772	0	ENST00000355710.3:c.1985A>G	p.Lys662Arg	p.K662R	ENST00000355710	NM_020975.4	662	aAg/aGg	11/20	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.241005827531155	2		772	411	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462366	89462366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	16	438	1	ENST00000336596.2:c.1838C>T	p.Ala613Val	p.A613V	ENST00000336596	NM_005233.5	613	gCc/gTc	10/17	1	2	FACETS	0.461	0.34	0.605	0.461	0.34	0.605	SUBCLONAL	1	TRUE	1	0.241005827531155	2		439	288	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281778	49281778	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	59	658	0	ENST00000282018.3:c.825A>T	p.Lys275Asn	p.K275N	ENST00000282018	NM_020377.2	275	aaA/aaT	1/1	0.241005827531155	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.241005827531155	1		658	303	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121644	108121644	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	32	581	0	ENST00000278616.4:c.1452G>T	p.Trp484Cys	p.W484C	ENST00000278616	NM_000051.3	484	tgG/tgT	10/63	1	2	FACETS	0.882	0.718	1	0.882	0.718	1	CLONAL	1	TRUE	1	0.241005827531155	2		581	301	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224559	36224559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	86	786	0	ENST00000222270.7:c.7021G>A	p.Gly2341Arg	p.G2341R	ENST00000222270	NM_014727.1	2341	Ggg/Agg	29/37	0.237650908878501	1	FACETS	0.824	0.734	0.919	1	0.982	1	CLONAL	2	TRUE	0	0.241005827531155	1		786	381	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056989	180056989	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	49	661	0	ENST00000261937.6:c.630G>T	p.Trp210Cys	p.W210C	ENST00000261937	NM_182925.4	210	tgG/tgT	5/30	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.241005827531155	2		661	392	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763848	76763848	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	32	533	0	ENST00000373344.5:c.7460C>A	p.Ser2487Tyr	p.S2487Y	ENST00000373344	NM_000489.3	2487	tCc/tAc	35/35	1	2	FACETS	0.888	0.723	1	0.888	0.723	1	CLONAL	1	TRUE	1	0.241005827531155	2		533	299	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129731	108129731	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	28	382	0	ENST00000278616.4:c.2395G>T	p.Ala799Ser	p.A799S	ENST00000278616	NM_000051.3	799	Gca/Tca	16/63	1	2	FACETS	0.901	0.723	1	0.901	0.723	1	CLONAL	1	TRUE	1	0.241005827531155	2		382	258	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129746	108129747	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	26	395	0	ENST00000278616.4:c.2411dup	p.Arg805AlafsTer10	p.R805Afs*10	ENST00000278616	NM_000051.3	804	ctg/cTtg	16/63	1	2	FACETS	0.87	0.692	1	0.87	0.692	1	CLONAL	1	TRUE	1	0.241005827531155	2		395	248	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355114	73355114	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	37	423	0	ENST00000377767.4:c.256A>T	p.Arg86Trp	p.R86W	ENST00000377767	NM_014953.3	86	Agg/Tgg	2/21	0.241005827531155	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.241005827531155	1		423	228	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916208	9916208	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	44	631	0	ENST00000330684.3:c.2081T>A	p.Ile694Asn	p.I694N	ENST00000330684	NM_001134407.1	694	aTt/aAt	10/13	1	2	FACETS	0.99	0.832	1	0.99	0.832	1	CLONAL	1	TRUE	1	0.241005827531155	2		631	369	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6222149	6222149	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	58	715	0	ENST00000252674.7:c.1093G>T	p.Ala365Ser	p.A365S	ENST00000252674	NM_005934.3	365	Gcc/Tcc	6/12	0.237650908878501	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.241005827531155	1		715	380	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973211	25973211	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	42	587	0	ENST00000435504.4:c.1214C>T	p.Pro405Leu	p.P405L	ENST00000435504		405	cCa/cTa	12/13	1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	1	0.241005827531155	2		587	345	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446304	29446304	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	61	706	0	ENST00000389048.3:c.3263T>C	p.Ile1088Thr	p.I1088T	ENST00000389048	NM_004304.4	1088	aTc/aCc	20/29	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.241005827531155	2		706	441	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281950	39281950	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	11	322	0	ENST00000402219.2:c.525G>T	p.Met175Ile	p.M175I	ENST00000402219	NM_005633.3	175	atG/atT	5/23	1	2	FACETS	0.697	0.484	0.958	0.697	0.484	0.958	SUBCLONAL	1	TRUE	1	0.241005827531155	2		322	131	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265156	198265156	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	30	468	0	ENST00000335508.6:c.2721C>G	p.Asp907Glu	p.D907E	ENST00000335508	NM_012433.2	907	gaC/gaG	19/25	1	2	FACETS	0.909	0.735	1	0.909	0.735	1	CLONAL	1	TRUE	1	0.241005827531155	2		468	274	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877433	40877433	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	58	626	0	ENST00000373198.4:c.2263G>T	p.Glu755Ter	p.E755*	ENST00000373198	NM_133170.3	755	Gag/Tag	15/32	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.241005827531155	2		626	341	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247445	71247445	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	43	612	0	ENST00000318789.4:c.88G>T	p.Gly30Cys	p.G30C	ENST00000318789	NM_032682.5	30	Ggc/Tgc	6/21	1	2	FACETS	0.927	0.777	1	0.927	0.777	1	CLONAL	1	TRUE	1	0.241005827531155	2		612	385	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170016876	170016876	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	32	326	0	ENST00000295797.4:c.1681G>T	p.Val561Phe	p.V561F	ENST00000295797	NM_002740.5	561	Gtc/Ttc	17/18	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.241005827531155	2		326	245	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133859	55133859	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	32	508	0	ENST00000257290.5:c.1072G>T	p.Glu358Ter	p.E358*	ENST00000257290	NM_006206.4	358	Gaa/Taa	7/23	1	2	FACETS	0.942	0.767	1	0.942	0.767	1	CLONAL	1	TRUE	1	0.241005827531155	2		508	282	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067033	143067033	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	46	441	0	ENST00000262992.4:c.1680G>T	p.Lys560Asn	p.K560N	ENST00000262992	NM_001101669.1	560	aaG/aaT	16/24	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.241005827531155	2		441	299	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534382	187534383	+	missense_variant	Missense_Mutation	DNP	AG	AG	TT	novel	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	34	608	0	ENST00000441802.2:c.9343_9344delinsAA	p.Leu3115Lys	p.L3115K	ENST00000441802	NM_005245.3	3115	CTa/AAa	13/27	1	2	FACETS	0.83	0.679	0.998	0.83	0.679	0.998	CLONAL	1	TRUE	1	0.241005827531155	2		608	340	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526550	31526550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770860452	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	28	457	1	ENST00000344624.3:c.490G>A	p.Val164Ile	p.V164I	ENST00000344624		164	Gtt/Att	2/33	1	2	FACETS	0.798	0.64	0.978	0.798	0.64	0.978	CLONAL	1	TRUE	1	0.241005827531155	2		458	291	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155669	56155669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	67	545	0	ENST00000399503.3:c.761G>T	p.Gly254Val	p.G254V	ENST00000399503	NM_005921.1	254	gGc/gTc	3/20	1	2	FACETS	0.772	0.675	0.876	1	0.975	1	SUBCLONAL	2	TRUE	1	0.241005827531155	2		545	360	SUCCESS
APC	324	MSKCC	GRCh37	5	112174040	112174040	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	41	565	0	ENST00000257430.4:c.2749G>T	p.Asp917Tyr	p.D917Y	ENST00000257430	NM_000038.5	917	Gat/Tat	16/16	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.241005827531155	2		565	334	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190525	32190525	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs752145572	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	58	716	0	ENST00000375023.3:c.214C>A	p.Gln72Lys	p.Q72K	ENST00000375023	NM_004557.3	72	Cag/Aag	3/30	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.241005827531155	2		716	405	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157519992	157519992	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	34	566	1	ENST00000346085.5:c.4061G>T	p.Gly1354Val	p.G1354V	ENST00000346085	NM_020732.3	1354	gGa/gTa	17/20	0.241005827531155	1	FACETS	0.909	0.746	1	0.909	0.746	1	CLONAL	1	TRUE	0	0.241005827531155	1		567	273	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444260	50444260	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs755068218	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	44	569	0	ENST00000331340.3:c.190G>T	p.Asp64Tyr	p.D64Y	ENST00000331340	NM_006060.4	64	Gat/Tat	4/8	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.241005827531155	2		569	344	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528728	8528728	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	65	634	0	ENST00000356435.5:c.404A>T	p.Lys135Met	p.K135M	ENST00000356435		135	aAg/aTg	4/35	0.241005827531155	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.241005827531155	1		634	318	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040974	47040974	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	78	785	0	ENST00000377604.3:c.1504G>T	p.Gly502Cys	p.G502C	ENST00000377604	NM_001204468.1	502	Ggt/Tgt	14/24	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.241005827531155	2		785	518	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044715	47044715	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	67	874	0	ENST00000377604.3:c.2115G>T	p.Glu705Asp	p.E705D	ENST00000377604	NM_001204468.1	705	gaG/gaT	19/24	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.241005827531155	2		874	497	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650593	48650593	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	51	835	0	ENST00000376670.3:c.563C>A	p.Pro188His	p.P188H	ENST00000376670	NM_002049.3	188	cCc/cAc	3/6	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.241005827531155	2		835	418	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53241072	53241072	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	39	572	0	ENST00000375401.3:c.1139del	p.Pro380GlnfsTer50	p.P380Qfs*50	ENST00000375401	NM_004187.3	380	cCa/ca	9/26	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.241005827531155	2		572	313	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412855	63412855	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	57	684	0	ENST00000330258.3:c.312T>A	p.His104Gln	p.H104Q	ENST00000330258	NM_152424.3	104	caT/caA	2/2	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.241005827531155	2		684	397	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339953	70339953	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	46	549	0	ENST00000374080.3:c.486G>T	p.Met162Ile	p.M162I	ENST00000374080		162	atG/atT	4/45	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.241005827531155	2		549	318	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181315	123181315	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021029-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	19	391	0	ENST00000218089.9:c.779C>A	p.Ala260Asp	p.A260D	ENST00000218089	NM_001042749.1	260	gCc/gAc	9/35	1	2	FACETS	0.848	0.647	1	0.848	0.647	1	CLONAL	1	TRUE	1	0.241005827531155	2		391	186	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	119	759	1				ENST00000310581	NM_198253.2	-/1132			0.215117283680433	4	FACETS	1	0.978	1	0.427	0.386	0.47	INDETERMINATE	1	TRUE	1	0.421606095107412	4		760	626	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929487	44929487	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	156	837	2	ENST00000377967.4:c.2587C>T	p.Gln863Ter	p.Q863*	ENST00000377967	NM_021140.2	863	Cag/Tag	17/29	0.215117283680433	4	FACETS	1	0.979	1	0.404	0.369	0.439	INDETERMINATE	1	TRUE	1	0.421606095107412	4		839	869	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599255	28599255	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	174	925	0	ENST00000253063.3:c.701C>G	p.Pro234Arg	p.P234R	ENST00000253063	NM_031459.4	234	cCt/cGt	5/10	0.215117283680433	4	FACETS	1	0.98	1	0.401	0.369	0.434	INDETERMINATE	1	TRUE	1	0.421606095107412	4		925	976	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740204	162740204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749040833	NA	P-0021532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	182	840	0	ENST00000367921.3:c.1406C>T	p.Ser469Leu	p.S469L	ENST00000367921	NM_006182.2	469	tCg/tTg	12/18	0.215117283680433	4	FACETS	1	0.987	1	0.445	0.411	0.481	INDETERMINATE	1	TRUE	1	0.421606095107412	4		840	919	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138140	64138140	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	190	856	0	ENST00000334205.4:c.2063C>G	p.Pro688Arg	p.P688R	ENST00000334205	NM_003942.2	688	cCc/cGc	16/17	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.421606095107412	2		856	752	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372495	118372495	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0021532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	158	894	0	ENST00000534358.1:c.6428C>G	p.Ser2143Ter	p.S2143*	ENST00000534358	NM_005933.3	2143	tCa/tGa	26/36	1	2	FACETS	0.88	0.806	0.956	0.88	0.806	0.956	CLONAL	1	TRUE	1	0.421606095107412	2		894	852	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427350	49427350	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0021532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	125	802	0	ENST00000301067.7:c.11138C>G	p.Ser3713Ter	p.S3713*	ENST00000301067	NM_003482.3	3713	tCa/tGa	39/54	NA	2	FACETS	0.843	0.764	0.927			1	INDETERMINATE	1	TRUE	NA	0.421606095107412	2		802	703	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864217	57864217	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	136	722	0	ENST00000228682.2:c.1694T>C	p.Phe565Ser	p.F565S	ENST00000228682	NM_005269.2	565	tTc/tCc	12/12	0.281175215594851	3	FACETS	1	0.95	1			1	CLONAL	1	TRUE	NA	0.421606095107412	3		722	734	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133290	30133290	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs746736375	NA	P-0021532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	158	852	1	ENST00000263025.4:c.208A>G	p.Ile70Val	p.I70V	ENST00000263025	NM_002746.2	70	Atc/Gtc	2/9	0.215117283680433	4	FACETS	1	0.972	1	0.38	0.348	0.414	INDETERMINATE	1	TRUE	1	0.421606095107412	4		853	934	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577019	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0021532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	302	853	2	ENST00000269305.4:c.919_919+1delinsTT		p.X307_splice	ENST00000269305	NM_001126112.2	307		8/11	0.421606095107412	2	FACETS	0.973	0.922	1	0.973	0.922	1	CLONAL	2	TRUE	0	0.421606095107412	2		855	736	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761480	59761480	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	114	656	0	ENST00000259008.2:c.2927A>T	p.Glu976Val	p.E976V	ENST00000259008	NM_032043.2	976	gAa/gTa	20/20	0.215117283680433	4	FACETS	1	0.98	1	0.447	0.404	0.493	INDETERMINATE	1	TRUE	1	0.421606095107412	4		656	573	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727073	41727073	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	173	1004	0	ENST00000301178.4:c.331G>C	p.Asp111His	p.D111H	ENST00000301178	NM_021913.4	111	Gac/Cac	3/20	0.215117283680433	4	FACETS	1	0.98	1	0.4	0.368	0.434	INDETERMINATE	1	TRUE	1	0.421606095107412	4		1004	972	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217460	142217460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	203	602	1	ENST00000350721.4:c.5537G>A	p.Arg1846Gln	p.R1846Q	ENST00000350721	NM_001184.3	1846	cGa/cAa	32/47	0.399222646967059	4	FACETS	0.913	0.849	0.978	0.913	0.849	0.978	CLONAL	2	TRUE	2	0.421606095107412	4		603	750	SUCCESS
ATR	545	MSKCC	GRCh37	3	142297528	142297541	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGGCCATGTTCC	CCAGGCCATGTTCC	-	novel	NA	P-0021532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	202	759	0	ENST00000350721.4:c.6_19del	p.Glu3AlafsTer20	p.E3Afs*20	ENST00000350721	NM_001184.3	2	ggGGAACATGGCCTGGag/ggag	1/47	0.215117283680433	4	FACETS	0.765	0.71	0.822	0.51	0.473	0.548	INDETERMINATE	2	TRUE	1	0.421606095107412	4		759	890	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950075	38950075	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	131	660	0	ENST00000357387.3:c.3875C>G	p.Ser1292Cys	p.S1292C	ENST00000357387	NM_152756.3	1292	tCt/tGt	31/38	0.215117283680433	4	FACETS	1	0.981	1	0.438	0.398	0.48	INDETERMINATE	1	TRUE	1	0.421606095107412	4		660	672	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778211	27778211	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	249	870	0	ENST00000369163.2:c.360C>G	p.Ile120Met	p.I120M	ENST00000369163	NM_003536.2	120	atC/atG	1/1	0.215117283680433	4	FACETS	0.939	0.88	1	0.626	0.586	0.667	INDETERMINATE	2	TRUE	1	0.421606095107412	4		870	894	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	167	243	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		243	463	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795757	42795757	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	314	766	1	ENST00000575354.2:c.2746C>T	p.Gln916Ter	p.Q916*	ENST00000575354	NM_015125.3	916	Cag/Tag	11/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		767	495	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106434	27106434	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	259	582	0	ENST00000324856.7:c.6046del	p.Leu2016CysfsTer14	p.L2016Cfs*14	ENST00000324856	NM_006015.4	2015	atC/at	20/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		582	698	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915524	112915524	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121918455	NA	P-0021729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	250	629	0	ENST00000351677.2:c.923A>C	p.Asn308Thr	p.N308T	ENST00000351677	NM_002834.3	308	aAt/aCt	8/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		629	656	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026125	36026125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367543241	NA	P-0021729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	278	771	1	ENST00000358208.4:c.727C>T	p.Arg243Cys	p.R243C	ENST00000358208		243	Cgc/Tgc	7/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		772	797	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169376	11169376	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	61	804	1	ENST00000361445.4:c.7499T>A	p.Ile2500Asn	p.I2500N	ENST00000361445	NM_004958.3	2500	aTt/aAt	56/58	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.517189748868342	2		805	214	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163376	47163377	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0021781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	16	462	0	ENST00000409792.3:c.2749dup	p.Ser917LysfsTer18	p.S917Kfs*18	ENST00000409792	NM_014159.6	917	agt/aAgt	3/21	0.517189748868342	1	FACETS	0.665	0.504	0.846	0.665	0.504	0.846	SUBCLONAL	1	TRUE	0	0.517189748868342	1		462	69	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271999	15271999	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs897705605	NA	P-0021781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	111	953	0	ENST00000263388.2:c.6440G>A	p.Gly2147Asp	p.G2147D	ENST00000263388	NM_000435.2	2147	gGt/gAt	33/33	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.517189748868342	2		953	393	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183725	10183726	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0021781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	130	947	0	ENST00000256474.2:c.194_195del	p.Ser65CysfsTer66	p.S65Cfs*66	ENST00000256474	NM_000551.3	65	tCG/t	1/3	0.517189748868342	1	FACETS	0.853	0.78	0.928	0.853	0.78	0.928	CLONAL	1	TRUE	0	0.517189748868342	1		947	437	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183738	10183738	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	149	976	0	ENST00000256474.2:c.207del	p.Glu70SerfsTer89	p.E70Sfs*89	ENST00000256474	NM_000551.3	69	cgC/cg	1/3	0.517189748868342	1	FACETS	0.973	0.897	1	0.973	0.897	1	CLONAL	1	TRUE	0	0.517189748868342	1		976	439	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637589	52637589	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	30	808	2	ENST00000394830.3:c.2727del	p.Lys909AsnfsTer6	p.K909Nfs*6	ENST00000394830	NM_018313.4	909	aaA/aa	18/30	0.517189748868342	1	FACETS	0.623	0.51	0.747	0.623	0.51	0.747	SUBCLONAL	1	TRUE	0	0.517189748868342	1		810	138	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231133	53231134	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0021781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	79	363	0	ENST00000375401.3:c.1767_1768dup	p.Ala590ValfsTer70	p.A590Vfs*70	ENST00000375401	NM_004187.3	590	gca/gTGca	13/26	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.517189748868342	1		363	151	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880984	37880985	+	inframe_insertion	In_Frame_Ins	INS	-	-	TACGTGATGGCT	rs397516977	NA	P-0022097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	321	859	0	ENST00000269571.5:c.2314_2325dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/TACGTGATGGCT	20/27	0.481279239689737	5	FACETS	1	0.99	1	0.79	0.748	0.833	CLONAL	2	TRUE	2	0.508821412072966	5		859	939	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30103718	30103718	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	1105	607	0	ENST00000331968.5:c.1220T>C	p.Met407Thr	p.M407T	ENST00000331968	NM_002742.2	407	aTg/aCg	8/18	0.508821412072966	16	FACETS	0.975	0.959	0.99			1	CLONAL	15	TRUE	NA	0.508821412072966	16		607	1355	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577045	7577045	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	262	847	0	ENST00000269305.4:c.893del	p.Glu298GlyfsTer47	p.E298Gfs*47	ENST00000269305	NM_001126112.2	298	gAg/gg	8/11	0.391569849550049	2	FACETS	0.807	0.762	0.853	0.807	0.762	0.853	CLONAL	2	TRUE	0	0.508821412072966	2		847	638	SUCCESS
APC	324	MSKCC	GRCh37	5	112173885	112173885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	136	460	0	ENST00000257430.4:c.2594C>T	p.Pro865Leu	p.P865L	ENST00000257430	NM_000038.5	865	cCa/cTa	16/16	0.449843295176381	4	FACETS	0.838	0.768	0.912	0.838	0.768	0.912	CLONAL	2	TRUE	2	0.508821412072966	4		460	481	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660462	227660462	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143760685	NA	P-0022097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	84	646	0	ENST00000305123.5:c.2993G>A	p.Arg998His	p.R998H	ENST00000305123	NM_005544.2	998	cGt/cAt	1/2	0.368647127557098	3	FACETS	0.74	0.654	0.831	0.37	0.327	0.416	SUBCLONAL	1	TRUE	1	0.508821412072966	3		646	560	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711311	114711311	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	94	470	0	ENST00000543371.1:c.326C>G	p.Pro109Arg	p.P109R	ENST00000543371	NM_001198531.1	109	cCc/cGc	3/14	0.350868868760324	4	FACETS	1	0.95	1	0.555	0.496	0.618	CLONAL	1	TRUE	2	0.508821412072966	4		470	502	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61761032	61761032	+	start_lost	Translation_Start_Site	SNP	T	T	A	novel	NA	P-0022381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	170	344	0	ENST00000401558.2:c.1A>T	p.Met1?	p.M1?	ENST00000401558	NM_003400.3	1	Atg/Ttg	2/25	0.439421929082196	6	FACETS	0.855	0.789	0.922	0.57	0.526	0.615	INDETERMINATE	2	TRUE	3	0.849584160490532	6		344	632	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056713	180056713	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	267	888	1	ENST00000261937.6:c.799G>T	p.Asp267Tyr	p.D267Y	ENST00000261937	NM_182925.4	267	Gac/Tac	6/30	0.849584160490532	3	FACETS	1	0.976	1	0.536	0.504	0.569	CLONAL	1	TRUE	1	0.849584160490532	3		889	835	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321058	137321058	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	222	783	0	ENST00000481739.1:c.1015A>T	p.Ser339Cys	p.S339C	ENST00000481739	NM_002957.4	339	Agc/Tgc	7/10	0.849584160490532	3	FACETS	0.985	0.92	1	0.328	0.306	0.351	CLONAL	1	TRUE	0	0.849584160490532	3		783	756	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0022504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	65	395	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.22406863727298	2		395	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0022504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	81	534	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.22406863727298	1	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	0	0.22406863727298	1		535	632	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0023248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	97	772	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.448789345350673	3	FACETS	1	0.955	1	0.562	0.503	0.624	CLONAL	1	TRUE	1	0.448789345350673	3		772	471	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593504	48593504	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	42	421	0	ENST00000342988.3:c.1255G>C	p.Gly419Arg	p.G419R	ENST00000342988	NM_005359.5	419	Ggg/Cgg	10/12	0.448789345350673	1	FACETS	0.444	0.372	0.523	0.444	0.372	0.523	SUBCLONAL	1	TRUE	0	0.448789345350673	1		421	327	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0023357-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	15	304	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.467	0.344	0.611	0.467	0.344	0.611	SUBCLONAL	1	TRUE	1	0.51	2		304	126	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0023357-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	15	331	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	1	2	FACETS	0.499	0.368	0.652	0.499	0.368	0.652	SUBCLONAL	1	TRUE	1	0.51	2		331	118	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226174	2226174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023357-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	15	678	2	ENST00000326181.6:c.1871C>T	p.Ser624Phe	p.S624F	ENST00000326181	NM_032271.2	624	tCc/tTc	19/21	0.122008971478617	0	FACETS	0.175	0.128	0.23			1	INDETERMINATE	1	TRUE	0	0.51	0		680	165	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270593	98270595	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs756897237	NA	P-0023357-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	9	0	0	ENST00000331920.6:c.49_51del	p.Gly17del	p.G17del	ENST00000331920	NM_000264.3	17	GGC/-	1/24	1	2	FACETS	0.082	0.054	0.119	0.082	0.054	0.119	SUBCLONAL	1	TRUE	1	0.51	2		0	429	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252880	36252880	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023357-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	63	541	0	ENST00000300305.3:c.482T>A	p.Leu161His	p.L161H	ENST00000300305		161	cTc/cAc	4/8	0.225297915844902	3	FACETS	0.861	0.76	0.966	0.861	0.76	0.966	INDETERMINATE	2	TRUE	1	0.51	3		541	180	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827262	72827262	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023357-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	13	660	0	ENST00000268489.5:c.9319C>T	p.Gln3107Ter	p.Q3107*	ENST00000268489	NM_006885.3	3107	Cag/Tag	9/10	0.225297915844902	1	FACETS	0.218	0.156	0.294	0.218	0.156	0.294	INDETERMINATE	1	TRUE	0	0.51	1		660	174	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217458	7217458	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023357-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	20	638	0	ENST00000380728.2:c.338C>A	p.Ser113Ter	p.S113*	ENST00000380728		113	tCa/tAa	5/11	1	2	FACETS	0.792	0.617	0.989	0.792	0.617	0.989	CLONAL	1	TRUE	1	0.51	2		638	99	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100041	157100055	+	inframe_deletion	In_Frame_Del	DEL	AGGAGGAGCAGGAGC	AGGAGGAGCAGGAGC	-	rs773423003	NA	P-0023357-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	25	804	0	ENST00000346085.5:c.993_1007del	p.Gly333_Gly337del	p.G333_G337del	ENST00000346085	NM_020732.3	326	ggAGGAGGAGCAGGAGCa/gga	1/20	1	2	FACETS	0.444	0.351	0.549	0.444	0.351	0.549	SUBCLONAL	1	TRUE	1	0.51	2		804	221	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849652	68849652	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023357-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	7	0	0	ENST00000261769.5:c.1555C>T	p.Gln519Ter	p.Q519*	ENST00000261769	NM_004360.3	519	Cag/Tag	10/16	0.225297915844902	1	FACETS	0.127	0.079	0.191	0.127	0.079	0.191	INDETERMINATE	1	TRUE	0	0.51	1		0	161	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016559	12016559	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023357-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	7	0	0	ENST00000353533.5:c.695C>T	p.Pro232Leu	p.P232L	ENST00000353533	NM_003010.3	232	cCt/cTt	7/11	1	2	FACETS	0.202	0.126	0.302	0.202	0.126	0.302	SUBCLONAL	1	TRUE	1	0.51	2		0	136	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911982	32911982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023357-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	14	510	0	ENST00000380152.3:c.3490C>T	p.Leu1164Phe	p.L1164F	ENST00000380152		1164	Ctt/Ttt	11/27	1	2	FACETS	0.352	0.255	0.468	0.352	0.255	0.468	SUBCLONAL	1	TRUE	1	0.51	2		510	156	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978815	13978815	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023357-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	11	507	0	ENST00000405192.2:c.292G>C	p.Glu98Gln	p.E98Q	ENST00000405192	NM_001163147.1	98	Gaa/Caa	6/12	0.225297915844902	3	FACETS	0.315	0.218	0.435	0.157	0.109	0.218	INDETERMINATE	1	TRUE	1	0.51	3		507	172	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44733219	44733219	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023357-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	91	402	0	ENST00000377967.4:c.211G>C	p.Ala71Pro	p.A71P	ENST00000377967	NM_021140.2	71	Gcc/Ccc	2/29	0.225297915844902	3	FACETS	0.922	0.832	1	0.922	0.832	1	INDETERMINATE	2	TRUE	1	0.51	3		402	243	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651959	36651959	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023411-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	74	516	0	ENST00000244741.5:c.81del	p.Ser27ArgfsTer4	p.S27Rfs*4	ENST00000244741	NM_000389.4	27	agC/ag	2/3	0.34371297488098	1	FACETS	0.586	0.514	0.665	0.586	0.514	0.665	SUBCLONAL	1	TRUE	0	0.34371297488098	1		516	608	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250268	39250268	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023411-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	104	622	0	ENST00000402219.2:c.1301G>C	p.Gly434Ala	p.G434A	ENST00000402219	NM_005633.3	434	gGa/gCa	10/23	1	2	FACETS	0.544	0.486	0.606	0.544	0.486	0.606	SUBCLONAL	1	TRUE	1	0.34371297488098	2		622	1112	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967759	90967759	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023411-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	32	213	0	ENST00000265433.3:c.1149A>C	p.Glu383Asp	p.E383D	ENST00000265433	NM_002485.4	383	gaA/gaC	10/16	1	2	FACETS	0.413	0.335	0.501	0.413	0.335	0.501	SUBCLONAL	1	TRUE	1	0.34371297488098	2		213	451	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	74	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.237853240826822	1	FACETS	0.827	0.724	0.938	0.827	0.724	0.938	CLONAL	1	TRUE	0	0.237853240826822	1		334	663	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0024429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	94	725	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.237853240826822	1	FACETS	0.986	0.878	1	0.986	0.878	1	CLONAL	1	TRUE	0	0.237853240826822	1		732	706	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584513	48584514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs377767334	NA	P-0024429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	41	367	0	ENST00000342988.3:c.692dup	p.Ser232GlnfsTer3	p.S232Qfs*3	ENST00000342988	NM_005359.5	229	ctg/ctGg	6/12	1	2	FACETS	0.839	0.7	0.993	0.839	0.7	0.993	CLONAL	1	TRUE	1	0.237853240826822	2		367	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0024429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	137	787	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.237853240826822	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.237853240826822	1		787	984	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102094419	102094420	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTCCCG	novel	NA	P-0024429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	72	562	0	ENST00000282441.5:c.1100_1105dup	p.Pro368_Gly369insAlaPro	p.P368_G369insAP	ENST00000282441	NM_001130145.2	367	tct/tCTCCCGct	7/9	0.237853240826822	3	FACETS	0.805	0.702	0.916	0.402	0.351	0.458	CLONAL	1	TRUE	1	0.237853240826822	3		562	842	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562489	21562489	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	13	116	0	ENST00000382592.4:c.1430C>T	p.Pro477Leu	p.P477L	ENST00000382592	NM_014572.2	477	cCc/cTc	4/8	1	2	FACETS	0.81	0.581	1	0.81	0.581	1	CLONAL	1	TRUE	1	0.237853240826822	2		116	135	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161274	56161274	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	45	345	0	ENST00000399503.3:c.1143G>T	p.Lys381Asn	p.K381N	ENST00000399503	NM_005921.1	381	aaG/aaT	5/20	1	2	FACETS	0.845	0.71	0.993	0.845	0.71	0.993	CLONAL	1	TRUE	1	0.237853240826822	2		345	448	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0024882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	112	410	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		410	624	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191536	185191536	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	60	583	1	ENST00000265026.3:c.2417G>T	p.Arg806Met	p.R806M	ENST00000265026	NM_004721.4	806	aGg/aTg	11/14	1	2	FACETS	0.792	0.681	0.914	0.792	0.681	0.914	CLONAL	1	TRUE	1	0.17	2		584	891	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044496	47044496	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	52	686	0	ENST00000377604.3:c.1993C>G	p.Gln665Glu	p.Q665E	ENST00000377604	NM_001204468.1	665	Caa/Gaa	18/24	1	2	FACETS	0.653	0.554	0.762	0.653	0.554	0.762	SUBCLONAL	1	TRUE	1	0.17	2		686	937	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070841	30070841	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	258	515	0	ENST00000338641.4:c.1357C>T	p.Gln453Ter	p.Q453*	ENST00000338641	NM_000268.3	453	Cag/Tag	13/16	0.739234695519513	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.739234695519513	1		515	427	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0025458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	105	243	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		243	283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	154	496	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		496	336	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560401	95560401	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	224	449	1	ENST00000393063.1:c.5188G>A	p.Gly1730Arg	p.G1730R	ENST00000393063	NM_030621.3	1730	Ggg/Agg	25/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		450	625	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281764	46281764	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	94	638	0	ENST00000371998.3:c.4211A>G	p.Gln1404Arg	p.Q1404R	ENST00000371998		1404	cAg/cGg	22/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		638	764	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593638	55593661	+	inframe_deletion	In_Frame_Del	DEL	TGTTTACATAGACCCAACACAACT	TGTTTACATAGACCCAACACAACT	-	novel	NA	P-0025633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	213	461	0	ENST00000288135.5:c.1705_1728del	p.Val569_Leu576del	p.V569_L576del	ENST00000288135	NM_000222.2	568	taTGTTTACATAGACCCAACACAACTt/tat	11/21	1	2	FACETS	0.865	0.81	0.92	0.865	0.81	0.92	CLONAL	1	TRUE	1	0.890868367719388	2		461	553	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275224	115275224	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0025633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	229	476	0	ENST00000438362.2:c.1188+1G>A		p.X396_splice	ENST00000438362	NM_001242891.1	396			0.890868367719388	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.890868367719388	1		476	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs747342068	NA	P-0025736-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	25	624	0	ENST00000269305.4:c.394A>C	p.Lys132Gln	p.K132Q	ENST00000269305	NM_001126112.2	132	Aag/Cag	5/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		624	473	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324690	31324690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1399078190	NA	P-0025736-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	18	107	4	ENST00000412585.2:c.118G>A	p.Gly40Ser	p.G40S	ENST00000412585	NM_005514.6	40	Ggc/Agc	2/8	0.121435366561496	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		111	86	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0026158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	45	536	0	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	1	2	FACETS	0.483	0.405	0.57	0.483	0.405	0.57	SUBCLONAL	1	TRUE	1	0.27685173145358	2		536	673	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739006	40739006	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	58	495	0	ENST00000373198.4:c.3278C>A	p.Pro1093His	p.P1093H	ENST00000373198	NM_133170.3	1093	cCc/cAc	24/32	1	2	FACETS	0.642	0.551	0.741	0.642	0.551	0.741	SUBCLONAL	1	TRUE	1	0.27685173145358	2		495	653	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563174	21563174	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	154	479	0	ENST00000382592.4:c.745C>T	p.Gln249Ter	p.Q249*	ENST00000382592	NM_014572.2	249	Cag/Tag	4/8	1	2	FACETS	0.947	0.871	1	0.947	0.871	1	CLONAL	1	TRUE	1	0.547289483459819	2		479	594	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945209	44945209	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1479629068	NA	P-0026299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	93	139	0	ENST00000377967.4:c.3533A>G	p.Asn1178Ser	p.N1178S	ENST00000377967	NM_021140.2	1178	aAt/aGt	24/29	1	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.547289483459819	1		139	210	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0026307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	68	395	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.317790266424825	2		395	331	SUCCESS
APC	324	MSKCC	GRCh37	5	112175539	112175539	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	29	138	0	ENST00000257430.4:c.4248del	p.Ile1417LeufsTer2	p.I1417Lfs*2	ENST00000257430	NM_000038.5	1416	ggC/gg	16/16	1	2	FACETS	0.873	0.706	1	0.873	0.706	1	CLONAL	1	TRUE	1	0.317790266424825	2		138	209	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0026307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	53	496	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.798	0.682	0.924	0.798	0.682	0.924	CLONAL	1	TRUE	1	0.317790266424825	2		497	418	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	99	193	0	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	0.317790266424825	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.317790266424825	2		193	271	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788618	3788618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398124146	NA	P-0026307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	69	238	0	ENST00000262367.5:c.4336C>T	p.Arg1446Cys	p.R1446C	ENST00000262367	NM_004380.2	1446	Cgc/Tgc	26/31	1	2	FACETS	0.942	0.823	1	0.942	0.823	1	CLONAL	1	TRUE	1	0.317790266424825	2		238	461	SUCCESS
APC	324	MSKCC	GRCh37	5	112174384	112174384	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0026307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	21	113	0	ENST00000257430.4:c.3093T>A	p.Tyr1031Ter	p.Y1031*	ENST00000257430	NM_000038.5	1031	taT/taA	16/16	1	2	FACETS	0.842	0.654	1	0.842	0.654	1	CLONAL	1	TRUE	1	0.317790266424825	2		113	157	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171611	36171615	+	frameshift_variant	Frame_Shift_Del	DEL	GGAAA	GGAAA	-	novel	NA	P-0026307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	51	133	0	ENST00000300305.3:c.950_954del	p.Leu317GlnfsTer281	p.L317Qfs*281	ENST00000300305		317	cTTTCC/c	7/8	1	2	FACETS	0.791	0.681	0.907	1	0.97	1	CLONAL	2	TRUE	1	0.317790266424825	2		133	203	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235345	235345	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs151170408	NA	P-0026307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	30	336	0	ENST00000264932.6:c.1151C>G	p.Ser384Ter	p.S384*	ENST00000264932	NM_004168.2	384	tCa/tGa	9/15	1	2	FACETS	0.34	0.273	0.417	0.34	0.273	0.417	SUBCLONAL	1	TRUE	1	0.317790266424825	2		336	555	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591118	67591126	+	inframe_deletion	In_Frame_Del	DEL	ATCCAGCTG	ATCCAGCTG	-	novel	NA	P-0026307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	47	152	0	ENST00000274335.5:c.1712_1720del	p.Ile571_Leu573del	p.I571_L573del	ENST00000274335		571	ATCCAGCTG/-	12/15	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.317790266424825	2		152	244	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	378	759	1				ENST00000310581	NM_198253.2	-/1132			0.443709817810327	3	FACETS	1	0.983	1	1	0.996	1	CLONAL	3	TRUE	1	0.443709817810327	3		760	663	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0026437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	155	454	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.443709817810327	2		454	642	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981202	201981202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750329636	NA	P-0026455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	104	837	1	ENST00000359651.3:c.281G>A	p.Arg94Gln	p.R94Q	ENST00000359651		94	cGa/cAa	2/8	0.384481788118455	3	FACETS	0.553	0.494	0.617	0.277	0.247	0.309	SUBCLONAL	1	TRUE	1	0.384481788118455	3		838	1166	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007666	45007666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1191507697	NA	P-0026455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	73	430	1	ENST00000558401.1:c.113G>A	p.Gly38Glu	p.G38E	ENST00000558401	NM_004048.2	38	gGa/gAa	2/4	0.256670221514872	1	FACETS	0.544	0.476	0.617	0.544	0.476	0.617	SUBCLONAL	1	TRUE	0	0.384481788118455	1		431	564	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2093576	2093576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3211977	NA	P-0026455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	153	666	1	ENST00000219066.1:c.701C>T	p.Ser234Leu	p.S234L	ENST00000219066	NM_002528.5	234	tCa/tTa	4/6	1	2	FACETS	0.889	0.813	0.969	0.889	0.813	0.969	CLONAL	1	TRUE	1	0.384481788118455	2		667	895	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190871	185190871	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0026455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	202	783	0	ENST00000265026.3:c.1752T>A	p.Tyr584Ter	p.Y584*	ENST00000265026	NM_004721.4	584	taT/taA	11/14	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.384481788118455	2		783	986	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205073	38205073	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0026455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	105	817	0	ENST00000317025.8:c.617C>G	p.Ser206Ter	p.S206*	ENST00000317025	NM_023034.1	206	tCa/tGa	2/24	0.384481788118455	2	FACETS	0.439	0.392	0.49	0.22	0.196	0.245	SUBCLONAL	1	TRUE	0	0.384481788118455	2		817	1243	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862871	117862871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	122	624	0	ENST00000297338.2:c.1606G>A	p.Asp536Asn	p.D536N	ENST00000297338	NM_006265.2	536	Gat/Aat	12/14	0.384481788118455	3	FACETS	0.739	0.667	0.815	0.246	0.222	0.272	SUBCLONAL	1	TRUE	0	0.384481788118455	3		624	1024	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016634	12016634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	61	477	0	ENST00000353533.5:c.770C>T	p.Ser257Phe	p.S257F	ENST00000353533	NM_003010.3	257	tCt/tTt	7/11	0.685879771964155	1	FACETS	0.489	0.427	0.555	0.489	0.427	0.555	SUBCLONAL	1	TRUE	0	0.685879771964155	1		477	239	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467502	25467502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	73	749	1	ENST00000264709.3:c.1574C>T	p.Ala525Val	p.A525V	ENST00000264709	NM_175629.2	525	gCg/gTg	14/23	0.184170979670742	2	FACETS	0.357	0.312	0.405	0.179	0.156	0.203	INDETERMINATE	1	TRUE	0	0.685879771964155	2		750	596	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0026660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	727	472	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	0.724100567521215	5	FACETS	0.925	0.902	0.947	0.925	0.902	0.947	CLONAL	4	TRUE	1	0.86886328062548	5		472	1042	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0026660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	516	1119	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.86886328062548	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.86886328062548	1		1119	630	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0026660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	891	958	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.868610665334302	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.86886328062548	2		958	1010	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202185	138202185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775745583	NA	P-0026660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	45	920	1	ENST00000237289.4:c.2102G>A	p.Arg701His	p.R701H	ENST00000237289	NM_001270507.1	701	cGc/cAc	9/9	1	2	FACETS	0.116	0.097	0.138	0.116	0.097	0.138	SUBCLONAL	1	TRUE	1	0.86886328062548	2		921	891	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490980	56490980	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs931676601	NA	P-0026660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	445	1045	0	ENST00000267101.3:c.2426A>G	p.Gln809Arg	p.Q809R	ENST00000267101	NM_001982.3	809	cAg/cGg	20/28	0.166632894791482	3	FACETS	1	0.996	1	0.735	0.704	0.767	INDETERMINATE	1	TRUE	1	0.86886328062548	3		1045	999	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0026660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	334	1146	10	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	0.86886328062548	1	FACETS	0.73	0.698	0.761	0.73	0.698	0.761	SUBCLONAL	1	TRUE	0	0.86886328062548	1		1156	596	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	372	1199	11	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	1	2	FACETS	0.874	0.832	0.917	0.874	0.832	0.917	CLONAL	1	TRUE	1	0.86886328062548	2		1210	980	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176354	24176354	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	43	781	0	ENST00000263121.7:c.1148del	p.Pro383ArgfsTer100	p.P383Rfs*100	ENST00000263121	NM_003073.3	382	gCc/gc	9/9	1	2	FACETS	0.129	0.107	0.153	0.129	0.107	0.153	SUBCLONAL	1	TRUE	1	0.86886328062548	2		781	767	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139804418	139804418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746259933	NA	P-0026660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	41	829	0	ENST00000247668.2:c.575G>A	p.Cys192Tyr	p.C192Y	ENST00000247668	NM_021138.3	192	tGc/tAc	6/11	1	2	FACETS	0.115	0.095	0.137	0.115	0.095	0.137	SUBCLONAL	1	TRUE	1	0.86886328062548	2		829	820	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274304	5274304	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	392	1025	3	ENST00000357368.4:c.143del	p.Gly48ValfsTer17	p.G48Vfs*17	ENST00000357368	NM_002850.3	48	gGt/gt	3/38	1	2	FACETS	0.961	0.917	1	0.961	0.917	1	CLONAL	1	TRUE	1	0.86886328062548	2		1028	939	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939260	71939260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	461	1178	2	ENST00000298229.2:c.209G>A	p.Arg70His	p.R70H	ENST00000298229	NM_001567.3	70	cGc/cAc	2/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.86886328062548	2		1180	1040	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0026660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	382	1179	2	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.802	0.762	0.841	0.802	0.762	0.841	CLONAL	1	TRUE	1	0.86886328062548	2		1181	1097	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506170	148506171	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs797045568	NA	P-0026660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	249	610	0	ENST00000320356.2:c.2187dup	p.Asp730Ter	p.D730*	ENST00000320356	NM_004456.4	729	-/T	19/20	1	2	FACETS	0.941	0.887	0.996	0.941	0.887	0.996	CLONAL	1	TRUE	1	0.86886328062548	2		610	609	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32438072	32438072	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	415	829	0	ENST00000332351.3:c.965G>T	p.Ser322Ile	p.S322I	ENST00000332351	NM_024426.4	322	aGc/aTc	5/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.86886328062548	2		829	856	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252024	133252024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	405	1000	0	ENST00000320574.5:c.1186del	p.Glu396SerfsTer16	p.E396Sfs*16	ENST00000320574	NM_006231.2	396	Gag/ag	12/49	1	2	FACETS	0.899	0.858	0.941	0.899	0.858	0.941	CLONAL	1	TRUE	1	0.86886328062548	2		1000	1037	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245912885	245912885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374803671	NA	P-0026660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	275	713	0	ENST00000388985.4:c.1267G>A	p.Ala423Thr	p.A423T	ENST00000388985		423	Gcc/Acc	12/12	0.166632894791482	3	FACETS	1	0.989	1	0.595	0.561	0.63	INDETERMINATE	1	TRUE	1	0.86886328062548	3		713	763	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210907	36210907	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770426704	NA	P-0026660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	516	1249	3	ENST00000222270.7:c.658C>T	p.Arg220Trp	p.R220W	ENST00000222270	NM_014727.1	220	Cgg/Tgg	3/37	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.86886328062548	2		1252	1143	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057831	27057832	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0026660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	633	1262	0	ENST00000324856.7:c.1542_1543del	p.Gln515AlafsTer107	p.Q515Afs*107	ENST00000324856	NM_006015.4	513	tcCTct/tcct	3/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.86886328062548	2		1262	1420	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755717	39755717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1333152977	NA	P-0026660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	354	1010	2	ENST00000288319.7:c.1048C>T	p.Arg350Cys	p.R350C	ENST00000288319	NM_182918.3	350	Cgc/Tgc	10/10	1	2	FACETS	0.939	0.893	0.985	0.939	0.893	0.985	CLONAL	1	TRUE	1	0.86886328062548	2		1012	868	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63898360	63898361	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCA	rs193922929	NA	P-0026660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	157	737	0	ENST00000398590.3:c.116_118dup	p.Gln39dup	p.Q39dup	ENST00000398590	NM_001177387.1	39	cgg/cgGCAg	3/14	0.86886328062548	1	FACETS	0.454	0.42	0.49	0.454	0.42	0.49	SUBCLONAL	1	TRUE	0	0.86886328062548	1		737	450	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1736014	1736014	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557889974	NA	P-0026660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	355	832	2	ENST00000378609.4:c.274G>A	p.Ala92Thr	p.A92T	ENST00000378609	NM_002074.3	92	Gcc/Acc	7/12	1	2	FACETS	0.999	0.952	1	0.999	0.952	1	CLONAL	1	TRUE	1	0.86886328062548	2		834	818	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50733661	50733661	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1567603601	NA	P-0026660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	41	232	0	ENST00000307179.4:c.226del	p.Arg76AspfsTer36	p.R76Dfs*36	ENST00000307179		74	Aaa/aa	3/20	1	2	FACETS	0.474	0.399	0.555	0.474	0.399	0.555	SUBCLONAL	1	TRUE	1	0.86886328062548	2		232	199	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379703	17379703	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	497	1027	0	ENST00000359435.4:c.88A>G	p.Asn30Asp	p.N30D	ENST00000359435	NM_001033549.1	30	Aat/Gat	2/9	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.86886328062548	2		1027	1035	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500558	149500558	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	428	1037	1	ENST00000261799.4:c.2479C>A	p.Leu827Met	p.L827M	ENST00000261799	NM_002609.3	827	Ctg/Atg	18/23	1	2	FACETS	0.994	0.951	1	0.994	0.951	1	CLONAL	1	TRUE	1	0.86886328062548	2		1038	991	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165247	32165247	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	468	1153	0	ENST00000375023.3:c.4881G>T	p.Gln1627His	p.Q1627H	ENST00000375023	NM_004557.3	1627	caG/caT	27/30	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.86886328062548	2		1153	1046	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229230	55229230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754646330	NA	P-0026660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	347	1042	2	ENST00000275493.2:c.1537G>A	p.Glu513Lys	p.E513K	ENST00000275493	NM_005228.3	513	Gag/Aag	13/28	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.86886328062548	2		1044	791	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873523	151873523	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	371	959	0	ENST00000262189.6:c.9015del	p.Thr3006GlnfsTer26	p.T3006Qfs*26	ENST00000262189	NM_170606.2	3005	ggG/gg	38/59	1	2	FACETS	0.947	0.902	0.992	0.947	0.902	0.992	CLONAL	1	TRUE	1	0.86886328062548	2		959	902	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0026772-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	237	418	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.714797371055552	4	FACETS	0.868	0.817	0.92	0.868	0.817	0.92	CLONAL	2	TRUE	2	0.858554451289949	4		418	591	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0026772-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	212	558	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.803640171313025	5	FACETS	0.984	0.921	1	0.656	0.614	0.699	CLONAL	2	TRUE	2	0.858554451289949	5		558	574	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923211	26923211	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026772-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	269	387	0	ENST00000381527.3:c.207A>C	p.Leu69Phe	p.L69F	ENST00000381527	NM_001260.1	69	ttA/ttC	3/13	0.803640171313025	5	FACETS	0.843	0.799	0.887	0.843	0.799	0.887	CLONAL	3	TRUE	2	0.858554451289949	5		387	567	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634343	23634343	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026772-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	698	609	0	ENST00000261584.4:c.2943del	p.Ser981ArgfsTer9	p.S981Rfs*9	ENST00000261584	NM_024675.3	981	agT/ag	9/13	0.858554451289949	4	FACETS	0.881	0.855	0.905	0.881	0.855	0.905	CLONAL	3	TRUE	1	0.858554451289949	4		609	1144	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294258	1294258	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026772-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	601	705	0	ENST00000310581.5:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000310581	NM_198253.2	248	cGg/cAg	2/16	0.426670998930507	6	FACETS	0.875	0.843	0.908	0.875	0.843	0.908	INDETERMINATE	3	TRUE	3	0.858554451289949	6		705	1449	SUCCESS
APC	324	MSKCC	GRCh37	5	112175437	112175438	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATGTTTAGCAGATGTACTT	novel	NA	P-0026772-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	123	338	0	ENST00000257430.4:c.4147_4165dup	p.Ser1389TyrfsTer3	p.S1389Yfs*3	ENST00000257430	NM_000038.5	1382	-/ATGTTTAGCAGATGTACTT	16/16	0.771881804429978	1	FACETS	0.44	0.402	0.479	0.44	0.402	0.479	SUBCLONAL	1	TRUE	0	0.858554451289949	1		338	372	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339575	70339575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266838743	NA	P-0026772-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	493	579	0	ENST00000374080.3:c.244C>T	p.Arg82Cys	p.R82C	ENST00000374080		82	Cgt/Tgt	3/45	0.858554451289949	3	FACETS	0.874	0.842	0.906			1	CLONAL	2	TRUE	NA	0.858554451289949	3		579	939	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672052	30672052	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026772-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1278	279	653	0	ENST00000376406.3:c.4908G>T	p.Arg1636Ser	p.R1636S	ENST00000376406	NM_014641.2	1636	agG/agT	10/15	0.858554451289949	3	FACETS	0.597	0.559	0.636	0.298	0.279	0.318	SUBCLONAL	1	TRUE	1	0.858554451289949	3		653	1557	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422688	47422688	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026772-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	233	522	0	ENST00000377045.4:c.160C>G	p.Leu54Val	p.L54V	ENST00000377045	NM_001654.4	54	Cta/Gta	3/16	0.858554451289949	3	FACETS	0.737	0.687	0.788			1	SUBCLONAL	1	TRUE	NA	0.858554451289949	3		522	1053	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0026811-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	296	834	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.385991237131421	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.385991237131421	2		834	649	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048238	180048238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324497116	NA	P-0026811-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	185	556	0	ENST00000261937.6:c.2035C>T	p.Arg679Trp	p.R679W	ENST00000261937	NM_182925.4	679	Cgg/Tgg	14/30	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.385991237131421	2		556	712	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029396	16029396	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026811-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	31	262	0	ENST00000268712.3:c.1634A>C	p.Lys545Thr	p.K545T	ENST00000268712	NM_006311.3	545	aAa/aCa	15/46	0.385991237131421	2	FACETS	0.744	0.606	0.897	0.372	0.303	0.449	SUBCLONAL	1	TRUE	0	0.385991237131421	2		262	216	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969093	93969093	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026811-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	144	694	0	ENST00000369303.4:c.1903A>C	p.Ile635Leu	p.I635L	ENST00000369303	NM_004440.3	635	Att/Ctt	10/17	0.385991237131421	4	FACETS	1	0.982	1	0.429	0.391	0.468	CLONAL	1	TRUE	1	0.385991237131421	4		694	804	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28903811	28903811	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199497877	NA	P-0027617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	363	602	3	ENST00000282397.4:c.2648C>T	p.Thr883Ile	p.T883I	ENST00000282397	NM_002019.4	883	aCc/aTc	19/30	1	2	FACETS	0.9	0.855	0.946	0.9	0.855	0.946	CLONAL	1	TRUE	1	0.770501107888275	2		605	1047	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034794	42034794	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	350	474	0	ENST00000219905.7:c.4636G>C	p.Val1546Leu	p.V1546L	ENST00000219905	NM_001164273.1	1546	Gtt/Ctt	15/24	1	2	FACETS	0.977	0.928	1	0.977	0.928	1	CLONAL	1	TRUE	1	0.770501107888275	2		474	930	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578204	7578204	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520001	NA	P-0027617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	509	604	1	ENST00000269305.4:c.645T>G	p.Ser215Arg	p.S215R	ENST00000269305	NM_001126112.2	215	agT/agG	6/11	0.756346386627629	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.770501107888275	1		605	781	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042504	37043233	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGATTTAGCCAGTATTTCTACCTATGGCTTTCGAGGTGAGGTAAGCTAAAGATTCAAGAAATGTGTAAAATATCCTCCTGTGATGACATTGTCTGTCATTTGTTAGTATGTATTTCTCAACATAGATAAATAAGGTTTGGTACCTTTTACTTGTTAAATGTATGCAAATCTGAGCAAACTTAATGAACTTTAACTTTCAAAGACTGAGAATTGTTCATAAATAAACTATTTTACCTGCAGAGACCTCTGATATATGTTTCTTGATGGAAGTACCCAGTACCACCTATGAAGTTTTCTTGTCAAAAAATCAAATGTGAATCTGATCATTACTTAGATCTAAGTACCAATATATGAAAAATATAGGAGACAAGGAAGCATGGTAAATGATACTGAGATTGGGAGACTACATGGAAAAAGACTTGTTCCCTTCAACAGATAGACAGCAGGGAAAAAAGAATAGAGAAAGGAGTAAAGAACCTGTAGATTAAAAGACATTTAAGGGACATATGAACCAGGTCCAGTGTATAGATCTTACCTAAATCCTGATGGAGCAAACTATAAAAAAATTTTTTTGAGACAAATGTTTGAATACAGGTTGACTATTTGATGGCATTAAGGAGAAATTATGAATTATCTTGGTATAAGAATATTGTCATGGGTTTTTTTTTTTGAGTCCTTACCTGTTAAGATACATACTAAAATATTTGTGGGTAAAATTATATGACGTAT	AGGATTTAGCCAGTATTTCTACCTATGGCTTTCGAGGTGAGGTAAGCTAAAGATTCAAGAAATGTGTAAAATATCCTCCTGTGATGACATTGTCTGTCATTTGTTAGTATGTATTTCTCAACATAGATAAATAAGGTTTGGTACCTTTTACTTGTTAAATGTATGCAAATCTGAGCAAACTTAATGAACTTTAACTTTCAAAGACTGAGAATTGTTCATAAATAAACTATTTTACCTGCAGAGACCTCTGATATATGTTTCTTGATGGAAGTACCCAGTACCACCTATGAAGTTTTCTTGTCAAAAAATCAAATGTGAATCTGATCATTACTTAGATCTAAGTACCAATATATGAAAAATATAGGAGACAAGGAAGCATGGTAAATGATACTGAGATTGGGAGACTACATGGAAAAAGACTTGTTCCCTTCAACAGATAGACAGCAGGGAAAAAAGAATAGAGAAAGGAGTAAAGAACCTGTAGATTAAAAGACATTTAAGGGACATATGAACCAGGTCCAGTGTATAGATCTTACCTAAATCCTGATGGAGCAAACTATAAAAAAATTTTTTTGAGACAAATGTTTGAATACAGGTTGACTATTTGATGGCATTAAGGAGAAATTATGAATTATCTTGGTATAAGAATATTGTCATGGGTTTTTTTTTTTGAGTCCTTACCTGTTAAGATACATACTAAAATATTTGTGGGTAAAATTATATGACGTAT	-	novel	NA	P-0027617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	199	575	0	ENST00000231790.2:c.270_306+693del		p.X90_splice	ENST00000231790	NM_000249.3	90		3/19	0.748925100171354	2	FACETS	0.604	0.56	0.65	0.302	0.28	0.325	SUBCLONAL	1	TRUE	0	0.770501107888275	2		575	855	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	207	759	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.82	2		760	471	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0027983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	298	499	1	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.82	2		500	702	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791758	42791758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1380826096	NA	P-0027983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	16	556	0	ENST00000575354.2:c.644G>A	p.Arg215Gln	p.R215Q	ENST00000575354	NM_015125.3	215	cGg/cAg	5/20	0.821434809810029	1	FACETS	0.057	0.042	0.075	0.057	0.042	0.075	SUBCLONAL	1	TRUE	0	0.82	1		556	404	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463586	25463586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761064473	NA	P-0027983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	207	532	1	ENST00000264709.3:c.2096G>A	p.Gly699Asp	p.G699D	ENST00000264709	NM_175629.2	699	gGc/gAc	18/23	1	2	FACETS	0.82	0.765	0.875	0.82	0.765	0.875	CLONAL	1	TRUE	1	0.82	2		533	616	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797274	42797274	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	93	668	0	ENST00000575354.2:c.3636del	p.Val1213SerfsTer89	p.V1213Sfs*89	ENST00000575354	NM_015125.3	1212	ccA/cc	15/20	0.821434809810029	1	FACETS	0.341	0.305	0.378	0.341	0.305	0.378	SUBCLONAL	1	TRUE	0	0.82	1		668	393	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797295	42797296	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0027983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	51	658	0	ENST00000575354.2:c.3659_3660del	p.Glu1220ValfsTer2	p.E1220Vfs*2	ENST00000575354	NM_015125.3	1219	ccAGag/ccag	15/20	0.821434809810029	1	FACETS	0.178	0.151	0.207	0.178	0.151	0.207	SUBCLONAL	1	TRUE	0	0.82	1		658	413	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798872	42798872	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	24	640	0	ENST00000575354.2:c.4445del	p.Gly1482AlafsTer28	p.G1482Afs*28	ENST00000575354	NM_015125.3	1482	Ggc/gc	19/20	0.821434809810029	1	FACETS	0.072	0.056	0.091	0.072	0.056	0.091	SUBCLONAL	1	TRUE	0	0.82	1		640	478	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90949274	90949275	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0027983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	60	241	0	ENST00000265433.3:c.2213dup	p.Leu739SerfsTer3	p.L739Sfs*3	ENST00000265433	NM_002485.4	738	tct/tcCt	15/16	1	2	FACETS	0.327	0.282	0.376	0.327	0.282	0.376	SUBCLONAL	1	TRUE	1	0.82	2		241	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0028070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	670	659	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.876827928497694	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.888091251604485	2		659	723	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0028070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	261	581	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.287551807867556	3	FACETS	0.857	0.814	0.901	0.857	0.814	0.901	INDETERMINATE	2	TRUE	1	0.888091251604485	3		581	495	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692839	89692839	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	168	205	0	ENST00000371953.3:c.323T>G	p.Leu108Arg	p.L108R	ENST00000371953	NM_000314.4	108	cTt/cGt	5/9	0.888091251604485	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.888091251604485	2		205	182	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47735799	47735799	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	370	657	0	ENST00000449228.1:c.61A>T	p.Thr21Ser	p.T21S	ENST00000449228	NM_001127240.2	21	Acg/Tcg	1/4	0.287551807867556	3	FACETS	0.805	0.77	0.841	0.805	0.77	0.841	INDETERMINATE	2	TRUE	1	0.888091251604485	3		657	747	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265542	198265542	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1402437917	NA	P-0028070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	378	656	0	ENST00000335508.6:c.2615T>C	p.Ile872Thr	p.I872T	ENST00000335508	NM_012433.2	872	aTt/aCt	18/25	0.539596834598129	5	FACETS	0.944	0.898	0.99	0.629	0.598	0.66	CLONAL	2	TRUE	2	0.888091251604485	5		656	1052	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589139	67589140	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAATAACAAATTAATCA	novel	NA	P-0028070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	51	268	0	ENST00000274335.5:c.1133_1149dup	p.Phe384ThrfsTer3	p.F384Tfs*3	ENST00000274335		376	gga/ggAAATAACAAATTAATCAa	9/15	0.793199030190096	3	FACETS	0.631	0.54	0.728	0.315	0.27	0.364	SUBCLONAL	1	TRUE	1	0.888091251604485	3		268	263	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589580	67589588	+	inframe_deletion	In_Frame_Del	DEL	AATTACATG	AATTACATG	-	novel	NA	P-0028070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	190	360	0	ENST00000274335.5:c.1346_1354del	p.Leu449_Glu451del	p.L449_E451del	ENST00000274335		448	aAATTACATGaa/aaa	10/15	0.793199030190096	3	FACETS	1	0.99	1	0.68	0.636	0.726	CLONAL	1	TRUE	1	0.888091251604485	3		360	454	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	74	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.94	0.821	1	0.94	0.821	1	CLONAL	1	TRUE	1	0.187070353169416	2		334	842	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0028084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	65	659	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.187070353169416	1	FACETS	0.79	0.684	0.906	0.79	0.684	0.906	CLONAL	1	TRUE	0	0.187070353169416	1		659	797	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95577788	95577788	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	21	216	0	ENST00000393063.1:c.2122C>G	p.Leu708Val	p.L708V	ENST00000393063	NM_030621.3	708	Ctg/Gtg	15/28	0.181803159719391	1	FACETS	0.577	0.443	0.732	0.577	0.443	0.732	SUBCLONAL	1	TRUE	0	0.187070353169416	1		216	353	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0028546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	356	476	0				ENST00000310581	NM_198253.2	-/1132			0.496756317534524	6	FACETS	1	0.966	1	1	0.966	1	INDETERMINATE	3	TRUE	3	0.923792760979371	6		476	722	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144146	11144146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	44	582	0	ENST00000358026.2:c.3727C>T	p.Arg1243Trp	p.R1243W	ENST00000358026	NM_001128849.1	1243	Cgg/Tgg	26/36	1	2	FACETS	0.181	0.151	0.214	0.181	0.151	0.214	SUBCLONAL	1	TRUE	1	0.923792760979371	2		582	526	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821930	59821930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200313471	NA	P-0028546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	506	354	0	ENST00000259008.2:c.2120G>A	p.Arg707His	p.R707H	ENST00000259008	NM_032043.2	707	cGt/cAt	15/20	0.90951023169993	5	FACETS	0.97	0.936	1	0.97	0.936	1	CLONAL	3	TRUE	2	0.923792760979371	5		354	898	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981167	201981168	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0028546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	174	611	0	ENST00000359651.3:c.248dup	p.Asn83LysfsTer9	p.N83Kfs*9	ENST00000359651		82	-/A	2/8	0.549085613826253	3	FACETS	0.642	0.591	0.695	0.214	0.197	0.232	INDETERMINATE	1	TRUE	0	0.923792760979371	3		611	858	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982367	201982367	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	644	707	0	ENST00000359651.3:c.746G>T	p.Arg249Leu	p.R249L	ENST00000359651		249	cGg/cTg	6/8	0.549085613826253	3	FACETS	1	0.997	1	0.814	0.795	0.832	INDETERMINATE	2	TRUE	0	0.923792760979371	3		707	835	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742916	17742916	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	364	592	0	ENST00000250003.3:c.824C>T	p.Pro275Leu	p.P275L	ENST00000250003	NM_002478.4	275	cCt/cTt	3/3	0.903766813825801	2	FACETS	0.983	0.963	1	0.983	0.963	1	CLONAL	2	TRUE	0	0.923792760979371	2		592	401	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492543	50492543	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	184	556	0	ENST00000394963.4:c.1439A>G	p.Glu480Gly	p.E480G	ENST00000394963	NM_003076.4	480	gAg/gGg	12/13	0.243391894702863	4	FACETS	1	0.98	1	0.289	0.267	0.311	INDETERMINATE	1	TRUE	0	0.923792760979371	4		556	663	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226519	41226519	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	205	417	0	ENST00000357654.3:c.4504C>A	p.Pro1502Thr	p.P1502T	ENST00000357654	NM_007294.3	1502	Cca/Aca	14/23	0.531688259927231	4	FACETS	1	0.991	1	0.464	0.433	0.496	INDETERMINATE	1	TRUE	1	0.923792760979371	4		417	613	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46275841	46275841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	383	513	0	ENST00000371998.3:c.3277G>A	p.Asp1093Asn	p.D1093N	ENST00000371998		1093	Gat/Aat	18/23	0.820809504301989	4	FACETS	0.893	0.852	0.934	0.893	0.852	0.934	CLONAL	2	TRUE	2	0.923792760979371	4		513	893	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092952	29092952	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs202051128	NA	P-0028546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	413	468	0	ENST00000328354.6:c.1032A>G	p.Ile344Met	p.I344M	ENST00000328354	NM_007194.3	344	atA/atG	10/15	0.820809504301989	4	FACETS	0.96	0.919	1	0.96	0.919	1	CLONAL	2	TRUE	2	0.923792760979371	4		468	896	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180254	32180254	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs751888857	NA	P-0028546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	400	416	0	ENST00000375023.3:c.2677C>A	p.Gln893Lys	p.Q893K	ENST00000375023	NM_004557.3	893	Caa/Aaa	17/30	0.609698311990097	3	FACETS	1	0.995	1	0.79	0.766	0.814	CLONAL	2	TRUE	0	0.923792760979371	3		416	534	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46254131	46254131	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	84	354	0	ENST00000371998.3:c.263C>T	p.Thr88Ile	p.T88I	ENST00000371998		88	aCt/aTt	5/23	1	2	FACETS	0.96	0.852	1	0.96	0.852	1	CLONAL	1	TRUE	1	0.417782122684364	2		354	419	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706977	117706977	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764959275	NA	P-0028895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	63	604	0	ENST00000368508.3:c.2173G>A	p.Asp725Asn	p.D725N	ENST00000368508	NM_002944.2	725	Gac/Aac	15/43	1	2	FACETS	0.624	0.54	0.717	0.624	0.54	0.717	SUBCLONAL	1	TRUE	1	0.31	2		604	651	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044463	12044463	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0028975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	66	245	0	ENST00000353533.5:c.1087-1G>A		p.X363_splice	ENST00000353533	NM_003010.3	363			0.352024455450926	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.352024455450926	1		245	248	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	118	572	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	1	2	FACETS	0.906	0.818	0.999	0.906	0.818	0.999	CLONAL	1	TRUE	1	0.352024455450926	2		572	740	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135729	64135729	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1312009585	NA	P-0028975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	98	499	0	ENST00000334205.4:c.1197G>A	p.Met399Ile	p.M399I	ENST00000334205	NM_003942.2	399	atG/atA	10/17	0.352024455450926	1	FACETS	0.94	0.842	1	0.94	0.842	1	CLONAL	1	TRUE	0	0.352024455450926	1		499	488	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831004	72831005	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0029204-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	40	432	0	ENST00000268489.5:c.5576_5577del	p.Ser1859TyrfsTer69	p.S1859Yfs*69	ENST00000268489	NM_006885.3	1859	tCT/t	9/10	1	2	FACETS	0.911	0.758	1	0.911	0.758	1	CLONAL	1	TRUE	1	0.23	2		432	382	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562254	95562254	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029204-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	16	351	0	ENST00000393063.1:c.5003A>C	p.Asn1668Thr	p.N1668T	ENST00000393063	NM_030621.3	1668	aAt/aCt	24/28	1	2	FACETS	0.679	0.503	0.888	0.679	0.503	0.888	SUBCLONAL	1	TRUE	1	0.23	2		351	205	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029204-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	35	499	0	ENST00000347630.2:c.305T>A	p.Phe102Tyr	p.F102Y	ENST00000347630	NM_001007230.1	102	tTc/tAc	5/11	1	2	FACETS	1	0.826	1	1	0.826	1	CLONAL	1	TRUE	1	0.23	2		499	303	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257568	19257568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029204-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	35	458	0	ENST00000162023.5:c.658G>A	p.Gly220Arg	p.G220R	ENST00000162023		220	Ggg/Agg	10/13	1	2	FACETS	0.69	0.565	0.83	0.69	0.565	0.83	SUBCLONAL	1	TRUE	1	0.23	2		458	441	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649047	86649047	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs952699191	NA	P-0029204-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	21	251	0	ENST00000274376.6:c.1327A>G	p.Met443Val	p.M443V	ENST00000274376	NM_002890.2	443	Atg/Gtg	9/25	1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.23	2		251	164	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0029830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	173	652	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		653	881	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220466	133220466	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	64	343	0	ENST00000320574.5:c.4247C>G	p.Ala1416Gly	p.A1416G	ENST00000320574	NM_006231.2	1416	gCt/gGt	33/49	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		343	624	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490369	29490381	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGTCTTTAGTC	GCAGTCTTTAGTC	-	novel	NA	P-0029830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	72	277	0	ENST00000356175.3:c.457_469del	p.Val153PhefsTer8	p.V153Ffs*8	ENST00000356175	NM_000267.3	152	GCAGTCTTTAGTCgc/gc	4/57	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		277	549	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943386	17943391	+	stop_gained	Nonsense_Mutation	ONP	GATCTG	GATCTG	CATCTA	novel	NA	P-0029830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	62	444	0	ENST00000458235.1:c.2617_2622delinsTAGATG	p.Gln873_Ile874delinsTer	p.Q873_I874delins*	ENST00000458235	NM_000215.3	873	CAGATC/TAGATG	19/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		444	845	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0030121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	208	693	2	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.381722620973931	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.381722620973931	1		695	806	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	43	283	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	1	2	FACETS	0.702	0.59	0.825	0.702	0.59	0.825	SUBCLONAL	1	TRUE	1	0.381722620973931	2		283	321	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006224	22006224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	126	469	0	ENST00000276925.6:c.179G>A	p.Arg60His	p.R60H	ENST00000276925	NM_004936.3	60	cGc/cAc	2/2	1	2	FACETS	0.99	0.898	1	0.99	0.898	1	CLONAL	1	TRUE	1	0.381722620973931	2		469	667	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438085	110438085	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	127	395	0	ENST00000375856.3:c.316G>T	p.Asp106Tyr	p.D106Y	ENST00000375856	NM_003749.2	106	Gac/Tac	1/2	0.381722620973931	3	FACETS	1	0.939	1	0.523	0.474	0.575	CLONAL	1	TRUE	1	0.381722620973931	3		395	757	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118989	70118990	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGGCAGA	novel	NA	P-0030121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	180	703	0	ENST00000245479.2:c.563_570dup	p.Glu191ArgfsTer31	p.E191Rfs*31	ENST00000245479	NM_000346.3	187	-/GAGGCAGA	2/3	1	2	FACETS	0.953	0.878	1	0.953	0.878	1	CLONAL	1	TRUE	1	0.381722620973931	2		703	990	SUCCESS
APC	324	MSKCC	GRCh37	5	112170760	112170761	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0030121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	133	533	0	ENST00000257430.4:c.1858_1859del	p.Leu620TyrfsTer13	p.L620Yfs*13	ENST00000257430	NM_000038.5	619	aCT/a	15/16	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.381722620973931	2		533	673	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100093	157100117	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCGGCGGCGGCAGCAGCAGGAG	GCGGCGGCGGCGGCAGCAGCAGGAG	-	novel	NA	P-0030121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	28	37	0	ENST00000346085.5:c.1044_1068del	p.Ala350MetfsTer11	p.A350Mfs*11	ENST00000346085	NM_020732.3	344	GCGGCGGCGGCGGCAGCAGCAGGAGgc/gc	1/20	0.348578218917212	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	0	0.381722620973931	2		37	61	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0030979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	479	690	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.656396111357968	4	FACETS	0.937	0.911	0.961	0.937	0.911	0.961	CLONAL	4	FALSE	0	0.68328621696079	4		690	630	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279674	123279674	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs77543610	NA	P-0030979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	323	297	0	ENST00000358487.5:c.758C>G	p.Pro253Arg	p.P253R	ENST00000358487	NM_000141.4	253	cCt/cGt	7/18	0.68328621696079	3	FACETS	0.997	0.964	1	0.997	0.964	1	CLONAL	3	FALSE	0	0.68328621696079	3		297	424	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5073748	5073748	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	205	363	0	ENST00000381652.3:c.1827G>C	p.Leu609Phe	p.L609F	ENST00000381652	NM_004972.3	609	ttG/ttC	14/25	0.68328621696079	6	FACETS	1	0.976	1	0.367	0.342	0.393	CLONAL	2	FALSE	0	0.68328621696079	6		363	645	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786876	135786885	+	frameshift_variant	Frame_Shift_Del	DEL	ACTCAGAGTC	ACTCAGAGTC	-	novel	NA	P-0030979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	472	328	0	ENST00000298552.3:c.984_993del	p.Gln328HisfsTer7	p.Q328Hfs*7	ENST00000298552	NM_001162426.1	328	caGACTCTGAGT/ca	10/23	0.668252391893951	4	FACETS	0.996	0.971	1	0.996	0.971	1	CLONAL	4	FALSE	0	0.68328621696079	4		328	584	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544675	65544675	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030979-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	58	502	0	ENST00000358664.4:c.251A>T	p.Asp84Val	p.D84V	ENST00000358664	NM_002382.4	84	gAt/gTt	4/5	0.68328621696079	2	FACETS	0.28	0.24	0.324	0.14	0.12	0.162	SUBCLONAL	1	FALSE	0	0.68328621696079	2		502	606	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0031154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	178	665	2	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		667	382	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0031206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	350	191	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.276479557885521	1	FACETS	0.653	0.623	0.684	0.653	0.623	0.684	INDETERMINATE	1	TRUE	0	0.831603594013678	1		191	753	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0031206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	501	932	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.831603594013678	1	FACETS	0.942	0.913	0.971	0.942	0.913	0.971	CLONAL	1	TRUE	0	0.831603594013678	1		932	747	SUCCESS
APC	324	MSKCC	GRCh37	5	112175876	112175876	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085992	NA	P-0031206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	245	350	0	ENST00000257430.4:c.4585C>T	p.Gln1529Ter	p.Q1529*	ENST00000257430	NM_000038.5	1529	Cag/Tag	16/16	0.831603594013678	1	FACETS	0.962	0.92	1	0.962	0.92	1	CLONAL	1	TRUE	0	0.831603594013678	1		350	358	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411411	63411411	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	474	628	0	ENST00000330258.3:c.1756C>T	p.Arg586Ter	p.R586*	ENST00000330258	NM_152424.3	586	Cga/Tga	2/2	0.831603594013678	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.831603594013678	1		628	663	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372555	118372555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	413	561	3	ENST00000534358.1:c.6488G>A	p.Arg2163Gln	p.R2163Q	ENST00000534358	NM_005933.3	2163	cGa/cAa	26/36	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.831603594013678	2		564	992	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662323	67662323	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0031206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	600	575	0	ENST00000264010.4:c.1569C>G	p.Tyr523Ter	p.Y523*	ENST00000264010	NM_006565.3	523	taC/taG	9/12	0.327185144327434	3	FACETS	0.801	0.772	0.829	0.801	0.772	0.829	INDETERMINATE	2	TRUE	1	0.831603594013678	3		575	1276	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209298	98209298	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149667902	NA	P-0031206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	511	696	1	ENST00000331920.6:c.4240G>A	p.Val1414Met	p.V1414M	ENST00000331920	NM_000264.3	1414	Gtg/Atg	23/24	0.831603594013678	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.831603594013678	1		697	698	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794554	42794554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150295260	NA	P-0031210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	188	768	0	ENST00000575354.2:c.1634C>T	p.Ser545Leu	p.S545L	ENST00000575354	NM_015125.3	545	tCg/tTg	10/20	0.556624423315494	2	FACETS	0.695	0.642	0.75	0.347	0.321	0.375	SUBCLONAL	1	TRUE	0	0.556624423315494	2		768	972	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520008	NA	P-0031210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	619	705	0	ENST00000269305.4:c.613T>G	p.Tyr205Asp	p.Y205D	ENST00000269305	NM_001126112.2	205	Tat/Gat	6/11	0.479019031676234	3	FACETS	0.977	0.949	1			1	CLONAL	3	TRUE	NA	0.556624423315494	3		705	970	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0031210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	89	337	1				ENST00000310581	NM_198253.2	-/1132			0.556624423315494	3	FACETS	1	0.902	1	0.506	0.451	0.564	CLONAL	1	TRUE	1	0.556624423315494	3		338	404	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456395	32456395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	215	629	0	ENST00000332351.3:c.497G>A	p.Gly166Asp	p.G166D	ENST00000332351	NM_024426.4	166	gGc/gAc	1/10	0.556624423315494	2	FACETS	1	0.974	1	0.542	0.505	0.579	CLONAL	1	TRUE	0	0.556624423315494	2		629	713	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933356	100933365	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTGGTGAA	ACCTGGTGAA	-	novel	NA	P-0031210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	312	578	1	ENST00000325455.5:c.2025_2034del	p.Ser676LysfsTer5	p.S676Kfs*5	ENST00000325455	NM_001202474.3	675	ttTTCACCAGGT/tt	4/8	0.419251290303695	4	FACETS	0.939	0.888	0.991	0.939	0.888	0.991	CLONAL	2	TRUE	2	0.556624423315494	4		579	929	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120796847	120796847	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769968859	NA	P-0031210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	166	750	0	ENST00000257552.2:c.412G>A	p.Ala138Thr	p.A138T	ENST00000257552	NM_002442.3	138	Gcc/Acc	7/15	0.290726652413809	4	FACETS	0.812	0.745	0.883	0.406	0.372	0.442	INDETERMINATE	1	TRUE	2	0.556624423315494	4		750	1143	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701139	29701139	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	146	492	0	ENST00000356175.3:c.8423G>T	p.Ser2808Ile	p.S2808I	ENST00000356175	NM_000267.3	2808	aGt/aTt	57/57	0.556624423315494	2	FACETS	0.919	0.842	0.998	0.459	0.421	0.499	CLONAL	1	TRUE	0	0.556624423315494	2		492	571	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47601082	47601082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224710	NA	P-0031210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	139	655	0	ENST00000263735.4:c.320C>T	p.Ala107Val	p.A107V	ENST00000263735	NM_002354.2	107	gCc/gTc	3/9	0.203729043287936	3	FACETS	0.744	0.677	0.814	0.248	0.225	0.272	INDETERMINATE	1	TRUE	0	0.556624423315494	3		655	858	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598056	55598056	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	125	443	0	ENST00000288135.5:c.2253T>A	p.Asp751Glu	p.D751E	ENST00000288135	NM_000222.2	751	gaT/gaA	16/21	0.556624423315494	2	FACETS	1	0.924	1	0.507	0.462	0.553	CLONAL	1	TRUE	0	0.556624423315494	2		443	443	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156145	106156145	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	65	431	0	ENST00000380013.4:c.1046G>C	p.Gly349Ala	p.G349A	ENST00000380013	NM_001127208.2	349	gGt/gCt	3/11	0.556624423315494	2	FACETS	0.508	0.441	0.579	0.254	0.22	0.29	SUBCLONAL	1	TRUE	0	0.556624423315494	2		431	460	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157520040	157520040	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	234	458	0	ENST00000346085.5:c.4109C>G	p.Pro1370Arg	p.P1370R	ENST00000346085	NM_020732.3	1370	cCg/cGg	17/20	0.550257347418296	3	FACETS	0.875	0.822	0.929	0.875	0.822	0.929	CLONAL	2	TRUE	1	0.556624423315494	3		458	614	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970931	70970931	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	194	715	0	ENST00000276594.2:c.1330C>G	p.Arg444Gly	p.R444G	ENST00000276594	NM_024504.3	444	Cgg/Ggg	6/8	0.556624423315494	2	FACETS	0.999	0.928	1	0.499	0.464	0.536	CLONAL	1	TRUE	0	0.556624423315494	2		715	698	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646015	215646015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755641562	NA	P-0031212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	89	565	0	ENST00000260947.4:c.583G>A	p.Ala195Thr	p.A195T	ENST00000260947	NM_000465.2	195	Gct/Act	4/11	0.473759898663689	1	FACETS	0.841	0.752	0.934	0.841	0.752	0.934	CLONAL	1	TRUE	0	0.473759898663689	1		565	341	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136209	2136209	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777539610	NA	P-0031214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	238	625	0	ENST00000219476.3:c.4678G>A	p.Ala1560Thr	p.A1560T	ENST00000219476	NM_000548.3	1560	Gcc/Acc	37/42	1	2	FACETS	0.907	0.851	0.964	0.907	0.851	0.964	CLONAL	1	FALSE	1	0.769526480604967	2		625	682	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444746	49444746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	470	896	0	ENST00000301067.7:c.2720C>T	p.Pro907Leu	p.P907L	ENST00000301067	NM_003482.3	907	cCt/cTt	10/54	0.107637973608091	4	FACETS	0.916	0.877	0.955	0.916	0.877	0.955	INDETERMINATE	2	FALSE	2	0.769526480604967	4		896	1180	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438151	110438151	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	243	377	0	ENST00000375856.3:c.250A>G	p.Ser84Gly	p.S84G	ENST00000375856	NM_003749.2	84	Agc/Ggc	1/2	1	2	FACETS	0.839	0.787	0.892	0.839	0.787	0.892	CLONAL	1	FALSE	1	0.769526480604967	2		377	753	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663657	29663657	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	122	453	1	ENST00000356175.3:c.6089T>C	p.Ile2030Thr	p.I2030T	ENST00000356175	NM_000267.3	2030	aTt/aCt	41/57	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.769526480604967	2		454	278	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064436	30064436	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1569302393	NA	P-0031214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	332	548	0	ENST00000338641.4:c.999+1G>A		p.X333_splice	ENST00000338641	NM_000268.3	333			0.769526480604967	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	0	0.769526480604967	1		548	510	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0031226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	154	243	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.455	0.416	0.494	0.455	0.416	0.494	SUBCLONAL	1	TRUE	1	0.897506069784179	2		243	755	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	226	1227	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	1	2	FACETS	0.536	0.499	0.573	0.536	0.499	0.573	SUBCLONAL	1	TRUE	1	0.897506069784179	2		1227	940	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155725	56155726	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0031226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	165	279	0	ENST00000399503.3:c.819_820del	p.Arg273SerfsTer27	p.R273Sfs*27	ENST00000399503	NM_005921.1	273	AGa/a	3/20	1	2	FACETS	0.449	0.413	0.488	0.449	0.413	0.488	SUBCLONAL	1	TRUE	1	0.897506069784179	2		279	818	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179381	56179381	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	96	530	0	ENST00000399503.3:c.3696del	p.Ala1233GlnfsTer12	p.A1233Qfs*12	ENST00000399503	NM_005921.1	1232	Aaa/aa	15/20	1	2	FACETS	0.461	0.413	0.512	0.461	0.413	0.512	SUBCLONAL	1	TRUE	1	0.897506069784179	2		530	464	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623625	28623625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1279372452	NA	P-0031448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	25	531	1	ENST00000241453.7:c.932G>A	p.Arg311Gln	p.R311Q	ENST00000241453	NM_004119.2	311	cGg/cAg	8/24	1	2	FACETS	0.331	0.26	0.413	0.331	0.26	0.413	SUBCLONAL	1	FALSE	1	0.315064504218558	2		532	479	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0031497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	56	481	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.991	0.848	1	0.991	0.848	1	CLONAL	1	TRUE	1	0.19	2		481	595	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	34	365	0	ENST00000342988.3:c.1610A>T	p.Asp537Val	p.D537V	ENST00000342988	NM_005359.5	537	gAc/gTc	12/12	1	2	FACETS	0.825	0.674	0.994	0.825	0.674	0.994	CLONAL	1	TRUE	1	0.19	2		365	434	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916946	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0031497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	44	448	0	ENST00000263967.3:c.332_334del	p.Lys111del	p.K111del	ENST00000263967	NM_006218.2	111	AAG/-	2/21	1	2	FACETS	0.78	0.653	0.92	0.78	0.653	0.92	CLONAL	1	TRUE	1	0.19	2		448	594	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022817	31022817	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770762273	NA	P-0031497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	58	515	0	ENST00000375687.4:c.2302C>T	p.Gln768Ter	p.Q768*	ENST00000375687	NM_015338.5	768	Caa/Taa	13/13	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.19	2		515	572	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006495	12006495	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1157133215	NA	P-0031497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	88	628	0	ENST00000396373.4:c.463G>A	p.Asp155Asn	p.D155N	ENST00000396373	NM_001987.4	155	Gat/Aat	4/8	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.19	2		628	907	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380328	25380328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	62	366	0	ENST00000311936.3:c.130G>A	p.Val44Ile	p.V44I	ENST00000311936	NM_004985.3	44	Gta/Ata	3/5	0.247232390302291	3	FACETS	1	0.965	1	0.695	0.601	0.797	CLONAL	1	TRUE	1	0.19	3		366	514	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400745	56400745	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0031497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	37	332	0	ENST00000348428.3:c.1339A>T	p.Lys447Ter	p.K447*	ENST00000348428	NM_006785.3	447	Aaa/Taa	11/17	1	2	FACETS	0.881	0.727	1	0.881	0.727	1	CLONAL	1	TRUE	1	0.19	2		332	442	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244185	5244185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774952239	NA	P-0031497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	39	568	2	ENST00000357368.4:c.1297G>A	p.Val433Met	p.V433M	ENST00000357368	NM_002850.3	433	Gtg/Atg	11/38	1	2	FACETS	0.676	0.559	0.807	0.676	0.559	0.807	SUBCLONAL	1	TRUE	1	0.19	2		570	607	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599332	55599332	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519710	NA	P-0031775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	227	393	0	ENST00000288135.5:c.2458G>T	p.Asp820Tyr	p.D820Y	ENST00000288135	NM_000222.2	820	Gat/Tat	17/21	0.930943528234769	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.930943528234769	1		393	258	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593582	55593597	+	protein_altering_variant,splice_region_variant	In_Frame_Del	DEL	AAACCCATGTATGAAG	AAACCCATGTATGAAG	T	novel	NA	P-0031775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	176	245	1	ENST00000288135.5:c.1648_1663delinsT	p.Lys550_Val555delinsLeu	p.K550_V555delinsL	ENST00000288135	NM_000222.2	550	AAACCCATGTATGAAGta/Tta	11/21	0.930943528234769	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.930943528234769	1		246	193	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0031818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	67	558	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	FALSE	1	0.445619116775965	2		558	298	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450909	70450909	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	89	524	0	ENST00000373644.4:c.5749G>T	p.Val1917Leu	p.V1917L	ENST00000373644	NM_030625.2	1917	Gtg/Ttg	12/12	1	2	FACETS	0.876	0.78	0.977	0.876	0.78	0.977	CLONAL	1	FALSE	1	0.445619116775965	2		524	456	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061241	38061244	+	frameshift_variant	Frame_Shift_Del	DEL	AGTC	AGTC	-	novel	NA	P-0032256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	144	589	0	ENST00000250448.2:c.745_748del	p.Asp249ProfsTer71	p.D249Pfs*71	ENST00000250448	NM_004496.3	249	GACTcc/cc	2/2	0.307561625373424	3	FACETS	1	0.988	1	0.718	0.664	0.773	INDETERMINATE	1	TRUE	1	0.800282369121613	3		589	351	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478157	138478157	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	86	369	0	ENST00000289153.2:c.29C>G	p.Ala10Gly	p.A10G	ENST00000289153	NM_006219.2	10	gCt/gGt	1/22	0.545160956201548	4	FACETS	0.98	0.872	1	0.327	0.29	0.365	CLONAL	1	TRUE	1	0.800282369121613	4		369	395	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859392	151859393	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0032256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	113	419	0	ENST00000262189.6:c.11269_11270del	p.Gln3757GlufsTer18	p.Q3757Efs*18	ENST00000262189	NM_170606.2	3757	CAg/g	43/59	1	2	FACETS	0.987	0.903	1	0.987	0.903	1	CLONAL	1	TRUE	1	0.800282369121613	2		419	286	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781328	135781328	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	43	578	0	ENST00000298552.3:c.1637A>C	p.Asp546Ala	p.D546A	ENST00000298552	NM_001162426.1	546	gAc/gCc	15/23	0.215342047304837	1	FACETS	0.202	0.169	0.238	0.202	0.169	0.238	INDETERMINATE	1	TRUE	0	0.800282369121613	1		578	319	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124723	108124738	+	protein_altering_variant	In_Frame_Del	DEL	TTCTGGGATTATCAGA	TTCTGGGATTATCAGA	C	novel	NA	P-0032256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	83	383	0	ENST00000278616.4:c.2081_2096delinsC	p.Leu694_Glu699delinsPro	p.L694_E699delinsP	ENST00000278616	NM_000051.3	694	cTTCTGGGATTATCAGAa/cCa	13/63	0.800282369121613	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.800282369121613	1		383	117	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0032339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	240	784	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.123216641126945	4	FACETS	1	0.964	1			1	INDETERMINATE	3	TRUE	NA	0.323810750536985	4		786	632	SUCCESS
ALK	238	MSKCC	GRCh37	2	29430098	29430098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024193740	NA	P-0032339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	36	466	0	ENST00000389048.3:c.3877G>A	p.Val1293Ile	p.V1293I	ENST00000389048	NM_004304.4	1293	Gtt/Att	26/29	0.323810750536985	3	FACETS	0.497	0.408	0.597	0.166	0.136	0.199	SUBCLONAL	1	TRUE	0	0.323810750536985	3		466	520	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431420	49431430	+	frameshift_variant	Frame_Shift_Del	DEL	AGTGAGCTCTC	AGTGAGCTCTC	GGAG	novel	NA	P-0032339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	134	576	1	ENST00000301067.7:c.9709_9719delinsCTCC	p.Glu3237LeufsTer3	p.E3237Lfs*3	ENST00000301067	NM_003482.3	3237	GAGAGCTCACTg/CTCCg	34/54	0.288194906241583	4	FACETS	0.959	0.875	1			1	CLONAL	2	TRUE	NA	0.323810750536985	4		577	571	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291059	10291059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	261	502	0	ENST00000340748.4:c.412C>T	p.Pro138Ser	p.P138S	ENST00000340748		138	Ccc/Tcc	4/40	0.297573810901075	4	FACETS	0.91	0.861	0.96	0.91	0.861	0.96	CLONAL	4	TRUE	0	0.323810750536985	4		502	586	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545762	106545762	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	146	448	0	ENST00000359195.3:c.3239G>A	p.Trp1080Ter	p.W1080*	ENST00000359195	NM_002649.2	1080	tGg/tAg	11/11	0.323810750536985	5	FACETS	1	0.974	1	0.771	0.707	0.838	CLONAL	2	TRUE	2	0.323810750536985	5		448	579	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007618	45007763	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGGTACTCCAAAGATTCAGGTTTACTCACGTCATCCAGCAGAGAATGGAAAGTCAAATTTCCTGAATTGCTATGTGTCTGGGTTTCATCCATCCGACATTGAAGTTGACTTACTGAAGAATGGAGAGAGAATTGAAAAAGTGGAG	CAGGTACTCCAAAGATTCAGGTTTACTCACGTCATCCAGCAGAGAATGGAAAGTCAAATTTCCTGAATTGCTATGTGTCTGGGTTTCATCCATCCGACATTGAAGTTGACTTACTGAAGAATGGAGAGAGAATTGAAAAAGTGGAG	-	novel	NA	P-0032339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	19	245	0	ENST00000558401.1:c.68-1_212del		p.X23_splice	ENST00000558401	NM_004048.2	23		2/4	0.297688567187408	2	FACETS	0.593	0.452	0.757	0.296	0.226	0.379	SUBCLONAL	1	TRUE	0	0.323810750536985	2		245	198	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547022	9547022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs58486349	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	24	204	0	ENST00000353224.5:c.1000G>A	p.Asp334Asn	p.D334N	ENST00000353224	NM_177990.2	334	Gat/Aat	5/10	1	2	FACETS	0.645	0.506	0.804	0.645	0.506	0.804	SUBCLONAL	1	TRUE	1	0.262167973364862	2		204	284	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	75	417	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.262167973364862	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.262167973364862	1		417	461	SUCCESS
APC	324	MSKCC	GRCh37	5	112177788	112177788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752091655	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	29	266	0	ENST00000257430.4:c.6497G>A	p.Arg2166Gln	p.R2166Q	ENST00000257430	NM_000038.5	2166	cGa/cAa	16/16	1	2	FACETS	0.679	0.545	0.83	0.679	0.545	0.83	SUBCLONAL	1	TRUE	1	0.262167973364862	2		266	326	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112029177	112029177	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	70	341	0	ENST00000368678.4:c.391G>A	p.Gly131Ser	p.G131S	ENST00000368678		131	Ggt/Agt	5/13	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.262167973364862	2		341	505	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116179	209116179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555882127	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	45	324	1	ENST00000345146.2:c.97C>T	p.Pro33Ser	p.P33S	ENST00000345146	NM_005896.2	33	Ccc/Tcc	3/10	1	2	FACETS	0.761	0.64	0.895	0.761	0.64	0.895	SUBCLONAL	1	TRUE	1	0.262167973364862	2		325	451	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446209	29446209	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs774951734	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	61	445	0	ENST00000389048.3:c.3358C>T	p.Arg1120Trp	p.R1120W	ENST00000389048	NM_004304.4	1120	Cgg/Tgg	20/29	1	2	FACETS	0.881	0.761	1	0.881	0.761	1	CLONAL	1	TRUE	1	0.262167973364862	2		445	528	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355540	15355540	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149185763	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	133	634	0	ENST00000263377.2:c.2192C>T	p.Pro731Leu	p.P731L	ENST00000263377	NM_058243.2	731	cCc/cTc	12/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.262167973364862	2		634	886	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924327	112924327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	90	522	0	ENST00000351677.2:c.1273G>A	p.Asp425Asn	p.D425N	ENST00000351677	NM_002834.3	425	Gac/Aac	11/16	0.262167973364862	1	FACETS	0.888	0.788	0.994	0.888	0.788	0.994	CLONAL	1	TRUE	0	0.262167973364862	1		522	672	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969075	93969075	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs992785889	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	39	252	0	ENST00000369303.4:c.1921G>T	p.Ala641Ser	p.A641S	ENST00000369303	NM_004440.3	641	Gca/Tca	10/17	1	2	FACETS	0.852	0.708	1	0.852	0.708	1	CLONAL	1	TRUE	1	0.262167973364862	2		252	349	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	103	749	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	1	2	FACETS	0.832	0.744	0.927	0.832	0.744	0.927	CLONAL	1	TRUE	1	0.262167973364862	2		749	944	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795392	39795392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	110	665	0	ENST00000288319.7:c.328G>A	p.Glu110Lys	p.E110K	ENST00000288319	NM_182918.3	110	Gag/Aag	3/10	1	2	FACETS	0.899	0.807	0.998	0.899	0.807	0.998	CLONAL	1	TRUE	1	0.262167973364862	2		665	933	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013719	170013719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388201066	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	68	246	1	ENST00000295797.4:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000295797	NM_002740.5	480	Cgc/Tgc	15/18	0.241704173774516	2	FACETS	0.933	0.813	1	0.467	0.406	0.532	CLONAL	1	TRUE	0	0.262167973364862	2		247	556	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295253	+	upstream_gene_variant	5'Flank	ONP	GAGG	GAGG	AAGA	novel	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	38	354	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.704	0.582	0.839	0.704	0.582	0.839	SUBCLONAL	1	TRUE	1	0.262167973364862	2		354	412	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710637	40710637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1161104430	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	66	485	0	ENST00000373198.4:c.4214G>A	p.Gly1405Glu	p.G1405E	ENST00000373198	NM_133170.3	1405	gGa/gAa	31/32	1	2	FACETS	0.772	0.67	0.883	0.772	0.67	0.883	SUBCLONAL	1	TRUE	1	0.262167973364862	2		485	652	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285173	212285173	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754420079	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	50	341	0	ENST00000342788.4:c.3128C>T	p.Ser1043Leu	p.S1043L	ENST00000342788	NM_005235.2	1043	tCg/tTg	25/28	1	2	FACETS	0.827	0.703	0.964	0.827	0.703	0.964	CLONAL	1	TRUE	1	0.262167973364862	2		341	461	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120783979	120783979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112244011	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	102	701	1	ENST00000257552.2:c.1006G>A	p.Ala336Thr	p.A336T	ENST00000257552	NM_002442.3	336	Gcc/Acc	13/15	0.262167973364862	1	FACETS	0.813	0.726	0.905	0.813	0.726	0.905	CLONAL	1	TRUE	0	0.262167973364862	1		702	832	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089707	27089708	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	79	504	0	ENST00000324856.7:c.2663_2664delinsAA	p.Gly888Glu	p.G888E	ENST00000324856	NM_006015.4	888	gGG/gAA	8/20	1	2	FACETS	0.961	0.846	1	0.961	0.846	1	CLONAL	1	TRUE	1	0.262167973364862	2		504	627	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812591	43812591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1305501233	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	62	423	0	ENST00000372470.3:c.1294C>T	p.His432Tyr	p.H432Y	ENST00000372470	NM_005373.2	432	Cat/Tat	8/12	1	2	FACETS	0.903	0.781	1	0.903	0.781	1	CLONAL	1	TRUE	1	0.262167973364862	2		423	524	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596041	43596041	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	60	603	0	ENST00000355710.3:c.208C>T	p.Gln70Ter	p.Q70*	ENST00000355710	NM_020975.4	70	Cag/Tag	2/20	1	2	FACETS	0.702	0.604	0.809	0.702	0.604	0.809	SUBCLONAL	1	TRUE	1	0.262167973364862	2		603	652	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022646	12022647	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	51	443	0	ENST00000396373.4:c.752_753delinsTT	p.Ser251Phe	p.S251F	ENST00000396373	NM_001987.4	251	tCC/tTT	5/8	0.194990215300155	3	FACETS	0.851	0.724	0.991	0.426	0.362	0.496	CLONAL	1	TRUE	1	0.262167973364862	3		443	517	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287320	46287320	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	64	417	0	ENST00000334344.6:c.5268del	p.Phe1756LeufsTer9	p.F1756Lfs*9	ENST00000334344	NM_152641.2	1755	gaT/ga	19/21	0.262167973364862	1	FACETS	0.771	0.668	0.883	0.771	0.668	0.883	SUBCLONAL	1	TRUE	0	0.262167973364862	1		417	550	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435476	49435476	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	98	731	0	ENST00000301067.7:c.6196G>C	p.Asp2066His	p.D2066H	ENST00000301067	NM_003482.3	2066	Gat/Cat	30/54	0.262167973364862	1	FACETS	0.807	0.719	0.9	0.807	0.719	0.9	CLONAL	1	TRUE	0	0.262167973364862	1		731	805	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348028	348028	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750117207	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	114	785	0	ENST00000262320.3:c.1478C>T	p.Ser493Phe	p.S493F	ENST00000262320	NM_003502.3	493	tCc/tTc	6/11	1	2	FACETS	0.897	0.806	0.993	0.897	0.806	0.993	CLONAL	1	TRUE	1	0.262167973364862	2		785	970	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640569	3640569	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	149	727	0	ENST00000294008.3:c.3070C>T	p.Pro1024Ser	p.P1024S	ENST00000294008	NM_032444.2	1024	Ccc/Tcc	12/15	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.262167973364862	2		727	1076	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991844	72991844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	109	564	2	ENST00000268489.5:c.2201C>T	p.Ser734Phe	p.S734F	ENST00000268489	NM_006885.3	734	tCc/tTc	2/10	1	2	FACETS	0.99	0.888	1	0.99	0.888	1	CLONAL	1	TRUE	1	0.262167973364862	2		566	840	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556227	29556227	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786203084	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	49	342	0	ENST00000356175.3:c.2594C>T	p.Pro865Leu	p.P865L	ENST00000356175	NM_000267.3	865	cCa/cTa	21/57	0.0439512068170891	3	FACETS	0.976	0.828	1			1	INDETERMINATE	1	TRUE	NA	0.262167973364862	3		342	433	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122916	7122916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	95	622	0	ENST00000302850.5:c.3343C>T	p.Leu1115Phe	p.L1115F	ENST00000302850	NM_000208.2	1115	Ctc/Ttc	18/22	1	2	FACETS	0.893	0.794	0.998	0.893	0.794	0.998	CLONAL	1	TRUE	1	0.262167973364862	2		622	812	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303329	15303329	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	112	661	0	ENST00000263388.2:c.199T>C	p.Cys67Arg	p.C67R	ENST00000263388	NM_000435.2	67	Tgc/Cgc	3/33	1	2	FACETS	0.941	0.845	1	0.941	0.845	1	CLONAL	1	TRUE	1	0.262167973364862	2		661	908	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273081	18273082	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	88	614	1	ENST00000222254.8:c.971_972delinsTT	p.Ser324Phe	p.S324F	ENST00000222254	NM_005027.3	324	tCC/tTT	8/16	1	2	FACETS	0.834	0.738	0.937	0.834	0.738	0.937	CLONAL	1	TRUE	1	0.262167973364862	2		615	805	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27016091	27016092	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	92	460	0	ENST00000335756.4:c.367_368delinsTT	p.Pro123Leu	p.P123L	ENST00000335756	NM_001809.3	123	CCa/TTa	4/5	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.262167973364862	2		460	627	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026317	48026317	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	73	419	0	ENST00000234420.5:c.1195C>T	p.Pro399Ser	p.P399S	ENST00000234420	NM_000179.2	399	Cct/Tct	4/10	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.262167973364862	2		419	505	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61753644	61753644	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	41	366	0	ENST00000401558.2:c.139C>T	p.Gln47Ter	p.Q47*	ENST00000401558	NM_003400.3	47	Caa/Taa	3/25	1	2	FACETS	0.677	0.564	0.803	0.677	0.564	0.803	SUBCLONAL	1	TRUE	1	0.262167973364862	2		366	462	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561387	9561387	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	68	541	0	ENST00000353224.5:c.395C>T	p.Ser132Phe	p.S132F	ENST00000353224	NM_177990.2	132	tCc/tTc	4/10	1	2	FACETS	0.797	0.693	0.909	0.797	0.693	0.909	CLONAL	1	TRUE	1	0.262167973364862	2		541	651	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375061	31375061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147421711	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	82	472	1	ENST00000328111.2:c.458C>T	p.Ser153Leu	p.S153L	ENST00000328111	NM_006892.3	153	tCg/tTg	6/23	1	2	FACETS	0.971	0.857	1	0.971	0.857	1	CLONAL	1	TRUE	1	0.262167973364862	2		473	644	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066761	94066761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	49	375	0	ENST00000369303.4:c.998C>T	p.Ser333Phe	p.S333F	ENST00000369303	NM_004440.3	333	tCt/tTt	5/17	1	2	FACETS	0.869	0.738	1	0.869	0.738	1	CLONAL	1	TRUE	1	0.262167973364862	2		375	430	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609677	117609677	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	45	383	0	ENST00000368508.3:c.7022G>A	p.Gly2341Glu	p.G2341E	ENST00000368508	NM_002944.2	2341	gGa/gAa	43/43	1	2	FACETS	0.726	0.61	0.853	0.726	0.61	0.853	SUBCLONAL	1	TRUE	1	0.262167973364862	2		383	473	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683824	117683824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754292558	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	69	507	0	ENST00000368508.3:c.3323C>T	p.Pro1108Leu	p.P1108L	ENST00000368508	NM_002944.2	1108	cCc/cTc	21/43	1	2	FACETS	0.834	0.726	0.951	0.834	0.726	0.951	CLONAL	1	TRUE	1	0.262167973364862	2		507	631	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974164	2974164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	118	610	0	ENST00000396946.4:c.1441G>A	p.Glu481Lys	p.E481K	ENST00000396946	NM_032415.4	481	Gag/Aag	10/25	0.194990215300155	3	FACETS	1	0.964	1	0.575	0.518	0.635	CLONAL	1	TRUE	1	0.262167973364862	3		610	886	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444296	50444296	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	47	309	0	ENST00000331340.3:c.226G>A	p.Glu76Lys	p.E76K	ENST00000331340	NM_006060.4	76	Gaa/Aaa	4/8	0.194990215300155	3	FACETS	1	0.861	1	0.509	0.431	0.596	CLONAL	1	TRUE	1	0.262167973364862	3		309	398	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56859022	56859022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	66	485	0	ENST00000519728.1:c.148C>T	p.Leu50Phe	p.L50F	ENST00000519728	NM_002350.3	50	Ctt/Ttt	3/13	1	2	FACETS	0.777	0.674	0.889	0.777	0.674	0.889	SUBCLONAL	1	TRUE	1	0.262167973364862	2		485	648	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968077	68968077	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567279949	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	57	414	0	ENST00000288368.4:c.1106G>A	p.Gly369Glu	p.G369E	ENST00000288368	NM_024870.2	369	gGa/gAa	10/40	1	2	FACETS	0.891	0.766	1	0.891	0.766	1	CLONAL	1	TRUE	1	0.262167973364862	2		414	488	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020422	69020422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	99	533	0	ENST00000288368.4:c.2794G>A	p.Asp932Asn	p.D932N	ENST00000288368	NM_024870.2	932	Gat/Aat	24/40	1	2	FACETS	0.87	0.776	0.971	0.87	0.776	0.971	CLONAL	1	TRUE	1	0.262167973364862	2		533	868	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933047	39933047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	91	806	0	ENST00000378444.4:c.1552G>A	p.Glu518Lys	p.E518K	ENST00000378444	NM_001123385.1	518	Gaa/Aaa	4/15	1	2	FACETS	0.759	0.672	0.851	0.759	0.672	0.851	SUBCLONAL	1	TRUE	1	0.262167973364862	2		806	915	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341181	70341181	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	70	487	0	ENST00000374080.3:c.740G>A	p.Gly247Glu	p.G247E	ENST00000374080		247	gGa/gAa	6/45	1	2	FACETS	0.883	0.77	1	0.883	0.77	1	CLONAL	1	TRUE	1	0.262167973364862	2		487	605	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937576	76937576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	63	419	0	ENST00000373344.5:c.3172G>A	p.Asp1058Asn	p.D1058N	ENST00000373344	NM_000489.3	1058	Gat/Aat	9/35	1	2	FACETS	0.888	0.769	1	0.888	0.769	1	CLONAL	1	TRUE	1	0.262167973364862	2		419	541	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937656	76937656	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782088552	NA	P-0032404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	60	438	0	ENST00000373344.5:c.3092G>A	p.Gly1031Asp	p.G1031D	ENST00000373344	NM_000489.3	1031	gGc/gAc	9/35	1	2	FACETS	0.776	0.668	0.893	0.776	0.668	0.893	SUBCLONAL	1	TRUE	1	0.262167973364862	2		438	590	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0032477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	48	420	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	1	2	FACETS	0.927	0.783	1	0.927	0.783	1	CLONAL	1	TRUE	1	0.19	2		420	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0032477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	65	746	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.144376874424344	1	FACETS	0.695	0.601	0.797	0.695	0.601	0.797	SUBCLONAL	1	TRUE	0	0.19	1		746	891	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	40	395	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.190141891969532	3	FACETS	1	0.906	1	0.568	0.473	0.674	CLONAL	1	TRUE	1	0.2	3		395	387	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048238	180048238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324497116	NA	P-0032756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	23	556	0	ENST00000261937.6:c.2035C>T	p.Arg679Trp	p.R679W	ENST00000261937	NM_182925.4	679	Cgg/Tgg	14/30	0.3	0	FACETS	0.902	0.707	1			1	CLONAL	1	TRUE	0	0.2	0		556	204	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs587781433	NA	P-0032756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	34	565	0	ENST00000269305.4:c.766A>C	p.Thr256Pro	p.T256P	ENST00000269305	NM_001126112.2	256	Aca/Cca	7/11	1	2	FACETS	0.787	0.648	0.941	1	0.952	1	CLONAL	2	TRUE	1	0.2	2		565	216	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591931	48591931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	19	460	0	ENST00000342988.3:c.1094G>A	p.Gly365Asp	p.G365D	ENST00000342988	NM_005359.5	365	gGt/gAt	9/12	1	2	FACETS	0.728	0.553	0.933	0.728	0.553	0.933	CLONAL	1	TRUE	1	0.2	2		460	261	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196243	106196243	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs777761555	NA	P-0032756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	17	270	0	ENST00000380013.4:c.4576C>T	p.Gln1526Ter	p.Q1526*	ENST00000380013	NM_001127208.2	1526	Cag/Tag	11/11	1	2	FACETS	0.806	0.603	1	0.806	0.603	1	CLONAL	1	TRUE	1	0.2	2		270	211	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074472	39074472	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs753147833	NA	P-0032756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	15	278	0	ENST00000357387.3:c.8C>G	p.Ala3Gly	p.A3G	ENST00000357387	NM_152756.3	3	gCg/gGg	1/38	0.190141891969532	3	FACETS	0.708	0.518	0.936	0.354	0.259	0.468	CLONAL	1	TRUE	1	0.2	3		278	233	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650332	48650332	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200599207	NA	P-0032756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	22	572	1	ENST00000376670.3:c.302C>T	p.Thr101Met	p.T101M	ENST00000376670	NM_002049.3	101	aCg/aTg	3/6	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.2	2		573	186	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0033615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	50	395	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.241152291804788	3	FACETS	0.654	0.555	0.762	0.327	0.277	0.381	SUBCLONAL	1	TRUE	1	0.347340415570953	3		395	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0033615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	271	538	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.248921223021532	2	FACETS	1	0.993	1	0.737	0.691	0.783	CLONAL	1	TRUE	0	0.347340415570953	2		538	1059	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0033615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	114	639	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	1	2	FACETS	0.795	0.715	0.879	0.795	0.715	0.879	SUBCLONAL	1	TRUE	1	0.347340415570953	2		639	826	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	87	1227	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	0.241152291804788	3	FACETS	0.614	0.543	0.691	0.307	0.271	0.346	SUBCLONAL	1	TRUE	1	0.347340415570953	3		1227	957	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242099	105242099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768800433	NA	P-0033615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	279	694	0	ENST00000349310.3:c.325G>A	p.Gly109Ser	p.G109S	ENST00000349310	NM_001014432.1	109	Ggc/Agc	6/15	0.215214025142425	5	FACETS	1	0.972	1	0.707	0.664	0.752	CLONAL	2	TRUE	2	0.347340415570953	5		694	1152	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793290	242793290	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143359677	NA	P-0033615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	88	747	0	ENST00000334409.5:c.787G>A	p.Ala263Thr	p.A263T	ENST00000334409	NM_005018.2	263	Gcc/Acc	5/5	1	2	FACETS	0.575	0.509	0.647	0.575	0.509	0.647	SUBCLONAL	1	TRUE	1	0.347340415570953	2		747	881	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986947	36986947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	243	706	1	ENST00000354822.5:c.742C>T	p.Arg248Cys	p.R248C	ENST00000354822	NM_001079668.2	248	Cgc/Tgc	3/3	0.215214025142425	5	FACETS	0.868	0.81	0.928	0.579	0.54	0.619	CLONAL	2	TRUE	2	0.347340415570953	5		707	1226	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260875	16260875	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	298	961	0	ENST00000375759.3:c.8140A>T	p.Thr2714Ser	p.T2714S	ENST00000375759	NM_015001.2	2714	Acg/Tcg	11/15	0.248921223021532	2	FACETS	1	0.993	1	0.723	0.68	0.766	CLONAL	1	TRUE	0	0.347340415570953	2		961	1187	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375575	118375575	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	299	622	0	ENST00000534358.1:c.8968G>T	p.Gly2990Cys	p.G2990C	ENST00000534358	NM_005933.3	2990	Ggc/Tgc	27/36	0.224698613714979	3	FACETS	1	0.982	1	0.727	0.687	0.769	CLONAL	2	TRUE	0	0.347340415570953	3		622	926	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428422	49428422	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs915492855	NA	P-0033615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	221	704	0	ENST00000301067.7:c.10383G>T	p.Arg3461Ser	p.R3461S	ENST00000301067	NM_003482.3	3461	agG/agT	36/54	0.241152291804788	3	FACETS	1	0.991	1	0.722	0.671	0.774	CLONAL	1	TRUE	1	0.347340415570953	3		704	1035	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	185	505	0	ENST00000267101.3:c.273G>C	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atC	3/28	0.241152291804788	3	FACETS	0.802	0.742	0.865	0.802	0.742	0.865	CLONAL	2	TRUE	1	0.347340415570953	3		505	779	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226451	133226451	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	75	460	0	ENST00000320574.5:c.3607G>C	p.Asp1203His	p.D1203H	ENST00000320574	NM_006231.2	1203	Gac/Cac	30/49	0.241152291804788	3	FACETS	0.783	0.686	0.888	0.392	0.343	0.444	SUBCLONAL	1	TRUE	1	0.347340415570953	3		460	647	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951140	48951141	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AT	novel	NA	P-0033615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	104	290	0	ENST00000267163.4:c.1302_1303delinsAT	p.Gly435Ter	p.G435*	ENST00000267163	NM_000321.2	434	gtGGga/gtATga	13/27	0.248921223021532	2	FACETS	1	0.98	1	0.685	0.617	0.756	CLONAL	1	TRUE	0	0.347340415570953	2		290	437	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472469	88472469	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	108	627	0	ENST00000360948.2:c.2086G>C	p.Gly696Arg	p.G696R	ENST00000360948	NM_001012338.2	696	Ggg/Cgg	16/19	1	2	FACETS	0.793	0.712	0.88	0.793	0.712	0.88	SUBCLONAL	1	TRUE	1	0.347340415570953	2		627	784	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876531	59876531	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	134	456	0	ENST00000259008.2:c.1270A>T	p.Ser424Cys	p.S424C	ENST00000259008	NM_032043.2	424	Agt/Tgt	9/20	0.241580316582498	4	FACETS	1	0.982	1	0.666	0.606	0.73	CLONAL	1	TRUE	2	0.347340415570953	4		456	780	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216495	2216495	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	225	725	0	ENST00000398665.3:c.2139G>C	p.Met713Ile	p.M713I	ENST00000398665	NM_032482.2	713	atG/atC	20/28	0.248921223021532	2	FACETS	1	0.992	1	0.732	0.683	0.783	CLONAL	1	TRUE	0	0.347340415570953	2		725	885	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17382451	17382451	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	151	424	0	ENST00000359435.4:c.331G>T	p.Glu111Ter	p.E111*	ENST00000359435	NM_001033549.1	111	Gag/Tag	3/9	0.248921223021532	2	FACETS	1	0.986	1	0.687	0.63	0.746	CLONAL	1	TRUE	0	0.347340415570953	2		424	633	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735395	204735395	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	101	707	0	ENST00000302823.3:c.196del	p.Ala66ProfsTer6	p.A66Pfs*6	ENST00000302823	NM_005214.4	66	Gcc/cc	2/4	1	2	FACETS	0.588	0.524	0.656	0.588	0.524	0.656	SUBCLONAL	1	TRUE	1	0.347340415570953	2		707	989	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267198	41267198	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	205	594	0	ENST00000349496.5:c.782A>G	p.Asn261Ser	p.N261S	ENST00000349496	NM_001904.3	261	aAc/aGc	6/15	0.248921223021532	2	FACETS	1	0.99	1	0.703	0.653	0.755	CLONAL	1	TRUE	0	0.347340415570953	2		594	839	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164198	47164198	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs776293901	NA	P-0033615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	120	369	0	ENST00000409792.3:c.1928A>G	p.His643Arg	p.H643R	ENST00000409792	NM_014159.6	643	cAt/cGt	3/21	0.248921223021532	2	FACETS	1	0.98	1	0.658	0.597	0.722	CLONAL	1	TRUE	0	0.347340415570953	2		369	525	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021817	71021817	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	142	496	0	ENST00000318789.4:c.1541G>T	p.Arg514Leu	p.R514L	ENST00000318789	NM_032682.5	514	cGt/cTt	18/21	0.248921223021532	2	FACETS	1	0.985	1	0.683	0.624	0.743	CLONAL	1	TRUE	0	0.347340415570953	2		496	599	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170015099	170015099	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	65	426	0	ENST00000295797.4:c.1505A>T	p.Lys502Met	p.K502M	ENST00000295797	NM_002740.5	502	aAg/aTg	16/18	0.247750238726687	4	FACETS	0.661	0.572	0.758	0.22	0.19	0.253	SUBCLONAL	1	TRUE	1	0.347340415570953	4		426	763	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356150	66356150	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1228970137	NA	P-0033615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	196	603	0	ENST00000273854.3:c.1347C>A	p.Asp449Glu	p.D449E	ENST00000273854	NM_004439.5	449	gaC/gaA	5/18	0.248921223021532	2	FACETS	1	0.99	1	0.705	0.654	0.758	CLONAL	1	TRUE	0	0.347340415570953	2		603	800	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542826	187542826	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	143	478	0	ENST00000441802.2:c.4914A>T	p.Lys1638Asn	p.K1638N	ENST00000441802	NM_005245.3	1638	aaA/aaT	10/27	0.248921223021532	2	FACETS	1	0.984	1	0.667	0.61	0.726	CLONAL	1	TRUE	0	0.347340415570953	2		478	617	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1721979	1721979	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	184	612	0	ENST00000378609.4:c.554G>C	p.Gly185Ala	p.G185A	ENST00000378609	NM_002074.3	185	gGa/gCa	9/12	0.248921223021532	2	FACETS	1	0.987	1	0.662	0.612	0.714	CLONAL	1	TRUE	0	0.347340415570953	2		612	800	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175996735	175996735	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	334	492	0	ENST00000367669.3:c.1702A>G	p.Arg568Gly	p.R568G	ENST00000367669	NM_022457.5	568	Aga/Gga	15/20	0.347340415570953	3	FACETS	0.866	0.822	0.91	0.866	0.822	0.91	CLONAL	3	TRUE	0	0.347340415570953	3		492	869	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097641	11097641	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	160	681	0	ENST00000358026.2:c.821G>T	p.Gly274Val	p.G274V	ENST00000358026	NM_001128849.1	274	gGc/gTc	5/36	0.248921223021532	2	FACETS	1	0.975	1	0.577	0.529	0.626	CLONAL	1	TRUE	0	0.347340415570953	2		681	799	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683656	162683656	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033615-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	71	568	0	ENST00000366898.1:c.313G>C	p.Val105Leu	p.V105L	ENST00000366898	NM_004562.2	105	Gtg/Ctg	3/12	0.347340415570953	3	FACETS	0.544	0.474	0.62	0.272	0.237	0.31	SUBCLONAL	1	TRUE	1	0.347340415570953	3		568	882	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458372	120458372	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033695-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	613	558	0	ENST00000256646.2:c.6973C>T	p.Gln2325Ter	p.Q2325*	ENST00000256646	NM_024408.3	2325	Cag/Tag	34/34	0.592069010759956	7	FACETS	0.962	0.935	0.987			1	CLONAL	6	TRUE	NA	0.592069010759956	7		558	890	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850925	63850925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033695-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	110	478	0	ENST00000279873.7:c.1703G>A	p.Ser568Asn	p.S568N	ENST00000279873	NM_032199.2	568	aGt/aAt	10/10	0.136264696928937	4	FACETS	0.855	0.777	0.936	0.855	0.777	0.936	INDETERMINATE	2	TRUE	2	0.592069010759956	4		478	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578466	7578466	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786202752	NA	P-0033695-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	328	836	0	ENST00000269305.4:c.464C>A	p.Thr155Asn	p.T155N	ENST00000269305	NM_001126112.2	155	aCc/aAc	5/11	0.586362261004493	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.592069010759956	2		836	535	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47643516	47643516	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033695-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	126	580	0	ENST00000233146.2:c.1024G>T	p.Val342Phe	p.V342F	ENST00000233146	NM_000251.2	342	Gtt/Ttt	6/16	0.382143943918253	5	FACETS	1	0.984	1	0.467	0.424	0.511	CLONAL	1	TRUE	2	0.592069010759956	5		580	574	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437822	52437822	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033695-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	195	827	0	ENST00000460680.1:c.1339del	p.Val447SerfsTer124	p.V447Sfs*124	ENST00000460680	NM_004656.3	447	Gtc/tc	13/17	0.592069010759956	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.592069010759956	1		827	411	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517762	176517762	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033695-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	97	697	0	ENST00000292408.4:c.372C>A	p.Ser124Arg	p.S124R	ENST00000292408	NM_213647.1	124	agC/agA	4/18	0.561388698105892	3	FACETS	0.744	0.665	0.828	0.248	0.221	0.276	SUBCLONAL	1	TRUE	0	0.592069010759956	3		697	571	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801006	135801007	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0033695-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	52	389	0	ENST00000298552.3:c.330_331del	p.Pro111SerfsTer14	p.P111Sfs*14	ENST00000298552	NM_001162426.1	110	gcACct/gcct	5/23	0.561388698105892	3	FACETS	0.802	0.687	0.925	0.267	0.229	0.309	CLONAL	1	TRUE	0	0.592069010759956	3		389	284	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0033840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	31	410	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.861	0.71	1	1	0.956	1	CLONAL	2	FALSE	1	0.290298431613893	2		410	124	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519886	NA	P-0033840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	53	325	0	ENST00000349496.5:c.97T>C	p.Ser33Pro	p.S33P	ENST00000349496	NM_001904.3	33	Tct/Cct	3/15	0.290298431613893	4	FACETS	0.906	0.795	1	1	0.955	1	CLONAL	4	FALSE	1	0.290298431613893	4		325	130	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515268	149515268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	18	654	0	ENST00000261799.4:c.214G>A	p.Glu72Lys	p.E72K	ENST00000261799	NM_002609.3	72	Gaa/Aaa	3/23	0.183121090448914	4	FACETS	0.816	0.625	1	0.816	0.625	1	CLONAL	2	FALSE	2	0.290298431613893	4		654	98	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440154	49440154	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	33	641	0	ENST00000301067.7:c.4472G>A	p.Trp1491Ter	p.W1491*	ENST00000301067	NM_003482.3	1491	tGg/tAg	16/54	0.24952533367805	5	FACETS	1	0.919	1	0.8	0.663	0.948	CLONAL	2	FALSE	2	0.290298431613893	5		641	136	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256662	16256662	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	29	517	0	ENST00000375759.3:c.3927T>G	p.Phe1309Leu	p.F1309L	ENST00000375759	NM_015001.2	1309	ttT/ttG	11/15	0.290298431613893	7	FACETS	0.884	0.721	1			1	CLONAL	3	FALSE	NA	0.290298431613893	7		517	130	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263299	115263299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	11	696	0	ENST00000438362.2:c.2051G>A	p.Gly684Glu	p.G684E	ENST00000438362	NM_001242891.1	684	gGg/gAg	17/20	1	2	FACETS	0.561	0.39	0.773	0.561	0.39	0.773	SUBCLONAL	1	FALSE	1	0.290298431613893	2		696	135	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047135	77047135	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	20	498	0	ENST00000356341.3:c.1409T>C	p.Leu470Pro	p.L470P	ENST00000356341	NM_002576.4	470	cTg/cCg	13/15	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	FALSE	1	0.290298431613893	2		498	92	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21629895	21629895	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	14	649	0	ENST00000421138.2:c.899T>G	p.Phe300Cys	p.F300C	ENST00000421138		300	tTt/tGt	9/16	0.290298431613893	0	FACETS	0.691	0.506	0.909			1	SUBCLONAL	1	FALSE	0	0.290298431613893	0		649	99	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007793	45007793	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	56	455	0	ENST00000558401.1:c.240G>A	p.Trp80Ter	p.W80*	ENST00000558401	NM_004048.2	80	tgG/tgA	2/4	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.290298431613893	2		455	261	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347404	89347404	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	23	684	0	ENST00000301030.4:c.5546G>A	p.Gly1849Glu	p.G1849E	ENST00000301030	NM_001256183.1	1849	gGg/gAg	9/13	0.231497584061019	3	FACETS	1	0.92	1	0.703	0.556	0.869	CLONAL	1	FALSE	1	0.290298431613893	3		684	129	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222483	39222483	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	15	787	0	ENST00000402219.2:c.3127T>C	p.Ser1043Pro	p.S1043P	ENST00000402219	NM_005633.3	1043	Tca/Cca	20/23	0.290298431613893	1	FACETS	0.669	0.493	0.877	0.669	0.493	0.877	SUBCLONAL	1	FALSE	0	0.290298431613893	1		787	132	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0033933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	178	241	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	1	2	FACETS	0.876	0.812	0.943	0.876	0.812	0.943	CLONAL	1	TRUE	1	0.667209645130759	2		241	609	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138376590	138376590	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	269	416	0	ENST00000289153.2:c.2884T>A	p.Tyr962Asn	p.Y962N	ENST00000289153	NM_006219.2	962	Tat/Aat	20/22	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.667209645130759	2		416	768	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851397	156851397	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	42	653	0	ENST00000524377.1:c.2354C>G	p.Ala785Gly	p.A785G	ENST00000524377	NM_002529.3	785	gCc/gGc	17/17	1	2	FACETS	0.154	0.128	0.184	0.154	0.128	0.184	SUBCLONAL	1	TRUE	1	0.667209645130759	2		653	815	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007630	45008460	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGATTCAGGTTTACTCACGTCATCCAGCAGAGAATGGAAAGTCAAATTTCCTGAATTGCTATGTGTCTGGGTTTCATCCATCCGACATTGAAGTTGACTTACTGAAGAATGGAGAGAGAATTGAAAAAGTGGAGCATTCAGACTTGTCTTTCAGCAAGGACTGGTCTTTCTATCTCTTGTACTACACTGAATTCACCCCCACTGAAAAAGATGAGTATGCCTGCCGTGTGAACCATGTGACTTTGTCACAGCCCAAGATAGTTAAGTGGGGTAAGTCTTACATTCTTTTGTAAGCTGCTGAAAGTTGTGTATGAGTAGTCATATCATAAAGCTGCTTTGATATAAAAAAGGTCTATGGCCATACTACCCTGAATGAGTCCCATCCCATCTGATATAAACAATCTGCATATTGGGATTGTCAGGGAATGTTCTTAAAGATCAGATTAGTGGCACCTGCTGAGATACTGATGCACAGCATGGTTTCTGAACCAGTAGTTTCCCTGCAGTTGAGCAGGGAGCAGCAGCAGCACTTGCACAAATACATATACACTCTTAACACTTCTTACCTACTGGCTTCCTCTAGCTTTTGTGGCAGCTTCAGGTATATTTAGCACTGAACGAACATCTCAAGAAGGTATAGGCCTTTGTTTGTAAGTCCTGCTGTCCTAGCATCCTATAATCCTGGACTTCTCCAGTACTTTCTGGCTGGATTGGTATCTGAGGCTAGTAGGAAGGGCTTGTTCCTGCTGGGTAGCTCTAAACAATGTATTCATGGGTAGGAACAGCAGCCTATTCTGCCAGCCTTATTTCTAACCATTTTAGACATTTGTT	AGATTCAGGTTTACTCACGTCATCCAGCAGAGAATGGAAAGTCAAATTTCCTGAATTGCTATGTGTCTGGGTTTCATCCATCCGACATTGAAGTTGACTTACTGAAGAATGGAGAGAGAATTGAAAAAGTGGAGCATTCAGACTTGTCTTTCAGCAAGGACTGGTCTTTCTATCTCTTGTACTACACTGAATTCACCCCCACTGAAAAAGATGAGTATGCCTGCCGTGTGAACCATGTGACTTTGTCACAGCCCAAGATAGTTAAGTGGGGTAAGTCTTACATTCTTTTGTAAGCTGCTGAAAGTTGTGTATGAGTAGTCATATCATAAAGCTGCTTTGATATAAAAAAGGTCTATGGCCATACTACCCTGAATGAGTCCCATCCCATCTGATATAAACAATCTGCATATTGGGATTGTCAGGGAATGTTCTTAAAGATCAGATTAGTGGCACCTGCTGAGATACTGATGCACAGCATGGTTTCTGAACCAGTAGTTTCCCTGCAGTTGAGCAGGGAGCAGCAGCAGCACTTGCACAAATACATATACACTCTTAACACTTCTTACCTACTGGCTTCCTCTAGCTTTTGTGGCAGCTTCAGGTATATTTAGCACTGAACGAACATCTCAAGAAGGTATAGGCCTTTGTTTGTAAGTCCTGCTGTCCTAGCATCCTATAATCCTGGACTTCTCCAGTACTTTCTGGCTGGATTGGTATCTGAGGCTAGTAGGAAGGGCTTGTTCCTGCTGGGTAGCTCTAAACAATGTATTCATGGGTAGGAACAGCAGCCTATTCTGCCAGCCTTATTTCTAACCATTTTAGACATTTGTT	-	novel	NA	P-0033933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	100	225	0	ENST00000558401.1:c.79_347-65del		p.X27_splice	ENST00000558401	NM_004048.2	27		2/4	0.667209645130759	1	FACETS	0.777	0.706	0.85	0.777	0.706	0.85	SUBCLONAL	1	TRUE	0	0.667209645130759	1		225	257	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41560073	41560073	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	193	256	0	ENST00000263253.7:c.3745G>C	p.Glu1249Gln	p.E1249Q	ENST00000263253	NM_001429.3	1249	Gag/Cag	22/31	1	2	FACETS	0.896	0.832	0.96	0.896	0.832	0.96	CLONAL	1	TRUE	1	0.667209645130759	2		256	646	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0033933-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	166	241	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.771274989860113	2		241	398	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138376590	138376590	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033933-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	255	416	0	ENST00000289153.2:c.2884T>A	p.Tyr962Asn	p.Y962N	ENST00000289153	NM_006219.2	962	Tat/Aat	20/22	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.771274989860113	2		416	618	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007630	45008460	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGATTCAGGTTTACTCACGTCATCCAGCAGAGAATGGAAAGTCAAATTTCCTGAATTGCTATGTGTCTGGGTTTCATCCATCCGACATTGAAGTTGACTTACTGAAGAATGGAGAGAGAATTGAAAAAGTGGAGCATTCAGACTTGTCTTTCAGCAAGGACTGGTCTTTCTATCTCTTGTACTACACTGAATTCACCCCCACTGAAAAAGATGAGTATGCCTGCCGTGTGAACCATGTGACTTTGTCACAGCCCAAGATAGTTAAGTGGGGTAAGTCTTACATTCTTTTGTAAGCTGCTGAAAGTTGTGTATGAGTAGTCATATCATAAAGCTGCTTTGATATAAAAAAGGTCTATGGCCATACTACCCTGAATGAGTCCCATCCCATCTGATATAAACAATCTGCATATTGGGATTGTCAGGGAATGTTCTTAAAGATCAGATTAGTGGCACCTGCTGAGATACTGATGCACAGCATGGTTTCTGAACCAGTAGTTTCCCTGCAGTTGAGCAGGGAGCAGCAGCAGCACTTGCACAAATACATATACACTCTTAACACTTCTTACCTACTGGCTTCCTCTAGCTTTTGTGGCAGCTTCAGGTATATTTAGCACTGAACGAACATCTCAAGAAGGTATAGGCCTTTGTTTGTAAGTCCTGCTGTCCTAGCATCCTATAATCCTGGACTTCTCCAGTACTTTCTGGCTGGATTGGTATCTGAGGCTAGTAGGAAGGGCTTGTTCCTGCTGGGTAGCTCTAAACAATGTATTCATGGGTAGGAACAGCAGCCTATTCTGCCAGCCTTATTTCTAACCATTTTAGACATTTGTT	AGATTCAGGTTTACTCACGTCATCCAGCAGAGAATGGAAAGTCAAATTTCCTGAATTGCTATGTGTCTGGGTTTCATCCATCCGACATTGAAGTTGACTTACTGAAGAATGGAGAGAGAATTGAAAAAGTGGAGCATTCAGACTTGTCTTTCAGCAAGGACTGGTCTTTCTATCTCTTGTACTACACTGAATTCACCCCCACTGAAAAAGATGAGTATGCCTGCCGTGTGAACCATGTGACTTTGTCACAGCCCAAGATAGTTAAGTGGGGTAAGTCTTACATTCTTTTGTAAGCTGCTGAAAGTTGTGTATGAGTAGTCATATCATAAAGCTGCTTTGATATAAAAAAGGTCTATGGCCATACTACCCTGAATGAGTCCCATCCCATCTGATATAAACAATCTGCATATTGGGATTGTCAGGGAATGTTCTTAAAGATCAGATTAGTGGCACCTGCTGAGATACTGATGCACAGCATGGTTTCTGAACCAGTAGTTTCCCTGCAGTTGAGCAGGGAGCAGCAGCAGCACTTGCACAAATACATATACACTCTTAACACTTCTTACCTACTGGCTTCCTCTAGCTTTTGTGGCAGCTTCAGGTATATTTAGCACTGAACGAACATCTCAAGAAGGTATAGGCCTTTGTTTGTAAGTCCTGCTGTCCTAGCATCCTATAATCCTGGACTTCTCCAGTACTTTCTGGCTGGATTGGTATCTGAGGCTAGTAGGAAGGGCTTGTTCCTGCTGGGTAGCTCTAAACAATGTATTCATGGGTAGGAACAGCAGCCTATTCTGCCAGCCTTATTTCTAACCATTTTAGACATTTGTT	-	novel	NA	P-0033933-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	63	225	0	ENST00000558401.1:c.79_347-65del		p.X27_splice	ENST00000558401	NM_004048.2	27		2/4	0.771274989860113	1	FACETS	0.851	0.764	0.937	0.851	0.764	0.937	CLONAL	1	TRUE	0	0.771274989860113	1		225	118	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41560073	41560073	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033933-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	136	256	0	ENST00000263253.7:c.3745G>C	p.Glu1249Gln	p.E1249Q	ENST00000263253	NM_001429.3	1249	Gag/Cag	22/31	1	2	FACETS	0.964	0.887	1	0.964	0.887	1	CLONAL	1	TRUE	1	0.771274989860113	2		256	366	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842335	151842335	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033933-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	149	315	0	ENST00000262189.6:c.14077C>G	p.Arg4693Gly	p.R4693G	ENST00000262189	NM_170606.2	4693	Cga/Gga	54/59	1	2	FACETS	0.996	0.921	1	0.996	0.921	1	CLONAL	1	TRUE	1	0.771274989860113	2		315	388	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588751	29588751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760703505	NA	P-0034053-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	94	303	0	ENST00000356175.3:c.4537C>T	p.Arg1513Ter	p.R1513*	ENST00000356175	NM_000267.3	1513	Cga/Tga	34/57	1	2	FACETS	0.618	0.554	0.684	0.618	0.554	0.684	SUBCLONAL	1	TRUE	1	0.83818075029891	2		303	363	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679366	29679366	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs866445127	NA	P-0034053-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	27	384	0	ENST00000356175.3:c.7486C>T	p.Arg2496Ter	p.R2496*	ENST00000356175	NM_000267.3	2496	Cga/Tga	50/57	1	2	FACETS	0.161	0.127	0.199	0.161	0.127	0.199	SUBCLONAL	1	TRUE	1	0.83818075029891	2		384	401	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258744	115258744	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121434596	NA	P-0034053-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	343	383	0	ENST00000369535.4:c.38G>T	p.Gly13Val	p.G13V	ENST00000369535	NM_002524.4	13	gGt/gTt	2/7	0.67318058079113	3	FACETS	0.981	0.94	1	0.981	0.94	1	CLONAL	2	TRUE	1	0.83818075029891	3		383	592	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29497003	29497003	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397514641	NA	P-0034053-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	116	218	0	ENST00000356175.3:c.574C>T	p.Arg192Ter	p.R192*	ENST00000356175	NM_000267.3	192	Cga/Tga	5/57	1	2	FACETS	0.708	0.644	0.774	0.708	0.644	0.774	SUBCLONAL	1	TRUE	1	0.83818075029891	2		218	391	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562745	29562745	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034053-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	55	550	0	ENST00000356175.3:c.3826del	p.Arg1276GlufsTer9	p.R1276Efs*9	ENST00000356175	NM_000267.3	1275	ttC/tt	28/57	1	2	FACETS	0.203	0.173	0.236	0.203	0.173	0.236	SUBCLONAL	1	TRUE	1	0.83818075029891	2		550	645	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0034126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	79	594	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.29082223251977	3	FACETS	0.993	0.882	1	0.993	0.882	1	CLONAL	2	TRUE	1	0.290145373808766	3		594	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577518	7577518	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519995	NA	P-0034126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	8	547	0	ENST00000269305.4:c.763A>T	p.Ile255Phe	p.I255F	ENST00000269305	NM_001126112.2	255	Atc/Ttc	7/11	0.29082223251977	3	FACETS	0.211	0.135	0.31	0.106	0.067	0.155	SUBCLONAL	1	TRUE	1	0.290145373808766	3		547	299	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32790091	32790091	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	20	178	0	ENST00000374899.4:c.1937C>A	p.Thr646Asn	p.T646N	ENST00000374899	NM_018833.2	646	aCc/aAc	12/12	0.170818354950691	5	FACETS	0.984	0.777	1	0.738	0.583	0.908	INDETERMINATE	3	TRUE	1	0.290145373808766	5		178	67	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0034268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	161	243	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.267497314877975	4	FACETS	0.816	0.754	0.881	0.816	0.754	0.881	INDETERMINATE	2	TRUE	2	0.601647948101448	4		243	525	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611203	100611203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555977836	NA	P-0034274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	43	529	0	ENST00000308731.7:c.1403G>A	p.Arg468His	p.R468H	ENST00000308731	NM_000061.2	468	cGc/cAc	15/19	1	2	FACETS	0.906	0.762	1	0.906	0.762	1	CLONAL	1	TRUE	1	0.289239536459194	2		529	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0034274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	101	626	3	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.289239536459194	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.289239536459194	1		629	519	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0034274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	78	317	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.956	0.842	1	0.956	0.842	1	CLONAL	1	TRUE	1	0.289239536459194	2		317	564	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868196	37868196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1308928763	NA	P-0034274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	108	527	2	ENST00000269571.5:c.917C>T	p.Thr306Met	p.T306M	ENST00000269571		306	aCg/aTg	8/27	0.152002633691865	3	FACETS	1	0.982	1	0.728	0.655	0.805	INDETERMINATE	1	TRUE	1	0.289239536459194	3		529	587	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856250	111856250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1246649893	NA	P-0034274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	26	129	0	ENST00000341259.2:c.301G>A	p.Glu101Lys	p.E101K	ENST00000341259	NM_005475.2	101	Gag/Aag	2/8	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.289239536459194	2		129	127	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265687	41266331	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTGCTCCATTTTCTGCTCACTCCTCCTAATGGCTTGGTGAAATAGCAAACAAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAA	TTTTGCTCCATTTTCTGCTCACTCCTCCTAATGGCTTGGTGAAATAGCAAACAAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAA	-	novel	NA	P-0034274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	59	150	0	ENST00000349496.5:c.13+116_241+88del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.216323806598905	3	FACETS	1	0.885	1	1	0.885	1	CLONAL	3	TRUE	0	0.289239536459194	3		150	155	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	472	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.439531521189823	5	FACETS	0.974	0.936	1			1	CLONAL	4	TRUE	NA	0.439531521189823	5		334	915	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577525	7577527	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0034324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	292	850	0	ENST00000269305.4:c.754_756del	p.Leu252del	p.L252del	ENST00000269305	NM_001126112.2	252	CTC/-	7/11	0.439531521189823	2	FACETS	0.955	0.904	1	0.955	0.904	1	CLONAL	2	TRUE	0	0.439531521189823	2		850	696	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0034888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	80	243	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.251222890906256	2		243	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0034888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	127	725	1	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	0.251222890906256	1	FACETS	0.984	0.891	1	0.984	0.891	1	CLONAL	1	TRUE	0	0.251222890906256	1		726	898	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412905	49412905	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519951	NA	P-0034888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	178	697	0	ENST00000418115.1:c.118G>A	p.Glu40Lys	p.E40K	ENST00000418115	NM_001664.2	40	Gag/Aag	2/5	0.251222890906256	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.251222890906256	1		697	1052	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643678	52643678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	130	612	0	ENST00000394830.3:c.2218G>A	p.Glu740Lys	p.E740K	ENST00000394830	NM_018313.4	740	Gag/Aag	17/30	0.251222890906256	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.251222890906256	1		612	813	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027776	152027776	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	80	713	0	ENST00000262189.6:c.299A>G	p.Asn100Ser	p.N100S	ENST00000262189	NM_170606.2	100	aAc/aGc	3/59	1	2	FACETS	0.493	0.432	0.559	0.493	0.432	0.559	SUBCLONAL	1	TRUE	1	0.251222890906256	2		713	1291	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939665	76939665	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	57	776	0	ENST00000373344.5:c.1083G>C	p.Glu361Asp	p.E361D	ENST00000373344	NM_000489.3	361	gaG/gaC	9/35	0.251222890906256	1	FACETS	0.377	0.322	0.437	0.377	0.322	0.437	SUBCLONAL	1	TRUE	0	0.251222890906256	1		776	1053	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845682	68845682	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	106	596	1	ENST00000261769.5:c.928G>T	p.Glu310Ter	p.E310*	ENST00000261769	NM_004360.3	310	Gag/Tag	7/16	0.282483996150214	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.282483996150214	1		597	537	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847225	68847226	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0035380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	19	439	0	ENST00000261769.5:c.1147_1148del	p.Gln383GlyfsTer3	p.Q383Gfs*3	ENST00000261769	NM_004360.3	383	CAg/g	9/16	0.282483996150214	1	FACETS	0.322	0.244	0.414	0.322	0.244	0.414	SUBCLONAL	1	TRUE	0	0.282483996150214	1		439	359	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459698	149459698	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	81	711	0	ENST00000286301.3:c.509T>A	p.Ile170Asn	p.I170N	ENST00000286301	NM_005211.3	170	aTt/aAt	4/22	1	2	FACETS	0.831	0.732	0.937	0.831	0.732	0.937	CLONAL	1	TRUE	1	0.282483996150214	2		711	690	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259433	55259433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371228501	NA	P-0035380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	21	379	0	ENST00000275493.2:c.2491C>T	p.Arg831Cys	p.R831C	ENST00000275493	NM_005228.3	831	Cgt/Tgt	21/28	1	2	FACETS	0.356	0.273	0.452	0.356	0.273	0.452	SUBCLONAL	1	TRUE	1	0.282483996150214	2		379	418	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196791	108196791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039471	NA	P-0035729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	56	246	0	ENST00000278616.4:c.6814G>A	p.Glu2272Lys	p.E2272K	ENST00000278616	NM_000051.3	2272	Gaa/Aaa	47/63	0.175514997434566	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	2	TRUE	0	0.175514997434566	2		246	303	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0035729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	48	531	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.16529313106294	1	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	0	0.175514997434566	1		531	474	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682991	241682991	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1226883651	NA	P-0035729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	25	255	0	ENST00000366560.3:c.32C>G	p.Ser11Trp	p.S11W	ENST00000366560	NM_000143.3	11	tCg/tGg	1/10	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.175514997434566	2		255	236	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404656	70404656	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	37	436	0	ENST00000373644.4:c.2170G>T	p.Gly724Ter	p.G724*	ENST00000373644	NM_030625.2	724	Gga/Tga	4/12	1	2	FACETS	0.781	0.643	0.936	0.781	0.643	0.936	CLONAL	1	TRUE	1	0.175514997434566	2		436	540	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235410	235410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258201485	NA	P-0035729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	61	539	0	ENST00000264932.6:c.1216G>A	p.Val406Met	p.V406M	ENST00000264932	NM_004168.2	406	Gtg/Atg	9/15	0.175514997434566	3	FACETS	1	0.948	1	0.608	0.524	0.699	CLONAL	1	TRUE	1	0.175514997434566	3		539	622	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556287	29556287	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	67	440	0	ENST00000356175.3:c.2654G>A	p.Gly885Glu	p.G885E	ENST00000356175	NM_000267.3	885	gGa/gAa	21/57	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.175514997434566	2		440	530	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813525	32813525	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	52	366	0	ENST00000354258.4:c.2258C>G	p.Ser753Cys	p.S753C	ENST00000354258	NM_000593.5	753	tCc/tGc	11/11	0.16529313106294	1	FACETS	0.777	0.664	0.899	1	0.967	1	SUBCLONAL	2	TRUE	0	0.175514997434566	1		366	348	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160239	22160239	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035767-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	243	678	0	ENST00000215832.6:c.392A>G	p.Tyr131Cys	p.Y131C	ENST00000215832	NM_002745.4	131	tAc/tGc	3/9	0.723825583680918	3	FACETS	1	0.971	1	0.531	0.497	0.565	CLONAL	1	TRUE	1	0.804786330475717	3		678	798	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476283	88476283	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035767-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	321	540	0	ENST00000360948.2:c.1849T>A	p.Phe617Ile	p.F617I	ENST00000360948	NM_001012338.2	617	Ttt/Att	15/19	0.804786330475717	4	FACETS	0.784	0.742	0.827			1	SUBCLONAL	2	TRUE	NA	0.804786330475717	4		540	918	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154805	2154805	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035767-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	237	826	0	ENST00000434045.2:c.416A>G	p.Tyr139Cys	p.Y139C	ENST00000434045	NM_001127598.1	139	tAc/tGc	4/5	0.804786330475717	2	FACETS	0.818	0.767	0.87	0.409	0.383	0.435	CLONAL	1	TRUE	0	0.804786330475717	2		826	720	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007168	62007168	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035767-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	243	768	0	ENST00000392795.3:c.514C>G	p.Leu172Val	p.L172V	ENST00000392795	NM_001039933.1	172	Ctc/Gtc	4/6	1	2	FACETS	0.976	0.918	1	0.976	0.918	1	CLONAL	1	TRUE	1	0.804786330475717	2		768	619	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967297	38967297	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035767-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	246	655	0	ENST00000357387.3:c.1184T>C	p.Ile395Thr	p.I395T	ENST00000357387	NM_152756.3	395	aTa/aCa	14/38	0.721096654287651	4	FACETS	0.992	0.927	1	0.496	0.463	0.53	CLONAL	1	TRUE	2	0.804786330475717	4		655	1112	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412045	116412045	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0035825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	419	612	0	ENST00000397752.3:c.3028+2T>C		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.243143821020983	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	0	0.243143821020983	3		612	1197	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956185	175956185	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	38	352	0	ENST00000367669.3:c.2027T>A	p.Leu676Gln	p.L676Q	ENST00000367669	NM_022457.5	676	cTa/cAa	18/20	1	2	FACETS	0.655	0.541	0.783	0.655	0.541	0.783	SUBCLONAL	1	TRUE	1	0.243143821020983	2		352	477	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974856	15974856	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	64	494	0	ENST00000268712.3:c.4019G>T	p.Gly1340Val	p.G1340V	ENST00000268712	NM_006311.3	1340	gGc/gTc	30/46	0.175277192720999	1	FACETS	0.758	0.656	0.868	0.758	0.656	0.868	SUBCLONAL	1	TRUE	0	0.243143821020983	1		494	610	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095917	178095917	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	51	496	0	ENST00000397062.3:c.1414A>G	p.Lys472Glu	p.K472E	ENST00000397062	NM_006164.4	472	Aaa/Gaa	5/5	1	2	FACETS	0.667	0.566	0.778	0.667	0.566	0.778	SUBCLONAL	1	TRUE	1	0.243143821020983	2		496	629	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215595178	215595184	+	frameshift_variant	Frame_Shift_Del	DEL	ATTTCAT	ATTTCAT	-	novel	NA	P-0035825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	40	407	0	ENST00000260947.4:c.1952_1958del	p.Tyr651PhefsTer61	p.Y651Ffs*61	ENST00000260947	NM_000465.2	651	tATGAAATt/tt	10/11	1	2	FACETS	0.533	0.442	0.635	0.533	0.442	0.635	SUBCLONAL	1	TRUE	1	0.243143821020983	2		407	617	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080581	5080581	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	52	337	0	ENST00000381652.3:c.2332G>T	p.Ala778Ser	p.A778S	ENST00000381652	NM_004972.3	778	Gca/Tca	18/25	1	2	FACETS	0.861	0.733	1	0.861	0.733	1	CLONAL	1	TRUE	1	0.243143821020983	2		337	497	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589808	28589808	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	42	444	0	ENST00000241453.7:c.2572G>C	p.Glu858Gln	p.E858Q	ENST00000241453	NM_004119.2	858	Gaa/Caa	21/24	1	2	FACETS	0.625	0.521	0.74	0.625	0.521	0.74	SUBCLONAL	1	TRUE	1	0.243143821020983	2		444	553	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589804	28589805	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	40	440	0	ENST00000241453.7:c.2575dup	p.Ser859LysfsTer4	p.S859Kfs*4	ENST00000241453	NM_004119.2	859	agc/aAgc	21/24	1	2	FACETS	0.586	0.487	0.698	0.586	0.487	0.698	SUBCLONAL	1	TRUE	1	0.243143821020983	2		440	561	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444120	49444120	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1162	71	561	1	ENST00000301067.7:c.3251del	p.Pro1084GlnfsTer35	p.P1084Qfs*35	ENST00000301067	NM_003482.3	1084	cCa/ca	11/54	1	2	FACETS	0.677	0.589	0.774	0.677	0.589	0.774	SUBCLONAL	1	TRUE	1	0.17	2		562	1233	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051629	30051630	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0035840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	38	445	0	ENST00000338641.4:c.564_565dup	p.Thr189IlefsTer21	p.T189Ifs*21	ENST00000338641	NM_000268.3	188	att/atTAt	6/16	0.240159568574147	1	FACETS	0.553	0.455	0.662	0.553	0.455	0.662	SUBCLONAL	1	TRUE	0	0.17	1		445	740	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442078	52442078	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	83	487	0	ENST00000460680.1:c.271T>G	p.Cys91Gly	p.C91G	ENST00000460680	NM_004656.3	91	Tgt/Ggt	5/17	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.17	2		487	967	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941314	71941314	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	177	625	0	ENST00000298229.2:c.1089del	p.Ile364SerfsTer48	p.I364Sfs*48	ENST00000298229	NM_001567.3	363	cgC/cg	9/28	0.835075576535382	3	FACETS	0.849	0.785	0.915	0.425	0.392	0.458	CLONAL	1	TRUE	1	0.891618944730221	3		625	676	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999558	100999558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	300	930	1	ENST00000325455.5:c.244G>A	p.Asp82Asn	p.D82N	ENST00000325455	NM_001202474.3	82	Gac/Aac	1/8	0.772443555810774	3	FACETS	0.914	0.862	0.968	0.457	0.431	0.484	CLONAL	1	TRUE	1	0.891618944730221	3		931	1064	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433446	138433446	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	110	523	0	ENST00000289153.2:c.1166T>C	p.Ile389Thr	p.I389T	ENST00000289153	NM_006219.2	389	aTt/aCt	7/22	1	2	FACETS	0.822	0.749	0.897	0.822	0.749	0.897	CLONAL	1	TRUE	1	0.891618944730221	2		523	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0036181-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	63	821	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.0808047586877367	4	FACETS	0.601	0.518	0.692	0.301	0.259	0.346	INDETERMINATE	1	FALSE	2	0.243058146848044	4		822	1072	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792278	33792278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036181-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	67	601	0	ENST00000498907.2:c.1043G>A	p.Ser348Asn	p.S348N	ENST00000498907	NM_004364.3	348	aGc/aAc	1/1	1	2	FACETS	0.605	0.524	0.693	0.605	0.524	0.693	SUBCLONAL	1	FALSE	1	0.243058146848044	2		601	911	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657369	29657369	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764782945	NA	P-0036181-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	33	439	1	ENST00000356175.3:c.5602G>A	p.Glu1868Lys	p.E1868K	ENST00000356175	NM_000267.3	1868	Gag/Aag	38/57	1	2	FACETS	0.471	0.382	0.571	0.471	0.382	0.571	SUBCLONAL	1	FALSE	1	0.243058146848044	2		440	577	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0036225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	106	573	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.220770320227981	1	FACETS	0.812	0.73	0.9	0.812	0.73	0.9	CLONAL	1	TRUE	0	0.351443939143216	1		573	612	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850951	128850951	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs767352128	NA	P-0036225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	69	479	0	ENST00000249373.3:c.1798G>T	p.Val600Leu	p.V600L	ENST00000249373	NM_005631.4	600	Gtg/Ttg	10/12	1	2	FACETS	0.778	0.678	0.884	0.778	0.678	0.884	SUBCLONAL	1	TRUE	1	0.351443939143216	2		479	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579374	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1060501195	NA	P-0036225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	125	731	0	ENST00000269305.4:c.313G>C	p.Gly105Arg	p.G105R	ENST00000269305	NM_001126112.2	105	Ggc/Cgc	4/11	0.351443939143216	1	FACETS	0.994	0.903	1	0.994	0.903	1	CLONAL	1	TRUE	0	0.351443939143216	1		731	590	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961005	55961005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	43	533	0	ENST00000263923.4:c.2935G>A	p.Glu979Lys	p.E979K	ENST00000263923	NM_002253.2	979	Gag/Aag	21/30	0.351443939143216	1	FACETS	0.335	0.279	0.396	0.335	0.279	0.396	SUBCLONAL	1	TRUE	0	0.351443939143216	1		533	603	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100850	27100850	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	39	547	0	ENST00000324856.7:c.4133del	p.Gly1378AlafsTer103	p.G1378Afs*103	ENST00000324856	NM_006015.4	1378	Ggc/gc	18/20	0.220770320227981	1	FACETS	0.399	0.331	0.476	0.399	0.331	0.476	SUBCLONAL	1	TRUE	0	0.351443939143216	1		547	458	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202743	133202743	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	55	535	0	ENST00000320574.5:c.6491G>T	p.Cys2164Phe	p.C2164F	ENST00000320574	NM_006231.2	2164	tGc/tTc	46/49	NA	2	FACETS	0.567	0.485	0.657			1	INDETERMINATE	1	TRUE	NA	0.351443939143216	2		535	552	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775179	73775180	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0036225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	115	539	0	ENST00000254810.4:c.76_77delinsTT	p.Ala26Phe	p.A26F	ENST00000254810	NM_005324.3	26	GCc/TTc	2/4	1	2	FACETS	0.968	0.873	1	0.968	0.873	1	CLONAL	1	TRUE	1	0.351443939143216	2		539	676	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264761	46264761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	148	510	1	ENST00000371998.3:c.1631C>T	p.Pro544Leu	p.P544L	ENST00000371998		544	cCa/cTa	12/23	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.351443939143216	2		511	632	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183697	10183697	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	59	479	0	ENST00000256474.2:c.166G>T	p.Ala56Ser	p.A56S	ENST00000256474	NM_000551.3	56	Gcc/Tcc	1/3	NA	2	FACETS	0.716	0.617	0.823			1	INDETERMINATE	1	TRUE	NA	0.351443939143216	2		479	469	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965658	93965658	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	74	503	1	ENST00000369303.4:c.2270G>T	p.Arg757Met	p.R757M	ENST00000369303	NM_004440.3	757	aGg/aTg	13/17	0.173437084146802	0	FACETS	0.552	0.484	0.624			1	INDETERMINATE	1	TRUE	0	0.351443939143216	0		504	495	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545731	106545731	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	117	621	0	ENST00000359195.3:c.3208G>C	p.Asp1070His	p.D1070H	ENST00000359195	NM_002649.2	1070	Gat/Cat	11/11	1	2	FACETS	0.905	0.816	0.998	0.905	0.816	0.998	CLONAL	1	TRUE	1	0.351443939143216	2		621	736	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0036252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	680	932	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.708777943981094	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.708777943981094	2		932	917	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998292	100998292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	17	58	0	ENST00000325455.5:c.1510G>A	p.Ala504Thr	p.A504T	ENST00000325455	NM_001202474.3	504	Gcc/Acc	1/8	0.306702847773163	2	FACETS	0.444	0.336	0.569	0.222	0.168	0.285	INDETERMINATE	1	TRUE	0	0.708777943981094	2		58	108	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681706	30681706	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56118863	NA	P-0036252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	586	451	2	ENST00000376406.3:c.391C>T	p.His131Tyr	p.H131Y	ENST00000376406	NM_014641.2	131	Cat/Tat	3/15	0.637909796100227	3	FACETS	0.866	0.841	0.89	0.866	0.841	0.89	CLONAL	3	TRUE	0	0.708777943981094	3		453	862	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729858	41729858	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	157	490	0	ENST00000242208.4:c.671C>G	p.Ser224Cys	p.S224C	ENST00000242208	NM_002192.2	224	tCc/tGc	3/3	0.200646551253915	5	FACETS	1	0.954	1	0.354	0.324	0.385	INDETERMINATE	1	TRUE	2	0.708777943981094	5		490	861	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0036619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	28	766	1	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.913	0.728	1	0.913	0.728	1	CLONAL	1	TRUE	1	0.13	2		767	472	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0036619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	13	462	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	1	2	FACETS	0.725	0.516	0.98	0.725	0.516	0.98	CLONAL	1	TRUE	1	0.13	2		462	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0036619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	29	765	2	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	1	2	FACETS	0.931	0.746	1	0.931	0.746	1	CLONAL	1	TRUE	1	0.13	2		767	479	SUCCESS
APC	324	MSKCC	GRCh37	5	112175223	112175223	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	24	195	0	ENST00000257430.4:c.3933del	p.Ile1311MetfsTer10	p.I1311Mfs*10	ENST00000257430	NM_000038.5	1311	aTt/at	16/16	1	2	FACETS	0.832	0.655	1	1	0.937	1	CLONAL	2	TRUE	1	0.13	2		195	222	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106366	27106383	+	inframe_deletion	In_Frame_Del	DEL	TTTGTGCCAGGCAATGAC	TTTGTGCCAGGCAATGAC	-	novel	NA	P-0036619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	28	493	1	ENST00000324856.7:c.5981_5998del	p.Val1994_Phe1999del	p.V1994_F1999del	ENST00000324856	NM_006015.4	1993	TTTGTGCCAGGCAATGAC/-	20/20	1	2	FACETS	1	0.814	1	1	0.814	1	CLONAL	1	TRUE	1	0.13	2		494	422	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	112	759	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.825	0.752	0.9	0.825	0.752	0.9	CLONAL	1	TRUE	1	0.867012885017876	2		760	313	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100375	27100375	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	290	492	0	ENST00000324856.7:c.4087C>T	p.Gln1363Ter	p.Q1363*	ENST00000324856	NM_006015.4	1363	Caa/Taa	17/20	1	2	FACETS	0.963	0.912	1	0.963	0.912	1	CLONAL	1	TRUE	1	0.867012885017876	2		492	695	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652129	36652129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34916193	NA	P-0036636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	332	516	0	ENST00000244741.5:c.251G>A	p.Arg84Gln	p.R84Q	ENST00000244741	NM_000389.4	84	cGa/cAa	2/3	0.867012885017876	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.867012885017876	1		516	409	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856113	68856113	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782750	NA	P-0036636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	294	446	1	ENST00000261769.5:c.1921C>T	p.Gln641Ter	p.Q641*	ENST00000261769	NM_004360.3	641	Cag/Tag	12/16	0.867012885017876	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.867012885017876	1		447	366	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953826	131953826	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs368980595	NA	P-0036636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	195	300	0	ENST00000265335.6:c.3229C>T	p.Arg1077Ter	p.R1077*	ENST00000265335		1077	Cga/Tga	21/25	1	2	FACETS	0.887	0.829	0.947	0.887	0.829	0.947	CLONAL	1	TRUE	1	0.867012885017876	2		300	507	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874215	155874215	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	349	495	1	ENST00000368323.3:c.316C>T	p.Arg106Ter	p.R106*	ENST00000368323	NM_006912.5	106	Cga/Tga	5/6	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.867012885017876	2		496	746	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606790	43606790	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs200334340	NA	P-0036636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	330	655	0	ENST00000355710.3:c.1399G>C	p.Val467Leu	p.V467L	ENST00000355710	NM_020975.4	467	Gtg/Ctg	7/20	1	2	FACETS	0.98	0.931	1	0.98	0.931	1	CLONAL	1	TRUE	1	0.867012885017876	2		655	777	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426196	49426196	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1388458596	NA	P-0036636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	368	636	0	ENST00000301067.7:c.12292C>T	p.Pro4098Ser	p.P4098S	ENST00000301067	NM_003482.3	4098	Cca/Tca	39/54	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.867012885017876	2		636	809	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037968	49037968	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	218	327	1	ENST00000267163.4:c.2209del	p.Glu737ArgfsTer7	p.E737Rfs*7	ENST00000267163	NM_000321.2	736	caG/ca	21/27	0.867012885017876	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.867012885017876	1		328	283	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726689	88726689	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	181	381	0	ENST00000360948.2:c.355C>A	p.Gln119Lys	p.Q119K	ENST00000360948	NM_001012338.2	119	Cag/Aag	4/19	1	2	FACETS	0.96	0.896	1	0.96	0.896	1	CLONAL	1	TRUE	1	0.867012885017876	2		381	435	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719780	52719780	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0036636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	236	444	0	ENST00000322088.6:c.994-2A>G		p.X332_splice	ENST00000322088	NM_014225.5	332			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.867012885017876	2		444	534	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593549	215593549	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	365	331	0	ENST00000260947.4:c.2185G>A	p.Asp729Asn	p.D729N	ENST00000260947	NM_000465.2	729	Gat/Aat	11/11	0.840227803315775	2	FACETS	0.946	0.92	0.97	0.946	0.92	0.97	CLONAL	2	TRUE	0	0.867012885017876	2		331	445	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12632328	12632328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	313	459	0	ENST00000251849.4:c.1339G>A	p.Asp447Asn	p.D447N	ENST00000251849	NM_002880.3	447	Gac/Aac	12/17	1	2	FACETS	0.967	0.917	1	0.967	0.917	1	CLONAL	1	TRUE	1	0.867012885017876	2		459	747	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31493367	31493367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	178	311	0	ENST00000344624.3:c.1789C>T	p.His597Tyr	p.H597Y	ENST00000344624		597	Cac/Tac	10/33	1	2	FACETS	0.898	0.837	0.961	0.898	0.837	0.961	CLONAL	1	TRUE	1	0.867012885017876	2		311	457	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652072	36652072	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	393	665	1	ENST00000244741.5:c.194G>A	p.Trp65Ter	p.W65*	ENST00000244741	NM_000389.4	65	tGg/tAg	2/3	0.867012885017876	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.867012885017876	1		666	487	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929578	44929578	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0036636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	148	161	0	ENST00000377967.4:c.2678C>G	p.Ser893Ter	p.S893*	ENST00000377967	NM_021140.2	893	tCa/tGa	17/29	1	1	FACETS	0.977	0.927	1	0.977	0.927	1	CLONAL	1	TRUE	0	0.867012885017876	1		161	198	SUCCESS
BTK	695	MSKCC	GRCh37	X	100604928	100604928	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41300892	NA	P-0036636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	210	196	0	ENST00000308731.7:c.1925C>T	p.Pro642Leu	p.P642L	ENST00000308731	NM_000061.2	642	cCc/cTc	19/19	1	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.867012885017876	1		196	268	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231773	36231773	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1569061762	NA	P-0036731-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	520	464	0	ENST00000300305.3:c.611G>A	p.Arg204Gln	p.R204Q	ENST00000300305		204	cGa/cAa	5/8	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.782076254390891	2		464	1232	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857311	68857312	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0036731-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	283	593	0	ENST00000261769.5:c.1947_1948insTT	p.Ile650LeufsTer4	p.I650Lfs*4	ENST00000261769	NM_004360.3	649	tct/tcTTt	13/16	0.782076254390891	1	FACETS	0.971	0.928	1	0.971	0.928	1	CLONAL	1	TRUE	0	0.782076254390891	1		593	454	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941851	71941853	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0036731-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	451	886	0	ENST00000298229.2:c.1211_1213del	p.Phe404del	p.F404del	ENST00000298229	NM_001567.3	403	gcCTTc/gcc	11/28	0.782076254390891	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.782076254390891	1		886	692	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510611	38510611	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036731-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	584	1096	0	ENST00000254066.5:c.865G>T	p.Gly289Trp	p.G289W	ENST00000254066	NM_000964.3	289	Ggg/Tgg	7/9	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.782076254390891	2		1096	1445	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0037002-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	152	583	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.393160554160417	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.393160554160417	1		583	443	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180648	56180649	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0037002-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	109	354	0	ENST00000399503.3:c.3979dup	p.Ala1327GlyfsTer11	p.A1327Gfs*11	ENST00000399503	NM_005921.1	1326	atg/atGg	16/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.393160554160417	2		354	475	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178587	56178587	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs150901136	NA	P-0037002-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	80	256	0	ENST00000399503.3:c.3560A>C	p.Glu1187Ala	p.E1187A	ENST00000399503	NM_005921.1	1187	gAa/gCa	14/20	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.393160554160417	2		256	386	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183288	56183289	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0037002-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	151	462	0	ENST00000399503.3:c.4199_4200dup	p.Gly1401LeufsTer22	p.G1401Lfs*22	ENST00000399503	NM_005921.1	1400	act/aCTct	18/20	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.393160554160417	2		462	762	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0037021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	51	407	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	0.836	0.712	0.973	0.836	0.712	0.973	CLONAL	1	TRUE	1	0.26	2		407	469	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99192856	99192856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	75	322	0	ENST00000268035.6:c.46C>T	p.Leu16Phe	p.L16F	ENST00000268035	NM_000875.3	16	Ctc/Ttc	1/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.26	2		322	428	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804154	46804154	+	stop_lost	Nonstop_Mutation	SNP	A	A	C	rs1555558440	NA	P-0037021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	56	619	0	ENST00000290295.7:c.853T>G	p.Ter285GluextTer32	p.*285Eext*32	ENST00000290295	NM_006361.5	285	Taa/Gaa	2/2	1	2	FACETS	0.695	0.595	0.804	0.695	0.595	0.804	SUBCLONAL	1	TRUE	1	0.26	2		619	620	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922961	44923000	+	frameshift_variant	Frame_Shift_Del	DEL	CCTTACCTGCAGCGAAACGCACTCACTCTACCTCATAACC	CCTTACCTGCAGCGAAACGCACTCACTCTACCTCATAACC	-	novel	NA	P-0037021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	68	299	0	ENST00000377967.4:c.1822_1861del	p.Pro608AlafsTer4	p.P608Afs*4	ENST00000377967	NM_021140.2	608	CCTTACCTGCAGCGAAACGCACTCACTCTACCTCATAACCgc/gc	16/29	1	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.26	1		299	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576865	7576865	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	rs879254077	NA	P-0037025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	438	678	0	ENST00000269305.4:c.981T>G	p.Tyr327Ter	p.Y327*	ENST00000269305	NM_001126112.2	327	taT/taG	9/11	0.479512965077594	1	FACETS	1	0.997	1	1	0.997	1	INDETERMINATE	1	TRUE	0	0.815263241235069	1		678	531	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395511	116395526	+	frameshift_variant	Frame_Shift_Del	DEL	AGAGTTCTCCTTGGAA	AGAGTTCTCCTTGGAA	TT	novel	NA	P-0037025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	98	509	0	ENST00000397752.3:c.1804_1819delinsTT	p.Arg602LeufsTer2	p.R602Lfs*2	ENST00000397752	NM_000245.2	602	AGAGTTCTCCTTGGAAat/TTat	6/21	1	2	FACETS	0.781	0.705	0.859	0.781	0.705	0.859	SUBCLONAL	1	TRUE	1	0.815263241235069	2		509	308	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0037065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	284	331	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.689386059034312	3	FACETS	0.951	0.904	0.999	0.951	0.904	0.999	CLONAL	2	TRUE	1	0.701295647787698	3		331	575	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0037065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	183	439	2	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	0.701295647787698	1	FACETS	0.934	0.876	0.991	0.934	0.876	0.991	CLONAL	1	TRUE	0	0.701295647787698	1		441	363	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117211	7117212	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0037065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	316	705	2	ENST00000302850.5:c.4004_4005del	p.Cys1335SerfsTer68	p.C1335Sfs*68	ENST00000302850	NM_000208.2	1335	tGT/t	22/22	1	2	FACETS	0.945	0.893	0.997	0.945	0.893	0.997	CLONAL	1	TRUE	1	0.701295647787698	2		707	954	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797120	42797120	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	348	765	0	ENST00000575354.2:c.3482C>G	p.Thr1161Ser	p.T1161S	ENST00000575354	NM_015125.3	1161	aCc/aGc	15/20	1	2	FACETS	0.976	0.926	1	0.976	0.926	1	CLONAL	1	TRUE	1	0.701295647787698	2		765	1017	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021635	31021659	+	frameshift_variant	Frame_Shift_Del	DEL	GTCAGTCCTTTCGTAACACAATTGA	GTCAGTCCTTTCGTAACACAATTGA	-	novel	NA	P-0037065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	212	571	0	ENST00000375687.4:c.1634_1658del	p.Arg545GlnfsTer150	p.R545Qfs*150	ENST00000375687	NM_015338.5	545	cGTCAGTCCTTTCGTAACACAATTGAa/ca	12/13	1	2	FACETS	0.881	0.822	0.942	0.881	0.822	0.942	CLONAL	1	TRUE	1	0.701295647787698	2		571	686	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0037085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	301	534	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.213600266777328	4	FACETS	0.88	0.835	0.924			1	CLONAL	4	FALSE	NA	0.34577331429624	4		535	666	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376681	8376681	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	150	442	0	ENST00000356435.5:c.4432G>C	p.Gly1478Arg	p.G1478R	ENST00000356435		1478	Gga/Cga	27/35	0.34577331429624	6	FACETS	0.853	0.78	0.93	0.427	0.39	0.465	CLONAL	2	FALSE	2	0.34577331429624	6		442	860	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983797	15983797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	224	429	1	ENST00000268712.3:c.3325G>A	p.Glu1109Lys	p.E1109K	ENST00000268712	NM_006311.3	1109	Gaa/Aaa	25/46	0.339052144887142	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	FALSE	0	0.34577331429624	2		430	581	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046312	69046312	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs769708831	NA	P-0037085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	52	371	1	ENST00000288368.4:c.3785G>T	p.Arg1262Leu	p.R1262L	ENST00000288368	NM_024870.2	1262	cGt/cTt	32/40	0.34577331429624	5	FACETS	0.748	0.636	0.87	0.249	0.212	0.29	SUBCLONAL	1	FALSE	2	0.34577331429624	5		372	611	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0037088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	72	380	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.20035416383072	2		380	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	92	546	0	ENST00000269305.4:c.376T>C	p.Tyr126His	p.Y126H	ENST00000269305	NM_001126112.2	126	Tac/Cac	5/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.20035416383072	2		546	781	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0037096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	290	558	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.997	0.944	1	0.997	0.944	1	CLONAL	1	TRUE	1	0.826173531469359	2		558	704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0037096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	558	934	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.826173531469359	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.826173531469359	1		934	754	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559859	29559862	+	frameshift_variant	Frame_Shift_Del	DEL	ACTC	ACTC	-	rs1321848637	NA	P-0037096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	159	308	0	ENST00000356175.3:c.3457_3460del	p.Leu1153MetfsTer4	p.L1153Mfs*4	ENST00000356175	NM_000267.3	1152	ttACTC/tt	26/57	0.746783672495984	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.826173531469359	1		308	226	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0037115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	96	761	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.253351518322258	1	FACETS	0.975	0.869	1	0.975	0.869	1	CLONAL	1	TRUE	0	0.253351518322258	1		764	679	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0037115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	68	321	1	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.253351518322258	2		322	420	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770587	40770587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776338672	NA	P-0037115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	790	509	0	ENST00000373198.4:c.2795G>A	p.Arg932His	p.R932H	ENST00000373198	NM_133170.3	932	cGc/cAc	19/32	0.253351518322258	9	FACETS	0.973	0.947	1			1	CLONAL	9	TRUE	NA	0.253351518322258	9		509	1343	SUCCESS
AR	367	MSKCC	GRCh37	X	66766357	66766386	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	-	rs746853821	NA	P-0037115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	25	163	1	ENST00000374690.3:c.1391_1420del	p.Gly464_Gly473del	p.G464_G473del	ENST00000374690	NM_000044.3	457	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGC/-	1/8	0.158446485507129	2	FACETS	0.866	0.685	1	0.433	0.342	0.536	CLONAL	1	TRUE	0	0.253351518322258	2		164	228	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741406	17741406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs993043194	NA	P-0037115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	246	930	2	ENST00000250003.3:c.77C>T	p.Thr26Met	p.T26M	ENST00000250003	NM_002478.4	26	aCg/aTg	1/3	1	2	FACETS	0.896	0.837	0.956	1	0.994	1	CLONAL	2	TRUE	1	0.253351518322258	2		932	1084	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480589	123480589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	80	584	0	ENST00000371139.4:c.97G>A	p.Asp33Asn	p.D33N	ENST00000371139	NM_001114937.2	33	Gac/Aac	1/4	0.158446485507129	2	FACETS	0.821	0.722	0.928	0.411	0.361	0.464	CLONAL	1	TRUE	0	0.253351518322258	2		584	769	SUCCESS
APC	324	MSKCC	GRCh37	5	112154999	112154999	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561542165	NA	P-0037115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	81	527	0	ENST00000257430.4:c.1270C>T	p.Gln424Ter	p.Q424*	ENST00000257430	NM_000038.5	424	Cag/Tag	10/16	1	2	FACETS	0.976	0.86	1	0.976	0.86	1	CLONAL	1	TRUE	1	0.253351518322258	2		527	655	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874188	151874194	+	frameshift_variant	Frame_Shift_Del	DEL	TATCATC	TATCATC	-	novel	NA	P-0037115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	84	565	0	ENST00000262189.6:c.8344_8350del	p.Asp2782SerfsTer2	p.D2782Sfs*2	ENST00000262189	NM_170606.2	2782	GATGATAag/ag	38/59	0.248023674205808	3	FACETS	1	0.919	1	0.526	0.464	0.592	CLONAL	1	TRUE	1	0.253351518322258	3		565	710	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913558	32913559	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359479	NA	P-0037151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	49	262	1	ENST00000380152.3:c.5073dup	p.Trp1692MetfsTer3	p.W1692Mfs*3	ENST00000380152		1689	gca/gcAa	11/27	0.663473775353531	1	FACETS	0.949	0.833	1	0.949	0.833	1	CLONAL	1	TRUE	0	0.663473775353531	1		263	104	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464402	120464402	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	95	408	0	ENST00000256646.2:c.5244C>G	p.Asn1748Lys	p.N1748K	ENST00000256646	NM_024408.3	1748	aaC/aaG	29/34	1	2	FACETS	0.77	0.691	0.852	0.77	0.691	0.852	SUBCLONAL	1	TRUE	1	0.663473775353531	2		408	372	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717948	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAAAAGGTTTGTACTTTACTTTCATTGGGAGAAATATCCAAAATAAGGACAGATTAAAAGCTATATTTTATTTTATGACATGTAAGGAACTATAATTTGTTTTCTATTAGATCTGCAGGTGTTTTGCTTACTCTGGCATTGGTGAGACATTATAAGGGTAAATAATCCTGTTTGAAGG	AAAAAAGGTTTGTACTTTACTTTCATTGGGAGAAATATCCAAAATAAGGACAGATTAAAAGCTATATTTTATTTTATGACATGTAAGGAACTATAATTTGTTTTCTATTAGATCTGCAGGTGTTTTGCTTACTCTGGCATTGGTGAGACATTATAAGGGTAAATAATCCTGTTTGAAGG	-	novel	NA	P-0037151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	14	219	0	ENST00000371953.3:c.799_801+176del		p.X267_splice	ENST00000371953	NM_000314.4	267		7/9	1	2	FACETS	0.508	0.374	0.666	0.508	0.374	0.666	SUBCLONAL	1	TRUE	1	0.663473775353531	2		219	83	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173748	108173793	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATGTGTGAAGTAAGAAGATTAATTAGTCTGATATAATTCCTTGTTT	ATGTGTGAAGTAAGAAGATTAATTAGTCTGATATAATTCCTTGTTT	-	novel	NA	P-0037151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	33	203	0	ENST00000278616.4:c.5491_5496+40del		p.X1831_splice	ENST00000278616	NM_000051.3	1831		36/63	1	2	FACETS	0.865	0.72	1	0.865	0.72	1	CLONAL	1	TRUE	1	0.663473775353531	2		203	115	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578393	7578396	+	protein_altering_variant	In_Frame_Del	DEL	ATGG	ATGG	T	novel	NA	P-0037162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	59	498	0	ENST00000269305.4:c.534_537delinsA	p.His178_His179delinsGln	p.H178_H179delinsQ	ENST00000269305	NM_001126112.2	178	caCCAT/caA	5/11	0.273855793949527	1	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	0	0.273855793949527	1		498	372	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302421	15302421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149307620	NA	P-0037171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1544	219	852	1	ENST00000263388.2:c.850G>A	p.Ala284Thr	p.A284T	ENST00000263388	NM_000435.2	284	Gcc/Acc	6/33	0.342161960470711	3	FACETS	0.85	0.788	0.915	0.425	0.394	0.458	CLONAL	1	TRUE	1	0.342161960470711	3		853	1763	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137784	64137784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1579	659	920	0	ENST00000334205.4:c.1885C>T	p.Arg629Cys	p.R629C	ENST00000334205	NM_003942.2	629	Cgc/Tgc	15/17	0.335411537385673	4	FACETS	1	0.994	1	0.77	0.74	0.8	CLONAL	2	TRUE	1	0.342161960470711	4		920	2238	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504407	186504408	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0037171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	59	545	0	ENST00000323963.5:c.745_746del	p.Gln249ValfsTer4	p.Q249Vfs*4	ENST00000323963		248	aaACag/aaag	7/11	0.191056583665995	3	FACETS	0.831	0.716	0.956	0.416	0.358	0.478	INDETERMINATE	1	TRUE	1	0.342161960470711	3		545	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0037177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	454	768	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.76885678766366	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.771728761896842	2		768	581	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918505	94918505	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	167	552	0	ENST00000536441.1:c.677T>G	p.Leu226Arg	p.L226R	ENST00000536441	NM_144665.3	226	cTa/cGa	5/10	0.771728761896842	3	FACETS	1	0.937	1	0.508	0.469	0.549	CLONAL	1	TRUE	1	0.771728761896842	3		552	590	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061274	38061274	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	501	713	0	ENST00000250448.2:c.715G>C	p.Gly239Arg	p.G239R	ENST00000250448	NM_004496.3	239	Ggc/Cgc	2/2	0.563246507073436	6	FACETS	0.951	0.913	0.99			1	CLONAL	3	TRUE	NA	0.771728761896842	6		713	1157	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56878477	56878477	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	135	433	0	ENST00000308159.5:c.2416G>A	p.Asp806Asn	p.D806N	ENST00000308159	NM_014669.4	806	Gac/Aac	22/22	NA	2	FACETS	0.918	0.844	0.994			1	INDETERMINATE	1	TRUE	NA	0.771728761896842	2		433	381	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049712	16049712	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	152	533	0	ENST00000268712.3:c.1060G>A	p.Glu354Lys	p.E354K	ENST00000268712	NM_006311.3	354	Gaa/Aaa	10/46	0.771728761896842	3	FACETS	0.85	0.78	0.923	0.425	0.39	0.462	CLONAL	1	TRUE	1	0.771728761896842	3		533	642	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50143339	50143339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	27	71	0	ENST00000246792.3:c.17C>T	p.Ala6Val	p.A6V	ENST00000246792	NM_006270.3	6	gCg/gTg	1/6	0.599303103518658	4	FACETS	1	0.901	1	0.59	0.48	0.711	CLONAL	1	TRUE	2	0.771728761896842	4		71	105	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022712	31022713	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	G	novel	NA	P-0037177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	175	546	0	ENST00000375687.4:c.2197_2198delinsG	p.Gln733GlyfsTer11	p.Q733Gfs*11	ENST00000375687	NM_015338.5	733	CAg/Gg	13/13	0.744487499963962	3	FACETS	1	0.969	1	0.543	0.503	0.584	CLONAL	1	TRUE	1	0.771728761896842	3		546	579	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0037198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	251	136	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.72747954236238	6	FACETS	1	0.984	1	1	0.984	1	CLONAL	5	TRUE	1	0.72747954236238	6		136	325	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	576	817	0	ENST00000269305.4:c.470T>G	p.Val157Gly	p.V157G	ENST00000269305	NM_001126112.2	157	gTc/gGc	5/11	0.72747954236238	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.72747954236238	2		817	746	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946810	17946810	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs149316157	NA	P-0037198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1459	175	658	1	ENST00000458235.1:c.1837C>T	p.Arg613Ter	p.R613*	ENST00000458235	NM_000215.3	613	Cga/Tga	14/24	0.72747954236238	6	FACETS	0.723	0.663	0.786	0.181	0.165	0.197	SUBCLONAL	1	TRUE	2	0.72747954236238	6		659	1634	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239503	123239503	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	256	800	0	ENST00000358487.5:c.2334G>C	p.Gln778His	p.Q778H	ENST00000358487	NM_000141.4	778	caG/caC	18/18	0.723587004993799	3	FACETS	1	0.989	1	0.607	0.57	0.644	CLONAL	1	TRUE	1	0.72747954236238	3		800	791	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202314	133202314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	69	645	0	ENST00000320574.5:c.6574G>A	p.Ala2192Thr	p.A2192T	ENST00000320574	NM_006231.2	2192	Gcg/Acg	47/49	0.58479289222723	2	FACETS	0.293	0.255	0.334	0.146	0.127	0.167	SUBCLONAL	1	TRUE	0	0.72747954236238	2		645	648	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241666	55241666	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	325	680	38	ENST00000275493.2:c.2114G>T	p.Arg705Met	p.R705M	ENST00000275493	NM_005228.3	705	aGg/aTg	18/28	0.334334928699159	3	FACETS	0.913	0.87	0.957	0.913	0.87	0.957	INDETERMINATE	2	TRUE	1	0.72747954236238	3		718	667	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	44	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.417	0.349	0.492	0.417	0.349	0.492	SUBCLONAL	1	FALSE	1	0.32336548093461	2		334	653	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	44	757	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	1	2	FACETS	0.333	0.278	0.394	0.333	0.278	0.394	SUBCLONAL	1	FALSE	1	0.32336548093461	2		757	817	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713886	30713886	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	39	606	0	ENST00000295754.5:c.1211T>G	p.Leu404Arg	p.L404R	ENST00000295754	NM_003242.5	404	cTg/cGg	4/7	1	2	FACETS	0.335	0.277	0.401	0.335	0.277	0.401	SUBCLONAL	1	FALSE	1	0.32336548093461	2		606	719	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981135	201981135	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	266	718	1	ENST00000359651.3:c.214G>T	p.Val72Phe	p.V72F	ENST00000359651		72	Gtt/Ttt	2/8	1	2	FACETS	0.997	0.936	1	0.997	0.936	1	CLONAL	1	TRUE	1	0.571254337049076	2		719	934	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022522	12022522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762232508	NA	P-0037228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	204	627	1	ENST00000396373.4:c.628C>T	p.Arg210Cys	p.R210C	ENST00000396373	NM_001987.4	210	Cgc/Tgc	5/8	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.571254337049076	2		628	690	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0037228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	121	378	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.796	0.723	0.873	0.796	0.723	0.873	SUBCLONAL	1	TRUE	1	0.571254337049076	2		378	532	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434150	49434150	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	227	784	1	ENST00000301067.7:c.7403A>G	p.Lys2468Arg	p.K2468R	ENST00000301067	NM_003482.3	2468	aAg/aGg	31/54	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.571254337049076	2		785	782	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482780	67482780	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	237	605	1	ENST00000327367.4:c.1184G>T	p.Trp395Leu	p.W395L	ENST00000327367	NM_005902.3	395	tGg/tTg	9/9	0.415650991069915	1	FACETS	0.965	0.907	1	0.965	0.907	1	CLONAL	1	TRUE	0	0.571254337049076	1		606	614	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467796	99467796	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	107	395	0	ENST00000268035.6:c.2665G>T	p.Gly889Ter	p.G889*	ENST00000268035	NM_000875.3	889	Gga/Tga	13/21	0.415650991069915	1	FACETS	0.769	0.697	0.844	0.769	0.697	0.844	SUBCLONAL	1	TRUE	0	0.571254337049076	1		395	348	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348830	11348830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	75	201	0	ENST00000332029.2:c.506G>A	p.Arg169His	p.R169H	ENST00000332029	NM_003745.1	169	cGc/cAc	2/2	0.415650991069915	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.571254337049076	1		201	163	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134499	30134499	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs955881745	NA	P-0037228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	89	265	0	ENST00000263025.4:c.32G>T	p.Gly11Val	p.G11V	ENST00000263025	NM_002746.2	11	gGc/gTc	1/9	0.290998838673601	1	FACETS	0.61	0.545	0.678	0.61	0.545	0.678	INDETERMINATE	1	TRUE	0	0.571254337049076	1		265	365	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993715	72993715	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	187	528	0	ENST00000268489.5:c.330G>T	p.Glu110Asp	p.E110D	ENST00000268489	NM_006885.3	110	gaG/gaT	2/10	0.290998838673601	1	FACETS	0.939	0.875	1	0.939	0.875	1	INDETERMINATE	1	TRUE	0	0.571254337049076	1		528	498	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222151	2222151	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760542574	NA	P-0037228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	297	860	0	ENST00000398665.3:c.2983C>T	p.Arg995Trp	p.R995W	ENST00000398665	NM_032482.2	995	Cgg/Tgg	24/28	0.426469465081465	3	FACETS	1	0.988	1	0.592	0.557	0.628	CLONAL	1	TRUE	1	0.571254337049076	3		860	1129	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950353	17950353	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	249	762	0	ENST00000458235.1:c.1374G>C	p.Trp458Cys	p.W458C	ENST00000458235	NM_000215.3	458	tgG/tgC	10/24	0.426469465081465	3	FACETS	0.976	0.912	1	0.488	0.456	0.521	CLONAL	1	TRUE	1	0.571254337049076	3		762	1148	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797206	42797206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	416	839	1	ENST00000575354.2:c.3568G>A	p.Gly1190Arg	p.G1190R	ENST00000575354	NM_015125.3	1190	Ggg/Agg	15/20	0.426469465081465	3	FACETS	0.861	0.822	0.901	0.861	0.822	0.901	CLONAL	2	TRUE	1	0.571254337049076	3		840	1087	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918165	50918165	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	210	845	0	ENST00000440232.2:c.2482G>C	p.Gly828Arg	p.G828R	ENST00000440232	NM_002691.3	828	Ggc/Cgc	20/27	0.426469465081465	3	FACETS	0.869	0.806	0.934	0.434	0.403	0.467	CLONAL	1	TRUE	1	0.571254337049076	3		845	1088	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380550	31380550	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs770469129	NA	P-0037228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	142	436	0	ENST00000328111.2:c.1040G>T	p.Gly347Val	p.G347V	ENST00000328111	NM_006892.3	347	gGc/gTc	9/23	0.441182310634912	5	FACETS	0.995	0.906	1			1	CLONAL	1	TRUE	NA	0.571254337049076	5		436	928	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324258	62324258	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1438	237	828	2	ENST00000360203.5:c.2753C>A	p.Ala918Asp	p.A918D	ENST00000360203	NM_001283009.1	918	gCc/gAc	29/35	0.558728038928337	5	FACETS	0.92	0.855	0.987	0.23	0.213	0.247	CLONAL	1	TRUE	1	0.571254337049076	5		830	1675	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161913	47161913	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0037228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	118	490	0	ENST00000409792.3:c.4213A>T	p.Lys1405Ter	p.K1405*	ENST00000409792	NM_014159.6	1405	Aaa/Taa	3/21	0.55993353456094	2	FACETS	0.754	0.683	0.828	0.377	0.341	0.414	SUBCLONAL	1	TRUE	0	0.571254337049076	2		490	548	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133466	55133466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	93	430	0	ENST00000257290.5:c.770G>A	p.Gly257Asp	p.G257D	ENST00000257290	NM_006206.4	257	gGc/gAc	6/23	0.366133168391488	1	FACETS	0.569	0.509	0.632	0.569	0.509	0.632	SUBCLONAL	1	TRUE	0	0.571254337049076	1		430	409	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599234	55599234	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0037228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	31	422	0	ENST00000288135.5:c.2362-2A>G		p.X788_splice	ENST00000288135	NM_000222.2	788			0.366133168391488	1	FACETS	0.195	0.158	0.238	0.195	0.158	0.238	SUBCLONAL	1	TRUE	0	0.571254337049076	1		422	397	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968597	55968597	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	216	686	0	ENST00000263923.4:c.2066C>G	p.Thr689Arg	p.T689R	ENST00000263923	NM_002253.2	689	aCg/aGg	14/30	0.366133168391488	1	FACETS	0.669	0.623	0.716	0.669	0.623	0.716	SUBCLONAL	1	TRUE	0	0.571254337049076	1		686	808	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532711	187532711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768440012	NA	P-0037228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	144	562	1	ENST00000441802.2:c.9682C>T	p.Pro3228Ser	p.P3228S	ENST00000441802	NM_005245.3	3228	Cct/Tct	14/27	1	2	FACETS	0.777	0.71	0.846	0.777	0.71	0.846	SUBCLONAL	1	TRUE	1	0.571254337049076	2		563	649	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31405808	31405808	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	113	309	0	ENST00000344624.3:c.3970G>T	p.Ala1324Ser	p.A1324S	ENST00000344624		1324	Gca/Tca	32/33	1	2	FACETS	0.992	0.9	1	0.992	0.9	1	CLONAL	1	TRUE	1	0.571254337049076	2		309	399	SUCCESS
APC	324	MSKCC	GRCh37	5	112173801	112173801	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs79512956	NA	P-0037228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	79	405	0	ENST00000257430.4:c.2510C>G	p.Ser837Ter	p.S837*	ENST00000257430	NM_000038.5	837	tCa/tGa	16/16	0.366133168391488	1	FACETS	0.488	0.431	0.548	0.488	0.431	0.548	SUBCLONAL	1	TRUE	0	0.571254337049076	1		405	405	SUCCESS
APC	324	MSKCC	GRCh37	5	112175282	112175282	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0037228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	106	265	0	ENST00000257430.4:c.3991A>T	p.Arg1331Ter	p.R1331*	ENST00000257430	NM_000038.5	1331	Aga/Tga	16/16	0.366133168391488	1	FACETS	0.717	0.648	0.788	0.717	0.648	0.788	SUBCLONAL	1	TRUE	0	0.571254337049076	1		265	370	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046060	180046060	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	46	339	0	ENST00000261937.6:c.2811C>A	p.Asn937Lys	p.N937K	ENST00000261937	NM_182925.4	937	aaC/aaA	20/30	0.366133168391488	1	FACETS	0.252	0.212	0.296	0.252	0.212	0.296	SUBCLONAL	1	TRUE	0	0.571254337049076	1		339	456	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046770	180046770	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0037228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	193	579	0	ENST00000261937.6:c.2543-1G>C		p.X848_splice	ENST00000261937	NM_182925.4	848			0.366133168391488	1	FACETS	0.79	0.735	0.847	0.79	0.735	0.847	SUBCLONAL	1	TRUE	0	0.571254337049076	1		579	611	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190349	32190349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	379	693	0	ENST00000375023.3:c.390G>T	p.Arg130Ser	p.R130S	ENST00000375023	NM_004557.3	130	agG/agT	3/30	0.327813456825263	2	FACETS	0.844	0.807	0.881	0.844	0.807	0.881	INDETERMINATE	2	TRUE	0	0.571254337049076	2		693	786	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339190	87339190	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200636057	NA	P-0037228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	51	564	0	ENST00000277120.3:c.772G>A	p.Asp258Asn	p.D258N	ENST00000277120		258	Gat/Aat	8/19	0.366133168391488	1	FACETS	0.199	0.168	0.232	0.199	0.168	0.232	SUBCLONAL	1	TRUE	0	0.571254337049076	1		564	642	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391964	139391964	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1022510242	NA	P-0037228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	202	798	0	ENST00000277541.6:c.6227C>T	p.Thr2076Ile	p.T2076I	ENST00000277541	NM_017617.3	2076	aCc/aTc	34/34	0.366133168391488	1	FACETS	0.554	0.514	0.596	0.554	0.514	0.596	SUBCLONAL	1	TRUE	0	0.571254337049076	1		798	912	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	65	759	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.672472223161767	2		760	190	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0037268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1564	426	816	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	0.672472223161767	7	FACETS	0.854	0.81	0.898			1	CLONAL	2	TRUE	NA	0.672472223161767	7		816	1990	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874261	155874261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352822	NA	P-0037268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	22	640	0	ENST00000368323.3:c.270G>A	p.Met90Ile	p.M90I	ENST00000368323	NM_006912.5	90	atG/atA	5/6	0.672472223161767	3	FACETS	0.101	0.078	0.129	0.051	0.039	0.065	SUBCLONAL	1	TRUE	1	0.672472223161767	3		640	864	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797258	135797258	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	98	388	0	ENST00000298552.3:c.611del	p.Arg204LeufsTer6	p.R204Lfs*6	ENST00000298552	NM_001162426.1	204	cGt/ct	7/23	0.672472223161767	1	FACETS	0.887	0.809	0.967	0.887	0.809	0.967	CLONAL	1	TRUE	0	0.672472223161767	1		388	218	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873820	35873820	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	92	307	0	ENST00000216797.5:c.31T>G	p.Trp11Gly	p.W11G	ENST00000216797	NM_020529.2	11	Tgg/Ggg	1/6	NA	2	FACETS	0.974	0.877	1			1	INDETERMINATE	1	TRUE	NA	0.672472223161767	2		307	281	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133748274	133748274	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	20	697	0	ENST00000318560.5:c.935A>T	p.Tyr312Phe	p.Y312F	ENST00000318560	NM_005157.4	312	tAt/tTt	6/11	0.672472223161767	1	FACETS	0.101	0.077	0.129	0.101	0.077	0.129	SUBCLONAL	1	TRUE	0	0.672472223161767	1		697	391	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0037281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	109	243	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.445766869677277	2		243	469	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0037281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	181	409	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.902	0.833	0.975	0.902	0.833	0.975	CLONAL	1	TRUE	1	0.445766869677277	2		409	900	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063347	67063347	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	88	293	0	ENST00000412916.2:c.37G>T	p.Glu13Ter	p.E13*	ENST00000412916		13	Gag/Tag	1/6	0.445766869677277	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.445766869677277	1		293	290	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0037281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	127	451	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.445766869677277	2		451	524	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200297	138200297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556022420	NA	P-0037281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	94	543	0	ENST00000237289.4:c.1715G>A	p.Arg572Gln	p.R572Q	ENST00000237289	NM_001270507.1	572	cGg/cAg	7/9	1	2	FACETS	0.852	0.761	0.948	0.852	0.761	0.948	CLONAL	1	TRUE	1	0.445766869677277	2		543	495	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593590	55593607	+	inframe_deletion	In_Frame_Del	DEL	GTATGAAGTACAGTGGAA	GTATGAAGTACAGTGGAA	-	novel	NA	P-0037282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	166	239	0	ENST00000288135.5:c.1657_1674del	p.Tyr553_Lys558del	p.Y553_K558del	ENST00000288135	NM_000222.2	552	atGTATGAAGTACAGTGGAAg/atg	11/21	1	2	FACETS	0.943	0.871	1	0.943	0.871	1	CLONAL	1	TRUE	1	0.623258795754673	2		239	565	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0037287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	181	410	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.483263240361789	2		410	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0037300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	469	919	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.480437126885092	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.480437126885092	2		919	888	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0037300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	142	324	1	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.480437126885092	2	FACETS	0.893	0.826	0.96	0.893	0.826	0.96	CLONAL	2	TRUE	0	0.480437126885092	2		325	331	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	330	482	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	0.480437126885092	4	FACETS	0.938	0.899	0.976	0.938	0.899	0.976	CLONAL	4	TRUE	0	0.480437126885092	4		482	542	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871249	12871249	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0037300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	80	194	0	ENST00000228872.4:c.475+1G>A		p.X159_splice	ENST00000228872	NM_004064.3	159			0.480437126885092	3	FACETS	0.894	0.8	0.991	0.894	0.8	0.991	CLONAL	2	TRUE	1	0.480437126885092	3		194	231	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455118	50455118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200163039	NA	P-0037300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	187	391	1	ENST00000331340.3:c.665G>A	p.Arg222His	p.R222H	ENST00000331340	NM_006060.4	222	cGc/cAc	6/8	0.333014582046152	4	FACETS	0.922	0.856	0.99	0.922	0.856	0.99	CLONAL	2	TRUE	2	0.480437126885092	4		392	625	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508683	106508683	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1490061702	NA	P-0037300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	280	630	0	ENST00000359195.3:c.677G>A	p.Arg226His	p.R226H	ENST00000359195	NM_002649.2	226	cGc/cAc	2/11	0.333014582046152	4	FACETS	0.959	0.903	1	0.959	0.903	1	CLONAL	2	TRUE	2	0.480437126885092	4		630	900	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280809	41280832	+	stop_lost,inframe_deletion	Nonstop_Mutation	DEL	GGCCTGGTTTGATACTGACCTGTA	GGCCTGGTTTGATACTGACCTGTA	-	novel	NA	P-0037300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	31	527	0	ENST00000349496.5:c.2322_2345del	p.Ala775_Ter782delextTer?	p.A775_*782delext*?	ENST00000349496	NM_001904.3	775	ctGGCCTGGTTTGATACTGACCTGTAa/cta	15/15	1	2	FACETS	0.249	0.201	0.304	0.249	0.201	0.304	SUBCLONAL	1	TRUE	1	0.480437126885092	2		527	518	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196542	106196542	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	39	496	0	ENST00000380013.4:c.4875T>A	p.Asn1625Lys	p.N1625K	ENST00000380013	NM_001127208.2	1625	aaT/aaA	11/11	0.480437126885092	4	FACETS	0.35	0.289	0.419	0.088	0.072	0.105	SUBCLONAL	1	TRUE	0	0.480437126885092	4		496	686	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0037302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	723	659	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.593244865649617	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.593244865649617	3		659	1041	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539736	187539736	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1400631217	NA	P-0037302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	111	458	0	ENST00000441802.2:c.8004C>A	p.Phe2668Leu	p.F2668L	ENST00000441802	NM_005245.3	2668	ttC/ttA	10/27	0.593244865649617	1	FACETS	0.668	0.606	0.733	0.668	0.606	0.733	SUBCLONAL	1	TRUE	0	0.593244865649617	1		458	394	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572538	64572538	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	202	561	0	ENST00000312049.6:c.1318C>A	p.Leu440Ile	p.L440I	ENST00000312049	NM_130799.2	440	Ctt/Att	9/10	0.362495819999889	5	FACETS	1	0.989	1	0.457	0.423	0.491	CLONAL	1	TRUE	2	0.593244865649617	5		561	939	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533176	63533176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1165490589	NA	P-0037302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	209	659	0	ENST00000307078.5:c.1718G>A	p.Ser573Asn	p.S573N	ENST00000307078	NM_004655.3	573	aGc/aAc	7/11	0.593244865649617	2	FACETS	1	0.98	1	0.561	0.524	0.599	CLONAL	1	TRUE	0	0.593244865649617	2		659	628	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444272	50444272	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	70	289	0	ENST00000331340.3:c.202G>T	p.Gly68Trp	p.G68W	ENST00000331340	NM_006060.4	68	Ggg/Tgg	4/8	0.593244865649617	6	FACETS	0.75	0.653	0.854	0.15	0.13	0.171	SUBCLONAL	1	TRUE	1	0.593244865649617	6		289	688	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0037305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	51	583	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		583	355	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0037305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	24	285	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		285	316	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0037305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	33	614	1	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		615	488	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0037305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	27	472	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		472	299	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041308	42041308	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0037305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	73	490	1	ENST00000219905.7:c.5504-1G>A		p.X1835_splice	ENST00000219905	NM_001164273.1	1835			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		491	578	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0037321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	102	479	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.914	0.83	1	0.914	0.83	1	CLONAL	1	TRUE	1	0.785532254308508	2		479	284	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57567469	57567469	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0037321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	80	273	0	ENST00000316660.6:c.58+2T>C		p.X20_splice	ENST00000316660	NM_021127.2	20			1	2	FACETS	0.821	0.734	0.912	0.821	0.734	0.912	CLONAL	1	TRUE	1	0.785532254308508	2		273	248	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0037321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1408	9551	453	1	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.785532254308508	54	FACETS	0.99	0.986	0.995	0.897	0.893	0.901	CLONAL	48	TRUE	1	0.785532254308508	54		454	10959	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247183	153247183	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	62	269	0	ENST00000281708.4:c.1619A>G	p.His540Arg	p.H540R	ENST00000281708	NM_033632.3	540	cAt/cGt	10/12	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.269862164820094	2		269	370	SUCCESS
APC	324	MSKCC	GRCh37	5	112174835	112174835	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0037327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	60	246	2	ENST00000257430.4:c.3544A>T	p.Lys1182Ter	p.K1182*	ENST00000257430	NM_000038.5	1182	Aaa/Taa	16/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.269862164820094	2		248	300	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67459188	67459188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760091844	NA	P-0037327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	79	464	0	ENST00000327367.4:c.604G>A	p.Ala202Thr	p.A202T	ENST00000327367	NM_005902.3	202	Gca/Aca	4/9	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.269862164820094	2		464	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579529	7579530	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0037327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	142	746	0	ENST00000269305.4:c.157dup	p.Trp53LeufsTer4	p.W53Lfs*4	ENST00000269305	NM_001126112.2	53	tgg/tTgg	4/11	0.203217142678663	2	FACETS	1	0.983	1	0.672	0.613	0.734	CLONAL	1	TRUE	0	0.269862164820094	2		746	783	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80171584	80171584	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	38	417	0	ENST00000265081.6:c.3317A>G	p.Tyr1106Cys	p.Y1106C	ENST00000265081	NM_002439.4	1106	tAt/tGt	24/24	1	2	FACETS	0.583	0.482	0.696	0.583	0.482	0.696	SUBCLONAL	1	TRUE	1	0.269862164820094	2		417	483	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	237	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.532325619964748	2	FACETS	0.871	0.823	0.919	0.871	0.823	0.919	CLONAL	2	TRUE	0	0.556415009516524	2		334	489	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0037331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	144	423	1	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	0.929	0.852	1	0.929	0.852	1	CLONAL	1	TRUE	1	0.556415009516524	2		424	557	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575080	48575080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	111	318	0	ENST00000342988.3:c.274C>T	p.His92Tyr	p.H92Y	ENST00000342988	NM_005359.5	92	Cat/Tat	3/12	1	2	FACETS	0.976	0.884	1	0.976	0.884	1	CLONAL	1	TRUE	1	0.556415009516524	2		318	409	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472523	88472523	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1419472052	NA	P-0037331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	165	511	0	ENST00000360948.2:c.2032C>T	p.Arg678Ter	p.R678*	ENST00000360948	NM_001012338.2	678	Cga/Tga	16/19	0.413266263747479	1	FACETS	0.624	0.575	0.675	0.624	0.575	0.675	SUBCLONAL	1	TRUE	0	0.556415009516524	1		511	686	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651532	52651532	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	133	365	0	ENST00000394830.3:c.1564C>T	p.Arg522Ter	p.R522*	ENST00000394830	NM_018313.4	522	Cga/Tga	15/30	1	2	FACETS	0.974	0.89	1	0.974	0.89	1	CLONAL	1	TRUE	1	0.556415009516524	2		365	491	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176330	24176330	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	225	543	0	ENST00000263121.7:c.1121G>C	p.Arg374Pro	p.R374P	ENST00000263121	NM_003073.3	374	cGg/cCg	9/9	1	2	FACETS	0.962	0.897	1	0.962	0.897	1	CLONAL	1	TRUE	1	0.556415009516524	2		543	841	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727152	41727153	+	splice_donor_variant	Splice_Site	DNP	GT	GT	AA	novel	NA	P-0037331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	173	519	1	ENST00000301178.4:c.409+1_409+2delinsAA		p.X137_splice	ENST00000301178	NM_021913.4	137			0.556415009516524	3	FACETS	0.756	0.695	0.82	0.378	0.347	0.41	SUBCLONAL	1	TRUE	1	0.556415009516524	3		520	1051	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408864	41408864	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	101	293	0	ENST00000373198.4:c.562C>A	p.Pro188Thr	p.P188T	ENST00000373198	NM_133170.3	188	Cca/Aca	4/32	0.413266263747479	1	FACETS	0.634	0.571	0.701	0.634	0.571	0.701	SUBCLONAL	1	TRUE	0	0.556415009516524	1		293	413	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589012	67589594	+	splice_donor_variant,splice_acceptor_variant,stop_lost,protein_altering_variant,intron_variant	Splice_Site	DEL	ATACTCTTACACTAAGGTAAGCCAGGGAATATAGCTGAAATTAGGGTTTTGGGCTGATATTAAAACATATTTCCTTATTCCAAAATGTTAATACCTTTATTTTTATATTGTTTTTACAGGAAAGGGGGAAATAACAAATTAATCAAAATATTTCATCGAGATGGGAAATATGGCTTCTCTGACCCATTAACCTTCAGTTCTGTGGTTGAATTAATAAACCACTACCGGAATGAATCTCTAGCTCAGTATAATCCCAAATTGGATGTGAAATTACTTTATCCAGTATCCAAATACCAACAGGTAATAAAAACTGAATGAATTATCCAGTTACGATGTTTAGACAAGATCCTTTTAATACTTAGAAAACATTTGAAGCAGATGAATTACATGTAATCAAGTCTAAAAAACTTGACACTCGTAATTACATAATTGCAATTTTAAAGATGTTTCCATGTCAGCTATTTTGTTAAACAATTGTTATTTGATTAAATACCTTATCCATTGAATTTATTTTAATCTTTCTAGGATCAAGTTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATTACATGAATATA	ATACTCTTACACTAAGGTAAGCCAGGGAATATAGCTGAAATTAGGGTTTTGGGCTGATATTAAAACATATTTCCTTATTCCAAAATGTTAATACCTTTATTTTTATATTGTTTTTACAGGAAAGGGGGAAATAACAAATTAATCAAAATATTTCATCGAGATGGGAAATATGGCTTCTCTGACCCATTAACCTTCAGTTCTGTGGTTGAATTAATAAACCACTACCGGAATGAATCTCTAGCTCAGTATAATCCCAAATTGGATGTGAAATTACTTTATCCAGTATCCAAATACCAACAGGTAATAAAAACTGAATGAATTATCCAGTTACGATGTTTAGACAAGATCCTTTTAATACTTAGAAAACATTTGAAGCAGATGAATTACATGTAATCAAGTCTAAAAAACTTGACACTCGTAATTACATAATTGCAATTTTAAAGATGTTTCCATGTCAGCTATTTTGTTAAACAATTGTTATTTGATTAAATACCTTATCCATTGAATTTATTTTAATCTTTCTAGGATCAAGTTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATTACATGAATATA	-	novel	NA	P-0037331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	79	208	0	ENST00000274335.5:c.1104_1358del		p.X368_splice	ENST00000274335		368	tATACTCTTACACTAAGGTAAGCCAGGGAATATAGCTGAAATTAGGGTTTTGGGCTGATATTAAAACATATTTCCTTATTCCAAAATGTTAATACCTTTATTTTTATATTGTTTTTACAGGAAAGGGGGAAATAACAAATTAATCAAAATATTTCATCGAGATGGGAAATATGGCTTCTCTGACCCATTAACCTTCAGTTCTGTGGTTGAATTAATAAACCACTACCGGAATGAATCTCTAGCTCAGTATAATCCCAAATTGGATGTGAAATTACTTTATCCAGTATCCAAATACCAACAGGTAATAAAAACTGAATGAATTATCCAGTTACGATGTTTAGACAAGATCCTTTTAATACTTAGAAAACATTTGAAGCAGATGAATTACATGTAATCAAGTCTAAAAAACTTGACACTCGTAATTACATAATTGCAATTTTAAAGATGTTTCCATGTCAGCTATTTTGTTAAACAATTGTTATTTGATTAAATACCTTATCCATTGAATTTATTTTAATCTTTCTAGGATCAAGTTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAac/tac	8-10/15	0.272977644678179	3	FACETS	1	0.975	1	0.685	0.61	0.763	INDETERMINATE	1	TRUE	1	0.556415009516524	3		208	265	SUCCESS
APC	324	MSKCC	GRCh37	5	112151271	112151271	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	93	301	0	ENST00000257430.4:c.914C>A	p.Thr305Lys	p.T305K	ENST00000257430	NM_000038.5	305	aCa/aAa	9/16	1	2	FACETS	0.887	0.795	0.983	0.887	0.795	0.983	CLONAL	1	TRUE	1	0.556415009516524	2		301	377	SUCCESS
APC	324	MSKCC	GRCh37	5	112174979	112174979	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs863225344	NA	P-0037331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	71	198	0	ENST00000257430.4:c.3688C>T	p.Gln1230Ter	p.Q1230*	ENST00000257430	NM_000038.5	1230	Cag/Tag	16/16	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.556415009516524	2		198	241	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38139056	38139056	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	135	547	0	ENST00000317025.8:c.3547G>T	p.Glu1183Ter	p.E1183*	ENST00000317025	NM_023034.1	1183	Gaa/Taa	20/24	1	2	FACETS	0.785	0.716	0.858	0.785	0.716	0.858	SUBCLONAL	1	TRUE	1	0.556415009516524	2		547	618	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0037341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	95	395	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	FALSE	1	0.423428085575077	2		395	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	154	628	0	ENST00000269305.4:c.383del	p.Pro128LeufsTer42	p.P128Lfs*42	ENST00000269305	NM_001126112.2	128	cCt/ct	5/11	0.423428085575077	1	FACETS	0.754	0.699	0.811	1	0.99	1	SUBCLONAL	2	FALSE	0	0.423428085575077	1		628	380	SUCCESS
APC	324	MSKCC	GRCh37	5	112175466	112175466	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786204170	NA	P-0037341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	131	348	0	ENST00000257430.4:c.4175C>A	p.Ser1392Ter	p.S1392*	ENST00000257430	NM_000038.5	1392	tCa/tAa	16/16	0.39179121338935	3	FACETS	0.915	0.847	0.984	0.915	0.847	0.984	CLONAL	3	FALSE	0	0.423428085575077	3		348	273	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925334	114925334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	50	437	0	ENST00000543371.1:c.1412G>A	p.Arg471His	p.R471H	ENST00000543371	NM_001198531.1	471	cGc/cAc	14/14	1	2	FACETS	0.875	0.748	1	0.875	0.748	1	CLONAL	1	FALSE	1	0.423428085575077	2		437	270	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456767	32456767	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	28	515	0	ENST00000332351.3:c.125A>C	p.Lys42Thr	p.K42T	ENST00000332351	NM_024426.4	42	aAg/aCg	1/10	1	2	FACETS	0.535	0.43	0.655	0.535	0.43	0.655	SUBCLONAL	1	FALSE	1	0.423428085575077	2		515	247	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41222965	41222965	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	159	645	0	ENST00000357654.3:c.4966G>T	p.Gly1656Cys	p.G1656C	ENST00000357654	NM_007294.3	1656	Ggc/Tgc	15/23	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.423428085575077	2		645	511	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501557	149501557	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	63	525	0	ENST00000261799.4:c.2230A>G	p.Ser744Gly	p.S744G	ENST00000261799	NM_002609.3	744	Agc/Ggc	16/23	0.39179121338935	3	FACETS	0.833	0.722	0.952	0.278	0.24	0.318	CLONAL	1	FALSE	0	0.423428085575077	3		525	433	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55231433	55231433	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1427028322	NA	P-0037341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	108	493	0	ENST00000275493.2:c.1639A>G	p.Arg547Gly	p.R547G	ENST00000275493	NM_005228.3	547	Agg/Ggg	14/28	0.423428085575077	3	FACETS	1	0.981	1	0.699	0.631	0.77	CLONAL	1	FALSE	1	0.423428085575077	3		493	442	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331663	8331663	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	126	486	1	ENST00000356435.5:c.5453A>T	p.Glu1818Val	p.E1818V	ENST00000356435		1818	gAa/gTa	33/35	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.423428085575077	2		487	448	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643504	38643504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1238094530	NA	P-0037373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	80	407	0	ENST00000299084.4:c.974G>A	p.Arg325Gln	p.R325Q	ENST00000299084	NM_152594.2	325	cGa/cAa	7/7	1	2	FACETS	0.494	0.437	0.556	0.494	0.437	0.556	SUBCLONAL	1	TRUE	1	0.712903581673429	2		407	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579347	7579348	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0037373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	339	588	0	ENST00000269305.4:c.339_340del	p.Leu114AlafsTer34	p.L114Afs*34	ENST00000269305	NM_001126112.2	113	ttCTtg/tttg	4/11	0.626621359388928	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.712903581673429	1		588	511	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246849	10246849	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1422	89	704	0	ENST00000340748.4:c.4556G>A	p.Trp1519Ter	p.W1519*	ENST00000340748		1519	tGg/tAg	37/40	NA	2	FACETS	0.165	0.145	0.187			1	INDETERMINATE	1	TRUE	NA	0.712903581673429	2		704	1511	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17389694	17389694	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	72	719	0	ENST00000359435.4:c.827C>G	p.Thr276Ser	p.T276S	ENST00000359435	NM_001033549.1	276	aCc/aGc	9/9	0.267710803644314	6	FACETS	0.409	0.356	0.467	0.102	0.089	0.117	INDETERMINATE	1	TRUE	2	0.712903581673429	6		719	1197	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0037375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	253	579	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.613939578024197	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.613939578024197	1		579	570	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910887	32910887	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs886040422	NA	P-0037375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	129	361	0	ENST00000380152.3:c.2397del	p.Gly800ValfsTer10	p.G800Vfs*10	ENST00000380152		799	Aaa/aa	11/27	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.613939578024197	2		361	383	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437800	52437800	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1165855820	NA	P-0037375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	294	738	0	ENST00000460680.1:c.1361A>T	p.Glu454Val	p.E454V	ENST00000460680	NM_004656.3	454	gAg/gTg	13/17	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.613939578024197	2		738	884	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412463	80412463	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	123	280	0	ENST00000286548.4:c.578C>G	p.Pro193Arg	p.P193R	ENST00000286548	NM_002072.3	193	cCc/cGc	4/7	1	2	FACETS	0.956	0.872	1	0.956	0.872	1	CLONAL	1	TRUE	1	0.613939578024197	2		280	419	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0037385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	88	513	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	0.397959192496218	3	FACETS	0.784	0.695	0.879	0.392	0.347	0.44	SUBCLONAL	1	TRUE	1	0.439447622226174	3		513	623	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129169	64129169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746466314	NA	P-0037385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	84	477	2	ENST00000334205.4:c.707C>T	p.Ser236Leu	p.S236L	ENST00000334205	NM_003942.2	236	tCg/tTg	7/17	1	2	FACETS	0.549	0.485	0.618	0.549	0.485	0.618	SUBCLONAL	1	TRUE	1	0.439447622226174	2		479	696	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519721	137519721	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0037385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	55	270	0	ENST00000367739.4:c.917C>G	p.Ser306Ter	p.S306*	ENST00000367739	NM_000416.2	306	tCa/tGa	7/7	0.366588979047748	2	FACETS	0.686	0.589	0.791	0.343	0.294	0.396	SUBCLONAL	1	TRUE	0	0.439447622226174	2		270	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0037385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	245	409	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.366588979047748	2	FACETS	0.842	0.792	0.893	0.842	0.792	0.893	CLONAL	2	TRUE	0	0.439447622226174	2		409	662	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406634	70406634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs980829577	NA	P-0037385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	122	479	0	ENST00000373644.4:c.4148C>T	p.Ser1383Leu	p.S1383L	ENST00000373644	NM_030625.2	1383	tCa/tTa	4/12	0.169704126004834	5	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.439447622226174	5		479	721	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748479	43748479	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	300	586	0	ENST00000382044.4:c.2327C>G	p.Ser776Cys	p.S776C	ENST00000382044	NM_001141980.1	776	tCt/tGt	12/28	0.366588979047748	2	FACETS	0.959	0.909	1	0.959	0.909	1	CLONAL	2	TRUE	0	0.439447622226174	2		586	712	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216566	7216566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	222	406	0	ENST00000380728.2:c.769G>A	p.Glu257Lys	p.E257K	ENST00000380728		257	Gaa/Aaa	9/11	0.366588979047748	2	FACETS	0.879	0.824	0.934	0.879	0.824	0.934	CLONAL	2	TRUE	0	0.439447622226174	2		406	575	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961853	15961853	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0037385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	229	405	0	ENST00000268712.3:c.5942C>G	p.Ser1981Ter	p.S1981*	ENST00000268712	NM_006311.3	1981	tCa/tGa	38/46	0.366588979047748	2	FACETS	0.883	0.829	0.938	0.883	0.829	0.938	CLONAL	2	TRUE	0	0.439447622226174	2		405	590	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871550	37871550	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3003	1570	457	0	ENST00000269571.5:c.1160C>G	p.Ser387Cys	p.S387C	ENST00000269571		387	tCc/tGc	10/27	0.439447622226174	24	FACETS	1	0.985	1			1	CLONAL	9	TRUE	NA	0.439447622226174	24		457	4573	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56171097	56171097	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs866945834	NA	P-0037385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	84	268	0	ENST00000399503.3:c.1925T>G	p.Val642Gly	p.V642G	ENST00000399503	NM_005921.1	642	gTc/gGc	10/20	0.439447622226174	5	FACETS	0.757	0.672	0.847	0.505	0.448	0.565	SUBCLONAL	2	TRUE	2	0.439447622226174	5		268	419	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945544	151945553	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGTGTAAC	GGTGTGTAAC	-	novel	NA	P-0037385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	114	303	0	ENST00000262189.6:c.1966_1975del	p.Val656ArgfsTer12	p.V656Rfs*12	ENST00000262189	NM_170606.2	656	GTTACACACCag/ag	14/59	0.366588979047748	2	FACETS	1	0.983	1	0.694	0.631	0.759	CLONAL	1	TRUE	0	0.439447622226174	2		303	374	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652261	48652261	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	154	508	0	ENST00000376670.3:c.932G>C	p.Gly311Ala	p.G311A	ENST00000376670	NM_002049.3	311	gGa/gCa	6/6	0.0883326429840466	6	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.439447622226174	6		508	1023	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0037387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	193	761	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.172925096357945	2	FACETS	0.851	0.788	0.915	0.851	0.788	0.915	CLONAL	2	TRUE	0	0.267909494020285	2		764	847	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0037393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	335	635	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.717717915225776	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.717717915225776	1		635	568	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064385	30064385	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	179	451	0	ENST00000338641.4:c.949G>T	p.Glu317Ter	p.E317*	ENST00000338641	NM_000268.3	317	Gaa/Taa	10/16	0.717717915225776	1	FACETS	0.963	0.905	1	0.963	0.905	1	CLONAL	1	TRUE	0	0.717717915225776	1		451	332	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6031631	6031631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377043696	NA	P-0037393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	92	360	0	ENST00000265849.7:c.961G>A	p.Val321Ile	p.V321I	ENST00000265849	NM_000535.5	321	Gtt/Att	9/15	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.717717915225776	2		360	249	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155725	56155726	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0037399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	35	279	0	ENST00000399503.3:c.819_820del	p.Arg273SerfsTer27	p.R273Sfs*27	ENST00000399503	NM_005921.1	273	AGa/a	3/20	1	2	FACETS	0.319	0.261	0.384	0.319	0.261	0.384	SUBCLONAL	1	TRUE	1	0.558169403901598	2		279	393	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519938	NA	P-0037399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	70	303	0	ENST00000263967.3:c.1034A>T	p.Asn345Ile	p.N345I	ENST00000263967	NM_006218.2	345	aAt/aTt	5/21	1	2	FACETS	0.59	0.516	0.669	0.59	0.516	0.669	SUBCLONAL	1	TRUE	1	0.558169403901598	2		303	425	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115435	115115437	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	rs1319662056	NA	P-0037399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	81	551	0	ENST00000257566.3:c.889_891del	p.Asn297del	p.N297del	ENST00000257566	NM_016569.3	297	AAC/-	5/8	1	2	FACETS	0.373	0.328	0.421	0.373	0.328	0.421	SUBCLONAL	1	TRUE	1	0.558169403901598	2		551	778	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521735	89521735	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	69	364	0	ENST00000336596.2:c.2812del	p.Ser938ValfsTer6	p.S938Vfs*6	ENST00000336596	NM_005233.5	938	Agt/gt	16/17	1	2	FACETS	0.512	0.447	0.582	0.512	0.447	0.582	SUBCLONAL	1	TRUE	1	0.558169403901598	2		364	483	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176561	56176579	+	frameshift_variant	Frame_Shift_Del	DEL	CAACACTGTTGGAACTGTG	CAACACTGTTGGAACTGTG	-	novel	NA	P-0037399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	61	379	0	ENST00000399503.3:c.2114_2132del	p.Thr705LysfsTer14	p.T705Kfs*14	ENST00000399503	NM_005921.1	704	tCAACACTGTTGGAACTGTGc/tc	12/20	1	2	FACETS	0.419	0.361	0.481	0.419	0.361	0.481	SUBCLONAL	1	TRUE	1	0.558169403901598	2		379	522	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184166	56184168	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0037399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	49	307	0	ENST00000399503.3:c.4372_4374del	p.Leu1458del	p.L1458del	ENST00000399503	NM_005921.1	1457	caTCTt/cat	19/20	1	2	FACETS	0.418	0.354	0.488	0.418	0.354	0.488	SUBCLONAL	1	TRUE	1	0.558169403901598	2		307	420	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189459	56189460	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0037399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	69	463	0	ENST00000399503.3:c.4493dup	p.Ser1499IlefsTer24	p.S1499Ifs*24	ENST00000399503	NM_005921.1	1497	-/C	20/20	1	2	FACETS	0.379	0.329	0.432	0.379	0.329	0.432	SUBCLONAL	1	TRUE	1	0.558169403901598	2		463	653	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0037411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	246	729	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.567582202842036	1	FACETS	0.931	0.875	0.987	0.931	0.875	0.987	CLONAL	1	TRUE	0	0.567582202842036	1		729	667	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753149	42753151	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs199960550	NA	P-0037411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	218	594	4	ENST00000222329.4:c.1113_1115del	p.Ser373del	p.S373del	ENST00000222329	NM_006494.2	371	tcTTCc/tcc	4/4	1	2	FACETS	0.91	0.848	0.974	0.91	0.848	0.974	CLONAL	1	TRUE	1	0.567582202842036	2		598	844	SUCCESS
APC	324	MSKCC	GRCh37	5	112175476	112175476	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	248	355	0	ENST00000257430.4:c.4188del	p.Phe1396LeufsTer19	p.F1396Lfs*19	ENST00000257430	NM_000038.5	1395	agT/ag	16/16	0.543459844620566	2	FACETS	0.918	0.87	0.966	0.918	0.87	0.966	CLONAL	2	TRUE	0	0.567582202842036	2		355	476	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775614	9775614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766440014	NA	P-0037411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	210	520	1	ENST00000377346.4:c.157G>A	p.Ala53Thr	p.A53T	ENST00000377346	NM_005026.3	53	Gcc/Acc	4/24	0.567582202842036	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.567582202842036	1		521	496	SUCCESS
APC	324	MSKCC	GRCh37	5	112179566	112179566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755366812	NA	P-0037411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	105	325	0	ENST00000257430.4:c.8275C>T	p.Arg2759Cys	p.R2759C	ENST00000257430	NM_000038.5	2759	Cgt/Tgt	16/16	0.543459844620566	2	FACETS	0.916	0.827	1	0.458	0.413	0.505	CLONAL	1	TRUE	0	0.567582202842036	2		325	404	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783216	9783216	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121480-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	239	742	0	ENST00000377346.4:c.2460C>A	p.Asp820Glu	p.D820E	ENST00000377346	NM_005026.3	820	gaC/gaA	20/24	0.849002026482152	3	FACETS	1	0.972	1	0.532	0.499	0.567	CLONAL	1	NA	1	0.857562641170123	3		742	748	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417167	417167	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121480-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	108	324	0	ENST00000399788.2:c.3383C>A	p.Ala1128Glu	p.A1128E	ENST00000399788	NM_001042603.1	1128	gCa/gAa	23/28	0.826001601137214	5	FACETS	0.976	0.878	1			1	CLONAL	1	NA	NA	0.857562641170123	5		324	590	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871133	12871134	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0121480-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	72	338	0	ENST00000228872.4:c.361_362dup	p.Pro122LeufsTer24	p.P122Lfs*24	ENST00000228872	NM_004064.3	120	-/GC	1/3	0.823867613103009	5	FACETS	0.93	0.816	1	0.31	0.272	0.351	CLONAL	1	NA	2	0.857562641170123	5		338	413	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432516	49432516	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121480-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	202	825	0	ENST00000301067.7:c.8623G>T	p.Ala2875Ser	p.A2875S	ENST00000301067	NM_003482.3	2875	Gcc/Tcc	34/54	0.823867613103009	5	FACETS	0.913	0.845	0.984	0.304	0.281	0.328	CLONAL	1	NA	2	0.857562641170123	5		825	1180	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435156	49435156	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121480-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	148	568	0	ENST00000301067.7:c.6397G>T	p.Ala2133Ser	p.A2133S	ENST00000301067	NM_003482.3	2133	Gcc/Tcc	31/54	0.823867613103009	5	FACETS	0.934	0.853	1	0.311	0.284	0.34	CLONAL	1	NA	2	0.857562641170123	5		568	845	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772478	56772478	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0121480-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	242	718	0	ENST00000337432.4:c.332T>C	p.Leu111Pro	p.L111P	ENST00000337432	NM_058216.2	111	cTt/cCt	2/9	0.797633686556471	5	FACETS	0.927	0.864	0.992	0.309	0.288	0.331	CLONAL	1	NA	2	0.857562641170123	5		718	1392	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796972	78796973	+	missense_variant	Missense_Mutation	DNP	GC	GC	CT	novel	NA	P-0121480-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	196	639	1	ENST00000306801.3:c.1085_1086delinsCT	p.Cys362Ser	p.C362S	ENST00000306801	NM_020761.2	362	tGC/tCT	9/34	0.797633686556471	5	FACETS	0.883	0.816	0.953	0.294	0.272	0.318	CLONAL	1	NA	2	0.857562641170123	5		640	1183	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636934	158636934	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121480-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	194	630	0	ENST00000263640.3:c.246G>T	p.Lys82Asn	p.K82N	ENST00000263640	NM_001105.4	82	aaG/aaT	4/11	0.857562641170123	3	FACETS	1	0.958	1	0.52	0.484	0.558	CLONAL	1	NA	1	0.857562641170123	3		630	621	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326263	62326263	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121480-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	340	958	0	ENST00000360203.5:c.3279C>A	p.Asp1093Glu	p.D1093E	ENST00000360203	NM_001283009.1	1093	gaC/gaA	32/35	0.685585854033424	5	FACETS	1	0.993	1	0.343	0.324	0.363	CLONAL	1	NA	1	0.857562641170123	5		958	1320	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117717425	117717425	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0121480-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	107	383	0	ENST00000368508.3:c.782T>A	p.Phe261Tyr	p.F261Y	ENST00000368508	NM_002944.2	261	tTt/tAt	8/43	0.857562641170123	3	FACETS	0.878	0.794	0.966	0.439	0.397	0.483	CLONAL	1	NA	1	0.857562641170123	3		383	406	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468213	50468213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0121480-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	392	720	2	ENST00000331340.3:c.1448G>A	p.Cys483Tyr	p.C483Y	ENST00000331340	NM_006060.4	483	tGc/tAc	8/8	0.751216903341438	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	NA	2	0.857562641170123	4		722	827	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161291	55161291	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0121480-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	137	423	0	ENST00000257290.5:c.3123-1G>A		p.X1041_splice	ENST00000257290	NM_006206.4	1041			0.857562641170123	3	FACETS	1	0.96	1	0.537	0.493	0.583	CLONAL	1	NA	1	0.857562641170123	3		423	425	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0037495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	54	479	0				ENST00000310581	NM_198253.2	-/1132			0.515443507630169	3	FACETS	0.955	0.822	1	0.477	0.411	0.549	CLONAL	1	TRUE	1	0.515443507630169	3		479	276	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720805	89720808	+	frameshift_variant	Frame_Shift_Del	DEL	CTTT	CTTT	-	rs398123330	NA	P-0037495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	44	240	0	ENST00000371953.3:c.956_959del	p.Thr319LysfsTer24	p.T319Kfs*24	ENST00000371953	NM_000314.4	319	aCTTTa/aa	8/9	0.515443507630169	1	FACETS	0.75	0.639	0.868	0.75	0.639	0.868	SUBCLONAL	1	TRUE	0	0.515443507630169	1		240	169	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556193	29556193	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555614261	NA	P-0037495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	44	159	1	ENST00000356175.3:c.2560C>T	p.Gln854Ter	p.Q854*	ENST00000356175	NM_000267.3	854	Cag/Tag	21/57	1	2	FACETS	0.899	0.764	1	0.899	0.764	1	CLONAL	1	TRUE	1	0.515443507630169	2		160	190	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665752	29665755	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1555535032	NA	P-0037495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	73	252	0	ENST00000356175.3:c.6789_6792del	p.Tyr2264ThrfsTer5	p.Y2264Tfs*5	ENST00000356175	NM_000267.3	2263	ACTTac/ac	45/57	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.515443507630169	2		252	274	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913351	NA	P-0037495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	128	449	1	ENST00000288602.6:c.1397G>A	p.Gly466Glu	p.G466E	ENST00000288602	NM_004333.4	466	gGa/gAa	11/18	0.488172491402563	4	FACETS	0.934	0.847	1	0.467	0.423	0.513	CLONAL	1	TRUE	2	0.515443507630169	4		450	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0037510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	22	538	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	1	2	FACETS	0.652	0.504	0.826	0.652	0.504	0.826	SUBCLONAL	1	TRUE	1	0.12	2		538	562	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0037510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	19	438	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.434	0.327	0.56	0.434	0.327	0.56	SUBCLONAL	1	TRUE	1	0.12	2		438	730	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435300	110435302	+	inframe_deletion	In_Frame_Del	DEL	GGT	GGT	-	rs765493638	NA	P-0037510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	11	94	0	ENST00000375856.3:c.3099_3101del	p.Pro1036del	p.P1036del	ENST00000375856	NM_003749.2	1033	ccACCg/ccg	1/2	1	2	FACETS	1	0.827	1	1	0.827	1	CLONAL	1	TRUE	1	0.12	2		94	138	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0037529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	216	191	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.272144559934063	4	FACETS	1	0.939	1	1	0.992	1	CLONAL	3	FALSE	2	0.336025916147152	4		191	571	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578397	7578397	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1555526004	NA	P-0037529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	127	566	0	ENST00000269305.4:c.533A>C	p.His178Pro	p.H178P	ENST00000269305	NM_001126112.2	178	cAc/cCc	5/11	0.254742088879091	3	FACETS	0.917	0.843	0.992	0.917	0.843	0.992	CLONAL	3	FALSE	0	0.336025916147152	3		566	321	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8246219	8246219	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	49	519	0	ENST00000335790.3:c.415C>T	p.Gln139Ter	p.Q139*	ENST00000335790	NM_002315.2	139	Cag/Tag	4/4	0.336025916147152	5	FACETS	0.923	0.783	1	0.231	0.195	0.27	CLONAL	1	FALSE	1	0.336025916147152	5		519	475	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0037537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	69	534	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.138394258803764	2	FACETS	0.977	0.849	1	0.489	0.424	0.559	CLONAL	1	TRUE	0	0.14909196019673	2		535	947	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0037537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	81	318	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	0.138394258803764	2	FACETS	0.848	0.747	0.955	0.848	0.747	0.955	CLONAL	2	TRUE	0	0.14909196019673	2		318	641	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129487	152129487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	44	152	0	ENST00000206249.3:c.440C>T	p.Pro147Leu	p.P147L	ENST00000206249	NM_000125.3	147	cCg/cTg	1/8	1	2	FACETS	0.975	0.829	1	0.975	0.829	1	CLONAL	1	TRUE	1	0.504428717432953	2		152	179	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	68	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.772	0.671	0.882	0.772	0.671	0.882	SUBCLONAL	1	TRUE	1	0.263216255124579	2		334	669	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0037573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	76	423	1	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.263216255124579	1	FACETS	0.963	0.846	1	0.963	0.846	1	CLONAL	1	TRUE	0	0.263216255124579	1		424	521	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422959	45422959	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	55	340	0	ENST00000262160.6:c.169C>T	p.Arg57Ter	p.R57*	ENST00000262160	NM_005901.5	57	Cga/Tga	2/11	0.263216255124579	1	FACETS	0.739	0.633	0.855	0.739	0.633	0.855	SUBCLONAL	1	TRUE	0	0.263216255124579	1		340	491	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484780	57484780	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	74	499	0	ENST00000371085.3:c.760A>G	p.Asn254Asp	p.N254D	ENST00000371085	NM_000516.4	254	Aac/Gac	10/13	1	2	FACETS	0.847	0.741	0.961	0.847	0.741	0.961	CLONAL	1	TRUE	1	0.263216255124579	2		499	664	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259296	89259296	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	43	392	0	ENST00000336596.2:c.440C>A	p.Ala147Glu	p.A147E	ENST00000336596	NM_005233.5	147	gCa/gAa	3/17	0.254167647590047	1	FACETS	0.555	0.464	0.656	0.555	0.464	0.656	SUBCLONAL	1	TRUE	0	0.263216255124579	1		392	511	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	49	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.626	0.53	0.732	0.626	0.53	0.732	SUBCLONAL	1	TRUE	1	0.26	2		334	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0037607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	49	652	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	0.548	0.463	0.642	0.548	0.463	0.642	SUBCLONAL	1	TRUE	1	0.26	2		653	688	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396667	396667	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	41	623	0	ENST00000262320.3:c.359C>A	p.Ala120Asp	p.A120D	ENST00000262320	NM_003502.3	120	gCc/gAc	2/11	1	2	FACETS	0.453	0.376	0.539	0.453	0.376	0.539	SUBCLONAL	1	TRUE	1	0.26	2		623	696	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305326	65305326	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	73	461	0	ENST00000342505.4:c.2802T>G	p.His934Gln	p.H934Q	ENST00000342505	NM_002227.2	934	caT/caG	20/25	1	2	FACETS	0.558	0.49	0.631	0.558	0.49	0.631	SUBCLONAL	1	TRUE	1	0.628880023480891	2		461	416	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0037670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	79	418	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.334041304553569	2		418	449	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0037670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	101	409	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.968	0.866	1	0.968	0.866	1	CLONAL	1	TRUE	1	0.334041304553569	2		409	625	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322567	39322567	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	39	347	0	ENST00000373001.3:c.425A>C	p.Tyr142Ser	p.Y142S	ENST00000373001	NM_022157.3	142	tAc/tCc	2/7	1	2	FACETS	0.437	0.362	0.522	0.437	0.362	0.522	SUBCLONAL	1	TRUE	1	0.334041304553569	2		347	534	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711861	89711875	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTCTGTCCACCAGG	TTTCTGTCCACCAGG	-	novel	NA	P-0037670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	106	303	0	ENST00000371953.3:c.493-14_493del		p.X165_splice	ENST00000371953	NM_000314.4	165		6/9	0.334041304553569	1	FACETS	0.764	0.692	0.838	1	0.985	1	SUBCLONAL	2	TRUE	0	0.334041304553569	1		303	346	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066772	30066772	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	81	353	0	ENST00000331968.5:c.2359G>A	p.Glu787Lys	p.E787K	ENST00000331968	NM_002742.2	787	Gaa/Aaa	16/18	1	2	FACETS	0.875	0.773	0.985	0.875	0.773	0.985	CLONAL	1	TRUE	1	0.334041304553569	2		353	554	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715615	30715615	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs104893817	NA	P-0037670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	100	208	0	ENST00000295754.5:c.1273A>G	p.Met425Val	p.M425V	ENST00000295754	NM_003242.5	425	Atg/Gtg	5/7	0.326312888041722	2	FACETS	0.93	0.84	1	0.93	0.84	1	CLONAL	2	TRUE	0	0.334041304553569	2		208	322	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165587	185165587	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	56	210	0	ENST00000265026.3:c.862A>G	p.Thr288Ala	p.T288A	ENST00000265026	NM_004721.4	288	Acc/Gcc	5/14	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.334041304553569	2		210	312	SUCCESS
APC	324	MSKCC	GRCh37	5	112173830	112173831	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0037670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	60	238	0	ENST00000257430.4:c.2544dup	p.Asp849ArgfsTer2	p.D849Rfs*2	ENST00000257430	NM_000038.5	847	gaa/gAaa	16/16	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.334041304553569	2		238	329	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0037670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	44	493	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.811	0.683	0.951	0.811	0.683	0.951	CLONAL	1	TRUE	1	0.334041304553569	2		493	325	SUCCESS
APC	324	MSKCC	GRCh37	5	112178717	112178717	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	69	309	0	ENST00000257430.4:c.7426A>G	p.Arg2476Gly	p.R2476G	ENST00000257430	NM_000038.5	2476	Agg/Ggg	16/16	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.334041304553569	2		309	412	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484335	8484335	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749208350	NA	P-0037670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	33	335	0	ENST00000356435.5:c.3197G>A	p.Arg1066Gln	p.R1066Q	ENST00000356435		1066	cGa/cAa	19/35	1	2	FACETS	0.423	0.344	0.512	0.423	0.344	0.512	SUBCLONAL	1	TRUE	1	0.334041304553569	2		335	467	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410124	63410124	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	186	547	0	ENST00000330258.3:c.3043G>T	p.Glu1015Ter	p.E1015*	ENST00000330258	NM_152424.3	1015	Gaa/Taa	2/2	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.334041304553569	2		547	811	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0037691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	263	821	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.790086315341927	1	FACETS	0.976	0.932	1	0.976	0.932	1	CLONAL	1	TRUE	0	0.789729995461279	1		822	413	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061191	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs879499034	NA	P-0037751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	181	441	1	ENST00000250448.2:c.798C>A	p.Phe266Leu	p.F266L	ENST00000250448	NM_004496.3	266	ttC/ttA	2/2	0.839085466492727	4	FACETS	1	0.974	1			1	CLONAL	1	TRUE	NA	0.846851698272797	4		442	709	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143273	58143273	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	15	339	0	ENST00000257904.6:c.647G>C	p.Gly216Ala	p.G216A	ENST00000257904	NM_000075.3	216	gGa/gCa	6/8	1	2	FACETS	0.539	0.394	0.714	0.539	0.394	0.714	SUBCLONAL	1	TRUE	1	0.21	2		339	265	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183259	56183259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	21	510	0	ENST00000399503.3:c.4169G>A	p.Gly1390Glu	p.G1390E	ENST00000399503	NM_005921.1	1390	gGa/gAa	18/20	1	2	FACETS	0.676	0.521	0.856	0.676	0.521	0.856	SUBCLONAL	1	TRUE	1	0.21	2		510	296	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0037905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	465	551	1	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.875486465584862	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.875486465584862	2		552	510	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359386	118359386	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	107	297	0	ENST00000534358.1:c.4390G>T	p.Glu1464Ter	p.E1464*	ENST00000534358	NM_005933.3	1464	Gag/Tag	11/36	0.618379352415334	3	FACETS	1	0.974	1	0.4	0.364	0.437	CLONAL	1	TRUE	0	0.875486465584862	3		297	293	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800491	32800492	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACTT	novel	NA	P-0037905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	243	733	0	ENST00000374899.4:c.1052_1055dup	p.Cys353SerfsTer5	p.C353Sfs*5	ENST00000374899	NM_018833.2	352	gtc/gtAAGTc	6/12	0.315671382212872	3	FACETS	1	0.981	1	0.555	0.521	0.59	INDETERMINATE	1	TRUE	1	0.875486465584862	3		733	719	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27209227	27209227	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs765053701	NA	P-0037905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	11	330	0	ENST00000380036.4:c.2684G>A	p.Arg895Gln	p.R895Q	ENST00000380036	NM_000459.3	895	cGa/cAa	16/23	0.230132810075496	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.875486465584862	0		330	218	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193202140	193202140	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	128	259	0	ENST00000367435.3:c.1172A>T	p.Glu391Val	p.E391V	ENST00000367435	NM_024529.4	391	gAa/gTa	14/17	0.65640913401076	6	FACETS	1	0.986	1	0.296	0.269	0.324	CLONAL	1	TRUE	1	0.828668658885687	6		259	555	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692920	89692921	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs398123323	NA	P-0037915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	169	493	2	ENST00000371953.3:c.405dup	p.Cys136MetfsTer44	p.C136Mfs*44	ENST00000371953	NM_000314.4	135	ata/atAa	5/9	0.828668658885687	1	FACETS	0.967	0.917	1	0.967	0.917	1	CLONAL	1	TRUE	0	0.828668658885687	1		495	247	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623152	52623152	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	221	472	0	ENST00000394830.3:c.2899G>T	p.Glu967Ter	p.E967*	ENST00000394830	NM_018313.4	967	Gaa/Taa	19/30	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.828668658885687	2		472	517	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0037915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	48	606	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.287	0.243	0.336	0.287	0.243	0.336	SUBCLONAL	1	TRUE	1	0.828668658885687	2		606	403	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0038287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	52	418	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.719	0.614	0.834	0.719	0.614	0.834	SUBCLONAL	1	TRUE	1	0.374487030444336	2		418	386	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0038287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	108	378	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.374487030444336	2	FACETS	1	0.983	1	0.719	0.651	0.791	CLONAL	1	TRUE	0	0.374487030444336	2		378	401	SUCCESS
APC	324	MSKCC	GRCh37	5	112175198	112175198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	39	222	0	ENST00000257430.4:c.3907C>T	p.Gln1303Ter	p.Q1303*	ENST00000257430	NM_000038.5	1303	Caa/Taa	16/16	1	2	FACETS	0.914	0.763	1	0.914	0.763	1	CLONAL	1	TRUE	1	0.374487030444336	2		222	228	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591125	67591125	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	64	346	0	ENST00000274335.5:c.1718T>C	p.Leu573Pro	p.L573P	ENST00000274335		573	cTg/cCg	12/15	1	2	FACETS	0.897	0.781	1	0.897	0.781	1	CLONAL	1	TRUE	1	0.374487030444336	2		346	381	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961688	41961688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	97	460	0	ENST00000219905.7:c.596G>A	p.Arg199His	p.R199H	ENST00000219905	NM_001164273.1	199	cGt/cAt	2/24	1	2	FACETS	0.992	0.888	1	0.992	0.888	1	CLONAL	1	TRUE	1	0.374487030444336	2		460	522	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26956950	26956950	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0038287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	96	227	0	ENST00000381527.3:c.457-1G>T		p.X153_splice	ENST00000381527	NM_001260.1	153			0.368895806883971	3	FACETS	0.939	0.846	1	0.939	0.846	1	CLONAL	2	TRUE	1	0.374487030444336	3		227	324	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332763	153332763	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0038287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	186	511	0	ENST00000281708.4:c.193A>T	p.Arg65Ter	p.R65*	ENST00000281708	NM_033632.3	65	Aga/Tga	2/12	0.374487030444336	2	FACETS	0.946	0.881	1	0.946	0.881	1	CLONAL	2	TRUE	0	0.374487030444336	2		511	525	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633858	86633858	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	73	344	1	ENST00000274376.6:c.967T>G	p.Leu323Val	p.L323V	ENST00000274376	NM_002890.2	323	Tta/Gta	5/25	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.374487030444336	2		345	364	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0038395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	118	395	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.270272391641525	2		395	738	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0038395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	60	471	1	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.65	0.559	0.749	0.65	0.559	0.749	SUBCLONAL	1	FALSE	1	0.270272391641525	2		472	683	SUCCESS
APC	324	MSKCC	GRCh37	5	112175182	112175182	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	64	282	0	ENST00000257430.4:c.3892del	p.Ser1298LeufsTer7	p.S1298Lfs*7	ENST00000257430	NM_000038.5	1297	gaT/ga	16/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.270272391641525	2		282	372	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578217	7578217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	192	810	0	ENST00000269305.4:c.632C>T	p.Thr211Ile	p.T211I	ENST00000269305	NM_001126112.2	211	aCt/aTt	6/11	0.270272391641525	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	0	0.270272391641525	1		810	1013	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720964	176720964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	81	637	1	ENST00000439151.2:c.6595C>T	p.Arg2199Cys	p.R2199C	ENST00000439151	NM_022455.4	2199	Cgt/Tgt	23/23	0.102774968113751	3	FACETS	0.725	0.637	0.819	0.362	0.318	0.41	INDETERMINATE	1	FALSE	1	0.270272391641525	3		638	939	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32814909	32814909	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121917702	NA	P-0038395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	110	838	0	ENST00000354258.4:c.2156G>A	p.Arg719Gln	p.R719Q	ENST00000354258	NM_000593.5	719	cGg/cAg	10/11	1	2	FACETS	0.733	0.657	0.814	0.733	0.657	0.814	SUBCLONAL	1	FALSE	1	0.270272391641525	2		838	1110	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885329	111885329	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	56	492	0	ENST00000341259.2:c.1217A>T	p.Asn406Ile	p.N406I	ENST00000341259	NM_005475.2	406	aAc/aTc	6/8	1	2	FACETS	0.737	0.632	0.853	0.737	0.632	0.853	SUBCLONAL	1	FALSE	1	0.270272391641525	2		492	562	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	23	759	1				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.744	0.582	0.931			1	INDETERMINATE	1	TRUE	NA	0.244321041148342	2		760	253	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29497003	29497003	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397514641	NA	P-0038523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	47	218	0	ENST00000356175.3:c.574C>T	p.Arg192Ter	p.R192*	ENST00000356175	NM_000267.3	192	Cga/Tga	5/57	1	2	FACETS	0.769	0.655	0.894	1	0.964	1	SUBCLONAL	2	TRUE	1	0.244321041148342	2		218	250	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041519	14041519	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161291089	NA	P-0038523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	39	339	0	ENST00000311895.7:c.2066G>A	p.Arg689His	p.R689H	ENST00000311895	NM_005236.2	689	cGt/cAt	11/11	1	2	FACETS	0.92	0.765	1	0.92	0.765	1	CLONAL	1	TRUE	1	0.244321041148342	2		339	347	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953897	17953897	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	69	740	2	ENST00000458235.1:c.505G>T	p.Asp169Tyr	p.D169Y	ENST00000458235	NM_000215.3	169	Gac/Tac	5/24	0.244321041148342	3	FACETS	0.796	0.692	0.909	0.398	0.346	0.455	CLONAL	1	TRUE	1	0.244321041148342	3		742	796	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295211	1295211	+	upstream_gene_variant	5'Flank	SNP	G	G	C	novel	NA	P-0038523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	19	310	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.643	0.489	0.823			1	INDETERMINATE	1	TRUE	NA	0.244321041148342	2		310	242	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589558	67589584	+	inframe_deletion	In_Frame_Del	DEL	AATATTGAAGCTGTAGGGAAAAAATTA	AATATTGAAGCTGTAGGGAAAAAATTA	-	novel	NA	P-0038523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	17	190	0	ENST00000274335.5:c.1321_1347del	p.Asn441_Leu449del	p.N441_L449del	ENST00000274335		441	AATATTGAAGCTGTAGGGAAAAAATTA/-	10/15	0.244321041148342	3	FACETS	0.688	0.514	0.893	0.344	0.257	0.447	SUBCLONAL	1	TRUE	1	0.244321041148342	3		190	227	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0039119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	142	628	1	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.938	0.868	1	0.938	0.868	1	CLONAL	1	TRUE	1	0.898103119289145	2		629	337	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427647	49427647	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0039119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	178	452	0	ENST00000301067.7:c.10841C>G	p.Ser3614Ter	p.S3614*	ENST00000301067	NM_003482.3	3614	tCa/tGa	39/54	1	2	FACETS	0.962	0.898	1	0.962	0.898	1	CLONAL	1	TRUE	1	0.898103119289145	2		452	412	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247190	153247190	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	139	300	0	ENST00000281708.4:c.1612C>T	p.Gln538Ter	p.Q538*	ENST00000281708	NM_033632.3	538	Cag/Tag	10/12	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.898103119289145	2		300	296	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434348	49434348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	305	661	0	ENST00000301067.7:c.7205C>A	p.Ser2402Ter	p.S2402*	ENST00000301067	NM_003482.3	2402	tCa/tAa	31/54	1	2	FACETS	0.92	0.873	0.969	0.92	0.873	0.969	CLONAL	1	TRUE	1	0.898103119289145	2		661	738	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866288	42866288	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	195	483	1	ENST00000398585.3:c.344C>A	p.Thr115Asn	p.T115N	ENST00000398585	NM_001135099.1	115	aCc/aAc	3/14	1	2	FACETS	0.934	0.874	0.995	0.934	0.874	0.995	CLONAL	1	TRUE	1	0.898103119289145	2		484	465	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400017	49400017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	197	484	0	ENST00000418115.1:c.320G>A	p.Cys107Tyr	p.C107Y	ENST00000418115	NM_001664.2	107	tGt/tAt	4/5	1	2	FACETS	0.877	0.82	0.936	0.877	0.82	0.936	CLONAL	1	TRUE	1	0.898103119289145	2		484	500	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925503	131925503	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	118	286	0	ENST00000265335.6:c.1426G>C	p.Glu476Gln	p.E476Q	ENST00000265335		476	Gaa/Caa	9/25	1	2	FACETS	0.885	0.811	0.96	0.885	0.811	0.96	CLONAL	1	TRUE	1	0.898103119289145	2		286	297	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197301	26197301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	37	461	1	ENST00000356476.2:c.178G>A	p.Glu60Lys	p.E60K	ENST00000356476		60	Gag/Aag	1/1	1	2	FACETS	0.191	0.157	0.229	0.191	0.157	0.229	SUBCLONAL	1	TRUE	1	0.898103119289145	2		462	431	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151847995	151847995	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0039119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	16	174	0	ENST00000262189.6:c.12764C>G	p.Ser4255Ter	p.S4255*	ENST00000262189	NM_170606.2	4255	tCa/tGa	51/59	1	2	FACETS	0.171	0.127	0.224	0.171	0.127	0.224	SUBCLONAL	1	TRUE	1	0.898103119289145	2		174	208	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151882717	151882717	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0039119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	44	166	0	ENST00000262189.6:c.5009-1G>C		p.X1670_splice	ENST00000262189	NM_170606.2	1670			1	2	FACETS	0.58	0.494	0.672	0.58	0.494	0.672	SUBCLONAL	1	TRUE	1	0.898103119289145	2		166	169	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5463075	5463075	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	103	217	0	ENST00000381577.3:c.636G>C	p.Arg212Ser	p.R212S	ENST00000381577	NM_014143.3	212	agG/agC	4/7	1	2	FACETS	0.84	0.764	0.918	0.84	0.764	0.918	CLONAL	1	TRUE	1	0.898103119289145	2		217	273	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179180	123179180	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0039119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	161	162	0	ENST00000218089.9:c.629C>G	p.Ser210Ter	p.S210*	ENST00000218089	NM_001042749.1	210	tCa/tGa	8/35	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.898103119289145	1		162	177	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920143	76920143	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	51	432	0	ENST00000373344.5:c.3934G>A	p.Gly1312Arg	p.G1312R	ENST00000373344	NM_000489.3	1312	Gga/Aga	11/35	1	2	FACETS	0.933	0.793	1	0.933	0.793	1	CLONAL	1	TRUE	1	0.22	2		432	497	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374249	118374249	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	76	406	0	ENST00000534358.1:c.7642G>C	p.Ala2548Pro	p.A2548P	ENST00000534358	NM_005933.3	2548	Gct/Cct	27/36	1	2	FACETS	0.855	0.754	0.963	1	0.98	1	CLONAL	2	TRUE	1	0.22	2		406	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579362	7579363	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACC	novel	NA	P-0039290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	61	589	0	ENST00000269305.4:c.322_324dup	p.Gly108dup	p.G108dup	ENST00000269305	NM_001126112.2	108	-/GGT	4/11	0.233020274102426	2	FACETS	1	0.954	1	0.624	0.54	0.716	CLONAL	1	TRUE	0	0.22	2		589	444	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210402	2210402	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	20	517	0	ENST00000398665.3:c.1009G>T	p.Glu337Ter	p.E337*	ENST00000398665	NM_032482.2	337	Gaa/Taa	13/28	0.3	1	FACETS	0.501	0.383	0.639	0.501	0.383	0.639	SUBCLONAL	1	TRUE	0	0.22	1		517	323	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0039302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	82	243	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.492183958532419	2		243	318	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771321	68771321	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs878854691	NA	P-0039302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	50	270	0	ENST00000261769.5:c.3G>A	p.Met1?	p.M1?	ENST00000261769	NM_004360.3	1	atG/atA	1/16	0.492183958532419	1	FACETS	0.976	0.845	1	0.976	0.845	1	CLONAL	1	TRUE	0	0.492183958532419	1		270	157	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405969	49405969	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	96	426	0	ENST00000418115.1:c.169T>G	p.Leu57Val	p.L57V	ENST00000418115	NM_001664.2	57	Ttg/Gtg	3/5	1	2	FACETS	0.771	0.689	0.857	0.771	0.689	0.857	SUBCLONAL	1	TRUE	1	0.492183958532419	2		426	506	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615812	1615812	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771807324	NA	P-0039302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	237	408	2	ENST00000344749.5:c.1459C>T	p.Arg487Ter	p.R487*	ENST00000344749	NM_001136139.2	487	Cga/Tga	17/19	0.478196112701935	3	FACETS	0.909	0.861	0.957	0.909	0.861	0.957	CLONAL	3	TRUE	0	0.492183958532419	3		410	440	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117878	70117888	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCAGGCGGC	GCGCAGGCGGC	-	novel	NA	P-0039302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	135	447	0	ENST00000245479.2:c.353_363del	p.Ala118GlufsTer130	p.A118Efs*130	ENST00000245479	NM_000346.3	116	GCGCAGGCGGCg/g	1/3	0.431718028785925	2	FACETS	0.821	0.757	0.886	0.821	0.757	0.886	CLONAL	2	TRUE	0	0.492183958532419	2		447	334	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107183	27107184	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTTG	novel	NA	P-0039302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	137	440	0	ENST00000324856.7:c.6795_6798dup	p.Met2267ValfsTer12	p.M2267Vfs*12	ENST00000324856	NM_006015.4	2265	ccg/ccGTTGg	20/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.492183958532419	2		440	505	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0039393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	189	418	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.922	0.856	0.99	0.922	0.856	0.99	CLONAL	1	TRUE	1	0.611017807095945	2		418	671	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805039	43805039	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	244	595	0	ENST00000372470.3:c.491del	p.Phe164SerfsTer2	p.F164Sfs*2	ENST00000372470	NM_005373.2	163	gaT/ga	4/12	1	2	FACETS	0.955	0.895	1	0.955	0.895	1	CLONAL	1	TRUE	1	0.611017807095945	2		595	836	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120130	70120130	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	182	188	0	ENST00000245479.2:c.1132C>T	p.Gln378Ter	p.Q378*	ENST00000245479	NM_000346.3	378	Cag/Tag	3/3	0.611017807095945	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.611017807095945	2		188	280	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937410	178937410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	56	109	0	ENST00000263967.3:c.1798G>A	p.Glu600Lys	p.E600K	ENST00000263967	NM_006218.2	600	Gaa/Aaa	12/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.611017807095945	2		109	150	SUCCESS
APC	324	MSKCC	GRCh37	5	112111435	112111435	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0039393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	90	251	0	ENST00000257430.4:c.531+1G>A		p.X177_splice	ENST00000257430	NM_000038.5	177			1	2	FACETS	0.839	0.751	0.932	0.839	0.751	0.932	CLONAL	1	TRUE	1	0.611017807095945	2		251	351	SUCCESS
APC	324	MSKCC	GRCh37	5	112175634	112175634	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	148	392	0	ENST00000257430.4:c.4344del	p.Lys1449SerfsTer24	p.K1449Sfs*24	ENST00000257430	NM_000038.5	1448	aCc/ac	16/16	1	2	FACETS	0.911	0.837	0.987	0.911	0.837	0.987	CLONAL	1	TRUE	1	0.611017807095945	2		392	532	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670590	30670590	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	224	539	0	ENST00000376406.3:c.5930A>G	p.Lys1977Arg	p.K1977R	ENST00000376406	NM_014641.2	1977	aAg/aGg	13/15	1	2	FACETS	0.859	0.801	0.918	0.859	0.801	0.918	CLONAL	1	TRUE	1	0.611017807095945	2		539	854	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265368	152265368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	219	469	0	ENST00000206249.3:c.821G>A	p.Gly274Glu	p.G274E	ENST00000206249	NM_000125.3	274	gGg/gAg	4/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.611017807095945	2		469	681	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157488190	157488190	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34786733	NA	P-0039393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	243	508	0	ENST00000346085.5:c.2896G>A	p.Gly966Ser	p.G966S	ENST00000346085	NM_020732.3	966	Ggc/Agc	10/20	1	2	FACETS	0.986	0.924	1	0.986	0.924	1	CLONAL	1	TRUE	1	0.611017807095945	2		508	807	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894987	101894987	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	142	252	1	ENST00000374994.4:c.540A>T	p.Leu180Phe	p.L180F	ENST00000374994	NM_004612.2	180	ttA/ttT	3/9	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.611017807095945	2		253	441	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412755	63412755	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	235	552	0	ENST00000330258.3:c.412G>T	p.Glu138Ter	p.E138*	ENST00000330258	NM_152424.3	138	Gag/Tag	2/2	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.611017807095945	2		552	753	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0039414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	202	784	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.507	0.469	0.546	0.507	0.469	0.546	SUBCLONAL	1	TRUE	1	0.749618429546036	2		786	1064	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913517	NA	P-0039414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	212	423	0	ENST00000288135.5:c.1676T>A	p.Val559Asp	p.V559D	ENST00000288135	NM_000222.2	559	gTt/gAt	11/21	1	2	FACETS	0.957	0.895	1	0.957	0.895	1	CLONAL	1	TRUE	1	0.749618429546036	2		423	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934573	NA	P-0039419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	375	628	0	ENST00000269305.4:c.722C>A	p.Ser241Tyr	p.S241Y	ENST00000269305	NM_001126112.2	241	tCc/tAc	7/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.758371999805793	2		628	989	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786767	3786767	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	337	528	1	ENST00000262367.5:c.4444T>A	p.Tyr1482Asn	p.Y1482N	ENST00000262367	NM_004380.2	1482	Tac/Aac	27/31	0.758371999805793	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.758371999805793	1		529	526	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925325	114925326	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	229	469	0	ENST00000543371.1:c.1404dup	p.Cys469ValfsTer8	p.C469Vfs*8	ENST00000543371	NM_001198531.1	468	aag/aaGg	14/14	0.758371999805793	1	FACETS	0.813	0.768	0.859	0.813	0.768	0.859	CLONAL	1	TRUE	0	0.758371999805793	1		469	461	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696410	47696410	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	284	508	0	ENST00000347630.2:c.413G>T	p.Arg138Leu	p.R138L	ENST00000347630	NM_001007230.1	138	cGt/cTt	6/11	1	2	FACETS	0.843	0.795	0.893	0.843	0.795	0.893	CLONAL	1	TRUE	1	0.758371999805793	2		508	888	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306550	41306550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	323	542	1	ENST00000373198.4:c.1109C>A	p.Thr370Lys	p.T370K	ENST00000373198	NM_133170.3	370	aCg/aAg	7/32	1	2	FACETS	0.942	0.893	0.993	0.942	0.893	0.993	CLONAL	1	TRUE	1	0.758371999805793	2		543	904	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456486	189456486	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	252	381	0	ENST00000264731.3:c.247G>C	p.Asp83His	p.D83H	ENST00000264731	NM_003722.4	83	Gat/Cat	3/14	0.758371999805793	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.758371999805793	1		381	407	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157583	106157583	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs914950397	NA	P-0039419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	153	317	0	ENST00000380013.4:c.2484C>A	p.Cys828Ter	p.C828*	ENST00000380013	NM_001127208.2	828	tgC/tgA	3/11	1	2	FACETS	0.925	0.855	0.998	0.925	0.855	0.998	CLONAL	1	TRUE	1	0.758371999805793	2		317	436	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925325	114925325	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1255971088	NA	P-0039419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	34	470	0	ENST00000543371.1:c.1403A>G	p.Lys468Arg	p.K468R	ENST00000543371	NM_001198531.1	468	aAg/aGg	14/14	0.758371999805793	1	FACETS	0.122	0.099	0.147	0.122	0.099	0.147	SUBCLONAL	1	TRUE	0	0.758371999805793	1		470	458	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	27	395	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.155005403923108	3	FACETS	0.815	0.648	1	0.408	0.324	0.504	CLONAL	1	TRUE	1	0.16	3		395	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0039424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	23	932	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.71	0.553	0.892	0.71	0.553	0.892	SUBCLONAL	1	TRUE	1	0.16	2		932	405	SUCCESS
APC	324	MSKCC	GRCh37	5	112175891	112175891	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	15	172	0	ENST00000257430.4:c.4602del	p.Asn1535MetfsTer30	p.N1535Mfs*30	ENST00000257430	NM_000038.5	1534	Ggg/gg	16/16	1	2	FACETS	0.966	0.709	1	0.966	0.709	1	CLONAL	1	TRUE	1	0.16	2		172	194	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411678	63411678	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	33	332	0	ENST00000330258.3:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000330258	NM_152424.3	497	Cga/Tga	2/2	0.3	2	FACETS	1	0.932	1	0.67	0.547	0.807	CLONAL	1	TRUE	0	0.16	2		332	308	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591925	48591925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660556	NA	P-0039424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	18	335	0	ENST00000342988.3:c.1088G>A	p.Cys363Tyr	p.C363Y	ENST00000342988	NM_005359.5	363	tGt/tAt	9/12	1	2	FACETS	0.65	0.489	0.842	0.65	0.489	0.842	SUBCLONAL	1	TRUE	1	0.16	2		335	346	SUCCESS
H3C13	653604	MSKCC	GRCh37	1	149784845	149784845	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	17	223	0	ENST00000331491.1:c.392T>C	p.Ile131Thr	p.I131T	ENST00000331491	NM_001123375.2	131	aTc/aCc	1/1	1	2	FACETS	0.979	0.733	1	0.979	0.733	1	CLONAL	1	TRUE	1	0.16	2		223	217	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0039432-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	121	542	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.838	0.757	0.922	0.838	0.757	0.922	CLONAL	1	TRUE	1	0.396828106068169	2		542	728	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039432-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	235	816	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.396828106068169	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.396828106068169	1		816	816	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028657	12028657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039432-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	112	375	1	ENST00000353533.5:c.860G>A	p.Arg287His	p.R287H	ENST00000353533	NM_003010.3	287	cGc/cAc	8/11	0.392031046784354	1	FACETS	0.868	0.784	0.957	0.868	0.784	0.957	CLONAL	1	TRUE	0	0.396828106068169	1		376	521	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070577	67070577	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039432-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	72	241	0	ENST00000412916.2:c.201G>T	p.Gln67His	p.Q67H	ENST00000412916		67	caG/caT	3/6	0.396828106068169	1	FACETS	0.892	0.786	1	0.892	0.786	1	CLONAL	1	TRUE	0	0.396828106068169	1		241	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0039467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	271	761	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.873626418695712	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.873626418695712	1		764	341	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951156	48951156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060503078	NA	P-0039467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	98	377	0	ENST00000267163.4:c.1318G>A	p.Glu440Lys	p.E440K	ENST00000267163	NM_000321.2	440	Gaa/Aaa	13/27	1	2	FACETS	0.801	0.725	0.88	0.801	0.725	0.88	CLONAL	1	TRUE	1	0.873626418695712	2		377	280	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857968	9857968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779746293	NA	P-0039467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	109	864	3	ENST00000330684.3:c.3433G>A	p.Val1145Met	p.V1145M	ENST00000330684	NM_001134407.1	1145	Gtg/Atg	13/13	0.609767292039032	1	FACETS	0.366	0.331	0.402	0.366	0.331	0.402	SUBCLONAL	1	TRUE	0	0.873626418695712	1		867	384	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420871	49420871	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555185969	NA	P-0039467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	261	841	0	ENST00000301067.7:c.14878C>T	p.Arg4960Ter	p.R4960*	ENST00000301067	NM_003482.3	4960	Cga/Tga	48/54	0.351872640579314	3	FACETS	0.793	0.751	0.836	0.793	0.751	0.836	INDETERMINATE	2	TRUE	1	0.873626418695712	3		841	541	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390766	139390766	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	303	1270	0	ENST00000277541.6:c.7425del	p.Val2476Ter	p.V2476*	ENST00000277541	NM_017617.3	2475	ccC/cc	34/34	0.236109795870706	1	FACETS	0.599	0.569	0.629	0.599	0.569	0.629	INDETERMINATE	1	TRUE	0	0.873626418695712	1		1270	652	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732806	44732807	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	226	620	0	ENST00000377967.4:c.10dup	p.Cys4LeufsTer17	p.C4Lfs*17	ENST00000377967	NM_021140.2	3	-/T	1/29	0.873626418695712	1	FACETS	0.952	0.913	0.99	0.952	0.913	0.99	CLONAL	1	TRUE	0	0.873626418695712	1		620	306	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289244	33289244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200370559	NA	P-0039494-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	440	571	3	ENST00000374542.5:c.308C>T	p.Ala103Val	p.A103V	ENST00000374542	NM_001141970.1	103	gCg/gTg	3/8	1	2	FACETS	0.999	0.958	1	0.999	0.958	1	CLONAL	1	TRUE	1	0.935242439503339	2		574	942	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725073	47725082	+	frameshift_variant	Frame_Shift_Del	DEL	TCTCGGGGGC	TCTCGGGGGC	-	novel	NA	P-0039494-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	652	827	0	ENST00000449228.1:c.662_671del	p.Ser221MetfsTer5	p.S221Mfs*5	ENST00000449228	NM_001127240.2	221	aGCCCCCGAGAt/at	4/4	1	2	FACETS	0.977	0.943	1	0.977	0.943	1	CLONAL	1	TRUE	1	0.935242439503339	2		827	1427	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127792	47127793	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039494-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	340	409	0	ENST00000409792.3:c.5289dup	p.Gln1764ThrfsTer25	p.Q1764Tfs*25	ENST00000409792	NM_014159.6	1763	-/A	11/21	0.935242439503339	1	FACETS	0.982	0.958	1	0.982	0.958	1	CLONAL	1	TRUE	0	0.935242439503339	1		409	394	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436817	52436848	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTCCTCCTTGAGGCACGCCTCATAGTTTGC	ACCTCCTCCTTGAGGCACGCCTCATAGTTTGC	GGT	novel	NA	P-0039494-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	276	712	2	ENST00000460680.1:c.1930_1961delinsACC	p.Ala644ThrfsTer10	p.A644Tfs*10	ENST00000460680	NM_004656.3	644	GCAAACTATGAGGCGTGCCTCAAGGAGGAGGTa/ACCa	15/17	0.935242439503339	1	FACETS	0.8	0.768	0.83	0.8	0.768	0.83	SUBCLONAL	1	TRUE	0	0.935242439503339	1		714	393	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864049	97864049	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039494-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	443	585	0	ENST00000289081.3:c.1617A>C	p.Glu539Asp	p.E539D	ENST00000289081	NM_000136.2	539	gaA/gaC	15/15	1	2	FACETS	0.988	0.947	1	0.988	0.947	1	CLONAL	1	TRUE	1	0.935242439503339	2		585	959	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0039513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	673	534	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.938716500660723	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.938716500660723	1		535	748	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882959	89882959	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs761341952	NA	P-0039513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	316	292	0	ENST00000389301.3:c.65G>A	p.Trp22Ter	p.W22*	ENST00000389301	NM_000135.2	22	tGg/tAg	1/43	0.168245250284138	3	FACETS	1	0.994	1	0.708	0.673	0.743	INDETERMINATE	1	TRUE	1	0.938716500660723	3		292	699	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983065	201983067	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0039513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1329	794	1020	0	ENST00000359651.3:c.915_917del	p.Phe305del	p.F305del	ENST00000359651		305	tTCCtg/ttg	7/8	0.572229948230876	3	FACETS	1	0.995	1	0.585	0.566	0.605	CLONAL	1	TRUE	1	0.938716500660723	3		1020	2123	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923483	9923483	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1555492804	NA	P-0039513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	415	614	0	ENST00000330684.3:c.1804G>T	p.Gly602Ter	p.G602*	ENST00000330684	NM_001134407.1	602	Gga/Tga	9/13	0.168245250284138	3	FACETS	1	0.996	1	0.702	0.672	0.733	INDETERMINATE	1	TRUE	1	0.938716500660723	3		614	925	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584607	48584607	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0039513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	310	466	0	ENST00000342988.3:c.780C>G	p.Tyr260Ter	p.Y260*	ENST00000342988	NM_005359.5	260	taC/taG	6/12	0.938716500660723	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.938716500660723	1		466	348	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568593	41568593	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	402	651	0	ENST00000263253.7:c.4543G>C	p.Glu1515Gln	p.E1515Q	ENST00000263253	NM_001429.3	1515	Gaa/Caa	28/31	0.243728046628139	6	FACETS	0.819	0.778	0.861			1	INDETERMINATE	2	TRUE	NA	0.938716500660723	6		651	1504	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0039558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	32	498	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.765410915249376	2		498	74	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0039558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	18	394	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.765410915249376	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.765410915249376	1		394	23	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0039558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	18	243	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.23929792055446	5	FACETS	0.864	0.69	1	0.864	0.69	1	INDETERMINATE	3	TRUE	2	0.765410915249376	5		243	39	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123722	11123722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263140481	NA	P-0039558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	28	598	0	ENST00000358026.2:c.2372C>T	p.Ala791Val	p.A791V	ENST00000358026	NM_001128849.1	791	gCg/gTg	16/36	0.318629452269932	4	FACETS	0.964	0.803	1	0.964	0.803	1	INDETERMINATE	2	TRUE	2	0.765410915249376	4		598	67	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0039558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	32	875	4	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	0.643381755661247	1	FACETS	0.374	0.308	0.445	0.374	0.308	0.445	SUBCLONAL	1	TRUE	0	0.765410915249376	1		879	138	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11210194	11210194	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs995332350	NA	P-0039558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	14	525	0	ENST00000361445.4:c.4559C>T	p.Ala1520Val	p.A1520V	ENST00000361445	NM_004958.3	1520	gCa/gTa	31/58	0.153437144937125	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.765410915249376	0		525	50	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	16	380	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	0.153437144937125	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.765410915249376	0		380	53	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0039558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	11	354	1	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	0.153437144937125	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.765410915249376	0		355	49	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874164	155874164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1213963509	NA	P-0039558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	12	674	0	ENST00000368323.3:c.367C>T	p.Arg123Cys	p.R123C	ENST00000368323	NM_006912.5	123	Cgt/Tgt	5/6	0.223336071592005	1	FACETS	0.293	0.21	0.391	0.293	0.21	0.391	INDETERMINATE	1	TRUE	0	0.765410915249376	1		674	66	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156107	119156107	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	31	646	0	ENST00000264033.4:c.1772T>C	p.Leu591Pro	p.L591P	ENST00000264033	NM_005188.3	591	cTg/cCg	11/16	1	2	FACETS	0.953	0.796	1	0.953	0.796	1	CLONAL	1	TRUE	1	0.765410915249376	2		646	85	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219536	133219536	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	170	698	0	ENST00000320574.5:c.4598A>G	p.Glu1533Gly	p.E1533G	ENST00000320574	NM_006231.2	1533	gAg/gGg	36/49	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.765410915249376	2		698	426	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219838	133219838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142508245	NA	P-0039558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	141	621	0	ENST00000320574.5:c.4523G>A	p.Arg1508His	p.R1508H	ENST00000320574	NM_006231.2	1508	cGc/cAc	35/49	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.765410915249376	2		621	308	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944594	32944594	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	29	528	0	ENST00000380152.3:c.8387C>A	p.Pro2796His	p.P2796H	ENST00000380152		2796	cCt/cAt	19/27	0.765410915249376	1	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	0	0.765410915249376	1		528	45	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95573958	95573958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1256068472	NA	P-0039558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	50	269	0	ENST00000393063.1:c.2791G>A	p.Val931Ile	p.V931I	ENST00000393063	NM_030621.3	931	Gtt/Att	18/28	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.765410915249376	2		269	115	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273878	10273878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	204	688	1	ENST00000330684.3:c.391G>A	p.Ala131Thr	p.A131T	ENST00000330684	NM_001134407.1	131	Gca/Aca	2/13	0.458788599703088	3	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.765410915249376	3		689	493	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831069	72831069	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	100	455	0	ENST00000268489.5:c.5512C>T	p.Gln1838Ter	p.Q1838*	ENST00000268489	NM_006885.3	1838	Cag/Tag	9/10	0.153437144937125	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.765410915249376	0		455	220	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436149	56436149	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	192	724	2	ENST00000407977.2:c.988C>T	p.Arg330Ter	p.R330*	ENST00000407977		330	Cga/Tga	9/10	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.765410915249376	2		726	497	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	96	510	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	0.765410915249376	1	FACETS	0.665	0.603	0.727	0.665	0.603	0.727	SUBCLONAL	1	TRUE	0	0.765410915249376	1		510	233	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940111	49940112	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760002850	NA	P-0039558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	199	660	0	ENST00000296474.3:c.931dup	p.Ala311GlyfsTer26	p.A311Gfs*26	ENST00000296474	NM_002447.2	311	gcc/gGcc	1/20	0.223336071592005	1	FACETS	0.602	0.562	0.643	0.602	0.562	0.643	INDETERMINATE	1	TRUE	0	0.765410915249376	1		660	533	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166497	32166497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	22	632	0	ENST00000375023.3:c.4546C>T	p.Pro1516Ser	p.P1516S	ENST00000375023	NM_004557.3	1516	Cca/Tca	25/30	0.223336071592005	1	FACETS	0.094	0.072	0.119	0.094	0.072	0.119	INDETERMINATE	1	TRUE	0	0.765410915249376	1		632	377	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527516	157527516	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	10	560	0	ENST00000346085.5:c.5241T>G	p.Asp1747Glu	p.D1747E	ENST00000346085	NM_020732.3	1747	gaT/gaG	20/20	1	2	FACETS	0.223	0.152	0.312	0.223	0.152	0.312	SUBCLONAL	1	TRUE	1	0.765410915249376	2		560	117	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874463	151874463	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	15	422	0	ENST00000262189.6:c.8075A>G	p.Asp2692Gly	p.D2692G	ENST00000262189	NM_170606.2	2692	gAt/gGt	38/59	0.223336071592005	1	FACETS	0.931	0.744	1	0.931	0.744	1	INDETERMINATE	1	TRUE	0	0.765410915249376	1		422	26	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426094	47426094	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	44	405	0	ENST00000377045.4:c.619del	p.Leu207TyrfsTer85	p.L207Yfs*85	ENST00000377045	NM_001654.4	205	gCc/gc	7/16	0.443459846054867	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	NA	0.765410915249376	0		405	61	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411366	63411366	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	33	340	0	ENST00000330258.3:c.1801C>T	p.Arg601Ter	p.R601*	ENST00000330258	NM_152424.3	601	Cga/Tga	2/2	0.443459846054867	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	NA	0.765410915249376	0		340	39	SUCCESS
AR	367	MSKCC	GRCh37	X	66937372	66937372	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	30	273	0	ENST00000374690.3:c.2226G>T	p.Trp742Cys	p.W742C	ENST00000374690	NM_000044.3	742	tgG/tgT	5/8	0.443459846054867	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	NA	0.765410915249376	0		273	36	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633500	3633500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199969428	NA	P-0039567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	356	663	0	ENST00000294008.3:c.4751G>A	p.Arg1584His	p.R1584H	ENST00000294008	NM_032444.2	1584	cGc/cAc	14/15	1	2	FACETS	0.909	0.865	0.953	0.909	0.865	0.953	CLONAL	1	TRUE	1	0.919331538956341	2		663	852	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074313	30074313	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0039567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	201	329	0	ENST00000338641.4:c.1574+1G>T		p.X525_splice	ENST00000338641	NM_000268.3	525			0.919331538956341	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.919331538956341	1		329	226	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437449	52437462	+	frameshift_variant	Frame_Shift_Del	DEL	CTCAGCACCCCATC	CTCAGCACCCCATC	-	novel	NA	P-0039567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	252	546	0	ENST00000460680.1:c.1699_1712del	p.Asp567SerfsTer71	p.D567Sfs*71	ENST00000460680	NM_004656.3	567	GATGGGGTGCTGAGt/t	13/17	1	2	FACETS	0.905	0.853	0.957	0.905	0.853	0.957	CLONAL	1	TRUE	1	0.919331538956341	2		546	606	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442509	52442509	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	339	446	0	ENST00000460680.1:c.236del	p.Asn79ThrfsTer8	p.N79Tfs*8	ENST00000460680	NM_004656.3	79	aAc/ac	4/17	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.919331538956341	2		446	731	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	33	759	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.22	0.179	0.267	0.22	0.179	0.267	SUBCLONAL	1	TRUE	1	0.544103500758004	2		760	551	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	216	395	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.544103500758004	2		395	632	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0039606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	128	318	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.544103500758004	2		318	435	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524215	18524215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769408892	NA	P-0039606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	60	512	0	ENST00000266497.5:c.1727C>T	p.Ala576Val	p.A576V	ENST00000266497		576	gCg/gTg	11/31	1	2	FACETS	0.273	0.234	0.315	0.273	0.234	0.315	SUBCLONAL	1	TRUE	1	0.544103500758004	2		512	808	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864800	117864800	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs905123790	NA	P-0039606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	165	348	0	ENST00000297338.2:c.1309C>T	p.Arg437Cys	p.R437C	ENST00000297338	NM_006265.2	437	Cgt/Tgt	10/14	0.544103500758004	3	FACETS	1	0.974	1	0.565	0.52	0.611	CLONAL	1	TRUE	1	0.544103500758004	3		348	683	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910883	114910883	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1477809102	NA	P-0039606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	177	463	0	ENST00000543371.1:c.1001+1G>A		p.X334_splice	ENST00000543371	NM_001198531.1	334			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.544103500758004	2		463	571	SUCCESS
APC	324	MSKCC	GRCh37	5	112175641	112175641	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	184	368	0	ENST00000257430.4:c.4350del	p.Glu1451LysfsTer22	p.E1451Kfs*22	ENST00000257430	NM_000038.5	1450	cgA/cg	16/16	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.544103500758004	2		368	460	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862766	9862766	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746978701	NA	P-0039606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	285	667	1	ENST00000330684.3:c.2537G>A	p.Arg846His	p.R846H	ENST00000330684	NM_001134407.1	846	cGc/cAc	12/13	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.544103500758004	2		668	882	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186839	108186839	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1565500074	NA	P-0039606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	121	328	0	ENST00000278616.4:c.6197A>G	p.Gln2066Arg	p.Q2066R	ENST00000278616	NM_000051.3	2066	cAg/cGg	42/63	0.544103500758004	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.544103500758004	1		328	322	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368252	45368252	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	24	438	0	ENST00000262160.6:c.1350C>A	p.Asp450Glu	p.D450E	ENST00000262160	NM_005901.5	450	gaC/gaA	11/11	0.544103500758004	1	FACETS	0.138	0.108	0.174	0.138	0.108	0.174	SUBCLONAL	1	TRUE	0	0.544103500758004	1		438	464	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553245	106553245	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	189	616	0	ENST00000369096.4:c.1210C>G	p.Pro404Ala	p.P404A	ENST00000369096	NM_001198.3	404	Ccc/Gcc	5/7	1	2	FACETS	0.862	0.798	0.928	0.862	0.798	0.928	CLONAL	1	TRUE	1	0.544103500758004	2		616	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs530941076	NA	P-0039702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	124	777	0	ENST00000269305.4:c.658T>C	p.Tyr220His	p.Y220H	ENST00000269305	NM_001126112.2	220	Tat/Cat	6/11	0.389947897700608	1	FACETS	0.84	0.762	0.922	0.84	0.762	0.922	CLONAL	1	TRUE	0	0.390076580559106	1		777	609	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771679	135771679	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	60	620	0	ENST00000298552.3:c.3438C>G	p.Asp1146Glu	p.D1146E	ENST00000298552	NM_001162426.1	1146	gaC/gaG	23/23	0.390076580559106	1	FACETS	0.445	0.383	0.512	0.445	0.383	0.512	SUBCLONAL	1	TRUE	0	0.390076580559106	1		620	557	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115873	8115874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0039706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	217	688	0	ENST00000346208.3:c.1220dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tCcg	6/6	1	2	FACETS	0.889	0.829	0.952	0.889	0.829	0.952	CLONAL	1	TRUE	1	0.590741513232714	2		688	826	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729515	41729515	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	193	681	0	ENST00000242208.4:c.1014G>C	p.Trp338Cys	p.W338C	ENST00000242208	NM_002192.2	338	tgG/tgC	3/3	1	2	FACETS	0.996	0.926	1	0.996	0.926	1	CLONAL	1	TRUE	1	0.590741513232714	2		681	656	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233525	69233525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	153	369	0	ENST00000462284.1:c.1390C>T	p.Leu464Phe	p.L464F	ENST00000462284	NM_002392.5	464	Ctt/Ttt	11/11	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.590741513232714	2		369	508	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32969019	32969020	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0039706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	156	371	0	ENST00000380152.3:c.9452_9453del	p.Lys3151ArgfsTer16	p.K3151Rfs*16	ENST00000380152		3150	ccAAaa/ccaa	25/27	0.590741513232714	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.590741513232714	1		371	348	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828423	72828423	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	205	626	0	ENST00000268489.5:c.8158T>C	p.Phe2720Leu	p.F2720L	ENST00000268489	NM_006885.3	2720	Ttc/Ctc	9/10	1	2	FACETS	0.924	0.86	0.99	0.924	0.86	0.99	CLONAL	1	TRUE	1	0.590741513232714	2		626	751	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934231	49934231	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768326110	NA	P-0039706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	260	870	0	ENST00000296474.3:c.2276C>A	p.Pro759His	p.P759H	ENST00000296474	NM_002447.2	759	cCt/cAt	8/20	0.590741513232714	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.590741513232714	1		870	579	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026111	71026111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	186	395	0	ENST00000318789.4:c.1511G>A	p.Arg504His	p.R504H	ENST00000318789	NM_032682.5	504	cGc/cAc	17/21	1	2	FACETS	0.911	0.845	0.98	0.911	0.845	0.98	CLONAL	1	TRUE	1	0.590741513232714	2		395	691	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680291	30680291	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	259	842	0	ENST00000376406.3:c.1428G>C	p.Lys476Asn	p.K476N	ENST00000376406	NM_014641.2	476	aaG/aaC	5/15	1	2	FACETS	0.972	0.912	1	0.972	0.912	1	CLONAL	1	TRUE	1	0.590741513232714	2		842	902	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411920	63411920	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1460320166	NA	P-0039706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	316	1091	0	ENST00000330258.3:c.1247A>G	p.Tyr416Cys	p.Y416C	ENST00000330258	NM_152424.3	416	tAt/tGt	2/2	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.590741513232714	2		1091	1064	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	88	759	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.76	0.683	0.84	0.76	0.683	0.84	SUBCLONAL	1	TRUE	1	0.87667854961775	2		760	264	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436083	51436083	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	220	465	1	ENST00000262662.1:c.43del	p.Arg15GlyfsTer4	p.R15Gfs*4	ENST00000262662		15	Agg/gg	3/4	1	2	FACETS	0.94	0.883	0.998	0.94	0.883	0.998	CLONAL	1	TRUE	1	0.87667854961775	2		466	534	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266831	198266831	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	265	483	0	ENST00000335508.6:c.2101G>T	p.Val701Phe	p.V701F	ENST00000335508	NM_012433.2	701	Gtt/Ttt	15/25	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.859817899122488	2		483	578	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115737	8115741	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGA	CCAGA	-	novel	NA	P-0039791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	143	426	0	ENST00000346208.3:c.1088_1092del	p.Thr363LysfsTer6	p.T363Kfs*6	ENST00000346208		361	atCCAGAcc/atcc	6/6	1	2	FACETS	0.88	0.812	0.949	0.88	0.812	0.949	CLONAL	1	TRUE	1	0.859817899122488	2		426	378	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777991	3778010	+	frameshift_variant	Frame_Shift_Del	DEL	GTGGAGACTGGACAGGGGCT	GTGGAGACTGGACAGGGGCT	-	novel	NA	P-0039791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1448	358	966	1	ENST00000262367.5:c.7038_7057del	p.Gln2350ProfsTer90	p.Q2350Pfs*90	ENST00000262367	NM_004380.2	2346	ccAGCCCCTGTCCAGTCTCCACgg/ccgg	31/31	0.830732213014523	4	FACETS	0.858	0.81	0.906	0.286	0.27	0.302	CLONAL	1	TRUE	1	0.859817899122488	4		967	1806	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614845	23614845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	194	432	0	ENST00000261584.4:c.3496G>A	p.Gly1166Ser	p.G1166S	ENST00000261584	NM_024675.3	1166	Ggt/Agt	13/13	0.830732213014523	4	FACETS	0.878	0.812	0.946	0.293	0.27	0.316	CLONAL	1	TRUE	1	0.859817899122488	4		432	956	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415523	152415523	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	173	437	0	ENST00000206249.3:c.1373T>C	p.Val458Ala	p.V458A	ENST00000206249	NM_000125.3	458	gTg/gCg	7/8	1	2	FACETS	0.925	0.861	0.99	0.925	0.861	0.99	CLONAL	1	TRUE	1	0.859817899122488	2		437	435	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0039794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	52	358	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.831	0.709	0.963	0.831	0.709	0.963	CLONAL	1	TRUE	1	0.314533191553836	2		358	398	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984848	11984848	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0039794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	128	330	0	ENST00000353533.5:c.393+1G>A		p.X131_splice	ENST00000353533	NM_003010.3	131			0.314533191553836	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.314533191553836	2		330	369	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0039794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	158	408	1	ENST00000304494.5:c.151-1G>A		p.X51_splice	ENST00000304494	NM_000077.4	51			0.314533191553836	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	0	0.314533191553836	2		409	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577561	7577561	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	203	527	0	ENST00000269305.4:c.720T>A	p.Ser240Arg	p.S240R	ENST00000269305	NM_001126112.2	240	agT/agA	7/11	0.314533191553836	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	0	0.314533191553836	2		527	641	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280675	115280675	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	71	394	0	ENST00000438362.2:c.356T>C	p.Val119Ala	p.V119A	ENST00000438362	NM_001242891.1	119	gTa/gCa	4/20	0.314533191553836	3	FACETS	0.971	0.849	1	0.486	0.424	0.552	CLONAL	1	TRUE	1	0.314533191553836	3		394	538	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604650	43604650	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	79	567	0	ENST00000355710.3:c.1235T>C	p.Val412Ala	p.V412A	ENST00000355710	NM_020975.4	412	gTg/gCg	6/20	1	2	FACETS	0.828	0.728	0.934	0.828	0.728	0.934	CLONAL	1	TRUE	1	0.314533191553836	2		567	607	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603127	48603127	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	63	388	0	ENST00000342988.3:c.1428del	p.Gly477GlufsTer2	p.G477Efs*2	ENST00000342988	NM_005359.5	476	ggT/gg	11/12	0.301017066381781	1	FACETS	0.825	0.717	0.943	0.825	0.717	0.943	CLONAL	1	TRUE	0	0.314533191553836	1		388	409	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957521	175957521	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	111	365	0	ENST00000367669.3:c.1875G>T	p.Trp625Cys	p.W625C	ENST00000367669	NM_022457.5	625	tgG/tgT	17/20	0.405326643557088	3	FACETS	0.972	0.875	1	0.486	0.437	0.537	CLONAL	1	NA	1	0.405326643557088	3		365	678	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0039864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	133	436	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.283801566690392	3	FACETS	0.961	0.876	1	0.961	0.876	1	CLONAL	2	TRUE	1	0.283801566690392	3		436	557	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0039864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	48	324	1	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.283801566690392	2		325	306	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0039864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	44	165	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.698	0.586	0.822	0.698	0.586	0.822	SUBCLONAL	1	TRUE	1	0.283801566690392	2		165	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577146	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0039864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	122	744	0	ENST00000269305.4:c.792_794del	p.Leu265del	p.L265del	ENST00000269305	NM_001126112.2	264	ctACTg/ctg	8/11	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.283801566690392	2		744	850	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028610	12028610	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0039864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	88	361	0	ENST00000353533.5:c.814-1G>A		p.X272_splice	ENST00000353533	NM_003010.3	272			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.283801566690392	2		361	447	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662577	227662577	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746823533	NA	P-0039864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	137	676	0	ENST00000305123.5:c.878C>T	p.Pro293Leu	p.P293L	ENST00000305123	NM_005544.2	293	cCg/cTg	1/2	0.21187789612429	3	FACETS	1	0.984	1	0.697	0.634	0.763	CLONAL	1	TRUE	1	0.283801566690392	3		676	791	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099479	27099479	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0039886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	39	376	0	ENST00000324856.7:c.3715+1G>T		p.X1239_splice	ENST00000324856	NM_006015.4	1239			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		376	692	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	69	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.303903307556775	4	FACETS	1	0.973	1	0.743	0.649	0.844	CLONAL	1	TRUE	2	0.26	4		334	450	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	70	636	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	0.256232673830043	4	FACETS	0.852	0.747	0.965	0.852	0.747	0.965	CLONAL	2	TRUE	2	0.26	4		637	398	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	38	725	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.182187634597059	3	FACETS	1	0.856	1	0.518	0.429	0.616	CLONAL	1	TRUE	1	0.26	3		732	319	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	37	495	1	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.985	0.816	1	0.985	0.816	1	CLONAL	1	TRUE	1	0.26	2		496	289	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	29	480	4	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.182187634597059	3	FACETS	1	0.939	1	0.733	0.594	0.887	CLONAL	1	TRUE	1	0.26	3		484	172	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933726	36933726	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	43	805	0	ENST00000361632.4:c.1673C>T	p.Pro558Leu	p.P558L	ENST00000361632		558	cCc/cTc	12/16	0.256232673830043	4	FACETS	1	0.958	1	0.747	0.629	0.876	CLONAL	1	TRUE	2	0.26	4		805	279	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733513	85733513	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs387906350	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	22	471	4	ENST00000370580.1:c.499del	p.Ser167LeufsTer6	p.S167Lfs*6	ENST00000370580	NM_003921.4	167	Tct/ct	3/3	0.256232673830043	4	FACETS	0.618	0.479	0.78	0.309	0.239	0.39	SUBCLONAL	1	TRUE	2	0.26	4		475	345	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263415	123263415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757125418	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	28	569	0	ENST00000358487.5:c.1328C>T	p.Pro443Leu	p.P443L	ENST00000358487	NM_000141.4	443	cCg/cTg	10/18	0.182187634597059	3	FACETS	0.763	0.611	0.936	0.381	0.305	0.468	CLONAL	1	TRUE	1	0.26	3		569	319	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136031	64136031	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	47	749	1	ENST00000334205.4:c.1292G>A	p.Arg431His	p.R431H	ENST00000334205	NM_003942.2	431	cGc/cAc	11/17	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.26	2		750	269	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138824	64138824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	35	779	1	ENST00000334205.4:c.2191C>T	p.Arg731Trp	p.R731W	ENST00000334205	NM_003942.2	731	Cgg/Tgg	17/17	1	2	FACETS	0.975	0.803	1	0.975	0.803	1	CLONAL	1	TRUE	1	0.26	2		780	276	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572546	64572546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555164188	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	33	731	0	ENST00000312049.6:c.1310C>T	p.Ala437Val	p.A437V	ENST00000312049	NM_130799.2	437	gCc/gTc	9/10	0.303866951809773	9	FACETS	1	0.896	1			1	CLONAL	1	TRUE	NA	0.26	9		731	420	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944191	71944191	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	23	621	0	ENST00000298229.2:c.2024A>T	p.Lys675Met	p.K675M	ENST00000298229	NM_001567.3	675	aAg/aTg	17/28	0.222045692086313	4	FACETS	0.829	0.647	1	0.414	0.323	0.519	CLONAL	1	TRUE	2	0.26	4		621	269	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	38	461	2	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	0.222045692086313	4	FACETS	0.767	0.639	0.909	0.767	0.639	0.909	CLONAL	2	TRUE	2	0.26	4		463	240	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417050	417050	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199716528	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	14	384	0	ENST00000399788.2:c.3500G>A	p.Arg1167His	p.R1167H	ENST00000399788	NM_001042603.1	1167	cGc/cAc	23/28	0.269121110825488	3	FACETS	0.621	0.45	0.827			1	SUBCLONAL	1	TRUE	NA	0.26	3		384	196	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425931	49425931	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	52	820	0	ENST00000301067.7:c.12557C>A	p.Pro4186His	p.P4186H	ENST00000301067	NM_003482.3	4186	cCt/cAt	39/54	0.303903307556775	4	FACETS	1	0.96	1	0.696	0.595	0.806	CLONAL	1	TRUE	2	0.26	4		820	362	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225574	133225574	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	79	755	1	ENST00000320574.5:c.4090del	p.Arg1364ValfsTer5	p.R1364Vfs*5	ENST00000320574	NM_006231.2	1364	Cgt/gt	32/49	0.220080559234093	1	FACETS	0.998	0.889	1	1	0.985	1	CLONAL	2	TRUE	0	0.26	1		756	265	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134102	41134102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218589643	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	48	503	0	ENST00000379561.5:c.1526G>A	p.Ser509Asn	p.S509N	ENST00000379561	NM_002015.3	509	aGc/aAc	2/3	0.303903307556775	4	FACETS	1	0.952	1	0.667	0.566	0.777	CLONAL	1	TRUE	2	0.26	4		503	349	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988284	41988284	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	37	572	0	ENST00000219905.7:c.1076G>T	p.Ser359Ile	p.S359I	ENST00000219905	NM_001164273.1	359	aGc/aTc	3/24	1	2	FACETS	0.862	0.713	1	0.862	0.713	1	CLONAL	1	TRUE	1	0.26	2		572	330	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134972	2134972	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	17	848	0	ENST00000219476.3:c.4514A>G	p.Tyr1505Cys	p.Y1505C	ENST00000219476	NM_000548.3	1505	tAc/tGc	35/42	1	2	FACETS	0.495	0.37	0.644	0.495	0.37	0.644	SUBCLONAL	1	TRUE	1	0.26	2		848	264	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781901	3781903	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs751071525	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	57	644	0	ENST00000262367.5:c.4764_4766del	p.Lys1588del	p.K1588del	ENST00000262367	NM_004380.2	1588	aaGAAc/aac	29/31	1	2	FACETS	0.97	0.843	1	1	0.978	1	CLONAL	2	TRUE	1	0.26	2		644	226	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900384	3900384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146887252	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	25	702	0	ENST00000262367.5:c.712G>A	p.Val238Met	p.V238M	ENST00000262367	NM_004380.2	238	Gtg/Atg	2/31	1	2	FACETS	0.626	0.494	0.778	0.626	0.494	0.778	SUBCLONAL	1	TRUE	1	0.26	2		702	307	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943716	9943716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1351978664	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	64	839	0	ENST00000330684.3:c.1225G>A	p.Val409Ile	p.V409I	ENST00000330684	NM_001134407.1	409	Gtc/Atc	5/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.26	2		839	349	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943779	9943779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1211198789	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	70	640	0	ENST00000330684.3:c.1162G>A	p.Ala388Thr	p.A388T	ENST00000330684	NM_001134407.1	388	Gcc/Acc	5/13	1	2	FACETS	0.928	0.817	1	1	0.981	1	CLONAL	2	TRUE	1	0.26	2		640	290	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828228	50828228	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	33	499	0	ENST00000398568.2:c.2566A>C	p.Met856Leu	p.M856L	ENST00000398568	NM_001042412.1	856	Atg/Ctg	17/18	1	2	FACETS	0.992	0.812	1	0.992	0.812	1	CLONAL	1	TRUE	1	0.26	2		499	256	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	36	843	10	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	0.182187634597059	3	FACETS	1	0.852	1	0.518	0.427	0.619	CLONAL	1	TRUE	1	0.26	3		853	302	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435732	56435732	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs775121749	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	45	618	0	ENST00000407977.2:c.1405G>T	p.Gly469Trp	p.G469W	ENST00000407977		469	Ggg/Tgg	9/10	0.182187634597059	3	FACETS	1	0.937	1	0.615	0.519	0.72	CLONAL	1	TRUE	1	0.26	3		618	318	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526472	66526472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	26	505	1	ENST00000358598.2:c.1028G>A	p.Gly343Asp	p.G343D	ENST00000358598	NM_212471.2	343	gGc/gAc	11/11	0.182187634597059	3	FACETS	0.483	0.382	0.599	0.241	0.191	0.3	SUBCLONAL	1	TRUE	1	0.26	3		506	468	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119780	70119781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	24	709	0	ENST00000245479.2:c.782_783insT	p.Glu261AspfsTer35	p.E261Dfs*35	ENST00000245479	NM_000346.3	261	gag/gaTg	3/3	0.182187634597059	3	FACETS	0.825	0.648	1	0.412	0.324	0.513	CLONAL	1	TRUE	1	0.26	3		709	253	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1627411	1627411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377688933	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	58	782	3	ENST00000344749.5:c.313C>T	p.Arg105Trp	p.R105W	ENST00000344749	NM_001136139.2	105	Cgg/Tgg	6/19	NA	2	FACETS	0.868	0.753	0.99			1	INDETERMINATE	2	TRUE	NA	0.26	2		785	257	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626892	14626892	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	92	701	0	ENST00000254322.2:c.883C>T	p.Arg295Ter	p.R295*	ENST00000254322	NM_006145.1	295	Cga/Tga	3/3	0.303866951809773	13	FACETS	1	0.968	1			1	CLONAL	2	TRUE	NA	0.26	13		701	690	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350553	15350553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	19	772	4	ENST00000263377.2:c.3362G>A	p.Arg1121His	p.R1121H	ENST00000263377	NM_058243.2	1121	cGc/cAc	16/20	1	2	FACETS	0.479	0.363	0.615	0.479	0.363	0.615	SUBCLONAL	1	TRUE	1	0.26	2		776	305	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375538	15375538	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	57	858	0	ENST00000263377.2:c.889C>A	p.Pro297Thr	p.P297T	ENST00000263377	NM_058243.2	297	Ccc/Acc	6/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.26	2		858	344	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228979	36228979	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555734923	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	42	746	1	ENST00000222270.7:c.7759C>T	p.Arg2587Ter	p.R2587*	ENST00000222270	NM_014727.1	2587	Cga/Tga	36/37	1	2	FACETS	0.739	0.618	0.874	0.739	0.618	0.874	SUBCLONAL	1	TRUE	1	0.26	2		747	437	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	57	705	6	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.26	2		711	306	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982440	25982440	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	80	400	0	ENST00000435504.4:c.850C>T	p.Arg284Ter	p.R284*	ENST00000435504		284	Cga/Tga	9/13	0.303903307556775	1	FACETS	0.872	0.775	0.973	1	0.983	1	CLONAL	2	TRUE	0	0.26	1		400	307	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027019	48027019	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	36	460	0	ENST00000234420.5:c.1897A>C	p.Thr633Pro	p.T633P	ENST00000234420	NM_000179.2	633	Act/Cct	4/10	1	2	FACETS	0.787	0.655	0.931	1	0.956	1	CLONAL	2	TRUE	1	0.26	2		460	176	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190708721	190708721	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	53	482	0	ENST00000441310.2:c.614A>G	p.Asp205Gly	p.D205G	ENST00000441310	NM_000534.4	205	gAt/gGt	6/13	0.12875758955603	4	FACETS	1	0.91	1	1	0.91	1	INDETERMINATE	2	TRUE	2	0.26	4		482	239	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661836	227661836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs577407654	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	23	968	3	ENST00000305123.5:c.1619C>T	p.Pro540Leu	p.P540L	ENST00000305123	NM_005544.2	540	cCg/cTg	1/2	0.12875758955603	4	FACETS	0.581	0.452	0.73	0.29	0.226	0.365	INDETERMINATE	1	TRUE	2	0.26	4		971	384	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023375	31023375	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	23	574	0	ENST00000375687.4:c.2860G>A	p.Asp954Asn	p.D954N	ENST00000375687	NM_015338.5	954	Gac/Aac	13/13	0.12875758955603	4	FACETS	0.937	0.733	1	0.468	0.366	0.586	INDETERMINATE	1	TRUE	2	0.26	4		574	238	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031762	36031762	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913314	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	41	613	0	ENST00000358208.4:c.1591C>T	p.Gln531Ter	p.Q531*	ENST00000358208		531	Cag/Tag	12/12	0.228892224385424	0	FACETS	1	0.89	1			1	CLONAL	1	TRUE	0	0.26	0		613	217	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031768	36031768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754707860	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	18	574	1	ENST00000358208.4:c.1597G>A	p.Gly533Arg	p.G533R	ENST00000358208		533	Ggg/Agg	12/12	0.228892224385424	0	FACETS	0.483	0.365	0.622			1	SUBCLONAL	1	TRUE	0	0.26	0		575	212	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306584	41306584	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	29	717	0	ENST00000373198.4:c.1075C>T	p.Arg359Ter	p.R359*	ENST00000373198	NM_133170.3	359	Cga/Tga	7/32	0.228892224385424	0	FACETS	0.855	0.692	1			1	CLONAL	1	TRUE	0	0.26	0		717	193	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385164	41385164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	17	779	1	ENST00000373198.4:c.797G>A	p.Arg266His	p.R266H	ENST00000373198	NM_133170.3	266	cGc/cAc	6/32	0.228892224385424	0	FACETS	0.389	0.29	0.505			1	SUBCLONAL	1	TRUE	0	0.26	0		780	249	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164486	36164486	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	60	549	0	ENST00000300305.3:c.1389del	p.Thr464ProfsTer130	p.T464Pfs*130	ENST00000300305		463	ccC/cc	8/8	0.12875758955603	4	FACETS	1	0.945	1	1	0.945	1	INDETERMINATE	2	TRUE	2	0.26	4		549	250	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656878	45656878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1306205252	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	63	705	1	ENST00000407780.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000407780	NM_001283052.1	93	cGg/cAg	3/7	0.12875758955603	4	FACETS	0.803	0.698	0.917	0.803	0.698	0.917	INDETERMINATE	2	TRUE	2	0.26	4		706	380	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127209	22127209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	26	592	1	ENST00000215832.6:c.919G>A	p.Ala307Thr	p.A307T	ENST00000215832	NM_002745.4	307	Gct/Act	7/9	1	2	FACETS	0.813	0.646	1	0.813	0.646	1	CLONAL	1	TRUE	1	0.26	2		593	246	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545790	41545790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749702423	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	48	611	1	ENST00000263253.7:c.2405C>T	p.Pro802Leu	p.P802L	ENST00000263253	NM_001429.3	802	cCg/cTg	14/31	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.26	2		612	327	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566520	41566520	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	21	448	0	ENST00000263253.7:c.4397G>T	p.Trp1466Leu	p.W1466L	ENST00000263253	NM_001429.3	1466	tGg/tTg	27/31	1	2	FACETS	0.651	0.503	0.824	0.651	0.503	0.824	SUBCLONAL	1	TRUE	1	0.26	2		448	248	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	41	462	1	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	0.256232673830043	4	FACETS	1	0.909	1	0.568	0.474	0.671	CLONAL	1	TRUE	2	0.26	4		463	350	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165213	47165213	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	11	298	0	ENST00000409792.3:c.913del	p.Thr305GlnfsTer35	p.T305Qfs*35	ENST00000409792	NM_014159.6	305	Aca/ca	3/21	0.256232673830043	4	FACETS	0.74	0.513	1	0.37	0.256	0.51	CLONAL	1	TRUE	2	0.26	4		298	144	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437608	52437608	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs535796204	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	84	823	1	ENST00000460680.1:c.1553G>A	p.Arg518Gln	p.R518Q	ENST00000460680	NM_004656.3	518	cGg/cAg	13/17	0.256232673830043	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.26	4		824	336	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69986988	69986988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs994568417	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	64	550	0	ENST00000394351.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000394351	NM_000248.3	17	Gaa/Aaa	2/9	0.256232673830043	4	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	2	0.26	4		550	276	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs753143066	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	64	715	7	ENST00000295797.4:c.826dup	p.Thr276AsnfsTer16	p.T276Nfs*16	ENST00000295797	NM_002740.5	273	tta/ttAa	9/18	0.222045692086313	4	FACETS	0.781	0.679	0.891	0.781	0.679	0.891	SUBCLONAL	2	TRUE	2	0.26	4		722	397	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	40	590	3	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	0.12875758955603	4	FACETS	1	0.886	1	0.541	0.451	0.642	INDETERMINATE	1	TRUE	2	0.26	4		593	358	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542109	187542110	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1560943587	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	19	419	0	ENST00000441802.2:c.5630dup	p.Val1878CysfsTer8	p.V1878Cfs*8	ENST00000441802	NM_005245.3	1877	cct/ccCt	10/27	0.12875758955603	4	FACETS	1	0.881	1	0.635	0.486	0.807	INDETERMINATE	1	TRUE	2	0.26	4		419	145	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225600	225600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777600956	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	21	250	0	ENST00000264932.6:c.379G>A	p.Val127Met	p.V127M	ENST00000264932	NM_004168.2	127	Gtg/Atg	4/15	0.303903307556775	1	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	0	0.26	1		250	121	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278821	1278821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150819225	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	72	800	0	ENST00000310581.5:c.2221G>A	p.Val741Met	p.V741M	ENST00000310581	NM_198253.2	741	Gtg/Atg	6/16	0.303903307556775	1	FACETS	1	0.912	1	1	0.984	1	CLONAL	2	TRUE	0	0.26	1		800	233	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439390	149439390	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	46	738	0	ENST00000286301.3:c.2005G>T	p.Gly669Cys	p.G669C	ENST00000286301	NM_005211.3	669	Ggc/Tgc	15/22	0.256232673830043	4	FACETS	1	0.952	1	0.676	0.571	0.79	CLONAL	1	TRUE	2	0.26	4		738	330	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324917	31324917	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	55	668	0	ENST00000412585.2:c.19del	p.Arg7GlufsTer13	p.R7Efs*13	ENST00000412585	NM_005514.6	7	Cga/ga	1/8	0.303866951809773	6	FACETS	0.76	0.652	0.878	0.38	0.326	0.439	SUBCLONAL	2	TRUE	2	0.26	6		668	423	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798218	32798218	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	46	570	0	ENST00000374899.4:c.1462-1G>T		p.X488_splice	ENST00000374899	NM_018833.2	488			0.303866951809773	7	FACETS	1	0.958	1			1	CLONAL	1	TRUE	NA	0.26	7		570	403	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805787	32805788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1174402903	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	59	821	0	ENST00000374899.4:c.223dup	p.Leu75ProfsTer92	p.L75Pfs*92	ENST00000374899	NM_018833.2	75	ctg/cCtg	2/12	0.303866951809773	15	FACETS	1	0.922	1			1	CLONAL	2	TRUE	NA	0.26	15		821	552	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818213	32818213	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs143800384	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	106	715	1	ENST00000354258.4:c.1312C>T	p.Arg438Ter	p.R438*	ENST00000354258	NM_000593.5	438	Cga/Tga	5/11	0.303866951809773	15	FACETS	0.921	0.825	1			1	CLONAL	3	TRUE	NA	0.26	15		716	794	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553255	106553255	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	72	630	0	ENST00000369096.4:c.1220A>G	p.Asn407Ser	p.N407S	ENST00000369096	NM_001198.3	407	aAc/aGc	5/7	0.303866951809773	7	FACETS	0.797	0.697	0.905			1	CLONAL	2	TRUE	NA	0.26	7		630	573	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001350	150001350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	55	636	0	ENST00000253339.5:c.2254G>A	p.Ala752Thr	p.A752T	ENST00000253339		752	Gct/Act	4/7	0.303903307556775	4	FACETS	1	0.871	1	1	0.871	1	CLONAL	2	TRUE	2	0.26	4		636	264	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979543	2979543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148083162	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	33	529	0	ENST00000396946.4:c.704G>A	p.Arg235Gln	p.R235Q	ENST00000396946	NM_032415.4	235	cGg/cAg	6/25	1	2	FACETS	0.76	0.627	0.906	1	0.95	1	CLONAL	2	TRUE	1	0.26	2		529	167	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729291	41729291	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	14	514	1	ENST00000242208.4:c.1238del	p.Lys413ArgfsTer6	p.K413Rfs*6	ENST00000242208	NM_002192.2	413	aAg/ag	3/3	1	2	FACETS	0.451	0.326	0.602	0.451	0.326	0.602	SUBCLONAL	1	TRUE	1	0.26	2		515	239	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398625	116398625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45587940	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	42	492	1	ENST00000397752.3:c.2215C>T	p.Arg739Cys	p.R739C	ENST00000397752	NM_000245.2	739	Cgt/Tgt	9/21	0.303866951809773	5	FACETS	1	0.947	1	0.451	0.378	0.532	CLONAL	1	TRUE	2	0.26	5		493	332	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411880	116411883	+	intron_variant	Intron	DEL	TCTT	TCTT	-	rs747887276	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	59	859	0	ENST00000397752.3:c.2888-16_2888-13del		p.*963*	ENST00000397752	NM_000245.2	-/1390			0.303866951809773	5	FACETS	1	0.939	1	0.389	0.335	0.449	CLONAL	1	TRUE	2	0.26	5		859	540	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864311	151864311	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760393462	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	26	581	1	ENST00000262189.6:c.9670C>T	p.Arg3224Cys	p.R3224C	ENST00000262189	NM_170606.2	3224	Cgt/Tgt	42/59	1	2	FACETS	0.631	0.5	0.78	0.631	0.5	0.78	SUBCLONAL	1	TRUE	1	0.26	2		582	317	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878863	151878863	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1563288201	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	49	616	0	ENST00000262189.6:c.6082C>T	p.Arg2028Ter	p.R2028*	ENST00000262189	NM_170606.2	2028	Cga/Tga	36/59	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.26	2		616	302	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981752	70981752	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	30	926	2	ENST00000276594.2:c.344T>C	p.Leu115Pro	p.L115P	ENST00000276594	NM_024504.3	115	cTg/cCg	2/8	0.303903307556775	0	FACETS	0.871	0.708	1			1	CLONAL	1	TRUE	0	0.26	0		928	196	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866587	117866587	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	37	518	0	ENST00000297338.2:c.1058T>G	p.Leu353Arg	p.L353R	ENST00000297338	NM_006265.2	353	cTg/cGg	9/14	0.256232673830043	4	FACETS	1	0.934	1	0.645	0.534	0.768	CLONAL	1	TRUE	2	0.26	4		518	278	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878932	117878932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	33	418	0	ENST00000297338.2:c.37C>T	p.Pro13Ser	p.P13S	ENST00000297338	NM_006265.2	13	Cct/Tct	2/14	0.256232673830043	4	FACETS	0.919	0.75	1	0.46	0.375	0.555	CLONAL	1	TRUE	2	0.26	4		418	348	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231211	98231211	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	34	722	0	ENST00000331920.6:c.2072C>A	p.Thr691Asn	p.T691N	ENST00000331920	NM_000264.3	691	aCc/aAc	14/24	0.182187634597059	3	FACETS	1	0.83	1	0.506	0.415	0.608	CLONAL	1	TRUE	1	0.26	3		722	292	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760702	133760702	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	96	1028	3	ENST00000318560.5:c.3025C>T	p.Arg1009Ter	p.R1009*	ENST00000318560	NM_005157.4	1009	Cga/Tga	11/11	0.182187634597059	3	FACETS	0.993	0.898	1	1	0.983	1	CLONAL	3	TRUE	1	0.26	3		1031	280	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760768	133760768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757631617	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	17	756	0	ENST00000318560.5:c.3091G>A	p.Val1031Met	p.V1031M	ENST00000318560	NM_005157.4	1031	Gtg/Atg	11/11	0.182187634597059	3	FACETS	0.613	0.458	0.797	0.307	0.229	0.399	SUBCLONAL	1	TRUE	1	0.26	3		756	241	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390936	139390936	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs746218012	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	19	918	1	ENST00000277541.6:c.7255C>A	p.Leu2419Ile	p.L2419I	ENST00000277541	NM_017617.3	2419	Ctt/Att	34/34	0.182187634597059	3	FACETS	0.547	0.415	0.702	0.273	0.207	0.351	SUBCLONAL	1	TRUE	1	0.26	3		919	302	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039405	47039405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	48	700	1	ENST00000377604.3:c.1028G>A	p.Arg343His	p.R343H	ENST00000377604	NM_001204468.1	343	cGc/cAc	10/24	0.303866951809773	1	FACETS	0.873	0.749	1	1	0.972	1	CLONAL	2	TRUE	0	0.26	1		701	184	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412095	63412095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852217	NA	P-0039888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	60	940	1	ENST00000330258.3:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000330258	NM_152424.3	358	Cga/Tga	2/2	0.303866951809773	1	FACETS	0.979	0.857	1	1	0.98	1	CLONAL	2	TRUE	0	0.26	1		941	205	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0039932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	404	676	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.692740649070036	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.692740649070036	1		676	747	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41219623	41219623	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0039932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	370	296	1	ENST00000357654.3:c.5074+2T>A		p.X1692_splice	ENST00000357654	NM_007294.3	1692			0.685390579839981	2	FACETS	0.998	0.963	1	0.998	0.963	1	CLONAL	2	TRUE	0	0.692740649070036	2		297	535	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125535	7125535	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	187	406	0	ENST00000302850.5:c.3017T>G	p.Phe1006Cys	p.F1006C	ENST00000302850	NM_000208.2	1006	tTt/tGt	17/22	0.119422760604031	6	FACETS	0.785	0.726	0.846			1	INDETERMINATE	2	TRUE	NA	0.692740649070036	6		406	820	SUCCESS
APC	324	MSKCC	GRCh37	5	112179394	112179394	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	110	439	0	ENST00000257430.4:c.8103G>T	p.Gln2701His	p.Q2701H	ENST00000257430	NM_000038.5	2701	caG/caT	16/16	0.542060339998119	3	FACETS	0.495	0.444	0.549			1	SUBCLONAL	1	TRUE	NA	0.692740649070036	3		439	864	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	138	759	1				ENST00000310581	NM_198253.2	-/1132			0.852193532362369	3	FACETS	1	0.955	1	0.354	0.325	0.384	CLONAL	1	TRUE	0	0.852193532362369	3		760	435	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508176	106508176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752039271	NA	P-0039963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	95	305	0	ENST00000359195.3:c.170C>T	p.Ala57Val	p.A57V	ENST00000359195	NM_002649.2	57	gCg/gTg	2/11	0.852193532362369	4	FACETS	1	0.932	1	0.525	0.471	0.582	CLONAL	1	TRUE	2	0.852193532362369	4		305	393	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259051	16259051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	178	568	1	ENST00000375759.3:c.6316G>A	p.Ala2106Thr	p.A2106T	ENST00000375759	NM_015001.2	2106	Gca/Aca	11/15	0.852193532362369	3	FACETS	0.972	0.9	1	0.324	0.3	0.349	CLONAL	1	TRUE	0	0.852193532362369	3		569	613	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921063	50921100	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCTGGTCCTGACCCTGCCCCTGCCCCCACCCGCAGCC	GGCTGGTCCTGACCCTGCCCCTGCCCCCACCCGCAGCC	-	novel	NA	P-0039963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	170	367	1	ENST00000440232.2:c.3219-34_3222del		p.X1073_splice	ENST00000440232	NM_002691.3	1073		27/27	0.852193532362369	3	FACETS	1	0.99	1	0.704	0.656	0.753	CLONAL	1	TRUE	1	0.852193532362369	3		368	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577074	7577075	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTCTC	novel	NA	P-0039996-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	321	738	0	ENST00000269305.4:c.859_863dup	p.Asn288LysfsTer59	p.N288Kfs*59	ENST00000269305	NM_001126112.2	288	aat/aaGAGAAt	8/11	0.494449927312043	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.516641215217155	2		738	620	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714655	52714655	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039996-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	92	664	0	ENST00000322088.6:c.413G>C	p.Gly138Ala	p.G138A	ENST00000322088	NM_014225.5	138	gGc/gCc	4/15	NA	2	FACETS	0.593	0.527	0.662			1	INDETERMINATE	1	TRUE	NA	0.516641215217155	2		664	601	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925621	114925621	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763934346	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	160	724	2	ENST00000543371.1:c.1699G>A	p.Ala567Thr	p.A567T	ENST00000543371	NM_001198531.1	567	Gcc/Acc	14/14	1	2	FACETS	0.955	0.876	1	0.955	0.876	1	CLONAL	1	TRUE	1	0.38	2		726	882	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	180	672	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.38	2		672	852	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	76	409	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.907	0.799	1	0.907	0.799	1	CLONAL	1	TRUE	1	0.38	2		409	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	41	932	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.245	0.203	0.292	0.245	0.203	0.292	SUBCLONAL	1	TRUE	1	0.38	2		932	880	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757396	40757396	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1374515118	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	71	574	1	ENST00000373198.4:c.2902G>A	p.Asp968Asn	p.D968N	ENST00000373198	NM_133170.3	968	Gac/Aac	20/32	1	2	FACETS	0.534	0.465	0.608	0.534	0.465	0.608	SUBCLONAL	1	TRUE	1	0.38	2		575	700	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986947	36986947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	179	706	1	ENST00000354822.5:c.742C>T	p.Arg248Cys	p.R248C	ENST00000354822	NM_001079668.2	248	Cgc/Tgc	3/3	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.38	2		707	855	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	134	524	0	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.38	2		524	610	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651532	52651532	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	38	365	0	ENST00000394830.3:c.1564C>T	p.Arg522Ter	p.R522*	ENST00000394830	NM_018313.4	522	Cga/Tga	15/30	1	2	FACETS	0.576	0.477	0.686	0.576	0.477	0.686	SUBCLONAL	1	TRUE	1	0.38	2		365	347	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784941	9784941	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778194087	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	50	725	0	ENST00000377346.4:c.2944C>T	p.Arg982Trp	p.R982W	ENST00000377346	NM_005026.3	982	Cgg/Tgg	23/24	1	2	FACETS	0.337	0.285	0.395	0.337	0.285	0.395	SUBCLONAL	1	TRUE	1	0.38	2		725	780	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298035	11298035	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	115	640	1	ENST00000361445.4:c.2073G>T	p.Glu691Asp	p.E691D	ENST00000361445	NM_004958.3	691	gaG/gaT	13/58	1	2	FACETS	0.735	0.661	0.812	0.735	0.661	0.812	SUBCLONAL	1	TRUE	1	0.38	2		641	824	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317108	11317108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	212	666	0	ENST00000361445.4:c.386C>T	p.Ala129Val	p.A129V	ENST00000361445	NM_004958.3	129	gCc/gTc	4/58	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.38	2		666	892	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255085	16255085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557758293	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	52	388	1	ENST00000375759.3:c.2350C>T	p.Arg784Cys	p.R784C	ENST00000375759	NM_015001.2	784	Cgc/Tgc	11/15	1	2	FACETS	0.563	0.48	0.654	0.563	0.48	0.654	SUBCLONAL	1	TRUE	1	0.38	2		389	486	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258976	16258976	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	104	638	0	ENST00000375759.3:c.6241C>T	p.Arg2081Ter	p.R2081*	ENST00000375759	NM_015001.2	2081	Cga/Tga	11/15	1	2	FACETS	0.745	0.667	0.827	0.745	0.667	0.827	SUBCLONAL	1	TRUE	1	0.38	2		638	735	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17354254	17354254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150437793	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	59	369	1	ENST00000375499.3:c.530G>A	p.Arg177His	p.R177H	ENST00000375499	NM_003000.2	177	cGt/cAt	5/8	1	2	FACETS	0.738	0.636	0.847	0.738	0.636	0.847	SUBCLONAL	1	TRUE	1	0.38	2		370	421	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17371323	17371323	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	145	571	0	ENST00000375499.3:c.133T>G	p.Tyr45Asp	p.Y45D	ENST00000375499	NM_003000.2	45	Tat/Gat	2/8	1	2	FACETS	0.975	0.89	1	0.975	0.89	1	CLONAL	1	TRUE	1	0.38	2		571	783	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058078	27058078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763739196	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	69	384	0	ENST00000324856.7:c.1786C>T	p.Arg596Cys	p.R596C	ENST00000324856	NM_006015.4	596	Cgc/Tgc	3/20	1	2	FACETS	0.722	0.63	0.821	0.722	0.63	0.821	SUBCLONAL	1	TRUE	1	0.38	2		384	503	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087377	27087377	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1341298575	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	58	591	0	ENST00000324856.7:c.1951A>G	p.Met651Val	p.M651V	ENST00000324856	NM_006015.4	651	Atg/Gtg	5/20	1	2	FACETS	0.42	0.36	0.486	0.42	0.36	0.486	SUBCLONAL	1	TRUE	1	0.38	2		591	726	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101508	27101508	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	49	843	0	ENST00000324856.7:c.4790A>G	p.Asn1597Ser	p.N1597S	ENST00000324856	NM_006015.4	1597	aAc/aGc	18/20	1	2	FACETS	0.263	0.222	0.309	0.263	0.222	0.309	SUBCLONAL	1	TRUE	1	0.38	2		843	979	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	75	592	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.602	0.527	0.682	0.602	0.527	0.682	SUBCLONAL	1	TRUE	1	0.38	2		593	656	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106355	27106355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773909963	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	51	578	1	ENST00000324856.7:c.5966G>A	p.Arg1989Gln	p.R1989Q	ENST00000324856	NM_006015.4	1989	cGa/cAa	20/20	1	2	FACETS	0.385	0.326	0.45	0.385	0.326	0.45	SUBCLONAL	1	TRUE	1	0.38	2		579	697	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814541	43814541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561818288	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	73	440	0	ENST00000372470.3:c.1336G>A	p.Gly446Arg	p.G446R	ENST00000372470	NM_005373.2	446	Gga/Aga	9/12	1	2	FACETS	0.682	0.597	0.774	0.682	0.597	0.774	SUBCLONAL	1	TRUE	1	0.38	2		440	563	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797948	45797948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	228	777	0	ENST00000450313.1:c.823C>T	p.Pro275Ser	p.P275S	ENST00000450313	NM_012222.2	275	Cca/Tca	10/16	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.38	2		777	969	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798286	45798286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147754007	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	97	673	0	ENST00000450313.1:c.650G>A	p.Arg217His	p.R217H	ENST00000450313	NM_012222.2	217	cGc/cAc	8/16	1	2	FACETS	0.646	0.576	0.721	0.646	0.576	0.721	SUBCLONAL	1	TRUE	1	0.38	2		673	790	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307227	65307227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	43	457	0	ENST00000342505.4:c.2461G>A	p.Ala821Thr	p.A821T	ENST00000342505	NM_002227.2	821	Gct/Act	18/25	1	2	FACETS	0.362	0.302	0.428	0.362	0.302	0.428	SUBCLONAL	1	TRUE	1	0.38	2		457	626	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166325	118166325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	62	398	0	ENST00000369448.3:c.835C>T	p.Pro279Ser	p.P279S	ENST00000369448	NM_017709.3	279	Ccg/Tcg	2/2	1	2	FACETS	0.716	0.62	0.819	0.716	0.62	0.819	SUBCLONAL	1	TRUE	1	0.38	2		398	456	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458236	120458236	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	127	727	0	ENST00000256646.2:c.7109T>A	p.Leu2370His	p.L2370H	ENST00000256646	NM_024408.3	2370	cTc/cAc	34/34	1	2	FACETS	0.796	0.721	0.875	0.796	0.721	0.875	SUBCLONAL	1	TRUE	1	0.38	2		727	840	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465267	120465267	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	84	404	0	ENST00000256646.2:c.4994C>A	p.Ser1665Tyr	p.S1665Y	ENST00000256646	NM_024408.3	1665	tCt/tAt	27/34	1	2	FACETS	0.929	0.823	1	0.929	0.823	1	CLONAL	1	TRUE	1	0.38	2		404	476	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120493361	120493361	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	32	499	0	ENST00000256646.2:c.2465T>C	p.Val822Ala	p.V822A	ENST00000256646	NM_024408.3	822	gTg/gCg	15/34	1	2	FACETS	0.28	0.227	0.341	0.28	0.227	0.341	SUBCLONAL	1	TRUE	1	0.38	2		499	601	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120508112	120508112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	94	389	0	ENST00000256646.2:c.1645G>A	p.Asp549Asn	p.D549N	ENST00000256646	NM_024408.3	549	Gat/Aat	10/34	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.38	2		389	494	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851324	156851324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759637817	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	54	786	0	ENST00000524377.1:c.2281C>T	p.Arg761Trp	p.R761W	ENST00000524377	NM_002529.3	761	Cgg/Tgg	17/17	1	2	FACETS	0.308	0.262	0.359	0.308	0.262	0.359	SUBCLONAL	1	TRUE	1	0.38	2		786	923	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161293415	161293415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767802663	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	52	385	0	ENST00000367975.2:c.32G>A	p.Arg11His	p.R11H	ENST00000367975	NM_003001.3	11	cGt/cAt	2/6	1	2	FACETS	0.484	0.411	0.563	0.484	0.411	0.563	SUBCLONAL	1	TRUE	1	0.38	2		385	566	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746132	162746132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1374086542	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	68	262	0	ENST00000367921.3:c.2255G>A	p.Arg752His	p.R752H	ENST00000367921	NM_006182.2	752	cGc/cAc	16/18	1	2	FACETS	0.873	0.763	0.991	0.873	0.763	0.991	CLONAL	1	TRUE	1	0.38	2		262	410	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318812	163318812	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	50	282	0	ENST00000271452.3:c.1202T>G	p.Ile401Ser	p.I401S	ENST00000271452	NM_145697.2	401	aTt/aGt	13/14	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.38	2		282	243	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193110979	193110979	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	25	132	0	ENST00000367435.3:c.513-1G>A		p.X171_splice	ENST00000367435	NM_024529.4	171			1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.38	2		132	103	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253478	226253478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	69	289	0	ENST00000366813.1:c.250C>T	p.Arg84Cys	p.R84C	ENST00000366813		84	Cgc/Tgc	2/3	1	2	FACETS	0.859	0.751	0.974	0.859	0.751	0.974	CLONAL	1	TRUE	1	0.38	2		289	423	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226579901	226579901	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	57	642	0	ENST00000366794.5:c.401A>G	p.Lys134Arg	p.K134R	ENST00000366794	NM_001618.3	134	aAg/aGg	3/23	1	2	FACETS	0.408	0.349	0.473	0.408	0.349	0.473	SUBCLONAL	1	TRUE	1	0.38	2		642	735	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675358	241675358	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	23	359	0	ENST00000366560.3:c.464A>G	p.Glu155Gly	p.E155G	ENST00000366560	NM_000143.3	155	gAa/gGa	4/10	1	2	FACETS	0.343	0.267	0.431	0.343	0.267	0.431	SUBCLONAL	1	TRUE	1	0.38	2		359	353	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800971	243800971	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	19	363	0	ENST00000263826.5:c.503A>T	p.Lys168Met	p.K168M	ENST00000263826	NM_005465.4	168	aAg/aTg	5/13	1	2	FACETS	0.345	0.262	0.443	0.345	0.262	0.443	SUBCLONAL	1	TRUE	1	0.38	2		363	290	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596108	43596108	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	39	631	0	ENST00000355710.3:c.275C>T	p.Thr92Ile	p.T92I	ENST00000355710	NM_020975.4	92	aCc/aTc	2/20	1	2	FACETS	0.267	0.22	0.319	0.267	0.22	0.319	SUBCLONAL	1	TRUE	1	0.38	2		631	769	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604602	43604602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781646869	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	191	762	0	ENST00000355710.3:c.1187C>T	p.Ser396Leu	p.S396L	ENST00000355710	NM_020975.4	396	tCg/tTg	6/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.38	2		762	901	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610101	43610101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753686782	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	62	763	0	ENST00000355710.3:c.2053G>A	p.Val685Ile	p.V685I	ENST00000355710	NM_020975.4	685	Gtc/Atc	11/20	1	2	FACETS	0.351	0.302	0.404	0.351	0.302	0.404	SUBCLONAL	1	TRUE	1	0.38	2		763	931	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620396	43620396	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763489828	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	160	572	1	ENST00000355710.3:c.3005G>A	p.Ser1002Asn	p.S1002N	ENST00000355710	NM_020975.4	1002	aGc/aAc	18/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.38	2		573	772	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623572	43623572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760625882	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	30	346	1	ENST00000355710.3:c.3200C>T	p.Pro1067Leu	p.P1067L	ENST00000355710	NM_020975.4	1067	cCg/cTg	20/20	1	2	FACETS	0.365	0.293	0.446	0.365	0.293	0.446	SUBCLONAL	1	TRUE	1	0.38	2		347	433	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623593	43623593	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	106	418	0	ENST00000355710.3:c.3221C>A	p.Pro1074His	p.P1074H	ENST00000355710	NM_020975.4	1074	cCt/cAt	20/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.38	2		418	493	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63829546	63829546	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	63	333	0	ENST00000279873.7:c.1189C>T	p.His397Tyr	p.H397Y	ENST00000279873	NM_032199.2	397	Cat/Tat	8/10	1	2	FACETS	0.679	0.589	0.778	0.679	0.589	0.778	SUBCLONAL	1	TRUE	1	0.38	2		333	488	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845589	63845589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759435915	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	46	223	0	ENST00000279873.7:c.1328G>A	p.Arg443His	p.R443H	ENST00000279873	NM_032199.2	443	cGc/cAc	9/10	1	2	FACETS	0.734	0.62	0.858	0.734	0.62	0.858	SUBCLONAL	1	TRUE	1	0.38	2		223	330	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845628	63845628	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	30	248	0	ENST00000279873.7:c.1370del	p.Asn457MetfsTer22	p.N457Mfs*22	ENST00000279873	NM_032199.2	456	gAa/ga	9/10	1	2	FACETS	0.466	0.376	0.568	0.466	0.376	0.568	SUBCLONAL	1	TRUE	1	0.38	2		248	339	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450805	70450805	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759636615	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	135	495	0	ENST00000373644.4:c.5645C>T	p.Thr1882Met	p.T1882M	ENST00000373644	NM_030625.2	1882	aCg/aTg	12/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.38	2		495	550	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88672025	88672025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782231	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	31	455	0	ENST00000372037.3:c.559C>T	p.Arg187Cys	p.R187C	ENST00000372037	NM_004329.2	187	Cgt/Tgt	8/13	1	2	FACETS	0.502	0.407	0.61	0.502	0.407	0.61	SUBCLONAL	1	TRUE	1	0.38	2		455	325	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690802	89690802	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1114167621	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	10	196	0	ENST00000371953.3:c.210-1G>A		p.X70_splice	ENST00000371953	NM_000314.4	70			1	2	FACETS	0.365	0.248	0.512	0.365	0.248	0.512	SUBCLONAL	1	TRUE	1	0.38	2		196	144	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104353781	104353781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369465986	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	97	626	1	ENST00000369902.3:c.715C>T	p.Arg239Trp	p.R239W	ENST00000369902	NM_016169.3	239	Cgg/Tgg	6/12	1	2	FACETS	0.604	0.538	0.675	0.604	0.538	0.675	SUBCLONAL	1	TRUE	1	0.38	2		627	845	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771549	112771549	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	77	464	1	ENST00000369452.4:c.1722G>A	p.Met574Ile	p.M574I	ENST00000369452	NM_007373.3	574	atG/atA	9/9	1	2	FACETS	0.763	0.671	0.862	0.763	0.671	0.862	SUBCLONAL	1	TRUE	1	0.38	2		465	531	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114799857	114799857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	78	603	0	ENST00000543371.1:c.524C>T	p.Ala175Val	p.A175V	ENST00000543371	NM_001198531.1	175	gCc/gTc	5/14	1	2	FACETS	0.433	0.379	0.49	0.433	0.379	0.49	SUBCLONAL	1	TRUE	1	0.38	2		603	949	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903687	114903687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	96	569	1	ENST00000543371.1:c.691C>T	p.Pro231Ser	p.P231S	ENST00000543371	NM_001198531.1	231	Cca/Tca	7/14	1	2	FACETS	0.7	0.623	0.781	0.7	0.623	0.781	SUBCLONAL	1	TRUE	1	0.38	2		570	722	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	532733	532733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778400	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	60	831	0	ENST00000451590.1:c.473C>T	p.Thr158Met	p.T158M	ENST00000451590	NM_001130442.1	158	aCg/aTg	5/5	1	2	FACETS	0.338	0.29	0.391	0.338	0.29	0.391	SUBCLONAL	1	TRUE	1	0.38	2		831	933	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533853	533853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730880461	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	120	905	0	ENST00000451590.1:c.203G>A	p.Arg68Gln	p.R68Q	ENST00000451590	NM_001130442.1	68	cGg/cAg	3/5	1	2	FACETS	0.59	0.531	0.652	0.59	0.531	0.652	SUBCLONAL	1	TRUE	1	0.38	2		905	1071	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456566	32456566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1311557029	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	14	49	0	ENST00000332351.3:c.326C>T	p.Ala109Val	p.A109V	ENST00000332351	NM_024426.4	109	gCg/gTg	1/10	1	2	FACETS	0.652	0.476	0.861	0.652	0.476	0.861	SUBCLONAL	1	TRUE	1	0.38	2		49	113	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572060	64572060	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs104894261	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	69	735	0	ENST00000312049.6:c.1579C>T	p.Arg527Ter	p.R527*	ENST00000312049	NM_130799.2	527	Cga/Tga	10/10	1	2	FACETS	0.358	0.311	0.41	0.358	0.311	0.41	SUBCLONAL	1	TRUE	1	0.38	2		735	1014	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573812	64573812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771645621	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	76	660	0	ENST00000312049.6:c.941G>A	p.Arg314Gln	p.R314Q	ENST00000312049	NM_130799.2	314	cGg/cAg	7/10	1	2	FACETS	0.547	0.479	0.62	0.547	0.479	0.62	SUBCLONAL	1	TRUE	1	0.38	2		660	731	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462909	69462909	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs777225097	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	44	648	0	ENST00000227507.2:c.722C>T	p.Pro241Leu	p.P241L	ENST00000227507	NM_053056.2	241	cCg/cTg	4/5	1	2	FACETS	0.287	0.24	0.34	0.287	0.24	0.34	SUBCLONAL	1	TRUE	1	0.38	2		648	807	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943693	71943693	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	117	619	0	ENST00000298229.2:c.1736T>C	p.Ile579Thr	p.I579T	ENST00000298229	NM_001567.3	579	aTc/aCc	15/28	1	2	FACETS	0.657	0.592	0.727	0.657	0.592	0.727	SUBCLONAL	1	TRUE	1	0.38	2		619	937	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047151	77047151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	135	554	0	ENST00000356341.3:c.1393C>T	p.Leu465Phe	p.L465F	ENST00000356341	NM_002576.4	465	Ctc/Ttc	13/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.38	2		554	611	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103511	77103511	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	112	328	0	ENST00000356341.3:c.55A>T	p.Asn19Tyr	p.N19Y	ENST00000356341	NM_002576.4	19	Aat/Tat	2/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.38	2		328	509	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94906441	94906441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	89	410	0	ENST00000536441.1:c.1457C>T	p.Ala486Val	p.A486V	ENST00000536441	NM_144665.3	486	gCc/gTc	10/10	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.38	2		410	460	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996737	100996737	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	21	404	0	ENST00000325455.5:c.1789+1G>A		p.X597_splice	ENST00000325455	NM_001202474.3	597			1	2	FACETS	0.278	0.213	0.353	0.278	0.213	0.353	SUBCLONAL	1	TRUE	1	0.38	2		404	398	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129749	108129749	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs780619951	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	20	322	0	ENST00000278616.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000278616	NM_000051.3	805	Cga/Tga	16/63	1	2	FACETS	0.384	0.294	0.49	0.384	0.294	0.49	SUBCLONAL	1	TRUE	1	0.38	2		322	274	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186765	108186765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	84	367	1	ENST00000278616.4:c.6123G>A	p.Met2041Ile	p.M2041I	ENST00000278616	NM_000051.3	2041	atG/atA	42/63	1	2	FACETS	0.855	0.757	0.959	0.855	0.757	0.959	CLONAL	1	TRUE	1	0.38	2		368	517	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205753	108205753	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	30	344	0	ENST00000278616.4:c.8068T>G	p.Phe2690Val	p.F2690V	ENST00000278616	NM_000051.3	2690	Ttt/Gtt	55/63	1	2	FACETS	0.504	0.407	0.614	0.504	0.407	0.614	SUBCLONAL	1	TRUE	1	0.38	2		344	313	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205808	108205808	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	30	390	0	ENST00000278616.4:c.8123A>G	p.Asp2708Gly	p.D2708G	ENST00000278616	NM_000051.3	2708	gAt/gGt	55/63	1	2	FACETS	0.388	0.312	0.474	0.388	0.312	0.474	SUBCLONAL	1	TRUE	1	0.38	2		390	407	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343084	118343084	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	34	312	0	ENST00000534358.1:c.1214del	p.Asn405IlefsTer25	p.N405Ifs*25	ENST00000534358	NM_005933.3	404	Aaa/aa	3/36	1	2	FACETS	0.468	0.383	0.564	0.468	0.383	0.564	SUBCLONAL	1	TRUE	1	0.38	2		312	382	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372558	118372558	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs533826575	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	84	432	0	ENST00000534358.1:c.6491C>T	p.Pro2164Leu	p.P2164L	ENST00000534358	NM_005933.3	2164	cCg/cTg	26/36	1	2	FACETS	0.626	0.553	0.705	0.626	0.553	0.705	SUBCLONAL	1	TRUE	1	0.38	2		432	706	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373158	118373158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555045986	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	108	384	0	ENST00000534358.1:c.6551C>T	p.Pro2184Leu	p.P2184L	ENST00000534358	NM_005933.3	2184	cCt/cTt	27/36	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.38	2		384	478	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373947	118373947	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	70	325	0	ENST00000534358.1:c.7340A>G	p.Lys2447Arg	p.K2447R	ENST00000534358	NM_005933.3	2447	aAa/aGa	27/36	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.38	2		325	329	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376803	118376803	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	28	424	0	ENST00000534358.1:c.10196C>A	p.Pro3399His	p.P3399H	ENST00000534358	NM_005933.3	3399	cCt/cAt	27/36	1	2	FACETS	0.353	0.281	0.434	0.353	0.281	0.434	SUBCLONAL	1	TRUE	1	0.38	2		424	418	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656262	18656262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774333984	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	66	442	0	ENST00000266497.5:c.2941C>T	p.Arg981Cys	p.R981C	ENST00000266497		981	Cgc/Tgc	21/31	1	2	FACETS	0.802	0.699	0.914	0.802	0.699	0.914	CLONAL	1	TRUE	1	0.38	2		442	433	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21630823	21630823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761204305	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	44	579	0	ENST00000421138.2:c.781G>A	p.Val261Ile	p.V261I	ENST00000421138		261	Gtt/Att	8/16	1	2	FACETS	0.34	0.284	0.401	0.34	0.284	0.401	SUBCLONAL	1	TRUE	1	0.38	2		579	682	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233228	46233228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374540100	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	33	298	0	ENST00000334344.6:c.1447C>T	p.Pro483Ser	p.P483S	ENST00000334344	NM_152641.2	483	Cca/Tca	11/21	1	2	FACETS	0.455	0.37	0.55	0.455	0.37	0.55	SUBCLONAL	1	TRUE	1	0.38	2		298	382	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245750	46245750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	101	441	0	ENST00000334344.6:c.3844G>A	p.Asp1282Asn	p.D1282N	ENST00000334344	NM_152641.2	1282	Gat/Aat	15/21	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.38	2		441	501	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415891	49415891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	80	467	1	ENST00000301067.7:c.16456G>A	p.Val5486Met	p.V5486M	ENST00000301067	NM_003482.3	5486	Gtg/Atg	53/54	1	2	FACETS	0.757	0.668	0.853	0.757	0.668	0.853	SUBCLONAL	1	TRUE	1	0.38	2		468	556	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420934	49420934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs569620684	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	77	625	0	ENST00000301067.7:c.14815G>A	p.Glu4939Lys	p.E4939K	ENST00000301067	NM_003482.3	4939	Gaa/Aaa	48/54	1	2	FACETS	0.595	0.522	0.674	0.595	0.522	0.674	SUBCLONAL	1	TRUE	1	0.38	2		625	681	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444228	49444228	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	102	1014	0	ENST00000301067.7:c.3143C>T	p.Pro1048Leu	p.P1048L	ENST00000301067	NM_003482.3	1048	cCa/cTa	11/54	1	2	FACETS	0.45	0.401	0.502	0.45	0.401	0.502	SUBCLONAL	1	TRUE	1	0.38	2		1014	1193	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478786	56478786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324972550	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	145	560	1	ENST00000267101.3:c.242G>A	p.Arg81Gln	p.R81Q	ENST00000267101	NM_001982.3	81	cGa/cAa	3/28	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.38	2		561	680	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495609	56495609	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs745487835	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	37	495	1	ENST00000267101.3:c.3799C>T	p.Arg1267Ter	p.R1267*	ENST00000267101	NM_001982.3	1267	Cga/Tga	28/28	1	2	FACETS	0.325	0.267	0.389	0.325	0.267	0.389	SUBCLONAL	1	TRUE	1	0.38	2		496	600	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864756	57864756	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	51	766	0	ENST00000228682.2:c.2233G>T	p.Ala745Ser	p.A745S	ENST00000228682	NM_005269.2	745	Gcg/Tcg	12/12	1	2	FACETS	0.316	0.267	0.369	0.316	0.267	0.369	SUBCLONAL	1	TRUE	1	0.38	2		766	850	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145099	58145099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3211612	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	44	584	0	ENST00000257904.6:c.245G>A	p.Arg82Gln	p.R82Q	ENST00000257904	NM_000075.3	82	cGa/cAa	3/8	1	2	FACETS	0.321	0.268	0.379	0.321	0.268	0.379	SUBCLONAL	1	TRUE	1	0.38	2		584	722	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856166	111856166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446024614	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	50	498	1	ENST00000341259.2:c.217C>T	p.Arg73Cys	p.R73C	ENST00000341259	NM_005475.2	73	Cgc/Tgc	2/8	1	2	FACETS	0.412	0.349	0.482	0.412	0.349	0.482	SUBCLONAL	1	TRUE	1	0.38	2		499	638	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112269	115112269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446220330	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	47	177	0	ENST00000257566.3:c.1471G>A	p.Ala491Thr	p.A491T	ENST00000257566	NM_016569.3	491	Gcg/Acg	7/8	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.38	2		177	197	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123892044	123892044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	64	520	0	ENST00000330479.4:c.853G>A	p.Asp285Asn	p.D285N	ENST00000330479	NM_020382.3	285	Gat/Aat	8/9	1	2	FACETS	0.526	0.455	0.603	0.526	0.455	0.603	SUBCLONAL	1	TRUE	1	0.38	2		520	640	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214661	133214661	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	62	530	0	ENST00000320574.5:c.5617C>A	p.Leu1873Ile	p.L1873I	ENST00000320574	NM_006231.2	1873	Ctc/Atc	41/49	1	2	FACETS	0.385	0.332	0.444	0.385	0.332	0.444	SUBCLONAL	1	TRUE	1	0.38	2		530	847	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238162	133238162	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	44	590	0	ENST00000320574.5:c.2815G>C	p.Ala939Pro	p.A939P	ENST00000320574	NM_006231.2	939	Gcc/Ccc	24/49	1	2	FACETS	0.294	0.245	0.347	0.294	0.245	0.347	SUBCLONAL	1	TRUE	1	0.38	2		590	789	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133242017	133242017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778288256	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	120	711	1	ENST00000320574.5:c.2339C>T	p.Ser780Leu	p.S780L	ENST00000320574	NM_006231.2	780	tCg/tTg	21/49	1	2	FACETS	0.725	0.654	0.8	0.725	0.654	0.8	SUBCLONAL	1	TRUE	1	0.38	2		712	871	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244968	133244968	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567031389	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	212	834	2	ENST00000320574.5:c.2147C>T	p.Ala716Val	p.A716V	ENST00000320574	NM_006231.2	716	gCg/gTg	19/49	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.38	2		836	1074	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563252	21563252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	83	950	0	ENST00000382592.4:c.667G>A	p.Gly223Arg	p.G223R	ENST00000382592	NM_014572.2	223	Ggg/Agg	4/8	1	2	FACETS	0.422	0.372	0.477	0.422	0.372	0.477	SUBCLONAL	1	TRUE	1	0.38	2		950	1034	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622518	28622518	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs778256828	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	28	403	0	ENST00000241453.7:c.1099T>G	p.Phe367Val	p.F367V	ENST00000241453	NM_004119.2	367	Ttt/Gtt	9/24	1	2	FACETS	0.447	0.357	0.548	0.447	0.357	0.548	SUBCLONAL	1	TRUE	1	0.38	2		403	330	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28883045	28883045	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	37	439	0	ENST00000282397.4:c.3655T>C	p.Phe1219Leu	p.F1219L	ENST00000282397	NM_002019.4	1219	Ttc/Ctc	28/30	1	2	FACETS	0.48	0.396	0.574	0.48	0.396	0.574	SUBCLONAL	1	TRUE	1	0.38	2		439	406	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895701	28895701	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	50	537	0	ENST00000282397.4:c.3073G>T	p.Ala1025Ser	p.A1025S	ENST00000282397	NM_002019.4	1025	Gcg/Tcg	23/30	1	2	FACETS	0.505	0.428	0.589	0.505	0.428	0.589	SUBCLONAL	1	TRUE	1	0.38	2		537	521	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893395	32893395	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	51	364	0	ENST00000380152.3:c.249G>T	p.Glu83Asp	p.E83D	ENST00000380152		83	gaG/gaT	3/27	1	2	FACETS	0.816	0.697	0.945	0.816	0.697	0.945	CLONAL	1	TRUE	1	0.38	2		364	329	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912025	32912025	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	93	587	0	ENST00000380152.3:c.3533G>T	p.Ser1178Ile	p.S1178I	ENST00000380152		1178	aGc/aTc	11/27	1	2	FACETS	0.876	0.78	0.977	0.876	0.78	0.977	CLONAL	1	TRUE	1	0.38	2		587	559	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913954	32913954	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555284238	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	73	416	0	ENST00000380152.3:c.5462A>G	p.Lys1821Arg	p.K1821R	ENST00000380152		1821	aAa/aGa	11/27	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.38	2		416	299	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930610	32930610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358973	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	109	370	0	ENST00000380152.3:c.7481G>A	p.Arg2494Gln	p.R2494Q	ENST00000380152		2494	cGa/cAa	15/27	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.38	2		370	474	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504591	103504591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778293	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	51	272	0	ENST00000355739.4:c.212G>A	p.Arg71His	p.R71H	ENST00000355739	NM_000123.3	71	cGt/cAt	2/15	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.38	2		272	258	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515241	103515241	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	32	282	0	ENST00000355739.4:c.1742T>C	p.Val581Ala	p.V581A	ENST00000355739	NM_000123.3	581	gTc/gCc	8/15	1	2	FACETS	0.497	0.404	0.602	0.497	0.404	0.602	SUBCLONAL	1	TRUE	1	0.38	2		282	339	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524624	103524624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377353991	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	110	326	0	ENST00000355739.4:c.2755C>T	p.Arg919Trp	p.R919W	ENST00000355739	NM_000123.3	919	Cgg/Tgg	13/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.38	2		326	513	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435273	110435273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775912180	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	63	273	0	ENST00000375856.3:c.3128G>A	p.Arg1043His	p.R1043H	ENST00000375856	NM_003749.2	1043	cGc/cAc	1/2	1	2	FACETS	0.829	0.72	0.946	0.829	0.72	0.946	CLONAL	1	TRUE	1	0.38	2		273	400	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436662	110436662	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1172028943	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	142	1018	1	ENST00000375856.3:c.1739C>T	p.Thr580Met	p.T580M	ENST00000375856	NM_003749.2	580	aCg/aTg	1/2	1	2	FACETS	0.683	0.621	0.748	0.683	0.621	0.748	SUBCLONAL	1	TRUE	1	0.38	2		1019	1094	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436740	110436740	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779681200	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	138	927	0	ENST00000375856.3:c.1661G>A	p.Arg554His	p.R554H	ENST00000375856	NM_003749.2	554	cGc/cAc	1/2	1	2	FACETS	0.718	0.653	0.788	0.718	0.653	0.788	SUBCLONAL	1	TRUE	1	0.38	2		927	1011	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093411	30093411	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs201154555	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	66	346	1	ENST00000331968.5:c.1852C>T	p.Arg618Ter	p.R618*	ENST00000331968	NM_002742.2	618	Cga/Tga	13/18	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.38	2		347	334	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132955	30132955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145651161	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	106	632	0	ENST00000331968.5:c.646C>T	p.Arg216Cys	p.R216C	ENST00000331968	NM_002742.2	216	Cgc/Tgc	4/18	1	2	FACETS	0.65	0.582	0.722	0.65	0.582	0.722	SUBCLONAL	1	TRUE	1	0.38	2		632	858	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986925	36986925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1192440323	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	40	612	1	ENST00000354822.5:c.764C>T	p.Ala255Val	p.A255V	ENST00000354822	NM_001079668.2	255	gCg/gTg	3/3	1	2	FACETS	0.273	0.226	0.326	0.273	0.226	0.326	SUBCLONAL	1	TRUE	1	0.38	2		613	771	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060970	38060970	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	74	423	0	ENST00000250448.2:c.1019C>T	p.Ala340Val	p.A340V	ENST00000250448	NM_004496.3	340	gCg/gTg	2/2	1	2	FACETS	0.83	0.729	0.939	0.83	0.729	0.939	CLONAL	1	TRUE	1	0.38	2		423	469	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352675	68352675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1416106631	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	15	283	0	ENST00000487270.1:c.542G>A	p.Arg181Gln	p.R181Q	ENST00000487270	NM_133509.3	181	cGg/cAg	6/11	1	2	FACETS	0.285	0.208	0.378	0.285	0.208	0.378	SUBCLONAL	1	TRUE	1	0.38	2		283	277	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609352	81609352	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	45	320	1	ENST00000298171.2:c.950C>A	p.Ala317Asp	p.A317D	ENST00000298171	NM_000369.2	317	gCc/gAc	10/10	1	2	FACETS	0.647	0.545	0.759	0.647	0.545	0.759	SUBCLONAL	1	TRUE	1	0.38	2		321	366	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562578	95562578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	55	335	0	ENST00000393063.1:c.4679C>T	p.Ala1560Val	p.A1560V	ENST00000393063	NM_030621.3	1560	gCg/gTg	24/28	1	2	FACETS	0.766	0.658	0.883	0.766	0.658	0.883	SUBCLONAL	1	TRUE	1	0.38	2		335	378	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571448	95571448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373412959	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	91	299	2	ENST00000393063.1:c.3229G>A	p.Asp1077Asn	p.D1077N	ENST00000393063	NM_030621.3	1077	Gat/Aat	21/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.38	2		301	366	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243030	105243030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1566818890	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	231	819	0	ENST00000349310.3:c.253G>A	p.Glu85Lys	p.E85K	ENST00000349310	NM_001014432.1	85	Gaa/Aaa	5/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.38	2		819	1032	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022896	33022896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	22	374	0	ENST00000300177.4:c.5G>A	p.Ser2Asn	p.S2N	ENST00000300177	NM_001191322.1	2	aGc/aAc	2/2	1	2	FACETS	0.283	0.219	0.358	0.283	0.219	0.358	SUBCLONAL	1	TRUE	1	0.38	2		374	409	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023207	33023207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	87	704	0	ENST00000300177.4:c.316G>A	p.Glu106Lys	p.E106K	ENST00000300177	NM_001191322.1	106	Gaa/Aaa	2/2	1	2	FACETS	0.549	0.485	0.617	0.549	0.485	0.617	SUBCLONAL	1	TRUE	1	0.38	2		704	834	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41022106	41022106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532630164	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	93	611	2	ENST00000267868.3:c.830C>T	p.Ala277Val	p.A277V	ENST00000267868	NM_002875.4	277	gCg/gTg	9/10	1	2	FACETS	0.742	0.66	0.829	0.742	0.66	0.829	SUBCLONAL	1	TRUE	1	0.38	2		613	660	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961588	41961588	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	40	510	0	ENST00000219905.7:c.496G>T	p.Gly166Cys	p.G166C	ENST00000219905	NM_001164273.1	166	Ggt/Tgt	2/24	1	2	FACETS	0.442	0.367	0.526	0.442	0.367	0.526	SUBCLONAL	1	TRUE	1	0.38	2		510	476	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032354	42032354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201349807	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	56	515	0	ENST00000219905.7:c.4538G>A	p.Arg1513His	p.R1513H	ENST00000219905	NM_001164273.1	1513	cGc/cAc	14/24	1	2	FACETS	0.471	0.403	0.545	0.471	0.403	0.545	SUBCLONAL	1	TRUE	1	0.38	2		515	626	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032375	42032375	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	66	519	1	ENST00000219905.7:c.4559C>T	p.Ala1520Val	p.A1520V	ENST00000219905	NM_001164273.1	1520	gCg/gTg	14/24	1	2	FACETS	0.594	0.515	0.679	0.594	0.515	0.679	SUBCLONAL	1	TRUE	1	0.38	2		520	585	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035286	42035286	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759260692	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	70	534	0	ENST00000219905.7:c.5128G>A	p.Val1710Met	p.V1710M	ENST00000219905	NM_001164273.1	1710	Gtg/Atg	15/24	1	2	FACETS	0.579	0.505	0.66	0.579	0.505	0.66	SUBCLONAL	1	TRUE	1	0.38	2		534	636	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707863	43707863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	204	796	1	ENST00000382044.4:c.5018G>A	p.Arg1673Lys	p.R1673K	ENST00000382044	NM_001141980.1	1673	aGa/aAa	23/28	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.38	2		797	1057	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720297	43720297	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	48	533	2	ENST00000382044.4:c.3745C>T	p.Arg1249Trp	p.R1249W	ENST00000382044	NM_001141980.1	1249	Cgg/Tgg	18/28	1	2	FACETS	0.334	0.281	0.392	0.334	0.281	0.392	SUBCLONAL	1	TRUE	1	0.38	2		535	757	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748360	43748360	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	42	640	0	ENST00000382044.4:c.2446G>T	p.Glu816Ter	p.E816*	ENST00000382044	NM_001141980.1	816	Gaa/Taa	12/28	1	2	FACETS	0.339	0.282	0.402	0.339	0.282	0.402	SUBCLONAL	1	TRUE	1	0.38	2		640	653	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748794	43748794	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	125	787	1	ENST00000382044.4:c.2012A>G	p.Glu671Gly	p.E671G	ENST00000382044	NM_001141980.1	671	gAa/gGa	12/28	1	2	FACETS	0.729	0.659	0.802	0.729	0.659	0.802	SUBCLONAL	1	TRUE	1	0.38	2		788	903	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477127	67477127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750756638	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	48	651	0	ENST00000327367.4:c.934G>A	p.Ala312Thr	p.A312T	ENST00000327367	NM_005902.3	312	Gct/Act	7/9	1	2	FACETS	0.292	0.246	0.343	0.292	0.246	0.343	SUBCLONAL	1	TRUE	1	0.38	2		651	865	SUCCESS
BLM	641	MSKCC	GRCh37	15	91326110	91326110	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	32	345	0	ENST00000355112.3:c.2618del	p.Lys873ArgfsTer7	p.K873Rfs*7	ENST00000355112	NM_000057.2	872	Aaa/aa	13/22	1	2	FACETS	0.554	0.451	0.67	0.554	0.451	0.67	SUBCLONAL	1	TRUE	1	0.38	2		345	304	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99451975	99451975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374465368	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	83	433	0	ENST00000268035.6:c.1309C>T	p.Arg437Cys	p.R437C	ENST00000268035	NM_000875.3	437	Cgc/Tgc	6/21	1	2	FACETS	0.734	0.649	0.826	0.734	0.649	0.826	SUBCLONAL	1	TRUE	1	0.38	2		433	595	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467176	99467176	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	39	478	0	ENST00000268035.6:c.2557C>T	p.Pro853Ser	p.P853S	ENST00000268035	NM_000875.3	853	Ccg/Tcg	12/21	1	2	FACETS	0.387	0.32	0.462	0.387	0.32	0.462	SUBCLONAL	1	TRUE	1	0.38	2		478	530	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348100	348100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266838158	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	74	825	1	ENST00000262320.3:c.1406G>A	p.Ser469Asn	p.S469N	ENST00000262320	NM_003502.3	469	aGc/aAc	6/11	1	2	FACETS	0.388	0.338	0.442	0.388	0.338	0.442	SUBCLONAL	1	TRUE	1	0.38	2		826	1004	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354425	354425	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548567255	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	195	834	1	ENST00000262320.3:c.1133C>T	p.Pro378Leu	p.P378L	ENST00000262320	NM_003502.3	378	cCg/cTg	5/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.38	2		835	987	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121604	2121604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746677177	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	99	771	0	ENST00000219476.3:c.1933G>A	p.Val645Ile	p.V645I	ENST00000219476	NM_000548.3	645	Gtc/Atc	18/42	1	2	FACETS	0.547	0.488	0.611	0.547	0.488	0.611	SUBCLONAL	1	TRUE	1	0.38	2		771	952	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126080	2126080	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs754849580	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	80	777	0	ENST00000219476.3:c.2651A>G	p.Tyr884Cys	p.Y884C	ENST00000219476	NM_000548.3	884	tAc/tGc	24/42	1	2	FACETS	0.426	0.374	0.483	0.426	0.374	0.483	SUBCLONAL	1	TRUE	1	0.38	2		777	988	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129134	2129134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555510327	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	228	838	0	ENST00000219476.3:c.3068C>T	p.Thr1023Met	p.T1023M	ENST00000219476	NM_000548.3	1023	aCg/aTg	27/42	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.38	2		838	972	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133701	2133701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45517319	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	44	714	2	ENST00000219476.3:c.3889G>A	p.Ala1297Thr	p.A1297T	ENST00000219476	NM_000548.3	1297	Gcc/Acc	33/42	1	2	FACETS	0.294	0.246	0.348	0.294	0.246	0.348	SUBCLONAL	1	TRUE	1	0.38	2		716	787	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133770	2133770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767495365	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	141	798	3	ENST00000219476.3:c.3958G>A	p.Val1320Ile	p.V1320I	ENST00000219476	NM_000548.3	1320	Gtt/Att	33/42	1	2	FACETS	0.771	0.701	0.843	0.771	0.701	0.843	SUBCLONAL	1	TRUE	1	0.38	2		801	963	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133798	2133798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45517323	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	175	680	0	ENST00000219476.3:c.3986G>A	p.Arg1329His	p.R1329H	ENST00000219476	NM_000548.3	1329	cGc/cAc	33/42	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.38	2		680	793	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639657	3639657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1394177026	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	287	1037	2	ENST00000294008.3:c.3982G>A	p.Val1328Ile	p.V1328I	ENST00000294008	NM_032444.2	1328	Gtc/Atc	12/15	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.38	2		1039	1262	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640235	3640235	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	228	988	1	ENST00000294008.3:c.3404G>A	p.Ser1135Asn	p.S1135N	ENST00000294008	NM_032444.2	1135	aGc/aAc	12/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.38	2		989	1082	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640538	3640538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150453226	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	100	876	1	ENST00000294008.3:c.3101G>A	p.Arg1034His	p.R1034H	ENST00000294008	NM_032444.2	1034	cGc/cAc	12/15	1	2	FACETS	0.488	0.435	0.545	0.488	0.435	0.545	SUBCLONAL	1	TRUE	1	0.38	2		877	1078	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647550	3647550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	109	939	1	ENST00000294008.3:c.1513G>A	p.Ala505Thr	p.A505T	ENST00000294008	NM_032444.2	505	Gcc/Acc	7/15	1	2	FACETS	0.603	0.54	0.669	0.603	0.54	0.669	SUBCLONAL	1	TRUE	1	0.38	2		940	952	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781225	3781225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	78	957	1	ENST00000262367.5:c.5140G>A	p.Val1714Met	p.V1714M	ENST00000262367	NM_004380.2	1714	Gtg/Atg	30/31	1	2	FACETS	0.341	0.298	0.387	0.341	0.298	0.387	SUBCLONAL	1	TRUE	1	0.38	2		958	1205	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807924	3807924	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	53	503	2	ENST00000262367.5:c.3495G>A	p.Trp1165Ter	p.W1165*	ENST00000262367	NM_004380.2	1165	tgG/tgA	18/31	1	2	FACETS	0.41	0.349	0.477	0.41	0.349	0.477	SUBCLONAL	1	TRUE	1	0.38	2		505	681	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823775	3823775	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	107	535	0	ENST00000262367.5:c.2440C>T	p.Pro814Ser	p.P814S	ENST00000262367	NM_004380.2	814	Cca/Tca	13/31	1	2	FACETS	0.834	0.749	0.924	0.834	0.749	0.924	CLONAL	1	TRUE	1	0.38	2		535	675	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862720	9862720	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	135	512	0	ENST00000330684.3:c.2583C>A	p.Phe861Leu	p.F861L	ENST00000330684	NM_001134407.1	861	ttC/ttA	12/13	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.38	2		512	668	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029218	14029218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41557814	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	50	288	0	ENST00000311895.7:c.1429C>T	p.Arg477Trp	p.R477W	ENST00000311895	NM_005236.2	477	Cgg/Tgg	8/11	1	2	FACETS	0.889	0.759	1	0.889	0.759	1	CLONAL	1	TRUE	1	0.38	2		288	296	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14031663	14031663	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373565480	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	72	392	0	ENST00000311895.7:c.1852C>T	p.Arg618Cys	p.R618C	ENST00000311895	NM_005236.2	618	Cgc/Tgc	9/11	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.38	2		392	370	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041629	14041629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777184889	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	47	438	1	ENST00000311895.7:c.2176C>T	p.Arg726Cys	p.R726C	ENST00000311895	NM_005236.2	726	Cgc/Tgc	11/11	1	2	FACETS	0.458	0.386	0.537	0.458	0.386	0.537	SUBCLONAL	1	TRUE	1	0.38	2		439	540	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646204	23646204	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	105	412	0	ENST00000261584.4:c.1663A>C	p.Lys555Gln	p.K555Q	ENST00000261584	NM_024675.3	555	Aaa/Caa	4/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.38	2		412	496	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646663	23646663	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1555461402	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	44	433	0	ENST00000261584.4:c.1204C>A	p.Leu402Ile	p.L402I	ENST00000261584	NM_024675.3	402	Ctt/Att	4/13	1	2	FACETS	0.453	0.38	0.535	0.453	0.38	0.535	SUBCLONAL	1	TRUE	1	0.38	2		433	511	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647098	23647098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780824	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	53	746	0	ENST00000261584.4:c.769G>A	p.Gly257Ser	p.G257S	ENST00000261584	NM_024675.3	257	Ggt/Agt	4/13	1	2	FACETS	0.374	0.318	0.436	0.374	0.318	0.436	SUBCLONAL	1	TRUE	1	0.38	2		746	746	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134476	30134476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	82	572	0	ENST00000263025.4:c.55G>A	p.Gly19Arg	p.G19R	ENST00000263025	NM_002746.2	19	Ggg/Agg	1/9	1	2	FACETS	0.655	0.578	0.738	0.655	0.578	0.738	SUBCLONAL	1	TRUE	1	0.38	2		572	659	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826570	50826570	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	27	190	0	ENST00000398568.2:c.2295A>C	p.Lys765Asn	p.K765N	ENST00000398568	NM_001042412.1	765	aaA/aaC	15/18	1	2	FACETS	0.967	0.779	1	0.967	0.779	1	CLONAL	1	TRUE	1	0.38	2		190	147	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782326	56782326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751835590	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	77	626	0	ENST00000308159.5:c.167C>T	p.Ala56Val	p.A56V	ENST00000308159	NM_014669.4	56	gCa/gTa	2/22	1	2	FACETS	0.503	0.441	0.57	0.503	0.441	0.57	SUBCLONAL	1	TRUE	1	0.38	2		626	806	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56867237	56867237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138281575	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	30	408	0	ENST00000308159.5:c.1456C>T	p.Arg486Cys	p.R486C	ENST00000308159	NM_014669.4	486	Cgc/Tgc	13/22	1	2	FACETS	0.302	0.242	0.37	0.302	0.242	0.37	SUBCLONAL	1	TRUE	1	0.38	2		408	523	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827655	72827655	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	158	588	0	ENST00000268489.5:c.8926T>C	p.Cys2976Arg	p.C2976R	ENST00000268489	NM_006885.3	2976	Tgt/Cgt	9/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.38	2		588	655	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829302	72829302	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs924588701	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	178	688	0	ENST00000268489.5:c.7279G>A	p.Asp2427Asn	p.D2427N	ENST00000268489	NM_006885.3	2427	Gat/Aat	9/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.38	2		688	894	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830895	72830895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770650936	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	71	561	0	ENST00000268489.5:c.5686G>A	p.Ala1896Thr	p.A1896T	ENST00000268489	NM_006885.3	1896	Gcc/Acc	9/10	1	2	FACETS	0.542	0.473	0.617	0.542	0.473	0.617	SUBCLONAL	1	TRUE	1	0.38	2		561	689	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831237	72831237	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1222142009	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	35	438	0	ENST00000268489.5:c.5344A>G	p.Met1782Val	p.M1782V	ENST00000268489	NM_006885.3	1782	Atg/Gtg	9/10	1	2	FACETS	0.317	0.259	0.382	0.317	0.259	0.382	SUBCLONAL	1	TRUE	1	0.38	2		438	582	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832274	72832274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1463858212	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	130	462	0	ENST00000268489.5:c.4307G>A	p.Arg1436His	p.R1436H	ENST00000268489	NM_006885.3	1436	cGc/cAc	9/10	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.38	2		462	657	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832340	72832340	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	75	453	0	ENST00000268489.5:c.4241A>G	p.Glu1414Gly	p.E1414G	ENST00000268489	NM_006885.3	1414	gAa/gGa	9/10	1	2	FACETS	0.652	0.572	0.739	0.652	0.572	0.739	SUBCLONAL	1	TRUE	1	0.38	2		453	605	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845582	72845582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370933867	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	210	692	3	ENST00000268489.5:c.3758G>A	p.Arg1253His	p.R1253H	ENST00000268489	NM_006885.3	1253	cGc/cAc	7/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.38	2		695	946	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984580	72984580	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	73	797	0	ENST00000268489.5:c.3004C>T	p.His1002Tyr	p.H1002Y	ENST00000268489	NM_006885.3	1002	Cac/Tac	3/10	1	2	FACETS	0.333	0.29	0.38	0.333	0.29	0.38	SUBCLONAL	1	TRUE	1	0.38	2		797	1153	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991508	72991508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755878058	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	112	811	0	ENST00000268489.5:c.2537G>A	p.Arg846His	p.R846H	ENST00000268489	NM_006885.3	846	cGc/cAc	2/10	1	2	FACETS	0.584	0.524	0.647	0.584	0.524	0.647	SUBCLONAL	1	TRUE	1	0.38	2		811	1010	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993674	72993674	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	47	676	0	ENST00000268489.5:c.371G>T	p.Ser124Ile	p.S124I	ENST00000268489	NM_006885.3	124	aGt/aTt	2/10	1	2	FACETS	0.289	0.243	0.34	0.289	0.243	0.34	SUBCLONAL	1	TRUE	1	0.38	2		676	856	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819655	81819655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	103	659	0	ENST00000359376.3:c.61G>A	p.Ala21Thr	p.A21T	ENST00000359376	NM_002661.3	21	Gcc/Acc	2/33	1	2	FACETS	0.684	0.611	0.76	0.684	0.611	0.76	SUBCLONAL	1	TRUE	1	0.38	2		659	793	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819778	81819778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	40	497	0	ENST00000359376.3:c.184G>A	p.Glu62Lys	p.E62K	ENST00000359376	NM_002661.3	62	Gag/Aag	2/33	1	2	FACETS	0.307	0.254	0.367	0.307	0.254	0.367	SUBCLONAL	1	TRUE	1	0.38	2		497	685	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81916896	81916896	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	63	642	0	ENST00000359376.3:c.715T>C	p.Ser239Pro	p.S239P	ENST00000359376	NM_002661.3	239	Tct/Cct	9/33	1	2	FACETS	0.372	0.32	0.428	0.372	0.32	0.428	SUBCLONAL	1	TRUE	1	0.38	2		642	892	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934252	81934252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	66	702	1	ENST00000359376.3:c.1229G>A	p.Ser410Asn	p.S410N	ENST00000359376	NM_002661.3	410	aGc/aAc	14/33	1	2	FACETS	0.426	0.369	0.488	0.426	0.369	0.488	SUBCLONAL	1	TRUE	1	0.38	2		703	816	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81954827	81954827	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	145	575	0	ENST00000359376.3:c.2260G>A	p.Asp754Asn	p.D754N	ENST00000359376	NM_002661.3	754	Gac/Aac	21/33	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.38	2		575	597	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348714	89348714	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	200	772	0	ENST00000301030.4:c.4236A>G	p.Ile1412Met	p.I1412M	ENST00000301030	NM_001256183.1	1412	atA/atG	9/13	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.38	2		772	1001	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349013	89349013	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	79	847	1	ENST00000301030.4:c.3937C>T	p.Gln1313Ter	p.Q1313*	ENST00000301030	NM_001256183.1	1313	Cag/Tag	9/13	1	2	FACETS	0.436	0.383	0.494	0.436	0.383	0.494	SUBCLONAL	1	TRUE	1	0.38	2		848	953	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89825072	89825072	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	44	621	0	ENST00000389301.3:c.2894C>T	p.Pro965Leu	p.P965L	ENST00000389301	NM_000135.2	965	cCt/cTt	30/43	1	2	FACETS	0.29	0.242	0.343	0.29	0.242	0.343	SUBCLONAL	1	TRUE	1	0.38	2		621	799	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7218299	7218299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	41	584	2	ENST00000380728.2:c.73G>A	p.Glu25Lys	p.E25K	ENST00000380728		25	Gag/Aag	2/11	1	2	FACETS	0.31	0.257	0.368	0.31	0.257	0.368	SUBCLONAL	1	TRUE	1	0.38	2		586	697	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7218344	7218344	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1309160387	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	50	614	1	ENST00000380728.2:c.28C>T	p.Leu10Phe	p.L10F	ENST00000380728		10	Ctt/Ttt	2/11	1	2	FACETS	0.326	0.276	0.382	0.326	0.276	0.382	SUBCLONAL	1	TRUE	1	0.38	2		615	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577590	7577590	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	66	565	0	ENST00000269305.4:c.691A>C	p.Thr231Pro	p.T231P	ENST00000269305	NM_001126112.2	231	Acc/Ccc	7/11	1	2	FACETS	0.44	0.381	0.504	0.44	0.381	0.504	SUBCLONAL	1	TRUE	1	0.38	2		565	790	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989346	7989346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397514526	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	149	797	1	ENST00000319144.4:c.340C>T	p.Arg114Trp	p.R114W	ENST00000319144	NM_001139.2	114	Cgg/Tgg	2/15	1	2	FACETS	0.867	0.792	0.946	0.867	0.792	0.946	CLONAL	1	TRUE	1	0.38	2		798	904	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990615	7990615	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs143526675	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	130	431	0	ENST00000319144.4:c.146C>T	p.Ala49Val	p.A49V	ENST00000319144	NM_001139.2	49	gCg/gTg	1/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.38	2		431	611	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8111146	8111146	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	39	561	0	ENST00000585124.1:c.61C>A	p.Leu21Met	p.L21M	ENST00000585124	NM_004217.3	21	Ctg/Atg	3/9	1	2	FACETS	0.288	0.238	0.344	0.288	0.238	0.344	SUBCLONAL	1	TRUE	1	0.38	2		561	713	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961847	15961847	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763880485	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	69	541	0	ENST00000268712.3:c.5948C>T	p.Ala1983Val	p.A1983V	ENST00000268712	NM_006311.3	1983	gCg/gTg	38/46	0.3	3	FACETS	0.644	0.561	0.734			1	SUBCLONAL	1	TRUE	NA	0.38	3		541	671	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15976805	15976805	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	21	434	0	ENST00000268712.3:c.3749T>C	p.Val1250Ala	p.V1250A	ENST00000268712	NM_006311.3	1250	gTg/gCg	28/46	0.3	3	FACETS	0.324	0.249	0.412			1	SUBCLONAL	1	TRUE	NA	0.38	3		434	406	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012152	16012152	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	42	479	0	ENST00000268712.3:c.2130G>T	p.Glu710Asp	p.E710D	ENST00000268712	NM_006311.3	710	gaG/gaT	19/46	0.3	3	FACETS	0.506	0.422	0.599			1	SUBCLONAL	1	TRUE	NA	0.38	3		479	520	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029445	16029446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	74	279	5	ENST00000268712.3:c.1584dup	p.Glu529ArgfsTer7	p.E529Rfs*7	ENST00000268712	NM_006311.3	528	-/A	15/46	0.3	3	FACETS	1	0.972	1			1	CLONAL	1	TRUE	NA	0.38	3		284	338	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131216	17131216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	213	855	0	ENST00000285071.4:c.236C>T	p.Ser79Leu	p.S79L	ENST00000285071	NM_144997.5	79	tCg/tTg	4/14	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.38	2		855	1051	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618854	37618854	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1236743086	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	116	608	0	ENST00000447079.4:c.530C>A	p.Ser177Tyr	p.S177Y	ENST00000447079	NM_015083.1	177	tCc/tAc	1/14	1	2	FACETS	0.707	0.637	0.782	0.707	0.637	0.782	SUBCLONAL	1	TRUE	1	0.38	2		608	863	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682300	37682300	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762780789	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	96	631	0	ENST00000447079.4:c.3491C>A	p.Thr1164Asn	p.T1164N	ENST00000447079	NM_015083.1	1164	aCt/aAt	13/14	1	2	FACETS	0.674	0.6	0.752	0.674	0.6	0.752	SUBCLONAL	1	TRUE	1	0.38	2		631	750	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864583	37864583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	81	511	0	ENST00000269571.5:c.235G>A	p.Glu79Lys	p.E79K	ENST00000269571		79	Gag/Aag	3/27	1	2	FACETS	0.715	0.631	0.806	0.715	0.631	0.806	SUBCLONAL	1	TRUE	1	0.38	2		511	596	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864706	37864706	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	119	732	0	ENST00000269571.5:c.358G>A	p.Gly120Arg	p.G120R	ENST00000269571		120	Gga/Aga	3/27	1	2	FACETS	0.668	0.602	0.737	0.668	0.602	0.737	SUBCLONAL	1	TRUE	1	0.38	2		732	938	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37882874	37882874	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758973569	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	73	735	0	ENST00000269571.5:c.2932C>T	p.Arg978Cys	p.R978C	ENST00000269571		978	Cgc/Tgc	24/27	1	2	FACETS	0.464	0.405	0.528	0.464	0.405	0.528	SUBCLONAL	1	TRUE	1	0.38	2		735	828	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883719	37883719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143958183	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	229	937	3	ENST00000269571.5:c.3331C>T	p.Arg1111Trp	p.R1111W	ENST00000269571		1111	Cgg/Tgg	26/27	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.38	2		940	1091	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359681	40359681	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148568485	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	147	669	0	ENST00000293328.3:c.1972G>A	p.Asp658Asn	p.D658N	ENST00000293328	NM_012448.3	658	Gac/Aac	16/19	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.38	2		669	767	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375486	40375486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138255473	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	194	691	0	ENST00000293328.3:c.464C>T	p.Thr155Met	p.T155M	ENST00000293328	NM_012448.3	155	aCg/aTg	5/19	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.38	2		691	895	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40458299	40458299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757085900	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	49	644	0	ENST00000345506.4:c.1514C>T	p.Pro505Leu	p.P505L	ENST00000345506	NM_003152.3	505	cCg/cTg	14/20	1	2	FACETS	0.315	0.266	0.369	0.315	0.266	0.369	SUBCLONAL	1	TRUE	1	0.38	2		644	819	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41199717	41199717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	43	644	0	ENST00000357654.3:c.5410G>A	p.Val1804Ile	p.V1804I	ENST00000357654	NM_007294.3	1804	Gtc/Atc	22/23	1	2	FACETS	0.279	0.233	0.331	0.279	0.233	0.331	SUBCLONAL	1	TRUE	1	0.38	2		644	810	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55334109	55334109	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	24	360	1	ENST00000284073.2:c.6G>T	p.Glu2Asp	p.E2D	ENST00000284073	NM_138962.2	2	gaG/gaT	1/14	1	2	FACETS	0.267	0.209	0.335	0.267	0.209	0.335	SUBCLONAL	1	TRUE	1	0.38	2		361	473	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435755	56435755	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	34	572	1	ENST00000407977.2:c.1382G>T	p.Gly461Val	p.G461V	ENST00000407977		461	gGg/gTg	9/10	1	2	FACETS	0.299	0.243	0.361	0.299	0.243	0.361	SUBCLONAL	1	TRUE	1	0.38	2		573	599	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734156	58734156	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	60	528	0	ENST00000305921.3:c.1214A>C	p.Glu405Ala	p.E405A	ENST00000305921	NM_003620.3	405	gAa/gCa	5/6	1	2	FACETS	0.528	0.455	0.608	0.528	0.455	0.608	SUBCLONAL	1	TRUE	1	0.38	2		528	598	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740623	58740624	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs763475304	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	56	519	0	ENST00000305921.3:c.1535dup	p.Asn512LysfsTer16	p.N512Kfs*16	ENST00000305921	NM_003620.3	510	caa/cAaa	6/6	1	2	FACETS	0.554	0.475	0.641	0.554	0.475	0.641	SUBCLONAL	1	TRUE	1	0.38	2		519	532	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740742	58740742	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	128	583	0	ENST00000305921.3:c.1647G>T	p.Lys549Asn	p.K549N	ENST00000305921	NM_003620.3	549	aaG/aaT	6/6	1	2	FACETS	0.988	0.897	1	0.988	0.897	1	CLONAL	1	TRUE	1	0.38	2		583	682	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59793369	59793369	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659410	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	27	472	0	ENST00000259008.2:c.2435C>T	p.Pro812Leu	p.P812L	ENST00000259008	NM_032043.2	812	cCt/cTt	17/20	1	2	FACETS	0.311	0.247	0.385	0.311	0.247	0.385	SUBCLONAL	1	TRUE	1	0.38	2		472	457	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861644	59861645	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	39	270	0	ENST00000259008.2:c.1614dup	p.Arg539Ter	p.R539*	ENST00000259008	NM_032043.2	538	-/T	11/20	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.38	2		270	184	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511578	66511578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	28	382	1	ENST00000358598.2:c.38G>A	p.Arg13His	p.R13H	ENST00000358598	NM_212471.2	13	cGc/cAc	2/11	1	2	FACETS	0.322	0.257	0.397	0.322	0.257	0.397	SUBCLONAL	1	TRUE	1	0.38	2		383	457	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118987	70118987	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771056492	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	54	852	1	ENST00000245479.2:c.559G>A	p.Ala187Thr	p.A187T	ENST00000245479	NM_000346.3	187	Gcg/Acg	2/3	1	2	FACETS	0.265	0.225	0.309	0.265	0.225	0.309	SUBCLONAL	1	TRUE	1	0.38	2		853	1073	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119809	70119809	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771635102	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	47	780	2	ENST00000245479.2:c.811C>T	p.Arg271Cys	p.R271C	ENST00000245479	NM_000346.3	271	Cgc/Tgc	3/3	1	2	FACETS	0.289	0.242	0.34	0.289	0.242	0.34	SUBCLONAL	1	TRUE	1	0.38	2		782	857	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796999	78796999	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	39	522	0	ENST00000306801.3:c.1112C>T	p.Pro371Leu	p.P371L	ENST00000306801	NM_020761.2	371	cCg/cTg	9/34	1	2	FACETS	0.307	0.253	0.367	0.307	0.253	0.367	SUBCLONAL	1	TRUE	1	0.38	2		522	669	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857650	78857650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184854653	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	132	784	0	ENST00000306801.3:c.1720C>T	p.Arg574Cys	p.R574C	ENST00000306801	NM_020761.2	574	Cgc/Tgc	16/34	1	2	FACETS	0.757	0.686	0.831	0.757	0.686	0.831	SUBCLONAL	1	TRUE	1	0.38	2		784	918	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896573	78896573	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	235	932	2	ENST00000306801.3:c.2570C>T	p.Thr857Met	p.T857M	ENST00000306801	NM_020761.2	857	aCg/aTg	22/34	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.38	2		934	1093	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422913	45422913	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	21	265	0	ENST00000262160.6:c.215C>A	p.Thr72Asn	p.T72N	ENST00000262160	NM_005901.5	72	aCt/aAt	2/11	1	2	FACETS	0.314	0.241	0.399	0.314	0.241	0.399	SUBCLONAL	1	TRUE	1	0.38	2		265	352	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56363666	56363666	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763701192	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	110	421	0	ENST00000348428.3:c.445C>T	p.Arg149Trp	p.R149W	ENST00000348428	NM_006785.3	149	Cgg/Tgg	3/17	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.38	2		421	556	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612274	1612274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377185315	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	205	786	2	ENST00000344749.5:c.1745C>T	p.Ala582Val	p.A582V	ENST00000344749	NM_001136139.2	582	gCg/gTg	18/19	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.38	2		788	919	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612308	1612308	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753925052	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	175	863	1	ENST00000344749.5:c.1711C>T	p.Arg571Cys	p.R571C	ENST00000344749	NM_001136139.2	571	Cgc/Tgc	18/19	1	2	FACETS	0.858	0.789	0.929	0.858	0.789	0.929	CLONAL	1	TRUE	1	0.38	2		864	1074	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615691	1615691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141432924	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	152	896	1	ENST00000344749.5:c.1580G>A	p.Arg527Gln	p.R527Q	ENST00000344749	NM_001136139.2	527	cGg/cAg	17/19	1	2	FACETS	0.721	0.658	0.787	0.721	0.658	0.787	SUBCLONAL	1	TRUE	1	0.38	2		897	1109	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217846	2217846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	132	824	1	ENST00000398665.3:c.2620G>A	p.Val874Met	p.V874M	ENST00000398665	NM_032482.2	874	Gtg/Atg	22/28	1	2	FACETS	0.678	0.615	0.746	0.678	0.615	0.746	SUBCLONAL	1	TRUE	1	0.38	2		825	1024	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226346	2226346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759369415	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	57	977	3	ENST00000398665.3:c.3826C>T	p.Arg1276Trp	p.R1276W	ENST00000398665	NM_032482.2	1276	Cgg/Tgg	27/28	1	2	FACETS	0.271	0.231	0.315	0.271	0.231	0.315	SUBCLONAL	1	TRUE	1	0.38	2		980	1107	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226589	2226589	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760808115	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	76	884	0	ENST00000398665.3:c.4069C>T	p.Arg1357Cys	p.R1357C	ENST00000398665	NM_032482.2	1357	Cgc/Tgc	27/28	1	2	FACETS	0.409	0.358	0.465	0.409	0.358	0.465	SUBCLONAL	1	TRUE	1	0.38	2		884	978	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222705	5222705	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	55	594	0	ENST00000357368.4:c.3098A>G	p.Asp1033Gly	p.D1033G	ENST00000357368	NM_002850.3	1033	gAc/gGc	18/38	1	2	FACETS	0.362	0.309	0.421	0.362	0.309	0.421	SUBCLONAL	1	TRUE	1	0.38	2		594	799	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273593	5273593	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs146675930	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	31	415	0	ENST00000357368.4:c.239C>T	p.Thr80Met	p.T80M	ENST00000357368	NM_002850.3	80	aCg/aTg	4/38	1	2	FACETS	0.312	0.252	0.381	0.312	0.252	0.381	SUBCLONAL	1	TRUE	1	0.38	2		415	523	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125431	7125431	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	207	893	1	ENST00000302850.5:c.3121A>G	p.Asn1041Asp	p.N1041D	ENST00000302850	NM_000208.2	1041	Aat/Gat	17/22	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.38	2		894	1005	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125515	7125515	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	90	589	0	ENST00000302850.5:c.3037C>T	p.Pro1013Ser	p.P1013S	ENST00000302850	NM_000208.2	1013	Ccg/Tcg	17/22	1	2	FACETS	0.65	0.576	0.728	0.65	0.576	0.728	SUBCLONAL	1	TRUE	1	0.38	2		589	729	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184349	7184349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	73	665	0	ENST00000302850.5:c.952G>T	p.Gly318Trp	p.G318W	ENST00000302850	NM_000208.2	318	Ggg/Tgg	3/22	1	2	FACETS	0.414	0.361	0.472	0.414	0.361	0.472	SUBCLONAL	1	TRUE	1	0.38	2		665	927	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184534	7184534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775222338	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	196	590	0	ENST00000302850.5:c.767G>A	p.Arg256His	p.R256H	ENST00000302850	NM_000208.2	256	cGc/cAc	3/22	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.38	2		590	880	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267556	7267556	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	66	684	0	ENST00000302850.5:c.452A>C	p.Glu151Ala	p.E151A	ENST00000302850	NM_000208.2	151	gAg/gCg	2/22	1	2	FACETS	0.348	0.301	0.399	0.348	0.301	0.399	SUBCLONAL	1	TRUE	1	0.38	2		684	999	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249230	10249230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779967013	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	45	687	1	ENST00000340748.4:c.3952G>A	p.Ala1318Thr	p.A1318T	ENST00000340748		1318	Gcg/Acg	34/40	1	2	FACETS	0.301	0.252	0.356	0.301	0.252	0.356	SUBCLONAL	1	TRUE	1	0.38	2		688	786	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10266541	10266541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	76	504	2	ENST00000340748.4:c.1432G>A	p.Gly478Ser	p.G478S	ENST00000340748		478	Ggc/Agc	18/40	1	2	FACETS	0.572	0.502	0.648	0.572	0.502	0.648	SUBCLONAL	1	TRUE	1	0.38	2		506	699	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610105	10610105	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775608603	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	112	737	1	ENST00000171111.5:c.605G>A	p.Arg202His	p.R202H	ENST00000171111	NM_203500.1	202	cGt/cAt	2/6	1	2	FACETS	0.637	0.572	0.705	0.637	0.572	0.705	SUBCLONAL	1	TRUE	1	0.38	2		738	926	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610562	10610562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752044333	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	189	827	1	ENST00000171111.5:c.148C>T	p.Arg50Cys	p.R50C	ENST00000171111	NM_203500.1	50	Cgc/Tgc	2/6	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.38	2		828	972	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031170	11031170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	77	835	0	ENST00000327064.4:c.1255C>T	p.Arg419Trp	p.R419W	ENST00000327064	NM_199141.1	419	Cgg/Tgg	11/16	1	2	FACETS	0.377	0.33	0.429	0.377	0.33	0.429	SUBCLONAL	1	TRUE	1	0.38	2		835	1074	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031619	11031619	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	82	895	0	ENST00000327064.4:c.1534G>T	p.Ala512Ser	p.A512S	ENST00000327064	NM_199141.1	512	Gca/Tca	13/16	1	2	FACETS	0.462	0.406	0.522	0.462	0.406	0.522	SUBCLONAL	1	TRUE	1	0.38	2		895	934	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097135	11097135	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778071122	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	144	810	0	ENST00000358026.2:c.626C>T	p.Pro209Leu	p.P209L	ENST00000358026	NM_001128849.1	209	cCg/cTg	4/36	1	2	FACETS	0.764	0.696	0.836	0.764	0.696	0.836	SUBCLONAL	1	TRUE	1	0.38	2		810	992	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107209	11107209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	253	700	1	ENST00000358026.2:c.1801C>T	p.Pro601Ser	p.P601S	ENST00000358026	NM_001128849.1	601	Ccg/Tcg	11/36	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.38	2		701	1034	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11114033	11114033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	42	490	0	ENST00000358026.2:c.1961G>A	p.Arg654Lys	p.R654K	ENST00000358026	NM_001128849.1	654	aGg/aAg	13/36	1	2	FACETS	0.36	0.3	0.427	0.36	0.3	0.427	SUBCLONAL	1	TRUE	1	0.38	2		490	614	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136141	11136141	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	68	761	0	ENST00000358026.2:c.3125T>A	p.Leu1042Gln	p.L1042Q	ENST00000358026	NM_001128849.1	1042	cTg/cAg	22/36	1	2	FACETS	0.342	0.296	0.391	0.342	0.296	0.391	SUBCLONAL	1	TRUE	1	0.38	2		761	1048	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11137009	11137009	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765857427	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	68	759	1	ENST00000358026.2:c.3202G>A	p.Gly1068Ser	p.G1068S	ENST00000358026	NM_001128849.1	1068	Ggc/Agc	23/36	1	2	FACETS	0.337	0.292	0.386	0.337	0.292	0.386	SUBCLONAL	1	TRUE	1	0.38	2		760	1063	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272495	15272495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	214	751	0	ENST00000263388.2:c.5944G>A	p.Glu1982Lys	p.E1982K	ENST00000263388	NM_000435.2	1982	Gag/Aag	33/33	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.38	2		751	968	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281305	15281305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	54	787	0	ENST00000263388.2:c.4951G>A	p.Ala1651Thr	p.A1651T	ENST00000263388	NM_000435.2	1651	Gct/Act	27/33	1	2	FACETS	0.272	0.231	0.317	0.272	0.231	0.317	SUBCLONAL	1	TRUE	1	0.38	2		787	1044	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284903	15284903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778647361	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	159	948	3	ENST00000263388.2:c.4712G>A	p.Arg1571Gln	p.R1571Q	ENST00000263388	NM_000435.2	1571	cGg/cAg	25/33	1	2	FACETS	0.745	0.681	0.811	0.745	0.681	0.811	SUBCLONAL	1	TRUE	1	0.38	2		951	1124	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290178	15290178	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	113	725	0	ENST00000263388.2:c.3457C>A	p.Leu1153Met	p.L1153M	ENST00000263388	NM_000435.2	1153	Ctg/Atg	21/33	1	2	FACETS	0.714	0.642	0.79	0.714	0.642	0.79	SUBCLONAL	1	TRUE	1	0.38	2		725	833	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291828	15291828	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376187165	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	250	936	1	ENST00000263388.2:c.2938G>A	p.Ala980Thr	p.A980T	ENST00000263388	NM_000435.2	980	Gcc/Acc	18/33	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.38	2		937	1070	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292410	15292410	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	115	845	0	ENST00000263388.2:c.2769G>T	p.Gln923His	p.Q923H	ENST00000263388	NM_000435.2	923	caG/caT	17/33	1	2	FACETS	0.655	0.589	0.725	0.655	0.589	0.725	SUBCLONAL	1	TRUE	1	0.38	2		845	924	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297773	15297773	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	241	915	4	ENST00000263388.2:c.1867G>A	p.Asp623Asn	p.D623N	ENST00000263388	NM_000435.2	623	Gac/Aac	12/33	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.38	2		919	1054	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300159	15300159	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1435305678	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	227	872	0	ENST00000263388.2:c.1117G>A	p.Gly373Ser	p.G373S	ENST00000263388	NM_000435.2	373	Ggc/Agc	7/33	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.38	2		872	1090	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303031	15303031	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	182	999	1	ENST00000263388.2:c.419G>A	p.Gly140Glu	p.G140E	ENST00000263388	NM_000435.2	140	gGa/gAa	4/33	1	2	FACETS	0.839	0.773	0.908	0.839	0.773	0.908	CLONAL	1	TRUE	1	0.38	2		1000	1142	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379814	17379814	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	189	1000	0	ENST00000359435.4:c.199G>T	p.Gly67Ter	p.G67*	ENST00000359435	NM_001033549.1	67	Gga/Tga	2/9	1	2	FACETS	0.774	0.713	0.837	0.774	0.713	0.837	SUBCLONAL	1	TRUE	1	0.38	2		1000	1286	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951064	17951064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	48	722	1	ENST00000458235.1:c.1229G>A	p.Ser410Asn	p.S410N	ENST00000458235	NM_000215.3	410	aGc/aAc	9/24	1	2	FACETS	0.265	0.223	0.312	0.265	0.223	0.312	SUBCLONAL	1	TRUE	1	0.38	2		723	952	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968331	18968331	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	57	776	1	ENST00000262803.5:c.2171G>A	p.Gly724Asp	p.G724D	ENST00000262803	NM_002911.3	724	gGt/gAt	15/24	1	2	FACETS	0.337	0.288	0.39	0.337	0.288	0.39	SUBCLONAL	1	TRUE	1	0.38	2		777	891	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974254	18974254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149336516	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	66	586	0	ENST00000262803.5:c.2608G>A	p.Val870Ile	p.V870I	ENST00000262803	NM_002911.3	870	Gtc/Atc	19/24	1	2	FACETS	0.515	0.447	0.59	0.515	0.447	0.59	SUBCLONAL	1	TRUE	1	0.38	2		586	674	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311657	30311657	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	47	374	0	ENST00000262643.3:c.511G>T	p.Asp171Tyr	p.D171Y	ENST00000262643	NM_001238.2	171	Gat/Tat	7/12	1	2	FACETS	0.663	0.561	0.775	0.663	0.561	0.775	SUBCLONAL	1	TRUE	1	0.38	2		374	373	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314649	30314649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764865470	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	117	649	0	ENST00000262643.3:c.1198G>A	p.Gly400Ser	p.G400S	ENST00000262643	NM_001238.2	400	Ggt/Agt	12/12	1	2	FACETS	0.682	0.614	0.754	0.682	0.614	0.754	SUBCLONAL	1	TRUE	1	0.38	2		649	903	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210898	36210898	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747219825	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	54	850	0	ENST00000222270.7:c.649C>T	p.Arg217Trp	p.R217W	ENST00000222270	NM_014727.1	217	Cgg/Tgg	3/37	1	2	FACETS	0.301	0.256	0.35	0.301	0.256	0.35	SUBCLONAL	1	TRUE	1	0.38	2		850	945	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213295	36213295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	59	798	0	ENST00000222270.7:c.2492G>A	p.Gly831Glu	p.G831E	ENST00000222270	NM_014727.1	831	gGg/gAg	4/37	1	2	FACETS	0.274	0.234	0.317	0.274	0.234	0.317	SUBCLONAL	1	TRUE	1	0.38	2		798	1134	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220138	36220138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1201006738	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	83	764	1	ENST00000222270.7:c.4858G>A	p.Glu1620Lys	p.E1620K	ENST00000222270	NM_014727.1	1620	Gag/Aag	22/37	1	2	FACETS	0.406	0.357	0.458	0.406	0.357	0.458	SUBCLONAL	1	TRUE	1	0.38	2		765	1077	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221273	36221273	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	223	846	0	ENST00000222270.7:c.5107C>A	p.Leu1703Ile	p.L1703I	ENST00000222270	NM_014727.1	1703	Ctc/Atc	24/37	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.38	2		846	1146	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223508	36223508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	118	878	1	ENST00000222270.7:c.6058C>T	p.Pro2020Ser	p.P2020S	ENST00000222270	NM_014727.1	2020	Ccg/Tcg	28/37	1	2	FACETS	0.633	0.57	0.7	0.633	0.57	0.7	SUBCLONAL	1	TRUE	1	0.38	2		879	981	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228065	36228065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1285582819	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	52	861	0	ENST00000222270.7:c.7451G>A	p.Arg2484His	p.R2484H	ENST00000222270	NM_014727.1	2484	cGt/cAt	33/37	1	2	FACETS	0.279	0.237	0.326	0.279	0.237	0.326	SUBCLONAL	1	TRUE	1	0.38	2		861	980	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229256	36229256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	66	737	0	ENST00000222270.7:c.7946G>A	p.Arg2649His	p.R2649H	ENST00000222270	NM_014727.1	2649	cGc/cAc	37/37	1	2	FACETS	0.399	0.346	0.458	0.399	0.346	0.458	SUBCLONAL	1	TRUE	1	0.38	2		737	870	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745212	41745212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1417369748	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	90	616	1	ENST00000301178.4:c.1278G>A	p.Trp426Ter	p.W426*	ENST00000301178	NM_021913.4	426	tgG/tgA	9/20	1	2	FACETS	0.649	0.576	0.727	0.649	0.576	0.727	SUBCLONAL	1	TRUE	1	0.38	2		617	730	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763501	41763501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200271277	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	31	507	0	ENST00000301178.4:c.2300G>A	p.Arg767His	p.R767H	ENST00000301178	NM_021913.4	767	cGc/cAc	19/20	1	2	FACETS	0.267	0.215	0.326	0.267	0.215	0.326	SUBCLONAL	1	TRUE	1	0.38	2		507	611	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383170	42383170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374041941	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	134	799	2	ENST00000221972.3:c.190G>A	p.Val64Ile	p.V64I	ENST00000221972	NM_021601.3	64	Gtc/Atc	2/5	1	2	FACETS	0.689	0.625	0.756	0.689	0.625	0.756	SUBCLONAL	1	TRUE	1	0.38	2		801	1024	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383298	42383298	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	166	683	0	ENST00000221972.3:c.318C>A	p.Cys106Ter	p.C106*	ENST00000221972	NM_021601.3	106	tgC/tgA	2/5	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.38	2		683	832	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793181	42793181	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143474767	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	69	917	0	ENST00000575354.2:c.1073G>A	p.Ser358Asn	p.S358N	ENST00000575354	NM_015125.3	358	aGc/aAc	7/20	1	2	FACETS	0.315	0.273	0.361	0.315	0.273	0.361	SUBCLONAL	1	TRUE	1	0.38	2		917	1153	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793472	42793472	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201067032	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	198	755	0	ENST00000575354.2:c.1274G>A	p.Arg425His	p.R425H	ENST00000575354	NM_015125.3	425	cGt/cAt	8/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.38	2		755	917	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798197	42798197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	208	784	0	ENST00000575354.2:c.4151G>A	p.Arg1384Gln	p.R1384Q	ENST00000575354	NM_015125.3	1384	cGg/cAg	17/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.38	2		784	964	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798803	42798803	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781618956	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	113	805	0	ENST00000575354.2:c.4375C>T	p.Pro1459Ser	p.P1459S	ENST00000575354	NM_015125.3	1459	Cca/Tca	19/20	1	2	FACETS	0.677	0.609	0.75	0.677	0.609	0.75	SUBCLONAL	1	TRUE	1	0.38	2		805	878	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906786	50906786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778843530	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	226	879	3	ENST00000440232.2:c.1174G>A	p.Val392Met	p.V392M	ENST00000440232	NM_002691.3	392	Gtg/Atg	10/27	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.38	2		882	1080	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705201	52705201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1372727039	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	104	434	1	ENST00000322088.6:c.83G>A	p.Arg28His	p.R28H	ENST00000322088	NM_014225.5	28	cGc/cAc	2/15	1	2	FACETS	0.928	0.833	1	0.928	0.833	1	CLONAL	1	TRUE	1	0.38	2		435	590	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714517	52714517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs950558629	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	165	502	1	ENST00000322088.6:c.275C>T	p.Pro92Leu	p.P92L	ENST00000322088	NM_014225.5	92	cCg/cTg	4/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.38	2		503	717	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082625	16082625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	40	160	0	ENST00000281043.3:c.439G>A	p.Ala147Thr	p.A147T	ENST00000281043	NM_005378.4	147	Gcc/Acc	2/3	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.38	2		160	171	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25462033	25462033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	41	544	1	ENST00000264709.3:c.2374C>T	p.Arg792Cys	p.R792C	ENST00000264709	NM_175629.2	792	Cgc/Tgc	20/23	1	2	FACETS	0.273	0.226	0.325	0.273	0.226	0.325	SUBCLONAL	1	TRUE	1	0.38	2		545	790	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469037	25469037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457323351	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	120	662	1	ENST00000264709.3:c.1421G>A	p.Arg474His	p.R474H	ENST00000264709	NM_175629.2	474	cGc/cAc	11/23	1	2	FACETS	0.849	0.767	0.935	0.849	0.767	0.935	CLONAL	1	TRUE	1	0.38	2		663	744	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523073	25523073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779208522	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	78	806	0	ENST00000264709.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000264709	NM_175629.2	38	Cgc/Tgc	3/23	1	2	FACETS	0.428	0.375	0.485	0.428	0.375	0.485	SUBCLONAL	1	TRUE	1	0.38	2		806	959	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965955	25965955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1330141951	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	61	682	0	ENST00000435504.4:c.3251C>T	p.Pro1084Leu	p.P1084L	ENST00000435504		1084	cCg/cTg	13/13	1	2	FACETS	0.359	0.309	0.414	0.359	0.309	0.414	SUBCLONAL	1	TRUE	1	0.38	2		682	894	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498010	29498010	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	143	587	0	ENST00000389048.3:c.1996C>A	p.Pro666Thr	p.P666T	ENST00000389048	NM_004304.4	666	Ccc/Acc	11/29	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.38	2		587	722	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213059	39213059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	229	945	0	ENST00000402219.2:c.3908C>T	p.Pro1303Leu	p.P1303L	ENST00000402219	NM_005633.3	1303	cCt/cTt	23/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.38	2		945	1121	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249864	39249864	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	48	523	0	ENST00000402219.2:c.1705C>A	p.Leu569Met	p.L569M	ENST00000402219	NM_005633.3	569	Ctg/Atg	10/23	1	2	FACETS	0.542	0.459	0.634	0.542	0.459	0.634	SUBCLONAL	1	TRUE	1	0.38	2		523	466	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033719	48033719	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	54	331	0	ENST00000234420.5:c.3930G>T	p.Glu1310Asp	p.E1310D	ENST00000234420	NM_000179.2	1310	gaG/gaT	9/10	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.38	2		331	277	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149452	61149452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	21	336	0	ENST00000295025.8:c.1642G>A	p.Ala548Thr	p.A548T	ENST00000295025	NM_002908.2	548	Gcc/Acc	11/11	1	2	FACETS	0.318	0.244	0.403	0.318	0.244	0.403	SUBCLONAL	1	TRUE	1	0.38	2		336	348	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99181169	99181169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778648043	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	41	627	1	ENST00000074304.5:c.2110C>T	p.Arg704Cys	p.R704C	ENST00000074304	NM_001134224.1	704	Cgc/Tgc	20/26	1	2	FACETS	0.286	0.237	0.341	0.286	0.237	0.341	SUBCLONAL	1	TRUE	1	0.38	2		628	754	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015243	128015243	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	166	624	1	ENST00000285398.2:c.2278G>A	p.Glu760Lys	p.E760K	ENST00000285398	NM_000122.1	760	Gag/Aag	15/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.38	2		625	781	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095985	178095985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs181294188	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	30	391	0	ENST00000397062.3:c.1346G>A	p.Arg449His	p.R449H	ENST00000397062	NM_006164.4	449	cGc/cAc	5/5	1	2	FACETS	0.335	0.269	0.41	0.335	0.269	0.41	SUBCLONAL	1	TRUE	1	0.38	2		391	471	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151297	202151297	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	34	348	0	ENST00000358485.4:c.1597C>A	p.Leu533Ile	p.L533I	ENST00000358485	NM_001080125.1	533	Ctt/Att	9/9	1	2	FACETS	0.388	0.317	0.469	0.388	0.317	0.469	SUBCLONAL	1	TRUE	1	0.38	2		348	461	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989569	212989569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	73	349	0	ENST00000342788.4:c.142G>A	p.Ala48Thr	p.A48T	ENST00000342788	NM_005235.2	48	Gcc/Acc	2/28	1	2	FACETS	0.854	0.749	0.966	0.854	0.749	0.966	CLONAL	1	TRUE	1	0.38	2		349	450	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440169	220440169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777288649	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	123	830	0	ENST00000243786.2:c.1022G>A	p.Arg341His	p.R341H	ENST00000243786	NM_002191.3	341	cGc/cAc	2/2	1	2	FACETS	0.7	0.632	0.771	0.7	0.632	0.771	SUBCLONAL	1	TRUE	1	0.38	2		830	925	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225360582	225360582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	10	184	0	ENST00000264414.4:c.1809G>A	p.Met603Ile	p.M603I	ENST00000264414	NM_003590.4	603	atG/atA	13/16	1	2	FACETS	0.269	0.182	0.378	0.269	0.182	0.378	SUBCLONAL	1	TRUE	1	0.38	2		184	196	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661555	227661555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	172	736	0	ENST00000305123.5:c.1900C>T	p.Pro634Ser	p.P634S	ENST00000305123	NM_005544.2	634	Ccc/Tcc	1/2	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.38	2		736	858	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661620	227661620	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	50	688	0	ENST00000305123.5:c.1835A>G	p.Tyr612Cys	p.Y612C	ENST00000305123	NM_005544.2	612	tAc/tGc	1/2	1	2	FACETS	0.368	0.311	0.43	0.368	0.311	0.43	SUBCLONAL	1	TRUE	1	0.38	2		688	716	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253829	30253829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759194807	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	175	543	0	ENST00000307677.4:c.625C>T	p.Arg209Cys	p.R209C	ENST00000307677	NM_138578.1	209	Cgc/Tgc	3/3	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.38	2		543	877	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019408	31019408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769717271	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	59	445	0	ENST00000375687.4:c.905G>A	p.Arg302His	p.R302H	ENST00000375687	NM_015338.5	302	cGt/cAt	10/13	1	2	FACETS	0.473	0.406	0.545	0.473	0.406	0.545	SUBCLONAL	1	TRUE	1	0.38	2		445	657	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374366	31374366	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757657111	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	56	646	1	ENST00000328111.2:c.365G>A	p.Arg122His	p.R122H	ENST00000328111	NM_006892.3	122	cGt/cAt	5/23	1	2	FACETS	0.344	0.294	0.4	0.344	0.294	0.4	SUBCLONAL	1	TRUE	1	0.38	2		647	856	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031708	36031708	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	69	814	0	ENST00000358208.4:c.1537G>A	p.Glu513Lys	p.E513K	ENST00000358208		513	Gag/Aag	12/12	1	2	FACETS	0.401	0.348	0.458	0.401	0.348	0.458	SUBCLONAL	1	TRUE	1	0.38	2		814	906	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750725	39750725	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	75	366	0	ENST00000361337.2:c.2125G>T	p.Glu709Ter	p.E709*	ENST00000361337	NM_003286.2	709	Gag/Tag	20/21	1	2	FACETS	0.849	0.746	0.959	0.849	0.746	0.959	CLONAL	1	TRUE	1	0.38	2		366	465	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100981	41100981	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188436636	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	138	625	0	ENST00000373198.4:c.1375C>T	p.Arg459Trp	p.R459W	ENST00000373198	NM_133170.3	459	Cgg/Tgg	8/32	1	2	FACETS	0.956	0.871	1	0.956	0.871	1	CLONAL	1	TRUE	1	0.38	2		625	760	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961423	54961423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767515238	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	53	214	1	ENST00000312783.6:c.209C>T	p.Pro70Leu	p.P70L	ENST00000312783	NM_198436.1	70	cCg/cTg	4/10	1	2	FACETS	0.989	0.85	1	0.989	0.85	1	CLONAL	1	TRUE	1	0.38	2		215	282	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961466	54961466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375420005	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	54	338	0	ENST00000312783.6:c.166C>T	p.Arg56Cys	p.R56C	ENST00000312783	NM_198436.1	56	Cgc/Tgc	4/10	1	2	FACETS	0.591	0.505	0.684	0.591	0.505	0.684	SUBCLONAL	1	TRUE	1	0.38	2		338	481	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961498	54961498	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	38	523	0	ENST00000312783.6:c.134A>G	p.Gln45Arg	p.Q45R	ENST00000312783	NM_198436.1	45	cAg/cGg	4/10	1	2	FACETS	0.281	0.231	0.336	0.281	0.231	0.336	SUBCLONAL	1	TRUE	1	0.38	2		523	713	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484231	57484231	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	42	419	0	ENST00000371085.3:c.545T>G	p.Ile182Ser	p.I182S	ENST00000371085	NM_000516.4	182	aTc/aGc	7/13	1	2	FACETS	0.33	0.275	0.392	0.33	0.275	0.392	SUBCLONAL	1	TRUE	1	0.38	2		419	670	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292823	62292823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	28	361	0	ENST00000360203.5:c.275C>T	p.Ala92Val	p.A92V	ENST00000360203	NM_001283009.1	92	gCt/gTt	3/35	1	2	FACETS	0.344	0.275	0.424	0.344	0.275	0.424	SUBCLONAL	1	TRUE	1	0.38	2		361	428	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171670	36171670	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	72	442	1	ENST00000300305.3:c.895G>T	p.Ala299Ser	p.A299S	ENST00000300305		299	Gca/Tca	7/8	1	2	FACETS	0.635	0.555	0.721	0.635	0.555	0.721	SUBCLONAL	1	TRUE	1	0.38	2		443	597	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259153	36259153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	190	621	0	ENST00000300305.3:c.338C>T	p.Pro113Leu	p.P113L	ENST00000300305		113	cCc/cTc	3/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.38	2		621	797	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513258	44513258	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	165	533	0	ENST00000291552.4:c.677G>A	p.Arg226His	p.R226H	ENST00000291552	NM_006758.2	226	cGt/cAt	8/8	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.38	2		533	843	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24134046	24134046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1268653633	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	33	445	0	ENST00000263121.7:c.197C>T	p.Ser66Leu	p.S66L	ENST00000263121	NM_003073.3	66	tCg/tTg	2/9	1	2	FACETS	0.308	0.25	0.374	0.308	0.25	0.374	SUBCLONAL	1	TRUE	1	0.38	2		445	564	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121073	29121073	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555926943	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	109	533	0	ENST00000328354.6:c.484G>T	p.Asp162Tyr	p.D162Y	ENST00000328354	NM_007194.3	162	Gat/Tat	4/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.38	2		533	500	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37628873	37628873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	160	867	0	ENST00000249071.6:c.193G>A	p.Asp65Asn	p.D65N	ENST00000249071	NM_002872.4	65	Gac/Aac	3/7	1	2	FACETS	0.8	0.733	0.871	0.8	0.733	0.871	SUBCLONAL	1	TRUE	1	0.38	2		867	1052	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572254	41572254	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057517732	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	80	638	0	ENST00000263253.7:c.4783T>G	p.Phe1595Val	p.F1595V	ENST00000263253	NM_001429.3	1595	Ttc/Gtc	30/31	1	2	FACETS	0.52	0.457	0.588	0.52	0.457	0.588	SUBCLONAL	1	TRUE	1	0.38	2		638	810	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37058999	37058999	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs63751194	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	72	358	0	ENST00000231790.2:c.793C>T	p.Arg265Cys	p.R265C	ENST00000231790	NM_000249.3	265	Cgt/Tgt	10/19	1	2	FACETS	0.964	0.847	1	0.964	0.847	1	CLONAL	1	TRUE	1	0.38	2		358	393	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070399	37070399	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63751472	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	65	336	0	ENST00000231790.2:c.1534G>T	p.Glu512Ter	p.E512*	ENST00000231790	NM_000249.3	512	Gaa/Taa	13/19	1	2	FACETS	0.932	0.813	1	0.932	0.813	1	CLONAL	1	TRUE	1	0.38	2		336	367	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098949	47098949	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	120	558	2	ENST00000409792.3:c.6325C>T	p.Arg2109Ter	p.R2109*	ENST00000409792	NM_014159.6	2109	Cga/Tga	15/21	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.38	2		560	627	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165255	47165255	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	36	232	0	ENST00000409792.3:c.871G>T	p.Glu291Ter	p.E291*	ENST00000409792	NM_014159.6	291	Gaa/Taa	3/21	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.38	2		232	149	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928639	49928639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1008363508	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	160	670	1	ENST00000296474.3:c.3635G>A	p.Arg1212Gln	p.R1212Q	ENST00000296474	NM_002447.2	1212	cGg/cAg	17/20	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.38	2		671	822	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940025	49940025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201546006	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	99	790	2	ENST00000296474.3:c.1018G>A	p.Ala340Thr	p.A340T	ENST00000296474	NM_002447.2	340	Gcc/Acc	1/20	1	2	FACETS	0.538	0.479	0.601	0.538	0.479	0.601	SUBCLONAL	1	TRUE	1	0.38	2		792	968	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436438	52436438	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	55	547	0	ENST00000460680.1:c.2057-1G>T		p.X686_splice	ENST00000460680	NM_004656.3	686			1	2	FACETS	0.45	0.384	0.522	0.45	0.384	0.522	SUBCLONAL	1	TRUE	1	0.38	2		547	643	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437206	52437206	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35448940	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	178	797	0	ENST00000460680.1:c.1838C>T	p.Thr613Met	p.T613M	ENST00000460680	NM_004656.3	613	aCg/aTg	14/17	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.38	2		797	933	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437516	52437516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	108	738	0	ENST00000460680.1:c.1645G>A	p.Ala549Thr	p.A549T	ENST00000460680	NM_004656.3	549	Gct/Act	13/17	1	2	FACETS	0.634	0.569	0.704	0.634	0.569	0.704	SUBCLONAL	1	TRUE	1	0.38	2		738	896	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582210	52582210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200020801	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	27	357	0	ENST00000394830.3:c.4618C>T	p.Arg1540Cys	p.R1540C	ENST00000394830	NM_018313.4	1540	Cgc/Tgc	30/30	1	2	FACETS	0.299	0.237	0.369	0.299	0.237	0.369	SUBCLONAL	1	TRUE	1	0.38	2		357	476	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651507	52651507	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	99	440	0	ENST00000394830.3:c.1589T>C	p.Val530Ala	p.V530A	ENST00000394830	NM_018313.4	530	gTt/gCt	15/30	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.38	2		440	445	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668619	52668619	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	52	298	0	ENST00000394830.3:c.1300C>T	p.Arg434Ter	p.R434*	ENST00000394830	NM_018313.4	434	Cga/Tga	12/30	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.38	2		298	267	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668691	52668691	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	34	398	0	ENST00000394830.3:c.1228C>A	p.His410Asn	p.H410N	ENST00000394830	NM_018313.4	410	Cat/Aat	12/30	1	2	FACETS	0.45	0.367	0.542	0.45	0.367	0.542	SUBCLONAL	1	TRUE	1	0.38	2		398	398	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928347	69928347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	48	368	0	ENST00000352241.4:c.167G>A	p.Arg56His	p.R56H	ENST00000352241	NM_198159.2	56	cGc/cAc	2/10	1	2	FACETS	0.543	0.46	0.635	0.543	0.46	0.635	SUBCLONAL	1	TRUE	1	0.38	2		368	465	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015179	71015179	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	65	272	0	ENST00000318789.4:c.1751T>C	p.Leu584Pro	p.L584P	ENST00000318789	NM_032682.5	584	cTa/cCa	20/21	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.38	2		272	293	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090642	71090642	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1207635648	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	61	285	0	ENST00000318789.4:c.706A>G	p.Thr236Ala	p.T236A	ENST00000318789	NM_032682.5	236	Aca/Gca	11/21	1	2	FACETS	0.809	0.7	0.926	0.809	0.7	0.926	CLONAL	1	TRUE	1	0.38	2		285	397	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495764	72495765	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	78	453	0	ENST00000477973.2:c.305dup	p.Arg103LysfsTer15	p.R103Kfs*15	ENST00000477973	NM_012234.5	103	aga/aAga	1/4	1	2	FACETS	0.603	0.529	0.682	0.603	0.529	0.682	SUBCLONAL	1	TRUE	1	0.38	2		453	681	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72861878	72861878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201983708	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	97	533	2	ENST00000325599.8:c.1004G>A	p.Arg335His	p.R335H	ENST00000325599	NM_018130.2	335	cGc/cAc	9/11	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.38	2		535	509	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448604	89448604	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	51	564	0	ENST00000336596.2:c.1568A>G	p.Lys523Arg	p.K523R	ENST00000336596	NM_005233.5	523	aAg/aGg	7/17	1	2	FACETS	0.381	0.323	0.445	0.381	0.323	0.445	SUBCLONAL	1	TRUE	1	0.38	2		564	704	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468382	89468382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs570346631	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	14	216	2	ENST00000336596.2:c.1916G>A	p.Arg639His	p.R639H	ENST00000336596	NM_005233.5	639	cGc/cAc	11/17	1	2	FACETS	0.301	0.217	0.402	0.301	0.217	0.402	SUBCLONAL	1	TRUE	1	0.38	2		218	245	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480511	89480511	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	15	227	0	ENST00000336596.2:c.2346+2T>C		p.X782_splice	ENST00000336596	NM_005233.5	782			1	2	FACETS	0.268	0.195	0.355	0.268	0.195	0.355	SUBCLONAL	1	TRUE	1	0.38	2		227	295	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528549	89528549	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	18	237	0	ENST00000336596.2:c.2849A>T	p.Asp950Val	p.D950V	ENST00000336596	NM_005233.5	950	gAc/gTc	17/17	1	2	FACETS	0.353	0.266	0.457	0.353	0.266	0.457	SUBCLONAL	1	TRUE	1	0.38	2		237	268	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119642287	119642287	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	46	491	0	ENST00000316626.5:c.410A>G	p.Glu137Gly	p.E137G	ENST00000316626		137	gAa/gGa	4/12	1	2	FACETS	0.543	0.457	0.637	0.543	0.457	0.637	SUBCLONAL	1	TRUE	1	0.38	2		491	446	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204927	128204927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	110	982	0	ENST00000341105.2:c.514G>A	p.Gly172Ser	p.G172S	ENST00000341105	NM_032638.4	172	Ggc/Agc	3/6	1	2	FACETS	0.533	0.477	0.592	0.533	0.477	0.592	SUBCLONAL	1	TRUE	1	0.38	2		982	1087	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670340	134670340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415689583	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	52	396	0	ENST00000398015.3:c.251G>A	p.Arg84His	p.R84H	ENST00000398015	NM_004441.4	84	cGc/cAc	3/16	1	2	FACETS	0.484	0.412	0.564	0.484	0.412	0.564	SUBCLONAL	1	TRUE	1	0.38	2		396	565	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960018	134960018	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	36	557	0	ENST00000398015.3:c.2375C>T	p.Ala792Val	p.A792V	ENST00000398015	NM_004441.4	792	gCt/gTt	13/16	1	2	FACETS	0.315	0.258	0.379	0.315	0.258	0.379	SUBCLONAL	1	TRUE	1	0.38	2		557	601	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960083	134960083	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	58	724	0	ENST00000398015.3:c.2440A>G	p.Met814Val	p.M814V	ENST00000398015	NM_004441.4	814	Atg/Gtg	13/16	1	2	FACETS	0.368	0.315	0.426	0.368	0.315	0.426	SUBCLONAL	1	TRUE	1	0.38	2		724	830	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226929	142226929	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	73	388	0	ENST00000350721.4:c.4875C>A	p.Asp1625Glu	p.D1625E	ENST00000350721	NM_001184.3	1625	gaC/gaA	28/47	1	2	FACETS	0.99	0.871	1	0.99	0.871	1	CLONAL	1	TRUE	1	0.38	2		388	388	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269072	142269072	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	31	465	0	ENST00000350721.4:c.2878C>T	p.Arg960Ter	p.R960*	ENST00000350721	NM_001184.3	960	Cga/Tga	14/47	1	2	FACETS	0.265	0.214	0.324	0.265	0.214	0.324	SUBCLONAL	1	TRUE	1	0.38	2		465	615	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281802	142281802	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	33	453	1	ENST00000350721.4:c.442G>T	p.Glu148Ter	p.E148*	ENST00000350721	NM_001184.3	148	Gaa/Taa	4/47	1	2	FACETS	0.456	0.371	0.551	0.456	0.371	0.551	SUBCLONAL	1	TRUE	1	0.38	2		454	381	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374775	149374775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	37	408	0	ENST00000360632.3:c.319G>A	p.Ala107Thr	p.A107T	ENST00000360632	NM_015472.4	107	Gcg/Acg	2/7	1	2	FACETS	0.38	0.312	0.455	0.38	0.312	0.455	SUBCLONAL	1	TRUE	1	0.38	2		408	513	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921566	178921566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793349	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	29	195	0	ENST00000263967.3:c.1048G>A	p.Asp350Asn	p.D350N	ENST00000263967	NM_006218.2	350	Gac/Aac	5/21	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.38	2		195	125	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928047	178928047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	34	390	0	ENST00000263967.3:c.1325C>T	p.Ala442Val	p.A442V	ENST00000263967	NM_006218.2	442	gCt/gTt	8/21	1	2	FACETS	0.563	0.461	0.677	0.563	0.461	0.677	SUBCLONAL	1	TRUE	1	0.38	2		390	318	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937008	178937008	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs758050864	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	31	349	0	ENST00000263967.3:c.1689A>C	p.Glu563Asp	p.E563D	ENST00000263967	NM_006218.2	563	gaA/gaC	11/21	1	2	FACETS	0.669	0.544	0.809	0.669	0.544	0.809	SUBCLONAL	1	TRUE	1	0.38	2		349	244	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430599	181430599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	36	568	0	ENST00000325404.1:c.451G>A	p.Ala151Thr	p.A151T	ENST00000325404	NM_003106.3	151	Gcg/Acg	1/1	1	2	FACETS	0.297	0.244	0.358	0.297	0.244	0.358	SUBCLONAL	1	TRUE	1	0.38	2		568	637	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431053	181431053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1226834656	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	103	661	2	ENST00000325404.1:c.905C>T	p.Pro302Leu	p.P302L	ENST00000325404	NM_003106.3	302	cCg/cTg	1/1	1	2	FACETS	0.617	0.551	0.687	0.617	0.551	0.687	SUBCLONAL	1	TRUE	1	0.38	2		663	879	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446229	187446229	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	211	814	0	ENST00000232014.4:c.1459G>T	p.Glu487Ter	p.E487*	ENST00000232014	NM_001130845.1	487	Gag/Tag	6/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.38	2		814	1024	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590708	189590708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	60	546	0	ENST00000264731.3:c.1273C>T	p.Gln425Ter	p.Q425*	ENST00000264731	NM_003722.4	425	Cag/Tag	10/14	1	2	FACETS	0.471	0.405	0.542	0.471	0.405	0.542	SUBCLONAL	1	TRUE	1	0.38	2		546	671	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608639	189608639	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	56	512	0	ENST00000264731.3:c.1714A>G	p.Thr572Ala	p.T572A	ENST00000264731	NM_003722.4	572	Acc/Gcc	13/14	1	2	FACETS	0.416	0.356	0.483	0.416	0.356	0.483	SUBCLONAL	1	TRUE	1	0.38	2		512	708	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801527	1801527	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	117	976	0	ENST00000260795.2:c.433G>T	p.Gly145Cys	p.G145C	ENST00000260795		145	Ggt/Tgt	3/17	1	2	FACETS	0.578	0.52	0.64	0.578	0.52	0.64	SUBCLONAL	1	TRUE	1	0.38	2		976	1065	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803630	1803630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780147591	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	134	836	0	ENST00000260795.2:c.808G>A	p.Asp270Asn	p.D270N	ENST00000260795		270	Gac/Aac	6/17	1	2	FACETS	0.693	0.628	0.761	0.693	0.628	0.761	SUBCLONAL	1	TRUE	1	0.38	2		836	1018	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807369	1807369	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519049	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	90	709	0	ENST00000260795.2:c.1618A>G	p.Asn540Asp	p.N540D	ENST00000260795		540	Aac/Gac	11/17	1	2	FACETS	0.557	0.494	0.625	0.557	0.494	0.625	SUBCLONAL	1	TRUE	1	0.38	2		709	850	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902690	1902690	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	221	755	0	ENST00000382891.5:c.309G>T	p.Gln103His	p.Q103H	ENST00000382891	NM_133335.3	103	caG/caT	2/22	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.38	2		755	1046	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957774	1957774	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	112	679	0	ENST00000382891.5:c.2740G>A	p.Glu914Lys	p.E914K	ENST00000382891	NM_133335.3	914	Gag/Aag	15/22	1	2	FACETS	0.668	0.6	0.74	0.668	0.6	0.74	SUBCLONAL	1	TRUE	1	0.38	2		679	882	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1959711	1959711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	24	345	0	ENST00000382891.5:c.2933C>T	p.Ala978Val	p.A978V	ENST00000382891	NM_133335.3	978	gCc/gTc	16/22	1	2	FACETS	0.266	0.208	0.333	0.266	0.208	0.333	SUBCLONAL	1	TRUE	1	0.38	2		345	475	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750512	41750512	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	145	588	0	ENST00000226382.2:c.116C>T	p.Ala39Val	p.A39V	ENST00000226382	NM_003924.3	39	gCc/gTc	1/3	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.38	2		588	632	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144556	55144556	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	53	424	0	ENST00000257290.5:c.2030G>T	p.Cys677Phe	p.C677F	ENST00000257290	NM_006206.4	677	tGc/tTc	15/23	1	2	FACETS	0.659	0.564	0.764	0.659	0.564	0.764	SUBCLONAL	1	TRUE	1	0.38	2		424	423	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144585	55144585	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	22	435	0	ENST00000257290.5:c.2059C>G	p.His687Asp	p.H687D	ENST00000257290	NM_006206.4	687	Cat/Gat	15/23	1	2	FACETS	0.265	0.205	0.335	0.265	0.205	0.335	SUBCLONAL	1	TRUE	1	0.38	2		435	437	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161366	55161366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775944809	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	75	484	0	ENST00000257290.5:c.3197C>T	p.Thr1066Ile	p.T1066I	ENST00000257290	NM_006206.4	1066	aCc/aTc	23/23	1	2	FACETS	0.595	0.521	0.675	0.595	0.521	0.675	SUBCLONAL	1	TRUE	1	0.38	2		484	663	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573269	55573269	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	14	195	0	ENST00000288135.5:c.931G>T	p.Gly311Ter	p.G311*	ENST00000288135	NM_000222.2	311	Gga/Tga	6/21	1	2	FACETS	0.452	0.328	0.601	0.452	0.328	0.601	SUBCLONAL	1	TRUE	1	0.38	2		195	163	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157497	106157497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748745799	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	38	274	0	ENST00000380013.4:c.2398C>T	p.His800Tyr	p.H800Y	ENST00000380013	NM_001127208.2	800	Cat/Tat	3/11	1	2	FACETS	0.901	0.751	1	0.901	0.751	1	CLONAL	1	TRUE	1	0.38	2		274	222	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157834	106157834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs4145756	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	67	252	0	ENST00000380013.4:c.2735C>T	p.Ala912Val	p.A912V	ENST00000380013	NM_001127208.2	912	gCg/gTg	3/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.38	2		252	310	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180847	106180847	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	26	324	0	ENST00000380013.4:c.3875G>T	p.Ser1292Ile	p.S1292I	ENST00000380013	NM_001127208.2	1292	aGc/aTc	7/11	1	2	FACETS	0.326	0.257	0.404	0.326	0.257	0.404	SUBCLONAL	1	TRUE	1	0.38	2		324	420	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244107	153244107	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	64	507	0	ENST00000281708.4:c.2050T>C	p.Cys684Arg	p.C684R	ENST00000281708	NM_033632.3	684	Tgt/Cgt	12/12	1	2	FACETS	0.479	0.414	0.55	0.479	0.414	0.55	SUBCLONAL	1	TRUE	1	0.38	2		507	703	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509969	187509969	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	42	406	1	ENST00000441802.2:c.13544C>A	p.Pro4515His	p.P4515H	ENST00000441802	NM_005245.3	4515	cCc/cAc	27/27	1	2	FACETS	0.472	0.394	0.559	0.472	0.394	0.559	SUBCLONAL	1	TRUE	1	0.38	2		407	468	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525091	187525091	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	135	440	0	ENST00000441802.2:c.10589A>G	p.Tyr3530Cys	p.Y3530C	ENST00000441802	NM_005245.3	3530	tAc/tGc	19/27	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.38	2		440	486	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539182	187539182	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771064453	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	45	396	0	ENST00000441802.2:c.8558G>A	p.Ser2853Asn	p.S2853N	ENST00000441802	NM_005245.3	2853	aGt/aAt	10/27	1	2	FACETS	0.604	0.509	0.709	0.604	0.509	0.709	SUBCLONAL	1	TRUE	1	0.38	2		396	392	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539924	187539924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765909046	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	33	410	0	ENST00000441802.2:c.7816G>A	p.Gly2606Arg	p.G2606R	ENST00000441802	NM_005245.3	2606	Ggg/Agg	10/27	1	2	FACETS	0.365	0.297	0.442	0.365	0.297	0.442	SUBCLONAL	1	TRUE	1	0.38	2		410	476	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542152	187542152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141937206	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	26	391	0	ENST00000441802.2:c.5588C>T	p.Ala1863Val	p.A1863V	ENST00000441802	NM_005245.3	1863	gCg/gTg	10/27	1	2	FACETS	0.363	0.287	0.45	0.363	0.287	0.45	SUBCLONAL	1	TRUE	1	0.38	2		391	377	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627885	187627885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752785176	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	191	652	0	ENST00000441802.2:c.3097G>A	p.Val1033Met	p.V1033M	ENST00000441802	NM_005245.3	1033	Gtg/Atg	2/27	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.38	2		652	871	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254521	1254521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200288187	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	170	879	0	ENST00000310581.5:c.3257G>A	p.Arg1086His	p.R1086H	ENST00000310581	NM_198253.2	1086	cGt/cAt	15/16	1	2	FACETS	0.765	0.702	0.831	0.765	0.702	0.831	SUBCLONAL	1	TRUE	1	0.38	2		879	1169	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293976	1293976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773366454	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	234	1058	0	ENST00000310581.5:c.1025G>A	p.Arg342Gln	p.R342Q	ENST00000310581	NM_198253.2	342	cGg/cAg	2/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.38	2		1058	1143	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294331	1294331	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750497661	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	79	669	0	ENST00000310581.5:c.670C>T	p.Arg224Cys	p.R224C	ENST00000310581	NM_198253.2	224	Cgc/Tgc	2/16	1	2	FACETS	0.515	0.452	0.583	0.515	0.452	0.583	SUBCLONAL	1	TRUE	1	0.38	2		669	807	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409413	31409413	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	14	345	0	ENST00000344624.3:c.3694A>G	p.Lys1232Glu	p.K1232E	ENST00000344624		1232	Aag/Gag	29/33	1	2	FACETS	0.304	0.22	0.407	0.304	0.22	0.407	SUBCLONAL	1	TRUE	1	0.38	2		345	242	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31431770	31431770	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs775775322	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	47	325	1	ENST00000344624.3:c.3058C>T	p.Arg1020Ter	p.R1020*	ENST00000344624		1020	Cga/Tga	23/33	1	2	FACETS	0.507	0.428	0.594	0.507	0.428	0.594	SUBCLONAL	1	TRUE	1	0.38	2		326	488	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952435	38952435	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138880117	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	72	292	2	ENST00000357387.3:c.2990G>A	p.Arg997His	p.R997H	ENST00000357387	NM_152756.3	997	cGc/cAc	30/38	1	2	FACETS	0.957	0.84	1	0.957	0.84	1	CLONAL	1	TRUE	1	0.38	2		294	396	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962651	38962651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	25	157	0	ENST00000357387.3:c.1604G>A	p.Ser535Asn	p.S535N	ENST00000357387	NM_152756.3	535	aGc/aAc	18/38	1	2	FACETS	0.907	0.724	1	0.907	0.724	1	CLONAL	1	TRUE	1	0.38	2		157	145	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168756	56168756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768818239	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	73	448	0	ENST00000399503.3:c.1610G>A	p.Ser537Asn	p.S537N	ENST00000399503	NM_005921.1	537	aGc/aAc	9/20	1	2	FACETS	0.74	0.649	0.839	0.74	0.649	0.839	SUBCLONAL	1	TRUE	1	0.38	2		448	519	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754643	57754643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	19	254	0	ENST00000274289.3:c.404G>A	p.Arg135Lys	p.R135K	ENST00000274289	NM_006622.3	135	aGa/aAa	3/14	1	2	FACETS	0.478	0.364	0.612	0.478	0.364	0.612	SUBCLONAL	1	TRUE	1	0.38	2		254	209	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592163	67592163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	75	205	0	ENST00000274335.5:c.1979C>T	p.Ser660Phe	p.S660F	ENST00000274335		660	tCt/tTt	14/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.38	2		205	311	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970928	79970928	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1362828312	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	88	516	0	ENST00000265081.6:c.1154A>G	p.Asn385Ser	p.N385S	ENST00000265081	NM_002439.4	385	aAc/aGc	7/24	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.38	2		516	439	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80071538	80071538	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	16	198	0	ENST00000265081.6:c.2279C>A	p.Ala760Asp	p.A760D	ENST00000265081	NM_002439.4	760	gCt/gAt	16/24	1	2	FACETS	0.569	0.423	0.74	0.569	0.423	0.74	SUBCLONAL	1	TRUE	1	0.38	2		198	148	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670711	86670711	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	20	126	0	ENST00000274376.6:c.1989G>T	p.Lys663Asn	p.K663N	ENST00000274376	NM_002890.2	663	aaG/aaT	15/25	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.38	2		126	92	SUCCESS
APC	324	MSKCC	GRCh37	5	112175670	112175670	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	82	313	0	ENST00000257430.4:c.4379C>A	p.Ala1460Asp	p.A1460D	ENST00000257430	NM_000038.5	1460	gCt/gAt	16/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.38	2		313	384	SUCCESS
APC	324	MSKCC	GRCh37	5	112175745	112175745	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	26	252	0	ENST00000257430.4:c.4454C>A	p.Ala1485Asp	p.A1485D	ENST00000257430	NM_000038.5	1485	gCt/gAt	16/16	1	2	FACETS	0.413	0.327	0.512	0.413	0.327	0.512	SUBCLONAL	1	TRUE	1	0.38	2		252	331	SUCCESS
APC	324	MSKCC	GRCh37	5	112177565	112177565	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	18	255	0	ENST00000257430.4:c.6274C>A	p.Leu2092Ile	p.L2092I	ENST00000257430	NM_000038.5	2092	Cta/Ata	16/16	1	2	FACETS	0.423	0.319	0.545	0.423	0.319	0.545	SUBCLONAL	1	TRUE	1	0.38	2		255	224	SUCCESS
APC	324	MSKCC	GRCh37	5	112178606	112178606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1311878041	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	28	354	0	ENST00000257430.4:c.7315C>T	p.Arg2439Cys	p.R2439C	ENST00000257430	NM_000038.5	2439	Cgc/Tgc	16/16	1	2	FACETS	0.546	0.437	0.668	0.546	0.437	0.668	SUBCLONAL	1	TRUE	1	0.38	2		354	270	SUCCESS
APC	324	MSKCC	GRCh37	5	112178969	112178969	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	26	304	0	ENST00000257430.4:c.7678C>T	p.Arg2560Ter	p.R2560*	ENST00000257430	NM_000038.5	2560	Cga/Tga	16/16	1	2	FACETS	0.425	0.337	0.526	0.425	0.337	0.526	SUBCLONAL	1	TRUE	1	0.38	2		304	322	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911502	131911502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	43	297	0	ENST00000265335.6:c.247C>T	p.Arg83Cys	p.R83C	ENST00000265335		83	Cgt/Tgt	3/25	1	2	FACETS	0.696	0.585	0.819	0.696	0.585	0.819	SUBCLONAL	1	TRUE	1	0.38	2		297	325	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911551	131911551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1372122953	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	18	326	0	ENST00000265335.6:c.296C>A	p.Ser99Tyr	p.S99Y	ENST00000265335		99	tCt/tAt	3/25	1	2	FACETS	0.3	0.225	0.388	0.3	0.225	0.388	SUBCLONAL	1	TRUE	1	0.38	2		326	316	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939071	131939071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369996457	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	40	310	1	ENST00000265335.6:c.2287C>T	p.Arg763Cys	p.R763C	ENST00000265335		763	Cgc/Tgc	14/25	1	2	FACETS	0.856	0.716	1	0.856	0.716	1	CLONAL	1	TRUE	1	0.38	2		311	246	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149498354	149498354	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	171	741	1	ENST00000261799.4:c.2860C>A	p.Leu954Met	p.L954M	ENST00000261799	NM_002609.3	954	Ctg/Atg	21/23	1	2	FACETS	0.938	0.862	1	0.938	0.862	1	CLONAL	1	TRUE	1	0.38	2		742	960	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499049	149499049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	63	658	0	ENST00000261799.4:c.2779G>A	p.Ala927Thr	p.A927T	ENST00000261799	NM_002609.3	927	Gcc/Acc	20/23	1	2	FACETS	0.414	0.358	0.477	0.414	0.358	0.477	SUBCLONAL	1	TRUE	1	0.38	2		658	800	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500540	149500540	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	133	687	0	ENST00000261799.4:c.2497C>T	p.Leu833Phe	p.L833F	ENST00000261799	NM_002609.3	833	Ctc/Ttc	18/23	1	2	FACETS	0.778	0.706	0.853	0.778	0.706	0.853	SUBCLONAL	1	TRUE	1	0.38	2		687	900	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512344	149512344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368602685	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	103	691	4	ENST00000261799.4:c.1096G>A	p.Ala366Thr	p.A366T	ENST00000261799	NM_002609.3	366	Gcc/Acc	7/23	1	2	FACETS	0.607	0.542	0.676	0.607	0.542	0.676	SUBCLONAL	1	TRUE	1	0.38	2		695	893	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515379	149515379	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568728923	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	185	706	1	ENST00000261799.4:c.103G>A	p.Val35Ile	p.V35I	ENST00000261799	NM_002609.3	35	Gtc/Atc	3/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.38	2		707	824	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518689	176518689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	42	611	0	ENST00000292408.4:c.607C>T	p.Arg203Cys	p.R203C	ENST00000292408	NM_213647.1	203	Cgc/Tgc	6/18	1	2	FACETS	0.268	0.223	0.319	0.268	0.223	0.319	SUBCLONAL	1	TRUE	1	0.38	2		611	824	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562765	176562765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	71	569	0	ENST00000439151.2:c.661G>A	p.Ala221Thr	p.A221T	ENST00000439151	NM_022455.4	221	Gca/Aca	2/23	1	2	FACETS	0.513	0.447	0.585	0.513	0.447	0.585	SUBCLONAL	1	TRUE	1	0.38	2		569	728	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638900	176638900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763399938	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	195	620	0	ENST00000439151.2:c.3500G>A	p.Arg1167His	p.R1167H	ENST00000439151	NM_022455.4	1167	cGc/cAc	5/23	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.38	2		620	847	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039610	180039610	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs202140363	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	44	664	0	ENST00000261937.6:c.3433C>T	p.Arg1145Cys	p.R1145C	ENST00000261937	NM_182925.4	1145	Cgc/Tgc	26/30	1	2	FACETS	0.305	0.255	0.361	0.305	0.255	0.361	SUBCLONAL	1	TRUE	1	0.38	2		664	760	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394951	394951	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	60	452	0	ENST00000380956.4:c.347T>C	p.Leu116Pro	p.L116P	ENST00000380956	NM_001195286.1	116	cTg/cCg	3/9	1	2	FACETS	0.482	0.415	0.555	0.482	0.415	0.555	SUBCLONAL	1	TRUE	1	0.38	2		452	655	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395931	395931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	55	425	0	ENST00000380956.4:c.488C>T	p.Ala163Val	p.A163V	ENST00000380956	NM_001195286.1	163	gCc/gTc	4/9	1	2	FACETS	0.599	0.513	0.693	0.599	0.513	0.693	SUBCLONAL	1	TRUE	1	0.38	2		425	483	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398927	398927	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751010198	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	119	520	0	ENST00000380956.4:c.737C>T	p.Ala246Val	p.A246V	ENST00000380956	NM_001195286.1	246	gCg/gTg	6/9	1	2	FACETS	0.964	0.871	1	0.964	0.871	1	CLONAL	1	TRUE	1	0.38	2		520	650	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407575	407575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748516736	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	69	308	0	ENST00000380956.4:c.1333C>T	p.Arg445Cys	p.R445C	ENST00000380956	NM_001195286.1	445	Cgc/Tgc	9/9	1	2	FACETS	0.915	0.8	1	0.915	0.8	1	CLONAL	1	TRUE	1	0.38	2		308	397	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20486918	20486918	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	45	220	0	ENST00000346618.3:c.885-2A>G		p.X295_splice	ENST00000346618	NM_001949.4	295			1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.38	2		220	202	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803444	32803444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779665536	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	92	812	0	ENST00000374899.4:c.715G>A	p.Gly239Ser	p.G239S	ENST00000374899	NM_018833.2	239	Ggt/Agt	4/12	1	2	FACETS	0.473	0.419	0.531	0.473	0.419	0.531	SUBCLONAL	1	TRUE	1	0.38	2		812	1024	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32814973	32814973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	148	564	0	ENST00000354258.4:c.2092G>A	p.Glu698Lys	p.E698K	ENST00000354258	NM_000593.5	698	Gag/Aag	10/11	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.38	2		564	753	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32819921	32819921	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140245535	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	152	809	0	ENST00000354258.4:c.989G>A	p.Arg330His	p.R330H	ENST00000354258	NM_000593.5	330	cGc/cAc	3/11	1	2	FACETS	0.699	0.638	0.764	0.699	0.638	0.764	SUBCLONAL	1	TRUE	1	0.38	2		809	1144	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32819964	32819964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531615408	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	252	813	3	ENST00000354258.4:c.946G>A	p.Val316Met	p.V316M	ENST00000354258	NM_000593.5	316	Gtg/Atg	3/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.38	2		816	1133	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289271	33289271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1303387799	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	66	481	0	ENST00000374542.5:c.281G>A	p.Arg94His	p.R94H	ENST00000374542	NM_001141970.1	94	cGt/cAt	3/8	1	2	FACETS	0.48	0.416	0.55	0.48	0.416	0.55	SUBCLONAL	1	TRUE	1	0.38	2		481	723	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652302	36652302	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774390644	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	90	607	0	ENST00000244741.5:c.424C>T	p.Arg142Trp	p.R142W	ENST00000244741	NM_000389.4	142	Cgg/Tgg	2/3	1	2	FACETS	0.634	0.562	0.711	0.634	0.562	0.711	SUBCLONAL	1	TRUE	1	0.38	2		607	747	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748519	43748519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267601048	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	45	465	0	ENST00000523873.1:c.473C>T	p.Ser158Phe	p.S158F	ENST00000523873		158	tCc/tTc	6/8	1	2	FACETS	0.353	0.296	0.416	0.353	0.296	0.416	SUBCLONAL	1	TRUE	1	0.38	2		465	671	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43749734	43749734	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	48	494	0	ENST00000523873.1:c.587T>C	p.Val196Ala	p.V196A	ENST00000523873		196	gTa/gCa	7/8	1	2	FACETS	0.329	0.277	0.386	0.329	0.277	0.386	SUBCLONAL	1	TRUE	1	0.38	2		494	768	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64290050	64290050	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs546134768	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	95	456	2	ENST00000370651.3:c.493G>A	p.Gly165Ser	p.G165S	ENST00000370651	NM_003463.4	165	Ggt/Agt	6/6	1	2	FACETS	0.945	0.844	1	0.945	0.844	1	CLONAL	1	TRUE	1	0.38	2		458	529	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956676	93956676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465960814	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	44	364	0	ENST00000369303.4:c.2560C>T	p.Arg854Cys	p.R854C	ENST00000369303	NM_004440.3	854	Cgt/Tgt	15/17	1	2	FACETS	0.541	0.454	0.637	0.541	0.454	0.637	SUBCLONAL	1	TRUE	1	0.38	2		364	428	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554912	106554912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	85	484	0	ENST00000369096.4:c.2029C>T	p.His677Tyr	p.H677Y	ENST00000369096	NM_001198.3	677	Cac/Tac	7/7	1	2	FACETS	0.722	0.638	0.81	0.722	0.638	0.81	SUBCLONAL	1	TRUE	1	0.38	2		484	620	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112029147	112029147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	26	408	2	ENST00000368678.4:c.421G>A	p.Val141Ile	p.V141I	ENST00000368678		141	Gtt/Att	5/13	1	2	FACETS	0.284	0.224	0.353	0.284	0.224	0.353	SUBCLONAL	1	TRUE	1	0.38	2		410	482	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631343	117631343	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	47	425	0	ENST00000368508.3:c.6335del	p.Asn2112MetfsTer22	p.N2112Mfs*22	ENST00000368508	NM_002944.2	2112	aAt/at	40/43	1	2	FACETS	0.525	0.443	0.615	0.525	0.443	0.615	SUBCLONAL	1	TRUE	1	0.38	2		425	471	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662788	117662788	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	27	227	0	ENST00000368508.3:c.4677G>T	p.Glu1559Asp	p.E1559D	ENST00000368508	NM_002944.2	1559	gaG/gaT	29/43	1	2	FACETS	0.621	0.496	0.761	0.621	0.496	0.761	SUBCLONAL	1	TRUE	1	0.38	2		227	229	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678076	117678076	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs373090808	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	34	283	0	ENST00000368508.3:c.3857G>A	p.Arg1286His	p.R1286H	ENST00000368508	NM_002944.2	1286	cGc/cAc	25/43	1	2	FACETS	0.668	0.548	0.801	0.668	0.548	0.801	SUBCLONAL	1	TRUE	1	0.38	2		283	268	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117680985	117680985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771443531	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	62	301	0	ENST00000368508.3:c.3635G>A	p.Arg1212His	p.R1212H	ENST00000368508	NM_002944.2	1212	cGc/cAc	23/43	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.38	2		301	273	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709080	117709080	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	74	494	0	ENST00000368508.3:c.1877del	p.Phe626SerfsTer2	p.F626Sfs*2	ENST00000368508	NM_002944.2	626	tTc/tc	13/43	1	2	FACETS	0.753	0.661	0.853	0.753	0.661	0.853	SUBCLONAL	1	TRUE	1	0.38	2		494	517	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200243	138200243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	35	467	0	ENST00000237289.4:c.1661G>A	p.Ser554Asn	p.S554N	ENST00000237289	NM_001270507.1	554	aGc/aAc	7/9	1	2	FACETS	0.271	0.221	0.327	0.271	0.221	0.327	SUBCLONAL	1	TRUE	1	0.38	2		467	680	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004256	150004256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	25	243	0	ENST00000253339.5:c.1969C>T	p.Arg657Cys	p.R657C	ENST00000253339		657	Cgt/Tgt	3/7	1	2	FACETS	0.633	0.501	0.782	0.633	0.501	0.782	SUBCLONAL	1	TRUE	1	0.38	2		243	208	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005260	150005260	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	25	420	0	ENST00000253339.5:c.965C>A	p.Ser322Tyr	p.S322Y	ENST00000253339		322	tCt/tAt	3/7	1	2	FACETS	0.265	0.208	0.331	0.265	0.208	0.331	SUBCLONAL	1	TRUE	1	0.38	2		420	496	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016233	150016233	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	82	363	0	ENST00000253339.5:c.473C>A	p.Pro158His	p.P158H	ENST00000253339		158	cCt/cAt	2/7	1	2	FACETS	0.92	0.814	1	0.92	0.814	1	CLONAL	1	TRUE	1	0.38	2		363	469	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016312	150016312	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	49	392	0	ENST00000253339.5:c.394G>A	p.Glu132Lys	p.E132K	ENST00000253339		132	Gaa/Aaa	2/7	1	2	FACETS	0.613	0.52	0.714	0.613	0.52	0.714	SUBCLONAL	1	TRUE	1	0.38	2		392	421	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265353	152265353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188957694	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	111	470	0	ENST00000206249.3:c.806G>A	p.Arg269His	p.R269H	ENST00000206249	NM_000125.3	269	cGc/cAc	4/8	1	2	FACETS	0.974	0.878	1	0.974	0.878	1	CLONAL	1	TRUE	1	0.38	2		470	600	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469934	157469934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	38	612	0	ENST00000346085.5:c.2728C>T	p.Pro910Ser	p.P910S	ENST00000346085	NM_020732.3	910	Cct/Tct	9/20	1	2	FACETS	0.266	0.219	0.318	0.266	0.219	0.318	SUBCLONAL	1	TRUE	1	0.38	2		612	753	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521974	157521974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772972321	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	48	563	2	ENST00000346085.5:c.4246C>T	p.Arg1416Cys	p.R1416C	ENST00000346085	NM_020732.3	1416	Cgc/Tgc	18/20	1	2	FACETS	0.369	0.311	0.433	0.369	0.311	0.433	SUBCLONAL	1	TRUE	1	0.38	2		565	685	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528051	157528051	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554237658	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	82	533	1	ENST00000346085.5:c.5776C>T	p.Arg1926Ter	p.R1926*	ENST00000346085	NM_020732.3	1926	Cga/Tga	20/20	1	2	FACETS	0.648	0.571	0.73	0.648	0.571	0.73	SUBCLONAL	1	TRUE	1	0.38	2		534	666	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161807872	161807872	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	37	397	0	ENST00000366898.1:c.1121A>G	p.Glu374Gly	p.E374G	ENST00000366898	NM_004562.2	374	gAa/gGa	10/12	1	2	FACETS	0.344	0.283	0.413	0.344	0.283	0.413	SUBCLONAL	1	TRUE	1	0.38	2		397	566	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962902	2962902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs186255478	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	113	909	0	ENST00000396946.4:c.2006C>T	p.Thr669Met	p.T669M	ENST00000396946	NM_032415.4	669	aCg/aTg	16/25	1	2	FACETS	0.554	0.497	0.615	0.554	0.497	0.615	SUBCLONAL	1	TRUE	1	0.38	2		909	1073	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042116	6042116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881916	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	55	177	0	ENST00000265849.7:c.505C>T	p.Arg169Cys	p.R169C	ENST00000265849	NM_000535.5	169	Cgc/Tgc	5/15	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.38	2		177	258	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940461	13940461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	30	290	0	ENST00000405192.2:c.1045G>A	p.Ala349Thr	p.A349T	ENST00000405192	NM_001163147.1	349	Gcc/Acc	11/12	1	2	FACETS	0.423	0.341	0.517	0.423	0.341	0.517	SUBCLONAL	1	TRUE	1	0.38	2		290	373	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975436	13975436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	35	405	0	ENST00000405192.2:c.451G>A	p.Ala151Thr	p.A151T	ENST00000405192	NM_001163147.1	151	Gca/Aca	7/12	1	2	FACETS	0.337	0.275	0.406	0.337	0.275	0.406	SUBCLONAL	1	TRUE	1	0.38	2		405	547	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	44	352	4	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	1	2	FACETS	0.541	0.454	0.637	0.541	0.454	0.637	SUBCLONAL	1	TRUE	1	0.38	2		356	428	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450243	50450243	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757521297	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	57	486	1	ENST00000331340.3:c.427C>T	p.Arg143Trp	p.R143W	ENST00000331340	NM_006060.4	143	Cgg/Tgg	5/8	1	2	FACETS	0.555	0.476	0.64	0.555	0.476	0.64	SUBCLONAL	1	TRUE	1	0.38	2		487	541	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467747	50467747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	126	657	0	ENST00000331340.3:c.982C>T	p.Arg328Cys	p.R328C	ENST00000331340	NM_006060.4	328	Cgc/Tgc	8/8	1	2	FACETS	0.857	0.776	0.942	0.857	0.776	0.942	CLONAL	1	TRUE	1	0.38	2		657	774	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508621	106508621	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	87	536	0	ENST00000359195.3:c.615G>T	p.Lys205Asn	p.K205N	ENST00000359195	NM_002649.2	205	aaG/aaT	2/11	1	2	FACETS	0.644	0.57	0.723	0.644	0.57	0.723	SUBCLONAL	1	TRUE	1	0.38	2		536	711	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435975	116435975	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	140	593	0	ENST00000397752.3:c.3970G>T	p.Ala1324Ser	p.A1324S	ENST00000397752	NM_000245.2	1324	Gcc/Tcc	21/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.38	2		593	691	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845511	128845511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs111694017	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	180	749	0	ENST00000249373.3:c.808G>A	p.Val270Ile	p.V270I	ENST00000249373	NM_005631.4	270	Gtc/Atc	4/12	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.38	2		749	878	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846357	128846357	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760560948	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	173	687	0	ENST00000249373.3:c.1193G>A	p.Arg398Gln	p.R398Q	ENST00000249373	NM_005631.4	398	cGa/cAa	6/12	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.38	2		687	848	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850838	128850838	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121918348	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	97	725	1	ENST00000249373.3:c.1685G>A	p.Arg562Gln	p.R562Q	ENST00000249373	NM_005631.4	562	cGg/cAg	10/12	1	2	FACETS	0.536	0.477	0.599	0.536	0.477	0.599	SUBCLONAL	1	TRUE	1	0.38	2		726	953	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850880	128850880	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs577512487	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	49	769	1	ENST00000249373.3:c.1727G>A	p.Arg576Gln	p.R576Q	ENST00000249373	NM_005631.4	576	cGg/cAg	10/12	1	2	FACETS	0.27	0.227	0.317	0.27	0.227	0.317	SUBCLONAL	1	TRUE	1	0.38	2		770	956	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481380	140481380	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	17	295	0	ENST00000288602.6:c.1428G>A	p.Trp476Ter	p.W476*	ENST00000288602	NM_004333.4	476	tgG/tgA	11/18	1	2	FACETS	0.352	0.263	0.458	0.352	0.263	0.458	SUBCLONAL	1	TRUE	1	0.38	2		295	254	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151164212	151164212	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	13	150	0	ENST00000262187.5:c.548T>C	p.Val183Ala	p.V183A	ENST00000262187	NM_005614.3	183	gTg/gCg	8/8	1	2	FACETS	0.324	0.231	0.438	0.324	0.231	0.438	SUBCLONAL	1	TRUE	1	0.38	2		150	211	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841862	151841862	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	44	308	0	ENST00000262189.6:c.14279C>T	p.Ser4760Leu	p.S4760L	ENST00000262189	NM_170606.2	4760	tCg/tTg	55/59	1	2	FACETS	0.487	0.408	0.573	0.487	0.408	0.573	SUBCLONAL	1	TRUE	1	0.38	2		308	476	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843697	151843697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151112171	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	68	348	0	ENST00000262189.6:c.14018G>A	p.Arg4673His	p.R4673H	ENST00000262189	NM_170606.2	4673	cGc/cAc	53/59	1	2	FACETS	0.65	0.566	0.74	0.65	0.566	0.74	SUBCLONAL	1	TRUE	1	0.38	2		348	551	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859407	151859407	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs749244367	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	44	427	0	ENST00000262189.6:c.11255C>A	p.Pro3752His	p.P3752H	ENST00000262189	NM_170606.2	3752	cCt/cAt	43/59	1	2	FACETS	0.391	0.327	0.462	0.391	0.327	0.462	SUBCLONAL	1	TRUE	1	0.38	2		427	592	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864284	151864284	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	72	434	0	ENST00000262189.6:c.9697C>G	p.Gln3233Glu	p.Q3233E	ENST00000262189	NM_170606.2	3233	Caa/Gaa	42/59	1	2	FACETS	0.808	0.708	0.915	0.808	0.708	0.915	CLONAL	1	TRUE	1	0.38	2		434	469	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874526	151874526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761335251	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	46	337	0	ENST00000262189.6:c.8012C>T	p.Thr2671Met	p.T2671M	ENST00000262189	NM_170606.2	2671	aCg/aTg	38/59	1	2	FACETS	0.624	0.527	0.731	0.624	0.527	0.731	SUBCLONAL	1	TRUE	1	0.38	2		337	388	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880191	151880191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	73	328	0	ENST00000262189.6:c.5133G>A	p.Met1711Ile	p.M1711I	ENST00000262189	NM_170606.2	1711	atG/atA	35/59	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.38	2		328	331	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38139034	38139034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201914561	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	81	415	0	ENST00000317025.8:c.3569G>A	p.Arg1190Gln	p.R1190Q	ENST00000317025	NM_023034.1	1190	cGa/cAa	20/24	1	2	FACETS	0.82	0.724	0.922	0.82	0.724	0.922	CLONAL	1	TRUE	1	0.38	2		415	520	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38156989	38156989	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	85	493	0	ENST00000317025.8:c.2731T>C	p.Ser911Pro	p.S911P	ENST00000317025	NM_023034.1	911	Tca/Cca	15/24	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.38	2		493	335	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272356	38272356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	70	565	0	ENST00000425967.3:c.2011G>A	p.Ala671Thr	p.A671T	ENST00000425967	NM_001174067.1	671	Gca/Aca	15/19	1	2	FACETS	0.525	0.457	0.598	0.525	0.457	0.598	SUBCLONAL	1	TRUE	1	0.38	2		565	702	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912039	56912039	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	132	653	0	ENST00000519728.1:c.1267A>G	p.Lys423Glu	p.K423E	ENST00000519728	NM_002350.3	423	Aag/Gag	12/13	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.38	2		653	638	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995514	68995514	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	37	488	0	ENST00000288368.4:c.1918A>G	p.Asn640Asp	p.N640D	ENST00000288368	NM_024870.2	640	Aat/Gat	18/40	1	2	FACETS	0.435	0.358	0.52	0.435	0.358	0.52	SUBCLONAL	1	TRUE	1	0.38	2		488	448	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129945	69129945	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748812788	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	109	334	0	ENST00000288368.4:c.4699C>T	p.Arg1567Trp	p.R1567W	ENST00000288368	NM_024870.2	1567	Cgg/Tgg	38/40	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.38	2		334	399	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970972	70970972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	72	715	0	ENST00000276594.2:c.1289G>A	p.Arg430Lys	p.R430K	ENST00000276594	NM_024504.3	430	aGg/aAg	6/8	1	2	FACETS	0.402	0.35	0.459	0.402	0.35	0.459	SUBCLONAL	1	TRUE	1	0.38	2		715	942	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955513	90955513	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1217913746	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	35	411	1	ENST00000265433.3:c.2152G>T	p.Glu718Ter	p.E718*	ENST00000265433	NM_002485.4	718	Gaa/Taa	14/16	1	2	FACETS	0.515	0.422	0.618	0.515	0.422	0.618	SUBCLONAL	1	TRUE	1	0.38	2		412	358	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976677	90976677	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876659969	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	54	405	0	ENST00000265433.3:c.955A>G	p.Thr319Ala	p.T319A	ENST00000265433	NM_002485.4	319	Aca/Gca	8/16	1	2	FACETS	0.723	0.62	0.836	0.723	0.62	0.836	SUBCLONAL	1	TRUE	1	0.38	2		405	393	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993113	90993113	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1355269482	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	11	202	0	ENST00000265433.3:c.329A>G	p.Tyr110Cys	p.Y110C	ENST00000265433	NM_002485.4	110	tAt/tGt	4/16	1	2	FACETS	0.343	0.237	0.473	0.343	0.237	0.473	SUBCLONAL	1	TRUE	1	0.38	2		202	169	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141557702	141557702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1431074938	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	80	770	1	ENST00000220592.5:c.1613C>T	p.Thr538Met	p.T538M	ENST00000220592	NM_012154.3	538	aCg/aTg	13/19	1	2	FACETS	0.467	0.41	0.529	0.467	0.41	0.529	SUBCLONAL	1	TRUE	1	0.38	2		771	901	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739029	145739029	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs947223466	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	161	658	1	ENST00000428558.2:c.2126G>A	p.Arg709Gln	p.R709Q	ENST00000428558	NM_004260.3	709	cGg/cAg	13/22	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.38	2		659	786	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341196	8341196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	38	339	0	ENST00000356435.5:c.5020C>T	p.Arg1674Cys	p.R1674C	ENST00000356435		1674	Cgc/Tgc	30/35	1	2	FACETS	0.714	0.593	0.848	0.714	0.593	0.848	SUBCLONAL	1	TRUE	1	0.38	2		339	280	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389371	8389371	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	46	433	0	ENST00000356435.5:c.4247T>C	p.Ile1416Thr	p.I1416T	ENST00000356435		1416	aTa/aCa	26/35	1	2	FACETS	0.596	0.503	0.699	0.596	0.503	0.699	SUBCLONAL	1	TRUE	1	0.38	2		433	406	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465651	8465651	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772237001	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	28	325	1	ENST00000356435.5:c.3529C>T	p.Arg1177Cys	p.R1177C	ENST00000356435		1177	Cgc/Tgc	21/35	1	2	FACETS	0.506	0.406	0.621	0.506	0.406	0.621	SUBCLONAL	1	TRUE	1	0.38	2		326	291	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499772	8499772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773166856	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	149	517	2	ENST00000356435.5:c.2197C>T	p.Arg733Cys	p.R733C	ENST00000356435		733	Cgc/Tgc	14/35	1	2	FACETS	0.968	0.885	1	0.968	0.885	1	CLONAL	1	TRUE	1	0.38	2		519	810	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524967	8524967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	48	326	0	ENST00000356435.5:c.637G>A	p.Ala213Thr	p.A213T	ENST00000356435		213	Gcg/Acg	7/35	1	2	FACETS	0.54	0.457	0.631	0.54	0.457	0.631	SUBCLONAL	1	TRUE	1	0.38	2		326	468	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202820	27202820	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	47	270	0	ENST00000380036.4:c.1912C>A	p.Leu638Ile	p.L638I	ENST00000380036	NM_000459.3	638	Ctt/Att	13/23	1	2	FACETS	0.906	0.77	1	0.906	0.77	1	CLONAL	1	TRUE	1	0.38	2		270	273	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202926	27202926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772637203	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	93	437	0	ENST00000380036.4:c.2018G>A	p.Arg673His	p.R673H	ENST00000380036	NM_000459.3	673	cGt/cAt	13/23	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.38	2		437	453	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212792	27212792	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1291636206	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	137	814	0	ENST00000380036.4:c.2774C>T	p.Ala925Val	p.A925V	ENST00000380036	NM_000459.3	925	gCa/gTa	17/23	1	2	FACETS	0.754	0.685	0.827	0.754	0.685	0.827	SUBCLONAL	1	TRUE	1	0.38	2		814	956	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336244	80336244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	89	270	0	ENST00000286548.4:c.1075G>A	p.Val359Ile	p.V359I	ENST00000286548	NM_002072.3	359	Gtc/Atc	7/7	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.38	2		270	399	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336303	80336303	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	71	372	1	ENST00000286548.4:c.1016T>A	p.Phe339Tyr	p.F339Y	ENST00000286548	NM_002072.3	339	tTt/tAt	7/7	1	2	FACETS	0.672	0.587	0.764	0.672	0.587	0.764	SUBCLONAL	1	TRUE	1	0.38	2		373	556	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285694	87285694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs78936193	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	80	634	0	ENST00000277120.3:c.31G>A	p.Ala11Thr	p.A11T	ENST00000277120		11	Gcc/Acc	2/19	1	2	FACETS	0.66	0.581	0.745	0.66	0.581	0.745	SUBCLONAL	1	TRUE	1	0.38	2		634	638	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317265	87317265	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	81	381	0	ENST00000277120.3:c.290C>T	p.Thr97Ile	p.T97I	ENST00000277120		97	aCa/aTa	4/19	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.38	2		381	391	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563530	87563530	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	86	525	0	ENST00000277120.3:c.1918G>T	p.Asp640Tyr	p.D640Y	ENST00000277120		640	Gac/Tac	16/19	1	2	FACETS	0.686	0.607	0.77	0.686	0.607	0.77	SUBCLONAL	1	TRUE	1	0.38	2		525	660	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650881	93650881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200438123	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	92	478	1	ENST00000375746.1:c.1807G>A	p.Asp603Asn	p.D603N	ENST00000375746	NM_001174167.1	603	Gat/Aat	13/14	1	2	FACETS	0.673	0.597	0.753	0.673	0.597	0.753	SUBCLONAL	1	TRUE	1	0.38	2		479	720	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97897758	97897758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	38	414	1	ENST00000289081.3:c.713C>T	p.Ala238Val	p.A238V	ENST00000289081	NM_000136.2	238	gCt/gTt	8/15	1	2	FACETS	0.411	0.339	0.491	0.411	0.339	0.491	SUBCLONAL	1	TRUE	1	0.38	2		415	487	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209387	98209387	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146447673	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	50	631	0	ENST00000331920.6:c.4151C>T	p.Pro1384Leu	p.P1384L	ENST00000331920	NM_000264.3	1384	cCg/cTg	23/24	1	2	FACETS	0.363	0.307	0.425	0.363	0.307	0.425	SUBCLONAL	1	TRUE	1	0.38	2		631	724	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209516	98209516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748609458	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	175	693	1	ENST00000331920.6:c.4022C>T	p.Pro1341Leu	p.P1341L	ENST00000331920	NM_000264.3	1341	cCt/cTt	23/24	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.38	2		694	781	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211581	98211581	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571420165	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	134	686	1	ENST00000331920.6:c.3574C>T	p.Arg1192Cys	p.R1192C	ENST00000331920	NM_000264.3	1192	Cgc/Tgc	22/24	1	2	FACETS	0.878	0.798	0.962	0.878	0.798	0.962	CLONAL	1	TRUE	1	0.38	2		687	803	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240450	98240450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370354759	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	38	447	1	ENST00000331920.6:c.1234G>A	p.Ala412Thr	p.A412T	ENST00000331920	NM_000264.3	412	Gca/Aca	9/24	1	2	FACETS	0.331	0.273	0.396	0.331	0.273	0.396	SUBCLONAL	1	TRUE	1	0.38	2		448	604	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268775	98268775	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	60	643	0	ENST00000331920.6:c.308T>C	p.Val103Ala	p.V103A	ENST00000331920	NM_000264.3	103	gTt/gCt	2/24	1	2	FACETS	0.384	0.33	0.443	0.384	0.33	0.443	SUBCLONAL	1	TRUE	1	0.38	2		643	823	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249660	110249660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376327952	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	85	1043	0	ENST00000374672.4:c.1015G>A	p.Gly339Ser	p.G339S	ENST00000374672	NM_004235.4	339	Ggc/Agc	3/5	1	2	FACETS	0.383	0.337	0.433	0.383	0.337	0.433	SUBCLONAL	1	TRUE	1	0.38	2		1043	1167	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771698	135771698	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751126355	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	233	656	1	ENST00000298552.3:c.3419C>T	p.Pro1140Leu	p.P1140L	ENST00000298552	NM_001162426.1	1140	cCg/cTg	23/23	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.38	2		657	942	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796757	135796757	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	60	294	0	ENST00000298552.3:c.730C>T	p.Pro244Ser	p.P244S	ENST00000298552	NM_001162426.1	244	Cct/Tct	8/23	1	2	FACETS	0.972	0.843	1	0.972	0.843	1	CLONAL	1	TRUE	1	0.38	2		294	325	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390912	139390912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370722609	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	168	888	4	ENST00000277541.6:c.7279G>A	p.Gly2427Ser	p.G2427S	ENST00000277541	NM_017617.3	2427	Ggc/Agc	34/34	1	2	FACETS	0.853	0.783	0.926	0.853	0.783	0.926	CLONAL	1	TRUE	1	0.38	2		892	1037	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400051	139400052	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	178	894	0	ENST00000277541.6:c.4296_4297insA	p.Gly1433ArgfsTer46	p.G1433Rfs*46	ENST00000277541	NM_017617.3	1432	-/A	25/34	1	2	FACETS	0.847	0.78	0.918	0.847	0.78	0.918	CLONAL	1	TRUE	1	0.38	2		894	1106	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1327743	1327743	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1319179000	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	100	673	0	ENST00000400841.2:c.138G>T	p.Trp46Cys	p.W46C	ENST00000400841		46	tgG/tgT	2/6	1	2	FACETS	0.599	0.534	0.668	0.599	0.534	0.668	SUBCLONAL	1	TRUE	1	0.38	2		673	879	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1327796	1327796	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	57	510	1	ENST00000400841.2:c.85G>T	p.Gly29Ter	p.G29*	ENST00000400841		29	Gga/Tga	2/6	1	2	FACETS	0.475	0.407	0.55	0.475	0.407	0.55	SUBCLONAL	1	TRUE	1	0.38	2		511	631	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15809119	15809119	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	139	426	0	ENST00000307771.7:c.104C>T	p.Ala35Val	p.A35V	ENST00000307771	NM_005089.3	35	gCt/gTt	2/11	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.38	2		426	714	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15833978	15833978	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1388592969	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	165	629	0	ENST00000307771.7:c.736G>A	p.Glu246Lys	p.E246K	ENST00000307771	NM_005089.3	246	Gag/Aag	8/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.38	2		629	801	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841159	15841159	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752029553	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	107	465	0	ENST00000307771.7:c.1243C>T	p.Arg415Trp	p.R415W	ENST00000307771	NM_005089.3	415	Cgg/Tgg	11/11	1	2	FACETS	0.857	0.77	0.949	0.857	0.77	0.949	CLONAL	1	TRUE	1	0.38	2		465	657	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933856	39933856	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771988446	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	65	802	1	ENST00000378444.4:c.743C>T	p.Pro248Leu	p.P248L	ENST00000378444	NM_001123385.1	248	cCg/cTg	4/15	1	2	FACETS	0.353	0.305	0.406	0.353	0.305	0.406	SUBCLONAL	1	TRUE	1	0.38	2		803	968	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820536	44820536	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772197961	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	36	271	0	ENST00000377967.4:c.233G>A	p.Arg78His	p.R78H	ENST00000377967	NM_021140.2	78	cGc/cAc	3/29	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.38	2		271	178	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44911008	44911008	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs142139890	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	15	283	0	ENST00000377967.4:c.709C>A	p.Leu237Ile	p.L237I	ENST00000377967	NM_021140.2	237	Ctt/Att	9/29	1	2	FACETS	0.325	0.237	0.43	0.325	0.237	0.43	SUBCLONAL	1	TRUE	1	0.38	2		283	243	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928872	44928872	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs755440519	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	72	388	0	ENST00000377967.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000377967	NM_021140.2	658	Cga/Tga	17/29	1	2	FACETS	0.73	0.639	0.828	0.73	0.639	0.828	SUBCLONAL	1	TRUE	1	0.38	2		388	519	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038791	47038791	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	221	873	2	ENST00000377604.3:c.798C>A	p.Ser266Arg	p.S266R	ENST00000377604	NM_001204468.1	266	agC/agA	9/24	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.38	2		875	1030	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045569	47045569	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1396222722	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	73	579	1	ENST00000377604.3:c.2536G>A	p.Val846Ile	p.V846I	ENST00000377604	NM_001204468.1	846	Gta/Ata	22/24	1	2	FACETS	0.616	0.538	0.699	0.616	0.538	0.699	SUBCLONAL	1	TRUE	1	0.38	2		580	624	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426690	47426690	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	132	870	0	ENST00000377045.4:c.935T>A	p.Leu312Gln	p.L312Q	ENST00000377045	NM_001654.4	312	cTg/cAg	10/16	1	2	FACETS	0.7	0.635	0.769	0.7	0.635	0.769	SUBCLONAL	1	TRUE	1	0.38	2		870	992	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430843	47430843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	181	678	2	ENST00000377045.4:c.1808G>A	p.Arg603His	p.R603H	ENST00000377045	NM_001654.4	603	cGc/cAc	16/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.38	2		680	834	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226001	53226001	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	151	911	0	ENST00000375401.3:c.2848A>G	p.Met950Val	p.M950V	ENST00000375401	NM_004187.3	950	Atg/Gtg	19/26	1	2	FACETS	0.679	0.619	0.741	0.679	0.619	0.741	SUBCLONAL	1	TRUE	1	0.38	2		911	1171	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231092	53231092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	118	725	0	ENST00000375401.3:c.1810G>A	p.Gly604Ser	p.G604S	ENST00000375401	NM_004187.3	604	Ggc/Agc	13/26	1	2	FACETS	0.642	0.578	0.709	0.642	0.578	0.709	SUBCLONAL	1	TRUE	1	0.38	2		725	968	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246390	53246390	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	133	785	1	ENST00000375401.3:c.592C>T	p.Arg198Ter	p.R198*	ENST00000375401	NM_004187.3	198	Cga/Tga	5/26	1	2	FACETS	0.692	0.627	0.76	0.692	0.627	0.76	SUBCLONAL	1	TRUE	1	0.38	2		786	1012	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247106	53247106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	118	568	2	ENST00000375401.3:c.394C>T	p.Arg132Cys	p.R132C	ENST00000375401	NM_004187.3	132	Cgt/Tgt	4/26	1	2	FACETS	0.827	0.746	0.912	0.827	0.746	0.912	CLONAL	1	TRUE	1	0.38	2		570	751	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247112	53247112	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	52	548	0	ENST00000375401.3:c.388A>G	p.Lys130Glu	p.K130E	ENST00000375401	NM_004187.3	130	Aag/Gag	4/26	1	2	FACETS	0.39	0.332	0.455	0.39	0.332	0.455	SUBCLONAL	1	TRUE	1	0.38	2		548	701	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411104	63411104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395903458	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	145	676	0	ENST00000330258.3:c.2063C>T	p.Thr688Ile	p.T688I	ENST00000330258	NM_152424.3	688	aCt/aTt	2/2	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.38	2		676	728	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413094	63413094	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	96	800	1	ENST00000330258.3:c.73G>T	p.Ala25Ser	p.A25S	ENST00000330258	NM_152424.3	25	Gca/Tca	2/2	1	2	FACETS	0.477	0.423	0.534	0.477	0.423	0.534	SUBCLONAL	1	TRUE	1	0.38	2		801	1060	SUCCESS
AR	367	MSKCC	GRCh37	X	66765047	66765047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1297947716	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	235	917	2	ENST00000374690.3:c.59G>A	p.Arg20Gln	p.R20Q	ENST00000374690	NM_000044.3	20	cGa/cAa	1/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.38	2		919	1095	SUCCESS
AR	367	MSKCC	GRCh37	X	66765406	66765406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1214854933	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	114	713	2	ENST00000374690.3:c.418G>A	p.Ala140Thr	p.A140T	ENST00000374690	NM_000044.3	140	Gcc/Acc	1/8	1	2	FACETS	0.743	0.668	0.821	0.743	0.668	0.821	SUBCLONAL	1	TRUE	1	0.38	2		715	808	SUCCESS
AR	367	MSKCC	GRCh37	X	66766421	66766421	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs760558682	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	24	222	0	ENST00000374690.3:c.1433T>C	p.Val478Ala	p.V478A	ENST00000374690	NM_000044.3	478	gTa/gCa	1/8	1	2	FACETS	0.453	0.355	0.564	0.453	0.355	0.564	SUBCLONAL	1	TRUE	1	0.38	2		222	279	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349253	70349253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	207	843	5	ENST00000374080.3:c.3665C>T	p.Ala1222Val	p.A1222V	ENST00000374080		1222	gCt/gTt	26/45	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.38	2		848	1038	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854952	76854952	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	109	631	0	ENST00000373344.5:c.5884T>C	p.Ser1962Pro	p.S1962P	ENST00000373344	NM_000489.3	1962	Tct/Cct	25/35	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.38	2		631	485	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76931733	76931733	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	77	319	0	ENST00000373344.5:c.3797A>C	p.Asp1266Ala	p.D1266A	ENST00000373344	NM_000489.3	1266	gAt/gCt	10/35	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.38	2		319	360	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937537	76937537	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143621153	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	13	255	0	ENST00000373344.5:c.3211G>A	p.Gly1071Arg	p.G1071R	ENST00000373344	NM_000489.3	1071	Gga/Aga	9/35	1	2	FACETS	0.405	0.289	0.545	0.405	0.289	0.545	SUBCLONAL	1	TRUE	1	0.38	2		255	169	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937678	76937678	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	43	324	0	ENST00000373344.5:c.3070G>T	p.Glu1024Ter	p.E1024*	ENST00000373344	NM_000489.3	1024	Gaa/Taa	9/35	1	2	FACETS	0.988	0.835	1	0.988	0.835	1	CLONAL	1	TRUE	1	0.38	2		324	229	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019547	123019547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	28	321	0	ENST00000355640.3:c.35G>A	p.Cys12Tyr	p.C12Y	ENST00000355640		12	tGt/tAt	2/7	1	2	FACETS	0.441	0.353	0.542	0.441	0.353	0.542	SUBCLONAL	1	TRUE	1	0.38	2		321	334	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220483	123220483	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	147	591	0	ENST00000218089.9:c.3140C>A	p.Ser1047Tyr	p.S1047Y	ENST00000218089	NM_001042749.1	1047	tCt/tAt	30/35	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.38	2		591	724	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860059	152860059	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	54	677	0	ENST00000406277.2:c.369G>T	p.Glu123Asp	p.E123D	ENST00000406277	NM_152274.4	123	gaG/gaT	5/7	1		FACETS		0.259	0.354				SUBCLONAL	1	TRUE	1	0.38	2		677	934	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2957006	2957006	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1175860108	NA	P-0040023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	90	464	2	ENST00000396946.4:c.2621C>T	p.Pro874Leu	p.P874L	ENST00000396946	NM_032415.4	874	cCa/cTa	20/25	1	2	FACETS	0.722	0.641	0.808	0.722	0.641	0.808	SUBCLONAL	1	TRUE	1	0.38	2		466	656	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0040024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	193	558	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.376473937233385	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.376473937233385	1		558	679	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679703	88679703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	60	332	0	ENST00000360948.2:c.760C>T	p.His254Tyr	p.H254Y	ENST00000360948	NM_001012338.2	254	Cac/Tac	7/19	0.20133902857942	1	FACETS	0.365	0.314	0.421	0.365	0.314	0.421	INDETERMINATE	1	TRUE	0	0.376473937233385	1		332	708	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578255	7578274	+	frameshift_variant	Frame_Shift_Del	DEL	TTCCACTCGGATAAGATGCT	TTCCACTCGGATAAGATGCT	-	novel	NA	P-0040024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	275	447	0	ENST00000269305.4:c.575_594del	p.Gln192ArgfsTer10	p.Q192Rfs*10	ENST00000269305	NM_001126112.2	192	cAGCATCTTATCCGAGTGGAA/c	6/11	0.336663290026982	2	FACETS	0.763	0.718	0.81	0.763	0.718	0.81	SUBCLONAL	2	TRUE	0	0.376473937233385	2		447	957	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0040027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	376	768	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.335977414365495	2	FACETS	0.967	0.92	1	0.967	0.92	1	CLONAL	2	TRUE	0	0.381364196752759	2		768	1020	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114905824	114905843	+	frameshift_variant	Frame_Shift_Del	DEL	CACAGCTCTGACCGTCAATG	CACAGCTCTGACCGTCAATG	-	novel	NA	P-0040027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	105	638	0	ENST00000543371.1:c.844_863del	p.Thr282PhefsTer39	p.T282Ffs*39	ENST00000543371	NM_001198531.1	281	ccCACAGCTCTGACCGTCAATGct/ccct	8/14	0.366758886725047	3	FACETS	0.802	0.718	0.891	0.401	0.359	0.446	CLONAL	1	TRUE	1	0.381364196752759	3		638	818	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467088	25467088	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs899717364	NA	P-0040027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	166	835	0	ENST00000264709.3:c.1787G>A	p.Arg596Gln	p.R596Q	ENST00000264709	NM_175629.2	596	cGg/cAg	15/23	0.381364196752759	3	FACETS	0.951	0.872	1	0.475	0.436	0.517	CLONAL	1	TRUE	1	0.381364196752759	3		835	1090	SUCCESS
APC	324	MSKCC	GRCh37	5	112116553	112116554	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	115	351	0	ENST00000257430.4:c.599dup	p.Met200IlefsTer52	p.M200Ifs*52	ENST00000257430	NM_000038.5	200	atg/aTtg	6/16	0.381364196752759	2	FACETS	0.9	0.821	0.982	0.9	0.821	0.982	CLONAL	2	TRUE	0	0.381364196752759	2		351	335	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0040036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	146	410	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.912	0.839	0.987	1	0.993	1	CLONAL	3	TRUE	1	0.23	2		410	464	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198264	185198264	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	250	605	0	ENST00000265026.3:c.2746G>A	p.Val916Met	p.V916M	ENST00000265026	NM_004721.4	916	Gtg/Atg	13/14	1	2	FACETS	0.928	0.87	0.987	0.928	0.87	0.987	CLONAL	1	TRUE	1	0.641554170443781	2		605	840	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0040136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	272	659	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	NA	2	FACETS	0.991	0.931	1			1	INDETERMINATE	2	TRUE	NA	0.28557133500763	2		659	961	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138376590	138376590	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	82	416	0	ENST00000289153.2:c.2884T>A	p.Tyr962Asn	p.Y962N	ENST00000289153	NM_006219.2	962	Tat/Aat	20/22	1	2	FACETS	0.884	0.779	0.995	0.884	0.779	0.995	CLONAL	1	TRUE	1	0.28557133500763	2		416	650	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985471	60985471	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	130	579	2	ENST00000333681.4:c.429C>A	p.Asn143Lys	p.N143K	ENST00000333681		143	aaC/aaA	2/3	0.28557133500763	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.28557133500763	1		581	751	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881711	111881711	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	218	491	1	ENST00000393256.3:c.389del	p.Ala130GlufsTer5	p.A130Efs*5	ENST00000393256	NM_006538.4	130	gCa/ga	2/4	0.28557133500763	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.28557133500763	3		492	853	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593303	67593324	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCTATAACTTGTACAGCTCT	GCCCTATAACTTGTACAGCTCT	-	novel	NA	P-0040136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	50	299	1	ENST00000274335.5:c.2049_2070del	p.Glu683AspfsTer2	p.E683Dfs*2	ENST00000274335		683	gaGCCCTATAACTTGTACAGCTCT/ga	15/15	0.28557133500763	1	FACETS	0.711	0.605	0.828	0.711	0.605	0.828	SUBCLONAL	1	TRUE	0	0.28557133500763	1		300	422	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0040146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	33	243	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.99	0.807	1	0.99	0.807	1	CLONAL	1	TRUE	1	0.19	2		243	351	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0040146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	86	583	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.212913420045797	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.19	2		583	403	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0040146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	12	505	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.304	0.212	0.417	0.304	0.212	0.417	SUBCLONAL	1	TRUE	1	0.19	2		505	416	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088672	27088672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	68	677	0	ENST00000324856.7:c.2281C>T	p.Gln761Ter	p.Q761*	ENST00000324856	NM_006015.4	761	Cag/Tag	7/20	1	2	FACETS	0.991	0.862	1	0.991	0.862	1	CLONAL	1	TRUE	1	0.19	2		677	722	SUCCESS
APC	324	MSKCC	GRCh37	5	112177043	112177043	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs776966222	NA	P-0040146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	46	415	0	ENST00000257430.4:c.5752A>G	p.Ile1918Val	p.I1918V	ENST00000257430	NM_000038.5	1918	Ata/Gta	16/16	1	2	FACETS	0.926	0.78	1	0.926	0.78	1	CLONAL	1	TRUE	1	0.19	2		415	523	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339329	70339329	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0040146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	52	445	0	ENST00000374080.3:c.204+2T>A		p.X68_splice	ENST00000374080		68			1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.19	2		445	488	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	25	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.318183007628578	1	FACETS	0.718	0.57	0.885	0.718	0.57	0.885	SUBCLONAL	1	TRUE	0	0.318183007628578	1		334	184	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0040152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	144	534	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.266693904557416	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.318183007628578	1		535	720	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221161	5221161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs575201235	NA	P-0040152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	134	663	1	ENST00000357368.4:c.3305G>A	p.Arg1102His	p.R1102H	ENST00000357368	NM_002850.3	1102	cGc/cAc	20/38	0.318183007628578	1	FACETS	0.923	0.84	1	0.923	0.84	1	CLONAL	1	TRUE	0	0.318183007628578	1		664	767	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573556	48573556	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	18	240	0	ENST00000342988.3:c.140T>C	p.Leu47Pro	p.L47P	ENST00000342988	NM_005359.5	47	cTg/cCg	2/12	0.266693904557416	1	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	0	0.318183007628578	1		240	73	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830786	72830786	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	146	537	0	ENST00000268489.5:c.5795T>A	p.Leu1932His	p.L1932H	ENST00000268489	NM_006885.3	1932	cTc/cAc	9/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.318183007628578	2		537	811	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974687	21974688	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCGG	novel	NA	P-0040152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	109	376	0	ENST00000304494.5:c.139_140insCCGA	p.Arg47ThrfsTer74	p.R47Tfs*74	ENST00000304494	NM_000077.4	47	agg/aCCGAgg	1/3	0.318183007628578	1	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	0	0.318183007628578	1		376	571	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141427	11141427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	60	574	2	ENST00000358026.2:c.3404G>A	p.Arg1135Gln	p.R1135Q	ENST00000358026	NM_001128849.1	1135	cGg/cAg	25/36	1	2	FACETS	0.863	0.742	0.996	0.863	0.742	0.996	CLONAL	1	TRUE	1	0.16	2		576	869	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463511	25463511	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1330225644	NA	P-0040244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	69	464	1	ENST00000264709.3:c.2171A>G	p.Tyr724Cys	p.Y724C	ENST00000264709	NM_175629.2	724	tAc/tGc	18/23	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.16	2		465	781	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163310	47163310	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0040244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	36	346	0	ENST00000409792.3:c.2816C>G	p.Ser939Ter	p.S939*	ENST00000409792	NM_014159.6	939	tCa/tGa	3/21	1	2	FACETS	0.974	0.801	1	0.974	0.801	1	CLONAL	1	TRUE	1	0.16	2		346	462	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338671	70338671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	210	838	0	ENST00000374080.3:c.67G>T	p.Asp23Tyr	p.D23Y	ENST00000374080		23	Gat/Tat	1/45	1	2	FACETS	0.959	0.891	1	0.959	0.891	1	CLONAL	1	TRUE	1	0.437925386389837	2		838	1000	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0040260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	134	136	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.437925386389837	2		136	561	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0040260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	103	290	1	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.437925386389837	2		291	466	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370985	55370985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	536	1054	0	ENST00000297316.4:c.287C>G	p.Ala96Gly	p.A96G	ENST00000297316	NM_022454.3	96	gCc/gGc	1/2	0.185299034210416	3	FACETS	1	0.992	1	1	0.992	1	INDETERMINATE	2	TRUE	1	0.437925386389837	3		1054	1338	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685315	89685316	+	splice_donor_variant	Splice_Site	INS	-	-	T	rs1064794925	NA	P-0040260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	125	204	0	ENST00000371953.3:c.209+2dup		p.X70_splice	ENST00000371953	NM_000314.4	70			0.437925386389837	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.437925386389837	2		204	277	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149465980	149465980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	259	902	0	ENST00000286301.3:c.11G>A	p.Gly4Glu	p.G4E	ENST00000286301	NM_005211.3	4	gGa/gAa	2/22	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.437925386389837	2		902	1160	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099064	27099064	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	315	591	1	ENST00000324856.7:c.3482del	p.Lys1161SerfsTer19	p.K1161Sfs*19	ENST00000324856	NM_006015.4	1160	ttA/tt	13/20	0.427271737964042	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.437925386389837	2		592	693	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406664	70406664	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	62	563	0	ENST00000373644.4:c.4178A>C	p.Lys1393Thr	p.K1393T	ENST00000373644	NM_030625.2	1393	aAa/aCa	4/12	1	2	FACETS	0.483	0.417	0.555	0.483	0.417	0.555	SUBCLONAL	1	TRUE	1	0.437925386389837	2		563	586	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486854	56486854	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	125	474	0	ENST00000267101.3:c.1268T>A	p.Leu423His	p.L423H	ENST00000267101	NM_001982.3	423	cTc/cAc	11/28	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.437925386389837	2		474	546	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244538	41244538	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	114	513	0	ENST00000357654.3:c.3010G>A	p.Glu1004Lys	p.E1004K	ENST00000357654	NM_007294.3	1004	Gag/Aag	10/23	1	2	FACETS	0.997	0.902	1	0.997	0.902	1	CLONAL	1	TRUE	1	0.437925386389837	2		513	522	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245003	41245003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	133	658	0	ENST00000357654.3:c.2545G>A	p.Glu849Lys	p.E849K	ENST00000357654	NM_007294.3	849	Gaa/Aaa	10/23	1	2	FACETS	0.904	0.823	0.989	0.904	0.823	0.989	CLONAL	1	TRUE	1	0.437925386389837	2		658	672	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246785	41246785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	131	469	0	ENST00000357654.3:c.763G>A	p.Glu255Lys	p.E255K	ENST00000357654	NM_007294.3	255	Gag/Aag	10/23	1	2	FACETS	0.973	0.886	1	0.973	0.886	1	CLONAL	1	TRUE	1	0.437925386389837	2		469	615	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92252362	92252362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	65	242	0	ENST00000265734.4:c.686G>A	p.Gly229Glu	p.G229E	ENST00000265734	NM_001259.6	229	gGa/gAa	6/8	1	2	FACETS	0.916	0.8	1	0.916	0.8	1	CLONAL	1	TRUE	1	0.437925386389837	2		242	324	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206600	108206600	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1565543359	NA	P-0040268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	99	296	0	ENST00000278616.4:c.8180T>C	p.Val2727Ala	p.V2727A	ENST00000278616	NM_000051.3	2727	gTc/gCc	56/63	0.468676228979384	1	FACETS	0.783	0.715	0.85	1	0.986	1	SUBCLONAL	2	TRUE	0	0.464677406098861	1		296	209	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15967400	15967400	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	166	594	0	ENST00000268712.3:c.5203G>C	p.Asp1735His	p.D1735H	ENST00000268712	NM_006311.3	1735	Gac/Cac	35/46	0.419087552930156	5	FACETS	1	0.979	1	0.401	0.367	0.435	CLONAL	1	TRUE	2	0.464677406098861	5		594	1009	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0040280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	268	626	3	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	NA	2	FACETS	0.948	0.898	0.997			1	INDETERMINATE	2	FALSE	NA	0.507620844845232	2		629	557	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591140	67591145	+	inframe_deletion	In_Frame_Del	DEL	ACCAAT	ACCAAT	-	rs751582616	NA	P-0040280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	137	361	0	ENST00000274335.5:c.1735_1740del	p.Gln579_Tyr580del	p.Q579_Y580del	ENST00000274335		578	gACCAATac/gac	12/15	0.507620844845232	4	FACETS	0.99	0.909	1	0.99	0.909	1	CLONAL	2	FALSE	2	0.507620844845232	4		361	411	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802645	139802645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762052203	NA	P-0040280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	49	650	0	ENST00000247668.2:c.490C>T	p.Arg164Trp	p.R164W	ENST00000247668	NM_021138.3	164	Cgg/Tgg	5/11	0.226325880298268	6	FACETS	0.457	0.385	0.536	0.152	0.128	0.179	INDETERMINATE	1	FALSE	3	0.507620844845232	6		650	852	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883113	37883113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780434636	NA	P-0040280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	282	819	1	ENST00000269571.5:c.3016C>T	p.Arg1006Cys	p.R1006C	ENST00000269571		1006	Cgc/Tgc	25/27	0.507620844845232	5	FACETS	0.919	0.864	0.975			1	CLONAL	2	FALSE	NA	0.507620844845232	5		820	1065	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105882	27105883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0040280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	353	623	0	ENST00000324856.7:c.5495_5496dup	p.Arg1833GlyfsTer51	p.R1833Gfs*51	ENST00000324856	NM_006015.4	1831	-/GG	20/20	0.507620844845232	4	FACETS	0.967	0.923	1	0.967	0.923	1	CLONAL	3	FALSE	1	0.507620844845232	4		623	723	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593284	67593285	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCTA	novel	NA	P-0040280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	101	368	0	ENST00000274335.5:c.2036_2041dup	p.Tyr679_Gly680dup	p.Y679_G680dup	ENST00000274335		679	act/acTGGCTAt	15/15	0.507620844845232	4	FACETS	1	0.976	1	0.648	0.582	0.717	CLONAL	1	FALSE	2	0.507620844845232	4		368	463	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053237	180053237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372947534	NA	P-0040280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	279	795	0	ENST00000261937.6:c.1132C>T	p.Arg378Cys	p.R378C	ENST00000261937	NM_182925.4	378	Cgc/Tgc	9/30	0.507620844845232	4	FACETS	0.924	0.87	0.979	0.924	0.87	0.979	CLONAL	2	FALSE	2	0.507620844845232	4		795	897	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32802947	32802947	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	106	425	0	ENST00000374899.4:c.929A>G	p.Tyr310Cys	p.Y310C	ENST00000374899	NM_018833.2	310	tAc/tGc	5/12	0.507620844845232	4	FACETS	0.966	0.867	1	0.322	0.289	0.357	CLONAL	1	FALSE	1	0.507620844845232	4		425	652	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650438	48650438	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	178	914	0	ENST00000376670.3:c.408G>C	p.Leu136Phe	p.L136F	ENST00000376670	NM_002049.3	136	ttG/ttC	3/6	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.507620844845232	2		914	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0040315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	71	563	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.194152582793923	1	FACETS	0.926	0.808	1	0.926	0.808	1	CLONAL	1	TRUE	0	0.206805480723091	1		563	665	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571903	64571903	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	148	805	0	ENST00000312049.6:c.1736T>A	p.Leu579His	p.L579H	ENST00000312049	NM_130799.2	579	cTc/cAc	10/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.206805480723091	2		805	1183	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55693361	55693361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	103	596	0	ENST00000284073.2:c.568G>A	p.Val190Ile	p.V190I	ENST00000284073	NM_138962.2	190	Gtc/Atc	9/14	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.206805480723091	2		596	888	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0040339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	53	766	1	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.49	0.417	0.571	0.49	0.417	0.571	SUBCLONAL	1	TRUE	1	0.29	2		767	746	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0040362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	30	165	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.703	0.568	0.855	0.703	0.568	0.855	SUBCLONAL	1	TRUE	1	0.288488382847355	2		165	296	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0040362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	111	410	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.24713581967374	4	FACETS	1	0.97	1	0.787	0.713	0.864	CLONAL	2	TRUE	1	0.288488382847355	4		410	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	127	472	0	ENST00000269305.4:c.398T>A	p.Met133Lys	p.M133K	ENST00000269305	NM_001126112.2	133	aTg/aAg	5/11	0.288488382847355	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.288488382847355	1		472	664	SUCCESS
APC	324	MSKCC	GRCh37	5	112175897	112175897	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	35	143	0	ENST00000257430.4:c.4606G>T	p.Glu1536Ter	p.E1536*	ENST00000257430	NM_000038.5	1536	Gaa/Taa	16/16	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.288488382847355	2		143	220	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720711	89720711	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	33	63	0	ENST00000371953.3:c.862G>T	p.Glu288Ter	p.E288*	ENST00000371953	NM_000314.4	288	Gaa/Taa	8/9	0.252996911451045	3	FACETS	0.992	0.834	1	0.992	0.834	1	CLONAL	3	TRUE	0	0.288488382847355	3		63	88	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121669	108121669	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750280306	NA	P-0040362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	55	298	1	ENST00000278616.4:c.1477C>T	p.Arg493Cys	p.R493C	ENST00000278616	NM_000051.3	493	Cgt/Tgt	10/63	1	2	FACETS	0.941	0.808	1	0.941	0.808	1	CLONAL	1	TRUE	1	0.288488382847355	2		299	405	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005429	29005429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372354806	NA	P-0040362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	23	210	0	ENST00000282397.4:c.832G>A	p.Val278Ile	p.V278I	ENST00000282397	NM_002019.4	278	Gta/Ata	7/30	1	2	FACETS	0.552	0.431	0.692	0.552	0.431	0.692	SUBCLONAL	1	TRUE	1	0.288488382847355	2		210	289	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509128	66509128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1439062174	NA	P-0040362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	23	388	0	ENST00000273854.3:c.199C>T	p.Arg67Cys	p.R67C	ENST00000273854	NM_004439.5	67	Cgc/Tgc	2/18	0.202456658344485	1	FACETS	0.552	0.432	0.691	0.552	0.432	0.691	SUBCLONAL	1	TRUE	0	0.288488382847355	1		388	247	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186602	108186602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	26	212	0	ENST00000278616.4:c.6059G>A	p.Gly2020Asp	p.G2020D	ENST00000278616	NM_000051.3	2020	gGc/gAc	41/63	1	2	FACETS	0.567	0.449	0.701	0.567	0.449	0.701	SUBCLONAL	1	TRUE	1	0.288488382847355	2		212	318	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822034	72822039	+	inframe_deletion	In_Frame_Del	DEL	GCTGCT	GCTGCT	-	rs372741038	NA	P-0040362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	41	245	0	ENST00000268489.5:c.10136_10141del	p.Gln3379_Gln3380del	p.Q3379_Q3380del	ENST00000268489	NM_006885.3	3379	cAGCAGCgg/cgg	10/10	1	2	FACETS	0.718	0.599	0.85	0.718	0.599	0.85	SUBCLONAL	1	TRUE	1	0.288488382847355	2		245	396	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513386	41513386	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	39	402	0	ENST00000263253.7:c.290T>G	p.Val97Gly	p.V97G	ENST00000263253	NM_001429.3	97	gTt/gGt	2/31	1	2	FACETS	0.503	0.416	0.599	0.503	0.416	0.599	SUBCLONAL	1	TRUE	1	0.288488382847355	2		402	538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0040442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	262	761	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.596342881758739	1	FACETS	0.958	0.904	1	0.958	0.904	1	CLONAL	1	TRUE	0	0.596342881758739	1		764	644	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224456	123224456	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	411	289	0	ENST00000218089.9:c.3309G>A	p.Trp1103Ter	p.W1103*	ENST00000218089	NM_001042749.1	1103	tgG/tgA	31/35	0.555000397245827	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.596342881758739	2		289	588	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120783981	120783981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	249	736	0	ENST00000257552.2:c.1004C>T	p.Ala335Val	p.A335V	ENST00000257552	NM_002442.3	335	gCc/gTc	13/15	1	2	FACETS	0.901	0.845	0.958	0.901	0.845	0.958	CLONAL	1	TRUE	1	0.669088026701006	2		736	826	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438033	438033	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	98	302	0	ENST00000399788.2:c.1936G>A	p.Glu646Lys	p.E646K	ENST00000399788	NM_001042603.1	646	Gaa/Aaa	14/28	0.242441730905214	5	FACETS	1	0.912	1			1	INDETERMINATE	1	TRUE	NA	0.669088026701006	5		302	574	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846039	68846039	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	153	571	0	ENST00000261769.5:c.1010G>T	p.Ser337Ile	p.S337I	ENST00000261769	NM_004360.3	337	aGt/aTt	8/16	1	2	FACETS	0.617	0.565	0.671	0.617	0.565	0.671	SUBCLONAL	1	TRUE	1	0.669088026701006	2		571	741	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220541	133220541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	207	459	0	ENST00000320574.5:c.4172C>T	p.Ser1391Phe	p.S1391F	ENST00000320574	NM_006231.2	1391	tCc/tTc	33/49	0.67484139171374	5	FACETS	1	0.964	1			1	CLONAL	1	TRUE	NA	0.740490580111666	5		459	1108	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266960	18266960	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752430880	NA	P-0040548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	134	164	0	ENST00000222254.8:c.271C>T	p.Arg91Trp	p.R91W	ENST00000222254	NM_005027.3	91	Cgg/Tgg	2/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.740490580111666	2		164	290	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040586-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	43	759	1				ENST00000310581	NM_198253.2	-/1132			0.463791483088749	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	1	0.458886152246607	3		760	94	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868168	45868168	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040586-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	24	825	0	ENST00000391945.4:c.522C>G	p.Ile174Met	p.I174M	ENST00000391945	NM_000400.3	174	atC/atG	7/23	0.463791483088749	4	FACETS	0.829	0.655	1	0.276	0.218	0.343	CLONAL	1	TRUE	1	0.458886152246607	4		825	184	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643566	38643578	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAATGTTAGGG	GAAAATGTTAGGG	-	novel	NA	P-0040586-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	25	643	0	ENST00000299084.4:c.1044_1056del	p.Gly350MetfsTer52	p.G350Mfs*52	ENST00000299084	NM_152594.2	346	GAAAATGTTAGGGga/ga	7/7	1	2	FACETS	0.633	0.504	0.78	0.633	0.504	0.78	SUBCLONAL	1	TRUE	1	0.458886152246607	2		643	172	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690362	117690362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040586-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	28	619	0	ENST00000369458.3:c.767C>T	p.Ser256Leu	p.S256L	ENST00000369458	NM_024626.3	256	tCa/tTa	5/6	0.235283356960197	4	FACETS	0.995	0.802	1	0.332	0.267	0.403	INDETERMINATE	1	TRUE	1	0.458886152246607	4		619	179	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551990	150551990	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040586-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	44	736	0	ENST00000369026.2:c.17G>C	p.Arg6Thr	p.R6T	ENST00000369026	NM_021960.4	6	aGa/aCa	1/3	0.458886152246607	6	FACETS	1	0.916	1	0.285	0.239	0.334	CLONAL	1	TRUE	2	0.458886152246607	6		736	323	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923090	48923090	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0040586-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	45	315	0	ENST00000267163.4:c.540-2A>G		p.X180_splice	ENST00000267163	NM_000321.2	180			0.179310652761997	5	FACETS	1	0.915	1			1	INDETERMINATE	3	TRUE	NA	0.458886152246607	5		315	103	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867571	45867571	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040586-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	38	1019	0	ENST00000391945.4:c.737C>G	p.Ser246Cys	p.S246C	ENST00000391945	NM_000400.3	246	tCc/tGc	9/23	0.463791483088749	4	FACETS	1	0.909	1	0.38	0.317	0.449	CLONAL	1	TRUE	1	0.458886152246607	4		1019	212	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942774	68942774	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040586-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	28	734	0	ENST00000288368.4:c.586G>C	p.Ala196Pro	p.A196P	ENST00000288368	NM_024870.2	196	Gca/Cca	6/40	0.463791483088749	3	FACETS	0.526	0.422	0.645	0.263	0.211	0.323	SUBCLONAL	1	TRUE	1	0.458886152246607	3		734	285	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1690553	1690553	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040586-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	21	681	0	ENST00000378625.1:c.562G>C	p.Gly188Arg	p.G188R	ENST00000378625	NM_001198994.1	188	Ggc/Cgc	5/14	0.281753755843469	4	FACETS	0.661	0.511	0.834	0.331	0.255	0.417	SUBCLONAL	1	TRUE	2	0.458886152246607	4		681	202	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93973601	93973602	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0040586-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	10	363	0	ENST00000369303.4:c.1774_1775delinsAT	p.Gly592Ile	p.G592I	ENST00000369303	NM_004440.3	592	GGc/ATc	9/17	0.105990582707514	4	FACETS	0.513	0.349	0.716	0.256	0.174	0.358	INDETERMINATE	1	TRUE	2	0.458886152246607	4		363	124	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396487	139396487	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs755659037	NA	P-0040586-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	21	843	0	ENST00000277541.6:c.5438G>T	p.Trp1813Leu	p.W1813L	ENST00000277541	NM_017617.3	1813	tGg/tTg	29/34	0.312223845673012	3	FACETS	0.765	0.595	0.96	0.383	0.297	0.48	CLONAL	1	TRUE	1	0.458886152246607	3		843	147	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922984	39922984	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040586-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	31	379	0	ENST00000378444.4:c.3724C>T	p.Gln1242Ter	p.Q1242*	ENST00000378444	NM_001123385.1	1242	Cag/Tag	8/15	0.458886152246607	3	FACETS	1	0.912	1			1	CLONAL	1	TRUE	NA	0.458886152246607	3		379	139	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0040635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	95	910	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.0699064136259873	2	FACETS	0.959	0.861	1			1	INDETERMINATE	2	TRUE	NA	0.27	2		910	367	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0040635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	115	634	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.3	1	FACETS	0.964	0.869	1	0.964	0.869	1	CLONAL	1	TRUE	0	0.27	1		635	764	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	123	608	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	0.168797664580798	2	FACETS	1	0.983	1	0.704	0.638	0.773	CLONAL	1	TRUE	0	0.27	2		608	647	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985441	60985441	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	54	701	0	ENST00000333681.4:c.459C>A	p.Phe153Leu	p.F153L	ENST00000333681		153	ttC/ttA	2/3	0.193543544127503	2	FACETS	0.491	0.418	0.571	0.245	0.209	0.286	SUBCLONAL	1	TRUE	0	0.27	2		701	815	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884502	151884502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	52	385	0	ENST00000262189.6:c.4853C>T	p.Ser1618Leu	p.S1618L	ENST00000262189	NM_170606.2	1618	tCa/tTa	33/59	1	2	FACETS	0.767	0.654	0.892	0.767	0.654	0.892	SUBCLONAL	1	TRUE	1	0.27	2		385	502	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542552	141542552	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1382113944	NA	P-0040635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	107	639	0	ENST00000220592.5:c.2434C>T	p.Arg812Trp	p.R812W	ENST00000220592	NM_012154.3	812	Cgg/Tgg	18/19	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.27	2		639	786	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0040639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	138	331	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.221207227264882	4	FACETS	1	0.955	1	1	0.955	1	INDETERMINATE	2	TRUE	2	0.469630115164918	4		331	408	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787737	135787737	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0040639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	230	506	0	ENST00000298552.3:c.845C>G	p.Ser282Ter	p.S282*	ENST00000298552	NM_001162426.1	282	tCa/tGa	9/23	0.469630115164918	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.469630115164918	1		506	593	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434092	121434092	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	283	567	0	ENST00000257555.6:c.983G>T	p.Ser328Ile	p.S328I	ENST00000257555		328	aGt/aTt	5/10	0.221207227264882	4	FACETS	0.937	0.882	0.993	0.937	0.882	0.993	INDETERMINATE	2	TRUE	2	0.469630115164918	4		567	945	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099313	157099339	+	inframe_deletion	In_Frame_Del	DEL	CACCACCACCACCACCATGCCCACCAC	CACCACCACCACCACCATGCCCACCAC	-	rs1234893556	NA	P-0040639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	49	295	0	ENST00000346085.5:c.261_287del	p.His88_His96del	p.H88_H96del	ENST00000346085	NM_020732.3	84	CACCACCACCACCACCATGCCCACCAC/-	1/20	1	2	FACETS	0.519	0.44	0.605	0.519	0.44	0.605	SUBCLONAL	1	TRUE	1	0.469630115164918	2		295	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578279	7578279	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	193	509	0	ENST00000269305.4:c.570del	p.Pro191LeufsTer56	p.P191Lfs*56	ENST00000269305	NM_001126112.2	190	ccT/cc	6/11	0.266483219550655	3	FACETS	0.915	0.856	0.974	0.915	0.856	0.974	CLONAL	3	TRUE	0	0.373395483194088	3		509	447	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682461	37682461	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs186741659	NA	P-0040647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	85	350	0	ENST00000447079.4:c.3652A>G	p.Met1218Val	p.M1218V	ENST00000447079	NM_015083.1	1218	Atg/Gtg	13/14	0.373395483194088	5	FACETS	0.83	0.737	0.928			1	CLONAL	2	TRUE	NA	0.373395483194088	5		350	428	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148644	20148644	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	101	355	0	ENST00000379607.5:c.419A>G	p.Asp140Gly	p.D140G	ENST00000379607	NM_001412.3	140	gAt/gGt	6/7	0.199063018221771	5	FACETS	0.963	0.866	1	0.642	0.577	0.71	INDETERMINATE	2	TRUE	2	0.373395483194088	5		355	438	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0040698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	337	761	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	0.223704806767545	1	FACETS	0.689	0.654	0.724	0.689	0.654	0.724	INDETERMINATE	1	TRUE	0	0.730803675381757	1		761	850	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144113	11144113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	53	762	0	ENST00000358026.2:c.3694G>A	p.Gly1232Ser	p.G1232S	ENST00000358026	NM_001128849.1	1232	Ggc/Agc	26/36	0.223704806767545	1	FACETS	0.111	0.094	0.129	0.111	0.094	0.129	INDETERMINATE	1	TRUE	0	0.730803675381757	1		762	832	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0040698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	210	440	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	0.894	0.834	0.955	0.894	0.834	0.955	CLONAL	1	TRUE	1	0.730803675381757	2		440	643	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	77	759	1				ENST00000310581	NM_198253.2	-/1132			0.192179043835392	2	FACETS	0.961	0.857	1	0.961	0.857	1	INDETERMINATE	2	TRUE	0	0.33957338102271	2		760	236	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0040700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	174	628	1	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.33957338102271	3	FACETS	0.996	0.937	1			1	CLONAL	4	TRUE	NA	0.33957338102271	3		629	301	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519893	NA	P-0040700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	197	912	1	ENST00000267101.3:c.310G>T	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ttg	3/28	0.33957338102271	5	FACETS	0.966	0.896	1	0.644	0.597	0.693	CLONAL	2	TRUE	2	0.33957338102271	5		913	906	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652198	36652199	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	146	811	1	ENST00000244741.5:c.322dup	p.Glu108GlyfsTer21	p.E108Gfs*21	ENST00000244741	NM_000389.4	107	gag/gaGg	2/3	0.319306959364323	4	FACETS	0.855	0.782	0.93	0.855	0.782	0.93	CLONAL	2	TRUE	2	0.33957338102271	4		812	674	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44910996	44910999	+	frameshift_variant	Frame_Shift_Del	DEL	CAGA	CAGA	-	novel	NA	P-0040700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	52	262	0	ENST00000377967.4:c.701_704del	p.Thr234ArgfsTer7	p.T234Rfs*7	ENST00000377967	NM_021140.2	233	CAGAca/ca	9/29	0.33957338102271	4	FACETS	1	0.946	1			1	CLONAL	1	TRUE	NA	0.33957338102271	4		262	332	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982387	201982387	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	76	866	0	ENST00000359651.3:c.766G>C	p.Glu256Gln	p.E256Q	ENST00000359651		256	Gag/Cag	6/8	0.33957338102271	3	FACETS	0.734	0.644	0.832	0.367	0.322	0.416	SUBCLONAL	1	TRUE	1	0.33957338102271	3		866	713	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45391495	45391495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	37	434	0	ENST00000262160.6:c.665C>T	p.Pro222Leu	p.P222L	ENST00000262160	NM_005901.5	222	cCt/cTt	6/11	0.318796802336736	3	FACETS	0.855	0.708	1	0.285	0.236	0.34	CLONAL	1	TRUE	0	0.33957338102271	3		434	298	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976923	18976923	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	59	769	0	ENST00000262803.5:c.3308G>A	p.Gly1103Glu	p.G1103E	ENST00000262803	NM_002911.3	1103	gGa/gAa	23/24	0.33957338102271	5	FACETS	0.772	0.664	0.891	0.257	0.221	0.297	SUBCLONAL	1	TRUE	2	0.33957338102271	5		769	679	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806555	1806555	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	318	710	0	ENST00000260795.2:c.1271C>G	p.Ser424Cys	p.S424C	ENST00000260795		424	tCc/tGc	9/17	0.33957338102271	3	FACETS	1	0.971	1			1	CLONAL	4	TRUE	NA	0.33957338102271	3		710	538	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807874	1807874	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1472731505	NA	P-0040700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	357	928	0	ENST00000260795.2:c.1933C>G	p.Leu645Val	p.L645V	ENST00000260795		645	Ctc/Gtc	13/17	0.33957338102271	3	FACETS	1	0.988	1			1	CLONAL	4	TRUE	NA	0.33957338102271	3		928	573	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436852	52436852	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1386810597	NA	P-0040725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	44	449	0	ENST00000460680.1:c.1926G>C	p.Glu642Asp	p.E642D	ENST00000460680	NM_004656.3	642	gaG/gaC	15/17	0.310346769534962	2	FACETS	0.383	0.32	0.452	0.191	0.16	0.226	SUBCLONAL	1	TRUE	0	0.364760719972034	2		449	630	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578516	7578610	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAA	GGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAA	-	novel	NA	P-0040725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	123	626	0	ENST00000269305.4:c.376-56_414del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	0.364614111662883	1	FACETS	0.73	0.661	0.804	0.73	0.661	0.804	SUBCLONAL	1	TRUE	0	0.364760719972034	1		626	755	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805721	46805721	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	274	610	0	ENST00000290295.7:c.235C>A	p.Pro79Thr	p.P79T	ENST00000290295	NM_006361.5	79	Cct/Act	1/2	0.349322960810591	4	FACETS	0.986	0.926	1	0.493	0.463	0.524	CLONAL	2	TRUE	0	0.364760719972034	4		610	1040	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420054	41420054	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	62	295	0	ENST00000373198.4:c.267C>G	p.His89Gln	p.H89Q	ENST00000373198	NM_133170.3	89	caC/caG	3/32	1	2	FACETS	0.794	0.688	0.909	0.794	0.688	0.909	CLONAL	1	TRUE	1	0.364760719972034	2		295	428	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436845	52436845	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	42	473	1	ENST00000460680.1:c.1933A>T	p.Asn645Tyr	p.N645Y	ENST00000460680	NM_004656.3	645	Aac/Tac	15/17	0.310346769534962	2	FACETS	0.352	0.293	0.418	0.176	0.146	0.209	SUBCLONAL	1	TRUE	0	0.364760719972034	2		474	654	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139794938	139794938	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	278	404	0	ENST00000247668.2:c.332G>C	p.Gly111Ala	p.G111A	ENST00000247668	NM_021138.3	111	gGa/gCa	4/11	0.306112244035739	3	FACETS	0.882	0.834	0.931	0.882	0.834	0.931	CLONAL	3	TRUE	0	0.364760719972034	3		404	681	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922944	44922944	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	32	435	0	ENST00000377967.4:c.1805G>T	p.Gly602Val	p.G602V	ENST00000377967	NM_021140.2	602	gGa/gTa	16/29	NA	2	FACETS	0.284	0.23	0.346			1	INDETERMINATE	1	TRUE	NA	0.364760719972034	2		435	618	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224523	53224523	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	98	605	0	ENST00000375401.3:c.3190G>C	p.Gly1064Arg	p.G1064R	ENST00000375401	NM_004187.3	1064	Ggg/Cgg	21/26	NA	2	FACETS	0.674	0.601	0.752			1	INDETERMINATE	1	TRUE	NA	0.364760719972034	2		605	797	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555526101	NA	P-0040746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	77	757	0	ENST00000269305.4:c.497C>G	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tGa	5/11	1	2	FACETS	0.86	0.754	0.976	0.86	0.754	0.976	CLONAL	1	TRUE	1	0.19	2		757	942	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477837	140477851	+	inframe_deletion	In_Frame_Del	DEL	TAGGTGCTGTCACAT	TAGGTGCTGTCACAT	-	novel	NA	P-0040746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	66	472	0	ENST00000288602.6:c.1457_1471del	p.Asn486_Pro490del	p.N486_P490del	ENST00000288602	NM_004333.4	486	aATGTGACAGCACCTAca/aca	12/18	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.19	2		472	628	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974690	21974691	+	missense_variant	Missense_Mutation	DNP	CG	CG	TT	novel	NA	P-0040746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	38	444	2	ENST00000304494.5:c.136_137delinsAA	p.Arg46Lys	p.R46K	ENST00000304494	NM_000077.4	46	CGg/AAg	1/3	0.124922663484397	1	FACETS	0.65	0.536	0.777	0.65	0.536	0.777	SUBCLONAL	1	TRUE	0	0.19	1		446	557	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	40	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.113335084677592	6	FACETS	1	0.954	1	0.489	0.409	0.577	INDETERMINATE	1	TRUE	3	0.369027301816854	6		334	257	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578502	7578502	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	191	965	0	ENST00000269305.4:c.428T>C	p.Val143Ala	p.V143A	ENST00000269305	NM_001126112.2	143	gTg/gCg	5/11	0.269023482976664	2	FACETS	0.77	0.715	0.827	0.77	0.715	0.827	SUBCLONAL	2	TRUE	0	0.369027301816854	2		965	672	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891277	101891277	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	85	512	0	ENST00000374994.4:c.238C>T	p.Arg80Ter	p.R80*	ENST00000374994	NM_004612.2	80	Cga/Tga	2/9	0.369027301816854	2	FACETS	0.835	0.747	0.925	0.835	0.747	0.925	CLONAL	2	TRUE	0	0.369027301816854	2		512	276	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981163	201981165	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0040777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	230	811	0	ENST00000359651.3:c.246_248del	p.Lys82del	p.K82del	ENST00000359651		81	gAGAag/gag	2/8	0.295662532645341	3	FACETS	1	0.984	1	0.761	0.713	0.809	CLONAL	2	TRUE	0	0.369027301816854	3		811	647	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420631	49420631	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	156	710	0	ENST00000301067.7:c.15118G>T	p.Asp5040Tyr	p.D5040Y	ENST00000301067	NM_003482.3	5040	Gac/Tac	48/54	0.113335084677592	6	FACETS	1	0.978	1	0.787	0.724	0.853	INDETERMINATE	2	TRUE	3	0.369027301816854	6		710	622	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457246	67457246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1343295267	NA	P-0040777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	115	643	3	ENST00000327367.4:c.220C>T	p.Arg74Trp	p.R74W	ENST00000327367	NM_005902.3	74	Cgg/Tgg	2/9	0.15108920277456	4	FACETS	1	0.983	1	0.733	0.662	0.807	INDETERMINATE	1	TRUE	2	0.369027301816854	4		646	582	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016601	12016601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	51	393	1	ENST00000353533.5:c.737G>A	p.Cys246Tyr	p.C246Y	ENST00000353533	NM_003010.3	246	tGt/tAt	7/11	0.269023482976664	2	FACETS	1	0.964	1	0.709	0.611	0.813	CLONAL	1	TRUE	0	0.369027301816854	2		394	195	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0040783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	115	395	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.445486764708438	2		395	477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0040783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	595	804	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.413996656437723	3	FACETS	0.852	0.821	0.883	0.852	0.821	0.883	CLONAL	3	FALSE	0	0.445486764708438	3		804	1278	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0040783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	118	383	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.148304434965414	5	FACETS	0.82	0.743	0.901	0.547	0.495	0.601	INDETERMINATE	2	FALSE	2	0.445486764708438	5		384	539	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937913	36937913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148747030	NA	P-0040783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	125	849	2	ENST00000361632.4:c.923G>A	p.Arg308His	p.R308H	ENST00000361632		308	cGc/cAc	7/16	0.106713095864072	5	FACETS	0.952	0.861	1	0.238	0.215	0.263	INDETERMINATE	1	FALSE	1	0.445486764708438	5		851	983	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473708	67473708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906855	NA	P-0040783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	288	582	1	ENST00000327367.4:c.788C>T	p.Pro263Leu	p.P263L	ENST00000327367	NM_005902.3	263	cCc/cTc	6/9	NA	2	FACETS	0.895	0.847	0.944			1	INDETERMINATE	2	FALSE	NA	0.445486764708438	2		583	722	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487487	38487487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173565250	NA	P-0040783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	34	377	0	ENST00000254066.5:c.17G>A	p.Ser6Asn	p.S6N	ENST00000254066	NM_000964.3	6	aGc/aAc	2/9	0.377587048884976	3	FACETS	0.332	0.271	0.402	0.111	0.09	0.134	SUBCLONAL	1	FALSE	0	0.445486764708438	3		377	562	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023480	31023480	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	280	498	0	ENST00000375687.4:c.2965T>C	p.Ser989Pro	p.S989P	ENST00000375687	NM_015338.5	989	Tct/Cct	13/13	0.325654458437277	5	FACETS	0.859	0.81	0.909	0.859	0.81	0.909	CLONAL	3	FALSE	2	0.445486764708438	5		498	814	SUCCESS
APC	324	MSKCC	GRCh37	5	112175530	112175547	+	frameshift_variant	Frame_Shift_Del	DEL	GGTAAGTGGCATTATAAG	GGTAAGTGGCATTATAAG	TATAACC	novel	NA	P-0040783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	118	309	2	ENST00000257430.4:c.4239_4256delinsTATAACC	p.Met1413IlefsTer6	p.M1413Ifs*6	ENST00000257430	NM_000038.5	1413	atGGTAAGTGGCATTATAAGc/atTATAACCc	16/16	0.148304434965414	5	FACETS	0.894	0.811	0.981	0.596	0.541	0.654	INDETERMINATE	2	FALSE	2	0.445486764708438	5		311	494	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292916	91292916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	99	466	0	ENST00000355112.3:c.418G>A	p.Glu140Lys	p.E140K	ENST00000355112	NM_000057.2	140	Gaa/Aaa	3/22	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.24	2		466	752	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0040834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	225	558	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.243536280404815	3	FACETS	0.755	0.703	0.81	0.755	0.703	0.81	SUBCLONAL	2	TRUE	1	0.31	3		558	1110	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	119	757	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.267249003405155	1	FACETS	0.94	0.85	1	0.94	0.85	1	CLONAL	1	TRUE	0	0.31	1		757	690	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0040854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	275	736	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	NA	2	FACETS	0.896	0.846	0.946			1	INDETERMINATE	2	TRUE	NA	0.428234142816708	2		737	717	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0040854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	184	243	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.428234142816708	3	FACETS	0.932	0.866	0.999	0.932	0.866	0.999	CLONAL	2	TRUE	1	0.428234142816708	3		243	560	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	131	674	3	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.422899095467012	2	FACETS	1	0.935	1	0.516	0.47	0.564	CLONAL	1	TRUE	0	0.428234142816708	2		677	593	SUCCESS
RET	5979	MSKCC	GRCh37	10	43614996	43614996	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79658334	NA	P-0040854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	116	724	1	ENST00000355710.3:c.2410G>C	p.Val804Leu	p.V804L	ENST00000355710	NM_020975.4	804	Gtg/Ctg	14/20	0.428234142816708	3	FACETS	0.877	0.791	0.968	0.439	0.395	0.484	CLONAL	1	TRUE	1	0.428234142816708	3		725	750	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658295	18658295	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	223	479	0	ENST00000266497.5:c.3100C>G	p.Arg1034Gly	p.R1034G	ENST00000266497		1034	Cgt/Ggt	22/31	0.420558742019815	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.428234142816708	4		479	705	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061730	38061730	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs770844920	NA	P-0040854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	94	526	0	ENST00000250448.2:c.259G>C	p.Gly87Arg	p.G87R	ENST00000250448	NM_004496.3	87	Ggg/Cgg	2/2	0.428234142816708	3	FACETS	0.564	0.501	0.632	0.282	0.25	0.316	SUBCLONAL	1	TRUE	1	0.428234142816708	3		526	945	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0040939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	58	436	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.899	0.775	1	0.899	0.775	1	CLONAL	1	TRUE	1	0.33	2		436	391	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0040939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	97	743	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	1	2	FACETS	0.995	0.889	1	0.995	0.889	1	CLONAL	1	TRUE	1	0.33	2		743	591	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916855	178916855	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	112	854	0	ENST00000263967.3:c.242A>C	p.Glu81Ala	p.E81A	ENST00000263967	NM_006218.2	81	gAa/gCa	2/21	1	2	FACETS	0.998	0.899	1	0.998	0.899	1	CLONAL	1	TRUE	1	0.33	2		854	680	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190825	32190825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779661107	NA	P-0040939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	88	995	0	ENST00000375023.3:c.112G>A	p.Gly38Arg	p.G38R	ENST00000375023	NM_004557.3	38	Gga/Aga	2/30	1	2	FACETS	0.86	0.763	0.964	0.86	0.763	0.964	CLONAL	1	TRUE	1	0.33	2		995	620	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0040957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	190	554	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.633572715148334	2		554	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577546	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGCCCATGCAG	GCCGCCCATGCAG	-	novel	NA	P-0040957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	177	634	1	ENST00000269305.4:c.723_735del	p.Cys242Ter	p.C242*	ENST00000269305	NM_001126112.2	241	tcCTGCATGGGCGGC/tc	7/11	0.633572715148334	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.633572715148334	1		635	321	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927964	49927964	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs539807742	NA	P-0040957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	67	690	1	ENST00000296474.3:c.3764C>T	p.Ala1255Val	p.A1255V	ENST00000296474	NM_002447.2	1255	gCg/gTg	18/20	0.171182753745616	2	FACETS	0.42	0.365	0.478	0.21	0.182	0.239	INDETERMINATE	1	TRUE	0	0.633572715148334	2		691	504	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940931	49940931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	237	768	0	ENST00000296474.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000296474	NM_002447.2	38	Cgc/Tgc	1/20	0.171182753745616	2	FACETS	1	0.993	1	0.728	0.687	0.769	INDETERMINATE	1	TRUE	0	0.633572715148334	2		768	514	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101768	71101768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	86	209	0	ENST00000318789.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000318789	NM_032682.5	144	Caa/Taa	9/21	0.171182753745616	2	FACETS	1	0.951	1	0.55	0.494	0.607	INDETERMINATE	1	TRUE	0	0.633572715148334	2		209	247	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0040957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	29	443	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.432	0.349	0.525	0.432	0.349	0.525	SUBCLONAL	1	TRUE	1	0.633572715148334	2		443	212	SUCCESS
APC	324	MSKCC	GRCh37	5	112175552	112175552	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	100	415	0	ENST00000257430.4:c.4261del	p.Ser1421ValfsTer52	p.S1421Vfs*52	ENST00000257430	NM_000038.5	1421	Agt/gt	16/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.633572715148334	2		415	272	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020768	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs926053251	NA	P-0040957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	191	610	0	ENST00000358127.4:c.77T>G	p.Val26Gly	p.V26G	ENST00000358127	NM_001280556.1	26	gTt/gGt	2/10	0.633572715148334	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.633572715148334	1		610	346	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	24	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.462	0.361	0.578	0.462	0.361	0.578	SUBCLONAL	1	TRUE	1	0.23	2		334	452	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0040977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	89	323	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.885	0.789	0.987	1	0.984	1	CLONAL	2	TRUE	1	0.23	2		323	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0040977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	70	659	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.151494331490401	0	FACETS	0.612	0.533	0.698			1	SUBCLONAL	1	TRUE	0	0.23	0		659	766	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0040977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	62	317	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.23	2		317	456	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0040977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	59	450	0	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	1	2	FACETS	0.744	0.639	0.858	0.744	0.639	0.858	SUBCLONAL	1	TRUE	1	0.23	2		450	690	SUCCESS
APC	324	MSKCC	GRCh37	5	112170777	112170780	+	frameshift_variant	Frame_Shift_Del	DEL	CAGA	CAGA	-	rs878853420	NA	P-0040977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	103	561	0	ENST00000257430.4:c.1875_1878del	p.Asn627LeufsTer2	p.N627Lfs*2	ENST00000257430	NM_000038.5	625	CAGAca/ca	15/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.23	2		561	773	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411246	63411246	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	117	647	0	ENST00000330258.3:c.1921C>T	p.Arg641Ter	p.R641*	ENST00000330258	NM_152424.3	641	Cga/Tga	2/2	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.23	2		647	836	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306568	41306568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	67	630	0	ENST00000373198.4:c.1091G>A	p.Arg364Gln	p.R364Q	ENST00000373198	NM_133170.3	364	cGa/cAa	7/32	0.14927459982688	3	FACETS	0.75	0.65	0.859	0.375	0.325	0.43	SUBCLONAL	1	TRUE	1	0.23	3		630	866	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937984	76937984	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373581602	NA	P-0040977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	45	447	0	ENST00000373344.5:c.2764G>A	p.Asp922Asn	p.D922N	ENST00000373344	NM_000489.3	922	Gat/Aat	9/35	1	2	FACETS	0.578	0.485	0.682	0.578	0.485	0.682	SUBCLONAL	1	TRUE	1	0.23	2		447	677	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944836	31944836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148314204	NA	P-0040977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	172	762	0	ENST00000340398.3:c.265G>A	p.Val89Ile	p.V89I	ENST00000340398	NM_001013699.2	89	Gtc/Atc	1/1	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.23	2		762	1159	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106352	27106352	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	62	602	0	ENST00000324856.7:c.5963T>A	p.Ile1988Asn	p.I1988N	ENST00000324856	NM_006015.4	1988	aTt/aAt	20/20	1	2	FACETS	0.722	0.622	0.83	0.722	0.622	0.83	SUBCLONAL	1	TRUE	1	0.23	2		602	747	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984365	201984366	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0040977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	154	607	0	ENST00000359651.3:c.1032_1033dup	p.Val345GlyfsTer103	p.V345Gfs*103	ENST00000359651		344	cgg/cGGgg	8/8	1	2	FACETS	0.887	0.813	0.964	1	0.99	1	CLONAL	2	TRUE	1	0.23	2		607	755	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114905815	114905816	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0040977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	54	526	0	ENST00000543371.1:c.836_837del	p.Pro279LeufsTer48	p.P279Lfs*48	ENST00000543371	NM_001198531.1	278	caCCcc/cacc	8/14	1	2	FACETS	0.553	0.471	0.643	0.553	0.471	0.643	SUBCLONAL	1	TRUE	1	0.23	2		526	849	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823889	3823889	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	219	698	0	ENST00000262367.5:c.2326A>G	p.Met776Val	p.M776V	ENST00000262367	NM_004380.2	776	Atg/Gtg	13/31	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.5	2		698	825	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417590	139417590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750242131	NA	P-0040987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	166	1084	2	ENST00000277541.6:c.454G>A	p.Gly152Ser	p.G152S	ENST00000277541	NM_017617.3	152	Ggt/Agt	4/34	0.625000988094756	3	FACETS	0.915	0.842	0.99	0.457	0.421	0.495	CLONAL	1	TRUE	1	0.673974200127983	3		1086	720	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0041010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	239	653	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.406856326734119	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.406856326734119	1		653	886	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206908	162206908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1233588284	NA	P-0041010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	165	330	0	ENST00000366898.1:c.767G>A	p.Arg256His	p.R256H	ENST00000366898	NM_004562.2	256	cGc/cAc	7/12	0.317680645521035	2	FACETS	0.78	0.721	0.84	0.78	0.721	0.84	SUBCLONAL	2	TRUE	0	0.406856326734119	2		330	520	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917736	29917736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150966028	NA	P-0041010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	199	692	0	ENST00000389048.3:c.932G>A	p.Arg311His	p.R311H	ENST00000389048	NM_004304.4	311	cGt/cAt	3/29	0.267293987202284	1	FACETS	0.843	0.782	0.907	0.843	0.782	0.907	CLONAL	1	TRUE	0	0.406856326734119	1		692	924	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106727	27106727	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	167	557	0	ENST00000324856.7:c.6341del	p.Pro2114ArgfsTer21	p.P2114Rfs*21	ENST00000324856	NM_006015.4	2113	tCc/tc	20/20	1	2	FACETS	0.888	0.816	0.964	0.888	0.816	0.964	CLONAL	1	TRUE	1	0.406856326734119	2		557	924	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983098	201983099	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCA	novel	NA	P-0041010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	206	740	0	ENST00000359651.3:c.948_950dup	p.Gly316_Gln317insHis	p.G316_Q317insH	ENST00000359651		316	ggc/ggCCAc	7/8	1	2	FACETS	0.912	0.846	0.982	0.912	0.846	0.982	CLONAL	1	TRUE	1	0.406856326734119	2		740	1110	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120461	70120461	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1197	327	918	0	ENST00000245479.2:c.1464del	p.Ile489SerfsTer34	p.I489Sfs*34	ENST00000245479	NM_000346.3	488	tCc/tc	3/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.406856326734119	2		918	1524	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593490	48593491	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs786201200	NA	P-0041010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	73	265	1	ENST00000342988.3:c.1242dup	p.Asp415ArgfsTer14	p.D415Rfs*14	ENST00000342988	NM_005359.5	414	tta/ttAa	10/12	0.406856326734119	1	FACETS	0.801	0.705	0.903	0.801	0.705	0.903	CLONAL	1	TRUE	0	0.406856326734119	1		266	357	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46266459	46266460	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	112	434	0	ENST00000371998.3:c.2446dup	p.Ser816PhefsTer7	p.S816Ffs*7	ENST00000371998		815	aat/aaTt	13/23	1	2	FACETS	0.988	0.892	1	0.988	0.892	1	CLONAL	1	TRUE	1	0.406856326734119	2		434	557	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597448	52597448	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	240	420	0	ENST00000394830.3:c.3862G>T	p.Glu1288Ter	p.E1288*	ENST00000394830	NM_018313.4	1288	Gaa/Taa	25/30	0.317680645521035	2	FACETS	0.939	0.883	0.996	0.939	0.883	0.996	CLONAL	2	TRUE	0	0.406856326734119	2		420	628	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587781702	NA	P-0041012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	128	482	0	ENST00000269305.4:c.920-1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.265258902599545	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.265258902599545	1		482	720	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843535	156843535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369367198	NA	P-0041012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	102	619	0	ENST00000524377.1:c.961G>A	p.Val321Met	p.V321M	ENST00000524377	NM_002529.3	321	Gtg/Atg	8/17	1	2	FACETS	0.919	0.821	1	0.919	0.821	1	CLONAL	1	TRUE	1	0.265258902599545	2		619	837	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508473	106508473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370328855	NA	P-0041012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	45	219	0	ENST00000359195.3:c.467C>T	p.Ala156Val	p.A156V	ENST00000359195	NM_002649.2	156	gCg/gTg	2/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.265258902599545	2		219	279	SUCCESS
APC	324	MSKCC	GRCh37	5	112175346	112175350	+	frameshift_variant	Frame_Shift_Del	DEL	TTGAA	TTGAA	-	novel	NA	P-0041012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	24	194	0	ENST00000257430.4:c.4057_4061del	p.Glu1353PhefsTer20	p.E1353Ffs*20	ENST00000257430	NM_000038.5	1352	gTTGAA/g	16/16	0.265258902599545	1	FACETS	0.577	0.453	0.719	0.577	0.453	0.719	SUBCLONAL	1	TRUE	0	0.265258902599545	1		194	272	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831482	72831482	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	134	506	0	ENST00000268489.5:c.5099A>C	p.Asn1700Thr	p.N1700T	ENST00000268489	NM_006885.3	1700	aAc/aCc	9/10	0.230976731509165	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.265258902599545	1		506	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	162	752	2	ENST00000269305.4:c.273del	p.Trp91CysfsTer32	p.W91Cfs*32	ENST00000269305	NM_001126112.2	91	tgG/tg	4/11	0.235905233952454	3	FACETS	1	0.982	1	0.796	0.738	0.855	CLONAL	2	TRUE	0	0.370686206495566	3		754	434	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007557	62007557	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	77	786	0	ENST00000392795.3:c.310T>C	p.Ser104Pro	p.S104P	ENST00000392795	NM_001039933.1	104	Tct/Cct	3/6	0.304434997817661	2	FACETS	0.929	0.819	1	0.465	0.409	0.524	CLONAL	1	TRUE	0	0.370686206495566	2		786	447	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976499	18976525	+	inframe_deletion	In_Frame_Del	DEL	CTCAGGGCGCCCTGACGCAGGGCTACA	CTCAGGGCGCCCTGACGCAGGGCTACA	-	novel	NA	P-0041035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	64	789	0	ENST00000262803.5:c.3149_3175del	p.Ser1050_Ile1059delinsPhe	p.S1050_I1059delinsF	ENST00000262803	NM_002911.3	1050	tCTCAGGGCGCCCTGACGCAGGGCTACAtc/ttc	22/24	0.370686206495566	3	FACETS	0.789	0.684	0.902	0.394	0.342	0.451	CLONAL	1	TRUE	1	0.370686206495566	3		789	519	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109321791	109321791	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs760197100	NA	P-0041035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	30	551	0	ENST00000436639.2:c.632A>G	p.Asn211Ser	p.N211S	ENST00000436639	NM_014454.2	211	aAt/aGt	4/10	0.212135865652212	3	FACETS	0.831	0.673	1	0.415	0.336	0.504	INDETERMINATE	1	TRUE	1	0.370686206495566	3		551	231	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	123	546	0	ENST00000206249.3:c.1610A>G	p.Tyr537Cys	p.Y537C	ENST00000206249	NM_000125.3	537	tAt/tGt	8/8	1	2	FACETS	0.494	0.447	0.543	0.494	0.447	0.543	SUBCLONAL	1	TRUE	1	0.704389085839388	2		546	707	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0041073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	131	290	1	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.905	0.829	0.983	0.905	0.829	0.983	CLONAL	1	TRUE	1	0.704389085839388	2		291	411	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589586	67589591	+	inframe_deletion	In_Frame_Del	DEL	ATGAAT	ATGAAT	-	novel	NA	P-0041073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	71	203	0	ENST00000274335.5:c.1351_1356del	p.Glu451_Tyr452del	p.E451_Y452del	ENST00000274335		450	cATGAATat/cat	10/15	0.194979819189284	3	FACETS	1	0.897	1	0.509	0.449	0.571	INDETERMINATE	1	TRUE	1	0.704389085839388	3		203	268	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119909	70119910	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0041073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	277	560	0	ENST00000245479.2:c.916dup	p.Val306GlyfsTer272	p.V306Gfs*272	ENST00000245479	NM_000346.3	304	ccg/ccGg	3/3	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.704389085839388	2		560	711	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110086	115110086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1314719430	NA	P-0041073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	345	747	0	ENST00000257566.3:c.1792G>A	p.Gly598Arg	p.G598R	ENST00000257566	NM_016569.3	598	Gga/Aga	8/8	1	2	FACETS	0.99	0.94	1	0.99	0.94	1	CLONAL	1	TRUE	1	0.704389085839388	2		747	989	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211939	36211939	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519283	NA	P-0041073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	417	879	0	ENST00000222270.7:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000222270	NM_014727.1	564	Cga/Tga	3/37	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.704389085839388	2		879	1171	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100175	27100176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0041073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	34	476	0	ENST00000324856.7:c.3976_3977dup	p.Gln1327ArgfsTer155	p.Q1327Rfs*155	ENST00000324856	NM_006015.4	1324	tac/taCCc	16/20	1	2	FACETS	0.179	0.146	0.217	0.179	0.146	0.217	SUBCLONAL	1	TRUE	1	0.704389085839388	2		476	538	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104359302	104359302	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776578	NA	P-0041073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	236	486	1	ENST00000369902.3:c.1022+1G>A		p.X341_splice	ENST00000369902	NM_016169.3	341			0.704389085839388	3	FACETS	1	0.952	1	0.341	0.318	0.364	CLONAL	1	TRUE	0	0.704389085839388	3		487	887	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100182	27100184	+	frameshift_variant	Frame_Shift_Del	DEL	GCA	GCA	CC	novel	NA	P-0041073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	81	461	0	ENST00000324856.7:c.3978_3980delinsCC	p.Gln1327ArgfsTer154	p.Q1327Rfs*154	ENST00000324856	NM_006015.4	1326	ccGCAg/ccCCg	16/20	1	2	FACETS	0.486	0.43	0.546	0.486	0.43	0.546	SUBCLONAL	1	TRUE	1	0.704389085839388	2		461	473	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436398	110436398	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	234	600	0	ENST00000375856.3:c.2003G>C	p.Gly668Ala	p.G668A	ENST00000375856	NM_003749.2	668	gGc/gCc	1/2	1	2	FACETS	0.955	0.895	1	0.955	0.895	1	CLONAL	1	TRUE	1	0.704389085839388	2		600	696	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370954	55370954	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	353	720	0	ENST00000297316.4:c.256C>A	p.Leu86Met	p.L86M	ENST00000297316	NM_022454.3	86	Ctg/Atg	1/2	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.704389085839388	2		720	981	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370960	55370960	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	361	719	1	ENST00000297316.4:c.262C>T	p.Gln88Ter	p.Q88*	ENST00000297316	NM_022454.3	88	Cag/Tag	1/2	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.704389085839388	2		720	993	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0041123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	45	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.424	0.357	0.498	0.424	0.357	0.498	SUBCLONAL	1	TRUE	1	0.530814552816851	2		334	400	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031708	36031708	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	191	814	0	ENST00000358208.4:c.1537G>A	p.Glu513Lys	p.E513K	ENST00000358208		513	Gag/Aag	12/12	1	2	FACETS	0.615	0.568	0.665	0.615	0.568	0.665	SUBCLONAL	1	TRUE	1	0.530814552816851	2		814	1170	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0041123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	64	466	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.512	0.444	0.585	0.512	0.444	0.585	SUBCLONAL	1	TRUE	1	0.530814552816851	2		466	471	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0041123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	206	794	0	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	1	2	FACETS	0.694	0.643	0.747	0.694	0.643	0.747	SUBCLONAL	1	TRUE	1	0.530814552816851	2		794	1118	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482864	67482864	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	183	479	0	ENST00000327367.4:c.1268G>T	p.Ser423Ile	p.S423I	ENST00000327367	NM_005902.3	423	aGt/aTt	9/9	0.278638640982254	2	FACETS	0.975	0.903	1	0.488	0.451	0.525	INDETERMINATE	1	TRUE	0	0.530814552816851	2		479	707	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117351	115117351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1234535767	NA	P-0041123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	60	300	0	ENST00000257566.3:c.823G>A	p.Glu275Lys	p.E275K	ENST00000257566	NM_016569.3	275	Gaa/Aaa	4/8	1	2	FACETS	0.506	0.437	0.581	0.506	0.437	0.581	SUBCLONAL	1	TRUE	1	0.530814552816851	2		300	447	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462635	29462635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747611056	NA	P-0041123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	158	796	1	ENST00000389048.3:c.2266G>A	p.Gly756Ser	p.G756S	ENST00000389048	NM_004304.4	756	Ggc/Agc	13/29	1	2	FACETS	0.518	0.474	0.565	0.518	0.474	0.565	SUBCLONAL	1	TRUE	1	0.530814552816851	2		797	1149	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120291	70120292	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	221	878	0	ENST00000245479.2:c.1294dup	p.Tyr432LeufsTer146	p.Y432Lfs*146	ENST00000245479	NM_000346.3	431	-/T	3/3	1	2	FACETS	0.644	0.598	0.692	0.644	0.598	0.692	SUBCLONAL	1	TRUE	1	0.530814552816851	2		878	1292	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371773	45371773	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0041123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	110	350	0	ENST00000262160.6:c.1218T>A	p.Tyr406Ter	p.Y406*	ENST00000262160	NM_005901.5	406	taT/taA	10/11	0.335188191873703	2	FACETS	0.957	0.866	1	0.479	0.433	0.526	CLONAL	1	TRUE	0	0.530814552816851	2		350	433	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79966007	79966007	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs772141055	NA	P-0041123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	82	465	0	ENST00000265081.6:c.671G>T	p.Arg224Leu	p.R224L	ENST00000265081	NM_002439.4	224	cGg/cTg	4/24	1	2	FACETS	0.592	0.523	0.665	0.592	0.523	0.665	SUBCLONAL	1	TRUE	1	0.530814552816851	2		465	522	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0041147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	238	479	0				ENST00000310581	NM_198253.2	-/1132			0.297201385308833	3	FACETS	0.975	0.918	1	0.975	0.918	1	INDETERMINATE	2	TRUE	1	0.527169916199848	3		479	585	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0041147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	95	975	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	0.210690041772596	2	FACETS	0.32	0.284	0.359	0.16	0.142	0.18	INDETERMINATE	1	TRUE	0	0.527169916199848	2		975	1126	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405870	49405870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	83	722	0	ENST00000418115.1:c.268G>A	p.Asp90Asn	p.D90N	ENST00000418115	NM_001664.2	90	Gat/Aat	3/5	0.210690041772596	2	FACETS	0.37	0.326	0.418	0.185	0.163	0.209	INDETERMINATE	1	TRUE	0	0.527169916199848	2		722	851	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106861	27106861	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	274	748	0	ENST00000324856.7:c.6472C>T	p.Arg2158Ter	p.R2158*	ENST00000324856	NM_006015.4	2158	Cga/Tga	20/20	0.349455864273296	1	FACETS	0.965	0.91	1	0.965	0.91	1	CLONAL	1	TRUE	0	0.527169916199848	1		748	793	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871992	45871992	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	104	797	0	ENST00000391945.4:c.256G>C	p.Glu86Gln	p.E86Q	ENST00000391945	NM_000400.3	86	Gag/Cag	5/23	0.349455864273296	1	FACETS	0.411	0.368	0.457	0.411	0.368	0.457	SUBCLONAL	1	TRUE	0	0.527169916199848	1		797	707	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248033	98248033	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	104	631	0	ENST00000331920.6:c.518A>T	p.Glu173Val	p.E173V	ENST00000331920	NM_000264.3	173	gAa/gTa	3/24	0.349455864273296	1	FACETS	0.424	0.38	0.471	0.424	0.38	0.471	SUBCLONAL	1	TRUE	0	0.527169916199848	1		631	685	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183655	10183655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	293	908	0	ENST00000256474.2:c.124G>A	p.Glu42Lys	p.E42K	ENST00000256474	NM_000551.3	42	Gag/Aag	1/3	0.210690041772596	2	FACETS	1	0.989	1	0.591	0.557	0.626	INDETERMINATE	1	TRUE	0	0.527169916199848	2		908	940	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434113	121434113	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0041147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	145	917	0	ENST00000257555.6:c.1004C>G	p.Ser335Ter	p.S335*	ENST00000257555		335	tCa/tGa	5/10	0.349455864273296	1	FACETS	0.403	0.367	0.441	0.403	0.367	0.441	SUBCLONAL	1	TRUE	0	0.527169916199848	1		917	1005	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187408	38187408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243215593	NA	P-0041147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	88	396	1	ENST00000317025.8:c.1069C>T	p.Arg357Trp	p.R357W	ENST00000317025	NM_023034.1	357	Cgg/Tgg	6/24	0.229129286001977	1	FACETS	0.442	0.392	0.495	0.442	0.392	0.495	INDETERMINATE	1	TRUE	0	0.527169916199848	1		397	556	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547265	106547265	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587778623	NA	P-0041147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	81	445	0	ENST00000369096.4:c.502C>G	p.Pro168Ala	p.P168A	ENST00000369096	NM_001198.3	168	Ccc/Gcc	4/7	0.279158843529747	1	FACETS	0.423	0.373	0.476	0.423	0.373	0.476	INDETERMINATE	1	TRUE	0	0.527169916199848	1		445	535	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567340	226567340	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	113	449	0	ENST00000366794.5:c.1546A>G	p.Ile516Val	p.I516V	ENST00000366794	NM_001618.3	516	Atc/Gtc	11/23	0.527169916199848	3	FACETS	0.807	0.727	0.892	0.404	0.363	0.446	CLONAL	1	TRUE	1	0.527169916199848	3		449	671	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497550	125497550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	73	360	0	ENST00000428830.2:c.114G>T	p.Lys38Asn	p.K38N	ENST00000428830	NM_001114121.2	38	aaG/aaT	3/14	0.279158843529747	1	FACETS	0.635	0.56	0.715	0.635	0.56	0.715	INDETERMINATE	1	TRUE	0	0.527169916199848	1		360	321	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427027	49427034	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGGCCC	GGGGGCCC	-	novel	NA	P-0041147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	114	803	2	ENST00000301067.7:c.11454_11461del	p.Gln3821SerfsTer188	p.Q3821Sfs*188	ENST00000301067	NM_003482.3	3818	ttGGGCCCCCag/ttag	39/54	0.279158843529747	1	FACETS	0.432	0.389	0.478	0.432	0.389	0.478	INDETERMINATE	1	TRUE	0	0.527169916199848	1		805	737	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32899228	32899228	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555280840	NA	P-0041147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	90	276	0	ENST00000380152.3:c.332A>G	p.Asn111Ser	p.N111S	ENST00000380152		111	aAt/aGt	4/27	1	2	FACETS	0.938	0.839	1	0.938	0.839	1	CLONAL	1	TRUE	1	0.527169916199848	2		276	364	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660066	12660066	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	251	586	0	ENST00000251849.4:c.155C>G	p.Ser52Cys	p.S52C	ENST00000251849	NM_002880.3	52	tCt/tGt	2/17	0.210690041772596	2	FACETS	1	0.991	1	0.643	0.604	0.683	INDETERMINATE	1	TRUE	0	0.527169916199848	2		586	740	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97887394	97887394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	101	632	0	ENST00000289081.3:c.970G>A	p.Glu324Lys	p.E324K	ENST00000289081	NM_000136.2	324	Gaa/Aaa	10/15	0.349455864273296	1	FACETS	0.387	0.345	0.43	0.387	0.345	0.43	SUBCLONAL	1	TRUE	0	0.527169916199848	1		632	730	SUCCESS
AR	367	MSKCC	GRCh37	X	66765136	66765277	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGGCGCCAGTTTGCTGCTGCTGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAAGAGACTAGCCCCAGGCAGCAGCAGCAGCAGCAGGGTGAGGATGGTTCTC	CCCGGCGCCAGTTTGCTGCTGCTGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAAGAGACTAGCCCCAGGCAGCAGCAGCAGCAGCAGGGTGAGGATGGTTCTC	-	novel	NA	P-0041147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	387	326	0	ENST00000374690.3:c.151_292del	p.Gly51LysfsTer77	p.G51Kfs*77	ENST00000374690	NM_000044.3	50	CCCGGCGCCAGTTTGCTGCTGCTGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAAGAGACTAGCCCCAGGCAGCAGCAGCAGCAGCAGGGTGAGGATGGTTCTCcc/cc	1/8	0.155746504430375	2	FACETS	0.866	0.836	0.895			1	INDETERMINATE	3	TRUE	NA	0.527169916199848	2		326	565	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	74	323	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.761	0.67	0.856	0.761	0.67	0.856	SUBCLONAL	1	TRUE	1	0.546577911256218	2		323	356	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	134	409	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.734	0.668	0.803	0.734	0.668	0.803	SUBCLONAL	1	TRUE	1	0.546577911256218	2		409	668	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	31	104	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	0.761	0.624	0.911	0.761	0.624	0.911	CLONAL	1	TRUE	1	0.546577911256218	2		104	149	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	65	493	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.695	0.607	0.79	0.695	0.607	0.79	SUBCLONAL	1	TRUE	1	0.546577911256218	2		493	342	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	120	768	2	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	0.45786719952483	3	FACETS	0.623	0.562	0.687	0.311	0.281	0.344	SUBCLONAL	1	TRUE	1	0.546577911256218	3		770	898	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	77	542	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.646	0.57	0.728	0.646	0.57	0.728	SUBCLONAL	1	TRUE	1	0.546577911256218	2		542	436	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358450	91358450	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	201	581	0	ENST00000355112.3:c.4195A>G	p.Met1399Val	p.M1399V	ENST00000355112	NM_000057.2	1399	Atg/Gtg	22/22	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.546577911256218	2		581	721	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	142	523	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.979	0.897	1	0.979	0.897	1	CLONAL	1	TRUE	1	0.546577911256218	2		523	531	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015055	37015055	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1414110836	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	119	586	1	ENST00000358127.4:c.349C>T	p.Arg117Trp	p.R117W	ENST00000358127	NM_001280556.1	117	Cgg/Tgg	3/10	1	2	FACETS	0.619	0.56	0.682	0.619	0.56	0.682	SUBCLONAL	1	TRUE	1	0.546577911256218	2		587	703	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007834	45007834	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	109	369	0	ENST00000558401.1:c.285del	p.Asp96MetfsTer7	p.D96Mfs*7	ENST00000558401	NM_004048.2	94	gAa/ga	2/4	1	2	FACETS	0.904	0.817	0.995	0.904	0.817	0.995	CLONAL	1	TRUE	1	0.546577911256218	2		369	441	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	155	624	4	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	0.82	0.752	0.89	0.82	0.752	0.89	CLONAL	1	TRUE	1	0.546577911256218	2		628	692	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491390	18491390	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1377942847	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	93	283	1	ENST00000266497.5:c.1309del	p.Ile437TyrfsTer5	p.I437Yfs*5	ENST00000266497		435	Aaa/aa	8/31	1	2	FACETS	0.937	0.841	1	0.937	0.841	1	CLONAL	1	TRUE	1	0.546577911256218	2		284	363	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	133	497	4	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.932	0.851	1	0.932	0.851	1	CLONAL	1	TRUE	1	0.546577911256218	2		501	522	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639588	47639588	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63749897	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	37	365	0	ENST00000233146.2:c.687del	p.Ala230LeufsTer16	p.A230Lfs*16	ENST00000233146	NM_000251.2	227	agA/ag	4/16	1	2	FACETS	0.294	0.242	0.352	0.294	0.242	0.352	SUBCLONAL	1	TRUE	1	0.546577911256218	2		365	461	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262139	10262139	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	194	701	2	ENST00000340748.4:c.2152del	p.Met718CysfsTer59	p.M718Cfs*59	ENST00000340748		718	Atg/tg	23/40	1	2	FACETS	0.908	0.842	0.976	0.908	0.842	0.976	CLONAL	1	TRUE	1	0.546577911256218	2		703	782	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354152	15354152	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs868796773	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	127	611	4	ENST00000263377.2:c.2728del	p.Gln910LysfsTer39	p.Q910Kfs*39	ENST00000263377	NM_058243.2	910	Caa/aa	14/20	1	2	FACETS	0.712	0.646	0.78	0.712	0.646	0.78	SUBCLONAL	1	TRUE	1	0.546577911256218	2		615	653	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652297	48652297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1055251352	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	236	928	0	ENST00000376670.3:c.968G>A	p.Gly323Asp	p.G323D	ENST00000376670	NM_002049.3	323	gGc/gAc	6/6	0.45786719952483	3	FACETS	0.949	0.884	1	0.474	0.442	0.508	CLONAL	1	TRUE	1	0.546577911256218	3		928	1159	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437288	220437288	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1190141661	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	196	890	1	ENST00000243786.2:c.197del	p.Gly66AlafsTer61	p.G66Afs*61	ENST00000243786	NM_002191.3	64	ctG/ct	1/2	1	2	FACETS	0.727	0.672	0.783	0.727	0.672	0.783	SUBCLONAL	1	TRUE	1	0.546577911256218	2		891	987	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170598	7170598	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750676016	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	152	595	2	ENST00000302850.5:c.1433G>A	p.Arg478His	p.R478H	ENST00000302850	NM_000208.2	478	cGc/cAc	6/22	1	2	FACETS	0.819	0.751	0.89	0.819	0.751	0.89	CLONAL	1	TRUE	1	0.546577911256218	2		597	679	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119780	70119781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	156	685	0	ENST00000245479.2:c.788dup	p.Arg264GlnfsTer32	p.R264Qfs*32	ENST00000245479	NM_000346.3	261	gag/gaGg	3/3	1	2	FACETS	0.813	0.746	0.883	0.813	0.746	0.883	CLONAL	1	TRUE	1	0.546577911256218	2		685	702	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412473	63412473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	201	801	0	ENST00000330258.3:c.694del	p.Gln232LysfsTer50	p.Q232Kfs*50	ENST00000330258	NM_152424.3	232	Caa/aa	2/2	0.45786719952483	3	FACETS	0.86	0.796	0.926	0.43	0.398	0.463	CLONAL	1	TRUE	1	0.546577911256218	3		801	1089	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953115	81953115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1336595726	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	79	313	1	ENST00000359376.3:c.2081G>A	p.Arg694His	p.R694H	ENST00000359376	NM_002661.3	694	cGc/cAc	20/33	1	2	FACETS	0.826	0.732	0.925	0.826	0.732	0.925	CLONAL	1	TRUE	1	0.546577911256218	2		314	350	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	171	729	5	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	1	2	FACETS	0.745	0.686	0.806	0.745	0.686	0.806	SUBCLONAL	1	TRUE	1	0.546577911256218	2		734	840	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185545	27185545	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1564083506	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	187	596	2	ENST00000380036.4:c.1250del	p.Pro417LeufsTer10	p.P417Lfs*10	ENST00000380036	NM_000459.3	415	ctC/ct	9/23	1	2	FACETS	0.884	0.818	0.952	0.884	0.818	0.952	CLONAL	1	TRUE	1	0.546577911256218	2		598	774	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15838418	15838418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	123	408	0	ENST00000307771.7:c.916C>T	p.Arg306Trp	p.R306W	ENST00000307771	NM_005089.3	306	Cgg/Tgg	10/11	0.45786719952483	3	FACETS	0.825	0.747	0.906	0.412	0.373	0.453	CLONAL	1	TRUE	1	0.546577911256218	3		408	695	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643503	38643503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057518683	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	150	502	2	ENST00000299084.4:c.973C>T	p.Arg325Ter	p.R325*	ENST00000299084	NM_152594.2	325	Cga/Tga	7/7	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.546577911256218	2		504	547	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134569	2134569	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs397514939	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	207	859	4	ENST00000219476.3:c.4351del	p.Arg1451AlafsTer25	p.R1451Afs*25	ENST00000219476	NM_000548.3	1449	tCc/tc	34/42	1	2	FACETS	0.842	0.782	0.904	0.842	0.782	0.904	CLONAL	1	TRUE	1	0.546577911256218	2		863	900	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247442	71247442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750746668	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	179	540	3	ENST00000318789.4:c.91G>A	p.Gly31Ser	p.G31S	ENST00000318789	NM_032682.5	31	Ggt/Agt	6/21	1	2	FACETS	0.933	0.863	1	0.933	0.863	1	CLONAL	1	TRUE	1	0.546577911256218	2		543	702	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251179	115251179	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	137	413	0	ENST00000369535.4:c.547G>T	p.Gly183Ter	p.G183*	ENST00000369535	NM_002524.4	183	Gga/Tga	5/7	1	2	FACETS	0.932	0.852	1	0.932	0.852	1	CLONAL	1	TRUE	1	0.546577911256218	2		413	538	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243293	123243293	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	180	725	0	ENST00000358487.5:c.2220G>T	p.Trp740Cys	p.W740C	ENST00000358487	NM_000141.4	740	tgG/tgT	17/18	1	2	FACETS	0.79	0.729	0.853	0.79	0.729	0.853	SUBCLONAL	1	TRUE	1	0.546577911256218	2		725	834	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138113	64138113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1449835853	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	207	695	3	ENST00000334205.4:c.2036C>T	p.Ala679Val	p.A679V	ENST00000334205	NM_003942.2	679	gCg/gTg	16/17	1	2	FACETS	0.969	0.901	1	0.969	0.901	1	CLONAL	1	TRUE	1	0.546577911256218	2		698	782	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118367045	118367045	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	134	397	0	ENST00000534358.1:c.5627G>A	p.Cys1876Tyr	p.C1876Y	ENST00000534358	NM_005933.3	1876	tGt/tAt	20/36	1	2	FACETS	0.866	0.79	0.945	0.866	0.79	0.945	CLONAL	1	TRUE	1	0.546577911256218	2		397	566	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	459914	459914	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	167	505	0	ENST00000399788.2:c.1181T>A	p.Phe394Tyr	p.F394Y	ENST00000399788	NM_001042603.1	394	tTt/tAt	10/28	1	2	FACETS	0.912	0.841	0.986	0.912	0.841	0.986	CLONAL	1	TRUE	1	0.546577911256218	2		505	670	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865675	57865675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	228	830	1	ENST00000228682.2:c.3152C>T	p.Ala1051Val	p.A1051V	ENST00000228682	NM_005269.2	1051	gCt/gTt	12/12	1	2	FACETS	0.946	0.883	1	0.946	0.883	1	CLONAL	1	TRUE	1	0.546577911256218	2		831	882	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121438970	121438970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	192	766	0	ENST00000257555.6:c.1871C>T	p.Thr624Ile	p.T624I	ENST00000257555		624	aCc/aTc	10/10	1	2	FACETS	0.788	0.729	0.848	0.788	0.729	0.848	SUBCLONAL	1	TRUE	1	0.546577911256218	2		766	892	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73995350	73995350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	74	311	0	ENST00000318443.5:c.656G>A	p.Ser219Asn	p.S219N	ENST00000318443	NM_001024736.1	219	aGc/aAc	4/10	1	2	FACETS	0.722	0.636	0.814	0.722	0.636	0.814	SUBCLONAL	1	TRUE	1	0.546577911256218	2		311	375	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830424	72830424	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	27	357	0	ENST00000268489.5:c.6157G>C	p.Ala2053Pro	p.A2053P	ENST00000268489	NM_006885.3	2053	Gca/Cca	9/10	1	2	FACETS	0.361	0.287	0.444	0.361	0.287	0.444	SUBCLONAL	1	TRUE	1	0.546577911256218	2		357	274	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347308	89347308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778263395	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	180	735	1	ENST00000301030.4:c.5642G>A	p.Gly1881Asp	p.G1881D	ENST00000301030	NM_001256183.1	1881	gGc/gAc	9/13	1	2	FACETS	0.839	0.775	0.905	0.839	0.775	0.905	CLONAL	1	TRUE	1	0.546577911256218	2		736	785	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78811769	78811769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370002882	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	154	620	1	ENST00000306801.3:c.1184C>T	p.Thr395Met	p.T395M	ENST00000306801	NM_020761.2	395	aCg/aTg	10/34	1	2	FACETS	0.887	0.815	0.963	0.887	0.815	0.963	CLONAL	1	TRUE	1	0.546577911256218	2		621	635	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976953	18976953	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764484697	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	146	586	0	ENST00000262803.5:c.3338C>T	p.Thr1113Met	p.T1113M	ENST00000262803	NM_002911.3	1113	aCg/aTg	23/24	1	2	FACETS	0.782	0.716	0.852	0.782	0.716	0.852	SUBCLONAL	1	TRUE	1	0.546577911256218	2		586	683	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956592	93956592	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	190	340	0	ENST00000369303.4:c.2644A>G	p.Lys882Glu	p.K882E	ENST00000369303	NM_004440.3	882	Aaa/Gaa	15/17	0.535608964700745	3	FACETS	0.892	0.833	0.953	0.892	0.833	0.953	CLONAL	2	TRUE	1	0.546577911256218	3		340	496	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984088	2984088	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	84	460	1	ENST00000396946.4:c.442C>T	p.Gln148Ter	p.Q148*	ENST00000396946	NM_032415.4	148	Caa/Taa	5/25	0.535608964700745	3	FACETS	0.632	0.559	0.711	0.316	0.279	0.356	SUBCLONAL	1	TRUE	1	0.546577911256218	3		461	619	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227684	53227684	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	98	522	1	ENST00000375401.3:c.2504G>A	p.Gly835Asp	p.G835D	ENST00000375401	NM_004187.3	835	gGc/gAc	17/26	0.45786719952483	3	FACETS	0.591	0.527	0.66	0.296	0.263	0.33	SUBCLONAL	1	TRUE	1	0.546577911256218	3		523	772	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	100	759	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.466	0.417	0.517	0.466	0.417	0.517	SUBCLONAL	1	TRUE	1	0.837210033710815	2		760	513	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0041214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	118	290	1	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.521	0.472	0.573	0.521	0.472	0.573	SUBCLONAL	1	TRUE	1	0.837210033710815	2		291	541	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115267880	115267880	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	158	577	0	ENST00000438362.2:c.1853A>G	p.Asn618Ser	p.N618S	ENST00000438362	NM_001242891.1	618	aAc/aGc	15/20	1	2	FACETS	0.461	0.422	0.501	0.461	0.422	0.501	SUBCLONAL	1	TRUE	1	0.837210033710815	2		577	819	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	490	759	1				ENST00000310581	NM_198253.2	-/1132			0.587071684965301	7	FACETS	0.926	0.892	0.959	1	0.994	1	CLONAL	5	TRUE	3	0.587071684965301	7		760	890	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953743	48953743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	139	270	0	ENST00000267163.4:c.1346G>A	p.Gly449Glu	p.G449E	ENST00000267163	NM_000321.2	449	gGa/gAa	14/27	NA	2	FACETS	0.89	0.828	0.952			1	INDETERMINATE	2	TRUE	NA	0.587071684965301	2		270	266	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355856	73355856	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	261	385	0	ENST00000377767.4:c.115T>C	p.Cys39Arg	p.C39R	ENST00000377767	NM_014953.3	39	Tgt/Cgt	1/21	0.587186502942444	4	FACETS	0.874	0.828	0.921	0.874	0.828	0.921	CLONAL	3	TRUE	1	0.587071684965301	4		385	538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0041271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	453	794	2	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.491981614334627	2	FACETS	0.961	0.925	0.996	0.961	0.925	0.996	CLONAL	2	TRUE	0	0.587071684965301	2		796	803	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244314	5244314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	206	686	2	ENST00000357368.4:c.1168G>A	p.Gly390Ser	p.G390S	ENST00000357368	NM_002850.3	390	Ggc/Agc	11/38	1	2	FACETS	0.886	0.824	0.95	0.886	0.824	0.95	CLONAL	1	TRUE	1	0.587071684965301	2		688	792	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739866	41739866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	110	522	1	ENST00000242208.4:c.107C>T	p.Pro36Leu	p.P36L	ENST00000242208	NM_002192.2	36	cCg/cTg	2/3	0.587186502942444	4	FACETS	0.771	0.693	0.854	0.257	0.231	0.285	SUBCLONAL	1	TRUE	1	0.587071684965301	4		523	771	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459453	50459453	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	139	312	0	ENST00000331340.3:c.742G>T	p.Glu248Ter	p.E248*	ENST00000331340	NM_006060.4	248	Gaa/Taa	7/8	0.587186502942444	4	FACETS	0.937	0.862	1	0.625	0.574	0.676	CLONAL	2	TRUE	1	0.587071684965301	4		312	401	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140500166	140500166	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs775040765	NA	P-0041271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	476	795	0	ENST00000288602.6:c.976A>G	p.Ile326Val	p.I326V	ENST00000288602	NM_004333.4	326	Att/Gtt	7/18	0.557556880854075	3	FACETS	0.987	0.947	1	0.987	0.947	1	CLONAL	2	TRUE	1	0.587071684965301	3		795	1063	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0041281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	85	395	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.25	2		395	607	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0041281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	106	507	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.208296043744443	2	FACETS	1	0.98	1	0.697	0.626	0.772	CLONAL	1	TRUE	0	0.25	2		507	608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0041281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	118	611	2	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.25	2		613	855	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119687	108119687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	25	263	0	ENST00000278616.4:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000278616	NM_000051.3	365	Gag/Aag	9/63	1	2	FACETS	0.562	0.443	0.699	0.562	0.443	0.699	SUBCLONAL	1	TRUE	1	0.25	2		263	356	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641058	23641058	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	86	759	0	ENST00000261584.4:c.2417C>G	p.Pro806Arg	p.P806R	ENST00000261584	NM_024675.3	806	cCg/cGg	5/13	1	2	FACETS	0.655	0.577	0.738	0.655	0.577	0.738	SUBCLONAL	1	TRUE	1	0.25	2		759	1051	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96930920	96930920	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	69	664	0	ENST00000258439.3:c.200G>A	p.Gly67Glu	p.G67E	ENST00000258439	NM_001193304.2	67	gGg/gAg	2/4	1	2	FACETS	0.566	0.491	0.647	0.566	0.491	0.647	SUBCLONAL	1	TRUE	1	0.25	2		664	976	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137522025	137522025	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	27	275	0	ENST00000367739.4:c.854A>T	p.Lys285Met	p.K285M	ENST00000367739	NM_000416.2	285	aAg/aTg	6/7	1	2	FACETS	0.55	0.437	0.678	0.55	0.437	0.678	SUBCLONAL	1	TRUE	1	0.25	2		275	393	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902215	151902215	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	52	543	0	ENST00000262189.6:c.3937G>T	p.Glu1313Ter	p.E1313*	ENST00000262189	NM_170606.2	1313	Gag/Tag	25/59	1	2	FACETS	0.561	0.476	0.654	0.561	0.476	0.654	SUBCLONAL	1	TRUE	1	0.25	2		543	742	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22008934	22008934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	140	625	0	ENST00000276925.6:c.19G>A	p.Gly7Ser	p.G7S	ENST00000276925	NM_004936.3	7	Ggc/Agc	1/2	0.208296043744443	2	FACETS	1	0.984	1	0.683	0.622	0.747	CLONAL	1	TRUE	0	0.25	2		625	820	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0041283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	520	919	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.548048026958242	2	FACETS	0.844	0.813	0.874	0.844	0.813	0.874	CLONAL	2	TRUE	0	0.616258182625222	2		919	1000	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857047	9857047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568622613	NA	P-0041283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	55	425	0	ENST00000330684.3:c.4354C>T	p.Arg1452Cys	p.R1452C	ENST00000330684	NM_001134407.1	1452	Cgc/Tgc	13/13	0.299403174695353	3	FACETS	0.385	0.329	0.447	0.128	0.109	0.149	INDETERMINATE	1	TRUE	0	0.616258182625222	3		425	606	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0041283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	274	403	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.590475987184264	2	FACETS	0.938	0.894	0.982	0.938	0.894	0.982	CLONAL	2	TRUE	0	0.616258182625222	2		403	474	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830778	72830778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781579217	NA	P-0041283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	117	844	0	ENST00000268489.5:c.5803C>T	p.Arg1935Cys	p.R1935C	ENST00000268489	NM_006885.3	1935	Cgc/Tgc	9/10	0.616258182625222	3	FACETS	0.451	0.406	0.499	0.226	0.203	0.25	SUBCLONAL	1	TRUE	1	0.616258182625222	3		844	1101	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434992	110434992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	478	836	0	ENST00000375856.3:c.3409C>T	p.Arg1137Cys	p.R1137C	ENST00000375856	NM_003749.2	1137	Cgc/Tgc	1/2	0.439690050264696	6	FACETS	1	0.965	1	0.506	0.483	0.53	CLONAL	2	TRUE	2	0.616258182625222	6		836	1710	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0041290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	13	743	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		743	555	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425589	49425589	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	36	802	0	ENST00000301067.7:c.12899del	p.Pro4300GlnfsTer84	p.P4300Qfs*84	ENST00000301067	NM_003482.3	4300	cCa/ca	39/54	0.123757355786879	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		802	548	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831381	72831382	+	stop_gained,inframe_insertion	Nonsense_Mutation	INS	-	-	TTGTTA	novel	NA	P-0041290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	18	346	0	ENST00000268489.5:c.5199_5200insTAACAA	p.Gln1733_Gln1734insTer	p.Q1733_Q1734ins*	ENST00000268489	NM_006885.3	1733	-/TAACAA	9/10	0.209874508952462	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		346	267	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0041318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	41	409	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.701	0.582	0.834	0.701	0.582	0.834	SUBCLONAL	1	TRUE	1	0.17	2		409	688	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0041318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	96	874	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.862	0.769	0.961	1	0.984	1	CLONAL	2	TRUE	1	0.17	2		874	655	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031170	11031170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	74	835	0	ENST00000327064.4:c.1255C>T	p.Arg419Trp	p.R419W	ENST00000327064	NM_199141.1	419	Cgg/Tgg	11/16	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.17	2		835	817	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0041318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	49	352	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.17	2		352	524	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0041318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	22	286	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	0.584	0.452	0.739	0.584	0.452	0.739	SUBCLONAL	1	TRUE	1	0.17	2		286	443	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654642	67654642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	57	353	1	ENST00000264010.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000264010	NM_006565.3	377	Cgt/Tgt	6/12	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.17	2		354	649	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111168	193111168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1452051467	NA	P-0041318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	37	250	0	ENST00000367435.3:c.701G>A	p.Arg234Gln	p.R234Q	ENST00000367435	NM_024529.4	234	cGa/cAa	7/17	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.17	2		250	371	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672842	86672842	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	21	161	0	ENST00000274376.6:c.2329G>T	p.Glu777Ter	p.E777*	ENST00000274376	NM_002890.2	777	Gaa/Taa	17/25	1	2	FACETS	0.939	0.725	1	0.939	0.725	1	CLONAL	1	TRUE	1	0.17	2		161	263	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258035	123258035	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	38	316	0	ENST00000358487.5:c.1646A>C	p.Asn549Thr	p.N549T	ENST00000358487	NM_000141.4	549	aAt/aCt	12/18	1	2	FACETS	0.808	0.667	0.966	0.808	0.667	0.966	CLONAL	1	TRUE	1	0.17	2		316	553	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692940	89692940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746152219	NA	P-0041318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	112	405	0	ENST00000371953.3:c.424C>T	p.Arg142Trp	p.R142W	ENST00000371953	NM_000314.4	142	Cgg/Tgg	5/9	1	2	FACETS	1	0.924	1	1	0.989	1	CLONAL	2	TRUE	1	0.17	2		405	640	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435289	121435289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371544082	NA	P-0041318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	33	439	0	ENST00000257555.6:c.1322C>T	p.Thr441Met	p.T441M	ENST00000257555		441	aCg/aTg	7/10	1	2	FACETS	0.71	0.577	0.86	0.71	0.577	0.86	SUBCLONAL	1	TRUE	1	0.17	2		439	547	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253151	133253151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	36	378	0	ENST00000320574.5:c.890C>T	p.Ser297Phe	p.S297F	ENST00000320574	NM_006231.2	297	tCc/tTc	9/49	1	2	FACETS	0.837	0.687	1	0.837	0.687	1	CLONAL	1	TRUE	1	0.17	2		378	506	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073692	8073692	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	33	308	0	ENST00000377482.5:c.967G>T	p.Glu323Ter	p.E323*	ENST00000377482	NM_018948.3	323	Gaa/Taa	4/4	1	2	FACETS	0.857	0.698	1	0.857	0.698	1	CLONAL	1	TRUE	1	0.17	2		308	453	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210116	55210116	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778638117	NA	P-0041318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	35	300	0	ENST00000275493.2:c.226C>A	p.Leu76Ile	p.L76I	ENST00000275493	NM_005228.3	76	Ctt/Att	2/28	1	2	FACETS	0.822	0.673	0.989	0.822	0.673	0.989	CLONAL	1	TRUE	1	0.17	2		300	501	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743281	162743281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	22	207	0	ENST00000367921.3:c.1751G>A	p.Gly584Glu	p.G584E	ENST00000367921	NM_006182.2	584	gGa/gAa	14/18	1	2	FACETS	0.857	0.665	1	0.857	0.665	1	CLONAL	1	TRUE	1	0.17	2		207	302	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210808	36210808	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	61	651	0	ENST00000222270.7:c.559G>T	p.Glu187Ter	p.E187*	ENST00000222270	NM_014727.1	187	Gaa/Taa	3/37	1	2	FACETS	0.763	0.656	0.879	0.763	0.656	0.879	SUBCLONAL	1	TRUE	1	0.17	2		651	941	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514527	103514527	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	17	199	0	ENST00000355739.4:c.1028G>T	p.Arg343Ile	p.R343I	ENST00000355739	NM_000123.3	343	aGa/aTa	8/15	1	2	FACETS	0.647	0.483	0.843	0.647	0.483	0.843	SUBCLONAL	1	TRUE	1	0.17	2		199	309	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2215893	2215893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370203279	NA	P-0041318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	63	545	1	ENST00000326181.6:c.95C>T	p.Thr32Met	p.T32M	ENST00000326181	NM_032271.2	32	aCg/aTg	3/21	1	2	FACETS	0.923	0.797	1	0.923	0.797	1	CLONAL	1	TRUE	1	0.17	2		546	803	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542870	187542870	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	30	266	0	ENST00000441802.2:c.4870G>T	p.Glu1624Ter	p.E1624*	ENST00000441802	NM_005245.3	1624	Gaa/Taa	10/27	1	2	FACETS	0.811	0.653	0.991	0.811	0.653	0.991	CLONAL	1	TRUE	1	0.17	2		266	435	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805116	43805116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	42	472	0	ENST00000372470.3:c.566C>T	p.Ala189Val	p.A189V	ENST00000372470	NM_005373.2	189	gCc/gTc	4/12	1	2	FACETS	0.811	0.676	0.962	0.811	0.676	0.962	CLONAL	1	TRUE	1	0.17	2		472	609	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717746	89717746	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1554825245	NA	P-0041318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	37	298	0	ENST00000371953.3:c.771C>A	p.Phe257Leu	p.F257L	ENST00000371953	NM_000314.4	257	ttC/ttA	7/9	1	2	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	TRUE	1	0.17	2		298	424	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640740	3640740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	42	529	0	ENST00000294008.3:c.2899G>A	p.Ala967Thr	p.A967T	ENST00000294008	NM_032444.2	967	Gca/Aca	12/15	1	2	FACETS	0.855	0.713	1	0.855	0.713	1	CLONAL	1	TRUE	1	0.17	2		529	578	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419994	41419994	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	61	454	1	ENST00000373198.4:c.327C>A	p.Phe109Leu	p.F109L	ENST00000373198	NM_133170.3	109	ttC/ttA	3/32	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.17	2		455	569	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902902	1902902	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	46	475	0	ENST00000382891.5:c.521A>G	p.Lys174Arg	p.K174R	ENST00000382891	NM_133335.3	174	aAa/aGa	2/22	1	2	FACETS	0.757	0.636	0.891	0.757	0.636	0.891	SUBCLONAL	1	TRUE	1	0.17	2		475	715	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80024750	80024750	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1379605717	NA	P-0041318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	67	306	0	ENST00000265081.6:c.1534G>T	p.Glu512Ter	p.E512*	ENST00000265081	NM_002439.4	512	Gaa/Taa	10/24	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.17	2		306	556	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339232	116339232	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	25	260	0	ENST00000397752.3:c.94A>C	p.Lys32Gln	p.K32Q	ENST00000397752	NM_000245.2	32	Aag/Cag	2/21	1	2	FACETS	0.774	0.61	0.963	0.774	0.61	0.963	CLONAL	1	TRUE	1	0.17	2		260	380	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008969	152008969	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	38	311	0	ENST00000262189.6:c.653A>G	p.Asp218Gly	p.D218G	ENST00000262189	NM_170606.2	218	gAt/gGt	5/59	1	2	FACETS	0.903	0.746	1	0.903	0.746	1	CLONAL	1	TRUE	1	0.17	2		311	495	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217335	123217335	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs934233502	NA	P-0041318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	42	446	0	ENST00000218089.9:c.2989T>G	p.Leu997Val	p.L997V	ENST00000218089	NM_001042749.1	997	Ttg/Gtg	29/35	1	2	FACETS	0.73	0.608	0.866	0.73	0.608	0.866	SUBCLONAL	1	TRUE	1	0.17	2		446	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0041341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	34	761	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.558	0.455	0.674	0.558	0.455	0.674	SUBCLONAL	1	TRUE	1	0.23	2		764	530	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0041341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	11	438	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.228	0.156	0.317	0.228	0.156	0.317	SUBCLONAL	1	TRUE	1	0.23	2		438	420	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023007	27023008	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGC	rs587779737	NA	P-0041341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	17	19	0	ENST00000324856.7:c.126_128dup	p.Ala45dup	p.A45dup	ENST00000324856	NM_006015.4	45	gag/gaGGCg	1/20	1	2	FACETS	1	0.851	1	1	0.939	1	CLONAL	2	TRUE	1	0.23	2		19	64	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	45	283	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	0.289594229494291	3	FACETS	0.865	0.74	0.996	0.576	0.493	0.664	CLONAL	2	TRUE	0	0.406706513845223	3		283	154	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782082	NA	P-0041420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	255	666	0	ENST00000269305.4:c.745A>T	p.Arg249Trp	p.R249W	ENST00000269305	NM_001126112.2	249	Agg/Tgg	7/11	0.274523756341672	3	FACETS	1	0.99	1	0.815	0.769	0.862	CLONAL	2	TRUE	0	0.406706513845223	3		666	617	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449535	32449535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779813097	NA	P-0041420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	182	830	0	ENST00000332351.3:c.839G>A	p.Ser280Asn	p.S280N	ENST00000332351	NM_024426.4	280	aGc/aAc	3/10	0.0800158171005503	5	FACETS	0.966	0.893	1	0.644	0.595	0.694	INDETERMINATE	2	TRUE	2	0.406706513845223	5		830	746	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624568	21624568	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	28	417	0	ENST00000421138.2:c.1461G>T	p.Lys487Asn	p.K487N	ENST00000421138		487	aaG/aaT	14/16	0.406706513845223	3	FACETS	0.549	0.439	0.673	0.183	0.146	0.225	SUBCLONAL	1	TRUE	0	0.406706513845223	3		417	302	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341526	89341526	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	36	606	0	ENST00000301030.4:c.7544T>G	p.Leu2515Arg	p.L2515R	ENST00000301030	NM_001256183.1	2515	cTg/cGg	10/13	0.0857504533184914	6	FACETS	0.586	0.481	0.704	0.195	0.16	0.235	INDETERMINATE	1	TRUE	3	0.406706513845223	6		606	548	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101008	41101008	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	144	674	0	ENST00000373198.4:c.1348C>T	p.Arg450Ter	p.R450*	ENST00000373198	NM_133170.3	450	Cga/Tga	8/32	0.406706513845223	8	FACETS	1	0.982	1	0.19	0.172	0.208	CLONAL	1	TRUE	1	0.406706513845223	8		674	1185	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435219	110435219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746894027	NA	P-0041434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	10	517	0	ENST00000375856.3:c.3182C>T	p.Ser1061Leu	p.S1061L	ENST00000375856	NM_003749.2	1061	tCg/tTg	1/2	1	2	FACETS	0.362	0.245	0.509	0.362	0.245	0.509	SUBCLONAL	1	FALSE	1	0.277738183043508	2		517	199	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462607	40462607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1387284839	NA	P-0041434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	10	692	0	ENST00000345506.4:c.2305C>T	p.Arg769Cys	p.R769C	ENST00000345506	NM_003152.3	769	Cgc/Tgc	20/20	1	2	FACETS	0.429	0.291	0.601	0.429	0.291	0.601	SUBCLONAL	1	FALSE	1	0.277738183043508	2		692	168	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0041439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	89	558	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.157134972101289	3	FACETS	0.802	0.713	0.896	0.802	0.713	0.896	CLONAL	2	TRUE	1	0.247454118857129	3		558	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579336	7579336	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	134	873	1	ENST00000269305.4:c.351del	p.Thr118GlnfsTer5	p.T118Qfs*5	ENST00000269305	NM_001126112.2	117	ggG/gg	4/11	0.247454118857129	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.247454118857129	1		874	834	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654643	67654643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs968244943	NA	P-0041439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	111	614	0	ENST00000264010.4:c.1130G>A	p.Arg377His	p.R377H	ENST00000264010	NM_006565.3	377	cGt/cAt	6/12	0.247454118857129	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.247454118857129	1		614	614	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998972	11998972	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	61	444	0	ENST00000353533.5:c.476del	p.Pro159HisfsTer38	p.P159Hfs*38	ENST00000353533	NM_003010.3	158	tgC/tg	4/11	0.247454118857129	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.247454118857129	1		444	391	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0041504-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	81	558	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.927	0.817	1	0.927	0.817	1	CLONAL	1	TRUE	1	0.28	2		558	624	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0041504-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	75	583	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.842	0.738	0.954	0.842	0.738	0.954	CLONAL	1	TRUE	1	0.28	2		583	636	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026864	6026864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs74902811	NA	P-0041504-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	40	571	0	ENST00000265849.7:c.1532C>T	p.Thr511Met	p.T511M	ENST00000265849	NM_000535.5	511	aCg/aTg	11/15	1	2	FACETS	0.422	0.35	0.503	0.422	0.35	0.503	SUBCLONAL	1	TRUE	1	0.28	2		571	677	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933761	39933761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763713717	NA	P-0041504-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	83	669	0	ENST00000378444.4:c.838G>A	p.Val280Ile	p.V280I	ENST00000378444	NM_001123385.1	280	Gtc/Atc	4/15	1	2	FACETS	0.896	0.791	1	0.896	0.791	1	CLONAL	1	TRUE	1	0.28	2		669	662	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438216	56438216	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041504-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	36	679	0	ENST00000407977.2:c.777G>A	p.Trp259Ter	p.W259*	ENST00000407977		259	tgG/tgA	7/10	1	2	FACETS	0.386	0.316	0.465	0.386	0.316	0.465	SUBCLONAL	1	TRUE	1	0.28	2		679	666	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023676	27023676	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs867647567	NA	P-0041504-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	17	251	0	ENST00000324856.7:c.782C>A	p.Ser261Ter	p.S261*	ENST00000324856	NM_006015.4	261	tCg/tAg	1/20	1	2	FACETS	0.402	0.3	0.524	0.402	0.3	0.524	SUBCLONAL	1	TRUE	1	0.28	2		251	302	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720877	89720877	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0041504-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	41	404	0	ENST00000371953.3:c.1026+2T>A		p.X342_splice	ENST00000371953	NM_000314.4	342			1	2	FACETS	0.547	0.455	0.65	0.547	0.455	0.65	SUBCLONAL	1	TRUE	1	0.28	2		404	535	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041504-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	42	187	0	ENST00000256196.4:c.68G>T	p.Gly23Val	p.G23V	ENST00000256196		23	gGc/gTc	1/6	1	2	FACETS	0.806	0.675	0.952	0.806	0.675	0.952	CLONAL	1	TRUE	1	0.28	2		187	372	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617533	158617533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751000395	NA	P-0041504-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	40	474	0	ENST00000263640.3:c.1123C>T	p.Arg375Cys	p.R375C	ENST00000263640	NM_001105.4	375	Cgt/Tgt	9/11	1	2	FACETS	0.431	0.357	0.514	0.431	0.357	0.514	SUBCLONAL	1	TRUE	1	0.28	2		474	663	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs149680468	NA	P-0041504-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	70	350	0	ENST00000281708.4:c.1513C>A	p.Arg505Ser	p.R505S	ENST00000281708	NM_033632.3	505	Cgc/Agc	10/12	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.28	2		350	478	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099416	27099417	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041504-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	108	585	0	ENST00000324856.7:c.3654dup	p.Asp1219Ter	p.D1219*	ENST00000324856	NM_006015.4	1218	tct/tcTt	14/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.28	2		585	583	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692855	89692855	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041504-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	23	175	0	ENST00000371953.3:c.339del	p.Ser113ArgfsTer21	p.S113Rfs*21	ENST00000371953	NM_000314.4	113	agT/ag	5/9	1	2	FACETS	0.637	0.498	0.797	0.637	0.498	0.797	SUBCLONAL	1	TRUE	1	0.28	2		175	258	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003509	42003509	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041504-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	35	431	0	ENST00000219905.7:c.3046C>T	p.Arg1016Ter	p.R1016*	ENST00000219905	NM_001164273.1	1016	Cga/Tga	8/24	1	2	FACETS	0.464	0.379	0.559	0.464	0.379	0.559	SUBCLONAL	1	TRUE	1	0.28	2		431	539	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55607075	55607075	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	104	555	0	ENST00000284073.2:c.444C>G	p.Asn148Lys	p.N148K	ENST00000284073	NM_138962.2	148	aaC/aaG	7/14	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.557264354348481	2		555	369	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188272	10188273	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs869025649	NA	P-0041509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	106	787	0	ENST00000256474.2:c.419_420del	p.Leu140GlnfsTer3	p.L140Qfs*3	ENST00000256474	NM_000551.3	139	TCt/t	2/3	0.536853701685321	1	FACETS	0.78	0.706	0.856	0.78	0.706	0.856	SUBCLONAL	1	TRUE	0	0.557264354348481	1		787	352	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1976590	1976590	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	77	765	0	ENST00000382891.5:c.3373G>A	p.Asp1125Asn	p.D1125N	ENST00000382891	NM_133335.3	1125	Gac/Aac	19/22	1	2	FACETS	0.837	0.741	0.939	0.837	0.741	0.939	CLONAL	1	TRUE	1	0.557264354348481	2		765	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	319	905	2	ENST00000269305.4:c.497C>A	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tAa	5/11	0.578837041523931	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.599005752513971	1		907	738	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261448	16261448	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1456771008	NA	P-0041510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	206	786	1	ENST00000375759.3:c.8713G>A	p.Asp2905Asn	p.D2905N	ENST00000375759	NM_015001.2	2905	Gat/Aat	11/15	0.466598315165256	3	FACETS	0.835	0.774	0.898	0.417	0.387	0.449	CLONAL	1	TRUE	1	0.599005752513971	3		787	1071	SUCCESS
APC	324	MSKCC	GRCh37	5	112173388	112173388	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1060503282	NA	P-0041510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	138	413	0	ENST00000257430.4:c.2097G>A	p.Trp699Ter	p.W699*	ENST00000257430	NM_000038.5	699	tgG/tgA	16/16	0.59004900152888	1	FACETS	0.927	0.855	1	0.927	0.855	1	CLONAL	1	TRUE	0	0.599005752513971	1		413	348	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462861	120462861	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1392588923	NA	P-0041510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	150	418	0	ENST00000256646.2:c.5470C>T	p.Arg1824Cys	p.R1824C	ENST00000256646	NM_024408.3	1824	Cgt/Tgt	30/34	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.599005752513971	2		418	462	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422316	422316	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	1516	602	0	ENST00000399788.2:c.2942C>G	p.Ala981Gly	p.A981G	ENST00000399788	NM_001042603.1	981	gCc/gGc	20/28	0.599005752513971	9	FACETS	0.947	0.932	0.962			1	CLONAL	8	TRUE	NA	0.599005752513971	9		602	2069	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593452	48593452	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	34	546	0	ENST00000342988.3:c.1203C>G	p.Cys401Trp	p.C401W	ENST00000342988	NM_005359.5	401	tgC/tgG	10/12	0.599005752513971	1	FACETS	0.152	0.124	0.184	0.152	0.124	0.184	SUBCLONAL	1	TRUE	0	0.599005752513971	1		546	522	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416647	29416647	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	367	606	0	ENST00000389048.3:c.4306C>G	p.Arg1436Gly	p.R1436G	ENST00000389048	NM_004304.4	1436	Cgc/Ggc	29/29	0.58026676590518	2	FACETS	0.962	0.923	1	0.962	0.923	1	CLONAL	2	TRUE	0	0.599005752513971	2		606	637	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411995	63411997	+	missense_variant	Missense_Mutation	TNP	TCT	TCT	ACA	novel	NA	P-0041510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	200	414	0	ENST00000330258.3:c.1170_1172delinsTGT	p.Leu390_Glu391delinsPheVal	p.L390_E391delinsFV	ENST00000330258	NM_152424.3	390	ttAGAg/ttTGTg	2/2	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.599005752513971	1		414	393	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0041512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	87	410	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.317069610495985	4	FACETS		NA	1			1	NA	NA	FALSE	2	NA	4		410	313	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0041517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	34	395	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.264162383499549	1	FACETS	0.381	0.31	0.46	0.381	0.31	0.46	SUBCLONAL	1	FALSE	0	0.264162383499549	1		395	587	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030478	49030479	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1566234123	NA	P-0041517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	47	371	0	ENST00000267163.4:c.1959dup	p.Val654SerfsTer14	p.V654Sfs*14	ENST00000267163	NM_000321.2	651	-/A	19/27	1	2	FACETS	0.659	0.556	0.773	0.659	0.556	0.773	SUBCLONAL	1	FALSE	1	0.264162383499549	2		371	540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578460	+	frameshift_variant	Frame_Shift_Del	DEL	CGGA	CGGA	-	novel	NA	P-0041517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	92	720	0	ENST00000269305.4:c.470_473del	p.Val157AlafsTer12	p.V157Afs*12	ENST00000269305	NM_001126112.2	157	gTCCGc/gc	5/11	0.264162383499549	1	FACETS	0.649	0.576	0.728	0.649	0.576	0.728	SUBCLONAL	1	FALSE	0	0.264162383499549	1		720	931	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968937	15968937	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762318164	NA	P-0041517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	49	497	0	ENST00000268712.3:c.4813G>A	p.Ala1605Thr	p.A1605T	ENST00000268712	NM_006311.3	1605	Gca/Aca	33/46	0.264162383499549	1	FACETS	0.53	0.449	0.621	0.53	0.449	0.621	SUBCLONAL	1	FALSE	0	0.264162383499549	1		497	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576868	7576868	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	392	567	0	ENST00000269305.4:c.978del	p.Glu326AspfsTer19	p.E326Dfs*19	ENST00000269305	NM_001126112.2	326	gaA/ga	9/11	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.809266234144905	2		567	457	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891308	101891308	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	343	574	0	ENST00000374994.4:c.269C>A	p.Ser90Ter	p.S90*	ENST00000374994	NM_004612.2	90	tCa/tAa	2/9	0.651274902051455	4	FACETS	0.962	0.916	1	0.962	0.916	1	CLONAL	2	TRUE	2	0.809266234144905	4		574	797	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117645564	117645564	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	249	535	0	ENST00000368508.3:c.5572C>G	p.Pro1858Ala	p.P1858A	ENST00000368508	NM_002944.2	1858	Cca/Gca	34/43	0.809266234144905	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.809266234144905	3		535	426	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15975497	15975497	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	272	492	0	ENST00000268712.3:c.3857T>C	p.Leu1286Pro	p.L1286P	ENST00000268712	NM_006311.3	1286	cTc/cCc	29/46	0.809266234144905	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.809266234144905	2		492	335	SUCCESS
BTK	695	MSKCC	GRCh37	X	100614300	100614300	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	350	250	0	ENST00000308731.7:c.875A>G	p.Glu292Gly	p.E292G	ENST00000308731	NM_000061.2	292	gAg/gGg	10/19	0.809266234144905	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.809266234144905	2		250	381	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814915	139814924	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGCCGGCA	GCAGCCGGCA	-	novel	NA	P-0041552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	214	536	0	ENST00000247668.2:c.911_920del	p.Ser304ThrfsTer11	p.S304Tfs*11	ENST00000247668	NM_021138.3	303	tGCAGCCGGCAg/tg	8/11	1	2	FACETS	0.776	0.721	0.832	0.776	0.721	0.832	SUBCLONAL	1	TRUE	1	0.597932446670174	2		536	923	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041110	180041110	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781402372	NA	P-0041573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	362	821	1	ENST00000261937.6:c.3289G>A	p.Val1097Met	p.V1097M	ENST00000261937	NM_182925.4	1097	Gtg/Atg	24/30	1	2	FACETS	0.991	0.942	1	0.991	0.942	1	CLONAL	1	TRUE	1	0.733795764789852	2		822	996	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0041573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	288	690	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.733795764789852	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.733795764789852	1		690	410	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247168	153247168	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1560758208	NA	P-0041573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	132	268	0	ENST00000281708.4:c.1634A>G	p.Tyr545Cys	p.Y545C	ENST00000281708	NM_033632.3	545	tAt/tGt	10/12	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.733795764789852	2		268	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0041586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	141	871	5	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.200988182557469	1	FACETS	0.78	0.711	0.852	1	0.988	1	SUBCLONAL	2	TRUE	0	0.200988182557469	1		876	809	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0041586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	99	643	1	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.200988182557469	1	FACETS	0.909	0.81	1	0.909	0.81	1	CLONAL	1	TRUE	0	0.200988182557469	1		644	975	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247812	59247813	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0041586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	104	735	0	ENST00000371222.2:c.930_931del	p.Lys311SerfsTer6	p.K311Sfs*6	ENST00000371222	NM_002228.3	310	caGAaa/caaa	1/1	0.200988182557469	1	FACETS	0.897	0.801	0.999	0.897	0.801	0.999	CLONAL	1	TRUE	0	0.200988182557469	1		735	1038	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412453	63412453	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	50	415	0	ENST00000330258.3:c.714A>C	p.Lys238Asn	p.K238N	ENST00000330258	NM_152424.3	238	aaA/aaC	2/2	1	1	FACETS	0.748	0.634	0.874	0.748	0.634	0.874	SUBCLONAL	1	TRUE	0	0.200988182557469	1		415	598	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724542	162724542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1041487062	NA	P-0041586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	84	442	0	ENST00000367921.3:c.314G>A	p.Arg105His	p.R105H	ENST00000367921	NM_006182.2	105	cGc/cAc	5/18	0.0776194705837645	4	FACETS	1	0.971	1	0.672	0.593	0.757	INDETERMINATE	1	TRUE	2	0.200988182557469	4		442	747	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15818054	15818054	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	48	161	0	ENST00000307771.7:c.181G>T	p.Glu61Ter	p.E61*	ENST00000307771	NM_005089.3	61	Gag/Tag	3/11	1	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.200988182557469	1		161	294	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630626	158630626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912678	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	102	361	1	ENST00000263640.3:c.617G>A	p.Arg206His	p.R206H	ENST00000263640	NM_001105.4	206	cGc/cAc	6/11	1	2	FACETS	0.962	0.867	1	0.962	0.867	1	CLONAL	1	TRUE	1	0.545137737113701	2		362	389	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	134	395	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.545137737113701	2		395	480	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	173	725	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.984	0.909	1	0.984	0.909	1	CLONAL	1	TRUE	1	0.545137737113701	2		732	645	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	216	896	5	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.545137737113701	2		901	768	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	133	496	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.8	0.729	0.874	0.8	0.729	0.874	SUBCLONAL	1	TRUE	1	0.545137737113701	2		497	610	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	34	370	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.491	0.403	0.589	0.491	0.403	0.589	SUBCLONAL	1	TRUE	1	0.545137737113701	2		370	254	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	171	572	5	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.545137737113701	2		577	588	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308382	15308383	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs749829137	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	162	798	1	ENST00000263388.2:c.125dup	p.Cys43LeufsTer32	p.C43Lfs*32	ENST00000263388	NM_000435.2	42	cct/ccCt	2/33	1	2	FACETS	0.772	0.709	0.837	0.772	0.709	0.837	SUBCLONAL	1	TRUE	1	0.545137737113701	2		799	770	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675562	30675562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769199645	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	250	861	0	ENST00000376406.3:c.2794G>A	p.Glu932Lys	p.E932K	ENST00000376406	NM_014641.2	932	Gag/Aag	8/15	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.545137737113701	2		861	907	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916728	178916728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	119	418	0	ENST00000263967.3:c.115G>A	p.Glu39Lys	p.E39K	ENST00000263967	NM_006218.2	39	Gag/Aag	2/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.545137737113701	2		418	365	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720741	89720741	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs371387815	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	34	270	1	ENST00000371953.3:c.892C>T	p.Gln298Ter	p.Q298*	ENST00000371953	NM_000314.4	298	Caa/Taa	8/9	1	2	FACETS	0.81	0.672	0.961	0.81	0.672	0.961	CLONAL	1	TRUE	1	0.545137737113701	2		271	154	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436026	56436026	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771831816	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	122	541	0	ENST00000407977.2:c.1111C>T	p.Arg371Ter	p.R371*	ENST00000407977		371	Cga/Tga	9/10	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.545137737113701	2		541	434	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793677	89793677	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	116	395	1	ENST00000336032.3:c.752del	p.Lys251SerfsTer14	p.K251Sfs*14	ENST00000336032	NM_006813.2	249	gAa/ga	2/2	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.545137737113701	2		396	424	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403254	213403254	+	frameshift_variant,start_lost,start_retained_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	124	452	2	ENST00000342788.4:c.1del	p.Met1?	p.M1?	ENST00000342788	NM_005235.2	1	Atg/tg	1/28	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.545137737113701	2		454	448	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	253	877	4	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.545137737113701	2		881	866	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916851	48916851	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1131690902	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	104	295	2	ENST00000267163.4:c.380+1G>A		p.X127_splice	ENST00000267163	NM_000321.2	127			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.545137737113701	2		297	337	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	90	920	2	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.439	0.389	0.492	0.439	0.389	0.492	SUBCLONAL	1	TRUE	1	0.545137737113701	2		922	753	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420184	49420184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555185701	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	209	761	2	ENST00000301067.7:c.15565G>A	p.Gly5189Arg	p.G5189R	ENST00000301067	NM_003482.3	5189	Gga/Aga	48/54	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.545137737113701	2		763	725	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372131	45372131	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	169	535	1	ENST00000262160.6:c.1038del	p.Phe346LeufsTer5	p.F346Lfs*5	ENST00000262160	NM_005901.5	346	ttT/tt	9/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.545137737113701	2		536	587	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941844	71941844	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1204907315	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	151	620	0	ENST00000298229.2:c.1202G>A	p.Arg401Gln	p.R401Q	ENST00000298229	NM_001567.3	401	cGg/cAg	11/28	1	2	FACETS	0.974	0.895	1	0.974	0.895	1	CLONAL	1	TRUE	1	0.545137737113701	2		620	569	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246903	10246903	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	259	899	0	ENST00000340748.4:c.4502C>T	p.Pro1501Leu	p.P1501L	ENST00000340748		1501	cCc/cTc	37/40	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.545137737113701	2		899	846	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435472	110435472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751311445	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	63	733	0	ENST00000375856.3:c.2929G>A	p.Asp977Asn	p.D977N	ENST00000375856	NM_003749.2	977	Gac/Aac	1/2	1	2	FACETS	0.296	0.255	0.34	0.296	0.255	0.34	SUBCLONAL	1	TRUE	1	0.545137737113701	2		733	782	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652330	206652330	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	207	872	2	ENST00000367120.3:c.1042del	p.Arg348AspfsTer32	p.R348Dfs*32	ENST00000367120	NM_014002.3	346	gCc/gc	10/22	0.545137737113701	4	FACETS	0.863	0.799	0.93	0.288	0.266	0.31	CLONAL	1	TRUE	1	0.545137737113701	4		874	1360	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258273	16258273	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	229	690	1	ENST00000375759.3:c.5538G>T	p.Arg1846Ser	p.R1846S	ENST00000375759	NM_015001.2	1846	agG/agT	11/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.545137737113701	2		691	789	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885763	23885763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769841287	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	220	792	0	ENST00000374561.5:c.155G>A	p.Arg52Gln	p.R52Q	ENST00000374561	NM_002167.4	52	cGg/cAg	1/3	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.545137737113701	2		792	728	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097673	27097673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	204	639	0	ENST00000324856.7:c.3262G>A	p.Ala1088Thr	p.A1088T	ENST00000324856	NM_006015.4	1088	Gct/Act	12/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.545137737113701	2		639	668	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243777015	243777015	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	188	540	0	ENST00000263826.5:c.654del	p.Asp219ThrfsTer6	p.D219Tfs*6	ENST00000263826	NM_005465.4	218	aaA/aa	7/13	0.545137737113701	4	FACETS	1	0.974	1	0.374	0.345	0.403	CLONAL	1	TRUE	1	0.545137737113701	4		540	951	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435391	18435391	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	90	344	0	ENST00000266497.5:c.376T>C	p.Trp126Arg	p.W126R	ENST00000266497		126	Tgg/Cgg	1/31	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.545137737113701	2		344	302	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939062	48939062	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	91	291	0	ENST00000267163.4:c.897del	p.Phe299LeufsTer2	p.F299Lfs*2	ENST00000267163	NM_000321.2	298	ccT/cc	9/27	1	2	FACETS	0.973	0.872	1	0.973	0.872	1	CLONAL	1	TRUE	1	0.545137737113701	2		291	343	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95584078	95584078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	104	343	0	ENST00000393063.1:c.1390G>A	p.Ala464Thr	p.A464T	ENST00000393063	NM_030621.3	464	Gct/Act	10/28	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.545137737113701	2		343	347	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396386	396386	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	244	855	0	ENST00000262320.3:c.640G>T	p.Gly214Cys	p.G214C	ENST00000262320	NM_003502.3	214	Ggc/Tgc	2/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.545137737113701	2		855	750	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831543	72831543	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	227	738	0	ENST00000268489.5:c.5038del	p.Leu1680Ter	p.L1680*	ENST00000268489	NM_006885.3	1680	Cta/ta	9/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.545137737113701	2		738	778	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438277	56438277	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	206	880	0	ENST00000407977.2:c.716C>A	p.Ala239Asp	p.A239D	ENST00000407977		239	gCc/gAc	7/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.545137737113701	2		880	672	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59878628	59878628	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	84	304	0	ENST00000259008.2:c.1126C>A	p.Gln376Lys	p.Q376K	ENST00000259008	NM_032043.2	376	Caa/Aaa	8/20	1	2	FACETS	0.934	0.832	1	0.934	0.832	1	CLONAL	1	TRUE	1	0.545137737113701	2		304	330	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221489	36221489	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	263	944	1	ENST00000222270.7:c.5248G>T	p.Glu1750Ter	p.E1750*	ENST00000222270	NM_014727.1	1750	Gag/Tag	25/37	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.545137737113701	2		945	885	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229279	36229279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	218	801	0	ENST00000222270.7:c.7969C>T	p.Pro2657Ser	p.P2657S	ENST00000222270	NM_014727.1	2657	Ccc/Tcc	37/37	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.545137737113701	2		801	754	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463512	25463512	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	45	643	0	ENST00000264709.3:c.2170T>C	p.Tyr724His	p.Y724H	ENST00000264709	NM_175629.2	724	Tac/Cac	18/23	1	2	FACETS	0.29	0.243	0.341	0.29	0.243	0.341	SUBCLONAL	1	TRUE	1	0.545137737113701	2		643	570	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279824	46279825	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAA	rs749655240	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	57	520	0	ENST00000371998.3:c.3752_3753insACA	p.Gln1276dup	p.Q1276dup	ENST00000371998		1276	-/CAA	20/23	1	2	FACETS	0.377	0.323	0.435	0.377	0.323	0.435	SUBCLONAL	1	TRUE	1	0.545137737113701	2		520	555	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22142620	22142620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	165	474	0	ENST00000215832.6:c.782G>A	p.Arg261Lys	p.R261K	ENST00000215832	NM_002745.4	261	aGg/aAg	6/9	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.545137737113701	2		474	540	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168677	56168678	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	149	445	0	ENST00000399503.3:c.1535dup	p.Ser513PhefsTer28	p.S513Ffs*28	ENST00000399503	NM_005921.1	511	tcc/tCcc	9/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.545137737113701	2		445	492	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100295	157100296	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	83	283	0	ENST00000346085.5:c.1235dup	p.Ser413ValfsTer122	p.S413Vfs*122	ENST00000346085	NM_020732.3	411	cac/caCc	1/20	1	2	FACETS	0.937	0.835	1	0.937	0.835	1	CLONAL	1	TRUE	1	0.545137737113701	2		283	325	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729727	41729727	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	146	578	1	ENST00000242208.4:c.802del	p.Glu268LysfsTer91	p.E268Kfs*91	ENST00000242208	NM_002192.2	268	Gaa/aa	3/3	1	2	FACETS	0.994	0.912	1	0.994	0.912	1	CLONAL	1	TRUE	1	0.545137737113701	2		579	539	SUCCESS
MET	4233	MSKCC	GRCh37	7	116417467	116417467	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	97	328	0	ENST00000397752.3:c.3284G>T	p.Gly1095Val	p.G1095V	ENST00000397752	NM_000245.2	1095	gGg/gTg	16/21	1	2	FACETS	0.962	0.865	1	0.962	0.865	1	CLONAL	1	TRUE	1	0.545137737113701	2		328	370	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020521	69020521	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	188	616	0	ENST00000288368.4:c.2893A>G	p.Arg965Gly	p.R965G	ENST00000288368	NM_024870.2	965	Agg/Ggg	24/40	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.545137737113701	2		616	689	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428390	47428390	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	215	794	0	ENST00000377045.4:c.1258C>A	p.Leu420Ile	p.L420I	ENST00000377045	NM_001654.4	420	Ctc/Atc	12/16	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.545137737113701	2		794	778	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589578	67589583	+	inframe_deletion	In_Frame_Del	DEL	AAAATT	AAAATT	-	novel	NA	P-0041605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	39	214	0	ENST00000274335.5:c.1342_1347del	p.Lys448_Leu449del	p.K448_L449del	ENST00000274335		447	aaAAAATTa/aaa	10/15	0.547313380576152	2	FACETS	0.923	0.778	1	0.462	0.389	0.539	CLONAL	1	TRUE	0	0.563288099217264	2		214	150	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374361	81374361	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1476385169	NA	P-0041605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	261	356	2	ENST00000222390.5:c.701G>A	p.Arg234His	p.R234H	ENST00000222390	NM_000601.4	234	cGc/cAc	6/18	0.563288099217264	4	FACETS	0.954	0.905	1	0.954	0.905	1	CLONAL	3	TRUE	1	0.563288099217264	4		358	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579578	7579582	+	frameshift_variant	Frame_Shift_Del	DEL	ACGGC	ACGGC	-	novel	NA	P-0041605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	291	701	0	ENST00000269305.4:c.105_109del	p.Leu35PhefsTer6	p.L35Ffs*6	ENST00000269305	NM_001126112.2	35	ttGCCGTcc/ttcc	4/11	NA	2	FACETS	0.969	0.924	1			1	INDETERMINATE	2	TRUE	NA	0.563288099217264	2		701	533	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80343494	80343494	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	23	420	0	ENST00000286548.4:c.825G>C	p.Lys275Asn	p.K275N	ENST00000286548	NM_002072.3	275	aaG/aaC	6/7	0.563288099217264	3	FACETS	0.263	0.204	0.331	0.131	0.102	0.166	SUBCLONAL	1	TRUE	1	0.563288099217264	3		420	398	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0041839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	159	479	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.834036683117534	2		479	305	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428471	78428471	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs369776228	NA	P-0041839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	144	413	0	ENST00000370768.2:c.1328T>C	p.Ile443Thr	p.I443T	ENST00000370768	NM_003902.3	443	aTa/aCa	14/20	1	2	FACETS	0.664	0.609	0.721	0.664	0.609	0.721	SUBCLONAL	1	TRUE	1	0.834036683117534	2		413	520	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230555	46230556	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0041839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	37	465	0	ENST00000334344.6:c.805_806del	p.Leu269IlefsTer10	p.L269Ifs*10	ENST00000334344	NM_152641.2	268	tcTTta/tcta	8/21	0.51475742719627	1	FACETS	0.13	0.107	0.156	0.13	0.107	0.156	SUBCLONAL	1	TRUE	0	0.834036683117534	1		465	398	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2097728	2097728	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	286	526	0	ENST00000219066.1:c.121A>G	p.Arg41Gly	p.R41G	ENST00000219066	NM_002528.5	41	Aga/Gga	1/6	0.113274573438997	5	FACETS	0.985	0.93	1			1	INDETERMINATE	2	TRUE	NA	0.834036683117534	5		526	784	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217289	66217289	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	135	319	2	ENST00000273854.3:c.2326del	p.Gln776SerfsTer6	p.Q776Sfs*6	ENST00000273854	NM_004439.5	776	Cag/ag	14/18	1	2	FACETS	0.894	0.823	0.967	0.894	0.823	0.967	CLONAL	1	TRUE	1	0.834036683117534	2		321	362	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798530	32798532	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0041839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	69	797	0	ENST00000374899.4:c.1324_1326del	p.Lys442del	p.K442del	ENST00000374899	NM_018833.2	442	AAG/-	8/12	1	2	FACETS	0.178	0.154	0.204	0.178	0.154	0.204	SUBCLONAL	1	TRUE	1	0.834036683117534	2		797	928	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885900	111885900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749430739	NA	P-0041864-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	205	742	0	ENST00000341259.2:c.1522C>T	p.Arg508Trp	p.R508W	ENST00000341259	NM_005475.2	508	Cgg/Tgg	8/8	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.818120232136377	2		742	484	SUCCESS
EED	8726	MSKCC	GRCh37	11	85955938	85956363	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	AGACATACTTAATACTGCCCTCTTAATCCAACGGACCTTACATCGTGTAGACTGCCGGGAGGGCGGCGGGAAAAGGGCAAGACGGGAGTTGGGGAAGGGAAGGAGCCAGGAAGCCGCGCGGGAGGGCGCGCGCGCGCGCCCCTTTTTCAGCAGTGTGGCGGGGTCGCACGCACGCCCGCCTCGGCGGCTGGGCGCGATTTGCGACAGTGGGGGGGGCGGTGGAGGTGGCGGCGGCAGCGGCAACTTTGCGGCAAGCTCGGGCCGGGCTTGCTTGACGGCGGTGTGGCGGAGGCCCCGCCCCAGGCGGCAGGAACCTGGAGGGAGGCGGAGGAATATGTCCGAGAGGGAAGTGTCGACTGCGCCGGCGGGAACAGACATGCCTGCGGCCAAGAAGCAGAAGCTGAGCAGTGACGAGAACAGCAATCC	AGACATACTTAATACTGCCCTCTTAATCCAACGGACCTTACATCGTGTAGACTGCCGGGAGGGCGGCGGGAAAAGGGCAAGACGGGAGTTGGGGAAGGGAAGGAGCCAGGAAGCCGCGCGGGAGGGCGCGCGCGCGCGCCCCTTTTTCAGCAGTGTGGCGGGGTCGCACGCACGCCCGCCTCGGCGGCTGGGCGCGATTTGCGACAGTGGGGGGGGCGGTGGAGGTGGCGGCGGCAGCGGCAACTTTGCGGCAAGCTCGGGCCGGGCTTGCTTGACGGCGGTGTGGCGGAGGCCCCGCCCCAGGCGGCAGGAACCTGGAGGGAGGCGGAGGAATATGTCCGAGAGGGAAGTGTCGACTGCGCCGGCGGGAACAGACATGCCTGCGGCCAAGAAGCAGAAGCTGAGCAGTGACGAGAACAGCAATCC	-	novel	NA	P-0041864-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3	65	12	0	ENST00000263360.6:c.-330_96del		p.*110*	ENST00000263360	NM_003797.3	?-31/441		1/12	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.818120232136377	NA		12	68	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0041867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	50	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.749	0.64	0.868	0.749	0.64	0.868	SUBCLONAL	1	TRUE	1	0.46819005848914	2		334	285	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	247	757	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.416913860738754	1	FACETS	0.846	0.792	0.902	0.846	0.792	0.902	CLONAL	1	TRUE	0	0.46819005848914	1		757	955	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207009	1207009	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	300	909	0	ENST00000326873.7:c.97G>T	p.Glu33Ter	p.E33*	ENST00000326873	NM_000455.4	33	Gag/Tag	1/10	0.465325728555172	1	FACETS	0.889	0.838	0.942	0.889	0.838	0.942	CLONAL	1	TRUE	0	0.46819005848914	1		909	1104	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069291	30069291	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	384	774	0	ENST00000338641.4:c.1156G>T	p.Glu386Ter	p.E386*	ENST00000338641	NM_000268.3	386	Gaa/Taa	12/16	0.361835909707347	2	FACETS	0.805	0.766	0.844	0.805	0.766	0.844	CLONAL	2	TRUE	0	0.46819005848914	2		774	1019	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743392	743392	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	44	236	0	ENST00000314574.4:c.748A>C	p.Lys250Gln	p.K250Q	ENST00000314574	NM_005433.3	250	Aag/Cag	7/12	0.217148675027682	4	FACETS	0.8	0.673	0.939			1	INDETERMINATE	1	TRUE	NA	0.46819005848914	4		236	345	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864118	57864118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200306754	NA	P-0041867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	232	738	0	ENST00000228682.2:c.1595G>A	p.Arg532His	p.R532H	ENST00000228682	NM_005269.2	532	cGc/cAc	12/12	1	2	FACETS	0.892	0.831	0.955	0.892	0.831	0.955	CLONAL	1	TRUE	1	0.46819005848914	2		738	1111	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032018	10032018	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	231	796	0	ENST00000330684.3:c.805C>G	p.Pro269Ala	p.P269A	ENST00000330684	NM_001134407.1	269	Cca/Gca	3/13	1	2	FACETS	0.969	0.904	1	0.969	0.904	1	CLONAL	1	TRUE	1	0.46819005848914	2		796	1018	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069267	30069267	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	316	686	0	ENST00000338641.4:c.1132G>C	p.Glu378Gln	p.E378Q	ENST00000338641	NM_000268.3	378	Gag/Cag	12/16	0.361835909707347	2	FACETS	0.77	0.73	0.812	0.77	0.73	0.812	SUBCLONAL	2	TRUE	0	0.46819005848914	2		686	876	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069345	30069345	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	457	800	1	ENST00000338641.4:c.1210G>C	p.Glu404Gln	p.E404Q	ENST00000338641	NM_000268.3	404	Gag/Cag	12/16	0.361835909707347	2	FACETS	0.821	0.785	0.857	0.821	0.785	0.857	CLONAL	2	TRUE	0	0.46819005848914	2		801	1189	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957467	1957467	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	246	707	0	ENST00000382891.5:c.2566G>C	p.Asp856His	p.D856H	ENST00000382891	NM_133335.3	856	Gac/Cac	14/22	1	2	FACETS	0.961	0.898	1	0.961	0.898	1	CLONAL	1	TRUE	1	0.46819005848914	2		707	1094	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	192	749	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	0.656921317347455	3	FACETS	0.932	0.863	1	0.466	0.431	0.502	CLONAL	1	TRUE	1	0.656921317347455	3		749	833	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039422	47039422	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	173	624	1	ENST00000377604.3:c.1045C>T	p.Gln349Ter	p.Q349*	ENST00000377604	NM_001204468.1	349	Cag/Tag	10/24	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.656921317347455	2		625	505	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873660	35873660	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs201559094	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	81	254	2	ENST00000303115.3:c.616C>T	p.Arg206Ter	p.R206*	ENST00000303115	NM_002185.3	206	Cga/Tga	5/8	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.656921317347455	2		256	240	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35860962	35860962	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	66	267	0	ENST00000303115.3:c.91G>A	p.Glu31Lys	p.E31K	ENST00000303115	NM_002185.3	31	Gaa/Aaa	2/8	1	2	FACETS	0.87	0.766	0.979	0.87	0.766	0.979	CLONAL	1	TRUE	1	0.656921317347455	2		267	231	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	137	277	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.656921317347455	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.656921317347455	3		277	270	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693002	89693003	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	115	261	0	ENST00000371953.3:c.491dup	p.Val166SerfsTer14	p.V166Sfs*14	ENST00000371953	NM_000314.4	162	-/A	5/9	0.656921317347455	2	FACETS	0.898	0.834	0.961	0.898	0.834	0.961	CLONAL	2	TRUE	0	0.656921317347455	2		261	195	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755678	39755678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	189	614	0	ENST00000288319.7:c.1087G>A	p.Asp363Asn	p.D363N	ENST00000288319	NM_182918.3	363	Gat/Aat	10/10	0.656921317347455	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.656921317347455	1		614	347	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869692	117869692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1337189031	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	105	248	0	ENST00000297338.2:c.502C>T	p.Arg168Cys	p.R168C	ENST00000297338	NM_006265.2	168	Cgt/Tgt	6/14	0.613917835480779	3	FACETS	0.948	0.868	1	0.948	0.868	1	CLONAL	2	TRUE	1	0.656921317347455	3		248	224	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385271	41385271	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	135	469	0	ENST00000373198.4:c.690G>A	p.Trp230Ter	p.W230*	ENST00000373198	NM_133170.3	230	tgG/tgA	6/32	1	2	FACETS	0.938	0.86	1	0.938	0.86	1	CLONAL	1	TRUE	1	0.656921317347455	2		469	438	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504590	103504590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1400329743	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	73	171	0	ENST00000355739.4:c.211C>T	p.Arg71Cys	p.R71C	ENST00000355739	NM_000123.3	71	Cgt/Tgt	2/15	1	2	FACETS	0.95	0.843	1	0.95	0.843	1	CLONAL	1	TRUE	1	0.656921317347455	2		171	234	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8497265	8497265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1270795879	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	39	146	0	ENST00000356435.5:c.2326G>A	p.Glu776Lys	p.E776K	ENST00000356435		776	Gaa/Aaa	15/35	1	2	FACETS	0.88	0.744	1	0.88	0.744	1	CLONAL	1	TRUE	1	0.656921317347455	2		146	135	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1272338	1272338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	189	770	1	ENST00000310581.5:c.2344G>A	p.Glu782Lys	p.E782K	ENST00000310581	NM_198253.2	782	Gag/Aag	7/16	1	2	FACETS	0.984	0.915	1	0.984	0.915	1	CLONAL	1	TRUE	1	0.656921317347455	2		771	585	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244889	46244889	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	165	514	0	ENST00000334344.6:c.2983C>T	p.Gln995Ter	p.Q995*	ENST00000334344	NM_152641.2	995	Caa/Taa	15/21	1	2	FACETS	0.961	0.888	1	0.961	0.888	1	CLONAL	1	TRUE	1	0.656921317347455	2		514	523	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281506	15281506	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	179	786	0	ENST00000263388.2:c.4867C>T	p.Pro1623Ser	p.P1623S	ENST00000263388	NM_000435.2	1623	Ccg/Tcg	26/33	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.656921317347455	2		786	540	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225582	26225582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752115135	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	185	504	0	ENST00000360408.1:c.200C>T	p.Pro67Leu	p.P67L	ENST00000360408	NM_003532.2	67	cCg/cTg	1/1	0.656921317347455	3	FACETS	1	0.931	1	0.503	0.465	0.542	CLONAL	1	TRUE	1	0.656921317347455	3		504	744	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937185	76937185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	57	287	0	ENST00000373344.5:c.3563C>T	p.Ser1188Phe	p.S1188F	ENST00000373344	NM_000489.3	1188	tCc/tTc	9/35	1	2	FACETS	0.913	0.797	1	0.913	0.797	1	CLONAL	1	TRUE	1	0.656921317347455	2		287	190	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228965	36228965	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	198	693	0	ENST00000222270.7:c.7745C>T	p.Ser2582Leu	p.S2582L	ENST00000222270	NM_014727.1	2582	tCa/tTa	36/37	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.656921317347455	2		693	596	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530432	187530432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	92	254	0	ENST00000441802.2:c.10111C>T	p.His3371Tyr	p.H3371Y	ENST00000441802	NM_005245.3	3371	Cac/Tac	16/27	1	2	FACETS	0.884	0.794	0.977	0.884	0.794	0.977	CLONAL	1	TRUE	1	0.656921317347455	2		254	317	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782187	9782187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	346	582	0	ENST00000377346.4:c.2210C>T	p.Pro737Leu	p.P737L	ENST00000377346	NM_005026.3	737	cCc/cTc	17/24	0.656921317347455	2	FACETS	0.99	0.952	1	0.99	0.952	1	CLONAL	2	TRUE	0	0.656921317347455	2		582	532	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106165	27106165	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	293	545	0	ENST00000324856.7:c.5776G>T	p.Gly1926Ter	p.G1926*	ENST00000324856	NM_006015.4	1926	Gga/Tga	20/20	0.656921317347455	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.656921317347455	2		545	438	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532683	46532683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	192	278	0	ENST00000262741.5:c.395C>T	p.Ser132Phe	p.S132F	ENST00000262741	NM_003629.3	132	tCc/tTc	4/10	0.656921317347455	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.656921317347455	2		278	291	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534244	534244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	208	752	0	ENST00000451590.1:c.79C>T	p.His27Tyr	p.H27Y	ENST00000451590	NM_001130442.1	27	Cat/Tat	2/5	1	2	FACETS	0.891	0.83	0.953	0.891	0.83	0.953	CLONAL	1	TRUE	1	0.656921317347455	2		752	711	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230438	46230439	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	64	262	0	ENST00000334344.6:c.772_772+1delinsAA		p.X258_splice	ENST00000334344	NM_152641.2	258		7/21	1	2	FACETS	0.882	0.775	0.994	0.882	0.775	0.994	CLONAL	1	TRUE	1	0.656921317347455	2		262	221	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856236	111856236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	54	113	0	ENST00000341259.2:c.287C>T	p.Pro96Leu	p.P96L	ENST00000341259	NM_005475.2	96	cCc/cTc	2/8	1	2	FACETS	0.903	0.785	1	0.903	0.785	1	CLONAL	1	TRUE	1	0.656921317347455	2		113	182	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647653	2647653	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	169	468	0	ENST00000342085.4:c.1556C>A	p.Pro519His	p.P519H	ENST00000342085	NM_002613.4	519	cCt/cAt	14/14	1	2	FACETS	0.953	0.882	1	0.953	0.882	1	CLONAL	1	TRUE	1	0.656921317347455	2		468	540	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128591	30128591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	128	434	1	ENST00000263025.4:c.791C>T	p.Pro264Leu	p.P264L	ENST00000263025	NM_002746.2	264	cCa/cTa	6/9	1	2	FACETS	0.95	0.869	1	0.95	0.869	1	CLONAL	1	TRUE	1	0.656921317347455	2		435	410	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414806	56414807	+	missense_variant	Missense_Mutation	DNP	CT	CT	TA	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	155	504	1	ENST00000348428.3:c.2207_2208delinsTA	p.Pro736Leu	p.P736L	ENST00000348428	NM_006785.3	736	cCT/cTA	17/17	1	2	FACETS	0.955	0.881	1	0.955	0.881	1	CLONAL	1	TRUE	1	0.656921317347455	2		505	494	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212197	36212197	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	238	679	0	ENST00000222270.7:c.1948C>T	p.Pro650Ser	p.P650S	ENST00000222270	NM_014727.1	650	Cct/Tct	3/37	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.656921317347455	2		679	662	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213299	39213299	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	244	749	0	ENST00000402219.2:c.3668C>T	p.Pro1223Leu	p.P1223L	ENST00000402219	NM_005633.3	1223	cCt/cTt	23/23	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.656921317347455	2		749	736	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793363	242793364	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	205	853	1	ENST00000334409.5:c.713_714delinsTT	p.Pro238Leu	p.P238L	ENST00000334409	NM_005018.2	238	cCC/cTT	5/5	1	2	FACETS	0.934	0.871	1	0.934	0.871	1	CLONAL	1	TRUE	1	0.656921317347455	2		854	668	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546773	9546773	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	100	347	0	ENST00000353224.5:c.1249G>A	p.Gly417Ser	p.G417S	ENST00000353224	NM_177990.2	417	Ggc/Agc	5/10	1	2	FACETS	0.943	0.852	1	0.943	0.852	1	CLONAL	1	TRUE	1	0.656921317347455	2		347	323	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755735	39755735	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	156	483	0	ENST00000288319.7:c.1030C>T	p.Pro344Ser	p.P344S	ENST00000288319	NM_182918.3	344	Ccc/Tcc	10/10	0.656921317347455	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.656921317347455	1		483	302	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72897364	72897364	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	113	408	0	ENST00000325599.8:c.128A>C	p.Lys43Thr	p.K43T	ENST00000325599	NM_018130.2	43	aAg/aCg	1/11	1	2	FACETS	0.808	0.732	0.886	0.808	0.732	0.886	CLONAL	1	TRUE	1	0.656921317347455	2		408	426	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953865	55953865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	193	338	0	ENST00000263923.4:c.3571G>A	p.Gly1191Arg	p.G1191R	ENST00000263923	NM_002253.2	1191	Gga/Aga	27/30	0.613917835480779	3	FACETS	0.957	0.897	1	0.957	0.897	1	CLONAL	2	TRUE	1	0.656921317347455	3		338	408	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539623	187539624	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	68	264	0	ENST00000441802.2:c.8116_8117delinsTT	p.Pro2706Phe	p.P2706F	ENST00000441802	NM_005245.3	2706	CCt/TTt	10/27	1	2	FACETS	0.828	0.729	0.932	0.828	0.729	0.932	CLONAL	1	TRUE	1	0.656921317347455	2		264	250	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628821	187628821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	152	563	0	ENST00000441802.2:c.2161C>T	p.Pro721Ser	p.P721S	ENST00000441802	NM_005245.3	721	Ccg/Tcg	2/27	1	2	FACETS	0.958	0.883	1	0.958	0.883	1	CLONAL	1	TRUE	1	0.656921317347455	2		563	483	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910803	29910803	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs41543912	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	67	166	0	ENST00000376809.5:c.343G>A	p.Gly115Ser	p.G115S	ENST00000376809	NM_002116.7	115	Ggt/Agt	2/8	0.656921317347455	3	FACETS	0.982	0.88	1	0.982	0.88	1	CLONAL	2	TRUE	1	0.656921317347455	3		166	138	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821536	32821536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	216	783	1	ENST00000354258.4:c.58C>T	p.Pro20Ser	p.P20S	ENST00000354258	NM_000593.5	20	Ccg/Tcg	1/11	0.656921317347455	3	FACETS	1	0.99	1	0.669	0.625	0.714	CLONAL	1	TRUE	1	0.656921317347455	3		784	653	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157954	27157954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	170	558	0	ENST00000380036.4:c.178G>A	p.Asp60Asn	p.D60N	ENST00000380036	NM_000459.3	60	Gac/Aac	2/23	1	2	FACETS	0.966	0.894	1	0.966	0.894	1	CLONAL	1	TRUE	1	0.656921317347455	2		558	536	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933563	39933563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	194	604	0	ENST00000378444.4:c.1036C>T	p.Pro346Ser	p.P346S	ENST00000378444	NM_001123385.1	346	Ccc/Tcc	4/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.656921317347455	2		604	543	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357059	70357060	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	215	780	1	ENST00000374080.3:c.5574_5575delinsTT	p.Arg1859Cys	p.R1859C	ENST00000374080		1858	taCCgt/taTTgt	39/45	1	2	FACETS	0.971	0.907	1	0.971	0.907	1	CLONAL	1	TRUE	1	0.656921317347455	2		781	674	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164974	123164974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	47	166	0	ENST00000218089.9:c.287A>G	p.Gln96Arg	p.Q96R	ENST00000218089	NM_001042749.1	96	cAg/cGg	5/35	1	2	FACETS	0.906	0.779	1	0.906	0.779	1	CLONAL	1	TRUE	1	0.656921317347455	2		166	158	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060639	38060639	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	72	884	0	ENST00000250448.2:c.1350C>G	p.Ile450Met	p.I450M	ENST00000250448	NM_004496.3	450	atC/atG	2/2	1	2	FACETS	0.355	0.309	0.405	0.355	0.309	0.405	SUBCLONAL	1	TRUE	1	0.371894008387784	2		884	1090	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0042017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	132	418	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.304722539193658	3	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	1	0.315787277464748	3		418	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0042017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	246	723	1	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.315787277464748	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.315787277464748	2		724	742	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265046	46265046	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs575619475	NA	P-0042017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	576	514	0	ENST00000371998.3:c.1916A>G	p.Asn639Ser	p.N639S	ENST00000371998		639	aAc/aGc	12/23	0.315787277464748	8	FACETS	1	0.974	1	1	0.974	1	CLONAL	7	TRUE	1	0.315787277464748	8		514	1007	SUCCESS
APC	324	MSKCC	GRCh37	5	112175339	112175350	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGCTGTTGAA	AAAGCTGTTGAA	G	novel	NA	P-0042017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	30	221	0	ENST00000257430.4:c.4048_4059delinsG	p.Lys1350ValfsTer21	p.K1350Vfs*21	ENST00000257430	NM_000038.5	1350	AAAGCTGTTGAA/G	16/16	0.304722539193658	3	FACETS	0.789	0.637	0.959	0.394	0.318	0.48	CLONAL	1	TRUE	1	0.315787277464748	3		221	279	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	76	759	1				ENST00000310581	NM_198253.2	-/1132			0.19242075622294	3	FACETS	0.771	0.683	0.863	0.771	0.683	0.863	INDETERMINATE	2	TRUE	1	0.409447262914775	3		760	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578184	7578184	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567551073	NA	P-0042021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	101	810	0	ENST00000269305.4:c.665del	p.Pro222ArgfsTer25	p.P222Rfs*25	ENST00000269305	NM_001126112.2	222	cCg/cg	6/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.409447262914775	2		810	383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577093	7577093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882008	NA	P-0042021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	119	818	1	ENST00000269305.4:c.845G>A	p.Arg282Gln	p.R282Q	ENST00000269305	NM_001126112.2	282	cGg/cAg	8/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.409447262914775	2		819	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540654	NA	P-0042021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	81	819	1	ENST00000269305.4:c.329G>A	p.Arg110His	p.R110H	ENST00000269305	NM_001126112.2	110	cGt/cAt	4/11	1	2	FACETS	0.887	0.785	0.996	0.887	0.785	0.996	CLONAL	1	TRUE	1	0.409447262914775	2		820	446	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720654	89720654	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	64	101	0	ENST00000371953.3:c.808del	p.Met270CysfsTer6	p.M270Cfs*6	ENST00000371953	NM_000314.4	269	Aaa/aa	8/9	0.395968929831594	5	FACETS	1	0.896	1	1	0.896	1	CLONAL	3	FALSE	2	0.589234499574683	5		101	136	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844245	68844245	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs878854697	NA	P-0042029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	83	227	0	ENST00000261769.5:c.832+1G>T		p.X278_splice	ENST00000261769	NM_004360.3	278			0.593537134926463	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	FALSE	0	0.589234499574683	2		227	128	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	116	759	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.943	0.859	1	0.943	0.859	1	CLONAL	1	TRUE	1	0.67401609798782	2		760	365	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710643	40710643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151076965	NA	P-0042119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	112	826	0	ENST00000373198.4:c.4208G>A	p.Arg1403His	p.R1403H	ENST00000373198	NM_133170.3	1403	cGt/cAt	31/32	0.153929726214754	3	FACETS	0.674	0.607	0.745	0.225	0.202	0.249	INDETERMINATE	1	TRUE	0	0.67401609798782	3		826	659	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726950	46726950	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775691979	NA	P-0042119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	314	682	1	ENST00000371975.4:c.784C>T	p.Arg262Cys	p.R262C	ENST00000371975	NM_003579.3	262	Cgt/Tgt	8/18	0.384871324154908	3	FACETS	0.827	0.785	0.87	0.827	0.785	0.87	INDETERMINATE	2	TRUE	1	0.67401609798782	3		683	753	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692938	89692938	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	274	904	0	ENST00000371953.3:c.422A>T	p.His141Leu	p.H141L	ENST00000371953	NM_000314.4	141	cAt/cTt	5/9	0.67401609798782	1	FACETS	0.946	0.897	0.995	0.946	0.897	0.995	CLONAL	1	TRUE	0	0.67401609798782	1		904	570	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425647	49425647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	229	1066	0	ENST00000301067.7:c.12841C>T	p.Pro4281Ser	p.P4281S	ENST00000301067	NM_003482.3	4281	Cct/Tct	39/54	NA	2	FACETS	0.927	0.867	0.988			1	INDETERMINATE	1	TRUE	NA	0.67401609798782	2		1066	733	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755462	39755462	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1403874321	NA	P-0042119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	186	791	0	ENST00000288319.7:c.1303C>A	p.Pro435Thr	p.P435T	ENST00000288319	NM_182918.3	435	Cct/Act	10/10	0.67401609798782	3	FACETS	1	0.941	1	0.509	0.471	0.548	CLONAL	1	TRUE	1	0.67401609798782	3		791	725	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0042122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	123	644	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.247009518918682	2	FACETS	0.992	0.902	1	0.992	0.902	1	CLONAL	2	TRUE	0	0.247009518918682	2		644	502	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426121	47426121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519786	NA	P-0042122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	184	492	0	ENST00000377045.4:c.641C>T	p.Ser214Phe	p.S214F	ENST00000377045	NM_001654.4	214	tCc/tTc	7/16	0.245987617882267	2	FACETS	1	0.952	1			1	CLONAL	4	TRUE	NA	0.247009518918682	2		492	366	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0042137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	133	686	0	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	0.490324064697357	1	FACETS	0.717	0.654	0.783	0.717	0.654	0.783	SUBCLONAL	1	TRUE	0	0.495469678629881	1		686	563	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229069	36229069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	151	985	1	ENST00000222270.7:c.7849C>T	p.Arg2617Trp	p.R2617W	ENST00000222270	NM_014727.1	2617	Cgg/Tgg	36/37	0.45504925865256	1	FACETS	0.449	0.409	0.49	0.449	0.409	0.49	SUBCLONAL	1	TRUE	0	0.495469678629881	1		986	1022	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282202	38282202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	64	823	1	ENST00000425967.3:c.854G>A	p.Arg285Gln	p.R285Q	ENST00000425967	NM_001174067.1	285	cGg/cAg	8/19	0.238265730544423	2	FACETS	0.293	0.253	0.337	0.146	0.126	0.169	INDETERMINATE	1	TRUE	0	0.495469678629881	2		824	882	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858895	57858895	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	212	725	0	ENST00000228682.2:c.391C>T	p.Pro131Ser	p.P131S	ENST00000228682	NM_005269.2	131	Cca/Tca	5/12	0.488388798134706	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.495469678629881	1		725	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578259	7578259	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	237	821	0	ENST00000269305.4:c.590del	p.Val197GlyfsTer50	p.V197Gfs*50	ENST00000269305	NM_001126112.2	197	gTg/gg	6/11	0.495469678629881	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.495469678629881	1		821	669	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0042143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	134	243	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.577765558105754	2		243	424	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061193	38061193	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	163	471	0	ENST00000250448.2:c.796T>G	p.Phe266Val	p.F266V	ENST00000250448	NM_004496.3	266	Ttc/Gtc	2/2	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.577765558105754	2		471	528	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524435	44524435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	110	278	0	ENST00000291552.4:c.122C>T	p.Thr41Met	p.T41M	ENST00000291552	NM_006758.2	41	aCg/aTg	2/8	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.577765558105754	NA		278	425	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180555	56180555	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	195	380	0	ENST00000399503.3:c.3884del	p.Ile1295LysfsTer3	p.I1295Kfs*3	ENST00000399503	NM_005921.1	1295	aTa/aa	16/20	0.540697406819192	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.577765558105754	2		380	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0042157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	192	626	3	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.255537867882245	2	FACETS	1	0.99	1	0.731	0.676	0.788	CLONAL	1	TRUE	0	0.269305872581257	2		629	975	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0042157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	196	773	1	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.255537867882245	2	FACETS	1	0.987	1	0.658	0.608	0.71	CLONAL	1	TRUE	0	0.269305872581257	2		774	1106	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575152	48575152	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	40	292	0	ENST00000342988.3:c.346C>T	p.Gln116Ter	p.Q116*	ENST00000342988	NM_005359.5	116	Cag/Tag	3/12	0.203553479527447	2	FACETS	0.689	0.573	0.818	0.345	0.286	0.409	SUBCLONAL	1	TRUE	0	0.269305872581257	2		292	431	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806689	1806689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	84	616	0	ENST00000260795.2:c.1405C>T	p.Arg469Trp	p.R469W	ENST00000260795		469	Cgg/Tgg	9/17	0.255537867882245	2	FACETS	0.646	0.57	0.729	0.323	0.285	0.365	SUBCLONAL	1	TRUE	0	0.269305872581257	2		616	965	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101683	27101683	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	102	762	0	ENST00000324856.7:c.4965G>C	p.Gln1655His	p.Q1655H	ENST00000324856	NM_006015.4	1655	caG/caC	18/20	NA	2	FACETS	0.654	0.583	0.729			1	INDETERMINATE	1	TRUE	NA	0.269305872581257	2		762	1159	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724968	162724968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	50	429	0	ENST00000367921.3:c.440C>T	p.Pro147Leu	p.P147L	ENST00000367921	NM_006182.2	147	cCc/cTc	6/18	0.241984107284411	4	FACETS	0.632	0.535	0.739	0.158	0.133	0.185	SUBCLONAL	1	TRUE	0	0.269305872581257	4		429	746	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46275849	46275849	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	68	599	0	ENST00000371998.3:c.3285C>A	p.Phe1095Leu	p.F1095L	ENST00000371998		1095	ttC/ttA	18/23	0.189353763815811	4	FACETS	0.612	0.53	0.7	0.306	0.265	0.35	SUBCLONAL	1	TRUE	2	0.269305872581257	4		599	1048	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182313	38182313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	47	506	0	ENST00000396334.3:c.749C>T	p.Thr250Ile	p.T250I	ENST00000396334	NM_002468.4	250	aCc/aTc	4/5	0.155898062544007	3	FACETS	0.516	0.434	0.606	0.258	0.217	0.303	INDETERMINATE	1	TRUE	1	0.269305872581257	3		506	768	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339974	116339974	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	152	376	0	ENST00000397752.3:c.836T>C	p.Ile279Thr	p.I279T	ENST00000397752	NM_000245.2	279	aTc/aCc	2/21	0.141100900616209	4	FACETS	1	0.976	1	1	0.976	1	INDETERMINATE	2	TRUE	2	0.269305872581257	4		376	615	SUCCESS
AR	367	MSKCC	GRCh37	X	66765269	66765269	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	62	337	0	ENST00000374690.3:c.281A>G	p.Asp94Gly	p.D94G	ENST00000374690	NM_000044.3	94	gAt/gGt	1/8	0.269305872581257	2	FACETS	1	0.913	1			1	CLONAL	1	TRUE	NA	0.269305872581257	2		337	430	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0042161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	79	368	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	0.284545042171118	3	FACETS	0.898	0.791	1	0.449	0.395	0.507	CLONAL	1	TRUE	1	0.33890810141234	3		368	607	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509420	106509420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622026	NA	P-0042161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	125	708	0	ENST00000359195.3:c.1414C>T	p.Arg472Cys	p.R472C	ENST00000359195	NM_002649.2	472	Cgt/Tgt	2/11	0.284545042171118	3	FACETS	1	0.907	1	0.501	0.453	0.552	CLONAL	1	TRUE	1	0.33890810141234	3		708	861	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611108	100611108	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	122	754	0	ENST00000308731.7:c.1498G>A	p.Glu500Lys	p.E500K	ENST00000308731	NM_000061.2	500	Gag/Aag	15/19	1	2	FACETS	0.961	0.869	1	0.961	0.869	1	CLONAL	1	TRUE	1	0.33890810141234	2		754	749	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624274	89624274	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs587782187	NA	P-0042161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	67	456	0	ENST00000371953.3:c.48T>G	p.Tyr16Ter	p.Y16*	ENST00000371953	NM_000314.4	16	taT/taG	1/9	0.33890810141234	3	FACETS	0.894	0.778	1	0.447	0.389	0.51	CLONAL	1	TRUE	1	0.33890810141234	3		456	517	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711892	89711892	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121909221	NA	P-0042161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	132	464	0	ENST00000371953.3:c.510T>A	p.Ser170Arg	p.S170R	ENST00000371953	NM_000314.4	170	agT/agA	6/9	0.33890810141234	3	FACETS	0.951	0.869	1	0.951	0.869	1	CLONAL	2	TRUE	1	0.33890810141234	3		464	479	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563357	21563357	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs185326327	NA	P-0042161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	147	1001	0	ENST00000382592.4:c.562G>A	p.Gly188Ser	p.G188S	ENST00000382592	NM_014572.2	188	Ggt/Agt	4/8	1	2	FACETS	0.89	0.812	0.972	0.89	0.812	0.972	CLONAL	1	TRUE	1	0.33890810141234	2		1001	975	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023932	27023939	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCCG	GGCGGCCG	-	novel	NA	P-0042161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	26	78	0	ENST00000324856.7:c.1038_1045del	p.Ala347LeufsTer50	p.A347Lfs*50	ENST00000324856	NM_006015.4	346	gcGGCGGCCGcc/gccc	1/20	1	2	FACETS	0.767	0.621	0.926	1	0.941	1	CLONAL	2	TRUE	1	0.33890810141234	2		78	100	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458895	120458896	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1553193574	NA	P-0042161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	113	798	0	ENST00000256646.2:c.6449_6450del	p.Pro2150ArgfsTer2	p.P2150Rfs*2	ENST00000256646	NM_024408.3	2150	cCT/c	34/34	1	2	FACETS	0.937	0.844	1	0.937	0.844	1	CLONAL	1	TRUE	1	0.33890810141234	2		798	712	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591081	67591082	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATTGACAAACGTATGAACAGCATT	novel	NA	P-0042161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	43	355	0	ENST00000274335.5:c.1676_1699dup	p.Ile559_Ile566dup	p.I559_I566dup	ENST00000274335		559	-/ATTGACAAACGTATGAACAGCATT	12/15	0.254945164105533	3	FACETS	0.689	0.577	0.812	0.344	0.288	0.406	SUBCLONAL	1	TRUE	1	0.33890810141234	3		355	431	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115269609	115269609	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	69	733	0	ENST00000438362.2:c.1597G>T	p.Asp533Tyr	p.D533Y	ENST00000438362	NM_001242891.1	533	Gat/Tat	13/20	0.237911774333287	2	FACETS	0.422	0.367	0.482	0.211	0.183	0.241	INDETERMINATE	1	TRUE	0	0.418887851829296	2		733	780	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528159	157528159	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	206	579	0	ENST00000346085.5:c.5884G>C	p.Asp1962His	p.D1962H	ENST00000346085	NM_020732.3	1962	Gat/Cat	20/20	1	2	FACETS	0.587	0.545	0.63	0.587	0.545	0.63	SUBCLONAL	1	TRUE	1	0.765607491805277	2		579	917	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228816	36228816	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867499379	NA	P-0042218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1615	98	770	0	ENST00000222270.7:c.7715C>T	p.Thr2572Met	p.T2572M	ENST00000222270	NM_014727.1	2572	aCg/aTg	35/37	0.578748134013179	3	FACETS	0.207	0.183	0.232	0.103	0.091	0.116	SUBCLONAL	1	TRUE	1	0.765607491805277	3		770	1713	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554935	187554935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	264	370	0	ENST00000441802.2:c.4226G>T	p.Gly1409Val	p.G1409V	ENST00000441802	NM_005245.3	1409	gGa/gTa	7/27	0.765607491805277	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.765607491805277	1		370	416	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527517	157527517	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554237164	NA	P-0042218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	162	464	0	ENST00000346085.5:c.5242G>T	p.Glu1748Ter	p.E1748*	ENST00000346085	NM_020732.3	1748	Gag/Tag	20/20	1	2	FACETS	0.504	0.462	0.547	0.504	0.462	0.547	SUBCLONAL	1	TRUE	1	0.765607491805277	2		464	840	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527966	157527966	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	220	585	0	ENST00000346085.5:c.5691G>C	p.Gln1897His	p.Q1897H	ENST00000346085	NM_020732.3	1897	caG/caC	20/20	1	2	FACETS	0.597	0.555	0.64	0.597	0.555	0.64	SUBCLONAL	1	TRUE	1	0.765607491805277	2		585	963	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528104	157528104	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	156	549	0	ENST00000346085.5:c.5829G>C	p.Lys1943Asn	p.K1943N	ENST00000346085	NM_020732.3	1943	aaG/aaC	20/20	1	2	FACETS	0.485	0.444	0.527	0.485	0.444	0.527	SUBCLONAL	1	TRUE	1	0.765607491805277	2		549	841	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104575	69104575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	231	622	1	ENST00000288368.4:c.4419G>A	p.Met1473Ile	p.M1473I	ENST00000288368	NM_024870.2	1473	atG/atA	37/40	0.242753931620942	5	FACETS	0.932	0.867	1	0.311	0.289	0.334	INDETERMINATE	1	TRUE	2	0.765607491805277	5		623	1391	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	200	759	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.999	0.937	1	0.999	0.937	1	CLONAL	1	TRUE	1	0.920850308097279	2		760	435	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225940	2225940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	378	461	0	ENST00000326181.6:c.1732G>A	p.Glu578Lys	p.E578K	ENST00000326181	NM_032271.2	578	Gag/Aag	18/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.920850308097279	2		461	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0042246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	464	780	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.996	0.955	1	0.996	0.955	1	CLONAL	1	TRUE	1	0.920850308097279	2		780	1012	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782006	NA	P-0042246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	485	519	0	ENST00000269305.4:c.859G>A	p.Glu287Lys	p.E287K	ENST00000269305	NM_001126112.2	287	Gag/Aag	8/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.920850308097279	2		519	1045	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	480	542	0	ENST00000269305.4:c.380C>A	p.Ser127Tyr	p.S127Y	ENST00000269305	NM_001126112.2	127	tCc/tAc	5/11	1	2	FACETS	0.934	0.896	0.973	0.934	0.896	0.973	CLONAL	1	TRUE	1	0.920850308097279	2		542	1116	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789661	3789661	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	264	342	0	ENST00000262367.5:c.4198G>C	p.Glu1400Gln	p.E1400Q	ENST00000262367	NM_004380.2	1400	Gag/Cag	25/31	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.920850308097279	2		342	540	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370822	225370822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1265558901	NA	P-0042246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	38	231	0	ENST00000264414.4:c.1057G>A	p.Asp353Asn	p.D353N	ENST00000264414	NM_003590.4	353	Gat/Aat	8/16	1	2	FACETS	0.598	0.504	0.699	0.598	0.504	0.699	SUBCLONAL	1	TRUE	1	0.920850308097279	2		231	138	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161272	185161272	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	141	360	0	ENST00000265026.3:c.699G>A	p.Met233Ile	p.M233I	ENST00000265026	NM_004721.4	233	atG/atA	4/14	1	2	FACETS	0.934	0.864	1	0.934	0.864	1	CLONAL	1	TRUE	1	0.920850308097279	2		360	328	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149488	61149488	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1460557137	NA	P-0042246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	71	198	0	ENST00000295025.8:c.1678G>C	p.Asp560His	p.D560H	ENST00000295025	NM_002908.2	560	Gat/Cat	11/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.920850308097279	2		198	136	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099479	27099479	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0042246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	131	235	0	ENST00000324856.7:c.3715+1G>C		p.X1239_splice	ENST00000324856	NM_006015.4	1239			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.920850308097279	2		235	267	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102067	27102068	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0042246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	171	346	0	ENST00000324856.7:c.4994-1_4994delinsTT		p.X1665_splice	ENST00000324856	NM_006015.4	1665		19/20	1	2	FACETS	0.787	0.73	0.844	0.787	0.73	0.844	SUBCLONAL	1	TRUE	1	0.920850308097279	2		346	472	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163325131	163325131	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	75	139	0	ENST00000271452.3:c.1267T>A	p.Phe423Ile	p.F423I	ENST00000271452	NM_145697.2	423	Ttt/Att	14/14	0.920850308097279	4	FACETS	0.948	0.873	1	0.948	0.873	1	CLONAL	3	TRUE	1	0.920850308097279	4		139	110	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149245720	149245720	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	232	332	0	ENST00000360632.3:c.808G>C	p.Glu270Gln	p.E270Q	ENST00000360632	NM_015472.4	270	Gag/Cag	5/7	1	2	FACETS	0.958	0.902	1	0.958	0.902	1	CLONAL	1	TRUE	1	0.920850308097279	2		332	526	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976821	55976821	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	197	360	1	ENST00000263923.4:c.1091G>A	p.Trp364Ter	p.W364*	ENST00000263923	NM_002253.2	364	tGg/tAg	8/30	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.920850308097279	2		361	381	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016258	150016258	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	99	218	0	ENST00000253339.5:c.448C>T	p.Gln150Ter	p.Q150*	ENST00000253339		150	Cag/Tag	2/7	1	2	FACETS	0.785	0.711	0.86	0.785	0.711	0.86	SUBCLONAL	1	TRUE	1	0.920850308097279	2		218	274	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150022920	150022920	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	43	208	1	ENST00000253339.5:c.343G>C	p.Asp115His	p.D115H	ENST00000253339		115	Gat/Cat	1/7	1	2	FACETS	0.826	0.712	0.946	0.826	0.712	0.946	CLONAL	1	TRUE	1	0.920850308097279	2		209	113	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405892	157405892	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1461225115	NA	P-0042246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	33	279	0	ENST00000346085.5:c.2134C>T	p.Gln712Ter	p.Q712*	ENST00000346085	NM_020732.3	712	Cag/Tag	6/20	1	2	FACETS	0.137	0.111	0.166	0.137	0.111	0.166	SUBCLONAL	1	TRUE	1	0.920850308097279	2		279	523	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411174	63411174	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	245	205	0	ENST00000330258.3:c.1993G>T	p.Gly665Cys	p.G665C	ENST00000330258	NM_152424.3	665	Ggc/Tgc	2/2	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.920850308097279	1		205	254	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	87	821	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.825	0.729	0.928	0.825	0.729	0.928	CLONAL	1	TRUE	1	0.22	2		822	959	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	65	409	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.796	0.689	0.913	0.796	0.689	0.913	CLONAL	1	TRUE	1	0.22	2		409	742	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	52	321	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.949	0.809	1	0.949	0.809	1	CLONAL	1	TRUE	1	0.22	2		321	498	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660469	67660469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	61	288	0	ENST00000264010.4:c.1369C>T	p.Arg457Ter	p.R457*	ENST00000264010	NM_006565.3	457	Cga/Tga	8/12	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.22	2		288	525	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013719	170013719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388201066	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	52	246	1	ENST00000295797.4:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000295797	NM_002740.5	480	Cgc/Tgc	15/18	1	2	FACETS	0.936	0.797	1	0.936	0.797	1	CLONAL	1	TRUE	1	0.22	2		247	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	91	574	1	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	1	2	FACETS	0.855	0.757	0.959	0.855	0.757	0.959	CLONAL	1	TRUE	1	0.22	2		575	968	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	62	485	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	0.795	0.686	0.914	0.795	0.686	0.914	CLONAL	1	TRUE	1	0.22	2		485	709	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803818	43803818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147938568	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	46	618	0	ENST00000372470.3:c.128G>A	p.Arg43Gln	p.R43Q	ENST00000372470	NM_005373.2	43	cGa/cAa	2/12	1	2	FACETS	0.5	0.419	0.589	0.5	0.419	0.589	SUBCLONAL	1	TRUE	1	0.22	2		618	837	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50481162	50481162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	63	315	0	ENST00000394963.4:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000394963	NM_003076.4	183	cGa/cAa	5/13	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.22	2		315	532	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690847	89690847	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776667	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	27	199	0	ENST00000371953.3:c.253+1G>A		p.X85_splice	ENST00000371953	NM_000314.4	85			1	2	FACETS	0.762	0.607	0.939	0.762	0.607	0.939	CLONAL	1	TRUE	1	0.22	2		199	322	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	11	457	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.244	0.168	0.341	0.244	0.168	0.341	SUBCLONAL	1	TRUE	1	0.22	2		457	409	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021428	42021428	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	53	332	1	ENST00000219905.7:c.3724C>T	p.Arg1242Ter	p.R1242*	ENST00000219905	NM_001164273.1	1242	Cga/Tga	11/24	1	2	FACETS	0.911	0.777	1	0.911	0.777	1	CLONAL	1	TRUE	1	0.22	2		333	529	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267600319	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	45	220	0	ENST00000257430.4:c.4199C>T	p.Ser1400Leu	p.S1400L	ENST00000257430	NM_000038.5	1400	tCg/tTg	16/16	1	2	FACETS	0.986	0.83	1	0.986	0.83	1	CLONAL	1	TRUE	1	0.22	2		220	415	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622419	28622419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776699712	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	41	259	2	ENST00000241453.7:c.1198G>A	p.Gly400Arg	p.G400R	ENST00000241453	NM_004119.2	400	Gga/Aga	9/24	1	2	FACETS	0.853	0.711	1	0.853	0.711	1	CLONAL	1	TRUE	1	0.22	2		261	437	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939417	76939417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781932965	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	60	462	0	ENST00000373344.5:c.1331G>A	p.Arg444Gln	p.R444Q	ENST00000373344	NM_000489.3	444	cGa/cAa	9/35	1	2	FACETS	0.795	0.684	0.916	0.795	0.684	0.916	CLONAL	1	TRUE	1	0.22	2		462	686	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649000	86649000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755634472	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	25	183	1	ENST00000274376.6:c.1280G>A	p.Arg427Gln	p.R427Q	ENST00000274376	NM_002890.2	427	cGa/cAa	9/25	1	2	FACETS	0.661	0.521	0.821	0.661	0.521	0.821	SUBCLONAL	1	TRUE	1	0.22	2		184	344	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662700	117662700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	41	297	0	ENST00000368508.3:c.4765G>A	p.Glu1589Lys	p.E1589K	ENST00000368508	NM_002944.2	1589	Gaa/Aaa	29/43	1	2	FACETS	0.849	0.708	1	0.849	0.708	1	CLONAL	1	TRUE	1	0.22	2		297	439	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	73	373	0	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.22	2		373	651	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205756	108205756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531980488	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	40	257	0	ENST00000278616.4:c.8071C>T	p.Arg2691Cys	p.R2691C	ENST00000278616	NM_000051.3	2691	Cgc/Tgc	55/63	1	2	FACETS	0.876	0.729	1	0.876	0.729	1	CLONAL	1	TRUE	1	0.22	2		257	415	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003283	42003283	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	38	439	0	ENST00000219905.7:c.2820G>T	p.Lys940Asn	p.K940N	ENST00000219905	NM_001164273.1	940	aaG/aaT	8/24	1	2	FACETS	0.482	0.398	0.578	0.482	0.398	0.578	SUBCLONAL	1	TRUE	1	0.22	2		439	716	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87322770	87322770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781137734	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	26	243	0	ENST00000277120.3:c.371G>A	p.Arg124Gln	p.R124Q	ENST00000277120		124	cGa/cAa	5/19	1	2	FACETS	0.579	0.458	0.718	0.579	0.458	0.718	SUBCLONAL	1	TRUE	1	0.22	2		243	408	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610695	52610695	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	55	202	0	ENST00000394830.3:c.3478C>T	p.Arg1160Ter	p.R1160*	ENST00000394830	NM_018313.4	1160	Cga/Tga	23/30	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.22	2		202	431	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011200	12011200	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	30	197	0	ENST00000353533.5:c.607G>T	p.Glu203Ter	p.E203*	ENST00000353533	NM_003010.3	203	Gaa/Taa	5/11	1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	1	0.22	2		197	258	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710983	117710983	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	37	148	0	ENST00000368508.3:c.1289G>A	p.Gly430Asp	p.G430D	ENST00000368508	NM_002944.2	430	gGc/gAc	12/43	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.22	2		148	268	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	48	279	0	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	1	2	FACETS	0.822	0.695	0.962	0.822	0.695	0.962	CLONAL	1	TRUE	1	0.22	2		279	531	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059183	27059183	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	36	245	0	ENST00000324856.7:c.1820C>A	p.Ser607Ter	p.S607*	ENST00000324856	NM_006015.4	607	tCa/tAa	4/20	1	2	FACETS	0.651	0.534	0.781	0.651	0.534	0.781	SUBCLONAL	1	TRUE	1	0.22	2		245	503	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256589	115256589	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	55	258	2	ENST00000369535.4:c.122G>T	p.Arg41Ile	p.R41I	ENST00000369535	NM_002524.4	41	aGa/aTa	3/7	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.22	2		260	439	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521385	187521385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426195084	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	43	361	0	ENST00000441802.2:c.11770C>T	p.Arg3924Cys	p.R3924C	ENST00000441802	NM_005245.3	3924	Cgc/Tgc	22/27	1	2	FACETS	0.654	0.546	0.773	0.654	0.546	0.773	SUBCLONAL	1	TRUE	1	0.22	2		361	598	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95592924	95592924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755944755	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	33	201	0	ENST00000393063.1:c.896C>T	p.Ser299Leu	p.S299L	ENST00000393063	NM_030621.3	299	tCg/tTg	8/28	1	2	FACETS	0.89	0.726	1	0.89	0.726	1	CLONAL	1	TRUE	1	0.22	2		201	337	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095644	178095644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763240080	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	33	254	0	ENST00000397062.3:c.1687G>A	p.Glu563Lys	p.E563K	ENST00000397062	NM_006164.4	563	Gaa/Aaa	5/5	1	2	FACETS	0.706	0.575	0.854	0.706	0.575	0.854	SUBCLONAL	1	TRUE	1	0.22	2		254	425	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103196	119103196	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	54	343	0	ENST00000264033.4:c.234G>T	p.Lys78Asn	p.K78N	ENST00000264033	NM_005188.3	78	aaG/aaT	2/16	1	2	FACETS	0.832	0.71	0.965	0.832	0.71	0.965	CLONAL	1	TRUE	1	0.22	2		343	590	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39708808	39708808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs183058581	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	33	181	0	ENST00000361337.2:c.419G>A	p.Arg140Gln	p.R140Q	ENST00000361337	NM_003286.2	140	cGa/cAa	6/21	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.22	2		181	266	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468381	89468381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754102338	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	28	136	0	ENST00000336596.2:c.1915C>T	p.Arg639Cys	p.R639C	ENST00000336596	NM_005233.5	639	Cgc/Tgc	11/17	1	2	FACETS	0.987	0.792	1	0.987	0.792	1	CLONAL	1	TRUE	1	0.22	2		136	258	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188404	32188404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763926116	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	73	422	0	ENST00000375023.3:c.937G>A	p.Glu313Lys	p.E313K	ENST00000375023	NM_004557.3	313	Gaa/Aaa	6/30	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.22	2		422	617	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268950	115268950	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs750855257	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	39	371	0	ENST00000438362.2:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000438362	NM_001242891.1	554	Cga/Tga	14/20	1	2	FACETS	0.539	0.445	0.644	0.539	0.445	0.644	SUBCLONAL	1	TRUE	1	0.22	2		371	658	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871249	35871249	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	32	302	0	ENST00000303115.3:c.471G>T	p.Lys157Asn	p.K157N	ENST00000303115	NM_002185.3	157	aaG/aaT	4/8	1	2	FACETS	0.66	0.535	0.801	0.66	0.535	0.801	SUBCLONAL	1	TRUE	1	0.22	2		302	441	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990631	7990631	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	82	440	0	ENST00000319144.4:c.130G>T	p.Asp44Tyr	p.D44Y	ENST00000319144	NM_001139.2	44	Gac/Tac	1/15	1	2	FACETS	0.792	0.697	0.895	0.792	0.697	0.895	SUBCLONAL	1	TRUE	1	0.22	2		440	941	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930564	32930564	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	21	193	0	ENST00000380152.3:c.7436-1G>T		p.X2479_splice	ENST00000380152		2479			1	2	FACETS	0.568	0.437	0.721	0.568	0.437	0.721	SUBCLONAL	1	TRUE	1	0.22	2		193	336	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917635	94917635	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	68	345	0	ENST00000536441.1:c.886G>T	p.Glu296Ter	p.E296*	ENST00000536441	NM_144665.3	296	Gaa/Taa	6/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.22	2		345	487	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31472304	31472304	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	35	368	0	ENST00000344624.3:c.2107C>A	p.Leu703Ile	p.L703I	ENST00000344624		703	Ctc/Atc	14/33	1	2	FACETS	0.488	0.399	0.589	0.488	0.399	0.589	SUBCLONAL	1	TRUE	1	0.22	2		368	652	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951934	178951934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	51	276	0	ENST00000263967.3:c.2989C>T	p.Leu997Phe	p.L997F	ENST00000263967	NM_006218.2	997	Ctc/Ttc	21/21	1	2	FACETS	0.997	0.849	1	0.997	0.849	1	CLONAL	1	TRUE	1	0.22	2		276	465	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242718	16242718	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	55	392	0	ENST00000375759.3:c.1339A>C	p.Lys447Gln	p.K447Q	ENST00000375759	NM_015001.2	447	Aaa/Caa	6/15	1	2	FACETS	0.779	0.666	0.903	0.779	0.666	0.903	CLONAL	1	TRUE	1	0.22	2		392	642	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117000	193117000	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	34	202	0	ENST00000367435.3:c.733T>A	p.Phe245Ile	p.F245I	ENST00000367435	NM_024529.4	245	Ttt/Att	8/17	1	2	FACETS	0.84	0.687	1	0.84	0.687	1	CLONAL	1	TRUE	1	0.22	2		202	368	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375222	118375222	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	55	270	0	ENST00000534358.1:c.8615C>A	p.Ser2872Ter	p.S2872*	ENST00000534358	NM_005933.3	2872	tCa/tAa	27/36	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.22	2		270	410	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953649	32953649	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	32	259	0	ENST00000380152.3:c.8950T>G	p.Ser2984Ala	p.S2984A	ENST00000380152		2984	Tca/Gca	22/27	1	2	FACETS	0.941	0.766	1	0.941	0.766	1	CLONAL	1	TRUE	1	0.22	2		259	309	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504563	103504563	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	30	230	0	ENST00000355739.4:c.184C>T	p.Leu62Phe	p.L62F	ENST00000355739	NM_000123.3	62	Ctc/Ttc	2/15	1	2	FACETS	0.775	0.625	0.944	0.775	0.625	0.944	CLONAL	1	TRUE	1	0.22	2		230	352	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103513946	103513946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	33	234	0	ENST00000355739.4:c.762G>T	p.Met254Ile	p.M254I	ENST00000355739	NM_000123.3	254	atG/atT	7/15	1	2	FACETS	0.758	0.617	0.916	0.758	0.617	0.916	CLONAL	1	TRUE	1	0.22	2		234	396	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042352	42042352	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1034708867	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	49	431	1	ENST00000219905.7:c.6547A>G	p.Thr2183Ala	p.T2183A	ENST00000219905	NM_001164273.1	2183	Acc/Gcc	17/24	1	2	FACETS	0.734	0.621	0.859	0.734	0.621	0.859	SUBCLONAL	1	TRUE	1	0.22	2		432	607	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3794909	3794909	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1305897515	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	44	311	0	ENST00000262367.5:c.3968A>C	p.Lys1323Thr	p.K1323T	ENST00000262367	NM_004380.2	1323	aAa/aCa	23/31	1	2	FACETS	0.697	0.584	0.822	0.697	0.584	0.822	SUBCLONAL	1	TRUE	1	0.22	2		311	574	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645195	67645195	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	86	543	0	ENST00000264010.4:c.460A>G	p.Ile154Val	p.I154V	ENST00000264010	NM_006565.3	154	Ata/Gta	3/12	1	2	FACETS	0.869	0.767	0.978	0.869	0.767	0.978	CLONAL	1	TRUE	1	0.22	2		543	900	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350510	89350510	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	72	487	0	ENST00000301030.4:c.2440T>G	p.Phe814Val	p.F814V	ENST00000301030	NM_001256183.1	814	Ttt/Gtt	9/13	1	2	FACETS	0.716	0.624	0.816	0.716	0.624	0.816	SUBCLONAL	1	TRUE	1	0.22	2		487	914	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352467	89352467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	86	511	0	ENST00000301030.4:c.872C>T	p.Ser291Phe	p.S291F	ENST00000301030	NM_001256183.1	291	tCc/tTc	8/13	1	2	FACETS	0.892	0.788	1	0.892	0.788	1	CLONAL	1	TRUE	1	0.22	2		511	876	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320332	30320332	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	49	226	0	ENST00000322652.5:c.1273A>C	p.Lys425Gln	p.K425Q	ENST00000322652	NM_015355.2	425	Aaa/Caa	11/16	1	2	FACETS	0.999	0.847	1	0.999	0.847	1	CLONAL	1	TRUE	1	0.22	2		226	446	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246494	41246494	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs80357472	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	68	445	0	ENST00000357654.3:c.1054G>T	p.Glu352Ter	p.E352*	ENST00000357654	NM_007294.3	352	Gaa/Taa	10/23	1	2	FACETS	0.861	0.748	0.983	0.861	0.748	0.983	CLONAL	1	TRUE	1	0.22	2		445	718	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39240665	39240665	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	38	258	0	ENST00000402219.2:c.2103C>A	p.Phe701Leu	p.F701L	ENST00000402219	NM_005633.3	701	ttC/ttA	13/23	1	2	FACETS	0.8	0.661	0.954	0.8	0.661	0.954	CLONAL	1	TRUE	1	0.22	2		258	432	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721151	61721151	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	46	343	0	ENST00000401558.2:c.1123C>A	p.His375Asn	p.H375N	ENST00000401558	NM_003400.3	375	Cat/Aat	12/25	1	2	FACETS	0.697	0.586	0.82	0.697	0.586	0.82	SUBCLONAL	1	TRUE	1	0.22	2		343	600	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268799	41268799	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	27	330	0	ENST00000349496.5:c.1037T>A	p.Val346Glu	p.V346E	ENST00000349496	NM_001904.3	346	gTg/gAg	7/15	1	2	FACETS	0.5	0.397	0.618	0.5	0.397	0.618	SUBCLONAL	1	TRUE	1	0.22	2		330	491	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155394	47155394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	62	310	0	ENST00000409792.3:c.4687G>A	p.Gly1563Ser	p.G1563S	ENST00000409792	NM_014159.6	1563	Ggc/Agc	5/21	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.22	2		310	536	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163347	47163347	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	39	212	0	ENST00000409792.3:c.2779G>T	p.Glu927Ter	p.E927*	ENST00000409792	NM_014159.6	927	Gaa/Taa	3/21	1	2	FACETS	0.948	0.787	1	0.948	0.787	1	CLONAL	1	TRUE	1	0.22	2		212	374	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155539	106155539	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs779231977	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	42	260	0	ENST00000380013.4:c.440A>C	p.Lys147Thr	p.K147T	ENST00000380013	NM_001127208.2	147	aAg/aCg	3/11	1	2	FACETS	0.957	0.8	1	0.957	0.8	1	CLONAL	1	TRUE	1	0.22	2		260	399	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003332	143003332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752612658	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	67	351	0	ENST00000262992.4:c.2494C>T	p.Arg832Cys	p.R832C	ENST00000262992	NM_001101669.1	832	Cgc/Tgc	23/24	1	2	FACETS	0.888	0.771	1	0.888	0.771	1	CLONAL	1	TRUE	1	0.22	2		351	686	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542078	187542078	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	46	284	0	ENST00000441802.2:c.5662C>A	p.Leu1888Ile	p.L1888I	ENST00000441802	NM_005245.3	1888	Ctt/Att	10/27	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.22	2		284	411	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31405827	31405827	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	20	158	0	ENST00000344624.3:c.3951T>G	p.Ile1317Met	p.I1317M	ENST00000344624		1317	atT/atG	32/33	1	2	FACETS	0.608	0.465	0.775	0.608	0.465	0.775	SUBCLONAL	1	TRUE	1	0.22	2		158	299	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876208	35876208	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	50	357	0	ENST00000303115.3:c.1000G>T	p.Glu334Ter	p.E334*	ENST00000303115	NM_002185.3	334	Gaa/Taa	8/8	1	2	FACETS	0.749	0.635	0.875	0.749	0.635	0.875	SUBCLONAL	1	TRUE	1	0.22	2		357	607	SUCCESS
APC	324	MSKCC	GRCh37	5	112111406	112111406	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	23	188	0	ENST00000257430.4:c.503G>T	p.Arg168Ile	p.R168I	ENST00000257430	NM_000038.5	168	aGa/aTa	5/16	1	2	FACETS	0.78	0.61	0.977	0.78	0.61	0.977	CLONAL	1	TRUE	1	0.22	2		188	268	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944857	131944857	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	11	147	0	ENST00000265335.6:c.2878G>T	p.Asp960Tyr	p.D960Y	ENST00000265335		960	Gac/Tac	18/25	1	2	FACETS	0.508	0.351	0.702	0.508	0.351	0.702	SUBCLONAL	1	TRUE	1	0.22	2		147	197	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670621	30670621	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	43	358	0	ENST00000376406.3:c.5899G>T	p.Glu1967Ter	p.E1967*	ENST00000376406	NM_014641.2	1967	Gaa/Taa	13/15	1	2	FACETS	0.597	0.498	0.706	0.597	0.498	0.706	SUBCLONAL	1	TRUE	1	0.22	2		358	655	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106534429	106534429	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	29	157	0	ENST00000369096.4:c.1A>G	p.Met1?	p.M1?	ENST00000369096	NM_001198.3	1	Atg/Gtg	1/7	1	2	FACETS	0.724	0.582	0.886	0.724	0.582	0.886	SUBCLONAL	1	TRUE	1	0.22	2		157	364	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555217	106555217	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	37	400	0	ENST00000369096.4:c.2334A>C	p.Arg778Ser	p.R778S	ENST00000369096	NM_001198.3	778	agA/agC	7/7	1	2	FACETS	0.497	0.408	0.596	0.497	0.408	0.596	SUBCLONAL	1	TRUE	1	0.22	2		400	677	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679070	117679070	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	43	257	0	ENST00000368508.3:c.3751G>A	p.Val1251Ile	p.V1251I	ENST00000368508	NM_002944.2	1251	Gta/Ata	24/43	1	2	FACETS	0.953	0.799	1	0.953	0.799	1	CLONAL	1	TRUE	1	0.22	2		257	410	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983517	90983517	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	24	138	0	ENST00000265433.3:c.586T>A	p.Phe196Ile	p.F196I	ENST00000265433	NM_002485.4	196	Ttt/Att	6/16	1	2	FACETS	0.957	0.753	1	0.957	0.753	1	CLONAL	1	TRUE	1	0.22	2		138	228	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8523511	8523511	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	33	179	0	ENST00000356435.5:c.691+2T>C		p.X231_splice	ENST00000356435		231			1	2	FACETS	0.796	0.649	0.961	0.796	0.649	0.961	CLONAL	1	TRUE	1	0.22	2		179	377	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133747542	133747542	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	39	339	0	ENST00000318560.5:c.849C>A	p.Phe283Leu	p.F283L	ENST00000318560	NM_005157.4	283	ttC/ttA	5/11	1	2	FACETS	0.545	0.45	0.65	0.545	0.45	0.65	SUBCLONAL	1	TRUE	1	0.22	2		339	651	SUCCESS
AR	367	MSKCC	GRCh37	X	66765865	66765865	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	120	703	0	ENST00000374690.3:c.877T>G	p.Ser293Ala	p.S293A	ENST00000374690	NM_000044.3	293	Tct/Gct	1/8	1	2	FACETS	0.927	0.835	1	0.927	0.835	1	CLONAL	1	TRUE	1	0.22	2		703	1177	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205138	123205138	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	34	247	0	ENST00000218089.9:c.2498T>C	p.Val833Ala	p.V833A	ENST00000218089	NM_001042749.1	833	gTc/gCc	25/35	1	2	FACETS	0.951	0.779	1	0.951	0.779	1	CLONAL	1	TRUE	1	0.22	2		247	325	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	74	395	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.814	0.715	0.92	0.814	0.715	0.92	CLONAL	1	TRUE	1	0.414105446393107	2		395	439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520008	NA	P-0042310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	154	781	0	ENST00000269305.4:c.613T>C	p.Tyr205His	p.Y205H	ENST00000269305	NM_001126112.2	205	Tat/Cat	6/11	0.378514217264236	1	FACETS	0.883	0.81	0.958	0.883	0.81	0.958	CLONAL	1	TRUE	0	0.414105446393107	1		781	668	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508169	106508169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381484125	NA	P-0042310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	38	410	0	ENST00000359195.3:c.163G>A	p.Glu55Lys	p.E55K	ENST00000359195	NM_002649.2	55	Gaa/Aaa	2/11	0.214135603555617	1	FACETS	0.403	0.334	0.48	0.403	0.334	0.48	INDETERMINATE	1	TRUE	0	0.414105446393107	1		410	361	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429266	78429268	+	inframe_deletion	In_Frame_Del	DEL	TAT	TAT	-	novel	NA	P-0042310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	96	371	0	ENST00000370768.2:c.1174_1176del	p.Ile392del	p.I392del	ENST00000370768	NM_003902.3	392	ATA/-	13/20	0.214135603555617	1	FACETS	0.806	0.722	0.895	0.806	0.722	0.895	INDETERMINATE	1	TRUE	0	0.414105446393107	1		371	456	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0042337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	70	243	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.811	0.708	0.922	0.811	0.708	0.922	CLONAL	1	TRUE	1	0.305578199548687	2		243	565	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114140	115114159	+	frameshift_variant	Frame_Shift_Del	DEL	AGTGGAGGCGGCTGGAGAAG	AGTGGAGGCGGCTGGAGAAG	-	novel	NA	P-0042337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	53	466	0	ENST00000257566.3:c.1058_1077del	p.Ser353CysfsTer15	p.S353Cfs*15	ENST00000257566	NM_016569.3	353	tCTTCTCCAGCCGCCTCCACT/t	6/8	1	2	FACETS	0.451	0.384	0.525	0.451	0.384	0.525	SUBCLONAL	1	TRUE	1	0.305578199548687	2		466	769	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0042508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	154	569	3	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.884	0.817	0.954	0.884	0.817	0.954	CLONAL	1	TRUE	1	0.775709516716126	2		572	449	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0042508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	127	496	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.825	0.754	0.897	0.825	0.754	0.897	CLONAL	1	TRUE	1	0.775709516716126	2		497	397	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	202	768	2	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.775709516716126	2		770	485	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0042508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	247	437	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.775709516716126	2	FACETS	0.977	0.939	1	0.977	0.939	1	CLONAL	2	TRUE	0	0.775709516716126	2		437	326	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486037	8486037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	112	559	0	ENST00000356435.5:c.2780C>T	p.Ser927Leu	p.S927L	ENST00000356435		927	tCa/tTa	17/35	1	2	FACETS	0.88	0.802	0.961	0.88	0.802	0.961	CLONAL	1	TRUE	1	0.775709516716126	2		559	328	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572810	41572810	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	186	646	1	ENST00000263253.7:c.5099del	p.Asn1700ThrfsTer9	p.N1700Tfs*9	ENST00000263253	NM_001429.3	1699	Aaa/aa	31/31	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.775709516716126	2		647	473	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0042508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	128	470	0	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.775709516716126	2		470	299	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347983	347983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760961378	NA	P-0042508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	226	923	6	ENST00000262320.3:c.1523del	p.Gly508ValfsTer197	p.G508Vfs*197	ENST00000262320	NM_003502.3	508	gGt/gt	6/11	1	2	FACETS	0.934	0.875	0.993	0.934	0.875	0.993	CLONAL	1	TRUE	1	0.775709516716126	2		929	624	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220476	133220476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372901803	NA	P-0042508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	181	610	0	ENST00000320574.5:c.4237G>A	p.Glu1413Lys	p.E1413K	ENST00000320574	NM_006231.2	1413	Gag/Aag	33/49	0.75668227702763	3	FACETS	1	0.972	1	0.548	0.508	0.589	CLONAL	1	TRUE	1	0.775709516716126	3		610	591	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101117	27101117	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	231	755	0	ENST00000324856.7:c.4403del	p.Pro1468LeufsTer13	p.P1468Lfs*13	ENST00000324856	NM_006015.4	1467	Ccc/cc	18/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.775709516716126	2		755	517	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935322	36935323	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs747437399	NA	P-0042508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	191	834	1	ENST00000361632.4:c.1404dup	p.Ser469GlnfsTer5	p.S469Qfs*5	ENST00000361632		468	-/C	10/16	1	2	FACETS	0.849	0.79	0.909	0.849	0.79	0.909	CLONAL	1	TRUE	1	0.775709516716126	2		835	580	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	258	887	2	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.952	0.896	1	0.952	0.896	1	CLONAL	1	TRUE	1	0.775709516716126	2		889	699	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	401960	401960	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200109736	NA	P-0042508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	86	326	0	ENST00000399788.2:c.4831G>A	p.Ala1611Thr	p.A1611T	ENST00000399788	NM_001042603.1	1611	Gca/Aca	27/28	0.52360804819092	3	FACETS	0.897	0.801	0.999			1	CLONAL	1	TRUE	NA	0.775709516716126	3		326	343	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107086	27107086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	152	421	1	ENST00000324856.7:c.6697C>T	p.Arg2233Trp	p.R2233W	ENST00000324856	NM_006015.4	2233	Cgg/Tgg	20/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.775709516716126	2		422	349	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400324	225400324	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	45	179	0	ENST00000264414.4:c.299A>G	p.Asn100Ser	p.N100S	ENST00000264414	NM_003590.4	100	aAc/aGc	3/16	1	2	FACETS	0.841	0.722	0.965	0.841	0.722	0.965	CLONAL	1	TRUE	1	0.775709516716126	2		179	138	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784122	9784124	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0042508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	87	591	0	ENST00000377346.4:c.2693_2695del	p.Asn898del	p.N898del	ENST00000377346	NM_005026.3	897	gACAac/gac	21/24	1	2	FACETS	0.618	0.551	0.688	0.618	0.551	0.688	SUBCLONAL	1	TRUE	1	0.775709516716126	2		591	363	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170821	99170821	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	108	576	0	ENST00000074304.5:c.1450T>C	p.Ser484Pro	p.S484P	ENST00000074304	NM_001134224.1	484	Tcc/Ccc	16/26	1	2	FACETS	0.751	0.68	0.824	0.751	0.68	0.824	SUBCLONAL	1	TRUE	1	0.775709516716126	2		576	371	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589260	67589261	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0042508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	81	233	0	ENST00000274335.5:c.1250dup	p.Asn417LysfsTer25	p.N417Kfs*25	ENST00000274335		416	-/A	9/15	1	2	FACETS	0.985	0.885	1	0.985	0.885	1	CLONAL	1	TRUE	1	0.775709516716126	2		233	212	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591115	67591116	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTA	novel	NA	P-0042508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	85	268	0	ENST00000274335.5:c.1710_1712dup	p.Ile571dup	p.I571dup	ENST00000274335		571	ctt/cTTAtt	12/15	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.775709516716126	2		268	204	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187253	38187254	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0042508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	174	623	0	ENST00000317025.8:c.1223dup	p.Ser409GlufsTer9	p.S409Efs*9	ENST00000317025	NM_023034.1	408	aag/aaAg	6/24	0.75668227702763	3	FACETS	0.889	0.821	0.96	0.445	0.41	0.48	CLONAL	1	TRUE	1	0.775709516716126	3		623	700	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0042512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	170	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.222559837749099	6	FACETS	0.942	0.872	1			1	INDETERMINATE	3	TRUE	NA	0.421596369299577	6		334	526	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0042512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	100	668	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.259749848222132	4	FACETS	0.855	0.763	0.952	0.427	0.381	0.476	CLONAL	1	TRUE	2	0.421596369299577	4		668	789	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576851	7576851	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0042512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	353	566	0	ENST00000269305.4:c.993+2T>C		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.134362181888415	4	FACETS	1	0.989	1			1	INDETERMINATE	3	TRUE	NA	0.421596369299577	4		566	716	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5462929	5462929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146495642	NA	P-0042512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	138	318	0	ENST00000381577.3:c.490G>A	p.Glu164Lys	p.E164K	ENST00000381577	NM_014143.3	164	Gaa/Aaa	4/7	0.259749848222132	4	FACETS	0.92	0.842	1	0.92	0.842	1	CLONAL	2	TRUE	2	0.421596369299577	4		318	506	SUCCESS
APC	324	MSKCC	GRCh37	5	112175758	112175759	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CATTTTGC	novel	NA	P-0042512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	77	317	0	ENST00000257430.4:c.4470_4477dup	p.Thr1493IlefsTer17	p.T1493Ifs*17	ENST00000257430	NM_000038.5	1489	-/CATTTTGC	16/16	0.421596369299577	2	FACETS	1	0.977	1	0.725	0.645	0.808	CLONAL	1	TRUE	0	0.421596369299577	2		317	252	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	16	347	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.859	0.656	1	0.859	0.656	1	CLONAL	1	TRUE	1	0.653299380735231	2		347	57	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	177	725	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.162194351157541	3	FACETS	1	0.986	1	0.642	0.595	0.69	INDETERMINATE	1	TRUE	1	0.653299380735231	3		732	560	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	11	481	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.185	0.128	0.256	0.185	0.128	0.256	SUBCLONAL	1	TRUE	1	0.653299380735231	2		481	182	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	14	590	1	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.227	0.164	0.302	0.227	0.164	0.302	SUBCLONAL	1	TRUE	1	0.653299380735231	2		591	189	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	29	608	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.807	0.662	0.965	0.807	0.662	0.965	CLONAL	1	TRUE	1	0.653299380735231	2		612	110	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426120	47426120	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	16	971	0	ENST00000377045.4:c.640T>C	p.Ser214Pro	p.S214P	ENST00000377045	NM_001654.4	214	Tcc/Ccc	7/16	0.379833326682568	1	FACETS	0.05	0.037	0.067	0.05	0.037	0.067	INDETERMINATE	1	TRUE	0	0.653299380735231	1		971	655	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	173	843	10	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	0.162194351157541	3	FACETS	1	0.968	1	0.545	0.503	0.588	INDETERMINATE	1	TRUE	1	0.653299380735231	3		853	645	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	193	592	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.2261745679859	4	FACETS	1	0.991	1	0.745	0.692	0.799	INDETERMINATE	1	TRUE	2	0.653299380735231	4		593	656	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	223	794	0	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	0.123344526972021	4	FACETS	0.751	0.702	0.802	0.751	0.702	0.802	INDETERMINATE	2	TRUE	2	0.653299380735231	4		794	751	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	45	624	4	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	0.162194351157541	3	FACETS	1	0.941	1	0.601	0.515	0.693	INDETERMINATE	1	TRUE	1	0.653299380735231	3		628	152	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039356	47039358	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	203	808	0	ENST00000377604.3:c.985_987del	p.Ser329del	p.S329del	ENST00000377604	NM_001204468.1	327	TCC/-	10/24	0.379833326682568	1	FACETS	0.634	0.591	0.679	0.634	0.591	0.679	INDETERMINATE	1	TRUE	0	0.653299380735231	1		808	660	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390736	139390736	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	287	1006	0	ENST00000277541.6:c.7455del	p.Ser2486ArgfsTer103	p.S2486Rfs*103	ENST00000277541	NM_017617.3	2485	ccC/cc	34/34	1	2	FACETS	0.856	0.805	0.907	0.856	0.805	0.907	CLONAL	1	TRUE	1	0.653299380735231	2		1006	1027	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992292	72992292	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140602496	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	204	913	1	ENST00000268489.5:c.1753G>A	p.Gly585Ser	p.G585S	ENST00000268489	NM_006885.3	585	Ggc/Agc	2/10	1	2	FACETS	0.983	0.917	1	0.983	0.917	1	CLONAL	1	TRUE	1	0.653299380735231	2		914	635	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	233	848	0	ENST00000269571.5:c.829G>A	p.Asp277Asn	p.D277N	ENST00000269571		277	Gac/Aac	7/27	0.162194351157541	3	FACETS	1	0.992	1	0.694	0.65	0.738	INDETERMINATE	1	TRUE	1	0.653299380735231	3		848	682	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804342	46804342	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770172581	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	217	624	0	ENST00000290295.7:c.665C>T	p.Pro222Leu	p.P222L	ENST00000290295	NM_006361.5	222	cCg/cTg	2/2	0.162194351157541	3	FACETS	1	0.991	1	0.708	0.663	0.755	INDETERMINATE	1	TRUE	1	0.653299380735231	3		624	622	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876454	35876454	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	79	656	0	ENST00000303115.3:c.1250del	p.Pro417LeufsTer10	p.P417Lfs*10	ENST00000303115	NM_002185.3	416	Ccc/cc	8/8	1	2	FACETS	0.756	0.671	0.845	0.756	0.671	0.845	SUBCLONAL	1	TRUE	1	0.653299380735231	2		656	320	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	225	1072	1	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	0.123344526972021	4	FACETS	1	0.99	1	0.684	0.638	0.731	INDETERMINATE	1	TRUE	2	0.653299380735231	4		1073	833	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193932	106193932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	44	356	1	ENST00000380013.4:c.4394G>A	p.Arg1465Gln	p.R1465Q	ENST00000380013	NM_001127208.2	1465	cGa/cAa	10/11	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.653299380735231	2		357	125	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224111	36224111	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	185	798	0	ENST00000222270.7:c.6666del	p.Thr2223ProfsTer38	p.T2223Pfs*38	ENST00000222270	NM_014727.1	2221	Ccc/cc	28/37	0.123344526972021	4	FACETS	1	0.99	1	0.725	0.672	0.779	INDETERMINATE	1	TRUE	2	0.653299380735231	4		798	646	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405960	157405960	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	139	579	0	ENST00000346085.5:c.2204del	p.Pro735HisfsTer10	p.P735Hfs*10	ENST00000346085	NM_020732.3	734	ggC/gg	6/20	0.2261745679859	4	FACETS	1	0.987	1	0.742	0.68	0.806	INDETERMINATE	1	TRUE	2	0.653299380735231	4		579	474	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439668	220439668	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs192760521	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	199	893	0	ENST00000243786.2:c.521C>A	p.Pro174His	p.P174H	ENST00000243786	NM_002191.3	174	cCt/cAt	2/2	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.653299380735231	2		893	572	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1036330	1036330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1352571686	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	218	696	0	ENST00000358495.3:c.448G>A	p.Gly150Arg	p.G150R	ENST00000358495	NM_134424.2	150	Ggg/Agg	6/12	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.653299380735231	2		696	614	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870953	12870953	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	153	383	0	ENST00000228872.4:c.180G>A	p.Trp60Ter	p.W60*	ENST00000228872	NM_004064.3	60	tgG/tgA	1/3	0.2261745679859	4	FACETS	0.805	0.742	0.87	0.805	0.742	0.87	INDETERMINATE	2	TRUE	2	0.653299380735231	4		383	481	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792033	42792034	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	171	747	0	ENST00000575354.2:c.839_840del	p.Glu280GlyfsTer34	p.E280Gfs*34	ENST00000575354	NM_015125.3	279	tcAGag/tcag	6/20	0.123344526972021	4	FACETS	1	0.987	1	0.68	0.628	0.734	INDETERMINATE	1	TRUE	2	0.653299380735231	4		747	636	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258863	16258863	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756454037	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	158	648	0	ENST00000375759.3:c.6128G>A	p.Arg2043His	p.R2043H	ENST00000375759	NM_015001.2	2043	cGt/cAt	11/15	0.2261745679859	4	FACETS	0.767	0.708	0.829	0.767	0.708	0.829	INDETERMINATE	2	TRUE	2	0.653299380735231	4		648	521	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46736339	46736339	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	82	510	0	ENST00000371975.4:c.1051C>A	p.His351Asn	p.H351N	ENST00000371975	NM_003579.3	351	Cat/Aat	10/18	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.653299380735231	2		510	244	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612723	228612723	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	196	787	0	ENST00000366696.1:c.304G>T	p.Val102Leu	p.V102L	ENST00000366696	NM_003493.2	102	Gtg/Ttg	1/1	1	2	FACETS	0.959	0.892	1	0.959	0.892	1	CLONAL	1	TRUE	1	0.653299380735231	2		787	626	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610167	43610167	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	153	900	1	ENST00000355710.3:c.2119G>T	p.Asp707Tyr	p.D707Y	ENST00000355710	NM_020975.4	707	Gat/Tat	11/20	1	2	FACETS	0.956	0.881	1	0.956	0.881	1	CLONAL	1	TRUE	1	0.653299380735231	2		901	490	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759890	63759890	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	89	352	0	ENST00000279873.7:c.547del	p.Gln183SerfsTer9	p.Q183Sfs*9	ENST00000279873	NM_032199.2	181	taC/ta	4/10	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.653299380735231	2		352	268	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112764536	112764536	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	15	327	0	ENST00000369452.4:c.1145G>T	p.Ser382Ile	p.S382I	ENST00000369452	NM_007373.3	382	aGt/aTt	5/9	1	2	FACETS	1	0.778	1	1	0.778	1	CLONAL	1	TRUE	1	0.653299380735231	2		327	45	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118355619	118355619	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	34	574	0	ENST00000534358.1:c.4261G>A	p.Gly1421Arg	p.G1421R	ENST00000534358	NM_005933.3	1421	Gga/Aga	10/36	0.239550619647259	1	FACETS	0.527	0.438	0.623	0.527	0.438	0.623	INDETERMINATE	1	TRUE	0	0.653299380735231	1		574	133	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856514	111856514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1565970517	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	124	445	1	ENST00000341259.2:c.565C>T	p.Arg189Trp	p.R189W	ENST00000341259	NM_005475.2	189	Cgg/Tgg	2/8	1	2	FACETS	0.857	0.781	0.936	0.857	0.781	0.936	CLONAL	1	TRUE	1	0.653299380735231	2		446	443	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912769	32912769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748591104	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	13	436	0	ENST00000380152.3:c.4277C>T	p.Thr1426Ile	p.T1426I	ENST00000380152		1426	aCa/aTa	11/27	0.480469477645245	1	FACETS	0.609	0.452	0.784	0.609	0.452	0.784	SUBCLONAL	1	TRUE	0	0.653299380735231	1		436	44	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129390	2129390	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	211	792	0	ENST00000219476.3:c.3245G>T	p.Gly1082Val	p.G1082V	ENST00000219476	NM_000548.3	1082	gGc/gTc	28/42	1	2	FACETS	0.973	0.908	1	0.973	0.908	1	CLONAL	1	TRUE	1	0.653299380735231	2		792	664	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647942	3647942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758029323	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	72	1125	2	ENST00000294008.3:c.1222C>T	p.Arg408Trp	p.R408W	ENST00000294008	NM_032444.2	408	Cgg/Tgg	6/15	1	2	FACETS	0.302	0.263	0.343	0.302	0.263	0.343	SUBCLONAL	1	TRUE	1	0.653299380735231	2		1127	731	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029134	14029134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1159571443	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	10	276	0	ENST00000311895.7:c.1345G>A	p.Val449Ile	p.V449I	ENST00000311895	NM_005236.2	449	Gtc/Atc	8/11	1	2	FACETS	0.419	0.288	0.579	0.419	0.288	0.579	SUBCLONAL	1	TRUE	1	0.653299380735231	2		276	73	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245859	5245859	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	86	1053	0	ENST00000357368.4:c.916T>C	p.Ser306Pro	p.S306P	ENST00000357368	NM_002850.3	306	Tcg/Ccg	10/38	0.123344526972021	4	FACETS	0.636	0.563	0.715	0.318	0.281	0.358	INDETERMINATE	1	TRUE	2	0.653299380735231	4		1053	684	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302945	15302945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28933696	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	259	966	0	ENST00000263388.2:c.505C>T	p.Arg169Cys	p.R169C	ENST00000263388	NM_000435.2	169	Cgc/Tgc	4/33	0.123344526972021	4	FACETS	0.81	0.761	0.86	0.81	0.761	0.86	INDETERMINATE	2	TRUE	2	0.653299380735231	4		966	809	SUCCESS
AXL	558	MSKCC	GRCh37	19	41736875	41736875	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	80	790	0	ENST00000301178.4:c.590T>G	p.Leu197Arg	p.L197R	ENST00000301178	NM_021913.4	197	cTg/cGg	5/20	0.123344526972021	4	FACETS	0.682	0.601	0.768	0.341	0.3	0.384	INDETERMINATE	1	TRUE	2	0.653299380735231	4		790	594	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012588	36012588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1212841399	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	178	561	0	ENST00000358208.4:c.32C>T	p.Ala11Val	p.A11V	ENST00000358208		11	gCc/gTc	2/12	1	2	FACETS	0.901	0.834	0.969	0.901	0.834	0.969	CLONAL	1	TRUE	1	0.653299380735231	2		561	605	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127562	55127562	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	11	325	0	ENST00000257290.5:c.350T>C	p.Ile117Thr	p.I117T	ENST00000257290	NM_006206.4	117	aTt/aCt	3/23	0.260353582989496	0	FACETS	0.101	0.07	0.139			1	INDETERMINATE	1	TRUE	0	0.653299380735231	0		325	116	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244121	153244121	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	81	529	1	ENST00000281708.4:c.2036del	p.Asn679ThrfsTer28	p.N679Tfs*28	ENST00000281708	NM_033632.3	679	aAc/ac	12/12	1	2	FACETS	0.579	0.513	0.65	0.579	0.513	0.65	SUBCLONAL	1	TRUE	1	0.653299380735231	2		530	428	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753404	57753404	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	27	355	0	ENST00000274289.3:c.720A>G	p.Ile240Met	p.I240M	ENST00000274289	NM_006622.3	240	atA/atG	6/14	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.653299380735231	2		355	60	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638842	176638842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	17	691	0	ENST00000439151.2:c.3442C>T	p.Leu1148Phe	p.L1148F	ENST00000439151	NM_022455.4	1148	Ctc/Ttc	5/23	1	2	FACETS	0.232	0.173	0.302	0.232	0.173	0.302	SUBCLONAL	1	TRUE	1	0.653299380735231	2		691	224	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046742	180046742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	216	899	0	ENST00000261937.6:c.2570G>A	p.Gly857Glu	p.G857E	ENST00000261937	NM_182925.4	857	gGg/gAg	18/30	1	2	FACETS	0.999	0.933	1	0.999	0.933	1	CLONAL	1	TRUE	1	0.653299380735231	2		899	662	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323266	31323266	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	145	251	0	ENST00000412585.2:c.723G>A	p.Trp241Ter	p.W241*	ENST00000412585	NM_005514.6	241	tgG/tgA	4/8	0.573062361849209	3	FACETS	0.846	0.794	0.897	0.846	0.794	0.897	CLONAL	3	TRUE	0	0.653299380735231	3		251	232	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430296	47430296	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377675069	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	42	916	2	ENST00000377045.4:c.1571G>A	p.Arg524His	p.R524H	ENST00000377045	NM_001654.4	524	cGt/cAt	15/16	0.379833326682568	1	FACETS	0.135	0.112	0.16	0.135	0.112	0.16	INDETERMINATE	1	TRUE	0	0.653299380735231	1		918	642	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273570	5273570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	127	596	0	ENST00000357368.4:c.262G>A	p.Gly88Arg	p.G88R	ENST00000357368	NM_002850.3	88	Ggg/Agg	4/38	0.123344526972021	4	FACETS	1	0.986	1	0.732	0.668	0.798	INDETERMINATE	1	TRUE	2	0.653299380735231	4		596	439	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0042588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	95	543	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.625	0.557	0.697	0.625	0.557	0.697	SUBCLONAL	1	TRUE	1	0.478796566306251	2		545	635	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0042588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	126	331	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.478796566306251	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.478796566306251	1		331	317	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440870	52440870	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	271	927	0	ENST00000460680.1:c.634G>T	p.Glu212Ter	p.E212*	ENST00000460680	NM_004656.3	212	Gag/Tag	8/17	0.478796566306251	1	FACETS	0.965	0.908	1	0.965	0.908	1	CLONAL	1	TRUE	0	0.478796566306251	1		927	892	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149447884	149447884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs538359948	NA	P-0042588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	252	954	1	ENST00000286301.3:c.1520C>T	p.Thr507Met	p.T507M	ENST00000286301	NM_005211.3	507	aCg/aTg	11/22	1	2	FACETS	0.923	0.863	0.985	0.923	0.863	0.985	CLONAL	1	TRUE	1	0.478796566306251	2		955	1140	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622198	162622198	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	126	534	0	ENST00000366898.1:c.499A>C	p.Ser167Arg	p.S167R	ENST00000366898	NM_004562.2	167	Agc/Cgc	4/12	0.478796566306251	1	FACETS	0.929	0.848	1	0.929	0.848	1	CLONAL	1	TRUE	0	0.478796566306251	1		534	431	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0042640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	142	910	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.29	2		910	863	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0042640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	177	761	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.214790556120674	3	FACETS	1	0.987	1	0.678	0.625	0.735	CLONAL	1	TRUE	1	0.29	3		764	1030	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0042640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	113	874	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.29	2		874	746	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0042640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	40	136	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.29	2		136	195	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0042640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	68	505	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.29	2		505	404	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370985	55370985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	261	1054	0	ENST00000297316.4:c.287C>G	p.Ala96Gly	p.A96G	ENST00000297316	NM_022454.3	96	gCc/gGc	1/2	0.214790556120674	3	FACETS	0.947	0.887	1	0.947	0.887	1	CLONAL	2	TRUE	1	0.29	3		1054	1088	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	24	238	0	ENST00000397062.3:c.101G>C	p.Arg34Pro	p.R34P	ENST00000397062	NM_006164.4	34	cGa/cCa	2/5	1	2	FACETS	0.985	0.779	1	0.985	0.779	1	CLONAL	1	TRUE	1	0.29	2		238	168	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0042640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	74	423	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	1	2	FACETS	1	0.95	1	1	0.985	1	CLONAL	2	TRUE	1	0.29	2		423	227	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984526	72984557	+	frameshift_variant	Frame_Shift_Del	DEL	CCTTGATGTGGGCCACCAGCTGGTACTTCTGC	CCTTGATGTGGGCCACCAGCTGGTACTTCTGC	-	novel	NA	P-0042640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	180	1192	0	ENST00000268489.5:c.3027_3058del	p.Gln1010GlyfsTer26	p.Q1010Gfs*26	ENST00000268489	NM_006885.3	1009	gtGCAGAAGTACCAGCTGGTGGCCCACATCAAGGag/gtag	3/10	0.295727729549548	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.29	1		1192	998	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098920	178098920	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	14	319	0	ENST00000397062.3:c.125G>C	p.Arg42Pro	p.R42P	ENST00000397062	NM_006164.4	42	cGa/cCa	2/5	1	2	FACETS	0.451	0.326	0.602	0.451	0.326	0.602	SUBCLONAL	1	TRUE	1	0.29	2		319	214	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961059	55961059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530419081	NA	P-0042656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	54	304	0	ENST00000263923.4:c.2881C>T	p.Arg961Trp	p.R961W	ENST00000263923	NM_002253.2	961	Cgg/Tgg	21/30	1	2	FACETS	0.27	0.23	0.314	0.27	0.23	0.314	SUBCLONAL	1	TRUE	1	0.581079193243549	2		304	688	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041266	47041266	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0042656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	427	220	0	ENST00000377604.3:c.1693+1G>A		p.X565_splice	ENST00000377604	NM_001204468.1	565			0.578144137447558	2	FACETS	0.836	0.81	0.861			1	CLONAL	3	TRUE	NA	0.581079193243549	2		220	586	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577567	7577568	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs1555525539	NA	P-0042656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	346	327	0	ENST00000269305.4:c.713_714del	p.Cys238Ter	p.C238*	ENST00000269305	NM_001126112.2	238	tGT/t	7/11	0.581079193243549	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.581079193243549	2		327	573	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983992	7983992	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769882996	NA	P-0042656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	166	212	0	ENST00000319144.4:c.634G>A	p.Val212Ile	p.V212I	ENST00000319144	NM_001139.2	212	Gtc/Atc	5/15	0.581079193243549	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.581079193243549	2		212	281	SUCCESS
APC	324	MSKCC	GRCh37	5	112174595	112174596	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0042656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	192	138	0	ENST00000257430.4:c.3305dup	p.Tyr1102Ter	p.Y1102*	ENST00000257430	NM_000038.5	1102	tac/tAac	16/16	0.555055316231145	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.581079193243549	2		138	330	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0042665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	116	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.367908807853121	2		334	584	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024001	27024002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0042665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	16	108	0	ENST00000324856.7:c.1113dup	p.Gln372AlafsTer28	p.Q372Afs*28	ENST00000324856	NM_006015.4	369	-/G	1/20	1	2	FACETS	0.635	0.473	0.825	0.635	0.473	0.825	SUBCLONAL	1	TRUE	1	0.367908807853121	2		108	137	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0042665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	136	761	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.367908807853121	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.367908807853121	1		764	557	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249348	110249348	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	163	761	0	ENST00000374672.4:c.1225A>C	p.Lys409Gln	p.K409Q	ENST00000374672	NM_004235.4	409	Aag/Cag	4/5	1	2	FACETS	0.872	0.8	0.948	0.872	0.8	0.948	CLONAL	1	TRUE	1	0.367908807853121	2		761	1016	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293661	1293661	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	108	642	0	ENST00000310581.5:c.1340G>A	p.Arg447His	p.R447H	ENST00000310581	NM_198253.2	447	cGc/cAc	2/16	1	2	FACETS	0.972	0.874	1	0.972	0.874	1	CLONAL	1	TRUE	1	0.367908807853121	2		642	604	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884563	151884563	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0042665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	53	267	0	ENST00000262189.6:c.4794-2A>T		p.X1598_splice	ENST00000262189	NM_170606.2	1598			1	2	FACETS	0.77	0.659	0.891	0.77	0.659	0.891	SUBCLONAL	1	TRUE	1	0.367908807853121	2		267	374	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584557	48584563	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCAGC	CCTCAGC	-	novel	NA	P-0042665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	102	372	0	ENST00000342988.3:c.731_737del	p.Pro244GlnfsTer90	p.P244Qfs*90	ENST00000342988	NM_005359.5	244	CCTCAGCca/ca	6/12	0.367908807853121	1	FACETS	0.992	0.892	1	0.992	0.892	1	CLONAL	1	TRUE	0	0.367908807853121	1		372	456	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	97	394	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.402019628462878	0	FACETS	0.851	0.767	0.939			1	CLONAL	1	TRUE	0	0.402019628462878	0		394	339	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	173	725	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.402019628462878	0	FACETS	0.759	0.701	0.819			1	SUBCLONAL	1	TRUE	0	0.402019628462878	0		732	678	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	117	472	5	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	0.402019628462878	0	FACETS	0.804	0.73	0.88			1	CLONAL	1	TRUE	0	0.402019628462878	0		477	433	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	133	875	4	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	0.402019628462878	0	FACETS	0.435	0.394	0.477			1	SUBCLONAL	1	TRUE	0	0.402019628462878	0		879	910	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	163	608	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.402019628462878	0	FACETS	0.903	0.834	0.974			1	CLONAL	1	TRUE	0	0.402019628462878	0		612	537	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	107	410	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.402019628462878	0	FACETS	0.982	0.892	1			1	CLONAL	1	TRUE	0	0.402019628462878	0		410	324	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508389	106508389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758375337	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	63	362	1	ENST00000359195.3:c.383C>T	p.Thr128Met	p.T128M	ENST00000359195	NM_002649.2	128	aCg/aTg	2/11	0.402019628462878	0	FACETS	0.741	0.648	0.839			1	SUBCLONAL	1	TRUE	0	0.402019628462878	0		363	253	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs753143066	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	156	715	7	ENST00000295797.4:c.826dup	p.Thr276AsnfsTer16	p.T276Nfs*16	ENST00000295797	NM_002740.5	273	tta/ttAa	9/18	0.402019628462878	0	FACETS	0.761	0.7	0.824			1	SUBCLONAL	1	TRUE	0	0.402019628462878	0		722	610	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031170	11031170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	298	835	0	ENST00000327064.4:c.1255C>T	p.Arg419Trp	p.R419W	ENST00000327064	NM_199141.1	419	Cgg/Tgg	11/16	0.402019628462878	0	FACETS	0.995	0.94	1			1	CLONAL	1	TRUE	0	0.402019628462878	0		835	891	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	310	523	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.402019628462878	0	FACETS		NA	1			1	NA	3	TRUE	0	0.402019628462878	0		523	480	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	100	497	4	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	0.402019628462878	0	FACETS	0.826	0.745	0.911			1	CLONAL	1	TRUE	0	0.402019628462878	0		501	360	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244098	5244098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs73545312	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	230	744	1	ENST00000357368.4:c.1384G>A	p.Val462Ile	p.V462I	ENST00000357368	NM_002850.3	462	Gtc/Atc	11/38	0.402019628462878	0	FACETS	0.827	0.773	0.883			1	CLONAL	1	TRUE	0	0.402019628462878	0		745	827	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574678	41574679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs754418509	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	219	836	1	ENST00000263253.7:c.6970dup	p.His2324ProfsTer55	p.H2324Pfs*55	ENST00000263253	NM_001429.3	2321	-/C	31/31	0.402019628462878	0	FACETS	0.751	0.699	0.803			1	SUBCLONAL	1	TRUE	0	0.402019628462878	0		837	868	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160588	56160588	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	82	267	0	ENST00000399503.3:c.862C>T	p.Arg288Ter	p.R288*	ENST00000399503	NM_005921.1	288	Cga/Tga	4/20	0.402019628462878	0	FACETS	0.897	0.801	0.997			1	CLONAL	1	TRUE	0	0.402019628462878	0		267	272	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	128	882	3	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	0.402019628462878	0	FACETS	0.44	0.398	0.484			1	SUBCLONAL	1	TRUE	0	0.402019628462878	0		885	866	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	122	570	3	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	0.402019628462878	0	FACETS	0.758	0.689	0.829			1	SUBCLONAL	1	TRUE	0	0.402019628462878	0		573	479	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394349	162394349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137853054	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	82	357	0	ENST00000366898.1:c.719C>T	p.Thr240Met	p.T240M	ENST00000366898	NM_004562.2	240	aCg/aTg	6/12	0.402019628462878	0	FACETS	0.724	0.644	0.808			1	SUBCLONAL	1	TRUE	0	0.402019628462878	0		357	337	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	120	504	0	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	0.402019628462878	0	FACETS	0.732	0.664	0.802			1	SUBCLONAL	1	TRUE	0	0.402019628462878	0		504	488	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962854	2962854	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	207	785	2	ENST00000396946.4:c.2054del	p.Gly685AlafsTer31	p.G685Afs*31	ENST00000396946	NM_032415.4	685	gGc/gc	16/25	0.402019628462878	0	FACETS	0.759	0.706	0.814			1	SUBCLONAL	1	TRUE	0	0.402019628462878	0		787	811	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086032	16086032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777508469	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	184	615	0	ENST00000281043.3:c.1208C>T	p.Thr403Met	p.T403M	ENST00000281043	NM_005378.4	403	aCg/aTg	3/3	0.402019628462878	0	FACETS	0.873	0.81	0.938			1	CLONAL	1	TRUE	0	0.402019628462878	0		615	627	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822586	72822586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	120	570	4	ENST00000268489.5:c.9589del	p.Gln3197SerfsTer44	p.Q3197Sfs*44	ENST00000268489	NM_006885.3	3197	Cag/ag	10/10	0.402019628462878	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.402019628462878	1		574	397	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432067	121432067	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555212014	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	291	868	2	ENST00000257555.6:c.814C>T	p.Arg272Cys	p.R272C	ENST00000257555		272	Cgc/Tgc	4/10	0.402019628462878	0	FACETS	0.945	0.891	1			1	CLONAL	1	TRUE	0	0.402019628462878	0		870	916	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381567	81381567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370760302	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	54	207	1	ENST00000222390.5:c.494C>T	p.Ser165Leu	p.S165L	ENST00000222390	NM_000601.4	165	tCg/tTg	5/18	0.402019628462878	0	FACETS	0.747	0.646	0.854			1	SUBCLONAL	1	TRUE	0	0.402019628462878	0		208	215	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	208	831	5	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	0.402019628462878	0	FACETS	0.843	0.785	0.903			1	CLONAL	1	TRUE	0	0.402019628462878	0		836	734	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125832	47125832	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	86	245	2	ENST00000409792.3:c.5438del	p.Asn1813IlefsTer25	p.N1813Ifs*25	ENST00000409792	NM_014159.6	1813	aAt/at	12/21	0.402019628462878	0	FACETS	1	0.928	1			1	CLONAL	1	TRUE	0	0.402019628462878	0		247	246	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681761	78681761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	246	714	1	ENST00000306801.3:c.469C>T	p.Arg157Trp	p.R157W	ENST00000306801	NM_020761.2	157	Cgg/Tgg	4/34	0.402019628462878	0	FACETS	0.921	0.863	0.979			1	CLONAL	1	TRUE	0	0.402019628462878	0		715	795	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096132	2096133	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs763525759	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	82	655	0	ENST00000219066.1:c.374dup	p.Val127GlyfsTer43	p.V127Gfs*43	ENST00000219066	NM_002528.5	125	cca/ccCa	2/6	0.402019628462878	1	FACETS	0.647	0.572	0.727	0.647	0.572	0.727	SUBCLONAL	1	TRUE	0	0.402019628462878	1		655	504	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795352	39795352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372598575	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	118	635	2	ENST00000288319.7:c.368G>A	p.Arg123His	p.R123H	ENST00000288319	NM_182918.3	123	cGc/cAc	3/10	0.402019628462878	0	FACETS	0.701	0.635	0.769			1	SUBCLONAL	1	TRUE	0	0.402019628462878	0		637	501	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427691	72427691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759180086	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	105	389	1	ENST00000477973.2:c.799C>T	p.Arg267Cys	p.R267C	ENST00000477973	NM_012234.5	267	Cgc/Tgc	4/4	0.402019628462878	0	FACETS	0.737	0.664	0.812			1	SUBCLONAL	1	TRUE	0	0.402019628462878	0		390	424	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280162	66280162	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	61	209	0	ENST00000273854.3:c.1528-1G>T		p.X510_splice	ENST00000273854	NM_004439.5	510			0.402019628462878	0	FACETS	0.903	0.792	1			1	CLONAL	1	TRUE	0	0.402019628462878	0		209	201	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030467	47030469	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs781998738	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	255	801	16	ENST00000377604.3:c.254_256del	p.Arg85del	p.R85del	ENST00000377604	NM_001204468.1	81	aGGCgg/agg	4/24	0.402019628462878	0	FACETS	0.892	0.838	0.949			1	CLONAL	1	TRUE	0	0.402019628462878	0		817	850	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599271	28599271	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs770146088	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	155	996	2	ENST00000253063.3:c.722del	p.Pro241GlnfsTer6	p.P241Qfs*6	ENST00000253063	NM_031459.4	239	agC/ag	5/10	0.402019628462878	0	FACETS	0.485	0.443	0.528			1	SUBCLONAL	1	TRUE	0	0.402019628462878	0		998	951	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155654	56155654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746479827	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	119	387	0	ENST00000399503.3:c.746G>A	p.Arg249His	p.R249H	ENST00000399503	NM_005921.1	249	cGc/cAc	3/20	0.402019628462878	0	FACETS	0.954	0.87	1			1	CLONAL	1	TRUE	0	0.402019628462878	0		387	371	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90971011	90971011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777259845	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	32	385	1	ENST00000265433.3:c.1066G>A	p.Ala356Thr	p.A356T	ENST00000265433	NM_002485.4	356	Gcc/Acc	9/16	0.374621229316082	3	FACETS	0.377	0.305	0.458	0.189	0.152	0.229	SUBCLONAL	1	TRUE	1	0.402019628462878	3		386	507	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223487	53223487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	33	625	2	ENST00000375401.3:c.3872G>A	p.Arg1291His	p.R1291H	ENST00000375401	NM_004187.3	1291	cGc/cAc	23/26	0.402019628462878	0	FACETS	0.192	0.156	0.233			1	SUBCLONAL	1	TRUE	0	0.402019628462878	0		627	512	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984828	72984828	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	188	593	0	ENST00000268489.5:c.2756del	p.Gly919AlafsTer9	p.G919Afs*9	ENST00000268489	NM_006885.3	919	gGc/gc	3/10	0.402019628462878	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.402019628462878	1		593	508	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250080	39250080	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	100	534	0	ENST00000402219.2:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000402219	NM_005633.3	497	Cga/Tga	10/23	0.402019628462878	0	FACETS	0.848	0.764	0.934			1	CLONAL	1	TRUE	0	0.402019628462878	0		534	351	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21627910	21627910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1176731657	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	81	404	0	ENST00000421138.2:c.1220G>A	p.Arg407Gln	p.R407Q	ENST00000421138		407	cGa/cAa	12/16	0.402019628462878	0	FACETS	0.798	0.71	0.89			1	SUBCLONAL	1	TRUE	0	0.402019628462878	0		404	302	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905174	50905175	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	110	1004	0	ENST00000440232.2:c.461dup	p.Gly155TrpfsTer9	p.G155Wfs*9	ENST00000440232	NM_002691.3	152	-/C	4/27	0.402019628462878	0	FACETS	0.474	0.426	0.524			1	SUBCLONAL	1	TRUE	0	0.402019628462878	0		1004	691	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212443	36212443	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	234	809	0	ENST00000222270.7:c.2194C>T	p.Gln732Ter	p.Q732*	ENST00000222270	NM_014727.1	732	Cag/Tag	3/37	0.402019628462878	0	FACETS	0.908	0.85	0.967			1	CLONAL	1	TRUE	0	0.402019628462878	0		809	767	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50143282	50143282	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	64	188	0	ENST00000246792.3:c.74del	p.Pro25ArgfsTer21	p.P25Rfs*21	ENST00000246792	NM_006270.3	25	cCg/cg	1/6	0.402019628462878	0	FACETS	0.911	0.802	1			1	CLONAL	1	TRUE	0	0.402019628462878	0		188	209	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573564	48573564	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs786203560	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	54	310	1	ENST00000342988.3:c.153del	p.Asp52MetfsTer6	p.D52Mfs*6	ENST00000342988	NM_005359.5	50	Aaa/aa	2/12	0.402019628462878	0	FACETS	0.744	0.643	0.85			1	SUBCLONAL	1	TRUE	0	0.402019628462878	0		311	216	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243872	53243872	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1261132692	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	200	707	0	ENST00000375401.3:c.1121C>T	p.Ala374Val	p.A374V	ENST00000375401	NM_004187.3	374	gCg/gTg	8/26	0.402019628462878	0	FACETS	0.833	0.775	0.893			1	CLONAL	1	TRUE	0	0.402019628462878	0		707	714	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260374	16260374	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	82	523	0	ENST00000375759.3:c.7639A>G	p.Thr2547Ala	p.T2547A	ENST00000375759	NM_015001.2	2547	Aca/Gca	11/15	0.402019628462878	0	FACETS	0.5	0.442	0.562			1	SUBCLONAL	1	TRUE	0	0.402019628462878	0		523	488	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023990	27023992	+	inframe_deletion	In_Frame_Del	DEL	AGC	AGC	-	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	18	78	0	ENST00000324856.7:c.1099_1101del	p.Ser367del	p.S367del	ENST00000324856	NM_006015.4	366	AGC/-	1/20	0.402019628462878	0	FACETS	0.47	0.358	0.598			1	SUBCLONAL	1	TRUE	0	0.402019628462878	0		78	114	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106730	27106730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773818181	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	167	670	0	ENST00000324856.7:c.6341C>T	p.Pro2114Leu	p.P2114L	ENST00000324856	NM_006015.4	2114	cCg/cTg	20/20	0.402019628462878	0	FACETS	0.814	0.752	0.879			1	CLONAL	1	TRUE	0	0.402019628462878	0		670	610	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799195	45799195	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	35	648	0	ENST00000450313.1:c.238T>G	p.Ser80Ala	p.S80A	ENST00000450313	NM_012222.2	80	Tct/Gct	3/16	0.402019628462878	0	FACETS	0.187	0.153	0.226			1	SUBCLONAL	1	TRUE	0	0.402019628462878	0		648	557	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983031	201983031	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	265	851	0	ENST00000359651.3:c.880A>G	p.Lys294Glu	p.K294E	ENST00000359651		294	Aag/Gag	7/8	0.402019628462878	0	FACETS	0.874	0.821	0.928			1	CLONAL	1	TRUE	0	0.402019628462878	0		851	902	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620366	43620366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758191409	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	175	518	1	ENST00000355710.3:c.2975C>T	p.Pro992Leu	p.P992L	ENST00000355710	NM_020975.4	992	cCg/cTg	18/20	0.402019628462878	0	FACETS	0.866	0.802	0.933			1	CLONAL	1	TRUE	0	0.402019628462878	0		519	601	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446281	70446281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471278863	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	168	560	1	ENST00000373644.4:c.5221C>T	p.Arg1741Cys	p.R1741C	ENST00000373644	NM_030625.2	1741	Cgc/Tgc	11/12	0.402019628462878	0	FACETS	0.8	0.738	0.863			1	SUBCLONAL	1	TRUE	0	0.402019628462878	0		561	625	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741690	17741690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	205	470	1	ENST00000250003.3:c.361C>T	p.Arg121Cys	p.R121C	ENST00000250003	NM_002478.4	121	Cgc/Tgc	1/3	0.402019628462878	0	FACETS	0.998	0.931	1			1	CLONAL	1	TRUE	0	0.402019628462878	0		471	611	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939250	71939250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	223	736	1	ENST00000298229.2:c.199C>T	p.His67Tyr	p.H67Y	ENST00000298229	NM_001567.3	67	Cac/Tac	2/28	0.402019628462878	0	FACETS	0.909	0.849	0.97			1	CLONAL	1	TRUE	0	0.402019628462878	0		737	730	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201815	102201816	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	128	427	0	ENST00000263464.3:c.1170dup	p.Ser391Ter	p.S391*	ENST00000263464	NM_001165.4	389	-/T	6/9	0.402019628462878	0	FACETS	1	0.927	1			1	CLONAL	1	TRUE	0	0.402019628462878	0		427	376	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245748	46245748	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1273340081	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	126	403	0	ENST00000334344.6:c.3842G>T	p.Gly1281Val	p.G1281V	ENST00000334344	NM_152641.2	1281	gGg/gTg	15/21	0.402019628462878	0	FACETS	0.866	0.79	0.944			1	CLONAL	1	TRUE	0	0.402019628462878	0		403	433	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442932	49442932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886049484	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	235	736	2	ENST00000301067.7:c.3976C>T	p.Arg1326Trp	p.R1326W	ENST00000301067	NM_003482.3	1326	Cgg/Tgg	12/54	0.402019628462878	0	FACETS	1	0.94	1			1	CLONAL	1	TRUE	0	0.402019628462878	0		738	697	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041261	29041261	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	82	364	0	ENST00000282397.4:c.167A>G	p.Glu56Gly	p.E56G	ENST00000282397	NM_002019.4	56	gAa/gGa	3/30	0.402019628462878	0	FACETS	0.835	0.745	0.93			1	CLONAL	1	TRUE	0	0.402019628462878	0		364	292	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73348112	73348112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	87	407	0	ENST00000377767.4:c.1073G>A	p.Gly358Asp	p.G358D	ENST00000377767	NM_014953.3	358	gGc/gAc	7/21	0.402019628462878	0	FACETS	0.911	0.817	1			1	CLONAL	1	TRUE	0	0.402019628462878	0		407	284	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436128	110436128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	126	849	2	ENST00000375856.3:c.2273G>A	p.Gly758Asp	p.G758D	ENST00000375856	NM_003749.2	758	gGc/gAc	1/2	0.402019628462878	0	FACETS	0.431	0.39	0.474			1	SUBCLONAL	1	TRUE	0	0.402019628462878	0		851	870	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560340	95560340	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	78	458	0	ENST00000393063.1:c.5249T>C	p.Val1750Ala	p.V1750A	ENST00000393063	NM_030621.3	1750	gTa/gCa	25/28	0.402019628462878	0	FACETS	0.424	0.373	0.479			1	SUBCLONAL	1	TRUE	0	0.402019628462878	0		458	547	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724465	43724465	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	270	889	0	ENST00000382044.4:c.3602T>C	p.Val1201Ala	p.V1201A	ENST00000382044	NM_001141980.1	1201	gTt/gCt	17/28	0.402019628462878	0	FACETS	0.845	0.794	0.897			1	CLONAL	1	TRUE	0	0.402019628462878	0		889	951	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996030	73996030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543666880	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	228	837	2	ENST00000318443.5:c.764C>T	p.Pro255Leu	p.P255L	ENST00000318443	NM_001024736.1	255	cCg/cTg	5/10	0.402019628462878	0	FACETS	0.792	0.74	0.847			1	SUBCLONAL	1	TRUE	0	0.402019628462878	0		839	856	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897439	78897439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1232044935	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	125	777	0	ENST00000306801.3:c.2774G>A	p.Arg925Gln	p.R925Q	ENST00000306801	NM_020761.2	925	cGg/cAg	23/34	0.402019628462878	0	FACETS	0.488	0.442	0.537			1	SUBCLONAL	1	TRUE	0	0.402019628462878	0		777	762	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222792	5222792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754813198	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	173	382	1	ENST00000357368.4:c.3011C>T	p.Thr1004Met	p.T1004M	ENST00000357368	NM_002850.3	1004	aCg/aTg	18/38	0.402019628462878	0	FACETS	0.929	0.86	0.999			1	CLONAL	1	TRUE	0	0.402019628462878	0		383	554	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313355	30313355	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	146	583	0	ENST00000262643.3:c.955T>C	p.Tyr319His	p.Y319H	ENST00000262643	NM_001238.2	319	Tat/Cat	11/12	0.402019628462878	0	FACETS	0.852	0.782	0.923			1	CLONAL	1	TRUE	0	0.402019628462878	0		583	510	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792331	33792331	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	69	834	2	ENST00000498907.2:c.990G>T	p.Gln330His	p.Q330H	ENST00000498907	NM_004364.3	330	caG/caT	1/1	0.402019628462878	0	FACETS	0.212	0.184	0.243			1	SUBCLONAL	1	TRUE	0	0.402019628462878	0		836	966	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574158	46574158	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	162	731	0	ENST00000263734.3:c.173G>C	p.Arg58Pro	p.R58P	ENST00000263734	NM_001430.4	58	cGa/cCa	2/16	0.402019628462878	0	FACETS	0.84	0.774	0.907			1	CLONAL	1	TRUE	0	0.402019628462878	0		731	574	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169953079	169953079	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs755677529	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	144	510	0	ENST00000295797.4:c.163C>T	p.Arg55Ter	p.R55*	ENST00000295797	NM_002740.5	55	Cga/Tga	2/18	0.402019628462878	0	FACETS	0.878	0.806	0.952			1	CLONAL	1	TRUE	0	0.402019628462878	0		510	488	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508799	31508799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	196	630	1	ENST00000344624.3:c.1516G>A	p.Ala506Thr	p.A506T	ENST00000344624		506	Gca/Aca	7/33	0.402019628462878	0	FACETS	0.707	0.655	0.76			1	SUBCLONAL	1	TRUE	0	0.402019628462878	0		631	825	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873582	35873582	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	39	182	0	ENST00000303115.3:c.538C>A	p.His180Asn	p.H180N	ENST00000303115	NM_002185.3	180	Cat/Aat	5/8	0.402019628462878	0	FACETS	0.959	0.814	1			1	CLONAL	1	TRUE	0	0.402019628462878	0		182	121	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021045	26021045	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs561395578	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	111	381	0	ENST00000357647.3:c.328C>A	p.Leu110Met	p.L110M	ENST00000357647	NM_003529.2	110	Ctg/Atg	1/1	0.402019628462878	0	FACETS	0.881	0.799	0.965			1	CLONAL	1	TRUE	0	0.402019628462878	0		381	375	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164717	32164717	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	212	682	0	ENST00000375023.3:c.5185del	p.Ala1729ProfsTer16	p.A1729Pfs*16	ENST00000375023	NM_004557.3	1729	Gcc/cc	28/30	0.402019628462878	0	FACETS	0.853	0.795	0.913			1	CLONAL	1	TRUE	0	0.402019628462878	0		682	739	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188411	32188411	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	118	512	0	ENST00000375023.3:c.930C>A	p.Asp310Glu	p.D310E	ENST00000375023	NM_004557.3	310	gaC/gaA	6/30	0.402019628462878	0	FACETS	0.9	0.82	0.983			1	CLONAL	1	TRUE	0	0.402019628462878	0		512	390	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964416	93964416	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	106	477	0	ENST00000369303.4:c.2481G>A	p.Trp827Ter	p.W827*	ENST00000369303	NM_004440.3	827	tgG/tgA	14/17	0.402019628462878	0	FACETS	0.869	0.786	0.954			1	CLONAL	1	TRUE	0	0.402019628462878	0		477	363	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188083	151188083	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	81	397	0	ENST00000262187.5:c.70A>G	p.Ile24Val	p.I24V	ENST00000262187	NM_005614.3	24	Att/Gtt	2/8	0.402019628462878	0	FACETS	0.775	0.689	0.865			1	SUBCLONAL	1	TRUE	0	0.402019628462878	0		397	311	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207684	29207684	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	111	268	0	ENST00000240100.2:c.112G>A	p.Gly38Arg	p.G38R	ENST00000240100	NM_001394.6	38	Ggg/Agg	1/4	0.374621229316082	3	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	1	0.402019628462878	3		268	319	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417476	139417476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	323	729	1	ENST00000277541.6:c.568C>T	p.Arg190Cys	p.R190C	ENST00000277541	NM_017617.3	190	Cgc/Tgc	4/34	0.402019628462878	0	FACETS	1	0.976	1			1	CLONAL	1	TRUE	0	0.402019628462878	0		730	913	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045902	47045902	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	157	704	1	ENST00000377604.3:c.2699del	p.Gly900ValfsTer24	p.G900Vfs*24	ENST00000377604	NM_001204468.1	899	ctG/ct	24/24	0.402019628462878	0	FACETS	0.707	0.649	0.766			1	SUBCLONAL	1	TRUE	0	0.402019628462878	0		705	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0042681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	175	768	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.108696827793656	1	FACETS	1	0.97	1	1	0.995	1	CLONAL	4	FALSE	0	0.108696827793656	1		768	693	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696688	47696688	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519971	NA	P-0042681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	54	483	0	ENST00000347630.2:c.260A>G	p.Tyr87Cys	p.Y87C	ENST00000347630	NM_001007230.1	87	tAc/tGc	5/11	0.108696827793656	1	FACETS	1	0.892	1	1	0.982	1	CLONAL	3	FALSE	0	0.108696827793656	1		483	300	SUCCESS
APC	324	MSKCC	GRCh37	5	112175861	112175862	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0042681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	14	223	0	ENST00000257430.4:c.4571_4572del	p.Ile1524AsnfsTer8	p.I1524Nfs*8	ENST00000257430	NM_000038.5	1524	ATa/a	16/16	0.108696827793656	1	FACETS	0.883	0.652	1	1	0.937	1	CLONAL	4	FALSE	0	0.108696827793656	1		223	69	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509338	149509349	+	inframe_deletion	In_Frame_Del	DEL	CCTCCTGCGTGT	CCTCCTGCGTGT	-	novel	NA	P-0042681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	46	563	0	ENST00000261799.4:c.1550_1561del	p.Asp517_Glu520del	p.D517_E520del	ENST00000261799	NM_002609.3	517	gACACGCAGGAGGtc/gtc	10/23	0.108696827793656	1	FACETS	1	0.897	1	1	0.974	1	CLONAL	2	FALSE	0	0.108696827793656	1		563	370	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	22	290	1	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.384	0.297	0.486	0.384	0.297	0.486	SUBCLONAL	1	TRUE	1	0.25	2		291	458	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	60	485	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	0.698	0.6	0.804	0.698	0.6	0.804	SUBCLONAL	1	TRUE	1	0.25	2		485	688	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803818	43803818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147938568	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	56	618	0	ENST00000372470.3:c.128G>A	p.Arg43Gln	p.R43Q	ENST00000372470	NM_005373.2	43	cGa/cAa	2/12	1	2	FACETS	0.649	0.555	0.752	0.649	0.555	0.752	SUBCLONAL	1	TRUE	1	0.25	2		618	690	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518099	8518099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764400127	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	54	357	0	ENST00000356435.5:c.1292C>T	p.Ser431Leu	p.S431L	ENST00000356435		431	tCg/tTg	10/35	1	2	FACETS	0.829	0.709	0.961	0.829	0.709	0.961	CLONAL	1	TRUE	1	0.25	2		357	521	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	88	371	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.25	2		371	609	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919244	48919244	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913296	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	27	149	0	ENST00000267163.4:c.409G>T	p.Glu137Ter	p.E137*	ENST00000267163	NM_000321.2	137	Gaa/Taa	4/27	1	2	FACETS	0.766	0.611	0.942	0.766	0.611	0.942	CLONAL	1	TRUE	1	0.25	2		149	282	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539951	187539951	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs777631605	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	57	333	0	ENST00000441802.2:c.7789C>T	p.Arg2597Ter	p.R2597*	ENST00000441802	NM_005245.3	2597	Cga/Tga	10/27	1	2	FACETS	0.896	0.769	1	0.896	0.769	1	CLONAL	1	TRUE	1	0.25	2		333	509	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7152900	7152900	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	70	436	0	ENST00000302850.5:c.2068G>A	p.Glu690Lys	p.E690K	ENST00000302850	NM_000208.2	690	Gag/Aag	10/22	1	2	FACETS	0.926	0.807	1	0.926	0.807	1	CLONAL	1	TRUE	1	0.25	2		436	605	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515141	103515141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770246574	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	29	270	0	ENST00000355739.4:c.1642G>A	p.Glu548Lys	p.E548K	ENST00000355739	NM_000123.3	548	Gaa/Aaa	8/15	1	2	FACETS	0.625	0.502	0.766	0.625	0.502	0.766	SUBCLONAL	1	TRUE	1	0.25	2		270	371	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685309	89685309	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs773176120	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	51	248	0	ENST00000371953.3:c.204C>G	p.Tyr68Ter	p.Y68*	ENST00000371953	NM_000314.4	68	taC/taG	3/9	1	2	FACETS	0.923	0.786	1	0.923	0.786	1	CLONAL	1	TRUE	1	0.25	2		248	442	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622457	28622457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751562024	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	38	516	0	ENST00000241453.7:c.1160G>A	p.Arg387Gln	p.R387Q	ENST00000241453	NM_004119.2	387	cGa/cAa	9/24	1	2	FACETS	0.408	0.336	0.488	0.408	0.336	0.488	SUBCLONAL	1	TRUE	1	0.25	2		516	746	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698180	47698180	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63751411	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	46	301	1	ENST00000233146.2:c.1738G>T	p.Glu580Ter	p.E580*	ENST00000233146	NM_000251.2	580	Gaa/Taa	11/16	1	2	FACETS	0.712	0.599	0.836	0.712	0.599	0.836	SUBCLONAL	1	TRUE	1	0.25	2		302	517	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	76	244	1	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.25	2		245	426	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205711	108205711	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	49	303	0	ENST00000278616.4:c.8026G>T	p.Glu2676Ter	p.E2676*	ENST00000278616	NM_000051.3	2676	Gaa/Taa	55/63	1	2	FACETS	0.885	0.751	1	0.885	0.751	1	CLONAL	1	TRUE	1	0.25	2		303	443	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937076	48937076	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	54	259	0	ENST00000267163.4:c.844G>T	p.Glu282Ter	p.E282*	ENST00000267163	NM_000321.2	282	Gaa/Taa	8/27	1	2	FACETS	0.989	0.846	1	0.989	0.846	1	CLONAL	1	TRUE	1	0.25	2		259	437	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344077	70344077	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	94	727	0	ENST00000374080.3:c.1813C>T	p.Arg605Ter	p.R605*	ENST00000374080		605	Cga/Tga	13/45	1	2	FACETS	0.742	0.659	0.832	0.742	0.659	0.832	SUBCLONAL	1	TRUE	1	0.25	2		727	1013	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	94	528	0	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	0.932	0.829	1	0.932	0.829	1	CLONAL	1	TRUE	1	0.25	2		528	807	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005419	29005419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55687105	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	30	309	0	ENST00000282397.4:c.842G>A	p.Arg281Gln	p.R281Q	ENST00000282397	NM_002019.4	281	cGa/cAa	7/30	1	2	FACETS	0.521	0.419	0.636	0.521	0.419	0.636	SUBCLONAL	1	TRUE	1	0.25	2		309	461	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024169	112024169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465963577	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	32	373	0	ENST00000368678.4:c.616C>T	p.Arg206Cys	p.R206C	ENST00000368678		206	Cgc/Tgc	7/13	1	2	FACETS	0.452	0.366	0.55	0.452	0.366	0.55	SUBCLONAL	1	TRUE	1	0.25	2		373	566	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379426	225379426	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	56	550	0	ENST00000264414.4:c.442C>T	p.Arg148Ter	p.R148*	ENST00000264414	NM_003590.4	148	Cga/Tga	4/16	1	2	FACETS	0.542	0.463	0.628	0.542	0.463	0.628	SUBCLONAL	1	TRUE	1	0.25	2		550	827	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830958	72830958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393698686	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	56	416	1	ENST00000268489.5:c.5623G>A	p.Glu1875Lys	p.E1875K	ENST00000268489	NM_006885.3	1875	Gaa/Aaa	9/10	1	2	FACETS	0.815	0.698	0.942	0.815	0.698	0.942	CLONAL	1	TRUE	1	0.25	2		417	550	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201966	102201966	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	34	176	1	ENST00000263464.3:c.1318G>T	p.Glu440Ter	p.E440*	ENST00000263464	NM_001165.4	440	Gaa/Taa	6/9	1	2	FACETS	0.968	0.794	1	0.968	0.794	1	CLONAL	1	TRUE	1	0.25	2		177	281	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850948	63850948	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	64	426	1	ENST00000279873.7:c.1726G>T	p.Glu576Ter	p.E576*	ENST00000279873	NM_032199.2	576	Gaa/Taa	10/10	1	2	FACETS	0.771	0.667	0.884	0.771	0.667	0.884	SUBCLONAL	1	TRUE	1	0.25	2		427	664	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81902830	81902830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766422892	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	51	431	0	ENST00000359376.3:c.491G>A	p.Arg164Gln	p.R164Q	ENST00000359376	NM_002661.3	164	cGa/cAa	6/33	1	2	FACETS	0.662	0.562	0.772	0.662	0.562	0.772	SUBCLONAL	1	TRUE	1	0.25	2		431	616	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692811	89692811	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	70	225	0	ENST00000371953.3:c.295G>T	p.Glu99Ter	p.E99*	ENST00000371953	NM_000314.4	99	Gaa/Taa	5/9	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.25	2		225	399	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519927	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	88	476	0	ENST00000263967.3:c.1625A>G	p.Glu542Gly	p.E542G	ENST00000263967	NM_006218.2	542	gAa/gGa	10/21	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.25	2		476	632	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190753	108190753	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587780635	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	84	333	0	ENST00000278616.4:c.6420C>A	p.Phe2140Leu	p.F2140L	ENST00000278616	NM_000051.3	2140	ttC/ttA	44/63	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.25	2		333	574	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984022	2984022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753614569	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	61	502	0	ENST00000396946.4:c.508C>T	p.Arg170Cys	p.R170C	ENST00000396946	NM_032415.4	170	Cgc/Tgc	5/25	1	2	FACETS	0.873	0.753	1	0.873	0.753	1	CLONAL	1	TRUE	1	0.25	2		502	559	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317623	163317623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747173543	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	46	361	0	ENST00000271452.3:c.1019C>T	p.Ser340Leu	p.S340L	ENST00000271452	NM_145697.2	340	tCg/tTg	12/14	1	2	FACETS	0.768	0.647	0.902	0.768	0.647	0.902	CLONAL	1	TRUE	1	0.25	2		361	479	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127414	55127414	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501504	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	79	525	0	ENST00000257290.5:c.202G>A	p.Asp68Asn	p.D68N	ENST00000257290	NM_006206.4	68	Gat/Aat	3/23	1	2	FACETS	0.894	0.786	1	0.894	0.786	1	CLONAL	1	TRUE	1	0.25	2		525	707	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59793411	59793411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375082407	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	70	349	0	ENST00000259008.2:c.2393G>A	p.Arg798Gln	p.R798Q	ENST00000259008	NM_032043.2	798	cGa/cAa	17/20	1	2	FACETS	0.956	0.834	1	0.956	0.834	1	CLONAL	1	TRUE	1	0.25	2		349	586	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144442	58144442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373619077	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	29	260	0	ENST00000257904.6:c.629G>A	p.Arg210Gln	p.R210Q	ENST00000257904	NM_000075.3	210	cGa/cAa	5/8	1	2	FACETS	0.789	0.635	0.963	0.789	0.635	0.963	CLONAL	1	TRUE	1	0.25	2		260	294	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183551	185183551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	39	282	0	ENST00000265026.3:c.1405C>T	p.Arg469Cys	p.R469C	ENST00000265026	NM_004721.4	469	Cgt/Tgt	9/14	1	2	FACETS	0.78	0.647	0.928	0.78	0.647	0.928	CLONAL	1	TRUE	1	0.25	2		282	400	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871986	45871986	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs748842373	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	72	477	0	ENST00000391945.4:c.262C>T	p.Arg88Ter	p.R88*	ENST00000391945	NM_000400.3	88	Cga/Tga	5/23	1	2	FACETS	0.903	0.789	1	0.903	0.789	1	CLONAL	1	TRUE	1	0.25	2		477	638	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836804	151836804	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	83	419	0	ENST00000262189.6:c.14416C>T	p.Arg4806Ter	p.R4806*	ENST00000262189	NM_170606.2	4806	Cga/Tga	56/59	1	2	FACETS	0.857	0.755	0.966	0.857	0.755	0.966	CLONAL	1	TRUE	1	0.25	2		419	775	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938788	76938788	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	73	573	0	ENST00000373344.5:c.1960C>T	p.Arg654Ter	p.R654*	ENST00000373344	NM_000489.3	654	Cga/Tga	9/35	1	2	FACETS	0.695	0.607	0.791	0.695	0.607	0.791	SUBCLONAL	1	TRUE	1	0.25	2		573	840	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434426	110434426	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs149826392	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	57	477	1	ENST00000375856.3:c.3975C>A	p.Phe1325Leu	p.F1325L	ENST00000375856	NM_003749.2	1325	ttC/ttA	1/2	1	2	FACETS	0.688	0.589	0.795	0.688	0.589	0.795	SUBCLONAL	1	TRUE	1	0.25	2		478	663	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115595	108115595	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs769166447	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	53	393	0	ENST00000278616.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000278616	NM_000051.3	248	cGa/cTa	7/63	1	2	FACETS	0.703	0.599	0.817	0.703	0.599	0.817	SUBCLONAL	1	TRUE	1	0.25	2		393	603	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374318	31374318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200236170	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	33	460	0	ENST00000328111.2:c.317G>A	p.Arg106Gln	p.R106Q	ENST00000328111	NM_006892.3	106	cGa/cAa	5/23	1	2	FACETS	0.48	0.39	0.582	0.48	0.39	0.582	SUBCLONAL	1	TRUE	1	0.25	2		460	550	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026133	71026133	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs775136381	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	73	343	0	ENST00000318789.4:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000318789	NM_032682.5	497	Cga/Tga	17/21	1	2	FACETS	0.98	0.858	1	0.98	0.858	1	CLONAL	1	TRUE	1	0.25	2		343	596	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431649	6431649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	80	473	0	ENST00000356142.4:c.202C>T	p.Arg68Cys	p.R68C	ENST00000356142	NM_018890.3	68	Cgc/Tgc	3/7	1	2	FACETS	0.968	0.852	1	0.968	0.852	1	CLONAL	1	TRUE	1	0.25	2		473	661	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850885	128850885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61740964	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	82	571	1	ENST00000249373.3:c.1732G>A	p.Glu578Lys	p.E578K	ENST00000249373	NM_005631.4	578	Gag/Aag	10/12	1	2	FACETS	0.919	0.81	1	0.919	0.81	1	CLONAL	1	TRUE	1	0.25	2		572	714	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295755	212295755	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	90	483	0	ENST00000342788.4:c.2558C>A	p.Ser853Tyr	p.S853Y	ENST00000342788	NM_005235.2	853	tCt/tAt	21/28	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.25	2		483	693	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112388	115112388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs565848855	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	27	175	0	ENST00000257566.3:c.1352C>T	p.Ala451Val	p.A451V	ENST00000257566	NM_016569.3	451	gCg/gTg	7/8	1	2	FACETS	0.85	0.679	1	0.85	0.679	1	CLONAL	1	TRUE	1	0.25	2		175	254	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410988	31410988	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1295265844	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	108	501	1	ENST00000344624.3:c.3532C>T	p.Arg1178Ter	p.R1178*	ENST00000344624		1178	Cga/Tga	28/33	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.25	2		502	743	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94910992	94910992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	105	533	1	ENST00000536441.1:c.1138C>T	p.Arg380Trp	p.R380W	ENST00000536441	NM_144665.3	380	Cgg/Tgg	8/10	1	2	FACETS	0.92	0.823	1	0.92	0.823	1	CLONAL	1	TRUE	1	0.25	2		534	913	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241093	39241093	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	90	454	2	ENST00000402219.2:c.1978C>T	p.Arg660Cys	p.R660C	ENST00000402219	NM_005633.3	660	Cgc/Tgc	12/23	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.25	2		456	632	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169036	32169036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745902446	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	91	710	1	ENST00000375023.3:c.3997C>T	p.Arg1333Cys	p.R1333C	ENST00000375023	NM_004557.3	1333	Cgt/Tgt	22/30	1	2	FACETS	0.98	0.87	1	0.98	0.87	1	CLONAL	1	TRUE	1	0.25	2		711	743	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145001	58145001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772938517	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	43	424	0	ENST00000257904.6:c.343G>A	p.Glu115Lys	p.E115K	ENST00000257904	NM_000075.3	115	Gaa/Aaa	3/8	1	2	FACETS	0.475	0.396	0.563	0.475	0.396	0.563	SUBCLONAL	1	TRUE	1	0.25	2		424	724	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56381317	56381317	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	32	180	0	ENST00000348428.3:c.961G>T	p.Glu321Ter	p.E321*	ENST00000348428	NM_006785.3	321	Gaa/Taa	8/17	1	2	FACETS	0.663	0.538	0.804	0.663	0.538	0.804	SUBCLONAL	1	TRUE	1	0.25	2		180	386	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484287	8484287	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	67	380	0	ENST00000356435.5:c.3245C>A	p.Ser1082Ter	p.S1082*	ENST00000356435		1082	tCa/tAa	19/35	1	2	FACETS	0.874	0.76	0.998	0.874	0.76	0.998	CLONAL	1	TRUE	1	0.25	2		380	613	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914722	39914722	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	80	460	1	ENST00000378444.4:c.4640G>T	p.Arg1547Leu	p.R1547L	ENST00000378444	NM_001123385.1	1547	cGa/cTa	12/15	1	2	FACETS	0.913	0.803	1	0.913	0.803	1	CLONAL	1	TRUE	1	0.25	2		461	701	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704605	117704605	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	56	321	1	ENST00000368508.3:c.2371G>T	p.Asp791Tyr	p.D791Y	ENST00000368508	NM_002944.2	791	Gac/Tac	16/43	1	2	FACETS	0.878	0.753	1	0.878	0.753	1	CLONAL	1	TRUE	1	0.25	2		322	510	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889176	76889176	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	49	334	0	ENST00000373344.5:c.4834C>A	p.Leu1612Ile	p.L1612I	ENST00000373344	NM_000489.3	1612	Ctt/Att	18/35	1	2	FACETS	0.654	0.554	0.766	0.654	0.554	0.766	SUBCLONAL	1	TRUE	1	0.25	2		334	599	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94170355	94170355	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	60	293	0	ENST00000323929.3:c.1914G>T	p.Lys638Asn	p.K638N	ENST00000323929	NM_005591.3	638	aaG/aaT	17/20	1	2	FACETS	0.901	0.777	1	0.901	0.777	1	CLONAL	1	TRUE	1	0.25	2		293	533	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727052	243727052	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	57	390	0	ENST00000263826.5:c.918C>A	p.Phe306Leu	p.F306L	ENST00000263826	NM_005465.4	306	ttC/ttA	9/13	1	2	FACETS	0.708	0.607	0.819	0.708	0.607	0.819	SUBCLONAL	1	TRUE	1	0.25	2		390	644	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858940	243858940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	64	417	0	ENST00000263826.5:c.125C>T	p.Pro42Leu	p.P42L	ENST00000263826	NM_005465.4	42	cCt/cTt	2/13	1	2	FACETS	0.919	0.797	1	0.919	0.797	1	CLONAL	1	TRUE	1	0.25	2		417	557	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332927	70332927	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	70	579	0	ENST00000373644.4:c.832G>T	p.Glu278Ter	p.E278*	ENST00000373644	NM_030625.2	278	Gaa/Taa	2/12	1	2	FACETS	0.718	0.625	0.819	0.718	0.625	0.819	SUBCLONAL	1	TRUE	1	0.25	2		579	780	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933223	100933223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1175582391	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	111	388	0	ENST00000325455.5:c.2167G>A	p.Glu723Lys	p.E723K	ENST00000325455	NM_001202474.3	723	Gag/Aag	4/8	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.25	2		388	796	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996807	100996831	+	frameshift_variant	Frame_Shift_Del	DEL	CTTCATCCCCACAGATTAAACAAAT	CTTCATCCCCACAGATTAAACAAAT	-	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	74	448	0	ENST00000325455.5:c.1696_1720del	p.Ile566HisfsTer75	p.I566Hfs*75	ENST00000325455	NM_001202474.3	566	ATTTGTTTAATCTGTGGGGATGAAGca/ca	2/8	1	2	FACETS	0.847	0.741	0.961	0.847	0.741	0.961	CLONAL	1	TRUE	1	0.25	2		448	699	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344075	118344075	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	49	310	0	ENST00000534358.1:c.2201G>T	p.Arg734Ile	p.R734I	ENST00000534358	NM_005933.3	734	aGa/aTa	3/36	1	2	FACETS	0.862	0.731	1	0.862	0.731	1	CLONAL	1	TRUE	1	0.25	2		310	455	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344743	118344743	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555036782	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	42	324	0	ENST00000534358.1:c.2869A>C	p.Lys957Gln	p.K957Q	ENST00000534358	NM_005933.3	957	Aaa/Caa	3/36	1	2	FACETS	0.778	0.65	0.919	0.778	0.65	0.919	CLONAL	1	TRUE	1	0.25	2		324	432	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811624	102811624	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	88	470	1	ENST00000307046.8:c.560C>T	p.Ala187Val	p.A187V	ENST00000307046	NM_001111285.1	187	gCt/gTt	4/4	1	2	FACETS	0.85	0.752	0.955	0.85	0.752	0.955	CLONAL	1	TRUE	1	0.25	2		471	828	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41999935	41999935	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	82	431	0	ENST00000219905.7:c.2198A>C	p.Lys733Thr	p.K733T	ENST00000219905	NM_001164273.1	733	aAa/aCa	6/24	1	2	FACETS	0.978	0.862	1	0.978	0.862	1	CLONAL	1	TRUE	1	0.25	2		431	671	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50830414	50830414	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	42	382	0	ENST00000398568.2:c.2857A>G	p.Lys953Glu	p.K953E	ENST00000398568	NM_001042412.1	953	Aaa/Gaa	18/18	1	2	FACETS	0.639	0.533	0.757	0.639	0.533	0.757	SUBCLONAL	1	TRUE	1	0.25	2		382	526	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819699	81819699	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	64	489	1	ENST00000359376.3:c.105G>T	p.Lys35Asn	p.K35N	ENST00000359376	NM_002661.3	35	aaG/aaT	2/33	1	2	FACETS	0.752	0.65	0.862	0.752	0.65	0.862	SUBCLONAL	1	TRUE	1	0.25	2		490	681	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627504	37627504	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	61	501	0	ENST00000447079.4:c.1419A>C	p.Lys473Asn	p.K473N	ENST00000447079	NM_015083.1	473	aaA/aaC	2/14	1	2	FACETS	0.67	0.577	0.772	0.67	0.577	0.772	SUBCLONAL	1	TRUE	1	0.25	2		501	728	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865301	40865301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	85	539	0	ENST00000428826.2:c.1130C>T	p.Ala377Val	p.A377V	ENST00000428826		377	gCc/gTc	11/21	1	2	FACETS	0.977	0.864	1	0.977	0.864	1	CLONAL	1	TRUE	1	0.25	2		539	696	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018249	48018249	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	82	411	0	ENST00000234420.5:c.444A>C	p.Leu148Phe	p.L148F	ENST00000234420	NM_000179.2	148	ttA/ttC	2/10	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.25	2		411	652	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735366	204735366	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	37	241	0	ENST00000302823.3:c.167T>G	p.Phe56Cys	p.F56C	ENST00000302823	NM_005214.4	56	tTt/tGt	2/4	1	2	FACETS	0.937	0.775	1	0.937	0.775	1	CLONAL	1	TRUE	1	0.25	2		241	316	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205176	128205176	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	75	528	0	ENST00000341105.2:c.265T>G	p.Leu89Val	p.L89V	ENST00000341105	NM_032638.4	89	Ttg/Gtg	3/6	1	2	FACETS	0.844	0.739	0.957	0.844	0.739	0.957	CLONAL	1	TRUE	1	0.25	2		528	711	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968334	134968334	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	25	429	0	ENST00000398015.3:c.2846+1G>T		p.X949_splice	ENST00000398015	NM_004441.4	949			1	2	FACETS	0.402	0.316	0.502	0.402	0.316	0.502	SUBCLONAL	1	TRUE	1	0.25	2		429	497	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143191816	143191816	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	52	314	0	ENST00000262992.4:c.615G>T	p.Lys205Asn	p.K205N	ENST00000262992	NM_001101669.1	205	aaG/aaT	8/24	1	2	FACETS	0.929	0.792	1	0.929	0.792	1	CLONAL	1	TRUE	1	0.25	2		314	448	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629221	187629221	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	73	469	0	ENST00000441802.2:c.1761A>C	p.Gln587His	p.Q587H	ENST00000441802	NM_005245.3	587	caA/caC	2/27	1	2	FACETS	0.765	0.669	0.87	0.765	0.669	0.87	SUBCLONAL	1	TRUE	1	0.25	2		469	763	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522808	67522808	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368742778	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	46	259	0	ENST00000274335.5:c.305C>T	p.Ser102Leu	p.S102L	ENST00000274335		102	tCg/tTg	1/15	1	2	FACETS	0.906	0.765	1	0.906	0.765	1	CLONAL	1	TRUE	1	0.25	2		259	406	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322566	109322566	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	79	569	0	ENST00000436639.2:c.471C>A	p.Phe157Leu	p.F157L	ENST00000436639	NM_014454.2	157	ttC/ttA	3/10	1	2	FACETS	0.732	0.643	0.829	0.732	0.643	0.829	SUBCLONAL	1	TRUE	1	0.25	2		569	863	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112035566	112035566	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	48	319	0	ENST00000368678.4:c.328C>A	p.Gln110Lys	p.Q110K	ENST00000368678		110	Caa/Aaa	4/13	1	2	FACETS	0.77	0.651	0.9	0.77	0.651	0.9	SUBCLONAL	1	TRUE	1	0.25	2		319	499	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138201358	138201358	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	76	398	0	ENST00000237289.4:c.2057T>G	p.Phe686Cys	p.F686C	ENST00000237289	NM_001270507.1	686	tTt/tGt	8/9	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.25	2		398	585	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229272	55229272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768627073	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	79	506	0	ENST00000275493.2:c.1579C>T	p.Arg527Trp	p.R527W	ENST00000275493	NM_005228.3	527	Cgg/Tgg	13/28	1	2	FACETS	0.928	0.816	1	0.928	0.816	1	CLONAL	1	TRUE	1	0.25	2		506	681	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874466	151874466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753744599	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	58	360	0	ENST00000262189.6:c.8072C>T	p.Ser2691Phe	p.S2691F	ENST00000262189	NM_170606.2	2691	tCt/tTt	38/59	1	2	FACETS	0.975	0.839	1	0.975	0.839	1	CLONAL	1	TRUE	1	0.25	2		360	476	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965439	68965439	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	119	655	0	ENST00000288368.4:c.1051G>T	p.Glu351Ter	p.E351*	ENST00000288368	NM_024870.2	351	Gaa/Taa	9/40	1	2	FACETS	0.886	0.798	0.98	0.886	0.798	0.98	CLONAL	1	TRUE	1	0.25	2		655	1074	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980587	70980587	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs761251088	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	81	601	0	ENST00000276594.2:c.790C>A	p.Pro264Thr	p.P264T	ENST00000276594	NM_024504.3	264	Cca/Aca	4/8	1	2	FACETS	0.89	0.784	1	0.89	0.784	1	CLONAL	1	TRUE	1	0.25	2		601	728	SUCCESS
BTK	695	MSKCC	GRCh37	X	100629595	100629595	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	73	456	0	ENST00000308731.7:c.169G>T	p.Asp57Tyr	p.D57Y	ENST00000308731	NM_000061.2	57	Gat/Tat	3/19	1	2	FACETS	0.886	0.775	1	0.886	0.775	1	CLONAL	1	TRUE	1	0.25	2		456	659	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020293	123020293	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1484649473	NA	P-0042702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	67	473	0	ENST00000355640.3:c.781T>C	p.Ser261Pro	p.S261P	ENST00000355640		261	Tcc/Ccc	2/7	1	2	FACETS	0.798	0.693	0.911	0.798	0.693	0.911	CLONAL	1	TRUE	1	0.25	2		473	672	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0042704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	31	389	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.821	0.663	1	0.821	0.663	1	CLONAL	1	TRUE	1	0.16	2		389	472	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937422	178937422	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	28	279	0	ENST00000263967.3:c.1810T>C	p.Cys604Arg	p.C604R	ENST00000263967	NM_006218.2	604	Tgt/Cgt	12/21	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.16	2		279	306	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772234	68772235	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0042704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	51	815	0	ENST00000261769.5:c.85dup	p.His29ProfsTer5	p.H29Pfs*5	ENST00000261769	NM_004360.3	28	tgc/tgCc	2/16	1	2	FACETS	0.7	0.593	0.818	0.7	0.593	0.818	SUBCLONAL	1	TRUE	1	0.16	2		815	911	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0042715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	86	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		334	629	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579716	7579716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1192416464	NA	P-0042715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	75	874	0	ENST00000269305.4:c.80del	p.Pro27LeufsTer17	p.P27Lfs*17	ENST00000269305	NM_001126112.2	27	cCt/ct	3/11	0.125576466484215	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		874	906	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263350	123263350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	58	611	0	ENST00000358487.5:c.1393G>A	p.Glu465Lys	p.E465K	ENST00000358487	NM_000141.4	465	Gag/Aag	10/18	0.125576466484215	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		611	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578410	7578410	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	97	702	0	ENST00000269305.4:c.520A>T	p.Arg174Trp	p.R174W	ENST00000269305	NM_001126112.2	174	Agg/Tgg	5/11	1	2	FACETS	0.527	0.469	0.589	0.527	0.469	0.589	SUBCLONAL	1	TRUE	1	0.400376847412953	2		702	919	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238339	98238339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753240797	NA	P-0042716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	47	514	1	ENST00000331920.6:c.1705G>A	p.Ala569Thr	p.A569T	ENST00000331920	NM_000264.3	569	Gct/Act	12/24	1	2	FACETS	0.278	0.233	0.327	0.278	0.233	0.327	SUBCLONAL	1	TRUE	1	0.400376847412953	2		515	846	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988128	85988128	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042748-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	310	385	0	ENST00000263360.6:c.1073A>G	p.Tyr358Cys	p.Y358C	ENST00000263360	NM_003797.3	358	tAc/tGc	10/12	0.203491728048387	1	FACETS	0.997	0.948	1	1	0.997	1	CLONAL	4	TRUE	0	0.203491728048387	1		385	686	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875985	76875985	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042748-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	220	266	0	ENST00000373344.5:c.5150T>G	p.Val1717Gly	p.V1717G	ENST00000373344	NM_000489.3	1717	gTt/gGt	20/35	0.203491728048387	1	FACETS	1	0.977	1	1	0.995	1	CLONAL	3	TRUE	0	0.203491728048387	1		266	595	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10785930	10785930	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042748-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	328	554	0	ENST00000361367.2:c.1360C>G	p.Leu454Val	p.L454V	ENST00000361367	NM_014633.3	454	Ctc/Gtc	11/25	0.203491728048387	1	FACETS	1	0.988	1	1	0.997	1	CLONAL	3	TRUE	0	0.203491728048387	1		554	849	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0042765-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	55	191	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.627	0.536	0.727	0.627	0.536	0.727	SUBCLONAL	1	TRUE	1	0.2897665914755	2		191	605	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0042765-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	128	493	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.2897665914755	2	FACETS	0.755	0.687	0.827	0.755	0.687	0.827	SUBCLONAL	2	TRUE	0	0.2897665914755	2		493	585	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0042765-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	59	457	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.823	0.709	0.946	0.823	0.709	0.946	CLONAL	1	TRUE	1	0.2897665914755	2		457	495	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900291	101900291	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042765-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	94	510	0	ENST00000374994.4:c.725G>A	p.Trp242Ter	p.W242*	ENST00000374994	NM_004612.2	242	tGg/tAg	4/9	0.2897665914755	1	FACETS	0.932	0.831	1	0.932	0.831	1	CLONAL	1	TRUE	0	0.2897665914755	1		510	595	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288967	212288967	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs537458255	NA	P-0042803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	39	459	0	ENST00000342788.4:c.2779C>T	p.Arg927Ter	p.R927*	ENST00000342788	NM_005235.2	927	Cga/Tga	23/28	0.234973919207204	2	FACETS	0.665	0.552	0.791	0.333	0.276	0.396	SUBCLONAL	1	TRUE	0	0.284612279440409	2		459	412	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482870	67482870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	78	534	0	ENST00000327367.4:c.1274C>T	p.Ser425Phe	p.S425F	ENST00000327367	NM_005902.3	425	tCt/tTt	9/9	1	2	FACETS	0.958	0.843	1	0.958	0.843	1	CLONAL	1	TRUE	1	0.284612279440409	2		534	572	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044850	47044850	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	124	993	1	ENST00000377604.3:c.2176C>T	p.Arg726Ter	p.R726*	ENST00000377604	NM_001204468.1	726	Cga/Tga	20/24	0.284612279440409	1	FACETS	0.87	0.787	0.958	0.87	0.787	0.958	CLONAL	1	TRUE	0	0.284612279440409	1		994	859	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058075	27058075	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	139	478	0	ENST00000324856.7:c.1783C>T	p.Gln595Ter	p.Q595*	ENST00000324856	NM_006015.4	595	Cag/Tag	3/20	0.234973919207204	2	FACETS	0.779	0.711	0.849	0.779	0.711	0.849	SUBCLONAL	2	TRUE	0	0.284612279440409	2		478	627	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591737	38591738	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0042803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	74	450	0	ENST00000299084.4:c.196_197del	p.Arg66GlyfsTer11	p.R66Gfs*11	ENST00000299084	NM_152594.2	66	AGg/g	2/7	1	2	FACETS	0.985	0.864	1	0.985	0.864	1	CLONAL	1	TRUE	1	0.284612279440409	2		450	528	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721360	176721360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772981865	NA	P-0042803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	69	587	0	ENST00000439151.2:c.6991G>A	p.Asp2331Asn	p.D2331N	ENST00000439151	NM_022455.4	2331	Gac/Aac	23/23	1	2	FACETS	0.79	0.688	0.9	0.79	0.688	0.9	SUBCLONAL	1	TRUE	1	0.284612279440409	2		587	614	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	256	922	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.631	0.591	0.672	0.631	0.591	0.672	SUBCLONAL	1	TRUE	1	0.818000526830423	2		922	992	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	108	583	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.393254473051354	3	FACETS	0.644	0.579	0.712	0.322	0.289	0.356	INDETERMINATE	1	TRUE	1	0.818000526830423	3		583	578	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	380	896	5	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.818000526830423	2		901	796	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	58	304	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.514	0.445	0.587	0.514	0.445	0.587	SUBCLONAL	1	TRUE	1	0.818000526830423	2		304	276	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057835	27057835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	233	842	0	ENST00000324856.7:c.1543C>T	p.Gln515Ter	p.Q515*	ENST00000324856	NM_006015.4	515	Cag/Tag	3/20	1	2	FACETS	0.629	0.588	0.672	0.629	0.588	0.672	SUBCLONAL	1	TRUE	1	0.818000526830423	2		842	905	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	98	495	1	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.385	0.344	0.429	0.385	0.344	0.429	SUBCLONAL	1	TRUE	1	0.818000526830423	2		496	622	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733513	85733513	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs387906350	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	47	471	4	ENST00000370580.1:c.499del	p.Ser167LeufsTer6	p.S167Lfs*6	ENST00000370580	NM_003921.4	167	Tct/ct	3/3	1	2	FACETS	0.239	0.201	0.28	0.239	0.201	0.28	SUBCLONAL	1	TRUE	1	0.818000526830423	2		475	481	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760702	133760702	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	306	1028	3	ENST00000318560.5:c.3025C>T	p.Arg1009Ter	p.R1009*	ENST00000318560	NM_005157.4	1009	Cga/Tga	11/11	1	2	FACETS	0.668	0.63	0.707	0.668	0.63	0.707	SUBCLONAL	1	TRUE	1	0.818000526830423	2		1031	1120	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	33	542	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.153	0.124	0.185	0.153	0.124	0.185	SUBCLONAL	1	TRUE	1	0.818000526830423	2		542	529	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	102	368	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.577	0.519	0.638	0.577	0.519	0.638	SUBCLONAL	1	TRUE	1	0.818000526830423	2		368	432	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	45	386	2	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.215	0.181	0.254	0.215	0.181	0.254	SUBCLONAL	1	TRUE	1	0.818000526830423	2		388	511	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	90	402	4	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.59	0.527	0.656	0.59	0.527	0.656	SUBCLONAL	1	TRUE	1	0.818000526830423	2		406	373	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	166	558	5	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.604	0.556	0.653	0.604	0.556	0.653	SUBCLONAL	1	TRUE	1	0.818000526830423	2		563	672	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743896	41743896	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	252	933	0	ENST00000301178.4:c.836del	p.Pro279GlnfsTer18	p.P279Qfs*18	ENST00000301178	NM_021913.4	277	gaC/ga	7/20	1	2	FACETS	0.631	0.591	0.673	0.631	0.591	0.673	SUBCLONAL	1	TRUE	1	0.818000526830423	2		933	976	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337296	89337296	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567537413	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	55	647	1	ENST00000301030.4:c.7735C>T	p.Arg2579Cys	p.R2579C	ENST00000301030	NM_001256183.1	2579	Cgc/Tgc	12/13	1	2	FACETS	0.151	0.129	0.176	0.151	0.129	0.176	SUBCLONAL	1	TRUE	1	0.818000526830423	2		648	889	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453124	140453124	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	31	431	1	ENST00000288602.6:c.1811G>T	p.Trp604Leu	p.W604L	ENST00000288602	NM_004333.4	604	tGg/tTg	15/18	1	2	FACETS	0.142	0.115	0.174	0.142	0.115	0.174	SUBCLONAL	1	TRUE	1	0.818000526830423	2		432	532	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759697	133759697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776289598	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	98	730	0	ENST00000318560.5:c.2020C>T	p.Arg674Trp	p.R674W	ENST00000318560	NM_005157.4	674	Cgg/Tgg	11/11	1	2	FACETS	0.355	0.317	0.396	0.355	0.317	0.396	SUBCLONAL	1	TRUE	1	0.818000526830423	2		730	675	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598124	52598124	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	46	571	0	ENST00000394830.3:c.3742G>T	p.Gly1248Ter	p.G1248*	ENST00000394830	NM_018313.4	1248	Gga/Tga	24/30	1	2	FACETS	0.148	0.124	0.175	0.148	0.124	0.175	SUBCLONAL	1	TRUE	1	0.818000526830423	2		571	759	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380350	14380350	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	149	366	1	ENST00000256196.4:c.67G>T	p.Gly23Cys	p.G23C	ENST00000256196		23	Ggc/Tgc	1/6	1	2	FACETS	0.737	0.678	0.798	0.737	0.678	0.798	SUBCLONAL	1	TRUE	1	0.818000526830423	2		367	494	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441816	49441816	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	81	724	1	ENST00000301067.7:c.4168del	p.Ala1390GlnfsTer27	p.A1390Qfs*27	ENST00000301067	NM_003482.3	1390	Gca/ca	14/54	1	2	FACETS	0.231	0.202	0.261	0.231	0.202	0.261	SUBCLONAL	1	TRUE	1	0.818000526830423	2		725	859	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345760	152345760	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	79	268	0	ENST00000359321.1:c.810del	p.Phe270LeufsTer27	p.F270Lfs*27	ENST00000359321	NM_005431.1	270	ttT/tt	3/3	1	2	FACETS	0.607	0.539	0.679	0.607	0.539	0.679	SUBCLONAL	1	TRUE	1	0.818000526830423	2		268	318	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302825	15302825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776600631	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	270	1011	2	ENST00000263388.2:c.625G>A	p.Gly209Arg	p.G209R	ENST00000263388	NM_000435.2	209	Ggg/Agg	4/33	1	2	FACETS	0.628	0.589	0.667	0.628	0.589	0.667	SUBCLONAL	1	TRUE	1	0.818000526830423	2		1013	1052	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120094	70120094	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	19	61	0	ENST00000245479.2:c.1100del	p.Pro367HisfsTer16	p.P367Hfs*16	ENST00000245479	NM_000346.3	366	Ccc/cc	3/3	1	2	FACETS	0.726	0.569	0.897	0.726	0.569	0.897	SUBCLONAL	1	TRUE	1	0.818000526830423	2		61	64	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360920	118360920	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1356402762	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	63	512	0	ENST00000534358.1:c.4652A>G	p.His1551Arg	p.H1551R	ENST00000534358	NM_005933.3	1551	cAt/cGt	13/36	1	2	FACETS	0.213	0.184	0.245	0.213	0.184	0.245	SUBCLONAL	1	TRUE	1	0.818000526830423	2		512	722	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420578	49420578	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	245	764	1	ENST00000301067.7:c.15171G>T	p.Trp5057Cys	p.W5057C	ENST00000301067	NM_003482.3	5057	tgG/tgT	48/54	1	2	FACETS	0.706	0.662	0.752	0.706	0.662	0.752	SUBCLONAL	1	TRUE	1	0.818000526830423	2		765	848	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123875278	123875278	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	25	245	0	ENST00000330479.4:c.234T>G	p.His78Gln	p.H78Q	ENST00000330479	NM_020382.3	78	caT/caG	3/9	1	2	FACETS	0.259	0.205	0.321	0.259	0.205	0.321	SUBCLONAL	1	TRUE	1	0.818000526830423	2		245	236	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555763	21555763	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	227	785	0	ENST00000382592.4:c.2507T>C	p.Met836Thr	p.M836T	ENST00000382592	NM_014572.2	836	aTg/aCg	6/8	1	2	FACETS	0.648	0.604	0.692	0.648	0.604	0.692	SUBCLONAL	1	TRUE	1	0.818000526830423	2		785	857	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223265	2223265	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	262	865	0	ENST00000326181.6:c.877C>T	p.Gln293Ter	p.Q293*	ENST00000326181	NM_032271.2	293	Cag/Tag	10/21	1	2	FACETS	0.625	0.586	0.665	0.625	0.586	0.665	SUBCLONAL	1	TRUE	1	0.818000526830423	2		865	1025	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660618	67660618	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	85	593	0	ENST00000264010.4:c.1518G>T	p.Gln506His	p.Q506H	ENST00000264010	NM_006565.3	506	caG/caT	8/12	1	2	FACETS	0.248	0.218	0.279	0.248	0.218	0.279	SUBCLONAL	1	TRUE	1	0.818000526830423	2		593	839	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610250	10610250	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	271	1000	1	ENST00000171111.5:c.460C>T	p.His154Tyr	p.H154Y	ENST00000171111	NM_203500.1	154	Cac/Tac	2/6	1	2	FACETS	0.573	0.537	0.61	0.573	0.537	0.61	SUBCLONAL	1	TRUE	1	0.818000526830423	2		1001	1157	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197645	106197645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs974556421	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	83	317	0	ENST00000380013.4:c.5978G>A	p.Arg1993Gln	p.R1993Q	ENST00000380013	NM_001127208.2	1993	cGg/cAg	11/11	1	2	FACETS	0.609	0.542	0.68	0.609	0.542	0.68	SUBCLONAL	1	TRUE	1	0.818000526830423	2		317	333	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38966817	38966817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771866090	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	26	280	0	ENST00000357387.3:c.1225G>A	p.Val409Ile	p.V409I	ENST00000357387	NM_152756.3	409	Gtt/Att	15/38	1	2	FACETS	0.195	0.154	0.242	0.195	0.154	0.242	SUBCLONAL	1	TRUE	1	0.818000526830423	2		280	326	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940562	131940562	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	108	343	0	ENST00000265335.6:c.2593del	p.Ser865ValfsTer6	p.S865Vfs*6	ENST00000265335		863	ctA/ct	16/25	1	2	FACETS	0.602	0.543	0.662	0.602	0.543	0.662	SUBCLONAL	1	TRUE	1	0.818000526830423	2		343	439	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032221	26032221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	71	308	0	ENST00000244661.2:c.68C>T	p.Thr23Ile	p.T23I	ENST00000244661	NM_003537.3	23	aCc/aTc	1/1	1	2	FACETS	0.534	0.47	0.603	0.534	0.47	0.603	SUBCLONAL	1	TRUE	1	0.818000526830423	2		308	325	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528422	157528422	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	170	704	0	ENST00000346085.5:c.6148del	p.Asp2050MetfsTer49	p.D2050Mfs*49	ENST00000346085	NM_020732.3	2049	ttG/tt	20/20	1	2	FACETS	0.561	0.517	0.607	0.561	0.517	0.607	SUBCLONAL	1	TRUE	1	0.818000526830423	2		704	741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0042823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	554	942	0	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	0.859468617713292	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.875325733425948	1		942	665	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577531	7577531	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567549203	NA	P-0042824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	131	720	1	ENST00000269305.4:c.750del	p.Ile251SerfsTer94	p.I251Sfs*94	ENST00000269305	NM_001126112.2	250	ccC/cc	7/11	0.367831744377053	1	FACETS	0.869	0.79	0.951	0.869	0.79	0.951	CLONAL	1	TRUE	0	0.367831744377053	1		721	669	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	225	759	1				ENST00000310581	NM_198253.2	-/1132			0.298766618017122	3	FACETS	0.996	0.935	1	0.996	0.935	1	CLONAL	2	TRUE	1	0.493332312971595	3		760	571	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085972	16085972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs998174759	NA	P-0042825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	190	751	1	ENST00000281043.3:c.1148G>A	p.Arg383His	p.R383H	ENST00000281043	NM_005378.4	383	cGc/cAc	3/3	0.493332312971595	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.493332312971595	1		752	578	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955394	48955394	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886043247	NA	P-0042825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	312	181	0	ENST00000267163.4:c.1510C>T	p.Gln504Ter	p.Q504*	ENST00000267163	NM_000321.2	504	Cag/Tag	17/27	0.493332312971595	6	FACETS	1	0.979	1	1	0.995	1	CLONAL	4	TRUE	3	0.493332312971595	6		181	601	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942673	48942673	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764547244	NA	P-0042825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	351	255	0	ENST00000267163.4:c.1060C>T	p.Gln354Ter	p.Q354*	ENST00000267163	NM_000321.2	354	Cag/Tag	11/27	0.493332312971595	6	FACETS	0.976	0.932	1	1	0.994	1	CLONAL	4	TRUE	3	0.493332312971595	6		255	724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577128	7577128	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519987	NA	P-0042825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	1317	849	0	ENST00000269305.4:c.810T>G	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	ttT/ttG	8/11	0.494798436970523	4	FACETS	0.977	0.971	0.983	1	0.999	1	CLONAL	6	TRUE	0	0.493332312971595	4		849	1360	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872189	45872189	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	591	780	0	ENST00000391945.4:c.245A>G	p.Lys82Arg	p.K82R	ENST00000391945	NM_000400.3	82	aAg/aGg	4/23	0.494798436970523	3	FACETS	1	0.989	1	1	0.998	1	CLONAL	3	TRUE	1	0.493332312971595	3		780	954	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793510	42793510	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1394050113	NA	P-0042825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	209	1017	1	ENST00000575354.2:c.1312G>A	p.Glu438Lys	p.E438K	ENST00000575354	NM_015125.3	438	Gag/Aag	8/20	0.494798436970523	3	FACETS	0.83	0.769	0.894	0.415	0.384	0.447	CLONAL	1	TRUE	1	0.493332312971595	3		1018	1272	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105524	27105524	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0042825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	342	445	0	ENST00000324856.7:c.5135T>A	p.Leu1712Ter	p.L1712*	ENST00000324856	NM_006015.4	1712	tTg/tAg	20/20	0.493332312971595	5	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.493332312971595	5		445	1037	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468426	120468426	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	331	644	0	ENST00000256646.2:c.4013C>G	p.Ser1338Cys	p.S1338C	ENST00000256646	NM_024408.3	1338	tCc/tGc	25/34	0.493332312971595	1	FACETS	0.893	0.855	0.931	1	0.996	1	CLONAL	2	TRUE	0	0.493332312971595	1		644	566	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567716	226567716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781134011	NA	P-0042825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	185	686	0	ENST00000366794.5:c.1450G>A	p.Glu484Lys	p.E484K	ENST00000366794	NM_001618.3	484	Gag/Aag	10/23	0.479610699738766	3	FACETS	0.967	0.893	1	0.483	0.446	0.522	CLONAL	1	TRUE	1	0.493332312971595	3		686	967	SUCCESS
BLM	641	MSKCC	GRCh37	15	91334070	91334070	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1567056762	NA	P-0042825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	198	355	1	ENST00000355112.3:c.3015A>G	p.Ile1005Met	p.I1005M	ENST00000355112	NM_000057.2	1005	atA/atG	15/22	1	2	FACETS	0.94	0.882	0.998	1	0.994	1	CLONAL	2	TRUE	1	0.493332312971595	2		356	427	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56855500	56855500	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	95	431	0	ENST00000308159.5:c.649G>C	p.Asp217His	p.D217H	ENST00000308159	NM_014669.4	217	Gat/Cat	7/22	0.25633090908259	6	FACETS	1	0.914	1			1	INDETERMINATE	1	TRUE	NA	0.493332312971595	6		431	742	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129474	152129474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	75	312	0	ENST00000206249.3:c.427G>A	p.Glu143Lys	p.E143K	ENST00000206249	NM_000125.3	143	Gag/Aag	1/8	0.479610699738766	3	FACETS	0.943	0.831	1	0.471	0.415	0.532	CLONAL	1	TRUE	1	0.493332312971595	3		312	402	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	125	136	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.661769209479604	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.661769209479604	3		136	210	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074199	8074199	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	160	548	0	ENST00000377482.5:c.460C>G	p.Pro154Ala	p.P154A	ENST00000377482	NM_018948.3	154	Cca/Gca	4/4	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.661769209479604	2		548	463	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190588	11190588	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	214	725	0	ENST00000361445.4:c.5611G>C	p.Glu1871Gln	p.E1871Q	ENST00000361445	NM_004958.3	1871	Gag/Cag	39/58	1	2	FACETS	0.884	0.824	0.945	0.884	0.824	0.945	CLONAL	1	TRUE	1	0.661769209479604	2		725	732	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282436	115282436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1314208666	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	52	576	0	ENST00000438362.2:c.214G>A	p.Glu72Lys	p.E72K	ENST00000438362	NM_001242891.1	72	Gaa/Aaa	3/20	0.661769209479604	6	FACETS	0.482	0.41	0.563	0.096	0.082	0.113	SUBCLONAL	1	TRUE	1	0.661769209479604	6		576	757	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120493424	120493424	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	141	554	0	ENST00000256646.2:c.2402C>G	p.Ser801Ter	p.S801*	ENST00000256646	NM_024408.3	801	tCa/tGa	15/34	0.661769209479604	6	FACETS	1	0.978	1	0.246	0.224	0.269	CLONAL	1	TRUE	1	0.661769209479604	6		554	806	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663871	241663871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1131691244	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	53	459	0	ENST00000366560.3:c.1256C>T	p.Ser419Leu	p.S419L	ENST00000366560	NM_000143.3	419	tCa/tTa	9/10	0.661769209479604	5	FACETS	0.654	0.558	0.759	0.164	0.139	0.19	SUBCLONAL	1	TRUE	1	0.661769209479604	5		459	488	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426820	70426820	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	148	416	0	ENST00000373644.4:c.4480G>T	p.Asp1494Tyr	p.D1494Y	ENST00000373644	NM_030625.2	1494	Gat/Tat	7/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.661769209479604	2		416	425	SUCCESS
EED	8726	MSKCC	GRCh37	11	85966327	85966327	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	25	225	0	ENST00000263360.6:c.424G>C	p.Asp142His	p.D142H	ENST00000263360	NM_003797.3	142	Gat/Cat	4/12	1	2	FACETS	0.787	0.635	0.953	0.787	0.635	0.953	CLONAL	1	TRUE	1	0.661769209479604	2		225	96	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374094	118374094	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	105	527	0	ENST00000534358.1:c.7487C>G	p.Ser2496Cys	p.S2496C	ENST00000534358	NM_005933.3	2496	tCt/tGt	27/36	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.661769209479604	2		527	295	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1022596	1022596	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1415589794	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	66	500	0	ENST00000358495.3:c.1218G>C	p.Lys406Asn	p.K406N	ENST00000358495	NM_134424.2	406	aaG/aaC	12/12	1	2	FACETS	0.911	0.803	1	0.911	0.803	1	CLONAL	1	TRUE	1	0.661769209479604	2		500	219	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023286	1023286	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs763741878	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	150	553	0	ENST00000358495.3:c.969G>C	p.Lys323Asn	p.K323N	ENST00000358495	NM_134424.2	323	aaG/aaC	11/12	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.661769209479604	2		553	437	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21639444	21639444	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766866319	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	33	155	0	ENST00000421138.2:c.470C>T	p.Ser157Leu	p.S157L	ENST00000421138		157	tCa/tTa	6/16	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.661769209479604	2		155	98	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424222	49424223	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	TC	TC	-	novel	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	39	229	0	ENST00000301067.7:c.13840-1_13840del		p.X4614_splice	ENST00000301067	NM_003482.3	4614		42/54	1	2	FACETS	0.477	0.398	0.564	0.477	0.398	0.564	SUBCLONAL	1	TRUE	1	0.661769209479604	2		229	247	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120752	115120758	+	frameshift_variant	Frame_Shift_Del	DEL	GCCTGGG	GCCTGGG	-	novel	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	321	1037	0	ENST00000257566.3:c.248_254del	p.Pro83ArgfsTer3	p.P83Rfs*3	ENST00000257566	NM_016569.3	83	cCCCAGGCg/cg	1/8	1	2	FACETS	0.907	0.857	0.958	0.907	0.857	0.958	CLONAL	1	TRUE	1	0.661769209479604	2		1037	1070	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061115	38061115	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	198	334	1	ENST00000250448.2:c.874G>T	p.Glu292Ter	p.E292*	ENST00000250448	NM_004496.3	292	Gag/Tag	2/2	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.661769209479604	2		335	457	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647241	2647241	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	64	744	0	ENST00000342085.4:c.1519G>C	p.Glu507Gln	p.E507Q	ENST00000342085	NM_002613.4	507	Gag/Cag	13/14	1	2	FACETS	0.352	0.305	0.403	0.352	0.305	0.403	SUBCLONAL	1	TRUE	1	0.661769209479604	2		744	549	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3634827	3634827	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs543847606	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	280	1097	0	ENST00000294008.3:c.4682C>T	p.Thr1561Met	p.T1561M	ENST00000294008	NM_032444.2	1561	aCg/aTg	13/15	1	2	FACETS	0.888	0.836	0.942	0.888	0.836	0.942	CLONAL	1	TRUE	1	0.661769209479604	2		1097	953	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640008	3640008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202032197	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	315	1172	1	ENST00000294008.3:c.3631G>A	p.Glu1211Lys	p.E1211K	ENST00000294008	NM_032444.2	1211	Gaa/Aaa	12/15	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.661769209479604	2		1173	949	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853277	68853277	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	296	818	0	ENST00000261769.5:c.1660G>T	p.Glu554Ter	p.E554*	ENST00000261769	NM_004360.3	554	Gag/Tag	11/16	0.298185433077401	1	FACETS	0.681	0.643	0.72	0.681	0.643	0.72	INDETERMINATE	1	TRUE	0	0.661769209479604	1		818	879	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347776	89347776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764002055	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	296	843	0	ENST00000301030.4:c.5174C>T	p.Pro1725Leu	p.P1725L	ENST00000301030	NM_001256183.1	1725	cCg/cTg	9/13	0.661769209479604	1	FACETS	0.965	0.917	1	0.965	0.917	1	CLONAL	1	TRUE	0	0.661769209479604	1		843	620	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320887	30320887	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	60	360	0	ENST00000322652.5:c.1297C>G	p.Leu433Val	p.L433V	ENST00000322652	NM_015355.2	433	Ctc/Gtc	12/16	1	2	FACETS	0.889	0.778	1	0.889	0.778	1	CLONAL	1	TRUE	1	0.661769209479604	2		360	204	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215951	41215951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	42	394	0	ENST00000357654.3:c.5092G>A	p.Glu1698Lys	p.E1698K	ENST00000357654	NM_007294.3	1698	Gaa/Aaa	17/23	1	2	FACETS	0.846	0.72	0.981	0.846	0.72	0.981	CLONAL	1	TRUE	1	0.661769209479604	2		394	150	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355050	15355050	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	433	1366	0	ENST00000263377.2:c.2573C>G	p.Ser858Cys	p.S858C	ENST00000263377	NM_058243.2	858	tCt/tGt	13/20	1	2	FACETS	0.939	0.895	0.984	0.939	0.895	0.984	CLONAL	1	TRUE	1	0.661769209479604	2		1366	1394	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719760	190719760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	23	158	0	ENST00000441310.2:c.1762C>T	p.Gln588Ter	p.Q588*	ENST00000441310	NM_000534.4	588	Cag/Tag	9/13	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.661769209479604	2		158	64	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288557	198288557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	65	504	0	ENST00000335508.6:c.170C>T	p.Ser57Leu	p.S57L	ENST00000335508	NM_012433.2	57	tCa/tTa	2/25	1	2	FACETS	0.829	0.728	0.935	0.829	0.728	0.935	CLONAL	1	TRUE	1	0.661769209479604	2		504	237	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178388	56178392	+	frameshift_variant	Frame_Shift_Del	DEL	AGATT	AGATT	-	novel	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	71	356	0	ENST00000399503.3:c.3365_3369del	p.Leu1122CysfsTer10	p.L1122Cfs*10	ENST00000399503	NM_005921.1	1121	AGATTa/a	14/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.661769209479604	2		356	173	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184179	56184179	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	30	221	0	ENST00000399503.3:c.4384T>A	p.Phe1462Ile	p.F1462I	ENST00000399503	NM_005921.1	1462	Ttt/Att	19/20	1	2	FACETS	0.743	0.61	0.888	0.743	0.61	0.888	SUBCLONAL	1	TRUE	1	0.661769209479604	2		221	122	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750411	57750411	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	48	385	0	ENST00000274289.3:c.2057G>C	p.Ter686SerextTer24	p.*686Sext*24	ENST00000274289	NM_006622.3	686	tGa/tCa	14/14	1	2	FACETS	0.748	0.641	0.862	0.748	0.641	0.862	SUBCLONAL	1	TRUE	1	0.661769209479604	2		385	194	SUCCESS
APC	324	MSKCC	GRCh37	5	112157655	112157655	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	35	299	0	ENST00000257430.4:c.1375G>C	p.Asp459His	p.D459H	ENST00000257430	NM_000038.5	459	Gat/Cat	11/16	1	2	FACETS	0.904	0.758	1	0.904	0.758	1	CLONAL	1	TRUE	1	0.661769209479604	2		299	117	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637507	176637507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	108	631	0	ENST00000439151.2:c.2107C>T	p.Leu703Phe	p.L703F	ENST00000439151	NM_022455.4	703	Ctc/Ttc	5/23	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.661769209479604	2		631	300	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638471	176638471	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	226	972	0	ENST00000439151.2:c.3071C>G	p.Ser1024Ter	p.S1024*	ENST00000439151	NM_022455.4	1024	tCa/tGa	5/23	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.661769209479604	2		972	677	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638480	176638480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	212	994	0	ENST00000439151.2:c.3080C>T	p.Ser1027Leu	p.S1027L	ENST00000439151	NM_022455.4	1027	tCa/tTa	5/23	1	2	FACETS	0.959	0.895	1	0.959	0.895	1	CLONAL	1	TRUE	1	0.661769209479604	2		994	668	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662458	117662458	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1441413725	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	71	454	0	ENST00000368508.3:c.4919C>G	p.Ser1640Cys	p.S1640C	ENST00000368508	NM_002944.2	1640	tCt/tGt	30/43	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.661769209479604	2		454	195	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157256633	157256633	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	81	378	0	ENST00000346085.5:c.1960C>G	p.Gln654Glu	p.Q654E	ENST00000346085	NM_020732.3	654	Caa/Gaa	5/20	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.661769209479604	2		378	233	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157431667	157431667	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	265	713	0	ENST00000346085.5:c.2343G>C	p.Leu781Phe	p.L781F	ENST00000346085	NM_020732.3	781	ttG/ttC	7/20	1	2	FACETS	0.901	0.846	0.957	0.901	0.846	0.957	CLONAL	1	TRUE	1	0.661769209479604	2		713	889	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157431693	157431693	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	241	630	0	ENST00000346085.5:c.2369G>C	p.Arg790Thr	p.R790T	ENST00000346085	NM_020732.3	790	aGa/aCa	7/20	1	2	FACETS	0.948	0.889	1	0.948	0.889	1	CLONAL	1	TRUE	1	0.661769209479604	2		630	768	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335688	81335688	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	61	494	0	ENST00000222390.5:c.1672G>C	p.Asp558His	p.D558H	ENST00000222390	NM_000601.4	558	Gat/Cat	15/18	1	2	FACETS	0.95	0.834	1	0.95	0.834	1	CLONAL	1	TRUE	1	0.661769209479604	2		494	194	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162143	38162143	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	108	565	0	ENST00000317025.8:c.2573C>G	p.Ser858Cys	p.S858C	ENST00000317025	NM_023034.1	858	tCt/tGt	14/24	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.661769209479604	2		565	321	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162233	38162233	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	120	538	0	ENST00000317025.8:c.2483C>G	p.Ser828Cys	p.S828C	ENST00000317025	NM_023034.1	828	tCt/tGt	14/24	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.661769209479604	2		538	341	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244421	98244421	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	37	466	0	ENST00000331920.6:c.649G>C	p.Asp217His	p.D217H	ENST00000331920	NM_000264.3	217	Gat/Cat	4/24	1	2	FACETS	0.618	0.515	0.729	0.618	0.515	0.729	SUBCLONAL	1	TRUE	1	0.661769209479604	2		466	181	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915952	127915952	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	71	527	0	ENST00000373547.4:c.529C>G	p.Arg177Gly	p.R177G	ENST00000373547	NM_002721.4	177	Cga/Gga	6/7	1	2	FACETS	0.975	0.865	1	0.975	0.865	1	CLONAL	1	TRUE	1	0.661769209479604	2		527	220	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	386	759	1				ENST00000310581	NM_198253.2	-/1132			0.874788296917597	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.874788296917597	3		760	594	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0042847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	502	871	5	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.874788296917597	2	FACETS	0.983	0.962	1	0.983	0.962	1	CLONAL	2	TRUE	0	0.874788296917597	2		876	584	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955130	17955130	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs565783591	NA	P-0042847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	736	1142	8	ENST00000458235.1:c.97C>T	p.Arg33Trp	p.R33W	ENST00000458235	NM_000215.3	33	Cgg/Tgg	2/24	0.874693916444157	2	FACETS	0.996	0.979	1	0.996	0.979	1	CLONAL	2	TRUE	0	0.874788296917597	2		1150	845	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795860	42795860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	98	1134	1	ENST00000575354.2:c.2849C>T	p.Ser950Leu	p.S950L	ENST00000575354	NM_015125.3	950	tCa/tTa	11/20	0.869069889782903	3	FACETS	0.273	0.242	0.306	0.136	0.121	0.153	SUBCLONAL	1	TRUE	1	0.874788296917597	3		1135	1180	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247295	153247295	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	101	445	1	ENST00000281708.4:c.1507G>A	p.Ala503Thr	p.A503T	ENST00000281708	NM_033632.3	503	Gca/Aca	10/12	1	2	FACETS	0.865	0.786	0.946	0.865	0.786	0.946	CLONAL	1	TRUE	1	0.874788296917597	2		446	267	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411694	116411694	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	19	498	0	ENST00000397752.3:c.2873G>A	p.Arg958Lys	p.R958K	ENST00000397752	NM_000245.2	958	aGa/aAa	13/21	0.873710359092955	1	FACETS	0.109	0.083	0.14	0.109	0.083	0.14	SUBCLONAL	1	TRUE	0	0.874788296917597	1		498	224	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052641	42052641	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	25	604	0	ENST00000219905.7:c.7312G>A	p.Glu2438Lys	p.E2438K	ENST00000219905	NM_001164273.1	2438	Gaa/Aaa	20/24	0.874788296917597	2	FACETS	0.115	0.09	0.144	0.057	0.045	0.072	SUBCLONAL	1	TRUE	0	0.874788296917597	2		604	498	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110617	4110617	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	267	930	3	ENST00000262948.5:c.340C>T	p.Gln114Ter	p.Q114*	ENST00000262948	NM_030662.3	114	Cag/Tag	3/11	0.874693916444157	2	FACETS	0.964	0.911	1	0.482	0.455	0.509	CLONAL	1	TRUE	0	0.874788296917597	2		933	633	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750440	133750440	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0042847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	233	824	1	ENST00000318560.5:c.1270+1G>A		p.X424_splice	ENST00000318560	NM_005157.4	424			1	2	FACETS	0.94	0.884	0.996	0.94	0.884	0.996	CLONAL	1	TRUE	1	0.874788296917597	2		825	567	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0042893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	122	243	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.381109334682075	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.381109334682075	3		243	353	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	165	395	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.953	1	1	0.993	1	CLONAL	2	TRUE	1	0.381109334682075	2		395	419	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089123	37089125	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs63751247	NA	P-0042893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	80	323	0	ENST00000231790.2:c.1852_1854del	p.Lys618del	p.K618del	ENST00000231790	NM_000249.3	615	ctGAAg/ctg	16/19	0.381109334682075	1	FACETS	0.918	0.814	1	0.918	0.814	1	CLONAL	1	TRUE	0	0.381109334682075	1		323	370	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157834	106157834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs4145756	NA	P-0042893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	23	252	0	ENST00000380013.4:c.2735C>T	p.Ala912Val	p.A912V	ENST00000380013	NM_001127208.2	912	gCg/gTg	3/11	1	2	FACETS	0.434	0.339	0.544	0.434	0.339	0.544	SUBCLONAL	1	TRUE	1	0.381109334682075	2		252	278	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0042893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	57	435	1	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	0.381109334682075	1	FACETS	0.492	0.423	0.568	0.492	0.423	0.568	SUBCLONAL	1	TRUE	0	0.381109334682075	1		436	492	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339111	65339111	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	55	383	1	ENST00000342505.4:c.425del	p.Lys142ArgfsTer26	p.K142Rfs*26	ENST00000342505	NM_002227.2	142	aAg/ag	5/25	0.381109334682075	1	FACETS	0.547	0.469	0.632	0.547	0.469	0.632	SUBCLONAL	1	TRUE	0	0.381109334682075	1		384	427	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860581	45860581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531021258	NA	P-0042893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	80	725	1	ENST00000391945.4:c.1426G>A	p.Val476Ile	p.V476I	ENST00000391945	NM_000400.3	476	Gtc/Atc	15/23	1	2	FACETS	0.401	0.351	0.454	0.401	0.351	0.454	SUBCLONAL	1	TRUE	1	0.381109334682075	2		726	1048	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342602	70342602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1268612180	NA	P-0042893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	108	483	0	ENST00000374080.3:c.1363C>T	p.Arg455Trp	p.R455W	ENST00000374080		455	Cgg/Tgg	10/45	0.309159516550563	3	FACETS	0.928	0.833	1	0.464	0.416	0.514	CLONAL	1	TRUE	1	0.381109334682075	3		483	727	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395624	31395624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756972254	NA	P-0042893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	137	541	0	ENST00000328111.2:c.2477G>A	p.Arg826His	p.R826H	ENST00000328111	NM_006892.3	826	cGc/cAc	23/23	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.381109334682075	2		541	709	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246078896	246078896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs987211168	NA	P-0042893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	150	468	0	ENST00000388985.4:c.749G>A	p.Arg250Gln	p.R250Q	ENST00000388985		250	cGg/cAg	8/12	NA	2	FACETS	0.93	0.851	1			1	INDETERMINATE	1	TRUE	NA	0.381109334682075	2		468	846	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060845	38060845	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	81	671	0	ENST00000250448.2:c.1144del	p.His382ThrfsTer7	p.H382Tfs*7	ENST00000250448	NM_004496.3	382	Cac/ac	2/2	1	2	FACETS	0.446	0.392	0.504	0.446	0.392	0.504	SUBCLONAL	1	TRUE	1	0.381109334682075	2		671	953	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724658	112724659	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0042893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	51	361	0	ENST00000369452.4:c.542_543del	p.Leu181GlnfsTer9	p.L181Qfs*9	ENST00000369452	NM_007373.3	181	cTG/c	2/9	1	2	FACETS	0.499	0.424	0.582	0.499	0.424	0.582	SUBCLONAL	1	TRUE	1	0.381109334682075	2		361	536	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427309	427309	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	52	394	0	ENST00000399788.2:c.2860C>T	p.Arg954Ter	p.R954*	ENST00000399788	NM_001042603.1	954	Cga/Tga	19/28	0.381109334682075	2	FACETS	0.463	0.393	0.539	0.231	0.196	0.27	SUBCLONAL	1	TRUE	0	0.381109334682075	2		394	590	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729202	66729202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	43	459	0	ENST00000307102.5:c.410G>A	p.Gly137Asp	p.G137D	ENST00000307102	NM_002755.3	137	gGc/gAc	3/11	0.381109334682075	1	FACETS	0.277	0.231	0.328	0.277	0.231	0.328	SUBCLONAL	1	TRUE	0	0.381109334682075	1		459	660	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911508	134911508	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	57	463	0	ENST00000398015.3:c.1973C>A	p.Ser658Ter	p.S658*	ENST00000398015	NM_004441.4	658	tCg/tAg	11/16	1	2	FACETS	0.42	0.359	0.486	0.42	0.359	0.486	SUBCLONAL	1	TRUE	1	0.381109334682075	2		463	713	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508966	106508966	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	97	401	0	ENST00000359195.3:c.960G>C	p.Lys320Asn	p.K320N	ENST00000359195	NM_002649.2	320	aaG/aaC	2/11	1	2	FACETS	0.946	0.846	1	0.946	0.846	1	CLONAL	1	TRUE	1	0.381109334682075	2		401	538	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853260	68853260	+	frameshift_variant	Frame_Shift_Ins	INS	T	T	AC	novel	NA	P-0042893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	159	488	0	ENST00000261769.5:c.1643delinsAC	p.Leu548HisfsTer7	p.L548Hfs*7	ENST00000261769	NM_004360.3	548	cTg/cACg	11/16	0.381109334682075	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.381109334682075	1		488	614	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142540	119142540	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730880431	NA	P-0042995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	118	418	1	ENST00000264033.4:c.539G>A	p.Arg180Gln	p.R180Q	ENST00000264033	NM_005188.3	180	cGg/cAg	3/16	1	2	FACETS	0.542	0.49	0.597	0.542	0.49	0.597	SUBCLONAL	1	TRUE	1	0.677638615301765	2		419	642	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849637	68849637	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	250	553	0	ENST00000261769.5:c.1540G>C	p.Asp514His	p.D514H	ENST00000261769	NM_004360.3	514	Gac/Cac	10/16	1	2	FACETS	0.901	0.845	0.958	0.901	0.845	0.958	CLONAL	1	TRUE	1	0.677638615301765	2		553	819	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118315	17118316	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGGCAGACGAGGCACTGG	novel	NA	P-0042995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	211	542	0	ENST00000285071.4:c.1503_1521dup	p.Lys508ProfsTer19	p.K508Pfs*19	ENST00000285071	NM_144997.5	507	-/CCAGTGCCTCGTCTGCCTC	13/14	0.676979812505936	1	FACETS	0.662	0.618	0.707	0.662	0.618	0.707	SUBCLONAL	1	TRUE	0	0.677638615301765	1		542	622	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082360	16082361	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0042995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	304	647	0	ENST00000281043.3:c.179dup	p.Leu61AlafsTer24	p.L61Afs*24	ENST00000281043	NM_005378.4	58	-/C	2/3	1	2	FACETS	0.897	0.847	0.949	0.897	0.847	0.949	CLONAL	1	TRUE	1	0.677638615301765	2		647	1000	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233747	233747	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	302	589	0	ENST00000264932.6:c.1051A>G	p.Ile351Val	p.I351V	ENST00000264932	NM_004168.2	351	Atc/Gtc	8/15	0.677638615301765	2	FACETS	0.986	0.931	1	0.493	0.465	0.521	CLONAL	1	TRUE	0	0.677638615301765	2		589	904	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317070	11317070	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766996808	NA	P-0042998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	175	733	1	ENST00000361445.4:c.424G>A	p.Ala142Thr	p.A142T	ENST00000361445	NM_004958.3	142	Gct/Act	4/58	0.215870216479868	1	FACETS	0.818	0.755	0.882	0.818	0.755	0.882	INDETERMINATE	1	TRUE	0	0.457837911279366	1		734	721	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374890	45374890	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	400	704	0	ENST00000262160.6:c.953A>T	p.Asn318Ile	p.N318I	ENST00000262160	NM_005901.5	318	aAt/aTt	8/11	0.441366641829073	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.457837911279366	2		704	870	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874169	155874169	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	141	732	0	ENST00000368323.3:c.362T>C	p.Val121Ala	p.V121A	ENST00000368323	NM_006912.5	121	gTc/gCc	5/6	0.215870216479868	1	FACETS	0.522	0.476	0.572	0.522	0.476	0.572	INDETERMINATE	1	TRUE	0	0.457837911279366	1		732	909	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88651892	88651892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	158	478	0	ENST00000372037.3:c.239G>A	p.Gly80Glu	p.G80E	ENST00000372037	NM_004329.2	80	gGa/gAa	5/13	0.457837911279366	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.457837911279366	1		478	486	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895641	28895641	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1475572191	NA	P-0042998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	343	565	0	ENST00000282397.4:c.3133C>T	p.Arg1045Trp	p.R1045W	ENST00000282397	NM_002019.4	1045	Cgg/Tgg	23/30	0.441366641829073	2	FACETS	0.986	0.939	1	0.986	0.939	1	CLONAL	2	TRUE	0	0.457837911279366	2		565	760	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99472846	99472846	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778465734	NA	P-0042998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	193	624	0	ENST00000268035.6:c.2842G>A	p.Val948Met	p.V948M	ENST00000268035	NM_000875.3	948	Gtg/Atg	14/21	0.215870216479868	1	FACETS	0.783	0.726	0.843	0.783	0.726	0.843	INDETERMINATE	1	TRUE	0	0.457837911279366	1		624	830	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577151	7577152	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0042998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	299	598	0	ENST00000269305.4:c.786dup	p.Asn263Ter	p.N263*	ENST00000269305	NM_001126112.2	262	-/T	8/11	0.435794921021664	2	FACETS	0.89	0.843	0.937	0.89	0.843	0.937	CLONAL	2	TRUE	0	0.457837911279366	2		598	734	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332874	152332874	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs755020320	NA	P-0042998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	89	585	0	ENST00000206249.3:c.1180C>A	p.Arg394Ser	p.R394S	ENST00000206249	NM_000125.3	394	Cgc/Agc	5/8	0.215870216479868	1	FACETS	0.528	0.469	0.591	0.528	0.469	0.591	INDETERMINATE	1	TRUE	0	0.457837911279366	1		585	568	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0043039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	126	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.574589732769451	1	FACETS	0.87	0.798	0.944	0.87	0.798	0.944	CLONAL	1	TRUE	0	0.592451172981958	1		334	344	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860121	152860121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782206940	NA	P-0043039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	180	698	3	ENST00000406277.2:c.307G>A	p.Gly103Ser	p.G103S	ENST00000406277	NM_152274.4	103	Ggt/Agt	5/7	1		FACETS		0.816	0.95				CLONAL	1	TRUE	1	0.592451172981958	2		701	689	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579462	7579462	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	255	719	0	ENST00000269305.4:c.225del	p.Ala76HisfsTer47	p.A76Hfs*47	ENST00000269305	NM_001126112.2	75	ccT/cc	4/11	0.566575453044524	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.592451172981958	1		719	606	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098937	178098938	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAA	novel	NA	P-0043039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	96	318	0	ENST00000397062.3:c.107_108insTTT	p.Val36_Phe37insLeu	p.V36_F37insL	ENST00000397062	NM_006164.4	36	gta/gtTTTa	2/5	1	2	FACETS	0.937	0.843	1	0.937	0.843	1	CLONAL	1	TRUE	1	0.592451172981958	2		318	346	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0043072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	171	479	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.583304091186443	2		479	548	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858195	40858195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777686988	NA	P-0043072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	475	706	0	ENST00000428826.2:c.1669C>T	p.Arg557Cys	p.R557C	ENST00000428826		557	Cgt/Tgt	16/21	0.574367813953708	2	FACETS	0.951	0.916	0.986	0.951	0.916	0.986	CLONAL	2	TRUE	0	0.583304091186443	2		706	856	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0043072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	466	634	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.574367813953708	2	FACETS	0.966	0.931	1	0.966	0.931	1	CLONAL	2	TRUE	0	0.583304091186443	2		635	827	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0043072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	174	565	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.583304091186443	2		565	572	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246137	46246137	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	87	330	0	ENST00000334344.6:c.4231C>T	p.Gln1411Ter	p.Q1411*	ENST00000334344	NM_152641.2	1411	Caa/Taa	15/21	0.583304091186443	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.583304091186443	1		330	200	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573894	18573894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759658584	NA	P-0043072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	70	293	1	ENST00000266497.5:c.2212C>T	p.Arg738Cys	p.R738C	ENST00000266497		738	Cgt/Tgt	15/31	0.583304091186443	1	FACETS	0.945	0.842	1	0.945	0.842	1	CLONAL	1	TRUE	0	0.583304091186443	1		294	180	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509768	187509768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766893768	NA	P-0043072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	93	327	0	ENST00000441802.2:c.13745C>T	p.Ser4582Phe	p.S4582F	ENST00000441802	NM_005245.3	4582	tCc/tTc	27/27	1	2	FACETS	0.811	0.727	0.9	0.811	0.727	0.9	CLONAL	1	TRUE	1	0.583304091186443	2		327	393	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564602	55564602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	193	698	0	ENST00000288135.5:c.490C>T	p.Pro164Ser	p.P164S	ENST00000288135	NM_000222.2	164	Cct/Tct	3/21	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.583304091186443	2		698	625	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201802	102201802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	113	303	0	ENST00000263464.3:c.1154C>T	p.Ala385Val	p.A385V	ENST00000263464	NM_001165.4	385	gCc/gTc	6/9	0.431009632773944	1	FACETS	0.88	0.802	0.959	0.88	0.802	0.959	CLONAL	1	TRUE	0	0.583304091186443	1		303	312	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857436	9857436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	139	566	0	ENST00000330684.3:c.3965G>A	p.Gly1322Glu	p.G1322E	ENST00000330684	NM_001134407.1	1322	gGa/gAa	13/13	1	2	FACETS	0.886	0.811	0.964	0.886	0.811	0.964	CLONAL	1	TRUE	1	0.583304091186443	2		566	538	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792611	33792611	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	22	24	0	ENST00000498907.2:c.710C>T	p.Pro237Leu	p.P237L	ENST00000498907	NM_004364.3	237	cCc/cTc	1/1	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.583304091186443	2		24	58	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625303	69625303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1335560620	NA	P-0043072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	318	971	0	ENST00000334134.2:c.490C>T	p.Arg164Cys	p.R164C	ENST00000334134	NM_005247.2	164	Cgc/Tgc	3/3	0.431009632773944	1	FACETS	0.979	0.929	1	0.979	0.929	1	CLONAL	1	TRUE	0	0.583304091186443	1		971	789	SUCCESS
ATR	545	MSKCC	GRCh37	3	142254994	142254994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	32	162	0	ENST00000350721.4:c.3775C>T	p.Pro1259Ser	p.P1259S	ENST00000350721	NM_001184.3	1259	Cca/Tca	20/47	1	2	FACETS	0.653	0.536	0.782	0.653	0.536	0.782	SUBCLONAL	1	TRUE	1	0.583304091186443	2		162	168	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978414	2978414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	330	943	0	ENST00000396946.4:c.916G>A	p.Glu306Lys	p.E306K	ENST00000396946	NM_032415.4	306	Gaa/Aaa	7/25	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.583304091186443	2		943	1109	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852443	42852443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139092674	NA	P-0043072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	272	706	0	ENST00000398585.3:c.643G>A	p.Glu215Lys	p.E215K	ENST00000398585	NM_001135099.1	215	Gag/Aag	6/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.583304091186443	2		706	857	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56872935	56872935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	84	309	0	ENST00000308159.5:c.2090C>T	p.Thr697Ile	p.T697I	ENST00000308159	NM_014669.4	697	aCc/aTc	19/22	1	2	FACETS	0.96	0.857	1	0.96	0.857	1	CLONAL	1	TRUE	1	0.583304091186443	2		309	300	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488219	56488219	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs371577741	NA	P-0043072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	192	611	1	ENST00000267101.3:c.1738C>T	p.Arg580Ter	p.R580*	ENST00000267101	NM_001982.3	580	Cga/Tga	15/28	0.583304091186443	1	FACETS	0.942	0.879	1	0.942	0.879	1	CLONAL	1	TRUE	0	0.583304091186443	1		612	495	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641097	3641097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	293	1081	0	ENST00000294008.3:c.2542G>A	p.Glu848Lys	p.E848K	ENST00000294008	NM_032444.2	848	Gaa/Aaa	12/15	1	2	FACETS	0.954	0.898	1	0.954	0.898	1	CLONAL	1	TRUE	1	0.583304091186443	2		1081	1053	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163295950	163295950	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	79	455	0	ENST00000271452.3:c.109T>C	p.Tyr37His	p.Y37H	ENST00000271452	NM_145697.2	37	Tat/Cat	2/14	1	2	FACETS	0.67	0.593	0.753	0.67	0.593	0.753	SUBCLONAL	1	TRUE	1	0.583304091186443	2		455	404	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246027136	246027136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	151	601	1	ENST00000388985.4:c.866C>T	p.Ser289Phe	p.S289F	ENST00000388985		289	tCc/tTc	9/12	1	2	FACETS	0.828	0.76	0.899	0.828	0.76	0.899	CLONAL	1	TRUE	1	0.583304091186443	2		602	625	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647848	3647848	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1175196086	NA	P-0043072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	341	1021	0	ENST00000294008.3:c.1316C>T	p.Pro439Leu	p.P439L	ENST00000294008	NM_032444.2	439	cCa/cTa	6/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.583304091186443	2		1021	1090	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658559	3658559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	259	879	0	ENST00000294008.3:c.407C>T	p.Ser136Phe	p.S136F	ENST00000294008	NM_032444.2	136	tCt/tTt	2/15	1	2	FACETS	0.92	0.863	0.979	0.92	0.863	0.979	CLONAL	1	TRUE	1	0.583304091186443	2		879	965	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348007	89348007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776941348	NA	P-0043072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	302	1177	0	ENST00000301030.4:c.4943C>T	p.Pro1648Leu	p.P1648L	ENST00000301030	NM_001256183.1	1648	cCa/cTa	9/13	1	2	FACETS	0.901	0.849	0.955	0.901	0.849	0.955	CLONAL	1	TRUE	1	0.583304091186443	2		1177	1149	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302408	15302408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	355	1092	0	ENST00000263388.2:c.863G>A	p.Gly288Glu	p.G288E	ENST00000263388	NM_000435.2	288	gGg/gAg	6/33	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.583304091186443	2		1092	1144	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972722	25972722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	141	525	0	ENST00000435504.4:c.1703G>A	p.Arg568Lys	p.R568K	ENST00000435504		568	aGg/aAg	12/13	1	2	FACETS	0.894	0.818	0.972	0.894	0.818	0.972	CLONAL	1	TRUE	1	0.583304091186443	2		525	541	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272230	21272230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1463139007	NA	P-0043072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	107	406	0	ENST00000354336.3:c.8C>T	p.Ser3Phe	p.S3F	ENST00000354336	NM_005207.3	3	tCc/tTc	1/3	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.583304091186443	2		406	344	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059193	47059193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772135964	NA	P-0043072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	173	550	0	ENST00000409792.3:c.7468C>T	p.Arg2490Trp	p.R2490W	ENST00000409792	NM_014159.6	2490	Cgg/Tgg	20/21	1	2	FACETS	0.957	0.885	1	0.957	0.885	1	CLONAL	1	TRUE	1	0.583304091186443	2		550	620	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902806	1902806	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	173	698	0	ENST00000382891.5:c.425C>T	p.Ser142Phe	p.S142F	ENST00000382891	NM_133335.3	142	tCc/tTc	2/22	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.583304091186443	2		698	580	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168668	56168668	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774985330	NA	P-0043072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	25	420	0	ENST00000399503.3:c.1522C>T	p.Pro508Ser	p.P508S	ENST00000399503	NM_005921.1	508	Cct/Tct	9/20	0.573981241260344	1	FACETS	0.162	0.128	0.202	0.162	0.128	0.202	SUBCLONAL	1	TRUE	0	0.583304091186443	1		420	374	SUCCESS
APC	324	MSKCC	GRCh37	5	112128144	112128144	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs76685252	NA	P-0043072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	70	287	0	ENST00000257430.4:c.647G>A	p.Arg216Gln	p.R216Q	ENST00000257430	NM_000038.5	216	cGa/cAa	7/16	0.573981241260344	1	FACETS	0.859	0.763	0.958	0.859	0.763	0.958	CLONAL	1	TRUE	0	0.583304091186443	1		287	198	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185627	27185627	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs748662110	NA	P-0043072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	199	562	1	ENST00000380036.4:c.1327G>A	p.Val443Ile	p.V443I	ENST00000380036	NM_000459.3	443	Gtt/Att	9/23	0.583304091186443	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.583304091186443	1		563	480	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231773	36231773	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1569061762	NA	P-0043090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	8	464	0	ENST00000300305.3:c.611G>A	p.Arg204Gln	p.R204Q	ENST00000300305		204	cGa/cAa	5/8	0.187593566580848	4	FACETS	0.183	0.117	0.268	0.091	0.058	0.134	INDETERMINATE	1	FALSE	2	0.513638936997026	4		464	258	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578249	7578250	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	45	541	0	ENST00000269305.4:c.599dup	p.Asn200LysfsTer9	p.N200Kfs*9	ENST00000269305	NM_001126112.2	200	aat/aaAt	6/11	0.287163963330916	3	FACETS	0.828	0.712	0.949	0.552	0.475	0.633	INDETERMINATE	2	FALSE	0	0.513638936997026	3		541	133	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48921968	48921968	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs587778826	NA	P-0043090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	24	271	0	ENST00000267163.4:c.508G>T	p.Glu170Ter	p.E170*	ENST00000267163	NM_000321.2	170	Gaa/Taa	5/27	0.28931495299147	3	FACETS	1	0.911	1	0.426	0.341	0.518	INDETERMINATE	1	FALSE	0	0.513638936997026	3		271	92	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260746	16260746	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	55	464	0	ENST00000375759.3:c.8011C>A	p.Pro2671Thr	p.P2671T	ENST00000375759	NM_015001.2	2671	Ccc/Acc	11/15	0.341968660519005	4	FACETS	1	0.874	1	1	0.874	1	CLONAL	2	FALSE	2	0.513638936997026	4		464	162	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424151	49424151	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	62	569	0	ENST00000301067.7:c.13911G>C	p.Lys4637Asn	p.K4637N	ENST00000301067	NM_003482.3	4637	aaG/aaC	42/54	0.513638936997026	5	FACETS	1	0.925	1	0.716	0.629	0.807	CLONAL	2	FALSE	2	0.513638936997026	5		569	199	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	131	759	1				ENST00000310581	NM_198253.2	-/1132			0.369228310060048	1	FACETS	0.619	0.57	0.669	0.619	0.57	0.669	INDETERMINATE	1	TRUE	0	0.79046004306852	1		760	324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0043121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	271	693	1	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.76670268968377	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.79046004306852	1		694	411	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918622	44918622	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	237	304	0	ENST00000377967.4:c.1105C>T	p.Gln369Ter	p.Q369*	ENST00000377967	NM_021140.2	369	Cag/Tag	12/29	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.79046004306852	1		304	300	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628266	187628266	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	270	707	2	ENST00000441802.2:c.2716C>T	p.Gln906Ter	p.Q906*	ENST00000441802	NM_005245.3	906	Cag/Tag	2/27	0.76670268968377	1	FACETS	0.926	0.884	0.968	0.926	0.884	0.968	CLONAL	1	TRUE	0	0.79046004306852	1		709	446	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223356	2223356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1376643409	NA	P-0043121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	266	760	1	ENST00000326181.6:c.968C>T	p.Ser323Leu	p.S323L	ENST00000326181	NM_032271.2	323	tCg/tTg	10/21	1	2	FACETS	0.893	0.841	0.945	0.893	0.841	0.945	CLONAL	1	TRUE	1	0.79046004306852	2		761	754	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799626	3799626	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0043121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	238	484	0	ENST00000262367.5:c.3836+2T>G		p.X1279_splice	ENST00000262367	NM_004380.2	1279			1	2	FACETS	0.858	0.805	0.912	0.858	0.805	0.912	CLONAL	1	TRUE	1	0.79046004306852	2		484	702	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981763	201981779	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCAGACCAGGGCAGCC	CCCAGACCAGGGCAGCC	-	novel	NA	P-0043121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	263	674	0	ENST00000359651.3:c.479-3_492del		p.X160_splice	ENST00000359651		160		4/8	1	2	FACETS	0.891	0.839	0.944	0.891	0.839	0.944	CLONAL	1	TRUE	1	0.79046004306852	2		674	747	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992795	72992795	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0043121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	241	631	0	ENST00000268489.5:c.1250C>G	p.Ser417Ter	p.S417*	ENST00000268489	NM_006885.3	417	tCa/tGa	2/10	1	2	FACETS	0.94	0.883	0.997	0.94	0.883	0.997	CLONAL	1	TRUE	1	0.79046004306852	2		631	649	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551003	41551003	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	107	386	0	ENST00000263253.7:c.3147C>G	p.Phe1049Leu	p.F1049L	ENST00000263253	NM_001429.3	1049	ttC/ttG	17/31	0.492537082083191	1	FACETS	0.391	0.353	0.43	0.391	0.353	0.43	SUBCLONAL	1	TRUE	0	0.79046004306852	1		386	419	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947413	38947413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	147	350	0	ENST00000357387.3:c.4267G>A	p.Asp1423Asn	p.D1423N	ENST00000357387	NM_152756.3	1423	Gat/Aat	32/38	NA	2	FACETS	0.817	0.753	0.884			1	INDETERMINATE	1	TRUE	NA	0.79046004306852	2		350	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0043122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	128	534	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.292221720624968	1	FACETS	0.877	0.795	0.964	0.877	0.795	0.964	CLONAL	1	TRUE	0	0.292221720624968	1		535	853	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591837	48591837	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867764109	NA	P-0043122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	70	413	0	ENST00000342988.3:c.1000C>T	p.Gln334Ter	p.Q334*	ENST00000342988	NM_005359.5	334	Cag/Tag	9/12	1	2	FACETS	0.992	0.867	1	0.992	0.867	1	CLONAL	1	TRUE	1	0.292221720624968	2		413	483	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0043122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	191	543	1	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.256267525436342	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.292221720624968	1		544	750	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436165	56436180	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGGAAAATGAATCT	CTGGGAAAATGAATCT	-	novel	NA	P-0043122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	69	645	0	ENST00000407977.2:c.957_972del	p.Asp320ProfsTer94	p.D320Pfs*94	ENST00000407977		319	ggAGATTCATTTTCCCAG/gg	9/10	0.292221720624968	1	FACETS	0.56	0.487	0.639	0.56	0.487	0.639	SUBCLONAL	1	TRUE	0	0.292221720624968	1		645	720	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218460	5218460	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	112	649	0	ENST00000357368.4:c.4019A>G	p.Glu1340Gly	p.E1340G	ENST00000357368	NM_002850.3	1340	gAa/gGa	25/38	1	2	FACETS	0.751	0.674	0.832	0.751	0.674	0.832	SUBCLONAL	1	TRUE	1	0.292221720624968	2		649	1021	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795002	242795015	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGTACCAGTTTA	GCGGTACCAGTTTA	-	novel	NA	P-0043122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	172	908	0	ENST00000334409.5:c.194_207del	p.Leu65HisfsTer36	p.L65Hfs*36	ENST00000334409	NM_005018.2	65	cTAAACTGGTACCGC/c	2/5	1	2	FACETS	0.882	0.809	0.958	0.882	0.809	0.958	CLONAL	1	TRUE	1	0.292221720624968	2		908	1335	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645703	12645703	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs397516825	NA	P-0043122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	72	310	0	ENST00000251849.4:c.766A>G	p.Arg256Gly	p.R256G	ENST00000251849	NM_002880.3	256	Agg/Ggg	7/17	1	2	FACETS	0.953	0.834	1	0.953	0.834	1	CLONAL	1	TRUE	1	0.292221720624968	2		310	517	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157552	106157553	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	86	270	0	ENST00000380013.4:c.2455dup	p.Tyr819LeufsTer2	p.Y819Lfs*2	ENST00000380013	NM_001127208.2	818	cct/ccTt	3/11	0.256267525436342	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.292221720624968	1		270	418	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004918	150004918	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0043122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	86	393	0	ENST00000253339.5:c.1307C>G	p.Ser436Ter	p.S436*	ENST00000253339		436	tCa/tGa	3/7	0.256267525436342	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.292221720624968	1		393	473	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0043130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	35	324	1	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.252289770665683	1	FACETS	0.892	0.766	1	0.892	0.766	1	INDETERMINATE	1	TRUE	0	0.711729647325176	1		325	71	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0043130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	216	634	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.572855579218955	1	FACETS	0.922	0.87	0.974	0.922	0.87	0.974	CLONAL	1	TRUE	0	0.711729647325176	1		635	424	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0043130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	58	411	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	1	2	FACETS	0.593	0.514	0.677	0.593	0.514	0.677	SUBCLONAL	1	TRUE	1	0.711729647325176	2		411	275	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554467	63554468	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGT	novel	NA	P-0043130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	331	636	0	ENST00000307078.5:c.269_271dup	p.Asp90dup	p.D90dup	ENST00000307078	NM_004655.3	90	ggt/gACGgt	2/11	0.711729647325176	3	FACETS	0.938	0.895	0.982	0.938	0.895	0.982	CLONAL	2	TRUE	1	0.711729647325176	3		636	672	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0043149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	24	407	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.164072611598084	5	FACETS	0.825	0.653	1	0.55	0.435	0.681	CLONAL	2	FALSE	2	0.226449406586738	5		407	172	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	169	817	0	ENST00000269305.4:c.470T>G	p.Val157Gly	p.V157G	ENST00000269305	NM_001126112.2	157	gTc/gGc	5/11	0.226449406586738	2	FACETS	0.946	0.871	1	0.946	0.871	1	CLONAL	2	FALSE	0	0.226449406586738	2		817	789	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483329	120483329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	46	400	0	ENST00000256646.2:c.3032G>A	p.Cys1011Tyr	p.C1011Y	ENST00000256646	NM_024408.3	1011	tGc/tAc	19/34	0.164072611598084	5	FACETS	0.904	0.766	1	0.603	0.51	0.704	CLONAL	2	FALSE	2	0.226449406586738	5		400	301	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418660	49418660	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555185337	NA	P-0043149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	123	586	0	ENST00000301067.7:c.15854C>G	p.Pro5285Arg	p.P5285R	ENST00000301067	NM_003482.3	5285	cCt/cGt	49/54	0.164072611598084	5	FACETS	1	0.973	1	0.797	0.722	0.874	CLONAL	2	FALSE	2	0.226449406586738	5		586	609	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28901663	28901663	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	36	342	0	ENST00000282397.4:c.2732A>G	p.Tyr911Cys	p.Y911C	ENST00000282397	NM_002019.4	911	tAc/tGc	20/30	0.226449406586738	5	FACETS	0.758	0.626	0.904	0.505	0.417	0.603	CLONAL	2	FALSE	2	0.226449406586738	5		342	281	SUCCESS
AR	367	MSKCC	GRCh37	X	66766149	66766149	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	76	673	0	ENST00000374690.3:c.1161C>G	p.Ile387Met	p.I387M	ENST00000374690	NM_000044.3	387	atC/atG	1/8	0.172775183344588	4	FACETS	0.931	0.82	1	0.931	0.82	1	CLONAL	2	FALSE	2	0.226449406586738	4		673	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577128	7577128	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519987	NA	P-0043152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	452	849	0	ENST00000269305.4:c.810T>G	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	ttT/ttG	8/11	0.602033577295474	2	FACETS	0.849	0.819	0.879	0.849	0.819	0.879	CLONAL	2	TRUE	0	0.71171168570682	2		849	748	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974718	21974718	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	241	547	0	ENST00000304494.5:c.109C>G	p.Leu37Val	p.L37V	ENST00000304494	NM_000077.4	37	Ctg/Gtg	1/3	0.637407917685224	2	FACETS	0.758	0.718	0.797	0.758	0.718	0.797	SUBCLONAL	2	TRUE	0	0.71171168570682	2		547	447	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299898	15299898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	281	1150	1	ENST00000263388.2:c.1280G>A	p.Arg427His	p.R427H	ENST00000263388	NM_000435.2	427	cGc/cAc	8/33	0.327666791303773	3	FACETS	1	0.963	1	0.517	0.486	0.549	INDETERMINATE	1	TRUE	1	0.71171168570682	3		1151	1036	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451373	70451373	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	119	702	0	ENST00000373644.4:c.6213A>C	p.Lys2071Asn	p.K2071N	ENST00000373644	NM_030625.2	2071	aaA/aaC	12/12	0.46316102059141	1	FACETS	0.704	0.645	0.764	0.704	0.645	0.764	SUBCLONAL	1	TRUE	0	0.71171168570682	1		702	306	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62322241	62322241	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	309	1171	1	ENST00000360203.5:c.2497G>A	p.Gly833Arg	p.G833R	ENST00000360203	NM_001283009.1	833	Ggg/Agg	27/35	0.511480829515405	4	FACETS	1	0.974	1	0.353	0.332	0.375	CLONAL	1	TRUE	1	0.71171168570682	4		1172	1402	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974724	21974765	+	inframe_deletion	In_Frame_Del	DEL	CCGCCTCCAGCAGCGCCCGCACCTCCTCTACCCGACCCCGGG	CCGCCTCCAGCAGCGCCCGCACCTCCTCTACCCGACCCCGGG	-	novel	NA	P-0043152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	212	533	0	ENST00000304494.5:c.62_103del	p.Ala21_Ala34del	p.A21_A34del	ENST00000304494	NM_000077.4	21	gCCCGGGGTCGGGTAGAGGAGGTGCGGGCGCTGCTGGAGGCGGgg/ggg	1/3	0.637407917685224	2	FACETS	1	0.992	1	0.704	0.664	0.745	CLONAL	1	TRUE	0	0.71171168570682	2		533	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0043160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	555	668	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.801652078405704	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.888630318458068	1		668	633	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs199469669	NA	P-0043160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	434	721	0	ENST00000374080.3:c.130G>C	p.Gly44Arg	p.G44R	ENST00000374080		44	Ggt/Cgt	2/45	0.888630318458068	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.888630318458068	1		721	524	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972798	32972798	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659246	NA	P-0043160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	175	523	0	ENST00000380152.3:c.10148A>G	p.Lys3383Arg	p.K3383R	ENST00000380152		3383	aAa/aGa	27/27	0.888630318458068	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.888630318458068	1		523	198	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433356	138433356	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	181	521	1	ENST00000289153.2:c.1256C>A	p.Thr419Asn	p.T419N	ENST00000289153	NM_006219.2	419	aCt/aAt	7/22	1	2	FACETS	0.989	0.924	1	0.989	0.924	1	CLONAL	1	TRUE	1	0.888630318458068	2		522	412	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587126	189587126	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	155	422	0	ENST00000264731.3:c.1143C>G	p.Asn381Lys	p.N381K	ENST00000264731	NM_003722.4	381	aaC/aaG	9/14	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.888630318458068	2		422	336	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890129	76890129	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	210	497	0	ENST00000373344.5:c.4765G>T	p.Gly1589Ter	p.G1589*	ENST00000373344	NM_000489.3	1589	Gga/Tga	17/35	0.888630318458068	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.888630318458068	1		497	258	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	54	759	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.43397775607928	2		760	228	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720741	89720741	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs371387815	NA	P-0043168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	13	270	1	ENST00000371953.3:c.892C>T	p.Gln298Ter	p.Q298*	ENST00000371953	NM_000314.4	298	Caa/Taa	8/9	0.43397775607928	1	FACETS	0.434	0.313	0.579	0.434	0.313	0.579	SUBCLONAL	1	TRUE	0	0.43397775607928	1		271	108	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528153	29528153	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	108	667	0	ENST00000356175.3:c.1163del	p.Pro388LeufsTer24	p.P388Lfs*24	ENST00000356175	NM_000267.3	387	agC/ag	10/57	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.43397775607928	2		667	386	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0043198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	66	665	2	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.526510744671286	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.57773336589423	1		667	146	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0043198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	14	418	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.184859441930887	2	FACETS	0.495	0.362	0.65	0.247	0.181	0.325	INDETERMINATE	1	TRUE	0	0.57773336589423	2		418	98	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0043198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	15	324	1	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.184859441930887	2	FACETS	0.618	0.46	0.801	0.309	0.23	0.401	INDETERMINATE	1	TRUE	0	0.57773336589423	2		325	84	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0043198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	193	820	2	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	0.536117524153845	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.57773336589423	2		822	320	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879576	151879576	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	22	409	2	ENST00000262189.6:c.5369C>T	p.Ser1790Phe	p.S1790F	ENST00000262189	NM_170606.2	1790	tCt/tTt	36/59	0.123119912581331	5	FACETS	0.941	0.737	1	0.314	0.245	0.392	INDETERMINATE	1	TRUE	2	0.57773336589423	5		411	151	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0043201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	136	558	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.52722318370634	6	FACETS	1	0.945	1	0.264	0.24	0.29	CLONAL	1	TRUE	2	0.52722318370634	6		558	1003	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0043201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	406	708	1	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.501160879885171	2	FACETS	0.978	0.938	1	0.978	0.938	1	CLONAL	2	TRUE	0	0.52722318370634	2		709	787	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098380	11098380	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	125	556	0	ENST00000358026.2:c.898C>T	p.Gln300Ter	p.Q300*	ENST00000358026	NM_001128849.1	300	Cag/Tag	6/36	0.52722318370634	6	FACETS	0.889	0.803	0.98	0.222	0.2	0.245	CLONAL	1	TRUE	2	0.52722318370634	6		556	1096	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729435	41729435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	44	639	0	ENST00000242208.4:c.1094C>T	p.Ser365Leu	p.S365L	ENST00000242208	NM_002192.2	365	tCa/tTa	3/3	0.455066268360448	3	FACETS	0.27	0.225	0.32	0.135	0.112	0.16	SUBCLONAL	1	TRUE	1	0.52722318370634	3		639	781	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118891	70118891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	129	656	0	ENST00000245479.2:c.463G>A	p.Val155Met	p.V155M	ENST00000245479	NM_000346.3	155	Gtg/Atg	2/3	0.52722318370634	3	FACETS	0.832	0.755	0.913	0.277	0.251	0.305	CLONAL	1	TRUE	0	0.52722318370634	3		656	743	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607673	43607673	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0043201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	169	844	0	ENST00000355710.3:c.1648+1G>A		p.X550_splice	ENST00000355710	NM_020975.4	550			0.513533969175379	3	FACETS	0.827	0.76	0.898	0.414	0.38	0.449	CLONAL	1	TRUE	1	0.52722318370634	3		844	979	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022701	12022701	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	130	542	0	ENST00000396373.4:c.807G>A	p.Met269Ile	p.M269I	ENST00000396373	NM_001987.4	269	atG/atA	5/8	0.52722318370634	3	FACETS	0.991	0.901	1	0.495	0.45	0.542	CLONAL	1	TRUE	1	0.52722318370634	3		542	629	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061200	38061200	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	72	442	0	ENST00000250448.2:c.789G>C	p.Gln263His	p.Q263H	ENST00000250448	NM_004496.3	263	caG/caC	2/2	0.261869411108734	1	FACETS	0.651	0.574	0.733	0.651	0.574	0.733	INDETERMINATE	1	TRUE	0	0.52722318370634	1		442	309	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063696	67063696	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	207	258	0	ENST00000412916.2:c.145C>T	p.Arg49Cys	p.R49C	ENST00000412916		49	Cgc/Tgc	2/6	0.501160879885171	2	FACETS	0.991	0.935	1	0.991	0.935	1	CLONAL	2	TRUE	0	0.52722318370634	2		258	396	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950351	38950351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369474390	NA	P-0043201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	115	557	0	ENST00000357387.3:c.3599G>A	p.Arg1200Gln	p.R1200Q	ENST00000357387	NM_152756.3	1200	cGa/cAa	31/38	0.402367030107365	4	FACETS	0.932	0.84	1	0.466	0.42	0.515	CLONAL	1	TRUE	2	0.52722318370634	4		557	715	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760077	133760128	+	frameshift_variant	Frame_Shift_Del	DEL	CATCATGGAGTCCAGCCCGGGCTCCAGCCCGCCCAACCTGACTCCAAAACCC	CATCATGGAGTCCAGCCCGGGCTCCAGCCCGCCCAACCTGACTCCAAAACCC	-	novel	NA	P-0043201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	178	852	0	ENST00000318560.5:c.2401_2452del	p.Ile801SerfsTer25	p.I801Sfs*25	ENST00000318560	NM_005157.4	800	gaCATCATGGAGTCCAGCCCGGGCTCCAGCCCGCCCAACCTGACTCCAAAACCC/ga	11/11	0.476137247234165	3	FACETS	0.952	0.878	1	0.476	0.439	0.515	CLONAL	1	TRUE	1	0.52722318370634	3		852	896	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0043226-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	804	821	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.569392342892471	3	FACETS	0.906	0.882	0.929	0.906	0.882	0.929	CLONAL	3	TRUE	0	0.609536002732294	3		822	1267	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509128	66509128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1439062174	NA	P-0043226-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	48	388	0	ENST00000273854.3:c.199C>T	p.Arg67Cys	p.R67C	ENST00000273854	NM_004439.5	67	Cgc/Tgc	2/18	0.383484976028625	1	FACETS	0.542	0.464	0.626	0.542	0.464	0.626	SUBCLONAL	1	TRUE	0	0.609536002732294	1		388	202	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056443	26056443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1252419231	NA	P-0043226-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	157	340	0	ENST00000343677.2:c.214G>A	p.Asp72Asn	p.D72N	ENST00000343677	NM_005319.3	72	Gat/Aat	1/1	0.609536002732294	3	FACETS	1	0.971	1	0.559	0.514	0.606	CLONAL	1	TRUE	1	0.609536002732294	3		340	601	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193202250	193202250	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043226-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	76	498	0	ENST00000367435.3:c.1282G>C	p.Val428Leu	p.V428L	ENST00000367435	NM_024529.4	428	Gta/Cta	14/17	0.211740939813906	2	FACETS	0.577	0.508	0.651	0.289	0.254	0.326	INDETERMINATE	1	TRUE	0	0.609536002732294	2		498	432	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1042212	1042212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043226-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1733	94	644	0	ENST00000358495.3:c.13G>A	p.Glu5Lys	p.E5K	ENST00000358495	NM_134424.2	5	Gag/Aag	2/12	0.604727619104126	4	FACETS	0.272	0.24	0.306			1	SUBCLONAL	1	TRUE	NA	0.609536002732294	4		644	1827	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923716	72923716	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043226-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	58	724	0	ENST00000268489.5:c.3362T>C	p.Leu1121Pro	p.L1121P	ENST00000268489	NM_006885.3	1121	cTg/cCg	4/10	0.56325475648478	2	FACETS	0.209	0.179	0.242	0.104	0.089	0.121	SUBCLONAL	1	TRUE	0	0.609536002732294	2		724	911	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346444	89346444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573380956	NA	P-0043226-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	238	787	1	ENST00000301030.4:c.6506G>A	p.Gly2169Glu	p.G2169E	ENST00000301030	NM_001256183.1	2169	gGg/gAg	9/13	0.56325475648478	2	FACETS	0.839	0.784	0.895	0.419	0.392	0.448	CLONAL	1	TRUE	0	0.609536002732294	2		788	931	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56378156	56378156	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043226-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	48	409	0	ENST00000348428.3:c.929G>A	p.Arg310Lys	p.R310K	ENST00000348428	NM_006785.3	310	aGa/aAa	7/17	0.609536002732294	1	FACETS	0.462	0.394	0.535	0.462	0.394	0.535	SUBCLONAL	1	TRUE	0	0.609536002732294	1		409	237	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622357	1622357	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs138005323	NA	P-0043226-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	63	808	0	ENST00000344749.5:c.607G>C	p.Ala203Pro	p.A203P	ENST00000344749	NM_001136139.2	203	Gcc/Ccc	9/19	0.56325475648478	2	FACETS	0.178	0.153	0.205	0.089	0.076	0.103	SUBCLONAL	1	TRUE	0	0.609536002732294	2		808	1161	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187081	38187081	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043226-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	267	859	0	ENST00000317025.8:c.1396G>A	p.Val466Ile	p.V466I	ENST00000317025	NM_023034.1	466	Gtt/Att	6/24	0.609536002732294	1	FACETS	0.586	0.549	0.623	0.586	0.549	0.623	SUBCLONAL	1	TRUE	0	0.609536002732294	1		859	1040	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189044	38189044	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043226-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	129	659	0	ENST00000317025.8:c.970G>C	p.Glu324Gln	p.E324Q	ENST00000317025	NM_023034.1	324	Gaa/Caa	5/24	0.609536002732294	1	FACETS	0.666	0.608	0.725	0.666	0.608	0.725	SUBCLONAL	1	TRUE	0	0.609536002732294	1		659	442	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518087	8518087	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043226-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	275	555	1	ENST00000356435.5:c.1304del	p.Leu435TrpfsTer33	p.L435Wfs*33	ENST00000356435		435	tTg/tg	10/35	0.609536002732294	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.609536002732294	1		556	544	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533767	63533767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881395	NA	P-0043226-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1246	78	701	0	ENST00000307078.5:c.1387C>T	p.Arg463Cys	p.R463C	ENST00000307078	NM_004655.3	463	Cgc/Tgc	6/11	0.609536002732294	3	FACETS	0.252	0.22	0.287	0.084	0.073	0.096	SUBCLONAL	1	TRUE	0	0.609536002732294	3		701	1324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0043233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	241	932	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.250341934173376	2	FACETS	1	0.991	1	0.674	0.631	0.719	CLONAL	1	TRUE	0	0.404470048646226	2		932	884	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038717	47038717	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0043233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	181	427	0	ENST00000377604.3:c.725-1G>C		p.X242_splice	ENST00000377604	NM_001204468.1	242			1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.404470048646226	1		427	480	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105898	27105898	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	260	715	0	ENST00000324856.7:c.5511del	p.Phe1837LeufsTer46	p.F1837Lfs*46	ENST00000324856	NM_006015.4	1837	Ttt/tt	20/20	0.105980470550526	3	FACETS	0.889	0.835	0.945	0.889	0.835	0.945	INDETERMINATE	2	TRUE	1	0.404470048646226	3		715	869	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941080	36941081	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0043233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	59	842	0	ENST00000361632.4:c.258_259insTA	p.Ile87Ter	p.I87*	ENST00000361632		86	-/TA	3/16	0.250341934173376	2	FACETS	0.291	0.249	0.337	0.145	0.124	0.169	SUBCLONAL	1	TRUE	0	0.404470048646226	2		842	1003	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913176	32913176	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397507737	NA	P-0043233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	82	632	0	ENST00000380152.3:c.4684C>T	p.Gln1562Ter	p.Q1562*	ENST00000380152		1562	Caa/Taa	11/27	1	2	FACETS	0.766	0.677	0.862	0.766	0.677	0.862	SUBCLONAL	1	TRUE	1	0.404470048646226	2		632	529	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061050	38061051	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	32	420	0	ENST00000250448.2:c.938dup	p.His314AlafsTer101	p.H314Afs*101	ENST00000250448	NM_004496.3	313	gtg/gtTg	2/2	1	2	FACETS	0.423	0.343	0.513	0.423	0.343	0.513	SUBCLONAL	1	TRUE	1	0.404470048646226	2		420	374	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397710	49397710	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	165	648	0	ENST00000418115.1:c.514G>C	p.Glu172Gln	p.E172Q	ENST00000418115	NM_001664.2	172	Gaa/Caa	5/5	0.404470048646226	1	FACETS	0.788	0.724	0.854	0.788	0.724	0.854	SUBCLONAL	1	TRUE	0	0.404470048646226	1		648	826	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0043237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	143	418	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.531897136229824	3	FACETS	0.963	0.891	1	0.963	0.891	1	CLONAL	2	FALSE	1	0.571558596252192	3		418	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0043237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	498	932	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.550280192481488	2	FACETS	0.94	0.906	0.974	0.94	0.906	0.974	CLONAL	2	FALSE	0	0.571558596252192	2		932	927	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729874	30729874	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0043237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	183	404	0	ENST00000295754.5:c.1397-2A>C		p.X466_splice	ENST00000295754	NM_003242.5	466			0.571558596252192	3	FACETS	0.957	0.894	1	0.957	0.894	1	CLONAL	2	FALSE	1	0.571558596252192	3		404	430	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934351	81934351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749548361	NA	P-0043237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	202	799	0	ENST00000359376.3:c.1328C>T	p.Ser443Leu	p.S443L	ENST00000359376	NM_002661.3	443	tCg/tTg	14/33	0.511917325407241	3	FACETS	0.928	0.861	0.999	0.464	0.43	0.5	CLONAL	1	FALSE	1	0.571558596252192	3		799	979	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0043248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	437	604	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.68283211524742	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	TRUE	0	0.68283211524742	3		604	572	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33290660	33290660	+	5_prime_UTR_variant	5'UTR	SNP	C	C	A	novel	NA	P-0043248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	162	669	1	ENST00000374542.5:c.-74G>T		p.*25*	ENST00000374542	NM_001141970.1	-/740		1/8	0.68283211524742	3	FACETS	1	0.927	1	0.504	0.464	0.545	CLONAL	1	TRUE	1	0.68283211524742	3		670	632	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105236731	105236731	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	398	732	0	ENST00000349310.3:c.1390G>T	p.Glu464Ter	p.E464*	ENST00000349310	NM_001014432.1	464	Gag/Tag	15/15	0.682544705055318	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.68283211524742	2		732	583	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458477	120458477	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	3292	688	0	ENST00000256646.2:c.6868G>T	p.Glu2290Ter	p.E2290*	ENST00000256646	NM_024408.3	2290	Gaa/Taa	34/34	0.68283211524742	23	FACETS	1	0.998	1			1	CLONAL	23	TRUE	NA	0.68283211524742	23		688	3409	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0043252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	30	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.85	0.686	1	0.85	0.686	1	CLONAL	1	TRUE	1	0.203316323368494	2		334	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579350	7579350	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587781642	NA	P-0043252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	95	617	0	ENST00000269305.4:c.337T>G	p.Phe113Val	p.F113V	ENST00000269305	NM_001126112.2	113	Ttc/Gtc	4/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.203316323368494	2		617	869	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438225	110438225	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	11	118	0	ENST00000375856.3:c.176A>G	p.Glu59Gly	p.E59G	ENST00000375856	NM_003749.2	59	gAg/gGg	1/2	1	2	FACETS	0.767	0.532	1	0.767	0.532	1	CLONAL	1	TRUE	1	0.203316323368494	2		118	141	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0043261-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	584	821	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	NA	2	FACETS	1	0.998	1			1	INDETERMINATE	2	TRUE	NA	0.937295622008114	2		822	599	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958042	54958042	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs779964295	NA	P-0043261-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	103	207	0	ENST00000312783.6:c.565C>T	p.Arg189Trp	p.R189W	ENST00000312783	NM_198436.1	189	Cgg/Tgg	6/10	0.937295622008114	5	FACETS	1	0.974	1	0.416	0.374	0.459	CLONAL	1	TRUE	2	0.937295622008114	5		207	424	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103249	119103249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781738309	NA	P-0043261-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	209	469	0	ENST00000264033.4:c.287G>A	p.Arg96His	p.R96H	ENST00000264033	NM_005188.3	96	cGt/cAt	2/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.937295622008114	2		469	437	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215595207	215595207	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043261-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	143	317	0	ENST00000260947.4:c.1929del	p.Val644TyrfsTer70	p.V644Yfs*70	ENST00000260947	NM_000465.2	643	aaA/aa	10/11	0.937295622008114	3	FACETS	0.916	0.841	0.994	0.458	0.42	0.497	CLONAL	1	TRUE	1	0.937295622008114	3		317	489	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260154	149260154	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043261-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	521	501	0	ENST00000360632.3:c.739A>T	p.Ile247Phe	p.I247F	ENST00000360632	NM_015472.4	247	Att/Ttt	4/7	0.937295622008114	5	FACETS	1	0.973	1	0.605	0.585	0.626	CLONAL	3	TRUE	0	0.937295622008114	5		501	884	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	469	759	1				ENST00000310581	NM_198253.2	-/1132			0.263856638873775	6	FACETS	1	0.981	1	1	0.981	1	CLONAL	5	TRUE	1	0.263856638873775	6		760	1046	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0043287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	157	768	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	1	2	FACETS	0.998	0.913	1	0.998	0.913	1	CLONAL	1	TRUE	1	0.263856638873775	2		768	1192	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0043287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	104	668	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	1	2	FACETS	0.677	0.605	0.755	0.677	0.605	0.755	SUBCLONAL	1	TRUE	1	0.263856638873775	2		668	1164	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	186	714	0	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.263856638873775	2		714	1181	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045024	47045024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	150	325	0	ENST00000377604.3:c.2350C>T	p.His784Tyr	p.H784Y	ENST00000377604	NM_001204468.1	784	Cac/Tac	20/24	1	1	FACETS	0.829	0.761	0.9	1	0.99	1	CLONAL	2	TRUE	0	0.263856638873775	1		325	595	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941739	48941739	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	37	256	0	ENST00000267163.4:c.1049G>A	p.Ser350Asn	p.S350N	ENST00000267163	NM_000321.2	350	aGt/aAt	10/27	1	2	FACETS	0.657	0.542	0.786	0.657	0.542	0.786	SUBCLONAL	1	TRUE	1	0.263856638873775	2		256	427	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951994	178951994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	86	425	0	ENST00000263967.3:c.3049G>A	p.Asp1017Asn	p.D1017N	ENST00000263967	NM_006218.2	1017	Gat/Aat	21/21	1	2	FACETS	0.909	0.804	1	0.909	0.804	1	CLONAL	1	TRUE	1	0.263856638873775	2		425	717	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852313	63852313	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	131	598	0	ENST00000279873.7:c.3091G>T	p.Val1031Leu	p.V1031L	ENST00000279873	NM_032199.2	1031	Gtg/Ttg	10/10	1	2	FACETS	0.941	0.853	1	0.941	0.853	1	CLONAL	1	TRUE	1	0.263856638873775	2		598	1055	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112767358	112767358	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs730881021	NA	P-0043287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	109	555	0	ENST00000369452.4:c.1231A>G	p.Thr411Ala	p.T411A	ENST00000369452	NM_007373.3	411	Act/Gct	6/9	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.263856638873775	2		555	652	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955394	48955412	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAATCTTGATTCTGGAA	CAGAATCTTGATTCTGGAA	-	novel	NA	P-0043287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	49	246	0	ENST00000267163.4:c.1514_1532del	p.Asn505IlefsTer8	p.N505Ifs*8	ENST00000267163	NM_000321.2	504	CAGAATCTTGATTCTGGAAca/ca	17/27	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.263856638873775	2		246	321	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81562991	81562991	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	43	451	0	ENST00000298171.2:c.554A>G	p.Tyr185Cys	p.Y185C	ENST00000298171	NM_000369.2	185	tAc/tGc	7/10	1	2	FACETS	0.505	0.422	0.598	0.505	0.422	0.598	SUBCLONAL	1	TRUE	1	0.263856638873775	2		451	645	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258614	19258614	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	112	669	0	ENST00000162023.5:c.286G>T	p.Asp96Tyr	p.D96Y	ENST00000162023		96	Gat/Tat	8/13	1	2	FACETS	0.747	0.67	0.828	0.747	0.67	0.828	SUBCLONAL	1	TRUE	1	0.263856638873775	2		669	1137	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622496	158622496	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	117	476	0	ENST00000263640.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000263640	NM_001105.4	335	Cga/Tga	8/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.263856638873775	2		476	726	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660583	227660583	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	137	613	0	ENST00000305123.5:c.2872A>T	p.Thr958Ser	p.T958S	ENST00000305123	NM_005544.2	958	Act/Tct	1/2	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.263856638873775	2		613	914	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324177	62324177	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs761295679	NA	P-0043287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	77	667	0	ENST00000360203.5:c.2672C>G	p.Ala891Gly	p.A891G	ENST00000360203	NM_001283009.1	891	gCa/gGa	29/35	1	2	FACETS	0.524	0.459	0.595	0.524	0.459	0.595	SUBCLONAL	1	TRUE	1	0.263856638873775	2		667	1113	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754321	57754322	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0043287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	57	431	0	ENST00000274289.3:c.528_529dup	p.Leu177CysfsTer2	p.L177Cfs*2	ENST00000274289	NM_006622.3	177	ttg/tGTtg	4/14	1	2	FACETS	0.652	0.558	0.754	0.652	0.558	0.754	SUBCLONAL	1	TRUE	1	0.263856638873775	2		431	663	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81340836	81340836	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0043287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	56	229	0	ENST00000222390.5:c.1406-1G>C		p.X469_splice	ENST00000222390	NM_000601.4	469			1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.263856638873775	2		229	411	SUCCESS
AR	367	MSKCC	GRCh37	X	66766489	66766489	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	131	238	0	ENST00000374690.3:c.1501G>T	p.Asp501Tyr	p.D501Y	ENST00000374690	NM_000044.3	501	Gat/Tat	1/8	1	1	FACETS	0.909	0.831	0.991	1	0.99	1	CLONAL	2	TRUE	0	0.263856638873775	1		238	474	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0043321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	153	327	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.993	0.917	1	0.993	0.917	1	CLONAL	1	TRUE	1	0.681676422863406	2		327	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0043321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	605	761	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.681676422863406	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.681676422863406	2		764	792	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937487	76937487	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0043321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	256	477	2	ENST00000373344.5:c.3261T>A	p.Tyr1087Ter	p.Y1087*	ENST00000373344	NM_000489.3	1087	taT/taA	9/35	0.681676422863406	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.681676422863406	1		479	486	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443657	29443657	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	257	757	0	ENST00000389048.3:c.3560T>A	p.Leu1187Gln	p.L1187Q	ENST00000389048	NM_004304.4	1187	cTg/cAg	23/29	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.681676422863406	2		757	732	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641231	93641231	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	157	375	0	ENST00000375746.1:c.1577A>G	p.Tyr526Cys	p.Y526C	ENST00000375746	NM_001174167.1	526	tAc/tGc	11/14	1	2	FACETS	0.944	0.871	1	0.944	0.871	1	CLONAL	1	TRUE	1	0.681676422863406	2		375	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0043331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	1116	729	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.8184553052514	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.8184553052514	3		729	1273	SUCCESS
APC	324	MSKCC	GRCh37	5	112175360	112175360	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	411	320	0	ENST00000257430.4:c.4069G>T	p.Gly1357Ter	p.G1357*	ENST00000257430	NM_000038.5	1357	Gga/Tga	16/16	0.814680677474283	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.8184553052514	3		320	463	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434820	110434820	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	620	603	0	ENST00000375856.3:c.3581C>G	p.Pro1194Arg	p.P1194R	ENST00000375856	NM_003749.2	1194	cCt/cGt	1/2	0.8184553052514	5	FACETS	1	0.977	1			1	CLONAL	2	TRUE	NA	0.8184553052514	5		603	1652	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95579460	95579460	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	167	426	0	ENST00000393063.1:c.2009C>T	p.Pro670Leu	p.P670L	ENST00000393063	NM_030621.3	670	cCa/cTa	13/28	0.8184553052514	2	FACETS	0.907	0.842	0.973	0.453	0.421	0.487	CLONAL	1	TRUE	0	0.8184553052514	2		426	450	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929465	81929465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766133588	NA	P-0043331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	768	582	2	ENST00000359376.3:c.1126C>T	p.Arg376Trp	p.R376W	ENST00000359376	NM_002661.3	376	Cgg/Tgg	13/33	0.625005684436013	5	FACETS	0.989	0.96	1	0.989	0.96	1	CLONAL	3	TRUE	2	0.8184553052514	5		584	1409	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0043333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	97	243	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.541637610992463	2		243	320	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0043333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	102	462	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.520399684578285	3	FACETS	1	0.965	1	0.581	0.523	0.641	CLONAL	1	TRUE	1	0.541637610992463	3		462	412	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0043333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	61	542	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.588	0.509	0.673	0.588	0.509	0.673	SUBCLONAL	1	TRUE	1	0.541637610992463	2		542	383	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913237	NA	P-0043333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	89	502	0	ENST00000369535.4:c.35G>T	p.Gly12Val	p.G12V	ENST00000369535	NM_002524.4	12	gGt/gTt	2/7	1	2	FACETS	0.845	0.754	0.94	0.845	0.754	0.94	CLONAL	1	TRUE	1	0.541637610992463	2		502	389	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	77	596	0	ENST00000355710.3:c.2753T>G	p.Met918Arg	p.M918R	ENST00000355710	NM_020975.4	918	aTg/aGg	16/20	0.219299061618557	0	FACETS	0.465	0.413	0.52			1	INDETERMINATE	1	TRUE	0	0.541637610992463	0		596	280	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058827	42058827	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	91	465	0	ENST00000219905.7:c.8547C>A	p.Ser2849Arg	p.S2849R	ENST00000219905	NM_001164273.1	2849	agC/agA	24/24	0.211777425846	3	FACETS	1	0.955	1	0.563	0.504	0.626	INDETERMINATE	1	TRUE	1	0.541637610992463	3		465	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0043333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	130	666	2	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	0.542088712520621	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.541637610992463	1		668	322	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727880	41727880	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756018335	NA	P-0043333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	157	806	0	ENST00000301178.4:c.505G>A	p.Val169Met	p.V169M	ENST00000301178	NM_021913.4	169	Gtg/Atg	4/20	0.542088712520621	3	FACETS	1	0.977	1	0.583	0.536	0.632	CLONAL	1	TRUE	1	0.541637610992463	3		806	632	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620674	52620674	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	93	403	0	ENST00000394830.3:c.3079C>T	p.Arg1027Ter	p.R1027*	ENST00000394830	NM_018313.4	1027	Cga/Tga	21/30	1	2	FACETS	0.992	0.891	1	0.992	0.891	1	CLONAL	1	TRUE	1	0.541637610992463	2		403	346	SUCCESS
APC	324	MSKCC	GRCh37	5	112175952	112175952	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587783031	NA	P-0043333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	55	323	0	ENST00000257430.4:c.4666del	p.Thr1556LeufsTer9	p.T1556Lfs*9	ENST00000257430	NM_000038.5	1554	gAa/ga	16/16	0.497652124694837	1	FACETS	0.926	0.809	1	0.926	0.809	1	CLONAL	1	TRUE	0	0.541637610992463	1		323	160	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903836	41903836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540997482	NA	P-0043333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	95	636	0	ENST00000372991.4:c.721C>T	p.Arg241Trp	p.R241W	ENST00000372991	NM_001760.3	241	Cgg/Tgg	5/5	0.541637610992463	2	FACETS	1	0.956	1	0.557	0.501	0.615	CLONAL	1	TRUE	0	0.541637610992463	2		636	315	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	105	759	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.42237522243005	2		760	459	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0043354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	204	410	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.42237522243005	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.42237522243005	1		410	595	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30061031	30061031	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0043354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	169	487	0	ENST00000338641.4:c.863C>G	p.Ser288Ter	p.S288*	ENST00000338641	NM_000268.3	288	tCa/tGa	9/16	0.42237522243005	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.42237522243005	1		487	615	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417866	138417866	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	180	501	0	ENST00000289153.2:c.1653T>G	p.Cys551Trp	p.C551W	ENST00000289153	NM_006219.2	551	tgT/tgG	11/22	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.42237522243005	2		501	786	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143326438	143326438	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs749451581	NA	P-0043354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	167	408	0	ENST00000262992.4:c.176T>C	p.Leu59Pro	p.L59P	ENST00000262992	NM_001101669.1	59	cTg/cCg	4/24	0.42237522243005	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.42237522243005	1		408	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0043377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	246	780	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.217047879567717	NA		780	1058	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110171	3110171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1335558363	NA	P-0043377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	75	556	0	ENST00000078429.4:c.161C>T	p.Thr54Met	p.T54M	ENST00000078429	NM_002067.2	54	aCg/aTg	2/7	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.217047879567717	NA		556	976	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289642	15289642	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	277	804	3	ENST00000263388.2:c.3829T>A	p.Cys1277Ser	p.C1277S	ENST00000263388	NM_000435.2	1277	Tgt/Agt	23/33	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.217047879567717	NA		807	1257	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851885	134851885	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	58	462	0	ENST00000398015.3:c.1291C>T	p.Gln431Ter	p.Q431*	ENST00000398015	NM_004441.4	431	Caa/Taa	5/16	0.217047879567717	3	FACETS	0.838	0.719	0.968	0.419	0.359	0.484	CLONAL	1	TRUE	1	0.217047879567717	3		462	707	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0043405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	152	410	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.313461895346004	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.323757659209148	3		410	503	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023168	33023168	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	90	575	0	ENST00000300177.4:c.277T>C	p.Trp93Arg	p.W93R	ENST00000300177	NM_001191322.1	93	Tgg/Cgg	2/2	0.149024768043398	0	FACETS	0.743	0.661	0.83			1	INDETERMINATE	1	TRUE	0	0.323757659209148	0		575	506	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023195	33023195	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	115	614	0	ENST00000300177.4:c.304A>T	p.Thr102Ser	p.T102S	ENST00000300177	NM_001191322.1	102	Acc/Tcc	2/2	0.149024768043398	0	FACETS	0.79	0.714	0.871			1	INDETERMINATE	1	TRUE	0	0.323757659209148	0		614	608	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294150	1294150	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1279190294	NA	P-0043405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	274	817	0	ENST00000310581.5:c.851C>T	p.Ser284Phe	p.S284F	ENST00000310581	NM_198253.2	284	tCt/tTt	2/16	0.323757659209148	4	FACETS	0.978	0.917	1	0.652	0.611	0.693	CLONAL	2	TRUE	1	0.323757659209148	4		817	1146	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144723	119144723	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs376182596	NA	P-0043415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	70	285	0	ENST00000264033.4:c.736C>T	p.Arg246Ter	p.R246*	ENST00000264033	NM_005188.3	246	Cga/Tga	4/16	0.336716096883585	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.377069549273539	1		285	263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578179	7578179	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	212	589	0	ENST00000269305.4:c.670G>T	p.Glu224Ter	p.E224*	ENST00000269305	NM_001126112.2	224	Gag/Tag	6/11	0.356148878300994	2	FACETS	0.959	0.898	1	0.959	0.898	1	CLONAL	2	TRUE	0	0.377069549273539	2		589	586	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222214	2222214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768756000	NA	P-0043415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	113	725	2	ENST00000398665.3:c.3046G>A	p.Ala1016Thr	p.A1016T	ENST00000398665	NM_032482.2	1016	Gcc/Acc	24/28	0.178842711527974	2	FACETS	0.88	0.793	0.972	0.44	0.396	0.486	INDETERMINATE	1	TRUE	0	0.377069549273539	2		727	681	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201792	66201792	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	38	418	2	ENST00000273854.3:c.2710C>A	p.Pro904Thr	p.P904T	ENST00000273854	NM_004439.5	904	Cct/Act	16/18	0.377069549273539	2	FACETS	0.333	0.275	0.399	0.167	0.137	0.2	SUBCLONAL	1	TRUE	0	0.377069549273539	2		420	605	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115928	8115929	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	38	438	0	ENST00000346208.3:c.1275dup	p.Ser426IlefsTer81	p.S426Ifs*81	ENST00000346208		425	cca/ccAa	6/6	1	2	FACETS	0.939	0.775	1	0.939	0.775	1	CLONAL	1	TRUE	1	0.16	2		438	506	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575362	64575362	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs794728622	NA	P-0043517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	52	516	0	ENST00000312049.6:c.654+1G>T		p.X218_splice	ENST00000312049	NM_130799.2	218			1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.16	2		516	567	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256469	16256472	+	frameshift_variant	Frame_Shift_Del	DEL	ACAG	ACAG	-	novel	NA	P-0043517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	43	582	0	ENST00000375759.3:c.3735_3738del	p.Tyr1245Ter	p.Y1245*	ENST00000375759	NM_015001.2	1245	tACAGa/ta	11/15	1	2	FACETS	0.823	0.687	0.974	0.823	0.687	0.974	CLONAL	1	TRUE	1	0.16	2		582	653	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262414	16262414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	26	359	0	ENST00000375759.3:c.9679C>T	p.Gln3227Ter	p.Q3227*	ENST00000375759	NM_015001.2	3227	Cag/Tag	11/15	1	2	FACETS	0.791	0.626	0.98	0.791	0.626	0.98	CLONAL	1	TRUE	1	0.16	2		359	411	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0043528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	15	243	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.501	0.365	0.666	0.501	0.365	0.666	SUBCLONAL	1	TRUE	1	0.15	2		243	399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0043558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	369	765	2	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.603959993786064	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.603959993786064	1		767	684	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245447	153245447	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	310	664	0	ENST00000281708.4:c.1744T>C	p.Ser582Pro	p.S582P	ENST00000281708	NM_033632.3	582	Tcg/Ccg	11/12	0.123756157678532	3	FACETS	0.859	0.814	0.904	0.573	0.543	0.603	INDETERMINATE	2	TRUE	0	0.603959993786064	3		664	778	SUCCESS
APC	324	MSKCC	GRCh37	5	112175770	112175770	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	69	377	1	ENST00000257430.4:c.4480del	p.Glu1494LysfsTer13	p.E1494Kfs*13	ENST00000257430	NM_000038.5	1493	acG/ac	16/16	1	2	FACETS	0.603	0.528	0.683	0.603	0.528	0.683	SUBCLONAL	1	TRUE	1	0.603959993786064	2		378	379	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518358	204518358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs557473906	NA	P-0043558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	42	559	0	ENST00000367182.3:c.1021C>T	p.Leu341Phe	p.L341F	ENST00000367182	NM_001278516.1	341	Ctc/Ttc	11/11	0.202536610634865	3	FACETS	0.246	0.205	0.292	0.123	0.102	0.146	INDETERMINATE	1	TRUE	1	0.603959993786064	3		559	736	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885006	111885006	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1252209646	NA	P-0043558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	238	733	0	ENST00000341259.2:c.1004C>G	p.Thr335Arg	p.T335R	ENST00000341259	NM_005475.2	335	aCa/aGa	5/8	0.603959993786064	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.603959993786064	1		733	542	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939051	48939051	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	39	328	0	ENST00000267163.4:c.883A>C	p.Asn295His	p.N295H	ENST00000267163	NM_000321.2	295	Aat/Cat	9/27	0.149503805698418	5	FACETS	0.452	0.374	0.539	0.113	0.093	0.135	INDETERMINATE	1	TRUE	1	0.603959993786064	5		328	545	SUCCESS
APC	324	MSKCC	GRCh37	5	112173806	112173806	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	124	409	0	ENST00000257430.4:c.2515G>T	p.Gly839Ter	p.G839*	ENST00000257430	NM_000038.5	839	Gga/Tga	16/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.603959993786064	2		409	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	91	496	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.261336996959734	4	FACETS	0.93	0.841	1	0.698	0.631	0.767	CLONAL	3	FALSE	0	0.379631810571437	4		496	237	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367336	50367336	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	82	456	0	ENST00000331340.3:c.143A>T	p.Lys48Met	p.K48M	ENST00000331340	NM_006060.4	48	aAg/aTg	3/8	0.379631810571437	5	FACETS	1	0.967	1	0.424	0.374	0.477	CLONAL	1	FALSE	2	0.379631810571437	5		456	533	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178244	56178245	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0043563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	17	307	0	ENST00000399503.3:c.3218_3219dup	p.Gly1074ArgfsTer9	p.G1074Rfs*9	ENST00000399503	NM_005921.1	1073	cag/cAGag	14/20	0.304504355761546	4	FACETS	1	0.898	1	0.473	0.36	0.603	CLONAL	1	FALSE	1	0.379631810571437	4		307	87	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0043586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	30	395	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.6	0.484	0.732	0.6	0.484	0.732	SUBCLONAL	1	TRUE	1	0.28	2		395	357	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0043586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	99	932	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.28	2		932	584	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897444	78897444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746953724	NA	P-0043586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	93	656	0	ENST00000306801.3:c.2779C>T	p.Arg927Trp	p.R927W	ENST00000306801	NM_020761.2	927	Cgg/Tgg	23/34	1	2	FACETS	0.94	0.836	1	0.94	0.836	1	CLONAL	1	TRUE	1	0.28	2		656	707	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0049605-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	220	542	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.377901550506469	2	FACETS	0.961	0.901	1	0.961	0.901	1	CLONAL	2	TRUE	0	0.390608645204174	2		542	586	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415537	152415537	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519714	NA	P-0049605-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	118	642	0	ENST00000206249.3:c.1387T>C	p.Ser463Pro	p.S463P	ENST00000206249	NM_000125.3	463	Tcc/Ccc	7/8	0.390608645204174	1	FACETS	0.921	0.834	1	0.921	0.834	1	CLONAL	1	TRUE	0	0.390608645204174	1		642	528	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049605-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	136	546	0	ENST00000206249.3:c.1610A>G	p.Tyr537Cys	p.Y537C	ENST00000206249	NM_000125.3	537	tAt/tGt	8/8	0.390608645204174	1	FACETS	0.899	0.82	0.982	0.899	0.82	0.982	CLONAL	1	TRUE	0	0.390608645204174	1		546	623	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049605-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	93	519	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	1	2	FACETS	0.958	0.855	1	0.958	0.855	1	CLONAL	1	TRUE	1	0.390608645204174	2		519	497	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0049605-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	121	975	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	1	2	FACETS	0.93	0.842	1	0.93	0.842	1	CLONAL	1	TRUE	1	0.390608645204174	2		975	666	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953011	2953011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1172378918	NA	P-0049605-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	129	726	0	ENST00000396946.4:c.2929G>A	p.Val977Met	p.V977M	ENST00000396946	NM_032415.4	977	Gtg/Atg	22/25	0.379053278312796	3	FACETS	0.989	0.897	1	0.495	0.448	0.543	CLONAL	1	TRUE	1	0.390608645204174	3		726	798	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118820	115118821	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0049605-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	114	606	0	ENST00000257566.3:c.520_521del	p.Gly174Ter	p.G174*	ENST00000257566	NM_016569.3	174	GGt/t	2/8	1	2	FACETS	0.929	0.839	1	0.929	0.839	1	CLONAL	1	TRUE	1	0.390608645204174	2		606	628	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120818	115120818	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049605-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	137	825	0	ENST00000257566.3:c.188del	p.Pro63ArgfsTer25	p.P63Rfs*25	ENST00000257566	NM_016569.3	63	cCg/cg	1/8	1	2	FACETS	0.918	0.836	1	0.918	0.836	1	CLONAL	1	TRUE	1	0.390608645204174	2		825	764	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188291	142188291	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049605-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	60	371	0	ENST00000350721.4:c.6440C>A	p.Ser2147Tyr	p.S2147Y	ENST00000350721	NM_001184.3	2147	tCt/tAt	38/47	1	2	FACETS	0.951	0.825	1	0.951	0.825	1	CLONAL	1	TRUE	1	0.390608645204174	2		371	323	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149450084	149450084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1419926665	NA	P-0049605-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	118	699	1	ENST00000286301.3:c.1133G>A	p.Arg378His	p.R378H	ENST00000286301	NM_005211.3	378	cGc/cAc	8/22	1	2	FACETS	0.883	0.798	0.973	0.883	0.798	0.973	CLONAL	1	TRUE	1	0.390608645204174	2		700	684	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939895	76939895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049605-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	87	529	0	ENST00000373344.5:c.853G>A	p.Glu285Lys	p.E285K	ENST00000373344	NM_000489.3	285	Gag/Aag	9/35	1	2	FACETS	0.87	0.773	0.974	0.87	0.773	0.974	CLONAL	1	TRUE	1	0.390608645204174	2		529	512	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842404	68842404	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	AG	novel	NA	P-0049605-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	190	634	0	ENST00000261769.5:c.465delinsAG	p.Asp155GlufsTer13	p.D155Efs*13	ENST00000261769	NM_004360.3	155	gaC/gaAG	4/16	0.377901550506469	2	FACETS	0.861	0.801	0.922	0.861	0.801	0.922	CLONAL	2	TRUE	0	0.390608645204174	2		634	565	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21336839	21336839	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049605-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	157	854	0	ENST00000215739.8:c.179G>A	p.Cys60Tyr	p.C60Y	ENST00000215739	NM_006767.3	60	tGc/tAc	1/21	0.390608645204174	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.390608645204174	1		854	640	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593606	55593611	+	inframe_deletion	In_Frame_Del	DEL	AAGGTT	AAGGTT	-	novel	NA	P-0052061-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	18	496	0	ENST00000288135.5:c.1672_1677del	p.Lys558_Val559del	p.K558_V559del	ENST00000288135	NM_000222.2	558	AAGGTT/-	11/21	0.264150277831214	0	FACETS	0.661	0.498	0.853			1	SUBCLONAL	1	TRUE	0	0.17	0		496	266	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593606	55593611	+	inframe_deletion	In_Frame_Del	DEL	AAGGTT	AAGGTT	-	novel	NA	P-0052061-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	8	496	0	ENST00000288135.5:c.1672_1677del	p.Lys558_Val559del	p.K558_V559del	ENST00000288135	NM_000222.2	558	AAGGTT/-	11/21	1	2	FACETS	0.151	0.097	0.223	0.151	0.097	0.223	SUBCLONAL	1	FALSE	1	0.307418773493175	2		496	344	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0052468-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	73	191	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.260987926266601	1	FACETS	0.626	0.558	0.695	0.626	0.558	0.695	INDETERMINATE	1	TRUE	0	0.746420651503721	1		191	196	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679724	88679724	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052468-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	123	401	0	ENST00000360948.2:c.739G>T	p.Gly247Trp	p.G247W	ENST00000360948	NM_001012338.2	247	Ggg/Tgg	7/19	0.746420651503721	1	FACETS	0.595	0.545	0.647	0.595	0.545	0.647	SUBCLONAL	1	TRUE	0	0.746420651503721	1		401	347	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218473	1218494	+	frameshift_variant	Frame_Shift_Del	DEL	GTTATACAACGAAGAGAAGCAG	GTTATACAACGAAGAGAAGCAG	-	novel	NA	P-0052468-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	147	418	0	ENST00000326873.7:c.348_369del	p.Leu117LysfsTer5	p.L117Kfs*5	ENST00000326873	NM_000455.4	116	gtGTTATACAACGAAGAGAAGCAG/gt	2/10	0.746420651503721	1	FACETS	0.771	0.716	0.827	0.771	0.716	0.827	SUBCLONAL	1	TRUE	0	0.746420651503721	1		418	320	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599949	10599950	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0052468-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	242	485	0	ENST00000171111.5:c.1626_1627del	p.Glu542AspfsTer31	p.E542Dfs*31	ENST00000171111	NM_203500.1	542	gaGAcg/gacg	5/6	0.746420651503721	1	FACETS	0.876	0.83	0.922	0.876	0.83	0.922	CLONAL	1	TRUE	0	0.746420651503721	1		485	464	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023441	31023441	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs776868653	NA	P-0052468-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	363	470	0	ENST00000375687.4:c.2926C>T	p.Gln976Ter	p.Q976*	ENST00000375687	NM_015338.5	976	Caa/Taa	13/13	0.712747474962429	2	FACETS	0.99	0.958	1	0.99	0.958	1	CLONAL	2	TRUE	0	0.746420651503721	2		470	491	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447190	187447190	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052468-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	224	519	1	ENST00000232014.4:c.1003C>T	p.Gln335Ter	p.Q335*	ENST00000232014	NM_001130845.1	335	Cag/Tag	5/10	0.746420651503721	1	FACETS	0.871	0.823	0.919	0.871	0.823	0.919	CLONAL	1	TRUE	0	0.746420651503721	1		520	432	SUCCESS
APC	324	MSKCC	GRCh37	5	112178205	112178205	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1561611221	NA	P-0052468-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	182	545	0	ENST00000257430.4:c.6914G>C	p.Arg2305Thr	p.R2305T	ENST00000257430	NM_000038.5	2305	aGa/aCa	16/16	0.746420651503721	1	FACETS	0.952	0.897	1	0.952	0.897	1	CLONAL	1	TRUE	0	0.746420651503721	1		545	321	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942807	68942807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052468-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	149	479	0	ENST00000288368.4:c.619G>T	p.Val207Phe	p.V207F	ENST00000288368	NM_024870.2	207	Gtc/Ttc	6/40	0.173617310310329	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.746420651503721	0		479	423	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317136	87317136	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052468-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	131	446	0	ENST00000277120.3:c.275G>T	p.Gly92Val	p.G92V	ENST00000277120		92	gGa/gTa	3/19	1	2	FACETS	0.886	0.812	0.962	0.886	0.812	0.962	CLONAL	1	TRUE	1	0.746420651503721	2		446	396	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485103	57485103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052522-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	163	567	0	ENST00000371085.3:c.937C>T	p.Pro313Ser	p.P313S	ENST00000371085	NM_000516.4	313	Cca/Tca	11/13	0.761415914680998	3	FACETS	0.911	0.84	0.985	0.456	0.42	0.493	CLONAL	1	TRUE	1	0.794782678544504	3		567	629	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426784	121426784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765432081	NA	P-0052522-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	400	644	0	ENST00000257555.6:c.475C>T	p.Arg159Trp	p.R159W	ENST00000257555		159	Cgg/Tgg	2/10	0.794782678544504	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.794782678544504	2		644	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578234	7578234	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs786202222	NA	P-0052522-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	390	633	0	ENST00000269305.4:c.615T>A	p.Tyr205Ter	p.Y205*	ENST00000269305	NM_001126112.2	205	taT/taA	6/11	0.794782678544504	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.794782678544504	2		633	475	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033965	49033965	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052522-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	338	479	1	ENST00000267163.4:c.2102A>G	p.Asp701Gly	p.D701G	ENST00000267163	NM_000321.2	701	gAc/gGc	20/27	0.794782678544504	3	FACETS	0.983	0.956	1	0.983	0.956	1	CLONAL	3	TRUE	0	0.794782678544504	3		480	403	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982426	201982426	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052522-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	194	562	0	ENST00000359651.3:c.805G>T	p.Ala269Ser	p.A269S	ENST00000359651		269	Gcg/Tcg	6/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.794782678544504	2		562	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0052625-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	432	676	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.257109857084559	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	3	FALSE	0	0.257109857084559	3		676	1261	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0052625-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	438	772	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.257109857084559	9	FACETS	1	0.979	1	0.837	0.797	0.878	CLONAL	4	FALSE	4	0.257109857084559	9		772	1546	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054947-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	58	759	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.918	0.793	1	0.918	0.793	1	CLONAL	1	TRUE	1	0.366201313239803	2		760	345	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225060	NA	P-0054947-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	122	545	0	ENST00000263967.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000263967	NM_006218.2	104	cCa/cTa	2/21	0.171859417894925	3	FACETS	1	0.971	1	0.594	0.537	0.653	INDETERMINATE	1	TRUE	1	0.366201313239803	3		545	664	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18747435	18747435	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054947-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	74	337	0	ENST00000266497.5:c.3896G>T	p.Cys1299Phe	p.C1299F	ENST00000266497		1299	tGt/tTt	28/31	0.171859417894925	3	FACETS	1	0.946	1	0.569	0.5	0.643	INDETERMINATE	1	TRUE	1	0.366201313239803	3		337	420	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602345	28602345	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054947-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	63	443	0	ENST00000241453.7:c.2023G>T	p.Val675Leu	p.V675L	ENST00000241453	NM_004119.2	675	Gtg/Ttg	16/24	1	2	FACETS	0.721	0.625	0.825	0.721	0.625	0.825	SUBCLONAL	1	TRUE	1	0.366201313239803	2		443	477	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81922859	81922859	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056089-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	45	335	0	ENST00000359376.3:c.848C>A	p.Pro283His	p.P283H	ENST00000359376	NM_002661.3	283	cCt/cAt	10/33	1	2	FACETS	0.153	0.128	0.181	0.153	0.128	0.181	SUBCLONAL	1	TRUE	1	0.88738786475816	2		335	663	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801030	1801030	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs143548893	NA	P-0056089-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	286	507	0	ENST00000260795.2:c.159C>A	p.Ser53Arg	p.S53R	ENST00000260795		53	agC/agA	2/17	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.88738786475816	2		507	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934571	NA	P-0057819-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	413	467	0	ENST00000269305.4:c.747G>C	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agC	7/11	0.728847090282264	4	FACETS	0.987	0.965	1	0.987	0.965	1	CLONAL	4	TRUE	0	0.793322218997454	4		467	473	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020733	37020733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057819-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	96	462	0	ENST00000358127.4:c.112C>T	p.Arg38Cys	p.R38C	ENST00000358127	NM_001280556.1	38	Cgc/Tgc	2/10	0.743481919447989	3	FACETS	0.98	0.881	1	0.327	0.293	0.361	CLONAL	1	TRUE	0	0.793322218997454	3		462	345	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62297419	62297419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1192425489	NA	P-0057819-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	175	438	0	ENST00000360203.5:c.601G>A	p.Gly201Arg	p.G201R	ENST00000360203	NM_001283009.1	201	Gga/Aga	7/35	0.793322218997454	6	FACETS	0.974	0.902	1	0.487	0.451	0.524	CLONAL	2	TRUE	2	0.793322218997454	6		438	586	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424752	49424752	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0058374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	622	742	0	ENST00000301067.7:c.13595T>A	p.Leu4532Ter	p.L4532*	ENST00000301067	NM_003482.3	4532	tTg/tAg	40/54	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.505330611117194	2		742	1115	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439295	52439295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1365625070	NA	P-0058374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	285	654	1	ENST00000460680.1:c.947C>T	p.Ala316Val	p.A316V	ENST00000460680	NM_004656.3	316	gCg/gTg	11/17	0.505330611117194	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.505330611117194	1		655	637	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0058651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	13	558	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.815	1	1	0.815	1	CLONAL	1	TRUE	1	0.16	2		558	136	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653840	89653840	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0058651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	10	235	0	ENST00000371953.3:c.138C>G	p.Tyr46Ter	p.Y46*	ENST00000371953	NM_000314.4	46	taC/taG	2/9	1	2	FACETS	0.845	0.574	1	0.845	0.574	1	CLONAL	1	TRUE	1	0.16	2		235	148	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058705-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	20	522	0	ENST00000269305.4:c.818del	p.Arg273LeufsTer72	p.R273Lfs*72	ENST00000269305	NM_001126112.2	273	cGt/ct	8/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		522	645	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138431082	138431082	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058705-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	23	321	0	ENST00000289153.2:c.1367A>C	p.Asp456Ala	p.D456A	ENST00000289153	NM_006219.2	456	gAc/gCc	8/22	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		321	459	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0059792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	337	766	1	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.270624882273236	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.270624882273236	3		767	1260	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0059792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	166	534	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.269110879775833	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	0	0.270624882273236	2		535	610	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125395	47125395	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	176	552	1	ENST00000409792.3:c.5875G>T	p.Glu1959Ter	p.E1959*	ENST00000409792	NM_014159.6	1959	Gaa/Taa	12/21	0.269110879775833	2	FACETS	0.993	0.918	1	0.993	0.918	1	CLONAL	2	TRUE	0	0.270624882273236	2		553	655	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942166	81942166	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	187	520	0	ENST00000359376.3:c.1703C>T	p.Thr568Ile	p.T568I	ENST00000359376	NM_002661.3	568	aCc/aTc	17/33	0.176589937792294	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	2	0.270624882273236	4		520	830	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24133997	24133997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	219	560	1	ENST00000263121.7:c.148C>T	p.Leu50Phe	p.L50F	ENST00000263121	NM_003073.3	50	Ctc/Ttc	2/9	0.227849471764254	3	FACETS	0.845	0.789	0.902	0.845	0.789	0.902	CLONAL	3	TRUE	0	0.270624882273236	3		561	725	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1296054	1296054	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0059792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	253	719	0				ENST00000310581	NM_198253.2	-/1132			0.239092353449827	5	FACETS	1	0.934	1	0.666	0.622	0.712	CLONAL	2	TRUE	2	0.270624882273236	5		719	1315	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921356	178921356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	48	383	0	ENST00000263967.3:c.838G>A	p.Gly280Arg	p.G280R	ENST00000263967	NM_006218.2	280	Ggg/Agg	5/21	0.247031232753867	3	FACETS	0.934	0.791	1	0.467	0.395	0.546	CLONAL	1	TRUE	1	0.270624882273236	3		383	431	SUCCESS
MET	4233	MSKCC	GRCh37	7	116381062	116381065	+	frameshift_variant	Frame_Shift_Del	DEL	CTGC	CTGC	-	novel	NA	P-0059792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	62	471	0	ENST00000397752.3:c.1688_1691del	p.Pro563GlnfsTer18	p.P563Qfs*18	ENST00000397752	NM_000245.2	562	CTGCct/ct	5/21	0.24419722597274	4	FACETS	0.768	0.662	0.883	0.384	0.331	0.442	SUBCLONAL	1	TRUE	2	0.270624882273236	4		471	758	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2047322	2047322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059792-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	10	100	0	ENST00000349721.2:c.884C>T	p.Ala295Val	p.A295V	ENST00000349721	NM_003070.3	295	gCg/gTg	5/34	0.269110879775833	2	FACETS	0.48	0.326	0.673	0.24	0.163	0.337	SUBCLONAL	1	TRUE	0	0.270624882273236	2		100	154	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0059792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	275	766	1	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.570716658547122	6	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	3	0.570716658547122	6		767	644	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0059792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	134	534	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.46460143884029	2	FACETS	0.995	0.927	1	0.995	0.927	1	CLONAL	2	TRUE	0	0.570716658547122	2		535	236	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0059792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	9	136	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.280597105616308	1	FACETS	0.207	0.137	0.294	0.207	0.137	0.294	INDETERMINATE	1	TRUE	0	0.570716658547122	1		136	109	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224161	98224161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56173896	NA	P-0059792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	27	494	0	ENST00000331920.6:c.2680G>A	p.Asp894Asn	p.D894N	ENST00000331920	NM_000264.3	894	Gat/Aat	16/24	0.23881867013494	3	FACETS	0.35	0.279	0.432	0.175	0.139	0.216	INDETERMINATE	1	TRUE	1	0.570716658547122	3		494	347	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125395	47125395	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	14	552	1	ENST00000409792.3:c.5875G>T	p.Glu1959Ter	p.E1959*	ENST00000409792	NM_014159.6	1959	Gaa/Taa	12/21	0.438224601166967	2	FACETS	0.177	0.127	0.237	0.089	0.063	0.119	SUBCLONAL	1	TRUE	0	0.570716658547122	2		553	277	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961068	55961068	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	31	380	0	ENST00000263923.4:c.2872G>T	p.Asp958Tyr	p.D958Y	ENST00000263923	NM_002253.2	958	Gat/Tat	21/30	1	2	FACETS	0.365	0.295	0.442	0.365	0.295	0.442	SUBCLONAL	1	TRUE	1	0.570716658547122	2		380	298	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942166	81942166	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	54	520	0	ENST00000359376.3:c.1703C>T	p.Thr568Ile	p.T568I	ENST00000359376	NM_002661.3	568	aCc/aTc	17/33	0.148466029808414	4	FACETS	1	0.967	1	0.718	0.622	0.82	INDETERMINATE	1	TRUE	2	0.570716658547122	4		520	207	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24133997	24133997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	121	560	1	ENST00000263121.7:c.148C>T	p.Leu50Phe	p.L50F	ENST00000263121	NM_003073.3	50	Ctc/Ttc	2/9	0.570716658547122	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.570716658547122	1		561	258	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1296054	1296054	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0059792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	97	719	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.570716658547122	2		719	265	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234501	41234501	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	27	470	0	ENST00000357654.3:c.4277C>G	p.Ser1426Cys	p.S1426C	ENST00000357654	NM_007294.3	1426	tCt/tGt	12/23	0.309007905937845	4	FACETS	0.473	0.377	0.583	0.237	0.188	0.292	INDETERMINATE	1	TRUE	2	0.570716658547122	4		470	314	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032110	26032110	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1297	107	677	0	ENST00000244661.2:c.179A>G	p.Glu60Gly	p.E60G	ENST00000244661	NM_003537.3	60	gAg/gGg	1/1	0.570716658547122	9	FACETS	0.801	0.715	0.892			1	CLONAL	1	TRUE	NA	0.570716658547122	9		677	1404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0059972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	391	531	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.392204604361476	2	FACETS	0.987	0.942	1	0.987	0.942	1	CLONAL	2	TRUE	0	0.426520973490038	2		531	929	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137323819	137323819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	173	452	0	ENST00000481739.1:c.1112G>A	p.Arg371His	p.R371H	ENST00000481739	NM_002957.4	371	cGc/cAc	8/10	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.426520973490038	2		452	769	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838380	156838380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202030811	NA	P-0059972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	178	531	0	ENST00000524377.1:c.658C>T	p.Arg220Trp	p.R220W	ENST00000524377	NM_002529.3	220	Cgg/Tgg	6/17	1	2	FACETS	0.932	0.859	1	0.932	0.859	1	CLONAL	1	TRUE	1	0.426520973490038	2		531	896	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2093599	2093599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	126	381	0	ENST00000219066.1:c.678G>A	p.Met226Ile	p.M226I	ENST00000219066	NM_002528.5	226	atG/atA	4/6	1	2	FACETS	0.926	0.841	1	0.926	0.841	1	CLONAL	1	TRUE	1	0.426520973490038	2		381	638	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112025275	112025275	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	138	336	0	ENST00000368678.4:c.474T>G	p.Asp158Glu	p.D158E	ENST00000368678		158	gaT/gaG	6/13	1	2	FACETS	0.831	0.756	0.908	0.831	0.756	0.908	CLONAL	1	TRUE	1	0.426520973490038	2		336	779	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647390	117647390	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	81	371	0	ENST00000368508.3:c.5554G>A	p.Gly1852Arg	p.G1852R	ENST00000368508	NM_002944.2	1852	Gga/Aga	33/43	1	2	FACETS	0.842	0.745	0.945	0.842	0.745	0.945	CLONAL	1	TRUE	1	0.426520973490038	2		371	451	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0060172-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	215	243	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.759812578748867	2		243	564	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0060172-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	510	420	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.760136730615278	4	FACETS	0.939	0.907	0.97	0.939	0.907	0.97	CLONAL	3	TRUE	1	0.759812578748867	4		420	839	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028880	47028880	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060172-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	468	702	0	ENST00000377604.3:c.184G>T	p.Glu62Ter	p.E62*	ENST00000377604	NM_001204468.1	62	Gag/Tag	3/24	0.633813983714895	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	2	0.759812578748867	4		702	1075	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69456169	69456169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs2220247	NA	P-0060172-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3329	287	765	0	ENST00000227507.2:c.88G>A	p.Ala30Thr	p.A30T	ENST00000227507	NM_053056.2	30	Gcc/Acc	1/5	0.759812578748867	9	FACETS	0.765	0.714	0.817			1	SUBCLONAL	1	TRUE	NA	0.759812578748867	9		765	3616	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831694	72831714	+	inframe_deletion	In_Frame_Del	DEL	CAGCTTGGCTGCCCGGGCCTT	CAGCTTGGCTGCCCGGGCCTT	-	novel	NA	P-0060172-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	238	710	0	ENST00000268489.5:c.4867_4887del	p.Lys1623_Leu1629del	p.K1623_L1629del	ENST00000268489	NM_006885.3	1623	AAGGCCCGGGCAGCCAAGCTG/-	9/10	0.754530368932575	3	FACETS	0.965	0.902	1	0.482	0.451	0.515	CLONAL	1	TRUE	1	0.759812578748867	3		710	896	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606909	47606909	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060172-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	172	396	0	ENST00000263735.4:c.659T>C	p.Val220Ala	p.V220A	ENST00000263735	NM_002354.2	220	gTt/gCt	7/9	0.760136730615278	4	FACETS	1	0.94	1	0.511	0.471	0.553	CLONAL	1	TRUE	2	0.759812578748867	4		396	779	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541363	187541363	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1002184454	NA	P-0060172-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	239	687	0	ENST00000441802.2:c.6377A>C	p.His2126Pro	p.H2126P	ENST00000441802	NM_005245.3	2126	cAc/cCc	10/27	0.746567973760106	3	FACETS	0.937	0.876	1	0.469	0.438	0.5	CLONAL	1	TRUE	1	0.759812578748867	3		687	926	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212519	133212519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371862779	NA	P-0060268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	262	466	0	ENST00000320574.5:c.5770G>A	p.Gly1924Arg	p.G1924R	ENST00000320574	NM_006231.2	1924	Gga/Aga	42/49	1	2	FACETS	0.939	0.883	0.997	0.939	0.883	0.997	CLONAL	1	TRUE	1	0.653245606981477	2		466	854	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245781	46245781	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	35	0	0	ENST00000334344.6:c.3875G>T	p.Ser1292Ile	p.S1292I	ENST00000334344	NM_152641.2	1292	aGt/aTt	15/21	1	2	FACETS	0.44	0.359	0.531	0.44	0.359	0.531	SUBCLONAL	1	TRUE	1	0.222503470132281	2		0	715	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	502	546	0	ENST00000206249.3:c.1610A>G	p.Tyr537Cys	p.Y537C	ENST00000206249	NM_000125.3	537	tAt/tGt	8/8	0.758107276361858	2	FACETS	1	0.976	1	0.513	0.491	0.535	CLONAL	1	TRUE	0	0.758107276361858	2		546	1291	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102080257	102080762	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AATATCAATCCCAGCACAGCAAATTCTCCAAAATGTCAGGTAGGCTCTTATCTGATGTTTTAGCACTGGAAAAAAAAAAAAAAAGATATTAAATTAGGAAAGAGAAACTTACATTCCAGGGTCCTGTCCTTATTGGACATTAGCCCAGAGAATAACTTTGAGCCATCTTTCTACCAAGATACTCAGGTTAACATTGCCCTTCCAAGAAAGTCTACACAGTCTGCTCCCTCCCTGCTCCTCCTAGGGAGTTTCTGTTTATTTTGATTCCATGGAGGTCTTTTTTATTCTATATTTAAATGTATTGTGTCTCAGTTGTACATCCTATCAGCTAGGTATGCCTAATTTTTATTTGAATAGCTTAAAATAGTATGTGTAATGATTTAAAGGAATTAATAAATTGAACAGTAACAAAAGCAGTATTTACTTGGATAGGCTACTTTAGGAAATTTTAGAGTCATGATACTATGAGGAAGAGAAAAATTCTTTCTAGTGGACATTCCAAAGGA	AATATCAATCCCAGCACAGCAAATTCTCCAAAATGTCAGGTAGGCTCTTATCTGATGTTTTAGCACTGGAAAAAAAAAAAAAAAGATATTAAATTAGGAAAGAGAAACTTACATTCCAGGGTCCTGTCCTTATTGGACATTAGCCCAGAGAATAACTTTGAGCCATCTTTCTACCAAGATACTCAGGTTAACATTGCCCTTCCAAGAAAGTCTACACAGTCTGCTCCCTCCCTGCTCCTCCTAGGGAGTTTCTGTTTATTTTGATTCCATGGAGGTCTTTTTTATTCTATATTTAAATGTATTGTGTCTCAGTTGTACATCCTATCAGCTAGGTATGCCTAATTTTTATTTGAATAGCTTAAAATAGTATGTGTAATGATTTAAAGGAATTAATAAATTGAACAGTAACAAAAGCAGTATTTACTTGGATAGGCTACTTTAGGAAATTTTAGAGTCATGATACTATGAGGAAGAGAAAAATTCTTTCTAGTGGACATTCCAAAGGA	-	novel	NA	P-0060393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	65	110	0	ENST00000282441.5:c.996_1032+469del		p.X332_splice	ENST00000282441	NM_001130145.2	332		6/9	0.758107276361858	1	FACETS	0.435	0.381	0.491	0.435	0.381	0.491	SUBCLONAL	1	TRUE	0	0.758107276361858	1		110	245	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911316	32911329	+	frameshift_variant	Frame_Shift_Del	DEL	TCAATTAAAAAAGA	TCAATTAAAAAAGA	-	novel	NA	P-0060393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	85	82	0	ENST00000380152.3:c.2825_2838del	p.Ser942PhefsTer12	p.S942Ffs*12	ENST00000380152		942	TCAATTAAAAAAGAt/t	11/27	0.758107276361858	1	FACETS	0.633	0.57	0.697	0.633	0.57	0.697	SUBCLONAL	1	TRUE	0	0.758107276361858	1		82	220	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544710	65544710	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	372	179	0	ENST00000358664.4:c.216G>C	p.Gln72His	p.Q72H	ENST00000358664	NM_002382.4	72	caG/caC	4/5	1	2	FACETS	0.792	0.752	0.833	0.792	0.752	0.833	SUBCLONAL	1	TRUE	1	0.758107276361858	2		179	1239	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279777	46279777	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2319	251	136	0	ENST00000371998.3:c.3703A>C	p.Ser1235Arg	p.S1235R	ENST00000371998		1235	Agt/Cgt	20/23	0.758107276361858	5	FACETS	0.551	0.512	0.591	0.184	0.17	0.197	SUBCLONAL	1	TRUE	2	0.758107276361858	5		136	2570	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411977	63411977	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060393-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	140	228	0	ENST00000330258.3:c.1190T>C	p.Val397Ala	p.V397A	ENST00000330258	NM_152424.3	397	gTt/gCt	2/2	0.758107276361858	1	FACETS	0.326	0.297	0.356	0.326	0.297	0.356	SUBCLONAL	1	TRUE	0	0.758107276361858	1		228	704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0060416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	449	690	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.545866323031282	4	FACETS	0.94	0.898	0.981	0.94	0.898	0.981	CLONAL	2	FALSE	2	0.705754485934238	4		690	1155	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983863	2983863	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	355	519	0	ENST00000396946.4:c.667C>T	p.Arg223Ter	p.R223*	ENST00000396946	NM_032415.4	223	Cga/Tga	5/25	0.705754485934238	5	FACETS	1	0.994	1	0.466	0.44	0.492	CLONAL	1	FALSE	2	0.705754485934238	5		519	1482	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0060416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	165	472	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.641110995205818	4	FACETS	0.758	0.701	0.817	0.758	0.701	0.817	SUBCLONAL	2	FALSE	2	0.705754485934238	4		472	526	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876343	35876343	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200570812	NA	P-0060416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	86	596	0	ENST00000303115.3:c.1135G>A	p.Ala379Thr	p.A379T	ENST00000303115	NM_002185.3	379	Gcc/Acc	8/8	0.479656051708858	3	FACETS	0.356	0.314	0.401			1	SUBCLONAL	1	FALSE	NA	0.705754485934238	3		596	927	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579592	7579592	+	splice_acceptor_variant	Splice_Site	DEL	T	T	-	rs1567557258	NA	P-0060416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	486	612	0	ENST00000269305.4:c.97-2del		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.545866323031282	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	FALSE	2	0.705754485934238	4		612	1133	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798302	45798302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	733	832	0	ENST00000450313.1:c.634C>A	p.Leu212Met	p.L212M	ENST00000450313	NM_012222.2	212	Ctg/Atg	8/16	0.641110995205818	4	FACETS	0.992	0.958	1	0.992	0.958	1	CLONAL	2	FALSE	2	0.705754485934238	4		832	1786	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873654	35873654	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	472	384	0	ENST00000216797.5:c.197G>A	p.Trp66Ter	p.W66*	ENST00000216797	NM_020529.2	66	tGg/tAg	1/6	0.634800691518886	2	FACETS	0.869	0.839	0.898	0.869	0.839	0.898	CLONAL	2	FALSE	0	0.705754485934238	2		384	770	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200748	128200748	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	457	507	0	ENST00000341105.2:c.1057C>G	p.Gln353Glu	p.Q353E	ENST00000341105	NM_032638.4	353	Cag/Gag	5/6	0.705754485934238	3	FACETS	0.776	0.743	0.81	0.517	0.495	0.54	SUBCLONAL	2	FALSE	0	0.705754485934238	3		507	1129	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060422-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	130	759	1				ENST00000310581	NM_198253.2	-/1132			0.485063147876934	3	FACETS	0.976	0.887	1	0.488	0.443	0.534	CLONAL	1	TRUE	1	0.519569973387835	3		760	646	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858492	9858492	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148669437	NA	P-0060422-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	144	676	0	ENST00000330684.3:c.2909G>A	p.Arg970Gln	p.R970Q	ENST00000330684	NM_001134407.1	970	cGg/cAg	13/13	0.480468143350811	2	FACETS	0.919	0.842	1	0.46	0.421	0.5	CLONAL	1	TRUE	0	0.519569973387835	2		676	603	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911617	39911617	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060422-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	145	268	0	ENST00000378444.4:c.5013G>C	p.Lys1671Asn	p.K1671N	ENST00000378444	NM_001123385.1	1671	aaG/aaC	15/15	0.388609893936667	2	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.519569973387835	2		268	428	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406207	70406207	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060422-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	136	590	0	ENST00000373644.4:c.3721C>G	p.Gln1241Glu	p.Q1241E	ENST00000373644	NM_030625.2	1241	Cag/Gag	4/12	NA	2	FACETS	1	0.934	1			1	INDETERMINATE	1	TRUE	NA	0.519569973387835	2		590	511	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663821	29663821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755791578	NA	P-0060422-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	157	580	1	ENST00000356175.3:c.6253G>A	p.Val2085Ile	p.V2085I	ENST00000356175	NM_000267.3	2085	Gtt/Att	41/57	0.519569973387835	4	FACETS	1	0.916	1	0.333	0.305	0.363	CLONAL	1	TRUE	1	0.519569973387835	4		581	918	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123722	11123722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263140481	NA	P-0060422-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	621	598	0	ENST00000358026.2:c.2372C>T	p.Ala791Val	p.A791V	ENST00000358026	NM_001128849.1	791	gCg/gTg	16/36	0.519569973387835	4	FACETS	0.981	0.948	1	0.981	0.948	1	CLONAL	3	TRUE	1	0.519569973387835	4		598	1234	SUCCESS
AXL	558	MSKCC	GRCh37	19	41725363	41725363	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060422-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	180	674	0	ENST00000301178.4:c.66G>T	p.Trp22Cys	p.W22C	ENST00000301178	NM_021913.4	22	tgG/tgT	1/20	0.519569973387835	4	FACETS	0.888	0.817	0.962	0.296	0.272	0.321	CLONAL	1	TRUE	1	0.519569973387835	4		674	1186	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	49	759	1				ENST00000310581	NM_198253.2	-/1132			0.671403904252586	3	FACETS	0.811	0.708	0.917	0.811	0.708	0.917	CLONAL	2	TRUE	1	0.687724225805989	3		760	118	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0060423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	221	652	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.683381605291717	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.687724225805989	2		653	319	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333266	70333266	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	93	291	0	ENST00000373644.4:c.1171G>A	p.Glu391Lys	p.E391K	ENST00000373644	NM_030625.2	391	Gag/Aag	2/12	0.687724225805989	3	FACETS	1	0.9	1	0.502	0.45	0.557	CLONAL	1	TRUE	1	0.687724225805989	3		291	362	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057835	27057835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	288	842	0	ENST00000324856.7:c.1543C>T	p.Gln515Ter	p.Q515*	ENST00000324856	NM_006015.4	515	Cag/Tag	3/20	0.522988741799666	4	FACETS	0.949	0.897	1			1	CLONAL	2	TRUE	NA	0.687724225805989	4		842	745	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923060	44923060	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	158	125	0	ENST00000377967.4:c.1921C>T	p.Gln641Ter	p.Q641*	ENST00000377967	NM_021140.2	641	Cag/Tag	16/29	0.62748757228963	2	FACETS	1	0.981	1			1	CLONAL	2	TRUE	NA	0.687724225805989	2		125	214	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670282	134670282	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748807854	NA	P-0060423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	116	469	0	ENST00000398015.3:c.193G>A	p.Glu65Lys	p.E65K	ENST00000398015	NM_004441.4	65	Gag/Aag	3/16	0.669724524255205	4	FACETS	1	0.985	1	0.484	0.44	0.53	CLONAL	1	TRUE	1	0.687724225805989	4		469	392	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250101	110250101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1169388589	NA	P-0060423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	88	194	0	ENST00000374672.4:c.574G>A	p.Asp192Asn	p.D192N	ENST00000374672	NM_004235.4	192	Gac/Aac	3/5	0.635994243393749	4	FACETS	1	0.935	1	0.535	0.476	0.596	CLONAL	1	TRUE	2	0.687724225805989	4		194	404	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207648	2207648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	138	362	0	ENST00000398665.3:c.932C>T	p.Ser311Phe	p.S311F	ENST00000398665	NM_032482.2	311	tCc/tTc	11/28	0.373843227503216	4	FACETS	0.836	0.769	0.906	0.836	0.769	0.906	INDETERMINATE	2	TRUE	2	0.687724225805989	4		362	405	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467835	66467835	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	57	142	0	ENST00000273854.3:c.434G>A	p.Gly145Glu	p.G145E	ENST00000273854	NM_004439.5	145	gGg/gAg	3/18	0.278476589983119	6	FACETS	1	0.955	1	0.318	0.274	0.364	INDETERMINATE	1	TRUE	2	0.687724225805989	6		142	310	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796535	42796535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs539384322	NA	P-0060423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	89	394	2	ENST00000575354.2:c.3092C>T	p.Ser1031Leu	p.S1031L	ENST00000575354	NM_015125.3	1031	tCg/tTg	13/20	0.687724225805989	5	FACETS	0.896	0.796	1	0.299	0.265	0.334	CLONAL	1	TRUE	2	0.687724225805989	5		396	587	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281904	39281904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886041241	NA	P-0060423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	13	54	0	ENST00000402219.2:c.571G>A	p.Glu191Lys	p.E191K	ENST00000402219	NM_005633.3	191	Gaa/Aaa	5/23	0.522988741799666	4	FACETS	0.541	0.389	0.723			1	SUBCLONAL	1	TRUE	NA	0.687724225805989	4		54	118	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242628	16242628	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	61	118	0	ENST00000375759.3:c.1249G>C	p.Glu417Gln	p.E417Q	ENST00000375759	NM_015001.2	417	Gaa/Caa	6/15	0.584197278237053	3	FACETS	0.795	0.691	0.906	0.397	0.345	0.453	CLONAL	1	TRUE	1	0.687724225805989	3		118	300	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023640	27023640	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	72	316	0	ENST00000324856.7:c.746C>T	p.Ser249Phe	p.S249F	ENST00000324856	NM_006015.4	249	tCc/tTc	1/20	0.522988741799666	4	FACETS	0.877	0.77	0.991			1	CLONAL	1	TRUE	NA	0.687724225805989	4		316	403	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439733	51439733	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	294	523	0	ENST00000262662.1:c.298G>C	p.Asp100His	p.D100H	ENST00000262662		100	Gat/Cat	4/4	0.599175198983346	4	FACETS	0.924	0.874	0.975	0.924	0.874	0.975	CLONAL	2	TRUE	2	0.687724225805989	4		523	781	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450702	70450702	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	249	423	0	ENST00000373644.4:c.5542T>A	p.Phe1848Ile	p.F1848I	ENST00000373644	NM_030625.2	1848	Ttc/Atc	12/12	0.687724225805989	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.687724225805989	3		423	475	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12043954	12043954	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	205	282	0	ENST00000396373.4:c.1333C>G	p.Gln445Glu	p.Q445E	ENST00000396373	NM_001987.4	445	Caa/Gaa	8/8	0.506826041784765	5	FACETS	0.836	0.784	0.889	0.836	0.784	0.889	CLONAL	3	TRUE	2	0.687724225805989	5		282	483	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061115	38061115	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	226	202	0	ENST00000250448.2:c.874G>C	p.Glu292Gln	p.E292Q	ENST00000250448	NM_004496.3	292	Gag/Cag	2/2	0.687724225805989	6	FACETS	1	0.981	1			1	CLONAL	3	TRUE	NA	0.687724225805989	6		202	476	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50789296	50789296	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	53	101	0	ENST00000307179.4:c.2906G>C	p.Arg969Thr	p.R969T	ENST00000307179		969	aGa/aCa	18/20	0.671403904252586	3	FACETS	1	0.913	1	0.537	0.464	0.613	CLONAL	1	TRUE	1	0.687724225805989	3		101	193	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383274	42383274	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	98	591	0	ENST00000221972.3:c.294G>C	p.Lys98Asn	p.K98N	ENST00000221972	NM_021601.3	98	aaG/aaC	2/5	0.466290359133445	4	FACETS	0.789	0.705	0.877			1	SUBCLONAL	1	TRUE	NA	0.687724225805989	4		591	610	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573916	41573916	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	91	465	0	ENST00000263253.7:c.6201G>C	p.Gln2067His	p.Q2067H	ENST00000263253	NM_001429.3	2067	caG/caC	31/31	0.310792868068111	3	FACETS	0.889	0.795	0.988			1	INDETERMINATE	1	TRUE	NA	0.687724225805989	3		465	400	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422848	12422848	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	187	124	0	ENST00000287820.6:c.338C>T	p.Pro113Leu	p.P113L	ENST00000287820	NM_015869.4	113	cCa/cTa	3/7	0.687724225805989	6	FACETS	0.905	0.838	0.973	0.452	0.419	0.487	CLONAL	2	TRUE	2	0.687724225805989	6		124	714	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274812	142274812	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	135	87	0	ENST00000350721.4:c.2248C>G	p.Gln750Glu	p.Q750E	ENST00000350721	NM_001184.3	750	Caa/Gaa	10/47	0.669724524255205	4	FACETS	0.898	0.836	0.959	0.898	0.836	0.959	CLONAL	3	TRUE	1	0.687724225805989	4		87	246	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197399	26197399	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	129	823	0	ENST00000356476.2:c.80G>C	p.Arg27Pro	p.R27P	ENST00000356476		27	cGa/cCa	1/1	0.316500960189034	4	FACETS	0.758	0.687	0.833	0.379	0.343	0.417	INDETERMINATE	1	TRUE	2	0.687724225805989	4		823	835	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005221	150005221	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1582877569	NA	P-0060423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	98	225	0	ENST00000253339.5:c.1004C>G	p.Ser335Cys	p.S335C	ENST00000253339		335	tCt/tGt	3/7	0.657981568054491	3	FACETS	0.95	0.854	1	0.475	0.427	0.526	CLONAL	1	TRUE	1	0.687724225805989	3		225	403	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730018	41730018	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	82	321	0	ENST00000242208.4:c.511G>T	p.Val171Phe	p.V171F	ENST00000242208	NM_002192.2	171	Gtc/Ttc	3/3	0.687724225805989	3	FACETS	0.83	0.737	0.929	0.415	0.368	0.465	CLONAL	1	TRUE	1	0.687724225805989	3		321	386	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069067	5069067	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1252513666	NA	P-0060423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	30	50	0	ENST00000381652.3:c.1372G>A	p.Glu458Lys	p.E458K	ENST00000381652	NM_004972.3	458	Gag/Aag	11/25	0.687724225805989	5	FACETS	0.795	0.644	0.963	0.265	0.214	0.321	CLONAL	1	TRUE	2	0.687724225805989	5		50	223	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933353	39933353	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	208	206	0	ENST00000378444.4:c.1246C>G	p.Gln416Glu	p.Q416E	ENST00000378444	NM_001123385.1	416	Caa/Gaa	4/15	0.62748757228963	2	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.687724225805989	2		206	258	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061215	38061235	+	inframe_deletion	In_Frame_Del	DEL	GCAGCCGTTCTCGAACATGTT	GCAGCCGTTCTCGAACATGTT	-	novel	NA	P-0060424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	28	699	0	ENST00000250448.2:c.754_774del	p.Asn252_Cys258del	p.N252_C258del	ENST00000250448	NM_004496.3	252	AACATGTTCGAGAACGGCTGC/-	2/2	1	2	FACETS	0.402	0.321	0.494	0.402	0.321	0.494	SUBCLONAL	1	FALSE	1	0.375755877478702	2		699	371	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0060424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	64	599	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	1	0.375755877478702	2		599	315	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532645	46532645	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	17	489	0	ENST00000262741.5:c.433C>G	p.Leu145Val	p.L145V	ENST00000262741	NM_003629.3	145	Ctt/Gtt	4/10	1	2	FACETS	0.374	0.279	0.486	0.374	0.279	0.486	SUBCLONAL	1	FALSE	1	0.375755877478702	2		489	242	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	224	479	0				ENST00000310581	NM_198253.2	-/1132			0.104332313894151	3	FACETS	0.855	0.806	0.904	0.855	0.806	0.904	INDETERMINATE	2	TRUE	1	0.791573453673936	3		479	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	586	690	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.791573453673936	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.791573453673936	2		690	740	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72866503	72866503	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs777239706	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	311	388	1	ENST00000325599.8:c.760C>T	p.Arg254Ter	p.R254*	ENST00000325599	NM_018130.2	254	Cga/Tga	7/11	0.791573453673936	4	FACETS	0.979	0.929	1	0.979	0.929	1	CLONAL	2	TRUE	2	0.791573453673936	4		389	719	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911144	40911144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776134993	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	102	292	0	ENST00000373198.4:c.2161C>T	p.Arg721Cys	p.R721C	ENST00000373198	NM_133170.3	721	Cgt/Tgt	13/32	0.171920212736878	3	FACETS	0.63	0.565	0.699	0.315	0.282	0.35	INDETERMINATE	1	TRUE	1	0.791573453673936	3		292	571	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561263	9561263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769939031	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	402	635	0	ENST00000353224.5:c.519G>A	p.Met173Ile	p.M173I	ENST00000353224	NM_177990.2	173	atG/atA	4/10	0.550233834760741	4	FACETS	0.946	0.903	0.989	0.946	0.903	0.989	CLONAL	2	TRUE	2	0.791573453673936	4		635	962	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875645	35875645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201449880	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	280	526	0	ENST00000303115.3:c.832G>A	p.Asp278Asn	p.D278N	ENST00000303115	NM_002185.3	278	Gat/Aat	7/8	0.104332313894151	3	FACETS	0.887	0.855	0.918	1	0.995	1	INDETERMINATE	3	TRUE	1	0.791573453673936	3		526	371	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518055	8518055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	142	765	0	ENST00000356435.5:c.1336G>A	p.Gly446Arg	p.G446R	ENST00000356435		446	Gga/Aga	10/35	0.791573453673936	3	FACETS	0.786	0.719	0.857	0.393	0.359	0.429	SUBCLONAL	1	TRUE	1	0.791573453673936	3		765	637	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510612	38510612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	252	993	0	ENST00000254066.5:c.866G>A	p.Gly289Glu	p.G289E	ENST00000254066	NM_000964.3	289	gGg/gAg	7/9	0.78904418075613	3	FACETS	0.915	0.857	0.975	0.458	0.428	0.488	CLONAL	1	TRUE	1	0.791573453673936	3		993	971	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162068	47162068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	170	668	0	ENST00000409792.3:c.4058C>T	p.Ser1353Phe	p.S1353F	ENST00000409792	NM_014159.6	1353	tCc/tTc	3/21	0.786274971240305	4	FACETS	0.839	0.772	0.909	0.28	0.257	0.303	CLONAL	1	TRUE	1	0.791573453673936	4		668	917	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317572	1317572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	86	276	0	ENST00000400841.2:c.493G>A	p.Glu165Lys	p.E165K	ENST00000400841		165	Gaa/Aaa	5/6	0.364818149908672	2	FACETS	0.817	0.733	0.904			1	INDETERMINATE	1	TRUE	NA	0.791573453673936	2		276	266	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	267	1028	2	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	0.618404388744602	3	FACETS	0.906	0.85	0.964	0.453	0.425	0.482	CLONAL	1	TRUE	1	0.791573453673936	3		1030	1039	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200062	128200062	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1345163538	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	299	1279	0	ENST00000341105.2:c.1243G>A	p.Glu415Lys	p.E415K	ENST00000341105	NM_032638.4	415	Gag/Aag	6/6	0.78904418075613	3	FACETS	1	0.947	1	0.503	0.474	0.532	CLONAL	1	TRUE	1	0.791573453673936	3		1279	1049	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367257	50367257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1245618829	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	426	852	0	ENST00000331340.3:c.64G>A	p.Asp22Asn	p.D22N	ENST00000331340	NM_006060.4	22	Gat/Aat	3/8	0.500989699203511	4	FACETS	0.979	0.936	1	0.979	0.936	1	CLONAL	2	TRUE	2	0.791573453673936	4		852	985	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350587	89350587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	91	266	0	ENST00000301030.4:c.2363C>T	p.Ser788Leu	p.S788L	ENST00000301030	NM_001256183.1	788	tCa/tTa	9/13	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.791573453673936	2		266	224	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053566	37053566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	170	433	0	ENST00000231790.2:c.653C>T	p.Ser218Phe	p.S218F	ENST00000231790	NM_000249.3	218	tCc/tTc	8/19	0.786274971240305	4	FACETS	1	0.962	1	0.357	0.329	0.386	CLONAL	1	TRUE	1	0.791573453673936	4		433	718	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991115	41991115	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	209	337	0	ENST00000219905.7:c.2068C>T	p.Gln690Ter	p.Q690*	ENST00000219905	NM_001164273.1	690	Cag/Tag	4/24	0.768622588298338	3	FACETS	0.869	0.818	0.92	0.869	0.818	0.92	CLONAL	2	TRUE	1	0.791573453673936	3		337	424	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730859	40730859	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	450	1126	0	ENST00000373198.4:c.3676C>T	p.Arg1226Ter	p.R1226*	ENST00000373198	NM_133170.3	1226	Cga/Tga	27/32	0.171920212736878	3	FACETS	1	0.996	1	0.695	0.664	0.725	INDETERMINATE	1	TRUE	1	0.791573453673936	3		1126	1142	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867745	45867745	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	561	1258	0	ENST00000391945.4:c.655G>A	p.Asp219Asn	p.D219N	ENST00000391945	NM_000400.3	219	Gac/Aac	8/23	0.768622588298338	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.791573453673936	3		1258	980	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434525	140434525	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	500	595	0	ENST00000288602.6:c.2173C>T	p.His725Tyr	p.H725Y	ENST00000288602	NM_004333.4	725	Cac/Tac	18/18	0.791573453673936	6	FACETS	1	0.981	1	0.522	0.499	0.545	CLONAL	2	TRUE	2	0.791573453673936	6		595	1564	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138384011	138384011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759151757	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	194	471	0	ENST00000289153.2:c.2539C>T	p.Arg847Cys	p.R847C	ENST00000289153	NM_006219.2	847	Cgc/Tgc	18/22	0.440001318480097	4	FACETS	1	0.986	1	0.417	0.387	0.448	INDETERMINATE	1	TRUE	1	0.791573453673936	4		471	702	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733280	40733280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370508724	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	444	837	0	ENST00000373198.4:c.3526C>T	p.Arg1176Cys	p.R1176C	ENST00000373198	NM_133170.3	1176	Cgt/Tgt	26/32	0.171920212736878	3	FACETS	0.799	0.765	0.832	0.799	0.765	0.832	INDETERMINATE	2	TRUE	1	0.791573453673936	3		837	980	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873796	45873796	+	start_lost,splice_region_variant	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	180	508	0	ENST00000391945.4:c.3G>A	p.Met1?	p.M1?	ENST00000391945	NM_000400.3	1	atG/atA	1/23	0.768622588298338	3	FACETS	1	0.979	1	0.571	0.53	0.613	CLONAL	1	TRUE	1	0.791573453673936	3		508	556	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54959363	54959363	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	11	28	0	ENST00000312783.6:c.337G>A	p.Glu113Lys	p.E113K	ENST00000312783	NM_198436.1	113	Gaa/Aaa	5/10	0.610109138563586	4	FACETS	1	0.737	1	0.519	0.369	0.692	CLONAL	1	TRUE	2	0.791573453673936	4		28	48	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561450	9561450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	545	997	0	ENST00000353224.5:c.332G>A	p.Gly111Glu	p.G111E	ENST00000353224	NM_177990.2	111	gGa/gAa	4/10	0.550233834760741	4	FACETS	0.944	0.907	0.981	0.944	0.907	0.981	CLONAL	2	TRUE	2	0.791573453673936	4		997	1307	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412494	80412494	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	464	721	0	ENST00000286548.4:c.547C>T	p.Arg183Ter	p.R183*	ENST00000286548	NM_002072.3	183	Cga/Tga	4/7	0.787240979745821	2	FACETS	0.994	0.967	1	0.994	0.967	1	CLONAL	2	TRUE	0	0.791573453673936	2		721	590	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857547	9857547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367543132	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	245	1117	1	ENST00000330684.3:c.3854G>A	p.Arg1285Lys	p.R1285K	ENST00000330684	NM_001134407.1	1285	aGg/aAg	13/13	1	2	FACETS	0.961	0.904	1	0.961	0.904	1	CLONAL	1	TRUE	1	0.791573453673936	2		1118	644	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247417	71247417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	294	1040	0	ENST00000318789.4:c.116G>A	p.Gly39Glu	p.G39E	ENST00000318789	NM_032682.5	39	gGa/gAa	6/21	0.791573453673936	4	FACETS	0.949	0.892	1	0.475	0.446	0.505	CLONAL	1	TRUE	2	0.791573453673936	4		1040	1402	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523617	41523617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1624	295	1027	0	ENST00000263253.7:c.1033C>T	p.Leu345Phe	p.L345F	ENST00000263253	NM_001429.3	345	Ctt/Ttt	4/31	0.791573453673936	6	FACETS	1	0.941	1	0.251	0.235	0.267	CLONAL	1	TRUE	2	0.791573453673936	6		1027	1919	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395473	116395473	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	387	425	0	ENST00000397752.3:c.1766G>A	p.Gly589Glu	p.G589E	ENST00000397752	NM_000245.2	589	gGa/gAa	6/21	0.791573453673936	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.791573453673936	4		425	869	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012219	16012219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	148	376	0	ENST00000268712.3:c.2063G>A	p.Arg688Gln	p.R688Q	ENST00000268712	NM_006311.3	688	cGa/cAa	19/46	0.791573453673936	2	FACETS	0.987	0.912	1	0.493	0.456	0.531	CLONAL	1	TRUE	0	0.791573453673936	2		376	379	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431395	121431395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs893256143	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	253	999	0	ENST00000257555.6:c.599G>A	p.Arg200Gln	p.R200Q	ENST00000257555		200	cGg/cAg	3/10	0.618404388744602	3	FACETS	1	0.962	1	0.517	0.485	0.55	CLONAL	1	TRUE	1	0.791573453673936	3		999	863	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039399	49039399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	189	683	0	ENST00000267163.4:c.2384C>T	p.Ser795Leu	p.S795L	ENST00000267163	NM_000321.2	795	tCa/tTa	23/27	0.206241596703969	3	FACETS	1	0.938	1	0.337	0.313	0.362	INDETERMINATE	1	TRUE	0	0.791573453673936	3		683	659	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755366	39755366	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	289	1089	0	ENST00000288319.7:c.1399C>T	p.Pro467Ser	p.P467S	ENST00000288319	NM_182918.3	467	Ccc/Tcc	10/10	0.775045213841205	3	FACETS	1	0.965	1	0.517	0.487	0.548	CLONAL	1	TRUE	1	0.791573453673936	3		1089	986	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932227	36932227	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147017250	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	308	1429	0	ENST00000361632.4:c.2242G>A	p.Asp748Asn	p.D748N	ENST00000361632		748	Gat/Aat	16/16	0.777153027526075	3	FACETS	0.968	0.913	1	0.323	0.304	0.342	CLONAL	1	TRUE	0	0.791573453673936	3		1429	1122	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755685	39755685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	501	1073	0	ENST00000288319.7:c.1080G>A	p.Met360Ile	p.M360I	ENST00000288319	NM_182918.3	360	atG/atA	10/10	0.775045213841205	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.791573453673936	3		1073	850	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946340	2946340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1171346123	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	208	1044	0	ENST00000396946.4:c.3397C>T	p.Arg1133Cys	p.R1133C	ENST00000396946	NM_032415.4	1133	Cgc/Tgc	25/25	0.198665217835756	4	FACETS	0.944	0.877	1	0.472	0.438	0.508	INDETERMINATE	1	TRUE	2	0.791573453673936	4		1044	997	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961321	54961321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs2230743	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	248	870	0	ENST00000312783.6:c.311C>T	p.Ser104Leu	p.S104L	ENST00000312783	NM_198436.1	104	tCg/tTg	4/10	0.610109138563586	4	FACETS	0.969	0.905	1	0.484	0.452	0.517	CLONAL	1	TRUE	2	0.791573453673936	4		870	1159	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202925	27202925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749958421	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	381	616	0	ENST00000380036.4:c.2017C>T	p.Arg673Cys	p.R673C	ENST00000380036	NM_000459.3	673	Cgt/Tgt	13/23	0.787240979745821	2	FACETS	0.944	0.914	0.972	0.944	0.914	0.972	CLONAL	2	TRUE	0	0.791573453673936	2		616	510	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966665	36966665	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	466	887	0	ENST00000358127.4:c.661C>T	p.Arg221Trp	p.R221W	ENST00000358127	NM_001280556.1	221	Cgg/Tgg	6/10	0.787240979745821	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.791573453673936	2		887	580	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149244	119149244	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs745896960	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	448	717	0	ENST00000264033.4:c.1252T>C	p.Phe418Leu	p.F418L	ENST00000264033	NM_005188.3	418	Ttc/Ctc	9/16	0.783734537835014	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.791573453673936	2		717	556	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346005	73346005	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	200	323	0	ENST00000377767.4:c.1533T>A	p.His511Gln	p.H511Q	ENST00000377767	NM_014953.3	511	caT/caA	11/21	0.206241596703969	3	FACETS	0.938	0.884	0.992	0.625	0.589	0.661	INDETERMINATE	2	TRUE	0	0.791573453673936	3		323	376	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485307	8485307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	96	309	0	ENST00000356435.5:c.3073C>T	p.His1025Tyr	p.H1025Y	ENST00000356435		1025	Cat/Tat	18/35	0.791573453673936	3	FACETS	0.91	0.818	1	0.455	0.409	0.504	CLONAL	1	TRUE	1	0.791573453673936	3		309	372	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376289	118376289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778675942	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	294	1036	0	ENST00000534358.1:c.9682C>T	p.Arg3228Cys	p.R3228C	ENST00000534358	NM_005933.3	3228	Cgt/Tgt	27/36	0.783734537835014	2	FACETS	1	0.974	1	0.522	0.495	0.55	CLONAL	1	TRUE	0	0.791573453673936	2		1036	711	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836354	89836354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762439008	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	316	1304	1	ENST00000389301.3:c.2395C>T	p.Pro799Ser	p.P799S	ENST00000389301	NM_000135.2	799	Cca/Tca	26/43	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.791573453673936	2		1305	768	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612277	189612277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	415	904	0	ENST00000264731.3:c.2029G>A	p.Glu677Lys	p.E677K	ENST00000264731	NM_003722.4	677	Gag/Aag	14/14	0.618404388744602	3	FACETS	0.915	0.878	0.952	0.915	0.878	0.952	CLONAL	2	TRUE	1	0.791573453673936	3		904	800	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69000044	69000044	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	194	589	0	ENST00000288368.4:c.2113G>A	p.Gly705Arg	p.G705R	ENST00000288368	NM_024870.2	705	Gga/Aga	19/40	0.768508461168577	4	FACETS	0.888	0.821	0.957	0.296	0.273	0.319	CLONAL	1	TRUE	1	0.791573453673936	4		589	989	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161339	55161339	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	179	714	0	ENST00000257290.5:c.3170C>T	p.Ser1057Phe	p.S1057F	ENST00000257290	NM_006206.4	1057	tCc/tTc	23/23	1	2	FACETS	0.958	0.892	1	0.958	0.892	1	CLONAL	1	TRUE	1	0.791573453673936	2		714	472	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240215	5240215	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141697567	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	433	1013	0	ENST00000357368.4:c.1699C>T	p.Arg567Trp	p.R567W	ENST00000357368	NM_002850.3	567	Cgg/Tgg	12/38	0.768622588298338	3	FACETS	0.999	0.962	1	0.999	0.962	1	CLONAL	2	TRUE	1	0.791573453673936	3		1013	764	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770576	40770576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	376	732	0	ENST00000373198.4:c.2806C>T	p.Arg936Ter	p.R936*	ENST00000373198	NM_133170.3	936	Cga/Tga	19/32	0.171920212736878	3	FACETS	0.78	0.744	0.816	0.78	0.744	0.816	INDETERMINATE	2	TRUE	1	0.791573453673936	3		732	850	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50784036	50784036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567421073	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	220	703	0	ENST00000398568.2:c.427C>T	p.Pro143Ser	p.P143S	ENST00000398568	NM_001042412.1	143	Cct/Tct	3/18	1	2	FACETS	0.942	0.883	1	0.942	0.883	1	CLONAL	1	TRUE	1	0.791573453673936	2		703	590	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157506	106157506	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs368508787	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	130	633	0	ENST00000380013.4:c.2407C>T	p.Gln803Ter	p.Q803*	ENST00000380013	NM_001127208.2	803	Caa/Taa	3/11	0.471111602228619	1	FACETS	0.587	0.54	0.636	0.587	0.54	0.636	INDETERMINATE	1	TRUE	0	0.791573453673936	1		633	338	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024885	31024885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	488	999	0	ENST00000375687.4:c.4370C>T	p.Ser1457Phe	p.S1457F	ENST00000375687	NM_015338.5	1457	tCc/tTc	13/13	0.550233834760741	4	FACETS	0.948	0.909	0.987	0.948	0.909	0.987	CLONAL	2	TRUE	2	0.791573453673936	4		999	1165	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849873	151849874	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1226	454	916	0	ENST00000262189.6:c.12442_12443delinsTT	p.Pro4148Leu	p.P4148L	ENST00000262189	NM_170606.2	4148	CCg/TTg	49/59	0.791573453673936	6	FACETS	0.882	0.84	0.924	0.441	0.42	0.462	CLONAL	2	TRUE	2	0.791573453673936	6		916	1680	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093456	30093456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1008608681	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	19	134	0	ENST00000331968.5:c.1807C>T	p.Arg603Cys	p.R603C	ENST00000331968	NM_002742.2	603	Cgt/Tgt	13/18	0.431935384622308	3	FACETS	0.469	0.359	0.595	0.156	0.119	0.199	INDETERMINATE	1	TRUE	0	0.791573453673936	3		134	143	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020509	69020509	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	151	597	0	ENST00000288368.4:c.2881C>T	p.Gln961Ter	p.Q961*	ENST00000288368	NM_024870.2	961	Cag/Tag	24/40	0.768508461168577	4	FACETS	0.853	0.781	0.929	0.284	0.26	0.31	CLONAL	1	TRUE	1	0.791573453673936	4		597	801	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199925	108199925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555122245	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	116	329	0	ENST00000278616.4:c.7267G>A	p.Glu2423Lys	p.E2423K	ENST00000278616	NM_000051.3	2423	Gaa/Aaa	49/63	0.783734537835014	2	FACETS	0.812	0.739	0.887	0.406	0.369	0.444	CLONAL	1	TRUE	0	0.791573453673936	2		329	361	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632393	3632393	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	229	1078	0	ENST00000294008.3:c.5455C>T	p.Gln1819Ter	p.Q1819*	ENST00000294008	NM_032444.2	1819	Cag/Tag	15/15	1	2	FACETS	0.977	0.918	1	0.977	0.918	1	CLONAL	1	TRUE	1	0.791573453673936	2		1078	592	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451005	70451005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	296	1130	0	ENST00000373644.4:c.5845C>T	p.Pro1949Ser	p.P1949S	ENST00000373644	NM_030625.2	1949	Cct/Tct	12/12	0.725192777445001	4	FACETS	1	0.952	1	0.508	0.477	0.539	CLONAL	1	TRUE	2	0.791573453673936	4		1130	1320	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239498	123239498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	204	868	0	ENST00000358487.5:c.2339C>T	p.Ser780Leu	p.S780L	ENST00000358487	NM_000141.4	780	tCa/tTa	18/18	0.725192777445001	4	FACETS	0.822	0.762	0.885	0.411	0.381	0.443	CLONAL	1	TRUE	2	0.791573453673936	4		868	1123	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821615	72821638	+	inframe_deletion	In_Frame_Del	DEL	GCCACCGCCGCCGCCGCCGCCACT	GCCACCGCCGCCGCCGCCGCCACT	-	rs750348888	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	192	1364	0	ENST00000268489.5:c.10537_10560del	p.Ser3513_Gly3520del	p.S3513_G3520del	ENST00000268489	NM_006885.3	3513	AGTGGCGGCGGCGGCGGCGGTGGC/-	10/10	1	2	FACETS	0.775	0.72	0.831	0.775	0.72	0.831	SUBCLONAL	1	TRUE	1	0.791573453673936	2		1364	626	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956610	93956610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748985745	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	179	646	0	ENST00000369303.4:c.2626G>A	p.Glu876Lys	p.E876K	ENST00000369303	NM_004440.3	876	Gag/Aag	15/17	1	2	FACETS	0.863	0.802	0.926	0.863	0.802	0.926	CLONAL	1	TRUE	1	0.791573453673936	2		646	524	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058530	69058530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	239	285	0	ENST00000288368.4:c.4174C>T	p.Pro1392Ser	p.P1392S	ENST00000288368	NM_024870.2	1392	Cct/Tct	34/40	0.768508461168577	4	FACETS	1	0.991	1	0.831	0.788	0.874	CLONAL	2	TRUE	1	0.791573453673936	4		285	434	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346139	89346139	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	239	1239	0	ENST00000301030.4:c.6811C>T	p.Pro2271Ser	p.P2271S	ENST00000301030	NM_001256183.1	2271	Cct/Tct	9/13	1	2	FACETS	0.993	0.934	1	0.993	0.934	1	CLONAL	1	TRUE	1	0.791573453673936	2		1239	608	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861085	35861085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	184	553	0	ENST00000303115.3:c.214G>A	p.Glu72Lys	p.E72K	ENST00000303115	NM_002185.3	72	Gaa/Aaa	2/8	0.104332313894151	3	FACETS	1	0.99	1	0.702	0.655	0.75	INDETERMINATE	1	TRUE	1	0.791573453673936	3		553	462	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453402	40453402	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	282	1065	0	ENST00000345506.4:c.1099C>T	p.Pro367Ser	p.P367S	ENST00000345506	NM_003152.3	367	Ccc/Tcc	10/20	0.78904418075613	3	FACETS	0.957	0.9	1	0.479	0.45	0.508	CLONAL	1	TRUE	1	0.791573453673936	3		1065	1039	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260455	16260455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	351	1197	0	ENST00000375759.3:c.7720C>T	p.Pro2574Ser	p.P2574S	ENST00000375759	NM_015001.2	2574	Ccg/Tcg	11/15	0.787206896459312	2	FACETS	1	0.981	1	0.53	0.504	0.556	CLONAL	1	TRUE	0	0.791573453673936	2		1197	837	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069575	69069575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	86	212	0	ENST00000288368.4:c.4250G>A	p.Gly1417Glu	p.G1417E	ENST00000288368	NM_024870.2	1417	gGa/gAa	35/40	0.768508461168577	4	FACETS	0.936	0.832	1	0.312	0.277	0.349	CLONAL	1	TRUE	1	0.791573453673936	4		212	416	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858028	9858028	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1200593226	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	239	965	0	ENST00000330684.3:c.3373G>A	p.Glu1125Lys	p.E1125K	ENST00000330684	NM_001134407.1	1125	Gag/Aag	13/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.791573453673936	2		965	584	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2218123	2218123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747417102	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	306	1045	0	ENST00000326181.6:c.185C>T	p.Ser62Phe	p.S62F	ENST00000326181	NM_032271.2	62	tCc/tTc	4/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.791573453673936	2		1045	724	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609930	43609930	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs754466051	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	742	1613	0	ENST00000355710.3:c.1882C>T	p.Pro628Ser	p.P628S	ENST00000355710	NM_020975.4	628	Cca/Tca	11/20	0.198665217835756	4	FACETS	1	0.994	1	1	0.994	1	INDETERMINATE	2	TRUE	2	0.791573453673936	4		1613	1518	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490506	20490506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	258	865	0	ENST00000346618.3:c.1243C>T	p.Pro415Ser	p.P415S	ENST00000346618	NM_001949.4	415	Cct/Tct	7/7	0.768622588298338	3	FACETS	0.946	0.887	1	0.473	0.443	0.503	CLONAL	1	TRUE	1	0.791573453673936	3		865	962	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102094470	102094470	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	183	499	0	ENST00000282441.5:c.1150C>T	p.Pro384Ser	p.P384S	ENST00000282441	NM_001130145.2	384	Cct/Tct	7/9	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.791573453673936	2		499	459	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686282	117686282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	163	472	0	ENST00000368508.3:c.3059C>T	p.Pro1020Leu	p.P1020L	ENST00000368508	NM_002944.2	1020	cCt/cTt	20/43	1	2	FACETS	0.964	0.895	1	0.964	0.895	1	CLONAL	1	TRUE	1	0.791573453673936	2		472	427	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295204	1295205	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	173	976	1				ENST00000310581	NM_198253.2	-/1132			0.104332313894151	3	FACETS	1	0.99	1	0.705	0.656	0.754	INDETERMINATE	1	TRUE	1	0.791573453673936	3		977	433	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486257	8486257	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	200	877	0	ENST00000356435.5:c.2560C>T	p.Gln854Ter	p.Q854*	ENST00000356435		854	Cag/Tag	17/35	0.791573453673936	3	FACETS	0.954	0.887	1	0.477	0.443	0.512	CLONAL	1	TRUE	1	0.791573453673936	3		877	739	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962271	2962271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867239716	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	361	723	0	ENST00000396946.4:c.2266G>A	p.Glu756Lys	p.E756K	ENST00000396946	NM_032415.4	756	Gaa/Aaa	17/25	0.198665217835756	4	FACETS	0.969	0.924	1	0.969	0.924	1	INDETERMINATE	2	TRUE	2	0.791573453673936	4		723	843	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828998	72828998	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	338	1278	0	ENST00000268489.5:c.7583T>A	p.Ile2528Asn	p.I2528N	ENST00000268489	NM_006885.3	2528	aTc/aAc	9/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.791573453673936	2		1278	832	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376158	118376158	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	312	1080	0	ENST00000534358.1:c.9551C>T	p.Pro3184Leu	p.P3184L	ENST00000534358	NM_005933.3	3184	cCt/cTt	27/36	0.783734537835014	2	FACETS	1	0.952	1	0.502	0.476	0.529	CLONAL	1	TRUE	0	0.791573453673936	2		1080	785	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803501	32803501	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs142794316	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	270	974	0	ENST00000374899.4:c.658C>T	p.Arg220Ter	p.R220*	ENST00000374899	NM_018833.2	220	Cga/Tga	4/12	0.768622588298338	3	FACETS	1	0.969	1	0.524	0.492	0.556	CLONAL	1	TRUE	1	0.791573453673936	3		974	909	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586455	189586455	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	508	861	0	ENST00000264731.3:c.1079G>A	p.Arg360Lys	p.R360K	ENST00000264731	NM_003722.4	360	aGa/aAa	8/14	0.618404388744602	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.791573453673936	3		861	895	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40468879	40468879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293678815	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	252	776	0	ENST00000264657.5:c.2185C>T	p.Arg729Cys	p.R729C	ENST00000264657	NM_139276.2	729	Cgc/Tgc	23/24	0.78904418075613	3	FACETS	0.977	0.915	1	0.488	0.457	0.52	CLONAL	1	TRUE	1	0.791573453673936	3		776	910	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425613	49425613	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	287	1345	0	ENST00000301067.7:c.12875C>T	p.Pro4292Leu	p.P4292L	ENST00000301067	NM_003482.3	4292	cCa/cTa	39/54	0.787240979745821	2	FACETS	1	0.966	1	0.514	0.486	0.542	CLONAL	1	TRUE	0	0.791573453673936	2		1345	705	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239729	53239729	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780372	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	392	546	0	ENST00000375401.3:c.1613C>T	p.Pro538Leu	p.P538L	ENST00000375401	NM_004187.3	538	cCc/cTc	12/26	0.364818149908672	2	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.791573453673936	2		546	472	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931887	68931887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	113	338	0	ENST00000288368.4:c.317G>A	p.Gly106Glu	p.G106E	ENST00000288368	NM_024870.2	106	gGa/gAa	3/40	0.768508461168577	4	FACETS	0.87	0.785	0.959	0.29	0.261	0.32	CLONAL	1	TRUE	1	0.791573453673936	4		338	588	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420076	41420076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	420	884	0	ENST00000373198.4:c.245G>A	p.Arg82Lys	p.R82K	ENST00000373198	NM_133170.3	82	aGa/aAa	3/32	0.610109138563586	4	FACETS	0.94	0.899	0.982	0.94	0.899	0.982	CLONAL	2	TRUE	2	0.791573453673936	4		884	1011	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754647	41754647	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs267605498	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	234	1076	0	ENST00000301178.4:c.1634-1G>A		p.X545_splice	ENST00000301178	NM_021913.4	545			0.768622588298338	3	FACETS	0.886	0.828	0.947	0.443	0.414	0.474	CLONAL	1	TRUE	1	0.791573453673936	3		1076	931	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009299	69009299	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1017780787	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	167	533	0	ENST00000288368.4:c.2416G>A	p.Glu806Lys	p.E806K	ENST00000288368	NM_024870.2	806	Gag/Aag	22/40	0.768508461168577	4	FACETS	0.875	0.804	0.948	0.292	0.268	0.317	CLONAL	1	TRUE	1	0.791573453673936	4		533	864	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860139	152860139	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	369	383	0	ENST00000406277.2:c.291-2A>T		p.X97_splice	ENST00000406277	NM_152274.4	97			0.664914732717213		FACETS		0.995	1				CLONAL	2	TRUE	NA	0.791573453673936	2		383	429	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174920	11174920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	241	369	0	ENST00000361445.4:c.7114C>T	p.Pro2372Ser	p.P2372S	ENST00000361445	NM_004958.3	2372	Cca/Tca	52/58	0.787206896459312	2	FACETS	0.951	0.914	0.987	0.951	0.914	0.987	CLONAL	2	TRUE	0	0.791573453673936	2		369	320	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150923915	150923915	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	205	704	0	ENST00000271640.5:c.2288C>T	p.Ser763Phe	p.S763F	ENST00000271640	NM_001145415.1	763	tCt/tTt	14/22	0.790540934191335	4	FACETS	0.86	0.797	0.925			1	CLONAL	1	TRUE	NA	0.791573453673936	4		704	1079	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163298045	163298045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	255	267	0	ENST00000271452.3:c.226C>T	p.Pro76Ser	p.P76S	ENST00000271452	NM_145697.2	76	Cca/Tca	4/14	0.756132145920367	4	FACETS	0.871	0.828	0.912	0.653	0.621	0.684	CLONAL	3	TRUE	0	0.791573453673936	4		267	442	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945713	206945713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	596	1011	2	ENST00000423557.1:c.68G>A	p.Gly23Asp	p.G23D	ENST00000423557	NM_000572.2	23	gGc/gAc	1/5	0.787206896459312	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.791573453673936	2		1013	739	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63816964	63816965	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	198	640	1	ENST00000279873.7:c.935_936delinsTT	p.Ala312Val	p.A312V	ENST00000279873	NM_032199.2	312	gCC/gTT	6/10	0.725192777445001	4	FACETS	0.88	0.815	0.948	0.44	0.407	0.474	CLONAL	1	TRUE	2	0.791573453673936	4		641	1018	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332691	70332691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	167	652	0	ENST00000373644.4:c.596C>T	p.Ser199Phe	p.S199F	ENST00000373644	NM_030625.2	199	tCc/tTc	2/12	0.725192777445001	4	FACETS	0.907	0.835	0.983	0.454	0.417	0.492	CLONAL	1	TRUE	2	0.791573453673936	4		652	833	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263332	123263332	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	173	686	0	ENST00000358487.5:c.1411G>A	p.Asp471Asn	p.D471N	ENST00000358487	NM_000141.4	471	Gac/Aac	10/18	0.605744457434633	4	FACETS	0.93	0.857	1			1	CLONAL	1	TRUE	NA	0.791573453673936	4		686	842	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10785690	10785690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	175	566	0	ENST00000361367.2:c.1226C>T	p.Pro409Leu	p.P409L	ENST00000361367	NM_014633.3	409	cCc/cTc	10/25	1	2	FACETS	0.886	0.823	0.951	0.886	0.823	0.951	CLONAL	1	TRUE	1	0.791573453673936	2		566	499	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129352	64129353	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	269	1373	0	ENST00000334205.4:c.784_785delinsTT	p.Pro262Phe	p.P262F	ENST00000334205	NM_003942.2	262	CCc/TTc	8/17	1	2	FACETS	0.997	0.941	1	0.997	0.941	1	CLONAL	1	TRUE	1	0.791573453673936	2		1373	682	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170464	108170464	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	127	420	0	ENST00000278616.4:c.5029G>C	p.Glu1677Gln	p.E1677Q	ENST00000278616	NM_000051.3	1677	Gaa/Caa	34/63	0.783734537835014	2	FACETS	0.816	0.747	0.888	0.408	0.373	0.444	CLONAL	1	TRUE	0	0.791573453673936	2		420	393	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524218	18524218	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	134	464	0	ENST00000266497.5:c.1730G>A	p.Trp577Ter	p.W577*	ENST00000266497		577	tGg/tAg	11/31	0.78904418075613	3	FACETS	0.841	0.767	0.917	0.42	0.383	0.459	CLONAL	1	TRUE	1	0.791573453673936	3		464	562	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915460	112915460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	165	508	0	ENST00000351677.2:c.859C>T	p.His287Tyr	p.H287Y	ENST00000351677	NM_002834.3	287	Cat/Tat	8/16	0.618404388744602	3	FACETS	1	0.967	1	0.541	0.5	0.583	CLONAL	1	TRUE	1	0.791573453673936	3		508	538	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416574	121416574	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	231	930	0	ENST00000257555.6:c.3G>A	p.Met1?	p.M1?	ENST00000257555		1	atG/atA	1/10	0.618404388744602	3	FACETS	1	0.983	1	0.568	0.532	0.605	CLONAL	1	TRUE	1	0.791573453673936	3		930	717	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931718	28931719	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	133	763	0	ENST00000282397.4:c.2220_2221delinsAA	p.Glu741Lys	p.E741K	ENST00000282397	NM_002019.4	740	gtGGaa/gtAAaa	15/30	0.280791512492841	2	FACETS	0.538	0.49	0.588	0.269	0.245	0.294	INDETERMINATE	1	TRUE	0	0.791573453673936	2		763	625	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913550	32913551	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	52	272	1	ENST00000380152.3:c.5058_5059delinsTT	p.Leu1686_Leu1687delinsPhePhe	p.L1686_L1687delinsFF	ENST00000380152		1686	ttACtt/ttTTtt	11/27	0.206241596703969	3	FACETS	0.65	0.558	0.75	0.217	0.186	0.25	INDETERMINATE	1	TRUE	0	0.791573453673936	3		273	282	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134121	41134121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	393	1126	0	ENST00000379561.5:c.1507G>A	p.Val503Ile	p.V503I	ENST00000379561	NM_002015.3	503	Gtc/Atc	2/3	0.206241596703969	3	FACETS	0.969	0.93	1	0.646	0.62	0.672	INDETERMINATE	2	TRUE	0	0.791573453673936	3		1126	715	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039462	49039462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	161	505	0	ENST00000267163.4:c.2447C>T	p.Ser816Leu	p.S816L	ENST00000267163	NM_000321.2	816	tCa/tTa	23/27	0.206241596703969	3	FACETS	1	0.942	1	0.342	0.315	0.369	INDETERMINATE	1	TRUE	0	0.791573453673936	3		505	554	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73649996	73649996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	421	962	0	ENST00000377687.4:c.1346C>T	p.Ala449Val	p.A449V	ENST00000377687	NM_001730.3	449	gCc/gTc	4/4	0.206241596703969	3	FACETS	0.916	0.88	0.953	0.611	0.586	0.636	INDETERMINATE	2	TRUE	0	0.791573453673936	3		962	810	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518040	103518040	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	218	577	0	ENST00000355739.4:c.1978G>A	p.Val660Met	p.V660M	ENST00000355739	NM_000123.3	660	Gtg/Atg	9/15	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.791573453673936	2		577	416	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023397	33023397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	273	951	0	ENST00000300177.4:c.506G>A	p.Arg169Lys	p.R169K	ENST00000300177	NM_001191322.1	169	aGa/aAa	2/2	0.768622588298338	3	FACETS	1	0.975	1	0.533	0.501	0.565	CLONAL	1	TRUE	1	0.791573453673936	3		951	904	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713286	43713286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	297	1150	0	ENST00000382044.4:c.4187C>T	p.Ala1396Val	p.A1396V	ENST00000382044	NM_001141980.1	1396	gCt/gTt	20/28	0.768622588298338	3	FACETS	0.976	0.92	1	0.488	0.46	0.517	CLONAL	1	TRUE	1	0.791573453673936	3		1150	1073	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310144	91310144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	31	94	0	ENST00000355112.3:c.2198C>T	p.Pro733Leu	p.P733L	ENST00000355112	NM_000057.2	733	cCa/cTa	10/22	0.768622588298338	3	FACETS	0.71	0.582	0.851	0.355	0.291	0.426	SUBCLONAL	1	TRUE	1	0.791573453673936	3		94	154	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094737	2094737	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	281	1022	1	ENST00000219066.1:c.443C>A	p.Ala148Glu	p.A148E	ENST00000219066	NM_002528.5	148	gCg/gAg	3/6	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.791573453673936	2		1023	664	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2115634	2115634	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	208	791	0	ENST00000219476.3:c.1714C>T	p.Gln572Ter	p.Q572*	ENST00000219476	NM_000548.3	572	Cag/Tag	16/42	1	2	FACETS	0.957	0.896	1	0.957	0.896	1	CLONAL	1	TRUE	1	0.791573453673936	2		791	549	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138235	2138235	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	245	1330	0	ENST00000219476.3:c.5168C>T	p.Ser1723Leu	p.S1723L	ENST00000219476	NM_000548.3	1723	tCa/tTa	41/42	1	2	FACETS	0.936	0.881	0.993	0.936	0.881	0.993	CLONAL	1	TRUE	1	0.791573453673936	2		1330	661	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647652	23647652	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	74	173	0	ENST00000261584.4:c.215C>T	p.Pro72Leu	p.P72L	ENST00000261584	NM_024675.3	72	cCt/cTt	4/13	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.791573453673936	2		173	156	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827196	72827196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	233	1010	0	ENST00000268489.5:c.9385C>T	p.Leu3129Phe	p.L3129F	ENST00000268489	NM_006885.3	3129	Ctc/Ttc	9/10	1	2	FACETS	0.95	0.892	1	0.95	0.892	1	CLONAL	1	TRUE	1	0.791573453673936	2		1010	620	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992169	72992169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758458326	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	309	1403	0	ENST00000268489.5:c.1876C>T	p.Leu626Phe	p.L626F	ENST00000268489	NM_006885.3	626	Ctc/Ttc	2/10	1	2	FACETS	0.973	0.922	1	0.973	0.922	1	CLONAL	1	TRUE	1	0.791573453673936	2		1403	802	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990361	81990361	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	250	999	0	ENST00000359376.3:c.3632A>G	p.Asn1211Ser	p.N1211S	ENST00000359376	NM_002661.3	1211	aAc/aGc	32/33	1	2	FACETS	0.88	0.827	0.934	0.88	0.827	0.934	CLONAL	1	TRUE	1	0.791573453673936	2		999	718	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346778	89346778	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	273	1223	1	ENST00000301030.4:c.6172C>A	p.Pro2058Thr	p.P2058T	ENST00000301030	NM_001256183.1	2058	Cct/Act	9/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.791573453673936	2		1224	626	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347092	89347093	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	231	1413	1	ENST00000301030.4:c.5857_5858delinsTT	p.Pro1953Phe	p.P1953F	ENST00000301030	NM_001256183.1	1953	CCc/TTc	9/13	1	2	FACETS	0.915	0.858	0.972	0.915	0.858	0.972	CLONAL	1	TRUE	1	0.791573453673936	2		1414	638	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805085	89805085	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1209919154	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	302	1136	0	ENST00000389301.3:c.4292A>G	p.Glu1431Gly	p.E1431G	ENST00000389301	NM_000135.2	1431	gAg/gGg	43/43	1	2	FACETS	0.977	0.925	1	0.977	0.925	1	CLONAL	1	TRUE	1	0.791573453673936	2		1136	781	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546085	29546086	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	427	745	0	ENST00000356175.3:c.1590_1591delinsTT	p.Gln531Ter	p.Q531*	ENST00000356175	NM_000267.3	530	gtCCaa/gtTTaa	14/57	0.78904418075613	3	FACETS	0.872	0.837	0.908	0.872	0.837	0.908	CLONAL	2	TRUE	1	0.791573453673936	3		745	863	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679392	33679392	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	405	883	0	ENST00000308377.4:c.2689C>T	p.Pro897Ser	p.P897S	ENST00000308377	NM_152270.3	897	Ccg/Tcg	5/5	0.78904418075613	3	FACETS	0.97	0.932	1	0.97	0.932	1	CLONAL	2	TRUE	1	0.791573453673936	3		883	736	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865370	40865370	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	237	816	0	ENST00000428826.2:c.1061G>T	p.Arg354Leu	p.R354L	ENST00000428826		354	cGc/cTc	11/21	0.78904418075613	3	FACETS	0.923	0.862	0.984	0.461	0.431	0.492	CLONAL	1	TRUE	1	0.791573453673936	3		816	906	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243997	41243997	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567791181	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	415	769	0	ENST00000357654.3:c.3551G>A	p.Gly1184Glu	p.G1184E	ENST00000357654	NM_007294.3	1184	gGa/gAa	10/23	0.78904418075613	3	FACETS	0.919	0.882	0.957	0.919	0.882	0.957	CLONAL	2	TRUE	1	0.791573453673936	3		769	796	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936292	78936292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	661	898	1	ENST00000306801.3:c.3724C>T	p.Arg1242Trp	p.R1242W	ENST00000306801	NM_020761.2	1242	Cgg/Tgg	32/34	0.664914732717213	4	FACETS	0.949	0.922	0.976			1	CLONAL	3	TRUE	NA	0.791573453673936	4		899	1051	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61305131	61305131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339226597	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	266	935	0	ENST00000341074.5:c.995C>T	p.Ala332Val	p.A332V	ENST00000341074	NM_002974.2	332	gCc/gTc	8/8	1	2	FACETS	0.968	0.913	1	0.968	0.913	1	CLONAL	1	TRUE	1	0.791573453673936	2		935	694	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097215	11097215	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	268	1084	0	ENST00000358026.2:c.706C>T	p.Pro236Ser	p.P236S	ENST00000358026	NM_001128849.1	236	Cct/Tct	4/36	0.768622588298338	3	FACETS	1	0.94	1	0.5	0.47	0.531	CLONAL	1	TRUE	1	0.791573453673936	3		1084	945	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097607	11097607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1270509173	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	491	1076	0	ENST00000358026.2:c.787C>T	p.Pro263Ser	p.P263S	ENST00000358026	NM_001128849.1	263	Cca/Tca	5/36	0.768622588298338	3	FACETS	0.997	0.962	1	0.997	0.962	1	CLONAL	2	TRUE	1	0.791573453673936	3		1076	868	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101934	11101934	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	240	1035	0	ENST00000358026.2:c.1354A>G	p.Ile452Val	p.I452V	ENST00000358026	NM_001128849.1	452	Atc/Gtc	8/36	0.768622588298338	3	FACETS	0.856	0.8	0.914	0.428	0.4	0.457	CLONAL	1	TRUE	1	0.791573453673936	3		1035	989	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290031	15290032	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	554	1397	2	ENST00000263388.2:c.3522_3523delinsTT	p.Arg1175Trp	p.R1175W	ENST00000263388	NM_000435.2	1174	ccCCgg/ccTTgg	22/33	0.768622588298338	3	FACETS	0.919	0.887	0.951	0.919	0.887	0.951	CLONAL	2	TRUE	1	0.791573453673936	3		1399	1063	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291945	15291945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	240	1157	0	ENST00000263388.2:c.2821G>A	p.Asp941Asn	p.D941N	ENST00000263388	NM_000435.2	941	Gac/Aac	18/33	0.768622588298338	3	FACETS	0.896	0.837	0.956	0.448	0.418	0.478	CLONAL	1	TRUE	1	0.791573453673936	3		1157	945	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280091	18280091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	247	989	0	ENST00000222254.8:c.2174C>T	p.Pro725Leu	p.P725L	ENST00000222254	NM_005027.3	725	cCt/cTt	16/16	0.768622588298338	3	FACETS	0.96	0.899	1	0.48	0.449	0.512	CLONAL	1	TRUE	1	0.791573453673936	3		989	907	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212150	36212150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	154	666	0	ENST00000222270.7:c.1901C>T	p.Pro634Leu	p.P634L	ENST00000222270	NM_014727.1	634	cCc/cTc	3/37	0.768622588298338	3	FACETS	1	0.96	1	0.532	0.49	0.576	CLONAL	1	TRUE	1	0.791573453673936	3		666	510	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794859	42794859	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	548	1246	0	ENST00000575354.2:c.1939G>A	p.Val647Met	p.V647M	ENST00000575354	NM_015125.3	647	Gtg/Atg	10/20	0.768622588298338	3	FACETS	0.854	0.823	0.886	0.854	0.823	0.886	CLONAL	2	TRUE	1	0.791573453673936	3		1246	1131	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795244	42795245	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	253	1331	0	ENST00000575354.2:c.2324_2325delinsTT	p.Pro775Leu	p.P775L	ENST00000575354	NM_015125.3	775	cCC/cTT	10/20	0.768622588298338	3	FACETS	0.799	0.748	0.853	0.4	0.374	0.427	SUBCLONAL	1	TRUE	1	0.791573453673936	3		1331	1116	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47503797	47503797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	310	1130	0	ENST00000404338.3:c.4352C>T	p.Ser1451Phe	p.S1451F	ENST00000404338	NM_004491.4	1451	tCc/tTc	6/6	0.768622588298338	3	FACETS	1	0.967	1	0.517	0.487	0.547	CLONAL	1	TRUE	1	0.791573453673936	3		1130	1058	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027529	48027529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	748	703	0	ENST00000234420.5:c.2407G>A	p.Asp803Asn	p.D803N	ENST00000234420	NM_000179.2	803	Gac/Aac	4/10	0.781634834561087	4	FACETS	0.989	0.973	1	0.989	0.973	1	CLONAL	4	TRUE	0	0.791573453673936	4		703	856	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793413	242793413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	584	1106	0	ENST00000334409.5:c.664G>A	p.Asp222Asn	p.D222N	ENST00000334409	NM_005018.2	222	Gac/Aac	5/5	0.791573453673936	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.791573453673936	2		1106	726	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253851	30253852	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	418	828	2	ENST00000307677.4:c.602_603delinsTT	p.Ala201Val	p.A201V	ENST00000307677	NM_138578.1	201	gCC/gTT	3/3	0.550233834760741	4	FACETS	0.927	0.885	0.968	0.927	0.885	0.968	CLONAL	2	TRUE	2	0.791573453673936	4		830	1021	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727191	40727191	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	372	915	0	ENST00000373198.4:c.3773G>A	p.Ser1258Asn	p.S1258N	ENST00000373198	NM_133170.3	1258	aGc/aAc	28/32	0.171920212736878	3	FACETS	1	0.994	1	0.671	0.638	0.704	INDETERMINATE	1	TRUE	1	0.791573453673936	3		915	978	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076949	41076949	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	306	576	0	ENST00000373198.4:c.1471G>A	p.Glu491Lys	p.E491K	ENST00000373198	NM_133170.3	491	Gaa/Aaa	9/32	0.171920212736878	3	FACETS	0.795	0.755	0.835	0.795	0.755	0.835	INDETERMINATE	2	TRUE	1	0.791573453673936	3		576	679	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306683	41306684	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	331	867	1	ENST00000373198.4:c.975_976delinsAA	p.Glu326Lys	p.E326K	ENST00000373198	NM_133170.3	325	gtGGaa/gtAAaa	7/32	0.171920212736878	3	FACETS	1	0.995	1	0.725	0.689	0.762	INDETERMINATE	1	TRUE	1	0.791573453673936	3		868	805	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44527567	44527567	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	215	869	0	ENST00000291552.4:c.38A>C	p.Lys13Thr	p.K13T	ENST00000291552	NM_006758.2	13	aAa/aCa	1/8	0.775045213841205	3	FACETS	0.945	0.881	1	0.473	0.44	0.506	CLONAL	1	TRUE	1	0.791573453673936	3		869	802	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446111	29446111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	483	1226	0	ENST00000544604.2:c.1942C>T	p.Pro648Ser	p.P648S	ENST00000544604	NM_001206998.1	648	Ccg/Tcg	8/9	0.725192777445001	4	FACETS	0.97	0.93	1	0.97	0.93	1	CLONAL	2	TRUE	2	0.791573453673936	4		1226	1127	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30733036	30733036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	215	999	0	ENST00000295754.5:c.1649G>A	p.Arg550Lys	p.R550K	ENST00000295754	NM_003242.5	550	aGg/aAg	7/7	0.786274971240305	4	FACETS	0.816	0.757	0.877	0.272	0.252	0.293	CLONAL	1	TRUE	1	0.791573453673936	4		999	1193	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30733072	30733072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	217	856	0	ENST00000295754.5:c.1685C>T	p.Ser562Phe	p.S562F	ENST00000295754	NM_003242.5	562	tCc/tTc	7/7	0.786274971240305	4	FACETS	0.957	0.89	1	0.319	0.296	0.343	CLONAL	1	TRUE	1	0.791573453673936	4		856	1026	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63965651	63965651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	267	827	0	ENST00000398590.3:c.560C>T	p.Ser187Phe	p.S187F	ENST00000398590	NM_001177387.1	187	tCc/tTc	6/14	0.791573453673936	4	FACETS	1	0.967	1	0.524	0.491	0.558	CLONAL	1	TRUE	2	0.791573453673936	4		827	1153	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008465	71008465	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	256	806	0	ENST00000318789.4:c.1967A>G	p.Asn656Ser	p.N656S	ENST00000318789	NM_032682.5	656	aAc/aGc	21/21	0.791573453673936	4	FACETS	0.958	0.896	1	0.479	0.448	0.511	CLONAL	1	TRUE	2	0.791573453673936	4		806	1210	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204959	128204959	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1350131138	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	288	1247	0	ENST00000341105.2:c.482C>T	p.Pro161Leu	p.P161L	ENST00000341105	NM_032638.4	161	cCt/cTt	3/6	0.78904418075613	3	FACETS	0.965	0.908	1	0.482	0.454	0.512	CLONAL	1	TRUE	1	0.791573453673936	3		1247	1053	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976914	55976914	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762779214	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	190	580	0	ENST00000263923.4:c.998G>A	p.Gly333Glu	p.G333E	ENST00000263923	NM_002253.2	333	gGa/gAa	8/30	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.791573453673936	2		580	463	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155665	56155666	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	249	729	0	ENST00000399503.3:c.757_758delinsTT	p.Pro253Phe	p.P253F	ENST00000399503	NM_005921.1	253	CCt/TTt	3/20	0.104332313894151	3	FACETS	1	0.991	1	0.661	0.622	0.701	INDETERMINATE	1	TRUE	1	0.791573453673936	3		729	664	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638059	176638060	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	147	669	0	ENST00000439151.2:c.2659_2660delinsTT	p.Pro887Leu	p.P887L	ENST00000439151	NM_022455.4	887	CCa/TTa	5/23	1	2	FACETS	0.79	0.727	0.855	0.79	0.727	0.855	SUBCLONAL	1	TRUE	1	0.791573453673936	2		669	470	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721444	176721445	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	281	1217	1	ENST00000439151.2:c.7075_7076delinsTT	p.Pro2359Leu	p.P2359L	ENST00000439151	NM_022455.4	2359	CCa/TTa	23/23	1	2	FACETS	0.913	0.861	0.965	0.913	0.861	0.965	CLONAL	1	TRUE	1	0.791573453673936	2		1218	778	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721984	176721984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	276	1248	1	ENST00000439151.2:c.7615C>T	p.Leu2539Phe	p.L2539F	ENST00000439151	NM_022455.4	2539	Ctt/Ttt	23/23	1	2	FACETS	0.9	0.849	0.952	0.9	0.849	0.952	CLONAL	1	TRUE	1	0.791573453673936	2		1249	775	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043963	180043963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	206	931	0	ENST00000261937.6:c.3033G>A	p.Met1011Ile	p.M1011I	ENST00000261937	NM_182925.4	1011	atG/atA	22/30	1	2	FACETS	0.988	0.924	1	0.988	0.924	1	CLONAL	1	TRUE	1	0.791573453673936	2		931	527	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672098	30672098	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774976533	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	569	1274	0	ENST00000376406.3:c.4862C>T	p.Pro1621Leu	p.P1621L	ENST00000376406	NM_014641.2	1621	cCt/cTt	10/15	0.768622588298338	3	FACETS	0.939	0.907	0.972	0.939	0.907	0.972	CLONAL	2	TRUE	1	0.791573453673936	3		1274	1068	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323193	31323194	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	305	1196	0	ENST00000412585.2:c.795_796delinsTT	p.Gln266Ter	p.Q266*	ENST00000412585	NM_005514.6	265	ttCCag/ttTTag	4/8	0.768622588298338	3	FACETS	0.963	0.908	1	0.481	0.454	0.51	CLONAL	1	TRUE	1	0.791573453673936	3		1196	1117	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964468	93964468	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	173	514	0	ENST00000369303.4:c.2429A>T	p.Tyr810Phe	p.Y810F	ENST00000369303	NM_004440.3	810	tAc/tTc	14/17	1	2	FACETS	0.926	0.86	0.993	0.926	0.86	0.993	CLONAL	1	TRUE	1	0.791573453673936	2		514	472	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066588	94066588	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	236	945	0	ENST00000369303.4:c.1171C>T	p.Gln391Ter	p.Q391*	ENST00000369303	NM_004440.3	391	Cag/Tag	5/17	1	2	FACETS	0.992	0.933	1	0.992	0.933	1	CLONAL	1	TRUE	1	0.791573453673936	2		945	601	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124442	94124442	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	69	264	0	ENST00000369303.4:c.141G>A	p.Trp47Ter	p.W47*	ENST00000369303	NM_004440.3	47	tgG/tgA	2/17	1	2	FACETS	0.918	0.815	1	0.918	0.815	1	CLONAL	1	TRUE	1	0.791573453673936	2		264	190	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708954	117708954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	196	786	0	ENST00000368508.3:c.2003C>T	p.Thr668Ile	p.T668I	ENST00000368508	NM_002944.2	668	aCc/aTc	13/43	1	2	FACETS	0.947	0.884	1	0.947	0.884	1	CLONAL	1	TRUE	1	0.791573453673936	2		786	523	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524780	137524780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55666220	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	180	449	0	ENST00000367739.4:c.589G>A	p.Glu197Lys	p.E197K	ENST00000367739	NM_000416.2	197	Gag/Aag	5/7	1	2	FACETS	0.944	0.878	1	0.944	0.878	1	CLONAL	1	TRUE	1	0.791573453673936	2		449	482	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004510	150004510	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760512152	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	291	1031	0	ENST00000253339.5:c.1715C>T	p.Pro572Leu	p.P572L	ENST00000253339		572	cCa/cTa	3/7	1	2	FACETS	0.87	0.821	0.92	0.87	0.821	0.92	CLONAL	1	TRUE	1	0.791573453673936	2		1031	845	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528639	157528639	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	256	1052	2	ENST00000346085.5:c.6364C>T	p.Arg2122Cys	p.R2122C	ENST00000346085	NM_020732.3	2122	Cgc/Tgc	20/20	1	2	FACETS	0.977	0.921	1	0.977	0.921	1	CLONAL	1	TRUE	1	0.791573453673936	2		1054	662	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962965	2962965	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	420	934	0	ENST00000396946.4:c.1943C>T	p.Pro648Leu	p.P648L	ENST00000396946	NM_032415.4	648	cCc/cTc	16/25	0.198665217835756	4	FACETS	1	0.969	1	1	0.969	1	INDETERMINATE	2	TRUE	2	0.791573453673936	4		934	936	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729712	41729712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1435204559	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	445	1170	0	ENST00000242208.4:c.817G>A	p.Gly273Ser	p.G273S	ENST00000242208	NM_002192.2	273	Ggc/Agc	3/3	0.791573453673936	4	FACETS	0.887	0.848	0.926	0.887	0.848	0.926	CLONAL	2	TRUE	2	0.791573453673936	4		1170	1136	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55269031	55269031	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	568	1117	0	ENST00000275493.2:c.3097C>T	p.Pro1033Ser	p.P1033S	ENST00000275493	NM_005228.3	1033	Ccc/Tcc	25/28	0.500989699203511	4	FACETS	0.963	0.927	1	0.963	0.927	1	CLONAL	2	TRUE	2	0.791573453673936	4		1117	1335	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339511	81339511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	289	377	0	ENST00000222390.5:c.1493G>A	p.Gly498Glu	p.G498E	ENST00000222390	NM_000601.4	498	gGg/gAg	13/18	0.791573453673936	4	FACETS	0.984	0.932	1	0.984	0.932	1	CLONAL	2	TRUE	2	0.791573453673936	4		377	665	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453075	140453075	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	301	416	0	ENST00000288602.6:c.1860G>A	p.Met620Ile	p.M620I	ENST00000288602	NM_004333.4	620	atG/atA	15/18	0.791573453673936	6	FACETS	0.912	0.86	0.966	0.456	0.43	0.483	CLONAL	2	TRUE	2	0.791573453673936	6		416	1077	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876962	151876962	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	380	839	0	ENST00000262189.6:c.7399C>T	p.Pro2467Ser	p.P2467S	ENST00000262189	NM_170606.2	2467	Cct/Tct	37/59	0.791573453673936	6	FACETS	0.865	0.82	0.911	0.432	0.41	0.456	CLONAL	2	TRUE	2	0.791573453673936	6		839	1434	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69012004	69012004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	123	437	0	ENST00000288368.4:c.2641C>T	p.Leu881Phe	p.L881F	ENST00000288368	NM_024870.2	881	Ctt/Ttt	23/40	0.768508461168577	4	FACETS	0.818	0.741	0.899	0.273	0.246	0.3	CLONAL	1	TRUE	1	0.791573453673936	4		437	681	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981783	70981783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	479	1135	1	ENST00000276594.2:c.313C>T	p.Pro105Ser	p.P105S	ENST00000276594	NM_024504.3	105	Ccc/Tcc	2/8	0.768508461168577	4	FACETS	0.996	0.955	1	0.664	0.637	0.691	CLONAL	2	TRUE	1	0.791573453673936	4		1136	1089	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738646	145738647	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	277	1354	0	ENST00000428558.2:c.2417_2418delinsAA	p.Gly806Glu	p.G806E	ENST00000428558	NM_004260.3	806	gGG/gAA	15/22	0.786274971240305	4	FACETS	0.968	0.908	1	0.323	0.302	0.344	CLONAL	1	TRUE	1	0.791573453673936	4		1354	1295	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2097445	2097445	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	103	426	0	ENST00000349721.2:c.3052C>T	p.His1018Tyr	p.H1018Y	ENST00000349721	NM_003070.3	1018	Cac/Tac	21/34	0.791573453673936	3	FACETS	0.741	0.666	0.82	0.371	0.333	0.41	SUBCLONAL	1	TRUE	1	0.791573453673936	3		426	490	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521457	8521457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	392	714	0	ENST00000356435.5:c.781G>A	p.Gly261Arg	p.G261R	ENST00000356435		261	Ggg/Agg	9/35	0.791573453673936	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.791573453673936	3		714	677	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974679	21974680	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GG	GG	TA	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	639	1169	0	ENST00000304494.5:c.147_148delinsTA	p.Gln50Lys	p.Q50K	ENST00000304494	NM_000077.4	49	atCCag/atTAag	1/3	0.787240979745821	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.791573453673936	2		1169	807	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27203112	27203112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	203	795	0	ENST00000380036.4:c.2204C>T	p.Ser735Phe	p.S735F	ENST00000380036	NM_000459.3	735	tCt/tTt	13/23	0.787240979745821	2	FACETS	0.948	0.886	1	0.474	0.443	0.506	CLONAL	1	TRUE	0	0.791573453673936	2		795	541	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931631	39931631	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	217	455	0	ENST00000378444.4:c.2968C>G	p.Gln990Glu	p.Q990E	ENST00000378444	NM_001123385.1	990	Cag/Gag	4/15	0.364818149908672	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.791573453673936	2		455	440	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428393	47428393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	153	475	0	ENST00000377045.4:c.1261C>T	p.His421Tyr	p.H421Y	ENST00000377045	NM_001654.4	421	Cat/Tat	12/16	0.364818149908672	2	FACETS	0.835	0.77	0.901			1	INDETERMINATE	1	TRUE	NA	0.791573453673936	2		475	463	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410439	63410439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1319125537	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	158	630	0	ENST00000330258.3:c.2728C>T	p.His910Tyr	p.H910Y	ENST00000330258	NM_152424.3	910	Cac/Tac	2/2	0.364818149908672	2	FACETS	0.758	0.699	0.818			1	INDETERMINATE	1	TRUE	NA	0.791573453673936	2		630	527	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347950	70347951	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	424	542	1	ENST00000374080.3:c.3189_3190delinsAA	p.Gly1064Arg	p.G1064R	ENST00000374080		1063	gtGGgg/gtAAgg	22/45	0.664914732717213	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.791573453673936	2		543	492	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912093	76912093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	205	117	0	ENST00000373344.5:c.4171G>A	p.Glu1391Lys	p.E1391K	ENST00000373344	NM_000489.3	1391	Gaa/Aaa	13/35	0.664914732717213	2	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.791573453673936	2		117	234	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183820	10183820	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060526-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	94	641	0	ENST00000256474.2:c.291del	p.Tyr98ThrfsTer61	p.Y98Tfs*61	ENST00000256474	NM_000551.3	97	Ccc/cc	1/3	0.367480862911316	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.367480862911316	1		641	341	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651408	52651408	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0060526-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	54	463	0	ENST00000394830.3:c.1688T>A	p.Leu563Ter	p.L563*	ENST00000394830	NM_018313.4	563	tTg/tAg	15/30	0.367480862911316	1	FACETS	0.766	0.659	0.883	0.766	0.659	0.883	SUBCLONAL	1	TRUE	0	0.367480862911316	1		463	313	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224527	53224531	+	frameshift_variant	Frame_Shift_Del	DEL	AGGTA	AGGTA	-	novel	NA	P-0060526-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	140	357	0	ENST00000375401.3:c.3182_3186del	p.Leu1061ArgfsTer67	p.L1061Rfs*67	ENST00000375401	NM_004187.3	1061	cTACCT/c	21/26	1	1	FACETS	0.972	0.899	1	1	0.992	1	CLONAL	2	TRUE	0	0.367480862911316	1		357	320	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0060580-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	262	401	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.492893537012383	4	FACETS	0.957	0.906	1	0.957	0.906	1	CLONAL	3	TRUE	1	0.492893537012383	4		401	553	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798299	45798299	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	215	649	0	ENST00000450313.1:c.637C>T	p.Pro213Ser	p.P213S	ENST00000450313	NM_012222.2	213	Cct/Tct	8/16	0.422689524339407	3	FACETS	1	0.954	1	0.519	0.481	0.558	CLONAL	1	TRUE	1	0.422689524339407	3		649	1188	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196953	108196965	+	splice_donor_variant,intron_variant	Splice_Site	DEL	GTTTGTTTTTTTT	GTTTGTTTTTTTT	-	novel	NA	P-0060582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	100	331	0	ENST00000278616.4:c.6975+1_6975+13del		p.X2325_splice	ENST00000278616	NM_000051.3	2325			0.422689524339407	1	FACETS	0.876	0.787	0.969	0.876	0.787	0.969	CLONAL	1	TRUE	0	0.422689524339407	1		331	426	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440918	52440918	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	170	464	0	ENST00000460680.1:c.586T>C	p.Trp196Arg	p.W196R	ENST00000460680	NM_004656.3	196	Tgg/Cgg	8/17	0.422689524339407	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.422689524339407	1		464	607	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633856	86633856	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	43	251	0	ENST00000274376.6:c.965A>T	p.Asn322Ile	p.N322I	ENST00000274376	NM_002890.2	322	aAt/aTt	5/25	1	2	FACETS	0.78	0.657	0.913	0.78	0.657	0.913	CLONAL	1	TRUE	1	0.422689524339407	2		251	261	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0060585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	180	932	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.238012150178201	2	FACETS	0.969	0.898	1	0.969	0.898	1	CLONAL	2	TRUE	0	0.288759898079737	2		932	643	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178095	56178095	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374455781	NA	P-0060585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	97	370	0	ENST00000399503.3:c.3068G>A	p.Arg1023His	p.R1023H	ENST00000399503	NM_005921.1	1023	cGc/cAc	14/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.288759898079737	2		370	611	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77064603	77064603	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767363828	NA	P-0060585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	79	340	0	ENST00000356341.3:c.814C>T	p.Arg272Trp	p.R272W	ENST00000356341	NM_002576.4	272	Cgg/Tgg	8/15	0.287859110391039	3	FACETS	0.913	0.803	1	0.456	0.401	0.516	CLONAL	1	TRUE	1	0.288759898079737	3		340	686	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412898	49412898	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519954	NA	P-0060585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	246	351	0	ENST00000418115.1:c.125A>G	p.Tyr42Cys	p.Y42C	ENST00000418115	NM_001664.2	42	tAt/tGt	2/5	0.288759898079737	3	FACETS	0.934	0.878	0.991	0.934	0.878	0.991	CLONAL	3	TRUE	0	0.288759898079737	3		351	696	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809769	36809769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	68	354	0	ENST00000373129.3:c.836C>T	p.Pro279Leu	p.P279L	ENST00000373129	NM_032017.1	279	cCg/cTg	9/12	0.287859110391039	3	FACETS	0.872	0.759	0.995	0.436	0.379	0.498	CLONAL	1	TRUE	1	0.288759898079737	3		354	618	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40500452	40500452	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	57	269	0	ENST00000264657.5:c.83T>C	p.Met28Thr	p.M28T	ENST00000264657	NM_139276.2	28	aTg/aCg	2/24	0.213423657069291	4	FACETS	0.811	0.696	0.938	0.406	0.348	0.469	CLONAL	1	TRUE	2	0.288759898079737	4		269	627	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0060586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	139	462	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.188002799827291	3	FACETS	0.801	0.731	0.873	0.801	0.731	0.873	CLONAL	2	TRUE	1	0.308289944629457	3		462	650	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929487	44929487	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	112	837	2	ENST00000377967.4:c.2587C>T	p.Gln863Ter	p.Q863*	ENST00000377967	NM_021140.2	863	Cag/Tag	17/29	1	1	FACETS	0.786	0.713	0.862	1	0.986	1	SUBCLONAL	2	TRUE	0	0.308289944629457	1		839	391	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858985	57858985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142957882	NA	P-0060586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	82	548	0	ENST00000228682.2:c.481C>T	p.Arg161Trp	p.R161W	ENST00000228682	NM_005269.2	161	Cgg/Tgg	5/12	1	2	FACETS	0.842	0.743	0.948	0.842	0.743	0.948	CLONAL	1	TRUE	1	0.308289944629457	2		548	632	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094413	27094414	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	193	520	0	ENST00000324856.7:c.3122dup	p.Pro1042AlafsTer5	p.P1042Afs*5	ENST00000324856	NM_006015.4	1041	ctg/cTtg	11/20	0.308289944629457	2	FACETS	0.987	0.918	1	0.987	0.918	1	CLONAL	2	TRUE	0	0.308289944629457	2		520	634	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120177	70120178	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0060586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	79	456	0	ENST00000245479.2:c.1180dup	p.Arg394ProfsTer184	p.R394Pfs*184	ENST00000245479	NM_000346.3	393	-/C	3/3	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.308289944629457	2		456	511	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136259	202136259	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	102	390	0	ENST00000358485.4:c.503C>A	p.Ser168Ter	p.S168*	ENST00000358485	NM_001080125.1	168	tCa/tAa	3/9	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.308289944629457	2		390	601	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405964	49405964	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	239	404	0	ENST00000418115.1:c.174G>C	p.Trp58Cys	p.W58C	ENST00000418115	NM_001664.2	58	tgG/tgC	3/5	0.286866034159939	3	FACETS	0.882	0.828	0.937	0.882	0.828	0.937	CLONAL	3	TRUE	0	0.308289944629457	3		404	676	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2039690	2039690	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764118923	NA	P-0060586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	98	566	1	ENST00000349721.2:c.580C>T	p.Arg194Ter	p.R194*	ENST00000349721	NM_003070.3	194	Cga/Tga	4/34	1	2	FACETS	0.929	0.83	1	0.929	0.83	1	CLONAL	1	TRUE	1	0.308289944629457	2		567	684	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570314	87570314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760629075	NA	P-0060586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	105	591	0	ENST00000277120.3:c.2054C>T	p.Ser685Phe	p.S685F	ENST00000277120		685	tCc/tTc	17/19	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.308289944629457	2		591	649	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863449	57863449	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781683841	NA	P-0060587-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	125	459	6	ENST00000228682.2:c.1544G>A	p.Arg515Gln	p.R515Q	ENST00000228682	NM_005269.2	515	cGg/cAg	11/12	1	2	FACETS	0.649	0.588	0.712	0.649	0.588	0.712	SUBCLONAL	1	TRUE	1	0.566790589618656	2		465	680	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555309	106555309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060587-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	134	431	0	ENST00000369096.4:c.2426C>T	p.Pro809Leu	p.P809L	ENST00000369096	NM_001198.3	809	cCt/cTt	7/7	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.566790589618656	2		431	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0060588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	444	932	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.835986775081685	2	FACETS	0.972	0.949	0.994	0.972	0.949	0.994	CLONAL	2	TRUE	0	0.863089310369461	2		932	529	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180310	27180310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1286718039	NA	P-0060588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	124	450	1	ENST00000380036.4:c.974G>A	p.Arg325His	p.R325H	ENST00000380036	NM_000459.3	325	cGc/cAc	7/23	1	2	FACETS	0.458	0.415	0.502	0.458	0.415	0.502	SUBCLONAL	1	TRUE	1	0.863089310369461	2		451	628	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182679101	182679101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs773792110	NA	P-0060588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1833	179	355	0	ENST00000292782.4:c.433G>C	p.Glu145Gln	p.E145Q	ENST00000292782	NM_020640.2	145	Gaa/Caa	4/7	0.863089310369461	9	FACETS	0.829	0.761	0.901	0.118	0.108	0.129	CLONAL	1	TRUE	2	0.863089310369461	9		355	2012	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2047278	2047301	+	inframe_deletion	In_Frame_Del	DEL	GCCCGCGCCCGGCGGCCGGCCCTC	GCCCGCGCCCGGCGGCCGGCCCTC	-	rs1297196554	NA	P-0060588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	43	64	0	ENST00000349721.2:c.850_873del	p.Gly284_Pro291del	p.G284_P291del	ENST00000349721	NM_003070.3	280	gtGCCCGCGCCCGGCGGCCGGCCCTCg/gtg	5/34	1	2	FACETS	0.94	0.812	1	0.94	0.812	1	CLONAL	1	TRUE	1	0.863089310369461	2		64	106	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	145	409	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.898	0.822	0.976	0.898	0.822	0.976	CLONAL	1	TRUE	1	0.548460817608579	2		409	589	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670282	134670282	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748807854	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	184	469	0	ENST00000398015.3:c.193G>A	p.Glu65Lys	p.E65K	ENST00000398015	NM_004441.4	65	Gag/Aag	3/16	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.548460817608579	2		469	601	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586470	189586470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147148566	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	207	510	0	ENST00000264731.3:c.1094C>T	p.Ser365Leu	p.S365L	ENST00000264731	NM_003722.4	365	tCg/tTg	8/14	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.548460817608579	2		510	688	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	289	321	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.548460817608579	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.548460817608579	2		321	485	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453486	138453486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451809865	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	130	345	0	ENST00000289153.2:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000289153	NM_006219.2	321	cGa/cAa	5/22	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.548460817608579	2		345	413	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	191	874	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.548460817608579	2		874	690	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	156	429	0	ENST00000394830.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000394830	NM_018313.4	710	Cga/Tga	17/30	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.548460817608579	2		429	551	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	237	458	0	ENST00000349496.5:c.101G>A	p.Gly34Glu	p.G34E	ENST00000349496	NM_001904.3	34	gGa/gAa	3/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.548460817608579	2		458	769	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056376	180056376	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	154	568	0	ENST00000261937.6:c.868G>T	p.Glu290Ter	p.E290*	ENST00000261937	NM_182925.4	290	Gaa/Taa	7/30	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.548460817608579	2		568	557	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	167	524	0	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.548460817608579	2		524	609	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32899248	32899248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375125172	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	85	309	0	ENST00000380152.3:c.352C>T	p.Arg118Cys	p.R118C	ENST00000380152		118	Cgc/Tgc	4/27	1	2	FACETS	0.975	0.87	1	0.975	0.87	1	CLONAL	1	TRUE	1	0.548460817608579	2		309	318	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115600	108115600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772821016	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	145	416	0	ENST00000278616.4:c.748C>T	p.Arg250Ter	p.R250*	ENST00000278616	NM_000051.3	250	Cga/Tga	7/63	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.548460817608579	2		416	526	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741458	39741458	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1346009286	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	217	416	0	ENST00000361337.2:c.1345C>T	p.Arg449Trp	p.R449W	ENST00000361337	NM_003286.2	449	Cgg/Tgg	14/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.548460817608579	2		416	705	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989557	85989557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	129	272	0	ENST00000263360.6:c.1316G>A	p.Arg439Gln	p.R439Q	ENST00000263360	NM_003797.3	439	cGa/cAa	12/12	1	2	FACETS	0.97	0.885	1	0.97	0.885	1	CLONAL	1	TRUE	1	0.548460817608579	2		272	485	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534356	187534356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770029391	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	180	458	1	ENST00000441802.2:c.9370G>A	p.Glu3124Lys	p.E3124K	ENST00000441802	NM_005245.3	3124	Gaa/Aaa	13/27	1	2	FACETS	0.95	0.879	1	0.95	0.879	1	CLONAL	1	TRUE	1	0.548460817608579	2		459	691	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521544	8521544	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	116	380	1	ENST00000356435.5:c.694C>T	p.Arg232Cys	p.R232C	ENST00000356435		232	Cgc/Tgc	9/35	1	2	FACETS	0.826	0.748	0.908	0.826	0.748	0.908	CLONAL	1	TRUE	1	0.548460817608579	2		381	512	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164385	47164385	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	149	387	0	ENST00000409792.3:c.1741G>T	p.Glu581Ter	p.E581*	ENST00000409792	NM_014159.6	581	Gaa/Taa	3/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.548460817608579	2		387	479	SUCCESS
REL	5966	MSKCC	GRCh37	2	61128173	61128173	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	100	291	0	ENST00000295025.8:c.349G>T	p.Glu117Ter	p.E117*	ENST00000295025	NM_002908.2	117	Gaa/Taa	4/11	1	2	FACETS	0.912	0.82	1	0.912	0.82	1	CLONAL	1	TRUE	1	0.548460817608579	2		291	400	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193884	106193884	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	193	408	0	ENST00000380013.4:c.4346C>A	p.Ser1449Tyr	p.S1449Y	ENST00000380013	NM_001127208.2	1449	tCt/tAt	10/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.548460817608579	2		408	664	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540815	187540815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1221788415	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	173	539	0	ENST00000441802.2:c.6925G>A	p.Asp2309Asn	p.D2309N	ENST00000441802	NM_005245.3	2309	Gat/Aat	10/27	1	2	FACETS	0.906	0.837	0.978	0.906	0.837	0.978	CLONAL	1	TRUE	1	0.548460817608579	2		539	696	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265446	152265446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371610514	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	216	444	0	ENST00000206249.3:c.899G>A	p.Arg300His	p.R300H	ENST00000206249	NM_000125.3	300	cGc/cAc	4/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.548460817608579	2		444	694	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349471	73349471	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777245855	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	179	441	0	ENST00000377767.4:c.865G>A	p.Glu289Lys	p.E289K	ENST00000377767	NM_014953.3	289	Gaa/Aaa	6/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.548460817608579	2		441	597	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589585	67589605	+	inframe_deletion	In_Frame_Del	DEL	CATGAATATAACACTCAGTTT	CATGAATATAACACTCAGTTT	-	novel	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	84	326	0	ENST00000274335.5:c.1350_1370del	p.His450_Phe456del	p.H450_F456del	ENST00000274335		450	CATGAATATAACACTCAGTTT/-	10/15	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.548460817608579	2		326	285	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258036	123258036	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	48	349	0	ENST00000358487.5:c.1645A>G	p.Asn549Asp	p.N549D	ENST00000358487	NM_000141.4	549	Aat/Gat	12/18	0.548460817608579	2	FACETS	0.392	0.331	0.458	0.196	0.165	0.229	SUBCLONAL	1	TRUE	0	0.548460817608579	2		349	447	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958042	54958042	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs779964295	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	149	207	0	ENST00000312783.6:c.565C>T	p.Arg189Trp	p.R189W	ENST00000312783	NM_198436.1	189	Cgg/Tgg	6/10	1	2	FACETS	0.96	0.881	1	0.96	0.881	1	CLONAL	1	TRUE	1	0.548460817608579	2		207	566	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181803	56181803	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	38	333	0	ENST00000399503.3:c.4027G>T	p.Glu1343Ter	p.E1343*	ENST00000399503	NM_005921.1	1343	Gaa/Taa	17/20	1	2	FACETS	0.285	0.235	0.341	0.285	0.235	0.341	SUBCLONAL	1	TRUE	1	0.548460817608579	2		333	486	SUCCESS
AR	367	MSKCC	GRCh37	X	66905929	66905929	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555990485	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	160	375	2	ENST00000374690.3:c.1846C>T	p.Arg616Cys	p.R616C	ENST00000374690	NM_000044.3	616	Cgt/Tgt	3/8	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.548460817608579	2		377	561	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024197	31024197	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	183	477	0	ENST00000375687.4:c.3682G>T	p.Glu1228Ter	p.E1228*	ENST00000375687	NM_015338.5	1228	Gaa/Taa	13/13	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.548460817608579	2		477	610	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198480	108198481	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	133	305	0	ENST00000278616.4:c.7088dup	p.Ala2364GlyfsTer9	p.A2364Gfs*9	ENST00000278616	NM_000051.3	2362	gaa/gAaa	48/63	1	2	FACETS	0.931	0.85	1	0.931	0.85	1	CLONAL	1	TRUE	1	0.548460817608579	2		305	521	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22417945	22417945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553196539	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	93	246	0	ENST00000344548.3:c.511G>A	p.Glu171Lys	p.E171K	ENST00000344548	NM_001039802.1	171	Gaa/Aaa	7/7	1	2	FACETS	0.953	0.854	1	0.953	0.854	1	CLONAL	1	TRUE	1	0.548460817608579	2		246	356	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733623	85733623	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1443772574	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	190	412	0	ENST00000370580.1:c.389C>T	p.Thr130Met	p.T130M	ENST00000370580	NM_003921.4	130	aCg/aTg	3/3	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.548460817608579	2		412	624	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958589	175958589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	141	348	0	ENST00000367669.3:c.1756C>T	p.Arg586Cys	p.R586C	ENST00000367669	NM_022457.5	586	Cgt/Tgt	16/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.548460817608579	2		348	490	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230459181	230459181	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138064546	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	151	501	0	ENST00000391860.1:c.1220C>T	p.Pro407Leu	p.P407L	ENST00000391860	NM_001258311.1	407	cCg/cTg	7/7	1	2	FACETS	0.949	0.872	1	0.949	0.872	1	CLONAL	1	TRUE	1	0.548460817608579	2		501	580	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10800360	10800360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758492695	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	227	537	0	ENST00000361367.2:c.3230G>A	p.Arg1077Gln	p.R1077Q	ENST00000361367	NM_014633.3	1077	cGa/cAa	25/25	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.548460817608579	2		537	726	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656239	18656239	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	178	401	0	ENST00000266497.5:c.2918C>A	p.Ala973Asp	p.A973D	ENST00000266497		973	gCt/gAt	21/31	1	2	FACETS	0.983	0.91	1	0.983	0.91	1	CLONAL	1	TRUE	1	0.548460817608579	2		401	660	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914532	32914532	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	192	452	0	ENST00000380152.3:c.6040G>A	p.Val2014Ile	p.V2014I	ENST00000380152		2014	Gta/Ata	11/27	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.548460817608579	2		452	682	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32931925	32931925	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	175	389	0	ENST00000380152.3:c.7664A>C	p.Lys2555Thr	p.K2555T	ENST00000380152		2555	aAa/aCa	16/27	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.548460817608579	2		389	570	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50733601	50733601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	128	336	0	ENST00000307179.4:c.160C>T	p.Arg54Cys	p.R54C	ENST00000307179		54	Cgt/Tgt	3/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.548460817608579	2		336	411	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649214	23649214	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	172	380	0	ENST00000261584.4:c.168T>G	p.Asp56Glu	p.D56E	ENST00000261584	NM_024675.3	56	gaT/gaG	3/13	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.548460817608579	2		380	543	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533316	29533316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1466678870	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	200	446	0	ENST00000356175.3:c.1319G>A	p.Arg440Gln	p.R440Q	ENST00000356175	NM_000267.3	440	cGa/cAa	12/57	1	2	FACETS	0.992	0.922	1	0.992	0.922	1	CLONAL	1	TRUE	1	0.548460817608579	2		446	735	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678240	58678240	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	175	480	0	ENST00000305921.3:c.465G>T	p.Lys155Asn	p.K155N	ENST00000305921	NM_003620.3	155	aaG/aaT	1/6	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.548460817608579	2		480	625	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505343	25505343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	172	487	0	ENST00000264709.3:c.415C>T	p.Pro139Ser	p.P139S	ENST00000264709	NM_175629.2	139	Ccc/Tcc	4/23	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.548460817608579	2		487	576	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114573	73114573	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	127	332	0	ENST00000356692.5:c.954G>T	p.Met318Ile	p.M318I	ENST00000356692		318	atG/atT	9/9	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.548460817608579	2		332	428	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156509	106156509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	178	540	0	ENST00000380013.4:c.1410C>A	p.Cys470Ter	p.C470*	ENST00000380013	NM_001127208.2	470	tgC/tgA	3/11	1	2	FACETS	0.978	0.904	1	0.978	0.904	1	CLONAL	1	TRUE	1	0.548460817608579	2		540	664	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177606	56177606	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1561199421	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	198	474	0	ENST00000399503.3:c.2579C>A	p.Ala860Glu	p.A860E	ENST00000399503	NM_005921.1	860	gCa/gAa	14/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.548460817608579	2		474	694	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131926973	131926973	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	121	333	0	ENST00000265335.6:c.1510G>T	p.Val504Leu	p.V504L	ENST00000265335		504	Gta/Tta	10/25	1	2	FACETS	0.923	0.839	1	0.923	0.839	1	CLONAL	1	TRUE	1	0.548460817608579	2		333	478	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036951	180036951	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	142	527	0	ENST00000261937.6:c.3761C>G	p.Thr1254Arg	p.T1254R	ENST00000261937	NM_182925.4	1254	aCa/aGa	28/30	1	2	FACETS	0.896	0.82	0.975	0.896	0.82	0.975	CLONAL	1	TRUE	1	0.548460817608579	2		527	578	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64286856	64286856	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	139	348	0	ENST00000370651.3:c.71A>C	p.Asn24Thr	p.N24T	ENST00000370651	NM_003463.4	24	aAt/aCt	2/6	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.548460817608579	2		348	489	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793788	89793788	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	178	459	0	ENST00000336032.3:c.857A>T	p.Asp286Val	p.D286V	ENST00000336032	NM_006813.2	286	gAt/gTt	2/2	1	2	FACETS	0.919	0.85	0.991	0.919	0.85	0.991	CLONAL	1	TRUE	1	0.548460817608579	2		459	706	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265336	152265336	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	152	419	0	ENST00000206249.3:c.789A>C	p.Arg263Ser	p.R263S	ENST00000206249	NM_000125.3	263	agA/agC	4/8	1	2	FACETS	0.978	0.899	1	0.978	0.899	1	CLONAL	1	TRUE	1	0.548460817608579	2		419	567	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38194883	38194883	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	198	358	0	ENST00000317025.8:c.850T>C	p.Trp284Arg	p.W284R	ENST00000317025	NM_023034.1	284	Tgg/Cgg	4/24	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.548460817608579	2		358	638	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53253972	53253972	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	194	550	0	ENST00000375401.3:c.100A>G	p.Ile34Val	p.I34V	ENST00000375401	NM_004187.3	34	Atc/Gtc	1/26	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.548460817608579	2		550	606	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937978	76937978	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1569538903	NA	P-0060589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	159	473	0	ENST00000373344.5:c.2770C>A	p.Leu924Ile	p.L924I	ENST00000373344	NM_000489.3	924	Ctt/Att	9/35	1	2	FACETS	0.909	0.836	0.984	0.909	0.836	0.984	CLONAL	1	TRUE	1	0.548460817608579	2		473	638	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0060590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	566	672	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	0.645572983002686	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	1	0.695186588997449	3		672	984	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091782	29091782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373073383	NA	P-0060590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	92	335	0	ENST00000328354.6:c.1175C>T	p.Ala392Val	p.A392V	ENST00000328354	NM_007194.3	392	gCg/gTg	11/15	0.643456866927911	2	FACETS	0.966	0.896	1	0.966	0.896	1	CLONAL	2	TRUE	0	0.695186588997449	2		335	137	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110566	4110566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397517413	NA	P-0060590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	141	674	2	ENST00000262948.5:c.391G>A	p.Val131Met	p.V131M	ENST00000262948	NM_030662.3	131	Gtg/Atg	3/11	0.56569231665735	3	FACETS	0.773	0.706	0.844	0.387	0.353	0.422	SUBCLONAL	1	TRUE	1	0.695186588997449	3		676	707	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577544	7577544	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587780074	NA	P-0060590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	264	523	0	ENST00000269305.4:c.737T>G	p.Met246Arg	p.M246R	ENST00000269305	NM_001126112.2	246	aTg/aGg	7/11	0.679911889594078	2	FACETS	0.986	0.945	1	0.986	0.945	1	CLONAL	2	TRUE	0	0.695186588997449	2		523	385	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261208	16261208	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779552895	NA	P-0060606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	79	633	0	ENST00000375759.3:c.8473G>A	p.Glu2825Lys	p.E2825K	ENST00000375759	NM_015001.2	2825	Gaa/Aaa	11/15	0.416894764893271	3	FACETS	0.564	0.495	0.638	0.282	0.247	0.319	SUBCLONAL	1	TRUE	1	0.416894764893271	3		633	812	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs864622237	NA	P-0060606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	233	472	0	ENST00000269305.4:c.700T>C	p.Tyr234His	p.Y234H	ENST00000269305	NM_001126112.2	234	Tac/Cac	7/11	0.416894764893271	3	FACETS	1	0.963	1			1	CLONAL	2	TRUE	NA	0.416894764893271	3		472	652	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508389	106508389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758375337	NA	P-0060606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	30	362	1	ENST00000359195.3:c.383C>T	p.Thr128Met	p.T128M	ENST00000359195	NM_002649.2	128	aCg/aTg	2/11	0.195152086808312	2	FACETS	0.241	0.193	0.295	0.121	0.096	0.148	INDETERMINATE	1	TRUE	0	0.416894764893271	2		363	597	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207120	1207120	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	273	634	0	ENST00000326873.7:c.208G>T	p.Glu70Ter	p.E70*	ENST00000326873	NM_000455.4	70	Gag/Tag	1/10	0.0867784588380576	4	FACETS	1	0.978	1			1	INDETERMINATE	2	TRUE	NA	0.416894764893271	4		634	861	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	147	460	0	ENST00000267101.3:c.273G>A	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atA	3/28	0.416894764893271	3	FACETS	1	0.953	1	0.533	0.486	0.581	CLONAL	1	TRUE	1	0.416894764893271	3		460	800	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207081	1207081	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs137854584	NA	P-0060606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	274	655	0	ENST00000326873.7:c.169G>T	p.Glu57Ter	p.E57*	ENST00000326873	NM_000455.4	57	Gaa/Taa	1/10	0.0867784588380576	4	FACETS	1	0.979	1			1	INDETERMINATE	2	TRUE	NA	0.416894764893271	4		655	860	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212215	36212215	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1010777622	NA	P-0060606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	127	520	0	ENST00000222270.7:c.1966G>A	p.Glu656Lys	p.E656K	ENST00000222270	NM_014727.1	656	Gaa/Aaa	3/37	0.142072703863394	6	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.416894764893271	6		520	753	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264403	16264403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61756184	NA	P-0060606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	100	599	0	ENST00000375759.3:c.10606C>T	p.Arg3536Trp	p.R3536W	ENST00000375759	NM_015001.2	3536	Cgg/Tgg	13/15	0.416894764893271	3	FACETS	0.725	0.647	0.807	0.362	0.323	0.404	SUBCLONAL	1	TRUE	1	0.416894764893271	3		599	800	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389219	31389219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	120	528	0	ENST00000328111.2:c.2132C>T	p.Ser711Leu	p.S711L	ENST00000328111	NM_006892.3	711	tCa/tTa	19/23	0.406316530714809	5	FACETS	1	0.976	1	0.418	0.377	0.46	CLONAL	1	TRUE	2	0.416894764893271	5		528	747	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075675	8075675	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1185940749	NA	P-0060606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	116	434	0	ENST00000377482.5:c.5C>G	p.Ser2Ter	p.S2*	ENST00000377482	NM_018948.3	2	tCa/tGa	2/4	0.101330364141492	3	FACETS	1	0.97	1	0.59	0.533	0.649	INDETERMINATE	1	TRUE	1	0.416894764893271	3		434	570	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260343	16260343	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	162	694	0	ENST00000375759.3:c.7608G>C	p.Lys2536Asn	p.K2536N	ENST00000375759	NM_015001.2	2536	aaG/aaC	11/15	0.416894764893271	3	FACETS	1	0.974	1	0.573	0.526	0.622	CLONAL	1	TRUE	1	0.416894764893271	3		694	819	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262035	16262035	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	78	742	0	ENST00000375759.3:c.9300G>T	p.Met3100Ile	p.M3100I	ENST00000375759	NM_015001.2	3100	atG/atT	11/15	0.416894764893271	3	FACETS	0.527	0.462	0.597	0.264	0.231	0.299	SUBCLONAL	1	TRUE	1	0.416894764893271	3		742	858	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437242	110437242	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	43	111	0	ENST00000375856.3:c.1159G>T	p.Gly387Trp	p.G387W	ENST00000375856	NM_003749.2	387	Ggg/Tgg	1/2	0.262809288975368	2	FACETS	1	0.915	1	0.561	0.475	0.652	CLONAL	1	TRUE	0	0.416894764893271	2		111	184	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144104	11144104	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	144	638	0	ENST00000358026.2:c.3685A>T	p.Ile1229Phe	p.I1229F	ENST00000358026	NM_001128849.1	1229	Atc/Ttc	26/36	0.26193843144621	3	FACETS	1	0.97	1	0.379	0.346	0.414	CLONAL	1	TRUE	0	0.416894764893271	3		638	734	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149468	61149468	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	59	472	0	ENST00000295025.8:c.1658C>G	p.Thr553Ser	p.T553S	ENST00000295025	NM_002908.2	553	aCt/aGt	11/11	0.158240966586093	3	FACETS	0.728	0.627	0.837	0.243	0.209	0.279	INDETERMINATE	1	TRUE	0	0.416894764893271	3		472	470	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715394	61715394	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	15	253	0	ENST00000401558.2:c.2219C>G	p.Thr740Arg	p.T740R	ENST00000401558	NM_003400.3	740	aCa/aGa	19/25	0.158240966586093	3	FACETS	0.572	0.421	0.752	0.191	0.14	0.251	INDETERMINATE	1	TRUE	0	0.416894764893271	3		253	152	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44515628	44515628	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	75	469	0	ENST00000291552.4:c.268G>T	p.Glu90Ter	p.E90*	ENST00000291552	NM_006758.2	90	Gag/Tag	5/8	0.416894764893271	4	FACETS	0.942	0.827	1	0.314	0.275	0.356	CLONAL	1	TRUE	1	0.416894764893271	4		469	541	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525953	41525953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	23	351	0	ENST00000263253.7:c.1228G>A	p.Asp410Asn	p.D410N	ENST00000263253	NM_001429.3	410	Gat/Aat	5/31	0.195152086808312	2	FACETS	0.355	0.277	0.445	0.177	0.138	0.223	INDETERMINATE	1	TRUE	0	0.416894764893271	2		351	311	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696232	52696232	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	104	487	0	ENST00000394830.3:c.445A>G	p.Asn149Asp	p.N149D	ENST00000394830	NM_018313.4	149	Aat/Gat	5/30	0.26193843144621	3	FACETS	1	0.979	1	0.451	0.406	0.498	CLONAL	1	TRUE	0	0.416894764893271	3		487	446	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902406	1902406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	93	496	0	ENST00000382891.5:c.25C>T	p.Pro9Ser	p.P9S	ENST00000382891	NM_133335.3	9	Ccc/Tcc	2/22	0.363426286200261	1	FACETS	0.748	0.668	0.833	0.748	0.668	0.833	SUBCLONAL	1	TRUE	0	0.416894764893271	1		496	472	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796339	57796339	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	72	407	0	ENST00000309042.7:c.1315G>C	p.Asp439His	p.D439H	ENST00000309042	NM_005612.4	439	Gat/Cat	4/4	0.216339806689801	3	FACETS	1	0.96	1	0.61	0.537	0.688	INDETERMINATE	1	TRUE	1	0.416894764893271	3		407	342	SUCCESS
REST	5978	MSKCC	GRCh37	4	57797936	57797936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	44	510	0	ENST00000309042.7:c.2912C>T	p.Ser971Leu	p.S971L	ENST00000309042	NM_005612.4	971	tCa/tTa	4/4	0.216339806689801	3	FACETS	0.481	0.403	0.568	0.241	0.201	0.284	INDETERMINATE	1	TRUE	1	0.416894764893271	3		510	530	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557939	187557939	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	49	609	0	ENST00000441802.2:c.3772G>T	p.Glu1258Ter	p.E1258*	ENST00000441802	NM_005245.3	1258	Gaa/Taa	5/27	0.416894764893271	1	FACETS	0.421	0.357	0.491	0.421	0.357	0.491	SUBCLONAL	1	TRUE	0	0.416894764893271	1		609	442	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140935	37140935	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	51	578	0	ENST00000373509.5:c.771G>C	p.Gln257His	p.Q257H	ENST00000373509	NM_002648.3	257	caG/caC	5/6	0.264598547699895	5	FACETS	0.463	0.392	0.541	0.093	0.078	0.109	SUBCLONAL	1	TRUE	0	0.416894764893271	5		578	859	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519210	137519210	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	102	468	0	ENST00000367739.4:c.1428G>C	p.Leu476Phe	p.L476F	ENST00000367739	NM_000416.2	476	ttG/ttC	7/7	0.314372921448417	3	FACETS	0.826	0.746	0.909	0.551	0.497	0.606	CLONAL	2	TRUE	0	0.416894764893271	3		468	358	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444428	50444428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	35	544	0	ENST00000331340.3:c.358G>A	p.Asp120Asn	p.D120N	ENST00000331340	NM_006060.4	120	Gat/Aat	4/8	0.262809288975368	2	FACETS	0.245	0.2	0.296	0.123	0.1	0.148	SUBCLONAL	1	TRUE	0	0.416894764893271	2		544	685	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949698	151949698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	22	443	0	ENST00000262189.6:c.1402C>T	p.Pro468Ser	p.P468S	ENST00000262189	NM_170606.2	468	Ccc/Tcc	10/59	0.195152086808312	2	FACETS	0.348	0.27	0.439	0.174	0.135	0.22	INDETERMINATE	1	TRUE	0	0.416894764893271	2		443	303	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913284	39913284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060606-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	48	288	0	ENST00000378444.4:c.4831G>A	p.Glu1611Lys	p.E1611K	ENST00000378444	NM_001123385.1	1611	Gaa/Aaa	14/15	0.118081986106322	2	FACETS	0.843	0.718	0.979			1	INDETERMINATE	1	TRUE	NA	0.416894764893271	2		288	273	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0060608-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	129	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.23	2		334	961	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0060608-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1409	165	729	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.912	0.834	0.993	0.912	0.834	0.993	CLONAL	1	TRUE	1	0.23	2		729	1574	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658393	206658393	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060608-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1596	226	694	0	ENST00000367120.3:c.1487G>T	p.Arg496Met	p.R496M	ENST00000367120	NM_014002.3	496	aGg/aTg	14/22	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.23	2		694	1822	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974758	21974759	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0060608-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1525	199	785	0	ENST00000304494.5:c.67_68dup	p.Arg24ValfsTer3	p.R24Vfs*3	ENST00000304494	NM_000077.4	23	ggt/ggGGt	1/3	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.23	2		785	1724	SUCCESS
ATM	472	MSKCC	GRCh37	11	108128323	108128323	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060609-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	74	210	0	ENST00000278616.4:c.2366A>G	p.Asn789Ser	p.N789S	ENST00000278616	NM_000051.3	789	aAc/aGc	15/63	0.385266558244763	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.398287781876745	1		210	282	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436677	52436677	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060609-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	220	529	0	ENST00000460680.1:c.1997G>C	p.Arg666Thr	p.R666T	ENST00000460680	NM_004656.3	666	aGa/aCa	16/17	0.33081835377355	2	FACETS	0.856	0.801	0.913	0.856	0.801	0.913	CLONAL	2	TRUE	0	0.398287781876745	2		529	645	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702571	52702571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060609-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	85	279	0	ENST00000394830.3:c.327del	p.Asn110IlefsTer3	p.N110Ifs*3	ENST00000394830	NM_018313.4	109	gtT/gt	4/30	0.33081835377355	2	FACETS	1	0.955	1	0.571	0.508	0.637	CLONAL	1	TRUE	0	0.398287781876745	2		279	374	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0060610-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	263	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.417633011748653	4	FACETS	0.984	0.931	1	0.984	0.931	1	CLONAL	3	TRUE	1	0.434659518230875	4		334	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0060610-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	176	506	0	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	0.434659518230875	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.434659518230875	1		506	617	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210674	2210674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	632	856	0	ENST00000398665.3:c.1171C>T	p.Pro391Ser	p.P391S	ENST00000398665	NM_032482.2	391	Ccc/Tcc	14/28	1	2	FACETS	0.915	0.882	0.948	0.915	0.882	0.948	CLONAL	1	TRUE	1	0.935645531242747	2		856	1476	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162688926	162688926	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	233	394	0	ENST00000367921.3:c.73G>T	p.Val25Phe	p.V25F	ENST00000367921	NM_006182.2	25	Gtt/Ttt	3/18	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.935645531242747	2		394	472	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951052	48951052	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0060611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	64	265	0	ENST00000267163.4:c.1216-2A>G		p.X406_splice	ENST00000267163	NM_000321.2	406			0.935645531242747	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.935645531242747	1		265	69	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	753	748	0	ENST00000269305.4:c.856del	p.Glu286LysfsTer59	p.E286Kfs*59	ENST00000269305	NM_001126112.2	286	Gaa/aa	8/11	0.935645531242747	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.935645531242747	1		748	798	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121536	193121536	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1425016725	NA	P-0060611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	87	320	0	ENST00000367435.3:c.934A>G	p.Met312Val	p.M312V	ENST00000367435	NM_024529.4	312	Atg/Gtg	10/17	1	2	FACETS	0.949	0.86	1	0.949	0.86	1	CLONAL	1	TRUE	1	0.935645531242747	2		320	196	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851995	63851995	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	74	686	0	ENST00000279873.7:c.2773G>T	p.Ala925Ser	p.A925S	ENST00000279873	NM_032199.2	925	Gct/Tct	10/10	1	2	FACETS	0.135	0.118	0.155	0.135	0.118	0.155	SUBCLONAL	1	TRUE	1	0.935645531242747	2		686	1168	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589669	69589669	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	971	1200	0	ENST00000168712.1:c.184G>T	p.Ala62Ser	p.A62S	ENST00000168712	NM_002007.2	62	Gcg/Tcg	1/3	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.935645531242747	2		1200	1916	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390456	118390456	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs564690648	NA	P-0060611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	522	721	0	ENST00000534358.1:c.11270A>G	p.Asn3757Ser	p.N3757S	ENST00000534358	NM_005933.3	3757	aAt/aGt	32/36	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.935645531242747	2		721	1102	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123880979	123880979	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	324	435	0	ENST00000330479.4:c.597G>T	p.Gln199His	p.Q199H	ENST00000330479	NM_020382.3	199	caG/caT	5/9	1	2	FACETS	0.967	0.92	1	0.967	0.92	1	CLONAL	1	TRUE	1	0.935645531242747	2		435	716	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21347187	21347187	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	625	687	0	ENST00000215739.8:c.1254G>T	p.Arg418Ser	p.R418S	ENST00000215739	NM_006767.3	418	agG/agT	11/21	0.935645531242747	2	FACETS	1	0.994	1	0.564	0.545	0.582	CLONAL	1	TRUE	0	0.935645531242747	2		687	1185	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609774	117609774	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060611-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	276	533	2	ENST00000368508.3:c.6925C>A	p.Pro2309Thr	p.P2309T	ENST00000368508	NM_002944.2	2309	Cca/Aca	43/43	0.220347300874327	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.935645531242747	0		535	584	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0060612-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	18	436	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.168507240959718	2	FACETS	0.311	0.233	0.405	0.156	0.116	0.203	SUBCLONAL	1	TRUE	0	0.168507240959718	2		436	686	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0060612-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	131	690	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	NA	2	FACETS	0.765	0.693	0.841			1	INDETERMINATE	2	TRUE	NA	0.168507240959718	2		690	1016	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024029	27024029	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060612-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	43	327	0	ENST00000324856.7:c.1135C>T	p.Gln379Ter	p.Q379*	ENST00000324856	NM_006015.4	379	Cag/Tag	1/20	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.168507240959718	2		327	425	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230492933	230492933	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768168936	NA	P-0060612-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	92	620	0	ENST00000391860.1:c.121G>A	p.Asp41Asn	p.D41N	ENST00000391860	NM_001258311.1	41	Gac/Aac	2/7	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.168507240959718	2		620	865	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246386	46246393	+	frameshift_variant	Frame_Shift_Del	DEL	TCCCATTC	TCCCATTC	-	novel	NA	P-0060612-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	147	598	0	ENST00000334344.6:c.4483_4490del	p.His1495CysfsTer5	p.H1495Cfs*5	ENST00000334344	NM_152641.2	1494	TCCCATTCt/t	15/21	0.168507240959718	3	FACETS	1	0.961	1	0.728	0.665	0.795	CLONAL	2	TRUE	0	0.168507240959718	3		598	866	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964104	28964104	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060612-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	39	498	0	ENST00000282397.4:c.1798A>G	p.Met600Val	p.M600V	ENST00000282397	NM_002019.4	600	Atg/Gtg	13/30	0.130929174450658	2	FACETS	0.756	0.626	0.903	0.378	0.313	0.452	CLONAL	1	TRUE	0	0.168507240959718	2		498	612	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221228	5221228	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774511967	NA	P-0060612-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	122	650	0	ENST00000357368.4:c.3238C>T	p.Arg1080Cys	p.R1080C	ENST00000357368	NM_002850.3	1080	Cgt/Tgt	20/38	0.130929174450658	2	FACETS	0.881	0.796	0.97	0.881	0.796	0.97	CLONAL	2	TRUE	0	0.168507240959718	2		650	822	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0060620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	662	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.517553108241941	6	FACETS	0.983	0.96	1	0.983	0.96	1	CLONAL	6	TRUE	0	0.540121897878148	6		334	865	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934576	NA	P-0060620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	623	671	1	ENST00000269305.4:c.818G>C	p.Arg273Pro	p.R273P	ENST00000269305	NM_001126112.2	273	cGt/cCt	8/11	0.527493770157024	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.540121897878148	2		672	1138	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180951	32180951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs978741176	NA	P-0060620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	239	670	0	ENST00000375023.3:c.2399C>T	p.Pro800Leu	p.P800L	ENST00000375023	NM_004557.3	800	cCg/cTg	15/30	1	2	FACETS	0.948	0.886	1	0.948	0.886	1	CLONAL	1	TRUE	1	0.540121897878148	2		670	934	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779271	3779271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370704436	NA	P-0060620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	256	722	0	ENST00000262367.5:c.5777G>A	p.Arg1926Gln	p.R1926Q	ENST00000262367	NM_004380.2	1926	cGg/cAg	31/31	0.540121897878148	3	FACETS	0.909	0.849	0.97	0.454	0.424	0.485	CLONAL	1	TRUE	1	0.540121897878148	3		722	1325	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39283913	39283913	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	112	452	0	ENST00000402219.2:c.440A>T	p.Asn147Ile	p.N147I	ENST00000402219	NM_005633.3	147	aAt/aTt	4/23	1	2	FACETS	0.992	0.899	1	0.992	0.899	1	CLONAL	1	TRUE	1	0.540121897878148	2		452	418	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142057	108142057	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs377244521	NA	P-0060620-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	214	554	0	ENST00000278616.4:c.3001C>G	p.Leu1001Val	p.L1001V	ENST00000278616	NM_000051.3	1001	Cta/Gta	20/63	0.540121897878148	3	FACETS	1	0.989	1	0.666	0.62	0.712	CLONAL	1	TRUE	1	0.540121897878148	3		554	756	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	12	759	1				ENST00000310581	NM_198253.2	-/1132			0.205014049388484	1	FACETS	1	0.785	1	1	0.785	1	CLONAL	1	FALSE	0	0.265555849396894	1		760	70	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0060636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	32	932	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.3	4	FACETS	0.947	0.779	1	0.631	0.519	0.755	CLONAL	2	FALSE	1	0.265555849396894	4		932	161	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	15	888	0	ENST00000269571.5:c.829G>C	p.Asp277His	p.D277H	ENST00000269571		277	Gac/Cac	7/27	1	2	FACETS	0.471	0.344	0.623	0.471	0.344	0.623	SUBCLONAL	1	FALSE	1	0.265555849396894	2		888	240	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022540	12022540	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	41	1004	0	ENST00000396373.4:c.646G>A	p.Glu216Lys	p.E216K	ENST00000396373	NM_001987.4	216	Gag/Aag	5/8	0.265555849396894	8	FACETS	0.984	0.824	1	0.492	0.412	0.58	CLONAL	2	FALSE	4	0.265555849396894	8		1004	282	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464409	464409	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	23	372	0	ENST00000399788.2:c.785T>A	p.Val262Asp	p.V262D	ENST00000399788	NM_001042603.1	262	gTc/gAc	7/28	0.174037556626072	1	FACETS	0.988	0.778	1	0.988	0.778	1	CLONAL	1	FALSE	0	0.265555849396894	1		372	152	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873579	37873579	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	31	838	0	ENST00000269571.5:c.1744G>A	p.Asp582Asn	p.D582N	ENST00000269571		582	Gac/Aac	15/27	1	2	FACETS	1	0.829	1	1	0.829	1	CLONAL	1	FALSE	1	0.265555849396894	2		838	229	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651914	36651930	+	frameshift_variant	Frame_Shift_Del	DEL	ATGCGGCAGCAAGGCCT	ATGCGGCAGCAAGGCCT	-	novel	NA	P-0060636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	41	832	0	ENST00000244741.5:c.36_52del	p.Cys13ProfsTer17	p.C13Pfs*17	ENST00000244741	NM_000389.4	12	ccATGCGGCAGCAAGGCCTgc/ccgc	2/3	0.265555849396894	13	FACETS	0.977	0.815	1	0.279	0.232	0.331	CLONAL	2	FALSE	6	0.265555849396894	13		832	389	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652051	36652051	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	20	892	0	ENST00000244741.5:c.173C>G	p.Pro58Arg	p.P58R	ENST00000244741	NM_000389.4	58	cCa/cGa	2/3	0.265555849396894	13	FACETS	1	0.807	1	0.152	0.116	0.195	CLONAL	1	FALSE	6	0.265555849396894	13		892	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0060648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	214	919	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.604166898470822	1	FACETS	0.984	0.925	1	0.984	0.925	1	CLONAL	1	TRUE	0	0.622662123860705	1		919	481	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037865	49037865	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0060648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	33	151	0	ENST00000267163.4:c.2107-2A>G		p.X703_splice	ENST00000267163	NM_000321.2	703			0.622662123860705	1	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	0	0.622662123860705	1		151	70	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969974	161969974	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	166	465	0	ENST00000366898.1:c.995G>T	p.Cys332Phe	p.C332F	ENST00000366898	NM_004562.2	332	tGc/tTc	9/12	1	2	FACETS	0.998	0.923	1	0.998	0.923	1	CLONAL	1	TRUE	1	0.622662123860705	2		465	534	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	68	759	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.723	0.636	0.816	0.723	0.636	0.816	SUBCLONAL	1	TRUE	1	0.673883929375544	2		760	279	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0060649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	173	195	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	0.673883929375544	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.673883929375544	1		195	285	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597858	43597858	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs79014735	NA	P-0060649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	157	737	0	ENST00000355710.3:c.406G>A	p.Glu136Lys	p.E136K	ENST00000355710	NM_020975.4	136	Gag/Aag	3/20	0.673883929375544	1	FACETS	0.842	0.782	0.902	0.842	0.782	0.902	CLONAL	1	TRUE	0	0.673883929375544	1		737	367	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926910	112926910	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	135	341	0	ENST00000351677.2:c.1530G>T	p.Gln510His	p.Q510H	ENST00000351677	NM_002834.3	510	caG/caT	13/16	1	2	FACETS	0.803	0.734	0.874	0.803	0.734	0.874	CLONAL	1	TRUE	1	0.673883929375544	2		341	499	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	46	759	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.863	0.743	0.988	0.863	0.743	0.988	CLONAL	1	TRUE	1	0.784126731396557	2		760	136	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0060650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	53	558	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.140920806978859	4	FACETS	1	0.91	1	1	0.91	1	INDETERMINATE	2	TRUE	2	0.784126731396557	4		558	116	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0060650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	133	494	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.478299137772473	1	FACETS	0.724	0.669	0.778	0.724	0.669	0.778	SUBCLONAL	1	TRUE	0	0.784126731396557	1		494	285	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374828	149374828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	43	335	0	ENST00000360632.3:c.266C>T	p.Ser89Leu	p.S89L	ENST00000360632	NM_015472.4	89	tCg/tTg	2/7	0.140920806978859	4	FACETS	0.588	0.493	0.691	0.294	0.246	0.346	INDETERMINATE	1	TRUE	2	0.784126731396557	4		335	333	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413079	139413079	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	22	408	0	ENST00000277541.6:c.1063G>C	p.Ala355Pro	p.A355P	ENST00000277541	NM_017617.3	355	Gcc/Ccc	6/34	1	2	FACETS	0.188	0.146	0.238	0.188	0.146	0.238	SUBCLONAL	1	TRUE	1	0.784126731396557	2		408	298	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564855	226564855	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138228205	NA	P-0060650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	47	345	0	ENST00000366794.5:c.1895C>T	p.Thr632Met	p.T632M	ENST00000366794	NM_001618.3	632	aCg/aTg	13/23	1	2	FACETS	0.504	0.429	0.585	0.504	0.429	0.585	SUBCLONAL	1	TRUE	1	0.784126731396557	2		345	238	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139438540	139438540	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1217905346	NA	P-0060650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	44	403	1	ENST00000277541.6:c.76C>T	p.Gln26Ter	p.Q26*	ENST00000277541	NM_017617.3	26	Cag/Tag	2/34	1	2	FACETS	0.342	0.288	0.402	0.342	0.288	0.402	SUBCLONAL	1	TRUE	1	0.784126731396557	2		404	328	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599066	28599066	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	61	286	0	ENST00000241453.7:c.2222G>A	p.Arg741Lys	p.R741K	ENST00000241453	NM_004119.2	741	aGa/aAa	18/24	0.239798861288355	1	FACETS	0.57	0.502	0.64	0.57	0.502	0.64	INDETERMINATE	1	TRUE	0	0.784126731396557	1		286	166	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868168	56868181	+	splice_donor_variant,intron_variant	Splice_Site	DEL	TAACATTTGCTTTT	TAACATTTGCTTTT	-	novel	NA	P-0060650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	18	362	0	ENST00000308159.5:c.1664+2_1664+15del		p.X555_splice	ENST00000308159	NM_014669.4	555			1	2	FACETS	0.14	0.105	0.181	0.14	0.105	0.181	SUBCLONAL	1	TRUE	1	0.784126731396557	2		362	329	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936585	49936585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	16	472	0	ENST00000296474.3:c.1342G>A	p.Val448Ile	p.V448I	ENST00000296474	NM_002447.2	448	Gtc/Atc	2/20	0.478299137772473	1	FACETS	0.101	0.074	0.133	0.101	0.074	0.133	SUBCLONAL	1	TRUE	0	0.784126731396557	1		472	246	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031735	69031735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	27	324	0	ENST00000288368.4:c.3490C>T	p.His1164Tyr	p.H1164Y	ENST00000288368	NM_024870.2	1164	Cat/Tat	28/40	1	2	FACETS	0.266	0.212	0.327	0.266	0.212	0.327	SUBCLONAL	1	TRUE	1	0.784126731396557	2		324	259	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97934338	97934338	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	25	187	0	ENST00000289081.3:c.437A>G	p.Tyr146Cys	p.Y146C	ENST00000289081	NM_000136.2	146	tAt/tGt	5/15	1	2	FACETS	0.425	0.339	0.522	0.425	0.339	0.522	SUBCLONAL	1	TRUE	1	0.784126731396557	2		187	150	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970978	21970979	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	TA	novel	NA	P-0060650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	306	551	0	ENST00000304494.5:c.379_380delinsTA	p.Ala127Ter	p.A127*	ENST00000304494	NM_000077.4	127	GCa/TAa	2/3	0.784126731396557	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.784126731396557	2		551	377	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023559	27023560	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0060652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	54	514	0	ENST00000324856.7:c.671dup	p.Pro225AlafsTer175	p.P225Afs*175	ENST00000324856	NM_006015.4	222	tac/taCc	1/20	NA	2	FACETS	0.919	0.793	1			1	INDETERMINATE	1	TRUE	NA	0.489697656553565	2		514	240	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436128	56436128	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	115	560	0	ENST00000407977.2:c.1009C>T	p.Arg337Ter	p.R337*	ENST00000407977		337	Cga/Tga	9/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.489697656553565	2		560	385	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891187	101891187	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	36	386	0	ENST00000374994.4:c.148A>G	p.Thr50Ala	p.T50A	ENST00000374994	NM_004612.2	50	Aca/Gca	2/9	0.435564020146322	1	FACETS	0.355	0.292	0.424	0.355	0.292	0.424	SUBCLONAL	1	TRUE	0	0.489697656553565	1		386	313	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0060652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	97	438	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.101685799274748	4	FACETS	0.878	0.791	0.969	0.878	0.791	0.969	INDETERMINATE	2	TRUE	2	0.489697656553565	4		438	336	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266558	115266558	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1570897128	NA	P-0060652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	21	400	0	ENST00000438362.2:c.1957A>G	p.Ser653Gly	p.S653G	ENST00000438362	NM_001242891.1	653	Agt/Ggt	16/20	0.465416235626347	1	FACETS	0.219	0.168	0.278	0.219	0.168	0.278	SUBCLONAL	1	TRUE	0	0.489697656553565	1		400	296	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199771	108199771	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0060652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	66	383	0	ENST00000278616.4:c.7113T>G	p.Tyr2371Ter	p.Y2371*	ENST00000278616	NM_000051.3	2371	taT/taG	49/63	0.469340800273101	1	FACETS	0.934	0.823	1	0.934	0.823	1	CLONAL	1	TRUE	0	0.489697656553565	1		383	218	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0060654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	112	672	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	0.2371651874348	3	FACETS	0.951	0.858	1	0.951	0.858	1	CLONAL	2	TRUE	1	0.237034316597757	3		672	556	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660469	67660469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	28	288	0	ENST00000264010.4:c.1369C>T	p.Arg457Ter	p.R457*	ENST00000264010	NM_006565.3	457	Cga/Tga	8/12	0.2371651874348	3	FACETS	0.692	0.553	0.85	0.346	0.276	0.425	SUBCLONAL	1	TRUE	1	0.237034316597757	3		288	382	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0060654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	140	603	1	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	0.2371651874348	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	1	0.237034316597757	3		604	634	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0060654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	99	937	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	0.203797506784582	2	FACETS	0.962	0.864	1	0.962	0.864	1	CLONAL	2	TRUE	0	0.237034316597757	2		937	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578397	7578397	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1555526004	NA	P-0060654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	148	566	0	ENST00000269305.4:c.533A>C	p.His178Pro	p.H178P	ENST00000269305	NM_001126112.2	178	cAc/cCc	5/11	0.200586480438041	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.237034316597757	2		566	554	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879580	37879580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	134	474	0	ENST00000269571.5:c.1955C>T	p.Thr652Met	p.T652M	ENST00000269571		652	aCg/aTg	17/27	0.2371651874348	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.237034316597757	3		474	548	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437518	52437518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779877855	NA	P-0060654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	133	585	0	ENST00000460680.1:c.1643G>A	p.Arg548His	p.R548H	ENST00000460680	NM_004656.3	548	cGt/cAt	13/17	0.180015678500488	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.237034316597757	4		585	622	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398255	25398255	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913236	NA	P-0060654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	72	283	0	ENST00000311936.3:c.64C>A	p.Gln22Lys	p.Q22K	ENST00000311936	NM_004985.3	22	Cag/Aag	2/5	0.237034316597757	5	FACETS	0.887	0.787	0.992	0.887	0.787	0.992	CLONAL	4	TRUE	1	0.237034316597757	5		283	232	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918198	50918198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	78	597	0	ENST00000440232.2:c.2515C>T	p.Leu839Phe	p.L839F	ENST00000440232	NM_002691.3	839	Ctc/Ttc	20/27	0.2371651874348	3	FACETS	1	0.973	1	0.697	0.614	0.786	CLONAL	1	TRUE	1	0.237034316597757	3		597	528	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0060660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	129	446	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	1	2	FACETS	0.944	0.859	1	0.944	0.859	1	CLONAL	1	TRUE	1	0.458732883701064	2		446	596	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0060660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	78	395	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.833	0.736	0.937	0.833	0.736	0.937	CLONAL	1	TRUE	1	0.458732883701064	2		395	408	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0060660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	173	693	2	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.458732883701064	1	FACETS	0.86	0.794	0.928	0.86	0.794	0.928	CLONAL	1	TRUE	0	0.458732883701064	1		695	676	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0060660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	129	481	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.883	0.803	0.967	0.883	0.803	0.967	CLONAL	1	TRUE	1	0.458732883701064	2		481	637	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0060660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	60	165	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.805	0.698	0.92	0.805	0.698	0.92	CLONAL	1	TRUE	1	0.458732883701064	2		165	325	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575209	48575209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767326	NA	P-0060660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	89	272	0	ENST00000342988.3:c.403C>T	p.Arg135Ter	p.R135*	ENST00000342988	NM_005359.5	135	Cga/Tga	3/12	0.458732883701064	1	FACETS	0.893	0.799	0.991	0.893	0.799	0.991	CLONAL	1	TRUE	0	0.458732883701064	1		272	335	SUCCESS
AR	367	MSKCC	GRCh37	X	66766207	66766207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	139	481	0	ENST00000374690.3:c.1219C>T	p.Arg407Cys	p.R407C	ENST00000374690	NM_000044.3	407	Cgc/Tgc	1/8	1	2	FACETS	0.921	0.841	1	0.921	0.841	1	CLONAL	1	TRUE	1	0.458732883701064	2		481	658	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117173	7117173	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764041031	NA	P-0060660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	144	501	0	ENST00000302850.5:c.4043C>T	p.Ser1348Leu	p.S1348L	ENST00000302850	NM_000208.2	1348	tCg/tTg	22/22	1	2	FACETS	0.896	0.818	0.976	0.896	0.818	0.976	CLONAL	1	TRUE	1	0.458732883701064	2		501	701	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023144	31023144	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	142	544	0	ENST00000375687.4:c.2629G>T	p.Glu877Ter	p.E877*	ENST00000375687	NM_015338.5	877	Gaa/Taa	13/13	1	2	FACETS	0.942	0.861	1	0.942	0.861	1	CLONAL	1	TRUE	1	0.458732883701064	2		544	657	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347856	128347856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	218	361	0	ENST00000265960.3:c.649G>A	p.Glu217Lys	p.E217K	ENST00000265960	NM_001006617.1	217	Gaa/Aaa	5/12	0.401416564801766	3	FACETS	0.942	0.882	1	0.942	0.882	1	CLONAL	2	TRUE	1	0.458732883701064	3		361	620	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679799	88679799	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1467942640	NA	P-0060660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	101	419	1	ENST00000360948.2:c.664C>T	p.Arg222Ter	p.R222*	ENST00000360948	NM_001012338.2	222	Cga/Tga	7/19	1	2	FACETS	0.987	0.888	1	0.987	0.888	1	CLONAL	1	TRUE	1	0.458732883701064	2		420	446	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905267	50905267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs969950434	NA	P-0060660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	175	685	0	ENST00000440232.2:c.475G>A	p.Glu159Lys	p.E159K	ENST00000440232	NM_002691.3	159	Gag/Aag	5/27	1	2	FACETS	0.9	0.829	0.973	0.9	0.829	0.973	CLONAL	1	TRUE	1	0.458732883701064	2		685	848	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983125	201983125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	172	510	0	ENST00000359651.3:c.974C>T	p.Thr325Ile	p.T325I	ENST00000359651		325	aCc/aTc	7/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.458732883701064	2		510	669	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288970	212288970	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	102	368	0	ENST00000342788.4:c.2776A>G	p.Thr926Ala	p.T926A	ENST00000342788	NM_005235.2	926	Acg/Gcg	23/28	1	2	FACETS	0.813	0.729	0.901	0.813	0.729	0.901	CLONAL	1	TRUE	1	0.458732883701064	2		368	547	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005302	150005302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	170	606	0	ENST00000253339.5:c.923C>T	p.Ser308Phe	p.S308F	ENST00000253339		308	tCc/tTc	3/7	1	2	FACETS	0.913	0.84	0.988	0.913	0.84	0.988	CLONAL	1	TRUE	1	0.458732883701064	2		606	812	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057230	180057230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780661773	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	75	512	1	ENST00000261937.6:c.508C>T	p.Arg170Cys	p.R170C	ENST00000261937	NM_182925.4	170	Cgc/Tgc	4/30	0.45524658006213	2	FACETS	0.439	0.384	0.498	0.219	0.192	0.249	SUBCLONAL	1	TRUE	0	0.490348634697944	2		513	697	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144589	55144589	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	33	378	0	ENST00000257290.5:c.2063A>C	p.Lys688Thr	p.K688T	ENST00000257290	NM_006206.4	688	aAg/aCg	15/23	1	2	FACETS	0.234	0.19	0.284	0.234	0.19	0.284	SUBCLONAL	1	TRUE	1	0.490348634697944	2		378	575	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372768	81372768	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	225	420	0	ENST00000222390.5:c.766G>T	p.Asp256Tyr	p.D256Y	ENST00000222390	NM_000601.4	256	Gat/Tat	7/18	0.490348634697944	5	FACETS	0.855	0.797	0.915	0.57	0.531	0.61	CLONAL	2	TRUE	2	0.490348634697944	5		420	931	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372707	81372707	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	156	399	0	ENST00000222390.5:c.827C>A	p.Pro276His	p.P276H	ENST00000222390	NM_000601.4	276	cCt/cAt	7/18	0.490348634697944	5	FACETS	1	0.979	1	0.403	0.369	0.439	CLONAL	1	TRUE	2	0.490348634697944	5		399	913	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020477	14020477	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145402255	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	184	432	0	ENST00000311895.7:c.448C>T	p.Arg150Cys	p.R150C	ENST00000311895	NM_005236.2	150	Cgc/Tgc	3/11	0.229620884645349	2	FACETS	1	0.989	1	0.672	0.625	0.721	INDETERMINATE	1	TRUE	0	0.490348634697944	2		432	558	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525927	41525927	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	40	292	0	ENST00000263253.7:c.1202C>A	p.Ser401Ter	p.S401*	ENST00000263253	NM_001429.3	401	tCa/tAa	5/31	0.451052628819199	2	FACETS	0.449	0.374	0.533	0.225	0.187	0.267	SUBCLONAL	1	TRUE	0	0.490348634697944	2		292	363	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023274	27023274	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	139	467	0	ENST00000324856.7:c.380G>C	p.Gly127Ala	p.G127A	ENST00000324856	NM_006015.4	127	gGc/gCc	1/20	1	2	FACETS	0.75	0.683	0.82	0.75	0.683	0.82	SUBCLONAL	1	TRUE	1	0.490348634697944	2		467	756	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46527745	46527745	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	136	239	0	ENST00000262741.5:c.622-2A>T		p.X208_splice	ENST00000262741	NM_003629.3	208			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.490348634697944	2		239	442	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466577	120466577	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	45	463	0	ENST00000256646.2:c.4542A>C	p.Lys1514Asn	p.K1514N	ENST00000256646	NM_024408.3	1514	aaA/aaC	26/34	1	2	FACETS	0.283	0.237	0.334	0.283	0.237	0.334	SUBCLONAL	1	TRUE	1	0.490348634697944	2		463	648	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608412	43608412	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	189	834	0	ENST00000355710.3:c.1759+1G>T		p.X587_splice	ENST00000355710	NM_020975.4	587			0.102109501545018	0	FACETS	0.39	0.36	0.421			1	INDETERMINATE	1	TRUE	0	0.490348634697944	0		834	1008	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77991659	77991659	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	126	486	0	ENST00000361507.4:c.364G>C	p.Glu122Gln	p.E122Q	ENST00000361507	NM_080491.2	122	Gag/Cag	2/10	0.229006834342872	5	FACETS	0.982	0.889	1	0.327	0.296	0.361	INDETERMINATE	1	TRUE	2	0.490348634697944	5		486	908	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125507343	125507343	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	149	242	0	ENST00000428830.2:c.719-1G>A		p.X240_splice	ENST00000428830	NM_001114121.2	240			0.229006834342872	5	FACETS	1	0.955	1	0.705	0.648	0.763	INDETERMINATE	2	TRUE	2	0.490348634697944	5		242	499	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298727	46298727	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	141	322	0	ENST00000334344.6:c.5374A>T	p.Arg1792Ter	p.R1792*	ENST00000334344	NM_152641.2	1792	Aga/Tga	21/21	0.45524658006213	2	FACETS	0.94	0.871	1	0.94	0.871	1	CLONAL	2	TRUE	0	0.490348634697944	2		322	306	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118799	115118799	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	301	535	0	ENST00000257566.3:c.542C>A	p.Pro181Gln	p.P181Q	ENST00000257566	NM_016569.3	181	cCa/cAa	2/8	0.45524658006213	2	FACETS	0.846	0.801	0.89	0.846	0.801	0.89	CLONAL	2	TRUE	0	0.490348634697944	2		535	726	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108043	30108043	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	150	317	0	ENST00000331968.5:c.764G>C	p.Arg255Pro	p.R255P	ENST00000331968	NM_002742.2	255	cGa/cCa	5/18	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.490348634697944	2		317	501	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569714	95569714	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	91	503	1	ENST00000393063.1:c.4019A>T	p.Glu1340Val	p.E1340V	ENST00000393063	NM_030621.3	1340	gAg/gTg	22/28	1	2	FACETS	0.433	0.383	0.485	0.433	0.383	0.485	SUBCLONAL	1	TRUE	1	0.490348634697944	2		504	858	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472437	88472437	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	261	512	0	ENST00000360948.2:c.2118C>G	p.Ser706Arg	p.S706R	ENST00000360948	NM_001012338.2	706	agC/agG	16/19	0.490348634697944	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.490348634697944	1		512	637	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858251	9858251	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	282	572	0	ENST00000330684.3:c.3150G>C	p.Arg1050Ser	p.R1050S	ENST00000330684	NM_001134407.1	1050	agG/agC	13/13	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.490348634697944	2		572	838	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274073	10274073	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	79	572	0	ENST00000330684.3:c.196G>C	p.Asp66His	p.D66H	ENST00000330684	NM_001134407.1	66	Gac/Cac	2/13	1	2	FACETS	0.369	0.323	0.418	0.369	0.323	0.418	SUBCLONAL	1	TRUE	1	0.490348634697944	2		572	874	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347480	89347480	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	431	648	0	ENST00000301030.4:c.5470C>A	p.Pro1824Thr	p.P1824T	ENST00000301030	NM_001256183.1	1824	Ccc/Acc	9/13	0.490348634697944	2	FACETS	0.966	0.926	1	0.966	0.926	1	CLONAL	2	TRUE	0	0.490348634697944	2		648	910	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838090	89838090	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	359	552	0	ENST00000389301.3:c.2147A>T	p.His716Leu	p.H716L	ENST00000389301	NM_000135.2	716	cAc/cTc	23/43	0.490348634697944	2	FACETS	0.945	0.901	0.988	0.945	0.901	0.988	CLONAL	2	TRUE	0	0.490348634697944	2		552	775	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576889	7576904	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTGGCTGGGGAGAG	CTTTGGCTGGGGAGAG	-	novel	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	191	675	0	ENST00000269305.4:c.942_957del	p.Ser315ArgfsTer25	p.S315Rfs*25	ENST00000269305	NM_001126112.2	314	tcCTCTCCCCAGCCAAAG/tc	9/11	0.490348634697944	1	FACETS	0.923	0.858	0.99	0.923	0.858	0.99	CLONAL	1	TRUE	0	0.490348634697944	1		675	637	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679559	33679559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376285868	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	464	518	0	ENST00000308377.4:c.2522C>T	p.Ala841Val	p.A841V	ENST00000308377	NM_152270.3	841	gCa/gTa	5/5	0.381158594706402	3	FACETS	1	0.994	1	0.802	0.769	0.834	CLONAL	2	TRUE	0	0.490348634697944	3		518	980	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761066	59761066	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1603275193	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	43	419	0	ENST00000259008.2:c.3341A>T	p.Gln1114Leu	p.Q1114L	ENST00000259008	NM_032043.2	1114	cAg/cTg	20/20	0.381158594706402	3	FACETS	0.33	0.275	0.391	0.11	0.091	0.131	SUBCLONAL	1	TRUE	0	0.490348634697944	3		419	662	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763304	59763304	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	45	458	0	ENST00000259008.2:c.2798A>G	p.Asn933Ser	p.N933S	ENST00000259008	NM_032043.2	933	aAt/aGt	19/20	0.381158594706402	3	FACETS	0.355	0.297	0.419	0.118	0.099	0.14	SUBCLONAL	1	TRUE	0	0.490348634697944	3		458	644	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955193	17955193	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	229	501	2	ENST00000458235.1:c.34C>A	p.Pro12Thr	p.P12T	ENST00000458235	NM_000215.3	12	Cct/Act	2/24	0.490348634697944	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.490348634697944	1		503	643	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635681	47635681	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	45	290	0	ENST00000233146.2:c.353A>T	p.Tyr118Phe	p.Y118F	ENST00000233146	NM_000251.2	118	tAt/tTt	2/16	0.229620884645349	2	FACETS	0.44	0.37	0.517	0.22	0.185	0.259	INDETERMINATE	1	TRUE	0	0.490348634697944	2		290	417	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499497	89499497	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	279	475	0	ENST00000336596.2:c.2667G>T	p.Lys889Asn	p.K889N	ENST00000336596	NM_005233.5	889	aaG/aaT	15/17	0.45524658006213	2	FACETS	0.859	0.813	0.906	0.859	0.813	0.906	CLONAL	2	TRUE	0	0.490348634697944	2		475	662	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876388	35876388	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	500	583	2	ENST00000303115.3:c.1180G>T	p.Gly394Cys	p.G394C	ENST00000303115	NM_002185.3	394	Ggc/Tgc	8/8	0.490348634697944	5	FACETS	0.956	0.917	0.996	0.956	0.917	0.996	CLONAL	3	TRUE	2	0.490348634697944	5		585	1234	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983910	2983910	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	205	450	0	ENST00000396946.4:c.620G>T	p.Arg207Leu	p.R207L	ENST00000396946	NM_032415.4	207	cGc/cTc	5/25	0.463235535167868	4	FACETS	1	0.977	1	0.377	0.349	0.406	CLONAL	1	TRUE	1	0.490348634697944	4		450	1101	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444413	50444413	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	222	502	0	ENST00000331340.3:c.343G>C	p.Gly115Arg	p.G115R	ENST00000331340	NM_006060.4	115	Gga/Cga	4/8	0.402577560000948	4	FACETS	1	0.987	1	0.415	0.385	0.445	CLONAL	1	TRUE	1	0.490348634697944	4		502	1085	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046431	69046431	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	86	432	0	ENST00000288368.4:c.3904G>C	p.Glu1302Gln	p.E1302Q	ENST00000288368	NM_024870.2	1302	Gaa/Caa	32/40	0.217167589108133	3	FACETS	0.55	0.486	0.619	0.183	0.162	0.207	INDETERMINATE	1	TRUE	0	0.490348634697944	3		432	794	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551426	141551426	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	364	422	0	ENST00000220592.5:c.1871G>T	p.Arg624Leu	p.R624L	ENST00000220592	NM_012154.3	624	cGc/cTc	15/19	0.490348634697944	2	FACETS	0.949	0.906	0.993	0.949	0.906	0.993	CLONAL	2	TRUE	0	0.490348634697944	2		422	782	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486095	8486095	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	115	570	0	ENST00000356435.5:c.2722G>T	p.Val908Leu	p.V908L	ENST00000356435		908	Gtg/Ttg	17/35	0.472842937078333	3	FACETS	0.67	0.603	0.741	0.223	0.201	0.247	SUBCLONAL	1	TRUE	0	0.490348634697944	3		570	872	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401270	139401270	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	301	612	0	ENST00000277541.6:c.3799del	p.Asp1267MetfsTer178	p.D1267Mfs*178	ENST00000277541	NM_017617.3	1267	Gat/at	23/34	0.451052628819199	2	FACETS	0.763	0.721	0.804	0.763	0.721	0.804	SUBCLONAL	2	TRUE	0	0.490348634697944	2		612	805	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271229	153271229	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	AA	novel	NA	P-0060661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	53	281	0	ENST00000281708.4:c.549delinsTT	p.Leu183PhefsTer73	p.L183Ffs*73	ENST00000281708	NM_033632.3	183	ttG/ttTT	3/12	1	2	FACETS	0.992	0.856	1	0.992	0.856	1	CLONAL	1	TRUE	1	0.490348634697944	2		281	218	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0060662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	178	243	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.348612646841458	5	FACETS	1	0.966	1	1	0.966	1	CLONAL	3	TRUE	2	0.348612646841458	5		243	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934573	NA	P-0060662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	189	628	0	ENST00000269305.4:c.722C>A	p.Ser241Tyr	p.S241Y	ENST00000269305	NM_001126112.2	241	tCc/tAc	7/11	0.287745272687338	3	FACETS	0.886	0.827	0.946	0.886	0.827	0.946	CLONAL	3	TRUE	0	0.348612646841458	3		628	479	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717776	89717776	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1554825266	NA	P-0060662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	51	302	0	ENST00000371953.3:c.801G>T	p.Lys267Asn	p.K267N	ENST00000371953	NM_000314.4	267	aaG/aaT	7/9	0.247311914962226	2	FACETS	0.846	0.731	0.966	0.846	0.731	0.966	CLONAL	2	TRUE	0	0.348612646841458	2		302	173	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200721	128200721	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	11	478	0	ENST00000341105.2:c.1084C>G	p.Arg362Gly	p.R362G	ENST00000341105	NM_032638.4	362	Cga/Gga	5/6	0.1143945237282	4	FACETS	0.184	0.126	0.256	0.092	0.063	0.128	INDETERMINATE	1	TRUE	2	0.348612646841458	4		478	463	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243045	105243045	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	114	593	0	ENST00000349310.3:c.238T>G	p.Trp80Gly	p.W80G	ENST00000349310	NM_001014432.1	80	Tgg/Ggg	5/15	0.1143945237282	4	FACETS	0.797	0.721	0.878	0.797	0.721	0.878	INDETERMINATE	2	TRUE	2	0.348612646841458	4		593	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0060663-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	258	729	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.288439332982669	3	FACETS	0.84	0.791	0.89	0.84	0.791	0.89	CLONAL	3	TRUE	0	0.33317736489003	3		729	717	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170354	119170354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507498	NA	P-0060663-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	173	461	0	ENST00000264033.4:c.2584G>A	p.Glu862Lys	p.E862K	ENST00000264033	NM_005188.3	862	Gag/Aag	16/16	0.291197993766476	2	FACETS	0.837	0.774	0.903	0.837	0.774	0.903	CLONAL	2	TRUE	0	0.33317736489003	2		461	620	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518383	204518383	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060663-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	87	530	0	ENST00000367182.3:c.1046T>A	p.Ile349Lys	p.I349K	ENST00000367182	NM_001278516.1	349	aTa/aAa	11/11	0.33317736489003	5	FACETS	0.771	0.681	0.868	0.193	0.17	0.217	SUBCLONAL	1	TRUE	1	0.33317736489003	5		530	1016	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912094	114912094	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060663-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	138	347	0	ENST00000543371.1:c.1164G>C	p.Trp388Cys	p.W388C	ENST00000543371	NM_001198531.1	388	tgG/tgC	11/14	0.291197993766476	2	FACETS	0.852	0.781	0.926	0.852	0.781	0.926	CLONAL	2	TRUE	0	0.33317736489003	2		347	486	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32928996	32928996	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs81002823	NA	P-0060663-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	120	302	0	ENST00000380152.3:c.7008-2A>T		p.X2336_splice	ENST00000380152		2336			0.291197993766476	2	FACETS	0.866	0.788	0.946	0.866	0.788	0.946	CLONAL	2	TRUE	0	0.33317736489003	2		302	416	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656986	45656986	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060663-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	195	447	0	ENST00000407780.3:c.170G>C	p.Ser57Thr	p.S57T	ENST00000407780	NM_001283052.1	57	aGt/aCt	3/7	0.271266978482101	4	FACETS	0.894	0.828	0.962	0.894	0.828	0.962	CLONAL	2	TRUE	2	0.33317736489003	4		447	873	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833947	44833948	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060663-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	30	201	0	ENST00000377967.4:c.372dup	p.Asp125Ter	p.D125*	ENST00000377967	NM_021140.2	124	tct/tcTt	4/29	1	2	FACETS	0.632	0.511	0.768	0.632	0.511	0.768	SUBCLONAL	1	TRUE	1	0.33317736489003	2		201	285	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0060665-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	157	761	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.270409938382047	2	FACETS	0.913	0.84	0.989	0.913	0.84	0.989	CLONAL	2	TRUE	0	0.282813481292195	2		764	608	SUCCESS
FH	2271	MSKCC	GRCh37	1	241671962	241671962	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060665-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	43	373	0	ENST00000366560.3:c.679C>G	p.Gln227Glu	p.Q227E	ENST00000366560	NM_000143.3	227	Cag/Gag	5/10	0.282813481292195	3	FACETS	0.821	0.687	0.968	0.41	0.343	0.484	CLONAL	1	TRUE	1	0.282813481292195	3		373	423	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042754	42042754	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060665-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	27	533	0	ENST00000219905.7:c.6949G>C	p.Asp2317His	p.D2317H	ENST00000219905	NM_001164273.1	2317	Gat/Cat	17/24	1	2	FACETS	0.399	0.316	0.493	0.399	0.316	0.493	SUBCLONAL	1	TRUE	1	0.282813481292195	2		533	479	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170011175	170011175	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1483055491	NA	P-0060665-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	30	386	0	ENST00000295797.4:c.1296C>G	p.Phe432Leu	p.F432L	ENST00000295797	NM_002740.5	432	ttC/ttG	14/18	0.2480231972291	5	FACETS	0.508	0.408	0.622	0.169	0.136	0.208	SUBCLONAL	1	TRUE	2	0.282813481292195	5		386	595	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0060666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	30	418	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.75	0.609	0.908	0.75	0.609	0.908	CLONAL	1	TRUE	1	0.379151484703952	2		418	211	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591891	48591891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912581	NA	P-0060666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	77	410	0	ENST00000342988.3:c.1054G>A	p.Gly352Arg	p.G352R	ENST00000342988	NM_005359.5	352	Gga/Aga	9/12	0.379151484703952	1	FACETS	0.859	0.759	0.966	0.859	0.759	0.966	CLONAL	1	TRUE	0	0.379151484703952	1		410	383	SUCCESS
ALB	213	MSKCC	GRCh37	4	74279233	74279233	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	125	410	0	ENST00000295897.4:c.940A>G	p.Ile314Val	p.I314V	ENST00000295897	NM_000477.5	314	Att/Gtt	8/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.379151484703952	2		410	500	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	153	323	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.34	2		323	818	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	125	922	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.995	0.901	1	0.995	0.901	1	CLONAL	1	TRUE	1	0.34	2		922	739	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	70	721	0	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	1	2	FACETS	0.427	0.371	0.487	0.427	0.371	0.487	SUBCLONAL	1	TRUE	1	0.34	2		721	965	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	51	636	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.333	0.281	0.389	0.333	0.281	0.389	SUBCLONAL	1	TRUE	1	0.34	2		637	902	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	50	656	3	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	1	2	FACETS	0.307	0.259	0.36	0.307	0.259	0.36	SUBCLONAL	1	TRUE	1	0.34	2		659	958	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	172	725	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.94	0.864	1	0.94	0.864	1	CLONAL	1	TRUE	1	0.34	2		732	1076	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9770625	9770625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765729544	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	151	553	0	ENST00000377346.4:c.112C>T	p.Arg38Cys	p.R38C	ENST00000377346	NM_005026.3	38	Cgc/Tgc	3/24	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.34	2		553	847	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272403	11272403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs557533784	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	137	510	0	ENST00000361445.4:c.3527C>T	p.Thr1176Met	p.T1176M	ENST00000361445	NM_004958.3	1176	aCg/aTg	23/58	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.34	2		510	755	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258536	16258536	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	121	718	0	ENST00000375759.3:c.5801T>C	p.Leu1934Ser	p.L1934S	ENST00000375759	NM_015001.2	1934	tTg/tCg	11/15	1	2	FACETS	0.703	0.634	0.776	0.703	0.634	0.776	SUBCLONAL	1	TRUE	1	0.34	2		718	1012	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259042	16259043	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	159	719	0	ENST00000375759.3:c.6313dup	p.Ala2105GlyfsTer18	p.A2105Gfs*18	ENST00000375759	NM_015001.2	2103	agg/aGgg	11/15	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.34	2		719	920	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022999	27022999	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1436957504	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	79	528	1	ENST00000324856.7:c.110del	p.Gly37AlafsTer14	p.G37Afs*14	ENST00000324856	NM_006015.4	35	gcG/gc	1/20	1	2	FACETS	0.6	0.527	0.678	0.6	0.527	0.678	SUBCLONAL	1	TRUE	1	0.34	2		529	775	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	37	104	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	0.371	0.305	0.446	0.371	0.305	0.446	SUBCLONAL	1	TRUE	1	0.34	2		104	586	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089705	27089706	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1286891446	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	101	720	0	ENST00000324856.7:c.2666dup	p.Met890HisfsTer46	p.M890Hfs*46	ENST00000324856	NM_006015.4	887	-/G	8/20	1	2	FACETS	0.612	0.546	0.682	0.612	0.546	0.682	SUBCLONAL	1	TRUE	1	0.34	2		720	971	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101322	27101322	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	157	686	0	ENST00000324856.7:c.4604C>G	p.Thr1535Arg	p.T1535R	ENST00000324856	NM_006015.4	1535	aCa/aGa	18/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.34	2		686	900	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933729	36933729	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs375011831	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	153	709	0	ENST00000361632.4:c.1670G>T	p.Ser557Ile	p.S557I	ENST00000361632		557	aGc/aTc	12/16	1	2	FACETS	0.929	0.849	1	0.929	0.849	1	CLONAL	1	TRUE	1	0.34	2		709	969	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322625	39322625	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	112	381	0	ENST00000373001.3:c.367T>G	p.Phe123Val	p.F123V	ENST00000373001	NM_022157.3	123	Ttt/Gtt	2/7	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.34	2		381	626	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428478	78428478	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	30	273	0	ENST00000370768.2:c.1321C>T	p.Gln441Ter	p.Q441*	ENST00000370768	NM_003902.3	441	Caa/Taa	14/20	1	2	FACETS	0.455	0.366	0.555	0.455	0.366	0.555	SUBCLONAL	1	TRUE	1	0.34	2		273	388	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462090	120462090	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	102	659	0	ENST00000256646.2:c.5626A>G	p.Thr1876Ala	p.T1876A	ENST00000256646	NM_024408.3	1876	Act/Gct	31/34	1	2	FACETS	0.678	0.605	0.755	0.678	0.605	0.755	SUBCLONAL	1	TRUE	1	0.34	2		659	885	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100696	8100696	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	87	631	0	ENST00000346208.3:c.670C>T	p.Pro224Ser	p.P224S	ENST00000346208		224	Ccc/Tcc	3/6	1	2	FACETS	0.624	0.552	0.702	0.624	0.552	0.702	SUBCLONAL	1	TRUE	1	0.34	2		631	820	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851485	63851485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750226503	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	127	607	0	ENST00000279873.7:c.2263G>A	p.Val755Ile	p.V755I	ENST00000279873	NM_032199.2	755	Gtc/Atc	10/10	1	2	FACETS	0.871	0.788	0.957	0.871	0.788	0.957	CLONAL	1	TRUE	1	0.34	2		607	858	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925543	114925543	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774534267	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	98	540	0	ENST00000543371.1:c.1621G>A	p.Ala541Thr	p.A541T	ENST00000543371	NM_001198531.1	541	Gct/Act	14/14	1	2	FACETS	0.711	0.634	0.793	0.711	0.634	0.793	SUBCLONAL	1	TRUE	1	0.34	2		540	811	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57004295	57004295	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	G	G	A	rs142394789	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	180	685	0	ENST00000257254.3:c.184C>T	p.Arg62Cys	p.R62C	ENST00000257254		62	Cgc/Tgc	1/2	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.34	2		685	934	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946411	71946411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776269568	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	88	704	1	ENST00000298229.2:c.2575C>T	p.Arg859Cys	p.R859C	ENST00000298229	NM_001567.3	859	Cgt/Tgt	23/28	1	2	FACETS	0.614	0.543	0.69	0.614	0.543	0.69	SUBCLONAL	1	TRUE	1	0.34	2		705	843	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102196033	102196033	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	57	539	0	ENST00000263464.3:c.793T>C	p.Trp265Arg	p.W265R	ENST00000263464	NM_001165.4	265	Tgg/Cgg	2/9	1	2	FACETS	0.493	0.422	0.571	0.493	0.422	0.571	SUBCLONAL	1	TRUE	1	0.34	2		539	680	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	31	472	5	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.352	0.284	0.429	0.352	0.284	0.429	SUBCLONAL	1	TRUE	1	0.34	2		477	518	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420402	49420402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	55	635	0	ENST00000301067.7:c.15347C>T	p.Ala5116Val	p.A5116V	ENST00000301067	NM_003482.3	5116	gCt/gTt	48/54	1	2	FACETS	0.356	0.303	0.413	0.356	0.303	0.413	SUBCLONAL	1	TRUE	1	0.34	2		635	910	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431640	49431640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370155635	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	154	794	1	ENST00000301067.7:c.9499C>T	p.Arg3167Trp	p.R3167W	ENST00000301067	NM_003482.3	3167	Cgg/Tgg	34/54	1	2	FACETS	0.978	0.895	1	0.978	0.895	1	CLONAL	1	TRUE	1	0.34	2		795	926	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	199	764	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.34	2		764	1038	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	58	875	4	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.404	0.346	0.468	0.404	0.346	0.468	SUBCLONAL	1	TRUE	1	0.34	2		879	844	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112217	115112217	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766332681	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	79	706	0	ENST00000257566.3:c.1523C>T	p.Ala508Val	p.A508V	ENST00000257566	NM_016569.3	508	gCg/gTg	7/8	1	2	FACETS	0.588	0.517	0.665	0.588	0.517	0.665	SUBCLONAL	1	TRUE	1	0.34	2		706	790	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233810	133233810	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	84	550	0	ENST00000320574.5:c.3494A>G	p.Asp1165Gly	p.D1165G	ENST00000320574	NM_006231.2	1165	gAc/gGc	29/49	1	2	FACETS	0.616	0.543	0.694	0.616	0.543	0.694	SUBCLONAL	1	TRUE	1	0.34	2		550	802	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133234500	133234500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs114315196	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	111	409	0	ENST00000320574.5:c.3332G>A	p.Arg1111Gln	p.R1111Q	ENST00000320574	NM_006231.2	1111	cGg/cAg	27/49	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.34	2		409	604	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918760	32918760	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	23	137	0	ENST00000380152.3:c.6907T>A	p.Ser2303Thr	p.S2303T	ENST00000380152		2303	Tcc/Acc	12/27	1	2	FACETS	0.701	0.55	0.874	0.701	0.55	0.874	SUBCLONAL	1	TRUE	1	0.34	2		137	193	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437134	110437134	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	51	448	0	ENST00000375856.3:c.1267G>T	p.Gly423Cys	p.G423C	ENST00000375856	NM_003749.2	423	Ggc/Tgc	1/2	1	2	FACETS	0.498	0.423	0.581	0.498	0.423	0.581	SUBCLONAL	1	TRUE	1	0.34	2		448	602	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437600	110437600	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	49	653	1	ENST00000375856.3:c.801del	p.Gly268AlafsTer24	p.G268Afs*24	ENST00000375856	NM_003749.2	267	ccC/cc	1/2	1	2	FACETS	0.336	0.283	0.394	0.336	0.283	0.394	SUBCLONAL	1	TRUE	1	0.34	2		654	859	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241994	105241994	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375990114	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	125	467	0	ENST00000349310.3:c.430C>T	p.Arg144Cys	p.R144C	ENST00000349310	NM_001014432.1	144	Cgc/Tgc	6/15	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.34	2		467	710	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727451	66727451	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519729	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	132	494	0	ENST00000307102.5:c.167A>C	p.Gln56Pro	p.Q56P	ENST00000307102	NM_002755.3	56	cAg/cCg	2/11	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.34	2		494	727	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434834	99434834	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	44	507	0	ENST00000268035.6:c.924del	p.Ser309ArgfsTer76	p.S309Rfs*76	ENST00000268035	NM_000875.3	307	tgC/tg	3/21	1	2	FACETS	0.343	0.287	0.406	0.343	0.287	0.406	SUBCLONAL	1	TRUE	1	0.34	2		507	754	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134604	2134604	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	149	795	0	ENST00000219476.3:c.4381T>C	p.Tyr1461His	p.Y1461H	ENST00000219476	NM_000548.3	1461	Tac/Cac	34/42	1	2	FACETS	0.817	0.745	0.892	0.817	0.745	0.892	CLONAL	1	TRUE	1	0.34	2		795	1073	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213983	2213983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	72	623	0	ENST00000326181.6:c.65del	p.Pro22GlnfsTer106	p.P22Qfs*106	ENST00000326181	NM_032271.2	21	aCc/ac	2/21	1	2	FACETS	0.445	0.387	0.507	0.445	0.387	0.507	SUBCLONAL	1	TRUE	1	0.34	2		623	952	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225940	2225940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	174	461	0	ENST00000326181.6:c.1732G>A	p.Glu578Lys	p.E578K	ENST00000326181	NM_032271.2	578	Gag/Aag	18/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.34	2		461	894	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778948	3778948	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	118	789	0	ENST00000262367.5:c.6100G>T	p.Gly2034Cys	p.G2034C	ENST00000262367	NM_004380.2	2034	Ggc/Tgc	31/31	1	2	FACETS	0.689	0.621	0.762	0.689	0.621	0.762	SUBCLONAL	1	TRUE	1	0.34	2		789	1007	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	104	590	1	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.716	0.641	0.797	0.716	0.641	0.797	SUBCLONAL	1	TRUE	1	0.34	2		591	854	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991509	72991509	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141276031	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	138	611	0	ENST00000268489.5:c.2536C>T	p.Arg846Cys	p.R846C	ENST00000268489	NM_006885.3	846	Cgc/Tgc	2/10	1	2	FACETS	0.991	0.902	1	0.991	0.902	1	CLONAL	1	TRUE	1	0.34	2		611	819	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	153	683	5	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.967	0.884	1	0.967	0.884	1	CLONAL	1	TRUE	1	0.34	2		688	931	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86546576	86546576	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs772446538	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	49	632	0	ENST00000262426.4:c.1025A>G	p.Lys342Arg	p.K342R	ENST00000262426	NM_001451.2	342	aAg/aGg	2/2	1	2	FACETS	0.369	0.311	0.432	0.369	0.311	0.432	SUBCLONAL	1	TRUE	1	0.34	2		632	782	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541491	29541491	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	13	49	0	ENST00000356175.3:c.1415T>C	p.Val472Ala	p.V472A	ENST00000356175	NM_000267.3	472	gTa/gCa	13/57	1	2	FACETS	0.702	0.505	0.936	0.702	0.505	0.936	CLONAL	1	TRUE	1	0.34	2		49	109	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858071	40858071	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	81	469	0	ENST00000428826.2:c.1793del	p.Lys598ArgfsTer32	p.K598Rfs*32	ENST00000428826		598	aAg/ag	16/21	1	2	FACETS	0.618	0.544	0.698	0.618	0.544	0.698	SUBCLONAL	1	TRUE	1	0.34	2		469	771	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533939	63533940	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs771001164	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	56	642	4	ENST00000307078.5:c.1214_1215del	p.Glu405GlyfsTer56	p.E405Gfs*56	ENST00000307078	NM_004655.3	405	gAG/g	6/11	1	2	FACETS	0.431	0.368	0.5	0.431	0.368	0.5	SUBCLONAL	1	TRUE	1	0.34	2		646	764	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619131	1619131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759729787	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	190	787	0	ENST00000344749.5:c.1429C>T	p.Arg477Trp	p.R477W	ENST00000344749	NM_001136139.2	477	Cgg/Tgg	16/19	1	2	FACETS	0.98	0.905	1	0.98	0.905	1	CLONAL	1	TRUE	1	0.34	2		787	1140	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110520	4110520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	119	632	0	ENST00000262948.5:c.437G>A	p.Cys146Tyr	p.C146Y	ENST00000262948	NM_030662.3	146	tGc/tAc	3/11	1	2	FACETS	0.717	0.646	0.792	0.717	0.646	0.792	SUBCLONAL	1	TRUE	1	0.34	2		632	976	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	153	569	3	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.34	2		572	629	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243957	5243957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1324477953	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	150	550	0	ENST00000357368.4:c.1525G>A	p.Asp509Asn	p.D509N	ENST00000357368	NM_002850.3	509	Gac/Aac	11/38	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.34	2		550	800	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6222256	6222256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144291468	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	143	771	0	ENST00000252674.7:c.986C>T	p.Pro329Leu	p.P329L	ENST00000252674	NM_005934.3	329	cCg/cTg	6/12	1	2	FACETS	0.852	0.776	0.932	0.852	0.776	0.932	CLONAL	1	TRUE	1	0.34	2		771	987	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291170	10291170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369196079	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	200	856	0	ENST00000340748.4:c.301C>T	p.Arg101Trp	p.R101W	ENST00000340748		101	Cgg/Tgg	4/40	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.34	2		856	1101	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215975	36215975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	43	595	0	ENST00000222270.7:c.3515G>A	p.Arg1172His	p.R1172H	ENST00000222270	NM_014727.1	1172	cGt/cAt	10/37	1	2	FACETS	0.31	0.258	0.368	0.31	0.258	0.368	SUBCLONAL	1	TRUE	1	0.34	2		595	816	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218098	36218098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	67	487	0	ENST00000222270.7:c.4045G>A	p.Asp1349Asn	p.D1349N	ENST00000222270	NM_014727.1	1349	Gac/Aac	15/37	1	2	FACETS	0.548	0.476	0.627	0.548	0.476	0.627	SUBCLONAL	1	TRUE	1	0.34	2		487	719	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218451	36218451	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs34078597	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	139	530	1	ENST00000222270.7:c.4235del	p.Gly1412AlafsTer10	p.G1412Afs*10	ENST00000222270	NM_014727.1	1410	caG/ca	16/37	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.34	2		531	731	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753149	42753151	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs199960550	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	176	594	4	ENST00000222329.4:c.1113_1115del	p.Ser373del	p.S373del	ENST00000222329	NM_006494.2	371	tcTTCc/tcc	4/4	1	2	FACETS	0.985	0.907	1	0.985	0.907	1	CLONAL	1	TRUE	1	0.34	2		598	1051	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791588	42791588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752629455	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	173	681	0	ENST00000575354.2:c.569G>A	p.Arg190His	p.R190H	ENST00000575354	NM_015125.3	190	cGc/cAc	4/20	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.34	2		681	978	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45864887	45864887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs186220206	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	177	702	0	ENST00000391945.4:c.1132C>T	p.Arg378Cys	p.R378C	ENST00000391945	NM_000400.3	378	Cgc/Tgc	12/23	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.34	2		702	1020	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902167	50902167	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	85	527	0	ENST00000440232.2:c.59G>T	p.Gly20Val	p.G20V	ENST00000440232	NM_002691.3	20	gGg/gTg	2/27	1	2	FACETS	0.723	0.639	0.812	0.723	0.639	0.812	SUBCLONAL	1	TRUE	1	0.34	2		527	692	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905324	50905324	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	167	731	2	ENST00000440232.2:c.537del	p.Arg180GlyfsTer3	p.R180Gfs*3	ENST00000440232	NM_002691.3	178	Ggg/gg	5/27	1	2	FACETS	0.986	0.906	1	0.986	0.906	1	CLONAL	1	TRUE	1	0.34	2		733	996	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702280	47702280	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	112	392	0	ENST00000233146.2:c.1876G>T	p.Glu626Ter	p.E626*	ENST00000233146	NM_000251.2	626	Gag/Tag	12/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.34	2		392	543	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	214	495	1	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.34	2		496	855	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630629	67630629	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	61	338	1	ENST00000272342.5:c.815A>G	p.Lys272Arg	p.K272R	ENST00000272342	NM_019002.3	272	aAg/aGg	5/6	1	2	FACETS	0.674	0.582	0.775	0.674	0.582	0.775	SUBCLONAL	1	TRUE	1	0.34	2		339	532	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737505	204737505	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	67	336	0	ENST00000302823.3:c.642A>T	p.Gln214His	p.Q214H	ENST00000302823	NM_005214.4	214	caA/caT	4/4	1	2	FACETS	0.855	0.745	0.973	0.855	0.745	0.973	CLONAL	1	TRUE	1	0.34	2		336	461	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757393	40757393	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs763353429	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	123	536	0	ENST00000373198.4:c.2904+1G>A		p.X968_splice	ENST00000373198	NM_133170.3	968			0.161636964463382	1	FACETS	0.823	0.745	0.905	0.823	0.745	0.905	INDETERMINATE	1	TRUE	0	0.34	1		536	730	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755427	39755427	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	90	712	2	ENST00000288319.7:c.1338del	p.Phe446LeufsTer59	p.F446Lfs*59	ENST00000288319	NM_182918.3	446	ttT/tt	10/10	1	2	FACETS	0.56	0.496	0.629	0.56	0.496	0.629	SUBCLONAL	1	TRUE	1	0.34	2		714	945	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21345976	21345976	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768361273	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	167	674	1	ENST00000215739.8:c.851G>A	p.Arg284His	p.R284H	ENST00000215739	NM_006767.3	284	cGc/cAc	9/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.34	2		675	924	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21346071	21346071	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370315661	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	161	651	1	ENST00000215739.8:c.946G>A	p.Val316Met	p.V316M	ENST00000215739	NM_006767.3	316	Gtg/Atg	9/21	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.34	2		652	885	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434182	12434182	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776687	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	59	378	0	ENST00000287820.6:c.556del	p.Ser186ValfsTer47	p.S186Vfs*47	ENST00000287820	NM_015869.4	184	Aaa/aa	4/7	1	2	FACETS	0.61	0.525	0.703	0.61	0.525	0.703	SUBCLONAL	1	TRUE	1	0.34	2		378	569	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	95	499	3	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.803	0.715	0.896	0.803	0.715	0.896	CLONAL	1	TRUE	1	0.34	2		502	696	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275669	41275669	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764576683	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	48	532	0	ENST00000349496.5:c.1564G>A	p.Ala522Thr	p.A522T	ENST00000349496	NM_001904.3	522	Gca/Aca	10/15	1	2	FACETS	0.375	0.316	0.441	0.375	0.316	0.441	SUBCLONAL	1	TRUE	1	0.34	2		532	752	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437234	52437234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369065146	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	174	680	0	ENST00000460680.1:c.1810G>A	p.Val604Met	p.V604M	ENST00000460680	NM_004656.3	604	Gtg/Atg	14/17	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.34	2		680	912	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200112	128200112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1420609104	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	150	664	0	ENST00000341105.2:c.1193G>A	p.Arg398Gln	p.R398Q	ENST00000341105	NM_032638.4	398	cGg/cAg	6/6	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.34	2		664	826	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927395	178927395	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	14	223	0	ENST00000263967.3:c.1158G>A	p.Trp386Ter	p.W386*	ENST00000263967	NM_006218.2	386	tgG/tgA	7/21	1	2	FACETS	0.339	0.245	0.453	0.339	0.245	0.453	SUBCLONAL	1	TRUE	1	0.34	2		223	243	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627981	187627981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	152	617	0	ENST00000441802.2:c.3001G>A	p.Val1001Met	p.V1001M	ENST00000441802	NM_005245.3	1001	Gtg/Atg	2/27	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.34	2		617	821	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629541	187629541	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	148	648	0	ENST00000441802.2:c.1441A>C	p.Thr481Pro	p.T481P	ENST00000441802	NM_005245.3	481	Act/Cct	2/27	1	2	FACETS	0.877	0.8	0.957	0.877	0.8	0.957	CLONAL	1	TRUE	1	0.34	2		648	993	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526755	31526755	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	80	525	0	ENST00000344624.3:c.285del	p.Cys96AlafsTer12	p.C96Afs*12	ENST00000344624		95	ccC/cc	2/33	1	2	FACETS	0.7	0.616	0.79	0.7	0.616	0.79	SUBCLONAL	1	TRUE	1	0.34	2		525	672	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160646	56160646	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343464548	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	142	595	0	ENST00000399503.3:c.920G>A	p.Arg307His	p.R307H	ENST00000399503	NM_005921.1	307	cGt/cAt	4/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.34	2		595	793	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180585	56180585	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	34	227	0	ENST00000399503.3:c.3914A>G	p.Asn1305Ser	p.N1305S	ENST00000399503	NM_005921.1	1305	aAc/aGc	16/20	1	2	FACETS	0.627	0.514	0.754	0.627	0.514	0.754	SUBCLONAL	1	TRUE	1	0.34	2		227	319	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	73	608	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.95	0.834	1	0.95	0.834	1	CLONAL	1	TRUE	1	0.34	2		612	452	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	58	471	1	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.912	0.787	1	0.912	0.787	1	CLONAL	1	TRUE	1	0.34	2		472	374	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721531	176721531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	66	662	0	ENST00000439151.2:c.7162C>T	p.Pro2388Ser	p.P2388S	ENST00000439151	NM_022455.4	2388	Ccg/Tcg	23/23	1	2	FACETS	0.398	0.344	0.456	0.398	0.344	0.456	SUBCLONAL	1	TRUE	1	0.34	2		662	976	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038353	180038353	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	137	588	0	ENST00000261937.6:c.3664C>T	p.Gln1222Ter	p.Q1222*	ENST00000261937	NM_182925.4	1222	Cag/Tag	27/30	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.34	2		588	718	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911044	29911044	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	59	571	0	ENST00000376809.5:c.344-1G>A		p.X115_splice	ENST00000376809	NM_002116.7	115			1	2	FACETS	0.451	0.387	0.521	0.451	0.387	0.521	SUBCLONAL	1	TRUE	1	0.34	2		571	769	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137528211	137528211	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	18	186	0	ENST00000367739.4:c.89C>A	p.Pro30His	p.P30H	ENST00000367739	NM_000416.2	30	cCt/cAt	2/7	1	2	FACETS	0.342	0.257	0.442	0.342	0.257	0.442	SUBCLONAL	1	TRUE	1	0.34	2		186	310	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729271	41729271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749989847	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	75	452	1	ENST00000242208.4:c.1258G>A	p.Val420Met	p.V420M	ENST00000242208	NM_002192.2	420	Gtg/Atg	3/3	1	2	FACETS	0.777	0.681	0.879	0.777	0.681	0.879	SUBCLONAL	1	TRUE	1	0.34	2		453	568	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730093	41730093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs979257752	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	66	547	0	ENST00000242208.4:c.436G>A	p.Asp146Asn	p.D146N	ENST00000242208	NM_002192.2	146	Gac/Aac	3/3	1	2	FACETS	0.559	0.484	0.639	0.559	0.484	0.639	SUBCLONAL	1	TRUE	1	0.34	2		547	695	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730106	41730106	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	57	514	0	ENST00000242208.4:c.423del	p.Lys142ArgfsTer18	p.K142Rfs*18	ENST00000242208	NM_002192.2	141	tcC/tc	3/3	1	2	FACETS	0.511	0.438	0.591	0.511	0.438	0.591	SUBCLONAL	1	TRUE	1	0.34	2		514	656	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148516753	148516753	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	27	412	0	ENST00000320356.2:c.934A>G	p.Lys312Glu	p.K312E	ENST00000320356	NM_004456.4	312	Aag/Gag	9/20	1	2	FACETS	0.318	0.252	0.394	0.318	0.252	0.394	SUBCLONAL	1	TRUE	1	0.34	2		412	499	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874007	151874009	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	100	387	0	ENST00000262189.6:c.8529_8531del	p.Asp2843del	p.D2843del	ENST00000262189	NM_170606.2	2843	gaTGAg/gag	38/59	1	2	FACETS	0.997	0.893	1	0.997	0.893	1	CLONAL	1	TRUE	1	0.34	2		387	590	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878653	151878653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781592244	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	53	613	0	ENST00000262189.6:c.6292C>T	p.Pro2098Ser	p.P2098S	ENST00000262189	NM_170606.2	2098	Ccc/Tcc	36/59	1	2	FACETS	0.375	0.319	0.437	0.375	0.319	0.437	SUBCLONAL	1	TRUE	1	0.34	2		613	831	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146045	38146045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200818177	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	122	536	0	ENST00000317025.8:c.3461G>A	p.Arg1154Gln	p.R1154Q	ENST00000317025	NM_023034.1	1154	cGg/cAg	19/24	1	2	FACETS	0.946	0.855	1	0.946	0.855	1	CLONAL	1	TRUE	1	0.34	2		536	759	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942745	68942745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781270008	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	89	488	0	ENST00000288368.4:c.557G>A	p.Arg186Gln	p.R186Q	ENST00000288368	NM_024870.2	186	cGg/cAg	6/40	1	2	FACETS	0.765	0.679	0.858	0.765	0.679	0.858	SUBCLONAL	1	TRUE	1	0.34	2		488	684	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878907	117878907	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	72	432	0	ENST00000297338.2:c.62C>T	p.Ala21Val	p.A21V	ENST00000297338	NM_006265.2	21	gCc/gTc	2/14	1	2	FACETS	0.67	0.585	0.761	0.67	0.585	0.761	SUBCLONAL	1	TRUE	1	0.34	2		432	632	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2115927	2115927	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs281875196	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	137	540	0	ENST00000349721.2:c.3562G>A	p.Ala1188Thr	p.A1188T	ENST00000349721	NM_003070.3	1188	Gca/Aca	25/34	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.34	2		540	707	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340418	8340418	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	83	577	0	ENST00000356435.5:c.5178A>T	p.Glu1726Asp	p.E1726D	ENST00000356435		1726	gaA/gaT	31/35	1	2	FACETS	0.664	0.586	0.748	0.664	0.586	0.748	SUBCLONAL	1	TRUE	1	0.34	2		577	735	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389359	8389359	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	62	391	0	ENST00000356435.5:c.4259G>T	p.Arg1420Met	p.R1420M	ENST00000356435		1420	aGg/aTg	26/35	1	2	FACETS	0.856	0.742	0.979	0.856	0.742	0.979	CLONAL	1	TRUE	1	0.34	2		391	426	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485313	8485313	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	53	312	0	ENST00000356435.5:c.3067A>C	p.Asn1023His	p.N1023H	ENST00000356435		1023	Aat/Cat	18/35	1	2	FACETS	0.734	0.627	0.85	0.734	0.627	0.85	SUBCLONAL	1	TRUE	1	0.34	2		312	425	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342734	87342734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	122	524	0	ENST00000277120.3:c.1019C>T	p.Thr340Met	p.T340M	ENST00000277120		340	aCg/aTg	9/19	1	2	FACETS	0.965	0.873	1	0.965	0.873	1	CLONAL	1	TRUE	1	0.34	2		524	744	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606273	93606273	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	92	563	0	ENST00000375746.1:c.98del	p.Gly33AlafsTer2	p.G33Afs*2	ENST00000375746	NM_001174167.1	31	caG/ca	2/14	1	2	FACETS	0.721	0.64	0.807	0.721	0.64	0.807	SUBCLONAL	1	TRUE	1	0.34	2		563	751	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772950	135772951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs118203724	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	58	407	0	ENST00000298552.3:c.2672dup	p.Asn891LysfsTer13	p.N891Kfs*13	ENST00000298552	NM_001162426.1	891	aac/aaAc	21/23	1	2	FACETS	0.618	0.531	0.713	0.618	0.531	0.713	SUBCLONAL	1	TRUE	1	0.34	2		407	552	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781141	135781141	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs118203585	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	145	580	0	ENST00000298552.3:c.1824del	p.Phe608LeufsTer21	p.F608Lfs*21	ENST00000298552	NM_001162426.1	608	ttT/tt	15/23	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.34	2		580	804	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137323776	137323776	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	125	565	0	ENST00000481739.1:c.1069A>C	p.Met357Leu	p.M357L	ENST00000481739	NM_002957.4	357	Atg/Ctg	8/10	1	2	FACETS	0.925	0.837	1	0.925	0.837	1	CLONAL	1	TRUE	1	0.34	2		565	795	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396536	139396536	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	115	642	0	ENST00000277541.6:c.5389C>A	p.Leu1797Met	p.L1797M	ENST00000277541	NM_017617.3	1797	Ctg/Atg	29/34	1	2	FACETS	0.725	0.652	0.802	0.725	0.652	0.802	SUBCLONAL	1	TRUE	1	0.34	2		642	933	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732860	44732860	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	63	276	0	ENST00000377967.4:c.64del	p.Glu22LysfsTer20	p.E22Kfs*20	ENST00000377967	NM_021140.2	21	gaG/ga	1/29	1	1	FACETS	0.899	0.783	1	0.899	0.783	1	CLONAL	1	TRUE	0	0.34	1		276	342	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820533	44820533	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	39	69	0	ENST00000377967.4:c.230T>C	p.Val77Ala	p.V77A	ENST00000377967	NM_021140.2	77	gTt/gCt	3/29	1	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.34	1		69	144	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357714	70357714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1009330609	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	153	336	0	ENST00000374080.3:c.5965C>T	p.Arg1989Cys	p.R1989C	ENST00000374080		1989	Cgc/Tgc	41/45	1	1	FACETS	0.836	0.771	0.901	1	0.991	1	CLONAL	2	TRUE	0	0.34	1		336	447	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779210	3779211	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs587783507	NA	P-0060667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	48	506	3	ENST00000262367.5:c.5837dup	p.Pro1947ThrfsTer19	p.P1947Tfs*19	ENST00000262367	NM_004380.2	1946	cca/ccCa	31/31	1	2	FACETS	0.467	0.395	0.548	0.467	0.395	0.548	SUBCLONAL	1	TRUE	1	0.34	2		509	604	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561263	9561263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769939031	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	70	635	0	ENST00000353224.5:c.519G>A	p.Met173Ile	p.M173I	ENST00000353224	NM_177990.2	173	atG/atA	4/10	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.305327685222426	2		635	429	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954668	17954668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	94	709	0	ENST00000458235.1:c.226G>A	p.Glu76Lys	p.E76K	ENST00000458235	NM_000215.3	76	Gag/Aag	3/24	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.305327685222426	2		709	478	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776561	9776561	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772233114	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	70	651	2	ENST00000377346.4:c.664C>T	p.Arg222Trp	p.R222W	ENST00000377346	NM_005026.3	222	Cgg/Tgg	6/24	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.305327685222426	2		653	457	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	58	385	0	ENST00000335508.6:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000335508	NM_012433.2	902	Gaa/Aaa	18/25	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.305327685222426	2		385	297	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524146	18524146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	60	506	0	ENST00000266497.5:c.1658C>T	p.Pro553Leu	p.P553L	ENST00000266497		553	cCa/cTa	11/31	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.305327685222426	2		506	390	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374369	31374369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767930436	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	166	685	0	ENST00000328111.2:c.368C>T	p.Ser123Phe	p.S123F	ENST00000328111	NM_006892.3	123	tCc/tTc	5/23	0.305355583654101	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.305327685222426	2		685	461	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984966	55984966	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	50	426	0	ENST00000263923.4:c.163G>A	p.Gly55Arg	p.G55R	ENST00000263923	NM_002253.2	55	Gga/Aga	3/30	0.187661533462889	1	FACETS	0.907	0.774	1	0.907	0.774	1	CLONAL	1	TRUE	0	0.305327685222426	1		426	306	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462683	29462683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766541301	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	23	645	0	ENST00000389048.3:c.2218G>A	p.Gly740Arg	p.G740R	ENST00000389048	NM_004304.4	740	Gga/Aga	13/29	0.227370984294069	1	FACETS	0.306	0.238	0.385	0.306	0.238	0.385	SUBCLONAL	1	TRUE	0	0.305327685222426	1		645	417	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553707	106553707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753053806	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	73	652	0	ENST00000369096.4:c.1672G>A	p.Gly558Ser	p.G558S	ENST00000369096	NM_001198.3	558	Ggc/Agc	5/7	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.305327685222426	2		652	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577540	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	rs1555525498	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	59	559	0	ENST00000269305.4:c.741_742delinsTT	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	247	aaCCgg/aaTTgg	7/11	0.305327685222426	1	FACETS	0.936	0.809	1	0.936	0.809	1	CLONAL	1	TRUE	0	0.305327685222426	1		559	350	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139408990	139408990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	56	739	0	ENST00000277541.6:c.2179C>T	p.His727Tyr	p.H727Y	ENST00000277541	NM_017617.3	727	Cac/Tac	13/34	1	2	FACETS	0.801	0.687	0.924	0.801	0.687	0.924	CLONAL	1	TRUE	1	0.305327685222426	2		739	458	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803246	1803246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886043613	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	88	813	0	ENST00000260795.2:c.598C>T	p.Arg200Cys	p.R200C	ENST00000260795		200	Cgc/Tgc	4/17	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.305327685222426	2		813	496	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79974803	79974803	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199659527	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	62	500	0	ENST00000265081.6:c.1231C>T	p.Arg411Cys	p.R411C	ENST00000265081	NM_002439.4	411	Cgt/Tgt	8/24	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.305327685222426	2		500	358	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425839	49425839	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	68	794	0	ENST00000301067.7:c.12649C>T	p.Gln4217Ter	p.Q4217*	ENST00000301067	NM_003482.3	4217	Cag/Tag	39/54	1	2	FACETS	0.909	0.793	1	0.909	0.793	1	CLONAL	1	TRUE	1	0.305327685222426	2		794	490	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068441	16068441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	12	141	0	ENST00000268712.3:c.470C>T	p.Ser157Phe	p.S157F	ENST00000268712	NM_006311.3	157	tCc/tTc	5/46	0.305327685222426	1	FACETS	0.622	0.441	0.841	0.622	0.441	0.841	SUBCLONAL	1	TRUE	0	0.305327685222426	1		141	107	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851903	63851903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776160603	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	72	736	0	ENST00000279873.7:c.2681C>T	p.Ser894Leu	p.S894L	ENST00000279873	NM_032199.2	894	tCg/tTg	10/10	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.305327685222426	2		736	447	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967641	26967641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	76	442	0	ENST00000381527.3:c.784C>T	p.Pro262Ser	p.P262S	ENST00000381527	NM_001260.1	262	Cct/Tct	7/13	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.305327685222426	2		442	371	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339484	81339484	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	50	408	0	ENST00000222390.5:c.1520G>A	p.Trp507Ter	p.W507*	ENST00000222390	NM_000601.4	507	tGg/tAg	13/18	1	2	FACETS	0.978	0.833	1	0.978	0.833	1	CLONAL	1	TRUE	1	0.305327685222426	2		408	335	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553044	106553044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	102	768	0	ENST00000369096.4:c.1009C>T	p.Pro337Ser	p.P337S	ENST00000369096	NM_001198.3	337	Ccc/Tcc	5/7	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.305327685222426	2		768	539	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622256	117622256	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	57	468	0	ENST00000368508.3:c.6614G>A	p.Arg2205Lys	p.R2205K	ENST00000368508	NM_002944.2	2205	aGa/aAa	42/43	0.114937876669756	0	FACETS	0.772	0.666	0.886			1	INDETERMINATE	1	TRUE	0	0.305327685222426	0		468	336	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897361	78897361	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1308946941	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	94	870	0	ENST00000306801.3:c.2696G>A	p.Arg899Gln	p.R899Q	ENST00000306801	NM_020761.2	899	cGa/cAa	23/34	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.305327685222426	2		870	529	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427404	49427404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	76	846	0	ENST00000301067.7:c.11084C>T	p.Pro3695Leu	p.P3695L	ENST00000301067	NM_003482.3	3695	cCt/cTt	39/54	1	2	FACETS	0.986	0.867	1	0.986	0.867	1	CLONAL	1	TRUE	1	0.305327685222426	2		846	505	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864780	57864780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769216016	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	91	818	0	ENST00000228682.2:c.2257C>T	p.Leu753Phe	p.L753F	ENST00000228682	NM_005269.2	753	Ctt/Ttt	12/12	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.305327685222426	2		818	538	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599046	28599046	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	82	455	0	ENST00000241453.7:c.2242G>A	p.Asp748Asn	p.D748N	ENST00000241453	NM_004119.2	748	Gac/Aac	18/24	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.305327685222426	2		455	374	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363555	40363555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	64	636	0	ENST00000397332.2:c.674C>T	p.Pro225Leu	p.P225L	ENST00000397332	NM_001033082.2	225	cCc/cTc	3/3	1	2	FACETS	0.951	0.826	1	0.951	0.826	1	CLONAL	1	TRUE	1	0.305327685222426	2		636	441	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301117	65301117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	53	556	0	ENST00000342505.4:c.3331G>A	p.Gly1111Arg	p.G1111R	ENST00000342505	NM_002227.2	1111	Gga/Aga	24/25	1	2	FACETS	0.967	0.828	1	0.967	0.828	1	CLONAL	1	TRUE	1	0.305327685222426	2		556	359	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551861	150551862	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	72	687	0	ENST00000369026.2:c.145_146delinsAA	p.Gly49Lys	p.G49K	ENST00000369026	NM_021960.4	49	GGg/AAg	1/3	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.305327685222426	2		687	438	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809224	243809224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	55	477	0	ENST00000263826.5:c.400G>A	p.Asp134Asn	p.D134N	ENST00000263826	NM_005465.4	134	Gat/Aat	4/13	1	2	FACETS	0.914	0.785	1	0.914	0.785	1	CLONAL	1	TRUE	1	0.305327685222426	2		477	394	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023096	1023097	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	76	551	0	ENST00000358495.3:c.1158_1159delinsAA	p.Trp386_Asp387delinsTer	p.W386_D387delins*	ENST00000358495	NM_134424.2	386	tgGGac/tgAAac	11/12	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.305327685222426	2		551	467	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037432	12037432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	72	739	2	ENST00000396373.4:c.1063G>A	p.Glu355Lys	p.E355K	ENST00000396373	NM_001987.4	355	Gaa/Aaa	6/8	1	2	FACETS	0.921	0.806	1	0.921	0.806	1	CLONAL	1	TRUE	1	0.305327685222426	2		741	512	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21639481	21639481	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1347153563	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	46	369	0	ENST00000421138.2:c.433G>A	p.Glu145Lys	p.E145K	ENST00000421138		145	Gaa/Aaa	6/16	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.305327685222426	2		369	285	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243404	46243405	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	59	573	0	ENST00000334344.6:c.1757_1758delinsTT	p.Ser586Phe	p.S586F	ENST00000334344	NM_152641.2	586	tCC/tTT	14/21	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.305327685222426	2		573	361	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120795663	120795663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	41	391	0	ENST00000257552.2:c.490G>A	p.Glu164Lys	p.E164K	ENST00000257552	NM_002442.3	164	Gag/Aag	8/15	1	2	FACETS	0.866	0.725	1	0.866	0.725	1	CLONAL	1	TRUE	1	0.305327685222426	2		391	310	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008270	29008270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	73	498	0	ENST00000282397.4:c.601G>A	p.Glu201Lys	p.E201K	ENST00000282397	NM_002019.4	201	Gaa/Aaa	5/30	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.305327685222426	2		498	373	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041264	29041264	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	67	497	0	ENST00000282397.4:c.164G>A	p.Gly55Glu	p.G55E	ENST00000282397	NM_002019.4	55	gGg/gAg	3/30	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.305327685222426	2		497	383	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465606	99465606	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	29	614	0	ENST00000268035.6:c.2431G>C	p.Glu811Gln	p.E811Q	ENST00000268035	NM_000875.3	811	Gag/Cag	11/21	1	2	FACETS	0.45	0.361	0.552	0.45	0.361	0.552	SUBCLONAL	1	TRUE	1	0.305327685222426	2		614	422	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640870	3640870	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567170716	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	80	841	0	ENST00000294008.3:c.2769G>A	p.Met923Ile	p.M923I	ENST00000294008	NM_032444.2	923	atG/atA	12/15	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.305327685222426	2		841	474	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641239	23641240	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	61	674	0	ENST00000261584.4:c.2235dup	p.Ala746SerfsTer27	p.A746Sfs*27	ENST00000261584	NM_024675.3	745	-/A	5/13	1	2	FACETS	0.91	0.787	1	0.91	0.787	1	CLONAL	1	TRUE	1	0.305327685222426	2		674	439	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849286	89849286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	65	550	0	ENST00000389301.3:c.1607C>T	p.Ser536Leu	p.S536L	ENST00000389301	NM_000135.2	536	tCa/tTa	17/43	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.305327685222426	2		550	423	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37876074	37876074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370514427	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	70	649	0	ENST00000269571.5:c.1933G>A	p.Glu645Lys	p.E645K	ENST00000269571		645	Gag/Aag	16/27	1	2	FACETS	0.969	0.848	1	0.969	0.848	1	CLONAL	1	TRUE	1	0.305327685222426	2		649	473	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435828	56435829	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	81	895	0	ENST00000407977.2:c.1308_1309delinsTT	p.Arg437Trp	p.R437W	ENST00000407977		436	cgCCgg/cgTTgg	9/10	1	2	FACETS	0.99	0.874	1	0.99	0.874	1	CLONAL	1	TRUE	1	0.305327685222426	2		895	536	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400686	56400687	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	48	490	1	ENST00000348428.3:c.1280_1281delinsTT	p.Pro427Leu	p.P427L	ENST00000348428	NM_006785.3	427	cCC/cTT	11/17	0.305327685222426	1	FACETS	0.873	0.743	1	0.873	0.743	1	CLONAL	1	TRUE	0	0.305327685222426	1		491	305	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2180731	2180731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	41	298	0	ENST00000398665.3:c.101C>T	p.Ala34Val	p.A34V	ENST00000398665	NM_032482.2	34	gCt/gTt	2/28	1	2	FACETS	0.973	0.815	1	0.973	0.815	1	CLONAL	1	TRUE	1	0.305327685222426	2		298	276	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254645	10254646	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	51	558	0	ENST00000340748.4:c.2864_2865delinsTT	p.Pro955Leu	p.P955L	ENST00000340748		955	cCC/cTT	28/40	1	2	FACETS	0.865	0.738	1	0.865	0.738	1	CLONAL	1	TRUE	1	0.305327685222426	2		558	386	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296185	15296186	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	70	856	0	ENST00000263388.2:c.2178_2179delinsTT	p.Pro727Ser	p.P727S	ENST00000263388	NM_000435.2	726	ggCCcc/ggTTcc	14/33	1	2	FACETS	0.942	0.823	1	0.942	0.823	1	CLONAL	1	TRUE	1	0.305327685222426	2		856	487	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219782	36219782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	52	742	0	ENST00000222270.7:c.4679C>T	p.Pro1560Leu	p.P1560L	ENST00000222270	NM_014727.1	1560	cCc/cTc	20/37	1	2	FACETS	0.733	0.624	0.851	0.733	0.624	0.851	SUBCLONAL	1	TRUE	1	0.305327685222426	2		742	465	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748806	41748806	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	57	513	0	ENST00000301178.4:c.1331C>T	p.Pro444Leu	p.P444L	ENST00000301178	NM_021913.4	444	cCt/cTt	11/20	1	2	FACETS	0.926	0.798	1	0.926	0.798	1	CLONAL	1	TRUE	1	0.305327685222426	2		513	403	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457288	25457289	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	50	594	0	ENST00000264709.3:c.2598_2599delinsAA	p.Val867Ile	p.V867I	ENST00000264709	NM_175629.2	866	agGGta/agAAta	23/23	1	2	FACETS	0.811	0.69	0.943	0.811	0.69	0.943	CLONAL	1	TRUE	1	0.305327685222426	2		594	404	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250064	39250064	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	62	484	0	ENST00000402219.2:c.1505A>T	p.Asn502Ile	p.N502I	ENST00000402219	NM_005633.3	502	aAt/aTt	10/23	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.305327685222426	2		484	370	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607820	46607820	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	81	716	0	ENST00000263734.3:c.2009C>T	p.Pro670Leu	p.P670L	ENST00000263734	NM_001430.4	670	cCt/cTt	12/16	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.305327685222426	2		716	496	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027608	48027609	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	64	559	0	ENST00000234420.5:c.2486_2487delinsAA	p.Gly829Glu	p.G829E	ENST00000234420	NM_000179.2	829	gGG/gAA	4/10	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.305327685222426	2		559	405	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924894	49924894	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	74	766	0	ENST00000296474.3:c.4049G>A	p.Gly1350Glu	p.G1350E	ENST00000296474	NM_002447.2	1350	gGg/gAg	20/20	1	2	FACETS	0.999	0.877	1	0.999	0.877	1	CLONAL	1	TRUE	1	0.305327685222426	2		766	485	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610667	52610667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	68	493	0	ENST00000394830.3:c.3506C>T	p.Pro1169Leu	p.P1169L	ENST00000394830	NM_018313.4	1169	cCc/cTc	23/30	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.305327685222426	2		493	388	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637546	52637546	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763328959	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	60	335	0	ENST00000394830.3:c.2770G>A	p.Glu924Lys	p.E924K	ENST00000394830	NM_018313.4	924	Gaa/Aaa	18/30	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.305327685222426	2		335	363	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55603385	55603385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	50	441	0	ENST00000288135.5:c.2741G>A	p.Arg914Lys	p.R914K	ENST00000288135	NM_000222.2	914	aGa/aAa	20/21	1	2	FACETS	0.995	0.849	1	0.995	0.849	1	CLONAL	1	TRUE	1	0.305327685222426	2		441	329	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144380627	144380627	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs767303107	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	41	491	0	ENST00000262995.4:c.1765C>T	p.Arg589Ter	p.R589*	ENST00000262995	NM_207123.2	589	Cga/Tga	8/11	1	2	FACETS	0.866	0.725	1	0.866	0.725	1	CLONAL	1	TRUE	1	0.305327685222426	2		491	310	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295730	1295730	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	73	892	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.305327685222426	2		892	435	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140772	37140773	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	145	581	0	ENST00000373509.5:c.608_609delinsAA	p.Gly203Glu	p.G203E	ENST00000373509	NM_002648.3	203	gGG/gAA	5/6	0.305355583654101	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	2	TRUE	0	0.305327685222426	2		581	467	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192446	138192446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	71	498	0	ENST00000237289.4:c.82G>A	p.Asp28Asn	p.D28N	ENST00000237289	NM_001270507.1	28	Gac/Aac	2/9	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.305327685222426	2		498	417	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441562	6441562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	27	147	0	ENST00000356142.4:c.409G>A	p.Asp137Asn	p.D137N	ENST00000356142	NM_018890.3	137	Gat/Aat	6/7	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.305327685222426	2		147	146	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2123818	2123818	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	24	630	0	ENST00000349721.2:c.3862G>A	p.Asp1288Asn	p.D1288N	ENST00000349721	NM_003070.3	1288	Gac/Aac	27/34	0.305355583654101	1	FACETS	0.345	0.27	0.432	0.345	0.27	0.432	SUBCLONAL	1	TRUE	0	0.305327685222426	1		630	386	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970890	21970905	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCAGTCCTCACCTGAG	TCAGTCCTCACCTGAG	-	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	48	640	0	ENST00000304494.5:c.453_457+11del		p.X151_splice	ENST00000304494	NM_000077.4	151		2/3	0.305355583654101	1	FACETS	0.843	0.716	0.981	0.843	0.716	0.981	CLONAL	1	TRUE	0	0.305327685222426	1		640	316	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128419967	128419967	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	92	478	0	ENST00000265960.3:c.461A>T	p.Asn154Ile	p.N154I	ENST00000265960	NM_001006617.1	154	aAt/aTt	4/12	1	2	FACETS	0.779	0.697	0.865	1	0.982	1	SUBCLONAL	2	TRUE	1	0.305327685222426	2		478	387	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395148	139395149	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	52	785	0	ENST00000277541.6:c.5789_5790delinsTT	p.Thr1930Ile	p.T1930I	ENST00000277541	NM_017617.3	1930	aCC/aTT	31/34	1	2	FACETS	0.687	0.585	0.798	0.687	0.585	0.798	SUBCLONAL	1	TRUE	1	0.305327685222426	2		785	496	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412601	139412601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	115	729	0	ENST00000277541.6:c.1243G>A	p.Glu415Lys	p.E415K	ENST00000277541	NM_017617.3	415	Gag/Aag	7/34	1	2	FACETS	0.753	0.682	0.828	1	0.985	1	SUBCLONAL	2	TRUE	1	0.305327685222426	2		729	500	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933791	39933791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs975085731	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	117	405	0	ENST00000378444.4:c.808C>T	p.Pro270Ser	p.P270S	ENST00000378444	NM_001123385.1	270	Cct/Tct	4/15	1	1	FACETS	1	0.975	1	1	0.991	1	CLONAL	2	TRUE	0	0.305327685222426	1		405	278	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855251	76855252	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0060669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	54	225	0	ENST00000373344.5:c.5735_5736delinsTT	p.Ala1912Val	p.A1912V	ENST00000373344	NM_000489.3	1912	gCC/gTT	24/35	1	1	FACETS	0.887	0.772	1	1	0.976	1	CLONAL	2	TRUE	0	0.305327685222426	1		225	169	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593594	55593608	+	inframe_deletion	In_Frame_Del	DEL	GAAGTACAGTGGAAG	GAAGTACAGTGGAAG	-	novel	NA	P-0060670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	6	507	0	ENST00000288135.5:c.1661_1675del	p.Glu554_Lys558del	p.E554_K558del	ENST00000288135	NM_000222.2	554	GAAGTACAGTGGAAG/-	11/21	0.188597900443709	0	FACETS	0.92	0.56	1			1	CLONAL	1	TRUE	0	0.213685567685367	0		507	48	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593594	55593608	+	inframe_deletion	In_Frame_Del	DEL	GAAGTACAGTGGAAG	GAAGTACAGTGGAAG	-	novel	NA	P-0060670-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	531	507	0	ENST00000288135.5:c.1661_1675del	p.Glu554_Lys558del	p.E554_K558del	ENST00000288135	NM_000222.2	554	GAAGTACAGTGGAAG/-	11/21	0.908070713240879	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.907558448923031	2		507	581	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368394	225368395	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0060670-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	112	245	0	ENST00000264414.4:c.1351dup	p.Glu451GlyfsTer7	p.E451Gfs*7	ENST00000264414	NM_003590.4	451	gaa/gGaa	9/16	1	2	FACETS	0.904	0.827	0.982	0.904	0.827	0.982	CLONAL	1	TRUE	1	0.907558448923031	2		245	273	SUCCESS
ALB	213	MSKCC	GRCh37	4	74283925	74283925	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779064435	NA	P-0060670-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1757	97	551	0	ENST00000295897.4:c.1549G>T	p.Val517Phe	p.V517F	ENST00000295897	NM_000477.5	517	Gtc/Ttc	12/15	0.908070713240879	5	FACETS	0.272	0.241	0.306			1	SUBCLONAL	1	TRUE	NA	0.907558448923031	5		551	1854	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0060671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	166	563	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.666998045868257	1	FACETS	0.984	0.92	1	0.984	0.92	1	CLONAL	1	TRUE	0	0.666998045868257	1		563	337	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925600	114925600	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	127	565	0	ENST00000543371.1:c.1678C>A	p.Pro560Thr	p.P560T	ENST00000543371	NM_001198531.1	560	Cca/Aca	14/14	0.666998045868257	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.666998045868257	1		565	235	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347183	89347183	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	147	651	0	ENST00000301030.4:c.5767A>G	p.Ile1923Val	p.I1923V	ENST00000301030	NM_001256183.1	1923	Atc/Gtc	9/13	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.666998045868257	2		651	362	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296473	15296473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1342458782	NA	P-0060671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	153	618	0	ENST00000263388.2:c.1969G>A	p.Glu657Lys	p.E657K	ENST00000263388	NM_000435.2	657	Gag/Aag	13/33	0.666998045868257	4	FACETS	1	0.929	1	0.339	0.31	0.368	CLONAL	1	TRUE	1	0.666998045868257	4		618	753	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056451	26056633	+	inframe_deletion	In_Frame_Del	DEL	GCGGCAGCCAACGCTTTTTTCAGAGCAGCCAGAGAAACTCCGCTACGCTCTTTAGAGGCGGCCACAGCCTTGGTGATGAGCTCTGACACCGGGGGACCAGACGCCTTACGAGGCGTACCCCCAGCCTTTTTGGCCGCCTTCTTCTTTACAGGGGCCTTCTCCGCAGGAGGCGCGGCAGCGGGA	GCGGCAGCCAACGCTTTTTTCAGAGCAGCCAGAGAAACTCCGCTACGCTCTTTAGAGGCGGCCACAGCCTTGGTGATGAGCTCTGACACCGGGGGACCAGACGCCTTACGAGGCGTACCCCCAGCCTTTTTGGCCGCCTTCTTCTTTACAGGGGCCTTCTCCGCAGGAGGCGCGGCAGCGGGA	-	novel	NA	P-0060671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	89	503	0	ENST00000343677.2:c.24_206del	p.Pro9_Ala69del	p.P9_A69del	ENST00000343677	NM_005319.3	8	gcTCCCGCTGCCGCGCCTCCTGCGGAGAAGGCCCCTGTAAAGAAGAAGGCGGCCAAAAAGGCTGGGGGTACGCCTCGTAAGGCGTCTGGTCCCCCGGTGTCAGAGCTCATCACCAAGGCTGTGGCCGCCTCTAAAGAGCGTAGCGGAGTTTCTCTGGCTGCTCTGAAAAAAGCGTTGGCTGCCGCc/gcc	1/1	1	2	FACETS	0.674	0.601	0.75	0.674	0.601	0.75	SUBCLONAL	1	TRUE	1	0.666998045868257	2		503	396	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692911	89692911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909241	NA	P-0060672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	10	497	0	ENST00000371953.3:c.395G>A	p.Gly132Asp	p.G132D	ENST00000371953	NM_000314.4	132	gGt/gAt	5/9	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		497	409	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589664	67589664	+	splice_donor_variant	Splice_Site	SNP	T	T	G	rs1554051075	NA	P-0060672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	10	382	0	ENST00000274335.5:c.1425+2T>G		p.X475_splice	ENST00000274335		475			1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		382	349	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692765	89692769	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CACAG	CACAG	-	novel	NA	P-0060673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	11	355	0	ENST00000371953.3:c.254-5_254-1del		p.X85_splice	ENST00000371953	NM_000314.4	85			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		355	79	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520000	NA	P-0060674-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	259	756	1	ENST00000269305.4:c.452C>A	p.Pro151His	p.P151H	ENST00000269305	NM_001126112.2	151	cCc/cAc	5/11	0.601281397609903	1	FACETS	0.961	0.907	1	0.961	0.907	1	CLONAL	1	TRUE	0	0.601281397609903	1		757	627	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120571	2120571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45469298	NA	P-0060674-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	50	595	0	ENST00000219476.3:c.1831C>T	p.Arg611Trp	p.R611W	ENST00000219476	NM_000548.3	611	Cgg/Tgg	17/42	0.596923022359369	1	FACETS	0.3	0.255	0.349	0.3	0.255	0.349	SUBCLONAL	1	TRUE	0	0.601281397609903	1		595	388	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777111	9777111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060674-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	34	781	0	ENST00000377346.4:c.875C>T	p.Pro292Leu	p.P292L	ENST00000377346	NM_005026.3	292	cCt/cTt	7/24	0.600438649503511	1	FACETS	0.167	0.136	0.202	0.167	0.136	0.202	SUBCLONAL	1	TRUE	0	0.601281397609903	1		781	474	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154808	2154808	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060674-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	172	794	1	ENST00000434045.2:c.413C>A	p.Thr138Lys	p.T138K	ENST00000434045	NM_001127598.1	138	aCg/aAg	4/5	0.601281397609903	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.601281397609903	1		795	392	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651108	206651108	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060674-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	150	698	0	ENST00000367120.3:c.718G>C	p.Glu240Gln	p.E240Q	ENST00000367120	NM_014002.3	240	Gag/Cag	8/22	1	2	FACETS	0.723	0.662	0.786	0.723	0.662	0.786	SUBCLONAL	1	TRUE	1	0.601281397609903	2		698	690	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0060675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	10	599	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	0.344	0.232	0.486	0.344	0.232	0.486	SUBCLONAL	1	FALSE	1	0.160146849050437	2		599	363	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560404	95560404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	195	701	2	ENST00000393063.1:c.5185C>T	p.Pro1729Ser	p.P1729S	ENST00000393063	NM_030621.3	1729	Ccg/Tcg	25/28	1	2	FACETS	0.885	0.82	0.953	0.885	0.82	0.953	CLONAL	1	TRUE	1	0.505670181080687	2		703	871	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969932	81969932	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024473204	NA	P-0060710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	283	722	0	ENST00000359376.3:c.3001C>T	p.Arg1001Cys	p.R1001C	ENST00000359376	NM_002661.3	1001	Cgc/Tgc	27/33	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.505670181080687	2		722	1008	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141564	11141564	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	230	719	0	ENST00000358026.2:c.3541C>T	p.His1181Tyr	p.H1181Y	ENST00000358026	NM_001128849.1	1181	Cac/Tac	25/36	1	2	FACETS	0.954	0.89	1	0.954	0.89	1	CLONAL	1	TRUE	1	0.505670181080687	2		719	954	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272140	15272140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	248	845	0	ENST00000263388.2:c.6299C>T	p.Ser2100Leu	p.S2100L	ENST00000263388	NM_000435.2	2100	tCg/tTg	33/33	1	2	FACETS	0.961	0.899	1	0.961	0.899	1	CLONAL	1	TRUE	1	0.505670181080687	2		845	1021	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295255	15295255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752312396	NA	P-0060710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	184	664	0	ENST00000263388.2:c.2417G>A	p.Arg806Gln	p.R806Q	ENST00000263388	NM_000435.2	806	cGa/cAa	16/33	1	2	FACETS	0.896	0.829	0.966	0.896	0.829	0.966	CLONAL	1	TRUE	1	0.505670181080687	2		664	812	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17949182	17949182	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	108	621	0	ENST00000458235.1:c.1459G>A	p.Val487Met	p.V487M	ENST00000458235	NM_000215.3	487	Gtg/Atg	11/24	1	2	FACETS	0.466	0.417	0.517	0.466	0.417	0.517	SUBCLONAL	1	TRUE	1	0.505670181080687	2		621	917	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520257	9520257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	227	632	1	ENST00000353224.5:c.2012C>T	p.Ser671Leu	p.S671L	ENST00000353224	NM_177990.2	671	tCa/tTa	10/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.505670181080687	2		633	856	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295250	+	upstream_gene_variant	5'Flank	DEL	GGGGGCTGGGCCGGGGACCCGGG	GGGGGCTGGGCCGGGGACCCGGG	-	novel	NA	P-0060710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	125	724	0				ENST00000310581	NM_198253.2	-/1132			0.505670181080687	1	FACETS	0.731	0.666	0.8	0.731	0.666	0.8	SUBCLONAL	1	TRUE	0	0.505670181080687	1		724	505	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460533	149460533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	256	817	0	ENST00000286301.3:c.104G>A	p.Gly35Glu	p.G35E	ENST00000286301	NM_005211.3	35	gGa/gAa	3/22	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.505670181080687	2		817	956	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678985	117678985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	122	296	0	ENST00000368508.3:c.3836C>T	p.Ser1279Phe	p.S1279F	ENST00000368508	NM_002944.2	1279	tCt/tTt	24/43	0.505670181080687	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.505670181080687	1		296	328	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0060710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	333	410	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.490318872977429	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.505670181080687	3		410	756	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68993050	68993050	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	102	375	0	ENST00000288368.4:c.1855G>A	p.Val619Ile	p.V619I	ENST00000288368	NM_024870.2	619	Gta/Ata	17/40	0.464119105067678	5	FACETS	0.923	0.825	1	0.231	0.206	0.257	CLONAL	1	TRUE	1	0.505670181080687	5		375	769	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938365	76938365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	63	569	0	ENST00000373344.5:c.2383G>A	p.Gly795Ser	p.G795S	ENST00000373344	NM_000489.3	795	Ggc/Agc	9/35	0.392333225143124	1	FACETS	0.271	0.234	0.311	0.271	0.234	0.311	SUBCLONAL	1	TRUE	0	0.505670181080687	1		569	687	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220503	123220503	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	70	571	0	ENST00000218089.9:c.3160G>A	p.Asp1054Asn	p.D1054N	ENST00000218089	NM_001042749.1	1054	Gat/Aat	30/35	0.392333225143124	1	FACETS	0.291	0.253	0.331	0.291	0.253	0.331	SUBCLONAL	1	TRUE	0	0.505670181080687	1		571	712	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	182	759	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.851	0.791	0.912	0.851	0.791	0.912	CLONAL	1	TRUE	1	0.808436871248798	2		760	529	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888166	112888166	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121918461	NA	P-0060712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	282	489	0	ENST00000351677.2:c.182A>C	p.Asp61Ala	p.D61A	ENST00000351677	NM_002834.3	61	gAt/gCt	3/16	0.606839795079884	1	FACETS	0.676	0.641	0.711	0.676	0.641	0.711	SUBCLONAL	1	TRUE	0	0.808436871248798	1		489	615	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588834	29588834	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555619041	NA	P-0060712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	215	425	0	ENST00000356175.3:c.4621del	p.Asn1542ThrfsTer11	p.N1542Tfs*11	ENST00000356175	NM_000267.3	1540	agC/ag	34/57	1	2	FACETS	0.897	0.84	0.955	0.897	0.84	0.955	CLONAL	1	TRUE	1	0.808436871248798	2		425	593	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677276	29677276	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs769052540	NA	P-0060712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	110	384	0	ENST00000356175.3:c.7336del	p.Ser2446GlnfsTer22	p.S2446Qfs*22	ENST00000356175	NM_000267.3	2445	aTt/at	49/57	1	2	FACETS	0.932	0.85	1	0.932	0.85	1	CLONAL	1	TRUE	1	0.808436871248798	2		384	292	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0060713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	148	804	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.24506285514152	1	FACETS	0.961	0.876	1	0.961	0.876	1	CLONAL	1	TRUE	0	0.24506285514152	1		804	1103	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0060713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	73	410	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.952	0.833	1	0.952	0.833	1	CLONAL	1	TRUE	1	0.24506285514152	2		410	626	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940402	49940402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760399844	NA	P-0060713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	59	622	0	ENST00000296474.3:c.641G>A	p.Arg214His	p.R214H	ENST00000296474	NM_002447.2	214	cGc/cAc	1/20	0.24506285514152	1	FACETS	0.409	0.351	0.474	0.409	0.351	0.474	SUBCLONAL	1	TRUE	0	0.24506285514152	1		622	1032	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158132	27158132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773256013	NA	P-0060713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	121	608	1	ENST00000380036.4:c.356G>A	p.Arg119His	p.R119H	ENST00000380036	NM_000459.3	119	cGt/cAt	2/23	1	2	FACETS	0.908	0.819	1	0.908	0.819	1	CLONAL	1	TRUE	1	0.24506285514152	2		609	1087	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597440	52597440	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	57	482	0	ENST00000394830.3:c.3870del	p.Lys1290AsnfsTer5	p.K1290Nfs*5	ENST00000394830	NM_018313.4	1290	aaA/aa	25/30	0.24506285514152	1	FACETS	0.504	0.431	0.584	0.504	0.431	0.584	SUBCLONAL	1	TRUE	0	0.24506285514152	1		482	810	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86658426	86658426	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776213397	NA	P-0060713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	34	336	0	ENST00000274376.6:c.1391G>A	p.Arg464His	p.R464H	ENST00000274376	NM_002890.2	464	cGt/cAt	10/25	0.24506285514152	1	FACETS	0.57	0.466	0.688	0.57	0.466	0.688	SUBCLONAL	1	TRUE	0	0.24506285514152	1		336	427	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0060715-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	55	418	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.547	0.467	0.634	0.547	0.467	0.634	SUBCLONAL	1	TRUE	1	0.314891180308826	2		418	639	SUCCESS
APC	324	MSKCC	GRCh37	5	112175240	112175240	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060715-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	84	512	0	ENST00000257430.4:c.3949G>T	p.Glu1317Ter	p.E1317*	ENST00000257430	NM_000038.5	1317	Gaa/Taa	16/16	1	2	FACETS	0.595	0.525	0.671	0.595	0.525	0.671	SUBCLONAL	1	TRUE	1	0.314891180308826	2		512	896	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174459	11174459	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557739557	NA	P-0060715-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	124	481	0	ENST00000361445.4:c.7216G>A	p.Val2406Met	p.V2406M	ENST00000361445	NM_004958.3	2406	Gtg/Atg	53/58	0.311566785904189	1	FACETS	0.877	0.794	0.964	0.877	0.794	0.964	CLONAL	1	TRUE	0	0.314891180308826	1		481	757	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204494707	204494707	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060715-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	124	429	0	ENST00000367182.3:c.61C>G	p.Pro21Ala	p.P21A	ENST00000367182	NM_001278516.1	21	Cct/Gct	2/11	1	2	FACETS	0.977	0.884	1	0.977	0.884	1	CLONAL	1	TRUE	1	0.314891180308826	2		429	806	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160342	108160342	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060715-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	126	272	0	ENST00000278616.4:c.4250A>G	p.Lys1417Arg	p.K1417R	ENST00000278616	NM_000051.3	1417	aAa/aGa	29/63	0.302228439708451	2	FACETS	0.868	0.791	0.947	0.868	0.791	0.947	CLONAL	2	TRUE	0	0.314891180308826	2		272	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577567	7577569	+	frameshift_variant	Frame_Shift_Del	DEL	ACA	ACA	G	novel	NA	P-0060715-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	181	470	0	ENST00000269305.4:c.712_714delinsC	p.Cys238GlnfsTer25	p.C238Qfs*25	ENST00000269305	NM_001126112.2	238	TGT/C	7/11	0.311566785904189	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.314891180308826	1		470	865	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0060717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	149	418	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.382124107166391	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	FALSE	1	0.382124107166391	3		418	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0060717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	96	919	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.382124107166391	1	FACETS	0.488	0.434	0.545	0.488	0.434	0.545	SUBCLONAL	1	FALSE	0	0.382124107166391	1		919	833	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0060717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	70	423	1	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.382124107166391	1	FACETS	0.5	0.436	0.569	0.5	0.436	0.569	SUBCLONAL	1	FALSE	0	0.382124107166391	1		424	593	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0060717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	265	748	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	0.382124107166391	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	0	0.382124107166391	1		748	962	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	9	452	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.105	0.069	0.151	0.105	0.069	0.151	SUBCLONAL	1	FALSE	1	0.382124107166391	2		452	449	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0060717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	153	541	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.382124107166391	0	FACETS	0.644	0.597	0.693			1	SUBCLONAL	2	FALSE	0	0.382124107166391	0		541	384	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73334690	73334690	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs575285131	NA	P-0060717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	98	373	0	ENST00000377767.4:c.2770C>T	p.Arg924Ter	p.R924*	ENST00000377767	NM_014953.3	924	Cga/Tga	20/21	0.215408695077714	3	FACETS	0.781	0.702	0.864	0.781	0.702	0.864	INDETERMINATE	2	FALSE	1	0.382124107166391	3		373	391	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0060717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	293	480	4	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.971	1	1	0.996	1	CLONAL	2	FALSE	1	0.382124107166391	2		484	739	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979624	55979624	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	30	413	0	ENST00000263923.4:c.823C>T	p.Arg275Ter	p.R275*	ENST00000263923	NM_002253.2	275	Cga/Tga	7/30	1	2	FACETS	0.312	0.25	0.381	0.312	0.25	0.381	SUBCLONAL	1	FALSE	1	0.382124107166391	2		413	504	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440168	220440168	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757864159	NA	P-0060717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	254	655	0	ENST00000243786.2:c.1021C>T	p.Arg341Cys	p.R341C	ENST00000243786	NM_002191.3	341	Cgc/Tgc	2/2	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	FALSE	1	0.382124107166391	2		655	901	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624942	9624942	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	246	483	0	ENST00000353224.5:c.35C>A	p.Ser12Tyr	p.S12Y	ENST00000353224	NM_177990.2	12	tCt/tAt	3/10	0.225644190057542	5	FACETS	1	0.989	1	0.823	0.772	0.876	INDETERMINATE	2	FALSE	2	0.382124107166391	5		483	820	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577414	64577418	+	frameshift_variant	Frame_Shift_Del	DEL	GGTAG	GGTAG	-	novel	NA	P-0060717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	207	727	0	ENST00000312049.6:c.164_168del	p.Pro55GlnfsTer60	p.P55Qfs*60	ENST00000312049	NM_130799.2	55	cCTACC/c	2/10	1	2	FACETS	0.896	0.83	0.965	0.896	0.83	0.965	CLONAL	1	FALSE	1	0.382124107166391	2		727	1209	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149743	202149754	+	inframe_deletion	In_Frame_Del	DEL	TGACATCTCAGT	TGACATCTCAGT	-	novel	NA	P-0060717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	116	702	0	ENST00000358485.4:c.1185_1196del	p.Ser397_Thr400del	p.S397_T400del	ENST00000358485	NM_001080125.1	395	cTGACATCTCAGTtc/ctc	8/9	1	2	FACETS	0.631	0.568	0.698	0.631	0.568	0.698	SUBCLONAL	1	FALSE	1	0.382124107166391	2		702	962	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0060718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	147	583	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.961	1	1	0.992	1	CLONAL	2	TRUE	1	0.362502346807368	2		583	381	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0060718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	138	937	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	1	2	FACETS	0.957	0.871	1	0.957	0.871	1	CLONAL	1	TRUE	1	0.362502346807368	2		937	796	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0060718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	92	396	1	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	1	2	FACETS	0.952	0.849	1	0.952	0.849	1	CLONAL	1	TRUE	1	0.362502346807368	2		397	533	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662313	227662313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771539785	NA	P-0060718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	173	676	0	ENST00000305123.5:c.1142G>A	p.Arg381His	p.R381H	ENST00000305123	NM_005544.2	381	cGc/cAc	1/2	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.362502346807368	2		676	764	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38957753	38957753	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0060718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	71	328	0	ENST00000357387.3:c.2499+1G>T		p.X833_splice	ENST00000357387	NM_152756.3	833			1	2	FACETS	0.97	0.85	1	0.97	0.85	1	CLONAL	1	TRUE	1	0.362502346807368	2		328	404	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591088	67591233	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAACGTATGAACAGCATTAAACCAGACCTTATCCAGCTGAGAAAGACGAGAGACCAATACTTGATGTAAGTATTTGAAATGGAATCCTATACATGAATAATTGGTGATTGCTACAATTCAGGATGAGTTAATGCGTTCTCTTTTCA	AAACGTATGAACAGCATTAAACCAGACCTTATCCAGCTGAGAAAGACGAGAGACCAATACTTGATGTAAGTATTTGAAATGGAATCCTATACATGAATAATTGGTGATTGCTACAATTCAGGATGAGTTAATGCGTTCTCTTTTCA	-	novel	NA	P-0060718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	89	451	0	ENST00000274335.5:c.1685_1746-11del		p.X562_splice	ENST00000274335		562		12/15	1	2	FACETS	0.909	0.808	1	0.909	0.808	1	CLONAL	1	TRUE	1	0.362502346807368	2		451	540	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265534	152265535	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAA	novel	NA	P-0060718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	109	579	0	ENST00000206249.3:c.989_990insAGA	p.Glu330dup	p.E330dup	ENST00000206249	NM_000125.3	330	-/GAA	4/8	1	2	FACETS	0.911	0.819	1	0.911	0.819	1	CLONAL	1	TRUE	1	0.362502346807368	2		579	660	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798433	45798439	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ACCTTCC	ACCTTCC	-	novel	NA	P-0060718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	140	732	0	ENST00000450313.1:c.572_576+2del		p.X191_splice	ENST00000450313	NM_012222.2	191		7/16	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.362502346807368	2		732	771	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0060719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	131	919	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.239937084167997	2		919	891	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589599	67589604	+	inframe_deletion	In_Frame_Del	DEL	TCAGTT	TCAGTT	-	novel	NA	P-0060719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	42	265	0	ENST00000274335.5:c.1365_1370del	p.Phe456_Gln457del	p.F456_Q457del	ENST00000274335		454	acTCAGTTt/act	10/15	0.239937084167997	1	FACETS	0.792	0.662	0.935	0.792	0.662	0.935	CLONAL	1	TRUE	0	0.239937084167997	1		265	389	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719107	52719107	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	60	634	0	ENST00000322088.6:c.883G>A	p.Glu295Lys	p.E295K	ENST00000322088	NM_014225.5	295	Gag/Aag	7/15	NA	2	FACETS	0.554	0.476	0.64			1	INDETERMINATE	1	TRUE	NA	0.239937084167997	2		634	902	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40498610	40498610	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	139	375	0	ENST00000264657.5:c.250C>T	p.Arg84Ter	p.R84*	ENST00000264657	NM_139276.2	84	Cga/Tga	3/24	0.238478046480947	2	FACETS	0.844	0.77	0.922	0.844	0.77	0.922	CLONAL	2	TRUE	0	0.239937084167997	2		375	686	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189822	11189822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760144268	NA	P-0060719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	59	425	0	ENST00000361445.4:c.5687G>A	p.Arg1896Gln	p.R1896Q	ENST00000361445	NM_004958.3	1896	cGa/cAa	40/58	0.238478046480947	2	FACETS	0.644	0.553	0.743	0.322	0.276	0.372	SUBCLONAL	1	TRUE	0	0.239937084167997	2		425	764	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189473	56189494	+	frameshift_variant	Frame_Shift_Del	DEL	TACTGAAGCATCCAGTCTTTCG	TACTGAAGCATCCAGTCTTTCG	-	novel	NA	P-0060719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	66	456	0	ENST00000399503.3:c.4509_4530del	p.Lys1504HisfsTer49	p.K1504Hfs*49	ENST00000399503	NM_005921.1	1502	cTACTGAAGCATCCAGTCTTTCGt/ct	20/20	0.239937084167997	1	FACETS	0.632	0.548	0.724	0.632	0.548	0.724	SUBCLONAL	1	TRUE	0	0.239937084167997	1		456	766	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0060810-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	160	469	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.832785039063297	1	FACETS	0.522	0.483	0.561	0.522	0.483	0.561	SUBCLONAL	1	TRUE	0	0.832785039063297	1		469	430	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636438	73636438	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060810-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	159	884	1	ENST00000377687.4:c.701C>A	p.Thr234Lys	p.T234K	ENST00000377687	NM_001730.3	234	aCa/aAa	2/4	1	2	FACETS	0.508	0.467	0.552	0.508	0.467	0.552	SUBCLONAL	1	TRUE	1	0.832785039063297	2		885	751	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50731361	50731362	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060810-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	122	468	0	ENST00000307179.4:c.92dup	p.Ser32LysfsTer3	p.S32Kfs*3	ENST00000307179		31	ata/aTta	2/20	1	2	FACETS	0.936	0.858	1	0.936	0.858	1	CLONAL	1	TRUE	1	0.832785039063297	2		468	313	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250542	110250542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060810-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	169	646	2	ENST00000374672.4:c.133C>T	p.Arg45Trp	p.R45W	ENST00000374672	NM_004235.4	45	Cgg/Tgg	3/5	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.832785039063297	2		648	402	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0060811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	49	910	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.194131999233214	2		910	496	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	38	397	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	1	2	FACETS	0.754	0.623	0.901	0.754	0.623	0.901	CLONAL	1	TRUE	1	0.194131999233214	2		397	519	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469672	NA	P-0060811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	16	332	0	ENST00000374080.3:c.131G>A	p.Gly44Asp	p.G44D	ENST00000374080		44	gGt/gAt	2/45	1	2	FACETS	0.305	0.224	0.403	0.305	0.224	0.403	SUBCLONAL	1	TRUE	1	0.194131999233214	2		332	540	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121909229	NA	P-0060811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	69	299	0	ENST00000371953.3:c.389G>T	p.Arg130Leu	p.R130L	ENST00000371953	NM_000314.4	130	cGa/cTa	5/9	0.194131999233214	2	FACETS	0.843	0.742	0.95	1	0.964	1	CLONAL	3	TRUE	0	0.194131999233214	2		299	281	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094454	27094455	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	65	422	0	ENST00000324856.7:c.3163dup	p.Tyr1055LeufsTer50	p.Y1055Lfs*50	ENST00000324856	NM_006015.4	1054	-/T	11/20	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.194131999233214	2		422	659	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792732	33792737	+	inframe_deletion	In_Frame_Del	DEL	GCGGGT	GCGGGT	-	rs762459325	NA	P-0060811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	13	423	1	ENST00000498907.2:c.584_589del	p.His195_Pro196del	p.H195_P196del	ENST00000498907	NM_004364.3	195	cACCCGCcg/ccg	1/1	1	2	FACETS	0.252	0.178	0.342	0.252	0.178	0.342	SUBCLONAL	1	TRUE	1	0.194131999233214	2		424	532	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481648	56481648	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs774589520	NA	P-0060811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	97	524	0	ENST00000267101.3:c.683A>G	p.His228Arg	p.H228R	ENST00000267101	NM_001982.3	228	cAt/cGt	6/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.194131999233214	2		524	760	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837945	156837945	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	71	526	0	ENST00000524377.1:c.478C>T	p.Gln160Ter	p.Q160*	ENST00000524377	NM_002529.3	160	Cag/Tag	5/17	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.194131999233214	2		526	664	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0060811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	37	810	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.194131999233214	2		810	336	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68758612	68758612	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	78	464	0	ENST00000487270.1:c.768del	p.Asn257IlefsTer7	p.N257Ifs*7	ENST00000487270	NM_133509.3	256	acG/ac	8/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.194131999233214	2		464	650	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701888	43701888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768497502	NA	P-0060811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	38	365	0	ENST00000382044.4:c.5357G>A	p.Arg1786Gln	p.R1786Q	ENST00000382044	NM_001141980.1	1786	cGa/cAa	25/28	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.194131999233214	2		365	380	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423475	47423475	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	44	445	0	ENST00000404338.3:c.1543G>T	p.Glu515Ter	p.E515*	ENST00000404338	NM_004491.4	515	Gag/Tag	1/6	1	2	FACETS	0.899	0.754	1	0.899	0.754	1	CLONAL	1	TRUE	1	0.194131999233214	2		445	504	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591147	67591147	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	86	362	0	ENST00000274335.5:c.1740C>A	p.Tyr580Ter	p.Y580*	ENST00000274335		580	taC/taA	12/15	0.194131999233214	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	2	TRUE	0	0.194131999233214	2		362	431	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984418	201984419	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0060813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	545	452	0	ENST00000359651.3:c.1085dup	p.Glu363GlyfsTer108	p.E363Gfs*108	ENST00000359651		361	-/A	8/8	0.787171047108073	5	FACETS	1	0.988	1	0.535	0.513	0.557	CLONAL	2	TRUE	1	0.787171047108073	5		452	1411	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0060813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	198	315	2	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	0.787171047108073	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.787171047108073	2		317	230	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0060813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	637	443	1	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.787171047108073	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.787171047108073	2		444	716	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056180	26056180	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	72	521	0	ENST00000343677.2:c.477G>C	p.Lys159Asn	p.K159N	ENST00000343677	NM_005319.3	159	aaG/aaC	1/1	0.787171047108073	3	FACETS	0.211	0.183	0.241	0.105	0.091	0.121	SUBCLONAL	1	TRUE	1	0.787171047108073	3		521	1211	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611203	100611203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555977836	NA	P-0060813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	378	529	0	ENST00000308731.7:c.1403G>A	p.Arg468His	p.R468H	ENST00000308731	NM_000061.2	468	cGc/cAc	15/19	0.598954626907155	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	2	0.787171047108073	4		529	858	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578485	7578485	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1064793929	NA	P-0060816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	119	565	0	ENST00000269305.4:c.445del	p.Ser149ProfsTer21	p.S149Pfs*21	ENST00000269305	NM_001126112.2	149	Tcc/cc	5/11	0.169823450294234	1	FACETS	0.903	0.816	0.995	1	0.988	1	CLONAL	2	FALSE	0	0.169823450294234	1		565	710	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919631	28919631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200840674	NA	P-0060816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	83	371	0	ENST00000282397.4:c.2306C>T	p.Ala769Val	p.A769V	ENST00000282397	NM_002019.4	769	gCg/gTg	16/30	1	2	FACETS	0.82	0.725	0.922	1	0.98	1	CLONAL	2	FALSE	1	0.169823450294234	2		371	596	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410439	139410439	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1334264743	NA	P-0060816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	71	455	0	ENST00000277541.6:c.1663A>G	p.Thr555Ala	p.T555A	ENST00000277541	NM_017617.3	555	Acg/Gcg	10/34	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.169823450294234	2		455	607	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974782	21974782	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs138677674	NA	P-0060816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	112	560	0	ENST00000304494.5:c.45G>A	p.Trp15Ter	p.W15*	ENST00000304494	NM_000077.4	15	tgG/tgA	1/3	0.169823450294234	1	FACETS	0.953	0.859	1	1	0.988	1	CLONAL	2	FALSE	0	0.169823450294234	1		560	633	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046462	69046462	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761455338	NA	P-0060816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	73	437	1	ENST00000288368.4:c.3935C>T	p.Ala1312Val	p.A1312V	ENST00000288368	NM_024870.2	1312	gCg/gTg	32/40	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.169823450294234	2		438	617	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0060816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	70	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.926	0.81	1	1	0.98	1	CLONAL	2	FALSE	1	0.169823450294234	2		334	445	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591926	48591926	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	122	480	0	ENST00000342988.3:c.1089T>G	p.Cys363Trp	p.C363W	ENST00000342988	NM_005359.5	363	tgT/tgG	9/12	0.169823450294234	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	FALSE	0	0.169823450294234	2		480	595	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288585	198288585	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	68	364	0	ENST00000335508.6:c.142G>T	p.Asp48Tyr	p.D48Y	ENST00000335508	NM_012433.2	48	Gac/Tac	2/25	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.169823450294234	2		364	592	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861013	35861013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	67	379	0	ENST00000303115.3:c.142G>A	p.Val48Met	p.V48M	ENST00000303115	NM_002185.3	48	Gtg/Atg	2/8	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.169823450294234	2		379	624	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0060817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	82	626	3	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	NA	2	FACETS	0.974	0.859	1			1	INDETERMINATE	1	TRUE	NA	0.24878762698393	2		629	677	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945087	31945087	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	102	528	0	ENST00000340398.3:c.14A>C	p.Lys5Thr	p.K5T	ENST00000340398	NM_001013699.2	5	aAg/aCg	1/1	1	2	FACETS	0.919	0.821	1	0.919	0.821	1	CLONAL	1	TRUE	1	0.24878762698393	2		528	892	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0060818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	251	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.240834790325775	6	FACETS	1	0.985	1			1	INDETERMINATE	3	TRUE	NA	0.701701992134127	6		334	515	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652097	36652098	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0060818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	203	472	0	ENST00000244741.5:c.222dup	p.Lys75GlnfsTer14	p.K75Qfs*14	ENST00000244741	NM_000389.4	73	-/C	2/3	1	2	FACETS	0.89	0.829	0.952	0.89	0.829	0.952	CLONAL	1	TRUE	1	0.701701992134127	2		472	650	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651338	52651338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1192414131	NA	P-0060818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	45	369	0	ENST00000394830.3:c.1758G>A	p.Met586Ile	p.M586I	ENST00000394830	NM_018313.4	586	atG/atA	15/30	1	2	FACETS	0.22	0.185	0.26	0.22	0.185	0.26	SUBCLONAL	1	TRUE	1	0.701701992134127	2		369	582	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0060818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	132	479	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.701701992134127	2		479	341	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652125	36652132	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCGAGG	CGGCGAGG	-	novel	NA	P-0060818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	188	472	0	ENST00000244741.5:c.248_255del	p.Arg83ProfsTer3	p.R83Pfs*3	ENST00000244741	NM_000389.4	83	CGGCGAGGc/c	2/3	1	2	FACETS	0.845	0.785	0.907	0.845	0.785	0.907	CLONAL	1	TRUE	1	0.701701992134127	2		472	634	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43766957	43766957	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0060818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	27	306	0	ENST00000382044.4:c.1094C>G	p.Ser365Ter	p.S365*	ENST00000382044	NM_001141980.1	365	tCa/tGa	10/28	1	2	FACETS	0.156	0.124	0.193	0.156	0.124	0.193	SUBCLONAL	1	TRUE	1	0.701701992134127	2		306	493	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63553967	63553967	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1183931601	NA	P-0060818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	47	478	2	ENST00000307078.5:c.772A>G	p.Thr258Ala	p.T258A	ENST00000307078	NM_004655.3	258	Acg/Gcg	2/11	1	2	FACETS	0.174	0.146	0.204	0.174	0.146	0.204	SUBCLONAL	1	TRUE	1	0.701701992134127	2		480	772	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61306462	61306462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	117	293	0	ENST00000341074.5:c.725G>A	p.Ser242Asn	p.S242N	ENST00000341074	NM_002974.2	242	aGc/aAc	7/8	1	2	FACETS	0.83	0.754	0.907	0.83	0.754	0.907	CLONAL	1	TRUE	1	0.701701992134127	2		293	402	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158633	26158633	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	51	161	0	ENST00000289316.2:c.236C>T	p.Ser79Phe	p.S79F	ENST00000289316	NM_138720.2	79	tCc/tTc	1/2	1	2	FACETS	0.803	0.694	0.919	0.803	0.694	0.919	CLONAL	1	TRUE	1	0.701701992134127	2		161	181	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0060819-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	67	479	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.250930029323379	2		479	508	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0060819-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	170	665	2	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.22560136658832	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.250930029323379	2		667	638	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858195	40858195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777686988	NA	P-0060819-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	95	706	0	ENST00000428826.2:c.1669C>T	p.Arg557Cys	p.R557C	ENST00000428826		557	Cgt/Tgt	16/21	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.250930029323379	2		706	657	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248001	98248001	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060819-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	108	457	0	ENST00000331920.6:c.550C>T	p.Gln184Ter	p.Q184*	ENST00000331920	NM_000264.3	184	Cag/Tag	3/24	0.250930029323379	1	FACETS	0.981	0.881	1	0.981	0.881	1	CLONAL	1	TRUE	0	0.250930029323379	1		457	767	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818219	43818219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060819-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	245	515	0	ENST00000372470.3:c.1684G>A	p.Glu562Lys	p.E562K	ENST00000372470	NM_005373.2	562	Gaa/Aaa	12/12	0.22560136658832	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.250930029323379	2		515	929	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849947	156849947	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060819-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	207	441	0	ENST00000524377.1:c.2203G>A	p.Glu735Lys	p.E735K	ENST00000524377	NM_002529.3	735	Gag/Aag	16/17	0.22560136658832	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.250930029323379	2		441	773	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911424	39911424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060819-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	81	418	0	ENST00000378444.4:c.5206C>A	p.Leu1736Met	p.L1736M	ENST00000378444	NM_001123385.1	1736	Ctg/Atg	15/15	1	2	FACETS	0.871	0.767	0.983	0.871	0.767	0.983	CLONAL	1	TRUE	1	0.250930029323379	2		418	741	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0060821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	17	608	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.124	0.092	0.163	0.124	0.092	0.163	SUBCLONAL	1	TRUE	1	0.39500867417796	2		608	694	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0060821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	108	498	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.39500867417796	2		498	492	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021658	31021658	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1569326367	NA	P-0060821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	36	641	0	ENST00000375687.4:c.1657G>T	p.Glu553Ter	p.E553*	ENST00000375687	NM_015338.5	553	Gaa/Taa	12/13	1	2	FACETS	0.266	0.218	0.321	0.266	0.218	0.321	SUBCLONAL	1	TRUE	1	0.39500867417796	2		641	684	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211107	55211107	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	95	534	0	ENST00000275493.2:c.350A>G	p.Tyr117Cys	p.Y117C	ENST00000275493	NM_005228.3	117	tAt/tGt	3/28	1	2	FACETS	0.938	0.838	1	0.938	0.838	1	CLONAL	1	TRUE	1	0.39500867417796	2		534	513	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860392	151860392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776155729	NA	P-0060821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	134	727	0	ENST00000262189.6:c.10270G>A	p.Ala3424Thr	p.A3424T	ENST00000262189	NM_170606.2	3424	Gct/Act	43/59	1	2	FACETS	0.973	0.886	1	0.973	0.886	1	CLONAL	1	TRUE	1	0.39500867417796	2		727	697	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	167	759	1				ENST00000310581	NM_198253.2	-/1132			0.520073094405705	4	FACETS	0.895	0.829	0.962	0.895	0.829	0.962	CLONAL	2	FALSE	2	0.631597065520379	4		760	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0060822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	371	736	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.335780092230352	6	FACETS	0.835	0.794	0.877	0.835	0.794	0.877	INDETERMINATE	3	FALSE	3	0.631597065520379	6		737	1061	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593519	48593519	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	117	409	0	ENST00000342988.3:c.1270G>C	p.Asp424His	p.D424H	ENST00000342988	NM_005359.5	424	Gat/Cat	10/12	0.301538076225453	5	FACETS	0.758	0.687	0.831	0.505	0.458	0.554	INDETERMINATE	2	FALSE	2	0.631597065520379	5		409	476	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461576	138461576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	51	328	0	ENST00000289153.2:c.445C>T	p.Arg149Ter	p.R149*	ENST00000289153	NM_006219.2	149	Cga/Tga	3/22	0.400213496169391	5	FACETS	0.659	0.561	0.767	0.22	0.187	0.256	SUBCLONAL	1	FALSE	2	0.631597065520379	5		328	477	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982095	201982096	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0060822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	514	698	0	ENST00000359651.3:c.622dup	p.His208ProfsTer9	p.H208Pfs*9	ENST00000359651		207	tcc/tCcc	5/8	0.631597065520379	3	FACETS	0.856	0.828	0.884	0.856	0.828	0.884	CLONAL	3	FALSE	0	0.631597065520379	3		698	834	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938435	44938435	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	139	164	0	ENST00000377967.4:c.2983G>T	p.Glu995Ter	p.E995*	ENST00000377967	NM_021140.2	995	Gaa/Taa	20/29	0.520722677375494	2	FACETS	1	0.969	1			1	CLONAL	2	FALSE	NA	0.631597065520379	2		164	210	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578410	7578411	+	inframe_insertion	In_Frame_Ins	INS	-	-	TAC	novel	NA	P-0060822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	309	713	0	ENST00000269305.4:c.519_520insGTA	p.Val173dup	p.V173dup	ENST00000269305	NM_001126112.2	173	-/GTA	5/11	0.335780092230352	6	FACETS	1	0.988	1	0.769	0.726	0.812	INDETERMINATE	2	FALSE	3	0.631597065520379	6		713	960	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222229	53222229	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	320	343	1	ENST00000375401.3:c.4603G>T	p.Gly1535Cys	p.G1535C	ENST00000375401	NM_004187.3	1535	Ggc/Tgc	26/26	0.520722677375494	2	FACETS	1	0.993	1			1	CLONAL	2	FALSE	NA	0.631597065520379	2		344	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0060823-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	206	626	3	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.320544199914258	2	FACETS	0.946	0.884	1	0.946	0.884	1	CLONAL	2	TRUE	0	0.398986258638365	2		629	546	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0060823-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	298	459	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.380085246781247	4	FACETS	0.958	0.908	1	0.958	0.908	1	CLONAL	3	TRUE	1	0.398986258638365	4		459	727	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0060823-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	73	418	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.320544199914258	2	FACETS	1	0.977	1	0.741	0.657	0.829	CLONAL	1	TRUE	0	0.398986258638365	2		418	247	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186802	11186802	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060823-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	96	496	0	ENST00000361445.4:c.6403G>T	p.Asp2135Tyr	p.D2135Y	ENST00000361445	NM_004958.3	2135	Gac/Tac	46/58	0.398986258638365	3	FACETS	0.934	0.833	1	0.467	0.416	0.521	CLONAL	1	TRUE	1	0.398986258638365	3		496	618	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955043	55955043	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060823-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	81	435	0	ENST00000263923.4:c.3502G>T	p.Ala1168Ser	p.A1168S	ENST00000263923	NM_002253.2	1168	Gct/Tct	26/30	0.380085246781247	4	FACETS	0.918	0.809	1	0.306	0.269	0.345	CLONAL	1	TRUE	1	0.398986258638365	4		435	619	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845262	151845262	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747850540	NA	P-0060823-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	417	682	0	ENST00000262189.6:c.13750C>T	p.Arg4584Trp	p.R4584W	ENST00000262189	NM_170606.2	4584	Cgg/Tgg	52/59	0.386241268017834	4	FACETS	0.924	0.882	0.966	1	0.995	1	CLONAL	3	TRUE	2	0.398986258638365	4		682	1055	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662226	227662226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060823-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	336	795	0	ENST00000305123.5:c.1229G>A	p.Arg410Gln	p.R410Q	ENST00000305123	NM_005544.2	410	cGg/cAg	1/2	0.397109157027187	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.398986258638365	3		795	969	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574035	7574035	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs867389695	NA	P-0060824-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	243	471	0	ENST00000269305.4:c.994-2A>G		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.593586417262308	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.599958840583273	1		471	535	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960183	151960183	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060824-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	64	166	0	ENST00000262189.6:c.1217G>T	p.Cys406Phe	p.C406F	ENST00000262189	NM_170606.2	406	tGt/tTt	9/59	1	2	FACETS	0.936	0.822	1	0.936	0.822	1	CLONAL	1	TRUE	1	0.599958840583273	2		166	228	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43730599	43730599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060824-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	187	480	0	ENST00000382044.4:c.3114G>A	p.Met1038Ile	p.M1038I	ENST00000382044	NM_001141980.1	1038	atG/atA	16/28	1	2	FACETS	0.88	0.816	0.947	0.88	0.816	0.947	CLONAL	1	TRUE	1	0.599958840583273	2		480	708	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	38	347	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	0.174129456489228	4	FACETS	1	0.937	1	1	0.937	1	INDETERMINATE	2	FALSE	2	0.350619879935871	4		347	119	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023559	27023560	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	113	514	0	ENST00000324856.7:c.671dup	p.Pro225AlafsTer175	p.P225Afs*175	ENST00000324856	NM_006015.4	222	tac/taCc	1/20	0.339040406937492	4	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	FALSE	2	0.350619879935871	4		514	409	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	17	89	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.174129456489228	4	FACETS	1	0.852	1	1	0.852	1	INDETERMINATE	2	FALSE	2	0.350619879935871	4		89	57	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024001	27024002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	137	108	0	ENST00000324856.7:c.1113dup	p.Gln372AlafsTer28	p.Q372Afs*28	ENST00000324856	NM_006015.4	369	-/G	1/20	0.339040406937492	4	FACETS	0.898	0.825	0.972	1	0.985	1	CLONAL	3	FALSE	2	0.350619879935871	4		108	392	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	13	143	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	FALSE	1	0.350619879935871	2		143	52	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238958	5238958	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	180	600	0	ENST00000357368.4:c.1821del	p.Val608TrpfsTer30	p.V608Wfs*30	ENST00000357368	NM_002850.3	607	ccC/cc	13/38	0.350619879935871	5	FACETS	1	0.96	1	1	0.96	1	CLONAL	3	FALSE	2	0.350619879935871	5		600	499	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	45	336	2	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	1	2	FACETS	0.812	0.695	0.937	1	0.968	1	CLONAL	2	FALSE	1	0.350619879935871	2		338	158	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884218	37884218	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	174	616	1	ENST00000269571.5:c.3694del	p.Ala1232LeufsTer70	p.A1232Lfs*70	ENST00000269571		1230	cGg/cg	27/27	0.339040406937492	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	FALSE	2	0.350619879935871	4		617	579	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687472	37687472	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	191	592	2	ENST00000447079.4:c.4382del	p.Gly1461AlafsTer38	p.G1461Afs*38	ENST00000447079	NM_015083.1	1459	tGg/tg	14/14	0.339040406937492	4	FACETS	0.938	0.874	1	1	0.99	1	CLONAL	3	FALSE	2	0.350619879935871	4		594	523	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630626	158630626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912678	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	63	361	1	ENST00000263640.3:c.617G>A	p.Arg206His	p.R206H	ENST00000263640	NM_001105.4	206	cGc/cAc	6/11	1	2	FACETS	0.802	0.703	0.906	1	0.976	1	CLONAL	2	FALSE	1	0.350619879935871	2		362	224	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	130	595	2	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	0.350619879935871	5	FACETS	0.907	0.83	0.986	1	0.984	1	CLONAL	3	FALSE	3	0.350619879935871	5		597	416	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176516607	176516607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545721160	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	124	420	2	ENST00000292408.4:c.4C>T	p.Arg2Trp	p.R2W	ENST00000292408	NM_213647.1	2	Cgg/Tgg	2/18	0.176684289960043	3	FACETS	1	0.974	1	1	0.974	1	INDETERMINATE	2	FALSE	1	0.350619879935871	3		422	357	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925621	114925621	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763934346	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	75	724	2	ENST00000543371.1:c.1699G>A	p.Ala567Thr	p.A567T	ENST00000543371	NM_001198531.1	567	Gcc/Acc	14/14	0.174129456489228	4	FACETS	0.944	0.835	1	0.944	0.835	1	INDETERMINATE	2	FALSE	2	0.350619879935871	4		726	306	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211118	36211118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200835025	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	130	696	2	ENST00000222270.7:c.869G>A	p.Arg290His	p.R290H	ENST00000222270	NM_014727.1	290	cGt/cAt	3/37	0.118439424805924	4	FACETS	0.959	0.875	1	0.959	0.875	1	INDETERMINATE	2	FALSE	2	0.350619879935871	4		698	522	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	150	601	3	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	0.118439424805924	4	FACETS	1	0.981	1	1	0.981	1	INDETERMINATE	2	FALSE	2	0.350619879935871	4		604	478	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	84	316	6	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	1	2	FACETS	0.887	0.804	0.971	1	0.989	1	CLONAL	3	FALSE	1	0.350619879935871	2		322	180	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042709	42042711	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs1159823543	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	67	486	0	ENST00000219905.7:c.6909_6911del	p.Glu2303del	p.E2303del	ENST00000219905	NM_001164273.1	2302	GAA/-	17/24	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.350619879935871	2		486	314	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001122	150001122	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	42	251	0	ENST00000253339.5:c.2482G>T	p.Asp828Tyr	p.D828Y	ENST00000253339		828	Gat/Tat	4/7	1	2	FACETS	0.887	0.757	1	1	0.969	1	CLONAL	2	FALSE	1	0.350619879935871	2		251	135	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274303	5274304	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs777078756	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	241	535	0	ENST00000357368.4:c.143dup	p.Val49CysfsTer11	p.V49Cfs*11	ENST00000357368	NM_002850.3	48	ggt/ggGt	3/38	0.350619879935871	5	FACETS	1	0.957	1	1	0.957	1	CLONAL	3	FALSE	2	0.350619879935871	5		535	683	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	76	418	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.223116601146281	4	FACETS	0.921	0.822	1	1	0.976	1	CLONAL	3	FALSE	2	0.350619879935871	4		418	212	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47594883	47594883	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs756343868	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	120	636	1	ENST00000430070.2:c.1204del	p.Glu402ArgfsTer27	p.E402Rfs*27	ENST00000430070	NM_018095.4	402	Gag/ag	4/4	1	2	FACETS	0.853	0.778	0.932	1	0.988	1	CLONAL	2	FALSE	1	0.350619879935871	2		637	401	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100125	30100125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770660969	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	68	406	1	ENST00000331968.5:c.1495G>A	p.Val499Ile	p.V499I	ENST00000331968	NM_002742.2	499	Gta/Ata	10/18	0.174129456489228	4	FACETS	0.924	0.82	1	1	0.974	1	INDETERMINATE	3	FALSE	2	0.350619879935871	4		407	189	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557629	95557629	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	136	437	0	ENST00000393063.1:c.5438A>G	p.Glu1813Gly	p.E1813G	ENST00000393063	NM_030621.3	1813	gAg/gGg	26/28	0.174129456489228	4	FACETS	0.992	0.914	1	1	0.988	1	INDETERMINATE	3	FALSE	2	0.350619879935871	4		437	352	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95597968	95597968	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	64	260	0	ENST00000393063.1:c.316G>T	p.Val106Phe	p.V106F	ENST00000393063	NM_030621.3	106	Gtt/Ttt	5/28	0.174129456489228	4	FACETS	0.939	0.831	1	1	0.973	1	INDETERMINATE	3	FALSE	2	0.350619879935871	4		260	175	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50782488	50782488	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767075041	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	40	339	0	ENST00000307179.4:c.2000G>A	p.Arg667His	p.R667H	ENST00000307179		667	cGt/cAt	14/20	1	2	FACETS	0.751	0.634	0.875	1	0.959	1	SUBCLONAL	2	FALSE	1	0.350619879935871	2		339	152	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293045	91293045	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	52	403	1	ENST00000355112.3:c.547G>T	p.Ala183Ser	p.A183S	ENST00000355112	NM_000057.2	183	Gct/Tct	3/22	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.350619879935871	2		404	199	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129653	2129653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746197874	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	199	561	0	ENST00000219476.3:c.3380G>A	p.Arg1127Gln	p.R1127Q	ENST00000219476	NM_000548.3	1127	cGg/cAg	29/42	0.350619879935871	5	FACETS	1	0.975	1	1	0.993	1	CLONAL	3	FALSE	3	0.350619879935871	5		561	530	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222592	2222593	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	117	397	0	ENST00000326181.6:c.788dup	p.Tyr264ValfsTer33	p.Y264Vfs*33	ENST00000326181	NM_032271.2	262	-/A	9/21	0.350619879935871	5	FACETS	1	0.919	1	1	0.986	1	CLONAL	3	FALSE	3	0.350619879935871	5		397	337	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544978	86544978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	54	570	0	ENST00000262426.4:c.803C>T	p.Ala268Val	p.A268V	ENST00000262426	NM_001451.2	268	gCg/gTg	1/2	0.350619879935871	0	FACETS	1	0.934	1			1	CLONAL	1	FALSE	0	0.350619879935871	0		570	178	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78797010	78797010	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	188	471	2	ENST00000306801.3:c.1123A>G	p.Met375Val	p.M375V	ENST00000306801	NM_020761.2	375	Atg/Gtg	9/34	0.174129456489228	4	FACETS	0.909	0.847	0.973	1	0.989	1	INDETERMINATE	3	FALSE	2	0.350619879935871	4		473	531	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727868	41727868	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	79	505	0	ENST00000301178.4:c.497del	p.Pro166GlnfsTer32	p.P166Qfs*32	ENST00000301178	NM_021913.4	165	Ccc/cc	4/20	0.118439424805924	4	FACETS	1	0.94	1	1	0.94	1	INDETERMINATE	2	FALSE	2	0.350619879935871	4		505	280	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795084	42795084	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	136	697	0	ENST00000575354.2:c.2164C>A	p.Pro722Thr	p.P722T	ENST00000575354	NM_015125.3	722	Ccg/Acg	10/20	0.350619879935871	4	FACETS	0.852	0.782	0.924	1	0.983	1	CLONAL	3	FALSE	2	0.350619879935871	4		697	410	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265436	46265436	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	31	415	0	ENST00000371998.3:c.2306G>A	p.Cys769Tyr	p.C769Y	ENST00000371998		769	tGc/tAc	12/23	1	2	FACETS	0.529	0.429	0.643	0.529	0.429	0.643	SUBCLONAL	1	FALSE	1	0.350619879935871	2		415	334	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326454	62326454	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745614952	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	114	630	0	ENST00000360203.5:c.3379C>T	p.Arg1127Cys	p.R1127C	ENST00000360203	NM_001283009.1	1127	Cgc/Tgc	33/35	1	2	FACETS	0.867	0.788	0.949	1	0.988	1	CLONAL	2	FALSE	1	0.350619879935871	2		630	375	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714480	117714480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	26	222	0	ENST00000368508.3:c.1169G>A	p.Cys390Tyr	p.C390Y	ENST00000368508	NM_002944.2	390	tGt/tAt	11/43	1	2	FACETS	0.872	0.711	1	1	0.951	1	CLONAL	2	FALSE	1	0.350619879935871	2		222	85	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739798	41739798	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	79	547	0	ENST00000242208.4:c.175A>G	p.Lys59Glu	p.K59E	ENST00000242208	NM_002192.2	59	Aag/Gag	2/3	0.145356206386209	0	FACETS	0.935	0.83	1			1	INDETERMINATE	1	FALSE	0	0.350619879935871	0		547	313	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5064955	5064955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060825-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	33	250	0	ENST00000381652.3:c.1129G>A	p.Ala377Thr	p.A377T	ENST00000381652	NM_004972.3	377	Gca/Aca	9/25	0.145356206386209	0	FACETS	0.97	0.806	1			1	INDETERMINATE	1	FALSE	0	0.350619879935871	0		250	126	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0060826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	266	327	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.952	0.898	1	0.952	0.898	1	CLONAL	1	TRUE	1	0.824186213405985	2		327	678	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797278	42797278	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs968289754	NA	P-0060826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	268	833	0	ENST00000575354.2:c.3640C>T	p.Arg1214Ter	p.R1214*	ENST00000575354	NM_015125.3	1214	Cga/Tga	15/20	0.824186213405985	1	FACETS	0.676	0.64	0.711	0.676	0.64	0.711	SUBCLONAL	1	TRUE	0	0.824186213405985	1		833	566	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	151	444	1	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	0.627	0.576	0.681	0.627	0.576	0.681	SUBCLONAL	1	TRUE	1	0.824186213405985	2		445	584	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798889	42798889	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0060826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	55	794	0	ENST00000575354.2:c.4459+2T>G		p.X1487_splice	ENST00000575354	NM_015125.3	1487			0.824186213405985	1	FACETS	0.145	0.123	0.168	0.145	0.123	0.168	SUBCLONAL	1	TRUE	0	0.824186213405985	1		794	543	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144904	47144904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	55	304	0	ENST00000409792.3:c.4849G>A	p.Ala1617Thr	p.A1617T	ENST00000409792	NM_014159.6	1617	Gcc/Acc	7/21	1	2	FACETS	0.404	0.348	0.466	0.404	0.348	0.466	SUBCLONAL	1	TRUE	1	0.824186213405985	2		304	330	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163046	47163047	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CATGACCA	novel	NA	P-0060826-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	127	479	0	ENST00000409792.3:c.3072_3079dup	p.Ala1027ValfsTer97	p.A1027Vfs*97	ENST00000409792	NM_014159.6	1027	gcc/gTGGTCATGcc	3/21	1	2	FACETS	0.542	0.492	0.593	0.542	0.492	0.593	SUBCLONAL	1	TRUE	1	0.824186213405985	2		479	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0060827-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	335	729	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.351598290796024	1	FACETS	0.945	0.906	0.983	1	0.997	1	CLONAL	3	TRUE	0	0.351598290796024	1		729	554	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879885	37879885	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060827-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	6278	755	0	ENST00000269571.5:c.2180G>C	p.Gly727Ala	p.G727A	ENST00000269571		727	gGa/gCa	18/27	0.351598290796024	38	FACETS	1	0.998	1	1	0.999	1	CLONAL	38	TRUE	1	0.351598290796024	38		755	6840	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0060827-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	5833	615	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.351598290796024	38	FACETS	0.996	0.99	1	1	0.999	1	CLONAL	38	TRUE	1	0.351598290796024	38		615	6427	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518025	8518025	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060827-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	147	445	0	ENST00000356435.5:c.1366A>G	p.Thr456Ala	p.T456A	ENST00000356435		456	Aca/Gca	10/35	1	2	FACETS	1	0.923	1	1	0.992	1	CLONAL	2	TRUE	1	0.351598290796024	2		445	418	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245723	46245723	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060827-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	244	495	0	ENST00000334344.6:c.3817C>T	p.Arg1273Ter	p.R1273*	ENST00000334344	NM_152641.2	1273	Cga/Tga	15/21	0.351598290796024	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	1	0.351598290796024	3		495	803	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589782	69589782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs906608234	NA	P-0060827-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	391	1107	1	ENST00000168712.1:c.71C>T	p.Ala24Val	p.A24V	ENST00000168712	NM_002007.2	24	gCg/gTg	1/3	0.130589442554288	5	FACETS	0.98	0.933	1	0.98	0.933	1	INDETERMINATE	3	TRUE	2	0.351598290796024	5		1108	1155	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546362	46546362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1467441428	NA	P-0060827-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	185	377	0	ENST00000262741.5:c.167G>A	p.Ser56Asn	p.S56N	ENST00000262741	NM_003629.3	56	aGt/aAt	2/10	1	2	FACETS	1	0.966	1	1	0.994	1	CLONAL	2	TRUE	1	0.351598290796024	2		377	497	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102080260	102080260	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060827-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	209	343	0	ENST00000282441.5:c.997A>T	p.Ile333Phe	p.I333F	ENST00000282441	NM_001130145.2	333	Atc/Ttc	6/9	0.130589442554288	5	FACETS	0.959	0.896	1	0.959	0.896	1	INDETERMINATE	3	TRUE	2	0.351598290796024	5		343	631	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18576900	18576900	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060827-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	123	309	1	ENST00000266497.5:c.2308C>A	p.Leu770Ile	p.L770I	ENST00000266497		770	Ctt/Att	16/31	0.351598290796024	3	FACETS	0.794	0.722	0.87	0.794	0.722	0.87	SUBCLONAL	2	TRUE	1	0.351598290796024	3		310	518	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431634	49431634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1460139650	NA	P-0060827-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	285	733	0	ENST00000301067.7:c.9505G>A	p.Gly3169Ser	p.G3169S	ENST00000301067	NM_003482.3	3169	Ggc/Agc	34/54	0.255840055767444	4	FACETS	1	0.972	1	0.704	0.662	0.746	CLONAL	2	TRUE	1	0.351598290796024	4		733	1038	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435895	49435895	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783723	NA	P-0060827-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	397	588	0	ENST00000301067.7:c.6086del	p.Pro2029LeufsTer18	p.P2029Lfs*18	ENST00000301067	NM_003482.3	2029	cCt/ct	28/54	0.255840055767444	4	FACETS	0.937	0.897	0.978	1	0.994	1	CLONAL	4	TRUE	1	0.351598290796024	4		588	814	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225301	2225301	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0060827-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	351	548	1	ENST00000326181.6:c.1387-1G>T		p.X463_splice	ENST00000326181	NM_032271.2	463			0.246619982693626	4	FACETS	0.889	0.848	0.93	1	0.992	1	CLONAL	4	TRUE	1	0.351598290796024	4		549	759	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210754	2210754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060827-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	42	668	0	ENST00000398665.3:c.1251G>A	p.Met417Ile	p.M417I	ENST00000398665	NM_032482.2	417	atG/atA	14/28	0.351598290796024	1	FACETS	0.277	0.231	0.329	0.277	0.231	0.329	SUBCLONAL	1	TRUE	0	0.351598290796024	1		668	710	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539336	187539336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217371070	NA	P-0060827-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	52	582	0	ENST00000441802.2:c.8404G>A	p.Ala2802Thr	p.A2802T	ENST00000441802	NM_005245.3	2802	Gca/Aca	10/27	1	2	FACETS	0.488	0.415	0.568	0.488	0.415	0.568	SUBCLONAL	1	TRUE	1	0.351598290796024	2		582	606	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0060828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	259	323	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.437376672235468	2	FACETS	0.908	0.857	0.961	0.908	0.857	0.961	CLONAL	2	TRUE	0	0.437376672235468	2		323	652	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0060828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	311	732	2	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.150955930790034	5	FACETS	0.838	0.792	0.884	0.838	0.792	0.884	INDETERMINATE	3	TRUE	2	0.437376672235468	5		734	937	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579861	7579861	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs876658627	NA	P-0060828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	475	591	0	ENST00000269305.4:c.52del	p.Thr18HisfsTer26	p.T18Hfs*26	ENST00000269305	NM_001126112.2	18	Aca/ca	2/11	0.437376672235468	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.437376672235468	3		591	827	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722761	49722761	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs62262682	NA	P-0060828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	16	39	0	ENST00000449682.2:c.1478G>T	p.Arg493Leu	p.R493L	ENST00000449682	NM_020998.3	493	cGt/cTt	13/18	0.150955930790034	5	FACETS	1	0.826	1	0.734	0.562	0.925	INDETERMINATE	2	TRUE	2	0.437376672235468	5		39	55	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432811	432811	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	175	539	0	ENST00000399788.2:c.2105A>G	p.His702Arg	p.H702R	ENST00000399788	NM_001042603.1	702	cAt/cGt	15/28	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.437376672235468	2		539	654	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589545	69589545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1331436166	NA	P-0060828-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	193	1463	2	ENST00000168712.1:c.308G>A	p.Arg103His	p.R103H	ENST00000168712	NM_002007.2	103	cGc/cAc	1/3	0.361091306669312	3	FACETS	0.85	0.785	0.918	0.425	0.392	0.459	CLONAL	1	TRUE	1	0.437376672235468	3		1465	1265	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0060829-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	411	479	0				ENST00000310581	NM_198253.2	-/1132			0.545129159671553	5	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	2	0.677260450519881	5		479	790	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0060829-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	383	628	1	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.677260450519881	3	FACETS	0.904	0.864	0.945	0.904	0.864	0.945	CLONAL	2	TRUE	1	0.677260450519881	3		629	837	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101195	27101195	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060829-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	250	791	0	ENST00000324856.7:c.4477C>T	p.Gln1493Ter	p.Q1493*	ENST00000324856	NM_006015.4	1493	Cag/Tag	18/20	0.585498611034866	4	FACETS	1	0.987	1	0.601	0.562	0.641	CLONAL	1	TRUE	2	0.677260450519881	4		791	1031	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060829-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	169	479	0	ENST00000267101.3:c.273G>T	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atT	3/28	0.677260450519881	3	FACETS	1	0.973	1	0.558	0.515	0.602	CLONAL	1	TRUE	1	0.677260450519881	3		479	599	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636113	73636113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060829-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	147	508	0	ENST00000377687.4:c.376G>A	p.Asp126Asn	p.D126N	ENST00000377687	NM_001730.3	126	Gac/Aac	2/4	0.677260450519881	4	FACETS	0.954	0.872	1	0.318	0.29	0.347	CLONAL	1	TRUE	1	0.677260450519881	4		508	763	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636119	73636119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060829-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	158	527	0	ENST00000377687.4:c.382G>A	p.Glu128Lys	p.E128K	ENST00000377687	NM_001730.3	128	Gaa/Aaa	2/4	0.677260450519881	4	FACETS	1	0.928	1	0.337	0.309	0.367	CLONAL	1	TRUE	1	0.677260450519881	4		527	773	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619838	1619838	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060829-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	370	695	0	ENST00000344749.5:c.1108C>T	p.Pro370Ser	p.P370S	ENST00000344749	NM_001136139.2	370	Cct/Tct	14/19	0.585498611034866	4	FACETS	0.897	0.853	0.941	0.897	0.853	0.941	CLONAL	2	TRUE	2	0.677260450519881	4		695	1022	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032069	26032069	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060829-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	225	779	0	ENST00000244661.2:c.220G>C	p.Glu74Gln	p.E74Q	ENST00000244661	NM_003537.3	74	Gaa/Caa	1/1	0.529775578010702	4	FACETS	1	0.973	1	0.362	0.337	0.388	CLONAL	1	TRUE	1	0.677260450519881	4		779	1027	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652028	36652028	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060829-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	476	748	0	ENST00000244741.5:c.150C>G	p.Asn50Lys	p.N50K	ENST00000244741	NM_000389.4	50	aaC/aaG	2/3	0.492881434301753	4	FACETS	0.893	0.86	0.926	0.893	0.86	0.926	CLONAL	3	TRUE	1	0.677260450519881	4		748	880	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36653540	36653540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060829-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	360	413	0	ENST00000244741.5:c.458C>T	p.Ser153Phe	p.S153F	ENST00000244741	NM_000389.4	153	tCc/tTc	3/3	0.492881434301753	4	FACETS	0.924	0.886	0.963	0.924	0.886	0.963	CLONAL	3	TRUE	1	0.677260450519881	4		413	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0060830-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	188	919	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.235810077242841	2	FACETS	0.94	0.87	1	0.94	0.87	1	CLONAL	2	TRUE	0	0.235810077242841	2		919	848	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0060830-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	40	405	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	0.775	0.644	0.92	0.775	0.644	0.92	CLONAL	1	TRUE	1	0.235810077242841	2		405	438	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175481	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0060830-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	80	645	0	ENST00000257430.4:c.4192_4193del	p.Arg1399PhefsTer9	p.R1399Ffs*9	ENST00000257430	NM_000038.5	1397	GAg/g	16/16	1	2	FACETS	0.937	0.825	1	0.937	0.825	1	CLONAL	1	TRUE	1	0.235810077242841	2		645	724	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038233	30038233	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060830-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	64	464	0	ENST00000338641.4:c.406G>A	p.Glu136Lys	p.E136K	ENST00000338641	NM_000268.3	136	Gag/Aag	4/16	1	2	FACETS	0.802	0.694	0.919	0.802	0.694	0.919	CLONAL	1	TRUE	1	0.235810077242841	2		464	677	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099552	157099552	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060830-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	93	655	0	ENST00000346085.5:c.489G>T	p.Lys163Asn	p.K163N	ENST00000346085	NM_020732.3	163	aaG/aaT	1/20	1	2	FACETS	0.812	0.721	0.91	0.812	0.721	0.91	CLONAL	1	TRUE	1	0.235810077242841	2		655	971	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0060831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	70	479	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.936	1			1	INDETERMINATE	1	TRUE	NA	0.475493532235679	2		479	269	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0060831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	141	487	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.297427622498252	2	FACETS	1	0.984	1	0.652	0.598	0.707	CLONAL	1	TRUE	0	0.475493532235679	2		487	455	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022526	12022526	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs111871763	NA	P-0060831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	134	752	0	ENST00000396373.4:c.632G>T	p.Arg211Leu	p.R211L	ENST00000396373	NM_001987.4	211	cGc/cTc	5/8	1	2	FACETS	0.765	0.696	0.837	0.765	0.696	0.837	SUBCLONAL	1	TRUE	1	0.475493532235679	2		752	737	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21342311	21342311	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060831-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	62	378	0	ENST00000215739.8:c.413G>A	p.Gly138Glu	p.G138E	ENST00000215739	NM_006767.3	138	gGg/gAg	5/21	0.475493532235679	1	FACETS	0.773	0.675	0.878	0.773	0.675	0.878	SUBCLONAL	1	TRUE	0	0.475493532235679	1		378	257	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782062	66782062	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060841-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	44	312	0	ENST00000307102.5:c.1034del	p.Asn345ThrfsTer8	p.N345Tfs*8	ENST00000307102	NM_002755.3	343	atA/at	10/11	1	2	FACETS	0.682	0.572	0.803	0.682	0.572	0.803	SUBCLONAL	1	TRUE	1	0.28	2		312	461	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295166	1295168	+	upstream_gene_variant	5'Flank	TNP	CTC	CTC	ATG	novel	NA	P-0060841-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	56	501	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	0.8	0.695	0.912	1	0.973	1	CLONAL	2	TRUE	0	0.28	1		501	215	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082750	16082750	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060841-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	13	291	0	ENST00000281043.3:c.564T>A	p.Asp188Glu	p.D188E	ENST00000281043	NM_005378.4	188	gaT/gaA	2/3	1	2	FACETS	0.36	0.256	0.487	0.36	0.256	0.487	SUBCLONAL	1	TRUE	1	0.28	2		291	258	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555032	106555032	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060841-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	164	489	0	ENST00000369096.4:c.2149G>T	p.Gly717Trp	p.G717W	ENST00000369096	NM_001198.3	717	Ggg/Tgg	7/7	1	2	FACETS	1	0.947	1	1	0.992	1	CLONAL	2	TRUE	1	0.28	2		489	567	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860293	151860293	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060841-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	46	518	0	ENST00000262189.6:c.10369G>T	p.Asp3457Tyr	p.D3457Y	ENST00000262189	NM_170606.2	3457	Gac/Tac	43/59	1	2	FACETS	0.565	0.475	0.664	0.565	0.475	0.664	SUBCLONAL	1	TRUE	1	0.28	2		518	582	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	136	759	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.561950267632113	2		760	467	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695809	117695809	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1042229408	NA	P-0060842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	118	253	0	ENST00000369458.3:c.628G>A	p.Val210Ile	p.V210I	ENST00000369458	NM_024626.3	210	Gtt/Att	4/6	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.561950267632113	2		253	419	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041110	180041110	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781402372	NA	P-0060842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	173	821	1	ENST00000261937.6:c.3289G>A	p.Val1097Met	p.V1097M	ENST00000261937	NM_182925.4	1097	Gtg/Atg	24/30	1	2	FACETS	0.924	0.854	0.997	0.924	0.854	0.997	CLONAL	1	TRUE	1	0.561950267632113	2		822	666	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0060842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	232	622	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	0.561950267632113	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.561950267632113	1		622	496	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843615	3843617	+	frameshift_variant	Frame_Shift_Del	DEL	TTT	TTT	G	novel	NA	P-0060842-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	150	351	0	ENST00000262367.5:c.986_988delinsC	p.Gln329ProfsTer20	p.Q329Pfs*20	ENST00000262367	NM_004380.2	329	cAAAca/cCca	4/31	0.561950267632113	1	FACETS	0.997	0.922	1	0.997	0.922	1	CLONAL	1	TRUE	0	0.561950267632113	1		351	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0060844-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	38	729	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.370435477453516	1	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	0	0.397578726900666	1		729	141	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856521	111856521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060844-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	20	643	0	ENST00000341259.2:c.572C>T	p.Pro191Leu	p.P191L	ENST00000341259	NM_005475.2	191	cCg/cTg	2/8	0.151011006532935	4	FACETS	0.99	0.765	1	0.495	0.382	0.624	INDETERMINATE	1	TRUE	2	0.397578726900666	4		643	142	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482550	56482550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060844-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	32	513	0	ENST00000267101.3:c.1007C>T	p.Ser336Phe	p.S336F	ENST00000267101	NM_001982.3	336	tCt/tTt	9/28	0.151011006532935	4	FACETS	1	0.899	1	0.577	0.472	0.693	INDETERMINATE	1	TRUE	2	0.397578726900666	4		513	195	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24133998	24133998	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060844-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	17	556	0	ENST00000263121.7:c.149T>G	p.Leu50Arg	p.L50R	ENST00000263121	NM_003073.3	50	cTc/cGc	2/9	0.349933949555062	1	FACETS	0.586	0.442	0.752	0.586	0.442	0.752	SUBCLONAL	1	TRUE	0	0.397578726900666	1		556	117	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060845-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	229	759	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.667045050266515	2		760	665	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0060845-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	307	436	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.667045050266515	2		436	831	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806089	1806089	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913479	NA	P-0060845-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	466	434	0	ENST00000260795.2:c.1108G>T	p.Gly370Cys	p.G370C	ENST00000260795		370	Ggc/Tgc	8/17	0.465816235783262	3	FACETS	0.839	0.803	0.874	0.839	0.803	0.874	CLONAL	2	TRUE	1	0.667045050266515	3		434	1111	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833925	44833925	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060845-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	124	219	0	ENST00000377967.4:c.349C>T	p.Gln117Ter	p.Q117*	ENST00000377967	NM_021140.2	117	Cag/Tag	4/29	0.607510023386298	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.667045050266515	1		219	230	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843480	3843480	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060845-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	197	453	0	ENST00000262367.5:c.1123G>T	p.Gly375Ter	p.G375*	ENST00000262367	NM_004380.2	375	Gga/Tga	4/31	1	2	FACETS	0.637	0.59	0.686	0.637	0.59	0.686	SUBCLONAL	1	TRUE	1	0.667045050266515	2		453	927	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150935505	150935505	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367609640	NA	P-0060845-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	363	422	0	ENST00000271640.5:c.3347G>A	p.Arg1116Gln	p.R1116Q	ENST00000271640	NM_001145415.1	1116	cGa/cAa	19/22	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.667045050266515	2		422	925	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132207	7132207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060845-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	327	449	0	ENST00000302850.5:c.2804C>T	p.Ser935Phe	p.S935F	ENST00000302850	NM_000208.2	935	tCt/tTt	14/22	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.667045050266515	2		449	962	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115958	8115966	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCCAGCA	CCTCCAGCA	ATGTG	novel	NA	P-0060845-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	470	446	1	ENST00000346208.3:c.1304_1312delinsATGTG	p.Pro435HisfsTer39	p.P435Hfs*39	ENST00000346208		435	cCCTCCAGCAtg/cATGTGtg	6/6	0.465816235783262	3	FACETS	0.76	0.727	0.793	0.76	0.727	0.793	SUBCLONAL	2	TRUE	1	0.667045050266515	3		447	1236	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060846-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	39	759	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.356	0.295	0.425	0.356	0.295	0.425	SUBCLONAL	1	TRUE	1	0.42	2		760	521	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1686020	1686020	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060846-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	44	498	1	ENST00000378625.1:c.1241T>A	p.Leu414Gln	p.L414Q	ENST00000378625	NM_001198994.1	414	cTg/cAg	10/14	1	2	FACETS	0.263	0.219	0.311	0.263	0.219	0.311	SUBCLONAL	1	TRUE	1	0.42	2		499	798	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578270	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0060846-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	63	552	0	ENST00000269305.4:c.579_580delinsAA	p.His193_Leu194delinsGlnIle	p.H193_L194delinsQI	ENST00000269305	NM_001126112.2	193	caTCtt/caAAtt	6/11	0.168171736868752	3	FACETS	0.436	0.376	0.501	0.218	0.188	0.251	INDETERMINATE	1	TRUE	1	0.42	3		552	833	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156492	106156492	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060846-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	57	448	5	ENST00000380013.4:c.1394del	p.Pro465HisfsTer21	p.P465Hfs*21	ENST00000380013	NM_001127208.2	465	Cca/ca	3/11	1	2	FACETS	0.463	0.397	0.535	0.463	0.397	0.535	SUBCLONAL	1	TRUE	1	0.42	2		453	586	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693003	89693003	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs786204900	NA	P-0060847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	64	260	0	ENST00000371953.3:c.491del	p.Lys164ArgfsTer3	p.K164Rfs*3	ENST00000371953	NM_000314.4	163	Aaa/aa	5/9	0.270997972084736	1	FACETS	0.763	0.662	0.873	0.763	0.662	0.873	SUBCLONAL	1	TRUE	0	0.270997972084736	1		260	535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579350	7579350	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587781642	NA	P-0060847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	128	617	0	ENST00000269305.4:c.337T>G	p.Phe113Val	p.F113V	ENST00000269305	NM_001126112.2	113	Ttc/Gtc	4/11	0.270997972084736	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.270997972084736	1		617	693	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696433	47696433	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	97	392	0	ENST00000347630.2:c.390C>G	p.Asp130Glu	p.D130E	ENST00000347630	NM_001007230.1	130	gaC/gaG	6/11	0.270997972084736	1	FACETS	0.917	0.818	1	0.917	0.818	1	CLONAL	1	TRUE	0	0.270997972084736	1		392	675	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061139	38061140	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCCGCTTCCGCT	novel	NA	P-0060847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	80	439	0	ENST00000250448.2:c.838_849dup	p.Ser280_Gly283dup	p.S280_G283dup	ENST00000250448	NM_004496.3	280	-/AGCGGAAGCGGG	2/2	1	2	FACETS	0.787	0.692	0.889	0.787	0.692	0.889	SUBCLONAL	1	TRUE	1	0.270997972084736	2		439	750	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061214	38061228	+	inframe_deletion	In_Frame_Del	DEL	AGCAGCCGTTCTCGA	AGCAGCCGTTCTCGA	-	novel	NA	P-0060847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	110	455	0	ENST00000250448.2:c.761_775del	p.Phe254_Cys258del	p.F254_C258del	ENST00000250448	NM_004496.3	254	tTCGAGAACGGCTGCTac/tac	2/2	1	2	FACETS	0.953	0.855	1	0.953	0.855	1	CLONAL	1	TRUE	1	0.270997972084736	2		455	852	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393585	139393585	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759643831	NA	P-0060847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	80	524	0	ENST00000277541.6:c.6061G>A	p.Val2021Ile	p.V2021I	ENST00000277541	NM_017617.3	2021	Gtc/Atc	32/34	1	2	FACETS	0.722	0.634	0.816	0.722	0.634	0.816	SUBCLONAL	1	TRUE	1	0.270997972084736	2		524	818	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591092	67591092	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	61	331	0	ENST00000274335.5:c.1685G>C	p.Arg562Pro	p.R562P	ENST00000274335		562	cGt/cCt	12/15	1	2	FACETS	0.85	0.732	0.979	0.85	0.732	0.979	CLONAL	1	TRUE	1	0.19	2		331	755	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0060848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	61	191	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.19	2		191	481	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428712	49428712	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	50	408	0	ENST00000301067.7:c.10238A>T	p.Asp3413Val	p.D3413V	ENST00000301067	NM_003482.3	3413	gAc/gTc	35/54	1	2	FACETS	0.7	0.592	0.819	0.7	0.592	0.819	SUBCLONAL	1	TRUE	1	0.19	2		408	752	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439511	220439511	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	42	584	0	ENST00000243786.2:c.364C>A	p.Arg122Ser	p.R122S	ENST00000243786	NM_002191.3	122	Cgc/Agc	2/2	1	2	FACETS	0.55	0.458	0.653	0.55	0.458	0.653	SUBCLONAL	1	TRUE	1	0.19	2		584	804	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401513	401513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	46	506	0	ENST00000380956.4:c.835G>T	p.Gly279Ter	p.G279*	ENST00000380956	NM_001195286.1	279	Gga/Tga	7/9	0.3	2	FACETS	0.631	0.53	0.744			1	SUBCLONAL	1	TRUE	NA	0.19	2		506	767	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578463	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371524413	NA	P-0060849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	136	368	0	ENST00000269305.4:c.467G>C	p.Arg156Pro	p.R156P	ENST00000269305	NM_001126112.2	156	cGc/cCc	5/11	0.232749974879275	1	FACETS	0.883	0.801	0.968	0.883	0.801	0.968	CLONAL	1	TRUE	0	0.260032817468906	1		368	1031	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971116	21971116	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs11552823	NA	P-0060849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	148	936	0	ENST00000304494.5:c.242C>G	p.Pro81Arg	p.P81R	ENST00000304494	NM_000077.4	81	cCc/cGc	2/3	0.260032817468906	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.260032817468906	1		936	982	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630459	187630459	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	121	777	0	ENST00000441802.2:c.523G>A	p.Asp175Asn	p.D175N	ENST00000441802	NM_005245.3	175	Gat/Aat	2/27	0.260032817468906	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.260032817468906	1		777	798	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88671966	88671966	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0060849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	35	290	0	ENST00000360948.2:c.1205-1G>A		p.X402_splice	ENST00000360948	NM_001012338.2	402			1	2	FACETS	0.744	0.61	0.893	0.744	0.61	0.893	SUBCLONAL	1	TRUE	1	0.260032817468906	2		290	362	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627582	14627582	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	130	725	0	ENST00000254322.2:c.488del	p.Pro163GlnfsTer21	p.P163Qfs*21	ENST00000254322	NM_006145.1	163	cCa/ca	2/3	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.260032817468906	2		725	946	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410807	63410807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	91	765	1	ENST00000330258.3:c.2360C>A	p.Ser787Tyr	p.S787Y	ENST00000330258	NM_152424.3	787	tCc/tAc	2/2	1	2	FACETS	0.887	0.787	0.994	0.887	0.787	0.994	CLONAL	1	TRUE	1	0.260032817468906	2		766	789	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168798	56168798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374345167	NA	P-0060849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	49	462	0	ENST00000399503.3:c.1652C>T	p.Pro551Leu	p.P551L	ENST00000399503	NM_005921.1	551	cCt/cTt	9/20	0.260032817468906	1	FACETS	0.701	0.594	0.818	0.701	0.594	0.818	SUBCLONAL	1	TRUE	0	0.260032817468906	1		462	468	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933694	36933694	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	106	900	0	ENST00000361632.4:c.1705G>C	p.Ala569Pro	p.A569P	ENST00000361632		569	Gct/Cct	12/16	0.260032817468906	1	FACETS	0.808	0.723	0.898	0.808	0.723	0.898	CLONAL	1	TRUE	0	0.260032817468906	1		900	878	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100563	8100563	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs987472805	NA	P-0060849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	117	927	0	ENST00000346208.3:c.537C>A	p.Asp179Glu	p.D179E	ENST00000346208		179	gaC/gaA	3/6	1	2	FACETS	0.821	0.739	0.909	0.821	0.739	0.909	CLONAL	1	TRUE	1	0.260032817468906	2		927	1096	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49419977	49419977	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	123	725	0	ENST00000301067.7:c.15772G>T	p.Ala5258Ser	p.A5258S	ENST00000301067	NM_003482.3	5258	Gcc/Tcc	48/54	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.260032817468906	2		725	900	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591640	38591654	+	inframe_deletion	In_Frame_Del	DEL	ACTTGGAGGGAGTGG	ACTTGGAGGGAGTGG	-	novel	NA	P-0060849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	77	530	0	ENST00000299084.4:c.102_116del	p.Gly35_Leu39del	p.G35_L39del	ENST00000299084	NM_152594.2	33	ccACTTGGAGGGAGTGGa/cca	2/7	1	2	FACETS	0.91	0.799	1	0.91	0.799	1	CLONAL	1	TRUE	1	0.260032817468906	2		530	651	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544685	86544685	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0060849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	114	883	0	ENST00000262426.4:c.510C>G	p.Tyr170Ter	p.Y170*	ENST00000262426	NM_001451.2	170	taC/taG	1/2	1	2	FACETS	0.87	0.782	0.963	0.87	0.782	0.963	CLONAL	1	TRUE	1	0.260032817468906	2		883	1008	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170433	11170433	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	72	636	0	ENST00000358026.2:c.4736A>G	p.Tyr1579Cys	p.Y1579C	ENST00000358026	NM_001128849.1	1579	tAt/tGt	34/36	1	2	FACETS	0.649	0.566	0.739	0.649	0.566	0.739	SUBCLONAL	1	TRUE	1	0.260032817468906	2		636	853	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565847	55565847	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	67	494	0	ENST00000288135.5:c.671G>C	p.Arg224Thr	p.R224T	ENST00000288135	NM_000222.2	224	aGg/aCg	4/21	1	2	FACETS	0.869	0.755	0.992	0.869	0.755	0.992	CLONAL	1	TRUE	1	0.260032817468906	2		494	593	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201672	66201672	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	61	609	0	ENST00000273854.3:c.2830A>T	p.Thr944Ser	p.T944S	ENST00000273854	NM_004439.5	944	Acg/Tcg	16/18	1	2	FACETS	0.675	0.582	0.777	0.675	0.582	0.777	SUBCLONAL	1	TRUE	1	0.260032817468906	2		609	695	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956694	93956694	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	43	348	0	ENST00000369303.4:c.2542G>A	p.Ala848Thr	p.A848T	ENST00000369303	NM_004440.3	848	Gca/Aca	15/17	1	2	FACETS	0.797	0.668	0.94	0.797	0.668	0.94	CLONAL	1	TRUE	1	0.260032817468906	2		348	415	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755928	133755928	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	88	716	0	ENST00000318560.5:c.1555G>C	p.Val519Leu	p.V519L	ENST00000318560	NM_005157.4	519	Gtg/Ctg	10/11	0.233635977685344	2	FACETS	0.816	0.722	0.917	0.408	0.361	0.459	CLONAL	1	TRUE	0	0.260032817468906	2		716	829	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401038	139401038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1227253271	NA	P-0060849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	120	822	0	ENST00000277541.6:c.3955G>A	p.Gly1319Arg	p.G1319R	ENST00000277541	NM_017617.3	1319	Ggg/Agg	24/34	0.233635977685344	2	FACETS	0.905	0.816	0.999	0.452	0.408	0.5	CLONAL	1	TRUE	0	0.260032817468906	2		822	1020	SUCCESS
AR	367	MSKCC	GRCh37	X	66765562	66765562	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	122	978	0	ENST00000374690.3:c.574C>G	p.Gln192Glu	p.Q192E	ENST00000374690	NM_000044.3	192	Caa/Gaa	1/8	1	2	FACETS	0.954	0.861	1	0.954	0.861	1	CLONAL	1	TRUE	1	0.260032817468906	2		978	984	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352751	70352751	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	82	550	0	ENST00000374080.3:c.4472G>T	p.Gly1491Val	p.G1491V	ENST00000374080		1491	gGg/gTg	32/45	1	2	FACETS	0.932	0.822	1	0.932	0.822	1	CLONAL	1	TRUE	1	0.260032817468906	2		550	677	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0060850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	32	558	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.318447029417299	1	FACETS	0.64	0.533	0.754	0.64	0.533	0.754	INDETERMINATE	1	TRUE	0	0.66213013902775	1		558	101	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692790	89692790	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554898067	NA	P-0060850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	59	270	0	ENST00000371953.3:c.274G>T	p.Asp92Tyr	p.D92Y	ENST00000371953	NM_000314.4	92	Gac/Tac	5/9	0.66213013902775	2	FACETS	0.958	0.867	1	0.958	0.867	1	CLONAL	2	TRUE	0	0.66213013902775	2		270	93	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652386	206652386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781784265	NA	P-0060850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	242	844	0	ENST00000367120.3:c.1093G>A	p.Val365Ile	p.V365I	ENST00000367120	NM_014002.3	365	Gtc/Atc	10/22	0.238160297930363	2	FACETS	1	0.992	1	0.657	0.62	0.695	INDETERMINATE	1	TRUE	0	0.66213013902775	2		844	556	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094420	27094421	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	278	817	0	ENST00000324856.7:c.3129dup	p.Val1044CysfsTer3	p.V1044Cfs*3	ENST00000324856	NM_006015.4	1043	gct/gcTt	11/20	0.548482166599789	2	FACETS	0.961	0.919	1	0.961	0.919	1	CLONAL	2	TRUE	0	0.66213013902775	2		817	437	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941041	71941041	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	116	1112	0	ENST00000298229.2:c.918del	p.Ile307SerfsTer8	p.I307Sfs*8	ENST00000298229	NM_001567.3	306	aCc/ac	8/28	0.318447029417299	1	FACETS	0.582	0.528	0.637	0.582	0.528	0.637	INDETERMINATE	1	TRUE	0	0.66213013902775	1		1112	403	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442777	99442777	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	144	724	0	ENST00000268035.6:c.1174C>T	p.His392Tyr	p.H392Y	ENST00000268035	NM_000875.3	392	Cat/Tat	5/21	0.203414591602396	0	FACETS	0.284	0.26	0.308			1	INDETERMINATE	1	TRUE	0	0.66213013902775	0		724	518	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662412	67662413	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCTT	novel	NA	P-0060850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	80	748	0	ENST00000264010.4:c.1659_1663dup	p.Phe555TrpfsTer31	p.F555Wfs*31	ENST00000264010	NM_006565.3	553	gcg/gcGGCTTg	9/12	0.3911007180151	1	FACETS	0.458	0.406	0.513	0.458	0.406	0.513	INDETERMINATE	1	TRUE	0	0.66213013902775	1		748	353	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492802	56492802	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	512	717	0	ENST00000407977.2:c.137C>A	p.Ala46Asp	p.A46D	ENST00000407977		46	gCt/gAt	2/10	0.652899595415867	2	FACETS	0.846	0.828	0.864	1	0.997	1	CLONAL	3	TRUE	0	0.66213013902775	2		717	609	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591151	67591155	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATGTA	ATGTA	-	novel	NA	P-0060850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	189	502	0	ENST00000274335.5:c.1745_1745+4del		p.X582_splice	ENST00000274335		582		12/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.66213013902775	2		502	473	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681190	86681190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs942447165	NA	P-0060850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	54	307	0	ENST00000274376.6:c.2831T>C	p.Val944Ala	p.V944A	ENST00000274376	NM_002890.2	944	gTg/gCg	22/25	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.66213013902775	2		307	143	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662418	67662418	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	75	733	0	ENST00000264010.4:c.1664T>G	p.Phe555Cys	p.F555C	ENST00000264010	NM_006565.3	555	tTt/tGt	9/12	0.3911007180151	1	FACETS	0.458	0.404	0.515	0.458	0.404	0.515	INDETERMINATE	1	TRUE	0	0.66213013902775	1		733	331	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0060857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	174	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.549900007626532	3	FACETS	0.855	0.795	0.916	0.855	0.795	0.916	CLONAL	2	TRUE	1	0.563593070854852	3		334	463	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0060857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	9	394	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.563593070854852	1	FACETS	0.052	0.033	0.075	0.052	0.033	0.075	SUBCLONAL	1	TRUE	0	0.563593070854852	1		394	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577111	7577111	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786202082	NA	P-0060857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	425	606	0	ENST00000269305.4:c.827C>A	p.Ala276Asp	p.A276D	ENST00000269305	NM_001126112.2	276	gCc/gAc	8/11	0.513134626441479	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.563593070854852	2		606	736	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142942	30142942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1442742511	NA	P-0060857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	125	689	0	ENST00000389048.3:c.584C>T	p.Ala195Val	p.A195V	ENST00000389048	NM_004304.4	195	gCg/gTg	1/29	0.549900007626532	3	FACETS	0.771	0.699	0.848	0.386	0.349	0.424	SUBCLONAL	1	TRUE	1	0.563593070854852	3		689	737	SUCCESS
APC	324	MSKCC	GRCh37	5	112173659	112173659	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0060857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	104	460	1	ENST00000257430.4:c.2368A>T	p.Arg790Ter	p.R790*	ENST00000257430	NM_000038.5	790	Aga/Tga	16/16	0.549900007626532	3	FACETS	0.843	0.757	0.934	0.422	0.378	0.467	CLONAL	1	TRUE	1	0.563593070854852	3		461	561	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120472	70120473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0060857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	149	754	0	ENST00000245479.2:c.1476_1477dup	p.His493ProfsTer31	p.H493Pfs*31	ENST00000245479	NM_000346.3	492	acc/aCCcc	3/3	0.513134626441479	2	FACETS	0.707	0.647	0.77	0.353	0.323	0.385	SUBCLONAL	1	TRUE	0	0.563593070854852	2		754	748	SUCCESS
APC	324	MSKCC	GRCh37	5	112176033	112176033	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	205	511	0	ENST00000257430.4:c.4742del	p.Ser1581LeufsTer69	p.S1581Lfs*69	ENST00000257430	NM_000038.5	1581	tCt/tt	16/16	0.549900007626532	3	FACETS	0.821	0.767	0.876	0.821	0.767	0.876	CLONAL	2	TRUE	1	0.563593070854852	3		511	568	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294022	1294022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060858-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	23184	757	0	ENST00000310581.5:c.979G>A	p.Glu327Lys	p.E327K	ENST00000310581	NM_198253.2	327	Gag/Aag	2/16	0.562772589814026	65	FACETS	1	0.999	1			1	CLONAL	66	TRUE	NA	0.562772589814026	65		757	23370	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306550	41306550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760520624	NA	P-0060858-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	139	426	1	ENST00000373198.4:c.1109C>T	p.Thr370Met	p.T370M	ENST00000373198	NM_133170.3	370	aCg/aTg	7/32	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.562772589814026	2		427	462	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549230	21549230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113238499	NA	P-0060858-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	201	695	0	ENST00000382592.4:c.3046G>A	p.Glu1016Lys	p.E1016K	ENST00000382592	NM_014572.2	1016	Gaa/Aaa	8/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.562772589814026	2		695	658	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938239	36938239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199991273	NA	P-0060858-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	178	723	0	ENST00000361632.4:c.722C>T	p.Ala241Val	p.A241V	ENST00000361632		241	gCg/gTg	6/16	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.562772589814026	2		723	625	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612100	189612100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1455505991	NA	P-0060858-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	186	647	0	ENST00000264731.3:c.1852C>T	p.Arg618Trp	p.R618W	ENST00000264731	NM_003722.4	618	Cgg/Tgg	14/14	0.322129178435185	1	FACETS	0.798	0.741	0.857	0.798	0.741	0.857	INDETERMINATE	1	TRUE	0	0.562772589814026	1		647	595	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291831	15291831	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1286854173	NA	P-0060858-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	167	689	0	ENST00000263388.2:c.2935G>A	p.Ala979Thr	p.A979T	ENST00000263388	NM_000435.2	979	Gcc/Acc	18/33	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.562772589814026	2		689	542	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056397	180056397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368167894	NA	P-0060858-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	198	689	3	ENST00000261937.6:c.847C>T	p.Arg283Cys	p.R283C	ENST00000261937	NM_182925.4	283	Cgc/Tgc	7/30	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.562772589814026	2		692	614	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295651	1295651	+	upstream_gene_variant	5'Flank	SNP	G	G	C	novel	NA	P-0060858-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	313	837	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.562772589814026	NA		837	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0060859-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	221	563	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.185478179527872	2	FACETS	0.773	0.718	0.83	0.773	0.718	0.83	SUBCLONAL	2	TRUE	0	0.215941286711646	2		563	1324	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412375	139412375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1341448592	NA	P-0060859-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	125	792	0	ENST00000277541.6:c.1270G>A	p.Glu424Lys	p.E424K	ENST00000277541	NM_017617.3	424	Gag/Aag	8/34	0.215941286711646	1	FACETS	0.987	0.892	1	0.987	0.892	1	CLONAL	1	TRUE	0	0.215941286711646	1		792	1046	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445818	49445818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060859-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1344	143	976	0	ENST00000301067.7:c.1648G>A	p.Glu550Lys	p.E550K	ENST00000301067	NM_003482.3	550	Gaa/Aaa	10/54	1	2	FACETS	0.891	0.809	0.977	0.891	0.809	0.977	CLONAL	1	TRUE	1	0.215941286711646	2		976	1487	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873191	35873890	+	splice_donor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	CCGCGGCCCCGGCGGGCGCCGGCCAGACCGCCCCGCCCTCCCGCCAGCTCGGAACGCCCTGTACTTCCCCTCCCGGCTGCTCGGCGCCCGCCAGCGGCCAGAAACTCCCGCCCCGCCTTATGCAACCGGGGACTTCGCGTCCCCGCTGCCGCCCCGCCCCCGGCCTAGAGGACGGGTCTGGGGGGAGGGGGCGTGTGGCGACGCTGCCATCCACCAGGGCCCAGCCGCCGCCCCTCCGAGTTGGGCCGGTGCCCCGCGCGGCCCTGCAGCCCTGCAGCGTTCGGGGCGGTGCAGGAGCCCCGGGGTGCCGCGGCGCCCGCCCGGCTGCATCGCTGGTCCCCCGGCTCGGGCTCCAGGCCCGGCGCCTCCCACCCCCAGGCCGCGCGCGTCCCGCCCTCCCGACGACCCCCAGCCCCGGGCCTCCGCCACTTACGAGTCCCCGTCCTCGGTGAGCTGCTGCTTCCAGGGCTCCGAGCCGCGCGGCACCTCCTGCGGCTCGAGGCGGATCTCCTGCAGCTCCTTGACCATCTGCTCGTACTCCTCGTCTTTCATGGAGTCCAGGCCGCTGTCGTGGCGGTCGTCCAGTAGCCGCTCCTTCTTCAGCCCGTCGCGGGGGCCCTCCATGGCCCACTCCTGGGGGCGCTCGGCCGCCTGGAACATGGCGCGGACGAGCTGCGGGCGCTGCTGCGGGTGCGCTGGG	CCGCGGCCCCGGCGGGCGCCGGCCAGACCGCCCCGCCCTCCCGCCAGCTCGGAACGCCCTGTACTTCCCCTCCCGGCTGCTCGGCGCCCGCCAGCGGCCAGAAACTCCCGCCCCGCCTTATGCAACCGGGGACTTCGCGTCCCCGCTGCCGCCCCGCCCCCGGCCTAGAGGACGGGTCTGGGGGGAGGGGGCGTGTGGCGACGCTGCCATCCACCAGGGCCCAGCCGCCGCCCCTCCGAGTTGGGCCGGTGCCCCGCGCGGCCCTGCAGCCCTGCAGCGTTCGGGGCGGTGCAGGAGCCCCGGGGTGCCGCGGCGCCCGCCCGGCTGCATCGCTGGTCCCCCGGCTCGGGCTCCAGGCCCGGCGCCTCCCACCCCCAGGCCGCGCGCGTCCCGCCCTCCCGACGACCCCCAGCCCCGGGCCTCCGCCACTTACGAGTCCCCGTCCTCGGTGAGCTGCTGCTTCCAGGGCTCCGAGCCGCGCGGCACCTCCTGCGGCTCGAGGCGGATCTCCTGCAGCTCCTTGACCATCTGCTCGTACTCCTCGTCTTTCATGGAGTCCAGGCCGCTGTCGTGGCGGTCGTCCAGTAGCCGCTCCTTCTTCAGCCCGTCGCGGGGGCCCTCCATGGCCCACTCCTGGGGGCGCTCGGCCGCCTGGAACATGGCGCGGACGAGCTGCGGGCGCTGCTGCGGGTGCGCTGGG	-	novel	NA	P-0060859-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	11	62	0	ENST00000216797.5:c.-40_228-187del		p.X14_splice	ENST00000216797	NM_020529.2	14		1/6	0.215941286711646	1	FACETS	0.937	0.654	1	0.937	0.654	1	CLONAL	1	TRUE	0	0.215941286711646	1		62	97	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733119	74733119	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060859-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	90	735	0	ENST00000359995.5:c.124G>T	p.Asp42Tyr	p.D42Y	ENST00000359995	NM_001195427.1	42	Gac/Tac	1/3	1	2	FACETS	0.714	0.632	0.803	0.714	0.632	0.803	SUBCLONAL	1	TRUE	1	0.215941286711646	2		735	1167	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405686	139406708	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGGGCACACGGGGCCAGCACCACCTCACACGTGGCACCTGCGGGAAGGAGACACACGTGACCCCGGGAGCCTCACCCAGAGGGATCTCCCAAATCGGCCACCGCCTGCTGGTCTTTCCGCCATCAGAGTGCCGTCTGCTGGTCCCGCCGGGAGGCAAATGTGCACCGAGACCCCTGAGCGCTCCCGGCTGTGCCAGGACCCTGACCCAGGGAGGAGTGGAGCACAGATGGGGGGACGCTGAAGACAAGCTGCACAAATGTCACGCTCAGAAGCCACCCCTCATTCCCGGTTGGCAGCGGGGCACAGCCTAGGCCTCACCCCACCAGGCGTGCCCAGGAACAAGGACTGCACCAGGAGAGGCGGCCTCAGTCGGGTGGGCTCCACGACACTGCAGGGACCTGGGCCCACCCCGGACGCAAGCCCCCTCATCTCTGGGTGACGAGGAAAGGCCCTGGCCTGAGACCGAGGCCTGAAACTAATCCTGGGGCTCCGTGTCACAGGCAGCAAACGCCCATCACGGGAGGCCAACAAACAAGGGCTGCGATGGAGGGGACAGGCCCAGGCCCCCAGCACATCCTGCGTGTCGGGGCACGGGGCACGGCCTGGAGACCTCCAGGGCCACGCAGGGTGTCTGGCAAAGGCTATGTGGGAACCACGTGCACAGCCGAGGGCCTTTTTCTGCACAAGCCCATGGCCGAGCTTCCTGTTTATAGCCGTGGGGACTGCGTTATCTTCCCTGTCCCCCATTATCTCCCTGGCCTGCTGGGGCGACTTTCCAGGGCCTCTCTTCCTATTGGTTTCCACGGTGACCCGGGCAGGCAGGAACTGCGCCAGAGTTTCCGACAATTGTGCGAAAGGAAGCAGGAAGCGGGCAGATAGGAAGCGGGTCAGCACCGCCGCTCCTCCTGCCGGCCCGATCGACGTGTCTGAAAGGGACAGGGGCGCCCAGCCGTGGAGGGAGGGTCCTCACTGACTGACACAGGAGAGAAAACCCAGGTCCTTAACTTCGGTCAAAGAAAACA	GGGGGCACACGGGGCCAGCACCACCTCACACGTGGCACCTGCGGGAAGGAGACACACGTGACCCCGGGAGCCTCACCCAGAGGGATCTCCCAAATCGGCCACCGCCTGCTGGTCTTTCCGCCATCAGAGTGCCGTCTGCTGGTCCCGCCGGGAGGCAAATGTGCACCGAGACCCCTGAGCGCTCCCGGCTGTGCCAGGACCCTGACCCAGGGAGGAGTGGAGCACAGATGGGGGGACGCTGAAGACAAGCTGCACAAATGTCACGCTCAGAAGCCACCCCTCATTCCCGGTTGGCAGCGGGGCACAGCCTAGGCCTCACCCCACCAGGCGTGCCCAGGAACAAGGACTGCACCAGGAGAGGCGGCCTCAGTCGGGTGGGCTCCACGACACTGCAGGGACCTGGGCCCACCCCGGACGCAAGCCCCCTCATCTCTGGGTGACGAGGAAAGGCCCTGGCCTGAGACCGAGGCCTGAAACTAATCCTGGGGCTCCGTGTCACAGGCAGCAAACGCCCATCACGGGAGGCCAACAAACAAGGGCTGCGATGGAGGGGACAGGCCCAGGCCCCCAGCACATCCTGCGTGTCGGGGCACGGGGCACGGCCTGGAGACCTCCAGGGCCACGCAGGGTGTCTGGCAAAGGCTATGTGGGAACCACGTGCACAGCCGAGGGCCTTTTTCTGCACAAGCCCATGGCCGAGCTTCCTGTTTATAGCCGTGGGGACTGCGTTATCTTCCCTGTCCCCCATTATCTCCCTGGCCTGCTGGGGCGACTTTCCAGGGCCTCTCTTCCTATTGGTTTCCACGGTGACCCGGGCAGGCAGGAACTGCGCCAGAGTTTCCGACAATTGTGCGAAAGGAAGCAGGAAGCGGGCAGATAGGAAGCGGGTCAGCACCGCCGCTCCTCCTGCCGGCCCGATCGACGTGTCTGAAAGGGACAGGGGCGCCCAGCCGTGGAGGGAGGGTCCTCACTGACTGACACAGGAGAGAAAACCCAGGTCCTTAACTTCGGTCAAAGAAAACA	-	novel	NA	P-0060859-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	65	639	0	ENST00000277541.6:c.2467+765_2505del		p.X823_splice	ENST00000277541	NM_017617.3	823		16/34	0.215941286711646	1	FACETS	0.55	0.475	0.632	0.55	0.475	0.632	SUBCLONAL	1	TRUE	0	0.215941286711646	1		639	976	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0060861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	102	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.905	0.811	1	0.905	0.811	1	CLONAL	1	TRUE	1	0.357136075618696	2		334	631	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0060861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	115	423	1	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.339596865266235	1	FACETS	0.644	0.58	0.712	0.644	0.58	0.712	SUBCLONAL	1	TRUE	0	0.357136075618696	1		424	821	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0060861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	237	676	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.339596865266235	1	FACETS	0.98	0.914	1	0.98	0.914	1	CLONAL	1	TRUE	0	0.357136075618696	1		676	1113	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0060861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	234	324	1	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.348517279164449	2	FACETS	0.757	0.707	0.808	0.757	0.707	0.808	SUBCLONAL	2	TRUE	0	0.357136075618696	2		325	866	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912149	114912149	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	139	525	0	ENST00000543371.1:c.1219C>T	p.Arg407Ter	p.R407*	ENST00000543371	NM_001198531.1	407	Cga/Tga	11/14	1	2	FACETS	0.816	0.742	0.894	0.816	0.742	0.894	CLONAL	1	TRUE	1	0.357136075618696	2		525	954	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101199	41101199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368237025	NA	P-0060861-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	127	568	0	ENST00000373198.4:c.1157C>T	p.Pro386Leu	p.P386L	ENST00000373198	NM_133170.3	386	cCg/cTg	8/32	NA	2	FACETS	0.741	0.67	0.815			1	INDETERMINATE	1	TRUE	NA	0.357136075618696	2		568	960	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0060862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	404	446	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.497569529712635	2	FACETS	0.944	0.903	0.985	0.944	0.903	0.985	CLONAL	2	TRUE	0	0.497569529712635	2		446	860	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	rs886039483	NA	P-0060862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	252	466	1	ENST00000269305.4:c.376T>A	p.Tyr126Asn	p.Y126N	ENST00000269305	NM_001126112.2	126	Tac/Aac	5/11	0.497569529712635	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.497569529712635	1		467	687	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982073	201982073	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0060862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	270	488	0	ENST00000359651.3:c.599-2A>T		p.X200_splice	ENST00000359651		200			0.348345687217383	1	FACETS	0.974	0.917	1	0.974	0.917	1	CLONAL	1	TRUE	0	0.497569529712635	1		488	837	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120741	94120741	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	92	382	0	ENST00000369303.4:c.310T>G	p.Phe104Val	p.F104V	ENST00000369303	NM_004440.3	104	Ttc/Gtc	3/17	1	2	FACETS	0.459	0.408	0.515	0.459	0.408	0.515	SUBCLONAL	1	TRUE	1	0.497569529712635	2		382	805	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0060863-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	1145	653	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.923441971956958	2		653	1239	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0060863-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4	72	108	0	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			0.923441971956958	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.923441971956958	1		108	76	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498343	29498343	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060863-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	212	560	0	ENST00000389048.3:c.1837G>T	p.Ala613Ser	p.A613S	ENST00000389048	NM_004304.4	613	Gca/Tca	10/29	0.466475056648301	1	FACETS	0.333	0.31	0.356	0.333	0.31	0.356	INDETERMINATE	1	TRUE	0	0.923441971956958	1		560	743	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994285	21994285	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060863-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	392	558	0	ENST00000579755.1:c.46G>T	p.Gly16Cys	p.G16C	ENST00000579755		16	Ggc/Tgc	1/3	1		FACETS		0.89	0.974				CLONAL	1	TRUE	1	0.923441971956958	2		558	911	SUCCESS
AR	367	MSKCC	GRCh37	X	66765079	66765079	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060863-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	479	679	0	ENST00000374690.3:c.91C>A	p.Arg31Ser	p.R31S	ENST00000374690	NM_000044.3	31	Cgc/Agc	1/8	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.923441971956958	2		679	1035	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696411	47696411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs968974699	NA	P-0060863-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	858	522	0	ENST00000347630.2:c.412C>T	p.Arg138Cys	p.R138C	ENST00000347630	NM_001007230.1	138	Cgt/Tgt	6/11	0.923441971956958	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.923441971956958	2		522	910	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658564	206658564	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060863-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	512	693	0	ENST00000367120.3:c.1537A>G	p.Ile513Val	p.I513V	ENST00000367120	NM_014002.3	513	Atc/Gtc	15/22	0.448660969827696	3	FACETS	1	0.991	1	0.558	0.534	0.582	INDETERMINATE	1	TRUE	1	0.923441971956958	3		693	1453	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448155	49448155	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060863-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	625	784	0	ENST00000301067.7:c.445G>T	p.Val149Leu	p.V149L	ENST00000301067	NM_003482.3	149	Gta/Tta	4/54	0.923441971956958	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.923441971956958	1		784	707	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155218	106155218	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060863-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	458	536	0	ENST00000380013.4:c.119T>A	p.Leu40Gln	p.L40Q	ENST00000380013	NM_001127208.2	40	cTg/cAg	3/11	0.923441971956958	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.923441971956958	1		536	527	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945057	151945057	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1383545815	NA	P-0060863-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	50	392	0	ENST00000262189.6:c.2462C>T	p.Pro821Leu	p.P821L	ENST00000262189	NM_170606.2	821	cCa/cTa	14/59	1	2	FACETS	0.22	0.186	0.256	0.22	0.186	0.256	SUBCLONAL	1	TRUE	1	0.923441971956958	2		392	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587780070	NA	P-0060865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	392	929	0	ENST00000269305.4:c.535C>G	p.His179Asp	p.H179D	ENST00000269305	NM_001126112.2	179	Cat/Gat	5/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.820551780968574	2		929	954	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577144	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	317	669	0	ENST00000269305.4:c.794T>G	p.Leu265Arg	p.L265R	ENST00000269305	NM_001126112.2	265	cTg/cGg	8/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.820551780968574	2		669	716	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033939	49033939	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0060865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	240	570	0	ENST00000267163.4:c.2076T>G	p.Tyr692Ter	p.Y692*	ENST00000267163	NM_000321.2	692	taT/taG	20/27	0.820551780968574	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.820551780968574	1		570	316	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578507	7578507	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519977	NA	P-0060866-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	202	752	0	ENST00000269305.4:c.423C>G	p.Cys141Trp	p.C141W	ENST00000269305	NM_001126112.2	141	tgC/tgG	5/11	0.219074559527667	2	FACETS	1	0.985	1	0.613	0.569	0.658	INDETERMINATE	1	TRUE	0	0.392109981214833	2		752	841	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442679	442679	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060866-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	79	716	0	ENST00000399788.2:c.1627A>T	p.Asn543Tyr	p.N543Y	ENST00000399788	NM_001042603.1	543	Aac/Tac	12/28	0.392109981214833	3	FACETS	0.406	0.356	0.461	0.203	0.178	0.231	SUBCLONAL	1	TRUE	1	0.392109981214833	3		716	1187	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472622	88472622	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060866-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	120	612	0	ENST00000360948.2:c.1933C>A	p.Arg645Ser	p.R645S	ENST00000360948	NM_001012338.2	645	Cgc/Agc	16/19	1	2	FACETS	0.83	0.75	0.915	0.83	0.75	0.915	CLONAL	1	TRUE	1	0.392109981214833	2		612	737	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016567	12016567	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060866-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	99	287	0	ENST00000353533.5:c.703A>G	p.Ile235Val	p.I235V	ENST00000353533	NM_003010.3	235	Att/Gtt	7/11	0.219074559527667	2	FACETS	1	0.976	1	0.652	0.587	0.721	INDETERMINATE	1	TRUE	0	0.392109981214833	2		287	387	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144005	11144005	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060866-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	174	636	0	ENST00000358026.2:c.3586C>T	p.Gln1196Ter	p.Q1196*	ENST00000358026	NM_001128849.1	1196	Cag/Tag	26/36	0.392109981214833	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.392109981214833	1		636	699	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977855	134977855	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1354688627	NA	P-0060866-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	91	433	0	ENST00000398015.3:c.2848G>A	p.Asp950Asn	p.D950N	ENST00000398015	NM_004441.4	950	Gac/Aac	16/16	0.392109981214833	3	FACETS	0.808	0.718	0.904	0.404	0.359	0.452	CLONAL	1	TRUE	1	0.392109981214833	3		433	687	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484318	8484318	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060866-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	98	386	0	ENST00000356435.5:c.3214A>T	p.Ile1072Phe	p.I1072F	ENST00000356435		1072	Att/Ttt	19/35	0.378644931082006	1	FACETS	0.926	0.831	1	0.926	0.831	1	CLONAL	1	TRUE	0	0.392109981214833	1		386	434	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484338	8484338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060866-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	84	333	0	ENST00000356435.5:c.3194G>A	p.Gly1065Asp	p.G1065D	ENST00000356435		1065	gGc/gAc	19/35	0.378644931082006	1	FACETS	0.921	0.819	1	0.921	0.819	1	CLONAL	1	TRUE	0	0.392109981214833	1		333	374	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0060867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	34	347	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.978	0.809	1	1	0.971	1	CLONAL	3	TRUE	1	0.134715777733883	2		347	172	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0060867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	92	243	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.926	0.833	1	1	0.991	1	CLONAL	5	TRUE	1	0.134715777733883	2		243	295	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0060867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	312	672	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	0.0969557068240725	4	FACETS	1	0.976	1	1	0.996	1	CLONAL	5	TRUE	2	0.134715777733883	4		672	995	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0060867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	77	428	5	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	1	2	FACETS	1	0.963	1	1	0.986	1	CLONAL	2	TRUE	1	0.134715777733883	2		433	459	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0060867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	126	483	0	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	1	2	FACETS	1	0.948	1	1	0.992	1	CLONAL	3	TRUE	1	0.134715777733883	2		483	586	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249510	153249510	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1157879635	NA	P-0060867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	87	355	0	ENST00000281708.4:c.1268G>T	p.Gly423Val	p.G423V	ENST00000281708	NM_033632.3	423	gGa/gTa	9/12	1	2	FACETS	0.946	0.849	1	1	0.99	1	CLONAL	5	TRUE	1	0.134715777733883	2		355	273	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027087	71027087	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	214	678	1	ENST00000318789.4:c.1240del	p.Leu414Ter	p.L414*	ENST00000318789	NM_032682.5	414	Ctg/tg	15/21	1	2	FACETS	0.975	0.906	1	1	0.995	1	CLONAL	3	TRUE	1	0.134715777733883	2		679	1086	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717609	89717609	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs876661024	NA	P-0060867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	46	357	0	ENST00000371953.3:c.635-1G>T		p.X212_splice	ENST00000371953	NM_000314.4	212			1	2	FACETS	1	0.935	1	1	0.976	1	CLONAL	2	TRUE	1	0.134715777733883	2		357	284	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991949	72991949	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs753977275	NA	P-0060867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	159	644	1	ENST00000268489.5:c.2096del	p.Gly699AlafsTer125	p.G699Afs*125	ENST00000268489	NM_006885.3	699	gGc/gc	2/10	0.0969557068240725	4	FACETS	1	0.968	1	1	0.99	1	CLONAL	3	TRUE	2	0.134715777733883	4		645	806	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0060867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	220	661	0	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	0.0969557068240725	4	FACETS	1	0.981	1	1	0.993	1	CLONAL	3	TRUE	2	0.134715777733883	4		661	1072	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0060867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	60	773	0	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	0.0969557068240725	4	FACETS	0.984	0.845	1	0.492	0.422	0.569	CLONAL	1	TRUE	2	0.134715777733883	4		773	1027	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647657	3647657	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs774532876	NA	P-0060867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	146	637	6	ENST00000294008.3:c.1406del	p.Pro469HisfsTer4	p.P469Hfs*4	ENST00000294008	NM_032444.2	469	cCa/ca	7/15	0.0969557068240725	4	FACETS	1	0.942	1	1	0.988	1	CLONAL	3	TRUE	2	0.134715777733883	4		643	789	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515378	103515378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	67	460	0	ENST00000355739.4:c.1879G>A	p.Ala627Thr	p.A627T	ENST00000355739	NM_000123.3	627	Gca/Aca	8/15	0.134715777733883	1	FACETS	1	0.958	1	1	0.984	1	CLONAL	2	TRUE	0	0.134715777733883	1		460	374	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955524	90955524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753270166	NA	P-0060867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	48	340	0	ENST00000265433.3:c.2141G>A	p.Arg714Gln	p.R714Q	ENST00000265433	NM_002485.4	714	cGa/cAa	14/16	0.0969557068240725	4	FACETS	0.991	0.844	1	1	0.963	1	CLONAL	3	TRUE	2	0.134715777733883	4		340	272	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246078851	246078851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61762672	NA	P-0060867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	97	452	0	ENST00000388985.4:c.794G>A	p.Arg265His	p.R265H	ENST00000388985		265	cGt/cAt	8/12	0.134715777733883	11	FACETS	1	0.962	1	0.237	0.211	0.265	CLONAL	2	TRUE	1	0.134715777733883	11		452	976	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0060867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	61	395	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.0965362375699161	3	FACETS	0.921	0.806	1	1	0.982	1	CLONAL	5	TRUE	1	0.134715777733883	3		395	210	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101704	27101705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTCAT	novel	NA	P-0060867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	219	623	0	ENST00000324856.7:c.4986_4987insTTCAT	p.Asp1663PhefsTer12	p.D1663Ffs*12	ENST00000324856	NM_006015.4	1662	-/TTCAT	18/20	1	2	FACETS	1	0.963	1	1	0.996	1	CLONAL	4	TRUE	1	0.134715777733883	2		623	777	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137358	64137358	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	164	550	1	ENST00000334205.4:c.1790T>C	p.Val597Ala	p.V597A	ENST00000334205	NM_003942.2	597	gTc/gCc	14/17	1	2	FACETS	1	0.972	1	1	0.994	1	CLONAL	3	TRUE	1	0.134715777733883	2		551	725	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943796	9943796	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1394587285	NA	P-0060867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	286	542	0	ENST00000330684.3:c.1145C>T	p.Thr382Met	p.T382M	ENST00000330684	NM_001134407.1	382	aCg/aTg	5/13	0.0969557068240725	4	FACETS	1	0.954	1	1	0.996	1	CLONAL	5	TRUE	2	0.134715777733883	4		542	950	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828884	72828884	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	209	648	0	ENST00000268489.5:c.7697del	p.Leu2566TrpfsTer46	p.L2566Wfs*46	ENST00000268489	NM_006885.3	2566	tTg/tg	9/10	0.0969557068240725	4	FACETS	0.98	0.911	1	1	0.994	1	CLONAL	4	TRUE	2	0.134715777733883	4		648	898	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234547	41234547	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587781768	NA	P-0060867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	38	467	0	ENST00000357654.3:c.4231A>G	p.Met1411Val	p.M1411V	ENST00000357654	NM_007294.3	1411	Atg/Gtg	12/23	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.134715777733883	2		467	487	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228542	36228542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1446310161	NA	P-0060867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	137	486	1	ENST00000222270.7:c.7556G>A	p.Cys2519Tyr	p.C2519Y	ENST00000222270	NM_014727.1	2519	tGc/tAc	34/37	0.0969557068240725	4	FACETS	1	0.961	1	1	0.988	1	CLONAL	3	TRUE	2	0.134715777733883	4		487	702	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530121	212530121	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1229347539	NA	P-0060867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	116	535	0	ENST00000342788.4:c.1798del	p.Ala600GlnfsTer53	p.A600Qfs*53	ENST00000342788	NM_005235.2	600	Gca/ca	15/28	1	2	FACETS	0.952	0.86	1	1	0.991	1	CLONAL	3	TRUE	1	0.134715777733883	2		535	603	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014010	70014010	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	93	443	0	ENST00000394351.3:c.871C>T	p.Gln291Ter	p.Q291*	ENST00000394351	NM_000248.3	291	Cag/Tag	9/9	1	2	FACETS	1	0.925	1	1	0.989	1	CLONAL	3	TRUE	1	0.134715777733883	2		443	441	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637289	176637289	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	138	544	0	ENST00000439151.2:c.1892del	p.Lys631SerfsTer22	p.K631Sfs*22	ENST00000439151	NM_022455.4	630	gAa/ga	5/23	1	2	FACETS	1	0.966	1	1	0.993	1	CLONAL	3	TRUE	1	0.134715777733883	2		544	613	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935615	13935615	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	176	506	0	ENST00000405192.2:c.1241A>C	p.Asp414Ala	p.D414A	ENST00000405192	NM_001163147.1	414	gAc/gCc	12/12	0.0965362375699161	3	FACETS	1	0.975	1	1	0.991	1	CLONAL	3	TRUE	1	0.134715777733883	3		506	821	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578213	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs864309495	NA	P-0060868-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	213	679	1	ENST00000269305.4:c.636del	p.Arg213AspfsTer34	p.R213Dfs*34	ENST00000269305	NM_001126112.2	212	ttT/tt	6/11	0.217597551625417	3	FACETS	0.991	0.924	1			1	CLONAL	3	TRUE	NA	0.217597551625417	3		680	730	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0060869-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	68	418	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.3643866582597	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.3643866582597	1		418	283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579397	7579397	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060869-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	227	588	0	ENST00000269305.4:c.290del	p.Val97AlafsTer26	p.V97Afs*26	ENST00000269305	NM_001126112.2	97	gTc/gc	4/11	0.20688417831225	3	FACETS	0.959	0.896	1	0.639	0.597	0.682	INDETERMINATE	2	TRUE	0	0.3643866582597	3		588	768	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912174	114912174	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060869-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	104	351	0	ENST00000543371.1:c.1244C>G	p.Pro415Arg	p.P415R	ENST00000543371	NM_001198531.1	415	cCc/cGc	11/14	0.2556923144735	3	FACETS	1	0.915	1	0.511	0.458	0.567	CLONAL	1	TRUE	1	0.3643866582597	3		351	660	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144381564	144381564	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060869-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	56	405	0	ENST00000262995.4:c.1817C>G	p.Thr606Arg	p.T606R	ENST00000262995	NM_207123.2	606	aCa/aGa	9/11	0.2556923144735	3	FACETS	0.711	0.61	0.822	0.356	0.305	0.411	SUBCLONAL	1	TRUE	1	0.3643866582597	3		405	511	SUCCESS
APC	324	MSKCC	GRCh37	5	112175566	112175567	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0060869-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	148	509	0	ENST00000257430.4:c.4276_4277dup	p.Ser1426ArgfsTer48	p.S1426Rfs*48	ENST00000257430	NM_000038.5	1425	-/AG	16/16	0.2556923144735	3	FACETS	0.85	0.78	0.922	0.85	0.78	0.922	CLONAL	2	TRUE	1	0.3643866582597	3		509	565	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061191	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	205	801	0	ENST00000250448.2:c.798C>G	p.Phe266Leu	p.F266L	ENST00000250448	NM_004496.3	266	ttC/ttG	2/2	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.541321864265183	2		801	605	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061516	38061517	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGC	rs763371315	NA	P-0060870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	87	688	0	ENST00000250448.2:c.470_472dup	p.Gly157dup	p.G157dup	ENST00000250448	NM_004496.3	157	gac/gGCGac	2/2	1	2	FACETS	0.694	0.617	0.776	0.694	0.617	0.776	SUBCLONAL	1	TRUE	1	0.541321864265183	2		688	463	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954022	32954023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs397507419	NA	P-0060870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	81	447	3	ENST00000380152.3:c.9097dup	p.Thr3033AsnfsTer11	p.T3033Nfs*11	ENST00000380152		3030	aca/acAa	23/27	0.541321864265183	1	FACETS	0.791	0.705	0.88	0.791	0.705	0.88	SUBCLONAL	1	TRUE	0	0.541321864265183	1		450	276	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245034	46245035	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0060870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	299	887	0	ENST00000334344.6:c.3128_3129del	p.Gln1043ProfsTer13	p.Q1043Pfs*13	ENST00000334344	NM_152641.2	1043	cAA/c	15/21	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.541321864265183	2		887	1007	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204012	142204012	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	145	500	0	ENST00000350721.4:c.6191T>C	p.Leu2064Pro	p.L2064P	ENST00000350721	NM_001184.3	2064	cTc/cCc	36/47	1	2	FACETS	0.979	0.898	1	0.979	0.898	1	CLONAL	1	TRUE	1	0.541321864265183	2		500	547	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953760	48953760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913302	NA	P-0060874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	90	228	0	ENST00000267163.4:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000267163	NM_000321.2	455	Cga/Tga	14/27	0.843573716076448	1	FACETS	0.956	0.889	1	0.956	0.889	1	CLONAL	1	TRUE	0	0.843573716076448	1		228	129	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0060874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	353	499	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.979	0.932	1	0.979	0.932	1	CLONAL	1	TRUE	1	0.843573716076448	2		499	855	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955540	90955540	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	213	350	0	ENST00000265433.3:c.2125A>G	p.Ile709Val	p.I709V	ENST00000265433	NM_002485.4	709	Ata/Gta	14/16	0.843573716076448	2	FACETS	0.99	0.929	1	0.495	0.464	0.526	CLONAL	1	TRUE	0	0.843573716076448	2		350	510	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0060875-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	28	729	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.165	0.131	0.204	0.165	0.131	0.204	SUBCLONAL	1	FALSE	1	0.513315203074328	2		729	660	SUCCESS
APC	324	MSKCC	GRCh37	5	112173656	112173656	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123117	NA	P-0060876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	94	353	0	ENST00000257430.4:c.2365C>T	p.Gln789Ter	p.Q789*	ENST00000257430	NM_000038.5	789	Cag/Tag	16/16	0.404008941089599	3	FACETS	1	0.969	1	0.783	0.71	0.859	CLONAL	2	TRUE	0	0.404008941089599	3		353	238	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097644	8097644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762722802	NA	P-0060876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	99	544	3	ENST00000346208.3:c.26G>A	p.Arg9His	p.R9H	ENST00000346208		9	cGc/cAc	2/6	0.18892041055369	3	FACETS	1	0.982	1	0.748	0.672	0.826	INDETERMINATE	1	TRUE	1	0.404008941089599	3		547	394	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165729	108165729	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs762083530	NA	P-0060876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	301	280	0	ENST00000278616.4:c.4852C>T	p.Arg1618Ter	p.R1618*	ENST00000278616	NM_000051.3	1618	Cga/Tga	32/63	0.404008941089599	11	FACETS	1	0.983	1	1	0.983	1	CLONAL	10	TRUE	1	0.404008941089599	11		280	407	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809525	36809525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	60	491	0	ENST00000373129.3:c.940G>A	p.Asp314Asn	p.D314N	ENST00000373129	NM_032017.1	314	Gac/Aac	10/12	0.18892041055369	3	FACETS	0.742	0.641	0.853	0.371	0.32	0.427	INDETERMINATE	1	TRUE	1	0.404008941089599	3		491	481	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739370	145739370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1420577458	NA	P-0060876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	72	494	0	ENST00000428558.2:c.2000C>T	p.Pro667Leu	p.P667L	ENST00000428558	NM_004260.3	667	cCa/cTa	12/22	0.241808276082851	5	FACETS	0.848	0.741	0.964	0.17	0.148	0.193	INDETERMINATE	1	TRUE	0	0.404008941089599	5		494	675	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508176	106508176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752039271	NA	P-0060878-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	104	305	0	ENST00000359195.3:c.170C>T	p.Ala57Val	p.A57V	ENST00000359195	NM_002649.2	57	gCg/gTg	2/11	0.156295526115777	3	FACETS	0.942	0.844	1	0.471	0.422	0.524	INDETERMINATE	1	TRUE	1	0.355667455282183	3		305	731	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441246	52441246	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060878-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	125	762	0	ENST00000460680.1:c.524C>G	p.Pro175Arg	p.P175R	ENST00000460680	NM_004656.3	175	cCt/cGt	7/17	0.355667455282183	1	FACETS	0.928	0.842	1	0.928	0.842	1	CLONAL	1	TRUE	0	0.355667455282183	1		762	623	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158509	106158509	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs772634266	NA	P-0060878-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	97	450	0	ENST00000380013.4:c.3409+1G>A		p.X1137_splice	ENST00000380013	NM_001127208.2	1137			0.253168391128923	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.355667455282183	1		450	416	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120752	115120752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777208877	NA	P-0060878-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	140	767	0	ENST00000257566.3:c.254C>T	p.Ala85Val	p.A85V	ENST00000257566	NM_016569.3	85	gCg/gTg	1/8	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.355667455282183	2		767	717	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197381	106197382	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGC	novel	NA	P-0060878-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	49	542	0	ENST00000380013.4:c.5715_5718dup	p.Met1907GlufsTer4	p.M1907Efs*4	ENST00000380013	NM_001127208.2	1905	aag/aaGAGCg	11/11	0.253168391128923	1	FACETS	0.398	0.337	0.466	0.398	0.337	0.466	SUBCLONAL	1	TRUE	0	0.355667455282183	1		542	569	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779118	135779118	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397514874	NA	P-0060878-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	123	548	0	ENST00000298552.3:c.2128C>T	p.Gln710Ter	p.Q710*	ENST00000298552	NM_001162426.1	710	Cag/Tag	17/23	0.253168391128923	1	FACETS	0.923	0.837	1	0.923	0.837	1	CLONAL	1	TRUE	0	0.355667455282183	1		548	616	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643779	52643796	+	inframe_deletion	In_Frame_Del	DEL	ATGTCCATGGGCTTTTTA	ATGTCCATGGGCTTTTTA	-	novel	NA	P-0060878-T01-IM7	NA	-	-	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	80	458	1	ENST00000394830.3:c.2100_2117del	p.Ile700_Asp705del	p.I700_D705del	ENST00000394830	NM_018313.4	700	atTAAAAAGCCCATGGACATg/atg	17/30	0.355667455282183	1	FACETS	0.824	0.728	0.926	0.824	0.728	0.926	CLONAL	1	TRUE	0	0.355667455282183	1		459	449	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	305	759	1				ENST00000310581	NM_198253.2	-/1132			0.4858285822324	4	FACETS	0.988	0.934	1	0.988	0.934	1	CLONAL	2	TRUE	2	0.522165203960433	4		760	900	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160485	108160485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	68	280	0	ENST00000278616.4:c.4393C>T	p.Leu1465Phe	p.L1465F	ENST00000278616	NM_000051.3	1465	Ctt/Ttt	29/63	0.522165203960433	3	FACETS	0.842	0.736	0.956	0.421	0.368	0.478	CLONAL	1	TRUE	1	0.522165203960433	3		280	390	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503192	125503192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	120	406	0	ENST00000428830.2:c.559G>A	p.Glu187Lys	p.E187K	ENST00000428830	NM_001114121.2	187	Gaa/Aaa	6/14	0.522165203960433	3	FACETS	0.979	0.887	1	0.49	0.443	0.538	CLONAL	1	TRUE	1	0.522165203960433	3		406	592	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0060879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	369	922	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	0.4858285822324	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.522165203960433	4		922	1012	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630800	90630800	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0060879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	218	557	0	ENST00000330062.3:c.686C>G	p.Ser229Ter	p.S229*	ENST00000330062	NM_002168.2	229	tCa/tGa	6/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.522165203960433	2		557	771	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041884	14041884	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	384	658	0	ENST00000311895.7:c.2431G>A	p.Glu811Lys	p.E811K	ENST00000311895	NM_005236.2	811	Gag/Aag	11/11	0.4858285822324	4	FACETS	0.991	0.942	1	0.991	0.942	1	CLONAL	2	TRUE	2	0.522165203960433	4		658	1130	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0060879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	370	761	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.4858285822324	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.522165203960433	4		764	1033	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0060879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	417	638	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.4858285822324	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.522165203960433	4		638	1199	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483095	29483095	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	73	252	0	ENST00000356175.3:c.155C>A	p.Ser52Tyr	p.S52Y	ENST00000356175	NM_000267.3	52	tCt/tAt	2/57	0.4858285822324	4	FACETS	0.994	0.873	1	0.497	0.436	0.562	CLONAL	1	TRUE	2	0.522165203960433	4		252	428	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721190	61721190	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	154	284	0	ENST00000401558.2:c.1084G>C	p.Glu362Gln	p.E362Q	ENST00000401558	NM_003400.3	362	Gaa/Caa	12/25	0.358383548486247	5	FACETS	1	0.963	1	0.717	0.661	0.775	CLONAL	2	TRUE	2	0.522165203960433	5		284	489	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137320992	137321003	+	inframe_deletion	In_Frame_Del	DEL	TCCATCGCCGTG	TCCATCGCCGTG	-	novel	NA	P-0060879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	598	675	0	ENST00000481739.1:c.949_960del	p.Ser317_Val320del	p.S317_V320del	ENST00000481739	NM_002957.4	317	TCCATCGCCGTG/-	7/10	0.522165203960433	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	0	0.522165203960433	3		675	950	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941963	44941963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	72	124	0	ENST00000377967.4:c.3213del	p.Arg1073GlyfsTer10	p.R1073Gfs*10	ENST00000377967	NM_021140.2	1071	tcT/tc	22/29	1	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.522165203960433	1		124	155	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0060880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	62	418	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.229531319355135	2	FACETS	0.777	0.676	0.884	0.777	0.676	0.884	SUBCLONAL	2	TRUE	0	0.265197341939826	2		418	301	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0060880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	81	418	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.116258607763332	3	FACETS	0.91	0.807	1	0.607	0.538	0.68	INDETERMINATE	2	TRUE	0	0.265197341939826	3		418	380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0060880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	174	821	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.216717903393381	2	FACETS	0.765	0.704	0.827	0.765	0.704	0.827	SUBCLONAL	2	TRUE	0	0.265197341939826	2		822	858	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604665	48604665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660045	NA	P-0060880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	76	678	0	ENST00000342988.3:c.1487G>A	p.Arg496His	p.R496H	ENST00000342988	NM_005359.5	496	cGt/cAt	12/12	0.265197341939826	1	FACETS	0.917	0.806	1	0.917	0.806	1	CLONAL	1	TRUE	0	0.265197341939826	1		678	542	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510895	157510895	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	81	736	1	ENST00000346085.5:c.3670A>G	p.Thr1224Ala	p.T1224A	ENST00000346085	NM_020732.3	1224	Act/Gct	14/20	1	2	FACETS	0.881	0.776	0.994	0.881	0.776	0.994	CLONAL	1	TRUE	1	0.265197341939826	2		737	693	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231488896	231488896	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	43	428	0	ENST00000295050.7:c.1259T>G	p.Phe420Cys	p.F420C	ENST00000295050	NM_032018.5	420	tTt/tGt	5/5	1	2	FACETS	0.992	0.833	1	0.992	0.833	1	CLONAL	1	TRUE	1	0.265197341939826	2		428	327	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845373	42845373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61735796	NA	P-0060884-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	59	697	0	ENST00000398585.3:c.889G>A	p.Glu297Lys	p.E297K	ENST00000398585	NM_001135099.1	297	Gag/Aag	9/14	0.211467711578381	1	FACETS	0.931	0.802	1	0.931	0.802	1	CLONAL	1	TRUE	0	0.211467711578381	1		697	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0060884-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	85	812	0	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.153916585447177	2	FACETS	1	0.966	1	0.623	0.551	0.7	CLONAL	1	TRUE	0	0.211467711578381	2		812	645	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0060884-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	58	608	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	0.211467711578381	1	FACETS	0.987	0.849	1	0.987	0.849	1	CLONAL	1	TRUE	0	0.211467711578381	1		608	497	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412297	139412297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060884-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	34	785	0	ENST00000277541.6:c.1348G>A	p.Glu450Lys	p.E450K	ENST00000277541	NM_017617.3	450	Gag/Aag	8/34	0.153916585447177	2	FACETS	0.542	0.442	0.656	0.271	0.221	0.328	SUBCLONAL	1	TRUE	0	0.211467711578381	2		785	593	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419022	419022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781079102	NA	P-0060884-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	67	512	0	ENST00000399788.2:c.3325C>T	p.Pro1109Ser	p.P1109S	ENST00000399788	NM_001042603.1	1109	Cct/Tct	22/28	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.211467711578381	2		512	438	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50769112	50769112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060884-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	28	521	0	ENST00000307179.4:c.916C>T	p.Leu306Phe	p.L306F	ENST00000307179		306	Ctt/Ttt	9/20	1	2	FACETS	0.573	0.457	0.706	0.573	0.457	0.706	SUBCLONAL	1	TRUE	1	0.211467711578381	2		521	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577080	7577080	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060884-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	34	714	0	ENST00000269305.4:c.858A>T	p.Glu286Asp	p.E286D	ENST00000269305	NM_001126112.2	286	gaA/gaT	8/11	0.153916585447177	2	FACETS	0.556	0.453	0.673	0.278	0.226	0.337	SUBCLONAL	1	TRUE	0	0.211467711578381	2		714	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578561	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTGTAGG	ACTGTAGG	-	novel	NA	P-0060884-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	63	663	0	ENST00000269305.4:c.376-7_376del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	0.153916585447177	2	FACETS	1	0.885	1	0.513	0.443	0.588	CLONAL	1	TRUE	0	0.211467711578381	2		663	581	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33689967	33689967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060884-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	51	703	1	ENST00000308377.4:c.860G>A	p.Cys287Tyr	p.C287Y	ENST00000308377	NM_152270.3	287	tGc/tAc	2/5	0.192345999816671	2	FACETS	0.75	0.637	0.875	0.375	0.318	0.438	SUBCLONAL	1	TRUE	0	0.211467711578381	2		704	643	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096550	178096550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060884-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	63	618	0	ENST00000397062.3:c.781G>A	p.Glu261Lys	p.E261K	ENST00000397062	NM_006164.4	261	Gaa/Aaa	5/5	0.211467711578381	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.211467711578381	1		618	490	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096580	178096580	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060884-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	58	610	0	ENST00000397062.3:c.751G>C	p.Glu251Gln	p.E251Q	ENST00000397062	NM_006164.4	251	Gag/Cag	5/5	0.211467711578381	1	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	0	0.211467711578381	1		610	466	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980913	40980913	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060884-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	30	671	0	ENST00000373198.4:c.1573G>C	p.Ala525Pro	p.A525P	ENST00000373198	NM_133170.3	525	Gct/Cct	10/32	0.211467711578381	0	FACETS	0.417	0.335	0.51			1	SUBCLONAL	1	TRUE	0	0.211467711578381	0		671	537	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100551	157100551	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs759078059	NA	P-0060884-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	34	422	0	ENST00000346085.5:c.1488G>C	p.Arg496Ser	p.R496S	ENST00000346085	NM_020732.3	496	agG/agC	1/20	0.211467711578381	1	FACETS	0.724	0.592	0.873	0.724	0.592	0.873	SUBCLONAL	1	TRUE	0	0.211467711578381	1		422	397	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0060888-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	135	395	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.907	0.831	0.985	0.907	0.831	0.985	CLONAL	1	TRUE	1	0.675024614527082	2		395	441	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0060888-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	292	507	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.675024614527082	2		507	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579314	7579314	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs1057520003	NA	P-0060888-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	191	483	0	ENST00000269305.4:c.373A>C	p.Thr125Pro	p.T125P	ENST00000269305	NM_001126112.2	125	Acg/Ccg	4/11	0.675024614527082	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.675024614527082	1		483	353	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591933	48591933	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060888-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	172	419	0	ENST00000342988.3:c.1096C>G	p.Gln366Glu	p.Q366E	ENST00000342988	NM_005359.5	366	Caa/Gaa	9/12	0.675024614527082	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.675024614527082	1		419	332	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958438	90958438	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060888-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	138	284	0	ENST00000265433.3:c.2000C>G	p.Ser667Cys	p.S667C	ENST00000265433	NM_002485.4	667	tCt/tGt	13/16	0.675024614527082	3	FACETS	0.77	0.702	0.842	0.385	0.351	0.421	SUBCLONAL	1	TRUE	1	0.675024614527082	3		284	710	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120502026	120502036	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGAGCAGAC	GGTGAGCAGAC	-	novel	NA	P-0060888-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	29	341	0	ENST00000256646.2:c.2005_2015del	p.Val669ArgfsTer8	p.V669Rfs*8	ENST00000256646	NM_024408.3	669	GTCTGCTCACCa/a	12/34	0.431272531913868	1	FACETS	0.134	0.107	0.165	0.134	0.107	0.165	SUBCLONAL	1	TRUE	0	0.675024614527082	1		341	424	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646222	3646222	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371325486	NA	P-0060888-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	136	479	0	ENST00000294008.3:c.1856C>T	p.Ala619Val	p.A619V	ENST00000294008	NM_032444.2	619	gCg/gTg	8/15	0.486116185152757	1	FACETS	0.737	0.679	0.797	0.737	0.679	0.797	SUBCLONAL	1	TRUE	0	0.675024614527082	1		479	362	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843552	3843552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060888-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	154	464	0	ENST00000262367.5:c.1051C>T	p.Arg351Cys	p.R351C	ENST00000262367	NM_004380.2	351	Cgc/Tgc	4/31	0.486116185152757	1	FACETS	0.511	0.469	0.553	0.511	0.469	0.553	SUBCLONAL	1	TRUE	0	0.675024614527082	1		464	592	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383895	15383895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200468125	NA	P-0060888-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	56	464	0	ENST00000263377.2:c.16G>A	p.Gly6Ser	p.G6S	ENST00000263377	NM_058243.2	6	Ggc/Agc	2/20	0.448151005052303	1	FACETS	0.3	0.258	0.346	0.3	0.258	0.346	SUBCLONAL	1	TRUE	0	0.675024614527082	1		464	366	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455223	29455223	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1194282326	NA	P-0060888-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	132	483	0	ENST00000389048.3:c.2579G>T	p.Arg860Ile	p.R860I	ENST00000389048	NM_004304.4	860	aGa/aTa	15/29	0.568736363829683	1	FACETS	0.626	0.573	0.68	0.626	0.573	0.68	SUBCLONAL	1	TRUE	0	0.675024614527082	1		483	414	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2949752	2949752	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1253214830	NA	P-0060888-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	98	371	0	ENST00000396946.4:c.3192G>C	p.Leu1064Phe	p.L1064F	ENST00000396946	NM_032415.4	1064	ttG/ttC	24/25	0.443767217875152	1	FACETS	0.576	0.519	0.635	0.576	0.519	0.635	SUBCLONAL	1	TRUE	0	0.675024614527082	1		371	334	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0060889-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	95	479	0				ENST00000310581	NM_198253.2	-/1132			0.257043421416428	0	FACETS	0.839	0.78	0.894			1	CLONAL	7	TRUE	0	0.19	0		479	138	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967632	26967633	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0060889-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	123	449	0	ENST00000381527.3:c.775_776del	p.Met259GlyfsTer6	p.M259Gfs*6	ENST00000381527	NM_001260.1	259	ATg/g	7/13	0.257043421416428	0	FACETS	0.816	0.753	0.879			1	CLONAL	5	TRUE	0	0.19	0		449	257	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108261	209108261	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756798008	NA	P-0060889-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	149	513	0	ENST00000345146.2:c.588del	p.Phe197SerfsTer13	p.F197Sfs*13	ENST00000345146	NM_005896.2	196	tcC/tc	6/10	1	2	FACETS	1	0.931	1	1	0.993	1	CLONAL	3	TRUE	1	0.19	2		513	516	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	22	759	1				ENST00000310581	NM_198253.2	-/1132			0.16096865995169	0	FACETS	1	0.811	1			1	CLONAL	1	TRUE	0	0.205704896306741	0		760	163	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520000	NA	P-0060892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	91	756	1	ENST00000269305.4:c.452C>A	p.Pro151His	p.P151H	ENST00000269305	NM_001126112.2	151	cCc/cAc	5/11	0.205944927861259	3	FACETS	0.951	0.847	1	0.951	0.847	1	CLONAL	2	TRUE	1	0.205704896306741	3		757	513	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865750	57865750	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs751486798	NA	P-0060892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	41	665	0	ENST00000228682.2:c.3227C>A	p.Pro1076His	p.P1076H	ENST00000228682	NM_005269.2	1076	cCt/cAt	12/12	0.158102796784976	4	FACETS	0.768	0.638	0.912	0.384	0.319	0.456	CLONAL	1	TRUE	2	0.205704896306741	4		665	626	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21348020	21348020	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775051211	NA	P-0060892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	46	550	0	ENST00000215739.8:c.1330G>A	p.Asp444Asn	p.D444N	ENST00000215739	NM_006767.3	444	Gac/Aac	12/21	0.109169821239234	4	FACETS	1	0.957	1	0.717	0.605	0.84	INDETERMINATE	1	TRUE	2	0.205704896306741	4		550	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	189	469	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.331091112195875	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.331091112195875	2		469	543	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	103	479	0				ENST00000310581	NM_198253.2	-/1132			0.331091112195875	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.331091112195875	3		479	337	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	397	554	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.331091112195875	7	FACETS	0.968	0.924	1	0.968	0.924	1	CLONAL	5	TRUE	2	0.331091112195875	7		554	906	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165834	118165834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780049033	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	224	515	0	ENST00000369448.3:c.344C>T	p.Ser115Phe	p.S115F	ENST00000369448	NM_017709.3	115	tCc/tTc	2/2	0.331091112195875	7	FACETS	1	0.98	1	0.455	0.423	0.488	CLONAL	2	TRUE	2	0.331091112195875	7		515	1088	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10797090	10797090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1340626013	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	172	364	0	ENST00000361367.2:c.3005C>T	p.Pro1002Leu	p.P1002L	ENST00000361367	NM_014633.3	1002	cCa/cTa	24/25	0.331091112195875	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.331091112195875	3		364	580	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77054863	77054864	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	CTGT	novel	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	91	366	0	ENST00000356341.3:c.995_998dup	p.Ser333ArgfsTer8	p.S333Rfs*8	ENST00000356341	NM_002576.4	333	agt/agACAGt		0.331091112195875	5	FACETS	1	0.969	1	0.315	0.28	0.353	CLONAL	1	TRUE	1	0.331091112195875	5		366	653	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	96	721	0	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	0.331091112195875	1	FACETS	0.846	0.755	0.942	0.846	0.755	0.942	CLONAL	1	TRUE	0	0.331091112195875	1		721	572	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944983	31944983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1175067252	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	121	536	0	ENST00000340398.3:c.118C>T	p.Arg40Cys	p.R40C	ENST00000340398	NM_001013699.2	40	Cgc/Tgc	1/1	0.272568712729913	4	FACETS	1	0.932	1	0.521	0.47	0.575	CLONAL	1	TRUE	2	0.331091112195875	4		536	934	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244824	46244824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	235	468	0	ENST00000334344.6:c.2918C>T	p.Ser973Leu	p.S973L	ENST00000334344	NM_152641.2	973	tCa/tTa	15/21	0.272568712729913	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.331091112195875	4		468	893	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480028	50480028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs759976916	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	186	414	0	ENST00000394963.4:c.262C>T	p.Arg88Ter	p.R88*	ENST00000394963	NM_003076.4	88	Cga/Tga	2/13	0.272568712729913	4	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	2	0.331091112195875	4		414	723	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347320	89347321	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	170	517	0	ENST00000301030.4:c.5629_5630delinsTT	p.Pro1877Leu	p.P1877L	ENST00000301030	NM_001256183.1	1877	CCg/TTg	9/13	0.331091112195875	3	FACETS	0.975	0.901	1	0.975	0.901	1	CLONAL	2	TRUE	1	0.331091112195875	3		517	614	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661982	29661982	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	140	412	1	ENST00000356175.3:c.5876del	p.Thr1959LysfsTer2	p.T1959Kfs*2	ENST00000356175	NM_000267.3	1959	aCa/aa	39/57	0.331091112195875	3	FACETS	0.903	0.826	0.982	0.903	0.826	0.982	CLONAL	2	TRUE	1	0.331091112195875	3		413	546	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61308147	61308147	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs145373357	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	11	13	0	ENST00000341074.5:c.430C>T	p.Arg144Ter	p.R144*	ENST00000341074	NM_002974.2	144	Cga/Tga	5/8	0.331091112195875	3	FACETS	0.993	0.714	1	0.993	0.714	1	CLONAL	2	TRUE	1	0.331091112195875	3		13	39	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61322991	61322991	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	90	465	0	ENST00000283752.5:c.1073C>T	p.Ser358Leu	p.S358L	ENST00000283752	NM_006919.2	358	tCa/tTa	8/8	0.331091112195875	3	FACETS	1	0.938	1	0.542	0.481	0.606	CLONAL	1	TRUE	1	0.331091112195875	3		465	585	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272402	15272403	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	171	521	0	ENST00000263388.2:c.6036_6037delinsTT	p.Gln2013Ter	p.Q2013*	ENST00000263388	NM_000435.2	2012	gcCCag/gcTTag	33/33	0.331091112195875	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.331091112195875	3		521	577	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36208991	36208991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	128	188	0	ENST00000222270.7:c.71C>T	p.Pro24Leu	p.P24L	ENST00000222270	NM_014727.1	24	cCg/cTg	1/37	0.331091112195875	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	TRUE	0	0.331091112195875	3		188	270	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451788	29451788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1490348940	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	77	282	0	ENST00000389048.3:c.2777G>A	p.Gly926Glu	p.G926E	ENST00000389048	NM_004304.4	926	gGg/gAg	16/29	0.277569181898608	4	FACETS	1	0.972	1	0.689	0.608	0.777	CLONAL	1	TRUE	2	0.331091112195875	4		282	449	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027464	48027464	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553413710	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	161	398	0	ENST00000234420.5:c.2342C>T	p.Pro781Leu	p.P781L	ENST00000234420	NM_000179.2	781	cCa/cTa	4/10	0.277569181898608	4	FACETS	0.97	0.893	1	0.97	0.893	1	CLONAL	2	TRUE	2	0.331091112195875	4		398	667	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42840343	42840344	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	79	456	0	ENST00000398585.3:c.1404_1405delinsAA	p.Gly469Arg	p.G469R	ENST00000398585	NM_001135099.1	468	caGGgg/caAAgg	12/14	0.331091112195875	3	FACETS	0.865	0.761	0.977	0.433	0.38	0.489	CLONAL	1	TRUE	1	0.331091112195875	3		456	643	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651327	45651327	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	85	383	0	ENST00000407780.3:c.698G>A	p.Gly233Glu	p.G233E	ENST00000407780	NM_001283052.1	233	gGa/gAa	5/7	0.331091112195875	3	FACETS	1	0.921	1	0.525	0.465	0.589	CLONAL	1	TRUE	1	0.331091112195875	3		383	570	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657031	45657031	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	94	405	0	ENST00000407780.3:c.125G>A	p.Gly42Glu	p.G42E	ENST00000407780	NM_001283052.1	42	gGa/gAa	3/7	0.331091112195875	3	FACETS	1	0.896	1	0.503	0.448	0.562	CLONAL	1	TRUE	1	0.331091112195875	3		405	658	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169953053	169953053	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	191	331	0	ENST00000295797.4:c.137C>T	p.Ser46Phe	p.S46F	ENST00000295797	NM_002740.5	46	tCc/tTc	2/18	0.277569181898608	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.331091112195875	4		331	667	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541172	187541172	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	405	448	0	ENST00000441802.2:c.6568G>A	p.Glu2190Lys	p.E2190K	ENST00000441802	NM_005245.3	2190	Gag/Aag	10/27	0.331091112195875	7	FACETS	0.924	0.882	0.966	0.924	0.882	0.966	CLONAL	5	TRUE	2	0.331091112195875	7		448	968	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956597	93956597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	90	403	0	ENST00000369303.4:c.2639G>A	p.Arg880Lys	p.R880K	ENST00000369303	NM_004440.3	880	aGg/aAg	15/17	0.331091112195875	3	FACETS	1	0.938	1	0.542	0.481	0.606	CLONAL	1	TRUE	1	0.331091112195875	3		403	585	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963978	2963978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	188	523	0	ENST00000396946.4:c.1829C>T	p.Ser610Phe	p.S610F	ENST00000396946	NM_032415.4	610	tCc/tTc	15/25	0.331091112195875	6	FACETS	1	0.967	1	0.54	0.499	0.582	CLONAL	2	TRUE	2	0.331091112195875	6		523	874	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729949	41729949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1165688714	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	201	421	0	ENST00000242208.4:c.580G>A	p.Glu194Lys	p.E194K	ENST00000242208	NM_002192.2	194	Gaa/Aaa	3/3	0.331091112195875	6	FACETS	1	0.939	1	0.508	0.47	0.546	CLONAL	2	TRUE	2	0.331091112195875	6		421	994	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211055	55211055	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866460345	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	189	406	0	ENST00000275493.2:c.298C>T	p.Pro100Ser	p.P100S	ENST00000275493	NM_005228.3	100	Cct/Tct	3/28	0.331091112195875	6	FACETS	1	0.965	1	0.536	0.496	0.578	CLONAL	2	TRUE	2	0.331091112195875	6		406	885	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221798	55221798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	95	599	0	ENST00000275493.2:c.842C>T	p.Pro281Leu	p.P281L	ENST00000275493	NM_005228.3	281	cCc/cTc	7/28	0.331091112195875	6	FACETS	0.881	0.782	0.986	0.22	0.195	0.247	CLONAL	1	TRUE	2	0.331091112195875	6		599	1083	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372725	81372725	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	375	391	0	ENST00000222390.5:c.809G>A	p.Trp270Ter	p.W270*	ENST00000222390	NM_000601.4	270	tGg/tAg	7/18	0.331091112195875	6	FACETS	0.907	0.866	0.949	1	0.99	1	CLONAL	5	TRUE	2	0.331091112195875	6		391	830	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843687	151843688	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCCG	novel	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	288	364	0	ENST00000262189.6:c.14024_14027dup	p.Glu4676AspfsTer8	p.E4676Dfs*8	ENST00000262189	NM_170606.2	4676	gaa/gaCGGAa	53/59	0.331091112195875	6	FACETS	1	0.984	1	0.838	0.79	0.886	CLONAL	3	TRUE	2	0.331091112195875	6		364	863	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851156	151851156	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	356	432	0	ENST00000262189.6:c.12215C>T	p.Pro4072Leu	p.P4072L	ENST00000262189	NM_170606.2	4072	cCa/cTa	48/59	0.331091112195875	6	FACETS	0.959	0.912	1	0.959	0.912	1	CLONAL	4	TRUE	2	0.331091112195875	6		432	932	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884833	151884833	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	183	399	0	ENST00000262189.6:c.4760C>T	p.Ser1587Phe	p.S1587F	ENST00000262189	NM_170606.2	1587	tCt/tTt	32/59	0.331091112195875	6	FACETS	1	0.973	1	0.557	0.514	0.601	CLONAL	2	TRUE	2	0.331091112195875	6		399	825	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974823	21974823	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	179	530	0	ENST00000304494.5:c.4G>T	p.Glu2Ter	p.E2*	ENST00000304494	NM_000077.4	2	Gag/Tag	1/3	0.331091112195875	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.331091112195875	2		530	518	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215872	98215872	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758520331	NA	P-0060893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	78	368	0	ENST00000331920.6:c.3337C>T	p.Arg1113Cys	p.R1113C	ENST00000331920	NM_000264.3	1113	Cgc/Tgc	20/24	0.131942473301909	3	FACETS	1	0.933	1	0.544	0.479	0.613	INDETERMINATE	1	TRUE	1	0.331091112195875	3		368	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0060894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	69	626	3	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.381308340121136	1	FACETS	0.959	0.847	1	0.959	0.847	1	CLONAL	1	TRUE	0	0.467245640792153	1		629	236	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0060894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	59	409	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.839	0.727	0.959	0.839	0.727	0.959	CLONAL	1	TRUE	1	0.467245640792153	2		409	301	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0060894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	50	358	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.892	0.764	1	0.892	0.764	1	CLONAL	1	TRUE	1	0.467245640792153	2		358	240	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967221	25967221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	55	594	0	ENST00000435504.4:c.1985C>T	p.Ala662Val	p.A662V	ENST00000435504		662	gCa/gTa	13/13	1	2	FACETS	0.973	0.841	1	0.973	0.841	1	CLONAL	1	TRUE	1	0.467245640792153	2		594	242	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631006	67631006	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	70	557	0	ENST00000272342.5:c.1192G>T	p.Asp398Tyr	p.D398Y	ENST00000272342	NM_019002.3	398	Gac/Tac	5/6	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.467245640792153	2		557	295	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880065	151880066	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0060894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	44	421	0	ENST00000262189.6:c.5258_5259del	p.Phe1753Ter	p.F1753*	ENST00000262189	NM_170606.2	1753	tTT/t	35/59	0.467245640792153	1	FACETS	0.902	0.77	1	0.902	0.77	1	CLONAL	1	TRUE	0	0.467245640792153	1		421	160	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0060895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	400	932	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.555407969167406	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.555407969167406	2		932	693	SUCCESS
APC	324	MSKCC	GRCh37	5	112175417	112175418	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	rs1554085533	NA	P-0060895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	268	512	0	ENST00000257430.4:c.4127_4128del	p.Tyr1376CysfsTer9	p.Y1376Cfs*9	ENST00000257430	NM_000038.5	1376	TAt/t	16/16	0.555407969167406	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.555407969167406	2		512	473	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120160	70120160	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	179	648	0	ENST00000245479.2:c.1162G>T	p.Glu388Ter	p.E388*	ENST00000245479	NM_000346.3	388	Gag/Tag	3/3	0.551224245441488	3	FACETS	1	0.987	1	0.656	0.607	0.706	CLONAL	1	TRUE	1	0.555407969167406	3		648	628	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819954	170819968	+	inframe_deletion	In_Frame_Del	DEL	GATGATGATGAAGAG	GATGATGATGAAGAG	-	rs764077801	NA	P-0060895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	52	394	0	ENST00000296930.5:c.511_524+1del		p.DDDEEdel	ENST00000296930	NM_002520.6	166	GATGATGATGAAGAG/-	6/11	0.555407969167406	3	FACETS	0.672	0.574	0.778	0.224	0.191	0.26	SUBCLONAL	1	TRUE	0	0.555407969167406	3		394	356	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793433	18793433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202143029	NA	P-0060895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	86	360	0	ENST00000266497.5:c.4130G>A	p.Arg1377His	p.R1377H	ENST00000266497		1377	cGt/cAt	30/31	0.555407969167406	3	FACETS	1	0.936	1	0.536	0.478	0.598	CLONAL	1	TRUE	1	0.555407969167406	3		360	369	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248560	8248560	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0060895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	277	495	0	ENST00000335790.3:c.327T>G	p.Tyr109Ter	p.Y109*	ENST00000335790	NM_002315.2	109	taT/taG	3/4	0.551224245441488	3	FACETS	0.97	0.918	1	0.97	0.918	1	CLONAL	2	TRUE	1	0.555407969167406	3		495	657	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123892084	123892091	+	frameshift_variant	Frame_Shift_Del	DEL	ATCACAGC	ATCACAGC	-	novel	NA	P-0060895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	22	237	0	ENST00000330479.4:c.894_901del	p.Asn298LysfsTer35	p.N298Kfs*35	ENST00000330479	NM_020382.3	298	aATCACAGC/a	8/9	0.555407969167406	3	FACETS	0.271	0.21	0.343	0.136	0.105	0.172	SUBCLONAL	1	TRUE	1	0.555407969167406	3		237	373	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86545128	86545128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1287705171	NA	P-0060895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	178	563	0	ENST00000262426.4:c.953G>A	p.Ser318Asn	p.S318N	ENST00000262426	NM_001451.2	318	aGc/aAc	1/2	0.359957129997743	5	FACETS	1	0.967	1	0.365	0.335	0.395	CLONAL	1	TRUE	2	0.555407969167406	5		563	1074	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	202	759	1				ENST00000310581	NM_198253.2	-/1132			0.549886838531205	5	FACETS	0.911	0.855	0.968	0.911	0.855	0.968	CLONAL	3	TRUE	2	0.636303961909095	5		760	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0060903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	201	453	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.516755492933153	4	FACETS	0.897	0.837	0.959	0.897	0.837	0.959	CLONAL	2	TRUE	2	0.636303961909095	4		453	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0060903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	288	693	2	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.516755492933153	4	FACETS	0.971	0.917	1	0.971	0.917	1	CLONAL	2	TRUE	2	0.636303961909095	4		695	763	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78425875	78425875	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	246	550	0	ENST00000370768.2:c.1570G>A	p.Asp524Asn	p.D524N	ENST00000370768	NM_003902.3	524	Gat/Aat	16/20	0.54183446621391	3	FACETS	0.93	0.878	0.982	0.93	0.878	0.982	CLONAL	2	TRUE	1	0.636303961909095	3		550	548	SUCCESS
ATM	472	MSKCC	GRCh37	11	108126979	108126979	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	73	348	0	ENST00000278616.4:c.2162T>C	p.Leu721Pro	p.L721P	ENST00000278616	NM_000051.3	721	cTt/cCt	14/63	0.636303961909095	3	FACETS	0.82	0.721	0.924	0.41	0.36	0.462	CLONAL	1	TRUE	1	0.636303961909095	3		348	369	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78921110	78921110	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	212	498	0	ENST00000306801.3:c.3224A>G	p.Tyr1075Cys	p.Y1075C	ENST00000306801	NM_020761.2	1075	tAt/tGt	27/34	0.516755492933153	4	FACETS	0.93	0.87	0.991	0.93	0.87	0.991	CLONAL	2	TRUE	2	0.636303961909095	4		498	586	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022433	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	GCCATCGGAG	GCCATCGGAG	-	novel	NA	P-0060903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	305	629	0	ENST00000375687.4:c.1919_1928del	p.Ala640GlyfsTer60	p.A640Gfs*60	ENST00000375687	NM_015338.5	640	GCCATCGGAGgg/gg	13/13	0.589504378893323	4	FACETS	0.869	0.827	0.91	0.869	0.827	0.91	CLONAL	3	TRUE	1	0.636303961909095	4		629	602	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294559	1294559	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745363596	NA	P-0060903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	252	700	0	ENST00000310581.5:c.442G>A	p.Val148Met	p.V148M	ENST00000310581	NM_198253.2	148	Gtg/Atg	2/16	0.549886838531205	5	FACETS	0.965	0.906	1	0.643	0.604	0.684	CLONAL	2	TRUE	2	0.636303961909095	5		700	802	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922749	44922749	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	225	508	0	ENST00000377967.4:c.1610C>A	p.Ser537Ter	p.S537*	ENST00000377967	NM_021140.2	537	tCa/tAa	16/29	0.632939186849457	2	FACETS	0.982	0.934	1	0.982	0.934	1	CLONAL	2	TRUE	0	0.636303961909095	2		508	360	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0060906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	205	910	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.67	2		910	596	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0060906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	100	661	0	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.339	0.302	0.378	0.339	0.302	0.378	SUBCLONAL	1	TRUE	1	0.67	2		661	881	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947865	178947865	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776932	NA	P-0060906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	174	358	0	ENST00000263967.3:c.2740G>A	p.Gly914Arg	p.G914R	ENST00000263967	NM_006218.2	914	Gga/Aga	19/21	1	2	FACETS	0.921	0.853	0.991	0.921	0.853	0.991	CLONAL	1	TRUE	1	0.67	2		358	564	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0060906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	155	583	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.987	0.911	1	0.987	0.911	1	CLONAL	1	TRUE	1	0.67	2		583	469	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	261	636	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.935	0.879	0.993	0.935	0.879	0.993	CLONAL	1	TRUE	1	0.67	2		637	833	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	257	656	3	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	1	2	FACETS	0.954	0.897	1	0.954	0.897	1	CLONAL	1	TRUE	1	0.67	2		659	804	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936096	178936096	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519940	NA	P-0060906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	89	214	0	ENST00000263967.3:c.1638G>T	p.Gln546His	p.Q546H	ENST00000263967	NM_006218.2	546	caG/caT	10/21	1	2	FACETS	0.959	0.862	1	0.959	0.862	1	CLONAL	1	TRUE	1	0.67	2		214	277	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0060906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	13	275	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	1	2	FACETS	0.081	0.057	0.111	0.081	0.057	0.111	SUBCLONAL	1	TRUE	1	0.67	2		275	478	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022917	27022939	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCCGCCAGCAGCCTGGGCAAC	CCGCCGCCAGCAGCCTGGGCAAC	-	novel	NA	P-0060906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	127	510	0	ENST00000324856.7:c.31_53del	p.Ser11AlafsTer92	p.S11Afs*92	ENST00000324856	NM_006015.4	8	gCCGCCGCCAGCAGCCTGGGCAAC/g	1/20	1	2	FACETS	0.711	0.647	0.778	0.711	0.647	0.778	SUBCLONAL	1	TRUE	1	0.67	2		510	533	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112490	115112490	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	254	545	0	ENST00000257566.3:c.1250del	p.Phe417SerfsTer215	p.F417Sfs*215	ENST00000257566	NM_016569.3	417	tTc/tc	7/8	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.67	2		545	739	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207152	1207153	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAG	novel	NA	P-0060906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	214	519	0	ENST00000326873.7:c.250_252dup	p.Lys84dup	p.K84dup	ENST00000326873	NM_000455.4	84	-/AAG	1/10	1	2	FACETS	0.835	0.778	0.893	0.835	0.778	0.893	CLONAL	1	TRUE	1	0.67	2		519	765	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	27	334	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	0.17	0.135	0.211	0.17	0.135	0.211	SUBCLONAL	1	TRUE	1	0.67	2		334	474	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142991	30142991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs62129830	NA	P-0060906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	248	610	0	ENST00000389048.3:c.535C>T	p.Arg179Cys	p.R179C	ENST00000389048	NM_004304.4	179	Cgc/Tgc	1/29	1	2	FACETS	0.876	0.821	0.932	0.876	0.821	0.932	CLONAL	1	TRUE	1	0.67	2		610	845	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624263	89624263	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	85	193	0	ENST00000371953.3:c.37A>G	p.Lys13Glu	p.K13E	ENST00000371953	NM_000314.4	13	Aaa/Gaa	1/9	1	2	FACETS	0.916	0.82	1	0.916	0.82	1	CLONAL	1	TRUE	1	0.67	2		193	277	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396919	139396919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	175	430	1	ENST00000277541.6:c.5189del	p.Pro1730ArgfsTer68	p.P1730Rfs*68	ENST00000277541	NM_017617.3	1730	cCg/cg	28/34	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.67	2		431	504	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057975	27057975	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	46	563	1	ENST00000324856.7:c.1683G>C	p.Gln561His	p.Q561H	ENST00000324856	NM_006015.4	561	caG/caC	3/20	1	2	FACETS	0.156	0.131	0.185	0.156	0.131	0.185	SUBCLONAL	1	TRUE	1	0.67	2		564	878	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459101	120459101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1223514910	NA	P-0060906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	290	586	0	ENST00000256646.2:c.6244C>T	p.Pro2082Ser	p.P2082S	ENST00000256646	NM_024408.3	2082	Cct/Tct	34/34	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.67	2		586	826	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655453	67655453	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	222	376	0	ENST00000264010.4:c.1316G>A	p.Cys439Tyr	p.C439Y	ENST00000264010	NM_006565.3	439	tGt/tAt	7/12	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.67	2		376	653	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257111	198257111	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	175	310	0	ENST00000335508.6:c.3831G>T	p.Gln1277His	p.Q1277H	ENST00000335508	NM_012433.2	1277	caG/caT	25/25	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.67	2		310	507	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513607	41513607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	276	518	0	ENST00000263253.7:c.511G>A	p.Ala171Thr	p.A171T	ENST00000263253	NM_001429.3	171	Gcg/Acg	2/31	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.67	2		518	817	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294782	1294782	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0060906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	215	524	0	ENST00000310581.5:c.220-1G>T		p.X74_splice	ENST00000310581	NM_198253.2	74			1	2	FACETS	0.987	0.923	1	0.987	0.923	1	CLONAL	1	TRUE	1	0.67	2		524	650	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295306	1295306	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0060906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	264	706	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.968	0.911	1	0.968	0.911	1	CLONAL	1	TRUE	1	0.67	2		707	814	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482927	140482928	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0060906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	284	462	0	ENST00000288602.6:c.1207_1208del	p.Pro403CysfsTer9	p.P403Cfs*9	ENST00000288602	NM_004333.4	403	CCt/t	10/18	1	2	FACETS	0.968	0.912	1	0.968	0.912	1	CLONAL	1	TRUE	1	0.67	2		462	876	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345948	152345948	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	284	456	0	ENST00000359321.1:c.622G>T	p.Glu208Ter	p.E208*	ENST00000359321	NM_005431.1	208	Gaa/Taa	3/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.67	2		456	780	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568524	41568524	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408820045	NA	P-0060908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	108	197	1	ENST00000263253.7:c.4474G>A	p.Glu1492Lys	p.E1492K	ENST00000263253	NM_001429.3	1492	Gaa/Aaa	28/31	1	2	FACETS	0.853	0.773	0.937	0.853	0.773	0.937	CLONAL	1	TRUE	1	0.673154303450411	2		198	376	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241873	72241873	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1252345844	NA	P-0060908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	122	385	1	ENST00000357731.5:c.517C>T	p.Arg173Ter	p.R173*	ENST00000357731	NM_173808.2	173	Cga/Tga	3/7	1	2	FACETS	0.988	0.902	1	0.988	0.902	1	CLONAL	1	TRUE	1	0.673154303450411	2		386	367	SUCCESS
APC	324	MSKCC	GRCh37	5	112177716	112177717	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0060908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	122	316	0	ENST00000257430.4:c.6430_6431del	p.Leu2144GlyfsTer9	p.L2144Gfs*9	ENST00000257430	NM_000038.5	2142	aTC/a	16/16	1	2	FACETS	0.826	0.752	0.902	0.826	0.752	0.902	CLONAL	1	TRUE	1	0.673154303450411	2		316	439	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196791	108196791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039471	NA	P-0060908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	27	246	0	ENST00000278616.4:c.6814G>A	p.Glu2272Lys	p.E2272K	ENST00000278616	NM_000051.3	2272	Gaa/Aaa	47/63	0.661400088080278	1	FACETS	0.229	0.183	0.282	0.229	0.183	0.282	SUBCLONAL	1	TRUE	0	0.673154303450411	1		246	232	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548264	41548264	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	138	351	0	ENST00000263253.7:c.3052G>C	p.Glu1018Gln	p.E1018Q	ENST00000263253	NM_001429.3	1018	Gag/Cag	16/31	1	2	FACETS	0.863	0.791	0.938	0.863	0.791	0.938	CLONAL	1	TRUE	1	0.673154303450411	2		351	475	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256735	16256735	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	176	395	0	ENST00000375759.3:c.4000G>A	p.Glu1334Lys	p.E1334K	ENST00000375759	NM_015001.2	1334	Gaa/Aaa	11/15	1	2	FACETS	0.93	0.862	1	0.93	0.862	1	CLONAL	1	TRUE	1	0.673154303450411	2		395	562	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872949	35872949	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	181	401	0	ENST00000216797.5:c.283del	p.Arg95AlafsTer3	p.R95Afs*3	ENST00000216797	NM_020529.2	95	Cgc/gc	2/6	0.666772711382089	1	FACETS	0.939	0.879	0.999	0.939	0.879	0.999	CLONAL	1	TRUE	0	0.673154303450411	1		401	380	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40854594	40854594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	315	541	1	ENST00000428826.2:c.2200G>A	p.Ala734Thr	p.A734T	ENST00000428826		734	Gct/Act	21/21	0.673178284634153	3	FACETS	0.952	0.906	0.998	0.952	0.906	0.998	CLONAL	2	TRUE	1	0.673154303450411	3		542	657	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548339	41549048	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGTCAAAGAAAAAGAGTGAGTCTCTGAAGCCATTCGTTCTGGAGGTAGCTGAAGAAACCAAAGACCCAGGGCAGAATTGCGGTCATGCCTCTTGGGCCTCAGAAGTTGCCATTATTGTGATTTCATTAACCTGGAAGCCCTGGGCCTGGTCTCTTCATTGTTACTAATAATTTTTCTTTCTTTTTTTTTTTTTTAATATTCACTTGCAGCAACCAATGAGTTAAGTCATTCCCCTCATTTCTTCAGGGTTCCCTGTGTTAGTACACCCTAAAAATTGTCTCATTTTTCAGGAGAGAGAAATGTTTGTAAATAGCCTTGACTAAAATGCAGGAAAGAATAGCAATAGTAATAGCATTTGTCATTCACCTGCTGTGTGCTAAGTATCCACATTGTCTCATTTAATAATTTCTTTCTTTCTTTTTCTTTTCTTTTTTGTTTGGAATCGGATTCTCACTTTTGTTGTTCAGGCTGGAGTGCAGTGGCGGGATCTGAGCTCACTGCAACCTCCACCTCCCAGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTATCTGGGACTGCATGCGCATGCCACCATGCCCGTCTAATTTTTGTATTTTTAGTAGAGACAGGATTTCACCGTGTTGGCCAGGATGGTCTCGATCTCTTGACCTGGTGATCCACCCGCTTCGAGCTCCCAAAGTGCTGGGATTACAGGCATGAGCTAC	CAGTCAAAGAAAAAGAGTGAGTCTCTGAAGCCATTCGTTCTGGAGGTAGCTGAAGAAACCAAAGACCCAGGGCAGAATTGCGGTCATGCCTCTTGGGCCTCAGAAGTTGCCATTATTGTGATTTCATTAACCTGGAAGCCCTGGGCCTGGTCTCTTCATTGTTACTAATAATTTTTCTTTCTTTTTTTTTTTTTTAATATTCACTTGCAGCAACCAATGAGTTAAGTCATTCCCCTCATTTCTTCAGGGTTCCCTGTGTTAGTACACCCTAAAAATTGTCTCATTTTTCAGGAGAGAGAAATGTTTGTAAATAGCCTTGACTAAAATGCAGGAAAGAATAGCAATAGTAATAGCATTTGTCATTCACCTGCTGTGTGCTAAGTATCCACATTGTCTCATTTAATAATTTCTTTCTTTCTTTTTCTTTTCTTTTTTGTTTGGAATCGGATTCTCACTTTTGTTGTTCAGGCTGGAGTGCAGTGGCGGGATCTGAGCTCACTGCAACCTCCACCTCCCAGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTATCTGGGACTGCATGCGCATGCCACCATGCCCGTCTAATTTTTGTATTTTTAGTAGAGACAGGATTTCACCGTGTTGGCCAGGATGGTCTCGATCTCTTGACCTGGTGATCCACCCGCTTCGAGCTCCCAAAGTGCTGGGATTACAGGCATGAGCTAC	-	novel	NA	P-0060908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	92	433	0	ENST00000263253.7:c.3129_3142+696del		p.X1043_splice	ENST00000263253	NM_001429.3	1043		16/31	1	2	FACETS	0.685	0.613	0.761	0.685	0.613	0.761	SUBCLONAL	1	TRUE	1	0.673154303450411	2		433	399	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034489	47034489	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	166	427	1	ENST00000377604.3:c.574C>G	p.Gln192Glu	p.Q192E	ENST00000377604	NM_001204468.1	192	Cag/Gag	6/24	0.44441910982882	3	FACETS	1	0.982	1	0.606	0.56	0.653	CLONAL	1	TRUE	1	0.673154303450411	3		428	544	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	33	759	1				ENST00000310581	NM_198253.2	-/1132			0.299703491149307	0	FACETS	0.468	0.382	0.563			1	SUBCLONAL	1	FALSE	0	0.347479791893778	0		760	265	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	136	374	0	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.153239873142238	3	FACETS	1	0.973	1	0.59	0.536	0.646	INDETERMINATE	1	FALSE	1	0.347479791893778	3		374	779	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782620	NA	P-0060910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	51	419	0	ENST00000269305.4:c.427G>A	p.Val143Met	p.V143M	ENST00000269305	NM_001126112.2	143	Gtg/Atg	5/11	0.153239873142238	3	FACETS	0.449	0.38	0.524	0.224	0.19	0.262	INDETERMINATE	1	FALSE	1	0.347479791893778	3		419	768	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115267844	115267844	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	89	276	0	ENST00000438362.2:c.1889C>T	p.Ser630Leu	p.S630L	ENST00000438362	NM_001242891.1	630	tCa/tTa	15/20	1	2	FACETS	0.775	0.687	0.868	0.775	0.687	0.868	SUBCLONAL	1	FALSE	1	0.347479791893778	2		276	661	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941137	36941137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	82	439	0	ENST00000361632.4:c.202G>A	p.Glu68Lys	p.E68K	ENST00000361632		68	Gag/Aag	3/16	1	2	FACETS	0.688	0.607	0.775	0.688	0.607	0.775	SUBCLONAL	1	FALSE	1	0.347479791893778	2		439	686	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363433	40363433	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	140	414	0	ENST00000397332.2:c.796G>C	p.Glu266Gln	p.E266Q	ENST00000397332	NM_001033082.2	266	Gag/Cag	3/3	1	2	FACETS	0.971	0.884	1	0.971	0.884	1	CLONAL	1	FALSE	1	0.347479791893778	2		414	830	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400903	72400903	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	109	286	0	ENST00000357731.5:c.268C>G	p.Arg90Gly	p.R90G	ENST00000357731	NM_173808.2	90	Cga/Gga	2/7	1	2	FACETS	0.824	0.74	0.913	0.824	0.74	0.913	CLONAL	1	FALSE	1	0.347479791893778	2		286	761	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813433	102813433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	52	367	0	ENST00000307046.8:c.256G>A	p.Ala86Thr	p.A86T	ENST00000307046	NM_001111285.1	86	Gcg/Acg	3/4	1	2	FACETS	0.442	0.376	0.515	0.442	0.376	0.515	SUBCLONAL	1	FALSE	1	0.347479791893778	2		367	677	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348054	89348054	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	210	475	0	ENST00000301030.4:c.4896G>C	p.Lys1632Asn	p.K1632N	ENST00000301030	NM_001256183.1	1632	aaG/aaC	9/13	0.00357945274787275	3	FACETS	0.822	0.764	0.881			1	INDETERMINATE	2	FALSE	NA	0.347479791893778	3		475	863	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902723	50902723	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	78	365	0	ENST00000440232.2:c.298G>C	p.Glu100Gln	p.E100Q	ENST00000440232	NM_002691.3	100	Gag/Cag	3/27	0.299703491149307	0	FACETS	0.637	0.562	0.717			1	SUBCLONAL	1	FALSE	0	0.347479791893778	0		365	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0060911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	334	871	5	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.711139767220944	2	FACETS	0.946	0.911	0.981	0.946	0.911	0.981	CLONAL	2	TRUE	0	0.723292694710437	2		876	488	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480055	50480055	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	169	469	0	ENST00000394963.4:c.289G>A	p.Asp97Asn	p.D97N	ENST00000394963	NM_003076.4	97	Gat/Aat	2/13	0.512189208847834	5	FACETS	0.803	0.736	0.872			1	CLONAL	1	TRUE	NA	0.723292694710437	5		469	1214	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579391	7579391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567556019	NA	P-0060911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	397	489	0	ENST00000269305.4:c.296C>T	p.Ser99Phe	p.S99F	ENST00000269305	NM_001126112.2	99	tCc/tTc	4/11	0.711139767220944	2	FACETS	0.929	0.896	0.96	0.929	0.896	0.96	CLONAL	2	TRUE	0	0.723292694710437	2		489	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0060913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	302	450	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.636735116362292	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	FALSE	0	0.638133424863613	2		450	444	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922341	178922341	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	128	150	0	ENST00000263967.3:c.1110T>G	p.Asn370Lys	p.N370K	ENST00000263967	NM_006218.2	370	aaT/aaG	6/21	0.636735116362292	5	FACETS	0.955	0.874	1	0.637	0.582	0.693	CLONAL	2	FALSE	2	0.638133424863613	5		150	411	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2645816	2645816	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	93	262	0	ENST00000342085.4:c.1366T>A	p.Leu456Ile	p.L456I	ENST00000342085	NM_002613.4	456	Tta/Ata	12/14	0.638133424863613	6	FACETS	0.942	0.838	1	0.236	0.209	0.264	CLONAL	1	FALSE	2	0.638133424863613	6		262	704	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778042	27778042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	419	692	0	ENST00000369163.2:c.191G>A	p.Arg64Lys	p.R64K	ENST00000369163	NM_003536.2	64	aGa/aAa	1/1	0.585354582779236	4	FACETS	0.96	0.916	1	0.96	0.916	1	CLONAL	2	FALSE	2	0.638133424863613	4		692	1120	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0060914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	236	761	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.529325052132444	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.529325052132444	1		764	612	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0060914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7786	9934	766	1	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.529325052132444	21	FACETS	0.982	0.974	0.99			1	CLONAL	13	TRUE	NA	0.529325052132444	21		767	17720	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604778	48604778	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767383	NA	P-0060914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	45	403	0	ENST00000342988.3:c.1600C>T	p.Gln534Ter	p.Q534*	ENST00000342988	NM_005359.5	534	Cag/Tag	12/12	0.529325052132444	1	FACETS	0.213	0.178	0.251	0.213	0.178	0.251	SUBCLONAL	1	TRUE	0	0.529325052132444	1		403	587	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518638	204518638	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	80	412	0	ENST00000367182.3:c.1301T>G	p.Leu434Trp	p.L434W	ENST00000367182	NM_001278516.1	434	tTg/tGg	11/11	1	2	FACETS	0.359	0.315	0.406	0.359	0.315	0.406	SUBCLONAL	1	TRUE	1	0.529325052132444	2		412	842	SUCCESS
ATR	545	MSKCC	GRCh37	3	142257382	142257382	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs554925737	NA	P-0060914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	31	293	0	ENST00000350721.4:c.3667A>G	p.Ile1223Val	p.I1223V	ENST00000350721	NM_001184.3	1223	Ata/Gta	19/47	1	2	FACETS	0.191	0.154	0.234	0.191	0.154	0.234	SUBCLONAL	1	TRUE	1	0.529325052132444	2		293	612	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437431	121437431	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0060915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	37	394	0	ENST00000257555.6:c.1768+1G>T		p.X590_splice	ENST00000257555		590			0.145151351806406	4	FACETS	0.736	0.605	0.883	0.368	0.302	0.442	SUBCLONAL	1	TRUE	2	0.186080099485622	4		394	641	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346783	225346783	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	21	269	0	ENST00000264414.4:c.1855G>C	p.Glu619Gln	p.E619Q	ENST00000264414	NM_003590.4	619	Gag/Cag	14/16	1	2	FACETS	0.548	0.421	0.696	0.548	0.421	0.696	SUBCLONAL	1	TRUE	1	0.186080099485622	2		269	412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0060916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	357	412	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.730875871546821	3	FACETS	0.954	0.925	0.982	0.954	0.925	0.982	CLONAL	3	FALSE	0	0.742017798359867	3		412	461	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971114	21971114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501269	NA	P-0060916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	18	591	1	ENST00000304494.5:c.244G>A	p.Val82Met	p.V82M	ENST00000304494	NM_000077.4	82	Gtg/Atg	2/3	0.726894869878701	2	FACETS	0.152	0.114	0.197	0.076	0.057	0.099	SUBCLONAL	1	FALSE	0	0.742017798359867	2		592	319	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056317	27056317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776238347	NA	P-0060916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	62	517	0	ENST00000324856.7:c.1313C>T	p.Ala438Val	p.A438V	ENST00000324856	NM_006015.4	438	gCg/gTg	2/20	0.742017798359867	4	FACETS	0.371	0.319	0.427	0.124	0.106	0.143	SUBCLONAL	1	FALSE	1	0.742017798359867	4		517	785	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416371	29416371	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	113	567	0	ENST00000389048.3:c.4582C>G	p.His1528Asp	p.H1528D	ENST00000389048	NM_004304.4	1528	Cac/Gac	29/29	0.742017798359867	5	FACETS	0.909	0.819	1	0.227	0.204	0.251	CLONAL	1	FALSE	1	0.742017798359867	5		567	708	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632260	215632260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501304	NA	P-0060916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	31	391	0	ENST00000260947.4:c.1514G>A	p.Gly505Glu	p.G505E	ENST00000260947	NM_000465.2	505	gGg/gAg	6/11	0.604794457774479	5	FACETS	0.343	0.277	0.418	0.114	0.092	0.14	SUBCLONAL	1	FALSE	2	0.742017798359867	5		391	515	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0060918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	34	558	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.116774790552102	4	FACETS	1	0.879	1	1	0.879	1	INDETERMINATE	2	TRUE	2	0.223901388557136	4		558	172	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0060918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	48	324	1	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.732	0.618	0.857	0.732	0.618	0.857	SUBCLONAL	1	TRUE	1	0.223901388557136	2		325	586	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0060918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	56	534	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.788	0.674	0.912	0.788	0.674	0.912	CLONAL	1	TRUE	1	0.223901388557136	2		535	635	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0060918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	74	422	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.223901388557136	2		422	459	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0060918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	12	319	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	0.499	0.35	0.681	0.499	0.35	0.681	SUBCLONAL	1	TRUE	1	0.223901388557136	2		319	215	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048632	180048632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	60	669	2	ENST00000261937.6:c.1930G>A	p.Ala644Thr	p.A644T	ENST00000261937	NM_182925.4	644	Gcg/Acg	13/30	0.223901388557136	1	FACETS	0.718	0.618	0.827	0.718	0.618	0.827	SUBCLONAL	1	TRUE	0	0.223901388557136	1		671	663	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563012	21563012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371362441	NA	P-0060918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	58	834	1	ENST00000382592.4:c.907G>A	p.Ala303Thr	p.A303T	ENST00000382592	NM_014572.2	303	Gct/Act	4/8	1	2	FACETS	0.607	0.52	0.703	0.607	0.52	0.703	SUBCLONAL	1	TRUE	1	0.223901388557136	2		835	853	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971039	21971039	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554654024	NA	P-0060918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	60	660	0	ENST00000304494.5:c.319C>T	p.Arg107Cys	p.R107C	ENST00000304494	NM_000077.4	107	Cgc/Tgc	2/3	1	2	FACETS	0.73	0.628	0.842	0.73	0.628	0.842	SUBCLONAL	1	TRUE	1	0.223901388557136	2		660	734	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102089	27102090	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0060918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	78	555	0	ENST00000324856.7:c.5016_5017dup	p.Met1673LysfsTer2	p.M1673Kfs*2	ENST00000324856	NM_006015.4	1672	gta/gtAAa	19/20	1	2	FACETS	0.906	0.795	1	0.906	0.795	1	CLONAL	1	TRUE	1	0.223901388557136	2		555	769	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852443	63852443	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	251	687	0	ENST00000279873.7:c.3221C>G	p.Ser1074Cys	p.S1074C	ENST00000279873	NM_032199.2	1074	tCc/tGc	10/10	0.213557889462025	4	FACETS	1	0.964	1			1	CLONAL	3	TRUE	NA	0.223901388557136	4		687	880	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587412	29587412	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060918-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	40	334	1	ENST00000356175.3:c.4393T>A	p.Cys1465Ser	p.C1465S	ENST00000356175	NM_000267.3	1465	Tgt/Agt	33/57	0.127563935048227	3	FACETS	0.903	0.751	1	0.451	0.375	0.536	INDETERMINATE	1	TRUE	1	0.223901388557136	3		335	440	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50784990	50784990	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs146125856	NA	P-0060919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	18	313	2	ENST00000307179.4:c.2327T>C	p.Leu776Pro	p.L776P	ENST00000307179		776	cTt/cCt	15/20	1	2	FACETS	0.198	0.149	0.256	0.198	0.149	0.256	SUBCLONAL	1	TRUE	1	0.664385680294113	2		315	274	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120927	115120927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	262	589	0	ENST00000257566.3:c.79G>A	p.Asp27Asn	p.D27N	ENST00000257566	NM_016569.3	27	Gac/Aac	1/8	0.479700594873046	4	FACETS	0.955	0.901	1	0.955	0.901	1	CLONAL	2	TRUE	2	0.664385680294113	4		589	687	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855219	76855250	+	frameshift_variant	Frame_Shift_Del	DEL	CTTAAACTCATGGAGGTTTCATCAGAATCTGA	CTTAAACTCATGGAGGTTTCATCAGAATCTGA	-	novel	NA	P-0060919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	134	219	0	ENST00000373344.5:c.5737_5768del	p.Ser1913LeufsTer3	p.S1913Lfs*3	ENST00000373344	NM_000489.3	1913	TCAGATTCTGATGAAACCTCCATGAGTTTAAGc/c	24/35	0.473870360455939	2	FACETS	1	0.959	1			1	CLONAL	2	TRUE	NA	0.664385680294113	2		219	197	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396919	139396919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	67	430	1	ENST00000277541.6:c.5189del	p.Pro1730ArgfsTer68	p.P1730Rfs*68	ENST00000277541	NM_017617.3	1730	cCg/cg	28/34	1	2	FACETS	0.385	0.335	0.439	0.385	0.335	0.439	SUBCLONAL	1	TRUE	1	0.715026890572154	2		431	487	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374293	138374293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	25	447	0	ENST00000289153.2:c.3151G>A	p.Glu1051Lys	p.E1051K	ENST00000289153	NM_006219.2	1051	Gaa/Aaa	22/22	1	2	FACETS	0.135	0.106	0.169	0.135	0.106	0.169	SUBCLONAL	1	TRUE	1	0.715026890572154	2		447	517	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0060920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	97	725	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.321	0.285	0.358	0.321	0.285	0.358	SUBCLONAL	1	TRUE	1	0.715026890572154	2		732	846	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	34	507	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.151	0.123	0.183	0.151	0.123	0.183	SUBCLONAL	1	TRUE	1	0.715026890572154	2		507	630	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030478	49030479	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1566234123	NA	P-0060920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	20	371	0	ENST00000267163.4:c.1959dup	p.Val654SerfsTer14	p.V654Sfs*14	ENST00000267163	NM_000321.2	651	-/A	19/27	0.636593041225484	1	FACETS	0.132	0.1	0.168	0.132	0.1	0.168	SUBCLONAL	1	TRUE	0	0.715026890572154	1		371	273	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878061	48878062	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1131690852	NA	P-0060920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	46	615	0	ENST00000267163.4:c.19dup	p.Arg7ProfsTer24	p.R7Pfs*24	ENST00000267163	NM_000321.2	5	acc/aCcc	1/27	0.636593041225484	1	FACETS	0.198	0.166	0.232	0.198	0.166	0.232	SUBCLONAL	1	TRUE	0	0.715026890572154	1		615	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0060920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	32	748	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	1	2	FACETS	0.105	0.084	0.128	0.105	0.084	0.128	SUBCLONAL	1	TRUE	1	0.715026890572154	2		748	856	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664761	138664761	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs797044528	NA	P-0060920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	30	409	2	ENST00000330315.3:c.804del	p.Gly269AlafsTer2	p.G269Afs*2	ENST00000330315	NM_023067.3	268	ccC/cc	1/1	1	2	FACETS	0.174	0.14	0.214	0.174	0.14	0.214	SUBCLONAL	1	TRUE	1	0.715026890572154	2		411	481	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023696	27023696	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	138	543	0	ENST00000324856.7:c.802C>T	p.Gln268Ter	p.Q268*	ENST00000324856	NM_006015.4	268	Cag/Tag	1/20	1	2	FACETS	0.716	0.655	0.78	0.716	0.655	0.78	SUBCLONAL	1	TRUE	1	0.715026890572154	2		543	539	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916726	178916726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772110575	NA	P-0060920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	10	351	0	ENST00000263967.3:c.113G>A	p.Arg38His	p.R38H	ENST00000263967	NM_006218.2	38	cGt/cAt	2/21	1	2	FACETS	0.089	0.059	0.125	0.089	0.059	0.125	SUBCLONAL	1	TRUE	1	0.715026890572154	2		351	316	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	57	597	3	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.218	0.187	0.253	0.218	0.187	0.253	SUBCLONAL	1	TRUE	1	0.715026890572154	2		600	730	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0060920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	102	896	5	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.404	0.361	0.449	0.404	0.361	0.449	SUBCLONAL	1	TRUE	1	0.715026890572154	2		901	707	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624271	89624272	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs786204883	NA	P-0060920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	173	270	0	ENST00000371953.3:c.46dup	p.Tyr16LeufsTer28	p.Y16Lfs*28	ENST00000371953	NM_000314.4	15	-/T	1/9	0.524041062949569	2	FACETS	1	0.992	1	0.744	0.698	0.79	CLONAL	1	TRUE	0	0.715026890572154	2		270	325	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1918645	1918645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372805518	NA	P-0060920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	53	449	0	ENST00000382891.5:c.808G>A	p.Ala270Thr	p.A270T	ENST00000382891	NM_133335.3	270	Gcc/Acc	4/22	1	2	FACETS	0.262	0.223	0.305	0.262	0.223	0.305	SUBCLONAL	1	TRUE	1	0.715026890572154	2		449	565	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17940939	17940939	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	59	555	0	ENST00000458235.1:c.3185C>T	p.Ala1062Val	p.A1062V	ENST00000458235	NM_000215.3	1062	gCg/gTg	23/24	1	2	FACETS	0.3	0.257	0.345	0.3	0.257	0.345	SUBCLONAL	1	TRUE	1	0.715026890572154	2		555	551	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175848	24175848	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	81	530	0	ENST00000263121.7:c.1076C>T	p.Ala359Val	p.A359V	ENST00000263121	NM_003073.3	359	gCt/gTt	8/9	1	2	FACETS	0.346	0.305	0.391	0.346	0.305	0.391	SUBCLONAL	1	TRUE	1	0.715026890572154	2		530	654	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268081	153268081	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0060920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	89	439	0	ENST00000281708.4:c.726+1G>T		p.X242_splice	ENST00000281708	NM_033632.3	242			1	2	FACETS	0.421	0.374	0.472	0.421	0.374	0.472	SUBCLONAL	1	TRUE	1	0.715026890572154	2		439	591	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347320	89347320	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768249075	NA	P-0060920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	114	616	0	ENST00000301030.4:c.5630C>T	p.Pro1877Leu	p.P1877L	ENST00000301030	NM_001256183.1	1877	cCg/cTg	9/13	1	2	FACETS	0.463	0.417	0.511	0.463	0.417	0.511	SUBCLONAL	1	TRUE	1	0.715026890572154	2		616	689	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272475	11272475	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	74	466	0	ENST00000361445.4:c.3455C>T	p.Ala1152Val	p.A1152V	ENST00000361445	NM_004958.3	1152	gCc/gTc	23/58	1	2	FACETS	0.334	0.293	0.379	0.334	0.293	0.379	SUBCLONAL	1	TRUE	1	0.715026890572154	2		466	619	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43739593	43739593	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1298106514	NA	P-0060920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	95	456	0	ENST00000382044.4:c.2807T>C	p.Leu936Ser	p.L936S	ENST00000382044	NM_001141980.1	936	tTg/tCg	13/28	1	2	FACETS	0.579	0.518	0.643	0.579	0.518	0.643	SUBCLONAL	1	TRUE	1	0.715026890572154	2		456	459	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89839716	89839716	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	166	483	0	ENST00000389301.3:c.1977G>T	p.Glu659Asp	p.E659D	ENST00000389301	NM_000135.2	659	gaG/gaT	22/43	1	2	FACETS	0.667	0.614	0.722	0.667	0.614	0.722	SUBCLONAL	1	TRUE	1	0.715026890572154	2		483	696	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128030509	128030511	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	novel	NA	P-0060920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	21	406	0	ENST00000285398.2:c.1757_1759del	p.Gln586_Gly587delinsArg	p.Q586_G587delinsR	ENST00000285398	NM_000122.1	586	cAGGgg/cgg	11/15	1	2	FACETS	0.154	0.118	0.196	0.154	0.118	0.196	SUBCLONAL	1	TRUE	1	0.715026890572154	2		406	381	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796750	57796750	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1199978831	NA	P-0060920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	66	546	2	ENST00000309042.7:c.1732del	p.Ser578ValfsTer7	p.S578Vfs*7	ENST00000309042	NM_005612.4	576	Aaa/aa	4/4	1	2	FACETS	0.333	0.289	0.381	0.333	0.289	0.381	SUBCLONAL	1	TRUE	1	0.715026890572154	2		548	554	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155675	56155675	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	156	485	0	ENST00000399503.3:c.770del	p.Pro257HisfsTer6	p.P257Hfs*6	ENST00000399503	NM_005921.1	256	tCc/tc	3/20	1	2	FACETS	0.609	0.559	0.662	0.609	0.559	0.662	SUBCLONAL	1	TRUE	1	0.715026890572154	2		485	716	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673703	176673703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1415003698	NA	P-0060920-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	41	420	0	ENST00000439151.2:c.4403C>T	p.Pro1468Leu	p.P1468L	ENST00000439151	NM_022455.4	1468	cCa/cTa	10/23	1	2	FACETS	0.209	0.174	0.249	0.209	0.174	0.249	SUBCLONAL	1	TRUE	1	0.715026890572154	2		420	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0060922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	313	563	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.354898586483794	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.381133216413373	2		563	817	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	90	356	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.381133216413373	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.381133216413373	1		356	371	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129160	2129160	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45465195	NA	P-0060922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	155	506	0	ENST00000219476.3:c.3094C>T	p.Arg1032Ter	p.R1032*	ENST00000219476	NM_000548.3	1032	Cga/Tga	27/42	0.361855255412844	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.381133216413373	1		506	595	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821601	72821618	+	inframe_deletion	In_Frame_Del	DEL	CCGCCGCCGCCGCCGCCA	CCGCCGCCGCCGCCGCCA	-	rs778016374	NA	P-0060922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	158	555	0	ENST00000268489.5:c.10557_10574del	p.Gly3522_Gly3527del	p.G3522_G3527del	ENST00000268489	NM_006885.3	3519	ggTGGCGGCGGCGGCGGCGGc/ggc	10/10	0.350982137395417	3	FACETS	1	0.987	1	0.697	0.64	0.756	CLONAL	1	TRUE	1	0.381133216413373	3		555	708	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169985715	169985715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567380681	NA	P-0060922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	72	316	0	ENST00000295797.4:c.377G>A	p.Arg126His	p.R126H	ENST00000295797	NM_002740.5	126	cGt/cAt	5/18	1	2	FACETS	0.771	0.675	0.874	0.771	0.675	0.874	SUBCLONAL	1	TRUE	1	0.381133216413373	2		316	490	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260809	16260809	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765749217	NA	P-0060922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	145	665	0	ENST00000375759.3:c.8074G>A	p.Val2692Ile	p.V2692I	ENST00000375759	NM_015001.2	2692	Gtc/Atc	11/15	1	2	FACETS	0.847	0.773	0.925	0.847	0.773	0.925	CLONAL	1	TRUE	1	0.381133216413373	2		665	898	SUCCESS
H3C13	653604	MSKCC	GRCh37	1	149784893	149784893	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782390772	NA	P-0060922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	29	173	0	ENST00000331491.1:c.344C>T	p.Ala115Val	p.A115V	ENST00000331491	NM_001123375.2	115	gCc/gTc	1/1	1	2	FACETS	0.662	0.534	0.805	0.662	0.534	0.805	SUBCLONAL	1	TRUE	1	0.381133216413373	2		173	230	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250877	153250878	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060922-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	85	285	0	ENST00000281708.4:c.1182dup	p.Val395SerfsTer2	p.V395Sfs*2	ENST00000281708	NM_033632.3	394	-/A	8/12	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.381133216413373	2		285	400	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0060923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	42	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.00164720727563994	4	FACETS	1	0.938	1	0.624	0.526	0.732	INDETERMINATE	1	FALSE	2	0.405969556049736	4		334	233	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0060923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	118	736	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.405969556049736	1	FACETS	0.999	0.907	1	0.999	0.907	1	CLONAL	1	FALSE	0	0.405969556049736	1		737	464	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0060923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	122	324	1	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.405969556049736	2	FACETS	0.884	0.809	0.961	0.884	0.809	0.961	CLONAL	2	FALSE	0	0.405969556049736	2		325	340	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971292	13971292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772105404	NA	P-0060923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	85	454	0	ENST00000405192.2:c.637C>T	p.Arg213Cys	p.R213C	ENST00000405192	NM_001163147.1	213	Cgc/Tgc	8/12	0.405969556049736	3	FACETS	0.89	0.788	0.999	0.445	0.394	0.5	CLONAL	1	FALSE	1	0.405969556049736	3		454	566	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118821	61118821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146326268	NA	P-0060923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	77	437	0	ENST00000295025.8:c.14C>T	p.Ala5Val	p.A5V	ENST00000295025	NM_002908.2	5	gCg/gTg	2/11	1	2	FACETS	0.944	0.833	1	0.944	0.833	1	CLONAL	1	FALSE	1	0.405969556049736	2		437	402	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434673	99434673	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	45	605	0	ENST00000268035.6:c.760T>C	p.Tyr254His	p.Y254H	ENST00000268035	NM_000875.3	254	Tac/Cac	3/21	0.405969556049736	1	FACETS	0.413	0.347	0.485	0.413	0.347	0.485	SUBCLONAL	1	FALSE	0	0.405969556049736	1		605	428	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946279	81946279	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	211	562	0	ENST00000359376.3:c.2012T>C	p.Ile671Thr	p.I671T	ENST00000359376	NM_002661.3	671	aTc/aCc	19/33	0.405969556049736	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	FALSE	1	0.405969556049736	3		562	578	SUCCESS
ALB	213	MSKCC	GRCh37	4	74279198	74279198	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060923-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	62	524	0	ENST00000295897.4:c.905G>T	p.Cys302Phe	p.C302F	ENST00000295897	NM_000477.5	302	tGc/tTc	8/15	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	FALSE	1	0.405969556049736	2		524	287	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0060924-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	29	495	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.496	0.396	0.61	0.496	0.396	0.61	SUBCLONAL	1	TRUE	1	0.15	2		495	780	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171593	36171596	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CTTA	CTTA	-	novel	NA	P-0060924-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	34	435	1	ENST00000300305.3:c.967+2_967+5del		p.X323_splice	ENST00000300305		323			1	2	FACETS	0.687	0.56	0.831	0.687	0.56	0.831	SUBCLONAL	1	TRUE	1	0.15	2		436	660	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0060941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	124	358	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.322063276026991	5	FACETS	1	0.966	1	1	0.966	1	CLONAL	4	TRUE	1	0.322063276026991	5		358	263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	74	757	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.322063276026991	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	2	TRUE	0	0.322063276026991	2		757	229	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604656	48604656	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	45	411	0	ENST00000342988.3:c.1478A>G	p.Asp493Gly	p.D493G	ENST00000342988	NM_005359.5	493	gAt/gGt	12/12	0.322063276026991	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.322063276026991	1		411	200	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971130	21971130	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	97	540	0	ENST00000304494.5:c.228del	p.Thr77LeufsTer69	p.T77Lfs*69	ENST00000304494	NM_000077.4	76	gcC/gc	2/3	0.322063276026991	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.322063276026991	2		540	283	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003772	57003772	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	C	C	A	rs199589565	NA	P-0060941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	42	554	0	ENST00000257254.3:c.707G>T	p.Arg236Leu	p.R236L	ENST00000257254		236	cGc/cTc	1/2	0.312741625897205	3	FACETS	0.964	0.809	1	0.482	0.404	0.568	CLONAL	1	TRUE	1	0.322063276026991	3		554	314	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249938	110249938	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	96	519	0	ENST00000374672.4:c.737C>A	p.Ser246Ter	p.S246*	ENST00000374672	NM_004235.4	246	tCg/tAg	3/5	0.294224184324471	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	2	TRUE	0	0.322063276026991	2		519	298	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092809	27092809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060982-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	51	626	0	ENST00000324856.7:c.2830C>T	p.Gln944Ter	p.Q944*	ENST00000324856	NM_006015.4	944	Cag/Tag	9/20	1	2	FACETS	0.53	0.45	0.619	0.53	0.45	0.619	SUBCLONAL	1	TRUE	1	0.29225667210661	2		626	658	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717769	89717770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0060982-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	83	283	1	ENST00000371953.3:c.800dup	p.Asp268GlyfsTer30	p.D268Gfs*30	ENST00000371953	NM_000314.4	265	cta/ctAa	7/9	0.255181945621208	2	FACETS	0.887	0.791	0.989	0.887	0.791	0.989	CLONAL	2	TRUE	0	0.29225667210661	2		284	320	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577144	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs879253942	NA	P-0060982-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	228	651	0	ENST00000269305.4:c.794T>C	p.Leu265Pro	p.L265P	ENST00000269305	NM_001126112.2	265	cTg/cCg	8/11	0.290386413688251	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.29225667210661	2		651	687	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21348558	21348558	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1232362523	NA	P-0060982-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	202	1038	0	ENST00000215739.8:c.1615G>A	p.Gly539Ser	p.G539S	ENST00000215739	NM_006767.3	539	Ggc/Agc	14/21	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.29225667210661	2		1038	927	SUCCESS
APC	324	MSKCC	GRCh37	5	112151216	112151216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060982-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	125	434	0	ENST00000257430.4:c.859G>A	p.Glu287Lys	p.E287K	ENST00000257430	NM_000038.5	287	Gaa/Aaa	9/16	0.255181945621208	2	FACETS	0.795	0.723	0.87	0.795	0.723	0.87	SUBCLONAL	2	TRUE	0	0.29225667210661	2		434	538	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139810997	139810997	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060982-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	89	523	0	ENST00000247668.2:c.608del	p.Gln203ArgfsTer25	p.Q203Rfs*25	ENST00000247668	NM_021138.3	203	cAg/cg	7/11	0.29225667210661	1	FACETS	0.909	0.808	1	0.909	0.808	1	CLONAL	1	TRUE	0	0.29225667210661	1		523	572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0060983-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	116	761	0	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.287177245219715	0	FACETS	0.409	0.37	0.451			1	INDETERMINATE	1	TRUE	0	0.499801483655914	0		761	567	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0060983-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	51	804	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.287177245219715	0	FACETS	0.203	0.172	0.236			1	INDETERMINATE	1	TRUE	0	0.499801483655914	0		804	504	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916753	48916753	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1555282775	NA	P-0060983-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	75	258	0	ENST00000267163.4:c.283A>T	p.Lys95Ter	p.K95*	ENST00000267163	NM_000321.2	95	Aaa/Taa	3/27	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.499801483655914	2		258	224	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878094	151878094	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0060983-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	191	703	0	ENST00000262189.6:c.6851C>G	p.Ser2284Ter	p.S2284*	ENST00000262189	NM_170606.2	2284	tCa/tGa	36/59	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.499801483655914	2		703	706	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426832	49426833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0060983-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	139	621	0	ENST00000301067.7:c.11655dup	p.Gln3886AlafsTer126	p.Q3886Afs*126	ENST00000301067	NM_003482.3	3885	-/G	39/54	1	2	FACETS	0.816	0.744	0.89	0.816	0.744	0.89	CLONAL	1	TRUE	1	0.499801483655914	2		621	682	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438646	49438646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060983-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	47	597	0	ENST00000301067.7:c.4844G>A	p.Arg1615Gln	p.R1615Q	ENST00000301067	NM_003482.3	1615	cGa/cAa	19/54	1	2	FACETS	0.333	0.28	0.391	0.333	0.28	0.391	SUBCLONAL	1	TRUE	1	0.499801483655914	2		597	565	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444499	49444499	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060983-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	128	656	0	ENST00000301067.7:c.2872G>T	p.Glu958Ter	p.E958*	ENST00000301067	NM_003482.3	958	Gag/Tag	11/54	1	2	FACETS	0.826	0.751	0.905	0.826	0.751	0.905	CLONAL	1	TRUE	1	0.499801483655914	2		656	620	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0060984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	31	810	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.21600652956489	1	FACETS	0.902	0.732	1	0.902	0.732	1	CLONAL	1	TRUE	0	0.21600652956489	1		810	284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0060984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	77	485	0	ENST00000269305.4:c.375+1G>T		p.X125_splice	ENST00000269305	NM_001126112.2	125			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.21600652956489	2		485	578	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154225	2154225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1014211286	NA	P-0060984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	80	554	0	ENST00000434045.2:c.703C>T	p.Arg235Trp	p.R235W	ENST00000434045	NM_001127598.1	235	Cgg/Tgg	5/5	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.21600652956489	2		554	593	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923263	78923263	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	69	411	0	ENST00000306801.3:c.3286T>C	p.Trp1096Arg	p.W1096R	ENST00000306801	NM_020761.2	1096	Tgg/Cgg	28/34	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.21600652956489	2		411	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0060985-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	230	693	1	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.585723929111539	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.585723929111539	2		694	374	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872105	76872105	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060985-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	122	169	0	ENST00000373344.5:c.5542C>T	p.Gln1848Ter	p.Q1848*	ENST00000373344	NM_000489.3	1848	Cag/Tag	22/35	0.531910529282844	2	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.585723929111539	2		169	173	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515154	31515154	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060985-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	258	602	0	ENST00000344624.3:c.1231G>T	p.Val411Leu	p.V411L	ENST00000344624		411	Gtg/Ttg	5/33	0.510037252303861	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	2	0.585723929111539	4		602	677	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89839792	89839792	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs151232042	NA	P-0060985-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	24	597	0	ENST00000389301.3:c.1901A>G	p.Asp634Gly	p.D634G	ENST00000389301	NM_000135.2	634	gAt/gGt	22/43	0.585723929111539	2	FACETS	0.173	0.135	0.217	0.086	0.067	0.109	SUBCLONAL	1	TRUE	0	0.585723929111539	2		597	474	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163767	72163767	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060985-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	173	502	0	ENST00000357731.5:c.591G>T	p.Gln197His	p.Q197H	ENST00000357731	NM_173808.2	197	caG/caT	4/7	0.120834907052628	6	FACETS	1	0.958	1			1	INDETERMINATE	3	TRUE	NA	0.585723929111539	6		502	412	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724637	162724637	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060985-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	220	604	0	ENST00000367921.3:c.411del	p.Lys138AsnfsTer15	p.K138Nfs*15	ENST00000367921	NM_006182.2	137	Ggg/gg	5/18	0.254129418359891	5	FACETS	1	0.988	1	0.812	0.762	0.864	INDETERMINATE	2	TRUE	2	0.585723929111539	5		604	579	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404744	404744	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs750084957	NA	P-0060985-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	75	493	0	ENST00000399788.2:c.4450A>G	p.Met1484Val	p.M1484V	ENST00000399788	NM_001042603.1	1484	Atg/Gtg	26/28	NA	2	FACETS	0.687	0.605	0.773			1	INDETERMINATE	1	TRUE	NA	0.585723929111539	2		493	373	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254211	133254211	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060985-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	97	624	0	ENST00000320574.5:c.673G>C	p.Asp225His	p.D225H	ENST00000320574	NM_006231.2	225	Gat/Cat	7/49	0.183083803589623	3	FACETS	0.917	0.821	1	0.306	0.273	0.34	INDETERMINATE	1	TRUE	0	0.585723929111539	3		624	467	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868128	56868129	+	missense_variant	Missense_Mutation	DNP	GG	GG	CC	novel	NA	P-0060985-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	102	674	0	ENST00000308159.5:c.1626_1627inv	p.Asp543His	p.D543H	ENST00000308159	NM_014669.4	542	acGGac/acCCac	14/22	0.585723929111539	3	FACETS	0.871	0.782	0.965	0.435	0.391	0.483	CLONAL	1	TRUE	1	0.585723929111539	3		674	517	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610282	10610282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060985-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	223	753	0	ENST00000171111.5:c.428C>T	p.Ala143Val	p.A143V	ENST00000171111	NM_203500.1	143	gCc/gTc	2/6	0.585723929111539	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.585723929111539	1		753	436	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170521	11170522	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0060985-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	223	744	0	ENST00000358026.2:c.4824_4825delinsTT	p.Glu1608_Glu1609delinsAspTer	p.E1608_E1609delinsD*	ENST00000358026	NM_001128849.1	1608	gaGGag/gaTTag	34/36	0.585723929111539	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.585723929111539	1		744	395	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52692301	52692301	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060985-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	172	440	0	ENST00000394830.3:c.559G>T	p.Glu187Ter	p.E187*	ENST00000394830	NM_018313.4	187	Gag/Tag	6/30	0.577809904922336	2	FACETS	0.912	0.855	0.968	0.912	0.855	0.968	CLONAL	2	TRUE	0	0.585723929111539	2		440	322	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562480	176562480	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs886060438	NA	P-0060985-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	288	719	0	ENST00000439151.2:c.376A>G	p.Met126Val	p.M126V	ENST00000439151	NM_022455.4	126	Atg/Gtg	2/23	0.585723929111539	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.585723929111539	2		719	491	SUCCESS
MET	4233	MSKCC	GRCh37	7	116399532	116399532	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060985-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	251	554	0	ENST00000397752.3:c.2352G>T	p.Arg784Ser	p.R784S	ENST00000397752	NM_000245.2	784	agG/agT	10/21	0.567497159497286	2	FACETS	0.906	0.859	0.952	0.906	0.859	0.952	CLONAL	2	TRUE	0	0.585723929111539	2		554	473	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2056675	2056675	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060985-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	114	551	0	ENST00000349721.2:c.1177A>G	p.Arg393Gly	p.R393G	ENST00000349721	NM_003070.3	393	Aga/Gga	7/34	0.577809904922336	2	FACETS	0.914	0.829	1	0.457	0.414	0.501	CLONAL	1	TRUE	0	0.585723929111539	2		551	426	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87475954	87475954	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0060985-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	84	421	0	ENST00000277120.3:c.1397-1G>C		p.X466_splice	ENST00000277120		466			0.585723929111539	2	FACETS	1	0.911	1	0.51	0.456	0.567	CLONAL	1	TRUE	0	0.585723929111539	2		421	281	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0000141-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1320	128	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.156929264431075	5	FACETS		NA	1			1	NA	NA	FALSE	2	NA	5		326	1448	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230731	46230731	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0000141-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	67	413	0	ENST00000334344.6:c.980T>A	p.Leu327Ter	p.L327*	ENST00000334344	NM_152641.2	327	tTa/tAa	8/21	0.156929264431075	5	FACETS		NA	1			1	NA	NA	FALSE	2	NA	5		413	915	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000141-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	105	378	0	ENST00000342988.3:c.1610A>T	p.Asp537Val	p.D537V	ENST00000342988	NM_005359.5	537	gAc/gTc	12/12	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		378	722	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0000141-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	43	491	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		492	1012	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0000476-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	358	814	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.660210101661715	2	FACETS	0.997	0.96	1	0.997	0.96	1	CLONAL	2	TRUE	0	0.660210101661715	2		814	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578516	7578517	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0000476-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	418	756	1	ENST00000269305.4:c.413_414delinsAA	p.Ala138Glu	p.A138E	ENST00000269305	NM_001126112.2	138	gCC/gAA	5/11	0.646481348641094	3	FACETS	0.939	0.899	0.979	0.939	0.899	0.979	CLONAL	2	TRUE	1	0.660210101661715	3		757	897	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211089	55211089	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs746631025	NA	P-0001193-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1529	86	703	0	ENST00000275493.2:c.332T>C	p.Met111Thr	p.M111T	ENST00000275493	NM_005228.3	111	aTg/aCg	3/28	1	2	FACETS	0.15	0.131	0.169	0.15	0.131	0.169	SUBCLONAL	1	TRUE	1	0.711747079416978	2		703	1615	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0002298-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	48	316	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.614736386427313	2		316	145	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794610	42794610	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002298-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	12	363	0	ENST00000575354.2:c.1690C>T	p.Gln564Ter	p.Q564*	ENST00000575354	NM_015125.3	564	Cag/Tag	10/20	0.614736386427313	1	FACETS	0.227	0.16	0.308	0.227	0.16	0.308	SUBCLONAL	1	TRUE	0	0.614736386427313	1		363	119	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	208	456	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.370619228395735	4	FACETS	1	0.935	1	0.669	0.623	0.717	CLONAL	2	TRUE	1	0.370619228395735	4		456	766	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0003185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	155	536	0	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	0.338256486260514	2	FACETS	1	0.988	1	0.739	0.68	0.8	CLONAL	1	TRUE	0	0.370619228395735	2		536	566	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111168	193111168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1452051467	NA	P-0003185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	46	231	0	ENST00000367435.3:c.701G>A	p.Arg234Gln	p.R234Q	ENST00000367435	NM_024529.4	234	cGa/cAa	7/17	0.370619228395735	5	FACETS	0.868	0.732	1	0.289	0.244	0.34	CLONAL	1	TRUE	2	0.370619228395735	5		231	445	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0003185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	89	404	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			0.363773763595172	3	FACETS	1	0.943	1	0.548	0.488	0.613	CLONAL	1	TRUE	1	0.370619228395735	3		404	519	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140349	50140349	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	109	559	0	ENST00000246792.3:c.192C>A	p.Asp64Glu	p.D64E	ENST00000246792	NM_006270.3	64	gaC/gaA	2/6	0.363773763595172	3	FACETS	1	0.927	1	0.519	0.466	0.574	CLONAL	1	TRUE	1	0.370619228395735	3		559	672	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541847	187541847	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747920188	NA	P-0003185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	61	382	1	ENST00000441802.2:c.5893G>A	p.Val1965Ile	p.V1965I	ENST00000441802	NM_005245.3	1965	Gtc/Atc	10/27	0.283697831544227	4	FACETS	0.91	0.786	1	0.455	0.393	0.522	CLONAL	1	TRUE	2	0.370619228395735	4		383	496	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	59	456	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.185720965056752	1	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	0	0.185720965056752	1		456	555	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754890	29754890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370848188	NA	P-0005145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	71	539	0	ENST00000389048.3:c.1045G>A	p.Val349Ile	p.V349I	ENST00000389048	NM_004304.4	349	Gtc/Atc	4/29	0.185720965056752	1	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	0	0.185720965056752	1		539	668	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313231	65313231	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	37	427	0	ENST00000342505.4:c.1883A>C	p.His628Pro	p.H628P	ENST00000342505	NM_002227.2	628	cAc/cCc	13/25	1	2	FACETS	0.868	0.716	1	0.868	0.716	1	CLONAL	1	TRUE	1	0.185720965056752	2		427	459	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917827	29917827	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	80	646	0	ENST00000389048.3:c.841C>G	p.His281Asp	p.H281D	ENST00000389048	NM_004304.4	281	Cat/Gat	3/29	0.185720965056752	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.185720965056752	1		646	719	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167795	56167795	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	61	560	0	ENST00000399503.3:c.1360G>A	p.Glu454Lys	p.E454K	ENST00000399503	NM_005921.1	454	Gaa/Aaa	7/20	0.185720965056752	3	FACETS	1	0.867	1	0.503	0.434	0.58	CLONAL	1	TRUE	1	0.185720965056752	3		560	713	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482843	67482843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	70	507	0	ENST00000327367.4:c.1247C>T	p.Ser416Phe	p.S416F	ENST00000327367	NM_005902.3	416	tCc/tTc	9/9	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.185720965056752	2		507	609	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313222	30313222	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005145-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	99	739	0	ENST00000262643.3:c.916C>A	p.His306Asn	p.H306N	ENST00000262643	NM_001238.2	306	Cat/Aat	10/12	1	2	FACETS	0.79	0.706	0.879	1	0.983	1	SUBCLONAL	2	TRUE	1	0.185720965056752	2		739	675	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0005242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	288	535	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.754062696295929	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	0	0.754062696295929	3		535	346	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0005242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	170	442	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.754062696295929	3	FACETS	0.848	0.805	0.89	0.848	0.805	0.89	CLONAL	3	TRUE	0	0.754062696295929	3		442	244	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255790	16255790	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	81	405	1	ENST00000375759.3:c.3055C>T	p.Gln1019Ter	p.Q1019*	ENST00000375759	NM_015001.2	1019	Cag/Tag	11/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.754062696295929	2		406	149	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105727	27105727	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772578230	NA	P-0005242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	44	312	0	ENST00000324856.7:c.5338G>A	p.Glu1780Lys	p.E1780K	ENST00000324856	NM_006015.4	1780	Gaa/Aaa	20/20	1	2	FACETS	0.997	0.86	1	0.997	0.86	1	CLONAL	1	TRUE	1	0.754062696295929	2		312	117	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936379	49936379	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	265	552	0	ENST00000296474.3:c.1469C>A	p.Ser490Ter	p.S490*	ENST00000296474	NM_002447.2	490	tCa/tAa	3/20	0.730557878631851	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.754062696295929	2		552	336	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178143	56178143	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	51	336	0	ENST00000399503.3:c.3116C>A	p.Ser1039Ter	p.S1039*	ENST00000399503	NM_005921.1	1039	tCa/tAa	14/20	1	2	FACETS	0.856	0.742	0.975	0.856	0.742	0.975	CLONAL	1	TRUE	1	0.754062696295929	2		336	158	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202720	133202720	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	108	509	0	ENST00000320574.5:c.6514G>C	p.Asp2172His	p.D2172H	ENST00000320574	NM_006231.2	2172	Gac/Cac	46/49	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.754062696295929	2		509	285	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237716	133237716	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	104	438	0	ENST00000320574.5:c.2899G>C	p.Glu967Gln	p.E967Q	ENST00000320574	NM_006231.2	967	Gag/Cag	25/49	1	2	FACETS	0.919	0.835	1	0.919	0.835	1	CLONAL	1	TRUE	1	0.754062696295929	2		438	300	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28901682	28901682	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	74	329	0	ENST00000282397.4:c.2713C>G	p.Leu905Val	p.L905V	ENST00000282397	NM_002019.4	905	Ctg/Gtg	20/30	1	2	FACETS	0.93	0.829	1	0.93	0.829	1	CLONAL	1	TRUE	1	0.754062696295929	2		329	211	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857532	68857532	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	C	novel	NA	P-0005242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	73	370	0	ENST00000261769.5:c.2164+3A>C		p.X722_splice	ENST00000261769	NM_004360.3	722			0.728333273953494	1	FACETS	0.914	0.829	0.998	0.914	0.829	0.998	CLONAL	1	TRUE	0	0.754062696295929	1		370	132	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752931	42752931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	199	727	0	ENST00000222329.4:c.1333G>A	p.Asp445Asn	p.D445N	ENST00000222329	NM_006494.2	445	Gat/Aat	4/4	1	2	FACETS	0.91	0.849	0.973	0.91	0.849	0.973	CLONAL	1	TRUE	1	0.754062696295929	2		727	580	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874386	151874386	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	138	430	0	ENST00000262189.6:c.8152G>A	p.Glu2718Lys	p.E2718K	ENST00000262189	NM_170606.2	2718	Gaa/Aaa	38/59	0.716257975867888	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.754062696295929	3		430	236	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519893	NA	P-0005342-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	86	1201	1	ENST00000267101.3:c.310G>T	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ttg	3/28	1	2	FACETS	0.787	0.709	0.867	0.787	0.709	0.867	SUBCLONAL	1	TRUE	1	0.979903955201179	2		1202	223	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005342-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	87	492	1	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	1	2	FACETS	0.906	0.821	0.992	0.906	0.821	0.992	CLONAL	1	TRUE	1	0.979903955201179	2		493	196	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846037	68846037	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0005342-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	55	978	0	ENST00000261769.5:c.1009-1G>C		p.X337_splice	ENST00000261769	NM_004360.3	337			0.935342887331516	1	FACETS	0.698	0.632	0.76	0.698	0.632	0.76	SUBCLONAL	1	TRUE	0	0.979903955201179	1		978	82	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051642	30051642	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005566-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	257	333	1	ENST00000338641.4:c.576C>A	p.Tyr192Ter	p.Y192*	ENST00000338641	NM_000268.3	192	taC/taA	6/16	0.678568498613906	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.678568498613906	1		334	500	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0006481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	150	316	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.166088405516974	6	FACETS	1	0.98	1	0.785	0.725	0.846	INDETERMINATE	2	TRUE	3	0.80051550707859	6		316	414	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413070	139413072	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0006481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	124	986	0	ENST00000277541.6:c.1070_1072del	p.Phe357del	p.F357del	ENST00000277541	NM_017617.3	357	tTCTac/tac	6/34	0.666534362928148	2	FACETS	0.352	0.318	0.388	0.176	0.159	0.194	SUBCLONAL	1	TRUE	0	0.80051550707859	2		986	880	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0006481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	408	341	0				ENST00000310581	NM_198253.2	-/1132			0.461547102059431	4	FACETS	0.988	0.944	1	0.988	0.944	1	INDETERMINATE	2	TRUE	2	0.80051550707859	4		341	929	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947827	178947827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	229	908	1	ENST00000263967.3:c.2702G>T	p.Cys901Phe	p.C901F	ENST00000263967	NM_006218.2	901	tGt/tTt	19/21	0.461547102059431	4	FACETS	0.789	0.739	0.839	0.789	0.739	0.839	INDETERMINATE	2	TRUE	2	0.80051550707859	4		909	653	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433848	78433851	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CAGT	CAGT	-	novel	NA	P-0006481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	182	692	0	ENST00000370768.2:c.248_250+1del		p.X83_splice	ENST00000370768	NM_003902.3	83		3/20	0.80051550707859	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.80051550707859	1		692	234	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291528	15291528	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1233	70	860	1	ENST00000263388.2:c.3106C>T	p.Arg1036Ter	p.R1036*	ENST00000263388	NM_000435.2	1036	Cga/Tga	19/33	0.562371304092255	4	FACETS	0.242	0.209	0.277	0.121	0.104	0.139	SUBCLONAL	1	TRUE	2	0.80051550707859	4		861	1303	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791752	42791752	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	493	800	0	ENST00000575354.2:c.638G>C	p.Arg213Pro	p.R213P	ENST00000575354	NM_015125.3	213	cGg/cCg	5/20	0.80051550707859	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.80051550707859	1		800	611	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263994	104263995	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0006481-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	162	621	0	ENST00000369902.3:c.87_88del	p.Phe30SerfsTer17	p.F30Sfs*17	ENST00000369902	NM_016169.3	29	CTc/c	1/12	0.461547102059431	4	FACETS	0.785	0.72	0.853	0.393	0.36	0.427	INDETERMINATE	1	TRUE	2	0.80051550707859	4		621	928	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0006771-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	184	826	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	1	2	FACETS	0.916	0.845	0.99	1	0.992	1	CLONAL	2	TRUE	1	0.19	2		826	1057	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1023835002	NA	P-0006771-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	68	655	0	ENST00000558401.1:c.1A>G	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Gtg	1/4	0.286807038417389	1	FACETS	0.521	0.451	0.597	0.521	0.451	0.597	SUBCLONAL	1	TRUE	0	0.19	1		655	1244	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041623	42041623	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006771-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	12	726	0	ENST00000219905.7:c.5818C>T	p.Gln1940Ter	p.Q1940*	ENST00000219905	NM_001164273.1	1940	Cag/Tag	17/24	0.286807038417389	1	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	0	0.19	1		726	77	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348278	89348278	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006771-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	98	844	0	ENST00000301030.4:c.4672T>G	p.Ser1558Ala	p.S1558A	ENST00000301030	NM_001256183.1	1558	Tcc/Gcc	9/13	0.3	3	FACETS	1	0.979	1	0.717	0.639	0.8	CLONAL	1	TRUE	1	0.19	3		844	788	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654634	29654634	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006771-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	45	618	0	ENST00000356175.3:c.5323G>T	p.Glu1775Ter	p.E1775*	ENST00000356175	NM_000267.3	1775	Gag/Tag	37/57	1	2	FACETS	1	0.851	1	1	0.972	1	CLONAL	2	TRUE	1	0.19	2		618	236	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806146	1806146	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006771-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	132	855	0	ENST00000260795.2:c.1165G>C	p.Val389Leu	p.V389L	ENST00000260795		389	Gtg/Ctg	8/17	1	2	FACETS	0.805	0.731	0.883	1	0.987	1	CLONAL	2	TRUE	1	0.19	2		855	863	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1253878	1253878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764841621	NA	P-0006771-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	71	819	0	ENST00000310581.5:c.3364G>A	p.Ala1122Thr	p.A1122T	ENST00000310581	NM_198253.2	1122	Gca/Aca	16/16	1	2	FACETS	0.661	0.575	0.755	0.661	0.575	0.755	SUBCLONAL	1	TRUE	1	0.19	2		819	1130	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218673	98218673	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368417828	NA	P-0006937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	37	263	0	ENST00000331920.6:c.3191C>T	p.Thr1064Met	p.T1064M	ENST00000331920	NM_000264.3	1064	aCg/aTg	19/24	1	2	FACETS	0.891	0.739	1	0.891	0.739	1	CLONAL	1	TRUE	1	0.330890310237732	2		263	251	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771330	68771330	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555509636	NA	P-0006937-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	82	298	0	ENST00000261769.5:c.12G>A	p.Trp4Ter	p.W4*	ENST00000261769	NM_004360.3	4	tgG/tgA	1/16	0.330890310237732	1	FACETS	0.878	0.799	0.957	1	0.989	1	CLONAL	3	TRUE	0	0.330890310237732	1		298	157	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449800	29449800	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008008-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	45	337	0	ENST00000389048.3:c.3055G>C	p.Val1019Leu	p.V1019L	ENST00000389048	NM_004304.4	1019	Gtc/Ctc	18/29	0.218643766249264	1	FACETS	0.917	0.773	1	0.917	0.773	1	CLONAL	1	TRUE	0	0.251030728744844	1		337	342	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341168	8341168	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008008-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	53	373	1	ENST00000356435.5:c.5048C>A	p.Ser1683Tyr	p.S1683Y	ENST00000356435		1683	tCc/tAc	30/35	1	2	FACETS	0.893	0.762	1	0.893	0.762	1	CLONAL	1	TRUE	1	0.251030728744844	2		374	473	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0008099-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	168	425	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.14993242261467	3	FACETS	1	0.95	1	0.691	0.638	0.745	INDETERMINATE	2	TRUE	0	0.318035264914476	3		426	591	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875627	35875627	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369971728	NA	P-0008099-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	57	292	0	ENST00000303115.3:c.814G>A	p.Val272Ile	p.V272I	ENST00000303115	NM_002185.3	272	Gta/Ata	7/8	0.318035264914476	3	FACETS	0.76	0.652	0.877	0.38	0.326	0.439	SUBCLONAL	1	TRUE	1	0.318035264914476	3		292	547	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020377	123020377	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008099-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	69	244	0	ENST00000355640.3:c.865T>C	p.Phe289Leu	p.F289L	ENST00000355640		289	Ttt/Ctt	2/7	0.318035264914476	1	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	0	0.318035264914476	1		244	363	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576916	7576917	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0008099-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	118	457	0	ENST00000269305.4:c.929_930insG	p.Asn310LysfsTer27	p.N310Kfs*27	ENST00000269305	NM_001126112.2	310	aac/aaGc	9/11	0.318035264914476	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.318035264914476	1		457	583	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009001-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	167	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.752	0.693	0.813	1	0.989	1	SUBCLONAL	2	TRUE	1	0.324990083206075	2		326	683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578525	7578525	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519976	NA	P-0009001-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	242	835	0	ENST00000269305.4:c.405C>G	p.Cys135Trp	p.C135W	ENST00000269305	NM_001126112.2	135	tgC/tgG	5/11	0.243450211400535	2	FACETS	1	0.989	1	0.643	0.6	0.688	CLONAL	1	TRUE	0	0.324990083206075	2		835	1158	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928075	178928095	+	inframe_deletion	In_Frame_Del	DEL	ATTAGAAGATTTGCTGAACCC	ATTAGAAGATTTGCTGAACCC	-	novel	NA	P-0009001-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	92	976	0	ENST00000263967.3:c.1353_1373del	p.Leu452_Pro458del	p.L452_P458del	ENST00000263967	NM_006218.2	451	ggATTAGAAGATTTGCTGAACCCt/ggt	8/21	0.206829804301818	3	FACETS	1	0.977	1	0.465	0.415	0.518	CLONAL	1	TRUE	0	0.324990083206075	3		976	472	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206756	36206757	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0009001-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	100	694	1	ENST00000300305.3:c.754_755dup	p.Leu253ProfsTer2	p.L253Pfs*2	ENST00000300305		252	tcc/tcTCc	6/8	0.282540264604401	3	FACETS	1	0.973	1	0.638	0.571	0.708	CLONAL	1	TRUE	1	0.324990083206075	3		695	561	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	132	425	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	1	TRUE	NA	0.31	2		426	750	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0009793-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	93	619	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	0.302179171068711	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.31	1		619	470	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009877-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	189	300	0				ENST00000310581	NM_198253.2	-/1132			0.724148083091856	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.724148083091856	3		300	349	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937542	32937542	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs397507396	NA	P-0009877-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	92	450	0	ENST00000380152.3:c.8206del	p.Leu2736SerfsTer2	p.L2736Sfs*2	ENST00000380152		2735	Ccc/cc	18/27	0.724148083091856	3	FACETS	0.732	0.653	0.815	0.366	0.326	0.408	SUBCLONAL	1	TRUE	1	0.724148083091856	3		450	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0010640-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	76	622	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.16	2		623	828	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242486	+	inframe_deletion	In_Frame_Del	DEL	TTAAGAGAAGCAACATCT	TTAAGAGAAGCAACATCT	-	rs121913440	NA	P-0010640-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	23	343	0	ENST00000275493.2:c.2239_2256del	p.Leu747_Ser752del	p.L747_S752del	ENST00000275493	NM_005228.3	747	TTAAGAGAAGCAACATCT/-	19/28	0.3	3	FACETS	0.591	0.46	0.745			1	SUBCLONAL	1	TRUE	NA	0.16	3		343	525	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984952	101984952	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1384754271	NA	P-0010640-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	30	303	0	ENST00000282441.5:c.399G>T	p.Gln133His	p.Q133H	ENST00000282441	NM_001130145.2	133	caG/caT	2/9	1	2	FACETS	0.933	0.752	1	0.933	0.752	1	CLONAL	1	TRUE	1	0.16	2		303	402	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0010703-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	30	278	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.119021447087629	4	FACETS	0.934	0.764	1	0.934	0.764	1	INDETERMINATE	2	TRUE	2	0.284377088317676	4		278	145	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0010703-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	22	442	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.119021447087629	4	FACETS	0.808	0.635	1	0.808	0.635	1	INDETERMINATE	2	TRUE	2	0.284377088317676	4		442	123	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395108	139395108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371414501	NA	P-0010703-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	8	332	1	ENST00000277541.6:c.5830G>A	p.Ala1944Thr	p.A1944T	ENST00000277541	NM_017617.3	1944	Gcc/Acc	31/34	1	2	FACETS	0.172	0.11	0.253	0.172	0.11	0.253	SUBCLONAL	1	TRUE	1	0.284377088317676	2		333	327	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729163	66729163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516792	NA	P-0010703-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	9	354	1	ENST00000307102.5:c.371C>T	p.Pro124Leu	p.P124L	ENST00000307102	NM_002755.3	124	cCg/cTg	3/11	1	2	FACETS	0.197	0.13	0.284	0.197	0.13	0.284	SUBCLONAL	1	TRUE	1	0.284377088317676	2		355	321	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155721	56155722	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0010703-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	40	225	0	ENST00000399503.3:c.816_817del	p.Arg273SerfsTer27	p.R273Sfs*27	ENST00000399503	NM_005921.1	271	agAAaa/agaa	3/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.284377088317676	2		225	195	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375134	104375134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1256959985	NA	P-0010703-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	78	288	2	ENST00000369902.3:c.1132G>A	p.Gly378Arg	p.G378R	ENST00000369902	NM_016169.3	378	Gga/Aga	9/12	0.119021447087629	4	FACETS	1	0.907	1	1	0.907	1	INDETERMINATE	2	TRUE	2	0.284377088317676	4		290	343	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160696	56160696	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010703-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	50	264	0	ENST00000399503.3:c.971del	p.Pro324LeufsTer5	p.P324Lfs*5	ENST00000399503	NM_005921.1	324	Cct/ct	4/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.284377088317676	2		264	244	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287448	38287448	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011048-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	80	594	0	ENST00000425967.3:c.209C>A	p.Pro70His	p.P70H	ENST00000425967	NM_001174067.1	70	cCt/cAt	4/19	0.124927470745074	3	FACETS	1	0.923	1	0.532	0.469	0.6	INDETERMINATE	1	TRUE	1	0.287046827431558	3		594	599	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796937	42796937	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011048-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	210	743	0	ENST00000575354.2:c.3395C>G	p.Thr1132Ser	p.T1132S	ENST00000575354	NM_015125.3	1132	aCc/aGc	14/20	0.121008705016901	5	FACETS	1	0.983	1	0.787	0.731	0.844	INDETERMINATE	2	TRUE	2	0.287046827431558	5		743	887	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864192	117864205	+	frameshift_variant	Frame_Shift_Del	DEL	TCACAGGCTCTGGG	TCACAGGCTCTGGG	-	novel	NA	P-0011048-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	116	452	0	ENST00000297338.2:c.1452_1465del	p.Pro485AlafsTer47	p.P485Afs*47	ENST00000297338	NM_006265.2	484	gaCCCAGAGCCTGTGAtg/gatg	11/14	0.287046827431558	8	FACETS	0.772	0.695	0.854	0.257	0.231	0.285	SUBCLONAL	2	TRUE	2	0.287046827431558	8		452	974	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343160	118343160	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011048-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	56	556	0	ENST00000534358.1:c.1286T>C	p.Ile429Thr	p.I429T	ENST00000534358	NM_005933.3	429	aTa/aCa	3/36	0.261165051266609	2	FACETS	0.783	0.672	0.905	0.392	0.336	0.453	CLONAL	1	TRUE	0	0.287046827431558	2		556	498	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118354931	118354934	+	frameshift_variant	Frame_Shift_Del	DEL	GCAG	GCAG	-	novel	NA	P-0011048-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	133	440	0	ENST00000534358.1:c.4123_4126del	p.Gly1375LeufsTer2	p.G1375Lfs*2	ENST00000534358	NM_005933.3	1374	GCAGgc/gc	9/36	0.261165051266609	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.287046827431558	2		440	416	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848649	151848649	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011048-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	87	405	0	ENST00000262189.6:c.12544G>T	p.Asp4182Tyr	p.D4182Y	ENST00000262189	NM_170606.2	4182	Gat/Tat	50/59	0.133518480161908	5	FACETS	1	0.945	1	0.732	0.652	0.816	INDETERMINATE	2	TRUE	2	0.287046827431558	5		405	395	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295475	1295475	+	upstream_gene_variant	5'Flank	SNP	C	C	T	rs1250692978	NA	P-0011048-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	75	730	0				ENST00000310581	NM_198253.2	-/1132			0.287046827431558	5	FACETS	0.95	0.831	1	0.317	0.277	0.36	CLONAL	1	TRUE	2	0.287046827431558	5		730	787	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295650	1295664	+	upstream_gene_variant	5'Flank	DEL	CGGGGCGTCGGGCTC	CGGGGCGTCGGGCTC	-	novel	NA	P-0011048-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	75	676	0				ENST00000310581	NM_198253.2	-/1132			0.287046827431558	5	FACETS	0.938	0.821	1	0.313	0.273	0.355	CLONAL	1	TRUE	2	0.287046827431558	5		676	797	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037957	49037971	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CATGCTGTTCAGGAG	CATGCTGTTCAGGAG	T	novel	NA	P-0011048-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	13	255	0	ENST00000267163.4:c.2197_2211delinsT	p.His733TyrfsTer13	p.H733Yfs*13	ENST00000267163	NM_000321.2	733	CATGCTGTTCAGGAG/T	21/27	0.287046827431558	1	FACETS	0.479	0.343	0.644	0.479	0.343	0.644	SUBCLONAL	1	TRUE	0	0.287046827431558	1		255	162	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024001	27024002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0011442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	59	10	0	ENST00000324856.7:c.1113dup	p.Gln372AlafsTer28	p.Q372Afs*28	ENST00000324856	NM_006015.4	369	-/G	1/20	0.766959938210039	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.766959938210039	1		10	80	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	453	535	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.733055240667778	7	FACETS	0.971	0.933	1	0.555	0.533	0.577	CLONAL	4	TRUE	0	0.733055240667778	7		535	901	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	40	281	1	ENST00000397062.3:c.101G>A	p.Arg34Gln	p.R34Q	ENST00000397062	NM_006164.4	34	cGa/cAa	2/5	0.694424247025569	4	FACETS	0.375	0.311	0.446	0.094	0.077	0.112	SUBCLONAL	1	TRUE	0	0.733055240667778	4		282	505	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163297	32163297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1239036035	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	113	689	0	ENST00000375023.3:c.5929G>A	p.Glu1977Lys	p.E1977K	ENST00000375023	NM_004557.3	1977	Gag/Aag	30/30	0.696545290735715	3	FACETS	0.691	0.623	0.762	0.23	0.207	0.254	SUBCLONAL	1	TRUE	0	0.733055240667778	3		689	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	242	608	1	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.72696390166739	2	FACETS	0.968	0.927	1	0.968	0.927	1	CLONAL	2	TRUE	0	0.733055240667778	2		609	341	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912815	100912815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1000609240	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	72	297	0	ENST00000325455.5:c.2507G>A	p.Arg836Gln	p.R836Q	ENST00000325455	NM_001202474.3	836	cGa/cAa	7/8	0.733055240667778	1	FACETS	0.584	0.519	0.652	0.584	0.519	0.652	SUBCLONAL	1	TRUE	0	0.733055240667778	1		297	213	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031750	36031750	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879255268	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	32	480	1	ENST00000358208.4:c.1579G>A	p.Glu527Lys	p.E527K	ENST00000358208		527	Gag/Aag	12/12	0.723594258132593	2	FACETS	0.195	0.158	0.237	0.098	0.079	0.119	SUBCLONAL	1	TRUE	0	0.733055240667778	2		481	447	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765576	41765576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763066660	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	36	569	0	ENST00000301178.4:c.2452G>A	p.Glu818Lys	p.E818K	ENST00000301178	NM_021913.4	818	Gaa/Aaa	20/20	0.733055240667778	2	FACETS	0.197	0.162	0.237	0.099	0.081	0.119	SUBCLONAL	1	TRUE	0	0.733055240667778	2		569	498	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355310	81355310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	32	242	0	ENST00000222390.5:c.1064G>A	p.Arg355Gln	p.R355Q	ENST00000222390	NM_000601.4	355	cGa/cAa	9/18	0.696468173096088	3	FACETS	0.506	0.413	0.609	0.169	0.137	0.203	SUBCLONAL	1	TRUE	0	0.733055240667778	3		242	236	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568569	41568569	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	32	419	0	ENST00000263253.7:c.4519G>A	p.Asp1507Asn	p.D1507N	ENST00000263253	NM_001429.3	1507	Gat/Aat	28/31	0.72696390166739	2	FACETS	0.249	0.202	0.302	0.124	0.101	0.151	SUBCLONAL	1	TRUE	0	0.733055240667778	2		419	351	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202741	16202741	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	50	404	0	ENST00000375759.3:c.449G>C	p.Gly150Ala	p.G150A	ENST00000375759	NM_015001.2	150	gGa/gCa	3/15	0.733055240667778	2	FACETS	0.244	0.207	0.285	0.122	0.103	0.143	SUBCLONAL	1	TRUE	0	0.733055240667778	2		404	559	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256174	16256174	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	37	498	0	ENST00000375759.3:c.3439C>T	p.Gln1147Ter	p.Q1147*	ENST00000375759	NM_015001.2	1147	Caa/Taa	11/15	0.669127169706671	4	FACETS	0.342	0.281	0.41	0.171	0.14	0.205	SUBCLONAL	1	TRUE	2	0.733055240667778	4		498	512	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546359	46546359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	31	333	1	ENST00000262741.5:c.170C>T	p.Ser57Phe	p.S57F	ENST00000262741	NM_003629.3	57	tCt/tTt	2/10	0.733055240667778	3	FACETS	0.279	0.225	0.34	0.093	0.075	0.114	SUBCLONAL	1	TRUE	0	0.733055240667778	3		334	414	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464424	120464424	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	18	346	0	ENST00000256646.2:c.5222C>T	p.Ser1741Leu	p.S1741L	ENST00000256646	NM_024408.3	1741	tCa/tTa	29/34	0.710935989229547	2	FACETS	0.191	0.144	0.247	0.096	0.072	0.124	SUBCLONAL	1	TRUE	0	0.733055240667778	2		346	257	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510155	120510155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	47	437	0	ENST00000256646.2:c.1354C>A	p.Arg452Ser	p.R452S	ENST00000256646	NM_024408.3	452	Cgt/Agt	8/34	0.710935989229547	2	FACETS	0.287	0.242	0.336	0.143	0.121	0.168	SUBCLONAL	1	TRUE	0	0.733055240667778	2		437	447	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845495	63845495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	33	217	0	ENST00000279873.7:c.1234G>A	p.Glu412Lys	p.E412K	ENST00000279873	NM_032199.2	412	Gaa/Aaa	9/10	0.614929650637461	4	FACETS	0.452	0.369	0.546			1	SUBCLONAL	1	TRUE	NA	0.733055240667778	4		217	345	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276944	123276944	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	23	267	0	ENST00000358487.5:c.973G>C	p.Glu325Gln	p.E325Q	ENST00000358487	NM_000141.4	325	Gag/Cag	8/18	0.733055240667778	2	FACETS	0.198	0.154	0.249	0.099	0.077	0.125	SUBCLONAL	1	TRUE	0	0.733055240667778	2		267	317	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456315	32456315	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs377072761	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	40	564	0	ENST00000332351.3:c.577G>T	p.Ala193Ser	p.A193S	ENST00000332351	NM_024426.4	193	Gcc/Tcc	1/10	0.697284877487756	2	FACETS	0.223	0.185	0.265	0.111	0.092	0.133	SUBCLONAL	1	TRUE	0	0.733055240667778	2		564	490	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948767	71948767	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	95	585	0	ENST00000298229.2:c.3479C>A	p.Ser1160Ter	p.S1160*	ENST00000298229	NM_001567.3	1160	tCg/tAg	26/28	0.728443176572236	3	FACETS	0.542	0.483	0.605	0.181	0.161	0.202	SUBCLONAL	1	TRUE	0	0.733055240667778	3		585	653	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201142	108201142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1266101531	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	11	253	0	ENST00000278616.4:c.7509G>A	p.Met2503Ile	p.M2503I	ENST00000278616	NM_000051.3	2503	atG/atA	50/63	0.733055240667778	1	FACETS	0.128	0.088	0.176	0.128	0.088	0.176	SUBCLONAL	1	TRUE	0	0.733055240667778	1		253	149	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155719	119155719	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	31	458	0	ENST00000264033.4:c.1472C>A	p.Ala491Asp	p.A491D	ENST00000264033	NM_005188.3	491	gCt/gAt	10/16	0.733055240667778	1	FACETS	0.138	0.111	0.168	0.138	0.111	0.168	SUBCLONAL	1	TRUE	0	0.733055240667778	1		458	389	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155917	119155917	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778239777	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	36	469	1	ENST00000264033.4:c.1582C>T	p.His528Tyr	p.H528Y	ENST00000264033	NM_005188.3	528	Cat/Tat	11/16	0.733055240667778	1	FACETS	0.18	0.148	0.216	0.18	0.148	0.216	SUBCLONAL	1	TRUE	0	0.733055240667778	1		470	345	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156142	119156142	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	51	487	0	ENST00000264033.4:c.1807C>T	p.Pro603Ser	p.P603S	ENST00000264033	NM_005188.3	603	Cca/Tca	11/16	0.733055240667778	1	FACETS	0.223	0.19	0.259	0.223	0.19	0.259	SUBCLONAL	1	TRUE	0	0.733055240667778	1		487	395	SUCCESS
CBL	867	MSKCC	GRCh37	11	119158623	119158623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	28	466	0	ENST00000264033.4:c.2003C>T	p.Ser668Leu	p.S668L	ENST00000264033	NM_005188.3	668	tCa/tTa	12/16	0.733055240667778	1	FACETS	0.209	0.167	0.255	0.209	0.167	0.255	SUBCLONAL	1	TRUE	0	0.733055240667778	1		466	232	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536716	120536716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	53	503	0	ENST00000229340.5:c.376G>A	p.Glu126Lys	p.E126K	ENST00000229340	NM_006861.6	126	Gag/Aag	5/6	0.702047499563026	2	FACETS	0.324	0.277	0.376	0.162	0.138	0.188	SUBCLONAL	1	TRUE	0	0.733055240667778	2		503	446	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614959	23614959	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	50	325	0	ENST00000261584.4:c.3382G>T	p.Ala1128Ser	p.A1128S	ENST00000261584	NM_024675.3	1128	Gca/Tca	13/13	0.72696390166739	2	FACETS	0.585	0.502	0.675	0.293	0.251	0.338	SUBCLONAL	1	TRUE	0	0.733055240667778	2		325	233	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827715	72827715	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	28	482	0	ENST00000268489.5:c.8866C>G	p.Leu2956Val	p.L2956V	ENST00000268489	NM_006885.3	2956	Ctg/Gtg	9/10	0.733055240667778	3	FACETS	0.197	0.157	0.244	0.066	0.052	0.082	SUBCLONAL	1	TRUE	0	0.733055240667778	3		482	529	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89866026	89866026	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs773057753	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	41	357	0	ENST00000389301.3:c.813G>T	p.Gln271His	p.Q271H	ENST00000389301	NM_000135.2	271	caG/caT	9/43	0.696468173096088	3	FACETS	0.485	0.406	0.573	0.162	0.135	0.191	SUBCLONAL	1	TRUE	0	0.733055240667778	3		357	315	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56383166	56383166	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	39	188	0	ENST00000348428.3:c.986-1G>C		p.X329_splice	ENST00000348428	NM_006785.3	329			0.72696390166739	2	FACETS	0.56	0.469	0.658	0.28	0.234	0.329	SUBCLONAL	1	TRUE	0	0.733055240667778	2		188	190	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942137	17942137	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	36	596	1	ENST00000458235.1:c.2878G>T	p.Glu960Ter	p.E960*	ENST00000458235	NM_000215.3	960	Gag/Tag	21/24	0.733055240667778	1	FACETS	0.146	0.12	0.176	0.146	0.12	0.176	SUBCLONAL	1	TRUE	0	0.733055240667778	1		597	425	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443612	29443612	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	200	580	0	ENST00000389048.3:c.3605G>T	p.Gly1202Val	p.G1202V	ENST00000389048	NM_004304.4	1202	gGa/gTa	23/29	0.696468173096088	3	FACETS	1	0.985	1	0.403	0.375	0.431	CLONAL	1	TRUE	0	0.733055240667778	3		580	617	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47601171	47601171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778548696	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	138	442	0	ENST00000263735.4:c.409G>A	p.Glu137Lys	p.E137K	ENST00000263735	NM_002354.2	137	Gag/Aag	3/9	0.696468173096088	3	FACETS	1	0.96	1	0.36	0.33	0.392	CLONAL	1	TRUE	0	0.733055240667778	3		442	476	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128016879	128016879	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	27	390	0	ENST00000285398.2:c.2210C>G	p.Ser737Cys	p.S737C	ENST00000285398	NM_000122.1	737	tCc/tGc	14/15	0.135236232009183	3	FACETS	0.224	0.178	0.277			1	INDETERMINATE	1	TRUE	NA	0.733055240667778	3		390	449	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116240	209116240	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	87	267	0	ENST00000345146.2:c.36G>C	p.Glu12Asp	p.E12D	ENST00000345146	NM_005896.2	12	gaG/gaC	3/10	0.694424247025569	4	FACETS	1	0.898	1	0.252	0.224	0.282	CLONAL	1	TRUE	0	0.733055240667778	4		267	408	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376255	225376255	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	44	293	0	ENST00000264414.4:c.699T>A	p.Tyr233Ter	p.Y233*	ENST00000264414	NM_003590.4	233	taT/taA	6/16	0.710935989229547	2	FACETS	0.603	0.512	0.702	0.302	0.256	0.351	SUBCLONAL	1	TRUE	0	0.733055240667778	2		293	199	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091838	29091838	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	20	230	0	ENST00000328354.6:c.1119G>C	p.Lys373Asn	p.K373N	ENST00000328354	NM_007194.3	373	aaG/aaC	11/15	0.72696390166739	2	FACETS	0.329	0.253	0.416	0.164	0.126	0.208	SUBCLONAL	1	TRUE	0	0.733055240667778	2		230	166	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513705	41513705	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	40	499	0	ENST00000263253.7:c.609G>C	p.Gln203His	p.Q203H	ENST00000263253	NM_001429.3	203	caG/caC	2/31	0.72696390166739	2	FACETS	0.239	0.199	0.285	0.12	0.099	0.143	SUBCLONAL	1	TRUE	0	0.733055240667778	2		499	456	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547886	41547886	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs61758152	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	34	410	0	ENST00000263253.7:c.2867C>G	p.Ser956Cys	p.S956C	ENST00000263253	NM_001429.3	956	tCt/tGt	15/31	0.72696390166739	2	FACETS	0.28	0.229	0.337	0.14	0.114	0.169	SUBCLONAL	1	TRUE	0	0.733055240667778	2		410	331	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205185	128205185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs924409987	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	110	536	0	ENST00000341105.2:c.256C>T	p.Arg86Cys	p.R86C	ENST00000341105	NM_032638.4	86	Cgc/Tgc	3/6	0.688015097869694	5	FACETS	0.726	0.652	0.805	0.145	0.13	0.161	SUBCLONAL	1	TRUE	0	0.733055240667778	5		536	868	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665540	138665540	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	100	333	0	ENST00000330315.3:c.25G>C	p.Glu9Gln	p.E9Q	ENST00000330315	NM_023067.3	9	Gag/Cag	1/1	0.688015097869694	5	FACETS	0.613	0.546	0.684	0.123	0.109	0.137	SUBCLONAL	1	TRUE	0	0.733055240667778	5		333	935	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244044	153244044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	43	326	0	ENST00000281708.4:c.2113G>A	p.Asp705Asn	p.D705N	ENST00000281708	NM_033632.3	705	Gac/Aac	12/12	0.733055240667778	1	FACETS	0.287	0.241	0.337	0.287	0.241	0.337	SUBCLONAL	1	TRUE	0	0.733055240667778	1		326	259	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630594	187630594	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	37	490	0	ENST00000441802.2:c.388G>C	p.Glu130Gln	p.E130Q	ENST00000441802	NM_005245.3	130	Gag/Cag	2/27	0.733055240667778	1	FACETS	0.207	0.171	0.247	0.207	0.171	0.247	SUBCLONAL	1	TRUE	0	0.733055240667778	1		490	309	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287383	33287383	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	77	418	0	ENST00000374542.5:c.1714G>A	p.Glu572Lys	p.E572K	ENST00000374542	NM_001141970.1	572	Gaa/Aaa	6/8	0.696545290735715	3	FACETS	0.623	0.548	0.702	0.208	0.182	0.234	SUBCLONAL	1	TRUE	0	0.733055240667778	3		418	461	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287800	33287800	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	152	624	0	ENST00000374542.5:c.1453G>A	p.Glu485Lys	p.E485K	ENST00000374542	NM_001141970.1	485	Gaa/Aaa	5/8	0.696545290735715	3	FACETS	0.723	0.662	0.787	0.241	0.22	0.263	SUBCLONAL	1	TRUE	0	0.733055240667778	3		624	784	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202334	138202334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	126	543	0	ENST00000237289.4:c.2251G>A	p.Glu751Lys	p.E751K	ENST00000237289	NM_001270507.1	751	Gag/Aag	9/9	0.645139162616734	4	FACETS	0.703	0.636	0.773	0.176	0.159	0.194	SUBCLONAL	1	TRUE	0	0.733055240667778	4		543	848	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983353	149983353	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	34	348	0	ENST00000253339.5:c.2905C>G	p.Leu969Val	p.L969V	ENST00000253339		969	Ctt/Gtt	7/7	0.645139162616734	4	FACETS	0.434	0.355	0.523	0.109	0.088	0.131	SUBCLONAL	1	TRUE	0	0.733055240667778	4		348	370	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891636	151891636	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	16	223	0	ENST00000262189.6:c.4396G>A	p.Asp1466Asn	p.D1466N	ENST00000262189	NM_170606.2	1466	Gat/Aat	29/59	0.697284877487756	2	FACETS	0.271	0.201	0.354	0.136	0.1	0.177	SUBCLONAL	1	TRUE	0	0.733055240667778	2		223	161	SUCCESS
AR	367	MSKCC	GRCh37	X	66931444	66931444	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	37	564	0	ENST00000374690.3:c.2086G>C	p.Asp696His	p.D696H	ENST00000374690	NM_000044.3	696	Gac/Cac	4/8	0.733055240667778	1	FACETS	0.138	0.113	0.165	0.138	0.113	0.165	SUBCLONAL	1	TRUE	0	0.733055240667778	1		564	464	SUCCESS
CBL	867	MSKCC	GRCh37	11	119158644	119158646	+	frameshift_variant	Frame_Shift_Del	DEL	CTC	CTC	TT	novel	NA	P-0012013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	14	392	0	ENST00000264033.4:c.2024_2026delinsTT	p.Ser675PhefsTer27	p.S675Ffs*27	ENST00000264033	NM_005188.3	675	tCTCtg/tTTtg	12/16	0.733055240667778	1	FACETS	0.121	0.087	0.162	0.121	0.087	0.162	SUBCLONAL	1	TRUE	0	0.733055240667778	1		392	200	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0012335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	199	341	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.897	0.84	0.956	0.897	0.84	0.956	CLONAL	1	TRUE	1	0.92007404264346	2		341	482	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0012335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	271	451	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.92007404264346	2		451	511	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0012335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	370	1154	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	0.418212540385685	1	FACETS	0.682	0.654	0.709	0.682	0.654	0.709	INDETERMINATE	1	TRUE	0	0.92007404264346	1		1154	637	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755612	39755612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776452839	NA	P-0012335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	615	449	0	ENST00000288319.7:c.1153C>T	p.Arg385Cys	p.R385C	ENST00000288319	NM_182918.3	385	Cgc/Tgc	10/10	0.36697922837669	3	FACETS	0.878	0.85	0.907	0.878	0.85	0.907	INDETERMINATE	2	TRUE	1	0.92007404264346	3		449	1111	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346550	81346550	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs148293411	NA	P-0012335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	115	532	1	ENST00000222390.5:c.1403G>A	p.Arg468His	p.R468H	ENST00000222390	NM_000601.4	468	cGt/cAt	11/18	1	2	FACETS	0.403	0.364	0.445	0.403	0.364	0.445	SUBCLONAL	1	TRUE	1	0.92007404264346	2		533	620	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461178	120461178	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0012335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	162	321	0	ENST00000256646.2:c.5782-2A>G		p.X1928_splice	ENST00000256646	NM_024408.3	1928			1	2	FACETS	0.806	0.747	0.866	0.806	0.747	0.866	CLONAL	1	TRUE	1	0.92007404264346	2		321	437	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877484	28877484	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	150	294	0	ENST00000282397.4:c.3837T>G	p.Ser1279Arg	p.S1279R	ENST00000282397	NM_002019.4	1279	agT/agG	30/30	1	2	FACETS	0.97	0.901	1	0.97	0.901	1	CLONAL	1	TRUE	1	0.92007404264346	2		294	336	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757396	40757396	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1374515118	NA	P-0012335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	279	629	1	ENST00000373198.4:c.2902G>A	p.Asp968Asn	p.D968N	ENST00000373198	NM_133170.3	968	Gac/Aac	20/32	0.418212540385685	1	FACETS	0.388	0.365	0.411	0.388	0.365	0.411	INDETERMINATE	1	TRUE	0	0.92007404264346	1		630	845	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077580	30077580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	359	458	0	ENST00000338641.4:c.1727C>T	p.Thr576Ile	p.T576I	ENST00000338641	NM_000268.3	576	aCc/aTc	15/16	0.445822405041119	3	FACETS	0.845	0.809	0.882	0.845	0.809	0.882	INDETERMINATE	2	TRUE	1	0.92007404264346	3		458	674	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113154	209113155	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0012335-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	281	520	0	ENST00000345146.2:c.352_353delinsAA	p.Pro118Asn	p.P118N	ENST00000345146	NM_005896.2	118	CCc/AAc	4/10	0.418212540385685	1	FACETS	0.62	0.59	0.65	0.62	0.59	0.65	INDETERMINATE	1	TRUE	0	0.92007404264346	1		520	532	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693002	89693003	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	93	274	0	ENST00000371953.3:c.491dup	p.Val166SerfsTer14	p.V166Sfs*14	ENST00000371953	NM_000314.4	162	-/A	5/9	0.522705101188873	2	FACETS	0.855	0.778	0.934	0.855	0.778	0.934	CLONAL	2	TRUE	0	0.522705101188873	2		274	208	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0012567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	235	407	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.476195369784262	4	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	2	0.522705101188873	4		407	684	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397516435	NA	P-0012567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	389	536	0	ENST00000269305.4:c.586C>G	p.Arg196Gly	p.R196G	ENST00000269305	NM_001126112.2	196	Cga/Gga	6/11	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.522705101188873	2		536	707	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231165	142231165	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	399	813	1	ENST00000350721.4:c.4789C>A	p.Gln1597Lys	p.Q1597K	ENST00000350721	NM_001184.3	1597	Cag/Aag	27/47	0.476195369784262	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.522705101188873	4		814	1072	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858199	9858199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1266	192	973	0	ENST00000330684.3:c.3202G>A	p.Ala1068Thr	p.A1068T	ENST00000330684	NM_001134407.1	1068	Gcc/Acc	13/13	0.522705101188873	5	FACETS	0.899	0.829	0.972	0.3	0.276	0.324	CLONAL	1	TRUE	2	0.522705101188873	5		973	1458	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874403	76874403	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012567-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	174	984	0	ENST00000373344.5:c.5319T>G	p.Ile1773Met	p.I1773M	ENST00000373344	NM_000489.3	1773	atT/atG	21/35	0.522705101188873	2	FACETS	1	0.976	1	0.564	0.522	0.608	CLONAL	1	TRUE	0	0.522705101188873	2		984	590	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	72	300	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.889	0.778	1	0.889	0.778	1	CLONAL	1	TRUE	1	0.331375111829757	2		300	489	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690169	47690169	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	130	419	0	ENST00000233146.2:c.1387-1G>A		p.X463_splice	ENST00000233146	NM_000251.2	463			1	2	FACETS	0.931	0.844	1	0.931	0.844	1	CLONAL	1	TRUE	1	0.331375111829757	2		419	843	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs267605076	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	174	676	0	ENST00000269305.4:c.672G>T	p.Glu224Asp	p.E224D	ENST00000269305	NM_001126112.2	224	gaG/gaT	6/11	0.325639059768192	1	FACETS	0.942	0.867	1	0.942	0.867	1	CLONAL	1	TRUE	0	0.331375111829757	1		676	930	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089556	27089556	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	145	642	3	ENST00000324856.7:c.2512G>T	p.Gly838Ter	p.G838*	ENST00000324856	NM_006015.4	838	Gga/Tga	8/20	1	2	FACETS	0.832	0.758	0.91	0.832	0.758	0.91	CLONAL	1	TRUE	1	0.331375111829757	2		645	1052	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31015986	31015986	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	108	477	0	ENST00000375687.4:c.308A>G	p.Glu103Gly	p.E103G	ENST00000375687	NM_015338.5	103	gAg/gGg	5/13	0.294739095305293	3	FACETS	0.821	0.736	0.912	0.411	0.368	0.456	CLONAL	1	TRUE	1	0.331375111829757	3		477	925	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684109	29684109	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1329683225	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	116	399	1	ENST00000356175.3:c.7806+1G>A		p.X2602_splice	ENST00000356175	NM_000267.3	2602			1	2	FACETS	0.853	0.768	0.942	0.853	0.768	0.942	CLONAL	1	TRUE	1	0.331375111829757	2		400	821	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272925	11272925	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	140	484	0	ENST00000361445.4:c.3326A>T	p.Asp1109Val	p.D1109V	ENST00000361445	NM_004958.3	1109	gAc/gTc	22/58	1	2	FACETS	0.937	0.853	1	0.937	0.853	1	CLONAL	1	TRUE	1	0.331375111829757	2		484	902	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099050	27099050	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	153	556	0	ENST00000324856.7:c.3466G>T	p.Glu1156Ter	p.E1156*	ENST00000324856	NM_006015.4	1156	Gaa/Taa	13/20	1	2	FACETS	0.942	0.861	1	0.942	0.861	1	CLONAL	1	TRUE	1	0.331375111829757	2		556	980	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739128	46739128	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	147	556	0	ENST00000371975.4:c.1477C>A	p.Gln493Lys	p.Q493K	ENST00000371975	NM_003579.3	493	Cag/Aag	13/18	1	2	FACETS	0.839	0.765	0.917	0.839	0.765	0.917	CLONAL	1	TRUE	1	0.331375111829757	2		556	1057	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653387	206653387	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	110	415	0	ENST00000367120.3:c.1271A>T	p.Gln424Leu	p.Q424L	ENST00000367120	NM_014002.3	424	cAg/cTg	12/22	1	2	FACETS	0.912	0.82	1	0.912	0.82	1	CLONAL	1	TRUE	1	0.331375111829757	2		415	728	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085855	16085855	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	87	336	0	ENST00000281043.3:c.1031C>A	p.Ala344Glu	p.A344E	ENST00000281043	NM_005378.4	344	gCa/gAa	3/3	1	2	FACETS	0.798	0.707	0.895	0.798	0.707	0.895	SUBCLONAL	1	TRUE	1	0.331375111829757	2		336	658	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469978	25469978	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	129	556	0	ENST00000264709.3:c.1064A>G	p.His355Arg	p.H355R	ENST00000264709	NM_175629.2	355	cAc/cGc	9/23	1	2	FACETS	0.838	0.759	0.921	0.838	0.759	0.921	CLONAL	1	TRUE	1	0.331375111829757	2		556	929	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416428	29416428	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	171	671	0	ENST00000389048.3:c.4525T>C	p.Ser1509Pro	p.S1509P	ENST00000389048	NM_004304.4	1509	Tcc/Ccc	29/29	1	2	FACETS	0.901	0.827	0.978	0.901	0.827	0.978	CLONAL	1	TRUE	1	0.331375111829757	2		671	1146	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010395	48010395	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	137	488	0	ENST00000234420.5:c.23A>G	p.Tyr8Cys	p.Y8C	ENST00000234420	NM_000179.2	8	tAc/tGc	1/10	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.331375111829757	2		488	806	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190717480	190717480	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	175	381	1	ENST00000441310.2:c.799G>T	p.Val267Leu	p.V267L	ENST00000441310	NM_000534.4	267	Gta/Tta	7/13	0.266553604405138	4	FACETS	0.852	0.786	0.921			1	CLONAL	2	TRUE	NA	0.331375111829757	4		382	825	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137360	202137360	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	171	292	0	ENST00000358485.4:c.589-1G>T		p.X197_splice	ENST00000358485	NM_001080125.1	197			0.33099411574949	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.331375111829757	2		292	493	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437293	220437293	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1369410899	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	428	809	2	ENST00000243786.2:c.197G>T	p.Gly66Val	p.G66V	ENST00000243786	NM_002191.3	66	gGc/gTc	1/2	0.33099411574949	2	FACETS	0.946	0.901	0.992	0.946	0.901	0.992	CLONAL	2	TRUE	0	0.331375111829757	2		811	1365	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47088113	47088113	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	72	315	0	ENST00000409792.3:c.6964-2A>G		p.X2322_splice	ENST00000409792	NM_014159.6	2322			1	2	FACETS	0.859	0.752	0.974	0.859	0.752	0.974	CLONAL	1	TRUE	1	0.331375111829757	2		315	506	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103759	47103759	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	215	752	0	ENST00000409792.3:c.6187A>T	p.Arg2063Ter	p.R2063*	ENST00000409792	NM_014159.6	2063	Aga/Tga	14/21	1	2	FACETS	0.961	0.891	1	0.961	0.891	1	CLONAL	1	TRUE	1	0.331375111829757	2		752	1350	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438482	52438482	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	108	552	0	ENST00000460680.1:c.1237A>T	p.Asn413Tyr	p.N413Y	ENST00000460680	NM_004656.3	413	Aac/Tac	12/17	1	2	FACETS	0.712	0.638	0.79	0.712	0.638	0.79	SUBCLONAL	1	TRUE	1	0.331375111829757	2		552	916	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799755	72799755	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	138	514	0	ENST00000325599.8:c.1414G>A	p.Gly472Ser	p.G472S	ENST00000325599	NM_018130.2	472	Ggc/Agc	11/11	1	2	FACETS	0.924	0.841	1	0.924	0.841	1	CLONAL	1	TRUE	1	0.331375111829757	2		514	901	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430297	181430297	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	90	356	0	ENST00000325404.1:c.149T>A	p.Val50Glu	p.V50E	ENST00000325404	NM_003106.3	50	gTg/gAg	1/1	1	2	FACETS	0.927	0.824	1	0.927	0.824	1	CLONAL	1	TRUE	1	0.331375111829757	2		356	586	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589827	55589827	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	153	569	0	ENST00000288135.5:c.1309A>T	p.Thr437Ser	p.T437S	ENST00000288135	NM_000222.2	437	Aca/Tca	8/21	1	2	FACETS	0.967	0.884	1	0.967	0.884	1	CLONAL	1	TRUE	1	0.331375111829757	2		569	955	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599314	55599314	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	112	459	0	ENST00000288135.5:c.2440G>T	p.Ala814Ser	p.A814S	ENST00000288135	NM_000222.2	814	Gcc/Tcc	17/21	1	2	FACETS	0.749	0.672	0.829	0.749	0.672	0.829	SUBCLONAL	1	TRUE	1	0.331375111829757	2		459	903	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955622	55955622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	150	571	0	ENST00000263923.4:c.3323G>A	p.Gly1108Glu	p.G1108E	ENST00000263923	NM_002253.2	1108	gGg/gAg	25/30	1	2	FACETS	0.877	0.801	0.958	0.877	0.801	0.958	CLONAL	1	TRUE	1	0.331375111829757	2		571	1032	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961007	55961007	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	148	501	0	ENST00000263923.4:c.2933T>A	p.Val978Glu	p.V978E	ENST00000263923	NM_002253.2	978	gTg/gAg	21/30	1	2	FACETS	0.987	0.901	1	0.987	0.901	1	CLONAL	1	TRUE	1	0.331375111829757	2		501	905	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968192	55968192	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	132	607	0	ENST00000263923.4:c.2138T>A	p.Ile713Asn	p.I713N	ENST00000263923	NM_002253.2	713	aTt/aAt	15/30	1	2	FACETS	0.796	0.721	0.874	0.796	0.721	0.874	SUBCLONAL	1	TRUE	1	0.331375111829757	2		607	1001	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971098	55971098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201069157	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	121	440	3	ENST00000263923.4:c.1699G>A	p.Val567Met	p.V567M	ENST00000263923	NM_002253.2	567	Gtg/Atg	13/30	1	2	FACETS	0.869	0.785	0.958	0.869	0.785	0.958	CLONAL	1	TRUE	1	0.331375111829757	2		443	840	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217184	66217184	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	192	588	0	ENST00000273854.3:c.2431A>T	p.Asn811Tyr	p.N811Y	ENST00000273854	NM_004439.5	811	Aac/Tac	14/18	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.331375111829757	2		588	1048	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029257	143029257	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	78	317	0	ENST00000262992.4:c.2363T>C	p.Met788Thr	p.M788T	ENST00000262992	NM_001101669.1	788	aTg/aCg	21/24	1	2	FACETS	0.74	0.651	0.836	0.74	0.651	0.836	SUBCLONAL	1	TRUE	1	0.331375111829757	2		317	636	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143129601	143129601	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	119	444	0	ENST00000262992.4:c.1049A>C	p.Gln350Pro	p.Q350P	ENST00000262992	NM_001101669.1	350	cAg/cCg	12/24	1	2	FACETS	0.936	0.846	1	0.936	0.846	1	CLONAL	1	TRUE	1	0.331375111829757	2		444	767	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516912	187516912	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1560916993	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	156	587	0	ENST00000441802.2:c.13069A>G	p.Ser4357Gly	p.S4357G	ENST00000441802	NM_005245.3	4357	Agt/Ggt	26/27	1	2	FACETS	0.977	0.894	1	0.977	0.894	1	CLONAL	1	TRUE	1	0.331375111829757	2		587	964	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524786	187524786	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	129	470	0	ENST00000441802.2:c.10894A>T	p.Arg3632Ter	p.R3632*	ENST00000441802	NM_005245.3	3632	Aga/Tga	19/27	1	2	FACETS	0.918	0.832	1	0.918	0.832	1	CLONAL	1	TRUE	1	0.331375111829757	2		470	848	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293626	1293626	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	81	390	0	ENST00000310581.5:c.1375T>C	p.Trp459Arg	p.W459R	ENST00000310581	NM_198253.2	459	Tgg/Cgg	2/16	1	2	FACETS	0.731	0.644	0.824	0.731	0.644	0.824	SUBCLONAL	1	TRUE	1	0.331375111829757	2		390	669	SUCCESS
APC	324	MSKCC	GRCh37	5	112176394	112176394	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	87	352	0	ENST00000257430.4:c.5103A>T	p.Gln1701His	p.Q1701H	ENST00000257430	NM_000038.5	1701	caA/caT	16/16	1	2	FACETS	0.841	0.746	0.944	0.841	0.746	0.944	CLONAL	1	TRUE	1	0.331375111829757	2		352	624	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176662936	176662936	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	93	357	0	ENST00000439151.2:c.3911A>C	p.Gln1304Pro	p.Q1304P	ENST00000439151	NM_022455.4	1304	cAg/cCg	6/23	1	2	FACETS	0.824	0.733	0.921	0.824	0.733	0.921	CLONAL	1	TRUE	1	0.331375111829757	2		357	681	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038337	180038337	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1398985437	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	121	467	2	ENST00000261937.6:c.3680C>A	p.Ala1227Asp	p.A1227D	ENST00000261937	NM_182925.4	1227	gCc/gAc	27/30	1	2	FACETS	0.931	0.842	1	0.931	0.842	1	CLONAL	1	TRUE	1	0.331375111829757	2		469	784	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052980	180052980	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866937901	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	133	575	0	ENST00000261937.6:c.1310G>T	p.Arg437Leu	p.R437L	ENST00000261937	NM_182925.4	437	cGt/cTt	10/30	1	2	FACETS	0.817	0.741	0.898	0.817	0.741	0.898	CLONAL	1	TRUE	1	0.331375111829757	2		575	982	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181612	32181612	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	163	519	0	ENST00000375023.3:c.2173A>T	p.Thr725Ser	p.T725S	ENST00000375023	NM_004557.3	725	Acc/Tcc	14/30	1	2	FACETS	0.959	0.879	1	0.959	0.879	1	CLONAL	1	TRUE	1	0.331375111829757	2		519	1026	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190389	32190389	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	124	524	0	ENST00000375023.3:c.350A>G	p.Lys117Arg	p.K117R	ENST00000375023	NM_004557.3	117	aAg/aGg	3/30	1	2	FACETS	0.761	0.687	0.838	0.761	0.687	0.838	SUBCLONAL	1	TRUE	1	0.331375111829757	2		524	984	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066642	94066642	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1391562093	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1252	222	850	0	ENST00000369303.4:c.1117A>C	p.Ser373Arg	p.S373R	ENST00000369303	NM_004440.3	373	Agt/Cgt	5/17	1	2	FACETS	0.909	0.844	0.977	0.909	0.844	0.977	CLONAL	1	TRUE	1	0.331375111829757	2		850	1474	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519473	137519473	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	82	380	1	ENST00000367739.4:c.1165C>A	p.Pro389Thr	p.P389T	ENST00000367739	NM_000416.2	389	Cct/Act	7/7	1	2	FACETS	0.738	0.65	0.831	0.738	0.65	0.831	SUBCLONAL	1	TRUE	1	0.331375111829757	2		381	671	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129498	152129498	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	33	131	0	ENST00000206249.3:c.451A>T	p.Arg151Trp	p.R151W	ENST00000206249	NM_000125.3	151	Agg/Tgg	1/8	1	2	FACETS	0.766	0.627	0.921	0.766	0.627	0.921	CLONAL	1	TRUE	1	0.331375111829757	2		131	260	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962852	2962852	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	145	547	1	ENST00000396946.4:c.2056A>C	p.Asn686His	p.N686H	ENST00000396946	NM_032415.4	686	Aac/Cac	16/25	1	2	FACETS	0.943	0.86	1	0.943	0.86	1	CLONAL	1	TRUE	1	0.331375111829757	2		548	928	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963909	2963909	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	193	696	0	ENST00000396946.4:c.1898T>A	p.Leu633Gln	p.L633Q	ENST00000396946	NM_032415.4	633	cTg/cAg	15/25	1	2	FACETS	0.904	0.834	0.976	0.904	0.834	0.976	CLONAL	1	TRUE	1	0.331375111829757	2		696	1289	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431643	6431643	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	80	305	0	ENST00000356142.4:c.196A>T	p.Arg66Ter	p.R66*	ENST00000356142	NM_018890.3	66	Aga/Tga	3/7	1	2	FACETS	0.896	0.79	1	0.896	0.79	1	CLONAL	1	TRUE	1	0.331375111829757	2		305	539	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367279	50367279	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	88	342	0	ENST00000331340.3:c.86A>G	p.Glu29Gly	p.E29G	ENST00000331340	NM_006060.4	29	gAg/gGg	3/8	1	2	FACETS	0.835	0.74	0.936	0.835	0.74	0.936	CLONAL	1	TRUE	1	0.331375111829757	2		342	636	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468217	50468217	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	126	416	1	ENST00000331340.3:c.1452C>A	p.His484Gln	p.H484Q	ENST00000331340	NM_006060.4	484	caC/caA	8/8	1	2	FACETS	0.997	0.903	1	0.997	0.903	1	CLONAL	1	TRUE	1	0.331375111829757	2		417	763	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358981	81358981	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	169	576	0	ENST00000222390.5:c.980A>T	p.Gln327Leu	p.Q327L	ENST00000222390	NM_000601.4	327	cAg/cTg	8/18	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.331375111829757	2		576	1006	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534489	140534489	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	119	459	0	ENST00000288602.6:c.424A>T	p.Thr142Ser	p.T142S	ENST00000288602	NM_004333.4	142	Aca/Tca	3/18	1	2	FACETS	0.816	0.736	0.901	0.816	0.736	0.901	CLONAL	1	TRUE	1	0.331375111829757	2		459	880	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739459	145739459	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	103	406	0	ENST00000428558.2:c.1911C>G	p.Phe637Leu	p.F637L	ENST00000428558	NM_004260.3	637	ttC/ttG	12/22	1	2	FACETS	0.904	0.809	1	0.904	0.809	1	CLONAL	1	TRUE	1	0.331375111829757	2		406	688	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518044	8518044	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	152	550	0	ENST00000356435.5:c.1347A>T	p.Gln449His	p.Q449H	ENST00000356435		449	caA/caT	10/35	1	2	FACETS	0.877	0.801	0.957	0.877	0.801	0.957	CLONAL	1	TRUE	1	0.331375111829757	2		550	1046	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971137	21971137	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	46	225	1	ENST00000304494.5:c.221A>T	p.Asp74Val	p.D74V	ENST00000304494	NM_000077.4	74	gAc/gTc	2/3	1	2	FACETS	0.646	0.544	0.757	0.646	0.544	0.757	SUBCLONAL	1	TRUE	1	0.331375111829757	2		226	430	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325646	87325646	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	159	555	0	ENST00000277120.3:c.523T>C	p.Tyr175His	p.Y175H	ENST00000277120		175	Tac/Cac	6/19	1	2	FACETS	0.941	0.862	1	0.941	0.862	1	CLONAL	1	TRUE	1	0.331375111829757	2		555	1020	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563504	87563504	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	96	377	0	ENST00000277120.3:c.1892T>C	p.Met631Thr	p.M631T	ENST00000277120		631	aTg/aCg	16/19	1	2	FACETS	0.944	0.842	1	0.944	0.842	1	CLONAL	1	TRUE	1	0.331375111829757	2		377	614	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401176	139401176	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs760966826	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	104	420	0	ENST00000277541.6:c.3893G>C	p.Gly1298Ala	p.G1298A	ENST00000277541	NM_017617.3	1298	gGt/gCt	23/34	1	2	FACETS	0.845	0.757	0.938	0.845	0.757	0.938	CLONAL	1	TRUE	1	0.331375111829757	2		420	743	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597853	43597853	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	184	817	0	ENST00000355710.3:c.401A>T	p.Glu134Val	p.E134V	ENST00000355710	NM_020975.4	134	gAg/gTg	3/20	1	2	FACETS	0.871	0.802	0.943	0.871	0.802	0.943	CLONAL	1	TRUE	1	0.331375111829757	2		817	1275	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610090	43610090	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	121	697	0	ENST00000355710.3:c.2042A>C	p.Gln681Pro	p.Q681P	ENST00000355710	NM_020975.4	681	cAg/cCg	11/20	1	2	FACETS	0.756	0.682	0.834	0.756	0.682	0.834	SUBCLONAL	1	TRUE	1	0.331375111829757	2		697	966	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88672034	88672034	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs771444196	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	61	236	0	ENST00000372037.3:c.568A>G	p.Asn190Asp	p.N190D	ENST00000372037	NM_004329.2	190	Aat/Gat	8/13	1	2	FACETS	0.87	0.753	0.997	0.87	0.753	0.997	CLONAL	1	TRUE	1	0.331375111829757	2		236	423	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717616	89717616	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	111	395	0	ENST00000371953.3:c.641A>G	p.Gln214Arg	p.Q214R	ENST00000371953	NM_000314.4	214	cAg/cGg	7/9	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.331375111829757	2		395	633	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180499	94180499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	154	532	1	ENST00000323929.3:c.1669G>A	p.Asp557Asn	p.D557N	ENST00000323929	NM_005591.3	557	Gac/Aac	15/20	1	2	FACETS	0.927	0.847	1	0.927	0.847	1	CLONAL	1	TRUE	1	0.331375111829757	2		533	1003	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491471	18491471	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs754123698	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	100	361	0	ENST00000266497.5:c.1384A>G	p.Arg462Gly	p.R462G	ENST00000266497		462	Aga/Gga	8/31	1	2	FACETS	0.829	0.741	0.923	0.829	0.741	0.923	CLONAL	1	TRUE	1	0.331375111829757	2		361	728	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422897	49422897	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	123	499	0	ENST00000301067.7:c.14198A>G	p.Glu4733Gly	p.E4733G	ENST00000301067	NM_003482.3	4733	gAg/gGg	44/54	1	2	FACETS	0.866	0.783	0.954	0.866	0.783	0.954	CLONAL	1	TRUE	1	0.331375111829757	2		499	857	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864441	57864441	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	219	740	0	ENST00000228682.2:c.1918A>G	p.Ser640Gly	p.S640G	ENST00000228682	NM_005269.2	640	Agt/Ggt	12/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.331375111829757	2		740	1232	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885271	111885271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	229	827	0	ENST00000341259.2:c.1159G>A	p.Gly387Arg	p.G387R	ENST00000341259	NM_005475.2	387	Gga/Aga	6/8	1	2	FACETS	0.965	0.897	1	0.965	0.897	1	CLONAL	1	TRUE	1	0.331375111829757	2		827	1432	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563389	21563389	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	190	747	1	ENST00000382592.4:c.530G>C	p.Gly177Ala	p.G177A	ENST00000382592	NM_014572.2	177	gGc/gCc	4/8	1	2	FACETS	0.964	0.889	1	0.964	0.889	1	CLONAL	1	TRUE	1	0.331375111829757	2		748	1190	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28885839	28885839	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	139	641	0	ENST00000282397.4:c.3523A>T	p.Ile1175Leu	p.I1175L	ENST00000282397	NM_002019.4	1175	Ata/Tta	27/30	1	2	FACETS	0.756	0.687	0.83	0.756	0.687	0.83	SUBCLONAL	1	TRUE	1	0.331375111829757	2		641	1109	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012444	29012444	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	123	448	1	ENST00000282397.4:c.427C>A	p.Pro143Thr	p.P143T	ENST00000282397	NM_002019.4	143	Ccc/Acc	4/30	1	2	FACETS	0.885	0.8	0.974	0.885	0.8	0.974	CLONAL	1	TRUE	1	0.331375111829757	2		449	839	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893220	32893220	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	87	260	0	ENST00000380152.3:c.74G>T	p.Gly25Val	p.G25V	ENST00000380152		25	gGa/gTa	3/27	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.331375111829757	2		260	511	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907437	32907437	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	132	508	0	ENST00000380152.3:c.1822G>C	p.Asp608His	p.D608H	ENST00000380152		608	Gac/Cac	10/27	1	2	FACETS	0.876	0.795	0.962	0.876	0.795	0.962	CLONAL	1	TRUE	1	0.331375111829757	2		508	909	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133692	41133692	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1344	225	886	0	ENST00000379561.5:c.1936A>G	p.Lys646Glu	p.K646E	ENST00000379561	NM_002015.3	646	Aag/Gag	2/3	1	2	FACETS	0.866	0.803	0.93	0.866	0.803	0.93	CLONAL	1	TRUE	1	0.331375111829757	2		886	1569	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519087	103519087	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	91	415	0	ENST00000355739.4:c.2425G>T	p.Asp809Tyr	p.D809Y	ENST00000355739	NM_000123.3	809	Gat/Tat	11/15	1	2	FACETS	0.844	0.75	0.944	0.844	0.75	0.944	CLONAL	1	TRUE	1	0.331375111829757	2		415	651	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557645	95557645	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs763241498	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	142	656	0	ENST00000393063.1:c.5422A>G	p.Met1808Val	p.M1808V	ENST00000393063	NM_030621.3	1808	Atg/Gtg	26/28	1	2	FACETS	0.792	0.721	0.867	0.792	0.721	0.867	SUBCLONAL	1	TRUE	1	0.331375111829757	2		656	1082	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476396	88476396	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	102	368	0	ENST00000360948.2:c.1736T>A	p.Leu579Gln	p.L579Q	ENST00000360948	NM_001012338.2	579	cTg/cAg	15/19	1	2	FACETS	0.996	0.893	1	0.996	0.893	1	CLONAL	1	TRUE	1	0.331375111829757	2		368	618	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396776	396776	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	143	566	0	ENST00000262320.3:c.250A>T	p.Lys84Ter	p.K84*	ENST00000262320	NM_003502.3	84	Aag/Tag	2/11	1	2	FACETS	0.901	0.821	0.985	0.901	0.821	0.985	CLONAL	1	TRUE	1	0.331375111829757	2		566	958	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828180	3828180	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	97	276	0	ENST00000262367.5:c.1945G>T	p.Glu649Ter	p.E649*	ENST00000262367	NM_004380.2	649	Gaa/Taa	10/31	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.331375111829757	2		276	559	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857941	9857941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	118	481	0	ENST00000330684.3:c.3460C>T	p.Pro1154Ser	p.P1154S	ENST00000330684	NM_001134407.1	1154	Ccc/Tcc	13/13	1	2	FACETS	0.88	0.794	0.971	0.88	0.794	0.971	CLONAL	1	TRUE	1	0.331375111829757	2		481	809	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671705	67671705	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	121	463	0	ENST00000264010.4:c.2114A>T	p.Gln705Leu	p.Q705L	ENST00000264010	NM_006565.3	705	cAg/cTg	12/12	1	2	FACETS	0.923	0.834	1	0.923	0.834	1	CLONAL	1	TRUE	1	0.331375111829757	2		463	791	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16021214	16021214	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	159	579	0	ENST00000268712.3:c.2043G>T	p.Gln681His	p.Q681H	ENST00000268712	NM_006311.3	681	caG/caT	18/46	0.325639059768192	1	FACETS	0.814	0.746	0.886	0.814	0.746	0.886	CLONAL	1	TRUE	0	0.331375111829757	1		579	983	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654515	29654515	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs1555533548	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	137	494	0	ENST00000356175.3:c.5206-2A>T		p.X1736_splice	ENST00000356175	NM_000267.3	1736			1	2	FACETS	0.932	0.848	1	0.932	0.848	1	CLONAL	1	TRUE	1	0.331375111829757	2		494	887	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264398	30264398	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	110	351	0	ENST00000322652.5:c.133A>T	p.Ser45Cys	p.S45C	ENST00000322652	NM_015355.2	45	Agc/Tgc	1/16	1	2	FACETS	0.992	0.893	1	0.992	0.893	1	CLONAL	1	TRUE	1	0.331375111829757	2		351	669	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441551	40441551	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	190	716	0	ENST00000345506.4:c.122A>T	p.Gln41Leu	p.Q41L	ENST00000345506	NM_003152.3	41	cAg/cTg	3/20	1	2	FACETS	0.932	0.86	1	0.932	0.86	1	CLONAL	1	TRUE	1	0.331375111829757	2		716	1230	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696719	47696719	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	133	467	0	ENST00000347630.2:c.229G>C	p.Asp77His	p.D77H	ENST00000347630	NM_001007230.1	77	Gat/Cat	5/11	1	2	FACETS	0.915	0.831	1	0.915	0.831	1	CLONAL	1	TRUE	1	0.331375111829757	2		467	877	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119788	70119788	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	161	553	0	ENST00000245479.2:c.790A>T	p.Arg264Ter	p.R264*	ENST00000245479	NM_000346.3	264	Aga/Tga	3/3	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.331375111829757	2		553	971	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120294	70120294	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1347	227	879	0	ENST00000245479.2:c.1296C>A	p.Tyr432Ter	p.Y432*	ENST00000245479	NM_000346.3	432	taC/taA	3/3	1	2	FACETS	0.87	0.808	0.935	0.87	0.808	0.935	CLONAL	1	TRUE	1	0.331375111829757	2		879	1574	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120335	70120335	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1361	222	904	1	ENST00000245479.2:c.1337A>T	p.Gln446Leu	p.Q446L	ENST00000245479	NM_000346.3	446	cAg/cTg	3/3	1	2	FACETS	0.846	0.785	0.91	0.846	0.785	0.91	CLONAL	1	TRUE	1	0.331375111829757	2		905	1583	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39607466	39607466	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	160	538	0	ENST00000262039.4:c.1544A>G	p.Glu515Gly	p.E515G	ENST00000262039	NM_002647.2	515	gAg/gGg	14/25	1	2	FACETS	0.926	0.848	1	0.926	0.848	1	CLONAL	1	TRUE	1	0.331375111829757	2		538	1043	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422919	45422919	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	154	710	0	ENST00000262160.6:c.209G>T	p.Cys70Phe	p.C70F	ENST00000262160	NM_005901.5	70	tGt/tTt	2/11	1	2	FACETS	0.808	0.737	0.881	0.808	0.737	0.881	CLONAL	1	TRUE	1	0.331375111829757	2		710	1151	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610180	10610180	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	166	599	0	ENST00000171111.5:c.530A>T	p.Gln177Leu	p.Q177L	ENST00000171111	NM_203500.1	177	cAg/cTg	2/6	1	2	FACETS	0.94	0.862	1	0.94	0.862	1	CLONAL	1	TRUE	1	0.331375111829757	2		599	1066	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745169	41745169	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	169	640	1	ENST00000301178.4:c.1235C>A	p.Ala412Asp	p.A412D	ENST00000301178	NM_021913.4	412	gCt/gAt	9/20	1	2	FACETS	0.895	0.821	0.972	0.895	0.821	0.972	CLONAL	1	TRUE	1	0.331375111829757	2		641	1140	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796319	42796319	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	178	721	1	ENST00000575354.2:c.2968A>T	p.Thr990Ser	p.T990S	ENST00000575354	NM_015125.3	990	Acc/Tcc	12/20	1	2	FACETS	0.902	0.83	0.978	0.902	0.83	0.978	CLONAL	1	TRUE	1	0.331375111829757	2		722	1191	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024824	31024824	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	310	667	0	ENST00000375687.4:c.4309A>T	p.Lys1437Ter	p.K1437*	ENST00000375687	NM_015338.5	1437	Aag/Tag	13/13	0.294739095305293	3	FACETS	0.856	0.806	0.907	0.856	0.806	0.907	CLONAL	2	TRUE	1	0.331375111829757	3		667	1274	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710629	40710629	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	168	380	0	ENST00000373198.4:c.4222T>A	p.Cys1408Ser	p.C1408S	ENST00000373198	NM_133170.3	1408	Tgt/Agt	31/32	0.294739095305293	3	FACETS	0.885	0.816	0.956	0.885	0.816	0.956	CLONAL	2	TRUE	1	0.331375111829757	3		380	668	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733319	40733319	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	158	309	0	ENST00000373198.4:c.3487T>C	p.Cys1163Arg	p.C1163R	ENST00000373198	NM_133170.3	1163	Tgc/Cgc	26/32	0.294739095305293	3	FACETS	0.849	0.78	0.92	0.849	0.78	0.92	CLONAL	2	TRUE	1	0.331375111829757	3		309	655	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911497	39911497	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	216	435	0	ENST00000378444.4:c.5133A>T	p.Lys1711Asn	p.K1711N	ENST00000378444	NM_001123385.1	1711	aaA/aaT	15/15	1	1	FACETS	0.769	0.718	0.822	1	0.992	1	SUBCLONAL	2	TRUE	0	0.331375111829757	1		435	707	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222716	53222716	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	156	298	0	ENST00000375401.3:c.4220A>C	p.Asp1407Ala	p.D1407A	ENST00000375401	NM_004187.3	1407	gAc/gCc	25/26	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.331375111829757	1		298	534	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44935984	44935984	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	217	403	0	ENST00000377967.4:c.2746del	p.Asp916IlefsTer21	p.D916Ifs*21	ENST00000377967	NM_021140.2	915	ttG/tt	18/29	1	1	FACETS	0.809	0.756	0.864	1	0.993	1	CLONAL	2	TRUE	0	0.331375111829757	1		403	675	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098635	47098636	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	146	598	0	ENST00000409792.3:c.6638_6639del	p.Ser2213TyrfsTer32	p.S2213Yfs*32	ENST00000409792	NM_014159.6	2213	tCT/t	15/21	1	2	FACETS	0.832	0.758	0.91	0.832	0.758	0.91	CLONAL	1	TRUE	1	0.331375111829757	2		598	1059	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191492	185191492	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	101	348	0	ENST00000265026.3:c.2373del	p.Thr792ProfsTer32	p.T792Pfs*32	ENST00000265026	NM_004721.4	791	ggC/gg	11/14	1	2	FACETS	0.983	0.88	1	0.983	0.88	1	CLONAL	1	TRUE	1	0.331375111829757	2		348	620	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343513	343514	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0013060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	133	605	0	ENST00000262320.3:c.2160_2161del	p.Arg720SerfsTer61	p.R720Sfs*61	ENST00000262320	NM_003502.3	720	agAGcc/agcc	8/11	1	2	FACETS	0.736	0.667	0.809	0.736	0.667	0.809	SUBCLONAL	1	TRUE	1	0.331375111829757	2		605	1091	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	103	300	0				ENST00000310581	NM_198253.2	-/1132			0.311779442832063	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.452152801158394	1		300	337	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11177082	11177082	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	78	533	0	ENST00000361445.4:c.6995A>G	p.Tyr2332Cys	p.Y2332C	ENST00000361445	NM_004958.3	2332	tAt/tGt	50/58	0.431153080389779	1	FACETS	0.678	0.599	0.761	0.678	0.599	0.761	SUBCLONAL	1	TRUE	0	0.452152801158394	1		533	394	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260523	16260523	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	215	670	0	ENST00000375759.3:c.7788A>G	p.Ile2596Met	p.I2596M	ENST00000375759	NM_015001.2	2596	atA/atG	11/15	0.189393872967014	3	FACETS	1	0.98	1	0.739	0.693	0.785	INDETERMINATE	2	TRUE	0	0.452152801158394	3		670	526	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105625	27105625	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	204	566	0	ENST00000324856.7:c.5236G>T	p.Asp1746Tyr	p.D1746Y	ENST00000324856	NM_006015.4	1746	Gat/Tat	20/20	0.200619229007641	2	FACETS	0.871	0.815	0.928	0.871	0.815	0.928	INDETERMINATE	2	TRUE	0	0.452152801158394	2		566	518	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809576	36809576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	109	902	0	ENST00000373129.3:c.889G>A	p.Gly297Arg	p.G297R	ENST00000373129	NM_032017.1	297	Gga/Aga	10/12	0.200619229007641	2	FACETS	0.839	0.755	0.926	0.419	0.377	0.463	INDETERMINATE	1	TRUE	0	0.452152801158394	2		902	575	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459016	120459016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1265351543	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	142	783	0	ENST00000256646.2:c.6329G>A	p.Ser2110Asn	p.S2110N	ENST00000256646	NM_024408.3	2110	aGt/aAt	34/34	0.200619229007641	2	FACETS	0.922	0.843	1	0.461	0.421	0.503	INDETERMINATE	1	TRUE	0	0.452152801158394	2		783	681	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226551667	226551667	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	287	614	0	ENST00000366794.5:c.2763G>T	p.Leu921Phe	p.L921F	ENST00000366794	NM_001618.3	921	ttG/ttT	20/23	0.32188444927233	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.452152801158394	3		614	709	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601929	43601929	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	121	918	0	ENST00000355710.3:c.973G>C	p.Ala325Pro	p.A325P	ENST00000355710	NM_020975.4	325	Gcc/Ccc	5/20	0.342689941853034	1	FACETS	0.713	0.646	0.783	0.713	0.646	0.783	SUBCLONAL	1	TRUE	0	0.452152801158394	1		918	581	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154326	2154326	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	106	1014	0	ENST00000434045.2:c.602A>T	p.Glu201Val	p.E201V	ENST00000434045	NM_001127598.1	201	gAg/gTg	5/5	0.311779442832063	1	FACETS	0.655	0.589	0.725	0.655	0.589	0.725	SUBCLONAL	1	TRUE	0	0.452152801158394	1		1014	554	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8252027	8252027	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	243	763	0	ENST00000335790.3:c.50C>A	p.Pro17His	p.P17H	ENST00000335790	NM_002315.2	17	cCc/cAc	2/4	0.311779442832063	1	FACETS	0.752	0.709	0.795	1	0.994	1	SUBCLONAL	2	TRUE	0	0.452152801158394	1		763	553	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8252048	8252048	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	90	639	1	ENST00000335790.3:c.29T>C	p.Val10Ala	p.V10A	ENST00000335790	NM_002315.2	10	gTg/gCg	2/4	0.311779442832063	1	FACETS	0.611	0.544	0.683	0.611	0.544	0.683	SUBCLONAL	1	TRUE	0	0.452152801158394	1		640	504	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207675	102207675	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	190	312	0	ENST00000263464.3:c.1657del	p.Glu553LysfsTer15	p.E553Kfs*15	ENST00000263464	NM_001165.4	553	Gaa/aa	9/9	0.311779442832063	1	FACETS	0.769	0.72	0.818	1	0.992	1	SUBCLONAL	2	TRUE	0	0.452152801158394	1		312	423	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383277	4383277	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	192	546	0	ENST00000261254.3:c.71A>T	p.Asp24Val	p.D24V	ENST00000261254	NM_001759.3	24	gAc/gTc	1/5	0.112176454647412	4	FACETS	1	0.976	1			1	INDETERMINATE	2	TRUE	NA	0.452152801158394	4		546	559	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50482418	50482418	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	70	664	0	ENST00000394963.4:c.769G>A	p.Glu257Lys	p.E257K	ENST00000394963	NM_003076.4	257	Gaa/Aaa	6/13	0.32188444927233	3	FACETS	0.521	0.453	0.594	0.26	0.226	0.297	SUBCLONAL	1	TRUE	1	0.452152801158394	3		664	729	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238159	133238159	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148382941	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	231	691	0	ENST00000320574.5:c.2818A>G	p.Met940Val	p.M940V	ENST00000320574	NM_006231.2	940	Atg/Gtg	24/49	0.150982591565867	2	FACETS	0.824	0.773	0.875	0.824	0.773	0.875	INDETERMINATE	2	TRUE	0	0.452152801158394	2		691	620	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549505	21549505	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	63	550	0	ENST00000382592.4:c.2773-2A>T		p.X925_splice	ENST00000382592	NM_014572.2	925			0.311779442832063	1	FACETS	0.482	0.418	0.552	0.482	0.418	0.552	SUBCLONAL	1	TRUE	0	0.452152801158394	1		550	447	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912226	32912226	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	281	573	0	ENST00000380152.3:c.3734A>T	p.Glu1245Val	p.E1245V	ENST00000380152		1245	gAg/gTg	11/27	0.311779442832063	1	FACETS	0.778	0.738	0.819	1	0.995	1	SUBCLONAL	2	TRUE	0	0.452152801158394	1		573	618	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436066	110436066	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	193	1090	0	ENST00000375856.3:c.2335A>T	p.Thr779Ser	p.T779S	ENST00000375856	NM_003749.2	779	Acc/Tcc	1/2	0.121692412354704	4	FACETS	0.851	0.79	0.915	0.851	0.79	0.915	INDETERMINATE	2	TRUE	2	0.452152801158394	4		1090	728	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	69061289	69061289	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	32	222	0	ENST00000487270.1:c.1124A>T	p.Gln375Leu	p.Q375L	ENST00000487270	NM_133509.3	375	cAg/cTg	11/11	0.261837436951967	0	FACETS	0.574	0.474	0.683			1	INDETERMINATE	1	TRUE	0	0.452152801158394	0		222	135	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041765	42041765	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	139	543	0	ENST00000219905.7:c.5960A>T	p.Glu1987Val	p.E1987V	ENST00000219905	NM_001164273.1	1987	gAg/gTg	17/24	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.452152801158394	2		543	422	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724669	43724669	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	313	879	0	ENST00000382044.4:c.3398A>T	p.Gln1133Leu	p.Q1133L	ENST00000382044	NM_001141980.1	1133	cAg/cTg	17/28	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.452152801158394	2		879	939	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310213	91310213	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	99	185	0	ENST00000355112.3:c.2267A>T	p.Lys756Ile	p.K756I	ENST00000355112	NM_000057.2	756	aAa/aTa	10/22	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.452152801158394	2		185	318	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354601	91354601	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	146	460	1	ENST00000355112.3:c.4041G>T	p.Arg1347Ser	p.R1347S	ENST00000355112	NM_000057.2	1347	agG/agT	21/22	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.452152801158394	2		461	578	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858451	89858451	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	229	734	0	ENST00000389301.3:c.1109A>C	p.Glu370Ala	p.E370A	ENST00000389301	NM_000135.2	370	gAg/gCg	13/43	0.368328752103886	0	FACETS	0.653	0.618	0.688			1	SUBCLONAL	2	TRUE	0	0.452152801158394	0		734	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764146326	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	457	859	0	ENST00000269305.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000269305	NM_001126112.2	281	Gac/Aac	8/11	0.452152801158394	1	FACETS	1	0.989	1	1	0.997	1	CLONAL	2	TRUE	0	0.452152801158394	1		859	741	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657380	29657380	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	160	786	0	ENST00000356175.3:c.5613A>T	p.Leu1871Phe	p.L1871F	ENST00000356175	NM_000267.3	1871	ttA/ttT	38/57	0.325805835253502	2	FACETS	0.794	0.728	0.863	0.397	0.364	0.432	SUBCLONAL	1	TRUE	0	0.452152801158394	2		786	891	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663651	29663651	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	75	400	0	ENST00000356175.3:c.6085-2A>C		p.X2029_splice	ENST00000356175	NM_000267.3	2029			0.325805835253502	2	FACETS	0.79	0.695	0.891	0.395	0.347	0.446	SUBCLONAL	1	TRUE	0	0.452152801158394	2		400	420	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243453	41243453	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	362	720	0	ENST00000357654.3:c.4095A>T	p.Leu1365Phe	p.L1365F	ENST00000357654	NM_007294.3	1365	ttA/ttT	10/23	0.325805835253502	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.452152801158394	2		720	701	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761359	59761359	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	428	700	0	ENST00000259008.2:c.3048A>G	p.Ile1016Met	p.I1016M	ENST00000259008	NM_032043.2	1016	atA/atG	20/20	0.308816638943394	3	FACETS	0.951	0.913	0.988	0.951	0.913	0.988	CLONAL	3	TRUE	0	0.452152801158394	3		700	814	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530045	63530045	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	71	655	0	ENST00000307078.5:c.2390A>G	p.Lys797Arg	p.K797R	ENST00000307078	NM_004655.3	797	aAa/aGa	10/11	0.308816638943394	3	FACETS	0.617	0.539	0.702	0.206	0.179	0.234	SUBCLONAL	1	TRUE	0	0.452152801158394	3		655	624	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554326	63554326	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	151	949	0	ENST00000307078.5:c.413A>G	p.Tyr138Cys	p.Y138C	ENST00000307078	NM_004655.3	138	tAc/tGc	2/11	0.308816638943394	3	FACETS	0.934	0.854	1	0.311	0.284	0.34	CLONAL	1	TRUE	0	0.452152801158394	3		949	877	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78617582	78617582	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	279	459	0	ENST00000306801.3:c.320A>G	p.Gln107Arg	p.Q107R	ENST00000306801	NM_020761.2	107	cAg/cGg	3/34	0.308816638943394	3	FACETS	1	0.987	1	0.762	0.721	0.803	CLONAL	2	TRUE	0	0.452152801158394	3		459	662	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219326	5219326	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	94	828	0	ENST00000357368.4:c.3918C>A	p.Tyr1306Ter	p.Y1306*	ENST00000357368	NM_002850.3	1306	taC/taA	23/38	0.419139902365883	1	FACETS	0.654	0.584	0.728	0.654	0.584	0.728	SUBCLONAL	1	TRUE	0	0.452152801158394	1		828	492	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231411	5231411	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	209	894	0	ENST00000357368.4:c.2065T>A	p.Trp689Arg	p.W689R	ENST00000357368	NM_002850.3	689	Tgg/Agg	14/38	0.419139902365883	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.452152801158394	1		894	589	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265048	5265048	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs774081095	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	106	1001	1	ENST00000357368.4:c.539G>T	p.Ser180Ile	p.S180I	ENST00000357368	NM_002850.3	180	aGc/aTc	5/38	0.419139902365883	1	FACETS	0.676	0.608	0.747	0.676	0.608	0.747	SUBCLONAL	1	TRUE	0	0.452152801158394	1		1002	537	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152020	11152020	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	80	642	0	ENST00000358026.2:c.4304A>G	p.Glu1435Gly	p.E1435G	ENST00000358026	NM_001128849.1	1435	gAg/gGg	31/36	0.419139902365883	1	FACETS	0.681	0.603	0.764	0.681	0.603	0.764	SUBCLONAL	1	TRUE	0	0.452152801158394	1		642	402	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271708	15271708	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	122	1298	0	ENST00000263388.2:c.6731A>T	p.Tyr2244Phe	p.Y2244F	ENST00000263388	NM_000435.2	2244	tAc/tTc	33/33	0.419139902365883	1	FACETS	0.695	0.63	0.763	0.695	0.63	0.763	SUBCLONAL	1	TRUE	0	0.452152801158394	1		1298	601	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366930	15366930	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	300	974	0	ENST00000263377.2:c.1696A>C	p.Lys566Gln	p.K566Q	ENST00000263377	NM_058243.2	566	Aag/Cag	9/20	0.419139902365883	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.452152801158394	1		974	687	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943606	17943606	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	155	959	0	ENST00000458235.1:c.2483T>A	p.Leu828Gln	p.L828Q	ENST00000458235	NM_000215.3	828	cTg/cAg	18/24	0.419139902365883	1	FACETS	0.813	0.746	0.881	0.813	0.746	0.881	CLONAL	1	TRUE	0	0.452152801158394	1		959	653	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971222	18971222	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	245	828	0	ENST00000262803.5:c.2275A>T	p.Ser759Cys	p.S759C	ENST00000262803	NM_002911.3	759	Agc/Tgc	16/24	0.419139902365883	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.452152801158394	1		828	569	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223710	36223710	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	230	1134	1	ENST00000222270.7:c.6260G>T	p.Gly2087Val	p.G2087V	ENST00000222270	NM_014727.1	2087	gGg/gTg	28/37	0.419139902365883	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.452152801158394	1		1135	620	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791167	42791167	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	124	862	0	ENST00000575354.2:c.227A>T	p.Glu76Val	p.E76V	ENST00000575354	NM_015125.3	76	gAg/gTg	3/20	0.419139902365883	1	FACETS	0.709	0.643	0.777	0.709	0.643	0.777	SUBCLONAL	1	TRUE	0	0.452152801158394	1		862	599	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798999	42798999	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	297	1098	0	ENST00000575354.2:c.4483G>T	p.Ala1495Ser	p.A1495S	ENST00000575354	NM_015125.3	1495	Gcc/Tcc	20/20	0.419139902365883	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.452152801158394	1		1098	729	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905333	50905333	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1060501833	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	315	1141	0	ENST00000440232.2:c.541G>T	p.Glu181Ter	p.E181*	ENST00000440232	NM_002691.3	181	Gag/Tag	5/27	0.419139902365883	1	FACETS	0.777	0.738	0.816	1	0.995	1	SUBCLONAL	2	TRUE	0	0.452152801158394	1		1141	694	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295785	212295785	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	153	669	1	ENST00000342788.4:c.2528A>G	p.Asp843Gly	p.D843G	ENST00000342788	NM_005235.2	843	gAt/gGt	21/28	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.452152801158394	2		670	609	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561223	9561223	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs34280805	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	418	618	0	ENST00000353224.5:c.559C>A	p.Pro187Thr	p.P187T	ENST00000353224	NM_177990.2	187	Cct/Act	4/10	0.452152801158394	2	FACETS	0.941	0.908	0.974	1	0.996	1	CLONAL	3	TRUE	0	0.452152801158394	2		618	655	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419953	41419953	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	203	648	0	ENST00000373198.4:c.368A>G	p.Tyr123Cys	p.Y123C	ENST00000373198	NM_133170.3	123	tAc/tGc	3/32	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.452152801158394	2		648	657	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288486	21288486	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1233334173	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	280	693	0	ENST00000354336.3:c.731A>G	p.Gln244Arg	p.Q244R	ENST00000354336	NM_005207.3	244	cAg/cGg	2/3	0.368328752103886	0	FACETS	0.681	0.649	0.713			1	SUBCLONAL	2	TRUE	0	0.452152801158394	0		693	498	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266928	41266928	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	223	500	0	ENST00000349496.5:c.599G>T	p.Arg200Leu	p.R200L	ENST00000349496	NM_001904.3	200	cGt/cTt	5/15	0.200619229007641	2	FACETS	0.895	0.841	0.95	0.895	0.841	0.95	INDETERMINATE	2	TRUE	0	0.452152801158394	2		500	551	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058606	47058606	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	280	698	2	ENST00000409792.3:c.7672A>G	p.Lys2558Glu	p.K2558E	ENST00000409792	NM_014159.6	2558	Aaa/Gaa	21/21	0.200619229007641	2	FACETS	0.912	0.863	0.962	0.912	0.863	0.962	INDETERMINATE	2	TRUE	0	0.452152801158394	2		700	679	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73112883	73112883	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	72	377	0	ENST00000356692.5:c.479C>A	p.Pro160Gln	p.P160Q	ENST00000356692		160	cCa/cAa	6/9	0.200619229007641	2	FACETS	0.852	0.748	0.962	0.426	0.374	0.481	INDETERMINATE	1	TRUE	0	0.452152801158394	2		377	374	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967204	134967204	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	84	588	0	ENST00000398015.3:c.2543A>G	p.Asp848Gly	p.D848G	ENST00000398015	NM_004441.4	848	gAc/gGc	14/16	0.247971117722096	3	FACETS	0.827	0.732	0.928	0.276	0.244	0.31	INDETERMINATE	1	TRUE	0	0.452152801158394	3		588	551	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138431097	138431097	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	314	380	0	ENST00000289153.2:c.1352A>G	p.Gln451Arg	p.Q451R	ENST00000289153	NM_006219.2	451	cAa/cGa	8/22	0.247971117722096	3	FACETS	0.954	0.91	0.998	0.954	0.91	0.998	INDETERMINATE	3	TRUE	0	0.452152801158394	3		380	595	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447184	187447184	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	131	823	0	ENST00000232014.4:c.1009T>G	p.Ser337Ala	p.S337A	ENST00000232014	NM_001130845.1	337	Tct/Gct	5/10	0.247971117722096	3	FACETS	0.903	0.82	0.99	0.301	0.273	0.33	INDETERMINATE	1	TRUE	0	0.452152801158394	3		823	787	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956236	55956236	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	168	549	0	ENST00000263923.4:c.3079A>T	p.Arg1027Trp	p.R1027W	ENST00000263923	NM_002253.2	1027	Agg/Tgg	23/30	0.419139902365883	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.452152801158394	1		549	502	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55974015	55974015	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	201	595	0	ENST00000263923.4:c.1301C>A	p.Ser434Tyr	p.S434Y	ENST00000263923	NM_002253.2	434	tCc/tAc	10/30	0.419139902365883	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.452152801158394	1		595	544	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189926	66189926	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	161	403	0	ENST00000273854.3:c.3020G>T	p.Arg1007Leu	p.R1007L	ENST00000273854	NM_004439.5	1007	cGg/cTg	18/18	0.419139902365883	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.452152801158394	1		403	472	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509135	66509135	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	101	316	0	ENST00000273854.3:c.192G>C	p.Leu64Phe	p.L64F	ENST00000273854	NM_004439.5	64	ttG/ttC	2/18	0.419139902365883	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.452152801158394	1		316	284	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155673	106155673	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs200585520	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	96	459	0	ENST00000380013.4:c.574T>C	p.Tyr192His	p.Y192H	ENST00000380013	NM_001127208.2	192	Tac/Cac	3/11	0.315104843137216	3	FACETS	1	0.972	1	0.626	0.561	0.694	CLONAL	1	TRUE	1	0.452152801158394	3		459	416	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155863	106155863	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	197	467	0	ENST00000380013.4:c.764A>T	p.Gln255Leu	p.Q255L	ENST00000380013	NM_001127208.2	255	cAg/cTg	3/11	0.315104843137216	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.452152801158394	3		467	468	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143044472	143044472	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	69	493	0	ENST00000262992.4:c.1990C>T	p.Gln664Ter	p.Q664*	ENST00000262992	NM_001101669.1	664	Caa/Taa	18/24	0.311779442832063	1	FACETS	0.607	0.531	0.688	0.607	0.531	0.688	SUBCLONAL	1	TRUE	0	0.452152801158394	1		493	389	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254620	1254620	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	128	545	0	ENST00000310581.5:c.3158G>T	p.Gly1053Val	p.G1053V	ENST00000310581	NM_198253.2	1053	gGg/gTg	15/16	0.311779442832063	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.452152801158394	1		545	354	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295017	1295017	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	59	117	1	ENST00000310581.5:c.88C>A	p.Arg30Ser	p.R30S	ENST00000310581	NM_198253.2	30	Cgc/Agc	1/16	0.311779442832063	1	FACETS	0.795	0.706	0.885	1	0.978	1	SUBCLONAL	2	TRUE	0	0.452152801158394	1		118	127	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522528	67522528	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs886043379	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	83	226	0	ENST00000274335.5:c.25A>G	p.Arg9Gly	p.R9G	ENST00000274335		9	Aga/Gga	1/15	0.315104843137216	3	FACETS	0.792	0.708	0.881	0.792	0.708	0.881	SUBCLONAL	2	TRUE	1	0.452152801158394	3		226	284	SUCCESS
APC	324	MSKCC	GRCh37	5	112173323	112173323	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	91	260	0	ENST00000257430.4:c.2032A>C	p.Ser678Arg	p.S678R	ENST00000257430	NM_000038.5	678	Agt/Cgt	16/16	0.315104843137216	3	FACETS	0.842	0.757	0.931	0.842	0.757	0.931	CLONAL	2	TRUE	1	0.452152801158394	3		260	293	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057717	180057717	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200071734	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	188	938	0	ENST00000261937.6:c.238G>A	p.Val80Met	p.V80M	ENST00000261937	NM_182925.4	80	Gtg/Atg	3/30	0.261837436951967	0	FACETS	0.704	0.653	0.756			1	INDETERMINATE	1	TRUE	0	0.452152801158394	0		938	647	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397176	397176	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	52	415	0	ENST00000380956.4:c.561C>A	p.His187Gln	p.H187Q	ENST00000380956	NM_001195286.1	187	caC/caA	5/9	NA	2	FACETS	0.691	0.591	0.799			1	INDETERMINATE	1	TRUE	NA	0.452152801158394	2		415	333	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187533	32187533	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	235	858	0	ENST00000375023.3:c.1346G>C	p.Gly449Ala	p.G449A	ENST00000375023	NM_004557.3	449	gGc/gCc	8/30	0.452152801158394	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.452152801158394	1		858	578	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017587	112017587	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	166	674	0	ENST00000368678.4:c.926T>A	p.Leu309His	p.L309H	ENST00000368678		309	cTt/cAt	9/13	0.419139902365883	1	FACETS	0.751	0.691	0.813	0.751	0.691	0.813	SUBCLONAL	1	TRUE	0	0.452152801158394	1		674	757	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677877	117677877	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	160	532	0	ENST00000368508.3:c.4056A>G	p.Ile1352Met	p.I1352M	ENST00000368508	NM_002944.2	1352	atA/atG	25/43	0.419139902365883	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.452152801158394	1		532	417	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527805	157527805	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	214	493	0	ENST00000346085.5:c.5530A>T	p.Arg1844Trp	p.R1844W	ENST00000346085	NM_020732.3	1844	Agg/Tgg	20/20	0.200619229007641	2	FACETS	0.972	0.913	1	0.972	0.913	1	INDETERMINATE	2	TRUE	0	0.452152801158394	2		493	487	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969956	161969956	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	200	621	0	ENST00000366898.1:c.1013G>T	p.Gly338Val	p.G338V	ENST00000366898	NM_004562.2	338	gGa/gTa	9/12	0.200619229007641	2	FACETS	1	0.991	1	0.741	0.691	0.792	INDETERMINATE	1	TRUE	0	0.452152801158394	2		621	597	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526637	106526637	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	166	539	0	ENST00000359195.3:c.2930G>T	p.Gly977Val	p.G977V	ENST00000359195	NM_002649.2	977	gGc/gTc	10/11	0.200619229007641	2	FACETS	1	0.99	1	0.748	0.692	0.804	INDETERMINATE	1	TRUE	0	0.452152801158394	2		539	491	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069638	69069638	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	116	531	0	ENST00000288368.4:c.4313T>A	p.Leu1438Gln	p.L1438Q	ENST00000288368	NM_024870.2	1438	cTg/cAg	35/40	0.452152801158394	4	FACETS	1	0.94	1	0.352	0.318	0.389	CLONAL	1	TRUE	1	0.452152801158394	4		531	705	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104025	69104025	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	116	501	0	ENST00000288368.4:c.4413+2T>C		p.X1471_splice	ENST00000288368	NM_024870.2	1471			0.452152801158394	4	FACETS	1	0.974	1	0.41	0.37	0.452	CLONAL	1	TRUE	1	0.452152801158394	4		501	606	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404543	8404543	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1055567731	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	152	322	0	ENST00000356435.5:c.4204A>G	p.Ile1402Val	p.I1402V	ENST00000356435		1402	Ata/Gta	25/35	0.452152801158394	1	FACETS	0.876	0.817	0.935	1	0.992	1	CLONAL	2	TRUE	0	0.452152801158394	1		322	297	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27209159	27209159	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	347	628	0	ENST00000380036.4:c.2616A>C	p.Glu872Asp	p.E872D	ENST00000380036	NM_000459.3	872	gaA/gaC	16/23	0.33771498709165	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.452152801158394	2		628	699	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002738	37002738	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	78	597	0	ENST00000358127.4:c.511A>T	p.Ser171Cys	p.S171C	ENST00000358127	NM_001280556.1	171	Agc/Tgc	5/10	0.33771498709165	2	FACETS	0.739	0.651	0.832	0.369	0.325	0.416	SUBCLONAL	1	TRUE	0	0.452152801158394	2		597	467	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801039	135801039	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	78	459	0	ENST00000298552.3:c.298C>A	p.Gln100Lys	p.Q100K	ENST00000298552	NM_001162426.1	100	Cag/Aag	5/23	0.33771498709165	2	FACETS	0.57	0.501	0.644	0.285	0.25	0.322	SUBCLONAL	1	TRUE	0	0.452152801158394	2		459	605	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814899	139814899	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013060-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	426	881	0	ENST00000247668.2:c.892A>G	p.Met298Val	p.M298V	ENST00000247668	NM_021138.3	298	Atg/Gtg	8/11	0.33771498709165	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.452152801158394	2		881	810	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934524	9934524	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013978-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	18	421	0	ENST00000330684.3:c.1631T>C	p.Val544Ala	p.V544A	ENST00000330684	NM_001134407.1	544	gTc/gCc	7/13	0.315852075072784	3	FACETS	1	0.783	1	0.341	0.261	0.431	CLONAL	1	FALSE	0	0.461005746701589	3		421	94	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0014074-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	190	475	0	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	1	2	FACETS	0.878	0.815	0.942	0.878	0.815	0.942	CLONAL	1	TRUE	1	0.656051460775734	2		475	660	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842603	68842603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	63	679	0	ENST00000261769.5:c.539C>T	p.Ser180Phe	p.S180F	ENST00000261769	NM_004360.3	180	tCc/tTc	5/16	1	2	FACETS	0.257	0.222	0.296	0.257	0.222	0.296	SUBCLONAL	1	TRUE	1	0.75	2		679	653	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288725	33288725	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	39	455	0	ENST00000374542.5:c.827A>G	p.Asn276Ser	p.N276S	ENST00000374542	NM_001141970.1	276	aAc/aGc	3/8	1	2	FACETS	0.196	0.162	0.234	0.196	0.162	0.234	SUBCLONAL	1	TRUE	1	0.75	2		455	530	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0014232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	112	435	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.201839328187058	2		435	877	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578525	7578525	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519976	NA	P-0014232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1453	287	835	0	ENST00000269305.4:c.405C>G	p.Cys135Trp	p.C135W	ENST00000269305	NM_001126112.2	135	tgC/tgG	5/11	0.158274778491959	2	FACETS	0.817	0.766	0.87	0.817	0.766	0.87	CLONAL	2	TRUE	0	0.201839328187058	2		835	1740	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212484000	212484000	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1369649105	NA	P-0014232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	63	277	0	ENST00000342788.4:c.2203G>T	p.Gly735Cys	p.G735C	ENST00000342788	NM_005235.2	735	Ggt/Tgt	19/28	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.201839328187058	2		277	618	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677762	47677762	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	88	363	0	ENST00000347630.2:c.1103G>T	p.Arg368Leu	p.R368L	ENST00000347630	NM_001007230.1	368	cGc/cTc	11/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.201839328187058	2		363	761	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610641	52610641	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	89	369	1	ENST00000394830.3:c.3532G>T	p.Glu1178Ter	p.E1178*	ENST00000394830	NM_018313.4	1178	Gag/Tag	23/30	0.201839328187058	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.201839328187058	1		370	727	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149452957	149452957	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	80	448	0	ENST00000286301.3:c.989G>C	p.Gly330Ala	p.G330A	ENST00000286301	NM_005211.3	330	gGc/gCc	7/22	1	2	FACETS	0.866	0.761	0.98	0.866	0.761	0.98	CLONAL	1	TRUE	1	0.201839328187058	2		448	915	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577077	7577077	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs748891343	NA	P-0014595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	393	858	0	ENST00000269305.4:c.861G>C	p.Glu287Asp	p.E287D	ENST00000269305	NM_001126112.2	287	gaG/gaC	8/11	0.669461946075824	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.758869926802073	1		858	596	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	84	407	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.184139250545556	4	FACETS	0.688	0.606	0.775	0.344	0.303	0.388	INDETERMINATE	1	TRUE	2	0.402549244594261	4		407	851	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0014810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	79	629	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.112787470048848	5	FACETS	0.864	0.759	0.976	0.288	0.253	0.326	INDETERMINATE	1	TRUE	2	0.402549244594261	5		630	729	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37666011	37666011	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	87	312	0	ENST00000447079.4:c.2663A>G	p.Glu888Gly	p.E888G	ENST00000447079	NM_015083.1	888	gAg/gGg	7/14	0.402549244594261	7	FACETS	0.732	0.646	0.825			1	SUBCLONAL	1	TRUE	NA	0.402549244594261	7		312	1184	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781504	NA	P-0015058-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	231	736	0	ENST00000269305.4:c.314G>A	p.Gly105Asp	p.G105D	ENST00000269305	NM_001126112.2	105	gGc/gAc	4/11	0.61528360313919	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.628074126511206	1		736	490	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0015058-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	49	267	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.628074126511206	1	FACETS	0.714	0.617	0.815	0.714	0.617	0.815	SUBCLONAL	1	TRUE	0	0.628074126511206	1		267	150	SUCCESS
APC	324	MSKCC	GRCh37	5	112176863	112176863	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1270783041	NA	P-0015058-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	89	569	1	ENST00000257430.4:c.5572C>T	p.Arg1858Ter	p.R1858*	ENST00000257430	NM_000038.5	1858	Cga/Tga	16/16	0.628074126511206	1	FACETS	0.967	0.877	1	0.967	0.877	1	CLONAL	1	TRUE	0	0.628074126511206	1		570	201	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509479	46509479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139622524	NA	P-0015058-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	330	366	3	ENST00000262741.5:c.1252C>T	p.Pro418Ser	p.P418S	ENST00000262741	NM_003629.3	418	Ccc/Tcc	10/10	0.587468789761565	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	2	0.628074126511206	4		369	742	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229398	98229398	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015058-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	73	220	0	ENST00000331920.6:c.2560G>T	p.Gly854Ter	p.G854*	ENST00000331920	NM_000264.3	854	Gga/Tga	15/24	0.587468789761565	4	FACETS	0.953	0.838	1	0.477	0.419	0.538	CLONAL	1	TRUE	2	0.628074126511206	4		220	397	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0015875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	124	210	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.359222414591806	2		210	547	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0015875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	208	582	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.359222414591806	1	FACETS	0.98	0.91	1	0.98	0.91	1	CLONAL	1	TRUE	0	0.359222414591806	1		582	969	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519896	NA	P-0015875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	139	447	0	ENST00000281708.4:c.1514G>T	p.Arg505Leu	p.R505L	ENST00000281708	NM_033632.3	505	cGc/cTc	10/12	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.359222414591806	2		447	651	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120478168	120478168	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	121	359	0	ENST00000256646.2:c.3582G>T	p.Gln1194His	p.Q1194H	ENST00000256646	NM_024408.3	1194	caG/caT	22/34	1	2	FACETS	0.957	0.866	1	0.957	0.866	1	CLONAL	1	TRUE	1	0.359222414591806	2		359	704	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2218080	2218080	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	259	705	0	ENST00000326181.6:c.142G>A	p.Asp48Asn	p.D48N	ENST00000326181	NM_032271.2	48	Gac/Aac	4/21	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.359222414591806	2		705	1126	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0016540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	349	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.686994550745874	2		336	1016	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149957	202149958	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	239	445	0	ENST00000358485.4:c.1400dup	p.Asn467LysfsTer31	p.N467Kfs*31	ENST00000358485	NM_001080125.1	466	-/A	8/9	1	2	FACETS	0.986	0.925	1	0.986	0.925	1	CLONAL	1	TRUE	1	0.686994550745874	2		445	706	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	137	535	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.25	2		535	976	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032474	12032474	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	81	356	0	ENST00000353533.5:c.910C>T	p.Arg304Ter	p.R304*	ENST00000353533	NM_003010.3	304	Cga/Tga	9/11	0.3	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.25	1		356	529	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692794	89692794	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121909238	NA	P-0017045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	86	337	0	ENST00000371953.3:c.278A>G	p.His93Arg	p.H93R	ENST00000371953	NM_000314.4	93	cAt/cGt	5/9	1	2	FACETS	0.814	0.719	0.916	0.814	0.719	0.916	CLONAL	1	TRUE	1	0.25	2		337	845	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38064140	38064140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	160	537	0	ENST00000250448.2:c.38G>A	p.Ser13Asn	p.S13N	ENST00000250448	NM_004496.3	13	aGc/aAc	1/2	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.25	2		537	1168	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530336	187530336	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0017045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	64	285	0	ENST00000441802.2:c.10206+1G>C		p.X3402_splice	ENST00000441802	NM_005245.3	3402			1	2	FACETS	0.871	0.754	0.997	0.871	0.754	0.997	CLONAL	1	TRUE	1	0.25	2		285	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0017593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	289	677	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.851391245816213	1	FACETS	0.96	0.923	0.996	0.96	0.923	0.996	CLONAL	1	TRUE	0	0.851391245816213	1		680	406	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509436	106509436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200175951	NA	P-0017593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	471	715	0	ENST00000359195.3:c.1430G>A	p.Arg477His	p.R477H	ENST00000359195	NM_002649.2	477	cGt/cAt	2/11	1	2	FACETS	0.905	0.866	0.944	0.905	0.866	0.944	CLONAL	1	TRUE	1	0.851391245816213	2		715	1223	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625456	69625456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781938977	NA	P-0017593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	443	599	0	ENST00000334134.2:c.337G>A	p.Ala113Thr	p.A113T	ENST00000334134	NM_005247.2	113	Gcc/Acc	3/3	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.851391245816213	2		599	1022	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411678	63411678	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	531	940	0	ENST00000330258.3:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000330258	NM_152424.3	497	Cga/Tga	2/2	1	2	FACETS	0.965	0.927	1	0.965	0.927	1	CLONAL	1	TRUE	1	0.851391245816213	2		940	1293	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622074	43622074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200989078	NA	P-0017593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	410	594	0	ENST00000355710.3:c.3091G>A	p.Asp1031Asn	p.D1031N	ENST00000355710	NM_020975.4	1031	Gac/Aac	19/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.851391245816213	2		594	935	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117888	70117888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	352	420	1	ENST00000245479.2:c.356C>T	p.Ala119Val	p.A119V	ENST00000245479	NM_000346.3	119	gCg/gTg	1/3	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.851391245816213	2		421	708	SUCCESS
APC	324	MSKCC	GRCh37	5	112128158	112128159	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	254	449	0	ENST00000257430.4:c.663dup	p.Gln222SerfsTer30	p.Q222Sfs*30	ENST00000257430	NM_000038.5	221	att/aTtt	7/16	0.851391245816213	1	FACETS	0.919	0.879	0.957	0.919	0.879	0.957	CLONAL	1	TRUE	0	0.851391245816213	1		449	373	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372301	55372301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1721	320	404	1	ENST00000297316.4:c.991G>A	p.Gly331Arg	p.G331R	ENST00000297316	NM_022454.3	331	Gga/Aga	2/2	0.851391245816213	6	FACETS	0.995	0.936	1	0.199	0.187	0.212	CLONAL	1	TRUE	1	0.851391245816213	6		405	2041	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391112	139391112	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	190	308	0	ENST00000277541.6:c.7079C>A	p.Ser2360Tyr	p.S2360Y	ENST00000277541	NM_017617.3	2360	tCc/tAc	34/34	1	2	FACETS	0.985	0.921	1	0.985	0.921	1	CLONAL	1	TRUE	1	0.851391245816213	2		308	453	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0017881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	57	326	1	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.605749511872393	3	FACETS	0.823	0.723	0.925	0.548	0.482	0.617	CLONAL	2	TRUE	0	0.611301594961728	3		327	148	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0017881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	179	945	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	0.605749511872393	3	FACETS	0.878	0.81	0.949	0.293	0.27	0.317	CLONAL	1	TRUE	0	0.611301594961728	3		945	871	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0017881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	127	123	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.934	0.852	1	0.934	0.852	1	CLONAL	1	TRUE	1	0.611301594961728	2		123	445	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844776	156844776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1292790967	NA	P-0017881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	223	844	1	ENST00000524377.1:c.1330C>T	p.Arg444Trp	p.R444W	ENST00000524377	NM_002529.3	444	Cgg/Tgg	11/17	1	2	FACETS	0.921	0.86	0.984	0.921	0.86	0.984	CLONAL	1	TRUE	1	0.611301594961728	2		845	792	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270120	66270120	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	176	798	0	ENST00000273854.3:c.1762G>T	p.Val588Leu	p.V588L	ENST00000273854	NM_004439.5	588	Gtg/Ttg	8/18	1	2	FACETS	0.775	0.716	0.837	0.775	0.716	0.837	SUBCLONAL	1	TRUE	1	0.611301594961728	2		798	743	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591133	67591154	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ACGAGAGACCAATACTTGATGT	ACGAGAGACCAATACTTGATGT	-	novel	NA	P-0017881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	27	568	0	ENST00000274335.5:c.1727_1745+3del		p.X576_splice	ENST00000274335		576		12/15	1	2	FACETS	0.499	0.401	0.609	0.499	0.401	0.609	SUBCLONAL	1	TRUE	1	0.611301594961728	2		568	177	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018200-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	44	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.721	0.61	0.843	0.721	0.61	0.843	SUBCLONAL	1	TRUE	1	0.489917487234257	2		326	249	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0018200-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	112	534	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.981	0.888	1	0.981	0.888	1	CLONAL	1	TRUE	1	0.489917487234257	2		535	466	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466378	120466378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779822957	NA	P-0018200-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	141	707	0	ENST00000256646.2:c.4741C>T	p.Arg1581Trp	p.R1581W	ENST00000256646	NM_024408.3	1581	Cgg/Tgg	26/34	1	2	FACETS	0.937	0.857	1	0.937	0.857	1	CLONAL	1	TRUE	1	0.489917487234257	2		707	614	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902211	50902211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs554554906	NA	P-0018200-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	135	714	0	ENST00000440232.2:c.103G>A	p.Glu35Lys	p.E35K	ENST00000440232	NM_002691.3	35	Gag/Aag	2/27	0.141200237342659	0	FACETS	0.557	0.509	0.606			1	INDETERMINATE	1	TRUE	0	0.489917487234257	0		714	505	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732957	30732957	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504421	NA	P-0018200-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	328	686	0	ENST00000295754.5:c.1570G>A	p.Asp524Asn	p.D524N	ENST00000295754	NM_003242.5	524	Gac/Aac	7/7	0.489917487234257	2	FACETS	0.973	0.927	1	0.973	0.927	1	CLONAL	2	TRUE	0	0.489917487234257	2		686	688	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201765	66201765	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs878919973	NA	P-0018200-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	135	577	0	ENST00000273854.3:c.2737G>T	p.Asp913Tyr	p.D913Y	ENST00000273854	NM_004439.5	913	Gat/Tat	16/18	1	2	FACETS	0.986	0.9	1	0.986	0.9	1	CLONAL	1	TRUE	1	0.489917487234257	2		577	559	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915167	131915167	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018200-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	75	173	0	ENST00000265335.6:c.524A>C	p.Lys175Thr	p.K175T	ENST00000265335		175	aAg/aCg	4/25	0.489917487234257	2	FACETS	0.994	0.897	1	0.994	0.897	1	CLONAL	2	TRUE	0	0.489917487234257	2		173	154	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367293	50367294	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0018200-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	143	617	0	ENST00000331340.3:c.100_101delinsAA	p.Pro34Asn	p.P34N	ENST00000331340	NM_006060.4	34	CCc/AAc	3/8	1	2	FACETS	0.995	0.911	1	0.995	0.911	1	CLONAL	1	TRUE	1	0.489917487234257	2		617	587	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133747527	133747528	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0018200-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	83	356	0	ENST00000318560.5:c.834_835delinsTT	p.Met278_Glu279delinsIleTer	p.M278_E279delinsI*	ENST00000318560	NM_005157.4	278	atGGag/atTTag	5/11	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.489917487234257	2		356	315	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0020130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	45	972	1	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.188728994679748	1	FACETS	0.812	0.682	0.956	0.812	0.682	0.956	CLONAL	1	TRUE	0	0.188728994679748	1		973	532	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115435	115115437	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	rs1319662056	NA	P-0020130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	31	951	0	ENST00000257566.3:c.889_891del	p.Asn297del	p.N297del	ENST00000257566	NM_016569.3	297	AAC/-	5/8	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.188728994679748	2		951	244	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644856	67644856	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	56	915	0	ENST00000264010.4:c.124del	p.Gln42ArgfsTer20	p.Q42Rfs*20	ENST00000264010	NM_006565.3	41	Ccc/cc	3/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.188728994679748	2		915	454	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120674	115120675	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	52	1171	1	ENST00000257566.3:c.331_332insT	p.Glu111ValfsTer27	p.E111Vfs*27	ENST00000257566	NM_016569.3	111	gaa/gTaa	1/8	1	2	FACETS	0.991	0.844	1	0.991	0.844	1	CLONAL	1	TRUE	1	0.188728994679748	2		1172	556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0020297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	23	683	2	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		685	591	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88672142	88672142	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0020297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	188	721	0	ENST00000372037.3:c.675+1G>T		p.X225_splice	ENST00000372037	NM_004329.2	225			0.325096524377404	3	FACETS		NA	1			1	NA	NA	TRUE	NA	NA	3		721	475	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233750	233750	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs746165168	NA	P-0020297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	78	444	0	ENST00000264932.6:c.1054C>T	p.Arg352Ter	p.R352*	ENST00000264932	NM_004168.2	352	Cga/Tga	8/15	0.325096524377404	0	FACETS		NA	1			1	NA	NA	TRUE	0	NA	0		444	333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0020609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	68	973	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.166574552293327	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		973	895	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0020609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	67	463	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		463	751	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970896	21970900	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CTCAC	CTCAC	GTGA	novel	NA	P-0020609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	79	705	2	ENST00000304494.5:c.457+1_457+5delinsTCAC		p.X153_splice	ENST00000304494	NM_000077.4	153			0.166574552293327	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		707	878	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0021000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	96	454	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.921	0.835	1	0.921	0.835	1	CLONAL	1	TRUE	1	0.861638862612989	2		454	242	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405936	49405936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	26	764	2	ENST00000418115.1:c.202C>T	p.Arg68Cys	p.R68C	ENST00000418115	NM_001664.2	68	Cgc/Tgc	3/5	0.698712395260025	3	FACETS	0.174	0.137	0.217			1	SUBCLONAL	1	TRUE	NA	0.861638862612989	3		766	495	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801805	3801806	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0021000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	77	776	1	ENST00000262367.5:c.3699_3700dup	p.Tyr1234CysfsTer17	p.Y1234Cfs*17	ENST00000262367	NM_004380.2	1234	tat/tGTat	20/31	0.130380547453239	4	FACETS	0.844	0.746	0.95	0.422	0.373	0.475	INDETERMINATE	1	TRUE	2	0.861638862612989	4		777	394	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	1308	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.825169643014826	8	FACETS	1	0.984	1	0.859	0.844	0.875	CLONAL	6	TRUE	1	0.825169643014826	8		326	1832	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543545	9543545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	195	697	0	ENST00000353224.5:c.1609C>T	p.His537Tyr	p.H537Y	ENST00000353224	NM_177990.2	537	Cac/Tac	6/10	0.825169643014826	3	FACETS	0.959	0.891	1	0.48	0.445	0.515	CLONAL	1	TRUE	1	0.825169643014826	3		697	696	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945127	44945127	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	135	339	0	ENST00000377967.4:c.3451A>G	p.Asn1151Asp	p.N1151D	ENST00000377967	NM_021140.2	1151	Aac/Gac	24/29	0.72319592962445	2	FACETS	0.951	0.876	1			1	CLONAL	1	TRUE	NA	0.825169643014826	2		339	344	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0021836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	241	567	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	1	2	FACETS	0.933	0.876	0.991	0.933	0.876	0.991	CLONAL	1	FALSE	1	0.750870858287156	2		567	688	SUCCESS
APC	324	MSKCC	GRCh37	5	112176863	112176863	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1270783041	NA	P-0022143-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	175	569	1	ENST00000257430.4:c.5572C>T	p.Arg1858Ter	p.R1858*	ENST00000257430	NM_000038.5	1858	Cga/Tga	16/16	0.836417603004432	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.849868402662551	1		570	231	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577524	7577524	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022143-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	922	799	0	ENST00000269305.4:c.757A>C	p.Thr253Pro	p.T253P	ENST00000269305	NM_001126112.2	253	Acc/Ccc	7/11	0.849868402662551	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.849868402662551	2		799	1052	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556727	41556727	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0022143-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	147	472	4	ENST00000263253.7:c.3671+1G>A		p.X1224_splice	ENST00000263253	NM_001429.3	1224			0.849868402662551	2	FACETS	0.918	0.848	0.988	0.459	0.424	0.494	CLONAL	1	TRUE	0	0.849868402662551	2		476	377	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335690	81335690	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022143-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	325	663	1	ENST00000222390.5:c.1670G>T	p.Gly557Val	p.G557V	ENST00000222390	NM_000601.4	557	gGa/gTa	15/18	0.672125867144759	6	FACETS	0.817	0.771	0.864			1	CLONAL	2	TRUE	NA	0.849868402662551	6		664	1264	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604648	48604649	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGTGTTG	novel	NA	P-0022143-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	210	369	0	ENST00000342988.3:c.1471_1477dup	p.Asp493GlyfsTer3	p.D493Gfs*3	ENST00000342988	NM_005359.5	490	-/GGTGTTG	12/12	0.849868402662551	1	FACETS	0.885	0.842	0.927	0.885	0.842	0.927	CLONAL	1	TRUE	0	0.849868402662551	1		369	321	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349966	15349966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022143-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1307	572	829	2	ENST00000263377.2:c.3686G>A	p.Arg1229His	p.R1229H	ENST00000263377	NM_058243.2	1229	cGc/cAc	18/20	0.79936645330251	3	FACETS	1	0.974	1	0.51	0.489	0.532	CLONAL	1	TRUE	1	0.849868402662551	3		831	1879	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192454	138192454	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1324617507	NA	P-0022143-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	155	380	0	ENST00000237289.4:c.90T>A	p.Phe30Leu	p.F30L	ENST00000237289	NM_001270507.1	30	ttT/ttA	2/9	0.84096138931829	3	FACETS	0.907	0.835	0.982	0.454	0.417	0.491	CLONAL	1	TRUE	1	0.849868402662551	3		380	573	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0022951-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	73	571	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.815	0.711	0.927	1	0.977	1	CLONAL	2	TRUE	1	0.109	2		571	822	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0022951-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	143	631	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	0.873	0.795	0.955	1	0.992	1	CLONAL	3	TRUE	1	0.109	2		631	1002	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307913	11307913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557482604	NA	P-0022951-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	68	611	1	ENST00000361445.4:c.1079G>A	p.Arg360Gln	p.R360Q	ENST00000361445	NM_004958.3	360	cGg/cAg	7/58	NA	2	FACETS	0.767	0.666	0.877			1	INDETERMINATE	2	TRUE	NA	0.109	2		612	813	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572651	64572651	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022951-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	111	576	0	ENST00000312049.6:c.1205C>A	p.Ser402Tyr	p.S402Y	ENST00000312049	NM_130799.2	402	tCc/tAc	9/10	1	2	FACETS	1	0.952	1	1	0.989	1	CLONAL	2	TRUE	1	0.109	2		576	924	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56367665	56367673	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTCACAGA	TTTCACAGA	-	novel	NA	P-0022951-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	30	203	0	ENST00000348428.3:c.499-6_501del		p.X167_splice	ENST00000348428	NM_006785.3	167		4/17	1	2	FACETS	0.76	0.613	0.927	1	0.941	1	CLONAL	2	TRUE	1	0.109	2		203	362	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0023280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	537	622	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.778811082181598	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.778811082181598	3		623	609	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0023280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	165	316	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.778811082181598	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.778811082181598	3		316	291	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0023280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	241	572	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	0.778811082181598	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.778811082181598	2		572	289	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338696	70338698	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0023280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	188	371	0	ENST00000374080.3:c.94_96del	p.Lys32del	p.K32del	ENST00000374080		31	cAGAag/cag	1/45	0.754882947208693	2	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.778811082181598	2		371	220	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068247	30068247	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	104	723	0	ENST00000331968.5:c.2152G>T	p.Asp718Tyr	p.D718Y	ENST00000331968	NM_002742.2	718	Gat/Tat	15/18	0.778811082181598	6	FACETS	0.972	0.871	1	0.243	0.217	0.27	CLONAL	1	TRUE	2	0.778811082181598	6		723	703	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133760	55133760	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8732	4224	772	5	ENST00000257290.5:c.973G>A	p.Glu325Lys	p.E325K	ENST00000257290	NM_006206.4	325	Gaa/Aaa	7/23	0.778811082181598	62	FACETS	1	0.994	1			1	CLONAL	20	TRUE	NA	0.778811082181598	62		777	12956	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0023364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	154	764	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.219980441470347	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	0	0.245884760224364	2		765	610	SUCCESS
APC	324	MSKCC	GRCh37	5	112137081	112137081	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1554076225	NA	P-0023364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	89	340	1	ENST00000257430.4:c.834+1G>A		p.X278_splice	ENST00000257430	NM_000038.5	278			0.245884760224364	3	FACETS	0.847	0.759	0.939	0.847	0.759	0.939	CLONAL	3	TRUE	0	0.245884760224364	3		341	320	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64126884	64126886	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0023364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	159	762	2	ENST00000334205.4:c.91_93del	p.Glu31del	p.E31del	ENST00000334205	NM_003942.2	30	gtGGAg/gtg	2/17	0.102112317652174	4	FACETS	0.949	0.87	1	0.949	0.87	1	INDETERMINATE	2	TRUE	2	0.245884760224364	4		764	849	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348565	89348565	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	213	1000	3	ENST00000301030.4:c.4385G>T	p.Arg1462Ile	p.R1462I	ENST00000301030	NM_001256183.1	1462	aGa/aTa	9/13	0.125061735195259	5	FACETS	1	0.948	1	0.684	0.634	0.735	INDETERMINATE	2	TRUE	2	0.245884760224364	5		1003	1156	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247112	153247255	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TATGATTCATCAGGAGAGCATTTAAGGGAGAGATAAGAGATCTTACCTGTAATGAATAGACTCTATTAGTATGCCCCTGCAACGTGTGTAGACAGGTTTCAGTCTCTGGATCCCACACCTTTACCATAAAATCATATGCTCCAC	TATGATTCATCAGGAGAGCATTTAAGGGAGAGATAAGAGATCTTACCTGTAATGAATAGACTCTATTAGTATGCCCCTGCAACGTGTGTAGACAGGTTTCAGTCTCTGGATCCCACACCTTTACCATAAAATCATATGCTCCAC	-	novel	NA	P-0023364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	16	103	0	ENST00000281708.4:c.1547_1644+46del		p.X516_splice	ENST00000281708	NM_033632.3	516		10/12	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.245884760224364	2		103	99	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	85	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.347212656394074	2		326	408	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0024388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	80	210	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.347212656394074	2		210	399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0024388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	124	698	2	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.347212656394074	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.347212656394074	1		700	543	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0024388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	66	469	1	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.99	0.864	1	0.99	0.864	1	CLONAL	1	TRUE	1	0.347212656394074	2		470	384	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074435	8074435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs980250925	NA	P-0024388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	24	252	2	ENST00000377482.5:c.224C>T	p.Pro75Leu	p.P75L	ENST00000377482	NM_018948.3	75	cCg/cTg	4/4	0.267949370062411	1	FACETS	0.438	0.344	0.545	0.438	0.344	0.545	SUBCLONAL	1	TRUE	0	0.347212656394074	1		254	261	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275439	38275439	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	125	676	0	ENST00000425967.3:c.1594G>T	p.Asp532Tyr	p.D532Y	ENST00000425967	NM_001174067.1	532	Gac/Tac	12/19	1	2	FACETS	0.889	0.805	0.978	0.889	0.805	0.978	CLONAL	1	TRUE	1	0.347212656394074	2		676	810	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223466	53223466	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	70	596	0	ENST00000375401.3:c.3893C>G	p.Ser1298Cys	p.S1298C	ENST00000375401	NM_004187.3	1298	tCt/tGt	23/26	0.347212656394074	1	FACETS	0.637	0.556	0.724	0.637	0.556	0.724	SUBCLONAL	1	TRUE	0	0.347212656394074	1		596	523	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0024521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	212	425	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.210046989092325	2	FACETS	1	0.969	1	0.533	0.497	0.57	INDETERMINATE	1	TRUE	0	0.544255130500375	2		426	731	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0024521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	273	770	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.484107237267195	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.544255130500375	1		770	553	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841252	15841252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1569074760	NA	P-0024521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	34	416	1	ENST00000307771.7:c.1336C>T	p.Arg446Trp	p.R446W	ENST00000307771	NM_005089.3	446	Cgg/Tgg	11/11	0.544255130500375	1	FACETS	0.271	0.222	0.327	0.271	0.222	0.327	SUBCLONAL	1	TRUE	0	0.544255130500375	1		417	335	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129867	55129867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373126818	NA	P-0024521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	125	709	0	ENST00000257290.5:c.401C>T	p.Thr134Met	p.T134M	ENST00000257290	NM_006206.4	134	aCg/aTg	4/23	0.544255130500375	1	FACETS	0.57	0.517	0.624	0.57	0.517	0.624	SUBCLONAL	1	TRUE	0	0.544255130500375	1		709	587	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356268	66356268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	112	652	0	ENST00000273854.3:c.1229G>A	p.Gly410Asp	p.G410D	ENST00000273854	NM_004439.5	410	gGt/gAt	5/18	0.544255130500375	1	FACETS	0.461	0.415	0.509	0.461	0.415	0.509	SUBCLONAL	1	TRUE	0	0.544255130500375	1		652	650	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	230998	230998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs940845256	NA	P-0024521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	67	817	1	ENST00000264932.6:c.778G>A	p.Gly260Arg	p.G260R	ENST00000264932	NM_004168.2	260	Ggg/Agg	7/15	NA	2	FACETS	0.27	0.234	0.309			1	INDETERMINATE	1	TRUE	NA	0.544255130500375	2		818	912	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123026600	123026600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	170	797	0	ENST00000355640.3:c.1076C>T	p.Thr359Ile	p.T359I	ENST00000355640		359	aCa/aTa	5/7	0.208099500192604	0	FACETS	0.417	0.385	0.451			1	INDETERMINATE	1	TRUE	0	0.544255130500375	0		797	682	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	307	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.687838456698812	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.687838456698812	1		326	565	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829066	128829066	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs41304185	NA	P-0024835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	13	9	0	ENST00000249373.3:c.74A>G	p.Asp25Gly	p.D25G	ENST00000249373	NM_005631.4	25	gAc/gGc	1/12	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.687838456698812	2		9	28	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0024835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	410	622	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.687838456698812	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.687838456698812	1		623	751	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076745	72076745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	338	644	1	ENST00000357731.5:c.752C>T	p.Pro251Leu	p.P251L	ENST00000357731	NM_173808.2	251	cCg/cTg	5/7	0.313347401776153	1	FACETS	0.699	0.663	0.735	0.699	0.663	0.735	INDETERMINATE	1	TRUE	0	0.687838456698812	1		645	923	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222730	5222730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374875451	NA	P-0024835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	319	433	1	ENST00000357368.4:c.3073G>A	p.Val1025Ile	p.V1025I	ENST00000357368	NM_002850.3	1025	Gtc/Atc	18/38	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.687838456698812	2		434	812	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816191	89816191	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1957	388	580	0	ENST00000389301.3:c.3186del	p.Trp1063GlyfsTer14	p.W1063Gfs*14	ENST00000389301	NM_000135.2	1062	ggG/gg	32/43	0.678164503976003	5	FACETS	0.977	0.924	1	0.244	0.231	0.258	CLONAL	1	TRUE	1	0.687838456698812	5		580	2345	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0025327-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	192	410	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	0.2738022346814	4	FACETS	1	0.991	1	0.745	0.694	0.798	INDETERMINATE	1	TRUE	2	0.804195136600988	4		410	578	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0025327-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	713	684	1	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	0.794820197354223	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	0	0.804195136600988	3		685	825	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843495	3843495	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1384496494	NA	P-0025327-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	367	515	0	ENST00000262367.5:c.1108C>G	p.Arg370Gly	p.R370G	ENST00000262367	NM_004380.2	370	Cga/Gga	4/31	0.366076912720422	4	FACETS	1	0.966	1	1	0.966	1	INDETERMINATE	2	TRUE	2	0.804195136600988	4		515	811	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69011953	69011953	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025327-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	238	598	0	ENST00000288368.4:c.2590G>C	p.Val864Leu	p.V864L	ENST00000288368	NM_024870.2	864	Gta/Cta	23/40	0.573777936257712	4	FACETS	1	0.946	1	0.338	0.316	0.362	CLONAL	1	TRUE	1	0.804195136600988	4		598	1052	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628340	187628340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536104649	NA	P-0025396-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	79	583	0	ENST00000441802.2:c.2642G>A	p.Arg881His	p.R881H	ENST00000441802	NM_005245.3	881	cGc/cAc	2/27	0.216859158133646	3	FACETS	0.668	0.588	0.754	0.223	0.196	0.252	INDETERMINATE	1	TRUE	0	0.449063756136886	3		583	645	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780830	9780830	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1185305370	NA	P-0025396-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	105	532	2	ENST00000377346.4:c.1552C>T	p.Arg518Trp	p.R518W	ENST00000377346	NM_005026.3	518	Cgg/Tgg	13/24	0.409495135540012	3	FACETS	1	0.96	1			1	CLONAL	1	TRUE	NA	0.449063756136886	3		534	506	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305329	39305329	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025396-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	55	490	0	ENST00000373001.3:c.1096G>T	p.Val366Phe	p.V366F	ENST00000373001	NM_022157.3	366	Gtt/Ttt	7/7	0.449063756136886	3	FACETS	0.51	0.436	0.591	0.255	0.218	0.296	SUBCLONAL	1	TRUE	1	0.449063756136886	3		490	588	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690405	117690405	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0025396-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	50	375	0	ENST00000369458.3:c.725-1G>T		p.X242_splice	ENST00000369458	NM_024626.3	242			0.217727223752699	2	FACETS	0.599	0.509	0.696	0.299	0.254	0.348	INDETERMINATE	1	TRUE	0	0.449063756136886	2		375	372	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464379	464379	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025396-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	51	546	1	ENST00000399788.2:c.815C>T	p.Ser272Leu	p.S272L	ENST00000399788	NM_001042603.1	272	tCa/tTa	7/28	1	2	FACETS	0.367	0.311	0.428	0.367	0.311	0.428	SUBCLONAL	1	TRUE	1	0.449063756136886	2		547	619	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428259	49428259	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025396-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	65	530	0	ENST00000301067.7:c.10441G>A	p.Glu3481Lys	p.E3481K	ENST00000301067	NM_003482.3	3481	Gag/Aag	37/54	0.367723618502424	3	FACETS	0.639	0.554	0.73			1	SUBCLONAL	1	TRUE	NA	0.449063756136886	3		530	555	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614571	38614571	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025396-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	57	580	0	ENST00000299084.4:c.337G>C	p.Asp113His	p.D113H	ENST00000299084	NM_152594.2	113	Gat/Cat	3/7	0.449063756136886	3	FACETS	0.516	0.442	0.596	0.258	0.221	0.298	SUBCLONAL	1	TRUE	1	0.449063756136886	3		580	603	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292893	91292893	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775197136	NA	P-0025396-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	75	551	0	ENST00000355112.3:c.395G>A	p.Arg132Gln	p.R132Q	ENST00000355112	NM_000057.2	132	cGg/cAg	3/22	0.449063756136886	3	FACETS	0.579	0.507	0.657	0.29	0.253	0.329	SUBCLONAL	1	TRUE	1	0.449063756136886	3		551	706	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646346	3646346	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1202254236	NA	P-0025396-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	53	663	0	ENST00000294008.3:c.1732G>C	p.Glu578Gln	p.E578Q	ENST00000294008	NM_032444.2	578	Gag/Cag	8/15	0.449063756136886	5	FACETS	0.628	0.535	0.73	0.157	0.133	0.183	SUBCLONAL	1	TRUE	1	0.449063756136886	5		663	629	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916146	9916146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025396-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	50	472	0	ENST00000330684.3:c.2143G>A	p.Asp715Asn	p.D715N	ENST00000330684	NM_001134407.1	715	Gac/Aac	10/13	0.449063756136886	5	FACETS	0.624	0.529	0.729	0.156	0.132	0.183	SUBCLONAL	1	TRUE	1	0.449063756136886	5		472	597	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244808	41244808	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs80357419	NA	P-0025396-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	85	697	0	ENST00000357654.3:c.2740G>C	p.Glu914Gln	p.E914Q	ENST00000357654	NM_007294.3	914	Gag/Cag	10/23	NA	2	FACETS	0.536	0.474	0.603			1	INDETERMINATE	1	TRUE	NA	0.449063756136886	2		697	706	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216751	2216751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025396-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	40	525	0	ENST00000398665.3:c.2395G>A	p.Glu799Lys	p.E799K	ENST00000398665	NM_032482.2	799	Gag/Aag	20/28	0.217727223752699	2	FACETS	0.409	0.339	0.485	0.204	0.169	0.243	INDETERMINATE	1	TRUE	0	0.449063756136886	2		525	436	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216640	36216640	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025396-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	65	553	0	ENST00000222270.7:c.3806A>G	p.Glu1269Gly	p.E1269G	ENST00000222270	NM_014727.1	1269	gAg/gGg	13/37	0.449063756136886	3	FACETS	0.515	0.445	0.589	0.257	0.222	0.295	SUBCLONAL	1	TRUE	1	0.449063756136886	3		553	689	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082466	16082466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025396-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	63	578	0	ENST00000281043.3:c.280G>A	p.Glu94Lys	p.E94K	ENST00000281043	NM_005378.4	94	Gag/Aag	2/3	1	2	FACETS	0.644	0.558	0.736	0.644	0.558	0.736	SUBCLONAL	1	TRUE	1	0.449063756136886	2		578	436	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443680	29443680	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025396-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	70	463	0	ENST00000389048.3:c.3537T>G	p.Ile1179Met	p.I1179M	ENST00000389048	NM_004304.4	1179	atT/atG	23/29	1	2	FACETS	0.595	0.519	0.676	0.595	0.519	0.676	SUBCLONAL	1	TRUE	1	0.449063756136886	2		463	524	SUCCESS
REL	5966	MSKCC	GRCh37	2	61144032	61144032	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025396-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	41	408	0	ENST00000295025.8:c.415G>C	p.Asp139His	p.D139H	ENST00000295025	NM_002908.2	139	Gat/Cat	5/11	0.449063756136886	3	FACETS	0.452	0.376	0.536	0.226	0.188	0.268	SUBCLONAL	1	TRUE	1	0.449063756136886	3		408	495	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021124	31021124	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748644253	NA	P-0025396-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	49	474	0	ENST00000375687.4:c.1123G>A	p.Val375Met	p.V375M	ENST00000375687	NM_015338.5	375	Gtg/Atg	12/13	0.449063756136886	6	FACETS	0.472	0.398	0.553	0.094	0.079	0.111	SUBCLONAL	1	TRUE	1	0.449063756136886	6		474	878	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530381	187530381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753202486	NA	P-0025396-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	84	347	1	ENST00000441802.2:c.10162G>A	p.Val3388Ile	p.V3388I	ENST00000441802	NM_005245.3	3388	Gtc/Atc	16/27	0.216859158133646	3	FACETS	1	0.952	1	0.378	0.336	0.423	INDETERMINATE	1	TRUE	0	0.449063756136886	3		348	404	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541457	187541457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025396-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	39	429	1	ENST00000441802.2:c.6283G>A	p.Glu2095Lys	p.E2095K	ENST00000441802	NM_005245.3	2095	Gag/Aag	10/27	0.216859158133646	3	FACETS	0.446	0.369	0.531	0.149	0.123	0.177	INDETERMINATE	1	TRUE	0	0.449063756136886	3		430	477	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497253	149497253	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025396-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	75	511	0	ENST00000261799.4:c.3065T>G	p.Ile1022Ser	p.I1022S	ENST00000261799	NM_002609.3	1022	aTc/aGc	22/23	0.214291022983294	2	FACETS	0.613	0.538	0.693	0.306	0.269	0.347	INDETERMINATE	1	TRUE	0	0.449063756136886	2		511	545	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637558	176637558	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025396-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	78	532	0	ENST00000439151.2:c.2158G>A	p.Glu720Lys	p.E720K	ENST00000439151	NM_022455.4	720	Gag/Aag	5/23	0.449063756136886	3	FACETS	0.683	0.6	0.771	0.341	0.3	0.386	SUBCLONAL	1	TRUE	1	0.449063756136886	3		532	623	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205449	38205449	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025396-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	93	729	1	ENST00000317025.8:c.241G>T	p.Glu81Ter	p.E81*	ENST00000317025	NM_023034.1	81	Gaa/Taa	2/24	0.416597527170054	5	FACETS	0.706	0.626	0.791			1	SUBCLONAL	1	TRUE	NA	0.449063756136886	5		730	982	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370965	55370965	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025396-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	50	517	0	ENST00000297316.4:c.267G>T	p.Gln89His	p.Q89H	ENST00000297316	NM_022454.3	89	caG/caT	1/2	0.449063756136886	3	FACETS	0.646	0.549	0.752	0.323	0.274	0.376	SUBCLONAL	1	TRUE	1	0.449063756136886	3		517	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0025449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	572	764	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.695482276042448	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.709350559132353	2		765	795	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913250	NA	P-0025449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	194	379	0	ENST00000369535.4:c.34G>T	p.Gly12Cys	p.G12C	ENST00000369535	NM_002524.4	12	Ggt/Tgt	2/7	1	2	FACETS	0.956	0.891	1	0.956	0.891	1	CLONAL	1	TRUE	1	0.709350559132353	2		379	572	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448631	89448631	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0025449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	142	453	0	ENST00000336596.2:c.1594+1G>C		p.X532_splice	ENST00000336596	NM_005233.5	532			0.709350559132353	4	FACETS	0.661	0.601	0.723	0.33	0.3	0.362	SUBCLONAL	1	TRUE	2	0.709350559132353	4		453	1036	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011144	12011144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025805-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	21	396	0	ENST00000353533.5:c.551C>T	p.Ser184Leu	p.S184L	ENST00000353533	NM_003010.3	184	tCg/tTg	5/11	0.418686046110728	1	FACETS	0.208	0.16	0.265	0.208	0.16	0.265	SUBCLONAL	1	TRUE	0	0.418686046110728	1		396	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0025805-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	149	789	0	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.418686046110728	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.418686046110728	1		789	533	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862207	68862207	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025805-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	92	536	0	ENST00000261769.5:c.2295G>C	p.Gln765His	p.Q765H	ENST00000261769	NM_004360.3	765	caG/caC	14/16	0.418686046110728	1	FACETS	0.917	0.821	1	0.917	0.821	1	CLONAL	1	TRUE	0	0.418686046110728	1		536	379	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984887	101984887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025805-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	109	550	0	ENST00000282441.5:c.334G>A	p.Ala112Thr	p.A112T	ENST00000282441	NM_001130145.2	112	Gca/Aca	2/9	1	2	FACETS	0.802	0.722	0.888	0.802	0.722	0.888	CLONAL	1	TRUE	1	0.418686046110728	2		550	649	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030357	49030357	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1359386263	NA	P-0025805-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	76	385	0	ENST00000267163.4:c.1832G>A	p.Arg611Lys	p.R611K	ENST00000267163	NM_000321.2	611	aGa/aAa	19/27	0.107625155453771	3	FACETS	0.825	0.725	0.933	0.413	0.362	0.467	INDETERMINATE	1	TRUE	1	0.418686046110728	3		385	532	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611777	1611777	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025805-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	57	602	0	ENST00000344749.5:c.1885G>A	p.Asp629Asn	p.D629N	ENST00000344749	NM_001136139.2	629	Gac/Aac	19/19	1	2	FACETS	0.434	0.371	0.501	0.434	0.371	0.501	SUBCLONAL	1	TRUE	1	0.418686046110728	2		602	628	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509436	106509436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200175951	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	121	715	0	ENST00000359195.3:c.1430G>A	p.Arg477His	p.R477H	ENST00000359195	NM_002649.2	477	cGt/cAt	2/11	1	2	FACETS	0.873	0.787	0.964	0.873	0.787	0.964	CLONAL	1	TRUE	1	0.25	2		715	1109	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073495	8073497	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	80	614	0	ENST00000377482.5:c.1162_1164del	p.Lys388del	p.K388del	ENST00000377482	NM_018948.3	388	AAG/-	4/4	1	2	FACETS	0.707	0.621	0.8	0.707	0.621	0.8	SUBCLONAL	1	TRUE	1	0.25	2		614	905	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105949	27105949	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	129	824	0	ENST00000324856.7:c.5560C>T	p.His1854Tyr	p.H1854Y	ENST00000324856	NM_006015.4	1854	Cat/Tat	20/20	1	2	FACETS	0.836	0.756	0.92	0.836	0.756	0.92	CLONAL	1	TRUE	1	0.25	2		824	1235	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106720	27106720	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770028290	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	150	819	0	ENST00000324856.7:c.6331G>A	p.Val2111Ile	p.V2111I	ENST00000324856	NM_006015.4	2111	Gtc/Atc	20/20	1	2	FACETS	0.976	0.89	1	0.976	0.89	1	CLONAL	1	TRUE	1	0.25	2		819	1229	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263316	115263316	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	80	463	0	ENST00000438362.2:c.2034T>A	p.Tyr678Ter	p.Y678*	ENST00000438362	NM_001242891.1	678	taT/taA	17/20	1	2	FACETS	0.843	0.742	0.953	0.843	0.742	0.953	CLONAL	1	TRUE	1	0.25	2		463	759	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332921	70332921	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	91	651	0	ENST00000373644.4:c.826C>T	p.Arg276Ter	p.R276*	ENST00000373644	NM_030625.2	276	Cga/Tga	2/12	1	2	FACETS	0.863	0.765	0.967	0.863	0.765	0.967	CLONAL	1	TRUE	1	0.25	2		651	844	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406016	70406016	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs867350355	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	76	635	0	ENST00000373644.4:c.3530A>G	p.Glu1177Gly	p.E1177G	ENST00000373644	NM_030625.2	1177	gAa/gGa	4/12	1	2	FACETS	0.77	0.674	0.873	0.77	0.674	0.873	SUBCLONAL	1	TRUE	1	0.25	2		635	790	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	45	371	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.25	2		371	352	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10785885	10785885	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	101	604	0	ENST00000361367.2:c.1315C>T	p.Arg439Ter	p.R439*	ENST00000361367	NM_014633.3	439	Cga/Tga	11/25	1	2	FACETS	0.888	0.793	0.99	0.888	0.793	0.99	CLONAL	1	TRUE	1	0.25	2		604	910	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138797	64138797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs902255820	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	114	528	0	ENST00000334205.4:c.2164G>A	p.Val722Met	p.V722M	ENST00000334205	NM_003942.2	722	Gtg/Atg	17/17	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.25	2		528	903	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631129	69631129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs281860303	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	127	764	2	ENST00000334134.2:c.283C>T	p.Arg95Trp	p.R95W	ENST00000334134	NM_005247.2	95	Cgg/Tgg	2/3	1	2	FACETS	0.999	0.904	1	0.999	0.904	1	CLONAL	1	TRUE	1	0.25	2		766	1017	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77931369	77931369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769709400	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	109	693	1	ENST00000361507.4:c.1883G>A	p.Arg628His	p.R628H	ENST00000361507	NM_080491.2	628	cGc/cAc	9/10	1	2	FACETS	0.902	0.808	1	0.902	0.808	1	CLONAL	1	TRUE	1	0.25	2		694	967	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989517	85989517	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1565707121	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	54	357	0	ENST00000263360.6:c.1276A>G	p.Ile426Val	p.I426V	ENST00000263360	NM_003797.3	426	Ata/Gta	12/12	1	2	FACETS	0.883	0.755	1	0.883	0.755	1	CLONAL	1	TRUE	1	0.25	2		357	489	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999653	100999653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	62	700	0	ENST00000325455.5:c.149C>T	p.Ala50Val	p.A50V	ENST00000325455	NM_001202474.3	50	gCc/gTc	1/8	1	2	FACETS	0.485	0.417	0.559	0.485	0.417	0.559	SUBCLONAL	1	TRUE	1	0.25	2		700	1023	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158382	108158382	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781785	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	59	433	0	ENST00000278616.4:c.4049C>T	p.Thr1350Met	p.T1350M	ENST00000278616	NM_000051.3	1350	aCg/aTg	27/63	1	2	FACETS	0.969	0.835	1	0.969	0.835	1	CLONAL	1	TRUE	1	0.25	2		433	487	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394830	394830	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	69	515	0	ENST00000399788.2:c.4867-2A>G		p.X1623_splice	ENST00000399788	NM_001042603.1	1623			1	2	FACETS	0.839	0.73	0.956	0.839	0.73	0.956	CLONAL	1	TRUE	1	0.25	2		515	658	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464349	464349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772720111	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	71	523	0	ENST00000399788.2:c.845G>A	p.Arg282Gln	p.R282Q	ENST00000399788	NM_001042603.1	282	cGg/cAg	7/28	1	2	FACETS	0.91	0.795	1	0.91	0.795	1	CLONAL	1	TRUE	1	0.25	2		523	624	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691191	18691191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774205366	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	64	510	0	ENST00000266497.5:c.3302G>A	p.Arg1101His	p.R1101H	ENST00000266497		1101	cGt/cAt	23/31	1	2	FACETS	0.936	0.811	1	0.936	0.811	1	CLONAL	1	TRUE	1	0.25	2		510	547	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420784	49420784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369790149	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	142	847	0	ENST00000301067.7:c.14965C>T	p.Arg4989Trp	p.R4989W	ENST00000301067	NM_003482.3	4989	Cgg/Tgg	48/54	1	2	FACETS	0.946	0.86	1	0.946	0.86	1	CLONAL	1	TRUE	1	0.25	2		847	1201	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433388	49433388	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555191598	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	132	781	0	ENST00000301067.7:c.8059C>T	p.Arg2687Ter	p.R2687*	ENST00000301067	NM_003482.3	2687	Cga/Tga	32/54	1	2	FACETS	0.92	0.833	1	0.92	0.833	1	CLONAL	1	TRUE	1	0.25	2		781	1148	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433620	49433620	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555191740	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	145	919	0	ENST00000301067.7:c.7933C>T	p.Arg2645Ter	p.R2645*	ENST00000301067	NM_003482.3	2645	Cga/Tga	31/54	1	2	FACETS	0.913	0.831	1	0.913	0.831	1	CLONAL	1	TRUE	1	0.25	2		919	1270	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433960	49433960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	147	835	0	ENST00000301067.7:c.7593del	p.Ser2532LeufsTer11	p.S2532Lfs*11	ENST00000301067	NM_003482.3	2531	ccC/cc	31/54	1	2	FACETS	0.962	0.876	1	0.962	0.876	1	CLONAL	1	TRUE	1	0.25	2		835	1223	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	117	857	2	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.919	0.827	1	0.919	0.827	1	CLONAL	1	TRUE	1	0.25	2		859	1019	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426695	121426695	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	153	877	0	ENST00000257555.6:c.386C>A	p.Pro129Gln	p.P129Q	ENST00000257555		129	cCa/cAa	2/10	1	2	FACETS	0.991	0.905	1	0.991	0.905	1	CLONAL	1	TRUE	1	0.25	2		877	1235	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879626	123879626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376869233	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	92	390	0	ENST00000330479.4:c.322G>A	p.Ala108Thr	p.A108T	ENST00000330479	NM_020382.3	108	Gcc/Acc	4/9	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.25	2		390	613	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562477	21562477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757658067	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	69	376	0	ENST00000382592.4:c.1442C>T	p.Ala481Val	p.A481V	ENST00000382592	NM_014572.2	481	gCg/gTg	4/8	1	2	FACETS	0.839	0.73	0.956	0.839	0.73	0.956	CLONAL	1	TRUE	1	0.25	2		376	658	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911443	32911443	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359365	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	22	302	0	ENST00000380152.3:c.2957del	p.Asn986IlefsTer5	p.N986Ifs*5	ENST00000380152		984	gAa/ga	11/27	1	2	FACETS	0.631	0.489	0.794	0.631	0.489	0.794	SUBCLONAL	1	TRUE	1	0.25	2		302	279	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914119	32914119	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs876660636	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	46	383	0	ENST00000380152.3:c.5630del	p.Asn1877ThrfsTer32	p.N1877Tfs*32	ENST00000380152		1876	gAa/ga	11/27	1	2	FACETS	0.934	0.788	1	0.934	0.788	1	CLONAL	1	TRUE	1	0.25	2		383	394	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435294	110435294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	180	847	0	ENST00000375856.3:c.3107C>T	p.Pro1036Leu	p.P1036L	ENST00000375856	NM_003749.2	1036	cCg/cTg	1/2	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.25	2		847	1312	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435487	110435487	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	117	695	0	ENST00000375856.3:c.2914C>T	p.Arg972Trp	p.R972W	ENST00000375856	NM_003749.2	972	Cgg/Tgg	1/2	1	2	FACETS	0.856	0.77	0.947	0.856	0.77	0.947	CLONAL	1	TRUE	1	0.25	2		695	1094	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	91	233	1	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	0.857	0.76	0.961	0.857	0.76	0.961	CLONAL	1	TRUE	1	0.25	2		234	849	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2107145	2107145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373818076	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	127	697	0	ENST00000219476.3:c.814G>A	p.Ala272Thr	p.A272T	ENST00000219476	NM_000548.3	272	Gcc/Acc	9/42	1	2	FACETS	0.974	0.881	1	0.974	0.881	1	CLONAL	1	TRUE	1	0.25	2		697	1043	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138267	2138267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751990617	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	152	797	0	ENST00000219476.3:c.5200G>A	p.Asp1734Asn	p.D1734N	ENST00000219476	NM_000548.3	1734	Gat/Aat	41/42	1	2	FACETS	0.988	0.901	1	0.988	0.901	1	CLONAL	1	TRUE	1	0.25	2		797	1231	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223493	2223493	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	133	830	0	ENST00000326181.6:c.1024G>A	p.Glu342Lys	p.E342K	ENST00000326181	NM_032271.2	342	Gaa/Aaa	11/21	1	2	FACETS	0.983	0.891	1	0.983	0.891	1	CLONAL	1	TRUE	1	0.25	2		830	1082	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225513	2225513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759408908	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	122	842	0	ENST00000326181.6:c.1516G>A	p.Val506Met	p.V506M	ENST00000326181	NM_032271.2	506	Gtg/Atg	17/21	1	2	FACETS	0.876	0.79	0.967	0.876	0.79	0.967	CLONAL	1	TRUE	1	0.25	2		842	1114	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56855488	56855488	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567027753	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	83	384	1	ENST00000308159.5:c.637G>A	p.Ala213Thr	p.A213T	ENST00000308159	NM_014669.4	213	Gca/Aca	7/22	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.25	2		385	618	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827804	72827804	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	98	687	0	ENST00000268489.5:c.8777C>T	p.Pro2926Leu	p.P2926L	ENST00000268489	NM_006885.3	2926	cCg/cTg	9/10	1	2	FACETS	0.807	0.718	0.901	0.807	0.718	0.901	CLONAL	1	TRUE	1	0.25	2		687	972	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828653	72828653	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777599986	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	106	727	0	ENST00000268489.5:c.7928G>A	p.Arg2643His	p.R2643H	ENST00000268489	NM_006885.3	2643	cGt/cAt	9/10	1	2	FACETS	0.912	0.816	1	0.912	0.816	1	CLONAL	1	TRUE	1	0.25	2		727	930	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829974	72829974	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	107	591	1	ENST00000268489.5:c.6607C>T	p.Arg2203Cys	p.R2203C	ENST00000268489	NM_006885.3	2203	Cgt/Tgt	9/10	1	2	FACETS	0.91	0.815	1	0.91	0.815	1	CLONAL	1	TRUE	1	0.25	2		592	941	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346892	89346892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755603365	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	119	786	0	ENST00000301030.4:c.6058G>A	p.Ala2020Thr	p.A2020T	ENST00000301030	NM_001256183.1	2020	Gcc/Acc	9/13	1	2	FACETS	0.878	0.791	0.971	0.878	0.791	0.971	CLONAL	1	TRUE	1	0.25	2		786	1084	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347668	89347668	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	164	926	1	ENST00000301030.4:c.5282del	p.Phe1761SerfsTer202	p.F1761Sfs*202	ENST00000301030	NM_001256183.1	1761	tTc/tc	9/13	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.25	2		927	1273	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845389	89845389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769158149	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	128	726	0	ENST00000389301.3:c.1738G>A	p.Val580Met	p.V580M	ENST00000389301	NM_000135.2	580	Gtg/Atg	19/43	1	2	FACETS	0.972	0.88	1	0.972	0.88	1	CLONAL	1	TRUE	1	0.25	2		726	1053	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577093	7577093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882008	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	124	703	0	ENST00000269305.4:c.845G>A	p.Arg282Gln	p.R282Q	ENST00000269305	NM_001126112.2	282	cGg/cAg	8/11	1	2	FACETS	0.908	0.819	1	0.908	0.819	1	CLONAL	1	TRUE	1	0.25	2		703	1093	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687306	37687306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1172789499	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	156	755	0	ENST00000447079.4:c.4210C>T	p.Arg1404Cys	p.R1404C	ENST00000447079	NM_015083.1	1404	Cgt/Tgt	14/14	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.25	2		755	1137	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485994	40485995	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	83	612	0	ENST00000264657.5:c.870dup	p.Val291SerfsTer24	p.V291Sfs*24	ENST00000264657	NM_139276.2	290	-/A	9/24	1	2	FACETS	0.801	0.706	0.903	0.801	0.706	0.903	CLONAL	1	TRUE	1	0.25	2		612	829	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677762	47677762	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1380705599	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	118	592	0	ENST00000347630.2:c.1103G>A	p.Arg368His	p.R368H	ENST00000347630	NM_001007230.1	368	cGc/cAc	11/11	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.25	2		592	923	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66525032	66525032	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303569195	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	62	435	0	ENST00000358598.2:c.791G>A	p.Arg264His	p.R264H	ENST00000358598	NM_212471.2	264	cGt/cAt	9/11	1	2	FACETS	0.834	0.72	0.957	0.834	0.72	0.957	CLONAL	1	TRUE	1	0.25	2		435	595	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857702	78857702	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	107	709	0	ENST00000306801.3:c.1772C>T	p.Ala591Val	p.A591V	ENST00000306801	NM_020761.2	591	gCg/gTg	16/34	1	2	FACETS	0.843	0.755	0.938	0.843	0.755	0.938	CLONAL	1	TRUE	1	0.25	2		709	1015	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371712	45371712	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	61	466	0	ENST00000262160.6:c.1279C>T	p.Arg427Ter	p.R427*	ENST00000262160	NM_005901.5	427	Cga/Tga	10/11	1	2	FACETS	0.827	0.714	0.951	0.827	0.714	0.951	CLONAL	1	TRUE	1	0.25	2		466	590	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621857	1621857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	143	780	0	ENST00000344749.5:c.935G>A	p.Ser312Asn	p.S312N	ENST00000344749	NM_001136139.2	312	aGc/aAc	11/19	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.25	2		780	1138	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622206	1622206	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	176	937	0	ENST00000344749.5:c.669del	p.Ser224GlnfsTer60	p.S224Qfs*60	ENST00000344749	NM_001136139.2	223	ccC/cc	10/19	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.25	2		937	1369	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214741	5214741	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs974923793	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	103	665	0	ENST00000357368.4:c.4325T>C	p.Met1442Thr	p.M1442T	ENST00000357368	NM_002850.3	1442	aTg/aCg	29/38	0.1443232718481	1	FACETS	0.841	0.752	0.936	0.841	0.752	0.936	INDETERMINATE	1	TRUE	0	0.25	1		665	857	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172373	7172373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	95	629	0	ENST00000302850.5:c.1196G>A	p.Arg399Gln	p.R399Q	ENST00000302850	NM_000208.2	399	cGa/cAa	5/22	1	2	FACETS	0.912	0.812	1	0.912	0.812	1	CLONAL	1	TRUE	1	0.25	2		629	833	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276311	15276311	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754537422	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	113	589	0	ENST00000263388.2:c.5683C>T	p.Arg1895Cys	p.R1895C	ENST00000263388	NM_000435.2	1895	Cgc/Tgc	31/33	1	2	FACETS	0.936	0.841	1	0.936	0.841	1	CLONAL	1	TRUE	1	0.25	2		589	966	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19261529	19261529	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	73	451	1	ENST00000162023.5:c.16del	p.Ile6SerfsTer14	p.I6Sfs*14	ENST00000162023		6	Atc/tc	6/13	1	2	FACETS	0.741	0.647	0.843	0.741	0.647	0.843	SUBCLONAL	1	TRUE	1	0.25	2		452	788	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210420	36210420	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1299531345	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	129	658	0	ENST00000222270.7:c.413G>A	p.Arg138His	p.R138H	ENST00000222270	NM_014727.1	138	cGc/cAc	2/37	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.25	2		658	1008	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214058	36214058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1385766471	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	140	778	0	ENST00000222270.7:c.2884C>T	p.Arg962Cys	p.R962C	ENST00000222270	NM_014727.1	962	Cgc/Tgc	6/37	1	2	FACETS	0.963	0.875	1	0.963	0.875	1	CLONAL	1	TRUE	1	0.25	2		778	1163	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223983	36223983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760774396	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	121	865	0	ENST00000222270.7:c.6533G>A	p.Gly2178Asp	p.G2178D	ENST00000222270	NM_014727.1	2178	gGc/gAc	28/37	1	2	FACETS	0.763	0.688	0.844	0.763	0.688	0.844	SUBCLONAL	1	TRUE	1	0.25	2		865	1268	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798842	42798842	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	125	685	1	ENST00000575354.2:c.4414G>A	p.Ala1472Thr	p.A1472T	ENST00000575354	NM_015125.3	1472	Gcc/Acc	19/20	1	2	FACETS	0.849	0.766	0.936	0.849	0.766	0.936	CLONAL	1	TRUE	1	0.25	2		686	1178	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860761	45860761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749815182	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	164	891	1	ENST00000391945.4:c.1348C>T	p.Arg450Cys	p.R450C	ENST00000391945	NM_000400.3	450	Cgt/Tgt	14/23	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.25	2		892	1312	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422128	47422128	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	97	679	0	ENST00000404338.3:c.196C>T	p.Arg66Ter	p.R66*	ENST00000404338	NM_004491.4	66	Cga/Tga	1/6	1	2	FACETS	0.785	0.698	0.877	0.785	0.698	0.877	SUBCLONAL	1	TRUE	1	0.25	2		679	989	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965049	25965049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780551383	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	99	700	1	ENST00000435504.4:c.4157C>T	p.Ala1386Val	p.A1386V	ENST00000435504		1386	gCg/gTg	13/13	1	2	FACETS	0.79	0.704	0.883	0.79	0.704	0.883	SUBCLONAL	1	TRUE	1	0.25	2		701	1002	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033392	48033393	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	72	451	0	ENST00000234420.5:c.3699dup	p.Glu1234ArgfsTer4	p.E1234Rfs*4	ENST00000234420	NM_000179.2	1232	-/A	8/10	1	2	FACETS	0.975	0.852	1	0.975	0.852	1	CLONAL	1	TRUE	1	0.25	2		451	591	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190742119	190742119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147566508	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	29	280	0	ENST00000441310.2:c.2756G>A	p.Arg919His	p.R919H	ENST00000441310	NM_000534.4	919	cGc/cAc	13/13	1	2	FACETS	0.806	0.648	0.983	0.806	0.648	0.983	CLONAL	1	TRUE	1	0.25	2		280	288	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265007	198265007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773349667	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	95	545	0	ENST00000335508.6:c.2870G>A	p.Arg957Gln	p.R957Q	ENST00000335508	NM_012433.2	957	cGa/cAa	19/25	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.25	2		545	747	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735405	204735405	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs757566658	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	126	816	0	ENST00000302823.3:c.206T>C	p.Val69Ala	p.V69A	ENST00000302823	NM_005214.4	69	gTc/gCc	2/4	1	2	FACETS	0.855	0.772	0.943	0.855	0.772	0.943	CLONAL	1	TRUE	1	0.25	2		816	1179	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793363	242793363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	113	875	0	ENST00000334409.5:c.714del	p.Val239CysfsTer39	p.V239Cfs*39	ENST00000334409	NM_005018.2	238	ccC/cc	5/5	1	2	FACETS	0.745	0.669	0.827	0.745	0.669	0.827	SUBCLONAL	1	TRUE	1	0.25	2		875	1213	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31025035	31025035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375101983	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	114	701	0	ENST00000375687.4:c.4520C>T	p.Ala1507Val	p.A1507V	ENST00000375687	NM_015338.5	1507	gCg/gTg	13/13	1	2	FACETS	0.904	0.812	1	0.904	0.812	1	CLONAL	1	TRUE	1	0.25	2		701	1009	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385183	41385183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1423243089	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	81	602	0	ENST00000373198.4:c.778C>T	p.Arg260Trp	p.R260W	ENST00000373198	NM_133170.3	260	Cgg/Tgg	6/32	0.1443232718481	1	FACETS	0.651	0.572	0.736	0.651	0.572	0.736	INDETERMINATE	1	TRUE	0	0.25	1		602	871	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651265	45651265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1195890520	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	117	619	0	ENST00000407780.3:c.760G>A	p.Ala254Thr	p.A254T	ENST00000407780	NM_001283052.1	254	Gcg/Acg	5/7	1	2	FACETS	0.971	0.874	1	0.971	0.874	1	CLONAL	1	TRUE	1	0.25	2		619	964	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29442779	29442779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747273571	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	115	623	2	ENST00000544604.2:c.820C>T	p.Arg274Cys	p.R274C	ENST00000544604	NM_001206998.1	274	Cgc/Tgc	6/9	1	2	FACETS	0.961	0.865	1	0.961	0.865	1	CLONAL	1	TRUE	1	0.25	2		625	957	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536193	41536193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	95	501	1	ENST00000263253.7:c.1810C>T	p.Arg604Trp	p.R604W	ENST00000263253	NM_001429.3	604	Cgg/Tgg	9/31	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.25	2		502	748	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566507	41566507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	91	494	0	ENST00000263253.7:c.4384C>T	p.Arg1462Ter	p.R1462*	ENST00000263253	NM_001429.3	1462	Cga/Tga	27/31	1	2	FACETS	0.95	0.843	1	0.95	0.843	1	CLONAL	1	TRUE	1	0.25	2		494	766	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277959	41277960	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1553632361	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	80	586	0	ENST00000349496.5:c.1925_1926del	p.Glu642ValfsTer5	p.E642Vfs*5	ENST00000349496	NM_001904.3	641	acAGag/acag	12/15	1	2	FACETS	0.748	0.657	0.845	0.748	0.657	0.845	SUBCLONAL	1	TRUE	1	0.25	2		586	856	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059133	47059133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	104	481	0	ENST00000409792.3:c.7528C>T	p.Arg2510Cys	p.R2510C	ENST00000409792	NM_014159.6	2510	Cgc/Tgc	20/21	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.25	2		481	815	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059214	47059214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141852778	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	114	607	0	ENST00000409792.3:c.7447G>A	p.Val2483Ile	p.V2483I	ENST00000409792	NM_014159.6	2483	Gtc/Atc	20/21	1	2	FACETS	0.958	0.861	1	0.958	0.861	1	CLONAL	1	TRUE	1	0.25	2		607	952	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164760	47164760	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	76	670	0	ENST00000409792.3:c.1366C>T	p.Arg456Ter	p.R456*	ENST00000409792	NM_014159.6	456	Cga/Tga	3/21	1	2	FACETS	0.767	0.672	0.869	0.767	0.672	0.869	SUBCLONAL	1	TRUE	1	0.25	2		670	793	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924781	49924781	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372825999	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	133	878	0	ENST00000296474.3:c.4162C>T	p.Arg1388Cys	p.R1388C	ENST00000296474	NM_002447.2	1388	Cgc/Tgc	20/20	1	2	FACETS	0.835	0.756	0.918	0.835	0.756	0.918	CLONAL	1	TRUE	1	0.25	2		878	1275	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643943	52643943	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	24	266	0	ENST00000394830.3:c.1953del	p.Lys651AsnfsTer5	p.K651Nfs*5	ENST00000394830	NM_018313.4	651	aaA/aa	17/30	1	2	FACETS	0.541	0.424	0.676	0.541	0.424	0.676	SUBCLONAL	1	TRUE	1	0.25	2		266	355	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72866457	72866457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375075276	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	82	569	0	ENST00000325599.8:c.806G>A	p.Arg269His	p.R269H	ENST00000325599	NM_018130.2	269	cGt/cAt	7/11	1	2	FACETS	0.932	0.821	1	0.932	0.821	1	CLONAL	1	TRUE	1	0.25	2		569	704	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182681684	182681684	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	58	468	0	ENST00000292782.4:c.374G>A	p.Gly125Asp	p.G125D	ENST00000292782	NM_020640.2	125	gGc/gAc	3/7	1	2	FACETS	0.711	0.61	0.821	0.711	0.61	0.821	SUBCLONAL	1	TRUE	1	0.25	2		468	653	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156811	106156811	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146049881	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	119	718	0	ENST00000380013.4:c.1712G>A	p.Arg571His	p.R571H	ENST00000380013	NM_001127208.2	571	cGt/cAt	3/11	1	2	FACETS	0.922	0.831	1	0.922	0.831	1	CLONAL	1	TRUE	1	0.25	2		718	1032	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158447	106158447	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	51	428	0	ENST00000380013.4:c.3353del	p.Asn1118IlefsTer19	p.N1118Ifs*19	ENST00000380013	NM_001127208.2	1116	atA/at	3/11	1	2	FACETS	0.915	0.779	1	0.915	0.779	1	CLONAL	1	TRUE	1	0.25	2		428	446	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155654	56155654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746479827	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	77	558	2	ENST00000399503.3:c.746G>A	p.Arg249His	p.R249H	ENST00000399503	NM_005921.1	249	cGc/cAc	3/20	1	2	FACETS	0.77	0.675	0.872	0.77	0.675	0.872	SUBCLONAL	1	TRUE	1	0.25	2		560	800	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155687	56155687	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768948038	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	108	528	0	ENST00000399503.3:c.779G>A	p.Arg260His	p.R260H	ENST00000399503	NM_005921.1	260	cGc/cAc	3/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.25	2		528	745	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	69	345	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	0.876	0.763	0.998	0.876	0.763	0.998	CLONAL	1	TRUE	1	0.25	2		345	630	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79966028	79966028	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201748817	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	64	487	0	ENST00000265081.6:c.692C>T	p.Pro231Leu	p.P231L	ENST00000265081	NM_002439.4	231	cCg/cTg	4/24	1	2	FACETS	0.853	0.739	0.977	0.853	0.739	0.977	CLONAL	1	TRUE	1	0.25	2		487	600	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176719015	176719015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1321310131	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	99	681	1	ENST00000439151.2:c.6319C>T	p.Arg2107Cys	p.R2107C	ENST00000439151	NM_022455.4	2107	Cgc/Tgc	22/23	1	2	FACETS	0.812	0.724	0.907	0.812	0.724	0.907	CLONAL	1	TRUE	1	0.25	2		682	975	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394897	394897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	136	642	0	ENST00000380956.4:c.293G>A	p.Arg98Gln	p.R98Q	ENST00000380956	NM_001195286.1	98	cGg/cAg	3/9	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.25	2		642	1071	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490474	20490474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	120	702	0	ENST00000346618.3:c.1211C>T	p.Ala404Val	p.A404V	ENST00000346618	NM_001949.4	404	gCc/gTc	7/7	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.25	2		702	935	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490525	20490525	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	119	712	0	ENST00000346618.3:c.1262C>A	p.Pro421Gln	p.P421Q	ENST00000346618	NM_001949.4	421	cCg/cAg	7/7	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.25	2		712	938	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056237	26056245	+	inframe_deletion	In_Frame_Del	DEL	CTTCTTGGG	CTTCTTGGG	-	rs749190253	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	119	827	0	ENST00000343677.2:c.412_420del	p.Pro138_Lys140del	p.P138_K140del	ENST00000343677	NM_005319.3	138	CCCAAGAAG/-	1/1	0.137974678350404	3	FACETS	0.837	0.753	0.926	0.418	0.376	0.463	INDETERMINATE	1	TRUE	1	0.25	3		827	1280	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178705	32178705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1309934695	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	102	587	0	ENST00000375023.3:c.2689G>A	p.Val897Ile	p.V897I	ENST00000375023	NM_004557.3	897	Gtc/Atc	18/30	1	2	FACETS	0.906	0.809	1	0.906	0.809	1	CLONAL	1	TRUE	1	0.25	2		587	901	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813532	32813532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747716612	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	126	522	0	ENST00000354258.4:c.2251C>T	p.Arg751Trp	p.R751W	ENST00000354258	NM_000593.5	751	Cgg/Tgg	11/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.25	2		522	895	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37141769	37141769	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761967890	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	91	603	0	ENST00000373509.5:c.844G>A	p.Glu282Lys	p.E282K	ENST00000373509	NM_002648.3	282	Gaa/Aaa	6/6	1	2	FACETS	0.752	0.666	0.844	0.752	0.666	0.844	SUBCLONAL	1	TRUE	1	0.25	2		603	968	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524803	137524803	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55881171	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	37	338	0	ENST00000367739.4:c.566C>T	p.Thr189Met	p.T189M	ENST00000367739	NM_000416.2	189	aCg/aTg	5/7	1	2	FACETS	0.661	0.545	0.791	0.661	0.545	0.791	SUBCLONAL	1	TRUE	1	0.25	2		338	448	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099566	157099566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1022306360	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	123	619	0	ENST00000346085.5:c.503G>A	p.Gly168Asp	p.G168D	ENST00000346085	NM_020732.3	168	gGc/gAc	1/20	1	2	FACETS	0.896	0.809	0.989	0.896	0.809	0.989	CLONAL	1	TRUE	1	0.25	2		619	1098	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522220	157522220	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1320072402	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	132	806	0	ENST00000346085.5:c.4492G>A	p.Asp1498Asn	p.D1498N	ENST00000346085	NM_020732.3	1498	Gat/Aat	18/20	1	2	FACETS	0.899	0.815	0.989	0.899	0.815	0.989	CLONAL	1	TRUE	1	0.25	2		806	1174	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55231515	55231515	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs370810719	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	89	540	1	ENST00000275493.2:c.1721G>A	p.Arg574Gln	p.R574Q	ENST00000275493	NM_005228.3	574	cGg/cAg	14/28	1	2	FACETS	0.904	0.8	1	0.904	0.8	1	CLONAL	1	TRUE	1	0.25	2		541	788	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335040	81335040	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751819844	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	59	457	0	ENST00000222390.5:c.1787C>T	p.Thr596Met	p.T596M	ENST00000222390	NM_000601.4	596	aCg/aTg	16/18	1	2	FACETS	0.967	0.833	1	0.967	0.833	1	CLONAL	1	TRUE	1	0.25	2		457	488	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339957	116339957	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	70	487	0	ENST00000397752.3:c.822del	p.His275ThrfsTer4	p.H275Tfs*4	ENST00000397752	NM_000245.2	273	acT/ac	2/21	1	2	FACETS	0.866	0.754	0.986	0.866	0.754	0.986	CLONAL	1	TRUE	1	0.25	2		487	647	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124493026	124493026	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	35	290	0	ENST00000357628.3:c.869del	p.Lys290ArgfsTer3	p.K290Rfs*3	ENST00000357628	NM_015450.2	290	aAg/ag	10/19	1	2	FACETS	0.867	0.712	1	0.867	0.712	1	CLONAL	1	TRUE	1	0.25	2		290	323	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534597	140534597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749247588	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	74	526	0	ENST00000288602.6:c.316G>A	p.Gly106Arg	p.G106R	ENST00000288602	NM_004333.4	106	Gga/Aga	3/18	1	2	FACETS	0.859	0.752	0.975	0.859	0.752	0.975	CLONAL	1	TRUE	1	0.25	2		526	689	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877818	151877818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749660959	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	64	495	0	ENST00000262189.6:c.7127C>T	p.Ala2376Val	p.A2376V	ENST00000262189	NM_170606.2	2376	gCa/gTa	36/59	1	2	FACETS	0.883	0.765	1	0.883	0.765	1	CLONAL	1	TRUE	1	0.25	2		495	580	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69103958	69103958	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1563581001	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	19	270	0	ENST00000288368.4:c.4348G>A	p.Ala1450Thr	p.A1450T	ENST00000288368	NM_024870.2	1450	Gca/Aca	36/40	1	2	FACETS	0.623	0.474	0.798	0.623	0.474	0.798	SUBCLONAL	1	TRUE	1	0.25	2		270	244	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859852	117859852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1283070450	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	81	534	0	ENST00000297338.2:c.1783G>A	p.Ala595Thr	p.A595T	ENST00000297338	NM_006265.2	595	Gca/Aca	14/14	1	2	FACETS	0.969	0.854	1	0.969	0.854	1	CLONAL	1	TRUE	1	0.25	2		534	669	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117870683	117870683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	41	400	0	ENST00000297338.2:c.389C>T	p.Ala130Val	p.A130V	ENST00000297338	NM_006265.2	130	gCc/gTc	5/14	1	2	FACETS	0.765	0.637	0.906	0.765	0.637	0.906	CLONAL	1	TRUE	1	0.25	2		400	429	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542214	141542214	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	116	638	0	ENST00000220592.5:c.2509C>T	p.Arg837Ter	p.R837*	ENST00000220592	NM_012154.3	837	Cga/Tga	19/19	1	2	FACETS	0.952	0.857	1	0.952	0.857	1	CLONAL	1	TRUE	1	0.25	2		638	975	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141557715	141557715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756553697	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	120	732	0	ENST00000220592.5:c.1600C>T	p.Arg534Cys	p.R534C	ENST00000220592	NM_012154.3	534	Cgc/Tgc	13/19	1	2	FACETS	0.89	0.802	0.983	0.89	0.802	0.983	CLONAL	1	TRUE	1	0.25	2		732	1079	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2039826	2039826	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752254994	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	136	827	2	ENST00000349721.2:c.716C>T	p.Pro239Leu	p.P239L	ENST00000349721	NM_003070.3	239	cCg/cTg	4/34	1	2	FACETS	0.924	0.839	1	0.924	0.839	1	CLONAL	1	TRUE	1	0.25	2		829	1177	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248138	98248138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763774051	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	71	425	0	ENST00000331920.6:c.413G>A	p.Arg138His	p.R138H	ENST00000331920	NM_000264.3	138	cGt/cAt	3/24	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.25	2		425	563	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249965	110249965	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	112	670	0	ENST00000374672.4:c.710C>T	p.Ala237Val	p.A237V	ENST00000374672	NM_004235.4	237	gCc/gTc	3/5	1	2	FACETS	0.905	0.813	1	0.905	0.813	1	CLONAL	1	TRUE	1	0.25	2		670	990	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759778	133759778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775106685	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	129	707	1	ENST00000318560.5:c.2101G>A	p.Gly701Ser	p.G701S	ENST00000318560	NM_005157.4	701	Ggc/Agc	11/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.25	2		708	989	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402583	139402583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370696201	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	121	855	0	ENST00000277541.6:c.3334G>A	p.Val1112Ile	p.V1112I	ENST00000277541	NM_017617.3	1112	Gtt/Att	21/34	1	2	FACETS	0.857	0.773	0.947	0.857	0.773	0.947	CLONAL	1	TRUE	1	0.25	2		855	1129	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028742	47028742	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	135	321	0	ENST00000377604.3:c.46T>C	p.Tyr16His	p.Y16H	ENST00000377604	NM_001204468.1	16	Tat/Cat	3/24	1	1	FACETS	0.89	0.813	0.97	1	0.99	1	CLONAL	2	TRUE	0	0.25	1		321	531	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223440	53223440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782631044	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	113	410	0	ENST00000375401.3:c.3919C>T	p.Arg1307Trp	p.R1307W	ENST00000375401	NM_004187.3	1307	Cgg/Tgg	23/26	1	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.25	1		410	534	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231148	53231148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	105	269	1	ENST00000375401.3:c.1754G>A	p.Arg585His	p.R585H	ENST00000375401	NM_004187.3	585	cGc/cAc	13/26	1	1	FACETS	0.849	0.765	0.936	1	0.986	1	CLONAL	2	TRUE	0	0.25	1		270	433	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250046	53250047	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs782600511	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	102	320	0	ENST00000375401.3:c.202dup	p.Arg68ProfsTer7	p.R68Pfs*7	ENST00000375401	NM_004187.3	68	cga/cCga	2/26	1	1	FACETS	0.75	0.674	0.83	1	0.982	1	SUBCLONAL	2	TRUE	0	0.25	1		320	476	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354957	70354957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776748297	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	130	346	0	ENST00000374080.3:c.4879C>T	p.Arg1627Cys	p.R1627C	ENST00000374080		1627	Cgc/Tgc	36/45	1	1	FACETS	0.775	0.706	0.848	1	0.987	1	SUBCLONAL	2	TRUE	0	0.25	1		346	587	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831357	72831358	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTG	rs34918837	NA	P-0025952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	151	818	1	ENST00000268489.5:c.5221_5223dup	p.Gln1741dup	p.Q1741dup	ENST00000268489	NM_006885.3	1741	-/CAA	9/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.25	2		819	1048	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	227	300	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.806111133305798	2		300	511	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577189	64577190	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0026301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	315	444	0	ENST00000312049.6:c.392_393del	p.Arg131LeufsTer48	p.R131Lfs*48	ENST00000312049	NM_130799.2	131	cGC/c	2/10	0.806111133305798	1	FACETS	0.966	0.927	1	0.966	0.927	1	CLONAL	1	TRUE	0	0.806111133305798	1		444	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0026468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	202	863	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.40783301594709	2	FACETS	1	0.964	1	0.531	0.492	0.571	CLONAL	1	TRUE	0	0.40783301594709	2		863	933	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0026468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	187	622	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.40783301594709	2	FACETS	0.98	0.905	1	0.49	0.452	0.529	CLONAL	1	TRUE	0	0.40783301594709	2		623	936	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0026468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	86	125	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.40783301594709	2		125	379	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916205	9916205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555491654	NA	P-0026468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	104	505	0	ENST00000330684.3:c.2084G>A	p.Arg695Gln	p.R695Q	ENST00000330684	NM_001134407.1	695	cGg/cAg	10/13	1	2	FACETS	0.847	0.76	0.939	0.847	0.76	0.939	CLONAL	1	TRUE	1	0.40783301594709	2		505	602	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468128	31468128	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	164	564	0	ENST00000344624.3:c.2284T>C	p.Phe762Leu	p.F762L	ENST00000344624		762	Ttc/Ctc	15/33	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.40783301594709	2		564	796	SUCCESS
APC	324	MSKCC	GRCh37	5	112175733	112175736	+	frameshift_variant	Frame_Shift_Del	DEL	TTCT	TTCT	-	novel	NA	P-0026468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	86	356	0	ENST00000257430.4:c.4443_4446del	p.Leu1482GlnfsTer24	p.L1482Qfs*24	ENST00000257430	NM_000038.5	1481	gTTCTt/gt	16/16	1	2	FACETS	0.88	0.782	0.985	0.88	0.782	0.985	CLONAL	1	TRUE	1	0.40783301594709	2		356	479	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026518-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	57	300	0				ENST00000310581	NM_198253.2	-/1132			0.29707208506934	1	FACETS	0.981	0.846	1	0.981	0.846	1	CLONAL	1	TRUE	0	0.28	1		300	357	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058620	72058620	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026518-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	20	321	0	ENST00000357731.5:c.820C>T	p.Gln274Ter	p.Q274*	ENST00000357731	NM_173808.2	274	Caa/Taa	6/7	1	2	FACETS	0.4	0.305	0.511	0.4	0.305	0.511	SUBCLONAL	1	TRUE	1	0.28	2		321	357	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981141	201981142	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0026518-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	56	699	0	ENST00000359651.3:c.220_221insT	p.Asp74ValfsTer18	p.D74Vfs*18	ENST00000359651		74	gac/gTac	2/8	1	2	FACETS	0.639	0.547	0.74	0.639	0.547	0.74	SUBCLONAL	1	TRUE	1	0.28	2		699	626	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129440	64129440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747947296	NA	P-0026518-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	59	918	0	ENST00000334205.4:c.872G>A	p.Gly291Glu	p.G291E	ENST00000334205	NM_003942.2	291	gGg/gAg	8/17	1	2	FACETS	0.495	0.425	0.572	0.495	0.425	0.572	SUBCLONAL	1	TRUE	1	0.28	2		918	851	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112460	115112460	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026518-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	120	968	0	ENST00000257566.3:c.1280G>C	p.Arg427Pro	p.R427P	ENST00000257566	NM_016569.3	427	cGg/cCg	7/8	0.0944286767244784	3	FACETS	1	0.935	1	0.524	0.472	0.578	INDETERMINATE	1	TRUE	1	0.28	3		968	933	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675070	40675070	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747846923	NA	P-0026518-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	59	709	0	ENST00000249776.8:c.34G>C	p.Val12Leu	p.V12L	ENST00000249776	NM_033286.3	12	Gtt/Ctt	1/9	1	2	FACETS	0.566	0.486	0.653	0.566	0.486	0.653	SUBCLONAL	1	TRUE	1	0.28	2		709	745	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907628	111907628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026518-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	111	552	0	ENST00000393256.3:c.402G>A	p.Met134Ile	p.M134I	ENST00000393256	NM_006538.4	134	atG/atA	3/4	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.28	2		552	724	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748098	41748098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026518-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	34	603	0	ENST00000226382.2:c.671C>T	p.Pro224Leu	p.P224L	ENST00000226382	NM_003924.3	224	cCg/cTg	3/3	1	2	FACETS	0.607	0.496	0.732	0.607	0.496	0.732	SUBCLONAL	1	TRUE	1	0.28	2		603	400	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137528156	137528156	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026518-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	25	244	0	ENST00000367739.4:c.144G>A	p.Trp48Ter	p.W48*	ENST00000367739	NM_000416.2	48	tgG/tgA	2/7	0.196778930847858	0	FACETS	0.44	0.347	0.547			1	SUBCLONAL	1	TRUE	0	0.28	0		244	292	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468240	50468240	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026518-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	118	840	0	ENST00000331340.3:c.1475G>T	p.Cys492Phe	p.C492F	ENST00000331340	NM_006060.4	492	tGc/tTc	8/8	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.28	2		840	817	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772823	135772823	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0026518-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	91	485	0	ENST00000298552.3:c.2800A>T	p.Lys934Ter	p.K934*	ENST00000298552	NM_001162426.1	934	Aaa/Taa	21/23	0.29707208506934	1	FACETS	0.995	0.885	1	0.995	0.885	1	CLONAL	1	TRUE	0	0.28	1		485	562	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248633	59248634	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0027293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	187	908	0	ENST00000371222.2:c.109_110del	p.Ser37HisfsTer69	p.S37Hfs*69	ENST00000371222	NM_002228.3	37	AGc/c	1/1	0.248836184370887	3	FACETS	1	0.985	1	0.639	0.59	0.691	CLONAL	1	TRUE	1	0.331382884797102	3		908	1029	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435201	18435202	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1565550462	NA	P-0027293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	37	308	1	ENST00000266497.5:c.192dup	p.Val65CysfsTer16	p.V65Cfs*16	ENST00000266497		62	-/T	1/31	0.196181633370761	4	FACETS	1	0.901	1	0.565	0.468	0.672	INDETERMINATE	1	TRUE	2	0.331382884797102	4		309	263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0027293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	206	658	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.106728602675901	5	FACETS	1	0.979	1	0.565	0.525	0.607	INDETERMINATE	2	TRUE	1	0.331382884797102	5		658	823	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509850	187509850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	35	330	0	ENST00000441802.2:c.13663G>A	p.Val4555Met	p.V4555M	ENST00000441802	NM_005245.3	4555	Gtg/Atg	27/27	0.166288547218746	3	FACETS	0.758	0.623	0.908	0.379	0.311	0.454	INDETERMINATE	1	TRUE	1	0.331382884797102	3		330	325	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	165	530	1	ENST00000206249.3:c.1607T>A	p.Leu536His	p.L536H	ENST00000206249	NM_000125.3	536	cTc/cAc	8/8	1	2	FACETS	0.752	0.693	0.813	0.752	0.693	0.813	SUBCLONAL	1	TRUE	1	0.668704740789242	2		531	656	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0028621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	133	254	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.863	0.789	0.939	0.863	0.789	0.939	CLONAL	1	TRUE	1	0.668704740789242	2		254	461	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0028621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	219	481	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.88	0.822	0.94	0.88	0.822	0.94	CLONAL	1	TRUE	1	0.668704740789242	2		481	744	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149778	202149778	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242650624	NA	P-0028621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	262	546	1	ENST00000358485.4:c.1219C>T	p.Leu407Phe	p.L407F	ENST00000358485	NM_001080125.1	407	Ctt/Ttt	8/9	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.668704740789242	2		547	729	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371799	55371820	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCCGCGCTGGGCCCCGAG	GGCGGCCGCGCTGGGCCCCGAG	-	novel	NA	P-0028621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	154	176	0	ENST00000297316.4:c.499_520del	p.Leu167TrpfsTer213	p.L167Wfs*213	ENST00000297316	NM_022454.3	163	caGGCGGCCGCGCTGGGCCCCGAG/ca	2/2	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.668704740789242	2		176	312	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653859	89653861	+	inframe_deletion	In_Frame_Del	DEL	GTA	GTA	-	rs1554893831	NA	P-0028621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	316	472	0	ENST00000371953.3:c.160_162del	p.Val54del	p.V54del	ENST00000371953	NM_000314.4	53	GTA/-	2/9	0.665198646050552	2	FACETS	0.9	0.862	0.938	0.9	0.862	0.938	CLONAL	2	TRUE	0	0.668704740789242	2		472	525	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106727	27106727	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	229	521	0	ENST00000324856.7:c.6341del	p.Pro2114ArgfsTer21	p.P2114Rfs*21	ENST00000324856	NM_006015.4	2113	tCc/tc	20/20	1	2	FACETS	0.98	0.918	1	0.98	0.918	1	CLONAL	1	TRUE	1	0.668704740789242	2		521	699	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196851	108196851	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	160	335	0	ENST00000278616.4:c.6874C>T	p.Gln2292Ter	p.Q2292*	ENST00000278616	NM_000051.3	2292	Cag/Tag	47/63	1	2	FACETS	0.971	0.897	1	0.971	0.897	1	CLONAL	1	TRUE	1	0.668704740789242	2		335	493	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641204	3641204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs983506423	NA	P-0028621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	344	792	0	ENST00000294008.3:c.2435C>T	p.Ala812Val	p.A812V	ENST00000294008	NM_032444.2	812	gCc/gTc	12/15	1	2	FACETS	0.982	0.931	1	0.982	0.931	1	CLONAL	1	TRUE	1	0.668704740789242	2		792	1048	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928072	178928107	+	inframe_deletion	In_Frame_Del	DEL	TGGATTAGAAGATTTGCTGAACCCTATTGGTGTTAC	TGGATTAGAAGATTTGCTGAACCCTATTGGTGTTAC	-	novel	NA	P-0028621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	135	530	0	ENST00000263967.3:c.1355_1390del	p.Leu452_Gly463del	p.L452_G463del	ENST00000263967	NM_006218.2	450	caTGGATTAGAAGATTTGCTGAACCCTATTGGTGTTACt/cat	8/21	1	2	FACETS	0.635	0.579	0.694	0.635	0.579	0.694	SUBCLONAL	1	TRUE	1	0.668704740789242	2		530	636	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33689937	33689937	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028742-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	67	547	0	ENST00000308377.4:c.890T>A	p.Leu297His	p.L297H	ENST00000308377	NM_152270.3	297	cTc/cAc	2/5	1	2	FACETS	0.714	0.624	0.81	0.714	0.624	0.81	SUBCLONAL	1	FALSE	1	0.527364472285603	2		547	356	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902235	50902235	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028742-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	29	674	0	ENST00000440232.2:c.127G>A	p.Glu43Lys	p.E43K	ENST00000440232	NM_002691.3	43	Gag/Aag	2/27	0.210090040631368	0	FACETS	0.207	0.167	0.253			1	INDETERMINATE	1	FALSE	0	0.527364472285603	0		674	251	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712532	52712536	+	frameshift_variant	Frame_Shift_Del	DEL	TAATG	TAATG	-	novel	NA	P-0028742-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	120	447	0	ENST00000394830.3:c.216_220del	p.Phe72LeufsTer13	p.F72Lfs*13	ENST00000394830	NM_018313.4	72	ttCATTAgg/ttgg	3/30	0.527364472285603	1	FACETS	0.952	0.87	1	0.952	0.87	1	CLONAL	1	FALSE	0	0.527364472285603	1		447	352	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38283669	38283669	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028742-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	91	551	0	ENST00000425967.3:c.809T>C	p.Ile270Thr	p.I270T	ENST00000425967	NM_001174067.1	270	aTc/aCc	7/19	1	2	FACETS	0.946	0.846	1	0.946	0.846	1	CLONAL	1	FALSE	1	0.527364472285603	2		551	365	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240767	53240767	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028742-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	65	265	0	ENST00000375401.3:c.1313T>A	p.Val438Asp	p.V438D	ENST00000375401	NM_004187.3	438	gTt/gAt	10/26	1	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	0	0.527364472285603	1		265	133	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0028809-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	226	826	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	1	2	FACETS	0.998	0.93	1	0.998	0.93	1	CLONAL	1	TRUE	1	0.454602566108098	2		826	996	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0028809-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	92	420	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	0.777	0.692	0.866	0.777	0.692	0.866	SUBCLONAL	1	TRUE	1	0.454602566108098	2		420	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578204	7578204	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028809-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	191	683	0	ENST00000269305.4:c.645T>A	p.Ser215Arg	p.S215R	ENST00000269305	NM_001126112.2	215	agT/agA	6/11	1	2	FACETS	0.908	0.84	0.979	0.908	0.84	0.979	CLONAL	1	TRUE	1	0.454602566108098	2		683	925	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591892	48591892	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028809-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	35	467	0	ENST00000342988.3:c.1055G>T	p.Gly352Val	p.G352V	ENST00000342988	NM_005359.5	352	gGa/gTa	9/12	0.197851090580902	0	FACETS	0.14	0.114	0.169			1	INDETERMINATE	1	TRUE	0	0.454602566108098	0		467	600	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219381	1219381	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028809-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	129	623	0	ENST00000326873.7:c.433G>T	p.Glu145Ter	p.E145*	ENST00000326873	NM_000455.4	145	Gag/Tag	3/10	0.454602566108098	1	FACETS	0.923	0.843	1	0.923	0.843	1	CLONAL	1	TRUE	0	0.454602566108098	1		623	475	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458740	120458740	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028809-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	61	584	0	ENST00000256646.2:c.6605C>G	p.Ser2202Cys	p.S2202C	ENST00000256646	NM_024408.3	2202	tCt/tGt	34/34	1	2	FACETS	0.521	0.45	0.598	0.521	0.45	0.598	SUBCLONAL	1	TRUE	1	0.454602566108098	2		584	515	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21630745	21630745	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028809-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	106	377	1	ENST00000421138.2:c.859T>A	p.Tyr287Asn	p.Y287N	ENST00000421138		287	Tat/Aat	8/16	1	2	FACETS	0.893	0.804	0.987	0.893	0.804	0.987	CLONAL	1	TRUE	1	0.454602566108098	2		378	522	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197716	66197716	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs563678006	NA	P-0028809-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	52	483	0	ENST00000273854.3:c.2983G>T	p.Asp995Tyr	p.D995Y	ENST00000273854	NM_004439.5	995	Gac/Tac	17/18	1	2	FACETS	0.392	0.333	0.456	0.392	0.333	0.456	SUBCLONAL	1	TRUE	1	0.454602566108098	2		483	584	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647402	117647402	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs765553432	NA	P-0028809-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	45	598	0	ENST00000368508.3:c.5542A>T	p.Ile1848Phe	p.I1848F	ENST00000368508	NM_002944.2	1848	Att/Ttt	33/43	1	2	FACETS	0.252	0.211	0.298	0.252	0.211	0.298	SUBCLONAL	1	TRUE	1	0.454602566108098	2		598	786	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0028970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	96	393	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.134997473187867	4	FACETS	0.815	0.736	0.897	0.815	0.736	0.897	INDETERMINATE	2	TRUE	2	0.708169311608072	4		393	284	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0028970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	75	425	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.134997473187867	4	FACETS	1	0.971	1	0.658	0.583	0.736	INDETERMINATE	1	TRUE	2	0.708169311608072	4		426	275	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0028970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	181	663	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.989	0.919	1	0.989	0.919	1	CLONAL	1	TRUE	1	0.708169311608072	2		663	517	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0028970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	49	111	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	0.76	0.654	0.873	0.76	0.654	0.873	SUBCLONAL	1	TRUE	1	0.708169311608072	2		111	182	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916726	178916726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772110575	NA	P-0028970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	73	398	0	ENST00000263967.3:c.113G>A	p.Arg38His	p.R38H	ENST00000263967	NM_006218.2	38	cGt/cAt	2/21	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.708169311608072	2		398	202	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0028970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	461	490	4	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	1	0.974	1	1	0.998	1	CLONAL	2	TRUE	1	0.708169311608072	2		494	648	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0028970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	126	346	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.883	0.807	0.961	0.883	0.807	0.961	CLONAL	1	TRUE	1	0.708169311608072	2		347	403	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0028970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	173	425	11	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.708169311608072	2		436	461	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	24	307	2	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.142	0.111	0.179	0.142	0.111	0.179	SUBCLONAL	1	TRUE	1	0.708169311608072	2		309	476	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424734	47424734	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	289	616	1	ENST00000377045.4:c.547del	p.Gln183ArgfsTer109	p.Q183Rfs*109	ENST00000377045	NM_001654.4	181	aCc/ac	6/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.708169311608072	2		617	779	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793466	18793466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193113798	NA	P-0028970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	80	459	2	ENST00000266497.5:c.4163C>T	p.Thr1388Met	p.T1388M	ENST00000266497		1388	aCg/aTg	30/31	0.134997473187867	4	FACETS	0.828	0.741	0.918	0.828	0.741	0.918	INDETERMINATE	2	TRUE	2	0.708169311608072	4		461	233	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922363	178922363	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	71	444	0	ENST00000263967.3:c.1132T>C	p.Cys378Arg	p.C378R	ENST00000263967	NM_006218.2	378	Tgt/Cgt	6/21	1	2	FACETS	0.76	0.671	0.853	0.76	0.671	0.853	SUBCLONAL	1	TRUE	1	0.708169311608072	2		444	264	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944516	71944516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293622519	NA	P-0028970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	230	693	0	ENST00000298229.2:c.2072G>A	p.Arg691Gln	p.R691Q	ENST00000298229	NM_001567.3	691	cGg/cAg	18/28	1	2	FACETS	0.936	0.877	0.996	0.936	0.877	0.996	CLONAL	1	TRUE	1	0.708169311608072	2		693	694	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852702	63852702	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	149	598	0	ENST00000279873.7:c.3480del	p.Asn1160LysfsTer6	p.N1160Kfs*6	ENST00000279873	NM_032199.2	1160	aaC/aa	10/10	0.134997473187867	4	FACETS	0.79	0.728	0.854	0.79	0.728	0.854	INDETERMINATE	2	TRUE	2	0.708169311608072	4		598	455	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720875	89720875	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	rs398123313	NA	P-0028970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	65	323	0	ENST00000371953.3:c.1026+1del		p.K342fs	ENST00000371953	NM_000314.4	342	aaG/aa	8/9	0.134997473187867	4	FACETS	1	0.968	1	0.673	0.591	0.759	INDETERMINATE	1	TRUE	2	0.708169311608072	4		323	233	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563155	21563155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1407362044	NA	P-0028970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	45	778	1	ENST00000382592.4:c.764G>A	p.Arg255Gln	p.R255Q	ENST00000382592	NM_014572.2	255	cGg/cAg	4/8	1	2	FACETS	0.189	0.158	0.223	0.189	0.158	0.223	SUBCLONAL	1	TRUE	1	0.708169311608072	2		779	673	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358613	67358613	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	587	681	0	ENST00000327367.4:c.121A>G	p.Lys41Glu	p.K41E	ENST00000327367	NM_005902.3	41	Aaa/Gaa	1/9	0.708169311608072	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.708169311608072	2		681	819	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209278	36209278	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs865852502	NA	P-0028970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	246	619	0	ENST00000222270.7:c.358G>T	p.Glu120Ter	p.E120*	ENST00000222270	NM_014727.1	120	Gag/Tag	1/37	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.708169311608072	2		619	693	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795157	42795157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	284	882	0	ENST00000575354.2:c.2237C>T	p.Ala746Val	p.A746V	ENST00000575354	NM_015125.3	746	gCt/gTt	10/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.708169311608072	2		882	683	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190708757	190708757	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	105	564	1	ENST00000441310.2:c.650C>T	p.Ala217Val	p.A217V	ENST00000441310	NM_000534.4	217	gCt/gTt	6/13	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.708169311608072	2		565	282	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540496	187540496	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs367553275	NA	P-0028970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	126	413	0	ENST00000441802.2:c.7244A>G	p.Tyr2415Cys	p.Y2415C	ENST00000441802	NM_005245.3	2415	tAt/tGt	10/27	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.708169311608072	2		413	323	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206804	162206804	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1262180713	NA	P-0028970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	156	499	0	ENST00000366898.1:c.871G>T	p.Ala291Ser	p.A291S	ENST00000366898	NM_004562.2	291	Gct/Tct	7/12	0.134997473187867	4	FACETS	0.938	0.869	1	0.938	0.869	1	INDETERMINATE	2	TRUE	2	0.708169311608072	4		499	401	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214428	55214428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	179	499	0	ENST00000275493.2:c.554G>A	p.Gly185Asp	p.G185D	ENST00000275493	NM_005228.3	185	gGc/gAc	4/28	1	2	FACETS	0.948	0.881	1	0.948	0.881	1	CLONAL	1	TRUE	1	0.708169311608072	2		499	533	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846095	151846095	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	205	464	1	ENST00000262189.6:c.12917C>A	p.Pro4306His	p.P4306H	ENST00000262189	NM_170606.2	4306	cCc/cAc	52/59	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.708169311608072	2		465	489	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739893	145739893	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377298374	NA	P-0028970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	269	649	0	ENST00000428558.2:c.1637C>T	p.Pro546Leu	p.P546L	ENST00000428558	NM_004260.3	546	cCg/cTg	10/22	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.708169311608072	2		649	708	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798840	135798840	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	92	375	0	ENST00000298552.3:c.403G>A	p.Val135Met	p.V135M	ENST00000298552	NM_001162426.1	135	Gtg/Atg	6/23	1	2	FACETS	0.921	0.83	1	0.921	0.83	1	CLONAL	1	TRUE	1	0.708169311608072	2		375	282	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044490	47044490	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	248	635	1	ENST00000377604.3:c.1987A>G	p.Asn663Asp	p.N663D	ENST00000377604	NM_001204468.1	663	Aac/Gac	18/24	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.708169311608072	2		636	658	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696425	47696425	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519967	NA	P-0029339-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	260	586	0	ENST00000347630.2:c.398T>C	p.Phe133Ser	p.F133S	ENST00000347630	NM_001007230.1	133	tTc/tCc	6/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.802606719514457	2		586	604	SUCCESS
APC	324	MSKCC	GRCh37	5	112175906	112175912	+	frameshift_variant	Frame_Shift_Del	DEL	TCAGAGC	TCAGAGC	-	novel	NA	P-0029339-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	113	450	0	ENST00000257430.4:c.4615_4621del	p.Glu1540LeufsTer23	p.E1540Lfs*23	ENST00000257430	NM_000038.5	1539	TCAGAGCag/ag	16/16	0.776290827915987	1	FACETS	0.974	0.909	1	0.974	0.909	1	CLONAL	1	TRUE	0	0.802606719514457	1		450	173	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196895	108196896	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0029339-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	198	466	0	ENST00000278616.4:c.6919_6920del	p.Leu2307CysfsTer65	p.L2307Cfs*65	ENST00000278616	NM_000051.3	2306	agTCtt/agtt	47/63	1	2	FACETS	0.914	0.853	0.976	0.914	0.853	0.976	CLONAL	1	TRUE	1	0.802606719514457	2		466	540	SUCCESS
APC	324	MSKCC	GRCh37	5	112175096	112175097	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs786203760	NA	P-0029708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	41	187	0	ENST00000257430.4:c.3807_3808del	p.Ile1269MetfsTer6	p.I1269Mfs*6	ENST00000257430	NM_000038.5	1269	ATa/a	16/16	1	2	FACETS	0.832	0.698	0.979	0.832	0.698	0.979	CLONAL	1	TRUE	1	0.385002816520361	2		187	256	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0029708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	361	475	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.385002816520361	5	FACETS	0.948	0.905	0.992			1	CLONAL	4	TRUE	NA	0.385002816520361	5		475	780	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0029708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	58	267	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.939	0.812	1	0.939	0.812	1	CLONAL	1	TRUE	1	0.385002816520361	2		267	321	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437230	220437230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs960266462	NA	P-0029708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1233	291	1139	4	ENST00000243786.2:c.134C>T	p.Ala45Val	p.A45V	ENST00000243786	NM_002191.3	45	gCg/gTg	1/2	0.385002816520361	3	FACETS	1	0.987	1	0.591	0.555	0.629	CLONAL	1	TRUE	1	0.385002816520361	3		1143	1524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0029708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	342	530	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.385002816520361	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.385002816520361	2		530	721	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59820411	59820411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555590382	NA	P-0029708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	258	577	0	ENST00000259008.2:c.2342C>T	p.Thr781Ile	p.T781I	ENST00000259008	NM_032043.2	781	aCa/aTa	16/20	0.252877309672636	3	FACETS	1	0.988	1	0.781	0.736	0.827	CLONAL	2	TRUE	0	0.385002816520361	3		577	682	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281248	15281248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754875491	NA	P-0029708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	523	997	1	ENST00000263388.2:c.5008G>A	p.Glu1670Lys	p.E1670K	ENST00000263388	NM_000435.2	1670	Gag/Aag	27/33	0.385002816520361	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	2	0.385002816520361	4		998	1653	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176579	142176579	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	50	582	0	ENST00000350721.4:c.7522C>T	p.Pro2508Ser	p.P2508S	ENST00000350721	NM_001184.3	2508	Cca/Tca	45/47	0.154049565747551	3	FACETS	0.462	0.391	0.54	0.231	0.195	0.27	INDETERMINATE	1	TRUE	1	0.385002816520361	3		582	670	SUCCESS
ATR	545	MSKCC	GRCh37	3	142255011	142255011	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	66	323	0	ENST00000350721.4:c.3758A>G	p.Tyr1253Cys	p.Y1253C	ENST00000350721	NM_001184.3	1253	tAt/tGt	20/47	0.154049565747551	3	FACETS	1	0.924	1	0.542	0.473	0.617	INDETERMINATE	1	TRUE	1	0.385002816520361	3		323	377	SUCCESS
APC	324	MSKCC	GRCh37	5	112154907	112154907	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	152	612	0	ENST00000257430.4:c.1178C>A	p.Ser393Ter	p.S393*	ENST00000257430	NM_000038.5	393	tCa/tAa	10/16	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.385002816520361	2		612	734	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	129	425	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.576075314047363	1	FACETS	0.811	0.743	0.882	0.811	0.743	0.882	CLONAL	1	TRUE	0	0.576075314047363	1		426	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0031052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	219	586	1	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	0.576075314047363	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.576075314047363	2		587	337	SUCCESS
APC	324	MSKCC	GRCh37	5	112137048	112137048	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1326410920	NA	P-0031052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	184	363	1	ENST00000257430.4:c.802G>T	p.Glu268Ter	p.E268*	ENST00000257430	NM_000038.5	268	Gaa/Taa	8/16	1	2	FACETS	0.877	0.812	0.945	0.877	0.812	0.945	CLONAL	1	TRUE	1	0.576075314047363	2		364	728	SUCCESS
APC	324	MSKCC	GRCh37	5	112175171	112175171	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085373	NA	P-0031052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	34	172	0	ENST00000257430.4:c.3880C>T	p.Gln1294Ter	p.Q1294*	ENST00000257430	NM_000038.5	1294	Cag/Tag	16/16	1	2	FACETS	0.837	0.696	0.99	0.837	0.696	0.99	CLONAL	1	TRUE	1	0.576075314047363	2		172	141	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263288	115263288	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0031052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	179	491	0	ENST00000438362.2:c.2062A>T	p.Lys688Ter	p.K688*	ENST00000438362	NM_001242891.1	688	Aaa/Taa	17/20	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.576075314047363	2		491	603	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753779	42753779	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1362941547	NA	P-0031052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	92	705	0	ENST00000222329.4:c.485C>T	p.Pro162Leu	p.P162L	ENST00000222329	NM_006494.2	162	cCa/cTa	4/4	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.576075314047363	2		705	271	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955052	55955052	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	152	346	1	ENST00000263923.4:c.3493C>A	p.Gln1165Lys	p.Q1165K	ENST00000263923	NM_002253.2	1165	Caa/Aaa	26/30	0.576075314047363	1	FACETS	0.978	0.906	1	0.978	0.906	1	CLONAL	1	TRUE	0	0.576075314047363	1		347	384	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	32	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.889	0.721	1	0.889	0.721	1	CLONAL	1	TRUE	1	0.15	2		326	480	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	33	210	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.967	0.787	1	0.967	0.787	1	CLONAL	1	TRUE	1	0.15	2		210	455	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	35	330	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.738	0.604	0.89	0.738	0.604	0.89	SUBCLONAL	1	TRUE	1	0.15	2		331	632	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138642	55138642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143344944	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	58	518	0	ENST00000257290.5:c.1319C>T	p.Thr440Met	p.T440M	ENST00000257290	NM_006206.4	440	aCg/aTg	9/23	1	2	FACETS	0.899	0.771	1	0.899	0.771	1	CLONAL	1	TRUE	1	0.15	2		518	860	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348128	348128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748975424	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	48	636	2	ENST00000262320.3:c.1378C>T	p.Arg460Trp	p.R460W	ENST00000262320	NM_003502.3	460	Cgg/Tgg	6/11	1	2	FACETS	0.798	0.673	0.937	0.798	0.673	0.937	CLONAL	1	TRUE	1	0.15	2		638	802	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	43	598	1	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.71	0.593	0.842	0.71	0.593	0.842	SUBCLONAL	1	TRUE	1	0.15	2		599	807	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472142	472142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1309760726	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	43	489	1	ENST00000399788.2:c.659G>A	p.Arg220His	p.R220H	ENST00000399788	NM_001042603.1	220	cGt/cAt	5/28	0.3	2	FACETS	0.766	0.64	0.908			1	CLONAL	1	TRUE	NA	0.15	2		490	748	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221936	98221936	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1064794260	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	51	479	0	ENST00000331920.6:c.2833C>T	p.Arg945Ter	p.R945*	ENST00000331920	NM_000264.3	945	Cga/Tga	17/24	1	2	FACETS	0.862	0.731	1	0.862	0.731	1	CLONAL	1	TRUE	1	0.15	2		479	789	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	62	552	1	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	0.847	0.729	0.976	0.847	0.729	0.976	CLONAL	1	TRUE	1	0.15	2		553	976	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	47	446	0	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	1	2	FACETS	0.813	0.684	0.956	0.813	0.684	0.956	CLONAL	1	TRUE	1	0.15	2		446	771	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624936	9624936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760501160	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	36	424	0	ENST00000353224.5:c.41C>T	p.Pro14Leu	p.P14L	ENST00000353224	NM_177990.2	14	cCg/cTg	3/10	1	2	FACETS	0.932	0.765	1	0.932	0.765	1	CLONAL	1	TRUE	1	0.15	2		424	515	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	43	371	1	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.866	0.723	1	0.866	0.723	1	CLONAL	1	TRUE	1	0.15	2		372	662	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924822	49924822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202007332	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	66	739	1	ENST00000296474.3:c.4121G>A	p.Arg1374His	p.R1374H	ENST00000296474	NM_002447.2	1374	cGt/cAt	20/20	1	2	FACETS	0.859	0.743	0.985	0.859	0.743	0.985	CLONAL	1	TRUE	1	0.15	2		740	1025	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197564	106197564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754215085	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	45	457	0	ENST00000380013.4:c.5897G>A	p.Arg1966His	p.R1966H	ENST00000380013	NM_001127208.2	1966	cGt/cAt	11/11	1	2	FACETS	0.872	0.731	1	0.872	0.731	1	CLONAL	1	TRUE	1	0.15	2		457	688	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656969	47656969	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779075	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	59	374	0	ENST00000233146.2:c.1165C>T	p.Arg389Ter	p.R389*	ENST00000233146	NM_000251.2	389	Cga/Tga	7/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.15	2		374	578	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111886074	111886074	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs72650662	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	59	541	0	ENST00000341259.2:c.1696C>T	p.Arg566Trp	p.R566W	ENST00000341259	NM_005475.2	566	Cgg/Tgg	8/8	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.15	2		541	760	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	67	706	2	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.871	0.754	0.998	0.871	0.754	0.998	CLONAL	1	TRUE	1	0.15	2		708	1026	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416416	49416416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123734	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	47	476	0	ENST00000301067.7:c.16295G>A	p.Arg5432Gln	p.R5432Q	ENST00000301067	NM_003482.3	5432	cGg/cAg	51/54	1	2	FACETS	0.791	0.666	0.93	0.791	0.666	0.93	CLONAL	1	TRUE	1	0.15	2		476	792	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214398	36214398	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs868041281	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	63	610	3	ENST00000222270.7:c.3057del	p.Gly1020AlafsTer4	p.G1020Afs*4	ENST00000222270	NM_014727.1	1018	Aaa/aa	7/37	1	2	FACETS	0.891	0.768	1	0.891	0.768	1	CLONAL	1	TRUE	1	0.15	2		613	943	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863054	56863054	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1266824391	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	32	567	2	ENST00000519728.1:c.327del	p.Glu110LysfsTer15	p.E110Kfs*15	ENST00000519728	NM_002350.3	107	acA/ac	5/13	1	2	FACETS	0.732	0.593	0.89	0.732	0.593	0.89	SUBCLONAL	1	TRUE	1	0.15	2		569	583	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459167	120459167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746551843	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	58	628	0	ENST00000256646.2:c.6178C>T	p.Arg2060Cys	p.R2060C	ENST00000256646	NM_024408.3	2060	Cgc/Tgc	34/34	1	2	FACETS	0.874	0.749	1	0.874	0.749	1	CLONAL	1	TRUE	1	0.15	2		628	885	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210704	5210704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766174955	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	52	631	2	ENST00000357368.4:c.5347C>T	p.Arg1783Trp	p.R1783W	ENST00000357368	NM_002850.3	1783	Cgg/Tgg	34/38	1	2	FACETS	0.824	0.7	0.962	0.824	0.7	0.962	CLONAL	1	TRUE	1	0.15	2		633	841	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107713	30107713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1160777726	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	55	520	0	ENST00000331968.5:c.967G>A	p.Glu323Lys	p.E323K	ENST00000331968	NM_002742.2	323	Gaa/Aaa	6/18	1	2	FACETS	0.98	0.837	1	0.98	0.837	1	CLONAL	1	TRUE	1	0.15	2		520	748	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838096	89838096	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1054636249	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	57	471	0	ENST00000389301.3:c.2141G>A	p.Arg714Gln	p.R714Q	ENST00000389301	NM_000135.2	714	cGg/cAg	23/43	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.15	2		471	740	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533668	63533668	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773033390	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	43	568	0	ENST00000307078.5:c.1486G>A	p.Ala496Thr	p.A496T	ENST00000307078	NM_004655.3	496	Gcc/Acc	6/11	1	2	FACETS	0.782	0.653	0.926	0.782	0.653	0.926	CLONAL	1	TRUE	1	0.15	2		568	733	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829115	72829115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	39	505	0	ENST00000268489.5:c.7466del	p.Pro2489LeufsTer39	p.P2489Lfs*39	ENST00000268489	NM_006885.3	2489	cCt/ct	9/10	1	2	FACETS	0.759	0.628	0.907	0.759	0.628	0.907	CLONAL	1	TRUE	1	0.15	2		505	685	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317159	11317159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	57	629	0	ENST00000361445.4:c.335G>A	p.Arg112Gln	p.R112Q	ENST00000361445	NM_004958.3	112	cGg/cAg	4/58	1	2	FACETS	0.819	0.701	0.949	0.819	0.701	0.949	CLONAL	1	TRUE	1	0.15	2		629	928	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138934	64138934	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	27	313	0	ENST00000334205.4:c.2305del	p.Leu769CysfsTer15	p.L769Cfs*15	ENST00000334205	NM_003942.2	767	ggC/gg	17/17	1	2	FACETS	0.732	0.581	0.905	0.732	0.581	0.905	CLONAL	1	TRUE	1	0.15	2		313	492	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456418	99456418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138992740	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	51	594	0	ENST00000268035.6:c.1735G>A	p.Val579Ile	p.V579I	ENST00000268035	NM_000875.3	579	Gtt/Att	8/21	1	2	FACETS	0.805	0.682	0.94	0.805	0.682	0.94	CLONAL	1	TRUE	1	0.15	2		594	845	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096258	2096258	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	67	687	0	ENST00000219066.1:c.249G>T	p.Lys83Asn	p.K83N	ENST00000219066	NM_002528.5	83	aaG/aaT	2/6	1	2	FACETS	0.848	0.734	0.971	0.848	0.734	0.971	CLONAL	1	TRUE	1	0.15	2		687	1054	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838148	89838148	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376888740	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	58	602	1	ENST00000389301.3:c.2089G>A	p.Val697Ile	p.V697I	ENST00000389301	NM_000135.2	697	Gtt/Att	23/43	1	2	FACETS	0.82	0.702	0.949	0.82	0.702	0.949	CLONAL	1	TRUE	1	0.15	2		603	943	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923324	78923324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759681695	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	40	587	0	ENST00000306801.3:c.3347C>T	p.Ser1116Leu	p.S1116L	ENST00000306801	NM_020761.2	1116	tCg/tTg	28/34	1	2	FACETS	0.744	0.616	0.887	0.744	0.616	0.887	SUBCLONAL	1	TRUE	1	0.15	2		587	717	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39613899	39613899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775480477	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	23	401	0	ENST00000262039.4:c.1817C>T	p.Pro606Leu	p.P606L	ENST00000262039	NM_002647.2	606	cCg/cTg	16/25	1	2	FACETS	0.845	0.658	1	0.845	0.658	1	CLONAL	1	TRUE	1	0.15	2		401	363	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224506	36224506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752337579	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	83	839	2	ENST00000222270.7:c.6968G>A	p.Arg2323His	p.R2323H	ENST00000222270	NM_014727.1	2323	cGt/cAt	29/37	1	2	FACETS	0.967	0.851	1	0.967	0.851	1	CLONAL	1	TRUE	1	0.15	2		841	1144	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182213	99182213	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs984538193	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	54	534	0	ENST00000074304.5:c.2278G>A	p.Val760Ile	p.V760I	ENST00000074304	NM_001134224.1	760	Gtc/Atc	21/26	1	2	FACETS	0.735	0.625	0.855	0.735	0.625	0.855	SUBCLONAL	1	TRUE	1	0.15	2		534	980	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714412	40714412	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	53	513	0	ENST00000373198.4:c.3985G>A	p.Glu1329Lys	p.E1329K	ENST00000373198	NM_133170.3	1329	Gag/Aag	29/32	1	2	FACETS	0.861	0.732	1	0.861	0.732	1	CLONAL	1	TRUE	1	0.15	2		513	821	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249511	153249511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	46	544	0	ENST00000281708.4:c.1267G>A	p.Gly423Arg	p.G423R	ENST00000281708	NM_033632.3	423	Gga/Aga	9/12	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.15	2		544	586	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435696	149435696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1214473761	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	47	574	0	ENST00000286301.3:c.2447G>A	p.Arg816His	p.R816H	ENST00000286301	NM_005211.3	816	cGc/cAc	19/22	1	2	FACETS	0.746	0.628	0.878	0.746	0.628	0.878	SUBCLONAL	1	TRUE	1	0.15	2		574	840	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923850	39923850	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs760373288	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	44	564	0	ENST00000378444.4:c.3241G>A	p.Glu1081Lys	p.E1081K	ENST00000378444	NM_001123385.1	1081	Gag/Aag	7/15	1	2	FACETS	0.776	0.649	0.917	0.776	0.649	0.917	CLONAL	1	TRUE	1	0.15	2		564	756	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229221	123229221	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0031211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	23	343	0	ENST00000218089.9:c.3706-1G>A		p.X1236_splice	ENST00000218089	NM_001042749.1	1236			1	2	FACETS	0.697	0.542	0.877	0.697	0.542	0.877	SUBCLONAL	1	TRUE	1	0.15	2		343	440	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0031217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	449	407	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.20625105312769	5	FACETS	1	0.978	1			1	INDETERMINATE	3	TRUE	NA	0.494386028464845	5		407	1023	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0031217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	311	764	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.494386028464845	1	FACETS	0.981	0.928	1	0.981	0.928	1	CLONAL	1	TRUE	0	0.494386028464845	1		765	965	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696716	47696716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	219	573	0	ENST00000347630.2:c.232G>A	p.Glu78Lys	p.E78K	ENST00000347630	NM_001007230.1	78	Gaa/Aaa	5/11	0.287728498021206	1	FACETS	0.895	0.836	0.956	0.895	0.836	0.956	INDETERMINATE	1	TRUE	0	0.494386028464845	1		573	745	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054540	42054541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0031217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	121	341	0	ENST00000219905.7:c.7731dup	p.Asp2578ArgfsTer45	p.D2578Rfs*45	ENST00000219905	NM_001164273.1	2575	aga/agAa	22/24	0.494386028464845	1	FACETS	0.755	0.686	0.827	0.755	0.686	0.827	SUBCLONAL	1	TRUE	0	0.494386028464845	1		341	488	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302646	15302646	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	400	897	0	ENST00000263388.2:c.712G>C	p.Asp238His	p.D238H	ENST00000263388	NM_000435.2	238	Gac/Cac	5/33	0.267119379658473	3	FACETS	1	0.993	1	0.635	0.603	0.668	INDETERMINATE	1	TRUE	1	0.494386028464845	3		897	1589	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302867	15302867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	428	966	0	ENST00000263388.2:c.583G>A	p.Glu195Lys	p.E195K	ENST00000263388	NM_000435.2	195	Gag/Aag	4/33	0.267119379658473	3	FACETS	1	0.995	1	0.689	0.655	0.723	INDETERMINATE	1	TRUE	1	0.494386028464845	3		966	1567	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744494	41744494	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	72	856	1	ENST00000301178.4:c.1114C>A	p.Gln372Lys	p.Q372K	ENST00000301178	NM_021913.4	372	Caa/Aaa	8/20	1	2	FACETS	0.258	0.225	0.295	0.258	0.225	0.295	SUBCLONAL	1	TRUE	1	0.494386028464845	2		857	1127	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248453	212248453	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	26	474	0	ENST00000342788.4:c.3814G>T	p.Gly1272Trp	p.G1272W	ENST00000342788	NM_005235.2	1272	Ggg/Tgg	28/28	0.320378126435333	1	FACETS	0.153	0.121	0.191	0.153	0.121	0.191	SUBCLONAL	1	TRUE	0	0.494386028464845	1		474	517	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659941	227659941	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	63	900	0	ENST00000305123.5:c.3514G>T	p.Gly1172Cys	p.G1172C	ENST00000305123	NM_005544.2	1172	Ggt/Tgt	1/2	0.320378126435333	1	FACETS	0.208	0.179	0.24	0.208	0.179	0.24	SUBCLONAL	1	TRUE	0	0.494386028464845	1		900	922	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0031282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	360	629	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.709902495493127	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.762177458052623	1		630	570	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007689	45007690	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0031282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	129	376	0	ENST00000558401.1:c.137_138del	p.Tyr46CysfsTer10	p.Y46Cfs*10	ENST00000558401	NM_004048.2	46	TAt/t	2/4	0.762177458052623	1	FACETS	0.53	0.485	0.577	0.53	0.485	0.577	SUBCLONAL	1	TRUE	0	0.762177458052623	1		376	395	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003812	45003812	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0031282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	94	389	0	ENST00000558401.1:c.67+1G>A		p.X23_splice	ENST00000558401	NM_004048.2	23			0.762177458052623	1	FACETS	0.387	0.347	0.43	0.387	0.347	0.43	SUBCLONAL	1	TRUE	0	0.762177458052623	1		389	394	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123889560	123889560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	34	156	0	ENST00000330479.4:c.787G>A	p.Ala263Thr	p.A263T	ENST00000330479	NM_020382.3	263	Gca/Aca	7/9	1	2	FACETS	0.397	0.326	0.474	0.397	0.326	0.474	SUBCLONAL	1	TRUE	1	0.762177458052623	2		156	225	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007761	45007761	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	25	397	0	ENST00000558401.1:c.208G>T	p.Glu70Ter	p.E70*	ENST00000558401	NM_004048.2	70	Gag/Tag	2/4	0.762177458052623	1	FACETS	0.099	0.077	0.123	0.099	0.077	0.123	SUBCLONAL	1	TRUE	0	0.762177458052623	1		397	411	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256204	41256204	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	318	445	0	ENST00000357654.3:c.376C>G	p.Gln126Glu	p.Q126E	ENST00000357654	NM_007294.3	126	Caa/Gaa	6/23	1	2	FACETS	0.925	0.876	0.975	0.925	0.876	0.975	CLONAL	1	TRUE	1	0.762177458052623	2		445	902	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656915	45656915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs558943057	NA	P-0031282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	123	729	1	ENST00000407780.3:c.241C>T	p.Arg81Trp	p.R81W	ENST00000407780	NM_001283052.1	81	Cgg/Tgg	3/7	1	2	FACETS	0.319	0.288	0.352	0.319	0.288	0.352	SUBCLONAL	1	TRUE	1	0.762177458052623	2		730	1012	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175391	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0031282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	268	301	0	ENST00000257430.4:c.4100dup	p.Thr1368AspfsTer7	p.T1368Dfs*7	ENST00000257430	NM_000038.5	1367	cag/cAag	16/16	0.759431974010828	2	FACETS	0.873	0.835	0.909	0.873	0.835	0.909	CLONAL	2	TRUE	0	0.762177458052623	2		301	403	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513452	149513452	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757668250	NA	P-0031282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	153	603	0	ENST00000261799.4:c.751C>T	p.Arg251Cys	p.R251C	ENST00000261799	NM_002609.3	251	Cgc/Tgc	5/23	0.759431974010828	2	FACETS	0.515	0.472	0.561	0.258	0.236	0.281	SUBCLONAL	1	TRUE	0	0.762177458052623	2		603	779	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111500	8111501	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0031377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	183	676	1	ENST00000346208.3:c.986_987insA	p.Arg330GlufsTer22	p.R330Efs*22	ENST00000346208		329	agg/agAg	5/6	0.342162226023735	4	FACETS	1	0.989	1	0.72	0.664	0.778	CLONAL	1	FALSE	2	0.373985635995527	4		677	934	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0031439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	188	407	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.360909951107718	3	FACETS	1	0.991	1	0.73	0.682	0.779	INDETERMINATE	1	TRUE	1	0.782408334090286	3		407	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579410	7579410	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567556123	NA	P-0031439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	423	742	0	ENST00000269305.4:c.277del	p.Leu93CysfsTer30	p.L93Cfs*30	ENST00000269305	NM_001126112.2	93	Ctg/tg	4/11	0.782408334090286	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.782408334090286	1		742	603	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123505237	123505237	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	132	376	0	ENST00000371139.4:c.383C>A	p.Pro128Gln	p.P128Q	ENST00000371139	NM_001114937.2	128	cCa/cAa	4/4	1	2	FACETS	0.863	0.792	0.936	0.863	0.792	0.936	CLONAL	1	TRUE	1	0.782408334090286	2		376	391	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359437	118359437	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	266	384	0	ENST00000534358.1:c.4441T>A	p.Phe1481Ile	p.F1481I	ENST00000534358	NM_005933.3	1481	Ttc/Atc	11/36	0.178718012159844	2	FACETS	1	0.991	1	0.616	0.583	0.648	INDETERMINATE	1	TRUE	0	0.782408334090286	2		384	552	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585498	29585498	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	101	231	0	ENST00000356175.3:c.4250del	p.Gly1417AlafsTer2	p.G1417Afs*2	ENST00000356175	NM_000267.3	1416	aGg/ag	31/57	0.782408334090286	1	FACETS	0.832	0.765	0.898	0.832	0.765	0.898	CLONAL	1	TRUE	0	0.782408334090286	1		231	189	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	G	rs1131691003	NA	P-0031766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	130	511	0	ENST00000269305.4:c.96+1G>C		p.X32_splice	ENST00000269305	NM_001126112.2	32			0.259047593307649	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.272111590535849	1		511	770	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47735817	47735817	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	76	503	0	ENST00000449228.1:c.43G>C	p.Val15Leu	p.V15L	ENST00000449228	NM_001127240.2	15	Gtg/Ctg	1/4	0.272111590535849	1	FACETS	0.482	0.422	0.548	0.482	0.422	0.548	SUBCLONAL	1	TRUE	0	0.272111590535849	1		503	1001	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0031810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	24	588	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	FALSE	1	0.187138099697016	2		588	213	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121556	193121556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	21	331	0	ENST00000367435.3:c.954G>A	p.Met318Ile	p.M318I	ENST00000367435	NM_024529.4	318	atG/atA	10/17	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	FALSE	1	0.187138099697016	2		331	175	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489526	40489526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	41	604	0	ENST00000264657.5:c.724G>A	p.Asp242Asn	p.D242N	ENST00000264657	NM_139276.2	242	Gac/Aac	8/24	1	2	FACETS	0.824	0.69	0.97	1	0.962	1	CLONAL	2	FALSE	1	0.187138099697016	2		604	266	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0031856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	316	520	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.511535325355047	3	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.511535325355047	3		520	652	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0031856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	101	252	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	NA	2	FACETS	0.796	0.725	0.869			1	INDETERMINATE	2	TRUE	NA	0.511535325355047	2		252	248	SUCCESS
AR	367	MSKCC	GRCh37	X	66943552	66943552	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137852578	NA	P-0031856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	636	119	2	ENST00000374690.3:c.2632A>G	p.Thr878Ala	p.T878A	ENST00000374690	NM_000044.3	878	Act/Gct	8/8	0.511535325355047	9	FACETS	0.966	0.938	0.994			1	CLONAL	7	TRUE	NA	0.511535325355047	9		121	1026	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457764	149457764	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	197	344	0	ENST00000286301.3:c.640C>T	p.Arg214Trp	p.R214W	ENST00000286301	NM_005211.3	214	Cgg/Tgg	5/22	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.511535325355047	2		344	636	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696688	47696688	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519971	NA	P-0031856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	119	277	0	ENST00000347630.2:c.260A>G	p.Tyr87Cys	p.Y87C	ENST00000347630	NM_001007230.1	87	tAc/tGc	5/11	1	2	FACETS	0.977	0.888	1	0.977	0.888	1	CLONAL	1	TRUE	1	0.511535325355047	2		277	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0031885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	279	973	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.360820358236195	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.360820358236195	1		973	979	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	115	425	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.957	0.864	1	0.957	0.864	1	CLONAL	1	TRUE	1	0.360820358236195	2		426	666	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	67	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.317948682926434	4	FACETS	1	0.95	1	0.589	0.515	0.67	CLONAL	1	TRUE	2	0.420465857984094	4		326	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0031918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	212	609	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.28118170163291	2	FACETS	0.922	0.863	0.981	0.922	0.863	0.981	CLONAL	2	TRUE	0	0.420465857984094	2		610	547	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591825	48591825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767342	NA	P-0031918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	47	134	0	ENST00000342988.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000342988	NM_005359.5	330	Gaa/Aaa	9/12	1	2	FACETS	0.884	0.752	1	0.884	0.752	1	CLONAL	1	TRUE	1	0.420465857984094	2		134	253	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971204	21971208	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	TGACC	TGACC	-	novel	NA	P-0031918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	63	170	0	ENST00000304494.5:c.151-1_154del		p.X51_splice	ENST00000304494	NM_000077.4	51		2/3	0.419402621566392	1	FACETS	0.805	0.702	0.915	0.805	0.702	0.915	CLONAL	1	TRUE	0	0.420465857984094	1		170	294	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455298	29455298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376091121	NA	P-0031918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	65	252	0	ENST00000389048.3:c.2504C>T	p.Pro835Leu	p.P835L	ENST00000389048	NM_004304.4	835	cCg/cTg	15/29	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.420465857984094	2		252	300	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398283	25398284	+	missense_variant	Missense_Mutation	DNP	AC	AC	GA	novel	NA	P-0031956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	49	346	0	ENST00000311936.3:c.35_36delinsTC	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGT/gTC	2/5	0.132334456224481	3	FACETS	1	0.96	1	0.694	0.594	0.802	INDETERMINATE	1	TRUE	1	0.37	3		346	226	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758332	41758332	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs370684779	NA	P-0031956-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	68	702	0	ENST00000301178.4:c.1788C>A	p.Asn596Lys	p.N596K	ENST00000301178	NM_021913.4	596	aaC/aaA	15/20	1	2	FACETS	0.813	0.71	0.925	0.813	0.71	0.925	CLONAL	1	TRUE	1	0.37	2		702	452	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0032081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	125	210	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.883	0.801	0.968	0.883	0.801	0.968	CLONAL	1	TRUE	1	0.459100725673251	2		210	617	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0032081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	131	475	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.991	0.903	1	0.991	0.903	1	CLONAL	1	TRUE	1	0.459100725673251	2		475	576	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0032081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	126	491	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.935	0.85	1	0.935	0.85	1	CLONAL	1	TRUE	1	0.459100725673251	2		492	587	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0032081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	100	183	1	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	0.459100725673251	2	FACETS	0.868	0.789	0.948	0.868	0.789	0.948	CLONAL	2	TRUE	0	0.459100725673251	2		184	251	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2185868	2185868	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	192	523	1	ENST00000398665.3:c.140A>T	p.Glu47Val	p.E47V	ENST00000398665	NM_032482.2	47	gAa/gTa	3/28	1	2	FACETS	0.988	0.915	1	0.988	0.915	1	CLONAL	1	TRUE	1	0.459100725673251	2		524	847	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250823	153250823	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1159697496	NA	P-0032081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	83	258	0	ENST00000281708.4:c.1236+1G>A		p.X412_splice	ENST00000281708	NM_033632.3	412			1	2	FACETS	0.869	0.771	0.973	0.869	0.771	0.973	CLONAL	1	TRUE	1	0.459100725673251	2		258	416	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554192	63554192	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	180	541	0	ENST00000307078.5:c.547G>A	p.Glu183Lys	p.E183K	ENST00000307078	NM_004655.3	183	Gag/Aag	2/11	1	2	FACETS	0.991	0.916	1	0.991	0.916	1	CLONAL	1	TRUE	1	0.459100725673251	2		541	791	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120504	70120505	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TACA	novel	NA	P-0032081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	172	663	0	ENST00000245479.2:c.1507_1510dup	p.Thr504IlefsTer75	p.T504Ifs*75	ENST00000245479	NM_000346.3	502	-/TACA	3/3	1	2	FACETS	0.806	0.741	0.873	0.806	0.741	0.873	CLONAL	1	TRUE	1	0.459100725673251	2		663	930	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72897475	72897475	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	48	181	0	ENST00000325599.8:c.17T>G	p.Phe6Cys	p.F6C	ENST00000325599	NM_018130.2	6	tTc/tGc	1/11	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.459100725673251	2		181	208	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662441	117662441	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs761904834	NA	P-0032081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	118	396	0	ENST00000368508.3:c.4936A>G	p.Thr1646Ala	p.T1646A	ENST00000368508	NM_002944.2	1646	Aca/Gca	30/43	1	2	FACETS	0.983	0.891	1	0.983	0.891	1	CLONAL	1	TRUE	1	0.459100725673251	2		396	523	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423763	47423763	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032283-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	23	678	0	ENST00000404338.3:c.1831G>A	p.Glu611Lys	p.E611K	ENST00000404338	NM_004491.4	611	Gag/Aag	1/6	1	2	FACETS	0.274	0.213	0.344	0.274	0.213	0.344	SUBCLONAL	1	TRUE	1	0.41	2		678	410	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	189	425	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.350046569797327	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	TRUE	1	0.350046569797327	4		426	453	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0032287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	189	456	3	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.350046569797327	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	1	0.350046569797327	4		459	450	SUCCESS
APC	324	MSKCC	GRCh37	5	112175606	112175606	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	49	276	0	ENST00000257430.4:c.4316del	p.Pro1439LeufsTer34	p.P1439Lfs*34	ENST00000257430	NM_000038.5	1439	Cct/ct	16/16	0.350046569797327	4	FACETS	1	0.914	1	0.371	0.315	0.431	CLONAL	1	TRUE	1	0.350046569797327	4		276	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579419	7579420	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0032287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	250	685	0	ENST00000269305.4:c.266_267dup	p.Ser90ProfsTer34	p.S90Pfs*34	ENST00000269305	NM_001126112.2	89	-/CC	4/11	0.350046569797327	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.350046569797327	2		685	705	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165141	47165141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372869995	NA	P-0032287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	53	365	0	ENST00000409792.3:c.985C>T	p.Arg329Trp	p.R329W	ENST00000409792	NM_014159.6	329	Cgg/Tgg	3/21	0.350046569797327	3	FACETS	1	0.937	1	0.585	0.502	0.675	CLONAL	1	TRUE	1	0.350046569797327	3		365	304	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917629	151917629	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	151	644	0	ENST00000262189.6:c.3691G>T	p.Gly1231Cys	p.G1231C	ENST00000262189	NM_170606.2	1231	Ggt/Tgt	23/59	0.350046569797327	5	FACETS	0.875	0.801	0.952	0.583	0.534	0.635	CLONAL	2	TRUE	2	0.350046569797327	5		644	752	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0032299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	149	542	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.88	0.808	0.954	0.88	0.808	0.954	CLONAL	1	TRUE	1	0.60502868004929	2		542	560	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926885	112926885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507544	NA	P-0032299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	53	638	0	ENST00000351677.2:c.1505C>T	p.Ser502Leu	p.S502L	ENST00000351677	NM_002834.3	502	tCa/tTa	13/16	1	2	FACETS	0.235	0.199	0.274	0.235	0.199	0.274	SUBCLONAL	1	TRUE	1	0.60502868004929	2		638	746	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs149840192	NA	P-0032299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8191	4508	447	0	ENST00000275493.2:c.866C>A	p.Ala289Asp	p.A289D	ENST00000275493	NM_005228.3	289	gCc/gAc	7/28	0.60502868004929	34	FACETS	0.964	0.95	0.978	0.38	0.374	0.386	CLONAL	13	TRUE	1	0.60502868004929	34		447	12699	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220467	133220467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146711942	NA	P-0032299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	223	593	0	ENST00000320574.5:c.4246G>A	p.Ala1416Thr	p.A1416T	ENST00000320574	NM_006231.2	1416	Gct/Act	33/49	1	2	FACETS	0.853	0.796	0.912	0.853	0.796	0.912	CLONAL	1	TRUE	1	0.60502868004929	2		593	864	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560109	29560109	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555615039	NA	P-0032299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	25	347	0	ENST00000356175.3:c.3586C>G	p.Leu1196Val	p.L1196V	ENST00000356175	NM_000267.3	1196	Ctt/Gtt	27/57	1	2	FACETS	0.171	0.134	0.213	0.171	0.134	0.213	SUBCLONAL	1	TRUE	1	0.60502868004929	2		347	484	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480119	20480119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1275994110	NA	P-0032299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	114	350	0	ENST00000346618.3:c.436C>T	p.Leu146Phe	p.L146F	ENST00000346618	NM_001949.4	146	Ctc/Ttc	2/7	1	2	FACETS	0.994	0.904	1	0.994	0.904	1	CLONAL	1	TRUE	1	0.60502868004929	2		350	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0032339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	335	810	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.838521270834103	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.838521270834103	1		810	457	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431420	49431430	+	frameshift_variant	Frame_Shift_Del	DEL	AGTGAGCTCTC	AGTGAGCTCTC	GGAG	novel	NA	P-0032339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	319	576	1	ENST00000301067.7:c.9709_9719delinsCTCC	p.Glu3237LeufsTer3	p.E3237Lfs*3	ENST00000301067	NM_003482.3	3237	GAGAGCTCACTg/CTCCg	34/54	NA	2	FACETS	0.958	0.909	1			1	INDETERMINATE	1	TRUE	NA	0.838521270834103	2		577	794	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291059	10291059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	570	502	0	ENST00000340748.4:c.412C>T	p.Pro138Ser	p.P138S	ENST00000340748		138	Ccc/Tcc	4/40	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.838521270834103	2		502	652	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545762	106545762	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	284	448	0	ENST00000359195.3:c.3239G>A	p.Trp1080Ter	p.W1080*	ENST00000359195	NM_002649.2	1080	tGg/tAg	11/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.838521270834103	2		448	631	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055681	152055681	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	115	515	0	ENST00000262189.6:c.241G>C	p.Val81Leu	p.V81L	ENST00000262189	NM_170606.2	81	Gtg/Ctg	2/59	1	2	FACETS	0.318	0.286	0.352	0.318	0.286	0.352	SUBCLONAL	1	TRUE	1	0.838521270834103	2		515	863	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845972	151845972	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	105	442	0	ENST00000262189.6:c.13040del	p.Pro4347ArgfsTer9	p.P4347Rfs*9	ENST00000262189	NM_170606.2	4347	cCg/cg	52/59	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		442	819	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566488	41566488	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	150	434	0	ENST00000263253.7:c.4365G>T	p.Gln1455His	p.Q1455H	ENST00000263253	NM_001429.3	1455	caG/caT	27/31	1	2	FACETS	0.957	0.881	1	0.957	0.881	1	CLONAL	1	FALSE	1	0.662896561402747	2		434	473	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645739	215645739	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	158	636	1	ENST00000260947.4:c.859G>C	p.Glu287Gln	p.E287Q	ENST00000260947	NM_000465.2	287	Gag/Cag	4/11	0.662896561402747	1	FACETS	0.924	0.86	0.988	0.924	0.86	0.988	CLONAL	1	FALSE	0	0.662896561402747	1		637	345	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448705	49448705	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	158	409	0	ENST00000301067.7:c.154C>T	p.Gln52Ter	p.Q52*	ENST00000301067	NM_003482.3	52	Cag/Tag	2/54	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	FALSE	1	0.662896561402747	2		409	462	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857187	9857187	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	68	418	1	ENST00000330684.3:c.4214T>C	p.Leu1405Ser	p.L1405S	ENST00000330684	NM_001134407.1	1405	tTg/tCg	13/13	0.102847405870024	0	FACETS	0.138	0.12	0.157			1	INDETERMINATE	1	FALSE	0	0.662896561402747	0		419	502	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600447	10600447	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	319	788	0	ENST00000171111.5:c.1408C>A	p.Arg470Ser	p.R470S	ENST00000171111	NM_203500.1	470	Cgt/Agt	4/6	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.662896561402747	2		788	900	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629328	187629328	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	102	749	0	ENST00000441802.2:c.1654G>T	p.Glu552Ter	p.E552*	ENST00000441802	NM_005245.3	552	Gaa/Taa	2/27	0.660016469117659	1	FACETS	0.365	0.327	0.406	0.365	0.327	0.406	SUBCLONAL	1	FALSE	0	0.662896561402747	1		749	563	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324628	31324628	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs151341114	NA	P-0032524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	38	171	0	ENST00000412585.2:c.180C>G	p.Phe60Leu	p.F60L	ENST00000412585	NM_005514.6	60	ttC/ttG	2/8	0.30024519911269	2	FACETS	0.948	0.802	1	0.474	0.401	0.551	INDETERMINATE	1	FALSE	0	0.662896561402747	2		171	121	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152009027	152009027	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	172	264	0	ENST00000262189.6:c.595C>T	p.Arg199Ter	p.R199*	ENST00000262189	NM_170606.2	199	Cga/Tga	5/59	NA	2	FACETS	0.947	0.894	0.999			1	INDETERMINATE	2	FALSE	NA	0.662896561402747	2		264	274	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972948	68972948	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	182	416	0	ENST00000288368.4:c.1273A>G	p.Ile425Val	p.I425V	ENST00000288368	NM_024870.2	425	Att/Gtt	11/40	0.102847405870024	0	FACETS	0.351	0.326	0.377			1	INDETERMINATE	1	FALSE	0	0.662896561402747	0		416	527	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401333	139401334	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0032524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1315	108	884	0	ENST00000277541.6:c.3735_3736delinsTT	p.Asp1246Tyr	p.D1246Y	ENST00000277541	NM_017617.3	1245	gtGGac/gtTTac	23/34	0.662896561402747	3	FACETS	0.305	0.272	0.34	0.152	0.136	0.17	SUBCLONAL	1	FALSE	1	0.662896561402747	3		884	1423	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0032597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	222	535	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.438777570102877	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.438777570102877	1		535	669	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0032597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	243	658	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.438777570102877	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.438777570102877	1		658	767	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451329	70451329	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	131	637	0	ENST00000373644.4:c.6169C>A	p.Pro2057Thr	p.P2057T	ENST00000373644	NM_030625.2	2057	Ccc/Acc	12/12	1	2	FACETS	0.694	0.629	0.761	0.694	0.629	0.761	SUBCLONAL	1	TRUE	1	0.438777570102877	2		637	861	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936781	32936781	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1566244896	NA	P-0032597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	145	463	0	ENST00000380152.3:c.7927G>A	p.Ala2643Thr	p.A2643T	ENST00000380152		2643	Gct/Act	17/27	0.438777570102877	3	FACETS	0.914	0.834	0.998	0.457	0.417	0.499	CLONAL	1	TRUE	1	0.438777570102877	3		463	882	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265805	41266404	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATG	CTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATG	-	novel	NA	P-0032597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	99	86	0	ENST00000349496.5:c.14-208_242-37del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.438777570102877	1	FACETS	0.952	0.875	1	1	0.989	1	CLONAL	2	TRUE	0	0.438777570102877	1		86	185	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481599	20481599	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	71	282	0	ENST00000346618.3:c.668A>G	p.Asn223Ser	p.N223S	ENST00000346618	NM_001949.4	223	aAc/aGc	3/7	1	2	FACETS	0.726	0.635	0.822	0.726	0.635	0.822	SUBCLONAL	1	TRUE	1	0.438777570102877	2		282	446	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0033856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	20	535	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.079	0.059	0.101	0.079	0.059	0.101	SUBCLONAL	1	TRUE	1	0.562351819680791	2		535	905	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0033856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	147	356	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	1	2	FACETS	0.83	0.76	0.902	0.83	0.76	0.902	CLONAL	1	TRUE	1	0.562351819680791	2		356	630	SUCCESS
APC	324	MSKCC	GRCh37	5	112175141	112175141	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	180	212	0	ENST00000257430.4:c.3850G>T	p.Glu1284Ter	p.E1284*	ENST00000257430	NM_000038.5	1284	Gaa/Taa	16/16	0.562351819680791	2	FACETS	0.947	0.89	1	0.947	0.89	1	CLONAL	2	TRUE	0	0.562351819680791	2		212	338	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372173	55372173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	79	312	0	ENST00000297316.4:c.863C>T	p.Ala288Val	p.A288V	ENST00000297316	NM_022454.3	288	gCg/gTg	2/2	1	2	FACETS	0.649	0.573	0.729	0.649	0.573	0.729	SUBCLONAL	1	TRUE	1	0.562351819680791	2		312	433	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981565	201981565	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs878935651	NA	P-0033856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	98	639	0	ENST00000359651.3:c.478+1G>A		p.X160_splice	ENST00000359651		160			1	2	FACETS	0.376	0.335	0.421	0.376	0.335	0.421	SUBCLONAL	1	TRUE	1	0.562351819680791	2		639	926	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119086	70119086	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	122	350	0	ENST00000245479.2:c.658G>T	p.Glu220Ter	p.E220*	ENST00000245479	NM_000346.3	220	Gag/Tag	2/3	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.562351819680791	2		350	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576863	7576875	+	frameshift_variant	Frame_Shift_Del	DEL	AAATATTCTCCAT	AAATATTCTCCAT	CAC	novel	NA	P-0033879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	77	957	2	ENST00000269305.4:c.971_983delinsGTG	p.Asp324GlyfsTer18	p.D324Gfs*18	ENST00000269305	NM_001126112.2	324	gATGGAGAATATTTc/gGTGc	9/11	0.292010796654147	3	FACETS	0.6	0.526	0.68	0.3	0.263	0.34	SUBCLONAL	1	FALSE	1	0.42150569480753	3		959	737	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0034127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	233	863	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.64112408961813	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.64112408961813	1		863	491	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720817	89720818	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	G	novel	NA	P-0034127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	76	199	0	ENST00000371953.3:c.968_969delinsG	p.Asn323ArgfsTer21	p.N323Rfs*21	ENST00000371953	NM_000314.4	323	aAT/aG	8/9	0.64112408961813	1	FACETS	0.937	0.842	1	0.937	0.842	1	CLONAL	1	TRUE	0	0.64112408961813	1		199	172	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0034128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	134	436	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.39059796959257	1	FACETS	0.96	0.878	1	0.96	0.878	1	CLONAL	1	TRUE	0	0.441199726211812	1		436	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0034128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	14	622	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.39059796959257	1	FACETS	0.088	0.063	0.119	0.088	0.063	0.119	SUBCLONAL	1	TRUE	0	0.441199726211812	1		622	559	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105743	27105743	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	75	342	0	ENST00000324856.7:c.5354A>G	p.Asp1785Gly	p.D1785G	ENST00000324856	NM_006015.4	1785	gAt/gGt	20/20	0.435442673709649	1	FACETS	0.911	0.806	1	0.911	0.806	1	CLONAL	1	TRUE	0	0.441199726211812	1		342	291	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670076	29670076	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	101	448	0	ENST00000356175.3:c.7049G>T	p.Cys2350Phe	p.C2350F	ENST00000356175	NM_000267.3	2350	tGc/tTc	47/57	0.441199726211812	3	FACETS	0.805	0.72	0.896	0.403	0.36	0.448	CLONAL	1	TRUE	1	0.441199726211812	3		448	694	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59934500	59934500	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	123	421	2	ENST00000259008.2:c.298A>T	p.Met100Leu	p.M100L	ENST00000259008	NM_032043.2	100	Atg/Ttg	4/20	1	2	FACETS	0.934	0.847	1	0.934	0.847	1	CLONAL	1	TRUE	1	0.441199726211812	2		423	597	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662789	117662789	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	51	214	0	ENST00000368508.3:c.4676A>T	p.Glu1559Val	p.E1559V	ENST00000368508	NM_002944.2	1559	gAg/gTg	29/43	1	2	FACETS	0.766	0.655	0.886	0.766	0.655	0.886	SUBCLONAL	1	TRUE	1	0.441199726211812	2		214	302	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101054	27101054	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	324	577	1	ENST00000324856.7:c.4336C>T	p.Arg1446Ter	p.R1446*	ENST00000324856	NM_006015.4	1446	Cga/Tga	18/20	0.477444594057451	3	FACETS	0.996	0.945	1	0.996	0.945	1	CLONAL	2	FALSE	1	0.477444594057451	3		578	844	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0034369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	5098	399	8	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	0.477444594057451	38	FACETS	0.991	0.983	0.998			1	CLONAL	33	FALSE	NA	0.477444594057451	38		407	6265	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974695	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691187	NA	P-0034369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	236	360	0	ENST00000304494.5:c.132del	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	taC/ta	1/3	0.453482571760275	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	FALSE	0	0.477444594057451	2		360	457	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944244	81944244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769887285	NA	P-0034369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	138	558	1	ENST00000359376.3:c.1853G>A	p.Arg618His	p.R618H	ENST00000359376	NM_002661.3	618	cGc/cAc	18/33	0.329766737184304	4	FACETS	0.973	0.885	1	0.486	0.442	0.533	CLONAL	1	FALSE	2	0.477444594057451	4		559	878	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579333	7579350	+	inframe_deletion	In_Frame_Del	DEL	TGTCCCAGAATGCAAGAA	TGTCCCAGAATGCAAGAA	-	novel	NA	P-0034369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	243	477	1	ENST00000269305.4:c.337_354del	p.Phe113_Thr118del	p.F113_T118del	ENST00000269305	NM_001126112.2	113	TTCTTGCATTCTGGGACA/-	4/11	0.453482571760275	2	FACETS	0.84	0.791	0.89	0.84	0.791	0.89	CLONAL	2	FALSE	0	0.477444594057451	2		478	606	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619347	37619358	+	inframe_deletion	In_Frame_Del	DEL	TCTGAGTCGGAG	TCTGAGTCGGAG	-	novel	NA	P-0034369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	153	342	0	ENST00000447079.4:c.1025_1036del	p.Leu342_Ser345del	p.L342_S345del	ENST00000447079	NM_015083.1	341	tcTCTGAGTCGGAGt/tct	1/14	0.329288004302214	4	FACETS	0.781	0.718	0.847			1	SUBCLONAL	2	FALSE	NA	0.477444594057451	4		342	606	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554267	63554267	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0034369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	205	689	0	ENST00000307078.5:c.472A>T	p.Arg158Ter	p.R158*	ENST00000307078	NM_004655.3	158	Aga/Tga	2/11	0.393276395732468	3	FACETS	1	0.955	1	0.52	0.482	0.56	CLONAL	1	FALSE	1	0.477444594057451	3		689	1022	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0034389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	234	590	1	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	0.464509608622484	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.464509608622484	1		591	743	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110319	3110319	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	198	511	0	ENST00000078429.4:c.309C>A	p.Tyr103Ter	p.Y103*	ENST00000078429	NM_002067.2	103	taC/taA	2/7	0.254795267044113	3	FACETS	1	0.989	1	0.68	0.631	0.73	INDETERMINATE	1	TRUE	1	0.464509608622484	3		511	773	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0034883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	85	315	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	1	2	FACETS	0.939	0.833	1	0.939	0.833	1	CLONAL	1	TRUE	1	0.377934207812512	2		315	479	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0121429-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	14	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA	2	FACETS	0.087	0.063	0.118			1	INDETERMINATE	1	NA	NA	0.756964748666731	2		336	423	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432664	29432664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113994087	NA	P-0121429-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	24	493	0	ENST00000389048.3:c.3824G>A	p.Arg1275Gln	p.R1275Q	ENST00000389048	NM_004304.4	1275	cGa/cAa	25/29	1	2	FACETS	0.119	0.092	0.149	0.119	0.092	0.149	SUBCLONAL	1	NA	1	0.756964748666731	2		493	534	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0035441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	276	520	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.596562517095758	4	FACETS	0.9	0.852	0.948	0.9	0.852	0.948	CLONAL	2	FALSE	2	0.940067108595085	4		520	633	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595329	141595329	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	376	827	0	ENST00000220592.5:c.104G>C	p.Gly35Ala	p.G35A	ENST00000220592	NM_012154.3	35	gGg/gCg	2/19	0.940067108595085	4	FACETS	0.765	0.727	0.802	0.765	0.727	0.802	SUBCLONAL	2	FALSE	2	0.940067108595085	4		827	1015	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	9	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.267	0.175	0.384	0.267	0.175	0.384	SUBCLONAL	1	TRUE	1	0.15	2		326	450	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797160	45797160	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587780744	NA	P-0035775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	160	786	0	ENST00000450313.1:c.1255G>C	p.Ala419Pro	p.A419P	ENST00000450313	NM_012222.2	419	Gcc/Ccc	13/16	1	2	FACETS	0.314	0.287	0.342	0.314	0.287	0.342	SUBCLONAL	1	TRUE	1	0.921410163584188	2		786	1106	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005628	42005628	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	194	360	0	ENST00000219905.7:c.3364G>T	p.Glu1122Ter	p.E1122*	ENST00000219905	NM_001164273.1	1122	Gaa/Taa	9/24	1	2	FACETS	0.894	0.836	0.953	0.894	0.836	0.953	CLONAL	1	TRUE	1	0.921410163584188	2		360	471	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816431	32816431	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs967210854	NA	P-0035775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	369	679	0	ENST00000354258.4:c.1744C>T	p.Gln582Ter	p.Q582*	ENST00000354258	NM_000593.5	582	Cag/Tag	7/11	0.878214972298196	3	FACETS	0.915	0.867	0.963	0.457	0.433	0.482	CLONAL	1	TRUE	1	0.921410163584188	3		679	1279	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs864622237	NA	P-0035859-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	58	619	0	ENST00000269305.4:c.700T>C	p.Tyr234His	p.Y234H	ENST00000269305	NM_001126112.2	234	Tac/Cac	7/11	1	2	FACETS	0.272	0.233	0.315	0.272	0.233	0.315	SUBCLONAL	1	TRUE	1	0.653711258089408	2		619	652	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574013	7574013	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035859-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	62	676	1	ENST00000269305.4:c.1014del	p.Phe338LeufsTer7	p.F338Lfs*7	ENST00000269305	NM_001126112.2	338	ttC/tt	10/11	1	2	FACETS	0.285	0.246	0.328	0.285	0.246	0.328	SUBCLONAL	1	TRUE	1	0.653711258089408	2		677	665	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0036317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	45	210	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.995	0.835	1	0.995	0.835	1	CLONAL	1	TRUE	1	0.14	2		210	646	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0036317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	31	346	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.14	2		347	391	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448592	89448592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543425684	NA	P-0036317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	52	529	0	ENST00000336596.2:c.1556C>T	p.Thr519Met	p.T519M	ENST00000336596	NM_005233.5	519	aCg/aTg	7/17	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.14	2		529	733	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712007	89712007	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs765433422	NA	P-0036317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	32	265	0	ENST00000371953.3:c.625G>T	p.Gly209Ter	p.G209*	ENST00000371953	NM_000314.4	209	Gga/Tga	6/9	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.14	2		265	316	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729604	41729604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	41	500	1	ENST00000242208.4:c.925C>T	p.Arg309Trp	p.R309W	ENST00000242208	NM_002192.2	309	Cgg/Tgg	3/3	1	2	FACETS	0.986	0.82	1	0.986	0.82	1	CLONAL	1	TRUE	1	0.14	2		501	594	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466026	69466028	+	inframe_deletion	In_Frame_Del	DEL	CGA	CGA	-	novel	NA	P-0036317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	46	705	0	ENST00000227507.2:c.866_868del	p.Asp289del	p.D289del	ENST00000227507	NM_053056.2	288	acCGAc/acc	5/5	1	2	FACETS	0.91	0.765	1	0.91	0.765	1	CLONAL	1	TRUE	1	0.14	2		705	722	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828579	72828579	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	52	755	1	ENST00000268489.5:c.8002C>T	p.Arg2668Ter	p.R2668*	ENST00000268489	NM_006885.3	2668	Cga/Tga	9/10	1	2	FACETS	0.802	0.681	0.936	0.802	0.681	0.936	CLONAL	1	TRUE	1	0.14	2		756	926	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944308	81944308	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	30	519	0	ENST00000359376.3:c.1921del	p.His641ThrfsTer11	p.H641Tfs*11	ENST00000359376	NM_002661.3	639	aaC/aa	18/33	1	2	FACETS	0.782	0.629	0.957	0.782	0.629	0.957	CLONAL	1	TRUE	1	0.14	2		519	548	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653846	89653846	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762518389	NA	P-0036317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	44	443	0	ENST00000371953.3:c.144C>A	p.Asn48Lys	p.N48K	ENST00000371953	NM_000314.4	48	aaC/aaA	2/9	1	2	FACETS	0.984	0.824	1	0.984	0.824	1	CLONAL	1	TRUE	1	0.14	2		443	639	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057838	27057839	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0036317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	61	789	0	ENST00000324856.7:c.1548_1549dup	p.Pro517LeufsTer103	p.P517Lfs*103	ENST00000324856	NM_006015.4	516	cct/cCTct	3/20	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.14	2		789	870	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530133	63530133	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	50	507	0	ENST00000307078.5:c.2302T>A	p.Tyr768Asn	p.Y768N	ENST00000307078	NM_004655.3	768	Tac/Aac	10/11	1	2	FACETS	0.96	0.813	1	0.96	0.813	1	CLONAL	1	TRUE	1	0.14	2		507	744	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178941918	178941918	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	43	457	0	ENST00000263967.3:c.2237A>T	p.Asp746Val	p.D746V	ENST00000263967	NM_006218.2	746	gAt/gTt	15/21	1	2	FACETS	0.984	0.822	1	0.984	0.822	1	CLONAL	1	TRUE	1	0.14	2		457	624	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468251	50468251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548117828	NA	P-0036317-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	32	541	1	ENST00000331340.3:c.1486G>A	p.Gly496Ser	p.G496S	ENST00000331340	NM_006060.4	496	Ggc/Agc	8/8	1	2	FACETS	0.775	0.627	0.942	0.775	0.627	0.942	CLONAL	1	TRUE	1	0.14	2		542	590	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0036903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	260	542	0				ENST00000310581	NM_198253.2	-/1132			0.514378653741911	3	FACETS	1	0.988	1	0.589	0.554	0.624	INDETERMINATE	1	TRUE	1	0.890459939752501	3		542	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573991	7573991	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567542019	NA	P-0036903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	635	775	0	ENST00000269305.4:c.1036G>T	p.Glu346Ter	p.E346*	ENST00000269305	NM_001126112.2	346	Gag/Tag	10/11	0.890459939752501	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.890459939752501	1		775	715	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521975	157521975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144424476	NA	P-0036903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	154	467	1	ENST00000346085.5:c.4247G>A	p.Arg1416His	p.R1416H	ENST00000346085	NM_020732.3	1416	cGc/cAc	18/20	0.372112233158201	1	FACETS	0.414	0.382	0.447	0.414	0.382	0.447	INDETERMINATE	1	TRUE	0	0.890459939752501	1		468	463	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432409	49432412	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	novel	NA	P-0036903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	394	787	0	ENST00000301067.7:c.8727_8730del	p.Ser2910ArgfsTer32	p.S2910Rfs*32	ENST00000301067	NM_003482.3	2909	gtAAGT/gt	34/54	1	2	FACETS	0.952	0.908	0.995	0.952	0.908	0.995	CLONAL	1	TRUE	1	0.890459939752501	2		787	930	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70005611	70005611	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs104893746	NA	P-0036903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	205	391	2	ENST00000394351.3:c.640C>T	p.Arg214Ter	p.R214*	ENST00000394351	NM_000248.3	214	Cga/Tga	7/9	0.546701287086415	2	FACETS	0.834	0.78	0.889	0.417	0.39	0.445	CLONAL	1	TRUE	0	0.890459939752501	2		393	552	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732533	74732533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	44	134	0	ENST00000359995.5:c.376C>T	p.Arg126Cys	p.R126C	ENST00000359995	NM_001195427.1	126	Cgc/Tgc	2/3	0.194087007940557	4	FACETS	0.898	0.762	1	0.449	0.381	0.523	INDETERMINATE	1	TRUE	2	0.890459939752501	4		134	208	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404765	404765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	150	551	0	ENST00000399788.2:c.4429G>A	p.Glu1477Lys	p.E1477K	ENST00000399788	NM_001042603.1	1477	Gaa/Aaa	26/28	NA	2	FACETS	0.438	0.4	0.477			1	INDETERMINATE	1	TRUE	NA	0.890459939752501	2		551	770	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643774	52643808	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	TTTCCATGTCCATGGGCTTTTTAATAGTCAGATAG	TTTCCATGTCCATGGGCTTTTTAATAGTCAGATAG	-	novel	NA	P-0036903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	116	730	0	ENST00000394830.3:c.2088_2122del	p.Tyr696Ter	p.Y696*	ENST00000394830	NM_018313.4	696	taCTATCTGACTATTAAAAAGCCCATGGACATGGAAAaa/taaa	17/30	0.546701287086415	2	FACETS	0.279	0.25	0.308	0.139	0.125	0.154	SUBCLONAL	1	TRUE	0	0.890459939752501	2		730	935	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961431	1961431	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	326	563	0	ENST00000382891.5:c.3219A>T	p.Lys1073Asn	p.K1073N	ENST00000382891	NM_133335.3	1073	aaA/aaT	17/22	0.146108908014968	3	FACETS	1	0.993	1	0.422	0.4	0.444	INDETERMINATE	1	TRUE	0	0.890459939752501	3		563	836	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748194	41748194	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	70	648	1	ENST00000226382.2:c.575C>A	p.Pro192Gln	p.P192Q	ENST00000226382	NM_003924.3	192	cCg/cAg	3/3	0.146108908014968	3	FACETS	0.265	0.23	0.303	0.088	0.076	0.101	INDETERMINATE	1	TRUE	0	0.890459939752501	3		649	858	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100088	157100088	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768271181	NA	P-0036903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	39	56	0	ENST00000346085.5:c.1025C>T	p.Ala342Val	p.A342V	ENST00000346085	NM_020732.3	342	gCg/gTg	1/20	0.372112233158201	1	FACETS	0.704	0.616	0.791	0.704	0.616	0.791	INDETERMINATE	1	TRUE	0	0.890459939752501	1		56	69	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0036931-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	145	210	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.462804871536429	2		210	572	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339680	116339680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036931-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	172	541	0	ENST00000397752.3:c.542G>A	p.Gly181Glu	p.G181E	ENST00000397752	NM_000245.2	181	gGa/gAa	2/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.462804871536429	2		541	646	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0036931-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	200	805	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	1	2	FACETS	0.932	0.864	1	0.932	0.864	1	CLONAL	1	TRUE	1	0.462804871536429	2		805	927	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046683	42046683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036931-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	164	712	1	ENST00000219905.7:c.7057G>A	p.Glu2353Lys	p.E2353K	ENST00000219905	NM_001164273.1	2353	Gag/Aag	18/24	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.462804871536429	2		713	699	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528097	29528097	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036931-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	98	463	0	ENST00000356175.3:c.1105C>T	p.Gln369Ter	p.Q369*	ENST00000356175	NM_000267.3	369	Cag/Tag	10/57	0.444353178824632	1	FACETS	0.841	0.756	0.93	0.841	0.756	0.93	CLONAL	1	TRUE	0	0.462804871536429	1		463	387	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964961	15964961	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036931-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	221	826	1	ENST00000268712.3:c.5635C>T	p.Gln1879Ter	p.Q1879*	ENST00000268712	NM_006311.3	1879	Cag/Tag	37/46	0.444353178824632	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.462804871536429	1		827	648	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176684035	176684035	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036931-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	260	828	1	ENST00000439151.2:c.4849G>A	p.Glu1617Lys	p.E1617K	ENST00000439151	NM_022455.4	1617	Gaa/Aaa	13/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.462804871536429	2		829	959	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162014	22162014	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036931-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	175	796	1	ENST00000215832.6:c.241G>A	p.Glu81Lys	p.E81K	ENST00000215832	NM_002745.4	81	Gag/Aag	2/9	1	2	FACETS	0.887	0.817	0.959	0.887	0.817	0.959	CLONAL	1	TRUE	1	0.462804871536429	2		797	853	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484303	120484303	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036931-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	139	568	0	ENST00000256646.2:c.2827G>T	p.Gly943Trp	p.G943W	ENST00000256646	NM_024408.3	943	Ggg/Tgg	18/34	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.462804871536429	2		568	589	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533611	533611	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs751137946	NA	P-0036931-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	173	739	0	ENST00000451590.1:c.292G>A	p.Glu98Lys	p.E98K	ENST00000451590	NM_001130442.1	98	Gag/Aag	4/5	1	2	FACETS	0.984	0.907	1	0.984	0.907	1	CLONAL	1	TRUE	1	0.462804871536429	2		739	760	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937599	32937599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036931-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	163	755	1	ENST00000380152.3:c.8260C>T	p.His2754Tyr	p.H2754Y	ENST00000380152		2754	Cat/Tat	18/27	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.462804871536429	2		756	691	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961377	41961377	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036931-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	194	710	0	ENST00000219905.7:c.285G>T	p.Met95Ile	p.M95I	ENST00000219905	NM_001164273.1	95	atG/atT	2/24	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.462804871536429	2		710	800	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752745	42752745	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036931-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	148	906	0	ENST00000222329.4:c.1519G>A	p.Glu507Lys	p.E507K	ENST00000222329	NM_006494.2	507	Gag/Aag	4/4	1	2	FACETS	0.855	0.782	0.931	0.855	0.782	0.931	CLONAL	1	TRUE	1	0.462804871536429	2		906	748	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051154	128051154	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036931-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	168	784	0	ENST00000285398.2:c.169G>T	p.Gly57Ter	p.G57*	ENST00000285398	NM_000122.1	57	Gga/Tga	2/15	1	2	FACETS	0.973	0.896	1	0.973	0.896	1	CLONAL	1	TRUE	1	0.462804871536429	2		784	746	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256665	46256665	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0036931-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	158	608	0	ENST00000371998.3:c.722-1G>A		p.X241_splice	ENST00000371998		241			1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.462804871536429	2		608	678	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22161969	22161969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs530183395	NA	P-0036931-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	168	746	0	ENST00000215832.6:c.286G>A	p.Glu96Lys	p.E96K	ENST00000215832	NM_002745.4	96	Gag/Aag	2/9	1	2	FACETS	0.882	0.812	0.956	0.882	0.812	0.956	CLONAL	1	TRUE	1	0.462804871536429	2		746	823	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191261	185191261	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036931-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	168	610	1	ENST00000265026.3:c.2142C>A	p.Asp714Glu	p.D714E	ENST00000265026	NM_004721.4	714	gaC/gaA	11/14	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.462804871536429	2		611	649	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741694	17741694	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	309	425	0	ENST00000250003.3:c.365T>G	p.Leu122Arg	p.L122R	ENST00000250003	NM_002478.4	122	cTg/cGg	1/3	0.500506703461359	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.500506703461359	2		425	560	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272338	38272338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	198	588	0	ENST00000425967.3:c.2029C>T	p.Arg677Trp	p.R677W	ENST00000425967	NM_001174067.1	677	Cgg/Tgg	15/19	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.500506703461359	2		588	780	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179180	123179180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	156	303	0	ENST00000218089.9:c.629C>T	p.Ser210Leu	p.S210L	ENST00000218089	NM_001042749.1	210	tCa/tTa	8/35	1	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.59011612472803	1		303	314	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711990	89711990	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	126	428	0	ENST00000371953.3:c.609del	p.Pro204GlnfsTer17	p.P204Qfs*17	ENST00000371953	NM_000314.4	203	aTt/at	6/9	0.59011612472803	1	FACETS	0.921	0.845	0.997	0.921	0.845	0.997	CLONAL	1	TRUE	0	0.59011612472803	1		428	327	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279929	18279929	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	327	665	0	ENST00000222254.8:c.2012A>G	p.Tyr671Cys	p.Y671C	ENST00000222254	NM_005027.3	671	tAc/tGc	16/16	1	2	FACETS	0.981	0.927	1	0.981	0.927	1	CLONAL	1	TRUE	1	0.59011612472803	2		665	1130	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354234	70354234	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	129	685	0	ENST00000374080.3:c.4645C>T	p.Arg1549Cys	p.R1549C	ENST00000374080		1549	Cgc/Tgc	34/45	0.182992060201934	4	FACETS	1	0.98	1	0.658	0.595	0.724	CLONAL	1	TRUE	2	0.21555042017855	4		685	1106	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1131691023	NA	P-0037028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	376	733	0	ENST00000269305.4:c.470T>C	p.Val157Ala	p.V157A	ENST00000269305	NM_001126112.2	157	gTc/gCc	5/11	0.21555042017855	2	FACETS	1	0.967	1	1	0.995	1	CLONAL	3	TRUE	0	0.21555042017855	2		733	1138	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943359	71943359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775327646	NA	P-0037028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	142	646	0	ENST00000298229.2:c.1691C>T	p.Ser564Leu	p.S564L	ENST00000298229	NM_001567.3	564	tCg/tTg	14/28	0.182992060201934	4	FACETS	0.762	0.693	0.834	0.762	0.693	0.834	SUBCLONAL	2	TRUE	2	0.21555042017855	4		646	1051	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782156	9782156	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	129	616	0	ENST00000377346.4:c.2179G>T	p.Ala727Ser	p.A727S	ENST00000377346	NM_005026.3	727	Gcc/Tcc	17/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.21555042017855	2		616	799	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462854	69462854	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	263	682	0	ENST00000227507.2:c.667T>G	p.Phe223Val	p.F223V	ENST00000227507	NM_053056.2	223	Ttc/Gtc	4/5	0.182992060201934	4	FACETS	0.877	0.822	0.934	1	0.991	1	CLONAL	3	TRUE	2	0.21555042017855	4		682	1127	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212852	94212852	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	40	489	0	ENST00000323929.3:c.390C>G	p.Asp130Glu	p.D130E	ENST00000323929	NM_005591.3	130	gaC/gaG	5/20	0.182992060201934	4	FACETS	0.806	0.669	0.959	0.403	0.334	0.48	CLONAL	1	TRUE	2	0.21555042017855	4		489	560	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039143	49039143	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	39	270	0	ENST00000267163.4:c.2221C>A	p.Arg741Ser	p.R741S	ENST00000267163	NM_000321.2	741	Cgt/Agt	22/27	0.21555042017855	5	FACETS	0.898	0.744	1	0.299	0.248	0.357	CLONAL	1	TRUE	2	0.21555042017855	5		270	533	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794890	42794890	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	58	629	0	ENST00000575354.2:c.1970A>C	p.Tyr657Ser	p.Y657S	ENST00000575354	NM_015125.3	657	tAt/tCt	10/20	1	2	FACETS	0.693	0.594	0.801	0.693	0.594	0.801	SUBCLONAL	1	TRUE	1	0.21555042017855	2		629	777	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945316	54945316	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	57	335	0	ENST00000312783.6:c.1110G>C	p.Gln370His	p.Q370H	ENST00000312783	NM_198436.1	370	caG/caC	10/10	0.21555042017855	6	FACETS	1	0.959	1	0.268	0.23	0.31	CLONAL	1	TRUE	1	0.21555042017855	6		335	564	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668656	52668656	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0037028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	123	572	0	ENST00000394830.3:c.1263C>G	p.Tyr421Ter	p.Y421*	ENST00000394830	NM_018313.4	421	taC/taG	12/30	0.21555042017855	3	FACETS	1	0.979	1	0.658	0.594	0.725	CLONAL	1	TRUE	1	0.21555042017855	3		572	961	SUCCESS
APC	324	MSKCC	GRCh37	5	112175407	112175407	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	134	373	0	ENST00000257430.4:c.4116del	p.Pro1373LeufsTer42	p.P1373Lfs*42	ENST00000257430	NM_000038.5	1372	ccA/cc	16/16	0.21555042017855	2	FACETS	0.836	0.764	0.91	1	0.98	1	CLONAL	3	TRUE	0	0.21555042017855	2		373	496	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370847	55370847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	87	370	2	ENST00000297316.4:c.149C>T	p.Ala50Val	p.A50V	ENST00000297316	NM_022454.3	50	gCg/gTg	1/2	0.21555042017855	10	FACETS	1	0.975	1	0.176	0.155	0.198	CLONAL	1	TRUE	2	0.21555042017855	10		372	1069	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	63	1014	11	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.833	0.723	0.952	0.833	0.723	0.952	CLONAL	1	TRUE	1	0.36	2		1025	420	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	56	484	4	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.827	0.712	0.953	0.827	0.712	0.953	CLONAL	1	TRUE	1	0.36	2		488	376	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	61	572	5	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.36	2		577	279	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	117	270	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.921	0.831	1	0.921	0.831	1	CLONAL	1	TRUE	1	0.36	2		271	706	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	51	840	6	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.807	0.689	0.936	0.807	0.689	0.936	CLONAL	1	TRUE	1	0.36	2		846	351	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	51	330	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.541	0.459	0.63	0.541	0.459	0.63	SUBCLONAL	1	TRUE	1	0.36	2		331	524	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	86	475	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.896	0.795	1	0.896	0.795	1	CLONAL	1	TRUE	1	0.36	2		475	533	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	128	857	2	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.36	2		859	657	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	55	307	2	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.751	0.644	0.867	0.751	0.644	0.867	SUBCLONAL	1	TRUE	1	0.36	2		309	407	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	55	371	1	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.856	0.735	0.986	0.856	0.735	0.986	CLONAL	1	TRUE	1	0.36	2		372	357	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434367	121434367	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	42	544	1	ENST00000257555.6:c.1136del	p.Pro379LeufsTer5	p.P379Lfs*5	ENST00000257555		377	ctC/ct	6/10	1	2	FACETS	0.697	0.583	0.821	0.697	0.583	0.821	SUBCLONAL	1	TRUE	1	0.36	2		545	335	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	27	224	1	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.575	0.459	0.706	0.575	0.459	0.706	SUBCLONAL	1	TRUE	1	0.36	2		225	261	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126730	5126730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1437629509	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	67	492	0	ENST00000381652.3:c.3338G>A	p.Arg1113His	p.R1113H	ENST00000381652	NM_004972.3	1113	cGc/cAc	25/25	1	2	FACETS	0.931	0.812	1	0.931	0.812	1	CLONAL	1	TRUE	1	0.36	2		492	400	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	19	176	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	0.648	0.495	0.824	0.648	0.495	0.824	SUBCLONAL	1	TRUE	1	0.36	2		176	163	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	59	695	5	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	1	2	FACETS	0.716	0.617	0.823	0.716	0.617	0.823	SUBCLONAL	1	TRUE	1	0.36	2		700	458	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777898	3777898	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	85	739	0	ENST00000262367.5:c.7150del	p.His2384ThrfsTer12	p.H2384Tfs*12	ENST00000262367	NM_004380.2	2384	Cac/ac	31/31	1	2	FACETS	0.809	0.716	0.908	0.809	0.716	0.908	CLONAL	1	TRUE	1	0.36	2		739	584	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	81	601	4	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.36	2		605	417	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455090	50455090	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	45	361	1	ENST00000331340.3:c.637C>T	p.Arg213Ter	p.R213*	ENST00000331340	NM_006060.4	213	Cga/Tga	6/8	1	2	FACETS	0.725	0.611	0.849	0.725	0.611	0.849	SUBCLONAL	1	TRUE	1	0.36	2		362	345	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	34	440	2	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	0.623	0.511	0.749	0.623	0.511	0.749	SUBCLONAL	1	TRUE	1	0.36	2		442	303	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785964	135785964	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs118203506	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	58	486	0	ENST00000298552.3:c.1257del	p.Arg420GlyfsTer20	p.R420Gfs*20	ENST00000298552	NM_001162426.1	419	ccC/cc	12/23	1	2	FACETS	0.748	0.644	0.86	0.748	0.644	0.86	SUBCLONAL	1	TRUE	1	0.36	2		486	431	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646981	23646981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	83	734	1	ENST00000261584.4:c.886del	p.Met296Ter	p.M296*	ENST00000261584	NM_024675.3	296	Atg/tg	4/13	1	2	FACETS	0.638	0.562	0.719	0.638	0.562	0.719	SUBCLONAL	1	TRUE	1	0.36	2		735	723	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934243	49934243	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1407832113	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	72	548	2	ENST00000296474.3:c.2264del	p.Gly755ValfsTer19	p.G755Vfs*19	ENST00000296474	NM_002447.2	755	gGt/gt	8/20	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.36	2		550	372	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	59	466	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.766	0.668	0.869	1	0.973	1	SUBCLONAL	2	TRUE	1	0.36	2		466	214	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143999	11143999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1171822727	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	66	420	0	ENST00000358026.2:c.3580G>A	p.Gly1194Arg	p.G1194R	ENST00000358026	NM_001128849.1	1194	Ggg/Agg	26/36	1	2	FACETS	0.945	0.824	1	0.945	0.824	1	CLONAL	1	TRUE	1	0.36	2		420	388	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246532	41246532	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357569	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	92	655	3	ENST00000357654.3:c.1016del	p.Lys339ArgfsTer2	p.K339Rfs*2	ENST00000357654	NM_007294.3	339	aAg/ag	10/23	1	2	FACETS	0.878	0.782	0.981	0.878	0.782	0.981	CLONAL	1	TRUE	1	0.36	2		658	582	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794623	42794623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564532974	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	47	587	1	ENST00000575354.2:c.1703C>T	p.Ala568Val	p.A568V	ENST00000575354	NM_015125.3	568	gCg/gTg	10/20	1	2	FACETS	0.721	0.611	0.843	0.721	0.611	0.843	SUBCLONAL	1	TRUE	1	0.36	2		588	362	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988303	36988303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	15	279	0	ENST00000354822.5:c.350G>A	p.Cys117Tyr	p.C117Y	ENST00000354822	NM_001079668.2	117	tGc/tAc	2/3	1	2	FACETS	0.311	0.227	0.412	0.311	0.227	0.412	SUBCLONAL	1	TRUE	1	0.36	2		279	268	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	141	571	1	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	0.865	0.794	0.937	1	0.99	1	CLONAL	2	TRUE	1	0.36	2		572	453	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797769	32797769	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs78328107	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	59	625	3	ENST00000374899.4:c.1733C>T	p.Ala578Val	p.A578V	ENST00000374899	NM_018833.2	578	gCg/gTg	10/12	1	2	FACETS	0.541	0.465	0.624	0.541	0.465	0.624	SUBCLONAL	1	TRUE	1	0.36	2		628	606	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300040	137300040	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	81	622	2	ENST00000481739.1:c.331del	p.Leu111TrpfsTer57	p.L111Wfs*57	ENST00000481739	NM_002957.4	109	Ccc/cc	3/10	1	2	FACETS	0.763	0.673	0.859	0.763	0.673	0.859	SUBCLONAL	1	TRUE	1	0.36	2		624	590	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351595	89351595	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	79	761	1	ENST00000301030.4:c.1355del	p.Asn452IlefsTer3	p.N452Ifs*3	ENST00000301030	NM_001256183.1	452	aAt/at	9/13	1	2	FACETS	0.61	0.536	0.69	0.61	0.536	0.69	SUBCLONAL	1	TRUE	1	0.36	2		762	719	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485116	57485116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1369025856	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	73	421	0	ENST00000371085.3:c.950G>A	p.Arg317His	p.R317H	ENST00000371085	NM_000516.4	317	cGc/cAc	11/13	1	2	FACETS	0.834	0.732	0.945	0.834	0.732	0.945	CLONAL	1	TRUE	1	0.36	2		421	486	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805713	43805713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913611	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	73	510	0	ENST00000372470.3:c.769C>T	p.Arg257Cys	p.R257C	ENST00000372470	NM_005373.2	257	Cgc/Tgc	5/12	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.36	2		510	390	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643348	52643348	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	47	431	0	ENST00000394830.3:c.2548C>T	p.Arg850Ter	p.R850*	ENST00000394830	NM_018313.4	850	Cga/Tga	17/30	1	2	FACETS	0.518	0.437	0.607	0.518	0.437	0.607	SUBCLONAL	1	TRUE	1	0.36	2		431	504	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191446	185191446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756793616	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	73	598	0	ENST00000265026.3:c.2327C>T	p.Thr776Met	p.T776M	ENST00000265026	NM_004721.4	776	aCg/aTg	11/14	1	2	FACETS	0.67	0.586	0.761	0.67	0.586	0.761	SUBCLONAL	1	TRUE	1	0.36	2		598	605	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	83	684	0	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	1	2	FACETS	0.761	0.672	0.856	0.761	0.672	0.856	SUBCLONAL	1	TRUE	1	0.36	2		684	606	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878910	117878910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	60	432	1	ENST00000297338.2:c.59C>T	p.Ala20Val	p.A20V	ENST00000297338	NM_006265.2	20	gCg/gTg	2/14	1	2	FACETS	0.604	0.52	0.695	0.604	0.52	0.695	SUBCLONAL	1	TRUE	1	0.36	2		433	552	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133981	38133981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	96	604	1	ENST00000317025.8:c.3905del	p.Asn1302MetfsTer4	p.N1302Mfs*4	ENST00000317025	NM_023034.1	1302	aAt/at	23/24	0.286186504431981	5	FACETS	0.761	0.676	0.852	0.19	0.169	0.213	SUBCLONAL	1	TRUE	1	0.36	5		605	1079	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38631981	38631981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1255149646	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	90	581	1	ENST00000299084.4:c.471del	p.Gln158SerfsTer16	p.Q158Sfs*16	ENST00000299084	NM_152594.2	156	cTt/ct	5/7	1	2	FACETS	0.856	0.761	0.957	0.856	0.761	0.957	CLONAL	1	TRUE	1	0.36	2		582	584	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845959	151845959	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	72	604	1	ENST00000262189.6:c.13053del	p.Lys4351AsnfsTer5	p.K4351Nfs*5	ENST00000262189	NM_170606.2	4351	aaA/aa	52/59	0.172018439167131	3	FACETS	0.843	0.737	0.957	0.421	0.368	0.479	INDETERMINATE	1	TRUE	1	0.36	3		605	560	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526679	31526679	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	69	640	1	ENST00000344624.3:c.361C>T	p.Pro121Ser	p.P121S	ENST00000344624		121	Cca/Tca	2/33	1	2	FACETS	0.966	0.845	1	0.966	0.845	1	CLONAL	1	TRUE	1	0.36	2		641	397	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652822	212652822	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780954188	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	79	467	0	ENST00000342788.4:c.484C>T	p.His162Tyr	p.H162Y	ENST00000342788	NM_005235.2	162	Cat/Tat	4/28	1	2	FACETS	0.971	0.857	1	0.971	0.857	1	CLONAL	1	TRUE	1	0.36	2		467	452	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010571	48010571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878853712	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	31	231	1	ENST00000234420.5:c.199C>T	p.Pro67Ser	p.P67S	ENST00000234420	NM_000179.2	67	Ccc/Tcc	1/10	1	2	FACETS	0.73	0.594	0.882	0.73	0.594	0.882	SUBCLONAL	1	TRUE	1	0.36	2		232	236	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29197675	29197675	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	83	519	1	ENST00000240100.2:c.519del	p.Ser174ValfsTer53	p.S174Vfs*53	ENST00000240100	NM_001394.6	173	ccC/cc	2/4	0.286186504431981	5	FACETS	0.985	0.869	1	0.246	0.217	0.278	CLONAL	1	TRUE	1	0.36	5		520	721	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279562	18279562	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	74	475	0	ENST00000222254.8:c.1835A>G	p.Asp612Gly	p.D612G	ENST00000222254	NM_005027.3	612	gAc/gGc	15/16	1	2	FACETS	0.806	0.707	0.912	0.806	0.707	0.912	CLONAL	1	TRUE	1	0.36	2		475	510	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969941	161969941	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529808032	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	40	442	0	ENST00000366898.1:c.1028C>T	p.Pro343Leu	p.P343L	ENST00000366898	NM_004562.2	343	cCg/cTg	9/12	1	2	FACETS	0.724	0.604	0.856	0.724	0.604	0.856	SUBCLONAL	1	TRUE	1	0.36	2		442	307	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918708	50918708	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768799892	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	43	344	0	ENST00000440232.2:c.2578G>A	p.Ala860Thr	p.A860T	ENST00000440232	NM_002691.3	860	Gcg/Acg	21/27	1	2	FACETS	0.829	0.698	0.973	0.829	0.698	0.973	CLONAL	1	TRUE	1	0.36	2		344	288	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789629	3789629	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	73	448	0	ENST00000262367.5:c.4230del	p.Phe1410LeufsTer49	p.F1410Lfs*49	ENST00000262367	NM_004380.2	1410	ttT/tt	25/31	1	2	FACETS	0.764	0.669	0.865	0.764	0.669	0.865	SUBCLONAL	1	TRUE	1	0.36	2		448	531	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551310	141551310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	95	700	0	ENST00000220592.5:c.1987C>T	p.Arg663Cys	p.R663C	ENST00000220592	NM_012154.3	663	Cgc/Tgc	15/19	1	2	FACETS	0.649	0.577	0.726	0.649	0.577	0.726	SUBCLONAL	1	TRUE	1	0.36	2		700	813	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288852	11288854	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	30	486	0	ENST00000361445.4:c.2901_2903del	p.His968del	p.H968del	ENST00000361445	NM_004958.3	967	caTCAc/cac	19/58	1	2	FACETS	0.469	0.378	0.573	0.469	0.378	0.573	SUBCLONAL	1	TRUE	1	0.36	2		486	355	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885769	23885769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1247524620	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	68	521	4	ENST00000374561.5:c.149G>A	p.Arg50His	p.R50H	ENST00000374561	NM_002167.4	50	cGc/cAc	1/3	1	2	FACETS	0.823	0.718	0.936	0.823	0.718	0.936	CLONAL	1	TRUE	1	0.36	2		525	459	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100424	8100425	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs772396478	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	52	553	1	ENST00000346208.3:c.404dup	p.Ala136GlyfsTer167	p.A136Gfs*167	ENST00000346208		133	tac/taCc	3/6	1	2	FACETS	0.703	0.6	0.815	0.703	0.6	0.815	SUBCLONAL	1	TRUE	1	0.36	2		554	411	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352652	118352652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	51	398	0	ENST00000534358.1:c.3857C>T	p.Ala1286Val	p.A1286V	ENST00000534358	NM_005933.3	1286	gCc/gTc	7/36	1	2	FACETS	0.748	0.637	0.868	0.748	0.637	0.868	SUBCLONAL	1	TRUE	1	0.36	2		398	379	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444035	49444045	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGGCTGGGG	CAGGGCTGGGG	-	rs1565813691	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	32	523	0	ENST00000301067.7:c.3326_3336del	p.Ala1109GlyfsTer2	p.A1109Gfs*2	ENST00000301067	NM_003482.3	1109	gCCCCAGCCCTG/g	11/54	1	2	FACETS	0.498	0.404	0.603	0.498	0.404	0.603	SUBCLONAL	1	TRUE	1	0.36	2		523	357	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495797	56495797	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	46	437	0	ENST00000267101.3:c.3987G>A	p.Trp1329Ter	p.W1329*	ENST00000267101	NM_001982.3	1329	tgG/tgA	28/28	1	2	FACETS	0.73	0.617	0.854	0.73	0.617	0.854	SUBCLONAL	1	TRUE	1	0.36	2		437	350	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023136	33023136	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	55	394	0	ENST00000300177.4:c.245A>T	p.His82Leu	p.H82L	ENST00000300177	NM_001191322.1	82	cAt/cTt	2/2	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.36	2		394	301	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805356	89805356	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	76	457	0	ENST00000389301.3:c.4194del	p.Ala1399LeufsTer8	p.A1399Lfs*8	ENST00000389301	NM_000135.2	1398	aaA/aa	42/43	1	2	FACETS	0.742	0.652	0.839	0.742	0.652	0.839	SUBCLONAL	1	TRUE	1	0.36	2		457	569	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527579	29527579	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	45	522	0	ENST00000356175.3:c.1028T>A	p.Phe343Tyr	p.F343Y	ENST00000356175	NM_000267.3	343	tTc/tAc	9/57	1	2	FACETS	0.498	0.418	0.586	0.498	0.418	0.586	SUBCLONAL	1	TRUE	1	0.36	2		522	502	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456575	40456575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs988135840	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	76	538	0	ENST00000345506.4:c.1285C>T	p.Arg429Trp	p.R429W	ENST00000345506	NM_003152.3	429	Cgg/Tgg	12/20	1	2	FACETS	0.828	0.728	0.935	0.828	0.728	0.935	CLONAL	1	TRUE	1	0.36	2		538	510	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550335	39550335	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	41	307	0	ENST00000262039.4:c.446T>C	p.Val149Ala	p.V149A	ENST00000262039	NM_002647.2	149	gTa/gCa	4/25	1	2	FACETS	0.571	0.476	0.676	0.571	0.476	0.676	SUBCLONAL	1	TRUE	1	0.36	2		307	399	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023325	31023325	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	56	524	0	ENST00000375687.4:c.2810C>A	p.Pro937His	p.P937H	ENST00000375687	NM_015338.5	937	cCt/cAt	13/13	1	2	FACETS	0.867	0.746	0.997	0.867	0.746	0.997	CLONAL	1	TRUE	1	0.36	2		524	359	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326237	62326237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1470891280	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	99	711	0	ENST00000360203.5:c.3253G>A	p.Ala1085Thr	p.A1085T	ENST00000360203	NM_001283009.1	1085	Gcc/Acc	32/35	1	2	FACETS	0.914	0.817	1	0.914	0.817	1	CLONAL	1	TRUE	1	0.36	2		711	602	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182677	38182677	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	55	450	0	ENST00000396334.3:c.830T>C	p.Phe277Ser	p.F277S	ENST00000396334	NM_002468.4	277	tTc/tCc	5/5	1	2	FACETS	0.717	0.615	0.828	0.717	0.615	0.828	SUBCLONAL	1	TRUE	1	0.36	2		450	426	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665035	138665035	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	15	39	0	ENST00000330315.3:c.530G>T	p.Gly177Val	p.G177V	ENST00000330315	NM_023067.3	177	gGc/gTc	1/1	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.36	2		39	63	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217223	66217223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	41	464	0	ENST00000273854.3:c.2392C>T	p.His798Tyr	p.H798Y	ENST00000273854	NM_004439.5	798	Cat/Tat	14/18	0.3	0	FACETS	0.405	0.338	0.479			1	SUBCLONAL	1	TRUE	0	0.36	0		464	360	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286224	66286224	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	81	533	0	ENST00000273854.3:c.1462T>C	p.Ser488Pro	p.S488P	ENST00000273854	NM_004439.5	488	Tct/Cct	6/18	0.3	0	FACETS	0.518	0.457	0.583			1	SUBCLONAL	1	TRUE	0	0.36	0		533	556	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31939994	31939994	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	39	400	1	ENST00000375333.2:c.220+1G>A		p.X74_splice	ENST00000375333	NM_032454.1	74			1	2	FACETS	0.768	0.64	0.91	0.768	0.64	0.91	CLONAL	1	TRUE	1	0.36	2		401	282	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652243	36652243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs558863376	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	72	519	0	ENST00000244741.5:c.365G>A	p.Arg122His	p.R122H	ENST00000244741	NM_000389.4	122	cGc/cAc	2/3	1	2	FACETS	0.93	0.816	1	0.93	0.816	1	CLONAL	1	TRUE	1	0.36	2		519	430	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200320	138200320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	41	449	0	ENST00000237289.4:c.1738C>A	p.His580Asn	p.H580N	ENST00000237289	NM_001270507.1	580	Cac/Aac	7/9	1	2	FACETS	0.631	0.527	0.746	0.631	0.527	0.746	SUBCLONAL	1	TRUE	1	0.36	2		449	361	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873683	151873683	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1489425164	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	124	551	1	ENST00000262189.6:c.8855C>T	p.Ser2952Leu	p.S2952L	ENST00000262189	NM_170606.2	2952	tCa/tTa	38/59	0.172018439167131	3	FACETS	1	0.984	1	0.716	0.65	0.784	INDETERMINATE	1	TRUE	1	0.36	3		552	568	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146220	38146220	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	104	597	0	ENST00000317025.8:c.3286C>T	p.Pro1096Ser	p.P1096S	ENST00000317025	NM_023034.1	1096	Ccc/Tcc	19/24	0.286186504431981	5	FACETS	0.99	0.885	1	0.247	0.221	0.276	CLONAL	1	TRUE	1	0.36	5		597	899	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779125	135779125	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	67	421	0	ENST00000298552.3:c.2121del	p.Phe707LeufsTer17	p.F707Lfs*17	ENST00000298552	NM_001162426.1	707	ttT/tt	17/23	1	2	FACETS	0.818	0.713	0.931	0.818	0.713	0.931	CLONAL	1	TRUE	1	0.36	2		421	455	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401171	139401171	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	50	537	0	ENST00000277541.6:c.3898A>G	p.Thr1300Ala	p.T1300A	ENST00000277541	NM_017617.3	1300	Acc/Gcc	23/34	1	2	FACETS	0.658	0.56	0.766	0.658	0.56	0.766	SUBCLONAL	1	TRUE	1	0.36	2		537	422	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0037045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	217	210	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.716407359809294	3	FACETS	1	0.972	1	0.538	0.502	0.576	CLONAL	1	TRUE	1	0.716407359809294	3		210	764	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518073	69518074	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0037045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	413	890	0	ENST00000294312.3:c.291_292del	p.Val98AlafsTer79	p.V98Afs*79	ENST00000294312	NM_005117.2	97	agCGtg/agtg	2/3	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.716407359809294	2		890	1114	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409096	4409096	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs771085906	NA	P-0037045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	473	494	0	ENST00000261254.3:c.791A>G	p.Asp264Gly	p.D264G	ENST00000261254	NM_001759.3	264	gAc/gGc	5/5	0.716407359809294	3	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.716407359809294	3		494	869	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350587	89350587	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0037045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	478	972	0	ENST00000301030.4:c.2363C>G	p.Ser788Ter	p.S788*	ENST00000301030	NM_001256183.1	788	tCa/tGa	9/13	0.716407359809294	2	FACETS	1	0.981	1	0.521	0.499	0.544	CLONAL	1	TRUE	0	0.716407359809294	2		972	1280	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913641	32913641	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs893978143	NA	P-0037086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	54	280	0	ENST00000380152.3:c.5149G>A	p.Glu1717Lys	p.E1717K	ENST00000380152		1717	Gaa/Aaa	11/27	0.216542881911981	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.216542881911981	1		280	412	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023612	31023612	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	71	426	0	ENST00000375687.4:c.3097G>T	p.Glu1033Ter	p.E1033*	ENST00000375687	NM_015338.5	1033	Gag/Tag	13/13	1	2	FACETS	0.953	0.831	1	0.953	0.831	1	CLONAL	1	TRUE	1	0.216542881911981	2		426	688	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713522	30713522	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	50	355	0	ENST00000295754.5:c.847G>T	p.Glu283Ter	p.E283*	ENST00000295754	NM_003242.5	283	Gag/Tag	4/7	0.216542881911981	1	FACETS	0.749	0.635	0.874	0.749	0.635	0.874	SUBCLONAL	1	TRUE	0	0.216542881911981	1		355	550	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17350557	17350557	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1045881797	NA	P-0037086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	65	314	0	ENST00000375499.3:c.553G>A	p.Glu185Lys	p.E185K	ENST00000375499	NM_003000.2	185	Gag/Aag	6/8	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.216542881911981	2		314	587	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726618	41726618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	77	488	1	ENST00000301178.4:c.163C>T	p.Arg55Trp	p.R55W	ENST00000301178	NM_021913.4	55	Cgg/Tgg	2/20	0.168860180371585	1	FACETS	0.704	0.617	0.798	0.704	0.617	0.798	SUBCLONAL	1	TRUE	0	0.216542881911981	1		489	901	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578262	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs483352697	NA	P-0037105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	237	623	0	ENST00000269305.4:c.587G>C	p.Arg196Pro	p.R196P	ENST00000269305	NM_001126112.2	196	cGa/cCa	6/11	0.615927494086676	2	FACETS	0.835	0.791	0.879	0.835	0.791	0.879	CLONAL	2	TRUE	0	0.639328266628456	2		623	444	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479718	67479720	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0037105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	83	524	1	ENST00000327367.4:c.1027_1029del	p.Phe343del	p.F343del	ENST00000327367	NM_005902.3	342	aTCTtc/atc	8/9	0.615927494086676	2	FACETS	0.535	0.474	0.601	0.268	0.237	0.301	SUBCLONAL	1	TRUE	0	0.639328266628456	2		525	485	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639946	3639946	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	138	786	0	ENST00000294008.3:c.3693G>T	p.Arg1231Ser	p.R1231S	ENST00000294008	NM_032444.2	1231	agG/agT	12/15	0.505493821469789	2	FACETS	0.717	0.655	0.782	0.359	0.327	0.391	SUBCLONAL	1	TRUE	0	0.639328266628456	2		786	602	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979267	93979267	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1417829621	NA	P-0037105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	45	408	1	ENST00000369303.4:c.1561G>T	p.Ala521Ser	p.A521S	ENST00000369303	NM_004440.3	521	Gct/Tct	7/17	0.444672559324039	4	FACETS	0.804	0.68	0.94	0.402	0.34	0.47	CLONAL	1	TRUE	2	0.639328266628456	4		409	287	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120592	94120592	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	96	537	1	ENST00000369303.4:c.459A>T	p.Glu153Asp	p.E153D	ENST00000369303	NM_004440.3	153	gaA/gaT	3/17	0.444672559324039	4	FACETS	1	0.979	1	0.691	0.622	0.764	CLONAL	1	TRUE	2	0.639328266628456	4		538	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0037120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	464	590	1	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	0.794358920389188	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.794358920389188	1		591	660	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0037120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	160	160	1	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.418623057473253	1	FACETS	0.747	0.697	0.797	0.747	0.697	0.797	INDETERMINATE	1	TRUE	0	0.794358920389188	1		161	325	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120451	70120452	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0037120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	391	851	0	ENST00000245479.2:c.1455_1456del	p.Val486ProfsTer91	p.V486Pfs*91	ENST00000245479	NM_000346.3	485	GGg/g	3/3	0.418623057473253	1	FACETS	0.39	0.369	0.41	0.39	0.369	0.41	INDETERMINATE	1	TRUE	0	0.794358920389188	1		851	1523	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5258120	5258120	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	248	670	0	ENST00000357368.4:c.614G>T	p.Ser205Ile	p.S205I	ENST00000357368	NM_002850.3	205	aGc/aTc	8/38	0.794358920389188	1	FACETS	0.489	0.459	0.52	0.489	0.459	0.52	SUBCLONAL	1	TRUE	0	0.794358920389188	1		670	769	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080325	5080325	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	76	289	0	ENST00000381652.3:c.2228T>C	p.Leu743Ser	p.L743S	ENST00000381652	NM_004972.3	743	tTg/tCg	17/25	1	2	FACETS	0.508	0.448	0.571	0.508	0.448	0.571	SUBCLONAL	1	TRUE	1	0.794358920389188	2		289	377	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158045	27158045	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	367	582	0	ENST00000380036.4:c.269G>C	p.Arg90Thr	p.R90T	ENST00000380036	NM_000459.3	90	aGa/aCa	2/23	1	2	FACETS	0.971	0.924	1	0.971	0.924	1	CLONAL	1	TRUE	1	0.794358920389188	2		582	952	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866483	56866483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1387477088	NA	P-0037124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	106	584	0	ENST00000519728.1:c.730C>T	p.Arg244Trp	p.R244W	ENST00000519728	NM_002350.3	244	Cgg/Tgg	8/13	1	2	FACETS	0.931	0.84	1	0.931	0.84	1	CLONAL	1	TRUE	1	0.50817855772309	2		584	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579406	7579406	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0037167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	305	679	0	ENST00000269305.4:c.281C>G	p.Ser94Ter	p.S94*	ENST00000269305	NM_001126112.2	94	tCa/tGa	4/11	0.496850701678636	2	FACETS	0.904	0.859	0.95	0.904	0.859	0.95	CLONAL	2	TRUE	0	0.496850701678636	2		679	679	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55963927	55963927	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	81	363	0	ENST00000263923.4:c.2516C>A	p.Pro839His	p.P839H	ENST00000263923	NM_002253.2	839	cCt/cAt	18/30	0.333957639275905	3	FACETS	0.899	0.795	1	0.449	0.397	0.505	CLONAL	1	TRUE	1	0.496850701678636	3		363	453	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90996788	90996788	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs746422391	NA	P-0037167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	162	431	0	ENST00000265433.3:c.2T>C	p.Met1?	p.M1?	ENST00000265433	NM_002485.4	1	aTg/aCg	1/16	0.461015612164915	4	FACETS	0.786	0.724	0.85	0.786	0.724	0.85	SUBCLONAL	2	TRUE	2	0.496850701678636	4		431	621	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0037190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	184	542	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		542	479	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682359	52682359	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0037190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	182	329	0	ENST00000394830.3:c.813+1G>T		p.X271_splice	ENST00000394830	NM_018313.4	271			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		329	283	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0037223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	251	1154	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.650327499634724	2		1154	698	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781244	3781245	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0037223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	80	993	0	ENST00000262367.5:c.5120dup	p.Cys1707TrpfsTer28	p.C1707Wfs*28	ENST00000262367	NM_004380.2	1707	tgc/tgGc	30/31	1	2	FACETS	0.358	0.314	0.404	0.358	0.314	0.404	SUBCLONAL	1	TRUE	1	0.650327499634724	2		993	688	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0037225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	150	415	2	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.966	0.889	1	0.966	0.889	1	CLONAL	1	TRUE	1	0.616229119576687	2		417	504	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0037225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	104	442	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.808	0.728	0.891	0.808	0.728	0.891	CLONAL	1	TRUE	1	0.616229119576687	2		442	418	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0037225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	346	1154	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.616229119576687	2		1154	1033	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692911	89692911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909241	NA	P-0037225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	371	600	0	ENST00000371953.3:c.395G>A	p.Gly132Asp	p.G132D	ENST00000371953	NM_000314.4	132	gGt/gAt	5/9	0.616229119576687	3	FACETS	0.983	0.949	1	0.983	0.949	1	CLONAL	3	TRUE	0	0.616229119576687	3		600	534	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591133	67591134	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0037225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	94	364	0	ENST00000274335.5:c.1727dup	p.Arg577GlufsTer25	p.R577Efs*25	ENST00000274335		576	acg/aCcg	12/15	1	2	FACETS	0.984	0.886	1	0.984	0.886	1	CLONAL	1	TRUE	1	0.616229119576687	2		364	310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0037241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	156	538	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.213289458741268	3	FACETS	0.88	0.81	0.952	0.88	0.81	0.952	CLONAL	3	TRUE	0	0.23	3		538	573	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202122968	202122968	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	102	387	0	ENST00000358485.4:c.14G>T	p.Arg5Ile	p.R5I	ENST00000358485	NM_001080125.1	5	aGa/aTa	1/9	0.300661863815121	5	FACETS	1	0.975	1	0.44	0.393	0.49	CLONAL	1	TRUE	2	0.23	5		387	904	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0037247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	126	698	2	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.163828183918224	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.163828183918224	2		700	702	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0037247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	104	491	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.163828183918224	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	2	TRUE	0	0.163828183918224	2		492	621	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057302	30057302	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315496	NA	P-0037247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	68	346	0	ENST00000338641.4:c.784C>T	p.Arg262Ter	p.R262*	ENST00000338641	NM_000268.3	262	Cga/Tga	8/16	0.163828183918224	2	FACETS	0.908	0.792	1	0.908	0.792	1	CLONAL	2	TRUE	0	0.163828183918224	2		346	457	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220644	1220644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1167609100	NA	P-0037247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	63	549	0	ENST00000326873.7:c.662C>T	p.Pro221Leu	p.P221L	ENST00000326873	NM_000455.4	221	cCg/cTg	5/10	0.163828183918224	2	FACETS	1	0.944	1	0.59	0.51	0.677	CLONAL	1	TRUE	0	0.163828183918224	2		549	652	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713383	40713383	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs773803715	NA	P-0037247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	50	523	1	ENST00000373198.4:c.4132C>T	p.Arg1378Ter	p.R1378*	ENST00000373198	NM_133170.3	1378	Cga/Tga	30/32	0.163828183918224	2	FACETS	0.926	0.785	1	0.463	0.392	0.541	CLONAL	1	TRUE	0	0.163828183918224	2		524	659	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463286	25463286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139293773	NA	P-0037247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	85	375	0	ENST00000264709.3:c.2207G>A	p.Arg736His	p.R736H	ENST00000264709	NM_175629.2	736	cGc/cAc	19/23	0.163828183918224	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	2	TRUE	0	0.163828183918224	2		375	503	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674233	86674233	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1463885690	NA	P-0037247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	30	371	2	ENST00000274376.6:c.2365C>T	p.Arg789Ter	p.R789*	ENST00000274376	NM_002890.2	789	Cga/Tga	18/25	0.163828183918224	4	FACETS	0.842	0.678	1	0.421	0.339	0.515	CLONAL	1	TRUE	2	0.163828183918224	4		373	506	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052725	42052725	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	91	420	0	ENST00000219905.7:c.7396C>T	p.Arg2466Ter	p.R2466*	ENST00000219905	NM_001164273.1	2466	Cga/Tga	20/24	0.163828183918224	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	2	TRUE	0	0.163828183918224	2		420	541	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471048	8471048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	68	393	0	ENST00000356435.5:c.3451C>T	p.Arg1151Cys	p.R1151C	ENST00000356435		1151	Cgc/Tgc	20/35	0.163828183918224	2	FACETS	0.835	0.728	0.951	0.835	0.728	0.951	CLONAL	2	TRUE	0	0.163828183918224	2		393	497	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149511632	149511632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167658274	NA	P-0037247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	39	422	0	ENST00000261799.4:c.1153C>T	p.Arg385Cys	p.R385C	ENST00000261799	NM_002609.3	385	Cgc/Tgc	8/23	0.163828183918224	3	FACETS	0.899	0.744	1	0.449	0.372	0.536	CLONAL	1	TRUE	1	0.163828183918224	3		422	573	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439919	56439919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765548407	NA	P-0037247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	112	420	0	ENST00000407977.2:c.673C>T	p.Arg225Cys	p.R225C	ENST00000407977		225	Cgc/Tgc	6/10	0.163828183918224	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.163828183918224	2		420	585	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31511250	31511250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767118229	NA	P-0037247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	85	667	0	ENST00000344624.3:c.1324C>T	p.Arg442Cys	p.R442C	ENST00000344624		442	Cgt/Tgt	6/33	0.163828183918224	4	FACETS	1	0.976	1	0.722	0.637	0.813	CLONAL	1	TRUE	2	0.163828183918224	4		667	836	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562904	21562904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1390242703	NA	P-0037247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	89	623	0	ENST00000382592.4:c.1015G>A	p.Ala339Thr	p.A339T	ENST00000382592	NM_014572.2	339	Gcc/Acc	4/8	1	2	FACETS	0.96	0.853	1	1	0.985	1	CLONAL	2	TRUE	1	0.163828183918224	2		623	566	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106003	27106003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775428237	NA	P-0037247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	81	422	0	ENST00000324856.7:c.5614G>A	p.Ala1872Thr	p.A1872T	ENST00000324856	NM_006015.4	1872	Gca/Aca	20/20	0.163828183918224	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	TRUE	0	0.163828183918224	2		422	468	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557911	21557911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	60	443	0	ENST00000382592.4:c.1934G>A	p.Arg645Gln	p.R645Q	ENST00000382592	NM_014572.2	645	cGg/cAg	5/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.163828183918224	2		443	515	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211753	36211753	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374554860	NA	P-0037247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	203	562	1	ENST00000222270.7:c.1504G>A	p.Ala502Thr	p.A502T	ENST00000222270	NM_014727.1	502	Gcc/Acc	3/37	0.163828183918224	4	FACETS	0.901	0.838	0.967	0.901	0.838	0.967	CLONAL	4	TRUE	0	0.163828183918224	4		563	800	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609650	46609650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761084491	NA	P-0037247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	149	604	0	ENST00000263734.3:c.2374G>A	p.Gly792Arg	p.G792R	ENST00000263734	NM_001430.4	792	Ggg/Agg	15/16	0.163828183918224	2	FACETS	0.834	0.763	0.908	1	0.981	1	CLONAL	3	TRUE	0	0.163828183918224	2		604	727	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397516435	NA	P-0037255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	36	536	0	ENST00000269305.4:c.586C>G	p.Arg196Gly	p.R196G	ENST00000269305	NM_001126112.2	196	Cga/Gga	6/11	0.104020572838656	0	FACETS	1	0.893	1			1	CLONAL	1	FALSE	0	0.161775775008246	0		536	333	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696689	47696689	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519972	NA	P-0037255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	47	458	0	ENST00000347630.2:c.259T>A	p.Tyr87Asn	p.Y87N	ENST00000347630	NM_001007230.1	87	Tac/Aac	5/11	0.104020572838656	0	FACETS	1	0.881	1			1	CLONAL	1	FALSE	0	0.161775775008246	0		458	463	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257007	16257007	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	76	563	0	ENST00000375759.3:c.4273del	p.Ser1425LeufsTer2	p.S1425Lfs*2	ENST00000375759	NM_015001.2	1424	agT/ag	11/15	1	2	FACETS	0.91	0.8	1	1	0.981	1	CLONAL	2	FALSE	1	0.161775775008246	2		563	516	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084125	47084125	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	55	554	0	ENST00000409792.3:c.7164del	p.Ile2389LeufsTer22	p.I2389Lfs*22	ENST00000409792	NM_014159.6	2388	acC/ac	17/21	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.161775775008246	2		554	533	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50481162	50481162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	192	416	0	ENST00000394963.4:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000394963	NM_003076.4	183	cGa/cAa	5/13	1	2	FACETS	0.933	0.866	1	0.933	0.866	1	CLONAL	1	TRUE	1	0.62	2		416	664	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	217	594	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.775	0.722	0.831	0.775	0.722	0.831	SUBCLONAL	1	TRUE	1	0.62	2		594	903	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546098	29546098	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1567843917	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	223	397	0	ENST00000356175.3:c.1603C>T	p.Gln535Ter	p.Q535*	ENST00000356175	NM_000267.3	535	Cag/Tag	14/57	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.62	2		397	683	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	208	465	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.62	2		465	642	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261434	16261434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	44	544	1	ENST00000375759.3:c.8699C>T	p.Ser2900Leu	p.S2900L	ENST00000375759	NM_015001.2	2900	tCg/tTg	11/15	1	2	FACETS	0.162	0.135	0.192	0.162	0.135	0.192	SUBCLONAL	1	TRUE	1	0.62	2		545	875	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149251	119149251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267606708	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	256	544	0	ENST00000264033.4:c.1259G>A	p.Arg420Gln	p.R420Q	ENST00000264033	NM_005188.3	420	cGa/cAa	9/16	1	2	FACETS	0.949	0.891	1	0.949	0.891	1	CLONAL	1	TRUE	1	0.62	2		544	870	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	19	350	0	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	1	2	FACETS	0.104	0.078	0.134	0.104	0.078	0.134	SUBCLONAL	1	TRUE	1	0.62	2		350	592	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855984	68855984	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121964877	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	255	561	1	ENST00000261769.5:c.1792C>T	p.Arg598Ter	p.R598*	ENST00000261769	NM_004360.3	598	Cga/Tga	12/16	1	2	FACETS	0.944	0.886	1	0.944	0.886	1	CLONAL	1	TRUE	1	0.62	2		562	871	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555216	226555216	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374662166	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	216	525	0	ENST00000366794.5:c.2371G>A	p.Asp791Asn	p.D791N	ENST00000366794	NM_001618.3	791	Gat/Aat	17/23	1	2	FACETS	0.8	0.745	0.857	0.8	0.745	0.857	SUBCLONAL	1	TRUE	1	0.62	2		525	871	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149710	202149710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	358	638	1	ENST00000358485.4:c.1151G>A	p.Gly384Asp	p.G384D	ENST00000358485	NM_001080125.1	384	gGc/gAc	8/9	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.62	2		639	1031	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181843	56181843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	171	398	0	ENST00000399503.3:c.4067G>A	p.Gly1356Asp	p.G1356D	ENST00000399503	NM_005921.1	1356	gGc/gAc	17/20	1	2	FACETS	0.906	0.837	0.976	0.906	0.837	0.976	CLONAL	1	TRUE	1	0.62	2		398	609	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777640	9777640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148703447	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	304	630	0	ENST00000377346.4:c.976G>A	p.Glu326Lys	p.E326K	ENST00000377346	NM_005026.3	326	Gag/Aag	8/24	1	2	FACETS	0.941	0.888	0.996	0.941	0.888	0.996	CLONAL	1	TRUE	1	0.62	2		630	1042	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268448	142268448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564283952	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	191	457	1	ENST00000350721.4:c.3044G>A	p.Arg1015Gln	p.R1015Q	ENST00000350721	NM_001184.3	1015	cGa/cAa	15/47	1	2	FACETS	0.963	0.894	1	0.963	0.894	1	CLONAL	1	TRUE	1	0.62	2		458	640	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720870	89720870	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1554825652	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	194	357	0	ENST00000371953.3:c.1021T>G	p.Phe341Val	p.F341V	ENST00000371953	NM_000314.4	341	Ttt/Gtt	8/9	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.62	2		357	595	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891035	112891035	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs755619262	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	140	333	0	ENST00000351677.2:c.369G>T	p.Glu123Asp	p.E123D	ENST00000351677	NM_002834.3	123	gaG/gaT	4/16	1	2	FACETS	0.887	0.813	0.964	0.887	0.813	0.964	CLONAL	1	TRUE	1	0.62	2		333	509	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	246	620	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	0.899	0.842	0.957	0.899	0.842	0.957	CLONAL	1	TRUE	1	0.62	2		620	883	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699360	47699360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	203	447	0	ENST00000347630.2:c.148G>A	p.Glu50Lys	p.E50K	ENST00000347630	NM_001007230.1	50	Gaa/Aaa	4/11	1	2	FACETS	0.866	0.805	0.929	0.866	0.805	0.929	CLONAL	1	TRUE	1	0.62	2		447	756	SUCCESS
AR	367	MSKCC	GRCh37	X	66942700	66942700	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs200801099	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	170	494	0	ENST00000374690.3:c.2481C>A	p.Phe827Leu	p.F827L	ENST00000374690	NM_000044.3	827	ttC/ttA	7/8	1	2	FACETS	0.809	0.746	0.874	0.809	0.746	0.874	CLONAL	1	TRUE	1	0.62	2		494	678	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126756	5126756	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	105	422	0	ENST00000381652.3:c.3364C>T	p.Arg1122Ter	p.R1122*	ENST00000381652	NM_004972.3	1122	Cga/Tga	25/25	0.142518776711173	0	FACETS	0.243	0.218	0.269			1	INDETERMINATE	1	TRUE	0	0.62	0		422	529	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695864	117695864	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	265	694	1	ENST00000369458.3:c.573C>A	p.Phe191Leu	p.F191L	ENST00000369458	NM_024626.3	191	ttC/ttA	4/6	1	2	FACETS	0.863	0.81	0.918	0.863	0.81	0.918	CLONAL	1	TRUE	1	0.62	2		695	990	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588626	28588626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548609046	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	180	474	0	ENST00000241453.7:c.2822C>T	p.Ser941Leu	p.S941L	ENST00000241453	NM_004119.2	941	tCg/tTg	23/24	1	2	FACETS	0.828	0.766	0.892	0.828	0.766	0.892	CLONAL	1	TRUE	1	0.62	2		474	701	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	503	621	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.918	0.886	0.95	1	0.997	1	CLONAL	2	TRUE	1	0.62	2		621	884	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881438	48881438	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	82	220	0	ENST00000267163.4:c.160G>T	p.Glu54Ter	p.E54*	ENST00000267163	NM_000321.2	54	Gaa/Taa	2/27	1	2	FACETS	0.778	0.692	0.869	0.778	0.692	0.869	SUBCLONAL	1	TRUE	1	0.62	2		220	340	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172385	108172385	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764389018	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	179	483	0	ENST00000278616.4:c.5188C>T	p.Arg1730Ter	p.R1730*	ENST00000278616	NM_000051.3	1730	Cga/Tga	35/63	1	2	FACETS	0.922	0.854	0.992	0.922	0.854	0.992	CLONAL	1	TRUE	1	0.62	2		483	626	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259262	89259262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770780950	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	213	438	0	ENST00000336596.2:c.406C>T	p.Arg136Ter	p.R136*	ENST00000336596	NM_005233.5	136	Cga/Tga	3/17	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.62	2		438	677	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027998	48027998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757653982	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	126	291	0	ENST00000234420.5:c.2876G>A	p.Arg959His	p.R959H	ENST00000234420	NM_000179.2	959	cGc/cAc	4/10	1	2	FACETS	0.836	0.762	0.914	0.836	0.762	0.914	CLONAL	1	TRUE	1	0.62	2		291	486	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622630	158622630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	237	498	0	ENST00000263640.3:c.869C>T	p.Ser290Leu	p.S290L	ENST00000263640	NM_001105.4	290	tCg/tTg	8/11	1	2	FACETS	0.932	0.873	0.994	0.932	0.873	0.994	CLONAL	1	TRUE	1	0.62	2		498	820	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149974	202149974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301592633	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	289	594	0	ENST00000358485.4:c.1415G>A	p.Arg472Gln	p.R472Q	ENST00000358485	NM_001080125.1	472	cGa/cAa	8/9	1	2	FACETS	0.96	0.905	1	0.96	0.905	1	CLONAL	1	TRUE	1	0.62	2		594	971	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267600319	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	46	337	0	ENST00000257430.4:c.4199C>T	p.Ser1400Leu	p.S1400L	ENST00000257430	NM_000038.5	1400	tCg/tTg	16/16	1	2	FACETS	0.259	0.218	0.305	0.259	0.218	0.305	SUBCLONAL	1	TRUE	1	0.62	2		337	572	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131418	17131418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751171641	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	233	575	0	ENST00000285071.4:c.34G>A	p.Glu12Lys	p.E12K	ENST00000285071	NM_144997.5	12	Gag/Aag	4/14	1	2	FACETS	0.827	0.772	0.883	0.827	0.772	0.883	CLONAL	1	TRUE	1	0.62	2		575	909	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752839	57752839	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	172	401	0	ENST00000274289.3:c.1089C>A	p.Phe363Leu	p.F363L	ENST00000274289	NM_006622.3	363	ttC/ttA	8/14	1	2	FACETS	0.884	0.817	0.953	0.884	0.817	0.953	CLONAL	1	TRUE	1	0.62	2		401	628	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575550	67575550	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	171	347	0	ENST00000274335.5:c.623C>A	p.Ser208Tyr	p.S208Y	ENST00000274335		208	tCt/tAt	4/15	1	2	FACETS	0.827	0.763	0.893	0.827	0.763	0.893	CLONAL	1	TRUE	1	0.62	2		347	667	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132542	11132542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	277	684	0	ENST00000358026.2:c.2758G>A	p.Glu920Lys	p.E920K	ENST00000358026	NM_001128849.1	920	Gag/Aag	19/36	1	2	FACETS	0.872	0.819	0.926	0.872	0.819	0.926	CLONAL	1	TRUE	1	0.62	2		684	1025	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342954	225342954	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	339	620	0	ENST00000264414.4:c.2138C>A	p.Ser713Tyr	p.S713Y	ENST00000264414	NM_003590.4	713	tCt/tAt	15/16	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.62	2		620	993	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274880	142274880	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs372610600	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	244	454	0	ENST00000350721.4:c.2180C>A	p.Ser727Tyr	p.S727Y	ENST00000350721	NM_001184.3	727	tCt/tAt	10/47	1	2	FACETS	0.907	0.849	0.966	0.907	0.849	0.966	CLONAL	1	TRUE	1	0.62	2		454	868	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407527	407527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs908661692	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	236	509	1	ENST00000380956.4:c.1285G>A	p.Asp429Asn	p.D429N	ENST00000380956	NM_001195286.1	429	Gat/Aat	9/9	1	2	FACETS	0.925	0.865	0.986	0.925	0.865	0.986	CLONAL	1	TRUE	1	0.62	2		510	823	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42002918	42002918	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	197	419	0	ENST00000219905.7:c.2455C>T	p.Arg819Cys	p.R819C	ENST00000219905	NM_001164273.1	819	Cgt/Tgt	8/24	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.62	2		419	623	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42002997	42002997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	284	610	0	ENST00000219905.7:c.2534C>T	p.Ser845Phe	p.S845F	ENST00000219905	NM_001164273.1	845	tCt/tTt	8/24	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.62	2		610	897	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417934	138417934	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1194965901	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	145	309	0	ENST00000289153.2:c.1585C>T	p.Arg529Ter	p.R529*	ENST00000289153	NM_006219.2	529	Cga/Tga	11/22	1	2	FACETS	0.896	0.822	0.972	0.896	0.822	0.972	CLONAL	1	TRUE	1	0.62	2		309	522	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	102	277	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	0.702	0.631	0.776	0.702	0.631	0.776	SUBCLONAL	1	TRUE	1	0.62	2		277	469	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203493	108203493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140263969	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	109	271	0	ENST00000278616.4:c.7793G>A	p.Arg2598Gln	p.R2598Q	ENST00000278616	NM_000051.3	2598	cGa/cAa	53/63	1	2	FACETS	0.918	0.832	1	0.918	0.832	1	CLONAL	1	TRUE	1	0.62	2		271	383	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672842	86672842	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	95	279	0	ENST00000274376.6:c.2329G>T	p.Glu777Ter	p.E777*	ENST00000274376	NM_002890.2	777	Gaa/Taa	17/25	1	2	FACETS	0.76	0.682	0.843	0.76	0.682	0.843	SUBCLONAL	1	TRUE	1	0.62	2		279	403	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156699	2156699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs975030738	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	259	614	0	ENST00000434045.2:c.223G>A	p.Ala75Thr	p.A75T	ENST00000434045	NM_001127598.1	75	Gcc/Acc	3/5	1	2	FACETS	0.92	0.863	0.978	0.92	0.863	0.978	CLONAL	1	TRUE	1	0.62	2		614	908	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982108	38982108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778526085	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	158	415	0	ENST00000357387.3:c.614G>A	p.Arg205Gln	p.R205Q	ENST00000357387	NM_152756.3	205	cGa/cAa	8/38	1	2	FACETS	0.907	0.836	0.981	0.907	0.836	0.981	CLONAL	1	TRUE	1	0.62	2		415	562	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593394	48593394	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	185	376	0	ENST00000342988.3:c.1145A>G	p.His382Arg	p.H382R	ENST00000342988	NM_005359.5	382	cAc/cGc	10/12	1	2	FACETS	0.943	0.875	1	0.943	0.875	1	CLONAL	1	TRUE	1	0.62	2		376	633	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546725	9546725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210292896	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	113	362	1	ENST00000353224.5:c.1297C>T	p.Arg433Trp	p.R433W	ENST00000353224	NM_177990.2	433	Cgg/Tgg	5/10	1	2	FACETS	0.862	0.781	0.946	0.862	0.781	0.946	CLONAL	1	TRUE	1	0.62	2		363	423	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604665	48604665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660045	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	161	347	0	ENST00000342988.3:c.1487G>A	p.Arg496His	p.R496H	ENST00000342988	NM_005359.5	496	cGt/cAt	12/12	1	2	FACETS	0.854	0.787	0.924	0.854	0.787	0.924	CLONAL	1	TRUE	1	0.62	2		347	608	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835623	68835623	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35606263	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	252	589	1	ENST00000261769.5:c.214G>A	p.Asp72Asn	p.D72N	ENST00000261769	NM_004360.3	72	Gac/Aac	3/16	1	2	FACETS	0.92	0.862	0.978	0.92	0.862	0.978	CLONAL	1	TRUE	1	0.62	2		590	884	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265635	152265635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367647625	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	158	402	0	ENST00000206249.3:c.1088G>A	p.Arg363Lys	p.R363K	ENST00000206249	NM_000125.3	363	aGg/aAg	4/8	1	2	FACETS	0.965	0.89	1	0.965	0.89	1	CLONAL	1	TRUE	1	0.62	2		402	528	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003192	42003192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764724458	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	54	597	1	ENST00000219905.7:c.2729G>A	p.Arg910Gln	p.R910Q	ENST00000219905	NM_001164273.1	910	cGa/cAa	8/24	1	2	FACETS	0.194	0.165	0.226	0.194	0.165	0.226	SUBCLONAL	1	TRUE	1	0.62	2		598	898	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729888	41729888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1043609570	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	191	504	1	ENST00000242208.4:c.641G>A	p.Arg214Gln	p.R214Q	ENST00000242208	NM_002192.2	214	cGg/cAg	3/3	1	2	FACETS	0.81	0.75	0.871	0.81	0.75	0.871	CLONAL	1	TRUE	1	0.62	2		505	761	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589618	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519838	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	82	196	0	ENST00000274335.5:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000274335		461	Cga/Tga	10/15	1	2	FACETS	0.915	0.816	1	0.915	0.816	1	CLONAL	1	TRUE	1	0.62	2		196	289	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045954	26045954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	190	396	0	ENST00000540144.1:c.316G>A	p.Glu106Lys	p.E106K	ENST00000540144	NM_003531.2	106	Gaa/Aaa	1/1	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.62	2		396	567	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059183	27059183	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	150	429	0	ENST00000324856.7:c.1820C>A	p.Ser607Ter	p.S607*	ENST00000324856	NM_006015.4	607	tCa/tAa	4/20	1	2	FACETS	0.793	0.728	0.861	0.793	0.728	0.861	SUBCLONAL	1	TRUE	1	0.62	2		429	610	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140487360	140487360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507472	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	211	545	2	ENST00000288602.6:c.1165C>T	p.Arg389Cys	p.R389C	ENST00000288602	NM_004333.4	389	Cgt/Tgt	9/18	1	2	FACETS	0.864	0.804	0.925	0.864	0.804	0.925	CLONAL	1	TRUE	1	0.62	2		547	788	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288786	33288786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752819224	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	230	499	0	ENST00000374542.5:c.766C>T	p.Arg256Cys	p.R256C	ENST00000374542	NM_001141970.1	256	Cgc/Tgc	3/8	1	2	FACETS	0.951	0.889	1	0.951	0.889	1	CLONAL	1	TRUE	1	0.62	2		499	780	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504590	103504590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1400329743	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	163	418	1	ENST00000355739.4:c.211C>T	p.Arg71Cys	p.R71C	ENST00000355739	NM_000123.3	71	Cgt/Tgt	2/15	1	2	FACETS	0.876	0.808	0.947	0.876	0.808	0.947	CLONAL	1	TRUE	1	0.62	2		419	600	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921533	178921533	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1428379257	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	170	396	0	ENST00000263967.3:c.1015C>A	p.Leu339Ile	p.L339I	ENST00000263967	NM_006218.2	339	Ctt/Att	5/21	1	2	FACETS	0.926	0.856	0.998	0.926	0.856	0.998	CLONAL	1	TRUE	1	0.62	2		396	592	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281219	46281219	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	44	500	0	ENST00000371998.3:c.4016G>T	p.Arg1339Ile	p.R1339I	ENST00000371998		1339	aGa/aTa	21/23	1	2	FACETS	0.17	0.141	0.201	0.17	0.141	0.201	SUBCLONAL	1	TRUE	1	0.62	2		500	837	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918943	76918943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782726588	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	53	584	0	ENST00000373344.5:c.4048G>A	p.Gly1350Arg	p.G1350R	ENST00000373344	NM_000489.3	1350	Gga/Aga	12/35	1	2	FACETS	0.166	0.141	0.194	0.166	0.141	0.194	SUBCLONAL	1	TRUE	1	0.62	2		584	1028	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268457	198268457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	51	508	0	ENST00000335508.6:c.1571G>A	p.Arg524His	p.R524H	ENST00000335508	NM_012433.2	524	cGt/cAt	12/25	1	2	FACETS	0.194	0.164	0.227	0.194	0.164	0.227	SUBCLONAL	1	TRUE	1	0.62	2		508	847	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461563	138461563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558261053	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	254	557	2	ENST00000289153.2:c.458G>A	p.Arg153His	p.R153H	ENST00000289153	NM_006219.2	153	cGc/cAc	3/22	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.62	2		559	815	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115397	115115397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866796237	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	221	571	3	ENST00000257566.3:c.929G>A	p.Arg310Gln	p.R310Q	ENST00000257566	NM_016569.3	310	cGa/cAa	5/8	1	2	FACETS	0.817	0.761	0.874	0.817	0.761	0.874	CLONAL	1	TRUE	1	0.62	2		574	873	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900873	3900873	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	294	653	3	ENST00000262367.5:c.223C>T	p.Arg75Ter	p.R75*	ENST00000262367	NM_004380.2	75	Cga/Tga	2/31	1	2	FACETS	0.95	0.896	1	0.95	0.896	1	CLONAL	1	TRUE	1	0.62	2		656	998	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107231	193107231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	125	259	0	ENST00000367435.3:c.440G>A	p.Arg147His	p.R147H	ENST00000367435	NM_024529.4	147	cGc/cAc	6/17	1	2	FACETS	0.797	0.725	0.872	0.797	0.725	0.872	SUBCLONAL	1	TRUE	1	0.62	2		259	506	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176614	56176614	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	189	356	0	ENST00000399503.3:c.2164G>T	p.Glu722Ter	p.E722*	ENST00000399503	NM_005921.1	722	Gaa/Taa	12/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.62	2		356	549	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120642	115120642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	287	703	0	ENST00000257566.3:c.364G>A	p.Glu122Lys	p.E122K	ENST00000257566	NM_016569.3	122	Gag/Aag	1/8	1	2	FACETS	0.882	0.83	0.935	0.882	0.83	0.935	CLONAL	1	TRUE	1	0.62	2		703	1050	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736474	85736474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	189	475	0	ENST00000370580.1:c.173G>A	p.Arg58Gln	p.R58Q	ENST00000370580	NM_003921.4	58	cGa/cAa	2/3	1	2	FACETS	0.836	0.775	0.899	0.836	0.775	0.899	CLONAL	1	TRUE	1	0.62	2		475	729	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201746	66201746	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	223	524	0	ENST00000273854.3:c.2756G>A	p.Arg919Gln	p.R919Q	ENST00000273854	NM_004439.5	919	cGa/cAa	16/18	1	2	FACETS	0.932	0.87	0.995	0.932	0.87	0.995	CLONAL	1	TRUE	1	0.62	2		524	772	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571448	95571448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373412959	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	146	307	0	ENST00000393063.1:c.3229G>A	p.Asp1077Asn	p.D1077N	ENST00000393063	NM_030621.3	1077	Gat/Aat	21/28	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.62	2		307	461	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871196	35871196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773491081	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	170	410	0	ENST00000303115.3:c.418C>T	p.Arg140Trp	p.R140W	ENST00000303115	NM_002185.3	140	Cgg/Tgg	4/8	1	2	FACETS	0.841	0.776	0.908	0.841	0.776	0.908	CLONAL	1	TRUE	1	0.62	2		410	652	SUCCESS
CBL	867	MSKCC	GRCh37	11	119145620	119145620	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755244263	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	173	437	1	ENST00000264033.4:c.826G>A	p.Glu276Lys	p.E276K	ENST00000264033	NM_005188.3	276	Gaa/Aaa	5/16	1	2	FACETS	0.883	0.816	0.952	0.883	0.816	0.952	CLONAL	1	TRUE	1	0.62	2		438	632	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486242	8486242	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	43	406	0	ENST00000356435.5:c.2575A>C	p.Lys859Gln	p.K859Q	ENST00000356435		859	Aaa/Caa	17/35	0.142518776711173	0	FACETS	0.108	0.09	0.127			1	INDETERMINATE	1	TRUE	0	0.62	0		406	490	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158095	27158095	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	184	477	1	ENST00000380036.4:c.319C>T	p.Arg107Ter	p.R107*	ENST00000380036	NM_000459.3	107	Cga/Tga	2/23	0.142518776711173	0	FACETS	0.327	0.302	0.352			1	INDETERMINATE	1	TRUE	0	0.62	0		478	690	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826539	50826539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1315227790	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	52	379	0	ENST00000398568.2:c.2264G>A	p.Arg755Gln	p.R755Q	ENST00000398568	NM_001042412.1	755	cGa/cAa	15/18	1	2	FACETS	0.351	0.299	0.408	0.351	0.299	0.408	SUBCLONAL	1	TRUE	1	0.62	2		379	478	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663630	117663630	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	202	542	0	ENST00000368508.3:c.4602T>A	p.Asn1534Lys	p.N1534K	ENST00000368508	NM_002944.2	1534	aaT/aaA	28/43	1	2	FACETS	0.939	0.874	1	0.939	0.874	1	CLONAL	1	TRUE	1	0.62	2		542	694	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128989	64128989	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	288	582	1	ENST00000334205.4:c.619G>A	p.Glu207Lys	p.E207K	ENST00000334205	NM_003942.2	207	Gaa/Aaa	6/17	1	2	FACETS	0.991	0.934	1	0.991	0.934	1	CLONAL	1	TRUE	1	0.62	2		583	937	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210688	36210688	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	236	568	2	ENST00000222270.7:c.439C>T	p.Arg147Ter	p.R147*	ENST00000222270	NM_014727.1	147	Cga/Tga	3/37	1	2	FACETS	0.9	0.842	0.96	0.9	0.842	0.96	CLONAL	1	TRUE	1	0.62	2		570	846	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001305	150001305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568586257	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	235	637	1	ENST00000253339.5:c.2299C>T	p.Arg767Cys	p.R767C	ENST00000253339		767	Cgt/Tgt	4/7	1	2	FACETS	0.815	0.761	0.871	0.815	0.761	0.871	CLONAL	1	TRUE	1	0.62	2		638	930	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14303198	14303198	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	295	650	0	ENST00000256196.4:c.477G>T	p.Lys159Asn	p.K159N	ENST00000256196		159	aaG/aaT	5/6	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.62	2		650	946	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013719	170013719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388201066	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	175	465	1	ENST00000295797.4:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000295797	NM_002740.5	480	Cgc/Tgc	15/18	1	2	FACETS	0.862	0.797	0.929	0.862	0.797	0.929	CLONAL	1	TRUE	1	0.62	2		466	655	SUCCESS
APC	324	MSKCC	GRCh37	5	112176555	112176555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771967537	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	130	307	0	ENST00000257430.4:c.5264C>T	p.Ala1755Val	p.A1755V	ENST00000257430	NM_000038.5	1755	gCg/gTg	16/16	1	2	FACETS	0.898	0.82	0.979	0.898	0.82	0.979	CLONAL	1	TRUE	1	0.62	2		307	467	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720857	89720857	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	160	319	0	ENST00000371953.3:c.1008C>A	p.Tyr336Ter	p.Y336*	ENST00000371953	NM_000314.4	336	taC/taA	8/9	1	2	FACETS	0.967	0.892	1	0.967	0.892	1	CLONAL	1	TRUE	1	0.62	2		319	534	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268399	46268399	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	159	371	0	ENST00000371998.3:c.2786G>T	p.Arg929Ile	p.R929I	ENST00000371998		929	aGa/aTa	15/23	1	2	FACETS	0.95	0.876	1	0.95	0.876	1	CLONAL	1	TRUE	1	0.62	2		371	540	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250820	99250820	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	182	454	2	ENST00000268035.6:c.124G>A	p.Asp42Asn	p.D42N	ENST00000268035	NM_000875.3	42	Gac/Aac	2/21	1	2	FACETS	0.92	0.853	0.99	0.92	0.853	0.99	CLONAL	1	TRUE	1	0.62	2		456	638	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884466	151884466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1435892915	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	212	394	2	ENST00000262189.6:c.4889C>T	p.Ser1630Leu	p.S1630L	ENST00000262189	NM_170606.2	1630	tCg/tTg	33/59	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.62	2		396	680	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805169	43805169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201385967	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	248	620	0	ENST00000372470.3:c.619G>A	p.Asp207Asn	p.D207N	ENST00000372470	NM_005373.2	207	Gac/Aac	4/12	1	2	FACETS	0.938	0.879	0.998	0.938	0.879	0.998	CLONAL	1	TRUE	1	0.62	2		620	853	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80021292	80021292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144798521	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	102	485	0	ENST00000265081.6:c.1361G>A	p.Arg454Gln	p.R454Q	ENST00000265081	NM_002439.4	454	cGa/cAa	9/24	1	2	FACETS	0.439	0.392	0.488	0.439	0.392	0.488	SUBCLONAL	1	TRUE	1	0.62	2		485	750	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312699	91312699	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	163	408	0	ENST00000355112.3:c.2438G>T	p.Arg813Ile	p.R813I	ENST00000355112	NM_000057.2	813	aGa/aTa	12/22	1	2	FACETS	0.913	0.842	0.986	0.913	0.842	0.986	CLONAL	1	TRUE	1	0.62	2		408	576	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285182	212285182	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	175	452	0	ENST00000342788.4:c.3119G>T	p.Arg1040Ile	p.R1040I	ENST00000342788	NM_005235.2	1040	aGa/aTa	25/28	1	2	FACETS	0.853	0.788	0.919	0.853	0.788	0.919	CLONAL	1	TRUE	1	0.62	2		452	662	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163297332	163297332	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1292835761	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	194	518	2	ENST00000271452.3:c.178C>T	p.Arg60Ter	p.R60*	ENST00000271452	NM_145697.2	60	Cga/Tga	3/14	1	2	FACETS	0.86	0.798	0.923	0.86	0.798	0.923	CLONAL	1	TRUE	1	0.62	2		520	728	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090886	5090886	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	54	149	0	ENST00000381652.3:c.3034G>T	p.Glu1012Ter	p.E1012*	ENST00000381652	NM_004972.3	1012	Gaa/Taa	22/25	0.142518776711173	0	FACETS	0.394	0.343	0.448			1	INDETERMINATE	1	TRUE	0	0.62	0		149	168	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615744	100615744	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	227	550	0	ENST00000308731.7:c.589-1G>A		p.X197_splice	ENST00000308731	NM_000061.2	197			1	2	FACETS	0.838	0.782	0.895	0.838	0.782	0.895	CLONAL	1	TRUE	1	0.62	2		550	874	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602770	55602770	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	190	476	1	ENST00000288135.5:c.2591C>A	p.Ser864Tyr	p.S864Y	ENST00000288135	NM_000222.2	864	tCt/tAt	18/21	1	2	FACETS	0.877	0.813	0.942	0.877	0.813	0.942	CLONAL	1	TRUE	1	0.62	2		477	699	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041149	47041149	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs963940626	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	287	690	1	ENST00000377604.3:c.1577C>T	p.Ser526Leu	p.S526L	ENST00000377604	NM_001204468.1	526	tCg/tTg	15/24	1	2	FACETS	0.987	0.93	1	0.987	0.93	1	CLONAL	1	TRUE	1	0.62	2		691	938	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763500	41763500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	226	505	0	ENST00000301178.4:c.2299C>T	p.Arg767Cys	p.R767C	ENST00000301178	NM_021913.4	767	Cgc/Tgc	19/20	1	2	FACETS	0.935	0.873	0.998	0.935	0.873	0.998	CLONAL	1	TRUE	1	0.62	2		505	780	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38315030	38315030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs548408836	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	366	589	0	ENST00000425967.3:c.34G>A	p.Glu12Lys	p.E12K	ENST00000425967	NM_001174067.1	12	Gag/Aag	3/19	0.210625489682174	3	FACETS	0.752	0.715	0.79	0.752	0.715	0.79	INDETERMINATE	2	TRUE	1	0.62	3		589	1028	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716081	52716081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	386	749	0	ENST00000322088.6:c.646G>A	p.Glu216Lys	p.E216K	ENST00000322088	NM_014225.5	216	Gag/Aag	5/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.62	2		749	1212	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026709	6026709	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587778618	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	330	683	1	ENST00000265849.7:c.1687C>T	p.Arg563Ter	p.R563*	ENST00000265849	NM_000535.5	563	Cga/Tga	11/15	1	2	FACETS	0.923	0.873	0.975	0.923	0.873	0.975	CLONAL	1	TRUE	1	0.62	2		684	1153	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457258	89457258	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779282250	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	190	526	0	ENST00000336596.2:c.1739G>T	p.Arg580Ile	p.R580I	ENST00000336596	NM_005233.5	580	aGa/aTa	9/17	1	2	FACETS	0.882	0.818	0.948	0.882	0.818	0.948	CLONAL	1	TRUE	1	0.62	2		526	695	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590927	95590927	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	156	410	0	ENST00000393063.1:c.982G>T	p.Glu328Ter	p.E328*	ENST00000393063	NM_030621.3	328	Gaa/Taa	9/28	1	2	FACETS	0.842	0.774	0.911	0.842	0.774	0.911	CLONAL	1	TRUE	1	0.62	2		410	598	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14317386	14317386	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	181	468	0	ENST00000256196.4:c.124G>A	p.Asp42Asn	p.D42N	ENST00000256196		42	Gat/Aat	2/6	1	2	FACETS	0.844	0.781	0.909	0.844	0.781	0.909	CLONAL	1	TRUE	1	0.62	2		468	692	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55987310	55987310	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	178	494	0	ENST00000263923.4:c.115G>T	p.Asp39Tyr	p.D39Y	ENST00000263923	NM_002253.2	39	Gac/Tac	2/30	1	2	FACETS	0.771	0.712	0.832	0.771	0.712	0.832	SUBCLONAL	1	TRUE	1	0.62	2		494	745	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724411	112724411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	248	556	0	ENST00000369452.4:c.295G>A	p.Glu99Lys	p.E99K	ENST00000369452	NM_007373.3	99	Gaa/Aaa	2/9	1	2	FACETS	0.959	0.899	1	0.959	0.899	1	CLONAL	1	TRUE	1	0.62	2		556	834	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541484	29541484	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	56	150	1	ENST00000356175.3:c.1408G>T	p.Glu470Ter	p.E470*	ENST00000356175	NM_000267.3	470	Gaa/Taa	13/57	1	2	FACETS	0.946	0.824	1	0.946	0.824	1	CLONAL	1	TRUE	1	0.62	2		151	191	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256796	16256796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	255	593	1	ENST00000375759.3:c.4061G>A	p.Ser1354Asn	p.S1354N	ENST00000375759	NM_015001.2	1354	aGt/aAt	11/15	1	2	FACETS	0.925	0.868	0.984	0.925	0.868	0.984	CLONAL	1	TRUE	1	0.62	2		594	889	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748582	43748582	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	383	884	0	ENST00000382044.4:c.2224G>T	p.Glu742Ter	p.E742*	ENST00000382044	NM_001141980.1	742	Gaa/Taa	12/28	1	2	FACETS	0.945	0.897	0.993	0.945	0.897	0.993	CLONAL	1	TRUE	1	0.62	2		884	1308	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374685	118374685	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	186	399	0	ENST00000534358.1:c.8078C>A	p.Ser2693Tyr	p.S2693Y	ENST00000534358	NM_005933.3	2693	tCt/tAt	27/36	1	2	FACETS	0.998	0.927	1	0.998	0.927	1	CLONAL	1	TRUE	1	0.62	2		399	601	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955517	48955517	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	160	349	0	ENST00000267163.4:c.1633G>T	p.Glu545Ter	p.E545*	ENST00000267163	NM_000321.2	545	Gaa/Taa	17/27	1	2	FACETS	0.879	0.81	0.951	0.879	0.81	0.951	CLONAL	1	TRUE	1	0.62	2		349	587	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873309	151873309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145953124	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	171	381	1	ENST00000262189.6:c.9229C>T	p.Arg3077Cys	p.R3077C	ENST00000262189	NM_170606.2	3077	Cgt/Tgt	38/59	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.62	2		382	551	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268823	41268823	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	40	498	0	ENST00000349496.5:c.1061A>C	p.Lys354Thr	p.K354T	ENST00000349496	NM_001904.3	354	aAg/aCg	7/15	1	2	FACETS	0.167	0.138	0.199	0.167	0.138	0.199	SUBCLONAL	1	TRUE	1	0.62	2		498	773	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720928	119720928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	249	545	0	ENST00000316626.5:c.247G>A	p.Ala83Thr	p.A83T	ENST00000316626		83	Gcc/Acc	2/12	1	2	FACETS	0.994	0.933	1	0.994	0.933	1	CLONAL	1	TRUE	1	0.62	2		545	808	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512179	120512179	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781979575	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	210	438	0	ENST00000256646.2:c.1063G>A	p.Asp355Asn	p.D355N	ENST00000256646	NM_024408.3	355	Gac/Aac	6/34	1	2	FACETS	0.999	0.932	1	0.999	0.932	1	CLONAL	1	TRUE	1	0.62	2		438	678	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780812	9780812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765797019	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	50	613	1	ENST00000377346.4:c.1534C>T	p.Arg512Trp	p.R512W	ENST00000377346	NM_005026.3	512	Cgg/Tgg	13/24	1	2	FACETS	0.189	0.159	0.221	0.189	0.159	0.221	SUBCLONAL	1	TRUE	1	0.62	2		614	855	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782066	9782066	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	274	744	2	ENST00000377346.4:c.2089G>T	p.Asp697Tyr	p.D697Y	ENST00000377346	NM_005026.3	697	Gac/Tac	17/24	1	2	FACETS	0.926	0.871	0.983	0.926	0.871	0.983	CLONAL	1	TRUE	1	0.62	2		746	954	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259367	11259367	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	72	613	0	ENST00000361445.4:c.4201G>T	p.Glu1401Ter	p.E1401*	ENST00000361445	NM_004958.3	1401	Gaa/Taa	28/58	1	2	FACETS	0.236	0.205	0.269	0.236	0.205	0.269	SUBCLONAL	1	TRUE	1	0.62	2		613	984	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298639	11298639	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	262	504	0	ENST00000361445.4:c.1822G>A	p.Asp608Asn	p.D608N	ENST00000361445	NM_004958.3	608	Gat/Aat	12/58	1	2	FACETS	0.929	0.872	0.987	0.929	0.872	0.987	CLONAL	1	TRUE	1	0.62	2		504	910	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256179	16256179	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	222	506	0	ENST00000375759.3:c.3444G>T	p.Glu1148Asp	p.E1148D	ENST00000375759	NM_015001.2	1148	gaG/gaT	11/15	1	2	FACETS	0.899	0.839	0.96	0.899	0.839	0.96	CLONAL	1	TRUE	1	0.62	2		506	797	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256478	16256478	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	273	602	0	ENST00000375759.3:c.3743C>A	p.Ser1248Ter	p.S1248*	ENST00000375759	NM_015001.2	1248	tCa/tAa	11/15	1	2	FACETS	0.958	0.901	1	0.958	0.901	1	CLONAL	1	TRUE	1	0.62	2		602	919	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023952	27023952	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1397136001	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	19	33	0	ENST00000324856.7:c.1058C>G	p.Ala353Gly	p.A353G	ENST00000324856	NM_006015.4	353	gCc/gGc	1/20	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.62	2		33	53	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058078	27058078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763739196	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	189	446	0	ENST00000324856.7:c.1786C>T	p.Arg596Cys	p.R596C	ENST00000324856	NM_006015.4	596	Cgc/Tgc	3/20	1	2	FACETS	0.867	0.804	0.932	0.867	0.804	0.932	CLONAL	1	TRUE	1	0.62	2		446	703	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36823895	36823895	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	269	685	0	ENST00000373129.3:c.287T>G	p.Leu96Arg	p.L96R	ENST00000373129	NM_032017.1	96	cTg/cGg	5/12	1	2	FACETS	0.955	0.897	1	0.955	0.897	1	CLONAL	1	TRUE	1	0.62	2		685	909	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739045	46739045	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	253	549	0	ENST00000371975.4:c.1394A>C	p.Asp465Ala	p.D465A	ENST00000371975	NM_003579.3	465	gAt/gCt	13/18	1	2	FACETS	0.967	0.907	1	0.967	0.907	1	CLONAL	1	TRUE	1	0.62	2		549	844	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330489	65330489	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	248	529	0	ENST00000342505.4:c.1157A>C	p.Lys386Thr	p.K386T	ENST00000342505	NM_002227.2	386	aAg/aCg	8/25	1	2	FACETS	0.909	0.852	0.968	0.909	0.852	0.968	CLONAL	1	TRUE	1	0.62	2		529	880	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332775	65332775	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	190	425	0	ENST00000342505.4:c.764C>G	p.Thr255Ser	p.T255S	ENST00000342505	NM_002227.2	255	aCc/aGc	7/25	1	2	FACETS	0.934	0.868	1	0.934	0.868	1	CLONAL	1	TRUE	1	0.62	2		425	656	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873235	71873235	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	121	348	0	ENST00000357731.5:c.959A>T	p.Tyr320Phe	p.Y320F	ENST00000357731	NM_173808.2	320	tAt/tTt	7/7	1	2	FACETS	0.849	0.772	0.928	0.849	0.772	0.928	CLONAL	1	TRUE	1	0.62	2		348	460	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276675	115276675	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	221	550	0	ENST00000438362.2:c.784T>G	p.Phe262Val	p.F262V	ENST00000438362	NM_001242891.1	262	Ttt/Gtt	8/20	1	2	FACETS	0.905	0.844	0.967	0.905	0.844	0.967	CLONAL	1	TRUE	1	0.62	2		550	788	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465333	120465333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs891328437	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	246	582	1	ENST00000256646.2:c.4928C>T	p.Thr1643Met	p.T1643M	ENST00000256646	NM_024408.3	1643	aCg/aTg	27/34	1	2	FACETS	0.895	0.838	0.953	0.895	0.838	0.953	CLONAL	1	TRUE	1	0.62	2		583	887	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193202143	193202143	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	126	287	0	ENST00000367435.3:c.1175A>C	p.Lys392Thr	p.K392T	ENST00000367435	NM_024529.4	392	aAg/aCg	14/17	1	2	FACETS	0.818	0.745	0.894	0.818	0.745	0.894	CLONAL	1	TRUE	1	0.62	2		287	497	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206943189	206943189	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	192	491	1	ENST00000423557.1:c.429G>T	p.Lys143Asn	p.K143N	ENST00000423557	NM_000572.2	143	aaG/aaT	4/5	1	2	FACETS	0.946	0.878	1	0.946	0.878	1	CLONAL	1	TRUE	1	0.62	2		492	655	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226590050	226590050	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	189	544	0	ENST00000366794.5:c.151T>G	p.Trp51Gly	p.W51G	ENST00000366794	NM_001618.3	51	Tgg/Ggg	2/23	1	2	FACETS	0.806	0.747	0.868	0.806	0.747	0.868	CLONAL	1	TRUE	1	0.62	2		544	756	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332931	70332931	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	284	648	0	ENST00000373644.4:c.836C>A	p.Ser279Tyr	p.S279Y	ENST00000373644	NM_030625.2	279	tCt/tAt	2/12	1	2	FACETS	0.924	0.869	0.979	0.924	0.869	0.979	CLONAL	1	TRUE	1	0.62	2		648	992	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685307	89685307	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs398123317	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	97	362	0	ENST00000371953.3:c.202T>G	p.Tyr68Asp	p.Y68D	ENST00000371953	NM_000314.4	68	Tac/Gac	3/9	1	2	FACETS	0.747	0.67	0.827	0.747	0.67	0.827	SUBCLONAL	1	TRUE	1	0.62	2		362	419	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717640	89717640	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	214	433	0	ENST00000371953.3:c.665T>C	p.Val222Ala	p.V222A	ENST00000371953	NM_000314.4	222	gTg/gCg	7/9	1	2	FACETS	0.901	0.84	0.964	0.901	0.84	0.964	CLONAL	1	TRUE	1	0.62	2		433	766	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175462	108175462	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	192	401	0	ENST00000278616.4:c.5557G>T	p.Asp1853Tyr	p.D1853Y	ENST00000278616	NM_000051.3	1853	Gat/Tat	37/63	1	2	FACETS	0.92	0.855	0.988	0.92	0.855	0.988	CLONAL	1	TRUE	1	0.62	2		401	673	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402132	402132	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	76	700	0	ENST00000399788.2:c.4659G>T	p.Lys1553Asn	p.K1553N	ENST00000399788	NM_001042603.1	1553	aaG/aaT	27/28	1	2	FACETS	0.247	0.216	0.281	0.247	0.216	0.281	SUBCLONAL	1	TRUE	1	0.62	2		700	993	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552613	18552613	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	175	411	0	ENST00000266497.5:c.2024G>A	p.Arg675Lys	p.R675K	ENST00000266497		675	aGa/aAa	14/31	1	2	FACETS	0.906	0.838	0.976	0.906	0.838	0.976	CLONAL	1	TRUE	1	0.62	2		411	623	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656333	18656333	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	166	406	0	ENST00000266497.5:c.3012A>C	p.Leu1004Phe	p.L1004F	ENST00000266497		1004	ttA/ttC	21/31	1	2	FACETS	0.882	0.814	0.952	0.882	0.814	0.952	CLONAL	1	TRUE	1	0.62	2		406	607	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246520	46246520	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	122	261	0	ENST00000334344.6:c.4614T>G	p.Ile1538Met	p.I1538M	ENST00000334344	NM_152641.2	1538	atT/atG	15/21	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.62	2		261	387	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861182	57861182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	37	505	0	ENST00000228682.2:c.979G>A	p.Gly327Ser	p.G327S	ENST00000228682	NM_005269.2	327	Ggt/Agt	9/12	1	2	FACETS	0.162	0.133	0.195	0.162	0.133	0.195	SUBCLONAL	1	TRUE	1	0.62	2		505	737	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861826	57861826	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	291	661	1	ENST00000228682.2:c.1127C>A	p.Pro376His	p.P376H	ENST00000228682	NM_005269.2	376	cCt/cAt	10/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.62	2		662	874	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865440	57865440	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	288	775	0	ENST00000228682.2:c.2917A>C	p.Asn973His	p.N973H	ENST00000228682	NM_005269.2	973	Aat/Cat	12/12	1	2	FACETS	0.829	0.78	0.88	0.829	0.78	0.88	CLONAL	1	TRUE	1	0.62	2		775	1120	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112893775	112893775	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	157	289	0	ENST00000351677.2:c.664A>C	p.Asn222His	p.N222H	ENST00000351677	NM_002834.3	222	Aat/Cat	6/16	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.62	2		289	500	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123888136	123888136	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	81	224	0	ENST00000330479.4:c.614G>T	p.Arg205Ile	p.R205I	ENST00000330479	NM_020382.3	205	aGa/aTa	6/9	1	2	FACETS	0.829	0.738	0.926	0.829	0.738	0.926	CLONAL	1	TRUE	1	0.62	2		224	315	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212500	133212500	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	215	473	0	ENST00000320574.5:c.5789C>A	p.Ser1930Ter	p.S1930*	ENST00000320574	NM_006231.2	1930	tCa/tAa	42/49	1	2	FACETS	0.928	0.866	0.993	0.928	0.866	0.993	CLONAL	1	TRUE	1	0.62	2		473	747	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622581	28622581	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	97	260	0	ENST00000241453.7:c.1037-1G>A		p.X346_splice	ENST00000241453	NM_004119.2	346			1	2	FACETS	0.928	0.836	1	0.928	0.836	1	CLONAL	1	TRUE	1	0.62	2		260	337	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907143	32907143	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs80358438	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	176	465	0	ENST00000380152.3:c.1528G>T	p.Glu510Ter	p.E510*	ENST00000380152		510	Gaa/Taa	10/27	1	2	FACETS	0.89	0.823	0.959	0.89	0.823	0.959	CLONAL	1	TRUE	1	0.62	2		465	638	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912320	32912320	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	143	465	0	ENST00000380152.3:c.3828A>C	p.Glu1276Asp	p.E1276D	ENST00000380152		1276	gaA/gaC	11/27	1	2	FACETS	0.934	0.857	1	0.934	0.857	1	CLONAL	1	TRUE	1	0.62	2		465	494	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953926	32953926	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587780664	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	120	420	0	ENST00000380152.3:c.8993C>A	p.Ser2998Tyr	p.S2998Y	ENST00000380152		2998	tCt/tAt	23/27	1	2	FACETS	0.721	0.654	0.791	0.721	0.654	0.791	SUBCLONAL	1	TRUE	1	0.62	2		420	537	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514919	103514919	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	35	317	0	ENST00000355739.4:c.1420G>T	p.Glu474Ter	p.E474*	ENST00000355739	NM_000123.3	474	Gaa/Taa	8/15	1	2	FACETS	0.259	0.212	0.312	0.259	0.212	0.312	SUBCLONAL	1	TRUE	1	0.62	2		317	436	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95592946	95592946	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	197	485	0	ENST00000393063.1:c.874G>T	p.Glu292Ter	p.E292*	ENST00000393063	NM_030621.3	292	Gaa/Taa	8/28	1	2	FACETS	0.928	0.862	0.995	0.928	0.862	0.995	CLONAL	1	TRUE	1	0.62	2		485	685	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95595862	95595862	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	165	516	0	ENST00000393063.1:c.681G>T	p.Glu227Asp	p.E227D	ENST00000393063	NM_030621.3	227	gaG/gaT	7/28	1	2	FACETS	0.78	0.719	0.844	0.78	0.719	0.844	SUBCLONAL	1	TRUE	1	0.62	2		516	682	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989117	41989117	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	245	526	0	ENST00000219905.7:c.1909A>C	p.Ile637Leu	p.I637L	ENST00000219905	NM_001164273.1	637	Att/Ctt	3/24	1	2	FACETS	0.912	0.854	0.971	0.912	0.854	0.971	CLONAL	1	TRUE	1	0.62	2		526	867	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052653	42052653	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	244	545	0	ENST00000219905.7:c.7324C>A	p.Leu2442Ile	p.L2442I	ENST00000219905	NM_001164273.1	2442	Ctc/Atc	20/24	1	2	FACETS	0.856	0.801	0.913	0.856	0.801	0.913	CLONAL	1	TRUE	1	0.62	2		545	919	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712872	43712872	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	282	669	0	ENST00000382044.4:c.4312G>T	p.Asp1438Tyr	p.D1438Y	ENST00000382044	NM_001141980.1	1438	Gat/Tat	21/28	1	2	FACETS	0.914	0.86	0.97	0.914	0.86	0.97	CLONAL	1	TRUE	1	0.62	2		669	995	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465588	99465588	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	40	611	0	ENST00000268035.6:c.2413A>G	p.Ser805Gly	p.S805G	ENST00000268035	NM_000875.3	805	Agc/Ggc	11/21	1	2	FACETS	0.162	0.134	0.193	0.162	0.134	0.193	SUBCLONAL	1	TRUE	1	0.62	2		611	798	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641077	3641077	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	390	1001	0	ENST00000294008.3:c.2562T>G	p.Ile854Met	p.I854M	ENST00000294008	NM_032444.2	854	atT/atG	12/15	1	2	FACETS	0.866	0.822	0.912	0.866	0.822	0.912	CLONAL	1	TRUE	1	0.62	2		1001	1452	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652302	3652302	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	189	518	0	ENST00000294008.3:c.767G>A	p.Gly256Glu	p.G256E	ENST00000294008	NM_032444.2	256	gGg/gAg	4/15	1	2	FACETS	0.902	0.837	0.969	0.902	0.837	0.969	CLONAL	1	TRUE	1	0.62	2		518	676	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658809	3658809	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	287	637	1	ENST00000294008.3:c.157G>T	p.Glu53Ter	p.E53*	ENST00000294008	NM_032444.2	53	Gaa/Taa	2/15	1	2	FACETS	0.894	0.842	0.948	0.894	0.842	0.948	CLONAL	1	TRUE	1	0.62	2		638	1035	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50784095	50784095	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	222	473	0	ENST00000398568.2:c.486C>A	p.Phe162Leu	p.F162L	ENST00000398568	NM_001042412.1	162	ttC/ttA	3/18	1	2	FACETS	0.848	0.791	0.907	0.848	0.791	0.907	CLONAL	1	TRUE	1	0.62	2		473	844	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831844	72831844	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	349	836	0	ENST00000268489.5:c.4737A>C	p.Glu1579Asp	p.E1579D	ENST00000268489	NM_006885.3	1579	gaA/gaC	9/10	1	2	FACETS	0.894	0.846	0.943	0.894	0.846	0.943	CLONAL	1	TRUE	1	0.62	2		836	1259	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89815114	89815114	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	221	592	0	ENST00000389301.3:c.3301A>G	p.Ile1101Val	p.I1101V	ENST00000389301	NM_000135.2	1101	Atc/Gtc	33/43	1	2	FACETS	0.84	0.783	0.898	0.84	0.783	0.898	CLONAL	1	TRUE	1	0.62	2		592	849	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562726	29562726	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	249	560	0	ENST00000356175.3:c.3806A>G	p.Asp1269Gly	p.D1269G	ENST00000356175	NM_000267.3	1269	gAc/gGc	28/57	1	2	FACETS	0.928	0.869	0.987	0.928	0.869	0.987	CLONAL	1	TRUE	1	0.62	2		560	866	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592288	29592288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs185660700	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	127	273	0	ENST00000356175.3:c.4703C>T	p.Thr1568Met	p.T1568M	ENST00000356175	NM_000267.3	1568	aCg/aTg	35/57	1	2	FACETS	0.862	0.786	0.942	0.862	0.786	0.942	CLONAL	1	TRUE	1	0.62	2		273	475	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805564	46805564	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	344	750	2	ENST00000290295.7:c.392C>T	p.Pro131Leu	p.P131L	ENST00000290295	NM_006361.5	131	cCg/cTg	1/2	1	2	FACETS	0.966	0.914	1	0.966	0.914	1	CLONAL	1	TRUE	1	0.62	2		752	1149	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926543	59926543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	282	697	0	ENST00000259008.2:c.454G>T	p.Asp152Tyr	p.D152Y	ENST00000259008	NM_032043.2	152	Gat/Tat	5/20	1	2	FACETS	0.933	0.878	0.989	0.933	0.878	0.989	CLONAL	1	TRUE	1	0.62	2		697	975	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736910	736910	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	267	597	0	ENST00000314574.4:c.1189C>A	p.Leu397Ile	p.L397I	ENST00000314574	NM_005433.3	397	Ctt/Att	10/12	1	2	FACETS	0.953	0.895	1	0.953	0.895	1	CLONAL	1	TRUE	1	0.62	2		597	904	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39600608	39600608	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	135	304	0	ENST00000262039.4:c.1423C>A	p.Leu475Ile	p.L475I	ENST00000262039	NM_002647.2	475	Ctc/Atc	13/25	1	2	FACETS	0.97	0.889	1	0.97	0.889	1	CLONAL	1	TRUE	1	0.62	2		304	449	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211118	2211118	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1156919758	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	354	826	0	ENST00000398665.3:c.1372A>G	p.Ser458Gly	p.S458G	ENST00000398665	NM_032482.2	458	Agc/Ggc	15/28	1	2	FACETS	0.984	0.933	1	0.984	0.933	1	CLONAL	1	TRUE	1	0.62	2		826	1160	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125494	7125494	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1378329388	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	48	623	3	ENST00000302850.5:c.3058C>T	p.Arg1020Ter	p.R1020*	ENST00000302850	NM_000208.2	1020	Cga/Tga	17/22	1	2	FACETS	0.167	0.14	0.197	0.167	0.14	0.197	SUBCLONAL	1	TRUE	1	0.62	2		626	927	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265047	10265047	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	273	659	2	ENST00000340748.4:c.1893C>A	p.Phe631Leu	p.F631L	ENST00000340748		631	ttC/ttA	21/40	1	2	FACETS	0.921	0.866	0.978	0.921	0.866	0.978	CLONAL	1	TRUE	1	0.62	2		661	956	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11114042	11114042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	207	449	1	ENST00000358026.2:c.1970G>A	p.Ser657Asn	p.S657N	ENST00000358026	NM_001128849.1	657	aGt/aAt	13/36	1	2	FACETS	0.9	0.838	0.964	0.9	0.838	0.964	CLONAL	1	TRUE	1	0.62	2		450	742	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355244	15355244	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	170	429	0	ENST00000263377.2:c.2379G>T	p.Met793Ile	p.M793I	ENST00000263377	NM_058243.2	793	atG/atT	13/20	1	2	FACETS	0.872	0.805	0.941	0.872	0.805	0.941	CLONAL	1	TRUE	1	0.62	2		429	629	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18956798	18956798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754519840	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	235	445	0	ENST00000262803.5:c.241G>A	p.Glu81Lys	p.E81K	ENST00000262803	NM_002911.3	81	Gaa/Aaa	2/24	1	2	FACETS	0.995	0.932	1	0.995	0.932	1	CLONAL	1	TRUE	1	0.62	2		445	762	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727124	41727124	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	326	651	0	ENST00000301178.4:c.382T>C	p.Ser128Pro	p.S128P	ENST00000301178	NM_021913.4	128	Tcc/Ccc	3/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.62	2		651	1046	SUCCESS
ALK	238	MSKCC	GRCh37	2	29430104	29430104	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	263	526	0	ENST00000389048.3:c.3871C>A	p.Leu1291Met	p.L1291M	ENST00000389048	NM_004304.4	1291	Ctg/Atg	26/29	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.62	2		526	836	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142907	30142907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	414	708	0	ENST00000389048.3:c.619G>A	p.Ala207Thr	p.A207T	ENST00000389048	NM_004304.4	207	Gca/Aca	1/29	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.62	2		708	1125	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47604200	47604200	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	293	475	0	ENST00000263735.4:c.539T>G	p.Phe180Cys	p.F180C	ENST00000263735	NM_002354.2	180	tTt/tGt	5/9	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.62	2		475	874	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47643551	47643551	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	210	421	0	ENST00000233146.2:c.1059G>T	p.Lys353Asn	p.K353N	ENST00000233146	NM_000251.2	353	aaG/aaT	6/16	1	2	FACETS	0.826	0.769	0.885	0.826	0.769	0.885	CLONAL	1	TRUE	1	0.62	2		421	820	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672697	47672697	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	215	486	0	ENST00000233146.2:c.1287G>T	p.Gln429His	p.Q429H	ENST00000233146	NM_000251.2	429	caG/caT	8/16	1	2	FACETS	0.987	0.921	1	0.987	0.921	1	CLONAL	1	TRUE	1	0.62	2		486	703	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145419	61145419	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	62	374	0	ENST00000295025.8:c.629A>C	p.Lys210Thr	p.K210T	ENST00000295025	NM_002908.2	210	aAa/aCa	6/11	1	2	FACETS	0.362	0.312	0.415	0.362	0.312	0.415	SUBCLONAL	1	TRUE	1	0.62	2		374	553	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715827	61715827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	148	504	0	ENST00000401558.2:c.2102C>A	p.Ala701Asp	p.A701D	ENST00000401558	NM_003400.3	701	gCt/gAt	18/25	1	2	FACETS	0.555	0.507	0.606	0.555	0.507	0.606	SUBCLONAL	1	TRUE	1	0.62	2		504	860	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293131	212293131	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	184	374	0	ENST00000342788.4:c.2719+2T>C		p.X907_splice	ENST00000342788	NM_005235.2	907			1	2	FACETS	0.933	0.865	1	0.933	0.865	1	CLONAL	1	TRUE	1	0.62	2		374	636	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225360563	225360563	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	109	251	0	ENST00000264414.4:c.1828A>C	p.Lys610Gln	p.K610Q	ENST00000264414	NM_003590.4	610	Aaa/Caa	13/16	1	2	FACETS	0.913	0.827	1	0.913	0.827	1	CLONAL	1	TRUE	1	0.62	2		251	385	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663285	227663285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	306	612	0	ENST00000305123.5:c.170C>T	p.Ser57Leu	p.S57L	ENST00000305123	NM_005544.2	57	tCg/tTg	1/2	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.62	2		612	932	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663322	227663322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	261	564	1	ENST00000305123.5:c.133G>A	p.Glu45Lys	p.E45K	ENST00000305123	NM_005544.2	45	Gag/Aag	1/2	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.62	2		565	840	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730774	40730774	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	242	532	5	ENST00000373198.4:c.3761C>A	p.Ala1254Glu	p.A1254E	ENST00000373198	NM_133170.3	1254	gCa/gAa	27/32	1	2	FACETS	0.938	0.879	0.999	0.938	0.879	0.999	CLONAL	1	TRUE	1	0.62	2		537	832	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40864872	40864872	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	144	345	0	ENST00000373198.4:c.2396A>G	p.Tyr799Cys	p.Y799C	ENST00000373198	NM_133170.3	799	tAc/tGc	16/32	1	2	FACETS	0.737	0.675	0.803	0.737	0.675	0.803	SUBCLONAL	1	TRUE	1	0.62	2		345	630	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038217	30038217	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	255	518	2	ENST00000338641.4:c.390G>T	p.Lys130Asn	p.K130N	ENST00000338641	NM_000268.3	130	aaG/aaT	4/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.62	2		520	790	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458546	12458546	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	304	692	0	ENST00000287820.6:c.1163T>C	p.Phe388Ser	p.F388S	ENST00000287820	NM_015869.4	388	tTt/tCt	6/7	1	2	FACETS	0.926	0.873	0.98	0.926	0.873	0.98	CLONAL	1	TRUE	1	0.62	2		692	1059	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127805	47127805	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	146	371	0	ENST00000409792.3:c.5278-1G>T		p.X1760_splice	ENST00000409792	NM_014159.6	1760			1	2	FACETS	0.776	0.711	0.844	0.776	0.711	0.844	SUBCLONAL	1	TRUE	1	0.62	2		371	607	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69788838	69788838	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	97	221	0	ENST00000352241.4:c.90A>C	p.Gln30His	p.Q30H	ENST00000352241	NM_198159.2	30	caA/caC	1/10	1	2	FACETS	0.915	0.824	1	0.915	0.824	1	CLONAL	1	TRUE	1	0.62	2		221	342	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89478311	89478311	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	135	376	0	ENST00000336596.2:c.2130C>A	p.Phe710Leu	p.F710L	ENST00000336596	NM_005233.5	710	ttC/ttA	12/17	1	2	FACETS	0.925	0.846	1	0.925	0.846	1	CLONAL	1	TRUE	1	0.62	2		376	471	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631635	119631635	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	147	270	0	ENST00000316626.5:c.631G>T	p.Glu211Ter	p.E211*	ENST00000316626		211	Gaa/Taa	6/12	1	2	FACETS	0.939	0.863	1	0.939	0.863	1	CLONAL	1	TRUE	1	0.62	2		270	505	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188340	142188340	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	245	530	0	ENST00000350721.4:c.6391A>C	p.Asn2131His	p.N2131H	ENST00000350721	NM_001184.3	2131	Aac/Cac	38/47	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.62	2		530	780	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170020830	170020830	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	146	379	0	ENST00000295797.4:c.1706A>G	p.Asp569Gly	p.D569G	ENST00000295797	NM_002740.5	569	gAc/gGc	18/18	1	2	FACETS	0.902	0.828	0.979	0.902	0.828	0.979	CLONAL	1	TRUE	1	0.62	2		379	522	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917673	178917673	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	111	186	0	ENST00000263967.3:c.548A>C	p.Asn183Thr	p.N183T	ENST00000263967	NM_006218.2	183	aAt/aCt	3/21	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.62	2		186	349	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178941927	178941927	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	210	479	0	ENST00000263967.3:c.2246A>G	p.Gln749Arg	p.Q749R	ENST00000263967	NM_006218.2	749	cAg/cGg	15/21	1	2	FACETS	0.881	0.82	0.943	0.881	0.82	0.943	CLONAL	1	TRUE	1	0.62	2		479	769	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446207	187446207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	298	691	0	ENST00000232014.4:c.1481G>A	p.Gly494Asp	p.G494D	ENST00000232014	NM_001130845.1	494	gGc/gAc	6/10	1	2	FACETS	0.907	0.855	0.96	0.907	0.855	0.96	CLONAL	1	TRUE	1	0.62	2		691	1060	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586465	189586465	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	152	413	0	ENST00000264731.3:c.1089A>C	p.Gln363His	p.Q363H	ENST00000264731	NM_003722.4	363	caA/caC	8/14	1	2	FACETS	0.863	0.793	0.935	0.863	0.793	0.935	CLONAL	1	TRUE	1	0.62	2		413	568	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594191	55594191	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	172	462	0	ENST00000288135.5:c.1894A>G	p.Thr632Ala	p.T632A	ENST00000288135	NM_000222.2	632	Aca/Gca	13/21	1	2	FACETS	0.854	0.788	0.921	0.854	0.788	0.921	CLONAL	1	TRUE	1	0.62	2		462	650	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356425	66356425	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	141	312	0	ENST00000273854.3:c.1072C>A	p.Pro358Thr	p.P358T	ENST00000273854	NM_004439.5	358	Ccc/Acc	5/18	1	2	FACETS	0.964	0.884	1	0.964	0.884	1	CLONAL	1	TRUE	1	0.62	2		312	472	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155548	106155548	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	40	392	1	ENST00000380013.4:c.449C>A	p.Ser150Tyr	p.S150Y	ENST00000380013	NM_001127208.2	150	tCt/tAt	3/11	1	2	FACETS	0.224	0.186	0.267	0.224	0.186	0.267	SUBCLONAL	1	TRUE	1	0.62	2		393	575	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156653	106156653	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	166	358	0	ENST00000380013.4:c.1554T>G	p.Ile518Met	p.I518M	ENST00000380013	NM_001127208.2	518	atT/atG	3/11	1	2	FACETS	0.984	0.91	1	0.984	0.91	1	CLONAL	1	TRUE	1	0.62	2		358	544	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114280	143114280	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	155	431	0	ENST00000262992.4:c.1141C>A	p.Leu381Ile	p.L381I	ENST00000262992	NM_001101669.1	381	Ctt/Att	13/24	1	2	FACETS	0.758	0.696	0.822	0.758	0.696	0.822	SUBCLONAL	1	TRUE	1	0.62	2		431	660	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521157	187521157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373469759	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	211	611	1	ENST00000441802.2:c.11998G>A	p.Glu4000Lys	p.E4000K	ENST00000441802	NM_005245.3	4000	Gaa/Aaa	22/27	1	2	FACETS	0.878	0.818	0.94	0.878	0.818	0.94	CLONAL	1	TRUE	1	0.62	2		612	775	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31422949	31422949	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1257594254	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	261	544	0	ENST00000344624.3:c.3364C>T	p.Arg1122Ter	p.R1122*	ENST00000344624		1122	Cga/Tga	26/33	1	2	FACETS	0.922	0.866	0.98	0.922	0.866	0.98	CLONAL	1	TRUE	1	0.62	2		544	913	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645085	86645085	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	172	381	0	ENST00000274376.6:c.1157A>G	p.Tyr386Cys	p.Y386C	ENST00000274376	NM_002890.2	386	tAt/tGt	8/25	1	2	FACETS	0.925	0.855	0.996	0.925	0.855	0.996	CLONAL	1	TRUE	1	0.62	2		381	600	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927585	131927585	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1554098469	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	70	208	0	ENST00000265335.6:c.1652A>G	p.Gln551Arg	p.Q551R	ENST00000265335		551	cAa/cGa	11/25	1	2	FACETS	0.706	0.62	0.796	0.706	0.62	0.796	SUBCLONAL	1	TRUE	1	0.62	2		208	320	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441354	149441354	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1173478824	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	318	683	0	ENST00000286301.3:c.1685C>A	p.Thr562Asn	p.T562N	ENST00000286301	NM_005211.3	562	aCt/aAt	12/22	1	2	FACETS	0.977	0.923	1	0.977	0.923	1	CLONAL	1	TRUE	1	0.62	2		683	1050	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176666839	176666839	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	29	297	0	ENST00000439151.2:c.4275G>T	p.Lys1425Asn	p.K1425N	ENST00000439151	NM_022455.4	1425	aaG/aaT	8/23	1	2	FACETS	0.193	0.154	0.237	0.193	0.154	0.237	SUBCLONAL	1	TRUE	1	0.62	2		297	484	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673715	176673715	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	152	340	0	ENST00000439151.2:c.4415A>C	p.Lys1472Thr	p.K1472T	ENST00000439151	NM_022455.4	1472	aAa/aCa	10/23	1	2	FACETS	0.827	0.76	0.897	0.827	0.76	0.897	CLONAL	1	TRUE	1	0.62	2		340	593	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041137	180041137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1376446971	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	343	762	2	ENST00000261937.6:c.3262G>A	p.Asp1088Asn	p.D1088N	ENST00000261937	NM_182925.4	1088	Gac/Aac	24/30	1	2	FACETS	0.989	0.936	1	0.989	0.936	1	CLONAL	1	TRUE	1	0.62	2		764	1119	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250692	26250692	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	207	572	1	ENST00000446824.2:c.142G>A	p.Ala48Thr	p.A48T	ENST00000446824	NM_021018.2	48	Gcc/Acc	1/1	1	2	FACETS	0.889	0.828	0.952	0.889	0.828	0.952	CLONAL	1	TRUE	1	0.62	2		573	751	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324873	31324873	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1326884077	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	57	338	0	ENST00000412585.2:c.63G>T	p.Glu21Asp	p.E21D	ENST00000412585	NM_005514.6	21	gaG/gaT	1/8	1	2	FACETS	0.371	0.319	0.429	0.371	0.319	0.429	SUBCLONAL	1	TRUE	1	0.62	2		338	495	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163542	32163542	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	187	486	0	ENST00000375023.3:c.5684C>A	p.Ser1895Tyr	p.S1895Y	ENST00000375023	NM_004557.3	1895	tCt/tAt	30/30	1	2	FACETS	0.954	0.886	1	0.954	0.886	1	CLONAL	1	TRUE	1	0.62	2		486	632	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169865	32169865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	68	650	0	ENST00000375023.3:c.3743C>T	p.Pro1248Leu	p.P1248L	ENST00000375023	NM_004557.3	1248	cCt/cTt	21/30	1	2	FACETS	0.226	0.196	0.259	0.226	0.196	0.259	SUBCLONAL	1	TRUE	1	0.62	2		650	969	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187563	32187563	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	263	531	1	ENST00000375023.3:c.1316C>T	p.Ala439Val	p.A439V	ENST00000375023	NM_004557.3	439	gCc/gTc	8/30	1	2	FACETS	0.981	0.922	1	0.981	0.922	1	CLONAL	1	TRUE	1	0.62	2		532	865	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286951	33286951	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1453165364	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	266	640	0	ENST00000374542.5:c.1986G>T	p.Lys662Asn	p.K662N	ENST00000374542	NM_001141970.1	662	aaG/aaT	7/8	1	2	FACETS	0.881	0.827	0.936	0.881	0.827	0.936	CLONAL	1	TRUE	1	0.62	2		640	974	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288258	33288258	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	240	569	0	ENST00000374542.5:c.1150G>A	p.Asp384Asn	p.D384N	ENST00000374542	NM_001141970.1	384	Gac/Aac	4/8	1	2	FACETS	0.898	0.84	0.957	0.898	0.84	0.957	CLONAL	1	TRUE	1	0.62	2		569	862	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138905	37138905	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs367638496	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	193	553	0	ENST00000373509.5:c.245A>C	p.Asn82Thr	p.N82T	ENST00000373509	NM_002648.3	82	aAt/aCt	4/6	1	2	FACETS	0.836	0.775	0.898	0.836	0.775	0.898	CLONAL	1	TRUE	1	0.62	2		553	745	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138907	37138907	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	252	556	1	ENST00000373509.5:c.247G>T	p.Gly83Cys	p.G83C	ENST00000373509	NM_002648.3	83	Ggc/Tgc	4/6	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.62	2		557	765	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864503	162864503	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	142	328	0	ENST00000366898.1:c.10T>C	p.Phe4Leu	p.F4L	ENST00000366898	NM_004562.2	4	Ttt/Ctt	2/12	1	2	FACETS	0.948	0.87	1	0.948	0.87	1	CLONAL	1	TRUE	1	0.62	2		328	483	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426883	6426883	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	49	537	0	ENST00000356142.4:c.76A>G	p.Asn26Asp	p.N26D	ENST00000356142	NM_018890.3	26	Aat/Gat	2/7	1	2	FACETS	0.168	0.141	0.197	0.168	0.141	0.197	SUBCLONAL	1	TRUE	1	0.62	2		537	941	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946090	13946090	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1419462186	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	150	347	1	ENST00000405192.2:c.1006C>T	p.Arg336Ter	p.R336*	ENST00000405192	NM_001163147.1	336	Cga/Tga	10/12	1	2	FACETS	0.852	0.782	0.924	0.852	0.782	0.924	CLONAL	1	TRUE	1	0.62	2		348	568	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227898	55227898	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	193	362	0	ENST00000275493.2:c.1365G>T	p.Glu455Asp	p.E455D	ENST00000275493	NM_005228.3	455	gaG/gaT	12/28	1	2	FACETS	0.968	0.9	1	0.968	0.9	1	CLONAL	1	TRUE	1	0.62	2		362	643	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339493	81339493	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	246	603	1	ENST00000222390.5:c.1511A>G	p.Asn504Ser	p.N504S	ENST00000222390	NM_000601.4	504	aAc/aGc	13/18	1	2	FACETS	0.963	0.903	1	0.963	0.903	1	CLONAL	1	TRUE	1	0.62	2		604	824	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412013	116412013	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	66	781	0	ENST00000397752.3:c.2998T>C	p.Ser1000Pro	p.S1000P	ENST00000397752	NM_000245.2	1000	Tct/Cct	14/21	1	2	FACETS	0.19	0.164	0.218	0.19	0.164	0.218	SUBCLONAL	1	TRUE	1	0.62	2		781	1121	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482891	140482891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	241	600	0	ENST00000288602.6:c.1244C>T	p.Ala415Val	p.A415V	ENST00000288602	NM_004333.4	415	gCc/gTc	10/18	1	2	FACETS	0.908	0.85	0.968	0.908	0.85	0.968	CLONAL	1	TRUE	1	0.62	2		600	856	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515066	148515066	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	51	567	0	ENST00000320356.2:c.1143G>T	p.Lys381Asn	p.K381N	ENST00000320356	NM_004456.4	381	aaG/aaT	10/20	1	2	FACETS	0.185	0.156	0.217	0.185	0.156	0.217	SUBCLONAL	1	TRUE	1	0.62	2		567	889	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859532	151859532	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	278	594	0	ENST00000262189.6:c.11130A>C	p.Glu3710Asp	p.E3710D	ENST00000262189	NM_170606.2	3710	gaA/gaC	43/59	1	2	FACETS	0.972	0.914	1	0.972	0.914	1	CLONAL	1	TRUE	1	0.62	2		594	923	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945012	151945012	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	10	54	0	ENST00000262189.6:c.2507C>A	p.Ser836Tyr	p.S836Y	ENST00000262189	NM_170606.2	836	tCt/tAt	14/59	1	2	FACETS	0.398	0.273	0.551	0.398	0.273	0.551	SUBCLONAL	1	TRUE	1	0.62	2		54	81	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146976	38146976	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	414	732	0	ENST00000317025.8:c.3166G>T	p.Glu1056Ter	p.E1056*	ENST00000317025	NM_023034.1	1056	Gaa/Taa	18/24	0.210625489682174	3	FACETS	1	0.995	1	0.726	0.692	0.761	INDETERMINATE	1	TRUE	1	0.62	3		732	1205	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275870	38275870	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	265	466	0	ENST00000425967.3:c.1399T>C	p.Ser467Pro	p.S467P	ENST00000425967	NM_001174067.1	467	Tcc/Ccc	11/19	0.210625489682174	3	FACETS	1	0.993	1	0.732	0.689	0.776	INDETERMINATE	1	TRUE	1	0.62	3		466	765	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972915	68972915	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs201372935	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	160	420	0	ENST00000288368.4:c.1240G>A	p.Glu414Lys	p.E414K	ENST00000288368	NM_024870.2	414	Gaa/Aaa	11/40	0.210625489682174	3	FACETS	0.966	0.888	1	0.483	0.444	0.524	INDETERMINATE	1	TRUE	1	0.62	3		420	700	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033194	69033194	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	244	508	0	ENST00000288368.4:c.3634A>C	p.Lys1212Gln	p.K1212Q	ENST00000288368	NM_024870.2	1212	Aaa/Caa	30/40	0.210625489682174	3	FACETS	1	0.987	1	0.601	0.563	0.64	INDETERMINATE	1	TRUE	1	0.62	3		508	858	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964427	70964427	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	284	575	0	ENST00000276594.2:c.1601G>T	p.Ser534Ile	p.S534I	ENST00000276594	NM_024504.3	534	aGc/aTc	8/8	0.210625489682174	3	FACETS	1	0.988	1	0.593	0.558	0.629	INDETERMINATE	1	TRUE	1	0.62	3		575	1012	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751173	128751173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	236	485	0	ENST00000377970.2:c.710C>T	p.Ser237Phe	p.S237F	ENST00000377970	NM_002467.4	237	tCt/tTt	2/3	0.210625489682174	3	FACETS	1	0.989	1	0.627	0.587	0.669	INDETERMINATE	1	TRUE	1	0.62	3		485	795	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5029900	5029900	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	99	409	0	ENST00000381652.3:c.344G>T	p.Arg115Ile	p.R115I	ENST00000381652	NM_004972.3	115	aGa/aTa	4/25	0.142518776711173	0	FACETS	0.268	0.24	0.297			1	INDETERMINATE	1	TRUE	0	0.62	0		409	453	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5055784	5055784	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	24	317	0	ENST00000381652.3:c.1052A>C	p.Asn351Thr	p.N351T	ENST00000381652	NM_004972.3	351	aAt/aCt	8/25	0.142518776711173	0	FACETS	0.085	0.066	0.106			1	INDETERMINATE	1	TRUE	0	0.62	0		317	348	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457214	5457214	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	26	403	0	ENST00000381577.3:c.188A>G	p.Asn63Ser	p.N63S	ENST00000381577	NM_014143.3	63	aAc/aGc	3/7	0.142518776711173	0	FACETS	0.064	0.05	0.08			1	INDETERMINATE	1	TRUE	0	0.62	0		403	495	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549563	5549563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1023826544	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	253	710	0	ENST00000397747.3:c.590C>T	p.Thr197Ile	p.T197I	ENST00000397747	NM_025239.3	197	aCt/aTt	4/7	0.142518776711173	0	FACETS	0.348	0.326	0.371			1	INDETERMINATE	1	TRUE	0	0.62	0		710	891	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27172700	27172700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	195	601	0	ENST00000380036.4:c.715G>A	p.Glu239Lys	p.E239K	ENST00000380036	NM_000459.3	239	Gaa/Aaa	5/23	0.142518776711173	0	FACETS	0.291	0.27	0.313			1	INDETERMINATE	1	TRUE	0	0.62	0		601	821	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912044	127912044	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	149	421	0	ENST00000373547.4:c.826G>T	p.Asp276Tyr	p.D276Y	ENST00000373547	NM_002721.4	276	Gat/Tat	7/7	0.142518776711173	0	FACETS	0.324	0.297	0.352			1	INDETERMINATE	1	TRUE	0	0.62	0		421	564	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399980	139399980	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	54	696	0	ENST00000277541.6:c.4368G>T	p.Glu1456Asp	p.E1456D	ENST00000277541	NM_017617.3	1456	gaG/gaT	25/34	0.142518776711173	0	FACETS	0.062	0.053	0.073			1	INDETERMINATE	1	TRUE	0	0.62	0		696	1062	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933296	39933296	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	322	748	0	ENST00000378444.4:c.1303G>T	p.Asp435Tyr	p.D435Y	ENST00000378444	NM_001123385.1	435	Gac/Tac	4/15	1	2	FACETS	0.886	0.836	0.936	0.886	0.836	0.936	CLONAL	1	TRUE	1	0.62	2		748	1173	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949014	44949014	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	64	506	0	ENST00000377967.4:c.3575C>A	p.Ser1192Tyr	p.S1192Y	ENST00000377967	NM_021140.2	1192	tCt/tAt	25/29	1	2	FACETS	0.276	0.238	0.317	0.276	0.238	0.317	SUBCLONAL	1	TRUE	1	0.62	2		506	748	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411030	63411030	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	207	691	0	ENST00000330258.3:c.2137G>T	p.Asp713Tyr	p.D713Y	ENST00000330258	NM_152424.3	713	Gat/Tat	2/2	1	2	FACETS	0.787	0.731	0.844	0.787	0.731	0.844	SUBCLONAL	1	TRUE	1	0.62	2		691	849	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412203	63412203	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	293	944	0	ENST00000330258.3:c.964T>G	p.Phe322Val	p.F322V	ENST00000330258	NM_152424.3	322	Ttt/Gtt	2/2	1	2	FACETS	0.802	0.754	0.851	0.802	0.754	0.851	CLONAL	1	TRUE	1	0.62	2		944	1179	SUCCESS
AR	367	MSKCC	GRCh37	X	66765289	66765289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	49	619	1	ENST00000374690.3:c.301C>T	p.Arg101Cys	p.R101C	ENST00000374690	NM_000044.3	101	Cgt/Tgt	1/8	1	2	FACETS	0.17	0.143	0.2	0.17	0.143	0.2	SUBCLONAL	1	TRUE	1	0.62	2		620	931	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341414	70341414	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	52	671	0	ENST00000374080.3:c.849C>A	p.Tyr283Ter	p.Y283*	ENST00000374080		283	taC/taA	7/45	1	2	FACETS	0.162	0.137	0.189	0.162	0.137	0.189	SUBCLONAL	1	TRUE	1	0.62	2		671	1037	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937783	76937783	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	49	642	1	ENST00000373344.5:c.2965A>T	p.Thr989Ser	p.T989S	ENST00000373344	NM_000489.3	989	Act/Tct	9/35	1	2	FACETS	0.186	0.157	0.219	0.186	0.157	0.219	SUBCLONAL	1	TRUE	1	0.62	2		643	849	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938873	76938873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	38	640	0	ENST00000373344.5:c.1875G>T	p.Glu625Asp	p.E625D	ENST00000373344	NM_000489.3	625	gaG/gaT	9/35	1	2	FACETS	0.128	0.105	0.154	0.128	0.105	0.154	SUBCLONAL	1	TRUE	1	0.62	2		640	957	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938917	76938917	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	222	648	0	ENST00000373344.5:c.1831G>T	p.Asp611Tyr	p.D611Y	ENST00000373344	NM_000489.3	611	Gat/Tat	9/35	1	2	FACETS	0.718	0.669	0.77	0.718	0.669	0.77	SUBCLONAL	1	TRUE	1	0.62	2		648	997	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940025	76940025	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	293	515	0	ENST00000373344.5:c.723G>T	p.Lys241Asn	p.K241N	ENST00000373344	NM_000489.3	241	aaG/aaT	9/35	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.62	2		515	816	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019580	123019580	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	203	533	0	ENST00000355640.3:c.68T>G	p.Phe23Cys	p.F23C	ENST00000355640		23	tTt/tGt	2/7	1	2	FACETS	0.915	0.851	0.98	0.915	0.851	0.98	CLONAL	1	TRUE	1	0.62	2		533	716	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123025119	123025119	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	108	489	0	ENST00000355640.3:c.1009G>T	p.Glu337Ter	p.E337*	ENST00000355640		337	Gaa/Taa	4/7	1	2	FACETS	0.682	0.614	0.753	0.682	0.614	0.753	SUBCLONAL	1	TRUE	1	0.62	2		489	511	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123234442	123234442	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	136	479	0	ENST00000218089.9:c.3802T>C	p.Phe1268Leu	p.F1268L	ENST00000218089	NM_001042749.1	1268	Ttt/Ctt	35/35	1	2	FACETS	0.795	0.726	0.866	0.795	0.726	0.866	SUBCLONAL	1	TRUE	1	0.62	2		479	552	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0037307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	191	395	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.987	0.92	1	0.987	0.92	1	CLONAL	1	TRUE	1	0.717880381614435	2		395	539	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949057	44949058	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0037307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	237	529	0	ENST00000377967.4:c.3621_3622dup	p.Tyr1208CysfsTer14	p.Y1208Cfs*14	ENST00000377967	NM_021140.2	1206	-/GT	25/29	1	2	FACETS	0.964	0.904	1	0.964	0.904	1	CLONAL	1	TRUE	1	0.717880381614435	2		529	685	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195638	123195638	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	94	210	0	ENST00000218089.9:c.1552G>T	p.Glu518Ter	p.E518*	ENST00000218089	NM_001042749.1	518	Gag/Tag	17/35	1	2	FACETS	0.966	0.873	1	0.966	0.873	1	CLONAL	1	TRUE	1	0.717880381614435	2		210	271	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0037311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	102	863	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.3	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	FALSE	0	0.3	1		863	543	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413009	49413009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519953	NA	P-0037317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	41	492	0	ENST00000418115.1:c.14G>A	p.Arg5Gln	p.R5Q	ENST00000418115	NM_001664.2	5	cGg/cAg	2/5	1	2	FACETS	0.943	0.784	1	0.943	0.784	1	CLONAL	1	TRUE	1	0.14	2		492	621	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652248	48652248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057518396	NA	P-0037317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	60	564	0	ENST00000376670.3:c.919C>T	p.Arg307Cys	p.R307C	ENST00000376670	NM_002049.3	307	Cgc/Tgc	6/6	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.14	2		564	674	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447165	187447165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	50	534	0	ENST00000232014.4:c.1028C>T	p.Ser343Leu	p.S343L	ENST00000232014	NM_001130845.1	343	tCg/tTg	5/10	1	2	FACETS	0.969	0.821	1	0.969	0.821	1	CLONAL	1	TRUE	1	0.14	2		534	737	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855929	68855955	+	inframe_deletion	In_Frame_Del	DEL	GACACTTCTGCTGATCCTGTCTGATGT	GACACTTCTGCTGATCCTGTCTGATGT	-	novel	NA	P-0037317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	21	394	0	ENST00000261769.5:c.1739_1765del	p.Thr580_Val588del	p.T580_V588del	ENST00000261769	NM_004360.3	579	ggGACACTTCTGCTGATCCTGTCTGATGTg/ggg	12/16	1	2	FACETS	0.765	0.588	0.972	0.765	0.588	0.972	CLONAL	1	TRUE	1	0.14	2		394	392	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0037323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	31	425	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.691388285306624	3	FACETS	0.191	0.153	0.233	0.095	0.076	0.117	SUBCLONAL	1	TRUE	1	0.691388285306624	3		426	633	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479795	67479795	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs757106110	NA	P-0037323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	44	604	1	ENST00000327367.4:c.1102C>T	p.Arg368Ter	p.R368*	ENST00000327367	NM_005902.3	368	Cga/Tga	8/9	0.603605748107383	3	FACETS	0.254	0.212	0.301	0.127	0.106	0.151	SUBCLONAL	1	TRUE	1	0.691388285306624	3		605	674	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304161	65304163	+	inframe_deletion	In_Frame_Del	DEL	ACG	ACG	-	novel	NA	P-0037323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	102	581	0	ENST00000342505.4:c.2952_2954del	p.Val985del	p.V985del	ENST00000342505	NM_002227.2	984	gcCGTt/gct	21/25	0.688028046238981	3	FACETS	0.595	0.533	0.662	0.198	0.177	0.221	SUBCLONAL	1	TRUE	0	0.691388285306624	3		581	667	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143277	108143284	+	frameshift_variant	Frame_Shift_Del	DEL	GAAATATA	GAAATATA	-	novel	NA	P-0037323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	273	364	0	ENST00000278616.4:c.3096_3103del	p.Arg1032SerfsTer13	p.R1032Sfs*13	ENST00000278616	NM_000051.3	1032	agGAAATATAta/agta	21/63	0.679019307145067	3	FACETS	0.968	0.932	1	0.968	0.932	1	CLONAL	3	TRUE	0	0.691388285306624	3		364	366	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0037324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	33	323	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.857	0.7	1	0.857	0.7	1	CLONAL	1	TRUE	1	0.25	2		323	308	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955096	17955096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201650430	NA	P-0037324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	60	731	0	ENST00000458235.1:c.131C>T	p.Ser44Phe	p.S44F	ENST00000458235	NM_000215.3	44	tCc/tTc	2/24	1	2	FACETS	0.72	0.619	0.829	0.72	0.619	0.829	SUBCLONAL	1	TRUE	1	0.25	2		731	667	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177075	56177075	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0037324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	30	362	0	ENST00000399503.3:c.2345C>G	p.Ser782Ter	p.S782*	ENST00000399503	NM_005921.1	782	tCa/tGa	13/20	1	2	FACETS	0.767	0.619	0.934	0.767	0.619	0.934	CLONAL	1	TRUE	1	0.25	2		362	313	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880076	151880076	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	87	488	0	ENST00000262189.6:c.5248G>T	p.Glu1750Ter	p.E1750*	ENST00000262189	NM_170606.2	1750	Gaa/Taa	35/59	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.25	2		488	468	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922813	44922813	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	36	476	0	ENST00000377967.4:c.1675del	p.Arg559ValfsTer34	p.R559Vfs*34	ENST00000377967	NM_021140.2	558	gtC/gt	16/29	1	2	FACETS	0.689	0.567	0.826	0.689	0.567	0.826	SUBCLONAL	1	TRUE	1	0.25	2		476	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578528	7578528	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	177	681	0	ENST00000269305.4:c.402T>G	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	ttT/ttG	5/11	0.178968091524558	3	FACETS	0.929	0.856	1	0.619	0.571	0.67	CLONAL	2	TRUE	0	0.236437475581471	3		681	901	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10283800	10283800	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143598088	NA	P-0037389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	110	502	0	ENST00000340748.4:c.686C>T	p.Thr229Met	p.T229M	ENST00000340748		229	aCg/aTg	8/40	0.236437475581471	6	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.236437475581471	6		502	1055	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564525	41564526	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0037389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	50	391	0	ENST00000263253.7:c.3947_3948del	p.Pro1316ArgfsTer8	p.P1316Rfs*8	ENST00000263253	NM_001429.3	1316	cCT/c	24/31	0.186304458908622	2	FACETS	0.806	0.684	0.94	0.403	0.342	0.47	CLONAL	1	TRUE	0	0.236437475581471	2		391	525	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024001	27024002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0037390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	10	10	0	ENST00000324856.7:c.1113dup	p.Gln372AlafsTer28	p.Q372Afs*28	ENST00000324856	NM_006015.4	369	-/G	1/20	1	2	FACETS	1	0.793	1	1	0.899	1	CLONAL	2	TRUE	1	0.16	2		10	52	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0037390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	125	481	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.879	0.795	0.967	1	0.988	1	CLONAL	2	TRUE	1	0.16	2		481	889	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231707	66231707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1211795184	NA	P-0037390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	27	408	0	ENST00000273854.3:c.1993G>A	p.Glu665Lys	p.E665K	ENST00000273854	NM_004439.5	665	Gaa/Aaa	11/18	1	2	FACETS	0.676	0.537	0.836	0.676	0.537	0.836	SUBCLONAL	1	TRUE	1	0.16	2		408	499	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974711	21974711	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	28	181	1	ENST00000304494.5:c.116A>T	p.Asn39Ile	p.N39I	ENST00000304494	NM_000077.4	39	aAc/aTc	1/3	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.16	2		182	295	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871748	35871748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	51	320	0	ENST00000216797.5:c.758C>T	p.Pro253Leu	p.P253L	ENST00000216797	NM_020529.2	253	cCc/cTc	5/6	1	2	FACETS	0.785	0.665	0.917	0.785	0.665	0.917	CLONAL	1	TRUE	1	0.16	2		320	812	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867469	35867469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs191585195	NA	P-0037390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	19	220	0	ENST00000303115.3:c.283G>A	p.Glu95Lys	p.E95K	ENST00000303115	NM_002185.3	95	Gag/Aag	3/8	0.180171201564939	1	FACETS	0.806	0.613	1	0.806	0.613	1	CLONAL	1	TRUE	0	0.16	1		220	271	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617430	43617430	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	29	360	0	ENST00000355710.3:c.2767C>T	p.Leu923Phe	p.L923F	ENST00000355710	NM_020975.4	923	Ctt/Ttt	16/20	1	2	FACETS	0.634	0.507	0.778	0.634	0.507	0.778	SUBCLONAL	1	TRUE	1	0.16	2		360	572	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258746	+	missense_variant	Missense_Mutation	DNP	CA	CA	AC	novel	NA	P-0037390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	35	259	0	ENST00000369535.4:c.36_37delinsGT	p.Gly13Cys	p.G13C	ENST00000369535	NM_002524.4	12	ggTGgt/ggGTgt	2/7	1	2	FACETS	0.696	0.569	0.839	0.696	0.569	0.839	SUBCLONAL	1	TRUE	1	0.16	2		259	629	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982980	201982980	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	96	441	0	ENST00000359651.3:c.829G>A	p.Glu277Lys	p.E277K	ENST00000359651		277	Gag/Aag	7/8	1	2	FACETS	0.786	0.7	0.878	1	0.982	1	SUBCLONAL	2	TRUE	1	0.16	2		441	763	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201540	133201540	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1566307187	NA	P-0037390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	50	417	0	ENST00000320574.5:c.6698C>T	p.Pro2233Leu	p.P2233L	ENST00000320574	NM_006231.2	2233	cCt/cTt	48/49	1	2	FACETS	0.907	0.768	1	0.907	0.768	1	CLONAL	1	TRUE	1	0.16	2		417	689	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042796	42042796	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	26	344	0	ENST00000219905.7:c.6991G>T	p.Val2331Phe	p.V2331F	ENST00000219905	NM_001164273.1	2331	Gtt/Ttt	17/24	1	2	FACETS	0.815	0.645	1	0.815	0.645	1	CLONAL	1	TRUE	1	0.16	2		344	399	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992024	72992024	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs558654045	NA	P-0037390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	57	418	0	ENST00000268489.5:c.2021C>T	p.Pro674Leu	p.P674L	ENST00000268489	NM_006885.3	674	cCc/cTc	2/10	0.180171201564939	1	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	0	0.16	1		418	623	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375247	31375247	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760734960	NA	P-0037390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	37	426	0	ENST00000328111.2:c.644C>T	p.Ser215Leu	p.S215L	ENST00000328111	NM_006892.3	215	tCa/tTa	6/23	1	2	FACETS	0.751	0.618	0.9	0.751	0.618	0.9	SUBCLONAL	1	TRUE	1	0.16	2		426	616	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932792	49932792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	50	513	0	ENST00000296474.3:c.3079G>A	p.Asp1027Asn	p.D1027N	ENST00000296474	NM_002447.2	1027	Gat/Aat	14/20	1	2	FACETS	0.758	0.642	0.888	0.758	0.642	0.888	SUBCLONAL	1	TRUE	1	0.16	2		513	824	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801065	1801066	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0037390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	49	554	2	ENST00000260795.2:c.194_195delinsAA	p.Gly65Glu	p.G65E	ENST00000260795		65	gGG/gAA	2/17	1	2	FACETS	0.7	0.591	0.821	0.7	0.591	0.821	SUBCLONAL	1	TRUE	1	0.16	2		556	875	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178127	56178128	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0037390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	24	225	0	ENST00000399503.3:c.3100_3101delinsTT	p.Pro1034Phe	p.P1034F	ENST00000399503	NM_005921.1	1034	CCt/TTt	14/20	1	2	FACETS	0.855	0.67	1	0.855	0.67	1	CLONAL	1	TRUE	1	0.16	2		225	351	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355332	81355332	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	19	203	0	ENST00000222390.5:c.1042G>A	p.Asp348Asn	p.D348N	ENST00000222390	NM_000601.4	348	Gac/Aac	9/18	1	2	FACETS	0.707	0.536	0.908	0.707	0.536	0.908	CLONAL	1	TRUE	1	0.16	2		203	336	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339172	116339172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764455004	NA	P-0037390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	23	224	0	ENST00000397752.3:c.34C>T	p.Leu12Phe	p.L12F	ENST00000397752	NM_000245.2	12	Ctc/Ttc	2/21	1	2	FACETS	0.747	0.582	0.938	0.747	0.582	0.938	CLONAL	1	TRUE	1	0.16	2		224	385	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202851	27202851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1204774906	NA	P-0037390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	51	434	0	ENST00000380036.4:c.1943C>T	p.Ser648Phe	p.S648F	ENST00000380036	NM_000459.3	648	tCc/tTc	13/23	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.16	2		434	472	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231413	98231413	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	57	334	0	ENST00000331920.6:c.1870C>T	p.Gln624Ter	p.Q624*	ENST00000331920	NM_000264.3	624	Cag/Tag	14/24	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.16	2		334	602	SUCCESS
AR	367	MSKCC	GRCh37	X	66905905	66905905	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886041128	NA	P-0037390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	42	322	0	ENST00000374690.3:c.1822C>T	p.Arg608Ter	p.R608*	ENST00000374690	NM_000044.3	608	Cga/Tga	3/8	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.16	2		322	489	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0037392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	151	237	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.193586136991846	1	FACETS	0.53	0.487	0.574	0.53	0.487	0.574	INDETERMINATE	1	TRUE	0	0.712505969972596	1		237	515	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579362	7579362	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057523496	NA	P-0037392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	472	530	0	ENST00000269305.4:c.325T>G	p.Phe109Val	p.F109V	ENST00000269305	NM_001126112.2	109	Ttc/Gtc	4/11	0.712505969972596	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.712505969972596	1		530	824	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934885	9934885	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1556	266	484	0	ENST00000330684.3:c.1405A>G	p.Arg469Gly	p.R469G	ENST00000330684	NM_001134407.1	469	Aga/Gga	6/13	0.640383211742175	5	FACETS	0.848	0.792	0.906			1	CLONAL	1	TRUE	NA	0.712505969972596	5		484	1822	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264628	46264634	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	AATTCAG	AATTCAG	-	novel	NA	P-0037392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	160	217	0	ENST00000371998.3:c.1505-7_1505-1del		p.X502_splice	ENST00000371998		502			0.625145671731892	4	FACETS	1	0.961	1	0.358	0.329	0.388	CLONAL	1	TRUE	1	0.712505969972596	4		217	716	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0037409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	169	629	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.262623749562609	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	FALSE	0	0.262623749562609	2		630	612	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186501402	186501402	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0037409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	91	300	0	ENST00000323963.5:c.3G>A	p.Met1?	p.M1?	ENST00000323963		1	atG/atA	1/11	0.166175294847665	4	FACETS	1	0.968	1	0.808	0.723	0.897	CLONAL	2	FALSE	1	0.262623749562609	4		300	361	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0037414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	83	252	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.256580055703121	0	FACETS	0.9	0.811	0.99			1	CLONAL	2	TRUE	0	0.315638083005121	0		252	200	SUCCESS
YES1	7525	MSKCC	GRCh37	18	751704	751704	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs368508541	NA	P-0037414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	38	378	0	ENST00000314574.4:c.371+1G>A		p.X124_splice	ENST00000314574	NM_005433.3	124			1	2	FACETS	0.774	0.642	0.92	0.774	0.642	0.92	CLONAL	1	TRUE	1	0.315638083005121	2		378	311	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828630	72828630	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	191	632	0	ENST00000268489.5:c.7951G>T	p.Glu2651Ter	p.E2651*	ENST00000268489	NM_006885.3	2651	Gaa/Taa	9/10	0.315638083005121	1	FACETS	1	0.944	1	1	0.994	1	CLONAL	2	TRUE	0	0.315638083005121	1		632	503	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0037415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	51	407	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.194419226734196	4	FACETS	1	0.913	1	0.706	0.617	0.798	INDETERMINATE	2	TRUE	1	0.595359348221384	4		407	129	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0037415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	134	764	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.509638214379232	2	FACETS	0.95	0.885	1	0.95	0.885	1	CLONAL	2	TRUE	0	0.595359348221384	2		765	237	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9787076	9787078	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0037415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	51	279	0	ENST00000377346.4:c.3109_3111del	p.Asn1037del	p.N1037del	ENST00000377346	NM_005026.3	1036	cACAac/cac	24/24	NA	2	FACETS	0.952	0.822	1			1	INDETERMINATE	1	TRUE	NA	0.595359348221384	2		279	180	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	226	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.515123290307088	2	FACETS	0.923	0.87	0.975	0.923	0.87	0.975	CLONAL	2	TRUE	0	0.520045470501017	2		326	471	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	247	393	0	ENST00000397062.3:c.101G>C	p.Arg34Pro	p.R34P	ENST00000397062	NM_006164.4	34	cGa/cCa	2/5	0.520045470501017	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.520045470501017	3		393	558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0037440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	227	792	1	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	1	2	FACETS	0.971	0.906	1	0.971	0.906	1	CLONAL	1	TRUE	1	0.520045470501017	2		793	899	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692887	89692887	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	230	342	0	ENST00000371953.3:c.371G>T	p.Cys124Phe	p.C124F	ENST00000371953	NM_000314.4	124	tGt/tTt	5/9	0.520045470501017	3	FACETS	0.904	0.857	0.951	0.904	0.857	0.951	CLONAL	3	TRUE	0	0.520045470501017	3		342	411	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562642	29562642	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs543387071	NA	P-0037440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	137	482	0	ENST00000356175.3:c.3722G>C	p.Arg1241Pro	p.R1241P	ENST00000356175	NM_000267.3	1241	cGa/cCa	28/57	1	2	FACETS	0.981	0.897	1	0.981	0.897	1	CLONAL	1	TRUE	1	0.520045470501017	2		482	537	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376161	225376161	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	252	706	0	ENST00000264414.4:c.793G>T	p.Glu265Ter	p.E265*	ENST00000264414	NM_003590.4	265	Gaa/Taa	6/16	0.520045470501017	3	FACETS	0.965	0.909	1	0.965	0.909	1	CLONAL	2	TRUE	1	0.520045470501017	3		706	633	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525645	187525645	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	149	499	0	ENST00000441802.2:c.10434del	p.Phe3478LeufsTer4	p.F3478Lfs*4	ENST00000441802	NM_005245.3	3478	ttT/tt	18/27	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.520045470501017	2		499	572	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591087	67591095	+	inframe_deletion	In_Frame_Del	DEL	CAAACGTAT	CAAACGTAT	-	novel	NA	P-0037440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	73	243	0	ENST00000274335.5:c.1680_1688del	p.Asp560_Met563delinsGlu	p.D560_M563delinsE	ENST00000274335		560	gaCAAACGTATg/gag	12/15	1	2	FACETS	0.903	0.797	1	0.903	0.797	1	CLONAL	1	TRUE	1	0.520045470501017	2		243	311	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631268	176631269	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs886041217	NA	P-0037440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	79	290	0	ENST00000439151.2:c.1212_1213del	p.Lys405ArgfsTer5	p.K405Rfs*5	ENST00000439151	NM_022455.4	404	cAG/c	4/23	1	2	FACETS	0.876	0.776	0.981	0.876	0.776	0.981	CLONAL	1	TRUE	1	0.520045470501017	2		290	347	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310860	123310860	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147987917	NA	P-0037461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	189	422	0	ENST00000358487.5:c.568C>T	p.Arg190Trp	p.R190W	ENST00000358487	NM_000141.4	190	Cgg/Tgg	5/18	0.749839442247518	2	FACETS	0.867	0.807	0.929	0.434	0.403	0.465	CLONAL	1	TRUE	0	0.75809404233456	2		422	575	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340255	116340255	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	116	224	0	ENST00000397752.3:c.1117T>A	p.Phe373Ile	p.F373I	ENST00000397752	NM_000245.2	373	Ttc/Atc	2/21	0.715823680129363	4	FACETS	1	0.915	1	0.506	0.457	0.556	CLONAL	1	TRUE	2	0.75809404233456	4		224	532	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783216	9783216	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	179	507	0	ENST00000377346.4:c.2460C>A	p.Asp820Glu	p.D820E	ENST00000377346	NM_005026.3	820	gaC/gaA	20/24	0.658651041647458	3	FACETS	1	0.965	1	0.536	0.495	0.577	CLONAL	1	NA	1	0.65925908100896	3		507	674	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417167	417167	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	85	311	0	ENST00000399788.2:c.3383C>A	p.Ala1128Glu	p.A1128E	ENST00000399788	NM_001042603.1	1128	gCa/gAa	23/28	0.65925908100896	5	FACETS	0.817	0.722	0.917	0.272	0.24	0.306	CLONAL	1	NA	2	0.65925908100896	5		311	628	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871133	12871134	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0121480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	59	251	0	ENST00000228872.4:c.361_362dup	p.Pro122LeufsTer24	p.P122Lfs*24	ENST00000228872	NM_004064.3	120	-/GC	1/3	0.65925908100896	5	FACETS	0.917	0.793	1	0.306	0.264	0.351	CLONAL	1	NA	2	0.65925908100896	5		251	388	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432516	49432516	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	201	608	1	ENST00000301067.7:c.8623G>T	p.Ala2875Ser	p.A2875S	ENST00000301067	NM_003482.3	2875	Gcc/Tcc	34/54	0.65925908100896	5	FACETS	1	0.985	1	0.415	0.384	0.447	CLONAL	1	NA	2	0.65925908100896	5		609	974	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435156	49435156	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	115	382	0	ENST00000301067.7:c.6397G>T	p.Ala2133Ser	p.A2133S	ENST00000301067	NM_003482.3	2133	Gcc/Tcc	31/54	0.65925908100896	5	FACETS	1	0.969	1	0.393	0.354	0.433	CLONAL	1	NA	2	0.65925908100896	5		382	589	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029430	16029430	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	64	440	1	ENST00000268712.3:c.1600G>T	p.Asp534Tyr	p.D534Y	ENST00000268712	NM_006311.3	534	Gat/Tat	15/46	0.294798914426046	3	FACETS	0.496	0.43	0.568	0.248	0.215	0.284	INDETERMINATE	1	NA	1	0.65925908100896	3		441	520	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772478	56772478	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0121480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	162	562	1	ENST00000337432.4:c.332T>C	p.Leu111Pro	p.L111P	ENST00000337432	NM_058216.2	111	cTt/cCt	2/9	0.65925908100896	5	FACETS	0.859	0.787	0.935	0.286	0.262	0.312	CLONAL	1	NA	2	0.65925908100896	5		563	1138	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796972	78796973	+	missense_variant	Missense_Mutation	DNP	GC	GC	CT	novel	NA	P-0121480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	123	545	2	ENST00000306801.3:c.1085_1086delinsCT	p.Cys362Ser	p.C362S	ENST00000306801	NM_020761.2	362	tGC/tCT	9/34	0.65925908100896	5	FACETS	0.657	0.593	0.726	0.219	0.197	0.242	SUBCLONAL	1	NA	2	0.65925908100896	5		547	1129	SUCCESS
YES1	7525	MSKCC	GRCh37	18	746023	746023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0121480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	26	466	0	ENST00000314574.4:c.499G>A	p.Asp167Asn	p.D167N	ENST00000314574	NM_005433.3	167	Gat/Aat	5/12	0.65925908100896	3	FACETS	0.225	0.177	0.279	0.112	0.088	0.14	SUBCLONAL	1	NA	1	0.65925908100896	3		466	467	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636934	158636934	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	163	540	0	ENST00000263640.3:c.246G>T	p.Lys82Asn	p.K82N	ENST00000263640	NM_001105.4	82	aaG/aaT	4/11	0.658651041647458	3	FACETS	0.995	0.916	1	0.497	0.458	0.538	CLONAL	1	NA	1	0.65925908100896	3		540	661	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326263	62326263	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	257	726	0	ENST00000360203.5:c.3279C>A	p.Asp1093Glu	p.D1093E	ENST00000360203	NM_001283009.1	1093	gaC/gaA	32/35	0.65925908100896	4	FACETS	1	0.98	1	0.37	0.346	0.395	CLONAL	1	NA	1	0.65925908100896	4		726	1165	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573870	41573870	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0121480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	112	749	0	ENST00000263253.7:c.6158del	p.Asn2053ThrfsTer81	p.N2053Tfs*81	ENST00000263253	NM_001429.3	2052	cAa/ca	31/31	0.65925908100896	3	FACETS	0.451	0.405	0.5	0.15	0.135	0.167	SUBCLONAL	1	NA	0	0.65925908100896	3		749	1002	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117717425	117717425	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0121480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	99	325	0	ENST00000368508.3:c.782T>A	p.Phe261Tyr	p.F261Y	ENST00000368508	NM_002944.2	261	tTt/tAt	8/43	0.65925908100896	3	FACETS	0.92	0.826	1	0.46	0.413	0.51	CLONAL	1	NA	1	0.65925908100896	3		325	434	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468213	50468213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0121480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	334	555	0	ENST00000331340.3:c.1448G>A	p.Cys483Tyr	p.C483Y	ENST00000331340	NM_006060.4	483	tGc/tAc	8/8	0.534907513558758	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	NA	2	0.65925908100896	4		555	835	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0037480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	142	535	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.888	0.813	0.967	0.888	0.813	0.967	CLONAL	1	TRUE	1	0.536356398230809	2		535	596	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178643	56178643	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	104	316	0	ENST00000399503.3:c.3617del	p.Pro1206LeufsTer39	p.P1206Lfs*39	ENST00000399503	NM_005921.1	1206	Cct/ct	14/20	1	2	FACETS	0.902	0.813	0.995	0.902	0.813	0.995	CLONAL	1	TRUE	1	0.536356398230809	2		316	430	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183339	56183422	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCACCTGAGGTGAGAAGCATCTTTGAGTGTGATGACAGAAAATATTTTGGAATTCTGTGTAACAGCATTATACTAAATTATCTT	GCACCTGAGGTGAGAAGCATCTTTGAGTGTGATGACAGAAAATATTTTGGAATTCTGTGTAACAGCATTATACTAAATTATCTT	-	novel	NA	P-0037480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	116	380	0	ENST00000399503.3:c.4252_4257+78del		p.X1418_splice	ENST00000399503	NM_005921.1	1418		18/20	1	2	FACETS	0.768	0.695	0.845	0.768	0.695	0.845	SUBCLONAL	1	TRUE	1	0.536356398230809	2		380	563	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851097	151851097	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	56	230	0	ENST00000262189.6:c.12274G>T	p.Glu4092Ter	p.E4092*	ENST00000262189	NM_170606.2	4092	Gag/Tag	48/59	0.409673246524672	3	FACETS	0.763	0.657	0.878	0.382	0.328	0.439	SUBCLONAL	1	TRUE	1	0.536356398230809	3		230	347	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0037625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	32	281	1	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	1	0.831	1	1	0.831	1	CLONAL	1	TRUE	1	0.15	2		282	416	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256572	133256572	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	34	462	1	ENST00000320574.5:c.391G>C	p.Val131Leu	p.V131L	ENST00000320574	NM_006231.2	131	Gtg/Ctg	5/49	1	2	FACETS	0.72	0.586	0.87	0.72	0.586	0.87	SUBCLONAL	1	TRUE	1	0.15	2		463	630	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0037653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	395	863	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.354812976742084	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	0	0.361606515604759	3		863	838	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0037653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	289	520	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.291569208773697	3	FACETS	0.965	0.915	1			1	CLONAL	3	TRUE	NA	0.361606515604759	3		520	652	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	135	574	0	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.361606515604759	2		574	593	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245372	153245372	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	109	557	0	ENST00000281708.4:c.1819del	p.Asp607IlefsTer21	p.D607Ifs*21	ENST00000281708	NM_033632.3	607	Gat/at	11/12	1	2	FACETS	0.943	0.849	1	0.943	0.849	1	CLONAL	1	TRUE	1	0.361606515604759	2		557	639	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699324	18699324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369934938	NA	P-0037653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	68	290	0	ENST00000266497.5:c.3425G>A	p.Arg1142His	p.R1142H	ENST00000266497		1142	cGt/cAt	24/31	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.361606515604759	2		290	353	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551216	29551216	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs749263944	NA	P-0037653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	132	527	2	ENST00000389048.3:c.1414C>T	p.Arg472Trp	p.R472W	ENST00000389048	NM_004304.4	472	Cgg/Tgg	6/29	0.356670819913108	3	FACETS	0.844	0.77	0.92	0.844	0.77	0.92	CLONAL	2	TRUE	1	0.361606515604759	3		529	511	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535403	66535403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	122	476	2	ENST00000273854.3:c.58G>A	p.Asp20Asn	p.D20N	ENST00000273854	NM_004439.5	20	Gac/Aac	1/18	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.361606515604759	2		478	533	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	56	327	0	ENST00000281708.4:c.1513del	p.Arg505AlafsTer19	p.R505Afs*19	ENST00000281708	NM_033632.3	505	Cgc/gc	10/12	1	2	FACETS	0.88	0.757	1	0.88	0.757	1	CLONAL	1	TRUE	1	0.361606515604759	2		327	352	SUCCESS
APC	324	MSKCC	GRCh37	5	112175604	112175604	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	152	269	0	ENST00000257430.4:c.4313del	p.Thr1438AsnfsTer35	p.T1438Nfs*35	ENST00000257430	NM_000038.5	1438	aCa/aa	16/16	0.354812976742084	3	FACETS	0.875	0.811	0.941	0.875	0.811	0.941	CLONAL	3	TRUE	0	0.361606515604759	3		269	378	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345256	70345256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	121	279	2	ENST00000374080.3:c.2282G>A	p.Gly761Glu	p.G761E	ENST00000374080		761	gGa/gAa	16/45	1	1	FACETS	0.781	0.714	0.85	1	0.987	1	SUBCLONAL	2	TRUE	0	0.361606515604759	1		281	351	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347943	70347943	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	156	374	0	ENST00000374080.3:c.3182T>G	p.Val1061Gly	p.V1061G	ENST00000374080		1061	gTc/gGc	22/45	1	1	FACETS	0.909	0.842	0.976	1	0.992	1	CLONAL	2	TRUE	0	0.361606515604759	1		374	389	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693002	89693003	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0037889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	38	274	0	ENST00000371953.3:c.491dup	p.Val166SerfsTer14	p.V166Sfs*14	ENST00000371953	NM_000314.4	162	-/A	5/9	1	2	FACETS	0.862	0.715	1	0.862	0.715	1	CLONAL	1	TRUE	1	0.29	2		274	304	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0037889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	81	594	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.884	0.779	0.996	0.884	0.779	0.996	CLONAL	1	TRUE	1	0.29	2		594	632	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0037889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	48	183	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.29	2		183	314	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs1057519842	NA	P-0037889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	34	271	0	ENST00000274335.5:c.1727_1729del	p.Thr576del	p.T576del	ENST00000274335		575	aaGACg/aag	12/15	1	2	FACETS	0.782	0.641	0.939	0.782	0.641	0.939	CLONAL	1	TRUE	1	0.29	2		271	300	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434991	110434991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	104	332	0	ENST00000375856.3:c.3410G>A	p.Arg1137His	p.R1137H	ENST00000375856	NM_003749.2	1137	cGc/cAc	1/2	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.29	2		332	582	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101713	27101713	+	splice_donor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0037889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	101	471	0	ENST00000324856.7:c.4993+2del		p.X1665_splice	ENST00000324856	NM_006015.4	1665			1	2	FACETS	0.973	0.87	1	0.973	0.87	1	CLONAL	1	TRUE	1	0.29	2		471	716	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106675	27106676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0037889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	86	484	0	ENST00000324856.7:c.6287dup	p.Ala2097SerfsTer2	p.A2097Sfs*2	ENST00000324856	NM_006015.4	2096	tca/tCca	20/20	1	2	FACETS	0.954	0.844	1	0.954	0.844	1	CLONAL	1	TRUE	1	0.29	2		484	622	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450715	70450715	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576727317	NA	P-0037889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	84	400	0	ENST00000373644.4:c.5555C>T	p.Pro1852Leu	p.P1852L	ENST00000373644	NM_030625.2	1852	cCg/cTg	12/12	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.29	2		400	578	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050933	49050933	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	62	318	0	ENST00000267163.4:c.2617A>G	p.Lys873Glu	p.K873E	ENST00000267163	NM_000321.2	873	Aaa/Gaa	25/27	1	2	FACETS	0.974	0.844	1	0.974	0.844	1	CLONAL	1	TRUE	1	0.29	2		318	439	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288377	15288379	+	inframe_deletion	In_Frame_Del	DEL	GTC	GTC	-	novel	NA	P-0037889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	88	486	1	ENST00000263388.2:c.4360_4362del	p.Asp1454del	p.D1454del	ENST00000263388	NM_000435.2	1454	GAC/-	24/33	1	2	FACETS	0.914	0.81	1	0.914	0.81	1	CLONAL	1	TRUE	1	0.29	2		487	664	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188048	151188050	+	inframe_deletion	In_Frame_Del	DEL	GTA	GTA	-	novel	NA	P-0037889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	43	292	0	ENST00000262187.5:c.103_105del	p.Tyr35del	p.Y35del	ENST00000262187	NM_005614.3	35	TAC/-	2/8	1	2	FACETS	0.793	0.665	0.934	0.793	0.665	0.934	CLONAL	1	TRUE	1	0.29	2		292	374	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0037963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	196	210	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.993	0.922	1	0.993	0.922	1	CLONAL	1	TRUE	1	0.54084305667863	2		210	730	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0037963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	33	682	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.54084305667863	1	FACETS	0.131	0.106	0.159	0.131	0.106	0.159	SUBCLONAL	1	TRUE	0	0.54084305667863	1		682	682	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257226	16257226	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	56	644	0	ENST00000375759.3:c.4491G>C	p.Lys1497Asn	p.K1497N	ENST00000375759	NM_015001.2	1497	aaG/aaC	11/15	1	2	FACETS	0.205	0.174	0.238	0.205	0.174	0.238	SUBCLONAL	1	TRUE	1	0.54084305667863	2		644	1012	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574493	64574493	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	296	672	0	ENST00000312049.6:c.902T>G	p.Leu301Arg	p.L301R	ENST00000312049	NM_130799.2	301	cTc/cGc	6/10	0.54084305667863	1	FACETS	0.983	0.93	1	0.983	0.93	1	CLONAL	1	TRUE	0	0.54084305667863	1		672	812	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298501	11298501	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	58	622	0	ENST00000361445.4:c.1960G>T	p.Asp654Tyr	p.D654Y	ENST00000361445	NM_004958.3	654	Gat/Tat	12/58	1	2	FACETS	0.231	0.197	0.267	0.231	0.197	0.267	SUBCLONAL	1	TRUE	1	0.54084305667863	2		622	930	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66518975	66518975	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	50	551	4	ENST00000358598.2:c.256C>T	p.Pro86Ser	p.P86S	ENST00000358598	NM_212471.2	86	Cca/Tca	3/11	1	2	FACETS	0.217	0.183	0.254	0.217	0.183	0.254	SUBCLONAL	1	TRUE	1	0.54084305667863	2		555	852	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285270	212285270	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	237	500	0	ENST00000342788.4:c.3031G>C	p.Glu1011Gln	p.E1011Q	ENST00000342788	NM_005235.2	1011	Gag/Cag	25/28	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.54084305667863	2		500	847	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495747	72495747	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	232	536	1	ENST00000477973.2:c.325G>T	p.Ala109Ser	p.A109S	ENST00000477973	NM_012234.5	109	Gca/Tca	1/4	1	2	FACETS	0.918	0.856	0.98	0.918	0.856	0.98	CLONAL	1	TRUE	1	0.54084305667863	2		537	935	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	28	1014	11	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.336	0.267	0.414	0.336	0.267	0.414	SUBCLONAL	1	FALSE	1	0.322823877237734	2		1025	517	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	166	484	4	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	0.322742556254865	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	FALSE	0	0.322823877237734	2		488	443	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	61	288	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.896	0.775	1	0.896	0.775	1	CLONAL	1	FALSE	1	0.322823877237734	2		290	422	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	95	210	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.751	0.673	0.832	1	0.982	1	SUBCLONAL	2	FALSE	1	0.322823877237734	2		210	392	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	35	330	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.591	0.485	0.709	0.591	0.485	0.709	SUBCLONAL	1	FALSE	1	0.322823877237734	2		331	367	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755612	39755612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776452839	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	71	449	0	ENST00000288319.7:c.1153C>T	p.Arg385Cys	p.R385C	ENST00000288319	NM_182918.3	385	Cgc/Tgc	10/10	1	2	FACETS	0.936	0.819	1	0.936	0.819	1	CLONAL	1	FALSE	1	0.322823877237734	2		449	470	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	79	469	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.77	0.683	0.861	1	0.979	1	SUBCLONAL	2	FALSE	1	0.322823877237734	2		469	318	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	59	294	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	FALSE	1	0.322823877237734	2		294	313	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725054	89725054	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1554826026	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	32	146	0	ENST00000371953.3:c.1037A>G	p.Tyr346Cys	p.Y346C	ENST00000371953	NM_000314.4	346	tAc/tGc	9/9	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	FALSE	1	0.322823877237734	2		146	157	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241726	55241726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767505234	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	30	425	1	ENST00000275493.2:c.2174C>T	p.Thr725Met	p.T725M	ENST00000275493	NM_005228.3	725	aCg/aTg	18/28	1	2	FACETS	0.356	0.286	0.436	0.356	0.286	0.436	SUBCLONAL	1	FALSE	1	0.322823877237734	2		426	522	SUCCESS
AR	367	MSKCC	GRCh37	X	66766238	66766238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1327366080	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	75	335	0	ENST00000374690.3:c.1250C>T	p.Ala417Val	p.A417V	ENST00000374690	NM_000044.3	417	gCg/gTg	1/8	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.322823877237734	2		335	386	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	61	390	1	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.945	0.818	1	0.945	0.818	1	CLONAL	1	FALSE	1	0.322823877237734	2		391	400	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223604	55223604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758748662	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	71	366	1	ENST00000275493.2:c.971G>A	p.Arg324His	p.R324H	ENST00000275493	NM_005228.3	324	cGc/cAc	8/28	1	2	FACETS	0.889	0.777	1	0.889	0.777	1	CLONAL	1	FALSE	1	0.322823877237734	2		367	495	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033352	48033352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750949	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	58	228	0	ENST00000234420.5:c.3656C>T	p.Thr1219Ile	p.T1219I	ENST00000234420	NM_000179.2	1219	aCt/aTt	8/10	1	2	FACETS	0.752	0.653	0.856	1	0.971	1	SUBCLONAL	2	FALSE	1	0.322823877237734	2		228	239	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014298	70014298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142372494	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	85	669	0	ENST00000394351.3:c.1159G>A	p.Gly387Ser	p.G387S	ENST00000394351	NM_000248.3	387	Ggt/Agt	9/9	1	2	FACETS	0.919	0.814	1	0.919	0.814	1	CLONAL	1	FALSE	1	0.322823877237734	2		669	573	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784137	9784137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202142608	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	72	395	0	ENST00000377346.4:c.2705G>A	p.Arg902Gln	p.R902Q	ENST00000377346	NM_005026.3	902	cGa/cAa	21/24	0.322742556254865	2	FACETS	1	0.929	1	0.543	0.476	0.614	CLONAL	1	FALSE	0	0.322823877237734	2		395	411	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645309	67645310	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	63	450	0	ENST00000264010.4:c.579dup	p.Asp194ArgfsTer36	p.D194Rfs*36	ENST00000264010	NM_006565.3	192	caa/cAaa	3/12	1	2	FACETS	0.703	0.609	0.806	0.703	0.609	0.806	SUBCLONAL	1	FALSE	1	0.322823877237734	2		450	555	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	67	591	2	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	1	2	FACETS	0.639	0.555	0.73	0.639	0.555	0.73	SUBCLONAL	1	FALSE	1	0.322823877237734	2		593	650	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144530	58144530	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	54	220	0	ENST00000257904.6:c.541C>T	p.Arg181Ter	p.R181*	ENST00000257904	NM_000075.3	181	Cga/Tga	5/8	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	FALSE	1	0.322823877237734	2		220	297	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420870	49420870	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370465399	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	110	418	0	ENST00000301067.7:c.14879G>A	p.Arg4960Gln	p.R4960Q	ENST00000301067	NM_003482.3	4960	cGa/cAa	48/54	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.322823877237734	2		418	529	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141567294	141567294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	46	489	2	ENST00000220592.5:c.920C>T	p.Thr307Met	p.T307M	ENST00000220592	NM_012154.3	307	aCg/aTg	8/19	1	2	FACETS	0.471	0.396	0.554	0.471	0.396	0.554	SUBCLONAL	1	FALSE	1	0.322823877237734	2		491	605	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221279	36221279	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555731976	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	127	640	0	ENST00000222270.7:c.5113C>T	p.Arg1705Ter	p.R1705*	ENST00000222270	NM_014727.1	1705	Cga/Tga	24/37	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.322823877237734	2		640	732	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350053	70350053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745627308	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	50	320	0	ENST00000374080.3:c.4036C>T	p.Arg1346Cys	p.R1346C	ENST00000374080		1346	Cgc/Tgc	28/45	1	2	FACETS	0.842	0.717	0.978	0.842	0.717	0.978	CLONAL	1	FALSE	1	0.322823877237734	2		320	368	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188126	11188126	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	170	291	0	ENST00000361445.4:c.5968G>A	p.Ala1990Thr	p.A1990T	ENST00000361445	NM_004958.3	1990	Gca/Aca	43/58	0.322742556254865	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	FALSE	0	0.322823877237734	2		291	494	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582014	95582014	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	15	148	0	ENST00000393063.1:c.1897C>T	p.His633Tyr	p.H633Y	ENST00000393063	NM_030621.3	633	Cac/Tac	12/28	1	2	FACETS	0.366	0.267	0.484	0.366	0.267	0.484	SUBCLONAL	1	FALSE	1	0.322823877237734	2		148	254	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858030	9858030	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	75	359	0	ENST00000330684.3:c.3371A>G	p.Lys1124Arg	p.K1124R	ENST00000330684	NM_001134407.1	1124	aAg/aGg	13/13	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	FALSE	1	0.322823877237734	2		359	434	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650878	37650878	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	141	384	0	ENST00000447079.4:c.2350C>T	p.Arg784Ter	p.R784*	ENST00000447079	NM_015083.1	784	Cga/Tga	5/14	1	2	FACETS	0.786	0.719	0.855	1	0.988	1	SUBCLONAL	2	FALSE	1	0.322823877237734	2		384	556	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271657	15271657	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	140	758	0	ENST00000263388.2:c.6782C>A	p.Pro2261His	p.P2261H	ENST00000263388	NM_000435.2	2261	cCc/cAc	33/33	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.322823877237734	2		758	796	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920465	50920465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779208942	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	95	556	0	ENST00000440232.2:c.3157C>T	p.Arg1053Cys	p.R1053C	ENST00000440232	NM_002691.3	1053	Cgc/Tgc	26/27	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.322823877237734	2		556	443	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660895	227660895	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	29	498	2	ENST00000305123.5:c.2560C>A	p.Arg854Ser	p.R854S	ENST00000305123	NM_005544.2	854	Cgc/Agc	1/2	1	2	FACETS	0.379	0.304	0.465	0.379	0.304	0.465	SUBCLONAL	1	FALSE	1	0.322823877237734	2		500	474	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030851	36030851	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	23	309	0	ENST00000358208.4:c.1130T>C	p.Met377Thr	p.M377T	ENST00000358208		377	aTg/aCg	10/12	0.322823877237734	1	FACETS	0.375	0.292	0.47	0.375	0.292	0.47	SUBCLONAL	1	FALSE	0	0.322823877237734	1		309	319	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169988254	169988254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	27	214	0	ENST00000295797.4:c.496C>T	p.Arg166Cys	p.R166C	ENST00000295797	NM_002740.5	166	Cgc/Tgc	6/18	1	2	FACETS	0.577	0.46	0.71	0.577	0.46	0.71	SUBCLONAL	1	FALSE	1	0.322823877237734	2		214	290	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806657	1806657	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	64	591	0	ENST00000260795.2:c.1373del	p.Glu458GlyfsTer15	p.E458Gfs*15	ENST00000260795		458	gAg/gg	9/17	1	2	FACETS	0.615	0.532	0.705	0.615	0.532	0.705	SUBCLONAL	1	FALSE	1	0.322823877237734	2		591	645	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539265	187539266	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	15	267	0	ENST00000441802.2:c.8474dup	p.Ser2826LysfsTer2	p.S2826Kfs*2	ENST00000441802	NM_005245.3	2825	gga/ggGa	10/27	1	2	FACETS	0.399	0.292	0.527	0.399	0.292	0.527	SUBCLONAL	1	FALSE	1	0.322823877237734	2		267	233	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751420	57751420	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	74	262	0	ENST00000274289.3:c.1571C>T	p.Thr524Ile	p.T524I	ENST00000274289	NM_006622.3	524	aCc/aTc	11/14	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.322823877237734	2		262	341	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651916	36651916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	114	448	0	ENST00000244741.5:c.38G>A	p.Cys13Tyr	p.C13Y	ENST00000244741	NM_000389.4	13	tGc/tAc	2/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.322823877237734	2		448	519	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956977	2956977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1450077193	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	110	441	0	ENST00000396946.4:c.2650C>T	p.Arg884Trp	p.R884W	ENST00000396946	NM_032415.4	884	Cgg/Tgg	20/25	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	FALSE	1	0.322823877237734	2		441	651	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729897	41729897	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	60	403	0	ENST00000242208.4:c.632T>C	p.Val211Ala	p.V211A	ENST00000242208	NM_002192.2	211	gTa/gCa	3/3	1	2	FACETS	0.754	0.651	0.866	0.754	0.651	0.866	SUBCLONAL	1	FALSE	1	0.322823877237734	2		403	493	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429012	47429012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754787460	NA	P-0038016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	98	575	0	ENST00000377045.4:c.1375G>A	p.Gly459Arg	p.G459R	ENST00000377045	NM_001654.4	459	Ggg/Agg	13/16	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	FALSE	1	0.322823877237734	2		575	582	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0038170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	78	194	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.49986580538443	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	0	0.49986580538443	1		194	231	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0038170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	176	545	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.49986580538443	1	FACETS	0.957	0.887	1	0.957	0.887	1	CLONAL	1	TRUE	0	0.49986580538443	1		545	552	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591755	48591872	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCATGGGAGGATGTTCTTTCCCATTTATTTCCTATAGCTCCTGAGTATTGGTGTTCCATTGCTTACTTTGAAATGGATGTTCAGGTAGGAGAGACATTTAAGGTTCCTTCAAGCTGC	CTCATGGGAGGATGTTCTTTCCCATTTATTTCCTATAGCTCCTGAGTATTGGTGTTCCATTGCTTACTTTGAAATGGATGTTCAGGTAGGAGAGACATTTAAGGTTCCTTCAAGCTGC	-	novel	NA	P-0038170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	10	246	0	ENST00000342988.3:c.956-37_1036del		p.X319_splice	ENST00000342988	NM_005359.5	319		9/12	0.374597131889389	0	FACETS	0.116	0.078	0.163			1	SUBCLONAL	1	TRUE	0	0.49986580538443	0		246	173	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18963067	18963067	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs775614318	NA	P-0038308-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	37	874	0	ENST00000262803.5:c.934C>A	p.Leu312Met	p.L312M	ENST00000262803	NM_002911.3	312	Ctg/Atg	6/24	1	2	FACETS	0.257	0.212	0.307	0.257	0.212	0.307	SUBCLONAL	1	TRUE	1	0.718795372049299	2		874	401	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18963073	18963073	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038308-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	37	855	0	ENST00000262803.5:c.940G>T	p.Ala314Ser	p.A314S	ENST00000262803	NM_002911.3	314	Gcc/Tcc	6/24	1	2	FACETS	0.261	0.215	0.312	0.261	0.215	0.312	SUBCLONAL	1	TRUE	1	0.718795372049299	2		855	395	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279875	46279875	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038308-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	42	598	2	ENST00000371998.3:c.3801G>T	p.Gln1267His	p.Q1267H	ENST00000371998		1267	caG/caT	20/23	1	2	FACETS	0.188	0.156	0.223	0.188	0.156	0.223	SUBCLONAL	1	TRUE	1	0.718795372049299	2		600	621	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	60	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.198645025256726	1	FACETS	0.549	0.48	0.621	0.549	0.48	0.621	INDETERMINATE	1	TRUE	0	0.695742657091873	1		326	205	SUCCESS
APC	324	MSKCC	GRCh37	5	112175147	112175147	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	30	190	0	ENST00000257430.4:c.3856G>T	p.Glu1286Ter	p.E1286*	ENST00000257430	NM_000038.5	1286	Gaa/Taa	16/16	0.655592590130011	3	FACETS	0.881	0.769	0.982	0.881	0.769	0.982	CLONAL	3	TRUE	0	0.695742657091873	3		190	44	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0038600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	103	210	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.316005639662466	5	FACETS	0.995	0.928	1	0.796	0.742	0.848	INDETERMINATE	4	TRUE	0	0.695742657091873	5		210	152	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0038600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	406	477	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.715095284131735	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	4	TRUE	0	0.695742657091873	4		477	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514495	NA	P-0038600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	8	519	0	ENST00000269305.4:c.542G>A	p.Arg181His	p.R181H	ENST00000269305	NM_001126112.2	181	cGc/cAc	5/11	0.715095284131735	4	FACETS	0.098	0.062	0.144	0.024	0.015	0.036	SUBCLONAL	1	TRUE	0	0.695742657091873	4		519	398	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0038600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	87	373	0	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	0.557302698438696	4	FACETS	0.828	0.744	0.915	0.828	0.744	0.915	CLONAL	2	TRUE	2	0.695742657091873	4		373	256	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120165	70120165	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	212	280	0	ENST00000245479.2:c.1169del	p.Gly390AlafsTer13	p.G390Afs*13	ENST00000245479	NM_000346.3	389	ccG/cc	3/3	0.715095284131735	4	FACETS		NA	1	1	0.996	1	NA	5	TRUE	0	0.695742657091873	4		280	219	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245369	46245369	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	52	363	0	ENST00000334344.6:c.3463del	p.Leu1155Ter	p.L1155*	ENST00000334344	NM_152641.2	1155	Ctg/tg	15/21	0.715095284131735	5	FACETS	0.756	0.653	0.866	0.504	0.435	0.578	SUBCLONAL	2	TRUE	2	0.695742657091873	5		363	202	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90645581	90645586	+	inframe_deletion	In_Frame_Del	DEL	GGCTCT	GGCTCT	-	novel	NA	P-0038600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	87	138	0	ENST00000330062.3:c.37_42del	p.Arg13_Ala14del	p.R13_A14del	ENST00000330062	NM_002168.2	13	AGAGCC/-	1/11	0.704216414031458	4	FACETS	0.895	0.818	0.97	1	0.982	1	CLONAL	3	TRUE	2	0.695742657091873	4		138	158	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533584	63533585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0038600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	605	674	0	ENST00000307078.5:c.1569dup	p.Val524ArgfsTer104	p.V524Rfs*104	ENST00000307078	NM_004655.3	523	-/C	6/11	0.715095284131735	4	FACETS	1	0.998	1	1	0.998	1	CLONAL	4	TRUE	0	0.695742657091873	4		674	656	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682811	190682811	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	18	265	0	ENST00000441310.2:c.487A>G	p.Lys163Glu	p.K163E	ENST00000441310	NM_000534.4	163	Aaa/Gaa	5/13	0.63764610469639	4	FACETS	0.68	0.517	0.868	0.34	0.258	0.434	SUBCLONAL	1	TRUE	2	0.695742657091873	4		265	129	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	32	300	0				ENST00000310581	NM_198253.2	-/1132			0.261337697701375	4	FACETS	1	0.851	1	0.528	0.429	0.641	CLONAL	1	TRUE	2	0.18	4		300	397	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257158	16257158	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	54	603	0	ENST00000375759.3:c.4423C>T	p.Arg1475Ter	p.R1475*	ENST00000375759	NM_015001.2	1475	Cga/Tga	11/15	1	2	FACETS	0.942	0.804	1	0.942	0.804	1	CLONAL	1	TRUE	1	0.18	2		603	637	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933425	36933425	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	67	768	0	ENST00000361632.4:c.1862C>T	p.Pro621Leu	p.P621L	ENST00000361632		621	cCa/cTa	13/16	1	2	FACETS	0.76	0.661	0.865	1	0.973	1	SUBCLONAL	2	TRUE	1	0.18	2		768	490	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939466	36939467	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	37	786	0	ENST00000361632.4:c.383dup	p.Asn128LysfsTer22	p.N128Kfs*22	ENST00000361632		128	aac/aaAc	4/16	1	2	FACETS	0.632	0.52	0.759	0.632	0.52	0.759	SUBCLONAL	1	TRUE	1	0.18	2		786	650	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163760	72163760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	31	582	0	ENST00000357731.5:c.598G>A	p.Glu200Lys	p.E200K	ENST00000357731	NM_173808.2	200	Gaa/Aaa	4/7	1	2	FACETS	0.632	0.51	0.771	0.632	0.51	0.771	SUBCLONAL	1	TRUE	1	0.18	2		582	545	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849818	156849818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761967383	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	65	609	1	ENST00000524377.1:c.2074C>T	p.Arg692Cys	p.R692C	ENST00000524377	NM_002529.3	692	Cgc/Tgc	16/17	1	2	FACETS	0.806	0.701	0.919	1	0.975	1	CLONAL	2	TRUE	1	0.18	2		610	448	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748454	162748454	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	63	459	0	ENST00000367921.3:c.2368T>A	p.Ser790Thr	p.S790T	ENST00000367921	NM_006182.2	790	Tcc/Acc	17/18	1	2	FACETS	0.86	0.747	0.982	1	0.976	1	CLONAL	2	TRUE	1	0.18	2		459	407	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015326	176015326	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	18	324	0	ENST00000367669.3:c.1412C>T	p.Ser471Leu	p.S471L	ENST00000367669	NM_022457.5	471	tCg/tTg	12/20	1	2	FACETS	0.671	0.505	0.867	0.671	0.505	0.867	SUBCLONAL	1	TRUE	1	0.18	2		324	298	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70442648	70442649	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	81	568	1	ENST00000373644.4:c.4970_4971delinsTT	p.Pro1657Leu	p.P1657L	ENST00000373644	NM_030625.2	1657	cCC/cTT	10/12	0.130360919893871	4	FACETS	0.922	0.813	1	0.922	0.813	1	CLONAL	2	TRUE	2	0.18	4		569	576	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205534	61205534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140191819	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	53	527	0	ENST00000301761.2:c.319C>T	p.Arg107Cys	p.R107C	ENST00000301761	NM_017841.2	107	Cgc/Tgc	3/4	0.172283635150495	3	FACETS	1	0.921	1	0.563	0.48	0.654	CLONAL	1	TRUE	1	0.18	3		527	570	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946406	71946407	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	92	915	0	ENST00000298229.2:c.2570_2571delinsTT	p.Ser857Phe	p.S857F	ENST00000298229	NM_001567.3	857	tCC/tTT	23/28	0.172283635150495	3	FACETS	1	0.978	1	0.721	0.64	0.807	CLONAL	1	TRUE	1	0.18	3		915	773	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195634	102195634	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	69	448	1	ENST00000263464.3:c.394G>A	p.Gly132Arg	p.G132R	ENST00000263464	NM_001165.4	132	Gga/Aga	2/9	0.172283635150495	3	FACETS	0.805	0.702	0.916	0.805	0.702	0.916	CLONAL	2	TRUE	1	0.18	3		449	519	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156224	119156224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	70	495	0	ENST00000264033.4:c.1889C>T	p.Pro630Leu	p.P630L	ENST00000264033	NM_005188.3	630	cCc/cTc	11/16	0.172283635150495	3	FACETS	0.938	0.82	1	0.938	0.82	1	CLONAL	2	TRUE	1	0.18	3		495	452	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624446	21624446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775015037	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	172	642	0	ENST00000421138.2:c.1583G>A	p.Arg528Lys	p.R528K	ENST00000421138		528	aGa/aAa	14/16	0.130360919893871	4	FACETS	1	0.939	1	1	0.99	1	CLONAL	3	TRUE	2	0.18	4		642	736	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420492	49420492	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775506569	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	53	742	0	ENST00000301067.7:c.15257G>A	p.Arg5086Gln	p.R5086Q	ENST00000301067	NM_003482.3	5086	cGa/cAa	48/54	0.130360919893871	4	FACETS	1	0.955	1	0.667	0.569	0.774	CLONAL	1	TRUE	2	0.18	4		742	521	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426034	49426035	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	78	838	1	ENST00000301067.7:c.12453_12454delinsTT	p.Leu4152Phe	p.L4152F	ENST00000301067	NM_003482.3	4151	aaCCtt/aaTTtt	39/54	0.130360919893871	4	FACETS	0.813	0.715	0.918	0.813	0.715	0.918	CLONAL	2	TRUE	2	0.18	4		839	629	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432471	49432471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	63	805	0	ENST00000301067.7:c.8668C>T	p.Pro2890Ser	p.P2890S	ENST00000301067	NM_003482.3	2890	Cct/Tct	34/54	0.130360919893871	4	FACETS	1	0.968	1	0.727	0.629	0.833	CLONAL	1	TRUE	2	0.18	4		805	568	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865368	57865368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1370254161	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	120	965	0	ENST00000228682.2:c.2845G>A	p.Gly949Arg	p.G949R	ENST00000228682	NM_005269.2	949	Gga/Aga	12/12	0.130360919893871	4	FACETS	0.939	0.847	1	0.939	0.847	1	CLONAL	2	TRUE	2	0.18	4		965	838	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244983	133244983	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	67	919	0	ENST00000320574.5:c.2132C>T	p.Ser711Phe	p.S711F	ENST00000320574	NM_006231.2	711	tCc/tTc	19/49	0.130360919893871	4	FACETS	1	0.94	1	0.575	0.499	0.658	CLONAL	1	TRUE	2	0.18	4		919	764	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336232	73336232	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	19	326	0	ENST00000377767.4:c.2171C>T	p.Ser724Phe	p.S724F	ENST00000377767	NM_014953.3	724	tCt/tTt	17/21	1	2	FACETS	0.841	0.639	1	0.841	0.639	1	CLONAL	1	TRUE	1	0.18	2		326	251	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606127	81606127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	90	592	0	ENST00000298171.2:c.797C>T	p.Ser266Phe	p.S266F	ENST00000298171	NM_000369.2	266	tCc/tTc	9/10	0.130360919893871	4	FACETS	0.887	0.788	0.993	0.887	0.788	0.993	CLONAL	2	TRUE	2	0.18	4		592	665	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562773	95562773	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753527258	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	54	353	0	ENST00000393063.1:c.4484C>T	p.Ser1495Leu	p.S1495L	ENST00000393063	NM_030621.3	1495	tCa/tTa	24/28	0.130360919893871	4	FACETS	1	0.86	1	1	0.86	1	CLONAL	2	TRUE	2	0.18	4		353	353	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582104	95582104	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	40	309	0	ENST00000393063.1:c.1807C>T	p.Pro603Ser	p.P603S	ENST00000393063	NM_030621.3	603	Cct/Tct	12/28	0.130360919893871	4	FACETS	1	0.949	1	0.707	0.588	0.838	CLONAL	1	TRUE	2	0.18	4		309	371	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242059	105242059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746934495	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	91	851	1	ENST00000349310.3:c.365C>T	p.Ser122Leu	p.S122L	ENST00000349310	NM_001014432.1	122	tCg/tTg	6/15	0.130360919893871	4	FACETS	0.88	0.782	0.985	0.88	0.782	0.985	CLONAL	2	TRUE	2	0.18	4		852	678	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028445	42028445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761761930	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	28	423	0	ENST00000219905.7:c.3983C>T	p.Ser1328Leu	p.S1328L	ENST00000219905	NM_001164273.1	1328	tCa/tTa	13/24	1	2	FACETS	0.937	0.75	1	0.937	0.75	1	CLONAL	1	TRUE	1	0.18	2		423	332	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035101	42035101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	93	764	0	ENST00000219905.7:c.4943C>T	p.Ser1648Phe	p.S1648F	ENST00000219905	NM_001164273.1	1648	tCt/tTt	15/24	1	2	FACETS	0.756	0.673	0.846	1	0.98	1	SUBCLONAL	2	TRUE	1	0.18	2		764	683	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223352	2223354	+	frameshift_variant	Frame_Shift_Del	DEL	CTC	CTC	TT	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	33	753	1	ENST00000326181.6:c.964_966delinsTT	p.Leu322PhefsTer8	p.L322Ffs*8	ENST00000326181	NM_032271.2	322	CTC/TT	10/21	1	2	FACETS	0.759	0.618	0.919	0.759	0.618	0.919	CLONAL	1	TRUE	1	0.18	2		754	483	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857349	9857349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	21	524	0	ENST00000330684.3:c.4052G>A	p.Ser1351Asn	p.S1351N	ENST00000330684	NM_001134407.1	1351	aGc/aAc	13/13	1	2	FACETS	0.741	0.57	0.939	0.741	0.57	0.939	CLONAL	1	TRUE	1	0.18	2		524	315	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857436	9857436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	24	515	0	ENST00000330684.3:c.3965G>A	p.Gly1322Glu	p.G1322E	ENST00000330684	NM_001134407.1	1322	gGa/gAa	13/13	1	2	FACETS	0.639	0.501	0.8	0.639	0.501	0.8	SUBCLONAL	1	TRUE	1	0.18	2		515	417	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923477	9923477	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	28	536	0	ENST00000330684.3:c.1810G>A	p.Ala604Thr	p.A604T	ENST00000330684	NM_001134407.1	604	Gct/Act	9/13	1	2	FACETS	0.792	0.633	0.973	0.792	0.633	0.973	CLONAL	1	TRUE	1	0.18	2		536	393	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032089	10032089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	32	682	0	ENST00000330684.3:c.734C>T	p.Ser245Phe	p.S245F	ENST00000330684	NM_001134407.1	245	tCc/tTc	3/13	1	2	FACETS	0.755	0.612	0.917	0.755	0.612	0.917	CLONAL	1	TRUE	1	0.18	2		682	471	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50821726	50821726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	74	418	0	ENST00000398568.2:c.2062C>T	p.His688Tyr	p.H688Y	ENST00000398568	NM_001042412.1	688	Cat/Tat	13/18	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.18	2		418	599	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992052	72992052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	82	714	0	ENST00000268489.5:c.1993C>T	p.Arg665Cys	p.R665C	ENST00000268489	NM_006885.3	665	Cgt/Tgt	2/10	1	2	FACETS	0.874	0.773	0.983	1	0.982	1	CLONAL	2	TRUE	1	0.18	2		714	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519986	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	141	663	0	ENST00000269305.4:c.809T>C	p.Phe270Ser	p.F270S	ENST00000269305	NM_001126112.2	270	tTt/tCt	8/11	0.172283635150495	3	FACETS	0.881	0.805	0.96	1	0.983	1	CLONAL	3	TRUE	1	0.18	3		663	646	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012135	16012135	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	90	434	0	ENST00000268712.3:c.2147C>G	p.Ala716Gly	p.A716G	ENST00000268712	NM_006311.3	716	gCc/gGc	19/46	0.172283635150495	3	FACETS	1	0.92	1	1	0.92	1	CLONAL	2	TRUE	1	0.18	3		434	523	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654535	29654535	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	67	260	0	ENST00000356175.3:c.5224C>T	p.Gln1742Ter	p.Q1742*	ENST00000356175	NM_000267.3	1742	Caa/Taa	37/57	0.172283635150495	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	1	0.18	3		260	355	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664864	29664864	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	31	412	0	ENST00000356175.3:c.6607A>T	p.Lys2203Ter	p.K2203*	ENST00000356175	NM_000267.3	2203	Aag/Tag	43/57	0.172283635150495	3	FACETS	0.804	0.65	0.979	0.402	0.325	0.49	CLONAL	1	TRUE	1	0.18	3		412	467	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62009599	62009599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	58	733	1	ENST00000392795.3:c.23C>T	p.Pro8Leu	p.P8L	ENST00000392795	NM_001039933.1	8	cCt/cTt	1/6	0.172283635150495	3	FACETS	1	0.921	1	0.555	0.476	0.641	CLONAL	1	TRUE	1	0.18	3		734	633	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533478	63533478	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	57	722	0	ENST00000307078.5:c.1676C>T	p.Ser559Phe	p.S559F	ENST00000307078	NM_004655.3	559	tCc/tTc	6/11	0.172283635150495	3	FACETS	1	0.883	1	0.517	0.443	0.599	CLONAL	1	TRUE	1	0.18	3		722	667	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218527	5218527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751229657	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	48	843	0	ENST00000357368.4:c.3952G>A	p.Glu1318Lys	p.E1318K	ENST00000357368	NM_002850.3	1318	Gaa/Aaa	25/38	1	2	FACETS	0.837	0.707	0.981	0.837	0.707	0.981	CLONAL	1	TRUE	1	0.18	2		843	637	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219382	5219382	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1385155560	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	39	815	0	ENST00000357368.4:c.3862G>A	p.Gly1288Arg	p.G1288R	ENST00000357368	NM_002850.3	1288	Ggg/Agg	23/38	1	2	FACETS	0.771	0.638	0.92	0.771	0.638	0.92	CLONAL	1	TRUE	1	0.18	2		815	562	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267676	7267677	+	missense_variant	Missense_Mutation	DNP	CC	CC	GT	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	37	721	0	ENST00000302850.5:c.331_332delinsAC	p.Gly111Thr	p.G111T	ENST00000302850	NM_000208.2	111	GGa/ACa	2/22	1	2	FACETS	0.604	0.496	0.725	0.604	0.496	0.725	SUBCLONAL	1	TRUE	1	0.18	2		721	681	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267680	7267680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	87	705	0	ENST00000302850.5:c.328C>T	p.Arg110Trp	p.R110W	ENST00000302850	NM_000208.2	110	Cgg/Tgg	2/22	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.18	2		705	664	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599892	10599892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199953210	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	102	846	0	ENST00000171111.5:c.1684C>T	p.His562Tyr	p.H562Y	ENST00000171111	NM_203500.1	562	Cac/Tac	5/6	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.18	2		846	806	SUCCESS
CALR	811	MSKCC	GRCh37	19	13049960	13049960	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	35	574	0	ENST00000316448.5:c.104C>T	p.Ser35Phe	p.S35F	ENST00000316448	NM_004343.3	35	tCc/tTc	2/9	1	2	FACETS	0.776	0.636	0.935	0.776	0.636	0.935	CLONAL	1	TRUE	1	0.18	2		574	501	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050388	13050388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	80	567	0	ENST00000316448.5:c.340C>T	p.Pro114Ser	p.P114S	ENST00000316448	NM_004343.3	114	Cct/Tct	3/9	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.18	2		567	595	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276875	15276875	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	44	716	0	ENST00000263388.2:c.5390C>T	p.Ser1797Phe	p.S1797F	ENST00000263388	NM_000435.2	1797	tCc/tTc	30/33	1	2	FACETS	0.777	0.651	0.918	0.777	0.651	0.918	CLONAL	1	TRUE	1	0.18	2		716	629	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273297	18273297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1470167636	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	73	475	0	ENST00000222254.8:c.1090G>A	p.Glu364Lys	p.E364K	ENST00000222254	NM_005027.3	364	Gag/Aag	9/16	1	2	FACETS	0.939	0.824	1	1	0.981	1	CLONAL	2	TRUE	1	0.18	2		475	432	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210742	36210742	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761150250	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	95	859	0	ENST00000222270.7:c.493C>T	p.Arg165Cys	p.R165C	ENST00000222270	NM_014727.1	165	Cgc/Tgc	3/37	1	2	FACETS	0.806	0.718	0.899	1	0.982	1	CLONAL	2	TRUE	1	0.18	2		859	655	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799318	42799318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1296828295	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	48	421	1	ENST00000575354.2:c.4802C>T	p.Pro1601Leu	p.P1601L	ENST00000575354	NM_015125.3	1601	cCc/cTc	20/20	1	2	FACETS	1	0.897	1	1	0.975	1	CLONAL	2	TRUE	1	0.18	2		422	250	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468189	25468189	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	105	807	0	ENST00000264709.3:c.1487C>T	p.Ser496Phe	p.S496F	ENST00000264709	NM_175629.2	496	tCc/tTc	13/23	0.172283635150495	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.18	3		807	564	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519902	29519902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200364883	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	34	582	1	ENST00000389048.3:c.1669C>T	p.Arg557Cys	p.R557C	ENST00000389048	NM_004304.4	557	Cgt/Tgt	9/29	0.172283635150495	3	FACETS	0.869	0.709	1	0.434	0.354	0.524	CLONAL	1	TRUE	1	0.18	3		583	474	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025798	48025798	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	27	231	0	ENST00000234420.5:c.676G>A	p.Glu226Lys	p.E226K	ENST00000234420	NM_000179.2	226	Gag/Aag	4/10	0.172283635150495	3	FACETS	0.768	0.614	0.94	0.768	0.614	0.94	CLONAL	2	TRUE	1	0.18	3		231	213	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617430	158617430	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	37	535	0	ENST00000263640.3:c.1226T>C	p.Leu409Pro	p.L409P	ENST00000263640	NM_001105.4	409	cTt/cCt	9/11	0.172283635150495	3	FACETS	0.9	0.741	1	0.45	0.37	0.539	CLONAL	1	TRUE	1	0.18	3		535	498	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719394	190719394	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	14	337	1	ENST00000441310.2:c.1396C>T	p.Gln466Ter	p.Q466*	ENST00000441310	NM_000534.4	466	Cag/Tag	9/13	0.172283635150495	3	FACETS	0.63	0.455	0.843	0.315	0.227	0.422	SUBCLONAL	1	TRUE	1	0.18	3		338	269	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131212	202131212	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	62	411	0	ENST00000358485.4:c.180G>T	p.Met60Ile	p.M60I	ENST00000358485	NM_001080125.1	60	atG/atT	2/9	0.172283635150495	3	FACETS	0.965	0.837	1	0.965	0.837	1	CLONAL	2	TRUE	1	0.18	3		411	389	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149886	202149886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	39	640	1	ENST00000358485.4:c.1327G>A	p.Asp443Asn	p.D443N	ENST00000358485	NM_001080125.1	443	Gat/Aat	8/9	0.172283635150495	3	FACETS	0.859	0.711	1	0.429	0.355	0.512	CLONAL	1	TRUE	1	0.18	3		641	550	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560859	9560859	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	38	513	0	ENST00000353224.5:c.923C>T	p.Pro308Leu	p.P308L	ENST00000353224	NM_177990.2	308	cCc/cTc	4/10	1	2	FACETS	0.975	0.806	1	0.975	0.806	1	CLONAL	1	TRUE	1	0.18	2		513	433	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561352	9561352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773981325	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	44	497	2	ENST00000353224.5:c.430G>A	p.Glu144Lys	p.E144K	ENST00000353224	NM_177990.2	144	Gaa/Aaa	4/10	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.18	2		499	408	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023136	31023136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	65	575	0	ENST00000375687.4:c.2621C>T	p.Pro874Leu	p.P874L	ENST00000375687	NM_015338.5	874	cCt/cTt	13/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.18	2		575	522	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39709819	39709819	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	40	234	0	ENST00000361337.2:c.446C>T	p.Pro149Leu	p.P149L	ENST00000361337	NM_003286.2	149	cCt/cTt	7/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.18	2		234	315	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076931	41076931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	63	553	0	ENST00000373198.4:c.1489C>T	p.Pro497Ser	p.P497S	ENST00000373198	NM_133170.3	497	Ccc/Tcc	9/32	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.18	2		553	491	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306763	41306763	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	39	507	0	ENST00000373198.4:c.896C>T	p.Ala299Val	p.A299V	ENST00000373198	NM_133170.3	299	gCt/gTt	7/32	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.18	2		507	336	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264695	46264695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	63	410	1	ENST00000371998.3:c.1565C>T	p.Ser522Phe	p.S522F	ENST00000371998		522	tCt/tTt	12/23	1	2	FACETS	0.921	0.8	1	1	0.978	1	CLONAL	2	TRUE	1	0.18	2		411	380	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252865	36252865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060499616	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	57	357	0	ENST00000300305.3:c.497G>A	p.Arg166Gln	p.R166Q	ENST00000300305		166	cGa/cAa	4/8	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.18	2		357	451	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143239	24143240	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	GT	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	45	789	0	ENST00000263121.7:c.471_472delinsGT	p.Arg158Ter	p.R158*	ENST00000263121	NM_003073.3	157	ggCCga/ggGTga	4/9	1	2	FACETS	0.85	0.714	1	0.85	0.714	1	CLONAL	1	TRUE	1	0.18	2		789	588	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434243	12434243	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	71	419	0	ENST00000287820.6:c.611C>T	p.Ser204Phe	p.S204F	ENST00000287820	NM_015869.4	204	tCt/tTt	4/7	1	2	FACETS	0.832	0.728	0.944	1	0.978	1	CLONAL	2	TRUE	1	0.18	2		419	474	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050356	37050356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	58	447	0	ENST00000231790.2:c.505C>T	p.Pro169Ser	p.P169S	ENST00000231790	NM_000249.3	169	Cca/Tca	6/19	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.18	2		447	537	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067242	37067242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750760	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	40	410	0	ENST00000231790.2:c.1153C>T	p.Arg385Cys	p.R385C	ENST00000231790	NM_000249.3	385	Cgt/Tgt	12/19	1	2	FACETS	0.988	0.821	1	0.988	0.821	1	CLONAL	1	TRUE	1	0.18	2		410	450	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164832	47164832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1017636782	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	33	311	0	ENST00000409792.3:c.1294C>T	p.Arg432Cys	p.R432C	ENST00000409792	NM_014159.6	432	Cgt/Tgt	3/21	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.18	2		311	282	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933693	49933693	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	90	894	1	ENST00000296474.3:c.2584C>T	p.Pro862Ser	p.P862S	ENST00000296474	NM_002447.2	862	Cca/Tca	10/20	1	2	FACETS	0.8	0.711	0.895	1	0.981	1	SUBCLONAL	2	TRUE	1	0.18	2		895	625	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587167	189587167	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1209841422	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	33	447	0	ENST00000264731.3:c.1184C>T	p.Ser395Phe	p.S395F	ENST00000264731	NM_003722.4	395	tCc/tTc	9/14	1	2	FACETS	0.857	0.698	1	0.857	0.698	1	CLONAL	1	TRUE	1	0.18	2		447	428	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607200	189607200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	62	780	0	ENST00000264731.3:c.1579C>T	p.Pro527Ser	p.P527S	ENST00000264731	NM_003722.4	527	Ccc/Tcc	12/14	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.18	2		780	556	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138657	55138658	+	missense_variant	Missense_Mutation	DNP	TT	TT	AC	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	35	454	1	ENST00000257290.5:c.1334_1335delinsAC	p.Ile445Asn	p.I445N	ENST00000257290	NM_006206.4	445	aTT/aAC	9/23	1	2	FACETS	0.827	0.678	0.996	0.827	0.678	0.996	CLONAL	1	TRUE	1	0.18	2		455	470	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518114	187518114	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	35	521	0	ENST00000441802.2:c.12580T>A	p.Leu4194Ile	p.L4194I	ENST00000441802	NM_005245.3	4194	Tta/Ata	25/27	1	2	FACETS	0.761	0.623	0.916	0.761	0.623	0.916	CLONAL	1	TRUE	1	0.18	2		521	511	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557338	187557338	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1031625322	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	32	673	0	ENST00000441802.2:c.4024C>T	p.His1342Tyr	p.H1342Y	ENST00000441802	NM_005245.3	1342	Cat/Tat	6/27	1	2	FACETS	0.697	0.565	0.847	0.697	0.565	0.847	SUBCLONAL	1	TRUE	1	0.18	2		673	510	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557340	187557340	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	31	644	0	ENST00000441802.2:c.4022T>A	p.Leu1341His	p.L1341H	ENST00000441802	NM_005245.3	1341	cTc/cAc	6/27	1	2	FACETS	0.688	0.555	0.838	0.688	0.555	0.838	SUBCLONAL	1	TRUE	1	0.18	2		644	501	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871202	35871202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200772681	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	47	315	0	ENST00000303115.3:c.424G>A	p.Gly142Arg	p.G142R	ENST00000303115	NM_002185.3	142	Gga/Aga	4/8	0.261337697701375	4	FACETS	1	0.953	1	0.686	0.58	0.804	CLONAL	1	TRUE	2	0.18	4		315	449	SUCCESS
APC	324	MSKCC	GRCh37	5	112179452	112179452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782312	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	26	522	0	ENST00000257430.4:c.8161C>T	p.Arg2721Cys	p.R2721C	ENST00000257430	NM_000038.5	2721	Cgc/Tgc	16/16	1	2	FACETS	0.651	0.515	0.807	0.651	0.515	0.807	SUBCLONAL	1	TRUE	1	0.18	2		522	444	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459633	149459633	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767113303	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	32	609	1	ENST00000286301.3:c.574C>T	p.Arg192Trp	p.R192W	ENST00000286301	NM_005211.3	192	Cgg/Tgg	4/22	1	2	FACETS	0.871	0.707	1	0.871	0.707	1	CLONAL	1	TRUE	1	0.18	2		610	408	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499034	149499034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs921756253	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	38	585	0	ENST00000261799.4:c.2794G>A	p.Glu932Lys	p.E932K	ENST00000261799	NM_002609.3	932	Gag/Aag	20/23	1	2	FACETS	0.904	0.747	1	0.904	0.747	1	CLONAL	1	TRUE	1	0.18	2		585	467	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190297	32190297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	25	449	1	ENST00000375023.3:c.442G>A	p.Gly148Arg	p.G148R	ENST00000375023	NM_004557.3	148	Gga/Aga	3/30	0.172283635150495	3	FACETS	1	0.811	1	0.515	0.406	0.639	CLONAL	1	TRUE	1	0.18	3		450	294	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956553	93956553	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1035177735	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	45	379	0	ENST00000369303.4:c.2683C>T	p.Arg895Ter	p.R895*	ENST00000369303	NM_004440.3	895	Cga/Tga	15/17	0.172283635150495	3	FACETS	1	0.958	1	0.733	0.617	0.859	CLONAL	1	TRUE	1	0.18	3		379	372	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124474	94124474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	62	477	0	ENST00000369303.4:c.109G>A	p.Asp37Asn	p.D37N	ENST00000369303	NM_004440.3	37	Gat/Aat	2/17	0.172283635150495	3	FACETS	0.76	0.658	0.871	0.76	0.658	0.871	SUBCLONAL	2	TRUE	1	0.18	3		477	494	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117632232	117632232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	46	642	0	ENST00000368508.3:c.6184G>A	p.Asp2062Asn	p.D2062N	ENST00000368508	NM_002944.2	2062	Gat/Aat	39/43	0.172283635150495	3	FACETS	0.976	0.821	1	0.488	0.41	0.574	CLONAL	1	TRUE	1	0.18	3		642	571	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642495	117642495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs9489124	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	68	747	0	ENST00000368508.3:c.5704G>A	p.Glu1902Lys	p.E1902K	ENST00000368508	NM_002944.2	1902	Gaa/Aaa	35/43	0.172283635150495	3	FACETS	1	0.955	1	0.614	0.533	0.701	CLONAL	1	TRUE	1	0.18	3		747	671	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117645576	117645576	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	47	659	0	ENST00000368508.3:c.5560G>A	p.Asp1854Asn	p.D1854N	ENST00000368508	NM_002944.2	1854	Gat/Aat	34/43	0.172283635150495	3	FACETS	1	0.849	1	0.504	0.425	0.591	CLONAL	1	TRUE	1	0.18	3		659	565	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658374	117658374	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	121	753	0	ENST00000368508.3:c.5209G>A	p.Glu1737Lys	p.E1737K	ENST00000368508	NM_002944.2	1737	Gaa/Aaa	31/43	0.172283635150495	3	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	1	0.18	3		753	704	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686282	117686282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	39	338	0	ENST00000368508.3:c.3059C>T	p.Pro1020Leu	p.P1020L	ENST00000368508	NM_002944.2	1020	cCt/cTt	20/43	0.172283635150495	3	FACETS	1	0.935	1	0.642	0.533	0.763	CLONAL	1	TRUE	1	0.18	3		338	368	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706910	117706910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	79	516	0	ENST00000368508.3:c.2240G>A	p.Gly747Glu	p.G747E	ENST00000368508	NM_002944.2	747	gGa/gAa	15/43	0.172283635150495	3	FACETS	0.893	0.787	1	0.893	0.787	1	CLONAL	2	TRUE	1	0.18	3		516	536	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708070	117708070	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	27	506	0	ENST00000368508.3:c.2107G>A	p.Asp703Asn	p.D703N	ENST00000368508	NM_002944.2	703	Gat/Aat	14/43	0.172283635150495	3	FACETS	0.794	0.631	0.98	0.397	0.315	0.49	CLONAL	1	TRUE	1	0.18	3		506	412	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710585	117710585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	20	314	0	ENST00000368508.3:c.1687G>A	p.Glu563Lys	p.E563K	ENST00000368508	NM_002944.2	563	Gag/Aag	12/43	0.172283635150495	3	FACETS	0.884	0.677	1	0.442	0.338	0.563	CLONAL	1	TRUE	1	0.18	3		314	274	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718196	117718196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	45	535	0	ENST00000368508.3:c.661C>T	p.Pro221Ser	p.P221S	ENST00000368508	NM_002944.2	221	Cca/Tca	7/43	0.172283635150495	3	FACETS	1	0.879	1	0.528	0.444	0.622	CLONAL	1	TRUE	1	0.18	3		535	516	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519446	137519446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	25	340	0	ENST00000367739.4:c.1192C>T	p.His398Tyr	p.H398Y	ENST00000367739	NM_000416.2	398	Cac/Tac	7/7	0.172283635150495	3	FACETS	1	0.807	1	0.511	0.404	0.635	CLONAL	1	TRUE	1	0.18	3		340	296	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954961	2954961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375594527	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	81	750	1	ENST00000396946.4:c.2749G>A	p.Glu917Lys	p.E917K	ENST00000396946	NM_032415.4	917	Gag/Aag	21/25	0.130360919893871	4	FACETS	1	0.976	1	0.743	0.654	0.838	CLONAL	1	TRUE	2	0.18	4		751	715	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984104	2984104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	48	524	0	ENST00000396946.4:c.426G>A	p.Met142Ile	p.M142I	ENST00000396946	NM_032415.4	142	atG/atA	5/25	0.130360919893871	4	FACETS	1	0.96	1	0.737	0.624	0.861	CLONAL	1	TRUE	2	0.18	4		524	427	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985473	2985473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	58	486	1	ENST00000396946.4:c.338G>A	p.Arg113Gln	p.R113Q	ENST00000396946	NM_032415.4	113	cGg/cAg	4/25	0.130360919893871	4	FACETS	0.762	0.655	0.878	0.762	0.655	0.878	SUBCLONAL	2	TRUE	2	0.18	4		487	499	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431631	6431631	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	70	478	0	ENST00000356142.4:c.184G>A	p.Glu62Lys	p.E62K	ENST00000356142	NM_018890.3	62	Gaa/Aaa	3/7	0.130360919893871	4	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	2	0.18	4		478	420	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971154	13971154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	30	326	0	ENST00000405192.2:c.775G>A	p.Glu259Lys	p.E259K	ENST00000405192	NM_001163147.1	259	Gaa/Aaa	8/12	0.130360919893871	4	FACETS	1	0.94	1	0.742	0.6	0.902	CLONAL	1	TRUE	2	0.18	4		326	265	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210120	55210120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	75	427	0	ENST00000275493.2:c.230C>T	p.Ser77Phe	p.S77F	ENST00000275493	NM_005228.3	77	tCc/tTc	2/28	0.130360919893871	4	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	2	0.18	4		427	441	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229285	55229285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1330512770	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	72	562	0	ENST00000275493.2:c.1592G>A	p.Arg531Gln	p.R531Q	ENST00000275493	NM_005228.3	531	cGa/cAa	13/28	0.130360919893871	4	FACETS	0.805	0.704	0.915	0.805	0.704	0.915	CLONAL	2	TRUE	2	0.18	4		562	586	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374353	81374353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	39	333	0	ENST00000222390.5:c.709C>T	p.His237Tyr	p.H237Y	ENST00000222390	NM_000601.4	237	Cat/Tat	6/18	0.130360919893871	4	FACETS	1	0.938	1	0.652	0.541	0.776	CLONAL	1	TRUE	2	0.18	4		333	392	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371896	116371896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	36	429	0	ENST00000397752.3:c.1375G>A	p.Glu459Lys	p.E459K	ENST00000397752	NM_000245.2	459	Gag/Aag	3/21	0.130360919893871	4	FACETS	1	0.883	1	0.55	0.452	0.66	CLONAL	1	TRUE	2	0.18	4		429	429	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523609	148523609	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	42	323	0	ENST00000320356.2:c.844C>T	p.His282Tyr	p.H282Y	ENST00000320356	NM_004456.4	282	Cat/Tat	8/20	0.130360919893871	4	FACETS	1	0.956	1	0.746	0.624	0.881	CLONAL	1	TRUE	2	0.18	4		323	369	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864428	151864428	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	29	360	0	ENST00000262189.6:c.9553C>T	p.Gln3185Ter	p.Q3185*	ENST00000262189	NM_170606.2	3185	Cag/Tag	42/59	0.130360919893871	4	FACETS	1	0.847	1	0.533	0.428	0.652	CLONAL	1	TRUE	2	0.18	4		360	357	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030790	69030790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	51	334	0	ENST00000288368.4:c.3332G>A	p.Cys1111Tyr	p.C1111Y	ENST00000288368	NM_024870.2	1111	tGc/tAc	27/40	0.172283635150495	3	FACETS	1	0.963	1	0.744	0.634	0.865	CLONAL	1	TRUE	1	0.18	3		334	415	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970924	70970924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1277239045	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	96	668	4	ENST00000276594.2:c.1337G>A	p.Arg446Gln	p.R446Q	ENST00000276594	NM_024504.3	446	cGg/cAg	6/8	0.172283635150495	3	FACETS	0.881	0.785	0.982	0.881	0.785	0.982	CLONAL	2	TRUE	1	0.18	3		672	660	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141582972	141582972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	112	745	1	ENST00000220592.5:c.275C>T	p.Pro92Leu	p.P92L	ENST00000220592	NM_012154.3	92	cCc/cTc	3/19	0.172283635150495	3	FACETS	0.818	0.735	0.906	0.818	0.735	0.906	CLONAL	2	TRUE	1	0.18	3		746	829	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317926	8317926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	44	458	0	ENST00000356435.5:c.5687C>T	p.Ser1896Phe	p.S1896F	ENST00000356435		1896	tCc/tTc	35/35	1	2	FACETS	0.771	0.65	0.904	1	0.961	1	CLONAL	2	TRUE	1	0.18	2		458	317	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341097	8341097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159861	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	47	441	0	ENST00000356435.5:c.5119G>A	p.Gly1707Arg	p.G1707R	ENST00000356435		1707	Gga/Aga	30/35	1	2	FACETS	0.873	0.741	1	1	0.969	1	CLONAL	2	TRUE	1	0.18	2		441	299	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518073	8518073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1480778931	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	40	437	0	ENST00000356435.5:c.1318G>A	p.Glu440Lys	p.E440K	ENST00000356435		440	Gaa/Aaa	10/35	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.18	2		437	330	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606379	93606379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757250931	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	40	700	3	ENST00000375746.1:c.199G>A	p.Glu67Lys	p.E67K	ENST00000375746	NM_001174167.1	67	Gag/Aag	2/14	1	2	FACETS	0.96	0.798	1	0.96	0.798	1	CLONAL	1	TRUE	1	0.18	2		703	463	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650812	93650812	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	21	390	0	ENST00000375746.1:c.1738G>A	p.Glu580Lys	p.E580K	ENST00000375746	NM_001174167.1	580	Gaa/Aaa	13/14	1	2	FACETS	0.626	0.481	0.794	0.626	0.481	0.794	SUBCLONAL	1	TRUE	1	0.18	2		390	373	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738415	133738416	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	28	434	0	ENST00000318560.5:c.815_816delinsTT	p.Thr272Ile	p.T272I	ENST00000318560	NM_005157.4	272	aCC/aTT	4/11	1	2	FACETS	1	0.819	1	1	0.819	1	CLONAL	1	TRUE	1	0.18	2		434	304	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781467	135781467	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203537	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	24	516	0	ENST00000298552.3:c.1498C>T	p.Arg500Ter	p.R500*	ENST00000298552	NM_001162426.1	500	Cga/Tga	15/23	1	2	FACETS	0.758	0.594	0.946	0.758	0.594	0.946	CLONAL	1	TRUE	1	0.18	2		516	352	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390593	139390593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	60	1028	1	ENST00000277541.6:c.7598C>T	p.Ser2533Phe	p.S2533F	ENST00000277541	NM_017617.3	2533	tCc/tTc	34/34	1	2	FACETS	0.881	0.757	1	0.881	0.757	1	CLONAL	1	TRUE	1	0.18	2		1029	757	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314905	1314905	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	69	487	0	ENST00000400841.2:c.756G>A	p.Trp252Ter	p.W252*	ENST00000400841		252	tgG/tgA	6/6	0.215818981493858	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.18	1		487	477	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932453	39932453	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	124	892	0	ENST00000378444.4:c.2146T>C	p.Tyr716His	p.Y716H	ENST00000378444	NM_001123385.1	716	Tac/Cac	4/15	0.3	3	FACETS	1	0.964	1			1	CLONAL	2	TRUE	NA	0.18	3		892	664	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922709	44922709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1188130009	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	67	427	0	ENST00000377967.4:c.1570C>T	p.Pro524Ser	p.P524S	ENST00000377967	NM_021140.2	524	Cct/Tct	16/29	0.3	3	FACETS	0.924	0.806	1			1	CLONAL	2	TRUE	NA	0.18	3		427	439	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250074	53250075	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	110	681	0	ENST00000375401.3:c.174_175delinsAA	p.Glu59Lys	p.E59K	ENST00000375401	NM_004187.3	58	gtGGaa/gtAAaa	2/26	0.3	3	FACETS	0.949	0.853	1			1	CLONAL	2	TRUE	NA	0.18	3		681	702	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412785	63412785	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1394216535	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	116	722	0	ENST00000330258.3:c.382C>T	p.Pro128Ser	p.P128S	ENST00000330258	NM_152424.3	128	Ccc/Tcc	2/2	0.3	3	FACETS	1	0.923	1			1	CLONAL	2	TRUE	NA	0.18	3		722	685	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413129	63413130	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	127	679	1	ENST00000330258.3:c.37_38delinsAA	p.Gly13Lys	p.G13K	ENST00000330258	NM_152424.3	13	GGa/AAa	2/2	0.3	3	FACETS	0.997	0.904	1			1	CLONAL	2	TRUE	NA	0.18	3		680	771	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357586	70357586	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	102	829	0	ENST00000374080.3:c.5837C>T	p.Pro1946Leu	p.P1946L	ENST00000374080		1946	cCt/cTt	41/45	0.23121525307873	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	2	TRUE	0	0.18	2		829	550	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111461	8111483	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGTGCGAACTGTCAGACCACC	CCTGTGCGAACTGTCAGACCACC	-	novel	NA	P-0038849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	71	462	0	ENST00000346208.3:c.947_969del	p.Ser316TyrfsTer28	p.S316Yfs*28	ENST00000346208		316	tCCTGTGCGAACTGTCAGACCACC/t	5/6	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.19	2		462	744	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406106	70406106	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	64	535	0	ENST00000373644.4:c.3620C>T	p.Pro1207Leu	p.P1207L	ENST00000373644	NM_030625.2	1207	cCt/cTt	4/12	1	2	FACETS	0.91	0.787	1	0.91	0.787	1	CLONAL	1	TRUE	1	0.19	2		535	740	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945335	71945335	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	57	563	0	ENST00000298229.2:c.2223G>C	p.Lys741Asn	p.K741N	ENST00000298229	NM_001567.3	741	aaG/aaC	20/28	1	2	FACETS	0.728	0.623	0.843	0.728	0.623	0.843	SUBCLONAL	1	TRUE	1	0.19	2		563	824	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	329	300	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.94	0.894	0.987	0.94	0.894	0.987	CLONAL	1	TRUE	1	0.935552686088054	2		300	748	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0038879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	798	921	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	1	2	FACETS	0.986	0.955	1	0.986	0.955	1	CLONAL	1	TRUE	1	0.935552686088054	2		921	1731	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692794	89692794	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121909238	NA	P-0038879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	201	337	0	ENST00000371953.3:c.278A>G	p.His93Arg	p.H93R	ENST00000371953	NM_000314.4	93	cAt/cGt	5/9	0.932092022558507	1	FACETS	0.973	0.94	1	0.973	0.94	1	CLONAL	1	TRUE	0	0.935552686088054	1		337	235	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0038879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	552	541	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	1	2	FACETS	0.984	0.948	1	0.984	0.948	1	CLONAL	1	TRUE	1	0.935552686088054	2		541	1199	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050363	176050363	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1301409514	NA	P-0038879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	35	394	2	ENST00000367669.3:c.1202G>A	p.Arg401Gln	p.R401Q	ENST00000367669	NM_022457.5	401	cGa/cAa	11/20	NA	2	FACETS	0.225	0.184	0.27			1	INDETERMINATE	1	TRUE	NA	0.935552686088054	2		396	333	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143293	30143293	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs748978993	NA	P-0038879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	520	662	0	ENST00000389048.3:c.233C>G	p.Ser78Trp	p.S78W	ENST00000389048	NM_004304.4	78	tCg/tGg	1/29	1	2	FACETS	0.992	0.954	1	0.992	0.954	1	CLONAL	1	TRUE	1	0.935552686088054	2		662	1121	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158629	26158629	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	174	185	0	ENST00000289316.2:c.232G>A	p.Ala78Thr	p.A78T	ENST00000289316	NM_138720.2	78	Gct/Act	1/2	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.935552686088054	2		185	356	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309890	65309890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	72	366	0	ENST00000342505.4:c.2260G>A	p.Glu754Lys	p.E754K	ENST00000342505	NM_002227.2	754	Gaa/Aaa	17/25	1	2	FACETS	0.209	0.182	0.239	0.209	0.182	0.239	SUBCLONAL	1	TRUE	1	0.935552686088054	2		366	735	SUCCESS
APC	324	MSKCC	GRCh37	5	112174605	112174605	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	38	347	0	ENST00000257430.4:c.3314G>T	p.Arg1105Leu	p.R1105L	ENST00000257430	NM_000038.5	1105	cGg/cTg	16/16	1	2	FACETS	0.136	0.111	0.163	0.136	0.111	0.163	SUBCLONAL	1	TRUE	1	0.935552686088054	2		347	599	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829847	72829847	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750842718	NA	P-0038879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	515	694	1	ENST00000268489.5:c.6734C>T	p.Ser2245Leu	p.S2245L	ENST00000268489	NM_006885.3	2245	tCa/tTa	9/10	0.932092022558507	1	FACETS	0.824	0.801	0.847	0.824	0.801	0.847	CLONAL	1	TRUE	0	0.935552686088054	1		695	711	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28624268	28624268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	74	447	1	ENST00000241453.7:c.706G>A	p.Glu236Lys	p.E236K	ENST00000241453	NM_004119.2	236	Gaa/Aaa	6/24	0.935552686088054	1	FACETS	0.188	0.165	0.213	0.188	0.165	0.213	SUBCLONAL	1	TRUE	0	0.935552686088054	1		448	448	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107122	27107122	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	423	445	0	ENST00000324856.7:c.6733G>T	p.Asp2245Tyr	p.D2245Y	ENST00000324856	NM_006015.4	2245	Gac/Tac	20/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.935552686088054	2		445	846	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447000	49447000	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	347	379	0	ENST00000301067.7:c.944G>C	p.Trp315Ser	p.W315S	ENST00000301067	NM_003482.3	315	tGg/tCg	7/54	1	2	FACETS	0.993	0.947	1	0.993	0.947	1	CLONAL	1	TRUE	1	0.935552686088054	2		379	747	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032558	12032558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1355543573	NA	P-0038879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	237	336	0	ENST00000353533.5:c.994G>A	p.Glu332Lys	p.E332K	ENST00000353533	NM_003010.3	332	Gag/Aag	9/11	1	2	FACETS	0.849	0.798	0.9	0.849	0.798	0.9	CLONAL	1	TRUE	1	0.935552686088054	2		336	597	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023595	31023595	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1462	112	520	0	ENST00000375687.4:c.3080C>G	p.Ser1027Cys	p.S1027C	ENST00000375687	NM_015338.5	1027	tCt/tGt	13/13	0.935552686088054	3	FACETS	0.223	0.2	0.249	0.112	0.1	0.125	SUBCLONAL	1	TRUE	1	0.935552686088054	3		520	1574	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024183	31024183	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1415	102	546	0	ENST00000375687.4:c.3668C>G	p.Ser1223Cys	p.S1223C	ENST00000375687	NM_015338.5	1223	tCt/tGt	13/13	0.935552686088054	3	FACETS	0.211	0.188	0.236	0.105	0.094	0.118	SUBCLONAL	1	TRUE	1	0.935552686088054	3		546	1517	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547861	41547861	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	330	413	0	ENST00000263253.7:c.2842G>C	p.Glu948Gln	p.E948Q	ENST00000263253	NM_001429.3	948	Gaa/Caa	15/31	0.935552686088054	1	FACETS	0.985	0.961	1	0.985	0.961	1	CLONAL	1	TRUE	0	0.935552686088054	1		413	381	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934729	49934729	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	420	617	0	ENST00000296474.3:c.2167G>C	p.Glu723Gln	p.E723Q	ENST00000296474	NM_002447.2	723	Gag/Cag	7/20	0.727080874461591	1	FACETS	0.649	0.624	0.674	0.649	0.624	0.674	SUBCLONAL	1	TRUE	0	0.935552686088054	1		617	736	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259063	89259063	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	212	268	0	ENST00000336596.2:c.207G>T	p.Gln69His	p.Q69H	ENST00000336596	NM_005233.5	69	caG/caT	3/17	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.935552686088054	2		268	441	SUCCESS
ATR	545	MSKCC	GRCh37	3	142185372	142185372	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	95	233	0	ENST00000350721.4:c.6691G>C	p.Asp2231His	p.D2231H	ENST00000350721	NM_001184.3	2231	Gat/Cat	40/47	1	2	FACETS	0.713	0.643	0.784	0.713	0.643	0.784	SUBCLONAL	1	TRUE	1	0.935552686088054	2		233	285	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998990	169998990	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	44	297	0	ENST00000295797.4:c.919G>C	p.Glu307Gln	p.E307Q	ENST00000295797	NM_002740.5	307	Gag/Cag	10/18	1	2	FACETS	0.212	0.177	0.25	0.212	0.177	0.25	SUBCLONAL	1	TRUE	1	0.935552686088054	2		297	444	SUCCESS
APC	324	MSKCC	GRCh37	5	112178697	112178697	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1561615265	NA	P-0038879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	215	376	0	ENST00000257430.4:c.7406C>G	p.Ser2469Cys	p.S2469C	ENST00000257430	NM_000038.5	2469	tCt/tGt	16/16	1	2	FACETS	0.739	0.691	0.788	0.739	0.691	0.788	SUBCLONAL	1	TRUE	1	0.935552686088054	2		376	622	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562202	176562202	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	60	552	0	ENST00000439151.2:c.98G>C	p.Gly33Ala	p.G33A	ENST00000439151	NM_022455.4	33	gGt/gCt	2/23	1	2	FACETS	0.12	0.102	0.139	0.12	0.102	0.139	SUBCLONAL	1	TRUE	1	0.935552686088054	2		552	1073	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652094	36652101	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGCCCA	CCTGCCCA	-	novel	NA	P-0038879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	526	642	0	ENST00000244741.5:c.216_223del	p.Leu73AlafsTer13	p.L73Afs*13	ENST00000244741	NM_000389.4	72	ggCCTGCCCAag/ggag	2/3	1	2	FACETS	0.929	0.892	0.965	0.929	0.892	0.965	CLONAL	1	TRUE	1	0.935552686088054	2		642	1211	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415150	116415150	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	328	476	0	ENST00000397752.3:c.3244G>A	p.Glu1082Lys	p.E1082K	ENST00000397752	NM_000245.2	1082	Gaa/Aaa	15/21	0.413706364460151	3	FACETS	1	0.991	1	0.603	0.572	0.634	INDETERMINATE	1	TRUE	1	0.935552686088054	3		476	854	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87322782	87322782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201256653	NA	P-0038879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	186	406	0	ENST00000277120.3:c.383C>T	p.Thr128Met	p.T128M	ENST00000277120		128	aCg/aTg	5/19	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.935552686088054	2		406	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs1202793339	NA	P-0038939-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	200	786	0	ENST00000269305.4:c.560-1G>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.508031486664049	1	FACETS	0.974	0.912	1	0.974	0.912	1	CLONAL	1	TRUE	0	0.599167500549065	1		786	480	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028089	69028089	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038939-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	150	576	0	ENST00000288368.4:c.3248A>T	p.Lys1083Ile	p.K1083I	ENST00000288368	NM_024870.2	1083	aAa/aTa	26/40	0.599167500549065	3	FACETS	0.977	0.896	1	0.489	0.448	0.531	CLONAL	1	TRUE	1	0.599167500549065	3		576	666	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115875	8115880	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCTT	GCCCTT	A	novel	NA	P-0038939-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	236	600	0	ENST00000346208.3:c.1221_1226delinsA	p.Pro408GlnfsTer97	p.P408Qfs*97	ENST00000346208		407	tcGCCCTTc/tcAc	6/6	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.599167500549065	2		600	722	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243365	46243365	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs76994389	NA	P-0039149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	66	255	0	ENST00000334344.6:c.1718C>T	p.Thr573Met	p.T573M	ENST00000334344	NM_152641.2	573	aCg/aTg	14/21	0.232642340682568	4	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	2	0.29	4		255	272	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546703	9546703	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	42	442	0	ENST00000353224.5:c.1319T>G	p.Val440Gly	p.V440G	ENST00000353224	NM_177990.2	440	gTc/gGc	5/10	0.232642340682568	4	FACETS	1	0.898	1	0.549	0.46	0.648	CLONAL	1	TRUE	2	0.29	4		442	340	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058563	72058563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1489300985	NA	P-0039149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	114	500	1	ENST00000357731.5:c.877G>A	p.Gly293Ser	p.G293S	ENST00000357731	NM_173808.2	293	Ggc/Agc	6/7	0.171772944199524	5	FACETS	1	0.964	1	0.755	0.683	0.83	INDETERMINATE	2	TRUE	2	0.29	5		501	498	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482437	56482437	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	123	649	0	ENST00000267101.3:c.985A>C	p.Lys329Gln	p.K329Q	ENST00000267101	NM_001982.3	329	Aaa/Caa	8/28	NA	2	FACETS	0.984	0.897	1			1	INDETERMINATE	2	TRUE	NA	0.29	2		649	431	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864976	57864976	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	166	776	0	ENST00000228682.2:c.2453A>C	p.Gln818Pro	p.Q818P	ENST00000228682	NM_005269.2	818	cAg/cCg	12/12	0.3	6	FACETS	1	0.93	1			1	CLONAL	2	TRUE	NA	0.29	6		776	893	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348236	348244	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCACCTT	CCTCACCTT	GGGCA	novel	NA	P-0039149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	252	862	2	ENST00000262320.3:c.1262_1270delinsTGCCC	p.Glu421ValfsTer58	p.E421Vfs*58	ENST00000262320	NM_003502.3	421	gAAGGTGAGGac/gTGCCCac	6/11	0.3	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.29	2		864	696	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661096	227661096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	160	773	0	ENST00000305123.5:c.2359C>G	p.Gln787Glu	p.Q787E	ENST00000305123	NM_005544.2	787	Cag/Gag	1/2	0.265812487117197	3	FACETS	0.889	0.817	0.963			1	CLONAL	2	TRUE	NA	0.29	3		773	711	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536266	106536266	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	127	534	0	ENST00000369096.4:c.233A>T	p.Gln78Leu	p.Q78L	ENST00000369096	NM_001198.3	78	cAg/cTg	2/7	0.3	3	FACETS	0.891	0.81	0.975	0.891	0.81	0.975	CLONAL	2	TRUE	1	0.29	3		534	563	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983114	111983114	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	69	524	0	ENST00000368678.4:c.1433G>C	p.Arg478Pro	p.R478P	ENST00000368678		478	cGa/cCa	13/13	0.3	3	FACETS	1	0.933	1	0.554	0.483	0.63	CLONAL	1	TRUE	1	0.29	3		524	492	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	80	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.928	0.821	1	0.928	0.821	1	CLONAL	1	TRUE	1	0.406578523319636	2		326	424	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0039264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	85	252	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.95	0.844	1	0.95	0.844	1	CLONAL	1	TRUE	1	0.406578523319636	2		252	440	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0039264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	170	698	2	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.406578523319636	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.406578523319636	1		700	548	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0039264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	58	311	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.822	0.71	0.943	0.822	0.71	0.943	CLONAL	1	TRUE	1	0.406578523319636	2		311	347	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480397	89480397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756739935	NA	P-0039264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	23	243	0	ENST00000336596.2:c.2234G>A	p.Arg745Gln	p.R745Q	ENST00000336596	NM_005233.5	745	cGa/cAa	13/17	1	2	FACETS	0.273	0.212	0.344	0.273	0.212	0.344	SUBCLONAL	1	TRUE	1	0.406578523319636	2		243	414	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920402	114920402	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	156	401	0	ENST00000543371.1:c.1345del	p.Ala449HisfsTer42	p.A449Hfs*42	ENST00000543371	NM_001198531.1	448	cGg/cg	13/14	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.406578523319636	2		401	709	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316307	14316307	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	105	453	0	ENST00000256196.4:c.298A>C	p.Ser100Arg	p.S100R	ENST00000256196		100	Agt/Cgt	3/6	1	2	FACETS	0.909	0.817	1	0.909	0.817	1	CLONAL	1	TRUE	1	0.406578523319636	2		453	568	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519152	103519152	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	40	337	0	ENST00000355739.4:c.2490G>T	p.Lys830Asn	p.K830N	ENST00000355739	NM_000123.3	830	aaG/aaT	11/15	0.390941149910189	4	FACETS	0.402	0.333	0.479	0.134	0.111	0.16	SUBCLONAL	1	TRUE	1	0.406578523319636	4		337	689	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703534	47703534	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1558519611	NA	P-0039264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	44	461	0	ENST00000233146.2:c.2034T>A	p.Tyr678Ter	p.Y678*	ENST00000233146	NM_000251.2	678	taT/taA	13/16	1	2	FACETS	0.405	0.339	0.478	0.405	0.339	0.478	SUBCLONAL	1	TRUE	1	0.406578523319636	2		461	534	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412131	63412132	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0039264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	201	667	0	ENST00000330258.3:c.1034_1035dup	p.Ser346ProfsTer19	p.S346Pfs*19	ENST00000330258	NM_152424.3	345	-/CC	2/2	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.406578523319636	2		667	969	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	158	316	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.962	0.894	1	0.962	0.894	1	CLONAL	1	TRUE	1	0.883117933838416	2		316	372	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459032	120459032	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372538600	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	310	669	1	ENST00000256646.2:c.6313C>T	p.Arg2105Trp	p.R2105W	ENST00000256646	NM_024408.3	2105	Cgg/Tgg	34/34	1	2	FACETS	0.989	0.939	1	0.989	0.939	1	CLONAL	1	TRUE	1	0.883117933838416	2		670	710	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412375	139412375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1341448592	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	88	610	0	ENST00000277541.6:c.1270G>A	p.Glu424Lys	p.E424K	ENST00000277541	NM_017617.3	424	Gag/Aag	8/34	0.232047838320056	2	FACETS	0.33	0.292	0.37	0.165	0.146	0.185	INDETERMINATE	1	TRUE	0	0.883117933838416	2		610	604	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416788	121416788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs905788991	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	316	793	0	ENST00000257555.6:c.217G>A	p.Glu73Lys	p.E73K	ENST00000257555		73	Gag/Aag	1/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.883117933838416	2		793	675	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027422	48027422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781462	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	185	472	0	ENST00000234420.5:c.2300C>T	p.Thr767Ile	p.T767I	ENST00000234420	NM_000179.2	767	aCt/aTt	4/10	1	2	FACETS	0.923	0.861	0.985	0.923	0.861	0.985	CLONAL	1	TRUE	1	0.883117933838416	2		472	454	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412252	139412252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057523819	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	176	680	2	ENST00000277541.6:c.1393G>A	p.Ala465Thr	p.A465T	ENST00000277541	NM_017617.3	465	Gcc/Acc	8/34	0.232047838320056	2	FACETS	0.52	0.479	0.561	0.26	0.239	0.281	INDETERMINATE	1	TRUE	0	0.883117933838416	2		682	767	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413072	139413072	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	51	649	0	ENST00000277541.6:c.1070T>C	p.Phe357Ser	p.F357S	ENST00000277541	NM_017617.3	357	tTc/tCc	6/34	0.232047838320056	2	FACETS	0.186	0.158	0.217	0.093	0.079	0.109	INDETERMINATE	1	TRUE	0	0.883117933838416	2		649	621	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572185	64572185	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	266	604	2	ENST00000312049.6:c.1454G>A	p.Arg485Gln	p.R485Q	ENST00000312049	NM_130799.2	485	cGg/cAg	10/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.883117933838416	2		606	526	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119812218	119812218	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	227	389	0	ENST00000316626.5:c.64G>A	p.Ala22Thr	p.A22T	ENST00000316626		22	Gct/Act	1/12	1	2	FACETS	0.972	0.914	1	0.972	0.914	1	CLONAL	1	TRUE	1	0.883117933838416	2		389	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577144	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs879253942	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	621	604	0	ENST00000269305.4:c.794T>C	p.Leu265Pro	p.L265P	ENST00000269305	NM_001126112.2	265	cTg/cCg	8/11	0.883117933838416	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.883117933838416	2		604	675	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317114	87317114	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	320	466	0	ENST00000277120.3:c.253G>A	p.Asp85Asn	p.D85N	ENST00000277120		85	Gat/Aat	3/19	0.232047838320056	2	FACETS	1	0.991	1	0.583	0.555	0.61	INDETERMINATE	1	TRUE	0	0.883117933838416	2		466	622	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470494	25470494	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs750966422	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	303	755	0	ENST00000264709.3:c.980G>A	p.Trp327Ter	p.W327*	ENST00000264709	NM_175629.2	327	tGg/tAg	8/23	1	2	FACETS	0.987	0.937	1	0.987	0.937	1	CLONAL	1	TRUE	1	0.883117933838416	2		755	695	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873426	151873426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	257	421	0	ENST00000262189.6:c.9112G>A	p.Ala3038Thr	p.A3038T	ENST00000262189	NM_170606.2	3038	Gca/Aca	38/59	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.883117933838416	2		421	532	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383628	15383628	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1409879003	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	183	391	0	ENST00000263377.2:c.283C>T	p.Pro95Ser	p.P95S	ENST00000263377	NM_058243.2	95	Cct/Tct	2/20	0.212786448090587	3	FACETS	1	0.989	1	0.67	0.625	0.715	INDETERMINATE	1	TRUE	1	0.883117933838416	3		391	446	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205401	38205401	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	386	672	0	ENST00000317025.8:c.289G>A	p.Ala97Thr	p.A97T	ENST00000317025	NM_023034.1	97	Gcc/Acc	2/24	1	2	FACETS	0.972	0.928	1	0.972	0.928	1	CLONAL	1	TRUE	1	0.883117933838416	2		672	899	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562607	21562607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750798997	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	27	377	1	ENST00000382592.4:c.1312G>A	p.Ala438Thr	p.A438T	ENST00000382592	NM_014572.2	438	Gcg/Acg	4/8	1	2	FACETS	0.18	0.143	0.222	0.18	0.143	0.222	SUBCLONAL	1	TRUE	1	0.883117933838416	2		378	340	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339563	70339563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs968474929	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	297	617	0	ENST00000374080.3:c.232G>A	p.Ala78Thr	p.A78T	ENST00000374080		78	Gca/Aca	3/45	1	2	FACETS	0.949	0.899	0.999	0.949	0.899	0.999	CLONAL	1	TRUE	1	0.883117933838416	2		617	709	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606544	93606544	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs962420195	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	223	645	1	ENST00000375746.1:c.364G>A	p.Asp122Asn	p.D122N	ENST00000375746	NM_001174167.1	122	Gat/Aat	2/14	0.232047838320056	2	FACETS	0.798	0.747	0.849	0.399	0.373	0.425	INDETERMINATE	1	TRUE	0	0.883117933838416	2		646	633	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437603	56437603	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770023953	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	199	544	0	ENST00000407977.2:c.859G>A	p.Val287Ile	p.V287I	ENST00000407977		287	Gtc/Atc	8/10	1	2	FACETS	0.867	0.81	0.924	0.867	0.81	0.924	CLONAL	1	TRUE	1	0.883117933838416	2		544	520	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194733	29194733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	258	700	0	ENST00000240100.2:c.995C>T	p.Ser332Phe	p.S332F	ENST00000240100	NM_001394.6	332	tCc/tTc	4/4	1	2	FACETS	0.953	0.9	1	0.953	0.9	1	CLONAL	1	TRUE	1	0.883117933838416	2		700	613	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298587	11298587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	283	653	0	ENST00000361445.4:c.1874C>T	p.Thr625Ile	p.T625I	ENST00000361445	NM_004958.3	625	aCc/aTc	12/58	1	2	FACETS	0.98	0.928	1	0.98	0.928	1	CLONAL	1	TRUE	1	0.883117933838416	2		653	654	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261649	16261649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	257	569	0	ENST00000375759.3:c.8914G>A	p.Val2972Ile	p.V2972I	ENST00000375759	NM_015001.2	2972	Gtc/Atc	11/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.883117933838416	2		569	574	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551723	150551723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	132	354	0	ENST00000369026.2:c.284G>A	p.Arg95Lys	p.R95K	ENST00000369026	NM_021960.4	95	aGg/aAg	1/3	1	2	FACETS	0.983	0.908	1	0.983	0.908	1	CLONAL	1	TRUE	1	0.883117933838416	2		354	304	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67197022	67197022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	269	469	0	ENST00000312629.5:c.265G>A	p.Gly89Ser	p.G89S	ENST00000312629	NM_003952.2	89	Ggc/Agc	4/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.883117933838416	2		469	590	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941270	71941270	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	367	787	0	ENST00000298229.2:c.1045C>T	p.Gln349Ter	p.Q349*	ENST00000298229	NM_001567.3	349	Cag/Tag	9/28	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.883117933838416	2		787	772	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948707	71948707	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	240	676	0	ENST00000298229.2:c.3419C>T	p.Pro1140Leu	p.P1140L	ENST00000298229	NM_001567.3	1140	cCt/cTt	26/28	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.883117933838416	2		676	536	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998372	100998372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	65	110	0	ENST00000325455.5:c.1430C>T	p.Pro477Leu	p.P477L	ENST00000325455	NM_001202474.3	477	cCg/cTg	1/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.883117933838416	2		110	105	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21627893	21627893	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	278	422	1	ENST00000421138.2:c.1237G>A	p.Asp413Asn	p.D413N	ENST00000421138		413	Gac/Aac	12/16	1	2	FACETS	0.935	0.885	0.987	0.935	0.885	0.987	CLONAL	1	TRUE	1	0.883117933838416	2		423	673	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448744	49448744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753608064	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	314	600	0	ENST00000301067.7:c.115G>A	p.Gly39Arg	p.G39R	ENST00000301067	NM_003482.3	39	Gga/Aga	2/54	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.883117933838416	2		600	668	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926905	112926905	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	124	415	0	ENST00000351677.2:c.1525G>A	p.Ala509Thr	p.A509T	ENST00000351677	NM_002834.3	509	Gca/Aca	13/16	1	2	FACETS	0.706	0.644	0.769	0.706	0.644	0.769	SUBCLONAL	1	TRUE	1	0.883117933838416	2		415	398	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120805994	120805994	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	225	630	0	ENST00000257552.2:c.182+1G>A		p.X61_splice	ENST00000257552	NM_002442.3	61			1	2	FACETS	0.932	0.875	0.988	0.932	0.875	0.988	CLONAL	1	TRUE	1	0.883117933838416	2		630	547	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416782	121416782	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	321	801	2	ENST00000257555.6:c.211G>T	p.Glu71Ter	p.E71*	ENST00000257555		71	Gag/Tag	1/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.883117933838416	2		803	681	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609630	81609630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908868	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	313	596	0	ENST00000298171.2:c.1228G>A	p.Asp410Asn	p.D410N	ENST00000298171	NM_000369.2	410	Gac/Aac	10/10	1	2	FACETS	0.954	0.905	1	0.954	0.905	1	CLONAL	1	TRUE	1	0.883117933838416	2		596	743	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631728	90631728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	305	588	0	ENST00000330062.3:c.541G>A	p.Ala181Thr	p.A181T	ENST00000330062	NM_002168.2	181	Gcc/Acc	5/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.883117933838416	2		588	634	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632635	3632635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	340	794	0	ENST00000294008.3:c.5213G>A	p.Gly1738Glu	p.G1738E	ENST00000294008	NM_032444.2	1738	gGg/gAg	15/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.883117933838416	2		794	739	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586113	29586113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	234	398	0	ENST00000356175.3:c.4333G>A	p.Asp1445Asn	p.D1445N	ENST00000356175	NM_000267.3	1445	Gat/Aat	32/57	1	2	FACETS	0.872	0.819	0.925	0.872	0.819	0.925	CLONAL	1	TRUE	1	0.883117933838416	2		398	608	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210493	2210493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	238	726	0	ENST00000398665.3:c.1100C>T	p.Pro367Leu	p.P367L	ENST00000398665	NM_032482.2	367	cCc/cTc	13/28	0.640795869546356	3	FACETS	1	0.941	1			1	CLONAL	1	TRUE	NA	0.883117933838416	3		726	773	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125359	7125359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	326	721	0	ENST00000302850.5:c.3193C>T	p.Leu1065Phe	p.L1065F	ENST00000302850	NM_000208.2	1065	Ctc/Ttc	17/22	0.212786448090587	3	FACETS	1	0.995	1	0.721	0.686	0.757	INDETERMINATE	1	TRUE	1	0.883117933838416	3		721	738	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42381415	42381415	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	255	647	0	ENST00000221972.3:c.41C>T	p.Thr14Ile	p.T14I	ENST00000221972	NM_021601.3	14	aCc/aTc	1/5	0.883117933838416	1	FACETS	0.971	0.935	1	0.971	0.935	1	CLONAL	1	TRUE	0	0.883117933838416	1		647	332	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451824	29451824	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358074797	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	271	699	1	ENST00000389048.3:c.2741G>A	p.Gly914Glu	p.G914E	ENST00000389048	NM_004304.4	914	gGg/gAg	16/29	1	2	FACETS	0.988	0.935	1	0.988	0.935	1	CLONAL	1	TRUE	1	0.883117933838416	2		700	621	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028115	48028115	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1281207200	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	191	402	0	ENST00000234420.5:c.2993C>T	p.Ser998Phe	p.S998F	ENST00000234420	NM_000179.2	998	tCt/tTt	4/10	1	2	FACETS	0.87	0.812	0.929	0.87	0.812	0.929	CLONAL	1	TRUE	1	0.883117933838416	2		402	497	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215674161	215674161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553628365	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	242	597	1	ENST00000260947.4:c.133G>A	p.Glu45Lys	p.E45K	ENST00000260947	NM_000465.2	45	Gag/Aag	1/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.883117933838416	2		598	535	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225360658	225360658	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	205	313	0	ENST00000264414.4:c.1733G>A	p.Gly578Glu	p.G578E	ENST00000264414	NM_003590.4	578	gGa/gAa	13/16	1	2	FACETS	0.969	0.909	1	0.969	0.909	1	CLONAL	1	TRUE	1	0.883117933838416	2		313	479	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775475	39775475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	323	592	0	ENST00000288319.7:c.545G>A	p.Ser182Asn	p.S182N	ENST00000288319	NM_182918.3	182	aGc/aAc	4/10	1	2	FACETS	0.987	0.938	1	0.987	0.938	1	CLONAL	1	TRUE	1	0.883117933838416	2		592	741	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721493	49721493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	282	499	1	ENST00000449682.2:c.2146G>A	p.Asp716Asn	p.D716N	ENST00000449682	NM_020998.3	716	Gac/Aac	18/18	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.883117933838416	2		500	527	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281165	142281165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751784387	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	261	422	1	ENST00000350721.4:c.1079G>A	p.Gly360Glu	p.G360E	ENST00000350721	NM_001184.3	360	gGg/gAg	4/47	1	2	FACETS	0.99	0.936	1	0.99	0.936	1	CLONAL	1	TRUE	1	0.883117933838416	2		423	597	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1952916	1952916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	252	596	0	ENST00000382891.5:c.1999G>A	p.Glu667Lys	p.E667K	ENST00000382891	NM_133335.3	667	Gag/Aag	10/22	1	2	FACETS	0.893	0.841	0.945	0.893	0.841	0.945	CLONAL	1	TRUE	1	0.883117933838416	2		596	639	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522583	67522583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	171	320	0	ENST00000274335.5:c.80G>A	p.Gly27Asp	p.G27D	ENST00000274335		27	gGt/gAt	1/15	1	2	FACETS	0.913	0.85	0.978	0.913	0.85	0.978	CLONAL	1	TRUE	1	0.883117933838416	2		320	424	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323974	31323974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41545114	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	311	449	0	ENST00000412585.2:c.589G>A	p.Glu197Lys	p.E197K	ENST00000412585	NM_005514.6	197	Gag/Aag	3/8	1	2	FACETS	0.984	0.958	1	1	0.997	1	CLONAL	2	TRUE	1	0.883117933838416	2		449	358	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196029	138196029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150717698	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	158	283	0	ENST00000237289.4:c.343G>A	p.Val115Ile	p.V115I	ENST00000237289	NM_001270507.1	115	Gtt/Att	3/9	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.883117933838416	2		283	355	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001010	150001010	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	160	231	0	ENST00000253339.5:c.2593+1G>A		p.X865_splice	ENST00000253339		865			1	2	FACETS	0.961	0.893	1	0.961	0.893	1	CLONAL	1	TRUE	1	0.883117933838416	2		231	377	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55228032	55228032	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	166	259	0	ENST00000275493.2:c.1498+1G>A		p.X500_splice	ENST00000275493	NM_005228.3	500			1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.883117933838416	2		259	375	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884548	151884548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	192	332	1	ENST00000262189.6:c.4807G>A	p.Ala1603Thr	p.A1603T	ENST00000262189	NM_170606.2	1603	Gcc/Acc	33/59	1	2	FACETS	0.895	0.836	0.955	0.895	0.836	0.955	CLONAL	1	TRUE	1	0.883117933838416	2		333	486	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69012025	69012025	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	345	566	0	ENST00000288368.4:c.2662C>T	p.Leu888Phe	p.L888F	ENST00000288368	NM_024870.2	888	Ctt/Ttt	23/40	1	2	FACETS	0.94	0.894	0.986	0.94	0.894	0.986	CLONAL	1	TRUE	1	0.883117933838416	2		566	831	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249671	110249671	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs959152350	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	348	759	0	ENST00000374672.4:c.1004C>T	p.Pro335Leu	p.P335L	ENST00000374672	NM_004235.4	335	cCg/cTg	3/5	0.232047838320056	2	FACETS	1	0.991	1	0.575	0.549	0.601	INDETERMINATE	1	TRUE	0	0.883117933838416	2		759	685	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730431	133730431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	290	465	0	ENST00000318560.5:c.497G>A	p.Arg166Lys	p.R166K	ENST00000318560	NM_005157.4	166	aGa/aAa	3/11	0.232047838320056	2	FACETS	1	0.991	1	0.586	0.558	0.615	INDETERMINATE	1	TRUE	0	0.883117933838416	2		465	560	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760399	133760399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	311	627	0	ENST00000318560.5:c.2722G>A	p.Gly908Arg	p.G908R	ENST00000318560	NM_005157.4	908	Ggg/Agg	11/11	0.232047838320056	2	FACETS	1	0.995	1	0.679	0.649	0.708	INDETERMINATE	1	TRUE	0	0.883117933838416	2		627	519	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409843	139409843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	233	771	0	ENST00000277541.6:c.1913G>A	p.Cys638Tyr	p.C638Y	ENST00000277541	NM_017617.3	638	tGc/tAc	12/34	0.232047838320056	2	FACETS	0.726	0.68	0.773	0.363	0.34	0.387	INDETERMINATE	1	TRUE	0	0.883117933838416	2		771	727	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412587	139412587	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	73	640	0	ENST00000277541.6:c.1255+2T>C		p.X419_splice	ENST00000277541	NM_017617.3	419			0.232047838320056	2	FACETS	0.319	0.279	0.361	0.159	0.139	0.181	INDETERMINATE	1	TRUE	0	0.883117933838416	2		640	519	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934271	39934271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	387	632	0	ENST00000378444.4:c.328G>A	p.Gly110Ser	p.G110S	ENST00000378444	NM_001123385.1	110	Ggt/Agt	4/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.883117933838416	2		632	822	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929472	44929472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	324	594	0	ENST00000377967.4:c.2572G>A	p.Gly858Arg	p.G858R	ENST00000377967	NM_021140.2	858	Ggg/Agg	17/29	1	2	FACETS	0.841	0.797	0.885	0.841	0.797	0.885	CLONAL	1	TRUE	1	0.883117933838416	2		594	873	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0039394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	36	535	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.386037310324128	2	FACETS	0.888	0.75	1	0.888	0.75	1	CLONAL	2	TRUE	0	0.386037310324128	2		535	105	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016549	12016549	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0039394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	26	335	0	ENST00000353533.5:c.686-1G>T		p.X229_splice	ENST00000353533	NM_003010.3	229			1	2	FACETS	0.765	0.623	0.919	1	0.942	1	CLONAL	2	TRUE	1	0.386037310324128	2		335	88	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645922	67645922	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	43	695	0	ENST00000264010.4:c.850C>G	p.His284Asp	p.H284D	ENST00000264010	NM_006565.3	284	Cac/Gac	4/12	0.386037310324128	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.386037310324128	1		695	158	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	580	520	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.662915226251752	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	2	0.661940807255425	4		520	1444	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0039452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	79	1014	11	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.405	0.355	0.46	0.405	0.355	0.46	SUBCLONAL	1	TRUE	1	0.357623161899303	2		1025	1090	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0039452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	133	840	6	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.734	0.665	0.806	0.734	0.665	0.806	SUBCLONAL	1	TRUE	1	0.357623161899303	2		846	1014	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0039452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	27	326	1	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.462	0.368	0.569	0.462	0.368	0.569	SUBCLONAL	1	TRUE	1	0.357623161899303	2		327	327	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0039452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	23	345	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	0.36	0.281	0.453	0.36	0.281	0.453	SUBCLONAL	1	TRUE	1	0.357623161899303	2		345	357	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459239	120459239	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	70	581	1	ENST00000256646.2:c.6106C>T	p.Arg2036Ter	p.R2036*	ENST00000256646	NM_024408.3	2036	Cga/Tga	34/34	1	2	FACETS	0.548	0.477	0.624	0.548	0.477	0.624	SUBCLONAL	1	TRUE	1	0.357623161899303	2		582	715	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444275	50444275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	39	243	0	ENST00000331340.3:c.205C>T	p.Arg69Cys	p.R69C	ENST00000331340	NM_006060.4	69	Cgt/Tgt	4/8	1	2	FACETS	0.503	0.417	0.598	0.503	0.417	0.598	SUBCLONAL	1	TRUE	1	0.357623161899303	2		243	434	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923738	72923738	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	79	764	0	ENST00000268489.5:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000268489	NM_006885.3	1114	Cga/Tga	4/10	1	2	FACETS	0.467	0.409	0.528	0.467	0.409	0.528	SUBCLONAL	1	TRUE	1	0.357623161899303	2		764	947	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092947	27092947	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0039452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	29	395	0	ENST00000324856.7:c.2879-1G>A		p.X960_splice	ENST00000324856	NM_006015.4	960			1	2	FACETS	0.353	0.282	0.433	0.353	0.282	0.433	SUBCLONAL	1	TRUE	1	0.357623161899303	2		395	460	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227863	36227863	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1568384928	NA	P-0039452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	86	1064	0	ENST00000222270.7:c.7348C>T	p.Arg2450Ter	p.R2450*	ENST00000222270	NM_014727.1	2450	Cga/Tga	32/37	1	2	FACETS	0.37	0.326	0.418	0.37	0.326	0.418	SUBCLONAL	1	TRUE	1	0.357623161899303	2		1064	1300	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662351	227662352	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs766624780	NA	P-0039452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	71	659	0	ENST00000305123.5:c.1103dup	p.Leu369AlafsTer28	p.L369Afs*28	ENST00000305123	NM_005544.2	368	ccg/ccCg	1/2	1	2	FACETS	0.448	0.39	0.511	0.448	0.39	0.511	SUBCLONAL	1	TRUE	1	0.357623161899303	2		659	886	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568866	212568866	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	26	470	0	ENST00000342788.4:c.1252del	p.Ser418LeufsTer4	p.S418Lfs*4	ENST00000342788	NM_005235.2	418	Tct/ct	11/28	1	2	FACETS	0.296	0.233	0.367	0.296	0.233	0.367	SUBCLONAL	1	TRUE	1	0.357623161899303	2		470	492	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	244006445	244006445	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	57	522	0	ENST00000263826.5:c.28G>T	p.Gly10Cys	p.G10C	ENST00000263826	NM_005465.4	10	Ggt/Tgt	1/13	0.357623161899303	3	FACETS	0.387	0.331	0.449	0.194	0.165	0.225	SUBCLONAL	1	TRUE	1	0.357623161899303	3		522	970	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830885	72830885	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	53	658	0	ENST00000268489.5:c.5696del	p.Gly1899GlufsTer15	p.G1899Efs*15	ENST00000268489	NM_006885.3	1899	gGa/ga	9/10	1	2	FACETS	0.326	0.277	0.381	0.326	0.277	0.381	SUBCLONAL	1	TRUE	1	0.357623161899303	2		658	908	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210796	36210796	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1342	102	999	1	ENST00000222270.7:c.547G>T	p.Glu183Ter	p.E183*	ENST00000222270	NM_014727.1	183	Gag/Tag	3/37	1	2	FACETS	0.395	0.352	0.441	0.395	0.352	0.441	SUBCLONAL	1	TRUE	1	0.357623161899303	2		1000	1444	SUCCESS
NF2	4771	MSKCC	GRCh37	22	29999991	29999991	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	27	361	0	ENST00000338641.4:c.4G>A	p.Ala2Thr	p.A2T	ENST00000338641	NM_000268.3	2	Gcc/Acc	1/16	1	2	FACETS	0.361	0.287	0.446	0.361	0.287	0.446	SUBCLONAL	1	TRUE	1	0.357623161899303	2		361	418	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665538	138665538	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	71	546	0	ENST00000330315.3:c.27G>T	p.Glu9Asp	p.E9D	ENST00000330315	NM_023067.3	9	gaG/gaT	1/1	1	2	FACETS	0.484	0.422	0.552	0.484	0.422	0.552	SUBCLONAL	1	TRUE	1	0.357623161899303	2		546	820	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607228	189607228	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	59	762	0	ENST00000264731.3:c.1607A>G	p.His536Arg	p.H536R	ENST00000264731	NM_003722.4	536	cAc/cGc	12/14	1	2	FACETS	0.343	0.294	0.397	0.343	0.294	0.397	SUBCLONAL	1	TRUE	1	0.357623161899303	2		762	961	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821202	32821202	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41540013	NA	P-0039452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	88	1004	0	ENST00000354258.4:c.392G>A	p.Gly131Glu	p.G131E	ENST00000354258	NM_000593.5	131	gGg/gAg	1/11	1	2	FACETS	0.394	0.348	0.444	0.394	0.348	0.444	SUBCLONAL	1	TRUE	1	0.357623161899303	2		1004	1249	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117874146	117874146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	34	390	1	ENST00000297338.2:c.308C>T	p.Ala103Val	p.A103V	ENST00000297338	NM_006265.2	103	gCa/gTa	4/14	1	2	FACETS	0.456	0.372	0.55	0.456	0.372	0.55	SUBCLONAL	1	TRUE	1	0.357623161899303	2		391	417	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0039574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	137	407	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.885	0.81	0.963	0.885	0.81	0.963	CLONAL	1	TRUE	1	0.618977607389247	2		407	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	255	564	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.5827591514547	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.618977607389247	1		564	524	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249348	110249348	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	801	868	0	ENST00000374672.4:c.1225A>C	p.Lys409Gln	p.K409Q	ENST00000374672	NM_004235.4	409	Aag/Cag	4/5	0.556440598571051	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.618977607389247	3		868	1636	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849586	68849586	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	294	662	0	ENST00000261769.5:c.1489G>T	p.Glu497Ter	p.E497*	ENST00000261769	NM_004360.3	497	Gag/Tag	10/16	0.51024141926958	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.618977607389247	1		662	627	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879888	37879888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	329	768	0	ENST00000269571.5:c.2183C>T	p.Ser728Phe	p.S728F	ENST00000269571		728	tCt/tTt	18/27	0.609189372269157	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.618977607389247	1		768	708	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133883	55133883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	136	373	0	ENST00000257290.5:c.1096G>A	p.Asp366Asn	p.D366N	ENST00000257290	NM_006206.4	366	Gat/Aat	7/23	1	2	FACETS	0.947	0.868	1	0.947	0.868	1	CLONAL	1	TRUE	1	0.618977607389247	2		373	464	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937038	76937038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1557136793	NA	P-0039574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	55	331	0	ENST00000373344.5:c.3710C>T	p.Ser1237Leu	p.S1237L	ENST00000373344	NM_000489.3	1237	tCa/tTa	9/35	1	2	FACETS	0.386	0.331	0.447	0.386	0.331	0.447	SUBCLONAL	1	TRUE	1	0.618977607389247	2		331	460	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114116	115114117	+	splice_donor_variant	Splice_Site	INS	-	-	C	novel	NA	P-0039574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	194	544	0	ENST00000257566.3:c.1099+1dup		p.X367_splice	ENST00000257566	NM_016569.3	367			NA	2	FACETS	0.979	0.911	1			1	INDETERMINATE	1	TRUE	NA	0.618977607389247	2		544	640	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77043786	77043786	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	233	589	0	ENST00000356341.3:c.1540G>C	p.Glu514Gln	p.E514Q	ENST00000356341	NM_002576.4	514	Gag/Cag	14/15	0.379159205319136	4	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.618977607389247	4		589	996	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202721	108202721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758128730	NA	P-0039574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	141	389	0	ENST00000278616.4:c.7745G>A	p.Arg2582Lys	p.R2582K	ENST00000278616	NM_000051.3	2582	aGa/aAa	52/63	1	2	FACETS	0.915	0.839	0.993	0.915	0.839	0.993	CLONAL	1	TRUE	1	0.618977607389247	2		389	498	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434226	49434226	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371053017	NA	P-0039574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	418	918	2	ENST00000301067.7:c.7327C>T	p.Arg2443Cys	p.R2443C	ENST00000301067	NM_003482.3	2443	Cgc/Tgc	31/54	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.618977607389247	2		920	1260	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030338	49030338	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0039574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	102	241	0	ENST00000267163.4:c.1815-2A>C		p.X605_splice	ENST00000267163	NM_000321.2	605			1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.618977607389247	2		241	320	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900341	3900341	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	292	690	0	ENST00000262367.5:c.755G>T	p.Gly252Val	p.G252V	ENST00000262367	NM_004380.2	252	gGt/gTt	2/31	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.618977607389247	2		690	926	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348650	89348650	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	295	787	0	ENST00000301030.4:c.4300G>T	p.Glu1434Ter	p.E1434*	ENST00000301030	NM_001256183.1	1434	Gag/Tag	9/13	0.618977607389247	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.618977607389247	1		787	648	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879654	37879654	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	275	720	0	ENST00000269571.5:c.2029C>G	p.Arg677Gly	p.R677G	ENST00000269571		677	Cga/Gga	17/27	0.609189372269157	1	FACETS	0.953	0.901	1	0.953	0.901	1	CLONAL	1	TRUE	0	0.618977607389247	1		720	644	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416370	29416370	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	330	761	1	ENST00000389048.3:c.4583A>T	p.His1528Leu	p.H1528L	ENST00000389048	NM_004304.4	1528	cAc/cTc	29/29	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.618977607389247	2		762	1035	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046305	128046305	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	236	495	0	ENST00000285398.2:c.958C>G	p.Gln320Glu	p.Q320E	ENST00000285398	NM_000122.1	320	Cag/Gag	7/15	1	2	FACETS	0.998	0.935	1	0.998	0.935	1	CLONAL	1	TRUE	1	0.618977607389247	2		495	764	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172292	38172292	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0039574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	147	355	0	ENST00000317025.8:c.2116-1G>A		p.X706_splice	ENST00000317025	NM_023034.1	706			1	2	FACETS	0.971	0.893	1	0.971	0.893	1	CLONAL	1	TRUE	1	0.618977607389247	2		355	489	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229514	98229514	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	36	432	0	ENST00000331920.6:c.2444T>G	p.Ile815Ser	p.I815S	ENST00000331920	NM_000264.3	815	aTc/aGc	15/24	1	2	FACETS	0.18	0.147	0.217	0.18	0.147	0.217	SUBCLONAL	1	TRUE	1	0.618977607389247	2		432	646	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141060	55141060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	55	426	0	ENST00000257290.5:c.1706G>A	p.Gly569Glu	p.G569E	ENST00000257290	NM_006206.4	569	gGa/gAa	12/23	0.552003319823495	3	FACETS	0.451	0.386	0.523	0.225	0.193	0.262	SUBCLONAL	1	TRUE	1	0.553065077704756	3		426	563	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101118	4101118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769471250	NA	P-0039721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	12	395	3	ENST00000262948.5:c.604G>A	p.Val202Met	p.V202M	ENST00000262948	NM_030662.3	202	Gtg/Atg	6/11	0.263240329284446	4	FACETS	0.286	0.201	0.391	0.095	0.067	0.131	INDETERMINATE	1	TRUE	1	0.616484660800383	4		398	220	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90960111	90960111	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	32	289	0	ENST00000265433.3:c.1855G>T	p.Glu619Ter	p.E619*	ENST00000265433	NM_002485.4	619	Gaa/Taa	12/16	0.616484660800383	5	FACETS	0.88	0.719	1	0.293	0.239	0.354	CLONAL	1	TRUE	2	0.616484660800383	5		289	227	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624275	89624276	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	113	491	0	ENST00000371953.3:c.51dup	p.Glu18ArgfsTer26	p.E18Rfs*26	ENST00000371953	NM_000314.4	17	caa/cAaa	1/9	0.576850200909031	2	FACETS	0.837	0.772	0.902	0.837	0.772	0.902	CLONAL	2	TRUE	0	0.616484660800383	2		491	219	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578405	7578406	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0039721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	165	648	0	ENST00000269305.4:c.524_525delinsAT	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGC/cAT	5/11	0.547523130799383	2	FACETS	0.949	0.892	1	0.949	0.892	1	CLONAL	2	TRUE	0	0.616484660800383	2		648	282	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	54	300	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.285283200359643	2		300	284	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652129	36652136	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGCCGG	GAGGCCGG	-	novel	NA	P-0039725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	151	614	0	ENST00000244741.5:c.253_260del	p.Gly85Ter	p.G85*	ENST00000244741	NM_000389.4	84	cGAGGCCGG/c	2/3	0.118749014068037	3	FACETS	1	0.98	1	0.623	0.569	0.68	INDETERMINATE	1	TRUE	1	0.285283200359643	3		614	971	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0039725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	40	334	0	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.285283200359643	2		334	244	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214607	133214607	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1337287611	NA	P-0039725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	97	488	0	ENST00000320574.5:c.5671A>G	p.Thr1891Ala	p.T1891A	ENST00000320574	NM_006231.2	1891	Acc/Gcc	41/49	1	2	FACETS	0.99	0.883	1	0.99	0.883	1	CLONAL	1	TRUE	1	0.285283200359643	2		488	687	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408924	41408924	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778928297	NA	P-0039725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	89	470	0	ENST00000373198.4:c.502G>T	p.Val168Phe	p.V168F	ENST00000373198	NM_133170.3	168	Gtc/Ttc	4/32	1	2	FACETS	0.937	0.831	1	0.937	0.831	1	CLONAL	1	TRUE	1	0.285283200359643	2		470	666	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268741	46268741	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	143	602	0	ENST00000371998.3:c.3026C>A	p.Ser1009Tyr	p.S1009Y	ENST00000371998		1009	tCc/tAc	16/23	1	2	FACETS	0.99	0.901	1	0.99	0.901	1	CLONAL	1	TRUE	1	0.285283200359643	2		602	1013	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121323	29121323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	111	749	0	ENST00000328354.6:c.352G>A	p.Asp118Asn	p.D118N	ENST00000328354	NM_007194.3	118	Gac/Aac	3/15	1	2	FACETS	0.904	0.812	1	0.904	0.812	1	CLONAL	1	TRUE	1	0.285283200359643	2		749	861	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645036	86645037	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0039725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	41	396	0	ENST00000274376.6:c.1109_1110insTA	p.Gln370HisfsTer8	p.Q370Hfs*8	ENST00000274376	NM_002890.2	370	caa/cATaa	8/25	1	2	FACETS	0.824	0.688	0.973	0.824	0.688	0.973	CLONAL	1	TRUE	1	0.285283200359643	2		396	349	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864506	162864506	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0039725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	40	393	0	ENST00000366898.1:c.8-1G>A		p.X3_splice	ENST00000366898	NM_004562.2	3			0.118749014068037	3	FACETS	0.482	0.399	0.574	0.241	0.199	0.287	INDETERMINATE	1	TRUE	1	0.285283200359643	3		393	665	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578204	7578204	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520001	NA	P-0039734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	332	689	0	ENST00000269305.4:c.645T>G	p.Ser215Arg	p.S215R	ENST00000269305	NM_001126112.2	215	agT/agG	6/11	0.737318123724961	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.737318123724961	1		689	544	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643619	38643619	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs140225135	NA	P-0039734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	30	505	0	ENST00000299084.4:c.1089A>G	p.Ile363Met	p.I363M	ENST00000299084	NM_152594.2	363	atA/atG	7/7	1	2	FACETS	0.156	0.125	0.191	0.156	0.125	0.191	SUBCLONAL	1	TRUE	1	0.737318123724961	2		505	521	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564274	86564298	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCCGAGGCCGGCAGTGAGGAG	GGCGGCCGAGGCCGGCAGTGAGGAG	-	novel	NA	P-0039734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	80	338	0	ENST00000274376.6:c.13_37del	p.Glu5ArgfsTer2	p.E5Rfs*2	ENST00000274376	NM_002890.2	2	atGGCGGCCGAGGCCGGCAGTGAGGAG/at	1/25	1	2	FACETS	0.795	0.708	0.885	0.795	0.708	0.885	SUBCLONAL	1	TRUE	1	0.737318123724961	2		338	273	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883190	37883723	+	splice_donor_variant,splice_acceptor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	CTGTCCAGACCCTGCCCCGGGCGCTGGGGGCATGGTCCACCACAGGCACCGCAGCTCATCTACCAGGGTCAGTGCCCTCGGTCACACTGTGTGGCTGTCTGCTTACCTCCCCCAACCCCGGTGGACTAGGGTCCCTTTCTCTGATGTTCCCTCAACTGTCACCTCTCAAGGAAACCCCATTATCCCTACAAAAAATTCTTACTGCCTTCCAACCCCTGTGACCCCATTCTCTCCACGGTGACTGTGTCATACCCCAAAGGTGACCTCTGTTTTTCTCCTGTGACCCTGTCACCTTCCATGGAGTCCCCATCCCAGATCCGTGAGTGACCCCCATCATGACTTTCTTTCTTGTCCCCAGAGTGGCGGTGGGGACCTGACACTAGGGCTGGAGCCCTCTGAAGAGGAGGCCCCCAGGTCTCCACTGGCACCCTCCGAAGGGGCTGGCTCCGATGTATTTGATGGTGACCTGGGAATGGGGGCAGCCAAGGGGCTGCAAAGCCTCCCCACACATGACCCCAGCCCTCTACAGCGGTA	CTGTCCAGACCCTGCCCCGGGCGCTGGGGGCATGGTCCACCACAGGCACCGCAGCTCATCTACCAGGGTCAGTGCCCTCGGTCACACTGTGTGGCTGTCTGCTTACCTCCCCCAACCCCGGTGGACTAGGGTCCCTTTCTCTGATGTTCCCTCAACTGTCACCTCTCAAGGAAACCCCATTATCCCTACAAAAAATTCTTACTGCCTTCCAACCCCTGTGACCCCATTCTCTCCACGGTGACTGTGTCATACCCCAAAGGTGACCTCTGTTTTTCTCCTGTGACCCTGTCACCTTCCATGGAGTCCCCATCCCAGATCCGTGAGTGACCCCCATCATGACTTTCTTTCTTGTCCCCAGAGTGGCGGTGGGGACCTGACACTAGGGCTGGAGCCCTCTGAAGAGGAGGCCCCCAGGTCTCCACTGGCACCCTCCGAAGGGGCTGGCTCCGATGTATTTGATGGTGACCTGGGAATGGGGGCAGCCAAGGGGCTGCAAAGCCTCCCCACACATGACCCCAGCCCTCTACAGCGGTA	-	novel	NA	P-0039734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	352	766	0	ENST00000269571.5:c.3094_3336del		p.X1032_splice	ENST00000269571		1032	ttCTGTCCAGACCCTGCCCCGGGCGCTGGGGGCATGGTCCACCACAGGCACCGCAGCTCATCTACCAGGGTCAGTGCCCTCGGTCACACTGTGTGGCTGTCTGCTTACCTCCCCCAACCCCGGTGGACTAGGGTCCCTTTCTCTGATGTTCCCTCAACTGTCACCTCTCAAGGAAACCCCATTATCCCTACAAAAAATTCTTACTGCCTTCCAACCCCTGTGACCCCATTCTCTCCACGGTGACTGTGTCATACCCCAAAGGTGACCTCTGTTTTTCTCCTGTGACCCTGTCACCTTCCATGGAGTCCCCATCCCAGATCCGTGAGTGACCCCCATCATGACTTTCTTTCTTGTCCCCAGAGTGGCGGTGGGGACCTGACACTAGGGCTGGAGCCCTCTGAAGAGGAGGCCCCCAGGTCTCCACTGGCACCCTCCGAAGGGGCTGGCTCCGATGTATTTGATGGTGACCTGGGAATGGGGGCAGCCAAGGGGCTGCAAAGCCTCCCCACACATGACCCCAGCCCTCTACAGCGGTAc/ttc	25-26/27	0.737318123724961	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.737318123724961	1		766	549	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416710	121416710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373180062	NA	P-0039757-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	63	757	0	ENST00000257555.6:c.139G>A	p.Gly47Arg	p.G47R	ENST00000257555		47	Ggg/Agg	1/10	0.160238163648642	2	FACETS	0.287	0.248	0.33	0.143	0.124	0.165	INDETERMINATE	1	TRUE	0	0.628144389474327	2		757	699	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934279	81934279	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039757-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	115	673	0	ENST00000359376.3:c.1256A>G	p.Lys419Arg	p.K419R	ENST00000359376	NM_002661.3	419	aAg/aGg	14/33	0.229447229553011	2	FACETS	0.469	0.422	0.518	0.234	0.211	0.259	INDETERMINATE	1	TRUE	0	0.628144389474327	2		673	781	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226566907	226566907	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039757-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	50	534	0	ENST00000366794.5:c.1681G>T	p.Asp561Tyr	p.D561Y	ENST00000366794	NM_001618.3	561	Gac/Tac	12/23	0.628144389474327	1	FACETS	0.189	0.16	0.221	0.189	0.16	0.221	SUBCLONAL	1	TRUE	0	0.628144389474327	1		534	577	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248823	133248823	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039757-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	141	545	0	ENST00000320574.5:c.1772A>T	p.Glu591Val	p.E591V	ENST00000320574	NM_006231.2	591	gAg/gTg	16/49	NA	2	FACETS	0.579	0.528	0.633			1	INDETERMINATE	1	TRUE	NA	0.628144389474327	2		545	775	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095014	11095014	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039757-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	165	834	0	ENST00000358026.2:c.187G>A	p.Gly63Arg	p.G63R	ENST00000358026	NM_001128849.1	63	Ggg/Agg	2/36	0.623628477831433	2	FACETS	0.74	0.681	0.801	0.37	0.34	0.401	SUBCLONAL	1	TRUE	0	0.628144389474327	2		834	710	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505447	25505447	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1315534478	NA	P-0039757-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	42	531	0	ENST00000264709.3:c.311G>A	p.Gly104Glu	p.G104E	ENST00000264709	NM_175629.2	104	gGg/gAg	4/23	1	2	FACETS	0.235	0.196	0.279	0.235	0.196	0.279	SUBCLONAL	1	TRUE	1	0.628144389474327	2		531	568	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178331	56178332	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0039757-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	33	286	0	ENST00000399503.3:c.3305_3306dup	p.Asn1103ValfsTer15	p.N1103Vfs*15	ENST00000399503	NM_005921.1	1102	agt/aGTgt	14/20	0.594956817630589	2	FACETS	0.307	0.25	0.371	0.154	0.125	0.186	SUBCLONAL	1	TRUE	0	0.628144389474327	2		286	342	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	192	425	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.593317231148835	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	1	0.593317231148835	3		426	408	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0039858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	462	732	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.588651109142374	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.593317231148835	2		732	749	SUCCESS
APC	324	MSKCC	GRCh37	5	112175760	112175761	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs398123122	NA	P-0039858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	73	310	0	ENST00000257430.4:c.4473dup	p.Ala1492CysfsTer22	p.A1492Cfs*22	ENST00000257430	NM_000038.5	1490	cat/caTt	16/16	0.143883762920478	0	FACETS	0.599	0.537	0.662			1	INDETERMINATE	1	TRUE	0	0.593317231148835	0		310	167	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450103	32450103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	186	710	1	ENST00000332351.3:c.709G>A	p.Ala237Thr	p.A237T	ENST00000332351	NM_024426.4	237	Gcg/Acg	2/10	0.593317231148835	3	FACETS	1	0.95	1	0.517	0.478	0.557	CLONAL	1	TRUE	1	0.593317231148835	3		711	786	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282215	38282215	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	138	551	3	ENST00000425967.3:c.841C>T	p.Arg281Trp	p.R281W	ENST00000425967	NM_001174067.1	281	Cgg/Tgg	8/19	0.593317231148835	3	FACETS	0.638	0.58	0.699	0.319	0.29	0.35	SUBCLONAL	1	TRUE	1	0.593317231148835	3		554	945	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873078	136873078	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	88	440	0	ENST00000241393.3:c.420C>G	p.His140Gln	p.H140Q	ENST00000241393	NM_003467.2	140	caC/caG	2/2	0.593317231148835	3	FACETS	0.86	0.766	0.96	0.43	0.383	0.48	CLONAL	1	TRUE	1	0.593317231148835	3		440	447	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37055952	37055952	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	66	372	0	ENST00000231790.2:c.707A>G	p.Lys236Arg	p.K236R	ENST00000231790	NM_000249.3	236	aAa/aGa	9/19	0.168397510594913	3	FACETS	1	0.953	1	0.589	0.517	0.664	INDETERMINATE	1	TRUE	1	0.593317231148835	3		372	245	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0039931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	132	546	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	0.762	0.692	0.835	0.762	0.692	0.835	SUBCLONAL	1	TRUE	1	0.469701478175548	2		546	738	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830711	72830712	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCAACTCAAAGCCAAAGTTCT	novel	NA	P-0039931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	128	734	1	ENST00000268489.5:c.5849_5869dup	p.Glu1950_Leu1956dup	p.E1950_L1956dup	ENST00000268489	NM_006885.3	1950	gtc/gAGAACTTTGGCTTTGAGTTGGtc	9/10	1	2	FACETS	0.704	0.638	0.773	0.704	0.638	0.773	SUBCLONAL	1	TRUE	1	0.469701478175548	2		735	774	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910569	29910569	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	94	525	0	ENST00000376809.5:c.109T>G	p.Ser37Ala	p.S37A	ENST00000376809	NM_002116.7	37	Tcc/Gcc	2/8	1	2	FACETS	0.702	0.626	0.783	0.702	0.626	0.783	SUBCLONAL	1	TRUE	1	0.469701478175548	2		525	570	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0039966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	79	435	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.736	0.648	0.832	0.736	0.648	0.832	SUBCLONAL	1	TRUE	1	0.327569267427153	2		435	655	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	147	348	0	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	0.289055725169285	3	FACETS	0.997	0.916	1	0.997	0.916	1	CLONAL	2	TRUE	1	0.327569267427153	3		348	524	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987204	36987204	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	50	576	0	ENST00000354822.5:c.485C>T	p.Ala162Val	p.A162V	ENST00000354822	NM_001079668.2	162	gCg/gTg	3/3	1	2	FACETS	0.374	0.316	0.437	0.374	0.316	0.437	SUBCLONAL	1	TRUE	1	0.327569267427153	2		576	817	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46738405	46738405	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	111	476	0	ENST00000371975.4:c.1306G>T	p.Glu436Ter	p.E436*	ENST00000371975	NM_003579.3	436	Gaa/Taa	12/18	1	2	FACETS	0.881	0.792	0.975	0.881	0.792	0.975	CLONAL	1	TRUE	1	0.327569267427153	2		476	769	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852740	63852740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	106	457	0	ENST00000279873.7:c.3518C>T	p.Ala1173Val	p.A1173V	ENST00000279873	NM_032199.2	1173	gCc/gTc	10/10	1	2	FACETS	0.898	0.805	0.996	0.898	0.805	0.996	CLONAL	1	TRUE	1	0.327569267427153	2		457	721	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946269	81946269	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	114	695	0	ENST00000359376.3:c.2002G>T	p.Ala668Ser	p.A668S	ENST00000359376	NM_002661.3	668	Gcc/Tcc	19/33	0.261832435203739	2	FACETS	0.715	0.642	0.791	0.357	0.321	0.396	SUBCLONAL	1	TRUE	0	0.327569267427153	2		695	974	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578194	7578195	+	inframe_insertion	In_Frame_Ins	INS	-	-	CACCAC	novel	NA	P-0039966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	233	677	0	ENST00000269305.4:c.649_654dup	p.Val217_Val218dup	p.V217_V218dup	ENST00000269305	NM_001126112.2	217	-/GTGGTG	6/11	0.261832435203739	2	FACETS	1	0.991	1	0.699	0.652	0.747	CLONAL	1	TRUE	0	0.327569267427153	2		677	1018	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584542	48584542	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	109	466	0	ENST00000342988.3:c.715C>T	p.Gln239Ter	p.Q239*	ENST00000342988	NM_005359.5	239	Cag/Tag	6/12	0.327569267427153	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.327569267427153	1		466	539	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958048	54958048	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	98	251	0	ENST00000312783.6:c.559C>A	p.His187Asn	p.H187N	ENST00000312783	NM_198436.1	187	Cac/Aac	6/10	0.328296617958281	5	FACETS	0.882	0.79	0.979	0.441	0.395	0.49	CLONAL	2	TRUE	1	0.327569267427153	5		251	506	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275252	142275252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	72	391	0	ENST00000350721.4:c.2051C>T	p.Ser684Phe	p.S684F	ENST00000350721	NM_001184.3	684	tCt/tTt	9/47	1	2	FACETS	0.778	0.68	0.883	0.778	0.68	0.883	SUBCLONAL	1	TRUE	1	0.327569267427153	2		391	565	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161744	56161744	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1406908752	NA	P-0039966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	41	415	1	ENST00000399503.3:c.1241G>A	p.Arg414His	p.R414H	ENST00000399503	NM_005921.1	414	cGc/cAc	6/20	0.289055725169285	3	FACETS	0.379	0.315	0.452	0.19	0.157	0.226	SUBCLONAL	1	TRUE	1	0.327569267427153	3		416	768	SUCCESS
APC	324	MSKCC	GRCh37	5	112174160	112174160	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	55	379	0	ENST00000257430.4:c.2870del	p.Lys957ArgfsTer8	p.K957Rfs*8	ENST00000257430	NM_000038.5	957	Aag/ag	16/16	0.289055725169285	3	FACETS	0.698	0.597	0.808	0.349	0.298	0.404	SUBCLONAL	1	TRUE	1	0.327569267427153	3		379	560	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760441	133760441	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	151	681	0	ENST00000318560.5:c.2764G>T	p.Ala922Ser	p.A922S	ENST00000318560	NM_005157.4	922	Gcg/Tcg	11/11	0.30609516571341	2	FACETS	1	0.949	1	0.526	0.481	0.574	CLONAL	1	TRUE	0	0.327569267427153	2		681	876	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317467	1317467	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs778213444	NA	P-0039966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	100	699	0	ENST00000400841.2:c.598C>G	p.Pro200Ala	p.P200A	ENST00000400841		200	Cca/Gca	5/6	0.272382041264559	2	FACETS	0.561	0.499	0.626			1	SUBCLONAL	1	TRUE	NA	0.327569267427153	2		699	1089	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24135758	24135758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	202	528	0	ENST00000263121.7:c.245C>T	p.Thr82Met	p.T82M	ENST00000263121	NM_003073.3	82	aCg/aTg	3/9	0.415745482210428	1	FACETS	0.969	0.902	1	0.969	0.902	1	CLONAL	1	TRUE	0	0.462077183808432	1		528	694	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421039	49421039	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123721	NA	P-0039981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	171	518	1	ENST00000301067.7:c.14710C>T	p.Arg4904Ter	p.R4904*	ENST00000301067	NM_003482.3	4904	Cga/Tga	48/54	0.462077183808432	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.462077183808432	1		519	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578548	7578553	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GGGAGT	GGGAGT	-	novel	NA	P-0039981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	265	784	1	ENST00000269305.4:c.377_382del	p.Tyr126_Pro128delinsSer	p.Y126_P128delinsS	ENST00000269305	NM_001126112.2	126	tACTCCCct/tct	5/11	0.462077183808432	1	FACETS	0.983	0.924	1	0.983	0.924	1	CLONAL	1	TRUE	0	0.462077183808432	1		785	897	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222748	5222748	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	211	710	0	ENST00000357368.4:c.3055G>T	p.Gly1019Cys	p.G1019C	ENST00000357368	NM_002850.3	1019	Ggc/Tgc	18/38	0.415745482210428	1	FACETS	0.823	0.766	0.883	0.823	0.766	0.883	CLONAL	1	TRUE	0	0.462077183808432	1		710	853	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245359	153245359	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	141	553	0	ENST00000281708.4:c.1832del	p.Gly611AspfsTer17	p.G611Dfs*17	ENST00000281708	NM_033632.3	611	gGa/ga	11/12	0.251424312561858	1	FACETS	0.892	0.817	0.97	0.892	0.817	0.97	INDETERMINATE	1	TRUE	0	0.462077183808432	1		553	526	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0040026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	78	210	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.309335712143919	2		210	444	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0040026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	163	435	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.309335712143919	3	FACETS	0.969	0.893	1	0.969	0.893	1	CLONAL	2	TRUE	1	0.309335712143919	3		435	628	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0040026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	92	260	3	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.956	0.851	1	0.956	0.851	1	CLONAL	1	TRUE	1	0.309335712143919	2		263	622	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0040026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	114	534	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.978	0.881	1	0.978	0.881	1	CLONAL	1	TRUE	1	0.309335712143919	2		535	754	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0040026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	433	857	2	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	0.309335712143919	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.309335712143919	3		859	1502	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0040026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	53	160	1	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	0.976	0.836	1	0.976	0.836	1	CLONAL	1	TRUE	1	0.309335712143919	2		161	351	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119884	70119884	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	169	673	1	ENST00000245479.2:c.886C>T	p.Gln296Ter	p.Q296*	ENST00000245479	NM_000346.3	296	Cag/Tag	3/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.309335712143919	2		674	948	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368208	45368208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	93	341	0	ENST00000262160.6:c.1394G>A	p.Ser465Asn	p.S465N	ENST00000262160	NM_005901.5	465	aGc/aAc	11/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.309335712143919	2		341	519	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50143283	50143283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1212916232	NA	P-0040026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	67	265	0	ENST00000246792.3:c.73C>T	p.Pro25Ser	p.P25S	ENST00000246792	NM_006270.3	25	Ccg/Tcg	1/6	1	2	FACETS	0.973	0.849	1	0.973	0.849	1	CLONAL	1	TRUE	1	0.309335712143919	2		265	445	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474129	29474129	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	99	560	0	ENST00000389048.3:c.2046T>A	p.His682Gln	p.H682Q	ENST00000389048	NM_004304.4	682	caT/caA	12/29	1	2	FACETS	0.951	0.85	1	0.951	0.85	1	CLONAL	1	TRUE	1	0.309335712143919	2		560	673	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723791	49723791	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	12	15	0	ENST00000449682.2:c.971A>G	p.Gln324Arg	p.Q324R	ENST00000449682	NM_020998.3	324	cAa/cGa	8/18	1	2	FACETS	1	0.802	1	1	0.916	1	CLONAL	2	TRUE	1	0.309335712143919	2		15	35	SUCCESS
APC	324	MSKCC	GRCh37	5	112175358	112175358	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	62	259	0	ENST00000257430.4:c.4067C>A	p.Ser1356Ter	p.S1356*	ENST00000257430	NM_000038.5	1356	tCa/tAa	16/16	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.309335712143919	2		259	350	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338684	70338698	+	inframe_deletion	In_Frame_Del	DEL	AGGACCCCAAACAGA	AGGACCCCAAACAGA	-	novel	NA	P-0040026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	113	357	0	ENST00000374080.3:c.84_98del	p.Asp28_Lys32del	p.D28_K32del	ENST00000374080		27	cAGGACCCCAAACAGAag/cag	1/45	1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.309335712143919	1		357	466	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0040030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	103	542	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.983	0.88	1	0.983	0.88	1	CLONAL	1	TRUE	1	0.27	2		542	776	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0040030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	67	425	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.24819204633172	3	FACETS	1	0.967	1	0.682	0.595	0.775	CLONAL	1	TRUE	1	0.27	3		426	413	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0040030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	46	123	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.744	0.627	0.873	0.744	0.627	0.873	SUBCLONAL	1	TRUE	1	0.27	2		123	458	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41276053	41276053	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs80357406	NA	P-0040030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	44	523	0	ENST00000357654.3:c.61A>G	p.Ile21Val	p.I21V	ENST00000357654	NM_007294.3	21	Atc/Gtc	2/23	1	2	FACETS	0.817	0.686	0.961	0.817	0.686	0.961	CLONAL	1	TRUE	1	0.27	2		523	399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577112	7577112	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1131691029	NA	P-0040044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	308	733	0	ENST00000269305.4:c.826G>C	p.Ala276Pro	p.A276P	ENST00000269305	NM_001126112.2	276	Gcc/Ccc	8/11	0.581209856507288	2	FACETS	0.878	0.838	0.919	0.878	0.838	0.919	CLONAL	2	TRUE	0	0.613134677426867	2		733	572	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508177	38508177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749735817	NA	P-0040044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	52	463	0	ENST00000254066.5:c.485G>A	p.Arg162Gln	p.R162Q	ENST00000254066	NM_000964.3	162	cGa/cAa	5/9	0.581209856507288	2	FACETS	0.527	0.451	0.609	0.263	0.225	0.305	SUBCLONAL	1	TRUE	0	0.613134677426867	2		463	322	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28607281	28607281	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756166147	NA	P-0040044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	119	570	2	ENST00000253063.3:c.1411G>A	p.Ala471Thr	p.A471T	ENST00000253063	NM_031459.4	471	Gcc/Acc	10/10	NA	2	FACETS	0.874	0.795	0.957			1	INDETERMINATE	1	TRUE	NA	0.613134677426867	2		572	444	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3795286	3795286	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	59	431	0	ENST00000262367.5:c.3906G>A	p.Trp1302Ter	p.W1302*	ENST00000262367	NM_004380.2	1302	tgG/tgA	22/31	1	2	FACETS	0.661	0.573	0.755	0.661	0.573	0.755	SUBCLONAL	1	TRUE	1	0.613134677426867	2		431	291	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	74	300	0				ENST00000310581	NM_198253.2	-/1132			0.261214226675325	8	FACETS	1	0.962	1			1	CLONAL	2	TRUE	NA	0.261214226675325	8		300	408	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0040109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	26	210	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.261214226675325	3	FACETS	0.421	0.332	0.523	0.21	0.166	0.262	SUBCLONAL	1	TRUE	1	0.261214226675325	3		210	535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0040109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	240	609	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.219856206294691	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.261214226675325	2		610	810	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917673	178917673	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	26	186	0	ENST00000263967.3:c.548A>C	p.Asn183Thr	p.N183T	ENST00000263967	NM_006218.2	183	aAt/aCt	3/21	0.261214226675325	3	FACETS	0.824	0.655	1			1	CLONAL	1	TRUE	NA	0.261214226675325	3		186	273	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121744	108121744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	123	429	1	ENST00000278616.4:c.1552G>A	p.Glu518Lys	p.E518K	ENST00000278616	NM_000051.3	518	Gag/Aag	10/63	0.219856206294691	2	FACETS	0.829	0.752	0.909	0.829	0.752	0.909	CLONAL	2	TRUE	0	0.261214226675325	2		430	568	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942124	81942125	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	34	568	0	ENST00000359376.3:c.1667dup	p.Lys557GlnfsTer16	p.K557Qfs*16	ENST00000359376	NM_002661.3	554	acg/acGg	17/33	1	2	FACETS	0.415	0.338	0.502	0.415	0.338	0.502	SUBCLONAL	1	TRUE	1	0.261214226675325	2		568	627	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682152	37682152	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	74	411	0	ENST00000447079.4:c.3343G>A	p.Glu1115Lys	p.E1115K	ENST00000447079	NM_015083.1	1115	Gaa/Aaa	13/14	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.261214226675325	2		411	500	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259130	16259130	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1017059236	NA	P-0040109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	86	570	1	ENST00000375759.3:c.6395G>A	p.Gly2132Asp	p.G2132D	ENST00000375759	NM_015001.2	2132	gGt/gAt	11/15	0.219856206294691	2	FACETS	1	0.935	1	0.541	0.479	0.607	CLONAL	1	TRUE	0	0.261214226675325	2		571	609	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670516	246670516	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	39	344	0	ENST00000388985.4:c.4G>C	p.Glu2Gln	p.E2Q	ENST00000388985		2	Gag/Cag	1/12	1	2	FACETS	0.73	0.606	0.868	0.73	0.606	0.868	SUBCLONAL	1	TRUE	1	0.261214226675325	2		344	409	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209306	133209306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479792502	NA	P-0040109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	129	674	0	ENST00000320574.5:c.6080G>A	p.Arg2027Lys	p.R2027K	ENST00000320574	NM_006231.2	2027	aGg/aAg	44/49	NA	2	FACETS	0.775	0.705	0.849			1	INDETERMINATE	2	TRUE	NA	0.261214226675325	2		674	637	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991596	72991596	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	44	553	0	ENST00000268489.5:c.2449A>G	p.Arg817Gly	p.R817G	ENST00000268489	NM_006885.3	817	Agg/Ggg	2/10	1	2	FACETS	0.521	0.436	0.615	0.521	0.436	0.615	SUBCLONAL	1	TRUE	1	0.261214226675325	2		553	647	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049826	16049826	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	88	282	0	ENST00000268712.3:c.946G>T	p.Glu316Ter	p.E316*	ENST00000268712	NM_006311.3	316	Gag/Tag	10/46	1	2	FACETS	0.894	0.797	0.995	1	0.984	1	CLONAL	2	TRUE	1	0.261214226675325	2		282	377	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948753	55948753	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	70	383	0	ENST00000263923.4:c.3712A>G	p.Thr1238Ala	p.T1238A	ENST00000263923	NM_002253.2	1238	Aca/Gca	28/30	1	2	FACETS	0.969	0.846	1	0.969	0.846	1	CLONAL	1	TRUE	1	0.261214226675325	2		383	553	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539600	187539600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	55	283	0	ENST00000441802.2:c.8140G>A	p.Glu2714Lys	p.E2714K	ENST00000441802	NM_005245.3	2714	Gag/Aag	10/27	NA	2	FACETS	1	0.913	1			1	INDETERMINATE	1	TRUE	NA	0.261214226675325	2		283	387	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169020	32169020	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs778683490	NA	P-0040109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	49	684	0	ENST00000375023.3:c.4013T>A	p.Met1338Lys	p.M1338K	ENST00000375023	NM_004557.3	1338	aTg/aAg	22/30	0.261214226675325	3	FACETS	0.484	0.408	0.567	0.161	0.136	0.189	SUBCLONAL	1	TRUE	0	0.261214226675325	3		684	877	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0040145-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	33	629	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.376	0.306	0.456	0.376	0.306	0.456	SUBCLONAL	1	TRUE	1	0.36	2		630	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0040145-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	90	809	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	1	2	FACETS	0.81	0.72	0.907	0.81	0.72	0.907	CLONAL	1	TRUE	1	0.36	2		809	617	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736188	204736188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040145-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	30	452	0	ENST00000302823.3:c.545C>T	p.Thr182Ile	p.T182I	ENST00000302823	NM_005214.4	182	aCa/aTa	3/4	1	2	FACETS	0.335	0.269	0.41	0.335	0.269	0.41	SUBCLONAL	1	TRUE	1	0.36	2		452	497	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039906	47039906	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0040145-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	49	547	0	ENST00000377604.3:c.1248+1G>T		p.X416_splice	ENST00000377604	NM_001204468.1	416			0.174065083549975	1	FACETS	0.704	0.599	0.818	0.704	0.599	0.818	INDETERMINATE	1	TRUE	0	0.36	1		547	317	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127456	55127456	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040145-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	32	634	0	ENST00000257290.5:c.244G>T	p.Val82Leu	p.V82L	ENST00000257290	NM_006206.4	82	Gtg/Ttg	3/23	1	2	FACETS	0.324	0.262	0.395	0.324	0.262	0.395	SUBCLONAL	1	TRUE	1	0.36	2		634	548	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182170	11182170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040145-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	37	669	0	ENST00000361445.4:c.6676G>A	p.Ala2226Thr	p.A2226T	ENST00000361445	NM_004958.3	2226	Gct/Act	48/58	1	2	FACETS	0.468	0.386	0.56	0.468	0.386	0.56	SUBCLONAL	1	TRUE	1	0.36	2		669	439	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601945	43601945	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040145-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	33	938	0	ENST00000355710.3:c.989G>T	p.Arg330Leu	p.R330L	ENST00000355710	NM_020975.4	330	cGg/cTg	5/20	1	2	FACETS	0.346	0.281	0.419	0.346	0.281	0.419	SUBCLONAL	1	TRUE	1	0.36	2		938	530	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615191	43615191	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040145-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	33	834	0	ENST00000355710.3:c.2605A>G	p.Lys869Glu	p.K869E	ENST00000355710	NM_020975.4	869	Aag/Gag	14/20	1	2	FACETS	0.374	0.304	0.453	0.374	0.304	0.453	SUBCLONAL	1	TRUE	1	0.36	2		834	490	SUCCESS
EED	8726	MSKCC	GRCh37	11	85967433	85967433	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040145-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	42	296	0	ENST00000263360.6:c.431A>T	p.Asp144Val	p.D144V	ENST00000263360	NM_003797.3	144	gAt/gTt	5/12	0.3	3	FACETS	0.575	0.48	0.68	0.287	0.24	0.34	SUBCLONAL	1	TRUE	1	0.36	3		296	479	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50482326	50482326	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040145-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	25	319	0	ENST00000394963.4:c.678del	p.Thr227LeufsTer15	p.T227Lfs*15	ENST00000394963	NM_003076.4	226	gCc/gc	6/13	1	2	FACETS	0.364	0.286	0.453	0.364	0.286	0.453	SUBCLONAL	1	TRUE	1	0.36	2		319	382	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569946	95569946	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040145-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	71	746	0	ENST00000393063.1:c.3787G>T	p.Gly1263Cys	p.G1263C	ENST00000393063	NM_030621.3	1263	Ggt/Tgt	22/28	0.15984709052525	3	FACETS	0.715	0.624	0.813	0.357	0.312	0.407	INDETERMINATE	1	TRUE	1	0.36	3		746	651	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239907	105239907	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040145-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	55	822	0	ENST00000349310.3:c.713A>G	p.His238Arg	p.H238R	ENST00000349310	NM_001014432.1	238	cAc/cGc	10/15	0.15984709052525	3	FACETS	0.714	0.611	0.826	0.357	0.305	0.413	INDETERMINATE	1	TRUE	1	0.36	3		822	505	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680731	88680731	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040145-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	60	645	0	ENST00000360948.2:c.526G>T	p.Glu176Ter	p.E176*	ENST00000360948	NM_001012338.2	176	Gag/Tag	6/19	0.253260164371758	3	FACETS	0.809	0.698	0.93			1	CLONAL	1	TRUE	NA	0.36	3		645	486	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347087	89347087	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040145-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	67	904	0	ENST00000301030.4:c.5863G>T	p.Glu1955Ter	p.E1955*	ENST00000301030	NM_001256183.1	1955	Gag/Tag	9/13	1	2	FACETS	0.797	0.694	0.908	0.797	0.694	0.908	CLONAL	1	TRUE	1	0.36	2		904	467	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676137	29676137	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0040145-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	60	267	0	ENST00000356175.3:c.7127-1G>T		p.X2376_splice	ENST00000356175	NM_000267.3	2376			1	2	FACETS	0.911	0.788	1	0.911	0.788	1	CLONAL	1	TRUE	1	0.36	2		267	366	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096020	11096020	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs757214683	NA	P-0040145-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	56	844	0	ENST00000358026.2:c.294G>T	p.Met98Ile	p.M98I	ENST00000358026	NM_001128849.1	98	atG/atT	3/36	1	2	FACETS	0.652	0.559	0.753	0.652	0.559	0.753	SUBCLONAL	1	TRUE	1	0.36	2		844	477	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144161	11144161	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040145-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	36	799	0	ENST00000358026.2:c.3742C>T	p.Gln1248Ter	p.Q1248*	ENST00000358026	NM_001128849.1	1248	Cag/Tag	26/36	1	2	FACETS	0.469	0.386	0.563	0.469	0.386	0.563	SUBCLONAL	1	TRUE	1	0.36	2		799	426	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11172470	11172470	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040145-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	50	569	0	ENST00000358026.2:c.5018G>T	p.Gly1673Val	p.G1673V	ENST00000358026	NM_001128849.1	1673	gGa/gTa	36/36	1	2	FACETS	0.749	0.637	0.87	0.749	0.637	0.87	SUBCLONAL	1	TRUE	1	0.36	2		569	371	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952246	17952247	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0040145-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	26	680	0	ENST00000458235.1:c.1093_1094delinsAA	p.Pro365Lys	p.P365K	ENST00000458235	NM_000215.3	365	CCg/AAg	8/24	1	2	FACETS	0.367	0.29	0.455	0.367	0.29	0.455	SUBCLONAL	1	TRUE	1	0.36	2		680	394	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495261	212495261	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040145-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	34	414	0	ENST00000342788.4:c.2005C>A	p.Leu669Met	p.L669M	ENST00000342788	NM_005235.2	669	Ctg/Atg	17/28	1	2	FACETS	0.343	0.279	0.414	0.343	0.279	0.414	SUBCLONAL	1	TRUE	1	0.36	2		414	551	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514532	41514532	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040145-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	75	502	0	ENST00000373198.4:c.129del	p.Tyr43Ter	p.Y43*	ENST00000373198	NM_133170.3	43	taT/ta	2/32	0.15984709052525	3	FACETS	1	0.929	1	0.54	0.475	0.61	INDETERMINATE	1	TRUE	1	0.36	3		502	455	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114277	73114277	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040145-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	37	386	0	ENST00000356692.5:c.913G>T	p.Glu305Ter	p.E305*	ENST00000356692		305	Gaa/Taa	8/9	1	2	FACETS	0.441	0.363	0.528	0.441	0.363	0.528	SUBCLONAL	1	TRUE	1	0.36	2		386	466	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391124	89391125	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040145-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	38	648	0	ENST00000336596.2:c.1191dup	p.Asp398ArgfsTer7	p.D398Rfs*7	ENST00000336596	NM_005233.5	397	aca/acAa	5/17	1	2	FACETS	0.423	0.349	0.506	0.423	0.349	0.506	SUBCLONAL	1	TRUE	1	0.36	2		648	499	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748102	41748102	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs747713899	NA	P-0040145-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	38	672	0	ENST00000226382.2:c.667G>T	p.Ala223Ser	p.A223S	ENST00000226382	NM_003924.3	223	Gct/Tct	3/3	1	2	FACETS	0.668	0.554	0.794	0.668	0.554	0.794	SUBCLONAL	1	TRUE	1	0.36	2		672	316	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968663	55968663	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040145-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	47	489	0	ENST00000263923.4:c.2000C>A	p.Pro667His	p.P667H	ENST00000263923	NM_002253.2	667	cCc/cAc	14/30	1	2	FACETS	0.503	0.424	0.59	0.503	0.424	0.59	SUBCLONAL	1	TRUE	1	0.36	2		489	519	SUCCESS
ALB	213	MSKCC	GRCh37	4	74283264	74283264	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040145-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	27	302	0	ENST00000295897.4:c.1306A>T	p.Thr436Ser	p.T436S	ENST00000295897	NM_000477.5	436	Acc/Tcc	11/15	1	2	FACETS	0.364	0.289	0.45	0.364	0.289	0.45	SUBCLONAL	1	TRUE	1	0.36	2		302	412	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86667933	86667933	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0040145-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	45	341	0	ENST00000274376.6:c.1699-2A>T		p.X567_splice	ENST00000274376	NM_002890.2	567			1	2	FACETS	0.533	0.448	0.627	0.533	0.448	0.627	SUBCLONAL	1	TRUE	1	0.36	2		341	469	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020865	112020865	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040145-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	47	384	0	ENST00000368678.4:c.706G>C	p.Asp236His	p.D236H	ENST00000368678		236	Gat/Cat	8/13	1	2	FACETS	0.566	0.478	0.663	0.566	0.478	0.663	SUBCLONAL	1	TRUE	1	0.36	2		384	461	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376638	8376638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040145-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	52	477	0	ENST00000356435.5:c.4475C>T	p.Thr1492Ile	p.T1492I	ENST00000356435		1492	aCa/aTa	27/35	1	2	FACETS	0.649	0.554	0.754	0.649	0.554	0.754	SUBCLONAL	1	TRUE	1	0.36	2		477	445	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93629470	93629470	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040145-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	49	498	0	ENST00000375746.1:c.904G>T	p.Gly302Cys	p.G302C	ENST00000375746	NM_001174167.1	302	Ggc/Tgc	7/14	1	2	FACETS	0.791	0.673	0.92	0.791	0.673	0.92	CLONAL	1	TRUE	1	0.36	2		498	344	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875949	76875949	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040145-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	14	200	0	ENST00000373344.5:c.5186C>A	p.Ser1729Tyr	p.S1729Y	ENST00000373344	NM_000489.3	1729	tCt/tAt	20/35	1	2	FACETS	0.344	0.249	0.46	0.344	0.249	0.46	SUBCLONAL	1	TRUE	1	0.36	2		200	226	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	11	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.37	0.254	0.515	0.37	0.254	0.515	SUBCLONAL	1	TRUE	1	0.14	2		326	425	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0040179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	33	491	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.956	0.778	1	0.956	0.778	1	CLONAL	1	TRUE	1	0.14	2		492	493	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0040179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	18	196	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.733	0.551	0.948	0.733	0.551	0.948	CLONAL	1	TRUE	1	0.14	2		196	351	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239419	105239419	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	49	426	0	ENST00000349310.3:c.968A>G	p.Asp323Gly	p.D323G	ENST00000349310	NM_001014432.1	323	gAc/gGc	12/15	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.14	2		426	603	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0040209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	147	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.34840722568938	4	FACETS	1	0.986	1	0.703	0.644	0.764	CLONAL	1	TRUE	2	0.510268521683386	4		336	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0040209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	370	541	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.456571942236262	3	FACETS	1	0.992	1	0.78	0.745	0.815	CLONAL	2	TRUE	0	0.510268521683386	3		541	778	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782172	135782172	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	150	632	0	ENST00000298552.3:c.1384T>C	p.Phe462Leu	p.F462L	ENST00000298552	NM_001162426.1	462	Ttt/Ctt	14/23	0.510268521683386	3	FACETS	0.926	0.847	1	0.463	0.423	0.504	CLONAL	1	TRUE	1	0.510268521683386	3		632	797	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998507	100998507	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	93	606	0	ENST00000325455.5:c.1295C>G	p.Ser432Cys	p.S432C	ENST00000325455	NM_001202474.3	432	tCc/tGc	1/8	0.241728003094342	2	FACETS	0.482	0.428	0.54	0.241	0.214	0.27	INDETERMINATE	1	TRUE	0	0.510268521683386	2		606	756	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26978154	26978154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1445	109	798	2	ENST00000381527.3:c.1331G>A	p.Ser444Asn	p.S444N	ENST00000381527	NM_001260.1	444	aGc/aAc	13/13	0.510268521683386	5	FACETS	0.485	0.434	0.54	0.162	0.144	0.18	SUBCLONAL	1	TRUE	2	0.510268521683386	5		800	1554	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436158	56436158	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs866430107	NA	P-0040209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	500	779	0	ENST00000407977.2:c.979G>T	p.Gly327Ter	p.G327*	ENST00000407977		327	Gga/Tga	9/10	0.456571942236262	3	FACETS	0.9	0.868	0.932	0.9	0.868	0.932	CLONAL	3	TRUE	0	0.510268521683386	3		779	911	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637640	176637640	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs779427675	NA	P-0040209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	67	676	0	ENST00000439151.2:c.2240C>A	p.Thr747Lys	p.T747K	ENST00000439151	NM_022455.4	747	aCa/aAa	5/23	0.463551568492914	2	FACETS	0.455	0.395	0.52	0.228	0.197	0.26	SUBCLONAL	1	TRUE	0	0.510268521683386	2		676	577	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	81	330	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.838	0.741	0.94	0.838	0.741	0.94	CLONAL	1	TRUE	1	0.425090896216988	2		331	455	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482927	140482927	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	36	517	3	ENST00000288602.6:c.1208del	p.Pro403LeufsTer8	p.P403Lfs*8	ENST00000288602	NM_004333.4	403	cCt/ct	10/18	0.340432944137736	3	FACETS	0.29	0.237	0.349	0.145	0.118	0.175	SUBCLONAL	1	TRUE	1	0.425090896216988	3		520	708	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0040259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	55	340	1	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.367684342186581	1	FACETS	0.605	0.52	0.696	0.605	0.52	0.696	SUBCLONAL	1	TRUE	0	0.425090896216988	1		341	337	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702265	47702265	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750508	NA	P-0040259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	106	450	0	ENST00000233146.2:c.1861C>T	p.Arg621Ter	p.R621*	ENST00000233146	NM_000251.2	621	Cga/Tga	12/16	0.425090896216988	1	FACETS	0.922	0.832	1	0.922	0.832	1	CLONAL	1	TRUE	0	0.425090896216988	1		450	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0040259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1244	28	784	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	1	2	FACETS	0.104	0.082	0.129	0.104	0.082	0.129	SUBCLONAL	1	TRUE	1	0.425090896216988	2		784	1272	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039356	47039358	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0040259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	256	467	0	ENST00000377604.3:c.985_987del	p.Ser329del	p.S329del	ENST00000377604	NM_001204468.1	327	TCC/-	10/24	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.425090896216988	1		467	668	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925330	114925330	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368331428	NA	P-0040259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	120	546	0	ENST00000543371.1:c.1408G>A	p.Val470Ile	p.V470I	ENST00000543371	NM_001198531.1	470	Gtt/Att	14/14	1	2	FACETS	0.796	0.72	0.877	0.796	0.72	0.877	SUBCLONAL	1	TRUE	1	0.425090896216988	2		546	709	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482242	87482242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	139	651	0	ENST00000277120.3:c.1529C>T	p.Ser510Leu	p.S510L	ENST00000277120		510	tCg/tTg	14/19	1	2	FACETS	0.838	0.764	0.917	0.838	0.764	0.917	CLONAL	1	TRUE	1	0.425090896216988	2		651	780	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945648	206945648	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs570050304	NA	P-0040259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	146	542	0	ENST00000423557.1:c.133C>T	p.Arg45Ter	p.R45*	ENST00000423557	NM_000572.2	45	Cga/Tga	1/5	1	2	FACETS	0.867	0.792	0.946	0.867	0.792	0.946	CLONAL	1	TRUE	1	0.425090896216988	2		542	792	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822586	72822586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	166	653	4	ENST00000268489.5:c.9589del	p.Gln3197SerfsTer44	p.Q3197Sfs*44	ENST00000268489	NM_006885.3	3197	Cag/ag	10/10	1	2	FACETS	0.944	0.868	1	0.944	0.868	1	CLONAL	1	TRUE	1	0.425090896216988	2		657	827	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307280	65307283	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0040259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	95	361	0	ENST00000342505.4:c.2405_2408del	p.Lys802ArgfsTer11	p.K802Rfs*11	ENST00000342505	NM_002227.2	802	aAAGAg/ag	18/25	1	2	FACETS	0.84	0.75	0.935	0.84	0.75	0.935	CLONAL	1	TRUE	1	0.425090896216988	2		361	532	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464501	25464501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	214	809	1	ENST00000264709.3:c.2012C>T	p.Thr671Met	p.T671M	ENST00000264709	NM_175629.2	671	aCg/aTg	17/23	1	2	FACETS	0.946	0.879	1	0.946	0.879	1	CLONAL	1	TRUE	1	0.425090896216988	2		810	1064	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664448	138664448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	195	414	0	ENST00000330315.3:c.1117C>T	p.Arg373Cys	p.R373C	ENST00000330315	NM_023067.3	373	Cgc/Tgc	1/1	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.425090896216988	2		414	797	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326255	62326255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559104198	NA	P-0040259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1272	320	1209	0	ENST00000360203.5:c.3271G>A	p.Asp1091Asn	p.D1091N	ENST00000360203	NM_001283009.1	1091	Gac/Aac	32/35	1	2	FACETS	0.946	0.89	1	0.946	0.89	1	CLONAL	1	TRUE	1	0.425090896216988	2		1209	1592	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040015	180040015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564369853	NA	P-0040259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1424	248	984	1	ENST00000261937.6:c.3427G>A	p.Ala1143Thr	p.A1143T	ENST00000261937	NM_182925.4	1143	Gcc/Acc	25/30	0.363299220599621	3	FACETS	0.846	0.788	0.906	0.423	0.394	0.453	CLONAL	1	TRUE	1	0.425090896216988	3		985	1672	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841488	156841488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1023556915	NA	P-0040259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1284	39	908	1	ENST00000524377.1:c.791C>T	p.Thr264Met	p.T264M	ENST00000524377	NM_002529.3	264	aCg/aTg	7/17	1	2	FACETS	0.139	0.114	0.167	0.139	0.114	0.167	SUBCLONAL	1	TRUE	1	0.425090896216988	2		909	1323	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438262	49438262	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	448	677	0	ENST00000301067.7:c.5007del	p.Val1670SerfsTer52	p.V1670Sfs*52	ENST00000301067	NM_003482.3	1669	ccC/cc	20/54	0.220473051292887	4	FACETS	1	0.993	1	1	0.993	1	INDETERMINATE	2	TRUE	2	0.425090896216988	4		677	1258	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900080	151900081	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	38	268	0	ENST00000262189.6:c.4030dup	p.Ile1344AsnfsTer11	p.I1344Nfs*11	ENST00000262189	NM_170606.2	1344	ata/aAta	26/59	0.340432944137736	3	FACETS	1	0.911	1	0.57	0.477	0.672	CLONAL	1	TRUE	1	0.425090896216988	3		268	190	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248450	212248450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1480034665	NA	P-0040259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	98	357	1	ENST00000342788.4:c.3817C>T	p.Arg1273Trp	p.R1273W	ENST00000342788	NM_005235.2	1273	Cgg/Tgg	28/28	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.425090896216988	2		358	439	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259751	16259751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	171	509	3	ENST00000375759.3:c.7016G>A	p.Arg2339His	p.R2339H	ENST00000375759	NM_015001.2	2339	cGc/cAc	11/15	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.425090896216988	2		512	794	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446988	187446988	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139744042	NA	P-0040259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	250	835	1	ENST00000232014.4:c.1205G>A	p.Arg402His	p.R402H	ENST00000232014	NM_001130845.1	402	cGc/cAc	5/10	1	2	FACETS	0.969	0.905	1	0.969	0.905	1	CLONAL	1	TRUE	1	0.425090896216988	2		836	1214	SUCCESS
MET	4233	MSKCC	GRCh37	7	116399449	116399449	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	79	376	1	ENST00000397752.3:c.2269G>T	p.Gly757Trp	p.G757W	ENST00000397752	NM_000245.2	757	Ggg/Tgg	10/21	0.340432944137736	3	FACETS	0.91	0.803	1	0.455	0.401	0.513	CLONAL	1	TRUE	1	0.425090896216988	3		377	495	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17349147	17349150	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	-	rs794728950	NA	P-0040259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	171	661	1	ENST00000375499.3:c.718_721del	p.Leu240ThrfsTer7	p.L240Tfs*7	ENST00000375499	NM_003000.2	240	CTATac/ac	7/8	1	2	FACETS	0.818	0.752	0.886	0.818	0.752	0.886	CLONAL	1	TRUE	1	0.425090896216988	2		662	984	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28600589	28600589	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	212	702	0	ENST00000253063.3:c.940T>C	p.Cys314Arg	p.C314R	ENST00000253063	NM_031459.4	314	Tgc/Cgc	7/10	1	2	FACETS	0.907	0.842	0.974	0.907	0.842	0.974	CLONAL	1	TRUE	1	0.425090896216988	2		702	1100	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472143	472143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752787643	NA	P-0040259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	116	443	1	ENST00000399788.2:c.658C>T	p.Arg220Cys	p.R220C	ENST00000399788	NM_001042603.1	220	Cgt/Tgt	5/28	0.41985115798436	3	FACETS	0.872	0.786	0.963	0.436	0.393	0.482	CLONAL	1	TRUE	1	0.425090896216988	3		444	759	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145030	58145030	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	215	656	0	ENST00000257904.6:c.314A>G	p.Asp105Gly	p.D105G	ENST00000257904	NM_000075.3	105	gAc/gGc	3/8	0.220473051292887	4	FACETS	1	0.978	1	0.567	0.525	0.609	INDETERMINATE	1	TRUE	2	0.425090896216988	4		656	1272	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435106	110435106	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	290	664	0	ENST00000375856.3:c.3295G>T	p.Ala1099Ser	p.A1099S	ENST00000375856	NM_003749.2	1099	Gcc/Tcc	1/2	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.425090896216988	2		664	1223	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849473	89849473	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	210	698	0	ENST00000389301.3:c.1508A>G	p.Tyr503Cys	p.Y503C	ENST00000389301	NM_000135.2	503	tAc/tGc	16/43	1	2	FACETS	0.893	0.828	0.96	0.893	0.828	0.96	CLONAL	1	TRUE	1	0.425090896216988	2		698	1107	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909728	50909728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1213	298	967	0	ENST00000440232.2:c.1448G>A	p.Gly483Asp	p.G483D	ENST00000440232	NM_002691.3	483	gGc/gAc	12/27	1	2	FACETS	0.928	0.872	0.986	0.928	0.872	0.986	CLONAL	1	TRUE	1	0.425090896216988	2		967	1511	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27183547	27183547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	91	420	0	ENST00000380036.4:c.1121G>A	p.Gly374Asp	p.G374D	ENST00000380036	NM_000459.3	374	gGc/gAc	8/23	1	2	FACETS	0.843	0.751	0.94	0.843	0.751	0.94	CLONAL	1	TRUE	1	0.425090896216988	2		420	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578509	7578509	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519978	NA	P-0040266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1184	202	962	3	ENST00000269305.4:c.421T>C	p.Cys141Arg	p.C141R	ENST00000269305	NM_001126112.2	141	Tgc/Cgc	5/11	0.218253491388257	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.218253491388257	1		965	1386	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	GT	novel	NA	P-0040266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	63	283	5	ENST00000257430.4:c.4199delinsGT	p.Ser1400CysfsTer9	p.S1400Cfs*9	ENST00000257430	NM_000038.5	1400	tCg/tGTg	16/16	0.218253491388257	2	FACETS	1	0.963	1	0.668	0.58	0.764	CLONAL	1	TRUE	0	0.218253491388257	2		288	432	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0040289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	465	676	0	ENST00000346208.3:c.1221_1222del	p.Pro408LeufsTer98	p.P408Lfs*98	ENST00000346208		407	tCG/t	6/6	0.734713996830596	4	FACETS	0.984	0.944	1	0.984	0.944	1	CLONAL	2	TRUE	2	0.836053255425124	4		676	1038	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0040289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	544	919	0	ENST00000269305.4:c.376-1G>C		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.836053255425124	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.836053255425124	2		919	603	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99472837	99472838	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGTTGATCGTGGGAGGGTTGGTGATTATGCAGTACG	novel	NA	P-0040289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	265	645	0	ENST00000268035.6:c.2863_2864insAGTACGTGTTGATCGTGGGAGGGTTGGTGATTATGC	p.Met954_Leu955insGlnTyrValLeuIleValGlyGlyLeuValIleMet	p.M954_L955insQYVLIVGGLVIM	ENST00000268035	NM_000875.3	945	ctg/cTGTTGATCGTGGGAGGGTTGGTGATTATGCAGTACGtg	14/21	0.734713996830596	4	FACETS	1	0.961	1	0.517	0.484	0.551	CLONAL	1	TRUE	2	0.836053255425124	4		645	1126	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56862894	56862894	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	236	340	0	ENST00000308159.5:c.800A>G	p.Lys267Arg	p.K267R	ENST00000308159	NM_014669.4	267	aAg/aGg	9/22	0.836053255425124	3	FACETS	0.967	0.918	1	0.645	0.612	0.677	CLONAL	2	TRUE	0	0.836053255425124	3		340	414	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982002	70982002	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs373117873	NA	P-0040289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1627	1132	1039	0	ENST00000276594.2:c.94C>G	p.Pro32Ala	p.P32A	ENST00000276594	NM_024504.3	32	Cct/Gct	2/8	0.836053255425124	9	FACETS	0.963	0.937	0.99	0.642	0.625	0.66	CLONAL	4	TRUE	3	0.836053255425124	9		1039	2759	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0040298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	59	278	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.578	0.499	0.663	0.578	0.499	0.663	SUBCLONAL	1	TRUE	1	0.507907918479007	2		278	402	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184137	56184137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	84	362	0	ENST00000399503.3:c.4342C>T	p.Pro1448Ser	p.P1448S	ENST00000399503	NM_005921.1	1448	Cca/Tca	19/20	1	2	FACETS	0.623	0.551	0.699	0.623	0.551	0.699	SUBCLONAL	1	TRUE	1	0.507907918479007	2		362	531	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922319	178922319	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs759188876	NA	P-0040298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	54	396	0	ENST00000263967.3:c.1088G>C	p.Gly363Ala	p.G363A	ENST00000263967	NM_006218.2	363	gGa/gCa	6/21	1	2	FACETS	0.373	0.318	0.433	0.373	0.318	0.433	SUBCLONAL	1	TRUE	1	0.507907918479007	2		396	570	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170876	56170877	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	73	264	0	ENST00000399503.3:c.1705dup	p.Val569GlyfsTer7	p.V569Gfs*7	ENST00000399503	NM_005921.1	568	-/G	10/20	1	2	FACETS	0.713	0.627	0.806	0.713	0.627	0.806	SUBCLONAL	1	TRUE	1	0.507907918479007	2		264	403	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	39	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.987	0.819	1	0.987	0.819	1	CLONAL	1	TRUE	1	0.19	2		326	416	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063359	67063359	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	39	306	0	ENST00000412916.2:c.54del	p.Phe18LeufsTer4	p.F18Lfs*4	ENST00000412916		17	Ttt/tt	1/6	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.19	2		306	376	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111444	8111445	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGGAG	novel	NA	P-0040314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	41	489	0	ENST00000346208.3:c.933_937dup	p.Ala313GlyfsTer44	p.A313Gfs*44	ENST00000346208		310	-/AGGAG	5/6	1	2	FACETS	0.788	0.655	0.935	0.788	0.655	0.935	CLONAL	1	TRUE	1	0.19	2		489	548	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916932	178916940	+	inframe_deletion	In_Frame_Del	DEL	AACCGTGAA	AACCGTGAA	-	novel	NA	P-0040314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	34	365	0	ENST00000263967.3:c.319_327del	p.Asn107_Glu109del	p.N107_E109del	ENST00000263967	NM_006218.2	107	AACCGTGAA/-	2/21	1	2	FACETS	0.736	0.601	0.889	0.736	0.601	0.889	SUBCLONAL	1	TRUE	1	0.19	2		365	486	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508793	106508793	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370152741	NA	P-0040316-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	71	469	2	ENST00000359195.3:c.787G>A	p.Glu263Lys	p.E263K	ENST00000359195	NM_002649.2	263	Gaa/Aaa	2/11	1	2	FACETS	0.207	0.18	0.237	0.207	0.18	0.237	SUBCLONAL	1	TRUE	1	0.779449433171036	2		471	879	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0040328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	181	677	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.793912843308081	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.793912843308081	1		680	266	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0040328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	15	407	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.230632767063134	3	FACETS	0.126	0.091	0.168	0.063	0.045	0.084	INDETERMINATE	1	TRUE	1	0.793912843308081	3		407	419	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0040328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	186	515	0	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	0.793912843308081	3	FACETS	1	0.96	1	0.525	0.487	0.564	CLONAL	1	TRUE	1	0.793912843308081	3		515	623	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589663	67589663	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587777709	NA	P-0040328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	23	161	0	ENST00000274335.5:c.1425+1G>A		p.X475_splice	ENST00000274335		475			0.793912843308081	1	FACETS	0.216	0.169	0.268	0.216	0.169	0.268	SUBCLONAL	1	TRUE	0	0.793912843308081	1		161	162	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791190	42791190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1225908345	NA	P-0040328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	229	784	2	ENST00000575354.2:c.250C>T	p.Arg84Trp	p.R84W	ENST00000575354	NM_015125.3	84	Cgg/Tgg	3/20	0.426958950447799	1	FACETS	0.568	0.532	0.603	0.568	0.532	0.603	INDETERMINATE	1	TRUE	0	0.793912843308081	1		786	613	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223810	2223810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	203	873	2	ENST00000326181.6:c.1108G>A	p.Ala370Thr	p.A370T	ENST00000326181	NM_032271.2	370	Gcg/Acg	12/21	0.793912843308081	2	FACETS	0.944	0.882	1	0.472	0.441	0.503	CLONAL	1	TRUE	0	0.793912843308081	2		875	542	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291104	10291104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	185	664	0	ENST00000340748.4:c.367G>A	p.Ala123Thr	p.A123T	ENST00000340748		123	Gca/Aca	4/40	0.426958950447799	1	FACETS	0.582	0.542	0.622	0.582	0.542	0.622	INDETERMINATE	1	TRUE	0	0.793912843308081	1		664	483	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144533	58144533	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs375372343	NA	P-0040328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	80	347	0	ENST00000257904.6:c.538T>C	p.Tyr180His	p.Y180H	ENST00000257904	NM_000075.3	180	Tac/Cac	5/8	0.418503007942211	1	FACETS	0.49	0.438	0.545	0.49	0.438	0.545	INDETERMINATE	1	TRUE	0	0.793912843308081	1		347	248	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233825	133233825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757902862	NA	P-0040328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	224	747	1	ENST00000320574.5:c.3479G>A	p.Arg1160His	p.R1160H	ENST00000320574	NM_006231.2	1160	cGt/cAt	29/49	0.793912843308081	1	FACETS	0.975	0.928	1	0.975	0.928	1	CLONAL	1	TRUE	0	0.793912843308081	1		748	349	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73995395	73995395	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs774649242	NA	P-0040328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	275	474	0	ENST00000318443.5:c.701C>G	p.Ser234Cys	p.S234C	ENST00000318443	NM_001024736.1	234	tCt/tGt	4/10	0.282349213822292	5	FACETS	1	0.984	1			1	INDETERMINATE	3	TRUE	NA	0.793912843308081	5		474	473	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842735	68842735	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201511530	NA	P-0040328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	159	371	0	ENST00000261769.5:c.671G>A	p.Arg224His	p.R224H	ENST00000261769	NM_004360.3	224	cGc/cAc	5/16	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.793912843308081	2		371	376	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573344	41573344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779646635	NA	P-0040328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	216	706	0	ENST00000263253.7:c.5629C>T	p.Pro1877Ser	p.P1877S	ENST00000263253	NM_001429.3	1877	Cct/Tct	31/31	0.793912843308081	3	FACETS	0.965	0.899	1	0.322	0.299	0.344	CLONAL	1	TRUE	0	0.793912843308081	3		706	788	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713589	52713589	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0040328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	123	344	0	ENST00000394830.3:c.138+1G>T		p.X46_splice	ENST00000394830	NM_018313.4	46			0.793912843308081	1	FACETS	0.978	0.915	1	0.978	0.915	1	CLONAL	1	TRUE	0	0.793912843308081	1		344	191	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028047	69028047	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	179	379	0	ENST00000288368.4:c.3206T>C	p.Ile1069Thr	p.I1069T	ENST00000288368	NM_024870.2	1069	aTa/aCa	26/40	0.793912843308081	5	FACETS	0.926	0.853	1	0.309	0.284	0.334	CLONAL	1	TRUE	2	0.793912843308081	5		379	1067	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0040357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	147	542	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.917667576134699	2		542	320	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0040357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	147	764	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.532586209221014	2	FACETS	0.483	0.442	0.526	0.242	0.221	0.263	INDETERMINATE	1	TRUE	0	0.917667576134699	2		765	663	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs149840192	NA	P-0040357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	287	447	0	ENST00000275493.2:c.866C>A	p.Ala289Asp	p.A289D	ENST00000275493	NM_005228.3	289	gCc/gAc	7/28	0.192620982556032	2	FACETS	0.821	0.776	0.867	0.41	0.388	0.434	INDETERMINATE	1	TRUE	0	0.917667576134699	2		447	762	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133814	55133814	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2547	546	303	1	ENST00000257290.5:c.1027C>T	p.Pro343Ser	p.P343S	ENST00000257290	NM_006206.4	343	Cca/Tca	7/23	0.917667576134699	16	FACETS	0.952	0.909	0.997	0.19	0.181	0.2	CLONAL	3	TRUE	1	0.917667576134699	16		304	3093	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224307	55224307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1164954595	NA	P-0040357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	213	283	0	ENST00000275493.2:c.1088C>T	p.Thr363Ile	p.T363I	ENST00000275493	NM_005228.3	363	aCc/aTc	9/28	0.192620982556032	2	FACETS	1	0.95	1	0.506	0.475	0.536	INDETERMINATE	1	TRUE	0	0.917667576134699	2		283	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0040357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	414	416	0	ENST00000269305.4:c.920-2del		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.532586209221014	2	FACETS	0.798	0.774	0.822	0.798	0.774	0.822	INDETERMINATE	2	TRUE	0	0.917667576134699	2		416	565	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0040361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	24	125	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	1	2	FACETS	0.972	0.764	1	0.972	0.764	1	CLONAL	1	TRUE	1	0.2	2		125	247	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0040361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	78	530	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.179894094444182	2	FACETS	0.842	0.743	0.948	0.842	0.743	0.948	CLONAL	2	TRUE	0	0.2	2		530	463	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0040361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	44	243	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.2	2		243	358	SUCCESS
APC	324	MSKCC	GRCh37	5	112175766	112175766	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	13	182	0	ENST00000257430.4:c.4476del	p.Thr1493ArgfsTer14	p.T1493Rfs*14	ENST00000257430	NM_000038.5	1492	gCc/gc	16/16	1	2	FACETS	0.537	0.383	0.726	0.537	0.383	0.726	SUBCLONAL	1	TRUE	1	0.2	2		182	242	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0040361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	10	116	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	1	2	FACETS	0.521	0.353	0.732	0.521	0.353	0.732	SUBCLONAL	1	TRUE	1	0.2	2		116	192	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413118	139413118	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	71	412	0	ENST00000277541.6:c.1024G>A	p.Ala342Thr	p.A342T	ENST00000277541	NM_017617.3	342	Gcc/Acc	6/34	1	2	FACETS	0.999	0.871	1	0.999	0.871	1	CLONAL	1	TRUE	1	0.2	2		412	711	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587780070	NA	P-0040368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	203	416	0	ENST00000269305.4:c.535C>G	p.His179Asp	p.H179D	ENST00000269305	NM_001126112.2	179	Cat/Gat	5/11	0.442855661615658	2	FACETS	0.895	0.838	0.954	0.895	0.838	0.954	CLONAL	2	TRUE	0	0.442855661615658	2		416	512	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0040368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	30	183	1	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	0.442855661615658	3	FACETS	0.692	0.561	0.84	0.346	0.28	0.42	SUBCLONAL	1	TRUE	1	0.442855661615658	3		184	239	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0040368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	66	160	1	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.442855661615658	3	FACETS	0.851	0.75	0.956	0.851	0.75	0.956	CLONAL	2	TRUE	1	0.442855661615658	3		161	214	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198179	185198179	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	182	335	0	ENST00000265026.3:c.2661C>A	p.Asp887Glu	p.D887E	ENST00000265026	NM_004721.4	887	gaC/gaA	13/14	0.387383612214165	4	FACETS	0.907	0.84	0.975	0.907	0.84	0.975	CLONAL	2	TRUE	2	0.442855661615658	4		335	654	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161878	47161878	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	51	415	0	ENST00000409792.3:c.4248A>C	p.Glu1416Asp	p.E1416D	ENST00000409792	NM_014159.6	1416	gaA/gaC	3/21	0.335529758025106	3	FACETS	0.79	0.673	0.918	0.395	0.336	0.459	CLONAL	1	TRUE	1	0.384806661541929	3		415	400	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610656	52610656	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	55	490	0	ENST00000394830.3:c.3517del	p.His1173ThrfsTer20	p.H1173Tfs*20	ENST00000394830	NM_018313.4	1173	Cac/ac	23/30	0.335529758025106	3	FACETS	1	0.903	1	0.531	0.457	0.611	CLONAL	1	TRUE	1	0.384806661541929	3		490	321	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0040446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	131	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.788	0.719	0.859	1	0.988	1	SUBCLONAL	2	TRUE	1	0.34	2		336	489	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264586	1264586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs547377569	NA	P-0040450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	325	671	0	ENST00000310581.5:c.2776G>A	p.Gly926Ser	p.G926S	ENST00000310581	NM_198253.2	926	Ggc/Agc	11/16	0.316287897521243	2	FACETS	0.944	0.894	0.995	0.944	0.894	0.995	CLONAL	2	TRUE	0	0.368588635711628	2		671	934	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0040450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	206	615	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.368588635711628	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.368588635711628	1		615	766	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874247	155874247	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs672601335	NA	P-0040450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	92	507	0	ENST00000368323.3:c.284G>C	p.Gly95Ala	p.G95A	ENST00000368323	NM_006912.5	95	gGg/gCg	5/6	0.147831256100396	3	FACETS	0.703	0.624	0.788	0.234	0.208	0.263	INDETERMINATE	1	TRUE	0	0.368588635711628	3		507	841	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958616	175958616	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0040450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	55	262	0	ENST00000367669.3:c.1730-1G>C		p.X577_splice	ENST00000367669	NM_022457.5	577			0.147831256100396	3	FACETS	0.787	0.675	0.91	0.262	0.225	0.304	INDETERMINATE	1	TRUE	0	0.368588635711628	3		262	449	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444578	187444578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147650939	NA	P-0040450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	341	687	1	ENST00000232014.4:c.1649G>A	p.Arg550His	p.R550H	ENST00000232014	NM_001130845.1	550	cGc/cAc	7/10	0.363159968131422	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.368588635711628	2		688	908	SUCCESS
APC	324	MSKCC	GRCh37	5	112175326	112175339	+	frameshift_variant	Frame_Shift_Del	DEL	ATCAGCCAGGCACA	ATCAGCCAGGCACA	TTC	novel	NA	P-0040450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	69	226	2	ENST00000257430.4:c.4035_4048delinsTTC	p.Glu1345AspfsTer5	p.E1345Dfs*5	ENST00000257430	NM_000038.5	1345	gaATCAGCCAGGCACAaa/gaTTCaa	16/16	0.316287897521243	2	FACETS	1	0.963	1	0.628	0.552	0.709	CLONAL	1	TRUE	0	0.368588635711628	2		228	298	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231203	98231203	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	97	699	0	ENST00000331920.6:c.2080C>A	p.Gln694Lys	p.Q694K	ENST00000331920	NM_000264.3	694	Cag/Aag	14/24	0.316287897521243	2	FACETS	0.585	0.52	0.654	0.292	0.26	0.327	SUBCLONAL	1	TRUE	0	0.368588635711628	2		699	900	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0040453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	225	677	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.382640416944238	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.382640416944238	1		680	939	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505570	157505570	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs886039699	NA	P-0040453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	45	238	0	ENST00000346085.5:c.3550+1G>A		p.X1184_splice	ENST00000346085	NM_020732.3	1184			1	2	FACETS	0.771	0.651	0.902	0.771	0.651	0.902	CLONAL	1	TRUE	1	0.382640416944238	2		238	305	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367944	15367944	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1568	196	829	0	ENST00000263377.2:c.1382C>A	p.Pro461His	p.P461H	ENST00000263377	NM_058243.2	461	cCt/cAt	8/20	0.382640416944238	4	FACETS	0.803	0.74	0.869	0.268	0.246	0.29	CLONAL	1	TRUE	1	0.382640416944238	4		829	1764	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	173	471	12	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.817	0.756	0.88	0.817	0.756	0.88	CLONAL	1	TRUE	1	0.702174980226687	2		483	603	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	208	572	5	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.702174980226687	2		577	551	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	252	270	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.936	0.879	0.994	0.936	0.879	0.994	CLONAL	1	TRUE	1	0.702174980226687	2		271	767	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	139	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.866	0.795	0.94	0.866	0.795	0.94	CLONAL	1	TRUE	1	0.702174980226687	2		326	457	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	65	305	5	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.701	0.614	0.793	0.701	0.614	0.793	SUBCLONAL	1	TRUE	1	0.702174980226687	2		310	264	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	232	425	11	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	0.949	0.89	1	0.949	0.89	1	CLONAL	1	TRUE	1	0.702174980226687	2		436	696	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054540	42054541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	127	341	0	ENST00000219905.7:c.7731dup	p.Asp2578ArgfsTer45	p.D2578Rfs*45	ENST00000219905	NM_001164273.1	2575	aga/agAa	22/24	1	2	FACETS	0.778	0.709	0.849	0.778	0.709	0.849	SUBCLONAL	1	TRUE	1	0.702174980226687	2		341	465	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712007	89712007	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs765433422	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	94	265	0	ENST00000371953.3:c.625G>T	p.Gly209Ter	p.G209*	ENST00000371953	NM_000314.4	209	Gga/Tga	6/9	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.702174980226687	2		265	234	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	142	466	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.911	0.837	0.987	0.911	0.837	0.987	CLONAL	1	TRUE	1	0.702174980226687	2		466	444	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	35	386	4	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.176	0.143	0.212	0.176	0.143	0.212	SUBCLONAL	1	TRUE	1	0.702174980226687	2		390	567	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	132	399	1	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.702174980226687	2		400	359	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803899	43803899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61754776	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	207	460	0	ENST00000372470.3:c.209C>T	p.Pro70Leu	p.P70L	ENST00000372470	NM_005373.2	70	cCg/cTg	2/12	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.702174980226687	2		460	575	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936093	178936093	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913275	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	211	619	0	ENST00000263967.3:c.1635G>T	p.Glu545Asp	p.E545D	ENST00000263967	NM_006218.2	545	gaG/gaT	10/21	1	2	FACETS	0.976	0.912	1	0.976	0.912	1	CLONAL	1	TRUE	1	0.702174980226687	2		619	616	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154242	2154242	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755455183	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	216	748	7	ENST00000434045.2:c.686del	p.Pro229GlnfsTer27	p.P229Qfs*27	ENST00000434045	NM_001127598.1	229	cCa/ca	5/5	1	2	FACETS	0.894	0.835	0.955	0.894	0.835	0.955	CLONAL	1	TRUE	1	0.702174980226687	2		755	688	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099397	27099397	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	236	541	0	ENST00000324856.7:c.3634C>T	p.Gln1212Ter	p.Q1212*	ENST00000324856	NM_006015.4	1212	Cag/Tag	14/20	1	2	FACETS	0.902	0.845	0.961	0.902	0.845	0.961	CLONAL	1	TRUE	1	0.702174980226687	2		541	745	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723126	49723128	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs751306787	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	316	626	0	ENST00000449682.2:c.1288_1290del	p.Glu430del	p.E430del	ENST00000449682	NM_020998.3	430	GAG/-	11/18	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.702174980226687	2		626	808	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027087	71027087	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	243	560	2	ENST00000318789.4:c.1240del	p.Leu414Ter	p.L414*	ENST00000318789	NM_032682.5	414	Ctg/tg	15/21	1	2	FACETS	0.948	0.89	1	0.948	0.89	1	CLONAL	1	TRUE	1	0.702174980226687	2		562	730	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	274	883	0	ENST00000222270.7:c.520_521dup	p.Lys175GlnfsTer20	p.K175Qfs*20	ENST00000222270	NM_014727.1	172	acc/aCCcc	3/37	1	2	FACETS	0.758	0.712	0.805	0.758	0.712	0.805	SUBCLONAL	1	TRUE	1	0.702174980226687	2		883	1030	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721106	61721106	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	214	524	0	ENST00000401558.2:c.1168G>A	p.Ala390Thr	p.A390T	ENST00000401558	NM_003400.3	390	Gcc/Acc	12/25	1	2	FACETS	0.944	0.882	1	0.944	0.882	1	CLONAL	1	TRUE	1	0.702174980226687	2		524	646	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180343	38180343	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761769496	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	52	766	0	ENST00000396334.3:c.191C>T	p.Ala64Val	p.A64V	ENST00000396334	NM_002468.4	64	gCg/gTg	1/5	1	2	FACETS	0.168	0.142	0.196	0.168	0.142	0.196	SUBCLONAL	1	TRUE	1	0.702174980226687	2		766	882	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258272	16258272	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	306	687	0	ENST00000375759.3:c.5537G>T	p.Arg1846Met	p.R1846M	ENST00000375759	NM_015001.2	1846	aGg/aTg	11/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.702174980226687	2		687	836	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023008	27023013	+	inframe_deletion	In_Frame_Del	DEL	GGCGGC	GGCGGC	-	rs587779737	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	31	16	0	ENST00000324856.7:c.123_128del	p.Ala44_Ala45del	p.A44_A45del	ENST00000324856	NM_006015.4	38	gaGGCGGCg/gag	1/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.702174980226687	2		16	61	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444658	78444659	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	208	433	0	ENST00000370768.2:c.30dup	p.Ser11LeufsTer18	p.S11Lfs*18	ENST00000370768	NM_003902.3	10	-/C	1/20	1	2	FACETS	0.834	0.777	0.893	0.834	0.777	0.893	CLONAL	1	TRUE	1	0.702174980226687	2		433	710	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841509	156841509	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1242358987	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	340	784	0	ENST00000524377.1:c.812T>C	p.Val271Ala	p.V271A	ENST00000524377	NM_002529.3	271	gTg/gCg	7/17	0.702174980226687	3	FACETS	1	0.981	1	0.54	0.511	0.57	CLONAL	1	TRUE	1	0.702174980226687	3		784	1211	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606836	43606836	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659821	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	279	909	0	ENST00000355710.3:c.1445A>G	p.His482Arg	p.H482R	ENST00000355710	NM_020975.4	482	cAc/cGc	7/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.702174980226687	2		909	792	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903759	114903759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	213	547	0	ENST00000543371.1:c.763C>T	p.His255Tyr	p.H255Y	ENST00000543371	NM_001198531.1	255	Cat/Tat	7/14	1	2	FACETS	0.995	0.93	1	0.995	0.93	1	CLONAL	1	TRUE	1	0.702174980226687	2		547	610	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380343	14380344	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGCCGCCCC	novel	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	89	266	0	ENST00000256196.4:c.65_73dup	p.Gly22_Gly24dup	p.G22_G24dup	ENST00000256196		22	gtg/gGGGGCGGCGtg	1/6	1	2	FACETS	0.685	0.612	0.762	0.685	0.612	0.762	SUBCLONAL	1	TRUE	1	0.702174980226687	2		266	370	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922253	100922253	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	125	393	0	ENST00000325455.5:c.2259T>A	p.Tyr753Ter	p.Y753*	ENST00000325455	NM_001202474.3	753	taT/taA	5/8	1	2	FACETS	0.881	0.805	0.96	0.881	0.805	0.96	CLONAL	1	TRUE	1	0.702174980226687	2		393	404	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998206	100998206	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	96	309	0	ENST00000325455.5:c.1596G>T	p.Glu532Asp	p.E532D	ENST00000325455	NM_001202474.3	532	gaG/gaT	1/8	1	2	FACETS	0.617	0.553	0.685	0.617	0.553	0.685	SUBCLONAL	1	TRUE	1	0.702174980226687	2		309	443	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190776	108190776	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs730881382	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	29	257	0	ENST00000278616.4:c.6443A>T	p.Lys2148Ile	p.K2148I	ENST00000278616	NM_000051.3	2148	aAa/aTa	44/63	1	2	FACETS	0.274	0.22	0.335	0.274	0.22	0.335	SUBCLONAL	1	TRUE	1	0.702174980226687	2		257	301	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498234	498235	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	93	231	0	ENST00000399788.2:c.23dup	p.Tyr9LeufsTer15	p.Y9Lfs*15	ENST00000399788	NM_001042603.1	8	ggc/ggGc	1/28	1	2	FACETS	0.748	0.671	0.829	0.748	0.671	0.829	SUBCLONAL	1	TRUE	1	0.702174980226687	2		231	354	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285825	46285825	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	160	446	0	ENST00000334344.6:c.5093C>T	p.Ala1698Val	p.A1698V	ENST00000334344	NM_152641.2	1698	gCa/gTa	18/21	1	2	FACETS	0.902	0.833	0.973	0.902	0.833	0.973	CLONAL	1	TRUE	1	0.702174980226687	2		446	505	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446482	49446482	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	242	468	0	ENST00000301067.7:c.1123C>A	p.Pro375Thr	p.P375T	ENST00000301067	NM_003482.3	375	Cca/Aca	9/54	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.702174980226687	2		468	626	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435309	110435309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	106	161	0	ENST00000375856.3:c.3092C>T	p.Pro1031Leu	p.P1031L	ENST00000375856	NM_003749.2	1031	cCg/cTg	1/2	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.702174980226687	2		161	253	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43700260	43700260	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	251	616	0	ENST00000382044.4:c.5627A>T	p.Asn1876Ile	p.N1876I	ENST00000382044	NM_001141980.1	1876	aAt/aTt	27/28	1	2	FACETS	0.915	0.859	0.973	0.915	0.859	0.973	CLONAL	1	TRUE	1	0.702174980226687	2		616	781	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106746	2106746	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	370	802	0	ENST00000219476.3:c.750G>T	p.Lys250Asn	p.K250N	ENST00000219476	NM_000548.3	250	aaG/aaT	8/42	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.702174980226687	2		802	923	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006638	62006638	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	252	652	0	ENST00000392795.3:c.641T>C	p.Leu214Pro	p.L214P	ENST00000392795	NM_001039933.1	214	cTg/cCg	6/6	1	2	FACETS	0.986	0.927	1	0.986	0.927	1	CLONAL	1	TRUE	1	0.702174980226687	2		652	728	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222827	36222828	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	367	859	0	ENST00000222270.7:c.5462dup	p.Leu1822ThrfsTer12	p.L1822Tfs*12	ENST00000222270	NM_014727.1	1819	gac/gaCc	27/37	1	2	FACETS	0.947	0.899	0.995	0.947	0.899	0.995	CLONAL	1	TRUE	1	0.702174980226687	2		859	1104	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274851	142274851	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	205	556	1	ENST00000350721.4:c.2209C>T	p.His737Tyr	p.H737Y	ENST00000350721	NM_001184.3	737	Cat/Tat	10/47	0.383721012294557	1	FACETS	0.586	0.546	0.626	0.586	0.546	0.626	INDETERMINATE	1	TRUE	0	0.702174980226687	1		557	647	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526955	31526955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	289	756	0	ENST00000344624.3:c.85C>T	p.Pro29Ser	p.P29S	ENST00000344624		29	Ccc/Tcc	2/33	1	2	FACETS	0.893	0.842	0.945	0.893	0.842	0.945	CLONAL	1	TRUE	1	0.702174980226687	2		756	922	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181849	56181849	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	159	318	0	ENST00000399503.3:c.4073C>G	p.Ser1358Trp	p.S1358W	ENST00000399503	NM_005921.1	1358	tCg/tGg	17/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.702174980226687	2		318	413	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099429	157099430	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCAA	novel	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	51	240	0	ENST00000346085.5:c.371_372insACAGCA	p.Gln130_Gln131dup	p.Q130_Q131dup	ENST00000346085	NM_020732.3	130	-/CAGCAA	1/20	1	2	FACETS	0.486	0.415	0.562	0.486	0.415	0.562	SUBCLONAL	1	TRUE	1	0.702174980226687	2		240	299	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852246	128852246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	283	743	0	ENST00000249373.3:c.2318C>T	p.Thr773Ile	p.T773I	ENST00000249373	NM_005631.4	773	aCc/aTc	12/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.702174980226687	2		743	754	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836331	151836331	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	176	441	0	ENST00000262189.6:c.14474A>G	p.Tyr4825Cys	p.Y4825C	ENST00000262189	NM_170606.2	4825	tAc/tGc	57/59	1	2	FACETS	0.71	0.656	0.766	0.71	0.656	0.766	SUBCLONAL	1	TRUE	1	0.702174980226687	2		441	706	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878639	151878664	+	frameshift_variant	Frame_Shift_Del	DEL	ATGTGGGGTAAGGGGAGGCTGACTAT	ATGTGGGGTAAGGGGAGGCTGACTAT	-	novel	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	193	535	0	ENST00000262189.6:c.6281_6306del	p.Tyr2094SerfsTer5	p.Y2094Sfs*5	ENST00000262189	NM_170606.2	2094	tATAGTCAGCCTCCCCTTACCCCACAT/t	36/59	1	2	FACETS	0.948	0.882	1	0.948	0.882	1	CLONAL	1	TRUE	1	0.702174980226687	2		535	580	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132781	152132781	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	289	489	0	ENST00000262189.6:c.91G>A	p.Ala31Thr	p.A31T	ENST00000262189	NM_170606.2	31	Gcc/Acc	1/59	1	2	FACETS	0.989	0.934	1	0.989	0.934	1	CLONAL	1	TRUE	1	0.702174980226687	2		489	832	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128268597	128268597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	349	779	3	ENST00000265960.3:c.1058G>A	p.Arg353His	p.R353H	ENST00000265960	NM_001006617.1	353	cGc/cAc	8/12	1	2	FACETS	0.987	0.937	1	0.987	0.937	1	CLONAL	1	TRUE	1	0.702174980226687	2		782	1007	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	204	1014	11	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.411902167049226	2		1025	855	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	256	270	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.909	0.856	0.962	1	0.995	1	CLONAL	2	TRUE	1	0.411902167049226	2		271	684	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	88	475	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.994	0.885	1	0.994	0.885	1	CLONAL	1	TRUE	1	0.411902167049226	2		475	430	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916726	178916726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772110575	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	64	398	0	ENST00000263967.3:c.113G>A	p.Arg38His	p.R38H	ENST00000263967	NM_006218.2	38	cGt/cAt	2/21	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.411902167049226	2		398	298	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	73	371	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.411902167049226	2		371	322	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	108	466	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.411902167049226	2		466	485	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444275	50444275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	80	243	0	ENST00000331340.3:c.205C>T	p.Arg69Cys	p.R69C	ENST00000331340	NM_006060.4	69	Cgt/Tgt	4/8	1	2	FACETS	0.981	0.869	1	0.981	0.869	1	CLONAL	1	TRUE	1	0.411902167049226	2		243	396	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	49	399	1	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.844	0.719	0.978	0.844	0.719	0.978	CLONAL	1	TRUE	1	0.411902167049226	2		400	282	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	144	670	4	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.953	0.87	1	0.953	0.87	1	CLONAL	1	TRUE	1	0.411902167049226	2		674	734	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366939	15366939	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	173	697	6	ENST00000263377.2:c.1687del	p.Ser563AlafsTer21	p.S563Afs*21	ENST00000263377	NM_058243.2	563	Agc/gc	9/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.411902167049226	2		703	773	SUCCESS
APC	324	MSKCC	GRCh37	5	112174758	112174761	+	frameshift_variant	Frame_Shift_Del	DEL	AAGA	AAGA	-	rs1554085029	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	39	275	0	ENST00000257430.4:c.3467_3470del	p.Glu1156GlyfsTer8	p.E1156Gfs*8	ENST00000257430	NM_000038.5	1156	gAAGAg/gg	16/16	1	2	FACETS	0.783	0.653	0.924	0.783	0.653	0.924	CLONAL	1	TRUE	1	0.411902167049226	2		275	242	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435300	110435302	+	inframe_deletion	In_Frame_Del	DEL	GGT	GGT	-	rs765493638	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	65	307	3	ENST00000375856.3:c.3099_3101del	p.Pro1036del	p.P1036del	ENST00000375856	NM_003749.2	1033	ccACCg/ccg	1/2	1	2	FACETS	0.727	0.632	0.829	0.727	0.632	0.829	SUBCLONAL	1	TRUE	1	0.411902167049226	2		310	434	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776037	9776037	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	158	801	0	ENST00000377346.4:c.505del	p.Leu169CysfsTer48	p.L169Cfs*48	ENST00000377346	NM_005026.3	167	ttC/tt	5/24	1	2	FACETS	0.942	0.864	1	0.942	0.864	1	CLONAL	1	TRUE	1	0.411902167049226	2		801	814	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216737	7216742	+	inframe_deletion	In_Frame_Del	DEL	GGCTGT	GGCTGT	-	rs748493582	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	105	536	0	ENST00000380728.2:c.681_686del	p.Gln228_Pro229del	p.Q228_P229del	ENST00000380728		227	ccACAGCCc/ccc	8/11	1	2	FACETS	0.924	0.83	1	0.924	0.83	1	CLONAL	1	TRUE	1	0.411902167049226	2		536	552	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905151	50905151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137953986	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	224	991	3	ENST00000440232.2:c.433G>A	p.Ala145Thr	p.A145T	ENST00000440232	NM_002691.3	145	Gct/Act	4/27	1	2	FACETS	0.969	0.901	1	0.969	0.901	1	CLONAL	1	TRUE	1	0.411902167049226	2		994	1123	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56411684	56411684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1004957123	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	66	420	0	ENST00000348428.3:c.1868C>T	p.Pro623Leu	p.P623L	ENST00000348428	NM_006785.3	623	cCg/cTg	15/17	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.411902167049226	2		420	312	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	249	440	2	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.98	1	1	0.995	1	CLONAL	2	TRUE	1	0.411902167049226	2		442	558	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149799	202149799	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	118	631	0	ENST00000358485.4:c.1245del	p.Phe415LeufsTer26	p.F415Lfs*26	ENST00000358485	NM_001080125.1	414	Ttt/tt	8/9	1	2	FACETS	0.891	0.806	0.981	0.891	0.806	0.981	CLONAL	1	TRUE	1	0.411902167049226	2		631	643	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348566	89348568	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs753054998	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	210	931	0	ENST00000301030.4:c.4382_4384del	p.Lys1461del	p.K1461del	ENST00000301030	NM_001256183.1	1461	aAGAga/aga	9/13	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.411902167049226	2		931	978	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120031	70120031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	21	74	1	ENST00000245479.2:c.1037del	p.Pro346ArgfsTer37	p.P346Rfs*37	ENST00000245479	NM_000346.3	345	Ccc/cc	3/3	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.411902167049226	2		75	77	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101117	27101117	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	153	787	1	ENST00000324856.7:c.4403del	p.Pro1468LeufsTer13	p.P1468Lfs*13	ENST00000324856	NM_006015.4	1467	Ccc/cc	18/20	1	2	FACETS	0.872	0.798	0.949	0.872	0.798	0.949	CLONAL	1	TRUE	1	0.411902167049226	2		788	852	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514571	149514571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540587683	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	78	386	0	ENST00000261799.4:c.373G>A	p.Val125Met	p.V125M	ENST00000261799	NM_002609.3	125	Gtg/Atg	4/23	1	2	FACETS	0.91	0.804	1	0.91	0.804	1	CLONAL	1	TRUE	1	0.411902167049226	2		386	416	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967511	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	rs1349928568	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	55	293	1	ENST00000265433.3:c.1396dup	p.Arg466LysfsTer5	p.R466Kfs*5	ENST00000265433	NM_002485.4	466	agg/aAgg	10/16	1	2	FACETS	0.832	0.716	0.957	0.832	0.716	0.957	CLONAL	1	TRUE	1	0.411902167049226	2		294	321	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107001	11107001	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1050237	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	182	704	0	ENST00000358026.2:c.1706G>A	p.Arg569Gln	p.R569Q	ENST00000358026	NM_001128849.1	569	cGg/cAg	10/36	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.411902167049226	2		704	813	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759977	63759977	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	42	338	1	ENST00000279873.7:c.635del	p.Gly212AlafsTer24	p.G212Afs*24	ENST00000279873	NM_032199.2	210	ctG/ct	4/10	1	2	FACETS	0.419	0.349	0.496	0.419	0.349	0.496	SUBCLONAL	1	TRUE	1	0.411902167049226	2		339	487	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039405	47039405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	174	691	1	ENST00000377604.3:c.1028G>A	p.Arg343His	p.R343H	ENST00000377604	NM_001204468.1	343	cGc/cAc	10/24	1	2	FACETS	0.961	0.885	1	0.961	0.885	1	CLONAL	1	TRUE	1	0.411902167049226	2		692	879	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647657	3647657	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs774532876	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	227	1030	5	ENST00000294008.3:c.1406del	p.Pro469HisfsTer4	p.P469Hfs*4	ENST00000294008	NM_032444.2	469	cCa/ca	7/15	1	2	FACETS	0.978	0.91	1	0.978	0.91	1	CLONAL	1	TRUE	1	0.411902167049226	2		1035	1127	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118361992	118361992	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782281385	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	62	373	1	ENST00000534358.1:c.4778G>A	p.Arg1593His	p.R1593H	ENST00000534358	NM_005933.3	1593	cGc/cAc	14/36	1	2	FACETS	0.86	0.747	0.981	0.86	0.747	0.981	CLONAL	1	TRUE	1	0.411902167049226	2		374	350	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16005023	16005023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775391836	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	212	698	0	ENST00000268712.3:c.2231G>A	p.Arg744Gln	p.R744Q	ENST00000268712	NM_006311.3	744	cGa/cAa	20/46	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.411902167049226	2		698	907	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865628	57865628	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	207	1025	0	ENST00000228682.2:c.3109del	p.Leu1037TrpfsTer23	p.L1037Wfs*23	ENST00000228682	NM_005269.2	1035	aaC/aa	12/12	1	2	FACETS	0.998	0.926	1	0.998	0.926	1	CLONAL	1	TRUE	1	0.411902167049226	2		1025	1007	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626102	12626102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs865905076	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	237	486	0	ENST00000251849.4:c.1858G>A	p.Ala620Thr	p.A620T	ENST00000251849	NM_002880.3	620	Gct/Act	17/17	0.411902167049226	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.411902167049226	2		486	535	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576881	212576881	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	67	437	0	ENST00000342788.4:c.1018G>T	p.Gly340Ter	p.G340*	ENST00000342788	NM_005235.2	340	Gga/Tga	9/28	1	2	FACETS	0.962	0.842	1	0.962	0.842	1	CLONAL	1	TRUE	1	0.411902167049226	2		437	338	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937719	36937719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	172	883	0	ENST00000361632.4:c.1019C>T	p.Thr340Ile	p.T340I	ENST00000361632		340	aCa/aTa	8/16	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.411902167049226	2		883	831	SUCCESS
ATM	472	MSKCC	GRCh37	11	108159797	108159797	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	31	226	0	ENST00000278616.4:c.4207del	p.Ser1403AlafsTer3	p.S1403Afs*3	ENST00000278616	NM_000051.3	1401	ttA/tt	28/63	1	2	FACETS	0.875	0.716	1	0.875	0.716	1	CLONAL	1	TRUE	1	0.411902167049226	2		226	172	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109887	115109887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762342872	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	198	827	1	ENST00000257566.3:c.1991C>T	p.Ala664Val	p.A664V	ENST00000257566	NM_016569.3	664	gCg/gTg	8/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.411902167049226	2		828	766	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913926	32913927	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	67	586	0	ENST00000380152.3:c.5436dup	p.Leu1813ThrfsTer4	p.L1813Tfs*4	ENST00000380152		1812	gaa/gAaa	11/27	1	2	FACETS	0.83	0.725	0.943	0.83	0.725	0.943	CLONAL	1	TRUE	1	0.411902167049226	2		586	392	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871633	35871634	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	97	321	0	ENST00000216797.5:c.872_873del	p.Thr291ArgfsTer15	p.T291Rfs*15	ENST00000216797	NM_020529.2	291	aCA/a	5/6	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.411902167049226	2		321	419	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040999	42041001	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	191	672	0	ENST00000219905.7:c.5379_5381del	p.Arg1793del	p.R1793del	ENST00000219905	NM_001164273.1	1793	AGG/-	16/24	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.411902167049226	2		672	880	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058313	42058313	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	66	325	0	ENST00000219905.7:c.8033G>A	p.Ser2678Asn	p.S2678N	ENST00000219905	NM_001164273.1	2678	aGc/aAc	24/24	1	2	FACETS	0.913	0.797	1	0.913	0.797	1	CLONAL	1	TRUE	1	0.411902167049226	2		325	351	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129039	30129039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	169	830	0	ENST00000263025.4:c.727C>T	p.Pro243Ser	p.P243S	ENST00000263025	NM_002746.2	243	Ccc/Tcc	5/9	1	2	FACETS	0.92	0.846	0.997	0.92	0.846	0.997	CLONAL	1	TRUE	1	0.411902167049226	2		830	892	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129720	30129720	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1173483036	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	230	649	1	ENST00000263025.4:c.493C>T	p.Arg165Ter	p.R165*	ENST00000263025	NM_002746.2	165	Cga/Tga	3/9	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.411902167049226	2		650	906	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603033	48603033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	98	326	0	ENST00000342988.3:c.1334G>A	p.Arg445Gln	p.R445Q	ENST00000342988	NM_005359.5	445	cGa/cAa	11/12	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.411902167049226	2		326	462	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139674	202139674	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	76	287	0	ENST00000358485.4:c.835C>T	p.Gln279Ter	p.Q279*	ENST00000358485	NM_001080125.1	279	Cag/Tag	6/9	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.411902167049226	2		287	329	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248736	212248737	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	62	371	0	ENST00000342788.4:c.3530dup	p.Asn1177LysfsTer9	p.N1177Kfs*9	ENST00000342788	NM_005235.2	1177	aat/aaAt	28/28	1	2	FACETS	0.962	0.837	1	0.962	0.837	1	CLONAL	1	TRUE	1	0.411902167049226	2		371	313	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41489031	41489031	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	173	548	0	ENST00000263253.7:c.23C>A	p.Pro8Gln	p.P8Q	ENST00000263253	NM_001429.3	8	cCg/cAg	1/31	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.411902167049226	2		548	754	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050344	37050344	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1553642707	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	150	465	0	ENST00000231790.2:c.493del	p.Ala165LeufsTer2	p.A165Lfs*2	ENST00000231790	NM_000249.3	165	Gct/ct	6/19	0.411902167049226	2	FACETS	0.754	0.694	0.815	0.754	0.694	0.815	SUBCLONAL	2	TRUE	0	0.411902167049226	2		465	483	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630426	187630426	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	213	708	0	ENST00000441802.2:c.556T>A	p.Tyr186Asn	p.Y186N	ENST00000441802	NM_005245.3	186	Tac/Aac	2/27	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.411902167049226	2		708	891	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021069	26021069	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	30	422	0	ENST00000357647.3:c.352G>A	p.Val118Ile	p.V118I	ENST00000357647	NM_003529.2	118	Gtc/Atc	1/1	1	2	FACETS	0.255	0.205	0.313	0.255	0.205	0.313	SUBCLONAL	1	TRUE	1	0.411902167049226	2		422	571	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324568	31324568	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	90	499	0	ENST00000412585.2:c.240del	p.Pro81ArgfsTer70	p.P81Rfs*70	ENST00000412585	NM_005514.6	80	ggG/gg	2/8	1	2	FACETS	0.741	0.658	0.828	0.741	0.658	0.828	SUBCLONAL	1	TRUE	1	0.411902167049226	2		499	590	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842262	151842262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	87	367	1	ENST00000262189.6:c.14150C>T	p.Ala4717Val	p.A4717V	ENST00000262189	NM_170606.2	4717	gCc/gTc	54/59	1	2	FACETS	0.836	0.743	0.936	0.836	0.743	0.936	CLONAL	1	TRUE	1	0.411902167049226	2		368	505	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389318	8389319	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	125	568	0	ENST00000356435.5:c.4299dup	p.Glu1434ArgfsTer33	p.E1434Rfs*33	ENST00000356435		1433	-/C	26/35	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.411902167049226	2		568	571	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324591	31324591	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	131	510	1	ENST00000412585.2:c.217del	p.Ala73ArgfsTer4	p.A73Rfs*4	ENST00000412585	NM_005514.6	73	Gcg/cg	2/8	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.411902167049226	2		511	574	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0040490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	196	677	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.30744167684299	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.30744167684299	1		680	883	SUCCESS
APC	324	MSKCC	GRCh37	5	112174658	112174658	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	83	367	0	ENST00000257430.4:c.3367C>T	p.Gln1123Ter	p.Q1123*	ENST00000257430	NM_000038.5	1123	Caa/Taa	16/16	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.30744167684299	2		367	528	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687445	29687602	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCAGATGGGGATTTACTTAAAAAAAAGGAACTAAAATAATTTCCTATTTTCCATTACAGCAAACACAAATTCCAGACTATGCTGAGCTTATTGTTAAGTTTCTTGATGCCTTGATTGACACGTACCTGCCTGGAATTGATGAAGAAACCAGTGAAGA	TTCAGATGGGGATTTACTTAAAAAAAAGGAACTAAAATAATTTCCTATTTTCCATTACAGCAAACACAAATTCCAGACTATGCTGAGCTTATTGTTAAGTTTCTTGATGCCTTGATTGACACGTACCTGCCTGGAATTGATGAAGAAACCAGTGAAGA	-	novel	NA	P-0040490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	15	178	0	ENST00000356175.3:c.8098-60_8195del		p.X2700_splice	ENST00000356175	NM_000267.3	2700		56/57	0.30744167684299	3	FACETS	0.39	0.284	0.516	0.195	0.142	0.258	SUBCLONAL	1	TRUE	1	0.30744167684299	3		178	289	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593487	48593487	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	94	316	0	ENST00000342988.3:c.1238A>T	p.Tyr413Phe	p.Y413F	ENST00000342988	NM_005359.5	413	tAc/tTc	10/12	0.30744167684299	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.30744167684299	1		316	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0040541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	334	829	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.583341988556838	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.606432789742383	2		829	541	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0040541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	17	194	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.173315688686906	3	FACETS	0.399	0.299	0.517	0.133	0.099	0.173	INDETERMINATE	1	TRUE	0	0.606432789742383	3		194	183	SUCCESS
APC	324	MSKCC	GRCh37	5	112174833	112174833	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1554085102	NA	P-0040541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	90	174	1	ENST00000257430.4:c.3542T>A	p.Leu1181Ter	p.L1181*	ENST00000257430	NM_000038.5	1181	tTa/tAa	16/16	0.173315688686906	3	FACETS	0.867	0.785	0.952	0.578	0.523	0.635	INDETERMINATE	2	TRUE	0	0.606432789742383	3		175	223	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322556	39322556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761415462	NA	P-0040541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	112	312	0	ENST00000373001.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000373001	NM_022157.3	146	Gca/Aca	2/7	1	2	FACETS	0.95	0.862	1	0.95	0.862	1	CLONAL	1	TRUE	1	0.606432789742383	2		312	389	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	54	300	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.21090266554325	2		300	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0040547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	75	541	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.981	0.859	1	0.981	0.859	1	CLONAL	1	TRUE	1	0.21090266554325	2		541	725	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888210	112888210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121918464	NA	P-0040547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	14	424	0	ENST00000351677.2:c.226G>A	p.Glu76Lys	p.E76K	ENST00000351677	NM_002834.3	76	Gag/Aag	3/16	1	2	FACETS	0.224	0.161	0.302	0.224	0.161	0.302	SUBCLONAL	1	TRUE	1	0.21090266554325	2		424	592	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17129496	17129496	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	68	484	0	ENST00000285071.4:c.390C>G	p.Ser130Arg	p.S130R	ENST00000285071	NM_144997.5	130	agC/agG	5/14	1	2	FACETS	0.824	0.715	0.941	0.824	0.715	0.941	CLONAL	1	TRUE	1	0.21090266554325	2		484	783	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743013	743013	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	48	373	0	ENST00000314574.4:c.965A>G	p.Gln322Arg	p.Q322R	ENST00000314574	NM_005433.3	322	cAg/cGg	8/12	1	2	FACETS	0.828	0.699	0.969	0.828	0.699	0.969	CLONAL	1	TRUE	1	0.21090266554325	2		373	550	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245357	53245357	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	81	453	0	ENST00000375401.3:c.680T>C	p.Ile227Thr	p.I227T	ENST00000375401	NM_004187.3	227	aTt/aCt	6/26	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.21090266554325	2		453	589	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413037	63413037	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	95	704	0	ENST00000330258.3:c.130C>A	p.Pro44Thr	p.P44T	ENST00000330258	NM_152424.3	44	Cca/Aca	2/2	1	2	FACETS	0.927	0.824	1	0.927	0.824	1	CLONAL	1	TRUE	1	0.21090266554325	2		704	972	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0040551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	233	475	0	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	1	2	FACETS	0.992	0.932	1	0.992	0.932	1	CLONAL	1	TRUE	1	0.795004635514789	2		475	591	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544702	65544702	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040561-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	364	765	0	ENST00000358664.4:c.224G>A	p.Arg75Gln	p.R75Q	ENST00000358664	NM_002382.4	75	cGa/cAa	4/5	1	2	FACETS	0.78	0.744	0.817	0.78	0.744	0.817	SUBCLONAL	1	TRUE	1	1.1	2		765	848	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0040568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	68	1014	11	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.14	2		1025	969	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0040568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	75	840	6	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.14	2		846	824	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717678	89717678	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554825200	NA	P-0040568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	73	486	0	ENST00000371953.3:c.703G>T	p.Glu235Ter	p.E235*	ENST00000371953	NM_000314.4	235	Gaa/Taa	7/9	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.14	2		486	781	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602620	10602620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	54	758	0	ENST00000171111.5:c.958C>T	p.Arg320Trp	p.R320W	ENST00000171111	NM_203500.1	320	Cgg/Tgg	3/6	1	2	FACETS	0.759	0.646	0.884	0.759	0.646	0.884	SUBCLONAL	1	TRUE	1	0.14	2		758	1016	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156732	20156732	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	40	365	0	ENST00000379607.5:c.25G>T	p.Gly9Cys	p.G9C	ENST00000379607	NM_001412.3	9	Ggt/Tgt	2/7	1	2	FACETS	0.786	0.651	0.937	0.786	0.651	0.937	CLONAL	1	TRUE	1	0.14	2		365	727	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584827	48584827	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0040568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	30	250	0	ENST00000342988.3:c.904+1G>A		p.X302_splice	ENST00000342988	NM_005359.5	302			0.0779248327694013	3	FACETS	0.831	0.668	1	0.415	0.334	0.508	INDETERMINATE	1	TRUE	1	0.14	3		250	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	326	522	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.794973984895158	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.794973984895158	1		522	467	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37665993	37665993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	396	317	0	ENST00000447079.4:c.2645G>A	p.Arg882Gln	p.R882Q	ENST00000447079	NM_015083.1	882	cGg/cAg	7/14	0.113588734737794	3	FACETS	0.941	0.915	0.966			1	INDETERMINATE	3	TRUE	NA	0.794973984895158	3		317	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0040630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	188	677	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.413379341032989	1	FACETS	0.874	0.808	0.941	0.874	0.808	0.941	CLONAL	1	TRUE	0	0.413379341032989	1		680	826	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175481	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0040630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	134	269	0	ENST00000257430.4:c.4192_4193del	p.Arg1399PhefsTer9	p.R1399Ffs*9	ENST00000257430	NM_000038.5	1397	GAg/g	16/16	0.352947000773516	2	FACETS	1	0.986	1	0.709	0.649	0.771	CLONAL	1	TRUE	0	0.413379341032989	2		269	457	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729399	41729399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	106	615	0	ENST00000242208.4:c.1130G>A	p.Arg377His	p.R377H	ENST00000242208	NM_002192.2	377	cGc/cAc	3/3	1	2	FACETS	0.589	0.528	0.655	0.589	0.528	0.655	SUBCLONAL	1	TRUE	1	0.413379341032989	2		615	870	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101266	4101266	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057517898	NA	P-0040630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	146	695	0	ENST00000262948.5:c.541T>A	p.Leu181Met	p.L181M	ENST00000262948	NM_030662.3	181	Ttg/Atg	5/11	0.307725517361199	1	FACETS	0.609	0.555	0.665	0.609	0.555	0.665	SUBCLONAL	1	TRUE	0	0.413379341032989	1		695	920	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	82	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.911	0.805	1	0.911	0.805	1	CLONAL	1	TRUE	1	0.314727402151574	2		326	572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0040632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	137	675	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.314727402151574	1	FACETS	0.956	0.871	1	0.956	0.871	1	CLONAL	1	TRUE	0	0.314727402151574	1		675	767	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971000	21971000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	122	540	0	ENST00000304494.5:c.358G>T	p.Glu120Ter	p.E120*	ENST00000304494	NM_000077.4	120	Gag/Tag	2/3	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.314727402151574	2		540	769	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0040632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	31	226	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	1	2	FACETS	0.785	0.638	0.949	0.785	0.638	0.949	CLONAL	1	TRUE	1	0.314727402151574	2		226	251	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	189	300	0				ENST00000310581	NM_198253.2	-/1132			0.442283369094754	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.442283369094754	3		300	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0040638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	200	622	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.442283369094754	2		622	858	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0040638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	257	792	1	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.442283369094754	2		793	1069	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980300	55980300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1438804033	NA	P-0040638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	74	435	1	ENST00000263923.4:c.791C>T	p.Ser264Phe	p.S264F	ENST00000263923	NM_002253.2	264	tCt/tTt	6/30	1	2	FACETS	0.499	0.437	0.567	0.499	0.437	0.567	SUBCLONAL	1	TRUE	1	0.442283369094754	2		436	670	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0040638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	187	512	1	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.442283369094754	2		513	737	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602314	10602314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	209	766	1	ENST00000171111.5:c.1264G>A	p.Asp422Asn	p.D422N	ENST00000171111	NM_203500.1	422	Gat/Aat	3/6	0.260304436146627	1	FACETS	0.804	0.747	0.863	0.804	0.747	0.863	INDETERMINATE	1	TRUE	0	0.442283369094754	1		767	916	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40879654	40879654	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	164	473	0	ENST00000428826.2:c.245A>T	p.Lys82Met	p.K82M	ENST00000428826		82	aAg/aTg	4/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.442283369094754	2		473	647	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156908	89156908	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	71	583	0	ENST00000336596.2:c.10C>T	p.Gln4Ter	p.Q4*	ENST00000336596	NM_005233.5	4	Cag/Tag	1/17	NA	2	FACETS	0.486	0.424	0.554			1	INDETERMINATE	1	TRUE	NA	0.442283369094754	2		583	660	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860252	151860252	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	85	515	0	ENST00000262189.6:c.10410G>T	p.Gln3470His	p.Q3470H	ENST00000262189	NM_170606.2	3470	caG/caT	43/59	1	2	FACETS	0.581	0.513	0.653	0.581	0.513	0.653	SUBCLONAL	1	TRUE	1	0.442283369094754	2		515	662	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0040724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	105	425	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.675557079021982	1	FACETS	0.953	0.874	1	0.953	0.874	1	CLONAL	1	TRUE	0	0.675557079021982	1		426	216	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203626	108203626	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	29	168	0	ENST00000278616.4:c.7926A>T	p.Arg2642Ser	p.R2642S	ENST00000278616	NM_000051.3	2642	agA/agT	53/63	1	2	FACETS	0.576	0.468	0.695	0.576	0.468	0.695	SUBCLONAL	1	TRUE	1	0.675557079021982	2		168	149	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236087	108236087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781894	NA	P-0040724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	179	415	0	ENST00000278616.4:c.9023G>A	p.Arg3008His	p.R3008H	ENST00000278616	NM_000051.3	3008	cGt/cAt	63/63	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.675557079021982	2		415	506	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575083	48575083	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	91	261	0	ENST00000342988.3:c.277G>A	p.Val93Met	p.V93M	ENST00000342988	NM_005359.5	93	Gtg/Atg	3/12	1	2	FACETS	0.962	0.866	1	0.962	0.866	1	CLONAL	1	TRUE	1	0.675557079021982	2		261	280	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480361	89480361	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	95	257	1	ENST00000336596.2:c.2198G>T	p.Gly733Val	p.G733V	ENST00000336596	NM_005233.5	733	gGc/gTc	13/17	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.675557079021982	2		258	277	SUCCESS
APC	324	MSKCC	GRCh37	5	112175672	112175672	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	87	275	0	ENST00000257430.4:c.4381G>T	p.Glu1461Ter	p.E1461*	ENST00000257430	NM_000038.5	1461	Gaa/Taa	16/16	0.675557079021982	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.675557079021982	1		275	167	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527809	157527809	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374035954	NA	P-0040724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	111	344	0	ENST00000346085.5:c.5534G>A	p.Arg1845His	p.R1845H	ENST00000346085	NM_020732.3	1845	cGc/cAc	20/20	1	2	FACETS	0.893	0.811	0.978	0.893	0.811	0.978	CLONAL	1	TRUE	1	0.675557079021982	2		344	368	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494163	140494163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	223	595	0	ENST00000288602.6:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000288602	NM_004333.4	362	cGa/cAa	8/18	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.675557079021982	2		595	655	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0040757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	237	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.83683496451775	3	FACETS	0.994	0.945	1	0.994	0.945	1	CLONAL	2	TRUE	1	0.83683496451775	3		336	404	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624293	89624293	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs876661244	NA	P-0040757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	564	588	0	ENST00000371953.3:c.67T>G	p.Leu23Val	p.L23V	ENST00000371953	NM_000314.4	23	Tta/Gta	1/9	0.83683496451775	3	FACETS	0.999	0.981	1			1	CLONAL	3	TRUE	NA	0.83683496451775	3		588	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0040757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	972	852	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.835950539870526	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.83683496451775	3		852	1066	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10273354	10273354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748515801	NA	P-0040757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	145	476	0	ENST00000340748.4:c.949G>A	p.Glu317Lys	p.E317K	ENST00000340748		317	Gag/Aag	12/40	1	2	FACETS	0.952	0.88	1	0.952	0.88	1	CLONAL	1	TRUE	1	0.83683496451775	2		476	364	SUCCESS
APC	324	MSKCC	GRCh37	5	112174919	112174920	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0040757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	147	211	1	ENST00000257430.4:c.3631_3632dup	p.Met1211IlefsTer55	p.M1211Ifs*55	ENST00000257430	NM_000038.5	1210	cat/cATat	16/16	0.83683496451775	2	FACETS	0.95	0.906	0.99	0.95	0.906	0.99	CLONAL	2	TRUE	0	0.83683496451775	2		212	185	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409745	139409745	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	596	881	0	ENST00000277541.6:c.2011A>G	p.Thr671Ala	p.T671A	ENST00000277541	NM_017617.3	671	Aca/Gca	12/34	0.83683496451775	3	FACETS	0.961	0.93	0.992	0.961	0.93	0.992	CLONAL	2	TRUE	1	0.83683496451775	3		881	1051	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0040766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	57	463	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.106448474393089	3	FACETS	1	0.942	1	0.597	0.513	0.689	INDETERMINATE	1	TRUE	1	0.211153474145447	3		463	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578432	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	142	867	0	ENST00000269305.4:c.498dup	p.Gln167ThrfsTer14	p.Q167Tfs*14	ENST00000269305	NM_001126112.2	166	-/A	5/11	0.211153474145447	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.211153474145447	1		867	1009	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974687	21974701	+	inframe_deletion	In_Frame_Del	DEL	CTCCGACCGTAACTA	CTCCGACCGTAACTA	-	novel	NA	P-0040766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	75	518	0	ENST00000304494.5:c.126_140del	p.Asn42_Arg47delinsLys	p.N42_R47delinsK	ENST00000304494	NM_000077.4	42	aaTAGTTACGGTCGGAGg/aag	1/3	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.211153474145447	2		518	561	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913233	NA	P-0040785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	349	786	0	ENST00000451590.1:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000451590	NM_001130442.1	61	cAg/cTg	3/5	0.292541078023729	1	FACETS	0.889	0.844	0.935	1	0.996	1	CLONAL	2	TRUE	0	0.337501371503972	1		786	967	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001438	29001438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1473309404	NA	P-0040785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	45	304	0	ENST00000282397.4:c.1294G>A	p.Glu432Lys	p.E432K	ENST00000282397	NM_002019.4	432	Gaa/Aaa	10/30	0.337501371503972	1	FACETS	0.542	0.456	0.637	0.542	0.456	0.637	SUBCLONAL	1	TRUE	0	0.337501371503972	1		304	409	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104619	69104619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753704	NA	P-0040785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	86	648	0	ENST00000288368.4:c.4463C>T	p.Ser1488Leu	p.S1488L	ENST00000288368	NM_024870.2	1488	tCg/tTg	37/40	1	2	FACETS	0.659	0.583	0.741	0.659	0.583	0.741	SUBCLONAL	1	TRUE	1	0.337501371503972	2		648	773	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143500	108143500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751714261	NA	P-0040785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	154	430	0	ENST00000278616.4:c.3205C>T	p.Pro1069Ser	p.P1069S	ENST00000278616	NM_000051.3	1069	Cct/Tct	22/63	0.215377910754437	2	FACETS	1	0.985	1	0.664	0.609	0.721	CLONAL	1	TRUE	0	0.337501371503972	2		430	687	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994376	25994376	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540066802	NA	P-0040785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	71	353	0	ENST00000435504.4:c.437C>T	p.Ser146Leu	p.S146L	ENST00000435504		146	tCa/tTa	6/13	1	2	FACETS	0.815	0.713	0.926	0.815	0.713	0.926	CLONAL	1	TRUE	1	0.337501371503972	2		353	516	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160372	99160372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	110	461	0	ENST00000074304.5:c.851C>T	p.Ser284Phe	p.S284F	ENST00000074304	NM_001134224.1	284	tCc/tTc	11/26	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.337501371503972	2		461	551	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288597	33288597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	77	392	0	ENST00000374542.5:c.955G>A	p.Asp319Asn	p.D319N	ENST00000374542	NM_001141970.1	319	Gat/Aat	3/8	1	2	FACETS	0.969	0.853	1	0.969	0.853	1	CLONAL	1	TRUE	1	0.337501371503972	2		392	471	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14026311	14026311	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0040785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	64	277	0	ENST00000405192.2:c.134-1G>A		p.X45_splice	ENST00000405192	NM_001163147.1	45			1	2	FACETS	0.837	0.727	0.956	0.837	0.727	0.956	CLONAL	1	TRUE	1	0.337501371503972	2		277	453	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978688	70978688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	125	661	1	ENST00000276594.2:c.965G>A	p.Gly322Glu	p.G322E	ENST00000276594	NM_024504.3	322	gGg/gAg	5/8	1	2	FACETS	0.858	0.777	0.945	0.858	0.777	0.945	CLONAL	1	TRUE	1	0.337501371503972	2		662	863	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957472	175957472	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	65	389	0	ENST00000367669.3:c.1924G>A	p.Glu642Lys	p.E642K	ENST00000367669	NM_022457.5	642	Gaa/Aaa	17/20	0.305832647767021	4	FACETS	0.773	0.67	0.884	0.258	0.223	0.295	SUBCLONAL	1	TRUE	1	0.35969598064962	4		389	636	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206942002	206942002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	52	272	0	ENST00000423557.1:c.516G>A	p.Met172Ile	p.M172I	ENST00000423557	NM_000572.2	172	atG/atA	5/5	0.305832647767021	4	FACETS	0.889	0.759	1	0.296	0.253	0.344	CLONAL	1	TRUE	1	0.35969598064962	4		272	442	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675413	241675413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	58	228	0	ENST00000366560.3:c.409C>T	p.Pro137Ser	p.P137S	ENST00000366560	NM_000143.3	137	Cct/Tct	4/10	0.35969598064962	6	FACETS	1	0.886	1	0.259	0.222	0.298	CLONAL	1	TRUE	2	0.35969598064962	6		228	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577093	7577119	+	inframe_deletion	In_Frame_Del	DEL	CGGTCTCTCCCAGGACAGGCACAAACA	CGGTCTCTCCCAGGACAGGCACAAACA	-	novel	NA	P-0040788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	194	678	0	ENST00000269305.4:c.819_845del	p.Val274_Arg282del	p.V274_R282del	ENST00000269305	NM_001126112.2	273	cgTGTTTGTGCCTGTCCTGGGAGAGACCGg/cgg	8/11	0.350416553047495	2	FACETS	1	0.99	1	0.729	0.676	0.783	CLONAL	1	TRUE	0	0.35969598064962	2		678	740	SUCCESS
YES1	7525	MSKCC	GRCh37	18	746014	746014	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	65	376	0	ENST00000314574.4:c.508A>G	p.Arg170Gly	p.R170G	ENST00000314574	NM_005433.3	170	Aga/Gga	5/12	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.35969598064962	2		376	321	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221326	36221326	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	142	697	0	ENST00000222270.7:c.5160G>C	p.Leu1720Phe	p.L1720F	ENST00000222270	NM_014727.1	1720	ttG/ttC	24/37	0.339951426779701	4	FACETS	0.98	0.892	1			1	CLONAL	1	TRUE	NA	0.35969598064962	4		697	1095	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251698	212251698	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	80	356	0	ENST00000342788.4:c.3361G>C	p.Glu1121Gln	p.E1121Q	ENST00000342788	NM_005235.2	1121	Gag/Cag	27/28	0.346492341313738	4	FACETS	1	0.892	1	0.338	0.297	0.381	CLONAL	1	TRUE	1	0.35969598064962	4		356	597	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252902	36252902	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	137	320	0	ENST00000300305.3:c.460C>T	p.Gln154Ter	p.Q154*	ENST00000300305		154	Cag/Tag	4/8	0.316828293558553	4	FACETS	0.899	0.821	0.98	0.899	0.821	0.98	CLONAL	2	TRUE	2	0.35969598064962	4		320	576	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259215	36259237	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGCGCACCAGCTCGCCCGGGT	GGTGCGCACCAGCTCGCCCGGGT	-	novel	NA	P-0040788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	250	640	0	ENST00000300305.3:c.254_276del	p.His85ArgfsTer45	p.H85Rfs*45	ENST00000300305		85	cACCCGGGCGAGCTGGTGCGCACC/c	3/8	0.316828293558553	4	FACETS	0.885	0.828	0.944	0.885	0.828	0.944	CLONAL	2	TRUE	2	0.35969598064962	4		640	1068	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156947	89156947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	70	459	0	ENST00000336596.2:c.49G>A	p.Asp17Asn	p.D17N	ENST00000336596	NM_005233.5	17	Gac/Aac	1/17	0.350416553047495	2	FACETS	0.661	0.576	0.752	0.33	0.288	0.376	SUBCLONAL	1	TRUE	0	0.35969598064962	2		459	589	SUCCESS
APC	324	MSKCC	GRCh37	5	112174218	112174218	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	52	318	0	ENST00000257430.4:c.2927G>C	p.Arg976Thr	p.R976T	ENST00000257430	NM_000038.5	976	aGa/aCa	16/16	0.350416553047495	2	FACETS	0.747	0.638	0.866	0.374	0.319	0.433	SUBCLONAL	1	TRUE	0	0.35969598064962	2		318	387	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552789	106552789	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	98	541	0	ENST00000369096.4:c.754G>T	p.Glu252Ter	p.E252*	ENST00000369096	NM_001198.3	252	Gaa/Taa	5/7	0.350416553047495	2	FACETS	0.817	0.729	0.91	0.408	0.364	0.455	CLONAL	1	TRUE	0	0.35969598064962	2		541	667	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710944	117710944	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1287758562	NA	P-0040788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	66	295	0	ENST00000368508.3:c.1328G>T	p.Cys443Phe	p.C443F	ENST00000368508	NM_002944.2	443	tGt/tTt	12/43	0.350416553047495	2	FACETS	1	0.895	1	0.514	0.449	0.584	CLONAL	1	TRUE	0	0.35969598064962	2		295	357	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055726	152055726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	94	421	0	ENST00000262189.6:c.196G>A	p.Glu66Lys	p.E66K	ENST00000262189	NM_170606.2	66	Gag/Aag	2/59	1	2	FACETS	0.959	0.856	1	0.959	0.856	1	CLONAL	1	TRUE	1	0.35969598064962	2		421	545	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0040802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	1079	463	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.682374395029834	10	FACETS	0.989	0.977	1			1	CLONAL	10	TRUE	NA	0.682374395029834	10		463	1193	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0040802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	370	732	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.550730512505994	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.682374395029834	1		732	675	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445412	29445412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748493584	NA	P-0040802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	325	892	2	ENST00000389048.3:c.3421G>A	p.Asp1141Asn	p.D1141N	ENST00000389048	NM_004304.4	1141	Gac/Aac	21/29	1	2	FACETS	0.905	0.856	0.956	0.905	0.856	0.956	CLONAL	1	TRUE	1	0.682374395029834	2		894	1052	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027638	48027638	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	83	343	0	ENST00000234420.5:c.2516A>G	p.Asp839Gly	p.D839G	ENST00000234420	NM_000179.2	839	gAc/gGc	4/10	1	2	FACETS	0.83	0.741	0.924	0.83	0.741	0.924	CLONAL	1	TRUE	1	0.682374395029834	2		343	293	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	66	300	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.982	0.855	1	0.982	0.855	1	CLONAL	1	TRUE	1	0.288471670523532	2		300	466	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609813	117609813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761155034	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	87	638	2	ENST00000368508.3:c.6886G>A	p.Glu2296Lys	p.E2296K	ENST00000368508	NM_002944.2	2296	Gaa/Aaa	43/43	1	2	FACETS	0.886	0.784	0.994	0.886	0.784	0.994	CLONAL	1	TRUE	1	0.288471670523532	2		640	681	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589913	212589913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	92	502	0	ENST00000342788.4:c.629G>A	p.Arg210Lys	p.R210K	ENST00000342788	NM_005235.2	210	aGg/aAg	6/28	1	2	FACETS	0.888	0.789	0.994	0.888	0.789	0.994	CLONAL	1	TRUE	1	0.288471670523532	2		502	718	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170021	32170021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	157	1030	1	ENST00000375023.3:c.3587G>A	p.Gly1196Glu	p.G1196E	ENST00000375023	NM_004557.3	1196	gGa/gAa	21/30	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.288471670523532	2		1031	1081	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423632	88423632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1478926904	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	73	586	0	ENST00000360948.2:c.2203C>T	p.Arg735Cys	p.R735C	ENST00000360948	NM_001012338.2	735	Cgc/Tgc	18/19	1	2	FACETS	0.834	0.73	0.946	0.834	0.73	0.946	CLONAL	1	TRUE	1	0.288471670523532	2		586	607	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166491	118166491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	68	484	0	ENST00000369448.3:c.1001C>T	p.Ser334Phe	p.S334F	ENST00000369448	NM_017709.3	334	tCc/tTc	2/2	1	2	FACETS	0.896	0.781	1	0.896	0.781	1	CLONAL	1	TRUE	1	0.288471670523532	2		484	526	SUCCESS
AR	367	MSKCC	GRCh37	X	66931523	66931523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769862197	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	96	367	0	ENST00000374690.3:c.2165C>T	p.Ala722Val	p.A722V	ENST00000374690	NM_000044.3	722	gCc/gTc	4/8	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.288471670523532	1		367	393	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405216	139405216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	261	911	0	ENST00000277541.6:c.2629C>T	p.Pro877Ser	p.P877S	ENST00000277541	NM_017617.3	877	Ccg/Tcg	17/34	1	2	FACETS	0.815	0.763	0.868	1	0.994	1	CLONAL	2	TRUE	1	0.288471670523532	2		911	1110	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562641	29562641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854562	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	62	472	0	ENST00000356175.3:c.3721C>T	p.Arg1241Ter	p.R1241*	ENST00000356175	NM_000267.3	1241	Cga/Tga	28/57	1	2	FACETS	0.722	0.624	0.829	0.722	0.624	0.829	SUBCLONAL	1	TRUE	1	0.288471670523532	2		472	595	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371953	55371953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	88	498	0	ENST00000297316.4:c.643G>A	p.Asp215Asn	p.D215N	ENST00000297316	NM_022454.3	215	Gac/Aac	2/2	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.288471670523532	2		498	581	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281334	142281334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754292203	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	201	559	0	ENST00000350721.4:c.910C>T	p.Pro304Ser	p.P304S	ENST00000350721	NM_001184.3	304	Ccc/Tcc	4/47	0.288471670523532	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.288471670523532	2		559	634	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486824	56486824	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1023742896	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	128	695	0	ENST00000267101.3:c.1238C>T	p.Ser413Phe	p.S413F	ENST00000267101	NM_001982.3	413	tCc/tTc	11/28	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.288471670523532	2		695	820	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169625	27169625	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs775884054	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	118	708	4	ENST00000380036.4:c.626G>A	p.Arg209Gln	p.R209Q	ENST00000380036	NM_000459.3	209	cGg/cAg	4/23	0.288471670523532	0	FACETS	0.833	0.752	0.918			1	CLONAL	1	TRUE	0	0.288471670523532	0		712	699	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024380	31024380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201302084	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	135	837	0	ENST00000375687.4:c.3865C>T	p.Arg1289Trp	p.R1289W	ENST00000375687	NM_015338.5	1289	Cgg/Tgg	13/13	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.288471670523532	2		837	933	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342551	118342551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	32	334	0	ENST00000534358.1:c.677C>T	p.Pro226Leu	p.P226L	ENST00000534358	NM_005933.3	226	cCc/cTc	3/36	1	2	FACETS	0.676	0.55	0.818	0.676	0.55	0.818	SUBCLONAL	1	TRUE	1	0.288471670523532	2		334	328	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546763	9546763	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	52	428	0	ENST00000353224.5:c.1259C>T	p.Ser420Phe	p.S420F	ENST00000353224	NM_177990.2	420	tCc/tTc	5/10	1	2	FACETS	0.969	0.828	1	0.969	0.828	1	CLONAL	1	TRUE	1	0.288471670523532	2		428	372	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509966	106509966	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	64	628	0	ENST00000359195.3:c.1960G>A	p.Asp654Asn	p.D654N	ENST00000359195	NM_002649.2	654	Gat/Aat	2/11	1	2	FACETS	0.669	0.579	0.767	0.669	0.579	0.767	SUBCLONAL	1	TRUE	1	0.288471670523532	2		628	663	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858351	9858351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	73	515	0	ENST00000330684.3:c.3050C>T	p.Ser1017Phe	p.S1017F	ENST00000330684	NM_001134407.1	1017	tCc/tTc	13/13	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.288471670523532	2		515	506	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397514	116397514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	244	433	0	ENST00000397752.3:c.1886C>T	p.Ala629Val	p.A629V	ENST00000397752	NM_000245.2	629	gCc/gTc	7/21	0.288471670523532	3	FACETS	0.964	0.907	1	1	0.993	1	CLONAL	3	TRUE	1	0.288471670523532	3		433	669	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354228	15354229	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	152	972	2	ENST00000263377.2:c.2651_2652delinsTT	p.Pro884Leu	p.P884L	ENST00000263377	NM_058243.2	884	cCC/cTT	14/20	1	2	FACETS	0.928	0.848	1	0.928	0.848	1	CLONAL	1	TRUE	1	0.288471670523532	2		974	1135	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748165	41748165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	108	621	0	ENST00000226382.2:c.604C>T	p.Pro202Ser	p.P202S	ENST00000226382	NM_003924.3	202	Ccc/Tcc	3/3	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.288471670523532	2		621	615	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846191	156846191	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	106	746	0	ENST00000524377.1:c.1633-1G>A		p.X545_splice	ENST00000524377	NM_002529.3	545			1	2	FACETS	0.98	0.879	1	0.98	0.879	1	CLONAL	1	TRUE	1	0.288471670523532	2		746	750	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749987	162749987	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	71	508	0	ENST00000367921.3:c.2519C>T	p.Pro840Leu	p.P840L	ENST00000367921	NM_006182.2	840	cCc/cTc	18/18	1	2	FACETS	0.706	0.616	0.804	0.706	0.616	0.804	SUBCLONAL	1	TRUE	1	0.288471670523532	2		508	697	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117012	193117012	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	77	347	0	ENST00000367435.3:c.745A>T	p.Ile249Phe	p.I249F	ENST00000367435	NM_024529.4	249	Att/Ttt	8/17	1	2	FACETS	0.971	0.854	1	0.971	0.854	1	CLONAL	1	TRUE	1	0.288471670523532	2		347	550	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577244	64577244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	143	949	0	ENST00000312049.6:c.338C>T	p.Ser113Phe	p.S113F	ENST00000312049	NM_130799.2	113	tCc/tTc	2/10	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.288471670523532	2		949	957	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518572	69518572	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	130	658	0	ENST00000294312.3:c.73C>T	p.Leu25Phe	p.L25F	ENST00000294312	NM_005117.2	25	Ctc/Ttc	1/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.288471670523532	2		658	693	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524151	18524151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	73	483	0	ENST00000266497.5:c.1663G>A	p.Glu555Lys	p.E555K	ENST00000266497		555	Gaa/Aaa	11/31	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.288471670523532	2		483	482	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18576910	18576910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	86	627	0	ENST00000266497.5:c.2318C>T	p.Pro773Leu	p.P773L	ENST00000266497		773	cCt/cTt	16/31	1	2	FACETS	0.777	0.687	0.874	0.777	0.687	0.874	SUBCLONAL	1	TRUE	1	0.288471670523532	2		627	767	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434621	49434621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	162	1062	0	ENST00000301067.7:c.6932C>T	p.Ser2311Phe	p.S2311F	ENST00000301067	NM_003482.3	2311	tCc/tTc	31/54	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.288471670523532	2		1062	965	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911028	32911028	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867554960	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	65	444	0	ENST00000380152.3:c.2536T>C	p.Ser846Pro	p.S846P	ENST00000380152		846	Tca/Cca	11/27	1	2	FACETS	0.945	0.821	1	0.945	0.821	1	CLONAL	1	TRUE	1	0.288471670523532	2		444	477	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878106	48878107	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	41	119	0	ENST00000267163.4:c.58_59delinsTT	p.Pro20Phe	p.P20F	ENST00000267163	NM_000321.2	20	CCc/TTc	1/27	1	2	FACETS	0.781	0.659	0.912	1	0.961	1	CLONAL	2	TRUE	1	0.288471670523532	2		119	182	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434390	110434390	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	124	816	0	ENST00000375856.3:c.4011del	p.Glu1338SerfsTer19	p.E1338Sfs*19	ENST00000375856	NM_003749.2	1337	aaA/aa	1/2	1	2	FACETS	0.839	0.757	0.925	0.839	0.757	0.925	CLONAL	1	TRUE	1	0.288471670523532	2		816	1025	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226162	2226162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	129	1060	0	ENST00000326181.6:c.1859C>T	p.Ser620Phe	p.S620F	ENST00000326181	NM_032271.2	620	tCc/tTc	19/21	1	2	FACETS	0.889	0.805	0.978	0.889	0.805	0.978	CLONAL	1	TRUE	1	0.288471670523532	2		1060	1006	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639791	3639791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140103960	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	167	948	1	ENST00000294008.3:c.3848C>T	p.Ala1283Val	p.A1283V	ENST00000294008	NM_032444.2	1283	gCc/gTc	12/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.288471670523532	2		949	998	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831299	3831299	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	67	378	0	ENST00000262367.5:c.1582C>T	p.Pro528Ser	p.P528S	ENST00000262367	NM_004380.2	528	Cca/Tca	7/31	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.288471670523532	2		378	438	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923429	9923429	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555492779	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	108	640	0	ENST00000330684.3:c.1858C>T	p.Gln620Ter	p.Q620*	ENST00000330684	NM_001134407.1	620	Cag/Tag	9/13	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.288471670523532	2		640	693	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274099	10274099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	136	836	0	ENST00000330684.3:c.170C>T	p.Pro57Leu	p.P57L	ENST00000330684	NM_001134407.1	57	cCc/cTc	2/13	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.288471670523532	2		836	905	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829373	72829373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766465283	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	114	736	0	ENST00000268489.5:c.7208C>T	p.Ser2403Phe	p.S2403F	ENST00000268489	NM_006885.3	2403	tCc/tTc	9/10	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.288471670523532	2		736	746	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349676	89349676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773172347	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	167	879	0	ENST00000301030.4:c.3274C>T	p.Pro1092Ser	p.P1092S	ENST00000301030	NM_001256183.1	1092	Cct/Tct	9/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.288471670523532	2		879	1063	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562935	29562936	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	45	396	0	ENST00000356175.3:c.3871-1_3871delinsAA		p.X1291_splice	ENST00000356175	NM_000267.3	1291		29/57	1	2	FACETS	0.675	0.568	0.794	0.675	0.568	0.794	SUBCLONAL	1	TRUE	1	0.288471670523532	2		396	462	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55339525	55339525	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	246	726	0	ENST00000284073.2:c.284T>C	p.Val95Ala	p.V95A	ENST00000284073	NM_138962.2	95	gTt/gCt	5/14	0.288471670523532	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.288471670523532	3		726	939	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223355	2223355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	148	957	0	ENST00000398665.3:c.3466C>T	p.Pro1156Ser	p.P1156S	ENST00000398665	NM_032482.2	1156	Ccc/Tcc	25/28	1	2	FACETS	0.991	0.904	1	0.991	0.904	1	CLONAL	1	TRUE	1	0.288471670523532	2		957	1035	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375522	15375522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	202	999	1	ENST00000263377.2:c.905C>T	p.Pro302Leu	p.P302L	ENST00000263377	NM_058243.2	302	cCc/cTc	6/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.288471670523532	2		1000	1139	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971786	18971786	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	124	737	0	ENST00000262803.5:c.2452T>C	p.Tyr818His	p.Y818H	ENST00000262803	NM_002911.3	818	Tac/Cac	17/24	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.288471670523532	2		737	785	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753003	42753003	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	164	898	0	ENST00000222329.4:c.1261C>T	p.Pro421Ser	p.P421S	ENST00000222329	NM_006494.2	421	Ccg/Tcg	4/4	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.288471670523532	2		898	969	SUCCESS
ALK	238	MSKCC	GRCh37	2	29541268	29541268	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	57	471	0	ENST00000389048.3:c.1549C>T	p.His517Tyr	p.H517Y	ENST00000389048	NM_004304.4	517	Cat/Tat	8/29	0.288471670523532	3	FACETS	0.754	0.646	0.871	0.377	0.323	0.436	SUBCLONAL	1	TRUE	1	0.288471670523532	3		471	600	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607769	46607769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs927242408	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	290	976	0	ENST00000263734.3:c.1958C>T	p.Ala653Val	p.A653V	ENST00000263734	NM_001430.4	653	gCc/gTc	12/16	0.288471670523532	3	FACETS	0.978	0.92	1	0.978	0.92	1	CLONAL	2	TRUE	1	0.288471670523532	3		976	1176	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306555	41306556	+	missense_variant	Missense_Mutation	DNP	CC	CC	GT	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	100	719	0	ENST00000373198.4:c.1103_1104delinsAC	p.Gly368Asp	p.G368D	ENST00000373198	NM_133170.3	368	gGG/gAC	7/32	1	2	FACETS	0.915	0.817	1	0.915	0.817	1	CLONAL	1	TRUE	1	0.288471670523532	2		719	758	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140789	37140789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	68	555	1	ENST00000373509.5:c.625C>T	p.Pro209Ser	p.P209S	ENST00000373509	NM_002648.3	209	Cct/Tct	5/6	1	2	FACETS	0.658	0.572	0.752	0.658	0.572	0.752	SUBCLONAL	1	TRUE	1	0.288471670523532	2		556	716	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552866	106552866	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	168	951	1	ENST00000369096.4:c.831A>T	p.Glu277Asp	p.E277D	ENST00000369096	NM_001198.3	277	gaA/gaT	5/7	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.288471670523532	2		952	1084	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137522130	137522130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	28	208	0	ENST00000367739.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000367739	NM_000416.2	250	cCa/cTa	6/7	1	2	FACETS	0.714	0.572	0.874	0.714	0.572	0.874	SUBCLONAL	1	TRUE	1	0.288471670523532	2		208	272	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781180	161781180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	132	755	0	ENST00000366898.1:c.1225G>A	p.Glu409Lys	p.E409K	ENST00000366898	NM_004562.2	409	Gaa/Aaa	11/12	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.288471670523532	2		755	903	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444485	50444485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	43	341	0	ENST00000331340.3:c.415C>T	p.His139Tyr	p.H139Y	ENST00000331340	NM_006060.4	139	Cac/Tac	4/8	1	2	FACETS	0.713	0.598	0.841	0.713	0.598	0.841	SUBCLONAL	1	TRUE	1	0.288471670523532	2		341	418	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930098	68930098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	81	459	0	ENST00000288368.4:c.159G>A	p.Met53Ile	p.M53I	ENST00000288368	NM_024870.2	53	atG/atA	2/40	1	2	FACETS	0.927	0.817	1	0.927	0.817	1	CLONAL	1	TRUE	1	0.288471670523532	2		459	606	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965642	90965642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	56	388	0	ENST00000265433.3:c.1675G>A	p.Glu559Lys	p.E559K	ENST00000265433	NM_002485.4	559	Gaa/Aaa	11/16	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.288471670523532	2		388	378	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412698	63412721	+	inframe_deletion	In_Frame_Del	DEL	CAGCCACAGCTTTCTCTGTGGCTC	CAGCCACAGCTTTCTCTGTGGCTC	-	rs768930991	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	99	325	0	ENST00000330258.3:c.446_469del	p.Gly149_Ala156del	p.G149_A156del	ENST00000330258	NM_152424.3	149	gGAGCCACAGAGAAAGCTGTGGCTGag/gag	2/2	1	1	FACETS	0.837	0.754	0.923	1	0.985	1	CLONAL	2	TRUE	0	0.288471670523532	1		325	351	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861590	152861596	+	frameshift_variant	Frame_Shift_Del	DEL	ATGGTAA	ATGGTAA	-	novel	NA	P-0040819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	124	406	0	ENST00000406277.2:c.156_162del	p.Tyr53SerfsTer15	p.Y53Sfs*15	ENST00000406277	NM_152274.4	52	atTTACCAT/at	4/7	1		FACETS		0.984	1				CLONAL	1	TRUE	0	0.288471670523532	1		406	515	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	150	1014	11	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.252491946854558	2		1025	834	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953730	48953730	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs3092891	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	17	181	0	ENST00000267163.4:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000267163	NM_000321.2	445	Cga/Tga	14/27	1	2	FACETS	0.446	0.332	0.581	0.446	0.332	0.581	SUBCLONAL	1	FALSE	1	0.252491946854558	2		181	302	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	20	594	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.192	0.146	0.247	0.192	0.146	0.247	SUBCLONAL	1	FALSE	1	0.252491946854558	2		594	823	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692901	89692901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786204929	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	12	468	1	ENST00000371953.3:c.385G>A	p.Gly129Arg	p.G129R	ENST00000371953	NM_000314.4	129	Gga/Aga	5/9	1	2	FACETS	0.185	0.129	0.255	0.185	0.129	0.255	SUBCLONAL	1	FALSE	1	0.252491946854558	2		469	513	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	23	622	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.187	0.144	0.236	0.187	0.144	0.236	SUBCLONAL	1	FALSE	1	0.252491946854558	2		623	976	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660414	227660414	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	33	589	1	ENST00000305123.5:c.3041A>G	p.Asp1014Gly	p.D1014G	ENST00000305123	NM_005544.2	1014	gAc/gGc	1/2	1	2	FACETS	0.559	0.454	0.676	0.559	0.454	0.676	SUBCLONAL	1	FALSE	1	0.252491946854558	2		590	468	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303199	15303199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769955930	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	86	820	2	ENST00000263388.2:c.329G>A	p.Arg110His	p.R110H	ENST00000263388	NM_000435.2	110	cGt/cAt	3/33	1	2	FACETS	0.686	0.605	0.773	0.686	0.605	0.773	SUBCLONAL	1	FALSE	1	0.252491946854558	2		822	993	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564642	55564642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	48	560	1	ENST00000288135.5:c.530G>A	p.Arg177His	p.R177H	ENST00000288135	NM_000222.2	177	cGc/cAc	3/21	1	2	FACETS	0.509	0.429	0.597	0.509	0.429	0.597	SUBCLONAL	1	FALSE	1	0.252491946854558	2		561	747	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	40	327	0	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	1	2	FACETS	0.62	0.515	0.737	0.62	0.515	0.737	SUBCLONAL	1	FALSE	1	0.252491946854558	2		327	511	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563107	21563107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542237961	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	61	716	0	ENST00000382592.4:c.812G>A	p.Arg271His	p.R271H	ENST00000382592	NM_014572.2	271	cGc/cAc	4/8	1	2	FACETS	0.599	0.516	0.691	0.599	0.516	0.691	SUBCLONAL	1	FALSE	1	0.252491946854558	2		716	806	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972504	32972504	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	64	603	1	ENST00000380152.3:c.9854C>T	p.Pro3285Leu	p.P3285L	ENST00000380152		3285	cCc/cTc	27/27	1	2	FACETS	0.653	0.565	0.75	0.653	0.565	0.75	SUBCLONAL	1	FALSE	1	0.252491946854558	2		604	776	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755666	39755666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	57	637	0	ENST00000288319.7:c.1099C>T	p.Arg367Cys	p.R367C	ENST00000288319	NM_182918.3	367	Cgc/Tgc	10/10	1	2	FACETS	0.55	0.471	0.637	0.55	0.471	0.637	SUBCLONAL	1	FALSE	1	0.252491946854558	2		637	821	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420308	88420308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367985043	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	50	482	1	ENST00000360948.2:c.2378G>A	p.Arg793Gln	p.R793Q	ENST00000360948	NM_001012338.2	793	cGa/cAa	19/19	1	2	FACETS	0.578	0.49	0.676	0.578	0.49	0.676	SUBCLONAL	1	FALSE	1	0.252491946854558	2		483	685	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665274	176665274	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121908070	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	37	330	0	ENST00000439151.2:c.3958C>T	p.Arg1320Ter	p.R1320*	ENST00000439151	NM_022455.4	1320	Cga/Tga	7/23	1	2	FACETS	0.507	0.417	0.608	0.507	0.417	0.608	SUBCLONAL	1	FALSE	1	0.252491946854558	2		330	578	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	85	500	5	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.992	0.877	1	0.992	0.877	1	CLONAL	1	FALSE	1	0.252491946854558	2		505	679	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	44	656	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	1	2	FACETS	0.465	0.389	0.55	0.465	0.389	0.55	SUBCLONAL	1	FALSE	1	0.252491946854558	2		656	749	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448564	89448564	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1184230536	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	81	500	0	ENST00000336596.2:c.1528C>T	p.Arg510Ter	p.R510*	ENST00000336596	NM_005233.5	510	Cga/Tga	7/17	1	2	FACETS	0.839	0.738	0.947	0.839	0.738	0.947	CLONAL	1	FALSE	1	0.252491946854558	2		500	765	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880887	134880887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	50	445	0	ENST00000398015.3:c.1450G>A	p.Ala484Thr	p.A484T	ENST00000398015	NM_004441.4	484	Gcc/Acc	7/16	1	2	FACETS	0.688	0.583	0.803	0.688	0.583	0.803	SUBCLONAL	1	FALSE	1	0.252491946854558	2		445	576	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416800	121416800	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770695671	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	126	883	1	ENST00000257555.6:c.229G>A	p.Asp77Asn	p.D77N	ENST00000257555		77	Gat/Aat	1/10	1	2	FACETS	0.905	0.818	0.997	0.905	0.818	0.997	CLONAL	1	FALSE	1	0.252491946854558	2		884	1103	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248860	133248860	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs116260568	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	91	662	0	ENST00000320574.5:c.1735C>T	p.Arg579Cys	p.R579C	ENST00000320574	NM_006231.2	579	Cgc/Tgc	16/49	1	2	FACETS	0.78	0.691	0.875	0.78	0.691	0.875	SUBCLONAL	1	FALSE	1	0.252491946854558	2		662	924	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052629	42052629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	67	471	2	ENST00000219905.7:c.7300C>T	p.Arg2434Trp	p.R2434W	ENST00000219905	NM_001164273.1	2434	Cgg/Tgg	20/24	1	2	FACETS	0.687	0.596	0.785	0.687	0.596	0.785	SUBCLONAL	1	FALSE	1	0.252491946854558	2		473	773	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740623	58740624	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs763475304	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	34	554	0	ENST00000305921.3:c.1535dup	p.Asn512LysfsTer16	p.N512Kfs*16	ENST00000305921	NM_003620.3	510	caa/cAaa	6/6	1	2	FACETS	0.419	0.341	0.507	0.419	0.341	0.507	SUBCLONAL	1	FALSE	1	0.252491946854558	2		554	643	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434164	121434164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	85	734	0	ENST00000257555.6:c.1055C>T	p.Ser352Phe	p.S352F	ENST00000257555		352	tCc/tTc	5/10	1	2	FACETS	0.707	0.624	0.797	0.707	0.624	0.797	SUBCLONAL	1	FALSE	1	0.252491946854558	2		734	952	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908877	101908877	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1469620887	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	36	485	0	ENST00000374994.4:c.1241G>A	p.Arg414Gln	p.R414Q	ENST00000374994	NM_004612.2	414	cGa/cAa	7/9	1	2	FACETS	0.462	0.379	0.556	0.462	0.379	0.556	SUBCLONAL	1	FALSE	1	0.252491946854558	2		485	617	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391890	139391890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	80	819	3	ENST00000277541.6:c.6301G>A	p.Ala2101Thr	p.A2101T	ENST00000277541	NM_017617.3	2101	Gca/Aca	34/34	1	2	FACETS	0.708	0.622	0.801	0.708	0.622	0.801	SUBCLONAL	1	FALSE	1	0.252491946854558	2		822	895	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222760	5222760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199829286	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	86	450	0	ENST00000357368.4:c.3043C>T	p.Arg1015Cys	p.R1015C	ENST00000357368	NM_002850.3	1015	Cgc/Tgc	18/38	1	2	FACETS	0.947	0.838	1	0.947	0.838	1	CLONAL	1	FALSE	1	0.252491946854558	2		450	719	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134687	41134687	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760747458	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	29	400	0	ENST00000379561.5:c.941G>A	p.Arg314His	p.R314H	ENST00000379561	NM_002015.3	314	cGc/cAc	2/3	1	2	FACETS	0.653	0.524	0.798	0.653	0.524	0.798	SUBCLONAL	1	FALSE	1	0.252491946854558	2		400	352	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971367	13971367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755892534	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	73	401	1	ENST00000405192.2:c.562C>T	p.Arg188Cys	p.R188C	ENST00000405192	NM_001163147.1	188	Cgc/Tgc	8/12	0.146861537554522	3	FACETS	1	0.935	1	0.555	0.485	0.629	INDETERMINATE	1	FALSE	1	0.252491946854558	3		402	587	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8338945	8338945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	29	405	0	ENST00000356435.5:c.5356G>A	p.Glu1786Lys	p.E1786K	ENST00000356435		1786	Gaa/Aaa	32/35	1	2	FACETS	0.477	0.382	0.585	0.477	0.382	0.585	SUBCLONAL	1	FALSE	1	0.252491946854558	2		405	482	SUCCESS
ATR	545	MSKCC	GRCh37	3	142168368	142168368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1034620994	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	32	399	1	ENST00000350721.4:c.7838C>T	p.Pro2613Leu	p.P2613L	ENST00000350721	NM_001184.3	2613	cCg/cTg	47/47	1	2	FACETS	0.638	0.518	0.774	0.638	0.518	0.774	SUBCLONAL	1	FALSE	1	0.252491946854558	2		400	397	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238951	5238951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237159914	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	61	394	0	ENST00000357368.4:c.1828C>T	p.Arg610Trp	p.R610W	ENST00000357368	NM_002850.3	610	Cgg/Tgg	13/38	1	2	FACETS	0.917	0.792	1	0.917	0.792	1	CLONAL	1	FALSE	1	0.252491946854558	2		394	527	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012617	36012617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367543238	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	41	347	0	ENST00000358208.4:c.61G>A	p.Ala21Thr	p.A21T	ENST00000358208		21	Gcc/Acc	2/12	1	2	FACETS	0.685	0.571	0.812	0.685	0.571	0.812	SUBCLONAL	1	FALSE	1	0.252491946854558	2		347	474	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101375	27101375	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	60	487	2	ENST00000324856.7:c.4661del	p.Pro1554HisfsTer11	p.P1554Hfs*11	ENST00000324856	NM_006015.4	1553	Ccc/cc	18/20	1	2	FACETS	0.727	0.626	0.837	0.727	0.626	0.837	SUBCLONAL	1	FALSE	1	0.252491946854558	2		489	654	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25368433	25368434	+	intron_variant	Intron	INS	-	-	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	25	285	1	ENST00000311936.3:c.451-5589dup		p.*151*	ENST00000311936	NM_004985.3	171/189			1	2	FACETS	0.569	0.448	0.708	0.569	0.448	0.708	SUBCLONAL	1	FALSE	1	0.252491946854558	2		286	348	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178554	32178554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759200326	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	64	590	3	ENST00000375023.3:c.2840C>T	p.Ala947Val	p.A947V	ENST00000375023	NM_004557.3	947	gCc/gTc	18/30	1	2	FACETS	0.664	0.574	0.762	0.664	0.574	0.762	SUBCLONAL	1	FALSE	1	0.252491946854558	2		593	764	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942055	17942055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	82	688	0	ENST00000458235.1:c.2960G>A	p.Gly987Asp	p.G987D	ENST00000458235	NM_000215.3	987	gGc/gAc	21/24	1	2	FACETS	0.773	0.681	0.873	0.773	0.681	0.873	SUBCLONAL	1	FALSE	1	0.252491946854558	2		688	840	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265049	46265049	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	39	480	0	ENST00000371998.3:c.1924del	p.Leu642Ter	p.L642*	ENST00000371998		640	tCc/tc	12/23	1	2	FACETS	0.554	0.458	0.66	0.554	0.458	0.66	SUBCLONAL	1	FALSE	1	0.252491946854558	2		480	558	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892293	9892293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs796052550	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	42	371	0	ENST00000330684.3:c.2197G>A	p.Ala733Thr	p.A733T	ENST00000330684	NM_001134407.1	733	Gca/Aca	11/13	1	2	FACETS	0.647	0.54	0.766	0.647	0.54	0.766	SUBCLONAL	1	FALSE	1	0.252491946854558	2		371	514	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379486	225379486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	23	390	0	ENST00000264414.4:c.382C>T	p.Arg128Cys	p.R128C	ENST00000264414	NM_003590.4	128	Cgt/Tgt	4/16	1	2	FACETS	0.505	0.393	0.634	0.505	0.393	0.634	SUBCLONAL	1	FALSE	1	0.252491946854558	2		390	361	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830135	72830135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	75	556	1	ENST00000268489.5:c.6446G>A	p.Arg2149His	p.R2149H	ENST00000268489	NM_006885.3	2149	cGc/cAc	9/10	1	2	FACETS	0.836	0.732	0.948	0.836	0.732	0.948	CLONAL	1	FALSE	1	0.252491946854558	2		557	711	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687001	176687001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	41	399	0	ENST00000439151.2:c.4978C>T	p.Arg1660Cys	p.R1660C	ENST00000439151	NM_022455.4	1660	Cgc/Tgc	14/23	1	2	FACETS	0.623	0.519	0.74	0.623	0.519	0.74	SUBCLONAL	1	FALSE	1	0.252491946854558	2		399	521	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828024	72828024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200701402	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	98	744	1	ENST00000268489.5:c.8557G>A	p.Ala2853Thr	p.A2853T	ENST00000268489	NM_006885.3	2853	Gca/Aca	9/10	1	2	FACETS	0.704	0.626	0.787	0.704	0.626	0.787	SUBCLONAL	1	FALSE	1	0.252491946854558	2		745	1103	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562629	95562629	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	48	360	0	ENST00000393063.1:c.4628C>T	p.Ser1543Phe	p.S1543F	ENST00000393063	NM_030621.3	1543	tCc/tTc	24/28	1	2	FACETS	0.927	0.786	1	0.927	0.786	1	CLONAL	1	FALSE	1	0.252491946854558	2		360	410	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396886	139396886	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752754662	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	59	524	0	ENST00000277541.6:c.5222C>T	p.Ala1741Val	p.A1741V	ENST00000277541	NM_017617.3	1741	gCg/gTg	28/34	1	2	FACETS	0.655	0.563	0.756	0.655	0.563	0.756	SUBCLONAL	1	FALSE	1	0.252491946854558	2		524	713	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	83	1318	2	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.656	0.577	0.741	0.656	0.577	0.741	SUBCLONAL	1	FALSE	1	0.252491946854558	2		1320	1002	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885286	111885286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770836648	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	69	612	2	ENST00000341259.2:c.1174C>T	p.Arg392Trp	p.R392W	ENST00000341259	NM_005475.2	392	Cgg/Tgg	6/8	1	2	FACETS	0.775	0.675	0.884	0.775	0.675	0.884	SUBCLONAL	1	FALSE	1	0.252491946854558	2		614	705	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612801	228612801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369460992	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	65	642	1	ENST00000366696.1:c.226G>A	p.Ala76Thr	p.A76T	ENST00000366696	NM_003493.2	76	Gct/Act	1/1	1	2	FACETS	0.704	0.61	0.807	0.704	0.61	0.807	SUBCLONAL	1	FALSE	1	0.252491946854558	2		643	731	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105512	30105512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768104173	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	79	585	0	ENST00000331968.5:c.1174G>A	p.Ala392Thr	p.A392T	ENST00000331968	NM_002742.2	392	Gcc/Acc	7/18	1	2	FACETS	0.858	0.754	0.97	0.858	0.754	0.97	CLONAL	1	FALSE	1	0.252491946854558	2		585	729	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279530	1279530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	68	833	0	ENST00000310581.5:c.2006G>A	p.Arg669Gln	p.R669Q	ENST00000310581	NM_198253.2	669	cGg/cAg	5/16	1	2	FACETS	0.569	0.493	0.651	0.569	0.493	0.651	SUBCLONAL	1	FALSE	1	0.252491946854558	2		833	947	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247617	123247617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	41	364	0	ENST00000358487.5:c.1874G>A	p.Arg625Gln	p.R625Q	ENST00000358487	NM_000141.4	625	cGa/cAa	14/18	1	2	FACETS	0.65	0.541	0.771	0.65	0.541	0.771	SUBCLONAL	1	FALSE	1	0.252491946854558	2		364	500	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125832	47125832	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	22	230	2	ENST00000409792.3:c.5438del	p.Asn1813IlefsTer25	p.N1813Ifs*25	ENST00000409792	NM_014159.6	1813	aAt/at	12/21	1	2	FACETS	0.526	0.408	0.664	0.526	0.408	0.664	SUBCLONAL	1	FALSE	1	0.252491946854558	2		232	331	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958212	11958212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760186886	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	44	301	0	ENST00000353533.5:c.122G>A	p.Arg41His	p.R41H	ENST00000353533	NM_003010.3	41	cGc/cAc	2/11	1	2	FACETS	0.869	0.73	1	0.869	0.73	1	CLONAL	1	FALSE	1	0.252491946854558	2		301	401	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190747	11190747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759603938	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	84	691	2	ENST00000361445.4:c.5452C>T	p.Arg1818Cys	p.R1818C	ENST00000361445	NM_004958.3	1818	Cgt/Tgt	39/58	1	2	FACETS	0.713	0.628	0.804	0.713	0.628	0.804	SUBCLONAL	1	FALSE	1	0.252491946854558	2		693	933	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395001	395001	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1300046652	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	43	402	3	ENST00000380956.4:c.402del	p.Gly135GlufsTer14	p.G135Efs*14	ENST00000380956	NM_001195286.1	133	Aaa/aa	3/9	1	2	FACETS	0.604	0.505	0.714	0.604	0.505	0.714	SUBCLONAL	1	FALSE	1	0.252491946854558	2		405	564	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670706	67670706	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762060506	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	70	543	1	ENST00000264010.4:c.1951C>T	p.Arg651Trp	p.R651W	ENST00000264010	NM_006565.3	651	Cgg/Tgg	11/12	1	2	FACETS	0.712	0.62	0.812	0.712	0.62	0.812	SUBCLONAL	1	FALSE	1	0.252491946854558	2		544	779	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434967	110434967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	80	604	0	ENST00000375856.3:c.3434G>A	p.Arg1145His	p.R1145H	ENST00000375856	NM_003749.2	1145	cGc/cAc	1/2	1	2	FACETS	0.692	0.608	0.783	0.692	0.608	0.783	SUBCLONAL	1	FALSE	1	0.252491946854558	2		604	916	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374486	118374486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555046878	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	26	391	0	ENST00000534358.1:c.7879C>T	p.Arg2627Cys	p.R2627C	ENST00000534358	NM_005933.3	2627	Cgt/Tgt	27/36	1	2	FACETS	0.426	0.337	0.529	0.426	0.337	0.529	SUBCLONAL	1	FALSE	1	0.252491946854558	2		391	483	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800901	18800901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767127006	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	30	390	0	ENST00000266497.5:c.4277G>A	p.Arg1426Gln	p.R1426Q	ENST00000266497		1426	cGa/cAa	31/31	1	2	FACETS	0.555	0.447	0.678	0.555	0.447	0.678	SUBCLONAL	1	FALSE	1	0.252491946854558	2		390	428	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606314	93606314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs16906862	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	78	702	1	ENST00000375746.1:c.134G>A	p.Arg45His	p.R45H	ENST00000375746	NM_001174167.1	45	cGc/cAc	2/14	1	2	FACETS	0.772	0.678	0.874	0.772	0.678	0.874	SUBCLONAL	1	FALSE	1	0.252491946854558	2		703	800	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245932	16245932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760738868	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	35	296	0	ENST00000375759.3:c.1555G>A	p.Val519Met	p.V519M	ENST00000375759	NM_015001.2	519	Gtg/Atg	8/15	1	2	FACETS	0.582	0.477	0.701	0.582	0.477	0.701	SUBCLONAL	1	FALSE	1	0.252491946854558	2		296	476	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523142	176523142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778323767	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	69	695	1	ENST00000292408.4:c.1906G>A	p.Gly636Ser	p.G636S	ENST00000292408	NM_213647.1	636	Ggc/Agc	14/18	1	2	FACETS	0.662	0.576	0.757	0.662	0.576	0.757	SUBCLONAL	1	FALSE	1	0.252491946854558	2		696	825	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216702	36216702	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748120825	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	55	553	0	ENST00000222270.7:c.3868C>T	p.Arg1290Cys	p.R1290C	ENST00000222270	NM_014727.1	1290	Cgc/Tgc	13/37	1	2	FACETS	0.617	0.527	0.716	0.617	0.527	0.716	SUBCLONAL	1	FALSE	1	0.252491946854558	2		553	706	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942514	17942514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1490602805	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	68	681	1	ENST00000458235.1:c.2774G>A	p.Arg925His	p.R925H	ENST00000458235	NM_000215.3	925	cGc/cAc	20/24	1	2	FACETS	0.657	0.57	0.751	0.657	0.57	0.751	SUBCLONAL	1	FALSE	1	0.252491946854558	2		682	820	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795060	45795060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374655042	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	73	543	0	ENST00000450313.1:c.1568G>A	p.Arg523His	p.R523H	ENST00000450313	NM_012222.2	523	cGc/cAc	16/16	1	2	FACETS	0.696	0.607	0.792	0.696	0.607	0.792	SUBCLONAL	1	FALSE	1	0.252491946854558	2		543	831	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867626	78867626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781190662	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	65	711	0	ENST00000306801.3:c.2362C>T	p.Arg788Cys	p.R788C	ENST00000306801	NM_020761.2	788	Cgc/Tgc	20/34	1	2	FACETS	0.5	0.432	0.575	0.5	0.432	0.575	SUBCLONAL	1	FALSE	1	0.252491946854558	2		711	1029	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410000	139410000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369522885	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	102	756	1	ENST00000277541.6:c.1838G>A	p.Arg613His	p.R613H	ENST00000277541	NM_017617.3	613	cGc/cAc	11/34	1	2	FACETS	0.783	0.699	0.873	0.783	0.699	0.873	SUBCLONAL	1	FALSE	1	0.252491946854558	2		757	1032	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008056	29008056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755339233	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	24	353	1	ENST00000282397.4:c.713G>A	p.Arg238His	p.R238H	ENST00000282397	NM_002019.4	238	cGc/cAc	6/30	1	2	FACETS	0.512	0.401	0.641	0.512	0.401	0.641	SUBCLONAL	1	FALSE	1	0.252491946854558	2		354	371	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934985	49934985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768318968	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	62	697	0	ENST00000296474.3:c.2014G>A	p.Gly672Ser	p.G672S	ENST00000296474	NM_002447.2	672	Ggc/Agc	6/20	1	2	FACETS	0.587	0.506	0.676	0.587	0.506	0.676	SUBCLONAL	1	FALSE	1	0.252491946854558	2		697	836	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900336	3900336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148781922	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	66	654	0	ENST00000262367.5:c.760G>A	p.Ala254Thr	p.A254T	ENST00000262367	NM_004380.2	254	Gcg/Acg	2/31	1	2	FACETS	0.631	0.547	0.723	0.631	0.547	0.723	SUBCLONAL	1	FALSE	1	0.252491946854558	2		654	828	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262616	39262616	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779162761	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	37	424	0	ENST00000402219.2:c.890C>T	p.Ser297Leu	p.S297L	ENST00000402219	NM_005633.3	297	tCg/tTg	7/23	0.252491946854558	1	FACETS	0.568	0.468	0.68	0.568	0.468	0.68	SUBCLONAL	1	FALSE	0	0.252491946854558	1		424	451	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735359	204735359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553657387	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	25	306	0	ENST00000302823.3:c.160G>A	p.Ala54Thr	p.A54T	ENST00000302823	NM_005214.4	54	Gcc/Acc	2/4	1	2	FACETS	0.654	0.516	0.812	0.654	0.516	0.812	SUBCLONAL	1	FALSE	1	0.252491946854558	2		306	303	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053171	180053171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369939230	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	60	818	2	ENST00000261937.6:c.1198G>A	p.Ala400Thr	p.A400T	ENST00000261937	NM_182925.4	400	Gcc/Acc	9/30	1	2	FACETS	0.562	0.483	0.648	0.562	0.483	0.648	SUBCLONAL	1	FALSE	1	0.252491946854558	2		820	846	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845504	151845504	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	44	545	1	ENST00000262189.6:c.13508G>A	p.Cys4503Tyr	p.C4503Y	ENST00000262189	NM_170606.2	4503	tGc/tAc	52/59	0.146861537554522	3	FACETS	0.533	0.445	0.63	0.266	0.222	0.315	INDETERMINATE	1	FALSE	1	0.252491946854558	3		546	737	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951105	48951105	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	23	291	0	ENST00000267163.4:c.1267G>T	p.Gly423Ter	p.G423*	ENST00000267163	NM_000321.2	423	Gga/Tga	13/27	1	2	FACETS	0.485	0.377	0.609	0.485	0.377	0.609	SUBCLONAL	1	FALSE	1	0.252491946854558	2		291	376	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545705	63545705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751143605	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	74	445	1	ENST00000307078.5:c.889G>A	p.Ala297Thr	p.A297T	ENST00000307078	NM_004655.3	297	Gcc/Acc	3/11	1	2	FACETS	0.87	0.761	0.987	0.87	0.761	0.987	CLONAL	1	FALSE	1	0.252491946854558	2		446	674	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430341	47430341	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	30	363	0	ENST00000377045.4:c.1616C>T	p.Pro539Leu	p.P539L	ENST00000377045	NM_001654.4	539	cCc/cTc	15/16	NA	2	FACETS	0.466	0.375	0.57			1	INDETERMINATE	1	FALSE	NA	0.252491946854558	2		363	510	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032353	42032353	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779785984	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	52	518	0	ENST00000219905.7:c.4537C>T	p.Arg1513Cys	p.R1513C	ENST00000219905	NM_001164273.1	1513	Cgc/Tgc	14/24	1	2	FACETS	0.63	0.535	0.734	0.63	0.535	0.734	SUBCLONAL	1	FALSE	1	0.252491946854558	2		518	654	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993624	72993624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs997674247	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	71	639	1	ENST00000268489.5:c.421G>A	p.Ala141Thr	p.A141T	ENST00000268489	NM_006885.3	141	Gcg/Acg	2/10	1	2	FACETS	0.753	0.656	0.857	0.753	0.656	0.857	SUBCLONAL	1	FALSE	1	0.252491946854558	2		640	747	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321323	65321323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201595595	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	63	622	0	ENST00000342505.4:c.1517G>A	p.Arg506His	p.R506H	ENST00000342505	NM_002227.2	506	cGc/cAc	11/25	1	2	FACETS	0.568	0.49	0.653	0.568	0.49	0.653	SUBCLONAL	1	FALSE	1	0.252491946854558	2		622	879	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518224	103518224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376753356	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	38	266	1	ENST00000355739.4:c.2162C>T	p.Ala721Val	p.A721V	ENST00000355739	NM_000123.3	721	gCg/gTg	9/15	1	2	FACETS	0.883	0.732	1	0.883	0.732	1	CLONAL	1	FALSE	1	0.252491946854558	2		267	341	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858177	27858177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1199392510	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	37	422	0	ENST00000359303.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000359303	NM_003535.2	132	Cgt/Tgt	1/1	1	2	FACETS	0.575	0.473	0.688	0.575	0.473	0.688	SUBCLONAL	1	FALSE	1	0.252491946854558	2		422	510	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487543	38487543	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371882393	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	48	594	0	ENST00000254066.5:c.73G>A	p.Ala25Thr	p.A25T	ENST00000254066	NM_000964.3	25	Gcc/Acc	2/9	1	2	FACETS	0.53	0.447	0.621	0.53	0.447	0.621	SUBCLONAL	1	FALSE	1	0.252491946854558	2		594	718	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851985	128851985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778688	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	136	732	2	ENST00000249373.3:c.2057C>T	p.Ala686Val	p.A686V	ENST00000249373	NM_005631.4	686	gCg/gTg	12/12	0.146861537554522	3	FACETS	1	0.985	1	0.719	0.653	0.787	INDETERMINATE	1	FALSE	1	0.252491946854558	3		734	844	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140814	37140814	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1244024334	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	71	514	0	ENST00000373509.5:c.650G>A	p.Arg217His	p.R217H	ENST00000373509	NM_002648.3	217	cGc/cAc	5/6	1	2	FACETS	0.808	0.705	0.92	0.808	0.705	0.92	CLONAL	1	FALSE	1	0.252491946854558	2		514	696	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984739	72984739	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113497421	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	78	707	0	ENST00000268489.5:c.2845G>A	p.Val949Ile	p.V949I	ENST00000268489	NM_006885.3	949	Gtc/Atc	3/10	1	2	FACETS	0.683	0.599	0.774	0.683	0.599	0.774	SUBCLONAL	1	FALSE	1	0.252491946854558	2		707	905	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168942	11168942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057523566	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	48	454	0	ENST00000358026.2:c.4532G>A	p.Arg1511His	p.R1511H	ENST00000358026	NM_001128849.1	1511	cGt/cAt	32/36	1	2	FACETS	0.623	0.526	0.731	0.623	0.526	0.731	SUBCLONAL	1	FALSE	1	0.252491946854558	2		454	610	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996221	73996221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	42	393	0	ENST00000318443.5:c.955G>A	p.Ala319Thr	p.A319T	ENST00000318443	NM_001024736.1	319	Gca/Aca	5/10	1	2	FACETS	0.601	0.501	0.712	0.601	0.501	0.712	SUBCLONAL	1	FALSE	1	0.252491946854558	2		393	554	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169536	11169536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	83	756	1	ENST00000358026.2:c.4702G>A	p.Ala1568Thr	p.A1568T	ENST00000358026	NM_001128849.1	1568	Gca/Aca	33/36	1	2	FACETS	0.712	0.627	0.803	0.712	0.627	0.803	SUBCLONAL	1	FALSE	1	0.252491946854558	2		757	924	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646279	3646279	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749277750	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	82	829	0	ENST00000294008.3:c.1799C>T	p.Pro600Leu	p.P600L	ENST00000294008	NM_032444.2	600	cCg/cTg	8/15	1	2	FACETS	0.741	0.652	0.836	0.741	0.652	0.836	SUBCLONAL	1	FALSE	1	0.252491946854558	2		829	877	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243872	53243872	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1261132692	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	22	378	0	ENST00000375401.3:c.1121C>T	p.Ala374Val	p.A374V	ENST00000375401	NM_004187.3	374	gCg/gTg	8/26	NA	2	FACETS	0.4	0.309	0.506			1	INDETERMINATE	1	FALSE	NA	0.252491946854558	2		378	436	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519945	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	28	497	0	ENST00000320574.5:c.1231G>A	p.Val411Met	p.V411M	ENST00000320574	NM_006231.2	411	Gtg/Atg	13/49	1	2	FACETS	0.415	0.331	0.512	0.415	0.331	0.512	SUBCLONAL	1	FALSE	1	0.252491946854558	2		497	534	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639525	3639525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369846826	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	108	815	1	ENST00000294008.3:c.4114C>T	p.Arg1372Trp	p.R1372W	ENST00000294008	NM_032444.2	1372	Cgg/Tgg	12/15	1	2	FACETS	0.872	0.781	0.969	0.872	0.781	0.969	CLONAL	1	FALSE	1	0.252491946854558	2		816	981	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016154	31016154	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777619874	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	55	486	0	ENST00000375687.4:c.400G>A	p.Ala134Thr	p.A134T	ENST00000375687	NM_015338.5	134	Gca/Aca	6/13	1	2	FACETS	0.649	0.555	0.753	0.649	0.555	0.753	SUBCLONAL	1	FALSE	1	0.252491946854558	2		486	671	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023402	31023402	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	37	511	1	ENST00000375687.4:c.2887C>T	p.Pro963Ser	p.P963S	ENST00000375687	NM_015338.5	963	Cca/Tca	13/13	1	2	FACETS	0.574	0.472	0.687	0.574	0.472	0.687	SUBCLONAL	1	FALSE	1	0.252491946854558	2		512	511	SUCCESS
ATR	545	MSKCC	GRCh37	3	142172007	142172007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762196224	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	51	493	0	ENST00000350721.4:c.7724C>T	p.Ala2575Val	p.A2575V	ENST00000350721	NM_001184.3	2575	gCg/gTg	46/47	1	2	FACETS	0.669	0.568	0.78	0.669	0.568	0.78	SUBCLONAL	1	FALSE	1	0.252491946854558	2		493	604	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240268	41240268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1232364332	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	35	243	0	ENST00000379561.5:c.82C>T	p.Pro28Ser	p.P28S	ENST00000379561	NM_002015.3	28	Ccc/Tcc	1/3	1	2	FACETS	0.702	0.576	0.843	0.702	0.576	0.843	SUBCLONAL	1	FALSE	1	0.252491946854558	2		243	395	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88672025	88672025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782231	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	32	480	0	ENST00000372037.3:c.559C>T	p.Arg187Cys	p.R187C	ENST00000372037	NM_004329.2	187	Cgt/Tgt	8/13	1	2	FACETS	0.479	0.388	0.582	0.479	0.388	0.582	SUBCLONAL	1	FALSE	1	0.252491946854558	2		480	529	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542552	141542552	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1382113944	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	114	563	0	ENST00000220592.5:c.2434C>T	p.Arg812Trp	p.R812W	ENST00000220592	NM_012154.3	812	Cgg/Tgg	18/19	0.146861537554522	3	FACETS	1	0.983	1	0.735	0.662	0.811	INDETERMINATE	1	FALSE	1	0.252491946854558	3		563	692	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260917	16260917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377314260	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	38	440	0	ENST00000375759.3:c.8182G>A	p.Ala2728Thr	p.A2728T	ENST00000375759	NM_015001.2	2728	Gct/Act	11/15	1	2	FACETS	0.59	0.487	0.705	0.59	0.487	0.705	SUBCLONAL	1	FALSE	1	0.252491946854558	2		440	510	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262141	16262141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201304481	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	27	303	0	ENST00000375759.3:c.9406C>T	p.Arg3136Cys	p.R3136C	ENST00000375759	NM_015001.2	3136	Cgt/Tgt	11/15	1	2	FACETS	0.804	0.642	0.988	0.804	0.642	0.988	CLONAL	1	FALSE	1	0.252491946854558	2		303	266	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265870	16265870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	51	668	0	ENST00000375759.3:c.10943C>T	p.Ala3648Val	p.A3648V	ENST00000375759	NM_015001.2	3648	gCc/gTc	15/15	1	2	FACETS	0.465	0.394	0.544	0.465	0.394	0.544	SUBCLONAL	1	FALSE	1	0.252491946854558	2		668	868	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100842	27100842	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	40	462	0	ENST00000324856.7:c.4124G>A	p.Gly1375Asp	p.G1375D	ENST00000324856	NM_006015.4	1375	gGc/gAc	18/20	1	2	FACETS	0.614	0.51	0.73	0.614	0.51	0.73	SUBCLONAL	1	FALSE	1	0.252491946854558	2		462	516	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258771	115258771	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	45	354	0	ENST00000369535.4:c.11A>G	p.Tyr4Cys	p.Y4C	ENST00000369535	NM_002524.4	4	tAc/tGc	2/7	1	2	FACETS	0.724	0.609	0.852	0.724	0.609	0.852	SUBCLONAL	1	FALSE	1	0.252491946854558	2		354	492	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317721	163317721	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	28	260	0	ENST00000271452.3:c.1117G>T	p.Val373Leu	p.V373L	ENST00000271452	NM_145697.2	373	Gta/Tta	12/14	1	2	FACETS	0.767	0.615	0.94	0.767	0.615	0.94	CLONAL	1	FALSE	1	0.252491946854558	2		260	289	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944710	206944710	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	44	442	0	ENST00000423557.1:c.216G>T	p.Glu72Asp	p.E72D	ENST00000423557	NM_000572.2	72	gaG/gaT	2/5	1	2	FACETS	0.547	0.458	0.646	0.547	0.458	0.646	SUBCLONAL	1	FALSE	1	0.252491946854558	2		442	637	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450102	32450102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	92	699	2	ENST00000332351.3:c.710C>T	p.Ala237Val	p.A237V	ENST00000332351	NM_024426.4	237	gCg/gTg	2/10	1	2	FACETS	0.784	0.696	0.879	0.784	0.696	0.879	SUBCLONAL	1	FALSE	1	0.252491946854558	2		701	929	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135674	64135674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199836004	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	85	793	0	ENST00000334205.4:c.1142C>T	p.Ala381Val	p.A381V	ENST00000334205	NM_003942.2	381	gCg/gTg	10/17	1	2	FACETS	0.704	0.621	0.794	0.704	0.621	0.794	SUBCLONAL	1	FALSE	1	0.252491946854558	2		793	956	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163503	108163503	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	23	479	0	ENST00000278616.4:c.4594G>A	p.Val1532Met	p.V1532M	ENST00000278616	NM_000051.3	1532	Gtg/Atg	30/63	1	2	FACETS	0.412	0.321	0.519	0.412	0.321	0.519	SUBCLONAL	1	FALSE	1	0.252491946854558	2		479	442	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111958643	111958643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	59	411	0	ENST00000375549.3:c.115C>T	p.Pro39Ser	p.P39S	ENST00000375549	NM_003002.3	39	Cct/Tct	2/4	1	2	FACETS	0.767	0.66	0.885	0.767	0.66	0.885	SUBCLONAL	1	FALSE	1	0.252491946854558	2		411	609	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4388080	4388080	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1417189054	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	19	285	0	ENST00000261254.3:c.566C>T	p.Ala189Val	p.A189V	ENST00000261254	NM_001759.3	189	gCc/gTc	3/5	0.242126209541466	0	FACETS	0.371	0.282	0.477			1	SUBCLONAL	1	FALSE	0	0.252491946854558	0		285	303	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432498	49432498	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763549369	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	83	691	0	ENST00000301067.7:c.8641C>T	p.Arg2881Trp	p.R2881W	ENST00000301067	NM_003482.3	2881	Cgg/Tgg	34/54	1	2	FACETS	0.853	0.752	0.961	0.853	0.752	0.961	CLONAL	1	FALSE	1	0.252491946854558	2		691	771	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435457	49435457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748389081	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	90	636	1	ENST00000301067.7:c.6215G>A	p.Arg2072His	p.R2072H	ENST00000301067	NM_003482.3	2072	cGc/cAc	30/54	1	2	FACETS	0.876	0.776	0.982	0.876	0.776	0.982	CLONAL	1	FALSE	1	0.252491946854558	2		637	814	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562765	21562765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1259441480	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	56	267	0	ENST00000382592.4:c.1154G>A	p.Gly385Asp	p.G385D	ENST00000382592	NM_014572.2	385	gGc/gAc	4/8	1	2	FACETS	0.986	0.846	1	0.986	0.846	1	CLONAL	1	FALSE	1	0.252491946854558	2		267	450	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21565503	21565503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	102	659	0	ENST00000382592.4:c.383G>A	p.Ser128Asn	p.S128N	ENST00000382592	NM_014572.2	128	aGc/aAc	3/8	1	2	FACETS	0.943	0.842	1	0.943	0.842	1	CLONAL	1	FALSE	1	0.252491946854558	2		659	857	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910701	32910701	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	41	490	0	ENST00000380152.3:c.2209G>A	p.Ala737Thr	p.A737T	ENST00000380152		737	Gca/Aca	11/27	1	2	FACETS	0.709	0.591	0.841	0.709	0.591	0.841	SUBCLONAL	1	FALSE	1	0.252491946854558	2		490	458	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32921027	32921027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748816192	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	27	433	0	ENST00000380152.3:c.7001C>T	p.Pro2334Leu	p.P2334L	ENST00000380152		2334	cCc/cTc	13/27	1	2	FACETS	0.446	0.354	0.551	0.446	0.354	0.551	SUBCLONAL	1	FALSE	1	0.252491946854558	2		433	480	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945130	32945130	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80359105	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	21	324	1	ENST00000380152.3:c.8525G>A	p.Arg2842His	p.R2842H	ENST00000380152		2842	cGc/cAc	20/27	1	2	FACETS	0.492	0.379	0.625	0.492	0.379	0.625	SUBCLONAL	1	FALSE	1	0.252491946854558	2		325	338	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134441	41134441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	78	552	0	ENST00000379561.5:c.1187G>A	p.Gly396Asp	p.G396D	ENST00000379561	NM_002015.3	396	gGc/gAc	2/3	1	2	FACETS	0.964	0.847	1	0.964	0.847	1	CLONAL	1	FALSE	1	0.252491946854558	2		552	641	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239783	41239783	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	87	579	1	ENST00000379561.5:c.567G>A	p.Trp189Ter	p.W189*	ENST00000379561	NM_002015.3	189	tgG/tgA	1/3	1	2	FACETS	0.733	0.648	0.825	0.733	0.648	0.825	SUBCLONAL	1	FALSE	1	0.252491946854558	2		580	940	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434964	110434964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	114	614	1	ENST00000375856.3:c.3437G>A	p.Arg1146His	p.R1146H	ENST00000375856	NM_003749.2	1146	cGc/cAc	1/2	1	2	FACETS	0.984	0.885	1	0.984	0.885	1	CLONAL	1	FALSE	1	0.252491946854558	2		615	918	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434970	110434970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	80	623	0	ENST00000375856.3:c.3431G>A	p.Arg1144His	p.R1144H	ENST00000375856	NM_003749.2	1144	cGc/cAc	1/2	1	2	FACETS	0.696	0.611	0.787	0.696	0.611	0.787	SUBCLONAL	1	FALSE	1	0.252491946854558	2		623	911	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434992	110434992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	68	614	0	ENST00000375856.3:c.3409C>T	p.Arg1137Cys	p.R1137C	ENST00000375856	NM_003749.2	1137	Cgc/Tgc	1/2	1	2	FACETS	0.634	0.55	0.725	0.634	0.55	0.725	SUBCLONAL	1	FALSE	1	0.252491946854558	2		614	850	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436687	110436687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	173	819	0	ENST00000375856.3:c.1714C>T	p.Arg572Cys	p.R572C	ENST00000375856	NM_003749.2	572	Cgc/Tgc	1/2	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.252491946854558	2		819	988	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331743	68331743	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	26	237	0	ENST00000487270.1:c.343del	p.Thr115LeufsTer5	p.T115Lfs*5	ENST00000487270	NM_133509.3	113	ggA/gg	5/11	1	2	FACETS	0.622	0.493	0.77	0.622	0.493	0.77	SUBCLONAL	1	FALSE	1	0.252491946854558	2		237	331	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054422	42054422	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	23	405	0	ENST00000219905.7:c.7606G>T	p.Asp2536Tyr	p.D2536Y	ENST00000219905	NM_001164273.1	2536	Gat/Tat	22/24	1	2	FACETS	0.522	0.407	0.656	0.522	0.407	0.656	SUBCLONAL	1	FALSE	1	0.252491946854558	2		405	349	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347978	347978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771101523	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	67	849	1	ENST00000262320.3:c.1528G>A	p.Ala510Thr	p.A510T	ENST00000262320	NM_003502.3	510	Gcc/Acc	6/11	1	2	FACETS	0.609	0.528	0.697	0.609	0.528	0.697	SUBCLONAL	1	FALSE	1	0.252491946854558	2		850	872	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396718	396718	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	75	616	0	ENST00000262320.3:c.308G>T	p.Arg103Met	p.R103M	ENST00000262320	NM_003502.3	103	aGg/aTg	2/11	1	2	FACETS	0.903	0.791	1	0.903	0.791	1	CLONAL	1	FALSE	1	0.252491946854558	2		616	658	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134473	2134473	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343536158	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	72	820	1	ENST00000219476.3:c.4250G>A	p.Arg1417Gln	p.R1417Q	ENST00000219476	NM_000548.3	1417	cGg/cAg	34/42	1	2	FACETS	0.559	0.486	0.637	0.559	0.486	0.637	SUBCLONAL	1	FALSE	1	0.252491946854558	2		821	1021	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134493	2134493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1216613310	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	67	815	0	ENST00000219476.3:c.4270G>A	p.Asp1424Asn	p.D1424N	ENST00000219476	NM_000548.3	1424	Gac/Aac	34/42	1	2	FACETS	0.552	0.478	0.633	0.552	0.478	0.633	SUBCLONAL	1	FALSE	1	0.252491946854558	2		815	961	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786794	3786794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	45	389	0	ENST00000262367.5:c.4417G>A	p.Ala1473Thr	p.A1473T	ENST00000262367	NM_004380.2	1473	Gcc/Acc	27/31	1	2	FACETS	0.762	0.64	0.896	0.762	0.64	0.896	SUBCLONAL	1	FALSE	1	0.252491946854558	2		389	468	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857586	9857586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	32	421	0	ENST00000330684.3:c.3815C>T	p.Ala1272Val	p.A1272V	ENST00000330684	NM_001134407.1	1272	gCa/gTa	13/13	1	2	FACETS	0.515	0.417	0.626	0.515	0.417	0.626	SUBCLONAL	1	FALSE	1	0.252491946854558	2		421	492	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641779	23641779	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746582620	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	15	267	0	ENST00000261584.4:c.1696C>T	p.Arg566Cys	p.R566C	ENST00000261584	NM_024675.3	566	Cgt/Tgt	5/13	1	2	FACETS	0.407	0.297	0.539	0.407	0.297	0.539	SUBCLONAL	1	FALSE	1	0.252491946854558	2		267	292	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72863735	72863735	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	66	524	0	ENST00000268489.5:c.3472G>T	p.Gly1158Ter	p.G1158*	ENST00000268489	NM_006885.3	1158	Gga/Tga	5/10	1	2	FACETS	0.712	0.617	0.815	0.712	0.617	0.815	SUBCLONAL	1	FALSE	1	0.252491946854558	2		524	734	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346600	89346600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749269329	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	41	536	0	ENST00000301030.4:c.6350C>T	p.Pro2117Leu	p.P2117L	ENST00000301030	NM_001256183.1	2117	cCg/cTg	9/13	1	2	FACETS	0.695	0.579	0.825	0.695	0.579	0.825	SUBCLONAL	1	FALSE	1	0.252491946854558	2		536	467	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348320	89348320	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761378635	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	67	882	1	ENST00000301030.4:c.4630G>A	p.Asp1544Asn	p.D1544N	ENST00000301030	NM_001256183.1	1544	Gac/Aac	9/13	1	2	FACETS	0.497	0.431	0.57	0.497	0.431	0.57	SUBCLONAL	1	FALSE	1	0.252491946854558	2		883	1067	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351934	89351934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1269	118	953	0	ENST00000301030.4:c.1016C>T	p.Ala339Val	p.A339V	ENST00000301030	NM_001256183.1	339	gCc/gTc	9/13	1	2	FACETS	0.674	0.606	0.746	0.674	0.606	0.746	SUBCLONAL	1	FALSE	1	0.252491946854558	2		953	1387	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075175	16075175	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	47	375	0	ENST00000268712.3:c.377T>C	p.Val126Ala	p.V126A	ENST00000268712	NM_006311.3	126	gTt/gCt	4/46	1	2	FACETS	0.63	0.531	0.739	0.63	0.531	0.739	SUBCLONAL	1	FALSE	1	0.252491946854558	2		375	591	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127300	17127300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	78	680	0	ENST00000285071.4:c.554C>T	p.Ser185Phe	p.S185F	ENST00000285071	NM_144997.5	185	tCc/tTc	6/14	1	2	FACETS	0.821	0.72	0.928	0.821	0.72	0.928	CLONAL	1	FALSE	1	0.252491946854558	2		680	753	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868246	37868246	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	77	679	0	ENST00000269571.5:c.967A>C	p.Thr323Pro	p.T323P	ENST00000269571		323	Aca/Cca	8/27	1	2	FACETS	0.685	0.6	0.777	0.685	0.6	0.777	SUBCLONAL	1	FALSE	1	0.252491946854558	2		679	890	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883225	37883225	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	60	701	0	ENST00000269571.5:c.3128T>C	p.Val1043Ala	p.V1043A	ENST00000269571		1043	gTc/gCc	25/27	1	2	FACETS	0.622	0.535	0.717	0.622	0.535	0.717	SUBCLONAL	1	FALSE	1	0.252491946854558	2		701	764	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866583	78866583	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	88	658	0	ENST00000306801.3:c.2156C>A	p.Ser719Tyr	p.S719Y	ENST00000306801	NM_020761.2	719	tCt/tAt	19/34	1	2	FACETS	0.687	0.607	0.773	0.687	0.607	0.773	SUBCLONAL	1	FALSE	1	0.252491946854558	2		658	1015	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899174	78899174	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199756138	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	68	414	1	ENST00000306801.3:c.2813C>T	p.Ala938Val	p.A938V	ENST00000306801	NM_020761.2	938	gCg/gTg	24/34	1	2	FACETS	0.798	0.694	0.911	0.798	0.694	0.911	CLONAL	1	FALSE	1	0.252491946854558	2		415	675	SUCCESS
YES1	7525	MSKCC	GRCh37	18	747948	747948	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	30	519	0	ENST00000314574.4:c.442G>A	p.Ala148Thr	p.A148T	ENST00000314574	NM_005433.3	148	Gcg/Acg	4/12	1	2	FACETS	0.451	0.362	0.552	0.451	0.362	0.552	SUBCLONAL	1	FALSE	1	0.252491946854558	2		519	527	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2199922	2199922	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	73	678	2	ENST00000398665.3:c.691C>T	p.Arg231Ter	p.R231*	ENST00000398665	NM_032482.2	231	Cga/Tga	8/28	1	2	FACETS	0.632	0.551	0.719	0.632	0.551	0.719	SUBCLONAL	1	FALSE	1	0.252491946854558	2		680	915	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265039	5265039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748364975	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	72	640	1	ENST00000357368.4:c.548G>A	p.Arg183His	p.R183H	ENST00000357368	NM_002850.3	183	cGc/cAc	5/38	1	2	FACETS	0.69	0.602	0.786	0.69	0.602	0.786	SUBCLONAL	1	FALSE	1	0.252491946854558	2		641	826	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955144	17955144	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	65	801	0	ENST00000458235.1:c.83T>C	p.Val28Ala	p.V28A	ENST00000458235	NM_000215.3	28	gTg/gCg	2/24	1	2	FACETS	0.583	0.504	0.669	0.583	0.504	0.669	SUBCLONAL	1	FALSE	1	0.252491946854558	2		801	883	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961631	18961631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339234477	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	92	661	1	ENST00000262803.5:c.764G>A	p.Arg255His	p.R255H	ENST00000262803	NM_002911.3	255	cGc/cAc	5/24	1	2	FACETS	0.921	0.818	1	0.921	0.818	1	CLONAL	1	FALSE	1	0.252491946854558	2		662	791	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18963101	18963101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	94	624	0	ENST00000262803.5:c.968C>T	p.Ser323Phe	p.S323F	ENST00000262803	NM_002911.3	323	tCc/tTc	6/24	1	2	FACETS	0.85	0.755	0.951	0.85	0.755	0.951	CLONAL	1	FALSE	1	0.252491946854558	2		624	876	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967719	18967719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1169322559	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	72	671	0	ENST00000262803.5:c.1858G>A	p.Ala620Thr	p.A620T	ENST00000262803	NM_002911.3	620	Gcc/Acc	14/24	1	2	FACETS	0.707	0.616	0.805	0.707	0.616	0.805	SUBCLONAL	1	FALSE	1	0.252491946854558	2		671	807	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758287	41758287	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	66	648	0	ENST00000301178.4:c.1743T>A	p.Asp581Glu	p.D581E	ENST00000301178	NM_021913.4	581	gaT/gaA	15/20	1	2	FACETS	0.689	0.597	0.789	0.689	0.597	0.789	SUBCLONAL	1	FALSE	1	0.252491946854558	2		648	759	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858973	45858973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	86	602	1	ENST00000391945.4:c.1493G>A	p.Gly498Asp	p.G498D	ENST00000391945	NM_000400.3	498	gGc/gAc	16/23	1	2	FACETS	0.799	0.705	0.899	0.799	0.705	0.899	SUBCLONAL	1	FALSE	1	0.252491946854558	2		603	853	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723484	52723484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	70	491	0	ENST00000322088.6:c.1345G>A	p.Ala449Thr	p.A449T	ENST00000322088	NM_014225.5	449	Gcc/Acc	11/15	1	2	FACETS	0.786	0.685	0.896	0.786	0.685	0.896	SUBCLONAL	1	FALSE	1	0.252491946854558	2		491	705	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285941	39285941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	39	346	0	ENST00000402219.2:c.218G>A	p.Arg73His	p.R73H	ENST00000402219	NM_005633.3	73	cGt/cAt	3/23	0.252491946854558	1	FACETS	0.823	0.684	0.976	0.823	0.684	0.976	CLONAL	1	FALSE	0	0.252491946854558	1		346	328	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919695	96919695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	48	536	0	ENST00000258439.3:c.568G>A	p.Ala190Thr	p.A190T	ENST00000258439	NM_001193304.2	190	Gcc/Acc	4/4	1	2	FACETS	0.654	0.553	0.767	0.654	0.553	0.767	SUBCLONAL	1	FALSE	1	0.252491946854558	2		536	581	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660127	227660127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	61	638	0	ENST00000305123.5:c.3328G>A	p.Ala1110Thr	p.A1110T	ENST00000305123	NM_005544.2	1110	Gcc/Acc	1/2	1	2	FACETS	0.645	0.555	0.743	0.645	0.555	0.743	SUBCLONAL	1	FALSE	1	0.252491946854558	2		638	749	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012599	36012599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	30	437	0	ENST00000358208.4:c.43C>T	p.Arg15Cys	p.R15C	ENST00000358208		15	Cgc/Tgc	2/12	1	2	FACETS	0.44	0.354	0.539	0.44	0.354	0.539	SUBCLONAL	1	FALSE	1	0.252491946854558	2		437	540	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480460	57480460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	27	260	0	ENST00000371085.3:c.455C>T	p.Ala152Val	p.A152V	ENST00000371085	NM_000516.4	152	gCt/gTt	6/13	1	2	FACETS	0.441	0.35	0.545	0.441	0.35	0.545	SUBCLONAL	1	FALSE	1	0.252491946854558	2		260	485	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167595	24167595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	47	451	0	ENST00000263121.7:c.979G>A	p.Ala327Thr	p.A327T	ENST00000263121	NM_003073.3	327	Gcc/Acc	7/9	1	2	FACETS	0.601	0.507	0.706	0.601	0.507	0.706	SUBCLONAL	1	FALSE	1	0.252491946854558	2		451	619	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627415	37627415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415916204	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	84	651	3	ENST00000249071.6:c.304C>T	p.Arg102Trp	p.R102W	ENST00000249071	NM_002872.4	102	Cgg/Tgg	5/7	1	2	FACETS	0.776	0.685	0.875	0.776	0.685	0.875	SUBCLONAL	1	FALSE	1	0.252491946854558	2		654	857	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547916	41547916	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	46	468	1	ENST00000263253.7:c.2897C>T	p.Ala966Val	p.A966V	ENST00000263253	NM_001429.3	966	gCc/gTc	15/31	1	2	FACETS	0.62	0.521	0.729	0.62	0.521	0.729	SUBCLONAL	1	FALSE	1	0.252491946854558	2		469	588	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645681	12645681	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397516830	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	32	289	0	ENST00000251849.4:c.788T>C	p.Val263Ala	p.V263A	ENST00000251849	NM_002880.3	263	gTc/gCc	7/17	1	2	FACETS	0.741	0.602	0.897	0.741	0.602	0.897	SUBCLONAL	1	FALSE	1	0.252491946854558	2		289	342	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928849	49928849	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	49	831	0	ENST00000296474.3:c.3517A>G	p.Ile1173Val	p.I1173V	ENST00000296474	NM_002447.2	1173	Atc/Gtc	16/20	1	2	FACETS	0.502	0.424	0.588	0.502	0.424	0.588	SUBCLONAL	1	FALSE	1	0.252491946854558	2		831	773	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259055	89259055	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	30	286	0	ENST00000336596.2:c.199A>G	p.Thr67Ala	p.T67A	ENST00000336596	NM_005233.5	67	Act/Gct	3/17	1	2	FACETS	0.757	0.611	0.921	0.757	0.611	0.921	CLONAL	1	FALSE	1	0.252491946854558	2		286	314	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119721051	119721051	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	88	509	1	ENST00000316626.5:c.124G>A	p.Ala42Thr	p.A42T	ENST00000316626		42	Gca/Aca	2/12	1	2	FACETS	0.876	0.775	0.983	0.876	0.775	0.983	CLONAL	1	FALSE	1	0.252491946854558	2		510	796	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664771	138664771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	18	173	0	ENST00000330315.3:c.794C>T	p.Ala265Val	p.A265V	ENST00000330315	NM_023067.3	265	gCg/gTg	1/1	1	2	FACETS	0.416	0.312	0.538	0.416	0.312	0.538	SUBCLONAL	1	FALSE	1	0.252491946854558	2		173	343	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260145	149260145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200641813	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	49	444	0	ENST00000360632.3:c.748C>T	p.Arg250Cys	p.R250C	ENST00000360632	NM_015472.4	250	Cgc/Tgc	4/7	1	2	FACETS	0.721	0.611	0.843	0.721	0.611	0.843	SUBCLONAL	1	FALSE	1	0.252491946854558	2		444	538	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456529	189456529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752080701	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	34	447	0	ENST00000264731.3:c.290G>A	p.Arg97His	p.R97H	ENST00000264731	NM_003722.4	97	cGc/cAc	3/14	1	2	FACETS	0.465	0.379	0.562	0.465	0.379	0.562	SUBCLONAL	1	FALSE	1	0.252491946854558	2		447	579	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592136	55592136	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1458834829	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	38	464	1	ENST00000288135.5:c.1460G>T	p.Gly487Val	p.G487V	ENST00000288135	NM_000222.2	487	gGc/gTc	9/21	1	2	FACETS	0.482	0.398	0.577	0.482	0.398	0.577	SUBCLONAL	1	FALSE	1	0.252491946854558	2		465	624	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84403335	84403335	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	26	361	0	ENST00000321945.7:c.150G>A	p.Met50Ile	p.M50I	ENST00000321945	NM_139076.2	50	atG/atA	2/9	1	2	FACETS	0.413	0.326	0.513	0.413	0.326	0.513	SUBCLONAL	1	FALSE	1	0.252491946854558	2		361	499	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143129680	143129680	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs977557624	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	20	311	0	ENST00000262992.4:c.970T>C	p.Ser324Pro	p.S324P	ENST00000262992	NM_001101669.1	324	Tcc/Ccc	12/24	1	2	FACETS	0.416	0.317	0.532	0.416	0.317	0.532	SUBCLONAL	1	FALSE	1	0.252491946854558	2		311	381	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510206	187510206	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	43	442	0	ENST00000441802.2:c.13307C>A	p.Pro4436His	p.P4436H	ENST00000441802	NM_005245.3	4436	cCt/cAt	27/27	1	2	FACETS	0.557	0.465	0.659	0.557	0.465	0.659	SUBCLONAL	1	FALSE	1	0.252491946854558	2		442	612	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508765	31508765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	90	656	0	ENST00000344624.3:c.1550G>A	p.Arg517Gln	p.R517Q	ENST00000344624		517	cGa/cAa	7/33	1	2	FACETS	0.678	0.6	0.762	0.678	0.6	0.762	SUBCLONAL	1	FALSE	1	0.252491946854558	2		656	1051	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508786	31508786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	99	633	0	ENST00000344624.3:c.1529G>A	p.Arg510His	p.R510H	ENST00000344624		510	cGc/cAc	7/33	1	2	FACETS	0.772	0.687	0.862	0.772	0.687	0.862	SUBCLONAL	1	FALSE	1	0.252491946854558	2		633	1016	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80171602	80171602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576204286	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	33	527	1	ENST00000265081.6:c.3335C>T	p.Thr1112Met	p.T1112M	ENST00000265081	NM_002439.4	1112	aCg/aTg	24/24	1	2	FACETS	0.459	0.372	0.556	0.459	0.372	0.556	SUBCLONAL	1	FALSE	1	0.252491946854558	2		528	570	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149506127	149506127	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	51	602	0	ENST00000261799.4:c.1630C>A	p.Leu544Ile	p.L544I	ENST00000261799	NM_002609.3	544	Ctc/Atc	11/23	1	2	FACETS	0.565	0.479	0.66	0.565	0.479	0.66	SUBCLONAL	1	FALSE	1	0.252491946854558	2		602	715	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402753	20402753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	20	207	1	ENST00000346618.3:c.290G>A	p.Ser97Asn	p.S97N	ENST00000346618	NM_001949.4	97	aGc/aAc	1/7	1	2	FACETS	0.461	0.352	0.588	0.461	0.352	0.588	SUBCLONAL	1	FALSE	1	0.252491946854558	2		208	344	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481613	20481613	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	19	263	0	ENST00000346618.3:c.682A>G	p.Ile228Val	p.I228V	ENST00000346618	NM_001949.4	228	Atc/Gtc	3/7	1	2	FACETS	0.426	0.323	0.548	0.426	0.323	0.548	SUBCLONAL	1	FALSE	1	0.252491946854558	2		263	353	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797235	32797235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768383489	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	103	787	1	ENST00000374899.4:c.1874C>T	p.Pro625Leu	p.P625L	ENST00000374899	NM_018833.2	625	cCg/cTg	11/12	1	2	FACETS	0.746	0.666	0.832	0.746	0.666	0.832	SUBCLONAL	1	FALSE	1	0.252491946854558	2		788	1093	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687431	117687431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	33	319	0	ENST00000368508.3:c.2620G>A	p.Glu874Lys	p.E874K	ENST00000368508	NM_002944.2	874	Gaa/Aaa	18/43	1	2	FACETS	0.657	0.535	0.794	0.657	0.535	0.794	SUBCLONAL	1	FALSE	1	0.252491946854558	2		319	398	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524761	137524761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258321707	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	39	413	1	ENST00000367739.4:c.608C>T	p.Ala203Val	p.A203V	ENST00000367739	NM_000416.2	203	gCg/gTg	5/7	1	2	FACETS	0.648	0.537	0.772	0.648	0.537	0.772	SUBCLONAL	1	FALSE	1	0.252491946854558	2		414	477	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935607	13935607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751525538	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	36	381	0	ENST00000405192.2:c.1249C>T	p.Arg417Cys	p.R417C	ENST00000405192	NM_001163147.1	417	Cgt/Tgt	12/12	0.146861537554522	3	FACETS	0.551	0.452	0.662	0.275	0.226	0.331	INDETERMINATE	1	FALSE	1	0.252491946854558	3		381	583	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508611	106508611	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	54	453	0	ENST00000359195.3:c.605T>C	p.Val202Ala	p.V202A	ENST00000359195	NM_002649.2	202	gTg/gCg	2/11	0.146861537554522	3	FACETS	0.796	0.68	0.924	0.398	0.34	0.462	INDETERMINATE	1	FALSE	1	0.252491946854558	3		453	605	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415023	116415023	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs575907920	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	36	547	0	ENST00000397752.3:c.3117C>A	p.Asp1039Glu	p.D1039E	ENST00000397752	NM_000245.2	1039	gaC/gaA	15/21	0.146861537554522	3	FACETS	0.506	0.415	0.608	0.253	0.207	0.304	INDETERMINATE	1	FALSE	1	0.252491946854558	3		547	635	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271703	38271703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1415925468	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	70	802	1	ENST00000425967.3:c.2246G>A	p.Arg749His	p.R749H	ENST00000425967	NM_001174067.1	749	cGc/cAc	17/19	0.146861537554522	3	FACETS	0.622	0.541	0.71	0.311	0.27	0.355	INDETERMINATE	1	FALSE	1	0.252491946854558	3		803	1004	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942777	68942777	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	55	492	1	ENST00000288368.4:c.589G>A	p.Val197Met	p.V197M	ENST00000288368	NM_024870.2	197	Gtg/Atg	6/40	0.146861537554522	3	FACETS	0.571	0.487	0.663	0.285	0.243	0.332	INDETERMINATE	1	FALSE	1	0.252491946854558	3		493	860	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054630	5054630	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772744665	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	27	306	2	ENST00000381652.3:c.682C>T	p.Arg228Ter	p.R228*	ENST00000381652	NM_004972.3	228	Cga/Tga	7/25	1	2	FACETS	0.745	0.594	0.917	0.745	0.594	0.917	CLONAL	1	FALSE	1	0.252491946854558	2		308	287	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517889	8517889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	36	290	0	ENST00000356435.5:c.1502G>A	p.Gly501Asp	p.G501D	ENST00000356435		501	gGt/gAt	10/35	1	2	FACETS	0.819	0.675	0.98	0.819	0.675	0.98	CLONAL	1	FALSE	1	0.252491946854558	2		290	348	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760508	133760508	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	83	711	0	ENST00000318560.5:c.2831A>G	p.Asp944Gly	p.D944G	ENST00000318560	NM_005157.4	944	gAc/gGc	11/11	1	2	FACETS	0.722	0.636	0.814	0.722	0.636	0.814	SUBCLONAL	1	FALSE	1	0.252491946854558	2		711	911	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781250	135781250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	57	568	0	ENST00000298552.3:c.1715G>A	p.Cys572Tyr	p.C572Y	ENST00000298552	NM_001162426.1	572	tGc/tAc	15/23	1	2	FACETS	0.675	0.578	0.781	0.675	0.578	0.781	SUBCLONAL	1	FALSE	1	0.252491946854558	2		568	669	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841268	15841269	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	14	133	0	ENST00000307771.7:c.1352_1353delinsAT	p.Arg451His	p.R451H	ENST00000307771	NM_005089.3	451	cGC/cAT	11/11	NA	2	FACETS	0.637	0.462	0.848			1	INDETERMINATE	1	FALSE	NA	0.252491946854558	2		133	174	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932841	39932841	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	28	368	0	ENST00000378444.4:c.1758C>A	p.Ser586Arg	p.S586R	ENST00000378444	NM_001123385.1	586	agC/agA	4/15	NA	2	FACETS	0.533	0.426	0.656			1	INDETERMINATE	1	FALSE	NA	0.252491946854558	2		368	416	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349961	70349961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	88	394	0	ENST00000374080.3:c.3944C>T	p.Ala1315Val	p.A1315V	ENST00000374080		1315	gCc/gTc	28/45	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	FALSE	NA	0.252491946854558	2		394	544	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	308	300	0				ENST00000310581	NM_198253.2	-/1132			0.667433401850025	2	FACETS	0.946	0.909	0.983	0.946	0.909	0.983	CLONAL	2	TRUE	0	0.704571361729643	2		300	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	741	663	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.704571361729643	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.704571361729643	2		663	984	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101612	27101612	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	420	839	0	ENST00000324856.7:c.4899del	p.Met1634Ter	p.M1634*	ENST00000324856	NM_006015.4	1632	Ccc/cc	18/20	0.14884044014954	3	FACETS	1	0.995	1	0.715	0.682	0.748	INDETERMINATE	1	TRUE	1	0.704571361729643	3		839	1128	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033967	49033967	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1131690865	NA	P-0040843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	167	367	0	ENST00000267163.4:c.2104C>T	p.Gln702Ter	p.Q702*	ENST00000267163	NM_000321.2	702	Caa/Taa	20/27	0.704571361729643	1	FACETS	0.936	0.876	0.996	0.936	0.876	0.996	CLONAL	1	TRUE	0	0.704571361729643	1		367	328	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134547	2134547	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs45469392	NA	P-0040843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	102	864	0	ENST00000219476.3:c.4324G>T	p.Glu1442Ter	p.E1442*	ENST00000219476	NM_000548.3	1442	Gag/Tag	34/42	1	2	FACETS	0.288	0.256	0.321	0.288	0.256	0.321	SUBCLONAL	1	TRUE	1	0.704571361729643	2		864	1007	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553117	106553117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750485966	NA	P-0040843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	250	529	0	ENST00000369096.4:c.1082C>T	p.Ser361Phe	p.S361F	ENST00000369096	NM_001198.3	361	tCc/tTc	5/7	0.288295156463194	3	FACETS	1	0.978	1	0.548	0.513	0.583	INDETERMINATE	1	TRUE	1	0.704571361729643	3		529	876	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0040885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	168	541	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.594965176194413	1	FACETS	0.977	0.909	1	0.977	0.909	1	CLONAL	1	TRUE	0	0.594965176194413	1		541	406	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	111	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.554914934287553	1	FACETS	0.964	0.881	1	0.964	0.881	1	CLONAL	1	TRUE	0	0.594965176194413	1		326	272	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	202	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.656596573930986	2		326	438	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0040916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	4313	535	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.656596573930986	32	FACETS	1	0.998	1			1	CLONAL	31	TRUE	NA	0.656596573930986	32		535	4571	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427276	49427276	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	158	568	0	ENST00000301067.7:c.11212C>T	p.Gln3738Ter	p.Q3738*	ENST00000301067	NM_003482.3	3738	Cag/Tag	39/54	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.656596573930986	2		568	445	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271507	15271507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771682246	NA	P-0040916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	240	782	1	ENST00000263388.2:c.6932C>T	p.Pro2311Leu	p.P2311L	ENST00000263388	NM_000435.2	2311	cCg/cTg	33/33	1	2	FACETS	0.952	0.892	1	0.952	0.892	1	CLONAL	1	TRUE	1	0.656596573930986	2		783	768	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555525585	NA	P-0040920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	52	481	0	ENST00000269305.4:c.673-2A>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.192211303287605	2	FACETS	0.806	0.696	0.924	0.806	0.696	0.924	CLONAL	2	TRUE	0	0.31464136401446	2		481	205	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259663	11259683	+	inframe_deletion	In_Frame_Del	DEL	GTGAGGTGAGGGCCAACTCGA	GTGAGGTGAGGGCCAACTCGA	-	novel	NA	P-0040920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	18	498	1	ENST00000361445.4:c.4022_4042del	p.Ile1341_Gln1348delinsLys	p.I1341_Q1348delinsK	ENST00000361445	NM_004958.3	1341	aTCGAGTTGGCCCTCACCTCACaa/aaa	27/58	0.199910696873656	2	FACETS	0.338	0.254	0.437	0.169	0.127	0.219	SUBCLONAL	1	TRUE	0	0.31464136401446	2		499	339	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16021327	16021327	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	32	240	0	ENST00000268712.3:c.1930G>T	p.Gly644Cys	p.G644C	ENST00000268712	NM_006311.3	644	Ggt/Tgt	18/46	0.192211303287605	2	FACETS	0.896	0.732	1	0.448	0.366	0.54	CLONAL	1	TRUE	0	0.31464136401446	2		240	227	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511529	38511529	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	19	546	0	ENST00000254066.5:c.1027G>C	p.Glu343Gln	p.E343Q	ENST00000254066	NM_000964.3	343	Gag/Cag	8/9	0.192211303287605	2	FACETS	0.595	0.453	0.76	0.297	0.226	0.38	SUBCLONAL	1	TRUE	0	0.31464136401446	2		546	203	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137406	202137406	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	58	385	0	ENST00000358485.4:c.634G>T	p.Gly212Ter	p.G212*	ENST00000358485	NM_001080125.1	212	Gga/Tga	4/9	0.134524170643763	3	FACETS	0.765	0.663	0.874	0.51	0.442	0.583	INDETERMINATE	2	TRUE	0	0.31464136401446	3		385	279	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148875	119148876	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0040983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	173	256	1	ENST00000264033.4:c.1096-1_1096delinsAA		p.X366_splice	ENST00000264033	NM_005188.3	366		8/16	0.738669155653335	2	FACETS	0.901	0.853	0.947	0.901	0.853	0.947	CLONAL	2	TRUE	0	0.738669155653335	2		257	260	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820773	3820773	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142047649	NA	P-0040983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	379	801	2	ENST00000262367.5:c.2678C>T	p.Ser893Leu	p.S893L	ENST00000262367	NM_004380.2	893	tCg/tTg	14/31	1	2	FACETS	0.985	0.937	1	0.985	0.937	1	CLONAL	1	TRUE	1	0.738669155653335	2		803	1042	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556852	29556852	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0040983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	138	296	0	ENST00000356175.3:c.2851-1G>A		p.X951_splice	ENST00000356175	NM_000267.3	951			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.738669155653335	2		296	338	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972861	55972861	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	151	401	0	ENST00000263923.4:c.1529A>C	p.Lys510Thr	p.K510T	ENST00000263923	NM_002253.2	510	aAa/aCa	11/30	0.738669155653335	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.738669155653335	1		401	238	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434077	121434077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	215	560	0	ENST00000257555.6:c.968G>A	p.Gly323Glu	p.G323E	ENST00000257555		323	gGa/gAa	5/10	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.738669155653335	2		560	581	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874197	155874197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375724784	NA	P-0040983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	322	595	0	ENST00000368323.3:c.334C>T	p.Arg112Cys	p.R112C	ENST00000368323	NM_006912.5	112	Cgt/Tgt	5/6	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.738669155653335	2		595	851	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483981	212483981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	107	349	0	ENST00000342788.4:c.2222G>A	p.Gly741Glu	p.G741E	ENST00000342788	NM_005235.2	741	gGa/gAa	19/28	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.738669155653335	2		349	272	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95573993	95573993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	99	281	0	ENST00000393063.1:c.2756C>T	p.Pro919Leu	p.P919L	ENST00000393063	NM_030621.3	919	cCc/cTc	18/28	1	2	FACETS	0.876	0.792	0.963	0.876	0.792	0.963	CLONAL	1	TRUE	1	0.738669155653335	2		281	306	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217310	66217310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	90	207	0	ENST00000273854.3:c.2305G>A	p.Asp769Asn	p.D769N	ENST00000273854	NM_004439.5	769	Gat/Aat	14/18	0.738669155653335	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.738669155653335	1		207	144	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38148059	38148059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	282	634	0	ENST00000317025.8:c.3052C>T	p.Pro1018Ser	p.P1018S	ENST00000317025	NM_023034.1	1018	Cct/Tct	17/24	1	2	FACETS	0.957	0.903	1	0.957	0.903	1	CLONAL	1	TRUE	1	0.738669155653335	2		634	798	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816536	32816536	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1392845171	NA	P-0040983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	346	725	0	ENST00000354258.4:c.1639C>T	p.Arg547Cys	p.R547C	ENST00000354258	NM_000593.5	547	Cgc/Tgc	7/11	1	2	FACETS	0.968	0.919	1	0.968	0.919	1	CLONAL	1	TRUE	1	0.738669155653335	2		725	968	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32438063	32438063	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762688982	NA	P-0040983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	211	498	0	ENST00000332351.3:c.974C>T	p.Ser325Leu	p.S325L	ENST00000332351	NM_024426.4	325	tCa/tTa	5/10	1	2	FACETS	0.999	0.935	1	0.999	0.935	1	CLONAL	1	TRUE	1	0.738669155653335	2		498	572	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912785	100912785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	299	380	0	ENST00000325455.5:c.2537C>T	p.Ser846Leu	p.S846L	ENST00000325455	NM_001202474.3	846	tCa/tTa	7/8	0.738669155653335	2	FACETS	0.968	0.932	1	0.968	0.932	1	CLONAL	2	TRUE	0	0.738669155653335	2		380	418	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650552	18650552	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0040983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	77	326	0	ENST00000266497.5:c.2764-1G>A		p.X922_splice	ENST00000266497		922			1	2	FACETS	0.79	0.702	0.881	0.79	0.702	0.881	SUBCLONAL	1	TRUE	1	0.738669155653335	2		326	264	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972722	32972722	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	185	400	0	ENST00000380152.3:c.10072G>A	p.Gly3358Arg	p.G3358R	ENST00000380152		3358	Gga/Aga	27/27	0.738669155653335	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.738669155653335	1		400	311	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027136	49027136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	88	272	0	ENST00000267163.4:c.1703C>T	p.Pro568Leu	p.P568L	ENST00000267163	NM_000321.2	568	cCt/cTt	18/27	0.732158261814431	2	FACETS	0.946	0.851	1	0.473	0.425	0.522	CLONAL	1	TRUE	0	0.738669155653335	2		272	252	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95597866	95597867	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	134	394	0	ENST00000393063.1:c.417_418delinsTT	p.Gln140Ter	p.Q140*	ENST00000393063	NM_030621.3	139	aaCCaa/aaTTaa	5/28	1	2	FACETS	0.881	0.808	0.956	0.881	0.808	0.956	CLONAL	1	TRUE	1	0.738669155653335	2		394	412	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88428932	88428932	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	152	405	0	ENST00000360948.2:c.2168G>A	p.Trp723Ter	p.W723*	ENST00000360948	NM_001012338.2	723	tGg/tAg	17/19	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.738669155653335	2		405	346	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641142	3641142	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	399	936	1	ENST00000294008.3:c.2497T>A	p.Leu833Met	p.L833M	ENST00000294008	NM_032444.2	833	Ttg/Atg	12/15	1	2	FACETS	0.941	0.896	0.987	0.941	0.896	0.987	CLONAL	1	TRUE	1	0.738669155653335	2		937	1148	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051135	13051135	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	228	592	0	ENST00000316448.5:c.571G>A	p.Val191Met	p.V191M	ENST00000316448	NM_004343.3	191	Gtg/Atg	5/9	1	2	FACETS	0.923	0.864	0.982	0.923	0.864	0.982	CLONAL	1	TRUE	1	0.738669155653335	2		592	669	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794832	242794832	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	206	582	0	ENST00000334409.5:c.377T>A	p.Ile126Asn	p.I126N	ENST00000334409	NM_005018.2	126	aTc/aAc	2/5	1	2	FACETS	0.923	0.862	0.986	0.923	0.862	0.986	CLONAL	1	TRUE	1	0.738669155653335	2		582	604	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293988	1293988	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1393461978	NA	P-0040983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	399	937	0	ENST00000310581.5:c.1013A>G	p.Lys338Arg	p.K338R	ENST00000310581	NM_198253.2	338	aAg/aGg	2/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.738669155653335	2		937	1035	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170022	32170022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	329	805	1	ENST00000375023.3:c.3586G>A	p.Gly1196Arg	p.G1196R	ENST00000375023	NM_004557.3	1196	Gga/Aga	21/30	1	2	FACETS	0.996	0.945	1	0.996	0.945	1	CLONAL	1	TRUE	1	0.738669155653335	2		806	894	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058470	69058470	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	113	422	0	ENST00000288368.4:c.4114G>C	p.Gly1372Arg	p.G1372R	ENST00000288368	NM_024870.2	1372	Gga/Cga	34/40	1	2	FACETS	0.93	0.847	1	0.93	0.847	1	CLONAL	1	TRUE	1	0.738669155653335	2		422	329	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293676	137293676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	276	733	0	ENST00000481739.1:c.227C>T	p.Ser76Phe	p.S76F	ENST00000481739	NM_002957.4	76	tCc/tTc	2/10	0.738669155653335	1	FACETS	0.928	0.883	0.973	0.928	0.883	0.973	CLONAL	1	TRUE	0	0.738669155653335	1		733	508	SUCCESS
BTK	695	MSKCC	GRCh37	X	100609651	100609651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	189	399	0	ENST00000308731.7:c.1598G>A	p.Gly533Glu	p.G533E	ENST00000308731	NM_000061.2	533	gGa/gAa	16/19	1	2	FACETS	0.971	0.905	1	0.971	0.905	1	CLONAL	1	TRUE	1	0.738669155653335	2		399	527	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586131	29586154	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTGATGCAGCACGCAGGTAATTT	TTTGATGCAGCACGCAGGTAATTT	-	novel	NA	P-0040983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	32	300	0	ENST00000356175.3:c.4352_4367+8del		p.X1451_splice	ENST00000356175	NM_000267.3	1451		32/57	1	2	FACETS	0.369	0.301	0.444	0.369	0.301	0.444	SUBCLONAL	1	TRUE	1	0.738669155653335	2		300	235	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050251	13050262	+	inframe_deletion	In_Frame_Del	DEL	CAAGCCAGGATG	CAAGCCAGGATG	-	novel	NA	P-0040989-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	190	416	0	ENST00000316448.5:c.205_216del	p.Ser69_Ala72del	p.S69_A72del	ENST00000316448	NM_004343.3	68	aCAAGCCAGGATGca/aca	3/9	0.780422115751134	1	FACETS	0.73	0.687	0.774	0.73	0.687	0.774	SUBCLONAL	1	TRUE	0	0.832201993372543	1		416	365	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040989-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	183	627	0	ENST00000206249.3:c.1610A>G	p.Tyr537Cys	p.Y537C	ENST00000206249	NM_000125.3	537	tAt/tGt	8/8	0.665557840379415	2	FACETS	0.683	0.633	0.734	0.341	0.316	0.367	SUBCLONAL	1	TRUE	0	0.832201993372543	2		627	644	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123050	5123050	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040989-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	57	424	0	ENST00000381652.3:c.3106G>T	p.Asp1036Tyr	p.D1036Y	ENST00000381652	NM_004972.3	1036	Gat/Tat	23/25	0.732389188701192	1	FACETS	0.308	0.266	0.352	0.308	0.266	0.352	SUBCLONAL	1	TRUE	0	0.832201993372543	1		424	260	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843396	128843396	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61746143	NA	P-0041006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	56	657	0	ENST00000249373.3:c.503G>A	p.Arg168His	p.R168H	ENST00000249373	NM_005631.4	168	cGc/cAc	2/12	0.195116465480574	3	FACETS	0.563	0.481	0.653	0.282	0.24	0.327	SUBCLONAL	1	FALSE	1	0.301573552661764	3		657	759	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0041006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	145	491	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.195116465480574	3	FACETS	0.912	0.835	0.991	0.912	0.835	0.991	CLONAL	2	FALSE	1	0.301573552661764	3		492	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0041006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	343	616	1	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.301573552661764	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	FALSE	0	0.301573552661764	3		617	777	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729529	41729529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138538132	NA	P-0041006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	45	590	0	ENST00000242208.4:c.1000G>A	p.Gly334Ser	p.G334S	ENST00000242208	NM_002192.2	334	Ggc/Agc	3/3	0.301573552661764	4	FACETS	0.439	0.367	0.519	0.219	0.183	0.26	SUBCLONAL	1	FALSE	2	0.301573552661764	4		590	885	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68301875	68301875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs965821237	NA	P-0041006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	32	503	0	ENST00000487270.1:c.277G>T	p.Ala93Ser	p.A93S	ENST00000487270	NM_133509.3	93	Gcc/Tcc	4/11	0.13309066188482	3	FACETS	0.39	0.316	0.475	0.195	0.158	0.238	INDETERMINATE	1	FALSE	1	0.301573552661764	3		503	626	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198264797	198264797	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	77	444	0	ENST00000335508.6:c.2995G>T	p.Ala999Ser	p.A999S	ENST00000335508	NM_012433.2	999	Gcc/Tcc	20/25	0.13309066188482	3	FACETS	1	0.923	1	0.533	0.469	0.602	INDETERMINATE	1	FALSE	1	0.301573552661764	3		444	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579463	7579463	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	231	672	0	ENST00000269305.4:c.224del	p.Pro75LeufsTer48	p.P75Lfs*48	ENST00000269305	NM_001126112.2	75	cCt/ct	4/11	0.628938612024386	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.628938612024386	1		672	494	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678539	88678539	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	22	397	0	ENST00000360948.2:c.997C>G	p.Leu333Val	p.L333V	ENST00000360948	NM_001012338.2	333	Ctg/Gtg	9/19	0.628938612024386	1	FACETS	0.209	0.163	0.263	0.209	0.163	0.263	SUBCLONAL	1	TRUE	0	0.628938612024386	1		397	229	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0041051-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	276	677	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.356969448747955	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.358990247812591	2		680	700	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041051-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	202	520	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.357468631285898	4	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	2	0.358990247812591	4		520	764	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0041051-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	104	210	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	0.357468631285898	4	FACETS	1	0.913	1	1	0.913	1	CLONAL	2	TRUE	2	0.358990247812591	4		210	389	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928225	178928225	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041051-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	202	343	0	ENST00000263967.3:c.1411C>G	p.Pro471Ala	p.P471A	ENST00000263967	NM_006218.2	471	Cca/Gca	9/21	0.357468631285898	4	FACETS	0.847	0.79	0.905	1	0.988	1	CLONAL	3	TRUE	2	0.358990247812591	4		343	602	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843386	3843386	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0041051-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	86	514	0	ENST00000262367.5:c.1216+1del		p.X406_splice	ENST00000262367	NM_004380.2	406			0.358990247812591	6	FACETS	1	0.887	1			1	CLONAL	1	TRUE	NA	0.358990247812591	6		514	820	SUCCESS
YES1	7525	MSKCC	GRCh37	18	742970	742971	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0041051-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	207	188	0	ENST00000314574.4:c.1007_1008del	p.Tyr336CysfsTer5	p.Y336Cfs*5	ENST00000314574	NM_005433.3	336	tAT/t	8/12	0.357015657529724	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	0	0.358990247812591	3		188	420	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378245	15378245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041051-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	102	423	1	ENST00000263377.2:c.541C>T	p.Arg181Cys	p.R181C	ENST00000263377	NM_058243.2	181	Cgt/Tgt	4/20	0.344198672230708	3	FACETS	1	0.954	1	0.558	0.5	0.619	CLONAL	1	TRUE	1	0.358990247812591	3		424	601	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860666	151860667	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041051-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	343	715	0	ENST00000262189.6:c.9995dup	p.Leu3332PhefsTer19	p.L3332Ffs*19	ENST00000262189	NM_170606.2	3332	tta/ttTa	43/59	0.319744172836001	3	FACETS	0.92	0.875	0.965	0.92	0.875	0.965	CLONAL	3	TRUE	0	0.358990247812591	3		715	817	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273109	198273109	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041051-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	85	473	0	ENST00000335508.6:c.1101G>T	p.Met367Ile	p.M367I	ENST00000335508	NM_012433.2	367	atG/atT	8/25	0.358990247812591	1	FACETS	0.932	0.828	1	0.932	0.828	1	CLONAL	1	TRUE	0	0.358990247812591	1		473	417	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987077	69987077	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041051-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	101	539	0	ENST00000394351.3:c.138C>A	p.Asn46Lys	p.N46K	ENST00000394351	NM_000248.3	46	aaC/aaA	2/9	0.344198672230708	3	FACETS	0.951	0.85	1	0.475	0.425	0.529	CLONAL	1	TRUE	1	0.358990247812591	3		539	698	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0041091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	337	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.330887836489486	4	FACETS	1	0.99	1	1	0.996	1	CLONAL	5	TRUE	0	0.330887836489486	4		326	501	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248633	59248634	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0041091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	179	908	0	ENST00000371222.2:c.109_110del	p.Ser37HisfsTer69	p.S37Hfs*69	ENST00000371222	NM_002228.3	37	AGc/c	1/1	1	2	FACETS	0.828	0.767	0.892	1	0.991	1	CLONAL	2	TRUE	1	0.330887836489486	2		908	653	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0041091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	44	407	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.704	0.591	0.827	0.704	0.591	0.827	SUBCLONAL	1	TRUE	1	0.330887836489486	2		407	378	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0041091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	32	579	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.395	0.32	0.48	0.395	0.32	0.48	SUBCLONAL	1	TRUE	1	0.330887836489486	2		579	490	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593520	48593520	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	71	260	0	ENST00000342988.3:c.1271A>T	p.Asp424Val	p.D424V	ENST00000342988	NM_005359.5	424	gAt/gTt	10/12	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.330887836489486	2		260	311	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650098	206650098	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	102	754	0	ENST00000367120.3:c.618C>A	p.Ser206Arg	p.S206R	ENST00000367120	NM_014002.3	206	agC/agA	7/22	0.330887836489486	4	FACETS	1	0.943	1	0.361	0.322	0.402	CLONAL	1	TRUE	1	0.330887836489486	4		754	758	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575155	48575156	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0041091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	94	329	0	ENST00000342988.3:c.350dup	p.Tyr117Ter	p.Y117*	ENST00000342988	NM_005359.5	117	tat/tAat	3/12	1	2	FACETS	0.882	0.793	0.975	1	0.986	1	CLONAL	2	TRUE	1	0.330887836489486	2		329	322	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18975048	18975048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	67	329	0	ENST00000262803.5:c.2845C>T	p.Arg949Trp	p.R949W	ENST00000262803	NM_002911.3	949	Cgg/Tgg	20/24	0.330887836489486	3	FACETS	1	0.972	1	0.719	0.63	0.815	CLONAL	1	TRUE	1	0.330887836489486	3		329	328	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170015128	170015128	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	39	691	0	ENST00000295797.4:c.1535del	p.Gly512AspfsTer18	p.G512Dfs*18	ENST00000295797	NM_002740.5	512	Gga/ga	16/18	1	2	FACETS	0.342	0.282	0.408	0.342	0.282	0.408	SUBCLONAL	1	TRUE	1	0.330887836489486	2		691	690	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342101	70342101	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	99	277	0	ENST00000374080.3:c.1153G>T	p.Asp385Tyr	p.D385Y	ENST00000374080		385	Gat/Tat	8/45	0.330887836489486	2	FACETS	0.757	0.681	0.837			1	SUBCLONAL	2	TRUE	NA	0.330887836489486	2		277	395	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	178	300	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.944	0.874	1	0.944	0.874	1	CLONAL	1	TRUE	1	0.57218679064661	2		300	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578262	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs483352697	NA	P-0041093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	298	623	0	ENST00000269305.4:c.587G>C	p.Arg196Pro	p.R196P	ENST00000269305	NM_001126112.2	196	cGa/cCa	6/11	0.57218679064661	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.57218679064661	1		623	740	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631837	90631837	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	278	583	0	ENST00000330062.3:c.516G>T	p.Arg172Ser	p.R172S	ENST00000330062	NM_002168.2	172	agG/agT	4/11	0.57218679064661	1	FACETS	0.977	0.923	1	0.977	0.923	1	CLONAL	1	TRUE	0	0.57218679064661	1		583	710	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133236063	133236063	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	210	452	1	ENST00000320574.5:c.3093G>C	p.Glu1031Asp	p.E1031D	ENST00000320574	NM_006231.2	1031	gaG/gaC	26/49	0.57218679064661	1	FACETS	0.96	0.899	1	0.96	0.899	1	CLONAL	1	TRUE	0	0.57218679064661	1		453	546	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0041126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	88	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		336	366	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0041142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	113	518	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.922	0.833	1	0.922	0.833	1	CLONAL	1	TRUE	1	0.459940454295955	2		518	533	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0041142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	107	210	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.809	0.728	0.895	0.809	0.728	0.895	CLONAL	1	TRUE	1	0.459940454295955	2		210	575	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0041142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	108	456	3	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.914	0.823	1	0.914	0.823	1	CLONAL	1	TRUE	1	0.459940454295955	2		459	514	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920469	134920469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	143	843	0	ENST00000398015.3:c.2284G>A	p.Asp762Asn	p.D762N	ENST00000398015	NM_004441.4	762	Gac/Aac	12/16	1	2	FACETS	0.843	0.769	0.919	0.843	0.769	0.919	CLONAL	1	TRUE	1	0.459940454295955	2		843	738	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920404	114920404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	132	578	0	ENST00000543371.1:c.1345G>A	p.Ala449Thr	p.A449T	ENST00000543371	NM_001198531.1	449	Gca/Aca	13/14	1	2	FACETS	0.759	0.69	0.832	0.759	0.69	0.832	SUBCLONAL	1	TRUE	1	0.459940454295955	2		578	756	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729478	41729478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	148	731	0	ENST00000242208.4:c.1051G>A	p.Glu351Lys	p.E351K	ENST00000242208	NM_002192.2	351	Gag/Aag	3/3	1	2	FACETS	0.874	0.8	0.952	0.874	0.8	0.952	CLONAL	1	TRUE	1	0.459940454295955	2		731	736	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378262	15378262	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	124	580	0	ENST00000263377.2:c.524A>T	p.Gln175Leu	p.Q175L	ENST00000263377	NM_058243.2	175	cAg/cTg	4/20	1	2	FACETS	0.928	0.843	1	0.928	0.843	1	CLONAL	1	TRUE	1	0.459940454295955	2		580	581	SUCCESS
APC	324	MSKCC	GRCh37	5	112175756	112175757	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TAAA	novel	NA	P-0041142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	80	356	0	ENST00000257430.4:c.4467_4468insAATA	p.His1490AsnfsTer25	p.H1490Nfs*25	ENST00000257430	NM_000038.5	1489	tta/tTAAAta	16/16	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.459940454295955	2		356	343	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562895	176562895	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	163	689	0	ENST00000439151.2:c.791A>T	p.Asn264Ile	p.N264I	ENST00000439151	NM_022455.4	264	aAc/aTc	2/23	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.459940454295955	2		689	708	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729847	41729847	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	114	555	0	ENST00000242208.4:c.682C>A	p.Gln228Lys	p.Q228K	ENST00000242208	NM_002192.2	228	Cag/Aag	3/3	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.459940454295955	2		555	466	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939479	68939479	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	93	437	0	ENST00000288368.4:c.464G>C	p.Arg155Pro	p.R155P	ENST00000288368	NM_024870.2	155	cGg/cCg	5/40	1	2	FACETS	0.958	0.857	1	0.958	0.857	1	CLONAL	1	TRUE	1	0.459940454295955	2		437	422	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759556	133759556	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	201	1055	1	ENST00000318560.5:c.1879C>T	p.Gln627Ter	p.Q627*	ENST00000318560	NM_005157.4	627	Cag/Tag	11/11	1	2	FACETS	0.942	0.873	1	0.942	0.873	1	CLONAL	1	TRUE	1	0.459940454295955	2		1056	928	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442059	52442059	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	17	712	0	ENST00000460680.1:c.290T>G	p.Leu97Arg	p.L97R	ENST00000460680	NM_004656.3	97	cTg/cGg	5/17	1	2	FACETS	1	0.807	1	1	0.807	1	CLONAL	1	TRUE	1	0.138467147592556	2		712	224	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0041153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	306	407	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.716672189801741	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.716672189801741	2		407	394	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0041153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	150	388	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	0.924	0.852	0.998	0.924	0.852	0.998	CLONAL	1	TRUE	1	0.716672189801741	2		388	453	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101259	27101260	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0041153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	530	814	10	ENST00000324856.7:c.4544dup	p.Ser1516LeufsTer16	p.S1516Lfs*16	ENST00000324856	NM_006015.4	1514	acg/acGg	18/20	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	2	TRUE	NA	0.716672189801741	2		824	732	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170832318	170832318	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	369	639	2	ENST00000296930.5:c.682T>G	p.Phe228Val	p.F228V	ENST00000296930	NM_002520.6	228	Ttc/Gtc	9/11	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.716672189801741	2		641	889	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5077490	5077491	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAT	novel	NA	P-0041153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	128	286	2	ENST00000381652.3:c.1903_1905dup	p.Asp635dup	p.D635dup	ENST00000381652	NM_004972.3	635	-/GAT	15/25	1	2	FACETS	0.942	0.863	1	0.942	0.863	1	CLONAL	1	TRUE	1	0.716672189801741	2		288	379	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0041169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	85	343	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.818	0.726	0.916	0.818	0.726	0.916	CLONAL	1	TRUE	1	0.443232635134615	2		343	469	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0041169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	76	407	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.843	0.743	0.949	0.843	0.743	0.949	CLONAL	1	TRUE	1	0.443232635134615	2		407	407	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0041169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	104	475	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.831	0.746	0.92	0.831	0.746	0.92	CLONAL	1	TRUE	1	0.443232635134615	2		475	565	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175481	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0041169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	82	269	0	ENST00000257430.4:c.4192_4193del	p.Arg1399PhefsTer9	p.R1399Ffs*9	ENST00000257430	NM_000038.5	1397	GAg/g	16/16	1	2	FACETS	0.871	0.771	0.976	0.871	0.771	0.976	CLONAL	1	TRUE	1	0.443232635134615	2		269	425	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	136	483	0	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.443232635134615	2		483	603	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468397	89468398	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1467832547	NA	P-0041169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	41	312	0	ENST00000336596.2:c.1938dup	p.Glu647ArgfsTer7	p.E647Rfs*7	ENST00000336596	NM_005233.5	644	tca/tcAa	11/17	1	2	FACETS	0.518	0.433	0.613	0.518	0.433	0.613	SUBCLONAL	1	TRUE	1	0.443232635134615	2		312	357	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227834	36227834	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	195	951	1	ENST00000222270.7:c.7319A>G	p.Glu2440Gly	p.E2440G	ENST00000222270	NM_014727.1	2440	gAg/gGg	32/37	1	2	FACETS	0.934	0.865	1	0.934	0.865	1	CLONAL	1	TRUE	1	0.443232635134615	2		952	942	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52649459	52649459	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	272	546	0	ENST00000394830.3:c.1832C>A	p.Ala611Glu	p.A611E	ENST00000394830	NM_018313.4	611	gCa/gAa	16/30	0.429530354013752	2	FACETS	0.983	0.93	1	0.983	0.93	1	CLONAL	2	TRUE	0	0.443232635134615	2		546	624	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111506	8111507	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	76	663	1	ENST00000346208.3:c.993dup	p.Ala332CysfsTer20	p.A332Cfs*20	ENST00000346208		331	aat/aaTt	5/6	1	2	FACETS	0.988	0.866	1	0.988	0.866	1	CLONAL	1	TRUE	1	0.20425194489953	2		664	753	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100043	157100043	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1455234951	NA	P-0041170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	11	80	0	ENST00000346085.5:c.980G>C	p.Gly327Ala	p.G327A	ENST00000346085	NM_020732.3	327	gGa/gCa	1/20	0.20425194489953	1	FACETS	0.761	0.529	1	0.761	0.529	1	CLONAL	1	TRUE	0	0.20425194489953	1		80	127	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0041211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	404	829	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.607203513883935	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.607203513883935	2		829	634	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371941	55371941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	139	430	0	ENST00000297316.4:c.631G>A	p.Ala211Thr	p.A211T	ENST00000297316	NM_022454.3	211	Gcg/Acg	2/2	0.256412658595211	5	FACETS	1	0.981	1	0.426	0.388	0.465	INDETERMINATE	1	TRUE	2	0.607203513883935	5		430	685	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521367	8521367	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	342	528	1	ENST00000356435.5:c.871C>A	p.Leu291Met	p.L291M	ENST00000356435		291	Ctg/Atg	9/35	0.607203513883935	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.607203513883935	2		529	507	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957484	175957484	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	314	454	0	ENST00000367669.3:c.1912G>A	p.Gly638Ser	p.G638S	ENST00000367669	NM_022457.5	638	Ggt/Agt	17/20	0.607203513883935	3	FACETS	0.976	0.927	1	0.976	0.927	1	CLONAL	2	TRUE	1	0.607203513883935	3		454	691	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0041222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	83	407	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.285237629985361	3	FACETS	1	0.951	1	0.572	0.506	0.643	CLONAL	1	FALSE	1	0.313070691496854	3		407	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577507	7577507	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	129	686	0	ENST00000269305.4:c.774A>C	p.Glu258Asp	p.E258D	ENST00000269305	NM_001126112.2	258	gaA/gaC	7/11	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	FALSE	1	0.313070691496854	2		686	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0041308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	303	863	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.305816649684368	1	FACETS	0.776	0.739	0.814	1	0.995	1	SUBCLONAL	2	TRUE	0	0.48603400978037	1		863	608	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0041308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	48	194	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.48603400978037	3	FACETS	0.959	0.832	1	0.959	0.832	1	CLONAL	2	TRUE	1	0.48603400978037	3		194	128	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473648	67473648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223736	NA	P-0041308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	93	587	0	ENST00000327367.4:c.728G>A	p.Arg243His	p.R243H	ENST00000327367	NM_005902.3	243	cGc/cAc	6/9	0.209145382542897	4	FACETS	0.781	0.694	0.874	0.391	0.347	0.437	INDETERMINATE	1	TRUE	2	0.48603400978037	4		587	728	SUCCESS
APC	324	MSKCC	GRCh37	5	112173965	112173965	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1561578889	NA	P-0041308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	35	367	0	ENST00000257430.4:c.2674G>T	p.Glu892Ter	p.E892*	ENST00000257430	NM_000038.5	892	Gaa/Taa	16/16	0.48603400978037	3	FACETS	0.635	0.522	0.76	0.317	0.261	0.38	SUBCLONAL	1	TRUE	1	0.48603400978037	3		367	282	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874878	151874878	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	43	346	0	ENST00000262189.6:c.7660C>G	p.Leu2554Val	p.L2554V	ENST00000262189	NM_170606.2	2554	Ctg/Gtg	38/59	0.48603400978037	3	FACETS	0.593	0.497	0.698	0.296	0.248	0.349	SUBCLONAL	1	TRUE	1	0.48603400978037	3		346	371	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0041320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	84	208	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.863	0.77	0.96	0.863	0.77	0.96	CLONAL	1	TRUE	1	0.634238112903528	2		208	307	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	72	492	1	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	1	2	FACETS	0.361	0.315	0.41	0.361	0.315	0.41	SUBCLONAL	1	TRUE	1	0.634238112903528	2		493	629	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0041320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	25	370	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.163	0.128	0.203	0.163	0.128	0.203	SUBCLONAL	1	TRUE	1	0.634238112903528	2		370	484	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063718	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0041320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	126	195	0	ENST00000412916.2:c.165+2dup		p.X55_splice	ENST00000412916		55			0.634238112903528	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.634238112903528	1		195	233	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884835	151884836	+	stop_gained	Nonsense_Mutation	DNP	GA	GA	TT	novel	NA	P-0041320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	195	417	0	ENST00000262189.6:c.4757_4758delinsAA	p.Phe1586Ter	p.F1586*	ENST00000262189	NM_170606.2	1586	tTC/tAA	32/59	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.634238112903528	2		417	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577067	7577067	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0041340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	528	694	0	ENST00000269305.4:c.871A>T	p.Lys291Ter	p.K291*	ENST00000269305	NM_001126112.2	291	Aag/Tag	8/11	0.533995646672215	3	FACETS	0.985	0.953	1	0.985	0.953	1	CLONAL	3	TRUE	0	0.532338888729287	3		694	850	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196252	108196252	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	50	337	0	ENST00000278616.4:c.6788G>C	p.Arg2263Thr	p.R2263T	ENST00000278616	NM_000051.3	2263	aGa/aCa	46/63	0.316989003987602	3	FACETS	0.61	0.519	0.709			1	INDETERMINATE	1	TRUE	NA	0.532338888729287	3		337	390	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196857	108196857	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	46	304	0	ENST00000278616.4:c.6880G>T	p.Glu2294Ter	p.E2294*	ENST00000278616	NM_000051.3	2294	Gaa/Taa	47/63	0.316989003987602	3	FACETS	0.61	0.515	0.713			1	INDETERMINATE	1	TRUE	NA	0.532338888729287	3		304	359	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198402	108198402	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	61	340	0	ENST00000278616.4:c.7006G>C	p.Glu2336Gln	p.E2336Q	ENST00000278616	NM_000051.3	2336	Gaa/Caa	48/63	0.316989003987602	3	FACETS	0.684	0.592	0.784			1	INDETERMINATE	1	TRUE	NA	0.532338888729287	3		340	424	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199772	108199772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	23	166	0	ENST00000278616.4:c.7114G>A	p.Asp2372Asn	p.D2372N	ENST00000278616	NM_000051.3	2372	Gat/Aat	49/63	0.316989003987602	3	FACETS	0.454	0.355	0.568			1	INDETERMINATE	1	TRUE	NA	0.532338888729287	3		166	241	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199778	108199778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	23	170	0	ENST00000278616.4:c.7120G>A	p.Glu2374Lys	p.E2374K	ENST00000278616	NM_000051.3	2374	Gaa/Aaa	49/63	0.316989003987602	3	FACETS	0.439	0.343	0.55			1	INDETERMINATE	1	TRUE	NA	0.532338888729287	3		170	249	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118339535	118339535	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555034779	NA	P-0041340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	144	457	1	ENST00000534358.1:c.478C>T	p.Arg160Ter	p.R160*	ENST00000534358	NM_005933.3	160	Cga/Tga	2/36	0.316989003987602	3	FACETS	0.839	0.774	0.907			1	INDETERMINATE	2	TRUE	NA	0.532338888729287	3		458	408	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0041372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	306	542	0				ENST00000310581	NM_198253.2	-/1132			0.5527114229097	4	FACETS	1	0.978	1			1	CLONAL	2	TRUE	NA	0.58213076816638	4		542	785	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0041372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	801	816	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.581588251820292	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.58213076816638	3		816	1143	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	266	234	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	0.581588251820292	2	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.58213076816638	2		234	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0041372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	633	655	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.581588251820292	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	0	0.58213076816638	3		655	920	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534545	140534545	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	131	509	0	ENST00000288602.6:c.368C>G	p.Ser123Cys	p.S123C	ENST00000288602	NM_004333.4	123	tCt/tGt	3/18	0.581588251820292	4	FACETS	0.864	0.784	0.948	0.432	0.392	0.474	CLONAL	1	TRUE	2	0.58213076816638	4		509	824	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2488158	2488158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1429446056	NA	P-0041372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	263	677	0	ENST00000355716.4:c.55G>A	p.Asp19Asn	p.D19N	ENST00000355716	NM_003820.2	19	Gac/Aac	1/8	0.581588251820292	4	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.58213076816638	4		677	1282	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325861	65325861	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	145	584	1	ENST00000342505.4:c.1261C>T	p.His421Tyr	p.H421Y	ENST00000342505	NM_002227.2	421	Cat/Tat	9/25	0.548566898028158	3	FACETS	0.95	0.869	1	0.475	0.434	0.518	CLONAL	1	TRUE	1	0.58213076816638	3		585	677	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38632043	38632043	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	142	587	0	ENST00000299084.4:c.529C>T	p.Pro177Ser	p.P177S	ENST00000299084	NM_152594.2	177	Ccc/Tcc	5/7	0.328873007949939	5	FACETS	1	0.965	1	0.371	0.338	0.405	INDETERMINATE	1	TRUE	2	0.58213076816638	5		587	822	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782077	66782077	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	80	381	0	ENST00000307102.5:c.1044G>C	p.Glu348Asp	p.E348D	ENST00000307102	NM_002755.3	348	gaG/gaC	10/11	0.558735329658649	4	FACETS	0.784	0.691	0.883	0.392	0.345	0.442	SUBCLONAL	1	TRUE	2	0.58213076816638	4		381	555	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819756	81819756	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	180	583	0	ENST00000359376.3:c.162G>C	p.Trp54Cys	p.W54C	ENST00000359376	NM_002661.3	54	tgG/tgC	2/33	0.328873007949939	5	FACETS	1	0.981	1	0.399	0.367	0.432	INDETERMINATE	1	TRUE	2	0.58213076816638	5		583	968	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858452	89858452	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	155	688	0	ENST00000389301.3:c.1108G>C	p.Glu370Gln	p.E370Q	ENST00000389301	NM_000135.2	370	Gag/Cag	13/43	0.328873007949939	5	FACETS	0.938	0.857	1	0.313	0.285	0.341	INDETERMINATE	1	TRUE	2	0.58213076816638	5		688	1064	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326544	62326544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	290	821	0	ENST00000360203.5:c.3469C>T	p.Pro1157Ser	p.P1157S	ENST00000360203	NM_001283009.1	1157	Cct/Tct	33/35	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.58213076816638	2		821	906	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537076	41537076	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	89	353	0	ENST00000263253.7:c.1903G>C	p.Glu635Gln	p.E635Q	ENST00000263253	NM_001429.3	635	Gag/Cag	10/31	0.581588251820292	3	FACETS	0.903	0.805	1	0.452	0.402	0.504	CLONAL	1	TRUE	1	0.58213076816638	3		353	437	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217549	142217549	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	119	436	0	ENST00000350721.4:c.5448C>G	p.Ile1816Met	p.I1816M	ENST00000350721	NM_001184.3	1816	atC/atG	32/47	0.558735329658649	4	FACETS	0.995	0.9	1	0.498	0.45	0.548	CLONAL	1	TRUE	2	0.58213076816638	4		436	650	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925375	131925375	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	56	223	0	ENST00000265335.6:c.1298G>C	p.Arg433Thr	p.R433T	ENST00000265335		433	aGa/aCa	9/25	0.581588251820292	3	FACETS	0.917	0.792	1	0.458	0.396	0.525	CLONAL	1	TRUE	1	0.58213076816638	3		223	271	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017509	112017509	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	135	422	0	ENST00000368678.4:c.1004T>A	p.Ile335Asn	p.I335N	ENST00000368678		335	aTc/aAc	9/13	0.343721182344369	3	FACETS	1	0.967	1	0.373	0.341	0.407	INDETERMINATE	1	TRUE	0	0.58213076816638	3		422	535	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069594	69069601	+	frameshift_variant	Frame_Shift_Del	DEL	TGTTTCTG	TGTTTCTG	-	novel	NA	P-0041372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	160	464	0	ENST00000288368.4:c.4271_4278del	p.Val1424GlyfsTer45	p.V1424Gfs*45	ENST00000288368	NM_024870.2	1423	aaTGTTTCTGtg/aatg	35/40	0.581588251820292	3	FACETS	0.967	0.899	1	0.967	0.899	1	CLONAL	2	TRUE	1	0.58213076816638	3		464	367	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740776	145740776	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	217	792	1	ENST00000428558.2:c.1324G>A	p.Glu442Lys	p.E442K	ENST00000428558	NM_004260.3	442	Gag/Aag	7/22	0.105955787827077	4	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.58213076816638	4		793	833	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038521	47038521	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	418	369	0	ENST00000377604.3:c.683A>T	p.Lys228Ile	p.K228I	ENST00000377604	NM_001204468.1	228	aAa/aTa	8/24	0.581588251820292	2	FACETS	0.849	0.823	0.874			1	CLONAL	3	TRUE	NA	0.58213076816638	2		369	564	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0041386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	183	425	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.241847774729691	3	FACETS	1	0.975	1			1	CLONAL	2	TRUE	NA	0.241762034067216	3		426	757	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0041386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	154	655	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.241762034067216	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.241762034067216	1		655	1011	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443642	49443729	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCAACTCCATGGACAGGGAGCCACCCCCCTCCGGGTCTGGAGAGCCCAGGAGGGGCTCTGAGCCAGGAAAACTGGCACTGGCATCA	CCCCAACTCCATGGACAGGGAGCCACCCCCCTCCGGGTCTGGAGAGCCCAGGAGGGGCTCTGAGCCAGGAAAACTGGCACTGGCATCA	-	novel	NA	P-0041386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	158	664	0	ENST00000301067.7:c.3642_3729del	p.Asp1215SerfsTer86	p.D1215Sfs*86	ENST00000301067	NM_003482.3	1214	ggTGATGCCAGTGCCAGTTTTCCTGGCTCAGAGCCCCTCCTGGGCTCTCCAGACCCGGAGGGGGGTGGCTCCCTGTCCATGGAGTTGGGG/gg	11/54	0.219045786168477	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.241762034067216	1		664	975	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56792511	56792512	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	83	474	0	ENST00000308159.5:c.242dup	p.Ser82GlufsTer7	p.S82Efs*7	ENST00000308159	NM_014669.4	81	ctg/cTtg	3/22	1	2	FACETS	0.783	0.69	0.883	0.783	0.69	0.883	SUBCLONAL	1	TRUE	1	0.241762034067216	2		474	877	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591952	48591952	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	AT	novel	NA	P-0041386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	58	322	2	ENST00000342988.3:c.1115delinsAT	p.Arg372AsnfsTer6	p.R372Nfs*6	ENST00000342988	NM_005359.5	372	aGg/aATg	9/12	1	2	FACETS	0.977	0.841	1	0.977	0.841	1	CLONAL	1	TRUE	1	0.241762034067216	2		324	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0041464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	215	732	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.53137139438784	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.53137139438784	1		732	560	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860287	151860287	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	23	566	0	ENST00000262189.6:c.10375C>T	p.Pro3459Ser	p.P3459S	ENST00000262189	NM_170606.2	3459	Cct/Tct	43/59	0.213276346406315	4	FACETS	0.414	0.323	0.52	0.207	0.161	0.26	INDETERMINATE	1	TRUE	2	0.53137139438784	4		566	320	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28886200	28886241	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGTCTCTGTGCCAGCAGTCCAGCATGATCTGATAGCTGGTG	GGGTCTCTGTGCCAGCAGTCCAGCATGATCTGATAGCTGGTG	-	novel	NA	P-0041464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	15	558	0	ENST00000282397.4:c.3387-6_3422del		p.X1129_splice	ENST00000282397	NM_002019.4	1129		26/30	1	2	FACETS	0.253	0.185	0.335	0.253	0.185	0.335	SUBCLONAL	1	TRUE	1	0.53137139438784	2		558	223	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844207	68844217	+	frameshift_variant	Frame_Shift_Del	DEL	GGTCTTTAAGG	GGTCTTTAAGG	-	novel	NA	P-0041469-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	128	528	0	ENST00000261769.5:c.800_810del	p.Phe267CysfsTer22	p.F267Cfs*22	ENST00000261769	NM_004360.3	265	gaGGTCTTTAAGGgg/gagg	6/16	0.455877562043561	1	FACETS	0.85	0.775	0.929	0.85	0.775	0.929	CLONAL	1	FALSE	0	0.455877562043561	1		528	510	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15938164	15938165	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCCGTTCCGTTCCTA	novel	NA	P-0041469-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	33	357	0	ENST00000268712.3:c.7034_7049dup	p.Ser2351ArgfsTer19	p.S2351Rfs*19	ENST00000268712	NM_006311.3	2350	ccc/ccTAGGAACGGAACGGCCc	45/46	0.327780170839651	1	FACETS	0.206	0.167	0.25	0.206	0.167	0.25	SUBCLONAL	1	FALSE	0	0.455877562043561	1		357	543	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226561931	226561931	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041469-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	26	288	0	ENST00000366794.5:c.2066A>G	p.Tyr689Cys	p.Y689C	ENST00000366794	NM_001618.3	689	tAt/tGt	14/23	1	2	FACETS	0.273	0.216	0.339	0.273	0.216	0.339	SUBCLONAL	1	FALSE	1	0.455877562043561	2		288	418	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692968	89692968	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041469-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	48	409	0	ENST00000371953.3:c.454del	p.Leu152Ter	p.L152*	ENST00000371953	NM_000314.4	151	gCc/gc	5/9	0.455877562043561	1	FACETS	0.572	0.487	0.665	0.572	0.487	0.665	SUBCLONAL	1	FALSE	0	0.455877562043561	1		409	284	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129712	108129712	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0041469-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	22	337	0	ENST00000278616.4:c.2377-1G>T		p.X793_splice	ENST00000278616	NM_000051.3	793			0.455877562043561	1	FACETS	0.416	0.325	0.521	0.416	0.325	0.521	SUBCLONAL	1	FALSE	0	0.455877562043561	1		337	179	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237652	133237652	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041469-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	82	578	0	ENST00000320574.5:c.2963C>G	p.Ser988Trp	p.S988W	ENST00000320574	NM_006231.2	988	tCg/tGg	25/49	1	2	FACETS	0.431	0.379	0.486	0.431	0.379	0.486	SUBCLONAL	1	FALSE	1	0.455877562043561	2		578	835	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76777759	76777759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	238	525	0	ENST00000373344.5:c.6957G>A	p.Met2319Ile	p.M2319I	ENST00000373344	NM_000489.3	2319	atG/atA	32/35	0.803239143534006	1	FACETS	0.953	0.909	0.997	0.953	0.909	0.997	CLONAL	1	TRUE	0	0.803239143534006	1		525	372	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0041478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	28	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.834	0.675	1	0.834	0.675	1	CLONAL	1	TRUE	1	0.466414520678493	2		326	144	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0041478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	190	545	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.451015101019611	1	FACETS	0.848	0.786	0.912	0.848	0.786	0.912	CLONAL	1	TRUE	0	0.466414520678493	1		545	737	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117779	70117779	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	273	638	0	ENST00000245479.2:c.247G>A	p.Gly83Ser	p.G83S	ENST00000245479	NM_000346.3	83	Ggc/Agc	1/3	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.466414520678493	2		638	1139	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0041507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	68	611	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.885	0.77	1	0.885	0.77	1	CLONAL	1	TRUE	1	0.24	2		611	640	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0041507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	55	407	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.917	0.785	1	0.917	0.785	1	CLONAL	1	TRUE	1	0.24	2		407	500	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250883	153250883	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	70	539	0	ENST00000281708.4:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000281708	NM_033632.3	393	Cga/Tga	8/12	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.24	2		539	564	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087458	27087458	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	97	920	1	ENST00000324856.7:c.2032C>T	p.Gln678Ter	p.Q678*	ENST00000324856	NM_006015.4	678	Cag/Tag	5/20	1	2	FACETS	0.848	0.755	0.948	0.848	0.755	0.948	CLONAL	1	TRUE	1	0.24	2		921	953	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717609	89717609	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs876661024	NA	P-0041507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	54	519	0	ENST00000371953.3:c.635-1G>C		p.X212_splice	ENST00000371953	NM_000314.4	212			1	2	FACETS	0.991	0.848	1	0.991	0.848	1	CLONAL	1	TRUE	1	0.24	2		519	454	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779220	3779220	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780545388	NA	P-0041507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	47	563	1	ENST00000262367.5:c.5828C>T	p.Pro1943Leu	p.P1943L	ENST00000262367	NM_004380.2	1943	cCg/cTg	31/31	1	2	FACETS	0.987	0.834	1	0.987	0.834	1	CLONAL	1	TRUE	1	0.24	2		564	397	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692922	89692922	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	67	762	0	ENST00000371953.3:c.406T>G	p.Cys136Gly	p.C136G	ENST00000371953	NM_000314.4	136	Tgt/Ggt	5/9	1	2	FACETS	0.716	0.621	0.819	0.716	0.621	0.819	SUBCLONAL	1	TRUE	1	0.24	2		762	780	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541127	187541127	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	72	569	0	ENST00000441802.2:c.6613C>T	p.Gln2205Ter	p.Q2205*	ENST00000441802	NM_005245.3	2205	Cag/Tag	10/27	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.24	2		569	578	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020851	112020851	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	58	457	0	ENST00000368678.4:c.720del	p.Phe240LeufsTer3	p.F240Lfs*3	ENST00000368678		240	ttT/tt	8/13	1	2	FACETS	0.69	0.592	0.798	0.69	0.592	0.798	SUBCLONAL	1	TRUE	1	0.24	2		457	700	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939243	76939243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	96	897	0	ENST00000373344.5:c.1505C>T	p.Pro502Leu	p.P502L	ENST00000373344	NM_000489.3	502	cCt/cTt	9/35	1	2	FACETS	0.837	0.744	0.936	0.837	0.744	0.936	CLONAL	1	TRUE	1	0.24	2		897	956	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828699	3828700	+	splice_donor_variant	Splice_Site	DNP	AC	AC	CT	novel	NA	P-0041555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	336	549	9	ENST00000262367.5:c.1941+1_1941+2delinsAG		p.X647_splice	ENST00000262367	NM_004380.2	647			1	2	FACETS	0.952	0.906	0.999	0.952	0.906	0.999	CLONAL	1	TRUE	1	0.902360198669614	2		558	782	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097144	11097144	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	454	803	10	ENST00000358026.2:c.635G>T	p.Gly212Val	p.G212V	ENST00000358026	NM_001128849.1	212	gGg/gTg	4/36	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.902360198669614	2		813	936	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399344	139399345	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCACGCGGCTGAGCTCCCGCAGGAAGTGGAAGGAGCTGTTGC	novel	NA	P-0041555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1407	395	800	19	ENST00000277541.6:c.4757_4798dup	p.Arg1586_Val1599dup	p.R1586_V1599dup	ENST00000277541	NM_017617.3	1586	ctg/cGCAACAGCTCCTTCCACTTCCTGCGGGAGCTCAGCCGCGTGCtg	26/34	0.787933027368496	3	FACETS	0.705	0.668	0.743			1	SUBCLONAL	1	TRUE	NA	0.902360198669614	3		819	1802	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0041568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	32	425	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.893	0.726	1	0.893	0.726	1	CLONAL	1	TRUE	1	0.206047292517624	2		426	348	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057923	27057924	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0041568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	64	547	0	ENST00000324856.7:c.1636dup	p.Gln546ProfsTer77	p.Q546Pfs*77	ENST00000324856	NM_006015.4	544	cac/caCc	3/20	0.206047292517624	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.206047292517624	1		547	479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577138	7577139	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTCCCAGTAGATTA	novel	NA	P-0041568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	49	612	0	ENST00000269305.4:c.786_799dup	p.Arg267LeufsTer83	p.R267Lfs*83	ENST00000269305	NM_001126112.2	267	cgg/cTAATCTACTGGGACgg	8/11	0.202272946510206	1	FACETS	0.864	0.732	1	0.864	0.732	1	CLONAL	1	TRUE	0	0.206047292517624	1		612	494	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732911	30732911	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0041568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	28	243	0	ENST00000295754.5:c.1525-1G>A		p.X509_splice	ENST00000295754	NM_003242.5	509			0.202272946510206	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.206047292517624	1		243	198	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174399	11174399	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	202	627	0	ENST00000361445.4:c.7276T>G	p.Leu2426Val	p.L2426V	ENST00000361445	NM_004958.3	2426	Ttg/Gtg	53/58	0.435066481103685	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.435066481103685	1		627	722	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37680934	37680935	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0041570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	104	384	0	ENST00000447079.4:c.3104_3105del	p.His1035LeufsTer6	p.H1035Lfs*6	ENST00000447079	NM_015083.1	1035	CAc/c	12/14	1	2	FACETS	0.914	0.822	1	0.914	0.822	1	CLONAL	1	TRUE	1	0.435066481103685	2		384	523	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0041600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	304	425	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.694474547861925	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.69554143490018	2		426	410	SUCCESS
APC	324	MSKCC	GRCh37	5	112174379	112174379	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs587779786	NA	P-0041600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	70	258	0	ENST00000257430.4:c.3088A>T	p.Lys1030Ter	p.K1030*	ENST00000257430	NM_000038.5	1030	Aaa/Taa	16/16	1	2	FACETS	0.932	0.826	1	0.932	0.826	1	CLONAL	1	TRUE	1	0.69554143490018	2		258	216	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0041600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	377	705	1	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	0.69554143490018	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.69554143490018	1		706	656	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	163	570	0	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	0.69554143490018	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.69554143490018	1		570	299	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0041600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	112	285	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	1	2	FACETS	0.9	0.818	0.984	0.9	0.818	0.984	CLONAL	1	TRUE	1	0.69554143490018	2		285	358	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411576	63411576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	574	408	2	ENST00000330258.3:c.1591C>T	p.Arg531Ter	p.R531*	ENST00000330258	NM_152424.3	531	Cga/Tga	2/2	0.641138873051708	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.69554143490018	2		410	690	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0041602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	163	469	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.482678600430591	1	FACETS	0.954	0.881	1	0.954	0.881	1	CLONAL	1	TRUE	0	0.482678600430591	1		469	537	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56377222	56377224	+	inframe_deletion	In_Frame_Del	DEL	TTT	TTT	-	novel	NA	P-0041602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	30	253	0	ENST00000348428.3:c.843_845del	p.Asp281_Leu282delinsGlu	p.D281_L282delinsE	ENST00000348428	NM_006785.3	281	gaTTTg/gag	6/17	0.482678600430591	1	FACETS	0.293	0.236	0.357	0.293	0.236	0.357	SUBCLONAL	1	TRUE	0	0.482678600430591	1		253	322	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168904	32168904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	249	837	0	ENST00000375023.3:c.4129C>T	p.Leu1377Phe	p.L1377F	ENST00000375023	NM_004557.3	1377	Ctc/Ttc	22/30	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.482678600430591	2		837	964	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424419	47424419	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	61	330	0	ENST00000377045.4:c.339C>G	p.Asp113Glu	p.D113E	ENST00000377045	NM_001654.4	113	gaC/gaG	5/16	1	1	FACETS	0.416	0.359	0.477	0.416	0.359	0.477	SUBCLONAL	1	TRUE	0	0.482678600430591	1		330	461	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175481	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0041612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	23	269	0	ENST00000257430.4:c.4192_4193del	p.Arg1399PhefsTer9	p.R1399Ffs*9	ENST00000257430	NM_000038.5	1397	GAg/g	16/16	1	2	FACETS	0.611	0.477	0.766	0.611	0.477	0.766	SUBCLONAL	1	TRUE	1	0.263146354143733	2		269	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	73	663	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.263146354143733	1	FACETS	0.884	0.774	1	0.884	0.774	1	CLONAL	1	TRUE	0	0.263146354143733	1		663	545	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748898	41748898	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1307122843	NA	P-0041612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	74	557	0	ENST00000301178.4:c.1423C>T	p.Arg475Ter	p.R475*	ENST00000301178	NM_021913.4	475	Cga/Tga	11/20	0.263146354143733	1	FACETS	0.838	0.734	0.949	0.838	0.734	0.949	CLONAL	1	TRUE	0	0.263146354143733	1		557	583	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037156	71037156	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	23	334	0	ENST00000318789.4:c.1135G>T	p.Ala379Ser	p.A379S	ENST00000318789	NM_032682.5	379	Gcc/Tcc	14/21	1	2	FACETS	0.382	0.297	0.48	0.382	0.297	0.48	SUBCLONAL	1	TRUE	1	0.263146354143733	2		334	458	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0041616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	153	425	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.523170867483166	2		426	582	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0041616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	136	458	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	0.927	0.846	1	0.927	0.846	1	CLONAL	1	TRUE	1	0.523170867483166	2		458	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578440	7578440	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs879254249	NA	P-0041616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	189	714	0	ENST00000269305.4:c.490A>G	p.Lys164Glu	p.K164E	ENST00000269305	NM_001126112.2	164	Aag/Gag	5/11	0.523170867483166	1	FACETS	0.92	0.855	0.986	0.92	0.855	0.986	CLONAL	1	TRUE	0	0.523170867483166	1		714	580	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0041698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	538	629	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.562967135035382	4	FACETS	0.992	0.964	1	0.992	0.964	1	CLONAL	4	TRUE	0	0.562967135035382	4		630	753	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0041698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	366	451	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	0.562967135035382	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	4	TRUE	0	0.562967135035382	4		451	500	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49423021	49423021	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0041698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	236	615	0	ENST00000301067.7:c.14076-2A>G		p.X4692_splice	ENST00000301067	NM_003482.3	4692			0.562967135035382	4	FACETS	1	0.965	1			1	CLONAL	2	TRUE	NA	0.562967135035382	4		615	631	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000040	42000040	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	228	653	0	ENST00000219905.7:c.2303C>G	p.Thr768Ser	p.T768S	ENST00000219905	NM_001164273.1	768	aCc/aGc	6/24	0.562967135035382	3	FACETS	0.923	0.868	0.98	0.923	0.868	0.98	CLONAL	2	TRUE	1	0.562967135035382	3		653	562	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971267	15971272	+	inframe_deletion	In_Frame_Del	DEL	CGATAA	CGATAA	-	novel	NA	P-0041698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	106	541	0	ENST00000268712.3:c.4677_4682del	p.Tyr1560_Arg1561del	p.Y1560_R1561del	ENST00000268712	NM_006311.3	1559	gtTTATCGg/gtg	32/46	0.562967135035382	4	FACETS	0.954	0.857	1	0.238	0.214	0.264	CLONAL	1	TRUE	0	0.562967135035382	4		541	617	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467820	66467820	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	54	361	0	ENST00000273854.3:c.449C>A	p.Thr150Asn	p.T150N	ENST00000273854	NM_004439.5	150	aCc/aAc	3/18	0.277012004678371	6	FACETS	0.966	0.828	1			1	INDETERMINATE	1	TRUE	NA	0.562967135035382	6		361	422	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268179	153268180	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTTT	novel	NA	P-0041698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	75	323	0	ENST00000281708.4:c.628_629insAAAA	p.Gly210GlufsTer47	p.G210Efs*47	ENST00000281708	NM_033632.3	210	ggg/gAAAAgg	4/12	1	2	FACETS	0.919	0.814	1	0.919	0.814	1	CLONAL	1	TRUE	1	0.562967135035382	2		323	290	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535392	187535392	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762496253	NA	P-0041698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	89	498	0	ENST00000441802.2:c.9182C>T	p.Thr3061Met	p.T3061M	ENST00000441802	NM_005245.3	3061	aCg/aTg	12/27	1	2	FACETS	0.909	0.813	1	0.909	0.813	1	CLONAL	1	TRUE	1	0.562967135035382	2		498	348	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372387	55372387	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	155	808	0	ENST00000297316.4:c.1077C>A	p.Asp359Glu	p.D359E	ENST00000297316	NM_022454.3	359	gaC/gaA	2/2	0.562967135035382	5	FACETS	0.876	0.8	0.955			1	CLONAL	1	TRUE	NA	0.562967135035382	5		808	1160	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	470	862	1	ENST00000269305.4:c.859G>T	p.Glu287Ter	p.E287*	ENST00000269305	NM_001126112.2	287	Gag/Tag	8/11	0.566563379900181	2	FACETS	0.984	0.949	1	0.984	0.949	1	CLONAL	2	TRUE	0	0.590297147435864	2		863	809	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182198	99182198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371798563	NA	P-0041702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	155	651	0	ENST00000074304.5:c.2263G>A	p.Ala755Thr	p.A755T	ENST00000074304	NM_001134224.1	755	Gca/Aca	21/26	0.588843570835259	3	FACETS	0.924	0.848	1	0.462	0.424	0.502	CLONAL	1	TRUE	1	0.590297147435864	3		651	736	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10257034	10257034	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	101	533	0	ENST00000340748.4:c.2839A>C	p.Thr947Pro	p.T947P	ENST00000340748		947	Acg/Ccg	27/40	1	2	FACETS	0.72	0.647	0.798	0.72	0.647	0.798	SUBCLONAL	1	TRUE	1	0.590297147435864	2		533	475	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181545	32181545	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	193	795	0	ENST00000375023.3:c.2240G>C	p.Ser747Thr	p.S747T	ENST00000375023	NM_004557.3	747	aGc/aCc	14/30	0.564977306096048	3	FACETS	0.943	0.873	1	0.314	0.291	0.339	CLONAL	1	TRUE	0	0.590297147435864	3		795	898	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951955	178951955	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	42	295	0	ENST00000263967.3:c.3010A>G	p.Met1004Val	p.M1004V	ENST00000263967	NM_006218.2	1004	Atg/Gtg	21/21	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.31	2		295	209	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169985727	169985727	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369872734	NA	P-0041838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	69	539	0	ENST00000295797.4:c.389G>A	p.Arg130His	p.R130H	ENST00000295797	NM_002740.5	130	cGc/cAc	5/18	1	2	FACETS	0.97	0.847	1	0.97	0.847	1	CLONAL	1	TRUE	1	0.31	2		539	459	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317719	163317719	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	11	109	0	ENST00000271452.3:c.1115C>A	p.Thr372Lys	p.T372K	ENST00000271452	NM_145697.2	372	aCa/aAa	12/14	1	2	FACETS	0.503	0.349	0.693	0.503	0.349	0.693	SUBCLONAL	1	TRUE	1	0.31	2		109	141	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0041870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	196	973	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.317801680622727	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.317801680622727	1		973	954	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0041870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	70	663	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.619	0.539	0.705	0.619	0.539	0.705	SUBCLONAL	1	TRUE	1	0.317801680622727	2		663	712	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087924	27087925	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0041870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	138	686	0	ENST00000324856.7:c.2212dup	p.His738ProfsTer79	p.H738Pfs*79	ENST00000324856	NM_006015.4	737	-/C	6/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.317801680622727	2		686	817	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711291	114711292	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0041870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	120	491	0	ENST00000543371.1:c.306_307insGG	p.Tyr103GlyfsTer6	p.Y103Gfs*6	ENST00000543371	NM_001198531.1	102	-/GG	3/14	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.317801680622727	2		491	653	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533923	63533924	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	122	585	0	ENST00000307078.5:c.1230dup	p.Leu411ThrfsTer51	p.L411Tfs*51	ENST00000307078	NM_004655.3	410	-/A	6/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.317801680622727	2		585	614	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356137	66356137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290982378	NA	P-0041870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	41	513	0	ENST00000273854.3:c.1360G>A	p.Ala454Thr	p.A454T	ENST00000273854	NM_004439.5	454	Gcc/Acc	5/18	0.317801680622727	1	FACETS	0.361	0.3	0.429	0.361	0.3	0.429	SUBCLONAL	1	TRUE	0	0.317801680622727	1		513	601	SUCCESS
APC	324	MSKCC	GRCh37	5	112175468	112175469	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	90	348	0	ENST00000257430.4:c.4179dup	p.Asp1394Ter	p.D1394*	ENST00000257430	NM_000038.5	1393	ctt/cTtt	16/16	1	2	FACETS	0.782	0.7	0.869	1	0.982	1	SUBCLONAL	2	TRUE	1	0.317801680622727	2		348	362	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	80	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.232563380470025	2		336	483	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	356	1014	11	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.933	0.889	0.978	1	0.997	1	CLONAL	4	TRUE	1	0.232563380470025	2		1025	820	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	196	1117	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.0731760363376575	3	FACETS	1	0.96	1	1	0.96	1	INDETERMINATE	2	TRUE	1	0.232563380470025	3		1117	893	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	123	270	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.0731760363376575	3	FACETS	0.836	0.757	0.919	0.836	0.757	0.919	INDETERMINATE	2	TRUE	1	0.232563380470025	3		271	706	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	53	123	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.76	0.652	0.876	1	0.967	1	SUBCLONAL	2	TRUE	1	0.232563380470025	2		123	300	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	149	233	1	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	1	0.959	1	1	0.992	1	CLONAL	2	TRUE	1	0.232563380470025	2		234	597	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444275	50444275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	56	243	0	ENST00000331340.3:c.205C>T	p.Arg69Cys	p.R69C	ENST00000331340	NM_006060.4	69	Cgt/Tgt	4/8	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.232563380470025	2		243	370	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	260	1318	2	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	0.232563380470025	1	FACETS	0.891	0.834	0.949	1	0.994	1	CLONAL	2	TRUE	0	0.232563380470025	1		1320	1109	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574383	41574383	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1046088	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	211	646	33	ENST00000263253.7:c.6668A>C	p.Gln2223Pro	p.Q2223P	ENST00000263253	NM_001429.3	2223	cAg/cCg	31/31	1	2	FACETS	0.998	0.933	1	1	0.995	1	CLONAL	3	TRUE	1	0.232563380470025	2		679	606	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	281	966	19	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	0.232563380470025	1	FACETS	0.875	0.825	0.925	1	0.996	1	CLONAL	3	TRUE	0	0.232563380470025	1		985	814	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528120	103528120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376411022	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	97	215	0	ENST00000355739.4:c.3428C>T	p.Ala1143Val	p.A1143V	ENST00000355739	NM_000123.3	1143	gCg/gTg	15/15	1	2	FACETS	0.909	0.814	1	1	0.986	1	CLONAL	2	TRUE	1	0.232563380470025	2		215	459	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129329	152129329	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	82	749	3	ENST00000206249.3:c.287del	p.Gly96ValfsTer13	p.G96Vfs*13	ENST00000206249	NM_000125.3	94	ctG/ct	1/8	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.232563380470025	2		752	656	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744385	41744385	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	156	891	0	ENST00000301178.4:c.1010del	p.Pro337LeufsTer29	p.P337Lfs*29	ENST00000301178	NM_021913.4	335	ggC/gg	8/20	0.232563380470025	1	FACETS	0.841	0.772	0.913	1	0.99	1	CLONAL	2	TRUE	0	0.232563380470025	1		891	705	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	170	959	7	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	0.795	0.731	0.861	1	0.99	1	SUBCLONAL	2	TRUE	1	0.232563380470025	2		966	920	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	135	798	7	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	1	2	FACETS	0.793	0.722	0.868	1	0.987	1	SUBCLONAL	2	TRUE	1	0.232563380470025	2		805	732	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	142	736	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	1	2	FACETS	0.79	0.721	0.863	1	0.988	1	SUBCLONAL	2	TRUE	1	0.232563380470025	2		736	773	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267410	7267410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	189	636	0	ENST00000302850.5:c.598G>A	p.Val200Ile	p.V200I	ENST00000302850	NM_000208.2	200	Gtc/Atc	2/22	0.232563380470025	1	FACETS	1	0.937	1	1	0.993	1	CLONAL	2	TRUE	0	0.232563380470025	1		636	710	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117594	70117594	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	147	827	0	ENST00000245479.2:c.66del	p.Ser23AlafsTer38	p.S23Afs*38	ENST00000245479	NM_000346.3	21	gCc/gc	1/3	1	2	FACETS	0.866	0.792	0.943	1	0.99	1	CLONAL	2	TRUE	1	0.232563380470025	2		827	730	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673724	30673724	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61733207	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	171	570	1	ENST00000376406.3:c.3236G>A	p.Arg1079His	p.R1079H	ENST00000376406	NM_014641.2	1079	cGt/cAt	10/15	0.232563380470025	1	FACETS	0.815	0.751	0.882	1	0.99	1	CLONAL	2	TRUE	0	0.232563380470025	1		571	797	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	54	152	0	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.232563380470025	2		152	430	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265522	152265522	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1467954450	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	206	508	0	ENST00000206249.3:c.975del	p.Ile326TyrfsTer17	p.I326Yfs*17	ENST00000206249	NM_000125.3	325	ccG/cc	4/8	0.232563380470025	0	FACETS	0.784	0.732	0.837			1	SUBCLONAL	3	TRUE	0	0.232563380470025	0		508	578	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255142	16255143	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	rs764595221	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	118	223	2	ENST00000375759.3:c.2417_2418del	p.Arg806ThrfsTer14	p.R806Tfs*14	ENST00000375759	NM_015001.2	803	GAg/g	11/15	1	2	FACETS	0.857	0.776	0.943	1	0.987	1	CLONAL	2	TRUE	1	0.232563380470025	2		225	592	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867533	78867533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs185118480	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	174	860	0	ENST00000306801.3:c.2269G>A	p.Gly757Arg	p.G757R	ENST00000306801	NM_020761.2	757	Gga/Aga	20/34	1	2	FACETS	0.988	0.912	1	1	0.992	1	CLONAL	2	TRUE	1	0.232563380470025	2		860	757	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209298	133209298	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060500809	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	194	1034	1	ENST00000320574.5:c.6088del	p.Ala2030ProfsTer18	p.A2030Pfs*18	ENST00000320574	NM_006231.2	2030	Gcc/cc	44/49	0.232563380470025	1	FACETS	0.954	0.885	1	1	0.993	1	CLONAL	2	TRUE	0	0.232563380470025	1		1035	773	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830754	3830754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	81	220	0	ENST00000262367.5:c.1802G>A	p.Arg601Gln	p.R601Q	ENST00000262367	NM_004380.2	601	cGg/cAg	8/31	0.232563380470025	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.232563380470025	1		220	490	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029445	16029446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	130	159	2	ENST00000268712.3:c.1584dup	p.Glu529ArgfsTer7	p.E529Rfs*7	ENST00000268712	NM_006311.3	528	-/A	15/46	1	2	FACETS	0.869	0.795	0.945	1	0.992	1	CLONAL	3	TRUE	1	0.232563380470025	2		161	429	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736510	85736511	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs387906351	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	53	125	0	ENST00000370580.1:c.136dup	p.Ile46AsnfsTer4	p.I46Nfs*4	ENST00000370580	NM_003921.4	46	ata/aAta	2/3	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.232563380470025	2		125	379	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274911	41274911	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs868651538	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	93	185	0	ENST00000349496.5:c.1161T>A	p.Asn387Lys	p.N387K	ENST00000349496	NM_001904.3	387	aaT/aaA	8/15	1	2	FACETS	0.854	0.763	0.951	1	0.984	1	CLONAL	2	TRUE	1	0.232563380470025	2		185	468	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738094	145738094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561220929	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	164	1183	3	ENST00000428558.2:c.2816C>T	p.Ala939Val	p.A939V	ENST00000428558	NM_004260.3	939	gCg/gTg	17/22	0.0301593770092723	4	FACETS	0.781	0.716	0.849	0.781	0.716	0.849	INDETERMINATE	2	TRUE	2	0.232563380470025	4		1186	1113	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138117	2138117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759420443	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	213	1146	1	ENST00000219476.3:c.5137C>T	p.Arg1713Cys	p.R1713C	ENST00000219476	NM_000548.3	1713	Cgc/Tgc	40/42	0.232563380470025	1	FACETS	0.834	0.775	0.895	1	0.993	1	CLONAL	2	TRUE	0	0.232563380470025	1		1147	970	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047959	180047959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs933223149	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	215	1165	0	ENST00000261937.6:c.2216G>A	p.Arg739His	p.R739H	ENST00000261937	NM_182925.4	739	cGc/cAc	15/30	0.232563380470025	1	FACETS	0.928	0.864	0.995	1	0.993	1	CLONAL	2	TRUE	0	0.232563380470025	1		1165	880	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537115	41537115	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853039	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	98	193	0	ENST00000263253.7:c.1942C>T	p.Arg648Ter	p.R648*	ENST00000263253	NM_001429.3	648	Cga/Tga	10/31	1	2	FACETS	0.964	0.865	1	1	0.987	1	CLONAL	2	TRUE	1	0.232563380470025	2		193	437	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179506	56179506	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	63	104	0	ENST00000399503.3:c.3819G>T	p.Gln1273His	p.Q1273H	ENST00000399503	NM_005921.1	1273	caG/caT	15/20	0.0731760363376575	3	FACETS	0.972	0.847	1	0.972	0.847	1	INDETERMINATE	2	TRUE	1	0.232563380470025	3		104	311	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562745	21562745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778627422	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	85	281	0	ENST00000382592.4:c.1174G>A	p.Ala392Thr	p.A392T	ENST00000382592	NM_014572.2	392	Gcg/Acg	4/8	1	2	FACETS	1	0.947	1	1	0.986	1	CLONAL	2	TRUE	1	0.232563380470025	2		281	332	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104359294	104359294	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773037813	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	165	716	0	ENST00000369902.3:c.1015C>T	p.Arg339Trp	p.R339W	ENST00000369902	NM_016169.3	339	Cgg/Tgg	8/12	1	2	FACETS	0.971	0.893	1	1	0.992	1	CLONAL	2	TRUE	1	0.232563380470025	2		716	731	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426634	121426634	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	154	662	0	ENST00000257555.6:c.327-2A>T		p.X109_splice	ENST00000257555		109			0.232563380470025	1	FACETS	0.832	0.764	0.904	1	0.99	1	CLONAL	2	TRUE	0	0.232563380470025	1		662	703	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324892	31324892	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs765875917	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	89	281	0	ENST00000412585.2:c.44del	p.Ala15GlyfsTer5	p.A15Gfs*5	ENST00000412585	NM_005514.6	15	gCg/gg	1/8	0.232563380470025	1	FACETS	1	0.963	1	1	0.988	1	CLONAL	2	TRUE	0	0.232563380470025	1		281	291	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324494	31324494	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs9266161	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	141	883	0	ENST00000412585.2:c.314T>C	p.Leu105Pro	p.L105P	ENST00000412585	NM_005514.6	105	cTg/cCg	2/8	0.232563380470025	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.232563380470025	1		883	746	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99491900	99491900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368518102	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	164	762	1	ENST00000268035.6:c.3685G>A	p.Gly1229Ser	p.G1229S	ENST00000268035	NM_000875.3	1229	Ggc/Agc	20/21	1	2	FACETS	0.827	0.759	0.897	1	0.99	1	CLONAL	2	TRUE	1	0.232563380470025	2		763	853	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438211	49438211	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	201	856	0	ENST00000301067.7:c.5058del	p.Lys1686AsnfsTer36	p.K1686Nfs*36	ENST00000301067	NM_003482.3	1686	aaA/aa	20/54	0.0731760363376575	3	FACETS	1	0.945	1	1	0.945	1	INDETERMINATE	2	TRUE	1	0.232563380470025	3		856	943	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349211	89349211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755642596	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	250	799	0	ENST00000301030.4:c.3739G>A	p.Ala1247Thr	p.A1247T	ENST00000301030	NM_001256183.1	1247	Gct/Act	9/13	0.232563380470025	1	FACETS	0.788	0.736	0.841	1	0.993	1	SUBCLONAL	2	TRUE	0	0.232563380470025	1		799	1206	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	184	967	5	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			0.232563380470025	1	FACETS	0.805	0.743	0.868	1	0.991	1	CLONAL	2	TRUE	0	0.232563380470025	1		972	869	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199493	16199493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752192287	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	120	268	0	ENST00000375759.3:c.266G>A	p.Arg89Gln	p.R89Q	ENST00000375759	NM_015001.2	89	cGg/cAg	2/15	1	2	FACETS	1	0.949	1	1	0.99	1	CLONAL	2	TRUE	1	0.232563380470025	2		268	484	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040033	180040033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	209	1204	0	ENST00000261937.6:c.3409C>T	p.Pro1137Ser	p.P1137S	ENST00000261937	NM_182925.4	1137	Ccg/Tcg	25/30	0.232563380470025	1	FACETS	0.902	0.839	0.968	1	0.993	1	CLONAL	2	TRUE	0	0.232563380470025	1		1204	880	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612894	228612894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746429747	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	174	871	0	ENST00000366696.1:c.133G>A	p.Gly45Ser	p.G45S	ENST00000366696	NM_003493.2	45	Ggc/Agc	1/1	1	2	FACETS	0.939	0.866	1	1	0.992	1	CLONAL	2	TRUE	1	0.232563380470025	2		871	797	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109843	115109843	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751621934	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	111	383	0	ENST00000257566.3:c.2035G>A	p.Ala679Thr	p.A679T	ENST00000257566	NM_016569.3	679	Gcc/Acc	8/8	0.0731760363376575	3	FACETS	0.886	0.803	0.972	1	0.98	1	INDETERMINATE	3	TRUE	1	0.232563380470025	3		383	401	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448408	49448408	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs797045661	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	185	838	5	ENST00000301067.7:c.303del	p.Ser102AlafsTer28	p.S102Afs*28	ENST00000301067	NM_003482.3	101	ggG/gg	3/54	0.0731760363376575	3	FACETS	1	0.98	1	1	0.98	1	INDETERMINATE	2	TRUE	1	0.232563380470025	3		843	764	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346177	89346177	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	64	345	0	ENST00000301030.4:c.6773C>T	p.Ala2258Val	p.A2258V	ENST00000301030	NM_001256183.1	2258	gCt/gTt	9/13	0.232563380470025	1	FACETS	0.803	0.701	0.911	1	0.975	1	CLONAL	2	TRUE	0	0.232563380470025	1		345	303	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988573	36988573	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	191	698	3	ENST00000354822.5:c.80G>A	p.Arg27His	p.R27H	ENST00000354822	NM_001079668.2	27	cGc/cAc	2/3	1	2	FACETS	0.789	0.729	0.851	1	0.991	1	SUBCLONAL	2	TRUE	1	0.232563380470025	2		701	1041	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218764	66218764	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	47	93	0	ENST00000273854.3:c.2294del	p.Leu765Ter	p.L765*	ENST00000273854	NM_004439.5	765	tTg/tg	13/18	1	2	FACETS	0.757	0.643	0.88	1	0.963	1	SUBCLONAL	2	TRUE	1	0.232563380470025	2		93	267	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528740	8528740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	89	347	0	ENST00000356435.5:c.392G>A	p.Gly131Asp	p.G131D	ENST00000356435		131	gGc/gAc	4/35	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.232563380470025	2		347	545	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118367017	118367017	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	140	214	0	ENST00000534358.1:c.5603del	p.Pro1868GlnfsTer3	p.P1868Qfs*3	ENST00000534358	NM_005933.3	1867	Ccc/cc	20/36	1	2	FACETS	1	0.944	1	1	0.991	1	CLONAL	2	TRUE	1	0.232563380470025	2		214	578	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466001	69466001	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	189	1020	5	ENST00000227507.2:c.839A>T	p.Glu280Val	p.E280V	ENST00000227507	NM_053056.2	280	gAg/gTg	5/5	1	2	FACETS	0.963	0.891	1	1	0.993	1	CLONAL	2	TRUE	1	0.232563380470025	2		1025	844	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494620	2494620	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	179	867	1	ENST00000355716.4:c.760G>T	p.Val254Phe	p.V254F	ENST00000355716	NM_003820.2	254	Gtc/Ttc	8/8	1	2	FACETS	0.931	0.859	1	1	0.992	1	CLONAL	2	TRUE	1	0.232563380470025	2		868	827	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258727	16258727	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	127	576	0	ENST00000375759.3:c.5996del	p.Lys1999ArgfsTer23	p.K1999Rfs*23	ENST00000375759	NM_015001.2	1998	Aaa/aa	11/15	1	2	FACETS	0.892	0.811	0.978	1	0.989	1	CLONAL	2	TRUE	1	0.232563380470025	2		576	612	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023320	27023321	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	21	47	0	ENST00000324856.7:c.428dup	p.Leu143PhefsTer257	p.L143Ffs*257	ENST00000324856	NM_006015.4	142	-/T	1/20	1	2	FACETS	1	0.823	1	1	0.946	1	CLONAL	2	TRUE	1	0.232563380470025	2		47	86	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120502072	120502072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	75	188	0	ENST00000256646.2:c.1969G>A	p.Gly657Arg	p.G657R	ENST00000256646	NM_024408.3	657	Gga/Aga	12/34	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.232563380470025	2		188	451	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619201	43619201	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	163	785	0	ENST00000355710.3:c.2884A>G	p.Asn962Asp	p.N962D	ENST00000355710	NM_020975.4	962	Aac/Gac	17/20	1	2	FACETS	0.95	0.873	1	1	0.992	1	CLONAL	2	TRUE	1	0.232563380470025	2		785	738	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404618	70404618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	167	199	0	ENST00000373644.4:c.2132C>T	p.Thr711Ile	p.T711I	ENST00000373644	NM_030625.2	711	aCa/aTa	4/12	1	2	FACETS	1	0.928	1	1	0.992	1	CLONAL	2	TRUE	1	0.232563380470025	2		199	713	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416835	416835	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1180218375	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	116	276	0	ENST00000399788.2:c.3715C>T	p.Arg1239Trp	p.R1239W	ENST00000399788	NM_001042603.1	1239	Cgg/Tgg	23/28	NA	2	FACETS	1	0.913	1			1	INDETERMINATE	2	TRUE	NA	0.232563380470025	2		276	495	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427046	49427046	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	29	843	0	ENST00000301067.7:c.11442C>G	p.His3814Gln	p.H3814Q	ENST00000301067	NM_003482.3	3814	caC/caG	39/54	0.0731760363376575	3	FACETS	0.546	0.437	0.67	0.273	0.218	0.335	INDETERMINATE	1	TRUE	1	0.232563380470025	3		843	510	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438550	49438550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	175	772	0	ENST00000301067.7:c.4940C>T	p.Thr1647Ile	p.T1647I	ENST00000301067	NM_003482.3	1647	aCc/aTc	19/54	0.0731760363376575	3	FACETS	1	0.927	1	1	0.927	1	INDETERMINATE	2	TRUE	1	0.232563380470025	3		772	835	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437386	121437386	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	110	932	0	ENST00000257555.6:c.1724T>G	p.Ile575Ser	p.I575S	ENST00000257555		575	aTc/aGc	9/10	0.232563380470025	1	FACETS	0.993	0.892	1	0.993	0.892	1	CLONAL	1	TRUE	0	0.232563380470025	1		932	842	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645901	67645901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	88	259	0	ENST00000264010.4:c.829C>T	p.Arg277Trp	p.R277W	ENST00000264010	NM_006565.3	277	Cgg/Tgg	4/12	0.232563380470025	1	FACETS	0.907	0.804	1	0.907	0.804	1	CLONAL	1	TRUE	0	0.232563380470025	1		259	737	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40368048	40368048	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	202	567	0	ENST00000293328.3:c.1457A>G	p.Asn486Ser	p.N486S	ENST00000293328	NM_012448.3	486	aAt/aGt	12/19	1	2	FACETS	0.906	0.84	0.974	1	0.993	1	CLONAL	2	TRUE	1	0.232563380470025	2		567	959	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120318	70120318	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs80338688	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	258	1272	0	ENST00000245479.2:c.1320C>G	p.Tyr440Ter	p.Y440*	ENST00000245479	NM_000346.3	440	taC/taG	3/3	1	2	FACETS	0.912	0.853	0.972	1	0.994	1	CLONAL	2	TRUE	1	0.232563380470025	2		1272	1217	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400627	56400627	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	44	94	0	ENST00000348428.3:c.1223-2A>G		p.X408_splice	ENST00000348428	NM_006785.3	408			1	2	FACETS	0.785	0.664	0.917	1	0.963	1	CLONAL	2	TRUE	1	0.232563380470025	2		94	241	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226491	2226491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748004837	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	237	1082	0	ENST00000398665.3:c.3971C>T	p.Ala1324Val	p.A1324V	ENST00000398665	NM_032482.2	1324	gCg/gTg	27/28	0.232563380470025	1	FACETS	0.85	0.794	0.909	1	0.993	1	CLONAL	2	TRUE	0	0.232563380470025	1		1082	1059	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184460	7184460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	170	911	3	ENST00000302850.5:c.841G>A	p.Val281Met	p.V281M	ENST00000302850	NM_000208.2	281	Gtg/Atg	3/22	0.232563380470025	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.232563380470025	1		914	1004	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937583	17937583	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	244	994	0	ENST00000458235.1:c.3344A>G	p.Glu1115Gly	p.E1115G	ENST00000458235	NM_000215.3	1115	gAg/gGg	24/24	0.232563380470025	1	FACETS	0.906	0.847	0.967	1	0.994	1	CLONAL	2	TRUE	0	0.232563380470025	1		994	1023	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731556	47731556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	13	11	0	ENST00000449228.1:c.236G>A	p.Gly79Asp	p.G79D	ENST00000449228	NM_001127240.2	79	gGc/gAc	2/4	0.232563380470025	1	FACETS	1	0.842	1	1	0.925	1	CLONAL	2	TRUE	0	0.232563380470025	1		11	41	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469500	25469500	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	134	851	0	ENST00000264709.3:c.1268A>G	p.Glu423Gly	p.E423G	ENST00000264709	NM_175629.2	423	gAg/gGg	10/23	1	2	FACETS	0.851	0.775	0.931	1	0.989	1	CLONAL	2	TRUE	1	0.232563380470025	2		851	677	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281940	39281940	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	49	96	0	ENST00000402219.2:c.535G>A	p.Asp179Asn	p.D179N	ENST00000402219	NM_005633.3	179	Gat/Aat	5/23	1	2	FACETS	0.777	0.663	0.901	1	0.966	1	CLONAL	2	TRUE	1	0.232563380470025	2		96	271	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097988	178097988	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	65	134	0	ENST00000397062.3:c.392A>G	p.Asp131Gly	p.D131G	ENST00000397062	NM_006164.4	131	gAt/gGt	3/5	1	2	FACETS	0.753	0.656	0.857	1	0.973	1	SUBCLONAL	2	TRUE	1	0.232563380470025	2		134	371	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662322	227662322	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	161	842	0	ENST00000305123.5:c.1133C>T	p.Pro378Leu	p.P378L	ENST00000305123	NM_005544.2	378	cCg/cTg	1/2	1	2	FACETS	1	0.934	1	1	0.992	1	CLONAL	2	TRUE	1	0.232563380470025	2		842	681	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538254	9538254	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs888019754	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	28	235	1	ENST00000353224.5:c.1743+1G>A		p.X581_splice	ENST00000353224	NM_177990.2	581			0.232563380470025	1	FACETS	0.383	0.305	0.472	0.383	0.305	0.472	SUBCLONAL	1	TRUE	0	0.232563380470025	1		236	556	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624915	9624915	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	98	330	0	ENST00000353224.5:c.62T>C	p.Val21Ala	p.V21A	ENST00000353224	NM_177990.2	21	gTt/gCt	3/10	0.232563380470025	1	FACETS	0.766	0.687	0.85	1	0.982	1	SUBCLONAL	2	TRUE	0	0.232563380470025	1		330	486	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383269	31383269	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	170	576	1	ENST00000328111.2:c.1181C>A	p.Pro394His	p.P394H	ENST00000328111	NM_006892.3	394	cCc/cAc	11/23	0.232563380470025	1	FACETS	0.885	0.816	0.957	1	0.991	1	CLONAL	2	TRUE	0	0.232563380470025	1		577	730	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565524	41565524	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	70	159	0	ENST00000263253.7:c.4190A>G	p.Tyr1397Cys	p.Y1397C	ENST00000263253	NM_001429.3	1397	tAc/tGc	26/31	1	2	FACETS	0.865	0.759	0.978	1	0.979	1	CLONAL	2	TRUE	1	0.232563380470025	2		159	348	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725269	49725269	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	65	302	0	ENST00000449682.2:c.156del	p.His53MetfsTer25	p.H53Mfs*25	ENST00000449682	NM_020998.3	52	ctA/ct	2/18	1	2	FACETS	1	0.907	1	1	0.982	1	CLONAL	2	TRUE	1	0.232563380470025	2		302	268	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447235	187447236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	155	750	1	ENST00000232014.4:c.957dup	p.Asn320GlnfsTer11	p.N320Qfs*11	ENST00000232014	NM_001130845.1	319	-/C	5/10	0.232563380470025	0	FACETS	1	0.978	1			1	CLONAL	1	TRUE	0	0.232563380470025	0		751	849	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972963	55972963	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	117	203	0	ENST00000263923.4:c.1427T>C	p.Val476Ala	p.V476A	ENST00000263923	NM_002253.2	476	gTg/gCg	11/30	1	2	FACETS	0.906	0.82	0.997	1	0.988	1	CLONAL	2	TRUE	1	0.232563380470025	2		203	555	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251134	251134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138723511	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	56	220	0	ENST00000264932.6:c.1579C>T	p.Arg527Cys	p.R527C	ENST00000264932	NM_004168.2	527	Cgt/Tgt	12/15	0.232563380470025	1	FACETS	0.755	0.652	0.865	1	0.969	1	SUBCLONAL	2	TRUE	0	0.232563380470025	1		220	282	SUCCESS
APC	324	MSKCC	GRCh37	5	112102920	112102920	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	85	199	0	ENST00000257430.4:c.258del	p.Lys86AsnfsTer39	p.K86Nfs*39	ENST00000257430	NM_000038.5	85	gtA/gt	4/16	0.0731760363376575	3	FACETS	1	0.922	1	1	0.922	1	INDETERMINATE	2	TRUE	1	0.232563380470025	3		199	390	SUCCESS
APC	324	MSKCC	GRCh37	5	112176330	112176330	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	68	141	0	ENST00000257430.4:c.5039A>G	p.Gln1680Arg	p.Q1680R	ENST00000257430	NM_000038.5	1680	cAg/cGg	16/16	0.0731760363376575	3	FACETS	0.909	0.796	1	0.909	0.796	1	INDETERMINATE	2	TRUE	1	0.232563380470025	3		141	359	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324016	31324016	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs72558118	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	26	505	0	ENST00000412585.2:c.547T>C	p.Tyr183His	p.Y183H	ENST00000412585	NM_005514.6	183	Tac/Cac	3/8	0.232563380470025	1	FACETS	0.455	0.36	0.565	0.455	0.36	0.565	SUBCLONAL	1	TRUE	0	0.232563380470025	1		505	434	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324064	31324064	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs41541519	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	84	805	0	ENST00000412585.2:c.499A>G	p.Thr167Ala	p.T167A	ENST00000412585	NM_005514.6	167	Acc/Gcc	3/8	0.232563380470025	1	FACETS	0.923	0.815	1	0.923	0.815	1	CLONAL	1	TRUE	0	0.232563380470025	1		805	692	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519538	137519538	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148158267	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	81	188	0	ENST00000367739.4:c.1100C>T	p.Pro367Leu	p.P367L	ENST00000367739	NM_000416.2	367	cCg/cTg	7/7	1	2	FACETS	0.924	0.819	1	1	0.983	1	CLONAL	2	TRUE	1	0.232563380470025	2		188	377	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81340824	81340824	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	47	93	0	ENST00000222390.5:c.1417A>G	p.Thr473Ala	p.T473A	ENST00000222390	NM_000601.4	473	Acc/Gcc	12/18	1	2	FACETS	0.867	0.739	1	1	0.97	1	CLONAL	2	TRUE	1	0.232563380470025	2		93	233	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151168524	151168524	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	26	160	0	ENST00000262187.5:c.336A>G	p.Ile112Met	p.I112M	ENST00000262187	NM_005614.3	112	atA/atG	6/8	1	2	FACETS	0.592	0.468	0.733	0.592	0.468	0.733	SUBCLONAL	1	TRUE	1	0.232563380470025	2		160	378	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345989	152345989	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775565256	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	125	228	0	ENST00000359321.1:c.581C>T	p.Thr194Met	p.T194M	ENST00000359321	NM_005431.1	194	aCg/aTg	3/3	1	2	FACETS	0.994	0.903	1	1	0.99	1	CLONAL	2	TRUE	1	0.232563380470025	2		228	541	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540131	23540131	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	46	172	0	ENST00000380871.4:c.272C>T	p.Ala91Val	p.A91V	ENST00000380871	NM_006167.3	91	gCa/gTa	1/2	0.0301593770092723	4	FACETS	1	0.859	1	1	0.859	1	INDETERMINATE	2	TRUE	2	0.232563380470025	4		172	241	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317930	8317930	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	62	165	0	ENST00000356435.5:c.5683T>G	p.Phe1895Val	p.F1895V	ENST00000356435		1895	Ttt/Gtt	35/35	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.232563380470025	2		165	362	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465510	8465510	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	92	215	0	ENST00000356435.5:c.3670G>T	p.Glu1224Ter	p.E1224*	ENST00000356435		1224	Gaa/Taa	21/35	NA	2	FACETS	0.809	0.722	0.901			1	INDETERMINATE	2	TRUE	NA	0.232563380470025	2		215	489	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857281	9857281	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	104	757	0	ENST00000330684.3:c.4120G>C	p.Asp1374His	p.D1374H	ENST00000330684	NM_001134407.1	1374	Gac/Cac	13/13	0.278184027368022	2	FACETS	1	0.941	1	0.537	0.481	0.596	CLONAL	1	TRUE	0	0.278184027368022	2		757	696	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573975	7573975	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	246	940	0	ENST00000269305.4:c.1052del	p.Lys351ArgfsTer19	p.K351Rfs*19	ENST00000269305	NM_001126112.2	351	aAg/ag	10/11	0.278184027368022	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.278184027368022	2		940	866	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967218	134967218	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	195	681	0	ENST00000398015.3:c.2557C>G	p.Leu853Val	p.L853V	ENST00000398015	NM_004441.4	853	Cta/Gta	14/16	0.278184027368022	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	1	0.278184027368022	3		681	774	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976925	55976925	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	47	497	0	ENST00000263923.4:c.987del	p.Phe329LeufsTer34	p.F329Lfs*34	ENST00000263923	NM_002253.2	329	ttT/tt	8/30	0.278184027368022	3	FACETS	0.589	0.496	0.691	0.294	0.248	0.346	SUBCLONAL	1	TRUE	1	0.278184027368022	3		497	654	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187392	32187392	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	105	767	1	ENST00000375023.3:c.1487C>A	p.Thr496Asn	p.T496N	ENST00000375023	NM_004557.3	496	aCc/aAc	8/30	0.278184027368022	2	FACETS	0.947	0.848	1	0.474	0.424	0.526	CLONAL	1	TRUE	0	0.278184027368022	2		768	797	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0041940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	152	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.693761487005449	3	FACETS	1	0.946	1	0.519	0.476	0.562	CLONAL	1	TRUE	1	0.693761487005449	3		336	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0041940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	179	764	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	NA	2	FACETS	0.592	0.546	0.64			1	INDETERMINATE	1	TRUE	NA	0.693761487005449	2		765	871	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0041940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	375	810	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.693761487005449	2		810	843	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0041940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	146	340	1	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.693761487005449	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.693761487005449	1		341	271	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150030	202150030	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs931648756	NA	P-0041940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	414	383	1	ENST00000358485.4:c.1471C>T	p.Arg491Ter	p.R491*	ENST00000358485	NM_001080125.1	491	Cga/Tga	8/9	0.374816214774729	3	FACETS	0.883	0.845	0.922	0.883	0.845	0.922	INDETERMINATE	2	TRUE	1	0.693761487005449	3		384	910	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105671	27105671	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs928266893	NA	P-0041940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	339	310	0	ENST00000324856.7:c.5282G>A	p.Gly1761Asp	p.G1761D	ENST00000324856	NM_006015.4	1761	gGt/gAt	20/20	0.297257114007824	3	FACETS	1	0.988	1	0.723	0.692	0.754	INDETERMINATE	2	TRUE	0	0.693761487005449	3		310	607	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455057	50455057	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	155	297	0	ENST00000331340.3:c.604A>C	p.Lys202Gln	p.K202Q	ENST00000331340	NM_006060.4	202	Aaa/Caa	6/8	0.693761487005449	3	FACETS	0.993	0.913	1	0.497	0.456	0.538	CLONAL	1	TRUE	1	0.693761487005449	3		297	606	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0041957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	221	407	0	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.507787198088183	1		407	441	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720726	89720726	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs878853944	NA	P-0041957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	12	180	0	ENST00000371953.3:c.877G>T	p.Gly293Ter	p.G293*	ENST00000371953	NM_000314.4	293	Gga/Tga	8/9	1	2	FACETS	0.675	0.483	0.901	0.675	0.483	0.901	SUBCLONAL	1	TRUE	1	0.507787198088183	2		180	70	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426687	212426687	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	274	597	0	ENST00000342788.4:c.2428G>C	p.Glu810Gln	p.E810Q	ENST00000342788	NM_005235.2	810	Gag/Cag	20/28	0.507787198088183	3	FACETS	0.945	0.892	0.999	0.945	0.892	0.999	CLONAL	2	TRUE	1	0.507787198088183	3		597	716	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720741	89720745	+	frameshift_variant	Frame_Shift_Del	DEL	CAAGA	CAAGA	-	novel	NA	P-0041957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	10	229	0	ENST00000371953.3:c.892_896del	p.Gln298AsnfsTer3	p.Q298Nfs*3	ENST00000371953	NM_000314.4	298	CAAGAa/a	8/9	1	2	FACETS	0.475	0.325	0.657	0.475	0.325	0.657	SUBCLONAL	1	TRUE	1	0.507787198088183	2		229	83	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564513	55564513	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	209	507	1	ENST00000288135.5:c.401T>C	p.Val134Ala	p.V134A	ENST00000288135	NM_000222.2	134	gTc/gCc	3/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.507787198088183	2		508	742	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517780	187517780	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780722653	NA	P-0041957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	73	334	0	ENST00000441802.2:c.12914C>T	p.Ala4305Val	p.A4305V	ENST00000441802	NM_005245.3	4305	gCg/gTg	25/27	1	2	FACETS	0.879	0.775	0.99	0.879	0.775	0.99	CLONAL	1	TRUE	1	0.507787198088183	2		334	327	SUCCESS
APC	324	MSKCC	GRCh37	5	112175147	112175147	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	27	190	0	ENST00000257430.4:c.3856G>T	p.Glu1286Ter	p.E1286*	ENST00000257430	NM_000038.5	1286	Gaa/Taa	16/16	0.234147586773414	3	FACETS	1	0.831	1	0.523	0.418	0.642	CLONAL	1	TRUE	1	0.23348665379472	3		190	247	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0041973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	331	619	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	0.234147586773414	3	FACETS	0.945	0.897	0.993	1	0.993	1	CLONAL	4	TRUE	0	0.23348665379472	3		619	838	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0041973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	93	283	0	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	0.234147586773414	3	FACETS	0.901	0.81	0.997	1	0.978	1	CLONAL	3	TRUE	1	0.23348665379472	3		283	329	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446318	70446318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1429461725	NA	P-0041973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	164	491	0	ENST00000373644.4:c.5258G>A	p.Arg1753His	p.R1753H	ENST00000373644	NM_030625.2	1753	cGt/cAt	11/12	0.227281678081439	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.23348665379472	2		491	615	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920444	114920469	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGTGCAGGTATATTACCACTGCGAGG	CGTGCAGGTATATTACCACTGCGAGG	-	novel	NA	P-0041973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	88	405	0	ENST00000543371.1:c.1386_1391+20del		p.X462_splice	ENST00000543371	NM_001198531.1	462		13/14	0.227281678081439	2	FACETS	0.818	0.727	0.913	0.818	0.727	0.913	CLONAL	2	TRUE	0	0.23348665379472	2		405	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0041975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	79	629	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.305606115949051	2		630	467	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592099	67592099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	32	261	0	ENST00000274335.5:c.1915C>T	p.Arg639Ter	p.R639*	ENST00000274335		639	Cga/Tga	14/15	1	2	FACETS	0.74	0.603	0.894	0.74	0.603	0.894	SUBCLONAL	1	TRUE	1	0.305606115949051	2		261	283	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785627	50785627	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	91	556	0	ENST00000398568.2:c.617A>G	p.Glu206Gly	p.E206G	ENST00000398568	NM_001042412.1	206	gAa/gGa	4/18	0.305606115949051	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.305606115949051	1		556	478	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577607	7577608	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	CCTAGGAG	novel	NA	P-0041975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	29	500	0	ENST00000269305.4:c.673-7_673dup	p.Val225AlafsTer25	p.V225Afs*25	ENST00000269305	NM_001126112.2	225	gtt/gCTCCTAGGtt	7/11	1	2	FACETS	0.527	0.423	0.645	0.527	0.423	0.645	SUBCLONAL	1	TRUE	1	0.305606115949051	2		500	360	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439518	220439518	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540215120	NA	P-0041975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	49	701	0	ENST00000243786.2:c.371G>A	p.Arg124His	p.R124H	ENST00000243786	NM_002191.3	124	cGc/cAc	2/2	0.305606115949051	1	FACETS	0.719	0.61	0.837	0.719	0.61	0.837	SUBCLONAL	1	TRUE	0	0.305606115949051	1		701	378	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	123	300	0				ENST00000310581	NM_198253.2	-/1132			0.199160208748514	4	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	2	TRUE	2	0.468282383717565	4		300	321	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549404	21549404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753026198	NA	P-0041991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	118	588	1	ENST00000382592.4:c.2872C>T	p.Arg958Cys	p.R958C	ENST00000382592	NM_014572.2	958	Cgc/Tgc	8/8	1	2	FACETS	0.821	0.742	0.903	0.821	0.742	0.903	CLONAL	1	TRUE	1	0.468282383717565	2		589	614	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	160	412	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	0.269724154134407	6	FACETS	0.922	0.86	0.985			1	CLONAL	6	TRUE	NA	0.269724154134407	6		412	330	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012157	16012157	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	19	548	0	ENST00000268712.3:c.2125C>T	p.Gln709Ter	p.Q709*	ENST00000268712	NM_006311.3	709	Cag/Tag	19/46	1	2	FACETS	0.383	0.29	0.492	0.383	0.29	0.492	SUBCLONAL	1	TRUE	1	0.269724154134407	2		548	368	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936096	178936096	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519940	NA	P-0042002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	101	589	1	ENST00000263967.3:c.1638G>T	p.Gln546His	p.Q546H	ENST00000263967	NM_006218.2	546	caG/caT	10/21	0.269724154134407	6	FACETS	1	0.907	1			1	CLONAL	4	TRUE	NA	0.269724154134407	6		590	288	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903779	41903779	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	78	641	1	ENST00000372991.4:c.778C>T	p.Gln260Ter	p.Q260*	ENST00000372991	NM_001760.3	260	Cag/Tag	5/5	1	2	FACETS	0.503	0.441	0.571	0.503	0.441	0.571	SUBCLONAL	1	TRUE	1	0.269724154134407	2		642	1149	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952513	17952513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199815093	NA	P-0042002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	67	759	1	ENST00000458235.1:c.920C>T	p.Pro307Leu	p.P307L	ENST00000458235	NM_000215.3	307	cCg/cTg	7/24	1	2	FACETS	0.417	0.361	0.478	0.417	0.361	0.478	SUBCLONAL	1	TRUE	1	0.269724154134407	2		760	1191	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422898	49422898	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	74	683	0	ENST00000301067.7:c.14197G>C	p.Glu4733Gln	p.E4733Q	ENST00000301067	NM_003482.3	4733	Gag/Cag	44/54	1	2	FACETS	0.491	0.428	0.559	0.491	0.428	0.559	SUBCLONAL	1	TRUE	1	0.269724154134407	2		683	1117	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852446	63852446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	79	607	2	ENST00000279873.7:c.3224C>T	p.Ser1075Phe	p.S1075F	ENST00000279873	NM_032199.2	1075	tCc/tTc	10/10	1	2	FACETS	0.545	0.478	0.618	0.545	0.478	0.618	SUBCLONAL	1	TRUE	1	0.269724154134407	2		609	1075	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375630	118375630	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	39	420	0	ENST00000534358.1:c.9023C>G	p.Ser3008Cys	p.S3008C	ENST00000534358	NM_005933.3	3008	tCt/tGt	27/36	1	2	FACETS	0.469	0.387	0.56	0.469	0.387	0.56	SUBCLONAL	1	TRUE	1	0.269724154134407	2		420	617	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375662	118375662	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	41	475	1	ENST00000534358.1:c.9055C>G	p.His3019Asp	p.H3019D	ENST00000534358	NM_005933.3	3019	Cat/Gat	27/36	1	2	FACETS	0.442	0.367	0.526	0.442	0.367	0.526	SUBCLONAL	1	TRUE	1	0.269724154134407	2		476	688	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431655	431655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373480934	NA	P-0042002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	22	520	0	ENST00000399788.2:c.2354G>A	p.Arg785Lys	p.R785K	ENST00000399788	NM_001042603.1	785	aGg/aAg	17/28	1	2	FACETS	0.386	0.298	0.488	0.386	0.298	0.488	SUBCLONAL	1	TRUE	1	0.269724154134407	2		520	423	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563132	21563132	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1206	97	720	1	ENST00000382592.4:c.787G>T	p.Glu263Ter	p.E263*	ENST00000382592	NM_014572.2	263	Gaa/Taa	4/8	NA	2	FACETS	0.552	0.49	0.618			1	INDETERMINATE	1	TRUE	NA	0.269724154134407	2		721	1303	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058501	42058501	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	16	414	0	ENST00000219905.7:c.8221G>C	p.Glu2741Gln	p.E2741Q	ENST00000219905	NM_001164273.1	2741	Gag/Cag	24/24	1	2	FACETS	0.406	0.3	0.534	0.406	0.3	0.534	SUBCLONAL	1	TRUE	1	0.269724154134407	2		414	292	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058535	42058535	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	13	356	0	ENST00000219905.7:c.8255G>C	p.Arg2752Thr	p.R2752T	ENST00000219905	NM_001164273.1	2752	aGa/aCa	24/24	1	2	FACETS	0.38	0.27	0.513	0.38	0.27	0.513	SUBCLONAL	1	TRUE	1	0.269724154134407	2		356	254	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7977046	7977046	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	78	516	0	ENST00000319144.4:c.1684G>C	p.Glu562Gln	p.E562Q	ENST00000319144	NM_001139.2	562	Gag/Cag	13/15	1	2	FACETS	0.6	0.526	0.68	0.6	0.526	0.68	SUBCLONAL	1	TRUE	1	0.269724154134407	2		516	964	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8109860	8109860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	52	606	0	ENST00000585124.1:c.635G>A	p.Gly212Glu	p.G212E	ENST00000585124	NM_004217.3	212	gGa/gAa	7/9	1	2	FACETS	0.377	0.319	0.44	0.377	0.319	0.44	SUBCLONAL	1	TRUE	1	0.269724154134407	2		606	1023	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965945	25965945	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1413476740	NA	P-0042002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	71	665	0	ENST00000435504.4:c.3261G>C	p.Gln1087His	p.Q1087H	ENST00000435504		1087	caG/caC	13/13	1	2	FACETS	0.491	0.427	0.561	0.491	0.427	0.561	SUBCLONAL	1	TRUE	1	0.269724154134407	2		665	1072	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62290847	62290847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	47	369	0	ENST00000360203.5:c.92G>A	p.Cys31Tyr	p.C31Y	ENST00000360203	NM_001283009.1	31	tGt/tAt	2/35	0.252939237030834	3	FACETS	0.567	0.478	0.667	0.284	0.239	0.334	SUBCLONAL	1	TRUE	1	0.269724154134407	3		369	697	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604653	55604653	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	66	587	0	ENST00000288135.5:c.2861C>G	p.Ser954Cys	p.S954C	ENST00000288135	NM_000222.2	954	tCt/tGt	21/21	1	2	FACETS	0.494	0.428	0.567	0.494	0.428	0.567	SUBCLONAL	1	TRUE	1	0.269724154134407	2		587	990	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735447	40735447	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs745862490	NA	P-0042004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	101	705	0	ENST00000373198.4:c.3426G>T	p.Arg1142Ser	p.R1142S	ENST00000373198	NM_133170.3	1142	agG/agT	25/32	0.403738376248096	6	FACETS	0.719	0.641	0.804	0.18	0.16	0.201	SUBCLONAL	1	TRUE	2	0.403738376248096	6		705	1257	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520008	NA	P-0042004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	286	746	0	ENST00000269305.4:c.613T>G	p.Tyr205Asp	p.Y205D	ENST00000269305	NM_001126112.2	205	Tat/Gat	6/11	0.34993120373199	2	FACETS	0.978	0.925	1	0.978	0.925	1	CLONAL	2	TRUE	0	0.403738376248096	2		746	724	SUCCESS
APC	324	MSKCC	GRCh37	5	112175133	112175133	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	71	229	0	ENST00000257430.4:c.3842C>A	p.Ser1281Ter	p.S1281*	ENST00000257430	NM_000038.5	1281	tCa/tAa	16/16	0.371702598486814	3	FACETS	1	0.925	1	0.701	0.623	0.782	CLONAL	2	TRUE	0	0.403738376248096	3		229	201	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515232	149515232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80162387	NA	P-0042004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	166	813	1	ENST00000261799.4:c.250G>A	p.Val84Met	p.V84M	ENST00000261799	NM_002609.3	84	Gtg/Atg	3/23	0.371702598486814	3	FACETS	1	0.962	1	0.36	0.33	0.391	CLONAL	1	TRUE	0	0.403738376248096	3		814	915	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0042008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	718	810	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.721444788294288	2	FACETS	0.995	0.971	1	0.995	0.971	1	CLONAL	2	TRUE	0	0.721444788294288	2		810	1000	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0042012-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	274	764	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.236152353851642	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.27	2		765	905	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933574	39933574	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042012-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	33	367	0	ENST00000378444.4:c.1025G>A	p.Arg342Gln	p.R342Q	ENST00000378444	NM_001123385.1	342	cGa/cAa	4/15	1	1	FACETS	0.493	0.401	0.596	0.493	0.401	0.596	SUBCLONAL	1	TRUE	0	0.27	1		367	429	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845590	128845590	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772693769	NA	P-0042012-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	34	576	1	ENST00000249373.3:c.887G>A	p.Arg296His	p.R296H	ENST00000249373	NM_005631.4	296	cGt/cAt	4/12	1	2	FACETS	0.389	0.316	0.47	0.389	0.316	0.47	SUBCLONAL	1	TRUE	1	0.27	2		577	648	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880250	37880250	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042012-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	378	620	0	ENST00000269571.5:c.2294A>T	p.Lys765Ile	p.K765I	ENST00000269571		765	aAa/aTa	19/27	0.3	6	FACETS	0.948	0.901	0.996			1	CLONAL	4	TRUE	NA	0.27	6		620	1137	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482628	56482628	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042012-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	175	727	0	ENST00000267101.3:c.1085A>C	p.Asp362Ala	p.D362A	ENST00000267101	NM_001982.3	362	gAc/gCc	9/28	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.27	2		727	907	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402559	139402582	+	inframe_deletion	In_Frame_Del	DEL	CTCCATGCTGGCACAGGCGGGCAA	CTCCATGCTGGCACAGGCGGGCAA	-	novel	NA	P-0042012-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	48	909	0	ENST00000277541.6:c.3335_3358del	p.Val1112_Gly1119del	p.V1112_G1119del	ENST00000277541	NM_017617.3	1112	gTTGCCCGCCTGTGCCAGCATGGAGgg/ggg	21/34	1	2	FACETS	0.415	0.35	0.488	0.415	0.35	0.488	SUBCLONAL	1	TRUE	1	0.27	2		909	856	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0042018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	269	682	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.622717416711219	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.622717416711219	1		682	562	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0042018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	228	262	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.619183016645945	2	FACETS	0.984	0.936	1	0.984	0.936	1	CLONAL	2	TRUE	0	0.622717416711219	2		262	372	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0042018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	176	420	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.622717416711219	2		420	536	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014298	70014298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142372494	NA	P-0042018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	237	669	0	ENST00000394351.3:c.1159G>A	p.Gly387Ser	p.G387S	ENST00000394351	NM_000248.3	387	Ggt/Agt	9/9	1	2	FACETS	0.957	0.896	1	0.957	0.896	1	CLONAL	1	TRUE	1	0.622717416711219	2		669	795	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097236	11097236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs545634451	NA	P-0042018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	227	695	0	ENST00000358026.2:c.727G>A	p.Gly243Ser	p.G243S	ENST00000358026	NM_001128849.1	243	Ggc/Agc	4/36	1	2	FACETS	0.983	0.919	1	0.983	0.919	1	CLONAL	1	TRUE	1	0.622717416711219	2		695	742	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	670	599	1	ENST00000397062.3:c.246A>T	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaT	2/5	0.674886550311246	3	FACETS	0.985	0.953	1	0.985	0.953	1	CLONAL	2	TRUE	1	0.674886550311246	3		600	1348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0042020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	534	696	0	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	0.674886550311246	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.674886550311246	2		696	768	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956772	68956772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199819614	NA	P-0042020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	470	775	1	ENST00000288368.4:c.890G>A	p.Arg297His	p.R297H	ENST00000288368	NM_024870.2	297	cGt/cAt	8/40	0.565794456774368	3	FACETS	1	0.996	1			1	CLONAL	1	TRUE	NA	0.674886550311246	3		776	1307	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715739	30715739	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0042020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	268	319	0	ENST00000295754.5:c.1396+1G>T		p.X466_splice	ENST00000295754	NM_003242.5	466			0.660206558978287	2	FACETS	0.898	0.857	0.939	0.898	0.857	0.939	CLONAL	2	TRUE	0	0.674886550311246	2		319	442	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42861457	42861457	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	194	544	0	ENST00000398585.3:c.413C>A	p.Ala138Asp	p.A138D	ENST00000398585	NM_001135099.1	138	gCc/gAc	4/14	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.674886550311246	2		544	567	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277059	38277059	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	332	545	0	ENST00000425967.3:c.1369C>A	p.Gln457Lys	p.Q457K	ENST00000425967	NM_001174067.1	457	Cag/Aag	10/19	0.565794456774368	3	FACETS	0.963	0.918	1			1	CLONAL	2	TRUE	NA	0.674886550311246	3		545	683	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0042066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	312	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.4490514401196	3	FACETS	0.896	0.848	0.946	0.896	0.848	0.946	CLONAL	2	TRUE	1	0.476817514849655	3		336	904	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398635	116398635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	375	589	0	ENST00000397752.3:c.2225C>T	p.Pro742Leu	p.P742L	ENST00000397752	NM_000245.2	742	cCc/cTc	9/21	0.4490514401196	3	FACETS	0.998	0.95	1	0.998	0.95	1	CLONAL	2	TRUE	1	0.476817514849655	3		589	976	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214636	5214636	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532712500	NA	P-0042066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	194	933	0	ENST00000357368.4:c.4430G>A	p.Arg1477His	p.R1477H	ENST00000357368	NM_002850.3	1477	cGt/cAt	29/38	0.476891475950732	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.476817514849655	1		933	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579502	7579503	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CATCTGGA	novel	NA	P-0042066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	186	941	0	ENST00000269305.4:c.177_184dup	p.Glu62ValfsTer64	p.E62Vfs*64	ENST00000269305	NM_001126112.2	62	gaa/gTCCAGATGaa	4/11	0.476891475950732	1	FACETS	0.862	0.799	0.927	0.862	0.799	0.927	CLONAL	1	TRUE	0	0.476817514849655	1		941	689	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435739	56435739	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	347	676	0	ENST00000407977.2:c.1398del	p.Ser467AlafsTer35	p.S467Afs*35	ENST00000407977		466	tcC/tc	9/10	0.476817514849655	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.476817514849655	2		676	669	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0042081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	657	622	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.453565755605939	3	FACETS	0.997	0.966	1	0.997	0.966	1	CLONAL	3	TRUE	0	0.46721514840686	3		623	1160	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210440	36210440	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	354	704	0	ENST00000222270.7:c.433C>T	p.Arg145Ter	p.R145*	ENST00000222270	NM_014727.1	145	Cga/Tga	2/37	0.347090724795633	4	FACETS	0.973	0.922	1	0.973	0.922	1	CLONAL	2	TRUE	2	0.46721514840686	4		704	1143	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374942	149374942	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	675	794	2	ENST00000360632.3:c.152C>A	p.Ser51Tyr	p.S51Y	ENST00000360632	NM_015472.4	51	tCt/tAt	2/7	0.46721514840686	5	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	2	0.46721514840686	5		796	1509	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0042082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	162	569	1	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.684714593985846	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	0	0.684714593985846	1		570	285	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426123	138426123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217537873	NA	P-0042082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	75	434	0	ENST00000289153.2:c.1408G>A	p.Glu470Lys	p.E470K	ENST00000289153	NM_006219.2	470	Gaa/Aaa	9/22	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.684714593985846	2		434	172	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100980	41100980	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868706902	NA	P-0042082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	179	776	1	ENST00000373198.4:c.1376G>A	p.Arg459Gln	p.R459Q	ENST00000373198	NM_133170.3	459	cGg/cAg	8/32	0.451066567589354	0	FACETS		NA	1			1	NA	1	FALSE	0	0.684714593985846	0		777	374	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846235	156846235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201564883	NA	P-0042082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	33	947	0	ENST00000524377.1:c.1676G>A	p.Arg559His	p.R559H	ENST00000524377	NM_002529.3	559	cGt/cAt	14/17	0.183575313436089	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.684714593985846	0		947	432	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22405066	22405066	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	96	384	0	ENST00000344548.3:c.95A>G	p.Tyr32Cys	p.Y32C	ENST00000344548	NM_001039802.1	32	tAt/tGt	3/7	0.0806285675944817	5	FACETS	0.97	0.876	1	0.647	0.584	0.712	INDETERMINATE	2	FALSE	2	0.684714593985846	5		384	293	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046917	128046917	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	122	736	0	ENST00000285398.2:c.818A>T	p.Lys273Met	p.K273M	ENST00000285398	NM_000122.1	273	aAg/aTg	6/15	0.358754012860775	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.684714593985846	0		736	381	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503805	186503805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	226	762	0	ENST00000323963.5:c.482G>A	p.Gly161Glu	p.G161E	ENST00000323963		161	gGg/gAg	5/11	1	2	FACETS	0.876	0.818	0.934	0.876	0.818	0.934	CLONAL	1	FALSE	1	0.684714593985846	2		762	754	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751450	57751450	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	218	647	0	ENST00000274289.3:c.1541A>G	p.Tyr514Cys	p.Y514C	ENST00000274289	NM_006622.3	514	tAt/tGt	11/14	0.124484504244047	3	FACETS	0.756	0.709	0.805	0.756	0.709	0.805	INDETERMINATE	2	FALSE	1	0.684714593985846	3		647	565	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513378	106513378	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	51	402	0	ENST00000359195.3:c.2282C>A	p.Ser761Tyr	p.S761Y	ENST00000359195	NM_002649.2	761	tCc/tAc	4/11	0.138447749997105	3	FACETS	0.635	0.542	0.735	0.212	0.18	0.245	INDETERMINATE	1	FALSE	0	0.684714593985846	3		402	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579349	7579349	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1567555667	NA	P-0042087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	578	868	0	ENST00000269305.4:c.338T>G	p.Phe113Cys	p.F113C	ENST00000269305	NM_001126112.2	113	tTc/tGc	4/11	0.73291814819973	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.73291814819973	1		868	871	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962298	2962298	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769577430	NA	P-0042087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	70	937	0	ENST00000396946.4:c.2239G>A	p.Val747Ile	p.V747I	ENST00000396946	NM_032415.4	747	Gtc/Atc	17/25	1	2	FACETS	0.165	0.143	0.189	0.165	0.143	0.189	SUBCLONAL	1	TRUE	1	0.73291814819973	2		937	1156	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226217	2226217	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749330602	NA	P-0042087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	433	928	1	ENST00000398665.3:c.3697G>A	p.Gly1233Ser	p.G1233S	ENST00000398665	NM_032482.2	1233	Ggc/Agc	27/28	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.73291814819973	2		929	1161	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966769	25966769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	404	845	0	ENST00000435504.4:c.2437G>A	p.Ala813Thr	p.A813T	ENST00000435504		813	Gcc/Acc	13/13	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.73291814819973	2		845	1019	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636735	8636735	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	110	482	0	ENST00000356435.5:c.174C>A	p.Asn58Lys	p.N58K	ENST00000356435		58	aaC/aaA	2/35	0.371493983869675	3	FACETS	0.501	0.45	0.556	0.167	0.15	0.186	INDETERMINATE	1	TRUE	0	0.73291814819973	3		482	818	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0042135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	58	210	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.299	0.256	0.345	0.299	0.256	0.345	SUBCLONAL	1	TRUE	1	0.686401258494793	2		210	566	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0042135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	175	355	1	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	0.966	0.896	1	0.966	0.896	1	CLONAL	1	TRUE	1	0.686401258494793	2		356	528	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250472	110250472	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs201986818	NA	P-0042135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	262	617	0	ENST00000374672.4:c.203C>G	p.Ala68Gly	p.A68G	ENST00000374672	NM_004235.4	68	gCg/gGg	3/5	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.686401258494793	2		617	669	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870865	12870866	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0042135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	43	355	0	ENST00000228872.4:c.92_93del	p.Asn31ThrfsTer93	p.N31Tfs*93	ENST00000228872	NM_004064.3	31	aAC/a	1/3	1	2	FACETS	0.315	0.264	0.371	0.315	0.264	0.371	SUBCLONAL	1	TRUE	1	0.686401258494793	2		355	398	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280043	18280044	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0042135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	51	427	1	ENST00000222254.8:c.2126_2127delinsAA	p.Thr709Lys	p.T709K	ENST00000222254	NM_005027.3	709	aCC/aAA	16/16	1	2	FACETS	0.326	0.277	0.379	0.326	0.277	0.379	SUBCLONAL	1	TRUE	1	0.686401258494793	2		428	456	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483949	212483949	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	199	548	0	ENST00000342788.4:c.2254A>G	p.Ile752Val	p.I752V	ENST00000342788	NM_005235.2	752	Att/Gtt	19/28	1	2	FACETS	0.907	0.845	0.972	0.907	0.845	0.972	CLONAL	1	TRUE	1	0.686401258494793	2		548	639	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42840414	42840415	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs193920966	NA	P-0042135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	214	595	0	ENST00000398585.3:c.1333_1334del	p.Gln445GlufsTer9	p.Q445Efs*9	ENST00000398585	NM_001135099.1	445	CAg/g	12/14	1	2	FACETS	0.913	0.852	0.975	0.913	0.852	0.975	CLONAL	1	TRUE	1	0.686401258494793	2		595	683	SUCCESS
ATR	545	MSKCC	GRCh37	3	142183962	142183962	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	141	356	0	ENST00000350721.4:c.7018del	p.Glu2340AsnfsTer5	p.E2340Nfs*5	ENST00000350721	NM_001184.3	2340	Gaa/aa	41/47	1	2	FACETS	0.851	0.78	0.923	0.851	0.78	0.923	CLONAL	1	TRUE	1	0.686401258494793	2		356	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0042148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	202	863	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.298021026155851	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.24	1		863	1010	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0042148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	66	407	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.225747056050251	3	FACETS	0.979	0.85	1	0.49	0.425	0.56	CLONAL	1	TRUE	1	0.24	3		407	629	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	113	439	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	0.298021026155851	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.24	1		439	685	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730125	41730125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142519810	NA	P-0042148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	45	485	1	ENST00000242208.4:c.404C>T	p.Thr135Met	p.T135M	ENST00000242208	NM_002192.2	135	aCg/aTg	3/3	1	2	FACETS	0.681	0.571	0.801	0.681	0.571	0.801	SUBCLONAL	1	TRUE	1	0.24	2		486	551	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	89	300	0				ENST00000310581	NM_198253.2	-/1132			0.428016489365736	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.428016489365736	1		300	318	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336232	73336232	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	82	326	0	ENST00000377767.4:c.2171C>T	p.Ser724Phe	p.S724F	ENST00000377767	NM_014953.3	724	tCt/tTt	17/21	1	2	FACETS	0.912	0.809	1	0.912	0.809	1	CLONAL	1	TRUE	1	0.428016489365736	2		326	420	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	158	669	0	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.428016489365736	2		669	650	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790641	89790641	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	202	900	1	ENST00000336032.3:c.28G>T	p.Glu10Ter	p.E10*	ENST00000336032	NM_006813.2	10	Gag/Tag	1/2	0.428016489365736	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.428016489365736	1		901	707	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517879	187517879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	159	553	0	ENST00000441802.2:c.12815C>T	p.Ser4272Phe	p.S4272F	ENST00000441802	NM_005245.3	4272	tCc/tTc	25/27	0.428016489365736	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.428016489365736	1		553	539	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421568	32421568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267602851	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	220	730	0	ENST00000332351.3:c.1024G>A	p.Asp342Asn	p.D342N	ENST00000332351	NM_024426.4	342	Gat/Aat	6/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.428016489365736	2		730	905	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615595	43615595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	150	685	0	ENST00000355710.3:c.2674G>A	p.Asp892Asn	p.D892N	ENST00000355710	NM_020975.4	892	Gat/Aat	15/20	0.428016489365736	1	FACETS	0.899	0.825	0.976	0.899	0.825	0.976	CLONAL	1	TRUE	0	0.428016489365736	1		685	613	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246350	46246350	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1275863291	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	123	457	0	ENST00000334344.6:c.4444C>T	p.Gln1482Ter	p.Q1482*	ENST00000334344	NM_152641.2	1482	Caa/Taa	15/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.428016489365736	2		457	546	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520257	9520257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	129	498	0	ENST00000353224.5:c.2012C>T	p.Ser671Leu	p.S671L	ENST00000353224	NM_177990.2	671	tCa/tTa	10/10	1	2	FACETS	0.996	0.906	1	0.996	0.906	1	CLONAL	1	TRUE	1	0.428016489365736	2		498	605	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000025	42000025	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	468	780	1	ENST00000219905.7:c.2288G>A	p.Trp763Ter	p.W763*	ENST00000219905	NM_001164273.1	763	tGg/tAg	6/24	0.428016489365736	3	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.428016489365736	3		781	1268	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138563	55138563	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	195	588	0	ENST00000257290.5:c.1240C>T	p.Pro414Ser	p.P414S	ENST00000257290	NM_006206.4	414	Cct/Tct	9/23	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.428016489365736	2		588	758	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948779	55948779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776015468	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	147	545	0	ENST00000263923.4:c.3686G>A	p.Arg1229Gln	p.R1229Q	ENST00000263923	NM_002253.2	1229	cGa/cAa	28/30	1	2	FACETS	0.913	0.835	0.995	0.913	0.835	0.995	CLONAL	1	TRUE	1	0.428016489365736	2		545	752	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486027	29486027	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	76	320	0	ENST00000356175.3:c.205-1G>A		p.X69_splice	ENST00000356175	NM_000267.3	69			1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.428016489365736	2		320	355	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912075	56912075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	148	780	1	ENST00000519728.1:c.1303G>A	p.Glu435Lys	p.E435K	ENST00000519728	NM_002350.3	435	Gaa/Aaa	12/13	1	2	FACETS	0.84	0.768	0.916	0.84	0.768	0.916	CLONAL	1	TRUE	1	0.428016489365736	2		781	823	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857172	9857172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555481986	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	149	648	2	ENST00000330684.3:c.4229C>T	p.Ser1410Leu	p.S1410L	ENST00000330684	NM_001134407.1	1410	tCg/tTg	13/13	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.428016489365736	2		650	657	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145424	61145424	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	110	383	0	ENST00000295025.8:c.634C>T	p.Gln212Ter	p.Q212*	ENST00000295025	NM_002908.2	212	Cag/Tag	6/11	0.105918653139357	3	FACETS	1	0.981	1	0.687	0.621	0.756	INDETERMINATE	1	TRUE	1	0.428016489365736	3		383	454	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504362	8504362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	164	656	0	ENST00000356435.5:c.1721G>A	p.Gly574Glu	p.G574E	ENST00000356435		574	gGa/gAa	12/35	1	2	FACETS	0.995	0.915	1	0.995	0.915	1	CLONAL	1	TRUE	1	0.428016489365736	2		656	770	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449812	149449812	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	222	989	0	ENST00000286301.3:c.1252T>A	p.Leu418Met	p.L418M	ENST00000286301	NM_005211.3	418	Ttg/Atg	9/22	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.428016489365736	2		989	989	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247772	10247772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769347864	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	244	878	1	ENST00000340748.4:c.4430C>T	p.Ser1477Phe	p.S1477F	ENST00000340748		1477	tCc/tTc	36/40	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.428016489365736	2		879	878	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965463	68965463	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1206854674	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	219	873	0	ENST00000288368.4:c.1075G>A	p.Glu359Lys	p.E359K	ENST00000288368	NM_024870.2	359	Gaa/Aaa	9/40	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.428016489365736	2		873	969	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961005	55961005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	170	654	1	ENST00000263923.4:c.2935G>A	p.Glu979Lys	p.E979K	ENST00000263923	NM_002253.2	979	Gag/Aag	21/30	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.428016489365736	2		655	754	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31372648	31372648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769220144	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	201	703	1	ENST00000328111.2:c.289C>T	p.Arg97Cys	p.R97C	ENST00000328111	NM_006892.3	97	Cgt/Tgt	4/23	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.428016489365736	2		704	915	SUCCESS
ALK	238	MSKCC	GRCh37	2	29497983	29497983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1469128263	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	190	667	0	ENST00000389048.3:c.2023C>T	p.Pro675Ser	p.P675S	ENST00000389048	NM_004304.4	675	Ccc/Tcc	11/29	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.428016489365736	2		667	758	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047257	180047257	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276261095	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	201	989	0	ENST00000261937.6:c.2458G>A	p.Gly820Arg	p.G820R	ENST00000261937	NM_182925.4	820	Ggg/Agg	17/30	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.428016489365736	2		989	828	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719947	18719947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437834329	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	100	519	0	ENST00000266497.5:c.3844C>T	p.His1282Tyr	p.H1282Y	ENST00000266497		1282	Cat/Tat	27/31	1	2	FACETS	0.813	0.728	0.903	0.813	0.728	0.903	CLONAL	1	TRUE	1	0.428016489365736	2		519	575	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999728	100999728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	176	926	1	ENST00000325455.5:c.74C>T	p.Ser25Phe	p.S25F	ENST00000325455	NM_001202474.3	25	tCc/tTc	1/8	0.428016489365736	1	FACETS	0.998	0.923	1	0.998	0.923	1	CLONAL	1	TRUE	0	0.428016489365736	1		927	648	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467978	50467978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	161	691	0	ENST00000331340.3:c.1213G>A	p.Glu405Lys	p.E405K	ENST00000331340	NM_006060.4	405	Gag/Aag	8/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.428016489365736	2		691	714	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211825	36211825	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	185	1002	1	ENST00000222270.7:c.1576C>T	p.Gln526Ter	p.Q526*	ENST00000222270	NM_014727.1	526	Cag/Tag	3/37	1	2	FACETS	0.954	0.881	1	0.954	0.881	1	CLONAL	1	TRUE	1	0.428016489365736	2		1003	906	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273916	10273916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	198	979	0	ENST00000330684.3:c.353C>T	p.Ser118Phe	p.S118F	ENST00000330684	NM_001134407.1	118	tCc/tTc	2/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.428016489365736	2		979	867	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188513	11188513	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	164	596	0	ENST00000361445.4:c.5908C>T	p.Gln1970Ter	p.Q1970*	ENST00000361445	NM_004958.3	1970	Cag/Tag	42/58	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.428016489365736	2		596	739	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088784	27088784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140683722	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	186	648	0	ENST00000324856.7:c.2393C>T	p.Pro798Leu	p.P798L	ENST00000324856	NM_006015.4	798	cCc/cTc	7/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.428016489365736	2		648	609	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941123	36941124	+	missense_variant	Missense_Mutation	DNP	CC	CC	GT	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	172	848	2	ENST00000361632.4:c.215_216delinsAC	p.Gly72Asp	p.G72D	ENST00000361632		72	gGG/gAC	3/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.428016489365736	2		850	731	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748132	72748132	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	117	625	1	ENST00000357731.5:c.46T>A	p.Trp16Arg	p.W16R	ENST00000357731	NM_173808.2	16	Tgg/Agg	1/7	1	2	FACETS	0.899	0.813	0.99	0.899	0.813	0.99	CLONAL	1	TRUE	1	0.428016489365736	2		626	608	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828104	243828104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	131	489	1	ENST00000263826.5:c.254G>A	p.Arg85Lys	p.R85K	ENST00000263826	NM_005465.4	85	aGa/aAa	3/13	1	2	FACETS	0.994	0.905	1	0.994	0.905	1	CLONAL	1	TRUE	1	0.428016489365736	2		490	616	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245246	46245247	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	127	604	0	ENST00000334344.6:c.3340_3341del	p.Gln1114AsnfsTer45	p.Q1114Nfs*45	ENST00000334344	NM_152641.2	1114	CAa/a	15/21	1	2	FACETS	0.866	0.786	0.95	0.866	0.786	0.95	CLONAL	1	TRUE	1	0.428016489365736	2		604	685	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863352	57863352	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	242	938	3	ENST00000228682.2:c.1447G>A	p.Glu483Lys	p.E483K	ENST00000228682	NM_005269.2	483	Gag/Aag	11/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.428016489365736	2		941	995	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222616	69222616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	174	733	0	ENST00000462284.1:c.589C>T	p.Leu197Phe	p.L197F	ENST00000462284	NM_002392.5	197	Ctt/Ttt	8/11	1	2	FACETS	0.995	0.917	1	0.995	0.917	1	CLONAL	1	TRUE	1	0.428016489365736	2		733	817	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134169	41134169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771279465	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	89	493	0	ENST00000379561.5:c.1459C>T	p.Pro487Ser	p.P487S	ENST00000379561	NM_002015.3	487	Ccc/Tcc	2/3	1	2	FACETS	0.806	0.717	0.901	0.806	0.717	0.901	CLONAL	1	TRUE	1	0.428016489365736	2		493	516	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641010	23641010	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	181	695	0	ENST00000261584.4:c.2465A>T	p.Gln822Leu	p.Q822L	ENST00000261584	NM_024675.3	822	cAg/cTg	5/13	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.428016489365736	2		695	840	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816247	89816248	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	153	813	0	ENST00000389301.3:c.3129_3130delinsTT	p.Gln1044Ter	p.Q1044*	ENST00000389301	NM_000135.2	1043	tcCCag/tcTTag	32/43	1	2	FACETS	0.862	0.789	0.939	0.862	0.789	0.939	CLONAL	1	TRUE	1	0.428016489365736	2		813	829	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982821	7982821	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	213	903	0	ENST00000319144.4:c.964G>A	p.Glu322Lys	p.E322K	ENST00000319144	NM_001139.2	322	Gag/Aag	8/15	0.428016489365736	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.428016489365736	1		903	654	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55339533	55339533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	216	747	0	ENST00000284073.2:c.292C>T	p.Pro98Ser	p.P98S	ENST00000284073	NM_138962.2	98	Cct/Tct	5/14	1	2	FACETS	0.952	0.885	1	0.952	0.885	1	CLONAL	1	TRUE	1	0.428016489365736	2		747	1060	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39595460	39595460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	118	559	1	ENST00000262039.4:c.1346C>T	p.Pro449Leu	p.P449L	ENST00000262039	NM_002647.2	449	cCc/cTc	12/25	1	2	FACETS	0.921	0.833	1	0.921	0.833	1	CLONAL	1	TRUE	1	0.428016489365736	2		560	599	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231453	5231453	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1238574782	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	252	862	0	ENST00000357368.4:c.2023C>T	p.Pro675Ser	p.P675S	ENST00000357368	NM_002850.3	675	Ccc/Tcc	14/38	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.428016489365736	2		862	971	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353903	15353903	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	155	589	0	ENST00000263377.2:c.2977C>T	p.Pro993Ser	p.P993S	ENST00000263377	NM_058243.2	993	Cct/Tct	14/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.428016489365736	2		589	592	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971634	18971635	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	156	813	0	ENST00000262803.5:c.2301-1_2301delinsAA		p.X767_splice	ENST00000262803	NM_002911.3	767		17/24	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.428016489365736	2		813	727	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229450	36229450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	96	575	0	ENST00000222270.7:c.8140C>T	p.Leu2714Phe	p.L2714F	ENST00000222270	NM_014727.1	2714	Ctt/Ttt	37/37	1	2	FACETS	0.929	0.831	1	0.929	0.831	1	CLONAL	1	TRUE	1	0.428016489365736	2		575	483	SUCCESS
ALK	238	MSKCC	GRCh37	2	29420440	29420441	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	182	789	1	ENST00000389048.3:c.4040_4041delinsAA	p.Arg1347Gln	p.R1347Q	ENST00000389048	NM_004304.4	1347	cGG/cAA	27/29	NA	2	FACETS	0.941	0.868	1			1	INDETERMINATE	1	TRUE	NA	0.428016489365736	2		790	904	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574042	46574043	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	222	821	2	ENST00000263734.3:c.57_58delinsTT	p.Arg20Trp	p.R20W	ENST00000263734	NM_001430.4	19	tcCCgg/tcTTgg	2/16	0.105918653139357	3	FACETS	1	0.991	1	0.731	0.682	0.782	INDETERMINATE	1	TRUE	1	0.428016489365736	3		823	861	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732675	204732675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	140	449	0	ENST00000302823.3:c.10C>T	p.Leu4Phe	p.L4F	ENST00000302823	NM_005214.4	4	Ctt/Ttt	1/4	1	2	FACETS	0.991	0.905	1	0.991	0.905	1	CLONAL	1	TRUE	1	0.428016489365736	2		449	660	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543852	212543852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767818461	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	155	506	0	ENST00000342788.4:c.1547G>A	p.Gly516Glu	p.G516E	ENST00000342788	NM_005235.2	516	gGg/gAg	13/28	1	2	FACETS	0.948	0.869	1	0.948	0.869	1	CLONAL	1	TRUE	1	0.428016489365736	2		506	764	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560889	9560889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1263199713	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	186	621	0	ENST00000353224.5:c.893C>T	p.Pro298Leu	p.P298L	ENST00000353224	NM_177990.2	298	cCa/cTa	4/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.428016489365736	2		621	732	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735541	40735541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	142	635	0	ENST00000373198.4:c.3332G>A	p.Gly1111Asp	p.G1111D	ENST00000373198	NM_133170.3	1111	gGc/gAc	25/32	1	2	FACETS	0.995	0.909	1	0.995	0.909	1	CLONAL	1	TRUE	1	0.428016489365736	2		635	667	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281194	46281194	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	211	720	0	ENST00000371998.3:c.3991C>T	p.Pro1331Ser	p.P1331S	ENST00000371998		1331	Cct/Tct	21/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.428016489365736	2		720	887	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485820	57485820	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	171	544	0	ENST00000371085.3:c.1121G>C	p.Arg374Pro	p.R374P	ENST00000371085	NM_000516.4	374	cGt/cCt	13/13	1	2	FACETS	0.994	0.915	1	0.994	0.915	1	CLONAL	1	TRUE	1	0.428016489365736	2		544	804	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817450	39817450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749235777	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	146	717	0	ENST00000288319.7:c.113C>T	p.Ser38Phe	p.S38F	ENST00000288319	NM_182918.3	38	tCc/tTc	2/10	1	2	FACETS	0.905	0.827	0.986	0.905	0.827	0.986	CLONAL	1	TRUE	1	0.428016489365736	2		717	754	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545852	41545852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	240	918	1	ENST00000263253.7:c.2467C>T	p.Pro823Ser	p.P823S	ENST00000263253	NM_001429.3	823	Cct/Tct	14/31	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.428016489365736	2		919	1059	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259202	89259202	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	133	481	0	ENST00000336596.2:c.346T>G	p.Cys116Gly	p.C116G	ENST00000336596	NM_005233.5	116	Tgc/Ggc	3/17	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.428016489365736	2		481	569	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433543	138433543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	128	448	0	ENST00000289153.2:c.1069C>T	p.Leu357Phe	p.L357F	ENST00000289153	NM_006219.2	357	Ctt/Ttt	7/22	0.428016489365736	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.428016489365736	1		448	461	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952481	38952481	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	123	370	0	ENST00000357387.3:c.2944T>C	p.Cys982Arg	p.C982R	ENST00000357387	NM_152756.3	982	Tgt/Cgt	30/38	0.428016489365736	1	FACETS	0.986	0.898	1	0.986	0.898	1	CLONAL	1	TRUE	0	0.428016489365736	1		370	458	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958598	38958598	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	77	304	0	ENST00000357387.3:c.2367G>T	p.Gln789His	p.Q789H	ENST00000357387	NM_152756.3	789	caG/caT	24/38	0.428016489365736	1	FACETS	0.87	0.77	0.975	0.87	0.77	0.975	CLONAL	1	TRUE	0	0.428016489365736	1		304	325	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672296	86672296	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	144	534	0	ENST00000274376.6:c.2098G>A	p.Gly700Ser	p.G700S	ENST00000274376	NM_002890.2	700	Ggt/Agt	16/25	1	2	FACETS	0.937	0.856	1	0.937	0.856	1	CLONAL	1	TRUE	1	0.428016489365736	2		534	718	SUCCESS
APC	324	MSKCC	GRCh37	5	112177321	112177321	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	137	414	0	ENST00000257430.4:c.6030A>T	p.Lys2010Asn	p.K2010N	ENST00000257430	NM_000038.5	2010	aaA/aaT	16/16	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.428016489365736	2		414	602	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721351	176721351	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	139	608	1	ENST00000439151.2:c.6982C>T	p.Gln2328Ter	p.Q2328*	ENST00000439151	NM_022455.4	2328	Cag/Tag	23/23	1	2	FACETS	0.948	0.865	1	0.948	0.865	1	CLONAL	1	TRUE	1	0.428016489365736	2		609	685	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038428	180038428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779959568	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	201	885	0	ENST00000261937.6:c.3589G>A	p.Gly1197Ser	p.G1197S	ENST00000261937	NM_182925.4	1197	Ggc/Agc	27/30	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.428016489365736	2		885	811	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171581	32171582	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	153	807	1	ENST00000375023.3:c.3196_3197delinsAA	p.Gly1066Lys	p.G1066K	ENST00000375023	NM_004557.3	1066	GGa/AAa	20/30	1	2	FACETS	0.848	0.776	0.923	0.848	0.776	0.923	CLONAL	1	TRUE	1	0.428016489365736	2		808	843	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287422	33287422	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	124	665	0	ENST00000374542.5:c.1675G>T	p.Glu559Ter	p.E559*	ENST00000374542	NM_001141970.1	559	Gaa/Taa	6/8	1	2	FACETS	0.841	0.762	0.924	0.841	0.762	0.924	CLONAL	1	TRUE	1	0.428016489365736	2		665	689	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969146	93969146	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373264389	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	123	524	1	ENST00000369303.4:c.1850C>T	p.Pro617Leu	p.P617L	ENST00000369303	NM_004440.3	617	cCa/cTa	10/17	0.428016489365736	1	FACETS	0.872	0.793	0.955	0.872	0.793	0.955	CLONAL	1	TRUE	0	0.428016489365736	1		525	518	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982111	93982111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	142	540	0	ENST00000369303.4:c.1354G>A	p.Glu452Lys	p.E452K	ENST00000369303	NM_004440.3	452	Gag/Aag	6/17	0.428016489365736	1	FACETS	0.948	0.869	1	0.948	0.869	1	CLONAL	1	TRUE	0	0.428016489365736	1		540	550	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663581	117663581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776176321	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	158	691	0	ENST00000368508.3:c.4651G>A	p.Gly1551Arg	p.G1551R	ENST00000368508	NM_002944.2	1551	Gga/Aga	28/43	0.428016489365736	1	FACETS	0.917	0.843	0.993	0.917	0.843	0.993	CLONAL	1	TRUE	0	0.428016489365736	1		691	633	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367293	50367293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	149	659	0	ENST00000331340.3:c.100C>T	p.Pro34Ser	p.P34S	ENST00000331340	NM_006060.4	34	Ccc/Tcc	3/8	1	2	FACETS	0.995	0.911	1	0.995	0.911	1	CLONAL	1	TRUE	1	0.428016489365736	2		659	700	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444289	50444289	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	111	448	1	ENST00000331340.3:c.219G>T	p.Met73Ile	p.M73I	ENST00000331340	NM_006060.4	73	atG/atT	4/8	1	2	FACETS	0.887	0.799	0.979	0.887	0.799	0.979	CLONAL	1	TRUE	1	0.428016489365736	2		449	585	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411694	116411694	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	239	895	0	ENST00000397752.3:c.2873G>A	p.Arg958Lys	p.R958K	ENST00000397752	NM_000245.2	958	aGa/aAa	13/21	1	2	FACETS	0.947	0.883	1	0.947	0.883	1	CLONAL	1	TRUE	1	0.428016489365736	2		895	1179	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965469	68965469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	224	864	0	ENST00000288368.4:c.1081G>A	p.Glu361Lys	p.E361K	ENST00000288368	NM_024870.2	361	Gaa/Aaa	9/40	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.428016489365736	2		864	961	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637014	93637014	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	150	631	0	ENST00000375746.1:c.1064C>T	p.Pro355Leu	p.P355L	ENST00000375746	NM_001174167.1	355	cCc/cTc	9/14	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.428016489365736	2		631	623	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412625	139412625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	255	915	0	ENST00000277541.6:c.1219C>T	p.Pro407Ser	p.P407S	ENST00000277541	NM_017617.3	407	Ccg/Tcg	7/34	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.428016489365736	2		915	978	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224544	53224544	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	241	452	0	ENST00000375401.3:c.3169G>T	p.Val1057Leu	p.V1057L	ENST00000375401	NM_004187.3	1057	Gtg/Ttg	21/26	1	1	FACETS	0.898	0.849	0.947	1	0.995	1	CLONAL	2	TRUE	0	0.428016489365736	1		452	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579582	7579584	+	frameshift_variant	Frame_Shift_Del	DEL	CAA	CAA	T	novel	NA	P-0042180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	157	738	0	ENST00000269305.4:c.103_105delinsA	p.Leu35ThrfsTer7	p.L35Tfs*7	ENST00000269305	NM_001126112.2	35	TTG/A	4/11	0.428016489365736	1	FACETS	0.977	0.9	1	0.977	0.9	1	CLONAL	1	TRUE	0	0.428016489365736	1		738	590	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0042181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	31	751	1	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.438	0.352	0.536	0.438	0.352	0.536	SUBCLONAL	1	TRUE	1	0.15	2		752	944	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	22	425	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.6	0.464	0.759	0.6	0.464	0.759	SUBCLONAL	1	TRUE	1	0.15	2		426	489	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	35	498	0	ENST00000263967.3:c.333G>T	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaT	2/21	1	2	FACETS	0.989	0.81	1	0.989	0.81	1	CLONAL	1	TRUE	1	0.15	2		498	472	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711875	89711875	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587782603	NA	P-0042181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	30	486	0	ENST00000371953.3:c.493G>A	p.Gly165Arg	p.G165R	ENST00000371953	NM_000314.4	165	Gga/Aga	6/9	1	2	FACETS	1	0.816	1	1	0.816	1	CLONAL	1	TRUE	1	0.15	2		486	395	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198482	108198482	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	20	482	0	ENST00000278616.4:c.7086A>C	p.Glu2362Asp	p.E2362D	ENST00000278616	NM_000051.3	2362	gaA/gaC	48/63	1	2	FACETS	0.675	0.515	0.863	0.675	0.515	0.863	SUBCLONAL	1	TRUE	1	0.15	2		482	395	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098800	178098800	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	42	827	0	ENST00000397062.3:c.245A>C	p.Glu82Ala	p.E82A	ENST00000397062	NM_006164.4	82	gAa/gCa	2/5	1	2	FACETS	0.607	0.505	0.722	0.607	0.505	0.722	SUBCLONAL	1	TRUE	1	0.15	2		827	922	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0042209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	64	944	0	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	1	2	FACETS	0.348	0.3	0.4	0.348	0.3	0.4	SUBCLONAL	1	TRUE	1	0.328385437359587	2		944	1121	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0042209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	25	858	1	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	1	2	FACETS	0.14	0.109	0.175	0.14	0.109	0.175	SUBCLONAL	1	TRUE	1	0.328385437359587	2		859	1089	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849414	68849416	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTA	CTA	-	novel	NA	P-0042209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	66	530	0	ENST00000261769.5:c.1321-4_1321-2del		p.X441_splice	ENST00000261769	NM_004360.3	441			1	2	FACETS	0.614	0.532	0.702	0.614	0.532	0.702	SUBCLONAL	1	TRUE	1	0.328385437359587	2		530	655	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938585	44938585	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	18	194	0	ENST00000377967.4:c.3133G>T	p.Glu1045Ter	p.E1045*	ENST00000377967	NM_021140.2	1045	Gaa/Taa	20/29	1	1	FACETS	0.49	0.37	0.63	0.49	0.37	0.63	SUBCLONAL	1	TRUE	0	0.328385437359587	1		194	187	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0042211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	173	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.84304173837807	1	FACETS	0.973	0.925	1	0.973	0.925	1	CLONAL	1	TRUE	0	0.84893401735778	1		326	241	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0042211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	235	393	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.84893401735778	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.84893401735778	1		393	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0042211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	296	545	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	1	2	FACETS	0.901	0.852	0.95	0.901	0.852	0.95	CLONAL	1	TRUE	1	0.84893401735778	2		545	774	SUCCESS
APC	324	MSKCC	GRCh37	5	112175417	112175418	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	rs1554085533	NA	P-0042211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	103	260	0	ENST00000257430.4:c.4127_4128del	p.Tyr1376CysfsTer9	p.Y1376Cfs*9	ENST00000257430	NM_000038.5	1376	TAt/t	16/16	0.106149997801983	4	FACETS	0.939	0.857	1	0.939	0.857	1	INDETERMINATE	2	TRUE	2	0.84893401735778	4		260	239	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0042211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	333	781	1	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.922	0.875	0.969	0.922	0.875	0.969	CLONAL	1	TRUE	1	0.84893401735778	2		782	851	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579584	7579585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0042211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	270	606	0	ENST00000269305.4:c.102dup	p.Pro36AlafsTer7	p.P36Afs*7	ENST00000269305	NM_001126112.2	34	-/C	4/11	1	2	FACETS	0.882	0.832	0.933	0.882	0.832	0.933	CLONAL	1	TRUE	1	0.84893401735778	2		606	721	SUCCESS
APC	324	MSKCC	GRCh37	5	112174745	112174745	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064795228	NA	P-0042211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	104	246	0	ENST00000257430.4:c.3454C>T	p.Gln1152Ter	p.Q1152*	ENST00000257430	NM_000038.5	1152	Cag/Tag	16/16	0.106149997801983	4	FACETS	1	0.949	1	1	0.949	1	INDETERMINATE	2	TRUE	2	0.84893401735778	4		246	216	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910737	29910738	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0042211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	136	655	0	ENST00000376809.5:c.280dup	p.Gln94ProfsTer5	p.Q94Pfs*5	ENST00000376809	NM_002116.7	93	gcc/gCcc	2/8	0.84893401735778	1	FACETS	0.715	0.665	0.765	0.715	0.665	0.765	SUBCLONAL	1	TRUE	0	0.84893401735778	1		655	258	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0042232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	56	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.872	0.749	1	0.872	0.749	1	CLONAL	1	TRUE	1	0.29	2		326	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0042232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	225	717	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.269070782842993	2	FACETS	0.999	0.933	1	0.999	0.933	1	CLONAL	2	TRUE	0	0.29	2		717	777	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954221	48954249	+	splice_donor_variant,intron_variant	Splice_Site	DEL	GTAAATTTTTTACTTTTAGTAAAAAATTT	GTAAATTTTTTACTTTTAGTAAAAAATTT	-	novel	NA	P-0042242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	112	246	0	ENST00000267163.4:c.1421+1_1421+29del		p.X474_splice	ENST00000267163	NM_000321.2	474			0.547075515133026	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.547075515133026	1		246	224	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023031	48023031	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0042242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	33	248	0	ENST00000234420.5:c.458-2A>T		p.X153_splice	ENST00000234420	NM_000179.2	153			0.206320511741981	2	FACETS	0.296	0.241	0.358	0.148	0.12	0.179	INDETERMINATE	1	TRUE	0	0.547075515133026	2		248	408	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024573	31024573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	97	627	1	ENST00000375687.4:c.4058G>A	p.Arg1353Lys	p.R1353K	ENST00000375687	NM_015338.5	1353	aGg/aAg	13/13	0.539211155865704	1	FACETS	0.27	0.24	0.302	0.27	0.24	0.302	SUBCLONAL	1	TRUE	0	0.547075515133026	1		628	953	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971268	13971268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781034658	NA	P-0042242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	121	498	0	ENST00000405192.2:c.661C>T	p.Pro221Ser	p.P221S	ENST00000405192	NM_001163147.1	221	Ccc/Tcc	8/12	0.248363698037473	3	FACETS	0.51	0.46	0.564	0.255	0.23	0.282	INDETERMINATE	1	TRUE	1	0.547075515133026	3		498	1104	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720805	89720808	+	frameshift_variant	Frame_Shift_Del	DEL	CTTT	CTTT	-	rs398123330	NA	P-0042249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	50	153	0	ENST00000371953.3:c.956_959del	p.Thr319LysfsTer24	p.T319Kfs*24	ENST00000371953	NM_000314.4	319	aCTTTa/aa	8/9	0.398846316436575	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	0	0.398846316436575	1		153	186	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782197	NA	P-0042249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	163	551	0	ENST00000269305.4:c.434T>C	p.Leu145Pro	p.L145P	ENST00000269305	NM_001126112.2	145	cTg/cCg	5/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.398846316436575	2		551	714	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592118	67592122	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTT	CTTTT	-	novel	NA	P-0042249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	33	152	0	ENST00000274335.5:c.1937_1941del	p.Phe646CysfsTer6	p.F646Cfs*6	ENST00000274335		645	aCTTTT/a	14/15	0.396963576342292	1	FACETS	0.55	0.45	0.66	0.55	0.45	0.66	SUBCLONAL	1	TRUE	0	0.398846316436575	1		152	241	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970955	21970955	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	166	353	1	ENST00000304494.5:c.403G>A	p.Gly135Arg	p.G135R	ENST00000304494	NM_000077.4	135	Ggg/Agg	2/3	0.344393899704345	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.398846316436575	1		354	625	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	26	425	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.764	0.607	0.941	0.764	0.607	0.941	CLONAL	1	TRUE	1	0.283731158803331	2		426	240	SUCCESS
ATM	472	MSKCC	GRCh37	11	108099919	108099919	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs754033733	NA	P-0042259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	10	124	0	ENST00000278616.4:c.200A>G	p.Tyr67Cys	p.Y67C	ENST00000278616	NM_000051.3	67	tAt/tGt	4/63	1	2	FACETS	0.438	0.297	0.614	0.438	0.297	0.614	SUBCLONAL	1	TRUE	1	0.283731158803331	2		124	161	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235894	133235894	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	22	459	0	ENST00000320574.5:c.3262C>T	p.Pro1088Ser	p.P1088S	ENST00000320574	NM_006231.2	1088	Cct/Tct	26/49	1	2	FACETS	0.383	0.296	0.484	0.383	0.296	0.484	SUBCLONAL	1	TRUE	1	0.283731158803331	2		459	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577147	7577155	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	AGATTACCA	AGATTACCA	-	novel	NA	P-0042259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	46	458	0	ENST00000269305.4:c.783_791del	p.Ser261_Leu264delinsArg	p.S261_L264delinsR	ENST00000269305	NM_001126112.2	261	agTGGTAATCTa/aga	8/11	1	2	FACETS	0.655	0.552	0.769	0.655	0.552	0.769	SUBCLONAL	1	TRUE	1	0.283731158803331	2		458	495	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46603779	46603779	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	38	532	0	ENST00000263734.3:c.1136A>C	p.Lys379Thr	p.K379T	ENST00000263734	NM_001430.4	379	aAg/aCg	9/16	1	2	FACETS	0.467	0.386	0.559	0.467	0.386	0.559	SUBCLONAL	1	TRUE	1	0.283731158803331	2		532	573	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	62	300	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.857	0.739	0.984	0.857	0.739	0.984	CLONAL	1	TRUE	1	0.22	2		300	658	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023151	27023179	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	-	novel	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	32	31	0	ENST00000324856.7:c.267_295del	p.Ser90ProfsTer11	p.S90Pfs*11	ENST00000324856	NM_006015.4	86	gGCGGAGCCGGCAGCGGCGGCGGGCCCGGC/g	1/20	1	2	FACETS	1	0.884	1	1	0.965	1	CLONAL	2	TRUE	1	0.22	2		31	133	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	149	711	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.22	2		711	1081	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	41	564	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	1	2	FACETS	0.458	0.38	0.545	0.458	0.38	0.545	SUBCLONAL	1	TRUE	1	0.22	2		564	814	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	96	699	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.851	0.757	0.953	0.851	0.757	0.953	CLONAL	1	TRUE	1	0.22	2		699	1025	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871059	12871060	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAGGTGCCTGC	novel	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	35	329	0	ENST00000228872.4:c.295_305dup	p.Gln104ArgfsTer19	p.Q104Rfs*19	ENST00000228872	NM_004064.3	96	aaa/aAAGGTGCCTGCaa	1/3	0.19880885551618	3	FACETS	0.686	0.561	0.826	0.343	0.28	0.413	SUBCLONAL	1	TRUE	1	0.22	3		329	515	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203543	108203543	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	26	256	0	ENST00000278616.4:c.7843C>T	p.Gln2615Ter	p.Q2615*	ENST00000278616	NM_000051.3	2615	Cag/Tag	53/63	1	2	FACETS	0.657	0.52	0.813	0.657	0.52	0.813	SUBCLONAL	1	TRUE	1	0.22	2		256	360	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643348	38643348	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs946203764	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	28	419	0	ENST00000299084.4:c.818G>C	p.Arg273Thr	p.R273T	ENST00000299084	NM_152594.2	273	aGa/aCa	7/7	0.3	1	FACETS	0.518	0.414	0.638	0.518	0.414	0.638	SUBCLONAL	1	TRUE	0	0.22	1		419	437	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164489	47164489	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	24	274	0	ENST00000409792.3:c.1637C>T	p.Ser546Phe	p.S546F	ENST00000409792	NM_014159.6	546	tCt/tTt	3/21	0.192214443811591	2	FACETS	0.678	0.531	0.846	0.339	0.265	0.423	SUBCLONAL	1	TRUE	0	0.22	2		274	322	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38064133	38064133	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	45	461	0	ENST00000250448.2:c.45G>A	p.Trp15Ter	p.W15*	ENST00000250448	NM_004496.3	15	tgG/tgA	1/2	1	2	FACETS	0.569	0.477	0.671	0.569	0.477	0.671	SUBCLONAL	1	TRUE	1	0.22	2		461	719	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662301	227662301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1289819083	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	138	729	0	ENST00000305123.5:c.1154C>T	p.Ser385Leu	p.S385L	ENST00000305123	NM_005544.2	385	tCg/tTg	1/2	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.22	2		729	997	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710987	114710987	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	40	440	1	ENST00000543371.1:c.211C>T	p.Arg71Cys	p.R71C	ENST00000543371	NM_001198531.1	71	Cgc/Tgc	2/14	0.3	1	FACETS	0.487	0.403	0.58	0.487	0.403	0.58	SUBCLONAL	1	TRUE	0	0.22	1		441	665	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420049	49420049	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1159189200	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	120	618	1	ENST00000301067.7:c.15700G>T	p.Glu5234Ter	p.E5234*	ENST00000301067	NM_003482.3	5234	Gag/Tag	48/54	0.19880885551618	3	FACETS	1	0.982	1	0.697	0.629	0.769	CLONAL	1	TRUE	1	0.22	3		619	869	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101288	27101288	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	70	695	0	ENST00000324856.7:c.4570C>T	p.His1524Tyr	p.H1524Y	ENST00000324856	NM_006015.4	1524	Cat/Tat	18/20	1	2	FACETS	0.763	0.664	0.87	0.763	0.664	0.87	SUBCLONAL	1	TRUE	1	0.22	2		695	834	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344722	118344722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1411269068	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	48	333	0	ENST00000534358.1:c.2848C>T	p.Leu950Phe	p.L950F	ENST00000534358	NM_005933.3	950	Ctt/Ttt	3/36	1	2	FACETS	0.996	0.844	1	0.996	0.844	1	CLONAL	1	TRUE	1	0.22	2		333	438	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363883	118363883	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	103	447	0	ENST00000534358.1:c.5116C>T	p.Gln1706Ter	p.Q1706*	ENST00000534358	NM_005933.3	1706	Cag/Tag	16/36	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.22	2		447	675	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248893	133248893	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	51	610	0	ENST00000320574.5:c.1702G>C	p.Asp568His	p.D568H	ENST00000320574	NM_006231.2	568	Gac/Cac	16/49	0.19880885551618	3	FACETS	0.529	0.448	0.619	0.265	0.224	0.31	SUBCLONAL	1	TRUE	1	0.22	3		610	972	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954333	48954333	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	17	264	0	ENST00000267163.4:c.1454C>T	p.Ser485Phe	p.S485F	ENST00000267163	NM_000321.2	485	tCt/tTt	16/27	1	2	FACETS	0.526	0.392	0.685	0.526	0.392	0.685	SUBCLONAL	1	TRUE	1	0.22	2		264	294	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81563040	81563040	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	37	346	0	ENST00000298171.2:c.603G>C	p.Lys201Asn	p.K201N	ENST00000298171	NM_000369.2	201	aaG/aaC	7/10	1	2	FACETS	0.743	0.612	0.889	0.743	0.612	0.889	SUBCLONAL	1	TRUE	1	0.22	2		346	453	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004694	16004694	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	43	563	0	ENST00000268712.3:c.2560G>C	p.Glu854Gln	p.E854Q	ENST00000268712	NM_006311.3	854	Gaa/Caa	20/46	1	2	FACETS	0.521	0.435	0.618	0.521	0.435	0.618	SUBCLONAL	1	TRUE	1	0.22	2		563	750	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50143304	50143304	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	36	130	0	ENST00000246792.3:c.52G>T	p.Gly18Ter	p.G18*	ENST00000246792	NM_006270.3	18	Gga/Tga	1/6	1	2	FACETS	0.861	0.716	1	1	0.96	1	CLONAL	2	TRUE	1	0.22	2		130	190	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505389	25505389	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	67	606	0	ENST00000264709.3:c.369G>C	p.Glu123Asp	p.E123D	ENST00000264709	NM_175629.2	123	gaG/gaC	4/23	0.19880885551618	3	FACETS	0.709	0.614	0.812	0.354	0.307	0.406	SUBCLONAL	1	TRUE	1	0.22	3		606	954	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273192	198273192	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	86	594	0	ENST00000335508.6:c.1018G>A	p.Glu340Lys	p.E340K	ENST00000335508	NM_012433.2	340	Gaa/Aaa	8/25	1	2	FACETS	0.918	0.811	1	0.918	0.811	1	CLONAL	1	TRUE	1	0.22	2		594	852	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662307	227662307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1446895458	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	136	726	0	ENST00000305123.5:c.1148C>T	p.Ser383Leu	p.S383L	ENST00000305123	NM_005544.2	383	tCg/tTg	1/2	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.22	2		726	1018	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735428	40735428	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	49	548	0	ENST00000373198.4:c.3445G>C	p.Glu1149Gln	p.E1149Q	ENST00000373198	NM_133170.3	1149	Gag/Cag	25/32	1	2	FACETS	0.608	0.513	0.712	0.608	0.513	0.712	SUBCLONAL	1	TRUE	1	0.22	2		548	733	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161851	47161851	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	50	382	0	ENST00000409792.3:c.4275G>C	p.Lys1425Asn	p.K1425N	ENST00000409792	NM_014159.6	1425	aaG/aaC	3/21	0.192214443811591	2	FACETS	0.902	0.766	1	0.451	0.383	0.526	CLONAL	1	TRUE	0	0.22	2		382	504	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027062	71027062	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1158652441	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	129	459	0	ENST00000318789.4:c.1265C>T	p.Ser422Phe	p.S422F	ENST00000318789	NM_032682.5	422	tCt/tTt	15/21	0.192214443811591	2	FACETS	0.887	0.806	0.972	0.887	0.806	0.972	CLONAL	2	TRUE	0	0.22	2		459	661	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259461	89259461	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	87	446	0	ENST00000336596.2:c.605G>T	p.Cys202Phe	p.C202F	ENST00000336596	NM_005233.5	202	tGc/tTc	3/17	0.192214443811591	2	FACETS	1	0.974	1	0.684	0.607	0.767	CLONAL	1	TRUE	0	0.22	2		446	578	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390923	89390923	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	45	297	0	ENST00000336596.2:c.989G>C	p.Arg330Thr	p.R330T	ENST00000336596	NM_005233.5	330	aGa/aCa	5/17	0.192214443811591	2	FACETS	0.917	0.772	1	0.459	0.386	0.539	CLONAL	1	TRUE	0	0.22	2		297	446	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946251	55946251	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	85	358	1	ENST00000263923.4:c.3928C>T	p.His1310Tyr	p.H1310Y	ENST00000263923	NM_002253.2	1310	Cac/Tac	30/30	0.19880885551618	3	FACETS	0.755	0.669	0.847	0.755	0.669	0.847	SUBCLONAL	2	TRUE	1	0.22	3		359	568	SUCCESS
APC	324	MSKCC	GRCh37	5	112111390	112111390	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	25	257	0	ENST00000257430.4:c.487C>G	p.Gln163Glu	p.Q163E	ENST00000257430	NM_000038.5	163	Cag/Gag	5/16	0.3	1	FACETS	0.655	0.516	0.813	0.655	0.516	0.813	SUBCLONAL	1	TRUE	0	0.22	1		257	309	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176662824	176662824	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	20	326	0	ENST00000439151.2:c.3799G>T	p.Val1267Leu	p.V1267L	ENST00000439151	NM_022455.4	1267	Gtg/Ttg	6/23	0.3	1	FACETS	0.433	0.33	0.553	0.433	0.33	0.553	SUBCLONAL	1	TRUE	0	0.22	1		326	374	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778088	27778088	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	41	511	0	ENST00000369163.2:c.237C>G	p.Phe79Leu	p.F79L	ENST00000369163	NM_003536.2	79	ttC/ttG	1/1	1	2	FACETS	0.603	0.501	0.717	0.603	0.501	0.717	SUBCLONAL	1	TRUE	1	0.22	2		511	618	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670961	30670961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	63	757	0	ENST00000376406.3:c.5785G>A	p.Asp1929Asn	p.D1929N	ENST00000376406	NM_014641.2	1929	Gat/Aat	12/15	1	2	FACETS	0.527	0.454	0.607	0.527	0.454	0.607	SUBCLONAL	1	TRUE	1	0.22	2		757	1087	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64288432	64288432	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	47	234	0	ENST00000370651.3:c.196C>T	p.Leu66Phe	p.L66F	ENST00000370651	NM_003463.4	66	Ctt/Ttt	3/6	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.22	2		234	316	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845886	151845886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	49	593	0	ENST00000262189.6:c.13126G>A	p.Glu4376Lys	p.E4376K	ENST00000262189	NM_170606.2	4376	Gag/Aag	52/59	1	2	FACETS	0.637	0.539	0.746	0.637	0.539	0.746	SUBCLONAL	1	TRUE	1	0.22	2		593	699	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929004	44929004	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	84	264	0	ENST00000377967.4:c.2104C>G	p.His702Asp	p.H702D	ENST00000377967	NM_021140.2	702	Cac/Gac	17/29	0.113204981560523	2	FACETS	0.972	0.864	1			1	INDETERMINATE	2	TRUE	NA	0.22	2		264	393	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358453	67358506	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	GCCGGGGGCGCTCCTCGCCGCCCGCGCGCCCTCCCCAGCCATGTCGTCCATCCT	GCCGGGGGCGCTCCTCGCCGCCCGCGCGCCCTCCCCAGCCATGTCGTCCATCCT	-	novel	NA	P-0042271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	24	106	0	ENST00000327367.4:c.-37_17del		p.*13*	ENST00000327367	NM_005902.3	?-5/425		1/9	1	2	FACETS	0.277	0.218	0.345	0.277	0.218	0.345	SUBCLONAL	1	TRUE	1	0.840112867829322	2		106	206	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273026	18273026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1317050980	NA	P-0042271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	656	903	1	ENST00000222254.8:c.916C>T	p.Pro306Ser	p.P306S	ENST00000222254	NM_005027.3	306	Ccc/Tcc	8/16	1	2	FACETS	0.904	0.871	0.937	0.904	0.871	0.937	CLONAL	1	TRUE	1	0.840112867829322	2		904	1728	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0042280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	43	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.753	0.63	0.89	0.753	0.63	0.89	SUBCLONAL	1	TRUE	1	0.22	2		326	519	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0042280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	85	714	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.22	2		714	755	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17947985	17947985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778414	NA	P-0042280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	88	844	3	ENST00000458235.1:c.1739C>T	p.Ser580Leu	p.S580L	ENST00000458235	NM_000215.3	580	tCg/tTg	13/24	1	2	FACETS	0.69	0.609	0.776	0.69	0.609	0.776	SUBCLONAL	1	TRUE	1	0.22	2		847	1160	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106554	27106554	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	106	715	0	ENST00000324856.7:c.6165del	p.Met2055IlefsTer80	p.M2055Ifs*80	ENST00000324856	NM_006015.4	2055	atG/at	20/20	1	2	FACETS	0.997	0.892	1	0.997	0.892	1	CLONAL	1	TRUE	1	0.22	2		715	967	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	299	300	0				ENST00000310581	NM_198253.2	-/1132			0.707765779949562	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.707765779949562	3		300	532	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0042342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	105	189	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.957	0.869	1	0.957	0.869	1	CLONAL	1	TRUE	1	0.707765779949562	2		189	310	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0042342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	288	287	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	0.707765779949562	5	FACETS	0.927	0.874	0.981	0.618	0.582	0.654	CLONAL	2	TRUE	2	0.707765779949562	5		287	905	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678470	88678470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1307510401	NA	P-0042342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	460	442	0	ENST00000360948.2:c.1066G>A	p.Gly356Arg	p.G356R	ENST00000360948	NM_001012338.2	356	Gga/Aga	9/19	0.707765779949562	3	FACETS	0.985	0.947	1	0.985	0.947	1	CLONAL	2	TRUE	1	0.707765779949562	3		442	893	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1042140	1042140	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0042342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	276	337	0	ENST00000358495.3:c.84+1G>A		p.X28_splice	ENST00000358495	NM_134424.2	28			1	2	FACETS	0.95	0.895	1	0.95	0.895	1	CLONAL	1	TRUE	1	0.707765779949562	2		337	821	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628671	21628671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	155	335	1	ENST00000421138.2:c.1037C>T	p.Ala346Val	p.A346V	ENST00000421138		346	gCc/gTc	10/16	1	2	FACETS	0.901	0.831	0.973	0.901	0.831	0.973	CLONAL	1	TRUE	1	0.707765779949562	2		336	486	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572540	95572540	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	116	199	0	ENST00000393063.1:c.2825C>T	p.Pro942Leu	p.P942L	ENST00000393063	NM_030621.3	942	cCt/cTt	19/28	1	2	FACETS	0.967	0.882	1	0.967	0.882	1	CLONAL	1	TRUE	1	0.707765779949562	2		199	339	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243078	105243078	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775892860	NA	P-0042342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	339	478	1	ENST00000349310.3:c.205C>T	p.Arg69Trp	p.R69W	ENST00000349310	NM_001014432.1	69	Cgg/Tgg	5/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.707765779949562	2		479	879	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729152	66729153	+	missense_variant	Missense_Mutation	DNP	GT	GT	AA	novel	NA	P-0042342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	499	399	0	ENST00000307102.5:c.360_361delinsAA	p.Cys121Ser	p.C121S	ENST00000307102	NM_002755.3	120	gaGTgc/gaAAgc	3/11	0.707765779949562	3	FACETS	0.928	0.892	0.963	0.928	0.892	0.963	CLONAL	2	TRUE	1	0.707765779949562	3		399	1029	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082487	16082488	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	245	416	2	ENST00000281043.3:c.301_302delinsAA	p.Gly101Lys	p.G101K	ENST00000281043	NM_005378.4	101	GGa/AAa	2/3	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.707765779949562	2		418	652	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663580	117663580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1417876029	NA	P-0042342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	399	344	0	ENST00000368508.3:c.4652G>A	p.Gly1551Glu	p.G1551E	ENST00000368508	NM_002944.2	1551	gGa/gAa	28/43	0.707765779949562	2	FACETS	0.938	0.905	0.97	0.938	0.905	0.97	CLONAL	2	TRUE	0	0.707765779949562	2		344	601	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962797	2962797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	254	447	0	ENST00000396946.4:c.2111C>T	p.Ala704Val	p.A704V	ENST00000396946	NM_032415.4	704	gCc/gTc	16/25	NA	2	FACETS	1	0.955	1			1	INDETERMINATE	1	TRUE	NA	0.707765779949562	2		447	705	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577052	7577070	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGCTCCCCTTTCTTGCG	GAGGCTCCCCTTTCTTGCG	-	novel	NA	P-0042348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	516	579	0	ENST00000269305.4:c.868_886del	p.Arg290ThrfsTer49	p.R290Tfs*49	ENST00000269305	NM_001126112.2	290	CGCAAGAAAGGGGAGCCTCac/ac	8/11	0.566213654304115	2	FACETS	0.845	0.813	0.877	0.845	0.813	0.877	CLONAL	2	TRUE	0	0.580004029525846	2		579	1053	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670131	29670181	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTGGTTGGACACCTTTTAAAAGGTAAAAAAGCCTTATTTAGAATATTTTT	ATTGGTTGGACACCTTTTAAAAGGTAAAAAAGCCTTATTTAGAATATTTTT	-	novel	NA	P-0042348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	234	277	0	ENST00000356175.3:c.7106_7126+30del		p.X2369_splice	ENST00000356175	NM_000267.3	2369		47/57	0.566213654304115	2	FACETS	0.812	0.766	0.858	0.812	0.766	0.858	CLONAL	2	TRUE	0	0.580004029525846	2		277	497	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30303539	30303539	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0042348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	26	31	0	ENST00000322652.5:c.824-1G>A		p.X275_splice	ENST00000322652	NM_015355.2	275			0.566213654304115	2	FACETS	1	0.943	1	0.723	0.598	0.852	CLONAL	1	TRUE	0	0.580004029525846	2		31	62	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797309	135797309	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	27	219	1	ENST00000298552.3:c.560T>C	p.Leu187Pro	p.L187P	ENST00000298552	NM_001162426.1	187	cTc/cCc	7/23	0.31726827377855	5	FACETS	0.507	0.404	0.625	0.169	0.134	0.209	INDETERMINATE	1	FALSE	2	0.681473723752426	5		220	316	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127672	2127676	+	missense_variant	Missense_Mutation	ONP	GCAGC	GCAGC	TGTTT	novel	NA	P-0042513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	184	529	2	ENST00000219476.3:c.2911_2915delinsTGTTT	p.Ala971_Ala972delinsCysPhe	p.A971_A972delinsCF	ENST00000219476	NM_000548.3	971	GCAGCc/TGTTTc	26/42	0.434280914022231	4	FACETS	1	0.983	1	0.302	0.279	0.326	CLONAL	1	FALSE	0	0.681473723752426	4		531	752	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938358	76938358	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	318	0	0	ENST00000373344.5:c.2390C>A	p.Ser797Ter	p.S797*	ENST00000373344	NM_000489.3	797	tCa/tAa	9/35	0.615234134599552	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	FALSE	2	0.681473723752426	4		0	757	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938358	76938358	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	34	0	0	ENST00000373344.5:c.2390C>A	p.Ser797Ter	p.S797*	ENST00000373344	NM_000489.3	797	tCa/tAa	9/35	1	2	FACETS	0.31	0.252	0.376	0.31	0.252	0.376	SUBCLONAL	1	FALSE	1	0.3	2		0	731	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0042513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	24	347	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	1	2	FACETS	0.395	0.309	0.494	0.395	0.309	0.494	SUBCLONAL	1	FALSE	1	0.3	2		347	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0042528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	160	711	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.305760260196478	2		711	751	SUCCESS
APC	324	MSKCC	GRCh37	5	112175360	112175360	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	56	255	0	ENST00000257430.4:c.4069G>T	p.Gly1357Ter	p.G1357*	ENST00000257430	NM_000038.5	1357	Gga/Tga	16/16	0.29477365112599	2	FACETS	1	0.968	1	0.73	0.631	0.835	CLONAL	1	FALSE	0	0.305760260196478	2		255	251	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022592	31022592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs373221034	NA	P-0042528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	108	588	2	ENST00000375687.4:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000375687	NM_015338.5	693	Cga/Tga	13/13	0.305760260196478	5	FACETS	1	0.966	1	0.393	0.352	0.437	CLONAL	1	FALSE	2	0.305760260196478	5		590	873	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144011	11144011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755541709	NA	P-0042528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	110	650	1	ENST00000358026.2:c.3592G>A	p.Glu1198Lys	p.E1198K	ENST00000358026	NM_001128849.1	1198	Gag/Aag	26/36	0.162565988540431	4	FACETS	0.884	0.792	0.981	0.442	0.396	0.491	INDETERMINATE	1	FALSE	2	0.305760260196478	4		651	1063	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0042598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	192	622	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.462402274180269	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.470638469939526	1		623	591	SUCCESS
APC	324	MSKCC	GRCh37	5	112174094	112174095	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs863225332	NA	P-0042598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	62	297	0	ENST00000257430.4:c.2804dup	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	tac/tAac	16/16	1	2	FACETS	0.794	0.69	0.905	0.794	0.69	0.905	CLONAL	1	TRUE	1	0.470638469939526	2		297	332	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539870	187539870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	65	355	0	ENST00000441802.2:c.7870G>A	p.Asp2624Asn	p.D2624N	ENST00000441802	NM_005245.3	2624	Gat/Aat	10/27	1	2	FACETS	0.759	0.661	0.863	0.759	0.661	0.863	SUBCLONAL	1	TRUE	1	0.470638469939526	2		355	364	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372527	55372527	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	230	782	0	ENST00000297316.4:c.1217T>C	p.Val406Ala	p.V406A	ENST00000297316	NM_022454.3	406	gTa/gCa	2/2	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.470638469939526	2		782	953	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0042609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	43	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.486596427507354	1	FACETS	0.452	0.38	0.531	0.452	0.38	0.531	SUBCLONAL	1	TRUE	0	0.486596427507354	1		326	296	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0042609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	247	698	2	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.486596427507354	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.486596427507354	1		700	726	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591892	48591892	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	140	467	0	ENST00000342988.3:c.1055G>T	p.Gly352Val	p.G352V	ENST00000342988	NM_005359.5	352	gGa/gTa	9/12	0.486596427507354	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.486596427507354	1		467	388	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591096	67591392	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAACAGCATTAAACCAGACCTTATCCAGCTGAGAAAGACGAGAGACCAATACTTGATGTAAGTATTTGAAATGGAATCCTATACATGAATAATTGGTGATTGCTACAATTCAGGATGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAAAAGGTGTTCGGCAAAAGAAGTTGAACGAGTGGTTGGGCAATGAAAACACTGAAGAGTAAGTAGTTACTAAAGATGGTGATAGCAGAAGATTTTTCTCATTTTAGGAAAATGCATGACTTGCTTTGTTTTTA	GAACAGCATTAAACCAGACCTTATCCAGCTGAGAAAGACGAGAGACCAATACTTGATGTAAGTATTTGAAATGGAATCCTATACATGAATAATTGGTGATTGCTACAATTCAGGATGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAAAAGGTGTTCGGCAAAAGAAGTTGAACGAGTGGTTGGGCAATGAAAACACTGAAGAGTAAGTAGTTACTAAAGATGGTGATAGCAGAAGATTTTTCTCATTTTAGGAAAATGCATGACTTGCTTTGTTTTTA	-	novel	NA	P-0042609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	14	297	0	ENST00000274335.5:c.1694_1814+81del		p.X565_splice	ENST00000274335		565		12-13/15	1	2	FACETS	0.281	0.203	0.374	0.281	0.203	0.374	SUBCLONAL	1	TRUE	1	0.486596427507354	2		297	205	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0042610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	137	829	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.383071712014148	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.383071712014148	1		829	561	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868145	56868145	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	96	661	1	ENST00000308159.5:c.1643del	p.Leu548ProfsTer23	p.L548Pfs*23	ENST00000308159	NM_014669.4	548	cTc/cc	14/22	0.344244280475467	4	FACETS	0.777	0.691	0.869	0.389	0.345	0.435	SUBCLONAL	1	TRUE	2	0.383071712014148	4		662	892	SUCCESS
APC	324	MSKCC	GRCh37	5	112175224	112175225	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0042610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	108	252	0	ENST00000257430.4:c.3935dup	p.Thr1313AsnfsTer2	p.T1313Nfs*2	ENST00000257430	NM_000038.5	1311	-/G	16/16	0.383071712014148	3	FACETS	0.978	0.897	1	0.978	0.897	1	CLONAL	3	TRUE	0	0.383071712014148	3		252	229	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0042648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	88	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.33098622970542	1	FACETS	0.566	0.506	0.628	0.566	0.506	0.628	INDETERMINATE	1	TRUE	0	0.64475525998064	1		326	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0042648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	318	677	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.64475525998064	1	FACETS	0.99	0.942	1	0.99	0.942	1	CLONAL	1	TRUE	0	0.64475525998064	1		680	675	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0042648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	47	160	1	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	0.814	0.698	0.939	0.814	0.698	0.939	CLONAL	1	TRUE	1	0.64475525998064	2		161	179	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	121	570	0	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	0.64475525998064	1	FACETS	0.978	0.902	1	0.978	0.902	1	CLONAL	1	TRUE	0	0.64475525998064	1		570	260	SUCCESS
APC	324	MSKCC	GRCh37	5	112175761	112175761	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	93	370	0	ENST00000257430.4:c.4473del	p.Phe1491LeufsTer16	p.F1491Lfs*16	ENST00000257430	NM_000038.5	1490	caT/ca	16/16	1	2	FACETS	0.925	0.831	1	0.925	0.831	1	CLONAL	1	TRUE	1	0.64475525998064	2		370	312	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164782	36164782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752616540	NA	P-0042648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	372	915	3	ENST00000300305.3:c.1093G>A	p.Gly365Ser	p.G365S	ENST00000300305		365	Ggc/Agc	8/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.64475525998064	2		918	1060	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604577	43604577	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776223166	NA	P-0042648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	162	914	1	ENST00000355710.3:c.1162G>A	p.Val388Ile	p.V388I	ENST00000355710	NM_020975.4	388	Gtc/Atc	6/20	0.33098622970542	1	FACETS	0.419	0.385	0.455	0.419	0.385	0.455	INDETERMINATE	1	TRUE	0	0.64475525998064	1		915	812	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805684	46805684	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	138	979	1	ENST00000290295.7:c.272G>A	p.Arg91Gln	p.R91Q	ENST00000290295	NM_006361.5	91	cGa/cAa	1/2	0.33852625759011	1	FACETS	0.381	0.346	0.416	0.381	0.346	0.416	INDETERMINATE	1	TRUE	0	0.64475525998064	1		980	762	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0042696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	42	184	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	1	0.3	2		184	278	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983071	201983072	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0042696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	87	786	0	ENST00000359651.3:c.921dup	p.Ser308LeufsTer163	p.S308Lfs*163	ENST00000359651		307	cgc/cgCc	7/8	1	2	FACETS	0.738	0.653	0.829	0.738	0.653	0.829	SUBCLONAL	1	TRUE	1	0.3	2		786	786	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918296	44918296	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs756644556	NA	P-0042696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	49	265	0	ENST00000377967.4:c.921C>A	p.Tyr307Ter	p.Y307*	ENST00000377967	NM_021140.2	307	taC/taA	11/29	1	1	FACETS	0.776	0.659	0.903	0.776	0.659	0.903	CLONAL	1	TRUE	0	0.3	1		265	358	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0042710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	85	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.289505334618643	2	FACETS	1	0.917	1	0.516	0.461	0.575	INDETERMINATE	1	TRUE	0	0.501753381482057	2		326	328	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101486	27101486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370907880	NA	P-0042710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	85	902	0	ENST00000324856.7:c.4768C>T	p.Pro1590Ser	p.P1590S	ENST00000324856	NM_006015.4	1590	Ccc/Tcc	18/20	0.232265192910702	2	FACETS	0.594	0.526	0.667	0.297	0.263	0.334	INDETERMINATE	1	TRUE	0	0.501753381482057	2		902	570	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256105	133256105	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375213599	NA	P-0042710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	80	626	1	ENST00000320574.5:c.556G>A	p.Ala186Thr	p.A186T	ENST00000320574	NM_006231.2	186	Gcg/Acg	6/49	0.501753381482057	1	FACETS	0.709	0.629	0.793	0.709	0.629	0.793	SUBCLONAL	1	TRUE	0	0.501753381482057	1		627	337	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549082	21549082	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	50	496	0	ENST00000382592.4:c.3194A>G	p.Gln1065Arg	p.Q1065R	ENST00000382592	NM_014572.2	1065	cAg/cGg	8/8	0.232265192910702	2	FACETS	0.546	0.465	0.635	0.273	0.232	0.318	INDETERMINATE	1	TRUE	0	0.501753381482057	2		496	365	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061021	38061021	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	17	117	0	ENST00000250448.2:c.968C>G	p.Ala323Gly	p.A323G	ENST00000250448	NM_004496.3	323	gCg/gGg	2/2	0.501753381482057	2	FACETS	0.443	0.333	0.572	0.221	0.166	0.286	SUBCLONAL	1	TRUE	0	0.501753381482057	2		117	153	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500663	99500663	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs773129173	NA	P-0042710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	47	475	0	ENST00000268035.6:c.4096A>C	p.Thr1366Pro	p.T1366P	ENST00000268035	NM_000875.3	1366	Acc/Ccc	21/21	0.238859553192664	2	FACETS	0.564	0.478	0.658	0.282	0.239	0.329	INDETERMINATE	1	TRUE	0	0.501753381482057	2		475	332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577135	7577143	+	inframe_deletion	In_Frame_Del	DEL	TTCCGTCCC	TTCCGTCCC	-	novel	NA	P-0042710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	129	782	2	ENST00000269305.4:c.795_803del	p.Gly266_Asn268del	p.G266_N268del	ENST00000269305	NM_001126112.2	265	ctGGGACGGAAc/ctc	8/11	0.501753381482057	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.501753381482057	1		784	384	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276608	15276608	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	115	838	0	ENST00000263388.2:c.5657G>T	p.Gly1886Val	p.G1886V	ENST00000263388	NM_000435.2	1886	gGt/gTt	30/33	0.238859553192664	2	FACETS	0.819	0.74	0.901	0.409	0.37	0.451	INDETERMINATE	1	TRUE	0	0.501753381482057	2		838	560	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211355	36211357	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs201152143	NA	P-0042710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	97	900	7	ENST00000222270.7:c.1117_1119del	p.Glu373del	p.E373del	ENST00000222270	NM_014727.1	369	aAAGaa/aaa	3/37	0.238859553192664	2	FACETS	0.581	0.519	0.648	0.291	0.259	0.324	INDETERMINATE	1	TRUE	0	0.501753381482057	2		907	665	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867048	45867048	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1477313928	NA	P-0042710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	34	519	0	ENST00000391945.4:c.1071C>G	p.Phe357Leu	p.F357L	ENST00000391945	NM_000400.3	357	ttC/ttG	11/23	0.238859553192664	2	FACETS	0.378	0.309	0.455	0.189	0.154	0.228	INDETERMINATE	1	TRUE	0	0.501753381482057	2		519	359	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279807	46279809	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	rs553605982	NA	P-0042710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	19	467	0	ENST00000371998.3:c.3739_3741del	p.Met1247del	p.M1247del	ENST00000371998		1245	ATG/-	20/23	0.232265192910702	2	FACETS	0.236	0.179	0.303	0.118	0.089	0.152	INDETERMINATE	1	TRUE	0	0.501753381482057	2		467	321	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430243	181430243	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	54	293	0	ENST00000325404.1:c.95G>C	p.Gly32Ala	p.G32A	ENST00000325404	NM_003106.3	32	gGc/gCc	1/1	0.501753381482057	3	FACETS	0.938	0.807	1	0.469	0.403	0.54	CLONAL	1	TRUE	1	0.501753381482057	3		293	287	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439403	149439403	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	140	717	0	ENST00000286301.3:c.1992G>C	p.Glu664Asp	p.E664D	ENST00000286301	NM_005211.3	664	gaG/gaC	15/22	0.289505334618643	2	FACETS	1	0.964	1	0.547	0.501	0.595	INDETERMINATE	1	TRUE	0	0.501753381482057	2		717	510	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380017	116380017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752842662	NA	P-0042710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	107	569	0	ENST00000397752.3:c.1406G>A	p.Arg469Gln	p.R469Q	ENST00000397752	NM_000245.2	469	cGa/cAa	4/21	0.289505334618643	2	FACETS	1	0.914	1	0.507	0.457	0.558	INDETERMINATE	1	TRUE	0	0.501753381482057	2		569	421	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26970433	26970433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	39	245	0	ENST00000381527.3:c.802G>A	p.Glu268Lys	p.E268K	ENST00000381527	NM_001260.1	268	Gaa/Aaa	8/13	0.554914631133828	1	FACETS	0.339	0.286	0.396	0.339	0.286	0.396	SUBCLONAL	1	TRUE	0	0.895026781345886	1		245	142	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919596	28919596	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	113	450	0	ENST00000282397.4:c.2341C>G	p.Arg781Gly	p.R781G	ENST00000282397	NM_002019.4	781	Cga/Gga	16/30	0.554914631133828	1	FACETS	0.321	0.29	0.352	0.321	0.29	0.352	SUBCLONAL	1	TRUE	0	0.895026781345886	1		450	435	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871621	35871621	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	195	301	0	ENST00000216797.5:c.885del	p.Phe295LeufsTer21	p.F295Lfs*21	ENST00000216797	NM_020529.2	295	ttC/tt	5/6	0.409564141429868	2	FACETS	1	0.993	1	0.694	0.657	0.73	INDETERMINATE	1	TRUE	0	0.895026781345886	2		301	314	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95573983	95573983	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	78	290	0	ENST00000393063.1:c.2766T>G	p.Phe922Leu	p.F922L	ENST00000393063	NM_030621.3	922	ttT/ttG	18/28	0.554914631133828	1	FACETS	0.422	0.377	0.469	0.422	0.377	0.469	SUBCLONAL	1	TRUE	0	0.895026781345886	1		290	228	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44919358	44919358	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	45	180	0	ENST00000377967.4:c.1286C>T	p.Ala429Val	p.A429V	ENST00000377967	NM_021140.2	429	gCa/gTa	13/29	0.842619259240709	2	FACETS	0.354	0.299	0.414			1	SUBCLONAL	1	TRUE	NA	0.895026781345886	2		180	284	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115845	8115846	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0042760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	255	725	0	ENST00000346208.3:c.1191_1192del	p.Arg398ThrfsTer108	p.R398Tfs*108	ENST00000346208		397	tcCAga/tcga	6/6	1	2	FACETS	0.881	0.826	0.938	0.881	0.826	0.938	CLONAL	1	TRUE	1	0.622377160129771	2		725	930	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528625	157528625	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747762304	NA	P-0042760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	236	773	0	ENST00000346085.5:c.6350G>C	p.Arg2117Thr	p.R2117T	ENST00000346085	NM_020732.3	2117	aGg/aCg	20/20	1	2	FACETS	0.891	0.833	0.95	0.891	0.833	0.95	CLONAL	1	TRUE	1	0.622377160129771	2		773	851	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971292	13971292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772105404	NA	P-0042790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	228	563	0	ENST00000405192.2:c.637C>T	p.Arg213Cys	p.R213C	ENST00000405192	NM_001163147.1	213	Cgc/Tgc	8/12	1	2	FACETS	0.97	0.908	1	0.97	0.908	1	CLONAL	1	TRUE	1	0.66	2		563	712	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930592	131930592	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	107	286	0	ENST00000265335.6:c.1825A>G	p.Asn609Asp	p.N609D	ENST00000265335		609	Aat/Gat	12/25	1	2	FACETS	0.968	0.878	1	0.968	0.878	1	CLONAL	1	TRUE	1	0.66	2		286	335	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	222	439	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	1	2	FACETS	0.996	0.936	1	0.996	0.936	1	CLONAL	1	TRUE	1	0.826697116720919	2		439	539	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0042797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	254	498	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	NA	2	FACETS	0.993	0.936	1			1	INDETERMINATE	1	TRUE	NA	0.826697116720919	2		498	619	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056053	26056067	+	inframe_deletion	In_Frame_Del	DEL	CCTTGGGCTTAGCGG	CCTTGGGCTTAGCGG	-	rs756916945	NA	P-0042797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	157	306	0	ENST00000343677.2:c.590_604del	p.Ala197_Lys201del	p.A197_K201del	ENST00000343677	NM_005319.3	197	gCCGCTAAGCCCAAGGtt/gtt	1/1	1	2	FACETS	0.887	0.821	0.955	0.887	0.821	0.955	CLONAL	1	TRUE	1	0.826697116720919	2		306	428	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481412	140481412	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913353	NA	P-0042797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	239	392	0	ENST00000288602.6:c.1396G>C	p.Gly466Arg	p.G466R	ENST00000288602	NM_004333.4	466	Gga/Cga	11/18	0.814977074558065	1	FACETS	0.998	0.955	1	0.998	0.955	1	CLONAL	1	TRUE	0	0.826697116720919	1		392	340	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595346	141595358	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTCTAGGTGGA	GGGTCTAGGTGGA	-	novel	NA	P-0042797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1460	343	806	0	ENST00000220592.5:c.75_87del	p.Pro26ThrfsTer109	p.P26Tfs*109	ENST00000220592	NM_012154.3	25	ccTCCACCTAGACCC/cc	2/19	0.808343801921646	4	FACETS	0.841	0.793	0.89	0.28	0.264	0.297	CLONAL	1	TRUE	1	0.826697116720919	4		806	1803	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0042807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	113	542	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		542	364	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0042814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	312	863	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.683414550245731	1	FACETS	0.953	0.907	0.998	0.953	0.907	0.998	CLONAL	1	TRUE	0	0.683414550245731	1		863	631	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	545	425	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.259267809726566	6	FACETS	1	0.991	1			1	INDETERMINATE	4	TRUE	NA	0.683414550245731	6		426	891	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593488	48593488	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs730881954	NA	P-0042814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	158	367	0	ENST00000342988.3:c.1239C>A	p.Tyr413Ter	p.Y413*	ENST00000342988	NM_005359.5	413	taC/taA	10/12	0.683414550245731	1	FACETS	0.92	0.857	0.982	0.92	0.857	0.982	CLONAL	1	TRUE	0	0.683414550245731	1		367	331	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437669	52437669	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	807	796	0	ENST00000460680.1:c.1492G>T	p.Glu498Ter	p.E498*	ENST00000460680	NM_004656.3	498	Gag/Tag	13/17	0.790318795463414	2	FACETS	0.981	0.961	1	0.981	0.961	1	CLONAL	2	TRUE	0	0.794395526480948	2		796	1036	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574031	7574032	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0042852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	816	780	2	ENST00000269305.4:c.995_996insA	p.Arg333ProfsTer4	p.R333Pfs*4	ENST00000269305	NM_001126112.2	332	atc/atAc	10/11	0.790318795463414	2	FACETS	0.975	0.956	0.995	0.975	0.956	0.995	CLONAL	2	TRUE	0	0.794395526480948	2		782	1053	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604740	48604740	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	290	550	1	ENST00000342988.3:c.1562C>A	p.Thr521Lys	p.T521K	ENST00000342988	NM_005359.5	521	aCa/aAa	12/12	1	2	FACETS	0.975	0.922	1	0.975	0.922	1	CLONAL	1	TRUE	1	0.794395526480948	2		551	749	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	97	425	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.193898753427093	5	FACETS	1	0.928	1	0.694	0.623	0.768	INDETERMINATE	2	TRUE	2	0.370849071146139	5		426	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0042882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	153	932	0	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.357635602603576	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.370849071146139	2		932	340	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575194	48575194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555685186	NA	P-0042882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	46	325	0	ENST00000342988.3:c.388C>T	p.Pro130Ser	p.P130S	ENST00000342988	NM_005359.5	130	Cca/Tca	3/12	0.358694454515003	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.370849071146139	1		325	153	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247764	59247764	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	82	650	0	ENST00000371222.2:c.979C>T	p.Gln327Ter	p.Q327*	ENST00000371222	NM_002228.3	327	Cag/Tag	1/1	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.370849071146139	2		650	404	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266577	142266577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	58	308	0	ENST00000350721.4:c.3347C>T	p.Pro1116Leu	p.P1116L	ENST00000350721	NM_001184.3	1116	cCt/cTt	16/47	0.14323727692046	3	FACETS	0.961	0.839	1	0.64	0.559	0.726	INDETERMINATE	2	TRUE	0	0.370849071146139	3		308	193	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960150	151960150	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	29	445	0	ENST00000262189.6:c.1250G>T	p.Cys417Phe	p.C417F	ENST00000262189	NM_170606.2	417	tGt/tTt	9/59	0.370849071146139	1	FACETS	0.724	0.587	0.877	0.724	0.587	0.877	SUBCLONAL	1	TRUE	0	0.370849071146139	1		445	176	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0042883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	285	545	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.532695270032505	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.532695270032505	2		545	521	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0042883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	211	516	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.102522827428667	6	FACETS	0.891	0.833	0.951			1	INDETERMINATE	3	TRUE	NA	0.532695270032505	6		516	612	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0042883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	83	251	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	0.996	0.888	1	0.996	0.888	1	CLONAL	1	TRUE	1	0.532695270032505	2		251	313	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0042895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	1064	535	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.645006395160778	7	FACETS	0.938	0.919	0.957			1	CLONAL	6	TRUE	NA	0.645006395160778	7		535	1531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0042895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	374	489	0	ENST00000269305.4:c.560-2A>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.645006395160778	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.645006395160778	2		489	568	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290063	15290063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	364	559	1	ENST00000263388.2:c.3491G>A	p.Cys1164Tyr	p.C1164Y	ENST00000263388	NM_000435.2	1164	tGc/tAc	22/33	0.370177043498798	2	FACETS	0.779	0.745	0.814	0.779	0.745	0.814	INDETERMINATE	2	TRUE	0	0.645006395160778	2		560	724	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228813	36228813	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	403	694	2	ENST00000222270.7:c.7712A>G	p.Lys2571Arg	p.K2571R	ENST00000222270	NM_014727.1	2571	aAg/aGg	35/37	0.134279619179362	4	FACETS	1	0.979	1	1	0.979	1	INDETERMINATE	2	TRUE	2	0.645006395160778	4		696	987	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645436	215645436	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	59	454	0	ENST00000260947.4:c.1162A>T	p.Ile388Phe	p.I388F	ENST00000260947	NM_000465.2	388	Att/Ttt	4/11	0.233857538857002	0	FACETS	0.105	0.09	0.122			1	INDETERMINATE	1	TRUE	0	0.645006395160778	0		454	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0042915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	472	973	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.464024854582036	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.474752806708475	2		973	950	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0042915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	88	475	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.78	0.694	0.872	0.78	0.694	0.872	SUBCLONAL	1	TRUE	1	0.474752806708475	2		475	475	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	54	157	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.474752806708475	2		157	204	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468174	25468174	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs149738328	NA	P-0042915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	222	734	0	ENST00000264709.3:c.1502A>G	p.Asn501Ser	p.N501S	ENST00000264709	NM_175629.2	501	aAt/aGt	13/23	1	2	FACETS	0.922	0.858	0.988	0.922	0.858	0.988	CLONAL	1	TRUE	1	0.474752806708475	2		734	1014	SUCCESS
APC	324	MSKCC	GRCh37	5	112175399	112175399	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0042915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	73	232	0	ENST00000257430.4:c.4108A>T	p.Lys1370Ter	p.K1370*	ENST00000257430	NM_000038.5	1370	Aaa/Taa	16/16	1	2	FACETS	0.989	0.873	1	0.989	0.873	1	CLONAL	1	TRUE	1	0.474752806708475	2		232	311	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226424	133226424	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	166	567	0	ENST00000320574.5:c.3634A>T	p.Met1212Leu	p.M1212L	ENST00000320574	NM_006231.2	1212	Atg/Ttg	30/49	1	2	FACETS	0.978	0.901	1	0.978	0.901	1	CLONAL	1	TRUE	1	0.474752806708475	2		567	715	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604767	48604767	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	127	350	0	ENST00000342988.3:c.1589A>C	p.His530Pro	p.H530P	ENST00000342988	NM_005359.5	530	cAc/cCc	12/12	0.474752806708475	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.474752806708475	1		350	406	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245512	153245512	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	96	323	0	ENST00000281708.4:c.1679A>G	p.Asp560Gly	p.D560G	ENST00000281708	NM_033632.3	560	gAt/gGt	11/12	1	2	FACETS	0.934	0.837	1	0.934	0.837	1	CLONAL	1	TRUE	1	0.474752806708475	2		323	433	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473635	67473635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906853	NA	P-0042932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	187	577	1	ENST00000327367.4:c.715G>A	p.Glu239Lys	p.E239K	ENST00000327367	NM_005902.3	239	Gag/Aag	6/9	0.513185370821755	4	FACETS	0.802	0.746	0.86	0.802	0.746	0.86	CLONAL	2	FALSE	2	0.682057296089271	4		578	575	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057705	27057705	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	232	768	0	ENST00000324856.7:c.1413C>A	p.Tyr471Ter	p.Y471*	ENST00000324856	NM_006015.4	471	taC/taA	3/20	0.628572346821182	3	FACETS	0.769	0.723	0.816	0.769	0.723	0.816	SUBCLONAL	2	FALSE	1	0.682057296089271	3		768	593	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652377	206652377	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782242787	NA	P-0042932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	49	695	1	ENST00000367120.3:c.1084G>A	p.Glu362Lys	p.E362K	ENST00000367120	NM_014002.3	362	Gag/Aag	10/22	0.579221710798762	5	FACETS	0.409	0.345	0.479	0.136	0.115	0.16	SUBCLONAL	1	FALSE	2	0.682057296089271	5		696	711	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482854	67482860	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CGCTGTT	CGCTGTT	TAAGAC	novel	NA	P-0042932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	115	494	2	ENST00000327367.4:c.1258_1264delinsTAAGAC	p.Arg420Ter	p.R420*	ENST00000327367	NM_005902.3	420	CGCTGTTcc/TAAGACcc	9/9	0.513185370821755	4	FACETS	1	0.965	1	0.571	0.516	0.627	CLONAL	1	FALSE	2	0.682057296089271	4		496	497	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696404	47696404	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	178	499	0	ENST00000347630.2:c.419A>T	p.Asp140Val	p.D140V	ENST00000347630	NM_001007230.1	140	gAt/gTt	6/11	0.682057296089271	5	FACETS	1	0.987	1	0.441	0.406	0.476	CLONAL	1	FALSE	2	0.682057296089271	5		499	799	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174395	11174395	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	37	696	0	ENST00000361445.4:c.7280T>G	p.Leu2427Arg	p.L2427R	ENST00000361445	NM_004958.3	2427	cTg/cGg	53/58	NA	2	FACETS	0.747	0.616	0.895			1	INDETERMINATE	1	FALSE	NA	0.215222307603276	2		696	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	rs886039483	NA	P-0042971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	112	836	0	ENST00000269305.4:c.376T>A	p.Tyr126Asn	p.Y126N	ENST00000269305	NM_001126112.2	126	Tac/Aac	5/11	0.215222307603276	2	FACETS	0.948	0.861	1	1	0.984	1	CLONAL	3	FALSE	0	0.215222307603276	2		836	366	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348536	70348536	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs387907360	NA	P-0042971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	13	347	1	ENST00000374080.3:c.3443G>T	p.Arg1148Leu	p.R1148L	ENST00000374080		1148	cGc/cTc	24/45	0.164798202139204	2	FACETS	0.523	0.373	0.706			1	SUBCLONAL	1	FALSE	NA	0.215222307603276	2		348	231	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0042974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	124	711	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.203034278846994	2	FACETS	1	0.977	1	0.625	0.566	0.688	CLONAL	1	TRUE	0	0.267209814236162	2		711	742	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222187	53222187	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	57	577	0	ENST00000375401.3:c.4645C>G	p.Leu1549Val	p.L1549V	ENST00000375401	NM_004187.3	1549	Ctg/Gtg	26/26	0.273295450697833	1	FACETS	0.705	0.606	0.814	0.705	0.606	0.814	SUBCLONAL	1	TRUE	0	0.267209814236162	1		577	524	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100303	27100303	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	90	606	0	ENST00000324856.7:c.4015T>G	p.Tyr1339Asp	p.Y1339D	ENST00000324856	NM_006015.4	1339	Tat/Gat	17/20	0.273295450697833	3	FACETS	1	0.952	1	0.566	0.503	0.635	CLONAL	1	TRUE	1	0.267209814236162	3		606	674	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891132	112891132	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	57	690	0	ENST00000351677.2:c.466G>T	p.Asp156Tyr	p.D156Y	ENST00000351677	NM_002834.3	156	Gac/Tac	4/16	0.203034278846994	2	FACETS	0.635	0.544	0.734	0.317	0.272	0.367	SUBCLONAL	1	TRUE	0	0.267209814236162	2		690	672	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672797	30672808	+	inframe_deletion	In_Frame_Del	DEL	GTGGGCTCAGGG	GTGGGCTCAGGG	-	novel	NA	P-0042974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	111	747	0	ENST00000376406.3:c.4152_4163del	p.Pro1385_Thr1388del	p.P1385_T1388del	ENST00000376406	NM_014641.2	1384	acCCCTGAGCCCACa/aca	10/15	0.267209814236162	5	FACETS	1	0.978	1	0.444	0.399	0.493	CLONAL	1	TRUE	2	0.267209814236162	5		747	873	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742000	145742000	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	64	657	0	ENST00000428558.2:c.503G>T	p.Arg168Met	p.R168M	ENST00000428558	NM_004260.3	168	aGg/aTg	5/22	0.267209814236162	7	FACETS	0.817	0.705	0.939	0.204	0.176	0.235	CLONAL	1	TRUE	3	0.267209814236162	7		657	978	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222169	53222169	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	46	534	0	ENST00000375401.3:c.4663C>G	p.Pro1555Ala	p.P1555A	ENST00000375401	NM_004187.3	1555	Ccg/Gcg	26/26	0.273295450697833	1	FACETS	0.65	0.548	0.763	0.65	0.548	0.763	SUBCLONAL	1	TRUE	0	0.267209814236162	1		534	459	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000100	30000100	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	258	709	0	ENST00000338641.4:c.113A>T	p.Glu38Val	p.E38V	ENST00000338641	NM_000268.3	38	gAg/gTg	1/16	0.765440206036882	1	FACETS	0.655	0.618	0.693	0.655	0.618	0.693	SUBCLONAL	1	TRUE	0	0.765440206036882	1		709	635	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100171	27100171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778051	NA	P-0042986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	341	597	0	ENST00000324856.7:c.3967C>T	p.Arg1323Cys	p.R1323C	ENST00000324856	NM_006015.4	1323	Cgc/Tgc	16/20	1	2	FACETS	0.994	0.944	1	0.994	0.944	1	CLONAL	1	TRUE	1	0.765440206036882	2		597	896	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950898	32950900	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0042986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	317	627	0	ENST00000380152.3:c.8727_8729del	p.Lys2909del	p.K2909del	ENST00000380152		2908	gtGAAg/gtg	21/27	0.765440206036882	1	FACETS	0.93	0.889	0.97	0.93	0.889	0.97	CLONAL	1	TRUE	0	0.765440206036882	1		627	550	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184388	7184388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765888394	NA	P-0043016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	118	644	0	ENST00000302850.5:c.913G>A	p.Val305Ile	p.V305I	ENST00000302850	NM_000208.2	305	Gtc/Atc	3/22	0.3264094125469	1	FACETS	0.914	0.826	1	0.914	0.826	1	CLONAL	1	TRUE	0	0.3264094125469	1		644	662	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0043016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	141	574	0	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.3264094125469	1	FACETS	0.752	0.689	0.816	1	0.988	1	SUBCLONAL	2	TRUE	0	0.3264094125469	1		574	481	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585516	29585516	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0043016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	15	123	0	ENST00000356175.3:c.4265C>G	p.Ser1422Ter	p.S1422*	ENST00000356175	NM_000267.3	1422	tCa/tGa	31/57	0.3264094125469	1	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	0	0.3264094125469	1		123	61	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716220	243716220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	67	505	0	ENST00000263826.5:c.974G>T	p.Arg325Leu	p.R325L	ENST00000263826	NM_005465.4	325	cGa/cTa	10/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.3264094125469	2		505	338	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0043030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	30	463	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.923	0.758	1	0.923	0.758	1	CLONAL	1	FALSE	1	0.532793341578809	2		463	122	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579861	7579861	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs876658627	NA	P-0043030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	77	746	0	ENST00000269305.4:c.52del	p.Thr18HisfsTer26	p.T18Hfs*26	ENST00000269305	NM_001126112.2	18	Aca/ca	2/11	0.484359330252523	1	FACETS	0.955	0.853	1	0.955	0.853	1	CLONAL	1	FALSE	0	0.532793341578809	1		746	222	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0043036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	169	407	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.504039832482232	2		407	537	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0043036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	128	435	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.864	0.786	0.945	0.864	0.786	0.945	CLONAL	1	TRUE	1	0.504039832482232	2		435	588	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023497	27023498	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0043036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	169	649	0	ENST00000324856.7:c.606_607del	p.His203ArgfsTer196	p.H203Rfs*196	ENST00000324856	NM_006015.4	201	aaCTct/aact	1/20	0.504039832482232	1	FACETS	0.978	0.906	1	0.978	0.906	1	CLONAL	1	TRUE	0	0.504039832482232	1		649	513	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098959	178098959	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	92	320	0	ENST00000397062.3:c.86A>C	p.Asp29Ala	p.D29A	ENST00000397062	NM_006164.4	29	gAt/gCt	2/5	1	2	FACETS	0.956	0.855	1	0.956	0.855	1	CLONAL	1	TRUE	1	0.504039832482232	2		320	382	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589219	67589219	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	40	321	0	ENST00000274335.5:c.1207G>T	p.Glu403Ter	p.E403*	ENST00000274335		403	Gaa/Taa	9/15	1	2	FACETS	0.375	0.312	0.446	0.375	0.312	0.446	SUBCLONAL	1	TRUE	1	0.504039832482232	2		321	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0043060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	93	973	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.258911991080363	5	FACETS	0.799	0.712	0.892	0.533	0.475	0.595	SUBCLONAL	2	TRUE	2	0.296526175818828	5		973	567	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281713	49281713	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	38	1008	0	ENST00000282018.3:c.760A>G	p.Ile254Val	p.I254V	ENST00000282018	NM_020377.2	254	Atc/Gtc	1/1	1	2	FACETS	0.54	0.446	0.644	0.54	0.446	0.644	SUBCLONAL	1	TRUE	1	0.296526175818828	2		1008	475	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921998	39921998	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0043060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	96	354	0	ENST00000378444.4:c.4173+1G>T		p.X1391_splice	ENST00000378444	NM_001123385.1	1391			0.297520955381849	2	FACETS	0.867	0.786	0.95			1	CLONAL	3	TRUE	NA	0.296526175818828	2		354	249	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577330	64577333	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	rs587776841	NA	P-0043063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	470	733	0	ENST00000312049.6:c.249_252del	p.Ile85SerfsTer33	p.I85Sfs*33	ENST00000312049	NM_130799.2	83	ctGTCT/ct	2/10	0.821645351915469	2	FACETS	0.839	0.813	0.864	0.839	0.813	0.864	CLONAL	2	TRUE	0	0.821645351915469	2		733	682	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0043063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	456	739	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.821645351915469	3	FACETS	1	0.996	1			1	CLONAL	1	TRUE	NA	0.821645351915469	3		739	1101	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56401549	56401549	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	42	343	0	ENST00000348428.3:c.1411G>A	p.Asp471Asn	p.D471N	ENST00000348428	NM_006785.3	471	Gat/Aat	12/17	0.821645351915469	4	FACETS	0.25	0.208	0.297	0.125	0.104	0.149	SUBCLONAL	1	TRUE	2	0.821645351915469	4		343	745	SUCCESS
AR	367	MSKCC	GRCh37	X	66766357	66766401	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	-	novel	NA	P-0043063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	88	117	0	ENST00000374690.3:c.1376_1420del	p.Gly459_Gly473del	p.G459_G473del	ENST00000374690	NM_000044.3	457	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC/-	1/8	0.423953093928762	5	FACETS	0.83	0.745	0.919	0.553	0.496	0.613	INDETERMINATE	2	TRUE	2	0.821645351915469	5		117	288	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0043074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	172	451	3	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.628595867693956	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.628595867693956	2		454	272	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0043074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	103	522	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	1	2	FACETS	0.936	0.846	1	0.936	0.846	1	CLONAL	1	TRUE	1	0.628595867693956	2		522	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0043074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	281	746	1	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	0.628595867693956	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.628595867693956	1		747	523	SUCCESS
CBL	867	MSKCC	GRCh37	11	119077232	119077233	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAC	rs373212940	NA	P-0043074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	130	733	1	ENST00000264033.4:c.125_127dup	p.His42dup	p.H42dup	ENST00000264033	NM_005188.3	42	-/CAC	1/16	1	2	FACETS	0.648	0.589	0.71	0.648	0.589	0.71	SUBCLONAL	1	TRUE	1	0.628595867693956	2		734	638	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517445	157517445	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs773740590	NA	P-0043074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	150	474	0	ENST00000346085.5:c.4009C>T	p.Arg1337Ter	p.R1337*	ENST00000346085	NM_020732.3	1337	Cga/Tga	16/20	1	2	FACETS	0.974	0.897	1	0.974	0.897	1	CLONAL	1	TRUE	1	0.628595867693956	2		474	490	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440290	187440290	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200887028	NA	P-0043074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	203	543	0	ENST00000232014.4:c.2077G>A	p.Val693Met	p.V693M	ENST00000232014	NM_001130845.1	693	Gtg/Atg	10/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.628595867693956	2		543	602	SUCCESS
APC	324	MSKCC	GRCh37	5	112175215	112175216	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAAAAGATTG	novel	NA	P-0043074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	36	244	0	ENST00000257430.4:c.3928_3937dup	p.Thr1313LysfsTer5	p.T1313Kfs*5	ENST00000257430	NM_000038.5	1308	-/GAAAAGATTG	16/16	0.628595867693956	1	FACETS	0.609	0.511	0.714	0.609	0.511	0.714	SUBCLONAL	1	TRUE	0	0.628595867693956	1		244	129	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372055	55372055	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	205	480	0	ENST00000297316.4:c.745G>A	p.Gly249Ser	p.G249S	ENST00000297316	NM_022454.3	249	Ggc/Agc	2/2	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.628595867693956	2		480	559	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	122	484	4	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.918	0.836	1	0.918	0.836	1	CLONAL	1	TRUE	1	0.63	2		488	422	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	37	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.0964628597882073	3	FACETS	1	0.912	1	0.568	0.477	0.665	INDETERMINATE	1	TRUE	1	0.63	3		326	136	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	38	343	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.868	0.731	1	0.868	0.731	1	CLONAL	1	TRUE	1	0.63	2		343	139	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863394	57863394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs533875222	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	129	711	1	ENST00000228682.2:c.1489C>T	p.Arg497Cys	p.R497C	ENST00000228682	NM_005269.2	497	Cgc/Tgc	11/12	0.0964628597882073	3	FACETS	1	0.967	1	0.562	0.513	0.613	INDETERMINATE	1	TRUE	1	0.63	3		712	479	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	93	425	11	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.63	2		436	289	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	91	440	2	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.63	2		442	250	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297996	15297996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142787620	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	166	820	2	ENST00000263388.2:c.1760G>A	p.Arg587His	p.R587H	ENST00000263388	NM_000435.2	587	cGc/cAc	11/33	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.63	2		822	470	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	19	186	1	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	0.3	2	FACETS	1	0.888	1	0.603	0.479	0.735	INDETERMINATE	1	TRUE	0	0.63	2		187	50	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950396	15950396	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201721277	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	58	496	0	ENST00000268712.3:c.6548G>A	p.Arg2183His	p.R2183H	ENST00000268712	NM_006311.3	2183	cGc/cAc	42/46	1	2	FACETS	0.885	0.772	1	0.885	0.772	1	CLONAL	1	TRUE	1	0.63	2		496	208	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589147	67589147	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	22	267	0	ENST00000274335.5:c.1135A>G	p.Lys379Glu	p.K379E	ENST00000274335		379	Aaa/Gaa	9/15	1	2	FACETS	0.776	0.615	0.954	0.776	0.615	0.954	CLONAL	1	TRUE	1	0.63	2		267	90	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	55	552	0	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	0.79	0.684	0.902	0.79	0.684	0.902	CLONAL	1	TRUE	1	0.63	2		552	221	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549884	187549884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756351356	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	57	317	1	ENST00000441802.2:c.4357C>T	p.Arg1453Cys	p.R1453C	ENST00000441802	NM_005245.3	1453	Cgt/Tgt	8/27	0.0964628597882073	3	FACETS	1	0.943	1	0.578	0.503	0.657	INDETERMINATE	1	TRUE	1	0.63	3		318	206	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17117087	17117087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764899882	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	143	582	2	ENST00000285071.4:c.1622C>T	p.Ala541Val	p.A541V	ENST00000285071	NM_144997.5	541	gCg/gTg	14/14	1	2	FACETS	0.901	0.826	0.978	0.901	0.826	0.978	CLONAL	1	TRUE	1	0.63	2		584	504	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852118	63852118	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	81	555	0	ENST00000279873.7:c.2901del	p.Lys967AsnfsTer15	p.K967Nfs*15	ENST00000279873	NM_032199.2	966	Aaa/aa	10/10	1	2	FACETS	0.768	0.682	0.858	0.768	0.682	0.858	SUBCLONAL	1	TRUE	1	0.63	2		555	335	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912103	50912103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237089094	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	151	809	0	ENST00000440232.2:c.1837G>A	p.Ala613Thr	p.A613T	ENST00000440232	NM_002691.3	613	Gcc/Acc	15/27	1	2	FACETS	0.925	0.852	1	0.925	0.852	1	CLONAL	1	TRUE	1	0.63	2		809	518	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136270	2136270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1371745883	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	137	721	0	ENST00000219476.3:c.4739G>A	p.Arg1580Gln	p.R1580Q	ENST00000219476	NM_000548.3	1580	cGg/cAg	37/42	1	2	FACETS	0.998	0.915	1	0.998	0.915	1	CLONAL	1	TRUE	1	0.63	2		721	436	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293833	1293833	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	124	920	4	ENST00000310581.5:c.1168C>T	p.Arg390Trp	p.R390W	ENST00000310581	NM_198253.2	390	Cgg/Tgg	2/16	1	2	FACETS	0.933	0.851	1	0.933	0.851	1	CLONAL	1	TRUE	1	0.63	2		924	422	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210837	2210837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753115153	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	89	466	0	ENST00000398665.3:c.1334C>T	p.Ala445Val	p.A445V	ENST00000398665	NM_032482.2	445	gCg/gTg	14/28	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.63	2		466	276	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044500	12044500	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367662793	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	36	331	0	ENST00000353533.5:c.1123G>A	p.Val375Ile	p.V375I	ENST00000353533	NM_003010.3	375	Gtt/Att	11/11	1	2	FACETS	0.71	0.592	0.838	0.71	0.592	0.838	SUBCLONAL	1	TRUE	1	0.63	2		331	161	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120115	70120115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	50	166	0	ENST00000245479.2:c.1121del	p.Pro374ArgfsTer9	p.P374Rfs*9	ENST00000245479	NM_000346.3	373	Ccc/cc	3/3	1	2	FACETS	1	0.944	1	1	0.982	1	CLONAL	2	TRUE	1	0.63	2		166	74	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261878	16261878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763414538	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	102	484	0	ENST00000375759.3:c.9143C>T	p.Thr3048Met	p.T3048M	ENST00000375759	NM_015001.2	3048	aCg/aTg	11/15	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.63	2		484	304	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014176	70014176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	129	598	0	ENST00000394351.3:c.1037G>A	p.Gly346Asp	p.G346D	ENST00000394351	NM_000248.3	346	gGc/gAc	9/9	1	2	FACETS	0.883	0.806	0.962	0.883	0.806	0.962	CLONAL	1	TRUE	1	0.63	2		598	464	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210692	5210692	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	121	634	0	ENST00000357368.4:c.5359C>T	p.Arg1787Trp	p.R1787W	ENST00000357368	NM_002850.3	1787	Cgg/Tgg	34/38	1	2	FACETS	0.9	0.819	0.983	0.9	0.819	0.983	CLONAL	1	TRUE	1	0.63	2		634	427	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206818	36206818	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	110	503	0	ENST00000300305.3:c.694C>T	p.Arg232Trp	p.R232W	ENST00000300305		232	Cgg/Tgg	6/8	0.0964628597882073	3	FACETS	0.985	0.89	1	0.493	0.445	0.543	INDETERMINATE	1	TRUE	1	0.63	3		503	466	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188297	32188297	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs753855314	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	107	741	4	ENST00000375023.3:c.1044del	p.Gly349AlafsTer49	p.G349Afs*49	ENST00000375023	NM_004557.3	348	ggC/gg	6/30	0.0964628597882073	3	FACETS	1	0.958	1	0.554	0.501	0.61	INDETERMINATE	1	TRUE	1	0.63	3		745	403	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610059	81610059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908872	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	47	379	0	ENST00000298171.2:c.1657G>A	p.Ala553Thr	p.A553T	ENST00000298171	NM_000369.2	553	Gcc/Acc	10/10	1	2	FACETS	0.612	0.52	0.71	0.612	0.52	0.71	SUBCLONAL	1	TRUE	1	0.63	2		379	244	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725324	49725324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748664213	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	28	523	1	ENST00000449682.2:c.101G>A	p.Arg34His	p.R34H	ENST00000449682	NM_020998.3	34	cGc/cAc	2/18	1	2	FACETS	0.211	0.168	0.259	0.211	0.168	0.259	SUBCLONAL	1	TRUE	1	0.63	2		524	422	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731065	162731065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747307320	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	74	433	0	ENST00000367921.3:c.920G>A	p.Arg307His	p.R307H	ENST00000367921	NM_006182.2	307	cGc/cAc	9/18	1	2	FACETS	0.918	0.814	1	0.918	0.814	1	CLONAL	1	TRUE	1	0.63	2		433	256	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354375	354375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910854855	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	190	754	0	ENST00000262320.3:c.1183C>T	p.Arg395Cys	p.R395C	ENST00000262320	NM_003502.3	395	Cgc/Tgc	5/11	1	2	FACETS	0.954	0.887	1	0.954	0.887	1	CLONAL	1	TRUE	1	0.63	2		754	632	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003788	45003788	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	129	461	0	ENST00000558401.1:c.44T>C	p.Leu15Pro	p.L15P	ENST00000558401	NM_004048.2	15	cTt/cCt	1/4	0.0964628597882073	0	FACETS	0.305	0.278	0.334			1	INDETERMINATE	1	TRUE	0	0.63	0		461	496	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031919	10031919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs901717931	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	80	699	0	ENST00000330684.3:c.904G>A	p.Ala302Thr	p.A302T	ENST00000330684	NM_001134407.1	302	Gct/Act	3/13	1	2	FACETS	0.694	0.615	0.777	0.694	0.615	0.777	SUBCLONAL	1	TRUE	1	0.63	2		699	366	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	100	638	5	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.971	0.877	1	0.971	0.877	1	CLONAL	1	TRUE	1	0.63	2		643	327	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631102	69631102	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121917704	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	93	655	0	ENST00000334134.2:c.310C>T	p.Arg104Ter	p.R104*	ENST00000334134	NM_005247.2	104	Cga/Tga	2/3	1	2	FACETS	0.937	0.843	1	0.937	0.843	1	CLONAL	1	TRUE	1	0.63	2		655	315	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435099	110435099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	172	719	2	ENST00000375856.3:c.3302C>T	p.Pro1101Leu	p.P1101L	ENST00000375856	NM_003749.2	1101	cCg/cTg	1/2	1	2	FACETS	0.894	0.826	0.963	0.894	0.826	0.963	CLONAL	1	TRUE	1	0.63	2		721	611	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993075	72993075	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	89	820	0	ENST00000268489.5:c.970G>A	p.Ala324Thr	p.A324T	ENST00000268489	NM_006885.3	324	Gct/Act	2/10	1	2	FACETS	0.71	0.633	0.79	0.71	0.633	0.79	SUBCLONAL	1	TRUE	1	0.63	2		820	398	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417875	32417875	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	94	472	0	ENST00000332351.3:c.1177T>C	p.Cys393Arg	p.C393R	ENST00000332351	NM_024426.4	393	Tgt/Cgt	7/10	1	2	FACETS	0.811	0.727	0.898	0.811	0.727	0.898	CLONAL	1	TRUE	1	0.63	2		472	368	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478220	99478220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	59	332	1	ENST00000268035.6:c.3124C>T	p.Arg1042Cys	p.R1042C	ENST00000268035	NM_000875.3	1042	Cgt/Tgt	16/21	0.0964628597882073	0	FACETS	0.322	0.281	0.366			1	INDETERMINATE	1	TRUE	0	0.63	0		333	215	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40993283	40993283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1428987216	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	28	377	0	ENST00000267868.3:c.109G>A	p.Asp37Asn	p.D37N	ENST00000267868	NM_002875.4	37	Gat/Aat	3/10	0.0964628597882073	0	FACETS	0.219	0.177	0.266			1	INDETERMINATE	1	TRUE	0	0.63	0		377	150	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570468	39570468	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs267605182	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	20	205	0	ENST00000262039.4:c.664C>T	p.Arg222Ter	p.R222*	ENST00000262039	NM_002647.2	222	Cga/Tga	6/25	1	2	FACETS	0.722	0.564	0.897	0.722	0.564	0.897	SUBCLONAL	1	TRUE	1	0.63	2		205	88	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294382	1294382	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs943176303	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	115	575	0	ENST00000310581.5:c.619G>A	p.Val207Ile	p.V207I	ENST00000310581	NM_198253.2	207	Gtc/Atc	2/16	1	2	FACETS	0.931	0.846	1	0.931	0.846	1	CLONAL	1	TRUE	1	0.63	2		575	392	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240069	41240069	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1482440466	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	10	25	0	ENST00000379561.5:c.281T>C	p.Val94Ala	p.V94A	ENST00000379561	NM_002015.3	94	gTg/gCg	1/3	1	2	FACETS	1	0.823	1	1	0.823	1	CLONAL	1	TRUE	1	0.63	2		25	26	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73342975	73342975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757306363	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	35	301	0	ENST00000377767.4:c.1831C>T	p.Arg611Cys	p.R611C	ENST00000377767	NM_014953.3	611	Cgt/Tgt	14/21	1	2	FACETS	0.717	0.596	0.848	0.717	0.596	0.848	SUBCLONAL	1	TRUE	1	0.63	2		301	155	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129249	152129249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771540162	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	123	695	2	ENST00000206249.3:c.202G>A	p.Ala68Thr	p.A68T	ENST00000206249	NM_000125.3	68	Gcc/Acc	1/8	0.0964628597882073	3	FACETS	1	0.981	1	0.643	0.587	0.702	INDETERMINATE	1	TRUE	1	0.63	3		697	399	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420213	49420213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267607237	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	145	646	0	ENST00000301067.7:c.15536G>A	p.Arg5179His	p.R5179H	ENST00000301067	NM_003482.3	5179	cGt/cAt	48/54	0.0964628597882073	3	FACETS	1	0.966	1	0.551	0.505	0.599	INDETERMINATE	1	TRUE	1	0.63	3		646	549	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226490	2226490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780810017	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	195	844	0	ENST00000398665.3:c.3970G>A	p.Ala1324Thr	p.A1324T	ENST00000398665	NM_032482.2	1324	Gcg/Acg	27/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.63	2		844	573	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928454	69928454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559222331	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	142	615	0	ENST00000352241.4:c.274G>A	p.Val92Met	p.V92M	ENST00000352241	NM_198159.2	92	Gtg/Atg	2/10	1	2	FACETS	0.851	0.779	0.924	0.851	0.779	0.924	CLONAL	1	TRUE	1	0.63	2		615	530	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200297	138200297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556022420	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	80	437	0	ENST00000237289.4:c.1715G>A	p.Arg572Gln	p.R572Q	ENST00000237289	NM_001270507.1	572	cGg/cAg	7/9	0.0964628597882073	3	FACETS	0.935	0.83	1	0.468	0.415	0.524	INDETERMINATE	1	TRUE	1	0.63	3		437	357	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906768	50906768	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373046355	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	132	774	0	ENST00000440232.2:c.1156C>T	p.Arg386Cys	p.R386C	ENST00000440232	NM_002691.3	386	Cgt/Tgt	10/27	1	2	FACETS	0.968	0.886	1	0.968	0.886	1	CLONAL	1	TRUE	1	0.63	2		774	433	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953083	2953083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1322611135	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	133	728	0	ENST00000396946.4:c.2857G>A	p.Glu953Lys	p.E953K	ENST00000396946	NM_032415.4	953	Gag/Aag	22/25	1	2	FACETS	0.862	0.788	0.939	0.862	0.788	0.939	CLONAL	1	TRUE	1	0.63	2		728	490	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781318	3781318	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	160	858	0	ENST00000262367.5:c.5047C>A	p.Arg1683Ser	p.R1683S	ENST00000262367	NM_004380.2	1683	Cgc/Agc	30/31	1	2	FACETS	0.888	0.819	0.96	0.888	0.819	0.96	CLONAL	1	TRUE	1	0.63	2		858	572	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829646	72829646	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767087836	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	51	627	0	ENST00000268489.5:c.6935G>A	p.Arg2312Gln	p.R2312Q	ENST00000268489	NM_006885.3	2312	cGg/cAg	9/10	1	2	FACETS	0.611	0.523	0.705	0.611	0.523	0.705	SUBCLONAL	1	TRUE	1	0.63	2		627	265	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944156	81944156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773800539	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	121	638	3	ENST00000359376.3:c.1765C>T	p.Arg589Cys	p.R589C	ENST00000359376	NM_002661.3	589	Cgc/Tgc	18/33	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.63	2		641	380	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030588	48030588	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63749843	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	70	356	1	ENST00000234420.5:c.3202C>T	p.Arg1068Ter	p.R1068*	ENST00000234420	NM_000179.2	1068	Cga/Tga	5/10	1	2	FACETS	0.829	0.731	0.932	0.829	0.731	0.932	CLONAL	1	TRUE	1	0.63	2		357	268	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743839	46743839	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs142058773	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	99	701	0	ENST00000371975.4:c.2129C>G	p.Thr710Ser	p.T710S	ENST00000371975	NM_003579.3	710	aCt/aGt	18/18	1	2	FACETS	0.75	0.674	0.83	0.75	0.674	0.83	SUBCLONAL	1	TRUE	1	0.63	2		701	419	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310435	65310435	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	95	431	0	ENST00000342505.4:c.2251+2T>G		p.X751_splice	ENST00000342505	NM_002227.2	751			1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.63	2		431	294	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344706	65344706	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	59	272	0	ENST00000342505.4:c.329+2T>C		p.X110_splice	ENST00000342505	NM_002227.2	110			1	2	FACETS	0.888	0.775	1	0.888	0.775	1	CLONAL	1	TRUE	1	0.63	2		272	211	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344711	65344711	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	63	281	0	ENST00000342505.4:c.326T>G	p.Met109Arg	p.M109R	ENST00000342505	NM_002227.2	109	aTg/aGg	4/25	1	2	FACETS	0.885	0.776	1	0.885	0.776	1	CLONAL	1	TRUE	1	0.63	2		281	226	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226259103	226259103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	11	27	0	ENST00000366813.1:c.334G>A	p.Ala112Thr	p.A112T	ENST00000366813		112	Gct/Act	3/3	1	2	FACETS	1	0.8	1	1	0.8	1	CLONAL	1	TRUE	1	0.63	2		27	31	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203728	94203728	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555012726	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	24	282	0	ENST00000323929.3:c.926T>C	p.Met309Thr	p.M309T	ENST00000323929	NM_005591.3	309	aTg/aCg	9/20	1	2	FACETS	0.68	0.543	0.833	0.68	0.543	0.833	SUBCLONAL	1	TRUE	1	0.63	2		282	112	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998573	100998573	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	139	691	0	ENST00000325455.5:c.1229A>G	p.Asn410Ser	p.N410S	ENST00000325455	NM_001202474.3	410	aAc/aGc	1/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.63	2		691	387	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422253	422253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374400044	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	60	497	0	ENST00000399788.2:c.3005G>A	p.Arg1002Gln	p.R1002Q	ENST00000399788	NM_001042603.1	1002	cGa/cAa	20/28	0.3	1	FACETS	0.59	0.515	0.669	0.59	0.515	0.669	INDETERMINATE	1	TRUE	0	0.63	1		497	221	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025633	1025633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754974791	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	22	575	0	ENST00000358495.3:c.742G>A	p.Ala248Thr	p.A248T	ENST00000358495	NM_134424.2	248	Gcc/Acc	9/12	0.3	1	FACETS	0.13	0.101	0.165	0.13	0.101	0.165	INDETERMINATE	1	TRUE	0	0.63	1		575	367	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205293	46205293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	43	429	0	ENST00000334344.6:c.377C>T	p.Ala126Val	p.A126V	ENST00000334344	NM_152641.2	126	gCa/gTa	4/21	0.0964628597882073	3	FACETS	0.981	0.832	1	0.49	0.416	0.571	INDETERMINATE	1	TRUE	1	0.63	3		429	183	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865699	57865699	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	145	805	0	ENST00000228682.2:c.3176T>C	p.Leu1059Pro	p.L1059P	ENST00000228682	NM_005269.2	1059	cTg/cCg	12/12	0.0964628597882073	3	FACETS	1	0.984	1	0.644	0.592	0.698	INDETERMINATE	1	TRUE	1	0.63	3		805	470	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120783437	120783437	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	99	637	0	ENST00000257552.2:c.1048-2A>G		p.X350_splice	ENST00000257552	NM_002442.3	350			0.0964628597882073	3	FACETS	1	0.978	1	0.66	0.596	0.726	INDETERMINATE	1	TRUE	1	0.63	3		637	313	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103520472	103520472	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1187994214	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	21	221	0	ENST00000355739.4:c.2543G>A	p.Arg848Gln	p.R848Q	ENST00000355739	NM_000123.3	848	cGg/cAg	12/15	1	2	FACETS	0.673	0.528	0.836	0.673	0.528	0.836	SUBCLONAL	1	TRUE	1	0.63	2		221	99	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528186	103528186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	82	388	0	ENST00000355739.4:c.3494C>T	p.Ala1165Val	p.A1165V	ENST00000355739	NM_000123.3	1165	gCc/gTc	15/15	1	2	FACETS	0.789	0.702	0.88	0.789	0.702	0.88	SUBCLONAL	1	TRUE	1	0.63	2		388	330	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436072	110436072	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	219	803	0	ENST00000375856.3:c.2329A>G	p.Thr777Ala	p.T777A	ENST00000375856	NM_003749.2	777	Acg/Gcg	1/2	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.63	2		803	673	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639155	3639155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777033175	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	144	771	2	ENST00000294008.3:c.4484C>T	p.Ala1495Val	p.A1495V	ENST00000294008	NM_032444.2	1495	gCg/gTg	12/15	1	2	FACETS	0.933	0.857	1	0.933	0.857	1	CLONAL	1	TRUE	1	0.63	2		773	490	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89383346	89383346	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	122	609	1	ENST00000301030.4:c.82A>G	p.Lys28Glu	p.K28E	ENST00000301030	NM_001256183.1	28	Aaa/Gaa	3/13	1	2	FACETS	0.866	0.789	0.947	0.866	0.789	0.947	CLONAL	1	TRUE	1	0.63	2		610	447	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7978924	7978924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145434489	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	100	388	0	ENST00000319144.4:c.1643G>A	p.Arg548Gln	p.R548Q	ENST00000319144	NM_001139.2	548	cGg/cAg	12/15	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.63	2		388	306	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223454	2223454	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	93	443	0	ENST00000398665.3:c.3565C>T	p.Pro1189Ser	p.P1189S	ENST00000398665	NM_032482.2	1189	Cca/Tca	25/28	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.63	2		443	257	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271900	15271900	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	126	856	0	ENST00000263388.2:c.6539C>A	p.Pro2180His	p.P2180H	ENST00000263388	NM_000435.2	2180	cCt/cAt	33/33	1	2	FACETS	0.928	0.847	1	0.928	0.847	1	CLONAL	1	TRUE	1	0.63	2		856	431	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276251	15276251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752426825	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	166	626	0	ENST00000263388.2:c.5743C>T	p.Arg1915Cys	p.R1915C	ENST00000263388	NM_000435.2	1915	Cgc/Tgc	31/33	1	2	FACETS	0.974	0.901	1	0.974	0.901	1	CLONAL	1	TRUE	1	0.63	2		626	541	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967069	18967069	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	137	711	0	ENST00000262803.5:c.1784A>G	p.Tyr595Cys	p.Y595C	ENST00000262803	NM_002911.3	595	tAc/tGc	13/24	1	2	FACETS	0.846	0.774	0.921	0.846	0.774	0.921	CLONAL	1	TRUE	1	0.63	2		711	514	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40761138	40761138	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	175	640	0	ENST00000392038.2:c.214A>G	p.Thr72Ala	p.T72A	ENST00000392038	NM_001626.4	72	Acc/Gcc	4/14	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.63	2		640	550	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753278	42753278	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1272093617	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	191	905	0	ENST00000222329.4:c.986G>A	p.Arg329His	p.R329H	ENST00000222329	NM_006494.2	329	cGc/cAc	4/4	1	2	FACETS	0.864	0.801	0.928	0.864	0.801	0.928	CLONAL	1	TRUE	1	0.63	2		905	702	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965986	25965986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	89	684	0	ENST00000435504.4:c.3220G>A	p.Val1074Ile	p.V1074I	ENST00000435504		1074	Gtt/Att	13/13	1	2	FACETS	0.829	0.741	0.92	0.829	0.741	0.92	CLONAL	1	TRUE	1	0.63	2		684	341	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551271	29551271	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	132	680	1	ENST00000389048.3:c.1359G>T	p.Gln453His	p.Q453H	ENST00000389048	NM_004304.4	453	caG/caT	6/29	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.63	2		681	409	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190742113	190742113	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	27	375	0	ENST00000441310.2:c.2750A>G	p.His917Arg	p.H917R	ENST00000441310	NM_000534.4	917	cAt/cGt	13/13	1	2	FACETS	0.51	0.41	0.622	0.51	0.41	0.622	SUBCLONAL	1	TRUE	1	0.63	2		375	168	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794348	242794348	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	106	712	0	ENST00000334409.5:c.592+2T>C		p.X198_splice	ENST00000334409	NM_005018.2	198			1	2	FACETS	0.825	0.745	0.908	0.825	0.745	0.908	CLONAL	1	TRUE	1	0.63	2		712	408	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387128	31387128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750849178	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	138	534	1	ENST00000328111.2:c.1753G>A	p.Ala585Thr	p.A585T	ENST00000328111	NM_006892.3	585	Gcg/Acg	16/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.63	2		535	387	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143163	24143163	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	108	624	0	ENST00000263121.7:c.395T>C	p.Val132Ala	p.V132A	ENST00000263121	NM_003073.3	132	gTa/gCa	4/9	1	2	FACETS	0.816	0.738	0.898	0.816	0.738	0.898	CLONAL	1	TRUE	1	0.63	2		624	420	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177952	142177952	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	22	291	0	ENST00000350721.4:c.7351T>C	p.Tyr2451His	p.Y2451H	ENST00000350721	NM_001184.3	2451	Tac/Cac	44/47	1	2	FACETS	0.541	0.425	0.673	0.541	0.425	0.673	SUBCLONAL	1	TRUE	1	0.63	2		291	129	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608661	189608661	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	41	400	0	ENST00000264731.3:c.1736A>G	p.Tyr579Cys	p.Y579C	ENST00000264731	NM_003722.4	579	tAc/tGc	13/14	1	2	FACETS	0.696	0.587	0.814	0.696	0.587	0.814	SUBCLONAL	1	TRUE	1	0.63	2		400	187	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177079	56177079	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	27	236	0	ENST00000399503.3:c.2349A>C	p.Gln783His	p.Q783H	ENST00000399503	NM_005921.1	783	caA/caC	13/20	1	2	FACETS	0.963	0.788	1	0.963	0.788	1	CLONAL	1	TRUE	1	0.63	2		236	89	SUCCESS
APC	324	MSKCC	GRCh37	5	112175684	112175684	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	51	295	0	ENST00000257430.4:c.4393del	p.Ser1465ValfsTer8	p.S1465Vfs*8	ENST00000257430	NM_000038.5	1465	Agt/gt	16/16	1	2	FACETS	0.915	0.791	1	0.915	0.791	1	CLONAL	1	TRUE	1	0.63	2		295	177	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170832331	170832331	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	71	477	0	ENST00000296930.5:c.700del	p.Thr234LeufsTer11	p.T234Lfs*11	ENST00000296930	NM_002520.6	232	gAa/ga	9/11	1	2	FACETS	0.909	0.804	1	0.909	0.804	1	CLONAL	1	TRUE	1	0.63	2		477	248	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652146	36652146	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	146	663	0	ENST00000244741.5:c.268G>T	p.Gly90Ter	p.G90*	ENST00000244741	NM_000389.4	90	Gga/Tga	2/3	0.0964628597882073	3	FACETS	1	0.981	1	0.616	0.566	0.667	INDETERMINATE	1	TRUE	1	0.63	3		663	495	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124419	94124419	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs528743765	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	26	329	0	ENST00000369303.4:c.162+2T>C		p.X54_splice	ENST00000369303	NM_004440.3	54			0.0964628597882073	3	FACETS	0.709	0.568	0.867	0.355	0.284	0.434	INDETERMINATE	1	TRUE	1	0.63	3		329	153	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106534452	106534452	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	52	248	1	ENST00000369096.4:c.24A>C	p.Lys8Asn	p.K8N	ENST00000369096	NM_001198.3	8	aaA/aaC	1/7	0.0964628597882073	3	FACETS	0.897	0.771	1	0.449	0.385	0.516	INDETERMINATE	1	TRUE	1	0.63	3		249	242	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92355092	92355092	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	10	207	0	ENST00000265734.4:c.385C>A	p.Leu129Ile	p.L129I	ENST00000265734	NM_001259.6	129	Ctt/Att	4/8	1	2	FACETS	0.181	0.123	0.255	0.181	0.123	0.255	SUBCLONAL	1	TRUE	1	0.63	2		207	175	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845609	151845609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369745886	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	66	576	1	ENST00000262189.6:c.13403C>T	p.Thr4468Met	p.T4468M	ENST00000262189	NM_170606.2	4468	aCg/aTg	52/59	1	2	FACETS	0.689	0.603	0.781	0.689	0.603	0.781	SUBCLONAL	1	TRUE	1	0.63	2		577	304	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271298	38271298	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	117	850	0	ENST00000425967.3:c.2410C>A	p.Leu804Met	p.L804M	ENST00000425967	NM_001174067.1	804	Ctg/Atg	19/19	1	2	FACETS	0.893	0.812	0.977	0.893	0.812	0.977	CLONAL	1	TRUE	1	0.63	2		850	416	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864735	68864735	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1459888665	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	137	550	1	ENST00000288368.4:c.106C>T	p.Arg36Trp	p.R36W	ENST00000288368	NM_024870.2	36	Cgg/Tgg	1/40	1	2	FACETS	0.88	0.806	0.957	0.88	0.806	0.957	CLONAL	1	TRUE	1	0.63	2		551	494	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759593	133759593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1476030646	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	187	806	0	ENST00000318560.5:c.1916G>A	p.Arg639Gln	p.R639Q	ENST00000318560	NM_005157.4	639	cGa/cAa	11/11	0.0964628597882073	0	FACETS	0.405	0.377	0.434			1	INDETERMINATE	1	TRUE	0	0.63	0		806	542	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314946	1314946	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754939213	NA	P-0043087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	50	472	0	ENST00000400841.2:c.715G>A	p.Ala239Thr	p.A239T	ENST00000400841		239	Gcc/Acc	6/6	0.3	2	FACETS	0.778	0.669	0.895	0.389	0.334	0.448	INDETERMINATE	1	TRUE	0	0.63	2		472	204	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	231	415	2	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.512313313478202	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.512313313478202	2		417	410	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	109	407	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.512313313478202	2		407	395	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822586	72822586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	161	653	4	ENST00000268489.5:c.9589del	p.Gln3197SerfsTer44	p.Q3197Sfs*44	ENST00000268489	NM_006885.3	3197	Cag/ag	10/10	1	2	FACETS	0.938	0.863	1	0.938	0.863	1	CLONAL	1	TRUE	1	0.512313313478202	2		657	670	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	136	399	1	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.819	0.756	0.883	1	0.99	1	CLONAL	2	TRUE	1	0.512313313478202	2		400	324	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	100	409	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.512313313478202	2		409	380	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641389	18641389	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1229278001	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	53	226	0	ENST00000266497.5:c.2393del	p.Asn798MetfsTer16	p.N798Mfs*16	ENST00000266497		796	ctA/ct	17/31	0.292580859336902	1	FACETS	0.709	0.612	0.812	0.709	0.612	0.812	INDETERMINATE	1	TRUE	0	0.512313313478202	1		226	217	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795103	242795104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768249210	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	251	1104	3	ENST00000334409.5:c.105dup	p.Thr36HisfsTer70	p.T36Hfs*70	ENST00000334409	NM_005018.2	35	-/C	2/5	1	2	FACETS	0.909	0.85	0.97	0.909	0.85	0.97	CLONAL	1	TRUE	1	0.512313313478202	2		1107	1078	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867540	35867541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs869312857	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	37	378	0	ENST00000303115.3:c.361dup	p.Ile121AsnfsTer8	p.I121Nfs*8	ENST00000303115	NM_002185.3	118	-/A	3/8	1	2	FACETS	0.412	0.34	0.491	0.412	0.34	0.491	SUBCLONAL	1	TRUE	1	0.512313313478202	2		378	351	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	160	559	11	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.512313313478202	2		570	602	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444659	78444659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs908264837	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	182	515	1	ENST00000370768.2:c.30del	p.Ser11LeufsTer43	p.S11Lfs*43	ENST00000370768	NM_003902.3	10	ccC/cc	1/20	1	2	FACETS	0.959	0.887	1	0.959	0.887	1	CLONAL	1	TRUE	1	0.512313313478202	2		516	741	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188297	10188297	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs869025653	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	92	649	0	ENST00000256474.2:c.444del	p.Phe148LeufsTer11	p.F148Lfs*11	ENST00000256474	NM_000551.3	147	aTt/at	2/3	0.512313313478202	2	FACETS	0.47	0.417	0.527	0.235	0.208	0.264	SUBCLONAL	1	TRUE	0	0.512313313478202	2		649	764	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481648	56481648	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs774589520	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	293	938	0	ENST00000267101.3:c.683A>G	p.His228Arg	p.H228R	ENST00000267101	NM_001982.3	228	cAt/cGt	6/28	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.512313313478202	2		938	1111	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610468	215610468	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	86	487	1	ENST00000260947.4:c.1788del	p.Lys596AsnfsTer9	p.K596Nfs*9	ENST00000260947	NM_000465.2	596	aaA/aa	8/11	1	2	FACETS	0.813	0.723	0.908	0.813	0.723	0.908	CLONAL	1	TRUE	1	0.512313313478202	2		488	413	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874013	151874013	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1248944002	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	37	569	3	ENST00000262189.6:c.8525del	p.Asn2842MetfsTer21	p.N2842Mfs*21	ENST00000262189	NM_170606.2	2842	aAt/at	38/59	1	2	FACETS	0.238	0.196	0.286	0.238	0.196	0.286	SUBCLONAL	1	TRUE	1	0.512313313478202	2		572	606	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837937	156837937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141021604	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	179	1093	3	ENST00000524377.1:c.470G>A	p.Arg157His	p.R157H	ENST00000524377	NM_002529.3	157	cGc/cAc	5/17	1	2	FACETS	0.585	0.538	0.634	0.585	0.538	0.634	SUBCLONAL	1	TRUE	1	0.512313313478202	2		1096	1195	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298519	11298519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748207893	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	45	727	1	ENST00000361445.4:c.1942G>A	p.Ala648Thr	p.A648T	ENST00000361445	NM_004958.3	648	Gca/Aca	12/58	1	2	FACETS	0.21	0.176	0.249	0.21	0.176	0.249	SUBCLONAL	1	TRUE	1	0.512313313478202	2		728	835	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682968	241682968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1194889415	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	217	678	0	ENST00000366560.3:c.55G>A	p.Ala19Thr	p.A19T	ENST00000366560	NM_000143.3	19	Gcc/Acc	1/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.512313313478202	2		678	814	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121662	108121663	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	151	606	0	ENST00000278616.4:c.1471dup	p.Thr491AsnfsTer8	p.T491Nfs*8	ENST00000278616	NM_000051.3	490	-/A	10/63	1	2	FACETS	0.966	0.887	1	0.966	0.887	1	CLONAL	1	TRUE	1	0.512313313478202	2		606	610	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427266	49427271	+	inframe_deletion	In_Frame_Del	DEL	TGCTGC	TGCTGC	-	rs398123707	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	45	816	0	ENST00000301067.7:c.11217_11222del	p.Gln3744_Gln3745del	p.Q3744_Q3745del	ENST00000301067	NM_003482.3	3739	caGCAGCAa/caa	39/54	1	2	FACETS	0.198	0.165	0.234	0.198	0.165	0.234	SUBCLONAL	1	TRUE	1	0.512313313478202	2		816	889	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434351	121434351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	213	848	0	ENST00000257555.6:c.1115C>T	p.Ala372Val	p.A372V	ENST00000257555		372	gCa/gTa	6/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.512313313478202	2		848	789	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986946	36986946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	258	860	0	ENST00000354822.5:c.743G>A	p.Arg248His	p.R248H	ENST00000354822	NM_001079668.2	248	cGc/cAc	3/3	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.512313313478202	2		860	997	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988527	41988527	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs765529103	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	59	651	0	ENST00000219905.7:c.1319A>G	p.His440Arg	p.H440R	ENST00000219905	NM_001164273.1	440	cAt/cGt	3/24	1	2	FACETS	0.317	0.272	0.366	0.317	0.272	0.366	SUBCLONAL	1	TRUE	1	0.512313313478202	2		651	726	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457690	67457690	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	49	792	0	ENST00000327367.4:c.500C>A	p.Pro167His	p.P167H	ENST00000327367	NM_005902.3	167	cCc/cAc	3/9	1	2	FACETS	0.222	0.187	0.261	0.222	0.187	0.261	SUBCLONAL	1	TRUE	1	0.512313313478202	2		792	860	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90645538	90645538	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	11	134	0	ENST00000330062.3:c.85C>A	p.Pro29Thr	p.P29T	ENST00000330062	NM_002168.2	29	Ccc/Acc	1/11	1	2	FACETS	0.23	0.158	0.318	0.23	0.158	0.318	SUBCLONAL	1	TRUE	1	0.512313313478202	2		134	187	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441439	40441439	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	194	652	0	ENST00000345506.4:c.10T>G	p.Trp4Gly	p.W4G	ENST00000345506	NM_003152.3	4	Tgg/Ggg	3/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.512313313478202	2		652	734	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554737	63554737	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1166564286	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	33	509	0	ENST00000307078.5:c.2T>C	p.Met1?	p.M1?	ENST00000307078	NM_004655.3	1	aTg/aCg	2/11	1	2	FACETS	0.237	0.193	0.288	0.237	0.193	0.288	SUBCLONAL	1	TRUE	1	0.512313313478202	2		509	543	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724354	52724354	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	200	619	1	ENST00000322088.6:c.1486C>A	p.Leu496Met	p.L496M	ENST00000322088	NM_014225.5	496	Ctg/Atg	12/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.512313313478202	2		620	725	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277897	41278261	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTGCTCAGGACAAGGAAGCTGCAGAAGCTATTGAAGCTGAGGGAGCCACAGCTCCTCTGACAGAGTTACTTCACTCTAGGAATGAAGGTGTGGGTAAGTAAAAAGGAACCAAAGCCTTTAGCAGATGTGTACATTGAAGTCTCAGTTTTTCCTCAAGGGCCTTTTTCTCCTTGTCTCTTAGCGACATATGCAGCTGCTGTTTTGTTCCGAATGTCTGAGGACAAGCCACAAGATTACAAGAAACGGCTTTCAGTTGAGCTGACCAGCTCTCTCTTCAGAACAGAGCCAATGGCTTGGAATGAGGTAGGGAAATGTGAGCAGTTATTTATCTGGTAGTTTCCTAGAGCAGGTATGGCAGCTTGTT	CTTGCTCAGGACAAGGAAGCTGCAGAAGCTATTGAAGCTGAGGGAGCCACAGCTCCTCTGACAGAGTTACTTCACTCTAGGAATGAAGGTGTGGGTAAGTAAAAAGGAACCAAAGCCTTTAGCAGATGTGTACATTGAAGTCTCAGTTTTTCCTCAAGGGCCTTTTTCTCCTTGTCTCTTAGCGACATATGCAGCTGCTGTTTTGTTCCGAATGTCTGAGGACAAGCCACAAGATTACAAGAAACGGCTTTCAGTTGAGCTGACCAGCTCTCTCTTCAGAACAGAGCCAATGGCTTGGAATGAGGTAGGGAAATGTGAGCAGTTATTTATCTGGTAGTTTCCTAGAGCAGGTATGGCAGCTTGTT	-	novel	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	115	498	0	ENST00000349496.5:c.1864_2076+64del		p.X622_splice	ENST00000349496	NM_001904.3	622		12-13/15	0.512313313478202	2	FACETS	1	0.981	1	0.656	0.598	0.716	CLONAL	1	TRUE	0	0.512313313478202	2		498	342	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499414	89499414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	154	572	0	ENST00000336596.2:c.2584C>T	p.Gln862Ter	p.Q862*	ENST00000336596	NM_005233.5	862	Cag/Tag	15/17	1	2	FACETS	0.944	0.867	1	0.944	0.867	1	CLONAL	1	TRUE	1	0.512313313478202	2		572	637	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	150	835	0	ENST00000295797.4:c.825_826dup	p.Thr276LysfsTer8	p.T276Kfs*8	ENST00000295797	NM_002740.5	273	tta/ttAAa	9/18	1	2	FACETS	0.69	0.63	0.752	0.69	0.63	0.752	SUBCLONAL	1	TRUE	1	0.512313313478202	2		835	849	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182681712	182681712	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	40	614	0	ENST00000292782.4:c.346G>A	p.Glu116Lys	p.E116K	ENST00000292782	NM_020640.2	116	Gag/Aag	3/7	1	2	FACETS	0.197	0.163	0.236	0.197	0.163	0.236	SUBCLONAL	1	TRUE	1	0.512313313478202	2		614	791	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198088	185198088	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	164	513	0	ENST00000265026.3:c.2570A>G	p.Asp857Gly	p.D857G	ENST00000265026	NM_004721.4	857	gAt/gGt	13/14	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.512313313478202	2		513	621	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1956903	1956903	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	288	944	0	ENST00000382891.5:c.2354G>A	p.Cys785Tyr	p.C785Y	ENST00000382891	NM_133335.3	785	tGt/tAt	13/22	1	2	FACETS	0.959	0.902	1	0.959	0.902	1	CLONAL	1	TRUE	1	0.512313313478202	2		944	1172	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143324111	143324111	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	17	306	0	ENST00000262992.4:c.352A>G	p.Lys118Glu	p.K118E	ENST00000262992	NM_001101669.1	118	Aag/Gag	5/24	1	2	FACETS	0.215	0.16	0.28	0.215	0.16	0.28	SUBCLONAL	1	TRUE	1	0.512313313478202	2		306	309	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332463	153332463	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	105	381	0	ENST00000281708.4:c.493del	p.Thr165GlnfsTer4	p.T165Qfs*4	ENST00000281708	NM_033632.3	165	Aca/ca	2/12	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.512313313478202	2		381	397	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13949263	13949264	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	15	305	0	ENST00000405192.2:c.864dup	p.Phe289IlefsTer36	p.F289Ifs*36	ENST00000405192	NM_001163147.1	288	-/A	9/12	1	2	FACETS	0.214	0.156	0.284	0.214	0.156	0.284	SUBCLONAL	1	TRUE	1	0.512313313478202	2		305	273	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336674	81336674	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	42	313	0	ENST00000222390.5:c.1548A>C	p.Lys516Asn	p.K516N	ENST00000222390	NM_000601.4	516	aaA/aaC	14/18	1	2	FACETS	0.785	0.662	0.917	0.785	0.662	0.917	CLONAL	1	TRUE	1	0.512313313478202	2		313	209	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392083	81392083	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	59	395	0	ENST00000222390.5:c.194A>G	p.Asn65Ser	p.N65S	ENST00000222390	NM_000601.4	65	aAt/aGt	2/18	1	2	FACETS	0.9	0.782	1	0.9	0.782	1	CLONAL	1	TRUE	1	0.512313313478202	2		395	256	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995615	68995615	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	100	557	0	ENST00000288368.4:c.2019G>T	p.Lys673Asn	p.K673N	ENST00000288368	NM_024870.2	673	aaG/aaT	18/40	0.512313313478202	4	FACETS	0.77	0.687	0.857	0.257	0.229	0.286	SUBCLONAL	1	TRUE	1	0.512313313478202	4		557	767	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739078	145739078	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1371868658	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	241	600	2	ENST00000428558.2:c.2077C>T	p.Gln693Ter	p.Q693*	ENST00000428558	NM_004260.3	693	Caa/Taa	13/22	0.512313313478202	4	FACETS	1	0.982	1	0.382	0.356	0.409	CLONAL	1	TRUE	1	0.512313313478202	4		602	1242	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391737	139391737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs116317506	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	284	1078	0	ENST00000277541.6:c.6454G>A	p.Gly2152Ser	p.G2152S	ENST00000277541	NM_017617.3	2152	Ggc/Agc	34/34	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.512313313478202	2		1078	1106	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652344	48652344	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	309	1231	2	ENST00000376670.3:c.1019del	p.Gly340AlafsTer14	p.G340Afs*14	ENST00000376670	NM_002049.3	339	Ggg/gg	6/6	1	2	FACETS	0.983	0.926	1	0.983	0.926	1	CLONAL	1	TRUE	1	0.512313313478202	2		1233	1227	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412124	63412124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	288	1085	0	ENST00000330258.3:c.1043G>A	p.Gly348Asp	p.G348D	ENST00000330258	NM_152424.3	348	gGc/gAc	2/2	1	2	FACETS	0.992	0.933	1	0.992	0.933	1	CLONAL	1	TRUE	1	0.512313313478202	2		1085	1133	SUCCESS
AR	367	MSKCC	GRCh37	X	66766042	66766042	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1362091565	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	94	1086	1	ENST00000374690.3:c.1054G>A	p.Ala352Thr	p.A352T	ENST00000374690	NM_000044.3	352	Gca/Aca	1/8	1	2	FACETS	0.322	0.285	0.361	0.322	0.285	0.361	SUBCLONAL	1	TRUE	1	0.512313313478202	2		1087	1141	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164850	123164850	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	19	360	0	ENST00000218089.9:c.163A>G	p.Lys55Glu	p.K55E	ENST00000218089	NM_001042749.1	55	Aaa/Gaa	5/35	1	2	FACETS	0.196	0.148	0.253	0.196	0.148	0.253	SUBCLONAL	1	TRUE	1	0.512313313478202	2		360	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0043157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	72	608	1	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	1	2	FACETS	0.97	0.847	1	0.97	0.847	1	CLONAL	1	TRUE	1	0.22	2		609	675	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0043158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	23	350	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.331	0.257	0.417	0.331	0.257	0.417	SUBCLONAL	1	TRUE	1	0.314364659485621	2		350	442	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	223682	223682	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs369321221	NA	P-0043159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	132	395	0	ENST00000264932.6:c.149C>T	p.Ser50Phe	p.S50F	ENST00000264932	NM_004168.2	50	tCc/tTc	2/15	1	2	FACETS	0.915	0.835	0.999	0.915	0.835	0.999	CLONAL	1	TRUE	1	0.549332791032788	2		395	525	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073913	8073913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	137	458	0	ENST00000377482.5:c.746C>T	p.Ser249Phe	p.S249F	ENST00000377482	NM_018948.3	249	tCt/tTt	4/4	1	2	FACETS	0.915	0.837	0.997	0.915	0.837	0.997	CLONAL	1	TRUE	1	0.549332791032788	2		458	545	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612977	228612977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151071964	NA	P-0043159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	130	477	0	ENST00000366696.1:c.50C>T	p.Pro17Leu	p.P17L	ENST00000366696	NM_003493.2	17	cCg/cTg	1/1	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.549332791032788	2		477	467	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416195	416195	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	108	413	0	ENST00000399788.2:c.3991T>G	p.Ser1331Ala	p.S1331A	ENST00000399788	NM_001042603.1	1331	Tct/Gct	24/28	NA	2	FACETS	0.746	0.672	0.824			1	INDETERMINATE	1	TRUE	NA	0.549332791032788	2		413	527	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0043184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	61	520	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.15	2		520	777	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0043184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	50	677	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.683	0.577	0.8	0.683	0.577	0.8	SUBCLONAL	1	TRUE	1	0.15	2		680	976	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427428	427428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373590748	NA	P-0043226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	82	563	0	ENST00000399788.2:c.2741C>T	p.Pro914Leu	p.P914L	ENST00000399788	NM_001042603.1	914	cCg/cTg	19/28	0.379047189160001	3	FACETS	0.514	0.452	0.58			1	SUBCLONAL	1	TRUE	NA	0.449398027709848	3		563	870	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260139	10260140	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0043226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	182	565	0	ENST00000340748.4:c.2527_2528del	p.Trp843GlyfsTer27	p.W843Gfs*27	ENST00000340748		843	TGg/g	25/40	0.386469239119374	3	FACETS	1	0.977	1	0.573	0.529	0.619	CLONAL	1	TRUE	1	0.449398027709848	3		565	865	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478235	99478236	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTC	novel	NA	P-0043226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	253	369	0	ENST00000268035.6:c.3141_3143dup	p.Leu1048dup	p.L1048dup	ENST00000268035	NM_000875.3	1048	ttt/tTTCtt	16/21	0.449398027709848	3	FACETS	0.972	0.922	1	0.972	0.922	1	CLONAL	3	TRUE	0	0.449398027709848	3		369	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0043254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	489	530	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.61732240640962	2		530	748	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0043254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	65	311	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.789	0.691	0.892	0.789	0.691	0.892	SUBCLONAL	1	TRUE	1	0.61732240640962	2		311	267	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0043254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	112	340	1	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.9	0.816	0.988	0.9	0.816	0.988	CLONAL	1	TRUE	1	0.61732240640962	2		341	403	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46602969	46602969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs574490008	NA	P-0043254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	454	670	0	ENST00000263734.3:c.1027G>A	p.Val343Ile	p.V343I	ENST00000263734	NM_001430.4	343	Gtc/Atc	8/16	0.313599704014	3	FACETS	0.961	0.922	1	0.961	0.922	1	INDETERMINATE	2	TRUE	1	0.61732240640962	3		670	1001	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652035	36652035	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	537	1048	0	ENST00000244741.5:c.159del	p.Phe53LeufsTer95	p.F53Lfs*95	ENST00000244741	NM_000389.4	53	Ttt/tt	2/3	0.673842036213184	2	FACETS	0.986	0.956	1	0.986	0.956	1	CLONAL	2	TRUE	0	0.678252608909062	2		1048	803	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288750	33288751	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0043324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	416	702	0	ENST00000374542.5:c.801_802insC	p.Asn268GlnfsTer5	p.N268Qfs*5	ENST00000374542	NM_001141970.1	267	-/C	3/8	0.673842036213184	2	FACETS	0.986	0.952	1	0.986	0.952	1	CLONAL	2	TRUE	0	0.678252608909062	2		702	622	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	48	300	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.793	0.671	0.926	0.793	0.671	0.926	CLONAL	1	TRUE	1	0.274636476182264	2		300	441	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0043338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	78	475	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.924	0.812	1	0.924	0.812	1	CLONAL	1	TRUE	1	0.274636476182264	2		475	615	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0043338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	50	535	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.535	0.453	0.625	0.535	0.453	0.625	SUBCLONAL	1	TRUE	1	0.274636476182264	2		535	681	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0043338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	95	534	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.864	0.768	0.965	0.864	0.768	0.965	CLONAL	1	TRUE	1	0.274636476182264	2		535	801	SUCCESS
APC	324	MSKCC	GRCh37	5	112175761	112175761	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	43	370	0	ENST00000257430.4:c.4473del	p.Phe1491LeufsTer16	p.F1491Lfs*16	ENST00000257430	NM_000038.5	1490	caT/ca	16/16	0.274636476182264	1	FACETS	0.624	0.522	0.736	0.624	0.522	0.736	SUBCLONAL	1	TRUE	0	0.274636476182264	1		370	433	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711915	89711915	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786204866	NA	P-0043338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	91	509	0	ENST00000371953.3:c.533A>G	p.Tyr178Cys	p.Y178C	ENST00000371953	NM_000314.4	178	tAt/tGt	6/9	0.274636476182264	1	FACETS	0.853	0.758	0.955	0.853	0.758	0.955	CLONAL	1	TRUE	0	0.274636476182264	1		509	670	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967309	134967309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs186851943	NA	P-0043338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	76	606	0	ENST00000398015.3:c.2648G>A	p.Arg883Gln	p.R883Q	ENST00000398015	NM_004441.4	883	cGg/cAg	14/16	1	2	FACETS	0.685	0.6	0.777	0.685	0.6	0.777	SUBCLONAL	1	TRUE	1	0.274636476182264	2		606	808	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522740	67522741	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	54	361	0	ENST00000274335.5:c.244dup	p.Ile82AsnfsTer24	p.I82Nfs*24	ENST00000274335		79	-/A	1/15	1	2	FACETS	0.874	0.748	1	0.874	0.748	1	CLONAL	1	TRUE	1	0.274636476182264	2		361	450	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915579	131915579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28903087	NA	P-0043338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	29	279	0	ENST00000265335.6:c.577C>T	p.Arg193Trp	p.R193W	ENST00000265335		193	Cgg/Tgg	5/25	0.274636476182264	1	FACETS	0.63	0.507	0.77	0.63	0.507	0.77	SUBCLONAL	1	TRUE	0	0.274636476182264	1		279	289	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875055	151875055	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	65	189	0	ENST00000262189.6:c.7483C>T	p.Gln2495Ter	p.Q2495*	ENST00000262189	NM_170606.2	2495	Caa/Taa	38/59	0.22447129683705	3	FACETS	0.841	0.735	0.955	0.841	0.735	0.955	CLONAL	2	TRUE	1	0.274636476182264	3		189	320	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262154	16262154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761478249	NA	P-0043338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	26	309	0	ENST00000375759.3:c.9419C>T	p.Pro3140Leu	p.P3140L	ENST00000375759	NM_015001.2	3140	cCg/cTg	11/15	1	2	FACETS	0.501	0.396	0.621	0.501	0.396	0.621	SUBCLONAL	1	TRUE	1	0.274636476182264	2		309	378	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692949	89692949	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	36	671	0	ENST00000371953.3:c.433T>A	p.Phe145Ile	p.F145I	ENST00000371953	NM_000314.4	145	Ttt/Att	5/9	0.274636476182264	1	FACETS	0.332	0.272	0.399	0.332	0.272	0.399	SUBCLONAL	1	TRUE	0	0.274636476182264	1		671	682	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758319	41758319	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	100	661	0	ENST00000301178.4:c.1775T>C	p.Phe592Ser	p.F592S	ENST00000301178	NM_021913.4	592	tTt/tCt	15/20	0.274636476182264	3	FACETS	0.837	0.747	0.935	0.419	0.373	0.468	CLONAL	1	TRUE	1	0.274636476182264	3		661	989	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441268	52441268	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	79	568	0	ENST00000460680.1:c.502T>C	p.Phe168Leu	p.F168L	ENST00000460680	NM_004656.3	168	Ttc/Ctc	7/17	1	2	FACETS	0.781	0.686	0.882	0.781	0.686	0.882	SUBCLONAL	1	TRUE	1	0.274636476182264	2		568	737	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374844	149374844	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	58	347	0	ENST00000360632.3:c.250C>A	p.His84Asn	p.H84N	ENST00000360632	NM_015472.4	84	Cat/Aat	2/7	1	2	FACETS	0.985	0.848	1	0.985	0.848	1	CLONAL	1	TRUE	1	0.274636476182264	2		347	429	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342361	70342361	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	96	591	0	ENST00000374080.3:c.1252C>T	p.Arg418Cys	p.R418C	ENST00000374080		418	Cgt/Tgt	9/45	1	2	FACETS	0.832	0.741	0.93	0.832	0.741	0.93	CLONAL	1	TRUE	1	0.274636476182264	2		591	840	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0043346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	607	425	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.475472190051336	6	FACETS	1	0.987	1	1	0.987	1	CLONAL	4	TRUE	2	0.475472190051336	6		426	1197	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0043346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	271	664	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.362576119846984	2	FACETS	1	0.993	1	0.722	0.68	0.765	CLONAL	1	TRUE	0	0.475472190051336	2		664	789	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170531	11170531	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	264	649	0	ENST00000358026.2:c.4834G>T	p.Glu1612Ter	p.E1612*	ENST00000358026	NM_001128849.1	1612	Gag/Tag	34/36	0.362576119846984	2	FACETS	1	0.993	1	0.716	0.674	0.759	CLONAL	1	TRUE	0	0.475472190051336	2		649	775	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0043361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	35	283	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.748	0.617	0.892	0.748	0.617	0.892	SUBCLONAL	1	TRUE	1	0.403523064071394	2		283	232	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0043361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	139	449	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	0.401719925132125	3	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	1	0.403523064071394	3		449	410	SUCCESS
APC	324	MSKCC	GRCh37	5	112175417	112175418	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	rs1554085533	NA	P-0043361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	52	260	0	ENST00000257430.4:c.4127_4128del	p.Tyr1376CysfsTer9	p.Y1376Cfs*9	ENST00000257430	NM_000038.5	1376	TAt/t	16/16	1	2	FACETS	0.859	0.736	0.992	0.859	0.736	0.992	CLONAL	1	TRUE	1	0.403523064071394	2		260	300	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041074	42041074	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	200	586	0	ENST00000219905.7:c.5452C>T	p.Arg1818Ter	p.R1818*	ENST00000219905	NM_001164273.1	1818	Cga/Tga	16/24	0.401719925132125	3	FACETS	0.976	0.91	1	0.976	0.91	1	CLONAL	2	TRUE	1	0.403523064071394	3		586	610	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236086	108236086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782292	NA	P-0043361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	72	457	0	ENST00000278616.4:c.9022C>T	p.Arg3008Cys	p.R3008C	ENST00000278616	NM_000051.3	3008	Cgt/Tgt	63/63	0.401719925132125	3	FACETS	0.962	0.843	1	0.481	0.421	0.544	CLONAL	1	TRUE	1	0.403523064071394	3		457	446	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172509	108172510	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	48	236	1	ENST00000278616.4:c.5318dup	p.Phe1774ValfsTer8	p.F1774Vfs*8	ENST00000278616	NM_000051.3	1771	aga/agAa	35/63	0.401719925132125	3	FACETS	0.916	0.79	1	0.916	0.79	1	CLONAL	2	TRUE	1	0.403523064071394	3		237	156	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0043364-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	478	863	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.590574370361463	2	FACETS	0.965	0.93	0.999	0.965	0.93	0.999	CLONAL	2	TRUE	0	0.590574370361463	2		863	839	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0043364-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	17	210	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.56648601849553	3	FACETS	0.811	0.615	1	0.405	0.307	0.517	CLONAL	1	TRUE	1	0.590574370361463	3		210	92	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0043364-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	205	260	3	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.56563139746451	3	FACETS	0.866	0.82	0.912	0.866	0.82	0.912	CLONAL	3	TRUE	0	0.590574370361463	3		263	346	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672177	30672177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762832250	NA	P-0043364-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	253	980	2	ENST00000376406.3:c.4783C>T	p.Arg1595Trp	p.R1595W	ENST00000376406	NM_014641.2	1595	Cgg/Tgg	10/15	0.59059404649947	3	FACETS	1	0.942	1	0.504	0.471	0.537	CLONAL	1	TRUE	1	0.590574370361463	3		982	1102	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110332	3110332	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0043364-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	586	787	1	ENST00000078429.4:c.321+1G>A		p.X107_splice	ENST00000078429	NM_002067.2	107			0.57867442296675	3	FACETS	0.953	0.925	0.981	0.953	0.925	0.981	CLONAL	3	TRUE	0	0.590574370361463	3		788	899	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729442	41729442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043364-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	219	834	0	ENST00000242208.4:c.1087G>A	p.Gly363Arg	p.G363R	ENST00000242208	NM_002192.2	363	Ggg/Agg	3/3	0.576465887188399	4	FACETS	0.925	0.859	0.994	0.308	0.286	0.332	CLONAL	1	TRUE	1	0.590574370361463	4		834	1275	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0043393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	162	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.869028122404656	3	FACETS	0.949	0.876	1	0.475	0.438	0.513	CLONAL	1	TRUE	1	0.883354394880575	3		336	557	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0043393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	180	261	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.546489989454446	1	FACETS	0.729	0.687	0.771	0.729	0.687	0.771	SUBCLONAL	1	TRUE	0	0.883354394880575	1		261	312	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344165	70344165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355367439	NA	P-0043393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	366	275	1	ENST00000374080.3:c.1901C>T	p.Pro634Leu	p.P634L	ENST00000374080		634	cCc/cTc	13/45	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.883354394880575	1		276	437	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0043393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	388	365	1				ENST00000310581	NM_198253.2	-/1132			0.476016392835629	3	FACETS	0.852	0.817	0.888	0.852	0.817	0.888	INDETERMINATE	2	TRUE	1	0.883354394880575	3		366	743	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933481	100933481	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs1209629034	NA	P-0043393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	54	205	0	ENST00000325455.5:c.1909C>T	p.Arg637Ter	p.R637*	ENST00000325455	NM_001202474.3	637	Cga/Tga	4/8	0.495408948577427	1	FACETS	0.336	0.291	0.384	0.336	0.291	0.384	INDETERMINATE	1	TRUE	0	0.883354394880575	1		205	203	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56171046	56171046	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	229	283	0	ENST00000399503.3:c.1874C>G	p.Thr625Ser	p.T625S	ENST00000399503	NM_005921.1	625	aCc/aGc	10/20	0.495408948577427	1	FACETS	0.797	0.759	0.835	0.797	0.759	0.835	INDETERMINATE	1	TRUE	0	0.883354394880575	1		283	363	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259436	55259436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745812480	NA	P-0043393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	279	403	0	ENST00000275493.2:c.2494C>T	p.Arg832Cys	p.R832C	ENST00000275493	NM_005228.3	832	Cgc/Tgc	21/28	1	2	FACETS	0.936	0.885	0.987	0.936	0.885	0.987	CLONAL	1	TRUE	1	0.883354394880575	2		403	675	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738406	145738406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774850992	NA	P-0043393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1992	241	712	1	ENST00000428558.2:c.2579C>T	p.Pro860Leu	p.P860L	ENST00000428558	NM_004260.3	860	cCg/cTg	16/22	0.740812984861023	5	FACETS	0.568	0.528	0.61	0.142	0.132	0.153	SUBCLONAL	1	TRUE	1	0.883354394880575	5		713	2233	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8339047	8339047	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	190	359	0	ENST00000356435.5:c.5254G>A	p.Glu1752Lys	p.E1752K	ENST00000356435		1752	Gag/Aag	32/35	0.546489989454446	1	FACETS	0.713	0.672	0.753	0.713	0.672	0.753	SUBCLONAL	1	TRUE	0	0.883354394880575	1		359	337	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249002	55249003	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGTGGA	rs397517109	NA	P-0043480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	99	527	0	ENST00000275493.2:c.2303_2311dup	p.Ser768_Asp770dup	p.S768_D770dup	ENST00000275493	NM_005228.3	768	gcc/gcCAGCGTGGAc	20/28	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		527	557	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	167	300	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.480116603631908	2		300	557	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074060	8074060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	97	396	0	ENST00000377482.5:c.599G>A	p.Ser200Asn	p.S200N	ENST00000377482	NM_018948.3	200	aGc/aAc	4/4	0.429190459347607	1	FACETS	0.742	0.666	0.822	0.742	0.666	0.822	SUBCLONAL	1	TRUE	0	0.480116603631908	1		396	414	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903759	114903759	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	99	493	0	ENST00000543371.1:c.763C>A	p.His255Asn	p.H255N	ENST00000543371	NM_001198531.1	255	Cat/Aat	7/14	0.480116603631908	1	FACETS	0.474	0.423	0.528	0.474	0.423	0.528	SUBCLONAL	1	TRUE	0	0.480116603631908	1		493	661	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201936	67201936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1325203087	NA	P-0043513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	294	659	0	ENST00000312629.5:c.1136G>A	p.Ser379Asn	p.S379N	ENST00000312629	NM_003952.2	379	aGt/aAt	13/15	0.480116603631908	6	FACETS	1	0.99	1	0.494	0.465	0.523	CLONAL	2	TRUE	1	0.480116603631908	6		659	972	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216543	108216543	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	80	306	0	ENST00000278616.4:c.8492T>C	p.Phe2831Ser	p.F2831S	ENST00000278616	NM_000051.3	2831	tTc/tCc	58/63	0.480116603631908	1	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	0	0.480116603631908	1		306	251	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478860	56478860	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs757425458	NA	P-0043513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	265	797	1	ENST00000267101.3:c.316C>T	p.Arg106Ter	p.R106*	ENST00000267101	NM_001982.3	106	Cga/Tga	3/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.480116603631908	2		798	1017	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888285	112888285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	111	435	0	ENST00000351677.2:c.301C>T	p.Pro101Ser	p.P101S	ENST00000351677	NM_002834.3	101	Cct/Tct	3/16	1	2	FACETS	0.912	0.824	1	0.912	0.824	1	CLONAL	1	TRUE	1	0.480116603631908	2		435	507	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543327	65543327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	257	621	0	ENST00000358664.4:c.350C>T	p.Ser117Phe	p.S117F	ENST00000358664	NM_002382.4	117	tCc/tTc	5/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.480116603631908	2		621	958	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347732	347732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	256	602	0	ENST00000262320.3:c.1774C>T	p.Leu592Phe	p.L592F	ENST00000262320	NM_003502.3	592	Ctc/Ttc	6/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.480116603631908	2		602	933	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032377	10032377	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	163	417	0	ENST00000330684.3:c.446C>G	p.Ala149Gly	p.A149G	ENST00000330684	NM_001134407.1	149	gCg/gGg	3/13	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.480116603631908	2		417	557	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527439	29527439	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs587781517	NA	P-0043513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	112	348	0	ENST00000356175.3:c.889-1G>A		p.X297_splice	ENST00000356175	NM_000267.3	297			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.480116603631908	2		348	397	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665053	29665053	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691093	NA	P-0043513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	120	473	0	ENST00000356175.3:c.6652C>T	p.Gln2218Ter	p.Q2218*	ENST00000356175	NM_000267.3	2218	Caa/Taa	44/57	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.480116603631908	2		473	453	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162245	47162246	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0043513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	90	445	1	ENST00000409792.3:c.3880_3881delinsAA	p.Gly1294Asn	p.G1294N	ENST00000409792	NM_014159.6	1294	GGt/AAt	3/21	1	2	FACETS	0.705	0.627	0.787	0.705	0.627	0.787	SUBCLONAL	1	TRUE	1	0.480116603631908	2		446	532	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268179	153268179	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	120	305	1	ENST00000281708.4:c.629G>A	p.Gly210Glu	p.G210E	ENST00000281708	NM_033632.3	210	gGg/gAg	4/12	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.480116603631908	2		306	462	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876520	35876520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	203	525	1	ENST00000303115.3:c.1312C>T	p.Leu438Phe	p.L438F	ENST00000303115	NM_002185.3	438	Ctt/Ttt	8/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.480116603631908	2		526	683	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682673	86682673	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	45	198	0	ENST00000274376.6:c.2878A>C	p.Ile960Leu	p.I960L	ENST00000274376	NM_002890.2	960	Atc/Ctc	23/25	1	2	FACETS	0.86	0.73	1	0.86	0.73	1	CLONAL	1	TRUE	1	0.480116603631908	2		198	218	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971121	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0043513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	220	512	0	ENST00000304494.5:c.237_238delinsTT	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	79	acCCga/acTTga	2/3	0.480116603631908	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.480116603631908	1		512	558	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923002	39923002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	254	653	1	ENST00000378444.4:c.3706G>A	p.Glu1236Lys	p.E1236K	ENST00000378444	NM_001123385.1	1236	Gaa/Aaa	8/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.480116603631908	2		654	924	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412002	63412002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	224	760	0	ENST00000330258.3:c.1165G>A	p.Glu389Lys	p.E389K	ENST00000330258	NM_152424.3	389	Gaa/Aaa	2/2	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.480116603631908	2		760	743	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0043532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	23	260	3	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.797	0.628	0.989	0.797	0.628	0.989	CLONAL	1	TRUE	1	0.374734138443326	2		263	154	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0043532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	187	582	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.281022545174778	1	FACETS	0.926	0.856	0.998	0.926	0.856	0.998	CLONAL	1	TRUE	0	0.374734138443326	1		582	876	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0043532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	17	160	1	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.357499846806858	1	FACETS	0.664	0.502	0.851	0.664	0.502	0.851	SUBCLONAL	1	TRUE	0	0.374734138443326	1		161	111	SUCCESS
APC	324	MSKCC	GRCh37	5	112175749	112175756	+	frameshift_variant	Frame_Shift_Del	DEL	TACTTTAT	TACTTTAT	-	novel	NA	P-0043532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	13	190	0	ENST00000257430.4:c.4461_4468del	p.Leu1488PhefsTer23	p.L1488Ffs*23	ENST00000257430	NM_000038.5	1486	gaTACTTTATta/gata	16/16	0.357499846806858	1	FACETS	0.286	0.204	0.386	0.286	0.204	0.386	SUBCLONAL	1	TRUE	0	0.374734138443326	1		190	197	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47735855	47735855	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	157	499	1	ENST00000449228.1:c.5A>T	p.Lys2Ile	p.K2I	ENST00000449228	NM_001127240.2	2	aAa/aTa	1/4	1	2	FACETS	0.907	0.83	0.987	0.907	0.83	0.987	CLONAL	1	TRUE	1	0.374734138443326	2		500	924	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172194	38172195	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0043532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	70	233	0	ENST00000317025.8:c.2212_2213del	p.Ser738GlnfsTer8	p.S738Qfs*8	ENST00000317025	NM_023034.1	738	AGc/c	12/24	0.31527533266284	4	FACETS	0.764	0.671	0.863			1	SUBCLONAL	2	TRUE	NA	0.374734138443326	4		233	336	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172997	38173013	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCACATCAGAAACGT	CTGCACATCAGAAACGT	-	novel	NA	P-0043532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	83	321	0	ENST00000317025.8:c.2036_2052del	p.Asp679ValfsTer15	p.D679Vfs*15	ENST00000317025	NM_023034.1	679	gACGTTTCTGATGTGCAG/g	11/24	0.31527533266284	4	FACETS	0.775	0.688	0.867			1	SUBCLONAL	2	TRUE	NA	0.374734138443326	4		321	393	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258658	16258658	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371899876	NA	P-0043577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	266	598	0	ENST00000375759.3:c.5923C>T	p.Leu1975Phe	p.L1975F	ENST00000375759	NM_015001.2	1975	Ctc/Ttc	11/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		598	871	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0043587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	696	658	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.732114092635385	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.732114092635385	2		658	949	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552810	226552810	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1486968445	NA	P-0043587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	185	541	0	ENST00000366794.5:c.2551T>A	p.Phe851Ile	p.F851I	ENST00000366794	NM_001618.3	851	Ttt/Att	19/23	0.639923986691086	3	FACETS	0.796	0.736	0.859	0.398	0.368	0.43	SUBCLONAL	1	TRUE	1	0.732114092635385	3		541	867	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131434	202131438	+	frameshift_variant	Frame_Shift_Del	DEL	GATTA	GATTA	-	novel	NA	P-0043587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	136	428	0	ENST00000358485.4:c.402_406del	p.Ile135LeufsTer5	p.I135Lfs*5	ENST00000358485	NM_001080125.1	134	ctGATTAcc/ctcc	2/9	0.732114092635385	3	FACETS	0.766	0.698	0.836	0.383	0.349	0.418	SUBCLONAL	1	TRUE	1	0.732114092635385	3		428	663	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0043591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	497	407	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.709026967203279	3	FACETS	0.927	0.9	0.952	0.927	0.9	0.952	CLONAL	3	TRUE	0	0.709026967203279	3		407	683	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061240	38061240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	248	567	0	ENST00000250448.2:c.749C>T	p.Ser250Phe	p.S250F	ENST00000250448	NM_004496.3	250	tCc/tTc	2/2	0.125657451983172	3	FACETS	1	0.991	1	0.645	0.606	0.686	INDETERMINATE	1	TRUE	1	0.709026967203279	3		567	734	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0043591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	595	633	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.676692134840609	2	FACETS	0.995	0.969	1	0.995	0.969	1	CLONAL	2	TRUE	0	0.709026967203279	2		633	843	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61753649	61753649	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	85	321	0	ENST00000401558.2:c.134T>A	p.Met45Lys	p.M45K	ENST00000401558	NM_003400.3	45	aTg/aAg	3/25	0.280463974690901	3	FACETS	0.594	0.526	0.666	0.198	0.175	0.222	INDETERMINATE	1	TRUE	0	0.709026967203279	3		321	547	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168490	56168491	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	270	282	0	ENST00000399503.3:c.1447dup	p.Arg483LysfsTer10	p.R483Kfs*10	ENST00000399503	NM_005921.1	482	-/A	8/20	0.676692134840609	2	FACETS	0.967	0.927	1	0.967	0.927	1	CLONAL	2	TRUE	0	0.709026967203279	2		282	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0043592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	529	921	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.44207855845932	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.443368363127233	2		921	1145	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0043592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	96	469	1	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.443368363127233	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.443368363127233	1		470	272	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	10	300	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.697	1	1	0.697	1	CLONAL	1	TRUE	1	0.319787054161925	2		300	62	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775625	39775625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140222241	NA	P-0043598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	21	407	0	ENST00000288319.7:c.395C>T	p.Thr132Met	p.T132M	ENST00000288319	NM_182918.3	132	aCg/aTg	4/10	1	2	FACETS	0.782	0.616	0.964	1	0.929	1	CLONAL	2	TRUE	1	0.319787054161925	2		407	84	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665110	29665110	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658541	NA	P-0043598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	20	658	1	ENST00000356175.3:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000356175	NM_000267.3	2237	Cga/Tga	44/57	0.112940740692436	1	FACETS	1	0.89	1	1	0.89	1	INDETERMINATE	1	TRUE	0	0.319787054161925	1		659	84	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717696	89717696	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	26	556	0	ENST00000371953.3:c.723del	p.Phe241LeufsTer15	p.F241Lfs*15	ENST00000371953	NM_000314.4	241	Ttt/tt	7/9	0.292571107021495	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.319787054161925	1		556	92	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0043617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	261	829	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	NA	2	FACETS	0.978	0.938	1			1	INDETERMINATE	2	TRUE	NA	0.723191395394307	2		829	369	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401472	401472	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	121	260	0	ENST00000380956.4:c.794A>G	p.Glu265Gly	p.E265G	ENST00000380956	NM_001195286.1	265	gAg/gGg	7/9	0.723191395394307	5	FACETS	0.843	0.768	0.92	0.337	0.307	0.368	CLONAL	2	TRUE	0	0.723191395394307	5		260	414	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873708	151873708	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1172527602	NA	P-0043617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	235	348	0	ENST00000262189.6:c.8830C>T	p.Pro2944Ser	p.P2944S	ENST00000262189	NM_170606.2	2944	Ccg/Tcg	38/59	0.723191395394307	7	FACETS	0.882	0.823	0.943	0.353	0.329	0.378	CLONAL	2	TRUE	2	0.723191395394307	7		348	1034	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	121	412	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.602010788177467	2		412	338	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027235	49027236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0043621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	85	241	0	ENST00000267163.4:c.1802_1803insG	p.Ala602CysfsTer51	p.A602Cfs*51	ENST00000267163	NM_000321.2	601	act/acGt	18/27	0.602010788177467	1	FACETS	0.851	0.765	0.939	0.851	0.765	0.939	CLONAL	1	TRUE	0	0.602010788177467	1		241	232	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285086	15285086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	116	617	0	ENST00000263388.2:c.4529G>A	p.Arg1510His	p.R1510H	ENST00000263388	NM_000435.2	1510	cGc/cAc	25/33	1	2	FACETS	0.417	0.375	0.461	0.417	0.375	0.461	SUBCLONAL	1	TRUE	1	0.602010788177467	2		617	925	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183772	10183772	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	115	636	0	ENST00000256474.2:c.241C>G	p.Pro81Ala	p.P81A	ENST00000256474	NM_000551.3	81	Ccg/Gcg	1/3	1	2	FACETS	0.427	0.384	0.473	0.427	0.384	0.473	SUBCLONAL	1	TRUE	1	0.602010788177467	2		636	894	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938440	76938440	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	147	131	0	ENST00000373344.5:c.2308C>T	p.Gln770Ter	p.Q770*	ENST00000373344	NM_000489.3	770	Cag/Tag	9/35	0.566307320906064	2	FACETS	1	0.949	1			1	CLONAL	2	TRUE	NA	0.602010788177467	2		131	241	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0043627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	135	542	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		542	435	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0043637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	36	515	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.794	0.657	0.946	0.794	0.657	0.946	CLONAL	1	TRUE	1	0.37	2		515	245	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	88	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.463029883743219	3	FACETS	0.78	0.7	0.863	0.78	0.7	0.863	SUBCLONAL	2	TRUE	1	0.497841569516562	3		336	283	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	447	1014	11	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.841	0.805	0.877	1	0.997	1	CLONAL	2	TRUE	1	0.497841569516562	2		1025	1068	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	132	296	2	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.497841569516562	2		298	357	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	118	374	1	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	0.767	0.694	0.844	0.767	0.694	0.844	SUBCLONAL	1	TRUE	1	0.497841569516562	2		375	618	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55143617	55143617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878854825	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	122	367	0	ENST00000257290.5:c.1849C>T	p.Arg617Trp	p.R617W	ENST00000257290	NM_006206.4	617	Cgg/Tgg	13/23	1	2	FACETS	0.89	0.807	0.976	0.89	0.807	0.976	CLONAL	1	TRUE	1	0.497841569516562	2		367	551	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972893	32972893	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	31	221	1	ENST00000380152.3:c.10248del	p.Lys3416AsnfsTer11	p.K3416Nfs*11	ENST00000380152		3415	Aaa/aa	27/27	1	2	FACETS	0.712	0.582	0.855	0.712	0.582	0.855	SUBCLONAL	1	TRUE	1	0.497841569516562	2		222	175	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	68	471	12	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.986	0.867	1	0.986	0.867	1	CLONAL	1	TRUE	1	0.497841569516562	2		483	277	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687472	37687472	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	120	335	0	ENST00000447079.4:c.4382del	p.Gly1461AlafsTer38	p.G1461Afs*38	ENST00000447079	NM_015083.1	1459	tGg/tg	14/14	1	2	FACETS	0.869	0.787	0.954	0.869	0.787	0.954	CLONAL	1	TRUE	1	0.497841569516562	2		335	555	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524933	187524933	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749223648	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	180	562	0	ENST00000441802.2:c.10747G>A	p.Asp3583Asn	p.D3583N	ENST00000441802	NM_005245.3	3583	Gac/Aac	19/27	1	2	FACETS	0.796	0.734	0.86	0.796	0.734	0.86	SUBCLONAL	1	TRUE	1	0.497841569516562	2		562	909	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736165	204736166	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	105	330	1	ENST00000302823.3:c.529dup	p.Tyr177LeufsTer2	p.Y177Lfs*2	ENST00000302823	NM_005214.4	174	-/T	3/4	1	2	FACETS	0.786	0.706	0.869	0.786	0.706	0.869	SUBCLONAL	1	TRUE	1	0.497841569516562	2		331	537	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528611	8528611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201846121	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	46	307	0	ENST00000356435.5:c.521G>A	p.Arg174His	p.R174H	ENST00000356435		174	cGt/cAt	4/35	0.129202433581432	3	FACETS	0.702	0.593	0.82	0.234	0.197	0.274	INDETERMINATE	1	TRUE	0	0.497841569516562	3		307	329	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933400	39933400	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	224	717	0	ENST00000378444.4:c.1199del	p.Gly400AlafsTer42	p.G400Afs*42	ENST00000378444	NM_001123385.1	400	gGc/gc	4/15	0.349310119445049	0	FACETS	0.542	0.505	0.579			1	SUBCLONAL	1	TRUE	0	0.497841569516562	0		717	834	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026852	48026852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376220212	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	45	315	0	ENST00000234420.5:c.1730G>A	p.Arg577His	p.R577H	ENST00000234420	NM_000179.2	577	cGc/cAc	4/10	1	2	FACETS	0.517	0.435	0.606	0.517	0.435	0.606	SUBCLONAL	1	TRUE	1	0.497841569516562	2		315	350	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138915	64138915	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	108	448	3	ENST00000334205.4:c.2287del	p.Arg763AlafsTer21	p.R763Afs*21	ENST00000334205	NM_003942.2	761	gCc/gc	17/17	1	2	FACETS	0.555	0.498	0.615	0.555	0.498	0.615	SUBCLONAL	1	TRUE	1	0.497841569516562	2		451	782	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408878	41408878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768757373	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	182	452	1	ENST00000373198.4:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000373198	NM_133170.3	183	cGg/cAg	4/32	1	2	FACETS	0.951	0.879	1	0.951	0.879	1	CLONAL	1	TRUE	1	0.497841569516562	2		453	769	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366679	40366679	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs777173419	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	159	435	0	ENST00000397332.2:c.518C>G	p.Ala173Gly	p.A173G	ENST00000397332	NM_001033082.2	173	gCc/gGc	2/3	1	2	FACETS	0.855	0.785	0.928	0.855	0.785	0.928	CLONAL	1	TRUE	1	0.497841569516562	2		435	747	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	127	652	2	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	1	2	FACETS	0.8	0.726	0.877	0.8	0.726	0.877	SUBCLONAL	1	TRUE	1	0.497841569516562	2		654	638	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1383	230	799	6	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	0.497841569516562	3	FACETS	0.715	0.665	0.768			1	SUBCLONAL	1	TRUE	NA	0.497841569516562	3		805	1613	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214871	36214871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	253	834	5	ENST00000222270.7:c.3302del	p.Pro1101LeufsTer81	p.P1101Lfs*81	ENST00000222270	NM_014727.1	1099	ggC/gg	8/37	1	2	FACETS	0.73	0.681	0.78	0.73	0.681	0.78	SUBCLONAL	1	TRUE	1	0.497841569516562	2		839	1393	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686962	37686962	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	207	454	1	ENST00000447079.4:c.3871del	p.Gln1291ArgfsTer3	p.Q1291Rfs*3	ENST00000447079	NM_015083.1	1289	gCc/gc	14/14	1	2	FACETS	0.87	0.807	0.934	0.87	0.807	0.934	CLONAL	1	TRUE	1	0.497841569516562	2		455	956	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757468	40757468	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	140	552	0	ENST00000373198.4:c.2830G>A	p.Asp944Asn	p.D944N	ENST00000373198	NM_133170.3	944	Gac/Aac	20/32	1	2	FACETS	0.712	0.649	0.778	0.712	0.649	0.778	SUBCLONAL	1	TRUE	1	0.497841569516562	2		552	790	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793676	89793677	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	40	215	0	ENST00000336032.3:c.752dup	p.Pro252AlafsTer3	p.P252Afs*3	ENST00000336032	NM_006813.2	249	gaa/gAaa	2/2	1	2	FACETS	0.724	0.607	0.852	0.724	0.607	0.852	SUBCLONAL	1	TRUE	1	0.497841569516562	2		215	222	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799180	88799180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	150	541	3	ENST00000360948.2:c.205G>A	p.Ala69Thr	p.A69T	ENST00000360948	NM_001012338.2	69	Gcc/Acc	2/19	1	2	FACETS	0.716	0.654	0.78	0.716	0.654	0.78	SUBCLONAL	1	TRUE	1	0.497841569516562	2		544	842	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213243	39213243	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	226	803	7	ENST00000402219.2:c.3724del	p.Ser1242ValfsTer37	p.S1242Vfs*37	ENST00000402219	NM_005633.3	1242	Agt/gt	23/23	1	2	FACETS	0.739	0.687	0.792	0.739	0.687	0.792	SUBCLONAL	1	TRUE	1	0.497841569516562	2		810	1229	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112323	115112324	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	rs1381943852	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	74	90	0	ENST00000257566.3:c.1416_1417del	p.Leu473ProfsTer218	p.L473Pfs*218	ENST00000257566	NM_016569.3	472	gcGCtc/gctc	7/8	0.463029883743219	3	FACETS	0.952	0.85	1	0.952	0.85	1	CLONAL	2	TRUE	1	0.497841569516562	3		90	195	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821344	72821344	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	121	383	1	ENST00000268489.5:c.10831del	p.His3611ThrfsTer83	p.H3611Tfs*83	ENST00000268489	NM_006885.3	3611	Cac/ac	10/10	1	2	FACETS	0.713	0.645	0.784	0.713	0.645	0.784	SUBCLONAL	1	TRUE	1	0.497841569516562	2		384	682	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32971138	32971138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507432	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	45	398	0	ENST00000380152.3:c.9605C>T	p.Pro3202Leu	p.P3202L	ENST00000380152		3202	cCg/cTg	26/27	1	2	FACETS	0.472	0.397	0.554	0.472	0.397	0.554	SUBCLONAL	1	TRUE	1	0.497841569516562	2		398	383	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117297	7117297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145697152	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	280	684	0	ENST00000302850.5:c.3919G>A	p.Glu1307Lys	p.E1307K	ENST00000302850	NM_000208.2	1307	Gag/Aag	22/22	1	2	FACETS	0.93	0.873	0.988	0.93	0.873	0.988	CLONAL	1	TRUE	1	0.497841569516562	2		684	1210	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162025	22162025	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	95	456	0	ENST00000215832.6:c.230G>A	p.Arg77His	p.R77H	ENST00000215832	NM_002745.4	77	cGc/cAc	2/9	1	2	FACETS	0.734	0.656	0.817	0.734	0.656	0.817	SUBCLONAL	1	TRUE	1	0.497841569516562	2		456	520	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259393	16259393	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	90	332	0	ENST00000375759.3:c.6658G>A	p.Gly2220Ser	p.G2220S	ENST00000375759	NM_015001.2	2220	Ggc/Agc	11/15	1	2	FACETS	0.703	0.626	0.786	0.703	0.626	0.786	SUBCLONAL	1	TRUE	1	0.497841569516562	2		332	514	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478757	57478757	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	136	365	0	ENST00000371085.3:c.348del	p.Val117TrpfsTer16	p.V117Wfs*16	ENST00000371085	NM_000516.4	115	Ccc/cc	5/13	1	2	FACETS	0.848	0.774	0.927	0.848	0.774	0.927	CLONAL	1	TRUE	1	0.497841569516562	2		365	644	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893641	28893641	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751031012	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	96	388	0	ENST00000282397.4:c.3205G>A	p.Glu1069Lys	p.E1069K	ENST00000282397	NM_002019.4	1069	Gaa/Aaa	24/30	1	2	FACETS	0.685	0.612	0.763	0.685	0.612	0.763	SUBCLONAL	1	TRUE	1	0.497841569516562	2		388	563	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864679	68864679	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	64	281	0	ENST00000288368.4:c.50T>C	p.Leu17Pro	p.L17P	ENST00000288368	NM_024870.2	17	cTg/cCg	1/40	0.463029883743219	3	FACETS	0.581	0.503	0.665	0.29	0.251	0.333	SUBCLONAL	1	TRUE	1	0.497841569516562	3		281	553	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105920	27105920	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	162	493	0	ENST00000324856.7:c.5531G>T	p.Trp1844Leu	p.W1844L	ENST00000324856	NM_006015.4	1844	tGg/tTg	20/20	1	2	FACETS	0.765	0.702	0.83	0.765	0.702	0.83	SUBCLONAL	1	TRUE	1	0.497841569516562	2		493	851	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936083	71936083	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	37	47	0	ENST00000298229.2:c.55C>T	p.Pro19Ser	p.P19S	ENST00000298229	NM_001567.3	19	Ccc/Tcc	1/28	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.497841569516562	2		47	135	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150261	108150261	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147112946	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	19	319	1	ENST00000278616.4:c.3328G>A	p.Ala1110Thr	p.A1110T	ENST00000278616	NM_000051.3	1110	Gca/Aca	23/63	1	2	FACETS	0.408	0.311	0.521	0.408	0.311	0.521	SUBCLONAL	1	TRUE	1	0.497841569516562	2		320	187	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464398	464398	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	54	436	1	ENST00000399788.2:c.796C>T	p.Arg266Ter	p.R266*	ENST00000399788	NM_001042603.1	266	Cga/Tga	7/28	0.497841569516562	3	FACETS	0.531	0.454	0.616	0.266	0.227	0.308	SUBCLONAL	1	TRUE	1	0.497841569516562	3		437	510	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246457	105246457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774836044	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	216	687	1	ENST00000349310.3:c.143G>A	p.Arg48His	p.R48H	ENST00000349310	NM_001014432.1	48	cGt/cAt	4/15	0.463029883743219	3	FACETS	0.825	0.766	0.888	0.413	0.383	0.444	CLONAL	1	TRUE	1	0.497841569516562	3		688	1313	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762061	43762061	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	107	495	0	ENST00000382044.4:c.1384del	p.Ser462LeufsTer29	p.S462Lfs*29	ENST00000382044	NM_001141980.1	462	Tct/ct	11/28	1	2	FACETS	0.679	0.61	0.752	0.679	0.61	0.752	SUBCLONAL	1	TRUE	1	0.497841569516562	2		495	633	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026104	14026104	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	28	139	0	ENST00000311895.7:c.1069del	p.Ile357TyrfsTer19	p.I357Yfs*19	ENST00000311895	NM_005236.2	355	gAa/ga	6/11	1	2	FACETS	0.735	0.595	0.891	0.735	0.595	0.891	SUBCLONAL	1	TRUE	1	0.497841569516562	2		139	153	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510617	38510617	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	259	757	0	ENST00000254066.5:c.871A>G	p.Thr291Ala	p.T291A	ENST00000254066	NM_000964.3	291	Acc/Gcc	7/9	1	2	FACETS	0.763	0.713	0.814	0.763	0.713	0.814	SUBCLONAL	1	TRUE	1	0.497841569516562	2		757	1364	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222772	5222772	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs770446171	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	165	439	0	ENST00000357368.4:c.3031C>T	p.Arg1011Ter	p.R1011*	ENST00000357368	NM_002850.3	1011	Cga/Tga	18/38	1	2	FACETS	0.807	0.742	0.875	0.807	0.742	0.875	CLONAL	1	TRUE	1	0.497841569516562	2		439	821	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952207	17952207	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1250190863	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	275	630	0	ENST00000458235.1:c.1133G>A	p.Gly378Asp	p.G378D	ENST00000458235	NM_000215.3	378	gGc/gAc	8/24	1	2	FACETS	0.906	0.85	0.964	0.906	0.85	0.964	CLONAL	1	TRUE	1	0.497841569516562	2		630	1219	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214143	36214143	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	282	864	0	ENST00000222270.7:c.2969T>C	p.Phe990Ser	p.F990S	ENST00000222270	NM_014727.1	990	tTt/tCt	6/37	1	2	FACETS	0.805	0.755	0.857	0.805	0.755	0.857	CLONAL	1	TRUE	1	0.497841569516562	2		864	1407	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40742001	40742001	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	248	718	0	ENST00000392038.2:c.971A>G	p.Asp324Gly	p.D324G	ENST00000392038	NM_001626.4	324	gAc/gGc	11/14	1	2	FACETS	0.908	0.849	0.969	0.908	0.849	0.969	CLONAL	1	TRUE	1	0.497841569516562	2		718	1097	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015101	27015101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	158	369	0	ENST00000335756.4:c.203G>A	p.Ser68Asn	p.S68N	ENST00000335756	NM_001809.3	68	aGc/aAc	2/5	1	2	FACETS	0.83	0.761	0.901	0.83	0.761	0.901	CLONAL	1	TRUE	1	0.497841569516562	2		369	765	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143114	30143114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	196	669	1	ENST00000389048.3:c.412G>A	p.Ala138Thr	p.A138T	ENST00000389048	NM_004304.4	138	Gcc/Acc	1/29	1	2	FACETS	0.839	0.777	0.904	0.839	0.777	0.904	CLONAL	1	TRUE	1	0.497841569516562	2		670	938	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170891	99170891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	232	692	0	ENST00000074304.5:c.1520C>T	p.Ala507Val	p.A507V	ENST00000074304	NM_001134224.1	507	gCc/gTc	16/26	1	2	FACETS	0.787	0.733	0.843	0.787	0.733	0.843	SUBCLONAL	1	TRUE	1	0.497841569516562	2		692	1184	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593610	215593610	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	95	324	0	ENST00000260947.4:c.2124G>T	p.Lys708Asn	p.K708N	ENST00000260947	NM_000465.2	708	aaG/aaT	11/11	1	2	FACETS	0.807	0.722	0.897	0.807	0.722	0.897	CLONAL	1	TRUE	1	0.497841569516562	2		324	473	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449623	187449623	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	135	402	0	ENST00000232014.4:c.257T>G	p.Leu86Arg	p.L86R	ENST00000232014	NM_001130845.1	86	cTc/cGc	4/10	1	2	FACETS	0.93	0.849	1	0.93	0.849	1	CLONAL	1	TRUE	1	0.497841569516562	2		402	583	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518870	187518870	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	135	430	0	ENST00000441802.2:c.12334G>T	p.Val4112Phe	p.V4112F	ENST00000441802	NM_005245.3	4112	Gtt/Ttt	24/27	1	2	FACETS	0.864	0.787	0.943	0.864	0.787	0.943	CLONAL	1	TRUE	1	0.497841569516562	2		430	628	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295262	1295263	+	upstream_gene_variant	5'Flank	INS	-	-	G	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	87	317	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.537	0.475	0.603	0.537	0.475	0.603	SUBCLONAL	1	TRUE	1	0.497841569516562	2		317	651	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526621	31526621	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	222	612	1	ENST00000344624.3:c.419G>A	p.Gly140Asp	p.G140D	ENST00000344624		140	gGc/gAc	2/33	1	2	FACETS	0.936	0.872	1	0.936	0.872	1	CLONAL	1	TRUE	1	0.497841569516562	2		613	953	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80088578	80088578	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	26	214	0	ENST00000265081.6:c.2570T>A	p.Ile857Asn	p.I857N	ENST00000265081	NM_002439.4	857	aTt/aAt	19/24	1	2	FACETS	0.785	0.631	0.957	0.785	0.631	0.957	CLONAL	1	TRUE	1	0.497841569516562	2		214	133	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911192	29911192	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	321	641	0	ENST00000376809.5:c.491C>T	p.Ala164Val	p.A164V	ENST00000376809	NM_002116.7	164	gCt/gTt	3/8	0.33609368501314	3	FACETS	1	0.991	1	0.42	0.396	0.445	CLONAL	1	TRUE	0	0.497841569516562	3		641	1278	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323154	31323154	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	520	700	0	ENST00000412585.2:c.835C>T	p.Gln279Ter	p.Q279*	ENST00000412585	NM_005514.6	279	Cag/Tag	4/8	0.33609368501314	3	FACETS	1	0.99	1	0.728	0.7	0.757	CLONAL	2	TRUE	0	0.497841569516562	3		700	1194	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815793	32815793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	608	746	3	ENST00000354258.4:c.1823C>T	p.Ala608Val	p.A608V	ENST00000354258	NM_000593.5	608	gCt/gTt	8/11	0.33609368501314	3	FACETS	1	0.994	1	0.759	0.732	0.786	CLONAL	2	TRUE	0	0.497841569516562	3		749	1340	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286994	33286994	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	308	469	0	ENST00000374542.5:c.1943A>G	p.Tyr648Cys	p.Y648C	ENST00000374542	NM_001141970.1	648	tAt/tGt	7/8	0.33609368501314	3	FACETS	1	0.989	1	0.764	0.726	0.803	CLONAL	2	TRUE	0	0.497841569516562	3		469	674	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528418	157528418	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	214	624	0	ENST00000346085.5:c.6146del	p.Leu2049TrpfsTer50	p.L2049Wfs*50	ENST00000346085	NM_020732.3	2048	aTt/at	20/20	1	2	FACETS	0.918	0.854	0.985	0.918	0.854	0.985	CLONAL	1	TRUE	1	0.497841569516562	2		624	936	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339281	116339281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80256822	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	205	346	0	ENST00000397752.3:c.143C>T	p.Ala48Val	p.A48V	ENST00000397752	NM_000245.2	48	gCg/gTg	2/21	0.463029883743219	3	FACETS	0.933	0.873	0.995	0.933	0.873	0.995	CLONAL	2	TRUE	1	0.497841569516562	3		346	551	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994239	21994239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528789830	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	225	554	1	ENST00000579755.1:c.92C>T	p.Thr31Met	p.T31M	ENST00000579755		31	aCg/aTg	1/3	0.129202433581432		FACETS		0.95	1				INDETERMINATE	1	TRUE	0	0.497841569516562	3		555	1101	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197507	27197507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	276	610	0	ENST00000380036.4:c.1819C>T	p.Pro607Ser	p.P607S	ENST00000380036	NM_000459.3	607	Ccc/Tcc	12/23	0.129202433581432	3	FACETS	1	0.993	1	0.497	0.467	0.527	INDETERMINATE	1	TRUE	0	0.497841569516562	3		610	929	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390930	139390930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373874935	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1389	310	895	1	ENST00000277541.6:c.7261G>A	p.Val2421Met	p.V2421M	ENST00000277541	NM_017617.3	2421	Gtg/Atg	34/34	0.129202433581432	3	FACETS	0.915	0.86	0.972	0.305	0.286	0.324	INDETERMINATE	1	TRUE	0	0.497841569516562	3		896	1699	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006797	47006799	+	5_prime_UTR_variant	5'UTR	DEL	AGC	AGC	-	novel	NA	P-0043652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	255	705	0	ENST00000377604.3:c.-78_-76del		p.*26*	ENST00000377604	NM_001204468.1	-/852		2/24	0.349310119445049	0	FACETS	0.582	0.546	0.619			1	SUBCLONAL	1	TRUE	0	0.497841569516562	0		705	884	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	231	829	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.29	2		829	1137	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	499	1014	11	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.966	1	1	0.998	1	CLONAL	3	TRUE	1	0.29	2		1025	1139	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023151	27023179	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	-	novel	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	182	31	0	ENST00000324856.7:c.267_295del	p.Ser90ProfsTer11	p.S90Pfs*11	ENST00000324856	NM_006015.4	86	gGCGGAGCCGGCAGCGGCGGCGGGCCCGGC/g	1/20	1	2	FACETS	0.984	0.937	1	1	0.995	1	CLONAL	5	TRUE	1	0.29	2		31	255	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	199	484	4	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.763	0.708	0.821	1	0.991	1	SUBCLONAL	2	TRUE	1	0.29	2		488	899	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812138	43812138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139770726	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	168	416	0	ENST00000372470.3:c.1003G>A	p.Glu335Lys	p.E335K	ENST00000372470	NM_005373.2	335	Gaa/Aaa	7/12	1	2	FACETS	0.857	0.79	0.926	1	0.991	1	CLONAL	2	TRUE	1	0.29	2		416	676	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458396	120458396	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs387906747	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	230	643	0	ENST00000256646.2:c.6949C>T	p.Gln2317Ter	p.Q2317*	ENST00000256646	NM_024408.3	2317	Caa/Taa	34/34	1	2	FACETS	0.822	0.767	0.879	1	0.993	1	CLONAL	2	TRUE	1	0.29	2		643	965	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	108	571	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.776	0.7	0.856	1	0.984	1	SUBCLONAL	2	TRUE	1	0.29	2		571	480	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945033	31945033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	284	781	2	ENST00000340398.3:c.68C>T	p.Thr23Met	p.T23M	ENST00000340398	NM_001013699.2	23	aCg/aTg	1/1	1	2	FACETS	0.768	0.721	0.817	1	0.994	1	SUBCLONAL	2	TRUE	1	0.29	2		783	1275	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	347	1117	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.852	0.805	0.899	1	0.995	1	CLONAL	2	TRUE	1	0.29	2		1117	1405	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437176	49437176	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371685892	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	266	640	1	ENST00000301067.7:c.5503C>T	p.Arg1835Cys	p.R1835C	ENST00000301067	NM_003482.3	1835	Cgt/Tgt	24/54	1	2	FACETS	0.826	0.775	0.88	1	0.994	1	CLONAL	2	TRUE	1	0.29	2		641	1110	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438067	49438067	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886043414	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	297	734	0	ENST00000301067.7:c.5104C>T	p.Arg1702Ter	p.R1702*	ENST00000301067	NM_003482.3	1702	Cga/Tga	21/54	1	2	FACETS	0.812	0.763	0.861	1	0.994	1	CLONAL	2	TRUE	1	0.29	2		734	1262	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856472	111856472	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	187	314	0	ENST00000341259.2:c.523C>T	p.Arg175Trp	p.R175W	ENST00000341259	NM_005475.2	175	Cgg/Tgg	2/8	1	2	FACETS	0.851	0.788	0.916	1	0.992	1	CLONAL	2	TRUE	1	0.29	2		314	758	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	106	271	3	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	1	2	FACETS	0.752	0.677	0.83	1	0.983	1	SUBCLONAL	2	TRUE	1	0.29	2		274	486	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987087	36987087	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	288	807	0	ENST00000354822.5:c.602C>T	p.Ala201Val	p.A201V	ENST00000354822	NM_001079668.2	201	gCg/gTg	3/3	1	2	FACETS	0.842	0.791	0.894	1	0.994	1	CLONAL	2	TRUE	1	0.29	2		807	1180	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591597	38591597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	147	430	0	ENST00000299084.4:c.56C>T	p.Ala19Val	p.A19V	ENST00000299084	NM_152594.2	19	gCt/gTt	2/7	1	2	FACETS	0.791	0.724	0.86	1	0.989	1	SUBCLONAL	2	TRUE	1	0.29	2		430	641	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251265	99251265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760481311	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	217	599	0	ENST00000268035.6:c.569C>T	p.Pro190Leu	p.P190L	ENST00000268035	NM_000875.3	190	cCg/cTg	2/21	1	2	FACETS	0.782	0.727	0.838	1	0.992	1	SUBCLONAL	2	TRUE	1	0.29	2		599	957	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349641	89349641	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs772267579	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	278	698	8	ENST00000301030.4:c.3309del	p.Asp1104MetfsTer214	p.D1104Mfs*214	ENST00000301030	NM_001256183.1	1103	aaA/aa	9/13	1	2	FACETS	0.877	0.824	0.932	1	0.995	1	CLONAL	2	TRUE	1	0.29	2		706	1093	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882974	89882974	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748624754	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	150	278	0	ENST00000389301.3:c.50del	p.Gly17AlafsTer27	p.G17Afs*27	ENST00000389301	NM_000135.2	17	gGc/gc	1/43	1	2	FACETS	0.94	0.864	1	1	0.991	1	CLONAL	2	TRUE	1	0.29	2		278	550	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	245	541	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.29	2		541	1135	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	221	572	5	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.765	0.712	0.82	1	0.992	1	SUBCLONAL	2	TRUE	1	0.29	2		577	996	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511652	38511652	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	279	689	0	ENST00000254066.5:c.1150C>A	p.Leu384Met	p.L384M	ENST00000254066	NM_000964.3	384	Ctg/Atg	8/9	1	2	FACETS	0.852	0.8	0.905	1	0.994	1	CLONAL	2	TRUE	1	0.29	2		689	1129	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774056	56774056	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	129	326	0	ENST00000337432.4:c.407T>C	p.Met136Thr	p.M136T	ENST00000337432	NM_058216.2	136	aTg/aCg	3/9	1	2	FACETS	0.775	0.705	0.848	1	0.987	1	SUBCLONAL	2	TRUE	1	0.29	2		326	574	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58733980	58733980	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	131	360	0	ENST00000305921.3:c.1038T>G	p.Cys346Trp	p.C346W	ENST00000305921	NM_003620.3	346	tgT/tgG	5/6	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.29	2		360	624	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18964077	18964077	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	191	534	0	ENST00000262803.5:c.1078del	p.Asp360MetfsTer46	p.D360Mfs*46	ENST00000262803	NM_002911.3	358	caG/ca	8/24	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.29	2		534	953	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221328	36221328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1308156549	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	366	870	2	ENST00000222270.7:c.5162C>T	p.Thr1721Met	p.T1721M	ENST00000222270	NM_014727.1	1721	aCg/aTg	24/37	1	2	FACETS	0.876	0.83	0.924	1	0.996	1	CLONAL	2	TRUE	1	0.29	2		872	1440	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905346	50905346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370292497	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1292	360	1005	0	ENST00000440232.2:c.554C>T	p.Pro185Leu	p.P185L	ENST00000440232	NM_002691.3	185	cCg/cTg	5/27	1	2	FACETS	0.751	0.71	0.794	1	0.995	1	SUBCLONAL	2	TRUE	1	0.29	2		1005	1652	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659847	227659847	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	145	617	1	ENST00000305123.5:c.3608del	p.Pro1203HisfsTer24	p.P1203Hfs*24	ENST00000305123	NM_005544.2	1203	cCa/ca	1/2	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.29	2		618	888	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017752	31017752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	429	722	0	ENST00000375687.4:c.614G>A	p.Ser205Asn	p.S205N	ENST00000375687	NM_015338.5	205	aGc/aAc	8/13	0.268381985951502	3	FACETS	0.941	0.898	0.985	1	0.995	1	CLONAL	3	TRUE	1	0.29	3		722	1200	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206868	36206868	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	182	391	0	ENST00000300305.3:c.644A>C	p.Lys215Thr	p.K215T	ENST00000300305		215	aAg/aCg	6/8	1	2	FACETS	0.83	0.768	0.895	1	0.991	1	CLONAL	2	TRUE	1	0.29	2		391	756	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12647737	12647737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773051648	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	90	311	0	ENST00000251849.4:c.643C>T	p.Arg215Cys	p.R215C	ENST00000251849	NM_002880.3	215	Cgt/Tgt	6/17	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.29	2		311	515	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181354	38181356	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GAG	GAG	-	novel	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	115	261	0	ENST00000396334.3:c.372_374del		p.X124_splice	ENST00000396334	NM_002468.4	124		2/5	1	2	FACETS	0.873	0.792	0.959	1	0.988	1	CLONAL	2	TRUE	1	0.29	2		261	454	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182679076	182679076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777384692	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	25	160	0	ENST00000292782.4:c.458G>A	p.Arg153Gln	p.R153Q	ENST00000292782	NM_020640.2	153	cGa/cAa	4/7	1	2	FACETS	0.641	0.506	0.795	0.641	0.506	0.795	SUBCLONAL	1	TRUE	1	0.29	2		160	269	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	153	491	0	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.29	2		491	795	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	93	270	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.29	2		271	457	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956523	93956523	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	75	179	0	ENST00000369303.4:c.2713G>T	p.Gly905Ter	p.G905*	ENST00000369303	NM_004440.3	905	Gga/Tga	15/17	1	2	FACETS	0.871	0.771	0.976	1	0.981	1	CLONAL	2	TRUE	1	0.29	2		179	297	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120512	94120512	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	78	326	0	ENST00000369303.4:c.539del	p.Lys180ArgfsTer10	p.K180Rfs*10	ENST00000369303	NM_004440.3	180	aAg/ag	3/17	1	2	FACETS	0.773	0.684	0.867	1	0.979	1	SUBCLONAL	2	TRUE	1	0.29	2		326	348	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202236	138202236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779416381	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	213	565	0	ENST00000237289.4:c.2153G>A	p.Arg718Gln	p.R718Q	ENST00000237289	NM_001270507.1	718	cGg/cAg	9/9	1	2	FACETS	0.809	0.752	0.867	1	0.992	1	CLONAL	2	TRUE	1	0.29	2		565	908	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100577	157100577	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1289149988	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	168	443	0	ENST00000346085.5:c.1518del	p.Gly507AspfsTer16	p.G507Dfs*16	ENST00000346085	NM_020732.3	505	aCc/ac	1/20	1	2	FACETS	0.752	0.693	0.814	1	0.989	1	SUBCLONAL	2	TRUE	1	0.29	2		443	770	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511249	157511250	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	193	511	0	ENST00000346085.5:c.3767_3768del	p.Pro1256GlnfsTer20	p.P1256Qfs*20	ENST00000346085	NM_020732.3	1256	cCA/c	15/20	1	2	FACETS	0.795	0.737	0.856	1	0.991	1	SUBCLONAL	2	TRUE	1	0.29	2		511	837	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748399150	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1334	327	952	5	ENST00000220592.5:c.1806del	p.Ala603ProfsTer92	p.A603Pfs*92	ENST00000220592	NM_012154.3	602	ccC/cc	14/19	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.29	2		957	1661	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376722	8376722	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	108	371	0	ENST00000356435.5:c.4391A>C	p.Lys1464Thr	p.K1464T	ENST00000356435		1464	aAg/aCg	27/35	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.29	2		371	567	SUCCESS
AR	367	MSKCC	GRCh37	X	66765598	66765598	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	343	508	1	ENST00000374690.3:c.610G>T	p.Glu204Ter	p.E204*	ENST00000374690	NM_000044.3	204	Gaa/Taa	1/8	1	1	FACETS	0.899	0.856	0.942	1	0.997	1	CLONAL	3	TRUE	0	0.29	1		509	750	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0043674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	124	751	1	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.231344137234304	0	FACETS	0.789	0.729	0.85			1	SUBCLONAL	4	FALSE	0	0.231344137234304	0		752	261	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725042	89725042	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1085308041	NA	P-0043674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	23	198	0	ENST00000371953.3:c.1027-2A>G		p.X343_splice	ENST00000371953	NM_000314.4	343			0.231344137234304	3	FACETS	1	0.87	1	1	0.87	1	CLONAL	2	FALSE	1	0.231344137234304	3		198	98	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692961	89692961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060500122	NA	P-0043674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	108	451	0	ENST00000371953.3:c.445C>T	p.Gln149Ter	p.Q149*	ENST00000371953	NM_000314.4	149	Caa/Taa	5/9	0.231344137234304	3	FACETS	0.923	0.842	1	1	0.989	1	CLONAL	4	FALSE	1	0.231344137234304	3		451	282	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519886	NA	P-0043674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	49	319	0	ENST00000349496.5:c.97T>G	p.Ser33Ala	p.S33A	ENST00000349496	NM_001904.3	33	Tct/Gct	3/15	1	2	FACETS	0.972	0.832	1	1	0.974	1	CLONAL	2	FALSE	1	0.231344137234304	2		319	218	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107152	27107152	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	127	532	0	ENST00000324856.7:c.6763G>T	p.Glu2255Ter	p.E2255*	ENST00000324856	NM_006015.4	2255	Gaa/Taa	20/20	0.194198939728631	3	FACETS	0.968	0.884	1	1	0.986	1	CLONAL	3	FALSE	1	0.231344137234304	3		532	422	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589583	67589585	+	inframe_deletion	In_Frame_Del	DEL	TAC	TAC	-	novel	NA	P-0043674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	83	151	0	ENST00000274335.5:c.1346_1348del	p.Leu449_His450delinsTyr	p.L449_H450delinsY	ENST00000274335		449	tTACat/tat	10/15	0.231344137234304	13	FACETS	0.939	0.845	1			1	CLONAL	8	FALSE	NA	0.231344137234304	13		151	217	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0043694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	308	973	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.389270067610745	2	FACETS	0.994	0.942	1	0.994	0.942	1	CLONAL	2	TRUE	0	0.403985179774303	2		973	767	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63531786	63531786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373911689	NA	P-0043694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	87	506	0	ENST00000307078.5:c.2195C>T	p.Thr732Met	p.T732M	ENST00000307078	NM_004655.3	732	aCg/aTg	9/11	0.304916287904977	3	FACETS	0.8	0.709	0.898	0.4	0.354	0.449	SUBCLONAL	1	TRUE	1	0.403985179774303	3		506	647	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052524	42052524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs918298619	NA	P-0043694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	48	247	0	ENST00000219905.7:c.7195C>T	p.Pro2399Ser	p.P2399S	ENST00000219905	NM_001164273.1	2399	Cca/Tca	20/24	0.27718062442392	3	FACETS	0.738	0.626	0.861	0.246	0.208	0.287	SUBCLONAL	1	TRUE	0	0.403985179774303	3		247	387	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712607	43712607	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	63	662	0	ENST00000382044.4:c.4577A>T	p.Asp1526Val	p.D1526V	ENST00000382044	NM_001141980.1	1526	gAt/gTt	21/28	0.27718062442392	3	FACETS	0.45	0.388	0.517	0.15	0.129	0.173	SUBCLONAL	1	TRUE	0	0.403985179774303	3		662	834	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933498	49933498	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1031624199	NA	P-0043694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	218	772	1	ENST00000296474.3:c.2692G>A	p.Val898Met	p.V898M	ENST00000296474	NM_002447.2	898	Gtg/Atg	11/20	0.304916287904977	3	FACETS	1	0.989	1	0.661	0.614	0.708	CLONAL	1	TRUE	1	0.403985179774303	3		773	982	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0043720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	34	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.555315669455291	4	FACETS	0.881	0.742	1	0.881	0.742	1	CLONAL	2	TRUE	2	0.671807231638607	4		326	96	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0043720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	189	528	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.591796925999	2	FACETS	0.82	0.772	0.868	0.82	0.772	0.868	CLONAL	2	TRUE	0	0.671807231638607	2		528	343	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971194	21971194	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	709	270	0	ENST00000304494.5:c.164del	p.Gly55AlafsTer91	p.G55Afs*91	ENST00000304494	NM_000077.4	55	gGc/gc	2/3	0.544050232082895	5	FACETS	1	0.996	1			1	CLONAL	3	TRUE	NA	0.671807231638607	5		270	1214	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945136	44945137	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGTTAAA	novel	NA	P-0043720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	26	332	0	ENST00000377967.4:c.3467_3468insACAGTTAA	p.Asn1156LysfsTer5	p.N1156Kfs*5	ENST00000377967	NM_021140.2	1154	tca/tCAGTTAAAca	24/29	0.47586247448431	3	FACETS	1	0.934	1	0.46	0.376	0.548	CLONAL	1	TRUE	0	0.671807231638607	3		332	75	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0043727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	40	863	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.47	0.388	0.561	0.47	0.388	0.561	SUBCLONAL	1	TRUE	1	0.15	2		863	1135	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572204	64572204	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	41	524	1	ENST00000312049.6:c.1435C>T	p.Arg479Trp	p.R479W	ENST00000312049	NM_130799.2	479	Cgg/Tgg	10/10	1	2	FACETS	0.668	0.555	0.795	0.668	0.555	0.795	SUBCLONAL	1	TRUE	1	0.15	2		525	818	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473696	67473696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	72	575	1	ENST00000327367.4:c.776G>A	p.Gly259Asp	p.G259D	ENST00000327367	NM_005902.3	259	gGc/gAc	6/9	1	2	FACETS	0.95	0.828	1	0.95	0.828	1	CLONAL	1	TRUE	1	0.15	2		576	1010	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0043734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	120	520	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.173932337691202	3	FACETS	0.713	0.644	0.785	0.356	0.322	0.393	INDETERMINATE	1	TRUE	1	0.620750377625094	3		520	711	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	113	300	0				ENST00000310581	NM_198253.2	-/1132			0.222084467947492	4	FACETS	0.945	0.865	1	0.945	0.865	1	INDETERMINATE	2	TRUE	2	0.789923417472926	4		300	271	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0043824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	252	208	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.473949132622621	5	FACETS	0.964	0.914	1	0.964	0.914	1	INDETERMINATE	3	TRUE	2	0.789923417472926	5		208	482	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599296	55599296	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	158	412	0	ENST00000288135.5:c.2422A>G	p.Ile808Val	p.I808V	ENST00000288135	NM_000222.2	808	Att/Gtt	17/21	0.123582901157314	4	FACETS	1	0.963	1	0.541	0.497	0.586	INDETERMINATE	1	TRUE	2	0.789923417472926	4		412	662	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495315	212495315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	52	330	0	ENST00000342788.4:c.1951C>T	p.Pro651Ser	p.P651S	ENST00000342788	NM_005235.2	651	Ccc/Tcc	17/28	1	2	FACETS	0.27	0.23	0.314	0.27	0.23	0.314	SUBCLONAL	1	TRUE	1	0.789923417472926	2		330	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567556006	NA	P-0043824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	383	583	0	ENST00000269305.4:c.298del	p.Gln100ArgfsTer23	p.Q100Rfs*23	ENST00000269305	NM_001126112.2	100	Cag/ag	4/11	0.789923417472926	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.789923417472926	1		583	496	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883987	37883987	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	170	612	0	ENST00000269571.5:c.3458G>C	p.Arg1153Pro	p.R1153P	ENST00000269571		1153	cGa/cCa	27/27	0.222084467947492	4	FACETS	0.855	0.786	0.927	0.428	0.393	0.464	INDETERMINATE	1	TRUE	2	0.789923417472926	4		612	901	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211537	46211537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	188	244	0	ENST00000334344.6:c.503G>A	p.Gly168Glu	p.G168E	ENST00000334344	NM_152641.2	168	gGa/gAa	5/21	0.264118808609829	4	FACETS	0.973	0.909	1	0.973	0.909	1	INDETERMINATE	2	TRUE	2	0.789923417472926	4		244	438	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000380	42000380	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs778558879	NA	P-0043824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	108	280	0	ENST00000219905.7:c.2399A>G	p.His800Arg	p.H800R	ENST00000219905	NM_001164273.1	800	cAt/cGt	7/24	0.159621205332584	4	FACETS	0.817	0.735	0.904	0.409	0.367	0.452	INDETERMINATE	1	TRUE	2	0.789923417472926	4		280	599	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348689	89348689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	55	646	0	ENST00000301030.4:c.4261G>A	p.Glu1421Lys	p.E1421K	ENST00000301030	NM_001256183.1	1421	Gaa/Aaa	9/13	0.180872952452128	2	FACETS	0.153	0.13	0.179	0.077	0.065	0.09	INDETERMINATE	1	TRUE	0	0.789923417472926	2		646	908	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216962	7216963	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	295	453	1	ENST00000380728.2:c.558dup	p.Ala187CysfsTer19	p.A187Cfs*19	ENST00000380728		186	-/T	7/11	0.789923417472926	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.789923417472926	1		454	400	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625587	1625587	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	101	552	0	ENST00000344749.5:c.487G>A	p.Asp163Asn	p.D163N	ENST00000344749	NM_001136139.2	163	Gac/Aac	7/19	0.638857764045673	2	FACETS	0.355	0.317	0.395	0.178	0.158	0.198	SUBCLONAL	1	TRUE	0	0.789923417472926	2		552	720	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982589	10982589	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1484713967	NA	P-0043824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	17	51	0	ENST00000327064.4:c.211C>G	p.Leu71Val	p.L71V	ENST00000327064	NM_199141.1	71	Ctc/Gtc	1/16	0.638857764045673	2	FACETS	0.489	0.372	0.623	0.245	0.186	0.312	SUBCLONAL	1	TRUE	0	0.789923417472926	2		51	88	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657079	45657079	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	89	266	0	ENST00000407780.3:c.77G>C	p.Arg26Thr	p.R26T	ENST00000407780	NM_001283052.1	26	aGa/aCa	3/7	0.222084467947492	4	FACETS	0.875	0.779	0.976	0.437	0.389	0.488	INDETERMINATE	1	TRUE	2	0.789923417472926	4		266	461	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958803	55958803	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	333	409	0	ENST00000263923.4:c.3050A>G	p.Glu1017Gly	p.E1017G	ENST00000263923	NM_002253.2	1017	gAg/gGg	22/30	0.123582901157314	4	FACETS	0.971	0.923	1	0.971	0.923	1	INDETERMINATE	2	TRUE	2	0.789923417472926	4		409	777	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645139	86645139	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1175378445	NA	P-0043824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	99	243	0	ENST00000274376.6:c.1211C>T	p.Thr404Met	p.T404M	ENST00000274376	NM_002890.2	404	aCg/aTg	8/25	0.236481264615104	2	FACETS	0.67	0.603	0.74	0.335	0.301	0.37	INDETERMINATE	1	TRUE	0	0.789923417472926	2		243	374	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195073	123195073	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0043824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	223	142	0	ENST00000218089.9:c.1417-1G>C		p.X473_splice	ENST00000218089	NM_001042749.1	473			0.642920738176094	2	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.789923417472926	2		142	256	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781871	9781871	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	176	842	1	ENST00000377346.4:c.2008G>A	p.Ala670Thr	p.A670T	ENST00000377346	NM_005026.3	670	Gcc/Acc	16/24	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.349648708777463	2		843	928	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291365	11291365	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	133	466	1	ENST00000361445.4:c.2641C>T	p.Arg881Cys	p.R881C	ENST00000361445	NM_004958.3	881	Cgc/Tgc	17/58	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.349648708777463	2		467	694	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202698	16202698	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs764320675	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	125	371	0	ENST00000375759.3:c.406G>A	p.Ala136Thr	p.A136T	ENST00000375759	NM_015001.2	136	Gct/Act	3/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.349648708777463	2		371	477	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258058	16258058	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766847660	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	125	432	1	ENST00000375759.3:c.5323G>A	p.Glu1775Lys	p.E1775K	ENST00000375759	NM_015001.2	1775	Gaa/Aaa	11/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.349648708777463	2		433	641	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258541	16258541	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	177	558	0	ENST00000375759.3:c.5806C>T	p.Arg1936Ter	p.R1936*	ENST00000375759	NM_015001.2	1936	Cga/Tga	11/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.349648708777463	2		558	878	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260611	16260611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	194	586	0	ENST00000375759.3:c.7876C>T	p.Pro2626Ser	p.P2626S	ENST00000375759	NM_015001.2	2626	Cct/Tct	11/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.349648708777463	2		586	866	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22417991	22417991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756680625	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	12	37	0	ENST00000344548.3:c.557G>A	p.Arg186His	p.R186H	ENST00000344548	NM_001039802.1	186	cGc/cAc	7/7	1	2	FACETS	0.995	0.713	1	0.995	0.713	1	CLONAL	1	TRUE	1	0.349648708777463	2		37	69	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101690	27101690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1442666063	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	243	775	0	ENST00000324856.7:c.4972C>T	p.Arg1658Trp	p.R1658W	ENST00000324856	NM_006015.4	1658	Cgg/Tgg	18/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.349648708777463	2		775	1176	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599897	28599897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145754239	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	146	608	1	ENST00000253063.3:c.779C>T	p.Ala260Val	p.A260V	ENST00000253063	NM_031459.4	260	gCg/gTg	6/10	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.349648708777463	2		609	828	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932347	36932347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	186	682	1	ENST00000361632.4:c.2122C>T	p.Pro708Ser	p.P708S	ENST00000361632		708	Ccc/Tcc	16/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.349648708777463	2		683	983	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803820	43803820	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	184	700	0	ENST00000372470.3:c.130A>C	p.Thr44Pro	p.T44P	ENST00000372470	NM_005373.2	44	Aca/Cca	2/12	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.349648708777463	2		700	934	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804262	43804262	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	64	551	0	ENST00000372470.3:c.262G>T	p.Gly88Ter	p.G88*	ENST00000372470	NM_005373.2	88	Gga/Tga	3/12	1	2	FACETS	0.428	0.37	0.492	0.428	0.37	0.492	SUBCLONAL	1	TRUE	1	0.349648708777463	2		551	855	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439625	51439625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142420524	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	89	334	1	ENST00000262662.1:c.190G>A	p.Asp64Asn	p.D64N	ENST00000262662		64	Gat/Aat	4/4	1	2	FACETS	0.89	0.791	0.996	0.89	0.791	0.996	CLONAL	1	TRUE	1	0.349648708777463	2		335	572	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439866	51439866	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	113	376	1	ENST00000262662.1:c.431C>T	p.Ala144Val	p.A144V	ENST00000262662		144	gCc/gTc	4/4	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.349648708777463	2		377	631	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344790	65344790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770735783	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	110	300	0	ENST00000342505.4:c.247G>A	p.Glu83Lys	p.E83K	ENST00000342505	NM_002227.2	83	Gag/Aag	4/25	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.349648708777463	2		300	596	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428591	78428591	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	36	295	1	ENST00000370768.2:c.1208G>T	p.Ser403Ile	p.S403I	ENST00000370768	NM_003902.3	403	aGc/aTc	14/20	1	2	FACETS	0.496	0.408	0.595	0.496	0.408	0.595	SUBCLONAL	1	TRUE	1	0.349648708777463	2		296	415	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273218	115273218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	132	500	0	ENST00000438362.2:c.1240C>T	p.Arg414Cys	p.R414C	ENST00000438362	NM_001242891.1	414	Cgt/Tgt	11/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.349648708777463	2		500	699	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466330	120466330	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	181	460	0	ENST00000256646.2:c.4789T>C	p.Ser1597Pro	p.S1597P	ENST00000256646	NM_024408.3	1597	Tca/Cca	26/34	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.349648708777463	2		460	718	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506383	120506383	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	139	429	0	ENST00000256646.2:c.1729G>A	p.Asp577Asn	p.D577N	ENST00000256646	NM_024408.3	577	Gat/Aat	11/34	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.349648708777463	2		429	736	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724542	162724542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1041487062	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	132	528	0	ENST00000367921.3:c.314G>A	p.Arg105His	p.R105H	ENST00000367921	NM_006182.2	105	cGc/cAc	5/18	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.349648708777463	2		528	658	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317623	163317623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747173543	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	74	333	0	ENST00000271452.3:c.1019C>T	p.Ser340Leu	p.S340L	ENST00000271452	NM_145697.2	340	tCg/tTg	12/14	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.349648708777463	2		333	419	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175729	176175729	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	229	737	0	ENST00000367669.3:c.386A>T	p.Asp129Val	p.D129V	ENST00000367669	NM_022457.5	129	gAc/gTc	1/20	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.349648708777463	2		737	1281	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091441	193091441	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	119	459	1	ENST00000367435.3:c.111G>T	p.Lys37Asn	p.K37N	ENST00000367435	NM_024529.4	37	aaG/aaT	1/17	1	2	FACETS	0.966	0.873	1	0.966	0.873	1	CLONAL	1	TRUE	1	0.349648708777463	2		460	705	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111048	193111048	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	57	202	0	ENST00000367435.3:c.581G>T	p.Arg194Ile	p.R194I	ENST00000367435	NM_024529.4	194	aGa/aTa	7/17	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.349648708777463	2		202	273	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117031	193117031	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	121	297	0	ENST00000367435.3:c.764C>A	p.Ser255Tyr	p.S255Y	ENST00000367435	NM_024529.4	255	tCt/tAt	8/17	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.349648708777463	2		297	637	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944320	206944320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	159	526	0	ENST00000423557.1:c.310G>T	p.Asp104Tyr	p.D104Y	ENST00000423557	NM_000572.2	104	Gac/Tac	3/5	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.349648708777463	2		526	843	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552729	226552729	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746139482	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	136	393	0	ENST00000366794.5:c.2632C>T	p.Arg878Trp	p.R878W	ENST00000366794	NM_001618.3	878	Cgg/Tgg	19/23	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.349648708777463	2		393	716	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226566960	226566960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371066735	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	149	422	1	ENST00000366794.5:c.1628C>T	p.Ala543Val	p.A543V	ENST00000366794	NM_001618.3	543	gCg/gTg	12/23	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.349648708777463	2		423	734	SUCCESS
FH	2271	MSKCC	GRCh37	1	241671902	241671902	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	73	360	0	ENST00000366560.3:c.738+1G>A		p.X246_splice	ENST00000366560	NM_000143.3	246			1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.349648708777463	2		360	385	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858945	243858945	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	31	379	0	ENST00000263826.5:c.120G>T	p.Glu40Asp	p.E40D	ENST00000263826	NM_005465.4	40	gaG/gaT	2/13	1	2	FACETS	0.426	0.344	0.519	0.426	0.344	0.519	SUBCLONAL	1	TRUE	1	0.349648708777463	2		379	416	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597870	43597870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	245	825	0	ENST00000355710.3:c.418C>T	p.Pro140Ser	p.P140S	ENST00000355710	NM_020975.4	140	Cca/Tca	3/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.349648708777463	2		825	1227	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63661997	63661997	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	130	412	0	ENST00000279873.7:c.101G>T	p.Arg34Ile	p.R34I	ENST00000279873	NM_032199.2	34	aGa/aTa	2/10	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.349648708777463	2		412	723	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845492	63845492	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs961794143	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	75	215	0	ENST00000279873.7:c.1231G>T	p.Gly411Ter	p.G411*	ENST00000279873	NM_032199.2	411	Gga/Tga	9/10	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.349648708777463	2		215	387	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332686	70332686	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	150	559	0	ENST00000373644.4:c.591G>T	p.Glu197Asp	p.E197D	ENST00000373644	NM_030625.2	197	gaG/gaT	2/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.349648708777463	2		559	764	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446279	70446279	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763447831	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	102	513	1	ENST00000373644.4:c.5219G>A	p.Arg1740His	p.R1740H	ENST00000373644	NM_030625.2	1740	cGc/cAc	11/12	1	2	FACETS	0.62	0.553	0.691	0.62	0.553	0.691	SUBCLONAL	1	TRUE	1	0.349648708777463	2		514	941	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649963	88649963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	124	518	0	ENST00000372037.3:c.212C>T	p.Ala71Val	p.A71V	ENST00000372037	NM_004329.2	71	gCt/gTt	4/13	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.349648708777463	2		518	678	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683441	88683441	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	29	102	0	ENST00000372037.3:c.1564G>T	p.Ala522Ser	p.A522S	ENST00000372037	NM_004329.2	522	Gcc/Tcc	13/13	1	2	FACETS	0.782	0.642	0.934	1	0.948	1	CLONAL	2	TRUE	1	0.349648708777463	2		102	106	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	113	393	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.349648708777463	2		393	481	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693002	89693003	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	84	274	0	ENST00000371953.3:c.491dup	p.Val166SerfsTer14	p.V166Sfs*14	ENST00000371953	NM_000314.4	162	-/A	5/9	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.349648708777463	2		274	475	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903708	114903708	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	171	537	0	ENST00000543371.1:c.712G>T	p.Asp238Tyr	p.D238Y	ENST00000543371	NM_001198531.1	238	Gat/Tat	7/14	1	2	FACETS	0.974	0.896	1	0.974	0.896	1	CLONAL	1	TRUE	1	0.349648708777463	2		537	1004	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251848	8251848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1470323179	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	160	567	0	ENST00000335790.3:c.229G>A	p.Asp77Asn	p.D77N	ENST00000335790	NM_002315.2	77	Gac/Aac	2/4	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.349648708777463	2		567	827	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741414	17741414	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	276	828	0	ENST00000250003.3:c.85T>G	p.Phe29Val	p.F29V	ENST00000250003	NM_002478.4	29	Ttc/Gtc	1/3	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.349648708777463	2		828	1295	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741792	17741792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	149	461	0	ENST00000250003.3:c.463C>T	p.Arg155Cys	p.R155C	ENST00000250003	NM_002478.4	155	Cgc/Tgc	1/3	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.349648708777463	2		461	734	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572285	64572285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863224810	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	165	659	2	ENST00000312049.6:c.1354C>T	p.Arg452Trp	p.R452W	ENST00000312049	NM_130799.2	452	Cgg/Tgg	10/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.349648708777463	2		661	817	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573215	64573215	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	90	631	1	ENST00000312049.6:c.1077G>T	p.Glu359Asp	p.E359D	ENST00000312049	NM_130799.2	359	gaG/gaT	8/10	1	2	FACETS	0.558	0.494	0.626	0.558	0.494	0.626	SUBCLONAL	1	TRUE	1	0.349648708777463	2		632	923	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573764	64573764	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373135175	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	72	713	0	ENST00000312049.6:c.989G>A	p.Arg330His	p.R330H	ENST00000312049	NM_130799.2	330	cGc/cAc	7/10	1	2	FACETS	0.442	0.385	0.504	0.442	0.385	0.504	SUBCLONAL	1	TRUE	1	0.349648708777463	2		713	931	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577320	64577320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	188	656	1	ENST00000312049.6:c.262G>A	p.Ala88Thr	p.A88T	ENST00000312049	NM_130799.2	88	Gcc/Acc	2/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.349648708777463	2		657	917	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200440	67200440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761131153	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	150	580	1	ENST00000312629.5:c.634G>A	p.Asp212Asn	p.D212N	ENST00000312629	NM_003952.2	212	Gac/Aac	8/15	1	2	FACETS	0.975	0.891	1	0.975	0.891	1	CLONAL	1	TRUE	1	0.349648708777463	2		581	880	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94169009	94169009	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	54	284	0	ENST00000323929.3:c.1983G>T	p.Lys661Asn	p.K661N	ENST00000323929	NM_005591.3	661	aaG/aaT	18/20	1	2	FACETS	0.856	0.734	0.988	0.856	0.734	0.988	CLONAL	1	TRUE	1	0.349648708777463	2		284	361	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189441	94189441	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1381679718	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	89	361	0	ENST00000323929.3:c.1563+1G>A		p.X521_splice	ENST00000323929	NM_005591.3	521			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.349648708777463	2		361	465	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94211920	94211920	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	93	389	0	ENST00000323929.3:c.525G>T	p.Lys175Asn	p.K175N	ENST00000323929	NM_005591.3	175	aaG/aaT	6/20	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.349648708777463	2		389	512	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102033294	102033294	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376161041	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	138	451	0	ENST00000282441.5:c.680C>T	p.Ser227Leu	p.S227L	ENST00000282441	NM_001130145.2	227	tCg/tTg	3/9	1	2	FACETS	0.963	0.876	1	0.963	0.876	1	CLONAL	1	TRUE	1	0.349648708777463	2		451	820	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114842	108114842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145355104	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	90	384	0	ENST00000278616.4:c.659C>T	p.Ala220Val	p.A220V	ENST00000278616	NM_000051.3	220	gCg/gTg	6/63	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.349648708777463	2		384	474	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206575	108206575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138526014	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	40	231	0	ENST00000278616.4:c.8155C>T	p.Arg2719Cys	p.R2719C	ENST00000278616	NM_000051.3	2719	Cgt/Tgt	56/63	1	2	FACETS	0.738	0.616	0.873	0.738	0.616	0.873	SUBCLONAL	1	TRUE	1	0.349648708777463	2		231	310	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235935	108235935	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770641163	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	85	349	0	ENST00000278616.4:c.8977C>T	p.Arg2993Ter	p.R2993*	ENST00000278616	NM_000051.3	2993	Cga/Tga	62/63	1	2	FACETS	0.95	0.842	1	0.95	0.842	1	CLONAL	1	TRUE	1	0.349648708777463	2		349	512	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376605	118376605	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	94	399	0	ENST00000534358.1:c.9998C>A	p.Ser3333Tyr	p.S3333Y	ENST00000534358	NM_005933.3	3333	tCt/tAt	27/36	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.349648708777463	2		399	496	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503180	125503180	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	60	300	0	ENST00000428830.2:c.547G>T	p.Glu183Ter	p.E183*	ENST00000428830	NM_001114121.2	183	Gaa/Taa	6/14	1	2	FACETS	0.871	0.753	0.998	0.871	0.753	0.998	CLONAL	1	TRUE	1	0.349648708777463	2		300	394	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404944	404944	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	40	413	0	ENST00000399788.2:c.4250G>T	p.Arg1417Met	p.R1417M	ENST00000399788	NM_001042603.1	1417	aGg/aTg	26/28	1	2	FACETS	0.383	0.318	0.457	0.383	0.318	0.457	SUBCLONAL	1	TRUE	1	0.349648708777463	2		413	597	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023246	1023246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs184776294	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	143	517	0	ENST00000358495.3:c.1009G>A	p.Asp337Asn	p.D337N	ENST00000358495	NM_134424.2	337	Gat/Aat	11/12	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.349648708777463	2		517	755	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435035	18435035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs191077735	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	63	246	0	ENST00000266497.5:c.20C>T	p.Thr7Met	p.T7M	ENST00000266497		7	aCg/aTg	1/31	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.349648708777463	2		246	285	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534768	18534768	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	134	402	0	ENST00000266497.5:c.1826C>A	p.Thr609Asn	p.T609N	ENST00000266497		609	aCt/aAt	12/31	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.349648708777463	2		402	753	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123836	46123837	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	105	267	0	ENST00000334344.6:c.109dup	p.Ile37AsnfsTer29	p.I37Nfs*29	ENST00000334344	NM_152641.2	34	-/A	2/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.349648708777463	2		267	470	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246094	46246094	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	76	336	0	ENST00000334344.6:c.4188A>T	p.Gln1396His	p.Q1396H	ENST00000334344	NM_152641.2	1396	caA/caT	15/21	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.349648708777463	2		336	355	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421877	49421877	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	204	644	0	ENST00000301067.7:c.14430G>T	p.Lys4810Asn	p.K4810N	ENST00000301067	NM_003482.3	4810	aaG/aaT	46/54	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.349648708777463	2		644	1033	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431915	49431915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	195	855	1	ENST00000301067.7:c.9224C>T	p.Ser3075Leu	p.S3075L	ENST00000301067	NM_003482.3	3075	tCg/tTg	34/54	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.349648708777463	2		856	980	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434647	49434648	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	203	902	0	ENST00000301067.7:c.6905dup	p.Asn2303LysfsTer6	p.N2303Kfs*6	ENST00000301067	NM_003482.3	2302	cca/ccCa	31/54	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.349648708777463	2		902	1113	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448776	49448776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	157	513	0	ENST00000301067.7:c.83C>T	p.Ala28Val	p.A28V	ENST00000301067	NM_003482.3	28	gCc/gTc	2/54	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.349648708777463	2		513	836	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50481162	50481162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	106	416	0	ENST00000394963.4:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000394963	NM_003076.4	183	cGa/cAa	5/13	1	2	FACETS	0.975	0.876	1	0.975	0.876	1	CLONAL	1	TRUE	1	0.349648708777463	2		416	622	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492761	50492761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	172	505	0	ENST00000394963.4:c.1526C>T	p.Ala509Val	p.A509V	ENST00000394963	NM_003076.4	509	gCc/gTc	13/13	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.349648708777463	2		505	711	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489544	56489544	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761002408	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	174	492	2	ENST00000267101.3:c.2009G>A	p.Arg670Gln	p.R670Q	ENST00000267101	NM_001982.3	670	cGg/cAg	17/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.349648708777463	2		494	851	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859015	57859015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776846382	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	221	718	2	ENST00000228682.2:c.511C>T	p.Arg171Trp	p.R171W	ENST00000228682	NM_005269.2	171	Cgg/Tgg	5/12	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.349648708777463	2		720	1021	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863334	57863334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	203	785	0	ENST00000228682.2:c.1429G>A	p.Asp477Asn	p.D477N	ENST00000228682	NM_005269.2	477	Gac/Aac	11/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.349648708777463	2		785	1057	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864396	57864396	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768202810	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	153	689	1	ENST00000228682.2:c.1873G>A	p.Glu625Lys	p.E625K	ENST00000228682	NM_005269.2	625	Gag/Aag	12/12	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.349648708777463	2		690	800	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145099	58145099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3211612	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	151	558	0	ENST00000257904.6:c.245G>A	p.Arg82Gln	p.R82Q	ENST00000257904	NM_000075.3	82	cGa/cAa	3/8	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.349648708777463	2		558	822	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813333	102813333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs539899150	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	213	540	2	ENST00000307046.8:c.356G>A	p.Arg119His	p.R119H	ENST00000307046	NM_001111285.1	119	cGc/cAc	3/4	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.349648708777463	2		542	930	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888240	112888240	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs925129380	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	69	456	0	ENST00000351677.2:c.256G>A	p.Gly86Arg	p.G86R	ENST00000351677	NM_002834.3	86	Ggg/Agg	3/16	1	2	FACETS	0.827	0.722	0.94	0.827	0.722	0.94	CLONAL	1	TRUE	1	0.349648708777463	2		456	477	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915481	112915481	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376007642	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	127	439	0	ENST00000351677.2:c.880G>A	p.Asp294Asn	p.D294N	ENST00000351677	NM_002834.3	294	Gat/Aat	8/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.349648708777463	2		439	577	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109974	115109974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1286841573	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	208	734	0	ENST00000257566.3:c.1904G>A	p.Arg635His	p.R635H	ENST00000257566	NM_016569.3	635	cGc/cAc	8/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.349648708777463	2		734	1010	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118949	115118949	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	48	205	0	ENST00000257566.3:c.392G>A	p.Arg131Gln	p.R131Q	ENST00000257566	NM_016569.3	131	cGa/cAa	2/8	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.349648708777463	2		205	258	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426644	121426644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853243	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	158	545	2	ENST00000257555.6:c.335C>T	p.Pro112Leu	p.P112L	ENST00000257555		112	cCg/cTg	2/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.349648708777463	2		547	849	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225520	133225520	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs5744904	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	136	595	0	ENST00000320574.5:c.4144C>T	p.Arg1382Cys	p.R1382C	ENST00000320574	NM_006231.2	1382	Cgc/Tgc	32/49	1	2	FACETS	0.992	0.903	1	0.992	0.903	1	CLONAL	1	TRUE	1	0.349648708777463	2		595	784	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250213	133250213	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs864622766	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	175	671	0	ENST00000320574.5:c.1307C>G	p.Pro436Arg	p.P436R	ENST00000320574	NM_006231.2	436	cCc/cGc	13/49	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.349648708777463	2		671	837	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549484	21549484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760026476	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	99	479	2	ENST00000382592.4:c.2792C>T	p.Thr931Met	p.T931M	ENST00000382592	NM_014572.2	931	aCg/aTg	8/8	1	2	FACETS	0.886	0.792	0.986	0.886	0.792	0.986	CLONAL	1	TRUE	1	0.349648708777463	2		481	639	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588695	28588695	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	76	279	0	ENST00000241453.7:c.2754-1G>T		p.X918_splice	ENST00000241453	NM_004119.2	918			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.349648708777463	2		279	388	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589312	28589312	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	23	339	0	ENST00000241453.7:c.2735T>A	p.Phe912Tyr	p.F912Y	ENST00000241453	NM_004119.2	912	tTt/tAt	22/24	1	2	FACETS	0.323	0.251	0.407	0.323	0.251	0.407	SUBCLONAL	1	TRUE	1	0.349648708777463	2		339	407	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601376	28601376	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	48	327	1	ENST00000241453.7:c.2056C>T	p.Pro686Ser	p.P686S	ENST00000241453	NM_004119.2	686	Cca/Tca	17/24	1	2	FACETS	0.808	0.685	0.941	0.808	0.685	0.941	CLONAL	1	TRUE	1	0.349648708777463	2		328	340	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897032	28897032	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	124	416	0	ENST00000282397.4:c.2848G>T	p.Glu950Ter	p.E950*	ENST00000282397	NM_002019.4	950	Gaa/Taa	21/30	1	2	FACETS	0.934	0.846	1	0.934	0.846	1	CLONAL	1	TRUE	1	0.349648708777463	2		416	759	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930564	32930564	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	74	228	1	ENST00000380152.3:c.7436-1G>T		p.X2479_splice	ENST00000380152		2479			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.349648708777463	2		229	338	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32931957	32931957	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs80358996	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	65	295	0	ENST00000380152.3:c.7696G>T	p.Asp2566Tyr	p.D2566Y	ENST00000380152		2566	Gat/Tat	16/27	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.349648708777463	2		295	332	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972336	32972336	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	63	430	0	ENST00000380152.3:c.9686C>A	p.Pro3229His	p.P3229H	ENST00000380152		3229	cCt/cAt	27/27	1	2	FACETS	0.656	0.568	0.752	0.656	0.568	0.752	SUBCLONAL	1	TRUE	1	0.349648708777463	2		430	549	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953730	48953730	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs3092891	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	47	181	0	ENST00000267163.4:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000267163	NM_000321.2	445	Cga/Tga	14/27	1	2	FACETS	0.985	0.837	1	0.985	0.837	1	CLONAL	1	TRUE	1	0.349648708777463	2		181	273	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955538	48955538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913303	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	61	337	1	ENST00000267163.4:c.1654C>T	p.Arg552Ter	p.R552*	ENST00000267163	NM_000321.2	552	Cga/Tga	17/27	1	2	FACETS	0.886	0.767	1	0.886	0.767	1	CLONAL	1	TRUE	1	0.349648708777463	2		338	394	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335641	73335641	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	58	227	1	ENST00000377767.4:c.2530G>T	p.Gly844Ter	p.G844*	ENST00000377767	NM_014953.3	844	Gga/Tga	19/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.349648708777463	2		228	283	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73348154	73348154	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	49	365	0	ENST00000377767.4:c.1031G>T	p.Arg344Ile	p.R344I	ENST00000377767	NM_014953.3	344	aGa/aTa	7/21	1	2	FACETS	0.687	0.583	0.801	0.687	0.583	0.801	SUBCLONAL	1	TRUE	1	0.349648708777463	2		365	408	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518064	103518064	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	107	331	0	ENST00000355739.4:c.2002G>A	p.Ala668Thr	p.A668T	ENST00000355739	NM_000123.3	668	Gca/Aca	9/15	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.349648708777463	2		331	488	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061291	38061291	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	209	742	1	ENST00000250448.2:c.698G>A	p.Arg233His	p.R233H	ENST00000250448	NM_004496.3	233	cGc/cAc	2/2	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.349648708777463	2		743	1113	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353867	68353867	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	100	385	1	ENST00000487270.1:c.702C>A	p.Phe234Leu	p.F234L	ENST00000487270	NM_133509.3	234	ttC/ttA	7/11	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.349648708777463	2		386	536	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95598872	95598872	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770567567	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	83	357	1	ENST00000393063.1:c.287C>T	p.Thr96Met	p.T96M	ENST00000393063	NM_030621.3	96	aCg/aTg	4/28	1	2	FACETS	0.973	0.861	1	0.973	0.861	1	CLONAL	1	TRUE	1	0.349648708777463	2		358	488	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023446	33023446	+	stop_lost	Nonstop_Mutation	SNP	A	A	C	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	209	689	0	ENST00000300177.4:c.555A>C	p.Ter185TyrextTer29	p.*185Yext*29	ENST00000300177	NM_001191322.1	185	taA/taC	2/2	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.349648708777463	2		689	1009	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38616972	38616972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764823722	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	96	257	0	ENST00000299084.4:c.385G>A	p.Glu129Lys	p.E129K	ENST00000299084	NM_152594.2	129	Gaa/Aaa	4/7	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.349648708777463	2		257	393	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961493	41961493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771815727	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	108	546	0	ENST00000219905.7:c.401G>A	p.Arg134His	p.R134H	ENST00000219905	NM_001164273.1	134	cGt/cAt	2/24	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.349648708777463	2		546	569	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991306	41991306	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	79	539	0	ENST00000219905.7:c.2137G>T	p.Asp713Tyr	p.D713Y	ENST00000219905	NM_001164273.1	713	Gat/Tat	5/24	1	2	FACETS	0.715	0.629	0.807	0.715	0.629	0.807	SUBCLONAL	1	TRUE	1	0.349648708777463	2		539	632	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019489	42019489	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	154	521	0	ENST00000219905.7:c.3542A>T	p.Glu1181Val	p.E1181V	ENST00000219905	NM_001164273.1	1181	gAg/gTg	10/24	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.349648708777463	2		521	651	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021428	42021428	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	129	421	1	ENST00000219905.7:c.3724C>T	p.Arg1242Ter	p.R1242*	ENST00000219905	NM_001164273.1	1242	Cga/Tga	11/24	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.349648708777463	2		422	628	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041957	42041957	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	92	489	0	ENST00000219905.7:c.6152C>T	p.Ser2051Phe	p.S2051F	ENST00000219905	NM_001164273.1	2051	tCc/tTc	17/24	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.349648708777463	2		489	508	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701243	43701243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769912966	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	155	519	0	ENST00000382044.4:c.5452C>T	p.Arg1818Trp	p.R1818W	ENST00000382044	NM_001141980.1	1818	Cgg/Tgg	26/28	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.349648708777463	2		519	887	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701889	43701889	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	51	225	0	ENST00000382044.4:c.5356C>T	p.Arg1786Ter	p.R1786*	ENST00000382044	NM_001141980.1	1786	Cga/Tga	25/28	1	2	FACETS	0.801	0.684	0.93	0.801	0.684	0.93	CLONAL	1	TRUE	1	0.349648708777463	2		225	364	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705321	43705321	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	115	653	0	ENST00000382044.4:c.5301G>T	p.Glu1767Asp	p.E1767D	ENST00000382044	NM_001141980.1	1767	gaG/gaT	24/28	1	2	FACETS	0.648	0.583	0.718	0.648	0.583	0.718	SUBCLONAL	1	TRUE	1	0.349648708777463	2		653	1015	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749242	43749242	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	137	605	1	ENST00000382044.4:c.1564C>T	p.Leu522Phe	p.L522F	ENST00000382044	NM_001141980.1	522	Ctt/Ttt	12/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.349648708777463	2		606	663	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457696	67457696	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772034969	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	148	587	1	ENST00000327367.4:c.506G>A	p.Gly169Asp	p.G169D	ENST00000327367	NM_005902.3	169	gGc/gAc	3/9	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.349648708777463	2		588	773	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476262	88476262	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	100	487	0	ENST00000360948.2:c.1870G>T	p.Asp624Tyr	p.D624Y	ENST00000360948	NM_001012338.2	624	Gac/Tac	15/19	1	2	FACETS	0.911	0.815	1	0.911	0.815	1	CLONAL	1	TRUE	1	0.349648708777463	2		487	628	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90634813	90634813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757504997	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	155	524	0	ENST00000330062.3:c.179G>A	p.Arg60His	p.R60H	ENST00000330062	NM_002168.2	60	cGt/cAt	2/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.349648708777463	2		524	818	SUCCESS
BLM	641	MSKCC	GRCh37	15	91298043	91298043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs755724766	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	43	276	1	ENST00000355112.3:c.962C>T	p.Thr321Met	p.T321M	ENST00000355112	NM_000057.2	321	aCg/aTg	5/22	1	2	FACETS	0.73	0.613	0.859	0.73	0.613	0.859	SUBCLONAL	1	TRUE	1	0.349648708777463	2		277	337	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465390	99465390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145300307	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	106	374	0	ENST00000268035.6:c.2215C>T	p.Arg739Trp	p.R739W	ENST00000268035	NM_000875.3	739	Cgg/Tgg	11/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.349648708777463	2		374	550	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347146	347146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	226	806	0	ENST00000262320.3:c.1865C>T	p.Ala622Val	p.A622V	ENST00000262320	NM_003502.3	622	gCc/gTc	7/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.349648708777463	2		806	1126	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112532	2112532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202187148	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	155	774	0	ENST00000219476.3:c.1292C>T	p.Ala431Val	p.A431V	ENST00000219476	NM_000548.3	431	gCg/gTg	13/42	1	2	FACETS	0.851	0.778	0.927	0.851	0.778	0.927	CLONAL	1	TRUE	1	0.349648708777463	2		774	1042	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126103	2126103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376801256	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	248	741	0	ENST00000219476.3:c.2674G>A	p.Val892Ile	p.V892I	ENST00000219476	NM_000548.3	892	Gtc/Atc	24/42	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.349648708777463	2		741	1166	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135250	2135250	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	188	889	0	ENST00000219476.3:c.4589C>A	p.Ser1530Ter	p.S1530*	ENST00000219476	NM_000548.3	1530	tCg/tAg	36/42	1	2	FACETS	0.989	0.913	1	0.989	0.913	1	CLONAL	1	TRUE	1	0.349648708777463	2		889	1087	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647685	3647685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1160715108	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	200	797	1	ENST00000294008.3:c.1378C>T	p.Arg460Cys	p.R460C	ENST00000294008	NM_032444.2	460	Cgc/Tgc	7/15	1	2	FACETS	0.992	0.918	1	0.992	0.918	1	CLONAL	1	TRUE	1	0.349648708777463	2		798	1153	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777838	3777838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863223334	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	249	973	3	ENST00000262367.5:c.7210G>A	p.Glu2404Lys	p.E2404K	ENST00000262367	NM_004380.2	2404	Gaa/Aaa	31/31	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.349648708777463	2		976	1405	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934524	9934524	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	109	421	0	ENST00000330684.3:c.1631T>C	p.Val544Ala	p.V544A	ENST00000330684	NM_001134407.1	544	gTc/gCc	7/13	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.349648708777463	2		421	612	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934525	9934525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	127	390	0	ENST00000330684.3:c.1630G>A	p.Val544Ile	p.V544I	ENST00000330684	NM_001134407.1	544	Gtc/Atc	7/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.349648708777463	2		390	606	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943680	9943680	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	158	630	0	ENST00000330684.3:c.1261G>T	p.Asp421Tyr	p.D421Y	ENST00000330684	NM_001134407.1	421	Gac/Tac	5/13	1	2	FACETS	0.935	0.856	1	0.935	0.856	1	CLONAL	1	TRUE	1	0.349648708777463	2		630	967	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032281	10032281	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	154	584	0	ENST00000330684.3:c.542G>T	p.Arg181Met	p.R181M	ENST00000330684	NM_001134407.1	181	aGg/aTg	3/13	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.349648708777463	2		584	774	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274037	10274037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	195	843	2	ENST00000330684.3:c.232G>A	p.Asp78Asn	p.D78N	ENST00000330684	NM_001134407.1	78	Gac/Aac	2/13	1	2	FACETS	0.999	0.923	1	0.999	0.923	1	CLONAL	1	TRUE	1	0.349648708777463	2		845	1117	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041765	14041765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	37	378	0	ENST00000311895.7:c.2312C>T	p.Ser771Phe	p.S771F	ENST00000311895	NM_005236.2	771	tCc/tTc	11/11	1	2	FACETS	0.315	0.259	0.378	0.315	0.259	0.378	SUBCLONAL	1	TRUE	1	0.349648708777463	2		378	672	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641672	23641672	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	110	475	0	ENST00000261584.4:c.1803G>T	p.Lys601Asn	p.K601N	ENST00000261584	NM_024675.3	601	aaG/aaT	5/13	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.349648708777463	2		475	523	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646395	23646395	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	147	544	0	ENST00000261584.4:c.1472C>A	p.Ala491Asp	p.A491D	ENST00000261584	NM_024675.3	491	gCt/gAt	4/13	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.349648708777463	2		544	780	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647241	23647241	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	139	597	0	ENST00000261584.4:c.626C>A	p.Ser209Tyr	p.S209Y	ENST00000261584	NM_024675.3	209	tCt/tAt	4/13	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.349648708777463	2		597	697	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825509	50825509	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	86	349	0	ENST00000398568.2:c.2140A>T	p.Ile714Phe	p.I714F	ENST00000398568	NM_001042412.1	714	Att/Ttt	14/18	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.349648708777463	2		349	410	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868319	56868319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748524706	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	76	291	0	ENST00000308159.5:c.1702C>T	p.Arg568Cys	p.R568C	ENST00000308159	NM_014669.4	568	Cgc/Tgc	15/22	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.349648708777463	2		291	418	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645159	67645159	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1175444753	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	119	624	0	ENST00000264010.4:c.424G>A	p.Val142Met	p.V142M	ENST00000264010	NM_006565.3	142	Gtg/Atg	3/12	1	2	FACETS	0.768	0.693	0.848	0.768	0.693	0.848	SUBCLONAL	1	TRUE	1	0.349648708777463	2		624	886	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654646	67654646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	154	476	0	ENST00000264010.4:c.1133C>T	p.Pro378Leu	p.P378L	ENST00000264010	NM_006565.3	378	cCg/cTg	6/12	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.349648708777463	2		476	841	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655431	67655431	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	146	539	2	ENST00000264010.4:c.1294G>T	p.Glu432Ter	p.E432*	ENST00000264010	NM_006565.3	432	Gaa/Taa	7/12	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.349648708777463	2		541	750	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844193	68844193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121964873	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	181	684	1	ENST00000261769.5:c.781G>A	p.Glu261Lys	p.E261K	ENST00000261769	NM_004360.3	261	Gaa/Aaa	6/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.349648708777463	2		685	885	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821815	72821815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770453754	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	98	507	2	ENST00000268489.5:c.10360G>A	p.Asp3454Asn	p.D3454N	ENST00000268489	NM_006885.3	3454	Gac/Aac	10/10	1	2	FACETS	0.557	0.495	0.622	0.557	0.495	0.622	SUBCLONAL	1	TRUE	1	0.349648708777463	2		509	1007	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827732	72827732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241554729	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	142	482	1	ENST00000268489.5:c.8849G>A	p.Arg2950His	p.R2950H	ENST00000268489	NM_006885.3	2950	cGc/cAc	9/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.349648708777463	2		483	732	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829922	72829922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	223	598	1	ENST00000268489.5:c.6659A>T	p.Glu2220Val	p.E2220V	ENST00000268489	NM_006885.3	2220	gAg/gTg	9/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.349648708777463	2		599	1024	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81971407	81971407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376667295	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	124	486	0	ENST00000359376.3:c.3097C>T	p.Arg1033Cys	p.R1033C	ENST00000359376	NM_002661.3	1033	Cgc/Tgc	28/33	1	2	FACETS	0.984	0.891	1	0.984	0.891	1	CLONAL	1	TRUE	1	0.349648708777463	2		486	721	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347080	89347080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs922813408	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	178	644	0	ENST00000301030.4:c.5870C>T	p.Ala1957Val	p.A1957V	ENST00000301030	NM_001256183.1	1957	gCg/gTg	9/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.349648708777463	2		644	833	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347486	89347486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373805397	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	160	660	0	ENST00000301030.4:c.5464G>A	p.Asp1822Asn	p.D1822N	ENST00000301030	NM_001256183.1	1822	Gac/Aac	9/13	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.349648708777463	2		660	807	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348669	89348669	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1421678693	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	207	869	1	ENST00000301030.4:c.4281G>T	p.Lys1427Asn	p.K1427N	ENST00000301030	NM_001256183.1	1427	aaG/aaT	9/13	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.349648708777463	2		870	1011	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350710	89350710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138898373	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	206	857	0	ENST00000301030.4:c.2240C>T	p.Ser747Leu	p.S747L	ENST00000301030	NM_001256183.1	747	tCg/tTg	9/13	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.349648708777463	2		857	1148	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805675	89805675	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	144	570	0	ENST00000389301.3:c.4033G>T	p.Asp1345Tyr	p.D1345Y	ENST00000389301	NM_000135.2	1345	Gac/Tac	41/43	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.349648708777463	2		570	722	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89828358	89828358	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs755546887	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	69	399	0	ENST00000389301.3:c.2851C>T	p.Arg951Trp	p.R951W	ENST00000389301	NM_000135.2	951	Cgg/Tgg	29/43	1	2	FACETS	0.631	0.55	0.72	0.631	0.55	0.72	SUBCLONAL	1	TRUE	1	0.349648708777463	2		399	625	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217622	7217622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	91	402	0	ENST00000380728.2:c.305G>A	p.Arg102Gln	p.R102Q	ENST00000380728		102	cGa/cAa	4/11	1	2	FACETS	0.832	0.739	0.93	0.832	0.739	0.93	CLONAL	1	TRUE	1	0.349648708777463	2		402	626	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983234	7983234	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	170	621	0	ENST00000319144.4:c.780G>T	p.Glu260Asp	p.E260D	ENST00000319144	NM_001139.2	260	gaG/gaT	7/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.349648708777463	2		621	791	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075199	16075199	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	169	340	0	ENST00000268712.3:c.353A>G	p.His118Arg	p.H118R	ENST00000268712	NM_006311.3	118	cAt/cGt	4/46	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.349648708777463	2		340	756	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554309	29554309	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	233	691	0	ENST00000356175.3:c.2325G>T	p.Glu775Asp	p.E775D	ENST00000356175	NM_000267.3	775	gaG/gaT	19/57	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.349648708777463	2		691	1190	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562981	29562981	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs376576925	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	84	443	1	ENST00000356175.3:c.3916C>T	p.Arg1306Ter	p.R1306*	ENST00000356175	NM_000267.3	1306	Cga/Tga	29/57	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.349648708777463	2		444	442	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654716	29654716	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	103	347	0	ENST00000356175.3:c.5405C>A	p.Ser1802Tyr	p.S1802Y	ENST00000356175	NM_000267.3	1802	tCt/tAt	37/57	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.349648708777463	2		347	571	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654842	29654842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	72	245	0	ENST00000356175.3:c.5531C>T	p.Ser1844Phe	p.S1844F	ENST00000356175	NM_000267.3	1844	tCt/tTt	37/57	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.349648708777463	2		245	407	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665149	29665149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	123	450	0	ENST00000356175.3:c.6748C>T	p.Leu2250Phe	p.L2250F	ENST00000356175	NM_000267.3	2250	Ctt/Ttt	44/57	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.349648708777463	2		450	625	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	65	320	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.349648708777463	2		320	338	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657596	37657596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748453656	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	108	556	1	ENST00000447079.4:c.2513C>T	p.Ser838Leu	p.S838L	ENST00000447079	NM_015083.1	838	tCg/tTg	6/14	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.349648708777463	2		557	552	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37856556	37856556	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs896376245	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	128	393	0	ENST00000269571.5:c.65G>A	p.Ser22Asn	p.S22N	ENST00000269571		22	aGc/aAc	1/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.349648708777463	2		393	574	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353772	40353772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752309096	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	187	624	0	ENST00000293328.3:c.2348C>T	p.Pro783Leu	p.P783L	ENST00000293328	NM_012448.3	783	cCg/cTg	19/19	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.349648708777463	2		624	1022	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40371822	40371822	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1396130852	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	148	678	0	ENST00000293328.3:c.589C>T	p.Arg197Cys	p.R197C	ENST00000293328	NM_012448.3	197	Cgt/Tgt	6/19	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.349648708777463	2		678	809	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375526	40375526	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	178	527	0	ENST00000293328.3:c.424C>A	p.Leu142Ile	p.L142I	ENST00000293328	NM_012448.3	142	Ctc/Atc	5/19	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.349648708777463	2		527	901	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870631	40870631	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs751414770	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	145	465	1	ENST00000428826.2:c.772C>T	p.Arg258Ter	p.R258*	ENST00000428826		258	Cga/Tga	9/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.349648708777463	2		466	660	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245603	41245603	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs80356907	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	156	609	0	ENST00000357654.3:c.1945G>T	p.Glu649Ter	p.E649*	ENST00000357654	NM_007294.3	649	Gag/Tag	10/23	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.349648708777463	2		609	675	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805786	46805786	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	133	682	2	ENST00000290295.7:c.170C>T	p.Ala57Val	p.A57V	ENST00000290295	NM_006361.5	57	gCg/gTg	1/2	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.349648708777463	2		684	692	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805840	46805840	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	130	597	0	ENST00000290295.7:c.116C>T	p.Ala39Val	p.A39V	ENST00000290295	NM_006361.5	39	gCg/gTg	1/2	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.349648708777463	2		597	623	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58701078	58701078	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	144	498	1	ENST00000305921.3:c.669G>T	p.Lys223Asn	p.K223N	ENST00000305921	NM_003620.3	223	aaG/aaT	2/6	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.349648708777463	2		499	810	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59820395	59820395	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	99	360	1	ENST00000259008.2:c.2358T>A	p.Phe786Leu	p.F786L	ENST00000259008	NM_032043.2	786	ttT/ttA	16/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.349648708777463	2		361	479	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66522016	66522016	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	69	244	0	ENST00000358598.2:c.674del	p.Gly225AlafsTer16	p.G225Afs*16	ENST00000358598	NM_212471.2	224	tGg/tg	7/11	1	2	FACETS	0.814	0.71	0.925	0.814	0.71	0.925	CLONAL	1	TRUE	1	0.349648708777463	2		244	485	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66523999	66523999	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	52	191	0	ENST00000358598.2:c.727C>T	p.Arg243Trp	p.R243W	ENST00000358598	NM_212471.2	243	Cgg/Tgg	8/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.349648708777463	2		191	234	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732523	74732523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	31	177	0	ENST00000359995.5:c.386G>A	p.Arg129Gln	p.R129Q	ENST00000359995	NM_001195427.1	129	cGa/cAa	2/3	1	2	FACETS	0.9	0.734	1	0.9	0.734	1	CLONAL	1	TRUE	1	0.349648708777463	2		177	197	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78831701	78831701	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1251049844	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	191	635	0	ENST00000306801.3:c.1509+1G>A		p.X503_splice	ENST00000306801	NM_020761.2	503			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.349648708777463	2		635	870	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866606	78866606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	157	627	0	ENST00000306801.3:c.2179C>T	p.Arg727Cys	p.R727C	ENST00000306801	NM_020761.2	727	Cgt/Tgt	19/34	1	2	FACETS	0.935	0.856	1	0.935	0.856	1	CLONAL	1	TRUE	1	0.349648708777463	2		627	960	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78933888	78933888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	161	614	1	ENST00000306801.3:c.3488C>T	p.Thr1163Met	p.T1163M	ENST00000306801	NM_020761.2	1163	aCg/aTg	30/34	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.349648708777463	2		615	798	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745706	745706	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	97	378	0	ENST00000314574.4:c.724+2T>C		p.X242_splice	ENST00000314574	NM_005433.3	242			1	2	FACETS	0.795	0.715	0.878	1	0.984	1	SUBCLONAL	2	TRUE	1	0.349648708777463	2		378	349	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615791	1615791	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs562975911	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	78	739	0	ENST00000344749.5:c.1480G>A	p.Ala494Thr	p.A494T	ENST00000344749	NM_001136139.2	494	Gcc/Acc	17/19	1	2	FACETS	0.47	0.412	0.533	0.47	0.412	0.533	SUBCLONAL	1	TRUE	1	0.349648708777463	2		739	949	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101240	4101240	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	153	777	0	ENST00000262948.5:c.567G>T	p.Gln189His	p.Q189H	ENST00000262948	NM_030662.3	189	caG/caT	5/11	1	2	FACETS	0.886	0.81	0.966	0.886	0.81	0.966	CLONAL	1	TRUE	1	0.349648708777463	2		777	988	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222993	5222993	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762510209	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	169	581	4	ENST00000357368.4:c.2810C>T	p.Ala937Val	p.A937V	ENST00000357368	NM_002850.3	937	gCg/gTg	18/38	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.349648708777463	2		585	793	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267416	7267416	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	182	452	0	ENST00000302850.5:c.592G>A	p.Ala198Thr	p.A198T	ENST00000302850	NM_000208.2	198	Gcc/Acc	2/22	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.349648708777463	2		452	821	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250770	10250770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1290055474	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	171	730	1	ENST00000340748.4:c.3710C>T	p.Ser1237Leu	p.S1237L	ENST00000340748		1237	tCg/tTg	32/40	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.349648708777463	2		731	946	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10257170	10257170	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	132	494	1	ENST00000340748.4:c.2703G>T	p.Glu901Asp	p.E901D	ENST00000340748		901	gaG/gaT	27/40	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.349648708777463	2		495	739	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10267124	10267124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751093624	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	215	491	0	ENST00000340748.4:c.1294G>A	p.Glu432Lys	p.E432K	ENST00000340748		432	Gaa/Aaa	17/40	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.349648708777463	2		491	962	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602404	10602404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1432914621	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	194	873	1	ENST00000171111.5:c.1174G>A	p.Ala392Thr	p.A392T	ENST00000171111	NM_203500.1	392	Gcc/Acc	3/6	1	2	FACETS	0.929	0.858	1	0.929	0.858	1	CLONAL	1	TRUE	1	0.349648708777463	2		874	1194	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123685	11123685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	195	643	0	ENST00000358026.2:c.2335G>A	p.Asp779Asn	p.D779N	ENST00000358026	NM_001128849.1	779	Gac/Aac	16/36	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.349648708777463	2		643	1026	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627456	14627456	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	176	588	0	ENST00000254322.2:c.614C>T	p.Thr205Ile	p.T205I	ENST00000254322	NM_006145.1	205	aCc/aTc	2/3	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.349648708777463	2		588	866	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272201	15272201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113178142	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	37	661	1	ENST00000263388.2:c.6238C>T	p.Arg2080Trp	p.R2080W	ENST00000263388	NM_000435.2	2080	Cgg/Tgg	33/33	1	2	FACETS	0.314	0.257	0.377	0.314	0.257	0.377	SUBCLONAL	1	TRUE	1	0.349648708777463	2		662	675	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212357	36212357	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1476081557	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	202	794	0	ENST00000222270.7:c.2108G>T	p.Ser703Ile	p.S703I	ENST00000222270	NM_014727.1	703	aGc/aTc	3/37	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.349648708777463	2		794	1072	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215951	36215951	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	237	734	0	ENST00000222270.7:c.3491C>A	p.Ser1164Tyr	p.S1164Y	ENST00000222270	NM_014727.1	1164	tCt/tAt	10/37	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.349648708777463	2		734	1213	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229027	36229027	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	227	727	1	ENST00000222270.7:c.7807G>A	p.Glu2603Lys	p.E2603K	ENST00000222270	NM_014727.1	2603	Gag/Aag	36/37	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.349648708777463	2		728	1152	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229239	36229239	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	195	718	0	ENST00000222270.7:c.7929G>A	p.Met2643Ile	p.M2643I	ENST00000222270	NM_014727.1	2643	atG/atA	37/37	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.349648708777463	2		718	885	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741173	40741173	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	155	735	0	ENST00000392038.2:c.1260G>T	p.Lys420Asn	p.K420N	ENST00000392038	NM_001626.4	420	aaG/aaT	12/14	1	2	FACETS	0.935	0.856	1	0.935	0.856	1	CLONAL	1	TRUE	1	0.349648708777463	2		735	948	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763456	41763456	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	153	595	0	ENST00000301178.4:c.2255G>A	p.Gly752Asp	p.G752D	ENST00000301178	NM_021913.4	752	gGc/gAc	19/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.349648708777463	2		595	812	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753276	42753276	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756887571	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	275	963	2	ENST00000222329.4:c.988G>A	p.Ala330Thr	p.A330T	ENST00000222329	NM_006494.2	330	Gcc/Acc	4/4	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.349648708777463	2		965	1342	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753644	42753644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759092904	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	233	826	0	ENST00000222329.4:c.620G>A	p.Arg207Gln	p.R207Q	ENST00000222329	NM_006494.2	207	cGa/cAa	4/4	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.349648708777463	2		826	1047	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754650	42754650	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	169	633	0	ENST00000222329.4:c.90G>T	p.Trp30Cys	p.W30C	ENST00000222329	NM_006494.2	30	tgG/tgT	2/4	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.349648708777463	2		633	777	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795121	42795121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778197	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	239	857	0	ENST00000575354.2:c.2201C>T	p.Ser734Leu	p.S734L	ENST00000575354	NM_015125.3	734	tCg/tTg	10/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.349648708777463	2		857	1091	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796254	42796254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	197	755	0	ENST00000575354.2:c.2903C>T	p.Pro968Leu	p.P968L	ENST00000575354	NM_015125.3	968	cCg/cTg	12/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.349648708777463	2		755	1033	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796987	42796987	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	238	865	1	ENST00000575354.2:c.3445A>G	p.Thr1149Ala	p.T1149A	ENST00000575354	NM_015125.3	1149	Act/Gct	14/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.349648708777463	2		866	1236	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797804	42797804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141205881	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	186	757	0	ENST00000575354.2:c.3856C>T	p.Arg1286Cys	p.R1286C	ENST00000575354	NM_015125.3	1286	Cgt/Tgt	16/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.349648708777463	2		757	978	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909556	50909556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs906743894	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	141	752	0	ENST00000440232.2:c.1360C>T	p.Arg454Cys	p.R454C	ENST00000440232	NM_002691.3	454	Cgc/Tgc	11/27	1	2	FACETS	0.99	0.902	1	0.99	0.902	1	CLONAL	1	TRUE	1	0.349648708777463	2		752	815	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909559	50909559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762670703	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	141	742	2	ENST00000440232.2:c.1363G>A	p.Val455Met	p.V455M	ENST00000440232	NM_002691.3	455	Gtg/Atg	11/27	1	2	FACETS	0.998	0.91	1	0.998	0.91	1	CLONAL	1	TRUE	1	0.349648708777463	2		744	808	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719064	52719064	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	132	557	0	ENST00000322088.6:c.840G>T	p.Lys280Asn	p.K280N	ENST00000322088	NM_014225.5	280	aaG/aaT	7/15	1	2	FACETS	0.923	0.838	1	0.923	0.838	1	CLONAL	1	TRUE	1	0.349648708777463	2		557	818	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966325	25966325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	62	629	0	ENST00000435504.4:c.2881G>A	p.Asp961Asn	p.D961N	ENST00000435504		961	Gat/Aat	13/13	1	2	FACETS	0.414	0.357	0.477	0.414	0.357	0.477	SUBCLONAL	1	TRUE	1	0.349648708777463	2		629	856	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416598	29416598	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	110	466	0	ENST00000389048.3:c.4355C>A	p.Ala1452Asp	p.A1452D	ENST00000389048	NM_004304.4	1452	gCt/gAt	29/29	1	2	FACETS	0.934	0.84	1	0.934	0.84	1	CLONAL	1	TRUE	1	0.349648708777463	2		466	674	SUCCESS
ALK	238	MSKCC	GRCh37	2	29448365	29448365	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	259	996	0	ENST00000389048.3:c.3134T>G	p.Val1045Gly	p.V1045G	ENST00000389048	NM_004304.4	1045	gTg/gGg	19/29	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.349648708777463	2		996	1263	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250353	39250353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	117	566	2	ENST00000402219.2:c.1216C>T	p.Arg406Trp	p.R406W	ENST00000402219	NM_005633.3	406	Cgg/Tgg	10/23	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.349648708777463	2		568	580	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39251201	39251201	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	103	513	0	ENST00000402219.2:c.1152G>T	p.Gln384His	p.Q384H	ENST00000402219	NM_005633.3	384	caG/caT	9/23	1	2	FACETS	0.859	0.769	0.954	0.859	0.769	0.954	CLONAL	1	TRUE	1	0.349648708777463	2		513	686	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281838	39281838	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	107	451	0	ENST00000402219.2:c.637C>T	p.Arg213Ter	p.R213*	ENST00000402219	NM_005633.3	213	Cga/Tga	5/23	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.349648708777463	2		451	559	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641516	47641516	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	84	316	0	ENST00000233146.2:c.901A>G	p.Lys301Glu	p.K301E	ENST00000233146	NM_000251.2	301	Aaa/Gaa	5/16	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.349648708777463	2		316	465	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698180	47698180	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63751411	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	72	269	0	ENST00000233146.2:c.1738G>T	p.Glu580Ter	p.E580*	ENST00000233146	NM_000251.2	580	Gaa/Taa	11/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.349648708777463	2		269	354	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027354	48027354	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	78	319	0	ENST00000234420.5:c.2232G>T	p.Glu744Asp	p.E744D	ENST00000234420	NM_000179.2	744	gaG/gaT	4/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.349648708777463	2		319	371	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	134	288	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.349648708777463	2		290	725	SUCCESS
REL	5966	MSKCC	GRCh37	2	61144132	61144132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253056300	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	111	459	0	ENST00000295025.8:c.515C>T	p.Ser172Leu	p.S172L	ENST00000295025	NM_002908.2	172	tCg/tTg	5/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.349648708777463	2		459	578	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152291	99152291	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	125	384	0	ENST00000074304.5:c.370G>T	p.Asp124Tyr	p.D124Y	ENST00000074304	NM_001134224.1	124	Gat/Tat	6/26	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.349648708777463	2		384	531	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99179935	99179935	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	193	704	0	ENST00000074304.5:c.1878G>A	p.Trp626Ter	p.W626*	ENST00000074304	NM_001134224.1	626	tgG/tgA	19/26	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.349648708777463	2		704	963	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907686	111907686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370016302	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	120	387	0	ENST00000393256.3:c.460C>T	p.Arg154Cys	p.R154C	ENST00000393256	NM_006538.4	154	Cgt/Tgt	3/4	1	2	FACETS	0.972	0.879	1	0.972	0.879	1	CLONAL	1	TRUE	1	0.349648708777463	2		387	706	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921737	111921737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1170116948	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	119	371	0	ENST00000393256.3:c.526G>A	p.Glu176Lys	p.E176K	ENST00000393256	NM_006538.4	176	Gaa/Aaa	4/4	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.349648708777463	2		371	617	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128030502	128030502	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	38	563	0	ENST00000285398.2:c.1766G>T	p.Arg589Met	p.R589M	ENST00000285398	NM_000122.1	589	aGg/aTg	11/15	1	2	FACETS	0.311	0.256	0.373	0.311	0.256	0.373	SUBCLONAL	1	TRUE	1	0.349648708777463	2		563	699	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038133	128038133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369244363	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	120	404	0	ENST00000285398.2:c.1417G>A	p.Glu473Lys	p.E473K	ENST00000285398	NM_000122.1	473	Gaa/Aaa	9/15	1	2	FACETS	0.938	0.848	1	0.938	0.848	1	CLONAL	1	TRUE	1	0.349648708777463	2		404	732	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046995	128046995	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	162	579	0	ENST00000285398.2:c.740A>G	p.Asp247Gly	p.D247G	ENST00000285398	NM_000122.1	247	gAc/gGc	6/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.349648708777463	2		579	828	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051271	128051271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	127	580	0	ENST00000285398.2:c.52C>T	p.His18Tyr	p.H18Y	ENST00000285398	NM_000122.1	18	Cac/Tac	2/15	1	2	FACETS	0.921	0.834	1	0.921	0.834	1	CLONAL	1	TRUE	1	0.349648708777463	2		580	789	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737491	204737491	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	74	354	0	ENST00000302823.3:c.628G>T	p.Glu210Ter	p.E210*	ENST00000302823	NM_005214.4	210	Gaa/Taa	4/4	1	2	FACETS	0.922	0.81	1	0.922	0.81	1	CLONAL	1	TRUE	1	0.349648708777463	2		354	459	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293145	212293145	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764667767	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	52	272	0	ENST00000342788.4:c.2707G>A	p.Val903Ile	p.V903I	ENST00000342788	NM_005235.2	903	Gtt/Att	22/28	1	2	FACETS	0.804	0.687	0.931	0.804	0.687	0.931	CLONAL	1	TRUE	1	0.349648708777463	2		272	370	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212615424	212615424	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752051535	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	47	430	0	ENST00000342788.4:c.562C>T	p.Arg188Cys	p.R188C	ENST00000342788	NM_005235.2	188	Cgt/Tgt	5/28	1	2	FACETS	0.349	0.294	0.411	0.349	0.294	0.411	SUBCLONAL	1	TRUE	1	0.349648708777463	2		430	770	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439504	220439504	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	153	594	1	ENST00000243786.2:c.357G>T	p.Gln119His	p.Q119H	ENST00000243786	NM_002191.3	119	caG/caT	2/2	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.349648708777463	2		595	813	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225365174	225365174	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	132	334	1	ENST00000264414.4:c.1516C>T	p.Arg506Trp	p.R506W	ENST00000264414	NM_003590.4	506	Cgg/Tgg	11/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.349648708777463	2		335	646	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379333	225379333	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	107	411	0	ENST00000264414.4:c.535G>T	p.Asp179Tyr	p.D179Y	ENST00000264414	NM_003590.4	179	Gac/Tac	4/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.349648708777463	2		411	497	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793286	242793286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757334336	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	227	943	0	ENST00000334409.5:c.791G>A	p.Arg264His	p.R264H	ENST00000334409	NM_005018.2	264	cGc/cAc	5/5	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.349648708777463	2		943	1092	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794111	242794111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	171	665	0	ENST00000334409.5:c.617G>A	p.Gly206Asp	p.G206D	ENST00000334409	NM_005018.2	206	gGc/gAc	4/5	1	2	FACETS	0.935	0.859	1	0.935	0.859	1	CLONAL	1	TRUE	1	0.349648708777463	2		665	1046	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525088	9525088	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	114	444	0	ENST00000353224.5:c.1797G>T	p.Lys599Asn	p.K599N	ENST00000353224	NM_177990.2	599	aaG/aaT	8/10	1	2	FACETS	0.967	0.872	1	0.967	0.872	1	CLONAL	1	TRUE	1	0.349648708777463	2		444	674	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021634	31021634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137920574	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	146	498	0	ENST00000375687.4:c.1633C>T	p.Arg545Cys	p.R545C	ENST00000375687	NM_015338.5	545	Cgt/Tgt	12/13	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.349648708777463	2		498	818	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383317	31383317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772079891	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	171	529	0	ENST00000328111.2:c.1229G>A	p.Arg410Gln	p.R410Q	ENST00000328111	NM_006892.3	410	cGa/cAa	11/23	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.349648708777463	2		529	858	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31390243	31390243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747182299	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	180	506	0	ENST00000328111.2:c.2198G>A	p.Arg733Gln	p.R733Q	ENST00000328111	NM_006892.3	733	cGa/cAa	20/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.349648708777463	2		506	876	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031588	36031588	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	164	686	1	ENST00000358208.4:c.1417G>A	p.Glu473Lys	p.E473K	ENST00000358208		473	Gag/Aag	12/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.349648708777463	2		687	852	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743943	40743943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763964405	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	118	459	0	ENST00000373198.4:c.3052C>T	p.Arg1018Ter	p.R1018*	ENST00000373198	NM_133170.3	1018	Cga/Tga	23/32	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.349648708777463	2		459	645	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656879	45656879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370218763	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	227	658	0	ENST00000407780.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000407780	NM_001283052.1	93	Cgg/Tgg	3/7	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.349648708777463	2		658	1139	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162026	22162026	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	137	509	1	ENST00000215832.6:c.229C>T	p.Arg77Cys	p.R77C	ENST00000215832	NM_002745.4	77	Cgc/Tgc	2/9	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.349648708777463	2		510	590	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24158976	24158976	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	143	586	0	ENST00000263121.7:c.648G>T	p.Glu216Asp	p.E216D	ENST00000263121	NM_003073.3	216	gaG/gaT	6/9	1	2	FACETS	0.958	0.873	1	0.958	0.873	1	CLONAL	1	TRUE	1	0.349648708777463	2		586	854	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130622	29130622	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	135	512	0	ENST00000328354.6:c.88G>T	p.Gly30Cys	p.G30C	ENST00000328354	NM_007194.3	30	Ggc/Tgc	2/15	1	2	FACETS	0.975	0.887	1	0.975	0.887	1	CLONAL	1	TRUE	1	0.349648708777463	2		512	792	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523588	41523588	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	180	562	0	ENST00000263253.7:c.1004G>A	p.Arg335His	p.R335H	ENST00000263253	NM_001429.3	335	cGc/cAc	4/31	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.349648708777463	2		562	899	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458377	12458377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	175	634	0	ENST00000287820.6:c.994C>T	p.Pro332Ser	p.P332S	ENST00000287820	NM_015869.4	332	Cct/Tct	6/7	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.349648708777463	2		634	939	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660097	12660097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200856000	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	73	447	2	ENST00000251849.4:c.124G>A	p.Ala42Thr	p.A42T	ENST00000251849	NM_002880.3	42	Gca/Aca	2/17	1	2	FACETS	0.599	0.523	0.681	0.599	0.523	0.681	SUBCLONAL	1	TRUE	1	0.349648708777463	2		449	697	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691841	30691841	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	99	387	0	ENST00000295754.5:c.343G>T	p.Asp115Tyr	p.D115Y	ENST00000295754	NM_003242.5	115	Gat/Tat	3/7	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.349648708777463	2		387	521	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732932	30732932	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	94	320	0	ENST00000295754.5:c.1545G>T	p.Glu515Asp	p.E515D	ENST00000295754	NM_003242.5	515	gaG/gaT	7/7	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.349648708777463	2		320	428	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275291	41275291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750554859	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	124	377	0	ENST00000349496.5:c.1457G>A	p.Arg486His	p.R486H	ENST00000349496	NM_001904.3	486	cGc/cAc	9/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.349648708777463	2		377	649	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139464	47139464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	137	499	0	ENST00000409792.3:c.5123G>A	p.Arg1708Gln	p.R1708Q	ENST00000409792	NM_014159.6	1708	cGa/cAa	9/21	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.349648708777463	2		499	716	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139557	47139557	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	96	329	0	ENST00000409792.3:c.5030A>T	p.Lys1677Ile	p.K1677I	ENST00000409792	NM_014159.6	1677	aAa/aTa	9/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.349648708777463	2		329	507	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162795	47162795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760289594	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	62	324	0	ENST00000409792.3:c.3331C>T	p.His1111Tyr	p.H1111Y	ENST00000409792	NM_014159.6	1111	Cat/Tat	3/21	1	2	FACETS	0.84	0.728	0.961	0.84	0.728	0.961	CLONAL	1	TRUE	1	0.349648708777463	2		324	422	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164132	47164132	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	48	271	0	ENST00000409792.3:c.1994G>T	p.Ser665Ile	p.S665I	ENST00000409792	NM_014159.6	665	aGt/aTt	3/21	1	2	FACETS	0.9	0.765	1	0.9	0.765	1	CLONAL	1	TRUE	1	0.349648708777463	2		271	305	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164311	47164311	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	59	291	0	ENST00000409792.3:c.1815A>C	p.Lys605Asn	p.K605N	ENST00000409792	NM_014159.6	605	aaA/aaC	3/21	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.349648708777463	2		291	299	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164856	47164856	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1278528667	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	65	276	0	ENST00000409792.3:c.1270C>T	p.Arg424Ter	p.R424*	ENST00000409792	NM_014159.6	424	Cga/Tga	3/21	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.349648708777463	2		276	364	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927934	49927934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764547217	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	131	516	0	ENST00000296474.3:c.3794C>T	p.Thr1265Ile	p.T1265I	ENST00000296474	NM_002447.2	1265	aCc/aTc	18/20	1	2	FACETS	0.926	0.841	1	0.926	0.841	1	CLONAL	1	TRUE	1	0.349648708777463	2		516	809	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442566	52442566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553646022	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	150	424	0	ENST00000460680.1:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000460680	NM_004656.3	60	cGa/cAa	4/17	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.349648708777463	2		424	726	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620566	52620566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746373271	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	161	460	0	ENST00000394830.3:c.3187C>T	p.Arg1063Trp	p.R1063W	ENST00000394830	NM_018313.4	1063	Cgg/Tgg	21/30	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.349648708777463	2		460	850	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014044	70014044	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	132	382	0	ENST00000394351.3:c.905C>A	p.Ser302Tyr	p.S302Y	ENST00000394351	NM_000248.3	302	tCc/tAc	9/9	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.349648708777463	2		382	640	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71064699	71064699	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	103	299	0	ENST00000318789.4:c.974+1G>T		p.X325_splice	ENST00000318789	NM_032682.5	325			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.349648708777463	2		299	516	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73112826	73112826	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	52	183	0	ENST00000356692.5:c.422A>C	p.Lys141Thr	p.K141T	ENST00000356692		141	aAa/aCa	6/9	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.349648708777463	2		183	277	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259104	89259104	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	77	275	0	ENST00000336596.2:c.248G>A	p.Arg83Lys	p.R83K	ENST00000336596	NM_005233.5	83	aGa/aAa	3/17	1	2	FACETS	0.962	0.847	1	0.962	0.847	1	CLONAL	1	TRUE	1	0.349648708777463	2		275	458	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259437	89259437	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	101	499	0	ENST00000336596.2:c.581C>A	p.Ser194Tyr	p.S194Y	ENST00000336596	NM_005233.5	194	tCt/tAt	3/17	1	2	FACETS	0.955	0.855	1	0.955	0.855	1	CLONAL	1	TRUE	1	0.349648708777463	2		499	605	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391088	89391088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767254790	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	191	624	0	ENST00000336596.2:c.1154G>A	p.Arg385Gln	p.R385Q	ENST00000336596	NM_005233.5	385	cGa/cAa	5/17	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.349648708777463	2		624	962	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457220	89457220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	62	252	0	ENST00000336596.2:c.1701C>A	p.Phe567Leu	p.F567L	ENST00000336596	NM_005233.5	567	ttC/ttA	9/17	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.349648708777463	2		252	340	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582302	119582302	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	141	336	1	ENST00000316626.5:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000316626		367	Cga/Tga	10/12	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.349648708777463	2		337	762	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582439	119582439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775606264	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	82	237	0	ENST00000316626.5:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000316626		321	cGa/cAa	10/12	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.349648708777463	2		237	452	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119595317	119595317	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	52	257	0	ENST00000316626.5:c.852G>T	p.Met284Ile	p.M284I	ENST00000316626		284	atG/atT	8/12	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.349648708777463	2		257	287	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202797	128202797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	219	688	0	ENST00000341105.2:c.923G>A	p.Arg308Gln	p.R308Q	ENST00000341105	NM_032638.4	308	cGg/cAg	4/6	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.349648708777463	2		688	1077	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967321	134967321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	149	459	0	ENST00000398015.3:c.2660G>A	p.Ser887Asn	p.S887N	ENST00000398015	NM_004441.4	887	aGt/aAt	14/16	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.349648708777463	2		459	795	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665249	138665249	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	223	888	2	ENST00000330315.3:c.316C>A	p.Leu106Ile	p.L106I	ENST00000330315	NM_023067.3	106	Ctc/Atc	1/1	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.349648708777463	2		890	1153	SUCCESS
ATR	545	MSKCC	GRCh37	3	142185243	142185243	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	53	450	1	ENST00000350721.4:c.6820C>A	p.Leu2274Met	p.L2274M	ENST00000350721	NM_001184.3	2274	Ctg/Atg	40/47	1	2	FACETS	0.563	0.48	0.654	0.563	0.48	0.654	SUBCLONAL	1	TRUE	1	0.349648708777463	2		451	538	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188268	142188268	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	62	373	0	ENST00000350721.4:c.6463G>T	p.Glu2155Ter	p.E2155*	ENST00000350721	NM_001184.3	2155	Gaa/Taa	38/47	1	2	FACETS	0.905	0.785	1	0.905	0.785	1	CLONAL	1	TRUE	1	0.349648708777463	2		373	392	SUCCESS
ATR	545	MSKCC	GRCh37	3	142254972	142254972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	36	193	0	ENST00000350721.4:c.3797C>T	p.Ala1266Val	p.A1266V	ENST00000350721	NM_001184.3	1266	gCc/gTc	20/47	1	2	FACETS	0.801	0.662	0.955	0.801	0.662	0.955	CLONAL	1	TRUE	1	0.349648708777463	2		193	257	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277581	142277581	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	77	312	0	ENST00000350721.4:c.1770A>T	p.Leu590Phe	p.L590F	ENST00000350721	NM_001184.3	590	ttA/ttT	8/47	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.349648708777463	2		312	401	SUCCESS
ATR	545	MSKCC	GRCh37	3	142286928	142286928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751709684	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	110	357	1	ENST00000350721.4:c.128G>A	p.Arg43Gln	p.R43Q	ENST00000350721	NM_001184.3	43	cGg/cAg	2/47	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.349648708777463	2		358	450	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260222	149260222	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766572084	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	231	747	2	ENST00000360632.3:c.671C>T	p.Ala224Val	p.A224V	ENST00000360632	NM_015472.4	224	gCg/gTg	4/7	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.349648708777463	2		749	1078	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	146	594	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.349648708777463	2		594	802	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430999	181430999	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	176	764	0	ENST00000325404.1:c.851C>A	p.Pro284Gln	p.P284Q	ENST00000325404	NM_003106.3	284	cCg/cAg	1/1	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.349648708777463	2		764	1002	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198253	185198253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370479462	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	187	533	0	ENST00000265026.3:c.2735C>T	p.Ala912Val	p.A912V	ENST00000265026	NM_004721.4	912	gCc/gTc	13/14	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.349648708777463	2		533	881	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443345	187443345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	127	404	2	ENST00000232014.4:c.1781G>A	p.Arg594Gln	p.R594Q	ENST00000232014	NM_001130845.1	594	cGa/cAa	8/10	1	2	FACETS	0.969	0.878	1	0.969	0.878	1	CLONAL	1	TRUE	1	0.349648708777463	2		406	750	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582168	189582168	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121908835	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	100	426	0	ENST00000264731.3:c.727C>T	p.Arg243Trp	p.R243W	ENST00000264731	NM_003722.4	243	Cgg/Tgg	5/14	1	2	FACETS	0.662	0.591	0.738	0.662	0.591	0.738	SUBCLONAL	1	TRUE	1	0.349648708777463	2		426	864	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612250	189612250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749906547	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	120	381	0	ENST00000264731.3:c.2002C>T	p.Arg668Cys	p.R668C	ENST00000264731	NM_003722.4	668	Cgc/Tgc	14/14	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.349648708777463	2		381	562	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1905952	1905955	+	frameshift_variant	Frame_Shift_Del	DEL	AAGA	AAGA	-	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	178	594	0	ENST00000382891.5:c.611_614del	p.Lys204SerfsTer14	p.K204Sfs*14	ENST00000382891	NM_133335.3	203	AAGAaa/aa	3/22	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.349648708777463	2		594	946	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920289	1920289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146822227	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	210	676	0	ENST00000382891.5:c.1349G>A	p.Arg450Gln	p.R450Q	ENST00000382891	NM_133335.3	450	cGa/cAa	5/22	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.349648708777463	2		676	974	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957776	1957776	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	203	622	0	ENST00000382891.5:c.2742G>T	p.Glu914Asp	p.E914D	ENST00000382891	NM_133335.3	914	gaG/gaT	15/22	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.349648708777463	2		622	903	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144558	55144558	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	106	339	0	ENST00000257290.5:c.2032T>G	p.Phe678Val	p.F678V	ENST00000257290	NM_006206.4	678	Ttc/Gtc	15/23	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.349648708777463	2		339	508	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151604	55151604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	130	558	0	ENST00000257290.5:c.2390G>A	p.Ser797Asn	p.S797N	ENST00000257290	NM_006206.4	797	aGc/aAc	17/23	1	2	FACETS	0.978	0.888	1	0.978	0.888	1	CLONAL	1	TRUE	1	0.349648708777463	2		558	760	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602916	55602916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372795544	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	85	380	0	ENST00000288135.5:c.2626G>A	p.Asp876Asn	p.D876N	ENST00000288135	NM_000222.2	876	Gat/Aat	19/21	1	2	FACETS	0.924	0.819	1	0.924	0.819	1	CLONAL	1	TRUE	1	0.349648708777463	2		380	526	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968609	55968609	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	165	687	0	ENST00000263923.4:c.2054A>G	p.Glu685Gly	p.E685G	ENST00000263923	NM_002253.2	685	gAa/gGa	14/30	1	2	FACETS	0.972	0.892	1	0.972	0.892	1	CLONAL	1	TRUE	1	0.349648708777463	2		687	971	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968610	55968610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374980446	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	97	684	0	ENST00000263923.4:c.2053G>A	p.Glu685Lys	p.E685K	ENST00000263923	NM_002253.2	685	Gaa/Aaa	14/30	1	2	FACETS	0.564	0.502	0.631	0.564	0.502	0.631	SUBCLONAL	1	TRUE	1	0.349648708777463	2		684	984	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981531	55981531	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35636987	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	81	353	0	ENST00000263923.4:c.406G>A	p.Val136Met	p.V136M	ENST00000263923	NM_002253.2	136	Gtg/Atg	4/30	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.349648708777463	2		353	410	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197757	66197757	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	100	408	0	ENST00000273854.3:c.2942G>T	p.Arg981Leu	p.R981L	ENST00000273854	NM_004439.5	981	cGg/cTg	17/18	1	2	FACETS	0.961	0.861	1	0.961	0.861	1	CLONAL	1	TRUE	1	0.349648708777463	2		408	595	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286284	66286284	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	50	233	0	ENST00000273854.3:c.1403-1G>T		p.X468_splice	ENST00000273854	NM_004439.5	468			1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.349648708777463	2		233	269	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361152	66361152	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	83	316	1	ENST00000273854.3:c.1020G>T	p.Lys340Asn	p.K340N	ENST00000273854	NM_004439.5	340	aaG/aaT	4/18	1	2	FACETS	0.989	0.876	1	0.989	0.876	1	CLONAL	1	TRUE	1	0.349648708777463	2		317	480	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467589	66467589	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772693559	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	41	336	0	ENST00000273854.3:c.680G>A	p.Arg227His	p.R227H	ENST00000273854	NM_004439.5	227	cGt/cAt	3/18	1	2	FACETS	0.513	0.427	0.608	0.513	0.427	0.608	SUBCLONAL	1	TRUE	1	0.349648708777463	2		336	457	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808233	99808233	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	160	576	0	ENST00000280892.6:c.456G>T	p.Glu152Asp	p.E152D	ENST00000280892	NM_001130678.1	152	gaG/gaT	5/7	1	2	FACETS	0.982	0.9	1	0.982	0.9	1	CLONAL	1	TRUE	1	0.349648708777463	2		576	932	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155933	106155933	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	73	262	2	ENST00000380013.4:c.834G>T	p.Gln278His	p.Q278H	ENST00000380013	NM_001127208.2	278	caG/caT	3/11	1	2	FACETS	0.918	0.805	1	0.918	0.805	1	CLONAL	1	TRUE	1	0.349648708777463	2		264	455	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156823	106156823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199640757	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	136	496	3	ENST00000380013.4:c.1724C>T	p.Ala575Val	p.A575V	ENST00000380013	NM_001127208.2	575	gCg/gTg	3/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.349648708777463	2		499	741	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193974	106193974	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	98	258	0	ENST00000380013.4:c.4436T>G	p.Leu1479Arg	p.L1479R	ENST00000380013	NM_001127208.2	1479	cTt/cGt	10/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.349648708777463	2		258	499	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003184	143003184	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	87	309	0	ENST00000262992.4:c.2642G>T	p.Arg881Ile	p.R881I	ENST00000262992	NM_001101669.1	881	aGa/aTa	23/24	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.349648708777463	2		309	453	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094807	143094807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	40	281	0	ENST00000262992.4:c.1337C>A	p.Ser446Tyr	p.S446Y	ENST00000262992	NM_001101669.1	446	tCt/tAt	14/24	1	2	FACETS	0.648	0.54	0.768	0.648	0.54	0.768	SUBCLONAL	1	TRUE	1	0.349648708777463	2		281	353	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250822	153250822	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	95	360	0	ENST00000281708.4:c.1236+2T>C		p.X412_splice	ENST00000281708	NM_033632.3	412			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.349648708777463	2		360	427	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259064	153259064	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	41	158	0	ENST00000281708.4:c.751C>A	p.Leu251Ile	p.L251I	ENST00000281708	NM_033632.3	251	Ctt/Att	5/12	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.349648708777463	2		158	202	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521150	187521150	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768613095	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	135	529	1	ENST00000441802.2:c.12005C>T	p.Ser4002Leu	p.S4002L	ENST00000441802	NM_005245.3	4002	tCg/tTg	22/27	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.349648708777463	2		530	744	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530978	187530978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376075512	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	134	409	0	ENST00000441802.2:c.10045G>A	p.Val3349Ile	p.V3349I	ENST00000441802	NM_005245.3	3349	Gtt/Att	15/27	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.349648708777463	2		409	682	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535426	187535426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370628880	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	107	421	1	ENST00000441802.2:c.9148G>A	p.Ala3050Thr	p.A3050T	ENST00000441802	NM_005245.3	3050	Gca/Aca	12/27	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.349648708777463	2		422	572	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540841	187540841	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761083769	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	81	295	1	ENST00000441802.2:c.6899C>T	p.Thr2300Met	p.T2300M	ENST00000441802	NM_005245.3	2300	aCg/aTg	10/27	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.349648708777463	2		296	447	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627849	187627849	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	195	648	0	ENST00000441802.2:c.3133G>T	p.Glu1045Ter	p.E1045*	ENST00000441802	NM_005245.3	1045	Gaa/Taa	2/27	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.349648708777463	2		648	988	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628125	187628125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1196972484	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	230	631	0	ENST00000441802.2:c.2857G>A	p.Asp953Asn	p.D953N	ENST00000441802	NM_005245.3	953	Gat/Aat	2/27	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.349648708777463	2		631	1018	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628196	187628196	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs937707929	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	151	630	1	ENST00000441802.2:c.2786C>A	p.Pro929Gln	p.P929Q	ENST00000441802	NM_005245.3	929	cCa/cAa	2/27	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.349648708777463	2		631	855	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628340	187628340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536104649	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	203	583	0	ENST00000441802.2:c.2642G>A	p.Arg881His	p.R881H	ENST00000441802	NM_005245.3	881	cGc/cAc	2/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.349648708777463	2		583	1001	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225663	225663	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375576259	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1231	231	925	1	ENST00000264932.6:c.442G>A	p.Ala148Thr	p.A148T	ENST00000264932	NM_004168.2	148	Gcc/Acc	4/15	1	2	FACETS	0.904	0.84	0.97	0.904	0.84	0.97	CLONAL	1	TRUE	1	0.349648708777463	2		926	1462	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293545	1293545	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	219	889	2	ENST00000310581.5:c.1456C>A	p.Arg486Ser	p.R486S	ENST00000310581	NM_198253.2	486	Cgc/Agc	2/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.349648708777463	2		891	1114	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293871	1293871	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756954938	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	229	917	2	ENST00000310581.5:c.1130G>A	p.Arg377His	p.R377H	ENST00000310581	NM_198253.2	377	cGc/cAc	2/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.349648708777463	2		919	1131	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294613	1294613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1389956132	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	56	394	1	ENST00000310581.5:c.388G>A	p.Ala130Thr	p.A130T	ENST00000310581	NM_198253.2	130	Gca/Aca	2/16	1	2	FACETS	0.424	0.362	0.491	0.424	0.362	0.491	SUBCLONAL	1	TRUE	1	0.349648708777463	2		395	756	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31421380	31421380	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	80	308	0	ENST00000344624.3:c.3524C>T	p.Thr1175Ile	p.T1175I	ENST00000344624		1175	aCt/aTt	27/33	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.349648708777463	2		308	359	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31483667	31483667	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	76	259	0	ENST00000344624.3:c.2065C>A	p.Leu689Ile	p.L689I	ENST00000344624		689	Ctt/Att	13/33	1	2	FACETS	0.955	0.841	1	0.955	0.841	1	CLONAL	1	TRUE	1	0.349648708777463	2		259	455	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38960032	38960032	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	54	252	0	ENST00000357387.3:c.1900C>T	p.Leu634Phe	p.L634F	ENST00000357387	NM_152756.3	634	Ctc/Ttc	21/38	1	2	FACETS	0.947	0.814	1	0.947	0.814	1	CLONAL	1	TRUE	1	0.349648708777463	2		252	326	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38975707	38975707	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	100	341	0	ENST00000357387.3:c.822-1G>T		p.X274_splice	ENST00000357387	NM_152756.3	274			1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.349648708777463	2		341	560	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176987	56176987	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	54	266	0	ENST00000399503.3:c.2257G>T	p.Glu753Ter	p.E753*	ENST00000399503	NM_005921.1	753	Gaa/Taa	13/20	1	2	FACETS	0.782	0.67	0.904	0.782	0.67	0.904	CLONAL	1	TRUE	1	0.349648708777463	2		266	395	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79968590	79968590	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	127	391	0	ENST00000265081.6:c.940G>A	p.Ala314Thr	p.A314T	ENST00000265081	NM_002439.4	314	Gca/Aca	6/24	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.349648708777463	2		391	662	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80071522	80071522	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	65	263	0	ENST00000265081.6:c.2263G>T	p.Glu755Ter	p.E755*	ENST00000265081	NM_002439.4	755	Gaa/Taa	16/24	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.349648708777463	2		263	345	SUCCESS
APC	324	MSKCC	GRCh37	5	112174134	112174134	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	65	343	0	ENST00000257430.4:c.2843C>A	p.Ser948Tyr	p.S948Y	ENST00000257430	NM_000038.5	948	tCt/tAt	16/16	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.349648708777463	2		343	347	SUCCESS
APC	324	MSKCC	GRCh37	5	112174674	112174674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	73	319	0	ENST00000257430.4:c.3383C>T	p.Ser1128Phe	p.S1128F	ENST00000257430	NM_000038.5	1128	tCt/tTt	16/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.349648708777463	2		319	363	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	72	252	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.822	0.72	0.932	0.822	0.72	0.932	CLONAL	1	TRUE	1	0.349648708777463	2		252	501	SUCCESS
APC	324	MSKCC	GRCh37	5	112176411	112176411	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	69	310	0	ENST00000257430.4:c.5120C>A	p.Ser1707Tyr	p.S1707Y	ENST00000257430	NM_000038.5	1707	tCt/tAt	16/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.349648708777463	2		310	325	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495372	149495372	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146614144	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	199	731	0	ENST00000261799.4:c.3275C>T	p.Ser1092Leu	p.S1092L	ENST00000261799	NM_002609.3	1092	tCg/tTg	23/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.349648708777463	2		731	911	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514342	149514342	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	54	479	0	ENST00000261799.4:c.602C>A	p.Ser201Tyr	p.S201Y	ENST00000261799	NM_002609.3	201	tCt/tAt	4/23	1	2	FACETS	0.566	0.483	0.656	0.566	0.483	0.656	SUBCLONAL	1	TRUE	1	0.349648708777463	2		479	546	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520306	176520306	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	156	650	0	ENST00000292408.4:c.1225C>A	p.Leu409Ile	p.L409I	ENST00000292408	NM_213647.1	409	Ctc/Atc	9/18	1	2	FACETS	0.997	0.913	1	0.997	0.913	1	CLONAL	1	TRUE	1	0.349648708777463	2		650	895	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522394	176522394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	205	723	2	ENST00000292408.4:c.1583G>A	p.Gly528Asp	p.G528D	ENST00000292408	NM_213647.1	528	gGc/gAc	12/18	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.349648708777463	2		725	1046	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638456	176638456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750354456	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	184	676	1	ENST00000439151.2:c.3056G>A	p.Arg1019His	p.R1019H	ENST00000439151	NM_022455.4	1019	cGc/cAc	5/23	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.349648708777463	2		677	978	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675287	176675287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	115	297	0	ENST00000439151.2:c.4603C>T	p.Arg1535Cys	p.R1535C	ENST00000439151	NM_022455.4	1535	Cgc/Tgc	11/23	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.349648708777463	2		297	608	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176678730	176678730	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	112	278	0	ENST00000439151.2:c.4642-1G>T		p.X1548_splice	ENST00000439151	NM_022455.4	1548			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.349648708777463	2		278	534	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696750	176696750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	92	354	0	ENST00000439151.2:c.5451G>T	p.Glu1817Asp	p.E1817D	ENST00000439151	NM_022455.4	1817	gaG/gaT	16/23	1	2	FACETS	0.948	0.845	1	0.948	0.845	1	CLONAL	1	TRUE	1	0.349648708777463	2		354	555	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707797	176707797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886041219	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	132	379	0	ENST00000439151.2:c.5854C>T	p.Arg1952Trp	p.R1952W	ENST00000439151	NM_022455.4	1952	Cgg/Tgg	18/23	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.349648708777463	2		379	717	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038451	180038451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370304760	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	153	729	1	ENST00000261937.6:c.3566G>A	p.Arg1189His	p.R1189H	ENST00000261937	NM_182925.4	1189	cGc/cAc	27/30	1	2	FACETS	0.896	0.819	0.976	0.896	0.819	0.976	CLONAL	1	TRUE	1	0.349648708777463	2		730	977	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043477	180043477	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	150	575	1	ENST00000261937.6:c.3109G>T	p.Asp1037Tyr	p.D1037Y	ENST00000261937	NM_182925.4	1037	Gac/Tac	23/30	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.349648708777463	2		576	794	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048587	180048587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	158	800	1	ENST00000261937.6:c.1975C>T	p.Arg659Cys	p.R659C	ENST00000261937	NM_182925.4	659	Cgc/Tgc	13/30	1	2	FACETS	0.98	0.898	1	0.98	0.898	1	CLONAL	1	TRUE	1	0.349648708777463	2		801	922	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048713	180048713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1176988485	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	157	750	1	ENST00000261937.6:c.1849G>A	p.Ala617Thr	p.A617T	ENST00000261937	NM_182925.4	617	Gcc/Acc	13/30	1	2	FACETS	0.999	0.915	1	0.999	0.915	1	CLONAL	1	TRUE	1	0.349648708777463	2		751	899	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052918	180052918	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	194	953	0	ENST00000261937.6:c.1372T>C	p.Trp458Arg	p.W458R	ENST00000261937	NM_182925.4	458	Tgg/Cgg	10/30	1	2	FACETS	0.978	0.903	1	0.978	0.903	1	CLONAL	1	TRUE	1	0.349648708777463	2		953	1135	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405045	405045	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377483798	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	141	429	1	ENST00000380956.4:c.1127G>A	p.Arg376His	p.R376H	ENST00000380956	NM_001195286.1	376	cGc/cAc	8/9	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.349648708777463	2		430	678	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481463	20481463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	73	261	0	ENST00000346618.3:c.532C>T	p.Arg178Trp	p.R178W	ENST00000346618	NM_001949.4	178	Cgg/Tgg	3/7	1	2	FACETS	0.9	0.79	1	0.9	0.79	1	CLONAL	1	TRUE	1	0.349648708777463	2		261	464	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910556	29910556	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	219	891	0	ENST00000376809.5:c.96C>A	p.Phe32Leu	p.F32L	ENST00000376809	NM_002116.7	32	ttC/ttA	2/8	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.349648708777463	2		891	992	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681924	30681924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754781804	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	39	441	0	ENST00000376406.3:c.173G>A	p.Arg58Gln	p.R58Q	ENST00000376406	NM_014641.2	58	cGa/cAa	3/15	1	2	FACETS	0.352	0.291	0.42	0.352	0.291	0.42	SUBCLONAL	1	TRUE	1	0.349648708777463	2		441	634	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30682905	30682905	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	153	413	0	ENST00000376406.3:c.48G>T	p.Glu16Asp	p.E16D	ENST00000376406	NM_014641.2	16	gaG/gaT	2/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.349648708777463	2		413	757	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322412	31322412	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs756666358	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	103	457	0	ENST00000412585.2:c.1043C>T	p.Ala348Val	p.A348V	ENST00000412585	NM_005514.6	348	gCg/gTg	6/8	1	2	FACETS	0.838	0.75	0.931	0.838	0.75	0.931	CLONAL	1	TRUE	1	0.349648708777463	2		457	703	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31946679	31946679	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	133	478	0	ENST00000375333.2:c.568-1G>T		p.X190_splice	ENST00000375333	NM_032454.1	190			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.349648708777463	2		478	686	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948503	31948503	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767624789	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	98	394	1	ENST00000375333.2:c.986G>A	p.Arg329Gln	p.R329Q	ENST00000375333	NM_032454.1	329	cGg/cAg	7/8	1	2	FACETS	0.965	0.863	1	0.965	0.863	1	CLONAL	1	TRUE	1	0.349648708777463	2		395	581	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166874	32166874	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	123	885	0	ENST00000375023.3:c.4364C>T	p.Ala1455Val	p.A1455V	ENST00000375023	NM_004557.3	1455	gCc/gTc	24/30	1	2	FACETS	0.569	0.513	0.629	0.569	0.513	0.629	SUBCLONAL	1	TRUE	1	0.349648708777463	2		885	1236	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180265	32180265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	128	527	0	ENST00000375023.3:c.2666C>T	p.Ala889Val	p.A889V	ENST00000375023	NM_004557.3	889	gCt/gTt	17/30	1	2	FACETS	0.86	0.78	0.946	0.86	0.78	0.946	CLONAL	1	TRUE	1	0.349648708777463	2		527	851	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185819	32185819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145916093	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	101	672	0	ENST00000375023.3:c.1577C>T	p.Ala526Val	p.A526V	ENST00000375023	NM_004557.3	526	gCg/gTg	9/30	1	2	FACETS	0.561	0.5	0.626	0.561	0.5	0.626	SUBCLONAL	1	TRUE	1	0.349648708777463	2		672	1030	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41904434	41904434	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	143	534	0	ENST00000372991.4:c.575-1G>T		p.X192_splice	ENST00000372991	NM_001760.3	192			1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.349648708777463	2		534	788	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94067982	94067982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	23	223	0	ENST00000369303.4:c.980C>T	p.Ala327Val	p.A327V	ENST00000369303	NM_004440.3	327	gCg/gTg	4/17	1	2	FACETS	0.346	0.269	0.435	0.346	0.269	0.435	SUBCLONAL	1	TRUE	1	0.349648708777463	2		223	380	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553357	106553357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	99	487	1	ENST00000369096.4:c.1322C>T	p.Pro441Leu	p.P441L	ENST00000369096	NM_001198.3	441	cCg/cTg	5/7	1	2	FACETS	0.958	0.857	1	0.958	0.857	1	CLONAL	1	TRUE	1	0.349648708777463	2		488	591	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322688	109322688	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	31	339	0	ENST00000436639.2:c.349C>A	p.Leu117Ile	p.L117I	ENST00000436639	NM_014454.2	117	Ctc/Atc	3/10	1	2	FACETS	0.317	0.256	0.387	0.317	0.256	0.387	SUBCLONAL	1	TRUE	1	0.349648708777463	2		339	559	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631356	117631356	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	117	344	1	ENST00000368508.3:c.6322G>T	p.Asp2108Tyr	p.D2108Y	ENST00000368508	NM_002944.2	2108	Gac/Tac	40/43	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.349648708777463	2		345	563	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683840	117683840	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	122	419	0	ENST00000368508.3:c.3307G>A	p.Ala1103Thr	p.A1103T	ENST00000368508	NM_002944.2	1103	Gct/Act	21/43	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.349648708777463	2		419	530	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686254	117686254	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	61	289	0	ENST00000368508.3:c.3087A>C	p.Lys1029Asn	p.K1029N	ENST00000368508	NM_002944.2	1029	aaA/aaC	20/43	1	2	FACETS	0.851	0.737	0.974	0.851	0.737	0.974	CLONAL	1	TRUE	1	0.349648708777463	2		289	410	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704658	117704658	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	71	249	0	ENST00000368508.3:c.2318C>A	p.Ser773Tyr	p.S773Y	ENST00000368508	NM_002944.2	773	tCt/tAt	16/43	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.349648708777463	2		249	354	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708061	117708061	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	97	366	0	ENST00000368508.3:c.2116A>C	p.Asn706His	p.N706H	ENST00000368508	NM_002944.2	706	Aat/Cat	14/43	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.349648708777463	2		366	392	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710904	117710904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	114	366	0	ENST00000368508.3:c.1368G>T	p.Lys456Asn	p.K456N	ENST00000368508	NM_002944.2	456	aaG/aaT	12/43	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.349648708777463	2		366	626	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715868	117715868	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	87	327	0	ENST00000368508.3:c.890G>T	p.Arg297Ile	p.R297I	ENST00000368508	NM_002944.2	297	aGa/aTa	9/43	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.349648708777463	2		327	442	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202424	138202424	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	164	672	1	ENST00000237289.4:c.2341G>A	p.Glu781Lys	p.E781K	ENST00000237289	NM_001270507.1	781	Gaa/Aaa	9/9	1	2	FACETS	0.974	0.894	1	0.974	0.894	1	CLONAL	1	TRUE	1	0.349648708777463	2		673	963	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163802	152163802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	147	449	0	ENST00000206249.3:c.523G>A	p.Ala175Thr	p.A175T	ENST00000206249	NM_000125.3	175	Gct/Act	2/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.349648708777463	2		449	667	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222566	157222566	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	174	578	0	ENST00000346085.5:c.1833G>T	p.Gln611His	p.Q611H	ENST00000346085	NM_020732.3	611	caG/caT	4/20	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.349648708777463	2		578	964	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157520001	157520001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773119970	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	176	604	0	ENST00000346085.5:c.4070C>T	p.Pro1357Leu	p.P1357L	ENST00000346085	NM_020732.3	1357	cCg/cTg	17/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.349648708777463	2		604	972	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978755	13978756	+	missense_variant	Missense_Mutation	DNP	GG	GG	TA	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	146	475	1	ENST00000405192.2:c.351_352delinsTA	p.Leu118Met	p.L118M	ENST00000405192	NM_001163147.1	117	tgCCtg/tgTAtg	6/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.349648708777463	2		476	739	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729320	41729320	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	163	454	0	ENST00000242208.4:c.1209C>A	p.Tyr403Ter	p.Y403*	ENST00000242208	NM_002192.2	403	taC/taA	3/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.349648708777463	2		454	714	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730009	41730009	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758496316	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	175	582	0	ENST00000242208.4:c.520C>T	p.Arg174Cys	p.R174C	ENST00000242208	NM_002192.2	174	Cgc/Tgc	3/3	1	2	FACETS	0.989	0.91	1	0.989	0.91	1	CLONAL	1	TRUE	1	0.349648708777463	2		582	1012	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739644	41739644	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	82	570	0	ENST00000242208.4:c.329G>T	p.Arg110Met	p.R110M	ENST00000242208	NM_002192.2	110	aGg/aTg	2/3	1	2	FACETS	0.545	0.48	0.616	0.545	0.48	0.616	SUBCLONAL	1	TRUE	1	0.349648708777463	2		570	860	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444317	50444317	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	91	363	0	ENST00000331340.3:c.247C>T	p.Arg83Ter	p.R83*	ENST00000331340	NM_006060.4	83	Cga/Tga	4/8	1	2	FACETS	0.941	0.838	1	0.941	0.838	1	CLONAL	1	TRUE	1	0.349648708777463	2		363	553	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467829	50467829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	118	549	0	ENST00000331340.3:c.1064C>T	p.Ala355Val	p.A355V	ENST00000331340	NM_006060.4	355	gCg/gTg	8/8	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.349648708777463	2		549	601	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468282	50468282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	206	544	0	ENST00000331340.3:c.1517C>T	p.Ser506Leu	p.S506L	ENST00000331340	NM_006060.4	506	tCg/tTg	8/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.349648708777463	2		544	909	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268009	55268009	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	89	518	2	ENST00000275493.2:c.2849G>T	p.Cys950Phe	p.C950F	ENST00000275493	NM_005228.3	950	tGc/tTc	24/28	1	2	FACETS	0.695	0.616	0.779	0.695	0.616	0.779	SUBCLONAL	1	TRUE	1	0.349648708777463	2		520	733	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55269022	55269022	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	215	746	0	ENST00000275493.2:c.3088T>C	p.Ser1030Pro	p.S1030P	ENST00000275493	NM_005228.3	1030	Tca/Cca	25/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.349648708777463	2		746	1068	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509953	106509953	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	113	535	0	ENST00000359195.3:c.1947G>T	p.Glu649Asp	p.E649D	ENST00000359195	NM_002649.2	649	gaG/gaT	2/11	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.349648708777463	2		535	643	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339865	116339865	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	80	410	1	ENST00000397752.3:c.727G>T	p.Asp243Tyr	p.D243Y	ENST00000397752	NM_000245.2	243	Gat/Tat	2/21	1	2	FACETS	0.995	0.879	1	0.995	0.879	1	CLONAL	1	TRUE	1	0.349648708777463	2		411	460	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339981	116339981	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	25	329	0	ENST00000397752.3:c.843C>A	p.Phe281Leu	p.F281L	ENST00000397752	NM_000245.2	281	ttC/ttA	2/21	1	2	FACETS	0.345	0.272	0.43	0.345	0.272	0.43	SUBCLONAL	1	TRUE	1	0.349648708777463	2		329	414	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340252	116340252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773200558	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	25	227	1	ENST00000397752.3:c.1114G>A	p.Asp372Asn	p.D372N	ENST00000397752	NM_000245.2	372	Gac/Aac	2/21	1	2	FACETS	0.348	0.274	0.434	0.348	0.274	0.434	SUBCLONAL	1	TRUE	1	0.349648708777463	2		228	411	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829066	128829066	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs41304185	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	18	9	0	ENST00000249373.3:c.74A>G	p.Asp25Gly	p.D25G	ENST00000249373	NM_005631.4	25	gAc/gGc	1/12	1	2	FACETS	1	0.868	1	1	0.945	1	CLONAL	2	TRUE	1	0.349648708777463	2		9	45	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843396	128843396	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61746143	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	143	657	0	ENST00000249373.3:c.503G>A	p.Arg168His	p.R168H	ENST00000249373	NM_005631.4	168	cGc/cAc	2/12	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.349648708777463	2		657	808	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846357	128846357	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760560948	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	155	671	0	ENST00000249373.3:c.1193G>A	p.Arg398Gln	p.R398Q	ENST00000249373	NM_005631.4	398	cGa/cAa	6/12	1	2	FACETS	0.925	0.847	1	0.925	0.847	1	CLONAL	1	TRUE	1	0.349648708777463	2		671	958	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128849189	128849189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17710891	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	168	609	1	ENST00000249373.3:c.1417G>A	p.Asp473Asn	p.D473N	ENST00000249373	NM_005631.4	473	Gac/Aac	8/12	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.349648708777463	2		610	904	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523717	148523717	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	62	187	0	ENST00000320356.2:c.736G>T	p.Glu246Ter	p.E246*	ENST00000320356	NM_004456.4	246	Gaa/Taa	8/20	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.349648708777463	2		187	328	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525883	148525883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778968366	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	23	350	0	ENST00000320356.2:c.574G>A	p.Asp192Asn	p.D192N	ENST00000320356	NM_004456.4	192	Gat/Aat	6/20	1	2	FACETS	0.301	0.234	0.379	0.301	0.234	0.379	SUBCLONAL	1	TRUE	1	0.349648708777463	2		350	437	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012410	152012410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	83	263	0	ENST00000262189.6:c.403G>A	p.Ala135Thr	p.A135T	ENST00000262189	NM_170606.2	135	Gct/Act	4/59	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.349648708777463	2		263	338	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132713	152132713	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	88	207	0	ENST00000262189.6:c.159G>T	p.Lys53Asn	p.K53N	ENST00000262189	NM_170606.2	53	aaG/aaT	1/59	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.349648708777463	2		207	366	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162263	38162263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	96	333	0	ENST00000317025.8:c.2453G>A	p.Arg818Lys	p.R818K	ENST00000317025	NM_023034.1	818	aGa/aAa	14/24	0.349648708777463	3	FACETS	1	0.962	1	0.584	0.522	0.65	CLONAL	1	TRUE	1	0.349648708777463	3		333	552	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189097	38189097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775871355	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	108	428	0	ENST00000317025.8:c.917G>A	p.Arg306Gln	p.R306Q	ENST00000317025	NM_023034.1	306	cGa/cAa	5/24	0.349648708777463	3	FACETS	0.961	0.863	1	0.481	0.431	0.533	CLONAL	1	TRUE	1	0.349648708777463	3		428	755	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205221	38205221	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1201	65	835	0	ENST00000317025.8:c.469del	p.Ile157Ter	p.I157*	ENST00000317025	NM_023034.1	157	Ata/ta	2/24	0.349648708777463	3	FACETS	0.345	0.298	0.397	0.173	0.149	0.199	SUBCLONAL	1	TRUE	1	0.349648708777463	3		835	1266	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272409	38272409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	69	393	0	ENST00000425967.3:c.1958G>A	p.Arg653Gln	p.R653Q	ENST00000425967	NM_001174067.1	653	cGa/cAa	15/19	0.349648708777463	3	FACETS	0.626	0.544	0.714	0.313	0.272	0.357	SUBCLONAL	1	TRUE	1	0.349648708777463	3		393	741	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274879	38274879	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	309	558	0	ENST00000425967.3:c.1701G>T	p.Lys567Asn	p.K567N	ENST00000425967	NM_001174067.1	567	aaG/aaT	13/19	0.349648708777463	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.349648708777463	3		558	930	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277050	38277050	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	154	409	0	ENST00000425967.3:c.1377+1G>A		p.X459_splice	ENST00000425967	NM_001174067.1	459			0.349648708777463	3	FACETS	1	0.98	1	0.616	0.564	0.67	CLONAL	1	TRUE	1	0.349648708777463	3		409	840	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931826	68931826	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs759461290	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	124	563	1	ENST00000288368.4:c.256G>T	p.Glu86Ter	p.E86*	ENST00000288368	NM_024870.2	86	Gaa/Taa	3/40	0.349648708777463	3	FACETS	1	0.969	1	0.583	0.528	0.641	CLONAL	1	TRUE	1	0.349648708777463	3		564	715	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021767	69021767	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	164	490	1	ENST00000288368.4:c.3055G>T	p.Asp1019Tyr	p.D1019Y	ENST00000288368	NM_024870.2	1019	Gac/Tac	25/40	0.349648708777463	3	FACETS	1	0.971	1	0.564	0.517	0.613	CLONAL	1	TRUE	1	0.349648708777463	3		491	977	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104637	69104637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746308010	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	194	581	0	ENST00000288368.4:c.4481G>A	p.Arg1494His	p.R1494H	ENST00000288368	NM_024870.2	1494	cGc/cAc	37/40	0.349648708777463	3	FACETS	1	0.966	1	0.54	0.499	0.583	CLONAL	1	TRUE	1	0.349648708777463	3		581	1207	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955513	90955513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	100	381	0	ENST00000265433.3:c.2152G>A	p.Glu718Lys	p.E718K	ENST00000265433	NM_002485.4	718	Gaa/Aaa	14/16	0.349648708777463	3	FACETS	1	0.929	1	0.525	0.469	0.584	CLONAL	1	TRUE	1	0.349648708777463	3		381	640	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859844	117859844	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	61	257	0	ENST00000297338.2:c.1791C>A	p.Phe597Leu	p.F597L	ENST00000297338	NM_006265.2	597	ttC/ttA	14/14	0.349648708777463	3	FACETS	0.838	0.724	0.962	0.419	0.362	0.481	CLONAL	1	TRUE	1	0.349648708777463	3		257	489	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868450	117868450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148308569	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	100	486	0	ENST00000297338.2:c.892C>T	p.Pro298Ser	p.P298S	ENST00000297338	NM_006265.2	298	Cca/Tca	8/14	0.349648708777463	3	FACETS	0.931	0.832	1	0.465	0.416	0.518	CLONAL	1	TRUE	1	0.349648708777463	3		486	722	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751056	128751056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	237	538	0	ENST00000377970.2:c.593C>T	p.Ala198Val	p.A198V	ENST00000377970	NM_002467.4	198	gCc/gTc	2/3	0.349648708777463	3	FACETS	0.925	0.865	0.986	0.925	0.865	0.986	CLONAL	2	TRUE	1	0.349648708777463	3		538	861	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542594	141542594	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	322	645	0	ENST00000220592.5:c.2392T>C	p.Ser798Pro	p.S798P	ENST00000220592	NM_012154.3	798	Tcc/Ccc	18/19	0.349648708777463	3	FACETS	0.983	0.929	1	0.983	0.929	1	CLONAL	2	TRUE	1	0.349648708777463	3		645	1101	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141570541	141570541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	412	791	1	ENST00000220592.5:c.587G>A	p.Arg196Gln	p.R196Q	ENST00000220592	NM_012154.3	196	cGa/cAa	5/19	0.349648708777463	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.349648708777463	3		792	1225	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738499	145738499	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375250269	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	152	674	1	ENST00000428558.2:c.2486G>A	p.Arg829His	p.R829H	ENST00000428558	NM_004260.3	829	cGc/cAc	16/22	0.349648708777463	3	FACETS	1	0.926	1	0.507	0.463	0.553	CLONAL	1	TRUE	1	0.349648708777463	3		675	1007	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054797	5054797	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs762791853	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	81	347	0	ENST00000381652.3:c.849G>T	p.Glu283Asp	p.E283D	ENST00000381652	NM_004972.3	283	gaG/gaT	7/25	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.349648708777463	2		347	406	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072579	5072579	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	79	379	0	ENST00000381652.3:c.1729G>T	p.Glu577Ter	p.E577*	ENST00000381652	NM_004972.3	577	Gaa/Taa	13/25	1	2	FACETS	0.893	0.788	1	0.893	0.788	1	CLONAL	1	TRUE	1	0.349648708777463	2		379	506	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089679	5089679	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	69	211	0	ENST00000381652.3:c.2580del	p.Phe860LeufsTer22	p.F860Lfs*22	ENST00000381652	NM_004972.3	859	aaT/aa	20/25	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.349648708777463	2		211	348	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504333	8504333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754609275	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	155	490	1	ENST00000356435.5:c.1750C>T	p.Arg584Cys	p.R584C	ENST00000356435		584	Cgt/Tgt	12/35	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.349648708777463	2		491	807	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517848	8517848	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	82	255	0	ENST00000356435.5:c.1543G>T	p.Val515Leu	p.V515L	ENST00000356435		515	Gta/Tta	10/35	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.349648708777463	2		255	336	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524966	8524966	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764474694	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	51	327	1	ENST00000356435.5:c.638C>T	p.Ala213Val	p.A213V	ENST00000356435		213	gCg/gTg	7/35	1	2	FACETS	0.548	0.466	0.639	0.548	0.466	0.639	SUBCLONAL	1	TRUE	1	0.349648708777463	2		328	532	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020738	37020738	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs564013593	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	128	554	0	ENST00000358127.4:c.107T>C	p.Val36Ala	p.V36A	ENST00000358127	NM_001280556.1	36	gTa/gCa	2/10	1	2	FACETS	0.8	0.725	0.88	0.8	0.725	0.88	SUBCLONAL	1	TRUE	1	0.349648708777463	2		554	915	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342807	87342807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	104	406	1	ENST00000277120.3:c.1092G>T	p.Lys364Asn	p.K364N	ENST00000277120		364	aaG/aaT	9/19	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.349648708777463	2		407	503	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359914	87359914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748744999	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	115	337	0	ENST00000277120.3:c.1222G>A	p.Gly408Arg	p.G408R	ENST00000277120		408	Ggg/Agg	11/19	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.349648708777463	2		337	603	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97933362	97933362	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs781542763	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	59	328	0	ENST00000289081.3:c.520C>T	p.Arg174Ter	p.R174*	ENST00000289081	NM_000136.2	174	Cga/Tga	6/15	1	2	FACETS	0.809	0.698	0.929	0.809	0.698	0.929	CLONAL	1	TRUE	1	0.349648708777463	2		328	417	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212182	98212182	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371346118	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	124	350	0	ENST00000331920.6:c.3490G>A	p.Val1164Ile	p.V1164I	ENST00000331920	NM_000264.3	1164	Gtt/Att	21/24	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.349648708777463	2		350	580	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224149	98224149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531947455	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	79	226	0	ENST00000331920.6:c.2692G>A	p.Asp898Asn	p.D898N	ENST00000331920	NM_000264.3	898	Gac/Aac	16/24	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.349648708777463	2		226	402	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900171	101900171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564161322	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	64	281	0	ENST00000374994.4:c.605C>T	p.Ala202Val	p.A202V	ENST00000374994	NM_004612.2	202	gCg/gTg	4/9	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.349648708777463	2		281	363	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760960	133760960	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750196179	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	199	769	1	ENST00000318560.5:c.3283C>T	p.Arg1095Trp	p.R1095W	ENST00000318560	NM_005157.4	1095	Cgg/Tgg	11/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.349648708777463	2		770	1111	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399348	139399348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543770603	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	250	839	0	ENST00000277541.6:c.4795G>A	p.Val1599Met	p.V1599M	ENST00000277541	NM_017617.3	1599	Gtg/Atg	26/34	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.349648708777463	2		839	1204	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412336	139412336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502238	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	221	773	0	ENST00000277541.6:c.1309G>A	p.Glu437Lys	p.E437K	ENST00000277541	NM_017617.3	437	Gag/Aag	8/34	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.349648708777463	2		773	1064	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922019	39922019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs577082253	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	58	633	1	ENST00000378444.4:c.4153G>A	p.Val1385Met	p.V1385M	ENST00000378444	NM_001123385.1	1385	Gtg/Atg	9/15	1	2	FACETS	0.359	0.307	0.416	0.359	0.307	0.416	SUBCLONAL	1	TRUE	1	0.349648708777463	2		634	924	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923826	39923826	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381312357	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	185	682	0	ENST00000378444.4:c.3265C>T	p.Arg1089Cys	p.R1089C	ENST00000378444	NM_001123385.1	1089	Cgt/Tgt	7/15	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.349648708777463	2		682	1010	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945153	44945153	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	130	482	0	ENST00000377967.4:c.3477T>G	p.Ile1159Met	p.I1159M	ENST00000377967	NM_021140.2	1159	atT/atG	24/29	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.349648708777463	2		482	594	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231039	53231039	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	107	518	1	ENST00000375401.3:c.1863C>A	p.Asp621Glu	p.D621E	ENST00000375401	NM_004187.3	621	gaC/gaA	13/26	1	2	FACETS	0.686	0.615	0.762	0.686	0.615	0.762	SUBCLONAL	1	TRUE	1	0.349648708777463	2		519	892	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247506	53247506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1556853080	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	152	625	0	ENST00000375401.3:c.303G>T	p.Lys101Asn	p.K101N	ENST00000375401	NM_004187.3	101	aaG/aaT	3/26	1	2	FACETS	0.977	0.893	1	0.977	0.893	1	CLONAL	1	TRUE	1	0.349648708777463	2		625	890	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410400	63410400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	82	712	0	ENST00000330258.3:c.2767G>A	p.Ala923Thr	p.A923T	ENST00000330258	NM_152424.3	923	Gcc/Acc	2/2	1	2	FACETS	0.545	0.48	0.616	0.545	0.48	0.616	SUBCLONAL	1	TRUE	1	0.349648708777463	2		712	860	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410458	63410458	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	132	645	0	ENST00000330258.3:c.2709G>T	p.Glu903Asp	p.E903D	ENST00000330258	NM_152424.3	903	gaG/gaT	2/2	1	2	FACETS	0.919	0.834	1	0.919	0.834	1	CLONAL	1	TRUE	1	0.349648708777463	2		645	822	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412452	63412452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	194	913	0	ENST00000330258.3:c.715G>A	p.Val239Ile	p.V239I	ENST00000330258	NM_152424.3	239	Gtt/Att	2/2	1	2	FACETS	0.995	0.92	1	0.995	0.92	1	CLONAL	1	TRUE	1	0.349648708777463	2		913	1115	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413103	63413103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	177	767	1	ENST00000330258.3:c.64G>A	p.Glu22Lys	p.E22K	ENST00000330258	NM_152424.3	22	Gaa/Aaa	2/2	1	2	FACETS	0.93	0.856	1	0.93	0.856	1	CLONAL	1	TRUE	1	0.349648708777463	2		768	1089	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340886	70340886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	69	651	0	ENST00000374080.3:c.619C>T	p.Pro207Ser	p.P207S	ENST00000374080		207	Cca/Tca	5/45	1	2	FACETS	0.44	0.382	0.502	0.44	0.382	0.502	SUBCLONAL	1	TRUE	1	0.349648708777463	2		651	898	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345240	70345240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	180	644	1	ENST00000374080.3:c.2266G>A	p.Val756Ile	p.V756I	ENST00000374080		756	Gta/Ata	16/45	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.349648708777463	2		645	898	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813089	76813089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057517707	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	114	459	0	ENST00000373344.5:c.6532C>T	p.Arg2178Trp	p.R2178W	ENST00000373344	NM_000489.3	2178	Cgg/Tgg	30/35	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.349648708777463	2		459	573	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855994	76855994	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	91	447	0	ENST00000373344.5:c.5606G>A	p.Gly1869Asp	p.G1869D	ENST00000373344	NM_000489.3	1869	gGt/gAt	23/35	1	2	FACETS	0.901	0.801	1	0.901	0.801	1	CLONAL	1	TRUE	1	0.349648708777463	2		447	578	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889188	76889188	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	66	358	0	ENST00000373344.5:c.4822C>A	p.Leu1608Ile	p.L1608I	ENST00000373344	NM_000489.3	1608	Ctt/Att	18/35	1	2	FACETS	0.892	0.778	1	0.892	0.778	1	CLONAL	1	TRUE	1	0.349648708777463	2		358	423	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76931767	76931767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	89	428	0	ENST00000373344.5:c.3763C>T	p.Pro1255Ser	p.P1255S	ENST00000373344	NM_000489.3	1255	Cct/Tct	10/35	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.349648708777463	2		428	509	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938570	76938570	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	90	476	0	ENST00000373344.5:c.2178T>A	p.Asp726Glu	p.D726E	ENST00000373344	NM_000489.3	726	gaT/gaA	9/35	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.349648708777463	2		476	399	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76953097	76953097	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	97	474	0	ENST00000373344.5:c.216G>T	p.Lys72Asn	p.K72N	ENST00000373344	NM_000489.3	72	aaG/aaT	4/35	1	2	FACETS	0.923	0.825	1	0.923	0.825	1	CLONAL	1	TRUE	1	0.349648708777463	2		474	601	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020177	123020177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1162866133	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	183	680	2	ENST00000355640.3:c.665G>A	p.Arg222Gln	p.R222Q	ENST00000355640		222	cGa/cAa	2/7	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.349648708777463	2		682	1038	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034431	123034431	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	87	420	0	ENST00000355640.3:c.1188A>T	p.Lys396Asn	p.K396N	ENST00000355640		396	aaA/aaT	6/7	1	2	FACETS	0.935	0.83	1	0.935	0.83	1	CLONAL	1	TRUE	1	0.349648708777463	2		420	532	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197708	123197708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	57	366	0	ENST00000218089.9:c.1832C>T	p.Ala611Val	p.A611V	ENST00000218089	NM_001042749.1	611	gCc/gTc	20/35	1	2	FACETS	0.953	0.822	1	0.953	0.822	1	CLONAL	1	TRUE	1	0.349648708777463	2		366	342	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205173	123205173	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	53	288	0	ENST00000218089.9:c.2533G>T	p.Asp845Tyr	p.D845Y	ENST00000218089	NM_001042749.1	845	Gat/Tat	25/35	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.349648708777463	2		288	277	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210233	123210233	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	113	491	1	ENST00000218089.9:c.2585G>T	p.Arg862Ile	p.R862I	ENST00000218089	NM_001042749.1	862	aGa/aTa	26/35	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.349648708777463	2		492	571	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480499	123480499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	95	448	0	ENST00000371139.4:c.7G>A	p.Ala3Thr	p.A3T	ENST00000371139	NM_001114937.2	3	Gca/Aca	1/4	1	2	FACETS	0.995	0.889	1	0.995	0.889	1	CLONAL	1	TRUE	1	0.349648708777463	2		448	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0043924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	211	829	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.472019023062916	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.495006093253482	1		829	614	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0043924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	40	283	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.199813026910621	0	FACETS	0.307	0.256	0.362			1	INDETERMINATE	1	TRUE	0	0.495006093253482	0		283	266	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936096	178936096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	14	528	0	ENST00000263967.3:c.1638G>C	p.Gln546His	p.Q546H	ENST00000263967	NM_006218.2	546	caG/caC	10/21	1	2	FACETS	0.093	0.066	0.125	0.093	0.066	0.125	SUBCLONAL	1	TRUE	1	0.495006093253482	2		528	611	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215674274	215674274	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	34	521	2	ENST00000260947.4:c.20C>T	p.Pro7Leu	p.P7L	ENST00000260947	NM_000465.2	7	cCg/cTg	1/11	0.390882595239069	2	FACETS	0.203	0.165	0.246	0.101	0.082	0.123	SUBCLONAL	1	TRUE	0	0.495006093253482	2		523	677	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254734	46254734	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0043924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	72	232	0	ENST00000334344.6:c.4922+2T>A		p.X1641_splice	ENST00000334344	NM_152641.2	1641			1	2	FACETS	0.903	0.796	1	0.903	0.796	1	CLONAL	1	TRUE	1	0.495006093253482	2		232	322	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243957	5243957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1324477953	NA	P-0043924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	208	525	1	ENST00000357368.4:c.1525G>A	p.Asp509Asn	p.D509N	ENST00000357368	NM_002850.3	509	Gac/Aac	11/38	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.495006093253482	2		526	758	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986548	36986549	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0043926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	43	626	0	ENST00000354822.5:c.1140dup	p.Asn381GlufsTer58	p.N381Efs*58	ENST00000354822	NM_001079668.2	380	-/G	3/3	1	2	FACETS	0.91	0.76	1	0.91	0.76	1	CLONAL	1	TRUE	1	0.14	2		626	675	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0043928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	103	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.218842936695474	3	FACETS	1	0.963	1	0.767	0.69	0.846	CLONAL	2	TRUE	0	0.230153349648646	3		326	434	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0043928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	29	410	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	0.167936203019948	3	FACETS	0.766	0.615	0.937	0.255	0.205	0.313	CLONAL	1	TRUE	0	0.230153349648646	3		410	367	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0043928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	80	603	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.230153349648646	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.230153349648646	1		603	448	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511205	148511205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	34	416	0	ENST00000320356.2:c.1697G>A	p.Arg566His	p.R566H	ENST00000320356	NM_004456.4	566	cGc/cAc	15/20	0.221742800314995	4	FACETS	0.751	0.613	0.906	0.25	0.204	0.302	CLONAL	1	TRUE	1	0.230153349648646	4		416	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0043932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	111	973	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.410569162699631	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.410569162699631	1		973	387	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0043932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	52	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.41029427164274	2	FACETS	0.632	0.539	0.733	0.316	0.269	0.367	SUBCLONAL	1	TRUE	0	0.410569162699631	2		326	401	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528621	89528621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780470195	NA	P-0043932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	31	195	0	ENST00000336596.2:c.2921C>T	p.Thr974Met	p.T974M	ENST00000336596	NM_005233.5	974	aCg/aTg	17/17	1	2	FACETS	0.956	0.783	1	0.956	0.783	1	CLONAL	1	TRUE	1	0.410569162699631	2		195	158	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998568	100998568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759171409	NA	P-0043932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	75	593	1	ENST00000325455.5:c.1234G>A	p.Ala412Thr	p.A412T	ENST00000325455	NM_001202474.3	412	Gca/Aca	1/8	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.410569162699631	2		594	334	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118382704	118382704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555050211	NA	P-0043932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	52	292	0	ENST00000534358.1:c.11110C>T	p.Arg3704Ter	p.R3704*	ENST00000534358	NM_005933.3	3704	Cga/Tga	31/36	1	2	FACETS	0.924	0.793	1	0.924	0.793	1	CLONAL	1	TRUE	1	0.410569162699631	2		292	274	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691826	30691826	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	66	394	0	ENST00000295754.5:c.328G>C	p.Asp110His	p.D110H	ENST00000295754	NM_003242.5	110	Gac/Cac	3/7	1	2	FACETS	0.957	0.836	1	0.957	0.836	1	CLONAL	1	TRUE	1	0.410569162699631	2		394	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0043943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	435	973	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.511252838512808	3	FACETS	0.871	0.839	0.903	0.871	0.839	0.903	CLONAL	3	TRUE	0	0.573495468053166	3		973	747	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0043943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	110	343	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.573495468053166	3	FACETS	0.979	0.897	1	0.979	0.897	1	CLONAL	2	TRUE	1	0.573495468053166	3		343	252	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714370	40714370	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs956451753	NA	P-0043943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	204	386	0	ENST00000373198.4:c.4027C>T	p.Arg1343Trp	p.R1343W	ENST00000373198	NM_133170.3	1343	Cgg/Tgg	29/32	NA	2	FACETS	1	0.955	1			1	INDETERMINATE	1	TRUE	NA	0.573495468053166	2		386	689	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612212	189612212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764601563	NA	P-0043943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	267	454	0	ENST00000264731.3:c.1964G>A	p.Arg655Gln	p.R655Q	ENST00000264731	NM_003722.4	655	cGa/cAa	14/14	0.573495468053166	5	FACETS	1	0.99	1	0.827	0.78	0.875	CLONAL	2	TRUE	2	0.573495468053166	5		454	698	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920430	114920430	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	287	457	0	ENST00000543371.1:c.1373del	p.Leu458TyrfsTer33	p.L458Yfs*33	ENST00000543371	NM_001198531.1	457	acT/ac	13/14	0.573495468053166	3	FACETS	0.997	0.945	1	0.997	0.945	1	CLONAL	2	TRUE	1	0.573495468053166	3		457	646	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398280	25398281	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0043943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	146	339	0	ENST00000311936.3:c.38_39delinsAT	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGC/gAT	2/5	0.346326896586825	6	FACETS	1	0.979	1	0.598	0.55	0.647	CLONAL	2	TRUE	2	0.573495468053166	6		339	457	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978405	2978405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370704955	NA	P-0043943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	126	645	0	ENST00000396946.4:c.925C>T	p.Arg309Cys	p.R309C	ENST00000396946	NM_032415.4	309	Cgc/Tgc	7/25	NA	2	FACETS	0.519	0.47	0.571			1	INDETERMINATE	1	TRUE	NA	0.573495468053166	2		645	846	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	29	176	0	ENST00000257430.4:c.3925del	p.Glu1309LysfsTer12	p.E1309Kfs*12	ENST00000257430	NM_000038.5	1309	Gaa/aa	16/16	0.573495468053166	3	FACETS	0.744	0.603	0.9	0.372	0.301	0.45	SUBCLONAL	1	TRUE	1	0.573495468053166	3		176	175	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0043950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	350	547	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.476967482310901	3	FACETS	0.992	0.95	1	0.992	0.95	1	CLONAL	3	TRUE	0	0.476967482310901	3		547	611	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217688	7217688	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	88	448	0	ENST00000380728.2:c.239del	p.Gln80ArgfsTer29	p.Q80Rfs*29	ENST00000380728		80	cAg/cg	4/11	0.476967482310901	3	FACETS	0.857	0.762	0.959	0.286	0.254	0.32	CLONAL	1	TRUE	0	0.476967482310901	3		448	533	SUCCESS
APC	324	MSKCC	GRCh37	5	112179385	112179385	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	83	404	0	ENST00000257430.4:c.8094A>T	p.Lys2698Asn	p.K2698N	ENST00000257430	NM_000038.5	2698	aaA/aaT	16/16	1	2	FACETS	0.902	0.801	1	0.902	0.801	1	CLONAL	1	TRUE	1	0.476967482310901	2		404	386	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577513	64577513	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	207	447	0	ENST00000312049.6:c.69del	p.Phe23LeufsTer96	p.F23Lfs*96	ENST00000312049	NM_130799.2	23	ttT/tt	2/10	0.697089190384061	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.697089190384061	1		447	387	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727451	66727451	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519729	NA	P-0044025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	441	397	0	ENST00000307102.5:c.167A>C	p.Gln56Pro	p.Q56P	ENST00000307102	NM_002755.3	56	cAg/cCg	2/11	0.675795452763222	2	FACETS	0.902	0.871	0.932	0.902	0.871	0.932	CLONAL	2	TRUE	0	0.721408795437819	2		397	678	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0044025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	552	692	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.649890845091811	2	FACETS	0.869	0.841	0.895	0.869	0.841	0.895	CLONAL	2	TRUE	0	0.721408795437819	2		692	881	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903747	114903747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	283	443	1	ENST00000543371.1:c.751G>A	p.Gly251Arg	p.G251R	ENST00000543371	NM_001198531.1	251	Gga/Aga	7/14	0.693860183288872	3	FACETS	1	0.987	1	0.388	0.366	0.412	CLONAL	1	TRUE	0	0.721408795437819	3		444	916	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127760	64127760	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	463	624	0	ENST00000334205.4:c.253G>A	p.Glu85Lys	p.E85K	ENST00000334205	NM_003942.2	85	Gag/Aag	3/17	0.295849990288709	3	FACETS	1	0.996	1	0.709	0.678	0.741	INDETERMINATE	1	TRUE	1	0.721408795437819	3		624	1231	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724420	43724420	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	121	607	0	ENST00000382044.4:c.3647G>T	p.Gly1216Val	p.G1216V	ENST00000382044	NM_001141980.1	1216	gGg/gTg	17/28	0.675795452763222	2	FACETS	0.352	0.317	0.388	0.176	0.158	0.194	SUBCLONAL	1	TRUE	0	0.721408795437819	2		607	954	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451872	29451872	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	216	671	0	ENST00000389048.3:c.2693A>T	p.Glu898Val	p.E898V	ENST00000389048	NM_004304.4	898	gAg/gTg	16/29	0.410975133049681	1	FACETS	0.418	0.389	0.449	0.418	0.389	0.449	INDETERMINATE	1	TRUE	0	0.721408795437819	1		671	915	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171642	32171643	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CACCTCA	novel	NA	P-0044025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	234	510	0	ENST00000375023.3:c.3129_3135dup	p.Glu1046Ter	p.E1046*	ENST00000375023	NM_004557.3	1045	-/TGAGGTG	20/30	0.295849990288709	3	FACETS	0.728	0.678	0.779	0.364	0.339	0.39	INDETERMINATE	1	TRUE	1	0.721408795437819	3		510	1213	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577330	64577333	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	rs587776841	NA	P-0044029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	172	733	0	ENST00000312049.6:c.249_252del	p.Ile85SerfsTer33	p.I85Sfs*33	ENST00000312049	NM_130799.2	83	ctGTCT/ct	2/10	0.336385412608127	2	FACETS	0.933	0.864	1	0.933	0.864	1	CLONAL	2	TRUE	0	0.336385412608127	2		733	548	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245235	46245235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753485118	NA	P-0044029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	61	456	0	ENST00000334344.6:c.3329G>A	p.Gly1110Glu	p.G1110E	ENST00000334344	NM_152641.2	1110	gGa/gAa	15/21	0.336385412608127	4	FACETS	0.772	0.665	0.888	0.386	0.332	0.444	SUBCLONAL	1	TRUE	2	0.336385412608127	4		456	628	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164127	47164127	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	53	267	1	ENST00000409792.3:c.1999del	p.Cys667ValfsTer3	p.C667Vfs*3	ENST00000409792	NM_014159.6	667	Tgt/gt	3/21	0.336385412608127	2	FACETS	1	0.956	1	0.648	0.558	0.745	CLONAL	1	TRUE	0	0.336385412608127	2		268	243	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0044047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	118	451	3	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.612882359459288	NA		454	148	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247168	153247168	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1560758208	NA	P-0044047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	106	228	0	ENST00000281708.4:c.1634A>G	p.Tyr545Cys	p.Y545C	ENST00000281708	NM_033632.3	545	tAt/tGt	10/12	0.612882359459288	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	FALSE	1	0.612882359459288	3		228	188	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057520006	NA	P-0044047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	515	603	0	ENST00000269305.4:c.821T>A	p.Val274Asp	p.V274D	ENST00000269305	NM_001126112.2	274	gTt/gAt	8/11	0.60038784350008	4	FACETS	0.974	0.947	0.999	0.974	0.947	0.999	CLONAL	4	FALSE	0	0.612882359459288	4		603	696	SUCCESS
APC	324	MSKCC	GRCh37	5	112175147	112175147	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	56	190	0	ENST00000257430.4:c.3856G>T	p.Glu1286Ter	p.E1286*	ENST00000257430	NM_000038.5	1286	Gaa/Taa	16/16	0.58515957083121	3	FACETS	0.947	0.859	1	0.947	0.859	1	CLONAL	3	FALSE	0	0.612882359459288	3		190	84	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455576	189455576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754361670	NA	P-0044047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	54	412	0	ENST00000264731.3:c.110G>A	p.Arg37Gln	p.R37Q	ENST00000264731	NM_003722.4	37	cGa/cAa	2/14	0.612882359459288	6	FACETS	1	0.937	1	0.234	0.201	0.27	CLONAL	1	FALSE	1	0.612882359459288	6		412	335	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22153365	22153365	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	100	373	0	ENST00000215832.6:c.545G>C	p.Gly182Ala	p.G182A	ENST00000215832	NM_002745.4	182	gGg/gCg	4/9	0.480777024570061	5	FACETS	1	0.976	1	0.435	0.39	0.482	CLONAL	1	FALSE	2	0.612882359459288	5		373	480	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282046	38282046	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	330	579	0	ENST00000425967.3:c.1010C>A	p.Pro337His	p.P337H	ENST00000425967	NM_001174067.1	337	cCt/cAt	8/19	0.58515957083121	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	FALSE	0	0.612882359459288	3		579	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0044051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	393	816	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.590197532963128	3	FACETS	0.89	0.859	0.92	0.89	0.859	0.92	CLONAL	3	TRUE	0	0.680629314684814	3		816	580	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977884	131977884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786203127	NA	P-0044051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	82	223	0	ENST00000265335.6:c.3767G>A	p.Arg1256His	p.R1256H	ENST00000265335		1256	cGc/cAc	25/25	0.638432076326367	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.680629314684814	1		223	139	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127640	64127640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	133	488	0	ENST00000334205.4:c.133G>A	p.Gly45Ser	p.G45S	ENST00000334205	NM_003942.2	45	Ggc/Agc	3/17	0.535762055717722	4	FACETS	0.969	0.882	1			1	CLONAL	1	TRUE	NA	0.680629314684814	4		488	678	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0044053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	471	863	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.875732618532981	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.875732618532981	2		863	537	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923024	48923118	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TATCTGGAAAACTTTCTTTCAGTGATACATTTTTCCTGTTTTTTTTCTGCTTTCTATTTGTTTAATAGGATATCTACTGAAATAAATTCTGCATT	TATCTGGAAAACTTTCTTTCAGTGATACATTTTTCCTGTTTTTTTTCTGCTTTCTATTTGTTTAATAGGATATCTACTGAAATAAATTCTGCATT	-	novel	NA	P-0044053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	32	93	0	ENST00000267163.4:c.540-68_566del		p.X180_splice	ENST00000267163	NM_000321.2	180		6/27	0.873067284675741	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.875732618532981	1		93	40	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535339	66535339	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	236	426	0	ENST00000273854.3:c.122G>T	p.Trp41Leu	p.W41L	ENST00000273854	NM_004439.5	41	tGg/tTg	1/18	0.823172425425795	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.875732618532981	1		426	292	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0044056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	331	711	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.497046768771921	3	FACETS	0.881	0.847	0.914	0.881	0.847	0.914	CLONAL	3	FALSE	0	0.67031405762365	3		711	499	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058083	27058083	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	201	362	0	ENST00000324856.7:c.1793del	p.Pro598LeufsTer21	p.P598Lfs*21	ENST00000324856	NM_006015.4	597	ttC/tt	3/20	0.572258490544152	4	FACETS	0.998	0.934	1	0.998	0.934	1	CLONAL	2	FALSE	2	0.67031405762365	4		362	502	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027153	49027153	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0044056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	73	372	0	ENST00000267163.4:c.1720A>T	p.Lys574Ter	p.K574*	ENST00000267163	NM_000321.2	574	Aaa/Taa	18/27	0.67031405762365	3	FACETS	0.836	0.764	0.905	0.836	0.764	0.905	CLONAL	3	FALSE	0	0.67031405762365	3		372	116	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247199	153247199	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	48	360	0	ENST00000281708.4:c.1603C>G	p.His535Asp	p.H535D	ENST00000281708	NM_033632.3	535	Cac/Gac	10/12	0.57961965014729	2	FACETS	1	0.969	1	0.716	0.628	0.804	CLONAL	1	FALSE	0	0.67031405762365	2		360	100	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020155	123020155	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	68	614	2	ENST00000355640.3:c.643C>A	p.Arg215Ser	p.R215S	ENST00000355640		215	Cgt/Agt	2/7	0.417480087781083	3	FACETS	0.912	0.801	1	0.456	0.4	0.515	CLONAL	1	FALSE	1	0.67031405762365	3		616	297	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0044084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	197	542	0				ENST00000310581	NM_198253.2	-/1132			0.620454946572819	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.620454946572819	1		542	338	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21553889	21553889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1565941238	NA	P-0044084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	50	470	0	ENST00000382592.4:c.2713G>A	p.Glu905Lys	p.E905K	ENST00000382592	NM_014572.2	905	Gag/Aag	7/8	0.620454946572819	1	FACETS	0.209	0.177	0.244	0.209	0.177	0.244	SUBCLONAL	1	TRUE	0	0.620454946572819	1		470	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579445	7579446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	354	640	0	ENST00000269305.4:c.241dup	p.Thr81AsnfsTer68	p.T81Nfs*68	ENST00000269305	NM_001126112.2	81	aca/aAca	4/11	0.620454946572819	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.620454946572819	1		640	655	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394890	394890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1459743512	NA	P-0044084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	397	456	0	ENST00000380956.4:c.286C>T	p.Arg96Cys	p.R96C	ENST00000380956	NM_001195286.1	96	Cgc/Tgc	3/9	0.599801088491461	4	FACETS	1	0.96	1			1	CLONAL	2	TRUE	NA	0.620454946572819	4		456	1029	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947542	48947561	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	ACTGTTATGAACACTATCCA	ACTGTTATGAACACTATCCA	-	novel	NA	P-0044084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	128	380	0	ENST00000267163.4:c.1131_1150del	p.Val378IlefsTer10	p.V378Ifs*10	ENST00000267163	NM_000321.2	377	ACTGTTATGAACACTATCCAa/a	12/27	0.620454946572819	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.620454946572819	1		380	275	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190867	185190867	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765143232	NA	P-0044084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	464	617	0	ENST00000265026.3:c.1748G>A	p.Arg583Gln	p.R583Q	ENST00000265026	NM_004721.4	583	cGa/cAa	11/14	0.612401623204924	4	FACETS	1	0.98	1	0.52	0.497	0.542	CLONAL	2	TRUE	0	0.620454946572819	4		617	1166	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36846847	36846847	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	40	403	0	ENST00000358127.4:c.1092del	p.Leu365CysfsTer38	p.L365Cfs*38	ENST00000358127	NM_001280556.1	364	ggG/gg	9/10	0.299614255342286	2	FACETS	0.259	0.215	0.308	0.129	0.107	0.154	INDETERMINATE	1	TRUE	0	0.620454946572819	2		403	498	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	79	300	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.801	0.705	0.904	0.801	0.705	0.904	CLONAL	1	TRUE	1	0.319142056156754	2		300	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0044133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	227	961	3	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.319142056156754	1	FACETS	0.945	0.879	1	0.945	0.879	1	CLONAL	1	TRUE	0	0.319142056156754	1		964	1265	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435950	49435950	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	199	872	1	ENST00000301067.7:c.6031G>T	p.Glu2011Ter	p.E2011*	ENST00000301067	NM_003482.3	2011	Gag/Tag	28/54	1	2	FACETS	0.995	0.92	1	0.995	0.92	1	CLONAL	1	TRUE	1	0.319142056156754	2		873	1253	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434443	110434443	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	177	767	0	ENST00000375856.3:c.3958T>C	p.Tyr1320His	p.Y1320H	ENST00000375856	NM_003749.2	1320	Tac/Cac	1/2	1	2	FACETS	0.946	0.87	1	0.946	0.87	1	CLONAL	1	TRUE	1	0.319142056156754	2		767	1172	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871253	35871255	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0044133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	73	383	0	ENST00000216797.5:c.918_920del	p.Asp307del	p.D307del	ENST00000216797	NM_020529.2	306	gaTGAc/gac	6/6	1	2	FACETS	0.665	0.581	0.755	0.665	0.581	0.755	SUBCLONAL	1	TRUE	1	0.319142056156754	2		383	688	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0044134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	543	463	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.51846971165964	5	FACETS	1	0.993	1	1	0.993	1	CLONAL	4	TRUE	1	0.51846971165964	5		463	857	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578359	7578375	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCAGCTGCTCACCATCG	CCAGCTGCTCACCATCG	-	novel	NA	P-0044134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	421	690	0	ENST00000269305.4:c.555_559+12del		p.X185_splice	ENST00000269305	NM_001126112.2	185		5/11	0.421296288656693	2	FACETS	0.838	0.801	0.875	0.838	0.801	0.875	CLONAL	2	TRUE	0	0.51846971165964	2		690	969	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252879	10252879	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	242	703	0	ENST00000340748.4:c.3086A>G	p.Lys1029Arg	p.K1029R	ENST00000340748		1029	aAg/aGg	29/40	0.51846971165964	1	FACETS	0.954	0.895	1	0.954	0.895	1	CLONAL	1	TRUE	0	0.51846971165964	1		703	725	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817433	39817433	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	219	634	0	ENST00000288319.7:c.130A>G	p.Thr44Ala	p.T44A	ENST00000288319	NM_182918.3	44	Act/Gct	2/10	1	2	FACETS	0.807	0.75	0.865	0.807	0.75	0.865	CLONAL	1	TRUE	1	0.51846971165964	2		634	1047	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0044141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	78	973	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.988	0.865	1	0.988	0.865	1	CLONAL	1	TRUE	1	0.14	2		973	1128	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0044141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	16	518	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.577	0.425	0.76	0.577	0.425	0.76	SUBCLONAL	1	TRUE	1	0.14	2		518	396	SUCCESS
APC	324	MSKCC	GRCh37	5	112175096	112175097	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs786203760	NA	P-0044141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	16	187	0	ENST00000257430.4:c.3807_3808del	p.Ile1269MetfsTer6	p.I1269Mfs*6	ENST00000257430	NM_000038.5	1269	ATa/a	16/16	1	2	FACETS	0.989	0.732	1	0.989	0.732	1	CLONAL	1	TRUE	1	0.14	2		187	231	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105967	27105967	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	44	493	0	ENST00000324856.7:c.5578G>T	p.Glu1860Ter	p.E1860*	ENST00000324856	NM_006015.4	1860	Gag/Tag	20/20	1	2	FACETS	0.82	0.685	0.969	0.82	0.685	0.969	CLONAL	1	TRUE	1	0.14	2		493	767	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224157	36224157	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	85	655	0	ENST00000222270.7:c.6707C>A	p.Pro2236Gln	p.P2236Q	ENST00000222270	NM_014727.1	2236	cCa/cAa	28/37	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.14	2		655	1033	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371734	116371734	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	25	297	0	ENST00000397752.3:c.1213A>G	p.Asn405Asp	p.N405D	ENST00000397752	NM_000245.2	405	Aat/Gat	3/21	1	2	FACETS	0.821	0.646	1	0.821	0.646	1	CLONAL	1	TRUE	1	0.14	2		297	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	380	1056	2	ENST00000269305.4:c.383del	p.Pro128LeufsTer42	p.P128Lfs*42	ENST00000269305	NM_001126112.2	128	cCt/ct	5/11	0.240825601012033	3	FACETS	1	0.989	1	0.756	0.718	0.795	CLONAL	2	TRUE	0	0.331867312785038	3		1058	1177	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324058	123324058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs938460066	NA	P-0044166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	86	574	1	ENST00000358487.5:c.412G>A	p.Asp138Asn	p.D138N	ENST00000358487	NM_000141.4	138	Gat/Aat	4/18	1	2	FACETS	0.782	0.692	0.878	0.782	0.692	0.878	SUBCLONAL	1	TRUE	1	0.331867312785038	2		575	663	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197163	26197163	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	79	494	0	ENST00000356476.2:c.316G>C	p.Glu106Gln	p.E106Q	ENST00000356476		106	Gag/Cag	1/1	0.316942968073824	4	FACETS	0.825	0.724	0.932	0.412	0.362	0.466	CLONAL	1	TRUE	2	0.331867312785038	4		494	769	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935692	15935692	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	60	426	0	ENST00000268712.3:c.7241A>G	p.His2414Arg	p.H2414R	ENST00000268712	NM_006311.3	2414	cAc/cGc	46/46	0.240825601012033	3	FACETS	0.76	0.655	0.874	0.253	0.218	0.292	SUBCLONAL	1	TRUE	0	0.331867312785038	3		426	555	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749580	41749580	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	79	911	0	ENST00000301178.4:c.1505A>C	p.Lys502Thr	p.K502T	ENST00000301178	NM_021913.4	502	aAg/aCg	12/20	1	2	FACETS	0.583	0.512	0.66	0.583	0.512	0.66	SUBCLONAL	1	TRUE	1	0.331867312785038	2		911	816	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26046002	26046002	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs548956477	NA	P-0044166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	97	362	0	ENST00000540144.1:c.364C>G	p.Pro122Ala	p.P122A	ENST00000540144	NM_003531.2	122	Ccc/Gcc	1/1	0.316942968073824	4	FACETS	0.752	0.672	0.835	0.752	0.672	0.835	SUBCLONAL	2	TRUE	2	0.331867312785038	4		362	518	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38194867	38194867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	91	603	0	ENST00000317025.8:c.866C>T	p.Ser289Leu	p.S289L	ENST00000317025	NM_023034.1	289	tCa/tTa	4/24	0.235950298266697	3	FACETS	0.729	0.646	0.818	0.365	0.323	0.409	SUBCLONAL	1	TRUE	1	0.331867312785038	3		603	877	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566386	141566386	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0044166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	44	306	0	ENST00000220592.5:c.1027-1G>A		p.X343_splice	ENST00000220592	NM_012154.3	343			0.273024205215617	3	FACETS	0.787	0.661	0.925			1	CLONAL	1	TRUE	NA	0.331867312785038	3		306	393	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249983	110249983	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1433770087	NA	P-0044166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	44	685	1	ENST00000374672.4:c.692T>G	p.Leu231Arg	p.L231R	ENST00000374672	NM_004235.4	231	cTg/cGg	3/5	1	2	FACETS	0.361	0.302	0.427	0.361	0.302	0.427	SUBCLONAL	1	TRUE	1	0.331867312785038	2		686	734	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730404	133730404	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	106	563	0	ENST00000318560.5:c.470G>T	p.Ser157Ile	p.S157I	ENST00000318560	NM_005157.4	157	aGt/aTt	3/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.331867312785038	2		563	524	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	84	425	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.414046887184509	3	FACETS	0.904	0.809	1	0.904	0.809	1	CLONAL	2	TRUE	1	0.414046887184509	3		426	271	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0044171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	134	677	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.414046887184509	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	0	0.414046887184509	2		680	321	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0044171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	9	415	2	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.414046887184509	4	FACETS	0.203	0.134	0.292	0.101	0.066	0.146	SUBCLONAL	1	TRUE	2	0.414046887184509	4		417	303	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912580	NA	P-0044171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	37	330	0	ENST00000342988.3:c.1157G>A	p.Gly386Asp	p.G386D	ENST00000342988	NM_005359.5	386	gGt/gAt	10/12	0.358799741643947	1	FACETS	0.886	0.741	1	0.886	0.741	1	CLONAL	1	TRUE	0	0.414046887184509	1		330	160	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030405	49030406	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	80	364	0	ENST00000267163.4:c.1881dup	p.Ala628CysfsTer25	p.A628Cfs*25	ENST00000267163	NM_000321.2	627	aat/aaTt	19/27	NA	2	FACETS	0.826	0.739	0.916			1	INDETERMINATE	2	TRUE	NA	0.414046887184509	2		364	234	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027166	48027166	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	50	414	0	ENST00000234420.5:c.2044T>C	p.Ser682Pro	p.S682P	ENST00000234420	NM_000179.2	682	Tct/Cct	4/10	0.414046887184509	4	FACETS	1	0.893	1	0.529	0.451	0.613	CLONAL	1	TRUE	2	0.414046887184509	4		414	323	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	189	456	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.39473199413579	1	FACETS	0.927	0.858	0.999	0.927	0.858	0.999	CLONAL	1	TRUE	0	0.39473199413579	1		456	829	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514515	103514515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	84	290	0	ENST00000355739.4:c.1016C>T	p.Pro339Leu	p.P339L	ENST00000355739	NM_000123.3	339	cCt/cTt	8/15	0.39473199413579	0	FACETS	1	0.92	1			1	CLONAL	1	TRUE	0	0.39473199413579	0		290	250	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117680986	117680986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780046038	NA	P-0044198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	70	313	0	ENST00000368508.3:c.3634C>T	p.Arg1212Cys	p.R1212C	ENST00000368508	NM_002944.2	1212	Cgc/Tgc	23/43	0.39473199413579	1	FACETS	0.887	0.779	1	0.887	0.779	1	CLONAL	1	TRUE	0	0.39473199413579	1		313	321	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279759	46279759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368683409	NA	P-0044198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	151	564	0	ENST00000371998.3:c.3685C>T	p.Arg1229Cys	p.R1229C	ENST00000371998		1229	Cgc/Tgc	20/23	0.39473199413579	3	FACETS	0.987	0.902	1	0.329	0.3	0.359	CLONAL	1	TRUE	0	0.39473199413579	3		564	928	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936077	178936083	+	protein_altering_variant	In_Frame_Del	DEL	TCTCTGA	TCTCTGA	AGAG	novel	NA	P-0044198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	149	413	1	ENST00000263967.3:c.1619_1625delinsAGAG	p.Leu540_Glu542delinsGlnArg	p.L540_E542delinsQR	ENST00000263967	NM_006218.2	540	cTCTCTGAa/cAGAGa	10/21	1	2	FACETS	0.79	0.727	0.854	1	0.989	1	SUBCLONAL	2	TRUE	1	0.39473199413579	2		414	478	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579310	7579310	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1555526469	NA	P-0044224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	399	654	0	ENST00000269305.4:c.375+2T>C		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.841606909493662	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.841606909493662	1		654	521	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171704	36171704	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121912499	NA	P-0044224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	332	442	0	ENST00000300305.3:c.861C>A	p.Tyr287Ter	p.Y287*	ENST00000300305		287	taC/taA	7/8	0.432714939246571	1	FACETS	0.614	0.584	0.644	0.614	0.584	0.644	INDETERMINATE	1	TRUE	0	0.841606909493662	1		442	744	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11293511	11293511	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	230	556	0	ENST00000361445.4:c.2365G>C	p.Asp789His	p.D789H	ENST00000361445	NM_004958.3	789	Gat/Cat	15/58	1	2	FACETS	0.981	0.923	1	0.981	0.923	1	CLONAL	1	TRUE	1	0.841606909493662	2		556	557	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552137	29552138	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0044224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	100	257	0	ENST00000356175.3:c.1871_1872del	p.Phe624SerfsTer9	p.F624Sfs*9	ENST00000356175	NM_000267.3	624	TTt/t	17/57	0.841606909493662	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.841606909493662	1		257	131	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878764	151878764	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	202	472	0	ENST00000262189.6:c.6181T>C	p.Ser2061Pro	p.S2061P	ENST00000262189	NM_170606.2	2061	Tca/Cca	36/59	1	2	FACETS	0.847	0.79	0.904	0.847	0.79	0.904	CLONAL	1	TRUE	1	0.841606909493662	2		472	567	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504056	123504056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1362460627	NA	P-0044255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	34	324	0	ENST00000371139.4:c.232C>T	p.Arg78Trp	p.R78W	ENST00000371139	NM_001114937.2	78	Cgg/Tgg	3/4	1	2	FACETS	0.967	0.8	1	0.967	0.8	1	CLONAL	1	TRUE	1	0.406386892774774	2		324	173	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710658	40710658	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0044255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	36	377	0	ENST00000373198.4:c.4194-1G>A		p.X1398_splice	ENST00000373198	NM_133170.3	1398			0.21299140673677	1	FACETS	0.654	0.542	0.777	0.654	0.542	0.777	INDETERMINATE	1	TRUE	0	0.406386892774774	1		377	216	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054951	176054951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	30	449	0	ENST00000367669.3:c.1102G>A	p.Glu368Lys	p.E368K	ENST00000367669	NM_022457.5	368	Gag/Aag	10/20	0.390426637761565	4	FACETS	0.67	0.541	0.815	0.335	0.27	0.408	SUBCLONAL	1	TRUE	2	0.406386892774774	4		449	310	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724427	112724427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	56	574	0	ENST00000369452.4:c.311G>A	p.Arg104His	p.R104H	ENST00000369452	NM_007373.3	104	cGt/cAt	2/9	0.406386892774774	2	FACETS	0.95	0.82	1	0.475	0.41	0.545	CLONAL	1	TRUE	0	0.406386892774774	2		574	290	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	221	1014	11	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.927	0.867	0.989	1	0.994	1	CLONAL	2	TRUE	1	0.354686233128073	2		1025	672	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	90	484	4	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.354686233128073	2		488	487	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913559	32913559	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359479	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	71	363	2	ENST00000380152.3:c.5073del	p.Lys1691AsnfsTer15	p.K1691Nfs*15	ENST00000380152		1689	gcA/gc	11/27	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.354686233128073	2		365	313	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350576	15350578	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs747153554	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	144	833	2	ENST00000263377.2:c.3337_3339del	p.Glu1113del	p.E1113del	ENST00000263377	NM_058243.2	1113	GAG/-	16/20	1	2	FACETS	0.919	0.838	1	0.919	0.838	1	CLONAL	1	TRUE	1	0.354686233128073	2		835	884	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024505	16024505	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	116	449	0	ENST00000268712.3:c.1713del	p.Arg572GlufsTer18	p.R572Efs*18	ENST00000268712	NM_006311.3	571	ggG/gg	16/46	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.354686233128073	2		449	525	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141426	11141426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	141	635	0	ENST00000358026.2:c.3403C>T	p.Arg1135Trp	p.R1135W	ENST00000358026	NM_001128849.1	1135	Cgg/Tgg	25/36	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.354686233128073	2		635	786	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404285	139404285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773902766	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	85	752	0	ENST00000277541.6:c.2869G>A	p.Gly957Arg	p.G957R	ENST00000277541	NM_017617.3	957	Ggg/Agg	18/34	1	2	FACETS	0.548	0.484	0.618	0.548	0.484	0.618	SUBCLONAL	1	TRUE	1	0.354686233128073	2		752	874	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522601	176522601	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	133	787	0	ENST00000292408.4:c.1703del	p.Pro568GlnfsTer53	p.P568Qfs*53	ENST00000292408	NM_213647.1	566	cgC/cg	13/18	1	2	FACETS	0.902	0.82	0.99	0.902	0.82	0.99	CLONAL	1	TRUE	1	0.354686233128073	2		787	831	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539105	23539105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	95	450	0	ENST00000380871.4:c.334G>A	p.Ala112Thr	p.A112T	ENST00000380871	NM_006167.3	112	Gcc/Acc	2/2	1	2	FACETS	0.998	0.891	1	0.998	0.891	1	CLONAL	1	TRUE	1	0.354686233128073	2		450	537	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687471	37687472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs760014508	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	29	314	2	ENST00000447079.4:c.4382dup	p.Thr1463AsnfsTer50	p.T1463Nfs*50	ENST00000447079	NM_015083.1	1459	tgg/tGgg	14/14	1	2	FACETS	0.513	0.412	0.627	0.513	0.412	0.627	SUBCLONAL	1	TRUE	1	0.354686233128073	2		316	319	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129338	152129338	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1361952517	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	91	613	4	ENST00000206249.3:c.296del	p.Pro99HisfsTer10	p.P99Hfs*10	ENST00000206249	NM_000125.3	97	ttC/tt	1/8	1	2	FACETS	0.86	0.764	0.961	0.86	0.764	0.961	CLONAL	1	TRUE	1	0.354686233128073	2		617	597	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736907	736907	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs986350587	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	36	474	0	ENST00000314574.4:c.1192C>T	p.Arg398Trp	p.R398W	ENST00000314574	NM_005433.3	398	Cgg/Tgg	10/12	1	2	FACETS	0.499	0.41	0.598	0.499	0.41	0.598	SUBCLONAL	1	TRUE	1	0.354686233128073	2		474	407	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589546	69589546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	67	158	0	ENST00000168712.1:c.307C>T	p.Arg103Cys	p.R103C	ENST00000168712	NM_002007.2	103	Cgc/Tgc	1/3	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.354686233128073	2		158	296	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148526849	148526849	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	14	306	1	ENST00000320356.2:c.455del	p.Asn152IlefsTer15	p.N152Ifs*15	ENST00000320356	NM_004456.4	152	aAt/at	5/20	1	2	FACETS	0.283	0.204	0.379	0.283	0.204	0.379	SUBCLONAL	1	TRUE	1	0.354686233128073	2		307	279	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564680	86564680	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	110	679	0	ENST00000274376.6:c.416del	p.Pro139LeufsTer35	p.P139Lfs*35	ENST00000274376	NM_002890.2	138	Ccc/cc	1/25	1	2	FACETS	0.911	0.819	1	0.911	0.819	1	CLONAL	1	TRUE	1	0.354686233128073	2		679	681	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26974623	26974623	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	63	424	0	ENST00000381527.3:c.967C>T	p.Arg323Ter	p.R323*	ENST00000381527	NM_001260.1	323	Cga/Tga	10/13	1	2	FACETS	0.745	0.645	0.852	0.745	0.645	0.852	SUBCLONAL	1	TRUE	1	0.354686233128073	2		424	477	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31372585	31372585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs545685689	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	97	537	0	ENST00000328111.2:c.226G>A	p.Gly76Arg	p.G76R	ENST00000328111	NM_006892.3	76	Ggg/Agg	4/23	1	2	FACETS	0.891	0.796	0.992	0.891	0.796	0.992	CLONAL	1	TRUE	1	0.354686233128073	2		537	614	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435882	149435882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777247	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	125	538	0	ENST00000286301.3:c.2342C>T	p.Ala781Val	p.A781V	ENST00000286301	NM_005211.3	781	gCg/gTg	18/22	1	2	FACETS	0.964	0.874	1	0.964	0.874	1	CLONAL	1	TRUE	1	0.354686233128073	2		538	731	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656840	45656840	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	56	644	0	ENST00000407780.3:c.316del	p.Gln106ArgfsTer11	p.Q106Rfs*11	ENST00000407780	NM_001283052.1	106	Cag/ag	3/7	NA	2	FACETS	0.513	0.439	0.594			1	INDETERMINATE	1	TRUE	NA	0.354686233128073	2		644	615	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897002	28897002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554058758	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	109	425	0	ENST00000282397.4:c.2878G>A	p.Val960Ile	p.V960I	ENST00000282397	NM_002019.4	960	Gtc/Atc	21/30	1	2	FACETS	0.953	0.857	1	0.953	0.857	1	CLONAL	1	TRUE	1	0.354686233128073	2		425	645	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	92	536	0	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	1	2	FACETS	0.745	0.662	0.834	0.745	0.662	0.834	SUBCLONAL	1	TRUE	1	0.354686233128073	2		536	696	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469956	157469956	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	66	477	0	ENST00000346085.5:c.2754del	p.Ser919ValfsTer20	p.S919Vfs*20	ENST00000346085	NM_020732.3	917	aCc/ac	9/20	1	2	FACETS	0.755	0.656	0.861	0.755	0.656	0.861	SUBCLONAL	1	TRUE	1	0.354686233128073	2		477	493	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096132	2096133	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs763525759	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	97	567	1	ENST00000219066.1:c.374dup	p.Val127GlyfsTer43	p.V127Gfs*43	ENST00000219066	NM_002528.5	125	cca/ccCa	2/6	1	2	FACETS	0.804	0.718	0.897	0.804	0.718	0.897	CLONAL	1	TRUE	1	0.354686233128073	2		568	680	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967091	18967092	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1384543747	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	62	699	0	ENST00000262803.5:c.1814_1815del	p.Glu605AlafsTer17	p.E605Afs*17	ENST00000262803	NM_002911.3	602	gcAGag/gcag	13/24	1	2	FACETS	0.417	0.359	0.48	0.417	0.359	0.48	SUBCLONAL	1	TRUE	1	0.354686233128073	2		699	838	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280012	18280012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1438495093	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	96	479	1	ENST00000222254.8:c.2095G>A	p.Ala699Thr	p.A699T	ENST00000222254	NM_005027.3	699	Gcc/Acc	16/16	1	2	FACETS	0.895	0.799	0.997	0.895	0.799	0.997	CLONAL	1	TRUE	1	0.354686233128073	2		480	605	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030691	48030692	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs267608092	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	48	336	0	ENST00000234420.5:c.3312dup	p.Gly1105TrpfsTer3	p.G1105Wfs*3	ENST00000234420	NM_000179.2	1102	act/acTt	5/10	1	2	FACETS	0.716	0.607	0.835	0.716	0.607	0.835	SUBCLONAL	1	TRUE	1	0.354686233128073	2		336	378	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964965	25964965	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	82	410	0	ENST00000435504.4:c.4241G>A	p.Gly1414Asp	p.G1414D	ENST00000435504		1414	gGc/gAc	13/13	1	2	FACETS	0.944	0.835	1	0.944	0.835	1	CLONAL	1	TRUE	1	0.354686233128073	2		410	490	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40857166	40857166	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	74	313	0	ENST00000428826.2:c.1875G>T	p.Trp625Cys	p.W625C	ENST00000428826		625	tgG/tgT	17/21	1	2	FACETS	0.929	0.817	1	0.929	0.817	1	CLONAL	1	TRUE	1	0.354686233128073	2		313	449	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038684	14038684	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56129764	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	49	233	0	ENST00000311895.7:c.2009G>A	p.Arg670Gln	p.R670Q	ENST00000311895	NM_005236.2	670	cGg/cAg	10/11	1	2	FACETS	0.83	0.706	0.965	0.83	0.706	0.965	CLONAL	1	TRUE	1	0.354686233128073	2		233	333	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915054	32915054	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507373	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	72	422	0	ENST00000380152.3:c.6566del	p.Asn2189ThrfsTer2	p.N2189Tfs*2	ENST00000380152		2188	Aaa/aa	11/27	1	2	FACETS	0.875	0.767	0.991	0.875	0.767	0.991	CLONAL	1	TRUE	1	0.354686233128073	2		422	464	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562799	95562799	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	44	314	0	ENST00000393063.1:c.4458del	p.Lys1486AsnfsTer4	p.K1486Nfs*4	ENST00000393063	NM_030621.3	1486	aaA/aa	24/28	1	2	FACETS	0.933	0.788	1	0.933	0.788	1	CLONAL	1	TRUE	1	0.354686233128073	2		314	266	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094737	2094737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750992242	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	170	763	1	ENST00000219066.1:c.443C>T	p.Ala148Val	p.A148V	ENST00000219066	NM_002528.5	148	gCg/gTg	3/6	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.354686233128073	2		764	917	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31511249	31511249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	112	672	0	ENST00000344624.3:c.1325G>A	p.Arg442His	p.R442H	ENST00000344624		442	cGt/cAt	6/33	1	2	FACETS	0.865	0.779	0.957	0.865	0.779	0.957	CLONAL	1	TRUE	1	0.354686233128073	2		672	730	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425694	49425694	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	136	705	0	ENST00000301067.7:c.12794del	p.Gly4265AlafsTer13	p.G4265Afs*13	ENST00000301067	NM_003482.3	4265	gGc/gc	39/54	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.354686233128073	2		705	689	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424442	49424443	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs797044740	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	110	597	0	ENST00000301067.7:c.13780dup	p.Ala4594GlyfsTer12	p.A4594Gfs*12	ENST00000301067	NM_003482.3	4594	gcc/gGcc	41/54	1	2	FACETS	0.912	0.821	1	0.912	0.821	1	CLONAL	1	TRUE	1	0.354686233128073	2		597	680	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946433	2946433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775862540	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	147	764	1	ENST00000396946.4:c.3304G>A	p.Val1102Met	p.V1102M	ENST00000396946	NM_032415.4	1102	Gtg/Atg	25/25	1	2	FACETS	0.944	0.862	1	0.944	0.862	1	CLONAL	1	TRUE	1	0.354686233128073	2		765	878	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319318	11319318	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	81	478	0	ENST00000361445.4:c.149T>C	p.Met50Thr	p.M50T	ENST00000361445	NM_004958.3	50	aTg/aCg	2/58	1	2	FACETS	0.813	0.717	0.915	0.813	0.717	0.915	CLONAL	1	TRUE	1	0.354686233128073	2		478	562	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163295926	163295926	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	77	553	0	ENST00000271452.3:c.89del	p.Asn30ThrfsTer18	p.N30Tfs*18	ENST00000271452	NM_145697.2	29	Aaa/aa	2/14	1	2	FACETS	0.967	0.852	1	0.967	0.852	1	CLONAL	1	TRUE	1	0.354686233128073	2		553	449	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683138	88683138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55932635	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	61	535	0	ENST00000372037.3:c.1348G>A	p.Val450Met	p.V450M	ENST00000372037	NM_004329.2	450	Gtg/Atg	12/13	1	2	FACETS	0.698	0.603	0.801	0.698	0.603	0.801	SUBCLONAL	1	TRUE	1	0.354686233128073	2		535	493	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860138	57860138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	135	624	0	ENST00000228682.2:c.878G>A	p.Arg293His	p.R293H	ENST00000228682	NM_005269.2	293	cGc/cAc	8/12	1	2	FACETS	0.928	0.844	1	0.928	0.844	1	CLONAL	1	TRUE	1	0.354686233128073	2		624	820	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143031	58143031	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs754187815	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	127	661	2	ENST00000257904.6:c.753del	p.Arg252GlufsTer25	p.R252Efs*25	ENST00000257904	NM_000075.3	251	ccC/cc	7/8	1	2	FACETS	0.897	0.813	0.986	0.897	0.813	0.986	CLONAL	1	TRUE	1	0.354686233128073	2		663	798	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281319	49281319	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201226412	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	104	731	0	ENST00000282018.3:c.366G>A	p.Met122Ile	p.M122I	ENST00000282018	NM_020377.2	122	atG/atA	1/1	1	2	FACETS	0.755	0.676	0.839	0.755	0.676	0.839	SUBCLONAL	1	TRUE	1	0.354686233128073	2		731	777	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052588	42052588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	80	423	0	ENST00000219905.7:c.7259C>T	p.Ala2420Val	p.A2420V	ENST00000219905	NM_001164273.1	2420	gCg/gTg	20/24	1	2	FACETS	0.892	0.787	1	0.892	0.787	1	CLONAL	1	TRUE	1	0.354686233128073	2		423	506	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348083	348083	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	141	749	0	ENST00000262320.3:c.1423del	p.Val475TyrfsTer5	p.V475Yfs*5	ENST00000262320	NM_003502.3	475	Gta/ta	6/11	1	2	FACETS	0.982	0.895	1	0.982	0.895	1	CLONAL	1	TRUE	1	0.354686233128073	2		749	810	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654642	67654642	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555535157	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	107	416	0	ENST00000264010.4:c.1129C>A	p.Arg377Ser	p.R377S	ENST00000264010	NM_006565.3	377	Cgt/Agt	6/12	1	2	FACETS	0.95	0.854	1	0.95	0.854	1	CLONAL	1	TRUE	1	0.354686233128073	2		416	635	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562750	29562750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	69	346	0	ENST00000356175.3:c.3830G>A	p.Gly1277Asp	p.G1277D	ENST00000356175	NM_000267.3	1277	gGc/gAc	28/57	1	2	FACETS	0.911	0.797	1	0.911	0.797	1	CLONAL	1	TRUE	1	0.354686233128073	2		346	427	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440659	56440659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1000142712	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	145	587	0	ENST00000407977.2:c.559G>A	p.Glu187Lys	p.E187K	ENST00000407977		187	Gag/Aag	5/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.354686233128073	2		587	753	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224374	36224374	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	115	846	0	ENST00000222270.7:c.6924G>T	p.Glu2308Asp	p.E2308D	ENST00000222270	NM_014727.1	2308	gaG/gaT	28/37	0.342473918787952	2	FACETS	0.656	0.59	0.726	0.328	0.295	0.363	SUBCLONAL	1	TRUE	0	0.354686233128073	2		846	989	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227590	36227590	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	124	375	0	ENST00000222270.7:c.7160-1G>C		p.X2387_splice	ENST00000222270	NM_014727.1	2387			0.342473918787952	2	FACETS	0.863	0.788	0.941	0.863	0.788	0.941	CLONAL	2	TRUE	0	0.354686233128073	2		375	405	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726592	41726592	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	61	640	0	ENST00000301178.4:c.137G>A	p.Gly46Asp	p.G46D	ENST00000301178	NM_021913.4	46	gGt/gAt	2/20	0.342473918787952	2	FACETS	0.432	0.372	0.498	0.216	0.186	0.249	SUBCLONAL	1	TRUE	0	0.354686233128073	2		640	796	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180820	106180820	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	53	268	2	ENST00000380013.4:c.3848C>T	p.Ala1283Val	p.A1283V	ENST00000380013	NM_001127208.2	1283	gCc/gTc	7/11	1	2	FACETS	0.861	0.738	0.995	0.861	0.738	0.995	CLONAL	1	TRUE	1	0.354686233128073	2		270	347	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251506	251506	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	54	267	0	ENST00000264932.6:c.1717C>A	p.Leu573Met	p.L573M	ENST00000264932	NM_004168.2	573	Ctg/Atg	13/15	1	2	FACETS	0.973	0.836	1	0.973	0.836	1	CLONAL	1	TRUE	1	0.354686233128073	2		267	313	SUCCESS
APC	324	MSKCC	GRCh37	5	112179578	112179578	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	67	351	0	ENST00000257430.4:c.8287A>G	p.Ser2763Gly	p.S2763G	ENST00000257430	NM_000038.5	2763	Agt/Ggt	16/16	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.354686233128073	2		351	340	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157519979	157519980	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCCTCCCTC	novel	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	103	576	0	ENST00000346085.5:c.4050_4059dup	p.Gly1354ProfsTer108	p.G1354Pfs*108	ENST00000346085	NM_020732.3	1350	ggc/gGCCCTCCCTCgc	17/20	1	2	FACETS	0.841	0.753	0.934	0.841	0.753	0.934	CLONAL	1	TRUE	1	0.354686233128073	2		576	691	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836271	151836271	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	96	432	0	ENST00000262189.6:c.14534G>T	p.Arg4845Met	p.R4845M	ENST00000262189	NM_170606.2	4845	aGg/aTg	57/59	1	2	FACETS	0.933	0.833	1	0.933	0.833	1	CLONAL	1	TRUE	1	0.354686233128073	2		432	580	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151850000	151850002	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	23	326	0	ENST00000262189.6:c.12314_12316del	p.Leu4105del	p.L4105del	ENST00000262189	NM_170606.2	4105	cTTCac/cac	49/59	1	2	FACETS	0.334	0.26	0.42	0.334	0.26	0.42	SUBCLONAL	1	TRUE	1	0.354686233128073	2		326	388	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500755	8500755	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	41	274	0	ENST00000356435.5:c.2127T>A	p.Asp709Glu	p.D709E	ENST00000356435		709	gaT/gaA	13/35	1	2	FACETS	0.784	0.656	0.924	0.784	0.656	0.924	CLONAL	1	TRUE	1	0.354686233128073	2		274	295	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	33	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.837	0.682	1	0.837	0.682	1	CLONAL	1	TRUE	1	0.216691314001101	2		326	364	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs864622237	NA	P-0044298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	64	619	0	ENST00000269305.4:c.700T>C	p.Tyr234His	p.Y234H	ENST00000269305	NM_001126112.2	234	Tac/Cac	7/11	0.216691314001101	1	FACETS	0.859	0.744	0.984	0.859	0.744	0.984	CLONAL	1	TRUE	0	0.216691314001101	1		619	613	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415917	49415918	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGGAA	novel	NA	P-0044298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	60	370	0	ENST00000301067.7:c.16425_16429dup	p.Cys5477PhefsTer12	p.C5477Ffs*12	ENST00000301067	NM_003482.3	5477	tgt/tTTCCTgt	53/54	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.216691314001101	2		370	523	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447415	49447415	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	91	505	0	ENST00000301067.7:c.683G>T	p.Arg228Leu	p.R228L	ENST00000301067	NM_003482.3	228	cGc/cTc	6/54	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.216691314001101	2		505	749	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974659	21974684	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGCAGACCCTCTACCCACCTGGATCG	TGCAGACCCTCTACCCACCTGGATCG	-	novel	NA	P-0044298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	53	540	0	ENST00000304494.5:c.143_150+18del		p.X48_splice	ENST00000304494	NM_000077.4	48		1/3	0.216691314001101	1	FACETS	0.767	0.653	0.891	0.767	0.653	0.891	SUBCLONAL	1	TRUE	0	0.216691314001101	1		540	569	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0044325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	154	542	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.923	0.848	1			1	INDETERMINATE	1	TRUE	NA	0.503856303619876	2		542	662	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0044325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	590	735	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	0.470588202307852	2	FACETS	0.852	0.82	0.883	0.852	0.82	0.883	CLONAL	2	TRUE	0	0.503856303619876	2		735	1375	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0044325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	145	360	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.969	0.888	1	0.969	0.888	1	CLONAL	1	TRUE	1	0.503856303619876	2		360	594	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176330	24176330	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1057517825	NA	P-0044325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	532	722	0	ENST00000263121.7:c.1121G>A	p.Arg374Gln	p.R374Q	ENST00000263121	NM_003073.3	374	cGg/cAg	9/9	0.470588202307852	2	FACETS	0.887	0.853	0.922	0.887	0.853	0.922	CLONAL	2	TRUE	0	0.503856303619876	2		722	1190	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0044325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	314	715	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.503856303619876	1	FACETS	0.878	0.829	0.928	0.878	0.829	0.928	CLONAL	1	TRUE	0	0.503856303619876	1		715	1062	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923245	26923245	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs997541090	NA	P-0044325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	98	273	0	ENST00000381527.3:c.241C>T	p.Leu81Phe	p.L81F	ENST00000381527	NM_001260.1	81	Ctt/Ttt	3/13	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.503856303619876	2		273	377	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913402	32913402	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs397507343	NA	P-0044325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	62	375	0	ENST00000380152.3:c.4910T>G	p.Val1637Gly	p.V1637G	ENST00000380152		1637	gTt/gGt	11/27	1	2	FACETS	0.988	0.864	1	0.988	0.864	1	CLONAL	1	TRUE	1	0.503856303619876	2		375	249	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549812	187549812	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	98	466	0	ENST00000441802.2:c.4429C>T	p.Gln1477Ter	p.Q1477*	ENST00000441802	NM_005245.3	1477	Caa/Taa	8/27	1	2	FACETS	0.796	0.713	0.883	0.796	0.713	0.883	SUBCLONAL	1	TRUE	1	0.503856303619876	2		466	489	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979315	93979315	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	63	452	0	ENST00000369303.4:c.1513C>G	p.Leu505Val	p.L505V	ENST00000369303	NM_004440.3	505	Ctg/Gtg	7/17	1	2	FACETS	0.695	0.604	0.792	0.695	0.604	0.792	SUBCLONAL	1	TRUE	1	0.503856303619876	2		452	360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0044360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	104	973	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.2	2		973	928	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0044360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	48	210	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.934	0.79	1	0.934	0.79	1	CLONAL	1	TRUE	1	0.2	2		210	514	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946426	2946426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471772603	NA	P-0044360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	87	537	1	ENST00000396946.4:c.3311G>A	p.Arg1104Gln	p.R1104Q	ENST00000396946	NM_032415.4	1104	cGg/cAg	25/25	1	2	FACETS	0.94	0.83	1	0.94	0.83	1	CLONAL	1	TRUE	1	0.2	2		538	926	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843595	156843595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139875058	NA	P-0044360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	87	539	1	ENST00000524377.1:c.1021G>A	p.Val341Met	p.V341M	ENST00000524377	NM_002529.3	341	Gtg/Atg	8/17	1	2	FACETS	0.976	0.863	1	0.976	0.863	1	CLONAL	1	TRUE	1	0.2	2		540	891	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	112	300	0				ENST00000310581	NM_198253.2	-/1132			0.319989307809427	1	FACETS	0.709	0.645	0.776	0.709	0.645	0.776	INDETERMINATE	1	TRUE	0	0.621916310135866	1		300	350	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397742	49397742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552757	NA	P-0044366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	581	548	1	ENST00000418115.1:c.482C>T	p.Ala161Val	p.A161V	ENST00000418115	NM_001664.2	161	gCa/gTa	5/5	0.247677026857867	3	FACETS	1	0.992	1	0.721	0.696	0.746	INDETERMINATE	2	TRUE	0	0.621916310135866	3		549	1133	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199980	128199980	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	670	541	0	ENST00000341105.2:c.1325A>G	p.His442Arg	p.H442R	ENST00000341105	NM_032638.4	442	cAc/cGc	6/6	0.247677026857867	3	FACETS	1	0.993	1	0.726	0.702	0.749	INDETERMINATE	2	TRUE	0	0.621916310135866	3		541	1297	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20150361	20150361	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	155	168	0	ENST00000379607.5:c.276T>G	p.Ile92Met	p.I92M	ENST00000379607	NM_001412.3	92	atT/atG	5/7	0.473188225737776	0	FACETS	0.751	0.706	0.795			1	SUBCLONAL	1	TRUE	NA	0.621916310135866	0		168	251	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513813	41513814	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	T	novel	NA	P-0044366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	299	472	1	ENST00000263253.7:c.717_718delinsT	p.Gln240SerfsTer7	p.Q240Sfs*7	ENST00000263253	NM_001429.3	239	ccCCag/ccTag	2/31	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.621916310135866	2		473	931	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636086	28636086	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	116	562	0	ENST00000241453.7:c.286G>T	p.Asp96Tyr	p.D96Y	ENST00000241453	NM_004119.2	96	Gac/Tac	3/24	0.478665145086375	1	FACETS	0.47	0.424	0.52	0.47	0.424	0.52	SUBCLONAL	1	TRUE	0	0.478665145086375	1		562	784	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986833	36986833	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	19	149	0	ENST00000354822.5:c.856C>T	p.Arg286Ter	p.R286*	ENST00000354822	NM_001079668.2	286	Cga/Tga	3/3	0.478665145086375	1	FACETS	0.181	0.137	0.233	0.181	0.137	0.233	SUBCLONAL	1	TRUE	0	0.478665145086375	1		149	333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934573	NA	P-0044372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	301	554	0	ENST00000269305.4:c.722C>A	p.Ser241Tyr	p.S241Y	ENST00000269305	NM_001126112.2	241	tCc/tAc	7/11	0.478665145086375	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.478665145086375	1		554	856	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082907	16082907	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs764416757	NA	P-0044372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	149	178	0	ENST00000281043.3:c.721G>T	p.Gly241Cys	p.G241C	ENST00000281043	NM_005378.4	241	Ggc/Tgc	2/3	0.333380823486093	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.478665145086375	1		178	317	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705494	47705494	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs63750346	NA	P-0044372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	78	342	0	ENST00000233146.2:c.2294del	p.Ala765ValfsTer47	p.A765Vfs*47	ENST00000233146	NM_000251.2	765	gCt/gt	14/16	0.333380823486093	1	FACETS	0.509	0.448	0.574	0.509	0.448	0.574	SUBCLONAL	1	TRUE	0	0.478665145086375	1		342	487	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732774	204732789	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTGAGTGAGACTTTT	GGTGAGTGAGACTTTT	-	novel	NA	P-0044372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	40	371	0	ENST00000302823.3:c.109+2_109+17del		p.X37_splice	ENST00000302823	NM_005214.4	37		1/4	0.333380823486093	1	FACETS	0.217	0.179	0.258	0.217	0.179	0.258	SUBCLONAL	1	TRUE	0	0.478665145086375	1		371	587	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202788	128202788	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	274	651	1	ENST00000341105.2:c.932C>A	p.Thr311Asn	p.T311N	ENST00000341105	NM_032638.4	311	aCc/aAc	4/6	1	2	FACETS	0.964	0.904	1	0.964	0.904	1	CLONAL	1	TRUE	1	0.478665145086375	2		652	1188	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268972	142268972	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0044372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	108	269	0	ENST00000350721.4:c.2976+2T>G		p.X992_splice	ENST00000350721	NM_001184.3	992			0.367363856769557	4	FACETS	0.938	0.843	1	0.313	0.281	0.347	CLONAL	1	TRUE	1	0.478665145086375	4		269	711	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33290691	33290691	+	5_prime_UTR_variant	5'UTR	SNP	T	T	A	novel	NA	P-0044372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	238	550	1	ENST00000374542.5:c.-105A>T		p.*35*	ENST00000374542	NM_001141970.1	-/740		1/8	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.478665145086375	2		551	990	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	389	1014	11	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.858	0.815	0.902	0.858	0.815	0.902	CLONAL	1	TRUE	1	0.716187681041634	2		1025	1266	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	324	572	5	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.92	0.87	0.97	0.92	0.87	0.97	CLONAL	1	TRUE	1	0.716187681041634	2		577	984	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	269	270	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.836	0.785	0.887	0.836	0.785	0.887	CLONAL	1	TRUE	1	0.716187681041634	2		271	899	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	383	751	1	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.716187681041634	2		752	1029	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720833	89720836	+	frameshift_variant	Frame_Shift_Del	DEL	AAAT	AAAT	-	rs587782304	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	151	326	0	ENST00000371953.3:c.987_990del	p.Asn329LysfsTer14	p.N329Kfs*14	ENST00000371953	NM_000314.4	328	gcAAAT/gc	8/9	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.716187681041634	2		326	416	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466022	69466022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	485	790	1	ENST00000227507.2:c.860C>T	p.Pro287Leu	p.P287L	ENST00000227507	NM_053056.2	287	cCc/cTc	5/5	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.716187681041634	2		791	1355	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	495	707	1	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.716187681041634	2		708	1378	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918921	76918921	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	270	639	6	ENST00000373344.5:c.4070del	p.Lys1357ArgfsTer18	p.K1357Rfs*18	ENST00000373344	NM_000489.3	1357	aAg/ag	12/35	1	2	FACETS	0.781	0.733	0.829	0.781	0.733	0.829	SUBCLONAL	1	TRUE	1	0.716187681041634	2		645	966	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	132	321	3	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	1	2	FACETS	0.906	0.83	0.984	0.906	0.83	0.984	CLONAL	1	TRUE	1	0.716187681041634	2		324	407	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528105	157528105	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1028186690	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	439	590	2	ENST00000346085.5:c.5830C>T	p.Arg1944Ter	p.R1944*	ENST00000346085	NM_020732.3	1944	Cga/Tga	20/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.716187681041634	2		592	1118	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	266	417	5	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.716187681041634	2		422	709	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428510	78428510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754770362	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	185	463	0	ENST00000370768.2:c.1289G>A	p.Arg430His	p.R430H	ENST00000370768	NM_003902.3	430	cGt/cAt	14/20	0.716187681041634	2	FACETS	0.882	0.819	0.946	0.441	0.409	0.473	CLONAL	1	TRUE	0	0.716187681041634	2		463	586	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370236	40370236	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs761761205	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	278	842	9	ENST00000293328.3:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000293328	NM_012448.3	368	Cag/ag	9/19	1	2	FACETS	0.56	0.524	0.596	0.56	0.524	0.596	SUBCLONAL	1	TRUE	1	0.716187681041634	2		851	1387	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692901	89692901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786204929	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	168	468	1	ENST00000371953.3:c.385G>A	p.Gly129Arg	p.G129R	ENST00000371953	NM_000314.4	129	Gga/Aga	5/9	1	2	FACETS	0.948	0.878	1	0.948	0.878	1	CLONAL	1	TRUE	1	0.716187681041634	2		469	495	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672758	86672758	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1204340475	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	113	376	0	ENST00000274376.6:c.2245C>T	p.Arg749Ter	p.R749*	ENST00000274376	NM_002890.2	749	Cga/Tga	17/25	1	2	FACETS	0.917	0.835	1	0.917	0.835	1	CLONAL	1	TRUE	1	0.716187681041634	2		376	344	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555255	226555255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	76	567	0	ENST00000366794.5:c.2332C>T	p.Leu778Phe	p.L778F	ENST00000366794	NM_001618.3	778	Ctc/Ttc	17/23	1	2	FACETS	0.194	0.169	0.221	0.194	0.169	0.221	SUBCLONAL	1	TRUE	1	0.716187681041634	2		567	1094	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	546	894	3	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.925	0.887	0.964	0.925	0.887	0.964	CLONAL	1	TRUE	1	0.716187681041634	2		897	1648	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	444	840	6	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.951	0.908	0.995	0.951	0.908	0.995	CLONAL	1	TRUE	1	0.716187681041634	2		846	1304	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86648999	86648999	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs975191415	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	121	338	2	ENST00000274376.6:c.1279C>T	p.Arg427Ter	p.R427*	ENST00000274376	NM_002890.2	427	Cga/Tga	9/25	1	2	FACETS	0.892	0.814	0.972	0.892	0.814	0.972	CLONAL	1	TRUE	1	0.716187681041634	2		340	379	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143345	30143345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	412	656	0	ENST00000389048.3:c.181C>T	p.Pro61Ser	p.P61S	ENST00000389048	NM_004304.4	61	Ccc/Tcc	1/29	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.716187681041634	2		656	1068	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223175	36223175	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	531	974	6	ENST00000222270.7:c.5730del	p.Arg1911AspfsTer23	p.R1911Dfs*23	ENST00000222270	NM_014727.1	1909	Ccc/cc	28/37	1	2	FACETS	0.874	0.837	0.912	0.874	0.837	0.912	CLONAL	1	TRUE	1	0.716187681041634	2		980	1696	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958917	38958917	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	83	198	1	ENST00000357387.3:c.2195C>T	p.Ala732Val	p.A732V	ENST00000357387	NM_152756.3	732	gCa/gTa	23/38	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.716187681041634	2		199	216	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949104	71949104	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	434	744	0	ENST00000298229.2:c.3571G>C	p.Gly1191Arg	p.G1191R	ENST00000298229	NM_001567.3	1191	Ggg/Cgg	27/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.716187681041634	2		744	1187	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524364	176524364	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759042869	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	501	789	1	ENST00000292408.4:c.2225C>T	p.Ala742Val	p.A742V	ENST00000292408	NM_213647.1	742	gCg/gTg	17/18	1	2	FACETS	0.983	0.941	1	0.983	0.941	1	CLONAL	1	TRUE	1	0.716187681041634	2		790	1423	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357087	89357087	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	476	647	1	ENST00000301030.4:c.547C>T	p.Arg183Cys	p.R183C	ENST00000301030	NM_001256183.1	183	Cgc/Tgc	6/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.716187681041634	2		648	1301	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252730	10252730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747265409	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	474	737	1	ENST00000340748.4:c.3235G>A	p.Gly1079Ser	p.G1079S	ENST00000340748		1079	Ggc/Agc	29/40	1	2	FACETS	0.994	0.95	1	0.994	0.95	1	CLONAL	1	TRUE	1	0.716187681041634	2		738	1332	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528243	157528243	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs797045283	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	396	730	1	ENST00000346085.5:c.5968C>T	p.Arg1990Ter	p.R1990*	ENST00000346085	NM_020732.3	1990	Cga/Tga	20/20	1	2	FACETS	0.943	0.897	0.989	0.943	0.897	0.989	CLONAL	1	TRUE	1	0.716187681041634	2		731	1173	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106139	27106139	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	788	644	0	ENST00000324856.7:c.5750del	p.Thr1917IlefsTer6	p.T1917Ifs*6	ENST00000324856	NM_006015.4	1917	aCt/at	20/20	0.716187681041634	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.716187681041634	2		644	1064	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429321	78429321	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	680	577	0	ENST00000370768.2:c.1121del	p.Gly374ValfsTer17	p.G374Vfs*17	ENST00000370768	NM_003902.3	374	gGt/gt	13/20	0.716187681041634	2	FACETS	0.916	0.891	0.94	0.916	0.891	0.94	CLONAL	2	TRUE	0	0.716187681041634	2		577	1037	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115976	8115976	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	200	384	0	ENST00000346208.3:c.1322C>T	p.Ala441Val	p.A441V	ENST00000346208		441	gCc/gTc	6/6	1	2	FACETS	0.87	0.81	0.931	0.87	0.81	0.931	CLONAL	1	TRUE	1	0.716187681041634	2		384	642	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948622	71948622	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	443	849	0	ENST00000298229.2:c.3334G>T	p.Glu1112Ter	p.E1112*	ENST00000298229	NM_001567.3	1112	Gaa/Taa	26/28	1	2	FACETS	0.898	0.857	0.941	0.898	0.857	0.941	CLONAL	1	TRUE	1	0.716187681041634	2		849	1377	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563252	21563252	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	427	821	0	ENST00000382592.4:c.667G>T	p.Gly223Trp	p.G223W	ENST00000382592	NM_014572.2	223	Ggg/Tgg	4/8	1	2	FACETS	0.973	0.928	1	0.973	0.928	1	CLONAL	1	TRUE	1	0.716187681041634	2		821	1225	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059201	42059201	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	284	474	0	ENST00000219905.7:c.8921A>G	p.Glu2974Gly	p.E2974G	ENST00000219905	NM_001164273.1	2974	gAg/gGg	24/24	0.699008024618121	2	FACETS	0.953	0.899	1	0.477	0.449	0.504	CLONAL	1	TRUE	0	0.716187681041634	2		474	832	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900750	3900750	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587778211	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	344	605	0	ENST00000262367.5:c.346A>G	p.Ser116Gly	p.S116G	ENST00000262367	NM_004380.2	116	Agt/Ggt	2/31	1	2	FACETS	0.948	0.899	0.998	0.948	0.899	0.998	CLONAL	1	TRUE	1	0.716187681041634	2		605	1013	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794746	42794746	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs759244964	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	459	746	0	ENST00000575354.2:c.1826T>C	p.Leu609Pro	p.L609P	ENST00000575354	NM_015125.3	609	cTg/cCg	10/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.716187681041634	2		746	1217	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583389	46583390	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGACATGATCTTTCTGTCAGAAAACAT	novel	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	300	600	0	ENST00000263734.3:c.319_345dup	p.Asp107_Ile115dup	p.D107_I115dup	ENST00000263734	NM_001430.4	107	ggc/ggCGACATGATCTTTCTGTCAGAAAACATc	3/16	1	2	FACETS	0.646	0.607	0.685	0.646	0.607	0.685	SUBCLONAL	1	TRUE	1	0.716187681041634	2		600	1297	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652831	212652831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	154	418	0	ENST00000342788.4:c.475G>A	p.Asp159Asn	p.D159N	ENST00000342788	NM_005235.2	159	Gac/Aac	4/28	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.716187681041634	2		418	416	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728793	39728793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	249	434	0	ENST00000361337.2:c.1073C>T	p.Pro358Leu	p.P358L	ENST00000361337	NM_003286.2	358	cCt/cTt	12/21	1	2	FACETS	0.874	0.82	0.929	0.874	0.82	0.929	CLONAL	1	TRUE	1	0.716187681041634	2		434	796	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47079181	47079181	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	344	553	0	ENST00000409792.3:c.7325C>T	p.Pro2442Leu	p.P2442L	ENST00000409792	NM_014159.6	2442	cCa/cTa	18/21	1	2	FACETS	0.945	0.896	0.994	0.945	0.896	0.994	CLONAL	1	TRUE	1	0.716187681041634	2		553	1017	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444636	187444636	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	326	468	0	ENST00000232014.4:c.1591G>A	p.Ala531Thr	p.A531T	ENST00000232014	NM_001130845.1	531	Gcc/Acc	7/10	1	2	FACETS	0.976	0.924	1	0.976	0.924	1	CLONAL	1	TRUE	1	0.716187681041634	2		468	933	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589610	67589611	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	101	281	0	ENST00000274335.5:c.1377_1378del	p.Glu462IlefsTer2	p.E462Ifs*2	ENST00000274335		458	gAA/g	10/15	1	2	FACETS	0.946	0.857	1	0.946	0.857	1	CLONAL	1	TRUE	1	0.716187681041634	2		281	298	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497220	149497220	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	402	667	0	ENST00000261799.4:c.3098C>T	p.Ala1033Val	p.A1033V	ENST00000261799	NM_002609.3	1033	gCt/gTt	22/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.716187681041634	2		667	1071	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638956	176638956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs973008371	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	432	606	0	ENST00000439151.2:c.3556G>A	p.Ala1186Thr	p.A1186T	ENST00000439151	NM_022455.4	1186	Gcc/Acc	5/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.716187681041634	2		606	1201	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665424	176665424	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	346	423	0	ENST00000439151.2:c.4108C>T	p.Gln1370Ter	p.Q1370*	ENST00000439151	NM_022455.4	1370	Cag/Tag	7/23	1	2	FACETS	0.996	0.945	1	0.996	0.945	1	CLONAL	1	TRUE	1	0.716187681041634	2		423	970	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052994	180052994	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	480	793	1	ENST00000261937.6:c.1296del	p.Ser433AlafsTer60	p.S433Afs*60	ENST00000261937	NM_182925.4	432	ccC/cc	10/30	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.716187681041634	2		794	1341	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056049	26056049	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	255	393	0	ENST00000343677.2:c.608T>A	p.Val203Asp	p.V203D	ENST00000343677	NM_005319.3	203	gTc/gAc	1/1	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.716187681041634	2		393	704	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392050	81392050	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	109	336	0	ENST00000222390.5:c.227G>T	p.Arg76Met	p.R76M	ENST00000222390	NM_000601.4	76	aGg/aTg	2/18	1	2	FACETS	0.939	0.854	1	0.939	0.854	1	CLONAL	1	TRUE	1	0.716187681041634	2		336	324	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851557	128851557	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200477210	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	484	719	0	ENST00000249373.3:c.1882C>T	p.Arg628Trp	p.R628W	ENST00000249373	NM_005631.4	628	Cgg/Tgg	11/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.716187681041634	2		719	1303	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411356	63411356	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587778023	NA	P-0044374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	394	760	0	ENST00000330258.3:c.1811A>G	p.Tyr604Cys	p.Y604C	ENST00000330258	NM_152424.3	604	tAt/tGt	2/2	1	2	FACETS	0.979	0.932	1	0.979	0.932	1	CLONAL	1	TRUE	1	0.716187681041634	2		760	1124	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0044378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	30	1014	11	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.174	0.139	0.213	0.174	0.139	0.213	SUBCLONAL	1	TRUE	1	0.662765708863771	2		1025	521	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349641	89349641	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs772267579	NA	P-0044378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	130	698	8	ENST00000301030.4:c.3309del	p.Asp1104MetfsTer214	p.D1104Mfs*214	ENST00000301030	NM_001256183.1	1103	aaA/aa	9/13	1	2	FACETS	0.796	0.726	0.868	0.796	0.726	0.868	SUBCLONAL	1	TRUE	1	0.662765708863771	2		706	493	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174459	11174459	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557739557	NA	P-0044378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	234	683	0	ENST00000361445.4:c.7216G>A	p.Val2406Met	p.V2406M	ENST00000361445	NM_004958.3	2406	Gtg/Atg	53/58	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.662765708863771	2		683	674	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056317	27056317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776238347	NA	P-0044378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	154	453	0	ENST00000324856.7:c.1313C>T	p.Ala438Val	p.A438V	ENST00000324856	NM_006015.4	438	gCg/gTg	2/20	1	2	FACETS	0.904	0.833	0.977	0.904	0.833	0.977	CLONAL	1	TRUE	1	0.662765708863771	2		453	514	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105892	27105892	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	137	595	0	ENST00000324856.7:c.5503C>T	p.Gln1835Ter	p.Q1835*	ENST00000324856	NM_006015.4	1835	Cag/Tag	20/20	1	2	FACETS	0.756	0.691	0.823	0.756	0.691	0.823	SUBCLONAL	1	TRUE	1	0.662765708863771	2		595	547	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0044378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	124	663	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.685	0.623	0.751	0.685	0.623	0.751	SUBCLONAL	1	TRUE	1	0.662765708863771	2		663	546	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	23	330	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.224	0.174	0.281	0.224	0.174	0.281	SUBCLONAL	1	TRUE	1	0.662765708863771	2		331	310	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78422373	78422373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766248444	NA	P-0044378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	21	308	0	ENST00000370768.2:c.1589C>T	p.Thr530Met	p.T530M	ENST00000370768	NM_003902.3	530	aCg/aTg	17/20	1	2	FACETS	0.166	0.128	0.212	0.166	0.128	0.212	SUBCLONAL	1	TRUE	1	0.662765708863771	2		308	381	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263282	115263282	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	32	662	0	ENST00000438362.2:c.2068del	p.Asp690IlefsTer38	p.D690Ifs*38	ENST00000438362	NM_001242891.1	690	Gat/at	17/20	1	2	FACETS	0.172	0.139	0.209	0.172	0.139	0.209	SUBCLONAL	1	TRUE	1	0.662765708863771	2		662	563	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0044378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	217	611	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.662765708863771	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.662765708863771	2		611	321	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444378	49444378	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	165	749	2	ENST00000301067.7:c.2993del	p.Pro998LeufsTer2	p.P998Lfs*2	ENST00000301067	NM_003482.3	998	cCt/ct	11/54	0.182749331160124	4	FACETS	0.755	0.698	0.815	0.755	0.698	0.815	INDETERMINATE	2	TRUE	2	0.662765708863771	4		751	548	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482392	56482392	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	113	631	0	ENST00000267101.3:c.944del	p.Asn315MetfsTer38	p.N315Mfs*38	ENST00000267101	NM_001982.3	314	Aaa/aa	8/28	0.182749331160124	4	FACETS	1	0.977	1	0.63	0.57	0.692	INDETERMINATE	1	TRUE	2	0.662765708863771	4		631	450	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219860	133219860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758114596	NA	P-0044378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	144	719	3	ENST00000320574.5:c.4501G>A	p.Gly1501Arg	p.G1501R	ENST00000320574	NM_006231.2	1501	Ggg/Agg	35/49	0.142567784726015	0	FACETS	0.306	0.281	0.332			1	INDETERMINATE	1	TRUE	0	0.662765708863771	0		722	479	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32971077	32971077	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	12	446	0	ENST00000380152.3:c.9544C>T	p.His3182Tyr	p.H3182Y	ENST00000380152		3182	Cat/Tat	26/27	1	2	FACETS	0.169	0.119	0.231	0.169	0.119	0.231	SUBCLONAL	1	TRUE	1	0.662765708863771	2		446	214	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678515	88678515	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775589367	NA	P-0044378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	100	493	1	ENST00000360948.2:c.1021C>T	p.Pro341Ser	p.P341S	ENST00000360948	NM_001012338.2	341	Cct/Tct	9/19	1	2	FACETS	0.784	0.706	0.865	0.784	0.706	0.865	SUBCLONAL	1	TRUE	1	0.662765708863771	2		494	385	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828990	72828990	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	214	772	1	ENST00000268489.5:c.7591C>T	p.Gln2531Ter	p.Q2531*	ENST00000268489	NM_006885.3	2531	Cag/Tag	9/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.662765708863771	2		773	621	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351031	89351031	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	154	775	0	ENST00000301030.4:c.1919del	p.Asn640ThrfsTer13	p.N640Tfs*13	ENST00000301030	NM_001256183.1	640	aAc/ac	9/13	1	2	FACETS	0.846	0.779	0.916	0.846	0.779	0.916	CLONAL	1	TRUE	1	0.662765708863771	2		775	549	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519008	66519008	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555813217	NA	P-0044378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	28	519	1	ENST00000358598.2:c.289C>T	p.Arg97Ter	p.R97*	ENST00000358598	NM_212471.2	97	Cga/Tga	3/11	1	2	FACETS	0.166	0.132	0.205	0.166	0.132	0.205	SUBCLONAL	1	TRUE	1	0.662765708863771	2		520	509	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251482	10251482	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	212	713	0	ENST00000340748.4:c.3450del	p.Leu1151CysfsTer29	p.L1151Cfs*29	ENST00000340748		1150	ggG/gg	31/40	1	2	FACETS	0.911	0.85	0.974	0.911	0.85	0.974	CLONAL	1	TRUE	1	0.662765708863771	2		713	702	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031124	11031124	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	246	761	0	ENST00000327064.4:c.1209G>A	p.Trp403Ter	p.W403*	ENST00000327064	NM_199141.1	403	tgG/tgA	11/16	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.662765708863771	2		761	727	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15280904	15280904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1251693132	NA	P-0044378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	133	656	1	ENST00000263388.2:c.5192G>A	p.Arg1731Gln	p.R1731Q	ENST00000263388	NM_000435.2	1731	cGg/cAg	28/33	1	2	FACETS	0.814	0.744	0.887	0.814	0.744	0.887	CLONAL	1	TRUE	1	0.662765708863771	2		657	493	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228026	36228026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157820452	NA	P-0044378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	37	828	2	ENST00000222270.7:c.7412C>T	p.Ala2471Val	p.A2471V	ENST00000222270	NM_014727.1	2471	gCt/gTt	33/37	1	2	FACETS	0.193	0.159	0.232	0.193	0.159	0.232	SUBCLONAL	1	TRUE	1	0.662765708863771	2		830	578	SUCCESS
NF2	4771	MSKCC	GRCh37	22	29999997	29999997	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	74	361	0	ENST00000338641.4:c.10G>T	p.Ala4Ser	p.A4S	ENST00000338641	NM_000268.3	4	Gcc/Tcc	1/16	1	2	FACETS	0.984	0.875	1	0.984	0.875	1	CLONAL	1	TRUE	1	0.662765708863771	2		361	227	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427558	72427558	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	81	249	0	ENST00000477973.2:c.932C>T	p.Ala311Val	p.A311V	ENST00000477973	NM_012234.5	311	gCa/gTa	4/4	1	2	FACETS	0.867	0.773	0.965	0.867	0.773	0.965	CLONAL	1	TRUE	1	0.662765708863771	2		249	282	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294682	1294682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	38	463	0	ENST00000310581.5:c.319G>A	p.Ala107Thr	p.A107T	ENST00000310581	NM_198253.2	107	Gcc/Acc	2/16	1	2	FACETS	0.546	0.455	0.645	0.546	0.455	0.645	SUBCLONAL	1	TRUE	1	0.662765708863771	2		463	210	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589610	67589612	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	novel	NA	P-0044378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	43	270	0	ENST00000274335.5:c.1376_1378del	p.Lys459del	p.K459del	ENST00000274335		458	gAAAaa/gaa	10/15	1	2	FACETS	0.746	0.633	0.866	0.746	0.633	0.866	SUBCLONAL	1	TRUE	1	0.662765708863771	2		270	174	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592130	67592130	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1389187507	NA	P-0044378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	116	292	0	ENST00000274335.5:c.1946G>A	p.Arg649Gln	p.R649Q	ENST00000274335		649	cGg/cAg	14/15	1	2	FACETS	0.989	0.901	1	0.989	0.901	1	CLONAL	1	TRUE	1	0.662765708863771	2		292	354	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517436	157517436	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	156	484	0	ENST00000346085.5:c.4000A>C	p.Ser1334Arg	p.S1334R	ENST00000346085	NM_020732.3	1334	Agt/Cgt	16/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.662765708863771	2		484	434	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482927	140482927	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	108	517	3	ENST00000288602.6:c.1208del	p.Pro403LeufsTer8	p.P403Lfs*8	ENST00000288602	NM_004333.4	403	cCt/ct	10/18	1	2	FACETS	0.967	0.878	1	0.967	0.878	1	CLONAL	1	TRUE	1	0.662765708863771	2		520	337	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0044378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	143	455	20	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	1	2	FACETS	0.782	0.728	0.836	1	0.991	1	SUBCLONAL	2	TRUE	1	0.662765708863771	2		475	276	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164817	123164817	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	32	259	0	ENST00000218089.9:c.135del	p.Gly46AlafsTer25	p.G46Afs*25	ENST00000218089	NM_001042749.1	44	Aaa/aa	5/35	0.356016798736994	1	FACETS	0.448	0.369	0.535	0.448	0.369	0.535	INDETERMINATE	1	TRUE	0	0.662765708863771	1		259	144	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0044399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	12	183	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	0.446	0.314	0.609	0.446	0.314	0.609	SUBCLONAL	1	TRUE	1	0.28	2		183	192	SUCCESS
APC	324	MSKCC	GRCh37	5	112175162	112175162	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561588104	NA	P-0044399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	11	183	0	ENST00000257430.4:c.3871C>T	p.Gln1291Ter	p.Q1291*	ENST00000257430	NM_000038.5	1291	Cag/Tag	16/16	1	2	FACETS	0.401	0.277	0.555	0.401	0.277	0.555	SUBCLONAL	1	TRUE	1	0.28	2		183	196	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579472	7579473	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	C	novel	NA	P-0044399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	104	695	1	ENST00000269305.4:c.214_215delinsG	p.Pro72AlafsTer51	p.P72Afs*51	ENST00000269305	NM_001126112.2	72	CCc/Gc	4/11	1	2	FACETS	0.718	0.642	0.8	0.718	0.642	0.8	SUBCLONAL	1	TRUE	1	0.28	2		696	1034	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307414	118307416	+	inframe_deletion	In_Frame_Del	DEL	GCG	GCG	-	rs781936420	NA	P-0044399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	10	32	0	ENST00000534358.1:c.200_202del	p.Ala67del	p.A67del	ENST00000534358	NM_005933.3	63	GCG/-	1/36	1	2	FACETS	1	0.692	1	1	0.692	1	CLONAL	1	TRUE	1	0.28	2		32	71	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212439	5212439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150241840	NA	P-0044399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	148	792	1	ENST00000357368.4:c.4678G>A	p.Val1560Met	p.V1560M	ENST00000357368	NM_002850.3	1560	Gtg/Atg	31/38	1	2	FACETS	0.798	0.727	0.873	0.798	0.727	0.873	SUBCLONAL	1	TRUE	1	0.28	2		793	1325	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32931914	32931914	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	22	225	0	ENST00000380152.3:c.7653A>T	p.Lys2551Asn	p.K2551N	ENST00000380152		2551	aaA/aaT	16/27	0.3	3	FACETS	0.807	0.628	1	0.403	0.314	0.507	CLONAL	1	TRUE	1	0.28	3		225	222	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881010	37881010	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1238	67	764	0	ENST00000269571.5:c.2339C>A	p.Pro780Gln	p.P780Q	ENST00000269571		780	cCa/cAa	20/27	1	2	FACETS	0.367	0.317	0.421	0.367	0.317	0.421	SUBCLONAL	1	TRUE	1	0.28	2		764	1305	SUCCESS
APC	324	MSKCC	GRCh37	5	112173516	112173516	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	17	266	0	ENST00000257430.4:c.2226del	p.Met743CysfsTer18	p.M743Cfs*18	ENST00000257430	NM_000038.5	742	aTt/at	16/16	1	2	FACETS	0.437	0.326	0.569	0.437	0.326	0.569	SUBCLONAL	1	TRUE	1	0.28	2		266	278	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0044433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	118	702	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	0.170330310959356	2	FACETS	1	0.972	1	0.603	0.544	0.664	CLONAL	1	TRUE	0	0.280585184676194	2		702	698	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524215	18524215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769408892	NA	P-0044433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	25	488	0	ENST00000266497.5:c.1727C>T	p.Ala576Val	p.A576V	ENST00000266497		576	gCg/gTg	11/31	0.253691181526532	0	FACETS	0.45	0.355	0.558			1	SUBCLONAL	1	TRUE	0	0.280585184676194	0		488	285	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0044433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	38	304	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.1419839823175	4	FACETS	0.945	0.783	1	0.473	0.391	0.563	INDETERMINATE	1	TRUE	2	0.280585184676194	4		304	367	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519815	29519815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs75158395	NA	P-0044433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	66	510	0	ENST00000389048.3:c.1756G>A	p.Ala586Thr	p.A586T	ENST00000389048	NM_004304.4	586	Gcc/Acc	9/29	0.239728973227435	1	FACETS	0.936	0.815	1	0.936	0.815	1	CLONAL	1	TRUE	0	0.280585184676194	1		510	432	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657409	29657409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465309384	NA	P-0044433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	69	548	0	ENST00000356175.3:c.5642C>T	p.Ala1881Val	p.A1881V	ENST00000356175	NM_000267.3	1881	gCc/gTc	38/57	0.238133604526699	4	FACETS	0.959	0.835	1	0.32	0.278	0.365	CLONAL	1	TRUE	1	0.280585184676194	4		548	657	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271150	38271150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758677681	NA	P-0044460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	12	515	2	ENST00000425967.3:c.2558G>A	p.Arg853His	p.R853H	ENST00000425967	NM_001174067.1	853	cGc/cAc	19/19	0.113342716810096	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		517	130	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419043	419043	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	10	544	0	ENST00000399788.2:c.3304G>A	p.Glu1102Lys	p.E1102K	ENST00000399788	NM_001042603.1	1102	Gaa/Aaa	22/28	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		544	90	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188253	10188256	+	protein_altering_variant	In_Frame_Del	DEL	AACT	AACT	C	novel	NA	P-0044460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	21	716	0	ENST00000256474.2:c.396_399delinsC	p.Gln132_Thr133delinsHis	p.Q132_T133delinsH	ENST00000256474	NM_000551.3	132	caAACT/caC	2/3	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		716	124	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380283	25380283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913528	NA	P-0044506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	72	459	0	ENST00000311936.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000311936	NM_004985.3	59	Gca/Aca	3/5	0.632507740617635	3	FACETS	0.444	0.388	0.505	0.148	0.129	0.169	SUBCLONAL	1	TRUE	0	0.658900250568153	3		459	654	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245506	153245506	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	40	418	0	ENST00000281708.4:c.1685C>A	p.Ser562Ter	p.S562*	ENST00000281708	NM_033632.3	562	tCa/tAa	11/12	0.658900250568153	1	FACETS	0.222	0.184	0.263	0.222	0.184	0.263	SUBCLONAL	1	TRUE	0	0.658900250568153	1		418	367	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579357	7579357	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	576	798	0	ENST00000269305.4:c.330del	p.Leu111TrpfsTer12	p.L111Wfs*12	ENST00000269305	NM_001126112.2	110	cgT/cg	4/11	0.658826442212907	2	FACETS	0.993	0.964	1	0.993	0.964	1	CLONAL	2	TRUE	0	0.658900250568153	2		798	880	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669390	241669390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772190176	NA	P-0044506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	26	346	0	ENST00000366560.3:c.817G>A	p.Ala273Thr	p.A273T	ENST00000366560	NM_000143.3	273	Gca/Aca	6/10	0.153957982978129	3	FACETS	0.226	0.178	0.281			1	INDETERMINATE	1	TRUE	NA	0.658900250568153	3		346	464	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440675	56440675	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	59	714	0	ENST00000407977.2:c.543G>T	p.Lys181Asn	p.K181N	ENST00000407977		181	aaG/aaT	5/10	NA	2	FACETS	0.184	0.158	0.213			1	INDETERMINATE	1	TRUE	NA	0.658900250568153	2		714	972	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947540	48947540	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0044506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	182	342	0	ENST00000267163.4:c.1128-1G>T		p.X376_splice	ENST00000267163	NM_000321.2	376			0.658900250568153	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.658900250568153	2		342	273	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748126	41748126	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	26	264	1	ENST00000226382.2:c.643G>A	p.Gly215Ser	p.G215S	ENST00000226382	NM_003924.3	215	Ggc/Agc	3/3	0.571346565018641	1	FACETS	0.195	0.155	0.241	0.195	0.155	0.241	SUBCLONAL	1	TRUE	0	0.658900250568153	1		265	271	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999347	100999347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1265	84	1057	2	ENST00000325455.5:c.455C>T	p.Pro152Leu	p.P152L	ENST00000325455	NM_001202474.3	152	cCg/cTg	1/8	0.136715544074271	5	FACETS	0.376	0.33	0.425	0.125	0.11	0.142	INDETERMINATE	1	TRUE	2	0.658900250568153	5		1059	1349	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206665081	206665081	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	45	391	1	ENST00000367120.3:c.1834A>G	p.Arg612Gly	p.R612G	ENST00000367120	NM_014002.3	612	Agg/Ggg	18/22	1	2	FACETS	0.277	0.232	0.326	0.277	0.232	0.326	SUBCLONAL	1	TRUE	1	0.658900250568153	2		392	494	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675293	241675293	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	43	409	0	ENST00000366560.3:c.529C>A	p.Pro177Thr	p.P177T	ENST00000366560	NM_000143.3	177	Ccc/Acc	4/10	0.153957982978129	3	FACETS	0.423	0.354	0.499			1	INDETERMINATE	1	TRUE	NA	0.658900250568153	3		409	410	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622068	43622068	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	57	424	0	ENST00000355710.3:c.3085T>C	p.Tyr1029His	p.Y1029H	ENST00000355710	NM_020975.4	1029	Tat/Cat	19/20	0.658900250568153	2	FACETS	0.274	0.235	0.317	0.137	0.117	0.159	SUBCLONAL	1	TRUE	0	0.658900250568153	2		424	631	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533604	533604	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	71	655	0	ENST00000451590.1:c.299T>A	p.Ile100Asn	p.I100N	ENST00000451590	NM_001130442.1	100	aTc/aAc	4/5	0.370032509428471	1	FACETS	0.193	0.168	0.221	0.193	0.168	0.221	INDETERMINATE	1	TRUE	0	0.658900250568153	1		655	747	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196084	108196084	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	30	510	0	ENST00000278616.4:c.6620A>T	p.Lys2207Ile	p.K2207I	ENST00000278616	NM_000051.3	2207	aAa/aTa	46/63	0.136715544074271	5	FACETS	0.413	0.333	0.505	0.138	0.111	0.169	INDETERMINATE	1	TRUE	2	0.658900250568153	5		510	438	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425759	49425759	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	138	738	0	ENST00000301067.7:c.12729C>A	p.Tyr4243Ter	p.Y4243*	ENST00000301067	NM_003482.3	4243	taC/taA	39/54	0.632507740617635	3	FACETS	0.606	0.551	0.664	0.202	0.183	0.222	SUBCLONAL	1	TRUE	0	0.658900250568153	3		738	919	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929256	32929256	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs730882169	NA	P-0044506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	69	569	0	ENST00000380152.3:c.7266T>A	p.Cys2422Ter	p.C2422*	ENST00000380152		2422	tgT/tgA	14/27	0.658900250568153	2	FACETS	0.427	0.372	0.485	0.213	0.186	0.243	SUBCLONAL	1	TRUE	0	0.658900250568153	2		569	491	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95556956	95556956	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1299000813	NA	P-0044506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	56	630	0	ENST00000393063.1:c.5648A>G	p.Glu1883Gly	p.E1883G	ENST00000393063	NM_030621.3	1883	gAa/gGa	28/28	0.629823142235689	2	FACETS	0.255	0.218	0.296	0.128	0.109	0.148	SUBCLONAL	1	TRUE	0	0.658900250568153	2		630	666	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128220	30128220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	80	698	1	ENST00000263025.4:c.1012G>A	p.Asp338Asn	p.D338N	ENST00000263025	NM_002746.2	338	Gat/Aat	7/9	NA	2	FACETS	0.226	0.198	0.256			1	INDETERMINATE	1	TRUE	NA	0.658900250568153	2		699	1076	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032519	12032519	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	233	353	0	ENST00000353533.5:c.955del	p.Gln319LysfsTer3	p.Q319Kfs*3	ENST00000353533	NM_003010.3	319	Caa/aa	9/11	0.658826442212907	2	FACETS	0.985	0.939	1	0.985	0.939	1	CLONAL	2	TRUE	0	0.658900250568153	2		353	359	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453473	40453473	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0044506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	143	809	0	ENST00000345506.4:c.1169+1G>A		p.X390_splice	ENST00000345506	NM_003152.3	390			0.658900250568153	2	FACETS	0.419	0.381	0.458	0.209	0.19	0.229	SUBCLONAL	1	TRUE	0	0.658900250568153	2		809	1037	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22143086	22143086	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	41	438	0	ENST00000215832.6:c.621G>C	p.Lys207Asn	p.K207N	ENST00000215832	NM_002745.4	207	aaG/aaC	5/9	0.658826442212907	2	FACETS	0.307	0.255	0.363	0.153	0.127	0.182	SUBCLONAL	1	TRUE	0	0.658900250568153	2		438	406	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55569983	55569983	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	21	384	0	ENST00000288135.5:c.850G>C	p.Asp284His	p.D284H	ENST00000288135	NM_000222.2	284	Gat/Cat	5/21	0.268395337288085	2	FACETS	0.19	0.146	0.242	0.095	0.073	0.121	INDETERMINATE	1	TRUE	0	0.658900250568153	2		384	335	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155342	106155342	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	157	421	0	ENST00000380013.4:c.243A>C	p.Glu81Asp	p.E81D	ENST00000380013	NM_001127208.2	81	gaA/gaC	3/11	0.658900250568153	1	FACETS	0.83	0.77	0.891	0.83	0.77	0.891	CLONAL	1	TRUE	0	0.658900250568153	1		421	385	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659179	86659179	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	25	177	0	ENST00000274376.6:c.1468T>G	p.Trp490Gly	p.W490G	ENST00000274376	NM_002890.2	490	Tgg/Ggg	11/25	0.658900250568153	1	FACETS	0.599	0.485	0.722	0.599	0.485	0.722	SUBCLONAL	1	TRUE	0	0.658900250568153	1		177	85	SUCCESS
APC	324	MSKCC	GRCh37	5	112178748	112178748	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	22	411	0	ENST00000257430.4:c.7457C>T	p.Pro2486Leu	p.P2486L	ENST00000257430	NM_000038.5	2486	cCt/cTt	16/16	NA	2	FACETS	0.157	0.121	0.199			1	INDETERMINATE	1	TRUE	NA	0.658900250568153	2		411	425	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149452910	149452910	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	65	597	0	ENST00000286301.3:c.1036C>A	p.Gln346Lys	p.Q346K	ENST00000286301	NM_005211.3	346	Cag/Aag	7/22	0.658900250568153	1	FACETS	0.187	0.162	0.215	0.187	0.162	0.215	SUBCLONAL	1	TRUE	0	0.658900250568153	1		597	707	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29195934	29195934	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1258	70	923	0	ENST00000240100.2:c.664A>G	p.Ile222Val	p.I222V	ENST00000240100	NM_001394.6	222	Atc/Gtc	3/4	0.269426509724672	3	FACETS	0.213	0.184	0.244	0.071	0.061	0.082	INDETERMINATE	1	TRUE	0	0.658900250568153	3		923	1328	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965667	90965667	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1554558368	NA	P-0044506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	17	340	0	ENST00000265433.3:c.1650A>C	p.Lys550Asn	p.K550N	ENST00000265433	NM_002485.4	550	aaA/aaC	11/16	0.241643185184363	3	FACETS	0.214	0.159	0.28	0.071	0.053	0.094	INDETERMINATE	1	TRUE	0	0.658900250568153	3		340	320	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966600	36966632	+	inframe_deletion	In_Frame_Del	DEL	CTCAAACACGCGGTCCAGCACCTCCAGCTGCTG	CTCAAACACGCGGTCCAGCACCTCCAGCTGCTG	-	novel	NA	P-0044506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	65	682	0	ENST00000358127.4:c.694_726del	p.Gln232_Glu242del	p.Q232_E242del	ENST00000358127	NM_001280556.1	232	CAGCAGCTGGAGGTGCTGGACCGCGTGTTTGAG/-	6/10	1	2	FACETS	0.248	0.214	0.285	0.248	0.214	0.285	SUBCLONAL	1	TRUE	1	0.658900250568153	2		682	796	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407503	139407503	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	72	721	0	ENST00000277541.6:c.2437T>A	p.Tyr813Asn	p.Y813N	ENST00000277541	NM_017617.3	813	Tac/Aac	15/34	0.116395153504044	3	FACETS	0.269	0.234	0.307	0.134	0.117	0.154	INDETERMINATE	1	TRUE	1	0.658900250568153	3		721	1082	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045689	47045716	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGTGACAACATTGGCAGTCGGATGCT	GCAGTGACAACATTGGCAGTCGGATGCT	-	novel	NA	P-0044506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	65	460	0	ENST00000377604.3:c.2574_2601del	p.Ser858ArgfsTer19	p.S858Rfs*19	ENST00000377604	NM_001204468.1	857	gGCAGTGACAACATTGGCAGTCGGATGCTg/gg	23/24	0.107342437568877	2	FACETS	0.3	0.259	0.344			1	INDETERMINATE	1	TRUE	NA	0.658900250568153	2		460	658	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553560	29553609	+	protein_altering_variant	In_Frame_Del	DEL	TCTGGTTGCCATGTCCTGTTTCCGCCACCTCTGTGAGGAAGCAGATATCC	TCTGGTTGCCATGTCCTGTTTCCGCCACCTCTGTGAGGAAGCAGATATCC	GG	novel	NA	P-0044506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	112	338	3	ENST00000356175.3:c.2109_2158delinsGG	p.Leu704_Arg720delinsGly	p.L704_R720delinsG	ENST00000356175	NM_000267.3	703	gtTCTGGTTGCCATGTCCTGTTTCCGCCACCTCTGTGAGGAAGCAGATATCCgg/gtGGgg	18/57	0.658826442212907	2	FACETS	0.808	0.732	0.886	0.404	0.366	0.443	CLONAL	1	TRUE	0	0.658900250568153	2		341	421	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696425	47696425	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519967	NA	P-0044509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	143	445	0	ENST00000347630.2:c.398T>G	p.Phe133Cys	p.F133C	ENST00000347630	NM_001007230.1	133	tTc/tGc	6/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.465865323980755	2		445	577	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044529-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	164	300	0				ENST00000310581	NM_198253.2	-/1132			0.636632136307197	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.636632136307197	1		300	322	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631839	90631839	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519906	NA	P-0044529-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	316	549	0	ENST00000330062.3:c.514A>T	p.Arg172Trp	p.R172W	ENST00000330062	NM_002168.2	172	Agg/Tgg	4/11	1	2	FACETS	0.931	0.88	0.984	0.931	0.88	0.984	CLONAL	1	TRUE	1	0.636632136307197	2		549	1066	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0044529-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	1011	921	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.636632136307197	2	FACETS	0.998	0.975	1	0.998	0.975	1	CLONAL	2	TRUE	0	0.636632136307197	2		921	1591	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455208	29455208	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044529-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	297	559	1	ENST00000389048.3:c.2594C>A	p.Ser865Tyr	p.S865Y	ENST00000389048	NM_004304.4	865	tCc/tAc	15/29	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.636632136307197	2		560	914	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420104	41420104	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044529-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	116	351	0	ENST00000373198.4:c.217T>C	p.Ser73Pro	p.S73P	ENST00000373198	NM_133170.3	73	Tct/Cct	3/32	0.636632136307197	1	FACETS	0.585	0.531	0.641	0.585	0.531	0.641	SUBCLONAL	1	TRUE	0	0.636632136307197	1		351	425	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	27	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.308873465645712	1	FACETS	0.83	0.667	1	0.83	0.667	1	CLONAL	1	TRUE	0	0.308873465645712	1		326	178	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0044534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	100	537	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.308873465645712	1	FACETS	0.778	0.695	0.866	0.778	0.695	0.866	SUBCLONAL	1	TRUE	0	0.308873465645712	1		537	704	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	73	300	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.764	0.67	0.864	1	0.976	1	SUBCLONAL	2	TRUE	1	0.206883506876084	2		300	462	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0044537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	76	407	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.809	0.712	0.913	1	0.979	1	CLONAL	2	TRUE	1	0.206883506876084	2		407	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0044537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	45	675	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.206883506876084	1	FACETS	0.476	0.399	0.562	0.476	0.399	0.562	SUBCLONAL	1	TRUE	0	0.206883506876084	1		675	819	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs864622237	NA	P-0044537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	13	511	0	ENST00000269305.4:c.700T>A	p.Tyr234Asn	p.Y234N	ENST00000269305	NM_001126112.2	234	Tac/Aac	7/11	0.206883506876084	1	FACETS	0.179	0.127	0.244	0.179	0.127	0.244	SUBCLONAL	1	TRUE	0	0.206883506876084	1		511	628	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475599	12475599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	37	471	0	ENST00000287820.6:c.1473G>A	p.Met491Ile	p.M491I	ENST00000287820	NM_015869.4	491	atG/atA	7/7	1	2	FACETS	0.579	0.476	0.694	0.579	0.476	0.694	SUBCLONAL	1	TRUE	1	0.206883506876084	2		471	618	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434142	49434142	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057518571	NA	P-0044537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	169	710	0	ENST00000301067.7:c.7411C>T	p.Arg2471Ter	p.R2471*	ENST00000301067	NM_003482.3	2471	Cga/Tga	31/54	1	2	FACETS	0.799	0.734	0.867	1	0.99	1	SUBCLONAL	2	TRUE	1	0.206883506876084	2		710	1022	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972611	32972611	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1566261240	NA	P-0044537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	48	345	0	ENST00000380152.3:c.9961C>T	p.Gln3321Ter	p.Q3321*	ENST00000380152		3321	Cag/Tag	27/27	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.206883506876084	2		345	444	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607794	46607794	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	135	684	1	ENST00000263734.3:c.1983C>A	p.Phe661Leu	p.F661L	ENST00000263734	NM_001430.4	661	ttC/ttA	12/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.206883506876084	2		685	999	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711346	114711346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	20	201	1	ENST00000543371.1:c.361C>T	p.Leu121Phe	p.L121F	ENST00000543371	NM_001198531.1	121	Ctc/Ttc	3/14	1	2	FACETS	0.618	0.472	0.788	0.618	0.472	0.788	SUBCLONAL	1	TRUE	1	0.206883506876084	2		202	313	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	443506	443506	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	71	368	0	ENST00000399788.2:c.1391C>G	p.Ser464Cys	p.S464C	ENST00000399788	NM_001042603.1	464	tCt/tGt	11/28	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.206883506876084	2		368	552	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445971	49445971	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	65	806	0	ENST00000301067.7:c.1495G>A	p.Glu499Lys	p.E499K	ENST00000301067	NM_003482.3	499	Gag/Aag	10/54	1	2	FACETS	0.518	0.447	0.595	0.518	0.447	0.595	SUBCLONAL	1	TRUE	1	0.206883506876084	2		806	1214	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109773	115109773	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs199572544	NA	P-0044537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	162	627	0	ENST00000257566.3:c.2105G>T	p.Ser702Ile	p.S702I	ENST00000257566	NM_016569.3	702	aGc/aTc	8/8	1	2	FACETS	0.936	0.859	1	1	0.991	1	CLONAL	2	TRUE	1	0.206883506876084	2		627	837	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739688	145739688	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1259051495	NA	P-0044537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	143	586	0	ENST00000428558.2:c.1763G>A	p.Gly588Glu	p.G588E	ENST00000428558	NM_004260.3	588	gGa/gAa	11/22	0.137734124655709	3	FACETS	0.846	0.771	0.924	0.846	0.771	0.924	CLONAL	2	TRUE	1	0.206883506876084	3		586	902	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577148	7577148	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1060501194	NA	P-0044572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	66	508	0	ENST00000269305.4:c.790del	p.Leu264TyrfsTer81	p.L264Yfs*81	ENST00000269305	NM_001126112.2	264	Cta/ta	8/11	1	2	FACETS	0.553	0.479	0.634	0.553	0.479	0.634	SUBCLONAL	1	TRUE	1	0.307366651783855	2		508	776	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144114	11144114	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	12	1007	0	ENST00000358026.2:c.3695G>A	p.Gly1232Asp	p.G1232D	ENST00000358026	NM_001128849.1	1232	gGc/gAc	26/36	0.734160073533682	2	FACETS	0.06	0.042	0.083	0.03	0.021	0.042	SUBCLONAL	1	TRUE	0	0.77819781342963	2		1007	511	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550583	29550583	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	63	290	0	ENST00000356175.3:c.1843A>G	p.Lys615Glu	p.K615E	ENST00000356175	NM_000267.3	615	Aag/Gag	16/57	0.77819781342963	3	FACETS	0.965	0.846	1	0.483	0.423	0.546	CLONAL	1	TRUE	1	0.77819781342963	3		290	233	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442054	52442054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	134	824	0	ENST00000460680.1:c.295G>A	p.Val99Met	p.V99M	ENST00000460680	NM_004656.3	99	Gtg/Atg	5/17	0.249125326252534	2	FACETS	0.881	0.804	0.962	0.881	0.804	0.962	CLONAL	2	TRUE	0	0.255091602152759	2		824	596	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11168301	11168301	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	144	781	1	ENST00000361445.4:c.7571A>T	p.Gln2524Leu	p.Q2524L	ENST00000361445	NM_004958.3	2524	cAa/cTa	57/58	0.255091602152759	1	FACETS	0.926	0.849	1	1	0.991	1	CLONAL	2	TRUE	0	0.255091602152759	1		782	532	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643806	52643807	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0044600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	146	722	0	ENST00000394830.3:c.2089_2090insC	p.Tyr697SerfsTer5	p.Y697Sfs*5	ENST00000394830	NM_018313.4	697	tat/tCat	17/30	0.249125326252534	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.255091602152759	2		722	501	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579716	7579716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1192416464	NA	P-0044609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	316	511	0	ENST00000269305.4:c.80del	p.Pro27LeufsTer17	p.P27Lfs*17	ENST00000269305	NM_001126112.2	27	cCt/ct	3/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.722513200004543	2		511	814	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0044609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	186	470	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			1	2	FACETS	0.785	0.728	0.844	0.785	0.728	0.844	SUBCLONAL	1	TRUE	1	0.722513200004543	2		470	656	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882030	36882030	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0044609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	359	635	0	ENST00000358127.4:c.983C>G	p.Ser328Ter	p.S328*	ENST00000358127	NM_001280556.1	328	tCa/tGa	8/10	0.674555971521897	1	FACETS	0.798	0.761	0.836	0.798	0.761	0.836	SUBCLONAL	1	TRUE	0	0.722513200004543	1		635	795	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136279	202136279	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	181	444	0	ENST00000358485.4:c.523G>A	p.Glu175Lys	p.E175K	ENST00000358485	NM_001080125.1	175	Gaa/Aaa	3/9	1	2	FACETS	0.798	0.739	0.858	0.798	0.739	0.858	SUBCLONAL	1	TRUE	1	0.722513200004543	2		444	628	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752413	57752413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs951811137	NA	P-0044609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	45	181	0	ENST00000274289.3:c.1160G>A	p.Arg387Lys	p.R387K	ENST00000274289	NM_006622.3	387	aGa/aAa	9/14	0.339674771747552	1	FACETS	0.612	0.527	0.701	0.612	0.527	0.701	INDETERMINATE	1	TRUE	0	0.722513200004543	1		181	130	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0044610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	25	751	1	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.465	0.364	0.581	0.465	0.364	0.581	SUBCLONAL	1	TRUE	1	0.12	2		752	897	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	15	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.377	0.274	0.502	0.377	0.274	0.502	SUBCLONAL	1	TRUE	1	0.12	2		326	663	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	34	599	1	ENST00000397062.3:c.246A>T	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaT	2/5	1	2	FACETS	0.571	0.464	0.692	0.571	0.464	0.692	SUBCLONAL	1	TRUE	1	0.12	2		600	993	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692790	89692790	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554898067	NA	P-0044610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	28	338	0	ENST00000371953.3:c.274G>T	p.Asp92Tyr	p.D92Y	ENST00000371953	NM_000314.4	92	Gac/Tac	5/9	1	2	FACETS	0.924	0.737	1	0.924	0.737	1	CLONAL	1	TRUE	1	0.12	2		338	505	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0044610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	11	111	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	1	0.733	1	1	0.733	1	CLONAL	1	TRUE	1	0.12	2		111	172	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117632251	117632251	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	24	449	0	ENST00000368508.3:c.6165C>A	p.Asp2055Glu	p.D2055E	ENST00000368508	NM_002944.2	2055	gaC/gaA	39/43	0.612978745077506	4	FACETS	0.681	0.538	0.844	0.341	0.269	0.422	SUBCLONAL	1	TRUE	2	0.66110804520883	4		449	177	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111493	8111494	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0044667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	287	636	1	ENST00000346208.3:c.981_982del	p.Trp328GlufsTer23	p.W328Efs*23	ENST00000346208		327	CTc/c	5/6	0.183544986068081	0	FACETS	0.553	0.522	0.584			1	INDETERMINATE	1	TRUE	0	0.562706304504836	0		637	807	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	130	300	0				ENST00000310581	NM_198253.2	-/1132			0.261910031226592	3	FACETS	0.793	0.73	0.859	0.793	0.73	0.859	INDETERMINATE	2	TRUE	1	0.64999198790046	3		300	334	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0044702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	205	395	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA	2	FACETS	0.809	0.762	0.855			1	INDETERMINATE	2	TRUE	NA	0.64999198790046	2		395	390	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546098	29546098	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1567843917	NA	P-0044702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	114	397	0	ENST00000356175.3:c.1603C>T	p.Gln535Ter	p.Q535*	ENST00000356175	NM_000267.3	535	Cag/Tag	14/57	0.123781023960542	3	FACETS	0.79	0.714	0.871	0.395	0.357	0.436	INDETERMINATE	1	TRUE	1	0.64999198790046	3		397	588	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808916	1808916	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0044702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	361	789	0	ENST00000260795.2:c.2348C>G	p.Ser783Ter	p.S783*	ENST00000260795		783	tCa/tGa	17/17	NA	2	FACETS	0.807	0.772	0.842			1	INDETERMINATE	2	TRUE	NA	0.64999198790046	2		789	688	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873483	151873483	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	254	456	1	ENST00000262189.6:c.9055C>T	p.Gln3019Ter	p.Q3019*	ENST00000262189	NM_170606.2	3019	Cag/Tag	38/59	0.4555960049162	5	FACETS	1	0.959	1	0.683	0.642	0.725	CLONAL	2	TRUE	2	0.64999198790046	5		457	753	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713670	52713670	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	241	392	0	ENST00000394830.3:c.58G>C	p.Asp20His	p.D20H	ENST00000394830	NM_018313.4	20	Gat/Cat	2/30	0.64999198790046	3	FACETS	0.934	0.882	0.987	0.934	0.882	0.987	CLONAL	2	TRUE	1	0.64999198790046	3		392	526	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088802	27088803	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0044702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	222	503	0	ENST00000324856.7:c.2414dup	p.Gln806ThrfsTer11	p.Q806Tfs*11	ENST00000324856	NM_006015.4	804	ggc/ggCc	7/20	0.643690777336235	2	FACETS	0.918	0.871	0.964	0.918	0.871	0.964	CLONAL	2	TRUE	0	0.64999198790046	2		503	372	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118339493	118339493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782605513	NA	P-0044702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	147	320	0	ENST00000534358.1:c.436G>A	p.Glu146Lys	p.E146K	ENST00000534358	NM_005933.3	146	Gag/Aag	2/36	0.211470111377861	2	FACETS	1	0.988	1	0.687	0.638	0.738	INDETERMINATE	1	TRUE	0	0.64999198790046	2		320	329	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342706	118342709	+	frameshift_variant	Frame_Shift_Del	DEL	CTCT	CTCT	-	novel	NA	P-0044702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	34	225	0	ENST00000534358.1:c.835_838del	p.Ser279LeufsTer13	p.S279Lfs*13	ENST00000534358	NM_005933.3	278	CTCTct/ct	3/36	0.211470111377861	2	FACETS	0.451	0.371	0.54	0.225	0.185	0.27	INDETERMINATE	1	TRUE	0	0.64999198790046	2		225	232	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437547	49437547	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	285	546	0	ENST00000301067.7:c.5338G>T	p.Glu1780Ter	p.E1780*	ENST00000301067	NM_003482.3	1780	Gag/Tag	23/54	0.215237511424873	4	FACETS	1	0.987	1	1	0.987	1	INDETERMINATE	2	TRUE	2	0.64999198790046	4		546	644	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443518	49443518	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	180	516	0	ENST00000301067.7:c.3853G>T	p.Glu1285Ter	p.E1285*	ENST00000301067	NM_003482.3	1285	Gag/Tag	11/54	0.215237511424873	4	FACETS	1	0.99	1	0.749	0.694	0.806	INDETERMINATE	1	TRUE	2	0.64999198790046	4		516	610	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733141	74733141	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	105	606	0	ENST00000359995.5:c.102C>G	p.Phe34Leu	p.F34L	ENST00000359995	NM_001195427.1	34	ttC/ttG	1/3	0.269721399466325	3	FACETS	0.664	0.595	0.736	0.221	0.198	0.246	INDETERMINATE	1	TRUE	0	0.64999198790046	3		606	645	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713620	52713621	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0044702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	206	394	0	ENST00000394830.3:c.107_108delinsAA	p.Arg36Lys	p.R36K	ENST00000394830	NM_018313.4	36	aGG/aAA	2/30	0.64999198790046	3	FACETS	0.83	0.777	0.883	0.83	0.777	0.883	CLONAL	2	TRUE	1	0.64999198790046	3		394	506	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602738	55602738	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	44	332	0	ENST00000288135.5:c.2559G>A	p.Trp853Ter	p.W853*	ENST00000288135	NM_000222.2	853	tgG/tgA	18/21	0.211470111377861	2	FACETS	0.362	0.304	0.426	0.181	0.152	0.213	INDETERMINATE	1	TRUE	0	0.64999198790046	2		332	374	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526428	31526428	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs781066515	NA	P-0044702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	350	673	0	ENST00000344624.3:c.612C>G	p.Phe204Leu	p.F204L	ENST00000344624		204	ttC/ttG	2/33	0.261910031226592	3	FACETS	1	0.995	1	0.719	0.683	0.756	INDETERMINATE	1	TRUE	1	0.64999198790046	3		673	992	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547180	106547180	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0044702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	47	207	0	ENST00000369096.4:c.417T>A	p.Tyr139Ter	p.Y139*	ENST00000369096	NM_001198.3	139	taT/taA	4/7	0.177903427171568	2	FACETS	0.727	0.621	0.84	0.363	0.31	0.42	INDETERMINATE	1	TRUE	0	0.64999198790046	2		207	199	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38148029	38148029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	325	554	0	ENST00000317025.8:c.3082G>A	p.Glu1028Lys	p.E1028K	ENST00000317025	NM_023034.1	1028	Gaa/Aaa	17/24	0.414822635523001	4	FACETS	0.948	0.899	0.998	0.948	0.899	0.998	CLONAL	2	TRUE	2	0.64999198790046	4		554	870	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0044784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	636	677	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.545699123666334	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	4	TRUE	0	0.549094805899952	4		680	889	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332882	70332882	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	125	680	0	ENST00000373644.4:c.787C>G	p.Gln263Glu	p.Q263E	ENST00000373644	NM_030625.2	263	Caa/Gaa	2/12	0.202731544354791	5	FACETS	1	0.978	1	0.421	0.382	0.463	INDETERMINATE	1	TRUE	2	0.549094805899952	5		680	657	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214313	55214313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs532655845	NA	P-0044784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	180	635	0	ENST00000275493.2:c.439G>A	p.Ala147Thr	p.A147T	ENST00000275493	NM_005228.3	147	Gcc/Acc	4/28	0.554822910281187	4	FACETS	1	0.986	1	0.43	0.397	0.464	CLONAL	1	TRUE	1	0.549094805899952	4		635	787	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169765	11169765	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	86	537	0	ENST00000361445.4:c.7388T>A	p.Leu2463His	p.L2463H	ENST00000361445	NM_004958.3	2463	cTt/cAt	55/58	0.554822910281187	3	FACETS	0.662	0.586	0.743	0.221	0.195	0.248	SUBCLONAL	1	TRUE	0	0.549094805899952	3		537	603	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941071	36941071	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	117	793	0	ENST00000361632.4:c.268C>A	p.Pro90Thr	p.P90T	ENST00000361632		90	Ccc/Acc	3/16	0.252402550355744	6	FACETS	0.914	0.823	1			1	INDETERMINATE	1	TRUE	NA	0.549094805899952	6		793	978	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77051761	77051761	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	84	575	0	ENST00000356341.3:c.1046G>C	p.Gly349Ala	p.G349A	ENST00000356341	NM_002576.4	349	gGa/gCa	11/15	0.554822910281187	3	FACETS	0.562	0.496	0.632			1	SUBCLONAL	1	TRUE	NA	0.549094805899952	3		575	694	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201082	108201082	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	128	397	0	ENST00000278616.4:c.7449G>T	p.Trp2483Cys	p.W2483C	ENST00000278616	NM_000051.3	2483	tgG/tgT	50/63	0.554822910281187	4	FACETS	0.778	0.71	0.849	0.389	0.355	0.425	SUBCLONAL	2	TRUE	0	0.549094805899952	4		397	464	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644427	18644427	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1419629305	NA	P-0044784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	49	333	0	ENST00000266497.5:c.2605C>G	p.Gln869Glu	p.Q869E	ENST00000266497		869	Caa/Gaa	18/31	0.554822910281187	4	FACETS	0.436	0.369	0.511	0.218	0.184	0.256	SUBCLONAL	1	TRUE	2	0.549094805899952	4		333	634	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934254	48934254	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	80	365	0	ENST00000267163.4:c.709G>C	p.Glu237Gln	p.E237Q	ENST00000267163	NM_000321.2	237	Gaa/Caa	7/27	0.488289377989776	3	FACETS	0.928	0.822	1	0.309	0.274	0.347	CLONAL	1	TRUE	0	0.549094805899952	3		365	400	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646920	23646920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658867	NA	P-0044784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	97	585	0	ENST00000261584.4:c.947C>T	p.Pro316Leu	p.P316L	ENST00000261584	NM_024675.3	316	cCc/cTc	4/13	0.287649092982745	2	FACETS	0.701	0.627	0.779	0.351	0.313	0.39	INDETERMINATE	1	TRUE	0	0.549094805899952	2		585	504	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541188	187541188	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	58	349	0	ENST00000441802.2:c.6552A>C	p.Lys2184Asn	p.K2184N	ENST00000441802	NM_005245.3	2184	aaA/aaC	10/27	0.554822910281187	2	FACETS	0.76	0.659	0.868	0.38	0.329	0.434	SUBCLONAL	1	TRUE	0	0.549094805899952	2		349	278	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92404100	92404100	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	80	451	1	ENST00000265734.4:c.279A>T	p.Lys93Asn	p.K93N	ENST00000265734	NM_001259.6	93	aaA/aaT	3/8	0.525368204264413	3	FACETS	0.641	0.565	0.723	0.321	0.282	0.362	SUBCLONAL	1	TRUE	1	0.549094805899952	3		452	579	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56910938	56910938	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	110	572	0	ENST00000519728.1:c.1084A>G	p.Asn362Asp	p.N362D	ENST00000519728	NM_002350.3	362	Aac/Gac	11/13	0.554822910281187	2	FACETS	0.787	0.71	0.868	0.394	0.355	0.434	SUBCLONAL	1	TRUE	0	0.549094805899952	2		572	509	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412698	139412698	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	120	930	0	ENST00000277541.6:c.1146C>G	p.Asn382Lys	p.N382K	ENST00000277541	NM_017617.3	382	aaC/aaG	7/34	0.554822910281187	2	FACETS	0.564	0.509	0.622	0.282	0.254	0.311	SUBCLONAL	1	TRUE	0	0.549094805899952	2		930	775	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929284	44929284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	127	690	0	ENST00000377967.4:c.2384G>A	p.Gly795Glu	p.G795E	ENST00000377967	NM_021140.2	795	gGa/gAa	17/29	0.545289965354302	1	FACETS	0.758	0.691	0.826	0.758	0.691	0.826	SUBCLONAL	1	TRUE	0	0.549094805899952	1		690	443	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	158	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.226321313331698	5	FACETS	0.874	0.811	0.938			1	INDETERMINATE	3	TRUE	NA	0.57610109261038	5		326	390	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971153	21971153	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913383	NA	P-0044786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	359	416	0	ENST00000304494.5:c.205G>T	p.Glu69Ter	p.E69*	ENST00000304494	NM_000077.4	69	Gag/Tag	2/3	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.57610109261038	2		416	577	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338657	70338657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	300	547	0	ENST00000374080.3:c.53G>A	p.Arg18Gln	p.R18Q	ENST00000374080		18	cGg/cAg	1/45	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.57610109261038	2		547	891	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578441	7578441	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	496	756	0	ENST00000269305.4:c.489del	p.Tyr163Ter	p.Y163*	ENST00000269305	NM_001126112.2	163	taC/ta	5/11	0.56445638065541	2	FACETS	0.953	0.919	0.988	0.953	0.919	0.988	CLONAL	2	TRUE	0	0.57610109261038	2		756	903	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603007	48603007	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0044786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	76	246	0	ENST00000342988.3:c.1309-1G>T		p.X437_splice	ENST00000342988	NM_005359.5	437			0.365740968721325	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.57610109261038	1		246	176	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	129	425	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.902	0.824	0.982	0.902	0.824	0.982	CLONAL	1	TRUE	1	0.65023817487821	2		426	440	SUCCESS
APC	324	MSKCC	GRCh37	5	112175755	112175755	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	120	188	0	ENST00000257430.4:c.4464del	p.Leu1488PhefsTer19	p.L1488Ffs*19	ENST00000257430	NM_000038.5	1488	ttA/tt	16/16	1	2	FACETS	0.956	0.872	1	0.956	0.872	1	CLONAL	1	TRUE	1	0.65023817487821	2		188	386	SUCCESS
APC	324	MSKCC	GRCh37	5	112174091	112174094	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1131691143	NA	P-0044856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	98	236	0	ENST00000257430.4:c.2802_2805del	p.Tyr935IlefsTer19	p.Y935Ifs*19	ENST00000257430	NM_000038.5	934	ACTTac/ac	16/16	1	2	FACETS	0.879	0.792	0.969	0.879	0.792	0.969	CLONAL	1	TRUE	1	0.65023817487821	2		236	343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578175	7578175	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0044856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	255	464	0	ENST00000269305.4:c.672+2T>C		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.645926865396745	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.65023817487821	1		464	515	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	340	300	0				ENST00000310581	NM_198253.2	-/1132			0.278349350722447	3	FACETS	0.79	0.754	0.827	0.79	0.754	0.827	INDETERMINATE	2	TRUE	1	0.885476734710333	3		300	701	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0044926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	426	682	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.885476734710333	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.885476734710333	1		682	494	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936983	48936983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690863	NA	P-0044926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	371	445	1	ENST00000267163.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000267163	NM_000321.2	251	Cga/Tga	8/27	0.789740146232407	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.885476734710333	1		446	444	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	140	234	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	0.789740146232407	0	FACETS		NA	1			1	NA	1	TRUE	NA	0.885476734710333	0		234	167	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872380	45872380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	417	770	0	ENST00000391945.4:c.131C>T	p.Ser44Leu	p.S44L	ENST00000391945	NM_000400.3	44	tCa/tTa	3/23	NA	2	FACETS	0.949	0.907	0.991			1	INDETERMINATE	1	TRUE	NA	0.885476734710333	2		770	993	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974714	21974714	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1563892591	NA	P-0044926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	122	431	1	ENST00000304494.5:c.113C>T	p.Pro38Leu	p.P38L	ENST00000304494	NM_000077.4	38	cCc/cTc	1/3	0.399433081829847	1	FACETS	0.288	0.261	0.316	0.288	0.261	0.316	INDETERMINATE	1	TRUE	0	0.885476734710333	1		432	534	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864632	68864632	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0044926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	62	168	0	ENST00000288368.4:c.3G>A	p.Met1?	p.M1?	ENST00000288368	NM_024870.2	1	atG/atA	1/40	0.399433081829847	1	FACETS	0.51	0.452	0.57	0.51	0.452	0.57	INDETERMINATE	1	TRUE	0	0.885476734710333	1		168	153	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923300	26923300	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	249	338	0	ENST00000381527.3:c.296A>G	p.Tyr99Cys	p.Y99C	ENST00000381527	NM_001260.1	99	tAt/tGt	3/13	1	2	FACETS	0.994	0.938	1	0.994	0.938	1	CLONAL	1	TRUE	1	0.885476734710333	2		338	566	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061321	38061324	+	frameshift_variant	Frame_Shift_Del	DEL	GACA	GACA	-	novel	NA	P-0044926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	146	731	0	ENST00000250448.2:c.665_668del	p.Leu222ProfsTer98	p.L222Pfs*98	ENST00000250448	NM_004496.3	222	cTGTCc/cc	2/2	0.885476734710333	2	FACETS	0.432	0.395	0.471	0.216	0.197	0.236	SUBCLONAL	1	TRUE	0	0.885476734710333	2		731	763	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651866	36651872	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TGCTGCA	TGCTGCA	-	novel	NA	P-0044926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	311	613	0	ENST00000244741.5:c.-5-8_-5-2del		p.X2_splice	ENST00000244741	NM_000389.4	2			0.457727475318866	1	FACETS	0.688	0.656	0.719	0.688	0.656	0.719	INDETERMINATE	1	TRUE	0	0.885476734710333	1		613	569	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37141752	37141752	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	370	630	0	ENST00000373509.5:c.827C>T	p.Ser276Leu	p.S276L	ENST00000373509	NM_002648.3	276	tCa/tTa	6/6	0.457727475318866	1	FACETS	0.751	0.721	0.781	0.751	0.721	0.781	INDETERMINATE	1	TRUE	0	0.885476734710333	1		630	620	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0044927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	219	181	0	ENST00000374690.3:c.2105T>A	p.Leu702His	p.L702H	ENST00000374690	NM_000044.3	702	cTc/cAc	4/8	0.1698054040279	24	FACETS	0.995	0.933	1			1	CLONAL	13	FALSE	NA	0.1698054040279	24		181	572	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061207	38061207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	232	275	1	ENST00000250448.2:c.782G>A	p.Arg261His	p.R261H	ENST00000250448	NM_004496.3	261	cGc/cAc	2/2	0.1698054040279	3	FACETS	1	0.971	1	1	0.996	1	CLONAL	7	FALSE	1	0.1698054040279	3		276	409	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166184	118166184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371434677	NA	P-0044927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	96	284	1	ENST00000369448.3:c.694G>A	p.Ala232Thr	p.A232T	ENST00000369448	NM_017709.3	232	Gcc/Acc	2/2	1	2	FACETS	1	0.955	1	1	0.991	1	CLONAL	5	FALSE	1	0.1698054040279	2		285	210	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618502	37618533	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGCATCCCTGGGCACAGTTATCAAACCTTT	GCAGCATCCCTGGGCACAGTTATCAAACCTTT	-	novel	NA	P-0044927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	63	361	0	ENST00000447079.4:c.179_210del	p.Ala60GlyfsTer4	p.A60Gfs*4	ENST00000447079	NM_015083.1	60	GCAGCATCCCTGGGCACAGTTATCAAACCTTTg/g	1/14	0.1698054040279	5	FACETS	1	0.936	1	0.84	0.734	0.954	CLONAL	3	FALSE	1	0.1698054040279	5		361	277	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667852	37667853	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0044927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	84	336	0	ENST00000447079.4:c.2738dup	p.Tyr913Ter	p.Y913*	ENST00000447079	NM_015083.1	913	tac/tAac	8/14	0.1698054040279	5	FACETS	0.933	0.844	1	1	0.984	1	CLONAL	7	FALSE	1	0.1698054040279	5		336	190	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158557	26158557	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	63	386	0	ENST00000289316.2:c.160G>C	p.Gly54Arg	p.G54R	ENST00000289316	NM_138720.2	54	Ggc/Cgc	1/2	0.1698054040279	9	FACETS	1	0.942	1	0.69	0.6	0.786	CLONAL	3	FALSE	4	0.1698054040279	9		386	343	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636826	8636826	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1353675904	NA	P-0044955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	171	496	0	ENST00000356435.5:c.83G>A	p.Arg28Gln	p.R28Q	ENST00000356435		28	cGa/cAa	2/35	0.340292948117918	1	FACETS	0.5	0.462	0.54	0.5	0.462	0.54	INDETERMINATE	1	TRUE	0	0.713595261142566	1		496	616	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120882	115120882	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	607	470	1	ENST00000257566.3:c.124C>A	p.Pro42Thr	p.P42T	ENST00000257566	NM_016569.3	42	Ccc/Acc	1/8	0.713595261142566	6	FACETS	0.997	0.961	1			1	CLONAL	3	TRUE	NA	0.713595261142566	6		471	1381	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690266	47690266	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs730881757	NA	P-0044955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	171	502	0	ENST00000233146.2:c.1483A>G	p.Thr495Ala	p.T495A	ENST00000233146	NM_000251.2	495	Aca/Gca	9/16	1	2	FACETS	0.876	0.811	0.943	0.876	0.811	0.943	CLONAL	1	TRUE	1	0.713595261142566	2		502	547	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506915	186506915	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	145	231	0	ENST00000323963.5:c.1081A>G	p.Ile361Val	p.I361V	ENST00000323963		361	Att/Gtt	11/11	1	2	FACETS	0.977	0.9	1	0.977	0.9	1	CLONAL	1	TRUE	1	0.713595261142566	2		231	416	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341250	8341250	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	74	305	0	ENST00000356435.5:c.4966del	p.Ala1656LeufsTer39	p.A1656Lfs*39	ENST00000356435		1656	Gct/ct	30/35	0.340292948117918	1	FACETS	0.556	0.493	0.621	0.556	0.493	0.621	INDETERMINATE	1	TRUE	0	0.713595261142566	1		305	240	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	341	300	0				ENST00000310581	NM_198253.2	-/1132			0.809474784247668	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	1	0.809474784247668	4		300	493	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0044959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	146	370	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.871	0.803	0.941	0.871	0.803	0.941	CLONAL	1	TRUE	1	0.809474784247668	2		370	414	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057835	27057835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	398	984	1	ENST00000324856.7:c.1543C>T	p.Gln515Ter	p.Q515*	ENST00000324856	NM_006015.4	515	Cag/Tag	3/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.809474784247668	2		985	930	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044971	47044971	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	429	581	0	ENST00000377604.3:c.2297G>C	p.Arg766Pro	p.R766P	ENST00000377604	NM_001204468.1	766	cGc/cCc	20/24	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.809474784247668	1		581	554	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047495	49047495	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0044959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	111	271	0	ENST00000267163.4:c.2490-1G>C		p.X830_splice	ENST00000267163	NM_000321.2	830			0.752119560629067	1	FACETS	0.897	0.833	0.959	0.897	0.833	0.959	CLONAL	1	TRUE	0	0.809474784247668	1		271	182	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651963	36651963	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	332	837	3	ENST00000244741.5:c.85C>T	p.Gln29Ter	p.Q29*	ENST00000244741	NM_000389.4	29	Cag/Tag	2/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.809474784247668	2		840	777	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445715	49445745	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGGGGACATGGGTGACTCCTCAGGTGGTG	GGAGGGGACATGGGTGACTCCTCAGGTGGTG	-	novel	NA	P-0044959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	579	1434	1	ENST00000301067.7:c.1721_1751del	p.Pro574HisfsTer346	p.P574Hfs*346	ENST00000301067	NM_003482.3	574	cCACCACCTGAGGAGTCACCCATGTCCCCTCCa/ca	10/54	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.809474784247668	2		1435	1395	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785538	50785538	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	301	712	0	ENST00000398568.2:c.528C>A	p.Phe176Leu	p.F176L	ENST00000398568	NM_001042412.1	176	ttC/ttA	4/18	1	2	FACETS	0.903	0.854	0.952	0.903	0.854	0.952	CLONAL	1	TRUE	1	0.809474784247668	2		712	824	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654651	67654651	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	254	568	1	ENST00000264010.4:c.1138C>T	p.Gln380Ter	p.Q380*	ENST00000264010	NM_006565.3	380	Cag/Tag	6/12	1	2	FACETS	0.961	0.905	1	0.961	0.905	1	CLONAL	1	TRUE	1	0.809474784247668	2		569	653	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182630	99182630	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	161	426	0	ENST00000074304.5:c.2433G>C	p.Glu811Asp	p.E811D	ENST00000074304	NM_001134224.1	811	gaG/gaC	22/26	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.809474784247668	2		426	389	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545177	41545177	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	250	556	0	ENST00000263253.7:c.2377C>T	p.Gln793Ter	p.Q793*	ENST00000263253	NM_001429.3	793	Caa/Taa	13/31	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.809474784247668	2		556	600	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49399979	49399979	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	245	742	0	ENST00000418115.1:c.358G>C	p.Asp120His	p.D120H	ENST00000418115	NM_001664.2	120	Gat/Cat	4/5	1	2	FACETS	0.788	0.739	0.838	0.788	0.739	0.838	SUBCLONAL	1	TRUE	1	0.809474784247668	2		742	768	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691039	NA	P-0045114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	335	1097	0	ENST00000269305.4:c.919+1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.429543564249849	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.429543564249849	2		1097	775	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0045114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	103	194	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.429543564249849	2	FACETS	0.847	0.77	0.927	0.847	0.77	0.927	CLONAL	2	TRUE	0	0.429543564249849	2		194	283	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0045114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	256	475	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.429543564249849	3	FACETS	0.981	0.923	1	0.981	0.923	1	CLONAL	2	TRUE	1	0.429543564249849	3		475	738	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604707	48604707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	113	383	0	ENST00000342988.3:c.1529G>A	p.Gly510Glu	p.G510E	ENST00000342988	NM_005359.5	510	gGa/gAa	12/12	0.429543564249849	1	FACETS	0.912	0.826	1	0.912	0.826	1	CLONAL	1	TRUE	0	0.429543564249849	1		383	453	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93626944	93626944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	112	426	0	ENST00000375746.1:c.791C>T	p.Thr264Ile	p.T264I	ENST00000375746	NM_001174167.1	264	aCa/aTa	5/14	1	2	FACETS	0.764	0.687	0.844	0.764	0.687	0.844	SUBCLONAL	1	TRUE	1	0.429543564249849	2		426	683	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0045167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	49	262	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.198829783378275	3	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	FALSE	1	0.198829783378275	3		262	240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	107	379	0	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	0.192853541618217	2	FACETS	0.891	0.801	0.986	0.891	0.801	0.986	CLONAL	2	FALSE	0	0.198829783378275	2		379	604	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250047	39250047	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs754823642	NA	P-0045167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	17	458	0	ENST00000402219.2:c.1522A>C	p.Asn508His	p.N508H	ENST00000402219	NM_005633.3	508	Aat/Cat	10/23	0.198829783378275	5	FACETS	0.716	0.534	0.933	0.239	0.178	0.311	CLONAL	1	FALSE	2	0.198829783378275	5		458	310	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505511	157505521	+	frameshift_variant	Frame_Shift_Del	DEL	GGAAGTCTTCA	GGAAGTCTTCA	-	novel	NA	P-0045167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	51	402	0	ENST00000346085.5:c.3493_3503del	p.Glu1165HisfsTer17	p.E1165Hfs*17	ENST00000346085	NM_020732.3	1164	ccGGAAGTCTTCAgc/ccgc	13/20	0.198829783378275	6	FACETS	0.953	0.813	1	0.477	0.406	0.553	CLONAL	2	FALSE	2	0.198829783378275	6		402	376	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630753	187630753	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377496399	NA	P-0045227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	115	536	0	ENST00000441802.2:c.229G>A	p.Gly77Arg	p.G77R	ENST00000441802	NM_005245.3	77	Gga/Aga	2/27	1	2	FACETS	0.441	0.398	0.487	0.441	0.398	0.487	SUBCLONAL	1	TRUE	1	0.72	2		536	724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934874	NA	P-0045257-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	500	587	0	ENST00000269305.4:c.451C>G	p.Pro151Ala	p.P151A	ENST00000269305	NM_001126112.2	151	Ccc/Gcc	5/11	0.57335645582317	2	FACETS	0.852	0.822	0.882	0.852	0.822	0.882	CLONAL	2	TRUE	0	0.663891476391561	2		587	884	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948787	55948787	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs751902659	NA	P-0045257-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	66	285	0	ENST00000263923.4:c.3678C>A	p.Asn1226Lys	p.N1226K	ENST00000263923	NM_002253.2	1226	aaC/aaA	28/30	0.663891476391561	1	FACETS	0.777	0.689	0.867	0.777	0.689	0.867	SUBCLONAL	1	TRUE	0	0.663891476391561	1		285	171	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661945	29661945	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854552	NA	P-0045257-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	166	321	0	ENST00000356175.3:c.5839C>T	p.Arg1947Ter	p.R1947*	ENST00000356175	NM_000267.3	1947	Cga/Tga	39/57	0.57335645582317	2	FACETS	0.786	0.736	0.836	0.786	0.736	0.836	SUBCLONAL	2	TRUE	0	0.663891476391561	2		321	318	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670671	86670671	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045257-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	38	168	0	ENST00000274376.6:c.1949del	p.Asp650AlafsTer7	p.D650Afs*7	ENST00000274376	NM_002890.2	650	gAc/gc	15/25	0.663891476391561	1	FACETS	0.84	0.72	0.965	0.84	0.72	0.965	CLONAL	1	TRUE	0	0.663891476391561	1		168	91	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813432	102813432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751304020	NA	P-0045570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	11	463	0	ENST00000307046.8:c.257C>T	p.Ala86Val	p.A86V	ENST00000307046	NM_001111285.1	86	gCg/gTg	3/4	1	2	FACETS	0.121	0.083	0.168	0.121	0.083	0.168	SUBCLONAL	1	TRUE	1	0.855749741383515	2		463	212	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087403	27087403	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	231	584	0	ENST00000324856.7:c.1977del	p.Gly660GlufsTer2	p.G660Efs*2	ENST00000324856	NM_006015.4	659	ccT/cc	5/20	0.855749741383515	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.855749741383515	2		584	261	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197851	123197851	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	133	372	0	ENST00000218089.9:c.1975G>A	p.Asp659Asn	p.D659N	ENST00000218089	NM_001042749.1	659	Gat/Aat	20/35	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.855749741383515	2		372	284	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111518	8111519	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0045736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	259	453	0	ENST00000346208.3:c.1007dup	p.Val337CysfsTer15	p.V337Cfs*15	ENST00000346208		335	gac/gaCc	5/6	1	2	FACETS	0.876	0.823	0.929	0.876	0.823	0.929	CLONAL	1	TRUE	1	0.755483175317024	2		453	783	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857866	89857866	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501879	NA	P-0045744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	84	625	0	ENST00000389301.3:c.1304G>A	p.Arg435His	p.R435H	ENST00000389301	NM_000135.2	435	cGc/cAc	14/43	0.278075405807608	3	FACETS	1	0.954	1	0.579	0.512	0.651	CLONAL	1	TRUE	1	0.278075405807608	3		625	594	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495056	56495056	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	172	630	0	ENST00000267101.3:c.3413G>T	p.Ser1138Ile	p.S1138I	ENST00000267101	NM_001982.3	1138	aGt/aTt	27/28	0.272753172696364	4	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	2	0.278075405807608	4		630	763	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912694	32912694	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	52	346	0	ENST00000380152.3:c.4202G>T	p.Gly1401Val	p.G1401V	ENST00000380152		1401	gGt/gTt	11/27	0.278075405807608	3	FACETS	1	0.867	1	0.508	0.434	0.59	CLONAL	1	TRUE	1	0.278075405807608	3		346	419	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15952217	15952218	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	73	612	0	ENST00000268712.3:c.6477dup	p.Glu2160Ter	p.E2160*	ENST00000268712	NM_006311.3	2159	-/T	41/46	0.278075405807608	3	FACETS	0.905	0.791	1	0.452	0.395	0.514	CLONAL	1	TRUE	1	0.278075405807608	3		612	661	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24135876	24135876	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1568937197	NA	P-0045744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	115	401	0	ENST00000263121.7:c.362+1G>A		p.X121_splice	ENST00000263121	NM_003073.3	121			0.278075405807608	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.278075405807608	2		401	375	SUCCESS
APC	324	MSKCC	GRCh37	5	112177215	112177215	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs751710222	NA	P-0045744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	34	249	0	ENST00000257430.4:c.5924T>A	p.Ile1975Asn	p.I1975N	ENST00000257430	NM_000038.5	1975	aTt/aAt	16/16	0.278075405807608	3	FACETS	0.944	0.774	1	0.472	0.387	0.567	CLONAL	1	TRUE	1	0.278075405807608	3		249	295	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930597	131930597	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	31	267	0	ENST00000265335.6:c.1830T>G	p.His610Gln	p.H610Q	ENST00000265335		610	caT/caG	12/25	0.278075405807608	3	FACETS	1	0.856	1	0.531	0.432	0.642	CLONAL	1	TRUE	1	0.278075405807608	3		267	239	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880065	151880065	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	100	381	0	ENST00000262189.6:c.5259del	p.Phe1753LeufsTer24	p.F1753Lfs*24	ENST00000262189	NM_170606.2	1753	ttT/tt	35/59	0.278075405807608	4	FACETS	0.95	0.852	1	0.95	0.852	1	CLONAL	2	TRUE	2	0.278075405807608	4		381	484	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	202	300	0				ENST00000310581	NM_198253.2	-/1132			0.621685554926547	3	FACETS	0.988	0.928	1	0.988	0.928	1	CLONAL	2	TRUE	1	0.621685554926547	3		300	431	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508805	106508805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762805000	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	94	402	0	ENST00000359195.3:c.799G>A	p.Glu267Lys	p.E267K	ENST00000359195	NM_002649.2	267	Gaa/Aaa	2/11	0.621685554926547	8	FACETS	0.824	0.731	0.923	0.165	0.146	0.185	CLONAL	1	TRUE	3	0.621685554926547	8		402	1052	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508281	106508281	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778832310	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	80	364	0	ENST00000359195.3:c.275G>A	p.Gly92Glu	p.G92E	ENST00000359195	NM_002649.2	92	gGa/gAa	2/11	0.621685554926547	8	FACETS	0.947	0.832	1	0.189	0.166	0.214	CLONAL	1	TRUE	3	0.621685554926547	8		364	779	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	316	382	0	ENST00000304494.5:c.143C>T	p.Pro48Leu	p.P48L	ENST00000304494	NM_000077.4	48	cCg/cTg	1/3	NA	2	FACETS	0.872	0.832	0.911			1	INDETERMINATE	2	TRUE	NA	0.621685554926547	2		382	583	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587782197	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	639	633	0	ENST00000269305.4:c.434T>A	p.Leu145Gln	p.L145Q	ENST00000269305	NM_001126112.2	145	cTg/cAg	5/11	0.53938359049122	4	FACETS	1	0.995	1	0.824	0.8	0.848	CLONAL	3	TRUE	0	0.621685554926547	4		633	1011	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589698	69589698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	48	81	0	ENST00000168712.1:c.155C>T	p.Ala52Val	p.A52V	ENST00000168712	NM_002007.2	52	gCg/gTg	1/3	0.621685554926547	3	FACETS	1	0.967	1	0.739	0.639	0.842	CLONAL	1	TRUE	1	0.621685554926547	3		81	137	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923216	26923216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	62	260	0	ENST00000381527.3:c.212G>A	p.Arg71Gln	p.R71Q	ENST00000381527	NM_001260.1	71	cGa/cAa	3/13	0.557228795108417	2	FACETS	1	0.977	1	0.744	0.663	0.827	CLONAL	1	TRUE	0	0.621685554926547	2		260	134	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148875	119148876	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	59	256	1	ENST00000264033.4:c.1096-1_1096delinsAA		p.X366_splice	ENST00000264033	NM_005188.3	366		8/16	0.621685554926547	3	FACETS	1	0.967	1	0.672	0.589	0.76	CLONAL	1	TRUE	1	0.621685554926547	3		257	185	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979559	7979559	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	476	526	1	ENST00000319144.4:c.1466G>A	p.Gly489Glu	p.G489E	ENST00000319144	NM_001139.2	489	gGg/gAg	11/15	0.53938359049122	4	FACETS	1	0.986	1	0.78	0.753	0.807	CLONAL	3	TRUE	0	0.621685554926547	4		527	796	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528612	8528612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	95	354	0	ENST00000356435.5:c.520C>T	p.Arg174Cys	p.R174C	ENST00000356435		174	Cgt/Tgt	4/35	0.621685554926547	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.621685554926547	1		354	184	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101199	41101199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368237025	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	242	499	0	ENST00000373198.4:c.1157C>T	p.Pro386Leu	p.P386L	ENST00000373198	NM_133170.3	386	cCg/cTg	8/32	NA	2	FACETS	0.78	0.737	0.823			1	INDETERMINATE	2	TRUE	NA	0.621685554926547	2		499	499	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40709539	40709539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159851	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	184	385	1	ENST00000373198.4:c.4363G>A	p.Glu1455Lys	p.E1455K	ENST00000373198	NM_133170.3	1455	Gaa/Aaa	32/32	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.621685554926547	2		386	395	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899063	40899063	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1405822046	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	100	540	0	ENST00000373198.4:c.2207G>A	p.Gly736Glu	p.G736E	ENST00000373198	NM_133170.3	736	gGg/gAg	14/32	NA	2	FACETS	0.444	0.396	0.494			1	INDETERMINATE	1	TRUE	NA	0.621685554926547	2		540	725	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730858	40730858	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200227405	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	362	610	0	ENST00000373198.4:c.3677G>A	p.Arg1226Gln	p.R1226Q	ENST00000373198	NM_133170.3	1226	cGa/cAa	27/32	NA	2	FACETS	0.837	0.8	0.873			1	INDETERMINATE	2	TRUE	NA	0.621685554926547	2		610	696	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245915	5245915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs724159894	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	159	628	0	ENST00000357368.4:c.860C>T	p.Pro287Leu	p.P287L	ENST00000357368	NM_002850.3	287	cCc/cTc	10/38	0.580606685534937	3	FACETS	0.88	0.808	0.955	0.44	0.404	0.478	CLONAL	1	TRUE	1	0.621685554926547	3		628	762	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748519	43748519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267601048	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	163	366	0	ENST00000523873.1:c.473C>T	p.Ser158Phe	p.S158F	ENST00000523873		158	tCc/tTc	6/8	0.484997433186138	5	FACETS	0.778	0.717	0.842	0.519	0.478	0.562	SUBCLONAL	2	TRUE	2	0.621685554926547	5		366	651	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739950	41739950	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1164410355	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	203	355	0	ENST00000242208.4:c.23G>A	p.Gly8Glu	p.G8E	ENST00000242208	NM_002192.2	8	gGa/gAa	2/3	0.621685554926547	4	FACETS	1	0.985	1	0.411	0.381	0.442	CLONAL	1	TRUE	1	0.621685554926547	4		355	859	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938617	76938617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	103	209	0	ENST00000373344.5:c.2131C>T	p.Pro711Ser	p.P711S	ENST00000373344	NM_000489.3	711	Cct/Tct	9/35	0.564952581192899	2	FACETS	1	0.969	1			1	CLONAL	2	TRUE	NA	0.621685554926547	2		209	154	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421265	12421265	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777067241	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	363	532	0	ENST00000287820.6:c.145G>A	p.Asp49Asn	p.D49N	ENST00000287820	NM_015869.4	49	Gat/Aat	2/7	0.621685554926547	6	FACETS	1	0.984	1	0.803	0.765	0.84	CLONAL	3	TRUE	2	0.621685554926547	6		532	816	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909887	100909887	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	17	273	0	ENST00000325455.5:c.2762T>C	p.Leu921Ser	p.L921S	ENST00000325455	NM_001202474.3	921	tTg/tCg	8/8	0.621685554926547	3	FACETS	0.815	0.619	1	0.407	0.309	0.519	CLONAL	1	TRUE	1	0.621685554926547	3		273	88	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105616	27105616	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	289	501	0	ENST00000324856.7:c.5227A>T	p.Thr1743Ser	p.T1743S	ENST00000324856	NM_006015.4	1743	Acg/Tcg	20/20	0.621685554926547	6	FACETS	1	0.988	1	0.786	0.742	0.832	CLONAL	2	TRUE	3	0.621685554926547	6		501	884	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812229	43812229	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	299	502	0	ENST00000372470.3:c.1094T>G	p.Leu365Arg	p.L365R	ENST00000372470	NM_005373.2	365	cTt/cGt	7/12	0.621685554926547	6	FACETS	1	0.988	1	0.776	0.732	0.82	CLONAL	2	TRUE	3	0.621685554926547	6		502	927	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799218	45799219	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	305	377	0	ENST00000450313.1:c.214_215delinsTT	p.Pro72Leu	p.P72L	ENST00000450313	NM_012222.2	72	CCg/TTg	3/16	0.621685554926547	6	FACETS	0.87	0.823	0.918	0.87	0.823	0.918	CLONAL	3	TRUE	3	0.621685554926547	6		377	843	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196662	67196662	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	170	469	0	ENST00000312629.5:c.191C>T	p.Pro64Leu	p.P64L	ENST00000312629	NM_003952.2	64	cCc/cTc	3/15	0.621685554926547	3	FACETS	0.8	0.736	0.867	0.4	0.368	0.434	SUBCLONAL	1	TRUE	1	0.621685554926547	3		469	896	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444061	49444061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	168	528	0	ENST00000301067.7:c.3310C>T	p.Pro1104Ser	p.P1104S	ENST00000301067	NM_003482.3	1104	Ccc/Tcc	11/54	0.525095754400156	5	FACETS	0.908	0.839	0.979	0.605	0.559	0.653	CLONAL	2	TRUE	2	0.621685554926547	5		528	575	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416888	121416888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	184	590	0	ENST00000257555.6:c.317C>T	p.Thr106Ile	p.T106I	ENST00000257555		106	aCc/aTc	1/10	0.0556553687842696	3	FACETS	1	0.974	1	0.555	0.514	0.598	INDETERMINATE	1	TRUE	1	0.621685554926547	3		590	699	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123875211	123875212	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	98	253	1	ENST00000330479.4:c.167_168delinsTT	p.Ser56Phe	p.S56F	ENST00000330479	NM_020382.3	56	tCC/tTT	3/9	0.0556553687842696	3	FACETS	1	0.978	1	0.658	0.594	0.725	INDETERMINATE	1	TRUE	1	0.621685554926547	3		254	314	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098738	2098738	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1385450866	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	168	481	0	ENST00000219476.3:c.122C>T	p.Thr41Ile	p.T41I	ENST00000219476	NM_000548.3	41	aCc/aTc	2/42	0.525095754400156	5	FACETS	1	0.986	1	0.44	0.404	0.476	CLONAL	1	TRUE	2	0.621685554926547	5		481	792	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779101	3779101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1326637502	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	145	579	0	ENST00000262367.5:c.5947C>T	p.Pro1983Ser	p.P1983S	ENST00000262367	NM_004380.2	1983	Cca/Tca	31/31	0.525095754400156	5	FACETS	1	0.981	1	0.423	0.386	0.461	CLONAL	1	TRUE	2	0.621685554926547	5		579	711	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682543	37682543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758668404	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	214	324	0	ENST00000447079.4:c.3734C>T	p.Pro1245Leu	p.P1245L	ENST00000447079	NM_015083.1	1245	cCc/cTc	13/14	0.539730582233494	3	FACETS	1	0.986	1	0.762	0.719	0.803	CLONAL	2	TRUE	0	0.621685554926547	3		324	395	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217049	2217049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	389	563	0	ENST00000398665.3:c.2504C>T	p.Pro835Leu	p.P835L	ENST00000398665	NM_032482.2	835	cCt/cTt	21/28	0.580606685534937	3	FACETS	0.989	0.946	1	0.989	0.946	1	CLONAL	2	TRUE	1	0.621685554926547	3		563	829	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11018760	11018760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	366	612	0	ENST00000327064.4:c.392C>T	p.Thr131Ile	p.T131I	ENST00000327064	NM_199141.1	131	aCc/aTc	3/16	0.451906114136876	4	FACETS	1	0.987	1	0.728	0.694	0.763	CLONAL	2	TRUE	1	0.621685554926547	4		612	874	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682862	190682862	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	51	430	0	ENST00000441310.2:c.538G>C	p.Gly180Arg	p.G180R	ENST00000441310	NM_000534.4	180	Ggt/Cgt	5/13	0.182689877388671	4	FACETS	0.872	0.746	1	0.291	0.248	0.337	INDETERMINATE	1	TRUE	1	0.621685554926547	4		430	305	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46276063	46276063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	177	449	0	ENST00000371998.3:c.3499C>T	p.Pro1167Ser	p.P1167S	ENST00000371998		1167	Ccc/Tcc	18/23	0.621685554926547	5	FACETS	1	0.985	1	0.321	0.295	0.347	CLONAL	1	TRUE	1	0.621685554926547	5		449	858	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281712	46281712	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	458	490	0	ENST00000371998.3:c.4159C>T	p.Pro1387Ser	p.P1387S	ENST00000371998		1387	Cct/Tct	22/23	0.621685554926547	5	FACETS	1	0.989	1	0.806	0.775	0.837	CLONAL	3	TRUE	1	0.621685554926547	5		490	883	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462347	89462347	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	222	458	0	ENST00000336596.2:c.1819C>T	p.Gln607Ter	p.Q607*	ENST00000336596	NM_005233.5	607	Caa/Taa	10/17	0.621685554926547	6	FACETS	1	0.985	1			1	CLONAL	3	TRUE	NA	0.621685554926547	6		458	470	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526312	189526312	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	157	353	0	ENST00000264731.3:c.576G>A	p.Trp192Ter	p.W192*	ENST00000264731	NM_003722.4	192	tgG/tgA	4/14	0.396386140005403	3	FACETS	1	0.949	1	0.681	0.635	0.728	CLONAL	2	TRUE	0	0.621685554926547	3		353	324	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747849	41747849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1420729662	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	88	293	0	ENST00000226382.2:c.920C>T	p.Ala307Val	p.A307V	ENST00000226382	NM_003924.3	307	gCc/gTc	3/3	1	2	FACETS	0.784	0.7	0.872	0.784	0.7	0.872	SUBCLONAL	1	TRUE	1	0.621685554926547	2		293	361	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127435	55127435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	119	520	0	ENST00000257290.5:c.223G>A	p.Glu75Lys	p.E75K	ENST00000257290	NM_006206.4	75	Gaa/Aaa	3/23	1	2	FACETS	0.862	0.784	0.944	0.862	0.784	0.944	CLONAL	1	TRUE	1	0.621685554926547	2		520	444	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981080	55981080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	43	374	0	ENST00000263923.4:c.619G>A	p.Glu207Lys	p.E207K	ENST00000263923	NM_002253.2	207	Gaa/Aaa	5/30	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.621685554926547	2		374	134	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984882	55984882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	125	414	0	ENST00000263923.4:c.247C>T	p.Leu83Phe	p.L83F	ENST00000263923	NM_002253.2	83	Ctc/Ttc	3/30	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.621685554926547	2		414	402	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751967	57751967	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	242	397	0	ENST00000274289.3:c.1270A>T	p.Thr424Ser	p.T424S	ENST00000274289	NM_006622.3	424	Acc/Tcc	10/14	0.451906114136876	4	FACETS	1	0.989	1	0.793	0.748	0.837	CLONAL	2	TRUE	1	0.621685554926547	4		397	531	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590977	67590977	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	15	137	0	ENST00000274335.5:c.1570A>T	p.Ile524Phe	p.I524F	ENST00000274335		524	Att/Ttt	12/15	0.451906114136876	4	FACETS	0.711	0.526	0.928	0.237	0.175	0.31	CLONAL	1	TRUE	1	0.621685554926547	4		137	110	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700241	117700241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	24	376	2	ENST00000368508.3:c.2578G>A	p.Ala860Thr	p.A860T	ENST00000368508	NM_002944.2	860	Gct/Act	17/43	0.282725877855429	0	FACETS	0.273	0.218	0.334			1	INDETERMINATE	1	TRUE	0	0.621685554926547	0		378	107	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710546	117710546	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	55	188	0	ENST00000368508.3:c.1726C>T	p.Gln576Ter	p.Q576*	ENST00000368508	NM_002944.2	576	Caa/Taa	12/43	0.282725877855429	0	FACETS	0.398	0.347	0.452			1	INDETERMINATE	1	TRUE	0	0.621685554926547	0		188	168	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508571	106508571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	185	351	0	ENST00000359195.3:c.565G>A	p.Ala189Thr	p.A189T	ENST00000359195	NM_002649.2	189	Gcc/Acc	2/11	0.621685554926547	8	FACETS	1	0.983	1	0.482	0.447	0.519	CLONAL	2	TRUE	3	0.621685554926547	8		351	707	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27183529	27183529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771578973	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	195	407	0	ENST00000380036.4:c.1103C>T	p.Pro368Leu	p.P368L	ENST00000380036	NM_000459.3	368	cCc/cTc	8/23	0.621685554926547	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.621685554926547	1		407	320	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923393	36923394	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	273	567	0	ENST00000358127.4:c.868_869delinsAA	p.Gly290Lys	p.G290K	ENST00000358127	NM_001280556.1	290	GGg/AAg	7/10	0.621685554926547	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.621685554926547	1		567	519	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250509	110250509	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	305	433	0	ENST00000374672.4:c.166C>T	p.Pro56Ser	p.P56S	ENST00000374672	NM_004235.4	56	Cca/Tca	3/5	0.451906114136876	4	FACETS	1	0.991	1	0.798	0.758	0.838	CLONAL	2	TRUE	1	0.621685554926547	4		433	665	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907621	76907621	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	26	224	0	ENST00000373344.5:c.4540C>T	p.Arg1514Ter	p.R1514*	ENST00000373344	NM_000489.3	1514	Cga/Tga	15/35	1	2	FACETS	0.471	0.372	0.585	0.471	0.372	0.585	SUBCLONAL	1	TRUE	1	0.24	2		224	460	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845724	68845725	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	53	245	0	ENST00000261769.5:c.970_971insT	p.Gly324ValfsTer26	p.G324Vfs*26	ENST00000261769	NM_004360.3	324	gga/gTga	7/16	1	2	FACETS	0.901	0.769	1	0.901	0.769	1	CLONAL	1	TRUE	1	0.24	2		245	490	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713524	30713524	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	74	302	0	ENST00000295754.5:c.849del	p.Glu283AspfsTer17	p.E283Dfs*17	ENST00000295754	NM_003242.5	283	gaG/ga	4/7	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.24	2		302	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0046149-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	27	826	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.3	2	FACETS	0.363	0.287	0.45			1	SUBCLONAL	1	TRUE	NA	0.17	2		826	875	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604706	48604706	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046149-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	40	688	1	ENST00000342988.3:c.1528G>T	p.Gly510Ter	p.G510*	ENST00000342988	NM_005359.5	510	Gga/Tga	12/12	1	2	FACETS	0.542	0.448	0.646	0.542	0.448	0.646	SUBCLONAL	1	TRUE	1	0.17	2		689	869	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0046149-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	40	334	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.962	0.799	1	0.962	0.799	1	CLONAL	1	TRUE	1	0.17	2		334	489	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435160	18435160	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046149-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	53	556	0	ENST00000266497.5:c.145G>T	p.Gly49Cys	p.G49C	ENST00000266497		49	Ggc/Tgc	1/31	1	2	FACETS	0.864	0.735	1	0.864	0.735	1	CLONAL	1	TRUE	1	0.17	2		556	722	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479162	50479162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046149-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	39	598	0	ENST00000394963.4:c.10C>T	p.Arg4Trp	p.R4W	ENST00000394963	NM_003076.4	4	Cgg/Tgg	1/13	1	2	FACETS	0.806	0.667	0.962	0.806	0.667	0.962	CLONAL	1	TRUE	1	0.17	2		598	569	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112372	115112372	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046149-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	42	747	0	ENST00000257566.3:c.1368C>A	p.Ser456Arg	p.S456R	ENST00000257566	NM_016569.3	456	agC/agA	7/8	1	2	FACETS	0.735	0.612	0.872	0.735	0.612	0.872	SUBCLONAL	1	TRUE	1	0.17	2		747	672	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916142	9916142	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519552	NA	P-0046149-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	57	636	0	ENST00000330684.3:c.2147C>A	p.Ala716Asp	p.A716D	ENST00000330684	NM_001134407.1	716	gCc/gAc	10/13	1	2	FACETS	0.838	0.718	0.971	0.838	0.718	0.971	CLONAL	1	TRUE	1	0.17	2		636	800	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31495424	31495424	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046149-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	75	523	0	ENST00000344624.3:c.1724G>T	p.Arg575Leu	p.R575L	ENST00000344624		575	cGg/cTg	9/33	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.17	2		523	816	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502652	149502652	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046149-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	41	674	1	ENST00000261799.4:c.2136C>A	p.Ser712Arg	p.S712R	ENST00000261799	NM_002609.3	712	agC/agA	15/23	1	2	FACETS	0.594	0.493	0.707	0.594	0.493	0.707	SUBCLONAL	1	TRUE	1	0.17	2		675	812	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048693	180048693	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046149-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	51	749	0	ENST00000261937.6:c.1869C>G	p.Ser623Arg	p.S623R	ENST00000261937	NM_182925.4	623	agC/agG	13/30	1	2	FACETS	0.788	0.669	0.921	0.788	0.669	0.921	CLONAL	1	TRUE	1	0.17	2		749	761	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061334	38061334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046826-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	183	697	1	ENST00000250448.2:c.655C>A	p.Arg219Ser	p.R219S	ENST00000250448	NM_004496.3	219	Cgc/Agc	2/2	0.196875397364187	3	FACETS	0.771	0.717	0.825	0.771	0.717	0.825	INDETERMINATE	2	TRUE	1	0.611595402024311	3		698	507	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16001793	16001793	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0046826-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	124	427	0	ENST00000268712.3:c.2708C>G	p.Ser903Ter	p.S903*	ENST00000268712	NM_006311.3	903	tCa/tGa	21/46	0.389000375396927	3	FACETS	1	0.982	1	0.654	0.597	0.713	CLONAL	1	TRUE	1	0.611595402024311	3		427	405	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372259	55372270	+	inframe_deletion	In_Frame_Del	DEL	CACCAGCACCAG	CACCAGCACCAG	-	rs564144826	NA	P-0046826-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	29	436	0	ENST00000297316.4:c.966_977del	p.Gln322_His325del	p.Q322_H325del	ENST00000297316	NM_022454.3	317	CACCAGCACCAG/-	2/2	1	2	FACETS	0.593	0.481	0.716	0.593	0.481	0.716	SUBCLONAL	1	TRUE	1	0.611595402024311	2		436	160	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574014	7574014	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1064796401	NA	P-0046826-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	100	626	0	ENST00000269305.4:c.1013T>C	p.Phe338Ser	p.F338S	ENST00000269305	NM_001126112.2	338	tTc/tCc	10/11	0.471160548046894	1	FACETS	0.805	0.73	0.883	0.805	0.73	0.883	CLONAL	1	TRUE	0	0.611595402024311	1		626	282	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923143	48923144	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTT	novel	NA	P-0046826-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	82	239	0	ENST00000267163.4:c.594_596dup	p.Phe198dup	p.F198dup	ENST00000267163	NM_000321.2	198	-/TTT	6/27	0.289805700828133	0	FACETS	0.563	0.508	0.618			1	INDETERMINATE	1	TRUE	0	0.611595402024311	0		239	185	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0047769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	21	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.407	0.313	0.516	0.407	0.313	0.516	SUBCLONAL	1	FALSE	1	0.325706766942626	2		326	317	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266713	198266713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776846119	NA	P-0047769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	35	473	0	ENST00000335508.6:c.2219G>A	p.Gly740Glu	p.G740E	ENST00000335508	NM_012433.2	740	gGa/gAa	15/25	1	2	FACETS	0.507	0.415	0.61	0.507	0.415	0.61	SUBCLONAL	1	FALSE	1	0.325706766942626	2		473	424	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593464	48593465	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0047769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	24	415	0	ENST00000342988.3:c.1217_1218del	p.Ala406GlyfsTer22	p.A406Gfs*22	ENST00000342988	NM_005359.5	405	caCGcg/cacg	10/12	1	2	FACETS	0.387	0.303	0.484	0.387	0.303	0.484	SUBCLONAL	1	FALSE	1	0.325706766942626	2		415	381	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266139	+	missense_variant	Missense_Mutation	TNP	CTC	CTC	TCT	novel	NA	P-0047769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	23	293	0	ENST00000349496.5:c.134_136delinsTCT	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCTCtg/tTCTtg	3/15	1	2	FACETS	0.432	0.337	0.542	0.432	0.337	0.542	SUBCLONAL	1	FALSE	1	0.325706766942626	2		293	327	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582131	52582131	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	121	286	0	ENST00000394830.3:c.4697T>A	p.Met1566Lys	p.M1566K	ENST00000394830	NM_018313.4	1566	aTg/aAg	30/30	0.567031648948331	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.567031648948331	1		286	264	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0048486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	1323	743	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	NA	2	FACETS	1	0.997	1			1	INDETERMINATE	2	TRUE	NA	0.728147232300032	2		743	1695	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0048486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	49	105	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.728147232300032	2		105	114	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0048889-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	225	278	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.230404440089697	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.230404440089697	3		278	964	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252988	36252988	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048889-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	87	686	0	ENST00000300305.3:c.374del	p.Pro125GlnfsTer8	p.P125Qfs*8	ENST00000300305		125	cCa/ca	4/8	0.230404440089697	3	FACETS	0.849	0.75	0.956	0.424	0.375	0.478	CLONAL	1	TRUE	1	0.230404440089697	3		686	992	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577579	7577579	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0048889-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	112	630	0	ENST00000269305.4:c.702C>G	p.Tyr234Ter	p.Y234*	ENST00000269305	NM_001126112.2	234	taC/taG	7/11	0.230404440089697	1	FACETS	0.986	0.887	1	0.986	0.887	1	CLONAL	1	TRUE	0	0.230404440089697	1		630	872	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627538	14627538	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048889-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	106	694	0	ENST00000254322.2:c.532G>T	p.Gly178Cys	p.G178C	ENST00000254322	NM_006145.1	178	Ggc/Tgc	2/3	1	2	FACETS	0.979	0.876	1	0.979	0.876	1	CLONAL	1	TRUE	1	0.230404440089697	2		694	940	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645700	215645700	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793050	NA	P-0048889-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	50	639	0	ENST00000260947.4:c.898C>T	p.Pro300Ser	p.P300S	ENST00000260947	NM_000465.2	300	Cct/Tct	4/11	1	2	FACETS	0.504	0.426	0.59	0.504	0.426	0.59	SUBCLONAL	1	TRUE	1	0.230404440089697	2		639	862	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0049537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	268	973	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.632827193693998	1	FACETS	0.977	0.926	1	0.977	0.926	1	CLONAL	1	TRUE	0	0.663311865996956	1		973	553	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0049537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	136	425	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.655753079556773	2	FACETS	0.951	0.873	1	0.476	0.436	0.517	CLONAL	1	TRUE	0	0.663311865996956	2		426	431	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374317	31374317	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	169	531	0	ENST00000328111.2:c.316C>T	p.Arg106Ter	p.R106*	ENST00000328111	NM_006892.3	106	Cga/Tga	5/23	1	2	FACETS	0.916	0.848	0.987	0.916	0.848	0.987	CLONAL	1	TRUE	1	0.663311865996956	2		531	556	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982345	201982346	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	302	630	0	ENST00000359651.3:c.725dup	p.His242GlnfsTer59	p.H242Qfs*59	ENST00000359651		242	cac/cAac	6/8	0.663311865996956	2	FACETS	1	0.985	1	0.556	0.526	0.587	CLONAL	1	TRUE	0	0.663311865996956	2		630	819	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440961	56440961	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	211	496	0	ENST00000407977.2:c.376G>C	p.Ala126Pro	p.A126P	ENST00000407977		126	Gct/Cct	4/10	0.663311865996956	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.663311865996956	1		496	415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0049639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	324	622	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.462162225273717	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.484683855938387	4		623	958	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0049639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	338	570	1	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	0.462162225273717	4	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	2	0.484683855938387	4		571	1035	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332868	152332868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745723014	NA	P-0049639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	68	415	0	ENST00000206249.3:c.1174G>A	p.Val392Ile	p.V392I	ENST00000206249	NM_000125.3	392	Gtc/Atc	5/8	0.484683855938387	3	FACETS	0.74	0.645	0.842	0.37	0.322	0.421	SUBCLONAL	1	TRUE	1	0.484683855938387	3		415	471	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	62	258	0	ENST00000263967.3:c.3132T>G	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaG	21/21	0.484683855938387	3	FACETS	0.906	0.787	1	0.453	0.393	0.517	CLONAL	1	TRUE	1	0.484683855938387	3		258	351	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863394	57863394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs533875222	NA	P-0049639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	180	711	1	ENST00000228682.2:c.1489C>T	p.Arg497Cys	p.R497C	ENST00000228682	NM_005269.2	497	Cgc/Tgc	11/12	0.102943524347383	6	FACETS	0.809	0.746	0.874			1	INDETERMINATE	2	TRUE	NA	0.484683855938387	6		712	904	SUCCESS
APC	324	MSKCC	GRCh37	5	112175398	112175399	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	87	224	0	ENST00000257430.4:c.4111dup	p.Ser1371LysfsTer4	p.S1371Kfs*4	ENST00000257430	NM_000038.5	1369	-/A	16/16	0.484683855938387	3	FACETS	0.933	0.84	1	0.933	0.84	1	CLONAL	2	TRUE	1	0.484683855938387	3		224	239	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248232	59248232	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	32	92	1	ENST00000371222.2:c.511G>T	p.Ala171Ser	p.A171S	ENST00000371222	NM_002228.3	171	Gca/Tca	1/1	0.484683855938387	3	FACETS	1	0.881	1	0.547	0.45	0.653	CLONAL	1	TRUE	1	0.484683855938387	3		93	150	SUCCESS
APC	324	MSKCC	GRCh37	5	112175395	112175396	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	42	223	0	ENST00000257430.4:c.4107dup	p.Lys1370GlnfsTer5	p.K1370Qfs*5	ENST00000257430	NM_000038.5	1368	-/C	16/16	0.484683855938387	3	FACETS	0.912	0.768	1	0.456	0.384	0.535	CLONAL	1	TRUE	1	0.484683855938387	3		223	236	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730910	40730910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370873414	NA	P-0049810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	285	716	3	ENST00000373198.4:c.3625C>T	p.Arg1209Trp	p.R1209W	ENST00000373198	NM_133170.3	1209	Cgg/Tgg	27/32	0.1358145833638	5	FACETS	1	0.978	1	0.717	0.676	0.759	INDETERMINATE	2	TRUE	2	0.526082080979312	5		719	901	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488229	56488229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	287	718	0	ENST00000267101.3:c.1748C>T	p.Pro583Leu	p.P583L	ENST00000267101	NM_001982.3	583	cCc/cTc	15/28	0.196592714866471	3	FACETS	1	0.992	1	0.679	0.639	0.72	INDETERMINATE	1	TRUE	1	0.526082080979312	3		718	1015	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226574115	226574115	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	231	599	0	ENST00000366794.5:c.746A>G	p.Lys249Arg	p.K249R	ENST00000366794	NM_001618.3	249	aAg/aGg	6/23	0.526082080979312	3	FACETS	0.995	0.927	1	0.497	0.463	0.533	CLONAL	1	TRUE	1	0.526082080979312	3		599	1115	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630388	47630388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1198168331	NA	P-0049810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	307	816	1	ENST00000233146.2:c.58G>A	p.Val20Met	p.V20M	ENST00000233146	NM_000251.2	20	Gtg/Atg	1/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.526082080979312	2		817	1068	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319907	8319907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	186	550	0	ENST00000356435.5:c.5594G>A	p.Arg1865Lys	p.R1865K	ENST00000356435		1865	aGa/aAa	34/35	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.526082080979312	2		550	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0050017-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	130	1088	1	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.184413499492529	2		1089	1202	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161166	56161166	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0050017-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	50	339	0	ENST00000399503.3:c.1036-1G>A		p.X346_splice	ENST00000399503	NM_005921.1	346			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.184413499492529	2		339	421	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974697	21974697	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050017-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	79	686	0	ENST00000304494.5:c.130del	p.Tyr44ThrfsTer9	p.Y44Tfs*9	ENST00000304494	NM_000077.4	44	Tac/ac	1/3	0.184413499492529	1	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	0	0.184413499492529	1		686	756	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541595	29541595	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050017-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	37	292	0	ENST00000356175.3:c.1520del	p.Leu507CysfsTer19	p.L507Cfs*19	ENST00000356175	NM_000267.3	507	Ttg/tg	13/57	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.184413499492529	2		292	271	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39214646	39214646	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050017-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	56	609	0	ENST00000402219.2:c.3478G>C	p.Glu1160Gln	p.E1160Q	ENST00000402219	NM_005633.3	1160	Gaa/Caa	22/23	1	2	FACETS	0.783	0.669	0.907	0.783	0.669	0.907	CLONAL	1	TRUE	1	0.184413499492529	2		609	776	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415159	109415159	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757998541	NA	P-0050017-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1192	105	973	0	ENST00000436639.2:c.118C>T	p.Arg40Cys	p.R40C	ENST00000436639	NM_014454.2	40	Cgt/Tgt	1/10	0.143837752856611	3	FACETS	0.959	0.856	1	0.479	0.428	0.535	CLONAL	1	TRUE	1	0.184413499492529	3		973	1297	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0050976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	70	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.379550700831312	2		336	334	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0050976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	48	304	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.201492796601745	3	FACETS	0.974	0.828	1	0.487	0.414	0.567	INDETERMINATE	1	TRUE	1	0.379550700831312	3		304	309	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644679	134644679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773064927	NA	P-0050976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	88	472	0	ENST00000398015.3:c.80C>T	p.Thr27Met	p.T27M	ENST00000398015	NM_004441.4	27	aCg/aTg	2/16	1	2	FACETS	0.842	0.747	0.942	0.842	0.747	0.942	CLONAL	1	TRUE	1	0.379550700831312	2		472	551	SUCCESS
APC	324	MSKCC	GRCh37	5	112175772	112175772	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	53	289	0	ENST00000257430.4:c.4483del	p.Ser1495ValfsTer12	p.S1495Vfs*12	ENST00000257430	NM_000038.5	1494	gAa/ga	16/16	0.201492796601745	3	FACETS	1	0.955	1	0.646	0.556	0.743	INDETERMINATE	1	TRUE	1	0.379550700831312	3		289	257	SUCCESS
AR	367	MSKCC	GRCh37	X	66941796	66941796	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	77	202	0	ENST00000374690.3:c.2440T>G	p.Phe814Val	p.F814V	ENST00000374690	NM_000044.3	814	Ttc/Gtc	6/8	0.379550700831312	2	FACETS	0.766	0.681	0.854			1	SUBCLONAL	2	TRUE	NA	0.379550700831312	2		202	265	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114917829	114917829	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0050976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	195	500	0	ENST00000543371.1:c.1318+1G>A		p.X440_splice	ENST00000543371	NM_001198531.1	440			0.379550700831312	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.379550700831312	2		500	451	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109690	115109690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1407667924	NA	P-0050976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	163	745	0	ENST00000257566.3:c.2188G>A	p.Gly730Ser	p.G730S	ENST00000257566	NM_016569.3	730	Ggc/Agc	8/8	1	2	FACETS	0.935	0.858	1	0.935	0.858	1	CLONAL	1	TRUE	1	0.379550700831312	2		745	919	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936083	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0050976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	77	422	1	ENST00000263967.3:c.1624_1625delinsTT	p.Glu542Leu	p.E542L	ENST00000263967	NM_006218.2	542	GAa/TTa	10/21	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.379550700831312	2		423	384	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	273	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.388069492043244	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.388069492043244	3		326	815	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0051049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	217	863	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.388069492043244	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.388069492043244	1		863	748	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828155	243828155	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	113	335	0	ENST00000263826.5:c.203A>C	p.Lys68Thr	p.K68T	ENST00000263826	NM_005465.4	68	aAg/aCg	3/13	0.328377185423143	3	FACETS	1	0.96	1	0.562	0.506	0.62	CLONAL	1	TRUE	1	0.388069492043244	3		335	619	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615155	43615155	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	218	667	0	ENST00000355710.3:c.2569C>T	p.Gln857Ter	p.Q857*	ENST00000355710	NM_020975.4	857	Cag/Tag	14/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.388069492043244	2		667	1091	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868346	45868346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776313922	NA	P-0051485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	141	692	0	ENST00000391945.4:c.431C>T	p.Ala144Val	p.A144V	ENST00000391945	NM_000400.3	144	gCg/gTg	6/23	0.139373007611202	5	FACETS	0.8	0.732	0.871	0.533	0.488	0.581	INDETERMINATE	2	TRUE	2	0.539788724084649	5		692	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579350	7579350	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587781642	NA	P-0051485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	217	598	0	ENST00000269305.4:c.337T>G	p.Phe113Val	p.F113V	ENST00000269305	NM_001126112.2	113	Ttc/Gtc	4/11	0.463199508843825	2	FACETS	0.962	0.908	1	0.962	0.908	1	CLONAL	2	TRUE	0	0.539788724084649	2		598	418	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971066	21971068	+	inframe_deletion	In_Frame_Del	DEL	GCA	GCA	-	novel	NA	P-0051485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	111	247	0	ENST00000304494.5:c.290_292del	p.Leu97del	p.L97del	ENST00000304494	NM_000077.4	97	cTGCac/cac	2/3	0.444972189641126	2	FACETS	0.86	0.79	0.931	0.86	0.79	0.931	CLONAL	2	TRUE	0	0.539788724084649	2		247	239	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955118	17955118	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs955716335	NA	P-0051485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	183	669	0	ENST00000458235.1:c.109C>G	p.Pro37Ala	p.P37A	ENST00000458235	NM_000215.3	37	Ccc/Gcc	2/24	0.139373007611202	5	FACETS	1	0.959	1	0.699	0.649	0.751	INDETERMINATE	2	TRUE	2	0.539788724084649	5		669	585	SUCCESS
ATR	545	MSKCC	GRCh37	3	142234320	142234320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	108	296	0	ENST00000350721.4:c.4420G>A	p.Val1474Ile	p.V1474I	ENST00000350721	NM_001184.3	1474	Gta/Ata	25/47	0.444972189641126	2	FACETS	0.955	0.863	1	0.478	0.431	0.526	CLONAL	1	TRUE	0	0.539788724084649	2		296	419	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594031	55594031	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	64	289	0	ENST00000288135.5:c.1817C>T	p.Ala606Val	p.A606V	ENST00000288135	NM_000222.2	606	gCa/gTa	12/21	0.461063946914242	2	FACETS	0.653	0.569	0.744	0.327	0.284	0.372	SUBCLONAL	1	TRUE	0	0.539788724084649	2		289	363	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0051731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	19	189	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.649	0.494	0.829	0.649	0.494	0.829	SUBCLONAL	1	TRUE	1	0.29	2		189	202	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020351	69020351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201443824	NA	P-0051731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	35	355	0	ENST00000288368.4:c.2723G>A	p.Arg908His	p.R908H	ENST00000288368	NM_024870.2	908	cGt/cAt	24/40	1	2	FACETS	0.789	0.649	0.945	0.789	0.649	0.945	CLONAL	1	TRUE	1	0.29	2		355	306	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11227561	11227561	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	48	386	0	ENST00000361445.4:c.4267C>A	p.Leu1423Ile	p.L1423I	ENST00000361445	NM_004958.3	1423	Cta/Ata	29/58	1	2	FACETS	0.817	0.692	0.954	0.817	0.692	0.954	CLONAL	1	TRUE	1	0.29	2		386	405	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288452	15288452	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	41	407	0	ENST00000263388.2:c.4287G>T	p.Glu1429Asp	p.E1429D	ENST00000263388	NM_000435.2	1429	gaG/gaT	24/33	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.29	2		407	238	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288457	21288457	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	84	504	0	ENST00000354336.3:c.702G>T	p.Gln234His	p.Q234H	ENST00000354336	NM_005207.3	234	caG/caT	2/3	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.29	2		504	408	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27172713	27172713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	62	447	1	ENST00000380036.4:c.728C>T	p.Pro243Leu	p.P243L	ENST00000380036	NM_000459.3	243	cCt/cTt	5/23	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.29	2		448	397	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644668	134644668	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051781-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	34	661	1	ENST00000398015.3:c.69G>T	p.Met23Ile	p.M23I	ENST00000398015	NM_004441.4	23	atG/atT	2/16	1	2	FACETS	0.926	0.755	1	0.926	0.755	1	CLONAL	1	TRUE	1	0.12	2		662	612	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846083	68846083	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051781-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	60	888	0	ENST00000261769.5:c.1054G>C	p.Gly352Arg	p.G352R	ENST00000261769	NM_004360.3	352	Ggt/Cgt	8/16	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.12	2		888	964	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058708	47058714	+	frameshift_variant	Frame_Shift_Del	DEL	AGTACTT	AGTACTT	-	novel	NA	P-0051781-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	39	580	0	ENST00000409792.3:c.7564_7570del	p.Lys2522ValfsTer13	p.K2522Vfs*13	ENST00000409792	NM_014159.6	2522	AAGTACTgt/gt	21/21	1	2	FACETS	0.875	0.723	1	0.875	0.723	1	CLONAL	1	TRUE	1	0.12	2		580	743	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155465	47155465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051781-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	32	373	0	ENST00000409792.3:c.4616G>A	p.Cys1539Tyr	p.C1539Y	ENST00000409792	NM_014159.6	1539	tGt/tAt	5/21	1	2	FACETS	0.959	0.777	1	0.959	0.777	1	CLONAL	1	TRUE	1	0.12	2		373	556	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43699645	43699645	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1044525239	NA	P-0052568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	72	493	0	ENST00000382044.4:c.5870T>C	p.Ile1957Thr	p.I1957T	ENST00000382044	NM_001141980.1	1957	aTt/aCt	28/28	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.221665204949061	2		493	628	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0052575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	120	435	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.467949001521164	2		435	457	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31015992	31015992	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749495615	NA	P-0052575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	183	544	0	ENST00000375687.4:c.314C>T	p.Thr105Met	p.T105M	ENST00000375687	NM_015338.5	105	aCg/aTg	5/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.467949001521164	2		544	732	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231202	46231202	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0052575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	63	326	0	ENST00000334344.6:c.1120+2T>G		p.X374_splice	ENST00000334344	NM_152641.2	374			1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.467949001521164	2		326	262	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761034	59761074	+	frameshift_variant	Frame_Shift_Del	DEL	CTTCTGTTTCAAAATCTCTATTTGAAGTGGACTGTTTATCT	CTTCTGTTTCAAAATCTCTATTTGAAGTGGACTGTTTATCT	-	novel	NA	P-0052575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	65	533	0	ENST00000259008.2:c.3333_3373del	p.Glu1111AspfsTer4	p.E1111Dfs*4	ENST00000259008	NM_032043.2	1111	gaAGATAAACAGTCCACTTCAAATAGAGATTTTGAAACAGAAGca/gaca	20/20	1	2	FACETS	0.601	0.523	0.686	0.601	0.523	0.686	SUBCLONAL	1	TRUE	1	0.467949001521164	2		533	462	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356229	66356229	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	166	591	0	ENST00000273854.3:c.1268A>T	p.Asn423Ile	p.N423I	ENST00000273854	NM_004439.5	423	aAc/aTc	5/18	0.467949001521164	1	FACETS	0.99	0.915	1	0.99	0.915	1	CLONAL	1	TRUE	0	0.467949001521164	1		591	549	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522557	157522558	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0052575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	36	739	0	ENST00000346085.5:c.4829_4830del	p.Pro1610ArgfsTer25	p.P1610Rfs*25	ENST00000346085	NM_020732.3	1610	cCT/c	18/20	0.467949001521164	1	FACETS	0.166	0.135	0.2	0.166	0.135	0.2	SUBCLONAL	1	TRUE	0	0.467949001521164	1		739	711	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052853-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	99	300	0				ENST00000310581	NM_198253.2	-/1132			0.287884995384498	4	FACETS	0.807	0.726	0.891	0.807	0.726	0.891	INDETERMINATE	2	TRUE	2	0.49226530426453	4		300	372	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052853-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	140	234	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	1	1	FACETS	0.831	0.774	0.887	1	0.991	1	CLONAL	2	TRUE	0	0.49226530426453	1		234	258	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578513	7578513	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052853-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	126	629	0	ENST00000269305.4:c.417G>C	p.Lys139Asn	p.K139N	ENST00000269305	NM_001126112.2	139	aaG/aaC	5/11	0.172251172925592	1	FACETS	0.889	0.812	0.97	0.889	0.812	0.97	INDETERMINATE	1	TRUE	0	0.49226530426453	1		629	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0052853-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	74	550	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	0.172251172925592	1	FACETS	0.482	0.423	0.545	0.482	0.423	0.545	INDETERMINATE	1	TRUE	0	0.49226530426453	1		550	470	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0052853-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	64	512	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	0.390065373079816	2	FACETS	0.584	0.507	0.667	0.292	0.253	0.334	SUBCLONAL	1	TRUE	0	0.49226530426453	2		512	445	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030378	49030378	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs267603840	NA	P-0052853-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	233	404	0	ENST00000267163.4:c.1853C>A	p.Ser618Ter	p.S618*	ENST00000267163	NM_000321.2	618	tCa/tAa	19/27	0.471406543376713	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.49226530426453	2		404	454	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670622	67670622	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052853-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	92	508	0	ENST00000264010.4:c.1867G>T	p.Glu623Ter	p.E623*	ENST00000264010	NM_006565.3	623	Gag/Tag	11/12	1	2	FACETS	0.918	0.821	1	0.918	0.821	1	CLONAL	1	TRUE	1	0.49226530426453	2		508	407	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309740	104309740	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052853-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	53	431	0	ENST00000369902.3:c.331G>C	p.Asp111His	p.D111H	ENST00000369902	NM_016169.3	111	Gat/Cat	3/12	0.271424475236909	1	FACETS	0.442	0.378	0.512	0.442	0.378	0.512	INDETERMINATE	1	TRUE	0	0.49226530426453	1		431	367	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024678	14024678	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052853-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	79	374	0	ENST00000311895.7:c.904G>C	p.Asp302His	p.D302H	ENST00000311895	NM_005236.2	302	Gat/Cat	5/11	0.49226530426453	5	FACETS	0.791	0.696	0.894	0.264	0.232	0.298	SUBCLONAL	1	TRUE	2	0.49226530426453	5		374	705	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244528	41244528	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs80357168	NA	P-0052853-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	66	523	0	ENST00000357654.3:c.3020C>G	p.Ser1007Ter	p.S1007*	ENST00000357654	NM_007294.3	1007	tCa/tGa	10/23	0.264323961958707	3	FACETS	0.583	0.506	0.666	0.194	0.168	0.222	INDETERMINATE	1	TRUE	0	0.49226530426453	3		523	573	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39567798	39567798	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052853-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	50	354	0	ENST00000262039.4:c.554G>A	p.Gly185Glu	p.G185E	ENST00000262039	NM_002647.2	185	gGa/gAa	5/25	0.460058941103971	3	FACETS	0.475	0.403	0.554	0.237	0.201	0.277	SUBCLONAL	1	TRUE	1	0.49226530426453	3		354	533	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030613	11030613	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052853-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	48	575	0	ENST00000327064.4:c.1167C>G	p.Phe389Leu	p.F389L	ENST00000327064	NM_199141.1	389	ttC/ttG	10/16	1	2	FACETS	0.48	0.407	0.561	0.48	0.407	0.561	SUBCLONAL	1	TRUE	1	0.49226530426453	2		575	406	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740561	145740561	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs768311526	NA	P-0052853-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	42	682	0	ENST00000428558.2:c.1456G>C	p.Glu486Gln	p.E486Q	ENST00000428558	NM_004260.3	486	Gag/Cag	8/22	0.275202964278807	4	FACETS	0.385	0.32	0.456	0.192	0.16	0.228	INDETERMINATE	1	TRUE	2	0.49226530426453	4		682	662	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231488731	231488731	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1318779022	NA	P-0052853-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	67	519	0	ENST00000295050.7:c.1094C>T	p.Ser365Phe	p.S365F	ENST00000295050	NM_032018.5	365	tCt/tTt	5/5	0.225527156983677	3	FACETS	0.695	0.605	0.792	0.232	0.201	0.264	INDETERMINATE	1	TRUE	0	0.49226530426453	3		519	488	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61305042	61305042	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052853-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	53	494	0	ENST00000341074.5:c.1084G>C	p.Glu362Gln	p.E362Q	ENST00000341074	NM_002974.2	362	Gag/Cag	8/8	0.460058941103971	3	FACETS	0.502	0.428	0.583	0.251	0.214	0.292	SUBCLONAL	1	TRUE	1	0.49226530426453	3		494	535	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61308179	61308179	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052853-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	25	133	0	ENST00000341074.5:c.398C>G	p.Ser133Cys	p.S133C	ENST00000341074	NM_002974.2	133	tCt/tGt	5/8	0.460058941103971	3	FACETS	0.753	0.599	0.927	0.377	0.299	0.464	CLONAL	1	TRUE	1	0.49226530426453	3		133	168	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2087011	2087011	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052853-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	230	537	0	ENST00000349721.2:c.2709T>G	p.Phe903Leu	p.F903L	ENST00000349721	NM_003070.3	903	ttT/ttG	18/34	0.34708760923381	2	FACETS	0.882	0.83	0.934	0.882	0.83	0.934	CLONAL	2	TRUE	0	0.49226530426453	2		537	530	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054215-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	102	456	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.17008690737631	3	FACETS	1	0.934	1	0.525	0.472	0.58	INDETERMINATE	1	TRUE	1	0.566882960434801	3		456	440	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160646	56160656	+	frameshift_variant	Frame_Shift_Del	DEL	GTGTTAACAAA	GTGTTAACAAA	-	novel	NA	P-0054215-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	236	643	0	ENST00000399503.3:c.923_933del	p.Val308AspfsTer14	p.V308Dfs*14	ENST00000399503	NM_005921.1	307	cGTGTTAACAAA/c	4/20	0.566882960434801	2	FACETS	0.925	0.876	0.974	0.925	0.876	0.974	CLONAL	2	TRUE	0	0.566882960434801	2		643	450	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402227	402227	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054215-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	187	375	0	ENST00000399788.2:c.4564C>G	p.Gln1522Glu	p.Q1522E	ENST00000399788	NM_001042603.1	1522	Cag/Gag	27/28	0.566882960434801	3	FACETS	0.951	0.889	1	0.951	0.889	1	CLONAL	2	TRUE	1	0.566882960434801	3		375	445	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358566	67358566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054215-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	138	762	1	ENST00000327367.4:c.74G>A	p.Gly25Glu	p.G25E	ENST00000327367	NM_005902.3	25	gGg/gAg	1/9	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.566882960434801	2		763	449	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218569	98218569	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054215-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	142	645	0	ENST00000331920.6:c.3295C>A	p.His1099Asn	p.H1099N	ENST00000331920	NM_000264.3	1099	Cac/Aac	19/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.566882960434801	2		645	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0055111-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	95	624	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.670196419129679	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.666211734358735	2		624	123	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402764	139402764	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758471372	NA	P-0056507-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	191	540	0	ENST00000277541.6:c.3245G>A	p.Arg1082His	p.R1082H	ENST00000277541	NM_017617.3	1082	cGc/cAc	20/34	1	2	FACETS	1	0.978	1	1	0.994	1	CLONAL	2	TRUE	1	0.29	2		540	587	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37680982	37680982	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	17	659	0	ENST00000447079.4:c.3151C>T	p.Arg1051Ter	p.R1051*	ENST00000447079	NM_015083.1	1051	Cga/Tga	12/14	0.364561205141144	1	FACETS	0.169	0.125	0.22	0.169	0.125	0.22	SUBCLONAL	1	TRUE	0	0.475936865624846	1		659	323	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39311716	39311716	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs779345543	NA	P-0057893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	49	434	0	ENST00000373001.3:c.943A>G	p.Met315Val	p.M315V	ENST00000373001	NM_022157.3	315	Atg/Gtg	6/7	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.475936865624846	2		434	183	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69210607	69210607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	35	306	0	ENST00000462284.1:c.190G>A	p.Gly64Ser	p.G64S	ENST00000462284	NM_002392.5	64	Ggc/Agc	4/11	0.364561205141144	1	FACETS	0.747	0.622	0.883	0.747	0.622	0.883	SUBCLONAL	1	TRUE	0	0.475936865624846	1		306	150	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022411	31022411	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	157	763	1	ENST00000375687.4:c.1897del	p.His633IlefsTer70	p.H633Ifs*70	ENST00000375687	NM_015338.5	632	tgC/tg	13/13	0.464416121208626	4	FACETS	0.992	0.915	1	0.661	0.61	0.713	CLONAL	2	TRUE	1	0.475936865624846	4		764	491	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709023	117709023	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057893-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	77	579	0	ENST00000368508.3:c.1934A>G	p.Tyr645Cys	p.Y645C	ENST00000368508	NM_002944.2	645	tAc/tGc	13/43	0.121722077079236	5	FACETS	1	0.972	1	0.458	0.404	0.515	INDETERMINATE	1	TRUE	2	0.475936865624846	5		579	404	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0058139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	210	542	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.579385348319454	2		542	522	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916838	178916838	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	95	566	0	ENST00000263967.3:c.225A>C	p.Gln75His	p.Q75H	ENST00000263967	NM_006218.2	75	caA/caC	2/21	1	2	FACETS	0.834	0.748	0.925	0.834	0.748	0.925	CLONAL	1	TRUE	1	0.579385348319454	2		566	393	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453148	140453148	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs397507483	NA	P-0058139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	73	487	0	ENST00000288602.6:c.1787G>T	p.Gly596Val	p.G596V	ENST00000288602	NM_004333.4	596	gGt/gTt	15/18	1	2	FACETS	0.726	0.64	0.818	0.726	0.64	0.818	SUBCLONAL	1	TRUE	1	0.579385348319454	2		487	347	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802587	135802587	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs118203348	NA	P-0058139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	167	492	0	ENST00000298552.3:c.210+1G>A		p.X70_splice	ENST00000298552	NM_001162426.1	70			0.579385348319454	1	FACETS	0.982	0.913	1	0.982	0.913	1	CLONAL	1	TRUE	0	0.579385348319454	1		492	417	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652006	36652007	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0058139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	223	654	0	ENST00000244741.5:c.130dup	p.Glu44GlyfsTer4	p.E44Gfs*4	ENST00000244741	NM_000389.4	43	cag/caGg	2/3	1	2	FACETS	0.935	0.873	1	0.935	0.873	1	CLONAL	1	TRUE	1	0.579385348319454	2		654	823	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894230	NA	P-0058139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	208	619	0	ENST00000451590.1:c.35G>A	p.Gly12Asp	p.G12D	ENST00000451590	NM_001130442.1	12	gGc/gAc	2/5	1	2	FACETS	0.954	0.888	1	0.954	0.888	1	CLONAL	1	TRUE	1	0.579385348319454	2		619	753	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094448	27094449	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0058139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	262	621	0	ENST00000324856.7:c.3156_3157insAG	p.Arg1053SerfsTer7	p.R1053Sfs*7	ENST00000324856	NM_006015.4	1052	-/AG	11/20	1	2	FACETS	0.969	0.91	1	0.969	0.91	1	CLONAL	1	TRUE	1	0.579385348319454	2		621	933	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098916	178098917	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAA	novel	NA	P-0058139-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	67	515	0	ENST00000397062.3:c.128_129insTTT	p.Arg43_Lys44insLeu	p.R43_K44insL	ENST00000397062	NM_006164.4	43	cgg/cgTTTg	2/5	0.138836012002064	0	FACETS	0.241	0.21	0.275			1	INDETERMINATE	1	TRUE	0	0.579385348319454	0		515	403	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144148	55144148	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519700	NA	P-0058889-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	153	523	0	ENST00000257290.5:c.1977C>G	p.Asn659Lys	p.N659K	ENST00000257290	NM_006206.4	659	aaC/aaG	14/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.590703745103368	2		523	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0059005-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	79	718	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	1	2	FACETS	0.868	0.763	0.982	0.868	0.763	0.982	CLONAL	1	TRUE	1	0.22	2		718	827	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0059005-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	13	326	1	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	1	0.787	1	1	0.787	1	CLONAL	1	TRUE	1	0.22	2		327	106	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971029	21971029	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519852	NA	P-0059005-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	52	601	0	ENST00000304494.5:c.329G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tGg/tAg	2/3	1	2	FACETS	0.671	0.571	0.783	0.671	0.571	0.783	SUBCLONAL	1	TRUE	1	0.22	2		601	704	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844247	68844247	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	G	rs1555515469	NA	P-0059005-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	30	461	0	ENST00000261769.5:c.832+3A>G		p.X278_splice	ENST00000261769	NM_004360.3	278			1	2	FACETS	0.585	0.471	0.715	0.585	0.471	0.715	SUBCLONAL	1	TRUE	1	0.22	2		461	466	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168977	11168977	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs758517117	NA	P-0059005-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	39	499	0	ENST00000358026.2:c.4567C>T	p.Arg1523Ter	p.R1523*	ENST00000358026	NM_001128849.1	1523	Cga/Tga	32/36	1	2	FACETS	0.589	0.487	0.703	0.589	0.487	0.703	SUBCLONAL	1	TRUE	1	0.22	2		499	602	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059250-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	53	425	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.24035639618143	2		426	348	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492938	56492938	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0059250-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	71	609	0	ENST00000407977.2:c.1A>G	p.Met1?	p.M1?	ENST00000407977		1	Atg/Gtg	2/10	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.24035639618143	2		609	504	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437664	49437664	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059250-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	72	790	0	ENST00000301067.7:c.5306C>T	p.Pro1769Leu	p.P1769L	ENST00000301067	NM_003482.3	1769	cCt/cTt	22/54	1	2	FACETS	0.954	0.834	1	0.954	0.834	1	CLONAL	1	TRUE	1	0.24035639618143	2		790	628	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395894	395894	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059250-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	66	671	0	ENST00000380956.4:c.451C>A	p.Pro151Thr	p.P151T	ENST00000380956	NM_001195286.1	151	Ccc/Acc	4/9	0.24035639618143	1	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	0	0.24035639618143	1		671	474	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0059255-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	314	449	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	0.493154835044879	9	FACETS	1	0.982	1	0.762	0.725	0.799	CLONAL	5	TRUE	2	0.493154835044879	9		449	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0059265-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	102	275	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.124496096679539	3	FACETS	1	0.925	1	0.69	0.62	0.763	INDETERMINATE	2	TRUE	0	0.242300007381912	3		275	456	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023307	27023307	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0059265-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	56	220	0	ENST00000324856.7:c.413C>G	p.Ser138Ter	p.S138*	ENST00000324856	NM_006015.4	138	tCa/tGa	1/20	0.124496096679539	3	FACETS	0.762	0.656	0.876	0.508	0.437	0.584	INDETERMINATE	2	TRUE	0	0.242300007381912	3		220	340	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0059265-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	40	522	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.228089222623657	1	FACETS	0.746	0.621	0.885	0.746	0.621	0.885	SUBCLONAL	1	TRUE	0	0.242300007381912	1		522	389	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006864	47006864	+	5_prime_UTR_variant	5'UTR	SNP	G	G	A	novel	NA	P-0059265-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	26	238	0	ENST00000377604.3:c.-17G>A		p.*6*	ENST00000377604	NM_001204468.1	-/852		2/24	1	2	FACETS	0.582	0.46	0.72	0.582	0.46	0.72	SUBCLONAL	1	TRUE	1	0.242300007381912	2		238	369	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016605	12016605	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059265-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	54	161	0	ENST00000353533.5:c.741C>G	p.Asp247Glu	p.D247E	ENST00000353533	NM_003010.3	247	gaC/gaG	7/11	0.124496096679539	3	FACETS	0.929	0.8	1	0.619	0.533	0.712	INDETERMINATE	2	TRUE	0	0.242300007381912	3		161	269	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985852	60985852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776360417	NA	P-0059265-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	22	257	0	ENST00000333681.4:c.48G>A	p.Met16Ile	p.M16I	ENST00000333681		16	atG/atA	2/3	1	2	FACETS	0.469	0.363	0.593	0.469	0.363	0.593	SUBCLONAL	1	TRUE	1	0.242300007381912	2		257	387	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624823	9624823	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059265-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	25	199	0	ENST00000353224.5:c.154C>A	p.Pro52Thr	p.P52T	ENST00000353224	NM_177990.2	52	Cct/Act	3/10	0.242300007381912	3	FACETS	0.552	0.434	0.688	0.184	0.144	0.23	SUBCLONAL	1	TRUE	0	0.242300007381912	3		199	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0059699-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	23	629	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.91	0.709	1	0.91	0.709	1	CLONAL	1	TRUE	1	0.14	2		630	361	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0059910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	14	326	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.136675782241199	3	FACETS	1	0.765	1	0.531	0.385	0.707	CLONAL	1	TRUE	1	0.16	3		326	178	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0059910-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	31	586	1	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	1	2	FACETS	0.823	0.665	1	0.823	0.665	1	CLONAL	1	TRUE	1	0.16	2		587	471	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0059911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	20	611	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.551	0.422	0.702	0.551	0.422	0.702	SUBCLONAL	1	FALSE	1	0.266904112119306	2		611	272	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0059911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	24	278	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.52	0.407	0.649	0.52	0.407	0.649	SUBCLONAL	1	FALSE	1	0.266904112119306	2		278	346	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279674	123279674	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs77543610	NA	P-0059911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	50	591	0	ENST00000358487.5:c.758C>G	p.Pro253Arg	p.P253R	ENST00000358487	NM_000141.4	253	cCt/cGt	7/18	1	2	FACETS	0.763	0.648	0.89	0.763	0.648	0.89	SUBCLONAL	1	FALSE	1	0.266904112119306	2		591	491	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650710	67650710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243010179	NA	P-0059911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	46	447	0	ENST00000264010.4:c.1015C>T	p.Arg339Trp	p.R339W	ENST00000264010	NM_006565.3	339	Cgg/Tgg	5/12	1	2	FACETS	0.645	0.543	0.758	0.645	0.543	0.758	SUBCLONAL	1	FALSE	1	0.266904112119306	2		447	534	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100934	27100934	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	58	576	0	ENST00000324856.7:c.4220del	p.Pro1407GlnfsTer74	p.P1407Qfs*74	ENST00000324856	NM_006015.4	1406	Ccc/cc	18/20	0.167616448477223	2	FACETS	1	0.934	1	0.57	0.492	0.655	CLONAL	1	FALSE	0	0.266904112119306	2		576	381	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217705	7217707	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs757139280	NA	P-0059911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	28	538	0	ENST00000380728.2:c.220_222del	p.Glu74del	p.E74del	ENST00000380728		74	GAG/-	4/11	1	2	FACETS	0.394	0.314	0.485	0.394	0.314	0.485	SUBCLONAL	1	FALSE	1	0.266904112119306	2		538	533	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416417	49416417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565753611	NA	P-0059911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	37	503	0	ENST00000301067.7:c.16294C>T	p.Arg5432Trp	p.R5432W	ENST00000301067	NM_003482.3	5432	Cgg/Tgg	51/54	1	2	FACETS	0.713	0.588	0.852	0.713	0.588	0.852	SUBCLONAL	1	FALSE	1	0.266904112119306	2		503	389	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514831	44514831	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	46	562	0	ENST00000291552.4:c.416C>T	p.Pro139Leu	p.P139L	ENST00000291552	NM_006758.2	139	cCg/cTg	6/8	1	2	FACETS	0.746	0.629	0.875	0.746	0.629	0.875	SUBCLONAL	1	FALSE	1	0.266904112119306	2		562	462	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627191	86627191	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	39	475	0	ENST00000274376.6:c.566del	p.Thr189ArgfsTer2	p.T189Rfs*2	ENST00000274376	NM_002890.2	189	aCg/ag	2/25	1	2	FACETS	0.699	0.58	0.832	0.699	0.58	0.832	SUBCLONAL	1	FALSE	1	0.266904112119306	2		475	418	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659181	86659181	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	21	205	0	ENST00000274376.6:c.1470G>C	p.Trp490Cys	p.W490C	ENST00000274376	NM_002890.2	490	tgG/tgC	11/25	1	2	FACETS	0.658	0.508	0.832	0.658	0.508	0.832	SUBCLONAL	1	FALSE	1	0.266904112119306	2		205	239	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466029	69466038	+	protein_altering_variant	In_Frame_Del	DEL	CGTGCGGGAC	CGTGCGGGAC	G	novel	NA	P-0059911-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	27	616	0	ENST00000227507.2:c.867_876delinsG	p.Asp289_Asp292delinsGlu	p.D289_D292delinsE	ENST00000227507	NM_053056.2	289	gaCGTGCGGGAC/gaG	5/5	1	2	FACETS	0.456	0.362	0.563	0.456	0.362	0.563	SUBCLONAL	1	FALSE	1	0.266904112119306	2		616	444	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0059912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	147	542	0				ENST00000310581	NM_198253.2	-/1132			0.345298924500285	3	FACETS	1	0.949	1	1	0.99	1	CLONAL	3	TRUE	1	0.345298924500285	3		542	324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	62	379	0	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	0.345298924500285	1	FACETS	0.946	0.823	1	0.946	0.823	1	CLONAL	1	TRUE	0	0.345298924500285	1		379	314	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561686	55561686	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs759129060	NA	P-0059912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	72	432	0	ENST00000288135.5:c.76C>G	p.Gln26Glu	p.Q26E	ENST00000288135	NM_000222.2	26	Caa/Gaa	2/21	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.345298924500285	2		432	403	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200961	108200961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782310	NA	P-0059912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	24	471	0	ENST00000278616.4:c.7328G>A	p.Arg2443Gln	p.R2443Q	ENST00000278616	NM_000051.3	2443	cGa/cAa	50/63	0.252734464277068	0	FACETS	0.275	0.215	0.344			1	SUBCLONAL	1	TRUE	0	0.345298924500285	0		471	331	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279958	18279958	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	26	453	0	ENST00000222254.8:c.2041G>A	p.Glu681Lys	p.E681K	ENST00000222254	NM_005027.3	681	Gag/Aag	16/16	1	2	FACETS	0.427	0.338	0.528	0.427	0.338	0.528	SUBCLONAL	1	TRUE	1	0.345298924500285	2		453	353	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982331	201982332	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0059912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	92	561	0	ENST00000359651.3:c.715dup	p.Asp239GlyfsTer62	p.D239Gfs*62	ENST00000359651		237	aag/aaGg	6/8	0.311979230251085	1	FACETS	0.971	0.867	1	0.971	0.867	1	CLONAL	1	TRUE	0	0.345298924500285	1		561	454	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482374	56482374	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	78	447	0	ENST00000267101.3:c.922G>C	p.Asp308His	p.D308H	ENST00000267101	NM_001982.3	308	Gac/Cac	8/28	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.345298924500285	2		447	399	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164163	108164164	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs864622164	NA	P-0059912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	19	321	0	ENST00000278616.4:c.4741dup	p.Ile1581AsnfsTer5	p.I1581Nfs*5	ENST00000278616	NM_000051.3	1579	caa/cAaa	31/63	0.252734464277068	0	FACETS	0.323	0.246	0.414			1	SUBCLONAL	1	TRUE	0	0.345298924500285	0		321	223	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458214	12458214	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	99	370	0	ENST00000287820.6:c.831C>G	p.Ile277Met	p.I277M	ENST00000287820	NM_015869.4	277	atC/atG	6/7	0.20255350835039	3	FACETS	0.841	0.756	0.929	0.841	0.756	0.929	INDETERMINATE	2	TRUE	1	0.345298924500285	3		370	400	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866407	37866407	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	97	501	0	ENST00000269571.5:c.712G>C	p.Glu238Gln	p.E238Q	ENST00000269571		238	Gag/Cag	6/27	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.345298924500285	2		501	451	SUCCESS
APC	324	MSKCC	GRCh37	5	112154981	112154981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	34	439	0	ENST00000257430.4:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000257430	NM_000038.5	418	Gaa/Aaa	10/16	1	2	FACETS	0.404	0.33	0.488	0.404	0.33	0.488	SUBCLONAL	1	TRUE	1	0.345298924500285	2		439	487	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776339	76776339	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	14	184	0	ENST00000373344.5:c.7127G>C	p.Arg2376Thr	p.R2376T	ENST00000373344	NM_000489.3	2376	aGa/aCa	34/35	1	1	FACETS	0.422	0.306	0.561	0.422	0.306	0.561	SUBCLONAL	1	TRUE	0	0.345298924500285	1		184	159	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737128	162737128	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	68	453	0	ENST00000367921.3:c.1272C>G	p.Phe424Leu	p.F424L	ENST00000367921	NM_006182.2	424	ttC/ttG	11/18	0.174666080628134	3	FACETS	0.843	0.734	0.96	0.281	0.244	0.32	INDETERMINATE	1	TRUE	0	0.345298924500285	3		453	548	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874016	123874016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1383461329	NA	P-0059912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	73	313	0	ENST00000330479.4:c.47C>T	p.Ala16Val	p.A16V	ENST00000330479	NM_020382.3	16	gCg/gTg	2/9	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.345298924500285	2		313	314	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720213	43720213	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0059912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	18	347	0	ENST00000382044.4:c.3828+1G>A		p.X1276_splice	ENST00000382044	NM_001141980.1	1276			0.311979230251085	1	FACETS	0.267	0.201	0.346	0.267	0.201	0.346	SUBCLONAL	1	TRUE	0	0.345298924500285	1		347	323	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99460026	99460026	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1198985271	NA	P-0059912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	41	438	0	ENST00000268035.6:c.2122G>A	p.Glu708Lys	p.E708K	ENST00000268035	NM_000875.3	708	Gag/Aag	10/21	0.311979230251085	1	FACETS	0.497	0.415	0.589	0.497	0.415	0.589	SUBCLONAL	1	TRUE	0	0.345298924500285	1		438	395	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89869741	89869741	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1184639006	NA	P-0059912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	57	382	0	ENST00000389301.3:c.718C>T	p.Gln240Ter	p.Q240*	ENST00000389301	NM_000135.2	240	Caa/Taa	8/43	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.345298924500285	NA		382	365	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876615	59876615	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1603342316	NA	P-0059912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	52	329	0	ENST00000259008.2:c.1186C>G	p.His396Asp	p.H396D	ENST00000259008	NM_032043.2	396	Cat/Gat	9/20	1	2	FACETS	0.803	0.686	0.93	0.803	0.686	0.93	CLONAL	1	TRUE	1	0.345298924500285	2		329	375	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424117	47424117	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	203	515	0	ENST00000404338.3:c.2185C>T	p.Gln729Ter	p.Q729*	ENST00000404338	NM_004491.4	729	Cag/Tag	1/6	0.345298924500285	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.345298924500285	3		515	577	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270157	198270157	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	70	410	0	ENST00000335508.6:c.1279C>G	p.Pro427Ala	p.P427A	ENST00000335508	NM_012433.2	427	Cca/Gca	10/25	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.345298924500285	2		410	347	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572260	41572260	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	70	356	0	ENST00000263253.7:c.4789G>T	p.Val1597Leu	p.V1597L	ENST00000263253	NM_001429.3	1597	Gtg/Ttg	30/31	1	2	FACETS	0.936	0.819	1	0.936	0.819	1	CLONAL	1	TRUE	1	0.345298924500285	2		356	433	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458492	12458492	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	142	478	0	ENST00000287820.6:c.1109C>A	p.Ser370Tyr	p.S370Y	ENST00000287820	NM_015869.4	370	tCc/tAc	6/7	0.20255350835039	3	FACETS	0.848	0.776	0.922	0.848	0.776	0.922	INDETERMINATE	2	TRUE	1	0.345298924500285	3		478	569	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191097	185191097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200211552	NA	P-0059912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	52	564	1	ENST00000265026.3:c.1978G>A	p.Gly660Arg	p.G660R	ENST00000265026	NM_004721.4	660	Gga/Aga	11/14	0.104020365863688	4	FACETS	0.681	0.579	0.793	0.34	0.289	0.397	INDETERMINATE	1	TRUE	2	0.345298924500285	4		565	595	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157224	106157224	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	63	483	0	ENST00000380013.4:c.2125G>A	p.Glu709Lys	p.E709K	ENST00000380013	NM_001127208.2	709	Gag/Aag	3/11	1	2	FACETS	0.704	0.61	0.807	0.704	0.61	0.807	SUBCLONAL	1	TRUE	1	0.345298924500285	2		483	518	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151216578	151216578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	19	155	0	ENST00000262187.5:c.20G>A	p.Arg7Gln	p.R7Q	ENST00000262187	NM_005614.3	7	cGg/cAg	1/8	0.311979230251085	1	FACETS	0.665	0.509	0.843	0.665	0.509	0.843	SUBCLONAL	1	TRUE	0	0.345298924500285	1		155	137	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781168	135781168	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	123	522	0	ENST00000298552.3:c.1797del	p.Gln600SerfsTer29	p.Q600Sfs*29	ENST00000298552	NM_001162426.1	599	ggG/gg	15/23	0.345298924500285	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.345298924500285	1		522	403	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938558	44938558	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059912-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	55	201	0	ENST00000377967.4:c.3106G>A	p.Ala1036Thr	p.A1036T	ENST00000377967	NM_021140.2	1036	Gca/Aca	20/29	1	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.345298924500285	1		201	182	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0059913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	26	407	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.170562315086176	1	FACETS	0.638	0.505	0.792	0.638	0.505	0.792	SUBCLONAL	1	TRUE	0	0.170562315086176	1		407	437	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332855	153332855	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059913-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	35	626	0	ENST00000281708.4:c.101A>G	p.Asn34Ser	p.N34S	ENST00000281708	NM_033632.3	34	aAt/aGt	2/12	1	2	FACETS	0.859	0.703	1	0.859	0.703	1	CLONAL	1	TRUE	1	0.170562315086176	2		626	478	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0059914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	55	305	5	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.873	0.751	1	0.873	0.751	1	CLONAL	1	TRUE	1	0.38897565996428	2		310	324	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245240	46245240	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	55	679	0	ENST00000334344.6:c.3334C>T	p.Gln1112Ter	p.Q1112*	ENST00000334344	NM_152641.2	1112	Cag/Tag	15/21	1	2	FACETS	0.892	0.768	1	0.892	0.768	1	CLONAL	1	TRUE	1	0.38897565996428	2		679	317	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830100	72830101	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0059914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	72	706	0	ENST00000268489.5:c.6480dup	p.Arg2161AlafsTer5	p.R2161Afs*5	ENST00000268489	NM_006885.3	2160	-/G	9/10	0.38897565996428	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.38897565996428	1		706	267	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189027	32189027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750178637	NA	P-0059914-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	74	759	0	ENST00000375023.3:c.527C>T	p.Pro176Leu	p.P176L	ENST00000375023	NM_004557.3	176	cCc/cTc	4/30	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.38897565996428	2		759	314	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0059915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	88	407	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.771	0.687	0.859	0.771	0.687	0.859	SUBCLONAL	1	FALSE	1	0.55832989782657	2		407	409	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0059915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	58	260	3	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.55	0.474	0.631	0.55	0.474	0.631	SUBCLONAL	1	FALSE	1	0.55832989782657	2		263	378	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	90	633	0	ENST00000227507.2:c.859C>T	p.Pro287Ser	p.P287S	ENST00000227507	NM_053056.2	287	Ccc/Tcc	5/5	1	2	FACETS	0.704	0.627	0.785	0.704	0.627	0.785	SUBCLONAL	1	FALSE	1	0.55832989782657	2		633	458	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692980	89692980	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060500126	NA	P-0059915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	76	347	0	ENST00000371953.3:c.464A>G	p.Tyr155Cys	p.Y155C	ENST00000371953	NM_000314.4	155	tAt/tGt	5/9	1	2	FACETS	0.654	0.577	0.737	0.654	0.577	0.737	SUBCLONAL	1	FALSE	1	0.55832989782657	2		347	416	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159743	20159743	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	29	308	0	ENST00000379607.5:c.16G>T	p.Gly6Cys	p.G6C	ENST00000379607	NM_001412.3	6	Ggt/Tgt	1/7	1	2	FACETS	0.594	0.481	0.719	0.594	0.481	0.719	SUBCLONAL	1	FALSE	1	0.55832989782657	2		308	175	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615698	1615698	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	64	672	0	ENST00000344749.5:c.1573del	p.Arg525GlyfsTer18	p.R525Gfs*18	ENST00000344749	NM_001136139.2	525	Cgg/gg	17/19	1	2	FACETS	0.657	0.572	0.748	0.657	0.572	0.748	SUBCLONAL	1	FALSE	1	0.55832989782657	2		672	349	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916726	178916726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772110575	NA	P-0059915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	58	398	0	ENST00000263967.3:c.113G>A	p.Arg38His	p.R38H	ENST00000263967	NM_006218.2	38	cGt/cAt	2/21	1	2	FACETS	0.615	0.531	0.705	0.615	0.531	0.705	SUBCLONAL	1	FALSE	1	0.55832989782657	2		398	338	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026147	36026147	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767829559	NA	P-0059915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	56	629	2	ENST00000358208.4:c.749C>T	p.Thr250Met	p.T250M	ENST00000358208		250	aCg/aTg	7/12	1	2	FACETS	0.612	0.527	0.703	0.612	0.527	0.703	SUBCLONAL	1	FALSE	1	0.55832989782657	2		631	328	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56171018	56171018	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	68	582	0	ENST00000399503.3:c.1850del	p.Gly617GlufsTer39	p.G617Efs*39	ENST00000399503	NM_005921.1	616	Ggg/gg	10/20	1	2	FACETS	0.603	0.527	0.685	0.603	0.527	0.685	SUBCLONAL	1	FALSE	1	0.55832989782657	2		582	404	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	65	816	3	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.558	0.486	0.636	0.558	0.486	0.636	SUBCLONAL	1	FALSE	1	0.55832989782657	2		819	417	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431874	49431874	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	62	727	2	ENST00000301067.7:c.9265del	p.Val3089TrpfsTer30	p.V3089Wfs*30	ENST00000301067	NM_003482.3	3089	Gtg/tg	34/54	1	2	FACETS	0.555	0.481	0.635	0.555	0.481	0.635	SUBCLONAL	1	FALSE	1	0.55832989782657	2		729	400	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543671	148543671	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1333628386	NA	P-0059915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	68	310	0	ENST00000320356.2:c.137G>A	p.Arg46His	p.R46H	ENST00000320356	NM_004456.4	46	cGt/cAt	3/20	1	2	FACETS	0.606	0.529	0.688	0.606	0.529	0.688	SUBCLONAL	1	FALSE	1	0.55832989782657	2		310	402	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420493	49420493	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs727503979	NA	P-0059915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	23	661	0	ENST00000301067.7:c.15256C>T	p.Arg5086Ter	p.R5086*	ENST00000301067	NM_003482.3	5086	Cga/Tga	48/54	1	2	FACETS	0.21	0.163	0.264	0.21	0.163	0.264	SUBCLONAL	1	FALSE	1	0.55832989782657	2		661	392	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023326	27023327	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0059915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	39	553	0	ENST00000324856.7:c.437dup	p.Ala147SerfsTer253	p.A147Sfs*253	ENST00000324856	NM_006015.4	144	-/C	1/20	1	2	FACETS	0.632	0.528	0.746	0.632	0.528	0.746	SUBCLONAL	1	FALSE	1	0.55832989782657	2		553	221	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692851	89692851	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	29	150	0	ENST00000371953.3:c.335T>G	p.Leu112Arg	p.L112R	ENST00000371953	NM_000314.4	112	cTa/cGa	5/9	1	2	FACETS	0.936	0.767	1	0.936	0.767	1	CLONAL	1	FALSE	1	0.55832989782657	2		150	111	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380522	31380522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1013448701	NA	P-0059915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	59	659	1	ENST00000328111.2:c.1012G>A	p.Gly338Arg	p.G338R	ENST00000328111	NM_006892.3	338	Ggg/Agg	9/23	1	2	FACETS	0.565	0.488	0.648	0.565	0.488	0.648	SUBCLONAL	1	FALSE	1	0.55832989782657	2		660	374	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247490	53247490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782091438	NA	P-0059915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	72	526	1	ENST00000375401.3:c.319C>T	p.Arg107Trp	p.R107W	ENST00000375401	NM_004187.3	107	Cgg/Tgg	3/26	1	2	FACETS	0.682	0.599	0.771	0.682	0.599	0.771	SUBCLONAL	1	FALSE	1	0.55832989782657	2		527	378	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294339	1294339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	47	676	0	ENST00000310581.5:c.662C>T	p.Ala221Val	p.A221V	ENST00000310581	NM_198253.2	221	gCg/gTg	2/16	1	2	FACETS	0.515	0.436	0.601	0.515	0.436	0.601	SUBCLONAL	1	FALSE	1	0.55832989782657	2		676	327	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106916	27106917	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0059915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	77	762	0	ENST00000324856.7:c.6531_6532dup	p.Asp2178GlyfsTer23	p.D2178Gfs*23	ENST00000324856	NM_006015.4	2176	cag/caGGg	20/20	1	2	FACETS	0.649	0.572	0.731	0.649	0.572	0.731	SUBCLONAL	1	FALSE	1	0.55832989782657	2		762	425	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927420	245927420	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	77	509	0	ENST00000388985.4:c.1108G>T	p.Gly370Trp	p.G370W	ENST00000388985		370	Ggg/Tgg	11/12	1	2	FACETS	0.676	0.596	0.761	0.676	0.596	0.761	SUBCLONAL	1	FALSE	1	0.55832989782657	2		509	408	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427492	427492	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1267802668	NA	P-0059915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	88	573	0	ENST00000399788.2:c.2677C>T	p.Arg893Ter	p.R893*	ENST00000399788	NM_001042603.1	893	Cga/Tga	19/28	1	2	FACETS	0.598	0.531	0.669	0.598	0.531	0.669	SUBCLONAL	1	FALSE	1	0.55832989782657	2		573	527	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799363	88799363	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	30	399	0	ENST00000360948.2:c.22G>A	p.Ala8Thr	p.A8T	ENST00000360948	NM_001012338.2	8	Gcc/Acc	2/19	1	2	FACETS	0.482	0.391	0.584	0.482	0.391	0.584	SUBCLONAL	1	FALSE	1	0.55832989782657	2		399	223	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654711	67654712	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0059915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	88	465	0	ENST00000264010.4:c.1201dup	p.His401ProfsTer8	p.H401Pfs*8	ENST00000264010	NM_006565.3	400	acc/aCcc	6/12	1	2	FACETS	0.773	0.689	0.861	0.773	0.689	0.861	SUBCLONAL	1	FALSE	1	0.55832989782657	2		465	408	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285110	15285110	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	71	639	0	ENST00000263388.2:c.4505G>A	p.Ser1502Asn	p.S1502N	ENST00000263388	NM_000435.2	1502	aGc/aAc	25/33	1	2	FACETS	0.761	0.669	0.859	0.761	0.669	0.859	SUBCLONAL	1	FALSE	1	0.55832989782657	2		639	334	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721864	176721864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	94	676	0	ENST00000439151.2:c.7495C>T	p.His2499Tyr	p.H2499Y	ENST00000439151	NM_022455.4	2499	Cat/Tat	23/23	1	2	FACETS	0.715	0.639	0.795	0.715	0.639	0.795	SUBCLONAL	1	FALSE	1	0.55832989782657	2		676	471	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538898	23538898	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	62	514	0	ENST00000380871.4:c.541C>T	p.Arg181Ter	p.R181*	ENST00000380871	NM_006167.3	181	Cga/Tga	2/2	1	2	FACETS	0.602	0.522	0.687	0.602	0.522	0.687	SUBCLONAL	1	FALSE	1	0.55832989782657	2		514	369	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194688	29194688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs919580482	NA	P-0059915-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	73	676	0	ENST00000240100.2:c.1040C>T	p.Ser347Leu	p.S347L	ENST00000240100	NM_001394.6	347	tCg/tTg	4/4	1	2	FACETS	0.797	0.703	0.897	0.797	0.703	0.897	SUBCLONAL	1	FALSE	1	0.55832989782657	2		676	328	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0059916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	77	542	0				ENST00000310581	NM_198253.2	-/1132			0.348861320326043	6	FACETS	0.914	0.825	1	1	0.962	1	CLONAL	5	TRUE	2	0.348861320326043	6		542	164	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31421483	31421483	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059916-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	48	399	0	ENST00000344624.3:c.3421G>T	p.Gly1141Cys	p.G1141C	ENST00000344624		1141	Ggc/Tgc	27/33	0.348861320326043	6	FACETS	0.92	0.784	1	0.46	0.392	0.533	CLONAL	2	TRUE	2	0.348861320326043	6		399	254	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782177	NA	P-0059917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	116	602	0	ENST00000269305.4:c.644G>T	p.Ser215Ile	p.S215I	ENST00000269305	NM_001126112.2	215	aGt/aTt	6/11	0.717185822925705	2	FACETS	1	0.969	1	0.561	0.514	0.608	CLONAL	1	TRUE	0	0.741633599311285	2		602	279	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098975	178098975	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	35	437	0	ENST00000397062.3:c.70T>G	p.Trp24Gly	p.W24G	ENST00000397062	NM_006164.4	24	Tgg/Ggg	2/5	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.741633599311285	2		437	88	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257542	16257542	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059917-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	46	623	0	ENST00000375759.3:c.4809del	p.Lys1603AsnfsTer29	p.K1603Nfs*29	ENST00000375759	NM_015001.2	1603	Aaa/aa	11/15	1	2	FACETS	0.867	0.746	0.995	0.867	0.746	0.995	CLONAL	1	TRUE	1	0.741633599311285	2		623	143	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0059919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	59	334	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.731	0.634	0.834	0.731	0.634	0.834	SUBCLONAL	1	TRUE	1	0.568555923920245	2		334	284	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591892	48591892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767345	NA	P-0059919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	145	482	0	ENST00000342988.3:c.1055G>A	p.Gly352Glu	p.G352E	ENST00000342988	NM_005359.5	352	gGa/gAa	9/12	0.568555923920245	1	FACETS	0.931	0.859	1	0.931	0.859	1	CLONAL	1	TRUE	0	0.568555923920245	1		482	392	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0059919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	148	514	0	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	1	2	FACETS	0.838	0.768	0.911	0.838	0.768	0.911	CLONAL	1	TRUE	1	0.568555923920245	2		514	621	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246516	46246516	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	32	517	0	ENST00000334344.6:c.4610G>T	p.Arg1537Ile	p.R1537I	ENST00000334344	NM_152641.2	1537	aGa/aTa	15/21	1	2	FACETS	0.204	0.165	0.249	0.204	0.165	0.249	SUBCLONAL	1	TRUE	1	0.568555923920245	2		517	551	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719086	190719086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059919-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	98	235	0	ENST00000441310.2:c.1088C>T	p.Thr363Ile	p.T363I	ENST00000441310	NM_000534.4	363	aCa/aTa	9/13	1	2	FACETS	0.884	0.795	0.977	0.884	0.795	0.977	CLONAL	1	TRUE	1	0.568555923920245	2		235	390	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188321	10188321	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs869025657	NA	P-0059928-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	90	333	0	ENST00000256474.2:c.463+1G>A		p.X155_splice	ENST00000256474	NM_000551.3	155			0.430109582567177	1	FACETS	0.952	0.852	1	0.952	0.852	1	CLONAL	1	TRUE	0	0.430109582567177	1		333	345	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979618	55979618	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059928-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	66	370	0	ENST00000263923.4:c.829C>A	p.Leu277Ile	p.L277I	ENST00000263923	NM_002253.2	277	Cta/Ata	7/30	1	2	FACETS	0.872	0.761	0.99	0.872	0.761	0.99	CLONAL	1	TRUE	1	0.430109582567177	2		370	352	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923432	9923432	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059928-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	81	519	1	ENST00000330684.3:c.1855G>T	p.Val619Phe	p.V619F	ENST00000330684	NM_001134407.1	619	Gtc/Ttc	9/13	0.295174940740057	3	FACETS	0.849	0.75	0.955	0.425	0.375	0.478	CLONAL	1	TRUE	1	0.430109582567177	3		520	539	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610579	52610590	+	frameshift_variant	Frame_Shift_Del	DEL	GGTTTCTTCCAG	GGTTTCTTCCAG	A	novel	NA	P-0059928-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	60	305	0	ENST00000394830.3:c.3583_3594delinsT	p.Glu1196ProfsTer24	p.E1196Pfs*24	ENST00000394830	NM_018313.4	1195	CTGGAAGAAACC/T	23/30	0.430109582567177	1	FACETS	0.89	0.776	1	0.89	0.776	1	CLONAL	1	TRUE	0	0.430109582567177	1		305	246	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913351	NA	P-0059929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	76	390	0	ENST00000288602.6:c.1397G>A	p.Gly466Glu	p.G466E	ENST00000288602	NM_004333.4	466	gGa/gAa	11/18	1	2	FACETS	0.813	0.721	0.908	0.813	0.721	0.908	CLONAL	1	TRUE	1	0.690298469460887	2		390	271	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250852	153250852	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0059929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	152	422	0	ENST00000281708.4:c.1208T>A	p.Leu403Ter	p.L403*	ENST00000281708	NM_033632.3	403	tTa/tAa	8/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.690298469460887	2		422	405	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362500	40362500	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219718677	NA	P-0059929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	190	547	0	ENST00000293328.3:c.1696C>T	p.Arg566Trp	p.R566W	ENST00000293328	NM_012448.3	566	Cgg/Tgg	14/19	1	2	FACETS	0.974	0.907	1	0.974	0.907	1	CLONAL	1	TRUE	1	0.690298469460887	2		547	565	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263220	115263220	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	202	510	0	ENST00000438362.2:c.2130A>T	p.Gln710His	p.Q710H	ENST00000438362	NM_001242891.1	710	caA/caT	17/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.690298469460887	2		510	552	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164482	47164487	+	inframe_deletion	In_Frame_Del	DEL	ATGCTT	ATGCTT	-	novel	NA	P-0059929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	173	633	0	ENST00000409792.3:c.1639_1644del	p.Lys547_His548del	p.K547_H548del	ENST00000409792	NM_014159.6	547	AAGCAT/-	3/21	1	2	FACETS	0.937	0.868	1	0.937	0.868	1	CLONAL	1	TRUE	1	0.690298469460887	2		633	535	SUCCESS
APC	324	MSKCC	GRCh37	5	112164613	112164613	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059929-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	148	554	0	ENST00000257430.4:c.1688del	p.Leu563CysfsTer7	p.L563Cfs*7	ENST00000257430	NM_000038.5	563	Ttg/tg	14/16	0.690298469460887	1	FACETS	0.883	0.82	0.946	0.883	0.82	0.946	CLONAL	1	TRUE	0	0.690298469460887	1		554	318	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	42	300	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.836	0.708	0.975	0.836	0.708	0.975	CLONAL	1	TRUE	1	0.551891730187012	2		300	182	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528243	157528243	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs797045283	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	115	730	1	ENST00000346085.5:c.5968C>T	p.Arg1990Ter	p.R1990*	ENST00000346085	NM_020732.3	1990	Cga/Tga	20/20	0.551891730187012	1	FACETS	0.914	0.834	0.997	0.914	0.834	0.997	CLONAL	1	TRUE	0	0.551891730187012	1		731	330	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526428	31526428	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs781066515	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	49	673	0	ENST00000344624.3:c.612C>G	p.Phe204Leu	p.F204L	ENST00000344624		204	ttC/ttG	2/33	1	2	FACETS	0.437	0.371	0.51	0.437	0.371	0.51	SUBCLONAL	1	TRUE	1	0.551891730187012	2		673	406	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	36	535	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.894	0.747	1	0.894	0.747	1	CLONAL	1	TRUE	1	0.551891730187012	2		535	146	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	76	369	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.551891730187012	2		369	211	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	73	393	0	ENST00000397062.3:c.101G>C	p.Arg34Pro	p.R34P	ENST00000397062	NM_006164.4	34	cGa/cCa	2/5	1	2	FACETS	0.928	0.82	1	0.928	0.82	1	CLONAL	1	TRUE	1	0.551891730187012	2		393	285	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057682	27057682	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520585	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	130	722	0	ENST00000324856.7:c.1390C>T	p.Gln464Ter	p.Q464*	ENST00000324856	NM_006015.4	464	Caa/Taa	3/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.551891730187012	2		722	416	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244124	153244124	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	131	706	0	ENST00000281708.4:c.2033C>G	p.Ser678Ter	p.S678*	ENST00000281708	NM_033632.3	678	tCa/tGa	12/12	1	2	FACETS	0.908	0.828	0.991	0.908	0.828	0.991	CLONAL	1	TRUE	1	0.551891730187012	2		706	523	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528895	157528895	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs763772159	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	17	596	0	ENST00000346085.5:c.6620G>C	p.Arg2207Thr	p.R2207T	ENST00000346085	NM_020732.3	2207	aGa/aCa	20/20	0.551891730187012	1	FACETS	0.16	0.119	0.208	0.16	0.119	0.208	SUBCLONAL	1	TRUE	0	0.551891730187012	1		596	279	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910507	32910507	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	65	357	0	ENST00000380152.3:c.2015G>C	p.Arg672Thr	p.R672T	ENST00000380152		672	aGa/aCa	11/27	1	2	FACETS	0.927	0.813	1	0.927	0.813	1	CLONAL	1	TRUE	1	0.551891730187012	2		357	254	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446909	18446909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	57	253	0	ENST00000266497.5:c.994C>A	p.His332Asn	p.H332N	ENST00000266497		332	Cat/Aat	4/31	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.551891730187012	2		253	193	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184592	11184592	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs774204282	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	124	491	0	ENST00000361445.4:c.6625C>G	p.Leu2209Val	p.L2209V	ENST00000361445	NM_004958.3	2209	Ctg/Gtg	47/58	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.551891730187012	2		491	347	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933743	49933743	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772397266	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	121	755	0	ENST00000296474.3:c.2534G>A	p.Arg845Gln	p.R845Q	ENST00000296474	NM_002447.2	845	cGa/cAa	10/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.551891730187012	2		755	413	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532590	187532590	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	89	511	0	ENST00000441802.2:c.9803C>G	p.Ser3268Ter	p.S3268*	ENST00000441802	NM_005245.3	3268	tCa/tGa	14/27	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.551891730187012	2		511	286	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251575	251575	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs371304688	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	132	681	0	ENST00000264932.6:c.1786G>C	p.Asp596His	p.D596H	ENST00000264932	NM_004168.2	596	Gac/Cac	13/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.551891730187012	2		681	434	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739397	46739397	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	122	671	0	ENST00000371975.4:c.1588G>C	p.Glu530Gln	p.E530Q	ENST00000371975	NM_003579.3	530	Gag/Cag	14/18	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.551891730187012	2		671	342	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216437	36216437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	120	763	0	ENST00000222270.7:c.3700G>A	p.Glu1234Lys	p.E1234K	ENST00000222270	NM_014727.1	1234	Gag/Aag	12/37	0.551891730187012	3	FACETS	1	0.97	1	0.579	0.526	0.635	CLONAL	1	TRUE	1	0.551891730187012	3		763	479	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349940	15349940	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	82	638	0	ENST00000263377.2:c.3712G>A	p.Glu1238Lys	p.E1238K	ENST00000263377	NM_058243.2	1238	Gag/Aag	18/20	0.551891730187012	3	FACETS	0.87	0.77	0.975	0.435	0.385	0.488	CLONAL	1	TRUE	1	0.551891730187012	3		638	436	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624605	93624605	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs746979231	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	94	575	0	ENST00000375746.1:c.696G>C	p.Lys232Asn	p.K232N	ENST00000375746	NM_001174167.1	232	aaG/aaC	4/14	1	2	FACETS	0.971	0.871	1	0.971	0.871	1	CLONAL	1	TRUE	1	0.551891730187012	2		575	351	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961963	41961963	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs753015602	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	102	619	0	ENST00000219905.7:c.871C>G	p.Arg291Gly	p.R291G	ENST00000219905	NM_001164273.1	291	Cgg/Ggg	2/24	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.551891730187012	2		619	346	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935647	15935647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	110	567	0	ENST00000268712.3:c.7286C>T	p.Ser2429Leu	p.S2429L	ENST00000268712	NM_006311.3	2429	tCa/tTa	46/46	1	2	FACETS	0.936	0.847	1	0.936	0.847	1	CLONAL	1	TRUE	1	0.551891730187012	2		567	426	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628296	187628296	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	119	701	0	ENST00000441802.2:c.2686G>A	p.Glu896Lys	p.E896K	ENST00000441802	NM_005245.3	896	Gag/Aag	2/27	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.551891730187012	2		701	421	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228990	36228990	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	92	757	0	ENST00000222270.7:c.7770C>G	p.Phe2590Leu	p.F2590L	ENST00000222270	NM_014727.1	2590	ttC/ttG	36/37	0.551891730187012	3	FACETS	0.806	0.718	0.899	0.403	0.359	0.45	CLONAL	1	TRUE	1	0.551891730187012	3		757	528	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218798	66218798	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	47	289	0	ENST00000273854.3:c.2260G>C	p.Glu754Gln	p.E754Q	ENST00000273854	NM_004439.5	754	Gag/Cag	13/18	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.551891730187012	2		289	166	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294268	1294268	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	102	763	0	ENST00000310581.5:c.733G>C	p.Glu245Gln	p.E245Q	ENST00000310581	NM_198253.2	245	Gag/Cag	2/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.551891730187012	2		763	344	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262414	16262414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	115	730	0	ENST00000375759.3:c.9679C>T	p.Gln3227Ter	p.Q3227*	ENST00000375759	NM_015001.2	3227	Cag/Tag	11/15	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.551891730187012	2		730	385	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337612	73337612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	68	463	0	ENST00000377767.4:c.2104C>T	p.Leu702Phe	p.L702F	ENST00000377767	NM_014953.3	702	Ctt/Ttt	16/21	1	2	FACETS	0.99	0.872	1	0.99	0.872	1	CLONAL	1	TRUE	1	0.551891730187012	2		463	249	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39708807	39708807	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	44	261	0	ENST00000361337.2:c.418C>G	p.Arg140Gly	p.R140G	ENST00000361337	NM_003286.2	140	Cga/Gga	6/21	1	2	FACETS	0.938	0.799	1	0.938	0.799	1	CLONAL	1	TRUE	1	0.551891730187012	2		261	170	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259667	16259667	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	123	740	0	ENST00000375759.3:c.6932C>G	p.Ser2311Ter	p.S2311*	ENST00000375759	NM_015001.2	2311	tCa/tGa	11/15	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.551891730187012	2		740	435	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522571	187522571	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	65	433	0	ENST00000441802.2:c.11492C>G	p.Ser3831Cys	p.S3831C	ENST00000441802	NM_005245.3	3831	tCt/tGt	21/27	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.551891730187012	2		433	228	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984233	7984233	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	86	678	0	ENST00000319144.4:c.496G>C	p.Val166Leu	p.V166L	ENST00000319144	NM_001139.2	166	Gtg/Ctg	4/15	1	2	FACETS	0.909	0.811	1	0.909	0.811	1	CLONAL	1	TRUE	1	0.551891730187012	2		678	343	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050948	49050948	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	72	493	0	ENST00000267163.4:c.2632G>C	p.Asp878His	p.D878H	ENST00000267163	NM_000321.2	878	Gat/Cat	25/27	1	2	FACETS	0.942	0.832	1	0.942	0.832	1	CLONAL	1	TRUE	1	0.551891730187012	2		493	277	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598290	28598290	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	121	664	0	ENST00000253063.3:c.262G>A	p.Asp88Asn	p.D88N	ENST00000253063	NM_031459.4	88	Gac/Aac	3/10	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.551891730187012	2		664	422	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140549992	140549992	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	43	254	0	ENST00000288602.6:c.159G>A	p.Met53Ile	p.M53I	ENST00000288602	NM_004333.4	53	atG/atA	2/18	1	2	FACETS	0.986	0.84	1	0.986	0.84	1	CLONAL	1	TRUE	1	0.551891730187012	2		254	158	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582123	52582123	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	127	541	0	ENST00000394830.3:c.4705G>A	p.Asp1569Asn	p.D1569N	ENST00000394830	NM_018313.4	1569	Gac/Aac	30/30	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.551891730187012	2		541	378	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030396	49030396	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	83	431	0	ENST00000267163.4:c.1871C>G	p.Ser624Cys	p.S624C	ENST00000267163	NM_000321.2	624	tCt/tGt	19/27	1	2	FACETS	0.943	0.84	1	0.943	0.84	1	CLONAL	1	TRUE	1	0.551891730187012	2		431	319	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270475	98270475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	71	484	0	ENST00000331920.6:c.169G>A	p.Asp57Asn	p.D57N	ENST00000331920	NM_000264.3	57	Gac/Aac	1/24	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.551891730187012	2		484	253	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255142	16255142	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	136	704	0	ENST00000375759.3:c.2407G>C	p.Glu803Gln	p.E803Q	ENST00000375759	NM_015001.2	803	Gag/Cag	11/15	1	2	FACETS	0.963	0.88	1	0.963	0.88	1	CLONAL	1	TRUE	1	0.551891730187012	2		704	512	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258841	16258841	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	140	813	0	ENST00000375759.3:c.6106G>T	p.Glu2036Ter	p.E2036*	ENST00000375759	NM_015001.2	2036	Gag/Tag	11/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.551891730187012	2		813	458	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259186	16259186	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	125	823	0	ENST00000375759.3:c.6451G>C	p.Glu2151Gln	p.E2151Q	ENST00000375759	NM_015001.2	2151	Gaa/Caa	11/15	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.551891730187012	2		823	435	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259426	16259426	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	151	793	0	ENST00000375759.3:c.6691G>C	p.Glu2231Gln	p.E2231Q	ENST00000375759	NM_015001.2	2231	Gaa/Caa	11/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.551891730187012	2		793	434	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259555	16259555	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	121	715	0	ENST00000375759.3:c.6820G>T	p.Glu2274Ter	p.E2274*	ENST00000375759	NM_015001.2	2274	Gaa/Taa	11/15	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.551891730187012	2		715	420	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023858	27023858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	82	716	0	ENST00000324856.7:c.964G>A	p.Asp322Asn	p.D322N	ENST00000324856	NM_006015.4	322	Gac/Aac	1/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.551891730187012	2		716	278	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366808	40366808	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	85	821	0	ENST00000397332.2:c.389C>G	p.Ser130Trp	p.S130W	ENST00000397332	NM_001033082.2	130	tCg/tGg	2/3	1	2	FACETS	0.969	0.865	1	0.969	0.865	1	CLONAL	1	TRUE	1	0.551891730187012	2		821	318	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649664	206649664	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	99	631	0	ENST00000367120.3:c.499G>C	p.Asp167His	p.D167H	ENST00000367120	NM_014002.3	167	Gat/Cat	6/22	1	2	FACETS	0.975	0.878	1	0.975	0.878	1	CLONAL	1	TRUE	1	0.551891730187012	2		631	368	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597902	43597902	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	99	711	2	ENST00000355710.3:c.450C>A	p.Phe150Leu	p.F150L	ENST00000355710	NM_020975.4	150	ttC/ttA	3/20	1	2	FACETS	0.892	0.802	0.987	0.892	0.802	0.987	CLONAL	1	TRUE	1	0.551891730187012	2		713	402	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125525191	125525191	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	106	446	0	ENST00000428830.2:c.1407G>C	p.Gln469His	p.Q469H	ENST00000428830	NM_001114121.2	469	caG/caC	13/14	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.551891730187012	2		446	337	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287316	46287316	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	96	562	0	ENST00000334344.6:c.5261G>A	p.Arg1754Gln	p.R1754Q	ENST00000334344	NM_152641.2	1754	cGa/cAa	19/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.551891730187012	2		562	297	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416114	49416114	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	65	510	0	ENST00000301067.7:c.16361G>C	p.Arg5454Pro	p.R5454P	ENST00000301067	NM_003482.3	5454	cGa/cCa	52/54	1	2	FACETS	0.879	0.77	0.994	0.879	0.77	0.994	CLONAL	1	TRUE	1	0.551891730187012	2		510	268	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426225	49426225	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	108	828	0	ENST00000301067.7:c.12263C>G	p.Ser4088Cys	p.S4088C	ENST00000301067	NM_003482.3	4088	tCt/tGt	39/54	1	2	FACETS	0.964	0.872	1	0.964	0.872	1	CLONAL	1	TRUE	1	0.551891730187012	2		828	406	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858980	57858980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	106	674	0	ENST00000228682.2:c.476C>T	p.Ser159Phe	p.S159F	ENST00000228682	NM_005269.2	159	tCt/tTt	5/12	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.551891730187012	2		674	347	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536669	120536669	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	129	742	0	ENST00000229340.5:c.423G>C	p.Gln141His	p.Q141H	ENST00000229340	NM_006861.6	141	caG/caC	5/6	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.551891730187012	2		742	439	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975443	26975443	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	92	481	0	ENST00000381527.3:c.1069G>C	p.Glu357Gln	p.E357Q	ENST00000381527	NM_001260.1	357	Gaa/Caa	11/13	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.551891730187012	2		481	326	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626739	28626739	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	102	515	0	ENST00000241453.7:c.557C>G	p.Ser186Cys	p.S186C	ENST00000241453	NM_004119.2	186	tCt/tGt	5/24	1	2	FACETS	0.931	0.839	1	0.931	0.839	1	CLONAL	1	TRUE	1	0.551891730187012	2		515	397	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907110	32907110	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1566223700	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	67	512	0	ENST00000380152.3:c.1495C>T	p.Gln499Ter	p.Q499*	ENST00000380152		499	Cag/Tag	10/27	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.551891730187012	2		512	237	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912639	32912639	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	60	383	0	ENST00000380152.3:c.4147G>C	p.Asp1383His	p.D1383H	ENST00000380152		1383	Gat/Cat	11/27	1	2	FACETS	0.782	0.68	0.891	0.782	0.68	0.891	SUBCLONAL	1	TRUE	1	0.551891730187012	2		383	278	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396716	30396716	+	start_lost	Translation_Start_Site	SNP	C	C	G	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	72	466	0	ENST00000331968.5:c.3G>C	p.Met1?	p.M1?	ENST00000331968	NM_002742.2	1	atG/atC	1/18	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.551891730187012	2		466	223	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582869	95582869	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	101	427	0	ENST00000393063.1:c.1673C>G	p.Ser558Cys	p.S558C	ENST00000393063	NM_030621.3	558	tCt/tGt	11/28	0.333929149479559	2	FACETS	1	0.984	1	0.723	0.658	0.79	CLONAL	1	TRUE	0	0.551891730187012	2		427	253	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50782500	50782500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	102	514	0	ENST00000307179.4:c.2012C>T	p.Ser671Leu	p.S671L	ENST00000307179		671	tCa/tTa	14/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.551891730187012	2		514	333	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51504520	51504520	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	72	423	0	ENST00000260433.2:c.1260G>C	p.Lys420Asn	p.K420N	ENST00000260433		420	aaG/aaC	9/10	1	2	FACETS	0.966	0.854	1	0.966	0.854	1	CLONAL	1	TRUE	1	0.551891730187012	2		423	270	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347499	91347499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	91	482	0	ENST00000355112.3:c.3661G>A	p.Glu1221Lys	p.E1221K	ENST00000355112	NM_000057.2	1221	Gaa/Aaa	19/22	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.551891730187012	2		482	299	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632500	3632500	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	123	721	0	ENST00000294008.3:c.5348C>G	p.Ala1783Gly	p.A1783G	ENST00000294008	NM_032444.2	1783	gCa/gGa	15/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.551891730187012	2		721	375	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843439	3843439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	90	616	0	ENST00000262367.5:c.1164G>A	p.Met388Ile	p.M388I	ENST00000262367	NM_004380.2	388	atG/atA	4/31	1	2	FACETS	0.865	0.773	0.962	0.865	0.773	0.962	CLONAL	1	TRUE	1	0.551891730187012	2		616	377	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14028120	14028120	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	46	440	0	ENST00000311895.7:c.1174G>C	p.Glu392Gln	p.E392Q	ENST00000311895	NM_005236.2	392	Gag/Cag	7/11	1	2	FACETS	0.79	0.673	0.916	0.79	0.673	0.916	CLONAL	1	TRUE	1	0.551891730187012	2		440	211	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632744	23632744	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	68	457	0	ENST00000261584.4:c.3052G>C	p.Glu1018Gln	p.E1018Q	ENST00000261584	NM_024675.3	1018	Gag/Cag	10/13	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.551891730187012	2		457	238	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646698	23646698	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	65	526	0	ENST00000261584.4:c.1169C>G	p.Ser390Cys	p.S390C	ENST00000261584	NM_024675.3	390	tCt/tGt	4/13	1	2	FACETS	0.743	0.649	0.843	0.743	0.649	0.843	SUBCLONAL	1	TRUE	1	0.551891730187012	2		526	317	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50815304	50815304	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	93	539	0	ENST00000398568.2:c.1657G>C	p.Glu553Gln	p.E553Q	ENST00000398568	NM_001042412.1	553	Gag/Cag	9/18	1	2	FACETS	0.991	0.89	1	0.991	0.89	1	CLONAL	1	TRUE	1	0.551891730187012	2		539	340	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831551	72831551	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	93	650	0	ENST00000268489.5:c.5030C>G	p.Ser1677Cys	p.S1677C	ENST00000268489	NM_006885.3	1677	tCt/tGt	9/10	1	2	FACETS	0.822	0.736	0.913	0.822	0.736	0.913	CLONAL	1	TRUE	1	0.551891730187012	2		650	410	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341336	89341336	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	73	361	0	ENST00000301030.4:c.7599G>C	p.Glu2533Asp	p.E2533D	ENST00000301030	NM_001256183.1	2533	gaG/gaC	11/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.551891730187012	2		361	192	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351154	89351154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1305076348	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	109	659	0	ENST00000301030.4:c.1796G>A	p.Arg599Lys	p.R599K	ENST00000301030	NM_001256183.1	599	aGg/aAg	9/13	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.551891730187012	2		659	383	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15976778	15976778	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	78	448	0	ENST00000268712.3:c.3776C>G	p.Ser1259Ter	p.S1259*	ENST00000268712	NM_006311.3	1259	tCa/tGa	28/46	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.551891730187012	2		448	205	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592283	29592283	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	69	283	0	ENST00000356175.3:c.4698G>C	p.Leu1566Phe	p.L1566F	ENST00000356175	NM_000267.3	1566	ttG/ttC	35/57	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.551891730187012	2		283	203	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40856696	40856696	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	58	343	0	ENST00000428826.2:c.1941C>G	p.Ile647Met	p.I647M	ENST00000428826		647	atC/atG	18/21	1	2	FACETS	0.891	0.774	1	0.891	0.774	1	CLONAL	1	TRUE	1	0.551891730187012	2		343	236	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621878	1621878	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141433039	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	97	717	0	ENST00000344749.5:c.914C>T	p.Ser305Phe	p.S305F	ENST00000344749	NM_001136139.2	305	tCc/tTc	11/19	0.551891730187012	3	FACETS	1	0.907	1	0.506	0.454	0.562	CLONAL	1	TRUE	1	0.551891730187012	3		717	443	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6213755	6213755	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	95	554	0	ENST00000252674.7:c.1461G>C	p.Lys487Asn	p.K487N	ENST00000252674	NM_005934.3	487	aaG/aaC	10/12	0.551891730187012	3	FACETS	1	0.958	1	0.568	0.509	0.629	CLONAL	1	TRUE	1	0.551891730187012	3		554	387	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6227001	6227001	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	210	704	0	ENST00000252674.7:c.533C>G	p.Ser178Cys	p.S178C	ENST00000252674	NM_005934.3	178	tCc/tGc	5/12	0.551891730187012	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.551891730187012	3		704	440	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262172	10262172	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	44	701	0	ENST00000340748.4:c.2119G>A	p.Asp707Asn	p.D707N	ENST00000340748		707	Gat/Aat	23/40	0.551891730187012	3	FACETS	0.395	0.331	0.466	0.198	0.165	0.233	SUBCLONAL	1	TRUE	1	0.551891730187012	3		701	515	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610334	10610334	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	121	824	0	ENST00000171111.5:c.376G>C	p.Glu126Gln	p.E126Q	ENST00000171111	NM_203500.1	126	Gag/Cag	2/6	0.551891730187012	3	FACETS	1	0.954	1	0.541	0.491	0.593	CLONAL	1	TRUE	1	0.551891730187012	3		824	517	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350772	15350772	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	109	550	0	ENST00000263377.2:c.3231G>C	p.Gln1077His	p.Q1077H	ENST00000263377	NM_058243.2	1077	caG/caC	15/20	0.551891730187012	3	FACETS	1	0.972	1	0.599	0.541	0.658	CLONAL	1	TRUE	1	0.551891730187012	3		550	421	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266750	18266750	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1038013455	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	81	633	0	ENST00000222254.8:c.61G>C	p.Glu21Gln	p.E21Q	ENST00000222254	NM_005027.3	21	Gag/Cag	2/16	0.551891730187012	3	FACETS	0.9	0.797	1	0.45	0.398	0.505	CLONAL	1	TRUE	1	0.551891730187012	3		633	416	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213956	36213956	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	124	807	0	ENST00000222270.7:c.2782G>C	p.Glu928Gln	p.E928Q	ENST00000222270	NM_014727.1	928	Gag/Cag	6/37	0.551891730187012	3	FACETS	0.992	0.901	1	0.496	0.45	0.544	CLONAL	1	TRUE	1	0.551891730187012	3		807	578	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216223	36216223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	112	692	0	ENST00000222270.7:c.3631G>A	p.Gly1211Arg	p.G1211R	ENST00000222270	NM_014727.1	1211	Gga/Aga	11/37	0.551891730187012	3	FACETS	1	0.903	1	0.5	0.451	0.551	CLONAL	1	TRUE	1	0.551891730187012	3		692	518	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754650	41754650	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	119	665	0	ENST00000301178.4:c.1636G>C	p.Glu546Gln	p.E546Q	ENST00000301178	NM_021913.4	546	Gag/Cag	14/20	0.551891730187012	3	FACETS	1	0.958	1	0.549	0.498	0.602	CLONAL	1	TRUE	1	0.551891730187012	3		665	501	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068426	26068426	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	42	153	0	ENST00000435504.4:c.64G>C	p.Glu22Gln	p.E22Q	ENST00000435504		22	Gaa/Caa	2/13	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.551891730187012	2		153	138	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61713079	61713079	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	75	545	0	ENST00000401558.2:c.2332C>T	p.Pro778Ser	p.P778S	ENST00000401558	NM_003400.3	778	Ccc/Tcc	20/25	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.551891730187012	2		545	256	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61760993	61760993	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	80	421	0	ENST00000401558.2:c.40C>G	p.Arg14Gly	p.R14G	ENST00000401558	NM_003400.3	14	Cgt/Ggt	2/25	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.551891730187012	2		421	272	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617392	158617392	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	85	503	0	ENST00000263640.3:c.1264G>A	p.Gly422Ser	p.G422S	ENST00000263640	NM_001105.4	422	Ggt/Agt	9/11	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.551891730187012	2		503	285	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198269898	198269898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	61	309	0	ENST00000335508.6:c.1441G>A	p.Asp481Asn	p.D481N	ENST00000335508	NM_012433.2	481	Gat/Aat	11/25	1	2	FACETS	0.81	0.705	0.921	0.81	0.705	0.921	CLONAL	1	TRUE	1	0.551891730187012	2		309	273	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324606	62324606	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	85	631	0	ENST00000360203.5:c.2962C>T	p.Gln988Ter	p.Q988*	ENST00000360203	NM_001283009.1	988	Cag/Tag	30/35	1	2	FACETS	0.863	0.769	0.962	0.863	0.769	0.962	CLONAL	1	TRUE	1	0.551891730187012	2		631	357	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272416	21272416	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	146	739	0	ENST00000354336.3:c.194C>G	p.Ser65Trp	p.S65W	ENST00000354336	NM_005207.3	65	tCg/tGg	1/3	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.551891730187012	2		739	446	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564595	41564595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	92	607	0	ENST00000263253.7:c.4017G>A	p.Met1339Ile	p.M1339I	ENST00000263253	NM_001429.3	1339	atG/atA	24/31	1	2	FACETS	0.899	0.805	0.997	0.899	0.805	0.997	CLONAL	1	TRUE	1	0.551891730187012	2		607	371	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627218	12627218	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	95	488	0	ENST00000251849.4:c.1498C>T	p.Gln500Ter	p.Q500*	ENST00000251849	NM_002880.3	500	Cag/Tag	14/17	1	2	FACETS	0.946	0.849	1	0.946	0.849	1	CLONAL	1	TRUE	1	0.551891730187012	2		488	364	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641694	12641694	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	113	624	0	ENST00000251849.4:c.947G>C	p.Arg316Thr	p.R316T	ENST00000251849	NM_002880.3	316	aGa/aCa	9/17	1	2	FACETS	0.957	0.867	1	0.957	0.867	1	CLONAL	1	TRUE	1	0.551891730187012	2		624	428	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72873606	72873606	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	65	329	0	ENST00000325599.8:c.696G>C	p.Lys232Asn	p.K232N	ENST00000325599	NM_018130.2	232	aaG/aaC	6/11	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.551891730187012	2		329	211	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890269	72890269	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1009568174	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	93	493	0	ENST00000325599.8:c.413C>G	p.Ser138Ter	p.S138*	ENST00000325599	NM_018130.2	138	tCa/tGa	4/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.551891730187012	2		493	314	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114568	73114568	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	61	309	0	ENST00000356692.5:c.949G>C	p.Glu317Gln	p.E317Q	ENST00000356692		317	Gaa/Caa	9/9	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.551891730187012	2		309	217	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825410	134825410	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	87	531	0	ENST00000398015.3:c.926G>C	p.Arg309Pro	p.R309P	ENST00000398015	NM_004441.4	309	cGa/cCa	4/16	1	2	FACETS	0.958	0.857	1	0.958	0.857	1	CLONAL	1	TRUE	1	0.551891730187012	2		531	329	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161352	185161352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	77	507	0	ENST00000265026.3:c.779C>T	p.Ser260Phe	p.S260F	ENST00000265026	NM_004721.4	260	tCc/tTc	4/14	1	2	FACETS	0.927	0.822	1	0.927	0.822	1	CLONAL	1	TRUE	1	0.551891730187012	2		507	301	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184726	185184726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	82	569	0	ENST00000265026.3:c.1618C>T	p.His540Tyr	p.H540Y	ENST00000265026	NM_004721.4	540	Cac/Tac	10/14	1	2	FACETS	0.835	0.742	0.933	0.835	0.742	0.933	CLONAL	1	TRUE	1	0.551891730187012	2		569	356	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526119	189526119	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	59	736	0	ENST00000264731.3:c.383C>G	p.Ser128Cys	p.S128C	ENST00000264731	NM_003722.4	128	tCc/tGc	4/14	1	2	FACETS	0.589	0.509	0.675	0.589	0.509	0.675	SUBCLONAL	1	TRUE	1	0.551891730187012	2		736	363	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156707	55156707	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	103	591	0	ENST00000257290.5:c.3108G>C	p.Lys1036Asn	p.K1036N	ENST00000257290	NM_006206.4	1036	aaG/aaC	22/23	1	2	FACETS	0.99	0.894	1	0.99	0.894	1	CLONAL	1	TRUE	1	0.551891730187012	2		591	377	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157549	106157549	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867783315	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	62	479	0	ENST00000380013.4:c.2450C>T	p.Ser817Phe	p.S817F	ENST00000380013	NM_001127208.2	817	tCc/tTc	3/11	1	2	FACETS	0.881	0.769	0.999	0.881	0.769	0.999	CLONAL	1	TRUE	1	0.551891730187012	2		479	255	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144361424	144361424	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	98	611	0	ENST00000262995.4:c.1474C>G	p.Pro492Ala	p.P492A	ENST00000262995	NM_207123.2	492	Cct/Gct	6/11	1	2	FACETS	0.968	0.871	1	0.968	0.871	1	CLONAL	1	TRUE	1	0.551891730187012	2		611	367	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539765	187539765	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	79	664	0	ENST00000441802.2:c.7975G>C	p.Glu2659Gln	p.E2659Q	ENST00000441802	NM_005245.3	2659	Gag/Cag	10/27	1	2	FACETS	0.954	0.848	1	0.954	0.848	1	CLONAL	1	TRUE	1	0.551891730187012	2		664	300	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540554	187540554	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	113	654	0	ENST00000441802.2:c.7186G>C	p.Glu2396Gln	p.E2396Q	ENST00000441802	NM_005245.3	2396	Gaa/Caa	10/27	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.551891730187012	2		654	400	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752858	57752858	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	67	530	0	ENST00000274289.3:c.1070C>G	p.Ser357Ter	p.S357*	ENST00000274289	NM_006622.3	357	tCa/tGa	8/14	1	2	FACETS	0.883	0.775	0.997	0.883	0.775	0.997	CLONAL	1	TRUE	1	0.551891730187012	2		530	275	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79968660	79968660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	73	412	0	ENST00000265081.6:c.1010C>T	p.Ser337Phe	p.S337F	ENST00000265081	NM_002439.4	337	tCt/tTt	6/24	1	2	FACETS	0.965	0.854	1	0.965	0.854	1	CLONAL	1	TRUE	1	0.551891730187012	2		412	274	SUCCESS
APC	324	MSKCC	GRCh37	5	112178939	112178939	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	99	596	0	ENST00000257430.4:c.7648G>A	p.Glu2550Lys	p.E2550K	ENST00000257430	NM_000038.5	2550	Gag/Aag	16/16	1	2	FACETS	0.999	0.9	1	0.999	0.9	1	CLONAL	1	TRUE	1	0.551891730187012	2		596	359	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495332	149495332	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	93	561	0	ENST00000261799.4:c.3315C>A	p.Phe1105Leu	p.F1105L	ENST00000261799	NM_002609.3	1105	ttC/ttA	23/23	NA	2	FACETS	1	0.955	1			1	INDETERMINATE	1	TRUE	NA	0.551891730187012	2		561	303	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031973	26031973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	57	853	0	ENST00000244661.2:c.316G>A	p.Glu106Lys	p.E106K	ENST00000244661	NM_003537.3	106	Gag/Aag	1/1	1	2	FACETS	0.413	0.355	0.477	0.413	0.355	0.477	SUBCLONAL	1	TRUE	1	0.551891730187012	2		853	500	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839699	27839699	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	92	698	0	ENST00000328488.2:c.395G>C	p.Arg132Pro	p.R132P	ENST00000328488	NM_003533.2	132	cGa/cCa	1/1	1	2	FACETS	0.857	0.767	0.952	0.857	0.767	0.952	CLONAL	1	TRUE	1	0.551891730187012	2		698	389	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31237139	31237139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	115	661	0	ENST00000376228.5:c.1072G>A	p.Asp358Asn	p.D358N	ENST00000376228	NM_002117.5	358	Gat/Aat	7/8	1	2	FACETS	0.992	0.901	1	0.992	0.901	1	CLONAL	1	TRUE	1	0.551891730187012	2		661	420	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188995	32188995	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	110	802	0	ENST00000375023.3:c.559G>C	p.Glu187Gln	p.E187Q	ENST00000375023	NM_004557.3	187	Gag/Cag	4/30	1	2	FACETS	0.997	0.903	1	0.997	0.903	1	CLONAL	1	TRUE	1	0.551891730187012	2		802	400	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805404	32805404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	106	617	0	ENST00000374899.4:c.518C>T	p.Ser173Phe	p.S173F	ENST00000374899	NM_018833.2	173	tCt/tTt	3/12	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.551891730187012	2		617	338	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552744	106552744	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	118	669	0	ENST00000369096.4:c.709G>C	p.Glu237Gln	p.E237Q	ENST00000369096	NM_001198.3	237	Gaa/Caa	5/7	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.551891730187012	2		669	391	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555110	106555110	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	111	718	0	ENST00000369096.4:c.2227G>C	p.Glu743Gln	p.E743Q	ENST00000369096	NM_001198.3	743	Gag/Cag	7/7	1	2	FACETS	0.933	0.845	1	0.933	0.845	1	CLONAL	1	TRUE	1	0.551891730187012	2		718	431	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117632244	117632244	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	57	370	0	ENST00000368508.3:c.6172G>C	p.Asp2058His	p.D2058H	ENST00000368508	NM_002944.2	2058	Gac/Cac	39/43	1	2	FACETS	0.974	0.848	1	0.974	0.848	1	CLONAL	1	TRUE	1	0.551891730187012	2		370	212	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864693	68864693	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	33	470	0	ENST00000288368.4:c.64C>G	p.Arg22Gly	p.R22G	ENST00000288368	NM_024870.2	22	Cgc/Ggc	1/40	1	2	FACETS	0.515	0.422	0.619	0.515	0.422	0.619	SUBCLONAL	1	TRUE	1	0.551891730187012	2		470	232	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436631	8436631	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	51	383	0	ENST00000356435.5:c.4047G>C	p.Leu1349Phe	p.L1349F	ENST00000356435		1349	ttG/ttC	24/35	1	2	FACETS	0.973	0.839	1	0.973	0.839	1	CLONAL	1	TRUE	1	0.551891730187012	2		383	190	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240369	98240369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	110	589	0	ENST00000331920.6:c.1315G>A	p.Val439Ile	p.V439I	ENST00000331920	NM_000264.3	439	Gtc/Atc	9/24	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.551891730187012	2		589	381	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391125	139391125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	89	774	0	ENST00000277541.6:c.7066G>A	p.Ala2356Thr	p.A2356T	ENST00000277541	NM_017617.3	2356	Gcc/Acc	34/34	1	2	FACETS	0.891	0.796	0.99	0.891	0.796	0.99	CLONAL	1	TRUE	1	0.551891730187012	2		774	362	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391279	139391279	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	120	880	0	ENST00000277541.6:c.6912G>C	p.Leu2304Phe	p.L2304F	ENST00000277541	NM_017617.3	2304	ttG/ttC	34/34	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.551891730187012	2		880	374	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396236	139396236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	107	698	0	ENST00000277541.6:c.5602G>A	p.Asp1868Asn	p.D1868N	ENST00000277541	NM_017617.3	1868	Gac/Aac	30/34	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.551891730187012	2		698	384	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405603	139405603	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	78	499	0	ENST00000277541.6:c.2587+1G>A		p.X863_splice	ENST00000277541	NM_017617.3	863			1	2	FACETS	0.988	0.878	1	0.988	0.878	1	CLONAL	1	TRUE	1	0.551891730187012	2		499	286	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342101	70342101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	116	590	0	ENST00000374080.3:c.1153G>A	p.Asp385Asn	p.D385N	ENST00000374080		385	Gat/Aat	8/45	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.551891730187012	2		590	364	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814297	76814297	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	40	262	0	ENST00000373344.5:c.6347C>G	p.Ser2116Cys	p.S2116C	ENST00000373344	NM_000489.3	2116	tCt/tGt	29/35	1	2	FACETS	0.947	0.801	1	0.947	0.801	1	CLONAL	1	TRUE	1	0.551891730187012	2		262	153	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849203	76849203	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	79	375	0	ENST00000373344.5:c.6073G>C	p.Glu2025Gln	p.E2025Q	ENST00000373344	NM_000489.3	2025	Gaa/Caa	26/35	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.551891730187012	2		375	253	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224529	123224529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059931-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	52	597	0	ENST00000218089.9:c.3382G>A	p.Glu1128Lys	p.E1128K	ENST00000218089	NM_001042749.1	1128	Gag/Aag	31/35	1	2	FACETS	0.624	0.534	0.721	0.624	0.534	0.721	SUBCLONAL	1	TRUE	1	0.551891730187012	2		597	302	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023559	27023560	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0059932-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	109	747	0	ENST00000324856.7:c.671dup	p.Pro225AlafsTer175	p.P225Afs*175	ENST00000324856	NM_006015.4	222	tac/taCc	1/20	0.332629957148268	6	FACETS	0.928	0.836	1	0.619	0.557	0.684	CLONAL	2	FALSE	3	0.332629957148268	6		747	588	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845910	156845910	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059932-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	51	960	0	ENST00000524377.1:c.1540T>G	p.Trp514Gly	p.W514G	ENST00000524377	NM_002529.3	514	Tgg/Ggg	13/17	0.332629957148268	6	FACETS	0.59	0.5	0.689	0.147	0.125	0.173	SUBCLONAL	1	FALSE	2	0.332629957148268	6		960	866	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243778435	243778435	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1360057195	NA	P-0059932-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	93	432	0	ENST00000263826.5:c.590G>A	p.Ser197Asn	p.S197N	ENST00000263826	NM_005465.4	197	aGc/aAc	6/13	0.332629957148268	5	FACETS	0.859	0.767	0.956	0.573	0.511	0.638	CLONAL	2	FALSE	2	0.332629957148268	5		432	488	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43767884	43767884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059932-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	182	611	0	ENST00000382044.4:c.964G>A	p.Asp322Asn	p.D322N	ENST00000382044	NM_001141980.1	322	Gat/Aat	9/28	0.332629957148268	5	FACETS	0.992	0.922	1	0.992	0.922	1	CLONAL	3	FALSE	2	0.332629957148268	5		611	551	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350611	15350611	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059932-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	131	645	0	ENST00000263377.2:c.3304G>C	p.Val1102Leu	p.V1102L	ENST00000263377	NM_058243.2	1102	Gtc/Ctc	16/20	0.332629957148268	5	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	FALSE	3	0.332629957148268	5		645	491	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260149	19260149	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059932-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	181	715	0	ENST00000162023.5:c.144del	p.Phe48LeufsTer20	p.F48Lfs*20	ENST00000162023		48	ttC/tt	7/13	0.332629957148268	5	FACETS	0.982	0.911	1	1	0.99	1	CLONAL	3	FALSE	3	0.332629957148268	5		715	554	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547248	106547248	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059932-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	153	632	0	ENST00000369096.4:c.485T>A	p.Val162Glu	p.V162E	ENST00000369096	NM_001198.3	162	gTg/gAg	4/7	0.32140099755199	3	FACETS	0.974	0.896	1	0.974	0.896	1	CLONAL	2	FALSE	1	0.332629957148268	3		632	551	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6029523	6029523	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059932-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	119	503	0	ENST00000265849.7:c.1052T>G	p.Leu351Trp	p.L351W	ENST00000265849	NM_000535.5	351	tTg/tGg	10/15	0.332629957148268	6	FACETS	1	0.947	1	0.533	0.483	0.586	CLONAL	2	FALSE	2	0.332629957148268	6		503	559	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211106	55211106	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059932-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	99	592	0	ENST00000275493.2:c.349T>G	p.Tyr117Asp	p.Y117D	ENST00000275493	NM_005228.3	117	Tat/Gat	3/28	1	2	FACETS	0.848	0.764	0.935	1	0.985	1	CLONAL	2	FALSE	1	0.332629957148268	2		592	351	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900150	151900150	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0059932-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	100	396	0	ENST00000262189.6:c.3962-1G>T		p.X1321_splice	ENST00000262189	NM_170606.2	1321			0.32140099755199	3	FACETS	0.851	0.765	0.941	0.851	0.765	0.941	CLONAL	2	FALSE	1	0.332629957148268	3		396	412	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0059933-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	46	410	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	0.238725823944202	3	FACETS	1	0.959	1	0.723	0.613	0.842	CLONAL	1	FALSE	1	0.268389735342356	3		410	269	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463330	463330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059933-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	38	433	0	ENST00000399788.2:c.941G>A	p.Cys314Tyr	p.C314Y	ENST00000399788	NM_001042603.1	314	tGt/tAt	8/28	0.238725823944202	3	FACETS	1	0.946	1	0.686	0.572	0.812	CLONAL	1	FALSE	1	0.268389735342356	3		433	234	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1296393	1296393	+	upstream_gene_variant	5'Flank	SNP	T	T	C	novel	NA	P-0059933-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	42	362	0				ENST00000310581	NM_198253.2	-/1132			0.238725823944202	3	FACETS	1	0.927	1	0.598	0.501	0.703	CLONAL	1	FALSE	1	0.268389735342356	3		362	297	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41962066	41962066	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059934-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	98	573	0	ENST00000219905.7:c.976del	p.Asn327IlefsTer2	p.N327Ifs*2	ENST00000219905	NM_001164273.1	325	tCc/tc	2/24	1	2	FACETS	0.914	0.815	1	0.914	0.815	1	CLONAL	1	TRUE	1	0.3	2		573	715	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350451	15350474	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGCAGGGAGAGCACTCACGCTGG	GGGCAGGGAGAGCACTCACGCTGG	-	novel	NA	P-0059934-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	71	633	0	ENST00000263377.2:c.3441_3445+19del		p.X1147_splice	ENST00000263377	NM_058243.2	1147		16/20	1	2	FACETS	0.949	0.83	1	0.949	0.83	1	CLONAL	1	TRUE	1	0.3	2		633	499	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410099	63410099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059935-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	266	395	0	ENST00000330258.3:c.3068C>T	p.Pro1023Leu	p.P1023L	ENST00000330258	NM_152424.3	1023	cCc/cTc	2/2	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.921187316813358	1		395	284	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94923092	94923093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0059938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	166	442	0	ENST00000536441.1:c.375_376insTT	p.Asn126LeufsTer9	p.N126Lfs*9	ENST00000536441	NM_144665.3	125	-/TT	4/10	1	2	FACETS	0.954	0.882	1	0.954	0.882	1	CLONAL	1	TRUE	1	0.659393055191601	2		442	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0059938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	203	717	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	1	2	FACETS	0.9	0.838	0.964	0.9	0.838	0.964	CLONAL	1	TRUE	1	0.659393055191601	2		717	684	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579518	7579518	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	249	641	0	ENST00000269305.4:c.169G>C	p.Asp57His	p.D57H	ENST00000269305	NM_001126112.2	57	Gac/Cac	4/11	1	2	FACETS	0.927	0.869	0.985	0.927	0.869	0.985	CLONAL	1	TRUE	1	0.659393055191601	2		641	815	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55974025	55974026	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0059938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	36	545	0	ENST00000263923.4:c.1290_1291del	p.Pro431CysfsTer52	p.P431Cfs*52	ENST00000263923	NM_002253.2	430	tcTCct/tcct	10/30	0.657421673980017	1	FACETS	0.156	0.128	0.188	0.156	0.128	0.188	SUBCLONAL	1	TRUE	0	0.659393055191601	1		545	469	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032546	47032546	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059938-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	240	295	0	ENST00000377604.3:c.452C>A	p.Ser151Ter	p.S151*	ENST00000377604	NM_001204468.1	151	tCg/tAg	5/24	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.659393055191601	1		295	372	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293475	1293475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554042799	NA	P-0059939-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	104	500	0	ENST00000310581.5:c.1526C>T	p.Thr509Met	p.T509M	ENST00000310581	NM_198253.2	509	aCg/aTg	2/16	0.236598182704668	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.708147233508283	0		500	240	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0059940-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	64	637	1	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	0.328059127635202	3	FACETS	1	0.971	1	0.716	0.626	0.811	CLONAL	1	FALSE	1	0.402086467844551	3		638	267	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578179	7578179	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059940-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	145	715	2	ENST00000269305.4:c.670G>T	p.Glu224Ter	p.E224*	ENST00000269305	NM_001126112.2	224	Gag/Tag	6/11	0.33820637713414	2	FACETS	0.761	0.699	0.824	0.761	0.699	0.824	SUBCLONAL	2	FALSE	0	0.402086467844551	2		717	474	SUCCESS
APC	324	MSKCC	GRCh37	5	112175351	112175351	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059940-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	27	595	0	ENST00000257430.4:c.4063del	p.Ser1355LeufsTer60	p.S1355Lfs*60	ENST00000257430	NM_000038.5	1354	Ttt/tt	16/16	0.328059127635202	3	FACETS	0.539	0.43	0.664	0.27	0.215	0.332	SUBCLONAL	1	FALSE	1	0.402086467844551	3		595	299	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120783979	120783979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112244011	NA	P-0059940-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	69	748	3	ENST00000257552.2:c.1006G>A	p.Ala336Thr	p.A336T	ENST00000257552	NM_002442.3	336	Gcc/Acc	13/15	0.277781170550498	3	FACETS	0.773	0.674	0.88	0.387	0.337	0.44	SUBCLONAL	1	FALSE	1	0.402086467844551	3		751	533	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101552	27101552	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0059941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	63	737	1	ENST00000324856.7:c.4834A>T	p.Lys1612Ter	p.K1612*	ENST00000324856	NM_006015.4	1612	Aaa/Taa	18/20	0.286553169450918	3	FACETS	0.842	0.729	0.965	0.421	0.364	0.483	CLONAL	1	TRUE	1	0.308989598378155	3		738	559	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180572	94180572	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	46	487	0	ENST00000323929.3:c.1596G>T	p.Gln532His	p.Q532H	ENST00000323929	NM_005591.3	532	caG/caT	15/20	0.308989598378155	3	FACETS	0.693	0.584	0.814	0.347	0.292	0.407	SUBCLONAL	1	TRUE	1	0.308989598378155	3		487	496	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170552	11170552	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568564931	NA	P-0059941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	30	731	0	ENST00000358026.2:c.4855G>A	p.Glu1619Lys	p.E1619K	ENST00000358026	NM_001128849.1	1619	Gaa/Aaa	34/36	0.218930273129823	2	FACETS	0.356	0.286	0.435	0.178	0.143	0.218	SUBCLONAL	1	TRUE	0	0.308989598378155	2		731	546	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726945	61726945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	86	387	0	ENST00000401558.2:c.493C>G	p.Gln165Glu	p.Q165E	ENST00000401558	NM_003400.3	165	Caa/Gaa	7/25	0.308989598378155	6	FACETS	0.813	0.721	0.911	0.542	0.48	0.608	CLONAL	2	TRUE	3	0.308989598378155	6		387	554	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945587	54945587	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	24	416	0	ENST00000312783.6:c.983C>G	p.Pro328Arg	p.P328R	ENST00000312783	NM_198436.1	328	cCt/cGt	9/10	0.30598057020883	4	FACETS	0.505	0.395	0.631	0.126	0.098	0.158	SUBCLONAL	1	TRUE	0	0.308989598378155	4		416	403	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074225	39074225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	35	491	0	ENST00000357387.3:c.85G>A	p.Asp29Asn	p.D29N	ENST00000357387	NM_152756.3	29	Gat/Aat	2/38	0.308989598378155	4	FACETS	0.567	0.464	0.683	0.189	0.154	0.228	SUBCLONAL	1	TRUE	1	0.308989598378155	4		491	523	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86686671	86686671	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	39	520	0	ENST00000274376.6:c.3115C>G	p.Gln1039Glu	p.Q1039E	ENST00000274376	NM_002890.2	1039	Cag/Gag	25/25	1	2	FACETS	0.497	0.411	0.592	0.497	0.411	0.592	SUBCLONAL	1	TRUE	1	0.308989598378155	2		520	508	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109315766	109315766	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	47	393	0	ENST00000436639.2:c.1019G>T	p.Arg340Met	p.R340M	ENST00000436639	NM_014454.2	340	aGg/aTg	6/10	0.281977812292935	4	FACETS	0.715	0.603	0.839	0.179	0.15	0.21	SUBCLONAL	1	TRUE	0	0.308989598378155	4		393	557	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412664	139412664	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	31	712	0	ENST00000277541.6:c.1180G>T	p.Gly394Cys	p.G394C	ENST00000277541	NM_017617.3	394	Ggc/Tgc	7/34	0.232231742418279	2	FACETS	0.376	0.304	0.459	0.188	0.152	0.23	SUBCLONAL	1	TRUE	0	0.308989598378155	2		712	533	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939847	76939847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	16	252	0	ENST00000373344.5:c.901G>A	p.Asp301Asn	p.D301N	ENST00000373344	NM_000489.3	301	Gac/Aac	9/35	0.280926777361091	2	FACETS	0.337	0.249	0.443			1	SUBCLONAL	1	TRUE	NA	0.308989598378155	2		252	307	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149799	202149809	+	frameshift_variant	Frame_Shift_Del	DEL	TTTTTTATTCA	TTTTTTATTCA	G	novel	NA	P-0059941-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	141	680	0	ENST00000358485.4:c.1240_1250delinsG	p.Phe414GlyfsTer24	p.F414Gfs*24	ENST00000358485	NM_001080125.1	414	TTTTTTATTCAg/Gg	8/9	0.308989598378155	3	FACETS	0.787	0.719	0.859	0.787	0.719	0.859	SUBCLONAL	2	TRUE	1	0.308989598378155	3		680	669	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200961	108200961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782310	NA	P-0059942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	97	471	0	ENST00000278616.4:c.7328G>A	p.Arg2443Gln	p.R2443Q	ENST00000278616	NM_000051.3	2443	cGa/cAa	50/63	0.244208414427425	2	FACETS	0.829	0.742	0.922	0.415	0.371	0.461	INDETERMINATE	1	TRUE	0	0.443859213042382	2		471	527	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528895	157528895	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs763772159	NA	P-0059942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	153	596	0	ENST00000346085.5:c.6620G>C	p.Arg2207Thr	p.R2207T	ENST00000346085	NM_020732.3	2207	aGa/aCa	20/20	0.443859213042382	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.443859213042382	1		596	513	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934874	NA	P-0059942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	224	651	2	ENST00000269305.4:c.451C>A	p.Pro151Thr	p.P151T	ENST00000269305	NM_001126112.2	151	Ccc/Acc	5/11	0.443859213042382	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.443859213042382	1		653	657	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087558	27087558	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0059942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	217	667	0	ENST00000324856.7:c.2132C>G	p.Ser711Ter	p.S711*	ENST00000324856	NM_006015.4	711	tCa/tGa	5/20	0.209616698644419	2	FACETS	1	0.991	1	0.692	0.647	0.74	INDETERMINATE	1	TRUE	0	0.443859213042382	2		667	706	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801749	3801749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	112	543	0	ENST00000262367.5:c.3757G>A	p.Asp1253Asn	p.D1253N	ENST00000262367	NM_004380.2	1253	Gac/Aac	20/31	1	2	FACETS	0.784	0.706	0.865	0.784	0.706	0.865	SUBCLONAL	1	TRUE	1	0.443859213042382	2		543	644	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045677	47045677	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	145	369	0	ENST00000377604.3:c.2560del	p.Asp854ThrfsTer32	p.D854Tfs*32	ENST00000377604	NM_001204468.1	853	cGg/cg	23/24	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.443859213042382	1		369	356	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335639	81335639	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	150	391	0	ENST00000222390.5:c.1721C>A	p.Pro574His	p.P574H	ENST00000222390	NM_000601.4	574	cCt/cAt	15/18	0.391166871703046	3	FACETS	1	0.985	1	0.67	0.615	0.728	CLONAL	1	TRUE	1	0.443859213042382	3		391	616	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42002891	42002891	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	99	313	0	ENST00000219905.7:c.2428G>T	p.Gly810Ter	p.G810*	ENST00000219905	NM_001164273.1	810	Gga/Tga	8/24	0.209616698644419	2	FACETS	1	0.96	1	0.568	0.51	0.627	INDETERMINATE	1	TRUE	0	0.443859213042382	2		313	393	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166916	32166916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	76	570	0	ENST00000375023.3:c.4322C>T	p.Pro1441Leu	p.P1441L	ENST00000375023	NM_004557.3	1441	cCt/cTt	24/30	0.290709176689229	1	FACETS	0.48	0.421	0.543	0.48	0.421	0.543	SUBCLONAL	1	TRUE	0	0.443859213042382	1		570	555	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948488	31948488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	40	250	0	ENST00000375333.2:c.971C>T	p.Ser324Leu	p.S324L	ENST00000375333	NM_032454.1	324	tCa/tTa	7/8	0.290709176689229	1	FACETS	0.626	0.525	0.737	0.626	0.525	0.737	SUBCLONAL	1	TRUE	0	0.443859213042382	1		250	224	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379701	17379701	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs775407791	NA	P-0059942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	63	633	0	ENST00000359435.4:c.86C>G	p.Ser29Cys	p.S29C	ENST00000359435	NM_001033549.1	29	tCc/tGc	2/9	0.443859213042382	1	FACETS	0.383	0.331	0.439	0.383	0.331	0.439	SUBCLONAL	1	TRUE	0	0.443859213042382	1		633	577	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1686819	1686819	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	63	499	0	ENST00000378625.1:c.1117A>C	p.Ile373Leu	p.I373L	ENST00000378625	NM_001198994.1	373	Ata/Cta	9/14	0.209616698644419	2	FACETS	0.513	0.444	0.588	0.257	0.222	0.294	INDETERMINATE	1	TRUE	0	0.443859213042382	2		499	553	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961330	41961331	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0059942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	82	539	0	ENST00000219905.7:c.240_241dup	p.Asn81IlefsTer16	p.N81Ifs*16	ENST00000219905	NM_001164273.1	80	gat/gATat	2/24	0.209616698644419	2	FACETS	0.555	0.489	0.625	0.277	0.244	0.313	INDETERMINATE	1	TRUE	0	0.443859213042382	2		539	666	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041575	42041575	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	227	584	0	ENST00000219905.7:c.5770T>C	p.Tyr1924His	p.Y1924H	ENST00000219905	NM_001164273.1	1924	Tat/Cat	17/24	0.209616698644419	2	FACETS	1	0.992	1	0.718	0.672	0.766	INDETERMINATE	1	TRUE	0	0.443859213042382	2		584	712	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786796	3786796	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	87	491	0	ENST00000262367.5:c.4415G>C	p.Trp1472Ser	p.W1472S	ENST00000262367	NM_004380.2	1472	tGg/tCg	27/31	1	2	FACETS	0.678	0.601	0.76	0.678	0.601	0.76	SUBCLONAL	1	TRUE	1	0.443859213042382	2		491	578	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923665	72923665	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	164	615	0	ENST00000268489.5:c.3413T>G	p.Ile1138Ser	p.I1138S	ENST00000268489	NM_006885.3	1138	aTc/aGc	4/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.443859213042382	2		615	650	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18972880	18972880	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	52	489	0	ENST00000262803.5:c.2519C>G	p.Ser840Cys	p.S840C	ENST00000262803	NM_002911.3	840	tCc/tGc	18/24	0.443859213042382	1	FACETS	0.354	0.301	0.412	0.354	0.301	0.412	SUBCLONAL	1	TRUE	0	0.443859213042382	1		489	515	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609697	46609697	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	54	606	0	ENST00000263734.3:c.2421G>C	p.Gln807His	p.Q807H	ENST00000263734	NM_001430.4	807	caG/caC	15/16	0.151519708333711	3	FACETS	0.4	0.341	0.465	0.133	0.113	0.155	INDETERMINATE	1	TRUE	0	0.443859213042382	3		606	743	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553269	41553269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767582855	NA	P-0059942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	177	499	0	ENST00000263253.7:c.3358G>A	p.Asp1120Asn	p.D1120N	ENST00000263253	NM_001429.3	1120	Gat/Aat	18/31	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.443859213042382	2		499	620	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056223	26056223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	68	659	0	ENST00000343677.2:c.434C>T	p.Ala145Val	p.A145V	ENST00000343677	NM_005319.3	145	gCa/gTa	1/1	0.290709176689229	1	FACETS	0.386	0.336	0.441	0.386	0.336	0.441	SUBCLONAL	1	TRUE	0	0.443859213042382	1		659	617	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508231	106508231	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	197	611	0	ENST00000359195.3:c.225G>C	p.Trp75Cys	p.W75C	ENST00000359195	NM_002649.2	75	tgG/tgC	2/11	0.391166871703046	3	FACETS	1	0.988	1	0.657	0.609	0.706	CLONAL	1	TRUE	1	0.443859213042382	3		611	826	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230751	53230751	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	119	247	0	ENST00000375401.3:c.2042G>T	p.Arg681Leu	p.R681L	ENST00000375401	NM_004187.3	681	cGa/cTa	14/26	1	1	FACETS	0.812	0.747	0.877	1	0.989	1	CLONAL	2	TRUE	0	0.443859213042382	1		247	257	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888829	76888829	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1557106489	NA	P-0059942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	136	262	0	ENST00000373344.5:c.5000A>G	p.Tyr1667Cys	p.Y1667C	ENST00000373344	NM_000489.3	1667	tAc/tGc	19/35	1	1	FACETS	0.848	0.787	0.91	1	0.991	1	CLONAL	2	TRUE	0	0.443859213042382	1		262	281	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26978156	26978156	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059943-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	153	371	0	ENST00000381527.3:c.1333del	p.Met445TrpfsTer37	p.M445Wfs*37	ENST00000381527	NM_001260.1	445	Atg/tg	13/13	0.193407003106825	4	FACETS	1	0.932	1	1	0.932	1	INDETERMINATE	2	TRUE	2	0.335257734459732	4		371	600	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060858	38060861	+	frameshift_variant	Frame_Shift_Del	DEL	GTGT	GTGT	-	novel	NA	P-0059943-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	96	654	0	ENST00000250448.2:c.1128_1131del	p.His377AlafsTer11	p.H377Afs*11	ENST00000250448	NM_004496.3	376	gcACAC/gc	2/2	0.251796682490735	4	FACETS	0.75	0.666	0.839	0.375	0.333	0.42	SUBCLONAL	1	TRUE	2	0.335257734459732	4		654	1020	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061226	38061229	+	frameshift_variant	Frame_Shift_Del	DEL	CGAA	CGAA	-	novel	NA	P-0059943-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	262	601	0	ENST00000250448.2:c.760_763del	p.Phe254ArgfsTer66	p.F254Rfs*66	ENST00000250448	NM_004496.3	254	TTCGag/ag	2/2	0.251796682490735	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.335257734459732	4		601	916	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80063772	80063772	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs773818431	NA	P-0059943-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	53	336	0	ENST00000265081.6:c.1917C>G	p.Phe639Leu	p.F639L	ENST00000265081	NM_002439.4	639	ttC/ttG	14/24	1	2	FACETS	0.985	0.845	1	0.985	0.845	1	CLONAL	1	TRUE	1	0.335257734459732	2		336	321	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0059944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	21	463	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.256996254466741	4	FACETS	1	0.863	1	0.387	0.301	0.485	CLONAL	1	TRUE	1	0.338933122711878	4		463	143	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156672	2156672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	80	553	0	ENST00000434045.2:c.250C>T	p.Pro84Ser	p.P84S	ENST00000434045	NM_001127598.1	84	Ccc/Tcc	3/5	0.317006961573064	3	FACETS	0.957	0.843	1	0.478	0.421	0.539	CLONAL	1	TRUE	1	0.338933122711878	3		553	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	70	584	0	ENST00000269305.4:c.991del	p.Gln331ArgfsTer14	p.Q331Rfs*14	ENST00000269305	NM_001126112.2	331	Cag/ag	9/11	0.349035120311484	4	FACETS	0.758	0.664	0.857			1	SUBCLONAL	2	TRUE	NA	0.338933122711878	4		584	365	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37865697	37865697	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	131	541	0	ENST00000269571.5:c.566C>T	p.Ser189Phe	p.S189F	ENST00000269571		189	tCt/tTt	4/27	0.338933122711878	6	FACETS	0.996	0.906	1	0.664	0.604	0.727	CLONAL	2	TRUE	3	0.338933122711878	6		541	651	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751491	57751492	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0059944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	30	510	0	ENST00000274289.3:c.1499dup	p.Phe501IlefsTer9	p.F501Ifs*9	ENST00000274289	NM_006622.3	500	tca/tcCa	11/14	0.212356133733407	3	FACETS	0.607	0.49	0.74	0.304	0.245	0.37	SUBCLONAL	1	TRUE	1	0.338933122711878	3		510	341	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245933	46245933	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059946-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	114	572	1	ENST00000334344.6:c.4027C>T	p.Gln1343Ter	p.Q1343*	ENST00000334344	NM_152641.2	1343	Caa/Taa	15/21	0.188883052504056	3	FACETS	1	0.962	1	0.746	0.675	0.819	CLONAL	2	TRUE	0	0.249228820237225	3		573	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578477	7578482	+	inframe_deletion	In_Frame_Del	DEL	GGGTGT	GGGTGT	-	novel	NA	P-0059946-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	240	721	0	ENST00000269305.4:c.448_453del	p.Thr150_Pro151del	p.T150_P151del	ENST00000269305	NM_001126112.2	150	ACACCC/-	5/11	0.249228820237225	4	FACETS	1	0.948	1	1	0.948	1	CLONAL	3	TRUE	1	0.249228820237225	4		721	791	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	142	582	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.254689840418282	2	FACETS	1	0.985	1	0.691	0.633	0.752	CLONAL	1	TRUE	0	0.36245566579607	2		582	567	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602493	10602493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	70	671	0	ENST00000171111.5:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000171111	NM_203500.1	362	cGg/cAg	3/6	0.273899400477779	3	FACETS	0.586	0.51	0.669	0.293	0.255	0.335	SUBCLONAL	1	TRUE	1	0.36245566579607	3		671	778	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602580	10602580	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	163	652	0	ENST00000171111.5:c.998G>T	p.Gly333Val	p.G333V	ENST00000171111	NM_203500.1	333	gGc/gTc	3/6	0.273899400477779	3	FACETS	1	0.987	1	0.704	0.647	0.763	CLONAL	1	TRUE	1	0.36245566579607	3		652	755	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602580	10602581	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	163	660	0	ENST00000171111.5:c.997_998delinsTT	p.Gly333Phe	p.G333F	ENST00000171111	NM_203500.1	333	GGc/TTc	3/6	0.273899400477779	3	FACETS	1	0.987	1	0.704	0.647	0.763	CLONAL	1	TRUE	1	0.36245566579607	3		660	755	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971095	21971096	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	107	567	0	ENST00000304494.5:c.262dup	p.Glu88GlyfsTer32	p.E88Gfs*32	ENST00000304494	NM_000077.4	88	gag/gGag	2/3	0.312579936160212	3	FACETS	0.966	0.867	1	0.322	0.289	0.357	CLONAL	1	TRUE	0	0.36245566579607	3		567	722	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979597	55979597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	27	396	0	ENST00000263923.4:c.850G>A	p.Glu284Lys	p.E284K	ENST00000263923	NM_002253.2	284	Gag/Aag	7/30	1	2	FACETS	0.497	0.396	0.611	0.497	0.396	0.611	SUBCLONAL	1	TRUE	1	0.36245566579607	2		396	300	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233726	133233726	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	177	537	0	ENST00000320574.5:c.3578G>C	p.Arg1193Thr	p.R1193T	ENST00000320574	NM_006231.2	1193	aGa/aCa	29/49	0.36245566579607	4	FACETS	0.895	0.827	0.966	0.448	0.413	0.483	CLONAL	2	TRUE	0	0.36245566579607	4		537	743	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971153	21971153	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	147	602	0	ENST00000304494.5:c.205del	p.Glu69SerfsTer77	p.E69Sfs*77	ENST00000304494	NM_000077.4	69	Gag/ag	2/3	0.312579936160212	3	FACETS	1	0.978	1	0.406	0.371	0.443	CLONAL	1	TRUE	0	0.36245566579607	3		602	786	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50143346	50143346	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	56	425	0	ENST00000246792.3:c.10G>T	p.Gly4Trp	p.G4W	ENST00000246792	NM_006270.3	4	Ggg/Tgg	1/6	0.273899400477779	3	FACETS	0.636	0.545	0.736	0.318	0.272	0.368	SUBCLONAL	1	TRUE	1	0.36245566579607	3		425	574	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747109	40747109	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	95	467	0	ENST00000373198.4:c.2973G>A	p.Trp991Ter	p.W991*	ENST00000373198	NM_133170.3	991	tgG/tgA	22/32	0.273899400477779	3	FACETS	1	0.968	1	0.612	0.547	0.681	CLONAL	1	TRUE	1	0.36245566579607	3		467	506	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564734	86564734	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	145	587	0	ENST00000274376.6:c.466G>T	p.Gly156Cys	p.G156C	ENST00000274376	NM_002890.2	156	Ggt/Tgt	1/25	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.36245566579607	2		587	702	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528514	157528514	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	88	547	0	ENST00000346085.5:c.6239G>C	p.Arg2080Thr	p.R2080T	ENST00000346085	NM_020732.3	2080	aGa/aCa	20/20	0.350128873379033	2	FACETS	0.862	0.766	0.965	0.431	0.383	0.483	CLONAL	1	TRUE	0	0.36245566579607	2		547	563	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256861	16256861	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	56	589	0	ENST00000375759.3:c.4126G>T	p.Gly1376Cys	p.G1376C	ENST00000375759	NM_015001.2	1376	Ggt/Tgt	11/15	1	2	FACETS	0.709	0.608	0.818	0.709	0.608	0.818	SUBCLONAL	1	TRUE	1	0.36245566579607	2		589	436	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202555	67202555	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	323	659	0	ENST00000312629.5:c.1364C>G	p.Pro455Arg	p.P455R	ENST00000312629	NM_003952.2	455	cCg/cGg	15/15	0.312579936160212	3	FACETS	1	0.99	1	0.788	0.747	0.831	CLONAL	2	TRUE	0	0.36245566579607	3		659	890	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21626553	21626553	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	35	448	0	ENST00000421138.2:c.1379A>T	p.Gln460Leu	p.Q460L	ENST00000421138		460	cAa/cTa	13/16	0.350128873379033	2	FACETS	0.924	0.764	1	0.462	0.382	0.55	CLONAL	1	TRUE	0	0.36245566579607	2		448	209	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120711	115120711	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	144	625	0	ENST00000257566.3:c.295G>T	p.Val99Leu	p.V99L	ENST00000257566	NM_016569.3	99	Gtg/Ttg	1/8	0.36245566579607	3	FACETS	1	0.975	1	0.394	0.359	0.43	CLONAL	1	TRUE	0	0.36245566579607	3		625	795	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636452	73636452	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	88	645	0	ENST00000377687.4:c.715A>G	p.Met239Val	p.M239V	ENST00000377687	NM_001730.3	239	Atg/Gtg	2/4	0.138995366784877	5	FACETS	1	0.899	1	0.339	0.3	0.38	INDETERMINATE	1	TRUE	2	0.36245566579607	5		645	738	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514848	103514848	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	122	609	0	ENST00000355739.4:c.1349G>T	p.Ser450Ile	p.S450I	ENST00000355739	NM_000123.3	450	aGt/aTt	8/15	0.138995366784877	5	FACETS	0.781	0.707	0.859	0.521	0.471	0.573	INDETERMINATE	2	TRUE	2	0.36245566579607	5		609	665	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749061	43749061	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	37	570	0	ENST00000382044.4:c.1745T>A	p.Val582Glu	p.V582E	ENST00000382044	NM_001141980.1	582	gTa/gAa	12/28	1	2	FACETS	0.665	0.55	0.792	0.665	0.55	0.792	SUBCLONAL	1	TRUE	1	0.36245566579607	2		570	307	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348891	11348891	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs760173376	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	69	464	0	ENST00000332029.2:c.445G>C	p.Glu149Gln	p.E149Q	ENST00000332029	NM_003745.1	149	Gag/Cag	2/2	0.254689840418282	2	FACETS	0.641	0.558	0.73	0.32	0.279	0.365	SUBCLONAL	1	TRUE	0	0.36245566579607	2		464	594	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86545044	86545044	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	56	502	0	ENST00000262426.4:c.869T>G	p.Leu290Arg	p.L290R	ENST00000262426	NM_001451.2	290	cTg/cGg	1/2	0.151018603992044	5	FACETS	0.798	0.683	0.923	0.266	0.227	0.308	INDETERMINATE	1	TRUE	2	0.36245566579607	5		502	598	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354466	40354466	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	79	588	0	ENST00000293328.3:c.2130-1G>T		p.X710_splice	ENST00000293328	NM_012448.3	710			0.347509850869123	4	FACETS	0.731	0.642	0.826	0.365	0.321	0.413	SUBCLONAL	1	TRUE	2	0.36245566579607	4		588	813	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226444	41226444	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	95	509	0	ENST00000357654.3:c.4579G>T	p.Glu1527Ter	p.E1527*	ENST00000357654	NM_007294.3	1527	Gag/Tag	14/23	0.347509850869123	4	FACETS	1	0.967	1	0.607	0.542	0.677	CLONAL	1	TRUE	2	0.36245566579607	4		509	588	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61310734	61310734	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	12	54	0	ENST00000341074.5:c.78C>G	p.Asn26Lys	p.N26K	ENST00000341074	NM_002974.2	26	aaC/aaG	2/8	0.254689840418282	2	FACETS	0.92	0.678	1	0.92	0.678	1	CLONAL	2	TRUE	0	0.36245566579607	2		54	36	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621888	1621888	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	97	556	0	ENST00000344749.5:c.904G>T	p.Gly302Cys	p.G302C	ENST00000344749	NM_001136139.2	302	Ggc/Tgc	11/19	0.273899400477779	3	FACETS	0.894	0.798	0.997	0.447	0.399	0.499	CLONAL	1	TRUE	1	0.36245566579607	3		556	707	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224533	36224533	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	186	669	0	ENST00000222270.7:c.6995G>T	p.Arg2332Leu	p.R2332L	ENST00000222270	NM_014727.1	2332	cGt/cTt	29/37	0.254689840418282	2	FACETS	0.763	0.707	0.82	0.763	0.707	0.82	SUBCLONAL	2	TRUE	0	0.36245566579607	2		669	673	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791307	42791307	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	158	534	0	ENST00000575354.2:c.367C>T	p.Pro123Ser	p.P123S	ENST00000575354	NM_015125.3	123	Ccg/Tcg	3/20	0.254689840418282	2	FACETS	1	0.988	1	0.711	0.654	0.77	CLONAL	1	TRUE	0	0.36245566579607	2		534	613	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45854976	45854976	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	119	472	0	ENST00000391945.4:c.2194G>T	p.Asp732Tyr	p.D732Y	ENST00000391945	NM_000400.3	732	Gat/Tat	23/23	0.254689840418282	2	FACETS	1	0.985	1	0.739	0.672	0.81	CLONAL	1	TRUE	0	0.36245566579607	2		472	444	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902277	50902277	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	61	553	0	ENST00000440232.2:c.169G>T	p.Glu57Ter	p.E57*	ENST00000440232	NM_002691.3	57	Gag/Tag	2/27	0.273899400477779	3	FACETS	0.564	0.486	0.649	0.282	0.243	0.325	SUBCLONAL	1	TRUE	1	0.36245566579607	3		553	705	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912425	50912425	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	63	501	0	ENST00000440232.2:c.1939G>T	p.Val647Leu	p.V647L	ENST00000440232	NM_002691.3	647	Gtg/Ttg	16/27	0.273899400477779	3	FACETS	0.703	0.608	0.806	0.352	0.304	0.403	SUBCLONAL	1	TRUE	1	0.36245566579607	3		501	584	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723065	52723065	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	147	608	0	ENST00000322088.6:c.1250G>A	p.Trp417Ter	p.W417*	ENST00000322088	NM_014225.5	417	tGg/tAg	10/15	0.273899400477779	3	FACETS	0.752	0.689	0.818	0.752	0.689	0.818	SUBCLONAL	2	TRUE	1	0.36245566579607	3		608	637	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082379	16082379	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	183	568	0	ENST00000281043.3:c.193C>A	p.Arg65Ser	p.R65S	ENST00000281043	NM_005378.4	65	Cgt/Agt	2/3	0.273899400477779	3	FACETS	0.856	0.792	0.921	0.856	0.792	0.921	CLONAL	2	TRUE	1	0.36245566579607	3		568	697	SUCCESS
ALK	238	MSKCC	GRCh37	2	29419722	29419722	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	46	441	0	ENST00000389048.3:c.4078C>G	p.Arg1360Gly	p.R1360G	ENST00000389048	NM_004304.4	1360	Cgg/Ggg	28/29	0.273899400477779	3	FACETS	0.833	0.704	0.975	0.416	0.352	0.488	CLONAL	1	TRUE	1	0.36245566579607	3		441	360	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455274	29455274	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	170	592	0	ENST00000389048.3:c.2528G>T	p.Gly843Val	p.G843V	ENST00000389048	NM_004304.4	843	gGa/gTa	15/29	0.273899400477779	3	FACETS	0.794	0.732	0.858	0.794	0.732	0.858	SUBCLONAL	2	TRUE	1	0.36245566579607	3		592	698	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100905	41100905	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	48	554	0	ENST00000373198.4:c.1450+1G>C		p.X484_splice	ENST00000373198	NM_133170.3	484			0.273899400477779	3	FACETS	0.641	0.542	0.75	0.321	0.271	0.375	SUBCLONAL	1	TRUE	1	0.36245566579607	3		554	488	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729984	30729984	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	95	476	0	ENST00000295754.5:c.1505G>C	p.Ser502Thr	p.S502T	ENST00000295754	NM_003242.5	502	aGc/aCc	6/7	0.264404107831053	3	FACETS	1	0.979	1	0.473	0.424	0.526	CLONAL	1	TRUE	0	0.36245566579607	3		476	436	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103765	47103765	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	52	511	0	ENST00000409792.3:c.6181A>T	p.Arg2061Ter	p.R2061*	ENST00000409792	NM_014159.6	2061	Aga/Tga	14/21	0.264404107831053	3	FACETS	0.634	0.539	0.737	0.211	0.179	0.246	SUBCLONAL	1	TRUE	0	0.36245566579607	3		511	535	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498373	89498373	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	33	393	0	ENST00000336596.2:c.2347-2A>G		p.X783_splice	ENST00000336596	NM_005233.5	783			0.309062992049305	4	FACETS	0.981	0.803	1	0.49	0.401	0.59	CLONAL	1	TRUE	2	0.36245566579607	4		393	253	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898759	134898759	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	134	553	0	ENST00000398015.3:c.1817C>G	p.Ala606Gly	p.A606G	ENST00000398015	NM_004441.4	606	gCt/gGt	10/16	0.36245566579607	4	FACETS	0.855	0.78	0.934	0.57	0.52	0.623	CLONAL	2	TRUE	1	0.36245566579607	4		553	589	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048608	180048608	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	108	578	0	ENST00000261937.6:c.1954G>A	p.Val652Met	p.V652M	ENST00000261937	NM_182925.4	652	Gtg/Atg	13/30	1	2	FACETS	0.998	0.898	1	0.998	0.898	1	CLONAL	1	TRUE	1	0.36245566579607	2		578	597	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948524	31948524	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	15	124	0	ENST00000375333.2:c.1007G>T	p.Arg336Leu	p.R336L	ENST00000375333	NM_032454.1	336	cGg/cTg	7/8	0.313693755488904	3	FACETS	0.679	0.5	0.891	0.226	0.166	0.297	SUBCLONAL	1	TRUE	0	0.36245566579607	3		124	144	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955024	93955024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	12	269	0	ENST00000369303.4:c.2874G>A	p.Met958Ile	p.M958I	ENST00000369303	NM_004440.3	958	atG/atA	16/17	0.264404107831053	3	FACETS	1	0.768	1	0.362	0.259	0.484	CLONAL	1	TRUE	0	0.36245566579607	3		269	72	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381544	81381544	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	75	377	0	ENST00000222390.5:c.517C>G	p.Gln173Glu	p.Q173E	ENST00000222390	NM_000601.4	173	Cag/Gag	5/18	0.36245566579607	4	FACETS	1	0.97	1	0.67	0.589	0.755	CLONAL	1	TRUE	2	0.36245566579607	4		377	421	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523561	148523561	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	54	358	0	ENST00000320356.2:c.892C>A	p.Arg298Ser	p.R298S	ENST00000320356	NM_004456.4	298	Cgt/Agt	8/20	0.36245566579607	3	FACETS	0.765	0.661	0.876	0.51	0.441	0.584	SUBCLONAL	2	TRUE	0	0.36245566579607	3		358	230	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228217	53228217	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	149	298	0	ENST00000375401.3:c.2185G>C	p.Val729Leu	p.V729L	ENST00000375401	NM_004187.3	729	Gtc/Ctc	15/26	0.326631533607057	2	FACETS	1	0.973	1			1	CLONAL	2	TRUE	NA	0.36245566579607	2		298	371	SUCCESS
AR	367	MSKCC	GRCh37	X	66942780	66942780	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	76	165	0	ENST00000374690.3:c.2561C>A	p.Ser854Ter	p.S854*	ENST00000374690	NM_000044.3	854	tCa/tAa	7/8	0.326631533607057	2	FACETS	1	0.931	1			1	CLONAL	2	TRUE	NA	0.36245566579607	2		165	199	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1232964733	NA	P-0059951-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	35	765	1	ENST00000324856.7:c.1015del	p.Ala339LeufsTer24	p.A339Lfs*24	ENST00000324856	NM_006015.4	337	tGg/tg	1/20	1	2	FACETS	0.57	0.467	0.685	0.57	0.467	0.685	SUBCLONAL	1	FALSE	1	0.292559217887027	2		766	420	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0059951-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	161	316	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.89	0.826	0.956	1	0.994	1	CLONAL	3	FALSE	1	0.292559217887027	2		316	412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587780070	NA	P-0059951-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	552	416	0	ENST00000269305.4:c.535C>G	p.His179Asp	p.H179D	ENST00000269305	NM_001126112.2	179	Cat/Gat	5/11	0.292559217887027	2	FACETS	0.971	0.951	0.989	1	0.998	1	CLONAL	6	FALSE	0	0.292559217887027	2		416	648	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352511	118352511	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059951-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	52	563	0	ENST00000534358.1:c.3716A>G	p.Asp1239Gly	p.D1239G	ENST00000534358	NM_005933.3	1239	gAc/gGc	7/36	1	2	FACETS	0.591	0.502	0.687	0.591	0.502	0.687	SUBCLONAL	1	FALSE	1	0.292559217887027	2		563	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0059952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	27	698	2	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		700	396	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0059952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	33	410	0	ENST00000311936.3:c.180_181delinsAA	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggAAaa	3/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		410	455	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437562	56437567	+	frameshift_variant	Frame_Shift_Del	DEL	GTCCAC	GTCCAC	TG	novel	NA	P-0059952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	41	627	1	ENST00000407977.2:c.895_900delinsCA	p.Val299HisfsTer119	p.V299Hfs*119	ENST00000407977		299	GTGGAC/CA	8/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		628	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0059953-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	35	677	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.336961625248435	4	FACETS	0.371	0.303	0.448	0.185	0.151	0.224	SUBCLONAL	1	TRUE	2	0.393651381318519	4		680	668	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413070	139413072	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0059953-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	16	986	0	ENST00000277541.6:c.1070_1072del	p.Phe357del	p.F357del	ENST00000277541	NM_017617.3	357	tTCTac/tac	6/34	0.217545582221142	4	FACETS	0.19	0.139	0.251	0.047	0.034	0.063	INDETERMINATE	1	TRUE	0	0.393651381318519	4		986	597	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412663	139412663	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1368532867	NA	P-0059953-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	51	720	0	ENST00000277541.6:c.1181G>T	p.Gly394Val	p.G394V	ENST00000277541	NM_017617.3	394	gGc/gTc	7/34	0.217545582221142	4	FACETS	0.545	0.462	0.636	0.136	0.115	0.159	INDETERMINATE	1	TRUE	0	0.393651381318519	4		720	663	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885949	59885949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs550031006	NA	P-0059953-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	24	559	0	ENST00000259008.2:c.797C>T	p.Thr266Met	p.T266M	ENST00000259008	NM_032043.2	266	aCg/aTg	7/20	0.139852713839338	4	FACETS	0.445	0.348	0.556	0.222	0.174	0.278	INDETERMINATE	1	TRUE	2	0.393651381318519	4		559	382	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984804	55984804	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059953-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	30	464	0	ENST00000263923.4:c.325G>A	p.Asp109Asn	p.D109N	ENST00000263923	NM_002253.2	109	Gac/Aac	3/30	1	2	FACETS	0.56	0.453	0.681	0.56	0.453	0.681	SUBCLONAL	1	TRUE	1	0.393651381318519	2		464	272	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971104	21971105	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	rs1064796336	NA	P-0059953-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	105	723	1	ENST00000304494.5:c.253_254delinsTT	p.Ala85Phe	p.A85F	ENST00000304494	NM_000077.4	85	GCt/TTt	2/3	0.393651381318519	3	FACETS	1	0.979	1	0.672	0.605	0.742	CLONAL	1	TRUE	1	0.393651381318519	3		724	475	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139414000	139414000	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059953-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	141	563	0	ENST00000277541.6:c.760T>A	p.Cys254Ser	p.C254S	ENST00000277541	NM_017617.3	254	Tgt/Agt	5/34	0.217545582221142	4	FACETS	0.937	0.858	1	0.468	0.429	0.509	INDETERMINATE	2	TRUE	0	0.393651381318519	4		563	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0059954-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	264	622	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.862580273114725	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.862580273114725	2		623	279	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518598	204518598	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059954-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	437	359	0	ENST00000367182.3:c.1261A>G	p.Arg421Gly	p.R421G	ENST00000367182	NM_001278516.1	421	Aga/Gga	11/11	0.862580273114725	6	FACETS	1	0.981	1	1	0.981	1	CLONAL	4	TRUE	2	0.862580273114725	6		359	675	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239745	41239745	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059954-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	155	527	0	ENST00000379561.5:c.605A>G	p.Asp202Gly	p.D202G	ENST00000379561	NM_002015.3	202	gAc/gGc	1/3	0.758640460200535	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.862580273114725	4		527	319	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51503100	51503100	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0059954-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	202	451	0	ENST00000260433.2:c.1417A>T	p.Lys473Ter	p.K473*	ENST00000260433		473	Aag/Tag	10/10	0.862580273114725	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.862580273114725	2		451	219	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587384	29587462	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGGTTTTTCCTTGATATAGCATCTGATTGTCCTACAAGTGATGCAGTAAATCATAGTCTTTCCTTCATAAGTGACGGC	AAGGTTTTTCCTTGATATAGCATCTGATTGTCCTACAAGTGATGCAGTAAATCATAGTCTTTCCTTCATAAGTGACGGC	-	novel	NA	P-0059954-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	119	226	0	ENST00000356175.3:c.4368-1_4445del		p.X1456_splice	ENST00000356175	NM_000267.3	1456		33/57	0.862580273114725	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.862580273114725	2		226	126	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243800	41243800	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs28897686	NA	P-0059954-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	222	389	0	ENST00000357654.3:c.3748G>T	p.Glu1250Ter	p.E1250*	ENST00000357654	NM_007294.3	1250	Gag/Tag	10/23	0.862580273114725	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.862580273114725	2		389	237	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441393	149441393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573212436	NA	P-0059954-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	209	595	0	ENST00000286301.3:c.1646G>A	p.Arg549His	p.R549H	ENST00000286301	NM_005211.3	549	cGc/cAc	12/22	0.758640460200535	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.862580273114725	4		595	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0059955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	65	629	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.338275253528351	1	FACETS	0.91	0.793	1	0.91	0.793	1	CLONAL	1	TRUE	0	0.338275253528351	1		630	351	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40855800	40855800	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1458266017	NA	P-0059955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	40	353	0	ENST00000428826.2:c.2056C>T	p.Arg686Ter	p.R686*	ENST00000428826		686	Cga/Tga	19/21	1	2	FACETS	0.624	0.519	0.74	0.624	0.519	0.74	SUBCLONAL	1	TRUE	1	0.338275253528351	2		353	379	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442599	52442599	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	91	596	0	ENST00000460680.1:c.146T>C	p.Leu49Pro	p.L49P	ENST00000460680	NM_004656.3	49	cTg/cCg	4/17	0.338275253528351	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.338275253528351	1		596	375	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044761	47044761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	106	890	0	ENST00000377604.3:c.2161C>A	p.Arg721Ser	p.R721S	ENST00000377604	NM_001204468.1	721	Cgc/Agc	19/24	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.338275253528351	2		890	625	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412311	63412311	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	77	669	0	ENST00000330258.3:c.856A>T	p.Ser286Cys	p.S286C	ENST00000330258	NM_152424.3	286	Agc/Tgc	2/2	1	2	FACETS	0.857	0.754	0.968	0.857	0.754	0.968	CLONAL	1	TRUE	1	0.338275253528351	2		669	531	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0059956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	94	343	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.921	0.828	1	0.921	0.828	1	CLONAL	1	TRUE	1	0.620258850321879	2		343	329	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0059956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	202	475	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.620258850321879	2	FACETS	0.933	0.882	0.983	0.933	0.882	0.983	CLONAL	2	TRUE	0	0.620258850321879	2		475	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0059956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	156	698	2	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.973	0.897	1	0.973	0.897	1	CLONAL	1	TRUE	1	0.620258850321879	2		700	517	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589575	67589576	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0059956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	61	232	0	ENST00000274335.5:c.1344dup	p.Leu449IlefsTer3	p.L449Ifs*3	ENST00000274335		446	-/A	10/15	1	2	FACETS	0.863	0.754	0.977	0.863	0.754	0.977	CLONAL	1	TRUE	1	0.620258850321879	2		232	228	SUCCESS
APC	324	MSKCC	GRCh37	5	112175770	112175770	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	150	623	0	ENST00000257430.4:c.4480del	p.Glu1494LysfsTer13	p.E1494Kfs*13	ENST00000257430	NM_000038.5	1493	acG/ac	16/16	1	2	FACETS	0.87	0.799	0.943	0.87	0.799	0.943	CLONAL	1	TRUE	1	0.620258850321879	2		623	556	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444345	50444345	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	182	680	0	ENST00000331340.3:c.275T>C	p.Met92Thr	p.M92T	ENST00000331340	NM_006060.4	92	aTg/aCg	4/8	0.620258850321879	3	FACETS	0.976	0.902	1	0.488	0.451	0.526	CLONAL	1	TRUE	1	0.620258850321879	3		680	788	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016672	12016672	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	134	512	0	ENST00000353533.5:c.808A>G	p.Met270Val	p.M270V	ENST00000353533	NM_003010.3	270	Atg/Gtg	7/11	0.620258850321879	1	FACETS	0.946	0.873	1	0.946	0.873	1	CLONAL	1	TRUE	0	0.620258850321879	1		512	315	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245873	5245873	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	178	668	0	ENST00000357368.4:c.902C>T	p.Thr301Ile	p.T301I	ENST00000357368	NM_002850.3	301	aCa/aTa	10/38	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.620258850321879	2		668	568	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0059956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	219	566	0	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.620258850321879	2		566	647	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382196	152382196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747099645	NA	P-0059956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	162	445	1	ENST00000206249.3:c.1306C>T	p.Arg436Cys	p.R436C	ENST00000206249	NM_000125.3	436	Cgc/Tgc	6/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.620258850321879	2		446	500	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0059957-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	57	435	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.223398598596901	3	FACETS	0.905	0.784	1	0.905	0.784	1	CLONAL	2	FALSE	1	0.273122032423855	3		435	262	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937036	36937036	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059957-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	41	709	0	ENST00000361632.4:c.1283G>A	p.Arg428Lys	p.R428K	ENST00000361632		428	aGa/aAa	9/16	1	2	FACETS	0.672	0.56	0.796	0.672	0.56	0.796	SUBCLONAL	1	FALSE	1	0.273122032423855	2		709	447	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910547	29910547	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059957-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	71	595	0	ENST00000376809.5:c.87G>C	p.Met29Ile	p.M29I	ENST00000376809	NM_002116.7	29	atG/atC	2/8	1	2	FACETS	0.938	0.828	1	1	0.982	1	CLONAL	2	FALSE	1	0.273122032423855	2		595	277	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11210213	11210213	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1420274633	NA	P-0059957-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	48	627	0	ENST00000361445.4:c.4540C>T	p.Arg1514Trp	p.R1514W	ENST00000361445	NM_004958.3	1514	Cgg/Tgg	31/58	1	2	FACETS	0.792	0.67	0.925	0.792	0.67	0.925	CLONAL	1	FALSE	1	0.273122032423855	2		627	444	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992213	11992218	+	inframe_deletion	In_Frame_Del	DEL	CTTTCG	CTTTCG	-	novel	NA	P-0059957-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	57	715	0	ENST00000396373.4:c.305_310del	p.Phe102_Arg103del	p.F102_R103del	ENST00000396373	NM_001987.4	101	gaCTTTCGc/gac	3/8	0.184863497600147	3	FACETS	0.784	0.672	0.906	0.392	0.336	0.453	CLONAL	1	FALSE	1	0.273122032423855	3		715	605	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068908	30068908	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059957-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	26	486	0	ENST00000331968.5:c.2021A>C	p.Glu674Ala	p.E674A	ENST00000331968	NM_002742.2	674	gAa/gCa	14/18	1	2	FACETS	0.589	0.467	0.729	0.589	0.467	0.729	SUBCLONAL	1	FALSE	1	0.273122032423855	2		486	323	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961196	41961196	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059957-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	64	674	0	ENST00000219905.7:c.104A>C	p.Lys35Thr	p.K35T	ENST00000219905	NM_001164273.1	35	aAa/aCa	2/24	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	1	0.273122032423855	2		674	425	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732961	30732961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059957-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	116	722	1	ENST00000295754.5:c.1574C>T	p.Pro525Leu	p.P525L	ENST00000295754	NM_003242.5	525	cCa/cTa	7/7	1	2	FACETS	0.86	0.779	0.944	1	0.987	1	CLONAL	2	FALSE	1	0.273122032423855	2		723	494	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253802	153253802	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059957-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	40	492	0	ENST00000281708.4:c.931T>A	p.Trp311Arg	p.W311R	ENST00000281708	NM_033632.3	311	Tgg/Agg	6/12	1	2	FACETS	0.942	0.786	1	0.942	0.786	1	CLONAL	1	FALSE	1	0.273122032423855	2		492	311	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512419	149512419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs942220808	NA	P-0059957-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	56	951	0	ENST00000261799.4:c.1021G>A	p.Glu341Lys	p.E341K	ENST00000261799	NM_002609.3	341	Gag/Aag	7/23	1	2	FACETS	0.759	0.651	0.878	0.759	0.651	0.878	SUBCLONAL	1	FALSE	1	0.273122032423855	2		951	540	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911171	29911171	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs199474533	NA	P-0059957-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	42	859	0	ENST00000376809.5:c.470G>C	p.Trp157Ser	p.W157S	ENST00000376809	NM_002116.7	157	tGg/tCg	3/8	1	2	FACETS	0.879	0.736	1	0.879	0.736	1	CLONAL	1	FALSE	1	0.273122032423855	2		859	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0059984-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	73	629	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.834	0.729	0.947	0.834	0.729	0.947	CLONAL	1	TRUE	1	0.262562322872007	2		630	667	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0059984-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	66	632	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.71	0.616	0.813	0.71	0.616	0.813	SUBCLONAL	1	TRUE	1	0.262562322872007	2		632	708	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900363	3900363	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059984-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	77	643	0	ENST00000262367.5:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000262367	NM_004380.2	245	Cag/Tag	2/31	1	2	FACETS	0.709	0.622	0.804	0.709	0.622	0.804	SUBCLONAL	1	TRUE	1	0.262562322872007	2		643	827	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271216	26271216	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059984-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	82	824	0	ENST00000305910.3:c.397G>T	p.Gly133Trp	p.G133W	ENST00000305910	NM_003534.2	133	Ggg/Tgg	1/1	1	2	FACETS	0.743	0.654	0.838	0.743	0.654	0.838	SUBCLONAL	1	TRUE	1	0.262562322872007	2		824	841	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104357035	104357035	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060121-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	307	248	1	ENST00000369902.3:c.895C>T	p.Arg299Ter	p.R299*	ENST00000369902	NM_016169.3	299	Cga/Tga	7/12	0.865812861989119	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.865812861989119	2		249	347	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230561506	230561506	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0060413-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	45	654	0				ENST00000391860	NM_001258311.1	-/409			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		654	636	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060463-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	29	300	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.665	0.533	0.815	0.665	0.533	0.815	SUBCLONAL	1	FALSE	1	0.200503236259601	2		300	435	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0060463-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	83	425	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.128974853788132	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	FALSE	1	0.200503236259601	3		426	410	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467448	25467448	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1164367418	NA	P-0060463-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	56	738	0	ENST00000264709.3:c.1628del	p.Gly543AlafsTer108	p.G543Afs*108	ENST00000264709	NM_175629.2	543	gGc/gc	14/23	1	2	FACETS	0.837	0.717	0.97	0.837	0.717	0.97	CLONAL	1	FALSE	1	0.200503236259601	2		738	667	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627290	12627290	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060463-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	48	422	0	ENST00000251849.4:c.1426C>T	p.Leu476Phe	p.L476F	ENST00000251849	NM_002880.3	476	Ctc/Ttc	14/17	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	FALSE	1	0.200503236259601	2		422	449	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137528167	137528167	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs777965499	NA	P-0060463-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	33	446	0	ENST00000367739.4:c.133A>G	p.Ile45Val	p.I45V	ENST00000367739	NM_000416.2	45	Atc/Gtc	2/7	1	2	FACETS	0.644	0.524	0.78	0.644	0.524	0.78	SUBCLONAL	1	FALSE	1	0.200503236259601	2		446	511	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039886	47039886	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060463-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	36	514	0	ENST00000377604.3:c.1231del	p.Gln411SerfsTer74	p.Q411Sfs*74	ENST00000377604	NM_001204468.1	410	gCc/gc	12/24	1	2	FACETS	0.791	0.65	0.949	0.791	0.65	0.949	CLONAL	1	FALSE	1	0.200503236259601	2		514	454	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854906	76854907	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0060463-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	31	461	0	ENST00000373344.5:c.5929_5930delinsAG	p.Pro1977Ser	p.P1977S	ENST00000373344	NM_000489.3	1977	CCt/AGt	25/35	1	2	FACETS	0.642	0.518	0.782	0.642	0.518	0.782	SUBCLONAL	1	FALSE	1	0.200503236259601	2		461	482	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	111	300	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.565	0.506	0.628	0.565	0.506	0.628	SUBCLONAL	1	TRUE	1	0.317712099075894	2		300	1237	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0060595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	31	336	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA	2	FACETS	0.895	0.729	1			1	INDETERMINATE	1	TRUE	NA	0.317712099075894	2		336	218	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0060595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	25	535	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.317712099075894	3	FACETS	1	0.847	1	0.54	0.429	0.664	CLONAL	1	TRUE	1	0.317712099075894	3		535	169	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163720	32163720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253487294	NA	P-0060595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	179	513	0	ENST00000375023.3:c.5506G>A	p.Glu1836Lys	p.E1836K	ENST00000375023	NM_004557.3	1836	Gag/Aag	30/30	1	2	FACETS	0.855	0.786	0.927	0.855	0.786	0.927	CLONAL	1	TRUE	1	0.317712099075894	2		513	1318	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827887	170827887	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1431020185	NA	P-0060595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	56	239	0	ENST00000296930.5:c.627G>C	p.Gln209His	p.Q209H	ENST00000296930	NM_002520.6	209	caG/caC	8/11	1	2	FACETS	0.814	0.699	0.939	0.814	0.699	0.939	CLONAL	1	TRUE	1	0.317712099075894	2		239	433	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404464	70404464	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	54	315	0	ENST00000373644.4:c.1978G>C	p.Asp660His	p.D660H	ENST00000373644	NM_030625.2	660	Gac/Cac	4/12	1	2	FACETS	0.809	0.693	0.936	0.809	0.693	0.936	CLONAL	1	TRUE	1	0.317712099075894	2		315	420	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904859	101904859	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	141	376	0	ENST00000374994.4:c.847C>G	p.His283Asp	p.H283D	ENST00000374994	NM_004612.2	283	Cat/Gat	5/9	0.268175223568127	2	FACETS	0.963	0.884	1	0.963	0.884	1	CLONAL	2	TRUE	0	0.317712099075894	2		376	461	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436173	116436176	+	frameshift_variant,stop_lost	Frame_Shift_Del	DEL	TCAT	TCAT	-	novel	NA	P-0060596-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	47	274	0	ENST00000397752.3:c.4168_4171del	p.Ter1391AlafsTer22	p.*1391Afs*22	ENST00000397752	NM_000245.2	1390	TCATag/ag	21/21	1	2	FACETS	0.674	0.568	0.792	0.674	0.568	0.792	SUBCLONAL	1	TRUE	1	0.21	2		274	664	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0060597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	489	732	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.807219788823407	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.819710057037206	2		732	587	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197309	106197309	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1417392445	NA	P-0060597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	289	491	0	ENST00000380013.4:c.5642A>G	p.His1881Arg	p.H1881R	ENST00000380013	NM_001127208.2	1881	cAt/cGt	11/11	0.742621563515881	3	FACETS	0.902	0.858	0.946	0.902	0.858	0.946	CLONAL	2	TRUE	1	0.819710057037206	3		491	551	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527265	187527265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373448625	NA	P-0060597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	197	472	0	ENST00000441802.2:c.10309G>A	p.Ala3437Thr	p.A3437T	ENST00000441802	NM_005245.3	3437	Gcg/Acg	17/27	0.742621563515881	3	FACETS	0.846	0.785	0.909	0.423	0.392	0.455	CLONAL	1	TRUE	1	0.819710057037206	3		472	801	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007234	62007234	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	306	566	0	ENST00000392795.3:c.448G>T	p.Ala150Ser	p.A150S	ENST00000392795	NM_001039933.1	150	Gca/Tca	4/6	0.436503934116559	5	FACETS	0.892	0.849	0.935	0.892	0.849	0.935	INDETERMINATE	3	TRUE	2	0.819710057037206	5		566	622	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938135	36938135	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201037400	NA	P-0060597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	118	549	0	ENST00000361632.4:c.826G>A	p.Glu276Lys	p.E276K	ENST00000361632		276	Gaa/Aaa	6/16	1	2	FACETS	0.778	0.709	0.849	0.778	0.709	0.849	SUBCLONAL	1	TRUE	1	0.819710057037206	2		549	370	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509450	46509450	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	46	499	0	ENST00000262741.5:c.1281G>T	p.Glu427Asp	p.E427D	ENST00000262741	NM_003629.3	427	gaG/gaT	10/10	1	2	FACETS	0.23	0.193	0.27	0.23	0.193	0.27	SUBCLONAL	1	TRUE	1	0.819710057037206	2		499	488	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497596	125497596	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0060597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	114	359	0	ENST00000428830.2:c.160A>T	p.Lys54Ter	p.K54*	ENST00000428830	NM_001114121.2	54	Aaa/Taa	3/14	0.222226826596354	3	FACETS	0.91	0.825	0.998	0.303	0.275	0.333	INDETERMINATE	1	TRUE	0	0.819710057037206	3		359	431	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124238	2124238	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	194	558	0	ENST00000219476.3:c.2393A>T	p.His798Leu	p.H798L	ENST00000219476	NM_000548.3	798	cAc/cTc	22/42	0.340819208060802	3	FACETS	1	0.989	1	0.654	0.611	0.699	INDETERMINATE	1	TRUE	1	0.819710057037206	3		558	510	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923328	9923328	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	198	377	0	ENST00000330684.3:c.1959G>T	p.Met653Ile	p.M653I	ENST00000330684	NM_001134407.1	653	atG/atT	9/13	0.340819208060802	3	FACETS	0.762	0.714	0.81	0.762	0.714	0.81	INDETERMINATE	2	TRUE	1	0.819710057037206	3		377	447	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032357	10032357	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	160	478	0	ENST00000330684.3:c.466A>T	p.Thr156Ser	p.T156S	ENST00000330684	NM_001134407.1	156	Acg/Tcg	3/13	0.340819208060802	3	FACETS	1	0.98	1	0.586	0.541	0.631	INDETERMINATE	1	TRUE	1	0.819710057037206	3		478	470	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278135	15278135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	29	531	0	ENST00000263388.2:c.5287G>A	p.Ala1763Thr	p.A1763T	ENST00000263388	NM_000435.2	1763	Gca/Aca	29/33	0.807219788823407	2	FACETS	0.148	0.118	0.182	0.074	0.059	0.091	SUBCLONAL	1	TRUE	0	0.819710057037206	2		531	479	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248743	212248743	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	117	462	0	ENST00000342788.4:c.3524G>T	p.Arg1175Ile	p.R1175I	ENST00000342788	NM_005235.2	1175	aGa/aTa	28/28	0.806462035071059	2	FACETS	0.678	0.616	0.742	0.339	0.308	0.371	SUBCLONAL	1	TRUE	0	0.819710057037206	2		462	421	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206812	36206812	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	86	598	0	ENST00000300305.3:c.700A>G	p.Thr234Ala	p.T234A	ENST00000300305		234	Aca/Gca	6/8	0.781188609785077	4	FACETS	0.449	0.397	0.506	0.112	0.099	0.127	SUBCLONAL	1	TRUE	0	0.819710057037206	4		598	850	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499435	89499435	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	371	518	0	ENST00000336596.2:c.2605C>G	p.Pro869Ala	p.P869A	ENST00000336596	NM_005233.5	869	Ccc/Gcc	15/17	0.806462035071059	2	FACETS	0.935	0.906	0.963	0.935	0.906	0.963	CLONAL	2	TRUE	0	0.819710057037206	2		518	484	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161366	185161366	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1248	83	413	0	ENST00000265026.3:c.793A>G	p.Ser265Gly	p.S265G	ENST00000265026	NM_004721.4	265	Agt/Ggt	4/14	0.819710057037206	6	FACETS	0.402	0.353	0.454	0.1	0.088	0.114	SUBCLONAL	1	TRUE	2	0.819710057037206	6		413	1331	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562486	176562486	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	205	553	0	ENST00000439151.2:c.382C>T	p.Gln128Ter	p.Q128*	ENST00000439151	NM_022455.4	128	Cag/Tag	2/23	0.769367330463169	4	FACETS	0.891	0.826	0.958	0.445	0.413	0.479	CLONAL	1	TRUE	2	0.819710057037206	4		553	1022	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324862	31324863	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	GG	novel	NA	P-0060597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	407	528	0	ENST00000412585.2:c.73_73+1inv		p.X25_splice	ENST00000412585	NM_005514.6	25		1/8	0.807219788823407	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.819710057037206	2		528	478	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0060598-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	37	535	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.536	0.446	0.635	0.536	0.446	0.635	SUBCLONAL	1	TRUE	1	0.642206854791652	2		535	215	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115849	8115850	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0060598-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	247	761	0	ENST00000346208.3:c.1196dup	p.His399GlnfsTer108	p.H399Qfs*108	ENST00000346208		399	cac/cAac	6/6	1	2	FACETS	0.998	0.936	1	0.998	0.936	1	CLONAL	1	TRUE	1	0.642206854791652	2		761	771	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0060599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	26	465	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	0.756	0.597	0.939	0.756	0.597	0.939	CLONAL	1	TRUE	1	0.13	2		465	529	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0060599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	36	350	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.782	0.641	0.941	0.782	0.641	0.941	CLONAL	1	TRUE	1	0.13	2		350	708	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	34	573	3	ENST00000227507.2:c.859C>G	p.Pro287Ala	p.P287A	ENST00000227507	NM_053056.2	287	Ccc/Gcc	5/5	1	2	FACETS	0.639	0.52	0.774	0.639	0.52	0.774	SUBCLONAL	1	TRUE	1	0.13	2		576	818	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692892	89692892	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	31	261	0	ENST00000371953.3:c.376G>C	p.Ala126Pro	p.A126P	ENST00000371953	NM_000314.4	126	Gct/Cct	5/9	1	2	FACETS	0.846	0.686	1	1	0.951	1	CLONAL	2	TRUE	1	0.13	2		261	282	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477794	140477794	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060600-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	127	356	0	ENST00000288602.6:c.1514T>A	p.Leu505His	p.L505H	ENST00000288602	NM_004333.4	505	cTc/cAc	12/18	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.521178432810144	2		356	442	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32439190	32439192	+	inframe_deletion	In_Frame_Del	DEL	ATA	ATA	-	novel	NA	P-0060600-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	63	441	0	ENST00000332351.3:c.881_883del	p.Leu294del	p.L294del	ENST00000332351	NM_024426.4	294	tTATac/tac	4/10	0.24964086268268	1	FACETS	0.389	0.337	0.446	0.389	0.337	0.446	INDETERMINATE	1	TRUE	0	0.521178432810144	1		441	459	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060714	38060714	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060600-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	294	767	0	ENST00000250448.2:c.1275A>C	p.Gln425His	p.Q425H	ENST00000250448	NM_004496.3	425	caA/caC	2/2	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.521178432810144	2		767	1052	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021515	42021515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060600-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	91	516	0	ENST00000219905.7:c.3811C>T	p.His1271Tyr	p.H1271Y	ENST00000219905	NM_001164273.1	1271	Cat/Tat	11/24	0.272344905654466	3	FACETS	0.536	0.475	0.6	0.268	0.237	0.3	INDETERMINATE	1	TRUE	1	0.521178432810144	3		516	822	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178596	56178596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060600-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	178	514	0	ENST00000399503.3:c.3569C>T	p.Ala1190Val	p.A1190V	ENST00000399503	NM_005921.1	1190	gCa/gTa	14/20	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.521178432810144	2		514	682	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060601-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	50	412	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	1	2	FACETS	0.986	0.836	1	0.986	0.836	1	CLONAL	1	TRUE	1	0.19	2		412	534	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0060601-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	31	425	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.811	1	1	0.811	1	CLONAL	1	TRUE	1	0.19	2		426	326	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720877	89720877	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0060601-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	10	125	0	ENST00000371953.3:c.1026+2T>A		p.X342_splice	ENST00000371953	NM_000314.4	342			1	2	FACETS	0.638	0.433	0.895	0.638	0.433	0.895	SUBCLONAL	1	TRUE	1	0.19	2		125	165	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591101	67591101	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060601-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	36	322	0	ENST00000274335.5:c.1694G>T	p.Ser565Ile	p.S565I	ENST00000274335		565	aGc/aTc	12/15	1	2	FACETS	0.723	0.594	0.869	0.723	0.594	0.869	SUBCLONAL	1	TRUE	1	0.19	2		322	524	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720805	89720805	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060601-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	10	83	0	ENST00000371953.3:c.956del	p.Thr319IlefsTer2	p.T319Ifs*2	ENST00000371953	NM_000314.4	319	aCt/at	8/9	1	2	FACETS	0.948	0.647	1	0.948	0.647	1	CLONAL	1	TRUE	1	0.19	2		83	111	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114178	115114178	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060601-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	52	497	0	ENST00000257566.3:c.1039A>C	p.Asn347His	p.N347H	ENST00000257566	NM_016569.3	347	Aac/Cac	6/8	1	2	FACETS	0.772	0.656	0.9	0.772	0.656	0.9	SUBCLONAL	1	TRUE	1	0.19	2		497	709	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796099	78796099	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs201102317	NA	P-0060601-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	34	457	0	ENST00000306801.3:c.989G>A	p.Arg330Gln	p.R330Q	ENST00000306801	NM_020761.2	330	cGg/cAg	8/34	1	2	FACETS	0.527	0.429	0.638	0.527	0.429	0.638	SUBCLONAL	1	TRUE	1	0.19	2		457	679	SUCCESS
YES1	7525	MSKCC	GRCh37	18	751796	751796	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060601-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	20	178	0	ENST00000314574.4:c.280del	p.Thr94LeufsTer27	p.T94Lfs*27	ENST00000314574	NM_005433.3	94	Act/ct	3/12	1	2	FACETS	0.97	0.745	1	0.97	0.745	1	CLONAL	1	TRUE	1	0.19	2		178	217	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579312	7579312	+	splice_region_variant,synonymous_variant	Splice_Region	SNP	C	C	T	rs55863639	NA	P-0060602-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	410	447	1	ENST00000269305.4:c.375G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125	acG/acA	4/11	0.850043450032343	2	FACETS	0.981	0.957	1	0.981	0.957	1	CLONAL	2	TRUE	0	0.862002320294919	2		448	485	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115952	8115953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0060602-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	323	610	1	ENST00000346208.3:c.1299_1300dup	p.His434ProfsTer42	p.H434Pfs*42	ENST00000346208		433	cac/caCCc	6/6	1	2	FACETS	0.956	0.908	1	0.956	0.908	1	CLONAL	1	TRUE	1	0.862002320294919	2		611	784	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057811	27057811	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060602-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	325	651	2	ENST00000324856.7:c.1519C>T	p.Gln507Ter	p.Q507*	ENST00000324856	NM_006015.4	507	Caa/Taa	3/20	1	2	FACETS	0.959	0.911	1	0.959	0.911	1	CLONAL	1	TRUE	1	0.862002320294919	2		653	786	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256598	16256602	+	frameshift_variant	Frame_Shift_Del	DEL	CTAAA	CTAAA	-	novel	NA	P-0060602-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	174	532	2	ENST00000375759.3:c.3863_3867del	p.Pro1288ArgfsTer3	p.P1288Rfs*3	ENST00000375759	NM_015001.2	1288	cCTAAA/c	11/15	0.813273917336572	1	FACETS	0.93	0.883	0.975	0.93	0.883	0.975	CLONAL	1	TRUE	0	0.862002320294919	1		534	247	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577260	64577260	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs794728647	NA	P-0060602-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	287	605	1	ENST00000312049.6:c.322C>T	p.Arg108Ter	p.R108*	ENST00000312049	NM_130799.2	108	Cga/Tga	2/10	0.854275344866081	1	FACETS	0.979	0.943	1	0.979	0.943	1	CLONAL	1	TRUE	0	0.862002320294919	1		606	387	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906565	32906566	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359770	NA	P-0060602-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	86	341	0	ENST00000380152.3:c.956dup	p.Asn319LysfsTer8	p.N319Kfs*8	ENST00000380152		317	aca/acAa	10/27	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.862002320294919	2		341	186	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060604-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	35	300	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.931	0.765	1			1	INDETERMINATE	1	TRUE	NA	0.223185518961694	2		300	337	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527502	29527503	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0060604-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	54	347	0	ENST00000356175.3:c.952_953del	p.Glu318LysfsTer11	p.E318Kfs*11	ENST00000356175	NM_000267.3	317	acAGaa/acaa	9/57	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.223185518961694	2		347	453	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684021	29684022	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0060604-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	55	299	0	ENST00000356175.3:c.7722dup	p.Val2575SerfsTer5	p.V2575Sfs*5	ENST00000356175	NM_000267.3	2573	-/A	52/57	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.223185518961694	2		299	412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0060605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	357	622	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.781704202490434	2	FACETS	0.957	0.927	0.986	0.957	0.927	0.986	CLONAL	2	TRUE	0	0.798674800167732	2		623	467	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939075	48939076	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	139	161	0	ENST00000267163.4:c.909dup	p.Gly304TrpfsTer6	p.G304Wfs*6	ENST00000267163	NM_000321.2	303	ctt/cTtt	9/27	0.781704202490434	2	FACETS	0.951	0.902	0.996	0.951	0.902	0.996	CLONAL	2	TRUE	0	0.798674800167732	2		161	183	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128028991	128029007	+	frameshift_variant	Frame_Shift_Del	DEL	GACATTTGCTTCCGGCA	GACATTTGCTTCCGGCA	-	novel	NA	P-0060605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	240	389	0	ENST00000285398.2:c.1850_1866del	p.Leu617ProfsTer25	p.L617Pfs*25	ENST00000285398	NM_000122.1	617	cTGCCGGAAGCAAATGTC/c	12/15	0.798674800167732	3	FACETS	0.883	0.836	0.931	0.883	0.836	0.931	CLONAL	2	TRUE	1	0.798674800167732	3		389	476	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0060605-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	1555	384	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.798674800167732	13	FACETS	0.995	0.984	1	0.995	0.984	1	CLONAL	12	TRUE	1	0.798674800167732	13		384	1759	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0060614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	76	711	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.448737034509584	1	FACETS	0.959	0.851	1	0.959	0.851	1	CLONAL	1	TRUE	0	0.448737034509584	1		711	274	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965472	68965472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200682883	NA	P-0060614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	39	516	0	ENST00000288368.4:c.1084C>T	p.Arg362Trp	p.R362W	ENST00000288368	NM_024870.2	362	Cgg/Tgg	9/40	0.448737034509584	3	FACETS	0.865	0.734	1	0.865	0.734	1	CLONAL	2	TRUE	1	0.448737034509584	3		516	123	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436789	110436789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	64	685	1	ENST00000375856.3:c.1612G>A	p.Glu538Lys	p.E538K	ENST00000375856	NM_003749.2	538	Gag/Aag	1/2	0.166328529216474	3	FACETS	0.88	0.765	1	0.44	0.382	0.502	INDETERMINATE	1	TRUE	1	0.448737034509584	3		686	397	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56402528	56402563	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	AAAATCACTGTGTTACTGGATGAAGTTGCAGAAGGT	AAAATCACTGTGTTACTGGATGAAGTTGCAGAAGGT	-	novel	NA	P-0060614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	12	306	0	ENST00000348428.3:c.1575_1603+7del		p.X525_splice	ENST00000348428	NM_006785.3	525		13/17	0.448737034509584	1	FACETS	0.553	0.395	0.74	0.553	0.395	0.74	SUBCLONAL	1	TRUE	0	0.448737034509584	1		306	75	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510281	187510281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	141	650	0	ENST00000441802.2:c.13232C>T	p.Pro4411Leu	p.P4411L	ENST00000441802	NM_005245.3	4411	cCc/cTc	27/27	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.29	2		650	896	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696431	47696431	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519969	NA	P-0060617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	41	627	0	ENST00000347630.2:c.392G>C	p.Trp131Ser	p.W131S	ENST00000347630	NM_001007230.1	131	tGg/tCg	6/11	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.16	2		627	476	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851977	63851977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776070701	NA	P-0060617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	44	746	0	ENST00000279873.7:c.2755G>A	p.Gly919Ser	p.G919S	ENST00000279873	NM_032199.2	919	Ggc/Agc	10/10	1	2	FACETS	0.945	0.792	1	0.945	0.792	1	CLONAL	1	TRUE	1	0.16	2		746	582	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374823	118374823	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060617-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	30	736	0	ENST00000534358.1:c.8216A>G	p.Lys2739Arg	p.K2739R	ENST00000534358	NM_005933.3	2739	aAa/aGa	27/36	1	2	FACETS	0.977	0.787	1	0.977	0.787	1	CLONAL	1	TRUE	1	0.16	2		736	384	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788617	3788617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519884	NA	P-0060619-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	8	231	0	ENST00000262367.5:c.4337G>A	p.Arg1446His	p.R1446H	ENST00000262367	NM_004380.2	1446	cGc/cAc	26/31	0.187957138036384	3	FACETS	0.126	0.081	0.186	0.063	0.04	0.093	INDETERMINATE	1	TRUE	1	0.383224768530884	3		231	394	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052584	42052584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060619-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	96	277	0	ENST00000219905.7:c.7255G>A	p.Glu2419Lys	p.E2419K	ENST00000219905	NM_001164273.1	2419	Gaa/Aaa	20/24	1	2	FACETS	0.767	0.684	0.855	0.767	0.684	0.855	SUBCLONAL	1	TRUE	1	0.383224768530884	2		277	653	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0001442-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	223	385	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.655734845111297	3	FACETS	1	0.955	1	0.515	0.48	0.552	CLONAL	1	TRUE	1	0.655734845111297	3		385	876	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0001442-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	160	408	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.796	0.733	0.861	0.796	0.733	0.861	SUBCLONAL	1	TRUE	1	0.655734845111297	2		408	613	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0001442-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	230	717	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.655734845111297	3	FACETS	0.903	0.841	0.966	0.451	0.42	0.483	CLONAL	1	TRUE	1	0.655734845111297	3		717	1032	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0001442-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	236	481	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.975	0.914	1	0.975	0.914	1	CLONAL	1	TRUE	1	0.655734845111297	2		481	738	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242511	55242511	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913418	NA	P-0001442-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	181	351	0	ENST00000275493.2:c.2281G>T	p.Asp761Tyr	p.D761Y	ENST00000275493	NM_005228.3	761	Gat/Tat	19/28	0.655734845111297	3	FACETS	1	0.951	1	0.518	0.479	0.559	CLONAL	1	TRUE	1	0.655734845111297	3		351	707	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725229	89725229	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	rs876660879	NA	P-0001442-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	23	38	0	ENST00000371953.3:c.1212A>G	p.Ter404TrpextTer8	p.*404Wext*8	ENST00000371953	NM_000314.4	404	tgA/tgG	9/9	1	2	FACETS	0.988	0.796	1	0.988	0.796	1	CLONAL	1	TRUE	1	0.655734845111297	2		38	71	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249091	55249091	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519861	NA	P-0001442-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	229	546	0	ENST00000275493.2:c.2389T>A	p.Cys797Ser	p.C797S	ENST00000275493	NM_005228.3	797	Tgc/Agc	20/28	0.655734845111297	3	FACETS	0.921	0.859	0.985	0.461	0.429	0.493	CLONAL	1	TRUE	1	0.655734845111297	3		546	1007	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0003784-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	172	541	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.441187922386197	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.441187922386197	1		541	603	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0003784-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	290	513	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.441187922386197	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.441187922386197	2		513	590	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480579	120480579	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003784-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	150	455	0	ENST00000256646.2:c.3238C>T	p.Gln1080Ter	p.Q1080*	ENST00000256646	NM_024408.3	1080	Cag/Tag	20/34	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.441187922386197	2		455	649	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112120	115112123	+	frameshift_variant	Frame_Shift_Del	DEL	ACCC	ACCC	-	novel	NA	P-0003784-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	185	690	0	ENST00000257566.3:c.1617_1620del	p.Met539IlefsTer92	p.M539Ifs*92	ENST00000257566	NM_016569.3	539	atGGGT/at	7/8	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.441187922386197	2		690	832	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645412	67645412	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003784-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	148	562	0	ENST00000264010.4:c.677A>G	p.Tyr226Cys	p.Y226C	ENST00000264010	NM_006565.3	226	tAc/tGc	3/12	0.441187922386197	1	FACETS	0.891	0.817	0.967	0.891	0.817	0.967	CLONAL	1	TRUE	0	0.441187922386197	1		562	587	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016550	12016550	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003784-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	97	330	1	ENST00000353533.5:c.686A>T	p.Asp229Val	p.D229V	ENST00000353533	NM_003010.3	229	gAt/gTt	7/11	0.441187922386197	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.441187922386197	1		331	304	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119113	70119113	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003784-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	170	572	0	ENST00000245479.2:c.685G>A	p.Gly229Arg	p.G229R	ENST00000245479	NM_000346.3	229	Ggg/Agg	2/3	0.25354070024044	1	FACETS	0.981	0.907	1	0.981	0.907	1	INDETERMINATE	1	TRUE	0	0.441187922386197	1		572	612	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612402	1612402	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003784-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	142	507	0	ENST00000344749.5:c.1617G>C	p.Glu539Asp	p.E539D	ENST00000344749	NM_001136139.2	539	gaG/gaC	18/19	0.189153938447271	1	FACETS	0.796	0.728	0.868	0.796	0.728	0.868	INDETERMINATE	1	TRUE	0	0.441187922386197	1		507	630	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546556	9546556	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003784-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	129	465	0	ENST00000353224.5:c.1466A>G	p.Glu489Gly	p.E489G	ENST00000353224	NM_177990.2	489	gAa/gGa	5/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.441187922386197	2		465	538	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564516	55564516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1174814949	NA	P-0003784-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	101	438	0	ENST00000288135.5:c.404G>A	p.Arg135His	p.R135H	ENST00000288135	NM_000222.2	135	cGc/cAc	3/21	1	2	FACETS	0.795	0.712	0.882	0.795	0.712	0.882	SUBCLONAL	1	TRUE	1	0.441187922386197	2		438	576	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450265	50450265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003784-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	107	500	0	ENST00000331340.3:c.449G>A	p.Cys150Tyr	p.C150Y	ENST00000331340	NM_006060.4	150	tGc/tAc	5/8	0.189153938447271	1	FACETS	0.614	0.551	0.679	0.614	0.551	0.679	INDETERMINATE	1	TRUE	0	0.441187922386197	1		500	616	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248153	98248153	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003784-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	125	341	0	ENST00000331920.6:c.398G>A	p.Gly133Glu	p.G133E	ENST00000331920	NM_000264.3	133	gGa/gAa	3/24	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.441187922386197	2		341	480	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817345	39817345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005342-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	108	545	0	ENST00000288319.7:c.218G>A	p.Ser73Asn	p.S73N	ENST00000288319	NM_182918.3	73	aGc/aAc	2/10	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.433055603558644	2		545	487	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981483	70981483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005342-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	142	758	1	ENST00000276594.2:c.613G>A	p.Val205Ile	p.V205I	ENST00000276594	NM_024504.3	205	Gtt/Att	2/8	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.433055603558644	2		759	610	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659648	88659648	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0005342-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	126	480	0	ENST00000372037.3:c.430+1G>T		p.X144_splice	ENST00000372037	NM_004329.2	144			1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.433055603558644	2		480	558	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006665-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	203	475	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.945	0.883	1	0.945	0.883	1	CLONAL	1	TRUE	1	0.777268811490297	2		475	553	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0006665-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	164	356	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.777268811490297	2		356	420	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210737	36210737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370168284	NA	P-0006665-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	335	491	0	ENST00000222270.7:c.488C>T	p.Pro163Leu	p.P163L	ENST00000222270	NM_014727.1	163	cCt/cTt	3/37	1	2	FACETS	0.973	0.923	1	0.973	0.923	1	CLONAL	1	TRUE	1	0.777268811490297	2		491	886	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0009307-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	50	433	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.391331862382795	1	FACETS	0.548	0.466	0.637	0.548	0.466	0.637	SUBCLONAL	1	TRUE	0	0.391331862382795	1		434	375	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39021158	39021158	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009307-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	36	404	0	ENST00000357387.3:c.178C>G	p.Leu60Val	p.L60V	ENST00000357387	NM_152756.3	60	Ctg/Gtg	3/38	0.111748655326505	4	FACETS	0.755	0.622	0.903	0.378	0.311	0.452	INDETERMINATE	1	TRUE	2	0.391331862382795	4		404	339	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333143	70333143	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009307-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	35	573	0	ENST00000373644.4:c.1048G>T	p.Glu350Ter	p.E350*	ENST00000373644	NM_030625.2	350	Gaa/Taa	2/12	0.329109705241446	1	FACETS	0.505	0.415	0.604	0.505	0.415	0.604	SUBCLONAL	1	TRUE	0	0.391331862382795	1		573	285	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43700202	43700202	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009307-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	66	547	0	ENST00000382044.4:c.5685G>C	p.Glu1895Asp	p.E1895D	ENST00000382044	NM_001141980.1	1895	gaG/gaC	27/28	0.391331862382795	1	FACETS	0.784	0.685	0.89	0.784	0.685	0.89	SUBCLONAL	1	TRUE	0	0.391331862382795	1		547	346	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39021232	39021232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1177276513	NA	P-0009307-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	26	415	1	ENST00000357387.3:c.104C>T	p.Ser35Phe	p.S35F	ENST00000357387	NM_152756.3	35	tCt/tTt	3/38	0.111748655326505	4	FACETS	0.524	0.415	0.649	0.262	0.207	0.325	INDETERMINATE	1	TRUE	2	0.391331862382795	4		416	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0010024-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	143	484	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.519461284453018	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	0	0.521228516563024	1		484	371	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0010024-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	275	781	0	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	0.521228516563024	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	FALSE	0	0.521228516563024	2		781	502	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162201	47162201	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0010024-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	141	816	0	ENST00000409792.3:c.3925A>T	p.Arg1309Ter	p.R1309*	ENST00000409792	NM_014159.6	1309	Aga/Tga	3/21	0.519461284453018	1	FACETS	0.86	0.79	0.933	0.86	0.79	0.933	CLONAL	1	FALSE	0	0.521228516563024	1		816	465	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724401	117724401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010024-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	45	696	0	ENST00000368508.3:c.478C>T	p.Pro160Ser	p.P160S	ENST00000368508	NM_002944.2	160	Ccc/Tcc	6/43	0.113138599353844	0	FACETS	0.167	0.14	0.197			1	INDETERMINATE	1	FALSE	0	0.521228516563024	0		696	494	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630393	90630393	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010024-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	79	944	0	ENST00000330062.3:c.918G>A	p.Trp306Ter	p.W306*	ENST00000330062	NM_002168.2	306	tgG/tgA	7/11	0.303693766201887	1	FACETS	0.353	0.31	0.399	0.353	0.31	0.399	INDETERMINATE	1	FALSE	0	0.521228516563024	1		944	635	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385119	41385119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010024-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	103	724	0	ENST00000373198.4:c.842C>T	p.Ala281Val	p.A281V	ENST00000373198	NM_133170.3	281	gCg/gTg	6/32	0.387240525752358	5	FACETS	0.899	0.805	1	0.3	0.268	0.334	CLONAL	1	FALSE	2	0.521228516563024	5		724	783	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013004-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	112	475	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.552274022160591	2		475	321	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147214	61147214	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs757728369	NA	P-0013004-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	73	191	0	ENST00000295025.8:c.892C>G	p.Leu298Val	p.L298V	ENST00000295025	NM_002908.2	298	Ctg/Gtg	8/11	1	2	FACETS	0.457	0.4	0.519	0.457	0.4	0.519	SUBCLONAL	1	TRUE	1	0.552274022160591	2		191	578	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968235	2968235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1188731718	NA	P-0013004-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	166	546	0	ENST00000396946.4:c.1751G>A	p.Arg584His	p.R584H	ENST00000396946	NM_032415.4	584	cGc/cAc	13/25	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.552274022160591	2		546	526	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877417	28877417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758531658	NA	P-0013004-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	82	426	0	ENST00000282397.4:c.3904G>A	p.Glu1302Lys	p.E1302K	ENST00000282397	NM_002019.4	1302	Gaa/Aaa	30/30	0.552274022160591	1	FACETS	0.587	0.521	0.657	0.587	0.521	0.657	SUBCLONAL	1	TRUE	0	0.552274022160591	1		426	366	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945099	151945099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219495191	NA	P-0013004-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	29	179	0	ENST00000262189.6:c.2420C>T	p.Ser807Phe	p.S807F	ENST00000262189	NM_170606.2	807	tCt/tTt	14/59	1	2	FACETS	0.337	0.27	0.412	0.337	0.27	0.412	SUBCLONAL	1	TRUE	1	0.552274022160591	2		179	312	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456601	32456601	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013004-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	64	428	1	ENST00000332351.3:c.291C>A	p.Ser97Arg	p.S97R	ENST00000332351	NM_024426.4	97	agC/agA	1/10	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.552274022160591	2		429	229	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427294	49427294	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013004-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	44	618	0	ENST00000301067.7:c.11194C>T	p.Gln3732Ter	p.Q3732*	ENST00000301067	NM_003482.3	3732	Cag/Tag	39/54	0.152733055377168	1	FACETS	0.222	0.186	0.262	0.222	0.186	0.262	INDETERMINATE	1	TRUE	0	0.552274022160591	1		618	519	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428450	49428450	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0013004-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	111	588	0	ENST00000301067.7:c.10356-1G>T		p.X3452_splice	ENST00000301067	NM_003482.3	3452			0.152733055377168	1	FACETS	0.538	0.485	0.593	0.538	0.485	0.593	INDETERMINATE	1	TRUE	0	0.552274022160591	1		588	541	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864169	57864169	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs200128720	NA	P-0013004-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	109	669	0	ENST00000228682.2:c.1646T>A	p.Ile549Asn	p.I549N	ENST00000228682	NM_005269.2	549	aTc/aAc	12/12	0.152733055377168	1	FACETS	0.508	0.458	0.562	0.508	0.458	0.562	INDETERMINATE	1	TRUE	0	0.552274022160591	1		669	562	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865770	56865770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013004-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	44	404	0	ENST00000308159.5:c.1102G>A	p.Glu368Lys	p.E368K	ENST00000308159	NM_014669.4	368	Gaa/Aaa	11/22	0.552274022160591	1	FACETS	0.394	0.332	0.461	0.394	0.332	0.461	SUBCLONAL	1	TRUE	0	0.552274022160591	1		404	293	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740478	58740479	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0013004-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	152	324	0	ENST00000305921.3:c.1383_1384delinsTT	p.Gln462Ter	p.Q462*	ENST00000305921	NM_003620.3	461	gtCCaa/gtTTaa	6/6	1	2	FACETS	0.936	0.86	1	0.936	0.86	1	CLONAL	1	TRUE	1	0.552274022160591	2		324	588	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220713	1220713	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013004-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	242	529	0	ENST00000326873.7:c.733del	p.Leu245SerfsTer42	p.L245Sfs*42	ENST00000326873	NM_000455.4	244	aCc/ac	5/10	0.180151408097159	5	FACETS	0.898	0.845	0.951			1	INDETERMINATE	3	TRUE	NA	0.552274022160591	5		529	595	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222007	1222007	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0013004-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	91	408	0	ENST00000326873.7:c.920+2T>G		p.X307_splice	ENST00000326873	NM_000455.4	307			0.180151408097159	5	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.552274022160591	5		408	437	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17947943	17947943	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013004-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	52	393	0	ENST00000458235.1:c.1781G>C	p.Gly594Ala	p.G594A	ENST00000458235	NM_000215.3	594	gGa/gCa	13/24	1	2	FACETS	0.479	0.409	0.556	0.479	0.409	0.556	SUBCLONAL	1	TRUE	1	0.552274022160591	2		393	393	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098661	47098661	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013004-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	59	611	0	ENST00000409792.3:c.6613C>T	p.His2205Tyr	p.H2205Y	ENST00000409792	NM_014159.6	2205	Cat/Tat	15/21	1	2	FACETS	0.334	0.287	0.386	0.334	0.287	0.386	SUBCLONAL	1	TRUE	1	0.552274022160591	2		611	639	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389275	8389275	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013004-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	132	234	0	ENST00000356435.5:c.4343G>T	p.Ser1448Ile	p.S1448I	ENST00000356435		1448	aGt/aTt	26/35	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.552274022160591	2		234	364	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868450	117868450	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs148308569	NA	P-0013793-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	139	99	0	ENST00000297338.2:c.892C>G	p.Pro298Ala	p.P298A	ENST00000297338	NM_006265.2	298	Cca/Gca	8/14	0.88399054634017	4	FACETS	1	0.938	1	0.515	0.471	0.562	CLONAL	1	TRUE	2	0.889132135254086	4		99	573	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116218	209116218	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs912110895	NA	P-0013793-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	111	108	0	ENST00000345146.2:c.58C>T	p.Arg20Ter	p.R20*	ENST00000345146	NM_005896.2	20	Cga/Tga	3/10	0.892385052322748	3	FACETS	0.794	0.719	0.874	0.397	0.359	0.437	SUBCLONAL	1	TRUE	1	0.889132135254086	3		108	454	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126545	2126545	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013793-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	569	512	0	ENST00000219476.3:c.2796C>G	p.Ser932Arg	p.S932R	ENST00000219476	NM_000548.3	932	agC/agG	25/42	0.892385052322748	5	FACETS	0.991	0.958	1	0.594	0.575	0.614	CLONAL	3	TRUE	0	0.889132135254086	5		512	1005	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402592	139402592	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0013793-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	206	624	0	ENST00000277541.6:c.3326-1G>C		p.X1109_splice	ENST00000277541	NM_017617.3	1109			0.892385052322748	3	FACETS	1	0.97	1	0.534	0.498	0.571	CLONAL	1	TRUE	1	0.889132135254086	3		624	627	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	213	769	0	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	0.3230403449138	1	FACETS	0.882	0.831	0.932	1	0.995	1	CLONAL	3	TRUE	0	0.3230403449138	1		769	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	269	584	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.14776798373303	3	FACETS	0.856	0.807	0.907	1	0.991	1	INDETERMINATE	3	TRUE	1	0.3230403449138	3		584	753	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	301	573	1	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	0.14776798373303	3	FACETS	1	0.986	1	1	0.995	1	INDETERMINATE	3	TRUE	1	0.3230403449138	3		574	654	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220135	5220135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269111261	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	190	758	0	ENST00000357368.4:c.3580C>T	p.Arg1194Cys	p.R1194C	ENST00000357368	NM_002850.3	1194	Cgc/Tgc	22/38	1	2	FACETS	1	0.979	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		758	523	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177584	56177584	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368201444	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	201	671	0	ENST00000399503.3:c.2557C>T	p.Arg853Cys	p.R853C	ENST00000399503	NM_005921.1	853	Cgt/Tgt	14/20	0.3230403449138	1	FACETS	1	0.96	1	1	0.994	1	CLONAL	2	TRUE	0	0.3230403449138	1		671	504	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798379	42798379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749470261	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	230	705	0	ENST00000575354.2:c.4250G>A	p.Arg1417His	p.R1417H	ENST00000575354	NM_015125.3	1417	cGc/cAc	18/20	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		705	622	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1688550	1688550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199931813	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	235	647	0	ENST00000378625.1:c.775G>A	p.Ala259Thr	p.A259T	ENST00000378625	NM_001198994.1	259	Gcc/Acc	6/14	1	2	FACETS	1	0.99	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		647	585	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1724742	1724742	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	27	612	0	ENST00000378609.4:c.439T>C	p.Ser147Pro	p.S147P	ENST00000378609	NM_002074.3	147	Tcc/Ccc	8/12	1	2	FACETS	0.32	0.253	0.396	0.32	0.253	0.396	SUBCLONAL	1	TRUE	1	0.3230403449138	2		612	523	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1747262	1747262	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756284066	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	262	664	0	ENST00000378609.4:c.136C>T	p.Arg46Cys	p.R46C	ENST00000378609	NM_002074.3	46	Cgc/Tgc	5/12	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.3230403449138	2		664	665	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778785	9778785	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759798937	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	195	712	0	ENST00000377346.4:c.1054G>A	p.Glu352Lys	p.E352K	ENST00000377346	NM_005026.3	352	Gag/Aag	9/24	1	2	FACETS	1	0.97	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		712	563	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783301	9783301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763402967	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	239	642	0	ENST00000377346.4:c.2545G>A	p.Ala849Thr	p.A849T	ENST00000377346	NM_005026.3	849	Gcc/Acc	20/24	1	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		642	643	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11172938	11172938	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555337942	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	229	595	0	ENST00000361445.4:c.7337C>T	p.Thr2446Met	p.T2446M	ENST00000361445	NM_004958.3	2446	aCg/aTg	54/58	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		595	602	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291078	11291078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	242	698	0	ENST00000361445.4:c.2683G>A	p.Asp895Asn	p.D895N	ENST00000361445	NM_004958.3	895	Gat/Aat	18/58	1	2	FACETS	1	0.981	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		698	677	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316113	11316113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs968103570	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	254	691	0	ENST00000361445.4:c.641G>A	p.Arg214His	p.R214H	ENST00000361445	NM_004958.3	214	cGt/cAt	5/58	1	2	FACETS	1	0.983	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		691	705	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319454	11319454	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774041749	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	254	725	0	ENST00000361445.4:c.13G>A	p.Gly5Arg	p.G5R	ENST00000361445	NM_004958.3	5	Gga/Aga	2/58	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		725	700	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254951	16254951	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759877253	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	274	674	0	ENST00000375759.3:c.2216C>T	p.Ala739Val	p.A739V	ENST00000375759	NM_015001.2	739	gCg/gTg	11/15	1	2	FACETS	0.84	0.794	0.887	1	0.996	1	CLONAL	3	TRUE	1	0.3230403449138	2		674	673	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257729	16257729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199930614	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	250	773	0	ENST00000375759.3:c.4994C>T	p.Ala1665Val	p.A1665V	ENST00000375759	NM_015001.2	1665	gCg/gTg	11/15	1	2	FACETS	1	0.964	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		773	747	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262373	16262373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372303430	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	220	807	0	ENST00000375759.3:c.9638C>T	p.Ala3213Val	p.A3213V	ENST00000375759	NM_015001.2	3213	gCg/gTg	11/15	1	2	FACETS	0.876	0.824	0.93	1	0.995	1	CLONAL	3	TRUE	1	0.3230403449138	2		807	518	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22417991	22417991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756680625	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	43	111	0	ENST00000344548.3:c.557G>A	p.Arg186His	p.R186H	ENST00000344548	NM_001039802.1	186	cGc/cAc	7/7	1	2	FACETS	1	0.947	1	1	0.977	1	CLONAL	2	TRUE	1	0.3230403449138	2		111	109	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101370	27101370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748819428	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	148	568	0	ENST00000324856.7:c.4652G>A	p.Arg1551His	p.R1551H	ENST00000324856	NM_006015.4	1551	cGc/cAc	18/20	1	2	FACETS	1	0.974	1	1	0.992	1	CLONAL	2	TRUE	1	0.3230403449138	2		568	406	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43806138	43806138	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1219805775	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	235	691	0	ENST00000372470.3:c.934C>A	p.Gln312Lys	p.Q312K	ENST00000372470	NM_005373.2	312	Caa/Aaa	6/12	1	2	FACETS	1	0.982	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		691	649	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726436	46726436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139448277	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	236	853	0	ENST00000371975.4:c.515G>A	p.Arg172His	p.R172H	ENST00000371975	NM_003579.3	172	cGc/cAc	7/18	1	2	FACETS	1	0.975	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		853	679	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78425885	78425885	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	92	768	0	ENST00000370768.2:c.1560G>T	p.Gln520His	p.Q520H	ENST00000370768	NM_003902.3	520	caG/caT	16/20	1	2	FACETS	0.917	0.816	1	0.917	0.816	1	CLONAL	1	TRUE	1	0.3230403449138	2		768	621	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428511	78428511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408536007	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	138	577	0	ENST00000370768.2:c.1288C>T	p.Arg430Cys	p.R430C	ENST00000370768	NM_003902.3	430	Cgt/Tgt	14/20	1	2	FACETS	1	0.979	1	1	0.992	1	CLONAL	2	TRUE	1	0.3230403449138	2		577	360	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695956	117695956	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	256	638	0	ENST00000369458.3:c.481G>A	p.Ala161Thr	p.A161T	ENST00000369458	NM_024626.3	161	Gcc/Acc	4/6	1	2	FACETS	0.863	0.815	0.912	1	0.996	1	CLONAL	3	TRUE	1	0.3230403449138	2		638	612	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165800	118165800	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	262	783	0	ENST00000369448.3:c.310G>T	p.Glu104Ter	p.E104*	ENST00000369448	NM_017709.3	104	Gaa/Taa	2/2	1	2	FACETS	1	0.985	1	1	0.996	1	CLONAL	2	TRUE	1	0.3230403449138	2		783	713	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120469168	120469168	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	261	741	0	ENST00000256646.2:c.3959C>A	p.Ala1320Asp	p.A1320D	ENST00000256646	NM_024408.3	1320	gCt/gAt	24/34	1	2	FACETS	1	0.986	1	1	0.996	1	CLONAL	2	TRUE	1	0.3230403449138	2		741	706	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484281	120484281	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553196472	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	223	708	0	ENST00000256646.2:c.2849T>C	p.Met950Thr	p.M950T	ENST00000256646	NM_024408.3	950	aTg/aCg	18/34	1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		708	576	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150917472	150917472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	223	732	0	ENST00000271640.5:c.1028G>A	p.Arg343His	p.R343H	ENST00000271640	NM_001145415.1	343	cGc/cAc	9/22	1	2	FACETS	1	0.981	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		732	619	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741970	162741970	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	256	654	0	ENST00000367921.3:c.1661C>A	p.Ala554Asp	p.A554D	ENST00000367921	NM_006182.2	554	gCt/gAt	13/18	1	2	FACETS	0.903	0.853	0.954	1	0.996	1	CLONAL	3	TRUE	1	0.3230403449138	2		654	585	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649613	206649613	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	229	767	0	ENST00000367120.3:c.448C>T	p.Gln150Ter	p.Q150*	ENST00000367120	NM_014002.3	150	Cag/Tag	6/22	1	2	FACETS	1	0.983	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		767	625	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552821	226552821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182639036	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	216	796	1	ENST00000366794.5:c.2540G>A	p.Arg847His	p.R847H	ENST00000366794	NM_001618.3	847	cGt/cAt	19/23	1	2	FACETS	1	0.97	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		797	630	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612740	228612740	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747322437	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	402	1042	0	ENST00000366696.1:c.287C>T	p.Ala96Val	p.A96V	ENST00000366696	NM_003493.2	96	gCg/gTg	1/1	1	2	FACETS	0.864	0.825	0.904	1	0.997	1	CLONAL	3	TRUE	1	0.3230403449138	2		1042	960	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230492801	230492801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41315609	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	223	735	1	ENST00000391860.1:c.253G>A	p.Ala85Thr	p.A85T	ENST00000391860	NM_001258311.1	85	Gcc/Acc	2/7	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		736	589	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622039	43622039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1371891301	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	213	664	1	ENST00000355710.3:c.3056C>T	p.Ala1019Val	p.A1019V	ENST00000355710	NM_020975.4	1019	gCg/gTg	19/20	1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		665	542	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759939	63759939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	199	652	0	ENST00000279873.7:c.592C>T	p.Pro198Ser	p.P198S	ENST00000279873	NM_032199.2	198	Cca/Tca	4/10	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		652	511	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659621	88659621	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	124	544	0	ENST00000372037.3:c.404A>T	p.Gln135Leu	p.Q135L	ENST00000372037	NM_004329.2	135	cAa/cTa	6/13	1	2	FACETS	1	0.951	1	1	0.991	1	CLONAL	2	TRUE	1	0.3230403449138	2		544	363	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112760215	112760215	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	131	510	0	ENST00000369452.4:c.884G>A	p.Arg295Lys	p.R295K	ENST00000369452	NM_007373.3	295	aGa/aAa	4/9	1	2	FACETS	1	0.972	1	1	0.992	1	CLONAL	2	TRUE	1	0.3230403449138	2		510	357	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925507	114925507	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	175	683	0	ENST00000543371.1:c.1585C>A	p.Leu529Met	p.L529M	ENST00000543371	NM_001198531.1	529	Ctg/Atg	14/14	1	2	FACETS	1	0.971	1	1	0.993	1	CLONAL	2	TRUE	1	0.3230403449138	2		683	499	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533808	533808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	219	746	0	ENST00000451590.1:c.248C>T	p.Ala83Val	p.A83V	ENST00000451590	NM_001130442.1	83	gCc/gTc	3/5	1	2	FACETS	1	0.98	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		746	609	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533838	533838	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	267	792	1	ENST00000451590.1:c.218G>A	p.Arg73His	p.R73H	ENST00000451590	NM_001130442.1	73	cGc/cAc	3/5	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.3230403449138	2		793	677	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456372	32456372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	134	785	0	ENST00000332351.3:c.520G>A	p.Ala174Thr	p.A174T	ENST00000332351	NM_024426.4	174	Gcc/Acc	1/10	1	2	FACETS	1	0.923	1	1	0.991	1	CLONAL	2	TRUE	1	0.3230403449138	2		785	412	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003736	57003736	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	203	804	0	ENST00000257254.3:c.743G>A	p.Ser248Asn	p.S248N	ENST00000257254		248	aGc/aAc	1/2	1	2	FACETS	1	0.983	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		804	546	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57004294	57004294	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	220	822	0	ENST00000257254.3:c.185G>A	p.Arg62His	p.R62H	ENST00000257254		62	cGc/cAc	1/2	1	2	FACETS	1	0.981	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		822	610	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127694	64127694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1387218415	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	176	692	0	ENST00000334205.4:c.187G>A	p.Ala63Thr	p.A63T	ENST00000334205	NM_003942.2	63	Gcc/Acc	3/17	1	2	FACETS	1	0.981	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		692	473	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136948	64136948	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767081339	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	177	530	1	ENST00000334205.4:c.1459C>T	p.Arg487Trp	p.R487W	ENST00000334205	NM_003942.2	487	Cgg/Tgg	13/17	1	2	FACETS	0.848	0.79	0.906	1	0.994	1	CLONAL	3	TRUE	1	0.3230403449138	2		531	431	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137020	64137020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1174133485	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	179	717	0	ENST00000334205.4:c.1531C>T	p.Arg511Cys	p.R511C	ENST00000334205	NM_003942.2	511	Cgc/Tgc	13/17	1	2	FACETS	0.857	0.799	0.916	1	0.994	1	CLONAL	3	TRUE	1	0.3230403449138	2		717	431	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137232	64137232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	234	748	0	ENST00000334205.4:c.1664C>T	p.Ala555Val	p.A555V	ENST00000334205	NM_003942.2	555	gCg/gTg	14/17	1	2	FACETS	0.838	0.789	0.889	1	0.995	1	CLONAL	3	TRUE	1	0.3230403449138	2		748	576	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200616	67200616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201207505	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	276	924	0	ENST00000312629.5:c.727C>T	p.Arg243Cys	p.R243C	ENST00000312629	NM_003952.2	243	Cgc/Tgc	9/15	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.3230403449138	2		924	716	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944716	71944716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750542712	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	203	768	0	ENST00000298229.2:c.2140G>A	p.Val714Ile	p.V714I	ENST00000298229	NM_001567.3	714	Gtc/Atc	19/28	0.3230403449138	1	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	0	0.3230403449138	1		768	448	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196936	108196936	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060501640	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	160	538	0	ENST00000278616.4:c.6959A>G	p.Asp2320Gly	p.D2320G	ENST00000278616	NM_000051.3	2320	gAt/gGt	47/63	0.3230403449138	1	FACETS	1	0.974	1	1	0.993	1	CLONAL	2	TRUE	0	0.3230403449138	1		538	377	SUCCESS
ATM	472	MSKCC	GRCh37	11	108213987	108213987	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs778269655	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	112	604	0	ENST00000278616.4:c.8307G>A	p.Trp2769Ter	p.W2769*	ENST00000278616	NM_000051.3	2769	tgG/tgA	57/63	0.3230403449138	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.3230403449138	1		604	400	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216546	108216546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529296539	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	105	495	0	ENST00000278616.4:c.8495G>A	p.Arg2832His	p.R2832H	ENST00000278616	NM_000051.3	2832	cGt/cAt	58/63	0.3230403449138	1	FACETS	0.943	0.857	1	1	0.988	1	CLONAL	2	TRUE	0	0.3230403449138	1		495	289	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344671	118344671	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782407414	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	170	681	1	ENST00000534358.1:c.2797C>T	p.Arg933Trp	p.R933W	ENST00000534358	NM_005933.3	933	Cgg/Tgg	3/36	0.3230403449138	1	FACETS	0.953	0.885	1	1	0.993	1	CLONAL	2	TRUE	0	0.3230403449138	1		682	463	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348795	118348795	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	286	630	0	ENST00000534358.1:c.3448C>T	p.Arg1150Cys	p.R1150C	ENST00000534358	NM_005933.3	1150	Cgt/Tgt	5/36	0.3230403449138	1	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	0	0.3230403449138	1		630	652	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376683	118376683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149340870	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	247	595	0	ENST00000534358.1:c.10076C>T	p.Ala3359Val	p.A3359V	ENST00000534358	NM_005933.3	3359	gCg/gTg	27/36	0.3230403449138	1	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	0	0.3230403449138	1		595	566	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432249	432249	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	123	373	0	ENST00000399788.2:c.2274del	p.Asp759IlefsTer2	p.D759Ifs*2	ENST00000399788	NM_001042603.1	758	aaA/aa	16/28	1	2	FACETS	1	0.965	1	1	0.991	1	CLONAL	2	TRUE	1	0.3230403449138	2		373	345	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21630862	21630862	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202110155	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	165	607	0	ENST00000421138.2:c.742G>A	p.Ala248Thr	p.A248T	ENST00000421138		248	Gca/Aca	8/16	1	2	FACETS	1	0.982	1	1	0.993	1	CLONAL	2	TRUE	1	0.3230403449138	2		607	430	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245612	46245612	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1020744272	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	223	721	0	ENST00000334344.6:c.3706C>T	p.Pro1236Ser	p.P1236S	ENST00000334344	NM_152641.2	1236	Cca/Tca	15/21	1	2	FACETS	1	0.975	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		721	638	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416516	49416516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	261	787	0	ENST00000301067.7:c.16195G>A	p.Val5399Met	p.V5399M	ENST00000301067	NM_003482.3	5399	Gtg/Atg	51/54	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.3230403449138	2		787	677	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420607	49420607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123724	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	263	898	0	ENST00000301067.7:c.15142C>T	p.Arg5048Cys	p.R5048C	ENST00000301067	NM_003482.3	5048	Cgt/Tgt	48/54	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.3230403449138	2		898	681	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433402	49433402	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	243	828	0	ENST00000301067.7:c.8047-2A>G		p.X2683_splice	ENST00000301067	NM_003482.3	2683			1	2	FACETS	0.925	0.873	0.978	1	0.996	1	CLONAL	3	TRUE	1	0.3230403449138	2		828	542	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436109	49436109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755573725	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	178	597	0	ENST00000301067.7:c.5872C>T	p.Arg1958Cys	p.R1958C	ENST00000301067	NM_003482.3	1958	Cgc/Tgc	28/54	1	2	FACETS	1	0.987	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		597	442	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436947	49436947	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	105	638	0	ENST00000301067.7:c.5556G>T	p.Lys1852Asn	p.K1852N	ENST00000301067	NM_003482.3	1852	aaG/aaT	25/54	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.3230403449138	2		638	522	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437710	49437710	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	227	806	0	ENST00000301067.7:c.5260C>T	p.Gln1754Ter	p.Q1754*	ENST00000301067	NM_003482.3	1754	Caa/Taa	22/54	1	2	FACETS	0.994	0.93	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		806	707	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50483736	50483736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768972786	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	197	475	0	ENST00000394963.4:c.841C>T	p.Arg281Trp	p.R281W	ENST00000394963	NM_003076.4	281	Cgg/Tgg	7/13	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		475	502	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863334	57863334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	213	758	0	ENST00000228682.2:c.1429G>A	p.Asp477Asn	p.D477N	ENST00000228682	NM_005269.2	477	Gac/Aac	11/12	1	2	FACETS	1	0.978	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		758	597	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856094	111856094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs895574020	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	155	740	0	ENST00000341259.2:c.145G>A	p.Ala49Thr	p.A49T	ENST00000341259	NM_005475.2	49	Gcc/Acc	2/8	1	2	FACETS	1	0.978	1	1	0.993	1	CLONAL	2	TRUE	1	0.3230403449138	2		740	416	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112910782	112910782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	139	451	0	ENST00000351677.2:c.791G>A	p.Ser264Asn	p.S264N	ENST00000351677	NM_002834.3	264	aGc/aAc	7/16	1	2	FACETS	1	0.983	1	1	0.993	1	CLONAL	2	TRUE	1	0.3230403449138	2		451	348	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120789188	120789188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	179	575	0	ENST00000257552.2:c.749G>A	p.Arg250Gln	p.R250Q	ENST00000257552	NM_002442.3	250	cGg/cAg	11/15	1	2	FACETS	1	0.971	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		575	511	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426830	121426830	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201934320	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	214	650	0	ENST00000257555.6:c.521C>T	p.Ala174Val	p.A174V	ENST00000257555		174	gCg/gTg	2/10	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		650	538	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432154	121432154	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555681479	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	254	794	0	ENST00000257555.6:c.901G>A	p.Ala301Thr	p.A301T	ENST00000257555		301	Gct/Act	4/10	1	2	FACETS	0.92	0.869	0.971	1	0.996	1	CLONAL	3	TRUE	1	0.3230403449138	2		794	570	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226445	133226445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	190	496	0	ENST00000320574.5:c.3613C>T	p.Pro1205Ser	p.P1205S	ENST00000320574	NM_006231.2	1205	Ccg/Tcg	30/49	1	2	FACETS	0.885	0.828	0.943	1	0.995	1	CLONAL	3	TRUE	1	0.3230403449138	2		496	443	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249829	133249829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555228490	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	204	630	1	ENST00000320574.5:c.1394C>T	p.Ala465Val	p.A465V	ENST00000320574	NM_006231.2	465	gCc/gTc	14/49	1	2	FACETS	1	0.983	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		631	547	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911893	32911893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	64	517	0	ENST00000380152.3:c.3401G>A	p.Ser1134Asn	p.S1134N	ENST00000380152		1134	aGc/aAc	11/27	0.3230403449138	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.3230403449138	1		517	313	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134255	41134255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs994659376	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	173	715	1	ENST00000379561.5:c.1373C>T	p.Ala458Val	p.A458V	ENST00000379561	NM_002015.3	458	gCg/gTg	2/3	0.3230403449138	1	FACETS	1	0.971	1	1	0.994	1	CLONAL	2	TRUE	0	0.3230403449138	1		716	416	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514928	103514928	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	457	702	0	ENST00000355739.4:c.1429T>C	p.Ser477Pro	p.S477P	ENST00000355739	NM_000123.3	477	Tca/Cca	8/15	0.3230403449138	4	FACETS	0.914	0.88	0.948	1	0.997	1	CLONAL	5	TRUE	1	0.3230403449138	4		702	819	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518693	103518693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142438319	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	185	540	0	ENST00000355739.4:c.2281G>A	p.Ala761Thr	p.A761T	ENST00000355739	NM_000123.3	761	Gct/Act	10/15	0.3230403449138	4	FACETS	1	0.982	1	0.79	0.733	0.849	CLONAL	2	TRUE	1	0.3230403449138	4		540	639	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524611	103524612	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs752661599	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	358	571	8	ENST00000355739.4:c.2751dup	p.Leu918IlefsTer12	p.L918Ifs*12	ENST00000355739	NM_000123.3	914	-/A	13/15	0.3230403449138	4	FACETS	0.965	0.921	1	1	0.994	1	CLONAL	4	TRUE	1	0.3230403449138	4		579	760	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528179	103528179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs183317723	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	366	594	0	ENST00000355739.4:c.3487G>A	p.Val1163Met	p.V1163M	ENST00000355739	NM_000123.3	1163	Gtg/Atg	15/15	0.3230403449138	4	FACETS	0.915	0.877	0.953	1	0.996	1	CLONAL	5	TRUE	1	0.3230403449138	4		594	655	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434592	110434592	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	170	823	3	ENST00000375856.3:c.3809C>A	p.Pro1270Gln	p.P1270Q	ENST00000375856	NM_003749.2	1270	cCg/cAg	1/2	0.3230403449138	4	FACETS	1	0.965	1	0.717	0.662	0.774	CLONAL	2	TRUE	1	0.3230403449138	4		826	647	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434823	110434823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1383650129	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	169	857	0	ENST00000375856.3:c.3578G>A	p.Gly1193Asp	p.G1193D	ENST00000375856	NM_003749.2	1193	gGc/gAc	1/2	0.3230403449138	4	FACETS	1	0.941	1	0.683	0.63	0.738	CLONAL	2	TRUE	1	0.3230403449138	4		857	676	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435355	110435355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1437839141	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	363	871	0	ENST00000375856.3:c.3046C>T	p.Pro1016Ser	p.P1016S	ENST00000375856	NM_003749.2	1016	Ccg/Tcg	1/2	0.3230403449138	4	FACETS	0.944	0.905	0.982	1	0.996	1	CLONAL	5	TRUE	1	0.3230403449138	4		871	630	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436057	110436057	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1204032443	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	218	831	1	ENST00000375856.3:c.2344G>A	p.Asp782Asn	p.D782N	ENST00000375856	NM_003749.2	782	Gac/Aac	1/2	0.3230403449138	4	FACETS	1	0.986	1	0.807	0.753	0.862	CLONAL	2	TRUE	1	0.3230403449138	4		832	738	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436287	110436287	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	156	922	0	ENST00000375856.3:c.2114C>T	p.Ala705Val	p.A705V	ENST00000375856	NM_003749.2	705	gCg/gTg	1/2	0.3230403449138	4	FACETS	0.819	0.751	0.89	0.546	0.501	0.594	CLONAL	2	TRUE	1	0.3230403449138	4		922	780	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436348	110436348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1373634609	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	431	1023	0	ENST00000375856.3:c.2053G>A	p.Ala685Thr	p.A685T	ENST00000375856	NM_003749.2	685	Gcc/Acc	1/2	0.3230403449138	4	FACETS	0.917	0.882	0.952	1	0.997	1	CLONAL	5	TRUE	1	0.3230403449138	4		1023	770	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436647	110436647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	165	840	0	ENST00000375856.3:c.1754G>A	p.Arg585Gln	p.R585Q	ENST00000375856	NM_003749.2	585	cGg/cAg	1/2	0.3230403449138	4	FACETS	1	0.953	1	0.698	0.644	0.755	CLONAL	2	TRUE	1	0.3230403449138	4		840	645	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046611	30046611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556530827	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	190	621	0	ENST00000331968.5:c.2572C>T	p.Arg858Cys	p.R858C	ENST00000331968	NM_002742.2	858	Cgc/Tgc	18/18	1	2	FACETS	1	0.986	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		621	481	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194789	30194789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761853569	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	165	602	4	ENST00000331968.5:c.356C>T	p.Ala119Val	p.A119V	ENST00000331968	NM_002742.2	119	gCg/gTg	2/18	1	2	FACETS	1	0.967	1	1	0.993	1	CLONAL	2	TRUE	1	0.3230403449138	2		606	475	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557552	95557552	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1447120867	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	193	698	0	ENST00000393063.1:c.5515C>T	p.Arg1839Trp	p.R1839W	ENST00000393063	NM_030621.3	1839	Cgg/Tgg	26/28	1	2	FACETS	1	0.982	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		698	519	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582851	95582851	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201298288	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	107	550	0	ENST00000393063.1:c.1691C>T	p.Ala564Val	p.A564V	ENST00000393063	NM_030621.3	564	gCg/gTg	11/28	1	2	FACETS	1	0.949	1	1	0.989	1	CLONAL	2	TRUE	1	0.3230403449138	2		550	311	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40685763	40685763	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777913445	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	146	554	0	ENST00000249776.8:c.916G>A	p.Ala306Thr	p.A306T	ENST00000249776	NM_033286.3	306	Gcc/Acc	9/9	1	2	FACETS	1	0.978	1	1	0.993	1	CLONAL	2	TRUE	1	0.3230403449138	2		554	389	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40993338	40993338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145617142	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	120	544	0	ENST00000267868.3:c.164C>T	p.Ala55Val	p.A55V	ENST00000267868	NM_002875.4	55	gCg/gTg	3/10	1	2	FACETS	1	0.914	1	1	0.99	1	CLONAL	2	TRUE	1	0.3230403449138	2		544	371	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712535	43712535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756376679	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	255	740	0	ENST00000382044.4:c.4649C>T	p.Thr1550Met	p.T1550M	ENST00000382044	NM_001141980.1	1550	aCg/aTg	21/28	1	2	FACETS	1	0.987	1	1	0.996	1	CLONAL	2	TRUE	1	0.3230403449138	2		740	679	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720329	43720329	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770349820	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	159	593	0	ENST00000382044.4:c.3713G>A	p.Gly1238Asp	p.G1238D	ENST00000382044	NM_001141980.1	1238	gGc/gAc	18/28	1	2	FACETS	1	0.935	1	1	0.992	1	CLONAL	2	TRUE	1	0.3230403449138	2		593	486	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729187	66729187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	225	696	1	ENST00000307102.5:c.395C>T	p.Ala132Val	p.A132V	ENST00000307102	NM_002755.3	132	gCg/gTg	3/11	1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		697	586	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73991994	73991994	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139808700	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	233	715	0	ENST00000318443.5:c.14G>A	p.Arg5Gln	p.R5Q	ENST00000318443	NM_001024736.1	5	cGg/cAg	2/10	1	2	FACETS	1	0.983	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		715	636	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994796	73994796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	171	644	1	ENST00000318443.5:c.280G>A	p.Ala94Thr	p.A94T	ENST00000318443	NM_001024736.1	94	Gcc/Acc	3/10	1	2	FACETS	1	0.983	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		645	443	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669547	88669547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56394626	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	156	568	1	ENST00000360948.2:c.1351G>A	p.Val451Ile	p.V451I	ENST00000360948	NM_001012338.2	451	Gtc/Atc	12/19	1	2	FACETS	1	0.971	1	1	0.993	1	CLONAL	2	TRUE	1	0.3230403449138	2		569	439	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295050	91295050	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	112	380	0	ENST00000355112.3:c.833C>T	p.Ala278Val	p.A278V	ENST00000355112	NM_000057.2	278	gCt/gTt	4/22	1	2	FACETS	1	0.939	1	1	0.99	1	CLONAL	2	TRUE	1	0.3230403449138	2		380	333	SUCCESS
BLM	641	MSKCC	GRCh37	15	91328208	91328208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367953471	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	192	574	1	ENST00000355112.3:c.2720C>T	p.Thr907Met	p.T907M	ENST00000355112	NM_000057.2	907	aCg/aTg	14/22	1	2	FACETS	1	0.965	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		575	562	SUCCESS
BLM	641	MSKCC	GRCh37	15	91352442	91352442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760554566	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	136	485	0	ENST00000355112.3:c.3827C>T	p.Ala1276Val	p.A1276V	ENST00000355112	NM_000057.2	1276	gCg/gTg	20/22	1	2	FACETS	1	0.951	1	1	0.991	1	CLONAL	2	TRUE	1	0.3230403449138	2		485	401	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251015	99251015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375153085	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	198	739	0	ENST00000268035.6:c.319C>T	p.Arg107Cys	p.R107C	ENST00000268035	NM_000875.3	107	Cgc/Tgc	2/21	1	2	FACETS	1	0.98	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		739	545	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251042	99251042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	189	726	1	ENST00000268035.6:c.346G>A	p.Ala116Thr	p.A116T	ENST00000268035	NM_000875.3	116	Gcc/Acc	2/21	1	2	FACETS	1	0.978	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		727	523	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	359996	359996	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324067997	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	172	724	0	ENST00000262320.3:c.1093C>T	p.Arg365Trp	p.R365W	ENST00000262320	NM_003502.3	365	Cgg/Tgg	4/11	1	2	FACETS	1	0.957	1	1	0.993	1	CLONAL	2	TRUE	1	0.3230403449138	2		724	509	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100432	2100432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397514949	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	196	534	0	ENST00000219476.3:c.170G>A	p.Arg57His	p.R57H	ENST00000219476	NM_000548.3	57	cGc/cAc	3/42	1	2	FACETS	1	0.986	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		534	501	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130378	2130378	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	177	787	1	ENST00000219476.3:c.3610G>T	p.Gly1204Trp	p.G1204W	ENST00000219476	NM_000548.3	1204	Ggg/Tgg	30/42	1	2	FACETS	1	0.969	1	1	0.993	1	CLONAL	2	TRUE	1	0.3230403449138	2		788	508	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134269	2134269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201979616	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	68	824	0	ENST00000219476.3:c.4046C>T	p.Ala1349Val	p.A1349V	ENST00000219476	NM_000548.3	1349	gCg/gTg	34/42	1	2	FACETS	0.712	0.62	0.812	0.712	0.62	0.812	SUBCLONAL	1	TRUE	1	0.3230403449138	2		824	591	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3634860	3634860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369852048	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	249	673	1	ENST00000294008.3:c.4649G>A	p.Arg1550Gln	p.R1550Q	ENST00000294008	NM_032444.2	1550	cGg/cAg	13/15	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.3230403449138	2		674	637	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652222	3652222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	29	688	0	ENST00000294008.3:c.847G>A	p.Ala283Thr	p.A283T	ENST00000294008	NM_032444.2	283	Gca/Aca	4/15	1	2	FACETS	0.312	0.249	0.383	0.312	0.249	0.383	SUBCLONAL	1	TRUE	1	0.3230403449138	2		688	576	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778362	3778362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1194793942	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	190	920	0	ENST00000262367.5:c.6686G>A	p.Gly2229Asp	p.G2229D	ENST00000262367	NM_004380.2	2229	gGc/gAc	31/31	1	2	FACETS	1	0.977	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		920	531	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779037	3779037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1279369054	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	222	835	1	ENST00000262367.5:c.6011G>A	p.Arg2004Gln	p.R2004Q	ENST00000262367	NM_004380.2	2004	cGa/cAa	31/31	1	2	FACETS	0.902	0.848	0.956	1	0.995	1	CLONAL	3	TRUE	1	0.3230403449138	2		836	508	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779475	3779475	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770325046	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	231	886	0	ENST00000262367.5:c.5573G>A	p.Arg1858His	p.R1858H	ENST00000262367	NM_004380.2	1858	cGc/cAc	31/31	1	2	FACETS	1	0.98	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		886	649	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781408	3781408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329802754	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	162	715	1	ENST00000262367.5:c.4957G>A	p.Asp1653Asn	p.D1653N	ENST00000262367	NM_004380.2	1653	Gac/Aac	30/31	1	2	FACETS	0.981	0.907	1	1	0.992	1	CLONAL	2	TRUE	1	0.3230403449138	2		716	511	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808917	3808917	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	235	639	0	ENST00000262367.5:c.3307C>T	p.Arg1103Ter	p.R1103*	ENST00000262367	NM_004380.2	1103	Cga/Tga	17/31	1	2	FACETS	1	0.99	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		639	585	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3827631	3827631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141098117	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	156	517	0	ENST00000262367.5:c.2141G>A	p.Arg714His	p.R714H	ENST00000262367	NM_004380.2	714	cGc/cAc	11/31	1	2	FACETS	1	0.979	1	1	0.993	1	CLONAL	2	TRUE	1	0.3230403449138	2		517	416	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900879	3900879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	195	654	1	ENST00000262367.5:c.217C>T	p.Leu73Phe	p.L73F	ENST00000262367	NM_004380.2	73	Ctt/Ttt	2/31	1	2	FACETS	1	0.973	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		655	556	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892293	9892293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs796052550	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	198	725	1	ENST00000330684.3:c.2197G>A	p.Ala733Thr	p.A733T	ENST00000330684	NM_001134407.1	733	Gca/Aca	11/13	1	2	FACETS	1	0.979	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		726	549	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041623	14041623	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1204895453	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	172	697	0	ENST00000311895.7:c.2170G>A	p.Val724Met	p.V724M	ENST00000311895	NM_005236.2	724	Gtg/Atg	11/11	1	2	FACETS	1	0.946	1	1	0.993	1	CLONAL	2	TRUE	1	0.3230403449138	2		697	520	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23635412	23635412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs515726094	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	116	467	0	ENST00000261584.4:c.2752C>T	p.Pro918Ser	p.P918S	ENST00000261584	NM_024675.3	918	Cca/Tca	8/13	1	2	FACETS	1	0.949	1	1	0.99	1	CLONAL	2	TRUE	1	0.3230403449138	2		467	339	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646329	23646329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778890869	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	207	666	0	ENST00000261584.4:c.1538C>T	p.Thr513Ile	p.T513I	ENST00000261584	NM_024675.3	513	aCa/aTa	4/13	1	2	FACETS	1	0.982	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		666	562	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875737	56875737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773614710	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	222	664	0	ENST00000308159.5:c.2341C>T	p.Arg781Cys	p.R781C	ENST00000308159	NM_014669.4	781	Cgc/Tgc	21/22	1	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		664	594	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650720	67650720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	248	652	0	ENST00000264010.4:c.1025G>A	p.Arg342His	p.R342H	ENST00000264010	NM_006565.3	342	cGt/cAt	5/12	1	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		652	670	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654642	67654642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	221	557	0	ENST00000264010.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000264010	NM_006565.3	377	Cgt/Tgt	6/12	1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		557	573	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832175	72832175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371424734	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	203	730	1	ENST00000268489.5:c.4406C>T	p.Ala1469Val	p.A1469V	ENST00000268489	NM_006885.3	1469	gCc/gTc	9/10	1	2	FACETS	1	0.979	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		731	562	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991508	72991508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755878058	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	219	738	2	ENST00000268489.5:c.2537G>A	p.Arg846His	p.R846H	ENST00000268489	NM_006885.3	846	cGc/cAc	2/10	1	2	FACETS	1	0.983	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		740	594	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993075	72993075	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	230	711	0	ENST00000268489.5:c.970G>A	p.Ala324Thr	p.A324T	ENST00000268489	NM_006885.3	324	Gct/Act	2/10	1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		711	596	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993348	72993348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759852645	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	216	755	0	ENST00000268489.5:c.697G>A	p.Val233Met	p.V233M	ENST00000268489	NM_006885.3	233	Gtg/Atg	2/10	1	2	FACETS	1	0.976	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		755	615	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969845	81969845	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369090249	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	216	714	0	ENST00000359376.3:c.2914G>A	p.Val972Ile	p.V972I	ENST00000359376	NM_002661.3	972	Gtc/Atc	27/33	1	2	FACETS	1	0.973	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		714	623	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86545019	86545019	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293500536	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	169	666	1	ENST00000262426.4:c.844G>A	p.Ala282Thr	p.A282T	ENST00000262426	NM_001451.2	282	Gcc/Acc	1/2	1	2	FACETS	0.953	0.889	1	1	0.994	1	CLONAL	3	TRUE	1	0.3230403449138	2		667	366	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346205	89346205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202081612	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	175	843	1	ENST00000301030.4:c.6745C>T	p.Arg2249Cys	p.R2249C	ENST00000301030	NM_001256183.1	2249	Cgc/Tgc	9/13	1	2	FACETS	1	0.981	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		844	470	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348938	89348938	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753576509	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	234	736	0	ENST00000301030.4:c.4012G>A	p.Ala1338Thr	p.A1338T	ENST00000301030	NM_001256183.1	1338	Gcc/Acc	9/13	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		736	622	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12043161	12043161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755523599	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	124	368	0	ENST00000353533.5:c.1046C>T	p.Thr349Met	p.T349M	ENST00000353533	NM_003010.3	349	aCg/aTg	10/11	0.14776798373303	3	FACETS	1	0.979	1	1	0.979	1	INDETERMINATE	2	TRUE	1	0.3230403449138	3		368	362	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935762	15935762	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	305	641	0	ENST00000268712.3:c.7171C>T	p.Arg2391Trp	p.R2391W	ENST00000268712	NM_006311.3	2391	Cgg/Tgg	46/46	0.14776798373303	3	FACETS	1	0.974	1	1	0.995	1	INDETERMINATE	3	TRUE	1	0.3230403449138	3		641	702	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968868	15968868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754505756	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	353	672	0	ENST00000268712.3:c.4882C>T	p.Arg1628Cys	p.R1628C	ENST00000268712	NM_006311.3	1628	Cgt/Tgt	33/46	0.14776798373303	3	FACETS	1	0.991	1	1	0.996	1	INDETERMINATE	3	TRUE	1	0.3230403449138	3		672	738	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974830	15974830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	193	597	0	ENST00000268712.3:c.4045C>T	p.Arg1349Cys	p.R1349C	ENST00000268712	NM_006311.3	1349	Cgt/Tgt	30/46	0.14776798373303	3	FACETS	1	0.98	1	1	0.98	1	INDETERMINATE	2	TRUE	1	0.3230403449138	3		597	606	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	180	464	0	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	0.14776798373303	3	FACETS	0.934	0.87	0.999	1	0.99	1	INDETERMINATE	3	TRUE	1	0.3230403449138	3		464	462	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118598	17118598	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41419545	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	249	638	5	ENST00000285071.4:c.1333G>A	p.Ala445Thr	p.A445T	ENST00000285071	NM_144997.5	445	Gca/Aca	12/14	0.14776798373303	3	FACETS	1	0.97	1	1	0.994	1	INDETERMINATE	3	TRUE	1	0.3230403449138	3		643	573	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556079	29556079	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886041347	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	124	390	0	ENST00000356175.3:c.2446C>T	p.Arg816Ter	p.R816*	ENST00000356175	NM_000267.3	816	Cga/Tga	21/57	0.14776798373303	3	FACETS	0.909	0.834	0.986	1	0.985	1	INDETERMINATE	3	TRUE	1	0.3230403449138	3		390	327	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559777	29559777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs902739109	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	272	485	2	ENST00000356175.3:c.3374C>T	p.Ala1125Val	p.A1125V	ENST00000356175	NM_000267.3	1125	gCg/gTg	26/57	0.14776798373303	3	FACETS	0.889	0.839	0.941	1	0.992	1	INDETERMINATE	3	TRUE	1	0.3230403449138	3		487	733	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657337	29657337	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	145	580	0	ENST00000356175.3:c.5570G>A	p.Cys1857Tyr	p.C1857Y	ENST00000356175	NM_000267.3	1857	tGt/tAt	38/57	0.14776798373303	3	FACETS	0.92	0.849	0.991	1	0.987	1	INDETERMINATE	3	TRUE	1	0.3230403449138	3		580	378	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	107	540	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	0.14776798373303	3	FACETS	1	0.949	1	1	0.949	1	INDETERMINATE	2	TRUE	1	0.3230403449138	3		540	359	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33446562	33446562	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	173	663	0	ENST00000345365.6:c.71G>T	p.Arg24Met	p.R24M	ENST00000345365	NM_002878.3	24	aGg/aTg	1/10	1	2	FACETS	0.877	0.818	0.938	1	0.994	1	CLONAL	3	TRUE	1	0.3230403449138	2		663	407	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690637	33690637	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	231	769	1	ENST00000308377.4:c.190G>A	p.Ala64Thr	p.A64T	ENST00000308377	NM_152270.3	64	Gcc/Acc	2/5	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		770	590	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866342	37866342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770976272	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	51	562	0	ENST00000269571.5:c.647C>T	p.Thr216Met	p.T216M	ENST00000269571		216	aCg/aTg	6/27	1	2	FACETS	0.87	0.742	1	0.87	0.742	1	CLONAL	1	TRUE	1	0.3230403449138	2		562	363	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38788488	38788488	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	194	547	0	ENST00000348513.6:c.673C>T	p.Gln225Ter	p.Q225*	ENST00000348513	NM_003079.4	225	Cag/Tag	8/11	1	2	FACETS	1	0.98	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		547	532	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40468908	40468908	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	147	492	0	ENST00000264657.5:c.2156G>A	p.Ser719Asn	p.S719N	ENST00000264657	NM_139276.2	719	aGc/aAc	23/24	1	2	FACETS	0.97	0.893	1	1	0.991	1	CLONAL	2	TRUE	1	0.3230403449138	2		492	469	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696709	47696709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	152	538	0	ENST00000347630.2:c.239G>A	p.Ser80Asn	p.S80N	ENST00000347630	NM_001007230.1	80	aGc/aAc	5/11	1	2	FACETS	1	0.965	1	1	0.992	1	CLONAL	2	TRUE	1	0.3230403449138	2		538	437	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511562	66511562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1224297486	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	215	458	0	ENST00000358598.2:c.22G>A	p.Ala8Thr	p.A8T	ENST00000358598	NM_212471.2	8	Gcc/Acc	2/11	1	2	FACETS	1	0.967	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		458	632	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39618815	39618815	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	93	378	0	ENST00000262039.4:c.2038+1G>A		p.X680_splice	ENST00000262039	NM_002647.2	680			1	2	FACETS	1	0.942	1	1	0.988	1	CLONAL	2	TRUE	1	0.3230403449138	2		378	271	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368313	45368313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747308534	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	121	526	2	ENST00000262160.6:c.1289C>T	p.Thr430Met	p.T430M	ENST00000262160	NM_005901.5	430	aCg/aTg	11/11	1	2	FACETS	1	0.968	1	1	0.991	1	CLONAL	2	TRUE	1	0.3230403449138	2		528	334	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1646375	1646375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528980993	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	263	726	0	ENST00000344749.5:c.124G>A	p.Gly42Arg	p.G42R	ENST00000344749	NM_001136139.2	42	Ggg/Agg	3/19	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.3230403449138	2		726	668	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191069	2191069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746714270	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	218	745	0	ENST00000398665.3:c.323G>A	p.Arg108His	p.R108H	ENST00000398665	NM_032482.2	108	cGc/cAc	5/28	1	2	FACETS	1	0.981	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		745	601	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226860	2226860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	230	933	0	ENST00000398665.3:c.4340C>T	p.Ala1447Val	p.A1447V	ENST00000398665	NM_032482.2	1447	gCg/gTg	27/28	1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		933	602	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119007	3119007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769503200	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	178	822	0	ENST00000078429.4:c.691G>A	p.Ala231Thr	p.A231T	ENST00000078429	NM_002067.2	231	Gcc/Acc	5/7	1	2	FACETS	1	0.977	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		822	492	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121089	3121089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	271	763	0	ENST00000078429.4:c.992C>T	p.Ala331Val	p.A331V	ENST00000078429	NM_002067.2	331	gCc/gTc	7/7	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.3230403449138	2		763	693	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121110	3121110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	259	741	0	ENST00000078429.4:c.1013G>A	p.Arg338His	p.R338H	ENST00000078429	NM_002067.2	338	cGc/cAc	7/7	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.3230403449138	2		741	678	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218488	5218488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1361339357	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	255	673	0	ENST00000357368.4:c.3991G>A	p.Ala1331Thr	p.A1331T	ENST00000357368	NM_002850.3	1331	Gcc/Acc	25/38	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.3230403449138	2		673	652	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229651	5229651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	103	503	0	ENST00000357368.4:c.2200G>A	p.Ala734Thr	p.A734T	ENST00000357368	NM_002850.3	734	Gcc/Acc	15/38	1	2	FACETS	1	0.975	1	1	0.99	1	CLONAL	2	TRUE	1	0.3230403449138	2		503	264	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238944	5238944	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs946180785	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	214	734	1	ENST00000357368.4:c.1835G>A	p.Arg612His	p.R612H	ENST00000357368	NM_002850.3	612	cGc/cAc	13/38	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		735	558	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265039	5265039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748364975	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	245	708	1	ENST00000357368.4:c.548G>A	p.Arg183His	p.R183H	ENST00000357368	NM_002850.3	183	cGc/cAc	5/38	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.3230403449138	2		709	612	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273512	5273512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	221	758	0	ENST00000357368.4:c.320G>A	p.Cys107Tyr	p.C107Y	ENST00000357368	NM_002850.3	107	tGt/tAt	4/38	1	2	FACETS	1	0.977	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		758	627	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142913	7142913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1283504748	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	234	782	0	ENST00000302850.5:c.2456G>A	p.Arg819His	p.R819H	ENST00000302850	NM_000208.2	819	cGc/cAc	12/22	1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		782	609	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184541	7184541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	182	668	1	ENST00000302850.5:c.760G>A	p.Ala254Thr	p.A254T	ENST00000302850	NM_000208.2	254	Gcc/Acc	3/22	1	2	FACETS	1	0.964	1	1	0.993	1	CLONAL	2	TRUE	1	0.3230403449138	2		669	532	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10259612	10259612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	234	631	0	ENST00000340748.4:c.2620G>A	p.Ala874Thr	p.A874T	ENST00000340748		874	Gcg/Acg	26/40	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		631	622	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600447	10600447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	87	775	0	ENST00000171111.5:c.1408C>T	p.Arg470Cys	p.R470C	ENST00000171111	NM_203500.1	470	Cgt/Tgt	4/6	1	2	FACETS	0.773	0.684	0.868	0.773	0.684	0.868	SUBCLONAL	1	TRUE	1	0.3230403449138	2		775	697	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11019846	11019846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	264	754	0	ENST00000327064.4:c.521G>A	p.Arg174His	p.R174H	ENST00000327064	NM_199141.1	174	cGc/cAc	4/16	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.3230403449138	2		754	683	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031413	11031413	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	240	848	0	ENST00000327064.4:c.1413C>A	p.Asn471Lys	p.N471K	ENST00000327064	NM_199141.1	471	aaC/aaA	12/16	1	2	FACETS	1	0.975	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		848	692	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101865	11101865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	207	771	0	ENST00000358026.2:c.1285G>A	p.Ala429Thr	p.A429T	ENST00000358026	NM_001128849.1	429	Gcg/Acg	8/36	1	2	FACETS	1	0.983	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		771	556	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118687	11118687	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1248744047	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	205	643	0	ENST00000358026.2:c.2111G>A	p.Arg704Gln	p.R704Q	ENST00000358026	NM_001128849.1	704	cGg/cAg	14/36	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		643	534	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132501	11132501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	280	869	0	ENST00000358026.2:c.2717G>A	p.Arg906His	p.R906H	ENST00000358026	NM_001128849.1	906	cGc/cAc	19/36	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.3230403449138	2		869	721	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136143	11136143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770014321	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	170	539	0	ENST00000358026.2:c.3127C>T	p.Arg1043Trp	p.R1043W	ENST00000358026	NM_001128849.1	1043	Cgg/Tgg	22/36	1	2	FACETS	1	0.981	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		539	454	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144146	11144146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	195	552	0	ENST00000358026.2:c.3727C>T	p.Arg1243Trp	p.R1243W	ENST00000358026	NM_001128849.1	1243	Cgg/Tgg	26/36	1	2	FACETS	1	0.956	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		552	583	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145645	11145645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	205	780	0	ENST00000358026.2:c.4007G>A	p.Arg1336His	p.R1336H	ENST00000358026	NM_001128849.1	1336	cGc/cAc	29/36	1	2	FACETS	1	0.98	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		780	567	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276215	15276215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748889237	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	215	648	0	ENST00000263388.2:c.5779G>A	p.Ala1927Thr	p.A1927T	ENST00000263388	NM_000435.2	1927	Gcc/Acc	31/33	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		648	540	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276250	15276250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747223569	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	235	722	3	ENST00000263388.2:c.5744G>A	p.Arg1915His	p.R1915H	ENST00000263388	NM_000435.2	1915	cGc/cAc	31/33	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		725	638	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288765	15288765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1317504991	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	123	531	0	ENST00000263388.2:c.3974G>A	p.Arg1325His	p.R1325H	ENST00000263388	NM_000435.2	1325	cGc/cAc	24/33	1	2	FACETS	1	0.963	1	1	0.991	1	CLONAL	2	TRUE	1	0.3230403449138	2		531	348	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302857	15302857	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140914494	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	218	793	0	ENST00000263388.2:c.593C>T	p.Ala198Val	p.A198V	ENST00000263388	NM_000435.2	198	gCg/gTg	4/33	1	2	FACETS	1	0.982	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		793	597	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367977	15367977	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	180	601	0	ENST00000263377.2:c.1349T>C	p.Phe450Ser	p.F450S	ENST00000263377	NM_058243.2	450	tTc/tCc	8/20	1	2	FACETS	1	0.98	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		601	488	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376376	15376376	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1055405627	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	258	773	0	ENST00000263377.2:c.638C>T	p.Pro213Leu	p.P213L	ENST00000263377	NM_058243.2	213	cCg/cTg	5/20	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.3230403449138	2		773	682	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945764	17945764	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201784993	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	236	728	0	ENST00000458235.1:c.2096C>T	p.Ala699Val	p.A699V	ENST00000458235	NM_000215.3	699	gCg/gTg	16/24	1	2	FACETS	0.841	0.791	0.892	1	0.995	1	CLONAL	3	TRUE	1	0.3230403449138	2		728	579	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967089	18967089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334288478	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	167	620	0	ENST00000262803.5:c.1804G>A	p.Ala602Thr	p.A602T	ENST00000262803	NM_002911.3	602	Gca/Aca	13/24	1	2	FACETS	1	0.959	1	1	0.993	1	CLONAL	2	TRUE	1	0.3230403449138	2		620	491	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313422	30313422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200042616	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	214	655	0	ENST00000262643.3:c.1022C>T	p.Thr341Met	p.T341M	ENST00000262643	NM_001238.2	341	aCg/aTg	11/12	1	2	FACETS	1	0.983	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		655	579	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210709	36210709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780868475	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	226	699	0	ENST00000222270.7:c.460C>T	p.Arg154Cys	p.R154C	ENST00000222270	NM_014727.1	154	Cgc/Tgc	3/37	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		699	611	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212526	36212526	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	280	846	0	ENST00000222270.7:c.2277G>T	p.Gln759His	p.Q759H	ENST00000222270	NM_014727.1	759	caG/caT	3/37	1	2	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	TRUE	1	0.3230403449138	2		846	703	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213515	36213515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746928288	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	213	676	2	ENST00000222270.7:c.2617C>T	p.Arg873Cys	p.R873C	ENST00000222270	NM_014727.1	873	Cgt/Tgt	5/37	1	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		678	563	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223533	36223533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1347423104	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	205	945	0	ENST00000222270.7:c.6083C>T	p.Ser2028Phe	p.S2028F	ENST00000222270	NM_014727.1	2028	tCc/tTc	28/37	1	2	FACETS	1	0.978	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		945	573	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228789	36228789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	282	795	0	ENST00000222270.7:c.7688C>T	p.Ala2563Val	p.A2563V	ENST00000222270	NM_014727.1	2563	gCc/gTc	35/37	1	2	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	TRUE	1	0.3230403449138	2		795	703	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754050	42754050	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	192	685	0	ENST00000222329.4:c.302G>A	p.Arg101Gln	p.R101Q	ENST00000222329	NM_006494.2	101	cGg/cAg	3/4	1	2	FACETS	1	0.97	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		685	554	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754574	42754574	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768322408	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	204	714	3	ENST00000222329.4:c.166G>A	p.Val56Ile	p.V56I	ENST00000222329	NM_006494.2	56	Gtc/Atc	2/4	1	2	FACETS	1	0.975	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		717	580	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423784	47423784	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	207	638	0	ENST00000404338.3:c.1852G>A	p.Ala618Thr	p.A618T	ENST00000404338	NM_004491.4	618	Gct/Act	1/6	1	2	FACETS	1	0.978	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		638	580	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905275	50905275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	262	878	0	ENST00000440232.2:c.483G>A	p.Met161Ile	p.M161I	ENST00000440232	NM_002691.3	161	atG/atA	5/27	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.3230403449138	2		878	684	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918709	50918709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501818	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	158	611	0	ENST00000440232.2:c.2579C>T	p.Ala860Val	p.A860V	ENST00000440232	NM_002691.3	860	gCg/gTg	21/27	1	2	FACETS	1	0.979	1	1	0.993	1	CLONAL	2	TRUE	1	0.3230403449138	2		611	424	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919665	50919665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs565328583	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	210	731	0	ENST00000440232.2:c.2833G>A	p.Val945Met	p.V945M	ENST00000440232	NM_002691.3	945	Gtg/Atg	23/27	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		731	560	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463271	25463271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770568549	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	208	667	0	ENST00000264709.3:c.2222C>T	p.Ala741Val	p.A741V	ENST00000264709	NM_175629.2	741	gCg/gTg	19/23	1	2	FACETS	1	0.98	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		667	575	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464541	25464541	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	241	634	0	ENST00000264709.3:c.1972G>T	p.Asp658Tyr	p.D658Y	ENST00000264709	NM_175629.2	658	Gac/Tac	17/23	1	2	FACETS	0.836	0.787	0.886	1	0.996	1	CLONAL	3	TRUE	1	0.3230403449138	2		634	595	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467047	25467047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	224	670	0	ENST00000264709.3:c.1828G>A	p.Ala610Thr	p.A610T	ENST00000264709	NM_175629.2	610	Gct/Act	15/23	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		670	593	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967305	25967305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766049052	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	248	643	0	ENST00000435504.4:c.1901C>T	p.Ser634Leu	p.S634L	ENST00000435504		634	tCg/tTg	13/13	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		643	641	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416496	29416496	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	74	846	0	ENST00000389048.3:c.4457C>G	p.Pro1486Arg	p.P1486R	ENST00000389048	NM_004304.4	1486	cCt/cGt	29/29	1	2	FACETS	0.713	0.624	0.808	0.713	0.624	0.808	SUBCLONAL	1	TRUE	1	0.3230403449138	2		846	643	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416647	29416647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201129468	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	268	836	1	ENST00000389048.3:c.4306C>T	p.Arg1436Cys	p.R1436C	ENST00000389048	NM_004304.4	1436	Cgc/Tgc	29/29	1	2	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	TRUE	1	0.3230403449138	2		837	668	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606697	29606697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779282861	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	197	716	0	ENST00000389048.3:c.1183C>T	p.Arg395Cys	p.R395C	ENST00000389048	NM_004304.4	395	Cgt/Tgt	5/29	1	2	FACETS	1	0.981	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		716	535	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702339	47702339	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587780684	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	157	440	0	ENST00000233146.2:c.1935A>C	p.Gln645His	p.Q645H	ENST00000233146	NM_000251.2	645	caA/caC	12/16	1	2	FACETS	1	0.985	1	1	0.993	1	CLONAL	2	TRUE	1	0.3230403449138	2		440	392	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026683	48026684	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	161	665	0	ENST00000234420.5:c.1564_1565del	p.Gln522AspfsTer8	p.Q522Dfs*8	ENST00000234420	NM_000179.2	521	ACa/a	4/10	1	2	FACETS	1	0.957	1	1	0.993	1	CLONAL	2	TRUE	1	0.3230403449138	2		665	475	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032123	48032124	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs63751327	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	201	568	0	ENST00000234420.5:c.3514dup	p.Arg1172LysfsTer5	p.R1172Kfs*5	ENST00000234420	NM_000179.2	1171	-/A	6/10	1	2	FACETS	1	0.975	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		568	570	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631036	67631036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	148	570	0	ENST00000272342.5:c.1222G>A	p.Ala408Thr	p.A408T	ENST00000272342	NM_019002.3	408	Gcc/Acc	5/6	1	2	FACETS	1	0.983	1	1	0.993	1	CLONAL	2	TRUE	1	0.3230403449138	2		570	371	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149894	99149894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368448330	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	167	622	0	ENST00000074304.5:c.206C>T	p.Ala69Val	p.A69V	ENST00000074304	NM_001134224.1	69	gCg/gTg	5/26	1	2	FACETS	0.902	0.834	0.973	1	0.992	1	CLONAL	2	TRUE	1	0.3230403449138	2		622	573	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172064	99172064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	243	759	1	ENST00000074304.5:c.1630C>T	p.Arg544Cys	p.R544C	ENST00000074304	NM_001134224.1	544	Cgt/Tgt	17/26	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		760	625	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050412	128050412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1246605943	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	206	552	0	ENST00000285398.2:c.245G>A	p.Gly82Asp	p.G82D	ENST00000285398	NM_000122.1	82	gGc/gAc	3/15	1	2	FACETS	0.869	0.815	0.924	1	0.995	1	CLONAL	3	TRUE	1	0.3230403449138	2		552	489	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634732	158634732	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771363719	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	280	730	0	ENST00000263640.3:c.454C>T	p.Arg152Cys	p.R152C	ENST00000263640	NM_001105.4	152	Cgc/Tgc	5/11	1	2	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	TRUE	1	0.3230403449138	2		730	705	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266725	198266725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	169	615	2	ENST00000335508.6:c.2207G>A	p.Arg736His	p.R736H	ENST00000335508	NM_012433.2	736	cGc/cAc	15/25	1	2	FACETS	1	0.979	1	1	0.993	1	CLONAL	2	TRUE	1	0.3230403449138	2		617	458	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149606	202149606	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	232	708	0	ENST00000358485.4:c.1047G>T	p.Glu349Asp	p.E349D	ENST00000358485	NM_001080125.1	349	gaG/gaT	8/9	1	2	FACETS	1	0.989	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		708	582	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103831	209103831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754957038	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	167	587	0	ENST00000345146.2:c.1118C>T	p.Thr373Ile	p.T373I	ENST00000345146	NM_005896.2	373	aCc/aTc	9/10	1	2	FACETS	0.898	0.836	0.96	1	0.994	1	CLONAL	3	TRUE	1	0.3230403449138	2		587	384	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593563	215593563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782662	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	228	689	1	ENST00000260947.4:c.2171C>T	p.Ala724Val	p.A724V	ENST00000260947	NM_000465.2	724	gCg/gTg	11/11	1	2	FACETS	1	0.958	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		690	685	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646007	215646007	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	173	714	0	ENST00000260947.4:c.591G>T	p.Lys197Asn	p.K197N	ENST00000260947	NM_000465.2	197	aaG/aaT	4/11	1	2	FACETS	1	0.983	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		714	453	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339039	225339039	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752958265	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	110	507	0	ENST00000264414.4:c.2230C>T	p.Arg744Cys	p.R744C	ENST00000264414	NM_003590.4	744	Cgt/Tgt	16/16	1	2	FACETS	1	0.945	1	1	0.99	1	CLONAL	2	TRUE	1	0.3230403449138	2		507	323	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371691	225371691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	145	582	0	ENST00000264414.4:c.913C>T	p.Arg305Cys	p.R305C	ENST00000264414	NM_003590.4	305	Cgt/Tgt	7/16	1	2	FACETS	0.845	0.782	0.91	1	0.993	1	CLONAL	3	TRUE	1	0.3230403449138	2		582	354	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400249	225400249	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	108	414	0	ENST00000264414.4:c.374A>G	p.Tyr125Cys	p.Y125C	ENST00000264414	NM_003590.4	125	tAc/tGc	3/16	1	2	FACETS	0.966	0.877	1	1	0.988	1	CLONAL	2	TRUE	1	0.3230403449138	2		414	346	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661663	227661664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761880048	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	158	829	11	ENST00000305123.5:c.1791dup	p.His598AlafsTer13	p.H598Afs*13	ENST00000305123	NM_005544.2	597	-/G	1/2	1	2	FACETS	0.98	0.905	1	1	0.992	1	CLONAL	2	TRUE	1	0.3230403449138	2		840	499	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31015992	31015992	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749495615	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	217	645	2	ENST00000375687.4:c.314C>T	p.Thr105Met	p.T105M	ENST00000375687	NM_015338.5	105	aCg/aTg	5/13	1	2	FACETS	1	0.954	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		647	655	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022830	31022830	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1463010740	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	188	757	0	ENST00000375687.4:c.2315C>T	p.Ala772Val	p.A772V	ENST00000375687	NM_015338.5	772	gCt/gTt	13/13	1	2	FACETS	1	0.958	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		757	559	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31025035	31025035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375101983	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	222	699	0	ENST00000375687.4:c.4520C>T	p.Ala1507Val	p.A1507V	ENST00000375687	NM_015338.5	1507	gCg/gTg	13/13	1	2	FACETS	1	0.981	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		699	614	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100906	41100906	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs560503250	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	211	704	0	ENST00000373198.4:c.1450G>A	p.Val484Ile	p.V484I	ENST00000373198	NM_133170.3	484	Gtt/Att	8/32	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		704	547	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256717	46256717	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	140	496	0	ENST00000371998.3:c.773G>T	p.Arg258Ile	p.R258I	ENST00000371998		258	aGa/aTa	8/23	1	2	FACETS	0.837	0.773	0.903	1	0.993	1	CLONAL	3	TRUE	1	0.3230403449138	2		496	345	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775583	39775583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369318352	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	252	708	0	ENST00000288319.7:c.437C>T	p.Ala146Val	p.A146V	ENST00000288319	NM_182918.3	146	gCg/gTg	4/10	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		708	690	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21348411	21348411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1329226132	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	193	922	0	ENST00000215739.8:c.1468G>A	p.Ala490Thr	p.A490T	ENST00000215739	NM_006767.3	490	Gcc/Acc	14/21	1	2	FACETS	1	0.983	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		922	515	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221649	22221649	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	116	437	0	ENST00000215832.6:c.82C>A	p.Leu28Ile	p.L28I	ENST00000215832	NM_002745.4	28	Ctc/Atc	1/9	1	2	FACETS	0.883	0.81	0.957	1	0.991	1	CLONAL	3	TRUE	1	0.3230403449138	2		437	271	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446636	29446636	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	147	833	1	ENST00000544604.2:c.2467C>T	p.Arg823Trp	p.R823W	ENST00000544604	NM_001206998.1	823	Cgg/Tgg	8/9	1	2	FACETS	0.946	0.87	1	1	0.991	1	CLONAL	2	TRUE	1	0.3230403449138	2		834	481	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572925	41572925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1389352663	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	282	851	0	ENST00000263253.7:c.5210G>A	p.Arg1737His	p.R1737H	ENST00000263253	NM_001429.3	1737	cGc/cAc	31/31	1	2	FACETS	0.882	0.835	0.929	1	0.996	1	CLONAL	3	TRUE	1	0.3230403449138	2		851	660	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721511	49721511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1255375162	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	183	507	0	ENST00000449682.2:c.2128C>T	p.Arg710Cys	p.R710C	ENST00000449682	NM_020998.3	710	Cgt/Tgt	18/18	1	2	FACETS	0.928	0.868	0.989	1	0.995	1	CLONAL	3	TRUE	1	0.3230403449138	2		507	407	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584478	52584478	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142726131	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	184	618	0	ENST00000394830.3:c.4535C>T	p.Ala1512Val	p.A1512V	ENST00000394830	NM_018313.4	1512	gCg/gTg	29/30	1	2	FACETS	1	0.957	1	1	0.993	1	CLONAL	2	TRUE	1	0.3230403449138	2		618	548	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63967897	63967897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777248770	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	199	641	0	ENST00000398590.3:c.788C>T	p.Pro263Leu	p.P263L	ENST00000398590	NM_001177387.1	263	cCg/cTg	7/14	1	2	FACETS	1	0.985	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		641	518	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981809	63981809	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367886296	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	263	898	0	ENST00000398590.3:c.2311C>T	p.Arg771Trp	p.R771W	ENST00000398590	NM_001177387.1	771	Cgg/Tgg	12/14	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.3230403449138	2		898	675	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987093	69987093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1221504326	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	279	726	0	ENST00000394351.3:c.154C>T	p.Pro52Ser	p.P52S	ENST00000394351	NM_000248.3	52	Cca/Tca	2/9	1	2	FACETS	0.871	0.824	0.918	1	0.996	1	CLONAL	3	TRUE	1	0.3230403449138	2		726	661	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027015	71027015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	255	799	0	ENST00000318789.4:c.1312C>T	p.Arg438Trp	p.R438W	ENST00000318789	NM_032682.5	438	Cgg/Tgg	15/21	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		799	700	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670340	134670340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415689583	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	214	636	1	ENST00000398015.3:c.251G>A	p.Arg84His	p.R84H	ENST00000398015	NM_004441.4	84	cGc/cAc	3/16	1	2	FACETS	1	0.979	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		637	597	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281651	142281651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759878676	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	28	505	0	ENST00000350721.4:c.593G>A	p.Ser198Asn	p.S198N	ENST00000350721	NM_001184.3	198	aGt/aAt	4/47	1	2	FACETS	0.54	0.432	0.663	0.54	0.432	0.663	SUBCLONAL	1	TRUE	1	0.3230403449138	2		505	321	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149243827	149243827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	215	563	0	ENST00000360632.3:c.991C>A	p.Leu331Ile	p.L331I	ENST00000360632	NM_015472.4	331	Ctc/Atc	6/7	1	2	FACETS	0.836	0.784	0.888	1	0.995	1	CLONAL	3	TRUE	1	0.3230403449138	2		563	531	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149290669	149290669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	202	563	0	ENST00000360632.3:c.550G>A	p.Val184Ile	p.V184I	ENST00000360632	NM_015472.4	184	Gta/Ata	3/7	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		563	501	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	130	367	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	1	0.931	1	1	0.991	1	CLONAL	2	TRUE	1	0.3230403449138	2		367	395	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922298	178922298	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	73	316	0	ENST00000263967.3:c.1067T>C	p.Val356Ala	p.V356A	ENST00000263967	NM_006218.2	356	gTt/gCt	6/21	1	2	FACETS	0.974	0.865	1	1	0.983	1	CLONAL	2	TRUE	1	0.3230403449138	2		316	232	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440290	187440290	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200887028	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	208	616	0	ENST00000232014.4:c.2077G>A	p.Val693Met	p.V693M	ENST00000232014	NM_001130845.1	693	Gtg/Atg	10/10	1	2	FACETS	1	0.975	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		616	592	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612028	189612028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs900140738	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	193	675	0	ENST00000264731.3:c.1780C>T	p.Arg594Ter	p.R594*	ENST00000264731	NM_003722.4	594	Cga/Tga	14/14	1	2	FACETS	1	0.975	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		675	544	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136880	55136880	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs397514549	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	120	378	0	ENST00000257290.5:c.1202C>A	p.Ala401Asp	p.A401D	ENST00000257290	NM_006206.4	401	gCt/gAt	8/23	0.3230403449138	1	FACETS	1	0.98	1	1	0.992	1	CLONAL	2	TRUE	0	0.3230403449138	1		378	258	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152027	55152027	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	110	647	0	ENST00000257290.5:c.2459C>T	p.Ala820Val	p.A820V	ENST00000257290	NM_006206.4	820	gCt/gTt	18/23	0.3230403449138	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.3230403449138	1		647	396	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968673	55968673	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs755067067	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	80	562	0	ENST00000263923.4:c.1990C>T	p.Arg664Cys	p.R664C	ENST00000263923	NM_002253.2	664	Cgt/Tgt	14/30	0.3230403449138	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.3230403449138	1		562	392	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796069	57796069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1419352292	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	145	617	0	ENST00000309042.7:c.1045C>T	p.Arg349Cys	p.R349C	ENST00000309042	NM_005612.4	349	Cgc/Tgc	4/4	0.3230403449138	1	FACETS	1	0.95	1	1	0.992	1	CLONAL	2	TRUE	0	0.3230403449138	1		617	363	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045791	143045791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	99	562	0	ENST00000262992.4:c.1843C>T	p.Pro615Ser	p.P615S	ENST00000262992	NM_001101669.1	615	Ccc/Tcc	17/24	0.3230403449138	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.3230403449138	1		562	402	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144361320	144361320	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369383480	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	188	700	0	ENST00000262995.4:c.1370G>A	p.Arg457Gln	p.R457Q	ENST00000262995	NM_207123.2	457	cGa/cAa	6/11	0.3230403449138	1	FACETS	1	0.985	1	1	0.994	1	CLONAL	2	TRUE	0	0.3230403449138	1		700	414	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268138	153268138	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1406877044	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	261	598	1	ENST00000281708.4:c.670C>T	p.Arg224Ter	p.R224*	ENST00000281708	NM_033632.3	224	Cga/Tga	4/12	0.3230403449138	1	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	0	0.3230403449138	1		599	562	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540032	187540032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	118	736	0	ENST00000441802.2:c.7708G>A	p.Ala2570Thr	p.A2570T	ENST00000441802	NM_005245.3	2570	Gct/Act	10/27	0.3230403449138	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.3230403449138	1		736	422	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557367	187557367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746932852	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	162	659	1	ENST00000441802.2:c.3995G>A	p.Arg1332His	p.R1332H	ENST00000441802	NM_005245.3	1332	cGc/cAc	6/27	0.3230403449138	1	FACETS	1	0.978	1	1	0.993	1	CLONAL	2	TRUE	0	0.3230403449138	1		660	373	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628365	187628365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143802989	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	138	746	0	ENST00000441802.2:c.2617G>A	p.Val873Met	p.V873M	ENST00000441802	NM_005245.3	873	Gtg/Atg	2/27	0.3230403449138	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.3230403449138	1		746	591	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228415	228415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745309710	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	55	464	0	ENST00000264932.6:c.737G>A	p.Arg246His	p.R246H	ENST00000264932	NM_004168.2	246	cGc/cAc	6/15	0.3230403449138	1	FACETS	0.825	0.709	0.95	0.825	0.709	0.95	CLONAL	1	TRUE	0	0.3230403449138	1		464	346	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1253902	1253902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	153	710	0	ENST00000310581.5:c.3340G>A	p.Ala1114Thr	p.A1114T	ENST00000310581	NM_198253.2	1114	Gcc/Acc	16/16	0.3230403449138	1	FACETS	0.898	0.83	0.969	1	0.991	1	CLONAL	2	TRUE	0	0.3230403449138	1		710	442	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293634	1293634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	175	831	0	ENST00000310581.5:c.1367G>A	p.Ser456Asn	p.S456N	ENST00000310581	NM_198253.2	456	aGc/aAc	2/16	0.3230403449138	1	FACETS	1	0.981	1	1	0.994	1	CLONAL	2	TRUE	0	0.3230403449138	1		831	397	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295909	1295909	+	upstream_gene_variant	5'Flank	SNP	C	C	T	rs1371469309	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	233	1002	0				ENST00000310581	NM_198253.2	-/1132			0.3230403449138	1	FACETS	1	0.982	1	1	0.995	1	CLONAL	2	TRUE	0	0.3230403449138	1		1002	548	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39002653	39002653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	117	466	0	ENST00000357387.3:c.376G>A	p.Asp126Asn	p.D126N	ENST00000357387	NM_152756.3	126	Gac/Aac	5/38	0.3230403449138	1	FACETS	0.937	0.856	1	1	0.989	1	CLONAL	2	TRUE	0	0.3230403449138	1		466	324	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522781	67522781	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765266397	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	162	661	0	ENST00000274335.5:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000274335		93	cGg/cAg	1/15	0.3230403449138	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.3230403449138	1		661	607	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645169	86645169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs191759701	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	70	484	0	ENST00000274376.6:c.1241G>A	p.Arg414Gln	p.R414Q	ENST00000274376	NM_002890.2	414	cGg/cAg	8/25	0.3230403449138	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.3230403449138	1		484	262	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672759	86672759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	119	584	1	ENST00000274376.6:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000274376	NM_002890.2	749	cGa/cAa	17/25	0.3230403449138	1	FACETS	1	0.955	1	1	0.991	1	CLONAL	2	TRUE	0	0.3230403449138	1		585	291	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685330	86685330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	190	512	0	ENST00000274376.6:c.3046C>T	p.Arg1016Cys	p.R1016C	ENST00000274376	NM_002890.2	1016	Cgt/Tgt	24/25	0.3230403449138	1	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	0	0.3230403449138	1		512	404	SUCCESS
APC	324	MSKCC	GRCh37	5	112173534	112173534	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1561575700	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	134	735	0	ENST00000257430.4:c.2243G>A	p.Ser748Asn	p.S748N	ENST00000257430	NM_000038.5	748	aGc/aAc	16/16	0.3230403449138	1	FACETS	0.925	0.85	1	1	0.99	1	CLONAL	2	TRUE	0	0.3230403449138	1		735	376	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923317	131923317	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	104	454	0	ENST00000265335.6:c.820G>A	p.Ala274Thr	p.A274T	ENST00000265335		274	Gcc/Acc	6/25	0.3230403449138	1	FACETS	0.975	0.886	1	1	0.989	1	CLONAL	2	TRUE	0	0.3230403449138	1		454	277	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517592	176517592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767045353	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	104	747	1	ENST00000292408.4:c.293G>A	p.Arg98His	p.R98H	ENST00000292408	NM_213647.1	98	cGc/cAc	3/18	0.3230403449138	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.3230403449138	1		748	369	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722000	176722000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758398402	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	235	789	0	ENST00000439151.2:c.7631C>T	p.Ala2544Val	p.A2544V	ENST00000439151	NM_022455.4	2544	gCc/gTc	23/23	0.3230403449138	1	FACETS	1	0.976	1	1	0.995	1	CLONAL	2	TRUE	0	0.3230403449138	1		789	569	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158764	26158764	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	166	542	0	ENST00000289316.2:c.367A>G	p.Thr123Ala	p.T123A	ENST00000289316	NM_138720.2	123	Acc/Gcc	1/2	1	2	FACETS	1	0.983	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		542	427	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679780	30679780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	222	865	1	ENST00000376406.3:c.1939G>A	p.Asp647Asn	p.D647N	ENST00000376406	NM_014641.2	647	Gat/Aat	5/15	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		866	569	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169083	32169083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1056526093	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	219	797	0	ENST00000375023.3:c.3950G>A	p.Arg1317Gln	p.R1317Q	ENST00000375023	NM_004557.3	1317	cGg/cAg	22/30	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		797	577	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818254	32818254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	216	698	0	ENST00000354258.4:c.1271G>A	p.Ser424Asn	p.S424N	ENST00000354258	NM_000593.5	424	aGc/aAc	5/11	1	2	FACETS	1	0.982	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		698	589	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41905105	41905105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	116	686	0	ENST00000372991.4:c.442C>T	p.Leu148Phe	p.L148F	ENST00000372991	NM_001760.3	148	Ctc/Ttc	3/5	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.3230403449138	2		686	610	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041025	112041025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779126684	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	231	696	0	ENST00000368678.4:c.230G>A	p.Arg77His	p.R77H	ENST00000368678		77	cGt/cAt	3/13	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		696	592	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710983	117710983	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	170	615	0	ENST00000368508.3:c.1289G>A	p.Gly430Asp	p.G430D	ENST00000368508	NM_002944.2	430	gGc/gAc	12/43	1	2	FACETS	1	0.98	1	1	0.993	1	CLONAL	2	TRUE	1	0.3230403449138	2		615	457	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198389	138198389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751123351	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	229	598	0	ENST00000237289.4:c.982G>A	p.Ala328Thr	p.A328T	ENST00000237289	NM_001270507.1	328	Gca/Aca	6/9	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		598	589	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202196	138202196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	226	684	0	ENST00000237289.4:c.2113C>T	p.Pro705Ser	p.P705S	ENST00000237289	NM_001270507.1	705	Cct/Tct	9/9	1	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		684	604	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001551	150001551	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	113	506	0	ENST00000253339.5:c.2053C>T	p.Leu685Phe	p.L685F	ENST00000253339		685	Ctt/Ttt	4/7	1	2	FACETS	1	0.962	1	1	0.99	1	CLONAL	2	TRUE	1	0.3230403449138	2		506	317	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100048	157100048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	143	841	0	ENST00000346085.5:c.985G>A	p.Ala329Thr	p.A329T	ENST00000346085	NM_020732.3	329	Gca/Aca	1/20	1	2	FACETS	1	0.978	1	1	0.992	1	CLONAL	2	TRUE	1	0.3230403449138	2		841	381	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100411	157100411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752684703	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	43	266	0	ENST00000346085.5:c.1348C>T	p.Pro450Ser	p.P450S	ENST00000346085	NM_020732.3	450	Ccg/Tcg	1/20	1	2	FACETS	1	0.948	1	1	0.977	1	CLONAL	2	TRUE	1	0.3230403449138	2		266	108	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968235	2968235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1188731718	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	189	546	0	ENST00000396946.4:c.1751G>A	p.Arg584His	p.R584H	ENST00000396946	NM_032415.4	584	cGc/cAc	13/25	1	2	FACETS	1	0.979	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		546	520	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2972186	2972186	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748468563	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	190	518	1	ENST00000396946.4:c.1553G>A	p.Arg518Gln	p.R518Q	ENST00000396946	NM_032415.4	518	cGa/cAa	11/25	1	2	FACETS	1	0.987	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		519	478	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233039	55233039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	213	640	0	ENST00000275493.2:c.1789G>A	p.Ala597Thr	p.A597T	ENST00000275493	NM_005228.3	597	Gca/Aca	15/28	1	2	FACETS	1	0.971	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		640	618	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508824	106508824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226994105	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	232	793	0	ENST00000359195.3:c.818G>A	p.Arg273His	p.R273H	ENST00000359195	NM_002649.2	273	cGc/cAc	2/11	1	2	FACETS	1	0.983	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		793	638	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513012	106513012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758968659	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	169	616	0	ENST00000359195.3:c.2026G>A	p.Ala676Thr	p.A676T	ENST00000359195	NM_002649.2	676	Gcc/Acc	3/11	1	2	FACETS	1	0.983	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		616	440	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434413	140434413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775889922	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	195	579	0	ENST00000288602.6:c.2285C>T	p.Ala762Val	p.A762V	ENST00000288602	NM_004333.4	762	gCg/gTg	18/18	1	2	FACETS	1	0.987	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		579	492	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845415	151845415	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	224	727	2	ENST00000262189.6:c.13597C>T	p.Arg4533Ter	p.R4533*	ENST00000262189	NM_170606.2	4533	Cga/Tga	52/59	1	2	FACETS	1	0.978	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		729	634	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877990	151877990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178963726	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	239	733	0	ENST00000262189.6:c.6955G>A	p.Ala2319Thr	p.A2319T	ENST00000262189	NM_170606.2	2319	Gcc/Acc	36/59	1	2	FACETS	1	0.989	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		733	604	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012253	152012253	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1563831738	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	139	565	0	ENST00000262189.6:c.560C>G	p.Ser187Ter	p.S187*	ENST00000262189	NM_170606.2	187	tCa/tGa	4/59	1	2	FACETS	1	0.97	1	1	0.992	1	CLONAL	2	TRUE	1	0.3230403449138	2		565	388	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194706	29194706	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs974286158	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	180	749	0	ENST00000240100.2:c.1022C>T	p.Ala341Val	p.A341V	ENST00000240100	NM_001394.6	341	gCg/gTg	4/4	1	2	FACETS	1	0.981	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		749	483	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194787	29194787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769407772	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	218	772	2	ENST00000240100.2:c.941G>A	p.Arg314His	p.R314H	ENST00000240100	NM_001394.6	314	cGc/cAc	4/4	1	2	FACETS	0.847	0.795	0.9	1	0.995	1	CLONAL	3	TRUE	1	0.3230403449138	2		774	531	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38139044	38139044	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	121	361	0	ENST00000317025.8:c.3559C>T	p.Arg1187Ter	p.R1187*	ENST00000317025	NM_023034.1	1187	Cga/Tga	20/24	1	2	FACETS	1	0.914	1	1	0.99	1	CLONAL	2	TRUE	1	0.3230403449138	2		361	374	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205614	38205614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	171	571	0	ENST00000317025.8:c.76G>A	p.Ala26Thr	p.A26T	ENST00000317025	NM_023034.1	26	Gcc/Acc	2/24	1	2	FACETS	1	0.977	1	1	0.993	1	CLONAL	2	TRUE	1	0.3230403449138	2		571	470	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863271	56863271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752739111	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	382	585	0	ENST00000519728.1:c.415G>A	p.Ala139Thr	p.A139T	ENST00000519728	NM_002350.3	139	Gca/Aca	6/13	0.3230403449138	5	FACETS	0.995	0.953	1	1	0.994	1	CLONAL	5	TRUE	1	0.3230403449138	5		585	706	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989642	68989642	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767992923	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	422	546	0	ENST00000288368.4:c.1580G>A	p.Arg527His	p.R527H	ENST00000288368	NM_024870.2	527	cGc/cAc	15/40	0.3230403449138	5	FACETS	1	0.991	1	1	0.996	1	CLONAL	5	TRUE	1	0.3230403449138	5		546	714	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129891	69129891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773214113	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	102	736	0	ENST00000288368.4:c.4645G>A	p.Ala1549Thr	p.A1549T	ENST00000288368	NM_024870.2	1549	Gcc/Acc	38/40	0.3230403449138	5	FACETS	0.812	0.724	0.906	0.203	0.181	0.227	CLONAL	1	TRUE	1	0.3230403449138	5		736	1155	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542602	141542602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	735	757	0	ENST00000220592.5:c.2384G>A	p.Arg795His	p.R795H	ENST00000220592	NM_012154.3	795	cGc/cAc	18/19	0.3230403449138	7	FACETS	1	0.987	1	1	0.997	1	CLONAL	7	TRUE	1	0.3230403449138	7		757	1149	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572622	141572622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772067763	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	250	768	0	ENST00000220592.5:c.448C>T	p.Arg150Trp	p.R150W	ENST00000220592	NM_012154.3	150	Cgg/Tgg	4/19	0.3230403449138	7	FACETS	1	0.988	1	0.413	0.385	0.441	CLONAL	2	TRUE	1	0.3230403449138	7		768	1130	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739881	145739881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764297840	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	173	701	0	ENST00000428558.2:c.1649C>T	p.Ala550Val	p.A550V	ENST00000428558	NM_004260.3	550	gCg/gTg	10/22	0.3230403449138	7	FACETS	1	0.947	1	0.345	0.318	0.374	CLONAL	2	TRUE	1	0.3230403449138	7		701	934	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2047474	2047474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	170	656	0	ENST00000349721.2:c.1036C>T	p.Arg346Trp	p.R346W	ENST00000349721	NM_003070.3	346	Cgg/Tgg	5/34	0.3230403449138	0	FACETS	0.797	0.749	0.844			1	SUBCLONAL	3	TRUE	0	0.3230403449138	0		656	298	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2058453	2058456	+	stop_gained	Nonsense_Mutation	ONP	CGGC	CGGC	TGGT	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	195	532	1	ENST00000349721.2:c.1510_1513delinsTGGT	p.Arg504_Arg505delinsTrpTer	p.R504_R505delinsW*	ENST00000349721	NM_003070.3	504	CGGCga/TGGTga	8/34	0.3230403449138	0	FACETS	0.843	0.798	0.888			1	CLONAL	3	TRUE	0	0.3230403449138	0		533	323	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971194	21971194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561034503	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	176	696	0	ENST00000304494.5:c.164G>A	p.Gly55Asp	p.G55D	ENST00000304494	NM_000077.4	55	gGc/gAc	2/3	0.3230403449138	0	FACETS	0.828	0.78	0.875			1	CLONAL	3	TRUE	0	0.3230403449138	0		696	297	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202926	27202926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772637203	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	156	612	0	ENST00000380036.4:c.2018G>A	p.Arg673His	p.R673H	ENST00000380036	NM_000459.3	673	cGt/cAt	13/23	0.3230403449138	0	FACETS	0.776	0.726	0.825			1	SUBCLONAL	3	TRUE	0	0.3230403449138	0		612	281	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894950	101894950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777965779	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	265	586	0	ENST00000374994.4:c.503G>A	p.Arg168His	p.R168H	ENST00000374994	NM_004612.2	168	cGc/cAc	3/9	0.222224206397799	3	FACETS	1	0.977	1	1	0.994	1	CLONAL	3	TRUE	1	0.3230403449138	3		586	600	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771908	135771908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060503200	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	262	863	0	ENST00000298552.3:c.3209C>T	p.Ala1070Val	p.A1070V	ENST00000298552	NM_001162426.1	1070	gCg/gTg	23/23	0.222224206397799	3	FACETS	0.856	0.806	0.906	1	0.991	1	CLONAL	3	TRUE	1	0.3230403449138	3		863	734	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321073	137321073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768721235	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	274	687	0	ENST00000481739.1:c.1030G>A	p.Ala344Thr	p.A344T	ENST00000481739	NM_002957.4	344	Gcc/Acc	7/10	0.222224206397799	3	FACETS	0.897	0.852	0.943	1	0.995	1	CLONAL	4	TRUE	1	0.3230403449138	3		687	549	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405170	139405170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199506721	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	272	787	3	ENST00000277541.6:c.2675G>A	p.Arg892His	p.R892H	ENST00000277541	NM_017617.3	892	cGc/cAc	17/34	0.222224206397799	3	FACETS	1	0.963	1	1	0.994	1	CLONAL	3	TRUE	1	0.3230403449138	3		790	637	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815530	139815530	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528114067	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	241	670	0	ENST00000247668.2:c.1001C>T	p.Ala334Val	p.A334V	ENST00000247668	NM_021138.3	334	gCg/gTg	9/11	0.222224206397799	3	FACETS	1	0.946	1	1	0.993	1	CLONAL	3	TRUE	1	0.3230403449138	3		670	575	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325383	1325383	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	186	614	0	ENST00000400841.2:c.292T>C	p.Ser98Pro	p.S98P	ENST00000400841		98	Tcc/Ccc	3/6	1	2	FACETS	1	0.978	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		614	514	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931873	39931873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	227	648	0	ENST00000378444.4:c.2726G>A	p.Gly909Asp	p.G909D	ENST00000378444	NM_001123385.1	909	gGc/gAc	4/15	1	2	FACETS	1	0.989	1	1	0.995	1	CLONAL	2	TRUE	1	0.3230403449138	2		648	572	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933535	39933535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747038834	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	265	835	0	ENST00000378444.4:c.1064C>T	p.Ser355Leu	p.S355L	ENST00000378444	NM_001123385.1	355	tCg/tTg	4/15	1	2	FACETS	0.892	0.843	0.941	1	0.996	1	CLONAL	3	TRUE	1	0.3230403449138	2		835	613	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034435	47034435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	178	522	0	ENST00000377604.3:c.520G>A	p.Ala174Thr	p.A174T	ENST00000377604	NM_001204468.1	174	Gcc/Acc	6/24	1	2	FACETS	1	0.982	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		522	473	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429048	47429048	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	221	679	0	ENST00000377045.4:c.1411C>A	p.Leu471Met	p.L471M	ENST00000377045	NM_001654.4	471	Ctg/Atg	13/16	1	2	FACETS	0.869	0.816	0.922	1	0.995	1	CLONAL	3	TRUE	1	0.3230403449138	2		679	525	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225983	53225983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1392496114	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	72	820	1	ENST00000375401.3:c.2866G>A	p.Ala956Thr	p.A956T	ENST00000375401	NM_004187.3	956	Gcg/Acg	19/26	1	2	FACETS	0.716	0.625	0.813	0.716	0.625	0.813	SUBCLONAL	1	TRUE	1	0.3230403449138	2		821	623	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240019	53240019	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	226	682	0	ENST00000375401.3:c.1422G>A	p.Trp474Ter	p.W474*	ENST00000375401	NM_004187.3	474	tgG/tgA	11/26	1	2	FACETS	0.864	0.812	0.916	1	0.995	1	CLONAL	3	TRUE	1	0.3230403449138	2		682	540	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246446	53246446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201805773	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	199	679	0	ENST00000375401.3:c.536G>A	p.Arg179His	p.R179H	ENST00000375401	NM_004187.3	179	cGt/cAt	5/26	1	2	FACETS	1	0.965	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		679	584	SUCCESS
AR	367	MSKCC	GRCh37	X	66766603	66766603	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	162	571	0	ENST00000374690.3:c.1615C>T	p.Arg539Cys	p.R539C	ENST00000374690	NM_000044.3	539	Cgt/Tgt	1/8	1	2	FACETS	1	0.98	1	1	0.993	1	CLONAL	2	TRUE	1	0.3230403449138	2		571	432	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354685	70354685	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753061449	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	180	669	0	ENST00000374080.3:c.4850C>T	p.Ala1617Val	p.A1617V	ENST00000374080		1617	gCg/gTg	35/45	1	2	FACETS	1	0.932	1	1	0.993	1	CLONAL	2	TRUE	1	0.3230403449138	2		669	555	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890104	76890104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	136	517	0	ENST00000373344.5:c.4790G>A	p.Gly1597Asp	p.G1597D	ENST00000373344	NM_000489.3	1597	gGc/gAc	17/35	1	2	FACETS	1	0.981	1	1	0.992	1	CLONAL	2	TRUE	1	0.3230403449138	2		517	345	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912062	76912062	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557119995	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	90	418	0	ENST00000373344.5:c.4202G>A	p.Arg1401Gln	p.R1401Q	ENST00000373344	NM_000489.3	1401	cGg/cAg	13/35	1	2	FACETS	0.991	0.891	1	1	0.987	1	CLONAL	2	TRUE	1	0.3230403449138	2		418	281	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940012	76940012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs122445105	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	121	538	0	ENST00000373344.5:c.736C>T	p.Arg246Cys	p.R246C	ENST00000373344	NM_000489.3	246	Cgc/Tgc	9/35	1	2	FACETS	1	0.947	1	1	0.99	1	CLONAL	2	TRUE	1	0.3230403449138	2		538	357	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630191	100630191	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	181	542	0	ENST00000308731.7:c.82C>T	p.Arg28Cys	p.R28C	ENST00000308731	NM_000061.2	28	Cgc/Tgc	2/19	1	2	FACETS	1	0.971	1	1	0.994	1	CLONAL	2	TRUE	1	0.3230403449138	2		542	518	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195701	123195701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777363856	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	110	456	0	ENST00000218089.9:c.1615G>A	p.Val539Met	p.V539M	ENST00000218089	NM_001042749.1	539	Gtg/Atg	17/35	1	2	FACETS	1	0.973	1	1	0.99	1	CLONAL	2	TRUE	1	0.3230403449138	2		456	290	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732506	74732506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1419789271	NA	P-0015081-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	142	762	0	ENST00000359995.5:c.403C>T	p.Arg135Cys	p.R135C	ENST00000359995	NM_001195427.1	135	Cgt/Tgt	2/3	1	2	FACETS	0.927	0.851	1	1	0.991	1	CLONAL	2	TRUE	1	0.3230403449138	2		762	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0016969-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	345	671	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.578889936500884	3	FACETS	0.873	0.839	0.906	0.873	0.839	0.906	CLONAL	3	TRUE	0	0.655154146963625	3		671	534	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016969-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	174	471	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.284766527739316	5	FACETS	0.768	0.709	0.828			1	INDETERMINATE	2	TRUE	NA	0.655154146963625	5		471	686	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661621	227661621	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016969-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	193	595	0	ENST00000305123.5:c.1834T>C	p.Tyr612His	p.Y612H	ENST00000305123	NM_005544.2	612	Tac/Cac	1/2	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.655154146963625	2		595	567	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928071	178928098	+	protein_altering_variant	In_Frame_Del	DEL	ATGGATTAGAAGATTTGCTGAACCCTAT	ATGGATTAGAAGATTTGCTGAACCCTAT	G	novel	NA	P-0016969-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	260	381	0	ENST00000263967.3:c.1349_1376delinsG	p.His450_Ile459delinsArg	p.H450_I459delinsR	ENST00000263967	NM_006218.2	450	cATGGATTAGAAGATTTGCTGAACCCTATt/cGt	8/21	0.64832553580697	3	FACETS	0.947	0.908	0.984	0.947	0.908	0.984	CLONAL	3	TRUE	0	0.655154146963625	3		381	371	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30954194	30954194	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016969-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	115	341	0	ENST00000375687.4:c.68del	p.Asn23ThrfsTer7	p.N23Tfs*7	ENST00000375687	NM_015338.5	22	gAa/ga	2/13	0.655154146963625	6	FACETS	0.927	0.834	1	0.309	0.278	0.342	CLONAL	1	TRUE	3	0.655154146963625	6		341	875	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976805	2976805	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016969-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	147	453	0	ENST00000396946.4:c.1207T>A	p.Tyr403Asn	p.Y403N	ENST00000396946	NM_032415.4	403	Tac/Aac	9/25	0.655154146963625	6	FACETS	1	0.956	1	0.179	0.163	0.196	CLONAL	1	TRUE	0	0.655154146963625	6		453	964	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018185-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	259	475	0				ENST00000310581	NM_198253.2	-/1132			0.529560978717285	3	FACETS	0.867	0.818	0.917	0.867	0.818	0.917	CLONAL	2	TRUE	1	0.591813750071711	3		475	654	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	G	rs11575997	NA	P-0018185-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	408	638	0	ENST00000269305.4:c.993+1G>C		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.543013485943583	3	FACETS	0.866	0.833	0.898	0.866	0.833	0.898	CLONAL	3	TRUE	0	0.591813750071711	3		638	688	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971099	21971099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749714198	NA	P-0018185-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	439	766	0	ENST00000304494.5:c.259C>T	p.Arg87Trp	p.R87W	ENST00000304494	NM_000077.4	87	Cgg/Tgg	2/3	0.503194645747125	3	FACETS	0.927	0.895	0.959	0.927	0.895	0.959	CLONAL	3	TRUE	0	0.591813750071711	3		766	691	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286244	66286244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018185-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	64	460	0	ENST00000273854.3:c.1442C>T	p.Ala481Val	p.A481V	ENST00000273854	NM_004439.5	481	gCa/gTa	6/18	0.207082490637846	2	FACETS	0.764	0.668	0.867	0.382	0.334	0.434	INDETERMINATE	1	TRUE	0	0.591813750071711	2		460	283	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169195	32169195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018185-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	192	749	0	ENST00000375023.3:c.3838G>A	p.Asp1280Asn	p.D1280N	ENST00000375023	NM_004557.3	1280	Gat/Aat	22/30	0.591813750071711	3	FACETS	0.961	0.89	1	0.32	0.296	0.345	CLONAL	1	TRUE	0	0.591813750071711	3		749	875	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18747480	18747480	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018185-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	38	219	0	ENST00000266497.5:c.3941A>G	p.Glu1314Gly	p.E1314G	ENST00000266497		1314	gAa/gGa	28/31	1	2	FACETS	0.937	0.79	1	0.937	0.79	1	CLONAL	1	TRUE	1	0.591813750071711	2		219	137	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352705	68352705	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018185-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	57	336	0	ENST00000487270.1:c.572G>T	p.Arg191Met	p.R191M	ENST00000487270	NM_133509.3	191	aGg/aTg	6/11	0.466929514943083	5	FACETS	0.975	0.84	1	0.244	0.21	0.281	CLONAL	1	TRUE	1	0.591813750071711	5		336	373	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989454	7989454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1466188561	NA	P-0018185-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	185	725	1	ENST00000319144.4:c.232C>T	p.Pro78Ser	p.P78S	ENST00000319144	NM_001139.2	78	Ccc/Tcc	2/15	0.543013485943583	3	FACETS	0.954	0.882	1	0.318	0.294	0.343	CLONAL	1	TRUE	0	0.591813750071711	3		726	849	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11071848	11071867	+	splice_donor_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	CTGGTAAGGAACGCGGGCCG	CTGGTAAGGAACGCGGGCCG	-	novel	NA	P-0018185-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	273	883	1	ENST00000358026.2:c.-33_-32+18del		p.X11_splice	ENST00000358026	NM_001128849.1	11		1/36	0.18093510876406	2	FACETS	1	0.992	1	0.642	0.606	0.679	INDETERMINATE	1	TRUE	0	0.591813750071711	2		884	718	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018541-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	573	475	0				ENST00000310581	NM_198253.2	-/1132			0.752179954182412	6	FACETS	0.913	0.887	0.938	1	0.996	1	CLONAL	5	TRUE	2	0.752179954182412	6		475	836	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047305	77047305	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018541-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	104	613	0	ENST00000356341.3:c.1239G>C	p.Gln413His	p.Q413H	ENST00000356341	NM_002576.4	413	caG/caC	13/15	0.660242488624512	3	FACETS	0.758	0.682	0.838	0.379	0.341	0.419	SUBCLONAL	1	TRUE	1	0.752179954182412	3		613	502	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878061	48878062	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1131690852	NA	P-0018541-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	149	755	1	ENST00000267163.4:c.19dup	p.Arg7ProfsTer24	p.R7Pfs*24	ENST00000267163	NM_000321.2	5	acc/aCcc	1/27	0.660242488624512	3	FACETS	0.648	0.592	0.707	0.324	0.296	0.354	SUBCLONAL	1	TRUE	1	0.752179954182412	3		756	841	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857925	9857925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs534440095	NA	P-0018541-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	158	776	0	ENST00000330684.3:c.3476G>A	p.Arg1159His	p.R1159H	ENST00000330684	NM_001134407.1	1159	cGc/cAc	13/13	0.686358088287576	3	FACETS	0.851	0.782	0.923	0.426	0.391	0.462	CLONAL	1	TRUE	1	0.752179954182412	3		776	679	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879855	37879855	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018541-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	1985	977	11	ENST00000269571.5:c.2150A>T	p.Glu717Val	p.E717V	ENST00000269571		717	gAg/gTg	18/27	0.752179954182412	9	FACETS	0.961	0.949	0.973			1	CLONAL	8	TRUE	NA	0.752179954182412	9		988	2493	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0018541-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	1879	818	5	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.752179954182412	9	FACETS	0.963	0.95	0.975			1	CLONAL	8	TRUE	NA	0.752179954182412	9		823	2357	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523588	41523588	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018541-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	206	747	1	ENST00000263253.7:c.1004G>A	p.Arg335His	p.R335H	ENST00000263253	NM_001429.3	335	cGc/cAc	4/31	0.660242488624512	3	FACETS	1	0.957	1	0.519	0.483	0.556	CLONAL	1	TRUE	1	0.752179954182412	3		748	726	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47168147	47168147	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018541-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	56	90	0	ENST00000409792.3:c.78A>T	p.Glu26Asp	p.E26D	ENST00000409792	NM_014159.6	26	gaA/gaT	2/21	0.653252692907254	4	FACETS	0.988	0.871	1	0.988	0.871	1	CLONAL	2	TRUE	2	0.752179954182412	4		90	132	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197077	26197077	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs373554594	NA	P-0018541-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	290	903	2	ENST00000356476.2:c.402G>C	p.Glu134Asp	p.E134D	ENST00000356476		134	gaG/gaC	1/1	0.752179954182412	4	FACETS	1	0.949	1			1	CLONAL	1	TRUE	NA	0.752179954182412	4		905	1335	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652056	36652056	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018541-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	648	851	2	ENST00000244741.5:c.178G>T	p.Glu60Ter	p.E60*	ENST00000244741	NM_000389.4	60	Gag/Tag	2/3	0.752179954182412	4	FACETS	0.94	0.913	0.968			1	CLONAL	3	TRUE	NA	0.752179954182412	4		853	1070	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0021850-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	454	257	0	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	0.507472358134326	3	FACETS	0.969	0.936	1	0.969	0.936	1	CLONAL	3	TRUE	0	0.568195871460815	3		257	706	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074229	8074229	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021850-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	370	285	0	ENST00000377482.5:c.430C>A	p.Pro144Thr	p.P144T	ENST00000377482	NM_018948.3	144	Cct/Act	4/4	0.450583829074228	3	FACETS	0.907	0.864	0.951			1	CLONAL	2	TRUE	NA	0.568195871460815	3		285	922	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418451	49418451	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021850-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	382	297	0	ENST00000301067.7:c.15962A>G	p.Tyr5321Cys	p.Y5321C	ENST00000301067	NM_003482.3	5321	tAt/tGt	50/54	0.490272593831283	3	FACETS	0.968	0.923	1	0.968	0.923	1	CLONAL	2	TRUE	1	0.568195871460815	3		297	892	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38792651	38792651	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021850-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	102	190	0	ENST00000348513.6:c.365A>G	p.Glu122Gly	p.E122G	ENST00000348513	NM_003079.4	122	gAa/gGa	6/11	0.47055480430207	4	FACETS	0.899	0.806	0.999			1	CLONAL	1	TRUE	NA	0.568195871460815	4		190	626	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260156	149260156	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021850-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	125	206	0	ENST00000360632.3:c.737G>T	p.Arg246Met	p.R246M	ENST00000360632	NM_015472.4	246	aGg/aTg	4/7	0.568195871460815	4	FACETS	0.753	0.681	0.829	0.377	0.34	0.415	SUBCLONAL	1	TRUE	2	0.568195871460815	4		206	916	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594029	55594029	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021850-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	83	186	0	ENST00000288135.5:c.1815G>C	p.Glu605Asp	p.E605D	ENST00000288135	NM_000222.2	605	gaG/gaC	12/21	0.366286468950012	3	FACETS	0.61	0.539	0.686	0.203	0.179	0.229	SUBCLONAL	1	TRUE	0	0.568195871460815	3		186	615	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0021873-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	149	238	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.572985041055228	2		238	516	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231836	36231836	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021873-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	306	287	1	ENST00000300305.3:c.548del	p.Pro183HisfsTer28	p.P183Hfs*28	ENST00000300305		183	cCa/ca	5/8	1	2	FACETS	0.983	0.927	1	0.983	0.927	1	CLONAL	1	TRUE	1	0.572985041055228	2		288	1087	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106926	27106926	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021873-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	368	320	0	ENST00000324856.7:c.6538del	p.Leu2180TrpfsTer20	p.L2180Wfs*20	ENST00000324856	NM_006015.4	2179	agC/ag	20/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.572985041055228	2		320	1206	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137702	64137702	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021873-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	259	243	0	ENST00000334205.4:c.1803G>T	p.Met601Ile	p.M601I	ENST00000334205	NM_003942.2	601	atG/atT	15/17	1	2	FACETS	0.954	0.894	1	0.954	0.894	1	CLONAL	1	TRUE	1	0.572985041055228	2		243	948	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640502	3640502	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021873-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	346	323	0	ENST00000294008.3:c.3137G>T	p.Arg1046Leu	p.R1046L	ENST00000294008	NM_032444.2	1046	cGc/cTc	12/15	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.572985041055228	2		323	1206	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600425	10600425	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021873-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	354	298	0	ENST00000171111.5:c.1430G>T	p.Gly477Val	p.G477V	ENST00000171111	NM_203500.1	477	gGc/gTc	4/6	0.572985041055228	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.572985041055228	1		298	827	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143965	11143965	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0021873-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	261	211	0	ENST00000358026.2:c.3547-1G>A		p.X1183_splice	ENST00000358026	NM_001128849.1	1183			0.572985041055228	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.572985041055228	1		211	614	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149440494	149440494	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021873-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	242	208	0	ENST00000286301.3:c.1900C>A	p.Leu634Met	p.L634M	ENST00000286301	NM_005211.3	634	Ctg/Atg	14/22	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.572985041055228	2		208	836	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443467	49443467	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023758-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	276	497	0	ENST00000301067.7:c.3904C>T	p.Gln1302Ter	p.Q1302*	ENST00000301067	NM_003482.3	1302	Cag/Tag	11/54	0.441278154597977	3	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	1	0.446109037339545	3		497	756	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041266	47041266	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0024878-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	22	558	0	ENST00000377604.3:c.1693+1G>T		p.X565_splice	ENST00000377604	NM_001204468.1	565			1	2	FACETS	0.152	0.118	0.193	0.152	0.118	0.193	SUBCLONAL	1	TRUE	1	0.795596102678171	2		558	363	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814532	43814532	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024878-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	85	468	0	ENST00000372470.3:c.1330del	p.Ala444ProfsTer52	p.A444Pfs*52	ENST00000372470	NM_005373.2	443	Ggg/gg	9/12	1	2	FACETS	0.848	0.761	0.938	0.848	0.761	0.938	CLONAL	1	TRUE	1	0.795596102678171	2		468	252	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908183	28908183	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024878-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	73	362	0	ENST00000282397.4:c.2572G>T	p.Val858Leu	p.V858L	ENST00000282397	NM_002019.4	858	Gtg/Ttg	18/30	1	2	FACETS	0.725	0.643	0.812	0.725	0.643	0.812	SUBCLONAL	1	TRUE	1	0.795596102678171	2		362	253	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005287	29005287	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024878-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	41	322	0	ENST00000282397.4:c.974C>A	p.Ser325Ter	p.S325*	ENST00000282397	NM_002019.4	325	tCa/tAa	7/30	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.795596102678171	2		322	103	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502250	186502250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778995582	NA	P-0024878-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	72	420	0	ENST00000323963.5:c.59C>T	p.Pro20Leu	p.P20L	ENST00000323963		20	cCc/cTc	2/11	1	2	FACETS	0.797	0.707	0.891	0.797	0.707	0.891	SUBCLONAL	1	TRUE	1	0.795596102678171	2		420	227	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0024878-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	41	238	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.758	0.645	0.878	0.758	0.645	0.878	SUBCLONAL	1	TRUE	1	0.795596102678171	2		238	136	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690522	33690522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024878-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	121	446	0	ENST00000308377.4:c.305G>A	p.Cys102Tyr	p.C102Y	ENST00000308377	NM_152270.3	102	tGt/tAt	2/5	1	2	FACETS	0.895	0.818	0.973	0.895	0.818	0.973	CLONAL	1	TRUE	1	0.795596102678171	2		446	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0025741-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	208	622	0	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	0.517377955189333	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.516573545448179	1		622	588	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	protein_altering_variant	In_Frame_Ins	INS	-	-	GTT	rs1554350347	NA	P-0025741-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	1231	685	0	ENST00000275493.2:c.2308_2309insGTT	p.Asp770delinsGlyTyr	p.D770delinsGY	ENST00000275493	NM_005228.3	770	gac/gGTTac	20/28	0.516573545448179	9	FACETS	0.939	0.918	0.959	0.939	0.918	0.959	CLONAL	7	TRUE	2	0.516573545448179	9		685	2037	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842606	68842606	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025741-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	125	662	0	ENST00000261769.5:c.542A>G	p.Asn181Ser	p.N181S	ENST00000261769	NM_004360.3	181	aAc/aGc	5/16	0.517377955189333	3	FACETS	0.964	0.874	1	0.482	0.437	0.529	CLONAL	1	TRUE	1	0.516573545448179	3		662	632	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719415	190719415	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025741-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	36	584	0	ENST00000441310.2:c.1417G>T	p.Asp473Tyr	p.D473Y	ENST00000441310	NM_000534.4	473	Gac/Tac	9/13	0.452508421684827	3	FACETS	1	0.931	1	0.412	0.344	0.484	CLONAL	1	TRUE	0	0.516573545448179	3		584	142	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972422	32972422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025741-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	24	607	0	ENST00000380152.3:c.9772G>A	p.Glu3258Lys	p.E3258K	ENST00000380152		3258	Gag/Aag	27/27	0.517377955189333	2	FACETS	0.215	0.168	0.27	0.108	0.084	0.135	SUBCLONAL	1	TRUE	0	0.516573545448179	2		607	432	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0026680-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	255	353	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.345073798784272	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.369458813680475	4		353	896	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031883	26031884	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs758780418	NA	P-0026680-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	136	474	0	ENST00000244661.2:c.405_406del	p.Arg135SerfsTer12	p.R135Sfs*12	ENST00000244661	NM_003537.3	135	agAGcg/agcg	1/1	0.369458813680475	3	FACETS	0.934	0.848	1	0.467	0.424	0.512	CLONAL	1	TRUE	1	0.369458813680475	3		474	934	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717733	89717733	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1554825235	NA	P-0026680-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	215	292	0	ENST00000371953.3:c.758T>A	p.Ile253Asn	p.I253N	ENST00000371953	NM_000314.4	253	aTc/aAc	7/9	0.369458813680475	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.369458813680475	2		292	531	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427614	49427614	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026680-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	373	577	0	ENST00000301067.7:c.10874C>T	p.Pro3625Leu	p.P3625L	ENST00000301067	NM_003482.3	3625	cCc/cTc	39/54	0.345073798784272	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.369458813680475	4		577	1332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574029	7574029	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026680-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	250	371	0	ENST00000269305.4:c.998G>C	p.Arg333Pro	p.R333P	ENST00000269305	NM_001126112.2	333	cGt/cCt	10/11	0.369458813680475	2	FACETS	0.952	0.895	1	0.952	0.895	1	CLONAL	2	TRUE	0	0.369458813680475	2		371	711	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78519487	78519487	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026680-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	187	455	0	ENST00000306801.3:c.58G>C	p.Asp20His	p.D20H	ENST00000306801	NM_020761.2	20	Gat/Cat	1/34	0.369458813680475	3	FACETS	1	0.98	1	0.587	0.542	0.634	CLONAL	1	TRUE	1	0.369458813680475	3		455	1021	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576268	88576268	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026680-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	122	386	0	ENST00000360948.2:c.1405G>C	p.Ala469Pro	p.A469P	ENST00000360948	NM_001012338.2	469	Gct/Cct	13/19	0.369458813680475	2	FACETS	0.937	0.848	1	0.468	0.424	0.515	CLONAL	1	TRUE	0	0.369458813680475	2		386	705	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21348492	21348492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748528782	NA	P-0026680-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	223	646	0	ENST00000215739.8:c.1549G>A	p.Glu517Lys	p.E517K	ENST00000215739	NM_006767.3	517	Gag/Aag	14/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.369458813680475	2		646	1002	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0026874-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	128	665	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.37125230692243	2		665	635	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0026874-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	101	499	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.37125230692243	2		499	473	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391716	139391716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371742334	NA	P-0026874-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	113	741	0	ENST00000277541.6:c.6475C>T	p.Arg2159Cys	p.R2159C	ENST00000277541	NM_017617.3	2159	Cgc/Tgc	34/34	0.37125230692243	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.37125230692243	1		741	450	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0026874-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	106	652	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.37125230692243	1	FACETS	0.969	0.873	1	0.969	0.873	1	CLONAL	1	TRUE	0	0.37125230692243	1		652	480	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651931	36651932	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0026874-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	118	670	0	ENST00000244741.5:c.55dup	p.Arg19ProfsTer17	p.R19Pfs*17	ENST00000244741	NM_000389.4	18	tgc/tgCc	2/3	1	2	FACETS	0.929	0.84	1	0.929	0.84	1	CLONAL	1	TRUE	1	0.37125230692243	2		670	684	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0029539-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	209	499	0				ENST00000310581	NM_198253.2	-/1132			0.630982118482116	4	FACETS	0.954	0.893	1	0.954	0.893	1	CLONAL	2	TRUE	2	0.636516178237489	4		499	563	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913381	NA	P-0029539-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	140	555	0	ENST00000304494.5:c.322G>A	p.Asp108Asn	p.D108N	ENST00000304494	NM_000077.4	108	Gat/Aat	2/3	0.645231614550939	3	FACETS	0.785	0.716	0.857	0.392	0.358	0.429	SUBCLONAL	1	TRUE	1	0.636516178237489	3		555	739	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045000	47045000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556782020	NA	P-0029539-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	210	316	0	ENST00000377604.3:c.2326C>T	p.Arg776Trp	p.R776W	ENST00000377604	NM_001204468.1	776	Cgg/Tgg	20/24	0.493443881524552	2	FACETS	0.937	0.888	0.986			1	CLONAL	2	TRUE	NA	0.636516178237489	2		316	352	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089755	27089755	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029539-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	113	491	0	ENST00000324856.7:c.2711C>T	p.Ala904Val	p.A904V	ENST00000324856	NM_006015.4	904	gCt/gTt	8/20	0.645231614550939	3	FACETS	0.687	0.619	0.759	0.344	0.309	0.38	SUBCLONAL	1	TRUE	1	0.636516178237489	3		491	681	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246498729	246498729	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029539-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	58	343	0	ENST00000388985.4:c.276C>A	p.Ser92Arg	p.S92R	ENST00000388985		92	agC/agA	3/12	0.447745447587373	5	FACETS	0.904	0.78	1	0.301	0.26	0.347	CLONAL	1	TRUE	2	0.636516178237489	5		343	394	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906987	32906987	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029539-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	71	449	0	ENST00000380152.3:c.1372C>G	p.Pro458Ala	p.P458A	ENST00000380152		458	Cca/Gca	10/27	0.645231614550939	3	FACETS	0.576	0.503	0.653	0.288	0.251	0.327	SUBCLONAL	1	TRUE	1	0.636516178237489	3		449	511	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274699	198274699	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029539-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	76	465	0	ENST00000335508.6:c.699T>A	p.Asp233Glu	p.D233E	ENST00000335508	NM_012433.2	233	gaT/gaA	7/25	NA	2	FACETS	0.623	0.55	0.702			1	INDETERMINATE	1	TRUE	NA	0.636516178237489	2		465	383	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945551	54945551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029539-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	69	456	1	ENST00000312783.6:c.1019G>A	p.Arg340Lys	p.R340K	ENST00000312783	NM_198436.1	340	aGa/aAa	9/10	0.372980177986908	4	FACETS	0.794	0.694	0.901	0.397	0.347	0.451	INDETERMINATE	1	TRUE	2	0.636516178237489	4		457	447	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983144	149983144	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029539-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	77	418	0	ENST00000253339.5:c.3114T>A	p.Asn1038Lys	p.N1038K	ENST00000253339		1038	aaT/aaA	7/7	0.645231614550939	3	FACETS	0.618	0.544	0.698	0.309	0.272	0.349	SUBCLONAL	1	TRUE	1	0.636516178237489	3		418	516	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923022	39923022	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029539-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	90	242	0	ENST00000378444.4:c.3686C>A	p.Pro1229His	p.P1229H	ENST00000378444	NM_001123385.1	1229	cCt/cAt	8/15	0.493443881524552	2	FACETS	0.865	0.775	0.959			1	CLONAL	1	TRUE	NA	0.636516178237489	2		242	327	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861754	59861754	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029539-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	81	337	0	ENST00000259008.2:c.1505A>G	p.Glu502Gly	p.E502G	ENST00000259008	NM_032043.2	502	gAa/gGa	11/20	0.520652112397764	5	FACETS	0.896	0.791	1	0.299	0.263	0.337	CLONAL	1	TRUE	2	0.636516178237489	5		337	555	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604368	43604526	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTGCGTGTTTGCACCAGTGTGAGTGCAGGGCTGTGTCTGGGAAGAGGTGTGCTACACATGAGGAAGCAGCCAGAGCAGCTTGGTGGTCATTGTTGTGCCCCTACCTGCAGGGCTGGTTCTCAACCGGAACCTCTCCATCTCGGAGAACCGCACCATGC	AGTGCGTGTTTGCACCAGTGTGAGTGCAGGGCTGTGTCTGGGAAGAGGTGTGCTACACATGAGGAAGCAGCCAGAGCAGCTTGGTGGTCATTGTTGTGCCCCTACCTGCAGGGCTGGTTCTCAACCGGAACCTCTCCATCTCGGAGAACCGCACCATGC	-	novel	NA	P-0029539-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	48	211	0	ENST00000355710.3:c.1064-109_1113del		p.X355_splice	ENST00000355710	NM_020975.4	355		6/20	0.530278168249094	3	FACETS	0.947	0.81	1	0.473	0.405	0.547	CLONAL	1	TRUE	1	0.636516178237489	3		211	210	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114679	108114679	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs778624615	NA	P-0029539-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	31	183	0	ENST00000278616.4:c.497-1G>A		p.X166_splice	ENST00000278616	NM_000051.3	166			0.645231614550939	4	FACETS	0.625	0.508	0.756	0.208	0.169	0.252	SUBCLONAL	1	TRUE	1	0.636516178237489	4		183	255	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487238	56487238	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029539-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	93	399	0	ENST00000267101.3:c.1384C>G	p.Leu462Val	p.L462V	ENST00000267101	NM_001982.3	462	Ctc/Gtc	12/28	0.593470757967711	4	FACETS	0.794	0.707	0.887	0.265	0.235	0.296	SUBCLONAL	1	TRUE	1	0.636516178237489	4		399	602	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40451775	40451775	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029539-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	46	549	0	ENST00000345506.4:c.557T>A	p.Phe186Tyr	p.F186Y	ENST00000345506	NM_003152.3	186	tTt/tAt	7/20	0.530278168249094	3	FACETS	0.371	0.312	0.436	0.185	0.156	0.218	SUBCLONAL	1	TRUE	1	0.636516178237489	3		549	514	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6222638	6222638	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs546615396	NA	P-0029539-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	91	583	1	ENST00000252674.7:c.604C>T	p.Arg202Trp	p.R202W	ENST00000252674	NM_005934.3	202	Cgg/Tgg	6/12	0.22465879224209	5	FACETS	0.938	0.834	1	0.313	0.278	0.35	INDETERMINATE	1	TRUE	2	0.636516178237489	5		584	596	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790123	40790123	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs757562149	NA	P-0029539-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	99	561	0	ENST00000373198.4:c.2608C>A	p.Arg870Ser	p.R870S	ENST00000373198	NM_133170.3	870	Cgc/Agc	18/32	0.441340695099799	4	FACETS	0.839	0.75	0.933	0.419	0.375	0.467	CLONAL	1	TRUE	2	0.636516178237489	4		561	607	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840010	27840010	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029539-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	124	770	0	ENST00000328488.2:c.84G>C	p.Lys28Asn	p.K28N	ENST00000328488	NM_003533.2	28	aaG/aaC	1/1	0.645231614550939	4	FACETS	0.643	0.58	0.709	0.214	0.193	0.237	SUBCLONAL	1	TRUE	1	0.636516178237489	4		770	992	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0031415-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	144	275	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	0.216382791742355	4	FACETS	0.835	0.769	0.903	0.835	0.769	0.903	INDETERMINATE	2	TRUE	2	0.674929841947088	4		275	428	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593667	55593669	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	rs1060502543	NA	P-0031415-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	180	328	0	ENST00000288135.5:c.1735_1737del	p.Asp579del	p.D579del	ENST00000288135	NM_000222.2	578	tATGat/tat	11/21	0.216382791742355	4	FACETS	0.915	0.852	0.98	0.915	0.852	0.98	INDETERMINATE	2	TRUE	2	0.674929841947088	4		328	488	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110651	8110651	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752234429	NA	P-0031415-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	214	452	0	ENST00000585124.1:c.241C>T	p.Arg81Cys	p.R81C	ENST00000585124	NM_004217.3	81	Cgt/Tgt	5/9	1	2	FACETS	0.976	0.912	1	0.976	0.912	1	CLONAL	1	TRUE	1	0.674929841947088	2		452	650	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125807	47125807	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031415-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	153	336	0	ENST00000409792.3:c.5463del	p.Pro1822GlnfsTer16	p.P1822Qfs*16	ENST00000409792	NM_014159.6	1821	ctT/ct	12/21	0.630504303408031	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.674929841947088	1		336	274	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625438	69625438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032111-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3943	248	567	0	ENST00000334134.2:c.355G>A	p.Glu119Lys	p.E119K	ENST00000334134	NM_005247.2	119	Gag/Aag	3/3	0.721660140969436	24	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.721660140969436	24		567	4191	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934576	NA	P-0032111-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	269	565	0	ENST00000269305.4:c.818G>C	p.Arg273Pro	p.R273P	ENST00000269305	NM_001126112.2	273	cGt/cCt	8/11	0.724122287946647	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.721660140969436	2		565	347	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89846317	89846317	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032111-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	139	541	0	ENST00000389301.3:c.1675G>C	p.Glu559Gln	p.E559Q	ENST00000389301	NM_000135.2	559	Gag/Cag	18/43	0.696921885236954	4	FACETS	1	0.949	1	0.352	0.321	0.384	CLONAL	1	TRUE	1	0.721660140969436	4		541	628	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416500	49416500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032111-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	349	552	0	ENST00000301067.7:c.16211C>T	p.Ser5404Phe	p.S5404F	ENST00000301067	NM_003482.3	5404	tCc/tTc	51/54	0.724122287946647	5	FACETS	1	0.988	1	0.749	0.712	0.787	CLONAL	2	TRUE	2	0.721660140969436	5		552	896	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440058	49440058	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032111-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	422	573	0	ENST00000301067.7:c.4568G>A	p.Cys1523Tyr	p.C1523Y	ENST00000301067	NM_003482.3	1523	tGc/tAc	16/54	0.724122287946647	5	FACETS	0.991	0.951	1	0.991	0.951	1	CLONAL	3	TRUE	2	0.721660140969436	5		573	819	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857892	9857892	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032111-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	415	590	0	ENST00000330684.3:c.3509A>T	p.Asn1170Ile	p.N1170I	ENST00000330684	NM_001134407.1	1170	aAc/aTc	13/13	0.626297584174115	5	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	2	0.721660140969436	5		590	737	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096569	178096569	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032111-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	109	482	0	ENST00000397062.3:c.762C>A	p.Phe254Leu	p.F254L	ENST00000397062	NM_006164.4	254	ttC/ttA	5/5	0.724122287946647	3	FACETS	1	0.932	1	0.518	0.469	0.569	CLONAL	1	TRUE	1	0.721660140969436	3		482	397	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129466	152129466	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032111-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	335	501	0	ENST00000206249.3:c.419C>G	p.Thr140Arg	p.T140R	ENST00000206249	NM_000125.3	140	aCg/aGg	1/8	0.724122287946647	5	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	2	0.721660140969436	5		501	590	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029284	14029284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032111-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	118	494	0	ENST00000311895.7:c.1495G>A	p.Gly499Arg	p.G499R	ENST00000311895	NM_005236.2	499	Gga/Aga	8/11	0.626297584174115	5	FACETS	0.966	0.872	1	0.322	0.29	0.355	CLONAL	1	TRUE	2	0.721660140969436	5		494	705	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646980	23646980	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032111-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	97	503	0	ENST00000261584.4:c.887T>C	p.Met296Thr	p.M296T	ENST00000261584	NM_024675.3	296	aTg/aCg	4/13	0.696921885236954	4	FACETS	1	0.931	1	0.35	0.313	0.388	CLONAL	1	TRUE	1	0.721660140969436	4		503	441	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971210	18971210	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032111-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	109	509	0	ENST00000262803.5:c.2263G>C	p.Glu755Gln	p.E755Q	ENST00000262803	NM_002911.3	755	Gag/Cag	16/24	0.721660140969436	6	FACETS	0.831	0.746	0.922	0.208	0.186	0.231	CLONAL	1	TRUE	2	0.721660140969436	6		509	888	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455642	189455642	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032111-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	57	408	0	ENST00000264731.3:c.176G>T	p.Trp59Leu	p.W59L	ENST00000264731	NM_003722.4	59	tGg/tTg	2/14	0.635442158605542	4	FACETS	0.76	0.655	0.873	0.253	0.218	0.291	SUBCLONAL	1	TRUE	1	0.721660140969436	4		408	358	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808931	3808936	+	frameshift_variant	Frame_Shift_Ins	INS	AGGGTT	AGGGTT	GTATCATGCCA	novel	NA	P-0032111-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	307	414	0	ENST00000262367.5:c.3288_3293delinsTGGCATGATAC	p.Thr1097GlyfsTer21	p.T1097Gfs*21	ENST00000262367	NM_004380.2	1096	ccAACCCTa/ccTGGCATGATACa	17/31	0.626297584174115	5	FACETS	0.871	0.827	0.915	0.871	0.827	0.915	CLONAL	3	TRUE	2	0.721660140969436	5		414	678	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7218344	7218344	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	107	724	2	ENST00000380728.2:c.28C>A	p.Leu10Ile	p.L10I	ENST00000380728		10	Ctt/Att	2/11	0.217754594808907	3	FACETS	1	0.948	1	0.54	0.486	0.596	INDETERMINATE	1	TRUE	1	0.515081822760377	3		726	484	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880257	37880257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034694-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	317	564	0	ENST00000269571.5:c.2301C>G	p.Ile767Met	p.I767M	ENST00000269571		767	atC/atG	19/27	0.45428778129295	1	FACETS	0.865	0.826	0.904	0.865	0.826	0.904	INDETERMINATE	1	TRUE	0	0.776631351101528	1		564	577	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480320	56480320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034694-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	421	377	0	ENST00000267101.3:c.427C>A	p.Leu143Met	p.L143M	ENST00000267101	NM_001982.3	143	Ctg/Atg	4/28	0.776631351101528	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.776631351101528	2		377	525	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008403	71008403	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034694-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	239	481	0	ENST00000318789.4:c.2029G>C	p.Glu677Gln	p.E677Q	ENST00000318789	NM_032682.5	677	Gag/Cag	21/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.776631351101528	2		481	550	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859006	57859006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034694-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	87	506	0	ENST00000228682.2:c.502C>T	p.Pro168Ser	p.P168S	ENST00000228682	NM_005269.2	168	Cct/Tct	5/12	0.776631351101528	2	FACETS	0.419	0.371	0.469	0.209	0.185	0.235	SUBCLONAL	1	TRUE	0	0.776631351101528	2		506	535	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441235	52441235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910211860	NA	P-0034694-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	253	632	0	ENST00000460680.1:c.535C>T	p.Arg179Trp	p.R179W	ENST00000460680	NM_004656.3	179	Cgg/Tgg	7/17	1	2	FACETS	0.96	0.903	1	0.96	0.903	1	CLONAL	1	TRUE	1	0.776631351101528	2		632	679	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265021	5265021	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034694-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	134	556	0	ENST00000357368.4:c.566C>T	p.Ser189Leu	p.S189L	ENST00000357368	NM_002850.3	189	tCa/tTa	5/38	0.776631351101528	1	FACETS	0.522	0.479	0.567	0.522	0.479	0.567	SUBCLONAL	1	TRUE	0	0.776631351101528	1		556	404	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023211	27023220	+	frameshift_variant	Frame_Shift_Del	DEL	ACGCGGGCCC	ACGCGGGCCC	-	novel	NA	P-0034694-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	196	468	0	ENST00000324856.7:c.317_326del	p.Asn106IlefsTer5	p.N106Ifs*5	ENST00000324856	NM_006015.4	106	aACGCGGGCCCt/at	1/20	0.616054326527141	2	FACETS	1	0.993	1	0.721	0.68	0.762	CLONAL	1	TRUE	0	0.776631351101528	2		468	350	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442562	52442573	+	inframe_deletion	In_Frame_Del	DEL	CTTTCGCCGGGA	CTTTCGCCGGGA	-	novel	NA	P-0034694-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	270	528	0	ENST00000460680.1:c.172_183del	p.Ser58_Lys61del	p.S58_K61del	ENST00000460680	NM_004656.3	58	TCCCGGCGAAAG/-	4/17	1	2	FACETS	0.978	0.923	1	0.978	0.923	1	CLONAL	1	TRUE	1	0.776631351101528	2		528	711	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348821	89348838	+	inframe_deletion	In_Frame_Del	DEL	CCTTCTCTTTCTTCTCGG	CCTTCTCTTTCTTCTCGG	-	rs754339551	NA	P-0034694-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	15	578	0	ENST00000301030.4:c.4112_4129del	p.Ala1371_Lys1376del	p.A1371_K1376del	ENST00000301030	NM_001256183.1	1371	gCCGAGAAGAAAGAGAAGGgc/ggc	9/13	0.45428778129295	1	FACETS	0.038	0.027	0.05	0.038	0.027	0.05	INDETERMINATE	1	TRUE	0	0.776631351101528	1		578	629	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647669	2647669	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0034694-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	85	453	0	ENST00000342085.4:c.1572T>A	p.Tyr524Ter	p.Y524*	ENST00000342085	NM_002613.4	524	taT/taA	14/14	1	2	FACETS	0.469	0.416	0.525	0.469	0.416	0.525	SUBCLONAL	1	TRUE	1	0.776631351101528	2		453	467	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251528	251528	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs372707443	NA	P-0034694-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	71	341	0	ENST00000264932.6:c.1739A>G	p.Tyr580Cys	p.Y580C	ENST00000264932	NM_004168.2	580	tAc/tGc	13/15	0.776631351101528	10	FACETS	0.594	0.516	0.678	0.066	0.057	0.076	SUBCLONAL	1	TRUE	1	0.776631351101528	10		341	1265	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356160	70356160	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034694-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	119	285	0	ENST00000374080.3:c.5055C>G	p.Ile1685Met	p.I1685M	ENST00000374080		1685	atC/atG	37/45	1	1	FACETS	0.615	0.563	0.667	0.615	0.563	0.667	SUBCLONAL	1	TRUE	0	0.776631351101528	1		285	305	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0039993-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	52	352	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.336467446523677	4	FACETS	0.808	0.689	0.94	0.269	0.229	0.314	CLONAL	1	TRUE	1	0.336467446523677	4		352	511	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944516	71944516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293622519	NA	P-0039993-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	34	453	0	ENST00000298229.2:c.2072G>A	p.Arg691Gln	p.R691Q	ENST00000298229	NM_001567.3	691	cGg/cAg	18/28	0.336467446523677	2	FACETS	0.36	0.294	0.436	0.18	0.147	0.218	SUBCLONAL	1	TRUE	0	0.336467446523677	2		453	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578404	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGGGGGCA	GGTGGGGGCA	-	novel	NA	P-0039993-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	144	423	0	ENST00000269305.4:c.526_535del	p.Cys176MetfsTer68	p.C176Mfs*68	ENST00000269305	NM_001126112.2	176	TGCCCCCACCat/at	5/11	0.233563881661664	2	FACETS	0.755	0.692	0.82	0.755	0.692	0.82	SUBCLONAL	2	TRUE	0	0.336467446523677	2		423	567	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870050	40870050	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039993-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	124	298	0	ENST00000428826.2:c.967A>C	p.Asn323His	p.N323H	ENST00000428826		323	Aat/Cat	10/21	0.332748312561412	3	FACETS	0.974	0.888	1	0.649	0.592	0.709	CLONAL	2	TRUE	0	0.336467446523677	3		298	442	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162405	47162405	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039993-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	59	404	0	ENST00000409792.3:c.3721T>G	p.Cys1241Gly	p.C1241G	ENST00000409792	NM_014159.6	1241	Tgt/Ggt	3/21	1	2	FACETS	0.706	0.608	0.812	0.706	0.608	0.812	SUBCLONAL	1	TRUE	1	0.336467446523677	2		404	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0041967-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	155	622	0	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	0.606790649230819	1	FACETS	0.964	0.895	1	0.964	0.895	1	CLONAL	1	TRUE	0	0.606790649230819	1		622	369	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998891	11998891	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0041967-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	63	294	0	ENST00000353533.5:c.394-1G>T		p.X132_splice	ENST00000353533	NM_003010.3	132			0.606790649230819	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.606790649230819	1		294	125	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443679	29443679	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041967-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	149	504	0	ENST00000389048.3:c.3538G>C	p.Val1180Leu	p.V1180L	ENST00000389048	NM_004304.4	1180	Gtt/Ctt	23/29	0.606790649230819	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.606790649230819	1		504	317	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274919	41274919	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041967-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	129	464	0	ENST00000349496.5:c.1169A>G	p.Asp390Gly	p.D390G	ENST00000349496	NM_001904.3	390	gAt/gGt	8/15	0.606790649230819	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.606790649230819	1		464	283	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17120451	17120461	+	frameshift_variant	Frame_Shift_Del	DEL	TGAGAACGTGC	TGAGAACGTGC	-	novel	NA	P-0041967-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	106	451	0	ENST00000285071.4:c.1098_1108del	p.Trp366CysfsTer20	p.W366Cfs*20	ENST00000285071	NM_144997.5	366	tgGCACGTTCTCAtg/tgtg	10/14	0.606790649230819	1	FACETS	0.817	0.742	0.893	0.817	0.742	0.893	CLONAL	1	TRUE	0	0.606790649230819	1		451	298	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927405	178927405	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041967-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	44	251	0	ENST00000263967.3:c.1168G>C	p.Asp390His	p.D390H	ENST00000263967	NM_006218.2	390	Gat/Cat	7/21	0.606790649230819	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.606790649230819	1		251	91	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0041987-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	87	137	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.875900561358886	2	FACETS	0.801	0.744	0.855	0.801	0.744	0.855	CLONAL	2	TRUE	0	0.875900561358886	2		137	124	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096129	178096129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1397390214	NA	P-0041987-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	405	619	0	ENST00000397062.3:c.1202G>A	p.Gly401Glu	p.G401E	ENST00000397062	NM_006164.4	401	gGg/gAg	5/5	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.875900561358886	2		619	876	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472553	88472553	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs761075951	NA	P-0041987-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	394	648	0	ENST00000360948.2:c.2002G>T	p.Val668Leu	p.V668L	ENST00000360948	NM_001012338.2	668	Gtg/Ttg	16/19	1	2	FACETS	0.964	0.92	1	0.964	0.92	1	CLONAL	1	TRUE	1	0.875900561358886	2		648	933	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041987-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	492	785	0	ENST00000269305.4:c.166G>T	p.Glu56Ter	p.E56*	ENST00000269305	NM_001126112.2	56	Gaa/Taa	4/11	0.862492592008475	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.875900561358886	1		785	588	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411948	63411948	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041987-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	406	783	0	ENST00000330258.3:c.1219G>T	p.Glu407Ter	p.E407*	ENST00000330258	NM_152424.3	407	Gaa/Taa	2/2	0.188040342794862	1	FACETS	0.527	0.503	0.551	0.527	0.503	0.551	INDETERMINATE	1	TRUE	0	0.875900561358886	1		783	989	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641489	18641489	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041987-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	151	447	0	ENST00000266497.5:c.2488A>C	p.Lys830Gln	p.K830Q	ENST00000266497		830	Aag/Cag	17/31	1	2	FACETS	0.564	0.518	0.613	0.564	0.518	0.613	SUBCLONAL	1	TRUE	1	0.875900561358886	2		447	611	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922004	39922004	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041987-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	721	550	0	ENST00000378444.4:c.4168G>T	p.Gly1390Cys	p.G1390C	ENST00000378444	NM_001123385.1	1390	Ggc/Tgc	9/15	0.851951371737313	3	FACETS	0.973	0.945	1	0.973	0.945	1	CLONAL	2	TRUE	1	0.875900561358886	3		550	1217	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28600566	28600566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041987-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	359	613	0	ENST00000253063.3:c.917C>T	p.Pro306Leu	p.P306L	ENST00000253063	NM_031459.4	306	cCc/cTc	7/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.875900561358886	2		613	795	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190734	11190734	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041987-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	453	724	0	ENST00000361445.4:c.5465G>T	p.Gly1822Val	p.G1822V	ENST00000361445	NM_004958.3	1822	gGg/gTg	39/58	1	2	FACETS	0.98	0.939	1	0.98	0.939	1	CLONAL	1	TRUE	1	0.875900561358886	2		724	1055	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552728	226552728	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041987-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	199	647	0	ENST00000366794.5:c.2633G>T	p.Arg878Leu	p.R878L	ENST00000366794	NM_001618.3	878	cGg/cTg	19/23	0.861402952102431	2	FACETS	0.619	0.575	0.664	0.31	0.287	0.332	SUBCLONAL	1	TRUE	0	0.875900561358886	2		647	734	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573200	64573200	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041987-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	439	697	0	ENST00000312049.6:c.1092C>G	p.Phe364Leu	p.F364L	ENST00000312049	NM_130799.2	364	ttC/ttG	8/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.875900561358886	2		697	995	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444391	49444391	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041987-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	456	848	0	ENST00000301067.7:c.2980G>T	p.Glu994Ter	p.E994*	ENST00000301067	NM_003482.3	994	Gag/Tag	11/54	1	2	FACETS	0.956	0.916	0.997	0.956	0.916	0.997	CLONAL	1	TRUE	1	0.875900561358886	2		848	1089	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954300	48954300	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0041987-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	164	264	0	ENST00000267163.4:c.1422-1G>C		p.X474_splice	ENST00000267163	NM_000321.2	474			0.875900561358886	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.875900561358886	1		264	193	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274128	18274128	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1219812893	NA	P-0041987-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	461	681	0	ENST00000222254.8:c.1346A>G	p.Tyr449Cys	p.Y449C	ENST00000222254	NM_005027.3	449	tAt/tGt	11/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.875900561358886	2		681	1018	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965767	25965767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041987-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	387	635	0	ENST00000435504.4:c.3439G>A	p.Glu1147Lys	p.E1147K	ENST00000435504		1147	Gaa/Aaa	13/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.875900561358886	2		635	873	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732675	204732675	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041987-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	318	479	0	ENST00000302823.3:c.10C>A	p.Leu4Ile	p.L4I	ENST00000302823	NM_005214.4	4	Ctt/Att	1/4	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.875900561358886	2		479	708	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370785	225370785	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041987-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	212	389	0	ENST00000264414.4:c.1094del	p.Leu365ProfsTer32	p.L365Pfs*32	ENST00000264414	NM_003590.4	365	cTc/cc	8/16	1	2	FACETS	0.905	0.848	0.963	0.905	0.848	0.963	CLONAL	1	TRUE	1	0.875900561358886	2		389	535	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264785	46264785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041987-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	370	555	0	ENST00000371998.3:c.1655C>T	p.Pro552Leu	p.P552L	ENST00000371998		552	cCc/cTc	12/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.875900561358886	2		555	807	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447688	187447694	+	frameshift_variant	Frame_Shift_Del	DEL	GTGGCAG	GTGGCAG	-	novel	NA	P-0041987-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	804	779	0	ENST00000232014.4:c.499_505del	p.Leu167Ter	p.L167*	ENST00000232014	NM_001130845.1	167	CTGCCACtg/tg	5/10	NA	2	FACETS	0.971	0.955	0.987			1	INDETERMINATE	2	TRUE	NA	0.875900561358886	2		779	945	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564665	86564665	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041987-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	446	749	0	ENST00000274376.6:c.397G>T	p.Gly133Cys	p.G133C	ENST00000274376	NM_002890.2	133	Ggt/Tgt	1/25	0.875900561358886	1	FACETS	0.997	0.97	1	0.997	0.97	1	CLONAL	1	TRUE	0	0.875900561358886	1		749	574	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965347	68965347	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041987-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	237	430	0	ENST00000288368.4:c.959G>T	p.Ser320Ile	p.S320I	ENST00000288368	NM_024870.2	320	aGt/aTt	9/40	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.875900561358886	2		430	529	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90994993	90994993	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041987-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	278	377	0	ENST00000265433.3:c.128G>T	p.Arg43Leu	p.R43L	ENST00000265433	NM_002485.4	43	cGa/cTa	2/16	1	2	FACETS	0.977	0.924	1	0.977	0.924	1	CLONAL	1	TRUE	1	0.875900561358886	2		377	650	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930936	39930936	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041987-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	326	307	0	ENST00000378444.4:c.3005G>C	p.Gly1002Ala	p.G1002A	ENST00000378444	NM_001123385.1	1002	gGa/gCa	5/15	0.851951371737313	3	FACETS	0.954	0.913	0.995	0.954	0.913	0.995	CLONAL	2	TRUE	1	0.875900561358886	3		307	561	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934199	39934199	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041987-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	748	707	0	ENST00000378444.4:c.400G>T	p.Ala134Ser	p.A134S	ENST00000378444	NM_001123385.1	134	Gct/Tct	4/15	0.851951371737313	3	FACETS	0.995	0.968	1	0.995	0.968	1	CLONAL	2	TRUE	1	0.875900561358886	3		707	1234	SUCCESS
AR	367	MSKCC	GRCh37	X	66766409	66766409	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041987-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	131	380	0	ENST00000374690.3:c.1421A>T	p.Glu474Val	p.E474V	ENST00000374690	NM_000044.3	474	gAg/gTg	1/8	0.188040342794862	1	FACETS	0.326	0.298	0.356	0.326	0.298	0.356	INDETERMINATE	1	TRUE	0	0.875900561358886	1		380	515	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043102-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	56	652	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.22	2		652	418	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426121	47426121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519786	NA	P-0043102-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	13	580	0	ENST00000377045.4:c.641C>T	p.Ser214Phe	p.S214F	ENST00000377045	NM_001654.4	214	tCc/tTc	7/16	0.296200343607403	3	FACETS	0.234	0.166	0.318			1	SUBCLONAL	1	TRUE	NA	0.22	3		580	561	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACT	novel	NA	P-0043102-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	75	563	0	ENST00000275493.2:c.2310_2311insTAC	p.Asp770_Asn771insTyr	p.D770_N771insY	ENST00000275493	NM_005228.3	770	gac/gACTac	20/28	0.3	3	FACETS	1	0.968	1	0.667	0.585	0.755	CLONAL	1	TRUE	1	0.22	3		563	567	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265477	198265477	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043102-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	28	294	0	ENST00000335508.6:c.2680G>A	p.Asp894Asn	p.D894N	ENST00000335508	NM_012433.2	894	Gat/Aat	18/25	1	2	FACETS	1	0.811	1	1	0.811	1	CLONAL	1	TRUE	1	0.22	2		294	252	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587781702	NA	P-0043614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	268	474	0	ENST00000269305.4:c.920-1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			NA	2	FACETS	0.899	0.848	0.951			1	INDETERMINATE	2	TRUE	NA	0.414590380656707	2		474	719	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403244	213403244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	85	398	0	ENST00000342788.4:c.11C>T	p.Ala4Val	p.A4V	ENST00000342788	NM_005235.2	4	gCg/gTg	1/28	1	2	FACETS	0.903	0.802	1	0.903	0.802	1	CLONAL	1	TRUE	1	0.414590380656707	2		398	454	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973904	55973904	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	89	353	0	ENST00000263923.4:c.1412G>T	p.Ser471Ile	p.S471I	ENST00000263923	NM_002253.2	471	aGc/aTc	10/30	0.414590380656707	1	FACETS	0.832	0.742	0.927	0.832	0.742	0.927	CLONAL	1	TRUE	0	0.414590380656707	1		353	409	SUCCESS
APC	324	MSKCC	GRCh37	5	112102961	112102961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199842850	NA	P-0043614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	77	339	0	ENST00000257430.4:c.296G>A	p.Arg99Gln	p.R99Q	ENST00000257430	NM_000038.5	99	cGg/cAg	4/16	0.369425708044526	1	FACETS	0.734	0.648	0.826	0.734	0.648	0.826	SUBCLONAL	1	TRUE	0	0.414590380656707	1		339	401	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0043622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	53	599	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.173019073843231	1	FACETS	0.708	0.602	0.824	0.708	0.602	0.824	SUBCLONAL	1	TRUE	0	0.18	1		599	757	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	34	243	0	ENST00000257430.4:c.4199del	p.Ser1400Ter	p.S1400*	ENST00000257430	NM_000038.5	1400	tCg/tg	16/16	1	2	FACETS	1	0.842	1	1	0.842	1	CLONAL	1	TRUE	1	0.18	2		243	366	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830777	72830777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752574946	NA	P-0043622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	54	458	0	ENST00000268489.5:c.5804G>A	p.Arg1935His	p.R1935H	ENST00000268489	NM_006885.3	1935	cGc/cAc	9/10	1	2	FACETS	0.834	0.711	0.97	0.834	0.711	0.97	CLONAL	1	TRUE	1	0.18	2		458	719	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916881	178916881	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	50	483	0	ENST00000263967.3:c.268T>G	p.Cys90Gly	p.C90G	ENST00000263967	NM_006218.2	90	Tgt/Ggt	2/21	1	2	FACETS	0.693	0.586	0.811	0.693	0.586	0.811	SUBCLONAL	1	TRUE	1	0.18	2		483	802	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31451710	31451710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1466433904	NA	P-0043622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	35	281	0	ENST00000344624.3:c.2612G>A	p.Arg871His	p.R871H	ENST00000344624		871	cGc/cAc	18/33	1	2	FACETS	0.939	0.77	1	0.939	0.77	1	CLONAL	1	TRUE	1	0.18	2		281	414	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675405	30675405	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	55	431	0	ENST00000376406.3:c.2951T>A	p.Val984Glu	p.V984E	ENST00000376406	NM_014641.2	984	gTa/gAa	8/15	1	2	FACETS	0.959	0.82	1	0.959	0.82	1	CLONAL	1	TRUE	1	0.18	2		431	637	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908790	101908790	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	32	248	0	ENST00000374994.4:c.1154A>G	p.Asp385Gly	p.D385G	ENST00000374994	NM_004612.2	385	gAt/gGt	7/9	1	2	FACETS	0.794	0.644	0.963	0.794	0.644	0.963	CLONAL	1	TRUE	1	0.18	2		248	448	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0043635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	140	457	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		457	365	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0043650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	99	279	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.723	0.648	0.801	0.723	0.648	0.801	SUBCLONAL	1	TRUE	1	0.574314468019682	2		279	477	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459758	149459758	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1029057991	NA	P-0043650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1707	782	862	0	ENST00000286301.3:c.449G>A	p.Arg150His	p.R150H	ENST00000286301	NM_005211.3	150	cGc/cAc	4/22	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.574314468019682	2		862	2489	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013719	170013719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388201066	NA	P-0043650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	50	275	0	ENST00000295797.4:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000295797	NM_002740.5	480	Cgc/Tgc	15/18	1	2	FACETS	0.741	0.635	0.855	0.741	0.635	0.855	SUBCLONAL	1	TRUE	1	0.574314468019682	2		275	235	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488685	212488685	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs138873985	NA	P-0043650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	156	485	0	ENST00000342788.4:c.2164A>G	p.Lys722Glu	p.K722E	ENST00000342788	NM_005235.2	722	Aaa/Gaa	18/28	1	2	FACETS	0.935	0.86	1	0.935	0.86	1	CLONAL	1	TRUE	1	0.574314468019682	2		485	581	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	220	475	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.838668154628228	2		475	509	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023126	27023126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	29	39	1	ENST00000324856.7:c.232G>A	p.Glu78Lys	p.E78K	ENST00000324856	NM_006015.4	78	Gag/Aag	1/20	1	2	FACETS	0.786	0.649	0.931	0.786	0.649	0.931	CLONAL	1	TRUE	1	0.838668154628228	2		40	88	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0043707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	57	256	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	1	2	FACETS	0.347	0.298	0.399	0.347	0.298	0.399	SUBCLONAL	1	TRUE	1	0.838668154628228	2		256	392	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971023	21971023	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	102	314	0	ENST00000304494.5:c.335G>C	p.Arg112Pro	p.R112P	ENST00000304494	NM_000077.4	112	cGt/cCt	2/3	0.838668154628228	1	FACETS	0.402	0.363	0.443	0.402	0.363	0.443	SUBCLONAL	1	TRUE	0	0.838668154628228	1		314	351	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0043707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	123	769	0	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	0.506	0.459	0.555	0.506	0.459	0.555	SUBCLONAL	1	TRUE	1	0.838668154628228	2		769	580	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0043707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	46	300	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.238	0.201	0.28	0.238	0.201	0.28	SUBCLONAL	1	TRUE	1	0.838668154628228	2		300	460	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974792	21974792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141798398	NA	P-0043707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	34	127	0	ENST00000304494.5:c.35C>T	p.Ser12Leu	p.S12L	ENST00000304494	NM_000077.4	12	tCg/tTg	1/3	0.838668154628228	1	FACETS	0.471	0.395	0.55	0.471	0.395	0.55	SUBCLONAL	1	TRUE	0	0.838668154628228	1		127	100	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295217	1295217	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs796849347	NA	P-0043707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	202	244	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.838668154628228	2		244	469	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943717	17943717	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	283	525	0	ENST00000458235.1:c.2372C>T	p.Pro791Leu	p.P791L	ENST00000458235	NM_000215.3	791	cCc/cTc	18/24	1	2	FACETS	0.997	0.943	1	0.997	0.943	1	CLONAL	1	TRUE	1	0.838668154628228	2		525	677	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100607	8100607	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1246283627	NA	P-0043707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	138	650	0	ENST00000346208.3:c.581T>G	p.Met194Arg	p.M194R	ENST00000346208		194	aTg/aGg	3/6	1	2	FACETS	0.414	0.377	0.453	0.414	0.377	0.453	SUBCLONAL	1	TRUE	1	0.838668154628228	2		650	795	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180547	94180547	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	87	302	0	ENST00000323929.3:c.1621A>G	p.Ser541Gly	p.S541G	ENST00000323929	NM_005591.3	541	Agt/Ggt	15/20	1	2	FACETS	0.43	0.381	0.481	0.43	0.381	0.481	SUBCLONAL	1	TRUE	1	0.838668154628228	2		302	483	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109984	115109984	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	131	627	0	ENST00000257566.3:c.1894A>G	p.Asn632Asp	p.N632D	ENST00000257566	NM_016569.3	632	Aac/Gac	8/8	1	2	FACETS	0.351	0.318	0.386	0.351	0.318	0.386	SUBCLONAL	1	TRUE	1	0.838668154628228	2		627	890	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248829	133248830	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0043707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	106	478	1	ENST00000320574.5:c.1765_1766delinsTT	p.Pro589Phe	p.P589F	ENST00000320574	NM_006231.2	589	CCt/TTt	16/49	0.308488350456083	1	FACETS	0.214	0.191	0.237	0.214	0.191	0.237	INDETERMINATE	1	TRUE	0	0.838668154628228	1		479	687	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549265	21549265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	330	612	0	ENST00000382592.4:c.3011C>T	p.Pro1004Leu	p.P1004L	ENST00000382592	NM_014572.2	1004	cCc/cTc	8/8	1	2	FACETS	0.847	0.803	0.892	0.847	0.803	0.892	CLONAL	1	TRUE	1	0.838668154628228	2		612	929	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805026	89805026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	147	656	0	ENST00000389301.3:c.4351G>A	p.Glu1451Lys	p.E1451K	ENST00000389301	NM_000135.2	1451	Gag/Aag	43/43	1	2	FACETS	0.409	0.373	0.446	0.409	0.373	0.446	SUBCLONAL	1	TRUE	1	0.838668154628228	2		656	858	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554708	63554708	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	99	401	0	ENST00000307078.5:c.31C>T	p.Pro11Ser	p.P11S	ENST00000307078	NM_004655.3	11	Ccg/Tcg	2/11	0.81567510899484	2	FACETS	0.436	0.39	0.484	0.218	0.195	0.242	SUBCLONAL	1	TRUE	0	0.838668154628228	2		401	542	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520264	9520264	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	186	302	0	ENST00000353224.5:c.2005G>A	p.Val669Ile	p.V669I	ENST00000353224	NM_177990.2	669	Gtt/Att	10/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.838668154628228	2		302	439	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031199	36031199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	135	592	1	ENST00000358208.4:c.1318G>A	p.Gly440Ser	p.G440S	ENST00000358208		440	Ggc/Agc	11/12	1	2	FACETS	0.391	0.355	0.428	0.391	0.355	0.428	SUBCLONAL	1	TRUE	1	0.838668154628228	2		593	824	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598169	52598169	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	217	393	0	ENST00000394830.3:c.3697G>T	p.Glu1233Ter	p.E1233*	ENST00000394830	NM_018313.4	1233	Gag/Tag	24/30	1	2	FACETS	0.846	0.791	0.901	0.846	0.791	0.901	CLONAL	1	TRUE	1	0.838668154628228	2		393	612	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52661304	52661304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	67	280	0	ENST00000394830.3:c.1526G>A	p.Ser509Asn	p.S509N	ENST00000394830	NM_018313.4	509	aGt/aAt	14/30	1	2	FACETS	0.352	0.306	0.401	0.352	0.306	0.401	SUBCLONAL	1	TRUE	1	0.838668154628228	2		280	454	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532539	187532540	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0043707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	37	244	0	ENST00000441802.2:c.9853_9853+1delinsAA		p.X3285_splice	ENST00000441802	NM_005245.3	3285		14/27	1	2	FACETS	0.327	0.271	0.389	0.327	0.271	0.389	SUBCLONAL	1	TRUE	1	0.838668154628228	2		244	270	SUCCESS
APC	324	MSKCC	GRCh37	5	112179425	112179425	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	74	358	1	ENST00000257430.4:c.8134C>A	p.Pro2712Thr	p.P2712T	ENST00000257430	NM_000038.5	2712	Ccc/Acc	16/16	1	2	FACETS	0.331	0.29	0.375	0.331	0.29	0.375	SUBCLONAL	1	TRUE	1	0.838668154628228	2		359	533	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100484	157100484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	35	32	0	ENST00000346085.5:c.1421G>A	p.Gly474Asp	p.G474D	ENST00000346085	NM_020732.3	474	gGc/gAc	1/20	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.838668154628228	2		32	73	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457093	5457093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1485681345	NA	P-0043707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	48	214	0	ENST00000381577.3:c.67G>A	p.Val23Ile	p.V23I	ENST00000381577	NM_014143.3	23	Gtt/Att	3/7	0.189086582763406	1	FACETS	0.238	0.202	0.277	0.238	0.202	0.277	INDETERMINATE	1	TRUE	0	0.838668154628228	1		214	279	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133748276	133748276	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	164	505	0	ENST00000318560.5:c.937A>G	p.Ile313Val	p.I313V	ENST00000318560	NM_005157.4	313	Atc/Gtc	6/11	1	2	FACETS	0.519	0.477	0.563	0.519	0.477	0.563	SUBCLONAL	1	TRUE	1	0.838668154628228	2		505	753	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0043719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	61	344	2	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.717233872152314	3	FACETS	0.969	0.895	1	0.969	0.895	1	CLONAL	3	TRUE	0	0.7232899935286	3		346	79	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912655	NA	P-0043719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	204	433	0	ENST00000269305.4:c.725G>C	p.Cys242Ser	p.C242S	ENST00000269305	NM_001126112.2	242	tGc/tCc	7/11	0.7232899935286	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.7232899935286	1		433	296	SUCCESS
APC	324	MSKCC	GRCh37	5	112175760	112175760	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	115	202	0	ENST00000257430.4:c.4469del	p.His1490LeufsTer17	p.H1490Lfs*17	ENST00000257430	NM_000038.5	1490	cAt/ct	16/16	0.7232899935286	3	FACETS	0.962	0.909	1	0.962	0.909	1	CLONAL	3	TRUE	0	0.7232899935286	3		202	150	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423605	88423605	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	74	351	0	ENST00000360948.2:c.2230T>A	p.Tyr744Asn	p.Y744N	ENST00000360948	NM_001012338.2	744	Tac/Aac	18/19	1	2	FACETS	0.718	0.635	0.805	0.718	0.635	0.805	SUBCLONAL	1	TRUE	1	0.7232899935286	2		351	285	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530443	187530443	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	36	173	0	ENST00000441802.2:c.10100A>G	p.Asn3367Ser	p.N3367S	ENST00000441802	NM_005245.3	3367	aAc/aGc	16/27	1	2	FACETS	0.429	0.355	0.511	0.429	0.355	0.511	SUBCLONAL	1	TRUE	1	0.7232899935286	2		173	232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0043730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	592	599	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.504951617531049	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.790107412141389	2		599	717	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0043730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	427	289	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.790107412141389	4	FACETS	0.916	0.883	0.949	0.916	0.883	0.949	CLONAL	3	TRUE	1	0.790107412141389	4		289	704	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0043730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	39	239	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.596194543783484	1	FACETS	0.334	0.28	0.392	0.334	0.28	0.392	SUBCLONAL	1	TRUE	0	0.790107412141389	1		239	179	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25458617	25458617	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	81	339	0	ENST00000264709.3:c.2556G>T	p.Met852Ile	p.M852I	ENST00000264709	NM_175629.2	852	atG/atT	22/23	0.428069128092428	3	FACETS	0.501	0.442	0.564	0.167	0.147	0.188	INDETERMINATE	1	TRUE	0	0.790107412141389	3		339	571	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790097	40790097	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	194	451	0	ENST00000373198.4:c.2634C>A	p.Ser878Arg	p.S878R	ENST00000373198	NM_133170.3	878	agC/agA	18/32	1	2	FACETS	0.754	0.701	0.809	0.754	0.701	0.809	SUBCLONAL	1	TRUE	1	0.790107412141389	2		451	651	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944620	40944620	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	100	224	0	ENST00000373198.4:c.1882G>T	p.Val628Phe	p.V628F	ENST00000373198	NM_133170.3	628	Gtc/Ttc	12/32	1	2	FACETS	0.83	0.751	0.912	0.83	0.751	0.912	CLONAL	1	TRUE	1	0.790107412141389	2		224	305	SUCCESS
APC	324	MSKCC	GRCh37	5	112173686	112173687	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0043730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	120	215	0	ENST00000257430.4:c.2396_2397del	p.Tyr799CysfsTer3	p.Y799Cfs*3	ENST00000257430	NM_000038.5	799	TAt/t	16/16	0.596194543783484	1	FACETS	0.792	0.732	0.852	0.792	0.732	0.852	SUBCLONAL	1	TRUE	0	0.790107412141389	1		215	232	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622182	117622182	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	60	214	0	ENST00000368508.3:c.6688A>G	p.Arg2230Gly	p.R2230G	ENST00000368508	NM_002944.2	2230	Aga/Gga	42/43	0.506890602845236	1	FACETS	0.344	0.299	0.392	0.344	0.299	0.392	SUBCLONAL	1	TRUE	0	0.790107412141389	1		214	267	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106336	27106337	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	137	467	0	ENST00000324856.7:c.5952_5953del	p.Ser1985GlnfsTer13	p.S1985Qfs*13	ENST00000324856	NM_006015.4	1983	TGt/t	20/20	1	2	FACETS	0.981	0.892	1	0.981	0.892	1	CLONAL	1	TRUE	1	0.32	2		467	873	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363268	40363268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201425251	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	156	471	0	ENST00000397332.2:c.961C>T	p.Arg321Cys	p.R321C	ENST00000397332	NM_001033082.2	321	Cgc/Tgc	3/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.32	2		471	857	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874274	155874274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1185965337	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	103	436	0	ENST00000368323.3:c.257G>A	p.Arg86Gln	p.R86Q	ENST00000368323	NM_006912.5	86	cGg/cAg	5/6	1	2	FACETS	0.894	0.8	0.993	0.894	0.8	0.993	CLONAL	1	TRUE	1	0.32	2		436	720	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175813	176175813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	36	342	0	ENST00000367669.3:c.302G>A	p.Gly101Asp	p.G101D	ENST00000367669	NM_022457.5	101	gGc/gAc	1/20	1	2	FACETS	0.452	0.371	0.543	0.452	0.371	0.543	SUBCLONAL	1	TRUE	1	0.32	2		342	498	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651652	206651652	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1430265856	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	180	634	2	ENST00000367120.3:c.962T>C	p.Leu321Pro	p.L321P	ENST00000367120	NM_014002.3	321	cTg/cCg	9/22	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.32	2		636	1091	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597893	43597895	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	130	673	0	ENST00000355710.3:c.443_445del	p.Ser148del	p.S148del	ENST00000355710	NM_020975.4	147	ttCTCc/ttc	3/20	1	2	FACETS	0.729	0.66	0.803	0.729	0.66	0.803	SUBCLONAL	1	TRUE	1	0.32	2		673	1114	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653780	89653781	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	rs1554893747	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	27	264	0	ENST00000371953.3:c.80-1_80del		p.X27_splice	ENST00000371953	NM_000314.4	27			1	2	FACETS	0.632	0.504	0.777	0.632	0.504	0.777	SUBCLONAL	1	TRUE	1	0.32	2		264	267	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692910	89692910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	75	394	0	ENST00000371953.3:c.394G>A	p.Gly132Ser	p.G132S	ENST00000371953	NM_000314.4	132	Ggt/Agt	5/9	1	2	FACETS	0.849	0.745	0.961	0.849	0.745	0.961	CLONAL	1	TRUE	1	0.32	2		394	552	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	132	372	2	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.32	2		374	631	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925589	114925589	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs749975791	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	145	581	0	ENST00000543371.1:c.1667T>C	p.Leu556Pro	p.L556P	ENST00000543371	NM_001198531.1	556	cTg/cCg	14/14	1	2	FACETS	0.881	0.802	0.963	0.881	0.802	0.963	CLONAL	1	TRUE	1	0.32	2		581	1029	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925646	114925646	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779491224	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	149	632	0	ENST00000543371.1:c.1724C>T	p.Pro575Leu	p.P575L	ENST00000543371	NM_001198531.1	575	cCg/cTg	14/14	1	2	FACETS	0.845	0.771	0.923	0.845	0.771	0.923	CLONAL	1	TRUE	1	0.32	2		632	1102	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941862	71941862	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	61	523	0	ENST00000298229.2:c.1220T>A	p.Leu407Gln	p.L407Q	ENST00000298229	NM_001567.3	407	cTg/cAg	11/28	1	2	FACETS	0.459	0.395	0.529	0.459	0.395	0.529	SUBCLONAL	1	TRUE	1	0.32	2		523	831	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421701	49421701	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	96	536	0	ENST00000301067.7:c.14528del	p.Lys4843ArgfsTer15	p.K4843Rfs*15	ENST00000301067	NM_003482.3	4843	aAg/ag	47/54	1	2	FACETS	0.656	0.584	0.734	0.656	0.584	0.734	SUBCLONAL	1	TRUE	1	0.32	2		536	914	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438691	49438691	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	95	643	0	ENST00000301067.7:c.4799T>G	p.Leu1600Arg	p.L1600R	ENST00000301067	NM_003482.3	1600	cTg/cGg	19/54	1	2	FACETS	0.536	0.476	0.601	0.536	0.476	0.601	SUBCLONAL	1	TRUE	1	0.32	2		643	1107	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614463	38614463	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	49	350	0	ENST00000299084.4:c.234del	p.Asp79ThrfsTer42	p.D79Tfs*42	ENST00000299084	NM_152594.2	77	Aaa/aa	3/7	1	2	FACETS	0.865	0.736	1	0.865	0.736	1	CLONAL	1	TRUE	1	0.32	2		350	354	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034986	42034986	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1469072500	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	85	533	0	ENST00000219905.7:c.4828A>G	p.Thr1610Ala	p.T1610A	ENST00000219905	NM_001164273.1	1610	Act/Gct	15/24	1	2	FACETS	0.613	0.541	0.69	0.613	0.541	0.69	SUBCLONAL	1	TRUE	1	0.32	2		533	867	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054396	42054396	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	79	301	0	ENST00000219905.7:c.7585del	p.Arg2529GlufsTer28	p.R2529Efs*28	ENST00000219905	NM_001164273.1	2527	cAa/ca	22/24	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.32	2		301	424	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007895	45007896	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	52	274	0	ENST00000558401.1:c.343_344del	p.Trp115GlyfsTer12	p.W115Gfs*12	ENST00000558401	NM_004048.2	114	aaGTgg/aagg	2/4	1	2	FACETS	0.686	0.584	0.797	0.686	0.584	0.797	SUBCLONAL	1	TRUE	1	0.32	2		274	474	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007896	45007897	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	70	269	0	ENST00000558401.1:c.346+1dup		p.W115fs	ENST00000558401	NM_004048.2	115	tgg/tGgg	2/4	1	2	FACETS	0.941	0.823	1	0.941	0.823	1	CLONAL	1	TRUE	1	0.32	2		269	465	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347095	89347095	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	113	522	0	ENST00000301030.4:c.5855A>G	p.His1952Arg	p.H1952R	ENST00000301030	NM_001256183.1	1952	cAc/cGc	9/13	1	2	FACETS	0.848	0.763	0.938	0.848	0.763	0.938	CLONAL	1	TRUE	1	0.32	2		522	833	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348062	89348062	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1466196842	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	224	860	2	ENST00000301030.4:c.4888G>A	p.Gly1630Arg	p.G1630R	ENST00000301030	NM_001256183.1	1630	Ggg/Agg	9/13	1	2	FACETS	0.962	0.893	1	0.962	0.893	1	CLONAL	1	TRUE	1	0.32	2		862	1456	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350035	89350035	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	85	641	0	ENST00000301030.4:c.2915A>G	p.His972Arg	p.H972R	ENST00000301030	NM_001256183.1	972	cAc/cGc	9/13	1	2	FACETS	0.485	0.427	0.547	0.485	0.427	0.547	SUBCLONAL	1	TRUE	1	0.32	2		641	1096	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	135	427	1	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	1	2	FACETS	0.953	0.866	1	0.953	0.866	1	CLONAL	1	TRUE	1	0.32	2		428	885	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665120	29665120	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs201336602	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	47	447	0	ENST00000356175.3:c.6719A>G	p.His2240Arg	p.H2240R	ENST00000356175	NM_000267.3	2240	cAt/cGt	44/57	1	2	FACETS	0.414	0.348	0.486	0.414	0.348	0.486	SUBCLONAL	1	TRUE	1	0.32	2		447	710	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687124	37687124	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	61	512	0	ENST00000447079.4:c.4028G>T	p.Gly1343Val	p.G1343V	ENST00000447079	NM_015083.1	1343	gGg/gTg	14/14	1	2	FACETS	0.441	0.379	0.508	0.441	0.379	0.508	SUBCLONAL	1	TRUE	1	0.32	2		512	865	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883561	37883561	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	126	537	0	ENST00000269571.5:c.3173A>G	p.Asp1058Gly	p.D1058G	ENST00000269571		1058	gAc/gGc	26/27	1	2	FACETS	0.862	0.779	0.948	0.862	0.779	0.948	CLONAL	1	TRUE	1	0.32	2		537	914	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677825	47677825	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	128	482	0	ENST00000347630.2:c.1040A>G	p.His347Arg	p.H347R	ENST00000347630	NM_001007230.1	347	cAc/cGc	11/11	1	2	FACETS	0.933	0.846	1	0.933	0.846	1	CLONAL	1	TRUE	1	0.32	2		482	857	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	143	602	3	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.852	0.776	0.932	0.852	0.776	0.932	CLONAL	1	TRUE	1	0.32	2		605	1049	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119910	70119910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1297203260	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	111	436	4	ENST00000245479.2:c.916del	p.Val306CysfsTer77	p.V306Cfs*77	ENST00000245479	NM_000346.3	304	ccG/cc	3/3	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.32	2		440	690	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119035	3119035	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1291813342	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	139	512	0	ENST00000078429.4:c.719T>C	p.Val240Ala	p.V240A	ENST00000078429	NM_002067.2	240	gTg/gCg	5/7	1	2	FACETS	0.977	0.889	1	0.977	0.889	1	CLONAL	1	TRUE	1	0.32	2		512	889	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210893	36210893	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	78	582	2	ENST00000222270.7:c.649del	p.Arg217GlyfsTer22	p.R217Gfs*22	ENST00000222270	NM_014727.1	215	aCc/ac	3/37	1	2	FACETS	0.494	0.433	0.561	0.494	0.433	0.561	SUBCLONAL	1	TRUE	1	0.32	2		584	986	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	171	832	5	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	0.988	0.907	1	0.988	0.907	1	CLONAL	1	TRUE	1	0.32	2		837	1082	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905875	50905875	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	142	605	2	ENST00000440232.2:c.847C>T	p.Gln283Ter	p.Q283*	ENST00000440232	NM_002691.3	283	Cag/Tag	8/27	1	2	FACETS	0.928	0.845	1	0.928	0.845	1	CLONAL	1	TRUE	1	0.32	2		607	956	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27016047	27016047	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	142	533	0	ENST00000335756.4:c.323A>G	p.Asp108Gly	p.D108G	ENST00000335756	NM_001809.3	108	gAc/gGc	4/5	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.32	2		533	874	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222520	39222520	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	89	371	2	ENST00000402219.2:c.3090del	p.Lys1030AsnfsTer6	p.K1030Nfs*6	ENST00000402219	NM_005633.3	1030	aaA/aa	20/23	1	2	FACETS	0.838	0.743	0.939	0.838	0.743	0.939	CLONAL	1	TRUE	1	0.32	2		373	664	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384651	31384651	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	153	603	2	ENST00000328111.2:c.1359del	p.Leu454SerfsTer136	p.L454Sfs*136	ENST00000328111	NM_006892.3	451	gaG/ga	13/23	1	2	FACETS	0.965	0.882	1	0.965	0.882	1	CLONAL	1	TRUE	1	0.32	2		605	991	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582098	52582098	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	32	247	0	ENST00000394830.3:c.4730A>G	p.Tyr1577Cys	p.Y1577C	ENST00000394830	NM_018313.4	1577	tAc/tGc	30/30	1	2	FACETS	0.394	0.319	0.479	0.394	0.319	0.479	SUBCLONAL	1	TRUE	1	0.32	2		247	508	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119666143	119666143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769576748	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	62	313	0	ENST00000316626.5:c.338G>A	p.Arg113His	p.R113H	ENST00000316626		113	cGt/cAt	3/12	1	2	FACETS	0.907	0.786	1	0.907	0.786	1	CLONAL	1	TRUE	1	0.32	2		313	427	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155466	106155466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749710391	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	88	345	1	ENST00000380013.4:c.367C>T	p.Arg123Cys	p.R123C	ENST00000380013	NM_001127208.2	123	Cgt/Tgt	3/11	1	2	FACETS	0.979	0.869	1	0.979	0.869	1	CLONAL	1	TRUE	1	0.32	2		346	562	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	120	663	3	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	0.891	0.804	0.982	0.891	0.804	0.982	CLONAL	1	TRUE	1	0.32	2		666	842	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253805	153253805	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	93	376	0	ENST00000281708.4:c.928T>C	p.Tyr310His	p.Y310H	ENST00000281708	NM_033632.3	310	Tac/Cac	6/12	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.32	2		376	496	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541358	187541359	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	86	346	0	ENST00000441802.2:c.6381dup	p.Gln2128SerfsTer7	p.Q2128Sfs*7	ENST00000441802	NM_005245.3	2127	-/T	10/27	1	2	FACETS	0.946	0.839	1	0.946	0.839	1	CLONAL	1	TRUE	1	0.32	2		346	568	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629661	187629663	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs760967821	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	145	481	0	ENST00000441802.2:c.1319_1321del	p.Thr440del	p.T440del	ENST00000441802	NM_005245.3	440	aCAAgt/agt	2/27	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.32	2		481	855	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874637	35874637	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	77	267	2	ENST00000303115.3:c.799del	p.Arg267GlyfsTer28	p.R267Gfs*28	ENST00000303115	NM_002185.3	265	Aaa/aa	6/8	1	2	FACETS	0.959	0.844	1	0.959	0.844	1	CLONAL	1	TRUE	1	0.32	2		269	502	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177828	56177828	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	101	331	1	ENST00000399503.3:c.2803del	p.Ser935GlnfsTer2	p.S935Qfs*2	ENST00000399503	NM_005921.1	934	aTt/at	14/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.32	2		332	552	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	56	317	1	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.742	0.636	0.856	0.742	0.636	0.856	SUBCLONAL	1	TRUE	1	0.32	2		318	472	SUCCESS
APC	324	MSKCC	GRCh37	5	112177265	112177265	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1554087123	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	55	292	0	ENST00000257430.4:c.5978del	p.Pro1993LeufsTer51	p.P1993Lfs*51	ENST00000257430	NM_000038.5	1992	Ccc/cc	16/16	1	2	FACETS	0.838	0.719	0.968	0.838	0.719	0.968	CLONAL	1	TRUE	1	0.32	2		292	410	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407567	407567	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	90	306	0	ENST00000380956.4:c.1325G>A	p.Arg442Lys	p.R442K	ENST00000380956	NM_001195286.1	442	aGa/aAa	9/9	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.32	2		306	539	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056566	26056566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1444425351	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	65	318	0	ENST00000343677.2:c.91A>G	p.Thr31Ala	p.T31A	ENST00000343677	NM_005319.3	31	Acg/Gcg	1/1	1	2	FACETS	0.991	0.862	1	0.991	0.862	1	CLONAL	1	TRUE	1	0.32	2		318	410	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324655	31324655	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs151341108	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	26	293	0	ENST00000412585.2:c.153C>A	p.Tyr51Ter	p.Y51*	ENST00000412585	NM_005514.6	51	taC/taA	2/8	1	2	FACETS	0.344	0.272	0.428	0.344	0.272	0.428	SUBCLONAL	1	TRUE	1	0.32	2		293	472	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816428	32816428	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	137	537	0	ENST00000354258.4:c.1746+1G>A		p.X582_splice	ENST00000354258	NM_000593.5	582			1	2	FACETS	0.918	0.834	1	0.918	0.834	1	CLONAL	1	TRUE	1	0.32	2		537	933	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821350	32821350	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	65	682	0	ENST00000354258.4:c.244T>G	p.Trp82Gly	p.W82G	ENST00000354258	NM_000593.5	82	Tgg/Ggg	1/11	1	2	FACETS	0.397	0.343	0.456	0.397	0.343	0.456	SUBCLONAL	1	TRUE	1	0.32	2		682	1023	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020823	112020823	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	100	302	0	ENST00000368678.4:c.748A>G	p.Thr250Ala	p.T250A	ENST00000368678		250	Acc/Gcc	8/13	1	2	FACETS	0.929	0.83	1	0.929	0.83	1	CLONAL	1	TRUE	1	0.32	2		302	673	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	57	760	5	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.396	0.339	0.459	0.396	0.339	0.459	SUBCLONAL	1	TRUE	1	0.32	2		765	899	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146945	38146945	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	103	635	1	ENST00000317025.8:c.3197del	p.Asn1066ThrfsTer16	p.N1066Tfs*16	ENST00000317025	NM_023034.1	1066	aAc/ac	18/24	1	2	FACETS	0.79	0.706	0.879	0.79	0.706	0.879	SUBCLONAL	1	TRUE	1	0.32	2		636	815	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205359	38205359	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	150	600	0	ENST00000317025.8:c.331T>C	p.Tyr111His	p.Y111H	ENST00000317025	NM_023034.1	111	Tat/Cat	2/24	1	2	FACETS	0.973	0.888	1	0.973	0.888	1	CLONAL	1	TRUE	1	0.32	2		600	964	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748399150	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	150	659	1	ENST00000220592.5:c.1806del	p.Ala603ProfsTer92	p.A603Pfs*92	ENST00000220592	NM_012154.3	602	ccC/cc	14/19	1	2	FACETS	0.883	0.806	0.964	0.883	0.806	0.964	CLONAL	1	TRUE	1	0.32	2		660	1062	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341773	8341773	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs761130552	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	100	513	0	ENST00000356435.5:c.4867A>G	p.Arg1623Gly	p.R1623G	ENST00000356435		1623	Aga/Gga	29/35	1	2	FACETS	0.874	0.781	0.973	0.874	0.781	0.973	CLONAL	1	TRUE	1	0.32	2		513	715	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879926	44879926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	81	505	0	ENST00000377967.4:c.515G>A	p.Arg172Gln	p.R172Q	ENST00000377967	NM_021140.2	172	cGa/cAa	6/29	0.0874144212037408	0	FACETS	0.652	0.576	0.734			1	INDETERMINATE	1	TRUE	0	0.32	0		505	528	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412473	63412473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	114	652	0	ENST00000330258.3:c.694del	p.Gln232LysfsTer50	p.Q232Kfs*50	ENST00000330258	NM_152424.3	232	Caa/aa	2/2	0.0874144212037408	0	FACETS	0.505	0.454	0.559			1	INDETERMINATE	1	TRUE	0	0.32	0		652	960	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019696	123019696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147946593	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	96	475	2	ENST00000355640.3:c.184C>T	p.Arg62Trp	p.R62W	ENST00000355640		62	Cgg/Tgg	2/7	0.0874144212037408	0	FACETS	0.538	0.479	0.601			1	INDETERMINATE	1	TRUE	0	0.32	0		477	758	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200029	123200029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	26	181	0	ENST00000218089.9:c.2101C>T	p.His701Tyr	p.H701Y	ENST00000218089	NM_001042749.1	701	Cat/Tat	22/35	0.0874144212037408	0	FACETS	0.476	0.379	0.587			1	INDETERMINATE	1	TRUE	0	0.32	0		181	232	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	23	233	2	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	0.0874144212037408	0	FACETS	0.331	0.258	0.416			1	INDETERMINATE	1	TRUE	0	0.32	0		235	295	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324886	31324887	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760037174	NA	P-0043781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	62	415	0	ENST00000412585.2:c.49_50insG	p.Leu17ArgfsTer82	p.L17Rfs*82	ENST00000412585	NM_005514.6	17	ctg/cGtg	1/8	1	2	FACETS	0.516	0.445	0.594	0.516	0.445	0.594	SUBCLONAL	1	TRUE	1	0.32	2		415	751	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0043816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	98	388	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.858	0.77	0.951	0.858	0.77	0.951	CLONAL	1	TRUE	1	0.534757657112869	2		388	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579855	7579855	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1131691018	NA	P-0043816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	197	482	0	ENST00000269305.4:c.58del	p.Ser20GlnfsTer24	p.S20Qfs*24	ENST00000269305	NM_001126112.2	20	Tca/ca	2/11	0.534757657112869	1	FACETS	0.924	0.861	0.989	0.924	0.861	0.989	CLONAL	1	TRUE	0	0.534757657112869	1		482	584	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004745	16004746	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	179	459	0	ENST00000268712.3:c.2508dup	p.Glu837Ter	p.E837*	ENST00000268712	NM_006311.3	836	-/T	20/46	0.534757657112869	1	FACETS	0.952	0.885	1	0.952	0.885	1	CLONAL	1	TRUE	0	0.534757657112869	1		459	515	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52722962	52722962	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	166	459	0	ENST00000322088.6:c.1148del	p.Asn383ThrfsTer9	p.N383Tfs*9	ENST00000322088	NM_014225.5	383	Aac/ac	10/15	0.133871615565175	5	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.534757657112869	5		459	898	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0043833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	194	392	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.359128866001025	1	FACETS	0.927	0.859	0.997	0.927	0.859	0.997	CLONAL	1	TRUE	0	0.414715079674447	1		392	800	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023151	27023179	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	-	novel	NA	P-0043833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	68	28	0	ENST00000324856.7:c.267_295del	p.Ser90ProfsTer11	p.S90Pfs*11	ENST00000324856	NM_006015.4	86	gGCGGAGCCGGCAGCGGCGGCGGGCCCGGC/g	1/20	0.359128866001025	1	FACETS	0.893	0.821	0.961	1	0.988	1	CLONAL	3	TRUE	0	0.414715079674447	1		28	97	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0043876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	222	439	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.643848079130002	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.643848079130002	3		439	442	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843495	3843495	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	60	469	0	ENST00000262367.5:c.1108C>T	p.Arg370Ter	p.R370*	ENST00000262367	NM_004380.2	370	Cga/Tga	4/31	0.534821791268544	4	FACETS	0.325	0.279	0.376	0.108	0.093	0.126	SUBCLONAL	1	TRUE	1	0.643848079130002	4		469	942	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0043876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	204	436	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.643848079130002	2		436	606	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38276891	38277223	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACAGACTCTAGAGCACTTAGTTCATGATATTCCACTGTGCCTTGCCCAGAAGCCAGAAAATAAGGCCCAAAGCTATAAATTAGGGACAATGGAGAGGGCAGGGCATTAGAGGCCCAGAGAGAGAGGTGGTGCTGAGTGTGCAAATCCCCCATCTACTTTCTGTTACCTGTCTGCGCAGAGGGATGCTCTTGGCCAGCTTGTGCACAGCCATCTGGCTGTGGAAGTCACTCTTCTTGGTACCACTCTTCATCTTGTAGACGATGACCGACCCCACCATGCAGGAGATGAGGAAGGCCCCTGTGCAATAGATGATGATCTCCAGGTACAGGGGCG	ACAGACTCTAGAGCACTTAGTTCATGATATTCCACTGTGCCTTGCCCAGAAGCCAGAAAATAAGGCCCAAAGCTATAAATTAGGGACAATGGAGAGGGCAGGGCATTAGAGGCCCAGAGAGAGAGGTGGTGCTGAGTGTGCAAATCCCCCATCTACTTTCTGTTACCTGTCTGCGCAGAGGGATGCTCTTGGCCAGCTTGTGCACAGCCATCTGGCTGTGGAAGTCACTCTTCTTGGTACCACTCTTCATCTTGTAGACGATGACCGACCCCACCATGCAGGAGATGAGGAAGGCCCCTGTGCAATAGATGATGATCTCCAGGTACAGGGGCG	-	novel	NA	P-0043876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	90	119	0	ENST00000425967.3:c.1205_1377+160del		p.X402_splice	ENST00000425967	NM_001174067.1	402		10/19	0.643848079130002	12	FACETS	1	0.935	1			1	CLONAL	4	TRUE	NA	0.643848079130002	12		119	280	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266833	198266837	+	protein_altering_variant	In_Frame_Del	DEL	TTCTG	TTCTG	CC	novel	NA	P-0043876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	165	507	0	ENST00000335508.6:c.2095_2099delinsGG	p.Gln699_Lys700delinsGly	p.Q699_K700delinsG	ENST00000335508	NM_012433.2	699	CAGAAa/GGa	15/25	1	2	FACETS	0.8	0.737	0.864	0.8	0.737	0.864	SUBCLONAL	1	TRUE	1	0.643848079130002	2		507	641	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913400	NA	P-0043912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	106	471	0	ENST00000349496.5:c.98C>A	p.Ser33Tyr	p.S33Y	ENST00000349496	NM_001904.3	33	tCt/tAt	3/15	1	2	FACETS	0.861	0.779	0.945	0.861	0.779	0.945	CLONAL	1	TRUE	1	0.69	2		471	357	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0043912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	50	137	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.792	0.683	0.908	0.792	0.683	0.908	CLONAL	1	TRUE	1	0.69	2		137	183	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845618	63845618	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	101	242	0	ENST00000279873.7:c.1359del	p.Glu454LysfsTer25	p.E454Kfs*25	ENST00000279873	NM_032199.2	453	Aaa/aa	9/10	1	2	FACETS	0.921	0.833	1	0.921	0.833	1	CLONAL	1	TRUE	1	0.69	2		242	318	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590496	67590496	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	66	186	0	ENST00000274335.5:c.1558G>T	p.Glu520Ter	p.E520*	ENST00000274335		520	Gaa/Taa	11/15	1	2	FACETS	0.811	0.713	0.913	0.811	0.713	0.913	CLONAL	1	TRUE	1	0.69	2		186	236	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106658	27106658	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	231	586	0	ENST00000324856.7:c.6269A>G	p.His2090Arg	p.H2090R	ENST00000324856	NM_006015.4	2090	cAc/cGc	20/20	1	2	FACETS	0.999	0.937	1	0.999	0.937	1	CLONAL	1	TRUE	1	0.69	2		586	670	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717656	89717657	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	150	433	0	ENST00000371953.3:c.683dup	p.Asn228LysfsTer15	p.N228Kfs*15	ENST00000371953	NM_000314.4	227	-/A	7/9	1	2	FACETS	0.97	0.895	1	0.97	0.895	1	CLONAL	1	TRUE	1	0.69	2		433	448	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514429	125514429	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1183852401	NA	P-0043912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	117	325	0	ENST00000428830.2:c.1124A>G	p.Lys375Arg	p.K375R	ENST00000428830	NM_001114121.2	375	aAa/aGa	11/14	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.69	2		325	312	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528465	157528466	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	198	501	0	ENST00000346085.5:c.6192dup	p.Asp2065ArgfsTer24	p.D2065Rfs*24	ENST00000346085	NM_020732.3	2064	caa/cAaa	20/20	0.106743250651658	3	FACETS	1	0.986	1	0.614	0.571	0.657	INDETERMINATE	1	TRUE	1	0.69	3		501	629	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	307	475	0				ENST00000310581	NM_198253.2	-/1132			0.722000269288785	4	FACETS	1	0.993	1	0.46	0.434	0.487	CLONAL	1	TRUE	1	0.722000269288785	4		475	1061	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0043929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	1063	526	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.722000269288785	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.722000269288785	3		526	1320	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333850	70333850	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs762232511	NA	P-0043929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	99	312	0	ENST00000373644.4:c.1755G>T	p.Lys585Asn	p.K585N	ENST00000373644	NM_030625.2	585	aaG/aaT	2/12	0.535139116538877	3	FACETS	0.742	0.665	0.823			1	SUBCLONAL	1	TRUE	NA	0.722000269288785	3		312	503	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911485	134911485	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	152	454	0	ENST00000398015.3:c.1950C>G	p.Ile650Met	p.I650M	ENST00000398015	NM_004441.4	650	atC/atG	11/16	0.299226941421837	4	FACETS	0.926	0.848	1	0.231	0.212	0.252	INDETERMINATE	1	TRUE	0	0.722000269288785	4		454	783	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184495	7184495	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1448475843	NA	P-0043929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	356	550	0	ENST00000302850.5:c.806C>T	p.Pro269Leu	p.P269L	ENST00000302850	NM_000208.2	269	cCg/cTg	3/22	0.154068471892878	4	FACETS	0.99	0.942	1	0.99	0.942	1	INDETERMINATE	2	TRUE	2	0.722000269288785	4		550	858	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076785	72076785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576347795	NA	P-0043929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	208	377	0	ENST00000357731.5:c.712G>A	p.Gly238Arg	p.G238R	ENST00000357731	NM_173808.2	238	Gga/Aga	5/7	0.228778136364217	4	FACETS	0.809	0.756	0.864	0.809	0.756	0.864	INDETERMINATE	2	TRUE	2	0.722000269288785	4		377	613	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426235	49426235	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	196	732	0	ENST00000301067.7:c.12253C>T	p.Gln4085Ter	p.Q4085*	ENST00000301067	NM_003482.3	4085	Cag/Tag	39/54	0.437271839197836	3	FACETS	0.675	0.624	0.728	0.225	0.208	0.243	SUBCLONAL	1	TRUE	0	0.722000269288785	3		732	1095	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027245	49027246	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	188	241	0	ENST00000267163.4:c.1813dup	p.Met605AsnfsTer48	p.M605Nfs*48	ENST00000267163	NM_000321.2	604	-/A	18/27	0.722000269288785	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.722000269288785	2		241	254	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554912	187554912	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	73	379	0	ENST00000441802.2:c.4249C>G	p.Leu1417Val	p.L1417V	ENST00000441802	NM_005245.3	1417	Ctt/Gtt	7/27	0.341698823946675	1	FACETS	0.422	0.372	0.475	0.422	0.372	0.475	INDETERMINATE	1	TRUE	0	0.722000269288785	1		379	306	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256735	16256735	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	121	390	0	ENST00000375759.3:c.4000G>A	p.Glu1334Lys	p.E1334K	ENST00000375759	NM_015001.2	1334	Gaa/Aaa	11/15	0.46320830263284	4	FACETS	0.875	0.792	0.962	0.437	0.396	0.481	CLONAL	1	TRUE	2	0.722000269288785	4		390	660	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913176	32913176	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397507737	NA	P-0043929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	119	389	0	ENST00000380152.3:c.4684C>T	p.Gln1562Ter	p.Q1562*	ENST00000380152		1562	Caa/Taa	11/27	0.684752708181694	4	FACETS	0.727	0.656	0.801	0.363	0.328	0.401	SUBCLONAL	1	TRUE	2	0.722000269288785	4		389	781	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041762	42041762	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	103	321	0	ENST00000219905.7:c.5957G>C	p.Arg1986Thr	p.R1986T	ENST00000219905	NM_001164273.1	1986	aGa/aCa	17/24	0.23881640428446	2	FACETS	0.811	0.733	0.892	0.405	0.366	0.446	INDETERMINATE	1	TRUE	0	0.722000269288785	2		321	352	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3929832	3929832	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0043929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	296	395	0	ENST00000262367.5:c.85+1G>T		p.X29_splice	ENST00000262367	NM_004380.2	29			0.23881640428446	2	FACETS	1	0.993	1	0.66	0.627	0.693	INDETERMINATE	1	TRUE	0	0.722000269288785	2		395	621	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81939032	81939032	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752906992	NA	P-0043929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	125	375	0	ENST00000359376.3:c.1387G>A	p.Asp463Asn	p.D463N	ENST00000359376	NM_002661.3	463	Gat/Aat	15/33	0.23881640428446	2	FACETS	0.64	0.582	0.701	0.32	0.291	0.351	INDETERMINATE	1	TRUE	0	0.722000269288785	2		375	541	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753000	42753017	+	inframe_deletion	In_Frame_Del	DEL	GCGGGGGCGGTGGGGCTA	GCGGGGGCGGTGGGGCTA	-	novel	NA	P-0043929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	180	628	0	ENST00000222329.4:c.1247_1264del	p.Leu416_Pro421del	p.L416_P421del	ENST00000222329	NM_006494.2	416	cTAGCCCCACCGCCCCCGCca/cca	4/4	0.154068471892878	4	FACETS	0.676	0.621	0.732	0.338	0.31	0.366	INDETERMINATE	1	TRUE	2	0.722000269288785	4		628	1271	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416416	29416416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374733353	NA	P-0043929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	187	556	0	ENST00000389048.3:c.4537G>A	p.Glu1513Lys	p.E1513K	ENST00000389048	NM_004304.4	1513	Gag/Aag	29/29	0.290887315458327	5	FACETS	0.992	0.915	1	0.198	0.183	0.215	INDETERMINATE	1	TRUE	0	0.722000269288785	5		556	1088	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538326	187538326	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	93	318	0	ENST00000441802.2:c.8908G>C	p.Glu2970Gln	p.E2970Q	ENST00000441802	NM_005245.3	2970	Gaa/Caa	11/27	0.341698823946675	1	FACETS	0.526	0.473	0.581	0.526	0.473	0.581	INDETERMINATE	1	TRUE	0	0.722000269288785	1		318	313	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39002640	39002640	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	61	190	0	ENST00000357387.3:c.389C>G	p.Ala130Gly	p.A130G	ENST00000357387	NM_152756.3	130	gCt/gGt	5/38	0.722000269288785	6	FACETS	0.656	0.565	0.754			1	SUBCLONAL	1	TRUE	NA	0.722000269288785	6		190	630	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553399	106553399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868421988	NA	P-0043929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	95	288	0	ENST00000369096.4:c.1364G>A	p.Ser455Asn	p.S455N	ENST00000369096	NM_001198.3	455	aGc/aAc	5/7	0.309914721922017	4	FACETS	0.819	0.732	0.913	0.41	0.366	0.457	INDETERMINATE	1	TRUE	2	0.722000269288785	4		288	553	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468047	50468047	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	129	400	0	ENST00000331340.3:c.1282C>G	p.Leu428Val	p.L428V	ENST00000331340	NM_006060.4	428	Ctc/Gtc	8/8	0.722000269288785	4	FACETS	0.629	0.57	0.692	0.21	0.19	0.231	SUBCLONAL	1	TRUE	1	0.722000269288785	4		400	978	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845932	151845932	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	93	447	0	ENST00000262189.6:c.13080G>A	p.Trp4360Ter	p.W4360*	ENST00000262189	NM_170606.2	4360	tgG/tgA	52/59	0.722000269288785	3	FACETS	0.495	0.44	0.554	0.248	0.22	0.277	SUBCLONAL	1	TRUE	1	0.722000269288785	3		447	708	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0043935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1549	107	66	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.808843971269367	11	FACETS	0.741	0.662	0.826	0.074	0.066	0.083	SUBCLONAL	1	TRUE	1	0.808843971269367	11		66	1656	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911072	29911072	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	138	532	1	ENST00000376809.5:c.371G>A	p.Gly124Asp	p.G124D	ENST00000376809	NM_002116.7	124	gGc/gAc	3/8	1	2	FACETS	0.432	0.393	0.473	0.432	0.393	0.473	SUBCLONAL	1	TRUE	1	0.808843971269367	2		533	790	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441147	149441147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	212	527	0	ENST00000286301.3:c.1765G>A	p.Gly589Arg	p.G589R	ENST00000286301	NM_005211.3	589	Gga/Aga	13/22	1	2	FACETS	0.726	0.677	0.777	0.726	0.677	0.777	SUBCLONAL	1	TRUE	1	0.808843971269367	2		527	722	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437457	49437458	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0043935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	287	503	0	ENST00000301067.7:c.5426_5427dup	p.Gly1810MetfsTer43	p.G1810Mfs*43	ENST00000301067	NM_003482.3	1809	-/AT	23/54	1	2	FACETS	0.951	0.899	1	0.951	0.899	1	CLONAL	1	TRUE	1	0.808843971269367	2		503	746	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828138	3828138	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0043935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	228	366	0	ENST00000262367.5:c.1987A>T	p.Lys663Ter	p.K663*	ENST00000262367	NM_004380.2	663	Aaa/Taa	10/31	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.808843971269367	2		366	541	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275345	142275345	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	237	359	0	ENST00000350721.4:c.1958C>A	p.Thr653Lys	p.T653K	ENST00000350721	NM_001184.3	653	aCa/aAa	9/47	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.808843971269367	2		359	528	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179364	56179365	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0043935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	51	139	0	ENST00000399503.3:c.3679_3680del	p.Leu1227ThrfsTer11	p.L1227Tfs*11	ENST00000399503	NM_005921.1	1226	aCT/a	15/20	1	2	FACETS	0.621	0.535	0.713	0.621	0.535	0.713	SUBCLONAL	1	TRUE	1	0.808843971269367	2		139	203	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188247	10188251	+	frameshift_variant	Frame_Shift_Del	DEL	TAACC	TAACC	-	novel	NA	P-0044026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	193	584	0	ENST00000256474.2:c.390_394del	p.Gln132Ter	p.Q132*	ENST00000256474	NM_000551.3	130	gtTAACCaa/gtaa	2/3	0.352581161623853	2	FACETS	0.96	0.894	1	0.96	0.894	1	CLONAL	2	TRUE	0	0.359740092387183	2		584	559	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584592	52584592	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	186	579	0	ENST00000394830.3:c.4421del	p.Ala1474ValfsTer15	p.A1474Vfs*15	ENST00000394830	NM_018313.4	1474	gCt/gt	29/30	0.352581161623853	2	FACETS	0.933	0.868	1	0.933	0.868	1	CLONAL	2	TRUE	0	0.359740092387183	2		579	554	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306676	41306676	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754008236	NA	P-0044062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	53	572	2	ENST00000373198.4:c.983G>A	p.Arg328His	p.R328H	ENST00000373198	NM_133170.3	328	cGc/cAc	7/32	1	2	FACETS	0.143	0.121	0.167	0.143	0.121	0.167	SUBCLONAL	1	TRUE	1	0.817005191920241	2		574	908	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577375	64577375	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1057517902	NA	P-0044062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	356	625	0	ENST00000312049.6:c.207del	p.Asp70ThrfsTer49	p.D70Tfs*49	ENST00000312049	NM_130799.2	69	ccC/cc	2/10	0.817005191920241	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.817005191920241	1		625	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0044101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	634	761	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.392080962353289	1	FACETS	1	0.991	1	1	0.998	1	CLONAL	3	TRUE	0	0.392080962353289	1		761	840	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720741	89720741	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs371387815	NA	P-0044101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	16	166	0	ENST00000371953.3:c.892C>T	p.Gln298Ter	p.Q298*	ENST00000371953	NM_000314.4	298	Caa/Taa	8/9	0.392080962353289	1	FACETS	0.381	0.283	0.498	0.381	0.283	0.498	SUBCLONAL	1	TRUE	0	0.392080962353289	1		166	172	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591109	67591109	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	137	300	0	ENST00000274335.5:c.1702C>G	p.Pro568Ala	p.P568A	ENST00000274335		568	Cca/Gca	12/15	1	2	FACETS	0.937	0.862	1	1	0.991	1	CLONAL	2	TRUE	1	0.392080962353289	2		300	373	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245518	153245518	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	187	436	0	ENST00000281708.4:c.1673C>A	p.Ser558Tyr	p.S558Y	ENST00000281708	NM_033632.3	558	tCt/tAt	11/12	0.308634011431248	1	FACETS	0.812	0.758	0.868	1	0.992	1	CLONAL	2	TRUE	0	0.392080962353289	1		436	472	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907626	111907627	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0044101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	307	295	0	ENST00000393256.3:c.400_401del	p.Met134GlufsTer4	p.M134Efs*4	ENST00000393256	NM_006538.4	134	ATg/g	3/4	0.392080962353289	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	3	TRUE	0	0.392080962353289	2		295	478	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	371	590	1	ENST00000269305.4:c.403del	p.Cys135AlafsTer35	p.C135Afs*35	ENST00000269305	NM_001126112.2	135	Tgc/gc	5/11	0.548807282793363	1	FACETS	0.974	0.927	1	0.974	0.927	1	CLONAL	1	TRUE	0	0.548807282793363	1		591	1007	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662554	227662554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866672328	NA	P-0044102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	322	597	1	ENST00000305123.5:c.901C>T	p.Arg301Cys	p.R301C	ENST00000305123	NM_005544.2	301	Cgc/Tgc	1/2	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.548807282793363	2		598	1109	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602733	55602733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555650901	NA	P-0044102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	149	384	0	ENST00000288135.5:c.2554G>A	p.Val852Ile	p.V852I	ENST00000288135	NM_000222.2	852	Gtc/Atc	18/21	1	2	FACETS	0.861	0.789	0.935	0.861	0.789	0.935	CLONAL	1	TRUE	1	0.548807282793363	2		384	631	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41999951	41999951	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	230	549	0	ENST00000219905.7:c.2214T>G	p.Asp738Glu	p.D738E	ENST00000219905	NM_001164273.1	738	gaT/gaG	6/24	1	2	FACETS	0.922	0.861	0.985	0.922	0.861	0.985	CLONAL	1	TRUE	1	0.548807282793363	2		549	909	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225572	26225572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	203	453	0	ENST00000360408.1:c.190C>T	p.Arg64Trp	p.R64W	ENST00000360408	NM_003532.2	64	Cgg/Tgg	1/1	0.195293412060661	1	FACETS	0.766	0.713	0.82	0.766	0.713	0.82	INDETERMINATE	1	TRUE	0	0.548807282793363	1		453	701	SUCCESS
MET	4233	MSKCC	GRCh37	7	116422147	116422150	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TGTA	TGTA	-	novel	NA	P-0044102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	52	321	0	ENST00000397752.3:c.3632_3632+3del		p.CM1210fs	ENST00000397752	NM_000245.2	1210	TGTAtg/tg	18/21	1	2	FACETS	0.285	0.242	0.332	0.285	0.242	0.332	SUBCLONAL	1	TRUE	1	0.548807282793363	2		321	665	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696432	47696432	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519968	NA	P-0044104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	60	636	0	ENST00000347630.2:c.391T>G	p.Trp131Gly	p.W131G	ENST00000347630	NM_001007230.1	131	Tgg/Ggg	6/11	1	2	FACETS	0.641	0.551	0.738	0.641	0.551	0.738	SUBCLONAL	1	TRUE	1	0.28	2		636	669	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403319	116403319	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	62	455	0	ENST00000397752.3:c.2580T>G	p.Ile860Met	p.I860M	ENST00000397752	NM_000245.2	860	atT/atG	11/21	1	2	FACETS	0.873	0.756	1	0.873	0.756	1	CLONAL	1	TRUE	1	0.28	2		455	507	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	131	475	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.693954013773723	2		475	307	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0044125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	49	230	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	1	2	FACETS	0.981	0.849	1	0.981	0.849	1	CLONAL	1	TRUE	1	0.693954013773723	2		230	144	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0044125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5255	9300	616	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.693954013773723	41	FACETS	0.991	0.983	0.999	0.653	0.647	0.658	CLONAL	27	TRUE	0	0.693954013773723	41		616	14555	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240690	55240690	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs772046081	NA	P-0044125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18500	1988	1187	0	ENST00000275493.2:c.1934C>G	p.Ser645Cys	p.S645C	ENST00000275493	NM_005228.3	645	tCc/tGc	17/28	0.693954013773723	41	FACETS	1	0.986	1	0.099	0.096	0.102	CLONAL	4	TRUE	0	0.693954013773723	41		1187	20488	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367315	50367315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751092583	NA	P-0044125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	197	510	0	ENST00000331340.3:c.122C>T	p.Ser41Leu	p.S41L	ENST00000331340	NM_006060.4	41	tCg/tTg	3/8	0.142508644880939	3	FACETS	1	0.991	1	0.478	0.446	0.511	INDETERMINATE	1	TRUE	0	0.693954013773723	3		510	533	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439614	51439614	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	116	450	4	ENST00000262662.1:c.179G>T	p.Gly60Val	p.G60V	ENST00000262662		60	gGt/gTt	4/4	1	2	FACETS	0.866	0.788	0.947	0.866	0.788	0.947	CLONAL	1	TRUE	1	0.693954013773723	2		454	386	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0044130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	65	348	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.485130681074466	2		348	208	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913492	NA	P-0044130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	71	645	0	ENST00000286548.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000286548	NM_002072.3	209	cAa/cTa	5/7	1	2	FACETS	0.944	0.831	1	0.944	0.831	1	CLONAL	1	TRUE	1	0.485130681074466	2		645	310	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567840	226567840	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	68	639	0	ENST00000366794.5:c.1326G>T	p.Lys442Asn	p.K442N	ENST00000366794	NM_001618.3	442	aaG/aaT	10/23	1	2	FACETS	0.663	0.579	0.753	0.663	0.579	0.753	SUBCLONAL	1	TRUE	1	0.485130681074466	2		639	423	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645424	67645424	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	21	519	0	ENST00000264010.4:c.689A>G	p.Glu230Gly	p.E230G	ENST00000264010	NM_006565.3	230	gAa/gGa	3/12	1	2	FACETS	0.328	0.253	0.415	0.328	0.253	0.415	SUBCLONAL	1	TRUE	1	0.485130681074466	2		519	264	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	397	289	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.696850355909688	2		289	804	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28934577	NA	P-0044135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	585	663	1	ENST00000269305.4:c.770T>C	p.Leu257Pro	p.L257P	ENST00000269305	NM_001126112.2	257	cTg/cCg	7/11	0.61913898244473	2	FACETS	0.857	0.83	0.884	0.857	0.83	0.884	CLONAL	2	TRUE	0	0.696850355909688	2		664	979	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0044138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	205	479	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.855953356092706	1	FACETS	0.961	0.918	1	0.961	0.918	1	CLONAL	1	TRUE	0	0.855953356092706	1		479	285	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777838	3777838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863223334	NA	P-0044138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	695	1179	1	ENST00000262367.5:c.7210G>A	p.Glu2404Lys	p.E2404K	ENST00000262367	NM_004380.2	2404	Gaa/Aaa	31/31	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.855953356092706	2		1180	1563	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221800	55221800	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199796955	NA	P-0044138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	428	870	0	ENST00000275493.2:c.844G>A	p.Glu282Lys	p.E282K	ENST00000275493	NM_005228.3	282	Gag/Aag	7/28	0.217335043692156	1	FACETS	0.542	0.518	0.566	0.542	0.518	0.566	INDETERMINATE	1	TRUE	0	0.855953356092706	1		870	1056	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771344	68771344	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	239	350	0	ENST00000261769.5:c.26C>G	p.Ser9Trp	p.S9W	ENST00000261769	NM_004360.3	9	tCg/tGg	1/16	0.855953356092706	3	FACETS	1	0.972	1			1	CLONAL	1	TRUE	NA	0.855953356092706	3		350	750	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149658	202149658	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	285	566	0	ENST00000358485.4:c.1099G>T	p.Asp367Tyr	p.D367Y	ENST00000358485	NM_001080125.1	367	Gac/Tac	8/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.855953356092706	2		566	645	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380683	118380683	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1450486073	NA	P-0044138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	230	418	0	ENST00000534358.1:c.10921G>A	p.Glu3641Lys	p.E3641K	ENST00000534358	NM_005933.3	3641	Gag/Aag	30/36	1	2	FACETS	0.995	0.936	1	0.995	0.936	1	CLONAL	1	TRUE	1	0.855953356092706	2		418	540	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404530	70404530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	256	543	0	ENST00000373644.4:c.2044G>A	p.Glu682Lys	p.E682K	ENST00000373644	NM_030625.2	682	Gaa/Aaa	4/12	1	2	FACETS	0.938	0.884	0.992	0.938	0.884	0.992	CLONAL	1	TRUE	1	0.855953356092706	2		543	638	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196788	123196788	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	127	572	0	ENST00000218089.9:c.1675G>A	p.Asp559Asn	p.D559N	ENST00000218089	NM_001042749.1	559	Gat/Aat	18/35	0.13449860634308	6	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.855953356092706	6		572	574	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325870	65325870	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	325	623	0	ENST00000342505.4:c.1252G>C	p.Asp418His	p.D418H	ENST00000342505	NM_002227.2	418	Gat/Cat	9/25	0.855953356092706	2	FACETS	0.966	0.918	1	0.483	0.459	0.508	CLONAL	1	TRUE	0	0.855953356092706	2		623	786	SUCCESS
CBL	867	MSKCC	GRCh37	11	119145650	119145650	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	230	328	1	ENST00000264033.4:c.856C>A	p.His286Asn	p.H286N	ENST00000264033	NM_005188.3	286	Cac/Aac	5/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.855953356092706	2		329	524	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431445	49431445	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	503	829	0	ENST00000301067.7:c.9694G>T	p.Glu3232Ter	p.E3232*	ENST00000301067	NM_003482.3	3232	Gag/Tag	34/54	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.855953356092706	2		829	1166	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445359	49445359	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	626	1152	3	ENST00000301067.7:c.2107G>T	p.Glu703Ter	p.E703*	ENST00000301067	NM_003482.3	703	Gag/Tag	10/54	1	2	FACETS	0.985	0.949	1	0.985	0.949	1	CLONAL	1	TRUE	1	0.855953356092706	2		1155	1485	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136289	202136289	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	285	563	0	ENST00000358485.4:c.533C>G	p.Ser178Cys	p.S178C	ENST00000358485	NM_001080125.1	178	tCt/tGt	3/9	1	2	FACETS	0.853	0.805	0.901	0.853	0.805	0.901	CLONAL	1	TRUE	1	0.855953356092706	2		563	781	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281833	142281833	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	240	488	0	ENST00000350721.4:c.411G>C	p.Lys137Asn	p.K137N	ENST00000350721	NM_001184.3	137	aaG/aaC	4/47	1	2	FACETS	0.913	0.859	0.968	0.913	0.859	0.968	CLONAL	1	TRUE	1	0.855953356092706	2		488	614	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288363	33288363	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	350	519	0	ENST00000374542.5:c.1045G>C	p.Asp349His	p.D349H	ENST00000374542	NM_001141970.1	349	Gac/Cac	4/8	0.855953356092706	2	FACETS	1	0.982	1	0.529	0.504	0.554	CLONAL	1	TRUE	0	0.855953356092706	2		519	773	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148507494	148507494	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	219	356	0	ENST00000320356.2:c.1960G>C	p.Asp654His	p.D654H	ENST00000320356	NM_004456.4	654	Gat/Cat	17/20	1	2	FACETS	0.96	0.901	1	0.96	0.901	1	CLONAL	1	TRUE	1	0.855953356092706	2		356	533	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220567	123220567	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0044138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	366	584	2	ENST00000218089.9:c.3224C>G	p.Ser1075Ter	p.S1075*	ENST00000218089	NM_001042749.1	1075	tCa/tGa	30/35	0.13449860634308	6	FACETS	1	0.95	1			1	INDETERMINATE	2	TRUE	NA	0.855953356092706	6		586	1158	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0044150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	95	487	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.698738529641416	1	FACETS	0.838	0.763	0.914	0.838	0.763	0.914	CLONAL	1	TRUE	0	0.698738529641416	1		487	211	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954198	48954198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123331	NA	P-0044150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	14	157	0	ENST00000267163.4:c.1399C>T	p.Arg467Ter	p.R467*	ENST00000267163	NM_000321.2	467	Cga/Tga	15/27	0.671601775308113	4	FACETS	0.314	0.227	0.419	0.105	0.075	0.14	SUBCLONAL	1	TRUE	1	0.698738529641416	4		157	217	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0044150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	238	584	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.698738529641416	1	FACETS	0.879	0.83	0.929	0.879	0.83	0.929	CLONAL	1	TRUE	0	0.698738529641416	1		584	504	SUCCESS
APC	324	MSKCC	GRCh37	5	112175273	112175273	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123121	NA	P-0044150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	118	280	0	ENST00000257430.4:c.3982C>T	p.Gln1328Ter	p.Q1328*	ENST00000257430	NM_000038.5	1328	Cag/Tag	16/16	0.694391115429336	2	FACETS	0.853	0.793	0.911	0.853	0.793	0.911	CLONAL	2	TRUE	0	0.698738529641416	2		280	198	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154760	2154760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143785521	NA	P-0044150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	263	916	0	ENST00000434045.2:c.461C>T	p.Pro154Leu	p.P154L	ENST00000434045	NM_001127598.1	154	cCg/cTg	4/5	1	2	FACETS	0.984	0.926	1	0.984	0.926	1	CLONAL	1	TRUE	1	0.698738529641416	2		916	765	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829907	72829907	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	172	724	0	ENST00000268489.5:c.6674A>C	p.Asp2225Ala	p.D2225A	ENST00000268489	NM_006885.3	2225	gAc/gCc	9/10	1	2	FACETS	0.71	0.656	0.767	0.71	0.656	0.767	SUBCLONAL	1	TRUE	1	0.698738529641416	2		724	693	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56415027	56415027	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	90	393	0	ENST00000348428.3:c.2428G>A	p.Glu810Lys	p.E810K	ENST00000348428	NM_006785.3	810	Gaa/Aaa	17/17	0.698738529641416	1	FACETS	0.86	0.781	0.939	0.86	0.781	0.939	CLONAL	1	TRUE	0	0.698738529641416	1		393	195	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	18	289	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.989	0.745	1	0.989	0.745	1	CLONAL	1	TRUE	1	0.14	2		289	260	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0044183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1456	127	853	2	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.14	2		855	1583	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350505	15350505	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540369634	NA	P-0044183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	92	683	1	ENST00000263377.2:c.3410C>T	p.Pro1137Leu	p.P1137L	ENST00000263377	NM_058243.2	1137	cCg/cTg	16/20	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.14	2		684	1270	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843609	3843609	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	34	347	0	ENST00000262367.5:c.994G>T	p.Val332Leu	p.V332L	ENST00000262367	NM_004380.2	332	Gtg/Ttg	4/31	1	2	FACETS	0.979	0.799	1	0.979	0.799	1	CLONAL	1	TRUE	1	0.14	2		347	496	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	48	475	0				ENST00000310581	NM_198253.2	-/1132			0.316456216177848	0	FACETS	0.703	0.6	0.815			1	SUBCLONAL	1	TRUE	0	0.355035461210441	0		475	248	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0044204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	186	665	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.158397294548951	4	FACETS	1	0.979	1			1	INDETERMINATE	2	TRUE	NA	0.355035461210441	4		665	620	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545060	41545060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	66	399	1	ENST00000263253.7:c.2260C>T	p.Arg754Cys	p.R754C	ENST00000263253	NM_001429.3	754	Cgt/Tgt	13/31	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.355035461210441	2		400	368	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431898	49431898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	107	796	1	ENST00000301067.7:c.9241G>A	p.Glu3081Lys	p.E3081K	ENST00000301067	NM_003482.3	3081	Gaa/Aaa	34/54	0.181698022881402	3	FACETS	0.998	0.896	1	0.499	0.448	0.553	INDETERMINATE	1	TRUE	1	0.355035461210441	3		797	711	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94963999	94963999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318902387	NA	P-0044204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	66	205	2	ENST00000536441.1:c.26C>T	p.Ser9Leu	p.S9L	ENST00000536441	NM_144665.3	9	tCg/tTg	1/10	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.355035461210441	2		207	337	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045806	180045806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1051985552	NA	P-0044204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	97	808	0	ENST00000261937.6:c.2965G>A	p.Glu989Lys	p.E989K	ENST00000261937	NM_182925.4	989	Gag/Aag	21/30	0.325102431243886	1	FACETS	0.713	0.637	0.795	0.713	0.637	0.795	SUBCLONAL	1	TRUE	0	0.355035461210441	1		808	630	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984343	201984344	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	141	581	0	ENST00000359651.3:c.1009dup	p.Tyr337LeufsTer134	p.Y337Lfs*134	ENST00000359651		336	-/T	8/8	0.355035461210441	3	FACETS	1	0.974	1	0.589	0.537	0.644	CLONAL	1	TRUE	1	0.355035461210441	3		581	794	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650645	18650645	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	28	328	0	ENST00000266497.5:c.2856G>C	p.Met952Ile	p.M952I	ENST00000266497		952	atG/atC	20/31	0.103033260638149	0	FACETS	0.524	0.422	0.639			1	INDETERMINATE	1	TRUE	0	0.355035461210441	0		328	194	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431430	49431430	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	108	655	0	ENST00000301067.7:c.9709G>C	p.Glu3237Gln	p.E3237Q	ENST00000301067	NM_003482.3	3237	Gag/Cag	34/54	0.181698022881402	3	FACETS	1	0.962	1	0.573	0.515	0.634	INDETERMINATE	1	TRUE	1	0.355035461210441	3		655	625	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907237	32907237	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	43	364	0	ENST00000380152.3:c.1622A>G	p.Glu541Gly	p.E541G	ENST00000380152		541	gAa/gGa	10/27	1	2	FACETS	0.997	0.841	1	0.997	0.841	1	CLONAL	1	TRUE	1	0.355035461210441	2		364	243	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68290342	68290342	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs761684336	NA	P-0044204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	36	272	0	ENST00000487270.1:c.82C>G	p.Gln28Glu	p.Q28E	ENST00000487270	NM_133509.3	28	Cag/Gag	2/11	1	2	FACETS	0.994	0.825	1	0.994	0.825	1	CLONAL	1	TRUE	1	0.355035461210441	2		272	204	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574334	95574334	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1182299033	NA	P-0044204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	25	247	0	ENST00000393063.1:c.2533T>G	p.Leu845Val	p.L845V	ENST00000393063	NM_030621.3	845	Ttg/Gtg	17/28	1	2	FACETS	0.897	0.714	1	0.897	0.714	1	CLONAL	1	TRUE	1	0.355035461210441	2		247	157	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41560080	41560080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1032317413	NA	P-0044204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	49	319	0	ENST00000263253.7:c.3752G>A	p.Gly1251Glu	p.G1251E	ENST00000263253	NM_001429.3	1251	gGa/gAa	22/31	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.355035461210441	2		319	260	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149245664	149245664	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	107	665	0	ENST00000360632.3:c.864G>C	p.Met288Ile	p.M288I	ENST00000360632	NM_015472.4	288	atG/atC	5/7	1	2	FACETS	0.933	0.838	1	0.933	0.838	1	CLONAL	1	TRUE	1	0.355035461210441	2		665	646	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176715865	176715865	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	87	597	0	ENST00000439151.2:c.6197G>C	p.Gly2066Ala	p.G2066A	ENST00000439151	NM_022455.4	2066	gGa/gCa	21/23	0.158397294548951	4	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.355035461210441	4		597	513	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983005	149983005	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	33	412	0	ENST00000253339.5:c.3253G>C	p.Asp1085His	p.D1085H	ENST00000253339		1085	Gat/Cat	7/7	0.355035461210441	3	FACETS	1	0.861	1	0.529	0.434	0.634	CLONAL	1	TRUE	1	0.355035461210441	3		412	207	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946376	2946376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866680537	NA	P-0044204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	143	895	0	ENST00000396946.4:c.3361G>A	p.Glu1121Lys	p.E1121K	ENST00000396946	NM_032415.4	1121	Gaa/Aaa	25/25	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.355035461210441	2		895	725	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797210	135797210	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	20	193	0	ENST00000298552.3:c.659T>A	p.Val220Asp	p.V220D	ENST00000298552	NM_001162426.1	220	gTc/gAc	7/23	0.355033579284965	1	FACETS	0.76	0.588	0.954	0.76	0.588	0.954	CLONAL	1	TRUE	0	0.355035461210441	1		193	122	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0044221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	296	392	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.491162753489113	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.491162753489113	2		392	595	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94908684	94908684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760970492	NA	P-0044221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	77	508	0	ENST00000536441.1:c.1370G>A	p.Arg457Gln	p.R457Q	ENST00000536441	NM_144665.3	457	cGg/cAg	9/10	1	2	FACETS	0.652	0.574	0.735	0.652	0.574	0.735	SUBCLONAL	1	TRUE	1	0.491162753489113	2		508	481	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665219	138665219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	208	796	0	ENST00000330315.3:c.346C>T	p.Pro116Ser	p.P116S	ENST00000330315	NM_023067.3	116	Ccg/Tcg	1/1	0.436912096587841	3	FACETS	1	0.985	1	0.608	0.565	0.652	CLONAL	1	TRUE	1	0.491162753489113	3		796	868	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332830	152332830	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3487	208	484	0	ENST00000206249.3:c.1136T>C	p.Leu379Pro	p.L379P	ENST00000206249	NM_000125.3	379	cTa/cCa	5/8	0.491162753489113	12	FACETS	0.792	0.73	0.857			1	SUBCLONAL	1	TRUE	NA	0.491162753489113	12		484	3695	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356342	70356342	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	99	673	0	ENST00000374080.3:c.5237C>A	p.Pro1746Gln	p.P1746Q	ENST00000374080		1746	cCa/cAa	37/45	1	2	FACETS	0.678	0.606	0.753	0.678	0.606	0.753	SUBCLONAL	1	TRUE	1	0.491162753489113	2		673	595	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0044225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	120	810	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.23097250496859	2		810	752	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0044225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	75	351	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	0.81	0.713	0.913	1	0.979	1	CLONAL	2	TRUE	1	0.23097250496859	2		351	401	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057964	27057965	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0044225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	97	529	0	ENST00000324856.7:c.1674_1675del	p.Pro559LeufsTer63	p.P559Lfs*63	ENST00000324856	NM_006015.4	558	TCt/t	3/20	1	2	FACETS	0.992	0.883	1	0.992	0.883	1	CLONAL	1	TRUE	1	0.23097250496859	2		529	847	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0044254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	14	399	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	1	2	FACETS	0.749	0.542	0.999	0.749	0.542	0.999	CLONAL	1	TRUE	1	0.17	2		399	220	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0044254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	12	616	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.947	0.669	1	0.947	0.669	1	CLONAL	1	TRUE	1	0.17	2		616	149	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0044254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	28	550	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	1	2	FACETS	0.707	0.564	0.87	0.707	0.564	0.87	SUBCLONAL	1	TRUE	1	0.17	2		550	466	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285792	46285792	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0044254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	13	256	0	ENST00000334344.6:c.5062-2A>G		p.X1688_splice	ENST00000334344	NM_152641.2	1688			0.226474415516466	3	FACETS	1	0.72	1	0.503	0.36	0.676	CLONAL	1	TRUE	1	0.17	3		256	165	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562482	21562483	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGGCG	rs550642106	NA	P-0044288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	25	142	7	ENST00000382592.4:c.1431_1436dup	p.Pro479_Ala480dup	p.P479_A480dup	ENST00000382592	NM_014572.2	479	ccg/ccCGCCCCg	4/8	0.925612294069641	2	FACETS	0.363	0.289	0.445	0.181	0.144	0.223	SUBCLONAL	1	TRUE	0	0.925612294069641	2		149	149	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0044288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	455	569	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.925612294069641	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.925612294069641	1		569	483	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857785	9857785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555482324	NA	P-0044288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	60	636	1	ENST00000330684.3:c.3616C>T	p.Arg1206Ter	p.R1206*	ENST00000330684	NM_001134407.1	1206	Cga/Tga	13/13	0.177421328330138	2	FACETS	0.225	0.193	0.259	0.112	0.096	0.13	INDETERMINATE	1	TRUE	0	0.925612294069641	2		637	577	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142885	30142885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766999851	NA	P-0044288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	427	598	2	ENST00000389048.3:c.641G>A	p.Arg214His	p.R214H	ENST00000389048	NM_004304.4	214	cGc/cAc	1/29	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.925612294069641	2		600	889	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829281	72829281	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	704	577	1	ENST00000268489.5:c.7300G>T	p.Glu2434Ter	p.E2434*	ENST00000268489	NM_006885.3	2434	Gaa/Taa	9/10	0.280906850595698	6	FACETS	1	0.973	1			1	INDETERMINATE	3	TRUE	NA	0.925612294069641	6		578	1437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28934577	NA	P-0044294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	252	663	1	ENST00000269305.4:c.770T>C	p.Leu257Pro	p.L257P	ENST00000269305	NM_001126112.2	257	cTg/cCg	7/11	0.682079927297836	1	FACETS	0.981	0.935	1	0.981	0.935	1	CLONAL	1	TRUE	0	0.776246602261771	1		664	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	208	529	0	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	0.347760140412608	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.347760140412608	2		529	581	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149728	202149728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	203	512	0	ENST00000358485.4:c.1173del	p.Ile392SerfsTer4	p.I392Sfs*4	ENST00000358485	NM_001080125.1	390	gCc/gc	8/9	0.290218012102728	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.347760140412608	3		512	641	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199469672	NA	P-0044305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	40	396	0	ENST00000374080.3:c.131G>T	p.Gly44Val	p.G44V	ENST00000374080		44	gGt/gTt	2/45	0.138439982251112	4	FACETS	0.351	0.29	0.419	0.175	0.145	0.21	INDETERMINATE	1	TRUE	2	0.347760140412608	4		396	884	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	190	475	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.813684212026949	2		475	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0044308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	351	553	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.767993767349741	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.813684212026949	1		553	469	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0044308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	239	61	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.78854360925113	3	FACETS	0.902	0.854	0.95	0.902	0.854	0.95	CLONAL	2	TRUE	1	0.813684212026949	3		61	458	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0044308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	349	566	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.984	0.936	1	0.984	0.936	1	CLONAL	1	TRUE	1	0.813684212026949	2		566	872	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175857	24175859	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs875989800	NA	P-0044308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	265	534	0	ENST00000263121.7:c.1091_1093del	p.Lys364del	p.K364del	ENST00000263121	NM_003073.3	362	gAGAag/gag	8/9	1	2	FACETS	0.892	0.841	0.945	0.892	0.841	0.945	CLONAL	1	TRUE	1	0.813684212026949	2		534	730	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652262	36652263	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0044308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	323	589	0	ENST00000244741.5:c.387dup	p.Ser130ValfsTer67	p.S130Vfs*67	ENST00000244741	NM_000389.4	128	-/G	2/3	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.813684212026949	2		589	789	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907677	111907677	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	238	375	0	ENST00000393256.3:c.451G>C	p.Glu151Gln	p.E151Q	ENST00000393256	NM_006538.4	151	Gag/Cag	3/4	0.813684212026949	1	FACETS	0.951	0.907	0.993	0.951	0.907	0.993	CLONAL	1	TRUE	0	0.813684212026949	1		375	365	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003545	42003545	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	168	310	0	ENST00000219905.7:c.3082C>T	p.Gln1028Ter	p.Q1028*	ENST00000219905	NM_001164273.1	1028	Caa/Taa	8/24	1	2	FACETS	0.871	0.808	0.936	0.871	0.808	0.936	CLONAL	1	TRUE	1	0.813684212026949	2		310	474	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087512	27087513	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0044308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	383	648	0	ENST00000324856.7:c.2090dup	p.Ser698ValfsTer119	p.S698Vfs*119	ENST00000324856	NM_006015.4	696	tcc/tCcc	5/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.813684212026949	2		648	937	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156203	119156203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	285	491	0	ENST00000264033.4:c.1868C>T	p.Ser623Leu	p.S623L	ENST00000264033	NM_005188.3	623	tCa/tTa	11/16	1	2	FACETS	0.96	0.907	1	0.96	0.907	1	CLONAL	1	TRUE	1	0.813684212026949	2		491	730	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964230	28964230	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	112	263	0	ENST00000282397.4:c.1672G>C	p.Gly558Arg	p.G558R	ENST00000282397	NM_002019.4	558	Ggg/Cgg	13/30	1	2	FACETS	0.9	0.821	0.981	0.9	0.821	0.981	CLONAL	1	TRUE	1	0.813684212026949	2		263	306	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039505	49039505	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0044308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	168	424	0	ENST00000267163.4:c.2489+1G>T		p.X830_splice	ENST00000267163	NM_000321.2	830			1	2	FACETS	0.938	0.872	1	0.938	0.872	1	CLONAL	1	TRUE	1	0.813684212026949	2		424	440	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462679	40462679	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	226	451	0	ENST00000345506.4:c.2377C>G	p.Leu793Val	p.L793V	ENST00000345506	NM_003152.3	793	Ctc/Gtc	20/20	1	2	FACETS	0.859	0.804	0.914	0.859	0.804	0.914	CLONAL	1	TRUE	1	0.813684212026949	2		451	647	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554505	63554505	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	102	589	0	ENST00000307078.5:c.234G>T	p.Trp78Cys	p.W78C	ENST00000307078	NM_004655.3	78	tgG/tgT	2/11	1	2	FACETS	0.301	0.269	0.336	0.301	0.269	0.336	SUBCLONAL	1	TRUE	1	0.813684212026949	2		589	832	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792762	33792762	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	69	77	0	ENST00000498907.2:c.559C>A	p.Pro187Thr	p.P187T	ENST00000498907	NM_004364.3	187	Ccg/Acg	1/1	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.813684212026949	2		77	148	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105717	27105723	+	frameshift_variant	Frame_Shift_Del	DEL	AGAAGAA	AGAAGAA	GAAGAC	novel	NA	P-0044309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	141	331	0	ENST00000324856.7:c.5328_5334delinsGAAGAC	p.Glu1777LysfsTer5	p.E1777Kfs*5	ENST00000324856	NM_006015.4	1776	gaAGAAGAA/gaGAAGAC	20/20	1	2	FACETS	0.903	0.83	0.977	0.903	0.83	0.977	CLONAL	1	TRUE	1	0.738324496588636	2		331	423	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0044309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	202	396	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.786	0.732	0.842	0.786	0.732	0.842	SUBCLONAL	1	TRUE	1	0.738324496588636	2		397	696	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653820	89653821	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	165	309	0	ENST00000371953.3:c.121dup	p.Arg41LysfsTer3	p.R41Kfs*3	ENST00000371953	NM_000314.4	40	gaa/gAaa	2/9	0.679551702043406	3	FACETS	0.809	0.754	0.866	0.809	0.754	0.866	CLONAL	2	TRUE	1	0.738324496588636	3		309	378	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725003	89725045	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTCATATTTGTGGGTTTTCATTTTAAATTTTCTTTCTCTAGGT	GTCATATTTGTGGGTTTTCATTTTAAATTTTCTTTCTCTAGGT	-	novel	NA	P-0044309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	17	159	0	ENST00000371953.3:c.1027-40_1029del		p.X343_splice	ENST00000371953	NM_000314.4	343		9/9	0.679551702043406	3	FACETS	0.432	0.325	0.557	0.216	0.162	0.279	SUBCLONAL	1	TRUE	1	0.738324496588636	3		159	146	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936196	71936197	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0044309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	167	230	0	ENST00000298229.2:c.168_169delinsAA	p.Phe56_Ala57delinsLeuThr	p.F56_A57delinsLT	ENST00000298229	NM_001567.3	56	ttCGcg/ttAAcg	1/28	1	2	FACETS	0.854	0.79	0.919	0.854	0.79	0.919	CLONAL	1	TRUE	1	0.738324496588636	2		230	530	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138453	2138453	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375075952	NA	P-0044309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	288	465	0	ENST00000219476.3:c.5266G>A	p.Glu1756Lys	p.E1756K	ENST00000219476	NM_000548.3	1756	Gag/Aag	42/42	1	2	FACETS	0.883	0.832	0.934	0.883	0.832	0.934	CLONAL	1	TRUE	1	0.738324496588636	2		465	884	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0044309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	159	250	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.84	0.775	0.906	0.84	0.775	0.906	CLONAL	1	TRUE	1	0.738324496588636	2		250	513	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994138	21994138	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	85	476	0	ENST00000579755.1:c.193G>A	p.Gly65Ser	p.G65S	ENST00000579755		65	Ggt/Agt	1/3	0.231677819713217		FACETS		0.684	0.867				SUBCLONAL	1	TRUE	0	0.331856287170842	1		476	553	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675706	30675706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	92	650	1	ENST00000376406.3:c.2650G>A	p.Glu884Lys	p.E884K	ENST00000376406	NM_014641.2	884	Gaa/Aaa	8/15	1	2	FACETS	0.772	0.686	0.864	0.772	0.686	0.864	SUBCLONAL	1	TRUE	1	0.331856287170842	2		651	718	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987269	2987269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	49	480	0	ENST00000396946.4:c.160G>A	p.Glu54Lys	p.E54K	ENST00000396946	NM_032415.4	54	Gag/Aag	3/25	1	2	FACETS	0.541	0.458	0.632	0.541	0.458	0.632	SUBCLONAL	1	TRUE	1	0.331856287170842	2		480	546	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842753	68842760	+	splice_donor_variant,intron_variant	Splice_Site	DEL	TAAGTATC	TAAGTATC	-	novel	NA	P-0044310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	54	326	0	ENST00000261769.5:c.687+3_687+10del		p.X229_splice	ENST00000261769	NM_004360.3	229			0.331856287170842	1	FACETS	0.998	0.86	1	0.998	0.86	1	CLONAL	1	TRUE	0	0.331856287170842	1		326	272	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0044311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	360	575	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	0.952	0.906	0.998			1	INDETERMINATE	2	TRUE	NA	0.428961359896199	2		575	882	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357432	70357432	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	174	581	0	ENST00000374080.3:c.5773T>A	p.Ser1925Thr	p.S1925T	ENST00000374080		1925	Tca/Aca	40/45	1	2	FACETS	0.962	0.887	1	0.962	0.887	1	CLONAL	1	TRUE	1	0.428961359896199	2		581	843	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199382	11199383	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	69	481	0	ENST00000361445.4:c.5108dup	p.Asn1703LysfsTer33	p.N1703Kfs*33	ENST00000361445	NM_004958.3	1703	aac/aaAc	36/58	1	2	FACETS	0.335	0.291	0.382	0.335	0.291	0.382	SUBCLONAL	1	TRUE	1	0.598581272369127	2		481	689	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298651	11298651	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	108	494	0	ENST00000361445.4:c.1810C>A	p.Arg604Ser	p.R604S	ENST00000361445	NM_004958.3	604	Cgc/Agc	12/58	1	2	FACETS	0.427	0.383	0.474	0.427	0.383	0.474	SUBCLONAL	1	TRUE	1	0.598581272369127	2		494	845	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023897	27023897	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	26	102	0	ENST00000324856.7:c.1003C>T	p.Gln335Ter	p.Q335*	ENST00000324856	NM_006015.4	335	Cag/Tag	1/20	1	2	FACETS	0.505	0.403	0.619	0.505	0.403	0.619	SUBCLONAL	1	TRUE	1	0.598581272369127	2		102	172	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	132	584	2	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.596	0.541	0.653	0.596	0.541	0.653	SUBCLONAL	1	TRUE	1	0.598581272369127	2		586	740	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	73	475	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.44	0.385	0.499	0.44	0.385	0.499	SUBCLONAL	1	TRUE	1	0.598581272369127	2		476	554	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330611	65330611	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	88	340	0	ENST00000342505.4:c.1035del	p.Lys345AsnfsTer32	p.K345Nfs*32	ENST00000342505	NM_002227.2	345	aaA/aa	8/25	1	2	FACETS	0.525	0.466	0.588	0.525	0.466	0.588	SUBCLONAL	1	TRUE	1	0.598581272369127	2		340	560	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115279377	115279377	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	16	265	0	ENST00000438362.2:c.638+2T>C		p.X213_splice	ENST00000438362	NM_001242891.1	213			1	2	FACETS	0.182	0.134	0.24	0.182	0.134	0.24	SUBCLONAL	1	TRUE	1	0.598581272369127	2		265	293	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163309260	163309260	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	17	257	0	ENST00000271452.3:c.604del	p.Thr202ArgfsTer2	p.T202Rfs*2	ENST00000271452	NM_145697.2	200	cAa/ca	8/14	0.5544502621403	3	FACETS	0.217	0.161	0.283	0.109	0.08	0.142	SUBCLONAL	1	TRUE	1	0.598581272369127	3		257	340	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243801030	243801030	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	33	160	0	ENST00000263826.5:c.444del	p.Phe148LeufsTer4	p.F148Lfs*4	ENST00000263826	NM_005465.4	148	ttT/tt	5/13	0.5544502621403	3	FACETS	0.345	0.281	0.418	0.173	0.14	0.209	SUBCLONAL	1	TRUE	1	0.598581272369127	3		160	415	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653782	89653783	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	TC	rs786203477	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	51	154	0	ENST00000371953.3:c.81_82insCT	p.Ile28LeufsTer27	p.I28Lfs*27	ENST00000371953	NM_000314.4	27	tat/taTCt	2/9	0.340062823905174	2	FACETS	0.888	0.766	1	0.444	0.383	0.509	INDETERMINATE	1	TRUE	0	0.598581272369127	2		154	192	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112764451	112764451	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	42	423	0	ENST00000369452.4:c.1063del	p.Ser355LeufsTer27	p.S355Lfs*27	ENST00000369452	NM_007373.3	354	Ttt/tt	5/9	0.340062823905174	2	FACETS	0.235	0.195	0.279	0.117	0.097	0.14	INDETERMINATE	1	TRUE	0	0.598581272369127	2		423	598	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	61	573	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.340062823905174	2	FACETS	0.443	0.383	0.508	0.222	0.191	0.254	INDETERMINATE	1	TRUE	0	0.598581272369127	2		573	460	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625249	69625249	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781935233	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	144	638	0	ENST00000334134.2:c.544G>A	p.Val182Met	p.V182M	ENST00000334134	NM_005247.2	182	Gtg/Atg	3/3	1	2	FACETS	0.525	0.478	0.574	0.525	0.478	0.574	SUBCLONAL	1	TRUE	1	0.598581272369127	2		638	917	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	219	656	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.85	0.792	0.91	0.85	0.792	0.91	CLONAL	1	TRUE	1	0.598581272369127	2		657	861	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981721	101981721	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555075353	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	40	287	1	ENST00000282441.5:c.147del	p.Ala50ProfsTer24	p.A50Pfs*24	ENST00000282441	NM_001130145.2	48	Ccc/cc	1/9	1	2	FACETS	0.406	0.338	0.481	0.406	0.338	0.481	SUBCLONAL	1	TRUE	1	0.598581272369127	2		288	329	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172510	108172510	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs876660289	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	34	197	1	ENST00000278616.4:c.5318del	p.Lys1773SerfsTer3	p.K1773Sfs*3	ENST00000278616	NM_000051.3	1771	agA/ag	35/63	1	2	FACETS	0.592	0.488	0.706	0.592	0.488	0.706	SUBCLONAL	1	TRUE	1	0.598581272369127	2		198	192	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003414	42003414	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269317379	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	102	456	1	ENST00000219905.7:c.2951G>A	p.Arg984His	p.R984H	ENST00000219905	NM_001164273.1	984	cGc/cAc	8/24	1	2	FACETS	0.424	0.379	0.472	0.424	0.379	0.472	SUBCLONAL	1	TRUE	1	0.598581272369127	2		457	804	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128018	30128018	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	108	600	0	ENST00000263025.4:c.1111T>C	p.Phe371Leu	p.F371L	ENST00000263025	NM_002746.2	371	Ttc/Ctc	8/9	1	2	FACETS	0.458	0.411	0.508	0.458	0.411	0.508	SUBCLONAL	1	TRUE	1	0.598581272369127	2		600	788	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644874	67644874	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	117	524	0	ENST00000264010.4:c.143del	p.Gly48ValfsTer14	p.G48Vfs*14	ENST00000264010	NM_006565.3	47	Ggg/gg	3/12	1	2	FACETS	0.504	0.454	0.556	0.504	0.454	0.556	SUBCLONAL	1	TRUE	1	0.598581272369127	2		524	776	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577123	7577123	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876660333	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	21	558	0	ENST00000269305.4:c.815T>C	p.Val272Ala	p.V272A	ENST00000269305	NM_001126112.2	272	gTg/gCg	8/11	1	2	FACETS	0.07	0.053	0.09	0.07	0.053	0.09	SUBCLONAL	1	TRUE	1	0.598581272369127	2		558	1003	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	164	393	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.581	0.533	0.631	0.581	0.533	0.631	SUBCLONAL	1	TRUE	1	0.598581272369127	2		393	943	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556991	29556991	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	20	104	0	ENST00000356175.3:c.2989A>G	p.Arg997Gly	p.R997G	ENST00000356175	NM_000267.3	997	Agg/Ggg	22/57	1	2	FACETS	0.548	0.424	0.688	0.548	0.424	0.688	SUBCLONAL	1	TRUE	1	0.598581272369127	2		104	122	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212058	5212058	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	120	610	0	ENST00000357368.4:c.4973C>T	p.Ala1658Val	p.A1658V	ENST00000357368	NM_002850.3	1658	gCa/gTa	32/38	1	2	FACETS	0.476	0.43	0.525	0.476	0.43	0.525	SUBCLONAL	1	TRUE	1	0.598581272369127	2		610	842	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	135	644	3	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.433	0.393	0.476	0.433	0.393	0.476	SUBCLONAL	1	TRUE	1	0.598581272369127	2		647	1041	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229342	36229342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	116	528	0	ENST00000222270.7:c.8032C>T	p.Arg2678Cys	p.R2678C	ENST00000222270	NM_014727.1	2678	Cgc/Tgc	37/37	1	2	FACETS	0.495	0.446	0.547	0.495	0.446	0.547	SUBCLONAL	1	TRUE	1	0.598581272369127	2		528	783	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	89	575	2	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.544	0.483	0.608	0.544	0.483	0.608	SUBCLONAL	1	TRUE	1	0.598581272369127	2		577	547	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149828	202149828	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	80	507	0	ENST00000358485.4:c.1269C>G	p.Asn423Lys	p.N423K	ENST00000358485	NM_001080125.1	423	aaC/aaG	8/9	1	2	FACETS	0.467	0.412	0.527	0.467	0.412	0.527	SUBCLONAL	1	TRUE	1	0.598581272369127	2		507	572	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30956850	30956850	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	112	441	0	ENST00000375687.4:c.176T>C	p.Met59Thr	p.M59T	ENST00000375687	NM_015338.5	59	aTg/aCg	4/13	1	2	FACETS	0.596	0.537	0.658	0.596	0.537	0.658	SUBCLONAL	1	TRUE	1	0.598581272369127	2		441	628	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069262	30069262	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs996964764	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	57	517	0	ENST00000338641.4:c.1127G>A	p.Arg376Gln	p.R376Q	ENST00000338641	NM_000268.3	376	cGg/cAg	12/16	1	2	FACETS	0.267	0.228	0.309	0.267	0.228	0.309	SUBCLONAL	1	TRUE	1	0.598581272369127	2		517	713	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933456	49933456	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	74	654	0	ENST00000296474.3:c.2734del	p.Asp912ThrfsTer24	p.D912Tfs*24	ENST00000296474	NM_002447.2	912	Gac/ac	11/20	1	2	FACETS	0.293	0.256	0.334	0.293	0.256	0.334	SUBCLONAL	1	TRUE	1	0.598581272369127	2		654	843	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	82	445	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.528	0.466	0.593	0.528	0.466	0.593	SUBCLONAL	1	TRUE	1	0.598581272369127	2		445	519	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928089	178928089	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	77	370	0	ENST00000263967.3:c.1367T>G	p.Leu456Arg	p.L456R	ENST00000263967	NM_006218.2	456	cTg/cGg	8/21	1	2	FACETS	0.601	0.53	0.677	0.601	0.53	0.677	SUBCLONAL	1	TRUE	1	0.598581272369127	2		370	428	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446270	187446270	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	125	604	0	ENST00000232014.4:c.1418del	p.Pro473ArgfsTer117	p.P473Rfs*117	ENST00000232014	NM_001130845.1	473	cCg/cg	6/10	1	2	FACETS	0.449	0.406	0.495	0.449	0.406	0.495	SUBCLONAL	1	TRUE	1	0.598581272369127	2		604	930	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950775	79950775	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1200938359	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	18	150	0	ENST00000265081.6:c.229C>T	p.Pro77Ser	p.P77S	ENST00000265081	NM_002439.4	77	Ccg/Tcg	1/24	1	2	FACETS	0.317	0.239	0.407	0.317	0.239	0.407	SUBCLONAL	1	TRUE	1	0.598581272369127	2		150	190	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163425	32163425	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	146	605	0	ENST00000375023.3:c.5801A>G	p.Tyr1934Cys	p.Y1934C	ENST00000375023	NM_004557.3	1934	tAc/tGc	30/30	1	2	FACETS	0.515	0.469	0.562	0.515	0.469	0.562	SUBCLONAL	1	TRUE	1	0.598581272369127	2		605	948	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128849148	128849148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	142	582	1	ENST00000249373.3:c.1376C>T	p.Ala459Val	p.A459V	ENST00000249373	NM_005631.4	459	gCc/gTc	8/12	1	2	FACETS	0.496	0.452	0.543	0.496	0.452	0.543	SUBCLONAL	1	TRUE	1	0.598581272369127	2		583	956	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863054	56863054	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1266824391	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	93	387	0	ENST00000519728.1:c.327del	p.Glu110LysfsTer15	p.E110Kfs*15	ENST00000519728	NM_002350.3	107	acA/ac	5/13	0.186928767512245	3	FACETS	0.639	0.569	0.714	0.319	0.284	0.357	INDETERMINATE	1	TRUE	1	0.598581272369127	3		387	632	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300040	137300040	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	132	666	0	ENST00000481739.1:c.331del	p.Leu111TrpfsTer57	p.L111Wfs*57	ENST00000481739	NM_002957.4	109	Ccc/cc	3/10	1	2	FACETS	0.456	0.413	0.501	0.456	0.413	0.501	SUBCLONAL	1	TRUE	1	0.598581272369127	2		666	967	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930311	39930311	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	158	626	0	ENST00000378444.4:c.3153G>T	p.Trp1051Cys	p.W1051C	ENST00000378444	NM_001123385.1	1051	tgG/tgT	6/15	1	2	FACETS	0.536	0.491	0.584	0.536	0.491	0.584	SUBCLONAL	1	TRUE	1	0.598581272369127	2		626	984	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0044361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	340	599	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.736582001041543	1	FACETS	0.857	0.82	0.895	0.857	0.82	0.895	CLONAL	1	TRUE	0	0.783212895029325	1		599	616	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0044361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	216	658	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.483496875609308	2	FACETS	1	0.992	1	0.684	0.646	0.722	CLONAL	1	TRUE	0	0.783212895029325	2		658	403	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502187	157502187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761227259	NA	P-0044361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	259	509	1	ENST00000346085.5:c.3220G>A	p.Asp1074Asn	p.D1074N	ENST00000346085	NM_020732.3	1074	Gac/Aac	12/20	1	2	FACETS	0.85	0.799	0.902	0.85	0.799	0.902	CLONAL	1	TRUE	1	0.783212895029325	2		510	778	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872795	136872795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1272938495	NA	P-0044361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	201	411	0	ENST00000241393.3:c.703C>T	p.Arg235Cys	p.R235C	ENST00000241393	NM_003467.2	235	Cgc/Tgc	2/2	1	2	FACETS	0.861	0.803	0.921	0.861	0.803	0.921	CLONAL	1	TRUE	1	0.783212895029325	2		411	596	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239441	123239442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	172	488	0	ENST00000358487.5:c.2395dup	p.Ser799PhefsTer22	p.S799Ffs*22	ENST00000358487	NM_000141.4	799	tct/tTct	18/18	1	2	FACETS	0.782	0.723	0.841	0.782	0.723	0.841	SUBCLONAL	1	TRUE	1	0.783212895029325	2		488	562	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346973	89346973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773403872	NA	P-0044361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	171	483	1	ENST00000301030.4:c.5977C>T	p.Arg1993Cys	p.R1993C	ENST00000301030	NM_001256183.1	1993	Cgt/Tgt	9/13	0.695621666312003	1	FACETS	0.791	0.74	0.841	0.791	0.74	0.841	SUBCLONAL	1	TRUE	0	0.783212895029325	1		484	336	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032026	10032026	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	266	663	0	ENST00000330684.3:c.797A>C	p.Glu266Ala	p.E266A	ENST00000330684	NM_001134407.1	266	gAg/gCg	3/13	1	2	FACETS	0.869	0.818	0.921	0.869	0.818	0.921	CLONAL	1	TRUE	1	0.783212895029325	2		663	782	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196773	106196773	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	133	344	0	ENST00000380013.4:c.5106G>C	p.Gln1702His	p.Q1702H	ENST00000380013	NM_001127208.2	1702	caG/caC	11/11	1	2	FACETS	0.962	0.885	1	0.962	0.885	1	CLONAL	1	TRUE	1	0.783212895029325	2		344	353	SUCCESS
APC	324	MSKCC	GRCh37	5	112162894	112162895	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0044361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	15	209	0	ENST00000257430.4:c.1499dup	p.Tyr500Ter	p.Y500*	ENST00000257430	NM_000038.5	500	tat/tAat	12/16	0.483496875609308	2	FACETS	0.199	0.146	0.263	0.1	0.073	0.132	SUBCLONAL	1	TRUE	0	0.783212895029325	2		209	192	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186751	11186751	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752458445	NA	P-0044373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	49	651	2	ENST00000361445.4:c.6454C>T	p.Arg2152Cys	p.R2152C	ENST00000361445	NM_004958.3	2152	Cgc/Tgc	46/58	1	2	FACETS	0.635	0.536	0.745	0.635	0.536	0.745	SUBCLONAL	1	TRUE	1	0.159620587834084	2		653	967	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929237	44929238	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0044373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	72	389	0	ENST00000377967.4:c.2342_2343dup	p.Ala782LeufsTer4	p.A782Lfs*4	ENST00000377967	NM_021140.2	779	-/CT	17/29	1	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.159620587834084	1		389	594	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422645	49422645	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0044417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	259	513	0	ENST00000301067.7:c.14348C>G	p.Ser4783Ter	p.S4783*	ENST00000301067	NM_003482.3	4783	tCa/tGa	45/54	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.571611216178174	2		513	906	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92244546	92244546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	139	255	0	ENST00000265734.4:c.889C>T	p.His297Tyr	p.H297Y	ENST00000265734	NM_001259.6	297	Cac/Tac	8/8	1	2	FACETS	0.878	0.803	0.956	0.878	0.803	0.956	CLONAL	1	TRUE	1	0.571611216178174	2		255	554	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960110	151960110	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	143	350	0	ENST00000262189.6:c.1290G>C	p.Trp430Cys	p.W430C	ENST00000262189	NM_170606.2	430	tgG/tgC	9/59	0.571611216178174	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.571611216178174	1		350	345	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247361	153247367	+	protein_altering_variant	In_Frame_Del	DEL	CATCTCG	CATCTCG	A	novel	NA	P-0044417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	85	213	0	ENST00000281708.4:c.1435_1441delinsT	p.Arg479_Ala481delinsSer	p.R479_A481delinsS	ENST00000281708	NM_033632.3	479	CGAGATGcc/Tcc	10/12	1	2	FACETS	0.799	0.712	0.892	0.799	0.712	0.892	SUBCLONAL	1	TRUE	1	0.571611216178174	2		213	372	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0044418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	97	66	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.944	0.843	1	0.944	0.843	1	CLONAL	1	TRUE	1	0.32165187933207	2		66	639	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419117	419117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1443684874	NA	P-0044418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	26	349	0	ENST00000399788.2:c.3230G>A	p.Arg1077Gln	p.R1077Q	ENST00000399788	NM_001042603.1	1077	cGg/cAg	22/28	1	2	FACETS	0.369	0.292	0.458	0.369	0.292	0.458	SUBCLONAL	1	TRUE	1	0.32165187933207	2		349	438	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087913	27087914	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0044418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	135	667	0	ENST00000324856.7:c.2201_2202insAA	p.Asp734GlufsTer9	p.D734Efs*9	ENST00000324856	NM_006015.4	734	gac/gAAac	6/20	1	2	FACETS	0.976	0.887	1	0.976	0.887	1	CLONAL	1	TRUE	1	0.32165187933207	2		667	860	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061070	38061070	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	29	141	0	ENST00000250448.2:c.919T>C	p.Ser307Pro	p.S307P	ENST00000250448	NM_004496.3	307	Tcg/Ccg	2/2	1	2	FACETS	0.843	0.681	1	0.843	0.681	1	CLONAL	1	TRUE	1	0.32165187933207	2		141	214	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207585	29207585	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	100	505	0	ENST00000240100.2:c.211A>G	p.Thr71Ala	p.T71A	ENST00000240100	NM_001394.6	71	Acc/Gcc	1/4	1	2	FACETS	0.891	0.796	0.991	0.891	0.796	0.991	CLONAL	1	TRUE	1	0.32165187933207	2		505	698	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578241	7578241	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	326	692	0	ENST00000269305.4:c.608T>A	p.Val203Glu	p.V203E	ENST00000269305	NM_001126112.2	203	gTg/gAg	6/11	0.863378361906581	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.863378361906581	1		692	407	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590719	95590719	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	163	294	0	ENST00000393063.1:c.1190G>C	p.Ser397Thr	p.S397T	ENST00000393063	NM_030621.3	397	aGc/aCc	9/28	1	2	FACETS	0.999	0.929	1	0.999	0.929	1	CLONAL	1	TRUE	1	0.863378361906581	2		294	378	SUCCESS
APC	324	MSKCC	GRCh37	5	112157592	112157593	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GT	GT	-	novel	NA	P-0044434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	166	353	0	ENST00000257430.4:c.1313_1314del		p.X438_splice	ENST00000257430	NM_000038.5	438		11/16	0.840979616928765	1	FACETS	0.98	0.933	1	0.98	0.933	1	CLONAL	1	TRUE	0	0.863378361906581	1		353	223	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250462	26250462	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	282	545	0	ENST00000446824.2:c.372del	p.Asp124GlufsTer17	p.D124Efs*17	ENST00000446824	NM_021018.2	124	gaC/ga	1/1	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.863378361906581	2		545	629	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0044445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	44	575	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.744	0.622	0.879	0.744	0.622	0.879	SUBCLONAL	1	TRUE	1	0.15	2		575	789	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0044445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	15	244	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.352	0.256	0.469	0.352	0.256	0.469	SUBCLONAL	1	TRUE	1	0.15	2		244	568	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481417	140481417	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913348	NA	P-0044445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	40	437	0	ENST00000288602.6:c.1391G>T	p.Gly464Val	p.G464V	ENST00000288602	NM_004333.4	464	gGa/gTa	11/18	1	2	FACETS	0.979	0.812	1	0.979	0.812	1	CLONAL	1	TRUE	1	0.15	2		437	545	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308098	30308098	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1240513553	NA	P-0044445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	66	605	0	ENST00000262643.3:c.235G>A	p.Asp79Asn	p.D79N	ENST00000262643	NM_001238.2	79	Gac/Aac	5/12	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.15	2		605	858	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952513	17952513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199815093	NA	P-0044445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	70	796	1	ENST00000458235.1:c.920C>T	p.Pro307Leu	p.P307L	ENST00000458235	NM_000215.3	307	cCg/cTg	7/24	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.15	2		797	879	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112362	115112362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1440126149	NA	P-0044445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	25	460	0	ENST00000257566.3:c.1378G>A	p.Glu460Lys	p.E460K	ENST00000257566	NM_016569.3	460	Gag/Aag	7/8	1	2	FACETS	0.672	0.528	0.838	0.672	0.528	0.838	SUBCLONAL	1	TRUE	1	0.15	2		460	496	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1039044	1039044	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	38	568	0	ENST00000358495.3:c.289G>C	p.Asp97His	p.D97H	ENST00000358495	NM_134424.2	97	Gac/Cac	5/12	1	2	FACETS	0.739	0.609	0.884	0.739	0.609	0.884	SUBCLONAL	1	TRUE	1	0.15	2		568	686	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5239023	5239023	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	74	820	0	ENST00000357368.4:c.1756C>G	p.Pro586Ala	p.P586A	ENST00000357368	NM_002850.3	586	Ccc/Gcc	13/38	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.15	2		820	928	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627451	14627451	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	42	626	0	ENST00000254322.2:c.619G>C	p.Glu207Gln	p.E207Q	ENST00000254322	NM_006145.1	207	Gaa/Caa	2/3	1	2	FACETS	0.697	0.58	0.828	0.697	0.58	0.828	SUBCLONAL	1	TRUE	1	0.15	2		626	803	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276203	15276203	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	32	549	0	ENST00000263388.2:c.5791G>C	p.Asp1931His	p.D1931H	ENST00000263388	NM_000435.2	1931	Gat/Cat	31/33	1	2	FACETS	0.711	0.576	0.865	0.711	0.576	0.865	SUBCLONAL	1	TRUE	1	0.15	2		549	600	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224577	36224577	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	63	1029	0	ENST00000222270.7:c.7039G>C	p.Glu2347Gln	p.E2347Q	ENST00000222270	NM_014727.1	2347	Gaa/Caa	29/37	1	2	FACETS	0.872	0.752	1	0.872	0.752	1	CLONAL	1	TRUE	1	0.15	2		1029	963	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139028	50139028	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769754956	NA	P-0044445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	85	948	0	ENST00000246792.3:c.535G>A	p.Val179Met	p.V179M	ENST00000246792	NM_006270.3	179	Gtg/Atg	5/6	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.15	2		948	1116	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	256491	256491	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375396913	NA	P-0044445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	22	190	0	ENST00000264932.6:c.1951G>A	p.Glu651Lys	p.E651K	ENST00000264932	NM_004168.2	651	Gag/Aag	15/15	1	2	FACETS	0.858	0.665	1	0.858	0.665	1	CLONAL	1	TRUE	1	0.15	2		190	342	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874008	151874008	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	32	491	0	ENST00000262189.6:c.8530G>A	p.Glu2844Lys	p.E2844K	ENST00000262189	NM_170606.2	2844	Gag/Aag	38/59	1	2	FACETS	0.697	0.564	0.848	0.697	0.564	0.848	SUBCLONAL	1	TRUE	1	0.15	2		491	612	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0044450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	79	66	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.325903746489718	2		66	456	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448693	49448693	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	75	335	1	ENST00000301067.7:c.166C>T	p.Gln56Ter	p.Q56*	ENST00000301067	NM_003482.3	56	Cag/Tag	2/54	0.325903746489718	3	FACETS	0.816	0.715	0.925	0.408	0.357	0.463	CLONAL	1	TRUE	1	0.325903746489718	3		336	656	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579444	7579444	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	178	611	0	ENST00000269305.4:c.243del	p.Pro82ArgfsTer41	p.P82Rfs*41	ENST00000269305	NM_001126112.2	81	acA/ac	4/11	0.325903746489718	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.325903746489718	1		611	742	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216750	2216750	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1030782681	NA	P-0044450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	92	717	0	ENST00000398665.3:c.2394T>A	p.Ser798Arg	p.S798R	ENST00000398665	NM_032482.2	798	agT/agA	20/28	1	2	FACETS	0.663	0.588	0.743	0.663	0.588	0.743	SUBCLONAL	1	TRUE	1	0.325903746489718	2		717	852	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0044450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	133	66	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.38145834120143	3	FACETS	0.767	0.7	0.837	0.767	0.7	0.837	SUBCLONAL	2	TRUE	1	0.38145834120143	3		66	541	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448693	49448693	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	144	335	1	ENST00000301067.7:c.166C>T	p.Gln56Ter	p.Q56*	ENST00000301067	NM_003482.3	56	Cag/Tag	2/54	0.38145834120143	3	FACETS	0.992	0.913	1	0.992	0.913	1	CLONAL	2	TRUE	1	0.38145834120143	3		336	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579444	7579444	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	229	611	0	ENST00000269305.4:c.243del	p.Pro82ArgfsTer41	p.P82Rfs*41	ENST00000269305	NM_001126112.2	81	acA/ac	4/11	0.307805395177114	2	FACETS	0.919	0.862	0.978	0.919	0.862	0.978	CLONAL	2	TRUE	0	0.38145834120143	2		611	653	SUCCESS
BLM	641	MSKCC	GRCh37	15	91290721	91290721	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs750293380	NA	P-0044450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	57	213	0	ENST00000355112.3:c.98+1G>A		p.X33_splice	ENST00000355112	NM_000057.2	33			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.38145834120143	2		213	210	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0044473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	45	450	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.16368169287193	5	FACETS	0.7	0.588	0.823	0.233	0.196	0.275	INDETERMINATE	1	TRUE	2	0.416347682061799	5		450	502	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111886057	111886057	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	76	537	0	ENST00000341259.2:c.1679C>T	p.Ser560Phe	p.S560F	ENST00000341259	NM_005475.2	560	tCc/tTc	8/8	1	2	FACETS	0.697	0.612	0.787	0.697	0.612	0.787	SUBCLONAL	1	TRUE	1	0.416347682061799	2		537	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0044473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	297	759	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.325205072269765	2	FACETS	0.82	0.774	0.866	0.82	0.774	0.866	CLONAL	2	TRUE	0	0.416347682061799	2		759	870	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021792	69021792	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	99	532	0	ENST00000288368.4:c.3080A>C	p.Gln1027Pro	p.Q1027P	ENST00000288368	NM_024870.2	1027	cAg/cCg	25/40	0.417256720397729	3	FACETS	0.752	0.671	0.838	0.376	0.335	0.419	SUBCLONAL	1	TRUE	1	0.416347682061799	3		532	764	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	144	289	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.215545557897366	3	FACETS	0.833	0.762	0.908	0.833	0.762	0.908	CLONAL	2	TRUE	1	0.277962328411993	3		289	708	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518738	176518738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200232395	NA	P-0044489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	85	828	0	ENST00000292408.4:c.656G>A	p.Arg219His	p.R219H	ENST00000292408	NM_213647.1	219	cGc/cAc	6/18	1	2	FACETS	0.952	0.841	1	0.952	0.841	1	CLONAL	1	TRUE	1	0.262301227276065	2		828	681	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224529	224529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370481102	NA	P-0044489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	44	465	0	ENST00000264932.6:c.205G>A	p.Ala69Thr	p.A69T	ENST00000264932	NM_004168.2	69	Gct/Act	3/15	0.262301227276065	5	FACETS	0.863	0.723	1	0.288	0.241	0.339	CLONAL	1	TRUE	2	0.262301227276065	5		465	542	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577571	7577571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	166	630	0	ENST00000269305.4:c.710del	p.Met237SerfsTer10	p.M237Sfs*10	ENST00000269305	NM_001126112.2	237	aTg/ag	7/11	0.204108625870471	3	FACETS	1	0.971	1	0.741	0.683	0.801	CLONAL	2	TRUE	0	0.262301227276065	3		630	644	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900314	101900314	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	70	295	0	ENST00000374994.4:c.748C>G	p.Gln250Glu	p.Q250E	ENST00000374994	NM_004612.2	250	Caa/Gaa	4/9	0.201197414660926	3	FACETS	1	0.956	1	0.609	0.532	0.691	CLONAL	1	TRUE	1	0.262301227276065	3		295	496	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006881	47006881	+	start_lost	Translation_Start_Site	SNP	A	A	T	novel	NA	P-0044489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	119	850	0	ENST00000377604.3:c.1A>T	p.Met1?	p.M1?	ENST00000377604	NM_001204468.1	1	Atg/Ttg	2/24	0.262301227276065	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.262301227276065	1		850	610	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257185	198257694	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTAAAATAATTGAACGGTTACATTATTTCAATTTTTAAGAACATACATAACCTTAACAAAATTAAGAAAACATAAAGATATGATTCAAAATTATTTCCCTTGGGGAGTTGGGGGGGGGGGAACCTACTAATTACACTGCTCTTAAGCTGCAATGGAAGAGACAAAACTCACTCCCCTGTCACCACACAATTGTTCTACCATATGGCACAATATACCCTAATGATAATCAGGAAAAGTAACTTAATTCAATACACTACTTTTCTTGCTAAGTAATCTTTTAAAAATCTTTAACTTACAGGCAGTGGGGGGAAAGGGGAGGGAGAGCATTAGGACAAATACCTAATGCATGCAGGGCTTAAAACCTAGATGACAGGTTGATAGGTGCAGCAAACCACCATGGCACATATATACCTATGTAACAAACCTGCACGTTCAGCACAAGTATCCCAGAACTTAAAGTATTATTTAAAAAAAAAAAATCACCGATTAAAAAAAAAATCTTTAACTTA	CCTAAAATAATTGAACGGTTACATTATTTCAATTTTTAAGAACATACATAACCTTAACAAAATTAAGAAAACATAAAGATATGATTCAAAATTATTTCCCTTGGGGAGTTGGGGGGGGGGGAACCTACTAATTACACTGCTCTTAAGCTGCAATGGAAGAGACAAAACTCACTCCCCTGTCACCACACAATTGTTCTACCATATGGCACAATATACCCTAATGATAATCAGGAAAAGTAACTTAATTCAATACACTACTTTTCTTGCTAAGTAATCTTTTAAAAATCTTTAACTTACAGGCAGTGGGGGGAAAGGGGAGGGAGAGCATTAGGACAAATACCTAATGCATGCAGGGCTTAAAACCTAGATGACAGGTTGATAGGTGCAGCAAACCACCATGGCACATATATACCTATGTAACAAACCTGCACGTTCAGCACAAGTATCCCAGAACTTAAAGTATTATTTAAAAAAAAAAAATCACCGATTAAAAAAAAAATCTTTAACTTA	-	novel	NA	P-0044498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	230	356	0	ENST00000335508.6:c.3756+2_3757del		p.X1252_splice	ENST00000335508	NM_012433.2	1252		25/25	0.687091516066857	3	FACETS	1	0.977	1	0.366	0.342	0.391	CLONAL	1	TRUE	0	0.716661887033798	3		356	794	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198262840	198263183	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTAATTTAAAAAATACACATATTAATTATTGTGACATTAAGAAAAGTTTTAAGGATAAATTTGCAAATTCAGTTCTAAAAACATGATTAACTCATTTTAAGCATTAAATAAAACTTACTACTCTTCAGAAAGGCTGAAGAGTTAGTCTTACAGGTTTAGTCCTAAAATTACATTGCCACCCCCATTACCATCCAAATTGAAATTTGACTGAAAATATTAATACTGGATAGCCTAATCTTTTACACTTATATTAGTGACATTAAGGAAATTTTGCTAATTGAATACAAAGTGGCCAAATTTGAAAATTGATACTGCTTATAAAAATGTGTGGGTAATCTGCTTA	CCTAATTTAAAAAATACACATATTAATTATTGTGACATTAAGAAAAGTTTTAAGGATAAATTTGCAAATTCAGTTCTAAAAACATGATTAACTCATTTTAAGCATTAAATAAAACTTACTACTCTTCAGAAAGGCTGAAGAGTTAGTCTTACAGGTTTAGTCCTAAAATTACATTGCCACCCCCATTACCATCCAAATTGAAATTTGACTGAAAATATTAATACTGGATAGCCTAATCTTTTACACTTATATTAGTGACATTAAGGAAATTTTGCTAATTGAATACAAAGTGGCCAAATTTGAAAATTGATACTGCTTATAAAAATGTGTGGGTAATCTGCTTA	-	novel	NA	P-0044498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	169	250	0	ENST00000335508.6:c.3134+2_3135del		p.X1045_splice	ENST00000335508	NM_012433.2	1045		22/25	0.687091516066857	3	FACETS	1	0.983	1	0.402	0.372	0.433	CLONAL	1	TRUE	0	0.716661887033798	3		250	531	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197468	27197468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	615	706	1	ENST00000380036.4:c.1780C>T	p.Pro594Ser	p.P594S	ENST00000380036	NM_000459.3	594	Cca/Tca	12/23	0.383477737823885	5	FACETS	0.852	0.822	0.883	0.852	0.822	0.883	INDETERMINATE	3	TRUE	2	0.716661887033798	5		707	1393	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132039	176132039	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	202	433	0	ENST00000367669.3:c.728A>T	p.Glu243Val	p.E243V	ENST00000367669	NM_022457.5	243	gAg/gTg	5/20	0.346912435865472	3	FACETS	1	0.977	1	0.556	0.517	0.595	INDETERMINATE	1	TRUE	1	0.716661887033798	3		433	689	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437463	49437463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	168	668	0	ENST00000301067.7:c.5422G>A	p.Gly1808Arg	p.G1808R	ENST00000301067	NM_003482.3	1808	Gga/Aga	23/54	0.365536092660033	1	FACETS	0.435	0.401	0.47	0.435	0.401	0.47	INDETERMINATE	1	TRUE	0	0.716661887033798	1		668	692	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286203	66286203	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	75	334	0	ENST00000273854.3:c.1483C>G	p.Pro495Ala	p.P495A	ENST00000273854	NM_004439.5	495	Ccc/Gcc	6/18	0.410389375521574	1	FACETS	0.385	0.339	0.433	0.385	0.339	0.433	INDETERMINATE	1	TRUE	0	0.716661887033798	1		334	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578213	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs864309495	NA	P-0044507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	645	799	1	ENST00000269305.4:c.636del	p.Arg213AspfsTer34	p.R213Dfs*34	ENST00000269305	NM_001126112.2	212	ttT/tt	6/11	0.463988449630978	3	FACETS	1	0.995	1	0.766	0.742	0.79	CLONAL	2	TRUE	0	0.634038645485335	3		800	1166	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046315	30046483	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	GTGCTAACAGTTTAACAGCTTTGTTCTCATCTGACAGAAAATAATGGCAGTTCTGCAAGGCAAATGTTAAACCTGACCGTATGTATTTATTAGTTCCACAGTGTTTTGACAGATTATAGGAGATGGAACTCAGAGGATGCTGACACGCTCACCGAGGGCTTTCATTTCT	GTGCTAACAGTTTAACAGCTTTGTTCTCATCTGACAGAAAATAATGGCAGTTCTGCAAGGCAAATGTTAAACCTGACCGTATGTATTTATTAGTTCCACAGTGTTTTGACAGATTATAGGAGATGGAACTCAGAGGATGCTGACACGCTCACCGAGGGCTTTCATTTCT	-	novel	NA	P-0044507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	64	102	0	ENST00000331968.5:c.2700_*129del		p.*900*	ENST00000331968	NM_002742.2	900		18/18	0.161871064312757	3	FACETS	1	0.952	1	1	0.952	1	INDETERMINATE	2	TRUE	1	0.634038645485335	3		102	120	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39644736	39644736	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	33	259	0	ENST00000262039.4:c.2465T>G	p.Leu822Trp	p.L822W	ENST00000262039	NM_002647.2	822	tTg/tGg	23/25	0.602003186399622	1	FACETS	0.224	0.183	0.271	0.224	0.183	0.271	SUBCLONAL	1	TRUE	0	0.634038645485335	1		259	317	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192347	138192349	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CAG	CAG	-	novel	NA	P-0044507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	18	125	0	ENST00000237289.4:c.-15-3_-15-1del		p.X5_splice	ENST00000237289	NM_001270507.1	5			0.343953832979842	4	FACETS	0.434	0.327	0.558	0.108	0.081	0.14	INDETERMINATE	1	TRUE	0	0.634038645485335	4		125	214	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922466	56922466	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0044507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	67	335	0	ENST00000519728.1:c.1337-1G>C		p.X446_splice	ENST00000519728	NM_002350.3	446			NA	2	FACETS	0.379	0.33	0.433			1	INDETERMINATE	1	TRUE	NA	0.634038645485335	2		335	557	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	28	239	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.866	0.697	1	0.866	0.697	1	CLONAL	1	TRUE	1	0.310924230805364	2		239	208	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	94	808	0	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	0.809	0.72	0.905	0.809	0.72	0.905	CLONAL	1	TRUE	1	0.310924230805364	2		808	747	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115277064	115277064	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	29	443	0	ENST00000438362.2:c.719A>C	p.Lys240Thr	p.K240T	ENST00000438362	NM_001242891.1	240	aAg/aCg	7/20	1	2	FACETS	0.372	0.298	0.457	0.372	0.298	0.457	SUBCLONAL	1	TRUE	1	0.310924230805364	2		443	501	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491175	120491175	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	113	534	0	ENST00000256646.2:c.2614A>G	p.Ile872Val	p.I872V	ENST00000256646	NM_024408.3	872	Att/Gtt	17/34	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.310924230805364	2		534	713	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577419	64577419	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	90	750	3	ENST00000312049.6:c.163C>A	p.Pro55Thr	p.P55T	ENST00000312049	NM_130799.2	55	Cct/Act	2/10	1	2	FACETS	0.602	0.533	0.676	0.602	0.533	0.676	SUBCLONAL	1	TRUE	1	0.310924230805364	2		753	962	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589633	69589633	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	56	272	0	ENST00000168712.1:c.220G>T	p.Gly74Cys	p.G74C	ENST00000168712	NM_002007.2	74	Ggc/Tgc	1/3	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.310924230805364	2		272	351	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	139	971	3	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.756	0.687	0.83	0.756	0.687	0.83	SUBCLONAL	1	TRUE	1	0.310924230805364	2		974	1182	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431718	431718	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747207978	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	91	339	0	ENST00000399788.2:c.2291G>A	p.Arg764Gln	p.R764Q	ENST00000399788	NM_001042603.1	764	cGa/cAa	17/28	0.308753429921432	3	FACETS	1	0.976	1	0.686	0.611	0.765	CLONAL	1	TRUE	1	0.310924230805364	3		339	493	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415622	49415622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	120	445	0	ENST00000301067.7:c.16555G>A	p.Asp5519Asn	p.D5519N	ENST00000301067	NM_003482.3	5519	Gat/Aat	54/54	0.308753429921432	3	FACETS	0.778	0.705	0.855	0.778	0.705	0.855	SUBCLONAL	2	TRUE	1	0.310924230805364	3		445	573	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420625	49420625	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	217	674	0	ENST00000301067.7:c.15124del	p.Ala5042ProfsTer9	p.A5042Pfs*9	ENST00000301067	NM_003482.3	5042	Gcc/cc	48/54	0.308753429921432	3	FACETS	0.82	0.762	0.879	0.82	0.762	0.879	CLONAL	2	TRUE	1	0.310924230805364	3		674	984	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541645	120541645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	112	607	0	ENST00000229340.5:c.212G>A	p.Arg71His	p.R71H	ENST00000229340	NM_006861.6	71	cGc/cAc	3/6	0.308753429921432	3	FACETS	0.801	0.719	0.888	0.401	0.359	0.444	CLONAL	1	TRUE	1	0.310924230805364	3		607	1039	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248830	133248830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	133	732	1	ENST00000320574.5:c.1765C>T	p.Pro589Ser	p.P589S	ENST00000320574	NM_006231.2	589	Cct/Tct	16/49	0.308753429921432	3	FACETS	0.917	0.831	1	0.458	0.415	0.504	CLONAL	1	TRUE	1	0.310924230805364	3		733	1078	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907364	32907365	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359301	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	27	325	0	ENST00000380152.3:c.1754dup	p.Lys586GlufsTer4	p.K586Efs*4	ENST00000380152		583	-/A	10/27	1	2	FACETS	0.634	0.506	0.779	0.634	0.506	0.779	SUBCLONAL	1	TRUE	1	0.310924230805364	2		325	274	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930634	32930634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56070345	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	61	460	0	ENST00000380152.3:c.7505G>A	p.Arg2502His	p.R2502H	ENST00000380152		2502	cGc/cAc	15/27	1	2	FACETS	0.715	0.617	0.821	0.715	0.617	0.821	SUBCLONAL	1	TRUE	1	0.310924230805364	2		460	549	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762174	43762174	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs776812022	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	157	744	0	ENST00000382044.4:c.1271A>C	p.Asn424Thr	p.N424T	ENST00000382044	NM_001141980.1	424	aAc/aCc	11/28	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.310924230805364	2		744	933	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	93	427	0	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.979	0.872	1	0.979	0.872	1	CLONAL	1	TRUE	1	0.310924230805364	2		427	611	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274171	10274171	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	81	582	0	ENST00000330684.3:c.98C>A	p.Ala33Glu	p.A33E	ENST00000330684	NM_001134407.1	33	gCg/gAg	2/13	1	2	FACETS	0.792	0.698	0.893	0.792	0.698	0.893	SUBCLONAL	1	TRUE	1	0.310924230805364	2		582	658	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50815168	50815168	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	90	499	0	ENST00000398568.2:c.1521T>G	p.Cys507Trp	p.C507W	ENST00000398568	NM_001042412.1	507	tgT/tgG	9/18	1	2	FACETS	0.843	0.748	0.944	0.843	0.748	0.944	CLONAL	1	TRUE	1	0.310924230805364	2		499	687	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81914545	81914545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769793664	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	55	447	0	ENST00000359376.3:c.679G>A	p.Val227Met	p.V227M	ENST00000359376	NM_002661.3	227	Gtg/Atg	8/33	1	2	FACETS	0.572	0.489	0.664	0.572	0.489	0.664	SUBCLONAL	1	TRUE	1	0.310924230805364	2		447	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578397	7578397	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1555526004	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	148	715	0	ENST00000269305.4:c.533A>C	p.His178Pro	p.H178P	ENST00000269305	NM_001126112.2	178	cAc/cCc	5/11	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.310924230805364	2		715	941	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138729528	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	142	545	0	ENST00000269305.4:c.523C>T	p.Arg175Cys	p.R175C	ENST00000269305	NM_001126112.2	175	Cgc/Tgc	5/11	1	2	FACETS	0.907	0.826	0.993	0.907	0.826	0.993	CLONAL	1	TRUE	1	0.310924230805364	2		545	1007	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118344	17118344	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	159	859	0	ENST00000285071.4:c.1493A>G	p.Asp498Gly	p.D498G	ENST00000285071	NM_144997.5	498	gAt/gGt	13/14	1	2	FACETS	0.948	0.868	1	0.948	0.868	1	CLONAL	1	TRUE	1	0.310924230805364	2		859	1079	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231333	5231333	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	121	634	0	ENST00000357368.4:c.2143A>G	p.Thr715Ala	p.T715A	ENST00000357368	NM_002850.3	715	Acc/Gcc	14/38	1	2	FACETS	0.861	0.777	0.95	0.861	0.777	0.95	CLONAL	1	TRUE	1	0.310924230805364	2		634	904	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308338	30308338	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	78	482	0	ENST00000262643.3:c.352A>T	p.Lys118Ter	p.K118*	ENST00000262643	NM_001238.2	118	Aaa/Taa	6/12	1	2	FACETS	0.89	0.783	1	0.89	0.783	1	CLONAL	1	TRUE	1	0.310924230805364	2		482	564	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224532	36224532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759167832	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	159	922	0	ENST00000222270.7:c.6994C>T	p.Arg2332Cys	p.R2332C	ENST00000222270	NM_014727.1	2332	Cgt/Tgt	29/37	1	2	FACETS	0.86	0.787	0.937	0.86	0.787	0.937	CLONAL	1	TRUE	1	0.310924230805364	2		922	1189	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907707	111907707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757046249	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	72	390	2	ENST00000393256.3:c.481G>A	p.Ala161Thr	p.A161T	ENST00000393256	NM_006538.4	161	Gct/Act	3/4	1	2	FACETS	0.763	0.667	0.867	0.763	0.667	0.867	SUBCLONAL	1	TRUE	1	0.310924230805364	2		392	607	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128030506	128030506	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs770925947	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	78	510	0	ENST00000285398.2:c.1762del	p.Glu588LysfsTer23	p.E588Kfs*23	ENST00000285398	NM_000122.1	588	Gaa/aa	11/15	1	2	FACETS	0.796	0.7	0.9	0.796	0.7	0.9	SUBCLONAL	1	TRUE	1	0.310924230805364	2		510	630	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137404	202137404	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	47	363	0	ENST00000358485.4:c.632T>C	p.Leu211Pro	p.L211P	ENST00000358485	NM_001080125.1	211	cTg/cCg	4/9	1	2	FACETS	0.703	0.594	0.823	0.703	0.594	0.823	SUBCLONAL	1	TRUE	1	0.310924230805364	2		363	430	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660476	227660476	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	89	630	0	ENST00000305123.5:c.2979G>T	p.Gln993His	p.Q993H	ENST00000305123	NM_005544.2	993	caG/caT	1/2	1	2	FACETS	0.804	0.713	0.902	0.804	0.713	0.902	CLONAL	1	TRUE	1	0.310924230805364	2		630	712	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31372633	31372633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149520896	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	105	653	2	ENST00000328111.2:c.274C>T	p.Arg92Trp	p.R92W	ENST00000328111	NM_006892.3	92	Cgg/Tgg	4/23	1	2	FACETS	0.77	0.689	0.856	0.77	0.689	0.856	SUBCLONAL	1	TRUE	1	0.310924230805364	2		655	877	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770625	40770625	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	29	423	0	ENST00000373198.4:c.2757G>T	p.Gln919His	p.Q919H	ENST00000373198	NM_133170.3	919	caG/caT	19/32	1	2	FACETS	0.401	0.321	0.492	0.401	0.321	0.492	SUBCLONAL	1	TRUE	1	0.310924230805364	2		423	465	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100998	41100998	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772057709	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	98	658	0	ENST00000373198.4:c.1358G>A	p.Arg453His	p.R453H	ENST00000373198	NM_133170.3	453	cGc/cAc	8/32	1	2	FACETS	0.828	0.739	0.924	0.828	0.739	0.924	CLONAL	1	TRUE	1	0.310924230805364	2		658	761	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29115459	29115460	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886039609	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	23	103	0	ENST00000328354.6:c.606dup	p.Asp203Ter	p.D203*	ENST00000328354	NM_007194.3	202	-/T	5/15	1	2	FACETS	0.643	0.503	0.804	0.643	0.503	0.804	SUBCLONAL	1	TRUE	1	0.310924230805364	2		103	230	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	29	350	0	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	0.357	0.286	0.439	0.357	0.286	0.439	SUBCLONAL	1	TRUE	1	0.310924230805364	2		350	522	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568501	41568501	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	18	226	0	ENST00000263253.7:c.4453-2A>T		p.X1485_splice	ENST00000263253	NM_001429.3	1485			1	2	FACETS	0.387	0.291	0.501	0.387	0.291	0.501	SUBCLONAL	1	TRUE	1	0.310924230805364	2		226	299	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691775	30691775	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766473954	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	66	424	0	ENST00000295754.5:c.277G>A	p.Glu93Lys	p.E93K	ENST00000295754	NM_003242.5	93	Gag/Aag	3/7	1	2	FACETS	0.829	0.721	0.946	0.829	0.721	0.946	CLONAL	1	TRUE	1	0.310924230805364	2		424	512	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125462	47125462	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	52	385	0	ENST00000409792.3:c.5808C>A	p.Cys1936Ter	p.C1936*	ENST00000409792	NM_014159.6	1936	tgC/tgA	12/21	1	2	FACETS	0.804	0.686	0.933	0.804	0.686	0.933	CLONAL	1	TRUE	1	0.310924230805364	2		385	416	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125698	47125698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	70	488	0	ENST00000409792.3:c.5572C>T	p.Pro1858Ser	p.P1858S	ENST00000409792	NM_014159.6	1858	Cct/Tct	12/21	1	2	FACETS	0.732	0.638	0.833	0.732	0.638	0.833	SUBCLONAL	1	TRUE	1	0.310924230805364	2		488	615	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451405	187451405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	94	512	1	ENST00000232014.4:c.77G>A	p.Arg26Gln	p.R26Q	ENST00000232014	NM_001130845.1	26	cGg/cAg	3/10	1	2	FACETS	0.912	0.812	1	0.912	0.812	1	CLONAL	1	TRUE	1	0.310924230805364	2		513	663	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955593	55955593	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs373654225	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	33	349	0	ENST00000263923.4:c.3352C>T	p.Arg1118Ter	p.R1118*	ENST00000263923	NM_002253.2	1118	Cga/Tga	25/30	1	2	FACETS	0.542	0.441	0.655	0.542	0.441	0.655	SUBCLONAL	1	TRUE	1	0.310924230805364	2		349	392	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955962	55955962	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	54	406	0	ENST00000263923.4:c.3200T>C	p.Leu1067Pro	p.L1067P	ENST00000263923	NM_002253.2	1067	cTc/cCc	24/30	1	2	FACETS	0.712	0.608	0.825	0.712	0.608	0.825	SUBCLONAL	1	TRUE	1	0.310924230805364	2		406	488	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244155	153244156	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	82	562	0	ENST00000281708.4:c.2001dup	p.Ser668GlufsTer26	p.S668Efs*26	ENST00000281708	NM_033632.3	667	-/G	12/12	1	2	FACETS	0.654	0.575	0.738	0.654	0.575	0.738	SUBCLONAL	1	TRUE	1	0.310924230805364	2		562	807	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	94	478	4	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.879	0.789	0.972	1	0.985	1	CLONAL	2	TRUE	1	0.310924230805364	2		482	344	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589576	67589576	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1289537429	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	19	73	0	ENST00000274335.5:c.1344del	p.Lys448AsnfsTer32	p.K448Nfs*32	ENST00000274335		447	Aaa/aa	10/15	1	2	FACETS	1	0.816	1	1	0.816	1	CLONAL	1	TRUE	1	0.310924230805364	2		73	114	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	17	575	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	0.344	0.256	0.448	0.344	0.256	0.448	SUBCLONAL	1	TRUE	1	0.310924230805364	2		575	318	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	49	264	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.310924230805364	2		264	314	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497299	149497299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142762235	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	128	756	0	ENST00000261799.4:c.3019G>A	p.Val1007Ile	p.V1007I	ENST00000261799	NM_002609.3	1007	Gtc/Atc	22/23	1	2	FACETS	0.831	0.752	0.914	0.831	0.752	0.914	CLONAL	1	TRUE	1	0.310924230805364	2		756	991	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	67	444	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	0.852	0.741	0.971	0.852	0.741	0.971	CLONAL	1	TRUE	1	0.310924230805364	2		444	506	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190344	32190344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146490163	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	93	691	2	ENST00000375023.3:c.395G>A	p.Arg132His	p.R132H	ENST00000375023	NM_004557.3	132	cGc/cAc	3/30	1	2	FACETS	0.751	0.667	0.84	0.751	0.667	0.84	SUBCLONAL	1	TRUE	1	0.310924230805364	2		693	797	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651913	36651914	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	99	669	0	ENST00000244741.5:c.36dup	p.Cys13MetfsTer23	p.C13Mfs*23	ENST00000244741	NM_000389.4	12	cca/ccAa	2/3	1	2	FACETS	0.705	0.629	0.787	0.705	0.629	0.787	SUBCLONAL	1	TRUE	1	0.310924230805364	2		669	903	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554315	106554315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1400919125	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	87	463	0	ENST00000369096.4:c.1843C>T	p.Leu615Phe	p.L615F	ENST00000369096	NM_001198.3	615	Ctc/Ttc	6/7	1	2	FACETS	0.785	0.695	0.881	0.785	0.695	0.881	SUBCLONAL	1	TRUE	1	0.310924230805364	2		463	713	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335047	81335048	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	27	321	0	ENST00000222390.5:c.1779dup	p.Val594CysfsTer2	p.V594Cfs*2	ENST00000222390	NM_000601.4	593	-/T	16/18	1	2	FACETS	0.665	0.531	0.818	0.665	0.531	0.818	SUBCLONAL	1	TRUE	1	0.310924230805364	2		321	261	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92355046	92355046	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	31	334	0	ENST00000265734.4:c.431G>A	p.Arg144His	p.R144H	ENST00000265734	NM_001259.6	144	cGc/cAc	4/8	1	2	FACETS	0.38	0.306	0.463	0.38	0.306	0.463	SUBCLONAL	1	TRUE	1	0.310924230805364	2		334	525	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	38	356	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.622	0.515	0.741	0.622	0.515	0.741	SUBCLONAL	1	TRUE	1	0.310924230805364	2		356	393	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370706	55370706	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	102	582	0	ENST00000297316.4:c.8G>T	p.Ser3Ile	p.S3I	ENST00000297316	NM_022454.3	3	aGc/aTc	1/2	1	2	FACETS	0.969	0.868	1	0.969	0.868	1	CLONAL	1	TRUE	1	0.310924230805364	2		582	677	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606403	93606403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs570398843	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	133	672	0	ENST00000375746.1:c.223G>A	p.Ala75Thr	p.A75T	ENST00000375746	NM_001174167.1	75	Gcc/Acc	2/14	1	2	FACETS	0.933	0.847	1	0.933	0.847	1	CLONAL	1	TRUE	1	0.310924230805364	2		672	917	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760523	133760523	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	145	851	1	ENST00000318560.5:c.2846G>T	p.Ser949Ile	p.S949I	ENST00000318560	NM_005157.4	949	aGc/aTc	11/11	1	2	FACETS	0.904	0.823	0.988	0.904	0.823	0.988	CLONAL	1	TRUE	1	0.310924230805364	2		852	1032	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399315	139399315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369467132	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	166	895	0	ENST00000277541.6:c.4828G>A	p.Ala1610Thr	p.A1610T	ENST00000277541	NM_017617.3	1610	Gca/Aca	26/34	1	2	FACETS	0.91	0.835	0.99	0.91	0.835	0.99	CLONAL	1	TRUE	1	0.310924230805364	2		895	1173	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841268	15841268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	91	475	0	ENST00000307771.7:c.1352G>A	p.Arg451His	p.R451H	ENST00000307771	NM_005089.3	451	cGc/cAc	11/11	1	2	FACETS	0.912	0.81	1	0.912	0.81	1	CLONAL	1	TRUE	1	0.310924230805364	2		475	642	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932958	39932959	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	102	699	0	ENST00000378444.4:c.1640dup	p.Met547IlefsTer10	p.M547Ifs*10	ENST00000378444	NM_001123385.1	547	atg/atTg	4/15	1	2	FACETS	0.815	0.729	0.907	0.815	0.729	0.907	CLONAL	1	TRUE	1	0.310924230805364	2		699	805	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426438	47426438	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	94	691	2	ENST00000377045.4:c.781G>T	p.Ala261Ser	p.A261S	ENST00000377045	NM_001654.4	261	Gcc/Tcc	9/16	1	2	FACETS	0.667	0.592	0.746	0.667	0.592	0.746	SUBCLONAL	1	TRUE	1	0.310924230805364	2		693	907	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937879	76937880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	42	333	0	ENST00000373344.5:c.2868dup	p.Val957SerfsTer7	p.V957Sfs*7	ENST00000373344	NM_000489.3	956	-/A	9/35	1	2	FACETS	0.651	0.544	0.769	0.651	0.544	0.769	SUBCLONAL	1	TRUE	1	0.310924230805364	2		333	415	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0044599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	76	388	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.926	0.815	1	0.926	0.815	1	CLONAL	1	TRUE	1	0.365650112218554	2		388	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587781845	NA	P-0044599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	115	802	0	ENST00000269305.4:c.511G>T	p.Glu171Ter	p.E171*	ENST00000269305	NM_001126112.2	171	Gag/Tag	5/11	0.365650112218554	1	FACETS	0.948	0.858	1	0.948	0.858	1	CLONAL	1	TRUE	0	0.365650112218554	1		802	542	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262096	10262096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	127	716	0	ENST00000340748.4:c.2195C>T	p.Ser732Phe	p.S732F	ENST00000340748		732	tCt/tTt	23/40	1	2	FACETS	0.869	0.788	0.955	0.869	0.788	0.955	CLONAL	1	TRUE	1	0.365650112218554	2		716	799	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853199	68853200	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	122	579	0	ENST00000261769.5:c.1583dup	p.Asp528GlufsTer9	p.D528Efs*9	ENST00000261769	NM_004360.3	528	gac/gAac	11/16	0.365650112218554	1	FACETS	0.96	0.871	1	0.96	0.871	1	CLONAL	1	TRUE	0	0.365650112218554	1		579	568	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309876	30309876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	37	690	0	ENST00000307677.4:c.146G>A	p.Ser49Asn	p.S49N	ENST00000307677	NM_138578.1	49	aGt/aAt	2/3	1	2	FACETS	0.325	0.267	0.391	0.325	0.267	0.391	SUBCLONAL	1	TRUE	1	0.365650112218554	2		690	622	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967859	93967859	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	99	548	2	ENST00000369303.4:c.2068G>A	p.Asp690Asn	p.D690N	ENST00000369303	NM_004440.3	690	Gac/Aac	11/17	1	2	FACETS	0.9	0.805	1	0.9	0.805	1	CLONAL	1	TRUE	1	0.365650112218554	2		550	602	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	40	289	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.673	0.561	0.796	0.673	0.561	0.796	SUBCLONAL	1	TRUE	1	0.378683524563246	2		289	314	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	97	372	2	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.378683524563246	2	FACETS	1	0.932	1	0.527	0.472	0.585	CLONAL	1	TRUE	0	0.378683524563246	2		374	486	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	297	656	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.992	0.938	1	1	0.996	1	CLONAL	2	TRUE	1	0.378683524563246	2		657	791	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	125	446	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.378683524563246	2		446	570	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	144	298	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.988	0.902	1	0.988	0.902	1	CLONAL	1	TRUE	1	0.378683524563246	2		299	770	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294665	1294665	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	29	1070	5	ENST00000310581.5:c.336del	p.Glu113ArgfsTer15	p.E113Rfs*15	ENST00000310581	NM_198253.2	112	ccC/cc	2/16	1	2	FACETS	0.272	0.217	0.334	0.272	0.217	0.334	SUBCLONAL	1	TRUE	1	0.378683524563246	2		1075	563	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	152	877	12	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.378683524563246	2		889	763	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438316	110438317	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	rs532810290	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	69	790	0	ENST00000375856.3:c.82_84dup	p.Asn28dup	p.N28dup	ENST00000375856	NM_003749.2	28	-/AAC	1/2	1	2	FACETS	0.616	0.536	0.701	0.616	0.536	0.701	SUBCLONAL	1	TRUE	1	0.378683524563246	2		790	592	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	111	202	0	ENST00000397062.3:c.246A>T	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaT	2/5	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.378683524563246	2		202	563	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673750	176673750	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	104	505	0	ENST00000439151.2:c.4455del	p.Val1486Ter	p.V1486*	ENST00000439151	NM_022455.4	1484	Aaa/aa	10/23	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.378683524563246	2		505	534	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692790	89692790	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554898067	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	48	305	1	ENST00000371953.3:c.274G>T	p.Asp92Tyr	p.D92Y	ENST00000371953	NM_000314.4	92	Gac/Tac	5/9	1	2	FACETS	0.818	0.705	0.936	1	0.97	1	CLONAL	2	TRUE	1	0.378683524563246	2		306	155	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539105	23539105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	178	909	0	ENST00000380871.4:c.334G>A	p.Ala112Thr	p.A112T	ENST00000380871	NM_006167.3	112	Gcc/Acc	2/2	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.378683524563246	2		909	811	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412400	63412400	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	130	1006	0	ENST00000330258.3:c.767A>G	p.Lys256Arg	p.K256R	ENST00000330258	NM_152424.3	256	aAa/aGa	2/2	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.378683524563246	2		1006	632	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983228	149983228	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	65	383	0	ENST00000253339.5:c.3030del	p.Phe1010LeufsTer10	p.F1010Lfs*10	ENST00000253339		1010	ttT/tt	7/7	1	2	FACETS	0.848	0.738	0.966	0.848	0.738	0.966	CLONAL	1	TRUE	1	0.378683524563246	2		383	405	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302962	15302962	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761209241	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	143	1149	0	ENST00000263388.2:c.488G>A	p.Arg163Gln	p.R163Q	ENST00000263388	NM_000435.2	163	cGg/cAg	4/33	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.378683524563246	2		1149	736	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917496	178917496	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	31	180	0	ENST00000263967.3:c.371C>A	p.Pro124Gln	p.P124Q	ENST00000263967	NM_006218.2	124	cCa/cAa	3/21	1	2	FACETS	0.819	0.668	0.986	0.819	0.668	0.986	CLONAL	1	TRUE	1	0.378683524563246	2		180	200	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512402	38512402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	100	781	11	ENST00000254066.5:c.1319del	p.Pro440ArgfsTer203	p.P440Rfs*203	ENST00000254066	NM_000964.3	438	gCc/gc	9/9	1	2	FACETS	0.962	0.862	1	0.962	0.862	1	CLONAL	1	TRUE	1	0.378683524563246	2		792	549	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822586	72822586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	128	526	1	ENST00000268489.5:c.9589del	p.Gln3197SerfsTer44	p.Q3197Sfs*44	ENST00000268489	NM_006885.3	3197	Cag/ag	10/10	1	2	FACETS	0.784	0.71	0.862	0.784	0.71	0.862	SUBCLONAL	1	TRUE	1	0.378683524563246	2		527	862	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	129	839	2	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	1	2	FACETS	0.953	0.865	1	0.953	0.865	1	CLONAL	1	TRUE	1	0.378683524563246	2		841	715	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	177	626	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.378683524563246	2		627	885	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281358	15281358	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375474414	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	143	1150	1	ENST00000263388.2:c.4898C>T	p.Pro1633Leu	p.P1633L	ENST00000263388	NM_000435.2	1633	cCg/cTg	27/33	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.378683524563246	2		1151	743	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996755	100996757	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	62	485	0	ENST00000325455.5:c.1770_1772del	p.Phe591del	p.F591del	ENST00000325455	NM_001202474.3	590	ttCTTt/ttt	2/8	1	2	FACETS	0.842	0.73	0.962	0.842	0.73	0.962	CLONAL	1	TRUE	1	0.378683524563246	2		485	389	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541552	187541552	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1344941217	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	157	872	0	ENST00000441802.2:c.6188C>T	p.Ala2063Val	p.A2063V	ENST00000441802	NM_005245.3	2063	gCc/gTc	10/27	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.378683524563246	2		872	739	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	150	1002	6	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.378683524563246	2		1008	663	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964756	15964756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1452521115	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	133	602	1	ENST00000268712.3:c.5840C>T	p.Ala1947Val	p.A1947V	ENST00000268712	NM_006311.3	1947	gCg/gTg	37/46	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.378683524563246	2		603	623	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214067	36214067	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	191	1015	0	ENST00000222270.7:c.2893C>T	p.Arg965Ter	p.R965*	ENST00000222270	NM_014727.1	965	Cga/Tga	6/37	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.378683524563246	2		1015	768	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993640	90993640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	29	169	0	ENST00000265433.3:c.283del	p.Asp95MetfsTer14	p.D95Mfs*14	ENST00000265433	NM_002485.4	95	Gat/at	3/16	1	2	FACETS	0.969	0.787	1	0.969	0.787	1	CLONAL	1	TRUE	1	0.378683524563246	2		169	158	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845352	151845352	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	150	896	0	ENST00000262189.6:c.13660A>G	p.Ile4554Val	p.I4554V	ENST00000262189	NM_170606.2	4554	Atc/Gtc	52/59	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.378683524563246	2		896	739	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741810	17741810	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	127	854	0	ENST00000250003.3:c.481C>T	p.Gln161Ter	p.Q161*	ENST00000250003	NM_002478.4	161	Cag/Tag	1/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.378683524563246	2		854	475	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850786	63850786	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	164	915	0	ENST00000279873.7:c.1564C>T	p.Gln522Ter	p.Q522*	ENST00000279873	NM_032199.2	522	Caa/Taa	10/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.378683524563246	2		915	794	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916642	178916642	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	45	335	0	ENST00000263967.3:c.29T>C	p.Leu10Pro	p.L10P	ENST00000263967	NM_006218.2	10	cTg/cCg	2/21	1	2	FACETS	0.874	0.739	1	0.874	0.739	1	CLONAL	1	TRUE	1	0.378683524563246	2		335	272	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294207	11294207	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	115	763	0	ENST00000361445.4:c.2324T>C	p.Ile775Thr	p.I775T	ENST00000361445	NM_004958.3	775	aTt/aCt	14/58	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.378683524563246	2		763	593	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087378	27087379	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	90	625	0	ENST00000324856.7:c.1955_1956dup	p.Thr653GlyfsTer6	p.T653Gfs*6	ENST00000324856	NM_006015.4	651	atg/atGGg	5/20	1	2	FACETS	0.943	0.84	1	0.943	0.84	1	CLONAL	1	TRUE	1	0.378683524563246	2		625	504	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699343	117699343	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781259290	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	134	687	0	ENST00000369458.3:c.298C>T	p.Arg100Trp	p.R100W	ENST00000369458	NM_024626.3	100	Cgg/Tgg	3/6	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.378683524563246	2		687	671	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458720	120458720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	147	1056	0	ENST00000256646.2:c.6625C>T	p.Pro2209Ser	p.P2209S	ENST00000256646	NM_024408.3	2209	Cct/Tct	34/34	1	2	FACETS	0.995	0.91	1	0.995	0.91	1	CLONAL	1	TRUE	1	0.378683524563246	2		1056	780	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653438	206653438	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	95	874	0	ENST00000367120.3:c.1326del	p.Leu443CysfsTer47	p.L443Cfs*47	ENST00000367120	NM_014002.3	441	cGg/cg	12/22	1	2	FACETS	0.725	0.646	0.809	0.725	0.646	0.809	SUBCLONAL	1	TRUE	1	0.378683524563246	2		874	692	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431307	49431307	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	179	1075	2	ENST00000301067.7:c.9832C>T	p.Gln3278Ter	p.Q3278*	ENST00000301067	NM_003482.3	3278	Caa/Taa	34/54	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.378683524563246	2		1077	820	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50741684	50741684	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	15	84	0	ENST00000307179.4:c.335+2T>C		p.X112_splice	ENST00000307179		112			1	2	FACETS	0.727	0.538	0.948	0.727	0.538	0.948	CLONAL	1	TRUE	1	0.378683524563246	2		84	109	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354434	354434	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs767850282	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	180	732	0	ENST00000262320.3:c.1124A>G	p.Tyr375Cys	p.Y375C	ENST00000262320	NM_003502.3	375	tAc/tGc	5/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.378683524563246	2		732	722	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14015994	14015994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	56	325	0	ENST00000311895.7:c.314G>A	p.Gly105Asp	p.G105D	ENST00000311895	NM_005236.2	105	gGt/gAt	2/11	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.378683524563246	2		325	284	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38792331	38792331	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	63	354	0	ENST00000348513.6:c.393G>T	p.Lys131Asn	p.K131N	ENST00000348513	NM_003079.4	131	aaG/aaT	7/11	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.378683524563246	2		354	320	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170805	11170805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1029465394	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	130	927	0	ENST00000358026.2:c.4949G>A	p.Arg1650Gln	p.R1650Q	ENST00000358026	NM_001128849.1	1650	cGa/cAa	35/36	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.378683524563246	2		927	652	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224265	36224265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1344846321	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	116	925	0	ENST00000222270.7:c.6815C>T	p.Pro2272Leu	p.P2272L	ENST00000222270	NM_014727.1	2272	cCc/cTc	28/37	1	2	FACETS	0.924	0.834	1	0.924	0.834	1	CLONAL	1	TRUE	1	0.378683524563246	2		925	663	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425572	47425572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1599820519	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	126	681	0	ENST00000404338.3:c.3640C>T	p.Arg1214Trp	p.R1214W	ENST00000404338	NM_004491.4	1214	Cgg/Tgg	1/6	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.378683524563246	2		681	610	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222428	39222428	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	95	599	0	ENST00000402219.2:c.3182G>T	p.Arg1061Met	p.R1061M	ENST00000402219	NM_005633.3	1061	aGg/aTg	20/23	1	2	FACETS	0.855	0.763	0.953	0.855	0.763	0.953	CLONAL	1	TRUE	1	0.378683524563246	2		599	587	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62311299	62311299	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs201938707	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	142	827	0	ENST00000360203.5:c.1135C>T	p.Arg379Cys	p.R379C	ENST00000360203	NM_001283009.1	379	Cgt/Tgt	13/35	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.378683524563246	2		827	688	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513198	41513201	+	frameshift_variant	Frame_Shift_Del	DEL	CTCT	CTCT	-	rs886037664	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	40	326	0	ENST00000263253.7:c.104_107del	p.Ser35TyrfsTer12	p.S35Yfs*12	ENST00000263253	NM_001429.3	34	ggCTCT/gg	2/31	1	2	FACETS	0.652	0.544	0.772	0.652	0.544	0.772	SUBCLONAL	1	TRUE	1	0.378683524563246	2		326	324	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114175	73114175	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	84	515	0	ENST00000356692.5:c.811G>C	p.Val271Leu	p.V271L	ENST00000356692		271	Gtt/Ctt	8/9	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.378683524563246	2		515	427	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884816	134884816	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	34	599	0	ENST00000398015.3:c.1592A>G	p.Tyr531Cys	p.Y531C	ENST00000398015	NM_004441.4	531	tAc/tGc	8/16	1	2	FACETS	0.371	0.303	0.448	0.371	0.303	0.448	SUBCLONAL	1	TRUE	1	0.378683524563246	2		599	484	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156403	106156403	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	110	700	0	ENST00000380013.4:c.1304A>G	p.His435Arg	p.H435R	ENST00000380013	NM_001127208.2	435	cAc/cGc	3/11	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.378683524563246	2		700	570	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111602	56111602	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	95	1029	0	ENST00000399503.3:c.202G>C	p.Val68Leu	p.V68L	ENST00000399503	NM_005921.1	68	Gtg/Ctg	1/20	1	2	FACETS	0.919	0.821	1	0.919	0.821	1	CLONAL	1	TRUE	1	0.378683524563246	2		1029	546	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370935	55370936	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	106	922	0	ENST00000297316.4:c.239dup	p.Asp81GlyfsTer81	p.D81Gfs*81	ENST00000297316	NM_022454.3	79	-/A	1/2	1	2	FACETS	0.993	0.893	1	0.993	0.893	1	CLONAL	1	TRUE	1	0.378683524563246	2		922	564	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2060827	2060827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	74	450	0	ENST00000349721.2:c.1533G>T	p.Glu511Asp	p.E511D	ENST00000349721	NM_003070.3	511	gaG/gaT	9/34	1	2	FACETS	0.92	0.809	1	0.92	0.809	1	CLONAL	1	TRUE	1	0.378683524563246	2		450	425	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239956	98239956	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140537949	NA	P-0044610-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	130	678	0	ENST00000331920.6:c.1376G>A	p.Arg459His	p.R459H	ENST00000331920	NM_000264.3	459	cGc/cAc	10/24	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.378683524563246	2		678	627	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	41	289	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.902	0.753	1	0.902	0.753	1	CLONAL	1	TRUE	1	0.22	2		289	413	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	46	575	2	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.22	2		577	378	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	70	445	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.856	0.746	0.976	0.856	0.746	0.976	CLONAL	1	TRUE	1	0.22	2		445	743	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	63	758	2	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	2	FACETS	0.919	0.795	1	0.919	0.795	1	CLONAL	1	TRUE	1	0.22	2		760	623	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	51	293	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.22	2		293	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs786202525	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	61	937	0	ENST00000269305.4:c.532del	p.His178ThrfsTer69	p.H178Tfs*69	ENST00000269305	NM_001126112.2	178	Cac/ac	5/11	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.22	2		937	530	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	38	389	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.22	2		389	318	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042196	14042196	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	32	292	0	ENST00000311895.7:c.2747del	p.Lys916SerfsTer4	p.K916Sfs*4	ENST00000311895	NM_005236.2	915	Aaa/aa	11/11	1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	1	0.22	2		292	278	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	61	699	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.894	0.771	1	0.894	0.771	1	CLONAL	1	TRUE	1	0.22	2		706	620	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70441157	70441157	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	rs764225020	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	40	405	0	ENST00000373644.4:c.4832del	p.Asn1611ThrfsTer13	p.N1611Tfs*13	ENST00000373644	NM_030625.2	1609	gAa/ga	9/12	1	2	FACETS	0.785	0.653	0.933	0.785	0.653	0.933	CLONAL	1	TRUE	1	0.22	2		405	463	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1232964733	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	16	136	0	ENST00000324856.7:c.1015del	p.Ala339LeufsTer24	p.A339Lfs*24	ENST00000324856	NM_006015.4	337	tGg/tg	1/20	1	2	FACETS	1	0.757	1	1	0.757	1	CLONAL	1	TRUE	1	0.22	2		136	143	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	33	501	0	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	0.471	0.382	0.571	0.471	0.382	0.571	SUBCLONAL	1	TRUE	1	0.22	2		501	637	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	29	324	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	1	2	FACETS	0.714	0.574	0.875	0.714	0.574	0.875	SUBCLONAL	1	TRUE	1	0.22	2		324	369	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415537	152415537	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519714	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	56	624	0	ENST00000206249.3:c.1387T>C	p.Ser463Pro	p.S463P	ENST00000206249	NM_000125.3	463	Tcc/Ccc	7/8	1	2	FACETS	0.97	0.831	1	0.97	0.831	1	CLONAL	1	TRUE	1	0.22	2		624	525	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	79	803	1	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	1	2	FACETS	0.945	0.83	1	0.945	0.83	1	CLONAL	1	TRUE	1	0.22	2		804	760	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217234	11217234	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1031980569	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	68	712	0	ENST00000361445.4:c.4444C>T	p.Arg1482Cys	p.R1482C	ENST00000361445	NM_004958.3	1482	Cgc/Tgc	30/58	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.22	2		712	558	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348211	348211	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1458136153	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	81	1028	2	ENST00000262320.3:c.1295del	p.Pro432GlnfsTer48	p.P432Qfs*48	ENST00000262320	NM_003502.3	432	cCa/ca	6/11	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.22	2		1030	693	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136070	64136070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	85	898	1	ENST00000334205.4:c.1331G>A	p.Arg444His	p.R444H	ENST00000334205	NM_003942.2	444	cGc/cAc	11/17	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.22	2		899	628	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519896	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	37	439	0	ENST00000281708.4:c.1514G>T	p.Arg505Leu	p.R505L	ENST00000281708	NM_033632.3	505	cGc/cTc	10/12	1	2	FACETS	0.795	0.656	0.951	0.795	0.656	0.951	CLONAL	1	TRUE	1	0.22	2		439	423	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885939	111885939	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	38	812	0	ENST00000341259.2:c.1566del	p.Glu523SerfsTer25	p.E523Sfs*25	ENST00000341259	NM_005475.2	521	Ccc/cc	8/8	1	2	FACETS	0.69	0.57	0.824	0.69	0.57	0.824	SUBCLONAL	1	TRUE	1	0.22	2		812	501	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510102	187510102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368666671	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	30	551	0	ENST00000441802.2:c.13411G>A	p.Ala4471Thr	p.A4471T	ENST00000441802	NM_005245.3	4471	Gcg/Acg	27/27	1	2	FACETS	0.634	0.511	0.775	0.634	0.511	0.775	SUBCLONAL	1	TRUE	1	0.22	2		551	430	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434182	12434182	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776687	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	46	481	2	ENST00000287820.6:c.556del	p.Ser186ValfsTer47	p.S186Vfs*47	ENST00000287820	NM_015869.4	184	Aaa/aa	4/7	1	2	FACETS	0.755	0.635	0.887	0.755	0.635	0.887	SUBCLONAL	1	TRUE	1	0.22	2		483	554	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440430	49440431	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	66	990	0	ENST00000301067.7:c.4379dup	p.Leu1461ThrfsTer30	p.L1461Tfs*30	ENST00000301067	NM_003482.3	1460	cca/ccCa	15/54	1	2	FACETS	0.798	0.692	0.913	0.798	0.692	0.913	CLONAL	1	TRUE	1	0.22	2		990	752	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752961	128752962	+	inframe_insertion	In_Frame_Ins	INS	-	-	AACGTCTTGGAGCGCCAGAGGAGG	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	30	566	0	ENST00000377970.2:c.1127_1150dup	p.Val376_Asn383dup	p.V376_N383dup	ENST00000377970	NM_002467.4	376	-/AACGTCTTGGAGCGCCAGAGGAGG	3/3	1	2	FACETS	0.49	0.393	0.599	0.49	0.393	0.599	SUBCLONAL	1	TRUE	1	0.22	2		566	557	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900080	151900081	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	34	343	0	ENST00000262189.6:c.4030dup	p.Ile1344AsnfsTer11	p.I1344Nfs*11	ENST00000262189	NM_170606.2	1344	ata/aAta	26/59	0.0751626354253057	3	FACETS	0.641	0.523	0.775	0.321	0.261	0.388	INDETERMINATE	1	TRUE	1	0.22	3		343	535	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818213	32818213	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs143800384	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	49	777	0	ENST00000354258.4:c.1312C>T	p.Arg438Ter	p.R438*	ENST00000354258	NM_000593.5	438	Cga/Tga	5/11	1	2	FACETS	0.621	0.525	0.728	0.621	0.525	0.728	SUBCLONAL	1	TRUE	1	0.22	2		777	717	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123875192	123875192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745678227	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	65	511	1	ENST00000330479.4:c.148G>A	p.Gly50Arg	p.G50R	ENST00000330479	NM_020382.3	50	Ggg/Agg	3/9	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.22	2		512	545	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273414	38273414	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	35	1109	0	ENST00000425967.3:c.1921G>T	p.Gly641Cys	p.G641C	ENST00000425967	NM_001174067.1	641	Ggc/Tgc	14/19	1	2	FACETS	0.464	0.379	0.561	0.464	0.379	0.561	SUBCLONAL	1	TRUE	1	0.22	2		1109	685	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393425	139393425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542300217	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	64	953	3	ENST00000277541.6:c.6106G>A	p.Ala2036Thr	p.A2036T	ENST00000277541	NM_017617.3	2036	Gcc/Acc	33/34	1	2	FACETS	0.785	0.679	0.901	0.785	0.679	0.901	CLONAL	1	TRUE	1	0.22	2		956	741	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779331	3779331	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	49	881	0	ENST00000262367.5:c.5717C>A	p.Pro1906His	p.P1906H	ENST00000262367	NM_004380.2	1906	cCt/cAt	31/31	1	2	FACETS	0.688	0.582	0.806	0.688	0.582	0.806	SUBCLONAL	1	TRUE	1	0.22	2		881	647	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458783	120458783	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139052054	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	34	741	1	ENST00000256646.2:c.6562G>A	p.Ala2188Thr	p.A2188T	ENST00000256646	NM_024408.3	2188	Gcc/Acc	34/34	1	2	FACETS	0.611	0.498	0.738	0.611	0.498	0.738	SUBCLONAL	1	TRUE	1	0.22	2		742	506	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260319	16260319	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	58	625	1	ENST00000375759.3:c.7584C>G	p.Asp2528Glu	p.D2528E	ENST00000375759	NM_015001.2	2528	gaC/gaG	11/15	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.22	2		626	496	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106757	27106757	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	65	780	2	ENST00000324856.7:c.6368G>A	p.Ser2123Asn	p.S2123N	ENST00000324856	NM_006015.4	2123	aGc/aAc	20/20	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.22	2		782	547	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983062	201983062	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	75	997	0	ENST00000359651.3:c.911A>G	p.Lys304Arg	p.K304R	ENST00000359651		304	aAg/aGg	7/8	1	2	FACETS	0.86	0.752	0.976	0.86	0.752	0.976	CLONAL	1	TRUE	1	0.22	2		997	793	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448360	49448360	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	52	814	2	ENST00000301067.7:c.351G>T	p.Gln117His	p.Q117H	ENST00000301067	NM_003482.3	117	caG/caT	3/54	1	2	FACETS	0.72	0.612	0.838	0.72	0.612	0.838	SUBCLONAL	1	TRUE	1	0.22	2		816	657	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495802	56495802	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	20	534	0	ENST00000267101.3:c.3992G>T	p.Ser1331Ile	p.S1331I	ENST00000267101	NM_001982.3	1331	aGc/aTc	28/28	1	2	FACETS	0.487	0.372	0.623	0.487	0.372	0.623	SUBCLONAL	1	TRUE	1	0.22	2		534	373	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519135	103519135	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs765932206	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	29	405	0	ENST00000355739.4:c.2478del	p.Phe826LeufsTer7	p.F826Lfs*7	ENST00000355739	NM_000123.3	825	Ttt/tt	11/15	1	2	FACETS	0.569	0.456	0.698	0.569	0.456	0.698	SUBCLONAL	1	TRUE	1	0.22	2		405	463	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820717	3820717	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	63	1306	0	ENST00000262367.5:c.2734A>C	p.Thr912Pro	p.T912P	ENST00000262367	NM_004380.2	912	Acc/Ccc	14/31	1	2	FACETS	0.613	0.528	0.705	0.613	0.528	0.705	SUBCLONAL	1	TRUE	1	0.22	2		1306	935	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783808	50783808	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	54	680	0	ENST00000398568.2:c.203del	p.Asn68IlefsTer5	p.N68Ifs*5	ENST00000398568	NM_001042412.1	67	Aaa/aa	3/18	1	2	FACETS	0.703	0.6	0.817	0.703	0.6	0.817	SUBCLONAL	1	TRUE	1	0.22	2		680	698	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829847	72829847	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	62	969	0	ENST00000268489.5:c.6734C>G	p.Ser2245Ter	p.S2245*	ENST00000268489	NM_006885.3	2245	tCa/tGa	9/10	1	2	FACETS	0.724	0.625	0.833	0.724	0.625	0.833	SUBCLONAL	1	TRUE	1	0.22	2		969	778	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991917	72991917	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	49	743	0	ENST00000268489.5:c.2128del	p.His710ThrfsTer114	p.H710Tfs*114	ENST00000268489	NM_006885.3	710	Cac/ac	2/10	1	2	FACETS	0.742	0.628	0.868	0.742	0.628	0.868	SUBCLONAL	1	TRUE	1	0.22	2		743	600	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577593	7577593	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	15	712	0	ENST00000269305.4:c.688A>C	p.Thr230Pro	p.T230P	ENST00000269305	NM_001126112.2	230	Acc/Ccc	7/11	1	2	FACETS	0.238	0.173	0.316	0.238	0.173	0.316	SUBCLONAL	1	TRUE	1	0.22	2		712	574	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348485	56348485	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	31	354	3	ENST00000348428.3:c.297del	p.Gly100ValfsTer7	p.G100Vfs*7	ENST00000348428	NM_006785.3	98	gAa/ga	2/17	1	2	FACETS	0.776	0.628	0.943	0.776	0.628	0.943	CLONAL	1	TRUE	1	0.22	2		357	363	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961526	18961526	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	49	656	0	ENST00000262803.5:c.659A>C	p.Lys220Thr	p.K220T	ENST00000262803	NM_002911.3	220	aAg/aCg	5/24	1	2	FACETS	0.865	0.733	1	0.865	0.733	1	CLONAL	1	TRUE	1	0.22	2		656	515	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104596	209104596	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	52	596	0	ENST00000345146.2:c.982A>C	p.Asn328His	p.N328H	ENST00000345146	NM_005896.2	328	Aat/Cat	8/10	1	2	FACETS	0.955	0.814	1	0.955	0.814	1	CLONAL	1	TRUE	1	0.22	2		596	495	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391240	89391240	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	23	326	0	ENST00000336596.2:c.1306G>T	p.Ala436Ser	p.A436S	ENST00000336596	NM_005233.5	436	Gct/Tct	5/17	1	2	FACETS	0.632	0.492	0.793	0.632	0.492	0.793	SUBCLONAL	1	TRUE	1	0.22	2		326	331	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1936885	1936885	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1445291234	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	49	555	3	ENST00000382891.5:c.1576del	p.Arg526GlufsTer72	p.R526Efs*72	ENST00000382891	NM_133335.3	524	Aaa/aa	7/22	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.22	2		558	432	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391367	84391367	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	38	539	0	ENST00000321945.7:c.465A>C	p.Lys155Asn	p.K155N	ENST00000321945	NM_139076.2	155	aaA/aaC	5/9	1	2	FACETS	0.657	0.542	0.785	0.657	0.542	0.785	SUBCLONAL	1	TRUE	1	0.22	2		539	526	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540632	187540632	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	17	435	0	ENST00000441802.2:c.7108C>A	p.Leu2370Met	p.L2370M	ENST00000441802	NM_005245.3	2370	Ctg/Atg	10/27	1	2	FACETS	0.481	0.359	0.628	0.481	0.359	0.628	SUBCLONAL	1	TRUE	1	0.22	2		435	321	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31511285	31511285	+	splice_acceptor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	42	602	0	ENST00000344624.3:c.1291-2del		p.X431_splice	ENST00000344624		431			1	2	FACETS	0.571	0.475	0.677	0.571	0.475	0.677	SUBCLONAL	1	TRUE	1	0.22	2		602	669	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588971	67588972	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	30	320	0	ENST00000274335.5:c.1066_1067dup	p.Leu356PhefsTer18	p.L356Ffs*18	ENST00000274335		354	-/TT	8/15	1	2	FACETS	0.921	0.744	1	0.921	0.744	1	CLONAL	1	TRUE	1	0.22	2		320	296	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858470	27858470	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	17	515	0	ENST00000359303.2:c.101G>A	p.Gly34Asp	p.G34D	ENST00000359303	NM_003535.2	34	gGc/gAc	1/1	1	2	FACETS	0.494	0.368	0.643	0.494	0.368	0.643	SUBCLONAL	1	TRUE	1	0.22	2		515	313	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672902	30672902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768639435	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	56	976	0	ENST00000376406.3:c.4058G>A	p.Ser1353Asn	p.S1353N	ENST00000376406	NM_014641.2	1353	aGc/aAc	10/15	1	2	FACETS	0.659	0.564	0.765	0.659	0.564	0.765	SUBCLONAL	1	TRUE	1	0.22	2		976	772	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815428	32815428	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	46	653	2	ENST00000354258.4:c.1945C>T	p.Gln649Ter	p.Q649*	ENST00000354258	NM_000593.5	649	Cag/Tag	9/11	1	2	FACETS	0.83	0.699	0.974	0.83	0.699	0.974	CLONAL	1	TRUE	1	0.22	2		655	504	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117632270	117632270	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	32	438	0	ENST00000368508.3:c.6146C>A	p.Pro2049His	p.P2049H	ENST00000368508	NM_002944.2	2049	cCt/cAt	39/43	1	2	FACETS	0.752	0.61	0.911	0.752	0.61	0.911	CLONAL	1	TRUE	1	0.22	2		438	387	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517355	157517355	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs387907140	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	33	603	2	ENST00000346085.5:c.3919C>T	p.Gln1307Ter	p.Q1307*	ENST00000346085	NM_020732.3	1307	Cag/Tag	16/20	1	2	FACETS	0.61	0.496	0.738	0.61	0.496	0.738	SUBCLONAL	1	TRUE	1	0.22	2		605	492	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729864	41729864	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	33	560	0	ENST00000242208.4:c.665C>A	p.Pro222His	p.P222H	ENST00000242208	NM_002192.2	222	cCt/cAt	3/3	0.0751626354253057	3	FACETS	0.822	0.67	0.994	0.411	0.335	0.497	INDETERMINATE	1	TRUE	1	0.22	3		560	405	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259548	55259548	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1440961719	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	57	859	0	ENST00000275493.2:c.2606A>G	p.Tyr869Cys	p.Y869C	ENST00000275493	NM_005228.3	869	tAc/tGc	21/28	0.0751626354253057	3	FACETS	0.997	0.855	1	0.498	0.427	0.576	INDETERMINATE	1	TRUE	1	0.22	3		859	577	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293538	137293538	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	69	1189	0	ENST00000481739.1:c.93del	p.Ser32ArgfsTer23	p.S32Rfs*23	ENST00000481739	NM_002957.4	30	gCc/gc	2/10	1	2	FACETS	0.852	0.741	0.972	0.852	0.741	0.972	CLONAL	1	TRUE	1	0.22	2		1189	736	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969403	44969403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	57	589	0	ENST00000377967.4:c.4085C>T	p.Ala1362Val	p.A1362V	ENST00000377967	NM_021140.2	1362	gCa/gTa	28/29	1	2	FACETS	0.834	0.715	0.964	0.834	0.715	0.964	CLONAL	1	TRUE	1	0.22	2		589	621	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039704	47039704	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	91	1082	0	ENST00000377604.3:c.1156A>G	p.Lys386Glu	p.K386E	ENST00000377604	NM_001204468.1	386	Aag/Gag	11/24	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.22	2		1082	695	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041265	47041265	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	81	1065	1	ENST00000377604.3:c.1693C>A	p.Pro565Thr	p.P565T	ENST00000377604	NM_001204468.1	565	Cct/Act	15/24	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.22	2		1066	710	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422624	47422624	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	59	680	0	ENST00000377045.4:c.97-1G>A		p.X33_splice	ENST00000377045	NM_001654.4	33			1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.22	2		680	522	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849183	76849183	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	31	319	0	ENST00000373344.5:c.6093G>T	p.Glu2031Asp	p.E2031D	ENST00000373344	NM_000489.3	2031	gaG/gaT	26/35	1	2	FACETS	0.867	0.703	1	0.867	0.703	1	CLONAL	1	TRUE	1	0.22	2		319	325	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325293	39325293	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	230	443	2	ENST00000373001.3:c.26A>T	p.Glu9Val	p.E9V	ENST00000373001	NM_022157.3	9	gAg/gTg	1/7	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.747959738184039	2		445	542	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65311261	65311261	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	151	442	1	ENST00000342505.4:c.2050G>A	p.Asp684Asn	p.D684N	ENST00000342505	NM_002227.2	684	Gat/Aat	15/25	1	2	FACETS	0.973	0.899	1	0.973	0.899	1	CLONAL	1	TRUE	1	0.747959738184039	2		443	415	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112764374	112764374	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	47	264	1	ENST00000369452.4:c.983C>T	p.Ser328Leu	p.S328L	ENST00000369452	NM_007373.3	328	tCa/tTa	5/9	0.747959738184039	1	FACETS	0.684	0.595	0.776	0.684	0.595	0.776	SUBCLONAL	1	TRUE	0	0.747959738184039	1		265	115	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281503	49281518	+	frameshift_variant	Frame_Shift_Del	DEL	GTCACATCATGCTTAG	GTCACATCATGCTTAG	-	novel	NA	P-0044745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	127	469	0	ENST00000282018.3:c.550_565del	p.Val184SerfsTer2	p.V184Sfs*2	ENST00000282018	NM_020377.2	184	GTCACATCATGCTTAGag/ag	1/1	0.592643786120777	1	FACETS	0.889	0.825	0.953	0.889	0.825	0.953	CLONAL	1	TRUE	0	0.747959738184039	1		469	239	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628078	90628078	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	301	708	0	ENST00000330062.3:c.1241A>T	p.Asp414Val	p.D414V	ENST00000330062	NM_002168.2	414	gAc/gTc	10/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.747959738184039	2		708	728	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439228	52439229	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0044745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	229	647	0	ENST00000460680.1:c.1013dup	p.Pro339SerfsTer59	p.P339Sfs*59	ENST00000460680	NM_004656.3	338	cct/ccCt	11/17	0.736784889347103	1	FACETS	0.988	0.938	1	0.988	0.938	1	CLONAL	1	TRUE	0	0.747959738184039	1		647	388	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261434	16261434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	105	647	0	ENST00000375759.3:c.8699C>T	p.Ser2900Leu	p.S2900L	ENST00000375759	NM_015001.2	2900	tCg/tTg	11/15	0.186541413595509	3	FACETS	0.941	0.844	1	0.941	0.844	1	CLONAL	2	TRUE	1	0.186541413595509	3		647	654	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0044756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	98	758	0	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.186541413595509	2		758	728	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0044756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	133	465	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.186541413595509	3	FACETS	0.885	0.807	0.967	1	0.983	1	CLONAL	3	TRUE	1	0.186541413595509	3		465	587	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230571	46230571	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	46	353	0	ENST00000334344.6:c.820C>T	p.Arg274Ter	p.R274*	ENST00000334344	NM_152641.2	274	Cga/Tga	8/21	0.186541413595509	2	FACETS	0.924	0.783	1	0.924	0.783	1	CLONAL	2	TRUE	0	0.186541413595509	2		353	267	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066618	94066618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	70	477	0	ENST00000369303.4:c.1141C>T	p.Pro381Ser	p.P381S	ENST00000369303	NM_004440.3	381	Ccc/Tcc	5/17	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.186541413595509	2		477	517	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683852	117683852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	38	312	0	ENST00000368508.3:c.3295G>A	p.Glu1099Lys	p.E1099K	ENST00000368508	NM_002944.2	1099	Gaa/Aaa	21/43	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.186541413595509	2		312	286	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295230	+	upstream_gene_variant	5'Flank	TNP	GGG	GGG	AAA	novel	NA	P-0044756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	35	449	1				ENST00000310581	NM_198253.2	-/1132			0.186541413595509	3	FACETS	1	0.924	1			1	CLONAL	1	TRUE	NA	0.186541413595509	3		450	327	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752724	42752724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764618715	NA	P-0044756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	142	861	1	ENST00000222329.4:c.1540C>T	p.Arg514Cys	p.R514C	ENST00000222329	NM_006494.2	514	Cgt/Tgt	4/4	0.186541413595509	3	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	1	0.186541413595509	3		862	795	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972744	25972744	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1348431069	NA	P-0044756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	87	436	0	ENST00000435504.4:c.1681C>T	p.Gln561Ter	p.Q561*	ENST00000435504		561	Cag/Tag	12/13	0.186085479608346	4	FACETS	1	0.906	1	1	0.906	1	CLONAL	2	TRUE	2	0.186541413595509	4		436	541	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458559	12458559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	81	677	0	ENST00000287820.6:c.1176G>A	p.Met392Ile	p.M392I	ENST00000287820	NM_015869.4	392	atG/atA	6/7	0.186541413595509	3	FACETS	0.78	0.687	0.878	0.78	0.687	0.878	SUBCLONAL	2	TRUE	1	0.186541413595509	3		677	609	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374685	118374685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	48	427	0	ENST00000534358.1:c.8078C>T	p.Ser2693Phe	p.S2693F	ENST00000534358	NM_005933.3	2693	tCt/tTt	27/36	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.186541413595509	2		427	345	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686270	117686270	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	36	295	0	ENST00000368508.3:c.3071G>A	p.Trp1024Ter	p.W1024*	ENST00000368508	NM_002944.2	1024	tGg/tAg	20/43	1	2	FACETS	0.843	0.698	1	1	0.959	1	CLONAL	2	TRUE	1	0.186541413595509	2		295	229	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695759	117695759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	66	354	0	ENST00000369458.3:c.678G>A	p.Met226Ile	p.M226I	ENST00000369458	NM_024626.3	226	atG/atA	4/6	0.186541413595509	3	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	1	0.186541413595509	3		354	352	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647681	206647681	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	28	518	0	ENST00000367120.3:c.95G>A	p.Gly32Glu	p.G32E	ENST00000367120	NM_014002.3	32	gGa/gAa	4/22	0.186541413595509	3	FACETS	0.685	0.547	0.844	0.343	0.273	0.422	SUBCLONAL	1	TRUE	1	0.186541413595509	3		518	479	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63760006	63760006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	62	396	0	ENST00000279873.7:c.659C>T	p.Pro220Leu	p.P220L	ENST00000279873	NM_032199.2	220	cCt/cTt	4/10	0.186541413595509	2	FACETS	0.875	0.759	0.999	0.875	0.759	0.999	CLONAL	2	TRUE	0	0.186541413595509	2		396	380	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156623	2156623	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	95	752	1	ENST00000434045.2:c.299T>A	p.Val100Asp	p.V100D	ENST00000434045	NM_001127598.1	100	gTc/gAc	3/5	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.186541413595509	2		753	719	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118770	115118770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	114	549	0	ENST00000257566.3:c.571C>T	p.Pro191Ser	p.P191S	ENST00000257566	NM_016569.3	191	Ccc/Tcc	2/8	0.186541413595509	2	FACETS	0.937	0.845	1	0.937	0.845	1	CLONAL	2	TRUE	0	0.186541413595509	2		549	652	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923417	9923417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	84	673	0	ENST00000330684.3:c.1870G>A	p.Gly624Arg	p.G624R	ENST00000330684	NM_001134407.1	624	Ggg/Agg	9/13	0.186541413595509	3	FACETS	0.827	0.732	0.93	0.827	0.732	0.93	CLONAL	2	TRUE	1	0.186541413595509	3		673	595	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604664	48604664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397518413	NA	P-0044756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	54	342	0	ENST00000342988.3:c.1486C>T	p.Arg496Cys	p.R496C	ENST00000342988	NM_005359.5	496	Cgt/Tgt	12/12	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.186541413595509	2		342	392	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367243	50367243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	32	340	1	ENST00000331340.3:c.50G>A	p.Ser17Asn	p.S17N	ENST00000331340	NM_006060.4	17	aGc/aAc	3/8	0.186541413595509	3	FACETS	1	0.815	1	0.501	0.407	0.608	CLONAL	1	TRUE	1	0.186541413595509	3		341	374	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55270316	55270316	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	205	853	3	ENST00000275493.2:c.3269C>T	p.Pro1090Leu	p.P1090L	ENST00000275493	NM_005228.3	1090	cCt/cTt	27/28	0.186541413595509	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.186541413595509	3		856	1029	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741433	145741433	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	92	1079	0	ENST00000428558.2:c.1070A>T	p.Asn357Ile	p.N357I	ENST00000428558	NM_004260.3	357	aAc/aTc	5/22	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.186541413595509	2		1079	963	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163695	32163695	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	345	551	0	ENST00000375023.3:c.5531G>C	p.Arg1844Pro	p.R1844P	ENST00000375023	NM_004557.3	1844	cGg/cCg	30/30	0.591728952183287	6	FACETS	0.884	0.841	0.928	0.663	0.631	0.696	CLONAL	3	TRUE	2	0.850360730937937	6		551	826	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0044764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	1139	580	0	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.85706957238853	4	FACETS	1	0.998	1	1	0.998	1	CLONAL	4	TRUE	0	0.850360730937937	4		580	1182	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432320	49432348	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGCCGGTGGGGCTGAGGGTTTCTGTGG	GGGGCCGGTGGGGCTGAGGGTTTCTGTGG	-	novel	NA	P-0044764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	395	812	1	ENST00000301067.7:c.8791_8819del	p.Pro2931Ter	p.P2931*	ENST00000301067	NM_003482.3	2931	CCACAGAAACCCTCAGCCCCACCGGCCCCt/t	34/54	0.788469229962918	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.850360730937937	1		813	484	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241414	105241414	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	49	631	0	ENST00000349310.3:c.566A>C	p.Lys189Thr	p.K189T	ENST00000349310	NM_001014432.1	189	aAg/aCg	7/15	0.85706957238853	3	FACETS	0.174	0.146	0.204	0.058	0.048	0.068	SUBCLONAL	1	TRUE	0	0.850360730937937	3		631	946	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439473	220439473	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs141659806	NA	P-0044764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	179	467	1	ENST00000243786.2:c.326G>T	p.Gly109Val	p.G109V	ENST00000243786	NM_002191.3	109	gGc/gTc	2/2	0.85706957238853	4	FACETS	0.86	0.793	0.929	0.287	0.264	0.31	CLONAL	1	TRUE	1	0.850360730937937	4		468	906	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72842073	72842073	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	79	205	0	ENST00000325599.8:c.1175A>C	p.Lys392Thr	p.K392T	ENST00000325599	NM_018130.2	392	aAa/aCa	10/11	0.606050335060525	4	FACETS	1	0.978	1	0.482	0.43	0.535	CLONAL	1	TRUE	1	0.850360730937937	4		205	238	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050752	69050752	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	13	198	0	ENST00000288368.4:c.4087A>G	p.Asn1363Asp	p.N1363D	ENST00000288368	NM_024870.2	1363	Aat/Gat	33/40	1	2	FACETS	0.223	0.16	0.299	0.223	0.16	0.299	SUBCLONAL	1	TRUE	1	0.850360730937937	2		198	137	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	46	475	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.972	0.823	1	0.972	0.823	1	CLONAL	1	TRUE	1	0.323195450061391	2		476	293	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0044767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	31	293	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	0.164480204855163	3	FACETS	1	0.933	1	0.671	0.549	0.806	INDETERMINATE	1	TRUE	1	0.323195450061391	3		293	166	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0044767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	78	66	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.164480204855163	3	FACETS	0.994	0.884	1	0.994	0.884	1	INDETERMINATE	2	TRUE	1	0.323195450061391	3		66	282	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0044767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	18	328	0	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	1	2	FACETS	0.615	0.466	0.791	0.615	0.466	0.791	SUBCLONAL	1	TRUE	1	0.323195450061391	2		328	181	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589589	67589591	+	inframe_deletion	In_Frame_Del	DEL	AAT	AAT	-	novel	NA	P-0044767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	26	156	0	ENST00000274335.5:c.1353_1355del	p.Glu451_Tyr452delinsAsp	p.E451_Y452delinsD	ENST00000274335		451	gAATat/gat	10/15	1	2	FACETS	0.781	0.632	0.944	1	0.942	1	CLONAL	2	TRUE	1	0.323195450061391	2		156	103	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991949	72991949	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs753977275	NA	P-0044767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	69	644	3	ENST00000268489.5:c.2096del	p.Gly699AlafsTer125	p.G699Afs*125	ENST00000268489	NM_006885.3	699	gGc/gc	2/10	1	2	FACETS	0.791	0.69	0.9	0.791	0.69	0.9	SUBCLONAL	1	TRUE	1	0.323195450061391	2		647	540	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588164	67588164	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	61	300	0	ENST00000274335.5:c.994G>T	p.Glu332Ter	p.E332*	ENST00000274335		332	Gaa/Taa	7/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.323195450061391	2		300	258	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451150	70451150	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564186545	NA	P-0044767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	85	650	0	ENST00000373644.4:c.5990G>A	p.Ser1997Asn	p.S1997N	ENST00000373644	NM_030625.2	1997	aGt/aAt	12/12	0.164480204855163	3	FACETS	1	0.923	1	0.528	0.467	0.592	INDETERMINATE	1	TRUE	1	0.323195450061391	3		650	579	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466022	69466023	+	inframe_insertion	In_Frame_Ins	INS	-	-	CACCGA	novel	NA	P-0044767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	179	783	0	ENST00000227507.2:c.862_867dup	p.Thr288_Asp289dup	p.T288_D289dup	ENST00000227507	NM_053056.2	288	ccc/ccCACCGAc	5/5	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.323195450061391	2		783	747	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491484	18491484	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0044767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	12	230	0	ENST00000266497.5:c.1395+2T>A		p.X465_splice	ENST00000266497		465			0.239999467467146	4	FACETS	0.717	0.507	0.973	0.359	0.253	0.487	CLONAL	1	TRUE	2	0.323195450061391	4		230	137	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426634	49426634	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	165	549	0	ENST00000301067.7:c.11854C>T	p.Gln3952Ter	p.Q3952*	ENST00000301067	NM_003482.3	3952	Caa/Taa	39/54	0.239999467467146	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.323195450061391	4		549	542	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438146	110438147	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	143	417	0	ENST00000375856.3:c.254dup	p.Ala86GlyfsTer111	p.A86Gfs*111	ENST00000375856	NM_003749.2	85	aag/aaAg	1/2	1	2	FACETS	0.832	0.762	0.903	1	0.989	1	CLONAL	2	TRUE	1	0.323195450061391	2		417	532	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645891	67645891	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	128	535	1	ENST00000264010.4:c.819C>A	p.Tyr273Ter	p.Y273*	ENST00000264010	NM_006565.3	273	taC/taA	4/12	1	2	FACETS	0.778	0.709	0.85	1	0.987	1	SUBCLONAL	2	TRUE	1	0.323195450061391	2		536	509	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984378	72984378	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	143	554	0	ENST00000268489.5:c.3206A>G	p.Lys1069Arg	p.K1069R	ENST00000268489	NM_006885.3	1069	aAg/aGg	3/10	1	2	FACETS	0.812	0.744	0.882	1	0.989	1	CLONAL	2	TRUE	1	0.323195450061391	2		554	545	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89825093	89825093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1374262828	NA	P-0044767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	145	477	1	ENST00000389301.3:c.2873C>T	p.Ala958Val	p.A958V	ENST00000389301	NM_000135.2	958	gCg/gTg	30/43	1	2	FACETS	0.776	0.711	0.844	1	0.988	1	SUBCLONAL	2	TRUE	1	0.323195450061391	2		478	578	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437565	52437565	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	194	712	0	ENST00000460680.1:c.1596del	p.Phe532LeufsTer39	p.F532Lfs*39	ENST00000460680	NM_004656.3	532	ttT/tt	13/17	1	2	FACETS	0.834	0.774	0.895	1	0.992	1	CLONAL	2	TRUE	1	0.323195450061391	2		712	720	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019961	123019961	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	89	638	0	ENST00000355640.3:c.449C>A	p.Ser150Ter	p.S150*	ENST00000355640		150	tCa/tAa	2/7	0.130145492630453	0	FACETS	1	0.929	1			1	INDETERMINATE	1	TRUE	0	0.323195450061391	0		638	355	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858050	152858050	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	113	606	0	ENST00000406277.2:c.565A>T	p.Ile189Phe	p.I189F	ENST00000406277	NM_152274.4	189	Atc/Ttc	6/7	0.130145492630453	0	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	0	0.323195450061391	0		606	418	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	54	279	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.240146031990621	3	FACETS	0.689	0.588	0.799	0.345	0.294	0.4	SUBCLONAL	1	TRUE	1	0.313081237259599	3		279	579	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604750	48604750	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	84	423	0	ENST00000342988.3:c.1572G>C	p.Trp524Cys	p.W524C	ENST00000342988	NM_005359.5	524	tgG/tgC	12/12	0.309924846339991	1	FACETS	0.913	0.809	1	0.913	0.809	1	CLONAL	1	TRUE	0	0.313081237259599	1		423	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0044779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	202	559	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.275932677336072	2	FACETS	0.866	0.805	0.929	0.866	0.805	0.929	CLONAL	2	TRUE	0	0.313081237259599	2		559	745	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100514	8100514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201023943	NA	P-0044779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	107	732	2	ENST00000346208.3:c.488C>T	p.Pro163Leu	p.P163L	ENST00000346208		163	cCg/cTg	3/6	0.240146031990621	3	FACETS	0.826	0.74	0.918	0.413	0.37	0.459	CLONAL	1	TRUE	1	0.313081237259599	3		734	957	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158588	26158588	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1415465556	NA	P-0044779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	69	417	0	ENST00000289316.2:c.191A>G	p.Asn64Ser	p.N64S	ENST00000289316	NM_138720.2	64	aAt/aGt	1/2	0.248374056460608	3	FACETS	0.843	0.734	0.96	0.421	0.367	0.48	CLONAL	1	TRUE	1	0.313081237259599	3		417	605	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	148	760	5	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.935	0.856	1	0.935	0.856	1	CLONAL	1	TRUE	1	0.443972787070912	2		765	713	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	100	478	4	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.443972787070912	2		482	400	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	106	356	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.443972787070912	2		356	458	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	141	298	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.996	0.91	1	0.996	0.91	1	CLONAL	1	TRUE	1	0.443972787070912	2		299	638	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	355	699	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.987	0.941	1	1	0.996	1	CLONAL	2	TRUE	1	0.443972787070912	2		706	810	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209721	98209721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749244396	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	146	647	0	ENST00000331920.6:c.3817G>A	p.Glu1273Lys	p.E1273K	ENST00000331920	NM_000264.3	1273	Gaa/Aaa	23/24	0.443972787070912	3	FACETS	0.937	0.855	1	0.468	0.427	0.511	CLONAL	1	TRUE	1	0.443972787070912	3		647	858	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	379	566	7	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.997	0.952	1	1	0.997	1	CLONAL	2	TRUE	1	0.443972787070912	2		573	856	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053022	180053023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750808726	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	150	610	1	ENST00000261937.6:c.1267dup	p.Gln423ProfsTer4	p.Q423Pfs*4	ENST00000261937	NM_182925.4	423	cag/cCag	10/30	1	2	FACETS	0.801	0.732	0.872	0.801	0.732	0.872	CLONAL	1	TRUE	1	0.443972787070912	2		611	844	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044348	128044348	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913047	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	158	550	0	ENST00000285398.2:c.1273C>T	p.Arg425Ter	p.R425*	ENST00000285398	NM_000122.1	425	Cga/Tga	8/15	1	2	FACETS	0.952	0.874	1	0.952	0.874	1	CLONAL	1	TRUE	1	0.443972787070912	2		550	748	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521103	187521103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs183364307	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	144	421	1	ENST00000441802.2:c.12052G>A	p.Ala4018Thr	p.A4018T	ENST00000441802	NM_005245.3	4018	Gcc/Acc	22/27	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.443972787070912	2		422	596	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	112	551	1	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	0.815	0.735	0.9	0.815	0.735	0.9	CLONAL	1	TRUE	1	0.443972787070912	2		552	619	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	128	620	3	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.924	0.84	1	0.924	0.84	1	CLONAL	1	TRUE	1	0.443972787070912	2		623	624	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260058	19260058	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143400241	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	194	647	3	ENST00000162023.5:c.235C>T	p.Arg79Cys	p.R79C	ENST00000162023		79	Cgc/Tgc	7/13	1	2	FACETS	0.978	0.905	1	0.978	0.905	1	CLONAL	1	TRUE	1	0.443972787070912	2		650	894	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120258	70120259	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	210	540	1	ENST00000245479.2:c.1261dup	p.Ser421LysfsTer157	p.S421Kfs*157	ENST00000245479	NM_000346.3	420	-/A	3/3	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.443972787070912	2		541	754	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155779	106155779	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	96	377	0	ENST00000380013.4:c.685del	p.Thr229HisfsTer21	p.T229Hfs*21	ENST00000380013	NM_001127208.2	227	gAa/ga	3/11	1	2	FACETS	0.881	0.788	0.979	0.881	0.788	0.979	CLONAL	1	TRUE	1	0.443972787070912	2		377	491	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105676	27105678	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs753766136	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	89	319	0	ENST00000324856.7:c.5299_5301del	p.Glu1767del	p.E1767del	ENST00000324856	NM_006015.4	1763	GAA/-	20/20	1	2	FACETS	0.791	0.703	0.884	0.791	0.703	0.884	SUBCLONAL	1	TRUE	1	0.443972787070912	2		319	507	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346220	152346220	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	141	459	5	ENST00000359321.1:c.350del	p.Leu117TrpfsTer17	p.L117Wfs*17	ENST00000359321	NM_005431.1	117	tTg/tg	3/3	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.443972787070912	2		464	623	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686961	37686962	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	123	468	0	ENST00000447079.4:c.3871dup	p.Gln1291ProfsTer19	p.Q1291Pfs*19	ENST00000447079	NM_015083.1	1289	gcc/gCcc	14/14	1	2	FACETS	0.888	0.805	0.975	0.888	0.805	0.975	CLONAL	1	TRUE	1	0.443972787070912	2		468	624	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288788	15288789	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	52	99	0	ENST00000263388.2:c.3950dup	p.Gly1318ArgfsTer245	p.G1318Rfs*245	ENST00000263388	NM_000435.2	1317	cca/ccCa	24/33	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.443972787070912	2		99	226	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794732	120794732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276733276	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	205	669	1	ENST00000257552.2:c.625G>A	p.Ala209Thr	p.A209T	ENST00000257552	NM_002442.3	209	Gcc/Acc	9/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.443972787070912	2		670	806	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	262	332	0	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.929	0.877	0.982	1	0.995	1	CLONAL	2	TRUE	1	0.443972787070912	2		332	635	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880988	37880988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772054394	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	205	655	0	ENST00000269571.5:c.2317G>A	p.Val773Met	p.V773M	ENST00000269571		773	Gtg/Atg	20/27	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.443972787070912	2		655	889	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913836	32913837	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359507	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	80	364	3	ENST00000380152.3:c.5351dup	p.Asn1784LysfsTer3	p.N1784Kfs*3	ENST00000380152		1782	caa/cAaa	11/27	1	2	FACETS	0.85	0.752	0.954	0.85	0.752	0.954	CLONAL	1	TRUE	1	0.443972787070912	2		367	424	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971039	21971039	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554654024	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	169	381	0	ENST00000304494.5:c.319C>T	p.Arg107Cys	p.R107C	ENST00000304494	NM_000077.4	107	Cgc/Tgc	2/3	0.443972787070912	3	FACETS	1	0.986	1	0.663	0.611	0.716	CLONAL	1	TRUE	1	0.443972787070912	3		381	702	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	162	493	3	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.898	0.824	0.974	0.898	0.824	0.974	CLONAL	1	TRUE	1	0.443972787070912	2		496	813	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38184289	38184289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149768452	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	93	436	1	ENST00000317025.8:c.1667C>T	p.Thr556Met	p.T556M	ENST00000317025	NM_023034.1	556	aCg/aTg	7/24	1	2	FACETS	0.689	0.614	0.769	0.689	0.614	0.769	SUBCLONAL	1	TRUE	1	0.443972787070912	2		437	608	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819239	3819239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772991403	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	154	472	2	ENST00000262367.5:c.2996C>T	p.Thr999Met	p.T999M	ENST00000262367	NM_004380.2	999	aCg/aTg	15/31	1	2	FACETS	0.918	0.841	0.997	0.918	0.841	0.997	CLONAL	1	TRUE	1	0.443972787070912	2		474	756	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240233	5240233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202189767	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	199	974	0	ENST00000357368.4:c.1681C>T	p.Arg561Trp	p.R561W	ENST00000357368	NM_002850.3	561	Cgg/Tgg	12/38	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.443972787070912	2		974	856	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022747	12022747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376242225	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	115	456	1	ENST00000396373.4:c.853G>A	p.Val285Met	p.V285M	ENST00000396373	NM_001987.4	285	Gtg/Atg	5/8	1	2	FACETS	0.874	0.789	0.962	0.874	0.789	0.962	CLONAL	1	TRUE	1	0.443972787070912	2		457	593	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300039	137300040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755912201	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	175	681	5	ENST00000481739.1:c.331dup	p.Leu111ProfsTer70	p.L111Pfs*70	ENST00000481739	NM_002957.4	108	-/C	3/10	0.443972787070912	3	FACETS	0.822	0.756	0.891	0.411	0.378	0.446	CLONAL	1	TRUE	1	0.443972787070912	3		686	1172	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851274	156851274	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	185	686	0	ENST00000524377.1:c.2231G>C	p.Arg744Pro	p.R744P	ENST00000524377	NM_002529.3	744	cGt/cCt	17/17	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.443972787070912	2		686	783	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430228	181430228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	138	358	0	ENST00000325404.1:c.80C>T	p.Ala27Val	p.A27V	ENST00000325404	NM_003106.3	27	gCg/gTg	1/1	0.443972787070912	2	FACETS	1	0.986	1	0.698	0.641	0.758	CLONAL	1	TRUE	0	0.443972787070912	2		358	445	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39002716	39002716	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	112	288	1	ENST00000357387.3:c.313C>T	p.Arg105Ter	p.R105*	ENST00000357387	NM_152756.3	105	Cga/Tga	5/38	1	2	FACETS	0.896	0.809	0.988	0.896	0.809	0.988	CLONAL	1	TRUE	1	0.443972787070912	2		289	563	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797891	45797891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199840380	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	184	676	0	ENST00000450313.1:c.880C>T	p.Arg294Cys	p.R294C	ENST00000450313	NM_012222.2	294	Cgc/Tgc	10/16	1	2	FACETS	0.983	0.909	1	0.983	0.909	1	CLONAL	1	TRUE	1	0.443972787070912	2		676	843	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169499	27169499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573385848	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	114	392	0	ENST00000380036.4:c.500G>A	p.Arg167Gln	p.R167Q	ENST00000380036	NM_000459.3	167	cGg/cAg	4/23	0.443972787070912	3	FACETS	0.947	0.854	1	0.473	0.427	0.522	CLONAL	1	TRUE	1	0.443972787070912	3		392	663	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555267	226555267	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	139	430	0	ENST00000366794.5:c.2320G>A	p.Ala774Thr	p.A774T	ENST00000366794	NM_001618.3	774	Gcc/Acc	17/23	1	2	FACETS	0.991	0.905	1	0.991	0.905	1	CLONAL	1	TRUE	1	0.443972787070912	2		430	632	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522532	67522532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767837787	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	70	168	0	ENST00000274335.5:c.29C>T	p.Ala10Val	p.A10V	ENST00000274335		10	gCg/gTg	1/15	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.443972787070912	2		168	287	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664771	138664771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	86	179	1	ENST00000330315.3:c.794C>T	p.Ala265Val	p.A265V	ENST00000330315	NM_023067.3	265	gCg/gTg	1/1	0.443972787070912	2	FACETS	0.922	0.82	1	0.461	0.41	0.515	CLONAL	1	TRUE	0	0.443972787070912	2		180	420	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244190	5244190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760369713	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	207	709	0	ENST00000357368.4:c.1292G>A	p.Arg431Gln	p.R431Q	ENST00000357368	NM_002850.3	431	cGg/cAg	11/38	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.443972787070912	2		709	806	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551958	150551958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs932863734	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	152	447	1	ENST00000369026.2:c.49G>A	p.Gly17Arg	p.G17R	ENST00000369026	NM_021960.4	17	Ggg/Agg	1/3	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.443972787070912	2		448	642	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982113	201982113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751933012	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	184	623	0	ENST00000359651.3:c.637G>A	p.Gly213Ser	p.G213S	ENST00000359651		213	Ggt/Agt	5/8	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.443972787070912	2		623	796	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942606	71942606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769074650	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	156	553	0	ENST00000298229.2:c.1562G>A	p.Arg521His	p.R521H	ENST00000298229	NM_001567.3	521	cGt/cAt	13/28	1	2	FACETS	0.909	0.834	0.988	0.909	0.834	0.988	CLONAL	1	TRUE	1	0.443972787070912	2		553	773	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920719	100920719	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	79	361	0	ENST00000325455.5:c.2429A>G	p.Lys810Arg	p.K810R	ENST00000325455	NM_001202474.3	810	aAg/aGg	6/8	1	2	FACETS	0.786	0.694	0.884	0.786	0.694	0.884	SUBCLONAL	1	TRUE	1	0.443972787070912	2		361	453	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285675	46285675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1201192337	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	45	306	0	ENST00000334344.6:c.5035C>T	p.Arg1679Trp	p.R1679W	ENST00000334344	NM_152641.2	1679	Cgg/Tgg	17/21	1	2	FACETS	0.356	0.298	0.419	0.356	0.298	0.419	SUBCLONAL	1	TRUE	1	0.443972787070912	2		306	570	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856326	111856326	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	19	59	1	ENST00000341259.2:c.377C>T	p.Pro126Leu	p.P126L	ENST00000341259	NM_005475.2	126	cCg/cTg	2/8	1	2	FACETS	0.856	0.661	1	0.856	0.661	1	CLONAL	1	TRUE	1	0.443972787070912	2		60	100	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562948	21562948	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	200	626	0	ENST00000382592.4:c.971del	p.Ala324GlyfsTer109	p.A324Gfs*109	ENST00000382592	NM_014572.2	324	gCg/gg	4/8	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.443972787070912	2		626	842	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039197	49039198	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCTTCA	novel	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	121	418	0	ENST00000267163.4:c.2277_2282dup	p.Phe760_Met761insIlePhe	p.F760_M761insIF	ENST00000267163	NM_000321.2	759	gtc/gTCTTCAtc	22/27	0.443972787070912	1	FACETS	0.942	0.857	1	0.942	0.857	1	CLONAL	1	TRUE	0	0.443972787070912	1		418	450	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423638	88423638	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	99	339	0	ENST00000360948.2:c.2197C>A	p.Pro733Thr	p.P733T	ENST00000360948	NM_001012338.2	733	Ccc/Acc	18/19	1	2	FACETS	0.989	0.888	1	0.989	0.888	1	CLONAL	1	TRUE	1	0.443972787070912	2		339	451	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134690	2134691	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	383	681	0	ENST00000219476.3:c.4470_4471del	p.Lys1491SerfsTer32	p.K1491Sfs*32	ENST00000219476	NM_000548.3	1489	gcAGag/gcag	34/42	0.443972787070912	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.443972787070912	2		681	809	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020487	14020487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913050	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	93	367	0	ENST00000311895.7:c.458G>A	p.Arg153His	p.R153H	ENST00000311895	NM_005236.2	153	cGc/cAc	3/11	1	2	FACETS	0.875	0.781	0.974	0.875	0.781	0.974	CLONAL	1	TRUE	1	0.443972787070912	2		367	479	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821368	72821368	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1458446159	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	82	261	0	ENST00000268489.5:c.10807G>A	p.Ala3603Thr	p.A3603T	ENST00000268489	NM_006885.3	3603	Gcc/Acc	10/10	1	2	FACETS	0.985	0.875	1	0.985	0.875	1	CLONAL	1	TRUE	1	0.443972787070912	2		261	375	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118551	17118552	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	rs1064793128	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	159	605	0	ENST00000285071.4:c.1379_1380del	p.Leu460GlnfsTer25	p.L460Qfs*25	ENST00000285071	NM_144997.5	460	cTC/c	12/14	1	2	FACETS	0.912	0.837	0.991	0.912	0.837	0.991	CLONAL	1	TRUE	1	0.443972787070912	2		605	785	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216310	2216310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780465036	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	168	566	1	ENST00000398665.3:c.1954C>T	p.Arg652Trp	p.R652W	ENST00000398665	NM_032482.2	652	Cgg/Tgg	20/28	1	2	FACETS	0.97	0.893	1	0.97	0.893	1	CLONAL	1	TRUE	1	0.443972787070912	2		567	780	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231461	5231461	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	198	636	0	ENST00000357368.4:c.2015A>G	p.Asn672Ser	p.N672S	ENST00000357368	NM_002850.3	672	aAc/aGc	14/38	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.443972787070912	2		636	849	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289889	15289889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	222	756	0	ENST00000263388.2:c.3665G>A	p.Cys1222Tyr	p.C1222Y	ENST00000263388	NM_000435.2	1222	tGc/tAc	22/33	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.443972787070912	2		756	996	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918193	50918194	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	184	717	0	ENST00000440232.2:c.2515dup	p.Leu839ProfsTer20	p.L839Pfs*20	ENST00000440232	NM_002691.3	837	tgc/tgCc	20/27	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.443972787070912	2		717	828	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374318	31374318	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	124	558	1	ENST00000328111.2:c.317G>T	p.Arg106Leu	p.R106L	ENST00000328111	NM_006892.3	106	cGa/cTa	5/23	1	2	FACETS	0.876	0.794	0.961	0.876	0.794	0.961	CLONAL	1	TRUE	1	0.443972787070912	2		559	638	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279201	142279201	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	100	351	1	ENST00000350721.4:c.1445T>C	p.Leu482Pro	p.L482P	ENST00000350721	NM_001184.3	482	cTa/cCa	6/47	0.443972787070912	2	FACETS	0.95	0.853	1	0.475	0.426	0.527	CLONAL	1	TRUE	0	0.443972787070912	2		352	474	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951992	178951992	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	190	373	0	ENST00000263967.3:c.3047T>C	p.Phe1016Ser	p.F1016S	ENST00000263967	NM_006218.2	1016	tTt/tCt	21/21	0.443972787070912	2	FACETS	0.92	0.86	0.982	0.92	0.86	0.982	CLONAL	2	TRUE	0	0.443972787070912	2		373	465	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562867	176562867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	147	430	0	ENST00000439151.2:c.763C>T	p.Pro255Ser	p.P255S	ENST00000439151	NM_022455.4	255	Cca/Tca	2/23	1	2	FACETS	0.97	0.887	1	0.97	0.887	1	CLONAL	1	TRUE	1	0.443972787070912	2		430	683	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323351	31323351	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	79	250	0	ENST00000412585.2:c.638T>C	p.Val213Ala	p.V213A	ENST00000412585	NM_005514.6	213	gTg/gCg	4/8	1	2	FACETS	0.811	0.716	0.911	0.811	0.716	0.911	CLONAL	1	TRUE	1	0.443972787070912	2		250	439	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748570	43748570	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	146	379	0	ENST00000523873.1:c.524C>A	p.Pro175His	p.P175H	ENST00000523873		175	cCc/cAc	6/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.443972787070912	2		379	586	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509318	106509318	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs772698550	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	156	504	0	ENST00000359195.3:c.1312G>T	p.Ala438Ser	p.A438S	ENST00000359195	NM_002649.2	438	Gct/Tct	2/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.443972787070912	2		504	669	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325439	1325439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1391352722	NA	P-0044791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	130	452	0	ENST00000400841.2:c.236G>A	p.Gly79Asp	p.G79D	ENST00000400841		79	gGt/gAt	3/6	1	1	FACETS	0.735	0.668	0.804	0.735	0.668	0.804	SUBCLONAL	1	TRUE	0	0.443972787070912	1		452	620	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245277	133245277	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	149	756	0	ENST00000320574.5:c.1970A>C	p.Asn657Thr	p.N657T	ENST00000320574	NM_006231.2	657	aAt/aCt	18/49	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.307842171361845	2		756	892	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0044824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	168	388	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.276857279166664	4	FACETS	0.992	0.918	1	0.992	0.918	1	CLONAL	2	TRUE	2	0.46078844629501	4		388	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577520	7577520	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	269	694	0	ENST00000269305.4:c.761T>A	p.Ile254Asn	p.I254N	ENST00000269305	NM_001126112.2	254	aTc/aAc	7/11	0.424984332622958	2	FACETS	0.857	0.809	0.906	0.857	0.809	0.906	CLONAL	2	TRUE	0	0.46078844629501	2		694	681	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190645	11190645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745409542	NA	P-0044824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	325	695	1	ENST00000361445.4:c.5554G>A	p.Glu1852Lys	p.E1852K	ENST00000361445	NM_004958.3	1852	Gag/Aag	39/58	0.424984332622958	2	FACETS	0.858	0.814	0.902	0.858	0.814	0.902	CLONAL	2	TRUE	0	0.46078844629501	2		696	822	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118674	11118674	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	306	751	0	ENST00000358026.2:c.2098G>A	p.Glu700Lys	p.E700K	ENST00000358026	NM_001128849.1	700	Gag/Aag	14/36	0.424984332622958	2	FACETS	0.884	0.838	0.931	0.884	0.838	0.931	CLONAL	2	TRUE	0	0.46078844629501	2		751	751	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097722	8097722	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	127	572	0	ENST00000346208.3:c.104A>T	p.Tyr35Phe	p.Y35F	ENST00000346208		35	tAc/tTc	2/6	0.106114570385452	3	FACETS	0.951	0.863	1			1	INDETERMINATE	1	TRUE	NA	0.46078844629501	3		572	713	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435424	18435424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	34	275	0	ENST00000266497.5:c.409G>T	p.Asp137Tyr	p.D137Y	ENST00000266497		137	Gat/Tat	1/31	0.46078844629501	3	FACETS	0.463	0.379	0.558	0.232	0.189	0.279	SUBCLONAL	1	TRUE	1	0.46078844629501	3		275	392	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014044	14014044	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs774510191	NA	P-0044824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	109	598	0	ENST00000311895.7:c.22C>G	p.Arg8Gly	p.R8G	ENST00000311895	NM_005236.2	8	Cga/Gga	1/11	0.46078844629501	6	FACETS	0.737	0.66	0.82			1	SUBCLONAL	1	TRUE	NA	0.46078844629501	6		598	1233	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206583	27206583	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	29	346	0	ENST00000380036.4:c.2368G>T	p.Glu790Ter	p.E790*	ENST00000380036	NM_000459.3	790	Gaa/Taa	15/23	0.248457837178558	3	FACETS	0.357	0.286	0.438	0.178	0.143	0.219	INDETERMINATE	1	TRUE	1	0.46078844629501	3		346	434	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563420	87563420	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs183344464	NA	P-0044824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	91	574	0	ENST00000277120.3:c.1808G>A	p.Arg603His	p.R603H	ENST00000277120		603	cGt/cAt	16/19	1	2	FACETS	0.57	0.506	0.638	0.57	0.506	0.638	SUBCLONAL	1	TRUE	1	0.46078844629501	2		574	693	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	107	798	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.368394479417412	5	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.368394479417412	5		798	700	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12647737	12647737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773051648	NA	P-0044829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	50	341	1	ENST00000251849.4:c.643C>T	p.Arg215Cys	p.R215C	ENST00000251849	NM_002880.3	215	Cgt/Tgt	6/17	1	2	FACETS	0.893	0.762	1	0.893	0.762	1	CLONAL	1	TRUE	1	0.368394479417412	2		342	304	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375406	118375409	+	frameshift_variant	Frame_Shift_Del	DEL	TCTG	TCTG	-	rs398122878	NA	P-0044829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	107	308	0	ENST00000534358.1:c.8806_8809del	p.Val2936Ter	p.V2936*	ENST00000534358	NM_005933.3	2933	gaTCTG/ga	27/36	NA	2	FACETS	0.934	0.849	1			1	INDETERMINATE	2	TRUE	NA	0.368394479417412	2		308	311	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	68	279	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.27113928952969	4	FACETS	1	0.966	1			1	CLONAL	1	TRUE	NA	0.27113928952969	4		279	475	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0044832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	219	689	1	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	0.244375243343974	2	FACETS	0.993	0.926	1	0.993	0.926	1	CLONAL	2	TRUE	0	0.27113928952969	2		690	813	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281250	15281250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184522923	NA	P-0044832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	287	999	1	ENST00000263388.2:c.5006G>A	p.Arg1669His	p.R1669H	ENST00000263388	NM_000435.2	1669	cGc/cAc	27/33	0.262148596139384	2	FACETS	0.928	0.872	0.985	0.928	0.872	0.985	CLONAL	2	TRUE	0	0.27113928952969	2		1000	1141	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602836	10602836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	282	869	0	ENST00000171111.5:c.742G>A	p.Ala248Thr	p.A248T	ENST00000171111	NM_203500.1	248	Gcc/Acc	3/6	0.262148596139384	2	FACETS	0.994	0.935	1	0.994	0.935	1	CLONAL	2	TRUE	0	0.27113928952969	2		869	1046	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3824594	3824594	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1389560620	NA	P-0044832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	60	524	0	ENST00000262367.5:c.2259G>A	p.Met753Ile	p.M753I	ENST00000262367	NM_004380.2	753	atG/atA	12/31	0.27113928952969	4	FACETS	0.807	0.694	0.93	0.404	0.347	0.465	CLONAL	1	TRUE	2	0.27113928952969	4		524	697	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	318	372	2	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.964	0.917	1	1	0.996	1	CLONAL	2	TRUE	1	0.460542566757198	2		374	716	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	323	832	5	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.460542566757198	2		837	1294	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	105	317	1	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.811	0.729	0.898	0.811	0.729	0.898	CLONAL	1	TRUE	1	0.460542566757198	2		318	562	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056566	26056566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1444425351	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	102	318	0	ENST00000343677.2:c.91A>G	p.Thr31Ala	p.T31A	ENST00000343677	NM_005319.3	31	Acg/Gcg	1/1	1	2	FACETS	0.938	0.844	1	0.938	0.844	1	CLONAL	1	TRUE	1	0.460542566757198	2		318	472	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	330	444	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	0.882	0.838	0.927	1	0.996	1	CLONAL	2	TRUE	1	0.460542566757198	2		444	812	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	359	332	0	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.954	0.909	0.999	1	0.996	1	CLONAL	2	TRUE	1	0.460542566757198	2		332	817	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099467	27099467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	42	348	0	ENST00000324856.7:c.3704G>A	p.Ser1235Asn	p.S1235N	ENST00000324856	NM_006015.4	1235	aGc/aAc	14/20	1	2	FACETS	0.274	0.228	0.326	0.274	0.228	0.326	SUBCLONAL	1	TRUE	1	0.460542566757198	2		348	665	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101417	27101417	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	263	491	0	ENST00000324856.7:c.4703del	p.Pro1568LeufsTer44	p.P1568Lfs*44	ENST00000324856	NM_006015.4	1567	Ccc/cc	18/20	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.460542566757198	2		491	883	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599234	28599234	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1198	84	754	2	ENST00000253063.3:c.685del	p.Gln229ArgfsTer18	p.Q229Rfs*18	ENST00000253063	NM_031459.4	227	gCc/gc	5/10	1	2	FACETS	0.285	0.25	0.322	0.285	0.25	0.322	SUBCLONAL	1	TRUE	1	0.460542566757198	2		756	1282	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	305	734	1	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.460542566757198	2		735	1245	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521525	46521525	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	162	398	0	ENST00000262741.5:c.883del	p.Met295Ter	p.M295*	ENST00000262741	NM_003629.3	295	Atg/tg	7/10	1	2	FACETS	0.961	0.884	1	0.961	0.884	1	CLONAL	1	TRUE	1	0.460542566757198	2		398	732	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468106	120468106	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	126	692	0	ENST00000256646.2:c.4333A>C	p.Ser1445Arg	p.S1445R	ENST00000256646	NM_024408.3	1445	Agc/Cgc	25/34	1	2	FACETS	0.497	0.448	0.547	0.497	0.448	0.547	SUBCLONAL	1	TRUE	1	0.460542566757198	2		692	1102	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129344	64129344	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs756803659	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	287	743	0	ENST00000334205.4:c.776C>A	p.Pro259His	p.P259H	ENST00000334205	NM_003942.2	259	cCt/cAt	8/17	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.460542566757198	2		743	1227	SUCCESS
EED	8726	MSKCC	GRCh37	11	85961474	85961474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1402767573	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	74	174	0	ENST00000263360.6:c.251G>A	p.Cys84Tyr	p.C84Y	ENST00000263360	NM_003797.3	84	tGt/tAt	2/12	1	2	FACETS	0.965	0.851	1	0.965	0.851	1	CLONAL	1	TRUE	1	0.460542566757198	2		174	333	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197308	94197308	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	157	337	0	ENST00000323929.3:c.1196del	p.Phe399SerfsTer29	p.F399Sfs*29	ENST00000323929	NM_005591.3	399	tTc/tc	11/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.460542566757198	2		337	595	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344558	118344558	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs200600434	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	43	372	1	ENST00000534358.1:c.2684A>G	p.Lys895Arg	p.K895R	ENST00000534358	NM_005933.3	895	aAg/aGg	3/36	1	2	FACETS	0.274	0.229	0.325	0.274	0.229	0.325	SUBCLONAL	1	TRUE	1	0.460542566757198	2		373	681	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118368661	118368661	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	92	280	0	ENST00000534358.1:c.5675G>A	p.Arg1892His	p.R1892H	ENST00000534358	NM_005933.3	1892	cGt/cAt	21/36	1	2	FACETS	0.908	0.811	1	0.908	0.811	1	CLONAL	1	TRUE	1	0.460542566757198	2		280	440	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	138	388	2	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.812	0.74	0.888	0.812	0.74	0.888	CLONAL	1	TRUE	1	0.460542566757198	2		390	738	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427743	49427743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	247	622	1	ENST00000301067.7:c.10745G>A	p.Arg3582Gln	p.R3582Q	ENST00000301067	NM_003482.3	3582	cGg/cAg	39/54	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.460542566757198	2		623	1063	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445257	49445257	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1328	74	859	5	ENST00000301067.7:c.2209del	p.Arg737GlyfsTer193	p.R737Gfs*193	ENST00000301067	NM_003482.3	737	Cgg/gg	10/54	1	2	FACETS	0.229	0.199	0.262	0.229	0.199	0.262	SUBCLONAL	1	TRUE	1	0.460542566757198	2		864	1402	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	195	482	3	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.67	0.619	0.723	0.67	0.619	0.723	SUBCLONAL	1	TRUE	1	0.460542566757198	2		485	1264	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856155	111856155	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1170508105	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	159	524	0	ENST00000341259.2:c.206A>G	p.Asp69Gly	p.D69G	ENST00000341259	NM_005475.2	69	gAc/gGc	2/8	1	2	FACETS	0.942	0.865	1	0.942	0.865	1	CLONAL	1	TRUE	1	0.460542566757198	2		524	733	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856196	111856196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	137	379	1	ENST00000341259.2:c.247C>T	p.Arg83Trp	p.R83W	ENST00000341259	NM_005475.2	83	Cgg/Tgg	2/8	1	2	FACETS	0.983	0.898	1	0.983	0.898	1	CLONAL	1	TRUE	1	0.460542566757198	2		380	605	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115385	115115386	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	73	386	1	ENST00000257566.3:c.940dup	p.Arg314LysfsTer13	p.R314Kfs*13	ENST00000257566	NM_016569.3	314	aga/aAga	5/8	1	2	FACETS	0.456	0.398	0.518	0.456	0.398	0.518	SUBCLONAL	1	TRUE	1	0.460542566757198	2		387	695	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975687	26975687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	148	384	0	ENST00000381527.3:c.1195C>T	p.Pro399Ser	p.P399S	ENST00000381527	NM_001260.1	399	Ccc/Tcc	12/13	1	2	FACETS	0.851	0.779	0.927	0.851	0.779	0.927	CLONAL	1	TRUE	1	0.460542566757198	2		384	755	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012358	29012359	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	154	367	0	ENST00000282397.4:c.512dup	p.Phe172ValfsTer4	p.F172Vfs*4	ENST00000282397	NM_002019.4	171	aag/aaAg	4/30	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.460542566757198	2		367	653	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913837	32913837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359507	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	138	370	1	ENST00000380152.3:c.5351del	p.Asn1784ThrfsTer7	p.N1784Tfs*7	ENST00000380152		1782	cAa/ca	11/27	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.460542566757198	2		371	550	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610503	81610503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137908024	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	118	408	0	ENST00000298171.2:c.2101C>T	p.Arg701Cys	p.R701C	ENST00000298171	NM_000369.2	701	Cgc/Tgc	10/10	1	2	FACETS	0.888	0.804	0.976	0.888	0.804	0.976	CLONAL	1	TRUE	1	0.460542566757198	2		408	577	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022990	33022990	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	110	491	0	ENST00000300177.4:c.104del	p.Pro35ArgfsTer49	p.P35Rfs*49	ENST00000300177	NM_001191322.1	33	atC/at	2/2	1	2	FACETS	0.59	0.53	0.654	0.59	0.53	0.654	SUBCLONAL	1	TRUE	1	0.460542566757198	2		491	809	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040841	42040841	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	145	366	0	ENST00000219905.7:c.5219C>T	p.Ala1740Val	p.A1740V	ENST00000219905	NM_001164273.1	1740	gCt/gTt	16/24	1	2	FACETS	0.97	0.888	1	0.97	0.888	1	CLONAL	1	TRUE	1	0.460542566757198	2		366	649	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43773126	43773126	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	49	549	0	ENST00000382044.4:c.466T>C	p.Ser156Pro	p.S156P	ENST00000382044	NM_001141980.1	156	Tca/Cca	5/28	1	2	FACETS	0.247	0.208	0.29	0.247	0.208	0.29	SUBCLONAL	1	TRUE	1	0.460542566757198	2		549	862	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420192	88420192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	166	441	0	ENST00000360948.2:c.2494C>T	p.Pro832Ser	p.P832S	ENST00000360948	NM_001012338.2	832	Cca/Tca	19/19	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.460542566757198	2		441	669	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347484	91347484	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	144	469	1	ENST00000355112.3:c.3651del	p.Lys1217AsnfsTer62	p.K1217Nfs*62	ENST00000355112	NM_000057.2	1216	Aaa/aa	19/22	1	2	FACETS	0.828	0.756	0.904	0.828	0.756	0.904	CLONAL	1	TRUE	1	0.460542566757198	2		470	755	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900369	3900369	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs762902238	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	261	622	2	ENST00000262367.5:c.727C>A	p.Leu243Ile	p.L243I	ENST00000262367	NM_004380.2	243	Cta/Ata	2/31	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.460542566757198	2		624	1108	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865869	56865869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761782738	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	125	347	1	ENST00000308159.5:c.1201G>A	p.Asp401Asn	p.D401N	ENST00000308159	NM_014669.4	401	Gac/Aac	11/22	1	2	FACETS	0.928	0.843	1	0.928	0.843	1	CLONAL	1	TRUE	1	0.460542566757198	2		348	585	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	137	742	2	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.842	0.767	0.92	0.842	0.767	0.92	CLONAL	1	TRUE	1	0.460542566757198	2		744	707	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979987	7979987	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746723399	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	256	662	2	ENST00000319144.4:c.1350del	p.Leu451SerfsTer16	p.L451Sfs*16	ENST00000319144	NM_001139.2	450	ggG/gg	10/15	1	2	FACETS	0.984	0.921	1	0.984	0.921	1	CLONAL	1	TRUE	1	0.460542566757198	2		664	1130	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110166	8110166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148133660	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	236	596	0	ENST00000585124.1:c.439C>T	p.Arg147Trp	p.R147W	ENST00000585124	NM_004217.3	147	Cgg/Tgg	6/9	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.460542566757198	2		596	986	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	176	601	4	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.792	0.729	0.857	0.792	0.729	0.857	SUBCLONAL	1	TRUE	1	0.460542566757198	2		605	965	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682428	37682428	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	185	429	0	ENST00000447079.4:c.3619C>T	p.Gln1207Ter	p.Q1207*	ENST00000447079	NM_015083.1	1207	Cag/Tag	13/14	1	2	FACETS	0.975	0.902	1	0.975	0.902	1	CLONAL	1	TRUE	1	0.460542566757198	2		429	824	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864757	37864757	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	52	499	0	ENST00000269571.5:c.409C>A	p.Leu137Met	p.L137M	ENST00000269571		137	Ctg/Atg	3/27	1	2	FACETS	0.275	0.233	0.321	0.275	0.233	0.321	SUBCLONAL	1	TRUE	1	0.460542566757198	2		499	821	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	283	684	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.460542566757198	2		684	1195	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	194	552	2	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	0.958	0.888	1	0.958	0.888	1	CLONAL	1	TRUE	1	0.460542566757198	2		554	879	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761414	59761417	+	frameshift_variant	Frame_Shift_Del	DEL	TTTG	TTTG	-	rs771028677	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	104	409	0	ENST00000259008.2:c.2990_2993del	p.Thr997ArgfsTer61	p.T997Rfs*61	ENST00000259008	NM_032043.2	997	aCAAAg/ag	20/20	1	2	FACETS	0.74	0.664	0.821	0.74	0.664	0.821	SUBCLONAL	1	TRUE	1	0.460542566757198	2		409	610	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	344	586	0	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.460542566757198	2		586	1435	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56376681	56376681	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	181	433	0	ENST00000348428.3:c.721G>T	p.Gly241Cys	p.G241C	ENST00000348428	NM_006785.3	241	Ggc/Tgc	5/17	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.460542566757198	2		433	741	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222772	5222772	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs770446171	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	259	783	0	ENST00000357368.4:c.3031C>T	p.Arg1011Ter	p.R1011*	ENST00000357368	NM_002850.3	1011	Cga/Tga	18/38	1	2	FACETS	0.962	0.901	1	0.962	0.901	1	CLONAL	1	TRUE	1	0.460542566757198	2		783	1169	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627687	14627687	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	213	604	0	ENST00000254322.2:c.383A>C	p.Asp128Ala	p.D128A	ENST00000254322	NM_006145.1	128	gAt/gCt	2/3	1	2	FACETS	0.875	0.813	0.94	0.875	0.813	0.94	CLONAL	1	TRUE	1	0.460542566757198	2		604	1057	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278138	15278138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756495084	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	288	809	0	ENST00000263388.2:c.5284G>A	p.Val1762Met	p.V1762M	ENST00000263388	NM_000435.2	1762	Gtg/Atg	29/33	1	2	FACETS	0.95	0.892	1	0.95	0.892	1	CLONAL	1	TRUE	1	0.460542566757198	2		809	1316	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288710	15288710	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	23	57	0	ENST00000263388.2:c.4029del	p.Cys1344ValfsTer76	p.C1344Vfs*76	ENST00000263388	NM_000435.2	1343	ccC/cc	24/33	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.460542566757198	2		57	96	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355060	15355060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199540579	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	357	868	1	ENST00000263377.2:c.2563G>A	p.Ala855Thr	p.A855T	ENST00000263377	NM_058243.2	855	Gca/Aca	13/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.460542566757198	2		869	1444	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950457	17950457	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	291	665	0	ENST00000458235.1:c.1270G>T	p.Asp424Tyr	p.D424Y	ENST00000458235	NM_000215.3	424	Gat/Tat	10/24	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.460542566757198	2		665	1184	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953977	17953977	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs964736085	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	297	811	0	ENST00000458235.1:c.425G>A	p.Arg142His	p.R142H	ENST00000458235	NM_000215.3	142	cGc/cAc	5/24	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.460542566757198	2		811	1223	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214871	36214871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	276	700	5	ENST00000222270.7:c.3302del	p.Pro1101LeufsTer81	p.P1101Lfs*81	ENST00000222270	NM_014727.1	1099	ggC/gg	8/37	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.460542566757198	2		705	1185	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42385003	42385003	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	277	697	0	ENST00000221972.3:c.637G>T	p.Val213Leu	p.V213L	ENST00000221972	NM_021601.3	213	Gtg/Ttg	5/5	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.460542566757198	2		697	1096	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906393	50906393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762330164	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	309	838	1	ENST00000440232.2:c.1054C>T	p.Arg352Cys	p.R352C	ENST00000440232	NM_002691.3	352	Cgc/Tgc	9/27	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.460542566757198	2		839	1312	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716301	52716301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	261	672	2	ENST00000322088.6:c.745C>T	p.Arg249Cys	p.R249C	ENST00000322088	NM_014225.5	249	Cgc/Tgc	6/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.460542566757198	2		674	1078	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605795	46605795	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	158	446	2	ENST00000263734.3:c.1444-1G>A		p.X482_splice	ENST00000263734	NM_001430.4	482			1	2	FACETS	0.9	0.826	0.978	0.9	0.826	0.978	CLONAL	1	TRUE	1	0.460542566757198	2		448	762	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046415	128046415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749390618	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	124	328	0	ENST00000285398.2:c.848G>A	p.Arg283His	p.R283H	ENST00000285398	NM_000122.1	283	cGt/cAt	7/15	1	2	FACETS	0.96	0.872	1	0.96	0.872	1	CLONAL	1	TRUE	1	0.460542566757198	2		328	561	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682809	190682810	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587778609	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	34	317	0	ENST00000441310.2:c.492dup	p.Cys165MetfsTer2	p.C165Mfs*2	ENST00000441310	NM_000534.4	162	gca/gcAa	5/13	1	2	FACETS	0.249	0.203	0.301	0.249	0.203	0.301	SUBCLONAL	1	TRUE	1	0.460542566757198	2		317	593	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150013	202150013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	52	477	1	ENST00000358485.4:c.1454G>A	p.Cys485Tyr	p.C485Y	ENST00000358485	NM_001080125.1	485	tGc/tAc	8/9	1	2	FACETS	0.241	0.204	0.282	0.241	0.204	0.282	SUBCLONAL	1	TRUE	1	0.460542566757198	2		478	936	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437222	220437223	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1286117855	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1346	88	992	1	ENST00000243786.2:c.132dup	p.Ala45ArgfsTer29	p.A45Rfs*29	ENST00000243786	NM_002191.3	42	-/C	1/2	1	2	FACETS	0.266	0.235	0.301	0.266	0.235	0.301	SUBCLONAL	1	TRUE	1	0.460542566757198	2		993	1434	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793431	242793431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376257658	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	232	626	0	ENST00000334409.5:c.646G>A	p.Val216Met	p.V216M	ENST00000334409	NM_005018.2	216	Gtg/Atg	5/5	1	2	FACETS	0.943	0.879	1	0.943	0.879	1	CLONAL	1	TRUE	1	0.460542566757198	2		626	1068	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560955	9560955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	168	425	0	ENST00000353224.5:c.827C>T	p.Thr276Ile	p.T276I	ENST00000353224	NM_177990.2	276	aCa/aTa	4/10	1	2	FACETS	0.977	0.9	1	0.977	0.9	1	CLONAL	1	TRUE	1	0.460542566757198	2		425	747	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39708808	39708808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs183058581	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	37	206	0	ENST00000361337.2:c.419G>A	p.Arg140Gln	p.R140Q	ENST00000361337	NM_003286.2	140	cGa/cAa	6/21	1	2	FACETS	0.499	0.412	0.595	0.499	0.412	0.595	SUBCLONAL	1	TRUE	1	0.460542566757198	2		206	322	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961495	54961495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769961096	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	161	470	0	ENST00000312783.6:c.137G>A	p.Arg46Gln	p.R46Q	ENST00000312783	NM_198436.1	46	cGg/cAg	4/10	1	2	FACETS	0.863	0.792	0.937	0.863	0.792	0.937	CLONAL	1	TRUE	1	0.460542566757198	2		470	810	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485851	57485851	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	152	407	0	ENST00000371085.3:c.1152G>T	p.Gln384His	p.Q384H	ENST00000371085	NM_000516.4	384	caG/caT	13/13	1	2	FACETS	0.924	0.847	1	0.924	0.847	1	CLONAL	1	TRUE	1	0.460542566757198	2		407	714	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527572	41527572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	64	420	0	ENST00000263253.7:c.1463C>T	p.Ala488Val	p.A488V	ENST00000263253	NM_001429.3	488	gCa/gTa	6/31	1	2	FACETS	0.35	0.303	0.403	0.35	0.303	0.403	SUBCLONAL	1	TRUE	1	0.460542566757198	2		420	793	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548281	41548281	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	112	290	0	ENST00000263253.7:c.3072del	p.Glu1025ArgfsTer34	p.E1025Rfs*34	ENST00000263253	NM_001429.3	1023	atA/at	16/31	1	2	FACETS	0.841	0.759	0.928	0.841	0.759	0.928	CLONAL	1	TRUE	1	0.460542566757198	2		290	578	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391168	89391168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772463834	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	153	438	0	ENST00000336596.2:c.1234G>A	p.Val412Ile	p.V412I	ENST00000336596	NM_005233.5	412	Gtt/Att	5/17	1	2	FACETS	0.96	0.881	1	0.96	0.881	1	CLONAL	1	TRUE	1	0.460542566757198	2		438	692	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851574	134851574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747682274	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	166	441	0	ENST00000398015.3:c.980G>A	p.Arg327His	p.R327H	ENST00000398015	NM_004441.4	327	cGc/cAc	5/16	1	2	FACETS	0.956	0.88	1	0.956	0.88	1	CLONAL	1	TRUE	1	0.460542566757198	2		441	754	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898710	134898710	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	86	264	1	ENST00000398015.3:c.1768G>T	p.Gly590Trp	p.G590W	ENST00000398015	NM_004441.4	590	Ggg/Tgg	10/16	1	2	FACETS	0.938	0.835	1	0.938	0.835	1	CLONAL	1	TRUE	1	0.460542566757198	2		265	398	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664989	138664989	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	24	278	0	ENST00000330315.3:c.576del	p.Lys193SerfsTer78	p.K193Sfs*78	ENST00000330315	NM_023067.3	192	ccC/cc	1/1	1	2	FACETS	0.255	0.199	0.319	0.255	0.199	0.319	SUBCLONAL	1	TRUE	1	0.460542566757198	2		278	409	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261554	142261555	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1043355995	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	105	294	0	ENST00000350721.4:c.3402dup	p.Asn1135Ter	p.N1135*	ENST00000350721	NM_001184.3	1134	-/T	17/47	1	2	FACETS	0.925	0.833	1	0.925	0.833	1	CLONAL	1	TRUE	1	0.460542566757198	2		294	493	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	97	283	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	0.955	0.856	1	0.955	0.856	1	CLONAL	1	TRUE	1	0.460542566757198	2		283	441	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79966007	79966007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772141055	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	148	450	0	ENST00000265081.6:c.671G>A	p.Arg224Gln	p.R224Q	ENST00000265081	NM_002439.4	224	cGg/cAg	4/24	1	2	FACETS	0.879	0.804	0.957	0.879	0.804	0.957	CLONAL	1	TRUE	1	0.460542566757198	2		450	731	SUCCESS
APC	324	MSKCC	GRCh37	5	112170762	112170765	+	frameshift_variant	Frame_Shift_Del	DEL	CTTA	CTTA	-	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	188	545	0	ENST00000257430.4:c.1863_1866del	p.Tyr622GlyfsTer7	p.Y622Gfs*7	ENST00000257430	NM_000038.5	620	CTTAct/ct	15/16	1	2	FACETS	0.961	0.889	1	0.961	0.889	1	CLONAL	1	TRUE	1	0.460542566757198	2		545	850	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512344	149512344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368602685	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	231	678	1	ENST00000261799.4:c.1096G>A	p.Ala366Thr	p.A366T	ENST00000261799	NM_002609.3	366	Gcc/Acc	7/23	1	2	FACETS	0.894	0.833	0.957	0.894	0.833	0.957	CLONAL	1	TRUE	1	0.460542566757198	2		679	1122	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048881	180048881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751002839	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	304	897	2	ENST00000261937.6:c.1681G>A	p.Glu561Lys	p.E561K	ENST00000261937	NM_182925.4	561	Gaa/Aaa	13/30	1	2	FACETS	0.94	0.884	0.998	0.94	0.884	0.998	CLONAL	1	TRUE	1	0.460542566757198	2		899	1404	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910570	29910574	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGG	CCCGG	-	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	160	332	0	ENST00000376809.5:c.117_121del	p.Gly40ArgfsTer57	p.G40Rfs*57	ENST00000376809	NM_002116.7	37	tCCCGG/t	2/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.460542566757198	2		332	572	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672551	30672551	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773270002	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	186	548	0	ENST00000376406.3:c.4409C>T	p.Thr1470Met	p.T1470M	ENST00000376406	NM_014641.2	1470	aCg/aTg	10/15	1	2	FACETS	0.863	0.797	0.931	0.863	0.797	0.931	CLONAL	1	TRUE	1	0.460542566757198	2		548	936	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188294	32188295	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs766348245	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	264	322	0	ENST00000375023.3:c.1046dup	p.Thr350HisfsTer4	p.T350Hfs*4	ENST00000375023	NM_004557.3	349	ggc/ggGc	6/30	1	2	FACETS	0.891	0.834	0.95	0.891	0.834	0.95	CLONAL	1	TRUE	1	0.460542566757198	2		322	1287	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405960	157405960	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	181	533	0	ENST00000346085.5:c.2204del	p.Pro735HisfsTer10	p.P735Hfs*10	ENST00000346085	NM_020732.3	734	ggC/gg	6/20	1	2	FACETS	0.878	0.81	0.949	0.878	0.81	0.949	CLONAL	1	TRUE	1	0.460542566757198	2		533	895	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259460	55259460	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143884981	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	181	536	0	ENST00000275493.2:c.2518G>A	p.Ala840Thr	p.A840T	ENST00000275493	NM_005228.3	840	Gcc/Acc	21/28	1	2	FACETS	0.942	0.87	1	0.942	0.87	1	CLONAL	1	TRUE	1	0.460542566757198	2		536	834	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874914	151874914	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	41	338	0	ENST00000262189.6:c.7624del	p.Ser2542HisfsTer20	p.S2542Hfs*20	ENST00000262189	NM_170606.2	2542	Tca/ca	38/59	1	2	FACETS	0.309	0.257	0.367	0.309	0.257	0.367	SUBCLONAL	1	TRUE	1	0.460542566757198	2		338	576	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38139101	38139101	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	130	316	0	ENST00000317025.8:c.3502G>T	p.Gly1168Cys	p.G1168C	ENST00000317025	NM_023034.1	1168	Ggt/Tgt	20/24	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.460542566757198	2		316	523	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205092	38205092	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	122	381	2	ENST00000317025.8:c.598del	p.Ser200AlafsTer20	p.S200Afs*20	ENST00000317025	NM_023034.1	200	Agc/gc	2/24	1	2	FACETS	0.641	0.579	0.706	0.641	0.579	0.706	SUBCLONAL	1	TRUE	1	0.460542566757198	2		383	827	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958480	90958480	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	61	300	1	ENST00000265433.3:c.1958del	p.Lys653SerfsTer4	p.K653Sfs*4	ENST00000265433	NM_002485.4	653	aAg/ag	13/16	1	2	FACETS	0.763	0.662	0.872	0.763	0.662	0.872	SUBCLONAL	1	TRUE	1	0.460542566757198	2		301	347	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864086	97864086	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	116	483	1	ENST00000289081.3:c.1580A>G	p.Asp527Gly	p.D527G	ENST00000289081	NM_000136.2	527	gAc/gGc	15/15	1	2	FACETS	0.58	0.522	0.641	0.58	0.522	0.641	SUBCLONAL	1	TRUE	1	0.460542566757198	2		484	869	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250050	110250050	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	295	794	0	ENST00000374672.4:c.625G>A	p.Asp209Asn	p.D209N	ENST00000374672	NM_004235.4	209	Gac/Aac	3/5	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.460542566757198	2		794	1216	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759526	133759526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773475680	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	277	680	1	ENST00000318560.5:c.1849C>T	p.Arg617Cys	p.R617C	ENST00000318560	NM_005157.4	617	Cgc/Tgc	11/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.460542566757198	2		681	1154	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405225	139405225	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776698364	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	332	873	1	ENST00000277541.6:c.2620G>A	p.Val874Ile	p.V874I	ENST00000277541	NM_017617.3	874	Gtt/Att	17/34	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.460542566757198	2		874	1411	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429012	47429012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754787460	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	252	713	0	ENST00000377045.4:c.1375G>A	p.Gly459Arg	p.G459R	ENST00000377045	NM_001654.4	459	Ggg/Agg	13/16	1	2	FACETS	0.974	0.911	1	0.974	0.911	1	CLONAL	1	TRUE	1	0.460542566757198	2		713	1123	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345231	70345231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	210	581	2	ENST00000374080.3:c.2257C>T	p.Arg753Trp	p.R753W	ENST00000374080		753	Cgg/Tgg	16/45	1	2	FACETS	0.917	0.851	0.984	0.917	0.851	0.984	CLONAL	1	TRUE	1	0.460542566757198	2		583	995	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197725	123197725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749851312	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	112	354	1	ENST00000218089.9:c.1849C>T	p.Arg617Trp	p.R617W	ENST00000218089	NM_001042749.1	617	Cgg/Tgg	20/35	1	2	FACETS	0.975	0.881	1	0.975	0.881	1	CLONAL	1	TRUE	1	0.460542566757198	2		355	499	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858192	152858192	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	303	833	0	ENST00000406277.2:c.424-1G>A		p.X142_splice	ENST00000406277	NM_152274.4	142			1	2	FACETS	0.978	0.92	1	0.978	0.92	1	CLONAL	1	TRUE	1	0.460542566757198	2		833	1346	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562487	21562487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	53	136	0	ENST00000382592.4:c.1432G>A	p.Ala478Thr	p.A478T	ENST00000382592	NM_014572.2	478	Gcc/Acc	4/8	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.460542566757198	2		136	228	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	793	798	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.685116523668081	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.688251322577436	2		798	1141	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201554	133201556	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs878854896	NA	P-0044859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	410	798	1	ENST00000320574.5:c.6682_6684del	p.Lys2228del	p.K2228del	ENST00000320574	NM_006231.2	2228	AAG/-	48/49	1	2	FACETS	0.945	0.9	0.991	0.945	0.9	0.991	CLONAL	1	TRUE	1	0.688251322577436	2		799	1261	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795096	45795096	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	282	562	0	ENST00000450313.1:c.1532C>A	p.Ser511Tyr	p.S511Y	ENST00000450313	NM_012222.2	511	tCc/tAc	16/16	1	2	FACETS	0.937	0.883	0.992	0.937	0.883	0.992	CLONAL	1	TRUE	1	0.688251322577436	2		562	875	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315498	30315507	+	frameshift_variant	Frame_Shift_Del	DEL	AAACCTACTC	AAACCTACTC	-	novel	NA	P-0044859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	210	363	0	ENST00000322652.5:c.1187_1196del	p.Pro396LeufsTer8	p.P396Lfs*8	ENST00000322652	NM_015355.2	395	AAACCTACTCaa/aa	10/16	1	2	FACETS	0.911	0.85	0.973	0.911	0.85	0.973	CLONAL	1	TRUE	1	0.688251322577436	2		363	670	SUCCESS
APC	324	MSKCC	GRCh37	5	112175147	112175147	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	34	211	0	ENST00000257430.4:c.3856G>T	p.Glu1286Ter	p.E1286*	ENST00000257430	NM_000038.5	1286	Gaa/Taa	16/16	0.502248330513101	1	FACETS	0.939	0.787	1	0.939	0.787	1	CLONAL	1	TRUE	0	0.502248330513101	1		211	108	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574010	7574026	+	frameshift_variant	Frame_Shift_Del	DEL	CTCGAAGCGCTCACGCC	CTCGAAGCGCTCACGCC	-	novel	NA	P-0044903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	125	701	0	ENST00000269305.4:c.1001_1017del	p.Gly334AspfsTer7	p.G334Dfs*7	ENST00000269305	NM_001126112.2	334	gGGCGTGAGCGCTTCGAG/g	10/11	0.322771884245607	1	FACETS	0.731	0.665	0.8	0.731	0.665	0.8	SUBCLONAL	1	TRUE	0	0.502248330513101	1		701	510	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120399	70120400	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0044903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	227	1029	0	ENST00000245479.2:c.1401_1402del	p.Tyr468HisfsTer109	p.Y468Hfs*109	ENST00000245479	NM_000346.3	467	acCTac/acac	3/3	0.322771884245607	1	FACETS	0.802	0.749	0.857	0.802	0.749	0.857	CLONAL	1	TRUE	0	0.502248330513101	1		1029	844	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266828	41266828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	55	289	0	ENST00000349496.5:c.499G>A	p.Val167Met	p.V167M	ENST00000349496	NM_001904.3	167	Gtg/Atg	5/15	1	2	FACETS	0.842	0.727	0.966	0.842	0.727	0.966	CLONAL	1	TRUE	1	0.502248330513101	2		289	260	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0044918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	554	526	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.541851794769528	2	FACETS	0.973	0.94	1	0.973	0.94	1	CLONAL	2	TRUE	0	0.589715180347948	2		526	966	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0044918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	797	646	0	ENST00000397752.3:c.3028+1G>C		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.525606727231956	4	FACETS	0.933	0.911	0.955	0.933	0.911	0.955	CLONAL	4	TRUE	0	0.589715180347948	4		646	1151	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11137023	11137023	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0044918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	340	631	0	ENST00000358026.2:c.3215+1G>C		p.X1072_splice	ENST00000358026	NM_001128849.1	1072			0.543935925808284	2	FACETS	0.806	0.769	0.844	0.806	0.769	0.844	CLONAL	2	TRUE	0	0.589715180347948	2		631	715	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645796	215645796	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	301	427	0	ENST00000260947.4:c.802G>A	p.Glu268Lys	p.E268K	ENST00000260947	NM_000465.2	268	Gaa/Aaa	4/11	0.554066789904162	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.589715180347948	3		427	661	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266483	41266483	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	248	354	0	ENST00000349496.5:c.280G>T	p.Val94Leu	p.V94L	ENST00000349496	NM_001904.3	94	Gta/Tta	4/15	0.543935925808284	2	FACETS	0.962	0.914	1	0.962	0.914	1	CLONAL	2	TRUE	0	0.589715180347948	2		354	437	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965481	68965481	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	115	575	0	ENST00000288368.4:c.1093G>C	p.Gly365Arg	p.G365R	ENST00000288368	NM_024870.2	365	Ggt/Cgt	9/40	1	2	FACETS	0.689	0.623	0.759	0.689	0.623	0.759	SUBCLONAL	1	TRUE	1	0.589715180347948	2		575	566	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974711	21975575	+	coding_sequence_variant,5_prime_UTR_variant	Frame_Shift_Del	DEL	TTGGGCAGCGCCCCCGCCTCCAGCAGCGCCCGCACCTCCTCTACCCGACCCCGGGCCGCGGCCGTGGCCAGCCAGTCAGCCGAAGGCTCCATGCTGCTCCCCGCCGCCGGCTCCATGCTGCTCCCCGCCGCCCGCTGCCTGCTCTCCCCCTCTCCGCAGCCGCCGAGCGCACGCGGTCCGCCCCACCCTCTGGTGACCAGCCAGCCCCTCCTCTTTCTTCCTCCGGTGCTGGCGGAAGAGCCCCCTCCGACCCTGTCCCTCAAATCCTCTGGAGGGACCGCGGTATCTTTCCAGGCAAGGGGACGCCGTGAGCGAGTGCTCGGAGGAGGTGCTATTAACTCCGAGCACTTAGCGAATGTGGCACCCCTGAAGTCGCCCCAGGTTGGGTCTCCCCCGGGGGCACCAGCCGGAAGCAGCCCTCGCCAGAGCCAGCGTTGGCAAGGAAGGAGGACTGGGCTCCTCCCCACCTGCCCCCCACACCGCCCTCCGGCCTCCCTGCTCCCAGCCGCGCTCCCCCGCCTGCCAGCAAAGGCGTGTTTGAGTGCGTTCACTCTGTTAAAAAGAAATCCGCCCCCGCCCCGTTTCCTTCCTCCGCGATACAACCTTCCTAACTGCCAAATTGAATCGGGGTGTTTGGTGTCATAGGGAAAGTATGGCTTCTTCTTTTAATCATAAGAAAAAGCAAAACTATTCTTTCCTAGTTGTGAGAGCCCCACCGAGAATCGAAATCACCTGTACGACTAGAAAGTGTCCCCCTACCCCCTCAACCCTTGATTTTCAGGAGCGCGGGGTTCACTAAGTCAGAAACCCTAGTTCAAAGGATTCCTTTTGGAGAGTCGGACTGCTCTCTCCTTCCCCTCCCCTT	TTGGGCAGCGCCCCCGCCTCCAGCAGCGCCCGCACCTCCTCTACCCGACCCCGGGCCGCGGCCGTGGCCAGCCAGTCAGCCGAAGGCTCCATGCTGCTCCCCGCCGCCGGCTCCATGCTGCTCCCCGCCGCCCGCTGCCTGCTCTCCCCCTCTCCGCAGCCGCCGAGCGCACGCGGTCCGCCCCACCCTCTGGTGACCAGCCAGCCCCTCCTCTTTCTTCCTCCGGTGCTGGCGGAAGAGCCCCCTCCGACCCTGTCCCTCAAATCCTCTGGAGGGACCGCGGTATCTTTCCAGGCAAGGGGACGCCGTGAGCGAGTGCTCGGAGGAGGTGCTATTAACTCCGAGCACTTAGCGAATGTGGCACCCCTGAAGTCGCCCCAGGTTGGGTCTCCCCCGGGGGCACCAGCCGGAAGCAGCCCTCGCCAGAGCCAGCGTTGGCAAGGAAGGAGGACTGGGCTCCTCCCCACCTGCCCCCCACACCGCCCTCCGGCCTCCCTGCTCCCAGCCGCGCTCCCCCGCCTGCCAGCAAAGGCGTGTTTGAGTGCGTTCACTCTGTTAAAAAGAAATCCGCCCCCGCCCCGTTTCCTTCCTCCGCGATACAACCTTCCTAACTGCCAAATTGAATCGGGGTGTTTGGTGTCATAGGGAAAGTATGGCTTCTTCTTTTAATCATAAGAAAAAGCAAAACTATTCTTTCCTAGTTGTGAGAGCCCCACCGAGAATCGAAATCACCTGTACGACTAGAAAGTGTCCCCCTACCCCCTCAACCCTTGATTTTCAGGAGCGCGGGGTTCACTAAGTCAGAAACCCTAGTTCAAAGGATTCCTTTTGGAGAGTCGGACTGCTCTCTCCTTCCCCTCCCCTT	-	novel	NA	P-0044918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	220	341	0				ENST00000304494	NM_000077.4	?-39/156		1/3	0.543935925808284	2	FACETS	0.905	0.856	0.955	0.905	0.856	0.955	CLONAL	2	TRUE	0	0.589715180347948	2		341	412	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480570	120480570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	48	451	0	ENST00000256646.2:c.3247G>A	p.Ala1083Thr	p.A1083T	ENST00000256646	NM_024408.3	1083	Gca/Aca	20/34	0.37704529287264	4	FACETS	0.326	0.275	0.383	0.163	0.137	0.192	SUBCLONAL	1	TRUE	2	0.539091622199675	4		451	840	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577076	7577083	+	frameshift_variant	Frame_Shift_Del	DEL	TCTCTTCC	TCTCTTCC	-	novel	NA	P-0044966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	339	810	0	ENST00000269305.4:c.855_862del	p.Glu286SerfsTer17	p.E286Sfs*17	ENST00000269305	NM_001126112.2	285	gaGGAAGAGAat/gaat	8/11	0.476340993585428	2	FACETS	0.802	0.763	0.841	0.802	0.763	0.841	CLONAL	2	TRUE	0	0.539091622199675	2		810	784	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62303972	62303972	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs778675789	NA	P-0044966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	245	639	0	ENST00000360203.5:c.763G>A	p.Val255Met	p.V255M	ENST00000360203	NM_001283009.1	255	Gtg/Atg	9/35	0.225332517464173	6	FACETS	0.893	0.834	0.953			1	INDETERMINATE	2	TRUE	NA	0.539091622199675	6		639	1058	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974701	21974715	+	frameshift_variant	Frame_Shift_Del	DEL	ATTCGGTGCGTTGGG	ATTCGGTGCGTTGGG	C	novel	NA	P-0044966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	155	437	0	ENST00000304494.5:c.112_126delinsG	p.Pro38GlufsTer77	p.P38Efs*77	ENST00000304494	NM_000077.4	38	CCCAACGCACCGAAT/G	1/3	0.539091622199675	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.539091622199675	1		437	391	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29195879	29195879	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs767641023	NA	P-0044973-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	18	609	0	ENST00000240100.2:c.719A>G	p.Tyr240Cys	p.Y240C	ENST00000240100	NM_001394.6	240	tAt/tGt	3/4	1	2	FACETS	0.528	0.398	0.68	0.528	0.398	0.68	SUBCLONAL	1	TRUE	1	0.29409810477416	2		609	232	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259338	89259338	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044973-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	13	560	0	ENST00000336596.2:c.482T>C	p.Ile161Thr	p.I161T	ENST00000336596	NM_005233.5	161	aTt/aCt	3/17	0.282764152323378	3	FACETS	0.654	0.469	0.879	0.327	0.234	0.44	SUBCLONAL	1	TRUE	1	0.29409810477416	3		560	155	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	14	289	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.319	0.229	0.428	0.319	0.229	0.428	SUBCLONAL	1	TRUE	1	0.201470744138468	2		289	436	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	33	566	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.347	0.281	0.422	0.347	0.281	0.422	SUBCLONAL	1	TRUE	1	0.201470744138468	2		566	945	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	46	445	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.746	0.627	0.878	0.746	0.627	0.878	SUBCLONAL	1	TRUE	1	0.201470744138468	2		445	612	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	92	66	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.201470744138468	2	FACETS	0.892	0.795	0.994	0.892	0.795	0.994	CLONAL	2	TRUE	0	0.201470744138468	2		66	512	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258380	16258380	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	91	463	0	ENST00000375759.3:c.5645A>G	p.Asn1882Ser	p.N1882S	ENST00000375759	NM_015001.2	1882	aAc/aGc	11/15	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.201470744138468	2		463	792	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101099	27101099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	107	539	0	ENST00000324856.7:c.4381C>T	p.Arg1461Ter	p.R1461*	ENST00000324856	NM_006015.4	1461	Cga/Tga	18/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.201470744138468	2		539	910	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106648	27106648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553153748	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	91	753	0	ENST00000324856.7:c.6259G>A	p.Gly2087Arg	p.G2087R	ENST00000324856	NM_006015.4	2087	Gga/Aga	20/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.201470744138468	2		753	784	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799267	45799267	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	51	302	0	ENST00000450313.1:c.166G>T	p.Gly56Trp	p.G56W	ENST00000450313	NM_012222.2	56	Ggg/Tgg	3/16	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.201470744138468	2		302	491	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459166	120459166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113023165	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	70	483	1	ENST00000256646.2:c.6179G>A	p.Arg2060His	p.R2060H	ENST00000256646	NM_024408.3	2060	cGc/cAc	34/34	1	2	FACETS	0.986	0.859	1	0.986	0.859	1	CLONAL	1	TRUE	1	0.201470744138468	2		484	705	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461161	120461161	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	40	287	1	ENST00000256646.2:c.5797C>T	p.Arg1933Ter	p.R1933*	ENST00000256646	NM_024408.3	1933	Cga/Tga	32/34	1	2	FACETS	0.812	0.675	0.965	0.812	0.675	0.965	CLONAL	1	TRUE	1	0.201470744138468	2		288	489	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843643	156843643	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	110	708	0	ENST00000524377.1:c.1069G>A	p.Gly357Ser	p.G357S	ENST00000524377	NM_002529.3	357	Ggc/Agc	8/17	1	2	FACETS	0.982	0.88	1	0.982	0.88	1	CLONAL	1	TRUE	1	0.201470744138468	2		708	1112	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850704	63850705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	35	282	0	ENST00000279873.7:c.1489dup	p.Ile497AsnfsTer31	p.I497Nfs*31	ENST00000279873	NM_032199.2	494	-/A	10/10	0.201470744138468	2	FACETS	0.765	0.627	0.921	0.383	0.313	0.461	CLONAL	1	TRUE	0	0.201470744138468	2		282	454	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851180	63851180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	81	455	0	ENST00000279873.7:c.1958C>T	p.Ser653Leu	p.S653L	ENST00000279873	NM_032199.2	653	tCg/tTg	10/10	0.201470744138468	2	FACETS	0.965	0.849	1	0.483	0.424	0.545	CLONAL	1	TRUE	0	0.201470744138468	2		455	833	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851575	63851575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376632312	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	77	411	0	ENST00000279873.7:c.2353C>T	p.Arg785Cys	p.R785C	ENST00000279873	NM_032199.2	785	Cgc/Tgc	10/10	0.201470744138468	2	FACETS	1	0.925	1	0.538	0.471	0.609	CLONAL	1	TRUE	0	0.201470744138468	2		411	711	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	57	367	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	0.888	0.762	1	0.888	0.762	1	CLONAL	1	TRUE	1	0.201470744138468	2		367	637	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571819	64571819	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	88	601	0	ENST00000312049.6:c.1820G>A	p.Arg607His	p.R607H	ENST00000312049	NM_130799.2	607	cGc/cAc	10/10	1	2	FACETS	0.893	0.79	1	0.893	0.79	1	CLONAL	1	TRUE	1	0.201470744138468	2		601	978	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175400	108175400	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs786203796	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	22	151	0	ENST00000278616.4:c.5497-2A>G		p.X1833_splice	ENST00000278616	NM_000051.3	1833			1	2	FACETS	0.843	0.655	1	0.843	0.655	1	CLONAL	1	TRUE	1	0.201470744138468	2		151	259	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236087	108236087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781894	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	59	352	0	ENST00000278616.4:c.9023G>A	p.Arg3008His	p.R3008H	ENST00000278616	NM_000051.3	3008	cGt/cAt	63/63	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.201470744138468	2		352	584	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992104	11992104	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	34	231	0	ENST00000396373.4:c.194A>G	p.Asp65Gly	p.D65G	ENST00000396373	NM_001987.4	65	gAc/gGc	3/8	1	2	FACETS	0.91	0.744	1	0.91	0.744	1	CLONAL	1	TRUE	1	0.201470744138468	2		231	371	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245108	46245108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753528071	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	76	410	0	ENST00000334344.6:c.3202C>T	p.Arg1068Cys	p.R1068C	ENST00000334344	NM_152641.2	1068	Cgt/Tgt	15/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.201470744138468	2		410	639	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420229	49420229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	89	519	1	ENST00000301067.7:c.15520C>T	p.Arg5174Trp	p.R5174W	ENST00000301067	NM_003482.3	5174	Cgg/Tgg	48/54	1	2	FACETS	0.984	0.871	1	0.984	0.871	1	CLONAL	1	TRUE	1	0.201470744138468	2		520	898	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440542	49440542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773033619	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	123	597	0	ENST00000301067.7:c.4268G>A	p.Arg1423His	p.R1423H	ENST00000301067	NM_003482.3	1423	cGt/cAt	15/54	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.201470744138468	2		597	1044	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56477655	56477655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142735651	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	57	471	1	ENST00000267101.3:c.203C>T	p.Thr68Met	p.T68M	ENST00000267101	NM_001982.3	68	aCg/aTg	2/28	1	2	FACETS	0.821	0.704	0.95	0.821	0.704	0.95	CLONAL	1	TRUE	1	0.201470744138468	2		472	689	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	104	415	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.201470744138468	2		415	1006	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861874	57861874	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	74	504	0	ENST00000228682.2:c.1175A>G	p.His392Arg	p.H392R	ENST00000228682	NM_005269.2	392	cAt/cGt	10/12	1	2	FACETS	0.955	0.835	1	0.955	0.835	1	CLONAL	1	TRUE	1	0.201470744138468	2		504	769	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813303	102813303	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	68	417	0	ENST00000307046.8:c.386T>C	p.Met129Thr	p.M129T	ENST00000307046	NM_001111285.1	129	aTg/aCg	3/4	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.201470744138468	2		417	669	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030387	49030387	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373601944	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	42	246	0	ENST00000267163.4:c.1862G>A	p.Arg621His	p.R621H	ENST00000267163	NM_000321.2	621	cGt/cAt	19/27	1	2	FACETS	0.954	0.797	1	0.954	0.797	1	CLONAL	1	TRUE	1	0.201470744138468	2		246	437	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107968	30107968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757900101	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	74	359	0	ENST00000331968.5:c.839G>A	p.Arg280Gln	p.R280Q	ENST00000331968	NM_002742.2	280	cGg/cAg	5/18	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.201470744138468	2		359	652	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562770	95562770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	36	209	0	ENST00000393063.1:c.4487C>T	p.Ser1496Leu	p.S1496L	ENST00000393063	NM_030621.3	1496	tCa/tTa	24/28	1	2	FACETS	0.81	0.666	0.972	0.81	0.666	0.972	CLONAL	1	TRUE	1	0.201470744138468	2		209	441	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035370	42035370	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	44	249	0	ENST00000219905.7:c.5212G>A	p.Glu1738Lys	p.E1738K	ENST00000219905	NM_001164273.1	1738	Gaa/Aaa	15/24	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.201470744138468	2		249	416	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058655	42058655	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	39	178	1	ENST00000219905.7:c.8375T>C	p.Leu2792Pro	p.L2792P	ENST00000219905	NM_001164273.1	2792	cTg/cCg	24/24	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.201470744138468	2		179	339	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121610	2121610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45509392	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	83	534	0	ENST00000219476.3:c.1939G>A	p.Asp647Asn	p.D647N	ENST00000219476	NM_000548.3	647	Gac/Aac	18/42	1	2	FACETS	0.861	0.758	0.972	0.861	0.758	0.972	CLONAL	1	TRUE	1	0.201470744138468	2		534	957	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788617	3788617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519884	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	32	291	0	ENST00000262367.5:c.4337G>A	p.Arg1446His	p.R1446H	ENST00000262367	NM_004380.2	1446	cGc/cAc	26/31	1	2	FACETS	0.652	0.529	0.792	0.652	0.529	0.792	SUBCLONAL	1	TRUE	1	0.201470744138468	2		291	487	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274173	10274173	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	55	380	1	ENST00000330684.3:c.96del	p.Ala33ArgfsTer2	p.A33Rfs*2	ENST00000330684	NM_001134407.1	32	ccC/cc	2/13	1	2	FACETS	0.794	0.678	0.921	0.794	0.678	0.921	CLONAL	1	TRUE	1	0.201470744138468	2		381	688	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347600	89347600	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	55	546	0	ENST00000301030.4:c.5350T>G	p.Ser1784Ala	p.S1784A	ENST00000301030	NM_001256183.1	1784	Tcc/Gcc	9/13	1	2	FACETS	0.657	0.56	0.763	0.657	0.56	0.763	SUBCLONAL	1	TRUE	1	0.201470744138468	2		546	831	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984230	7984230	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	72	490	1	ENST00000319144.4:c.499C>T	p.Arg167Trp	p.R167W	ENST00000319144	NM_001139.2	167	Cgg/Tgg	4/15	1	2	FACETS	0.873	0.761	0.993	0.873	0.761	0.993	CLONAL	1	TRUE	1	0.201470744138468	2		491	819	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965426	15965426	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567776756	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	43	247	0	ENST00000268712.3:c.5380C>T	p.Arg1794Ter	p.R1794*	ENST00000268712	NM_006311.3	1794	Cga/Tga	36/46	1	2	FACETS	0.97	0.813	1	0.97	0.813	1	CLONAL	1	TRUE	1	0.201470744138468	2		247	440	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15976869	15976869	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	38	219	0	ENST00000268712.3:c.3685C>T	p.Arg1229Ter	p.R1229*	ENST00000268712	NM_006311.3	1229	Cga/Tga	28/46	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.201470744138468	2		219	359	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871746	37871746	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142783371	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	113	543	0	ENST00000269571.5:c.1270G>A	p.Val424Ile	p.V424I	ENST00000269571		424	Gtc/Atc	11/27	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.201470744138468	2		543	1011	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119978	70119978	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	43	284	0	ENST00000245479.2:c.983del	p.Pro328ArgfsTer55	p.P328Rfs*55	ENST00000245479	NM_000346.3	327	aCc/ac	3/3	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.201470744138468	2		284	403	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5225818	5225818	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	90	544	0	ENST00000357368.4:c.2414A>G	p.Tyr805Cys	p.Y805C	ENST00000357368	NM_002850.3	805	tAc/tGc	17/38	1	2	FACETS	0.999	0.885	1	0.999	0.885	1	CLONAL	1	TRUE	1	0.201470744138468	2		544	894	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349565	15349565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	103	667	0	ENST00000263377.2:c.4009C>T	p.Arg1337Cys	p.R1337C	ENST00000263377	NM_058243.2	1337	Cgc/Tgc	19/20	1	2	FACETS	0.91	0.813	1	0.91	0.813	1	CLONAL	1	TRUE	1	0.201470744138468	2		667	1123	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350023	15350023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1489035830	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	102	640	1	ENST00000263377.2:c.3629C>T	p.Pro1210Leu	p.P1210L	ENST00000263377	NM_058243.2	1210	cCg/cTg	18/20	1	2	FACETS	0.934	0.833	1	0.934	0.833	1	CLONAL	1	TRUE	1	0.201470744138468	2		641	1084	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277075	18277075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376215289	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	51	415	0	ENST00000222254.8:c.1522C>T	p.Arg508Cys	p.R508C	ENST00000222254	NM_005027.3	508	Cgc/Tgc	12/16	1	2	FACETS	0.786	0.667	0.917	0.786	0.667	0.917	CLONAL	1	TRUE	1	0.201470744138468	2		415	644	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917102	50917102	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	99	635	0	ENST00000440232.2:c.2354A>G	p.His785Arg	p.H785R	ENST00000440232	NM_002691.3	785	cAc/cGc	19/27	1	2	FACETS	0.952	0.848	1	0.952	0.848	1	CLONAL	1	TRUE	1	0.201470744138468	2		635	1032	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	72	709	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.897	0.782	1	0.897	0.782	1	CLONAL	1	TRUE	1	0.201470744138468	2		709	797	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716329	52716329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863225094	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	16	473	0	ENST00000322088.6:c.773G>A	p.Arg258His	p.R258H	ENST00000322088	NM_014225.5	258	cGc/cAc	6/15	1	2	FACETS	0.207	0.152	0.274	0.207	0.152	0.274	SUBCLONAL	1	TRUE	1	0.201470744138468	2		473	767	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185045	99185045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778972642	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	53	310	1	ENST00000074304.5:c.2447C>T	p.Thr816Met	p.T816M	ENST00000074304	NM_001134224.1	816	aCg/aTg	23/26	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.201470744138468	2		311	475	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159098	24159098	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	53	331	0	ENST00000263121.7:c.770A>G	p.Gln257Arg	p.Q257R	ENST00000263121	NM_003073.3	257	cAg/cGg	6/9	1	2	FACETS	0.913	0.779	1	0.913	0.779	1	CLONAL	1	TRUE	1	0.201470744138468	2		331	576	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163533	47163533	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	18	185	0	ENST00000409792.3:c.2593A>G	p.Asn865Asp	p.N865D	ENST00000409792	NM_014159.6	865	Aat/Gat	3/21	1	2	FACETS	0.541	0.407	0.701	0.541	0.407	0.701	SUBCLONAL	1	TRUE	1	0.201470744138468	2		185	330	SUCCESS
ATR	545	MSKCC	GRCh37	3	142257337	142257337	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1210104615	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	51	210	1	ENST00000350721.4:c.3712A>G	p.Ile1238Val	p.I1238V	ENST00000350721	NM_001184.3	1238	Ata/Gta	19/47	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.201470744138468	2		211	451	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181425	185181425	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1435276633	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	33	497	0	ENST00000265026.3:c.1366C>T	p.Arg456Ter	p.R456*	ENST00000265026	NM_004721.4	456	Cga/Tga	8/14	1	2	FACETS	0.743	0.605	0.899	0.743	0.605	0.899	SUBCLONAL	1	TRUE	1	0.201470744138468	2		497	441	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190762	185190762	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	54	421	0	ENST00000265026.3:c.1644-1G>T		p.X548_splice	ENST00000265026	NM_004721.4	548			1	2	FACETS	0.842	0.718	0.977	0.842	0.718	0.977	CLONAL	1	TRUE	1	0.201470744138468	2		421	637	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604643	55604643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745651409	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	66	381	0	ENST00000288135.5:c.2851G>A	p.Val951Ile	p.V951I	ENST00000288135	NM_000222.2	951	Gta/Ata	21/21	1	2	FACETS	0.932	0.808	1	0.932	0.808	1	CLONAL	1	TRUE	1	0.201470744138468	2		381	703	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235405	235405	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	89	454	0	ENST00000264932.6:c.1211C>G	p.Pro404Arg	p.P404R	ENST00000264932	NM_004168.2	404	cCc/cGc	9/15	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.201470744138468	2		454	832	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31493322	31493322	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	29	225	0	ENST00000344624.3:c.1834del	p.Leu612Ter	p.L612*	ENST00000344624		612	Ctg/tg	10/33	1	2	FACETS	0.729	0.585	0.893	0.729	0.585	0.893	SUBCLONAL	1	TRUE	1	0.201470744138468	2		225	395	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31495439	31495439	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	68	382	0	ENST00000344624.3:c.1709G>T	p.Arg570Ile	p.R570I	ENST00000344624		570	aGa/aTa	9/33	1	2	FACETS	0.99	0.861	1	0.99	0.861	1	CLONAL	1	TRUE	1	0.201470744138468	2		382	682	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751901	57751901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148954251	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	57	347	0	ENST00000274289.3:c.1336C>T	p.Arg446Trp	p.R446W	ENST00000274289	NM_006622.3	446	Cgg/Tgg	10/14	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.201470744138468	2		347	563	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673711	176673711	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs570278338	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	85	225	0	ENST00000439151.2:c.4411C>T	p.Arg1471Ter	p.R1471*	ENST00000439151	NM_022455.4	1471	Cga/Tga	10/23	0.201470744138468	3	FACETS	0.948	0.841	1	0.948	0.841	1	CLONAL	2	TRUE	1	0.201470744138468	3		225	490	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687160	176687160	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	48	286	0	ENST00000439151.2:c.5137T>C	p.Cys1713Arg	p.C1713R	ENST00000439151	NM_022455.4	1713	Tgc/Cgc	14/23	0.201470744138468	3	FACETS	0.982	0.83	1	0.491	0.415	0.575	CLONAL	1	TRUE	1	0.201470744138468	3		286	534	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777871	27777871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	23	254	0	ENST00000369163.2:c.20C>T	p.Thr7Ile	p.T7I	ENST00000369163	NM_003536.2	7	aCt/aTt	1/1	1	2	FACETS	0.698	0.544	0.876	0.698	0.544	0.876	SUBCLONAL	1	TRUE	1	0.201470744138468	2		254	327	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777910	27777910	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	29	302	0	ENST00000369163.2:c.59A>G	p.Gln20Arg	p.Q20R	ENST00000369163	NM_003536.2	20	cAg/cGg	1/1	1	2	FACETS	0.718	0.576	0.879	0.718	0.576	0.879	SUBCLONAL	1	TRUE	1	0.201470744138468	2		302	401	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180993	32180993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	70	579	0	ENST00000375023.3:c.2357C>T	p.Pro786Leu	p.P786L	ENST00000375023	NM_004557.3	786	cCt/cTt	15/30	1	2	FACETS	0.734	0.638	0.838	0.734	0.638	0.838	SUBCLONAL	1	TRUE	1	0.201470744138468	2		579	947	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041026	112041026	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746134687	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	30	312	1	ENST00000368678.4:c.229C>T	p.Arg77Cys	p.R77C	ENST00000368678		77	Cgt/Tgt	3/13	0.186489831139603	1	FACETS	0.527	0.424	0.645	0.527	0.424	0.645	SUBCLONAL	1	TRUE	0	0.201470744138468	1		313	508	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441974	6441974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	69	522	0	ENST00000356142.4:c.533C>T	p.Ala178Val	p.A178V	ENST00000356142	NM_018890.3	178	gCg/gTg	7/7	1	2	FACETS	0.822	0.715	0.939	0.822	0.715	0.939	CLONAL	1	TRUE	1	0.201470744138468	2		522	833	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241726	55241726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767505234	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	91	388	0	ENST00000275493.2:c.2174C>T	p.Thr725Met	p.T725M	ENST00000275493	NM_005228.3	725	aCg/aTg	18/28	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.201470744138468	2		388	614	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508259	106508259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	60	264	0	ENST00000359195.3:c.253G>A	p.Ala85Thr	p.A85T	ENST00000359195	NM_002649.2	85	Gcg/Acg	2/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.201470744138468	2		264	452	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965403	68965403	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	69	422	0	ENST00000288368.4:c.1015T>C	p.Phe339Leu	p.F339L	ENST00000288368	NM_024870.2	339	Ttt/Ctt	9/40	1	2	FACETS	0.916	0.797	1	0.916	0.797	1	CLONAL	1	TRUE	1	0.201470744138468	2		422	748	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741681	145741681	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	85	625	1	ENST00000428558.2:c.822G>T	p.Gln274His	p.Q274H	ENST00000428558	NM_004260.3	274	caG/caT	5/22	1	2	FACETS	0.843	0.743	0.95	0.843	0.743	0.95	CLONAL	1	TRUE	1	0.201470744138468	2		626	1001	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460517	8460517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370994760	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	60	359	0	ENST00000356435.5:c.3769C>T	p.Pro1257Ser	p.P1257S	ENST00000356435		1257	Ccg/Tcg	22/35	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.201470744138468	2		359	547	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399471	139399471	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751810380	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	97	639	1	ENST00000277541.6:c.4672G>A	p.Gly1558Arg	p.G1558R	ENST00000277541	NM_017617.3	1558	Ggg/Agg	26/34	1	2	FACETS	0.962	0.856	1	0.962	0.856	1	CLONAL	1	TRUE	1	0.201470744138468	2		640	1001	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418358	139418358	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	97	687	0	ENST00000277541.6:c.214G>T	p.Gly72Trp	p.G72W	ENST00000277541	NM_017617.3	72	Ggg/Tgg	3/34	1	2	FACETS	0.919	0.817	1	0.919	0.817	1	CLONAL	1	TRUE	1	0.201470744138468	2		687	1048	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156720	20156720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	44	251	0	ENST00000379607.5:c.37C>T	p.Arg13Cys	p.R13C	ENST00000379607	NM_001412.3	13	Cgc/Tgc	2/7	1	2	FACETS	0.899	0.754	1	0.899	0.754	1	CLONAL	1	TRUE	1	0.201470744138468	2		251	486	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923024	44923024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	66	434	0	ENST00000377967.4:c.1885G>A	p.Glu629Lys	p.E629K	ENST00000377967	NM_021140.2	629	Gag/Aag	16/29	1	2	FACETS	0.919	0.797	1	0.919	0.797	1	CLONAL	1	TRUE	1	0.201470744138468	2		434	713	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226990	53226990	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	71	531	0	ENST00000375401.3:c.2585A>G	p.Asn862Ser	p.N862S	ENST00000375401	NM_004187.3	862	aAc/aGc	18/26	1	2	FACETS	0.856	0.746	0.976	0.856	0.746	0.976	CLONAL	1	TRUE	1	0.201470744138468	2		531	823	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829713	76829713	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	36	313	0	ENST00000373344.5:c.6326+2T>C		p.X2109_splice	ENST00000373344	NM_000489.3	2109			1	2	FACETS	0.82	0.674	0.983	0.82	0.674	0.983	CLONAL	1	TRUE	1	0.201470744138468	2		313	436	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829819	76829819	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	46	339	0	ENST00000373344.5:c.6222G>T	p.Glu2074Asp	p.E2074D	ENST00000373344	NM_000489.3	2074	gaG/gaT	28/35	1	2	FACETS	0.967	0.815	1	0.967	0.815	1	CLONAL	1	TRUE	1	0.201470744138468	2		339	472	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215282	123215282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	39	273	0	ENST00000218089.9:c.2828C>T	p.Ser943Phe	p.S943F	ENST00000218089	NM_001042749.1	943	tCt/tTt	28/35	1	2	FACETS	0.849	0.704	1	0.849	0.704	1	CLONAL	1	TRUE	1	0.201470744138468	2		273	456	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217361	123217361	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	63	303	0	ENST00000218089.9:c.3015A>T	p.Glu1005Asp	p.E1005D	ENST00000218089	NM_001042749.1	1005	gaA/gaT	29/35	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.201470744138468	2		303	561	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858138	152858138	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	113	690	1	ENST00000406277.2:c.477G>A	p.Trp159Ter	p.W159*	ENST00000406277	NM_152274.4	159	tgG/tgA	6/7	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.201470744138468	2		691	1108	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874451	76874451	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0044987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	27	162	0	ENST00000373344.5:c.5273-2A>G		p.X1758_splice	ENST00000373344	NM_000489.3	1758			1	2	FACETS	0.893	0.712	1	0.893	0.712	1	CLONAL	1	TRUE	1	0.201470744138468	2		162	300	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	257	289	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.87510236986194	2		289	277	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266503	55266503	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	204	516	12	ENST00000275493.2:c.2795G>A	p.Arg932His	p.R932H	ENST00000275493	NM_005228.3	932	cGc/cAc	23/28	0.87510236986194	3	FACETS	0.99	0.922	1	0.495	0.461	0.53	CLONAL	1	TRUE	1	0.87510236986194	3		528	677	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604790	48604790	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1568211615	NA	P-0044990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	114	282	0	ENST00000342988.3:c.1612G>T	p.Glu538Ter	p.E538*	ENST00000342988	NM_005359.5	538	Gaa/Taa	12/12	0.872679937047637	1	FACETS	0.97	0.915	1	0.97	0.915	1	CLONAL	1	TRUE	0	0.87510236986194	1		282	151	SUCCESS
APC	324	MSKCC	GRCh37	5	112128142	112128142	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0044990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	65	246	2	ENST00000257430.4:c.646-1G>A		p.X216_splice	ENST00000257430	NM_000038.5	216			0.87510236986194	3	FACETS	0.841	0.737	0.95	0.42	0.368	0.475	CLONAL	1	TRUE	1	0.87510236986194	3		248	254	SUCCESS
APC	324	MSKCC	GRCh37	5	112174268	112174268	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0044990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	142	264	2	ENST00000257430.4:c.2977A>T	p.Lys993Ter	p.K993*	ENST00000257430	NM_000038.5	993	Aag/Tag	16/16	0.87510236986194	3	FACETS	0.997	0.934	1	0.997	0.934	1	CLONAL	2	TRUE	1	0.87510236986194	3		266	234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0044990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	532	598	10	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.87510236986194	2	FACETS	0.962	0.941	0.981	0.962	0.941	0.981	CLONAL	2	TRUE	0	0.87510236986194	2		608	632	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920450	114920450	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	398	357	3	ENST00000543371.1:c.1391G>A	p.Arg464Lys	p.R464K	ENST00000543371	NM_001198531.1	464	aGg/aAg	13/14	0.87510236986194	3	FACETS	0.921	0.884	0.957	0.921	0.884	0.957	CLONAL	2	TRUE	1	0.87510236986194	3		360	710	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468092	120468092	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	212	595	0	ENST00000256646.2:c.4347G>C	p.Gln1449His	p.Q1449H	ENST00000256646	NM_024408.3	1449	caG/caC	25/34	0.308821491394426	6	FACETS	1	0.987	1	0.428	0.397	0.46	INDETERMINATE	1	TRUE	3	0.87510236986194	6		595	1037	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609646	81609646	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	200	508	1	ENST00000298171.2:c.1244A>T	p.Lys415Met	p.K415M	ENST00000298171	NM_000369.2	415	aAg/aTg	10/10	0.87510236986194	2	FACETS	1	0.938	1	0.5	0.469	0.532	CLONAL	1	TRUE	0	0.87510236986194	2		509	457	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243037	105243038	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTGGTCCACTGCAGGCAGCGGATG	novel	NA	P-0044999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	205	1050	0	ENST00000349310.3:c.222_245dup	p.Ile75_Thr82dup	p.I75_T82dup	ENST00000349310	NM_001014432.1	75	act/acCATCCGCTGCCTGCAGTGGACCACt	5/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.264017468553517	2		1050	1334	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121338	29121338	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	96	562	0	ENST00000328354.6:c.337T>C	p.Tyr113His	p.Y113H	ENST00000328354	NM_007194.3	113	Tac/Cac	3/15	0.23773133476723	1	FACETS	0.842	0.75	0.94	0.842	0.75	0.94	CLONAL	1	TRUE	0	0.264017468553517	1		562	750	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	131	584	2	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.282683473877875	2		586	875	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	34	332	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	0.209538155233034	1	FACETS	0.435	0.355	0.525	0.435	0.355	0.525	SUBCLONAL	1	TRUE	0	0.282683473877875	1		332	475	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682399	52682400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0045008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	84	298	0	ENST00000394830.3:c.773dup	p.Asn258LysfsTer6	p.N258Kfs*6	ENST00000394830	NM_018313.4	258	aat/aaAt	8/30	0.239170085549304	2	FACETS	1	0.972	1	0.66	0.586	0.74	CLONAL	1	TRUE	0	0.282683473877875	2		298	450	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602341	10602341	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	114	821	0	ENST00000171111.5:c.1237del	p.Arg413ValfsTer45	p.R413Vfs*45	ENST00000171111	NM_203500.1	413	Cgt/gt	3/6	1	2	FACETS	0.717	0.644	0.795	0.717	0.644	0.795	SUBCLONAL	1	TRUE	1	0.282683473877875	2		821	1125	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207153	1207155	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs587782056	NA	P-0045008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	90	802	0	ENST00000326873.7:c.250_252del	p.Lys84del	p.K84del	ENST00000326873	NM_000455.4	81	AAG/-	1/10	1	2	FACETS	0.567	0.501	0.637	0.567	0.501	0.637	SUBCLONAL	1	TRUE	1	0.282683473877875	2		802	1123	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183817	10183817	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690959	NA	P-0045008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	185	639	0	ENST00000256474.2:c.286C>T	p.Gln96Ter	p.Q96*	ENST00000256474	NM_000551.3	96	Cag/Tag	1/3	0.239170085549304	2	FACETS	1	0.99	1	0.747	0.69	0.806	CLONAL	1	TRUE	0	0.282683473877875	2		639	876	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0045008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	191	1097	6	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.282683473877875	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.282683473877875	1		1103	989	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244280	153244280	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	28	227	0	ENST00000281708.4:c.1877C>A	p.Ala626Asp	p.A626D	ENST00000281708	NM_033632.3	626	gCt/gAt	12/12	0.282683473877875	1	FACETS	0.561	0.449	0.688	0.561	0.449	0.688	SUBCLONAL	1	TRUE	0	0.282683473877875	1		227	303	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161950	47161951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0045008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	96	310	0	ENST00000409792.3:c.4175dup	p.Asn1392LysfsTer6	p.N1392Kfs*6	ENST00000409792	NM_014159.6	1392	aac/aaAc	3/21	0.239170085549304	2	FACETS	0.795	0.713	0.882	0.795	0.713	0.882	SUBCLONAL	2	TRUE	0	0.282683473877875	2		310	427	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500476	99500476	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	68	698	1	ENST00000268035.6:c.3913del	p.Leu1305TrpfsTer45	p.L1305Wfs*45	ENST00000268035	NM_000875.3	1303	gtC/gt	21/21	0.209538155233034	1	FACETS	0.555	0.482	0.634	0.555	0.482	0.634	SUBCLONAL	1	TRUE	0	0.282683473877875	1		699	744	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043407	180043407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757396801	NA	P-0045008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	129	741	4	ENST00000261937.6:c.3179G>A	p.Arg1060Gln	p.R1060Q	ENST00000261937	NM_182925.4	1060	cGg/cAg	23/30	1	2	FACETS	0.915	0.828	1	0.915	0.828	1	CLONAL	1	TRUE	1	0.282683473877875	2		745	998	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259391	36259391	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	72	574	0	ENST00000300305.3:c.100G>A	p.Ala34Thr	p.A34T	ENST00000300305		34	Gcc/Acc	3/8	0.209538155233034	1	FACETS	0.545	0.476	0.621	0.545	0.476	0.621	SUBCLONAL	1	TRUE	0	0.282683473877875	1		574	802	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600363	10600363	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	158	758	0	ENST00000171111.5:c.1492C>T	p.Arg498Ter	p.R498*	ENST00000171111	NM_203500.1	498	Cga/Tga	4/6	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.282683473877875	2		758	1033	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41247864	41247865	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	rs80357537	NA	P-0045008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	30	396	0	ENST00000357654.3:c.668dup	p.Ala224GlyfsTer4	p.A224Gfs*4	ENST00000357654	NM_007294.3	223	aag/aaAg	9/23	1	2	FACETS	0.357	0.286	0.437	0.357	0.286	0.437	SUBCLONAL	1	TRUE	1	0.282683473877875	2		396	595	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022898	27022898	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1333869920	NA	P-0045008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	11	45	0	ENST00000324856.7:c.4G>A	p.Ala2Thr	p.A2T	ENST00000324856	NM_006015.4	2	Gcc/Acc	1/20	1	2	FACETS	0.998	0.7	1	0.998	0.7	1	CLONAL	1	TRUE	1	0.282683473877875	2		45	78	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274812	123274812	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	47	410	0	ENST00000358487.5:c.1106T>A	p.Ile369Asn	p.I369N	ENST00000358487	NM_000141.4	369	aTt/aAt	9/18	1	2	FACETS	0.542	0.456	0.636	0.542	0.456	0.636	SUBCLONAL	1	TRUE	1	0.282683473877875	2		410	614	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061690	38061690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	26	396	0	ENST00000250448.2:c.299G>A	p.Gly100Asp	p.G100D	ENST00000250448	NM_004496.3	100	gGc/gAc	2/2	0.282683473877875	1	FACETS	0.394	0.311	0.488	0.394	0.311	0.488	SUBCLONAL	1	TRUE	0	0.282683473877875	1		396	401	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774181	66774181	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	69	1022	0	ENST00000307102.5:c.657G>T	p.Met219Ile	p.M219I	ENST00000307102	NM_002755.3	219	atG/atT	6/11	0.209538155233034	1	FACETS	0.333	0.289	0.382	0.333	0.289	0.382	SUBCLONAL	1	TRUE	0	0.282683473877875	1		1022	1258	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348476	89348476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567568714	NA	P-0045008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	167	789	1	ENST00000301030.4:c.4474C>T	p.Leu1492Phe	p.L1492F	ENST00000301030	NM_001256183.1	1492	Ctc/Ttc	9/13	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.282683473877875	2		790	1166	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627347	37627347	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	48	602	0	ENST00000447079.4:c.1262A>C	p.Lys421Thr	p.K421T	ENST00000447079	NM_015083.1	421	aAg/aCg	2/14	1	2	FACETS	0.365	0.307	0.429	0.365	0.307	0.429	SUBCLONAL	1	TRUE	1	0.282683473877875	2		602	931	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213585	36213585	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1181	117	946	0	ENST00000222270.7:c.2687T>G	p.Leu896Arg	p.L896R	ENST00000222270	NM_014727.1	896	cTc/cGc	5/37	1	2	FACETS	0.638	0.573	0.707	0.638	0.573	0.707	SUBCLONAL	1	TRUE	1	0.282683473877875	2		946	1298	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223593	36223593	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	61	866	1	ENST00000222270.7:c.6147del	p.Ser2050AlafsTer41	p.S2050Afs*41	ENST00000222270	NM_014727.1	2048	gCc/gc	28/37	1	2	FACETS	0.365	0.313	0.421	0.365	0.313	0.421	SUBCLONAL	1	TRUE	1	0.282683473877875	2		867	1184	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719839	190719839	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	20	209	0	ENST00000441310.2:c.1841A>G	p.Glu614Gly	p.E614G	ENST00000441310	NM_000534.4	614	gAa/gGa	9/13	1	2	FACETS	0.571	0.437	0.726	0.571	0.437	0.726	SUBCLONAL	1	TRUE	1	0.282683473877875	2		209	248	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37059036	37059036	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1064794122	NA	P-0045008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	123	417	0	ENST00000231790.2:c.832del	p.Thr278GlnfsTer19	p.T278Qfs*19	ENST00000231790	NM_000249.3	277	gAa/ga	10/19	0.239170085549304	2	FACETS	1	0.984	1	0.716	0.649	0.786	CLONAL	1	TRUE	0	0.282683473877875	2		417	608	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149243894	149243894	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	69	539	0	ENST00000360632.3:c.924G>T	p.Arg308Ser	p.R308S	ENST00000360632	NM_015472.4	308	agG/agT	6/7	0.133313101076913	3	FACETS	0.623	0.541	0.711	0.311	0.27	0.356	INDETERMINATE	1	TRUE	1	0.282683473877875	3		539	895	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	24	291	0	ENST00000263967.3:c.3145G>T	p.Gly1049Cys	p.G1049C	ENST00000263967	NM_006218.2	1049	Ggt/Tgt	21/21	0.133313101076913	3	FACETS	0.403	0.315	0.505	0.201	0.157	0.253	INDETERMINATE	1	TRUE	1	0.282683473877875	3		291	481	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140847	37140847	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	49	531	0	ENST00000373509.5:c.683T>C	p.Leu228Pro	p.L228P	ENST00000373509	NM_002648.3	228	cTg/cCg	5/6	1	2	FACETS	0.448	0.379	0.526	0.448	0.379	0.526	SUBCLONAL	1	TRUE	1	0.282683473877875	2		531	773	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28934577	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	29	663	1	ENST00000269305.4:c.770T>C	p.Leu257Pro	p.L257P	ENST00000269305	NM_001126112.2	257	cTg/cCg	7/11	1	2	FACETS	0.111	0.089	0.137	0.111	0.089	0.137	SUBCLONAL	1	TRUE	1	0.71399737408342	2		664	729	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857785	9857785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555482324	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	45	636	1	ENST00000330684.3:c.3616C>T	p.Arg1206Ter	p.R1206*	ENST00000330684	NM_001134407.1	1206	Cga/Tga	13/13	1	2	FACETS	0.228	0.191	0.269	0.228	0.191	0.269	SUBCLONAL	1	TRUE	1	0.71399737408342	2		637	553	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	205	475	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.791	0.747	0.834	1	0.994	1	SUBCLONAL	2	TRUE	1	0.71399737408342	2		476	363	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	145	808	0	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	0.706	0.647	0.768	0.706	0.647	0.768	SUBCLONAL	1	TRUE	1	0.71399737408342	2		808	575	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	160	356	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.71399737408342	3	FACETS	1	0.954	1	0.524	0.483	0.567	CLONAL	1	TRUE	1	0.71399737408342	3		356	580	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	384	699	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.85	0.817	0.882	1	0.997	1	CLONAL	2	TRUE	1	0.71399737408342	2		706	633	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991949	72991949	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs753977275	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	156	644	3	ENST00000268489.5:c.2096del	p.Gly699AlafsTer125	p.G699Afs*125	ENST00000268489	NM_006885.3	699	gGc/gc	2/10	1	2	FACETS	0.811	0.747	0.877	0.811	0.747	0.877	CLONAL	1	TRUE	1	0.71399737408342	2		647	539	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	39	551	1	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	0.199	0.165	0.238	0.199	0.165	0.238	SUBCLONAL	1	TRUE	1	0.71399737408342	2		552	548	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	281	586	0	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.969	0.914	1	0.969	0.914	1	CLONAL	1	TRUE	1	0.71399737408342	2		586	812	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682399	52682400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	120	298	0	ENST00000394830.3:c.773dup	p.Asn258LysfsTer6	p.N258Kfs*6	ENST00000394830	NM_018313.4	258	aat/aaAt	8/30	1	2	FACETS	0.86	0.784	0.938	0.86	0.784	0.938	CLONAL	1	TRUE	1	0.71399737408342	2		298	391	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777063	9777063	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	188	674	0	ENST00000377346.4:c.827T>C	p.Met276Thr	p.M276T	ENST00000377346	NM_005026.3	276	aTg/aCg	7/24	1	2	FACETS	0.879	0.817	0.943	0.879	0.817	0.943	CLONAL	1	TRUE	1	0.71399737408342	2		674	599	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461166	120461166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200693165	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	141	411	0	ENST00000256646.2:c.5792G>A	p.Arg1931His	p.R1931H	ENST00000256646	NM_024408.3	1931	cGc/cAc	32/34	1	2	FACETS	0.839	0.77	0.91	0.839	0.77	0.91	CLONAL	1	TRUE	1	0.71399737408342	2		411	471	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617431	43617431	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	170	435	2	ENST00000355710.3:c.2772del	p.Phe924LeufsTer22	p.F924Lfs*22	ENST00000355710	NM_020975.4	923	cTt/ct	16/20	1	2	FACETS	0.976	0.905	1	0.976	0.905	1	CLONAL	1	TRUE	1	0.71399737408342	2		437	488	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332459	70332459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751344073	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	196	633	2	ENST00000373644.4:c.364G>A	p.Val122Ile	p.V122I	ENST00000373644	NM_030625.2	122	Gta/Ata	2/12	1	2	FACETS	0.871	0.811	0.934	0.871	0.811	0.934	CLONAL	1	TRUE	1	0.71399737408342	2		635	630	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88635807	88635807	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	115	366	0	ENST00000372037.3:c.32T>C	p.Leu11Ser	p.L11S	ENST00000372037	NM_004329.2	11	tTg/tCg	3/13	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.71399737408342	2		366	320	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	190	343	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.71399737408342	2		343	517	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	137	349	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	0.872	0.8	0.947	0.872	0.8	0.947	CLONAL	1	TRUE	1	0.71399737408342	2		349	440	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742476	17742476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	196	735	1	ENST00000250003.3:c.658G>A	p.Ala220Thr	p.A220T	ENST00000250003	NM_002478.4	220	Gcc/Acc	2/3	1	2	FACETS	0.989	0.923	1	0.989	0.923	1	CLONAL	1	TRUE	1	0.71399737408342	2		736	555	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575119	64575119	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	98	598	0	ENST00000312049.6:c.688T>G	p.Cys230Gly	p.C230G	ENST00000312049	NM_130799.2	230	Tgt/Ggt	4/10	0.438688451697672	3	FACETS	0.553	0.493	0.616	0.276	0.246	0.308	SUBCLONAL	1	TRUE	1	0.71399737408342	3		598	674	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589791	69589791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	77	89	0	ENST00000168712.1:c.62C>T	p.Ala21Val	p.A21V	ENST00000168712	NM_002007.2	21	gCg/gTg	1/3	0.438688451697672	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.71399737408342	3		89	126	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981720	101981721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	59	297	0	ENST00000282441.5:c.147dup	p.Ala50ArgfsTer62	p.A50Rfs*62	ENST00000282441	NM_001130145.2	47	-/C	1/9	0.438688451697672	3	FACETS	0.758	0.657	0.866	0.379	0.328	0.433	SUBCLONAL	1	TRUE	1	0.71399737408342	3		297	296	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195514	102195514	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	246	436	0	ENST00000263464.3:c.274A>G	p.Ser92Gly	p.S92G	ENST00000263464	NM_001165.4	92	Agc/Ggc	2/9	0.438688451697672	3	FACETS	0.861	0.813	0.909	0.861	0.813	0.909	CLONAL	2	TRUE	1	0.71399737408342	3		436	543	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641498	18641498	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	119	380	0	ENST00000266497.5:c.2497A>G	p.Lys833Glu	p.K833E	ENST00000266497		833	Aaa/Gaa	17/31	1	2	FACETS	0.906	0.826	0.988	0.906	0.826	0.988	CLONAL	1	TRUE	1	0.71399737408342	2		380	368	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245702	46245702	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	135	487	0	ENST00000334344.6:c.3796A>G	p.Met1266Val	p.M1266V	ENST00000334344	NM_152641.2	1266	Atg/Gtg	15/21	1	2	FACETS	0.903	0.828	0.979	0.903	0.828	0.979	CLONAL	1	TRUE	1	0.71399737408342	2		487	419	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287417	46287417	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	115	314	1	ENST00000334344.6:c.5280del	p.Glu1761ArgfsTer4	p.E1761Rfs*4	ENST00000334344	NM_152641.2	1759	gAa/ga	20/21	1	2	FACETS	0.805	0.732	0.882	0.805	0.732	0.882	CLONAL	1	TRUE	1	0.71399737408342	2		315	400	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426973	49426973	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1565778024	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	53	723	3	ENST00000301067.7:c.11515del	p.Gln3839SerfsTer42	p.Q3839Sfs*42	ENST00000301067	NM_003482.3	3839	Cag/ag	39/54	1	2	FACETS	0.251	0.213	0.292	0.251	0.213	0.292	SUBCLONAL	1	TRUE	1	0.71399737408342	2		726	592	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222651	69222651	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	202	592	1	ENST00000462284.1:c.624A>G	p.Ile208Met	p.I208M	ENST00000462284	NM_002392.5	208	atA/atG	8/11	1	2	FACETS	0.907	0.845	0.97	0.907	0.845	0.97	CLONAL	1	TRUE	1	0.71399737408342	2		593	624	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	384	567	2	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.904	0.871	0.936	1	0.997	1	CLONAL	2	TRUE	1	0.71399737408342	2		569	595	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257836	133257836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	163	533	0	ENST00000320574.5:c.92C>T	p.Ala31Val	p.A31V	ENST00000320574	NM_006231.2	31	gCa/gTa	2/49	1	2	FACETS	0.915	0.846	0.986	0.915	0.846	0.986	CLONAL	1	TRUE	1	0.71399737408342	2		533	499	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437458	110437458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866284428	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	168	562	0	ENST00000375856.3:c.943C>T	p.His315Tyr	p.H315Y	ENST00000375856	NM_003749.2	315	Cac/Tac	1/2	0.71399737408342	3	FACETS	0.888	0.818	0.961	0.444	0.409	0.481	CLONAL	1	TRUE	1	0.71399737408342	3		562	719	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438317	110438322	+	inframe_deletion	In_Frame_Del	DEL	GTTGTT	GTTGTT	-	rs532810290	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	121	223	1	ENST00000375856.3:c.79_84del	p.Asn27_Asn28del	p.N27_N28del	ENST00000375856	NM_003749.2	27	AACAAC/-	1/2	0.71399737408342	3	FACETS	1	0.98	1	0.635	0.58	0.692	CLONAL	1	TRUE	1	0.71399737408342	3		224	362	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986832	36986832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	138	254	0	ENST00000354822.5:c.857G>A	p.Arg286Gln	p.R286Q	ENST00000354822	NM_001079668.2	286	cGa/cAa	3/3	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.71399737408342	2		254	351	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562840	95562840	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	67	315	0	ENST00000393063.1:c.4417del	p.Ser1473GlnfsTer17	p.S1473Qfs*17	ENST00000393063	NM_030621.3	1473	Tca/ca	24/28	1	2	FACETS	0.659	0.578	0.744	0.659	0.578	0.744	SUBCLONAL	1	TRUE	1	0.71399737408342	2		315	285	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562983	95562994	+	inframe_deletion	In_Frame_Del	DEL	TCCTCCTCCTCA	TCCTCCTCCTCA	-	rs1566756845	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	81	345	0	ENST00000393063.1:c.4263_4274del	p.Asp1421_Glu1424del	p.D1421_E1424del	ENST00000393063	NM_030621.3	1421	gaTGAGGAGGAGGAg/gag	24/28	1	2	FACETS	0.622	0.551	0.696	0.622	0.551	0.696	SUBCLONAL	1	TRUE	1	0.71399737408342	2		345	365	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643312	38643312	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	163	424	0	ENST00000299084.4:c.782A>G	p.Tyr261Cys	p.Y261C	ENST00000299084	NM_152594.2	261	tAc/tGc	7/7	1	2	FACETS	0.993	0.919	1	0.993	0.919	1	CLONAL	1	TRUE	1	0.71399737408342	2		424	460	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628303	90628303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	273	955	0	ENST00000330062.3:c.1108G>A	p.Ala370Thr	p.A370T	ENST00000330062	NM_002168.2	370	Gcc/Acc	9/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.71399737408342	2		955	745	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	148	503	2	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.871	0.802	0.942	0.871	0.802	0.942	CLONAL	1	TRUE	1	0.71399737408342	2		505	476	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112603	2112603	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs397515301	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	159	672	0	ENST00000219476.3:c.1361+2T>C		p.X454_splice	ENST00000219476	NM_000548.3	454			1	2	FACETS	0.875	0.808	0.944	0.875	0.808	0.944	CLONAL	1	TRUE	1	0.71399737408342	2		672	509	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134496	2134496	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	217	919	0	ENST00000219476.3:c.4276del	p.Glu1426LysfsTer50	p.E1426Kfs*50	ENST00000219476	NM_000548.3	1425	Ggg/gg	34/42	1	2	FACETS	0.814	0.759	0.87	0.814	0.759	0.87	CLONAL	1	TRUE	1	0.71399737408342	2		919	747	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789642	3789642	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	198	549	0	ENST00000262367.5:c.4217A>G	p.Asp1406Gly	p.D1406G	ENST00000262367	NM_004380.2	1406	gAt/gGt	25/31	1	2	FACETS	0.886	0.825	0.949	0.886	0.825	0.949	CLONAL	1	TRUE	1	0.71399737408342	2		549	626	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348058	89348058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886568838	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	304	1057	0	ENST00000301030.4:c.4892G>A	p.Arg1631Gln	p.R1631Q	ENST00000301030	NM_001256183.1	1631	cGg/cAg	9/13	1	2	FACETS	0.957	0.904	1	0.957	0.904	1	CLONAL	1	TRUE	1	0.71399737408342	2		1057	890	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349946	89349946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779328307	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	282	791	0	ENST00000301030.4:c.3004C>T	p.Arg1002Trp	p.R1002W	ENST00000301030	NM_001256183.1	1002	Cgg/Tgg	9/13	1	2	FACETS	0.99	0.934	1	0.99	0.934	1	CLONAL	1	TRUE	1	0.71399737408342	2		791	798	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876659675	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	38	664	0	ENST00000269305.4:c.764T>G	p.Ile255Ser	p.I255S	ENST00000269305	NM_001126112.2	255	aTc/aGc	7/11	1	2	FACETS	0.146	0.12	0.176	0.146	0.12	0.176	SUBCLONAL	1	TRUE	1	0.71399737408342	2		664	728	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	225	803	0	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	1	2	FACETS	0.86	0.804	0.917	0.86	0.804	0.917	CLONAL	1	TRUE	1	0.71399737408342	2		803	733	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998959	11998959	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1208900089	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	121	318	1	ENST00000353533.5:c.461G>A	p.Arg154Gln	p.R154Q	ENST00000353533	NM_003010.3	154	cGg/cAg	4/11	1	2	FACETS	0.931	0.85	1	0.931	0.85	1	CLONAL	1	TRUE	1	0.71399737408342	2		319	364	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	111	328	0	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	0.772	0.699	0.847	0.772	0.699	0.847	SUBCLONAL	1	TRUE	1	0.71399737408342	2		328	403	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687472	37687472	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	130	414	0	ENST00000447079.4:c.4382del	p.Gly1461AlafsTer38	p.G1461Afs*38	ENST00000447079	NM_015083.1	1459	tGg/tg	14/14	1	2	FACETS	0.936	0.858	1	0.936	0.858	1	CLONAL	1	TRUE	1	0.71399737408342	2		414	389	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526499	66526499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	187	439	1	ENST00000358598.2:c.1055G>A	p.Arg352Gln	p.R352Q	ENST00000358598	NM_212471.2	352	cGa/cAa	11/11	1	2	FACETS	0.935	0.87	1	0.935	0.87	1	CLONAL	1	TRUE	1	0.71399737408342	2		440	560	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119962	70119962	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	116	434	0	ENST00000245479.2:c.964A>G	p.Ser322Gly	p.S322G	ENST00000245479	NM_000346.3	322	Agc/Ggc	3/3	1	2	FACETS	0.846	0.77	0.925	0.846	0.77	0.925	CLONAL	1	TRUE	1	0.71399737408342	2		434	384	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218447	1218447	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs886041996	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	197	667	0	ENST00000326873.7:c.326del	p.Asn109MetfsTer20	p.N109Mfs*20	ENST00000326873	NM_000455.4	108	Aaa/aa	2/10	1	2	FACETS	0.857	0.797	0.918	0.857	0.797	0.918	CLONAL	1	TRUE	1	0.71399737408342	2		667	644	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	185	836	2	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	1	2	FACETS	0.826	0.767	0.888	0.826	0.767	0.888	CLONAL	1	TRUE	1	0.71399737408342	2		838	627	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226817	2226817	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749350627	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	203	533	2	ENST00000398665.3:c.4297G>A	p.Val1433Met	p.V1433M	ENST00000398665	NM_032482.2	1433	Gtg/Atg	27/28	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.71399737408342	2		535	539	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602799	10602799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	317	956	0	ENST00000171111.5:c.779G>A	p.Arg260Gln	p.R260Q	ENST00000171111	NM_203500.1	260	cGa/cAa	3/6	1	2	FACETS	0.999	0.946	1	0.999	0.946	1	CLONAL	1	TRUE	1	0.71399737408342	2		956	889	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123782	11123783	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	41	555	0	ENST00000358026.2:c.2437_2438del	p.Ser813AsnfsTer10	p.S813Nfs*10	ENST00000358026	NM_001128849.1	811	cCT/c	16/36	1	2	FACETS	0.204	0.169	0.243	0.204	0.169	0.243	SUBCLONAL	1	TRUE	1	0.71399737408342	2		555	563	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141541	11141541	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	208	769	0	ENST00000358026.2:c.3522del	p.Phe1174LeufsTer42	p.F1174Lfs*42	ENST00000358026	NM_001128849.1	1173	aTt/at	25/36	1	2	FACETS	0.868	0.81	0.928	0.868	0.81	0.928	CLONAL	1	TRUE	1	0.71399737408342	2		769	671	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288867	15288867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	120	357	0	ENST00000263388.2:c.3872G>A	p.Arg1291His	p.R1291H	ENST00000263388	NM_000435.2	1291	cGc/cAc	24/33	1	2	FACETS	0.95	0.867	1	0.95	0.867	1	CLONAL	1	TRUE	1	0.71399737408342	2		357	354	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210926	36210926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373933410	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	238	857	0	ENST00000222270.7:c.677G>A	p.Arg226Gln	p.R226Q	ENST00000222270	NM_014727.1	226	cGg/cAg	3/37	1	2	FACETS	0.956	0.897	1	0.956	0.897	1	CLONAL	1	TRUE	1	0.71399737408342	2		857	697	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229429	36229429	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356978354	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	148	492	0	ENST00000222270.7:c.8119G>A	p.Ala2707Thr	p.A2707T	ENST00000222270	NM_014727.1	2707	Gcc/Acc	37/37	1	2	FACETS	0.923	0.851	0.998	0.923	0.851	0.998	CLONAL	1	TRUE	1	0.71399737408342	2		492	449	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40747868	40747868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752597471	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	222	727	0	ENST00000392038.2:c.550C>T	p.Arg184Trp	p.R184W	ENST00000392038	NM_001626.4	184	Cgg/Tgg	6/14	1	2	FACETS	0.866	0.809	0.924	0.866	0.809	0.924	CLONAL	1	TRUE	1	0.71399737408342	2		727	718	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42384807	42384807	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	138	514	1	ENST00000221972.3:c.567+2T>C		p.X189_splice	ENST00000221972	NM_021601.3	189			1	2	FACETS	0.918	0.843	0.995	0.918	0.843	0.995	CLONAL	1	TRUE	1	0.71399737408342	2		515	421	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795176	42795177	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	240	898	0	ENST00000575354.2:c.2258_2259del	p.Val753GlyfsTer9	p.V753Gfs*9	ENST00000575354	NM_015125.3	752	acTGtg/actg	10/20	1	2	FACETS	0.94	0.882	1	0.94	0.882	1	CLONAL	1	TRUE	1	0.71399737408342	2		898	715	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639588	47639588	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63749897	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	164	388	0	ENST00000233146.2:c.687del	p.Ala230LeufsTer16	p.A230Lfs*16	ENST00000233146	NM_000251.2	227	agA/ag	4/16	1	2	FACETS	0.928	0.859	0.999	0.928	0.859	0.999	CLONAL	1	TRUE	1	0.71399737408342	2		388	495	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	185	462	14	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	0.946	0.879	1	0.946	0.879	1	CLONAL	1	TRUE	1	0.71399737408342	2		476	548	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149799	202149799	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	185	589	0	ENST00000358485.4:c.1245del	p.Phe415LeufsTer26	p.F415Lfs*26	ENST00000358485	NM_001080125.1	414	Ttt/tt	8/9	1	2	FACETS	0.824	0.764	0.885	0.824	0.764	0.885	CLONAL	1	TRUE	1	0.71399737408342	2		589	629	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022443	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	rs750318549	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	78	338	0	ENST00000375687.4:c.1933_1934del	p.Gly645TrpfsTer12	p.G645Wfs*12	ENST00000375687	NM_015338.5	643	GGg/g	13/13	1	2	FACETS	0.922	0.823	1	0.922	0.823	1	CLONAL	1	TRUE	1	0.71399737408342	2		338	237	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279824	46279825	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAA	rs749655240	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	32	506	0	ENST00000371998.3:c.3752_3753insACA	p.Gln1276dup	p.Q1276dup	ENST00000371998		1276	-/CAA	20/23	1	2	FACETS	0.238	0.193	0.289	0.238	0.193	0.289	SUBCLONAL	1	TRUE	1	0.71399737408342	2		506	376	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164805	36164805	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	231	908	0	ENST00000300305.3:c.1070del	p.Pro357ArgfsTer237	p.P357Rfs*237	ENST00000300305		357	cCg/cg	8/8	1	2	FACETS	0.894	0.837	0.952	0.894	0.837	0.952	CLONAL	1	TRUE	1	0.71399737408342	2		908	724	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171723	36171723	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	132	394	0	ENST00000300305.3:c.842A>G	p.Tyr281Cys	p.Y281C	ENST00000300305		281	tAc/tGc	7/8	1	2	FACETS	0.82	0.75	0.892	0.82	0.75	0.892	CLONAL	1	TRUE	1	0.71399737408342	2		394	451	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691872	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs79375991	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	247	422	13	ENST00000295754.5:c.383del	p.Lys128SerfsTer35	p.K128Sfs*35	ENST00000295754	NM_003242.5	125	gAa/ga	3/7	1	2	FACETS	0.806	0.766	0.846	1	0.995	1	CLONAL	2	TRUE	1	0.71399737408342	2		435	429	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713184	30713184	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	25	361	0	ENST00000295754.5:c.509T>C	p.Ile170Thr	p.I170T	ENST00000295754	NM_003242.5	170	aTc/aCc	4/7	1	2	FACETS	0.195	0.153	0.243	0.195	0.153	0.243	SUBCLONAL	1	TRUE	1	0.71399737408342	2		361	359	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933680	49933680	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	315	894	0	ENST00000296474.3:c.2597C>A	p.Pro866His	p.P866H	ENST00000296474	NM_002447.2	866	cCc/cAc	10/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.71399737408342	2		894	864	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217556	142217557	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1268253442	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	128	414	1	ENST00000350721.4:c.5440dup	p.Arg1814LysfsTer8	p.R1814Kfs*8	ENST00000350721	NM_001184.3	1814	aga/aAga	32/47	1	2	FACETS	0.795	0.726	0.867	0.795	0.726	0.867	SUBCLONAL	1	TRUE	1	0.71399737408342	2		415	451	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374895	149374895	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1193595953	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	153	599	0	ENST00000360632.3:c.199A>G	p.Thr67Ala	p.T67A	ENST00000360632	NM_015472.4	67	Acc/Gcc	2/7	1	2	FACETS	0.791	0.728	0.856	0.791	0.728	0.856	SUBCLONAL	1	TRUE	1	0.71399737408342	2		599	542	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919194	178919194	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	91	231	0	ENST00000263967.3:c.685del	p.Thr229LeufsTer11	p.T229Lfs*11	ENST00000263967	NM_006218.2	227	Aaa/aa	4/21	1	2	FACETS	0.891	0.802	0.984	0.891	0.802	0.984	CLONAL	1	TRUE	1	0.71399737408342	2		231	286	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871287	35871287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149161098	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	103	319	0	ENST00000303115.3:c.509G>A	p.Arg170His	p.R170H	ENST00000303115	NM_002185.3	170	cGc/cAc	4/8	1	2	FACETS	0.782	0.706	0.861	0.782	0.706	0.861	SUBCLONAL	1	TRUE	1	0.71399737408342	2		319	369	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945763	38945763	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	69	263	0	ENST00000357387.3:c.4463G>T	p.Ser1488Ile	p.S1488I	ENST00000357387	NM_152756.3	1488	aGt/aTt	34/38	1	2	FACETS	0.773	0.682	0.869	0.773	0.682	0.869	SUBCLONAL	1	TRUE	1	0.71399737408342	2		263	250	SUCCESS
APC	324	MSKCC	GRCh37	5	112178033	112178033	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	117	423	0	ENST00000257430.4:c.6742A>T	p.Lys2248Ter	p.K2248*	ENST00000257430	NM_000038.5	2248	Aaa/Taa	16/16	1	2	FACETS	0.898	0.818	0.98	0.898	0.818	0.98	CLONAL	1	TRUE	1	0.71399737408342	2		423	365	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944976	131944976	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	71	168	0	ENST00000265335.6:c.2928del	p.Glu977LysfsTer7	p.E977Kfs*7	ENST00000265335		975	cAa/ca	19/25	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.71399737408342	2		168	198	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046754	180046754	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	205	814	0	ENST00000261937.6:c.2558A>G	p.Tyr853Cys	p.Y853C	ENST00000261937	NM_182925.4	853	tAc/tGc	18/30	1	2	FACETS	0.869	0.81	0.929	0.869	0.81	0.929	CLONAL	1	TRUE	1	0.71399737408342	2		814	661	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056961	180056961	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	201	861	0	ENST00000261937.6:c.658T>C	p.Phe220Leu	p.F220L	ENST00000261937	NM_182925.4	220	Ttc/Ctc	5/30	1	2	FACETS	0.795	0.74	0.852	0.795	0.74	0.852	SUBCLONAL	1	TRUE	1	0.71399737408342	2		861	708	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681463	30681463	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	145	438	0	ENST00000376406.3:c.549del	p.Lys183AsnfsTer9	p.K183Nfs*9	ENST00000376406	NM_014641.2	183	aaA/aa	4/15	1	2	FACETS	0.853	0.784	0.924	0.853	0.784	0.924	CLONAL	1	TRUE	1	0.71399737408342	2		438	476	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681120	117681120	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs748436511	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	139	385	2	ENST00000368508.3:c.3500del	p.Leu1167Ter	p.L1167*	ENST00000368508	NM_002944.2	1167	tTa/ta	23/43	1	2	FACETS	0.752	0.688	0.817	0.752	0.688	0.817	SUBCLONAL	1	TRUE	1	0.71399737408342	2		387	518	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161807896	161807896	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	134	361	0	ENST00000366898.1:c.1097G>T	p.Arg366Leu	p.R366L	ENST00000366898	NM_004562.2	366	cGg/cTg	10/12	1	2	FACETS	0.934	0.857	1	0.934	0.857	1	CLONAL	1	TRUE	1	0.71399737408342	2		361	402	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	179	406	2	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	0.71399737408342	3	FACETS	0.784	0.731	0.838	0.784	0.731	0.838	SUBCLONAL	2	TRUE	1	0.71399737408342	3		408	434	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	180	530	2	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	0.71399737408342	3	FACETS	0.846	0.781	0.913	0.423	0.39	0.457	CLONAL	1	TRUE	1	0.71399737408342	3		532	809	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514997	148514999	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	290	454	3	ENST00000320356.2:c.1210_1212del	p.Glu404del	p.E404del	ENST00000320356	NM_004456.4	404	GAG/-	10/20	0.71399737408342	3	FACETS	0.798	0.755	0.84	0.798	0.755	0.84	SUBCLONAL	2	TRUE	1	0.71399737408342	3		457	691	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	261	432	9	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	0.71399737408342	3	FACETS	0.819	0.773	0.864	0.819	0.773	0.864	CLONAL	2	TRUE	1	0.71399737408342	3		441	606	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750677	128750677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28933407	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	204	668	1	ENST00000377970.2:c.214C>T	p.Pro72Ser	p.P72S	ENST00000377970	NM_002467.4	72	Ccc/Tcc	2/3	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.71399737408342	2		669	552	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5064988	5064988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	108	335	0	ENST00000381652.3:c.1162G>A	p.Ala388Thr	p.A388T	ENST00000381652	NM_004972.3	388	Gca/Aca	9/25	1	2	FACETS	0.805	0.729	0.883	0.805	0.729	0.883	CLONAL	1	TRUE	1	0.71399737408342	2		335	376	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006062	22006062	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	195	683	1	ENST00000276925.6:c.341G>A	p.Arg114His	p.R114H	ENST00000276925	NM_004936.3	114	cGt/cAt	2/2	1	2	FACETS	0.935	0.871	1	0.935	0.871	1	CLONAL	1	TRUE	1	0.71399737408342	2		684	584	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434747	128434747	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	213	686	0	ENST00000265960.3:c.107T>C	p.Val36Ala	p.V36A	ENST00000265960	NM_001006617.1	36	gTt/gCt	2/12	1	2	FACETS	0.95	0.888	1	0.95	0.888	1	CLONAL	1	TRUE	1	0.71399737408342	2		686	628	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938488	44938488	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	175	516	0	ENST00000377967.4:c.3036G>C	p.Trp1012Cys	p.W1012C	ENST00000377967	NM_021140.2	1012	tgG/tgC	20/29	1	2	FACETS	0.98	0.91	1	0.98	0.91	1	CLONAL	1	TRUE	1	0.71399737408342	2		516	500	SUCCESS
AR	367	MSKCC	GRCh37	X	66765149	66765151	+	inframe_deletion	In_Frame_Del	DEL	TGC	TGC	-	rs752055010	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	20	400	0	ENST00000374690.3:c.170_172del	p.Leu57del	p.L57del	ENST00000374690	NM_000044.3	54	tTGCtg/ttg	1/8	1	2	FACETS	0.235	0.18	0.3	0.235	0.18	0.3	SUBCLONAL	1	TRUE	1	0.71399737408342	2		400	238	SUCCESS
AR	367	MSKCC	GRCh37	X	66766418	66766418	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	42	207	0	ENST00000374690.3:c.1430C>G	p.Ala477Gly	p.A477G	ENST00000374690	NM_000044.3	477	gCt/gGt	1/8	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.71399737408342	2		207	117	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343559	70343559	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	150	568	0	ENST00000374080.3:c.1733C>T	p.Ala578Val	p.A578V	ENST00000374080		578	gCt/gTt	12/45	1	2	FACETS	0.794	0.73	0.86	0.794	0.73	0.86	SUBCLONAL	1	TRUE	1	0.71399737408342	2		568	529	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357070	70357070	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773713291	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	270	873	0	ENST00000374080.3:c.5585G>A	p.Arg1862His	p.R1862H	ENST00000374080		1862	cGc/cAc	39/45	1	2	FACETS	0.977	0.921	1	0.977	0.921	1	CLONAL	1	TRUE	1	0.71399737408342	2		873	774	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448297	56448297	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	254	744	2	ENST00000407977.2:c.350del	p.Arg117ProfsTer41	p.R117Pfs*41	ENST00000407977		117	cGc/cc	3/10	1	2	FACETS	0.918	0.863	0.975	0.918	0.863	0.975	CLONAL	1	TRUE	1	0.71399737408342	2		746	775	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0045017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	47	316	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.851	0.725	0.986	0.851	0.725	0.986	CLONAL	1	TRUE	1	0.486726342971243	2		316	227	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879885	37879885	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	750	870	0	ENST00000269571.5:c.2180G>C	p.Gly727Ala	p.G727A	ENST00000269571		727	gGa/gCa	18/27	0.1848102180759	6	FACETS	0.956	0.927	0.985			1	CLONAL	8	FALSE	NA	0.1848102180759	6		870	1453	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0045147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	285	534	0	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	1	2	FACETS	1	0.969	1	1	0.997	1	CLONAL	4	FALSE	1	0.1848102180759	2		534	744	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0045147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	464	469	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.1848102180759	1	FACETS	1	0.979	1	1	0.998	1	CLONAL	7	FALSE	0	0.1848102180759	1		469	644	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244882	41244882	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	53	441	0	ENST00000357654.3:c.2666C>G	p.Ser889Cys	p.S889C	ENST00000357654	NM_007294.3	889	tCt/tGt	10/23	1	2	FACETS	0.79	0.672	0.919	0.79	0.672	0.919	CLONAL	1	FALSE	1	0.1848102180759	2		441	726	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0045147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	273	618	2	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	1	2	FACETS	1	0.95	1	1	0.996	1	CLONAL	4	FALSE	1	0.1848102180759	2		620	733	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061461	38061461	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	317	639	0	ENST00000250448.2:c.528C>G	p.Ile176Met	p.I176M	ENST00000250448	NM_004496.3	176	atC/atG	2/2	1	2	FACETS	1	0.967	1	1	0.997	1	CLONAL	4	FALSE	1	0.1848102180759	2		639	835	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202218	138202218	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0045147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	249	608	0	ENST00000237289.4:c.2135C>G	p.Ser712Ter	p.S712*	ENST00000237289	NM_001270507.1	712	tCa/tGa	9/9	1	2	FACETS	1	0.984	1	1	0.996	1	CLONAL	3	FALSE	1	0.1848102180759	2		608	791	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2493140	2493140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	280	610	0	ENST00000355716.4:c.580G>A	p.Ala194Thr	p.A194T	ENST00000355716	NM_003820.2	194	Gct/Act	6/8	1	2	FACETS	1	0.947	1	1	0.997	1	CLONAL	4	FALSE	1	0.1848102180759	2		610	755	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609528	81609528	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	62	432	0	ENST00000298171.2:c.1126G>C	p.Glu376Gln	p.E376Q	ENST00000298171	NM_000369.2	376	Gag/Cag	10/10	1	2	FACETS	0.99	0.854	1	0.99	0.854	1	CLONAL	1	FALSE	1	0.1848102180759	2		432	678	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845656	68845659	+	frameshift_variant	Frame_Shift_Del	DEL	CTTA	CTTA	-	novel	NA	P-0045147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	335	584	0	ENST00000261769.5:c.903_906del	p.Tyr302ProfsTer53	p.Y302Pfs*53	ENST00000261769	NM_004360.3	301	gCTTAc/gc	7/16	0.1848102180759	0	FACETS	0.886	0.849	0.922			1	CLONAL	6	FALSE	0	0.1848102180759	0		584	556	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244820	41244820	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397509004	NA	P-0045147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	49	435	0	ENST00000357654.3:c.2728C>G	p.Gln910Glu	p.Q910E	ENST00000357654	NM_007294.3	910	Caa/Gaa	10/23	1	2	FACETS	0.686	0.579	0.804	0.686	0.579	0.804	SUBCLONAL	1	FALSE	1	0.1848102180759	2		435	773	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245866	41245866	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	48	338	0	ENST00000357654.3:c.1682C>G	p.Ser561Cys	p.S561C	ENST00000357654	NM_007294.3	561	tCt/tGt	10/23	1	2	FACETS	0.803	0.678	0.941	0.803	0.678	0.941	CLONAL	1	FALSE	1	0.1848102180759	2		338	647	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046391	69046391	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	123	539	0	ENST00000288368.4:c.3864G>C	p.Gln1288His	p.Q1288H	ENST00000288368	NM_024870.2	1288	caG/caC	32/40	0.1848102180759	5	FACETS	0.837	0.755	0.923			1	CLONAL	2	FALSE	NA	0.1848102180759	5		539	1016	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220483	123220483	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	68	553	0	ENST00000218089.9:c.3140C>G	p.Ser1047Cys	p.S1047C	ENST00000218089	NM_001042749.1	1047	tCt/tGt	30/35	0.1848102180759	1	FACETS	0.863	0.75	0.986	0.863	0.75	0.986	CLONAL	1	FALSE	0	0.1848102180759	1		553	774	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0045543-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	57	499	0				ENST00000310581	NM_198253.2	-/1132			0.464255239379958	3	FACETS	0.789	0.682	0.903	0.263	0.227	0.301	CLONAL	1	TRUE	0	0.692390943117975	3		499	281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0045543-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	158	670	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.220725509823481	4	FACETS	1	0.989	1	0.736	0.678	0.795	INDETERMINATE	1	TRUE	2	0.692390943117975	4		670	525	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0045543-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	245	721	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.220725509823481	4	FACETS	1	0.967	1	1	0.967	1	INDETERMINATE	2	TRUE	2	0.692390943117975	4		721	577	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941653	48941653	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0045543-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	61	226	0	ENST00000267163.4:c.963C>G	p.Tyr321Ter	p.Y321*	ENST00000267163	NM_000321.2	321	taC/taG	10/27	NA	2	FACETS	0.864	0.78	0.945			1	INDETERMINATE	2	TRUE	NA	0.692390943117975	2		226	102	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs121913468	NA	P-0045543-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	329	537	0	ENST00000269571.5:c.2305G>C	p.Asp769His	p.D769H	ENST00000269571		769	Gac/Cac	19/27	0.692390943117975	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	1	0.692390943117975	3		537	526	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910587	29910587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41549014	NA	P-0045543-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	392	959	0	ENST00000376809.5:c.127G>A	p.Glu43Lys	p.E43K	ENST00000376809	NM_002116.7	43	Gag/Aag	2/8	0.264956447398486	2	FACETS	0.808	0.775	0.84	0.808	0.775	0.84	INDETERMINATE	2	TRUE	0	0.692390943117975	2		959	701	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105892	27105892	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045543-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	811	760	0	ENST00000324856.7:c.5503C>T	p.Gln1835Ter	p.Q1835*	ENST00000324856	NM_006015.4	1835	Cag/Tag	20/20	0.692390943117975	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.692390943117975	3		760	965	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10277291	10277291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257025095	NA	P-0045543-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	96	696	0	ENST00000340748.4:c.826G>A	p.Glu276Lys	p.E276K	ENST00000340748		276	Gaa/Aaa	10/40	1	2	FACETS	0.541	0.483	0.601	0.541	0.483	0.601	SUBCLONAL	1	TRUE	1	0.692390943117975	2		696	513	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264627	11264627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045543-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	320	634	0	ENST00000361445.4:c.3935C>T	p.Pro1312Leu	p.P1312L	ENST00000361445	NM_004958.3	1312	cCg/cTg	26/58	0.692390943117975	3	FACETS	1	0.98	1	0.698	0.667	0.73	CLONAL	2	TRUE	0	0.692390943117975	3		634	594	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623894	28623894	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045543-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	108	495	0	ENST00000241453.7:c.760C>G	p.Gln254Glu	p.Q254E	ENST00000241453	NM_004119.2	254	Cag/Gag	7/24	NA	2	FACETS	0.969	0.88	1			1	INDETERMINATE	1	TRUE	NA	0.692390943117975	2		495	322	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671985	30671985	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045543-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	201	812	0	ENST00000376406.3:c.4975G>A	p.Asp1659Asn	p.D1659N	ENST00000376406	NM_014641.2	1659	Gat/Aat	10/15	0.534025268305777	3	FACETS	1	0.989	1	0.657	0.612	0.702	CLONAL	1	TRUE	1	0.692390943117975	3		812	595	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139804433	139804433	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1250915147	NA	P-0045543-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	319	565	0	ENST00000247668.2:c.590T>A	p.Ile197Asn	p.I197N	ENST00000247668	NM_021138.3	197	aTc/aAc	6/11	0.290760373834477	5	FACETS	1	0.992	1	0.809	0.768	0.851	INDETERMINATE	2	TRUE	2	0.692390943117975	5		565	774	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139804439	139804439	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045543-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	303	562	0	ENST00000247668.2:c.596G>C	p.Arg199Pro	p.R199P	ENST00000247668	NM_021138.3	199	cGg/cCg	6/11	0.290760373834477	5	FACETS	1	0.99	1	0.792	0.75	0.834	INDETERMINATE	2	TRUE	2	0.692390943117975	5		562	751	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091372	193091388	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGAAGGAGATTGTGG	GAAGAAGGAGATTGTGG	-	novel	NA	P-0045543-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	68	604	0	ENST00000367435.3:c.42_58del	p.Gln14HisfsTer46	p.Q14Hfs*46	ENST00000367435	NM_024529.4	14	caGAAGAAGGAGATTGTGGtg/catg	1/17	0.627388153290805	3	FACETS	0.325	0.282	0.372	0.108	0.094	0.124	SUBCLONAL	1	TRUE	0	0.692390943117975	3		604	813	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917776	29917776	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045543-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	54	589	0	ENST00000389048.3:c.892G>C	p.Ala298Pro	p.A298P	ENST00000389048	NM_004304.4	298	Gcc/Ccc	3/29	0.324248903241816	3	FACETS	0.397	0.339	0.46	0.132	0.113	0.154	INDETERMINATE	1	TRUE	0	0.692390943117975	3		589	529	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014103	70014103	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs756384799	NA	P-0045543-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	71	651	0	ENST00000394351.3:c.964G>C	p.Glu322Gln	p.E322Q	ENST00000394351	NM_000248.3	322	Gag/Cag	9/9	0.397481767482347	1	FACETS	0.324	0.284	0.367	0.324	0.284	0.367	INDETERMINATE	1	TRUE	0	0.692390943117975	1		651	414	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500854	149500854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045543-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	57	627	0	ENST00000261799.4:c.2376C>G	p.Ile792Met	p.I792M	ENST00000261799	NM_002609.3	792	atC/atG	17/23	1	2	FACETS	0.339	0.291	0.392	0.339	0.291	0.392	SUBCLONAL	1	TRUE	1	0.692390943117975	2		627	485	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0045543-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	166	499	0				ENST00000310581	NM_198253.2	-/1132			0.449400408690296	3	FACETS	1	0.987	1	0.655	0.608	0.703	INDETERMINATE	1	TRUE	1	0.830256008662969	3		499	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0045543-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	271	670	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.451505968367443	1	FACETS	0.784	0.746	0.822	0.784	0.746	0.822	INDETERMINATE	1	TRUE	0	0.830256008662969	1		670	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0045543-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	178	721	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.451505968367443	1	FACETS	0.428	0.396	0.46	0.428	0.396	0.46	INDETERMINATE	1	TRUE	0	0.830256008662969	1		721	586	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941653	48941653	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0045543-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	101	226	0	ENST00000267163.4:c.963C>G	p.Tyr321Ter	p.Y321*	ENST00000267163	NM_000321.2	321	taC/taG	10/27	0.810337800685938	2	FACETS	0.882	0.826	0.934	0.882	0.826	0.934	CLONAL	2	TRUE	0	0.830256008662969	2		226	138	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs121913468	NA	P-0045543-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	355	537	0	ENST00000269571.5:c.2305G>C	p.Asp769His	p.D769H	ENST00000269571		769	Gac/Cac	19/27	0.830256008662969	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.830256008662969	1		537	399	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910587	29910587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41549014	NA	P-0045543-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	822	959	0	ENST00000376809.5:c.127G>A	p.Glu43Lys	p.E43K	ENST00000376809	NM_002116.7	43	Gag/Aag	2/8	0.824324652989031	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.830256008662969	2		959	941	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105892	27105892	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045543-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	758	760	0	ENST00000324856.7:c.5503C>T	p.Gln1835Ter	p.Q1835*	ENST00000324856	NM_006015.4	1835	Cag/Tag	20/20	0.830256008662969	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.830256008662969	2		760	856	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10277291	10277291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257025095	NA	P-0045543-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	172	696	0	ENST00000340748.4:c.826G>A	p.Glu276Lys	p.E276K	ENST00000340748		276	Gaa/Aaa	10/40	0.540613772209868	1	FACETS	0.471	0.437	0.507	0.471	0.437	0.507	SUBCLONAL	1	TRUE	0	0.830256008662969	1		696	514	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264627	11264627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045543-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	424	634	0	ENST00000361445.4:c.3935C>T	p.Pro1312Leu	p.P1312L	ENST00000361445	NM_004958.3	1312	cCg/cTg	26/58	0.830256008662969	2	FACETS	0.808	0.781	0.835	0.808	0.781	0.835	CLONAL	2	TRUE	0	0.830256008662969	2		634	632	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623894	28623894	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045543-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	176	495	0	ENST00000241453.7:c.760C>G	p.Gln254Glu	p.Q254E	ENST00000241453	NM_004119.2	254	Cag/Gag	7/24	0.830256008662969	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.830256008662969	1		495	236	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671985	30671985	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045543-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	158	812	0	ENST00000376406.3:c.4975G>A	p.Asp1659Asn	p.D1659N	ENST00000376406	NM_014641.2	1659	Gat/Aat	10/15	0.797891861639606	2	FACETS	0.685	0.631	0.74	0.342	0.315	0.37	SUBCLONAL	1	TRUE	0	0.830256008662969	2		812	556	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139804433	139804433	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1250915147	NA	P-0045543-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	155	565	0	ENST00000247668.2:c.590T>A	p.Ile197Asn	p.I197N	ENST00000247668	NM_021138.3	197	aTc/aAc	6/11	0.488491617183411	2	FACETS	0.509	0.467	0.554	0.255	0.233	0.277	INDETERMINATE	1	TRUE	0	0.830256008662969	2		565	733	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139804439	139804439	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045543-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	148	562	0	ENST00000247668.2:c.596G>C	p.Arg199Pro	p.R199P	ENST00000247668	NM_021138.3	199	cGg/cCg	6/11	0.488491617183411	2	FACETS	0.485	0.444	0.528	0.243	0.222	0.264	INDETERMINATE	1	TRUE	0	0.830256008662969	2		562	735	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014103	70014103	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs756384799	NA	P-0045543-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	116	651	0	ENST00000394351.3:c.964G>C	p.Glu322Gln	p.E322Q	ENST00000394351	NM_000248.3	322	Gag/Cag	9/9	0.502839474304612	1	FACETS	0.343	0.311	0.377	0.343	0.311	0.377	SUBCLONAL	1	TRUE	0	0.830256008662969	1		651	476	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273273	55273273	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs768074018	NA	P-0045543-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	47	610	0	ENST00000275493.2:c.3596G>C	p.Arg1199Thr	p.R1199T	ENST00000275493	NM_005228.3	1199	aGg/aCg	28/28	0.557398496700332	1	FACETS	0.135	0.114	0.159	0.135	0.114	0.159	SUBCLONAL	1	TRUE	0	0.830256008662969	1		610	489	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135286	30135286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1179272987	NA	P-0045543-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	58	525	0	ENST00000331968.5:c.532G>A	p.Glu178Lys	p.E178K	ENST00000331968	NM_002742.2	178	Gaa/Aaa	3/18	0.408600411325613	1	FACETS	0.248	0.214	0.285	0.248	0.214	0.285	INDETERMINATE	1	TRUE	0	0.830256008662969	1		525	329	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70353052	70353052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045543-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	38	280	0	ENST00000374080.3:c.4607G>A	p.Arg1536Gln	p.R1536Q	ENST00000374080		1536	cGg/cAg	33/45	0.830256008662969	0	FACETS		NA	1			1	NA	1	TRUE	NA	0.830256008662969	0		280	182	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528627	89528627	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0045543-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	116	485	1	ENST00000336596.2:c.2927C>G	p.Ser976Ter	p.S976*	ENST00000336596	NM_005233.5	976	tCa/tGa	17/17	1	2	FACETS	0.457	0.412	0.503	0.457	0.412	0.503	SUBCLONAL	1	TRUE	1	0.830256008662969	2		486	612	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15280981	15280982	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AG	novel	NA	P-0045543-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	67	736	1	ENST00000263388.2:c.5115-1_5115delinsCT		p.X1705_splice	ENST00000263388	NM_000435.2	1705		28/33	0.41779396204016	5	FACETS	0.4	0.346	0.458			1	INDETERMINATE	1	TRUE	NA	0.830256008662969	5		737	906	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177480	56177480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045543-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	42	583	0	ENST00000399503.3:c.2453G>A	p.Arg818Lys	p.R818K	ENST00000399503	NM_005921.1	818	aGg/aAg	14/20	0.449400408690296	3	FACETS	0.354	0.296	0.419	0.177	0.148	0.21	INDETERMINATE	1	TRUE	1	0.830256008662969	3		583	404	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144002	11144002	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	140	410	0	ENST00000358026.2:c.3583C>A	p.Gln1195Lys	p.Q1195K	ENST00000358026	NM_001128849.1	1195	Cag/Aag	26/36	0.596791347283836	1	FACETS	0.917	0.846	0.989	0.917	0.846	0.989	CLONAL	1	TRUE	0	0.596791347283836	1		410	359	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442041	52442110	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGTTCAGGAGCACGCTCAGCAAGGCATGAGTTGCACAAGAGTTGGGTATCAGCTGTGAAACCAAGAATA	CAGTTCAGGAGCACGCTCAGCAAGGCATGAGTTGCACAAGAGTTGGGTATCAGCTGTGAAACCAAGAATA	-	novel	NA	P-0045658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	75	349	0	ENST00000460680.1:c.256-17_308del		p.X86_splice	ENST00000460680	NM_004656.3	86		5/17	0.409596845677312	1	FACETS	0.487	0.429	0.548	0.487	0.429	0.548	SUBCLONAL	1	TRUE	0	0.596791347283836	1		349	362	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593613	55593613	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913521	NA	P-0045969-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	117	406	0	ENST00000288135.5:c.1679T>A	p.Val560Asp	p.V560D	ENST00000288135	NM_000222.2	560	gTt/gAt	11/21	1	2	FACETS	0.892	0.816	0.971	1	0.992	1	CLONAL	4	TRUE	1	0.208151193202518	2		406	315	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0046156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	91	499	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.610407560426644	2		499	287	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610123	28610123	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	37	623	0	ENST00000241453.7:c.1367G>A	p.Gly456Glu	p.G456E	ENST00000241453	NM_004119.2	456	gGa/gAa	11/24	1	2	FACETS	0.219	0.18	0.263	0.219	0.18	0.263	SUBCLONAL	1	TRUE	1	0.610407560426644	2		623	553	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158201	47158202	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CA	CA	-	novel	NA	P-0046156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	135	438	0	ENST00000409792.3:c.4497_4498del	p.Cys1499Ter	p.C1499*	ENST00000409792	NM_014159.6	1499	tgTGag/tgag	4/21	1	2	FACETS	0.943	0.863	1	0.943	0.863	1	CLONAL	1	TRUE	1	0.610407560426644	2		438	469	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683511	182683512	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	163	455	0	ENST00000292782.4:c.33dup	p.Val12SerfsTer11	p.V12Sfs*11	ENST00000292782	NM_020640.2	11	-/A	2/7	1	2	FACETS	0.939	0.866	1	0.939	0.866	1	CLONAL	1	TRUE	1	0.610407560426644	2		455	569	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609759	28609759	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046156-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	37	588	0	ENST00000241453.7:c.1470del	p.Val491CysfsTer11	p.V491Cfs*11	ENST00000241453	NM_004119.2	490	aaA/aa	12/24	1	2	FACETS	0.192	0.158	0.231	0.192	0.158	0.231	SUBCLONAL	1	TRUE	1	0.610407560426644	2		588	631	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046400-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	30	475	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.581	0.466	0.713	0.581	0.466	0.713	SUBCLONAL	1	TRUE	1	0.12	2		475	860	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0046400-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	44	356	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.98	0.82	1	0.98	0.82	1	CLONAL	1	TRUE	1	0.12	2		356	748	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562482	21562483	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGGCG	rs550642106	NA	P-0047083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	16	142	7	ENST00000382592.4:c.1431_1436dup	p.Pro479_Ala480dup	p.P479_A480dup	ENST00000382592	NM_014572.2	479	ccg/ccCGCCCCg	4/8	1	2	FACETS	0.736	0.561	0.93	0.736	0.561	0.93	CLONAL	1	TRUE	1	0.737018746124461	2		149	59	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692790	89692790	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554898067	NA	P-0047083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	94	305	1	ENST00000371953.3:c.274G>T	p.Asp92Tyr	p.D92Y	ENST00000371953	NM_000314.4	92	Gac/Tac	5/9	0.737018746124461	2	FACETS	0.924	0.859	0.986	0.924	0.859	0.986	CLONAL	2	TRUE	0	0.737018746124461	2		306	138	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844151	68844151	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	78	634	0	ENST00000261769.5:c.739G>T	p.Glu247Ter	p.E247*	ENST00000261769	NM_004360.3	247	Gag/Tag	6/16	0.737018746124461	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.737018746124461	1		634	106	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004549	16004660	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGAACGAGCCTCACCTCTGCCTCTCTGGCTCTCCATCCACATCCTCATCAGCGCTGCACGTGGCACTGGAATCATTGTCTGACTGGGGCTCGGGCCTTTGGGCATTTATTT	TGGAACGAGCCTCACCTCTGCCTCTCTGGCTCTCCATCCACATCCTCATCAGCGCTGCACGTGGCACTGGAATCATTGTCTGACTGGGGCTCGGGCCTTTGGGCATTTATTT	-	novel	NA	P-0047083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	61	371	0	ENST00000268712.3:c.2594_2690+15del		p.X865_splice	ENST00000268712	NM_006311.3	865		20/46	0.653803278462458	1	FACETS	0.942	0.846	1	0.942	0.846	1	CLONAL	1	TRUE	0	0.737018746124461	1		371	111	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189385	56189386	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	122	536	0	ENST00000399503.3:c.4418dup	p.Ser1475PhefsTer48	p.S1475Ffs*48	ENST00000399503	NM_005921.1	1473	atc/aTtc	20/20	0.605318609929165	3	FACETS	0.899	0.847	0.948	0.899	0.847	0.948	CLONAL	3	TRUE	0	0.737018746124461	3		536	168	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	100	475	0				ENST00000310581	NM_198253.2	-/1132			0.706900380261643	3	FACETS	0.992	0.91	1	0.992	0.91	1	CLONAL	2	TRUE	1	0.706900380261643	3		475	193	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0047119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	279	473	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.706900380261643	3	FACETS	0.945	0.898	0.993	0.945	0.898	0.993	CLONAL	2	TRUE	1	0.706900380261643	3		473	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578520	7578520	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	574	878	2	ENST00000269305.4:c.410T>A	p.Leu137Gln	p.L137Q	ENST00000269305	NM_001126112.2	137	cTg/cAg	5/11	0.688771177681861	2	FACETS	0.952	0.924	0.979	0.952	0.924	0.979	CLONAL	2	TRUE	0	0.706900380261643	2		880	853	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796754	135796754	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203434	NA	P-0047119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	176	303	0	ENST00000298552.3:c.733C>T	p.Arg245Ter	p.R245*	ENST00000298552	NM_001162426.1	245	Cga/Tga	8/23	0.706900380261643	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.706900380261643	2		303	247	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56857716	56857716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370111038	NA	P-0047119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	306	499	2	ENST00000308159.5:c.752G>A	p.Arg251His	p.R251H	ENST00000308159	NM_014669.4	251	cGc/cAc	8/22	0.5121978221914	4	FACETS	0.842	0.796	0.888	0.842	0.796	0.888	CLONAL	2	TRUE	2	0.706900380261643	4		501	878	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40460301	40460301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266628382	NA	P-0047119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	348	696	4	ENST00000345506.4:c.2012C>T	p.Pro671Leu	p.P671L	ENST00000345506	NM_003152.3	671	cCt/cTt	17/20	0.381544251814195	4	FACETS	0.898	0.853	0.943	0.898	0.853	0.943	INDETERMINATE	2	TRUE	2	0.706900380261643	4		700	936	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546903	9546903	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0047119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	544	524	0	ENST00000353224.5:c.1119C>G	p.Tyr373Ter	p.Y373*	ENST00000353224	NM_177990.2	373	taC/taG	5/10	0.706900380261643	4	FACETS	0.839	0.809	0.869	1	0.996	1	CLONAL	3	TRUE	2	0.706900380261643	4		524	1044	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0047148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	68	273	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.936	0.822	1	0.936	0.822	1	CLONAL	1	TRUE	1	0.480939674538986	2		273	302	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275687	41275687	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756737848	NA	P-0047148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	123	441	0	ENST00000349496.5:c.1582C>T	p.Arg528Cys	p.R528C	ENST00000349496	NM_001904.3	528	Cgt/Tgt	10/15	1	2	FACETS	0.951	0.864	1	0.951	0.864	1	CLONAL	1	TRUE	1	0.480939674538986	2		441	538	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0047572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	138	300	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.632597050882663	2		300	415	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720649	89720649	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs587782455	NA	P-0047572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	95	332	1	ENST00000371953.3:c.802-2A>T		p.X268_splice	ENST00000371953	NM_000314.4	268			1	2	FACETS	0.758	0.68	0.841	0.758	0.68	0.841	SUBCLONAL	1	TRUE	1	0.632597050882663	2		333	396	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730802	40730802	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747513450	NA	P-0047572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	362	604	3	ENST00000373198.4:c.3733G>A	p.Gly1245Arg	p.G1245R	ENST00000373198	NM_133170.3	1245	Gga/Aga	27/32	0.62341006514487	3	FACETS	0.937	0.894	0.98	0.937	0.894	0.98	CLONAL	2	TRUE	1	0.632597050882663	3		607	804	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	rs786202799	NA	P-0047572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	356	706	0	ENST00000269305.4:c.376-2A>T		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.632597050882663	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.632597050882663	1		706	674	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624252	89624252	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	82	214	0	ENST00000371953.3:c.27del	p.Ser10AlafsTer14	p.S10Afs*14	ENST00000371953	NM_000314.4	9	gTt/gt	1/9	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.632597050882663	2		214	257	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368277	45368277	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	20	308	0	ENST00000262160.6:c.1325del	p.Leu442ArgfsTer12	p.L442Rfs*12	ENST00000262160	NM_005901.5	442	cTg/cg	11/11	0.632597050882663	1	FACETS	0.162	0.124	0.207	0.162	0.124	0.207	SUBCLONAL	1	TRUE	0	0.632597050882663	1		308	267	SUCCESS
APC	324	MSKCC	GRCh37	5	112174093	112174097	+	frameshift_variant	Frame_Shift_Del	DEL	TTACA	TTACA	-	novel	NA	P-0047572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	86	258	0	ENST00000257430.4:c.2802_2806del	p.Tyr935PhefsTer3	p.Y935Ffs*3	ENST00000257430	NM_000038.5	934	acTTACAat/acat	16/16	1	2	FACETS	0.944	0.845	1	0.944	0.845	1	CLONAL	1	TRUE	1	0.632597050882663	2		258	288	SUCCESS
APC	324	MSKCC	GRCh37	5	112175933	112175936	+	frameshift_variant	Frame_Shift_Del	DEL	AACC	AACC	-	novel	NA	P-0047572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	54	173	0	ENST00000257430.4:c.4644_4647del	p.Asn1548LysfsTer16	p.N1548Kfs*16	ENST00000257430	NM_000038.5	1548	AACCaa/aa	16/16	1	2	FACETS	0.908	0.788	1	0.908	0.788	1	CLONAL	1	TRUE	1	0.632597050882663	2		173	188	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197350	27197351	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0047572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	126	376	0	ENST00000380036.4:c.1662_1663insG	p.Ser555GlufsTer19	p.S555Efs*19	ENST00000380036	NM_000459.3	554	-/G	12/23	1	2	FACETS	0.76	0.692	0.832	0.76	0.692	0.832	SUBCLONAL	1	TRUE	1	0.632597050882663	2		376	524	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0047971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	76	665	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.746	0.653	0.845	0.746	0.653	0.845	SUBCLONAL	1	TRUE	1	0.27	2		665	755	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087961	27087961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	66	349	0	ENST00000324856.7:c.2248C>T	p.Arg750Ter	p.R750*	ENST00000324856	NM_006015.4	750	Cga/Tga	6/20	0.3	1	FACETS	0.763	0.663	0.872	0.763	0.663	0.872	SUBCLONAL	1	TRUE	0	0.27	1		349	554	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709505	176709505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	42	194	0	ENST00000439151.2:c.5932G>A	p.Glu1978Lys	p.E1978K	ENST00000439151	NM_022455.4	1978	Gaa/Aaa	19/23	1	2	FACETS	0.972	0.815	1	0.972	0.815	1	CLONAL	1	TRUE	1	0.27	2		194	320	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	37	235	0	ENST00000335508.6:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000335508	NM_012433.2	902	Gaa/Aaa	18/25	1	2	FACETS	0.867	0.717	1	0.867	0.717	1	CLONAL	1	TRUE	1	0.27	2		235	316	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0047971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	70	520	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.995	0.869	1	0.995	0.869	1	CLONAL	1	TRUE	1	0.27	2		520	521	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397678	139397678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778830490	NA	P-0047971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	112	623	0	ENST00000277541.6:c.5123C>T	p.Ser1708Leu	p.S1708L	ENST00000277541	NM_017617.3	1708	tCg/tTg	27/34	0.3	1	FACETS	0.838	0.753	0.928	0.838	0.753	0.928	CLONAL	1	TRUE	0	0.27	1		623	856	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878356	151878356	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	116	405	0	ENST00000262189.6:c.6589C>T	p.Gln2197Ter	p.Q2197*	ENST00000262189	NM_170606.2	2197	Cag/Tag	36/59	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.27	2		405	588	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271357	26271357	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	79	433	0	ENST00000305910.3:c.256C>T	p.Gln86Ter	p.Q86*	ENST00000305910	NM_003534.2	86	Cag/Tag	1/1	0.158763859396261	2	FACETS	0.955	0.84	1	0.477	0.42	0.539	INDETERMINATE	1	TRUE	0	0.27	2		433	613	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73334705	73334705	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	22	153	0	ENST00000377767.4:c.2755C>A	p.Gln919Lys	p.Q919K	ENST00000377767	NM_014953.3	919	Caa/Aaa	20/21	1	2	FACETS	0.595	0.462	0.749	0.595	0.462	0.749	SUBCLONAL	1	TRUE	1	0.27	2		153	274	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856044	68856044	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	101	380	0	ENST00000261769.5:c.1852G>C	p.Asp618His	p.D618H	ENST00000261769	NM_004360.3	618	Gac/Cac	12/16	0.158763859396261	2	FACETS	1	0.972	1	0.624	0.559	0.694	INDETERMINATE	1	TRUE	0	0.27	2		380	599	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833955	44833956	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0047971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	77	197	0	ENST00000377967.4:c.381dup	p.Lys128GlufsTer17	p.K128Efs*17	ENST00000377967	NM_021140.2	127	tgg/tGgg	4/29	0.262593018099753	2	FACETS	0.98	0.87	1			1	CLONAL	2	TRUE	NA	0.27	2		197	291	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578275	+	stop_gained	Nonsense_Mutation	ONP	TGCTG	TGCTG	CGCTA	novel	NA	P-0047971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	56	471	0	ENST00000269305.4:c.574_578delinsTAGCG	p.Gln192_His193delinsTer	p.Q192_H193delins*	ENST00000269305	NM_001126112.2	192	CAGCAt/TAGCGt	6/11	1	2	FACETS	0.689	0.59	0.797	0.689	0.59	0.797	SUBCLONAL	1	TRUE	1	0.27	2		471	602	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013719	170013719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388201066	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	17	275	0	ENST00000295797.4:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000295797	NM_002740.5	480	Cgc/Tgc	15/18	1	2	FACETS	0.231	0.172	0.303	0.231	0.172	0.303	SUBCLONAL	1	TRUE	1	0.34	2		275	432	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181425	185181425	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1435276633	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	118	497	0	ENST00000265026.3:c.1366C>T	p.Arg456Ter	p.R456*	ENST00000265026	NM_004721.4	456	Cga/Tga	8/14	1	2	FACETS	0.934	0.843	1	0.934	0.843	1	CLONAL	1	TRUE	1	0.34	2		497	743	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	340	541	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.839	0.794	0.885	1	0.995	1	CLONAL	2	TRUE	1	0.34	2		541	1192	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004242	29004242	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766441216	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	148	592	0	ENST00000282397.4:c.1051C>T	p.Arg351Trp	p.R351W	ENST00000282397	NM_002019.4	351	Cgg/Tgg	8/30	1	2	FACETS	0.998	0.912	1	0.998	0.912	1	CLONAL	1	TRUE	1	0.34	2		592	872	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672759	86672759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	117	584	1	ENST00000274376.6:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000274376	NM_002890.2	749	cGa/cAa	17/25	1	2	FACETS	0.883	0.797	0.975	0.883	0.797	0.975	CLONAL	1	TRUE	1	0.34	2		585	779	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1720642	1720642	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367544631	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	188	733	0	ENST00000378609.4:c.766C>T	p.Arg256Cys	p.R256C	ENST00000378609	NM_002074.3	256	Cgt/Tgt	10/12	1	2	FACETS	0.917	0.846	0.991	0.917	0.846	0.991	CLONAL	1	TRUE	1	0.34	2		733	1206	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073530	8073530	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs535836763	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	169	740	0	ENST00000377482.5:c.1129C>T	p.Pro377Ser	p.P377S	ENST00000377482	NM_018948.3	377	Cct/Tct	4/4	1	2	FACETS	0.906	0.832	0.984	0.906	0.832	0.984	CLONAL	1	TRUE	1	0.34	2		740	1097	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11269467	11269467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	170	649	0	ENST00000361445.4:c.3703C>T	p.Arg1235Trp	p.R1235W	ENST00000361445	NM_004958.3	1235	Cgg/Tgg	25/58	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.34	2		649	948	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272943	11272943	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	164	588	0	ENST00000361445.4:c.3308T>A	p.Phe1103Tyr	p.F1103Y	ENST00000361445	NM_004958.3	1103	tTt/tAt	22/58	1	2	FACETS	0.998	0.915	1	0.998	0.915	1	CLONAL	1	TRUE	1	0.34	2		588	967	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254623	16254623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749814808	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	146	618	0	ENST00000375759.3:c.1888C>T	p.Arg630Cys	p.R630C	ENST00000375759	NM_015001.2	630	Cgt/Tgt	11/15	1	2	FACETS	0.9	0.821	0.983	0.9	0.821	0.983	CLONAL	1	TRUE	1	0.34	2		618	954	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094336	27094336	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	95	745	0	ENST00000324856.7:c.3044G>T	p.Gly1015Val	p.G1015V	ENST00000324856	NM_006015.4	1015	gGt/gTt	11/20	1	2	FACETS	0.495	0.439	0.555	0.495	0.439	0.555	SUBCLONAL	1	TRUE	1	0.34	2		745	1129	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101309	27101309	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1268	105	923	0	ENST00000324856.7:c.4591G>T	p.Glu1531Ter	p.E1531*	ENST00000324856	NM_006015.4	1531	Gaa/Taa	18/20	1	2	FACETS	0.45	0.401	0.502	0.45	0.401	0.502	SUBCLONAL	1	TRUE	1	0.34	2		923	1373	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106582	27106582	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1359226978	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	256	943	1	ENST00000324856.7:c.6193G>A	p.Ala2065Thr	p.A2065T	ENST00000324856	NM_006015.4	2065	Gcc/Acc	20/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.34	2		944	1464	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932167	36932167	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	239	919	0	ENST00000361632.4:c.2302C>A	p.Leu768Ile	p.L768I	ENST00000361632		768	Ctc/Atc	16/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.34	2		919	1375	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305238	39305238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs890472037	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	155	707	0	ENST00000373001.3:c.1187G>A	p.Arg396Gln	p.R396Q	ENST00000373001	NM_022157.3	396	cGa/cAa	7/7	1	2	FACETS	0.895	0.818	0.975	0.895	0.818	0.975	CLONAL	1	TRUE	1	0.34	2		707	1019	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804269	43804269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766638870	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	90	813	0	ENST00000372470.3:c.269G>A	p.Arg90Gln	p.R90Q	ENST00000372470	NM_005373.2	90	cGa/cAa	3/12	1	2	FACETS	0.429	0.379	0.482	0.429	0.379	0.482	SUBCLONAL	1	TRUE	1	0.34	2		813	1235	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795032	45795032	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768671057	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	188	792	0	ENST00000450313.1:c.1596C>A	p.Phe532Leu	p.F532L	ENST00000450313	NM_012222.2	532	ttC/ttA	16/16	1	2	FACETS	0.885	0.816	0.958	0.885	0.816	0.958	CLONAL	1	TRUE	1	0.34	2		792	1249	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521529	46521529	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	155	503	0	ENST00000262741.5:c.879A>C	p.Lys293Asn	p.K293N	ENST00000262741	NM_003629.3	293	aaA/aaC	7/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.34	2		503	776	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521540	46521540	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	132	480	0	ENST00000262741.5:c.868G>T	p.Glu290Ter	p.E290*	ENST00000262741	NM_003629.3	290	Gaa/Taa	7/10	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.34	2		480	762	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726593	46726593	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	202	884	0	ENST00000371975.4:c.672G>T	p.Lys224Asn	p.K224N	ENST00000371975	NM_003579.3	224	aaG/aaT	7/18	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.34	2		884	1166	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439638	51439638	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750990884	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	181	666	1	ENST00000262662.1:c.203G>A	p.Arg68Gln	p.R68Q	ENST00000262662		68	cGa/cAa	4/4	1	2	FACETS	0.965	0.889	1	0.965	0.889	1	CLONAL	1	TRUE	1	0.34	2		667	1103	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301128	65301128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1198988820	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	88	598	1	ENST00000342505.4:c.3320C>T	p.Thr1107Met	p.T1107M	ENST00000342505	NM_002227.2	1107	aCg/aTg	24/25	1	2	FACETS	0.551	0.487	0.62	0.551	0.487	0.62	SUBCLONAL	1	TRUE	1	0.34	2		599	939	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309886	65309886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	157	631	0	ENST00000342505.4:c.2264G>A	p.Arg755Gln	p.R755Q	ENST00000342505	NM_002227.2	755	cGa/cAa	17/25	1	2	FACETS	0.999	0.915	1	0.999	0.915	1	CLONAL	1	TRUE	1	0.34	2		631	924	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414985	78414985	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	88	528	0	ENST00000370768.2:c.1781G>C	p.Gly594Ala	p.G594A	ENST00000370768	NM_003902.3	594	gGt/gCt	19/20	1	2	FACETS	0.692	0.613	0.777	0.692	0.613	0.777	SUBCLONAL	1	TRUE	1	0.34	2		528	748	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736388	85736388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs949558985	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	133	677	0	ENST00000370580.1:c.259C>T	p.Arg87Trp	p.R87W	ENST00000370580	NM_003921.4	87	Cgg/Tgg	2/3	1	2	FACETS	0.907	0.823	0.994	0.907	0.823	0.994	CLONAL	1	TRUE	1	0.34	2		677	863	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165875	118165875	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	176	795	0	ENST00000369448.3:c.385A>C	p.Ile129Leu	p.I129L	ENST00000369448	NM_017709.3	129	Atc/Ctc	2/2	1	2	FACETS	0.887	0.816	0.962	0.887	0.816	0.962	CLONAL	1	TRUE	1	0.34	2		795	1167	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458147	120458147	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1325403451	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	232	916	1	ENST00000256646.2:c.7198C>T	p.Arg2400Ter	p.R2400*	ENST00000256646	NM_024408.3	2400	Cga/Tga	34/34	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.34	2		917	1292	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461167	120461167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs983208690	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	121	604	0	ENST00000256646.2:c.5791C>T	p.Arg1931Cys	p.R1931C	ENST00000256646	NM_024408.3	1931	Cgc/Tgc	32/34	1	2	FACETS	0.827	0.746	0.911	0.827	0.746	0.911	CLONAL	1	TRUE	1	0.34	2		604	861	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483310	120483310	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	84	739	0	ENST00000256646.2:c.3051C>A	p.Phe1017Leu	p.F1017L	ENST00000256646	NM_024408.3	1017	ttC/ttA	19/34	1	2	FACETS	0.427	0.376	0.482	0.427	0.376	0.482	SUBCLONAL	1	TRUE	1	0.34	2		739	1157	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510825	120510825	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	76	677	0	ENST00000256646.2:c.1139T>A	p.Ile380Asn	p.I380N	ENST00000256646	NM_024408.3	380	aTc/aAc	7/34	1	2	FACETS	0.434	0.379	0.493	0.434	0.379	0.493	SUBCLONAL	1	TRUE	1	0.34	2		677	1030	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150936528	150936528	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	167	771	0	ENST00000271640.5:c.3727C>T	p.Arg1243Cys	p.R1243C	ENST00000271640	NM_001145415.1	1243	Cgc/Tgc	21/22	0.3	2	FACETS	0.882	0.809	0.958			1	CLONAL	1	TRUE	NA	0.34	2		771	1114	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163315554	163315554	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	99	493	0	ENST00000271452.3:c.894G>T	p.Lys298Asn	p.K298N	ENST00000271452	NM_145697.2	298	aaG/aaT	11/14	1	2	FACETS	0.938	0.839	1	0.938	0.839	1	CLONAL	1	TRUE	1	0.34	2		493	621	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111168	193111168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1452051467	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	117	649	0	ENST00000367435.3:c.701G>A	p.Arg234Gln	p.R234Q	ENST00000367435	NM_024529.4	234	cGa/cAa	7/17	1	2	FACETS	0.808	0.728	0.892	0.808	0.728	0.892	CLONAL	1	TRUE	1	0.34	2		649	852	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578208	226578208	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	110	767	0	ENST00000366794.5:c.520C>G	p.Pro174Ala	p.P174A	ENST00000366794	NM_001618.3	174	Ccc/Gcc	4/23	1	2	FACETS	0.523	0.468	0.581	0.523	0.468	0.581	SUBCLONAL	1	TRUE	1	0.34	2		767	1237	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230561391	230561391	+	5_prime_UTR_variant	5'UTR	SNP	C	C	T	rs545256509	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1259	260	1157	1	ENST00000391860.1:c.-62G>A		p.*21*	ENST00000391860	NM_001258311.1	-/409		1/7	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.34	2		1158	1519	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669348	241669348	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	58	428	0	ENST00000366560.3:c.859A>C	p.Ile287Leu	p.I287L	ENST00000366560	NM_000143.3	287	Att/Ctt	6/10	1	2	FACETS	0.521	0.447	0.602	0.521	0.447	0.602	SUBCLONAL	1	TRUE	1	0.34	2		428	655	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675359	241675359	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	86	469	0	ENST00000366560.3:c.463G>T	p.Glu155Ter	p.E155*	ENST00000366560	NM_000143.3	155	Gaa/Taa	4/10	1	2	FACETS	0.74	0.654	0.831	0.74	0.654	0.831	SUBCLONAL	1	TRUE	1	0.34	2		469	684	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680556	241680556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769956664	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	80	436	0	ENST00000366560.3:c.193G>T	p.Asp65Tyr	p.D65Y	ENST00000366560	NM_000143.3	65	Gat/Tat	2/10	1	2	FACETS	0.716	0.631	0.808	0.716	0.631	0.808	SUBCLONAL	1	TRUE	1	0.34	2		436	657	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809194	243809194	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	44	474	0	ENST00000263826.5:c.429+1G>A		p.X143_splice	ENST00000263826	NM_005465.4	143			1	2	FACETS	0.428	0.358	0.505	0.428	0.358	0.505	SUBCLONAL	1	TRUE	1	0.34	2		474	605	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809199	243809199	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	130	479	0	ENST00000263826.5:c.425G>T	p.Arg142Ile	p.R142I	ENST00000263826	NM_005465.4	142	aGa/aTa	4/13	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.34	2		479	611	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609930	43609930	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs754466051	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1297	101	1023	0	ENST00000355710.3:c.1882C>T	p.Pro628Ser	p.P628S	ENST00000355710	NM_020975.4	628	Cca/Tca	11/20	1	2	FACETS	0.425	0.378	0.475	0.425	0.378	0.475	SUBCLONAL	1	TRUE	1	0.34	2		1023	1398	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610159	43610159	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	112	875	0	ENST00000355710.3:c.2111T>C	p.Val704Ala	p.V704A	ENST00000355710	NM_020975.4	704	gTc/gCc	11/20	1	2	FACETS	0.519	0.465	0.577	0.519	0.465	0.577	SUBCLONAL	1	TRUE	1	0.34	2		875	1269	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612095	43612095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	100	924	0	ENST00000355710.3:c.2200G>A	p.Glu734Lys	p.E734K	ENST00000355710	NM_020975.4	734	Gaa/Aaa	12/20	1	2	FACETS	0.469	0.417	0.524	0.469	0.417	0.524	SUBCLONAL	1	TRUE	1	0.34	2		924	1255	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615538	43615538	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	85	828	0	ENST00000355710.3:c.2617C>G	p.Arg873Gly	p.R873G	ENST00000355710	NM_020975.4	873	Cgg/Ggg	15/20	1	2	FACETS	0.471	0.415	0.531	0.471	0.415	0.531	SUBCLONAL	1	TRUE	1	0.34	2		828	1062	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63810678	63810678	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1464829578	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	67	563	0	ENST00000279873.7:c.765G>T	p.Lys255Asn	p.K255N	ENST00000279873	NM_032199.2	255	aaG/aaT	5/10	1	2	FACETS	0.408	0.353	0.468	0.408	0.353	0.468	SUBCLONAL	1	TRUE	1	0.34	2		563	966	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850777	63850777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374377066	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	220	788	0	ENST00000279873.7:c.1555G>A	p.Glu519Lys	p.E519K	ENST00000279873	NM_032199.2	519	Gaa/Aaa	10/10	1	2	FACETS	0.98	0.91	1	0.98	0.91	1	CLONAL	1	TRUE	1	0.34	2		788	1321	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851755	63851755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749293931	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	219	780	0	ENST00000279873.7:c.2533G>A	p.Glu845Lys	p.E845K	ENST00000279873	NM_032199.2	845	Gag/Aag	10/10	1	2	FACETS	0.969	0.899	1	0.969	0.899	1	CLONAL	1	TRUE	1	0.34	2		780	1330	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852632	63852632	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	97	771	0	ENST00000279873.7:c.3410C>A	p.Ser1137Tyr	p.S1137Y	ENST00000279873	NM_032199.2	1137	tCt/tAt	10/10	1	2	FACETS	0.511	0.454	0.572	0.511	0.454	0.572	SUBCLONAL	1	TRUE	1	0.34	2		771	1117	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332336	70332336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775380660	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	170	691	1	ENST00000373644.4:c.241C>T	p.Arg81Cys	p.R81C	ENST00000373644	NM_030625.2	81	Cgc/Tgc	2/12	1	2	FACETS	0.961	0.883	1	0.961	0.883	1	CLONAL	1	TRUE	1	0.34	2		692	1041	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333539	70333539	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs570151139	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	172	673	0	ENST00000373644.4:c.1444A>C	p.Asn482His	p.N482H	ENST00000373644	NM_030625.2	482	Aac/Cac	2/12	1	2	FACETS	0.997	0.917	1	0.997	0.917	1	CLONAL	1	TRUE	1	0.34	2		673	1015	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333960	70333960	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	94	693	0	ENST00000373644.4:c.1865G>T	p.Arg622Ile	p.R622I	ENST00000373644	NM_030625.2	622	aGa/aTa	2/12	1	2	FACETS	0.527	0.468	0.591	0.527	0.468	0.591	SUBCLONAL	1	TRUE	1	0.34	2		693	1049	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404890	70404890	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	70	592	0	ENST00000373644.4:c.2404A>C	p.Asn802His	p.N802H	ENST00000373644	NM_030625.2	802	Aac/Cac	4/12	1	2	FACETS	0.493	0.429	0.563	0.493	0.429	0.563	SUBCLONAL	1	TRUE	1	0.34	2		592	835	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406122	70406122	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	84	609	0	ENST00000373644.4:c.3636A>C	p.Lys1212Asn	p.K1212N	ENST00000373644	NM_030625.2	1212	aaA/aaC	4/12	1	2	FACETS	0.535	0.472	0.604	0.535	0.472	0.604	SUBCLONAL	1	TRUE	1	0.34	2		609	923	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406586	70406586	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	80	575	0	ENST00000373644.4:c.4100T>C	p.Val1367Ala	p.V1367A	ENST00000373644	NM_030625.2	1367	gTt/gCt	4/12	1	2	FACETS	0.494	0.433	0.559	0.494	0.433	0.559	SUBCLONAL	1	TRUE	1	0.34	2		575	953	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406732	70406732	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768683199	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	54	510	0	ENST00000373644.4:c.4246G>T	p.Asp1416Tyr	p.D1416Y	ENST00000373644	NM_030625.2	1416	Gat/Tat	4/12	1	2	FACETS	0.421	0.359	0.49	0.421	0.359	0.49	SUBCLONAL	1	TRUE	1	0.34	2		510	754	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692874	89692874	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786204930	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	55	258	0	ENST00000371953.3:c.358G>A	p.Ala120Thr	p.A120T	ENST00000371953	NM_000314.4	120	Gca/Aca	5/9	1	2	FACETS	0.919	0.79	1	0.919	0.79	1	CLONAL	1	TRUE	1	0.34	2		258	352	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720816	89720816	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	42	172	0	ENST00000371953.3:c.967A>C	p.Asn323His	p.N323H	ENST00000371953	NM_000314.4	323	Aat/Cat	8/9	1	2	FACETS	0.973	0.818	1	0.973	0.818	1	CLONAL	1	TRUE	1	0.34	2		172	254	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	157	635	0	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	1	2	FACETS	0.904	0.827	0.984	0.904	0.827	0.984	CLONAL	1	TRUE	1	0.34	2		635	1022	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258036	123258036	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519045	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	24	503	0	ENST00000358487.5:c.1645A>C	p.Asn549His	p.N549H	ENST00000358487	NM_000141.4	549	Aat/Cat	12/18	1	2	FACETS	0.201	0.156	0.252	0.201	0.156	0.252	SUBCLONAL	1	TRUE	1	0.34	2		503	704	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161460	2161460	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	206	752	0	ENST00000434045.2:c.67C>A	p.Gln23Lys	p.Q23K	ENST00000434045	NM_001127598.1	23	Caa/Aaa	2/5	1	2	FACETS	0.944	0.874	1	0.944	0.874	1	CLONAL	1	TRUE	1	0.34	2		752	1283	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316108	14316108	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	46	216	0	ENST00000256196.4:c.317A>C	p.Lys106Thr	p.K106T	ENST00000256196		106	aAg/aCg	4/6	1	2	FACETS	0.881	0.746	1	0.881	0.746	1	CLONAL	1	TRUE	1	0.34	2		216	307	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741684	17741684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1384940737	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	72	741	0	ENST00000250003.3:c.355C>T	p.Arg119Trp	p.R119W	ENST00000250003	NM_002478.4	119	Cgg/Tgg	1/3	1	2	FACETS	0.404	0.351	0.461	0.404	0.351	0.461	SUBCLONAL	1	TRUE	1	0.34	2		741	1049	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417904	32417904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	182	696	0	ENST00000332351.3:c.1148C>T	p.Ser383Phe	p.S383F	ENST00000332351	NM_024426.4	383	tCt/tTt	7/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.34	2		696	995	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47599447	47599447	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	102	711	0	ENST00000430070.2:c.153G>A	p.Met51Ile	p.M51I	ENST00000430070	NM_018095.4	51	atG/atA	2/4	1	2	FACETS	0.485	0.433	0.542	0.485	0.433	0.542	SUBCLONAL	1	TRUE	1	0.34	2		711	1236	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625333	69625333	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	194	946	0	ENST00000334134.2:c.460T>C	p.Tyr154His	p.Y154H	ENST00000334134	NM_005247.2	154	Tac/Cac	3/3	1	2	FACETS	0.921	0.851	0.995	0.921	0.851	0.995	CLONAL	1	TRUE	1	0.34	2		946	1239	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625354	69625354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	183	921	0	ENST00000334134.2:c.439C>T	p.Pro147Ser	p.P147S	ENST00000334134	NM_005247.2	147	Ccc/Tcc	3/3	1	2	FACETS	0.89	0.82	0.964	0.89	0.82	0.964	CLONAL	1	TRUE	1	0.34	2		921	1209	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943323	71943323	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	117	806	0	ENST00000298229.2:c.1655G>C	p.Gly552Ala	p.G552A	ENST00000298229	NM_001567.3	552	gGc/gCc	14/28	1	2	FACETS	0.527	0.473	0.584	0.527	0.473	0.584	SUBCLONAL	1	TRUE	1	0.34	2		806	1306	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944711	71944711	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	89	745	1	ENST00000298229.2:c.2135A>G	p.Asp712Gly	p.D712G	ENST00000298229	NM_001567.3	712	gAc/gGc	19/28	1	2	FACETS	0.469	0.414	0.527	0.469	0.414	0.527	SUBCLONAL	1	TRUE	1	0.34	2		746	1117	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988988	85988988	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	77	332	0	ENST00000263360.6:c.1154A>C	p.Lys385Thr	p.K385T	ENST00000263360	NM_003797.3	385	aAa/aCa	11/12	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.34	2		332	447	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94922975	94922975	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1286895936	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	58	491	0	ENST00000536441.1:c.493C>T	p.Arg165Ter	p.R165*	ENST00000536441	NM_144665.3	165	Cga/Tga	4/10	1	2	FACETS	0.495	0.425	0.572	0.495	0.425	0.572	SUBCLONAL	1	TRUE	1	0.34	2		491	689	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912801	100912801	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	98	561	0	ENST00000325455.5:c.2521T>C	p.Phe841Leu	p.F841L	ENST00000325455	NM_001202474.3	841	Ttt/Ctt	7/8	1	2	FACETS	0.793	0.707	0.884	0.793	0.707	0.884	SUBCLONAL	1	TRUE	1	0.34	2		561	727	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076800	102076800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768834182	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	93	759	0	ENST00000282441.5:c.979C>T	p.Arg327Trp	p.R327W	ENST00000282441	NM_001130145.2	327	Cgg/Tgg	5/9	1	2	FACETS	0.513	0.455	0.576	0.513	0.455	0.576	SUBCLONAL	1	TRUE	1	0.34	2		759	1066	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102080254	102080254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193100333	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	98	480	0	ENST00000282441.5:c.991C>T	p.Arg331Trp	p.R331W	ENST00000282441	NM_001130145.2	331	Cgg/Tgg	6/9	1	2	FACETS	0.804	0.717	0.896	0.804	0.717	0.896	CLONAL	1	TRUE	1	0.34	2		480	717	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100496	102100496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	208	691	0	ENST00000282441.5:c.1340C>T	p.Ala447Val	p.A447V	ENST00000282441	NM_001130145.2	447	gCc/gTc	9/9	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.34	2		691	1029	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206719	102206719	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	44	384	0	ENST00000263464.3:c.1347G>T	p.Lys449Asn	p.K449N	ENST00000263464	NM_001165.4	449	aaG/aaT	7/9	1	2	FACETS	0.494	0.414	0.583	0.494	0.414	0.583	SUBCLONAL	1	TRUE	1	0.34	2		384	524	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098519	108098519	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs876658520	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	33	422	0	ENST00000278616.4:c.89T>G	p.Phe30Cys	p.F30C	ENST00000278616	NM_000051.3	30	tTt/tGt	3/63	1	2	FACETS	0.317	0.257	0.384	0.317	0.257	0.384	SUBCLONAL	1	TRUE	1	0.34	2		422	613	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114842	108114842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145355104	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	85	427	0	ENST00000278616.4:c.659C>T	p.Ala220Val	p.A220V	ENST00000278616	NM_000051.3	220	gCg/gTg	6/63	1	2	FACETS	0.84	0.744	0.943	0.84	0.744	0.943	CLONAL	1	TRUE	1	0.34	2		427	595	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115600	108115600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772821016	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	98	533	0	ENST00000278616.4:c.748C>T	p.Arg250Ter	p.R250*	ENST00000278616	NM_000051.3	250	Cga/Tga	7/63	1	2	FACETS	0.887	0.792	0.987	0.887	0.792	0.987	CLONAL	1	TRUE	1	0.34	2		533	650	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124717	108124717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751515818	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	115	530	0	ENST00000278616.4:c.2075G>A	p.Arg692His	p.R692H	ENST00000278616	NM_000051.3	692	cGc/cAc	13/63	1	2	FACETS	0.901	0.812	0.995	0.901	0.812	0.995	CLONAL	1	TRUE	1	0.34	2		530	751	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175544	108175544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780628	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	127	607	0	ENST00000278616.4:c.5639C>T	p.Thr1880Met	p.T1880M	ENST00000278616	NM_000051.3	1880	aCg/aTg	37/63	1	2	FACETS	0.903	0.818	0.993	0.903	0.818	0.993	CLONAL	1	TRUE	1	0.34	2		607	827	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216627	108216627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786203542	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	108	438	0	ENST00000278616.4:c.8576C>T	p.Ser2859Phe	p.S2859F	ENST00000278616	NM_000051.3	2859	tCt/tTt	58/63	1	2	FACETS	0.971	0.873	1	0.971	0.873	1	CLONAL	1	TRUE	1	0.34	2		438	654	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236086	108236086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782292	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	164	686	0	ENST00000278616.4:c.9022C>T	p.Arg3008Cys	p.R3008C	ENST00000278616	NM_000051.3	3008	Cgt/Tgt	63/63	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.34	2		686	954	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118365111	118365111	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs999060359	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	111	414	0	ENST00000534358.1:c.5287C>T	p.Arg1763Trp	p.R1763W	ENST00000534358	NM_005933.3	1763	Cgg/Tgg	17/36	1	2	FACETS	0.972	0.875	1	0.972	0.875	1	CLONAL	1	TRUE	1	0.34	2		414	672	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142447	119142447	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs199739868	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	107	480	0	ENST00000264033.4:c.446G>A	p.Arg149Gln	p.R149Q	ENST00000264033	NM_005188.3	149	cGa/cAa	3/16	1	2	FACETS	0.826	0.741	0.916	0.826	0.741	0.916	CLONAL	1	TRUE	1	0.34	2		480	762	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514012	125514012	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	131	592	0	ENST00000428830.2:c.950C>A	p.Ser317Tyr	p.S317Y	ENST00000428830	NM_001114121.2	317	tCt/tAt	10/14	1	2	FACETS	0.861	0.781	0.945	0.861	0.781	0.945	CLONAL	1	TRUE	1	0.34	2		592	895	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402085	402085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	168	757	0	ENST00000399788.2:c.4706C>T	p.Ala1569Val	p.A1569V	ENST00000399788	NM_001042603.1	1569	gCt/gTt	27/28	1	2	FACETS	0.914	0.839	0.993	0.914	0.839	0.993	CLONAL	1	TRUE	1	0.34	2		757	1081	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416138	416138	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	157	635	0	ENST00000399788.2:c.4048C>T	p.Arg1350Ter	p.R1350*	ENST00000399788	NM_001042603.1	1350	Cga/Tga	24/28	1	2	FACETS	0.928	0.85	1	0.928	0.85	1	CLONAL	1	TRUE	1	0.34	2		635	995	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431664	431664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	117	586	0	ENST00000399788.2:c.2345G>A	p.Arg782Gln	p.R782Q	ENST00000399788	NM_001042603.1	782	cGa/cAa	17/28	1	2	FACETS	0.832	0.75	0.919	0.832	0.75	0.919	CLONAL	1	TRUE	1	0.34	2		586	827	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	465601	465601	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	111	435	0	ENST00000399788.2:c.775G>T	p.Glu259Ter	p.E259*	ENST00000399788	NM_001042603.1	259	Gaa/Taa	6/28	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.34	2		435	611	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	465607	465607	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	111	473	0	ENST00000399788.2:c.769G>T	p.Asp257Tyr	p.D257Y	ENST00000399788	NM_001042603.1	257	Gat/Tat	6/28	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.34	2		473	636	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475141	475141	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	67	544	0	ENST00000399788.2:c.496C>A	p.Leu166Ile	p.L166I	ENST00000399788	NM_001042603.1	166	Ctc/Atc	4/28	1	2	FACETS	0.485	0.42	0.555	0.485	0.42	0.555	SUBCLONAL	1	TRUE	1	0.34	2		544	813	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385283	4385283	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	179	701	0	ENST00000261254.3:c.308C>T	p.Ala103Val	p.A103V	ENST00000261254	NM_001759.3	103	gCt/gTt	2/5	1	2	FACETS	0.915	0.842	0.991	0.915	0.842	0.991	CLONAL	1	TRUE	1	0.34	2		701	1151	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435490	18435490	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs760928254	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	71	414	0	ENST00000266497.5:c.475G>T	p.Glu159Ter	p.E159*	ENST00000266497		159	Gaa/Taa	1/31	0.3	1	FACETS	0.628	0.549	0.713	0.628	0.549	0.713	SUBCLONAL	1	TRUE	0	0.34	1		414	552	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435588	18435588	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	92	583	0	ENST00000266497.5:c.573G>T	p.Glu191Asp	p.E191D	ENST00000266497		191	gaG/gaT	1/31	0.3	1	FACETS	0.544	0.483	0.609	0.544	0.483	0.609	SUBCLONAL	1	TRUE	0	0.34	1		583	826	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443796	18443796	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1185264920	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	53	432	0	ENST00000266497.5:c.769G>T	p.Glu257Ter	p.E257*	ENST00000266497		257	Gaa/Taa	3/31	0.3	1	FACETS	0.475	0.405	0.552	0.475	0.405	0.552	SUBCLONAL	1	TRUE	0	0.34	1		432	545	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466933	18466933	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	106	462	0	ENST00000266497.5:c.1072G>T	p.Asp358Tyr	p.D358Y	ENST00000266497		358	Gat/Tat	5/31	0.3	1	FACETS	0.752	0.675	0.834	0.752	0.675	0.834	SUBCLONAL	1	TRUE	0	0.34	1		462	688	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18473938	18473938	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	80	353	0	ENST00000266497.5:c.1180G>T	p.Glu394Ter	p.E394*	ENST00000266497		394	Gaa/Taa	6/31	0.3	1	FACETS	0.894	0.79	1	0.894	0.79	1	CLONAL	1	TRUE	0	0.34	1		353	437	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491360	18491360	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	48	307	0	ENST00000266497.5:c.1273G>A	p.Glu425Lys	p.E425K	ENST00000266497		425	Gaa/Aaa	8/31	0.3	1	FACETS	0.632	0.536	0.737	0.632	0.536	0.737	SUBCLONAL	1	TRUE	0	0.34	1		307	371	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552613	18552613	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1371859788	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	93	529	0	ENST00000266497.5:c.2024G>T	p.Arg675Ile	p.R675I	ENST00000266497		675	aGa/aTa	14/31	0.3	1	FACETS	0.729	0.649	0.814	0.729	0.649	0.814	SUBCLONAL	1	TRUE	0	0.34	1		529	623	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699323	18699323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199904184	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	70	602	0	ENST00000266497.5:c.3424C>T	p.Arg1142Cys	p.R1142C	ENST00000266497		1142	Cgt/Tgt	24/31	1	2	FACETS	0.487	0.423	0.556	0.487	0.423	0.556	SUBCLONAL	1	TRUE	1	0.34	2		602	846	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716359	18716359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	118	590	0	ENST00000266497.5:c.3706G>A	p.Glu1236Lys	p.E1236K	ENST00000266497		1236	Gaa/Aaa	26/31	1	2	FACETS	0.893	0.806	0.985	0.893	0.806	0.985	CLONAL	1	TRUE	1	0.34	2		590	777	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18762492	18762492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	84	471	0	ENST00000266497.5:c.3988C>T	p.Pro1330Ser	p.P1330S	ENST00000266497		1330	Cct/Tct	29/31	1	2	FACETS	0.837	0.741	0.941	0.837	0.741	0.941	CLONAL	1	TRUE	1	0.34	2		471	590	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123895	46123895	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	179	798	0	ENST00000334344.6:c.161T>G	p.Val54Gly	p.V54G	ENST00000334344	NM_152641.2	54	gTc/gGc	2/21	1	2	FACETS	0.898	0.826	0.972	0.898	0.826	0.972	CLONAL	1	TRUE	1	0.34	2		798	1173	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242710	46242710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777576250	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	73	431	0	ENST00000334344.6:c.1672C>T	p.Arg558Cys	p.R558C	ENST00000334344	NM_152641.2	558	Cgt/Tgt	13/21	1	2	FACETS	0.94	0.825	1	0.94	0.825	1	CLONAL	1	TRUE	1	0.34	2		431	457	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426266	49426266	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	191	912	0	ENST00000301067.7:c.12222A>C	p.Gln4074His	p.Q4074H	ENST00000301067	NM_003482.3	4074	caA/caC	39/54	1	2	FACETS	0.834	0.769	0.902	0.834	0.769	0.902	CLONAL	1	TRUE	1	0.34	2		912	1347	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432623	49432623	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555191147	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	212	852	0	ENST00000301067.7:c.8516C>G	p.Ser2839Ter	p.S2839*	ENST00000301067	NM_003482.3	2839	tCa/tGa	34/54	1	2	FACETS	0.928	0.86	0.999	0.928	0.86	0.999	CLONAL	1	TRUE	1	0.34	2		852	1344	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433373	49433373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771966959	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	188	831	0	ENST00000301067.7:c.8074C>T	p.Arg2692Trp	p.R2692W	ENST00000301067	NM_003482.3	2692	Cgg/Tgg	32/54	1	2	FACETS	0.883	0.814	0.954	0.883	0.814	0.954	CLONAL	1	TRUE	1	0.34	2		831	1253	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437986	49437986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747363115	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	208	773	0	ENST00000301067.7:c.5185G>A	p.Glu1729Lys	p.E1729K	ENST00000301067	NM_003482.3	1729	Gag/Aag	21/54	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.34	2		773	1171	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442540	49442540	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	57	595	0	ENST00000301067.7:c.4033G>T	p.Asp1345Tyr	p.D1345Y	ENST00000301067	NM_003482.3	1345	Gat/Tat	13/54	1	2	FACETS	0.373	0.319	0.432	0.373	0.319	0.432	SUBCLONAL	1	TRUE	1	0.34	2		595	899	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444297	49444297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746163543	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1306	123	930	0	ENST00000301067.7:c.3074C>T	p.Ser1025Leu	p.S1025L	ENST00000301067	NM_003482.3	1025	tCg/tTg	11/54	1	2	FACETS	0.506	0.456	0.56	0.506	0.456	0.56	SUBCLONAL	1	TRUE	1	0.34	2		930	1429	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50488303	50488303	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs750857733	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	139	591	0	ENST00000394963.4:c.1217C>A	p.Ser406Tyr	p.S406Y	ENST00000394963	NM_003076.4	406	tCt/tAt	10/13	1	2	FACETS	0.87	0.791	0.953	0.87	0.791	0.953	CLONAL	1	TRUE	1	0.34	2		591	940	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481824	56481824	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	192	747	0	ENST00000267101.3:c.752A>G	p.Asp251Gly	p.D251G	ENST00000267101	NM_001982.3	251	gAc/gGc	7/28	1	2	FACETS	0.96	0.887	1	0.96	0.887	1	CLONAL	1	TRUE	1	0.34	2		747	1176	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857489	57857489	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	203	839	0	ENST00000228682.2:c.15G>T	p.Met5Ile	p.M5I	ENST00000228682	NM_005269.2	5	atG/atT	2/12	1	2	FACETS	0.994	0.92	1	0.994	0.92	1	CLONAL	1	TRUE	1	0.34	2		839	1201	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102874103	102874103	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	88	423	0	ENST00000307046.8:c.57C>A	p.Phe19Leu	p.F19L	ENST00000307046	NM_001111285.1	19	ttC/ttA	1/4	1	2	FACETS	0.869	0.771	0.973	0.869	0.771	0.973	CLONAL	1	TRUE	1	0.34	2		423	596	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891037	112891037	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	124	515	0	ENST00000351677.2:c.371A>C	p.Lys124Thr	p.K124T	ENST00000351677	NM_002834.3	124	aAa/aCa	4/16	1	2	FACETS	0.969	0.877	1	0.969	0.877	1	CLONAL	1	TRUE	1	0.34	2		515	753	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117320	115117320	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	164	583	0	ENST00000257566.3:c.854A>C	p.Gln285Pro	p.Q285P	ENST00000257566	NM_016569.3	285	cAg/cCg	4/8	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.34	2		583	926	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416625	121416625	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	163	716	0	ENST00000257555.6:c.54G>C	p.Glu18Asp	p.E18D	ENST00000257555		18	gaG/gaC	1/10	1	2	FACETS	0.948	0.87	1	0.948	0.87	1	CLONAL	1	TRUE	1	0.34	2		716	1011	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123888136	123888136	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	74	593	0	ENST00000330479.4:c.614G>T	p.Arg205Ile	p.R205I	ENST00000330479	NM_020382.3	205	aGa/aTa	6/9	1	2	FACETS	0.484	0.422	0.55	0.484	0.422	0.55	SUBCLONAL	1	TRUE	1	0.34	2		593	900	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240670	133240670	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1208731306	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	169	731	0	ENST00000320574.5:c.2626T>G	p.Phe876Val	p.F876V	ENST00000320574	NM_006231.2	876	Ttt/Gtt	23/49	1	2	FACETS	0.936	0.86	1	0.936	0.86	1	CLONAL	1	TRUE	1	0.34	2		731	1062	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245434	133245434	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	228	804	0	ENST00000320574.5:c.1886C>A	p.Ala629Asp	p.A629D	ENST00000320574	NM_006231.2	629	gCc/gAc	17/49	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.34	2		804	1194	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252703	133252703	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	171	750	0	ENST00000320574.5:c.997T>A	p.Cys333Ser	p.C333S	ENST00000320574	NM_006231.2	333	Tgt/Agt	10/49	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.34	2		750	975	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253212	133253212	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	140	634	0	ENST00000320574.5:c.829G>C	p.Glu277Gln	p.E277Q	ENST00000320574	NM_006231.2	277	Gag/Cag	9/49	1	2	FACETS	0.846	0.77	0.927	0.846	0.77	0.927	CLONAL	1	TRUE	1	0.34	2		634	973	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253957	133253957	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	143	578	0	ENST00000320574.5:c.793G>A	p.Glu265Lys	p.E265K	ENST00000320574	NM_006231.2	265	Gaa/Aaa	8/49	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.34	2		578	820	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975443	26975443	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	121	586	0	ENST00000381527.3:c.1069G>T	p.Glu357Ter	p.E357*	ENST00000381527	NM_001260.1	357	Gaa/Taa	11/13	1	2	FACETS	0.836	0.755	0.922	0.836	0.755	0.922	CLONAL	1	TRUE	1	0.34	2		586	851	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597525	28597525	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	109	516	0	ENST00000241453.7:c.2380C>A	p.Gln794Lys	p.Q794K	ENST00000241453	NM_004119.2	794	Caa/Aaa	19/24	1	2	FACETS	0.919	0.826	1	0.919	0.826	1	CLONAL	1	TRUE	1	0.34	2		516	698	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599042	28599042	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1355239392	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	89	529	0	ENST00000241453.7:c.2246C>T	p.Ser749Leu	p.S749L	ENST00000241453	NM_004119.2	749	tCg/tTg	18/24	1	2	FACETS	0.72	0.638	0.808	0.72	0.638	0.808	SUBCLONAL	1	TRUE	1	0.34	2		529	727	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608270	28608270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	153	645	0	ENST00000241453.7:c.1786G>A	p.Glu596Lys	p.E596K	ENST00000241453	NM_004119.2	596	Gaa/Aaa	14/24	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.34	2		645	898	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609763	28609763	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	155	639	0	ENST00000241453.7:c.1466G>T	p.Arg489Ile	p.R489I	ENST00000241453	NM_004119.2	489	aGa/aTa	12/24	1	2	FACETS	0.991	0.907	1	0.991	0.907	1	CLONAL	1	TRUE	1	0.34	2		639	920	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611338	28611338	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	71	462	0	ENST00000241453.7:c.1293C>A	p.Phe431Leu	p.F431L	ENST00000241453	NM_004119.2	431	ttC/ttA	10/24	1	2	FACETS	0.709	0.619	0.806	0.709	0.619	0.806	SUBCLONAL	1	TRUE	1	0.34	2		462	589	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28883029	28883029	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs370986273	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	54	500	0	ENST00000282397.4:c.3671G>T	p.Arg1224Ile	p.R1224I	ENST00000282397	NM_002019.4	1224	aGa/aTa	28/30	1	2	FACETS	0.486	0.415	0.565	0.486	0.415	0.565	SUBCLONAL	1	TRUE	1	0.34	2		500	653	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895653	28895653	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	135	621	0	ENST00000282397.4:c.3121T>G	p.Phe1041Val	p.F1041V	ENST00000282397	NM_002019.4	1041	Ttt/Gtt	23/30	1	2	FACETS	0.903	0.821	0.99	0.903	0.821	0.99	CLONAL	1	TRUE	1	0.34	2		621	879	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28903838	28903838	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1319953709	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	133	699	0	ENST00000282397.4:c.2621C>T	p.Ala874Val	p.A874V	ENST00000282397	NM_002019.4	874	gCt/gTt	19/30	1	2	FACETS	0.818	0.742	0.898	0.818	0.742	0.898	CLONAL	1	TRUE	1	0.34	2		699	956	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964128	28964128	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	132	588	0	ENST00000282397.4:c.1774C>A	p.Leu592Met	p.L592M	ENST00000282397	NM_002019.4	592	Ctg/Atg	13/30	1	2	FACETS	0.921	0.836	1	0.921	0.836	1	CLONAL	1	TRUE	1	0.34	2		588	843	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964139	28964139	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	59	592	0	ENST00000282397.4:c.1763C>A	p.Thr588Asn	p.T588N	ENST00000282397	NM_002019.4	588	aCt/aAt	13/30	1	2	FACETS	0.422	0.362	0.488	0.422	0.362	0.488	SUBCLONAL	1	TRUE	1	0.34	2		592	822	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29002009	29002009	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750711298	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	58	553	0	ENST00000282397.4:c.1156C>T	p.Arg386Cys	p.R386C	ENST00000282397	NM_002019.4	386	Cgt/Tgt	9/30	1	2	FACETS	0.444	0.381	0.514	0.444	0.381	0.514	SUBCLONAL	1	TRUE	1	0.34	2		553	768	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005332	29005332	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	116	500	0	ENST00000282397.4:c.929C>A	p.Thr310Asn	p.T310N	ENST00000282397	NM_002019.4	310	aCt/aAt	7/30	1	2	FACETS	0.954	0.861	1	0.954	0.861	1	CLONAL	1	TRUE	1	0.34	2		500	715	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012437	29012437	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	139	591	0	ENST00000282397.4:c.434T>G	p.Ile145Ser	p.I145S	ENST00000282397	NM_002019.4	145	aTt/aGt	4/30	1	2	FACETS	0.953	0.868	1	0.953	0.868	1	CLONAL	1	TRUE	1	0.34	2		591	858	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907124	32907124	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	120	627	0	ENST00000380152.3:c.1509G>T	p.Lys503Asn	p.K503N	ENST00000380152		503	aaG/aaT	10/27	1	2	FACETS	0.919	0.83	1	0.919	0.83	1	CLONAL	1	TRUE	1	0.34	2		627	768	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914260	32914260	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	106	534	0	ENST00000380152.3:c.5768A>G	p.Asp1923Gly	p.D1923G	ENST00000380152		1923	gAc/gGc	11/27	1	2	FACETS	0.875	0.784	0.97	0.875	0.784	0.97	CLONAL	1	TRUE	1	0.34	2		534	713	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950837	32950837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80359124	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	121	454	0	ENST00000380152.3:c.8663G>A	p.Arg2888His	p.R2888H	ENST00000380152		2888	cGt/cAt	21/27	1	2	FACETS	0.928	0.839	1	0.928	0.839	1	CLONAL	1	TRUE	1	0.34	2		454	767	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878127	48878127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1309325353	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	92	852	0	ENST00000267163.4:c.79C>T	p.Pro27Ser	p.P27S	ENST00000267163	NM_000321.2	27	Ccc/Tcc	1/27	0.3	2	FACETS	0.461	0.408	0.518			1	SUBCLONAL	1	TRUE	NA	0.34	2		852	1173	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936983	48936983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690863	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	120	485	0	ENST00000267163.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000267163	NM_000321.2	251	Cga/Tga	8/27	0.3	2	FACETS	0.993	0.898	1			1	CLONAL	1	TRUE	NA	0.34	2		485	711	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941657	48941657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1060503077	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	50	189	0	ENST00000267163.4:c.967G>T	p.Glu323Ter	p.E323*	ENST00000267163	NM_000321.2	323	Gaa/Taa	10/27	0.3	2	FACETS	1	0.923	1			1	CLONAL	1	TRUE	NA	0.34	2		189	261	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953781	48953781	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	66	260	0	ENST00000267163.4:c.1384A>C	p.Lys462Gln	p.K462Q	ENST00000267163	NM_000321.2	462	Aaa/Caa	14/27	0.3	2	FACETS	0.978	0.853	1			1	CLONAL	1	TRUE	NA	0.34	2		260	397	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281206	49281206	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	156	609	0	ENST00000282018.3:c.253C>A	p.Leu85Ile	p.L85I	ENST00000282018	NM_020377.2	85	Ctc/Atc	1/1	1	2	FACETS	0.988	0.904	1	0.988	0.904	1	CLONAL	1	TRUE	1	0.34	2		609	929	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281447	49281447	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	167	762	0	ENST00000282018.3:c.494T>G	p.Leu165Arg	p.L165R	ENST00000282018	NM_020377.2	165	cTt/cGt	1/1	1	2	FACETS	0.939	0.862	1	0.939	0.862	1	CLONAL	1	TRUE	1	0.34	2		762	1046	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73334768	73334768	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	71	352	0	ENST00000377767.4:c.2692G>T	p.Asp898Tyr	p.D898Y	ENST00000377767	NM_014953.3	898	Gat/Tat	20/21	1	2	FACETS	0.994	0.872	1	0.994	0.872	1	CLONAL	1	TRUE	1	0.34	2		352	420	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345070	73345070	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	78	388	0	ENST00000377767.4:c.1727A>C	p.Lys576Thr	p.K576T	ENST00000377767	NM_014953.3	576	aAg/aCg	13/21	1	2	FACETS	0.916	0.807	1	0.916	0.807	1	CLONAL	1	TRUE	1	0.34	2		388	501	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346314	73346314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs575448022	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	97	409	0	ENST00000377767.4:c.1486G>A	p.Glu496Lys	p.E496K	ENST00000377767	NM_014953.3	496	Gaa/Aaa	10/21	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.34	2		409	569	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504513	103504513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140917545	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	120	512	0	ENST00000355739.4:c.134G>A	p.Arg45His	p.R45H	ENST00000355739	NM_000123.3	45	cGc/cAc	2/15	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.34	2		512	682	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514595	103514595	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs966111552	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	194	815	0	ENST00000355739.4:c.1096C>T	p.Arg366Ter	p.R366*	ENST00000355739	NM_000123.3	366	Cga/Tga	8/15	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.34	2		815	1135	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527822	103527822	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs768440346	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	75	698	0	ENST00000355739.4:c.3130G>T	p.Glu1044Ter	p.E1044*	ENST00000355739	NM_000123.3	1044	Gaa/Taa	15/15	1	2	FACETS	0.449	0.392	0.511	0.449	0.392	0.511	SUBCLONAL	1	TRUE	1	0.34	2		698	982	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30095743	30095743	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	75	357	0	ENST00000331968.5:c.1745A>C	p.Gln582Pro	p.Q582P	ENST00000331968	NM_002742.2	582	cAg/cCg	12/18	1	2	FACETS	0.967	0.851	1	0.967	0.851	1	CLONAL	1	TRUE	1	0.34	2		357	456	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30102098	30102098	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	83	409	0	ENST00000331968.5:c.1369G>T	p.Asp457Tyr	p.D457Y	ENST00000331968	NM_002742.2	457	Gac/Tac	9/18	1	2	FACETS	0.81	0.715	0.911	0.81	0.715	0.911	CLONAL	1	TRUE	1	0.34	2		409	603	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105579	30105579	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1036795627	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	166	735	0	ENST00000331968.5:c.1107G>T	p.Glu369Asp	p.E369D	ENST00000331968	NM_002742.2	369	gaG/gaT	7/18	1	2	FACETS	0.926	0.849	1	0.926	0.849	1	CLONAL	1	TRUE	1	0.34	2		735	1055	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133041	30133041	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	116	531	0	ENST00000331968.5:c.560G>T	p.Arg187Ile	p.R187I	ENST00000331968	NM_002742.2	187	aGa/aTa	4/18	1	2	FACETS	0.912	0.823	1	0.912	0.823	1	CLONAL	1	TRUE	1	0.34	2		531	748	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353757	68353757	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs774910383	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	67	306	0	ENST00000487270.1:c.592G>T	p.Glu198Ter	p.E198*	ENST00000487270	NM_133509.3	198	Gaa/Taa	7/11	1	2	FACETS	0.876	0.763	0.997	0.876	0.763	0.997	CLONAL	1	TRUE	1	0.34	2		306	450	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353867	68353867	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	63	570	0	ENST00000487270.1:c.702C>A	p.Phe234Leu	p.F234L	ENST00000487270	NM_133509.3	234	ttC/ttA	7/11	1	2	FACETS	0.427	0.368	0.491	0.427	0.368	0.491	SUBCLONAL	1	TRUE	1	0.34	2		570	868	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554305	81554305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777252114	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	189	488	0	ENST00000298171.2:c.325C>T	p.Arg109Trp	p.R109W	ENST00000298171	NM_000369.2	109	Cgg/Tgg	4/10	1	2	FACETS	0.794	0.736	0.854	1	0.991	1	SUBCLONAL	2	TRUE	1	0.34	2		488	700	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557695	95557695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	110	498	0	ENST00000393063.1:c.5372G>A	p.Arg1791Lys	p.R1791K	ENST00000393063	NM_030621.3	1791	aGa/aAa	26/28	1	2	FACETS	0.857	0.77	0.949	0.857	0.77	0.949	CLONAL	1	TRUE	1	0.34	2		498	755	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570365	95570365	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	145	587	0	ENST00000393063.1:c.3368A>C	p.Lys1123Thr	p.K1123T	ENST00000393063	NM_030621.3	1123	aAg/aCg	22/28	1	2	FACETS	0.911	0.831	0.996	0.911	0.831	0.996	CLONAL	1	TRUE	1	0.34	2		587	936	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022896	33022896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	63	614	0	ENST00000300177.4:c.5G>A	p.Ser2Asn	p.S2N	ENST00000300177	NM_001191322.1	2	aGc/aAc	2/2	1	2	FACETS	0.425	0.367	0.489	0.425	0.367	0.489	SUBCLONAL	1	TRUE	1	0.34	2		614	871	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000323	42000323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	103	507	0	ENST00000219905.7:c.2342C>A	p.Ser781Tyr	p.S781Y	ENST00000219905	NM_001164273.1	781	tCt/tAt	7/24	1	2	FACETS	0.919	0.824	1	0.919	0.824	1	CLONAL	1	TRUE	1	0.34	2		507	659	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003374	42003374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372252914	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	153	686	0	ENST00000219905.7:c.2911C>T	p.Arg971Trp	p.R971W	ENST00000219905	NM_001164273.1	971	Cgg/Tgg	8/24	1	2	FACETS	0.835	0.763	0.911	0.835	0.763	0.911	CLONAL	1	TRUE	1	0.34	2		686	1078	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028765	42028765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	201	782	0	ENST00000219905.7:c.4303G>A	p.Asp1435Asn	p.D1435N	ENST00000219905	NM_001164273.1	1435	Gat/Aat	13/24	1	2	FACETS	0.976	0.903	1	0.976	0.903	1	CLONAL	1	TRUE	1	0.34	2		782	1211	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040978	42040978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755286142	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	182	799	0	ENST00000219905.7:c.5356C>T	p.Arg1786Trp	p.R1786W	ENST00000219905	NM_001164273.1	1786	Cgg/Tgg	16/24	1	2	FACETS	0.886	0.815	0.959	0.886	0.815	0.959	CLONAL	1	TRUE	1	0.34	2		799	1209	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041074	42041074	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	166	832	1	ENST00000219905.7:c.5452C>T	p.Arg1818Ter	p.R1818*	ENST00000219905	NM_001164273.1	1818	Cga/Tga	16/24	1	2	FACETS	0.809	0.741	0.88	0.809	0.741	0.88	CLONAL	1	TRUE	1	0.34	2		833	1207	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042025	42042025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199971244	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	153	653	0	ENST00000219905.7:c.6220C>T	p.Arg2074Cys	p.R2074C	ENST00000219905	NM_001164273.1	2074	Cgt/Tgt	17/24	1	2	FACETS	0.956	0.875	1	0.956	0.875	1	CLONAL	1	TRUE	1	0.34	2		653	941	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052661	42052661	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	189	641	0	ENST00000219905.7:c.7332G>T	p.Glu2444Asp	p.E2444D	ENST00000219905	NM_001164273.1	2444	gaG/gaT	20/24	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.34	2		641	1037	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701889	43701889	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	126	448	1	ENST00000382044.4:c.5356C>T	p.Arg1786Ter	p.R1786*	ENST00000382044	NM_001141980.1	1786	Cga/Tga	25/28	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.34	2		449	736	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707863	43707863	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	192	721	0	ENST00000382044.4:c.5018G>T	p.Arg1673Ile	p.R1673I	ENST00000382044	NM_001141980.1	1673	aGa/aTa	23/28	1	2	FACETS	0.988	0.913	1	0.988	0.913	1	CLONAL	1	TRUE	1	0.34	2		721	1143	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749137	43749137	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	137	632	0	ENST00000382044.4:c.1669T>C	p.Ser557Pro	p.S557P	ENST00000382044	NM_001141980.1	557	Tct/Cct	12/28	1	2	FACETS	0.816	0.741	0.894	0.816	0.741	0.894	CLONAL	1	TRUE	1	0.34	2		632	988	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749297	43749297	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs748115671	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	121	534	0	ENST00000382044.4:c.1509G>T	p.Lys503Asn	p.K503N	ENST00000382044	NM_001141980.1	503	aaG/aaT	12/28	1	2	FACETS	0.857	0.774	0.944	0.857	0.774	0.944	CLONAL	1	TRUE	1	0.34	2		534	831	SUCCESS
B2M	567	MSKCC	GRCh37	15	45008529	45008529	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	97	434	0	ENST00000558401.1:c.349C>T	p.Arg117Ter	p.R117*	ENST00000558401	NM_004048.2	117	Cga/Tga	3/4	1	2	FACETS	0.926	0.827	1	0.926	0.827	1	CLONAL	1	TRUE	1	0.34	2		434	616	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50773906	50773906	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs942688916	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	151	701	0	ENST00000307179.4:c.1447C>T	p.Arg483Trp	p.R483W	ENST00000307179		483	Cgg/Tgg	11/20	1	2	FACETS	0.905	0.826	0.987	0.905	0.826	0.987	CLONAL	1	TRUE	1	0.34	2		701	982	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50786463	50786463	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	97	429	0	ENST00000307179.4:c.2644G>T	p.Glu882Ter	p.E882*	ENST00000307179		882	Gaa/Taa	16/20	1	2	FACETS	0.896	0.8	0.998	0.896	0.8	0.998	CLONAL	1	TRUE	1	0.34	2		429	637	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50789381	50789381	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	112	516	0	ENST00000307179.4:c.2991G>T	p.Lys997Asn	p.K997N	ENST00000307179		997	aaG/aaT	18/20	1	2	FACETS	0.867	0.78	0.959	0.867	0.78	0.959	CLONAL	1	TRUE	1	0.34	2		516	760	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51504742	51504742	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	63	431	0	ENST00000260433.2:c.1038G>T	p.Lys346Asn	p.K346N	ENST00000260433		346	aaG/aaT	9/10	1	2	FACETS	0.567	0.49	0.65	0.567	0.49	0.65	SUBCLONAL	1	TRUE	1	0.34	2		431	654	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51514699	51514699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201842322	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	189	715	0	ENST00000260433.2:c.475C>T	p.Arg159Cys	p.R159C	ENST00000260433		159	Cgt/Tgt	5/10	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.34	2		715	1097	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727423	66727423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1049040928	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	175	643	0	ENST00000307102.5:c.139C>T	p.Arg47Ter	p.R47*	ENST00000307102	NM_002755.3	47	Cga/Tga	2/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.34	2		643	1010	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358533	67358533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	203	790	0	ENST00000327367.4:c.41G>A	p.Arg14His	p.R14H	ENST00000327367	NM_005902.3	14	cGc/cAc	1/9	1	2	FACETS	0.987	0.913	1	0.987	0.913	1	CLONAL	1	TRUE	1	0.34	2		790	1210	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473770	67473770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	171	613	0	ENST00000327367.4:c.850G>A	p.Glu284Lys	p.E284K	ENST00000327367	NM_005902.3	284	Gag/Aag	6/9	1	2	FACETS	0.942	0.865	1	0.942	0.865	1	CLONAL	1	TRUE	1	0.34	2		613	1068	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679159	88679159	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	135	582	0	ENST00000360948.2:c.878G>T	p.Ser293Ile	p.S293I	ENST00000360948	NM_001012338.2	293	aGc/aTc	8/19	1	2	FACETS	0.912	0.828	0.999	0.912	0.828	0.999	CLONAL	1	TRUE	1	0.34	2		582	871	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726674	88726674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	118	622	0	ENST00000360948.2:c.370G>A	p.Ala124Thr	p.A124T	ENST00000360948	NM_001012338.2	124	Gcc/Acc	4/19	1	2	FACETS	0.827	0.746	0.913	0.827	0.746	0.913	CLONAL	1	TRUE	1	0.34	2		622	839	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440050	99440050	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs768385917	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	88	579	0	ENST00000268035.6:c.1018A>G	p.Thr340Ala	p.T340A	ENST00000268035	NM_000875.3	340	Acc/Gcc	4/21	1	2	FACETS	0.52	0.46	0.585	0.52	0.46	0.585	SUBCLONAL	1	TRUE	1	0.34	2		579	995	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347200	347200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	143	616	0	ENST00000262320.3:c.1811G>T	p.Arg604Ile	p.R604I	ENST00000262320	NM_003502.3	604	aGa/aTa	7/11	1	2	FACETS	0.889	0.81	0.972	0.889	0.81	0.972	CLONAL	1	TRUE	1	0.34	2		616	946	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639238	3639238	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	196	843	0	ENST00000294008.3:c.4401T>G	p.Cys1467Trp	p.C1467W	ENST00000294008	NM_032444.2	1467	tgT/tgG	12/15	1	2	FACETS	0.978	0.904	1	0.978	0.904	1	CLONAL	1	TRUE	1	0.34	2		843	1179	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640689	3640689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750906921	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	179	919	0	ENST00000294008.3:c.2950G>A	p.Glu984Lys	p.E984K	ENST00000294008	NM_032444.2	984	Gaa/Aaa	12/15	1	2	FACETS	0.803	0.738	0.871	0.803	0.738	0.871	CLONAL	1	TRUE	1	0.34	2		919	1311	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788659	3788659	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	106	472	0	ENST00000262367.5:c.4295C>A	p.Ser1432Tyr	p.S1432Y	ENST00000262367	NM_004380.2	1432	tCt/tAt	26/31	1	2	FACETS	0.823	0.737	0.913	0.823	0.737	0.913	CLONAL	1	TRUE	1	0.34	2		472	758	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790473	3790473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	73	672	0	ENST00000262367.5:c.4060G>A	p.Ala1354Thr	p.A1354T	ENST00000262367	NM_004380.2	1354	Gcc/Acc	24/31	1	2	FACETS	0.404	0.352	0.461	0.404	0.352	0.461	SUBCLONAL	1	TRUE	1	0.34	2		672	1062	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842075	3842075	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1302427305	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	126	530	0	ENST00000262367.5:c.1237C>T	p.Arg413Ter	p.R413*	ENST00000262367	NM_004380.2	413	Cga/Tga	5/31	1	2	FACETS	0.894	0.81	0.983	0.894	0.81	0.983	CLONAL	1	TRUE	1	0.34	2		530	829	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3929909	3929909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	156	700	0	ENST00000262367.5:c.9G>T	p.Glu3Asp	p.E3D	ENST00000262367	NM_004380.2	3	gaG/gaT	1/31	1	2	FACETS	0.894	0.817	0.973	0.894	0.817	0.973	CLONAL	1	TRUE	1	0.34	2		700	1027	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857757	9857757	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	202	939	0	ENST00000330684.3:c.3644G>T	p.Arg1215Ile	p.R1215I	ENST00000330684	NM_001134407.1	1215	aGa/aTa	13/13	1	2	FACETS	0.908	0.84	0.98	0.908	0.84	0.98	CLONAL	1	TRUE	1	0.34	2		939	1308	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858072	9858072	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	167	726	0	ENST00000330684.3:c.3329C>A	p.Ser1110Ter	p.S1110*	ENST00000330684	NM_001134407.1	1110	tCa/tAa	13/13	1	2	FACETS	0.908	0.833	0.986	0.908	0.833	0.986	CLONAL	1	TRUE	1	0.34	2		726	1082	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923344	9923344	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	145	611	0	ENST00000330684.3:c.1943A>C	p.Asn648Thr	p.N648T	ENST00000330684	NM_001134407.1	648	aAt/aCt	9/13	1	2	FACETS	0.876	0.798	0.957	0.876	0.798	0.957	CLONAL	1	TRUE	1	0.34	2		611	974	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9927978	9927978	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	42	550	0	ENST00000330684.3:c.1761C>A	p.Asn587Lys	p.N587K	ENST00000330684	NM_001134407.1	587	aaC/aaA	8/13	1	2	FACETS	0.324	0.27	0.385	0.324	0.27	0.385	SUBCLONAL	1	TRUE	1	0.34	2		550	762	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032274	10032274	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	148	683	0	ENST00000330684.3:c.549C>A	p.Phe183Leu	p.F183L	ENST00000330684	NM_001134407.1	183	ttC/ttA	3/13	1	2	FACETS	0.905	0.826	0.988	0.905	0.826	0.988	CLONAL	1	TRUE	1	0.34	2		683	962	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273941	10273941	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	180	845	0	ENST00000330684.3:c.328G>T	p.Ala110Ser	p.A110S	ENST00000330684	NM_001134407.1	110	Gcc/Tcc	2/13	1	2	FACETS	0.957	0.882	1	0.957	0.882	1	CLONAL	1	TRUE	1	0.34	2		845	1106	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134459	30134460	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	99	613	1	ENST00000263025.4:c.71dup	p.Glu27GlyfsTer35	p.E27Gfs*35	ENST00000263025	NM_002746.2	24	gtc/gtTc	1/9	1	2	FACETS	0.666	0.593	0.743	0.666	0.593	0.743	SUBCLONAL	1	TRUE	1	0.34	2		614	875	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783612	50783612	+	start_lost	Translation_Start_Site	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	94	456	0	ENST00000398568.2:c.3G>T	p.Met1?	p.M1?	ENST00000398568	NM_001042412.1	1	atG/atT	3/18	1	2	FACETS	0.917	0.817	1	0.917	0.817	1	CLONAL	1	TRUE	1	0.34	2		456	603	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50818289	50818289	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	80	459	0	ENST00000398568.2:c.1867G>T	p.Glu623Ter	p.E623*	ENST00000398568	NM_001042412.1	623	Gaa/Taa	11/18	1	2	FACETS	0.802	0.706	0.904	0.802	0.706	0.904	CLONAL	1	TRUE	1	0.34	2		459	587	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56878418	56878418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374875893	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	170	708	0	ENST00000308159.5:c.2357G>A	p.Arg786Gln	p.R786Q	ENST00000308159	NM_014669.4	786	cGa/cAa	22/22	1	2	FACETS	0.91	0.836	0.988	0.91	0.836	0.988	CLONAL	1	TRUE	1	0.34	2		708	1099	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132617	67132617	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	119	404	0	ENST00000412916.2:c.500G>T	p.Arg167Ile	p.R167I	ENST00000412916		167	aGa/aTa	6/6	1	2	FACETS	0.945	0.853	1	0.945	0.853	1	CLONAL	1	TRUE	1	0.34	2		404	741	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645414	67645414	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772804334	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	179	707	0	ENST00000264010.4:c.679G>A	p.Asp227Asn	p.D227N	ENST00000264010	NM_006565.3	227	Gat/Aat	3/12	1	2	FACETS	0.963	0.887	1	0.963	0.887	1	CLONAL	1	TRUE	1	0.34	2		707	1093	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835732	68835732	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	222	815	0	ENST00000261769.5:c.323G>T	p.Arg108Ile	p.R108I	ENST00000261769	NM_004360.3	108	aGa/aTa	3/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.34	2		815	1225	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828294	72828294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	198	855	0	ENST00000268489.5:c.8287G>A	p.Asp2763Asn	p.D2763N	ENST00000268489	NM_006885.3	2763	Gat/Aat	9/10	1	2	FACETS	0.948	0.876	1	0.948	0.876	1	CLONAL	1	TRUE	1	0.34	2		855	1229	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923722	72923722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1169589589	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	189	844	0	ENST00000268489.5:c.3356G>A	p.Arg1119Gln	p.R1119Q	ENST00000268489	NM_006885.3	1119	cGa/cAa	4/10	1	2	FACETS	0.961	0.887	1	0.961	0.887	1	CLONAL	1	TRUE	1	0.34	2		844	1157	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992268	72992268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746207124	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	223	821	0	ENST00000268489.5:c.1777G>A	p.Glu593Lys	p.E593K	ENST00000268489	NM_006885.3	593	Gaa/Aaa	2/10	1	2	FACETS	0.96	0.891	1	0.96	0.891	1	CLONAL	1	TRUE	1	0.34	2		821	1367	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992274	72992274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767435394	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	222	825	0	ENST00000268489.5:c.1771G>A	p.Ala591Thr	p.A591T	ENST00000268489	NM_006885.3	591	Gct/Act	2/10	1	2	FACETS	0.946	0.879	1	0.946	0.879	1	CLONAL	1	TRUE	1	0.34	2		825	1380	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993242	72993242	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	89	821	0	ENST00000268489.5:c.803A>C	p.Lys268Thr	p.K268T	ENST00000268489	NM_006885.3	268	aAa/aCa	2/10	1	2	FACETS	0.416	0.367	0.469	0.416	0.367	0.469	SUBCLONAL	1	TRUE	1	0.34	2		821	1258	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993335	72993335	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773329700	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	132	832	0	ENST00000268489.5:c.710G>A	p.Arg237Gln	p.R237Q	ENST00000268489	NM_006885.3	237	cGa/cAa	2/10	1	2	FACETS	0.598	0.541	0.658	0.598	0.541	0.658	SUBCLONAL	1	TRUE	1	0.34	2		832	1298	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993350	72993350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765589758	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1224	66	859	0	ENST00000268489.5:c.695G>A	p.Arg232His	p.R232H	ENST00000268489	NM_006885.3	232	cGc/cAc	2/10	1	2	FACETS	0.301	0.26	0.346	0.301	0.26	0.346	SUBCLONAL	1	TRUE	1	0.34	2		859	1290	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544459	86544459	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	173	833	0	ENST00000262426.4:c.284C>T	p.Ser95Phe	p.S95F	ENST00000262426	NM_001451.2	95	tCc/tTc	1/2	1	2	FACETS	0.847	0.778	0.919	0.847	0.778	0.919	CLONAL	1	TRUE	1	0.34	2		833	1202	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544981	86544981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	158	757	1	ENST00000262426.4:c.806C>T	p.Ala269Val	p.A269V	ENST00000262426	NM_001451.2	269	gCc/gTc	1/2	1	2	FACETS	0.963	0.882	1	0.963	0.882	1	CLONAL	1	TRUE	1	0.34	2		758	965	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349532	89349532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369869329	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	229	882	2	ENST00000301030.4:c.3418G>A	p.Ala1140Thr	p.A1140T	ENST00000301030	NM_001256183.1	1140	Gcc/Acc	9/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.34	2		884	1275	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805570	89805570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs775234845	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	225	759	0	ENST00000389301.3:c.4138G>T	p.Ala1380Ser	p.A1380S	ENST00000389301	NM_000135.2	1380	Gct/Tct	41/43	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.34	2		759	1190	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838195	89838195	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	228	718	0	ENST00000389301.3:c.2042C>A	p.Ser681Tyr	p.S681Y	ENST00000389301	NM_000135.2	681	tCt/tAt	23/43	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.34	2		718	1249	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989624	15989624	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	76	639	0	ENST00000268712.3:c.3149C>A	p.Ser1050Tyr	p.S1050Y	ENST00000268712	NM_006311.3	1050	tCt/tAt	23/46	1	2	FACETS	0.468	0.409	0.531	0.468	0.409	0.531	SUBCLONAL	1	TRUE	1	0.34	2		639	956	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012219	16012219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	92	432	0	ENST00000268712.3:c.2063G>A	p.Arg688Gln	p.R688Q	ENST00000268712	NM_006311.3	688	cGa/cAa	19/46	1	2	FACETS	0.886	0.788	0.99	0.886	0.788	0.99	CLONAL	1	TRUE	1	0.34	2		432	611	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16022758	16022758	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	123	447	0	ENST00000268712.3:c.1894G>T	p.Glu632Ter	p.E632*	ENST00000268712	NM_006311.3	632	Gaa/Taa	17/46	1	2	FACETS	0.998	0.903	1	0.998	0.903	1	CLONAL	1	TRUE	1	0.34	2		447	725	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049769	16049769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	107	519	0	ENST00000268712.3:c.1003G>A	p.Glu335Lys	p.E335K	ENST00000268712	NM_006311.3	335	Gaa/Aaa	10/46	1	2	FACETS	0.868	0.779	0.963	0.868	0.779	0.963	CLONAL	1	TRUE	1	0.34	2		519	725	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068450	16068450	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	16	118	0	ENST00000268712.3:c.461A>G	p.Glu154Gly	p.E154G	ENST00000268712	NM_006311.3	154	gAa/gGa	5/46	1	2	FACETS	0.45	0.333	0.589	0.45	0.333	0.589	SUBCLONAL	1	TRUE	1	0.34	2		118	209	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075295	16075295	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	65	555	0	ENST00000268712.3:c.257G>T	p.Arg86Ile	p.R86I	ENST00000268712	NM_006311.3	86	aGa/aTa	4/46	1	2	FACETS	0.465	0.402	0.534	0.465	0.402	0.534	SUBCLONAL	1	TRUE	1	0.34	2		555	822	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17129591	17129591	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	88	818	1	ENST00000285071.4:c.295G>T	p.Asp99Tyr	p.D99Y	ENST00000285071	NM_144997.5	99	Gat/Tat	5/14	1	2	FACETS	0.425	0.375	0.479	0.425	0.375	0.479	SUBCLONAL	1	TRUE	1	0.34	2		819	1218	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486064	29486064	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782772	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	57	315	0	ENST00000356175.3:c.241C>A	p.Leu81Ile	p.L81I	ENST00000356175	NM_000267.3	81	Ctc/Atc	3/57	1	2	FACETS	0.791	0.68	0.911	0.791	0.68	0.911	CLONAL	1	TRUE	1	0.34	2		315	424	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	85	684	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	1	2	FACETS	0.52	0.459	0.587	0.52	0.459	0.587	SUBCLONAL	1	TRUE	1	0.34	2		684	961	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562982	29562982	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1306237220	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	145	557	1	ENST00000356175.3:c.3917G>A	p.Arg1306Gln	p.R1306Q	ENST00000356175	NM_000267.3	1306	cGa/cAa	29/57	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.34	2		558	782	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684332	29684332	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	56	513	0	ENST00000356175.3:c.7852C>A	p.Leu2618Ile	p.L2618I	ENST00000356175	NM_000267.3	2618	Ctt/Att	53/57	1	2	FACETS	0.455	0.389	0.527	0.455	0.389	0.527	SUBCLONAL	1	TRUE	1	0.34	2		513	724	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315354	30315354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1480541649	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	136	537	0	ENST00000322652.5:c.1039G>A	p.Glu347Lys	p.E347K	ENST00000322652	NM_015355.2	347	Gaa/Aaa	10/16	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.34	2		537	787	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325698	30325698	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	59	356	0	ENST00000322652.5:c.1896G>T	p.Met632Ile	p.M632I	ENST00000322652	NM_015355.2	632	atG/atT	16/16	1	2	FACETS	0.674	0.58	0.776	0.674	0.58	0.776	SUBCLONAL	1	TRUE	1	0.34	2		356	515	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679887	33679887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200734680	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	135	679	0	ENST00000308377.4:c.2194C>T	p.Arg732Cys	p.R732C	ENST00000308377	NM_152270.3	732	Cgc/Tgc	5/5	1	2	FACETS	0.736	0.668	0.808	0.736	0.668	0.808	SUBCLONAL	1	TRUE	1	0.34	2		679	1079	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33680998	33680998	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	154	568	0	ENST00000308377.4:c.1279A>C	p.Ile427Leu	p.I427L	ENST00000308377	NM_152270.3	427	Ata/Cta	4/5	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.34	2		568	867	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690068	33690068	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	64	705	0	ENST00000308377.4:c.759G>T	p.Lys253Asn	p.K253N	ENST00000308377	NM_152270.3	253	aaG/aaT	2/5	1	2	FACETS	0.362	0.312	0.416	0.362	0.312	0.416	SUBCLONAL	1	TRUE	1	0.34	2		705	1041	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690100	33690100	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	66	630	0	ENST00000308377.4:c.727G>T	p.Gly243Ter	p.G243*	ENST00000308377	NM_152270.3	243	Gga/Tga	2/5	1	2	FACETS	0.377	0.326	0.433	0.377	0.326	0.433	SUBCLONAL	1	TRUE	1	0.34	2		630	1030	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690321	33690321	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	145	705	0	ENST00000308377.4:c.506T>G	p.Ile169Ser	p.I169S	ENST00000308377	NM_152270.3	169	aTt/aGt	2/5	1	2	FACETS	0.852	0.776	0.932	0.852	0.776	0.932	CLONAL	1	TRUE	1	0.34	2		705	1001	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690360	33690360	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	130	672	0	ENST00000308377.4:c.467G>T	p.Arg156Met	p.R156M	ENST00000308377	NM_152270.3	156	aGg/aTg	2/5	1	2	FACETS	0.772	0.699	0.848	0.772	0.699	0.848	SUBCLONAL	1	TRUE	1	0.34	2		672	991	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686970	37686970	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	199	650	0	ENST00000447079.4:c.3874G>A	p.Glu1292Lys	p.E1292K	ENST00000447079	NM_015083.1	1292	Gag/Aag	14/14	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.34	2		650	1079	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40458275	40458275	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	122	496	0	ENST00000345506.4:c.1490C>A	p.Ala497Asp	p.A497D	ENST00000345506	NM_003152.3	497	gCc/gAc	14/20	1	2	FACETS	0.867	0.783	0.955	0.867	0.783	0.955	CLONAL	1	TRUE	1	0.34	2		496	828	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40458327	40458327	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	10	108	0	ENST00000345506.4:c.1542A>C	p.Lys514Asn	p.K514N	ENST00000345506	NM_003152.3	514	aaA/aaC	14/20	1	2	FACETS	0.338	0.229	0.475	0.338	0.229	0.475	SUBCLONAL	1	TRUE	1	0.34	2		108	174	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40857127	40857127	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	57	520	0	ENST00000428826.2:c.1914C>A	p.Phe638Leu	p.F638L	ENST00000428826		638	ttC/ttA	17/21	1	2	FACETS	0.415	0.355	0.481	0.415	0.355	0.481	SUBCLONAL	1	TRUE	1	0.34	2		520	807	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243774	41243774	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs431825399	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	140	664	0	ENST00000357654.3:c.3774G>T	p.Glu1258Asp	p.E1258D	ENST00000357654	NM_007294.3	1258	gaG/gaT	10/23	1	2	FACETS	0.853	0.776	0.934	0.853	0.776	0.934	CLONAL	1	TRUE	1	0.34	2		664	965	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244826	41244826	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs80356978	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	140	545	0	ENST00000357654.3:c.2722G>T	p.Glu908Ter	p.E908*	ENST00000357654	NM_007294.3	908	Gaa/Taa	10/23	1	2	FACETS	0.956	0.871	1	0.956	0.871	1	CLONAL	1	TRUE	1	0.34	2		545	861	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244869	41244869	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781771	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	138	587	0	ENST00000357654.3:c.2679G>T	p.Lys893Asn	p.K893N	ENST00000357654	NM_007294.3	893	aaG/aaT	10/23	1	2	FACETS	0.907	0.825	0.993	0.907	0.825	0.993	CLONAL	1	TRUE	1	0.34	2		587	895	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245263	41245263	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	85	628	0	ENST00000357654.3:c.2285G>T	p.Arg762Ile	p.R762I	ENST00000357654	NM_007294.3	762	aGa/aTa	10/23	1	2	FACETS	0.548	0.483	0.618	0.548	0.483	0.618	SUBCLONAL	1	TRUE	1	0.34	2		628	912	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55754375	55754375	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	57	473	0	ENST00000284073.2:c.973A>C	p.Asn325His	p.N325H	ENST00000284073	NM_138962.2	325	Aat/Cat	13/14	1	2	FACETS	0.421	0.36	0.487	0.421	0.36	0.487	SUBCLONAL	1	TRUE	1	0.34	2		473	797	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448309	56448309	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781449421	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	226	891	0	ENST00000407977.2:c.338G>A	p.Arg113Gln	p.R113Q	ENST00000407977		113	cGa/cAa	3/10	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.34	2		891	1304	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740668	58740668	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs759850701	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	191	717	0	ENST00000305921.3:c.1573G>T	p.Glu525Ter	p.E525*	ENST00000305921	NM_003620.3	525	Gaa/Taa	6/6	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.34	2		717	1116	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740814	58740814	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	187	768	0	ENST00000305921.3:c.1719G>T	p.Lys573Asn	p.K573N	ENST00000305921	NM_003620.3	573	aaG/aaT	6/6	1	2	FACETS	0.941	0.868	1	0.941	0.868	1	CLONAL	1	TRUE	1	0.34	2		768	1169	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926518	59926518	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1330277587	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	89	438	0	ENST00000259008.2:c.479G>T	p.Arg160Ile	p.R160I	ENST00000259008	NM_032043.2	160	aGa/aTa	5/20	1	2	FACETS	0.903	0.802	1	0.903	0.802	1	CLONAL	1	TRUE	1	0.34	2		438	580	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554341	63554341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767445163	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	196	769	1	ENST00000307078.5:c.398C>T	p.Ala133Val	p.A133V	ENST00000307078	NM_004655.3	133	gCg/gTg	2/11	1	2	FACETS	0.971	0.898	1	0.971	0.898	1	CLONAL	1	TRUE	1	0.34	2		770	1187	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78765281	78765281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1361255662	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	140	512	0	ENST00000306801.3:c.862C>T	p.Pro288Ser	p.P288S	ENST00000306801	NM_020761.2	288	Cct/Tct	7/34	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.34	2		512	810	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867622	78867622	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	209	840	0	ENST00000306801.3:c.2358G>T	p.Lys786Asn	p.K786N	ENST00000306801	NM_020761.2	786	aaG/aaT	20/34	1	2	FACETS	0.977	0.906	1	0.977	0.906	1	CLONAL	1	TRUE	1	0.34	2		840	1258	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756651	756651	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	89	631	0	ENST00000314574.4:c.177G>T	p.Met59Ile	p.M59I	ENST00000314574	NM_005433.3	59	atG/atT	2/12	1	2	FACETS	0.493	0.436	0.555	0.493	0.436	0.555	SUBCLONAL	1	TRUE	1	0.34	2		631	1061	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604790	48604790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	163	710	0	ENST00000342988.3:c.1612G>A	p.Glu538Lys	p.E538K	ENST00000342988	NM_005359.5	538	Gaa/Aaa	12/12	1	2	FACETS	0.943	0.864	1	0.943	0.864	1	CLONAL	1	TRUE	1	0.34	2		710	1017	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56409133	56409133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	90	389	0	ENST00000348428.3:c.1640C>T	p.Ala547Val	p.A547V	ENST00000348428	NM_006785.3	547	gCt/gTt	14/17	1	2	FACETS	0.954	0.848	1	0.954	0.848	1	CLONAL	1	TRUE	1	0.34	2		389	555	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212111	5212111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	189	918	0	ENST00000357368.4:c.4920C>A	p.Phe1640Leu	p.F1640L	ENST00000357368	NM_002850.3	1640	ttC/ttA	32/38	1	2	FACETS	0.932	0.86	1	0.932	0.86	1	CLONAL	1	TRUE	1	0.34	2		918	1193	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7163175	7163175	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1283232736	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	194	651	0	ENST00000302850.5:c.1897A>G	p.Asn633Asp	p.N633D	ENST00000302850	NM_000208.2	633	Aac/Gac	9/22	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.34	2		651	1090	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123685	11123685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	174	701	0	ENST00000358026.2:c.2335G>A	p.Asp779Asn	p.D779N	ENST00000358026	NM_001128849.1	779	Gac/Aac	16/36	1	2	FACETS	0.922	0.848	1	0.922	0.848	1	CLONAL	1	TRUE	1	0.34	2		701	1110	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130361	11130361	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	165	586	1	ENST00000358026.2:c.2600A>C	p.Lys867Thr	p.K867T	ENST00000358026	NM_001128849.1	867	aAg/aCg	18/36	1	2	FACETS	0.989	0.908	1	0.989	0.908	1	CLONAL	1	TRUE	1	0.34	2		587	981	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15364969	15364969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1394299823	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	74	491	0	ENST00000263377.2:c.2152G>A	p.Glu718Lys	p.E718K	ENST00000263377	NM_058243.2	718	Gaa/Aaa	11/20	1	2	FACETS	0.491	0.429	0.559	0.491	0.429	0.559	SUBCLONAL	1	TRUE	1	0.34	2		491	886	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15365064	15365064	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	149	545	0	ENST00000263377.2:c.2057T>G	p.Val686Gly	p.V686G	ENST00000263377	NM_058243.2	686	gTt/gGt	11/20	1	2	FACETS	0.914	0.834	0.997	0.914	0.834	0.997	CLONAL	1	TRUE	1	0.34	2		545	959	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366129	15366129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1468704458	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	184	643	0	ENST00000263377.2:c.2026C>T	p.Arg676Trp	p.R676W	ENST00000263377	NM_058243.2	676	Cgg/Tgg	10/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.34	2		643	957	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950424	17950424	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	153	669	0	ENST00000458235.1:c.1303A>G	p.Thr435Ala	p.T435A	ENST00000458235	NM_000215.3	435	Aca/Gca	10/24	1	2	FACETS	0.847	0.773	0.924	0.847	0.773	0.924	CLONAL	1	TRUE	1	0.34	2		669	1063	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954674	17954674	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	205	866	0	ENST00000458235.1:c.220G>T	p.Ala74Ser	p.A74S	ENST00000458235	NM_000215.3	74	Gcc/Tcc	3/24	1	2	FACETS	0.893	0.827	0.963	0.893	0.827	0.963	CLONAL	1	TRUE	1	0.34	2		866	1350	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211219	36211219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765836382	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	214	785	0	ENST00000222270.7:c.970G>A	p.Glu324Lys	p.E324K	ENST00000222270	NM_014727.1	324	Gaa/Aaa	3/37	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.34	2		785	1255	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211894	36211894	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	227	837	0	ENST00000222270.7:c.1645G>T	p.Glu549Ter	p.E549*	ENST00000222270	NM_014727.1	549	Gaa/Taa	3/37	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.34	2		837	1309	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222962	36222962	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs181607228	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	266	1000	0	ENST00000222270.7:c.5591G>A	p.Arg1864Gln	p.R1864Q	ENST00000222270	NM_014727.1	1864	cGa/cAa	27/37	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.34	2		1000	1382	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383677	42383677	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1221821073	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	215	819	0	ENST00000221972.3:c.452T>C	p.Ile151Thr	p.I151T	ENST00000221972	NM_021601.3	151	aTc/aCc	3/5	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.34	2		819	1221	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423433	47423433	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	150	618	0	ENST00000404338.3:c.1501G>T	p.Glu501Ter	p.E501*	ENST00000404338	NM_004491.4	501	Gaa/Taa	1/6	1	2	FACETS	0.918	0.839	1	0.918	0.839	1	CLONAL	1	TRUE	1	0.34	2		618	961	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964903	25964903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561088610	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	200	722	1	ENST00000435504.4:c.4303C>T	p.Arg1435Trp	p.R1435W	ENST00000435504		1435	Cgg/Tgg	13/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.34	2		723	1018	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966540	25966540	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	196	737	0	ENST00000435504.4:c.2666C>A	p.Ser889Tyr	p.S889Y	ENST00000435504		889	tCt/tAt	13/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.34	2		737	1101	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976476	25976476	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	94	512	0	ENST00000435504.4:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000435504		357	Cga/Tga	11/13	1	2	FACETS	0.839	0.747	0.937	0.839	0.747	0.937	CLONAL	1	TRUE	1	0.34	2		512	659	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015053	27015053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151098324	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	144	647	0	ENST00000335756.4:c.155G>A	p.Arg52Gln	p.R52Q	ENST00000335756	NM_001809.3	52	cGa/cAa	2/5	1	2	FACETS	0.877	0.799	0.959	0.877	0.799	0.959	CLONAL	1	TRUE	1	0.34	2		647	966	SUCCESS
ALK	238	MSKCC	GRCh37	2	29420510	29420510	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	74	636	0	ENST00000389048.3:c.3971C>A	p.Ser1324Tyr	p.S1324Y	ENST00000389048	NM_004304.4	1324	tCt/tAt	27/29	1	2	FACETS	0.449	0.392	0.511	0.449	0.392	0.511	SUBCLONAL	1	TRUE	1	0.34	2		636	969	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443676	29443676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56315533	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	94	688	0	ENST00000389048.3:c.3541C>T	p.Arg1181Cys	p.R1181C	ENST00000389048	NM_004304.4	1181	Cgc/Tgc	23/29	1	2	FACETS	0.517	0.458	0.579	0.517	0.458	0.579	SUBCLONAL	1	TRUE	1	0.34	2		688	1070	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449913	29449913	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	246	895	0	ENST00000389048.3:c.2942T>G	p.Ile981Ser	p.I981S	ENST00000389048	NM_004304.4	981	aTt/aGt	18/29	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.34	2		895	1392	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606679	29606679	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs865931787	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	240	702	0	ENST00000389048.3:c.1201C>T	p.Arg401Ter	p.R401*	ENST00000389048	NM_004304.4	401	Cga/Tga	5/29	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.34	2		702	1014	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222281	39222281	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572955351	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	53	489	0	ENST00000402219.2:c.3329C>T	p.Ser1110Leu	p.S1110L	ENST00000402219	NM_005633.3	1110	tCg/tTg	20/23	1	2	FACETS	0.438	0.373	0.51	0.438	0.373	0.51	SUBCLONAL	1	TRUE	1	0.34	2		489	711	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234311	39234311	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	66	308	0	ENST00000402219.2:c.2534T>G	p.Leu845Ter	p.L845*	ENST00000402219	NM_005633.3	845	tTa/tGa	16/23	1	2	FACETS	0.828	0.72	0.944	0.828	0.72	0.944	CLONAL	1	TRUE	1	0.34	2		308	469	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234312	39234312	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	31	304	0	ENST00000402219.2:c.2533T>G	p.Leu845Val	p.L845V	ENST00000402219	NM_005633.3	845	Tta/Gta	16/23	1	2	FACETS	0.39	0.315	0.475	0.39	0.315	0.475	SUBCLONAL	1	TRUE	1	0.34	2		304	468	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241973	39241973	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	60	293	0	ENST00000402219.2:c.1873C>T	p.Arg625Trp	p.R625W	ENST00000402219	NM_005633.3	625	Cgg/Tgg	11/23	1	2	FACETS	0.931	0.806	1	0.931	0.806	1	CLONAL	1	TRUE	1	0.34	2		293	379	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698180	47698180	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63751411	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	66	129	0	ENST00000233146.2:c.1738G>T	p.Glu580Ter	p.E580*	ENST00000233146	NM_000251.2	580	Gaa/Taa	11/16	1	2	FACETS	0.761	0.662	0.869	0.761	0.662	0.869	SUBCLONAL	1	TRUE	1	0.34	2		129	510	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702410	47702410	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs267607986	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	69	324	0	ENST00000233146.2:c.2005+1G>A		p.X669_splice	ENST00000233146	NM_000251.2	669			1	2	FACETS	0.88	0.769	1	0.88	0.769	1	CLONAL	1	TRUE	1	0.34	2		324	461	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026290	48026290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147737737	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	154	733	1	ENST00000234420.5:c.1168G>A	p.Asp390Asn	p.D390N	ENST00000234420	NM_000179.2	390	Gat/Aat	4/10	1	2	FACETS	0.886	0.81	0.966	0.886	0.81	0.966	CLONAL	1	TRUE	1	0.34	2		734	1022	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027750	48027750	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	130	537	0	ENST00000234420.5:c.2628A>C	p.Glu876Asp	p.E876D	ENST00000234420	NM_000179.2	876	gaA/gaC	4/10	1	2	FACETS	0.945	0.858	1	0.945	0.858	1	CLONAL	1	TRUE	1	0.34	2		537	809	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033961	48033961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	34	417	0	ENST00000234420.5:c.4045G>A	p.Ala1349Thr	p.A1349T	ENST00000234420	NM_000179.2	1349	Gct/Act	10/10	1	2	FACETS	0.328	0.267	0.397	0.328	0.267	0.397	SUBCLONAL	1	TRUE	1	0.34	2		417	610	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61706056	61706056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	123	525	0	ENST00000401558.2:c.3115G>A	p.Glu1039Lys	p.E1039K	ENST00000401558	NM_003400.3	1039	Gaa/Aaa	25/25	1	2	FACETS	0.883	0.799	0.973	0.883	0.799	0.973	CLONAL	1	TRUE	1	0.34	2		525	819	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715373	61715373	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	87	413	0	ENST00000401558.2:c.2240G>T	p.Ser747Ile	p.S747I	ENST00000401558	NM_003400.3	747	aGt/aTt	19/25	1	2	FACETS	0.939	0.833	1	0.939	0.833	1	CLONAL	1	TRUE	1	0.34	2		413	545	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719832	61719832	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	92	504	0	ENST00000401558.2:c.1436A>C	p.Lys479Thr	p.K479T	ENST00000401558	NM_003400.3	479	aAg/aCg	14/25	1	2	FACETS	0.842	0.749	0.941	0.842	0.749	0.941	CLONAL	1	TRUE	1	0.34	2		504	643	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61720080	61720080	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	89	361	0	ENST00000401558.2:c.1354A>C	p.Asn452His	p.N452H	ENST00000401558	NM_003400.3	452	Aat/Cat	13/25	1	2	FACETS	0.95	0.844	1	0.95	0.844	1	CLONAL	1	TRUE	1	0.34	2		361	551	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726855	61726855	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	82	342	0	ENST00000401558.2:c.583A>C	p.Lys195Gln	p.K195Q	ENST00000401558	NM_003400.3	195	Aaa/Caa	7/25	1	2	FACETS	0.921	0.814	1	0.921	0.814	1	CLONAL	1	TRUE	1	0.34	2		342	524	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99203949	99203949	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1370549873	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	109	550	0	ENST00000074304.5:c.2812C>T	p.Arg938Ter	p.R938*	ENST00000074304	NM_001134224.1	938	Cga/Tga	26/26	1	2	FACETS	0.762	0.684	0.845	0.762	0.684	0.845	SUBCLONAL	1	TRUE	1	0.34	2		550	841	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872622	136872622	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	173	813	0	ENST00000241393.3:c.876C>A	p.Phe292Leu	p.F292L	ENST00000241393	NM_003467.2	292	ttC/ttA	2/2	1	2	FACETS	0.877	0.806	0.952	0.877	0.806	0.952	CLONAL	1	TRUE	1	0.34	2		813	1160	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873397	136873397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	161	643	1	ENST00000241393.3:c.101C>T	p.Ala34Val	p.A34V	ENST00000241393	NM_003467.2	34	gCt/gTt	2/2	1	2	FACETS	0.961	0.88	1	0.961	0.88	1	CLONAL	1	TRUE	1	0.34	2		644	986	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594066	158594066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769751827	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	110	562	0	ENST00000263640.3:c.1507G>A	p.Asp503Asn	p.D503N	ENST00000263640	NM_001105.4	503	Gac/Aac	11/11	1	2	FACETS	0.767	0.688	0.85	0.767	0.688	0.85	SUBCLONAL	1	TRUE	1	0.34	2		562	844	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096135	178096135	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	206	742	0	ENST00000397062.3:c.1196C>A	p.Ser399Tyr	p.S399Y	ENST00000397062	NM_006164.4	399	tCt/tAt	5/5	1	2	FACETS	0.993	0.92	1	0.993	0.92	1	CLONAL	1	TRUE	1	0.34	2		742	1220	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273266	198273266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	127	649	0	ENST00000335508.6:c.944G>A	p.Arg315Gln	p.R315Q	ENST00000335508	NM_012433.2	315	cGa/cAa	8/25	1	2	FACETS	0.796	0.721	0.876	0.796	0.721	0.876	SUBCLONAL	1	TRUE	1	0.34	2		649	938	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285193	198285193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	121	617	0	ENST00000335508.6:c.374C>T	p.Thr125Ile	p.T125I	ENST00000335508	NM_012433.2	125	aCc/aTc	4/25	1	2	FACETS	0.824	0.744	0.908	0.824	0.744	0.908	CLONAL	1	TRUE	1	0.34	2		617	864	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131278	202131278	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	89	664	0	ENST00000358485.4:c.246G>T	p.Lys82Asn	p.K82N	ENST00000358485	NM_001080125.1	82	aaG/aaT	2/9	1	2	FACETS	0.51	0.451	0.573	0.51	0.451	0.573	SUBCLONAL	1	TRUE	1	0.34	2		664	1027	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136289	202136289	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	138	528	0	ENST00000358485.4:c.533C>A	p.Ser178Tyr	p.S178Y	ENST00000358485	NM_001080125.1	178	tCt/tAt	3/9	1	2	FACETS	0.982	0.893	1	0.982	0.893	1	CLONAL	1	TRUE	1	0.34	2		528	827	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149974	202149974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301592633	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	106	835	0	ENST00000358485.4:c.1415G>A	p.Arg472Gln	p.R472Q	ENST00000358485	NM_001080125.1	472	cGa/cAa	8/9	1	2	FACETS	0.495	0.442	0.552	0.495	0.442	0.552	SUBCLONAL	1	TRUE	1	0.34	2		835	1259	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736197	204736197	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	71	512	0	ENST00000302823.3:c.554C>A	p.Ser185Tyr	p.S185Y	ENST00000302823	NM_005214.4	185	tCt/tAt	3/4	1	2	FACETS	0.461	0.402	0.526	0.461	0.402	0.526	SUBCLONAL	1	TRUE	1	0.34	2		512	905	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437278	220437278	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	66	788	0	ENST00000243786.2:c.182G>T	p.Arg61Ile	p.R61I	ENST00000243786	NM_002191.3	61	aGa/aTa	1/2	1	2	FACETS	0.323	0.279	0.371	0.323	0.279	0.371	SUBCLONAL	1	TRUE	1	0.34	2		788	1203	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346750	225346750	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	34	459	0	ENST00000264414.4:c.1888G>A	p.Ala630Thr	p.A630T	ENST00000264414	NM_003590.4	630	Gcc/Acc	14/16	1	2	FACETS	0.323	0.263	0.391	0.323	0.263	0.391	SUBCLONAL	1	TRUE	1	0.34	2		459	619	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661884	227661884	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	217	852	0	ENST00000305123.5:c.1571G>T	p.Arg524Ile	p.R524I	ENST00000305123	NM_005544.2	524	aGa/aTa	1/2	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.34	2		852	1231	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242800926	242800926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	147	747	0	ENST00000334409.5:c.65G>A	p.Gly22Glu	p.G22E	ENST00000334409	NM_005018.2	22	gGa/gAa	1/5	1	2	FACETS	0.823	0.75	0.899	0.823	0.75	0.899	CLONAL	1	TRUE	1	0.34	2		747	1051	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546557	9546557	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	161	630	0	ENST00000353224.5:c.1465G>T	p.Glu489Ter	p.E489*	ENST00000353224	NM_177990.2	489	Gaa/Taa	5/10	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.34	2		630	892	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546725	9546725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210292896	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	160	843	0	ENST00000353224.5:c.1297C>T	p.Arg433Trp	p.R433W	ENST00000353224	NM_177990.2	433	Cgg/Tgg	5/10	1	2	FACETS	0.873	0.799	0.95	0.873	0.799	0.95	CLONAL	1	TRUE	1	0.34	2		843	1078	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546847	9546847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	188	808	0	ENST00000353224.5:c.1175C>T	p.Ser392Leu	p.S392L	ENST00000353224	NM_177990.2	392	tCg/tTg	5/10	1	2	FACETS	0.925	0.853	1	0.925	0.853	1	CLONAL	1	TRUE	1	0.34	2		808	1196	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024197	31024197	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	181	729	0	ENST00000375687.4:c.3682G>T	p.Glu1228Ter	p.E1228*	ENST00000375687	NM_015338.5	1228	Gaa/Taa	13/13	1	2	FACETS	0.961	0.885	1	0.961	0.885	1	CLONAL	1	TRUE	1	0.34	2		729	1108	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383226	31383226	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs376213530	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	63	748	0	ENST00000328111.2:c.1138C>T	p.Arg380Ter	p.R380*	ENST00000328111	NM_006892.3	380	Cga/Tga	11/23	1	2	FACETS	0.339	0.292	0.39	0.339	0.292	0.39	SUBCLONAL	1	TRUE	1	0.34	2		748	1094	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39690063	39690063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	120	596	0	ENST00000361337.2:c.88G>A	p.Asp30Asn	p.D30N	ENST00000361337	NM_003286.2	30	Gat/Aat	3/21	1	2	FACETS	0.858	0.774	0.946	0.858	0.774	0.946	CLONAL	1	TRUE	1	0.34	2		596	823	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39726971	39726971	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	109	447	0	ENST00000361337.2:c.969G>T	p.Glu323Asp	p.E323D	ENST00000361337	NM_003286.2	323	gaG/gaT	11/21	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.34	2		447	637	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40864896	40864896	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	33	410	0	ENST00000373198.4:c.2372G>T	p.Arg791Ile	p.R791I	ENST00000373198	NM_133170.3	791	aGa/aTa	16/32	1	2	FACETS	0.36	0.293	0.437	0.36	0.293	0.437	SUBCLONAL	1	TRUE	1	0.34	2		410	539	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944562	40944562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868189942	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	82	712	0	ENST00000373198.4:c.1940C>T	p.Ser647Leu	p.S647L	ENST00000373198	NM_133170.3	647	tCg/tTg	12/32	1	2	FACETS	0.472	0.415	0.534	0.472	0.415	0.534	SUBCLONAL	1	TRUE	1	0.34	2		712	1022	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944600	40944600	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	157	660	0	ENST00000373198.4:c.1902G>T	p.Gln634His	p.Q634H	ENST00000373198	NM_133170.3	634	caG/caT	12/32	1	2	FACETS	0.966	0.884	1	0.966	0.884	1	CLONAL	1	TRUE	1	0.34	2		660	956	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262885	46262885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761607812	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	134	528	0	ENST00000371998.3:c.1058G>A	p.Arg353Gln	p.R353Q	ENST00000371998		353	cGa/cAa	10/23	1	2	FACETS	0.985	0.896	1	0.985	0.896	1	CLONAL	1	TRUE	1	0.34	2		528	800	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268333	46268333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747268479	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	134	650	0	ENST00000371998.3:c.2720G>A	p.Arg907Gln	p.R907Q	ENST00000371998		907	cGa/cAa	15/23	1	2	FACETS	0.875	0.794	0.96	0.875	0.794	0.96	CLONAL	1	TRUE	1	0.34	2		650	901	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281208	46281208	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	110	695	0	ENST00000371998.3:c.4005G>T	p.Met1335Ile	p.M1335I	ENST00000371998		1335	atG/atT	21/23	1	2	FACETS	0.62	0.556	0.689	0.62	0.556	0.689	SUBCLONAL	1	TRUE	1	0.34	2		695	1043	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252889	36252889	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	155	626	0	ENST00000300305.3:c.473T>G	p.Phe158Cys	p.F158C	ENST00000300305		158	tTt/tGt	4/8	1	2	FACETS	0.959	0.877	1	0.959	0.877	1	CLONAL	1	TRUE	1	0.34	2		626	951	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39762950	39762950	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	102	454	0	ENST00000288319.7:c.886C>A	p.Leu296Ile	p.L296I	ENST00000288319	NM_182918.3	296	Ctt/Att	9/10	1	2	FACETS	0.885	0.792	0.983	0.885	0.792	0.983	CLONAL	1	TRUE	1	0.34	2		454	678	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657017	45657017	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	176	692	0	ENST00000407780.3:c.139T>G	p.Leu47Val	p.L47V	ENST00000407780	NM_001283052.1	47	Tta/Gta	3/7	1	2	FACETS	0.884	0.813	0.959	0.884	0.813	0.959	CLONAL	1	TRUE	1	0.34	2		692	1171	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24134006	24134006	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	180	773	1	ENST00000263121.7:c.157C>T	p.Arg53Ter	p.R53*	ENST00000263121	NM_003073.3	53	Cga/Tga	2/9	1	2	FACETS	0.933	0.859	1	0.933	0.859	1	CLONAL	1	TRUE	1	0.34	2		774	1135	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29106023	29106023	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587782152	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	29	230	0	ENST00000328354.6:c.817G>T	p.Glu273Ter	p.E273*	ENST00000328354	NM_007194.3	273	Gaa/Taa	7/15	1	2	FACETS	0.517	0.415	0.632	0.517	0.415	0.632	SUBCLONAL	1	TRUE	1	0.34	2		230	330	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29383089	29383089	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	61	667	0	ENST00000544604.2:c.326A>C	p.Asn109Thr	p.N109T	ENST00000544604	NM_001206998.1	109	aAc/aCc	2/9	1	2	FACETS	0.373	0.32	0.43	0.373	0.32	0.43	SUBCLONAL	1	TRUE	1	0.34	2		667	963	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038196	30038196	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	129	546	0	ENST00000338641.4:c.369G>T	p.Lys123Asn	p.K123N	ENST00000338641	NM_000268.3	123	aaG/aaT	4/16	1	2	FACETS	0.928	0.841	1	0.928	0.841	1	CLONAL	1	TRUE	1	0.34	2		546	818	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458537	12458537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140204299	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	92	730	0	ENST00000287820.6:c.1154G>A	p.Arg385Gln	p.R385Q	ENST00000287820	NM_015869.4	385	cGa/cAa	6/7	1	2	FACETS	0.496	0.44	0.557	0.496	0.44	0.557	SUBCLONAL	1	TRUE	1	0.34	2		730	1090	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37059066	37059066	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	159	652	0	ENST00000231790.2:c.860A>G	p.Asn287Ser	p.N287S	ENST00000231790	NM_000249.3	287	aAc/aGc	10/19	1	2	FACETS	0.978	0.896	1	0.978	0.896	1	CLONAL	1	TRUE	1	0.34	2		652	956	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37061871	37061871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750796	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	97	663	0	ENST00000231790.2:c.955G>A	p.Glu319Lys	p.E319K	ENST00000231790	NM_000249.3	319	Gag/Aag	11/19	1	2	FACETS	0.534	0.475	0.598	0.534	0.475	0.598	SUBCLONAL	1	TRUE	1	0.34	2		663	1068	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180299	38180299	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1356	115	901	0	ENST00000396334.3:c.147C>A	p.Phe49Leu	p.F49L	ENST00000396334	NM_002468.4	49	ttC/ttA	1/5	1	2	FACETS	0.46	0.412	0.51	0.46	0.412	0.51	SUBCLONAL	1	TRUE	1	0.34	2		901	1471	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266016	41266016	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	65	583	0	ENST00000349496.5:c.14-1G>A		p.X5_splice	ENST00000349496	NM_001904.3	5			1	2	FACETS	0.489	0.423	0.561	0.489	0.423	0.561	SUBCLONAL	1	TRUE	1	0.34	2		583	782	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277291	41277291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	130	412	1	ENST00000349496.5:c.1760G>A	p.Arg587Gln	p.R587Q	ENST00000349496	NM_001904.3	587	cGa/cAa	11/15	1	2	FACETS	0.881	0.799	0.968	0.881	0.799	0.968	CLONAL	1	TRUE	1	0.34	2		413	868	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164259	47164259	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	50	514	0	ENST00000409792.3:c.1867G>T	p.Asp623Tyr	p.D623Y	ENST00000409792	NM_014159.6	623	Gat/Tat	3/21	1	2	FACETS	0.403	0.341	0.471	0.403	0.341	0.471	SUBCLONAL	1	TRUE	1	0.34	2		514	730	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165140	47165140	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540015912	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	105	466	0	ENST00000409792.3:c.986G>A	p.Arg329Gln	p.R329Q	ENST00000409792	NM_014159.6	329	cGg/cAg	3/21	1	2	FACETS	0.885	0.793	0.982	0.885	0.793	0.982	CLONAL	1	TRUE	1	0.34	2		466	698	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165167	47165167	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326993979	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	118	498	0	ENST00000409792.3:c.959G>A	p.Gly320Asp	p.G320D	ENST00000409792	NM_014159.6	320	gGt/gAt	3/21	1	2	FACETS	0.99	0.894	1	0.99	0.894	1	CLONAL	1	TRUE	1	0.34	2		498	701	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165465	47165465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	191	768	1	ENST00000409792.3:c.661G>A	p.Val221Ile	p.V221I	ENST00000409792	NM_014159.6	221	Gtt/Att	3/21	1	2	FACETS	0.897	0.827	0.969	0.897	0.827	0.969	CLONAL	1	TRUE	1	0.34	2		769	1253	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165843	47165843	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	151	693	0	ENST00000409792.3:c.283G>T	p.Glu95Ter	p.E95*	ENST00000409792	NM_014159.6	95	Gaa/Taa	3/21	1	2	FACETS	0.808	0.738	0.882	0.808	0.738	0.882	CLONAL	1	TRUE	1	0.34	2		693	1099	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49929262	49929262	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	177	571	0	ENST00000296474.3:c.3281G>A	p.Gly1094Glu	p.G1094E	ENST00000296474	NM_002447.2	1094	gGa/gAa	15/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.34	2		571	963	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	136	577	0	ENST00000394830.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000394830	NM_018313.4	710	Cga/Tga	17/30	1	2	FACETS	0.897	0.815	0.983	0.897	0.815	0.983	CLONAL	1	TRUE	1	0.34	2		577	892	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651331	52651331	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	150	590	0	ENST00000394830.3:c.1765G>A	p.Asp589Asn	p.D589N	ENST00000394830	NM_018313.4	589	Gac/Aac	15/30	1	2	FACETS	0.955	0.872	1	0.955	0.872	1	CLONAL	1	TRUE	1	0.34	2		590	924	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63898395	63898395	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	153	620	0	ENST00000398590.3:c.121C>A	p.Pro41Thr	p.P41T	ENST00000398590	NM_001177387.1	41	Ccg/Acg	3/14	1	2	FACETS	0.965	0.882	1	0.965	0.882	1	CLONAL	1	TRUE	1	0.34	2		620	933	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63898579	63898579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253633126	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	212	939	0	ENST00000398590.3:c.305C>T	p.Ser102Phe	p.S102F	ENST00000398590	NM_001177387.1	102	tCc/tTc	3/14	1	2	FACETS	0.886	0.821	0.954	0.886	0.821	0.954	CLONAL	1	TRUE	1	0.34	2		939	1408	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63975917	63975917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	197	901	0	ENST00000398590.3:c.1427C>T	p.Ser476Phe	p.S476F	ENST00000398590	NM_001177387.1	476	tCt/tTt	10/14	1	2	FACETS	0.899	0.831	0.97	0.899	0.831	0.97	CLONAL	1	TRUE	1	0.34	2		901	1289	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014097	70014097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757354709	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	197	721	0	ENST00000394351.3:c.958G>A	p.Val320Ile	p.V320I	ENST00000394351	NM_000248.3	320	Gtt/Att	9/9	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.34	2		721	1045	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021785	71021785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs112795301	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	179	556	4	ENST00000318789.4:c.1573C>T	p.Arg525Ter	p.R525*	ENST00000318789	NM_032682.5	525	Cga/Tga	18/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.34	2		560	981	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72881574	72881574	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774166433	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	52	458	0	ENST00000325599.8:c.545G>A	p.Arg182Gln	p.R182Q	ENST00000325599	NM_018130.2	182	cGa/cAa	5/11	1	2	FACETS	0.394	0.334	0.459	0.394	0.334	0.459	SUBCLONAL	1	TRUE	1	0.34	2		458	777	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114601	73114601	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs775783057	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	31	354	0	ENST00000356692.5:c.982G>T	p.Glu328Ter	p.E328*	ENST00000356692		328	Gaa/Taa	9/9	1	2	FACETS	0.389	0.314	0.474	0.389	0.314	0.474	SUBCLONAL	1	TRUE	1	0.34	2		354	469	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259409	89259409	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	145	592	0	ENST00000336596.2:c.553G>T	p.Asp185Tyr	p.D185Y	ENST00000336596	NM_005233.5	185	Gat/Tat	3/17	1	2	FACETS	0.863	0.787	0.944	0.863	0.787	0.944	CLONAL	1	TRUE	1	0.34	2		592	988	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670362	134670362	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	191	757	0	ENST00000398015.3:c.273C>A	p.Phe91Leu	p.F91L	ENST00000398015	NM_004441.4	91	ttC/ttA	3/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.34	2		757	987	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884812	134884812	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	65	595	0	ENST00000398015.3:c.1588G>T	p.Asp530Tyr	p.D530Y	ENST00000398015	NM_004441.4	530	Gat/Tat	8/16	1	2	FACETS	0.455	0.393	0.522	0.455	0.393	0.522	SUBCLONAL	1	TRUE	1	0.34	2		595	841	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453486	138453486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451809865	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	78	408	0	ENST00000289153.2:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000289153	NM_006219.2	321	cGa/cAa	5/22	1	2	FACETS	0.842	0.741	0.95	0.842	0.741	0.95	CLONAL	1	TRUE	1	0.34	2		408	545	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178201	142178201	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	86	444	0	ENST00000350721.4:c.7217T>G	p.Leu2406Arg	p.L2406R	ENST00000350721	NM_001184.3	2406	cTt/cGt	43/47	1	2	FACETS	0.806	0.713	0.904	0.806	0.713	0.904	CLONAL	1	TRUE	1	0.34	2		444	628	SUCCESS
ATR	545	MSKCC	GRCh37	3	142224146	142224146	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	124	527	0	ENST00000350721.4:c.5032-1G>T		p.X1678_splice	ENST00000350721	NM_001184.3	1678			1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.34	2		527	704	SUCCESS
ATR	545	MSKCC	GRCh37	3	142232476	142232476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755364026	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	100	480	0	ENST00000350721.4:c.4508G>A	p.Arg1503Gln	p.R1503Q	ENST00000350721	NM_001184.3	1503	cGa/cAa	26/47	1	2	FACETS	0.836	0.747	0.93	0.836	0.747	0.93	CLONAL	1	TRUE	1	0.34	2		480	704	SUCCESS
ATR	545	MSKCC	GRCh37	3	142253965	142253965	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	51	453	0	ENST00000350721.4:c.3902T>G	p.Ile1301Ser	p.I1301S	ENST00000350721	NM_001184.3	1301	aTt/aGt	21/47	1	2	FACETS	0.554	0.47	0.645	0.554	0.47	0.645	SUBCLONAL	1	TRUE	1	0.34	2		453	542	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259851	142259851	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	132	539	0	ENST00000350721.4:c.3476T>C	p.Met1159Thr	p.M1159T	ENST00000350721	NM_001184.3	1159	aTg/aCg	18/47	1	2	FACETS	0.977	0.887	1	0.977	0.887	1	CLONAL	1	TRUE	1	0.34	2		539	795	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281637	142281637	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	111	450	1	ENST00000350721.4:c.607G>T	p.Glu203Ter	p.E203*	ENST00000350721	NM_001184.3	203	Gaa/Taa	4/47	1	2	FACETS	0.98	0.883	1	0.98	0.883	1	CLONAL	1	TRUE	1	0.34	2		451	666	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281802	142281802	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	103	483	0	ENST00000350721.4:c.442G>T	p.Glu148Ter	p.E148*	ENST00000350721	NM_001184.3	148	Gaa/Taa	4/47	1	2	FACETS	0.903	0.809	1	0.903	0.809	1	CLONAL	1	TRUE	1	0.34	2		483	671	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260177	149260177	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	176	683	0	ENST00000360632.3:c.716G>T	p.Arg239Ile	p.R239I	ENST00000360632	NM_015472.4	239	aGa/aTa	4/7	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.34	2		683	1006	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916651	178916651	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	118	471	0	ENST00000263967.3:c.38T>C	p.Ile13Thr	p.I13T	ENST00000263967	NM_006218.2	13	aTc/aCc	2/21	1	2	FACETS	0.912	0.823	1	0.912	0.823	1	CLONAL	1	TRUE	1	0.34	2		471	761	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952049	178952049	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242945375	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	145	549	0	ENST00000263967.3:c.3104C>T	p.Ala1035Val	p.A1035V	ENST00000263967	NM_006218.2	1035	gCt/gTt	21/21	1	2	FACETS	0.945	0.862	1	0.945	0.862	1	CLONAL	1	TRUE	1	0.34	2		549	903	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502876	186502876	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	176	626	0	ENST00000323963.5:c.334G>T	p.Glu112Ter	p.E112*	ENST00000323963		112	Gaa/Taa	4/11	1	2	FACETS	0.972	0.895	1	0.972	0.895	1	CLONAL	1	TRUE	1	0.34	2		626	1065	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451474	187451474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145456310	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	172	629	0	ENST00000232014.4:c.8C>T	p.Ser3Leu	p.S3L	ENST00000232014	NM_001130845.1	3	tCg/tTg	3/10	1	2	FACETS	0.978	0.899	1	0.978	0.899	1	CLONAL	1	TRUE	1	0.34	2		629	1035	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980404	1980404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	222	742	0	ENST00000382891.5:c.3866G>A	p.Gly1289Asp	p.G1289D	ENST00000382891	NM_133335.3	1289	gGc/gAc	22/22	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.34	2		742	1091	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129983	55129983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763718380	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	163	794	0	ENST00000257290.5:c.517G>A	p.Asp173Asn	p.D173N	ENST00000257290	NM_006206.4	173	Gac/Aac	4/23	1	2	FACETS	0.87	0.797	0.946	0.87	0.797	0.946	CLONAL	1	TRUE	1	0.34	2		794	1102	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131211	55131211	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	71	541	0	ENST00000257290.5:c.754G>T	p.Glu252Ter	p.E252*	ENST00000257290	NM_006206.4	252	Gaa/Taa	5/23	1	2	FACETS	0.52	0.453	0.593	0.52	0.453	0.593	SUBCLONAL	1	TRUE	1	0.34	2		541	803	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133894	55133894	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	134	501	1	ENST00000257290.5:c.1107G>T	p.Lys369Asn	p.K369N	ENST00000257290	NM_006206.4	369	aaG/aaT	7/23	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.34	2		502	724	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146523	55146523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	155	543	0	ENST00000257290.5:c.2197G>A	p.Asp733Asn	p.D733N	ENST00000257290	NM_006206.4	733	Gac/Aac	16/23	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.34	2		543	842	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146592	55146592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555347387	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	148	527	0	ENST00000257290.5:c.2266G>A	p.Asp756Asn	p.D756N	ENST00000257290	NM_006206.4	756	Gac/Aac	16/23	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.34	2		527	801	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152120	55152120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745464928	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	71	680	0	ENST00000257290.5:c.2552C>T	p.Ser851Leu	p.S851L	ENST00000257290	NM_006206.4	851	tCg/tTg	18/23	1	2	FACETS	0.442	0.385	0.505	0.442	0.385	0.505	SUBCLONAL	1	TRUE	1	0.34	2		680	944	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593628	55593628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	115	557	0	ENST00000288135.5:c.1694G>A	p.Gly565Glu	p.G565E	ENST00000288135	NM_000222.2	565	gGa/gAa	11/21	1	2	FACETS	0.854	0.769	0.944	0.854	0.769	0.944	CLONAL	1	TRUE	1	0.34	2		557	792	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602916	55602916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372795544	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	114	555	0	ENST00000288135.5:c.2626G>A	p.Asp876Asn	p.D876N	ENST00000288135	NM_000222.2	876	Gat/Aat	19/21	1	2	FACETS	0.822	0.74	0.909	0.822	0.74	0.909	CLONAL	1	TRUE	1	0.34	2		555	816	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953804	55953804	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	152	674	0	ENST00000263923.4:c.3632A>C	p.Lys1211Thr	p.K1211T	ENST00000263923	NM_002253.2	1211	aAa/aCa	27/30	1	2	FACETS	0.967	0.884	1	0.967	0.884	1	CLONAL	1	TRUE	1	0.34	2		674	925	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961766	55961766	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	89	496	0	ENST00000263923.4:c.2795G>T	p.Arg932Ile	p.R932I	ENST00000263923	NM_002253.2	932	aGa/aTa	20/30	1	2	FACETS	0.752	0.667	0.843	0.752	0.667	0.843	SUBCLONAL	1	TRUE	1	0.34	2		496	696	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968136	55968136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747362899	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	55	506	0	ENST00000263923.4:c.2194G>A	p.Glu732Lys	p.E732K	ENST00000263923	NM_002253.2	732	Gaa/Aaa	15/30	1	2	FACETS	0.411	0.351	0.478	0.411	0.351	0.478	SUBCLONAL	1	TRUE	1	0.34	2		506	787	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970882	55970882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	150	697	0	ENST00000263923.4:c.1915G>A	p.Asp639Asn	p.D639N	ENST00000263923	NM_002253.2	639	Gac/Aac	13/30	1	2	FACETS	0.947	0.865	1	0.947	0.865	1	CLONAL	1	TRUE	1	0.34	2		697	932	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970985	55970985	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	159	603	0	ENST00000263923.4:c.1812G>T	p.Lys604Asn	p.K604N	ENST00000263923	NM_002253.2	604	aaG/aaT	13/30	1	2	FACETS	0.99	0.907	1	0.99	0.907	1	CLONAL	1	TRUE	1	0.34	2		603	945	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976672	55976672	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	71	617	0	ENST00000263923.4:c.1153A>C	p.Ile385Leu	p.I385L	ENST00000263923	NM_002253.2	385	Att/Ctt	9/30	1	2	FACETS	0.495	0.431	0.565	0.495	0.431	0.565	SUBCLONAL	1	TRUE	1	0.34	2		617	843	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979589	55979589	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	119	550	0	ENST00000263923.4:c.858G>T	p.Lys286Asn	p.K286N	ENST00000263923	NM_002253.2	286	aaG/aaT	7/30	1	2	FACETS	0.874	0.789	0.964	0.874	0.789	0.964	CLONAL	1	TRUE	1	0.34	2		550	801	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981172	55981172	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	110	485	0	ENST00000263923.4:c.527G>T	p.Arg176Ile	p.R176I	ENST00000263923	NM_002253.2	176	aGa/aTa	5/30	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.34	2		485	634	SUCCESS
REST	5978	MSKCC	GRCh37	4	57797177	57797177	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	230	1126	0	ENST00000309042.7:c.2153C>T	p.Ser718Phe	p.S718F	ENST00000309042	NM_005612.4	718	tCt/tTt	4/4	1	2	FACETS	0.95	0.883	1	0.95	0.883	1	CLONAL	1	TRUE	1	0.34	2		1126	1424	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230813	66230813	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	37	558	0	ENST00000273854.3:c.2158G>T	p.Asp720Tyr	p.D720Y	ENST00000273854	NM_004439.5	720	Gat/Tat	12/18	1	2	FACETS	0.304	0.25	0.366	0.304	0.25	0.366	SUBCLONAL	1	TRUE	1	0.34	2		558	715	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361171	66361171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	161	709	1	ENST00000273854.3:c.1001C>T	p.Thr334Ile	p.T334I	ENST00000273854	NM_004439.5	334	aCc/aTc	4/18	1	2	FACETS	0.993	0.91	1	0.993	0.91	1	CLONAL	1	TRUE	1	0.34	2		710	954	SUCCESS
ALB	213	MSKCC	GRCh37	4	74270114	74270114	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867930468	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	125	518	0	ENST00000295897.4:c.70C>T	p.Arg24Ter	p.R24*	ENST00000295897	NM_000477.5	24	Cga/Tga	1/15	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.34	2		518	726	SUCCESS
ALB	213	MSKCC	GRCh37	4	74279174	74279174	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774294755	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	102	612	0	ENST00000295897.4:c.881C>T	p.Ser294Leu	p.S294L	ENST00000295897	NM_000477.5	294	tCg/tTg	8/15	1	2	FACETS	0.745	0.666	0.83	0.745	0.666	0.83	SUBCLONAL	1	TRUE	1	0.34	2		612	805	SUCCESS
ALB	213	MSKCC	GRCh37	4	74283255	74283255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141626688	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	91	441	0	ENST00000295897.4:c.1297G>A	p.Val433Ile	p.V433I	ENST00000295897	NM_000477.5	433	Gtt/Att	11/15	1	2	FACETS	0.81	0.72	0.906	0.81	0.72	0.906	CLONAL	1	TRUE	1	0.34	2		441	661	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99823081	99823081	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	47	318	0	ENST00000280892.6:c.131C>A	p.Ser44Tyr	p.S44Y	ENST00000280892	NM_001130678.1	44	tCt/tAt	2/7	1	2	FACETS	0.554	0.467	0.65	0.554	0.467	0.65	SUBCLONAL	1	TRUE	1	0.34	2		318	499	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106162587	106162587	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	97	425	0	ENST00000380013.4:c.3500+1G>A		p.X1167_splice	ENST00000380013	NM_001127208.2	1167			1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.34	2		425	563	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196499	106196499	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs527895107	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	264	719	0	ENST00000380013.4:c.4832C>A	p.Ser1611Tyr	p.S1611Y	ENST00000380013	NM_001127208.2	1611	tCt/tAt	11/11	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.34	2		719	1061	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007320	143007320	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	101	372	0	ENST00000262992.4:c.2464G>T	p.Glu822Ter	p.E822*	ENST00000262992	NM_001101669.1	822	Gaa/Taa	22/24	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.34	2		372	548	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029259	143029259	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	49	299	0	ENST00000262992.4:c.2361G>T	p.Lys787Asn	p.K787N	ENST00000262992	NM_001101669.1	787	aaG/aaT	21/24	1	2	FACETS	0.698	0.592	0.814	0.698	0.592	0.814	SUBCLONAL	1	TRUE	1	0.34	2		299	413	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143129648	143129648	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs768272420	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	68	315	0	ENST00000262992.4:c.1002G>T	p.Glu334Asp	p.E334D	ENST00000262992	NM_001101669.1	334	gaG/gaT	12/24	1	2	FACETS	0.783	0.682	0.891	0.783	0.682	0.891	SUBCLONAL	1	TRUE	1	0.34	2		315	511	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130163	143130163	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	78	385	0	ENST00000262992.4:c.853G>T	p.Glu285Ter	p.E285*	ENST00000262992	NM_001101669.1	285	Gaa/Taa	11/24	1	2	FACETS	0.872	0.768	0.984	0.872	0.768	0.984	CLONAL	1	TRUE	1	0.34	2		385	526	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251901	153251901	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	139	551	0	ENST00000281708.4:c.1105G>T	p.Glu369Ter	p.E369*	ENST00000281708	NM_033632.3	369	Gaa/Taa	7/12	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.34	2		551	744	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251927	153251927	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	50	518	0	ENST00000281708.4:c.1079G>T	p.Arg360Ile	p.R360I	ENST00000281708	NM_033632.3	360	aGa/aTa	7/12	1	2	FACETS	0.411	0.348	0.481	0.411	0.348	0.481	SUBCLONAL	1	TRUE	1	0.34	2		518	715	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271212	153271212	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs770911310	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	48	316	0	ENST00000281708.4:c.566A>G	p.Lys189Arg	p.K189R	ENST00000281708	NM_033632.3	189	aAa/aGa	3/12	1	2	FACETS	0.798	0.677	0.93	0.798	0.677	0.93	CLONAL	1	TRUE	1	0.34	2		316	354	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524374	187524374	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	165	766	0	ENST00000441802.2:c.11306T>C	p.Phe3769Ser	p.F3769S	ENST00000441802	NM_005245.3	3769	tTt/tCt	19/27	1	2	FACETS	0.916	0.84	0.995	0.916	0.84	0.995	CLONAL	1	TRUE	1	0.34	2		766	1060	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540113	187540113	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	149	694	0	ENST00000441802.2:c.7627A>C	p.Asn2543His	p.N2543H	ENST00000441802	NM_005245.3	2543	Aat/Cat	10/27	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.34	2		694	875	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540605	187540605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	200	833	0	ENST00000441802.2:c.7135G>A	p.Asp2379Asn	p.D2379N	ENST00000441802	NM_005245.3	2379	Gac/Aac	10/27	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.34	2		833	1169	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541943	187541943	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	180	676	0	ENST00000441802.2:c.5797A>G	p.Thr1933Ala	p.T1933A	ENST00000441802	NM_005245.3	1933	Act/Gct	10/27	1	2	FACETS	0.94	0.865	1	0.94	0.865	1	CLONAL	1	TRUE	1	0.34	2		676	1127	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557804	187557804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1321370436	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	144	653	0	ENST00000441802.2:c.3907G>A	p.Glu1303Lys	p.E1303K	ENST00000441802	NM_005245.3	1303	Gaa/Aaa	5/27	1	2	FACETS	0.851	0.776	0.931	0.851	0.776	0.931	CLONAL	1	TRUE	1	0.34	2		653	995	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628125	187628125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1196972484	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	178	746	0	ENST00000441802.2:c.2857G>A	p.Asp953Asn	p.D953N	ENST00000441802	NM_005245.3	953	Gat/Aat	2/27	1	2	FACETS	0.991	0.912	1	0.991	0.912	1	CLONAL	1	TRUE	1	0.34	2		746	1057	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225555	225555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751114575	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	58	466	0	ENST00000264932.6:c.334G>A	p.Gly112Arg	p.G112R	ENST00000264932	NM_004168.2	112	Ggg/Agg	4/15	1	2	FACETS	0.502	0.431	0.581	0.502	0.431	0.581	SUBCLONAL	1	TRUE	1	0.34	2		466	679	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233619	233619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457666982	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	46	220	0	ENST00000264932.6:c.923C>T	p.Thr308Met	p.T308M	ENST00000264932	NM_004168.2	308	aCg/aTg	8/15	1	2	FACETS	0.82	0.693	0.958	0.82	0.693	0.958	CLONAL	1	TRUE	1	0.34	2		220	330	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	901465	901465	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	79	628	0	ENST00000166345.3:c.454T>G	p.Tyr152Asp	p.Y152D	ENST00000166345	NM_004237.3	152	Tat/Gat	5/13	1	2	FACETS	0.504	0.442	0.571	0.504	0.442	0.571	SUBCLONAL	1	TRUE	1	0.34	2		628	922	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294166	1294166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61748181	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1188	81	947	2	ENST00000310581.5:c.835G>A	p.Ala279Thr	p.A279T	ENST00000310581	NM_198253.2	279	Gcc/Acc	2/16	1	2	FACETS	0.375	0.329	0.425	0.375	0.329	0.425	SUBCLONAL	1	TRUE	1	0.34	2		949	1269	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410987	31410987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1236254462	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	152	635	0	ENST00000344624.3:c.3533G>A	p.Arg1178Gln	p.R1178Q	ENST00000344624		1178	cGa/cAa	28/33	1	2	FACETS	0.888	0.811	0.968	0.888	0.811	0.968	CLONAL	1	TRUE	1	0.34	2		635	1007	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874597	35874597	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	147	605	0	ENST00000303115.3:c.753C>A	p.Phe251Leu	p.F251L	ENST00000303115	NM_002185.3	251	ttC/ttA	6/8	1	2	FACETS	0.982	0.896	1	0.982	0.896	1	CLONAL	1	TRUE	1	0.34	2		605	881	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945727	38945727	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	105	517	0	ENST00000357387.3:c.4499C>T	p.Ala1500Val	p.A1500V	ENST00000357387	NM_152756.3	1500	gCc/gTc	34/38	1	2	FACETS	0.843	0.755	0.935	0.843	0.755	0.935	CLONAL	1	TRUE	1	0.34	2		517	733	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947377	38947377	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	87	445	0	ENST00000357387.3:c.4303G>T	p.Asp1435Tyr	p.D1435Y	ENST00000357387	NM_152756.3	1435	Gat/Tat	32/38	1	2	FACETS	0.815	0.722	0.914	0.815	0.722	0.914	CLONAL	1	TRUE	1	0.34	2		445	628	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950099	38950099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757900166	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	150	768	0	ENST00000357387.3:c.3851C>T	p.Ser1284Leu	p.S1284L	ENST00000357387	NM_152756.3	1284	tCg/tTg	31/38	1	2	FACETS	0.811	0.74	0.886	0.811	0.74	0.886	CLONAL	1	TRUE	1	0.34	2		768	1088	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950364	38950364	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	159	573	0	ENST00000357387.3:c.3586G>T	p.Glu1196Ter	p.E1196*	ENST00000357387	NM_152756.3	1196	Gaa/Taa	31/38	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.34	2		573	838	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950622	38950622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748585755	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	135	625	0	ENST00000357387.3:c.3328C>T	p.Arg1110Cys	p.R1110C	ENST00000357387	NM_152756.3	1110	Cgt/Tgt	31/38	1	2	FACETS	0.993	0.903	1	0.993	0.903	1	CLONAL	1	TRUE	1	0.34	2		625	800	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958874	38958874	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	72	419	0	ENST00000357387.3:c.2238C>A	p.Phe746Leu	p.F746L	ENST00000357387	NM_152756.3	746	ttC/ttA	23/38	1	2	FACETS	0.759	0.664	0.861	0.759	0.664	0.861	SUBCLONAL	1	TRUE	1	0.34	2		419	558	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959396	38959396	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	53	356	0	ENST00000357387.3:c.2079C>A	p.Asn693Lys	p.N693K	ENST00000357387	NM_152756.3	693	aaC/aaA	22/38	1	2	FACETS	0.827	0.708	0.957	0.827	0.708	0.957	CLONAL	1	TRUE	1	0.34	2		356	377	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962617	38962617	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	63	316	0	ENST00000357387.3:c.1638G>A	p.Trp546Ter	p.W546*	ENST00000357387	NM_152756.3	546	tgG/tgA	18/38	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.34	2		316	354	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38996935	38996935	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	95	514	1	ENST00000357387.3:c.442C>T	p.Arg148Ter	p.R148*	ENST00000357387	NM_152756.3	148	Cga/Tga	6/38	1	2	FACETS	0.879	0.783	0.98	0.879	0.783	0.98	CLONAL	1	TRUE	1	0.34	2		515	636	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39003697	39003697	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	109	427	0	ENST00000357387.3:c.223G>T	p.Glu75Ter	p.E75*	ENST00000357387	NM_152756.3	75	Gaa/Taa	4/38	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.34	2		427	600	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522690	67522690	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1444581630	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	64	745	0	ENST00000274335.5:c.187A>C	p.Thr63Pro	p.T63P	ENST00000274335		63	Aca/Cca	1/15	1	2	FACETS	0.362	0.312	0.416	0.362	0.312	0.416	SUBCLONAL	1	TRUE	1	0.34	2		745	1041	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575478	67575478	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	176	552	0	ENST00000274335.5:c.551A>C	p.Asp184Ala	p.D184A	ENST00000274335		184	gAc/gCc	4/15	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.34	2		552	995	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79952236	79952236	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	119	470	0	ENST00000265081.6:c.244G>T	p.Glu82Ter	p.E82*	ENST00000265081	NM_002439.4	82	Gaa/Taa	2/24	1	2	FACETS	0.863	0.779	0.952	0.863	0.779	0.952	CLONAL	1	TRUE	1	0.34	2		470	811	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79960969	79960969	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1472947441	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	48	508	0	ENST00000265081.6:c.366G>T	p.Lys122Asn	p.K122N	ENST00000265081	NM_002439.4	122	aaG/aaT	3/24	1	2	FACETS	0.389	0.328	0.457	0.389	0.328	0.457	SUBCLONAL	1	TRUE	1	0.34	2		508	725	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961137	79961137	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs569679162	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	248	458	0	ENST00000265081.6:c.534G>T	p.Lys178Asn	p.K178N	ENST00000265081	NM_002439.4	178	aaG/aaT	3/24	1	2	FACETS	0.945	0.887	1	1	0.995	1	CLONAL	2	TRUE	1	0.34	2		458	772	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80021286	80021286	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	99	411	0	ENST00000265081.6:c.1355G>T	p.Arg452Ile	p.R452I	ENST00000265081	NM_002439.4	452	aGa/aTa	9/24	1	2	FACETS	0.913	0.816	1	0.913	0.816	1	CLONAL	1	TRUE	1	0.34	2		411	638	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80057459	80057459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200337887	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	121	501	0	ENST00000265081.6:c.1858G>A	p.Asp620Asn	p.D620N	ENST00000265081	NM_002439.4	620	Gac/Aac	13/24	1	2	FACETS	0.945	0.855	1	0.945	0.855	1	CLONAL	1	TRUE	1	0.34	2		501	753	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672324	86672324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs976081140	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	51	587	0	ENST00000274376.6:c.2126G>A	p.Arg709Gln	p.R709Q	ENST00000274376	NM_002890.2	709	cGa/cAa	16/25	1	2	FACETS	0.365	0.309	0.427	0.365	0.309	0.427	SUBCLONAL	1	TRUE	1	0.34	2		587	821	SUCCESS
APC	324	MSKCC	GRCh37	5	112090693	112090693	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	83	357	0	ENST00000257430.4:c.106A>C	p.Lys36Gln	p.K36Q	ENST00000257430	NM_000038.5	36	Aaa/Caa	2/16	1	2	FACETS	0.849	0.75	0.954	0.849	0.75	0.954	CLONAL	1	TRUE	1	0.34	2		357	575	SUCCESS
APC	324	MSKCC	GRCh37	5	112176660	112176660	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	115	528	0	ENST00000257430.4:c.5369G>T	p.Arg1790Ile	p.R1790I	ENST00000257430	NM_000038.5	1790	aGa/aTa	16/16	1	2	FACETS	0.897	0.809	0.991	0.897	0.809	0.991	CLONAL	1	TRUE	1	0.34	2		528	754	SUCCESS
APC	324	MSKCC	GRCh37	5	112176873	112176873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	61	589	0	ENST00000257430.4:c.5582C>A	p.Ser1861Tyr	p.S1861Y	ENST00000257430	NM_000038.5	1861	tCt/tAt	16/16	1	2	FACETS	0.402	0.345	0.463	0.402	0.345	0.463	SUBCLONAL	1	TRUE	1	0.34	2		589	893	SUCCESS
APC	324	MSKCC	GRCh37	5	112179582	112179582	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	174	677	0	ENST00000257430.4:c.8291C>A	p.Ser2764Tyr	p.S2764Y	ENST00000257430	NM_000038.5	2764	tCt/tAt	16/16	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.34	2		677	1012	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925500	131925500	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs867459964	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	104	378	0	ENST00000265335.6:c.1423C>A	p.Leu475Ile	p.L475I	ENST00000265335		475	Ctt/Att	9/25	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.34	2		378	583	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131951738	131951738	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs77642085	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	69	314	0	ENST00000265335.6:c.3080G>T	p.Arg1027Ile	p.R1027I	ENST00000265335		1027	aGa/aTa	20/25	1	2	FACETS	0.976	0.853	1	0.976	0.853	1	CLONAL	1	TRUE	1	0.34	2		314	416	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131976418	131976418	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	86	730	0	ENST00000265335.6:c.3673T>G	p.Cys1225Gly	p.C1225G	ENST00000265335		1225	Tgt/Ggt	24/25	1	2	FACETS	0.446	0.393	0.503	0.446	0.393	0.503	SUBCLONAL	1	TRUE	1	0.34	2		730	1135	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499611	149499611	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	152	613	1	ENST00000261799.4:c.2662T>C	p.Ser888Pro	p.S888P	ENST00000261799	NM_002609.3	888	Tcc/Ccc	19/23	1	2	FACETS	0.973	0.89	1	0.973	0.89	1	CLONAL	1	TRUE	1	0.34	2		614	919	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513278	149513278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	198	800	0	ENST00000261799.4:c.805C>T	p.Pro269Ser	p.P269S	ENST00000261799	NM_002609.3	269	Cct/Tct	6/23	1	2	FACETS	0.901	0.832	0.972	0.901	0.832	0.972	CLONAL	1	TRUE	1	0.34	2		800	1293	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149516607	149516607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148272095	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	184	567	0	ENST00000261799.4:c.4C>T	p.Arg2Trp	p.R2W	ENST00000261799	NM_002609.3	2	Cgg/Tgg	2/23	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.34	2		567	1076	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523297	176523297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1372	120	1008	1	ENST00000292408.4:c.1954C>T	p.Pro652Ser	p.P652S	ENST00000292408	NM_213647.1	652	Cct/Tct	15/18	1	2	FACETS	0.473	0.425	0.524	0.473	0.425	0.524	SUBCLONAL	1	TRUE	1	0.34	2		1009	1492	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638900	176638900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763399938	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	175	721	0	ENST00000439151.2:c.3500G>A	p.Arg1167His	p.R1167H	ENST00000439151	NM_022455.4	1167	cGc/cAc	5/23	1	2	FACETS	0.881	0.81	0.956	0.881	0.81	0.956	CLONAL	1	TRUE	1	0.34	2		721	1168	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709529	176709529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777258117	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	100	461	0	ENST00000439151.2:c.5956C>T	p.Arg1986Cys	p.R1986C	ENST00000439151	NM_022455.4	1986	Cgc/Tgc	19/23	1	2	FACETS	0.89	0.796	0.99	0.89	0.796	0.99	CLONAL	1	TRUE	1	0.34	2		461	661	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721382	176721382	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	124	873	0	ENST00000439151.2:c.7013G>T	p.Ser2338Ile	p.S2338I	ENST00000439151	NM_022455.4	2338	aGc/aTc	23/23	1	2	FACETS	0.573	0.517	0.633	0.573	0.517	0.633	SUBCLONAL	1	TRUE	1	0.34	2		873	1272	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722214	176722214	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	109	857	0	ENST00000439151.2:c.7845G>T	p.Lys2615Asn	p.K2615N	ENST00000439151	NM_022455.4	2615	aaG/aaT	23/23	1	2	FACETS	0.534	0.478	0.594	0.534	0.478	0.594	SUBCLONAL	1	TRUE	1	0.34	2		857	1201	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038418	180038418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530977029	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	157	752	0	ENST00000261937.6:c.3599C>T	p.Ser1200Leu	p.S1200L	ENST00000261937	NM_182925.4	1200	tCg/tTg	27/30	1	2	FACETS	0.874	0.799	0.952	0.874	0.799	0.952	CLONAL	1	TRUE	1	0.34	2		752	1057	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045921	180045921	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	185	829	0	ENST00000261937.6:c.2851-1G>A		p.X951_splice	ENST00000261937	NM_182925.4	951			1	2	FACETS	0.935	0.862	1	0.935	0.862	1	CLONAL	1	TRUE	1	0.34	2		829	1164	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401770	401770	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	106	831	0	ENST00000380956.4:c.1092C>A	p.Phe364Leu	p.F364L	ENST00000380956	NM_001195286.1	364	ttC/ttA	7/9	1	2	FACETS	0.507	0.453	0.565	0.507	0.453	0.565	SUBCLONAL	1	TRUE	1	0.34	2		831	1230	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20486949	20486949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188266138	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	95	375	0	ENST00000346618.3:c.914G>A	p.Arg305Gln	p.R305Q	ENST00000346618	NM_001949.4	305	cGa/cAa	5/7	1	2	FACETS	0.938	0.836	1	0.938	0.836	1	CLONAL	1	TRUE	1	0.34	2		375	596	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30676062	30676062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	176	696	0	ENST00000376406.3:c.2294C>T	p.Thr765Ile	p.T765I	ENST00000376406	NM_014641.2	765	aCc/aTc	8/15	1	2	FACETS	0.88	0.809	0.955	0.88	0.809	0.955	CLONAL	1	TRUE	1	0.34	2		696	1176	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163542	32163542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1187763031	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	218	747	0	ENST00000375023.3:c.5684C>T	p.Ser1895Phe	p.S1895F	ENST00000375023	NM_004557.3	1895	tCt/tTt	30/30	1	2	FACETS	0.961	0.891	1	0.961	0.891	1	CLONAL	1	TRUE	1	0.34	2		747	1335	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166773	32166773	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1231739465	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	102	789	0	ENST00000375023.3:c.4465C>T	p.Arg1489Ter	p.R1489*	ENST00000375023	NM_004557.3	1489	Cga/Tga	24/30	1	2	FACETS	0.492	0.439	0.549	0.492	0.439	0.549	SUBCLONAL	1	TRUE	1	0.34	2		789	1219	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169036	32169036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745902446	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	192	880	0	ENST00000375023.3:c.3997C>T	p.Arg1333Cys	p.R1333C	ENST00000375023	NM_004557.3	1333	Cgt/Tgt	22/30	1	2	FACETS	0.931	0.86	1	0.931	0.86	1	CLONAL	1	TRUE	1	0.34	2		880	1213	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800433	32800433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	205	839	0	ENST00000374899.4:c.1114G>A	p.Glu372Lys	p.E372K	ENST00000374899	NM_018833.2	372	Gaa/Aaa	6/12	1	2	FACETS	0.984	0.912	1	0.984	0.912	1	CLONAL	1	TRUE	1	0.34	2		839	1225	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289240	33289240	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	203	773	0	ENST00000374542.5:c.312G>T	p.Glu104Asp	p.E104D	ENST00000374542	NM_001141970.1	104	gaG/gaT	3/8	0.3	2	FACETS	1	0.93	1			1	CLONAL	1	TRUE	NA	0.34	2		773	1189	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956553	93956553	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1035177735	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	138	594	0	ENST00000369303.4:c.2683C>T	p.Arg895Ter	p.R895*	ENST00000369303	NM_004440.3	895	Cga/Tga	15/17	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.34	2		594	806	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066675	94066675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	152	636	0	ENST00000369303.4:c.1084G>A	p.Asp362Asn	p.D362N	ENST00000369303	NM_004440.3	362	Gat/Aat	5/17	1	2	FACETS	0.946	0.865	1	0.946	0.865	1	CLONAL	1	TRUE	1	0.34	2		636	945	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609843	117609843	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	144	656	0	ENST00000368508.3:c.6856G>T	p.Glu2286Ter	p.E2286*	ENST00000368508	NM_002944.2	2286	Gaa/Taa	43/43	1	2	FACETS	0.939	0.856	1	0.939	0.856	1	CLONAL	1	TRUE	1	0.34	2		656	902	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622152	117622152	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	48	441	0	ENST00000368508.3:c.6718A>C	p.Asn2240His	p.N2240H	ENST00000368508	NM_002944.2	2240	Aat/Cat	42/43	1	2	FACETS	0.495	0.418	0.58	0.495	0.418	0.58	SUBCLONAL	1	TRUE	1	0.34	2		441	570	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665230	117665230	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1258207555	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	78	456	0	ENST00000368508.3:c.4517G>T	p.Arg1506Ile	p.R1506I	ENST00000368508	NM_002944.2	1506	aGa/aTa	27/43	1	2	FACETS	0.776	0.683	0.877	0.776	0.683	0.877	SUBCLONAL	1	TRUE	1	0.34	2		456	591	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686322	117686322	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141385549	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	101	445	0	ENST00000368508.3:c.3019G>A	p.Gly1007Arg	p.G1007R	ENST00000368508	NM_002944.2	1007	Gga/Aga	20/43	1	2	FACETS	0.854	0.763	0.949	0.854	0.763	0.949	CLONAL	1	TRUE	1	0.34	2		445	696	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686823	117686823	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	117	478	0	ENST00000368508.3:c.2894T>A	p.Phe965Tyr	p.F965Y	ENST00000368508	NM_002944.2	965	tTt/tAt	19/43	1	2	FACETS	0.864	0.779	0.953	0.864	0.779	0.953	CLONAL	1	TRUE	1	0.34	2		478	797	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710875	117710875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140178288	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	170	797	0	ENST00000368508.3:c.1397G>A	p.Arg466Gln	p.R466Q	ENST00000368508	NM_002944.2	466	cGa/cAa	12/43	1	2	FACETS	0.923	0.847	1	0.923	0.847	1	CLONAL	1	TRUE	1	0.34	2		797	1084	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710987	117710987	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	79	633	0	ENST00000368508.3:c.1285G>T	p.Asp429Tyr	p.D429Y	ENST00000368508	NM_002944.2	429	Gat/Tat	12/43	1	2	FACETS	0.513	0.45	0.581	0.513	0.45	0.581	SUBCLONAL	1	TRUE	1	0.34	2		633	905	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192545	138192545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs970781981	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	179	757	0	ENST00000237289.4:c.181C>T	p.Arg61Trp	p.R61W	ENST00000237289	NM_001270507.1	61	Cgg/Tgg	2/9	1	2	FACETS	0.91	0.838	0.986	0.91	0.838	0.986	CLONAL	1	TRUE	1	0.34	2		757	1157	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023160	150023160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	158	586	0	ENST00000253339.5:c.103C>T	p.Arg35Trp	p.R35W	ENST00000253339		35	Cgg/Tgg	1/7	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.34	2		586	915	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201885	152201885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778449608	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	131	544	0	ENST00000206249.3:c.739G>A	p.Glu247Lys	p.E247K	ENST00000206249	NM_000125.3	247	Gaa/Aaa	3/8	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.34	2		544	749	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265535	152265535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571716552	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	163	679	2	ENST00000206249.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000206249	NM_000125.3	330	Gag/Aag	4/8	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.34	2		681	946	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382257	152382257	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	94	411	0	ENST00000206249.3:c.1367C>A	p.Ser456Tyr	p.S456Y	ENST00000206249	NM_000125.3	456	tCt/tAt	6/8	1	2	FACETS	0.958	0.855	1	0.958	0.855	1	CLONAL	1	TRUE	1	0.34	2		411	577	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100045	157100045	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	184	862	0	ENST00000346085.5:c.982G>T	p.Gly328Ter	p.G328*	ENST00000346085	NM_020732.3	328	Gga/Tga	1/20	1	2	FACETS	0.852	0.785	0.923	0.852	0.785	0.923	CLONAL	1	TRUE	1	0.34	2		862	1270	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100502	157100502	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771204934	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	124	503	0	ENST00000346085.5:c.1439G>A	p.Gly480Asp	p.G480D	ENST00000346085	NM_020732.3	480	gGc/gAc	1/20	1	2	FACETS	0.983	0.89	1	0.983	0.89	1	CLONAL	1	TRUE	1	0.34	2		503	742	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522598	157522598	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554236040	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	146	606	0	ENST00000346085.5:c.4870C>T	p.Arg1624Ter	p.R1624*	ENST00000346085	NM_020732.3	1624	Cga/Tga	18/20	1	2	FACETS	0.875	0.797	0.956	0.875	0.797	0.956	CLONAL	1	TRUE	1	0.34	2		606	982	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528546	157528546	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	198	756	0	ENST00000346085.5:c.6271A>C	p.Ile2091Leu	p.I2091L	ENST00000346085	NM_020732.3	2091	Atc/Ctc	20/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.34	2		756	1121	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042116	6042116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881916	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	80	329	2	ENST00000265849.7:c.505C>T	p.Arg169Cys	p.R169C	ENST00000265849	NM_000535.5	169	Cgc/Tgc	5/15	1	2	FACETS	0.868	0.766	0.978	0.868	0.766	0.978	CLONAL	1	TRUE	1	0.34	2		331	542	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946090	13946090	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1419462186	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	117	549	0	ENST00000405192.2:c.1006C>T	p.Arg336Ter	p.R336*	ENST00000405192	NM_001163147.1	336	Cga/Tga	10/12	1	2	FACETS	0.993	0.897	1	0.993	0.897	1	CLONAL	1	TRUE	1	0.34	2		549	693	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14027749	14027749	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	131	444	0	ENST00000405192.2:c.95G>T	p.Arg32Ile	p.R32I	ENST00000405192	NM_001163147.1	32	aGa/aTa	3/12	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.34	2		444	697	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459453	50459453	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	132	582	0	ENST00000331340.3:c.742G>T	p.Glu248Ter	p.E248*	ENST00000331340	NM_006060.4	248	Gaa/Taa	7/8	1	2	FACETS	0.927	0.841	1	0.927	0.841	1	CLONAL	1	TRUE	1	0.34	2		582	838	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210116	55210116	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778638117	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	102	449	0	ENST00000275493.2:c.226C>A	p.Leu76Ile	p.L76I	ENST00000275493	NM_005228.3	76	Ctt/Att	2/28	1	2	FACETS	0.913	0.818	1	0.913	0.818	1	CLONAL	1	TRUE	1	0.34	2		449	657	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221725	55221725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138847501	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	121	808	0	ENST00000275493.2:c.769G>A	p.Glu257Lys	p.E257K	ENST00000275493	NM_005228.3	257	Gaa/Aaa	7/28	1	2	FACETS	0.568	0.512	0.628	0.568	0.512	0.628	SUBCLONAL	1	TRUE	1	0.34	2		808	1253	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259480	55259480	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	76	679	0	ENST00000275493.2:c.2538A>T	p.Lys846Asn	p.K846N	ENST00000275493	NM_005228.3	846	aaA/aaT	21/28	1	2	FACETS	0.457	0.4	0.519	0.457	0.4	0.519	SUBCLONAL	1	TRUE	1	0.34	2		679	978	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331962	81331962	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs201768315	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	97	546	0	ENST00000222390.5:c.2122C>T	p.Arg708Ter	p.R708*	ENST00000222390	NM_000601.4	708	Cga/Tga	18/18	1	2	FACETS	0.784	0.699	0.874	0.784	0.699	0.874	SUBCLONAL	1	TRUE	1	0.34	2		546	728	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381567	81381567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370760302	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	103	495	1	ENST00000222390.5:c.494C>T	p.Ser165Leu	p.S165L	ENST00000222390	NM_000601.4	165	tCg/tTg	5/18	1	2	FACETS	0.842	0.753	0.935	0.842	0.753	0.935	CLONAL	1	TRUE	1	0.34	2		496	720	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386512	81386512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	76	460	0	ENST00000222390.5:c.475G>A	p.Glu159Lys	p.E159K	ENST00000222390	NM_000601.4	159	Gaa/Aaa	4/18	1	2	FACETS	0.779	0.684	0.881	0.779	0.684	0.881	SUBCLONAL	1	TRUE	1	0.34	2		460	574	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481451	140481451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	125	461	0	ENST00000288602.6:c.1357C>T	p.Pro453Ser	p.P453S	ENST00000288602	NM_004333.4	453	Cct/Tct	11/18	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.34	2		461	728	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140500178	140500178	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762305547	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	81	837	2	ENST00000288602.6:c.964G>A	p.Ala322Thr	p.A322T	ENST00000288602	NM_004333.4	322	Gcc/Acc	7/18	1	2	FACETS	0.431	0.378	0.488	0.431	0.378	0.488	SUBCLONAL	1	TRUE	1	0.34	2		839	1105	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148504755	148504755	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	121	495	0	ENST00000320356.2:c.2239G>T	p.Glu747Ter	p.E747*	ENST00000320356	NM_004456.4	747	Gaa/Taa	20/20	1	2	FACETS	0.916	0.828	1	0.916	0.828	1	CLONAL	1	TRUE	1	0.34	2		495	777	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148513849	148513849	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	144	566	0	ENST00000320356.2:c.1432G>T	p.Glu478Ter	p.E478*	ENST00000320356	NM_004456.4	478	Gaa/Taa	12/20	1	2	FACETS	0.868	0.791	0.949	0.868	0.791	0.949	CLONAL	1	TRUE	1	0.34	2		566	976	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524317	148524317	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	109	467	0	ENST00000320356.2:c.667A>T	p.Ile223Phe	p.I223F	ENST00000320356	NM_004456.4	223	Att/Ttt	7/20	1	2	FACETS	0.966	0.868	1	0.966	0.868	1	CLONAL	1	TRUE	1	0.34	2		467	664	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836804	151836804	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	138	567	0	ENST00000262189.6:c.14416C>T	p.Arg4806Ter	p.R4806*	ENST00000262189	NM_170606.2	4806	Cga/Tga	56/59	1	2	FACETS	0.893	0.812	0.978	0.893	0.812	0.978	CLONAL	1	TRUE	1	0.34	2		567	909	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845865	151845865	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	99	680	0	ENST00000262189.6:c.13147C>A	p.Leu4383Ile	p.L4383I	ENST00000262189	NM_170606.2	4383	Cta/Ata	52/59	1	2	FACETS	0.598	0.533	0.668	0.598	0.533	0.668	SUBCLONAL	1	TRUE	1	0.34	2		680	974	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860083	151860083	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	83	814	0	ENST00000262189.6:c.10579C>A	p.Pro3527Thr	p.P3527T	ENST00000262189	NM_170606.2	3527	Cca/Aca	43/59	1	2	FACETS	0.439	0.386	0.496	0.439	0.386	0.496	SUBCLONAL	1	TRUE	1	0.34	2		814	1113	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873896	151873896	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	156	668	0	ENST00000262189.6:c.8642G>T	p.Arg2881Ile	p.R2881I	ENST00000262189	NM_170606.2	2881	aGa/aTa	38/59	1	2	FACETS	0.949	0.868	1	0.949	0.868	1	CLONAL	1	TRUE	1	0.34	2		668	967	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877882	151877882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1284609025	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	100	776	0	ENST00000262189.6:c.7063C>T	p.Leu2355Phe	p.L2355F	ENST00000262189	NM_170606.2	2355	Ctt/Ttt	36/59	1	2	FACETS	0.529	0.471	0.59	0.529	0.471	0.59	SUBCLONAL	1	TRUE	1	0.34	2		776	1113	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879203	151879203	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	153	848	0	ENST00000262189.6:c.5742T>A	p.Phe1914Leu	p.F1914L	ENST00000262189	NM_170606.2	1914	ttT/ttA	36/59	1	2	FACETS	0.819	0.748	0.894	0.819	0.748	0.894	CLONAL	1	TRUE	1	0.34	2		848	1099	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880126	151880126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146495785	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	118	467	0	ENST00000262189.6:c.5198C>T	p.Ser1733Leu	p.S1733L	ENST00000262189	NM_170606.2	1733	tCg/tTg	35/59	1	2	FACETS	0.932	0.841	1	0.932	0.841	1	CLONAL	1	TRUE	1	0.34	2		467	745	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132811	152132811	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	140	562	0	ENST00000262189.6:c.61G>T	p.Glu21Ter	p.E21*	ENST00000262189	NM_170606.2	21	Gag/Tag	1/59	1	2	FACETS	0.872	0.794	0.955	0.872	0.794	0.955	CLONAL	1	TRUE	1	0.34	2		562	944	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539127	23539127	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	171	741	0	ENST00000380871.4:c.312G>T	p.Leu104Phe	p.L104F	ENST00000380871	NM_006167.3	104	ttG/ttT	2/2	1	2	FACETS	0.897	0.824	0.974	0.897	0.824	0.974	CLONAL	1	TRUE	1	0.34	2		741	1121	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187104	38187104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758646155	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	147	640	0	ENST00000317025.8:c.1373C>T	p.Ala458Val	p.A458V	ENST00000317025	NM_023034.1	458	gCg/gTg	6/24	1	2	FACETS	0.882	0.805	0.964	0.882	0.805	0.964	CLONAL	1	TRUE	1	0.34	2		640	980	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912075	56912075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	112	461	0	ENST00000519728.1:c.1303G>A	p.Glu435Lys	p.E435K	ENST00000519728	NM_002350.3	435	Gaa/Aaa	12/13	1	2	FACETS	0.883	0.795	0.977	0.883	0.795	0.977	CLONAL	1	TRUE	1	0.34	2		461	746	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931805	68931805	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	90	420	0	ENST00000288368.4:c.235G>T	p.Asp79Tyr	p.D79Y	ENST00000288368	NM_024870.2	79	Gac/Tac	3/40	1	2	FACETS	0.871	0.774	0.974	0.871	0.774	0.974	CLONAL	1	TRUE	1	0.34	2		420	608	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931896	68931896	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	72	459	0	ENST00000288368.4:c.326T>G	p.Phe109Cys	p.F109C	ENST00000288368	NM_024870.2	109	tTt/tGt	3/40	1	2	FACETS	0.706	0.617	0.802	0.706	0.617	0.802	SUBCLONAL	1	TRUE	1	0.34	2		459	600	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934337	68934337	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	34	368	0	ENST00000288368.4:c.403G>A	p.Glu135Lys	p.E135K	ENST00000288368	NM_024870.2	135	Gaa/Aaa	4/40	1	2	FACETS	0.436	0.356	0.526	0.436	0.356	0.526	SUBCLONAL	1	TRUE	1	0.34	2		368	459	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939490	68939490	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	42	459	0	ENST00000288368.4:c.475G>T	p.Asp159Tyr	p.D159Y	ENST00000288368	NM_024870.2	159	Gat/Tat	5/40	1	2	FACETS	0.474	0.395	0.562	0.474	0.395	0.562	SUBCLONAL	1	TRUE	1	0.34	2		459	521	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950493	68950493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760821149	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	85	438	0	ENST00000288368.4:c.805G>A	p.Asp269Asn	p.D269N	ENST00000288368	NM_024870.2	269	Gat/Aat	7/40	1	2	FACETS	0.891	0.789	1	0.891	0.789	1	CLONAL	1	TRUE	1	0.34	2		438	561	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021660	69021660	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs554090253	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	127	526	0	ENST00000288368.4:c.2948G>A	p.Ser983Asn	p.S983N	ENST00000288368	NM_024870.2	983	aGc/aAc	25/40	1	2	FACETS	0.978	0.886	1	0.978	0.886	1	CLONAL	1	TRUE	1	0.34	2		526	764	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028028	69028028	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	96	546	0	ENST00000288368.4:c.3187A>C	p.Lys1063Gln	p.K1063Q	ENST00000288368	NM_024870.2	1063	Aag/Cag	26/40	1	2	FACETS	0.81	0.722	0.904	0.81	0.722	0.904	CLONAL	1	TRUE	1	0.34	2		546	697	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136820	69136820	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	73	597	0	ENST00000288368.4:c.4734G>T	p.Lys1578Asn	p.K1578N	ENST00000288368	NM_024870.2	1578	aaG/aaT	39/40	1	2	FACETS	0.539	0.471	0.614	0.539	0.471	0.614	SUBCLONAL	1	TRUE	1	0.34	2		597	796	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136830	69136830	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	74	610	0	ENST00000288368.4:c.4744G>C	p.Val1582Leu	p.V1582L	ENST00000288368	NM_024870.2	1582	Gtc/Ctc	39/40	1	2	FACETS	0.537	0.47	0.611	0.537	0.47	0.611	SUBCLONAL	1	TRUE	1	0.34	2		610	810	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868912	117868912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746064262	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	110	417	0	ENST00000297338.2:c.787G>A	p.Asp263Asn	p.D263N	ENST00000297338	NM_006265.2	263	Gat/Aat	7/14	1	2	FACETS	0.947	0.852	1	0.947	0.852	1	CLONAL	1	TRUE	1	0.34	2		417	683	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2170448	2170448	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	132	498	0	ENST00000349721.2:c.4229C>A	p.Ser1410Tyr	p.S1410Y	ENST00000349721	NM_003070.3	1410	tCt/tAt	29/34	1	2	FACETS	0.956	0.868	1	0.956	0.868	1	CLONAL	1	TRUE	1	0.34	2		498	812	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2191349	2191349	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs747368303	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	235	809	2	ENST00000349721.2:c.4678C>T	p.Arg1560Ter	p.R1560*	ENST00000349721	NM_003070.3	1560	Cga/Tga	33/34	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.34	2		811	1091	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072524	5072524	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	50	445	1	ENST00000381652.3:c.1674G>T	p.Lys558Asn	p.K558N	ENST00000381652	NM_004972.3	558	aaG/aaT	13/25	1	2	FACETS	0.455	0.385	0.531	0.455	0.385	0.531	SUBCLONAL	1	TRUE	1	0.34	2		446	647	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5462929	5462929	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	167	681	1	ENST00000381577.3:c.490G>T	p.Glu164Ter	p.E164*	ENST00000381577	NM_014143.3	164	Gaa/Taa	4/7	1	2	FACETS	0.905	0.831	0.983	0.905	0.831	0.983	CLONAL	1	TRUE	1	0.34	2		682	1085	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5563174	5563174	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	102	521	1	ENST00000397747.3:c.779G>T	p.Arg260Ile	p.R260I	ENST00000397747	NM_025239.3	260	aGa/aTa	6/7	1	2	FACETS	0.91	0.815	1	0.91	0.815	1	CLONAL	1	TRUE	1	0.34	2		522	659	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341130	8341130	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	119	615	1	ENST00000356435.5:c.5086G>T	p.Gly1696Ter	p.G1696*	ENST00000356435		1696	Gga/Tga	30/35	1	2	FACETS	0.937	0.846	1	0.937	0.846	1	CLONAL	1	TRUE	1	0.34	2		616	747	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376627	8376627	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	98	551	0	ENST00000356435.5:c.4486C>T	p.Arg1496Ter	p.R1496*	ENST00000356435		1496	Cga/Tga	27/35	1	2	FACETS	0.725	0.646	0.809	0.725	0.646	0.809	SUBCLONAL	1	TRUE	1	0.34	2		551	795	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485858	8485858	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	120	672	0	ENST00000356435.5:c.2959G>T	p.Asp987Tyr	p.D987Y	ENST00000356435		987	Gat/Tat	17/35	1	2	FACETS	0.79	0.713	0.872	0.79	0.713	0.872	SUBCLONAL	1	TRUE	1	0.34	2		672	893	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521502	8521502	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	161	632	0	ENST00000356435.5:c.736G>T	p.Glu246Ter	p.E246*	ENST00000356435		246	Gaa/Taa	9/35	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.34	2		632	912	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636723	8636723	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	97	591	0	ENST00000356435.5:c.186G>T	p.Lys62Asn	p.K62N	ENST00000356435		62	aaG/aaT	2/35	1	2	FACETS	0.692	0.617	0.773	0.692	0.617	0.773	SUBCLONAL	1	TRUE	1	0.34	2		591	824	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158029	27158029	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	82	747	0	ENST00000380036.4:c.253A>C	p.Lys85Gln	p.K85Q	ENST00000380036	NM_000459.3	85	Aaa/Caa	2/23	1	2	FACETS	0.442	0.388	0.5	0.442	0.388	0.5	SUBCLONAL	1	TRUE	1	0.34	2		747	1091	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27168511	27168511	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	44	450	0	ENST00000380036.4:c.383C>A	p.Thr128Asn	p.T128N	ENST00000380036	NM_000459.3	128	aCt/aAt	3/23	1	2	FACETS	0.412	0.345	0.487	0.412	0.345	0.487	SUBCLONAL	1	TRUE	1	0.34	2		450	628	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27183521	27183521	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	71	545	0	ENST00000380036.4:c.1095A>C	p.Lys365Asn	p.K365N	ENST00000380036	NM_000459.3	365	aaA/aaC	8/23	1	2	FACETS	0.498	0.433	0.568	0.498	0.433	0.568	SUBCLONAL	1	TRUE	1	0.34	2		545	839	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197484	27197484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756064806	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	146	531	0	ENST00000380036.4:c.1796C>T	p.Ser599Leu	p.S599L	ENST00000380036	NM_000459.3	599	tCg/tTg	12/23	1	2	FACETS	0.926	0.845	1	0.926	0.845	1	CLONAL	1	TRUE	1	0.34	2		531	927	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966671	36966671	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	155	656	0	ENST00000358127.4:c.655T>G	p.Phe219Val	p.F219V	ENST00000358127	NM_001280556.1	219	Ttc/Gtc	6/10	1	2	FACETS	0.903	0.826	0.984	0.903	0.826	0.984	CLONAL	1	TRUE	1	0.34	2		656	1010	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412494	80412494	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	185	394	0	ENST00000286548.4:c.547C>T	p.Arg183Ter	p.R183*	ENST00000286548	NM_002072.3	183	Cga/Tga	4/7	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.34	2		394	1040	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430668	80430668	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	58	327	0	ENST00000286548.4:c.340C>T	p.Arg114Ter	p.R114*	ENST00000286548	NM_002072.3	114	Cga/Tga	3/7	1	2	FACETS	0.81	0.698	0.932	0.81	0.698	0.932	CLONAL	1	TRUE	1	0.34	2		327	421	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342691	87342691	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	130	654	0	ENST00000277120.3:c.976G>T	p.Glu326Ter	p.E326*	ENST00000277120		326	Gag/Tag	9/19	1	2	FACETS	0.81	0.734	0.89	0.81	0.734	0.89	CLONAL	1	TRUE	1	0.34	2		654	944	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342828	87342828	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	142	715	0	ENST00000277120.3:c.1113G>T	p.Glu371Asp	p.E371D	ENST00000277120		371	gaG/gaT	9/19	1	2	FACETS	0.922	0.84	1	0.922	0.84	1	CLONAL	1	TRUE	1	0.34	2		715	906	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864002	97864002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369636116	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	75	539	0	ENST00000289081.3:c.1664G>A	p.Arg555Gln	p.R555Q	ENST00000289081	NM_000136.2	555	cGa/cAa	15/15	1	2	FACETS	0.533	0.466	0.605	0.533	0.466	0.605	SUBCLONAL	1	TRUE	1	0.34	2		539	828	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239054	98239054	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	83	575	0	ENST00000331920.6:c.1589G>T	p.Arg530Ile	p.R530I	ENST00000331920	NM_000264.3	530	aGa/aTa	11/24	1	2	FACETS	0.545	0.48	0.615	0.545	0.48	0.615	SUBCLONAL	1	TRUE	1	0.34	2		575	896	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270558	98270558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	154	596	0	ENST00000331920.6:c.86G>A	p.Gly29Glu	p.G29E	ENST00000331920	NM_000264.3	29	gGa/gAa	1/24	1	2	FACETS	0.981	0.898	1	0.981	0.898	1	CLONAL	1	TRUE	1	0.34	2		596	923	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894935	101894935	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	138	605	0	ENST00000374994.4:c.488A>G	p.Asp163Gly	p.D163G	ENST00000374994	NM_004612.2	163	gAc/gGc	3/9	1	2	FACETS	0.893	0.812	0.978	0.893	0.812	0.978	CLONAL	1	TRUE	1	0.34	2		605	909	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250350	110250350	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768719572	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	192	757	0	ENST00000374672.4:c.325C>A	p.Leu109Ile	p.L109I	ENST00000374672	NM_004235.4	109	Ctc/Atc	3/5	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.34	2		757	1069	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128246746	128246746	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	139	650	3	ENST00000265960.3:c.1183C>T	p.Arg395Ter	p.R395*	ENST00000265960	NM_001006617.1	395	Cga/Tga	9/12	1	2	FACETS	0.806	0.733	0.884	0.806	0.733	0.884	CLONAL	1	TRUE	1	0.34	2		653	1014	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755947	133755947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	163	750	0	ENST00000318560.5:c.1574C>T	p.Ala525Val	p.A525V	ENST00000318560	NM_005157.4	525	gCc/gTc	10/11	1	2	FACETS	0.855	0.783	0.93	0.855	0.783	0.93	CLONAL	1	TRUE	1	0.34	2		750	1122	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772842	135772842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	145	617	0	ENST00000298552.3:c.2781G>T	p.Lys927Asn	p.K927N	ENST00000298552	NM_001162426.1	927	aaG/aaT	21/23	1	2	FACETS	0.872	0.795	0.953	0.872	0.795	0.953	CLONAL	1	TRUE	1	0.34	2		617	978	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393687	139393687	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	200	739	1	ENST00000277541.6:c.5959G>T	p.Asp1987Tyr	p.D1987Y	ENST00000277541	NM_017617.3	1987	Gac/Tac	32/34	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.34	2		740	1163	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564417	139564417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143123347	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	180	749	1	ENST00000308874.7:c.365G>A	p.Arg122His	p.R122H	ENST00000308874		122	cGc/cAc	6/10	1	2	FACETS	0.992	0.914	1	0.992	0.914	1	CLONAL	1	TRUE	1	0.34	2		750	1067	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841310	15841310	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	201	789	0	ENST00000307771.7:c.1394G>T	p.Gly465Val	p.G465V	ENST00000307771	NM_005089.3	465	gGc/gTc	11/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.34	2		789	1116	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20150333	20150333	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	69	391	0	ENST00000379607.5:c.304A>T	p.Ser102Cys	p.S102C	ENST00000379607	NM_001412.3	102	Agt/Tgt	5/7	1	2	FACETS	0.712	0.621	0.811	0.712	0.621	0.811	SUBCLONAL	1	TRUE	1	0.34	2		391	570	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921447	39921447	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	169	632	0	ENST00000378444.4:c.4373T>C	p.Val1458Ala	p.V1458A	ENST00000378444	NM_001123385.1	1458	gTc/gCc	10/15	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.34	2		632	989	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930376	39930376	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	75	659	0	ENST00000378444.4:c.3088G>T	p.Glu1030Ter	p.E1030*	ENST00000378444	NM_001123385.1	1030	Gaa/Taa	6/15	1	2	FACETS	0.431	0.376	0.49	0.431	0.376	0.49	SUBCLONAL	1	TRUE	1	0.34	2		659	1024	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932170	39932170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780523057	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	176	699	0	ENST00000378444.4:c.2429G>A	p.Arg810Gln	p.R810Q	ENST00000378444	NM_001123385.1	810	cGa/cAa	4/15	1	2	FACETS	0.925	0.851	1	0.925	0.851	1	CLONAL	1	TRUE	1	0.34	2		699	1119	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932683	39932683	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	196	859	0	ENST00000378444.4:c.1916T>G	p.Phe639Cys	p.F639C	ENST00000378444	NM_001123385.1	639	tTt/tGt	4/15	1	2	FACETS	0.937	0.866	1	0.937	0.866	1	CLONAL	1	TRUE	1	0.34	2		859	1230	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820533	44820533	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	69	379	0	ENST00000377967.4:c.230T>G	p.Val77Gly	p.V77G	ENST00000377967	NM_021140.2	77	gTt/gGt	3/29	1	2	FACETS	0.775	0.676	0.881	0.775	0.676	0.881	SUBCLONAL	1	TRUE	1	0.34	2		379	524	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918694	44918694	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	111	518	0	ENST00000377967.4:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000377967	NM_021140.2	393	Cga/Tga	12/29	1	2	FACETS	0.922	0.83	1	0.922	0.83	1	CLONAL	1	TRUE	1	0.34	2		518	708	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041645	47041645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782408699	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	179	860	0	ENST00000377604.3:c.1870G>A	p.Asp624Asn	p.D624N	ENST00000377604	NM_001204468.1	624	Gac/Aac	17/24	1	2	FACETS	0.847	0.779	0.918	0.847	0.779	0.918	CLONAL	1	TRUE	1	0.34	2		860	1243	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426078	47426078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	83	747	0	ENST00000377045.4:c.598C>T	p.Pro200Ser	p.P200S	ENST00000377045	NM_001654.4	200	Cct/Tct	7/16	1	2	FACETS	0.447	0.393	0.505	0.447	0.393	0.505	SUBCLONAL	1	TRUE	1	0.34	2		747	1092	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247028	53247028	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	136	681	0	ENST00000375401.3:c.472G>A	p.Glu158Lys	p.E158K	ENST00000375401	NM_004187.3	158	Gaa/Aaa	4/26	1	2	FACETS	0.781	0.709	0.857	0.781	0.709	0.857	SUBCLONAL	1	TRUE	1	0.34	2		681	1024	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247039	53247039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556852808	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	148	696	0	ENST00000375401.3:c.461G>A	p.Arg154His	p.R154H	ENST00000375401	NM_004187.3	154	cGc/cAc	4/26	1	2	FACETS	0.84	0.766	0.918	0.84	0.766	0.918	CLONAL	1	TRUE	1	0.34	2		696	1036	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411810	63411810	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	177	867	0	ENST00000330258.3:c.1357C>A	p.Leu453Ile	p.L453I	ENST00000330258	NM_152424.3	453	Ctt/Att	2/2	1	2	FACETS	0.872	0.802	0.945	0.872	0.802	0.945	CLONAL	1	TRUE	1	0.34	2		867	1194	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338650	70338650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	136	548	1	ENST00000374080.3:c.46C>T	p.Arg16Trp	p.R16W	ENST00000374080		16	Cgg/Tgg	1/45	1	2	FACETS	0.882	0.802	0.967	0.882	0.802	0.967	CLONAL	1	TRUE	1	0.34	2		549	907	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776304	76776304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	105	546	0	ENST00000373344.5:c.7162G>A	p.Glu2388Lys	p.E2388K	ENST00000373344	NM_000489.3	2388	Gaa/Aaa	34/35	1	2	FACETS	0.914	0.819	1	0.914	0.819	1	CLONAL	1	TRUE	1	0.34	2		546	676	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776955	76776955	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	75	488	0	ENST00000373344.5:c.6997G>T	p.Glu2333Ter	p.E2333*	ENST00000373344	NM_000489.3	2333	Gaa/Taa	33/35	1	2	FACETS	0.801	0.703	0.906	0.801	0.703	0.906	CLONAL	1	TRUE	1	0.34	2		488	551	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778812	76778812	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	106	569	0	ENST00000373344.5:c.6767C>A	p.Ser2256Tyr	p.S2256Y	ENST00000373344	NM_000489.3	2256	tCt/tAt	31/35	1	2	FACETS	0.921	0.827	1	0.921	0.827	1	CLONAL	1	TRUE	1	0.34	2		569	677	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855046	76855046	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	74	410	0	ENST00000373344.5:c.5790G>T	p.Lys1930Asn	p.K1930N	ENST00000373344	NM_000489.3	1930	aaG/aaT	25/35	1	2	FACETS	0.862	0.756	0.975	0.862	0.756	0.975	CLONAL	1	TRUE	1	0.34	2		410	505	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889193	76889193	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	92	418	0	ENST00000373344.5:c.4817G>T	p.Ser1606Ile	p.S1606I	ENST00000373344	NM_000489.3	1606	aGt/aTt	18/35	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.34	2		418	523	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890192	76890192	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	76	423	0	ENST00000373344.5:c.4702G>A	p.Val1568Ile	p.V1568I	ENST00000373344	NM_000489.3	1568	Gtt/Att	17/35	1	2	FACETS	0.726	0.637	0.821	0.726	0.637	0.821	SUBCLONAL	1	TRUE	1	0.34	2		423	616	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907720	76907720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	110	499	0	ENST00000373344.5:c.4441C>T	p.Arg1481Trp	p.R1481W	ENST00000373344	NM_000489.3	1481	Cgg/Tgg	15/35	1	2	FACETS	0.936	0.842	1	0.936	0.842	1	CLONAL	1	TRUE	1	0.34	2		499	691	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912075	76912075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782228142	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	74	458	1	ENST00000373344.5:c.4189G>A	p.Glu1397Lys	p.E1397K	ENST00000373344	NM_000489.3	1397	Gaa/Aaa	13/35	1	2	FACETS	0.8	0.702	0.906	0.8	0.702	0.906	CLONAL	1	TRUE	1	0.34	2		459	544	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920242	76920242	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	40	393	0	ENST00000373344.5:c.3835G>T	p.Glu1279Ter	p.E1279*	ENST00000373344	NM_000489.3	1279	Gaa/Taa	11/35	1	2	FACETS	0.446	0.37	0.531	0.446	0.37	0.531	SUBCLONAL	1	TRUE	1	0.34	2		393	527	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937356	76937356	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	82	434	0	ENST00000373344.5:c.3392G>T	p.Arg1131Ile	p.R1131I	ENST00000373344	NM_000489.3	1131	aGa/aTa	9/35	1	2	FACETS	0.89	0.786	1	0.89	0.786	1	CLONAL	1	TRUE	1	0.34	2		434	542	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937587	76937587	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	96	509	0	ENST00000373344.5:c.3161C>A	p.Ser1054Tyr	p.S1054Y	ENST00000373344	NM_000489.3	1054	tCt/tAt	9/35	1	2	FACETS	0.927	0.828	1	0.927	0.828	1	CLONAL	1	TRUE	1	0.34	2		509	609	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937850	76937850	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs138256318	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	102	569	0	ENST00000373344.5:c.2898G>T	p.Glu966Asp	p.E966D	ENST00000373344	NM_000489.3	966	gaG/gaT	9/35	1	2	FACETS	0.77	0.689	0.857	0.77	0.689	0.857	SUBCLONAL	1	TRUE	1	0.34	2		569	779	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938337	76938337	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	92	509	0	ENST00000373344.5:c.2411C>A	p.Ser804Tyr	p.S804Y	ENST00000373344	NM_000489.3	804	tCt/tAt	9/35	1	2	FACETS	0.83	0.738	0.928	0.83	0.738	0.928	CLONAL	1	TRUE	1	0.34	2		509	652	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938406	76938406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	101	369	2	ENST00000373344.5:c.2342G>A	p.Arg781Gln	p.R781Q	ENST00000373344	NM_000489.3	781	cGa/cAa	9/35	1	2	FACETS	0.936	0.838	1	0.936	0.838	1	CLONAL	1	TRUE	1	0.34	2		371	635	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938640	76938640	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	88	513	0	ENST00000373344.5:c.2108C>A	p.Ser703Tyr	p.S703Y	ENST00000373344	NM_000489.3	703	tCt/tAt	9/35	1	2	FACETS	0.81	0.718	0.908	0.81	0.718	0.908	CLONAL	1	TRUE	1	0.34	2		513	639	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938659	76938659	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	39	517	0	ENST00000373344.5:c.2089A>T	p.Lys697Ter	p.K697*	ENST00000373344	NM_000489.3	697	Aaa/Taa	9/35	1	2	FACETS	0.331	0.273	0.396	0.331	0.273	0.396	SUBCLONAL	1	TRUE	1	0.34	2		517	693	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938995	76938995	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs886044898	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	127	524	0	ENST00000373344.5:c.1753G>T	p.Glu585Ter	p.E585*	ENST00000373344	NM_000489.3	585	Gaa/Taa	9/35	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.34	2		524	710	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939077	76939077	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs376761153	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	69	601	0	ENST00000373344.5:c.1671G>T	p.Glu557Asp	p.E557D	ENST00000373344	NM_000489.3	557	gaG/gaT	9/35	1	2	FACETS	0.474	0.412	0.542	0.474	0.412	0.542	SUBCLONAL	1	TRUE	1	0.34	2		601	856	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939417	76939417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781932965	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	106	560	0	ENST00000373344.5:c.1331G>A	p.Arg444Gln	p.R444Q	ENST00000373344	NM_000489.3	444	cGa/cAa	9/35	1	2	FACETS	0.782	0.701	0.869	0.782	0.701	0.869	SUBCLONAL	1	TRUE	1	0.34	2		560	797	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613678	100613678	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	152	541	0	ENST00000308731.7:c.901G>T	p.Glu301Ter	p.E301*	ENST00000308731	NM_000061.2	301	Gaa/Taa	11/19	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.34	2		541	872	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630232	100630232	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520682	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	46	611	0	ENST00000308731.7:c.41C>A	p.Ser14Tyr	p.S14Y	ENST00000308731	NM_000061.2	14	tCc/tAc	2/19	1	2	FACETS	0.32	0.268	0.377	0.32	0.268	0.377	SUBCLONAL	1	TRUE	1	0.34	2		611	846	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020225	123020225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	196	600	0	ENST00000355640.3:c.713G>A	p.Arg238Gln	p.R238Q	ENST00000355640		238	cGa/cAa	2/7	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.34	2		600	915	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034462	123034462	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	79	331	0	ENST00000355640.3:c.1219C>A	p.Leu407Ile	p.L407I	ENST00000355640		407	Ctt/Att	6/7	1	2	FACETS	0.822	0.724	0.927	0.822	0.724	0.927	CLONAL	1	TRUE	1	0.34	2		331	565	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190069	123190069	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	90	436	0	ENST00000218089.9:c.1288G>T	p.Glu430Ter	p.E430*	ENST00000218089	NM_001042749.1	430	Gaa/Taa	14/35	1	2	FACETS	0.806	0.715	0.902	0.806	0.715	0.902	CLONAL	1	TRUE	1	0.34	2		436	657	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202452	123202452	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	61	297	0	ENST00000218089.9:c.2304T>G	p.Phe768Leu	p.F768L	ENST00000218089	NM_001042749.1	768	ttT/ttG	24/35	1	2	FACETS	0.805	0.696	0.922	0.805	0.696	0.922	CLONAL	1	TRUE	1	0.34	2		297	446	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211862	123211862	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	122	646	0	ENST00000218089.9:c.2729T>A	p.Ile910Lys	p.I910K	ENST00000218089	NM_001042749.1	910	aTa/aAa	27/35	1	2	FACETS	0.865	0.781	0.953	0.865	0.781	0.953	CLONAL	1	TRUE	1	0.34	2		646	830	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215251	123215251	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	60	268	0	ENST00000218089.9:c.2797G>T	p.Glu933Ter	p.E933*	ENST00000218089	NM_001042749.1	933	Gaa/Taa	28/35	1	2	FACETS	0.997	0.864	1	0.997	0.864	1	CLONAL	1	TRUE	1	0.34	2		268	354	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217281	123217281	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	37	370	1	ENST00000218089.9:c.2935G>T	p.Glu979Ter	p.E979*	ENST00000218089	NM_001042749.1	979	Gaa/Taa	29/35	1	2	FACETS	0.387	0.318	0.464	0.387	0.318	0.464	SUBCLONAL	1	TRUE	1	0.34	2		371	563	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220483	123220483	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	125	570	0	ENST00000218089.9:c.3140C>A	p.Ser1047Tyr	p.S1047Y	ENST00000218089	NM_001042749.1	1047	tCt/tAt	30/35	1	2	FACETS	0.833	0.753	0.917	0.833	0.753	0.917	CLONAL	1	TRUE	1	0.34	2		570	883	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224466	123224466	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	136	622	0	ENST00000218089.9:c.3319G>T	p.Glu1107Ter	p.E1107*	ENST00000218089	NM_001042749.1	1107	Gaa/Taa	31/35	1	2	FACETS	0.935	0.85	1	0.935	0.85	1	CLONAL	1	TRUE	1	0.34	2		622	856	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504048	123504048	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	69	308	0	ENST00000371139.4:c.224G>T	p.Arg75Ile	p.R75I	ENST00000371139	NM_001114937.2	75	aGa/aTa	3/4	1	2	FACETS	0.89	0.778	1	0.89	0.778	1	CLONAL	1	TRUE	1	0.34	2		308	456	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861577	152861577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149734965	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	149	779	0	ENST00000406277.2:c.175G>A	p.Glu59Lys	p.E59K	ENST00000406277	NM_152274.4	59	Gag/Aag	4/7	1		FACETS		0.736	0.882				CLONAL	1	TRUE	1	0.34	2		779	1086	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447310	49447310	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	211	797	0	ENST00000301067.7:c.788G>T	p.Arg263Leu	p.R263L	ENST00000301067	NM_003482.3	263	cGc/cTc	6/54	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.34	2		797	1192	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447309	49447309	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048298-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	207	804	0	ENST00000301067.7:c.789del	p.Lys264AsnfsTer40	p.K264Nfs*40	ENST00000301067	NM_003482.3	263	cgC/cg	6/54	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.34	2		804	1189	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346338	73346338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048335-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	303	423	0	ENST00000377767.4:c.1462G>A	p.Asp488Asn	p.D488N	ENST00000377767	NM_014953.3	488	Gat/Aat	10/21	0.139049464700367	4	FACETS	0.925	0.877	0.973	0.925	0.877	0.973	INDETERMINATE	2	TRUE	2	0.845595409345681	4		423	715	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560494	65560494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048335-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	339	553	0	ENST00000358664.4:c.103C>T	p.Arg35Cys	p.R35C	ENST00000358664	NM_002382.4	35	Cgt/Tgt	3/5	0.845595409345681	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.845595409345681	1		553	455	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048650-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	47	475	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.348	0.293	0.407	0.348	0.293	0.407	SUBCLONAL	1	TRUE	1	0.6147545556126	2		475	440	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0048650-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	57	639	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.233	0.199	0.27	0.233	0.199	0.27	SUBCLONAL	1	TRUE	1	0.6147545556126	2		639	797	SUCCESS
AR	367	MSKCC	GRCh37	X	66766193	66766193	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866450936	NA	P-0048650-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	42	601	1	ENST00000374690.3:c.1205C>T	p.Ala402Val	p.A402V	ENST00000374690	NM_000044.3	402	gCg/gTg	1/8	1	2	FACETS	0.168	0.14	0.2	0.168	0.14	0.2	SUBCLONAL	1	TRUE	1	0.6147545556126	2		602	812	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397742	49397742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552757	NA	P-0048650-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	41	518	0	ENST00000418115.1:c.482C>T	p.Ala161Val	p.A161V	ENST00000418115	NM_001664.2	161	gCa/gTa	5/5	1	2	FACETS	0.157	0.13	0.187	0.157	0.13	0.187	SUBCLONAL	1	TRUE	1	0.6147545556126	2		518	851	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779172	135779172	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203631	NA	P-0048650-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	49	1325	0	ENST00000298552.3:c.2074C>T	p.Arg692Ter	p.R692*	ENST00000298552	NM_001162426.1	692	Cga/Tga	17/23	1	2	FACETS	0.201	0.169	0.236	0.201	0.169	0.236	SUBCLONAL	1	TRUE	1	0.6147545556126	2		1325	793	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021729	71021729	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	44	298	0	ENST00000318789.4:c.1629del	p.Lys543AsnfsTer56	p.K543Nfs*56	ENST00000318789	NM_032682.5	543	aaA/aa	18/21	0.468722126410983	9	FACETS	0.95	0.809	1			1	CLONAL	3	TRUE	NA	0.468722126410983	9		298	174	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633314	3633314	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	10	859	1	ENST00000294008.3:c.4937A>T	p.Glu1646Val	p.E1646V	ENST00000294008	NM_032444.2	1646	gAg/gTg	14/15	1	2	FACETS	0.333	0.227	0.466	0.333	0.227	0.466	SUBCLONAL	1	TRUE	1	0.468722126410983	2		860	128	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18972933	18972933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	42	612	1	ENST00000262803.5:c.2572C>T	p.Arg858Cys	p.R858C	ENST00000262803	NM_002911.3	858	Cgt/Tgt	18/24	0.2684532215364	4	FACETS	0.833	0.707	0.967	0.833	0.707	0.967	INDETERMINATE	2	TRUE	2	0.468722126410983	4		613	158	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753612	42753612	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1425504754	NA	P-0048791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	47	871	1	ENST00000222329.4:c.652C>T	p.Arg218Ter	p.R218*	ENST00000222329	NM_006494.2	218	Cga/Tga	4/4	0.2684532215364	4	FACETS	1	0.864	1	0.51	0.432	0.593	INDETERMINATE	1	TRUE	2	0.468722126410983	4		872	289	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453135	140453136	+	missense_variant	Missense_Mutation	DNP	CA	CA	TT	rs121913377	NA	P-0049901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	9	337	2	ENST00000288602.6:c.1799_1800delinsAA	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTG/gAA	15/18	1	2	FACETS	0.794	0.525	1	0.794	0.525	1	CLONAL	1	TRUE	1	0.12	2		339	189	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0049901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	30	613	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	1	2	FACETS	1	0.808	1	1	0.808	1	CLONAL	1	TRUE	1	0.12	2		613	498	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170994	56170994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	21	329	0	ENST00000399503.3:c.1822G>A	p.Gly608Ser	p.G608S	ENST00000399503	NM_005921.1	608	Ggc/Agc	10/20	1	2	FACETS	1	0.776	1	1	0.776	1	CLONAL	1	TRUE	1	0.12	2		329	347	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057874	27057874	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	203	933	0	ENST00000324856.7:c.1582C>T	p.Gln528Ter	p.Q528*	ENST00000324856	NM_006015.4	528	Cag/Tag	3/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.590645575812467	2		933	635	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023948	27023948	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	91	837	0	ENST00000324856.7:c.1057del	p.Ala353ProfsTer10	p.A353Pfs*10	ENST00000324856	NM_006015.4	352	Ggg/gg	1/20	1	2	FACETS	0.856	0.766	0.95	0.856	0.766	0.95	CLONAL	1	TRUE	1	0.590645575812467	2		837	360	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863605	68863612	+	frameshift_variant	Frame_Shift_Del	DEL	GTGACTCG	GTGACTCG	A	novel	NA	P-0050374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	127	723	0	ENST00000261769.5:c.2344_2351delinsA	p.Val782IlefsTer9	p.V782Ifs*9	ENST00000261769	NM_004360.3	782	GTGACTCGt/At	15/16	0.590645575812467	1	FACETS	0.905	0.83	0.98	0.905	0.83	0.98	CLONAL	1	TRUE	0	0.590645575812467	1		723	335	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0050573-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	236	836	2	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.320215252706403	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.320215252706403	1		838	1067	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610322	10610322	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050573-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	380	1022	0	ENST00000171111.5:c.388C>T	p.Pro130Ser	p.P130S	ENST00000171111	NM_203500.1	130	Ccc/Tcc	2/6	0.229392832689162	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.320215252706403	2		1022	1176	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0050573-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	269	519	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.320215252706403	2	FACETS	0.855	0.803	0.909	0.855	0.803	0.909	CLONAL	2	TRUE	0	0.320215252706403	2		520	982	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050573-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	229	759	0	ENST00000269305.4:c.811G>C	p.Glu271Gln	p.E271Q	ENST00000269305	NM_001126112.2	271	Gag/Cag	8/11	0.320215252706403	2	FACETS	0.779	0.727	0.833	0.779	0.727	0.833	SUBCLONAL	2	TRUE	0	0.320215252706403	2		759	918	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21553861	21553862	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0050573-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	104	562	0	ENST00000382592.4:c.2740_2741del	p.Leu914GlyfsTer29	p.L914Gfs*29	ENST00000382592	NM_014572.2	914	TTg/g	7/8	0.320215252706403	1	FACETS	0.886	0.795	0.982	0.886	0.795	0.982	CLONAL	1	TRUE	0	0.320215252706403	1		562	616	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003183	45003745	+	coding_sequence_variant,5_prime_UTR_variant	Frame_Shift_Del	DEL	TGTCCTCAGGATGCTTTTGGGACTATTTTTCTTACCCAGAGAATGGAGAAACCCTGCAGGGAATTCCCAAGCTGTAGTTATAAACAGAAGTTCTCCTTCTGCTAGGTAGCATTCAAAGATCTTAATCTTCTGGGTTTCCGTTTTCTCGAATGAAAAATGCAGGTCCGAGCAGTTAACTGGCTGGGGCACCATTAGCAAGTCACTTAGCATCTCTGGGGCCAGTCTGCAAAGCGAGGGGGCAGCCTTAATGTGCCTCCAGCCTGAAGTCCTAGAATGAGCGCCCGGTGTCCCAAGCTGGGGCGCGCACCCCAGATCGGAGGGCGCCGATGTACAGACAGCAAACTCACCCAGTCTAGTGCATGCCTTCTTAAACATCACGAGACTCTAAGAAAAGGAAACTGAAAACGGGAAAGTCCCTCTCTCTAACCTGGCACTGCGTCGCTGGCTTGGAGACAGGTGACGGTCCCTGCGGGCCTTGTCCTGATTGGCTGGGCACGCGTTTAATATAAGTGGAGGCGTCGCGCTGGCGGGCATTCCTGAAGCTGACAGCATTCGGGCCGAGA	TGTCCTCAGGATGCTTTTGGGACTATTTTTCTTACCCAGAGAATGGAGAAACCCTGCAGGGAATTCCCAAGCTGTAGTTATAAACAGAAGTTCTCCTTCTGCTAGGTAGCATTCAAAGATCTTAATCTTCTGGGTTTCCGTTTTCTCGAATGAAAAATGCAGGTCCGAGCAGTTAACTGGCTGGGGCACCATTAGCAAGTCACTTAGCATCTCTGGGGCCAGTCTGCAAAGCGAGGGGGCAGCCTTAATGTGCCTCCAGCCTGAAGTCCTAGAATGAGCGCCCGGTGTCCCAAGCTGGGGCGCGCACCCCAGATCGGAGGGCGCCGATGTACAGACAGCAAACTCACCCAGTCTAGTGCATGCCTTCTTAAACATCACGAGACTCTAAGAAAAGGAAACTGAAAACGGGAAAGTCCCTCTCTCTAACCTGGCACTGCGTCGCTGGCTTGGAGACAGGTGACGGTCCCTGCGGGCCTTGTCCTGATTGGCTGGGCACGCGTTTAATATAAGTGGAGGCGTCGCGCTGGCGGGCATTCCTGAAGCTGACAGCATTCGGGCCGAGA	-	novel	NA	P-0050573-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	0	79	3	0				ENST00000558401	NM_004048.2	?-1/119		1/4	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	6	TRUE	1	0.320215252706403	2		3	79	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348800	89348800	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050573-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	165	869	0	ENST00000301030.4:c.4150G>C	p.Gly1384Arg	p.G1384R	ENST00000301030	NM_001256183.1	1384	Ggt/Cgt	9/13	0.297126139699777	1	FACETS	0.985	0.905	1	0.985	0.905	1	CLONAL	1	TRUE	0	0.320215252706403	1		869	879	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122765	7122765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050573-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	224	794	0	ENST00000302850.5:c.3389C>T	p.Pro1130Leu	p.P1130L	ENST00000302850	NM_000208.2	1130	cCc/cTc	19/22	0.229392832689162	2	FACETS	0.775	0.722	0.829	0.775	0.722	0.829	SUBCLONAL	2	TRUE	0	0.320215252706403	2		794	903	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765756	41765756	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050573-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	127	872	0	ENST00000301178.4:c.2632C>T	p.Gln878Ter	p.Q878*	ENST00000301178	NM_021913.4	878	Cag/Tag	20/20	0.320215252706403	1	FACETS	0.644	0.582	0.709	0.644	0.582	0.709	SUBCLONAL	1	TRUE	0	0.320215252706403	1		872	1035	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0050683-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	88	526	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.223749606651221	3	FACETS	0.784	0.693	0.882	0.392	0.346	0.441	SUBCLONAL	1	FALSE	1	0.229604960016641	3		526	1090	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0050683-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	75	557	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.162362528996833	2	FACETS	1	0.92	1	0.533	0.467	0.604	CLONAL	1	FALSE	0	0.229604960016641	2		557	613	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123260405	123260405	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050683-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	59	775	0	ENST00000358487.5:c.1496A>C	p.Glu499Ala	p.E499A	ENST00000358487	NM_000141.4	499	gAa/gCa	11/18	1	2	FACETS	0.643	0.552	0.743	0.643	0.552	0.743	SUBCLONAL	1	FALSE	1	0.229604960016641	2		775	799	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050975-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	56	475	0				ENST00000310581	NM_198253.2	-/1132			0.191681123627366	4	FACETS	0.76	0.649	0.881	0.38	0.324	0.441	SUBCLONAL	1	TRUE	2	0.218577220237551	4		475	822	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0050975-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	109	541	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.218577220237551	2		541	873	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0050975-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	8	497	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.229	0.146	0.336	0.229	0.146	0.336	SUBCLONAL	1	TRUE	1	0.218577220237551	2		497	320	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0050975-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	319	513	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.218577220237551	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.218577220237551	2		513	1439	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448360	49448360	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050975-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	46	866	0	ENST00000301067.7:c.351G>C	p.Gln117His	p.Q117H	ENST00000301067	NM_003482.3	117	caG/caC	3/54	1	2	FACETS	0.473	0.397	0.558	0.473	0.397	0.558	SUBCLONAL	1	TRUE	1	0.218577220237551	2		866	890	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136286	202136286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050975-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	17	436	0	ENST00000358485.4:c.530G>A	p.Arg177Lys	p.R177K	ENST00000358485	NM_001080125.1	177	aGg/aAg	3/9	1	2	FACETS	0.701	0.524	0.91	0.701	0.524	0.91	CLONAL	1	TRUE	1	0.218577220237551	2		436	222	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090646	71090646	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050975-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	20	509	0	ENST00000318789.4:c.702A>T	p.Glu234Asp	p.E234D	ENST00000318789	NM_032682.5	234	gaA/gaT	11/21	1	2	FACETS	0.475	0.363	0.608	0.475	0.363	0.608	SUBCLONAL	1	TRUE	1	0.218577220237551	2		509	385	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968335	134968335	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0050975-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	58	575	0	ENST00000398015.3:c.2846+2T>C		p.X949_splice	ENST00000398015	NM_004441.4	949			1	2	FACETS	0.818	0.702	0.944	0.818	0.702	0.944	CLONAL	1	TRUE	1	0.218577220237551	2		575	649	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275777	38275777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs923019674	NA	P-0050975-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	51	819	0	ENST00000425967.3:c.1492G>A	p.Glu498Lys	p.E498K	ENST00000425967	NM_001174067.1	498	Gaa/Aaa	11/19	1	2	FACETS	0.591	0.501	0.691	0.591	0.501	0.691	SUBCLONAL	1	TRUE	1	0.218577220237551	2		819	789	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0051024-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	59	499	0				ENST00000310581	NM_198253.2	-/1132			0.138573447238191	4	FACETS	0.962	0.831	1	0.962	0.831	1	CLONAL	2	TRUE	2	0.206159763600948	4		499	359	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127460	55127460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779332376	NA	P-0051024-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	75	618	0	ENST00000257290.5:c.248C>T	p.Thr83Met	p.T83M	ENST00000257290	NM_006206.4	83	aCg/aTg	3/23	0.206159763600948	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.206159763600948	1		618	518	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420601	49420618	+	inframe_deletion	In_Frame_Del	DEL	GCAGACGGGCAGGCCCAT	GCAGACGGGCAGGCCCAT	-	novel	NA	P-0051024-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	49	775	0	ENST00000301067.7:c.15131_15148del	p.Asp5044_Leu5050delinsVal	p.D5044_L5050delinsV	ENST00000301067	NM_003482.3	5044	gATGGGCCTGCCCGTCTGCtg/gtg	48/54	0.206159763600948	2	FACETS	0.77	0.652	0.901	0.385	0.326	0.451	CLONAL	1	TRUE	0	0.206159763600948	2		775	617	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636032	73636032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051024-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	46	461	0	ENST00000377687.4:c.295C>T	p.Gln99Ter	p.Q99*	ENST00000377687	NM_001730.3	99	Cag/Tag	2/4	0.206159763600948	3	FACETS	0.931	0.783	1	0.465	0.391	0.547	CLONAL	1	TRUE	1	0.206159763600948	3		461	529	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593580	55593606	+	splice_acceptor_variant,coding_sequence_variant	In_Frame_Del	DEL	AGAAACCCATGTATGAAGTACAGTGGA	AGAAACCCATGTATGAAGTACAGTGGA	-	rs121913234	NA	P-0052033-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	362	549	0	ENST00000288135.5:c.1648_1674del		p.K550_K558del	ENST00000288135	NM_000222.2	550		11/21	0.783396375676648	3	FACETS	0.897	0.857	0.936	0.897	0.857	0.936	CLONAL	2	TRUE	1	0.783396375676648	3		549	717	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061219	38061229	+	protein_altering_variant	In_Frame_Del	DEL	CCGTTCTCGAA	CCGTTCTCGAA	AACTTGCG	novel	NA	P-0052056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	68	501	1	ENST00000250448.2:c.760_770delinsCGCAAGTT	p.Phe254_Gly257delinsArgLysPhe	p.F254_G257delinsRKF	ENST00000250448	NM_004496.3	254	TTCGAGAACGGc/CGCAAGTTc	2/2	0.152099098014903	4	FACETS	1	0.906	1	0.523	0.457	0.595	INDETERMINATE	1	FALSE	2	0.404625151785114	4		502	451	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593606	55593611	+	inframe_deletion	In_Frame_Del	DEL	AAGGTT	AAGGTT	-	novel	NA	P-0052061-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	92	459	0	ENST00000288135.5:c.1672_1677del	p.Lys558_Val559del	p.K558_V559del	ENST00000288135	NM_000222.2	558	AAGGTT/-	11/21	0.560017862540541	6	FACETS	1	0.96	1	0.759	0.682	0.839	CLONAL	2	TRUE	3	0.560017862540541	6		459	306	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0052265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	18	239	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.529513750404095	1	FACETS	0.153	0.115	0.198	0.153	0.115	0.198	SUBCLONAL	1	TRUE	0	0.529513750404095	1		239	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0052265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	229	573	1	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	1	2	FACETS	0.939	0.876	1	0.939	0.876	1	CLONAL	1	TRUE	1	0.529513750404095	2		574	921	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932410	36932410	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201699446	NA	P-0052265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	244	624	0	ENST00000361632.4:c.2059G>A	p.Gly687Ser	p.G687S	ENST00000361632		687	Ggc/Agc	16/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.529513750404095	2		624	907	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383228	42383228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782110924	NA	P-0052265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	282	547	0	ENST00000221972.3:c.248C>T	p.Pro83Leu	p.P83L	ENST00000221972	NM_021601.3	83	cCg/cTg	2/5	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.529513750404095	2		547	1028	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131345	202131345	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	276	442	0	ENST00000358485.4:c.313C>T	p.Gln105Ter	p.Q105*	ENST00000358485	NM_001080125.1	105	Cag/Tag	2/9	0.41093692676774	2	FACETS	1	0.994	1	0.741	0.7	0.783	CLONAL	1	TRUE	0	0.529513750404095	2		442	703	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912821	100912821	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	136	313	0	ENST00000325455.5:c.2501G>A	p.Gly834Glu	p.G834E	ENST00000325455	NM_001202474.3	834	gGg/gAg	7/8	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.529513750404095	2		313	498	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0052265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	225	459	0	ENST00000269305.4:c.783-1del		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.529513750404095	2		459	827	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1206989	1207002	+	frameshift_variant	Frame_Shift_Del	DEL	TCCACCGCATCGAC	TCCACCGCATCGAC	-	novel	NA	P-0052265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	115	606	1	ENST00000326873.7:c.84_97del	p.Ile29GlyfsTer129	p.I29Gfs*129	ENST00000326873	NM_000455.4	26	aTCCACCGCATCGAC/a	1/10	1	2	FACETS	0.492	0.443	0.545	0.492	0.443	0.545	SUBCLONAL	1	TRUE	1	0.529513750404095	2		607	882	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39713173	39713173	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	87	292	0	ENST00000361337.2:c.579G>T	p.Lys193Asn	p.K193N	ENST00000361337	NM_003286.2	193	aaG/aaT	8/21	1	2	FACETS	0.843	0.751	0.939	0.843	0.751	0.939	CLONAL	1	TRUE	1	0.529513750404095	2		292	390	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029300	143029300	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	141	296	0	ENST00000262992.4:c.2320T>G	p.Phe774Val	p.F774V	ENST00000262992	NM_001101669.1	774	Ttc/Gtc	21/24	0.347759546121681	1	FACETS	0.859	0.789	0.931	0.859	0.789	0.931	CLONAL	1	TRUE	0	0.529513750404095	1		296	456	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042251	6042251	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	124	456	0	ENST00000265849.7:c.370A>T	p.Thr124Ser	p.T124S	ENST00000265849	NM_000535.5	124	Acc/Tcc	5/15	NA	2	FACETS	0.599	0.542	0.659			1	INDETERMINATE	1	TRUE	NA	0.529513750404095	2		456	782	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486322	8486322	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	19	235	0	ENST00000356435.5:c.2495A>C	p.Asn832Thr	p.N832T	ENST00000356435		832	aAc/aCc	17/35	0.493740918382668	1	FACETS	0.165	0.125	0.213	0.165	0.125	0.213	SUBCLONAL	1	TRUE	0	0.529513750404095	1		235	319	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732862	44732862	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	80	372	0	ENST00000377967.4:c.68del	p.Lys23ArgfsTer19	p.K23Rfs*19	ENST00000377967	NM_021140.2	22	gAa/ga	1/29	NA	2	FACETS	0.415	0.365	0.469			1	INDETERMINATE	1	TRUE	NA	0.529513750404095	2		372	728	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410277	63410277	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	188	640	2	ENST00000330258.3:c.2890T>C	p.Cys964Arg	p.C964R	ENST00000330258	NM_152424.3	964	Tgt/Cgt	2/2	0.18907171443425	1	FACETS	0.552	0.51	0.596	0.552	0.51	0.596	INDETERMINATE	1	TRUE	0	0.529513750404095	1		642	945	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367293	50367293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	94	707	0	ENST00000331340.3:c.100C>T	p.Pro34Ser	p.P34S	ENST00000331340	NM_006060.4	34	Ccc/Tcc	3/8	0.250492837003177	3	FACETS	0.8	0.714	0.891	0.8	0.714	0.891	SUBCLONAL	2	TRUE	1	0.250492837003177	3		707	528	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491397	2491397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194006438	NA	P-0052363-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	58	726	0	ENST00000355716.4:c.440G>A	p.Gly147Asp	p.G147D	ENST00000355716	NM_003820.2	147	gGc/gAc	4/8	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.250492837003177	2		726	432	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541652	120541652	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052964-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	275	415	0	ENST00000229340.5:c.205C>T	p.Arg69Cys	p.R69C	ENST00000229340	NM_006861.6	69	Cgc/Tgc	3/6	0.804879266814813	3	FACETS	1	0.956	1	0.51	0.479	0.541	CLONAL	1	TRUE	1	0.804879266814813	3		415	940	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782936	66782936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052964-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	154	205	0	ENST00000307102.5:c.1165C>T	p.His389Tyr	p.H389Y	ENST00000307102	NM_002755.3	389	Cat/Tat	11/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.804879266814813	2		205	366	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217241	7217241	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052964-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	230	340	0	ENST00000380728.2:c.464G>T	p.Gly155Val	p.G155V	ENST00000380728		155	gGa/gTa	6/11	1	2	FACETS	0.98	0.921	1	0.98	0.921	1	CLONAL	1	TRUE	1	0.804879266814813	2		340	583	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311679	15311679	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052964-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	41	470	0	ENST00000263388.2:c.38G>T	p.Arg13Leu	p.R13L	ENST00000263388	NM_000435.2	13	cGc/cTc	1/33	1	2	FACETS	0.156	0.13	0.186	0.156	0.13	0.186	SUBCLONAL	1	TRUE	1	0.804879266814813	2		470	651	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052976-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	103	475	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.846	0.768	0.925	0.846	0.768	0.925	CLONAL	1	TRUE	1	0.876188407558459	2		475	278	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0052976-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	28	66	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.876188407558459	1	FACETS	0.185	0.149	0.226	0.185	0.149	0.226	SUBCLONAL	1	TRUE	0	0.876188407558459	1		66	194	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718716	190718716	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052976-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	46	509	0	ENST00000441310.2:c.874T>C	p.Tyr292His	p.Y292H	ENST00000441310	NM_000534.4	292	Tat/Cat	8/13	1	2	FACETS	0.245	0.207	0.288	0.245	0.207	0.288	SUBCLONAL	1	TRUE	1	0.876188407558459	2		509	428	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087333	27087346	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TATATATGTTCTAG	TATATATGTTCTAG	-	novel	NA	P-0052976-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	221	449	0	ENST00000324856.7:c.1921-14_1921-1del		p.X641_splice	ENST00000324856	NM_006015.4	641			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.876188407558459	2		449	470	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55225428	55225429	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0052976-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10499	7965	565	0	ENST00000275493.2:c.1280_1281delinsTT	p.Arg427Leu	p.R427L	ENST00000275493	NM_005228.3	427	cGC/cTT	11/28	0.876188407558459	43	FACETS	0.983	0.972	0.993	0.445	0.44	0.45	CLONAL	19	TRUE	1	0.876188407558459	43		565	18464	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729104	66729109	+	inframe_deletion	In_Frame_Del	DEL	ACCCGC	ACCCGC	-	novel	NA	P-0053193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	55	579	0	ENST00000307102.5:c.313_318del	p.Pro105_Ala106del	p.P105_A106del	ENST00000307102	NM_002755.3	104	aaACCCGCa/aaa	3/11	1	2	FACETS	0.71	0.607	0.822	0.71	0.607	0.822	SUBCLONAL	1	TRUE	1	0.273425368167188	2		579	567	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309037	137309037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs537231520	NA	P-0053193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	76	801	1	ENST00000481739.1:c.644G>A	p.Arg215Gln	p.R215Q	ENST00000481739	NM_002957.4	215	cGg/cAg	5/10	0.273425368167188	4	FACETS	0.757	0.662	0.859	0.189	0.165	0.215	SUBCLONAL	1	TRUE	0	0.273425368167188	4		802	935	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111855955	111855955	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs759758469	NA	P-0053193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	62	608	0	ENST00000341259.2:c.6C>G	p.Asn2Lys	p.N2K	ENST00000341259	NM_005475.2	2	aaC/aaG	2/8	0.245564183006907	3	FACETS	0.877	0.757	1	0.438	0.378	0.503	CLONAL	1	TRUE	1	0.273425368167188	3		608	588	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914069	32914070	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs397507790	NA	P-0053193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	110	416	0	ENST00000380152.3:c.5583dup	p.Val1862SerfsTer11	p.V1862Sfs*11	ENST00000380152		1859	-/A	11/27	0.19813318149499	2	FACETS	0.949	0.859	1	0.949	0.859	1	CLONAL	2	TRUE	0	0.273425368167188	2		416	424	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313250	30313250	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	65	465	0	ENST00000262643.3:c.944A>G	p.Lys315Arg	p.K315R	ENST00000262643	NM_001238.2	315	aAg/aGg	10/12	0.185885187768668	4	FACETS	1	0.878	1	0.506	0.439	0.579	CLONAL	1	TRUE	2	0.273425368167188	4		465	598	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484228	57484507	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGATCGACGTGATCAAGCAGGCTGACTATGTGCCGAGCGATCAGGTGTGCAAAACCCCTCCCCACCAGAGGACTCTGAGCCCTCTTTCCAAACTACTCCAGACCTTTGCTTTAGATTGGCAATTATTACTGTTTCGGTTGGCTTTGGTGAGATCCATTGACCTCAATTTTGTTTCAGGACCTGCTTCGCTGCCGTGTCCTGACTTCTGGAATCTTTGAGACCAAGTTCCAGGTGGACAAAGTCAACTTCCAGTAAGCCAACTGTTACCTTTTTATATAAC	AGATCGACGTGATCAAGCAGGCTGACTATGTGCCGAGCGATCAGGTGTGCAAAACCCCTCCCCACCAGAGGACTCTGAGCCCTCTTTCCAAACTACTCCAGACCTTTGCTTTAGATTGGCAATTATTACTGTTTCGGTTGGCTTTGGTGAGATCCATTGACCTCAATTTTGTTTCAGGACCTGCTTCGCTGCCGTGTCCTGACTTCTGGAATCTTTGAGACCAAGTTCCAGGTGGACAAAGTCAACTTCCAGTAAGCCAACTGTTACCTTTTTATATAAC	-	novel	NA	P-0053193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	91	377	0	ENST00000371085.3:c.545_659+32del		p.X182_splice	ENST00000371085	NM_000516.4	182		7-8/13	0.245564183006907	3	FACETS	0.953	0.852	1	0.953	0.852	1	CLONAL	2	TRUE	1	0.273425368167188	3		377	397	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84393394	84393394	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	36	307	0	ENST00000321945.7:c.263T>G	p.Ile88Arg	p.I88R	ENST00000321945	NM_139076.2	88	aTa/aGa	4/9	0.273425368167188	3	FACETS	0.673	0.553	0.807	0.336	0.276	0.404	SUBCLONAL	1	TRUE	1	0.273425368167188	3		307	445	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589537	67589554	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GATCAAGTTGTCAAAGAA	GATCAAGTTGTCAAAGAA	-	novel	NA	P-0053193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	19	174	0	ENST00000274335.5:c.1303_1320del	p.Gln435_Asp440del	p.Q435_D440del	ENST00000274335		434	GATCAAGTTGTCAAAGAA/-	10/15	1	2	FACETS	0.739	0.564	0.943	0.739	0.564	0.943	CLONAL	1	TRUE	1	0.273425368167188	2		174	188	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624258	89624259	+	frameshift_variant	Frame_Shift_Ins	INS	GA	GA	TATCAAGAACAAC	novel	NA	P-0053193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	19	252	0	ENST00000371953.3:c.32_33delinsTATCAAGAACAAC	p.Arg11IlefsTer17	p.R11Ifs*17	ENST00000371953	NM_000314.4	11	aGA/aTATCAAGAACAAC	1/9	0.185885187768668	4	FACETS	0.634	0.482	0.814	0.317	0.241	0.407	SUBCLONAL	1	TRUE	2	0.273425368167188	4		252	279	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651513	52651513	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053509-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	22	356	0	ENST00000394830.3:c.1583A>T	p.Asn528Ile	p.N528I	ENST00000394830	NM_018313.4	528	aAt/aTt	15/30	0.470451417141648	1	FACETS	0.862	0.685	1	0.862	0.685	1	CLONAL	1	FALSE	0	0.470451417141648	1		356	83	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864331	151864331	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775712660	NA	P-0053509-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	37	474	0	ENST00000262189.6:c.9650G>A	p.Arg3217His	p.R3217H	ENST00000262189	NM_170606.2	3217	cGt/cAt	42/59	1	2	FACETS	0.874	0.729	1	0.874	0.729	1	CLONAL	1	FALSE	1	0.470451417141648	2		474	180	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900698	3900698	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053509-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	40	721	0	ENST00000262367.5:c.398T>C	p.Leu133Pro	p.L133P	ENST00000262367	NM_004380.2	133	cTg/cCg	2/31	0.158026754742296	0	FACETS	0.687	0.584	0.797			1	INDETERMINATE	1	FALSE	0	0.470451417141648	0		721	131	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188303	10188303	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053509-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	45	387	0	ENST00000256474.2:c.446C>A	p.Ala149Asp	p.A149D	ENST00000256474	NM_000551.3	149	gCc/gAc	2/3	0.470451417141648	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	0	0.470451417141648	1		387	105	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231085	53231085	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1556842070	NA	P-0053509-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	51	310	0	ENST00000375401.3:c.1817A>T	p.Asn606Ile	p.N606I	ENST00000375401	NM_004187.3	606	aAc/aTc	13/26	0.470451417141648	0	FACETS	0.668	0.596	0.737			1	SUBCLONAL	2	FALSE	NA	0.470451417141648	0		310	86	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0054325-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	181	388	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.246095736818122	5	FACETS	0.904	0.835	0.974	0.904	0.835	0.974	CLONAL	3	TRUE	2	0.246095736818122	5		388	743	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs786201838	NA	P-0054325-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	213	718	0	ENST00000269305.4:c.578A>C	p.His193Pro	p.H193P	ENST00000269305	NM_001126112.2	193	cAt/cCt	6/11	0.242854941654954	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.246095736818122	2		718	775	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817493	39817493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755303168	NA	P-0054325-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	297	592	0	ENST00000288319.7:c.70G>A	p.Gly24Arg	p.G24R	ENST00000288319	NM_182918.3	24	Gga/Aga	2/10	0.246095736818122	5	FACETS	0.913	0.862	0.965	0.913	0.862	0.965	CLONAL	4	TRUE	1	0.246095736818122	5		592	905	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134614	2134614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054325-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	119	828	0	ENST00000219476.3:c.4391C>T	p.Ser1464Phe	p.S1464F	ENST00000219476	NM_000548.3	1464	tCc/tTc	34/42	0.199177057019952	4	FACETS	1	0.983	1	0.728	0.657	0.803	CLONAL	1	TRUE	2	0.246095736818122	4		828	828	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134918	41134918	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054325-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	100	504	0	ENST00000379561.5:c.710G>A	p.Trp237Ter	p.W237*	ENST00000379561	NM_002015.3	237	tGg/tAg	2/3	0.246095736818122	4	FACETS	0.903	0.808	1	0.903	0.808	1	CLONAL	2	TRUE	2	0.246095736818122	4		504	561	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56854546	56854546	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054325-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	112	364	0	ENST00000519728.1:c.128G>T	p.Arg43Met	p.R43M	ENST00000519728	NM_002350.3	43	aGg/aTg	2/13	0.246095736818122	4	FACETS	0.998	0.901	1			1	CLONAL	2	TRUE	NA	0.246095736818122	4		364	568	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913400	NA	P-0055117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	31	471	0	ENST00000349496.5:c.98C>A	p.Ser33Tyr	p.S33Y	ENST00000349496	NM_001904.3	33	tCt/tAt	3/15	0.376536319566391	3	FACETS	0.772	0.637	0.916	0.514	0.425	0.611	CLONAL	2	TRUE	0	0.423300110042679	3		471	115	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0055117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	61	385	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.359713820461128	4	FACETS	1	0.947	1			1	CLONAL	2	TRUE	NA	0.423300110042679	4		385	179	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	36	486	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.256659723034482	3	FACETS	0.778	0.643	0.927	0.259	0.214	0.309	CLONAL	1	TRUE	0	0.423300110042679	3		486	265	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573996	7574005	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTCTCGGA	AGCTCTCGGA	-	novel	NA	P-0055117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	50	511	0	ENST00000269305.4:c.1022_1031del	p.Phe341Ter	p.F341*	ENST00000269305	NM_001126112.2	341	tTCCGAGAGCTg/tg	10/11	0.423300110042679	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	0	0.423300110042679	2		511	109	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520264	9520264	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs368616079	NA	P-0055117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	42	515	0	ENST00000353224.5:c.2005G>T	p.Val669Phe	p.V669F	ENST00000353224	NM_177990.2	669	Gtt/Ttt	10/10	1	2	FACETS	0.834	0.714	0.958	1	0.968	1	CLONAL	2	TRUE	1	0.423300110042679	2		515	119	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651334	52651334	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	55	492	0	ENST00000394830.3:c.1762G>T	p.Glu588Ter	p.E588*	ENST00000394830	NM_018313.4	588	Gaa/Taa	15/30	0.423300110042679	2	FACETS	0.841	0.749	0.932	1	0.967	1	CLONAL	3	TRUE	0	0.423300110042679	2		492	103	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858134	152858134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1393228949	NA	P-0055117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	26	649	0	ENST00000406277.2:c.481C>T	p.Arg161Trp	p.R161W	ENST00000406277	NM_152274.4	161	Cgg/Tgg	6/7	0.421331158162063	4	FACETS	1	0.921	1	0.445	0.357	0.542	CLONAL	1	TRUE	1	0.423300110042679	4		649	131	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483958	88483958	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	13	563	0	ENST00000360948.2:c.1612A>G	p.Ile538Val	p.I538V	ENST00000360948	NM_001012338.2	538	Atc/Gtc	14/19	1	2	FACETS	0.591	0.426	0.787	0.591	0.426	0.787	SUBCLONAL	1	TRUE	1	0.423300110042679	2		563	104	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842359	151842359	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055117-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	34	518	0	ENST00000262189.6:c.14053G>A	p.Glu4685Lys	p.E4685K	ENST00000262189	NM_170606.2	4685	Gaa/Aaa	54/59	0.389190681619514	5	FACETS	1	0.921	1	0.409	0.337	0.489	CLONAL	1	TRUE	2	0.423300110042679	5		518	214	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0055453-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	103	247	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.242644565631663	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.242644565631663	2		247	392	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940561	71940561	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055453-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	60	631	0	ENST00000298229.2:c.712C>T	p.Gln238Ter	p.Q238*	ENST00000298229	NM_001567.3	238	Cag/Tag	6/28	0.148589008408566	4	FACETS	0.999	0.861	1	0.5	0.43	0.575	CLONAL	1	TRUE	2	0.242644565631663	4		631	615	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988188	36988188	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0055453-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	109	553	0	ENST00000354822.5:c.463+2T>A		p.X155_splice	ENST00000354822	NM_001079668.2	155			0.242644565631663	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.242644565631663	2		553	362	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570421	87570421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1564499587	NA	P-0055453-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	67	591	0	ENST00000277120.3:c.2161G>A	p.Asp721Asn	p.D721N	ENST00000277120		721	Gac/Aac	17/19	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.242644565631663	2		591	501	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143984	11143984	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs267607070	NA	P-0055453-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	167	598	0	ENST00000358026.2:c.3565C>T	p.Arg1189Ter	p.R1189*	ENST00000358026	NM_001128849.1	1189	Cga/Tga	26/36	0.239742054652694	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	0	0.242644565631663	3		598	449	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0055577-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	70	377	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.748	0.655	0.849	0.748	0.655	0.849	SUBCLONAL	1	FALSE	1	0.418443344714899	2		377	447	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207162	1207162	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs137853076	NA	P-0055577-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	288	276	0	ENST00000326873.7:c.250A>T	p.Lys84Ter	p.K84*	ENST00000326873	NM_000455.4	84	Aag/Tag	1/10	0.418443344714899	5	FACETS	0.835	0.788	0.884			1	CLONAL	3	FALSE	NA	0.418443344714899	5		276	894	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181227	123181227	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055577-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	181	144	0	ENST00000218089.9:c.691G>A	p.Val231Met	p.V231M	ENST00000218089	NM_001042749.1	231	Gtg/Atg	9/35	0.418443344714899	2	FACETS	0.901	0.848	0.953			1	CLONAL	3	FALSE	NA	0.418443344714899	2		144	320	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597490	10597491	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0055577-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	196	221	0	ENST00000171111.5:c.1712_1713delinsTT	p.Gly571Val	p.G571V	ENST00000171111	NM_203500.1	571	gGC/gTT	6/6	0.371630293116344	4	FACETS	0.899	0.835	0.965			1	CLONAL	2	FALSE	NA	0.418443344714899	4		221	739	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392668	118392668	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055577-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	103	400	0	ENST00000534358.1:c.11700G>T	p.Met3900Ile	p.M3900I	ENST00000534358	NM_005933.3	3900	atG/atT	36/36	0.260658374160245	4	FACETS	0.925	0.828	1			1	CLONAL	1	FALSE	NA	0.418443344714899	4		400	755	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912238	32912238	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055577-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	65	456	1	ENST00000380152.3:c.3746A>G	p.Glu1249Gly	p.E1249G	ENST00000380152		1249	gAg/gGg	11/27	1	2	FACETS	0.675	0.587	0.771	0.675	0.587	0.771	SUBCLONAL	1	FALSE	1	0.418443344714899	2		457	460	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843252	128843252	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055577-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	117	508	0	ENST00000249373.3:c.359C>G	p.Ala120Gly	p.A120G	ENST00000249373	NM_005631.4	120	gCa/gGa	2/12	0.116332447894669	3	FACETS	0.701	0.632	0.776	0.234	0.21	0.259	INDETERMINATE	1	FALSE	0	0.418443344714899	3		508	964	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056417-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	42	798	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.631	0.524	0.751	0.631	0.524	0.751	SUBCLONAL	1	TRUE	1	0.11	2		798	1210	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111496	8111512	+	frameshift_variant	Frame_Shift_Del	DEL	TGGAGGAGGAATGCCAA	TGGAGGAGGAATGCCAA	-	novel	NA	P-0056417-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	58	680	0	ENST00000346208.3:c.985_1001del	p.Arg329GlyfsTer17	p.R329Gfs*17	ENST00000346208		328	TGGAGGAGGAATGCCAAt/t	5/6	1	2	FACETS	0.95	0.813	1	0.95	0.813	1	CLONAL	1	TRUE	1	0.11	2		680	1110	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0056656-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	611	875	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.470186696585797	3	FACETS	1	0.996	1	0.828	0.801	0.853	CLONAL	2	TRUE	0	0.610750492383661	3		875	1052	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467623	66467623	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056656-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	88	533	0	ENST00000273854.3:c.646G>T	p.Asp216Tyr	p.D216Y	ENST00000273854	NM_004439.5	216	Gat/Tat	3/18	0.370243316760713	3	FACETS	0.463	0.409	0.52	0.154	0.136	0.174	SUBCLONAL	1	TRUE	0	0.610750492383661	3		533	813	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897351	78897351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056656-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	140	1112	1	ENST00000306801.3:c.2686C>T	p.Pro896Ser	p.P896S	ENST00000306801	NM_020761.2	896	Ccg/Tcg	23/34	0.545309073969325	3	FACETS	0.495	0.449	0.543	0.165	0.149	0.181	SUBCLONAL	1	TRUE	0	0.610750492383661	3		1113	1209	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636849	73636849	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056656-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1201	229	580	0	ENST00000377687.4:c.1112G>A	p.Arg371His	p.R371H	ENST00000377687	NM_001730.3	371	cGc/cAc	2/4	0.610750492383661	4	FACETS	0.845	0.785	0.907	0.211	0.196	0.227	CLONAL	1	TRUE	0	0.610750492383661	4		580	1430	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208054	5208054	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056656-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	432	867	0	ENST00000357368.4:c.5657G>T	p.Arg1886Met	p.R1886M	ENST00000357368	NM_002850.3	1886	aGg/aTg	37/38	0.53740916771397	2	FACETS	0.879	0.844	0.913	0.879	0.844	0.913	CLONAL	2	TRUE	0	0.610750492383661	2		867	805	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542516	141542516	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056656-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	201	735	0	ENST00000220592.5:c.2470A>T	p.Ser824Cys	p.S824C	ENST00000220592	NM_012154.3	824	Agt/Tgt	18/19	0.569832851695484	1	FACETS	0.831	0.776	0.887	0.831	0.776	0.887	CLONAL	1	TRUE	0	0.610750492383661	1		735	550	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0057132-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	25	527	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.453	0.355	0.567	0.453	0.355	0.567	SUBCLONAL	1	TRUE	1	0.13	2		528	849	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841241	15841241	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770119952	NA	P-0057132-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	60	911	1	ENST00000307771.7:c.1325G>A	p.Arg442Gln	p.R442Q	ENST00000307771	NM_005089.3	442	cGg/cAg	11/11	1	2	FACETS	0.799	0.685	0.923	0.799	0.685	0.923	CLONAL	1	TRUE	1	0.13	2		912	1156	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0057385-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	231	388	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.202597268952651	4	FACETS	0.902	0.841	0.964			1	CLONAL	3	TRUE	NA	0.21	4		388	984	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0057385-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	76	527	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	1	2	FACETS	0.871	0.763	0.988	0.871	0.763	0.988	CLONAL	1	TRUE	1	0.21	2		527	831	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891584	151891584	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0057385-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	93	418	0	ENST00000262189.6:c.4448T>G	p.Leu1483Ter	p.L1483*	ENST00000262189	NM_170606.2	1483	tTa/tGa	29/59	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.21	2		418	842	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0057387-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	256	279	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.406055341873413	5	FACETS	0.987	0.93	1	0.987	0.93	1	CLONAL	3	TRUE	2	0.406055341873413	5		279	685	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0057387-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	361	606	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.406055341873413	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.406055341873413	2		606	866	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017705	31017743	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GTTCTCGGGCTGCCACGCCGATGGCGAGAGCGGCAGCCC	GTTCTCGGGCTGCCACGCCGATGGCGAGAGCGGCAGCCC	-	novel	NA	P-0057387-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	115	385	0	ENST00000375687.4:c.569_607del	p.Phe190_Pro202del	p.F190_P202del	ENST00000375687	NM_015338.5	189	ggGTTCTCGGGCTGCCACGCCGATGGCGAGAGCGGCAGCCCg/ggg	8/13	0.366253907491966	4	FACETS	1	0.931	1	0.521	0.469	0.575	CLONAL	1	TRUE	2	0.406055341873413	4		385	765	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047989	180047989	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057387-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	434	662	0	ENST00000261937.6:c.2186C>T	p.Ser729Phe	p.S729F	ENST00000261937	NM_182925.4	729	tCc/tTc	15/30	0.366253907491966	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	2	0.406055341873413	4		662	1205	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	26	279	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.739	0.585	0.914	0.739	0.585	0.914	CLONAL	1	TRUE	1	0.215982917276406	2		279	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	57	489	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.215982917276406	1	FACETS	0.823	0.706	0.951	0.823	0.706	0.951	CLONAL	1	TRUE	0	0.215982917276406	1		489	572	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016609	12016609	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	66	448	0	ENST00000353533.5:c.745G>T	p.Gly249Cys	p.G249C	ENST00000353533	NM_003010.3	249	Ggc/Tgc	7/11	0.215982917276406	1	FACETS	0.95	0.825	1	0.95	0.825	1	CLONAL	1	TRUE	0	0.215982917276406	1		448	574	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115260837	115260837	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	54	375	0	ENST00000438362.2:c.2488G>T	p.Gly830Trp	p.G830W	ENST00000438362	NM_001242891.1	830	Ggg/Tgg	20/20	1	2	FACETS	0.982	0.84	1	0.982	0.84	1	CLONAL	1	TRUE	1	0.215982917276406	2		375	509	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356195	66356195	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	106	623	0	ENST00000273854.3:c.1302C>A	p.His434Gln	p.H434Q	ENST00000273854	NM_004439.5	434	caC/caA	5/18	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.215982917276406	2		623	932	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150457	157150457	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554256715	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	78	552	0	ENST00000346085.5:c.1639G>T	p.Gly547Ter	p.G547*	ENST00000346085	NM_020732.3	547	Gga/Tga	2/20	0.215982917276406	3	FACETS	0.982	0.862	1	0.491	0.431	0.556	CLONAL	1	TRUE	1	0.215982917276406	3		552	815	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080613	5080613	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	48	357	0	ENST00000381652.3:c.2364G>T	p.Met788Ile	p.M788I	ENST00000381652	NM_004972.3	788	atG/atT	18/25	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.215982917276406	2		357	394	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611246	100611246	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	54	366	0	ENST00000308731.7:c.1360C>A	p.His454Asn	p.H454N	ENST00000308731	NM_000061.2	454	Cat/Aat	15/19	1	2	FACETS	0.963	0.823	1	0.963	0.823	1	CLONAL	1	TRUE	1	0.215982917276406	2		366	519	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451206	70451206	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	92	655	0	ENST00000373644.4:c.6046G>T	p.Gly2016Cys	p.G2016C	ENST00000373644	NM_030625.2	2016	Ggc/Tgc	12/12	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.215982917276406	2		655	750	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514736	103514736	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	180	608	0	ENST00000355739.4:c.1237G>C	p.Gly413Arg	p.G413R	ENST00000355739	NM_000123.3	413	Ggg/Cgg	8/15	0.215982917276406	3	FACETS	0.877	0.808	0.949	0.877	0.808	0.949	CLONAL	2	TRUE	1	0.215982917276406	3		608	1053	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99439984	99439984	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	61	406	0	ENST00000268035.6:c.954-2A>T		p.X318_splice	ENST00000268035	NM_000875.3	318			0.215982917276406	1	FACETS	0.986	0.852	1	0.986	0.852	1	CLONAL	1	TRUE	0	0.215982917276406	1		406	511	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984937	9984937	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1231057100	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	32	371	0	ENST00000330684.3:c.1028G>T	p.Trp343Leu	p.W343L	ENST00000330684	NM_001134407.1	343	tGg/tTg	4/13	1	2	FACETS	0.661	0.536	0.803	0.661	0.536	0.803	SUBCLONAL	1	TRUE	1	0.215982917276406	2		371	448	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31015983	31015983	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	72	554	0	ENST00000375687.4:c.305C>G	p.Pro102Arg	p.P102R	ENST00000375687	NM_015338.5	102	cCa/cGa	5/13	1	2	FACETS	0.822	0.717	0.936	0.822	0.717	0.936	CLONAL	1	TRUE	1	0.215982917276406	2		554	811	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628829	187628829	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	60	533	0	ENST00000441802.2:c.2153G>T	p.Ser718Ile	p.S718I	ENST00000441802	NM_005245.3	718	aGc/aTc	2/27	1	2	FACETS	0.794	0.683	0.915	0.794	0.683	0.915	CLONAL	1	TRUE	1	0.215982917276406	2		533	700	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509506	149509506	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	51	603	0	ENST00000261799.4:c.1393C>A	p.Leu465Met	p.L465M	ENST00000261799	NM_002609.3	465	Ctg/Atg	10/23	0.215982917276406	1	FACETS	0.728	0.618	0.848	0.728	0.618	0.848	SUBCLONAL	1	TRUE	0	0.215982917276406	1		603	579	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402482	20402482	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	64	508	0	ENST00000346618.3:c.19C>G	p.Pro7Ala	p.P7A	ENST00000346618	NM_001949.4	7	Ccc/Gcc	1/7	1	2	FACETS	0.872	0.754	0.999	0.872	0.754	0.999	CLONAL	1	TRUE	1	0.215982917276406	2		508	680	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374426	81374426	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	39	345	0	ENST00000222390.5:c.636G>C	p.Met212Ile	p.M212I	ENST00000222390	NM_000601.4	212	atG/atC	6/18	1	2	FACETS	0.813	0.674	0.968	0.813	0.674	0.968	CLONAL	1	TRUE	1	0.215982917276406	2		345	444	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960183	151960183	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	20	175	0	ENST00000262189.6:c.1217G>T	p.Cys406Phe	p.C406F	ENST00000262189	NM_170606.2	406	tGt/tTt	9/59	0.187239243977452	3	FACETS	1	0.889	1	0.645	0.497	0.816	CLONAL	1	TRUE	1	0.215982917276406	3		175	159	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38314921	38314921	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	48	449	0	ENST00000425967.3:c.143del	p.Thr48LysfsTer88	p.T48Kfs*88	ENST00000425967	NM_001174067.1	48	aCa/aa	3/19	1	2	FACETS	0.828	0.7	0.969	0.828	0.7	0.969	CLONAL	1	TRUE	1	0.215982917276406	2		449	537	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220524	98220524	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	52	579	0	ENST00000331920.6:c.2939G>T	p.Gly980Val	p.G980V	ENST00000331920	NM_000264.3	980	gGc/gTc	18/24	1	2	FACETS	0.774	0.658	0.901	0.774	0.658	0.901	CLONAL	1	TRUE	1	0.215982917276406	2		579	622	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411855	63411855	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	79	700	0	ENST00000330258.3:c.1312C>A	p.Leu438Ile	p.L438I	ENST00000330258	NM_152424.3	438	Ctc/Atc	2/2	1	2	FACETS	0.849	0.745	0.96	0.849	0.745	0.96	CLONAL	1	TRUE	1	0.215982917276406	2		700	862	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132876	64132876	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	39	694	0	ENST00000334205.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000334205	NM_003942.2	337	cGg/cTg	9/17	0.215982917276406	1	FACETS	0.438	0.361	0.523	0.438	0.361	0.523	SUBCLONAL	1	TRUE	0	0.215982917276406	1		694	736	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913206	32913206	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	65	552	0	ENST00000380152.3:c.4714G>T	p.Ala1572Ser	p.A1572S	ENST00000380152		1572	Gcc/Tcc	11/27	0.215982917276406	1	FACETS	0.809	0.701	0.926	0.809	0.701	0.926	CLONAL	1	TRUE	0	0.215982917276406	1		552	664	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100131	30100131	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	43	474	0	ENST00000331968.5:c.1489G>T	p.Ala497Ser	p.A497S	ENST00000331968	NM_002742.2	497	Gca/Tca	10/18	1	2	FACETS	0.675	0.564	0.798	0.675	0.564	0.798	SUBCLONAL	1	TRUE	1	0.215982917276406	2		474	590	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562968	95562968	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	80	544	0	ENST00000393063.1:c.4289G>T	p.Arg1430Met	p.R1430M	ENST00000393063	NM_030621.3	1430	aGg/aTg	24/28	1	2	FACETS	0.878	0.771	0.992	0.878	0.771	0.992	CLONAL	1	TRUE	1	0.215982917276406	2		544	844	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980319	7980319	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	58	613	0	ENST00000319144.4:c.1264C>A	p.Pro422Thr	p.P422T	ENST00000319144	NM_001139.2	422	Ccc/Acc	9/15	0.215982917276406	1	FACETS	0.848	0.729	0.978	0.848	0.729	0.978	CLONAL	1	TRUE	0	0.215982917276406	1		613	565	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312686	30312686	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	39	498	0	ENST00000262643.3:c.667G>T	p.Gly223Ter	p.G223*	ENST00000262643	NM_001238.2	223	Gga/Tga	8/12	1	2	FACETS	0.727	0.602	0.866	0.727	0.602	0.866	SUBCLONAL	1	TRUE	1	0.215982917276406	2		498	497	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046918	128046918	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	54	509	0	ENST00000285398.2:c.817A>T	p.Lys273Ter	p.K273*	ENST00000285398	NM_000122.1	273	Aag/Tag	6/15	1	2	FACETS	0.816	0.696	0.947	0.816	0.696	0.947	CLONAL	1	TRUE	1	0.215982917276406	2		509	613	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456436	89456436	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	39	396	0	ENST00000336596.2:c.1612G>T	p.Glu538Ter	p.E538*	ENST00000336596	NM_005233.5	538	Gaa/Taa	8/17	1	2	FACETS	0.634	0.524	0.756	0.634	0.524	0.756	SUBCLONAL	1	TRUE	1	0.215982917276406	2		396	570	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134514531	134514531	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	33	432	0	ENST00000398015.3:c.58G>T	p.Glu20Ter	p.E20*	ENST00000398015	NM_004441.4	20	Gaa/Taa	1/16	1	2	FACETS	0.907	0.74	1	0.907	0.74	1	CLONAL	1	TRUE	1	0.215982917276406	2		432	337	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161990437	161990437	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	128	448	0	ENST00000366898.1:c.883A>T	p.Asn295Tyr	p.N295Y	ENST00000366898	NM_004562.2	295	Aac/Tac	8/12	0.215982917276406	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	1	0.215982917276406	3		448	625	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042242	6042242	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	75	461	0	ENST00000265849.7:c.379G>T	p.Ala127Ser	p.A127S	ENST00000265849	NM_000535.5	127	Gca/Tca	5/15	1	2	FACETS	0.928	0.813	1	0.928	0.813	1	CLONAL	1	TRUE	1	0.215982917276406	2		461	748	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151933005	151933005	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	21	160	0	ENST00000262189.6:c.2666G>T	p.Gly889Val	p.G889V	ENST00000262189	NM_170606.2	889	gGa/gTa	16/59	0.187239243977452	3	FACETS	0.7	0.539	0.887	0.35	0.269	0.444	SUBCLONAL	1	TRUE	1	0.215982917276406	3		160	308	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518340	8518340	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	36	402	0	ENST00000356435.5:c.1051G>A	p.Val351Ile	p.V351I	ENST00000356435		351	Gtt/Att	10/35	1	2	FACETS	0.539	0.442	0.649	0.539	0.442	0.649	SUBCLONAL	1	TRUE	1	0.215982917276406	2		402	618	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098488	11098490	+	missense_variant	Missense_Mutation	TNP	CCG	CCG	TCC	novel	NA	P-0057588-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	60	712	0	ENST00000358026.2:c.1006_1008delinsTCC	p.Pro336Ser	p.P336S	ENST00000358026	NM_001128849.1	336	CCG/TCC	6/36	1	2	FACETS	0.921	0.794	1	0.921	0.794	1	CLONAL	1	TRUE	1	0.215982917276406	2		712	603	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100975	41100975	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057683-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	674	1672	0	ENST00000373198.4:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000373198	NM_133170.3	461	Cga/Tga	8/32	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.918331963829164	2		1672	1429	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988167	85988167	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057683-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	306	405	0	ENST00000263360.6:c.1112A>T	p.Asp371Val	p.D371V	ENST00000263360	NM_003797.3	371	gAt/gTt	10/12	0.918331963829164	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.918331963829164	1		405	356	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183800	10183800	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs143985153	NA	P-0058182-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	67	560	0	ENST00000256474.2:c.269A>T	p.Asn90Ile	p.N90I	ENST00000256474	NM_000551.3	90	aAc/aTc	1/3	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		560	364	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188262	10188263	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058182-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	68	465	0	ENST00000256474.2:c.408dup	p.Val137CysfsTer7	p.V137Cfs*7	ENST00000256474	NM_000551.3	135	-/T	2/3	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		465	456	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0058209-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	248	499	0				ENST00000310581	NM_198253.2	-/1132			0.633492843107844	3	FACETS	0.863	0.823	0.903	1	0.993	1	CLONAL	3	TRUE	1	0.633492843107844	3		499	398	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325233	39325242	+	protein_altering_variant	In_Frame_Del	DEL	CCGTAGCCGA	CCGTAGCCGA	ACTTCGG	novel	NA	P-0058209-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	45	1419	2	ENST00000373001.3:c.77_86delinsCCGAAGT	p.Phe26_Gly29delinsSerGluVal	p.F26_G29delinsSEV	ENST00000373001	NM_022157.3	26	tTCGGCTACGGc/tCCGAAGTc	1/7	1	2	FACETS	0.292	0.245	0.343	0.292	0.245	0.343	SUBCLONAL	1	TRUE	1	0.633492843107844	2		1421	487	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150902492	150902492	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058209-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	99	864	1	ENST00000271640.5:c.310G>T	p.Gly104Ter	p.G104*	ENST00000271640	NM_001145415.1	104	Gga/Tga	3/22	0.230903413559382	6	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.633492843107844	6		865	584	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28980031	28980031	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1309375561	NA	P-0058209-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	64	595	1	ENST00000282397.4:c.1437G>T	p.Arg479Ser	p.R479S	ENST00000282397	NM_002019.4	479	agG/agT	11/30	0.601422364322753	0	FACETS	0.365	0.321	0.411			1	SUBCLONAL	1	TRUE	0	0.633492843107844	0		596	203	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595948	52595948	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058209-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	101	1055	0	ENST00000394830.3:c.3967G>T	p.Glu1323Ter	p.E1323*	ENST00000394830	NM_018313.4	1323	Gaa/Taa	26/30	1	2	FACETS	0.689	0.619	0.762	0.689	0.619	0.762	SUBCLONAL	1	TRUE	1	0.633492843107844	2		1055	463	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055897	180055897	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058209-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	138	1199	1	ENST00000261937.6:c.1088C>A	p.Pro363Gln	p.P363Q	ENST00000261937	NM_182925.4	363	cCg/cAg	8/30	0.292401287355868	3	FACETS	1	0.985	1	0.677	0.621	0.733	INDETERMINATE	1	TRUE	1	0.633492843107844	3		1200	424	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032006	26032006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058209-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	164	1352	0	ENST00000244661.2:c.283G>A	p.Glu95Lys	p.E95K	ENST00000244661	NM_003537.3	95	Gag/Aag	1/1	0.125018945980158	4	FACETS	1	0.983	1	0.626	0.577	0.678	INDETERMINATE	1	TRUE	2	0.633492843107844	4		1352	675	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587778720	NA	P-0058299-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	514	587	0	ENST00000269305.4:c.638G>C	p.Arg213Pro	p.R213P	ENST00000269305	NM_001126112.2	213	cGa/cCa	6/11	0.729220614948249	3	FACETS	0.978	0.953	1	0.978	0.953	1	CLONAL	3	TRUE	0	0.719902828569636	3		587	662	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380347	14380347	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058299-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	720	458	0	ENST00000256196.4:c.70G>T	p.Gly24Cys	p.G24C	ENST00000256196		24	Ggc/Tgc	1/6	0.513128922231025	3	FACETS	0.961	0.93	0.991	0.961	0.93	0.991	CLONAL	2	TRUE	1	0.719902828569636	3		458	1416	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971369	13971369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779937870	NA	P-0058299-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	77	454	0	ENST00000405192.2:c.560G>A	p.Arg187His	p.R187H	ENST00000405192	NM_001163147.1	187	cGc/cAc	8/12	0.454765057371995	5	FACETS	1	0.914	1	0.348	0.307	0.392	CLONAL	1	TRUE	2	0.719902828569636	5		454	426	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245219	46245219	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058299-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	320	561	0	ENST00000334344.6:c.3313C>T	p.Gln1105Ter	p.Q1105*	ENST00000334344	NM_152641.2	1105	Caa/Taa	15/21	0.347021949557971	6	FACETS	1	0.977	1	0.686	0.657	0.715	INDETERMINATE	4	TRUE	0	0.719902828569636	6		561	527	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237715	16237715	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058299-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	163	429	0	ENST00000375759.3:c.1162G>T	p.Asp388Tyr	p.D388Y	ENST00000375759	NM_015001.2	388	Gac/Tac	5/15	0.729220614948249	4	FACETS	1	0.979	1	0.753	0.702	0.803	CLONAL	2	TRUE	1	0.719902828569636	4		429	345	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148891	119148905	+	inframe_deletion	In_Frame_Del	DEL	TACTGTGAGATGGGC	TACTGTGAGATGGGC	-	novel	NA	P-0058299-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	67	216	0	ENST00000264033.4:c.1112_1126del	p.Tyr371_Gly375del	p.Y371_G375del	ENST00000264033	NM_005188.3	371	TACTGTGAGATGGGC/-	8/16	0.682655918010136	4	FACETS	1	0.972	1	0.861	0.792	0.924	CLONAL	3	TRUE	0	0.719902828569636	4		216	93	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220274	55220274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4201	363	455	0	ENST00000275493.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000275493	NM_005228.3	222	Cgc/Tgc	6/28	0.28379905723979	55	FACETS	0.955	0.899	1			1	CLONAL	5	TRUE	NA	0.28379905723979	55		455	4564	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867333	45867333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765839639	NA	P-0058478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	77	721	0	ENST00000391945.4:c.860G>A	p.Arg287His	p.R287H	ENST00000391945	NM_000400.3	287	cGt/cAt	10/23	0.28379905723979	3	FACETS	1	0.91	1	0.522	0.458	0.59	CLONAL	1	TRUE	1	0.28379905723979	3		721	594	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861149	57861149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774058977	NA	P-0058478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	92	571	0	ENST00000228682.2:c.946G>A	p.Glu316Lys	p.E316K	ENST00000228682	NM_005269.2	316	Gaa/Aaa	9/12	1	2	FACETS	0.937	0.833	1	0.937	0.833	1	CLONAL	1	TRUE	1	0.28379905723979	2		571	692	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414970	56414970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146335154	NA	P-0058478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	68	538	0	ENST00000348428.3:c.2371G>A	p.Ala791Thr	p.A791T	ENST00000348428	NM_006785.3	791	Gct/Act	17/17	1	2	FACETS	0.931	0.811	1	0.931	0.811	1	CLONAL	1	TRUE	1	0.28379905723979	2		538	515	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0058478-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	41	499	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.973	0.814	1	0.973	0.814	1	CLONAL	1	TRUE	1	0.28379905723979	2		499	297	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058486-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	634	475	0				ENST00000310581	NM_198253.2	-/1132			0.658974463695718	11	FACETS	1	0.975	1	1	0.975	1	CLONAL	9	TRUE	2	0.658974463695718	11		475	848	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0058486-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	636	575	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.658974463695718	4	FACETS	1	0.979	1			1	CLONAL	4	TRUE	NA	0.658974463695718	4		575	800	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428615	78428615	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058486-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	60	316	0	ENST00000370768.2:c.1184G>A	p.Gly395Glu	p.G395E	ENST00000370768	NM_003902.3	395	gGa/gAa	14/20	0.658974463695718	5	FACETS	0.926	0.801	1	0.309	0.267	0.354	CLONAL	1	TRUE	2	0.658974463695718	5		316	391	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102033215	102033215	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058486-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	108	449	0	ENST00000282441.5:c.601G>A	p.Asp201Asn	p.D201N	ENST00000282441	NM_001130145.2	201	Gac/Aac	3/9	0.607664317561228	4	FACETS	0.874	0.786	0.967	0.291	0.262	0.323	CLONAL	1	TRUE	1	0.658974463695718	4		449	622	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196089	108196089	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058486-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	71	378	0	ENST00000278616.4:c.6625T>C	p.Ser2209Pro	p.S2209P	ENST00000278616	NM_000051.3	2209	Tcc/Ccc	46/63	0.607664317561228	4	FACETS	0.77	0.674	0.873	0.257	0.224	0.291	SUBCLONAL	1	TRUE	1	0.658974463695718	4		378	464	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976236	18976236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1431836450	NA	P-0058486-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	123	620	0	ENST00000262803.5:c.2996G>A	p.Gly999Glu	p.G999E	ENST00000262803	NM_002911.3	999	gGa/gAa	21/24	0.607664317561228	4	FACETS	0.895	0.81	0.984	0.298	0.27	0.328	CLONAL	1	TRUE	1	0.658974463695718	4		620	692	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268519	46268519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058486-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	108	592	0	ENST00000371998.3:c.2906C>T	p.Pro969Leu	p.P969L	ENST00000371998		969	cCa/cTa	15/23	0.49835143380572	6	FACETS	0.875	0.785	0.971	0.292	0.261	0.324	CLONAL	1	TRUE	3	0.658974463695718	6		592	868	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990433	69990433	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058486-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	298	302	0	ENST00000394351.3:c.392A>G	p.Asn131Ser	p.N131S	ENST00000394351	NM_000248.3	131	aAt/aGt	4/9	0.658974463695718	5	FACETS	0.923	0.883	0.963	0.923	0.883	0.963	CLONAL	4	TRUE	1	0.658974463695718	5		302	487	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751564	57751564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1209851623	NA	P-0058486-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	117	422	0	ENST00000274289.3:c.1427C>T	p.Ala476Val	p.A476V	ENST00000274289	NM_006622.3	476	gCa/gTa	11/14	0.60000429122576	3	FACETS	0.984	0.892	1	0.492	0.446	0.54	CLONAL	1	TRUE	1	0.658974463695718	3		422	480	SUCCESS
APC	324	MSKCC	GRCh37	5	112176821	112176821	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058486-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	82	382	0	ENST00000257430.4:c.5530C>T	p.His1844Tyr	p.H1844Y	ENST00000257430	NM_000038.5	1844	Cat/Tat	16/16	0.60000429122576	3	FACETS	0.813	0.721	0.911	0.406	0.36	0.456	CLONAL	1	TRUE	1	0.658974463695718	3		382	407	SUCCESS
MTAP	4507	MSKCC	GRCh37	9	21838005	21838005	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058486-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	76	351	0	ENST00000380172.4:c.446G>A	p.Arg149Lys	p.R149K	ENST00000380172	NM_002451.3	149	aGa/aAa	5/8	0.658974463695718	4	FACETS	0.841	0.74	0.949	0.28	0.246	0.317	CLONAL	1	TRUE	1	0.658974463695718	4		351	455	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058486-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	737	475	0				ENST00000310581	NM_198253.2	-/1132			0.775229639072189	8	FACETS	0.958	0.938	0.978	0.958	0.938	0.978	CLONAL	7	TRUE	1	0.775229639072189	8		475	943	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0058486-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	573	433	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.659301747829661	4	FACETS	0.955	0.935	0.974	0.955	0.935	0.974	CLONAL	4	TRUE	0	0.775229639072189	4		434	687	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0058486-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	43	519	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.659301747829661	4	FACETS	0.235	0.196	0.279	0.059	0.049	0.07	SUBCLONAL	1	TRUE	0	0.775229639072189	4		520	837	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196089	108196089	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058486-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	298	378	0	ENST00000278616.4:c.6625T>C	p.Ser2209Pro	p.S2209P	ENST00000278616	NM_000051.3	2209	Tcc/Ccc	46/63	0.775229639072189	3	FACETS	0.963	0.918	1	0.963	0.918	1	CLONAL	2	TRUE	1	0.775229639072189	3		378	554	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990433	69990433	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058486-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	141	302	0	ENST00000394351.3:c.392A>G	p.Asn131Ser	p.N131S	ENST00000394351	NM_000248.3	131	aAt/aGt	4/9	0.775229639072189	3	FACETS	1	0.973	1	0.568	0.522	0.616	CLONAL	1	TRUE	1	0.775229639072189	3		302	444	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0058486-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	30	407	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	0.775229639072189	3	FACETS	0.168	0.134	0.206	0.056	0.044	0.069	SUBCLONAL	1	TRUE	0	0.775229639072189	3		407	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579408	7579430	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGGGCCAGGAGGGGGCTGGTG	CAGGGGCCAGGAGGGGGCTGGTG	-	rs886041861	NA	P-0058486-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	47	633	0	ENST00000269305.4:c.257_279del	p.Ala86ValfsTer55	p.A86Vfs*55	ENST00000269305	NM_001126112.2	86	gCACCAGCCCCCTCCTGGCCCCTG/g	4/11	0.659301747829661	4	FACETS	0.243	0.204	0.286	0.061	0.051	0.072	SUBCLONAL	1	TRUE	0	0.775229639072189	4		633	887	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672392	30672392	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058486-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	233	698	0	ENST00000376406.3:c.4568C>T	p.Ser1523Phe	p.S1523F	ENST00000376406	NM_014641.2	1523	tCt/tTt	10/15	0.775229639072189	4	FACETS	0.909	0.847	0.973	0.454	0.423	0.487	CLONAL	1	TRUE	2	0.775229639072189	4		698	1174	SUCCESS
AR	367	MSKCC	GRCh37	X	66765677	66765677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1315081227	NA	P-0058486-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	20	302	0	ENST00000374690.3:c.689C>T	p.Ser230Leu	p.S230L	ENST00000374690	NM_000044.3	230	tCg/tTg	1/8	1	1	FACETS	0.095	0.072	0.122	0.095	0.072	0.122	SUBCLONAL	1	TRUE	0	0.775229639072189	1		302	332	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482898	140482898	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377093637	NA	P-0058486-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	178	522	0	ENST00000288602.6:c.1237G>A	p.Val413Met	p.V413M	ENST00000288602	NM_004333.4	413	Gtg/Atg	10/18	0.775229639072189	3	FACETS	0.855	0.79	0.923			1	CLONAL	1	TRUE	NA	0.775229639072189	3		522	745	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295554	1295554	+	upstream_gene_variant	5'Flank	SNP	G	G	C	novel	NA	P-0058486-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1542	185	656	0				ENST00000310581	NM_198253.2	-/1132			0.775229639072189	8	FACETS	0.919	0.845	0.997	0.131	0.12	0.143	CLONAL	1	TRUE	1	0.775229639072189	8		656	1727	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032052	26032052	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058486-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	225	689	0	ENST00000244661.2:c.237C>G	p.Phe79Leu	p.F79L	ENST00000244661	NM_003537.3	79	ttC/ttG	1/1	0.775229639072189	4	FACETS	0.926	0.862	0.992	0.463	0.431	0.496	CLONAL	1	TRUE	2	0.775229639072189	4		689	1113	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675711	30675711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058486-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	204	489	0	ENST00000376406.3:c.2645G>A	p.Ser882Asn	p.S882N	ENST00000376406	NM_014641.2	882	aGt/aAt	8/15	0.775229639072189	4	FACETS	1	0.965	1	0.532	0.494	0.572	CLONAL	1	TRUE	2	0.775229639072189	4		489	878	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156699	20156699	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058486-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	136	158	0	ENST00000379607.5:c.58G>T	p.Glu20Ter	p.E20*	ENST00000379607	NM_001412.3	20	Gaa/Taa	2/7	0.775229639072189	2	FACETS	0.956	0.88	1			1	CLONAL	1	TRUE	NA	0.775229639072189	2		158	367	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913381	NA	P-0058560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	179	555	0	ENST00000304494.5:c.322G>A	p.Asp108Asn	p.D108N	ENST00000304494	NM_000077.4	108	Gat/Aat	2/3	0.673175761052703	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.674082317757093	1		555	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0058560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	364	634	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.673175761052703	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.674082317757093	2		634	492	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023174	48023174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	153	519	0	ENST00000234420.5:c.599C>T	p.Ser200Leu	p.S200L	ENST00000234420	NM_000179.2	200	tCa/tTa	3/10	0.673175761052703	6	FACETS	1	0.932	1	0.205	0.187	0.224	CLONAL	1	TRUE	1	0.674082317757093	6		519	1042	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252856	36252856	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	269	366	0	ENST00000300305.3:c.506G>A	p.Arg169Lys	p.R169K	ENST00000300305		169	aGa/aAa	4/8	0.640928594522507	5	FACETS	1	0.98	1			1	CLONAL	3	TRUE	NA	0.674082317757093	5		366	505	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531825	41531825	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	85	346	0	ENST00000263253.7:c.1537C>T	p.Pro513Ser	p.P513S	ENST00000263253	NM_001429.3	513	Cct/Tct	7/31	0.673175761052703	3	FACETS	0.883	0.786	0.985	0.294	0.262	0.329	CLONAL	1	TRUE	0	0.674082317757093	3		346	382	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426469	49426469	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs188017299	NA	P-0058560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	1276	644	0	ENST00000301067.7:c.12019C>T	p.Gln4007Ter	p.Q4007*	ENST00000301067	NM_003482.3	4007	Caa/Taa	39/54	0.674082317757093	7	FACETS	1	0.995	1			1	CLONAL	6	TRUE	NA	0.674082317757093	7		644	1649	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426751	49426751	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1491	196	662	0	ENST00000301067.7:c.11737C>T	p.Gln3913Ter	p.Q3913*	ENST00000301067	NM_003482.3	3913	Cag/Tag	39/54	0.674082317757093	7	FACETS	0.926	0.854	1			1	CLONAL	1	TRUE	NA	0.674082317757093	7		662	1687	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779816	135779816	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768189353	NA	P-0058560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	200	266	0	ENST00000298552.3:c.2023G>A	p.Asp675Asn	p.D675N	ENST00000298552	NM_001162426.1	675	Gac/Aac	16/23	0.231390374233673	5	FACETS	1	0.955	1	0.61	0.574	0.646	INDETERMINATE	3	TRUE	0	0.674082317757093	5		266	391	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214009	108214009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	141	478	0	ENST00000278616.4:c.8329G>A	p.Gly2777Ser	p.G2777S	ENST00000278616	NM_000051.3	2777	Ggt/Agt	57/63	0.673175761052703	3	FACETS	1	0.97	1	0.562	0.515	0.61	CLONAL	1	TRUE	1	0.674082317757093	3		478	498	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143448	108143448	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0058560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	148	392	0	ENST00000278616.4:c.3154-1G>C		p.X1052_splice	ENST00000278616	NM_000051.3	1052			0.673175761052703	3	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	1	0.674082317757093	3		392	292	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050365	13050365	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	186	523	0	ENST00000316448.5:c.317G>A	p.Gly106Glu	p.G106E	ENST00000316448	NM_004343.3	106	gGg/gAg	3/9	0.673175761052703	3	FACETS	1	0.948	1	0.515	0.476	0.554	CLONAL	1	TRUE	1	0.674082317757093	3		523	717	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873688	35873688	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	258	388	0	ENST00000216797.5:c.163G>C	p.Glu55Gln	p.E55Q	ENST00000216797	NM_020529.2	55	Gag/Cag	1/6	0.673175761052703	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.674082317757093	2		388	374	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77934677	77934677	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	135	420	1	ENST00000361507.4:c.1348G>A	p.Asp450Asn	p.D450N	ENST00000361507	NM_080491.2	450	Gac/Aac	6/10	0.673175761052703	3	FACETS	1	0.918	1	0.502	0.459	0.548	CLONAL	1	TRUE	1	0.674082317757093	3		421	533	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246464	46246464	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	1243	516	0	ENST00000334344.6:c.4558G>C	p.Glu1520Gln	p.E1520Q	ENST00000334344	NM_152641.2	1520	Gag/Cag	15/21	0.674082317757093	7	FACETS	1	0.995	1			1	CLONAL	6	TRUE	NA	0.674082317757093	7		516	1600	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420123	49420123	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1394	147	595	0	ENST00000301067.7:c.15626del	p.Gly5209AlafsTer34	p.G5209Afs*34	ENST00000301067	NM_003482.3	5209	gGc/gc	48/54	0.674082317757093	7	FACETS	0.76	0.691	0.833			1	SUBCLONAL	1	TRUE	NA	0.674082317757093	7		595	1541	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112593	115112593	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	206	569	0	ENST00000257566.3:c.1147G>C	p.Glu383Gln	p.E383Q	ENST00000257566	NM_016569.3	383	Gag/Cag	7/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.674082317757093	2		569	498	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652303	3652303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	319	501	0	ENST00000294008.3:c.766G>A	p.Gly256Arg	p.G256R	ENST00000294008	NM_032444.2	256	Ggg/Agg	4/15	0.475041899384247	4	FACETS	0.971	0.921	1	0.971	0.921	1	CLONAL	2	TRUE	2	0.674082317757093	4		501	816	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989736	15989736	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	311	448	0	ENST00000268712.3:c.3037C>T	p.Gln1013Ter	p.Q1013*	ENST00000268712	NM_006311.3	1013	Caa/Taa	23/46	0.673175761052703	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.674082317757093	2		448	448	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456650	40456650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754704026	NA	P-0058560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	370	612	0	ENST00000345506.4:c.1360G>A	p.Glu454Lys	p.E454K	ENST00000345506	NM_003152.3	454	Gag/Aag	12/20	0.673175761052703	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.674082317757093	3		612	706	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222247	2222247	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	164	597	0	ENST00000398665.3:c.3079G>C	p.Asp1027His	p.D1027H	ENST00000398665	NM_032482.2	1027	Gac/Cac	24/28	0.673175761052703	3	FACETS	1	0.933	1	0.507	0.467	0.548	CLONAL	1	TRUE	1	0.674082317757093	3		597	642	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313489	30313489	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	122	515	0	ENST00000262643.3:c.1089C>G	p.His363Gln	p.H363Q	ENST00000262643	NM_001238.2	363	caC/caG	11/12	0.475041899384247	4	FACETS	0.804	0.727	0.885	0.402	0.363	0.443	CLONAL	1	TRUE	2	0.674082317757093	4		515	754	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21346593	21346593	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs189150283	NA	P-0058560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	180	543	0	ENST00000215739.8:c.1084C>T	p.Arg362Ter	p.R362*	ENST00000215739	NM_006767.3	362	Cga/Tga	10/21	0.475041899384247	4	FACETS	1	0.978	1	0.577	0.533	0.622	CLONAL	1	TRUE	2	0.674082317757093	4		543	775	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24158967	24158967	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	248	458	0	ENST00000263121.7:c.639G>C	p.Met213Ile	p.M213I	ENST00000263121	NM_003073.3	213	atG/atC	6/9	0.475041899384247	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.674082317757093	4		458	568	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275348	142275348	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	246	448	0	ENST00000350721.4:c.1955G>A	p.Arg652Lys	p.R652K	ENST00000350721	NM_001184.3	652	aGa/aAa	9/47	0.673175761052703	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	2	0.674082317757093	4		448	587	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242871	98242871	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0058560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	486	419	0	ENST00000331920.6:c.747-1G>C		p.X249_splice	ENST00000331920	NM_000264.3	249			0.612107457143019	5	FACETS	1	0.978	1			1	CLONAL	4	TRUE	NA	0.674082317757093	5		419	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0058573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	318	753	0	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	0.611293452083318	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.611293452083318	1		753	695	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948220	71948221	+	missense_variant	Missense_Mutation	DNP	AA	AA	TT	novel	NA	P-0058573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	277	723	0	ENST00000298229.2:c.2932_2933inv	p.Lys978Leu	p.K978L	ENST00000298229	NM_001567.3	978	AAg/TTg	26/28	1	2	FACETS	0.95	0.894	1	0.95	0.894	1	CLONAL	1	TRUE	1	0.611293452083318	2		723	954	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989524	85989524	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	143	383	0	ENST00000263360.6:c.1283T>C	p.Val428Ala	p.V428A	ENST00000263360	NM_003797.3	428	gTt/gCt	12/12	0.533137784607735	3	FACETS	0.985	0.901	1	0.493	0.45	0.537	CLONAL	1	TRUE	1	0.611293452083318	3		383	620	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586147	29586147	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1060500293	NA	P-0058573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	105	302	0	ENST00000356175.3:c.4367G>A	p.Arg1456Lys	p.R1456K	ENST00000356175	NM_000267.3	1456	aGg/aAg	32/57	0.611293452083318	1	FACETS	0.871	0.792	0.95	0.871	0.792	0.95	CLONAL	1	TRUE	0	0.611293452083318	1		302	274	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679285	29679285	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	199	400	0	ENST00000356175.3:c.7405G>T	p.Glu2469Ter	p.E2469*	ENST00000356175	NM_000267.3	2469	Gag/Tag	50/57	0.611293452083318	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.611293452083318	1		400	413	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0058646-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	163	499	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.549410085103685	2		499	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0058646-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	263	814	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.223522201182152	3	FACETS	0.79	0.744	0.838	0.79	0.744	0.838	INDETERMINATE	2	TRUE	1	0.549410085103685	3		814	772	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0058646-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	172	247	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.223522201182152	3	FACETS	1	0.99	1	0.731	0.677	0.786	INDETERMINATE	1	TRUE	1	0.549410085103685	3		247	546	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058646-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	322	777	1	ENST00000324856.7:c.4555del	p.Gln1519ArgfsTer8	p.Q1519Rfs*8	ENST00000324856	NM_006015.4	1517	gCc/gc	18/20	0.549410085103685	2	FACETS	0.932	0.889	0.975	0.932	0.889	0.975	CLONAL	2	TRUE	0	0.549410085103685	2		778	629	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295254	1295254	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0058646-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	150	712	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.549410085103685	2		712	457	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851097	151851097	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058646-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	125	480	0	ENST00000262189.6:c.12274G>A	p.Glu4092Lys	p.E4092K	ENST00000262189	NM_170606.2	4092	Gag/Aag	48/59	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.549410085103685	2		480	433	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295239	1295239	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0058646-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	136	540	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.549410085103685	2		540	398	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984369	201984370	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0058646-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	361	645	0	ENST00000359651.3:c.1036dup	p.Asp346GlyfsTer125	p.D346Gfs*125	ENST00000359651		345	gtg/gtGg	8/8	0.520575395034783	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.549410085103685	2		645	629	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453547	138453547	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058646-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	240	497	0	ENST00000289153.2:c.901G>A	p.Glu301Lys	p.E301K	ENST00000289153	NM_006219.2	301	Gag/Aag	5/22	0.456371948074488	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.549410085103685	3		497	546	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737677	145737677	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058646-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	158	987	0	ENST00000428558.2:c.3086A>C	p.Glu1029Ala	p.E1029A	ENST00000428558	NM_004260.3	1029	gAg/gCg	19/22	0.157233079152201	2	FACETS	0.748	0.686	0.812	0.374	0.343	0.406	INDETERMINATE	1	TRUE	0	0.549410085103685	2		987	769	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112201	115112201	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058670-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	106	756	1	ENST00000257566.3:c.1539C>A	p.Phe513Leu	p.F513L	ENST00000257566	NM_016569.3	513	ttC/ttA	7/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.517316459845937	2		757	374	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089638	27089639	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0058670-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	129	832	0	ENST00000324856.7:c.2596dup	p.Arg866ProfsTer6	p.R866Pfs*6	ENST00000324856	NM_006015.4	865	aac/aaCc	8/20	0.463129630869037	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.517316459845937	1		832	344	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740606	58740606	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058670-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	90	692	0	ENST00000305921.3:c.1511C>A	p.Thr504Lys	p.T504K	ENST00000305921	NM_003620.3	504	aCa/aAa	6/6	0.51516590890448	4	FACETS	0.907	0.806	1	0.302	0.268	0.338	CLONAL	1	TRUE	1	0.517316459845937	4		692	582	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100058	157100058	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058670-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	66	841	0	ENST00000346085.5:c.995G>A	p.Gly332Glu	p.G332E	ENST00000346085	NM_020732.3	332	gGa/gAa	1/20	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.517316459845937	2		841	253	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527968	157527968	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058670-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	119	758	0	ENST00000346085.5:c.5693C>G	p.Thr1898Ser	p.T1898S	ENST00000346085	NM_020732.3	1898	aCc/aGc	20/20	1	2	FACETS	0.985	0.895	1	0.985	0.895	1	CLONAL	1	TRUE	1	0.517316459845937	2		758	467	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923036	44923037	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0058670-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	95	307	0	ENST00000377967.4:c.1900_1901del	p.Asn634ProfsTer4	p.N634Pfs*4	ENST00000377967	NM_021140.2	633	AAa/a	16/29	1	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.517316459845937	1		307	213	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989558	212989563	+	inframe_deletion	In_Frame_Del	DEL	CTTGCG	CTTGCG	-	novel	NA	P-0058670-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	89	536	0	ENST00000342788.4:c.148_153del	p.Arg50_Lys51del	p.R50_K51del	ENST00000342788	NM_005235.2	50	CGCAAG/-	2/28	1	2	FACETS	0.887	0.792	0.987	0.887	0.792	0.987	CLONAL	1	TRUE	1	0.517316459845937	2		536	388	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458222	12458222	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058670-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	78	511	0	ENST00000287820.6:c.839T>C	p.Met280Thr	p.M280T	ENST00000287820	NM_015869.4	280	aTg/aCg	6/7	1	2	FACETS	0.954	0.846	1	0.954	0.846	1	CLONAL	1	TRUE	1	0.517316459845937	2		511	316	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210321	123210321	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058670-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	44	163	0	ENST00000218089.9:c.2673G>C	p.Lys891Asn	p.K891N	ENST00000218089	NM_001042749.1	891	aaG/aaC	26/35	1	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.517316459845937	1		163	111	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936995	48936995	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778842	NA	P-0058734-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3	446	0	0	ENST00000267163.4:c.763C>T	p.Arg255Ter	p.R255*	ENST00000267163	NM_000321.2	255	Cga/Tga	8/27	0.899536594703225	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.937215619755377	1		0	449	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183846	10183846	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058762-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	15	596	0	ENST00000256474.2:c.317del	p.Gly106AlafsTer53	p.G106Afs*53	ENST00000256474	NM_000551.3	105	acG/ac	1/3	1	2	FACETS	0.531	0.387	0.706	0.531	0.387	0.706	SUBCLONAL	1	TRUE	1	0.12	2		596	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0058775-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	226	584	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.559300005982279	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.559300005982279	1		584	526	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259442	55259442	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397517127	NA	P-0058775-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	575	555	0	ENST00000275493.2:c.2500G>C	p.Val834Leu	p.V834L	ENST00000275493	NM_005228.3	834	Gtg/Ctg	21/28	0.560364179396322	5	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	2	0.559300005982279	5		555	1210	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259514	55259515	+	missense_variant	Missense_Mutation	DNP	CT	CT	AG	rs1057519847	NA	P-0058775-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	471	636	1	ENST00000275493.2:c.2572_2573inv	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	CTg/AGg	21/28	0.560364179396322	5	FACETS	0.933	0.895	0.972	0.933	0.895	0.972	CLONAL	3	TRUE	2	0.559300005982279	5		637	1106	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821646	72821646	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058775-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	177	606	0	ENST00000268489.5:c.10529G>T	p.Gly3510Val	p.G3510V	ENST00000268489	NM_006885.3	3510	gGc/gTc	10/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.559300005982279	2		606	490	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311687	30311687	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058775-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	50	473	0	ENST00000262643.3:c.541G>T	p.Glu181Ter	p.E181*	ENST00000262643	NM_001238.2	181	Gaa/Taa	7/12	0.141155796927185	3	FACETS	0.88	0.753	1	0.44	0.376	0.509	INDETERMINATE	1	TRUE	1	0.559300005982279	3		473	260	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272308	38272308	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs869320694	NA	P-0058824-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	226	469	0	ENST00000425967.3:c.2059A>G	p.Lys687Glu	p.K687E	ENST00000425967	NM_001174067.1	687	Aag/Gag	15/19	0.90389055811007	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.90389055811007	1		469	261	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs199469669	NA	P-0058824-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	228	371	0	ENST00000374080.3:c.130G>C	p.Gly44Arg	p.G44R	ENST00000374080		44	Ggt/Cgt	2/45	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.90389055811007	2		371	480	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828258	72828258	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058824-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	274	568	0	ENST00000268489.5:c.8323C>T	p.Pro2775Ser	p.P2775S	ENST00000268489	NM_006885.3	2775	Cca/Tca	9/10	1	2	FACETS	0.989	0.936	1	0.989	0.936	1	CLONAL	1	TRUE	1	0.90389055811007	2		568	613	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106648	27106648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553153748	NA	P-0058882-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	265	753	0	ENST00000324856.7:c.6259G>A	p.Gly2087Arg	p.G2087R	ENST00000324856	NM_006015.4	2087	Gga/Aga	20/20	0.341138977946189	4	FACETS	0.915	0.863	0.966	0.915	0.863	0.966	INDETERMINATE	2	TRUE	2	0.797540832831691	4		753	653	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024014	27024018	+	frameshift_variant	Frame_Shift_Del	DEL	CTCGC	CTCGC	-	novel	NA	P-0058882-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	124	441	0	ENST00000324856.7:c.1121_1125del	p.Leu374ProfsTer24	p.L374Pfs*24	ENST00000324856	NM_006015.4	374	CTCGCc/c	1/20	0.341138977946189	4	FACETS	0.842	0.772	0.913	0.842	0.772	0.913	INDETERMINATE	2	TRUE	2	0.797540832831691	4		441	332	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807382	36807382	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058882-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	130	562	0	ENST00000373129.3:c.1282C>G	p.Leu428Val	p.L428V	ENST00000373129	NM_032017.1	428	Ctg/Gtg	12/12	0.22215906101156	3	FACETS	1	0.953	1	0.531	0.486	0.579	INDETERMINATE	1	TRUE	1	0.797540832831691	3		562	429	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981851	201981852	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0058882-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	403	736	0	ENST00000359651.3:c.567dup	p.Ser190LeufsTer6	p.S190Lfs*6	ENST00000359651		188	gcc/gCcc	4/8	0.797540832831691	3	FACETS	0.843	0.807	0.88	0.843	0.807	0.88	CLONAL	2	TRUE	1	0.797540832831691	3		736	838	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518527	69518527	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058882-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	27	578	0	ENST00000294312.3:c.118G>A	p.Asp40Asn	p.D40N	ENST00000294312	NM_005117.2	40	Gac/Aac	1/3	1	2	FACETS	0.205	0.163	0.253	0.205	0.163	0.253	SUBCLONAL	1	TRUE	1	0.797540832831691	2		578	330	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195424	102195424	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058882-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	173	531	0	ENST00000263464.3:c.184G>C	p.Asp62His	p.D62H	ENST00000263464	NM_001165.4	62	Gac/Cac	2/9	1	2	FACETS	0.958	0.89	1	0.958	0.89	1	CLONAL	1	TRUE	1	0.797540832831691	2		531	453	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042423	42042423	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058882-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	231	640	0	ENST00000219905.7:c.6618G>C	p.Lys2206Asn	p.K2206N	ENST00000219905	NM_001164273.1	2206	aaG/aaC	17/24	0.158928320147136	5	FACETS	1	0.978	1	0.725	0.681	0.769	INDETERMINATE	2	TRUE	2	0.797540832831691	5		640	585	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782280	56782280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781486427	NA	P-0058882-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	21	480	0	ENST00000308159.5:c.121G>A	p.Glu41Lys	p.E41K	ENST00000308159	NM_014669.4	41	Gag/Aag	2/22	0.724446966007112	1	FACETS	0.113	0.087	0.144	0.113	0.087	0.144	SUBCLONAL	1	TRUE	0	0.797540832831691	1		480	279	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690145	33690145	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0058882-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	131	552	0	ENST00000308377.4:c.682A>T	p.Lys228Ter	p.K228*	ENST00000308377	NM_152270.3	228	Aaa/Taa	2/5	NA	2	FACETS	0.947	0.87	1			1	INDETERMINATE	1	TRUE	NA	0.797540832831691	2		552	347	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78934001	78934001	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058882-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	27	635	0	ENST00000306801.3:c.3601G>A	p.Glu1201Lys	p.E1201K	ENST00000306801	NM_020761.2	1201	Gaa/Aaa	30/34	0.22215906101156	3	FACETS	0.229	0.182	0.283	0.114	0.091	0.142	INDETERMINATE	1	TRUE	1	0.797540832831691	3		635	414	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220150	36220150	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058882-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	200	717	0	ENST00000222270.7:c.4870G>A	p.Gly1624Ser	p.G1624S	ENST00000222270	NM_014727.1	1624	Ggc/Agc	22/37	0.22215906101156	3	FACETS	1	0.989	1	0.651	0.608	0.695	INDETERMINATE	1	TRUE	1	0.797540832831691	3		717	539	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873328	136873328	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058882-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	154	619	0	ENST00000241393.3:c.170G>C	p.Gly57Ala	p.G57A	ENST00000241393	NM_003467.2	57	gGa/gCa	2/2	0.797540832831691	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.797540832831691	1		619	228	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0058882-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	691	574	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.776088829136325	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	4	TRUE	0	0.797540832831691	4		574	775	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225564	225564	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058882-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	85	328	0	ENST00000264932.6:c.343G>C	p.Glu115Gln	p.E115Q	ENST00000264932	NM_004168.2	115	Gag/Cag	4/15	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.797540832831691	2		328	212	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915717	131915717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773887771	NA	P-0058882-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	148	375	0	ENST00000265335.6:c.715G>A	p.Glu239Lys	p.E239K	ENST00000265335		239	Gaa/Aaa	5/25	0.339457787924647	4	FACETS	0.902	0.834	0.97			1	INDETERMINATE	2	TRUE	NA	0.797540832831691	4		375	370	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651956	36651957	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0058882-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	241	660	0	ENST00000244741.5:c.79dup	p.Ser27LysfsTer9	p.S27Kfs*9	ENST00000244741	NM_000389.4	26	-/A	2/3	0.138776530552271	5	FACETS	1	0.981	1	0.733	0.689	0.776	INDETERMINATE	2	TRUE	2	0.797540832831691	5		660	604	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0058882-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	154	400	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	0.180889368337393	5	FACETS	1	0.982	1			1	INDETERMINATE	2	TRUE	NA	0.797540832831691	5		400	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0058926-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	356	393	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.533239361636426	3	FACETS	0.959	0.922	0.995	0.959	0.922	0.995	CLONAL	3	TRUE	0	0.574090981739295	3		393	555	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981163	201981165	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0058926-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	515	498	0	ENST00000359651.3:c.246_248del	p.Lys82del	p.K82del	ENST00000359651		81	gAGAag/gag	2/8	0.545375856086304	4	FACETS	0.921	0.892	0.948	0.921	0.892	0.948	CLONAL	4	TRUE	0	0.574090981739295	4		498	767	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024613	11024613	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058926-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	123	560	0	ENST00000327064.4:c.730G>T	p.Glu244Ter	p.E244*	ENST00000327064	NM_199141.1	244	Gag/Tag	6/16	0.574090981739295	6	FACETS	0.863	0.779	0.952	0.173	0.155	0.191	CLONAL	1	TRUE	1	0.574090981739295	6		560	1067	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032221	26032221	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058926-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	292	631	0	ENST00000244661.2:c.68C>G	p.Thr23Ser	p.T23S	ENST00000244661	NM_003537.3	23	aCc/aGc	1/1	0.574090981739295	7	FACETS	0.87	0.817	0.925	0.249	0.233	0.265	CLONAL	2	TRUE	0	0.574090981739295	7		631	1423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578510	+	frameshift_variant	Frame_Shift_Del	DEL	GCACAGGGCAG	GCACAGGGCAG	-	novel	NA	P-0058935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	111	791	0	ENST00000269305.4:c.420_430del	p.Cys141AlafsTer4	p.C141Afs*4	ENST00000269305	NM_001126112.2	140	acCTGCCCTGTGCag/acag	5/11	0.284498652729691	1	FACETS	0.823	0.74	0.912	0.823	0.74	0.912	CLONAL	1	TRUE	0	0.284498652729691	1		791	813	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813090	76813090	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058935-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	71	440	0	ENST00000373344.5:c.6531T>G	p.Asp2177Glu	p.D2177E	ENST00000373344	NM_000489.3	2177	gaT/gaG	30/35	0.284498652729691	3	FACETS	1	0.95	1	0.585	0.512	0.664	CLONAL	1	TRUE	1	0.284498652729691	3		440	487	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111543	8111544	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058938-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	261	416	0	ENST00000346208.3:c.1030dup	p.Tyr344LeufsTer8	p.Y344Lfs*8	ENST00000346208		343	-/T	5/6	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.643953975045239	2		416	748	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955394	48955394	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886043247	NA	P-0058938-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	51	253	0	ENST00000267163.4:c.1510C>T	p.Gln504Ter	p.Q504*	ENST00000267163	NM_000321.2	504	Cag/Tag	17/27	0.643953975045239	1	FACETS	0.846	0.739	0.955	0.846	0.739	0.955	CLONAL	1	TRUE	0	0.643953975045239	1		253	127	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855970	68855971	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CATACCAGAACCTCGAACTATAT	novel	NA	P-0058938-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	190	496	0	ENST00000261769.5:c.1779_1801dup	p.Phe601SerfsTer20	p.F601Sfs*20	ENST00000261769	NM_004360.3	593	ccc/ccCATACCAGAACCTCGAACTATATc	12/16	0.643953975045239	1	FACETS	0.654	0.608	0.701	0.654	0.608	0.701	SUBCLONAL	1	TRUE	0	0.643953975045239	1		496	612	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39542507	39542507	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058938-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	179	364	0	ENST00000262039.4:c.311C>A	p.Ala104Asp	p.A104D	ENST00000262039	NM_002647.2	104	gCc/gAc	3/25	1	2	FACETS	0.89	0.824	0.957	0.89	0.824	0.957	CLONAL	1	TRUE	1	0.643953975045239	2		364	625	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252994	36252995	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0058938-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	261	409	0	ENST00000300305.3:c.366_367dup	p.Asp123GlyfsTer11	p.D123Gfs*11	ENST00000300305		123	gat/gGGat	4/8	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.643953975045239	2		409	784	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910349	29910349	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs749604425	NA	P-0058938-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	276	648	0	ENST00000376809.5:c.19C>G	p.Arg7Gly	p.R7G	ENST00000376809	NM_002116.7	7	Cga/Gga	1/8	0.643953975045239	1	FACETS	0.947	0.896	0.997	0.947	0.896	0.997	CLONAL	1	TRUE	0	0.643953975045239	1		648	614	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288996	212288996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059023-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	27	301	0	ENST00000342788.4:c.2750G>A	p.Gly917Glu	p.G917E	ENST00000342788	NM_005235.2	917	gGa/gAa	23/28	0.476760054958739	3	FACETS	0.271	0.215	0.336	0.136	0.107	0.168	SUBCLONAL	1	TRUE	1	0.476760054958739	3		301	517	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059038-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	14	475	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.959	0.718	1	0.959	0.718	1	CLONAL	1	TRUE	1	0.583698858762919	2		475	50	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685300	89685300	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs878853936	NA	P-0059038-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	24	125	0	ENST00000371953.3:c.195C>G	p.Tyr65Ter	p.Y65*	ENST00000371953	NM_000314.4	65	taC/taG	3/9	0.583698858762919	1	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	0	0.583698858762919	1		125	56	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390071	89390071	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760135022	NA	P-0059038-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	30	331	0	ENST00000336596.2:c.820C>T	p.Arg274Ter	p.R274*	ENST00000336596	NM_005233.5	274	Cga/Tga	4/17	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.583698858762919	2		331	85	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519920	NA	P-0059038-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	10	361	0	ENST00000397062.3:c.85G>A	p.Asp29Asn	p.D29N	ENST00000397062	NM_006164.4	29	Gat/Aat	2/5	0.17372803091165	4	FACETS	0.714	0.49	0.986	0.357	0.245	0.493	INDETERMINATE	1	TRUE	2	0.583698858762919	4		361	76	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056165	27056165	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059038-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	29	463	0	ENST00000324856.7:c.1163del	p.Gly388AlafsTer3	p.G388Afs*3	ENST00000324856	NM_006015.4	387	atG/at	2/20	1	2	FACETS	0.857	0.701	1	0.857	0.701	1	CLONAL	1	TRUE	1	0.583698858762919	2		463	116	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087524	27087524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059038-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	38	616	0	ENST00000324856.7:c.2098G>A	p.Val700Ile	p.V700I	ENST00000324856	NM_006015.4	700	Gtt/Att	5/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.583698858762919	2		616	94	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089777	27089777	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0059038-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	45	501	0	ENST00000324856.7:c.2732+1G>C		p.X911_splice	ENST00000324856	NM_006015.4	911			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.583698858762919	2		501	105	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243904	41243904	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786203310	NA	P-0059038-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	19	476	0	ENST00000357654.3:c.3644A>G	p.Asn1215Ser	p.N1215S	ENST00000357654	NM_007294.3	1215	aAc/aGc	10/23	0.285149670346536	3	FACETS	1	0.835	1	0.546	0.425	0.681	INDETERMINATE	1	TRUE	1	0.583698858762919	3		476	77	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007565	62007565	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059038-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	39	565	0	ENST00000392795.3:c.302A>G	p.Gln101Arg	p.Q101R	ENST00000392795	NM_001039933.1	101	cAg/cGg	3/6	0.285149670346536	3	FACETS	0.785	0.668	0.906	0.785	0.668	0.906	INDETERMINATE	2	TRUE	1	0.583698858762919	3		565	110	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157519944	157519944	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs886044620	NA	P-0059038-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	34	375	0	ENST00000346085.5:c.4014-1G>A		p.X1338_splice	ENST00000346085	NM_020732.3	1338			1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.583698858762919	2		375	101	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197047	123197047	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059038-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	16	254	0	ENST00000218089.9:c.1814del	p.Leu605Ter	p.L605*	ENST00000218089	NM_001042749.1	605	Tta/ta	19/35	NA	2	FACETS	0.731	0.552	0.934			1	INDETERMINATE	1	TRUE	NA	0.583698858762919	2		254	75	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930931	39930931	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059160-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	122	347	0	ENST00000378444.4:c.3010C>T	p.Gln1004Ter	p.Q1004*	ENST00000378444	NM_001123385.1	1004	Caa/Taa	5/15	1	2	FACETS	0.957	0.879	1	0.957	0.879	1	CLONAL	1	TRUE	1	0.876557886650646	2		347	291	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131161	55131161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059167-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1335	5655	347	0	ENST00000257290.5:c.704G>A	p.Cys235Tyr	p.C235Y	ENST00000257290	NM_006206.4	235	tGt/tAt	5/23	0.882457725830645	25	FACETS	1	0.998	1	0.852	0.845	0.858	CLONAL	20	TRUE	1	0.882457725830645	25		347	6990	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416781	29416781	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059167-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	237	462	0	ENST00000389048.3:c.4172A>G	p.Asp1391Gly	p.D1391G	ENST00000389048	NM_004304.4	1391	gAt/gGt	29/29	0.213467873216926	2	FACETS	1	0.988	1	0.583	0.551	0.614	INDETERMINATE	1	TRUE	0	0.882457725830645	2		462	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0059248-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	63	484	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.297772300681158	0	FACETS	0.572	0.501	0.646			1	SUBCLONAL	1	TRUE	0	0.491529614053607	0		484	228	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0059256-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	1701	385	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.296691995675379	38	FACETS	1	0.993	1	1	0.993	1	CLONAL	36	TRUE	2	0.27	38		385	2037	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0059256-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	146	796	3	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.296691995675379	5	FACETS	1	0.976	1	0.861	0.793	0.931	CLONAL	3	TRUE	1	0.27	5		799	441	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268969	55268969	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059256-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	2047	722	46	ENST00000275493.2:c.3035A>T	p.Asp1012Val	p.D1012V	ENST00000275493	NM_005228.3	1012	gAt/gTt	25/28	0.296691995675379	38	FACETS	1	0.995	1	0.984	0.972	0.995	CLONAL	35	TRUE	2	0.27	38		768	2509	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475456	12475456	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059256-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	58	643	3	ENST00000287820.6:c.1330G>T	p.Ala444Ser	p.A444S	ENST00000287820	NM_015869.4	444	Gcc/Tcc	7/7	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.27	2		646	407	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778149	27778149	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059256-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	33	762	0	ENST00000369163.2:c.298T>A	p.Tyr100Asn	p.Y100N	ENST00000369163	NM_003536.2	100	Tac/Aac	1/1	0.296691995675379	5	FACETS	0.529	0.43	0.642	0.176	0.143	0.214	SUBCLONAL	1	TRUE	2	0.27	5		762	649	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0059385-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	76	499	0				ENST00000310581	NM_198253.2	-/1132			0.479941980171928	1	FACETS	0.593	0.526	0.665	0.593	0.526	0.665	SUBCLONAL	1	TRUE	0	0.60828620560372	1		499	293	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0059385-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	281	406	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.613217646641073	3	FACETS	0.914	0.865	0.964			1	CLONAL	2	TRUE	NA	0.60828620560372	3		406	659	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971138	21971138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760640852	NA	P-0059385-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	271	630	1	ENST00000304494.5:c.220G>A	p.Asp74Asn	p.D74N	ENST00000304494	NM_000077.4	74	Gac/Aac	2/3	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.60828620560372	2		631	753	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376453	118376454	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0059385-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	186	526	1	ENST00000534358.1:c.9846_9847delinsTT	p.Arg3283Ter	p.R3283*	ENST00000534358	NM_005933.3	3282	caCCga/caTTga	27/36	0.613217646641073	3	FACETS	1	0.966	1	0.537	0.497	0.579	CLONAL	1	TRUE	1	0.60828620560372	3		527	742	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634336	23634336	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059385-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	159	345	0	ENST00000261584.4:c.2950C>T	p.Leu984Phe	p.L984F	ENST00000261584	NM_024675.3	984	Ctt/Ttt	9/13	0.477295992120607	3	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.60828620560372	3		345	564	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681642	30681642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754211812	NA	P-0059385-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	541	551	0	ENST00000376406.3:c.455G>A	p.Arg152Lys	p.R152K	ENST00000376406	NM_014641.2	152	aGa/aAa	3/15	0.558737003500193	5	FACETS	1	0.989	1			1	CLONAL	3	TRUE	NA	0.60828620560372	5		551	1067	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954942	2954942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371300769	NA	P-0059385-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	100	583	0	ENST00000396946.4:c.2768C>T	p.Ser923Leu	p.S923L	ENST00000396946	NM_032415.4	923	tCg/tTg	21/25	NA	2	FACETS	0.551	0.493	0.612			1	INDETERMINATE	1	TRUE	NA	0.60828620560372	2		583	597	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971138	21971139	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGGTGAGAGTGGCGGGGTT	novel	NA	P-0059385-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	165	624	0	ENST00000304494.5:c.219_220insAACCCCGCCACTCTCACCC	p.Asp74AsnfsTer52	p.D74Nfs*52	ENST00000304494	NM_000077.4	73	-/AACCCCGCCACTCTCACCC	2/3	NA	2	FACETS	0.858	0.791	0.928			1	INDETERMINATE	1	TRUE	NA	0.60828620560372	2		624	632	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115036	3115036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1317391449	NA	P-0059468-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	101	589	0	ENST00000078429.4:c.571G>A	p.Glu191Lys	p.E191K	ENST00000078429	NM_002067.2	191	Gag/Aag	4/7	1	2	FACETS	0.969	0.864	1	0.969	0.864	1	CLONAL	1	TRUE	1	0.18	2		589	1158	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239397	123239397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059468-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	48	437	0	ENST00000358487.5:c.2440C>T	p.His814Tyr	p.H814Y	ENST00000358487	NM_000141.4	814	Cac/Tac	18/18	1	2	FACETS	0.78	0.658	0.914	0.78	0.658	0.914	CLONAL	1	TRUE	1	0.18	2		437	684	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21346018	21346018	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059468-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	181	563	0	ENST00000215739.8:c.893T>G	p.Val298Gly	p.V298G	ENST00000215739	NM_006767.3	298	gTg/gGg	9/21	0.3	1	FACETS	0.863	0.795	0.934	1	0.991	1	CLONAL	2	TRUE	0	0.18	1		563	1060	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165971	118165971	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	92	675	0	ENST00000369448.3:c.481A>T	p.Asn161Tyr	p.N161Y	ENST00000369448	NM_017709.3	161	Aac/Tac	2/2	0.16920858293756	4	FACETS	1	0.974	1	0.663	0.592	0.739	INDETERMINATE	1	TRUE	2	0.392565826289262	4		675	492	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405821	70405821	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	19	498	0	ENST00000373644.4:c.3335T>A	p.Val1112Glu	p.V1112E	ENST00000373644	NM_030625.2	1112	gTa/gAa	4/12	0.229433501006268	3	FACETS	0.6	0.457	0.766	0.3	0.228	0.383	INDETERMINATE	1	TRUE	1	0.392565826289262	3		498	193	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037378	12037378	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0059469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	52	733	0	ENST00000396373.4:c.1010-1G>C		p.X337_splice	ENST00000396373	NM_001987.4	337			0.392565826289262	5	FACETS	0.822	0.7	0.956	0.274	0.233	0.319	CLONAL	1	TRUE	2	0.392565826289262	5		733	512	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433935	49433935	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	46	850	0	ENST00000301067.7:c.7618C>G	p.Gln2540Glu	p.Q2540E	ENST00000301067	NM_003482.3	2540	Cag/Gag	31/54	0.225051692827519	4	FACETS	0.755	0.637	0.886	0.252	0.212	0.296	INDETERMINATE	1	TRUE	1	0.392565826289262	4		850	432	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435410	121435410	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	42	805	1	ENST00000257555.6:c.1443G>C	p.Gln481His	p.Q481H	ENST00000257555		481	caG/caC	7/10	1	2	FACETS	0.554	0.464	0.655	0.554	0.464	0.655	SUBCLONAL	1	TRUE	1	0.392565826289262	2		806	386	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582103	95582103	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	82	579	0	ENST00000393063.1:c.1808C>G	p.Pro603Arg	p.P603R	ENST00000393063	NM_030621.3	603	cCt/cGt	12/28	0.272653777884394	2	FACETS	1	0.977	1	0.703	0.627	0.783	CLONAL	1	TRUE	0	0.392565826289262	2		579	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577535	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0059469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	90	562	0	ENST00000269305.4:c.746_747delinsTT	p.Arg249Ile	p.R249I	ENST00000269305	NM_001126112.2	249	aGG/aTT	7/11	0.268040164951804	3	FACETS	1	0.978	1	0.469	0.419	0.522	CLONAL	1	TRUE	0	0.392565826289262	3		562	390	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920444	134920444	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	42	613	0	ENST00000398015.3:c.2259C>A	p.Asn753Lys	p.N753K	ENST00000398015	NM_004441.4	753	aaC/aaA	12/16	0.392565826289262	1	FACETS	0.462	0.387	0.546	0.462	0.387	0.546	SUBCLONAL	1	TRUE	0	0.392565826289262	1		613	372	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340214	116340214	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	38	595	0	ENST00000397752.3:c.1076G>C	p.Arg359Pro	p.R359P	ENST00000397752	NM_000245.2	359	cGa/cCa	2/21	0.392565826289262	6	FACETS	0.789	0.652	0.941	0.197	0.163	0.236	CLONAL	1	TRUE	2	0.392565826289262	6		595	438	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971116	21971116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552823	NA	P-0059469-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	78	677	0	ENST00000304494.5:c.242C>T	p.Pro81Leu	p.P81L	ENST00000304494	NM_000077.4	81	cCc/cTc	2/3	0.392565826289262	1	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	0	0.392565826289262	1		677	314	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0059508-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	261	499	0				ENST00000310581	NM_198253.2	-/1132			0.267331432042262	1	FACETS	1	0.986	1	1	0.996	1	CLONAL	3	FALSE	0	0.267331432042262	1		499	506	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888189	112888189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507511	NA	P-0059508-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	12	357	0	ENST00000351677.2:c.205G>A	p.Glu69Lys	p.E69K	ENST00000351677	NM_002834.3	69	Gag/Aag	3/16	1	2	FACETS	0.182	0.127	0.25	0.182	0.127	0.25	SUBCLONAL	1	FALSE	1	0.267331432042262	2		357	494	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023203	33023203	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059508-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	427	682	0	ENST00000300177.4:c.312C>A	p.His104Gln	p.H104Q	ENST00000300177	NM_001191322.1	104	caC/caA	2/2	1	2	FACETS	0.903	0.866	0.941	1	0.998	1	CLONAL	4	FALSE	1	0.267331432042262	2		682	884	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059525-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	41	475	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.647	0.537	0.769	0.647	0.537	0.769	SUBCLONAL	1	TRUE	1	0.17	2		475	746	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059525-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	43	575	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	0.777	0.649	0.92	0.777	0.649	0.92	CLONAL	1	TRUE	1	0.17	2		575	651	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534287	534288	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0059525-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	58	775	0	ENST00000451590.1:c.35_36delinsTT	p.Gly12Val	p.G12V	ENST00000451590	NM_001130442.1	12	gGC/gTT	2/5	1	2	FACETS	0.804	0.689	0.93	0.804	0.689	0.93	CLONAL	1	TRUE	1	0.17	2		775	849	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707902	43707903	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0059525-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	49	837	0	ENST00000382044.4:c.4978_4979del	p.Glu1660LysfsTer19	p.E1660Kfs*19	ENST00000382044	NM_001141980.1	1660	GAa/a	23/28	1	2	FACETS	0.622	0.525	0.729	0.622	0.525	0.729	SUBCLONAL	1	TRUE	1	0.17	2		837	927	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0059643-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	38	61	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.994	0.824	1	0.994	0.824	1	CLONAL	1	TRUE	1	0.22698118760217	2		61	337	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849569	68849570	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs876659208	NA	P-0059643-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	95	459	0	ENST00000261769.5:c.1476_1477del	p.Arg492SerfsTer44	p.R492Sfs*44	ENST00000261769	NM_004360.3	491	aAG/a	10/16	0.22698118760217	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.22698118760217	1		459	675	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374979	118374979	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059643-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	74	496	0	ENST00000534358.1:c.8372G>C	p.Arg2791Thr	p.R2791T	ENST00000534358	NM_005933.3	2791	aGa/aCa	27/36	1	2	FACETS	0.856	0.748	0.972	0.856	0.748	0.972	CLONAL	1	TRUE	1	0.22698118760217	2		496	762	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104000	69104000	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059643-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	93	328	0	ENST00000288368.4:c.4390T>C	p.Ser1464Pro	p.S1464P	ENST00000288368	NM_024870.2	1464	Tcc/Ccc	36/40	0.22698118760217	5	FACETS	1	0.969	1	0.316	0.28	0.354	CLONAL	1	TRUE	1	0.22698118760217	5		328	869	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0059679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	9	61	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.59	0.392	0.839	0.59	0.392	0.839	SUBCLONAL	1	TRUE	1	0.25	2		61	122	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	44	298	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.949	0.798	1	0.949	0.798	1	CLONAL	1	TRUE	1	0.25	2		299	371	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	24	202	0	ENST00000397062.3:c.246A>T	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaT	2/5	1	2	FACETS	0.696	0.546	0.867	0.696	0.546	0.867	SUBCLONAL	1	TRUE	1	0.25	2		202	276	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188294	32188295	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs766348245	NA	P-0059679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	28	322	0	ENST00000375023.3:c.1046dup	p.Thr350HisfsTer4	p.T350Hfs*4	ENST00000375023	NM_004557.3	349	ggc/ggGc	6/30	1	2	FACETS	0.638	0.51	0.784	0.638	0.51	0.784	SUBCLONAL	1	TRUE	1	0.25	2		322	351	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	22	238	1	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.552	0.428	0.696	0.552	0.428	0.696	SUBCLONAL	1	TRUE	1	0.25	2		239	319	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0059679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	17	136	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	0.907	0.682	1	0.907	0.682	1	CLONAL	1	TRUE	1	0.25	2		136	150	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717769	89717770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0059679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	16	109	0	ENST00000371953.3:c.800dup	p.Asp268GlyfsTer30	p.D268Gfs*30	ENST00000371953	NM_000314.4	265	cta/ctAa	7/9	1	2	FACETS	0.81	0.602	1	0.81	0.602	1	CLONAL	1	TRUE	1	0.25	2		109	158	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444659	78444659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs908264837	NA	P-0059679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	28	242	0	ENST00000370768.2:c.30del	p.Ser11LeufsTer43	p.S11Lfs*43	ENST00000370768	NM_003902.3	10	ccC/cc	1/20	1	2	FACETS	0.614	0.491	0.754	0.614	0.491	0.754	SUBCLONAL	1	TRUE	1	0.25	2		242	365	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505443	157505443	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554231830	NA	P-0059679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	24	202	0	ENST00000346085.5:c.3428del	p.Lys1143SerfsTer68	p.K1143Sfs*68	ENST00000346085	NM_020732.3	1142	Aaa/aa	13/20	1	2	FACETS	0.736	0.578	0.916	0.736	0.578	0.916	CLONAL	1	TRUE	1	0.25	2		202	261	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416659	29416659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	26	269	0	ENST00000389048.3:c.4294C>T	p.Arg1432Trp	p.R1432W	ENST00000389048	NM_004304.4	1432	Cgg/Tgg	29/29	1	2	FACETS	0.644	0.51	0.797	0.644	0.51	0.797	SUBCLONAL	1	TRUE	1	0.25	2		269	323	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0059679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	43	324	0	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.25	2		324	295	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223858	36223858	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	23	335	0	ENST00000222270.7:c.6413del	p.Pro2138ArgfsTer15	p.P2138Rfs*15	ENST00000222270	NM_014727.1	2136	ctC/ct	28/37	1	2	FACETS	0.54	0.42	0.677	0.54	0.42	0.677	SUBCLONAL	1	TRUE	1	0.25	2		335	341	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87338511	87338511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs117250170	NA	P-0059679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	40	177	0	ENST00000277120.3:c.607G>A	p.Ala203Thr	p.A203T	ENST00000277120		203	Gca/Aca	7/19	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.25	2		177	246	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061154	38061154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	32	251	0	ENST00000250448.2:c.835G>A	p.Gly279Arg	p.G279R	ENST00000250448	NM_004496.3	279	Ggg/Agg	2/2	1	2	FACETS	0.895	0.729	1	0.895	0.729	1	CLONAL	1	TRUE	1	0.25	2		251	286	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805537	32805539	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0059679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	41	277	0	ENST00000374899.4:c.472_474del	p.Phe158del	p.F158del	ENST00000374899	NM_018833.2	158	TTC/-	2/12	1	2	FACETS	0.796	0.664	0.943	0.796	0.664	0.943	CLONAL	1	TRUE	1	0.25	2		277	412	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659222	86659225	+	frameshift_variant	Frame_Shift_Del	DEL	TTAT	TTAT	-	novel	NA	P-0059679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	24	87	0	ENST00000274376.6:c.1517_1520del	p.Tyr506LeufsTer13	p.Y506Lfs*13	ENST00000274376	NM_002890.2	504	cTTATt/ct	11/25	1	2	FACETS	1	0.835	1	1	0.835	1	CLONAL	1	TRUE	1	0.25	2		87	180	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194830	29194830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	21	263	0	ENST00000240100.2:c.898C>T	p.Arg300Trp	p.R300W	ENST00000240100	NM_001394.6	300	Cgg/Tgg	4/4	1	2	FACETS	0.515	0.397	0.654	0.515	0.397	0.654	SUBCLONAL	1	TRUE	1	0.25	2		263	326	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219153	133219153	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs565413729	NA	P-0059679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	29	282	0	ENST00000320574.5:c.4891C>T	p.Arg1631Cys	p.R1631C	ENST00000320574	NM_006231.2	1631	Cgc/Tgc	37/49	1	2	FACETS	0.748	0.602	0.914	0.748	0.602	0.914	CLONAL	1	TRUE	1	0.25	2		282	310	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264371	30264371	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	21	243	0	ENST00000322652.5:c.106G>A	p.Ala36Thr	p.A36T	ENST00000322652	NM_015355.2	36	Gct/Act	1/16	1	2	FACETS	0.669	0.516	0.847	0.669	0.516	0.847	SUBCLONAL	1	TRUE	1	0.25	2		243	251	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885607	111885607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs577495609	NA	P-0059679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	32	261	0	ENST00000341259.2:c.1384G>A	p.Val462Met	p.V462M	ENST00000341259	NM_005475.2	462	Gtg/Atg	7/8	1	2	FACETS	0.753	0.612	0.911	0.753	0.612	0.911	CLONAL	1	TRUE	1	0.25	2		261	340	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101469	27101469	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs558739370	NA	P-0059679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	32	256	0	ENST00000324856.7:c.4751A>G	p.Gln1584Arg	p.Q1584R	ENST00000324856	NM_006015.4	1584	cAg/cGg	18/20	1	2	FACETS	1	0.816	1	1	0.816	1	CLONAL	1	TRUE	1	0.25	2		256	256	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685314	89685314	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121909226	NA	P-0059679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	10	56	1	ENST00000371953.3:c.209T>C	p.Leu70Pro	p.L70P	ENST00000371953	NM_000314.4	70	cTt/cCt	3/9	1	2	FACETS	0.792	0.541	1	0.792	0.541	1	CLONAL	1	TRUE	1	0.25	2		57	101	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47594883	47594883	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs756343868	NA	P-0059679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	32	279	2	ENST00000430070.2:c.1204del	p.Glu402ArgfsTer27	p.E402Rfs*27	ENST00000430070	NM_018095.4	402	Gag/ag	4/4	1	2	FACETS	0.723	0.588	0.876	0.723	0.588	0.876	SUBCLONAL	1	TRUE	1	0.25	2		281	354	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022472	12022474	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0059679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	47	343	0	ENST00000396373.4:c.580_582del	p.Pro194del	p.P194del	ENST00000396373	NM_001987.4	193	tCTCct/tct	5/8	1	2	FACETS	0.972	0.822	1	0.972	0.822	1	CLONAL	1	TRUE	1	0.25	2		343	387	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32932051	32932053	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs80359682	NA	P-0059679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	23	146	0	ENST00000380152.3:c.7795_7797del	p.Glu2599del	p.E2599del	ENST00000380152		2597	aAAGaa/aaa	16/27	1	2	FACETS	0.8	0.626	1	0.8	0.626	1	CLONAL	1	TRUE	1	0.25	2		146	230	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050308	37050308	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	16	139	0	ENST00000231790.2:c.457G>T	p.Glu153Ter	p.E153*	ENST00000231790	NM_000249.3	153	Gag/Tag	6/19	1	2	FACETS	0.557	0.412	0.729	0.557	0.412	0.729	SUBCLONAL	1	TRUE	1	0.25	2		139	230	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090018	37090018	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	29	192	0	ENST00000231790.2:c.1907T>G	p.Leu636Arg	p.L636R	ENST00000231790	NM_000249.3	636	cTg/cGg	17/19	1	2	FACETS	0.892	0.719	1	0.892	0.719	1	CLONAL	1	TRUE	1	0.25	2		192	260	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564693	86564867	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCTGCCCCCTTTGGGGGCGGGCCTCGGGACAGTGGACGAAGGTGACTCTCTGGATGGACCAGAATACGAGGAGGAAGAGGTGGCCATACCGTTGACCGCTCCTCCAACTAACCAGTAAGTTAAGACTGCTGTTCAGGAATTTGGGAAGCTGGCTCCAGAAAAGAAGTGGAAATG	ACCTGCCCCCTTTGGGGGCGGGCCTCGGGACAGTGGACGAAGGTGACTCTCTGGATGGACCAGAATACGAGGAGGAAGAGGTGGCCATACCGTTGACCGCTCCTCCAACTAACCAGTAAGTTAAGACTGCTGTTCAGGAATTTGGGAAGCTGGCTCCAGAAAAGAAGTGGAAATG	-	novel	NA	P-0059679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	32	287	0	ENST00000274376.6:c.426_539+61del		p.X142_splice	ENST00000274376	NM_002890.2	142		1/25	1	2	FACETS	0.85	0.692	1	0.85	0.692	1	CLONAL	1	TRUE	1	0.25	2		287	301	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840010	27840011	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0059679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	37	344	0	ENST00000328488.2:c.83dup	p.Ser29GlufsTer52	p.S29Efs*52	ENST00000328488	NM_003533.2	28	aag/aaAg	1/1	1	2	FACETS	0.783	0.646	0.935	0.783	0.646	0.935	CLONAL	1	TRUE	1	0.25	2		344	378	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339455	116339455	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	19	225	0	ENST00000397752.3:c.317A>C	p.Asn106Thr	p.N106T	ENST00000397752	NM_000245.2	106	aAt/aCt	2/21	1	2	FACETS	0.514	0.39	0.659	0.514	0.39	0.659	SUBCLONAL	1	TRUE	1	0.25	2		225	296	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209576	98209576	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059679-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	17	255	0	ENST00000331920.6:c.3962A>G	p.Asp1321Gly	p.D1321G	ENST00000331920	NM_000264.3	1321	gAc/gGc	23/24	1	2	FACETS	0.482	0.36	0.628	0.482	0.36	0.628	SUBCLONAL	1	TRUE	1	0.25	2		255	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0059714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	57	575	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.123907129258673	4	FACETS	0.799	0.689	0.918	0.799	0.689	0.918	INDETERMINATE	2	TRUE	2	0.251557418227659	4		575	355	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812293	43812293	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	36	494	0	ENST00000372470.3:c.1158C>A	p.His386Gln	p.H386Q	ENST00000372470	NM_005373.2	386	caC/caA	7/12	1	2	FACETS	0.583	0.479	0.7	0.583	0.479	0.7	SUBCLONAL	1	TRUE	1	0.251557418227659	2		494	491	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912345	32912346	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359406	NA	P-0059714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	19	337	0	ENST00000380152.3:c.3860dup	p.Asn1287LysfsTer2	p.N1287Kfs*2	ENST00000380152		1285	gaa/gAaa	11/27	0.251557418227659	1	FACETS	0.93	0.712	1	0.93	0.712	1	CLONAL	1	TRUE	0	0.251557418227659	1		337	142	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012193	16012194	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	G	novel	NA	P-0059714-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	88	356	0	ENST00000268712.3:c.2088_2089delinsC	p.Ser697LeufsTer71	p.S697Lfs*71	ENST00000268712	NM_006311.3	696	gtGTct/gtCct	19/46	0.172981437327776	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.251557418227659	1		356	420	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059768-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	131	429	0	ENST00000425967.3:c.1731C>G	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaG	13/19	1	2	FACETS	0.901	0.824	0.98	1	0.992	1	CLONAL	3	FALSE	1	0.216439914241032	2		429	448	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888199	112888199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918454	NA	P-0059768-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	78	452	0	ENST00000351677.2:c.215C>T	p.Ala72Val	p.A72V	ENST00000351677	NM_002834.3	72	gCc/gTc	3/16	1	2	FACETS	1	0.941	1	1	0.985	1	CLONAL	2	FALSE	1	0.216439914241032	2		452	328	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807902	3807902	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059768-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	79	502	0	ENST00000262367.5:c.3517C>T	p.Arg1173Ter	p.R1173*	ENST00000262367	NM_004380.2	1173	Cga/Tga	18/31	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.216439914241032	2		502	512	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560068	29560068	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059768-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	63	477	0	ENST00000356175.3:c.3545T>C	p.Val1182Ala	p.V1182A	ENST00000356175	NM_000267.3	1182	gTt/gCt	27/57	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.216439914241032	2		477	395	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698180	47698180	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63751411	NA	P-0059779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	8	129	0	ENST00000233146.2:c.1738G>T	p.Glu580Ter	p.E580*	ENST00000233146	NM_000251.2	580	Gaa/Taa	11/16	0.0760966175134232	3	FACETS	0.481	0.308	0.705	0.24	0.154	0.353	SUBCLONAL	1	TRUE	1	0.12	3		129	294	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412494	80412494	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	8	394	0	ENST00000286548.4:c.547C>T	p.Arg183Ter	p.R183*	ENST00000286548	NM_002072.3	183	Cga/Tga	4/7	1	2	FACETS	0.337	0.216	0.495	0.337	0.216	0.495	SUBCLONAL	1	TRUE	1	0.12	2		394	396	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191507	10191507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs5030821	NA	P-0059779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	15	312	0	ENST00000256474.2:c.500G>A	p.Arg167Gln	p.R167Q	ENST00000256474	NM_000551.3	167	cGg/cAg	3/3	1	2	FACETS	0.656	0.478	0.871	0.656	0.478	0.871	SUBCLONAL	1	TRUE	1	0.12	2		312	381	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0059779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	31	364	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	0.76	0.615	0.923	1	0.943	1	CLONAL	2	TRUE	1	0.12	2		364	340	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936984	48936984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772678500	NA	P-0059779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	13	268	0	ENST00000267163.4:c.752G>A	p.Arg251Gln	p.R251Q	ENST00000267163	NM_000321.2	251	cGa/cAa	8/27	1	2	FACETS	0.745	0.53	1	0.745	0.53	1	CLONAL	1	TRUE	1	0.12	2		268	291	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681708	78681708	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767783333	NA	P-0059779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	12	358	0	ENST00000306801.3:c.416G>A	p.Arg139His	p.R139H	ENST00000306801	NM_020761.2	139	cGc/cAc	4/34	1	2	FACETS	0.575	0.402	0.788	0.575	0.402	0.788	SUBCLONAL	1	TRUE	1	0.12	2		358	348	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134988	41134988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	19	261	0	ENST00000379561.5:c.640C>T	p.Arg214Cys	p.R214C	ENST00000379561	NM_002015.3	214	Cgt/Tgt	2/3	1	2	FACETS	0.94	0.713	1	0.94	0.713	1	CLONAL	1	TRUE	1	0.12	2		261	337	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249847	133249847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	9	333	0	ENST00000320574.5:c.1376C>T	p.Ser459Phe	p.S459F	ENST00000320574	NM_006231.2	459	tCt/tTt	14/49	1	2	FACETS	0.462	0.304	0.663	0.462	0.304	0.663	SUBCLONAL	1	TRUE	1	0.12	2		333	325	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258035	123258035	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	16	312	0	ENST00000358487.5:c.1646A>C	p.Asn549Thr	p.N549T	ENST00000358487	NM_000141.4	549	aAt/aCt	12/18	1	2	FACETS	0.801	0.591	1	0.801	0.591	1	CLONAL	1	TRUE	1	0.12	2		312	333	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14303198	14303198	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	15	267	0	ENST00000256196.4:c.477G>T	p.Lys159Asn	p.K159N	ENST00000256196		159	aaG/aaT	5/6	1	2	FACETS	0.951	0.695	1	0.951	0.695	1	CLONAL	1	TRUE	1	0.12	2		267	263	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488717	212488717	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1269407579	NA	P-0059779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	18	425	0	ENST00000342788.4:c.2132G>A	p.Arg711His	p.R711H	ENST00000342788	NM_005235.2	711	cGt/cAt	18/28	1	2	FACETS	0.647	0.485	0.838	0.647	0.485	0.838	SUBCLONAL	1	TRUE	1	0.12	2		425	464	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099344	157099344	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	18	359	0	ENST00000346085.5:c.281A>G	p.His94Arg	p.H94R	ENST00000346085	NM_020732.3	94	cAc/cGc	1/20	1	2	FACETS	0.855	0.643	1	0.855	0.643	1	CLONAL	1	TRUE	1	0.12	2		359	351	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94910900	94910900	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	13	231	0	ENST00000536441.1:c.1230C>A	p.His410Gln	p.H410Q	ENST00000536441	NM_144665.3	410	caC/caA	8/10	1	2	FACETS	0.874	0.623	1	0.874	0.623	1	CLONAL	1	TRUE	1	0.12	2		231	248	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443878	18443878	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	15	228	0	ENST00000266497.5:c.851C>A	p.Ser284Tyr	p.S284Y	ENST00000266497		284	tCt/tAt	3/31	1	2	FACETS	1	0.743	1	1	0.743	1	CLONAL	1	TRUE	1	0.12	2		228	246	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233257	46233257	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	21	294	0	ENST00000334344.6:c.1476G>T	p.Gln492His	p.Q492H	ENST00000334344	NM_152641.2	492	caG/caT	11/21	1	2	FACETS	0.833	0.64	1	0.833	0.64	1	CLONAL	1	TRUE	1	0.12	2		294	420	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676183	29676183	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	16	208	0	ENST00000356175.3:c.7172T>G	p.Ile2391Ser	p.I2391S	ENST00000356175	NM_000267.3	2391	aTt/aGt	48/57	1	2	FACETS	0.923	0.682	1	0.923	0.682	1	CLONAL	1	TRUE	1	0.12	2		208	289	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264483	30264483	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	14	326	0	ENST00000322652.5:c.218A>C	p.Lys73Thr	p.K73T	ENST00000322652	NM_015355.2	73	aAg/aCg	1/16	1	2	FACETS	0.884	0.638	1	0.884	0.638	1	CLONAL	1	TRUE	1	0.12	2		326	264	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55334866	55334866	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	15	228	0	ENST00000284073.2:c.143G>T	p.Arg48Ile	p.R48I	ENST00000284073	NM_138962.2	48	aGa/aTa	3/14	1	2	FACETS	0.842	0.615	1	0.842	0.615	1	CLONAL	1	TRUE	1	0.12	2		228	297	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928022	178928022	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	15	193	0	ENST00000263967.3:c.1300G>T	p.Asp434Tyr	p.D434Y	ENST00000263967	NM_006218.2	434	Gac/Tac	8/21	1	2	FACETS	0.853	0.623	1	0.853	0.623	1	CLONAL	1	TRUE	1	0.12	2		193	293	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447515	187447515	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	30	491	0	ENST00000232014.4:c.678G>T	p.Lys226Asn	p.K226N	ENST00000232014	NM_001130845.1	226	aaG/aaT	5/10	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.12	2		491	459	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144336729	144336729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1363184155	NA	P-0059779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	18	270	0	ENST00000262995.4:c.172C>T	p.Arg58Cys	p.R58C	ENST00000262995	NM_207123.2	58	Cgt/Tgt	2/11	1	2	FACETS	0.993	0.748	1	0.993	0.748	1	CLONAL	1	TRUE	1	0.12	2		270	302	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351467	70351467	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	19	335	0	ENST00000374080.3:c.4115A>C	p.Asn1372Thr	p.N1372T	ENST00000374080		1372	aAc/aCc	29/45	1	2	FACETS	0.983	0.746	1	0.983	0.746	1	CLONAL	1	TRUE	1	0.12	2		335	322	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849197	76849197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059779-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	16	247	0	ENST00000373344.5:c.6079C>T	p.Leu2027Phe	p.L2027F	ENST00000373344	NM_000489.3	2027	Ctt/Ttt	26/35	1	2	FACETS	0.995	0.736	1	0.995	0.736	1	CLONAL	1	TRUE	1	0.12	2		247	268	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589592	67589594	+	inframe_deletion	In_Frame_Del	DEL	ATA	ATA	-	novel	NA	P-0059788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	52	258	0	ENST00000274335.5:c.1356_1358del	p.Asn453del	p.N453del	ENST00000274335		452	tATAac/tac	10/15	0.287805713761404	2	FACETS	0.936	0.813	1	0.936	0.813	1	CLONAL	2	TRUE	0	0.347123106642464	2		258	160	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747342068	NA	P-0059788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	89	714	0	ENST00000269305.4:c.394A>G	p.Lys132Glu	p.K132E	ENST00000269305	NM_001126112.2	132	Aag/Gag	5/11	0.347123106642464	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.347123106642464	1		714	408	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2086866	2086866	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1471482709	NA	P-0059788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	22	634	0	ENST00000349721.2:c.2564G>A	p.Arg855Gln	p.R855Q	ENST00000349721	NM_003070.3	855	cGa/cAa	18/34	0.287805713761404	2	FACETS	0.304	0.235	0.384	0.152	0.117	0.192	SUBCLONAL	1	TRUE	0	0.347123106642464	2		634	417	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244248	46244248	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	42	701	0	ENST00000334344.6:c.2342G>C	p.Gly781Ala	p.G781A	ENST00000334344	NM_152641.2	781	gGa/gCa	15/21	NA	3	FACETS	0.753	0.63	0.889	0.377	0.315	0.445	INDETERMINATE	1	TRUE	1	0.347123106642464	3		701	377	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900579	3900579	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	205	736	0	ENST00000262367.5:c.517C>T	p.Pro173Ser	p.P173S	ENST00000262367	NM_004380.2	173	Cct/Tct	2/31	0.347123106642464	5	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	2	0.347123106642464	5		736	538	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832251	72832251	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	183	652	0	ENST00000268489.5:c.4330C>G	p.Leu1444Val	p.L1444V	ENST00000268489	NM_006885.3	1444	Ctg/Gtg	9/10	0.226623645265473	4	FACETS	0.878	0.817	0.942	0.878	0.817	0.942	CLONAL	3	TRUE	1	0.347123106642464	4		652	539	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873961	151873961	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	124	638	0	ENST00000262189.6:c.8577C>G	p.His2859Gln	p.H2859Q	ENST00000262189	NM_170606.2	2859	caC/caG	38/59	0.334713202155021	3	FACETS	0.984	0.898	1	0.984	0.898	1	CLONAL	2	TRUE	1	0.347123106642464	3		638	426	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150039	202150039	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	28	741	0	ENST00000358485.4:c.1480C>G	p.Arg494Gly	p.R494G	ENST00000358485	NM_001080125.1	494	Cga/Gga	8/9	0.30261032531118	3	FACETS	0.375	0.299	0.462	0.187	0.149	0.231	SUBCLONAL	1	TRUE	1	0.347123106642464	3		741	505	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0059795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	70	457	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.492	0.429	0.56	0.492	0.429	0.56	SUBCLONAL	1	TRUE	1	0.473096288928517	2		457	601	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913400	NA	P-0059795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	58	471	0	ENST00000349496.5:c.98C>A	p.Ser33Tyr	p.S33Y	ENST00000349496	NM_001904.3	33	tCt/tAt	3/15	1	2	FACETS	0.399	0.342	0.46	0.399	0.342	0.46	SUBCLONAL	1	TRUE	1	0.473096288928517	2		471	615	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0059795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	102	573	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.458637353905125	3	FACETS	0.631	0.564	0.703	0.21	0.188	0.235	SUBCLONAL	1	TRUE	0	0.473096288928517	3		573	845	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589149	67589151	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	novel	NA	P-0059795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	50	402	0	ENST00000274335.5:c.1138_1140del	p.Leu380del	p.L380del	ENST00000274335		379	aaATTa/aaa	9/15	1	2	FACETS	0.829	0.709	0.958	0.829	0.709	0.958	CLONAL	1	TRUE	1	0.473096288928517	2		402	255	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655352	67655352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	23	416	0	ENST00000264010.4:c.1215del	p.Lys405AsnfsTer18	p.K405Nfs*18	ENST00000264010	NM_006565.3	405	aaG/aa	7/12	1	2	FACETS	0.257	0.2	0.323	0.257	0.2	0.323	SUBCLONAL	1	TRUE	1	0.473096288928517	2		416	378	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663327	67663328	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTGC	novel	NA	P-0059795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	93	518	1	ENST00000264010.4:c.1731_1735dup	p.Gly579ValfsTer7	p.G579Vfs*7	ENST00000264010	NM_006565.3	576	-/TGTGC	10/12	1	2	FACETS	0.669	0.596	0.746	0.669	0.596	0.746	SUBCLONAL	1	TRUE	1	0.473096288928517	2		519	588	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40476865	40476865	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0059795-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	133	505	0	ENST00000264657.5:c.1465-1G>C		p.X489_splice	ENST00000264657	NM_139276.2	489			1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.473096288928517	2		505	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0059802-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	117	540	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.234763717286452	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.23	1		540	682	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0059802-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	2636	477	0	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	0.3	25	FACETS	1	0.993	1			1	CLONAL	26	TRUE	NA	0.23	25		477	3202	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535283	66535283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs547670481	NA	P-0059802-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	51	516	0	ENST00000273854.3:c.178G>A	p.Glu60Lys	p.E60K	ENST00000273854	NM_004439.5	60	Gaa/Aaa	1/18	1	2	FACETS	0.569	0.482	0.664	0.569	0.482	0.664	SUBCLONAL	1	TRUE	1	0.23	2		516	780	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965567	15965567	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs747836235	NA	P-0059802-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	116	546	0	ENST00000268712.3:c.5239C>T	p.Arg1747Ter	p.R1747*	ENST00000268712	NM_006311.3	1747	Cga/Tga	36/46	0.234763717286452	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.23	1		546	733	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413566	32413566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121907900	NA	P-0059802-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	95	441	0	ENST00000332351.3:c.1384C>T	p.Arg462Trp	p.R462W	ENST00000332351	NM_024426.4	462	Cgg/Tgg	9/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.23	2		441	748	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230492780	230492780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059802-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	61	585	1	ENST00000391860.1:c.274C>T	p.Arg92Cys	p.R92C	ENST00000391860	NM_001258311.1	92	Cgc/Tgc	2/7	1	2	FACETS	0.66	0.568	0.76	0.66	0.568	0.76	SUBCLONAL	1	TRUE	1	0.23	2		586	804	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537914	212537914	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059802-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	61	590	0	ENST00000342788.4:c.1691A>G	p.Asp564Gly	p.D564G	ENST00000342788	NM_005235.2	564	gAt/gGt	14/28	0.188864541014747	3	FACETS	0.59	0.507	0.681	0.295	0.253	0.341	SUBCLONAL	1	TRUE	1	0.23	3		590	1002	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028126	69028126	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059802-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	102	415	0	ENST00000288368.4:c.3285A>C	p.Glu1095Asp	p.E1095D	ENST00000288368	NM_024870.2	1095	gaA/gaC	26/40	0.3	3	FACETS	1	0.978	1	0.685	0.613	0.762	CLONAL	1	TRUE	1	0.23	3		415	722	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457112	5457116	+	frameshift_variant	Frame_Shift_Del	DEL	TGGTA	TGGTA	AGTT	novel	NA	P-0059802-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	49	417	0	ENST00000381577.3:c.86_90delinsAGTT	p.Val29GlufsTer8	p.V29Efs*8	ENST00000381577	NM_014143.3	29	gTGGTA/gAGTT	3/7	1	2	FACETS	0.606	0.512	0.71	0.606	0.512	0.71	SUBCLONAL	1	TRUE	1	0.23	2		417	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0059804-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	622	864	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.758267128730757	3	FACETS	0.98	0.96	0.999	0.98	0.96	0.999	CLONAL	3	FALSE	0	0.788381035586319	3		864	748	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060852	38060852	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059804-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	281	946	0	ENST00000250448.2:c.1137G>T	p.Leu379Phe	p.L379F	ENST00000250448	NM_004496.3	379	ttG/ttT	2/2	0.788753146446891	3	FACETS	0.987	0.928	1	0.329	0.309	0.349	CLONAL	1	FALSE	0	0.788381035586319	3		946	1007	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256730	16256730	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059804-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	247	574	0	ENST00000375759.3:c.3995A>G	p.Asn1332Ser	p.N1332S	ENST00000375759	NM_015001.2	1332	aAt/aGt	11/15	0.788753146446891	3	FACETS	1	0.975	1			1	CLONAL	1	FALSE	NA	0.788381035586319	3		574	813	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259054	16259054	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059804-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	114	777	0	ENST00000375759.3:c.6319G>C	p.Ala2107Pro	p.A2107P	ENST00000375759	NM_015001.2	2107	Gca/Cca	11/15	0.788753146446891	3	FACETS	0.397	0.357	0.44			1	SUBCLONAL	1	FALSE	NA	0.788381035586319	3		777	1015	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872010	35872069	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGCTCCACGATGCCCAGGTAGCCATGGATAGAGGCTAAGTGTAGACACGTGTGGCCTGG	AAGCTCCACGATGCCCAGGTAGCCATGGATAGAGGCTAAGTGTAGACACGTGTGGCCTGG	-	novel	NA	P-0059804-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	218	732	0	ENST00000216797.5:c.548-4_603del		p.X183_splice	ENST00000216797	NM_020529.2	183		4/6	0.788753146446891	3	FACETS	0.864	0.805	0.926	0.288	0.268	0.309	CLONAL	1	FALSE	0	0.788381035586319	3		732	892	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987143	36987143	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059804-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	188	674	0	ENST00000354822.5:c.546C>A	p.Asn182Lys	p.N182K	ENST00000354822	NM_001079668.2	182	aaC/aaA	3/3	0.788753146446891	3	FACETS	0.934	0.866	1	0.311	0.288	0.335	CLONAL	1	FALSE	0	0.788381035586319	3		674	712	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032190	10032190	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs771580780	NA	P-0059804-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	190	733	0	ENST00000330684.3:c.633G>C	p.Glu211Asp	p.E211D	ENST00000330684	NM_001134407.1	211	gaG/gaC	3/13	0.605225839907757	3	FACETS	0.987	0.916	1			1	CLONAL	1	FALSE	NA	0.788381035586319	3		733	681	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215617212	215617212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059804-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	299	426	0	ENST00000260947.4:c.1636C>T	p.Pro546Ser	p.P546S	ENST00000260947	NM_000465.2	546	Cca/Tca	7/11	0.788753146446891	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	FALSE	0	0.788381035586319	2		426	372	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573076	41573077	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0059804-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	309	848	0	ENST00000263253.7:c.5364_5365dup	p.Cys1789SerfsTer20	p.C1789Sfs*20	ENST00000263253	NM_001429.3	1787	-/CT	31/31	0.187143166997095	3	FACETS	1	0.994	1	0.702	0.666	0.74	INDETERMINATE	1	FALSE	1	0.788381035586319	3		848	778	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641889	12641889	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0059804-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	188	543	0	ENST00000251849.4:c.860C>G	p.Ser287Ter	p.S287*	ENST00000251849	NM_002880.3	287	tCa/tGa	8/17	0.788753146446891	5	FACETS	0.911	0.841	0.985	0.228	0.21	0.247	CLONAL	1	FALSE	1	0.788381035586319	5		543	1142	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376651	8376651	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059804-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	186	470	0	ENST00000356435.5:c.4462G>C	p.Val1488Leu	p.V1488L	ENST00000356435		1488	Gtg/Ctg	27/35	0.680841953559418	4	FACETS	1	0.976	1	0.376	0.348	0.405	CLONAL	1	FALSE	1	0.788381035586319	4		470	748	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293606	137293606	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059804-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	269	888	0	ENST00000481739.1:c.157A>T	p.Thr53Ser	p.T53S	ENST00000481739	NM_002957.4	53	Acc/Tcc	2/10	0.788753146446891	2	FACETS	0.978	0.923	1	0.489	0.461	0.517	CLONAL	1	FALSE	0	0.788381035586319	2		888	698	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249037	55249038	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0059806-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	586	560	0	ENST00000275493.2:c.2335_2336delinsTT	p.Gly779Phe	p.G779F	ENST00000275493	NM_005228.3	779	GGc/TTc	20/28	0.392112621723076	7	FACETS	0.963	0.929	0.998	0.963	0.929	0.998	CLONAL	5	TRUE	2	0.392112621723076	7		560	1229	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0059806-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	217	504	0	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.392112621723076	3	FACETS	0.966	0.903	1	0.966	0.903	1	CLONAL	2	TRUE	1	0.392112621723076	3		504	685	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0059806-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	130	718	0	ENST00000269305.4:c.560-1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.392112621723076	3	FACETS	0.902	0.818	0.991	0.451	0.409	0.496	CLONAL	1	TRUE	1	0.392112621723076	3		718	879	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274231	10274231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367543131	NA	P-0059806-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	54	513	0	ENST00000330684.3:c.38C>T	p.Pro13Leu	p.P13L	ENST00000330684	NM_001134407.1	13	cCg/cTg	2/13	0.31903378881852	4	FACETS	0.54	0.46	0.628	0.18	0.153	0.21	SUBCLONAL	1	TRUE	1	0.392112621723076	4		513	710	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342676	87342676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779160638	NA	P-0059806-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	114	553	0	ENST00000277120.3:c.961G>A	p.Gly321Arg	p.G321R	ENST00000277120		321	Ggg/Agg	9/19	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.392112621723076	2		553	554	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486248	8486248	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768330226	NA	P-0059806-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	118	474	0	ENST00000356435.5:c.2569C>A	p.Arg857Ser	p.R857S	ENST00000356435		857	Cgt/Agt	17/35	0.392112621723076	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.392112621723076	1		474	454	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295650	1295650	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0059806-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	124	690	0				ENST00000310581	NM_198253.2	-/1132			0.191026331574349	3	FACETS	0.941	0.851	1	0.314	0.283	0.345	INDETERMINATE	1	TRUE	0	0.392112621723076	3		690	804	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846327	156846327	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059806-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	113	582	0	ENST00000524377.1:c.1768G>C	p.Glu590Gln	p.E590Q	ENST00000524377	NM_002529.3	590	Gag/Cag	14/17	0.359038623447331	4	FACETS	0.92	0.827	1	0.307	0.275	0.34	CLONAL	1	TRUE	1	0.392112621723076	4		582	872	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604668	43604668	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059806-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	156	551	0	ENST00000355710.3:c.1253G>T	p.Arg418Leu	p.R418L	ENST00000355710	NM_020975.4	418	cGa/cTa	6/20	0.392112621723076	3	FACETS	1	0.987	1	0.707	0.649	0.767	CLONAL	1	TRUE	1	0.392112621723076	3		551	673	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661904	29661904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059806-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	201	469	0	ENST00000356175.3:c.5798C>T	p.Ser1933Leu	p.S1933L	ENST00000356175	NM_000267.3	1933	tCa/tTa	39/57	0.392112621723076	5	FACETS	1	0.963	1	0.704	0.654	0.755	CLONAL	2	TRUE	2	0.392112621723076	5		469	771	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584318	39584318	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0059806-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	86	324	0	ENST00000262039.4:c.985-2A>C		p.X329_splice	ENST00000262039	NM_002647.2	329			0.386753207833016	4	FACETS	1	0.955	1	0.289	0.256	0.324	CLONAL	1	TRUE	0	0.392112621723076	4		324	529	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543677	29543677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059806-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	121	632	0	ENST00000389048.3:c.1486C>T	p.Pro496Ser	p.P496S	ENST00000389048	NM_004304.4	496	Ccc/Tcc	7/29	0.359038623447331	4	FACETS	0.902	0.814	0.996	0.301	0.271	0.332	CLONAL	1	TRUE	1	0.392112621723076	4		632	952	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46251053	46251053	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059806-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	74	329	0	ENST00000371998.3:c.62C>T	p.Pro21Leu	p.P21L	ENST00000371998		21	cCa/cTa	3/23	0.351944294906372	4	FACETS	0.9	0.788	1	0.45	0.394	0.51	CLONAL	1	TRUE	2	0.392112621723076	4		329	584	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413637	138413637	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059806-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	142	403	0	ENST00000289153.2:c.1883G>T	p.Arg628Leu	p.R628L	ENST00000289153	NM_006219.2	628	cGa/cTa	12/22	0.18176300201612	3	FACETS	1	0.987	1	0.746	0.682	0.811	INDETERMINATE	1	TRUE	1	0.392112621723076	3		403	581	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1253889	1253889	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059806-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	130	588	0	ENST00000310581.5:c.3353C>T	p.Ala1118Val	p.A1118V	ENST00000310581	NM_198253.2	1118	gCa/gTa	16/16	0.191026331574349	3	FACETS	1	0.966	1	0.377	0.342	0.414	INDETERMINATE	1	TRUE	0	0.392112621723076	3		588	701	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495429	149495429	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059806-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	145	701	0	ENST00000261799.4:c.3218A>T	p.Glu1073Val	p.E1073V	ENST00000261799	NM_002609.3	1073	gAg/gTg	23/23	0.392112621723076	3	FACETS	0.996	0.909	1	0.498	0.454	0.544	CLONAL	1	TRUE	1	0.392112621723076	3		701	888	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928931	44928931	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059806-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	79	376	0	ENST00000377967.4:c.2031G>C	p.Gln677His	p.Q677H	ENST00000377967	NM_021140.2	677	caG/caC	17/29	0.191026331574349	3	FACETS	1	0.913	1	0.347	0.306	0.391	INDETERMINATE	1	TRUE	0	0.392112621723076	3		376	463	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0059831-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	58	460	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.972	0.839	1	1	0.977	1	CLONAL	2	TRUE	1	0.16	2		461	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0059831-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	56	554	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	1	2	FACETS	0.759	0.652	0.876	1	0.968	1	SUBCLONAL	2	TRUE	1	0.16	2		554	461	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	106	475	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.759	0.686	0.835	0.759	0.686	0.835	SUBCLONAL	1	TRUE	1	0.703427345065221	2		475	397	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	239	613	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	0.347591710004347	1	FACETS	0.792	0.746	0.839	0.792	0.746	0.839	INDETERMINATE	1	TRUE	0	0.703427345065221	1		613	556	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481403	140481403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913357	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	109	376	0	ENST00000288602.6:c.1405G>A	p.Gly469Arg	p.G469R	ENST00000288602	NM_004333.4	469	Gga/Aga	11/18	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.703427345065221	2		376	263	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170217	32170217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	548	689	0	ENST00000375023.3:c.3391C>T	p.Pro1131Ser	p.P1131S	ENST00000375023	NM_004557.3	1131	Cct/Tct	21/30	0.579193043086865	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.703427345065221	4		689	1298	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443612	29443612	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1244270149	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	262	552	0	ENST00000389048.3:c.3605G>A	p.Gly1202Glu	p.G1202E	ENST00000389048	NM_004304.4	1202	gGa/gAa	23/29	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.703427345065221	2		552	733	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217364	123217364	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	83	189	0	ENST00000218089.9:c.3018T>G	p.Phe1006Leu	p.F1006L	ENST00000218089	NM_001042749.1	1006	ttT/ttG	29/35	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.703427345065221	1		189	105	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041725	29041725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	144	344	0	ENST00000282397.4:c.94C>T	p.Pro32Ser	p.P32S	ENST00000282397	NM_002019.4	32	Cct/Tct	2/30	0.241183301178765	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.703427345065221	0		344	404	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606081	81606081	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746685925	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	252	553	0	ENST00000298171.2:c.751G>A	p.Glu251Lys	p.E251K	ENST00000298171	NM_000369.2	251	Gaa/Aaa	9/10	1	2	FACETS	0.964	0.906	1	0.964	0.906	1	CLONAL	1	TRUE	1	0.703427345065221	2		553	743	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104594	69104594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	230	503	0	ENST00000288368.4:c.4438G>A	p.Asp1480Asn	p.D1480N	ENST00000288368	NM_024870.2	1480	Gat/Aat	37/40	0.703427345065221	3	FACETS	1	0.97	1	0.532	0.497	0.569	CLONAL	1	TRUE	1	0.703427345065221	3		503	830	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541553	187541553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	68	632	0	ENST00000441802.2:c.6187G>A	p.Ala2063Thr	p.A2063T	ENST00000441802	NM_005245.3	2063	Gcc/Acc	10/27	0.625504249305346	1	FACETS	0.206	0.179	0.235	0.206	0.179	0.235	SUBCLONAL	1	TRUE	0	0.703427345065221	1		632	608	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967278	25967278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	277	614	0	ENST00000435504.4:c.1928C>T	p.Pro643Leu	p.P643L	ENST00000435504		643	cCa/cTa	13/13	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.703427345065221	2		614	770	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11293519	11293519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	95	398	0	ENST00000361445.4:c.2357C>T	p.Pro786Leu	p.P786L	ENST00000361445	NM_004958.3	786	cCa/cTa	15/58	0.703427345065221	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.703427345065221	1		398	161	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106019	8106019	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	355	646	0	ENST00000346208.3:c.839G>A	p.Gly280Glu	p.G280E	ENST00000346208		280	gGa/gAa	4/6	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.703427345065221	2		646	946	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435269	18435270	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	146	561	0	ENST00000266497.5:c.254_255delinsTT	p.Ser85Phe	p.S85F	ENST00000266497		85	tCC/tTT	1/31	1	2	FACETS	0.847	0.779	0.918	0.847	0.779	0.918	CLONAL	1	TRUE	1	0.703427345065221	2		561	490	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	79	341	0	ENST00000311936.3:c.34_35delinsAA	p.Gly12Asn	p.G12N	ENST00000311936	NM_004985.3	12	GGt/AAt	2/5	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.703427345065221	2		341	205	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859694	57859694	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	289	588	0	ENST00000228682.2:c.748G>A	p.Glu250Lys	p.E250K	ENST00000228682	NM_005269.2	250	Gag/Aag	7/12	1	2	FACETS	0.934	0.881	0.988	0.934	0.881	0.988	CLONAL	1	TRUE	1	0.703427345065221	2		588	880	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115422	115115422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	141	506	0	ENST00000257566.3:c.904G>A	p.Gly302Ser	p.G302S	ENST00000257566	NM_016569.3	302	Ggt/Agt	5/8	0.703427345065221	3	FACETS	1	0.975	1	0.578	0.53	0.627	CLONAL	1	TRUE	1	0.703427345065221	3		506	469	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434166	121434166	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	572	722	0	ENST00000257555.6:c.1057C>T	p.Pro353Ser	p.P353S	ENST00000257555		353	Ccc/Tcc	5/10	0.703427345065221	3	FACETS	0.997	0.962	1	0.997	0.962	1	CLONAL	2	TRUE	1	0.703427345065221	3		722	1103	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959449	26959449	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	149	413	0	ENST00000381527.3:c.616C>T	p.Leu206Phe	p.L206F	ENST00000381527	NM_001260.1	206	Ctt/Ttt	6/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.703427345065221	2		413	336	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916821	48916823	+	frameshift_variant	Frame_Shift_Del	DEL	TAC	TAC	AT	novel	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	49	318	0	ENST00000267163.4:c.351_353delinsAT	p.Phe117LeufsTer8	p.F117Lfs*8	ENST00000267163	NM_000321.2	117	ttTACt/ttATt	3/27	1	2	FACETS	0.929	0.803	1	0.929	0.803	1	CLONAL	1	TRUE	1	0.703427345065221	2		318	150	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039171	49039175	+	frameshift_variant	Frame_Shift_Del	DEL	ATTCT	ATTCT	-	novel	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	73	294	0	ENST00000267163.4:c.2252_2256del	p.Ser751TyrfsTer5	p.S751Yfs*5	ENST00000267163	NM_000321.2	750	gATTCT/g	22/27	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.703427345065221	2		294	194	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988499	36988499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	229	670	0	ENST00000354822.5:c.154G>A	p.Glu52Lys	p.E52K	ENST00000354822	NM_001079668.2	52	Gaa/Aaa	2/3	1	2	FACETS	0.916	0.857	0.976	0.916	0.857	0.976	CLONAL	1	TRUE	1	0.703427345065221	2		670	711	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66777515	66777516	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	277	640	1	ENST00000307102.5:c.881_882delinsAA	p.Gly294Glu	p.G294E	ENST00000307102	NM_002755.3	294	gGG/gAA	7/11	0.347591710004347	1	FACETS	0.682	0.643	0.721	0.682	0.643	0.721	INDETERMINATE	1	TRUE	0	0.703427345065221	1		641	749	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727481	88727481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	234	585	0	ENST00000360948.2:c.298G>A	p.Glu100Lys	p.E100K	ENST00000360948	NM_001012338.2	100	Gag/Aag	3/19	0.347591710004347	1	FACETS	0.516	0.482	0.551	0.516	0.482	0.551	INDETERMINATE	1	TRUE	0	0.703427345065221	1		585	836	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843438	3843439	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CATGGTTCGA	novel	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	213	586	0	ENST00000262367.5:c.1155_1164dup	p.Lys389SerfsTer41	p.K389Sfs*41	ENST00000262367	NM_004380.2	388	-/TCGAACCATG	4/31	0.703427345065221	1	FACETS	0.82	0.77	0.87	0.82	0.77	0.87	CLONAL	1	TRUE	0	0.703427345065221	1		586	479	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533271	29533271	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	166	543	0	ENST00000356175.3:c.1274G>A	p.Trp425Ter	p.W425*	ENST00000356175	NM_000267.3	425	tGg/tAg	12/57	1	2	FACETS	0.985	0.913	1	0.985	0.913	1	CLONAL	1	TRUE	1	0.703427345065221	2		543	479	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657361	29657361	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	155	478	0	ENST00000356175.3:c.5594T>C	p.Leu1865Ser	p.L1865S	ENST00000356175	NM_000267.3	1865	tTa/tCa	38/57	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.703427345065221	2		478	321	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61324085	61324085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	53	374	0	ENST00000283752.5:c.748G>A	p.Glu250Lys	p.E250K	ENST00000283752	NM_006919.2	250	Gaa/Aaa	7/8	1	2	FACETS	0.685	0.591	0.785	0.685	0.591	0.785	SUBCLONAL	1	TRUE	1	0.703427345065221	2		374	220	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387320	17387320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	264	620	0	ENST00000359435.4:c.586C>T	p.Leu196Phe	p.L196F	ENST00000359435	NM_001033549.1	196	Ctt/Ttt	7/9	1	2	FACETS	0.984	0.926	1	0.984	0.926	1	CLONAL	1	TRUE	1	0.703427345065221	2		620	763	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215615	36215615	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	257	514	0	ENST00000222270.7:c.3412C>T	p.Arg1138Ter	p.R1138*	ENST00000222270	NM_014727.1	1138	Cga/Tga	9/37	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.703427345065221	2		514	703	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257749	198257749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	183	487	0	ENST00000335508.6:c.3703G>A	p.Glu1235Lys	p.E1235K	ENST00000335508	NM_012433.2	1235	Gag/Aag	24/25	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.703427345065221	2		487	492	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736197	204736197	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	179	454	0	ENST00000302823.3:c.554C>T	p.Ser185Phe	p.S185F	ENST00000302823	NM_005214.4	185	tCt/tTt	3/4	0.536484302660289	3	FACETS	1	0.956	1	0.524	0.484	0.564	CLONAL	1	TRUE	1	0.703427345065221	3		454	657	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260166	149260166	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	288	526	0	ENST00000360632.3:c.727G>A	p.Glu243Lys	p.E243K	ENST00000360632	NM_015472.4	243	Gag/Aag	4/7	1	2	FACETS	0.982	0.927	1	0.982	0.927	1	CLONAL	1	TRUE	1	0.703427345065221	2		526	834	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196448	106196448	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	45	621	0	ENST00000380013.4:c.4781C>A	p.Pro1594His	p.P1594H	ENST00000380013	NM_001127208.2	1594	cCt/cAt	11/11	0.625504249305346	1	FACETS	0.205	0.172	0.241	0.205	0.172	0.241	SUBCLONAL	1	TRUE	0	0.703427345065221	1		621	404	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345791	152345791	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	113	442	0	ENST00000359321.1:c.779del	p.Leu260Ter	p.L260*	ENST00000359321	NM_005431.1	260	tTa/ta	3/3	1	2	FACETS	0.931	0.848	1	0.931	0.848	1	CLONAL	1	TRUE	1	0.703427345065221	2		442	345	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859750	117859750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	282	427	0	ENST00000297338.2:c.1885C>T	p.His629Tyr	p.H629Y	ENST00000297338	NM_006265.2	629	Cat/Tat	14/14	0.703427345065221	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.703427345065221	3		427	515	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197322	27197322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	98	398	0	ENST00000380036.4:c.1634C>T	p.Pro545Leu	p.P545L	ENST00000380036	NM_000459.3	545	cCt/cTt	12/23	1	2	FACETS	0.92	0.831	1	0.92	0.831	1	CLONAL	1	TRUE	1	0.703427345065221	2		398	303	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858020	152858020	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059832-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	308	326	0	ENST00000406277.2:c.595C>T	p.Gln199Ter	p.Q199*	ENST00000406277	NM_152274.4	199	Cag/Tag	6/7	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.703427345065221	1		326	446	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858738	9858738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149698593	NA	P-0059834-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	68	522	0	ENST00000330684.3:c.2663C>T	p.Thr888Met	p.T888M	ENST00000330684	NM_001134407.1	888	aCg/aTg	13/13	0.494589501452817	2	FACETS	1	0.973	1	0.677	0.601	0.754	CLONAL	1	TRUE	0	0.558237683810778	2		522	180	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068325	30068325	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758594741	NA	P-0059834-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	36	260	0	ENST00000331968.5:c.2074G>A	p.Val692Met	p.V692M	ENST00000331968	NM_002742.2	692	Gtg/Atg	15/18	0.195783361098814	5	FACETS	0.898	0.764	1	0.898	0.764	1	INDETERMINATE	3	TRUE	2	0.558237683810778	5		260	88	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574815	41574815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748953233	NA	P-0059834-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	309	593	0	ENST00000263253.7:c.7100C>T	p.Pro2367Leu	p.P2367L	ENST00000263253	NM_001429.3	2367	cCg/cTg	31/31	0.469931061891217	3	FACETS	0.892	0.853	0.931	0.892	0.853	0.931	CLONAL	3	TRUE	0	0.558237683810778	3		593	529	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30060979	30060979	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059834-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	70	319	0	ENST00000338641.4:c.813del	p.Phe271LeufsTer25	p.F271Lfs*25	ENST00000338641	NM_000268.3	271	Ttt/tt	9/16	0.469931061891217	3	FACETS	0.849	0.768	0.928	0.849	0.768	0.928	CLONAL	3	TRUE	0	0.558237683810778	3		319	126	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0059848-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	70	462	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	FALSE	1	0.665376790220533	2		462	197	SUCCESS
REST	5978	MSKCC	GRCh37	4	57798097	57798097	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059848-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	69	583	0	ENST00000309042.7:c.3073G>T	p.Glu1025Ter	p.E1025*	ENST00000309042	NM_005612.4	1025	Gag/Tag	4/4	0.205025252009889	0	FACETS	0.344	0.304	0.384			1	INDETERMINATE	1	FALSE	0	0.665376790220533	0		583	202	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262645	16262645	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059849-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	261	611	0	ENST00000375759.3:c.9910C>G	p.Gln3304Glu	p.Q3304E	ENST00000375759	NM_015001.2	3304	Caa/Gaa	11/15	0.612380220427718	4	FACETS	0.942	0.887	0.998	0.942	0.887	0.998	CLONAL	2	TRUE	2	0.61039289507103	4		611	731	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741944	162741944	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059849-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	250	644	2	ENST00000367921.3:c.1635G>T	p.Met545Ile	p.M545I	ENST00000367921	NM_006182.2	545	atG/atT	13/18	0.459540496272609	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	2	0.61039289507103	4		646	647	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745634	162745634	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0059849-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	250	603	0	ENST00000367921.3:c.2048+1G>T		p.X683_splice	ENST00000367921	NM_006182.2	683			0.459540496272609	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	2	0.61039289507103	4		603	650	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600462	43600462	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059849-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	144	744	0	ENST00000355710.3:c.688G>C	p.Asp230His	p.D230H	ENST00000355710	NM_020975.4	230	Gac/Cac	4/20	0.110812539821381	0	FACETS	0.389	0.357	0.421			1	INDETERMINATE	1	TRUE	0	0.61039289507103	0		744	473	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604678	43604678	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059849-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	150	529	0	ENST00000355710.3:c.1263G>T	p.Gln421His	p.Q421H	ENST00000355710	NM_020975.4	421	caG/caT	6/20	0.110812539821381	0	FACETS	0.443	0.409	0.479			1	INDETERMINATE	1	TRUE	0	0.61039289507103	0		529	432	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998409	100998409	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1171387034	NA	P-0059849-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	231	571	0	ENST00000325455.5:c.1393G>T	p.Ala465Ser	p.A465S	ENST00000325455	NM_001202474.3	465	Gcg/Tcg	1/8	0.584197203835994	3	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	1	0.61039289507103	3		571	493	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434357	121434357	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059849-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	144	683	0	ENST00000257555.6:c.1121G>T	p.Gly374Val	p.G374V	ENST00000257555		374	gGg/gTg	6/10	1	2	FACETS	0.942	0.865	1	0.942	0.865	1	CLONAL	1	TRUE	1	0.61039289507103	2		683	501	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134846	41134846	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059849-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	128	593	0	ENST00000379561.5:c.782G>T	p.Ser261Ile	p.S261I	ENST00000379561	NM_002015.3	261	aGt/aTt	2/3	0.612380220427718	2	FACETS	0.932	0.851	1	0.466	0.425	0.508	CLONAL	1	TRUE	0	0.61039289507103	2		593	450	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281216	49281216	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059849-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	212	564	3	ENST00000282018.3:c.263del	p.Ile88LysfsTer42	p.I88Kfs*42	ENST00000282018	NM_020377.2	88	aTa/aa	1/1	0.612380220427718	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.61039289507103	2		567	346	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506191	103506191	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs760467381	NA	P-0059849-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	21	467	0	ENST00000355739.4:c.349C>A	p.Gln117Lys	p.Q117K	ENST00000355739	NM_000123.3	117	Caa/Aaa	3/15	0.612380220427718	2	FACETS	0.181	0.139	0.23	0.091	0.069	0.115	SUBCLONAL	1	TRUE	0	0.61039289507103	2		467	380	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023231	33023232	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0059849-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	354	711	0	ENST00000300177.4:c.341dup	p.Asn115GlnfsTer46	p.N115Qfs*46	ENST00000300177	NM_001191322.1	114	atc/aTtc	2/2	0.612380220427718	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.61039289507103	2		711	568	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129433	30129433	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059849-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	296	620	0	ENST00000263025.4:c.595G>T	p.Gly199Cys	p.G199C	ENST00000263025	NM_002746.2	199	Ggc/Tgc	4/9	0.111528670035446	6	FACETS	1	0.985	1			1	INDETERMINATE	4	TRUE	NA	0.61039289507103	6		620	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059849-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	332	711	0	ENST00000269305.4:c.542G>C	p.Arg181Pro	p.R181P	ENST00000269305	NM_001126112.2	181	cGc/cCc	5/11	0.597632419163948	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.61039289507103	2		711	539	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602763	10602763	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs774469695	NA	P-0059849-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	342	716	0	ENST00000171111.5:c.815G>T	p.Arg272Leu	p.R272L	ENST00000171111	NM_203500.1	272	cGc/cTc	3/6	0.612380220427718	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.61039289507103	2		716	546	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530203	212530203	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0059849-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	193	493	0	ENST00000342788.4:c.1717-1G>T		p.X573_splice	ENST00000342788	NM_005235.2	573			0.379300557728663	5	FACETS	0.836	0.781	0.892	0.836	0.781	0.892	CLONAL	3	TRUE	2	0.61039289507103	5		493	483	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446840	29446840	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059849-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	31	620	0	ENST00000544604.2:c.2671G>T	p.Gly891Cys	p.G891C	ENST00000544604	NM_001206998.1	891	Ggc/Tgc	8/9	0.464615411117975	2	FACETS	0.221	0.178	0.269	0.11	0.089	0.135	SUBCLONAL	1	TRUE	0	0.61039289507103	2		620	460	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961069	79961069	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059849-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	201	560	0	ENST00000265081.6:c.466C>G	p.Leu156Val	p.L156V	ENST00000265081	NM_002439.4	156	Ctg/Gtg	3/24	0.612380220427718	2	FACETS	0.922	0.871	0.973	0.922	0.871	0.973	CLONAL	2	TRUE	0	0.61039289507103	2		560	357	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864374	162864374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059849-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	216	529	2	ENST00000366898.1:c.139G>T	p.Gly47Trp	p.G47W	ENST00000366898	NM_004562.2	47	Ggg/Tgg	2/12	NA	2	FACETS	0.997	0.946	1			1	INDETERMINATE	2	TRUE	NA	0.61039289507103	2		531	355	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971158	21971158	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059849-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	294	731	0	ENST00000304494.5:c.200G>T	p.Gly67Val	p.G67V	ENST00000304494	NM_000077.4	67	gGc/gTc	2/3	0.612380220427718	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.61039289507103	2		731	445	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0059856-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	154	238	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.750952598043558	2		238	339	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581229	48581229	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059856-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	301	498	0	ENST00000342988.3:c.533C>A	p.Ser178Ter	p.S178*	ENST00000342988	NM_005359.5	178	tCa/tAa	5/12	0.750952598043558	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.750952598043558	1		498	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0059856-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	295	612	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.750952598043558	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.750952598043558	1		612	469	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426133	47426133	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059856-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	384	641	0	ENST00000377045.4:c.653T>C	p.Val218Ala	p.V218A	ENST00000377045	NM_001654.4	218	gTc/gCc	7/16	0.750952598043558	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.750952598043558	1		641	560	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522552	176522552	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519793	NA	P-0059859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	104	764	0	ENST00000292408.4:c.1649T>A	p.Val550Glu	p.V550E	ENST00000292408	NM_213647.1	550	gTg/gAg	13/18	0.269526609268242	3	FACETS	1	0.969	1	0.608	0.544	0.675	CLONAL	1	TRUE	1	0.271971833484107	3		764	715	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056119	26056119	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	74	583	0	ENST00000343677.2:c.538G>C	p.Ala180Pro	p.A180P	ENST00000343677	NM_005319.3	180	Gcg/Ccg	1/1	0.271971833484107	6	FACETS	0.918	0.802	1	0.23	0.2	0.261	CLONAL	1	TRUE	2	0.271971833484107	6		583	915	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	33	475	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.24	2		475	230	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	20	66	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.24	2		66	121	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	29	88	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.905	0.729	1	0.905	0.729	1	CLONAL	1	TRUE	1	0.24	2		88	267	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	34	333	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	1	2	FACETS	0.623	0.508	0.751	0.623	0.508	0.751	SUBCLONAL	1	TRUE	1	0.24	2		333	455	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292409	15292409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	34	538	0	ENST00000263388.2:c.2770G>A	p.Asp924Asn	p.D924N	ENST00000263388	NM_000435.2	924	Gac/Aac	17/33	0.191908977397165	3	FACETS	0.682	0.557	0.824	0.341	0.278	0.412	SUBCLONAL	1	TRUE	1	0.24	3		538	465	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057682	27057682	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520585	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	65	520	0	ENST00000324856.7:c.1390C>T	p.Gln464Ter	p.Q464*	ENST00000324856	NM_006015.4	464	Caa/Taa	3/20	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.24	2		520	501	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446909	18446909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	24	102	0	ENST00000266497.5:c.994C>A	p.His332Asn	p.H332N	ENST00000266497		332	Cat/Aat	4/31	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.24	2		102	170	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604655	48604655	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121912578	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	35	416	0	ENST00000342988.3:c.1477G>C	p.Asp493His	p.D493H	ENST00000342988	NM_005359.5	493	Gat/Cat	12/12	1	2	FACETS	0.666	0.546	0.801	0.666	0.546	0.801	SUBCLONAL	1	TRUE	1	0.24	2		416	438	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532590	187532590	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	50	268	0	ENST00000441802.2:c.9803C>G	p.Ser3268Ter	p.S3268*	ENST00000441802	NM_005245.3	3268	tCa/tGa	14/27	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.24	2		268	304	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058045	27058045	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	48	509	0	ENST00000324856.7:c.1753C>T	p.Gln585Ter	p.Q585*	ENST00000324856	NM_006015.4	585	Cag/Tag	3/20	1	2	FACETS	0.775	0.655	0.907	0.775	0.655	0.907	CLONAL	1	TRUE	1	0.24	2		509	516	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182125	11182125	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	27	390	1	ENST00000361445.4:c.6721C>T	p.Pro2241Ser	p.P2241S	ENST00000361445	NM_004958.3	2241	Ccc/Tcc	48/58	1	2	FACETS	0.521	0.414	0.643	0.521	0.414	0.643	SUBCLONAL	1	TRUE	1	0.24	2		391	432	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294268	1294268	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	30	614	0	ENST00000310581.5:c.733G>C	p.Glu245Gln	p.E245Q	ENST00000310581	NM_198253.2	245	Gag/Cag	2/16	1	2	FACETS	0.708	0.571	0.863	0.708	0.571	0.863	SUBCLONAL	1	TRUE	1	0.24	2		614	353	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385171	41385171	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	18	383	0	ENST00000373198.4:c.790A>C	p.Lys264Gln	p.K264Q	ENST00000373198	NM_133170.3	264	Aag/Cag	6/32	1	2	FACETS	0.464	0.349	0.601	0.464	0.349	0.601	SUBCLONAL	1	TRUE	1	0.24	2		383	323	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259667	16259667	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	66	538	0	ENST00000375759.3:c.6932C>G	p.Ser2311Ter	p.S2311*	ENST00000375759	NM_015001.2	2311	tCa/tGa	11/15	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.24	2		538	481	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582123	52582123	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	60	435	0	ENST00000394830.3:c.4705G>A	p.Asp1569Asn	p.D1569N	ENST00000394830	NM_018313.4	1569	Gac/Aac	30/30	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.24	2		435	462	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258841	16258841	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	75	544	0	ENST00000375759.3:c.6106G>T	p.Glu2036Ter	p.E2036*	ENST00000375759	NM_015001.2	2036	Gag/Tag	11/15	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.24	2		544	587	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259186	16259186	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	67	562	0	ENST00000375759.3:c.6451G>C	p.Glu2151Gln	p.E2151Q	ENST00000375759	NM_015001.2	2151	Gaa/Caa	11/15	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.24	2		562	489	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259426	16259426	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	55	544	0	ENST00000375759.3:c.6691G>C	p.Glu2231Gln	p.E2231Q	ENST00000375759	NM_015001.2	2231	Gaa/Caa	11/15	1	2	FACETS	0.943	0.808	1	0.943	0.808	1	CLONAL	1	TRUE	1	0.24	2		544	486	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259555	16259555	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	50	487	0	ENST00000375759.3:c.6820G>T	p.Glu2274Ter	p.E2274*	ENST00000375759	NM_015001.2	2274	Gaa/Taa	11/15	1	2	FACETS	0.904	0.768	1	0.904	0.768	1	CLONAL	1	TRUE	1	0.24	2		487	461	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51504520	51504520	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	38	293	0	ENST00000260433.2:c.1260G>C	p.Lys420Asn	p.K420N	ENST00000260433		420	aaG/aaC	9/10	1	2	FACETS	0.993	0.823	1	0.993	0.823	1	CLONAL	1	TRUE	1	0.24	2		293	319	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831551	72831551	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	51	497	0	ENST00000268489.5:c.5030C>G	p.Ser1677Cys	p.S1677C	ENST00000268489	NM_006885.3	1677	tCt/tGt	9/10	1	2	FACETS	0.966	0.822	1	0.966	0.822	1	CLONAL	1	TRUE	1	0.24	2		497	440	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6227001	6227001	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	103	468	0	ENST00000252674.7:c.533C>G	p.Ser178Cys	p.S178C	ENST00000252674	NM_005934.3	178	tCc/tGc	5/12	0.191908977397165	3	FACETS	0.995	0.895	1	0.995	0.895	1	CLONAL	2	TRUE	1	0.24	3		468	483	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754650	41754650	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	60	545	0	ENST00000301178.4:c.1636G>C	p.Glu546Gln	p.E546Q	ENST00000301178	NM_021913.4	546	Gag/Cag	14/20	0.191908977397165	3	FACETS	1	0.897	1	0.524	0.452	0.603	CLONAL	1	TRUE	1	0.24	3		545	534	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324606	62324606	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	37	497	0	ENST00000360203.5:c.2962C>T	p.Gln988Ter	p.Q988*	ENST00000360203	NM_001283009.1	988	Cag/Tag	30/35	1	2	FACETS	0.824	0.681	0.985	0.824	0.681	0.985	CLONAL	1	TRUE	1	0.24	2		497	374	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72873606	72873606	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	37	99	0	ENST00000325599.8:c.696G>C	p.Lys232Asn	p.K232N	ENST00000325599	NM_018130.2	232	aaG/aaC	6/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.24	2		99	208	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890269	72890269	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1009568174	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	38	277	0	ENST00000325599.8:c.413C>G	p.Ser138Ter	p.S138*	ENST00000325599	NM_018130.2	138	tCa/tGa	4/11	1	2	FACETS	0.808	0.669	0.963	0.808	0.669	0.963	CLONAL	1	TRUE	1	0.24	2		277	392	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839699	27839699	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	60	542	0	ENST00000328488.2:c.395G>C	p.Arg132Pro	p.R132P	ENST00000328488	NM_003533.2	132	cGa/cCa	1/1	1	2	FACETS	0.899	0.775	1	0.899	0.775	1	CLONAL	1	TRUE	1	0.24	2		542	556	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405603	139405603	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	52	394	0	ENST00000277541.6:c.2587+1G>A		p.X863_splice	ENST00000277541	NM_017617.3	863			1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.24	2		394	377	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814297	76814297	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	17	49	0	ENST00000373344.5:c.6347C>G	p.Ser2116Cys	p.S2116C	ENST00000373344	NM_000489.3	2116	tCt/tGt	29/35	1	2	FACETS	0.944	0.71	1	0.944	0.71	1	CLONAL	1	TRUE	1	0.24	2		49	150	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849203	76849203	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	38	151	0	ENST00000373344.5:c.6073G>C	p.Glu2025Gln	p.E2025Q	ENST00000373344	NM_000489.3	2025	Gaa/Caa	26/35	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.24	2		151	249	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933468	36933468	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1469371601	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	64	624	1	ENST00000361632.4:c.1819G>A	p.Gly607Arg	p.G607R	ENST00000361632		607	Ggg/Agg	13/16	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.24	2		625	532	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446099	49446099	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	63	729	0	ENST00000301067.7:c.1367C>G	p.Ser456Ter	p.S456*	ENST00000301067	NM_003482.3	456	tCa/tGa	10/54	1	2	FACETS	0.872	0.754	1	0.872	0.754	1	CLONAL	1	TRUE	1	0.24	2		729	602	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007897	45007897	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	20	276	0	ENST00000558401.1:c.344G>C	p.Trp115Ser	p.W115S	ENST00000558401	NM_004048.2	115	tGg/tCg	2/4	1	2	FACETS	0.43	0.328	0.549	0.43	0.328	0.549	SUBCLONAL	1	TRUE	1	0.24	2		276	388	SUCCESS
B2M	567	MSKCC	GRCh37	15	45008526	45008526	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	27	131	0	ENST00000558401.1:c.347-1G>C		p.X116_splice	ENST00000558401	NM_004048.2	116			1	2	FACETS	0.872	0.696	1	0.872	0.696	1	CLONAL	1	TRUE	1	0.24	2		131	258	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849526	68849526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	49	463	0	ENST00000261769.5:c.1429G>A	p.Val477Met	p.V477M	ENST00000261769	NM_004360.3	477	Gtg/Atg	10/16	1	2	FACETS	0.768	0.65	0.897	0.768	0.65	0.897	SUBCLONAL	1	TRUE	1	0.24	2		463	532	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690388	33690388	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	23	425	0	ENST00000308377.4:c.439G>C	p.Glu147Gln	p.E147Q	ENST00000308377	NM_152270.3	147	Gag/Cag	2/5	1	2	FACETS	0.44	0.342	0.553	0.44	0.342	0.553	SUBCLONAL	1	TRUE	1	0.24	2		425	436	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593429	48593429	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	31	307	0	ENST00000342988.3:c.1180G>A	p.Glu394Lys	p.E394K	ENST00000342988	NM_005359.5	394	Gaa/Aaa	10/12	1	2	FACETS	0.546	0.441	0.665	0.546	0.441	0.665	SUBCLONAL	1	TRUE	1	0.24	2		307	473	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207114	1207114	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	39	545	0	ENST00000326873.7:c.202G>T	p.Asp68Tyr	p.D68Y	ENST00000326873	NM_000455.4	68	Gac/Tac	1/10	0.191908977397165	3	FACETS	0.692	0.573	0.825	0.346	0.286	0.413	SUBCLONAL	1	TRUE	1	0.24	3		545	526	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278099	18278099	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	27	464	0	ENST00000222254.8:c.1719C>G	p.Ile573Met	p.I573M	ENST00000222254	NM_005027.3	573	atC/atG	13/16	0.191908977397165	3	FACETS	0.575	0.457	0.711	0.288	0.228	0.356	SUBCLONAL	1	TRUE	1	0.24	3		464	438	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422413	47422413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	33	385	0	ENST00000404338.3:c.481C>T	p.Leu161Phe	p.L161F	ENST00000404338	NM_004491.4	161	Ctt/Ttt	1/6	0.191908977397165	3	FACETS	0.662	0.539	0.802	0.331	0.269	0.401	SUBCLONAL	1	TRUE	1	0.24	3		385	465	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076936	41076936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1031395862	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	25	319	0	ENST00000373198.4:c.1484G>A	p.Gly495Glu	p.G495E	ENST00000373198	NM_133170.3	495	gGg/gAg	9/32	1	2	FACETS	0.763	0.603	0.946	0.763	0.603	0.946	CLONAL	1	TRUE	1	0.24	2		319	273	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592173	55592173	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	17	245	0	ENST00000288135.5:c.1497G>C	p.Lys499Asn	p.K499N	ENST00000288135	NM_000222.2	499	aaG/aaC	9/21	1	2	FACETS	0.519	0.387	0.675	0.519	0.387	0.675	SUBCLONAL	1	TRUE	1	0.24	2		245	273	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821456	32821456	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	35	505	0	ENST00000354258.4:c.138G>C	p.Glu46Asp	p.E46D	ENST00000354258	NM_000593.5	46	gaG/gaC	1/11	1	2	FACETS	0.583	0.477	0.702	0.583	0.477	0.702	SUBCLONAL	1	TRUE	1	0.24	2		505	500	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120760	94120760	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	23	359	0	ENST00000369303.4:c.291G>C	p.Arg97Ser	p.R97S	ENST00000369303	NM_004440.3	97	agG/agC	3/17	1	2	FACETS	0.519	0.405	0.653	0.519	0.405	0.653	SUBCLONAL	1	TRUE	1	0.24	2		359	369	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510866	157511225	+	splice_donor_variant,splice_acceptor_variant,frameshift_variant,stop_lost,intron_variant	Splice_Site	DEL	CCCCAGCCTCCACCCCTCACGGCCAGATGACTCCAATGCAAGGTGGAAGGTATGTTCAAATAACTCTGTGAGGCATACAAAGTCACATTTGTTCATCTTTTAGTTTTCTGGGGCAAACTTCACAGAGAGAAGAAATGGTATTCCCTAGAGAGTTTTTAAATGTTGATGACTGCCAGTTTTCTTCATGTCATTTATCTTGAATGGTTTTTGCATTTGCACATTTCAAGATGGGTTCATCTTCTGAATGTACTGTTTGGAGGTAACTCCTGCTGTATCATTAAGCTTTCATTCTTTGCCTCTCTTCAGAAGCAGTACAATCAGTGTGCACGACCCATTCTCAGATGTGAGTGATTCATCCTT	CCCCAGCCTCCACCCCTCACGGCCAGATGACTCCAATGCAAGGTGGAAGGTATGTTCAAATAACTCTGTGAGGCATACAAAGTCACATTTGTTCATCTTTTAGTTTTCTGGGGCAAACTTCACAGAGAGAAGAAATGGTATTCCCTAGAGAGTTTTTAAATGTTGATGACTGCCAGTTTTCTTCATGTCATTTATCTTGAATGGTTTTTGCATTTGCACATTTCAAGATGGGTTCATCTTCTGAATGTACTGTTTGGAGGTAACTCCTGCTGTATCATTAAGCTTTCATTCTTTGCCTCTCTTCAGAAGCAGTACAATCAGTGTGCACGACCCATTCTCAGATGTGAGTGATTCATCCTT	-	novel	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	61	471	0	ENST00000346085.5:c.3644_3746del		p.X1215_splice	ENST00000346085	NM_020732.3	1215	aCCCCAGCCTCCACCCCTCACGGCCAGATGACTCCAATGCAAGGTGGAAGGTATGTTCAAATAACTCTGTGAGGCATACAAAGTCACATTTGTTCATCTTTTAGTTTTCTGGGGCAAACTTCACAGAGAGAAGAAATGGTATTCCCTAGAGAGTTTTTAAATGTTGATGACTGCCAGTTTTCTTCATGTCATTTATCTTGAATGGTTTTTGCATTTGCACATTTCAAGATGGGTTCATCTTCTGAATGTACTGTTTGGAGGTAACTCCTGCTGTATCATTAAGCTTTCATTCTTTGCCTCTCTTCAGAAGCAGTACAATCAGTGTGCACGACCCATTCTCAGATGTGAGTGATTCATCCTTc/ac	14-15/20	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.24	2		471	468	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528797	157528797	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs527775865	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	53	459	0	ENST00000346085.5:c.6522G>C	p.Gln2174His	p.Q2174H	ENST00000346085	NM_020732.3	2174	caG/caC	20/20	1	2	FACETS	0.885	0.755	1	0.885	0.755	1	CLONAL	1	TRUE	1	0.24	2		459	499	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97897761	97897761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881715	NA	P-0059931-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	21	337	0	ENST00000289081.3:c.710C>T	p.Ser237Leu	p.S237L	ENST00000289081	NM_000136.2	237	tCa/tTa	8/15	1	2	FACETS	0.522	0.402	0.663	0.522	0.402	0.663	SUBCLONAL	1	TRUE	1	0.24	2		337	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0059938-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	151	399	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	1	2	FACETS	0.947	0.876	1	0.947	0.876	1	CLONAL	1	TRUE	1	0.830545023040617	2		399	384	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94923092	94923093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0059938-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	91	384	0	ENST00000536441.1:c.375_376insTT	p.Asn126LeufsTer9	p.N126Lfs*9	ENST00000536441	NM_144665.3	125	-/TT	4/10	1	2	FACETS	0.849	0.766	0.935	0.849	0.766	0.935	CLONAL	1	TRUE	1	0.830545023040617	2		384	258	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579518	7579518	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059938-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	218	544	0	ENST00000269305.4:c.169G>C	p.Asp57His	p.D57H	ENST00000269305	NM_001126112.2	57	Gac/Cac	4/11	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.830545023040617	2		544	523	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55974025	55974026	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0059938-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	205	410	0	ENST00000263923.4:c.1290_1291del	p.Pro431CysfsTer52	p.P431Cfs*52	ENST00000263923	NM_002253.2	430	tcTCct/tcct	10/30	1	2	FACETS	0.957	0.896	1	0.957	0.896	1	CLONAL	1	TRUE	1	0.830545023040617	2		410	516	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032546	47032546	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059938-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	214	211	0	ENST00000377604.3:c.452C>A	p.Ser151Ter	p.S151*	ENST00000377604	NM_001204468.1	151	tCg/tAg	5/24	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.830545023040617	1		211	251	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141687	202141687	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs777561102	NA	P-0059938-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	45	459	0	ENST00000358485.4:c.975T>A	p.Asp325Glu	p.D325E	ENST00000358485	NM_001080125.1	325	gaT/gaA	7/9	0.830545023040617	1	FACETS	0.305	0.259	0.354	0.305	0.259	0.354	SUBCLONAL	1	TRUE	0	0.830545023040617	1		459	208	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0059938-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	206	399	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	1	2	FACETS	0.979	0.916	1	0.979	0.916	1	CLONAL	1	TRUE	1	0.793969995795952	2		399	530	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94923092	94923093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0059938-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	174	384	0	ENST00000536441.1:c.375_376insTT	p.Asn126LeufsTer9	p.N126Lfs*9	ENST00000536441	NM_144665.3	125	-/TT	4/10	1	2	FACETS	0.937	0.87	1	0.937	0.87	1	CLONAL	1	TRUE	1	0.793969995795952	2		384	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579518	7579518	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059938-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	298	544	0	ENST00000269305.4:c.169G>C	p.Asp57His	p.D57H	ENST00000269305	NM_001126112.2	57	Gac/Cac	4/11	1	2	FACETS	0.98	0.928	1	0.98	0.928	1	CLONAL	1	TRUE	1	0.793969995795952	2		544	766	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55974025	55974026	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0059938-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	220	410	0	ENST00000263923.4:c.1290_1291del	p.Pro431CysfsTer52	p.P431Cfs*52	ENST00000263923	NM_002253.2	430	tcTCct/tcct	10/30	1	2	FACETS	0.907	0.849	0.966	0.907	0.849	0.966	CLONAL	1	TRUE	1	0.793969995795952	2		410	611	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032546	47032546	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059938-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	276	211	0	ENST00000377604.3:c.452C>A	p.Ser151Ter	p.S151*	ENST00000377604	NM_001204468.1	151	tCg/tAg	5/24	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.793969995795952	1		211	346	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141687	202141687	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs777561102	NA	P-0059938-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	65	459	0	ENST00000358485.4:c.975T>A	p.Asp325Glu	p.D325E	ENST00000358485	NM_001080125.1	325	gaT/gaA	7/9	0.793969995795952	1	FACETS	0.258	0.224	0.294	0.258	0.224	0.294	SUBCLONAL	1	TRUE	0	0.793969995795952	1		459	383	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	37	475	0				ENST00000310581	NM_198253.2	-/1132			0.22412525317547	2	FACETS	0.79	0.658	0.934	0.79	0.658	0.934	CLONAL	2	TRUE	0	0.235370493391696	2		475	199	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	43	497	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.0986787710614392	4	FACETS	1	0.94	1	0.638	0.535	0.75	INDETERMINATE	1	TRUE	2	0.235370493391696	4		497	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577064	7577064	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	113	514	0	ENST00000269305.4:c.874A>T	p.Lys292Ter	p.K292*	ENST00000269305	NM_001126112.2	292	Aaa/Taa	8/11	1	2	FACETS	0.97	0.877	1	1	0.988	1	CLONAL	2	TRUE	1	0.235370493391696	2		514	495	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498004	29498004	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1208550472	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	54	485	0	ENST00000389048.3:c.2002G>A	p.Glu668Lys	p.E668K	ENST00000389048	NM_004304.4	668	Gaa/Aaa	11/29	0.0986787710614392	4	FACETS	1	0.908	1	0.543	0.464	0.63	INDETERMINATE	1	TRUE	2	0.235370493391696	4		485	522	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892266	9892266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868291959	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	52	492	0	ENST00000330684.3:c.2224G>A	p.Asp742Asn	p.D742N	ENST00000330684	NM_001134407.1	742	Gat/Aat	11/13	0.223302711279621	3	FACETS	1	0.877	1	0.517	0.44	0.6	CLONAL	1	TRUE	1	0.235370493391696	3		492	478	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78933971	78933971	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771723844	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	46	529	0	ENST00000306801.3:c.3571C>T	p.Arg1191Cys	p.R1191C	ENST00000306801	NM_020761.2	1191	Cgc/Tgc	30/34	0.0986787710614392	4	FACETS	0.911	0.767	1	0.456	0.383	0.535	INDETERMINATE	1	TRUE	2	0.235370493391696	4		529	530	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636727	8636727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159852	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	42	429	0	ENST00000356435.5:c.182G>A	p.Gly61Glu	p.G61E	ENST00000356435		61	gGa/gAa	2/35	0.235370493391696	1	FACETS	0.91	0.762	1	0.91	0.762	1	CLONAL	1	TRUE	0	0.235370493391696	1		429	346	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546826	9546826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	38	578	0	ENST00000353224.5:c.1196C>T	p.Ser399Phe	p.S399F	ENST00000353224	NM_177990.2	399	tCc/tTc	5/10	0.0986787710614392	4	FACETS	0.788	0.651	0.942	0.394	0.325	0.471	INDETERMINATE	1	TRUE	2	0.235370493391696	4		578	506	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306568	41306568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	33	459	0	ENST00000373198.4:c.1091G>A	p.Arg364Gln	p.R364Q	ENST00000373198	NM_133170.3	364	cGa/cAa	7/32	0.0986787710614392	4	FACETS	1	0.848	1	0.522	0.426	0.629	INDETERMINATE	1	TRUE	2	0.235370493391696	4		459	332	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942171	81942171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	51	460	0	ENST00000359376.3:c.1708C>T	p.Pro570Ser	p.P570S	ENST00000359376	NM_002661.3	570	Ccc/Tcc	17/33	0.223302711279621	3	FACETS	1	0.929	1	0.578	0.492	0.672	CLONAL	1	TRUE	1	0.235370493391696	3		460	419	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670282	134670282	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748807854	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	26	485	0	ENST00000398015.3:c.193G>A	p.Glu65Lys	p.E65K	ENST00000398015	NM_004441.4	65	Gag/Aag	3/16	0.223302711279621	3	FACETS	0.581	0.46	0.721	0.291	0.23	0.361	SUBCLONAL	1	TRUE	1	0.235370493391696	3		485	425	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971187	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	44	529	0	ENST00000304494.5:c.171_172delinsTT	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	57	gcCCga/gcTTga	2/3	0.235370493391696	1	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	0	0.235370493391696	1		529	320	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81954866	81954866	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	35	432	0	ENST00000359376.3:c.2299C>T	p.Pro767Ser	p.P767S	ENST00000359376	NM_002661.3	767	Ccg/Tcg	21/33	0.223302711279621	3	FACETS	0.815	0.668	0.979	0.407	0.334	0.49	CLONAL	1	TRUE	1	0.235370493391696	3		432	408	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942739	44942739	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760394554	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	40	186	0	ENST00000377967.4:c.3319C>T	p.Pro1107Ser	p.P1107S	ENST00000377967	NM_021140.2	1107	Cct/Tct	23/29	0.181660089788533	2	FACETS	0.924	0.777	1			1	CLONAL	2	TRUE	NA	0.235370493391696	2		186	184	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858202	9858202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	103	604	2	ENST00000330684.3:c.3199C>T	p.Arg1067Trp	p.R1067W	ENST00000330684	NM_001134407.1	1067	Cgg/Tgg	13/13	0.223302711279621	3	FACETS	0.952	0.855	1	0.952	0.855	1	CLONAL	2	TRUE	1	0.235370493391696	3		606	514	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867256	45867256	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780129241	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	48	504	0	ENST00000391945.4:c.937G>A	p.Glu313Lys	p.E313K	ENST00000391945	NM_000400.3	313	Gaa/Aaa	10/23	0.115585481921423	5	FACETS	1	0.925	1	0.387	0.327	0.453	INDETERMINATE	1	TRUE	2	0.235370493391696	5		504	475	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793432	18793432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187869576	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	32	390	0	ENST00000266497.5:c.4129C>T	p.Arg1377Cys	p.R1377C	ENST00000266497		1377	Cgt/Tgt	30/31	0.223302711279621	3	FACETS	1	0.851	1	0.526	0.428	0.635	CLONAL	1	TRUE	1	0.235370493391696	3		390	289	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672972	30672972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	60	690	0	ENST00000376406.3:c.3988C>T	p.Pro1330Ser	p.P1330S	ENST00000376406	NM_014641.2	1330	Cct/Tct	10/15	0.0986787710614392	4	FACETS	0.805	0.693	0.929	0.403	0.346	0.465	INDETERMINATE	1	TRUE	2	0.235370493391696	4		690	782	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857878	9857878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867464241	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	98	597	0	ENST00000330684.3:c.3523G>A	p.Glu1175Lys	p.E1175K	ENST00000330684	NM_001134407.1	1175	Gaa/Aaa	13/13	0.223302711279621	3	FACETS	0.948	0.849	1	0.948	0.849	1	CLONAL	2	TRUE	1	0.235370493391696	3		597	491	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346880	89346880	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1272359896	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	47	492	0	ENST00000301030.4:c.6070C>T	p.Pro2024Ser	p.P2024S	ENST00000301030	NM_001256183.1	2024	Ccg/Tcg	9/13	0.223302711279621	3	FACETS	0.996	0.842	1	0.498	0.421	0.583	CLONAL	1	TRUE	1	0.235370493391696	3		492	448	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790000	40790000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159843	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	30	454	0	ENST00000373198.4:c.2731G>A	p.Glu911Lys	p.E911K	ENST00000373198	NM_133170.3	911	Gaa/Aaa	18/32	0.0986787710614392	4	FACETS	0.722	0.582	0.882	0.361	0.291	0.441	INDETERMINATE	1	TRUE	2	0.235370493391696	4		454	436	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923328	9923328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	45	422	0	ENST00000330684.3:c.1959G>A	p.Met653Ile	p.M653I	ENST00000330684	NM_001134407.1	653	atG/atA	9/13	0.223302711279621	3	FACETS	1	0.914	1	0.565	0.476	0.663	CLONAL	1	TRUE	1	0.235370493391696	3		422	378	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790003	40790003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	64	454	0	ENST00000373198.4:c.2728G>A	p.Glu910Lys	p.E910K	ENST00000373198	NM_133170.3	910	Gag/Aag	18/32	0.0986787710614392	4	FACETS	0.774	0.672	0.884	0.774	0.672	0.884	INDETERMINATE	2	TRUE	2	0.235370493391696	4		454	434	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236616	236616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1296066077	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	21	284	0	ENST00000264932.6:c.1334C>T	p.Ser445Leu	p.S445L	ENST00000264932	NM_004168.2	445	tCg/tTg	10/15	0.22412525317547	2	FACETS	0.747	0.576	0.944	0.373	0.288	0.472	CLONAL	1	TRUE	0	0.235370493391696	2		284	239	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458899	120458899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	98	544	0	ENST00000256646.2:c.6446C>T	p.Ser2149Phe	p.S2149F	ENST00000256646	NM_024408.3	2149	tCc/tTc	34/34	0.0986787710614392	4	FACETS	0.982	0.879	1	0.982	0.879	1	INDETERMINATE	2	TRUE	2	0.235370493391696	4		544	524	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350616	15350616	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1305915305	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	43	486	0	ENST00000263377.2:c.3299C>T	p.Ser1100Phe	p.S1100F	ENST00000263377	NM_058243.2	1100	tCc/tTc	16/20	0.0986787710614392	4	FACETS	1	0.866	1	0.519	0.434	0.612	INDETERMINATE	1	TRUE	2	0.235370493391696	4		486	435	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068102	94068102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	26	399	0	ENST00000369303.4:c.860C>T	p.Ser287Phe	p.S287F	ENST00000369303	NM_004440.3	287	tCc/tTc	4/17	0.0986787710614392	4	FACETS	0.793	0.629	0.982	0.397	0.314	0.491	INDETERMINATE	1	TRUE	2	0.235370493391696	4		399	344	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980726	40980726	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	42	485	0	ENST00000373198.4:c.1760C>T	p.Ser587Leu	p.S587L	ENST00000373198	NM_133170.3	587	tCa/tTa	10/32	0.0986787710614392	4	FACETS	0.928	0.775	1	0.464	0.387	0.549	INDETERMINATE	1	TRUE	2	0.235370493391696	4		485	475	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609791	81609791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	58	615	0	ENST00000298171.2:c.1389G>A	p.Met463Ile	p.M463I	ENST00000298171	NM_000369.2	463	atG/atA	10/10	1	2	FACETS	0.932	0.801	1	0.932	0.801	1	CLONAL	1	TRUE	1	0.235370493391696	2		615	529	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217913	2217913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770910000	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	39	487	0	ENST00000398665.3:c.2687G>A	p.Arg896Lys	p.R896K	ENST00000398665	NM_032482.2	896	aGg/aAg	22/28	0.0799100803295905	4	FACETS	0.832	0.689	0.991	0.416	0.344	0.496	INDETERMINATE	1	TRUE	2	0.235370493391696	4		487	492	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342713	118342713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	22	531	0	ENST00000534358.1:c.839C>T	p.Pro280Leu	p.P280L	ENST00000534358	NM_005933.3	280	cCt/cTt	3/36	0.158733754984001	3	FACETS	0.657	0.509	0.829	0.329	0.254	0.415	SUBCLONAL	1	TRUE	1	0.235370493391696	3		531	318	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012402	29012402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	77	457	0	ENST00000282397.4:c.469C>T	p.Pro157Ser	p.P157S	ENST00000282397	NM_002019.4	157	Ccc/Tcc	4/30	1	2	FACETS	0.808	0.713	0.909	1	0.979	1	CLONAL	2	TRUE	1	0.235370493391696	2		457	405	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450372	50450372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	50	612	0	ENST00000331340.3:c.556G>A	p.Asp186Asn	p.D186N	ENST00000331340	NM_006060.4	186	Gac/Aac	5/8	0.0986787710614392	4	FACETS	1	0.867	1	0.512	0.434	0.597	INDETERMINATE	1	TRUE	2	0.235370493391696	4		612	513	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639890	93639890	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	32	433	0	ENST00000375746.1:c.1219G>A	p.Glu407Lys	p.E407K	ENST00000375746	NM_001174167.1	407	Gag/Aag	10/14	0.147911535331023	3	FACETS	0.918	0.747	1	0.459	0.373	0.556	CLONAL	1	TRUE	1	0.235370493391696	3		433	331	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89818581	89818581	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142377616	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	50	482	0	ENST00000389301.3:c.3031C>T	p.Arg1011Cys	p.R1011C	ENST00000389301	NM_000135.2	1011	Cgc/Tgc	31/43	0.223302711279621	3	FACETS	0.998	0.847	1	0.499	0.423	0.582	CLONAL	1	TRUE	1	0.235370493391696	3		482	476	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522299	157522299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867707366	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	49	582	0	ENST00000346085.5:c.4571C>T	p.Ser1524Leu	p.S1524L	ENST00000346085	NM_020732.3	1524	tCg/tTg	18/20	0.22412525317547	2	FACETS	0.955	0.81	1	0.477	0.405	0.557	CLONAL	1	TRUE	0	0.235370493391696	2		582	436	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139563	47139563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	42	392	0	ENST00000409792.3:c.5024C>T	p.Ala1675Val	p.A1675V	ENST00000409792	NM_014159.6	1675	gCc/gTc	9/21	0.223302711279621	3	FACETS	1	0.883	1	0.535	0.447	0.631	CLONAL	1	TRUE	1	0.235370493391696	3		392	373	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11308061	11308061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200901835	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	52	541	0	ENST00000361445.4:c.931C>T	p.Arg311Cys	p.R311C	ENST00000361445	NM_004958.3	311	Cgt/Tgt	7/58	0.0986787710614392	4	FACETS	0.971	0.827	1	0.486	0.413	0.565	INDETERMINATE	1	TRUE	2	0.235370493391696	4		541	562	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88671957	88671957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs574695821	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	35	324	0	ENST00000360948.2:c.1213G>A	p.Asp405Asn	p.D405N	ENST00000360948	NM_001012338.2	405	Gat/Aat	10/19	0.22669752103346	3	FACETS	1	0.939	1	0.45	0.371	0.538	CLONAL	1	TRUE	0	0.235370493391696	3		324	246	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073599	8073599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	48	538	0	ENST00000377482.5:c.1060C>T	p.Pro354Ser	p.P354S	ENST00000377482	NM_018948.3	354	Cct/Tct	4/4	0.0986787710614392	4	FACETS	0.969	0.819	1	0.484	0.409	0.567	INDETERMINATE	1	TRUE	2	0.235370493391696	4		538	520	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11168247	11168247	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	40	418	0	ENST00000361445.4:c.7625A>T	p.Tyr2542Phe	p.Y2542F	ENST00000361445	NM_004958.3	2542	tAt/tTt	57/58	0.0986787710614392	4	FACETS	1	0.888	1	0.544	0.453	0.645	INDETERMINATE	1	TRUE	2	0.235370493391696	4		418	386	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023483	27023483	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	27	408	0	ENST00000324856.7:c.589G>C	p.Gly197Arg	p.G197R	ENST00000324856	NM_006015.4	197	Ggg/Cgg	1/20	0.0986787710614392	4	FACETS	0.794	0.632	0.979	0.397	0.316	0.49	INDETERMINATE	1	TRUE	2	0.235370493391696	4		408	357	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933681	36933681	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752378580	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	38	527	0	ENST00000361632.4:c.1718C>T	p.Ser573Phe	p.S573F	ENST00000361632		573	tCc/tTc	12/16	0.0986787710614392	4	FACETS	0.822	0.68	0.982	0.411	0.34	0.491	INDETERMINATE	1	TRUE	2	0.235370493391696	4		527	485	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344766	65344766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	59	516	0	ENST00000342505.4:c.271C>T	p.Pro91Ser	p.P91S	ENST00000342505	NM_002227.2	91	Cca/Tca	4/25	0.0986787710614392	4	FACETS	1	0.916	1	0.545	0.469	0.628	INDETERMINATE	1	TRUE	2	0.235370493391696	4		516	568	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003967	57003967	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	C	C	T	rs761532425	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	34	570	0	ENST00000257254.3:c.512G>A	p.Gly171Glu	p.G171E	ENST00000257254		171	gGg/gAg	1/2	0.158733754984001	3	FACETS	0.749	0.612	0.903	0.375	0.306	0.452	CLONAL	1	TRUE	1	0.235370493391696	3		570	431	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94209566	94209566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	13	259	0	ENST00000323929.3:c.548C>T	p.Ser183Phe	p.S183F	ENST00000323929	NM_005591.3	183	tCc/tTc	7/20	0.158733754984001	3	FACETS	0.882	0.633	1	0.441	0.316	0.591	CLONAL	1	TRUE	1	0.235370493391696	3		259	140	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195656	102195656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	30	500	0	ENST00000263464.3:c.416C>T	p.Ser139Leu	p.S139L	ENST00000263464	NM_001165.4	139	tCa/tTa	2/9	0.158733754984001	3	FACETS	0.768	0.619	0.937	0.384	0.309	0.469	CLONAL	1	TRUE	1	0.235370493391696	3		500	371	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143477	108143477	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	44	385	0	ENST00000278616.4:c.3182T>C	p.Leu1061Pro	p.L1061P	ENST00000278616	NM_000051.3	1061	cTt/cCt	22/63	0.158733754984001	3	FACETS	0.897	0.759	1	0.897	0.759	1	CLONAL	2	TRUE	1	0.235370493391696	3		385	233	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170268	119170268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	30	585	0	ENST00000264033.4:c.2498C>T	p.Ser833Phe	p.S833F	ENST00000264033	NM_005188.3	833	tCt/tTt	16/16	0.158733754984001	3	FACETS	0.569	0.457	0.695	0.284	0.228	0.348	SUBCLONAL	1	TRUE	1	0.235370493391696	3		585	501	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442703	442703	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs867104192	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	66	547	0	ENST00000399788.2:c.1603C>T	p.Gln535Ter	p.Q535*	ENST00000399788	NM_001042603.1	535	Cag/Tag	12/28	0.223302711279621	3	FACETS	1	0.957	1	0.624	0.543	0.712	CLONAL	1	TRUE	1	0.235370493391696	3		547	502	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435018	18435018	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	24	318	0	ENST00000266497.5:c.3G>A	p.Met1?	p.M1?	ENST00000266497		1	atG/atA	1/31	0.223302711279621	3	FACETS	0.873	0.687	1	0.437	0.343	0.544	CLONAL	1	TRUE	1	0.235370493391696	3		318	261	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562502	21562503	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	27	314	0	ENST00000382592.4:c.1416_1417delinsTT	p.Pro473Ser	p.P473S	ENST00000382592	NM_014572.2	472	gcCCcc/gcTTcc	4/8	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.235370493391696	2		314	197	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623811	28623811	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	34	450	1	ENST00000241453.7:c.843del	p.Phe281LeufsTer7	p.F281Lfs*7	ENST00000241453	NM_004119.2	281	ttC/tt	7/24	1	2	FACETS	0.816	0.668	0.982	0.816	0.668	0.982	CLONAL	1	TRUE	1	0.235370493391696	2		451	354	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28963966	28963966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	43	480	0	ENST00000282397.4:c.1936G>A	p.Glu646Lys	p.E646K	ENST00000282397	NM_002019.4	646	Gaa/Aaa	13/30	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.235370493391696	2		480	339	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912573	32912573	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587780652	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	28	414	0	ENST00000380152.3:c.4081C>T	p.Gln1361Ter	p.Q1361*	ENST00000380152		1361	Cag/Tag	11/27	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.235370493391696	2		414	184	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134882	41134882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370153409	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	26	516	0	ENST00000379561.5:c.746C>T	p.Ser249Phe	p.S249F	ENST00000379561	NM_002015.3	249	tCt/tTt	2/3	1	2	FACETS	0.525	0.415	0.651	0.525	0.415	0.651	SUBCLONAL	1	TRUE	1	0.235370493391696	2		516	421	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95599679	95599679	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	36	341	0	ENST00000393063.1:c.117T>G	p.Asp39Glu	p.D39E	ENST00000393063	NM_030621.3	39	gaT/gaG	3/28	1	2	FACETS	0.968	0.798	1	0.968	0.798	1	CLONAL	1	TRUE	1	0.235370493391696	2		341	316	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576190	88576190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112443158	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	52	563	0	ENST00000360948.2:c.1483G>A	p.Asp495Asn	p.D495N	ENST00000360948	NM_001012338.2	495	Gat/Aat	13/19	0.22669752103346	3	FACETS	0.984	0.838	1	0.328	0.279	0.381	CLONAL	1	TRUE	0	0.235370493391696	3		563	502	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2218146	2218147	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	43	547	2	ENST00000326181.6:c.208_209delinsTT	p.Pro70Leu	p.P70L	ENST00000326181	NM_032271.2	70	CCg/TTg	4/21	0.235370493391696	1	FACETS	0.829	0.695	0.976	0.829	0.695	0.976	CLONAL	1	TRUE	0	0.235370493391696	1		549	389	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900384	3900384	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs146887252	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	65	521	0	ENST00000262367.5:c.712G>T	p.Val238Leu	p.V238L	ENST00000262367	NM_004380.2	238	Gtg/Ttg	2/31	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.235370493391696	NA		521	399	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857323	9857323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	36	525	0	ENST00000330684.3:c.4078G>A	p.Asp1360Asn	p.D1360N	ENST00000330684	NM_001134407.1	1360	Gac/Aac	13/13	0.223302711279621	3	FACETS	0.806	0.663	0.967	0.403	0.331	0.484	CLONAL	1	TRUE	1	0.235370493391696	3		525	424	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679772	33679772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	95	588	0	ENST00000308377.4:c.2309C>T	p.Ser770Phe	p.S770F	ENST00000308377	NM_152270.3	770	tCc/tTc	5/5	0.0986787710614392	4	FACETS	1	0.91	1	1	0.91	1	INDETERMINATE	2	TRUE	2	0.235370493391696	4		588	489	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679788	33679788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150521243	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	40	581	0	ENST00000308377.4:c.2293C>T	p.Pro765Ser	p.P765S	ENST00000308377	NM_152270.3	765	Cct/Tct	5/5	0.0986787710614392	4	FACETS	0.862	0.716	1	0.431	0.358	0.513	INDETERMINATE	1	TRUE	2	0.235370493391696	4		581	487	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690082	33690082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	25	503	0	ENST00000308377.4:c.745G>A	p.Gly249Arg	p.G249R	ENST00000308377	NM_152270.3	249	Gga/Aga	2/5	0.0986787710614392	4	FACETS	0.678	0.534	0.844	0.339	0.267	0.422	INDETERMINATE	1	TRUE	2	0.235370493391696	4		503	387	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690822	33690822	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	29	455	0	ENST00000308377.4:c.5A>T	p.Glu2Val	p.E2V	ENST00000308377	NM_152270.3	2	gAg/gTg	2/5	0.0986787710614392	4	FACETS	0.66	0.529	0.81	0.33	0.264	0.405	INDETERMINATE	1	TRUE	2	0.235370493391696	4		455	461	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256183	41256183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357457	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	62	409	0	ENST00000357654.3:c.397C>T	p.Arg133Cys	p.R133C	ENST00000357654	NM_007294.3	133	Cgt/Tgt	6/23	0.0986787710614392	4	FACETS	1	0.899	1	1	0.899	1	INDETERMINATE	2	TRUE	2	0.235370493391696	4		409	313	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47700154	47700154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	49	444	0	ENST00000347630.2:c.19C>T	p.Pro7Ser	p.P7S	ENST00000347630	NM_001007230.1	7	Cct/Tct	3/11	0.0986787710614392	4	FACETS	1	0.853	1	0.503	0.426	0.588	INDETERMINATE	1	TRUE	2	0.235370493391696	4		444	511	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211969	36211969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773918376	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	50	555	0	ENST00000222270.7:c.1720C>T	p.Pro574Ser	p.P574S	ENST00000222270	NM_014727.1	574	Ccc/Tcc	3/37	0.115585481921423	5	FACETS	0.986	0.836	1	0.329	0.278	0.384	INDETERMINATE	1	TRUE	2	0.235370493391696	5		555	583	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213569	36213569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	54	596	0	ENST00000222270.7:c.2671C>T	p.Pro891Ser	p.P891S	ENST00000222270	NM_014727.1	891	Cct/Tct	5/37	0.115585481921423	5	FACETS	1	0.878	1	0.344	0.293	0.399	INDETERMINATE	1	TRUE	2	0.235370493391696	5		596	602	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36217176	36217176	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	54	401	0	ENST00000222270.7:c.3925A>G	p.Thr1309Ala	p.T1309A	ENST00000222270	NM_014727.1	1309	Act/Gct	14/37	0.115585481921423	5	FACETS	1	0.956	1	0.444	0.38	0.514	INDETERMINATE	1	TRUE	2	0.235370493391696	5		401	466	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42381382	42381383	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	44	515	0	ENST00000221972.3:c.8_9delinsAA	p.Gly3Glu	p.G3E	ENST00000221972	NM_021601.3	3	gGG/gAA	1/5	0.115585481921423	5	FACETS	0.994	0.833	1	0.331	0.277	0.391	INDETERMINATE	1	TRUE	2	0.235370493391696	5		515	509	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609632	46609632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	59	554	0	ENST00000263734.3:c.2356C>T	p.Pro786Ser	p.P786S	ENST00000263734	NM_001430.4	786	Cca/Tca	15/16	0.0986787710614392	4	FACETS	1	0.921	1	0.552	0.475	0.636	INDETERMINATE	1	TRUE	2	0.235370493391696	4		554	561	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630652	67630652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1451862986	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	27	435	0	ENST00000272342.5:c.838G>A	p.Ala280Thr	p.A280T	ENST00000272342	NM_019002.3	280	Gca/Aca	5/6	0.0986787710614392	4	FACETS	0.849	0.676	1	0.424	0.338	0.523	INDETERMINATE	1	TRUE	2	0.235370493391696	4		435	334	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015262	128015263	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	42	466	0	ENST00000285398.2:c.2258_2259delinsTT	p.Ala753Val	p.A753V	ENST00000285398	NM_000122.1	753	gCC/gTT	15/15	0.0986787710614392	4	FACETS	0.875	0.73	1	0.437	0.365	0.518	INDETERMINATE	1	TRUE	2	0.235370493391696	4		466	504	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149795	202149795	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	102	509	0	ENST00000358485.4:c.1236A>T	p.Lys412Asn	p.K412N	ENST00000358485	NM_001080125.1	412	aaA/aaT	8/9	0.0986787710614392	4	FACETS	1	0.923	1	1	0.923	1	INDETERMINATE	2	TRUE	2	0.235370493391696	4		509	518	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732672	204732672	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	35	390	0	ENST00000302823.3:c.7T>C	p.Cys3Arg	p.C3R	ENST00000302823	NM_005214.4	3	Tgc/Cgc	1/4	0.0986787710614392	4	FACETS	0.824	0.675	0.991	0.412	0.337	0.496	INDETERMINATE	1	TRUE	2	0.235370493391696	4		390	446	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285322	212285322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	15	449	0	ENST00000342788.4:c.2979G>A	p.Met993Ile	p.M993I	ENST00000342788	NM_005235.2	993	atG/atA	25/28	0.0986787710614392	4	FACETS	0.635	0.464	0.84	0.317	0.232	0.42	INDETERMINATE	1	TRUE	2	0.235370493391696	4		449	248	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530124	212530124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	36	468	0	ENST00000342788.4:c.1795G>A	p.Gly599Arg	p.G599R	ENST00000342788	NM_005235.2	599	Ggg/Agg	15/28	0.0986787710614392	4	FACETS	0.838	0.689	1	0.419	0.344	0.503	INDETERMINATE	1	TRUE	2	0.235370493391696	4		468	451	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546919	9546919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868370722	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	70	578	0	ENST00000353224.5:c.1103C>T	p.Ser368Leu	p.S368L	ENST00000353224	NM_177990.2	368	tCa/tTa	5/10	0.0986787710614392	4	FACETS	0.772	0.675	0.876	0.772	0.675	0.876	INDETERMINATE	2	TRUE	2	0.235370493391696	4		578	476	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714396	40714396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	50	482	0	ENST00000373198.4:c.4001G>A	p.Arg1334Lys	p.R1334K	ENST00000373198	NM_133170.3	1334	aGa/aAa	29/32	0.0986787710614392	4	FACETS	1	0.89	1	0.53	0.45	0.618	INDETERMINATE	1	TRUE	2	0.235370493391696	4		482	495	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743921	40743921	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	45	485	0	ENST00000373198.4:c.3074A>C	p.Glu1025Ala	p.E1025A	ENST00000373198	NM_133170.3	1025	gAg/gCg	23/32	0.0986787710614392	4	FACETS	1	0.854	1	0.508	0.427	0.597	INDETERMINATE	1	TRUE	2	0.235370493391696	4		485	465	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264866	46264866	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	58	528	0	ENST00000371998.3:c.1736C>T	p.Pro579Leu	p.P579L	ENST00000371998		579	cCa/cTa	12/23	0.0986787710614392	4	FACETS	1	0.946	1	0.605	0.52	0.697	INDETERMINATE	1	TRUE	2	0.235370493391696	4		528	503	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163103	47163103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	21	399	0	ENST00000409792.3:c.3023C>T	p.Thr1008Ile	p.T1008I	ENST00000409792	NM_014159.6	1008	aCc/aTc	3/21	0.223302711279621	3	FACETS	0.75	0.578	0.949	0.375	0.289	0.475	CLONAL	1	TRUE	1	0.235370493391696	3		399	266	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205031	128205031	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	45	550	0	ENST00000341105.2:c.410C>T	p.Pro137Leu	p.P137L	ENST00000341105	NM_032638.4	137	cCa/cTa	3/6	0.223302711279621	3	FACETS	0.781	0.656	0.92	0.391	0.328	0.46	CLONAL	1	TRUE	1	0.235370493391696	3		550	547	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433735	149433735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	38	489	0	ENST00000286301.3:c.2816G>A	p.Ser939Asn	p.S939N	ENST00000286301	NM_005211.3	939	aGc/aAc	22/22	0.22412525317547	2	FACETS	0.856	0.709	1	0.428	0.354	0.51	CLONAL	1	TRUE	0	0.235370493391696	2		489	377	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519420	176519420	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750977138	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	46	570	0	ENST00000292408.4:c.826G>A	p.Asp276Asn	p.D276N	ENST00000292408	NM_213647.1	276	Gat/Aat	7/18	0.22412525317547	2	FACETS	0.865	0.729	1	0.432	0.364	0.507	CLONAL	1	TRUE	0	0.235370493391696	2		570	452	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225776	26225776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1186783518	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	50	600	0	ENST00000360408.1:c.394C>T	p.Arg132Cys	p.R132C	ENST00000360408	NM_003532.2	132	Cgt/Tgt	1/1	0.0986787710614392	4	FACETS	0.908	0.77	1	0.454	0.385	0.53	INDETERMINATE	1	TRUE	2	0.235370493391696	4		600	578	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679078	117679078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	16	388	0	ENST00000368508.3:c.3743G>A	p.Gly1248Glu	p.G1248E	ENST00000368508	NM_002944.2	1248	gGa/gAa	24/43	0.22412525317547	2	FACETS	0.647	0.48	0.847	0.324	0.24	0.424	SUBCLONAL	1	TRUE	0	0.235370493391696	2		388	210	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954940	2954940	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	66	633	1	ENST00000396946.4:c.2770G>A	p.Gly924Arg	p.G924R	ENST00000396946	NM_032415.4	924	Ggg/Agg	21/25	0.0986787710614392	4	FACETS	1	0.902	1	0.524	0.454	0.6	INDETERMINATE	1	TRUE	2	0.235370493391696	4		634	661	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214421	55214421	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	32	438	0	ENST00000275493.2:c.547C>T	p.His183Tyr	p.H183Y	ENST00000275493	NM_005228.3	183	Cac/Tac	4/28	0.0986787710614392	4	FACETS	0.657	0.533	0.799	0.329	0.266	0.4	INDETERMINATE	1	TRUE	2	0.235370493391696	4		438	511	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55272970	55272970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	70	441	0	ENST00000275493.2:c.3293C>T	p.Pro1098Leu	p.P1098L	ENST00000275493	NM_005228.3	1098	cCc/cTc	28/28	0.0986787710614392	4	FACETS	0.806	0.705	0.914	0.806	0.705	0.914	INDETERMINATE	2	TRUE	2	0.235370493391696	4		441	456	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520008	106520008	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	49	406	0	ENST00000359195.3:c.2436G>A	p.Trp812Ter	p.W812*	ENST00000359195	NM_002649.2	812	tgG/tgA	6/11	0.0986787710614392	4	FACETS	0.832	0.709	0.966	0.832	0.709	0.966	INDETERMINATE	2	TRUE	2	0.235370493391696	4		406	309	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965443	68965443	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	27	392	0	ENST00000288368.4:c.1055G>A	p.Trp352Ter	p.W352*	ENST00000288368	NM_024870.2	352	tGg/tAg	9/40	1	2	FACETS	0.879	0.702	1	0.879	0.702	1	CLONAL	1	TRUE	1	0.235370493391696	2		392	261	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046380	69046380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	30	490	2	ENST00000288368.4:c.3853G>A	p.Ala1285Thr	p.A1285T	ENST00000288368	NM_024870.2	1285	Gcc/Acc	32/40	1	2	FACETS	0.575	0.463	0.703	0.575	0.463	0.703	SUBCLONAL	1	TRUE	1	0.235370493391696	2		492	443	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595285	141595285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	32	425	0	ENST00000220592.5:c.148C>T	p.Pro50Ser	p.P50S	ENST00000220592	NM_012154.3	50	Ccc/Tcc	2/19	1	2	FACETS	0.779	0.633	0.943	0.779	0.633	0.943	CLONAL	1	TRUE	1	0.235370493391696	2		425	349	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069193	5069193	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759440902	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	14	389	0	ENST00000381652.3:c.1498C>T	p.Pro500Ser	p.P500S	ENST00000381652	NM_004972.3	500	Ccc/Tcc	11/25	0.235370493391696	1	FACETS	0.766	0.557	1	0.766	0.557	1	CLONAL	1	TRUE	0	0.235370493391696	1		389	137	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27190527	27190527	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	39	349	0	ENST00000380036.4:c.1328T>C	p.Val443Ala	p.V443A	ENST00000380036	NM_000459.3	443	gTt/gCt	10/23	0.235370493391696	1	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	0	0.235370493391696	1		349	284	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949064	44949065	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	65	159	0	ENST00000377967.4:c.3627dup	p.Phe1210ValfsTer41	p.F1210Vfs*41	ENST00000377967	NM_021140.2	1209	agg/aGgg	25/29	0.181660089788533	2	FACETS	0.864	0.761	0.972			1	CLONAL	3	TRUE	NA	0.235370493391696	2		159	213	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424716	47424716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	104	239	1	ENST00000377045.4:c.524C>T	p.Pro175Leu	p.P175L	ENST00000377045	NM_001654.4	175	cCc/cTc	6/16	0.181660089788533	2	FACETS	1	0.936	1			1	CLONAL	3	TRUE	NA	0.235370493391696	2		240	284	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344869	70344870	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0059958-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	35	265	0	ENST00000374080.3:c.2099_2100delinsTT	p.Ser700Phe	p.S700F	ENST00000374080		700	tCC/tTT	15/45	0.181660089788533	2	FACETS	1	0.909	1			1	CLONAL	1	TRUE	NA	0.235370493391696	2		265	254	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029453	16029454	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0059960-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	90	382	0	ENST00000268712.3:c.1576_1577del	p.Glu526LysfsTer9	p.E526Kfs*9	ENST00000268712	NM_006311.3	526	GAa/a	15/46	0.429686550466658	1	FACETS	0.966	0.865	1	0.966	0.865	1	CLONAL	1	TRUE	0	0.434295465494999	1		382	336	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175481	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0059962-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	51	634	0	ENST00000257430.4:c.4192_4193del	p.Arg1399PhefsTer9	p.R1399Ffs*9	ENST00000257430	NM_000038.5	1397	GAg/g	16/16	1	2	FACETS	0.918	0.781	1	0.918	0.781	1	CLONAL	1	TRUE	1	0.23	2		634	483	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710652	114710652	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059962-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	70	597	0	ENST00000543371.1:c.137C>A	p.Ser46Ter	p.S46*	ENST00000543371	NM_001198531.1	46	tCg/tAg	1/14	1	2	FACETS	0.995	0.867	1	0.995	0.867	1	CLONAL	1	TRUE	1	0.23	2		597	612	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710669	114710669	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059962-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	70	588	1	ENST00000543371.1:c.154T>A	p.Ser52Thr	p.S52T	ENST00000543371	NM_001198531.1	52	Tca/Aca	1/14	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.23	2		589	602	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754483	42754483	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs765295141	NA	P-0059962-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	69	694	0	ENST00000222329.4:c.257G>A	p.Arg86His	p.R86H	ENST00000222329	NM_006494.2	86	cGc/cAc	2/4	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.23	2		694	541	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165403	47165404	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0059962-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	60	570	0	ENST00000409792.3:c.722_723insT	p.Pro242ThrfsTer14	p.P242Tfs*14	ENST00000409792	NM_014159.6	241	cca/ccTa	3/21	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.23	2		570	510	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497304	149497304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059962-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	67	573	0	ENST00000261799.4:c.3014G>A	p.Ser1005Asn	p.S1005N	ENST00000261799	NM_002609.3	1005	aGc/aAc	22/23	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.23	2		573	550	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511338	157511338	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1554233176	NA	P-0059962-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	59	546	0	ENST00000346085.5:c.3856A>T	p.Arg1286Ter	p.R1286*	ENST00000346085	NM_020732.3	1286	Aga/Tga	15/20	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.23	2		546	507	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0059963-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	223	289	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.790962316193184	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.790962316193184	2		289	270	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0059963-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	454	671	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.790962316193184	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.790962316193184	2		671	513	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5256125	5256125	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059963-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	137	414	0	ENST00000357368.4:c.712C>T	p.Arg238Ter	p.R238*	ENST00000357368	NM_002850.3	238	Cga/Tga	9/38	0.790962316193184	3	FACETS	1	0.959	1	0.537	0.492	0.583	CLONAL	1	TRUE	1	0.790962316193184	3		414	450	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604655	48604655	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059963-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	343	567	0	ENST00000342988.3:c.1477G>T	p.Asp493Tyr	p.D493Y	ENST00000342988	NM_005359.5	493	Gat/Tat	12/12	0.790962316193184	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.790962316193184	2		567	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	107	584	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.27	2		584	696	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	15	709	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.162	0.118	0.217	0.162	0.118	0.217	SUBCLONAL	1	TRUE	1	0.27	2		709	684	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	67	273	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.27	2		273	476	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867333	45867333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765839639	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	50	721	0	ENST00000391945.4:c.860G>A	p.Arg287His	p.R287H	ENST00000391945	NM_000400.3	287	cGt/cAt	10/23	1	2	FACETS	0.628	0.532	0.733	0.628	0.532	0.733	SUBCLONAL	1	TRUE	1	0.27	2		721	590	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	896786	896786	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	75	613	0	ENST00000166345.3:c.265G>A	p.Asp89Asn	p.D89N	ENST00000166345	NM_004237.3	89	Gat/Aat	3/13	1	2	FACETS	0.932	0.817	1	0.932	0.817	1	CLONAL	1	TRUE	1	0.27	2		613	596	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556079	29556079	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886041347	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	75	390	0	ENST00000356175.3:c.2446C>T	p.Arg816Ter	p.R816*	ENST00000356175	NM_000267.3	816	Cga/Tga	21/57	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.27	2		390	437	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	49	367	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.695	0.589	0.812	0.695	0.589	0.812	SUBCLONAL	1	TRUE	1	0.27	2		367	522	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012465	29012465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373801409	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	60	448	0	ENST00000282397.4:c.406G>A	p.Val136Ile	p.V136I	ENST00000282397	NM_002019.4	136	Gta/Ata	4/30	1	2	FACETS	0.884	0.762	1	0.884	0.762	1	CLONAL	1	TRUE	1	0.27	2		448	503	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149516607	149516607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148272095	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	45	567	0	ENST00000261799.4:c.4C>T	p.Arg2Trp	p.R2W	ENST00000261799	NM_002609.3	2	Cgg/Tgg	2/23	1	2	FACETS	0.56	0.47	0.66	0.56	0.47	0.66	SUBCLONAL	1	TRUE	1	0.27	2		567	595	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1718810	1718810	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1235217579	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	81	520	0	ENST00000378609.4:c.983C>T	p.Ala328Val	p.A328V	ENST00000378609	NM_002074.3	328	gCg/gTg	11/12	1	2	FACETS	0.957	0.844	1	0.957	0.844	1	CLONAL	1	TRUE	1	0.27	2		520	627	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2488147	2488147	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532636628	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	72	585	1	ENST00000355716.4:c.44C>T	p.Thr15Ile	p.T15I	ENST00000355716	NM_003820.2	15	aCc/aTc	1/8	1	2	FACETS	0.964	0.844	1	0.964	0.844	1	CLONAL	1	TRUE	1	0.27	2		586	553	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075419	8075419	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	107	569	1	ENST00000377482.5:c.151A>G	p.Thr51Ala	p.T51A	ENST00000377482	NM_018948.3	51	Acc/Gcc	3/4	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.27	2		570	687	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782378	9782378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200226248	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	75	621	0	ENST00000377346.4:c.2311G>A	p.Gly771Ser	p.G771S	ENST00000377346	NM_005026.3	771	Ggc/Agc	18/24	1	2	FACETS	0.923	0.809	1	0.923	0.809	1	CLONAL	1	TRUE	1	0.27	2		621	602	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298033	11298033	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	120	666	0	ENST00000361445.4:c.2075A>C	p.Asn692Thr	p.N692T	ENST00000361445	NM_004958.3	692	aAc/aCc	13/58	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.27	2		666	766	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245962	16245962	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	64	516	0	ENST00000375759.3:c.1585T>C	p.Ser529Pro	p.S529P	ENST00000375759	NM_015001.2	529	Tca/Cca	8/15	1	2	FACETS	0.851	0.738	0.974	0.851	0.738	0.974	CLONAL	1	TRUE	1	0.27	2		516	557	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254692	16254692	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	84	573	0	ENST00000375759.3:c.1957C>T	p.Arg653Ter	p.R653*	ENST00000375759	NM_015001.2	653	Cga/Tga	11/15	1	2	FACETS	0.833	0.735	0.938	0.833	0.735	0.938	CLONAL	1	TRUE	1	0.27	2		573	747	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256866	16256866	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	92	625	0	ENST00000375759.3:c.4131G>T	p.Glu1377Asp	p.E1377D	ENST00000375759	NM_015001.2	1377	gaG/gaT	11/15	1	2	FACETS	0.922	0.819	1	0.922	0.819	1	CLONAL	1	TRUE	1	0.27	2		625	739	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261752	16261752	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	126	722	0	ENST00000375759.3:c.9017G>T	p.Ser3006Ile	p.S3006I	ENST00000375759	NM_015001.2	3006	aGc/aTc	11/15	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.27	2		722	760	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262493	16262493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	43	432	0	ENST00000375759.3:c.9758C>A	p.Pro3253His	p.P3253H	ENST00000375759	NM_015001.2	3253	cCt/cAt	11/15	1	2	FACETS	0.806	0.676	0.95	0.806	0.676	0.95	CLONAL	1	TRUE	1	0.27	2		432	395	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17359626	17359626	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	58	390	0	ENST00000375499.3:c.215T>C	p.Val72Ala	p.V72A	ENST00000375499	NM_003000.2	72	gTa/gCa	3/8	1	2	FACETS	0.877	0.754	1	0.877	0.754	1	CLONAL	1	TRUE	1	0.27	2		390	490	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023326	27023327	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	58	500	0	ENST00000324856.7:c.437dup	p.Ala147SerfsTer253	p.A147Sfs*253	ENST00000324856	NM_006015.4	144	-/C	1/20	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.27	2		500	402	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	83	580	0	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	1	2	FACETS	0.9	0.794	1	0.9	0.794	1	CLONAL	1	TRUE	1	0.27	2		580	683	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938248	36938248	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	103	650	0	ENST00000361632.4:c.713G>A	p.Ser238Asn	p.S238N	ENST00000361632		238	aGc/aAc	6/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.27	2		650	595	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39311721	39311721	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	64	295	0	ENST00000373001.3:c.938A>T	p.Glu313Val	p.E313V	ENST00000373001	NM_022157.3	313	gAa/gTa	6/7	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.27	2		295	446	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46733154	46733154	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	98	585	1	ENST00000371975.4:c.915G>T	p.Glu305Asp	p.E305D	ENST00000371975	NM_003579.3	305	gaG/gaT	9/18	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.27	2		586	565	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301864	65301864	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	92	463	0	ENST00000342505.4:c.3175T>G	p.Tyr1059Asp	p.Y1059D	ENST00000342505	NM_002227.2	1059	Tat/Gat	23/25	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.27	2		463	524	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321216	65321216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1306467125	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	80	626	0	ENST00000342505.4:c.1624C>T	p.Arg542Cys	p.R542C	ENST00000342505	NM_002227.2	542	Cgc/Tgc	11/25	1	2	FACETS	0.829	0.729	0.936	0.829	0.729	0.936	CLONAL	1	TRUE	1	0.27	2		626	715	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430865	78430865	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	110	509	1	ENST00000370768.2:c.524C>A	p.Pro175His	p.P175H	ENST00000370768	NM_003902.3	175	cCt/cAt	8/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.27	2		510	654	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251271	115251271	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	66	393	0	ENST00000369535.4:c.455T>G	p.Val152Gly	p.V152G	ENST00000369535	NM_002524.4	152	gTt/gGt	5/7	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.27	2		393	439	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258751	115258751	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	67	381	0	ENST00000369535.4:c.31G>T	p.Ala11Ser	p.A11S	ENST00000369535	NM_002524.4	11	Gca/Tca	2/7	1	2	FACETS	0.909	0.791	1	0.909	0.791	1	CLONAL	1	TRUE	1	0.27	2		381	546	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115267948	115267948	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	65	413	0	ENST00000438362.2:c.1785C>A	p.Phe595Leu	p.F595L	ENST00000438362	NM_001242891.1	595	ttC/ttA	15/20	1	2	FACETS	0.94	0.817	1	0.94	0.817	1	CLONAL	1	TRUE	1	0.27	2		413	512	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471614	120471614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1399178397	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	98	545	1	ENST00000256646.2:c.3877C>T	p.Arg1293Cys	p.R1293C	ENST00000256646	NM_024408.3	1293	Cgt/Tgt	23/34	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.27	2		546	624	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471740	120471740	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782797192	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	107	700	0	ENST00000256646.2:c.3751C>T	p.Arg1251Cys	p.R1251C	ENST00000256646	NM_024408.3	1251	Cgc/Tgc	23/34	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.27	2		700	707	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510170	120510170	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	49	642	2	ENST00000256646.2:c.1339G>T	p.Gly447Cys	p.G447C	ENST00000256646	NM_024408.3	447	Ggt/Tgt	8/34	1	2	FACETS	0.542	0.458	0.634	0.542	0.458	0.634	SUBCLONAL	1	TRUE	1	0.27	2		644	670	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150936071	150936071	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	105	562	0	ENST00000271640.5:c.3523A>G	p.Ile1175Val	p.I1175V	ENST00000271640	NM_001145415.1	1175	Att/Gtt	20/22	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.27	2		562	736	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874163	155874163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs977405637	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	97	581	1	ENST00000368323.3:c.368G>A	p.Arg123His	p.R123H	ENST00000368323	NM_006912.5	123	cGt/cAt	5/6	1	2	FACETS	0.97	0.865	1	0.97	0.865	1	CLONAL	1	TRUE	1	0.27	2		582	741	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837999	156837999	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	86	735	0	ENST00000524377.1:c.532C>T	p.His178Tyr	p.H178Y	ENST00000524377	NM_002529.3	178	Cat/Tat	5/17	1	2	FACETS	0.861	0.761	0.968	0.861	0.761	0.968	CLONAL	1	TRUE	1	0.27	2		735	740	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846217	156846217	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	73	648	0	ENST00000524377.1:c.1658C>A	p.Ala553Asp	p.A553D	ENST00000524377	NM_002529.3	553	gCt/gAt	14/17	1	2	FACETS	0.841	0.735	0.955	0.841	0.735	0.955	CLONAL	1	TRUE	1	0.27	2		648	643	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162688870	162688870	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	65	412	0	ENST00000367921.3:c.17G>T	p.Arg6Ile	p.R6I	ENST00000367921	NM_006182.2	6	aGa/aTa	3/18	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.27	2		412	476	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163315592	163315592	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	45	308	0	ENST00000271452.3:c.932C>T	p.Ala311Val	p.A311V	ENST00000271452	NM_145697.2	311	gCc/gTc	11/14	1	2	FACETS	0.731	0.615	0.859	0.731	0.615	0.859	SUBCLONAL	1	TRUE	1	0.27	2		308	456	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518240	204518240	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	101	541	0	ENST00000367182.3:c.904-1G>T		p.X302_splice	ENST00000367182	NM_001278516.1	302			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.27	2		541	607	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649596	206649596	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	129	714	0	ENST00000367120.3:c.431T>C	p.Leu144Pro	p.L144P	ENST00000367120	NM_014002.3	144	cTc/cCc	6/22	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.27	2		714	698	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246091253	246091253	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	62	505	0	ENST00000388985.4:c.682G>T	p.Asp228Tyr	p.D228Y	ENST00000388985		228	Gac/Tac	7/12	1	2	FACETS	0.89	0.77	1	0.89	0.77	1	CLONAL	1	TRUE	1	0.27	2		505	516	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100351	8100351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776412274	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	108	931	0	ENST00000346208.3:c.325G>A	p.Ala109Thr	p.A109T	ENST00000346208		109	Gcc/Acc	3/6	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.27	2		931	791	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600582	43600582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	64	698	0	ENST00000355710.3:c.808C>T	p.Pro270Ser	p.P270S	ENST00000355710	NM_020975.4	270	Ccc/Tcc	4/20	1	2	FACETS	0.864	0.748	0.988	0.864	0.748	0.988	CLONAL	1	TRUE	1	0.27	2		698	549	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610128	43610128	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193922700	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	81	733	0	ENST00000355710.3:c.2080C>T	p.Arg694Trp	p.R694W	ENST00000355710	NM_020975.4	694	Cgg/Tgg	11/20	1	2	FACETS	0.843	0.742	0.951	0.843	0.742	0.951	CLONAL	1	TRUE	1	0.27	2		733	712	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851074	63851074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143074852	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	83	651	0	ENST00000279873.7:c.1852G>A	p.Ala618Thr	p.A618T	ENST00000279873	NM_032199.2	618	Gcc/Acc	10/10	1	2	FACETS	0.873	0.771	0.984	0.873	0.771	0.984	CLONAL	1	TRUE	1	0.27	2		651	704	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717720	89717720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	31	351	0	ENST00000371953.3:c.745G>A	p.Val249Met	p.V249M	ENST00000371953	NM_000314.4	249	Gtg/Atg	7/9	1	2	FACETS	0.48	0.388	0.585	0.48	0.388	0.585	SUBCLONAL	1	TRUE	1	0.27	2		351	478	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112760223	112760223	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1296115550	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	91	382	0	ENST00000369452.4:c.892G>A	p.Ala298Thr	p.A298T	ENST00000369452	NM_007373.3	298	Gca/Aca	4/9	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.27	2		382	565	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910801	114910801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1336546841	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	75	600	1	ENST00000543371.1:c.920C>T	p.Thr307Met	p.T307M	ENST00000543371	NM_001198531.1	307	aCg/aTg	9/14	1	2	FACETS	0.789	0.691	0.895	0.789	0.691	0.895	SUBCLONAL	1	TRUE	1	0.27	2		601	704	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910844	114910844	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	45	614	0	ENST00000543371.1:c.963G>T	p.Gln321His	p.Q321H	ENST00000543371	NM_001198531.1	321	caG/caT	9/14	1	2	FACETS	0.494	0.414	0.582	0.494	0.414	0.582	SUBCLONAL	1	TRUE	1	0.27	2		614	675	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276974	123276974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918504	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	99	652	0	ENST00000358487.5:c.943G>A	p.Ala315Thr	p.A315T	ENST00000358487	NM_000141.4	315	Gcc/Acc	8/18	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.27	2		652	657	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156654	2156654	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	83	794	0	ENST00000434045.2:c.268G>T	p.Gly90Cys	p.G90C	ENST00000434045	NM_001127598.1	90	Ggc/Tgc	3/5	1	2	FACETS	0.896	0.791	1	0.896	0.791	1	CLONAL	1	TRUE	1	0.27	2		794	686	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14317397	14317397	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	59	319	0	ENST00000256196.4:c.113A>C	p.Tyr38Ser	p.Y38S	ENST00000256196		38	tAt/tCt	2/6	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.27	2		319	400	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380350	14380350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	51	596	0	ENST00000256196.4:c.67G>A	p.Gly23Ser	p.G23S	ENST00000256196		23	Ggc/Agc	1/6	1	2	FACETS	0.789	0.671	0.918	0.789	0.671	0.918	CLONAL	1	TRUE	1	0.27	2		596	479	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410710	32410710	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	101	529	0	ENST00000332351.3:c.1448G>T	p.Ser483Ile	p.S483I	ENST00000332351	NM_024426.4	483	aGc/aTc	10/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.27	2		529	589	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456609	32456609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567200038	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	40	514	0	ENST00000332351.3:c.283C>T	p.Pro95Ser	p.P95S	ENST00000332351	NM_024426.4	95	Cct/Tct	1/10	1	2	FACETS	0.737	0.613	0.875	0.737	0.613	0.875	SUBCLONAL	1	TRUE	1	0.27	2		514	402	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57004404	57004404	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	T	T	G	rs564912523	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	95	649	1	ENST00000257254.3:c.75A>C	p.Lys25Asn	p.K25N	ENST00000257254		25	aaA/aaC	1/2	0.109974236728309	0	FACETS	0.837	0.746	0.933			1	INDETERMINATE	1	TRUE	0	0.27	0		650	614	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127991	64127991	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	116	779	0	ENST00000334205.4:c.389G>A	p.Arg130His	p.R130H	ENST00000334205	NM_003942.2	130	cGc/cAc	4/17	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.27	2		779	741	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573229	64573229	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863224807	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	74	633	0	ENST00000312049.6:c.1063C>T	p.Arg355Trp	p.R355W	ENST00000312049	NM_130799.2	355	Cgg/Tgg	8/10	1	2	FACETS	0.88	0.771	0.998	0.88	0.771	0.998	CLONAL	1	TRUE	1	0.27	2		633	623	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573764	64573764	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373135175	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	113	739	0	ENST00000312049.6:c.989G>A	p.Arg330His	p.R330H	ENST00000312049	NM_130799.2	330	cGc/cAc	7/10	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.27	2		739	780	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69458713	69458713	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	88	557	0	ENST00000227507.2:c.528G>T	p.Gln176His	p.Q176H	ENST00000227507	NM_053056.2	176	caG/caT	3/5	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.27	2		557	560	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514344	69514344	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	74	520	0	ENST00000294312.3:c.337C>T	p.Leu113Phe	p.L113F	ENST00000294312	NM_005117.2	113	Ctt/Ttt	3/3	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.27	2		520	493	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940586	71940586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1255360958	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	124	781	0	ENST00000298229.2:c.737G>A	p.Arg246His	p.R246H	ENST00000298229	NM_001567.3	246	cGc/cAc	6/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.27	2		781	782	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942232	71942232	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs775939148	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	87	636	0	ENST00000298229.2:c.1496C>T	p.Pro499Leu	p.P499L	ENST00000298229	NM_001567.3	499	cCg/cTg	12/28	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.27	2		636	571	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94211927	94211927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	82	339	0	ENST00000323929.3:c.518G>A	p.Ser173Asn	p.S173N	ENST00000323929	NM_005591.3	173	aGc/aAc	6/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.27	2		339	457	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962529	100962529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767360879	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	29	444	0	ENST00000325455.5:c.1868G>A	p.Arg623His	p.R623H	ENST00000325455	NM_001202474.3	623	cGc/cAc	3/8	1	2	FACETS	0.405	0.324	0.497	0.405	0.324	0.497	SUBCLONAL	1	TRUE	1	0.27	2		444	531	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195248	102195248	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1435803547	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	89	398	0	ENST00000263464.3:c.8T>C	p.Ile3Thr	p.I3T	ENST00000263464	NM_001165.4	3	aTa/aCa	2/9	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.27	2		398	535	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115639	108115639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876659531	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	65	367	0	ENST00000278616.4:c.787C>T	p.Leu263Phe	p.L263F	ENST00000278616	NM_000051.3	263	Ctt/Ttt	7/63	1	2	FACETS	0.935	0.812	1	0.935	0.812	1	CLONAL	1	TRUE	1	0.27	2		367	515	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122569	108122569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1565385040	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	85	505	0	ENST00000278616.4:c.1613C>T	p.Ala538Val	p.A538V	ENST00000278616	NM_000051.3	538	gCa/gTa	11/63	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.27	2		505	607	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151845	108151845	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	37	421	0	ENST00000278616.4:c.3526C>A	p.Leu1176Met	p.L1176M	ENST00000278616	NM_000051.3	1176	Ctg/Atg	24/63	1	2	FACETS	0.49	0.403	0.588	0.49	0.403	0.588	SUBCLONAL	1	TRUE	1	0.27	2		421	559	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205724	108205724	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	62	393	0	ENST00000278616.4:c.8039T>G	p.Leu2680Arg	p.L2680R	ENST00000278616	NM_000051.3	2680	cTg/cGg	55/63	1	2	FACETS	0.928	0.803	1	0.928	0.803	1	CLONAL	1	TRUE	1	0.27	2		393	495	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216612	108216612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501605	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	67	456	0	ENST00000278616.4:c.8561G>A	p.Arg2854His	p.R2854H	ENST00000278616	NM_000051.3	2854	cGc/cAc	58/63	1	2	FACETS	0.853	0.741	0.973	0.853	0.741	0.973	CLONAL	1	TRUE	1	0.27	2		456	582	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111959676	111959676	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199517389	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	44	231	0	ENST00000375549.3:c.255G>T	p.Leu85Phe	p.L85F	ENST00000375549	NM_003002.3	85	ttG/ttT	3/4	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.27	2		231	312	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342733	118342733	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	94	583	0	ENST00000534358.1:c.859A>G	p.Thr287Ala	p.T287A	ENST00000534358	NM_005933.3	287	Aca/Gca	3/36	1	2	FACETS	0.942	0.838	1	0.942	0.838	1	CLONAL	1	TRUE	1	0.27	2		583	739	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344458	118344458	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	110	704	0	ENST00000534358.1:c.2584C>T	p.Arg862Ter	p.R862*	ENST00000534358	NM_005933.3	862	Cga/Tga	3/36	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.27	2		704	783	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360556	118360556	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	51	603	0	ENST00000534358.1:c.4529T>C	p.Leu1510Pro	p.L1510P	ENST00000534358	NM_005933.3	1510	cTg/cCg	12/36	1	2	FACETS	0.513	0.435	0.599	0.513	0.435	0.599	SUBCLONAL	1	TRUE	1	0.27	2		603	736	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377091	118377091	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	83	681	0	ENST00000534358.1:c.10484G>A	p.Ser3495Asn	p.S3495N	ENST00000534358	NM_005933.3	3495	aGc/aAc	27/36	1	2	FACETS	0.806	0.71	0.908	0.806	0.71	0.908	CLONAL	1	TRUE	1	0.27	2		681	763	SUCCESS
CBL	867	MSKCC	GRCh37	11	119167720	119167720	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	82	502	0	ENST00000264033.4:c.2129C>T	p.Pro710Leu	p.P710L	ENST00000264033	NM_005188.3	710	cCt/cTt	13/16	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.27	2		502	580	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170283	119170283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	98	640	2	ENST00000264033.4:c.2513G>A	p.Gly838Asp	p.G838D	ENST00000264033	NM_005188.3	838	gGc/gAc	16/16	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.27	2		642	666	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497646	125497646	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	78	382	0	ENST00000428830.2:c.210C>A	p.Phe70Leu	p.F70L	ENST00000428830	NM_001114121.2	70	ttC/ttA	3/14	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.27	2		382	489	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435332	18435332	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	98	565	0	ENST00000266497.5:c.317C>T	p.Ala106Val	p.A106V	ENST00000266497		106	gCa/gTa	1/31	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.27	2		565	722	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534755	18534755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776582655	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	93	488	0	ENST00000266497.5:c.1813G>A	p.Val605Ile	p.V605I	ENST00000266497		605	Gta/Ata	12/31	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.27	2		488	625	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628759	21628759	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	36	340	0	ENST00000421138.2:c.950-1G>T		p.X317_splice	ENST00000421138		317			1	2	FACETS	0.565	0.464	0.678	0.565	0.464	0.678	SUBCLONAL	1	TRUE	1	0.27	2		340	472	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245002	46245002	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	100	732	0	ENST00000334344.6:c.3096G>T	p.Gln1032His	p.Q1032H	ENST00000334344	NM_152641.2	1032	caG/caT	15/21	1	2	FACETS	0.891	0.796	0.993	0.891	0.796	0.993	CLONAL	1	TRUE	1	0.27	2		732	831	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246222	46246222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	101	609	0	ENST00000334344.6:c.4316C>T	p.Thr1439Ile	p.T1439I	ENST00000334344	NM_152641.2	1439	aCa/aTa	15/21	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.27	2		609	686	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432333	49432333	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	91	788	0	ENST00000301067.7:c.8806G>A	p.Ala2936Thr	p.A2936T	ENST00000301067	NM_003482.3	2936	Gcc/Acc	34/54	1	2	FACETS	0.87	0.772	0.974	0.87	0.772	0.974	CLONAL	1	TRUE	1	0.27	2		788	775	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432378	49432378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	111	796	0	ENST00000301067.7:c.8761C>T	p.Leu2921Phe	p.L2921F	ENST00000301067	NM_003482.3	2921	Ctt/Ttt	34/54	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.27	2		796	811	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435226	49435226	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	82	600	0	ENST00000301067.7:c.6327G>T	p.Gln2109His	p.Q2109H	ENST00000301067	NM_003482.3	2109	caG/caT	31/54	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.27	2		600	576	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436025	49436025	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	68	648	0	ENST00000301067.7:c.5956A>G	p.Thr1986Ala	p.T1986A	ENST00000301067	NM_003482.3	1986	Acc/Gcc	28/54	1	2	FACETS	0.741	0.644	0.846	0.741	0.644	0.846	SUBCLONAL	1	TRUE	1	0.27	2		648	680	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50490681	50490681	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	54	502	0	ENST00000394963.4:c.1318T>G	p.Phe440Val	p.F440V	ENST00000394963	NM_003076.4	440	Ttc/Gtc	11/13	1	2	FACETS	0.704	0.601	0.817	0.704	0.601	0.817	SUBCLONAL	1	TRUE	1	0.27	2		502	568	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495751	56495751	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573158454	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	113	656	0	ENST00000267101.3:c.3941G>A	p.Arg1314His	p.R1314H	ENST00000267101	NM_001982.3	1314	cGt/cAt	28/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.27	2		656	653	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858974	57858974	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1039477087	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	37	778	0	ENST00000228682.2:c.470A>G	p.His157Arg	p.H157R	ENST00000228682	NM_005269.2	157	cAt/cGt	5/12	1	2	FACETS	0.373	0.306	0.448	0.373	0.306	0.448	SUBCLONAL	1	TRUE	1	0.27	2		778	735	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864154	57864154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	88	799	0	ENST00000228682.2:c.1631G>A	p.Ser544Asn	p.S544N	ENST00000228682	NM_005269.2	544	aGc/aAc	12/12	1	2	FACETS	0.863	0.765	0.969	0.863	0.765	0.969	CLONAL	1	TRUE	1	0.27	2		799	755	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112473	115112473	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1218376949	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	69	767	0	ENST00000257566.3:c.1267C>T	p.Arg423Trp	p.R423W	ENST00000257566	NM_016569.3	423	Cgg/Tgg	7/8	1	2	FACETS	0.869	0.757	0.99	0.869	0.757	0.99	CLONAL	1	TRUE	1	0.27	2		767	588	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115397	115115397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866796237	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	86	463	0	ENST00000257566.3:c.929G>A	p.Arg310Gln	p.R310Q	ENST00000257566	NM_016569.3	310	cGa/cAa	5/8	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.27	2		463	546	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120535059	120535059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	88	552	0	ENST00000229340.5:c.596G>A	p.Arg199His	p.R199H	ENST00000229340	NM_006861.6	199	cGc/cAc	6/6	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.27	2		552	610	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784078	120784078	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	89	816	2	ENST00000257552.2:c.907C>T	p.Arg303Cys	p.R303C	ENST00000257552	NM_002442.3	303	Cgc/Tgc	13/15	1	2	FACETS	0.929	0.823	1	0.929	0.823	1	CLONAL	1	TRUE	1	0.27	2		818	710	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218901	133218901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768244569	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	80	750	0	ENST00000320574.5:c.5035C>T	p.Arg1679Cys	p.R1679C	ENST00000320574	NM_006231.2	1679	Cgc/Tgc	38/49	1	2	FACETS	0.832	0.732	0.94	0.832	0.732	0.94	CLONAL	1	TRUE	1	0.27	2		750	712	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226017	133226017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770966534	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	95	656	1	ENST00000320574.5:c.3880C>T	p.Arg1294Cys	p.R1294C	ENST00000320574	NM_006231.2	1294	Cgt/Tgt	31/49	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.27	2		657	670	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250189	133250189	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	109	688	0	ENST00000320574.5:c.1331T>A	p.Met444Lys	p.M444K	ENST00000320574	NM_006231.2	444	aTg/aAg	13/49	0.3	2	FACETS	1	0.972	1			1	CLONAL	1	TRUE	NA	0.27	2		688	655	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256616	133256616	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	97	545	0	ENST00000320574.5:c.347T>G	p.Val116Gly	p.V116G	ENST00000320574	NM_006231.2	116	gTt/gGt	5/49	0.3	2	FACETS	1	0.959	1			1	CLONAL	1	TRUE	NA	0.27	2		545	623	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619844	21619844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762892798	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	87	547	0	ENST00000382592.4:c.322G>A	p.Val108Met	p.V108M	ENST00000382592	NM_014572.2	108	Gtg/Atg	2/8	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.27	2		547	543	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828836	26828836	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	98	623	0	ENST00000381527.3:c.58T>C	p.Phe20Leu	p.F20L	ENST00000381527	NM_001260.1	20	Ttt/Ctt	1/13	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.27	2		623	628	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967566	26967566	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs369889152	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	73	399	0	ENST00000381527.3:c.709C>T	p.Arg237Ter	p.R237*	ENST00000381527	NM_001260.1	237	Cga/Tga	7/13	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.27	2		399	491	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588594	28588594	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	85	497	0	ENST00000241453.7:c.2854G>T	p.Glu952Ter	p.E952*	ENST00000241453	NM_004119.2	952	Gaa/Taa	23/24	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.27	2		497	516	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592705	28592705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201208287	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	84	528	0	ENST00000241453.7:c.2440G>A	p.Ala814Thr	p.A814T	ENST00000241453	NM_004119.2	814	Gcc/Acc	20/24	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.27	2		528	571	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32890655	32890655	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	80	337	1	ENST00000380152.3:c.58A>G	p.Asn20Asp	p.N20D	ENST00000380152		20	Aac/Gac	2/27	0.162131334930246	3	FACETS	1	0.967	1	0.641	0.565	0.721	CLONAL	1	TRUE	1	0.27	3		338	525	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907389	32907389	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	95	385	0	ENST00000380152.3:c.1774T>C	p.Tyr592His	p.Y592H	ENST00000380152		592	Tat/Cat	10/27	0.162131334930246	3	FACETS	1	0.973	1	0.647	0.577	0.722	CLONAL	1	TRUE	1	0.27	3		385	617	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936759	32936759	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	89	532	0	ENST00000380152.3:c.7905A>C	p.Glu2635Asp	p.E2635D	ENST00000380152		2635	gaA/gaC	17/27	0.162131334930246	3	FACETS	1	0.962	1	0.598	0.53	0.669	CLONAL	1	TRUE	1	0.27	3		532	626	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941739	48941739	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1368390928	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	31	103	0	ENST00000267163.4:c.1049G>T	p.Ser350Ile	p.S350I	ENST00000267163	NM_000321.2	350	aGt/aTt	10/27	0.162131334930246	3	FACETS	0.841	0.682	1	0.42	0.341	0.51	CLONAL	1	TRUE	1	0.27	3		103	310	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514527	103514527	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	101	664	0	ENST00000355739.4:c.1028G>T	p.Arg343Ile	p.R343I	ENST00000355739	NM_000123.3	343	aGa/aTa	8/15	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.27	2		664	746	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528228	103528228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs998046185	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	92	516	0	ENST00000355739.4:c.3536C>T	p.Ala1179Val	p.A1179V	ENST00000355739	NM_000123.3	1179	gCg/gTg	15/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.27	2		516	593	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132969	30132969	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	76	598	0	ENST00000331968.5:c.632G>A	p.Gly211Glu	p.G211E	ENST00000331968	NM_002742.2	211	gGg/gAg	4/18	1	2	FACETS	0.995	0.874	1	0.995	0.874	1	CLONAL	1	TRUE	1	0.27	2		598	566	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060613	38060613	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	128	844	0	ENST00000250448.2:c.1376A>G	p.Tyr459Cys	p.Y459C	ENST00000250448	NM_004496.3	459	tAc/tGc	2/2	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.27	2		844	881	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81563035	81563035	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs559898532	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	46	514	0	ENST00000298171.2:c.598A>G	p.Thr200Ala	p.T200A	ENST00000298171	NM_000369.2	200	Aca/Gca	7/10	1	2	FACETS	0.625	0.526	0.735	0.625	0.526	0.735	SUBCLONAL	1	TRUE	1	0.27	2		514	545	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609492	81609492	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs774376871	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	59	620	0	ENST00000298171.2:c.1090A>T	p.Ile364Phe	p.I364F	ENST00000298171	NM_000369.2	364	Att/Ttt	10/10	1	2	FACETS	0.621	0.533	0.716	0.621	0.533	0.716	SUBCLONAL	1	TRUE	1	0.27	2		620	704	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560416	95560416	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756827508	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	95	614	0	ENST00000393063.1:c.5173C>T	p.Arg1725Trp	p.R1725W	ENST00000393063	NM_030621.3	1725	Cgg/Tgg	25/28	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.27	2		614	671	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560476	95560476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	86	583	0	ENST00000393063.1:c.5113G>A	p.Glu1705Lys	p.E1705K	ENST00000393063	NM_030621.3	1705	Gaa/Aaa	25/28	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.27	2		583	610	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562655	95562655	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	100	681	0	ENST00000393063.1:c.4602C>A	p.Asn1534Lys	p.N1534K	ENST00000393063	NM_030621.3	1534	aaC/aaA	24/28	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.27	2		681	728	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569726	95569726	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	113	664	0	ENST00000393063.1:c.4007C>T	p.Pro1336Leu	p.P1336L	ENST00000393063	NM_030621.3	1336	cCt/cTt	22/28	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.27	2		664	732	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574313	95574313	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	85	371	0	ENST00000393063.1:c.2554T>C	p.Tyr852His	p.Y852H	ENST00000393063	NM_030621.3	852	Tat/Cat	17/28	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.27	2		371	564	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105237125	105237125	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1159942120	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	85	546	0	ENST00000349310.3:c.1320G>T	p.Glu440Asp	p.E440D	ENST00000349310	NM_001014432.1	440	gaG/gaT	14/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.27	2		546	538	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243030	105243030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1566818890	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	90	642	0	ENST00000349310.3:c.253G>A	p.Glu85Lys	p.E85K	ENST00000349310	NM_001014432.1	85	Gaa/Aaa	5/15	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.27	2		642	664	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028712	42028712	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	106	651	0	ENST00000219905.7:c.4250C>A	p.Pro1417His	p.P1417H	ENST00000219905	NM_001164273.1	1417	cCt/cAt	13/24	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.27	2		651	749	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041770	42041770	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1555434669	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	103	620	0	ENST00000219905.7:c.5965G>T	p.Glu1989Ter	p.E1989*	ENST00000219905	NM_001164273.1	1989	Gaa/Taa	17/24	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.27	2		620	732	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052557	42052557	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	96	575	0	ENST00000219905.7:c.7228T>G	p.Trp2410Gly	p.W2410G	ENST00000219905	NM_001164273.1	2410	Tgg/Ggg	20/24	1	2	FACETS	0.997	0.889	1	0.997	0.889	1	CLONAL	1	TRUE	1	0.27	2		575	713	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058417	42058417	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	114	672	0	ENST00000219905.7:c.8137T>G	p.Leu2713Val	p.L2713V	ENST00000219905	NM_001164273.1	2713	Ttg/Gtg	24/24	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.27	2		672	770	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43773136	43773136	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	99	539	0	ENST00000382044.4:c.456A>C	p.Glu152Asp	p.E152D	ENST00000382044	NM_001141980.1	152	gaA/gaC	5/28	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.27	2		539	586	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007620	45007620	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs111947448	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	45	495	0	ENST00000558401.1:c.68-1G>T		p.X23_splice	ENST00000558401	NM_004048.2	23			1	2	FACETS	0.57	0.478	0.671	0.57	0.478	0.671	SUBCLONAL	1	TRUE	1	0.27	2		495	585	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007686	45007686	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	89	567	0	ENST00000558401.1:c.133T>C	p.Cys45Arg	p.C45R	ENST00000558401	NM_004048.2	45	Tgc/Cgc	2/4	1	2	FACETS	0.949	0.841	1	0.949	0.841	1	CLONAL	1	TRUE	1	0.27	2		567	695	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50773822	50773822	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	109	549	0	ENST00000307179.4:c.1363C>A	p.Leu455Ile	p.L455I	ENST00000307179		455	Ctc/Atc	11/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.27	2		549	726	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727553	66727553	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	76	462	0	ENST00000307102.5:c.269C>A	p.Ser90Tyr	p.S90Y	ENST00000307102	NM_002755.3	90	tCt/tAt	2/11	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.27	2		462	556	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472463	88472463	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	61	662	0	ENST00000360948.2:c.2092T>A	p.Phe698Ile	p.F698I	ENST00000360948	NM_001012338.2	698	Ttc/Atc	16/19	1	2	FACETS	0.708	0.611	0.815	0.708	0.611	0.815	SUBCLONAL	1	TRUE	1	0.27	2		662	638	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669576	88669576	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	75	491	0	ENST00000360948.2:c.1322T>C	p.Phe441Ser	p.F441S	ENST00000360948	NM_001012338.2	441	tTt/tCt	12/19	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.27	2		491	511	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678629	88678629	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	67	497	0	ENST00000360948.2:c.908-1G>A		p.X303_splice	ENST00000360948	NM_001012338.2	303			1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.27	2		497	479	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90645541	90645541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	33	397	0	ENST00000330062.3:c.82G>A	p.Ala28Thr	p.A28T	ENST00000330062	NM_002168.2	28	Gcc/Acc	1/11	1	2	FACETS	0.685	0.558	0.827	0.685	0.558	0.827	SUBCLONAL	1	TRUE	1	0.27	2		397	357	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778468	3778468	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766744145	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	84	697	0	ENST00000262367.5:c.6580C>T	p.Arg2194Trp	p.R2194W	ENST00000262367	NM_004380.2	2194	Cgg/Tgg	31/31	0.3	2	FACETS	0.847	0.747	0.953			1	CLONAL	1	TRUE	NA	0.27	2		697	735	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778738	3778738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1489860615	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	113	656	0	ENST00000262367.5:c.6310C>T	p.Arg2104Cys	p.R2104C	ENST00000262367	NM_004380.2	2104	Cgc/Tgc	31/31	0.3	2	FACETS	1	0.97	1			1	CLONAL	1	TRUE	NA	0.27	2		656	699	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778767	3778767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	86	671	0	ENST00000262367.5:c.6281C>T	p.Pro2094Leu	p.P2094L	ENST00000262367	NM_004380.2	2094	cCg/cTg	31/31	0.3	2	FACETS	0.868	0.767	0.975			1	CLONAL	1	TRUE	NA	0.27	2		671	734	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779715	3779715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1220965943	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	105	697	0	ENST00000262367.5:c.5333C>T	p.Ser1778Leu	p.S1778L	ENST00000262367	NM_004380.2	1778	tCg/tTg	31/31	0.3	2	FACETS	1	0.95	1			1	CLONAL	1	TRUE	NA	0.27	2		697	707	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801726	3801726	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs587783483	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	111	566	0	ENST00000262367.5:c.3779+1G>A		p.X1260_splice	ENST00000262367	NM_004380.2	1260			0.3	2	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.27	2		566	652	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828735	3828735	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	87	600	1	ENST00000262367.5:c.1907T>C	p.Val636Ala	p.V636A	ENST00000262367	NM_004380.2	636	gTg/gCg	9/31	0.3	2	FACETS	0.982	0.87	1			1	CLONAL	1	TRUE	NA	0.27	2		601	656	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934881	9934881	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs752320310	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	77	517	0	ENST00000330684.3:c.1409C>A	p.Thr470Asn	p.T470N	ENST00000330684	NM_001134407.1	470	aCt/aAt	6/13	1	2	FACETS	0.985	0.866	1	0.985	0.866	1	CLONAL	1	TRUE	1	0.27	2		517	579	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031840	10031840	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	100	565	1	ENST00000330684.3:c.983A>G	p.Glu328Gly	p.E328G	ENST00000330684	NM_001134407.1	328	gAg/gGg	3/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.27	2		566	564	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857514	68857514	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	87	463	0	ENST00000261769.5:c.2149A>G	p.Ile717Val	p.I717V	ENST00000261769	NM_004360.3	717	Att/Gtt	13/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.27	2		463	524	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867223	68867223	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	62	583	0	ENST00000261769.5:c.2470G>T	p.Ala824Ser	p.A824S	ENST00000261769	NM_004360.3	824	Gcc/Tcc	16/16	1	2	FACETS	0.788	0.681	0.904	0.788	0.681	0.904	CLONAL	1	TRUE	1	0.27	2		583	583	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827732	72827732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241554729	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	82	568	1	ENST00000268489.5:c.8849G>A	p.Arg2950His	p.R2950H	ENST00000268489	NM_006885.3	2950	cGc/cAc	9/10	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.27	2		569	571	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830501	72830501	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	76	629	0	ENST00000268489.5:c.6080A>G	p.Asp2027Gly	p.D2027G	ENST00000268489	NM_006885.3	2027	gAt/gGt	9/10	1	2	FACETS	0.948	0.832	1	0.948	0.832	1	CLONAL	1	TRUE	1	0.27	2		629	594	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832605	72832605	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	88	438	0	ENST00000268489.5:c.3976G>T	p.Glu1326Ter	p.E1326*	ENST00000268489	NM_006885.3	1326	Gag/Tag	9/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.27	2		438	475	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992345	72992345	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	94	663	0	ENST00000268489.5:c.1700G>T	p.Arg567Met	p.R567M	ENST00000268489	NM_006885.3	567	aGg/aTg	2/10	1	2	FACETS	0.92	0.818	1	0.92	0.818	1	CLONAL	1	TRUE	1	0.27	2		663	757	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819766	81819766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766974268	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	81	589	1	ENST00000359376.3:c.172G>A	p.Ala58Thr	p.A58T	ENST00000359376	NM_002661.3	58	Gct/Act	2/33	1	2	FACETS	0.936	0.825	1	0.936	0.825	1	CLONAL	1	TRUE	1	0.27	2		590	641	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346925	89346925	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	88	719	0	ENST00000301030.4:c.6025A>G	p.Ser2009Gly	p.S2009G	ENST00000301030	NM_001256183.1	2009	Agc/Ggc	9/13	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.27	2		719	630	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347639	89347639	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761323554	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	133	748	0	ENST00000301030.4:c.5311C>T	p.Leu1771Phe	p.L1771F	ENST00000301030	NM_001256183.1	1771	Ctt/Ttt	9/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.27	2		748	790	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89806483	89806483	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	81	578	0	ENST00000389301.3:c.3853T>G	p.Phe1285Val	p.F1285V	ENST00000389301	NM_000135.2	1285	Ttc/Gtc	39/43	1	2	FACETS	0.876	0.772	0.988	0.876	0.772	0.988	CLONAL	1	TRUE	1	0.27	2		578	685	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882335	89882335	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190475225	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	74	621	0	ENST00000389301.3:c.139G>A	p.Ala47Thr	p.A47T	ENST00000389301	NM_000135.2	47	Gct/Act	2/43	1	2	FACETS	0.888	0.778	1	0.888	0.778	1	CLONAL	1	TRUE	1	0.27	2		621	617	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577055	7577055	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1131691006	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	107	807	0	ENST00000269305.4:c.883C>T	p.Pro295Ser	p.P295S	ENST00000269305	NM_001126112.2	295	Cct/Tct	8/11	1	2	FACETS	0.979	0.877	1	0.979	0.877	1	CLONAL	1	TRUE	1	0.27	2		807	810	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	120	736	0	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.27	2		736	772	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976991	7976991	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	85	481	0	ENST00000319144.4:c.1739C>T	p.Ala580Val	p.A580V	ENST00000319144	NM_001139.2	580	gCt/gTt	13/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.27	2		481	480	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924295	11924295	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	99	881	0	ENST00000353533.5:c.92A>G	p.His31Arg	p.H31R	ENST00000353533	NM_003010.3	31	cAc/cGc	1/11	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.27	2		881	663	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679366	29679366	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs866445127	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	74	563	0	ENST00000356175.3:c.7486C>T	p.Arg2496Ter	p.R2496*	ENST00000356175	NM_000267.3	2496	Cga/Tga	50/57	1	2	FACETS	0.858	0.751	0.973	0.858	0.751	0.973	CLONAL	1	TRUE	1	0.27	2		563	639	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33689800	33689800	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	84	589	0	ENST00000308377.4:c.1027A>C	p.Thr343Pro	p.T343P	ENST00000308377	NM_152270.3	343	Aca/Cca	2/5	1	2	FACETS	0.95	0.839	1	0.95	0.839	1	CLONAL	1	TRUE	1	0.27	2		589	655	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866644	37866644	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	93	765	0	ENST00000269571.5:c.811C>A	p.Leu271Met	p.L271M	ENST00000269571		271	Ctg/Atg	7/27	1	2	FACETS	0.883	0.785	0.988	0.883	0.785	0.988	CLONAL	1	TRUE	1	0.27	2		765	780	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40477041	40477041	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	96	631	0	ENST00000264657.5:c.1404T>G	p.Cys468Trp	p.C468W	ENST00000264657	NM_139276.2	468	tgT/tgG	16/24	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.27	2		631	698	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244242	41244242	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	82	452	0	ENST00000357654.3:c.3306T>G	p.Asn1102Lys	p.N1102K	ENST00000357654	NM_007294.3	1102	aaT/aaG	10/23	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.27	2		452	596	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804162	46804162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	62	637	0	ENST00000290295.7:c.845C>T	p.Ala282Val	p.A282V	ENST00000290295	NM_006361.5	282	gCt/gTt	2/2	1	2	FACETS	0.885	0.765	1	0.885	0.765	1	CLONAL	1	TRUE	1	0.27	2		637	519	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56801451	56801451	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781287	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	74	449	0	ENST00000337432.4:c.955C>T	p.Arg319Ter	p.R319*	ENST00000337432	NM_058216.2	319	Cga/Tga	7/9	1	2	FACETS	0.942	0.825	1	0.942	0.825	1	CLONAL	1	TRUE	1	0.27	2		449	582	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761469	59761469	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	70	359	0	ENST00000259008.2:c.2938G>T	p.Ala980Ser	p.A980S	ENST00000259008	NM_032043.2	980	Gca/Tca	20/20	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.27	2		359	508	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763302	59763302	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs863224801	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	89	439	0	ENST00000259008.2:c.2800T>G	p.Phe934Val	p.F934V	ENST00000259008	NM_032043.2	934	Ttt/Gtt	19/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.27	2		439	611	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66525064	66525064	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	79	495	0	ENST00000358598.2:c.823C>T	p.Gln275Ter	p.Q275*	ENST00000358598	NM_212471.2	275	Cag/Tag	9/11	1	2	FACETS	0.888	0.781	1	0.888	0.781	1	CLONAL	1	TRUE	1	0.27	2		495	659	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857603	78857603	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	88	606	0	ENST00000306801.3:c.1673T>G	p.Leu558Arg	p.L558R	ENST00000306801	NM_020761.2	558	cTc/cGc	16/34	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.27	2		606	572	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923252	78923252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	47	519	0	ENST00000306801.3:c.3275C>T	p.Ala1092Val	p.A1092V	ENST00000306801	NM_020761.2	1092	gCc/gTc	28/34	1	2	FACETS	0.645	0.544	0.756	0.645	0.544	0.756	SUBCLONAL	1	TRUE	1	0.27	2		519	540	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736915	736915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs910562293	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	63	358	0	ENST00000314574.4:c.1184G>A	p.Arg395Gln	p.R395Q	ENST00000314574	NM_005433.3	395	cGa/cAa	10/12	1	2	FACETS	0.935	0.81	1	0.935	0.81	1	CLONAL	1	TRUE	1	0.27	2		358	499	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1627411	1627411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377688933	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	93	690	3	ENST00000344749.5:c.313C>T	p.Arg105Trp	p.R105W	ENST00000344749	NM_001136139.2	105	Cgg/Tgg	6/19	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.27	2		693	637	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222934	5222934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768350891	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	102	665	0	ENST00000357368.4:c.2869G>A	p.Glu957Lys	p.E957K	ENST00000357368	NM_002850.3	957	Gag/Aag	18/38	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.27	2		665	579	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6222328	6222328	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141047642	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	39	775	0	ENST00000252674.7:c.914C>T	p.Ser305Leu	p.S305L	ENST00000252674	NM_005934.3	305	tCg/tTg	6/12	1	2	FACETS	0.41	0.339	0.49	0.41	0.339	0.49	SUBCLONAL	1	TRUE	1	0.27	2		775	704	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122673	7122673	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913139	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	86	632	0	ENST00000302850.5:c.3481G>A	p.Ala1161Thr	p.A1161T	ENST00000302850	NM_000208.2	1161	Gca/Aca	19/22	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.27	2		632	628	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032303	11032303	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	108	716	0	ENST00000327064.4:c.1697C>A	p.Ala566Asp	p.A566D	ENST00000327064	NM_199141.1	566	gCc/gAc	16/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.27	2		716	703	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132400	11132400	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	88	784	1	ENST00000358026.2:c.2617-1G>T		p.X873_splice	ENST00000358026	NM_001128849.1	873			1	2	FACETS	0.949	0.841	1	0.949	0.841	1	CLONAL	1	TRUE	1	0.27	2		785	687	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145624	11145624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555785361	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	96	616	0	ENST00000358026.2:c.3986G>A	p.Arg1329His	p.R1329H	ENST00000358026	NM_001128849.1	1329	cGc/cAc	29/36	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.27	2		616	666	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278149	15278149	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	82	643	0	ENST00000263388.2:c.5273C>A	p.Ala1758Asp	p.A1758D	ENST00000263388	NM_000435.2	1758	gCt/gAt	29/33	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.27	2		643	578	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290034	15290034	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258221482	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	92	899	0	ENST00000263388.2:c.3520C>T	p.Pro1174Ser	p.P1174S	ENST00000263388	NM_000435.2	1174	Ccc/Tcc	22/33	1	2	FACETS	0.877	0.779	0.982	0.877	0.779	0.982	CLONAL	1	TRUE	1	0.27	2		899	777	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303019	15303019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568361985	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	86	767	0	ENST00000263388.2:c.431G>A	p.Cys144Tyr	p.C144Y	ENST00000263388	NM_000435.2	144	tGc/tAc	4/33	1	2	FACETS	0.938	0.83	1	0.938	0.83	1	CLONAL	1	TRUE	1	0.27	2		767	679	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308368	15308368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	91	665	0	ENST00000263388.2:c.140G>A	p.Ser47Asn	p.S47N	ENST00000263388	NM_000435.2	47	aGc/aAc	2/33	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.27	2		665	576	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350060	15350060	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	55	601	0	ENST00000263377.2:c.3592A>G	p.Asn1198Asp	p.N1198D	ENST00000263377	NM_058243.2	1198	Aac/Gac	18/20	1	2	FACETS	0.694	0.593	0.804	0.694	0.593	0.804	SUBCLONAL	1	TRUE	1	0.27	2		601	587	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375223	15375223	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	84	541	0	ENST00000263377.2:c.1204A>G	p.Thr402Ala	p.T402A	ENST00000263377	NM_058243.2	402	Aca/Gca	6/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.27	2		541	543	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17947941	17947941	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	81	434	0	ENST00000458235.1:c.1783G>T	p.Asp595Tyr	p.D595Y	ENST00000458235	NM_000215.3	595	Gac/Tac	13/24	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.27	2		434	488	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954259	17954259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	92	643	1	ENST00000458235.1:c.350G>A	p.Arg117His	p.R117H	ENST00000458235	NM_000215.3	117	cGc/cAc	4/24	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.27	2		644	660	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278019	18278019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762411607	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	66	581	0	ENST00000222254.8:c.1639C>T	p.Arg547Trp	p.R547W	ENST00000222254	NM_005027.3	547	Cgg/Tgg	13/16	1	2	FACETS	0.847	0.736	0.968	0.847	0.736	0.968	CLONAL	1	TRUE	1	0.27	2		581	577	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36208925	36208925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	42	410	0	ENST00000222270.7:c.5C>T	p.Ala2Val	p.A2V	ENST00000222270	NM_014727.1	2	gCg/gTg	1/37	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.27	2		410	286	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210694	36210694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1270556414	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	96	591	2	ENST00000222270.7:c.445C>T	p.Pro149Ser	p.P149S	ENST00000222270	NM_014727.1	149	Ccc/Tcc	3/37	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.27	2		593	642	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211341	36211341	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	119	705	0	ENST00000222270.7:c.1092G>T	p.Glu364Asp	p.E364D	ENST00000222270	NM_014727.1	364	gaG/gaT	3/37	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.27	2		705	763	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212417	36212417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1319017297	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	78	769	0	ENST00000222270.7:c.2168G>A	p.Gly723Glu	p.G723E	ENST00000222270	NM_014727.1	723	gGg/gAg	3/37	1	2	FACETS	0.807	0.709	0.913	0.807	0.709	0.913	CLONAL	1	TRUE	1	0.27	2		769	716	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216388	36216388	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	99	635	0	ENST00000222270.7:c.3651C>A	p.Phe1217Leu	p.F1217L	ENST00000222270	NM_014727.1	1217	ttC/ttA	12/37	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.27	2		635	649	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216465	36216465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	76	701	0	ENST00000222270.7:c.3728C>T	p.Thr1243Ile	p.T1243I	ENST00000222270	NM_014727.1	1243	aCc/aTc	12/37	1	2	FACETS	0.816	0.715	0.924	0.816	0.715	0.924	CLONAL	1	TRUE	1	0.27	2		701	690	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216480	36216480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	68	669	2	ENST00000222270.7:c.3743G>A	p.Arg1248His	p.R1248H	ENST00000222270	NM_014727.1	1248	cGc/cAc	12/37	1	2	FACETS	0.788	0.686	0.899	0.788	0.686	0.899	SUBCLONAL	1	TRUE	1	0.27	2		671	639	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40744812	40744812	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	80	676	1	ENST00000392038.2:c.708G>T	p.Glu236Asp	p.E236D	ENST00000392038	NM_001626.4	236	gaG/gaT	8/14	1	2	FACETS	0.97	0.855	1	0.97	0.855	1	CLONAL	1	TRUE	1	0.27	2		677	611	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758342	41758342	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	44	572	0	ENST00000301178.4:c.1798C>A	p.Leu600Ile	p.L600I	ENST00000301178	NM_021913.4	600	Ctc/Atc	15/20	1	2	FACETS	0.58	0.486	0.684	0.58	0.486	0.684	SUBCLONAL	1	TRUE	1	0.27	2		572	562	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754683	42754683	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	51	368	0	ENST00000222329.4:c.57G>T	p.Glu19Asp	p.E19D	ENST00000222329	NM_006494.2	19	gaG/gaT	2/4	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.27	2		368	375	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794583	42794583	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	46	700	0	ENST00000575354.2:c.1663G>T	p.Gly555Ter	p.G555*	ENST00000575354	NM_015125.3	555	Gga/Tga	10/20	1	2	FACETS	0.497	0.417	0.585	0.497	0.417	0.585	SUBCLONAL	1	TRUE	1	0.27	2		700	686	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794934	42794934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	92	785	0	ENST00000575354.2:c.2014G>A	p.Val672Ile	p.V672I	ENST00000575354	NM_015125.3	672	Gtc/Atc	10/20	1	2	FACETS	0.979	0.87	1	0.979	0.87	1	CLONAL	1	TRUE	1	0.27	2		785	696	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798450	42798450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142012810	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	81	636	0	ENST00000575354.2:c.4321C>T	p.Arg1441Cys	p.R1441C	ENST00000575354	NM_015125.3	1441	Cgt/Tgt	18/20	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.27	2		636	598	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918754	50918754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754832710	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	74	611	0	ENST00000440232.2:c.2624G>A	p.Arg875His	p.R875H	ENST00000440232	NM_002691.3	875	cGc/cAc	21/27	1	2	FACETS	0.977	0.857	1	0.977	0.857	1	CLONAL	1	TRUE	1	0.27	2		611	561	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716250	52716250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769334090	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	100	710	1	ENST00000322088.6:c.694G>A	p.Ala232Thr	p.A232T	ENST00000322088	NM_014225.5	232	Gcc/Acc	6/15	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.27	2		711	735	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469130	25469130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	89	631	0	ENST00000264709.3:c.1328C>A	p.Pro443His	p.P443H	ENST00000264709	NM_175629.2	443	cCt/cAt	11/23	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.27	2		631	627	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965401	25965401	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	118	695	0	ENST00000435504.4:c.3805G>A	p.Ala1269Thr	p.A1269T	ENST00000435504		1269	Gca/Aca	13/13	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.27	2		695	823	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451853	29451853	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	64	435	0	ENST00000389048.3:c.2712T>G	p.His904Gln	p.H904Q	ENST00000389048	NM_004304.4	904	caT/caG	16/29	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.27	2		435	426	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39283895	39283895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761951846	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	68	281	0	ENST00000402219.2:c.458G>A	p.Arg153Gln	p.R153Q	ENST00000402219	NM_005633.3	153	cGg/cAg	4/23	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.27	2		281	465	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574097	46574097	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	92	677	0	ENST00000263734.3:c.112G>A	p.Ala38Thr	p.A38T	ENST00000263734	NM_001430.4	38	Gcc/Acc	2/16	1	2	FACETS	0.948	0.842	1	0.948	0.842	1	CLONAL	1	TRUE	1	0.27	2		677	719	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47601031	47601031	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587780764	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	88	531	0	ENST00000263735.4:c.269A>G	p.Asn90Ser	p.N90S	ENST00000263735	NM_002354.2	90	aAc/aGc	3/9	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.27	2		531	647	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47602407	47602407	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	65	270	0	ENST00000263735.4:c.460G>T	p.Glu154Ter	p.E154*	ENST00000263735	NM_002354.2	154	Gaa/Taa	4/9	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.27	2		270	421	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635632	47635632	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	60	268	0	ENST00000233146.2:c.304G>T	p.Val102Phe	p.V102F	ENST00000233146	NM_000251.2	102	Gtt/Ttt	2/16	1	2	FACETS	0.932	0.804	1	0.932	0.804	1	CLONAL	1	TRUE	1	0.27	2		268	477	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47710020	47710020	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	25	249	0	ENST00000233146.2:c.2737G>T	p.Ala913Ser	p.A913S	ENST00000233146	NM_000251.2	913	Gct/Tct	16/16	1	2	FACETS	0.423	0.332	0.527	0.423	0.332	0.527	SUBCLONAL	1	TRUE	1	0.27	2		249	438	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027244	48027244	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1064795960	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	80	541	0	ENST00000234420.5:c.2122G>T	p.Glu708Ter	p.E708*	ENST00000234420	NM_000179.2	708	Gaa/Taa	4/10	1	2	FACETS	0.962	0.848	1	0.962	0.848	1	CLONAL	1	TRUE	1	0.27	2		541	616	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027317	48027317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749746725	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	81	608	1	ENST00000234420.5:c.2195G>A	p.Arg732Gln	p.R732Q	ENST00000234420	NM_000179.2	732	cGa/cAa	4/10	1	2	FACETS	0.893	0.787	1	0.893	0.787	1	CLONAL	1	TRUE	1	0.27	2		609	672	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149129	61149129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144119768	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	54	649	0	ENST00000295025.8:c.1319C>T	p.Ser440Leu	p.S440L	ENST00000295025	NM_002908.2	440	tCg/tTg	11/11	1	2	FACETS	0.554	0.472	0.644	0.554	0.472	0.644	SUBCLONAL	1	TRUE	1	0.27	2		649	722	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711081	61711081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs996736538	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	61	387	0	ENST00000401558.2:c.2668G>A	p.Ala890Thr	p.A890T	ENST00000401558	NM_003400.3	890	Gca/Aca	21/25	0.3	4	FACETS	1	0.944	1			1	CLONAL	1	TRUE	NA	0.27	4		387	485	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	40	303	0	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	0.3	4	FACETS	0.814	0.677	0.968			1	CLONAL	1	TRUE	NA	0.27	4		303	462	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67626754	67626754	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	46	152	0	ENST00000272342.5:c.425C>A	p.Pro142His	p.P142H	ENST00000272342	NM_019002.3	142	cCt/cAt	3/6	1	2	FACETS	0.89	0.751	1	0.89	0.751	1	CLONAL	1	TRUE	1	0.27	2		152	383	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630599	67630599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	45	419	0	ENST00000272342.5:c.785C>T	p.Ser262Phe	p.S262F	ENST00000272342	NM_019002.3	262	tCt/tTt	5/6	1	2	FACETS	0.527	0.442	0.622	0.527	0.442	0.622	SUBCLONAL	1	TRUE	1	0.27	2		419	632	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630625	67630625	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	79	456	0	ENST00000272342.5:c.811C>T	p.Gln271Ter	p.Q271*	ENST00000272342	NM_019002.3	271	Cag/Tag	5/6	1	2	FACETS	0.902	0.793	1	0.902	0.793	1	CLONAL	1	TRUE	1	0.27	2		456	649	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67632141	67632141	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	83	313	0	ENST00000272342.5:c.2327T>C	p.Leu776Ser	p.L776S	ENST00000272342	NM_019002.3	776	tTg/tCg	5/6	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.27	2		313	514	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96930970	96930970	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	86	660	0	ENST00000258439.3:c.150G>T	p.Glu50Asp	p.E50D	ENST00000258439	NM_001193304.2	50	gaG/gaT	2/4	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.27	2		660	596	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99181174	99181174	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	101	652	0	ENST00000074304.5:c.2115G>T	p.Gln705His	p.Q705H	ENST00000074304	NM_001134224.1	705	caG/caT	20/26	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.27	2		652	625	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99204026	99204026	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	27	465	0	ENST00000074304.5:c.2889G>T	p.Lys963Asn	p.K963N	ENST00000074304	NM_001134224.1	963	aaG/aaT	26/26	1	2	FACETS	0.372	0.295	0.46	0.372	0.295	0.46	SUBCLONAL	1	TRUE	1	0.27	2		465	538	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907686	111907686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370016302	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	90	582	1	ENST00000393256.3:c.460C>T	p.Arg154Cys	p.R154C	ENST00000393256	NM_006538.4	154	Cgt/Tgt	3/4	1	2	FACETS	0.978	0.868	1	0.978	0.868	1	CLONAL	1	TRUE	1	0.27	2		583	682	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046272	128046272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745564603	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	86	572	0	ENST00000285398.2:c.991G>A	p.Gly331Arg	p.G331R	ENST00000285398	NM_000122.1	331	Ggg/Agg	7/15	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.27	2		572	606	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728565	190728565	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs764521118	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	73	556	0	ENST00000441310.2:c.1958del	p.Lys653ArgfsTer2	p.K653Rfs*2	ENST00000441310	NM_000534.4	651	agA/ag	10/13	1	2	FACETS	0.819	0.716	0.93	0.819	0.716	0.93	CLONAL	1	TRUE	1	0.27	2		556	660	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268478	198268478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	31	468	0	ENST00000335508.6:c.1550G>A	p.Arg517His	p.R517H	ENST00000335508	NM_012433.2	517	cGt/cAt	12/25	1	2	FACETS	0.435	0.351	0.53	0.435	0.351	0.53	SUBCLONAL	1	TRUE	1	0.27	2		468	528	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273120	198273120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	103	554	0	ENST00000335508.6:c.1090G>A	p.Ala364Thr	p.A364T	ENST00000335508	NM_012433.2	364	Gcc/Acc	8/25	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.27	2		554	679	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202122968	202122968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	99	597	0	ENST00000358485.4:c.14G>A	p.Arg5Lys	p.R5K	ENST00000358485	NM_001080125.1	5	aGa/aAa	1/9	1	2	FACETS	0.983	0.878	1	0.983	0.878	1	CLONAL	1	TRUE	1	0.27	2		597	746	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149741	202149741	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	62	760	0	ENST00000358485.4:c.1182G>T	p.Glu394Asp	p.E394D	ENST00000358485	NM_001080125.1	394	gaG/gaT	8/9	1	2	FACETS	0.593	0.511	0.682	0.593	0.511	0.682	SUBCLONAL	1	TRUE	1	0.27	2		760	775	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652847	212652847	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	69	442	0	ENST00000342788.4:c.459A>T	p.Lys153Asn	p.K153N	ENST00000342788	NM_005235.2	153	aaA/aaT	4/28	1	2	FACETS	0.985	0.859	1	0.985	0.859	1	CLONAL	1	TRUE	1	0.27	2		442	519	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645765	215645765	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	86	564	0	ENST00000260947.4:c.833T>C	p.Val278Ala	p.V278A	ENST00000260947	NM_000465.2	278	gTc/gCc	4/11	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.27	2		564	637	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657077	215657077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145629242	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	66	500	0	ENST00000260947.4:c.308G>A	p.Ser103Asn	p.S103N	ENST00000260947	NM_000465.2	103	aGc/aAc	3/11	1	2	FACETS	0.875	0.76	0.999	0.875	0.76	0.999	CLONAL	1	TRUE	1	0.27	2		500	559	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339003	225339003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	64	469	0	ENST00000264414.4:c.2266C>T	p.Arg756Ter	p.R756*	ENST00000264414	NM_003590.4	756	Cga/Tga	16/16	1	2	FACETS	0.884	0.767	1	0.884	0.767	1	CLONAL	1	TRUE	1	0.27	2		469	536	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242800920	242800920	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	64	664	1	ENST00000334409.5:c.71T>A	p.Phe24Tyr	p.F24Y	ENST00000334409	NM_005018.2	24	tTc/tAc	1/5	1	2	FACETS	0.862	0.747	0.986	0.862	0.747	0.986	CLONAL	1	TRUE	1	0.27	2		665	550	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560890	9560890	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	75	698	0	ENST00000353224.5:c.892C>A	p.Pro298Thr	p.P298T	ENST00000353224	NM_177990.2	298	Cca/Aca	4/10	1	2	FACETS	0.809	0.708	0.917	0.809	0.708	0.917	CLONAL	1	TRUE	1	0.27	2		698	687	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023577	31023577	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	87	608	0	ENST00000375687.4:c.3062C>A	p.Ala1021Asp	p.A1021D	ENST00000375687	NM_015338.5	1021	gCt/gAt	13/13	1	2	FACETS	0.984	0.872	1	0.984	0.872	1	CLONAL	1	TRUE	1	0.27	2		608	655	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012647	36012647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1437496392	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	78	581	2	ENST00000358208.4:c.91G>A	p.Ala31Thr	p.A31T	ENST00000358208		31	Gct/Act	2/12	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.27	2		583	555	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026110	36026110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1433113895	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	93	634	0	ENST00000358208.4:c.712G>A	p.Asp238Asn	p.D238N	ENST00000358208		238	Gat/Aat	7/12	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.27	2		634	630	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031235	36031235	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	54	612	0	ENST00000358208.4:c.1354G>A	p.Gly452Arg	p.G452R	ENST00000358208		452	Ggg/Agg	11/12	1	2	FACETS	0.727	0.621	0.843	0.727	0.621	0.843	SUBCLONAL	1	TRUE	1	0.27	2		612	550	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39751897	39751897	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	69	564	0	ENST00000361337.2:c.2258C>T	p.Ala753Val	p.A753V	ENST00000361337	NM_003286.2	753	gCc/gTc	21/21	0.109974236728309	0	FACETS	0.612	0.533	0.697			1	INDETERMINATE	1	TRUE	0	0.27	0		564	610	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408893	41408893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	71	500	0	ENST00000373198.4:c.533C>T	p.Ala178Val	p.A178V	ENST00000373198	NM_133170.3	178	gCc/gTc	4/32	0.109974236728309	0	FACETS	0.774	0.677	0.878			1	INDETERMINATE	1	TRUE	0	0.27	0		500	496	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256699	46256699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749607074	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	93	406	0	ENST00000371998.3:c.755G>A	p.Arg252His	p.R252H	ENST00000371998		252	cGc/cAc	8/23	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.27	2		406	564	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164889	36164889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1358657401	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	104	625	0	ENST00000300305.3:c.986C>T	p.Ala329Val	p.A329V	ENST00000300305		329	gCg/gTg	8/8	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.27	2		625	733	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866282	42866282	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	84	644	0	ENST00000398585.3:c.349+1G>T		p.X117_splice	ENST00000398585	NM_001135099.1	117			1	2	FACETS	0.999	0.883	1	0.999	0.883	1	CLONAL	1	TRUE	1	0.27	2		644	623	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21348931	21348931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372417941	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	99	744	0	ENST00000215739.8:c.1700G>A	p.Arg567His	p.R567H	ENST00000215739	NM_006767.3	567	cGc/cAc	15/21	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.27	2		744	703	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29107984	29107984	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	96	477	0	ENST00000328354.6:c.705G>T	p.Lys235Asn	p.K235N	ENST00000328354	NM_007194.3	235	aaG/aaT	6/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.27	2		477	562	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035183	30035183	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	80	528	0	ENST00000338641.4:c.345A>C	p.Gln115His	p.Q115H	ENST00000338641	NM_000268.3	115	caA/caC	3/16	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.27	2		528	590	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074284	30074284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762588182	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	76	540	0	ENST00000338641.4:c.1546C>T	p.Arg516Trp	p.R516W	ENST00000338641	NM_000268.3	516	Cgg/Tgg	14/16	1	2	FACETS	0.941	0.826	1	0.941	0.826	1	CLONAL	1	TRUE	1	0.27	2		540	598	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077532	30077532	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	83	641	0	ENST00000338641.4:c.1679T>A	p.Ile560Asn	p.I560N	ENST00000338641	NM_000268.3	560	aTt/aAt	15/16	1	2	FACETS	0.95	0.839	1	0.95	0.839	1	CLONAL	1	TRUE	1	0.27	2		641	647	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41562638	41562638	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764929476	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	59	217	0	ENST00000263253.7:c.3842G>A	p.Arg1281Gln	p.R1281Q	ENST00000263253	NM_001429.3	1281	cGa/cAa	23/31	0.3	3	FACETS	1	0.927	1			1	CLONAL	1	TRUE	NA	0.27	3		217	444	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183691	10183691	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	33	621	0	ENST00000256474.2:c.160A>G	p.Met54Val	p.M54V	ENST00000256474	NM_000551.3	54	Atg/Gtg	1/3	1	2	FACETS	0.424	0.345	0.515	0.424	0.345	0.515	SUBCLONAL	1	TRUE	1	0.27	2		621	576	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191507	10191507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs5030821	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	21	312	0	ENST00000256474.2:c.500G>A	p.Arg167Gln	p.R167Q	ENST00000256474	NM_000551.3	167	cGg/cAg	3/3	1	2	FACETS	0.255	0.195	0.325	0.255	0.195	0.325	SUBCLONAL	1	TRUE	1	0.27	2		312	611	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067388	37067388	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	82	641	0	ENST00000231790.2:c.1299A>C	p.Glu433Asp	p.E433D	ENST00000231790	NM_000249.3	433	gaA/gaC	12/19	1	2	FACETS	0.912	0.804	1	0.912	0.804	1	CLONAL	1	TRUE	1	0.27	2		641	666	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090398	37090398	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1251779788	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	82	419	0	ENST00000231790.2:c.1993A>G	p.Asn665Asp	p.N665D	ENST00000231790	NM_000249.3	665	Aat/Gat	18/19	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.27	2		419	478	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098949	47098949	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	86	475	1	ENST00000409792.3:c.6325C>T	p.Arg2109Ter	p.R2109*	ENST00000409792	NM_014159.6	2109	Cga/Tga	15/21	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.27	2		476	589	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936346	49936346	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1299694918	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	102	893	0	ENST00000296474.3:c.1502A>G	p.Asp501Gly	p.D501G	ENST00000296474	NM_002447.2	501	gAt/gGt	3/20	1	2	FACETS	0.942	0.842	1	0.942	0.842	1	CLONAL	1	TRUE	1	0.27	2		893	802	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643331	52643331	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	78	390	0	ENST00000394830.3:c.2565T>G	p.Asn855Lys	p.N855K	ENST00000394830	NM_018313.4	855	aaT/aaG	17/30	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.27	2		390	513	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643893	52643893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	84	390	0	ENST00000394830.3:c.2003C>T	p.Ala668Val	p.A668V	ENST00000394830	NM_018313.4	668	gCt/gTt	17/30	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.27	2		390	508	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63973760	63973760	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	72	561	0	ENST00000398590.3:c.1121C>A	p.Ala374Asp	p.A374D	ENST00000398590	NM_001177387.1	374	gCt/gAt	9/14	1	2	FACETS	0.772	0.674	0.878	0.772	0.674	0.878	SUBCLONAL	1	TRUE	1	0.27	2		561	691	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63973837	63973837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	83	663	0	ENST00000398590.3:c.1198C>T	p.Arg400Cys	p.R400C	ENST00000398590	NM_001177387.1	400	Cgc/Tgc	9/14	1	2	FACETS	0.878	0.775	0.989	0.878	0.775	0.989	CLONAL	1	TRUE	1	0.27	2		663	700	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015044	71015044	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754297044	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	93	510	0	ENST00000318789.4:c.1886C>T	p.Ala629Val	p.A629V	ENST00000318789	NM_032682.5	629	gCc/gTc	20/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.27	2		510	575	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72891538	72891538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs529764235	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	75	543	0	ENST00000325599.8:c.224G>A	p.Arg75His	p.R75H	ENST00000325599	NM_018130.2	75	cGc/cAc	3/11	1	2	FACETS	0.953	0.836	1	0.953	0.836	1	CLONAL	1	TRUE	1	0.27	2		543	583	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259587	89259587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	70	611	0	ENST00000336596.2:c.731G>A	p.Cys244Tyr	p.C244Y	ENST00000336596	NM_005233.5	244	tGc/tAc	3/17	1	2	FACETS	0.851	0.743	0.969	0.851	0.743	0.969	CLONAL	1	TRUE	1	0.27	2		611	609	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521680	89521680	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	50	567	0	ENST00000336596.2:c.2757G>A	p.Trp919Ter	p.W919*	ENST00000336596	NM_005233.5	919	tgG/tgA	16/17	1	2	FACETS	0.536	0.454	0.627	0.536	0.454	0.627	SUBCLONAL	1	TRUE	1	0.27	2		567	691	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631633	119631633	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	32	423	0	ENST00000316626.5:c.633A>C	p.Glu211Asp	p.E211D	ENST00000316626		211	gaA/gaC	6/12	1	2	FACETS	0.428	0.346	0.52	0.428	0.346	0.52	SUBCLONAL	1	TRUE	1	0.27	2		423	554	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911466	134911466	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	75	628	0	ENST00000398015.3:c.1931G>T	p.Arg644Met	p.R644M	ENST00000398015	NM_004441.4	644	aGg/aTg	11/16	1	2	FACETS	0.914	0.801	1	0.914	0.801	1	CLONAL	1	TRUE	1	0.27	2		628	608	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911488	134911488	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	35	599	1	ENST00000398015.3:c.1953G>T	p.Lys651Asn	p.K651N	ENST00000398015	NM_004441.4	651	aaG/aaT	11/16	1	2	FACETS	0.456	0.373	0.55	0.456	0.373	0.55	SUBCLONAL	1	TRUE	1	0.27	2		600	568	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664959	138664959	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	64	521	0	ENST00000330315.3:c.606C>A	p.Asn202Lys	p.N202K	ENST00000330315	NM_023067.3	202	aaC/aaA	1/1	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.27	2		521	437	SUCCESS
ATR	545	MSKCC	GRCh37	3	142168375	142168375	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	74	421	0	ENST00000350721.4:c.7831G>T	p.Gly2611Ter	p.G2611*	ENST00000350721	NM_001184.3	2611	Gga/Tga	47/47	1	2	FACETS	0.982	0.861	1	0.982	0.861	1	CLONAL	1	TRUE	1	0.27	2		421	558	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430887	181430887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	127	869	0	ENST00000325404.1:c.739G>A	p.Glu247Lys	p.E247K	ENST00000325404	NM_003106.3	247	Gag/Aag	1/1	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.27	2		869	764	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506990	186506990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	94	521	0	ENST00000323963.5:c.1156C>T	p.Arg386Cys	p.R386C	ENST00000323963		386	Cgt/Tgt	11/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.27	2		521	627	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446845	187446845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201771435	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	88	644	0	ENST00000232014.4:c.1348G>A	p.Val450Ile	p.V450I	ENST00000232014	NM_001130845.1	450	Gtt/Att	5/10	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.27	2		644	644	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586449	189586449	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	111	613	0	ENST00000264731.3:c.1073G>T	p.Ser358Ile	p.S358I	ENST00000264731	NM_003722.4	358	aGc/aTc	8/14	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.27	2		613	718	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1800997	1800997	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs770464815	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	101	668	0	ENST00000260795.2:c.126G>T	p.Glu42Asp	p.E42D	ENST00000260795		42	gaG/gaT	2/17	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.27	2		668	642	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156637	55156637	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1307047645	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	83	631	0	ENST00000257290.5:c.3038G>T	p.Ser1013Ile	p.S1013I	ENST00000257290	NM_006206.4	1013	aGc/aTc	22/23	1	2	FACETS	0.87	0.767	0.979	0.87	0.767	0.979	CLONAL	1	TRUE	1	0.27	2		631	707	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604659	55604659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139694927	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	84	567	0	ENST00000288135.5:c.2867G>A	p.Arg956Gln	p.R956Q	ENST00000288135	NM_000222.2	956	cGg/cAg	21/21	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.27	2		567	581	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231715	66231715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458893557	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	70	426	0	ENST00000273854.3:c.1985C>T	p.Ala662Val	p.A662V	ENST00000273854	NM_004439.5	662	gCt/gTt	11/18	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.27	2		426	511	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270150	66270150	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	82	521	0	ENST00000273854.3:c.1732T>C	p.Ser578Pro	p.S578P	ENST00000273854	NM_004439.5	578	Tct/Cct	8/18	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.27	2		521	599	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286196	66286196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	68	425	0	ENST00000273854.3:c.1490G>A	p.Gly497Glu	p.G497E	ENST00000273854	NM_004439.5	497	gGa/gAa	6/18	1	2	FACETS	0.992	0.864	1	0.992	0.864	1	CLONAL	1	TRUE	1	0.27	2		425	508	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467964	66467964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	62	450	0	ENST00000273854.3:c.305G>A	p.Cys102Tyr	p.C102Y	ENST00000273854	NM_004439.5	102	tGc/tAc	3/18	1	2	FACETS	0.801	0.693	0.92	0.801	0.693	0.92	CLONAL	1	TRUE	1	0.27	2		450	573	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535337	66535337	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	66	637	1	ENST00000273854.3:c.124A>G	p.Thr42Ala	p.T42A	ENST00000273854	NM_004439.5	42	Acg/Gcg	1/18	1	2	FACETS	0.907	0.788	1	0.907	0.788	1	CLONAL	1	TRUE	1	0.27	2		638	539	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114268	143114268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	50	434	0	ENST00000262992.4:c.1153C>T	p.Leu385Phe	p.L385F	ENST00000262992	NM_001101669.1	385	Ctc/Ttc	13/24	1	2	FACETS	0.756	0.642	0.881	0.756	0.642	0.881	SUBCLONAL	1	TRUE	1	0.27	2		434	490	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249457	153249457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	84	518	0	ENST00000281708.4:c.1321C>T	p.Arg441Trp	p.R441W	ENST00000281708	NM_033632.3	441	Cgg/Tgg	9/12	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.27	2		518	602	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510062	187510062	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	89	622	0	ENST00000441802.2:c.13451T>C	p.Phe4484Ser	p.F4484S	ENST00000441802	NM_005245.3	4484	tTc/tCc	27/27	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.27	2		622	621	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510264	187510264	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	82	571	1	ENST00000441802.2:c.13249C>A	p.Pro4417Thr	p.P4417T	ENST00000441802	NM_005245.3	4417	Cca/Aca	27/27	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.27	2		572	529	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530348	187530348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768392442	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	83	599	0	ENST00000441802.2:c.10195G>A	p.Asp3399Asn	p.D3399N	ENST00000441802	NM_005245.3	3399	Gac/Aac	16/27	1	2	FACETS	0.982	0.867	1	0.982	0.867	1	CLONAL	1	TRUE	1	0.27	2		599	626	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532728	187532728	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	87	608	0	ENST00000441802.2:c.9665A>G	p.Asp3222Gly	p.D3222G	ENST00000441802	NM_005245.3	3222	gAc/gGc	14/27	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.27	2		608	626	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542790	187542790	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	79	577	0	ENST00000441802.2:c.4950A>G	p.Ile1650Met	p.I1650M	ENST00000441802	NM_005245.3	1650	atA/atG	10/27	1	2	FACETS	0.927	0.816	1	0.927	0.816	1	CLONAL	1	TRUE	1	0.27	2		577	631	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549490	187549490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1050292453	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	92	654	1	ENST00000441802.2:c.4628G>A	p.Arg1543His	p.R1543H	ENST00000441802	NM_005245.3	1543	cGc/cAc	9/27	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.27	2		655	637	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271253	1271253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778051907	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	40	549	1	ENST00000310581.5:c.2449G>A	p.Ala817Thr	p.A817T	ENST00000310581	NM_198253.2	817	Gcc/Acc	8/16	1	2	FACETS	0.64	0.532	0.76	0.64	0.532	0.76	SUBCLONAL	1	TRUE	1	0.27	2		550	463	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294191	1294191	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	102	724	0	ENST00000310581.5:c.810C>A	p.Phe270Leu	p.F270L	ENST00000310581	NM_198253.2	270	ttC/ttA	2/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.27	2		724	667	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410963	31410963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	89	655	0	ENST00000344624.3:c.3557C>T	p.Thr1186Ile	p.T1186I	ENST00000344624		1186	aCt/aTt	28/33	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.27	2		655	644	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468160	31468160	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	74	423	0	ENST00000344624.3:c.2252C>A	p.Ser751Tyr	p.S751Y	ENST00000344624		751	tCt/tAt	15/33	1	2	FACETS	0.993	0.871	1	0.993	0.871	1	CLONAL	1	TRUE	1	0.27	2		423	552	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867418	35867418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200687605	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	79	518	0	ENST00000303115.3:c.232G>A	p.Val78Met	p.V78M	ENST00000303115	NM_002185.3	78	Gtg/Atg	3/8	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.27	2		518	581	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867543	35867543	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	72	314	0	ENST00000303115.3:c.357A>C	p.Lys119Asn	p.K119N	ENST00000303115	NM_002185.3	119	aaA/aaC	3/8	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.27	2		314	456	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950267	38950267	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	98	543	1	ENST00000357387.3:c.3683G>A	p.Gly1228Asp	p.G1228D	ENST00000357387	NM_152756.3	1228	gGc/gAc	31/38	1	2	FACETS	0.976	0.87	1	0.976	0.87	1	CLONAL	1	TRUE	1	0.27	2		544	744	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959996	38959996	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	54	401	0	ENST00000357387.3:c.1936C>A	p.Leu646Ile	p.L646I	ENST00000357387	NM_152756.3	646	Ctt/Att	21/38	1	2	FACETS	0.825	0.705	0.955	0.825	0.705	0.955	CLONAL	1	TRUE	1	0.27	2		401	485	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963109	38963109	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	35	399	0	ENST00000357387.3:c.1435T>G	p.Phe479Val	p.F479V	ENST00000357387	NM_152756.3	479	Ttc/Gtc	17/38	1	2	FACETS	0.439	0.359	0.53	0.439	0.359	0.53	SUBCLONAL	1	TRUE	1	0.27	2		399	590	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152530	56152530	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	100	609	0	ENST00000399503.3:c.586G>T	p.Ala196Ser	p.A196S	ENST00000399503	NM_005921.1	196	Gcc/Tcc	2/20	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.27	2		609	731	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160643	56160643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375262853	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	124	639	0	ENST00000399503.3:c.917G>A	p.Arg306His	p.R306H	ENST00000399503	NM_005921.1	306	cGc/cAc	4/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.27	2		639	801	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	78	364	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.27	2		364	565	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86676375	86676375	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	65	374	0	ENST00000274376.6:c.2653T>C	p.Trp885Arg	p.W885R	ENST00000274376	NM_002890.2	885	Tgg/Cgg	20/25	1	2	FACETS	0.942	0.818	1	0.942	0.818	1	CLONAL	1	TRUE	1	0.27	2		374	511	SUCCESS
APC	324	MSKCC	GRCh37	5	112177788	112177788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752091655	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	77	413	0	ENST00000257430.4:c.6497G>A	p.Arg2166Gln	p.R2166Q	ENST00000257430	NM_000038.5	2166	cGa/cAa	16/16	1	2	FACETS	0.985	0.866	1	0.985	0.866	1	CLONAL	1	TRUE	1	0.27	2		413	579	SUCCESS
APC	324	MSKCC	GRCh37	5	112179011	112179011	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876659753	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	85	446	0	ENST00000257430.4:c.7720C>A	p.Leu2574Ile	p.L2574I	ENST00000257430	NM_000038.5	2574	Ctt/Att	16/16	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.27	2		446	623	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131895051	131895051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370769989	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	52	194	0	ENST00000265335.6:c.205G>A	p.Asp69Asn	p.D69N	ENST00000265335		69	Gat/Aat	2/25	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.27	2		194	343	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977969	131977969	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	70	416	0	ENST00000265335.6:c.3852G>T	p.Glu1284Asp	p.E1284D	ENST00000265335		1284	gaG/gaT	25/25	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.27	2		416	496	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435835	149435835	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	105	605	0	ENST00000286301.3:c.2389T>A	p.Phe797Ile	p.F797I	ENST00000286301	NM_005211.3	797	Ttc/Atc	18/22	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.27	2		605	581	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449847	149449847	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	91	779	0	ENST00000286301.3:c.1217T>A	p.Val406Asp	p.V406D	ENST00000286301	NM_005211.3	406	gTc/gAc	9/22	1	2	FACETS	0.96	0.853	1	0.96	0.853	1	CLONAL	1	TRUE	1	0.27	2		779	702	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497347	149497347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140261309	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	80	615	1	ENST00000261799.4:c.2971C>T	p.Arg991Cys	p.R991C	ENST00000261799	NM_002609.3	991	Cgc/Tgc	22/23	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.27	2		616	588	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509413	149509413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1225116257	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	91	676	2	ENST00000261799.4:c.1486C>T	p.Arg496Cys	p.R496C	ENST00000261799	NM_002609.3	496	Cgt/Tgt	10/23	1	2	FACETS	0.921	0.818	1	0.921	0.818	1	CLONAL	1	TRUE	1	0.27	2		678	732	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524657	176524657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200649056	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	68	687	0	ENST00000292408.4:c.2389G>A	p.Gly797Arg	p.G797R	ENST00000292408	NM_213647.1	797	Ggg/Agg	18/18	1	2	FACETS	0.74	0.643	0.844	0.74	0.643	0.844	SUBCLONAL	1	TRUE	1	0.27	2		687	681	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637458	176637458	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	82	495	0	ENST00000439151.2:c.2058T>G	p.Tyr686Ter	p.Y686*	ENST00000439151	NM_022455.4	686	taT/taG	5/23	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.27	2		495	580	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707758	176707758	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064796690	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	116	597	0	ENST00000439151.2:c.5815C>T	p.Arg1939Cys	p.R1939C	ENST00000439151	NM_022455.4	1939	Cgc/Tgc	18/23	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.27	2		597	788	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046752	180046752	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	72	704	0	ENST00000261937.6:c.2560G>A	p.Gly854Ser	p.G854S	ENST00000261937	NM_182925.4	854	Ggc/Agc	18/30	1	2	FACETS	0.871	0.762	0.99	0.871	0.762	0.99	CLONAL	1	TRUE	1	0.27	2		704	612	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048772	180048772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758587669	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	88	678	0	ENST00000261937.6:c.1790C>T	p.Thr597Met	p.T597M	ENST00000261937	NM_182925.4	597	aCg/aTg	13/30	1	2	FACETS	0.953	0.845	1	0.953	0.845	1	CLONAL	1	TRUE	1	0.27	2		678	684	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021123	26021123	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	56	757	0	ENST00000357647.3:c.406G>A	p.Ala136Thr	p.A136T	ENST00000357647	NM_003529.2	136	Gcg/Acg	1/1	0.162131334930246	3	FACETS	0.599	0.512	0.695	0.3	0.256	0.348	SUBCLONAL	1	TRUE	1	0.27	3		757	786	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225573	26225573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343949085	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	140	838	0	ENST00000360408.1:c.191G>A	p.Arg64Gln	p.R64Q	ENST00000360408	NM_003532.2	64	cGg/cAg	1/1	0.162131334930246	3	FACETS	1	0.963	1	0.555	0.505	0.609	CLONAL	1	TRUE	1	0.27	3		838	1060	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858276	27858276	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs935367274	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	100	836	0	ENST00000359303.2:c.295G>A	p.Ala99Thr	p.A99T	ENST00000359303	NM_003535.2	99	Gcc/Acc	1/1	1	2	FACETS	0.838	0.748	0.934	0.838	0.748	0.934	CLONAL	1	TRUE	1	0.27	2		836	884	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672852	30672852	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	61	975	0	ENST00000376406.3:c.4108G>T	p.Ala1370Ser	p.A1370S	ENST00000376406	NM_014641.2	1370	Gcc/Tcc	10/15	1	2	FACETS	0.433	0.372	0.5	0.433	0.372	0.5	SUBCLONAL	1	TRUE	1	0.27	2		975	1043	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675746	30675746	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	44	524	0	ENST00000376406.3:c.2610G>T	p.Gln870His	p.Q870H	ENST00000376406	NM_014641.2	870	caG/caT	8/15	1	2	FACETS	0.441	0.369	0.522	0.441	0.369	0.522	SUBCLONAL	1	TRUE	1	0.27	2		524	739	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323230	31323230	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	95	600	1	ENST00000412585.2:c.759G>T	p.Glu253Asp	p.E253D	ENST00000412585	NM_005514.6	253	gaG/gaT	4/8	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.27	2		601	613	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165155	32165155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	101	696	0	ENST00000375023.3:c.4973C>T	p.Ala1658Val	p.A1658V	ENST00000375023	NM_004557.3	1658	gCc/gTc	27/30	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.27	2		696	710	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168682	32168682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs935064991	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	53	626	0	ENST00000375023.3:c.4241C>T	p.Ala1414Val	p.A1414V	ENST00000375023	NM_004557.3	1414	gCg/gTg	23/30	1	2	FACETS	0.569	0.484	0.662	0.569	0.484	0.662	SUBCLONAL	1	TRUE	1	0.27	2		626	690	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797789	32797789	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	77	586	0	ENST00000374899.4:c.1713C>A	p.Cys571Ter	p.C571*	ENST00000374899	NM_018833.2	571	tgC/tgA	10/12	1	2	FACETS	0.858	0.753	0.97	0.858	0.753	0.97	CLONAL	1	TRUE	1	0.27	2		586	665	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797867	32797867	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	70	561	0	ENST00000374899.4:c.1636-1G>T		p.X546_splice	ENST00000374899	NM_018833.2	546			1	2	FACETS	0.84	0.733	0.957	0.84	0.733	0.957	CLONAL	1	TRUE	1	0.27	2		561	617	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815426	32815426	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	74	536	0	ENST00000354258.4:c.1947G>T	p.Gln649His	p.Q649H	ENST00000354258	NM_000593.5	649	caG/caT	9/11	1	2	FACETS	0.915	0.802	1	0.915	0.802	1	CLONAL	1	TRUE	1	0.27	2		536	599	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43749695	43749695	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	96	663	0	ENST00000523873.1:c.548C>T	p.Pro183Leu	p.P183L	ENST00000523873		183	cCc/cTc	7/8	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.27	2		663	696	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790826	89790826	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	91	700	0	ENST00000336032.3:c.213G>T	p.Gln71His	p.Q71H	ENST00000336032	NM_006813.2	71	caG/caT	1/2	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.27	2		700	658	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793872	89793872	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	93	537	0	ENST00000336032.3:c.941T>C	p.Leu314Pro	p.L314P	ENST00000336032	NM_006813.2	314	cTg/cCg	2/2	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.27	2		537	635	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553145	106553145	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	98	723	0	ENST00000369096.4:c.1110C>A	p.His370Gln	p.H370Q	ENST00000369096	NM_001198.3	370	caC/caA	5/7	1	2	FACETS	0.974	0.869	1	0.974	0.869	1	CLONAL	1	TRUE	1	0.27	2		723	745	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322609	109322609	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	84	517	0	ENST00000436639.2:c.428T>C	p.Ile143Thr	p.I143T	ENST00000436639	NM_014454.2	143	aTt/aCt	3/10	1	2	FACETS	0.94	0.83	1	0.94	0.83	1	CLONAL	1	TRUE	1	0.27	2		517	662	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041037	112041037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761032788	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	85	647	0	ENST00000368678.4:c.218C>T	p.Thr73Met	p.T73M	ENST00000368678		73	aCg/aTg	3/13	1	2	FACETS	0.882	0.779	0.992	0.882	0.779	0.992	CLONAL	1	TRUE	1	0.27	2		647	714	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117629975	117629975	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	54	464	0	ENST00000368508.3:c.6551G>A	p.Arg2184Lys	p.R2184K	ENST00000368508	NM_002944.2	2184	aGa/aAa	41/43	1	2	FACETS	0.778	0.665	0.902	0.778	0.665	0.902	CLONAL	1	TRUE	1	0.27	2		464	514	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665225	117665225	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	32	355	0	ENST00000368508.3:c.4522C>A	p.Leu1508Met	p.L1508M	ENST00000368508	NM_002944.2	1508	Ctg/Atg	27/43	1	2	FACETS	0.464	0.376	0.564	0.464	0.376	0.564	SUBCLONAL	1	TRUE	1	0.27	2		355	511	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681518	117681518	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	46	400	0	ENST00000368508.3:c.3432G>T	p.Lys1144Asn	p.K1144N	ENST00000368508	NM_002944.2	1144	aaG/aaT	22/43	1	2	FACETS	0.725	0.611	0.851	0.725	0.611	0.851	SUBCLONAL	1	TRUE	1	0.27	2		400	470	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718076	117718076	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	65	370	0	ENST00000368508.3:c.779+2T>C		p.X260_splice	ENST00000368508	NM_002944.2	260			1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.27	2		370	443	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117746814	117746814	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	50	387	0	ENST00000368508.3:c.6G>T	p.Lys2Asn	p.K2N	ENST00000368508	NM_002944.2	2	aaG/aaT	1/43	1	2	FACETS	0.708	0.601	0.826	0.708	0.601	0.826	SUBCLONAL	1	TRUE	1	0.27	2		387	523	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199624	138199624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	109	576	0	ENST00000237289.4:c.1042C>T	p.Leu348Phe	p.L348F	ENST00000237289	NM_001270507.1	348	Ctt/Ttt	7/9	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.27	2		576	717	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200183	138200183	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	99	669	0	ENST00000237289.4:c.1601G>T	p.Gly534Val	p.G534V	ENST00000237289	NM_001270507.1	534	gGg/gTg	7/9	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.27	2		669	732	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202332	138202332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1016313423	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	79	733	0	ENST00000237289.4:c.2249G>A	p.Gly750Asp	p.G750D	ENST00000237289	NM_001270507.1	750	gGt/gAt	9/9	1	2	FACETS	0.814	0.715	0.92	0.814	0.715	0.92	CLONAL	1	TRUE	1	0.27	2		733	719	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983017	149983017	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757876116	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	77	496	0	ENST00000253339.5:c.3241C>T	p.Arg1081Ter	p.R1081*	ENST00000253339		1081	Cga/Tga	7/7	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.27	2		496	563	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001394	150001394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774100617	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	100	535	0	ENST00000253339.5:c.2210G>A	p.Arg737Gln	p.R737Q	ENST00000253339		737	cGa/cAa	4/7	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.27	2		535	645	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005711	150005711	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	92	478	0	ENST00000253339.5:c.514G>T	p.Val172Phe	p.V172F	ENST00000253339		172	Gtt/Ttt	3/7	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.27	2		478	628	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023004	150023004	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	81	516	0	ENST00000253339.5:c.259C>T	p.Pro87Ser	p.P87S	ENST00000253339		87	Cca/Tca	1/7	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.27	2		516	596	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265611	152265611	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	34	586	0	ENST00000206249.3:c.1064T>C	p.Val355Ala	p.V355A	ENST00000206249	NM_000125.3	355	gTt/gCt	4/8	1	2	FACETS	0.378	0.307	0.457	0.378	0.307	0.457	SUBCLONAL	1	TRUE	1	0.27	2		586	667	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528742	157528742	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	86	676	0	ENST00000346085.5:c.6467T>C	p.Ile2156Thr	p.I2156T	ENST00000346085	NM_020732.3	2156	aTt/aCt	20/20	1	2	FACETS	0.852	0.753	0.957	0.852	0.753	0.957	CLONAL	1	TRUE	1	0.27	2		676	748	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781125	161781125	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	80	494	0	ENST00000366898.1:c.1280A>C	p.Lys427Thr	p.K427T	ENST00000366898	NM_004562.2	427	aAa/aCa	11/12	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.27	2		494	566	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268956	55268956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1162232225	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	108	718	0	ENST00000275493.2:c.3022G>A	p.Asp1008Asn	p.D1008N	ENST00000275493	NM_005228.3	1008	Gac/Aac	25/28	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.27	2		718	773	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92244495	92244495	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	42	606	0	ENST00000265734.4:c.940C>A	p.Leu314Met	p.L314M	ENST00000265734	NM_001259.6	314	Ctg/Atg	8/8	1	2	FACETS	0.491	0.409	0.583	0.491	0.409	0.583	SUBCLONAL	1	TRUE	1	0.27	2		606	633	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508092	106508092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	37	608	0	ENST00000359195.3:c.86C>T	p.Ala29Val	p.A29V	ENST00000359195	NM_002649.2	29	gCg/gTg	2/11	1	2	FACETS	0.45	0.37	0.54	0.45	0.37	0.54	SUBCLONAL	1	TRUE	1	0.27	2		608	609	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508210	106508210	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	92	624	0	ENST00000359195.3:c.204G>T	p.Glu68Asp	p.E68D	ENST00000359195	NM_002649.2	68	gaG/gaT	2/11	1	2	FACETS	0.975	0.867	1	0.975	0.867	1	CLONAL	1	TRUE	1	0.27	2		624	699	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508451	106508451	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1192283060	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	71	556	0	ENST00000359195.3:c.445G>A	p.Ala149Thr	p.A149T	ENST00000359195	NM_002649.2	149	Gcc/Acc	2/11	1	2	FACETS	0.881	0.769	1	0.881	0.769	1	CLONAL	1	TRUE	1	0.27	2		556	597	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508893	106508893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	93	654	0	ENST00000359195.3:c.887G>A	p.Cys296Tyr	p.C296Y	ENST00000359195	NM_002649.2	296	tGc/tAc	2/11	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.27	2		654	685	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513165	106513165	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs778461029	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	81	507	0	ENST00000359195.3:c.2069G>T	p.Arg690Ile	p.R690I	ENST00000359195	NM_002649.2	690	aGa/aTa	4/11	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.27	2		507	596	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523578	106523578	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	90	527	0	ENST00000359195.3:c.2730G>A	p.Trp910Ter	p.W910*	ENST00000359195	NM_002649.2	910	tgG/tgA	8/11	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.27	2		527	646	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339979	116339979	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	76	497	0	ENST00000397752.3:c.841T>G	p.Phe281Val	p.F281V	ENST00000397752	NM_000245.2	281	Ttc/Gtc	2/21	1	2	FACETS	0.909	0.798	1	0.909	0.798	1	CLONAL	1	TRUE	1	0.27	2		497	619	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124503417	124503417	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	67	410	0	ENST00000357628.3:c.533C>A	p.Ser178Ter	p.S178*	ENST00000357628	NM_015450.2	178	tCa/tAa	8/19	1	2	FACETS	0.964	0.839	1	0.964	0.839	1	CLONAL	1	TRUE	1	0.27	2		410	515	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829251	128829251	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	30	617	0	ENST00000249373.3:c.259G>A	p.Ala87Thr	p.A87T	ENST00000249373	NM_005631.4	87	Gcc/Acc	1/12	1	2	FACETS	0.386	0.31	0.473	0.386	0.31	0.473	SUBCLONAL	1	TRUE	1	0.27	2		617	575	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856027	151856027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774117324	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	104	559	0	ENST00000262189.6:c.11591G>A	p.Arg3864His	p.R3864H	ENST00000262189	NM_170606.2	3864	cGc/cAc	44/59	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.27	2		559	694	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860184	151860184	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	119	704	0	ENST00000262189.6:c.10478T>C	p.Ile3493Thr	p.I3493T	ENST00000262189	NM_170606.2	3493	aTt/aCt	43/59	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.27	2		704	774	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146180	38146180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	77	563	0	ENST00000317025.8:c.3326G>A	p.Gly1109Asp	p.G1109D	ENST00000317025	NM_023034.1	1109	gGc/gAc	19/24	1	2	FACETS	0.825	0.724	0.934	0.825	0.724	0.934	CLONAL	1	TRUE	1	0.27	2		563	691	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934284	68934284	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146218789	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	33	228	0	ENST00000288368.4:c.350G>A	p.Arg117His	p.R117H	ENST00000288368	NM_024870.2	117	cGt/cAt	4/40	1	2	FACETS	0.664	0.541	0.802	0.664	0.541	0.802	SUBCLONAL	1	TRUE	1	0.27	2		228	368	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965356	68965356	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	66	380	0	ENST00000288368.4:c.968T>A	p.Ile323Asn	p.I323N	ENST00000288368	NM_024870.2	323	aTt/aAt	9/40	1	2	FACETS	0.875	0.76	0.999	0.875	0.76	0.999	CLONAL	1	TRUE	1	0.27	2		380	559	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68982089	68982089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376775544	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	28	138	0	ENST00000288368.4:c.1463G>A	p.Arg488His	p.R488H	ENST00000288368	NM_024870.2	488	cGt/cAt	13/40	1	2	FACETS	0.757	0.607	0.927	0.757	0.607	0.927	CLONAL	1	TRUE	1	0.27	2		138	274	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020366	69020366	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	62	487	0	ENST00000288368.4:c.2738G>T	p.Arg913Met	p.R913M	ENST00000288368	NM_024870.2	913	aGg/aTg	24/40	1	2	FACETS	0.786	0.679	0.903	0.786	0.679	0.903	CLONAL	1	TRUE	1	0.27	2		487	584	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033249	69033249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs114811202	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	36	505	0	ENST00000288368.4:c.3689G>A	p.Arg1230Gln	p.R1230Q	ENST00000288368	NM_024870.2	1230	cGg/cAg	30/40	1	2	FACETS	0.406	0.333	0.488	0.406	0.333	0.488	SUBCLONAL	1	TRUE	1	0.27	2		505	657	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864875	117864875	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	91	479	0	ENST00000297338.2:c.1234A>C	p.Asn412His	p.N412H	ENST00000297338	NM_006265.2	412	Aat/Cat	10/14	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.27	2		479	665	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737684	145737684	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	65	898	1	ENST00000428558.2:c.3079C>A	p.Leu1027Ile	p.L1027I	ENST00000428558	NM_004260.3	1027	Ctt/Att	19/22	1	2	FACETS	0.537	0.465	0.617	0.537	0.465	0.617	SUBCLONAL	1	TRUE	1	0.27	2		899	896	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2070461	2070461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768235436	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	72	463	0	ENST00000349721.2:c.1736C>T	p.Pro579Leu	p.P579L	ENST00000349721	NM_003070.3	579	cCg/cTg	10/34	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.27	2		463	473	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2123821	2123821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1402226729	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	85	647	0	ENST00000349721.2:c.3865G>A	p.Ala1289Thr	p.A1289T	ENST00000349721	NM_003070.3	1289	Gct/Act	27/34	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.27	2		647	620	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054855	5054855	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	70	342	0	ENST00000381652.3:c.907C>G	p.His303Asp	p.H303D	ENST00000381652	NM_004972.3	303	Cat/Gat	7/25	1	2	FACETS	0.905	0.79	1	0.905	0.79	1	CLONAL	1	TRUE	1	0.27	2		342	573	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449796	8449796	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	32	532	0	ENST00000356435.5:c.3917A>G	p.Asn1306Ser	p.N1306S	ENST00000356435		1306	aAc/aGc	23/35	1	2	FACETS	0.419	0.339	0.509	0.419	0.339	0.509	SUBCLONAL	1	TRUE	1	0.27	2		532	566	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465651	8465651	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772237001	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	64	512	0	ENST00000356435.5:c.3529C>T	p.Arg1177Cys	p.R1177C	ENST00000356435		1177	Cgc/Tgc	21/35	1	2	FACETS	0.798	0.691	0.914	0.798	0.691	0.914	CLONAL	1	TRUE	1	0.27	2		512	594	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492894	8492894	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	31	475	1	ENST00000356435.5:c.2435G>T	p.Ser812Ile	p.S812I	ENST00000356435		812	aGc/aTc	16/35	1	2	FACETS	0.434	0.35	0.529	0.434	0.35	0.529	SUBCLONAL	1	TRUE	1	0.27	2		476	529	SUCCESS
MTAP	4507	MSKCC	GRCh37	9	21815520	21815520	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	42	249	0	ENST00000380172.4:c.120+2T>C		p.X40_splice	ENST00000380172	NM_002451.3	40			1	2	FACETS	0.902	0.755	1	0.902	0.755	1	CLONAL	1	TRUE	1	0.27	2		249	345	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006078	22006078	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	46	767	0	ENST00000276925.6:c.325C>T	p.Arg109Cys	p.R109C	ENST00000276925	NM_004936.3	109	Cgc/Tgc	2/2	1	2	FACETS	0.471	0.396	0.555	0.471	0.396	0.555	SUBCLONAL	1	TRUE	1	0.27	2		767	723	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537100	80537100	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	85	590	0	ENST00000286548.4:c.298C>T	p.Pro100Ser	p.P100S	ENST00000286548	NM_002072.3	100	Cca/Tca	2/7	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.27	2		590	583	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93636496	93636496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	83	535	0	ENST00000375746.1:c.926C>T	p.Ala309Val	p.A309V	ENST00000375746	NM_001174167.1	309	gCc/gTc	8/14	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.27	2		535	597	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639960	93639960	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	77	611	0	ENST00000375746.1:c.1289C>T	p.Pro430Leu	p.P430L	ENST00000375746	NM_001174167.1	430	cCg/cTg	10/14	1	2	FACETS	0.927	0.815	1	0.927	0.815	1	CLONAL	1	TRUE	1	0.27	2		611	615	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908873	101908873	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200595614	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	99	580	0	ENST00000374994.4:c.1237C>T	p.Arg413Ter	p.R413*	ENST00000374994	NM_004612.2	413	Cga/Tga	7/9	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.27	2		580	624	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250071	110250071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	105	623	0	ENST00000374672.4:c.604G>A	p.Glu202Lys	p.E202K	ENST00000374672	NM_004235.4	202	Gag/Aag	3/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.27	2		623	528	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133729570	133729570	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138924193	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	90	493	0	ENST00000318560.5:c.199G>A	p.Val67Ile	p.V67I	ENST00000318560	NM_005157.4	67	Gtt/Att	2/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.27	2		493	581	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738400	133738400	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1191034511	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	110	619	0	ENST00000318560.5:c.800C>T	p.Thr267Met	p.T267M	ENST00000318560	NM_005157.4	267	aCg/aTg	4/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.27	2		619	667	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750259	133750259	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	75	506	0	ENST00000318560.5:c.1090C>A	p.Leu364Ile	p.L364I	ENST00000318560	NM_005157.4	364	Ctt/Att	7/11	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.27	2		506	532	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753948	133753948	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	67	431	1	ENST00000318560.5:c.1417C>T	p.Arg473Ter	p.R473*	ENST00000318560	NM_005157.4	473	Cga/Tga	8/11	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.27	2		432	482	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759811	133759811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1312773585	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	42	598	0	ENST00000318560.5:c.2134C>T	p.Arg712Cys	p.R712C	ENST00000318560	NM_005157.4	712	Cgc/Tgc	11/11	1	2	FACETS	0.573	0.478	0.679	0.573	0.478	0.679	SUBCLONAL	1	TRUE	1	0.27	2		598	543	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760592	133760592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2229067	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	111	785	0	ENST00000318560.5:c.2915C>T	p.Ser972Leu	p.S972L	ENST00000318560	NM_005157.4	972	tCg/tTg	11/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.27	2		785	710	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772091	135772091	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	95	641	0	ENST00000298552.3:c.3026A>G	p.Glu1009Gly	p.E1009G	ENST00000298552	NM_001162426.1	1009	gAa/gGa	23/23	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.27	2		641	680	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779042	135779042	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs746535706	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	63	576	0	ENST00000298552.3:c.2204C>A	p.Ala735Asp	p.A735D	ENST00000298552	NM_001162426.1	735	gCc/gAc	17/23	1	2	FACETS	0.863	0.747	0.988	0.863	0.747	0.988	CLONAL	1	TRUE	1	0.27	2		576	541	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407871	139407871	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377286829	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	87	708	0	ENST00000277541.6:c.2326G>A	p.Val776Met	p.V776M	ENST00000277541	NM_017617.3	776	Gtg/Atg	14/34	1	2	FACETS	0.958	0.848	1	0.958	0.848	1	CLONAL	1	TRUE	1	0.27	2		708	673	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15833865	15833865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	15	203	0	ENST00000307771.7:c.623C>T	p.Thr208Met	p.T208M	ENST00000307771	NM_005089.3	208	aCg/aTg	8/11	1	2	FACETS	0.607	0.445	0.8	0.607	0.445	0.8	SUBCLONAL	1	TRUE	1	0.27	2		203	183	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15838375	15838375	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	68	378	0	ENST00000307771.7:c.873G>A	p.Trp291Ter	p.W291*	ENST00000307771	NM_005089.3	291	tgG/tgA	10/11	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.27	2		378	476	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922926	44922926	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	76	600	0	ENST00000377967.4:c.1787A>C	p.Asn596Thr	p.N596T	ENST00000377967	NM_021140.2	596	aAt/aCt	16/29	1	2	FACETS	0.854	0.749	0.967	0.854	0.749	0.967	CLONAL	1	TRUE	1	0.27	2		600	659	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942835	44942835	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	72	430	0	ENST00000377967.4:c.3415C>T	p.Pro1139Ser	p.P1139S	ENST00000377967	NM_021140.2	1139	Cca/Tca	23/29	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.27	2		430	485	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030632	47030632	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	33	539	0	ENST00000377604.3:c.407T>C	p.Leu136Pro	p.L136P	ENST00000377604	NM_001204468.1	136	cTg/cCg	4/24	1	2	FACETS	0.583	0.475	0.706	0.583	0.475	0.706	SUBCLONAL	1	TRUE	1	0.27	2		539	419	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228018	53228018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199422238	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	88	647	0	ENST00000375401.3:c.2296C>T	p.Arg766Trp	p.R766W	ENST00000375401	NM_004187.3	766	Cgg/Tgg	16/26	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.27	2		647	633	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410466	63410466	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	87	728	0	ENST00000330258.3:c.2701A>G	p.Thr901Ala	p.T901A	ENST00000330258	NM_152424.3	901	Acc/Gcc	2/2	1	2	FACETS	0.909	0.805	1	0.909	0.805	1	CLONAL	1	TRUE	1	0.27	2		728	709	SUCCESS
AR	367	MSKCC	GRCh37	X	66905920	66905920	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	61	497	0	ENST00000374690.3:c.1837C>T	p.Pro613Ser	p.P613S	ENST00000374690	NM_000044.3	613	Cca/Tca	3/8	1	2	FACETS	0.906	0.782	1	0.906	0.782	1	CLONAL	1	TRUE	1	0.27	2		497	499	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344231	70344231	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	53	498	0	ENST00000374080.3:c.1967A>C	p.Lys656Thr	p.K656T	ENST00000374080		656	aAg/aCg	13/45	1	2	FACETS	0.758	0.647	0.88	0.758	0.647	0.88	SUBCLONAL	1	TRUE	1	0.27	2		498	518	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344921	70344921	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	91	591	0	ENST00000374080.3:c.2151G>T	p.Lys717Asn	p.K717N	ENST00000374080		717	aaG/aaT	15/45	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.27	2		591	567	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814268	76814268	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	75	249	0	ENST00000373344.5:c.6376C>A	p.Leu2126Met	p.L2126M	ENST00000373344	NM_000489.3	2126	Ctg/Atg	29/35	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.27	2		249	437	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855030	76855030	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs782332504	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	61	387	0	ENST00000373344.5:c.5806A>C	p.Lys1936Gln	p.K1936Q	ENST00000373344	NM_000489.3	1936	Aag/Cag	25/35	1	2	FACETS	0.9	0.778	1	0.9	0.778	1	CLONAL	1	TRUE	1	0.27	2		387	502	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937602	76937603	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	49	328	1	ENST00000373344.5:c.3145dup	p.Ile1049AsnfsTer4	p.I1049Nfs*4	ENST00000373344	NM_000489.3	1049	ata/aAta	9/35	1	2	FACETS	0.726	0.615	0.848	0.726	0.615	0.848	SUBCLONAL	1	TRUE	1	0.27	2		329	500	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939439	76939439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	73	492	0	ENST00000373344.5:c.1309G>A	p.Ala437Thr	p.A437T	ENST00000373344	NM_000489.3	437	Gct/Act	9/35	1	2	FACETS	0.952	0.834	1	0.952	0.834	1	CLONAL	1	TRUE	1	0.27	2		492	568	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939565	76939565	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1569539366	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	82	548	0	ENST00000373344.5:c.1183T>G	p.Phe395Val	p.F395V	ENST00000373344	NM_000489.3	395	Ttt/Gtt	9/35	1	2	FACETS	0.922	0.813	1	0.922	0.813	1	CLONAL	1	TRUE	1	0.27	2		548	659	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615626	100615626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782467781	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	68	564	0	ENST00000308731.7:c.706C>T	p.Arg236Trp	p.R236W	ENST00000308731	NM_000061.2	236	Cgg/Tgg	8/19	1	2	FACETS	0.909	0.792	1	0.909	0.792	1	CLONAL	1	TRUE	1	0.27	2		564	554	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181264	123181264	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	35	333	0	ENST00000218089.9:c.728A>T	p.Asn243Ile	p.N243I	ENST00000218089	NM_001042749.1	243	aAt/aTt	9/35	1	2	FACETS	0.583	0.477	0.701	0.583	0.477	0.701	SUBCLONAL	1	TRUE	1	0.27	2		333	445	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190075	123190075	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	42	345	0	ENST00000218089.9:c.1294C>A	p.Leu432Ile	p.L432I	ENST00000218089	NM_001042749.1	432	Ctc/Atc	14/35	1	2	FACETS	0.662	0.553	0.783	0.662	0.553	0.783	SUBCLONAL	1	TRUE	1	0.27	2		345	470	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191725	123191725	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	50	339	0	ENST00000218089.9:c.1314T>G	p.Ser438Arg	p.S438R	ENST00000218089	NM_001042749.1	438	agT/agG	15/35	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.27	2		339	355	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1296454	1296454	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0059964-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	24	183	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	1	0.27	2		183	163	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0059965-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	144	465	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.197527155987117	6	FACETS	1	0.958	1	1	0.958	1	INDETERMINATE	3	TRUE	3	0.43569562824558	6		465	390	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056291	180056291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199942873	NA	P-0059965-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	102	596	0	ENST00000261937.6:c.953G>A	p.Arg318Gln	p.R318Q	ENST00000261937	NM_182925.4	318	cGa/cAa	7/30	0.311619200177476	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.43569562824558	1		596	302	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627234	86627238	+	frameshift_variant	Frame_Shift_Del	DEL	TTATC	TTATC	-	rs1060503441	NA	P-0059965-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	193	537	0	ENST00000274376.6:c.613_617del	p.Leu205LysfsTer4	p.L205Kfs*4	ENST00000274376	NM_002890.2	203	agTTATCtt/agtt	2/25	0.43569562824558	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	3	TRUE	0	0.43569562824558	3		537	350	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101327	27101327	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059965-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	169	678	0	ENST00000324856.7:c.4609C>T	p.Gln1537Ter	p.Q1537*	ENST00000324856	NM_006015.4	1537	Cag/Tag	18/20	0.43569562824558	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.43569562824558	2		678	331	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342827	118342827	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059965-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	36	545	0	ENST00000534358.1:c.953T>C	p.Leu318Pro	p.L318P	ENST00000534358	NM_005933.3	318	cTc/cCc	3/36	1	2	FACETS	0.643	0.532	0.766	0.643	0.532	0.766	SUBCLONAL	1	TRUE	1	0.43569562824558	2		545	257	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69210686	69210686	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059965-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	86	373	0	ENST00000462284.1:c.269A>T	p.Asp90Val	p.D90V	ENST00000462284	NM_002392.5	90	gAt/gTt	4/11	0.43569562824558	4	FACETS	0.961	0.86	1	0.961	0.86	1	CLONAL	2	TRUE	2	0.43569562824558	4		373	295	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73649897	73649897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059965-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	66	475	0	ENST00000377687.4:c.1247G>A	p.Arg416Gln	p.R416Q	ENST00000377687	NM_001730.3	416	cGa/cAa	4/4	0.43569562824558	3	FACETS	1	0.962	1	0.636	0.557	0.72	CLONAL	1	TRUE	1	0.43569562824558	3		475	290	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651460	52651460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059965-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	111	489	0	ENST00000394830.3:c.1636T>G	p.Phe546Val	p.F546V	ENST00000394830	NM_018313.4	546	Ttt/Gtt	15/30	0.43569562824558	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.43569562824558	2		489	217	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430311	181430311	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059965-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	85	378	0	ENST00000325404.1:c.163C>G	p.Gln55Glu	p.Q55E	ENST00000325404	NM_003106.3	55	Cag/Gag	1/1	0.197527155987117	6	FACETS	1	0.954	1	1	0.954	1	INDETERMINATE	3	TRUE	3	0.43569562824558	6		378	220	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	41	279	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.762	0.637	0.9	0.762	0.637	0.9	SUBCLONAL	1	FALSE	1	0.326037736924414	2		279	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0059966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	88	584	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.176043571220957	2	FACETS	1	0.97	1	0.629	0.56	0.702	INDETERMINATE	1	FALSE	0	0.326037736924414	2		584	429	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546832	9546832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1018346655	NA	P-0059966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	125	662	0	ENST00000353224.5:c.1190C>T	p.Thr397Met	p.T397M	ENST00000353224	NM_177990.2	397	aCg/aTg	5/10	0.326037736924414	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	FALSE	1	0.326037736924414	3		662	418	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628266	90628266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1402492889	NA	P-0059966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	53	731	0	ENST00000330062.3:c.1145G>A	p.Arg382Gln	p.R382Q	ENST00000330062	NM_002168.2	382	cGg/cAg	9/11	1	2	FACETS	0.758	0.648	0.878	0.758	0.648	0.878	SUBCLONAL	1	FALSE	1	0.326037736924414	2		731	429	SUCCESS
APC	324	MSKCC	GRCh37	5	112175612	112175617	+	frameshift_variant	Frame_Shift_Del	DEL	CCACCT	CCACCT	ACACA	novel	NA	P-0059966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	84	660	0	ENST00000257430.4:c.4321_4326delinsACACA	p.Pro1441ThrfsTer32	p.P1441Tfs*32	ENST00000257430	NM_000038.5	1441	CCACCT/ACACA	16/16	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	FALSE	1	0.326037736924414	2		660	499	SUCCESS
APC	324	MSKCC	GRCh37	5	112175642	112175643	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAGTACCTAAAAATA	novel	NA	P-0059966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	42	635	0	ENST00000257430.4:c.4355_4369dup	p.Val1452_Lys1456dup	p.V1452_K1456dup	ENST00000257430	NM_000038.5	1452	gaa/gAAGTACCTAAAAATAaa	16/16	1	2	FACETS	0.509	0.425	0.603	0.509	0.425	0.603	SUBCLONAL	1	FALSE	1	0.326037736924414	2		635	506	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638278	176638278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059966-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	97	578	0	ENST00000439151.2:c.2878G>A	p.Gly960Ser	p.G960S	ENST00000439151	NM_022455.4	960	Ggc/Agc	5/23	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.326037736924414	2		578	494	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464487	25464487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375399431	NA	P-0059967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	220	551	0	ENST00000264709.3:c.2026C>T	p.Arg676Trp	p.R676W	ENST00000264709	NM_175629.2	676	Cgg/Tgg	17/23	0.487934947735941	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.487934947735941	1		551	588	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023895	27023895	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	225	607	0	ENST00000324856.7:c.1001C>G	p.Ser334Trp	p.S334W	ENST00000324856	NM_006015.4	334	tCg/tGg	1/20	0.487934947735941	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.487934947735941	1		607	612	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023696	27023696	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	220	529	0	ENST00000324856.7:c.802C>T	p.Gln268Ter	p.Q268*	ENST00000324856	NM_006015.4	268	Cag/Tag	1/20	0.487934947735941	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.487934947735941	1		529	658	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25462006	25462006	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753567076	NA	P-0059967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	180	482	0	ENST00000264709.3:c.2401A>G	p.Met801Val	p.M801V	ENST00000264709	NM_175629.2	801	Atg/Gtg	20/23	0.487934947735941	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.487934947735941	1		482	557	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809464	36809464	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	163	498	0	ENST00000373129.3:c.1001C>A	p.Ser334Ter	p.S334*	ENST00000373129	NM_032017.1	334	tCa/tAa	10/12	0.487934947735941	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.487934947735941	1		498	478	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051617	30051617	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555993293	NA	P-0059967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	124	396	0	ENST00000338641.4:c.551G>A	p.Trp184Ter	p.W184*	ENST00000338641	NM_000268.3	184	tGg/tAg	6/16	0.487934947735941	1	FACETS	0.875	0.798	0.956	0.875	0.798	0.956	CLONAL	1	TRUE	0	0.487934947735941	1		396	439	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020764	26020764	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1265819917	NA	P-0059967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	215	595	0	ENST00000357647.3:c.47C>T	p.Ala16Val	p.A16V	ENST00000357647	NM_003529.2	16	gCg/gTg	1/1	0.113105084012757	4	FACETS	1	0.988	1	0.648	0.603	0.696	INDETERMINATE	1	TRUE	2	0.487934947735941	4		595	1011	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008970	152008970	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	152	445	0	ENST00000262189.6:c.652G>C	p.Asp218His	p.D218H	ENST00000262189	NM_170606.2	218	Gat/Cat	5/59	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.487934947735941	2		445	591	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058575	69058575	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs746957295	NA	P-0059967-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	102	340	0	ENST00000288368.4:c.4219C>G	p.Leu1407Val	p.L1407V	ENST00000288368	NM_024870.2	1407	Ctt/Gtt	34/40	1	2	FACETS	0.813	0.73	0.901	0.813	0.73	0.901	CLONAL	1	TRUE	1	0.487934947735941	2		340	514	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0059969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	96	66	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.838	0.753	0.925	0.838	0.753	0.925	CLONAL	1	TRUE	1	0.658755615428099	2		66	348	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0059969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	131	238	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.658755615428099	2		238	378	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057727	27057727	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	213	692	0	ENST00000324856.7:c.1435C>T	p.Gln479Ter	p.Q479*	ENST00000324856	NM_006015.4	479	Cag/Tag	3/20	1	2	FACETS	0.862	0.804	0.922	0.862	0.804	0.922	CLONAL	1	TRUE	1	0.658755615428099	2		692	750	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984060	2984060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781530962	NA	P-0059969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	168	628	0	ENST00000396946.4:c.470G>A	p.Arg157Gln	p.R157Q	ENST00000396946	NM_032415.4	157	cGg/cAg	5/25	1	2	FACETS	0.875	0.808	0.943	0.875	0.808	0.943	CLONAL	1	TRUE	1	0.658755615428099	2		628	583	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023637	27023638	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTCCAAGCCGC	novel	NA	P-0059969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	122	623	0	ENST00000324856.7:c.748_758dup	p.Ser255ArgfsTer112	p.S255Rfs*112	ENST00000324856	NM_006015.4	248	ggc/ggCTCCAAGCCGCc	1/20	1	2	FACETS	0.677	0.614	0.743	0.677	0.614	0.743	SUBCLONAL	1	TRUE	1	0.658755615428099	2		623	547	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624258	89624259	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0059969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	54	173	0	ENST00000371953.3:c.35dup	p.Asn12LysfsTer32	p.N12Kfs*32	ENST00000371953	NM_000314.4	11	aga/agAa	1/9	1	2	FACETS	0.745	0.644	0.853	0.745	0.644	0.853	SUBCLONAL	1	TRUE	1	0.658755615428099	2		173	220	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456353	32456353	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	136	705	1	ENST00000332351.3:c.539T>C	p.Phe180Ser	p.F180S	ENST00000332351	NM_024426.4	180	tTc/tCc	1/10	1	2	FACETS	0.805	0.736	0.876	0.805	0.736	0.876	CLONAL	1	TRUE	1	0.658755615428099	2		706	513	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589583	67589584	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATATTC	novel	NA	P-0059969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	62	174	0	ENST00000274335.5:c.1347_1348insTATTCA	p.Leu449_His450insTyrSer	p.L449_H450insYS	ENST00000274335		449	tta/ttATATTCa	10/15	1	2	FACETS	0.721	0.629	0.819	0.721	0.629	0.819	SUBCLONAL	1	TRUE	1	0.658755615428099	2		174	261	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934574	NA	P-0059970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	503	817	0	ENST00000269305.4:c.844C>G	p.Arg282Gly	p.R282G	ENST00000269305	NM_001126112.2	282	Cgg/Ggg	8/11	0.515727397967202	2	FACETS	0.969	0.932	1	0.969	0.932	1	CLONAL	2	TRUE	0	0.512918817878315	2		817	1012	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910647	29910647	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199474387	NA	P-0059970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1620	226	1275	0	ENST00000376809.5:c.187G>T	p.Asp63Tyr	p.D63Y	ENST00000376809	NM_002116.7	63	Gac/Tac	2/8	0.515727397967202	3	FACETS	0.6	0.556	0.645	0.3	0.278	0.323	SUBCLONAL	1	TRUE	1	0.512918817878315	3		1275	1846	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331617	8331617	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	160	610	1	ENST00000356435.5:c.5499G>T	p.Gln1833His	p.Q1833H	ENST00000356435		1833	caG/caT	33/35	0.512918817878315	5	FACETS	0.929	0.85	1	0.31	0.283	0.338	CLONAL	1	TRUE	2	0.512918817878315	5		611	1188	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150915530	150915530	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0059970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1356	187	666	0	ENST00000271640.5:c.875+1G>T		p.X292_splice	ENST00000271640	NM_001145415.1	292			0.512918817878315	6	FACETS	0.957	0.881	1			1	CLONAL	1	TRUE	NA	0.512918817878315	6		666	1543	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176153824	176153885	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGGGCTAAAAAGAAAAGAAAAATAATTGATTTTTTTTTAAAAGTAGAGTGATTACAAATTG	TGGGGCTAAAAAGAAAAGAAAAATAATTGATTTTTTTTTAAAAGTAGAGTGATTACAAATTG	-	novel	NA	P-0059970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	24	231	0	ENST00000367669.3:c.408-57_412del		p.X136_splice	ENST00000367669	NM_022457.5	136		2/20	NA	2	FACETS	0.592	0.469	0.732			1	INDETERMINATE	1	TRUE	NA	0.512918817878315	2		231	158	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559729	29559729	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	133	518	0	ENST00000356175.3:c.3326T>C	p.Leu1109Ser	p.L1109S	ENST00000356175	NM_000267.3	1109	tTa/tCa	26/57	0.515727397967202	2	FACETS	1	0.939	1	0.518	0.473	0.564	CLONAL	1	TRUE	0	0.512918817878315	2		518	501	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0059971-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	295	575	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.522842714028342	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.522842714028342	1		575	751	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133268	38133268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770152981	NA	P-0059971-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	233	675	0	ENST00000317025.8:c.4205G>A	p.Arg1402His	p.R1402H	ENST00000317025	NM_023034.1	1402	cGc/cAc	24/24	1	2	FACETS	0.986	0.921	1	0.986	0.921	1	CLONAL	1	TRUE	1	0.522842714028342	2		675	904	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	157	475	0				ENST00000310581	NM_198253.2	-/1132			0.245399346484914	6	FACETS	1	0.943	1	1	0.943	1	INDETERMINATE	3	TRUE	3	0.895214110988454	6		475	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0059973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	272	547	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.895214110988454	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.895214110988454	2		547	302	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100198	27100198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	461	925	1	ENST00000324856.7:c.3994C>T	p.Gln1332Ter	p.Q1332*	ENST00000324856	NM_006015.4	1332	Cag/Tag	16/20	0.736586649746464	4	FACETS	0.989	0.949	1	0.989	0.949	1	CLONAL	2	TRUE	2	0.895214110988454	4		926	987	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248409	59248409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184098204	NA	P-0059973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	418	1082	0	ENST00000371222.2:c.334G>A	p.Glu112Lys	p.E112K	ENST00000371222	NM_002228.3	112	Gag/Aag	1/1	0.736586649746464	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	2	0.895214110988454	4		1082	804	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998756	100998756	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs749674024	NA	P-0059973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	161	815	1	ENST00000325455.5:c.1046C>A	p.Ser349Ter	p.S349*	ENST00000325455	NM_001202474.3	349	tCg/tAg	1/8	0.895214110988454	2	FACETS	1	0.942	1	0.507	0.472	0.542	CLONAL	1	TRUE	0	0.895214110988454	2		816	355	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437151	49437152	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0059973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	414	731	0	ENST00000301067.7:c.5527dup	p.Thr1843AsnfsTer5	p.T1843Nfs*5	ENST00000301067	NM_003482.3	1843	aca/aAca	24/54	0.895214110988454	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.895214110988454	2		731	458	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249458	153249460	+	inframe_deletion	In_Frame_Del	DEL	ATC	ATC	-	novel	NA	P-0059973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	319	619	0	ENST00000281708.4:c.1318_1320del	p.Asp440del	p.D440del	ENST00000281708	NM_033632.3	440	GAT/-	9/12	0.538065810424391	3	FACETS	1	0.995	1	0.815	0.787	0.841	CLONAL	2	TRUE	0	0.895214110988454	3		619	422	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	122	475	0				ENST00000310581	NM_198253.2	-/1132			0.782488257740845	3	FACETS	0.776	0.705	0.851	0.388	0.352	0.426	SUBCLONAL	1	TRUE	1	0.821132297943708	3		475	540	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	570	684	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.821132297943708	3	FACETS	1	0.99	1			1	CLONAL	2	TRUE	NA	0.821132297943708	3		684	933	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	625	639	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.821132297943708	3	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.821132297943708	3		639	1014	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946352	2946352	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	299	654	0	ENST00000396946.4:c.3385G>C	p.Glu1129Gln	p.E1129Q	ENST00000396946	NM_032415.4	1129	Gag/Cag	25/25	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.821132297943708	2		654	677	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	91	174	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.943	0.853	1	0.943	0.853	1	CLONAL	1	TRUE	1	0.821132297943708	2		174	235	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572928	7572928	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	255	640	0	ENST00000269305.4:c.1181G>C	p.Ter394SerextTer9	p.*394Sext*9	ENST00000269305	NM_001126112.2	394	tGa/tCa	11/11	0.820875367330779	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.821132297943708	1		640	348	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455091	50455091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1422790468	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	213	541	0	ENST00000331340.3:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000331340	NM_006060.4	213	cGa/cAa	6/8	1	2	FACETS	0.996	0.934	1	0.996	0.934	1	CLONAL	1	TRUE	1	0.821132297943708	2		541	521	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652198	36652199	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	251	631	0	ENST00000244741.5:c.322dup	p.Glu108GlyfsTer21	p.E108Gfs*21	ENST00000244741	NM_000389.4	107	gag/gaGg	2/3	1	2	FACETS	0.914	0.86	0.968	0.914	0.86	0.968	CLONAL	1	TRUE	1	0.821132297943708	2		631	669	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670844	134670844	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	288	595	0	ENST00000398015.3:c.755G>C	p.Arg252Pro	p.R252P	ENST00000398015	NM_004441.4	252	cGa/cCa	3/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.821132297943708	2		595	677	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246017	46246017	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	220	553	0	ENST00000334344.6:c.4111C>G	p.His1371Asp	p.H1371D	ENST00000334344	NM_152641.2	1371	Cat/Gat	15/21	0.312519850779774	1	FACETS	0.784	0.741	0.826	0.784	0.741	0.826	INDETERMINATE	1	TRUE	0	0.821132297943708	1		553	403	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651906	36651906	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	312	662	1	ENST00000244741.5:c.28C>T	p.Gln10Ter	p.Q10*	ENST00000244741	NM_000389.4	10	Cag/Tag	2/3	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.821132297943708	2		663	705	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021828	71021828	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	207	498	0	ENST00000318789.4:c.1531-1G>C		p.X511_splice	ENST00000318789	NM_032682.5	511			1	2	FACETS	0.953	0.892	1	0.953	0.892	1	CLONAL	1	TRUE	1	0.821132297943708	2		498	529	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883158	37883158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	559	580	0	ENST00000269571.5:c.3061G>A	p.Glu1021Lys	p.E1021K	ENST00000269571		1021	Gag/Aag	25/27	0.821132297943708	3	FACETS	1	0.99	1			1	CLONAL	2	TRUE	NA	0.821132297943708	3		580	911	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99204042	99204042	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529481819	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	217	475	0	ENST00000074304.5:c.2905G>A	p.Glu969Lys	p.E969K	ENST00000074304	NM_001134224.1	969	Gaa/Aaa	26/26	0.312519850779774	1	FACETS	0.669	0.629	0.708	0.669	0.629	0.708	INDETERMINATE	1	TRUE	0	0.821132297943708	1		475	466	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099408	27099408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	267	665	0	ENST00000324856.7:c.3645G>A	p.Met1215Ile	p.M1215I	ENST00000324856	NM_006015.4	1215	atG/atA	14/20	1	2	FACETS	0.969	0.915	1	0.969	0.915	1	CLONAL	1	TRUE	1	0.821132297943708	2		665	671	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479969	50479969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	159	594	0	ENST00000394963.4:c.203G>A	p.Arg68Gln	p.R68Q	ENST00000394963	NM_003076.4	68	cGa/cAa	2/13	0.312519850779774	1	FACETS	0.45	0.415	0.486	0.45	0.415	0.486	INDETERMINATE	1	TRUE	0	0.821132297943708	1		594	507	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490547	56490547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	226	602	0	ENST00000267101.3:c.2191G>A	p.Glu731Lys	p.E731K	ENST00000267101	NM_001982.3	731	Gag/Aag	19/28	0.312519850779774	1	FACETS	0.64	0.602	0.678	0.64	0.602	0.678	INDETERMINATE	1	TRUE	0	0.821132297943708	1		602	507	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136252	202136252	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	211	475	0	ENST00000358485.4:c.496C>T	p.Gln166Ter	p.Q166*	ENST00000358485	NM_001080125.1	166	Cag/Tag	3/9	0.427757951447045	1	FACETS	0.73	0.688	0.772	0.73	0.688	0.772	INDETERMINATE	1	TRUE	0	0.821132297943708	1		475	415	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199697	11199697	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	254	502	0	ENST00000361445.4:c.4891G>C	p.Glu1631Gln	p.E1631Q	ENST00000361445	NM_004958.3	1631	Gag/Cag	35/58	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.821132297943708	2		502	557	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982111	201982111	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	304	676	0	ENST00000359651.3:c.636del	p.Gly213ValfsTer41	p.G213Vfs*41	ENST00000359651		212	tCc/tc	5/8	0.74148156560699	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.821132297943708	1		676	417	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100445	8100445	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	370	844	0	ENST00000346208.3:c.419C>A	p.Ser140Tyr	p.S140Y	ENST00000346208		140	tCc/tAc	3/6	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.821132297943708	2		844	858	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94926629	94926629	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	36	300	0	ENST00000536441.1:c.136G>C	p.Glu46Gln	p.E46Q	ENST00000536441	NM_144665.3	46	Gag/Cag	2/10	0.427757951447045	1	FACETS	0.286	0.237	0.338	0.286	0.237	0.338	INDETERMINATE	1	TRUE	0	0.821132297943708	1		300	181	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417120	417120	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	195	646	0	ENST00000399788.2:c.3430C>G	p.Leu1144Val	p.L1144V	ENST00000399788	NM_001042603.1	1144	Ctc/Gtc	23/28	0.312519850779774	1	FACETS	0.427	0.397	0.458	0.427	0.397	0.458	INDETERMINATE	1	TRUE	0	0.821132297943708	1		646	656	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120842	115120842	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	193	649	0	ENST00000257566.3:c.164C>G	p.Ser55Trp	p.S55W	ENST00000257566	NM_016569.3	55	tCg/tGg	1/8	0.312519850779774	1	FACETS	0.497	0.462	0.531	0.497	0.462	0.531	INDETERMINATE	1	TRUE	0	0.821132297943708	1		649	558	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868063	56868063	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777975365	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	299	645	0	ENST00000308159.5:c.1561C>T	p.Pro521Ser	p.P521S	ENST00000308159	NM_014669.4	521	Cct/Tct	14/22	0.821132297943708	3	FACETS	1	0.962	1	0.513	0.484	0.543	CLONAL	1	TRUE	1	0.821132297943708	3		645	1001	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670622	67670622	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	558	619	0	ENST00000264010.4:c.1867G>C	p.Glu623Gln	p.E623Q	ENST00000264010	NM_006565.3	623	Gag/Cag	11/12	0.821132297943708	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.821132297943708	3		619	918	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670652	67670652	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	567	586	0	ENST00000264010.4:c.1897G>A	p.Glu633Lys	p.E633K	ENST00000264010	NM_006565.3	633	Gaa/Aaa	11/12	0.821132297943708	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.821132297943708	3		586	934	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671674	67671674	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	571	648	0	ENST00000264010.4:c.2083G>A	p.Glu695Lys	p.E695K	ENST00000264010	NM_006565.3	695	Gag/Aag	12/12	0.821132297943708	3	FACETS	0.993	0.96	1	0.993	0.96	1	CLONAL	2	TRUE	1	0.821132297943708	3		648	988	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877375	89877375	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	320	640	0	ENST00000389301.3:c.388G>T	p.Glu130Ter	p.E130*	ENST00000389301	NM_000135.2	130	Gag/Tag	4/43	0.821132297943708	3	FACETS	1	0.976	1	0.528	0.498	0.557	CLONAL	1	TRUE	1	0.821132297943708	3		640	1042	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217834	7217837	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	novel	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	259	625	1	ENST00000380728.2:c.174_177del	p.Arg59CysfsTer3	p.R59Cfs*3	ENST00000380728		58	gaGAGA/ga	3/11	0.820875367330779	1	FACETS	0.979	0.937	1	0.979	0.937	1	CLONAL	1	TRUE	0	0.821132297943708	1		626	380	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883647	37883647	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	587	716	0	ENST00000269571.5:c.3259G>C	p.Asp1087His	p.D1087H	ENST00000269571		1087	Gat/Cat	26/27	0.821132297943708	3	FACETS	1	0.981	1			1	CLONAL	2	TRUE	NA	0.821132297943708	3		716	991	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244002	41244002	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	315	709	0	ENST00000357654.3:c.3546G>C	p.Gln1182His	p.Q1182H	ENST00000357654	NM_007294.3	1182	caG/caC	10/23	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.821132297943708	2		709	681	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422455	47422455	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	271	604	0	ENST00000404338.3:c.523G>C	p.Asp175His	p.D175H	ENST00000404338	NM_004491.4	175	Gat/Cat	1/6	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.821132297943708	2		604	614	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423225	47423225	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	339	675	0	ENST00000404338.3:c.1293G>C	p.Glu431Asp	p.E431D	ENST00000404338	NM_004491.4	431	gaG/gaC	1/6	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.821132297943708	2		675	799	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719175	61719175	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	162	385	0	ENST00000401558.2:c.1882C>G	p.Gln628Glu	p.Q628E	ENST00000401558	NM_003400.3	628	Caa/Gaa	16/25	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.821132297943708	2		385	379	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090596	71090596	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	274	566	0	ENST00000318789.4:c.752G>C	p.Ser251Thr	p.S251T	ENST00000318789	NM_032682.5	251	aGt/aCt	11/21	1	2	FACETS	0.948	0.895	1	0.948	0.895	1	CLONAL	1	TRUE	1	0.821132297943708	2		566	704	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683388	182683388	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	77	431	0	ENST00000292782.4:c.157C>G	p.Arg53Gly	p.R53G	ENST00000292782	NM_020640.2	53	Cga/Gga	2/7	1	2	FACETS	0.735	0.654	0.82	0.735	0.654	0.82	SUBCLONAL	1	TRUE	1	0.821132297943708	2		431	255	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161393	55161393	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	260	553	0	ENST00000257290.5:c.3224del	p.Asp1075AlafsTer4	p.D1075Afs*4	ENST00000257290	NM_006206.4	1075	gAc/gc	23/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.821132297943708	2		553	589	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264533	1264533	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	238	613	0	ENST00000310581.5:c.2829G>C	p.Gln943His	p.Q943H	ENST00000310581	NM_198253.2	943	caG/caC	11/16	0.782488257740845	3	FACETS	1	0.972	1	0.533	0.499	0.568	CLONAL	1	TRUE	1	0.821132297943708	3		613	767	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106201	27106201	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0059976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	161	790	0	ENST00000324856.7:c.5812A>T	p.Lys1938Ter	p.K1938*	ENST00000324856	NM_006015.4	1938	Aag/Tag	20/20	0.572521991292205	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	0	0.572521991292205	1		790	358	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188321	10188321	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs869025657	NA	P-0059977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	84	517	0	ENST00000256474.2:c.463+1G>A		p.X155_splice	ENST00000256474	NM_000551.3	155			0.369657226677911	1	FACETS	0.86	0.763	0.962	0.86	0.763	0.962	CLONAL	1	TRUE	0	0.369657226677911	1		517	431	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441328	52441328	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	122	827	0	ENST00000460680.1:c.442G>T	p.Glu148Ter	p.E148*	ENST00000460680	NM_004656.3	148	Gag/Tag	7/17	0.369657226677911	1	FACETS	0.894	0.81	0.981	0.894	0.81	0.981	CLONAL	1	TRUE	0	0.369657226677911	1		827	602	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374837	149374837	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	107	648	0	ENST00000360632.3:c.257G>T	p.Arg86Leu	p.R86L	ENST00000360632	NM_015472.4	86	cGc/cTc	2/7	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.369657226677911	2		648	435	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059230	47059230	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs777018406	NA	P-0059977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	101	607	0	ENST00000409792.3:c.7432-1G>T		p.X2478_splice	ENST00000409792	NM_014159.6	2478			0.369657226677911	1	FACETS	0.839	0.752	0.93	0.839	0.752	0.93	CLONAL	1	TRUE	0	0.369657226677911	1		607	531	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668617	52668617	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0059977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	94	417	0	ENST00000394830.3:c.1301+1G>T		p.X434_splice	ENST00000394830	NM_018313.4	434			0.369657226677911	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.369657226677911	1		417	364	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540950	187540950	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	142	677	0	ENST00000441802.2:c.6790C>T	p.His2264Tyr	p.H2264Y	ENST00000441802	NM_005245.3	2264	Cat/Tat	10/27	1	2	FACETS	0.999	0.912	1	0.999	0.912	1	CLONAL	1	TRUE	1	0.369657226677911	2		677	769	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469877	157469877	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	125	767	0	ENST00000346085.5:c.2671T>G	p.Cys891Gly	p.C891G	ENST00000346085	NM_020732.3	891	Tgt/Ggt	9/20	1	2	FACETS	0.977	0.886	1	0.977	0.886	1	CLONAL	1	TRUE	1	0.369657226677911	2		767	692	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0059983-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	1854	353	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.361575742156121	21	FACETS	1	0.995	1			1	CLONAL	18	TRUE	NA	0.361575742156121	21		353	2480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882019	NA	P-0059983-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	179	611	0	ENST00000269305.4:c.455del	p.Pro152ArgfsTer18	p.P152Rfs*18	ENST00000269305	NM_001126112.2	152	cCg/cg	5/11	0.196365327865075	3	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.361575742156121	3		611	974	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059983-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	132	588	0	ENST00000269305.4:c.314G>C	p.Gly105Ala	p.G105A	ENST00000269305	NM_001126112.2	105	gGc/gCc	4/11	0.196365327865075	3	FACETS	1	0.93	1			1	INDETERMINATE	1	TRUE	NA	0.361575742156121	3		588	838	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807340	3807340	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059983-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	109	341	0	ENST00000262367.5:c.3647A>C	p.Lys1216Thr	p.K1216T	ENST00000262367	NM_004380.2	1216	aAg/aCg	19/31	1	2	FACETS	0.945	0.85	1	0.945	0.85	1	CLONAL	1	TRUE	1	0.361575742156121	2		341	638	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324081	31324081	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs151341256	NA	P-0059983-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	29	170	0	ENST00000412585.2:c.482A>G	p.Asp161Gly	p.D161G	ENST00000412585	NM_005514.6	161	gAc/gGc	3/8	0.363894463240282	3	FACETS	0.596	0.479	0.728	0.298	0.239	0.364	SUBCLONAL	1	TRUE	1	0.361575742156121	3		170	318	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0059984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	180	392	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.920747752082207	2	FACETS	0.935	0.903	0.965	0.935	0.903	0.965	CLONAL	2	TRUE	0	0.920747752082207	2		392	209	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0059984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	2057	385	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.920747752082207	19	FACETS	0.994	0.987	1	0.994	0.987	1	CLONAL	18	TRUE	1	0.920747752082207	19		385	2204	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987418	2987418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	93	312	0	ENST00000396946.4:c.11G>A	p.Gly4Glu	p.G4E	ENST00000396946	NM_032415.4	4	gGa/gAa	3/25	0.409927737768878	5	FACETS	1	0.956	1	0.377	0.337	0.42	INDETERMINATE	1	TRUE	2	0.920747752082207	5		312	425	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900363	3900363	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	67	445	0	ENST00000262367.5:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000262367	NM_004380.2	245	Cag/Tag	2/31	0.206859177967414	4	FACETS	1	0.902	1	0.516	0.453	0.582	INDETERMINATE	1	TRUE	2	0.920747752082207	4		445	271	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271216	26271216	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059984-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	161	505	1	ENST00000305910.3:c.397G>T	p.Gly133Trp	p.G133W	ENST00000305910	NM_003534.2	133	Ggg/Tgg	1/1	0.132663050349012	3	FACETS	1	0.991	1	0.744	0.694	0.795	INDETERMINATE	1	TRUE	1	0.920747752082207	3		506	343	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0059985-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	11	66	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.211	0.146	0.291	0.211	0.146	0.291	SUBCLONAL	1	TRUE	1	0.813012882931437	2		66	128	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0059985-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	207	460	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.813012882931437	2		460	425	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939112	36939112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059985-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	21	464	0	ENST00000361632.4:c.597G>A	p.Met199Ile	p.M199I	ENST00000361632		199	atG/atA	5/16	1	2	FACETS	0.129	0.099	0.165	0.129	0.099	0.165	SUBCLONAL	1	TRUE	1	0.813012882931437	2		464	400	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625347	69625347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059985-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	27	423	0	ENST00000334134.2:c.446C>T	p.Ala149Val	p.A149V	ENST00000334134	NM_005247.2	149	gCc/gTc	3/3	0.813012882931437	3	FACETS	0.191	0.151	0.236	0.095	0.075	0.118	SUBCLONAL	1	TRUE	1	0.813012882931437	3		423	490	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771188	161771188	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059985-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	88	292	0	ENST00000366898.1:c.1341G>C	p.Trp447Cys	p.W447C	ENST00000366898	NM_004562.2	447	tgG/tgC	12/12	0.373468068891417	1	FACETS	0.424	0.38	0.47	0.424	0.38	0.47	INDETERMINATE	1	TRUE	0	0.813012882931437	1		292	303	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026970	6026970	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059985-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	27	82	0	ENST00000265849.7:c.1426A>T	p.Ser476Cys	p.S476C	ENST00000265849	NM_000535.5	476	Agt/Tgt	11/15	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.813012882931437	2		82	59	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450288	50450288	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059985-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	28	368	0	ENST00000331340.3:c.472G>T	p.Gly158Cys	p.G158C	ENST00000331340	NM_006060.4	158	Ggc/Tgc	5/8	1	2	FACETS	0.199	0.159	0.245	0.199	0.159	0.245	SUBCLONAL	1	TRUE	1	0.813012882931437	2		368	346	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146069	38146099	+	frameshift_variant	Frame_Shift_Del	DEL	TCAGGGTATAGTCTCTTTGTAAAGCACTGGT	TCAGGGTATAGTCTCTTTGTAAAGCACTGGT	-	novel	NA	P-0059985-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	31	330	0	ENST00000317025.8:c.3407_3437del	p.Asn1136MetfsTer26	p.N1136Mfs*26	ENST00000317025	NM_023034.1	1136	aACCAGTGCTTTACAAAGAGACTATACCCTGAt/at	19/24	0.373468068891417	1	FACETS	0.141	0.114	0.172	0.141	0.114	0.172	INDETERMINATE	1	TRUE	0	0.813012882931437	1		330	321	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059986-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	10	475	0				ENST00000310581	NM_198253.2	-/1132			0.189740079089386	0	FACETS	0.905	0.615	1			1	CLONAL	1	TRUE	0	0.12	0		475	162	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797313	135797313	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059986-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	21	189	0	ENST00000298552.3:c.556del	p.Ala186HisfsTer24	p.A186Hfs*24	ENST00000298552	NM_001162426.1	186	Gca/ca	7/23	1	2	FACETS	0.931	0.716	1	0.931	0.716	1	CLONAL	1	TRUE	1	0.12	2		189	376	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0059987-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	35	244	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.355368349572529	1	FACETS	0.947	0.786	1	0.947	0.786	1	CLONAL	1	TRUE	0	0.355368349572529	1		244	171	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0059987-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	65	406	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.355368349572529	2		406	365	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610129	28610129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059987-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	78	421	0	ENST00000241453.7:c.1361C>T	p.Ser454Leu	p.S454L	ENST00000241453	NM_004119.2	454	tCg/tTg	11/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.355368349572529	2		421	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579421	7579422	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGGCTGGT	novel	NA	P-0059987-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	66	604	0	ENST00000269305.4:c.258_265dup	p.Pro89HisfsTer37	p.P89Hfs*37	ENST00000269305	NM_001126112.2	89	ccc/cACCAGCCCcc	4/11	0.355368349572529	1	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	0	0.355368349572529	1		604	305	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898764	134898764	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs185655852	NA	P-0059987-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	61	457	0	ENST00000398015.3:c.1822C>T	p.Arg608Trp	p.R608W	ENST00000398015	NM_004441.4	608	Cgg/Tgg	10/16	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.355368349572529	2		457	296	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0059988-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	22	289	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.166	0.128	0.211	0.166	0.128	0.211	SUBCLONAL	1	TRUE	1	0.61	2		289	434	SUCCESS
APC	324	MSKCC	GRCh37	5	112175760	112175761	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs398123122	NA	P-0059988-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	39	572	0	ENST00000257430.4:c.4473dup	p.Ala1492CysfsTer22	p.A1492Cfs*22	ENST00000257430	NM_000038.5	1490	cat/caTt	16/16	1	2	FACETS	0.191	0.158	0.229	0.191	0.158	0.229	SUBCLONAL	1	TRUE	1	0.61	2		572	669	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449495	31449495	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs886369396	NA	P-0059988-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	48	366	0	ENST00000344624.3:c.2714A>G	p.Asn905Ser	p.N905S	ENST00000344624		905	aAt/aGt	19/33	1	2	FACETS	0.321	0.271	0.375	0.321	0.271	0.375	SUBCLONAL	1	TRUE	1	0.61	2		366	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578223	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059988-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	37	547	0	ENST00000269305.4:c.626del	p.Arg209LysfsTer38	p.R209Kfs*38	ENST00000269305	NM_001126112.2	209	aGa/aa	6/11	1	2	FACETS	0.181	0.149	0.218	0.181	0.149	0.218	SUBCLONAL	1	TRUE	1	0.61	2		547	669	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71064699	71064699	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0059988-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	28	352	0	ENST00000318789.4:c.974+1G>A		p.X325_splice	ENST00000318789	NM_032682.5	325			1	2	FACETS	0.187	0.149	0.231	0.187	0.149	0.231	SUBCLONAL	1	TRUE	1	0.61	2		352	491	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	30	475	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.26	0.209	0.318	0.26	0.209	0.318	SUBCLONAL	1	TRUE	1	0.431574898883151	2		476	535	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0059989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	70	656	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.662	0.578	0.752	0.662	0.578	0.752	SUBCLONAL	1	TRUE	1	0.431574898883151	2		657	490	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0059989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	105	66	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.431574898883151	2		66	368	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0059989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	51	566	7	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.509	0.433	0.593	0.509	0.433	0.593	SUBCLONAL	1	TRUE	1	0.431574898883151	2		573	464	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0059989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	28	567	2	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.281	0.224	0.347	0.281	0.224	0.347	SUBCLONAL	1	TRUE	1	0.431574898883151	2		569	461	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0059989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	38	518	2	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.326	0.269	0.39	0.326	0.269	0.39	SUBCLONAL	1	TRUE	1	0.431574898883151	2		520	540	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0059989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	139	377	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.431574898883151	2		377	527	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0059989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	150	468	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.431574898883151	2		468	541	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058083	27058083	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	138	470	0	ENST00000324856.7:c.1793del	p.Pro598LeufsTer21	p.P598Lfs*21	ENST00000324856	NM_006015.4	597	ttC/tt	3/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.431574898883151	2		470	526	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932123	36932123	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	26	616	0	ENST00000361632.4:c.2346del	p.Ser783AlafsTer19	p.S783Afs*19	ENST00000361632		782	ccC/cc	16/16	1	2	FACETS	0.252	0.199	0.313	0.252	0.199	0.313	SUBCLONAL	1	TRUE	1	0.431574898883151	2		616	478	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720671	89720671	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587782607	NA	P-0059989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	25	28	0	ENST00000371953.3:c.822G>A	p.Trp274Ter	p.W274*	ENST00000371953	NM_000314.4	274	tgG/tgA	8/9	1	2	FACETS	0.884	0.707	1	0.884	0.707	1	CLONAL	1	TRUE	1	0.431574898883151	2		28	131	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911639	114911639	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	61	446	0	ENST00000543371.1:c.1157G>A	p.Arg386Gln	p.R386Q	ENST00000543371	NM_001198531.1	386	cGg/cAg	10/14	1	2	FACETS	0.675	0.584	0.773	0.675	0.584	0.773	SUBCLONAL	1	TRUE	1	0.431574898883151	2		446	419	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597588	28597588	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1566063342	NA	P-0059989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	31	129	1	ENST00000241453.7:c.2317del	p.Arg773GlyfsTer8	p.R773Gfs*8	ENST00000241453	NM_004119.2	773	Agg/gg	19/24	1	2	FACETS	0.362	0.292	0.44	0.362	0.292	0.44	SUBCLONAL	1	TRUE	1	0.431574898883151	2		130	397	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001328	29001328	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	66	330	0	ENST00000282397.4:c.1404G>A	p.Trp468Ter	p.W468*	ENST00000282397	NM_002019.4	468	tgG/tgA	10/30	1	2	FACETS	0.617	0.536	0.703	0.617	0.536	0.703	SUBCLONAL	1	TRUE	1	0.431574898883151	2		330	496	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969813	81969813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371326699	NA	P-0059989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	43	404	0	ENST00000359376.3:c.2882C>T	p.Thr961Met	p.T961M	ENST00000359376	NM_002661.3	961	aCg/aTg	27/33	1	2	FACETS	0.425	0.355	0.502	0.425	0.355	0.502	SUBCLONAL	1	TRUE	1	0.431574898883151	2		404	469	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544836	86544836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1336836103	NA	P-0059989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	45	565	0	ENST00000262426.4:c.661G>A	p.Gly221Ser	p.G221S	ENST00000262426	NM_001451.2	221	Ggc/Agc	1/2	1	2	FACETS	0.535	0.45	0.628	0.535	0.45	0.628	SUBCLONAL	1	TRUE	1	0.431574898883151	2		565	390	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346158	89346158	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs878855327	NA	P-0059989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	14	627	0	ENST00000301030.4:c.6792del	p.Ala2265ProfsTer72	p.A2265Pfs*72	ENST00000301030	NM_001256183.1	2264	ccC/cc	9/13	1	2	FACETS	0.141	0.101	0.19	0.141	0.101	0.19	SUBCLONAL	1	TRUE	1	0.431574898883151	2		627	460	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351069	89351069	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	22	474	0	ENST00000301030.4:c.1881del	p.Val628LeufsTer25	p.V628Lfs*25	ENST00000301030	NM_001256183.1	627	aaA/aa	9/13	1	2	FACETS	0.173	0.133	0.22	0.173	0.133	0.22	SUBCLONAL	1	TRUE	1	0.431574898883151	2		474	589	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012100	16012100	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	100	122	0	ENST00000268712.3:c.2182G>T	p.Val728Phe	p.V728F	ENST00000268712	NM_006311.3	728	Gtt/Ttt	19/46	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.431574898883151	2		122	377	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353796	40353796	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	80	543	0	ENST00000293328.3:c.2324G>T	p.Arg775Leu	p.R775L	ENST00000293328	NM_012448.3	775	cGg/cTg	19/19	1	2	FACETS	0.653	0.575	0.736	0.653	0.575	0.736	SUBCLONAL	1	TRUE	1	0.431574898883151	2		543	568	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267575	7267575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	126	473	1	ENST00000302850.5:c.433C>T	p.Arg145Cys	p.R145C	ENST00000302850	NM_000208.2	145	Cgc/Tgc	2/22	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.431574898883151	2		474	516	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661341	227661341	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	40	575	0	ENST00000305123.5:c.2114del	p.Gly705AlafsTer29	p.G705Afs*29	ENST00000305123	NM_005544.2	705	gGc/gc	1/2	1	2	FACETS	0.307	0.254	0.366	0.307	0.254	0.366	SUBCLONAL	1	TRUE	1	0.431574898883151	2		575	604	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715721	30715721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893816	NA	P-0059989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	43	265	0	ENST00000295754.5:c.1379G>A	p.Arg460His	p.R460H	ENST00000295754	NM_003242.5	460	cGc/cAc	5/7	1	2	FACETS	0.441	0.369	0.52	0.441	0.369	0.52	SUBCLONAL	1	TRUE	1	0.431574898883151	2		265	452	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186507029	186507029	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	35	211	0	ENST00000323963.5:c.1195A>G	p.Met399Val	p.M399V	ENST00000323963		399	Atg/Gtg	11/11	1	2	FACETS	0.345	0.282	0.416	0.345	0.282	0.416	SUBCLONAL	1	TRUE	1	0.431574898883151	2		211	470	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235282	235282	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	32	299	0	ENST00000264932.6:c.1088A>G	p.His363Arg	p.H363R	ENST00000264932	NM_004168.2	363	cAc/cGc	9/15	1	2	FACETS	0.463	0.377	0.561	0.463	0.377	0.561	SUBCLONAL	1	TRUE	1	0.431574898883151	2		299	320	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591128	67591129	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0059989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	116	114	0	ENST00000274335.5:c.1724dup	p.Thr576AspfsTer26	p.T576Dfs*26	ENST00000274335		574	aga/agAa	12/15	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.431574898883151	2		114	506	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592108	67592108	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1419325070	NA	P-0059989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	58	328	0	ENST00000274335.5:c.1924C>T	p.Arg642Ter	p.R642*	ENST00000274335		642	Cga/Tga	14/15	1	2	FACETS	0.571	0.491	0.657	0.571	0.491	0.657	SUBCLONAL	1	TRUE	1	0.431574898883151	2		328	471	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710992	117710992	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	38	236	1	ENST00000368508.3:c.1280T>C	p.Leu427Pro	p.L427P	ENST00000368508	NM_002944.2	427	cTg/cCg	12/43	1	2	FACETS	0.47	0.389	0.56	0.47	0.389	0.56	SUBCLONAL	1	TRUE	1	0.431574898883151	2		237	375	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042170	6042170	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1562689635	NA	P-0059989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	45	460	2	ENST00000265849.7:c.451del	p.Arg151AlafsTer50	p.R151Afs*50	ENST00000265849	NM_000535.5	151	Cgc/gc	5/15	1	2	FACETS	0.4	0.336	0.471	0.4	0.336	0.471	SUBCLONAL	1	TRUE	1	0.431574898883151	2		462	521	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371697	55371698	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0059989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	120	593	0	ENST00000297316.4:c.388dup	p.Gln130ProfsTer32	p.Q130Pfs*32	ENST00000297316	NM_022454.3	129	-/C	2/2	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.431574898883151	2		593	494	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400036	139400036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746077264	NA	P-0059989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	149	689	1	ENST00000277541.6:c.4312C>T	p.Arg1438Cys	p.R1438C	ENST00000277541	NM_017617.3	1438	Cgc/Tgc	25/34	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.431574898883151	2		690	570	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	108	279	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.434355358491729	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	0	0.434355358491729	2		279	245	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0059990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	149	645	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.404462474196265	2	FACETS	0.91	0.842	0.979	0.91	0.842	0.979	CLONAL	2	TRUE	0	0.434355358491729	2		645	377	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066637	94066637	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	111	504	0	ENST00000369303.4:c.1122G>T	p.Trp374Cys	p.W374C	ENST00000369303	NM_004440.3	374	tgG/tgT	5/17	0.434355358491729	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.434355358491729	1		504	356	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409937	63409937	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	54	540	0	ENST00000330258.3:c.3230C>A	p.Pro1077His	p.P1077H	ENST00000330258	NM_152424.3	1077	cCt/cAt	2/2	0.208053233864879	2	FACETS	0.731	0.628	0.843	0.366	0.314	0.422	INDETERMINATE	1	TRUE	0	0.434355358491729	2		540	340	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31237272	31237272	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs139702282	NA	P-0059990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	34	375	0	ENST00000376228.5:c.1046C>T	p.Ala349Val	p.A349V	ENST00000376228	NM_002117.5	349	gCg/gTg	6/8	0.227531575216088	3	FACETS	0.546	0.447	0.657	0.273	0.223	0.329	INDETERMINATE	1	TRUE	1	0.434355358491729	3		375	349	SUCCESS
AR	367	MSKCC	GRCh37	X	66937342	66937342	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	37	470	0	ENST00000374690.3:c.2196C>A	p.Asp732Glu	p.D732E	ENST00000374690	NM_000044.3	732	gaC/gaA	5/8	0.208053233864879	2	FACETS	0.512	0.423	0.61	0.256	0.211	0.305	INDETERMINATE	1	TRUE	0	0.434355358491729	2		470	333	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671929	30671929	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	141	622	0	ENST00000376406.3:c.5031G>T	p.Gln1677His	p.Q1677H	ENST00000376406	NM_014641.2	1677	caG/caT	10/15	0.227531575216088	3	FACETS	0.837	0.768	0.908	0.837	0.768	0.908	INDETERMINATE	2	TRUE	1	0.434355358491729	3		622	472	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528564	89528564	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	73	353	0	ENST00000336596.2:c.2864G>A	p.Gly955Asp	p.G955D	ENST00000336596	NM_005233.5	955	gGt/gAt	17/17	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.434355358491729	2		353	272	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197187	26197187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	57	803	0	ENST00000356476.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000356476		98	Gag/Aag	1/1	0.227531575216088	3	FACETS	0.569	0.488	0.658	0.285	0.244	0.329	INDETERMINATE	1	TRUE	1	0.434355358491729	3		803	561	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303341	11303341	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	75	439	0	ENST00000361445.4:c.1242del	p.Asp415IlefsTer3	p.D415Ifs*3	ENST00000361445	NM_004958.3	414	caA/ca	9/58	0.2322834158581	1	FACETS	0.864	0.764	0.969	0.864	0.764	0.969	INDETERMINATE	1	TRUE	0	0.434355358491729	1		439	313	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023948	27023948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	31	478	0	ENST00000324856.7:c.1054G>A	p.Gly352Arg	p.G352R	ENST00000324856	NM_006015.4	352	Ggg/Agg	1/20	0.2322834158581	1	FACETS	0.556	0.453	0.67	0.556	0.453	0.67	INDETERMINATE	1	TRUE	0	0.434355358491729	1		478	201	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937941	36937941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	79	626	0	ENST00000361632.4:c.895C>T	p.Pro299Ser	p.P299S	ENST00000361632		299	Cca/Tca	7/16	0.2322834158581	1	FACETS	0.835	0.74	0.935	0.835	0.74	0.935	INDETERMINATE	1	TRUE	0	0.434355358491729	1		626	341	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506410	120506411	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CA	CA	-	novel	NA	P-0059990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	58	416	0	ENST00000256646.2:c.1701_1702del	p.Cys567Ter	p.C567*	ENST00000256646	NM_024408.3	567	tgTGag/tgag	11/34	0.2322834158581	1	FACETS	0.553	0.477	0.635	0.553	0.477	0.635	INDETERMINATE	1	TRUE	0	0.434355358491729	1		416	378	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573777	64573777	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	98	552	0	ENST00000312049.6:c.976G>T	p.Gly326Cys	p.G326C	ENST00000312049	NM_130799.2	326	Ggc/Tgc	7/10	0.434355358491729	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.434355358491729	1		552	327	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041842	42041842	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs779273324	NA	P-0059990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	96	513	0	ENST00000219905.7:c.6037G>T	p.Gly2013Ter	p.G2013*	ENST00000219905	NM_001164273.1	2013	Gga/Tga	17/24	0.434355358491729	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.434355358491729	1		513	272	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396892	396892	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	118	557	0	ENST00000262320.3:c.134G>T	p.Cys45Phe	p.C45F	ENST00000262320	NM_003502.3	45	tGc/tTc	2/11	0.434355358491729	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.434355358491729	1		557	398	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110531	8110531	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	49	458	0	ENST00000585124.1:c.361C>T	p.Gln121Ter	p.Q121*	ENST00000585124	NM_004217.3	121	Cag/Tag	5/9	0.404462474196265	2	FACETS	0.673	0.573	0.783	0.337	0.286	0.392	SUBCLONAL	1	TRUE	0	0.434355358491729	2		458	335	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110589	8110589	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	58	427	0	ENST00000585124.1:c.303C>A	p.Phe101Leu	p.F101L	ENST00000585124	NM_004217.3	101	ttC/ttA	5/9	0.404462474196265	2	FACETS	0.734	0.633	0.842	0.367	0.316	0.421	SUBCLONAL	1	TRUE	0	0.434355358491729	2		427	364	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007710	62007710	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	41	459	0	ENST00000392795.3:c.157T>A	p.Phe53Ile	p.F53I	ENST00000392795	NM_001039933.1	53	Ttc/Atc	3/6	0.404462474196265	2	FACETS	0.597	0.499	0.705	0.299	0.249	0.353	SUBCLONAL	1	TRUE	0	0.434355358491729	2		459	316	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141502	11141502	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	90	553	1	ENST00000358026.2:c.3479G>T	p.Gly1160Val	p.G1160V	ENST00000358026	NM_001128849.1	1160	gGg/gTg	25/36	0.434355358491729	1	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	0	0.434355358491729	1		554	317	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211259	36211259	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	125	568	0	ENST00000222270.7:c.1010A>T	p.Gln337Leu	p.Q337L	ENST00000222270	NM_014727.1	337	cAg/cTg	3/37	0.227531575216088	3	FACETS	1	0.98	1	0.646	0.587	0.708	INDETERMINATE	1	TRUE	1	0.434355358491729	3		568	542	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198264847	198264847	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	68	421	1	ENST00000335508.6:c.2945T>C	p.Leu982Ser	p.L982S	ENST00000335508	NM_012433.2	982	tTg/tCg	20/25	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.434355358491729	2		422	312	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064376	30064376	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	99	395	0	ENST00000338641.4:c.940G>T	p.Asp314Tyr	p.D314Y	ENST00000338641	NM_000268.3	314	Gat/Tat	10/16	0.434355358491729	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.434355358491729	1		395	298	SUCCESS
ALB	213	MSKCC	GRCh37	4	74275145	74275145	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0059990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	95	419	0	ENST00000295897.4:c.556A>T	p.Lys186Ter	p.K186*	ENST00000295897	NM_000477.5	186	Aaa/Taa	5/15	0.434355358491729	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.434355358491729	1		419	253	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352342	143352342	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	27	316	0	ENST00000262992.4:c.71C>A	p.Pro24His	p.P24H	ENST00000262992	NM_001101669.1	24	cCc/cAc	2/24	0.208053233864879	2	FACETS	0.401	0.319	0.494	0.201	0.159	0.247	INDETERMINATE	1	TRUE	0	0.434355358491729	2		316	310	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180035975	180035975	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	76	494	0	ENST00000261937.6:c.3886G>T	p.Gly1296Cys	p.G1296C	ENST00000261937	NM_182925.4	1296	Ggc/Tgc	29/30	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.434355358491729	2		494	341	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467735	50467735	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	105	507	1	ENST00000331340.3:c.970G>T	p.Ala324Ser	p.A324S	ENST00000331340	NM_006060.4	324	Gcc/Tcc	8/8	0.2322834158581	1	FACETS	1	0.924	1	1	0.924	1	INDETERMINATE	1	TRUE	0	0.434355358491729	1		508	369	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509656	106509656	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	47	512	0	ENST00000359195.3:c.1650G>T	p.Gln550His	p.Q550H	ENST00000359195	NM_002649.2	550	caG/caT	2/11	0.2322834158581	1	FACETS	0.465	0.394	0.544	0.465	0.394	0.544	INDETERMINATE	1	TRUE	0	0.434355358491729	1		512	364	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513336	106513336	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	69	379	0	ENST00000359195.3:c.2240T>A	p.Leu747His	p.L747H	ENST00000359195	NM_002649.2	747	cTt/cAt	4/11	0.2322834158581	1	FACETS	0.957	0.843	1	0.957	0.843	1	INDETERMINATE	1	TRUE	0	0.434355358491729	1		379	260	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523498	106523498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	43	333	0	ENST00000359195.3:c.2650G>A	p.Asp884Asn	p.D884N	ENST00000359195	NM_002649.2	884	Gac/Aac	8/11	0.2322834158581	1	FACETS	0.403	0.337	0.475	0.403	0.337	0.475	INDETERMINATE	1	TRUE	0	0.434355358491729	1		333	385	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354950	70354950	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	41	515	0	ENST00000374080.3:c.4872G>C	p.Leu1624Phe	p.L1624F	ENST00000374080		1624	ttG/ttC	36/45	0.208053233864879	2	FACETS	0.456	0.38	0.54	0.228	0.19	0.27	INDETERMINATE	1	TRUE	0	0.434355358491729	2		515	414	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179147	123179147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	16	339	0	ENST00000218089.9:c.596C>T	p.Thr199Ile	p.T199I	ENST00000218089	NM_001042749.1	199	aCa/aTa	8/35	0.208053233864879	2	FACETS	0.433	0.322	0.565	0.217	0.161	0.283	INDETERMINATE	1	TRUE	0	0.434355358491729	2		339	170	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	108	279	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.238392782333246	3	FACETS	1	0.971	1	0.602	0.543	0.664	INDETERMINATE	1	TRUE	1	0.451788164425453	3		279	487	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	80	475	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.515	0.453	0.581	0.515	0.453	0.581	SUBCLONAL	1	TRUE	1	0.451788164425453	2		476	688	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	77	626	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.463	0.406	0.525	0.463	0.406	0.525	SUBCLONAL	1	TRUE	1	0.451788164425453	2		627	736	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0059991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	42	316	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.491	0.41	0.579	0.491	0.41	0.579	SUBCLONAL	1	TRUE	1	0.451788164425453	2		316	379	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0059991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	30	174	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.492	0.398	0.598	0.492	0.398	0.598	SUBCLONAL	1	TRUE	1	0.451788164425453	2		174	270	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0059991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	87	486	0	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	1	2	FACETS	0.556	0.492	0.624	0.556	0.492	0.624	SUBCLONAL	1	TRUE	1	0.451788164425453	2		486	693	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929516	81929516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760949449	NA	P-0059991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	98	489	0	ENST00000359376.3:c.1177G>A	p.Ala393Thr	p.A393T	ENST00000359376	NM_002661.3	393	Gcc/Acc	13/33	1	2	FACETS	0.643	0.574	0.716	0.643	0.574	0.716	SUBCLONAL	1	TRUE	1	0.451788164425453	2		489	675	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023327	27023327	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	40	397	0	ENST00000324856.7:c.437del	p.Pro146GlnfsTer86	p.P146Qfs*86	ENST00000324856	NM_006015.4	145	Ccc/cc	1/20	1	2	FACETS	0.527	0.439	0.624	0.527	0.439	0.624	SUBCLONAL	1	TRUE	1	0.451788164425453	2		397	336	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952142	178952142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253171657	NA	P-0059991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	64	361	0	ENST00000263967.3:c.3197C>T	p.Ala1066Val	p.A1066V	ENST00000263967	NM_006218.2	1066	gCa/gTa	21/21	1	2	FACETS	0.567	0.491	0.648	0.567	0.491	0.648	SUBCLONAL	1	TRUE	1	0.451788164425453	2		361	500	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022999	27022999	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1436957504	NA	P-0059991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	50	445	0	ENST00000324856.7:c.110del	p.Gly37AlafsTer14	p.G37Afs*14	ENST00000324856	NM_006015.4	35	gcG/gc	1/20	1	2	FACETS	0.552	0.469	0.642	0.552	0.469	0.642	SUBCLONAL	1	TRUE	1	0.451788164425453	2		445	401	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262680	16262680	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	94	459	1	ENST00000375759.3:c.9950del	p.Pro3317ArgfsTer83	p.P3317Rfs*83	ENST00000375759	NM_015001.2	3315	caC/ca	11/15	1	2	FACETS	0.664	0.591	0.741	0.664	0.591	0.741	SUBCLONAL	1	TRUE	1	0.451788164425453	2		460	627	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426106	47426106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	79	512	0	ENST00000377045.4:c.626G>A	p.Arg209His	p.R209H	ENST00000377045	NM_001654.4	209	cGc/cAc	7/16	1	2	FACETS	0.537	0.472	0.607	0.537	0.472	0.607	SUBCLONAL	1	TRUE	1	0.451788164425453	2		512	651	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384650	31384651	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs756395138	NA	P-0059991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	67	477	1	ENST00000328111.2:c.1359dup	p.Leu454AlafsTer11	p.L454Afs*11	ENST00000328111	NM_006892.3	451	gag/gaGg	13/23	1	2	FACETS	0.48	0.417	0.548	0.48	0.417	0.548	SUBCLONAL	1	TRUE	1	0.451788164425453	2		478	618	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31435934	31435936	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0059991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	52	348	0	ENST00000344624.3:c.2978_2980del	p.Glu993del	p.E993del	ENST00000344624		993	gAAGga/gga	22/33	1	2	FACETS	0.48	0.408	0.557	0.48	0.408	0.557	SUBCLONAL	1	TRUE	1	0.451788164425453	2		348	480	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500519	99500519	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138696883	NA	P-0059991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	99	593	0	ENST00000268035.6:c.3952G>A	p.Asp1318Asn	p.D1318N	ENST00000268035	NM_000875.3	1318	Gac/Aac	21/21	1	2	FACETS	0.629	0.561	0.7	0.629	0.561	0.7	SUBCLONAL	1	TRUE	1	0.451788164425453	2		593	697	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31464401	31464401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	83	396	0	ENST00000344624.3:c.2516C>T	p.Thr839Met	p.T839M	ENST00000344624		839	aCg/aTg	17/33	1	2	FACETS	0.58	0.512	0.652	0.58	0.512	0.652	SUBCLONAL	1	TRUE	1	0.451788164425453	2		396	634	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933839	39933839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749475374	NA	P-0059991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	95	561	0	ENST00000378444.4:c.760G>A	p.Gly254Ser	p.G254S	ENST00000378444	NM_001123385.1	254	Ggt/Agt	4/15	1	2	FACETS	0.603	0.537	0.673	0.603	0.537	0.673	SUBCLONAL	1	TRUE	1	0.451788164425453	2		561	698	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615045	43615045	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	69	602	0	ENST00000355710.3:c.2459G>A	p.Arg820His	p.R820H	ENST00000355710	NM_020975.4	820	cGc/cAc	14/20	1	2	FACETS	0.548	0.478	0.624	0.548	0.478	0.624	SUBCLONAL	1	TRUE	1	0.451788164425453	2		602	557	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100259	157100260	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1554248082	NA	P-0059991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	30	348	0	ENST00000346085.5:c.1202dup	p.Phe402LeufsTer133	p.F402Lfs*133	ENST00000346085	NM_020732.3	399	gcg/gcGg	1/20	1	2	FACETS	0.415	0.335	0.506	0.415	0.335	0.506	SUBCLONAL	1	TRUE	1	0.451788164425453	2		348	320	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055896	180055897	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0059991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	58	407	1	ENST00000261937.6:c.1088dup	p.Pro364AlafsTer63	p.P364Afs*63	ENST00000261937	NM_182925.4	363	ccg/ccCg	8/30	1	2	FACETS	0.484	0.416	0.558	0.484	0.416	0.558	SUBCLONAL	1	TRUE	1	0.451788164425453	2		408	531	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456524	32456524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	30	347	0	ENST00000332351.3:c.368C>T	p.Ala123Val	p.A123V	ENST00000332351	NM_024426.4	123	gCg/gTg	1/10	1	2	FACETS	0.428	0.346	0.522	0.428	0.346	0.522	SUBCLONAL	1	TRUE	1	0.451788164425453	2		347	310	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12043874	12043874	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0059991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	41	359	0	ENST00000396373.4:c.1254-1G>T		p.X418_splice	ENST00000396373	NM_001987.4	418			0.238392782333246	3	FACETS	0.386	0.321	0.459	0.193	0.16	0.23	INDETERMINATE	1	TRUE	1	0.451788164425453	3		359	576	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984392	201984393	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0059991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	90	502	0	ENST00000359651.3:c.1057_1058del	p.Lys353ValfsTer117	p.K353Vfs*117	ENST00000359651		353	AAg/g	8/8	0.451788164425453	3	FACETS	0.536	0.474	0.601	0.268	0.237	0.301	SUBCLONAL	1	TRUE	1	0.451788164425453	3		502	912	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573177	64573177	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	89	559	0	ENST00000312049.6:c.1115T>C	p.Ile372Thr	p.I372T	ENST00000312049	NM_130799.2	372	aTc/aCc	8/10	1	2	FACETS	0.597	0.529	0.669	0.597	0.529	0.669	SUBCLONAL	1	TRUE	1	0.451788164425453	2		559	660	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436093	110436093	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	96	511	0	ENST00000375856.3:c.2308T>C	p.Ser770Pro	p.S770P	ENST00000375856	NM_003749.2	770	Tcc/Ccc	1/2	1	2	FACETS	0.67	0.598	0.747	0.67	0.598	0.747	SUBCLONAL	1	TRUE	1	0.451788164425453	2		511	634	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778720	3778720	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1433842236	NA	P-0059991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	87	543	0	ENST00000262367.5:c.6328G>T	p.Ala2110Ser	p.A2110S	ENST00000262367	NM_004380.2	2110	Gcc/Tcc	31/31	1	2	FACETS	0.602	0.533	0.675	0.602	0.533	0.675	SUBCLONAL	1	TRUE	1	0.451788164425453	2		543	640	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204106	142204106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	62	354	0	ENST00000350721.4:c.6097C>T	p.Pro2033Ser	p.P2033S	ENST00000350721	NM_001184.3	2033	Cca/Tca	36/47	1	2	FACETS	0.522	0.451	0.599	0.522	0.451	0.599	SUBCLONAL	1	TRUE	1	0.451788164425453	2		354	526	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	900663	900663	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	rs749626469	NA	P-0059991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	62	350	0	ENST00000166345.3:c.443A>T	p.His148Leu	p.H148L	ENST00000166345	NM_004237.3	148	cAt/cTt	4/13	1	2	FACETS	0.595	0.515	0.682	0.595	0.515	0.682	SUBCLONAL	1	TRUE	1	0.451788164425453	2		350	461	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457680	149457680	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1297158711	NA	P-0059991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	51	483	0	ENST00000286301.3:c.724A>G	p.Thr242Ala	p.T242A	ENST00000286301	NM_005211.3	242	Acc/Gcc	5/22	1	2	FACETS	0.421	0.358	0.491	0.421	0.358	0.491	SUBCLONAL	1	TRUE	1	0.451788164425453	2		483	536	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187222	38187222	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	99	424	1	ENST00000317025.8:c.1255del	p.Thr419ProfsTer8	p.T419Pfs*8	ENST00000317025	NM_023034.1	419	Acc/cc	6/24	1	2	FACETS	0.589	0.526	0.656	0.589	0.526	0.656	SUBCLONAL	1	TRUE	1	0.451788164425453	2		425	744	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2084186	2084186	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	60	287	0	ENST00000349721.2:c.2516T>C	p.Ile839Thr	p.I839T	ENST00000349721	NM_003070.3	839	aTt/aCt	17/34	1	2	FACETS	0.592	0.511	0.679	0.592	0.511	0.679	SUBCLONAL	1	TRUE	1	0.451788164425453	2		287	449	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2115921	2115921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059991-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	81	457	0	ENST00000349721.2:c.3556G>A	p.Ala1186Thr	p.A1186T	ENST00000349721	NM_003070.3	1186	Gcg/Acg	25/34	1	2	FACETS	0.514	0.452	0.58	0.514	0.452	0.58	SUBCLONAL	1	TRUE	1	0.451788164425453	2		457	698	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs104886003	NA	P-0059993-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	227	277	0	ENST00000263967.3:c.1633G>C	p.Glu545Gln	p.E545Q	ENST00000263967	NM_006218.2	545	Gag/Cag	10/21	0.670596110702481	3	FACETS	1	0.979	1	0.714	0.676	0.752	CLONAL	2	TRUE	0	0.670596110702481	3		277	422	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0059993-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	345	577	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.668959702878551	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.670596110702481	2		577	499	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902229	151902229	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0059993-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	98	217	0	ENST00000262189.6:c.3923C>G	p.Ser1308Ter	p.S1308*	ENST00000262189	NM_170606.2	1308	tCa/tGa	25/59	1	2	FACETS	0.987	0.893	1	0.987	0.893	1	CLONAL	1	TRUE	1	0.670596110702481	2		217	296	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295404	1295404	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0059993-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	127	590	0				ENST00000310581	NM_198253.2	-/1132			0.621250808605409	4	FACETS	0.971	0.881	1	0.485	0.44	0.532	CLONAL	1	TRUE	2	0.670596110702481	4		590	652	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223589	36223589	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059993-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	369	759	0	ENST00000222270.7:c.6139C>G	p.Leu2047Val	p.L2047V	ENST00000222270	NM_014727.1	2047	Ctg/Gtg	28/37	0.521809002836923	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.670596110702481	4		759	856	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437197	52437198	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0059993-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	438	545	0	ENST00000460680.1:c.1846dup	p.Val616GlyfsTer27	p.V616Gfs*27	ENST00000460680	NM_004656.3	616	gtg/gGtg	14/17	0.670596110702481	3	FACETS	0.979	0.95	1	0.979	0.95	1	CLONAL	3	TRUE	0	0.670596110702481	3		545	594	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225674	26225674	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059993-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	279	787	0	ENST00000360408.1:c.292G>A	p.Glu98Lys	p.E98K	ENST00000360408	NM_003532.2	98	Gag/Aag	1/1	0.670596110702481	2	FACETS	1	0.985	1	0.558	0.527	0.59	CLONAL	1	TRUE	0	0.670596110702481	2		787	745	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228223	53228223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059993-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	166	302	0	ENST00000375401.3:c.2179G>A	p.Gly727Ser	p.G727S	ENST00000375401	NM_004187.3	727	Ggc/Agc	15/26	0.670596110702481	2	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.670596110702481	2		302	419	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0059994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	154	300	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.319283952046586	3	FACETS	0.888	0.822	0.956	1	0.987	1	CLONAL	3	TRUE	1	0.32723736494604	3		300	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0059994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	231	526	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.303171255376081	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.32723736494604	2		526	639	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368287	45368287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	162	353	0	ENST00000262160.6:c.1315G>A	p.Glu439Lys	p.E439K	ENST00000262160	NM_005901.5	439	Gaa/Aaa	11/11	0.32723736494604	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.32723736494604	2		353	452	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446276	29446276	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	180	554	0	ENST00000389048.3:c.3291C>A	p.Cys1097Ter	p.C1097*	ENST00000389048	NM_004304.4	1097	tgC/tgA	20/29	0.319283952046586	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.32723736494604	3		554	624	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875645	35875645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059995-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	191	396	0	ENST00000303115.3:c.832G>T	p.Asp278Tyr	p.D278Y	ENST00000303115	NM_002185.3	278	Gat/Tat	7/8	0.662004968736011	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.750045470688695	3		396	321	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509853	187509853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748762429	NA	P-0059995-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	138	635	0	ENST00000441802.2:c.13660G>A	p.Glu4554Lys	p.E4554K	ENST00000441802	NM_005245.3	4554	Gaa/Aaa	27/27	1	2	FACETS	0.783	0.732	0.833	1	0.991	1	SUBCLONAL	2	TRUE	1	0.750045470688695	2		635	235	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630078	117630078	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059995-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	96	380	0	ENST00000368508.3:c.6448C>G	p.Leu2150Val	p.L2150V	ENST00000368508	NM_002944.2	2150	Ctg/Gtg	41/43	0.754178894550436	4	FACETS	1	0.974	1	0.633	0.569	0.699	CLONAL	1	TRUE	2	0.750045470688695	4		380	354	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10800335	10800335	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150955197	NA	P-0059995-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	203	606	0	ENST00000361367.2:c.3205G>A	p.Glu1069Lys	p.E1069K	ENST00000361367	NM_014633.3	1069	Gag/Aag	25/25	0.662004968736011	3	FACETS	1	0.992	1	0.74	0.692	0.788	CLONAL	1	TRUE	1	0.750045470688695	3		606	503	SUCCESS
ATM	472	MSKCC	GRCh37	11	108159816	108159816	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1565455224	NA	P-0059995-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	28	112	1	ENST00000278616.4:c.4222C>T	p.Leu1408Phe	p.L1408F	ENST00000278616	NM_000051.3	1408	Ctt/Ttt	28/63	0.662004968736011	3	FACETS	0.969	0.82	1	0.969	0.82	1	CLONAL	2	TRUE	1	0.750045470688695	3		113	53	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185112	99185112	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059995-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	297	439	0	ENST00000074304.5:c.2514G>C	p.Lys838Asn	p.K838N	ENST00000074304	NM_001134224.1	838	aaG/aaC	23/26	0.754178894550436	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	1	0.750045470688695	3		439	441	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0059996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	240	344	2	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.458595275414204	7	FACETS	1	0.967	1	0.628	0.589	0.667	CLONAL	3	TRUE	2	0.458595275414204	7		346	716	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0059996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	423	810	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.465663868341021	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	0	0.458595275414204	3		810	745	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0059996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	48	684	1	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	0.465663868341021	3	FACETS	0.38	0.32	0.445	0.19	0.16	0.223	SUBCLONAL	1	TRUE	1	0.458595275414204	3		685	678	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974715	21974732	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCCCCCGCCTCCA	GCAGCGCCCCCGCCTCCA	-	novel	NA	P-0059996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	185	718	0	ENST00000304494.5:c.95_112del	p.Leu32_Leu37del	p.L32_L37del	ENST00000304494	NM_000077.4	32	cTGGAGGCGGGGGCGCTGCcc/ccc	1/3	NA	2	FACETS	0.853	0.795	0.911			1	INDETERMINATE	2	TRUE	NA	0.458595275414204	2		718	473	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575194	48575194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555685186	NA	P-0059996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	31	381	0	ENST00000342988.3:c.388C>T	p.Pro130Ser	p.P130S	ENST00000342988	NM_005359.5	130	Cca/Tca	3/12	0.434242502894852	3	FACETS	0.428	0.346	0.521	0.214	0.173	0.261	SUBCLONAL	1	TRUE	1	0.458595275414204	3		381	388	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27093045	27093045	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	40	528	0	ENST00000324856.7:c.2976A>T	p.Glu992Asp	p.E992D	ENST00000324856	NM_006015.4	992	gaA/gaT	10/20	0.465663868341021	3	FACETS	0.356	0.295	0.424	0.119	0.098	0.142	SUBCLONAL	1	TRUE	0	0.458595275414204	3		528	603	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77048426	77048426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	35	488	0	ENST00000356341.3:c.1159C>T	p.His387Tyr	p.H387Y	ENST00000356341	NM_002576.4	387	Cac/Tac	12/15	0.275694736407943	5	FACETS	0.409	0.334	0.493	0.136	0.111	0.165	SUBCLONAL	1	TRUE	2	0.458595275414204	5		488	630	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885248	111885248	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	161	688	0	ENST00000341259.2:c.1136A>C	p.Gln379Pro	p.Q379P	ENST00000341259	NM_005475.2	379	cAg/cCg	6/8	0.206858013023837	5	FACETS	0.859	0.79	0.93	0.573	0.526	0.62	INDETERMINATE	2	TRUE	2	0.458595275414204	5		688	690	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712903	43712903	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	83	682	0	ENST00000382044.4:c.4281A>G	p.Ile1427Met	p.I1427M	ENST00000382044	NM_001141980.1	1427	atA/atG	21/28	0.458595275414204	5	FACETS	0.694	0.612	0.783	0.231	0.204	0.261	SUBCLONAL	1	TRUE	2	0.458595275414204	5		682	880	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556119	29556119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567848794	NA	P-0059996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	43	354	0	ENST00000356175.3:c.2486C>T	p.Ser829Phe	p.S829F	ENST00000356175	NM_000267.3	829	tCt/tTt	21/57	0.449417765048204	3	FACETS	0.659	0.553	0.775			1	SUBCLONAL	1	TRUE	NA	0.458595275414204	3		354	350	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872039	37872039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	162	821	0	ENST00000269571.5:c.1360G>A	p.Gly454Arg	p.G454R	ENST00000269571		454	Ggg/Agg	12/27	0.369901690412681	4	FACETS	1	0.979	1	0.301	0.276	0.327	CLONAL	1	TRUE	0	0.458595275414204	4		821	855	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850210	128850210	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	161	489	0	ENST00000249373.3:c.1473G>T	p.Gln491His	p.Q491H	ENST00000249373	NM_005631.4	491	caG/caT	9/12	0.206858013023837	5	FACETS	1	0.967	1	0.726	0.67	0.784	INDETERMINATE	2	TRUE	2	0.458595275414204	5		489	544	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	45	475	0				ENST00000310581	NM_198253.2	-/1132			0.233382366966878	3	FACETS	0.909	0.766	1	0.455	0.383	0.534	CLONAL	1	TRUE	1	0.283191933510769	3		475	399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0059997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	139	614	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	0.219899726058561	2	FACETS	1	0.986	1	0.73	0.666	0.797	CLONAL	1	TRUE	0	0.283191933510769	2		614	672	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668813	52668813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	18	373	0	ENST00000394830.3:c.1106G>A	p.Gly369Glu	p.G369E	ENST00000394830	NM_018313.4	369	gGa/gAa	12/30	1	2	FACETS	0.368	0.277	0.477	0.368	0.277	0.477	SUBCLONAL	1	TRUE	1	0.283191933510769	2		373	345	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332160	70332161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0059997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	63	416	0	ENST00000373644.4:c.65_66insT	p.Lys22AsnfsTer38	p.K22Nfs*38	ENST00000373644	NM_030625.2	22	aag/aaTg	2/12	1	2	FACETS	0.941	0.815	1	0.941	0.815	1	CLONAL	1	TRUE	1	0.283191933510769	2		416	473	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333446	70333446	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	65	505	0	ENST00000373644.4:c.1351G>T	p.Glu451Ter	p.E451*	ENST00000373644	NM_030625.2	451	Gag/Tag	2/12	1	2	FACETS	0.964	0.838	1	0.964	0.838	1	CLONAL	1	TRUE	1	0.283191933510769	2		505	476	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861952	57861952	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	80	555	0	ENST00000228682.2:c.1253G>T	p.Arg418Leu	p.R418L	ENST00000228682	NM_005269.2	418	cGg/cTg	10/12	1	2	FACETS	0.883	0.777	0.996	0.883	0.777	0.996	CLONAL	1	TRUE	1	0.283191933510769	2		555	640	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103510628	103510628	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	36	295	0	ENST00000355739.4:c.532G>C	p.Glu178Gln	p.E178Q	ENST00000355739	NM_000123.3	178	Gag/Cag	6/15	0.283191933510769	1	FACETS	0.906	0.749	1	0.906	0.749	1	CLONAL	1	TRUE	0	0.283191933510769	1		295	241	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061207	38061207	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	58	546	0	ENST00000250448.2:c.782G>T	p.Arg261Leu	p.R261L	ENST00000250448	NM_004496.3	261	cGc/cTc	2/2	1	2	FACETS	0.707	0.608	0.816	0.707	0.608	0.816	SUBCLONAL	1	TRUE	1	0.283191933510769	2		546	579	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348652	89348652	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	34	497	0	ENST00000301030.4:c.4298C>G	p.Ser1433Cys	p.S1433C	ENST00000301030	NM_001256183.1	1433	tCc/tGc	9/13	1	2	FACETS	0.538	0.44	0.65	0.538	0.44	0.65	SUBCLONAL	1	TRUE	1	0.283191933510769	2		497	446	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604724	48604724	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	29	486	0	ENST00000342988.3:c.1546C>A	p.Gln516Lys	p.Q516K	ENST00000342988	NM_005359.5	516	Cag/Aag	12/12	1	2	FACETS	0.356	0.285	0.438	0.356	0.285	0.438	SUBCLONAL	1	TRUE	1	0.283191933510769	2		486	575	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966366	25966366	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	59	554	0	ENST00000435504.4:c.2840C>T	p.Pro947Leu	p.P947L	ENST00000435504		947	cCt/cTt	13/13	1	2	FACETS	0.772	0.664	0.888	0.772	0.664	0.888	SUBCLONAL	1	TRUE	1	0.283191933510769	2		554	540	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474023	29474023	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	41	445	0	ENST00000389048.3:c.2152G>T	p.Gly718Cys	p.G718C	ENST00000389048	NM_004304.4	718	Ggc/Tgc	12/29	1	2	FACETS	0.611	0.509	0.724	0.611	0.509	0.724	SUBCLONAL	1	TRUE	1	0.283191933510769	2		445	474	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646144	215646144	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0059997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	46	417	0	ENST00000260947.4:c.454A>T	p.Lys152Ter	p.K152*	ENST00000260947	NM_000465.2	152	Aag/Tag	4/11	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.283191933510769	2		417	312	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256482	46256482	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	88	475	0	ENST00000371998.3:c.710A>C	p.Glu237Ala	p.E237A	ENST00000371998		237	gAg/gCg	7/23	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.283191933510769	2		475	574	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156944	89156944	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	91	376	0	ENST00000336596.2:c.46C>A	p.Leu16Ile	p.L16I	ENST00000336596	NM_005233.5	16	Ctc/Atc	1/17	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.283191933510769	2		376	488	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628927	187628927	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	55	516	0	ENST00000441802.2:c.2055G>C	p.Glu685Asp	p.E685D	ENST00000441802	NM_005245.3	685	gaG/gaC	2/27	0.178115215380508	0	FACETS	0.571	0.488	0.66			1	SUBCLONAL	1	TRUE	0	0.283191933510769	0		516	488	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509378	106509378	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	45	529	0	ENST00000359195.3:c.1372G>C	p.Val458Leu	p.V458L	ENST00000359195	NM_002649.2	458	Gtt/Ctt	2/11	1	2	FACETS	0.513	0.43	0.604	0.513	0.43	0.604	SUBCLONAL	1	TRUE	1	0.283191933510769	2		529	620	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874488	151874488	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	90	535	0	ENST00000262189.6:c.8050G>T	p.Gly2684Cys	p.G2684C	ENST00000262189	NM_170606.2	2684	Ggt/Tgt	38/59	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.283191933510769	2		535	463	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878375	151878376	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0059997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	42	494	0	ENST00000262189.6:c.6569_6570del	p.Phe2190CysfsTer11	p.F2190Cfs*11	ENST00000262189	NM_170606.2	2190	tTT/t	36/59	1	2	FACETS	0.491	0.409	0.582	0.491	0.409	0.582	SUBCLONAL	1	TRUE	1	0.283191933510769	2		494	604	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209573	98209573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1054532927	NA	P-0059997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	134	505	0	ENST00000331920.6:c.3965C>T	p.Ala1322Val	p.A1322V	ENST00000331920	NM_000264.3	1322	gCt/gTt	23/24	0.274131605046476	2	FACETS	0.935	0.855	1	0.935	0.855	1	CLONAL	2	TRUE	0	0.283191933510769	2		505	506	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0059998-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	74	300	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.167043561448922	2	FACETS	0.929	0.823	1	0.465	0.411	0.521	INDETERMINATE	1	TRUE	0	0.568663603954646	2		300	280	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577107	7577107	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1057523347	NA	P-0059998-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	248	497	0	ENST00000269305.4:c.831T>A	p.Cys277Ter	p.C277*	ENST00000269305	NM_001126112.2	277	tgT/tgA	8/11	0.568663603954646	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.568663603954646	1		497	512	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570063	212570063	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746784831	NA	P-0059998-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	56	390	1	ENST00000342788.4:c.1178G>A	p.Arg393Gln	p.R393Q	ENST00000342788	NM_005235.2	393	cGg/cAg	10/28	1	2	FACETS	0.738	0.638	0.845	0.738	0.638	0.845	SUBCLONAL	1	TRUE	1	0.568663603954646	2		391	267	SUCCESS
APC	324	MSKCC	GRCh37	5	112174058	112174058	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0059998-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	78	473	0	ENST00000257430.4:c.2767A>T	p.Arg923Ter	p.R923*	ENST00000257430	NM_000038.5	923	Aga/Tga	16/16	1	2	FACETS	0.797	0.706	0.894	0.797	0.706	0.894	SUBCLONAL	1	TRUE	1	0.568663603954646	2		473	344	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435201	18435202	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1565550462	NA	P-0059998-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	100	495	0	ENST00000266497.5:c.192dup	p.Val65CysfsTer16	p.V65Cfs*16	ENST00000266497		62	-/T	1/31	0.568663603954646	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.568663603954646	1		495	247	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433689	49433689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760968358	NA	P-0059998-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	69	626	0	ENST00000301067.7:c.7864G>A	p.Asp2622Asn	p.D2622N	ENST00000301067	NM_003482.3	2622	Gac/Aac	31/54	0.167043561448922	2	FACETS	0.453	0.395	0.515	0.226	0.197	0.258	INDETERMINATE	1	TRUE	0	0.568663603954646	2		626	536	SUCCESS
APC	324	MSKCC	GRCh37	5	112175656	112175656	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059998-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	168	513	0	ENST00000257430.4:c.4365del	p.Asn1455LysfsTer18	p.N1455Kfs*18	ENST00000257430	NM_000038.5	1455	aaT/aa	16/16	1	2	FACETS	0.962	0.889	1	0.962	0.889	1	CLONAL	1	TRUE	1	0.568663603954646	2		513	614	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603039	48603039	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059998-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	184	389	0	ENST00000342988.3:c.1340T>G	p.Met447Arg	p.M447R	ENST00000342988	NM_005359.5	447	aTg/aGg	11/12	0.568663603954646	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.568663603954646	1		389	423	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003197	143003197	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059998-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	53	305	0	ENST00000262992.4:c.2629G>C	p.Asp877His	p.D877H	ENST00000262992	NM_001101669.1	877	Gat/Cat	23/24	0.393018313409881	1	FACETS	0.554	0.477	0.636	0.554	0.477	0.636	SUBCLONAL	1	TRUE	0	0.568663603954646	1		305	241	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123199732	123199732	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059998-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	15	293	0	ENST00000218089.9:c.2032G>T	p.Glu678Ter	p.E678*	ENST00000218089	NM_001042749.1	678	Gaa/Taa	21/35	1	2	FACETS	0.44	0.324	0.575	0.44	0.324	0.575	SUBCLONAL	1	TRUE	1	0.568663603954646	2		293	120	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0059999-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	255	569	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.584443879511174	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.584443879511174	1		569	590	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0059999-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	1517	497	2	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.584443879511174	7	FACETS	1	0.995	1			1	CLONAL	7	TRUE	NA	0.584443879511174	7		499	1798	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920413	114920413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767830105	NA	P-0059999-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	194	421	1	ENST00000543371.1:c.1354G>A	p.Gly452Arg	p.G452R	ENST00000543371	NM_001198531.1	452	Ggg/Agg	13/14	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.584443879511174	2		422	634	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55974004	55974004	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754979123	NA	P-0059999-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	166	541	0	ENST00000263923.4:c.1312G>A	p.Gly438Ser	p.G438S	ENST00000263923	NM_002253.2	438	Ggc/Agc	10/30	0.180379256849737	1	FACETS	0.595	0.548	0.643	0.595	0.548	0.643	INDETERMINATE	1	TRUE	0	0.584443879511174	1		541	676	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488222	56488222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059999-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	238	566	0	ENST00000267101.3:c.1741G>A	p.Asp581Asn	p.D581N	ENST00000267101	NM_001982.3	581	Gat/Aat	15/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.584443879511174	2		566	724	SUCCESS
APC	324	MSKCC	GRCh37	5	112176021	112176021	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059999-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	178	531	0	ENST00000257430.4:c.4731del	p.Glu1577AspfsTer73	p.E1577Dfs*73	ENST00000257430	NM_000038.5	1577	gAa/ga	16/16	1	2	FACETS	0.848	0.784	0.915	0.848	0.784	0.915	CLONAL	1	TRUE	1	0.584443879511174	2		531	718	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953041	2953041	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149857605	NA	P-0059999-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	202	544	0	ENST00000396946.4:c.2899C>T	p.Arg967Cys	p.R967C	ENST00000396946	NM_032415.4	967	Cgc/Tgc	22/25	0.584443879511174	3	FACETS	1	0.965	1	0.532	0.494	0.572	CLONAL	1	TRUE	1	0.584443879511174	3		544	839	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434174	12434174	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059999-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	155	500	1	ENST00000287820.6:c.542G>T	p.Arg181Leu	p.R181L	ENST00000287820	NM_015869.4	181	cGg/cTg	4/7	1	2	FACETS	0.768	0.704	0.833	0.768	0.704	0.833	SUBCLONAL	1	TRUE	1	0.584443879511174	2		501	691	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430250	181430251	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0059999-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	285	498	0	ENST00000325404.1:c.107dup	p.Asn36LysfsTer60	p.N36Kfs*60	ENST00000325404	NM_003106.3	34	-/A	1/1	0.380853862478799	3	FACETS	0.884	0.836	0.932	0.884	0.836	0.932	CLONAL	2	TRUE	1	0.584443879511174	3		498	713	SUCCESS
APC	324	MSKCC	GRCh37	5	112174004	112174007	+	frameshift_variant	Frame_Shift_Del	DEL	AGTT	AGTT	-	novel	NA	P-0059999-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	198	571	0	ENST00000257430.4:c.2713_2716del	p.Ser905LeufsTer10	p.S905Lfs*10	ENST00000257430	NM_000038.5	905	AGTTct/ct	16/16	1	2	FACETS	0.935	0.868	1	0.935	0.868	1	CLONAL	1	TRUE	1	0.584443879511174	2		571	725	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370757	55370757	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059999-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	176	556	3	ENST00000297316.4:c.59del	p.Leu20ArgfsTer4	p.L20Rfs*4	ENST00000297316	NM_022454.3	20	cTg/cg	1/2	1	2	FACETS	0.983	0.91	1	0.983	0.91	1	CLONAL	1	TRUE	1	0.584443879511174	2		559	613	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0060012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	92	332	0	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.426308972148249	3	FACETS	0.568	0.505	0.634	0.189	0.168	0.212	INDETERMINATE	1	TRUE	0	0.816833468769356	3		332	559	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691872	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs79375991	NA	P-0060012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	345	422	13	ENST00000295754.5:c.383del	p.Lys128SerfsTer35	p.K128Sfs*35	ENST00000295754	NM_003242.5	125	gAa/ga	3/7	0.816833468769356	2	FACETS	1	0.995	1	0.692	0.663	0.722	CLONAL	1	TRUE	0	0.816833468769356	2		435	610	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0060012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	206	280	2	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			0.806037489039283	2	FACETS	0.959	0.921	0.995	0.959	0.921	0.995	CLONAL	2	TRUE	0	0.816833468769356	2		282	263	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233090	69233090	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746910913	NA	P-0060012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	108	505	2	ENST00000462284.1:c.961del	p.Leu321PhefsTer52	p.L321Ffs*52	ENST00000462284	NM_002392.5	319	Ccc/cc	11/11	0.816833468769356	2	FACETS	0.462	0.416	0.511	0.231	0.208	0.256	SUBCLONAL	1	TRUE	0	0.816833468769356	2		507	572	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950860	32950860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373203204	NA	P-0060012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	60	467	0	ENST00000380152.3:c.8686C>T	p.Arg2896Cys	p.R2896C	ENST00000380152		2896	Cgt/Tgt	21/27	0.806037489039283	2	FACETS	0.305	0.263	0.351	0.153	0.131	0.176	SUBCLONAL	1	TRUE	0	0.816833468769356	2		467	481	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696740	47696740	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	433	397	0	ENST00000347630.2:c.208C>T	p.Arg70Ter	p.R70*	ENST00000347630	NM_001007230.1	70	Cga/Tga	5/11	0.816833468769356	2	FACETS	0.987	0.961	1	0.987	0.961	1	CLONAL	2	TRUE	0	0.816833468769356	2		397	537	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042545	37042545	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs267607734	NA	P-0060012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	317	348	0	ENST00000231790.2:c.306+1G>A		p.X102_splice	ENST00000231790	NM_000249.3	102			0.816833468769356	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.816833468769356	2		348	376	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751214	128751214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766666917	NA	P-0060012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	125	524	0	ENST00000377970.2:c.751G>A	p.Glu251Lys	p.E251K	ENST00000377970	NM_002467.4	251	Gag/Aag	2/3	0.816833468769356	2	FACETS	0.518	0.47	0.568	0.259	0.235	0.284	SUBCLONAL	1	TRUE	0	0.816833468769356	2		524	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577497	7577497	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0060012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	520	470	0	ENST00000269305.4:c.782+2T>C		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.816833468769356	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.816833468769356	2		470	609	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451273	70451273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	168	688	0	ENST00000373644.4:c.6113G>A	p.Arg2038His	p.R2038H	ENST00000373644	NM_030625.2	2038	cGt/cAt	12/12	0.789272612315006	2	FACETS	0.687	0.634	0.741	0.343	0.317	0.371	SUBCLONAL	1	TRUE	0	0.816833468769356	2		688	599	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459495	50459495	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	91	460	0	ENST00000331340.3:c.784C>A	p.Leu262Ile	p.L262I	ENST00000331340	NM_006060.4	262	Ctc/Atc	7/8	0.787489838272797	2	FACETS	0.459	0.409	0.512	0.23	0.204	0.256	SUBCLONAL	1	TRUE	0	0.816833468769356	2		460	485	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588751	29588751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760703505	NA	P-0060012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	392	382	0	ENST00000356175.3:c.4537C>T	p.Arg1513Ter	p.R1513*	ENST00000356175	NM_000267.3	1513	Cga/Tga	34/57	0.787638983243479	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.816833468769356	2		382	477	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150923040	150923040	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	386	481	0	ENST00000271640.5:c.1687T>G	p.Ser563Ala	p.S563A	ENST00000271640	NM_001145415.1	563	Tcc/Gcc	13/22	0.789272612315006	2	FACETS	0.93	0.902	0.957	0.93	0.902	0.957	CLONAL	2	TRUE	0	0.816833468769356	2		481	508	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225531	133225531	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	373	510	0	ENST00000320574.5:c.4133G>T	p.Gly1378Val	p.G1378V	ENST00000320574	NM_006231.2	1378	gGt/gTt	32/49	0.816833468769356	2	FACETS	0.961	0.933	0.988	0.961	0.933	0.988	CLONAL	2	TRUE	0	0.816833468769356	2		510	475	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61305180	61305180	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	586	552	0	ENST00000341074.5:c.946G>T	p.Gly316Cys	p.G316C	ENST00000341074	NM_002974.2	316	Ggc/Tgc	8/8	0.816833468769356	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.816833468769356	3		552	665	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6216515	6216515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780435265	NA	P-0060012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	82	404	0	ENST00000252674.7:c.1208G>A	p.Arg403His	p.R403H	ENST00000252674	NM_005934.3	403	cGc/cAc	8/12	0.816833468769356	3	FACETS	0.45	0.396	0.506	0.15	0.132	0.169	SUBCLONAL	1	TRUE	0	0.816833468769356	3		404	629	SUCCESS
REL	5966	MSKCC	GRCh37	2	61148949	61148949	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	107	496	0	ENST00000295025.8:c.1139T>G	p.Val380Gly	p.V380G	ENST00000295025	NM_002908.2	380	gTt/gGt	11/11	0.816833468769356	2	FACETS	0.452	0.407	0.501	0.226	0.203	0.251	SUBCLONAL	1	TRUE	0	0.816833468769356	2		496	579	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713601	30713601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202168735	NA	P-0060012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	530	620	0	ENST00000295754.5:c.926C>T	p.Thr309Met	p.T309M	ENST00000295754	NM_003242.5	309	aCg/aTg	4/7	0.816833468769356	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.816833468769356	2		620	637	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803453	1803453	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	395	696	0	ENST00000260795.2:c.722A>G	p.Tyr241Cys	p.Y241C	ENST00000260795		241	tAc/tGc	5/17	0.816833468769356	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.816833468769356	1		696	524	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230806	66230806	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1560456953	NA	P-0060012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	170	466	0	ENST00000273854.3:c.2165T>C	p.Leu722Pro	p.L722P	ENST00000273854	NM_004439.5	722	cTa/cCa	12/18	0.816833468769356	2	FACETS	1	0.957	1	0.519	0.483	0.555	CLONAL	1	TRUE	0	0.816833468769356	2		466	401	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927100	131927100	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0060012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	303	359	0	ENST00000265335.6:c.1635+2T>C		p.X545_splice	ENST00000265335		545			0.426308972148249	3	FACETS	1	0.993	1	0.786	0.755	0.816	INDETERMINATE	2	TRUE	0	0.816833468769356	3		359	443	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855199	76855199	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0060012-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	188	188	0	ENST00000373344.5:c.5786+2T>C		p.X1929_splice	ENST00000373344	NM_000489.3	1929			1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.816833468769356	1		188	226	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0060015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	131	569	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.386660351833692	1	FACETS	0.356	0.323	0.391	0.356	0.323	0.391	SUBCLONAL	1	TRUE	0	0.637074844994697	1		569	787	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	251	554	0	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	0.386660351833692	1	FACETS	0.824	0.775	0.872	0.824	0.775	0.872	CLONAL	1	TRUE	0	0.637074844994697	1		554	652	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0060015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	116	533	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.386660351833692	1	FACETS	0.369	0.333	0.407	0.369	0.333	0.407	SUBCLONAL	1	TRUE	0	0.637074844994697	1		533	673	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81971386	81971386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774452862	NA	P-0060015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	260	508	0	ENST00000359376.3:c.3076G>A	p.Ala1026Thr	p.A1026T	ENST00000359376	NM_002661.3	1026	Gca/Aca	28/33	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.637074844994697	2		508	774	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578453	7578453	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	324	634	0	ENST00000269305.4:c.477del	p.Met160TrpfsTer10	p.M160Wfs*10	ENST00000269305	NM_001126112.2	159	gcC/gc	5/11	0.386660351833692	1	FACETS	0.796	0.754	0.838	0.796	0.754	0.838	SUBCLONAL	1	TRUE	0	0.637074844994697	1		634	871	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620403	43620403	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060015-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	286	534	0	ENST00000355710.3:c.3012C>A	p.Asp1004Glu	p.D1004E	ENST00000355710	NM_020975.4	1004	gaC/gaA	18/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.637074844994697	2		534	848	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251216	99251216	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060016-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	74	525	0	ENST00000268035.6:c.520C>T	p.Pro174Ser	p.P174S	ENST00000268035	NM_000875.3	174	Ccc/Tcc	2/21	1	2	FACETS	0.795	0.7	0.894	1	0.978	1	SUBCLONAL	2	TRUE	1	0.266851080178214	2		525	349	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0060017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	49	439	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.182064311798724	3	FACETS	0.976	0.826	1	0.488	0.413	0.571	CLONAL	1	TRUE	1	0.18	3		439	608	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0060017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	38	446	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.821	0.678	0.981	0.821	0.678	0.981	CLONAL	1	TRUE	1	0.18	2		446	514	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519927	NA	P-0060017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	8	220	0	ENST00000263967.3:c.1625A>C	p.Glu542Ala	p.E542A	ENST00000263967	NM_006218.2	542	gAa/gCa	10/21	0.182064311798724	3	FACETS	0.394	0.253	0.577	0.197	0.126	0.289	SUBCLONAL	1	TRUE	1	0.18	3		220	246	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0060017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	41	238	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.18	2		238	378	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0060017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	31	377	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	1	2	FACETS	0.59	0.476	0.72	0.59	0.476	0.72	SUBCLONAL	1	TRUE	1	0.18	2		377	584	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	51	614	0	ENST00000227507.2:c.859C>T	p.Pro287Ser	p.P287S	ENST00000227507	NM_053056.2	287	Ccc/Tcc	5/5	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.18	2		614	539	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692911	89692911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909241	NA	P-0060017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	11	360	0	ENST00000371953.3:c.395G>A	p.Gly132Asp	p.G132D	ENST00000371953	NM_000314.4	132	gGt/gAt	5/9	1	2	FACETS	0.243	0.166	0.338	0.243	0.166	0.338	SUBCLONAL	1	TRUE	1	0.18	2		360	504	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720699	89720699	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs786202840	NA	P-0060017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	12	79	0	ENST00000371953.3:c.850G>T	p.Glu284Ter	p.E284*	ENST00000371953	NM_000314.4	284	Gag/Tag	8/9	1	2	FACETS	1	0.777	1	1	0.777	1	CLONAL	1	TRUE	1	0.18	2		79	119	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693002	89693003	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0060017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	25	368	0	ENST00000371953.3:c.491dup	p.Val166SerfsTer14	p.V166Sfs*14	ENST00000371953	NM_000314.4	162	-/A	5/9	1	2	FACETS	0.604	0.475	0.753	0.604	0.475	0.753	SUBCLONAL	1	TRUE	1	0.18	2		368	460	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116168	67116168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1467426352	NA	P-0060017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	57	381	1	ENST00000412916.2:c.452G>A	p.Arg151His	p.R151H	ENST00000412916		151	cGc/cAc	5/6	1	2	FACETS	0.997	0.855	1	0.997	0.855	1	CLONAL	1	TRUE	1	0.18	2		382	635	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288140	21288140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	31	492	2	ENST00000354336.3:c.385C>T	p.Arg129Trp	p.R129W	ENST00000354336	NM_005207.3	129	Cgg/Tgg	2/3	1	2	FACETS	0.577	0.465	0.704	0.577	0.465	0.704	SUBCLONAL	1	TRUE	1	0.18	2		494	597	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50143282	50143282	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	27	462	0	ENST00000246792.3:c.74del	p.Pro25ArgfsTer21	p.P25Rfs*21	ENST00000246792	NM_006270.3	25	cCg/cg	1/6	1	2	FACETS	0.804	0.64	0.992	0.804	0.64	0.992	CLONAL	1	TRUE	1	0.18	2		462	373	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100343	27100344	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0060017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	47	583	0	ENST00000324856.7:c.4059dup	p.Phe1354LeufsTer91	p.F1354Lfs*91	ENST00000324856	NM_006015.4	1352	agc/agCc	17/20	1	2	FACETS	0.812	0.684	0.954	0.812	0.684	0.954	CLONAL	1	TRUE	1	0.18	2		583	643	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653837	89653869	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATACAGGAACAATATTGATGATGTAGTAAGGTA	ATACAGGAACAATATTGATGATGTAGTAAGGTA	-	novel	NA	P-0060017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	17	302	0	ENST00000371953.3:c.136_164+4del		p.X46_splice	ENST00000371953	NM_000314.4	46		2/9	1	2	FACETS	0.651	0.486	0.848	0.651	0.486	0.848	SUBCLONAL	1	TRUE	1	0.18	2		302	290	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426065	49426065	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	40	617	0	ENST00000301067.7:c.12423A>C	p.Leu4141Phe	p.L4141F	ENST00000301067	NM_003482.3	4141	ttA/ttC	39/54	1	2	FACETS	0.762	0.632	0.907	0.762	0.632	0.907	CLONAL	1	TRUE	1	0.18	2		617	583	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950348	17950348	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060017-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	48	538	0	ENST00000458235.1:c.1379G>T	p.Gly460Val	p.G460V	ENST00000458235	NM_000215.3	460	gGg/gTg	10/24	1	2	FACETS	0.904	0.763	1	0.904	0.763	1	CLONAL	1	TRUE	1	0.18	2		538	590	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0060018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	115	388	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.751	0.678	0.828	0.751	0.678	0.828	SUBCLONAL	1	TRUE	1	0.463958514679407	2		388	660	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0060018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	107	478	4	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.613	0.549	0.68	0.613	0.549	0.68	SUBCLONAL	1	TRUE	1	0.463958514679407	2		482	753	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822586	72822586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	104	526	1	ENST00000268489.5:c.9589del	p.Gln3197SerfsTer44	p.Q3197Sfs*44	ENST00000268489	NM_006885.3	3197	Cag/ag	10/10	1	2	FACETS	0.56	0.501	0.622	0.56	0.501	0.622	SUBCLONAL	1	TRUE	1	0.463958514679407	2		527	801	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0060018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	90	465	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	0.643	0.572	0.72	0.643	0.572	0.72	SUBCLONAL	1	TRUE	1	0.463958514679407	2		465	603	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053022	180053023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750808726	NA	P-0060018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	76	610	1	ENST00000261937.6:c.1267dup	p.Gln423ProfsTer4	p.Q423Pfs*4	ENST00000261937	NM_182925.4	423	cag/cCag	10/30	1	2	FACETS	0.473	0.415	0.536	0.473	0.415	0.536	SUBCLONAL	1	TRUE	1	0.463958514679407	2		611	692	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0060018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	145	620	3	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.677	0.617	0.74	0.677	0.617	0.74	SUBCLONAL	1	TRUE	1	0.463958514679407	2		623	923	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0060018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	120	586	0	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.644	0.582	0.71	0.644	0.582	0.71	SUBCLONAL	1	TRUE	1	0.463958514679407	2		586	803	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0060018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	96	415	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.656	0.585	0.731	0.656	0.585	0.731	SUBCLONAL	1	TRUE	1	0.463958514679407	2		415	631	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	67	503	0	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.56	0.487	0.638	0.56	0.487	0.638	SUBCLONAL	1	TRUE	1	0.463958514679407	2		503	516	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176540	56176540	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1305030339	NA	P-0060018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	104	359	0	ENST00000399503.3:c.2090G>A	p.Arg697His	p.R697H	ENST00000399503	NM_005921.1	697	cGc/cAc	12/20	1	2	FACETS	0.668	0.599	0.742	0.668	0.599	0.742	SUBCLONAL	1	TRUE	1	0.463958514679407	2		359	671	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101054	27101054	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	102	454	0	ENST00000324856.7:c.4336C>T	p.Arg1446Ter	p.R1446*	ENST00000324856	NM_006015.4	1446	Cga/Tga	18/20	1	2	FACETS	0.698	0.625	0.775	0.698	0.625	0.775	SUBCLONAL	1	TRUE	1	0.463958514679407	2		454	630	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	110	544	0	ENST00000227507.2:c.859C>G	p.Pro287Ala	p.P287A	ENST00000227507	NM_053056.2	287	Ccc/Gcc	5/5	1	2	FACETS	0.643	0.577	0.711	0.643	0.577	0.711	SUBCLONAL	1	TRUE	1	0.463958514679407	2		544	738	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	134	569	1	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.63	0.572	0.691	0.63	0.572	0.691	SUBCLONAL	1	TRUE	1	0.463958514679407	2		570	917	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449475	149449475	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576921324	NA	P-0060018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	90	467	0	ENST00000286301.3:c.1471G>A	p.Val491Met	p.V491M	ENST00000286301	NM_005211.3	491	Gtg/Atg	10/22	1	2	FACETS	0.637	0.566	0.713	0.637	0.566	0.713	SUBCLONAL	1	TRUE	1	0.463958514679407	2		467	609	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267002	41267002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	125	559	2	ENST00000349496.5:c.673C>T	p.Arg225Cys	p.R225C	ENST00000349496	NM_001904.3	225	Cgt/Tgt	5/15	1	2	FACETS	0.641	0.58	0.706	0.641	0.58	0.706	SUBCLONAL	1	TRUE	1	0.463958514679407	2		561	840	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717719	89717720	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs780264945	NA	P-0060018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	66	338	0	ENST00000371953.3:c.750_751del	p.Cys250TrpfsTer2	p.C250Wfs*2	ENST00000371953	NM_000314.4	248	ccTGtg/cctg	7/9	1	2	FACETS	0.544	0.473	0.621	0.544	0.473	0.621	SUBCLONAL	1	TRUE	1	0.463958514679407	2		338	523	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566114	141566114	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	219	438	0	ENST00000220592.5:c.1150C>T	p.Arg384Ter	p.R384*	ENST00000220592	NM_012154.3	384	Cga/Tga	10/19	0.303605661893279	3	FACETS	1	0.991	1	0.697	0.65	0.746	CLONAL	1	TRUE	1	0.463958514679407	3		438	834	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720869	89720869	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1564568689	NA	P-0060018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	48	191	0	ENST00000371953.3:c.1023del	p.Phe341LeufsTer3	p.F341Lfs*3	ENST00000371953	NM_000314.4	340	aaT/aa	8/9	1	2	FACETS	0.645	0.547	0.75	0.645	0.547	0.75	SUBCLONAL	1	TRUE	1	0.463958514679407	2		191	321	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778839	9778839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143521812	NA	P-0060018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	87	558	2	ENST00000377346.4:c.1108G>A	p.Val370Met	p.V370M	ENST00000377346	NM_005026.3	370	Gtg/Atg	9/24	1	2	FACETS	0.509	0.45	0.572	0.509	0.45	0.572	SUBCLONAL	1	TRUE	1	0.463958514679407	2		560	737	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584488	39584488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs375465653	NA	P-0060018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	105	458	0	ENST00000262039.4:c.1153C>T	p.Arg385Ter	p.R385*	ENST00000262039	NM_002647.2	385	Cga/Tga	10/25	1	2	FACETS	0.548	0.49	0.609	0.548	0.49	0.609	SUBCLONAL	1	TRUE	1	0.463958514679407	2		458	826	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180522	56180524	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs1397309724	NA	P-0060018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	57	335	0	ENST00000399503.3:c.3857_3859del	p.Glu1286del	p.E1286del	ENST00000399503	NM_005921.1	1284	cAAGaa/caa	16/20	1	2	FACETS	0.608	0.523	0.7	0.608	0.523	0.7	SUBCLONAL	1	TRUE	1	0.463958514679407	2		335	404	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250938	153250938	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0060018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	48	265	0	ENST00000281708.4:c.1123-1G>T		p.X375_splice	ENST00000281708	NM_033632.3	375			1	2	FACETS	0.623	0.529	0.726	0.623	0.529	0.726	SUBCLONAL	1	TRUE	1	0.463958514679407	2		265	332	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905432	11905432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34966596	NA	P-0060018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	80	420	0	ENST00000396373.4:c.82G>A	p.Ala28Thr	p.A28T	ENST00000396373	NM_001987.4	28	Gct/Act	2/8	1	2	FACETS	0.527	0.463	0.594	0.527	0.463	0.594	SUBCLONAL	1	TRUE	1	0.463958514679407	2		420	655	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188182	11188182	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	22	433	0	ENST00000361445.4:c.5912C>A	p.Ala1971Asp	p.A1971D	ENST00000361445	NM_004958.3	1971	gCc/gAc	43/58	1	2	FACETS	0.128	0.098	0.162	0.128	0.098	0.162	SUBCLONAL	1	TRUE	1	0.463958514679407	2		433	743	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204615	108204615	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	68	251	0	ENST00000278616.4:c.7930G>T	p.Gly2644Cys	p.G2644C	ENST00000278616	NM_000051.3	2644	Ggc/Tgc	54/63	1	2	FACETS	0.552	0.481	0.629	0.552	0.481	0.629	SUBCLONAL	1	TRUE	1	0.463958514679407	2		251	531	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500356	99500358	+	inframe_deletion	In_Frame_Del	DEL	CAG	CAG	-	novel	NA	P-0060018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	93	538	0	ENST00000268035.6:c.3794_3796del	p.Ser1265del	p.S1265del	ENST00000268035	NM_000875.3	1263	atCAGc/atc	21/21	1	2	FACETS	0.616	0.548	0.688	0.616	0.548	0.688	SUBCLONAL	1	TRUE	1	0.463958514679407	2		538	651	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715356	61715356	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	65	316	0	ENST00000401558.2:c.2257A>G	p.Arg753Gly	p.R753G	ENST00000401558	NM_003400.3	753	Agg/Ggg	19/25	1	2	FACETS	0.605	0.526	0.691	0.605	0.526	0.691	SUBCLONAL	1	TRUE	1	0.463958514679407	2		316	463	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39762965	39762965	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0060018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	61	302	0	ENST00000288319.7:c.872-1G>T		p.X291_splice	ENST00000288319	NM_182918.3	291			1	2	FACETS	0.607	0.525	0.696	0.607	0.525	0.696	SUBCLONAL	1	TRUE	1	0.463958514679407	2		302	433	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184151	123184151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060018-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	67	338	0	ENST00000218089.9:c.1009C>T	p.His337Tyr	p.H337Y	ENST00000218089	NM_001042749.1	337	Cat/Tat	11/35	1	2	FACETS	0.555	0.483	0.633	0.555	0.483	0.633	SUBCLONAL	1	TRUE	1	0.463958514679407	2		338	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0060019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	165	810	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.580353514068053	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.580353514068053	1		810	371	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984413	201984413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167293860	NA	P-0060019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	238	517	0	ENST00000359651.3:c.1078G>A	p.Gly360Ser	p.G360S	ENST00000359651		360	Ggc/Agc	8/8	0.17890384420477	2	FACETS	1	0.992	1	0.706	0.664	0.748	INDETERMINATE	1	TRUE	0	0.580353514068053	2		517	581	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123888	46123889	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0060019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	234	535	0	ENST00000334344.6:c.156dup	p.Arg53GlnfsTer13	p.R53Qfs*13	ENST00000334344	NM_152641.2	52	acc/aCcc	2/21	0.580353514068053	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.580353514068053	1		535	465	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024218	31024222	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTC	TTCTC	-	novel	NA	P-0060019-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	117	549	0	ENST00000375687.4:c.3706_3710del	p.Ser1236LeufsTer2	p.S1236Lfs*2	ENST00000375687	NM_015338.5	1235	TTCTCt/t	13/13	1	2	FACETS	0.892	0.81	0.978	0.892	0.81	0.978	CLONAL	1	TRUE	1	0.580353514068053	2		549	452	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0060020-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	10	289	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		289	239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs530941076	NA	P-0060020-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	44	499	0	ENST00000269305.4:c.658T>C	p.Tyr220His	p.Y220H	ENST00000269305	NM_001126112.2	220	Tat/Cat	6/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		499	397	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0060026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	60	568	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	1	2	FACETS	0.779	0.67	0.897	1	0.97	1	SUBCLONAL	2	TRUE	1	0.12	2		568	642	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426673	49426673	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060026-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	34	737	0	ENST00000301067.7:c.11815C>T	p.Gln3939Ter	p.Q3939*	ENST00000301067	NM_003482.3	3939	Cag/Tag	39/54	1	2	FACETS	0.842	0.686	1	0.842	0.686	1	CLONAL	1	TRUE	1	0.12	2		737	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0060026-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	278	568	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	0.42807689670804	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.42807689670804	1		568	1000	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570245	87570245	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060026-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	142	871	0	ENST00000277120.3:c.1985C>T	p.Thr662Met	p.T662M	ENST00000277120		662	aCg/aTg	17/19	0.219454498440765	1	FACETS	0.496	0.451	0.543	0.496	0.451	0.543	INDETERMINATE	1	TRUE	0	0.42807689670804	1		871	1052	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426673	49426673	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060026-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	206	737	0	ENST00000301067.7:c.11815C>T	p.Gln3939Ter	p.Q3939*	ENST00000301067	NM_003482.3	3939	Cag/Tag	39/54	1	2	FACETS	0.889	0.824	0.956	0.889	0.824	0.956	CLONAL	1	TRUE	1	0.42807689670804	2		737	1083	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438042	49438051	+	frameshift_variant	Frame_Shift_Del	DEL	GTGCGTGTGT	GTGCGTGTGT	-	novel	NA	P-0060026-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	206	862	0	ENST00000301067.7:c.5120_5129del	p.His1707ArgfsTer12	p.H1707Rfs*12	ENST00000301067	NM_003482.3	1707	cACACACGCACg/cg	21/54	1	2	FACETS	0.823	0.762	0.886	0.823	0.762	0.886	CLONAL	1	TRUE	1	0.42807689670804	2		862	1170	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020242	123020242	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060027-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	109	464	0	ENST00000355640.3:c.730G>T	p.Val244Leu	p.V244L	ENST00000355640		244	Gtg/Ttg	2/7	0.191862038345505	0	FACETS	0.449	0.404	0.496			1	INDETERMINATE	1	TRUE	0	0.474810299022764	0		464	537	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223757	53223757	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060027-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	188	652	0	ENST00000375401.3:c.3602A>G	p.Gln1201Arg	p.Q1201R	ENST00000375401	NM_004187.3	1201	cAg/cGg	23/26	1	2	FACETS	0.928	0.859	1	0.928	0.859	1	CLONAL	1	TRUE	1	0.474810299022764	2		652	853	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0060028-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	206	247	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.707180300102006	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	FALSE	0	0.707180300102006	2		247	275	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56857628	56857628	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759345823	NA	P-0060028-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	105	198	0	ENST00000308159.5:c.664G>A	p.Asp222Asn	p.D222N	ENST00000308159	NM_014669.4	222	Gac/Aac	8/22	0.707180300102006	2	FACETS	1	0.978	1	0.616	0.563	0.67	CLONAL	1	FALSE	0	0.707180300102006	2		198	241	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0060029-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	230	569	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.462590726614267	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.462590726614267	2		569	439	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747084	40747084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762809890	NA	P-0060029-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	338	427	0	ENST00000373198.4:c.2998G>A	p.Ala1000Thr	p.A1000T	ENST00000373198	NM_133170.3	1000	Gcc/Acc	22/32	0.462590726614267	7	FACETS	0.958	0.915	1	0.958	0.915	1	CLONAL	5	TRUE	2	0.462590726614267	7		427	658	SUCCESS
APC	324	MSKCC	GRCh37	5	112174112	112174112	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060029-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	105	393	0	ENST00000257430.4:c.2821G>T	p.Glu941Ter	p.E941*	ENST00000257430	NM_000038.5	941	Gaa/Taa	16/16	0.462590726614267	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.462590726614267	2		393	214	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372459	55372459	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1261506897	NA	P-0060029-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	98	617	0	ENST00000297316.4:c.1149C>G	p.Asp383Glu	p.D383E	ENST00000297316	NM_022454.3	383	gaC/gaG	2/2	0.424106277717876	5	FACETS	1	0.944	1	0.363	0.324	0.405	CLONAL	1	TRUE	2	0.462590726614267	5		617	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579369	7579369	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555526581	NA	P-0060030-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	438	565	0	ENST00000269305.4:c.318C>G	p.Ser106Arg	p.S106R	ENST00000269305	NM_001126112.2	106	agC/agG	4/11	0.852680722231087	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.857462540585543	1		565	541	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107258	193107258	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060030-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	59	357	0	ENST00000367435.3:c.467G>A	p.Arg156His	p.R156H	ENST00000367435	NM_024529.4	156	cGt/cAt	6/17	1	2	FACETS	0.181	0.155	0.21	0.181	0.155	0.21	SUBCLONAL	1	TRUE	1	0.857462540585543	2		357	759	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21351190	21351190	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060030-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	35	642	0	ENST00000215739.8:c.2341G>T	p.Asp781Tyr	p.D781Y	ENST00000215739	NM_006767.3	781	Gac/Tac	20/21	0.857462540585543	1	FACETS	0.085	0.069	0.103	0.085	0.069	0.103	SUBCLONAL	1	TRUE	0	0.857462540585543	1		642	547	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161807854	161807854	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060030-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	280	403	0	ENST00000366898.1:c.1139T>A	p.Val380Glu	p.V380E	ENST00000366898	NM_004562.2	380	gTa/gAa	10/12	0.440079298791906	1	FACETS	0.711	0.676	0.745	0.711	0.676	0.745	INDETERMINATE	1	TRUE	0	0.857462540585543	1		403	525	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878344	151878344	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060030-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	143	486	0	ENST00000262189.6:c.6601G>T	p.Asp2201Tyr	p.D2201Y	ENST00000262189	NM_170606.2	2201	Gat/Tat	36/59	0.431391953277911	1	FACETS	0.315	0.288	0.344	0.315	0.288	0.344	INDETERMINATE	1	TRUE	0	0.857462540585543	1		486	604	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	57	475	0				ENST00000310581	NM_198253.2	-/1132			0.226316691782894	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.884932140224895	0		475	130	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0060031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	201	574	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.884932140224895	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.884932140224895	1		574	228	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432379	78432379	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	124	255	0	ENST00000370768.2:c.472C>T	p.Gln158Ter	p.Q158*	ENST00000370768	NM_003902.3	158	Cag/Tag	7/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.884932140224895	2		255	267	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965562	93965562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	68	293	0	ENST00000369303.4:c.2366C>T	p.Ala789Val	p.A789V	ENST00000369303	NM_004440.3	789	gCt/gTt	13/17	1	2	FACETS	0.735	0.65	0.824	0.735	0.65	0.824	SUBCLONAL	1	TRUE	1	0.884932140224895	2		293	209	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272089	15272089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	144	588	0	ENST00000263388.2:c.6350C>T	p.Ser2117Phe	p.S2117F	ENST00000263388	NM_000435.2	2117	tCc/tTc	33/33	0.108577088741944	4	FACETS	0.899	0.832	0.967	0.899	0.832	0.967	INDETERMINATE	2	TRUE	2	0.884932140224895	4		588	341	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606929	47606929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	120	304	0	ENST00000263735.4:c.679C>T	p.His227Tyr	p.H227Y	ENST00000263735	NM_002354.2	227	Cat/Tat	7/9	1	2	FACETS	0.935	0.858	1	0.935	0.858	1	CLONAL	1	TRUE	1	0.884932140224895	2		304	290	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979219	93979219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1009626356	NA	P-0060031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	92	355	0	ENST00000369303.4:c.1609G>A	p.Glu537Lys	p.E537K	ENST00000369303	NM_004440.3	537	Gaa/Aaa	7/17	1	2	FACETS	0.941	0.853	1	0.941	0.853	1	CLONAL	1	TRUE	1	0.884932140224895	2		355	221	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959121	2959121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778152	NA	P-0060031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	94	422	0	ENST00000396946.4:c.2395G>A	p.Asp799Asn	p.D799N	ENST00000396946	NM_032415.4	799	Gat/Aat	18/25	NA	2	FACETS	0.857	0.775	0.94			1	INDETERMINATE	1	TRUE	NA	0.884932140224895	2		422	248	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344357	118344357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	214	435	0	ENST00000534358.1:c.2483C>T	p.Ser828Leu	p.S828L	ENST00000534358	NM_005933.3	828	tCa/tTa	3/36	0.882575955105226	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.884932140224895	1		435	265	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998178	100998178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1452692847	NA	P-0060031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	78	361	0	ENST00000325455.5:c.1624C>T	p.Leu542Phe	p.L542F	ENST00000325455	NM_001202474.3	542	Ctc/Ttc	1/8	0.882575955105226	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.884932140224895	1		361	97	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202413	123202413	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0060031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	30	180	0	ENST00000218089.9:c.2266-1G>A		p.X756_splice	ENST00000218089	NM_001042749.1	756			0.610845568493225	1	FACETS	0.394	0.326	0.466	0.394	0.326	0.466	SUBCLONAL	1	TRUE	0	0.884932140224895	1		180	96	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117541	4117541	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519808	NA	P-0060031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	94	146	0	ENST00000262948.5:c.179A>C	p.Gln60Pro	p.Q60P	ENST00000262948	NM_030662.3	60	cAg/cCg	2/11	0.108577088741944	4	FACETS	0.834	0.768	0.899	1	0.981	1	INDETERMINATE	3	TRUE	2	0.884932140224895	4		146	160	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916538	39916538	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	91	313	0	ENST00000378444.4:c.4465G>A	p.Asp1489Asn	p.D1489N	ENST00000378444	NM_001123385.1	1489	Gat/Aat	11/15	0.162595342220539	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.884932140224895	0		313	260	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435412	121435412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1479408304	NA	P-0060031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	198	504	0	ENST00000257555.6:c.1445G>A	p.Ser482Asn	p.S482N	ENST00000257555		482	aGc/aAc	7/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.884932140224895	2		504	414	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115277070	115277070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	118	269	0	ENST00000438362.2:c.713C>T	p.Ala238Val	p.A238V	ENST00000438362	NM_001242891.1	238	gCc/gTc	7/20	1	2	FACETS	0.929	0.852	1	0.929	0.852	1	CLONAL	1	TRUE	1	0.884932140224895	2		269	287	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150923356	150923356	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199613890	NA	P-0060031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	171	408	0	ENST00000271640.5:c.2003G>A	p.Arg668Gln	p.R668Q	ENST00000271640	NM_001145415.1	668	cGa/cAa	13/22	0.277923162879881	4	FACETS	0.845	0.786	0.905	0.845	0.786	0.905	INDETERMINATE	2	TRUE	2	0.884932140224895	4		408	431	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712679	43712679	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	164	422	0	ENST00000382044.4:c.4505C>T	p.Ser1502Phe	p.S1502F	ENST00000382044	NM_001141980.1	1502	tCc/tTc	21/28	0.108577088741944	4	FACETS	0.863	0.801	0.925	0.863	0.801	0.925	INDETERMINATE	2	TRUE	2	0.884932140224895	4		422	405	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724633	43724633	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	166	431	0	ENST00000382044.4:c.3434G>C	p.Ser1145Thr	p.S1145T	ENST00000382044	NM_001141980.1	1145	aGt/aCt	17/28	0.108577088741944	4	FACETS	0.938	0.874	1	0.938	0.874	1	INDETERMINATE	2	TRUE	2	0.884932140224895	4		431	377	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343711	343712	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0060031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	159	431	0	ENST00000262320.3:c.1962_1963delinsAA	p.Gly655Arg	p.G655R	ENST00000262320	NM_003502.3	654	tcGGgg/tcAAgg	8/11	0.214899278351877	4	FACETS	0.871	0.808	0.934	0.871	0.808	0.934	INDETERMINATE	2	TRUE	2	0.884932140224895	4		431	389	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528100	29528100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878853862	NA	P-0060031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	83	210	0	ENST00000356175.3:c.1108C>T	p.Pro370Ser	p.P370S	ENST00000356175	NM_000267.3	370	Cct/Tct	10/57	0.138553104836204	4	FACETS	0.945	0.855	1	0.945	0.855	1	INDETERMINATE	2	TRUE	2	0.884932140224895	4		210	187	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619072	37619072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1177110993	NA	P-0060031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	205	478	1	ENST00000447079.4:c.748C>T	p.Pro250Ser	p.P250S	ENST00000447079	NM_015083.1	250	Ccc/Tcc	1/14	0.138553104836204	4	FACETS	1	0.966	1	1	0.966	1	INDETERMINATE	2	TRUE	2	0.884932140224895	4		479	420	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744024	41744024	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs868431544	NA	P-0060031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	173	564	0	ENST00000301178.4:c.959G>A	p.Trp320Ter	p.W320*	ENST00000301178	NM_021913.4	320	tGg/tAg	7/20	NA	2	FACETS	0.958	0.893	1			1	INDETERMINATE	1	TRUE	NA	0.884932140224895	2		564	408	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422413	47422414	+	missense_variant	Missense_Mutation	DNP	CT	CT	TA	novel	NA	P-0060031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	185	424	0	ENST00000404338.3:c.481_482delinsTA	p.Leu161Tyr	p.L161Y	ENST00000404338	NM_004491.4	161	CTt/TAt	1/6	0.673042498649274	3	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.884932140224895	3		424	466	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67626304	67626304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	79	246	0	ENST00000272342.5:c.227G>A	p.Arg76Lys	p.R76K	ENST00000272342	NM_019002.3	76	aGg/aAg	2/6	1	2	FACETS	0.875	0.785	0.967	0.875	0.785	0.967	CLONAL	1	TRUE	1	0.884932140224895	2		246	204	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158637016	158637016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	202	432	0	ENST00000263640.3:c.164C>T	p.Ser55Phe	p.S55F	ENST00000263640	NM_001105.4	55	tCc/tTc	4/11	0.882800658735593	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.884932140224895	1		432	228	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170011233	170011233	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	149	335	0	ENST00000295797.4:c.1354C>T	p.Pro452Ser	p.P452S	ENST00000295797	NM_002740.5	452	Cca/Tca	14/18	0.884932140224895	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.884932140224895	1		335	169	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168921	32168921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	269	545	0	ENST00000375023.3:c.4112G>A	p.Gly1371Asp	p.G1371D	ENST00000375023	NM_004557.3	1371	gGc/gAc	22/30	0.277923162879881	4	FACETS	0.927	0.877	0.978	0.927	0.877	0.978	INDETERMINATE	2	TRUE	2	0.884932140224895	4		545	618	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120737	94120737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	120	334	0	ENST00000369303.4:c.314C>T	p.Thr105Ile	p.T105I	ENST00000369303	NM_004440.3	105	aCc/aTc	3/17	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.884932140224895	2		334	252	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545693	106545693	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	189	346	0	ENST00000359195.3:c.3170T>C	p.Val1057Ala	p.V1057A	ENST00000359195	NM_002649.2	1057	gTg/gCg	11/11	0.138553104836204	4	FACETS	0.895	0.836	0.954	0.895	0.836	0.954	INDETERMINATE	2	TRUE	2	0.884932140224895	4		346	450	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76953122	76953122	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060031-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	54	186	0	ENST00000373344.5:c.191G>A	p.Gly64Glu	p.G64E	ENST00000373344	NM_000489.3	64	gGa/gAa	4/35	0.610845568493225	1	FACETS	0.558	0.491	0.625	0.558	0.491	0.625	SUBCLONAL	1	TRUE	0	0.884932140224895	1		186	122	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0060032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	60	300	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.204936671925513	1	FACETS	0.804	0.697	0.918	1	0.973	1	CLONAL	2	TRUE	0	0.203823537099745	1		300	329	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0060032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	74	541	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.963	0.842	1	0.963	0.842	1	CLONAL	1	TRUE	1	0.203823537099745	2		541	754	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912580	NA	P-0060032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	95	323	0	ENST00000342988.3:c.1157G>A	p.Gly386Asp	p.G386D	ENST00000342988	NM_005359.5	386	gGt/gAt	10/12	0.190462837869798	2	FACETS	0.99	0.885	1	0.99	0.885	1	CLONAL	2	TRUE	0	0.203823537099745	2		323	471	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265323	152265323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866869178	NA	P-0060032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	37	370	0	ENST00000206249.3:c.776G>A	p.Arg259Gln	p.R259Q	ENST00000206249	NM_000125.3	259	cGa/cAa	4/8	0.190462837869798	2	FACETS	0.708	0.583	0.848	0.354	0.291	0.424	SUBCLONAL	1	TRUE	0	0.203823537099745	2		370	513	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0060032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	47	468	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			1	2	FACETS	0.797	0.671	0.935	0.797	0.671	0.935	CLONAL	1	TRUE	1	0.203823537099745	2		468	579	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972499	81972501	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0060032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	104	398	0	ENST00000359376.3:c.3292_3294del	p.Lys1098del	p.K1098del	ENST00000359376	NM_002661.3	1098	AAG/-	29/33	1	2	FACETS	0.869	0.78	0.963	1	0.986	1	CLONAL	2	TRUE	1	0.203823537099745	2		398	587	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66468020	66468020	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	30	275	0	ENST00000273854.3:c.249G>A	p.Trp83Ter	p.W83*	ENST00000273854	NM_004439.5	83	tgG/tgA	3/18	0.203823537099745	1	FACETS	0.747	0.602	0.91	0.747	0.602	0.91	CLONAL	1	TRUE	0	0.203823537099745	1		275	354	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0060035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	72	289	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.649833983023375	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.654603831549406	1		289	138	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0060035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	137	810	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.654603831549406	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.654603831549406	1		810	244	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14317322	14317322	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782597266	NA	P-0060035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	75	291	0	ENST00000256196.4:c.188G>A	p.Arg63Gln	p.R63Q	ENST00000256196		63	cGg/cAg	2/6	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.654603831549406	2		291	220	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs730881677	NA	P-0060035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	109	590	0	ENST00000304494.5:c.151-1G>C		p.X51_splice	ENST00000304494	NM_000077.4	51			1	2	FACETS	0.946	0.859	1	0.946	0.859	1	CLONAL	1	TRUE	1	0.654603831549406	2		590	352	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0060035-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	109	656	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	1	2	FACETS	0.943	0.856	1	0.943	0.856	1	CLONAL	1	TRUE	1	0.654603831549406	2		656	353	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907651	76907651	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	335	243	0	ENST00000373344.5:c.4510C>T	p.Arg1504Ter	p.R1504*	ENST00000373344	NM_000489.3	1504	Cga/Tga	15/35	0.867700208081001	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.867700208081001	2		243	360	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857662	9857662	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	415	677	0	ENST00000330684.3:c.3739G>C	p.Asp1247His	p.D1247H	ENST00000330684	NM_001134407.1	1247	Gac/Cac	13/13	0.48678707588453	4	FACETS	0.893	0.86	0.925	0.893	0.86	0.925	INDETERMINATE	3	TRUE	1	0.867700208081001	4		677	667	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0060037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	54	519	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.163106736486555	2	FACETS	1	0.885	1	0.522	0.445	0.605	CLONAL	1	FALSE	0	0.180383732177612	2		520	574	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0060037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	31	500	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	1	2	FACETS	0.664	0.536	0.809	0.664	0.536	0.809	SUBCLONAL	1	FALSE	1	0.180383732177612	2		500	518	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045872	47045872	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0060037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	91	498	0	ENST00000377604.3:c.2668-1G>T		p.X890_splice	ENST00000377604	NM_001204468.1	890			1	1	FACETS	1	0.943	1	1	0.987	1	CLONAL	2	FALSE	0	0.180383732177612	1		498	423	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265353	152265353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188957694	NA	P-0060037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	55	658	0	ENST00000206249.3:c.806G>A	p.Arg269His	p.R269H	ENST00000206249	NM_000125.3	269	cGc/cAc	4/8	0.180383732177612	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	FALSE	0	0.180383732177612	1		658	472	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058536	69058536	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753703	NA	P-0060037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	36	466	0	ENST00000288368.4:c.4180C>T	p.Arg1394Trp	p.R1394W	ENST00000288368	NM_024870.2	1394	Cgg/Tgg	34/40	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	FALSE	1	0.180383732177612	2		466	314	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576121	88576121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374272958	NA	P-0060037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	51	735	0	ENST00000360948.2:c.1552C>T	p.Arg518Cys	p.R518C	ENST00000360948	NM_001012338.2	518	Cgt/Tgt	13/19	1	2	FACETS	0.89	0.756	1	0.89	0.756	1	CLONAL	1	FALSE	1	0.180383732177612	2		735	635	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603018	48603018	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0060037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	43	432	0	ENST00000342988.3:c.1319T>A	p.Leu440Ter	p.L440*	ENST00000342988	NM_005359.5	440	tTg/tAg	11/12	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	1	0.180383732177612	2		432	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0060038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	136	575	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.866	0.786	0.95	1	0.988	1	CLONAL	2	TRUE	1	0.14	2		575	1122	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554452	63554452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	69	722	0	ENST00000307078.5:c.287G>A	p.Arg96Gln	p.R96Q	ENST00000307078	NM_004655.3	96	cGa/cAa	2/11	0.227081937328641	2	FACETS	0.883	0.767	1	0.442	0.383	0.505	CLONAL	1	TRUE	0	0.14	2		722	1116	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295801	212295801	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1423325504	NA	P-0060039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	210	402	0	ENST00000342788.4:c.2512C>T	p.Arg838Ter	p.R838*	ENST00000342788	NM_005235.2	838	Cga/Tga	21/28	1	2	FACETS	0.931	0.869	0.994	0.931	0.869	0.994	CLONAL	1	TRUE	1	0.711490071977148	2		402	634	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561560	9561560	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060041-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	139	473	0	ENST00000353224.5:c.222C>A	p.Asn74Lys	p.N74K	ENST00000353224	NM_177990.2	74	aaC/aaA	4/10	1	2	FACETS	0.851	0.782	0.923	0.851	0.782	0.923	CLONAL	1	TRUE	1	0.76112169552891	2		473	429	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871019	12871020	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0060042-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	57	617	0	ENST00000228872.4:c.247dup	p.Ser83LysfsTer42	p.S83Kfs*42	ENST00000228872	NM_004064.3	82	-/A	1/3	1	2	FACETS	0.216	0.185	0.251	0.216	0.185	0.251	SUBCLONAL	1	TRUE	1	0.614289705346923	2		617	859	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578464	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	498	901	0	ENST00000269305.4:c.466del	p.Arg156AlafsTer14	p.R156Afs*14	ENST00000269305	NM_001126112.2	156	Cgc/gc	5/11	0.498584627052265	2	FACETS	0.988	0.95	1	0.988	0.95	1	CLONAL	2	TRUE	0	0.498584627052265	2		901	1011	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422254	422254	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1448384274	NA	P-0060043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	123	486	0	ENST00000399788.2:c.3004C>G	p.Arg1002Gly	p.R1002G	ENST00000399788	NM_001042603.1	1002	Cga/Gga	20/28	1	2	FACETS	0.987	0.897	1	0.987	0.897	1	CLONAL	1	TRUE	1	0.498584627052265	2		486	500	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437770	49437770	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	189	837	0	ENST00000301067.7:c.5200del	p.Asp1734ThrfsTer12	p.D1734Tfs*12	ENST00000301067	NM_003482.3	1734	Gac/ac	22/54	1	2	FACETS	0.939	0.87	1	0.939	0.87	1	CLONAL	1	TRUE	1	0.498584627052265	2		837	807	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041151	112041151	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060043-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	183	744	0	ENST00000368678.4:c.104C>A	p.Thr35Asn	p.T35N	ENST00000368678		35	aCc/aAc	3/13	0.498584627052265	3	FACETS	0.933	0.861	1	0.466	0.43	0.504	CLONAL	1	TRUE	1	0.498584627052265	3		744	983	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0060044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	20	289	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.229	0.174	0.294	0.229	0.174	0.294	SUBCLONAL	1	TRUE	1	0.318068675528243	2		289	549	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0060044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	126	392	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.318068675528243	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.318068675528243	1		392	614	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0060044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	49	658	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.318068675528243	1	FACETS	0.362	0.306	0.424	0.362	0.306	0.424	SUBCLONAL	1	TRUE	0	0.318068675528243	1		658	716	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016675	12016675	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	41	519	0	ENST00000353533.5:c.811G>A	p.Ala271Thr	p.A271T	ENST00000353533	NM_003010.3	271	Gca/Aca	7/11	0.318068675528243	1	FACETS	0.381	0.317	0.453	0.381	0.317	0.453	SUBCLONAL	1	TRUE	0	0.318068675528243	1		519	569	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602334	10602334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1379198956	NA	P-0060044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	52	873	2	ENST00000171111.5:c.1244G>A	p.Arg415His	p.R415H	ENST00000171111	NM_203500.1	415	cGc/cAc	3/6	1	2	FACETS	0.386	0.327	0.451	0.386	0.327	0.451	SUBCLONAL	1	TRUE	1	0.318068675528243	2		875	847	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991794	72991794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	41	721	0	ENST00000268489.5:c.2251C>T	p.Leu751Phe	p.L751F	ENST00000268489	NM_006885.3	751	Ctc/Ttc	2/10	1	2	FACETS	0.374	0.31	0.444	0.374	0.31	0.444	SUBCLONAL	1	TRUE	1	0.318068675528243	2		721	690	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109651	115109651	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	75	550	0	ENST00000257566.3:c.2227C>A	p.Pro743Thr	p.P743T	ENST00000257566	NM_016569.3	743	Ccg/Acg	8/8	1	2	FACETS	0.797	0.699	0.902	0.797	0.699	0.902	CLONAL	1	TRUE	1	0.318068675528243	2		550	592	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207131	1207131	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	48	654	0	ENST00000326873.7:c.219C>A	p.Cys73Ter	p.C73*	ENST00000326873	NM_000455.4	73	tgC/tgA	1/10	0.318068675528243	1	FACETS	0.368	0.311	0.432	0.368	0.311	0.432	SUBCLONAL	1	TRUE	0	0.318068675528243	1		654	689	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144113	11144113	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	70	622	2	ENST00000358026.2:c.3694G>T	p.Gly1232Cys	p.G1232C	ENST00000358026	NM_001128849.1	1232	Ggc/Tgc	26/36	1	2	FACETS	0.562	0.489	0.641	0.562	0.489	0.641	SUBCLONAL	1	TRUE	1	0.318068675528243	2		624	783	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719324	52719324	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	88	612	0	ENST00000322088.6:c.990C>G	p.Ile330Met	p.I330M	ENST00000322088	NM_014225.5	330	atC/atG	8/15	0.318068675528243	1	FACETS	0.812	0.721	0.909	0.812	0.721	0.909	CLONAL	1	TRUE	0	0.318068675528243	1		612	573	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27016112	27016112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	100	486	0	ENST00000335756.4:c.388C>T	p.Arg130Trp	p.R130W	ENST00000335756	NM_001809.3	130	Cgg/Tgg	4/5	1	2	FACETS	0.973	0.871	1	0.973	0.871	1	CLONAL	1	TRUE	1	0.318068675528243	2		486	646	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566710	212566710	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	112	406	0	ENST00000342788.4:c.1471A>G	p.Arg491Gly	p.R491G	ENST00000342788	NM_005235.2	491	Aga/Gga	12/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.318068675528243	2		406	544	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099333	157099338	+	inframe_deletion	In_Frame_Del	DEL	CCACCA	CCACCA	-	rs754114025	NA	P-0060044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	159	659	2	ENST00000346085.5:c.282_287del	p.His95_His96del	p.H95_H96del	ENST00000346085	NM_020732.3	90	gcCCACCAc/gcc	1/20	0.105647376192479	5	FACETS	1	0.987	1	0.48	0.44	0.523	INDETERMINATE	1	TRUE	2	0.318068675528243	5		661	1025	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465594	8465594	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	92	467	0	ENST00000356435.5:c.3586T>G	p.Phe1196Val	p.F1196V	ENST00000356435		1196	Ttt/Gtt	21/35	0.318068675528243	1	FACETS	0.911	0.812	1	0.911	0.812	1	CLONAL	1	TRUE	0	0.318068675528243	1		467	534	SUCCESS
AR	367	MSKCC	GRCh37	X	66765740	66765740	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	123	425	0	ENST00000374690.3:c.752T>C	p.Val251Ala	p.V251A	ENST00000374690	NM_000044.3	251	gTg/gCg	1/8	0.0406809475599101	2	FACETS	0.919	0.837	1			1	INDETERMINATE	2	TRUE	NA	0.318068675528243	2		425	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0060045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	323	864	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.352759940154081	4	FACETS	0.939	0.886	0.992	0.939	0.886	0.992	CLONAL	2	TRUE	2	0.405247024340558	4		864	1193	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579463	7579463	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	355	846	0	ENST00000269305.4:c.224del	p.Pro75LeufsTer48	p.P75Lfs*48	ENST00000269305	NM_001126112.2	75	cCt/ct	4/11	0.352759940154081	4	FACETS	0.935	0.886	0.986	0.935	0.886	0.986	CLONAL	2	TRUE	2	0.405247024340558	4		846	1316	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528596	8528596	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	193	467	0	ENST00000356435.5:c.536G>T	p.Arg179Leu	p.R179L	ENST00000356435		179	cGa/cTa	4/35	0.405454823596257	3	FACETS	0.963	0.896	1	0.963	0.896	1	CLONAL	2	TRUE	1	0.405247024340558	3		467	595	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264927	46264927	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	136	646	0	ENST00000371998.3:c.1797G>T	p.Lys599Asn	p.K599N	ENST00000371998		599	aaG/aaT	12/23	0.400226158267446	5	FACETS	0.963	0.874	1	0.321	0.291	0.353	CLONAL	1	TRUE	2	0.405247024340558	5		646	1121	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55597574	55597574	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	82	360	0	ENST00000288135.5:c.2222C>T	p.Ser741Phe	p.S741F	ENST00000288135	NM_000222.2	741	tCt/tTt	15/21	0.405454823596257	3	FACETS	0.917	0.81	1	0.458	0.405	0.515	CLONAL	1	TRUE	1	0.405247024340558	3		360	531	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287828	33287828	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	174	726	0	ENST00000374542.5:c.1425G>T	p.Glu475Asp	p.E475D	ENST00000374542	NM_001141970.1	475	gaG/gaT	5/8	0.405247024340558	5	FACETS	1	0.959	1	0.267	0.245	0.291	CLONAL	1	TRUE	1	0.405247024340558	5		726	1291	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101438	27101438	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	227	494	0	ENST00000324856.7:c.4724del	p.Pro1575HisfsTer37	p.P1575Hfs*37	ENST00000324856	NM_006015.4	1574	Ccc/cc	18/20	0.405454823596257	3	FACETS	0.757	0.706	0.809			1	SUBCLONAL	2	TRUE	NA	0.405247024340558	3		494	890	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210761	36210761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1969	163	880	0	ENST00000222270.7:c.512C>T	p.Pro171Leu	p.P171L	ENST00000222270	NM_014727.1	171	cCt/cTt	3/37	0.405247024340558	8	FACETS	0.836	0.763	0.913	0.139	0.127	0.153	CLONAL	1	TRUE	2	0.405247024340558	8		880	2132	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46725684	46725684	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	611	708	1	ENST00000371975.4:c.320G>T	p.Arg107Leu	p.R107L	ENST00000371975	NM_003579.3	107	cGg/cTg	5/18	0.405247024340558	6	FACETS	1	0.974	1			1	CLONAL	4	TRUE	NA	0.405247024340558	6		709	1349	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443803	49443803	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1206669578	NA	P-0060045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	334	866	0	ENST00000301067.7:c.3568G>C	p.Ala1190Pro	p.A1190P	ENST00000301067	NM_003482.3	1190	Gca/Cca	11/54	0.401595936253623	3	FACETS	0.949	0.898	1	0.949	0.898	1	CLONAL	2	TRUE	1	0.405247024340558	3		866	1045	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30099993	30099993	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs143339301	NA	P-0060045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	154	593	0	ENST00000331968.5:c.1627G>T	p.Val543Phe	p.V543F	ENST00000331968	NM_002742.2	543	Gtc/Ttc	10/18	0.405247024340558	6	FACETS	1	0.974	1	0.291	0.265	0.318	CLONAL	1	TRUE	2	0.405247024340558	6		593	1182	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135415	30135415	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0060045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	60	451	0	ENST00000331968.5:c.404-1G>C		p.X135_splice	ENST00000331968	NM_002742.2	135			0.405247024340558	6	FACETS	0.605	0.52	0.698	0.151	0.13	0.175	SUBCLONAL	1	TRUE	2	0.405247024340558	6		451	886	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396621	396623	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs1225958459	NA	P-0060045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	272	667	0	ENST00000262320.3:c.403_405del	p.Glu135del	p.E135del	ENST00000262320	NM_003502.3	135	GAG/-	2/11	0.405247024340558	6	FACETS	0.895	0.838	0.953			1	CLONAL	2	TRUE	NA	0.405247024340558	6		667	1358	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222512	2222512	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	162	800	0	ENST00000326181.6:c.706A>C	p.Asn236His	p.N236H	ENST00000326181	NM_032271.2	236	Aac/Cac	9/21	0.333423287028677	4	FACETS	0.943	0.863	1			1	CLONAL	1	TRUE	NA	0.405247024340558	4		800	1192	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642755	3642755	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	173	645	0	ENST00000294008.3:c.2272G>C	p.Ala758Pro	p.A758P	ENST00000294008	NM_032444.2	758	Gcg/Ccg	11/15	0.405454823596257	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.405247024340558	1		645	586	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369269	40369269	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	295	632	0	ENST00000293328.3:c.1289G>T	p.Arg430Leu	p.R430L	ENST00000293328	NM_012448.3	430	cGt/cTt	11/19	0.286051982400612	5	FACETS	1	0.986	1	0.757	0.713	0.802	CLONAL	2	TRUE	2	0.405247024340558	5		632	1031	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714401	40714401	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	136	602	0	ENST00000373198.4:c.3996C>G	p.Ile1332Met	p.I1332M	ENST00000373198	NM_133170.3	1332	atC/atG	29/32	0.400226158267446	5	FACETS	0.979	0.889	1	0.326	0.296	0.359	CLONAL	1	TRUE	2	0.405247024340558	5		602	1102	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206811	36206834	+	inframe_deletion	In_Frame_Del	DEL	GTGCGCCGCAGCTGCTCCAGTTCA	GTGCGCCGCAGCTGCTCCAGTTCA	-	novel	NA	P-0060045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1402	144	775	0	ENST00000300305.3:c.678_701del	p.Ser226_Thr234delinsArg	p.S226_T234delinsR	ENST00000300305		226	agTGAACTGGAGCAGCTGCGGCGCACa/aga	6/8	0.405247024340558	6	FACETS	0.832	0.756	0.913			1	CLONAL	1	TRUE	NA	0.405247024340558	6		775	1546	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247451	71247451	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	132	612	1	ENST00000318789.4:c.82G>T	p.Glu28Ter	p.E28*	ENST00000318789	NM_032682.5	28	Gag/Tag	6/21	0.112046360633729	5	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.405247024340558	5		613	819	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72842088	72842088	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	83	419	0	ENST00000325599.8:c.1160G>T	p.Cys387Phe	p.C387F	ENST00000325599	NM_018130.2	387	tGt/tTt	10/11	0.112046360633729	5	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.405247024340558	5		419	497	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898732	134898732	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	118	619	0	ENST00000398015.3:c.1790C>G	p.Pro597Arg	p.P597R	ENST00000398015	NM_004441.4	597	cCc/cGc	10/16	0.400226158267446	5	FACETS	0.954	0.86	1	0.318	0.286	0.352	CLONAL	1	TRUE	2	0.405247024340558	5		619	981	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561699	55561699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	124	552	0	ENST00000288135.5:c.89G>A	p.Ser30Asn	p.S30N	ENST00000288135	NM_000222.2	30	aGt/aAt	2/21	0.405454823596257	3	FACETS	1	0.926	1	0.513	0.465	0.564	CLONAL	1	TRUE	1	0.405247024340558	3		552	717	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915068	131915068	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs745933578	NA	P-0060045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	158	387	0	ENST00000265335.6:c.425G>T	p.Ser142Ile	p.S142I	ENST00000265335		142	aGt/aTt	4/25	0.401595936253623	3	FACETS	0.928	0.857	1	0.928	0.857	1	CLONAL	2	TRUE	1	0.405247024340558	3		387	505	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460413	149460413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748096324	NA	P-0060045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	148	698	0	ENST00000286301.3:c.224C>T	p.Thr75Ile	p.T75I	ENST00000286301	NM_005211.3	75	aCc/aTc	3/22	0.401595936253623	3	FACETS	0.928	0.847	1	0.464	0.423	0.507	CLONAL	1	TRUE	1	0.405247024340558	3		698	947	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523648	176523648	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	311	846	0	ENST00000292408.4:c.2059G>T	p.Gly687Cys	p.G687C	ENST00000292408	NM_213647.1	687	Ggc/Tgc	16/18	0.405454823596257	3	FACETS	0.807	0.762	0.854	0.807	0.762	0.854	CLONAL	2	TRUE	1	0.405247024340558	3		846	1143	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250602	26250602	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1229	171	824	0	ENST00000446824.2:c.232G>T	p.Asp78Tyr	p.D78Y	ENST00000446824	NM_021018.2	78	Gac/Tac	1/1	0.405247024340558	5	FACETS	0.969	0.889	1	0.242	0.222	0.264	CLONAL	1	TRUE	1	0.405247024340558	5		824	1400	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864407	162864408	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0060045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	110	639	0	ENST00000366898.1:c.105_106delinsTT	p.Val36Phe	p.V36F	ENST00000366898	NM_004562.2	35	ggGGtt/ggTTtt	2/12	1	2	FACETS	0.88	0.792	0.972	0.88	0.792	0.972	CLONAL	1	TRUE	1	0.405247024340558	2		639	617	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935622	13935622	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0060045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	129	600	0	ENST00000405192.2:c.1234A>T	p.Lys412Ter	p.K412*	ENST00000405192	NM_001163147.1	412	Aag/Tag	12/12	0.405454823596257	3	FACETS	1	0.907	1	0.5	0.453	0.549	CLONAL	1	TRUE	1	0.405247024340558	3		600	766	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633340	8633340	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	78	531	0	ENST00000356435.5:c.329C>A	p.Ser110Tyr	p.S110Y	ENST00000356435		110	tCc/tAc	3/35	0.405454823596257	3	FACETS	0.685	0.602	0.774	0.342	0.301	0.387	SUBCLONAL	1	TRUE	1	0.405247024340558	3		531	676	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143129658	143129659	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	A	novel	NA	P-0060045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	52	323	0	ENST00000262992.4:c.991_992delinsT	p.Gly333GlufsTer5	p.G333Efs*5	ENST00000262992	NM_001101669.1	331	AGc/Tc	12/24	1	2	FACETS	0.844	0.723	0.975	0.844	0.723	0.975	CLONAL	1	TRUE	1	0.405247024340558	2		323	304	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481403	140481403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913357	NA	P-0060046-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	25	376	0	ENST00000288602.6:c.1405G>A	p.Gly469Arg	p.G469R	ENST00000288602	NM_004333.4	469	Gga/Aga	11/18	1	2	FACETS	0.782	0.617	0.973	0.782	0.617	0.973	CLONAL	1	TRUE	1	0.18	2		376	355	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266165	+	inframe_deletion	In_Frame_Del	DEL	TCTCTGAGTGGTAAAGGCAATCCTGAGGAA	TCTCTGAGTGGTAAAGGCAATCCTGAGGAA	-	novel	NA	P-0060046-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	63	529	0	ENST00000349496.5:c.133_162del	p.Ser45_Glu54del	p.S45_E54del	ENST00000349496	NM_001904.3	45	TCTCTGAGTGGTAAAGGCAATCCTGAGGAA/-	3/15	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.18	2		529	559	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636209	73636210	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060067-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	100	552	0	ENST00000377687.4:c.473dup	p.Thr159AsnfsTer16	p.T159Nfs*16	ENST00000377687	NM_001730.3	158	gta/gTta	2/4	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.376526076961324	2		552	515	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0060075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	50	289	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.379311411925418	2		289	243	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971194	21971194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561034503	NA	P-0060075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	86	696	0	ENST00000304494.5:c.164G>A	p.Gly55Asp	p.G55D	ENST00000304494	NM_000077.4	55	gGc/gAc	2/3	0.379311411925418	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.379311411925418	1		696	341	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577530	7577530	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060075-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	62	561	0	ENST00000269305.4:c.751A>T	p.Ile251Phe	p.I251F	ENST00000269305	NM_001126112.2	251	Atc/Ttc	7/11	0.379311411925418	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.379311411925418	1		561	245	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578441	7578441	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1567553246	NA	P-0060076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	182	795	0	ENST00000269305.4:c.489C>G	p.Tyr163Ter	p.Y163*	ENST00000269305	NM_001126112.2	163	taC/taG	5/11	0.299819416213963	5	FACETS	0.919	0.857	0.982	0.919	0.857	0.982	CLONAL	4	TRUE	1	0.32	5		795	458	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246040	41246044	+	frameshift_variant	Frame_Shift_Del	DEL	TTTAA	TTTAA	-	rs80357888	NA	P-0060076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	181	512	0	ENST00000357654.3:c.1504_1508del	p.Leu502AlafsTer2	p.L502Afs*2	ENST00000357654	NM_007294.3	502	TTAAAg/g	10/23	0.297536370029253	7	FACETS	0.988	0.924	1	0.824	0.77	0.878	CLONAL	5	TRUE	1	0.32	7		512	412	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239815	105239815	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1167819752	NA	P-0060076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	57	745	0	ENST00000349310.3:c.805A>G	p.Asn269Asp	p.N269D	ENST00000349310	NM_001014432.1	269	Aac/Gac	10/15	0.152113811654424	3	FACETS	1	0.963	1	0.458	0.395	0.525	INDETERMINATE	1	TRUE	0	0.32	3		745	301	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020256	123020256	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060076-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	50	503	0	ENST00000355640.3:c.744G>T	p.Arg248Ser	p.R248S	ENST00000355640		248	agG/agT	2/7	0.299819416213963	0	FACETS	0.681	0.59	0.777			1	SUBCLONAL	2	TRUE	0	0.32	0		503	156	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572608	64572609	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1555164305	NA	P-0060077-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	200	858	0	ENST00000312049.6:c.1247dup	p.Tyr417LeufsTer32	p.Y417Lfs*32	ENST00000312049	NM_130799.2	416	ttc/ttTc	9/10	0.406100298498682	1	FACETS	0.892	0.827	0.959	0.892	0.827	0.959	CLONAL	1	TRUE	0	0.406100298498682	1		858	880	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732481	74732481	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060077-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	164	683	0	ENST00000359995.5:c.428G>C	p.Arg143Pro	p.R143P	ENST00000359995	NM_001195427.1	143	cGc/cCc	2/3	0.398741650047751	3	FACETS	0.894	0.819	0.972	0.447	0.409	0.486	CLONAL	1	TRUE	1	0.406100298498682	3		683	1087	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115863	8115891	+	frameshift_variant	Frame_Shift_Del	DEL	GAGCCACATCTCGCCCTTCAGCCACTCCA	GAGCCACATCTCGCCCTTCAGCCACTCCA	-	novel	NA	P-0060080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	153	856	0	ENST00000346208.3:c.1210_1238del	p.Ser404ProfsTer93	p.S404Pfs*93	ENST00000346208		403	ctGAGCCACATCTCGCCCTTCAGCCACTCCAgc/ctgc	6/6	0.393208630107504	4	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	2	TRUE	2	0.659970788187281	4		856	341	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206606	108206606	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	21	567	0	ENST00000278616.4:c.8186A>G	p.Gln2729Arg	p.Q2729R	ENST00000278616	NM_000051.3	2729	cAa/cGa	56/63	0.477989895570679	2	FACETS	0.493	0.384	0.617	0.247	0.192	0.309	SUBCLONAL	1	TRUE	0	0.659970788187281	2		567	129	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112557	115112576	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTGGCCGCGTCGCAGGCC	TCTTGGCCGCGTCGCAGGCC	-	novel	NA	P-0060080-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	137	845	0	ENST00000257566.3:c.1164_1183del	p.Glu388AspfsTer12	p.E388Dfs*12	ENST00000257566	NM_016569.3	388	gaGGCCTGCGACGCGGCCAAGAtc/gatc	7/8	0.659970788187281	8	FACETS	1	0.953	1			1	CLONAL	3	TRUE	NA	0.659970788187281	8		845	392	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0060081-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	337	570	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	0.75951231788012	2	FACETS	0.944	0.911	0.976	0.944	0.911	0.976	CLONAL	2	FALSE	0	0.75951231788012	2		570	470	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382221	152382221	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060081-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	253	575	0	ENST00000206249.3:c.1331A>T	p.Glu444Val	p.E444V	ENST00000206249	NM_000125.3	444	gAg/gTg	6/8	0.133193279379358	3	FACETS	0.762	0.719	0.806	0.762	0.719	0.806	INDETERMINATE	2	FALSE	1	0.75951231788012	3		575	603	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110007	115110017	+	frameshift_variant	Frame_Shift_Del	DEL	TGCACCGAGCT	TGCACCGAGCT	C	novel	NA	P-0060081-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	330	735	0	ENST00000257566.3:c.1861_1871delinsG	p.Ser621AlafsTer8	p.S621Afs*8	ENST00000257566	NM_016569.3	621	AGCTCGGTGCAc/Gc	8/8	0.75951231788012	3	FACETS	1	0.986	1	0.558	0.528	0.589	CLONAL	1	FALSE	1	0.75951231788012	3		735	1074	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0060082-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	604	460	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.35364586657713	4	FACETS	0.933	0.901	0.964	0.7	0.676	0.723	INDETERMINATE	3	TRUE	0	0.601000453256923	4		460	1150	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301111	65301111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370434553	NA	P-0060082-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	282	537	0	ENST00000342505.4:c.3337C>T	p.Arg1113Cys	p.R1113C	ENST00000342505	NM_002227.2	1113	Cgc/Tgc	24/25	0.504143218960405	3	FACETS	1	0.992	1	0.666	0.627	0.706	CLONAL	1	TRUE	1	0.601000453256923	3		537	916	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518419	69518419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060082-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	1534	367	6	ENST00000294312.3:c.226G>A	p.Ala76Thr	p.A76T	ENST00000294312	NM_005117.2	76	Gcg/Acg	1/3	0.601000453256923	8	FACETS	1	0.998	1			1	CLONAL	7	TRUE	NA	0.601000453256923	8		373	1920	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099060	27099073	+	frameshift_variant	Frame_Shift_Del	DEL	ACTTAAAGCCACCA	ACTTAAAGCCACCA	-	novel	NA	P-0060082-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	229	821	0	ENST00000324856.7:c.3479_3492del	p.Leu1160SerfsTer28	p.L1160Sfs*28	ENST00000324856	NM_006015.4	1159	gACTTAAAGCCACCA/g	13/20	0.504143218960405	3	FACETS	0.723	0.672	0.776	0.361	0.336	0.388	SUBCLONAL	1	TRUE	1	0.601000453256923	3		821	1371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0060084-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	24	634	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	1	2	FACETS	0.341	0.266	0.429	0.341	0.266	0.429	SUBCLONAL	1	TRUE	1	0.14	2		634	1004	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0060084-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	40	377	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	1	0.14	2		377	560	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	287	663	3	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	0.867	0.816	0.92	0.867	0.816	0.92	CLONAL	1	TRUE	1	0.65	2		666	1018	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	113	399	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	1	2	FACETS	0.838	0.76	0.919	0.838	0.76	0.919	CLONAL	1	TRUE	1	0.65	2		399	415	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857785	9857785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555482324	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	248	636	1	ENST00000330684.3:c.3616C>T	p.Arg1206Ter	p.R1206*	ENST00000330684	NM_001134407.1	1206	Cga/Tga	13/13	1	2	FACETS	0.927	0.869	0.986	0.927	0.869	0.986	CLONAL	1	TRUE	1	0.65	2		637	823	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	160	445	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.963	0.89	1	0.963	0.89	1	CLONAL	1	TRUE	1	0.65	2		445	511	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461166	120461166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200693165	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	167	411	0	ENST00000256646.2:c.5792G>A	p.Arg1931His	p.R1931H	ENST00000256646	NM_024408.3	1931	cGc/cAc	32/34	1	2	FACETS	0.878	0.811	0.948	0.878	0.811	0.948	CLONAL	1	TRUE	1	0.65	2		411	585	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	119	343	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.998	0.91	1	0.998	0.91	1	CLONAL	1	TRUE	1	0.65	2		343	367	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	157	503	2	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.82	0.755	0.888	0.82	0.755	0.888	CLONAL	1	TRUE	1	0.65	2		505	589	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	194	433	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.883	0.82	0.947	0.883	0.82	0.947	CLONAL	1	TRUE	1	0.65	2		434	676	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715678	30715678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039551	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	217	497	0	ENST00000295754.5:c.1336G>A	p.Asp446Asn	p.D446N	ENST00000295754	NM_003242.5	446	Gat/Aat	5/7	1	2	FACETS	0.944	0.882	1	0.944	0.882	1	CLONAL	1	TRUE	1	0.65	2		497	707	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376683	118376683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149340870	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	255	595	0	ENST00000534358.1:c.10076C>T	p.Ala3359Val	p.A3359V	ENST00000534358	NM_005933.3	3359	gCg/gTg	27/36	1	2	FACETS	0.937	0.88	0.996	0.937	0.88	0.996	CLONAL	1	TRUE	1	0.65	2		595	837	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559777	29559777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs902739109	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	276	485	2	ENST00000356175.3:c.3374C>T	p.Ala1125Val	p.A1125V	ENST00000356175	NM_000267.3	1125	gCg/gTg	26/57	1	2	FACETS	0.956	0.9	1	0.956	0.9	1	CLONAL	1	TRUE	1	0.65	2		487	888	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511562	66511562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1224297486	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	61	458	0	ENST00000358598.2:c.22G>A	p.Ala8Thr	p.A8T	ENST00000358598	NM_212471.2	8	Gcc/Acc	2/11	1	2	FACETS	0.236	0.203	0.273	0.236	0.203	0.273	SUBCLONAL	1	TRUE	1	0.65	2		458	794	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144146	11144146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	239	552	0	ENST00000358026.2:c.3727C>T	p.Arg1243Trp	p.R1243W	ENST00000358026	NM_001128849.1	1243	Cgg/Tgg	26/36	1	2	FACETS	0.939	0.88	1	0.939	0.88	1	CLONAL	1	TRUE	1	0.65	2		552	783	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213515	36213515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746928288	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	237	676	2	ENST00000222270.7:c.2617C>T	p.Arg873Cys	p.R873C	ENST00000222270	NM_014727.1	873	Cgt/Tgt	5/37	1	2	FACETS	0.886	0.829	0.944	0.886	0.829	0.944	CLONAL	1	TRUE	1	0.65	2		678	823	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38139044	38139044	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	144	361	0	ENST00000317025.8:c.3559C>T	p.Arg1187Ter	p.R1187*	ENST00000317025	NM_023034.1	1187	Cga/Tga	20/24	1	2	FACETS	0.957	0.88	1	0.957	0.88	1	CLONAL	1	TRUE	1	0.65	2		361	463	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520087	106520087	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774448553	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	105	328	0	ENST00000359195.3:c.2515C>T	p.Arg839Cys	p.R839C	ENST00000359195	NM_002649.2	839	Cgc/Tgc	6/11	1	2	FACETS	0.936	0.848	1	0.936	0.848	1	CLONAL	1	TRUE	1	0.65	2		328	345	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277291	41277291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	178	412	1	ENST00000349496.5:c.1760G>A	p.Arg587Gln	p.R587Q	ENST00000349496	NM_001904.3	587	cGa/cAa	11/15	1	2	FACETS	0.78	0.721	0.841	0.78	0.721	0.841	SUBCLONAL	1	TRUE	1	0.65	2		413	702	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197484	27197484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756064806	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	176	531	0	ENST00000380036.4:c.1796C>T	p.Ser599Leu	p.S599L	ENST00000380036	NM_000459.3	599	tCg/tTg	12/23	1	2	FACETS	0.853	0.789	0.919	0.853	0.789	0.919	CLONAL	1	TRUE	1	0.65	2		531	635	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938406	76938406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	104	369	2	ENST00000373344.5:c.2342G>A	p.Arg781Gln	p.R781Q	ENST00000373344	NM_000489.3	781	cGa/cAa	9/35	1	2	FACETS	0.722	0.651	0.797	0.722	0.651	0.797	SUBCLONAL	1	TRUE	1	0.65	2		371	443	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923252	78923252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	178	519	0	ENST00000306801.3:c.3275C>T	p.Ala1092Val	p.A1092V	ENST00000306801	NM_020761.2	1092	gCc/gTc	28/34	1	2	FACETS	0.905	0.839	0.974	0.905	0.839	0.974	CLONAL	1	TRUE	1	0.65	2		519	605	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643893	52643893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	137	390	0	ENST00000394830.3:c.2003C>T	p.Ala668Val	p.A668V	ENST00000394830	NM_018313.4	668	gCt/gTt	17/30	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.65	2		390	420	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	120	364	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	0.894	0.814	0.977	0.894	0.814	0.977	CLONAL	1	TRUE	1	0.65	2		364	413	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	19	381	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	1	2	FACETS	0.133	0.1	0.171	0.133	0.1	0.171	SUBCLONAL	1	TRUE	1	0.65	2		381	441	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982440	25982440	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	183	442	0	ENST00000435504.4:c.850C>T	p.Arg284Ter	p.R284*	ENST00000435504		284	Cga/Tga	9/13	1	2	FACETS	0.86	0.797	0.925	0.86	0.797	0.925	CLONAL	1	TRUE	1	0.65	2		442	655	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366939	15366939	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	225	474	0	ENST00000263377.2:c.1687del	p.Ser563AlafsTer21	p.S563Afs*21	ENST00000263377	NM_058243.2	563	Agc/gc	9/20	1	2	FACETS	0.917	0.857	0.979	0.917	0.857	0.979	CLONAL	1	TRUE	1	0.65	2		474	755	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2645847	2645847	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1378928701	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	146	361	0	ENST00000342085.4:c.1397G>A	p.Arg466Gln	p.R466Q	ENST00000342085	NM_002613.4	466	cGg/cAg	12/14	1	2	FACETS	0.897	0.824	0.972	0.897	0.824	0.972	CLONAL	1	TRUE	1	0.65	2		361	501	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424409	47424409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779648831	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	274	670	0	ENST00000377045.4:c.329C>T	p.Ala110Val	p.A110V	ENST00000377045	NM_001654.4	110	gCg/gTg	5/16	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.65	2		670	832	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17371320	17371320	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs74315370	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	199	387	0	ENST00000375499.3:c.136C>T	p.Arg46Ter	p.R46*	ENST00000375499	NM_003000.2	46	Cga/Tga	2/8	1	2	FACETS	0.999	0.931	1	0.999	0.931	1	CLONAL	1	TRUE	1	0.65	2		387	613	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339111	65339111	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	265	572	2	ENST00000342505.4:c.425del	p.Lys142ArgfsTer26	p.K142Rfs*26	ENST00000342505	NM_002227.2	142	aAg/ag	5/25	1	2	FACETS	0.96	0.903	1	0.96	0.903	1	CLONAL	1	TRUE	1	0.65	2		574	849	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299832	15299832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465285176	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	272	570	0	ENST00000263388.2:c.1346G>A	p.Arg449His	p.R449H	ENST00000263388	NM_000435.2	449	cGc/cAc	8/33	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.65	2		570	827	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417422	139417422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745817995	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	289	707	1	ENST00000277541.6:c.622G>A	p.Ala208Thr	p.A208T	ENST00000277541	NM_017617.3	208	Gcc/Acc	4/34	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.65	2		708	852	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671655	67671655	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1400980130	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	221	463	0	ENST00000264010.4:c.2070del	p.Glu691SerfsTer30	p.E691Sfs*30	ENST00000264010	NM_006565.3	688	gtA/gt	12/12	1	2	FACETS	0.99	0.926	1	0.99	0.926	1	CLONAL	1	TRUE	1	0.65	2		463	687	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	213	498	1	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	1	2	FACETS	0.879	0.819	0.94	0.879	0.819	0.94	CLONAL	1	TRUE	1	0.65	2		499	746	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923645	39923645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368780561	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	212	575	0	ENST00000378444.4:c.3446C>T	p.Ala1149Val	p.A1149V	ENST00000378444	NM_001123385.1	1149	gCg/gTg	7/15	1	2	FACETS	0.879	0.819	0.94	0.879	0.819	0.94	CLONAL	1	TRUE	1	0.65	2		575	742	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	550	557	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.935	0.905	0.965	1	0.998	1	CLONAL	2	TRUE	1	0.65	2		557	905	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685287	89685287	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs398123316	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	71	216	0	ENST00000371953.3:c.182A>G	p.His61Arg	p.H61R	ENST00000371953	NM_000314.4	61	cAt/cGt	3/9	1	2	FACETS	0.803	0.709	0.903	0.803	0.709	0.903	CLONAL	1	TRUE	1	0.65	2		216	272	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857766	9857766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	241	660	1	ENST00000330684.3:c.3635C>T	p.Thr1212Met	p.T1212M	ENST00000330684	NM_001134407.1	1212	aCg/aTg	13/13	1	2	FACETS	0.88	0.824	0.937	0.88	0.824	0.937	CLONAL	1	TRUE	1	0.65	2		661	843	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890203	72890203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758931723	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	170	369	0	ENST00000325599.8:c.479G>A	p.Arg160Gln	p.R160Q	ENST00000325599	NM_018130.2	160	cGg/cAg	4/11	1	2	FACETS	0.923	0.853	0.994	0.923	0.853	0.994	CLONAL	1	TRUE	1	0.65	2		369	567	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026984	71026984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763413735	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	233	589	0	ENST00000318789.4:c.1343C>T	p.Ser448Leu	p.S448L	ENST00000318789	NM_032682.5	448	tCg/tTg	15/21	1	2	FACETS	0.918	0.859	0.978	0.918	0.859	0.978	CLONAL	1	TRUE	1	0.65	2		589	781	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730335	133730335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	241	524	0	ENST00000318560.5:c.401G>A	p.Arg134His	p.R134H	ENST00000318560	NM_005157.4	134	cGc/cAc	3/11	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.65	2		524	739	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922301	178922301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	50	212	0	ENST00000263967.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000263967	NM_006218.2	357	cGa/cAa	6/21	1	2	FACETS	0.655	0.561	0.755	0.655	0.561	0.755	SUBCLONAL	1	TRUE	1	0.65	2		212	235	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	179	592	0	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	1	2	FACETS	0.873	0.808	0.939	0.873	0.808	0.939	CLONAL	1	TRUE	1	0.65	2		592	631	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225663	225663	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375576259	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	180	587	0	ENST00000264932.6:c.442G>A	p.Ala148Thr	p.A148T	ENST00000264932	NM_004168.2	148	Gcc/Acc	4/15	1	2	FACETS	0.715	0.66	0.771	0.715	0.66	0.771	SUBCLONAL	1	TRUE	1	0.65	2		587	775	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645069	67645069	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	234	548	0	ENST00000264010.4:c.334G>T	p.Glu112Ter	p.E112*	ENST00000264010	NM_006565.3	112	Gaa/Taa	3/12	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.65	2		548	700	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028632	12028632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753665559	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	151	414	0	ENST00000353533.5:c.835G>A	p.Ala279Thr	p.A279T	ENST00000353533	NM_003010.3	279	Gca/Aca	8/11	1	2	FACETS	0.846	0.778	0.917	0.846	0.778	0.917	CLONAL	1	TRUE	1	0.65	2		414	549	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615593	43615593	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	224	557	1	ENST00000355710.3:c.2672C>T	p.Ser891Leu	p.S891L	ENST00000355710	NM_020975.4	891	tCg/tTg	15/20	1	2	FACETS	0.907	0.847	0.968	0.907	0.847	0.968	CLONAL	1	TRUE	1	0.65	2		558	760	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120479966	120479966	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367562640	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	274	540	1	ENST00000256646.2:c.3461C>T	p.Ala1154Val	p.A1154V	ENST00000256646	NM_024408.3	1154	gCg/gTg	21/34	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.65	2		541	831	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681119	117681120	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs748436511	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	29	439	0	ENST00000368508.3:c.3500dup	p.Leu1167PhefsTer26	p.L1167Ffs*26	ENST00000368508	NM_002944.2	1167	tta/ttTa	23/43	1	2	FACETS	0.183	0.146	0.225	0.183	0.146	0.225	SUBCLONAL	1	TRUE	1	0.65	2		439	487	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637690	52637690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239654517	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	109	318	0	ENST00000394830.3:c.2626C>T	p.Arg876Cys	p.R876C	ENST00000394830	NM_018313.4	876	Cgt/Tgt	18/30	1	2	FACETS	0.81	0.733	0.891	0.81	0.733	0.891	CLONAL	1	TRUE	1	0.65	2		318	414	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039844	47039844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	34	483	0	ENST00000377604.3:c.1187G>A	p.Arg396His	p.R396H	ENST00000377604	NM_001204468.1	396	cGc/cAc	12/24	1	2	FACETS	0.192	0.156	0.232	0.192	0.156	0.232	SUBCLONAL	1	TRUE	1	0.65	2		483	545	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70412277	70412277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	124	304	0	ENST00000373644.4:c.4387G>A	p.Ala1463Thr	p.A1463T	ENST00000373644	NM_030625.2	1463	Gca/Aca	6/12	1	2	FACETS	0.933	0.851	1	0.933	0.851	1	CLONAL	1	TRUE	1	0.65	2		304	409	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295789	212295789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1240072004	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	188	464	0	ENST00000342788.4:c.2524C>T	p.Arg842Trp	p.R842W	ENST00000342788	NM_005235.2	842	Cgg/Tgg	21/28	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.65	2		464	563	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687328	37687328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766205887	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	271	612	0	ENST00000447079.4:c.4232C>T	p.Ala1411Val	p.A1411V	ENST00000447079	NM_015083.1	1411	gCg/gTg	14/14	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.65	2		612	812	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117323	115117323	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	164	419	0	ENST00000257566.3:c.851A>G	p.Tyr284Cys	p.Y284C	ENST00000257566	NM_016569.3	284	tAc/tGc	4/8	1	2	FACETS	0.986	0.911	1	0.986	0.911	1	CLONAL	1	TRUE	1	0.65	2		419	512	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589618	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519838	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	67	252	0	ENST00000274335.5:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000274335		461	Cga/Tga	10/15	1	2	FACETS	0.75	0.658	0.846	0.75	0.658	0.846	SUBCLONAL	1	TRUE	1	0.65	2		252	275	SUCCESS
BLM	641	MSKCC	GRCh37	15	91352484	91352484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1031421025	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	138	390	0	ENST00000355112.3:c.3869C>T	p.Ser1290Leu	p.S1290L	ENST00000355112	NM_000057.2	1290	tCg/tTg	20/22	1	2	FACETS	0.905	0.83	0.983	0.905	0.83	0.983	CLONAL	1	TRUE	1	0.65	2		390	469	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021439	31021439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs545224250	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	244	557	0	ENST00000375687.4:c.1438G>A	p.Glu480Lys	p.E480K	ENST00000375687	NM_015338.5	480	Gaa/Aaa	12/13	1	2	FACETS	0.942	0.883	1	0.942	0.883	1	CLONAL	1	TRUE	1	0.65	2		557	797	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345759	152345760	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs730882049	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	141	347	0	ENST00000359321.1:c.810dup	p.Ile271TyrfsTer8	p.I271Yfs*8	ENST00000359321	NM_005431.1	270	-/T	3/3	1	2	FACETS	0.844	0.774	0.917	0.844	0.774	0.917	CLONAL	1	TRUE	1	0.65	2		347	514	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572350	41572350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	225	653	0	ENST00000263253.7:c.4879C>T	p.Arg1627Trp	p.R1627W	ENST00000263253	NM_001429.3	1627	Cgg/Tgg	30/31	1	2	FACETS	0.856	0.799	0.914	0.856	0.799	0.914	CLONAL	1	TRUE	1	0.65	2		653	809	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991344	72991344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148024459	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	197	531	1	ENST00000268489.5:c.2701G>A	p.Ala901Thr	p.A901T	ENST00000268489	NM_006885.3	901	Gcc/Acc	2/10	1	2	FACETS	0.876	0.814	0.939	0.876	0.814	0.939	CLONAL	1	TRUE	1	0.65	2		532	692	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937236	76937236	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	122	372	0	ENST00000373344.5:c.3512G>T	p.Arg1171Ile	p.R1171I	ENST00000373344	NM_000489.3	1171	aGa/aTa	9/35	1	2	FACETS	0.963	0.878	1	0.963	0.878	1	CLONAL	1	TRUE	1	0.65	2		372	390	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402695	139402695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778118508	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	234	595	0	ENST00000277541.6:c.3314C>T	p.Ala1105Val	p.A1105V	ENST00000277541	NM_017617.3	1105	gCg/gTg	20/34	1	2	FACETS	0.863	0.807	0.921	0.863	0.807	0.921	CLONAL	1	TRUE	1	0.65	2		595	834	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651277	45651277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	245	539	0	ENST00000407780.3:c.748G>A	p.Gly250Ser	p.G250S	ENST00000407780	NM_001283052.1	250	Ggc/Agc	5/7	1	2	FACETS	0.904	0.847	0.962	0.904	0.847	0.962	CLONAL	1	TRUE	1	0.65	2		539	834	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755755	39755755	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	231	517	0	ENST00000288319.7:c.1010G>A	p.Gly337Glu	p.G337E	ENST00000288319	NM_182918.3	337	gGg/gAg	10/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.65	2		517	703	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980608	1980608	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753305456	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	243	608	0	ENST00000382891.5:c.4070G>A	p.Gly1357Asp	p.G1357D	ENST00000382891	NM_133335.3	1357	gGc/gAc	22/22	1	2	FACETS	0.962	0.902	1	0.962	0.902	1	CLONAL	1	TRUE	1	0.65	2		608	777	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218668	98218668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	260	506	0	ENST00000331920.6:c.3196G>A	p.Glu1066Lys	p.E1066K	ENST00000331920	NM_000264.3	1066	Gag/Aag	19/24	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.65	2		506	772	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858456	9858456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768295624	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	225	503	0	ENST00000330684.3:c.2945G>A	p.Gly982Glu	p.G982E	ENST00000330684	NM_001134407.1	982	gGa/gAa	13/13	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.65	2		503	657	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100283	8100283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	240	668	1	ENST00000346208.3:c.257G>A	p.Arg86His	p.R86H	ENST00000346208		86	cGc/cAc	3/6	1	2	FACETS	0.911	0.853	0.97	0.911	0.853	0.97	CLONAL	1	TRUE	1	0.65	2		669	811	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532732	187532732	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	229	512	0	ENST00000441802.2:c.9661C>A	p.Leu3221Ile	p.L3221I	ENST00000441802	NM_005245.3	3221	Ctt/Att	14/27	1	2	FACETS	0.901	0.842	0.961	0.901	0.842	0.961	CLONAL	1	TRUE	1	0.65	2		512	782	SUCCESS
APC	324	MSKCC	GRCh37	5	112154771	112154771	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1314843920	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	173	466	1	ENST00000257430.4:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000257430	NM_000038.5	348	Cga/Tga	10/16	1	2	FACETS	0.942	0.872	1	0.942	0.872	1	CLONAL	1	TRUE	1	0.65	2		467	565	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216712	36216712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780411851	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	204	593	0	ENST00000222270.7:c.3878G>A	p.Arg1293His	p.R1293H	ENST00000222270	NM_014727.1	1293	cGc/cAc	13/37	1	2	FACETS	0.826	0.768	0.885	0.826	0.768	0.885	CLONAL	1	TRUE	1	0.65	2		593	760	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78704367	78704367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780768526	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	189	459	0	ENST00000306801.3:c.515C>T	p.Thr172Met	p.T172M	ENST00000306801	NM_020761.2	172	aCg/aTg	5/34	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.65	2		459	456	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622451	28622451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	127	441	0	ENST00000241453.7:c.1166C>T	p.Ser389Leu	p.S389L	ENST00000241453	NM_004119.2	389	tCa/tTa	9/24	1	2	FACETS	0.762	0.694	0.833	0.762	0.694	0.833	SUBCLONAL	1	TRUE	1	0.65	2		441	513	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100181	27100182	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCA	rs374564889	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	189	702	0	ENST00000324856.7:c.3999_4001dup	p.Gln1334dup	p.Q1334dup	ENST00000324856	NM_006015.4	1334	ccg/ccGCAg	16/20	1	2	FACETS	0.612	0.566	0.66	0.612	0.566	0.66	SUBCLONAL	1	TRUE	1	0.65	2		702	950	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029333	14029333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766111215	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	242	572	0	ENST00000311895.7:c.1544G>A	p.Arg515His	p.R515H	ENST00000311895	NM_005236.2	515	cGt/cAt	8/11	1	2	FACETS	0.918	0.86	0.978	0.918	0.86	0.978	CLONAL	1	TRUE	1	0.65	2		572	811	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11269466	11269466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	208	480	0	ENST00000361445.4:c.3704G>A	p.Arg1235Gln	p.R1235Q	ENST00000361445	NM_004958.3	1235	cGg/cAg	25/58	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.65	2		480	637	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223862	53223862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	107	650	0	ENST00000375401.3:c.3497G>A	p.Arg1166His	p.R1166H	ENST00000375401	NM_004187.3	1166	cGc/cAc	23/26	1	2	FACETS	0.44	0.395	0.488	0.44	0.395	0.488	SUBCLONAL	1	TRUE	1	0.65	2		650	748	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279760	46279760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757419594	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	78	492	0	ENST00000371998.3:c.3686G>A	p.Arg1229His	p.R1229H	ENST00000371998		1229	cGc/cAc	20/23	1	2	FACETS	0.31	0.271	0.351	0.31	0.271	0.351	SUBCLONAL	1	TRUE	1	0.65	2		492	775	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942026	81942027	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	61	483	0	ENST00000359376.3:c.1568dup	p.Thr524TyrfsTer49	p.T524Yfs*49	ENST00000359376	NM_002661.3	521	-/C	17/33	1	2	FACETS	0.297	0.256	0.342	0.297	0.256	0.342	SUBCLONAL	1	TRUE	1	0.65	2		483	632	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619279	23619279	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587776527	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	232	502	0	ENST00000261584.4:c.3256C>T	p.Arg1086Ter	p.R1086*	ENST00000261584	NM_024675.3	1086	Cga/Tga	12/13	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.65	2		502	676	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403622	138403622	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	112	270	0	ENST00000289153.2:c.2160A>C	p.Lys720Asn	p.K720N	ENST00000289153	NM_006219.2	720	aaA/aaC	15/22	1	2	FACETS	0.841	0.762	0.922	0.841	0.762	0.922	CLONAL	1	TRUE	1	0.65	2		270	410	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741598	17741598	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	233	529	1	ENST00000250003.3:c.269C>T	p.Ala90Val	p.A90V	ENST00000250003	NM_002478.4	90	gCg/gTg	1/3	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.65	2		530	655	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122886	2122886	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs574205203	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	216	495	2	ENST00000219476.3:c.2257G>A	p.Ala753Thr	p.A753T	ENST00000219476	NM_000548.3	753	Gcc/Acc	21/42	1	2	FACETS	0.945	0.883	1	0.945	0.883	1	CLONAL	1	TRUE	1	0.65	2		497	703	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445095	49445095	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	246	654	1	ENST00000301067.7:c.2371del	p.Gln791ArgfsTer139	p.Q791Rfs*139	ENST00000301067	NM_003482.3	791	Cag/ag	10/54	1	2	FACETS	0.919	0.861	0.978	0.919	0.861	0.978	CLONAL	1	TRUE	1	0.65	2		655	824	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976372	18976372	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	219	578	0	ENST00000262803.5:c.3022C>T	p.Arg1008Ter	p.R1008*	ENST00000262803	NM_002911.3	1008	Cga/Tga	22/24	1	2	FACETS	0.941	0.879	1	0.941	0.879	1	CLONAL	1	TRUE	1	0.65	2		578	716	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639237	3639237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760497928	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	272	666	0	ENST00000294008.3:c.4402C>T	p.Arg1468Cys	p.R1468C	ENST00000294008	NM_032444.2	1468	Cgc/Tgc	12/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.65	2		666	807	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435129	110435129	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	240	649	6	ENST00000375856.3:c.3272del	p.Pro1091ArgfsTer15	p.P1091Rfs*15	ENST00000375856	NM_003749.2	1091	cCg/cg	1/2	1	2	FACETS	0.995	0.933	1	0.995	0.933	1	CLONAL	1	TRUE	1	0.65	2		655	742	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345918	70345918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751774081	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	56	438	0	ENST00000374080.3:c.2455C>T	p.Arg819Trp	p.R819W	ENST00000374080		819	Cgg/Tgg	18/45	1	2	FACETS	0.255	0.217	0.295	0.255	0.217	0.295	SUBCLONAL	1	TRUE	1	0.65	2		438	677	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130418	29130418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1300016035	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	254	597	0	ENST00000328354.6:c.292G>A	p.Ala98Thr	p.A98T	ENST00000328354	NM_007194.3	98	Gcc/Acc	2/15	1	2	FACETS	0.935	0.877	0.994	0.935	0.877	0.994	CLONAL	1	TRUE	1	0.65	2		597	836	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729808	41729808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150182559	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	190	603	0	ENST00000242208.4:c.721C>T	p.Arg241Trp	p.R241W	ENST00000242208	NM_002192.2	241	Cgg/Tgg	3/3	1	2	FACETS	0.766	0.71	0.824	0.766	0.71	0.824	SUBCLONAL	1	TRUE	1	0.65	2		603	763	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394020	31394020	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	130	341	0	ENST00000328111.2:c.2307G>T	p.Lys769Asn	p.K769N	ENST00000328111	NM_006892.3	769	aaG/aaT	22/23	1	2	FACETS	0.83	0.758	0.905	0.83	0.758	0.905	CLONAL	1	TRUE	1	0.65	2		341	482	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314945	1314945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1256843059	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	190	459	0	ENST00000400841.2:c.716C>T	p.Ala239Val	p.A239V	ENST00000400841		239	gCc/gTc	6/6	1	2	FACETS	0.847	0.786	0.91	0.847	0.786	0.91	CLONAL	1	TRUE	1	0.65	2		459	690	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943698	71943698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761761079	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	273	571	2	ENST00000298229.2:c.1741C>T	p.Arg581Trp	p.R581W	ENST00000298229	NM_001567.3	581	Cgg/Tgg	15/28	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.65	2		573	818	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90971071	90971071	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1554560506	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	171	365	0	ENST00000265433.3:c.1006A>G	p.Thr336Ala	p.T336A	ENST00000265433	NM_002485.4	336	Aca/Gca	9/16	1	2	FACETS	0.928	0.859	0.999	0.928	0.859	0.999	CLONAL	1	TRUE	1	0.65	2		365	567	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046462	69046462	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761455338	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	169	419	0	ENST00000288368.4:c.3935C>T	p.Ala1312Val	p.A1312V	ENST00000288368	NM_024870.2	1312	gCg/gTg	32/40	1	2	FACETS	0.884	0.817	0.953	0.884	0.817	0.953	CLONAL	1	TRUE	1	0.65	2		419	588	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649869	88649869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781556	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	96	246	0	ENST00000372037.3:c.118G>A	p.Asp40Asn	p.D40N	ENST00000372037	NM_004329.2	40	Gac/Aac	4/13	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.65	2		246	287	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568635	41568635	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1569118537	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	166	453	0	ENST00000263253.7:c.4585C>T	p.Arg1529Ter	p.R1529*	ENST00000263253	NM_001429.3	1529	Cga/Tga	28/31	1	2	FACETS	0.944	0.873	1	0.944	0.873	1	CLONAL	1	TRUE	1	0.65	2		453	541	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323193	31323193	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	305	805	1	ENST00000412585.2:c.796C>T	p.Gln266Ter	p.Q266*	ENST00000412585	NM_005514.6	266	Cag/Tag	4/8	1	2	FACETS	0.969	0.915	1	0.969	0.915	1	CLONAL	1	TRUE	1	0.65	2		806	968	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163313635	163313635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149575845	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	82	231	0	ENST00000271452.3:c.782C>T	p.Thr261Met	p.T261M	ENST00000271452	NM_145697.2	261	aCg/aTg	10/14	1	2	FACETS	0.774	0.689	0.864	0.774	0.689	0.864	SUBCLONAL	1	TRUE	1	0.65	2		231	326	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110004	115110004	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1201751425	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	223	560	0	ENST00000257566.3:c.1874G>A	p.Arg625His	p.R625H	ENST00000257566	NM_016569.3	625	cGc/cAc	8/8	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.65	2		560	599	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67197058	67197058	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	240	461	0	ENST00000312629.5:c.301C>A	p.Leu101Ile	p.L101I	ENST00000312629	NM_003952.2	101	Cta/Ata	4/15	1	2	FACETS	0.99	0.928	1	0.99	0.928	1	CLONAL	1	TRUE	1	0.65	2		461	746	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223469	2223469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1462122341	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	247	573	0	ENST00000398665.3:c.3580G>A	p.Glu1194Lys	p.E1194K	ENST00000398665	NM_032482.2	1194	Gag/Aag	25/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.65	2		573	709	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228998	36228998	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	295	673	4	ENST00000222270.7:c.7778G>A	p.Arg2593His	p.R2593H	ENST00000222270	NM_014727.1	2593	cGc/cAc	36/37	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.65	2		677	896	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631089	69631089	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs143593259	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	208	532	0	ENST00000334134.2:c.323C>T	p.Ser108Leu	p.S108L	ENST00000334134	NM_005247.2	108	tCg/tTg	2/3	1	2	FACETS	0.94	0.876	1	0.94	0.876	1	CLONAL	1	TRUE	1	0.65	2		532	681	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880926	134880926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371083718	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	186	479	1	ENST00000398015.3:c.1489C>T	p.Arg497Trp	p.R497W	ENST00000398015	NM_004441.4	497	Cgg/Tgg	7/16	1	2	FACETS	0.861	0.798	0.925	0.861	0.798	0.925	CLONAL	1	TRUE	1	0.65	2		480	665	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43699598	43699598	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766550469	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	174	427	0	ENST00000382044.4:c.5917G>A	p.Asp1973Asn	p.D1973N	ENST00000382044	NM_001141980.1	1973	Gat/Aat	28/28	1	2	FACETS	0.879	0.813	0.947	0.879	0.813	0.947	CLONAL	1	TRUE	1	0.65	2		427	609	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696405	47696405	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	214	433	0	ENST00000347630.2:c.418G>T	p.Asp140Tyr	p.D140Y	ENST00000347630	NM_001007230.1	140	Gat/Tat	6/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.65	2		433	615	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821341	72821341	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200494604	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	144	374	0	ENST00000268489.5:c.10834G>A	p.Ala3612Thr	p.A3612T	ENST00000268489	NM_006885.3	3612	Gcc/Acc	10/10	1	2	FACETS	0.935	0.859	1	0.935	0.859	1	CLONAL	1	TRUE	1	0.65	2		374	474	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562303	21562303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	232	605	0	ENST00000382592.4:c.1616G>A	p.Gly539Asp	p.G539D	ENST00000382592	NM_014572.2	539	gGc/gAc	4/8	1	2	FACETS	0.938	0.878	1	0.938	0.878	1	CLONAL	1	TRUE	1	0.65	2		605	761	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456496	99456496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223089854	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	185	483	0	ENST00000268035.6:c.1813C>T	p.Arg605Cys	p.R605C	ENST00000268035	NM_000875.3	605	Cgc/Tgc	8/21	1	2	FACETS	0.985	0.915	1	0.985	0.915	1	CLONAL	1	TRUE	1	0.65	2		483	578	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639525	3639525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369846826	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	163	732	0	ENST00000294008.3:c.4114C>T	p.Arg1372Trp	p.R1372W	ENST00000294008	NM_032444.2	1372	Cgg/Tgg	12/15	1	2	FACETS	0.618	0.568	0.671	0.618	0.568	0.671	SUBCLONAL	1	TRUE	1	0.65	2		732	811	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244124	133244124	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794759	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	259	539	0	ENST00000320574.5:c.2284C>T	p.Arg762Trp	p.R762W	ENST00000320574	NM_006231.2	762	Cgg/Tgg	20/49	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.65	2		539	740	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004302	150004302	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs35163691	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	161	338	0	ENST00000253339.5:c.1923C>A	p.Phe641Leu	p.F641L	ENST00000253339		641	ttC/ttA	3/7	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.65	2		338	452	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177000	56177000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs553060905	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	150	374	0	ENST00000399503.3:c.2270G>A	p.Arg757His	p.R757H	ENST00000399503	NM_005921.1	757	cGc/cAc	13/20	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.65	2		374	457	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778977	3778977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745551441	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	249	686	0	ENST00000262367.5:c.6071C>T	p.Ala2024Val	p.A2024V	ENST00000262367	NM_004380.2	2024	gCg/gTg	31/31	1	2	FACETS	0.951	0.892	1	0.951	0.892	1	CLONAL	1	TRUE	1	0.65	2		686	806	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266692	142266692	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	94	407	0	ENST00000350721.4:c.3232G>T	p.Glu1078Ter	p.E1078*	ENST00000350721	NM_001184.3	1078	Gaa/Taa	16/47	1	2	FACETS	0.784	0.703	0.868	0.784	0.703	0.868	SUBCLONAL	1	TRUE	1	0.65	2		407	369	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849900	151849900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773458258	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	265	545	0	ENST00000262189.6:c.12416G>A	p.Arg4139Gln	p.R4139Q	ENST00000262189	NM_170606.2	4139	cGa/cAa	49/59	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.65	2		545	797	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006000	22006000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	235	643	0	ENST00000276925.6:c.403G>A	p.Ala135Thr	p.A135T	ENST00000276925	NM_004936.3	135	Gcc/Acc	2/2	1	2	FACETS	0.876	0.82	0.935	0.876	0.82	0.935	CLONAL	1	TRUE	1	0.65	2		643	825	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39745020	39745020	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	210	505	0	ENST00000361337.2:c.1810G>T	p.Glu604Ter	p.E604*	ENST00000361337	NM_003286.2	604	Gaa/Taa	17/21	1	2	FACETS	0.95	0.886	1	0.95	0.886	1	CLONAL	1	TRUE	1	0.65	2		505	680	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266472	41266472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	185	456	0	ENST00000349496.5:c.269G>A	p.Arg90Gln	p.R90Q	ENST00000349496	NM_001904.3	90	cGa/cAa	4/15	1	2	FACETS	0.918	0.852	0.986	0.918	0.852	0.986	CLONAL	1	TRUE	1	0.65	2		456	620	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101511	27101511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748573855	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	222	658	2	ENST00000324856.7:c.4793G>A	p.Arg1598His	p.R1598H	ENST00000324856	NM_006015.4	1598	cGc/cAc	18/20	1	2	FACETS	0.879	0.821	0.939	0.879	0.821	0.939	CLONAL	1	TRUE	1	0.65	2		660	777	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541861	187541861	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	258	556	0	ENST00000441802.2:c.5879C>T	p.Ala1960Val	p.A1960V	ENST00000441802	NM_005245.3	1960	gCc/gTc	10/27	1	2	FACETS	0.959	0.901	1	0.959	0.901	1	CLONAL	1	TRUE	1	0.65	2		556	828	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905522	50905522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1408031137	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	250	726	0	ENST00000440232.2:c.650C>T	p.Pro217Leu	p.P217L	ENST00000440232	NM_002691.3	217	cCg/cTg	6/27	1	2	FACETS	0.928	0.87	0.987	0.928	0.87	0.987	CLONAL	1	TRUE	1	0.65	2		726	829	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418445	49418445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745599611	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	281	648	0	ENST00000301067.7:c.15968G>A	p.Arg5323His	p.R5323H	ENST00000301067	NM_003482.3	5323	cGc/cAc	50/54	1	2	FACETS	0.989	0.932	1	0.989	0.932	1	CLONAL	1	TRUE	1	0.65	2		648	874	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852046	63852046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756275189	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	237	596	0	ENST00000279873.7:c.2824G>A	p.Val942Ile	p.V942I	ENST00000279873	NM_032199.2	942	Gtc/Atc	10/10	1	2	FACETS	0.893	0.835	0.951	0.893	0.835	0.951	CLONAL	1	TRUE	1	0.65	2		596	817	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455139	50455139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1359632331	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	175	440	0	ENST00000331340.3:c.686G>A	p.Ser229Asn	p.S229N	ENST00000331340	NM_006060.4	229	aGc/aAc	6/8	1	2	FACETS	0.963	0.893	1	0.963	0.893	1	CLONAL	1	TRUE	1	0.65	2		440	559	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007560	62007560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	257	678	0	ENST00000392795.3:c.307G>A	p.Glu103Lys	p.E103K	ENST00000392795	NM_001039933.1	103	Gaa/Aaa	3/6	1	2	FACETS	0.995	0.935	1	0.995	0.935	1	CLONAL	1	TRUE	1	0.65	2		678	795	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182104	11182104	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs181023452	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	241	544	1	ENST00000361445.4:c.6742G>A	p.Ala2248Thr	p.A2248T	ENST00000361445	NM_004958.3	2248	Gcc/Acc	48/58	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.65	2		545	693	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172091	99172091	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776893699	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	250	653	0	ENST00000074304.5:c.1657C>T	p.Arg553Trp	p.R553W	ENST00000074304	NM_001134224.1	553	Cgg/Tgg	17/26	1	2	FACETS	0.89	0.835	0.947	0.89	0.835	0.947	CLONAL	1	TRUE	1	0.65	2		653	864	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019434	31019434	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	261	505	0	ENST00000375687.4:c.931G>A	p.Glu311Lys	p.E311K	ENST00000375687	NM_015338.5	311	Gag/Aag	10/13	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.65	2		505	796	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187791	11187791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	222	522	0	ENST00000361445.4:c.6106C>T	p.Arg2036Cys	p.R2036C	ENST00000361445	NM_004958.3	2036	Cgt/Tgt	44/58	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.65	2		522	672	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104572	193104572	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	142	406	0	ENST00000367435.3:c.359G>A	p.Arg120Gln	p.R120Q	ENST00000367435	NM_024529.4	120	cGa/cAa	4/17	0.3	0	FACETS	0.323	0.296	0.35			1	INDETERMINATE	1	TRUE	0	0.65	0		406	474	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223724	53223724	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141544076	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	247	675	0	ENST00000375401.3:c.3635G>A	p.Arg1212Gln	p.R1212Q	ENST00000375401	NM_004187.3	1212	cGg/cAg	23/26	1	2	FACETS	0.882	0.826	0.939	0.882	0.826	0.939	CLONAL	1	TRUE	1	0.65	2		675	862	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059323	42059323	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	286	620	0	ENST00000219905.7:c.9043G>A	p.Ala3015Thr	p.A3015T	ENST00000219905	NM_001164273.1	3015	Gca/Aca	24/24	1	2	FACETS	0.984	0.928	1	0.984	0.928	1	CLONAL	1	TRUE	1	0.65	2		620	894	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610111	43610111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	271	699	0	ENST00000355710.3:c.2063C>T	p.Ser688Phe	p.S688F	ENST00000355710	NM_020975.4	688	tCc/tTc	11/20	1	2	FACETS	0.987	0.929	1	0.987	0.929	1	CLONAL	1	TRUE	1	0.65	2		699	845	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164805	36164805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745561479	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	244	754	0	ENST00000300305.3:c.1070C>T	p.Pro357Leu	p.P357L	ENST00000300305		357	cCg/cTg	8/8	1	2	FACETS	0.893	0.836	0.951	0.893	0.836	0.951	CLONAL	1	TRUE	1	0.65	2		754	841	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427665	49427667	+	inframe_deletion	In_Frame_Del	DEL	TGC	TGC	-	rs747016071	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	216	636	7	ENST00000301067.7:c.10821_10823del	p.Gln3612del	p.Q3612del	ENST00000301067	NM_003482.3	3607	caGCAa/caa	39/54	1	2	FACETS	0.836	0.779	0.894	0.836	0.779	0.894	CLONAL	1	TRUE	1	0.65	2		643	795	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596150	43596150	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	211	544	0	ENST00000355710.3:c.317G>T	p.Trp106Leu	p.W106L	ENST00000355710	NM_020975.4	106	tGg/tTg	2/20	1	2	FACETS	0.88	0.82	0.941	0.88	0.82	0.941	CLONAL	1	TRUE	1	0.65	2		544	738	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522409	157522409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	228	616	0	ENST00000346085.5:c.4681C>T	p.Arg1561Cys	p.R1561C	ENST00000346085	NM_020732.3	1561	Cgc/Tgc	18/20	1	2	FACETS	0.886	0.828	0.945	0.886	0.828	0.945	CLONAL	1	TRUE	1	0.65	2		616	792	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	401930	401930	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	260	486	0	ENST00000399788.2:c.4861G>A	p.Asp1621Asn	p.D1621N	ENST00000399788	NM_001042603.1	1621	Gac/Aac	27/28	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.65	2		486	785	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422997	49422997	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369583907	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	219	648	0	ENST00000301067.7:c.14098G>A	p.Asp4700Asn	p.D4700N	ENST00000301067	NM_003482.3	4700	Gat/Aat	44/54	1	2	FACETS	0.923	0.862	0.986	0.923	0.862	0.986	CLONAL	1	TRUE	1	0.65	2		648	730	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300475	11300475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	50	633	0	ENST00000361445.4:c.1671G>A	p.Met557Ile	p.M557I	ENST00000361445	NM_004958.3	557	atG/atA	11/58	1	2	FACETS	0.185	0.156	0.217	0.185	0.156	0.217	SUBCLONAL	1	TRUE	1	0.65	2		633	831	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282396	115282396	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	153	380	0	ENST00000438362.2:c.254T>G	p.Phe85Cys	p.F85C	ENST00000438362	NM_001242891.1	85	tTt/tGt	3/20	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.65	2		380	467	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462974	120462974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587634422	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	236	552	0	ENST00000256646.2:c.5357G>A	p.Arg1786Gln	p.R1786Q	ENST00000256646	NM_024408.3	1786	cGa/cAa	30/34	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.65	2		552	719	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150919368	150919368	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	177	510	0	ENST00000271640.5:c.1150del	p.Arg384AspfsTer18	p.R384Dfs*18	ENST00000271640	NM_001145415.1	383	Aaa/aa	10/22	1	2	FACETS	0.903	0.837	0.972	0.903	0.837	0.972	CLONAL	1	TRUE	1	0.65	2		510	603	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150921596	150921596	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	211	493	2	ENST00000271640.5:c.1268-2A>G		p.X423_splice	ENST00000271640	NM_001145415.1	423			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.65	2		495	635	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150923882	150923882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	209	486	0	ENST00000271640.5:c.2255C>T	p.Ala752Val	p.A752V	ENST00000271640	NM_001145415.1	752	gCc/gTc	14/22	1	2	FACETS	0.961	0.897	1	0.961	0.897	1	CLONAL	1	TRUE	1	0.65	2		486	669	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021954	246021954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	174	456	0	ENST00000388985.4:c.920C>T	p.Ala307Val	p.A307V	ENST00000388985		307	gCc/gTc	10/12	1	2	FACETS	0.953	0.882	1	0.953	0.882	1	CLONAL	1	TRUE	1	0.65	2		456	562	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607562	43607562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149238501	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	373	925	0	ENST00000355710.3:c.1538C>T	p.Ala513Val	p.A513V	ENST00000355710	NM_020975.4	513	gCg/gTg	8/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.65	2		925	1148	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57004340	57004340	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	C	C	T	rs1238295474	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	282	659	0	ENST00000257254.3:c.139G>A	p.Gly47Ser	p.G47S	ENST00000257254		47	Ggt/Agt	1/2	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.65	2		659	807	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090412	77090412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769079461	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	203	516	0	ENST00000356341.3:c.313C>T	p.Arg105Cys	p.R105C	ENST00000356341	NM_002576.4	105	Cgc/Tgc	4/15	1	2	FACETS	0.833	0.774	0.893	0.833	0.774	0.893	CLONAL	1	TRUE	1	0.65	2		516	750	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212853	94212853	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	123	365	0	ENST00000323929.3:c.389A>G	p.Asp130Gly	p.D130G	ENST00000323929	NM_005591.3	130	gAc/gGc	5/20	1	2	FACETS	0.845	0.769	0.923	0.845	0.769	0.923	CLONAL	1	TRUE	1	0.65	2		365	448	SUCCESS
ATM	472	MSKCC	GRCh37	11	108159766	108159766	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	42	186	0	ENST00000278616.4:c.4172C>T	p.Ala1391Val	p.A1391V	ENST00000278616	NM_000051.3	1391	gCc/gTc	28/63	1	2	FACETS	0.525	0.442	0.616	0.525	0.442	0.616	SUBCLONAL	1	TRUE	1	0.65	2		186	246	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	465653	465653	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	179	369	0	ENST00000399788.2:c.723T>G	p.Ile241Met	p.I241M	ENST00000399788	NM_001042603.1	241	atT/atG	6/28	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.65	2		369	551	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022716	12022716	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	264	778	0	ENST00000396373.4:c.822G>T	p.Met274Ile	p.M274I	ENST00000396373	NM_001987.4	274	atG/atT	5/8	1	2	FACETS	0.801	0.751	0.852	0.801	0.751	0.852	CLONAL	1	TRUE	1	0.65	2		778	1014	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435304	18435304	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	186	503	0	ENST00000266497.5:c.289T>G	p.Ser97Ala	p.S97A	ENST00000266497		97	Tcc/Gcc	1/31	1	2	FACETS	0.91	0.844	0.977	0.91	0.844	0.977	CLONAL	1	TRUE	1	0.65	2		503	629	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479277	50479277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1357450761	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	189	515	0	ENST00000394963.4:c.125C>T	p.Pro42Leu	p.P42L	ENST00000394963	NM_003076.4	42	cCg/cTg	1/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.65	2		515	551	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492285	56492285	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	167	409	0	ENST00000267101.3:c.2618C>T	p.Thr873Ile	p.T873I	ENST00000267101	NM_001982.3	873	aCt/aTt	22/28	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.65	2		409	514	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930630	32930630	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886040711	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	234	486	0	ENST00000380152.3:c.7501C>T	p.Gln2501Ter	p.Q2501*	ENST00000380152		2501	Caa/Taa	15/27	1	2	FACETS	0.946	0.886	1	0.946	0.886	1	CLONAL	1	TRUE	1	0.65	2		486	761	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951122	48951122	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	126	279	0	ENST00000267163.4:c.1284G>T	p.Glu428Asp	p.E428D	ENST00000267163	NM_000321.2	428	gaG/gaT	13/27	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.65	2		279	380	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033959	49033959	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	208	440	0	ENST00000267163.4:c.2096A>G	p.His699Arg	p.H699R	ENST00000267163	NM_000321.2	699	cAt/cGt	20/27	1	2	FACETS	0.983	0.917	1	0.983	0.917	1	CLONAL	1	TRUE	1	0.65	2		440	651	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039187	49039187	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	96	296	0	ENST00000267163.4:c.2265C>A	p.Phe755Leu	p.F755L	ENST00000267163	NM_000321.2	755	ttC/ttA	22/27	1	2	FACETS	0.849	0.763	0.938	0.849	0.763	0.938	CLONAL	1	TRUE	1	0.65	2		296	348	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337670	73337670	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	144	365	0	ENST00000377767.4:c.2046T>G	p.Phe682Leu	p.F682L	ENST00000377767	NM_014953.3	682	ttT/ttG	16/21	1	2	FACETS	0.937	0.861	1	0.937	0.861	1	CLONAL	1	TRUE	1	0.65	2		365	473	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103525608	103525608	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	133	350	0	ENST00000355739.4:c.2880-1T>C		p.X960_splice	ENST00000355739	NM_000123.3	960			1	2	FACETS	0.905	0.829	0.985	0.905	0.829	0.985	CLONAL	1	TRUE	1	0.65	2		350	452	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436030	110436030	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	245	674	0	ENST00000375856.3:c.2371G>T	p.Gly791Cys	p.G791C	ENST00000375856	NM_003749.2	791	Ggc/Tgc	1/2	1	2	FACETS	0.951	0.891	1	0.951	0.891	1	CLONAL	1	TRUE	1	0.65	2		674	793	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748815	43748815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	225	600	0	ENST00000382044.4:c.1991C>T	p.Ser664Phe	p.S664F	ENST00000382044	NM_001141980.1	664	tCt/tTt	12/28	1	2	FACETS	0.99	0.927	1	0.99	0.927	1	CLONAL	1	TRUE	1	0.65	2		600	699	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479822	67479822	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730880216	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	261	586	1	ENST00000327367.4:c.1129G>A	p.Val377Ile	p.V377I	ENST00000327367	NM_005902.3	377	Gtc/Atc	8/9	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.65	2		587	744	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679841	88679841	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	173	399	0	ENST00000360948.2:c.623-1G>A		p.X208_splice	ENST00000360948	NM_001012338.2	208			1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.65	2		399	531	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103395	2103395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1222477746	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	61	420	1	ENST00000219476.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000219476	NM_000548.3	93	cGg/cAg	4/42	1	2	FACETS	0.348	0.3	0.399	0.348	0.3	0.399	SUBCLONAL	1	TRUE	1	0.65	2		421	540	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857619	9857619	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	262	667	0	ENST00000330684.3:c.3782C>T	p.Ala1261Val	p.A1261V	ENST00000330684	NM_001134407.1	1261	gCc/gTc	13/13	1	2	FACETS	0.969	0.911	1	0.969	0.911	1	CLONAL	1	TRUE	1	0.65	2		667	832	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827571	72827571	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	229	510	0	ENST00000268489.5:c.9010T>C	p.Ser3004Pro	p.S3004P	ENST00000268489	NM_006885.3	3004	Tcc/Ccc	9/10	1	2	FACETS	0.969	0.907	1	0.969	0.907	1	CLONAL	1	TRUE	1	0.65	2		510	727	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831910	72831910	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	205	563	0	ENST00000268489.5:c.4671G>T	p.Lys1557Asn	p.K1557N	ENST00000268489	NM_006885.3	1557	aaG/aaT	9/10	1	2	FACETS	0.932	0.868	0.997	0.932	0.868	0.997	CLONAL	1	TRUE	1	0.65	2		563	677	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982722	7982722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	172	466	0	ENST00000319144.4:c.1063G>A	p.Ala355Thr	p.A355T	ENST00000319144	NM_001139.2	355	Gcc/Acc	8/15	1	2	FACETS	0.925	0.856	0.996	0.925	0.856	0.996	CLONAL	1	TRUE	1	0.65	2		466	572	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17120474	17120474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559055296	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	199	507	0	ENST00000285071.4:c.1085G>A	p.Arg362His	p.R362H	ENST00000285071	NM_144997.5	362	cGc/cAc	10/14	1	2	FACETS	0.832	0.773	0.893	0.832	0.773	0.893	CLONAL	1	TRUE	1	0.65	2		507	736	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533325	29533325	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555611581	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	175	497	0	ENST00000356175.3:c.1328T>C	p.Phe443Ser	p.F443S	ENST00000356175	NM_000267.3	443	tTt/tCt	12/57	1	2	FACETS	0.88	0.814	0.947	0.88	0.814	0.947	CLONAL	1	TRUE	1	0.65	2		497	612	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745848	745848	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	112	435	0	ENST00000314574.4:c.584C>A	p.Ser195Tyr	p.S195Y	ENST00000314574	NM_005433.3	195	tCc/tAc	6/12	1	2	FACETS	0.838	0.76	0.92	0.838	0.76	0.92	CLONAL	1	TRUE	1	0.65	2		435	411	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56411698	56411698	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	87	281	0	ENST00000348428.3:c.1882T>C	p.Cys628Arg	p.C628R	ENST00000348428	NM_006785.3	628	Tgt/Cgt	15/17	1	2	FACETS	0.872	0.78	0.968	0.872	0.78	0.968	CLONAL	1	TRUE	1	0.65	2		281	307	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61324626	61324626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	109	292	0	ENST00000283752.5:c.490C>T	p.Pro164Ser	p.P164S	ENST00000283752	NM_006919.2	164	Cct/Tct	6/8	1	2	FACETS	0.897	0.813	0.984	0.897	0.813	0.984	CLONAL	1	TRUE	1	0.65	2		292	374	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619329	1619329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781628625	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	52	766	4	ENST00000344749.5:c.1312C>T	p.Arg438Trp	p.R438W	ENST00000344749	NM_001136139.2	438	Cgg/Tgg	15/19	1	2	FACETS	0.181	0.153	0.212	0.181	0.153	0.212	SUBCLONAL	1	TRUE	1	0.65	2		770	884	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118953	3118953	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777912441	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	246	577	1	ENST00000078429.4:c.637C>T	p.Arg213Trp	p.R213W	ENST00000078429	NM_002067.2	213	Cgg/Tgg	5/7	1	2	FACETS	0.968	0.908	1	0.968	0.908	1	CLONAL	1	TRUE	1	0.65	2		578	782	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215399	5215399	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	239	634	0	ENST00000357368.4:c.4219A>G	p.Thr1407Ala	p.T1407A	ENST00000357368	NM_002850.3	1407	Aca/Gca	28/38	1	2	FACETS	0.922	0.863	0.981	0.922	0.863	0.981	CLONAL	1	TRUE	1	0.65	2		634	798	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030356	11030356	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	124	541	0	ENST00000327064.4:c.1106G>T	p.Arg369Met	p.R369M	ENST00000327064	NM_199141.1	369	aGg/aTg	9/16	1	2	FACETS	0.571	0.518	0.627	0.571	0.518	0.627	SUBCLONAL	1	TRUE	1	0.65	2		541	668	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134251	11134251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218643327	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	221	474	0	ENST00000358026.2:c.2917C>T	p.Arg973Trp	p.R973W	ENST00000358026	NM_001128849.1	973	Cgg/Tgg	20/36	1	2	FACETS	0.947	0.885	1	0.947	0.885	1	CLONAL	1	TRUE	1	0.65	2		474	718	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277081	18277081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1279824134	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	274	553	0	ENST00000222254.8:c.1528C>T	p.Arg510Trp	p.R510W	ENST00000222254	NM_005027.3	510	Cgg/Tgg	12/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.65	2		553	808	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214803	36214803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	185	464	0	ENST00000222270.7:c.3229C>T	p.Arg1077Trp	p.R1077W	ENST00000222270	NM_014727.1	1077	Cgg/Tgg	8/37	1	2	FACETS	0.955	0.887	1	0.955	0.887	1	CLONAL	1	TRUE	1	0.65	2		464	596	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216449	36216449	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	228	638	0	ENST00000222270.7:c.3715del	p.Gln1239SerfsTer116	p.Q1239Sfs*116	ENST00000222270	NM_014727.1	1238	Ccc/cc	12/37	1	2	FACETS	0.894	0.835	0.954	0.894	0.835	0.954	CLONAL	1	TRUE	1	0.65	2		638	785	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227822	36227822	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	282	741	0	ENST00000222270.7:c.7307G>T	p.Arg2436Ile	p.R2436I	ENST00000222270	NM_014727.1	2436	aGa/aTa	32/37	1	2	FACETS	0.993	0.936	1	0.993	0.936	1	CLONAL	1	TRUE	1	0.65	2		741	874	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964981	25964981	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	237	582	0	ENST00000435504.4:c.4225A>G	p.Met1409Val	p.M1409V	ENST00000435504		1409	Atg/Gtg	13/13	1	2	FACETS	0.907	0.849	0.966	0.907	0.849	0.966	CLONAL	1	TRUE	1	0.65	2		582	804	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726987	61726987	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	133	370	0	ENST00000401558.2:c.451A>G	p.Ser151Gly	p.S151G	ENST00000401558	NM_003400.3	151	Agt/Ggt	7/25	1	2	FACETS	0.894	0.818	0.972	0.894	0.818	0.972	CLONAL	1	TRUE	1	0.65	2		370	458	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375048	31375048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200405601	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	230	643	1	ENST00000328111.2:c.445C>T	p.Arg149Trp	p.R149W	ENST00000328111	NM_006892.3	149	Cgg/Tgg	6/23	1	2	FACETS	0.941	0.88	1	0.941	0.88	1	CLONAL	1	TRUE	1	0.65	2		644	752	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388037	31388037	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1568857280	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	264	567	0	ENST00000328111.2:c.1838T>C	p.Val613Ala	p.V613A	ENST00000328111	NM_006892.3	613	gTt/gCt	17/23	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.65	2		567	794	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39690124	39690124	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	213	434	0	ENST00000361337.2:c.149G>A	p.Ser50Asn	p.S50N	ENST00000361337	NM_003286.2	50	aGc/aAc	3/21	1	2	FACETS	0.915	0.854	0.979	0.915	0.854	0.979	CLONAL	1	TRUE	1	0.65	2		434	716	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42851178	42851178	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	142	406	0	ENST00000398585.3:c.715G>A	p.Asp239Asn	p.D239N	ENST00000398585	NM_001135099.1	239	Gat/Aat	7/14	1	2	FACETS	0.894	0.82	0.97	0.894	0.82	0.97	CLONAL	1	TRUE	1	0.65	2		406	489	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514612	44514612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	236	470	0	ENST00000291552.4:c.544C>T	p.Arg182Trp	p.R182W	ENST00000291552	NM_006758.2	182	Cgg/Tgg	7/8	1	2	FACETS	0.932	0.873	0.993	0.932	0.873	0.993	CLONAL	1	TRUE	1	0.65	2		470	779	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21348457	21348457	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201773172	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	239	772	0	ENST00000215739.8:c.1514G>A	p.Arg505Gln	p.R505Q	ENST00000215739	NM_006767.3	505	cGg/cAg	14/21	1	2	FACETS	0.877	0.82	0.934	0.877	0.82	0.934	CLONAL	1	TRUE	1	0.65	2		772	839	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130528	29130528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1569170658	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	230	548	0	ENST00000328354.6:c.182G>A	p.Ser61Asn	p.S61N	ENST00000328354	NM_007194.3	61	aGc/aAc	2/15	1	2	FACETS	0.993	0.929	1	0.993	0.929	1	CLONAL	1	TRUE	1	0.65	2		548	713	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446744	29446744	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1457204359	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	250	571	0	ENST00000544604.2:c.2575C>T	p.Arg859Ter	p.R859*	ENST00000544604	NM_001206998.1	859	Cga/Tga	8/9	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.65	2		571	706	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042521	37042521	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	106	311	0	ENST00000231790.2:c.283T>C	p.Ser95Pro	p.S95P	ENST00000231790	NM_000249.3	95	Tct/Cct	3/19	1	2	FACETS	0.766	0.691	0.844	0.766	0.691	0.844	SUBCLONAL	1	TRUE	1	0.65	2		311	426	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181881	38181881	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	197	541	0	ENST00000396334.3:c.505C>T	p.His169Tyr	p.H169Y	ENST00000396334	NM_002468.4	169	Cat/Tat	3/5	1	2	FACETS	0.878	0.817	0.942	0.878	0.817	0.942	CLONAL	1	TRUE	1	0.65	2		541	690	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163041	47163041	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	146	405	0	ENST00000409792.3:c.3085G>T	p.Glu1029Ter	p.E1029*	ENST00000409792	NM_014159.6	1029	Gaa/Taa	3/21	1	2	FACETS	0.883	0.811	0.957	0.883	0.811	0.957	CLONAL	1	TRUE	1	0.65	2		405	509	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723581	49723581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	16	27	0	ENST00000449682.2:c.1061C>T	p.Ala354Val	p.A354V	ENST00000449682	NM_020998.3	354	gCg/gTg	9/18	1	2	FACETS	1	0.818	1	1	0.818	1	CLONAL	1	TRUE	1	0.65	2		27	46	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480379	89480379	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	180	416	0	ENST00000336596.2:c.2216A>C	p.Asp739Ala	p.D739A	ENST00000336596	NM_005233.5	739	gAc/gCc	13/17	1	2	FACETS	0.892	0.826	0.959	0.892	0.826	0.959	CLONAL	1	TRUE	1	0.65	2		416	621	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430239	181430239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1386163785	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	203	564	0	ENST00000325404.1:c.91G>A	p.Gly31Ser	p.G31S	ENST00000325404	NM_003106.3	31	Ggc/Agc	1/1	1	2	FACETS	0.942	0.878	1	0.942	0.878	1	CLONAL	1	TRUE	1	0.65	2		564	663	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748324	41748324	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	215	482	0	ENST00000226382.2:c.445C>T	p.Arg149Cys	p.R149C	ENST00000226382	NM_003924.3	149	Cgc/Tgc	3/3	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.65	2		482	622	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968081	55968081	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	136	333	0	ENST00000263923.4:c.2249C>G	p.Ala750Gly	p.A750G	ENST00000263923	NM_002253.2	750	gCa/gGa	15/30	1	2	FACETS	0.932	0.854	1	0.932	0.854	1	CLONAL	1	TRUE	1	0.65	2		333	449	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144359747	144359747	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1458245713	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	162	399	0	ENST00000262995.4:c.1189C>T	p.Arg397Ter	p.R397*	ENST00000262995	NM_207123.2	397	Cga/Tga	4/11	1	2	FACETS	0.946	0.874	1	0.946	0.874	1	CLONAL	1	TRUE	1	0.65	2		399	527	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524809	187524809	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	228	469	0	ENST00000441802.2:c.10871T>C	p.Val3624Ala	p.V3624A	ENST00000441802	NM_005245.3	3624	gTg/gCg	19/27	1	2	FACETS	0.871	0.814	0.93	0.871	0.814	0.93	CLONAL	1	TRUE	1	0.65	2		469	805	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541337	187541337	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	188	524	0	ENST00000441802.2:c.6403A>G	p.Ile2135Val	p.I2135V	ENST00000441802	NM_005245.3	2135	Att/Gtt	10/27	1	2	FACETS	0.875	0.812	0.94	0.875	0.812	0.94	CLONAL	1	TRUE	1	0.65	2		524	661	SUCCESS
APC	324	MSKCC	GRCh37	5	112176727	112176727	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	106	357	0	ENST00000257430.4:c.5436G>T	p.Lys1812Asn	p.K1812N	ENST00000257430	NM_000038.5	1812	aaG/aaT	16/16	1	2	FACETS	0.73	0.658	0.805	0.73	0.658	0.805	SUBCLONAL	1	TRUE	1	0.65	2		357	447	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930711	131930711	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	88	288	0	ENST00000265335.6:c.1944A>C	p.Glu648Asp	p.E648D	ENST00000265335		648	gaA/gaC	12/25	1	2	FACETS	0.767	0.685	0.853	0.767	0.685	0.853	SUBCLONAL	1	TRUE	1	0.65	2		288	353	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778105	27778105	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	281	792	0	ENST00000369163.2:c.254T>C	p.Phe85Ser	p.F85S	ENST00000369163	NM_003536.2	85	tTc/tCc	1/1	1	2	FACETS	0.95	0.895	1	0.95	0.895	1	CLONAL	1	TRUE	1	0.65	2		792	910	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778185	27778185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	305	687	0	ENST00000369163.2:c.334G>A	p.Ala112Thr	p.A112T	ENST00000369163	NM_003536.2	112	Gcc/Acc	1/1	1	2	FACETS	0.964	0.91	1	0.964	0.91	1	CLONAL	1	TRUE	1	0.65	2		687	974	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681612	30681612	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	284	624	0	ENST00000376406.3:c.485T>A	p.Leu162His	p.L162H	ENST00000376406	NM_014641.2	162	cTt/cAt	3/15	1	2	FACETS	0.957	0.902	1	0.957	0.902	1	CLONAL	1	TRUE	1	0.65	2		624	913	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956648	93956648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	185	459	0	ENST00000369303.4:c.2588C>T	p.Ala863Val	p.A863V	ENST00000369303	NM_004440.3	863	gCt/gTt	15/17	1	2	FACETS	0.953	0.885	1	0.953	0.885	1	CLONAL	1	TRUE	1	0.65	2		459	597	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042090	6042090	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs863224679	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	52	135	0	ENST00000265849.7:c.531T>G	p.Ile177Met	p.I177M	ENST00000265849	NM_000535.5	177	atT/atG	5/15	1	2	FACETS	0.804	0.694	0.921	0.804	0.694	0.921	CLONAL	1	TRUE	1	0.65	2		135	199	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210132	55210132	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	135	288	0	ENST00000275493.2:c.240+2T>C		p.X80_splice	ENST00000275493	NM_005228.3	80			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.65	2		288	397	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374380	81374380	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs139457161	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	132	372	0	ENST00000222390.5:c.682T>G	p.Ser228Ala	p.S228A	ENST00000222390	NM_000601.4	228	Tca/Gca	6/18	1	2	FACETS	0.923	0.845	1	0.923	0.845	1	CLONAL	1	TRUE	1	0.65	2		372	440	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148529826	148529826	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	122	281	0	ENST00000320356.2:c.263A>G	p.Asp88Gly	p.D88G	ENST00000320356	NM_004456.4	88	gAc/gGc	4/20	1	2	FACETS	0.967	0.883	1	0.967	0.883	1	CLONAL	1	TRUE	1	0.65	2		281	388	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38137195	38137195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	157	418	0	ENST00000317025.8:c.3623G>A	p.Arg1208His	p.R1208H	ENST00000317025	NM_023034.1	1208	cGt/cAt	21/24	1	2	FACETS	0.87	0.802	0.941	0.87	0.802	0.941	CLONAL	1	TRUE	1	0.65	2		418	555	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38173523	38173523	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	197	395	0	ENST00000317025.8:c.1893G>T	p.Lys631Asn	p.K631N	ENST00000317025	NM_023034.1	631	aaG/aaT	10/24	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.65	2		395	595	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189055	38189055	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1250796714	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	146	395	2	ENST00000317025.8:c.959C>T	p.Ala320Val	p.A320V	ENST00000317025	NM_023034.1	320	gCg/gTg	5/24	1	2	FACETS	0.908	0.834	0.983	0.908	0.834	0.983	CLONAL	1	TRUE	1	0.65	2		397	495	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981966	70981966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	204	607	0	ENST00000276594.2:c.130G>A	p.Ala44Thr	p.A44T	ENST00000276594	NM_024504.3	44	Gcc/Acc	2/8	1	2	FACETS	0.941	0.877	1	0.941	0.877	1	CLONAL	1	TRUE	1	0.65	2		607	667	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74868160	74868160	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	116	286	0	ENST00000284811.8:c.134T>G	p.Met45Arg	p.M45R	ENST00000284811		45	aTg/aGg	3/4	1	2	FACETS	0.908	0.826	0.993	0.908	0.826	0.993	CLONAL	1	TRUE	1	0.65	2		286	393	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965738	90965738	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	116	350	0	ENST00000265433.3:c.1579G>A	p.Asp527Asn	p.D527N	ENST00000265433	NM_002485.4	527	Gat/Aat	11/16	1	2	FACETS	0.875	0.795	0.958	0.875	0.795	0.958	CLONAL	1	TRUE	1	0.65	2		350	408	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965863	90965863	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200891292	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	92	306	0	ENST00000265433.3:c.1454C>T	p.Thr485Met	p.T485M	ENST00000265433	NM_002485.4	485	aCg/aTg	11/16	1	2	FACETS	0.776	0.695	0.86	0.776	0.695	0.86	SUBCLONAL	1	TRUE	1	0.65	2		306	365	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2032958	2032958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762444118	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	97	402	0	ENST00000349721.2:c.232G>A	p.Asp78Asn	p.D78N	ENST00000349721	NM_003070.3	78	Gat/Aat	3/34	1	2	FACETS	0.624	0.559	0.693	0.624	0.559	0.693	SUBCLONAL	1	TRUE	1	0.65	2		402	478	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2181578	2181578	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	111	297	0	ENST00000349721.2:c.4261C>T	p.Arg1421Ter	p.R1421*	ENST00000349721	NM_003070.3	1421	Cga/Tga	30/34	1	2	FACETS	0.787	0.712	0.865	0.787	0.712	0.865	SUBCLONAL	1	TRUE	1	0.65	2		297	434	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471042	8471042	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1471848912	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	135	393	0	ENST00000356435.5:c.3457A>G	p.Lys1153Glu	p.K1153E	ENST00000356435		1153	Aaa/Gaa	20/35	1	2	FACETS	0.999	0.916	1	0.999	0.916	1	CLONAL	1	TRUE	1	0.65	2		393	416	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485309	8485309	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	85	307	0	ENST00000356435.5:c.3071T>G	p.Phe1024Cys	p.F1024C	ENST00000356435		1024	tTt/tGt	18/35	1	2	FACETS	0.672	0.598	0.751	0.672	0.598	0.751	SUBCLONAL	1	TRUE	1	0.65	2		307	389	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486233	8486233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763867237	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	184	506	0	ENST00000356435.5:c.2584C>T	p.Arg862Cys	p.R862C	ENST00000356435		862	Cgc/Tgc	17/35	1	2	FACETS	0.944	0.876	1	0.944	0.876	1	CLONAL	1	TRUE	1	0.65	2		506	600	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002728	37002728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	250	606	1	ENST00000358127.4:c.521C>T	p.Ser174Leu	p.S174L	ENST00000358127	NM_001280556.1	174	tCg/tTg	5/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.65	2		607	721	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325668	87325668	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	155	416	0	ENST00000277120.3:c.545A>C	p.Lys182Thr	p.K182T	ENST00000277120		182	aAg/aCg	6/19	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.65	2		416	476	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915930	127915930	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	175	421	0	ENST00000373547.4:c.551A>C	p.Glu184Ala	p.E184A	ENST00000373547	NM_002721.4	184	gAa/gCa	6/7	1	2	FACETS	0.924	0.855	0.994	0.924	0.855	0.994	CLONAL	1	TRUE	1	0.65	2		421	583	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920648	127920648	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	89	298	0	ENST00000373547.4:c.251A>G	p.Asp84Gly	p.D84G	ENST00000373547	NM_002721.4	84	gAc/gGc	4/7	1	2	FACETS	0.843	0.755	0.935	0.843	0.755	0.935	CLONAL	1	TRUE	1	0.65	2		298	325	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760738	133760738	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776649059	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	230	625	0	ENST00000318560.5:c.3061C>T	p.Arg1021Trp	p.R1021W	ENST00000318560	NM_005157.4	1021	Cgg/Tgg	11/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.65	2		625	700	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356243	70356243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374390933	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	191	552	0	ENST00000374080.3:c.5138G>A	p.Arg1713Gln	p.R1713Q	ENST00000374080		1713	cGa/cAa	37/45	1	2	FACETS	0.841	0.78	0.903	0.841	0.78	0.903	CLONAL	1	TRUE	1	0.65	2		552	699	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938220	76938220	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	108	427	0	ENST00000373344.5:c.2528A>G	p.Asn843Ser	p.N843S	ENST00000373344	NM_000489.3	843	aAt/aGt	9/35	1	2	FACETS	0.786	0.71	0.864	0.786	0.71	0.864	SUBCLONAL	1	TRUE	1	0.65	2		427	423	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224495	123224495	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774149981	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	159	488	0	ENST00000218089.9:c.3348G>A	p.Met1116Ile	p.M1116I	ENST00000218089	NM_001042749.1	1116	atG/atA	31/35	1	2	FACETS	0.818	0.753	0.885	0.818	0.753	0.885	CLONAL	1	TRUE	1	0.65	2		488	598	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61308146	61308146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201629395	NA	P-0060107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	12	21	0	ENST00000341074.5:c.431G>A	p.Arg144Gln	p.R144Q	ENST00000341074	NM_002974.2	144	cGa/cAa	5/8	1	2	FACETS	0.998	0.734	1	0.998	0.734	1	CLONAL	1	TRUE	1	0.65	2		21	37	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0060108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	23	360	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	0.364387777557287	1	FACETS	0.2	0.155	0.253	0.2	0.155	0.253	SUBCLONAL	1	TRUE	0	0.364387777557287	1		360	515	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577595	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0060108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	178	523	0	ENST00000269305.4:c.686_687del	p.Cys229TyrfsTer10	p.C229Yfs*10	ENST00000269305	NM_001126112.2	229	tGT/t	7/11	0.364387777557287	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.364387777557287	1		523	688	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974721	21974721	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	188	699	3	ENST00000304494.5:c.106del	p.Ala36ArgfsTer17	p.A36Rfs*17	ENST00000304494	NM_000077.4	36	Gcg/cg	1/3	0.364387777557287	1	FACETS	0.947	0.876	1	0.947	0.876	1	CLONAL	1	TRUE	0	0.364387777557287	1		702	891	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730916	40730916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765075213	NA	P-0060108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	169	600	0	ENST00000373198.4:c.3619C>T	p.Arg1207Cys	p.R1207C	ENST00000373198	NM_133170.3	1207	Cgt/Tgt	27/32	1	2	FACETS	0.972	0.894	1	0.972	0.894	1	CLONAL	1	TRUE	1	0.364387777557287	2		600	954	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023216	27023222	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCCTA	GGCCCTA	-	novel	NA	P-0060108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	160	558	0	ENST00000324856.7:c.327_333del	p.Arg110ProfsTer2	p.R110Pfs*2	ENST00000324856	NM_006015.4	108	GGCCCTAgg/gg	1/20	1	2	FACETS	0.978	0.897	1	0.978	0.897	1	CLONAL	1	TRUE	1	0.364387777557287	2		558	898	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0060108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	121	306	0	ENST00000311936.3:c.34_35delinsCT	p.Gly12Leu	p.G12L	ENST00000311936	NM_004985.3	12	GGt/CTt	2/5	0.364387777557287	3	FACETS	1	0.985	1	0.741	0.672	0.812	CLONAL	1	TRUE	1	0.364387777557287	3		306	530	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311664	15311688	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCGACATCGGGCGACGGCGGC	GGCGGCGACATCGGGCGACGGCGGC	-	novel	NA	P-0060108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	247	1009	0	ENST00000263388.2:c.29_53del	p.Arg10HisfsTer16	p.R10Hfs*16	ENST00000263388	NM_000435.2	10	cGCCGCCGTCGCCCGATGTCGCCGCCa/ca	1/33	1	2	FACETS	0.966	0.901	1	0.966	0.901	1	CLONAL	1	TRUE	1	0.364387777557287	2		1009	1404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0060109-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	128	484	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.292455379471796	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.292455379471796	1		484	631	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060109-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	108	562	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	1	2	FACETS	0.937	0.841	1	0.937	0.841	1	CLONAL	1	TRUE	1	0.292455379471796	2		562	788	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37059000	37059000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63751448	NA	P-0060109-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	101	412	0	ENST00000231790.2:c.794G>A	p.Arg265His	p.R265H	ENST00000231790	NM_000249.3	265	cGt/cAt	10/19	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.292455379471796	2		412	659	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612352	1612352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748738693	NA	P-0060109-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	133	570	0	ENST00000344749.5:c.1667G>A	p.Arg556Gln	p.R556Q	ENST00000344749	NM_001136139.2	556	cGg/cAg	18/19	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.292455379471796	2		570	826	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982427	201982428	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0060109-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	155	580	0	ENST00000359651.3:c.805+2dup		p.X269_splice	ENST00000359651		269			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.292455379471796	2		580	836	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50782672	50782672	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060109-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	142	585	0	ENST00000307179.4:c.2184G>T	p.Glu728Asp	p.E728D	ENST00000307179		728	gaG/gaT	14/20	0.292455379471796	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.292455379471796	1		585	753	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654517	29654517	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060109-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	106	386	0	ENST00000356175.3:c.5206G>A	p.Val1736Ile	p.V1736I	ENST00000356175	NM_000267.3	1736	Gtt/Att	37/57	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.292455379471796	2		386	679	SUCCESS
APC	324	MSKCC	GRCh37	5	112175023	112175026	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	novel	NA	P-0060109-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	80	397	0	ENST00000257430.4:c.3732_3735del	p.Lys1245LeufsTer19	p.K1245Lfs*19	ENST00000257430	NM_000038.5	1244	caAAAG/ca	16/16	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.292455379471796	2		397	530	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398538	116398539	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATA	novel	NA	P-0060109-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	78	392	0	ENST00000397752.3:c.2129_2131dup	p.Tyr710_Thr711insAsn	p.Y710_T711insN	ENST00000397752	NM_000245.2	710	tat/tATAat	9/21	0.287960213661786	3	FACETS	1	0.884	1	0.503	0.442	0.568	CLONAL	1	TRUE	1	0.292455379471796	3		392	608	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962788	2962788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201948130	NA	P-0060110-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	194	447	0	ENST00000396946.4:c.2120G>A	p.Arg707His	p.R707H	ENST00000396946	NM_032415.4	707	cGt/cAt	16/25	0.754677827258436	3	FACETS	1	0.969	1	0.538	0.5	0.577	CLONAL	1	TRUE	1	0.754677827258436	3		447	658	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518687	103518687	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs570252494	NA	P-0060111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	77	492	0	ENST00000355739.4:c.2275C>T	p.Arg759Trp	p.R759W	ENST00000355739	NM_000123.3	759	Cgg/Tgg	10/15	1	2	FACETS	0.767	0.675	0.865	0.767	0.675	0.865	SUBCLONAL	1	TRUE	1	0.40737329959822	2		492	493	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1693463	1693463	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs771216147	NA	P-0060111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	234	637	0	ENST00000378625.1:c.191C>G	p.Ser64Cys	p.S64C	ENST00000378625	NM_001198994.1	64	tCt/tGt	3/14	0.385979899237408	3	FACETS	0.955	0.895	1	0.955	0.895	1	CLONAL	2	TRUE	1	0.40737329959822	3		637	724	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416576	49416576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	106	791	0	ENST00000301067.7:c.16135C>T	p.Gln5379Ter	p.Q5379*	ENST00000301067	NM_003482.3	5379	Cag/Tag	51/54	1	2	FACETS	0.685	0.614	0.76	0.685	0.614	0.76	SUBCLONAL	1	TRUE	1	0.40737329959822	2		791	760	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311691	30311691	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	84	400	0	ENST00000262643.3:c.545A>T	p.Asn182Ile	p.N182I	ENST00000262643	NM_001238.2	182	aAt/aTt	7/12	1	2	FACETS	0.918	0.815	1	0.918	0.815	1	CLONAL	1	TRUE	1	0.40737329959822	2		400	449	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162862	47162864	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0060111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	114	519	0	ENST00000409792.3:c.3262_3264del	p.Ser1088del	p.S1088del	ENST00000409792	NM_014159.6	1088	TCT/-	3/21	1	2	FACETS	0.913	0.824	1	0.913	0.824	1	CLONAL	1	TRUE	1	0.40737329959822	2		519	613	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176700729	176700729	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784151	NA	P-0060111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	90	555	0	ENST00000439151.2:c.5566C>T	p.Gln1856Ter	p.Q1856*	ENST00000439151	NM_022455.4	1856	Cag/Tag	17/23	1	2	FACETS	0.74	0.658	0.828	0.74	0.658	0.828	SUBCLONAL	1	TRUE	1	0.40737329959822	2		555	597	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151866335	151866335	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0060111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	117	326	0	ENST00000262189.6:c.9454-1G>A		p.X3152_splice	ENST00000262189	NM_170606.2	3152			0.325560160126436	2	FACETS	0.892	0.815	0.971	0.892	0.815	0.971	CLONAL	2	TRUE	0	0.40737329959822	2		326	322	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060112-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	80	475	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.903	0.801	1	0.903	0.801	1	CLONAL	1	TRUE	1	0.503632135198815	2		475	352	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0060112-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	206	564	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.503632135198815	2		564	665	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916932	178916932	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060112-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	206	438	0	ENST00000263967.3:c.319A>T	p.Asn107Tyr	p.N107Y	ENST00000263967	NM_006218.2	107	Aac/Tac	2/21	0.436214293919496	3	FACETS	0.914	0.855	0.975	0.914	0.855	0.975	CLONAL	2	TRUE	1	0.503632135198815	3		438	560	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031768	36031768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754707860	NA	P-0060112-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	189	585	0	ENST00000358208.4:c.1597G>A	p.Gly533Arg	p.G533R	ENST00000358208		533	Ggg/Agg	12/12	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.503632135198815	2		585	673	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983028	201983029	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060112-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	198	632	0	ENST00000359651.3:c.878dup	p.Met293IlefsTer8	p.M293Ifs*8	ENST00000359651		293	atg/aTtg	7/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.503632135198815	2		632	675	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343762	118343787	+	frameshift_variant	Frame_Shift_Del	DEL	CAATACTTTTCCTCAGCAAAGTATGC	CAATACTTTTCCTCAGCAAAGTATGC	-	novel	NA	P-0060112-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	156	555	0	ENST00000534358.1:c.1891_1916del	p.Tyr631ArgfsTer10	p.Y631Rfs*10	ENST00000534358	NM_005933.3	630	CAATACTTTTCCTCAGCAAAGTATGCc/c	3/36	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.503632135198815	2		555	579	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004495	150004495	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060112-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	221	606	0	ENST00000253339.5:c.1730G>C	p.Ser577Thr	p.S577T	ENST00000253339		577	aGt/aCt	3/7	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.503632135198815	2		606	718	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891146	101891146	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060112-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	143	348	0	ENST00000374994.4:c.107G>T	p.Cys36Phe	p.C36F	ENST00000374994	NM_004612.2	36	tGt/tTt	2/9	0.503632135198815	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.503632135198815	1		348	339	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918491	44918491	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0060112-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	146	191	0	ENST00000377967.4:c.975-1G>T		p.X325_splice	ENST00000377967	NM_021140.2	325			1	1	FACETS	0.955	0.899	1	1	0.993	1	CLONAL	2	TRUE	0	0.503632135198815	1		191	227	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199469672	NA	P-0060113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	14	396	0	ENST00000374080.3:c.131G>T	p.Gly44Val	p.G44V	ENST00000374080		44	gGt/gTt	2/45	1	2	FACETS	0.142	0.102	0.192	0.142	0.102	0.192	SUBCLONAL	1	TRUE	1	0.328136040246539	2		396	599	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0060113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	127	575	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.328136040246539	1	FACETS	0.923	0.837	1	0.923	0.837	1	CLONAL	1	TRUE	0	0.328136040246539	1		575	701	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0060113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	130	445	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.328136040246539	2		445	756	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0060113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	91	438	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.876	0.779	0.98	0.876	0.779	0.98	CLONAL	1	TRUE	1	0.328136040246539	2		438	633	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274157	18274157	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1350762892	NA	P-0060113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	140	621	0	ENST00000222254.8:c.1375G>A	p.Glu459Lys	p.E459K	ENST00000222254	NM_005027.3	459	Gag/Aag	11/16	0.328136040246539	4	FACETS	0.946	0.859	1	0.315	0.286	0.346	CLONAL	1	TRUE	1	0.328136040246539	4		621	1198	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422294	47422295	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	123	464	0	ENST00000404338.3:c.363dup	p.Ala122CysfsTer8	p.A122Cfs*8	ENST00000404338	NM_004491.4	121	gct/gcTt	1/6	1	2	FACETS	0.953	0.862	1	0.953	0.862	1	CLONAL	1	TRUE	1	0.328136040246539	2		464	787	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317111	87317111	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	112	446	0	ENST00000277120.3:c.250G>C	p.Glu84Gln	p.E84Q	ENST00000277120		84	Gaa/Caa	3/19	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.328136040246539	2		446	681	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0060114-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	143	353	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.301441781128089	3	FACETS	0.939	0.861	1	0.939	0.861	1	CLONAL	2	TRUE	1	0.351026486707973	3		353	510	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0060115-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	83	467	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.26	2		467	576	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987149	36987149	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060115-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	70	680	0	ENST00000354822.5:c.540C>G	p.Ser180Arg	p.S180R	ENST00000354822	NM_001079668.2	180	agC/agG	3/3	1	2	FACETS	0.877	0.765	0.998	0.877	0.765	0.998	CLONAL	1	TRUE	1	0.26	2		680	614	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0060122-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	58	289	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.999	0.868	1	0.999	0.868	1	CLONAL	1	FALSE	1	0.477740012994674	2		289	243	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0060122-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	124	515	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.377721006253954	3	FACETS	1	0.98	1	0.803	0.741	0.866	CLONAL	2	FALSE	0	0.477740012994674	3		515	267	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935252	36935252	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0060122-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	93	504	0	ENST00000361632.4:c.1474+1G>A		p.X492_splice	ENST00000361632		492			0.471177345002337	2	FACETS	0.779	0.704	0.855	0.779	0.704	0.855	SUBCLONAL	2	FALSE	0	0.477740012994674	2		504	250	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426650	212426650	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060122-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	34	477	0	ENST00000342788.4:c.2465A>C	p.Asn822Thr	p.N822T	ENST00000342788	NM_005235.2	822	aAc/aCc	20/28	1	2	FACETS	0.453	0.371	0.545	0.453	0.371	0.545	SUBCLONAL	1	FALSE	1	0.477740012994674	2		477	314	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221204	1221219	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAATGAAGCTACAACA	AAATGAAGCTACAACA	GG	novel	NA	P-0060122-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	64	509	0	ENST00000326873.7:c.735-8_742delinsGG		p.X245_splice	ENST00000326873	NM_000455.4	245		6/10	0.477740012994674	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	FALSE	0	0.477740012994674	1		509	194	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0060123-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	271	580	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.452473065302396	2	FACETS	0.942	0.891	0.994	0.942	0.891	0.994	CLONAL	2	TRUE	0	0.453573177451364	2		580	634	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022914	27022945	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCCGCCGCCAGCAGCCTGGGCAACCCGCCG	CCGCCGCCGCCAGCAGCCTGGGCAACCCGCCG	-	novel	NA	P-0060123-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	82	483	1	ENST00000324856.7:c.31_62del	p.Ser11LeufsTer89	p.S11Lfs*89	ENST00000324856	NM_006015.4	7	cCCGCCGCCGCCAGCAGCCTGGGCAACCCGCCG/c	1/20	1	2	FACETS	0.606	0.535	0.682	0.606	0.535	0.682	SUBCLONAL	1	TRUE	1	0.453573177451364	2		484	597	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57004063	57004063	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	C	C	T	rs780546020	NA	P-0060123-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	119	613	1	ENST00000257254.3:c.416G>A	p.Arg139Gln	p.R139Q	ENST00000257254		139	cGg/cAg	1/2	0.442864378873826	3	FACETS	0.851	0.769	0.939	0.426	0.384	0.47	CLONAL	1	TRUE	1	0.453573177451364	3		614	756	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847249	68847269	+	inframe_deletion	In_Frame_Del	DEL	GTCGTAATCACCACACTGAAA	GTCGTAATCACCACACTGAAA	-	novel	NA	P-0060123-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	208	412	0	ENST00000261769.5:c.1173_1193del	p.Val392_Val398del	p.V392_V398del	ENST00000261769	NM_004360.3	391	GTCGTAATCACCACACTGAAA/-	9/16	0.260617194392604	5	FACETS	1	0.98	1	0.752	0.701	0.804	INDETERMINATE	2	TRUE	2	0.453573177451364	5		412	683	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023544	31023544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs116112525	NA	P-0060123-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	117	465	0	ENST00000375687.4:c.3029C>T	p.Thr1010Met	p.T1010M	ENST00000375687	NM_015338.5	1010	aCg/aTg	13/13	0.453573177451364	6	FACETS	0.949	0.854	1	0.237	0.213	0.263	CLONAL	1	TRUE	2	0.453573177451364	6		465	1037	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420014	41420014	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs200831045	NA	P-0060123-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	211	501	0	ENST00000373198.4:c.307A>T	p.Ile103Phe	p.I103F	ENST00000373198	NM_133170.3	103	Atc/Ttc	3/32	0.453573177451364	4	FACETS	1	0.99	1	0.477	0.443	0.512	CLONAL	1	TRUE	1	0.453573177451364	4		501	945	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960187	151960187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060123-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	67	163	0	ENST00000262189.6:c.1213G>A	p.Val405Met	p.V405M	ENST00000262189	NM_170606.2	405	Gtg/Atg	9/59	0.3843379774108	5	FACETS	0.937	0.823	1	0.624	0.549	0.705	CLONAL	2	TRUE	2	0.453573177451364	5		163	265	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2182151	2182151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060123-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	181	319	0	ENST00000349721.2:c.4370G>A	p.Arg1457His	p.R1457H	ENST00000349721	NM_003070.3	1457	cGt/cAt	31/34	0.453573177451364	2	FACETS	0.993	0.928	1	0.993	0.928	1	CLONAL	2	TRUE	0	0.453573177451364	2		319	402	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231238	98231238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1366288601	NA	P-0060123-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	293	517	0	ENST00000331920.6:c.2045G>A	p.Arg682His	p.R682H	ENST00000331920	NM_000264.3	682	cGc/cAc	14/24	0.424326786244403	3	FACETS	0.964	0.911	1	0.964	0.911	1	CLONAL	2	TRUE	1	0.453573177451364	3		517	822	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121912580	NA	P-0060124-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	29	351	0	ENST00000342988.3:c.1157G>T	p.Gly386Val	p.G386V	ENST00000342988	NM_005359.5	386	gGt/gTt	10/12	1	2	FACETS	0.73	0.584	0.896	0.73	0.584	0.896	SUBCLONAL	1	TRUE	1	0.15	2		351	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0060126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	65	422	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.477671209256596	2		422	233	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220371	1220371	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0060126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	79	530	0	ENST00000326873.7:c.465-1G>T		p.X155_splice	ENST00000326873	NM_000455.4	155			0.477671209256596	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.477671209256596	1		530	218	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602584	10602584	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1208201314	NA	P-0060126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	89	520	0	ENST00000171111.5:c.994G>T	p.Gly332Cys	p.G332C	ENST00000171111	NM_203500.1	332	Ggc/Tgc	3/6	0.477671209256596	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.477671209256596	1		520	258	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273024	55273024	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	85	469	0	ENST00000275493.2:c.3347A>T	p.Asn1116Ile	p.N1116I	ENST00000275493	NM_005228.3	1116	aAc/aTc	28/28	0.455479123770682	3	FACETS	1	0.961	1	0.393	0.35	0.439	CLONAL	1	TRUE	0	0.477671209256596	3		469	374	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858941	45858941	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	52	367	0	ENST00000391945.4:c.1525G>C	p.Glu509Gln	p.E509Q	ENST00000391945	NM_000400.3	509	Gag/Cag	16/23	0.477671209256596	2	FACETS	1	0.887	1	0.516	0.445	0.592	CLONAL	1	TRUE	0	0.477671209256596	2		367	211	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679212	88679212	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	52	429	0	ENST00000360948.2:c.825T>G	p.Ser275Arg	p.S275R	ENST00000360948	NM_001012338.2	275	agT/agG	8/19	0.477671209256596	2	FACETS	0.985	0.849	1	0.493	0.424	0.566	CLONAL	1	TRUE	0	0.477671209256596	2		429	221	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769547	112769547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	58	373	0	ENST00000369452.4:c.1499G>A	p.Gly500Asp	p.G500D	ENST00000369452	NM_007373.3	500	gGc/gAc	8/9	0.477671209256596	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.477671209256596	1		373	174	SUCCESS
APC	324	MSKCC	GRCh37	5	112154775	112154775	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	95	397	1	ENST00000257430.4:c.1046A>T	p.Gln349Leu	p.Q349L	ENST00000257430	NM_000038.5	349	cAg/cTg	10/16	0.452882436439903	2	FACETS	0.952	0.867	1	0.952	0.867	1	CLONAL	2	TRUE	0	0.477671209256596	2		398	209	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0060132-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	65	385	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.899	0.779	1	0.899	0.779	1	CLONAL	1	TRUE	1	0.239817298953174	2		385	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121912651	NA	P-0060132-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	70	580	0	ENST00000269305.4:c.742C>G	p.Arg248Gly	p.R248G	ENST00000269305	NM_001126112.2	248	Cgg/Ggg	7/11	1	2	FACETS	0.995	0.868	1	0.995	0.868	1	CLONAL	1	TRUE	1	0.239817298953174	2		580	587	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627996	187627996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060132-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	80	647	0	ENST00000441802.2:c.2986G>A	p.Val996Met	p.V996M	ENST00000441802	NM_005245.3	996	Gtg/Atg	2/27	1	2	FACETS	0.975	0.859	1	0.975	0.859	1	CLONAL	1	TRUE	1	0.239817298953174	2		647	684	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518250	8518250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060133-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	34	425	0	ENST00000356435.5:c.1141G>A	p.Ala381Thr	p.A381T	ENST00000356435		381	Gct/Act	10/35	0.228654750805573	2	FACETS	0.354	0.288	0.427	0.177	0.144	0.214	SUBCLONAL	1	TRUE	0	0.343467596671126	2		425	560	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77933154	77933154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060133-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	43	417	0	ENST00000361507.4:c.1655C>T	p.Ala552Val	p.A552V	ENST00000361507	NM_080491.2	552	gCc/gTc	7/10	1	2	FACETS	0.386	0.322	0.458	0.386	0.322	0.458	SUBCLONAL	1	TRUE	1	0.343467596671126	2		417	648	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998576	100998576	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1274438915	NA	P-0060133-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	52	559	0	ENST00000325455.5:c.1226C>A	p.Ala409Asp	p.A409D	ENST00000325455	NM_001202474.3	409	gCc/gAc	1/8	1	2	FACETS	0.408	0.346	0.475	0.408	0.346	0.475	SUBCLONAL	1	TRUE	1	0.343467596671126	2		559	743	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411880	116411898	+	splice_region_variant,intron_variant	Splice_Region	DEL	TCTTTCTTTCTCTCTGTTT	TCTTTCTTTCTCTCTGTTT	-	novel	NA	P-0060133-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	147	602	0	ENST00000397752.3:c.2888-22_2888-4del		p.X963_splice	ENST00000397752	NM_000245.2	963			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.343467596671126	2		602	704	SUCCESS
AR	367	MSKCC	GRCh37	X	66766180	66766180	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060133-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	99	595	0	ENST00000374690.3:c.1192G>A	p.Ala398Thr	p.A398T	ENST00000374690	NM_000044.3	398	Gcc/Acc	1/8	1	2	FACETS	0.699	0.623	0.779	0.699	0.623	0.779	SUBCLONAL	1	TRUE	1	0.343467596671126	2		595	825	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0060134-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	120	353	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.147683118578479	4	FACETS	0.945	0.857	1	0.945	0.857	1	INDETERMINATE	2	TRUE	2	0.305301478952573	4		353	543	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045115	47045115	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060134-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	170	743	0	ENST00000377604.3:c.2356C>T	p.Gln786Ter	p.Q786*	ENST00000377604	NM_001204468.1	786	Caa/Taa	21/24	0.180417877432481	3	FACETS	0.889	0.82	0.961	0.889	0.82	0.961	INDETERMINATE	2	TRUE	1	0.305301478952573	3		743	722	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729094	66729099	+	inframe_deletion	In_Frame_Del	DEL	TGGAGA	TGGAGA	-	novel	NA	P-0060135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	67	511	0	ENST00000307102.5:c.303_308del	p.Glu102_Ile103del	p.E102_I103del	ENST00000307102	NM_002755.3	101	cTGGAGAtc/ctc	3/11	1	2	FACETS	0.939	0.817	1	0.939	0.817	1	CLONAL	1	TRUE	1	0.262237770771493	2		511	544	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186791	11186791	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	75	461	0	ENST00000361445.4:c.6414G>C	p.Leu2138Phe	p.L2138F	ENST00000361445	NM_004958.3	2138	ttG/ttC	46/58	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.262237770771493	2		461	446	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0060136-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	1346	385	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.433498652161981	17	FACETS	0.996	0.975	1	0.996	0.975	1	CLONAL	12	TRUE	5	0.433498652161981	17		385	2209	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0060136-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1972	536	717	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.433498652161981	17	FACETS	1	0.981	1	0.349	0.333	0.366	CLONAL	4	TRUE	5	0.433498652161981	17		717	2508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121912651	NA	P-0060136-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	435	580	0	ENST00000269305.4:c.742C>G	p.Arg248Gly	p.R248G	ENST00000269305	NM_001126112.2	248	Cgg/Ggg	7/11	0.366778790040813	4	FACETS	0.933	0.897	0.968	0.933	0.897	0.968	CLONAL	4	TRUE	0	0.433498652161981	4		580	771	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940457	13940457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060136-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	65	387	0	ENST00000405192.2:c.1049G>A	p.Arg350Gln	p.R350Q	ENST00000405192	NM_001163147.1	350	cGa/cAa	11/12	0.433498652161981	6	FACETS	0.803	0.696	0.92	0.161	0.139	0.184	CLONAL	1	TRUE	1	0.433498652161981	6		387	697	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209110124	209110125	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAC	novel	NA	P-0060136-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	64	444	0	ENST00000345146.2:c.436_438dup	p.Val146dup	p.V146dup	ENST00000345146	NM_005896.2	146	-/GTT	5/10	0.435976327822816	3	FACETS	0.66	0.572	0.756	0.33	0.286	0.378	SUBCLONAL	1	TRUE	1	0.433498652161981	3		444	544	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0060137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	207	520	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.650789073021921	2		520	521	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0060137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	319	564	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.650789073021921	2		564	761	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935538	13935538	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	299	560	0	ENST00000405192.2:c.1318G>A	p.Gly440Arg	p.G440R	ENST00000405192	NM_001163147.1	440	Ggg/Agg	12/12	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.650789073021921	2		560	689	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308353	15308353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	325	623	0	ENST00000263388.2:c.155G>A	p.Gly52Glu	p.G52E	ENST00000263388	NM_000435.2	52	gGa/gAa	2/33	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.650789073021921	2		623	796	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43817921	43817921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1214203929	NA	P-0060137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	298	633	0	ENST00000372470.3:c.1600G>A	p.Asp534Asn	p.D534N	ENST00000372470	NM_005373.2	534	Gac/Aac	11/12	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.650789073021921	2		633	749	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644486	18644486	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	120	390	0	ENST00000266497.5:c.2664T>A	p.Asp888Glu	p.D888E	ENST00000266497		888	gaT/gaA	18/31	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.650789073021921	2		390	297	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210605	5210605	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	362	706	0	ENST00000357368.4:c.5362G>T	p.Glu1788Ter	p.E1788*	ENST00000357368	NM_002850.3	1788	Gag/Tag	35/38	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.650789073021921	2		706	929	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267672	198267672	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0060137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	179	393	0	ENST00000335508.6:c.1806+1G>T		p.X602_splice	ENST00000335508	NM_012433.2	602			1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.650789073021921	2		393	443	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095861	29095863	+	missense_variant	Missense_Mutation	TNP	TGC	TGC	GCA	novel	NA	P-0060137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	201	441	1	ENST00000328354.6:c.971_973inv	p.Cys324_Lys325delinsLeuGln	p.C324_K325delinsLQ	ENST00000328354	NM_007194.3	324	tGCAag/tTGCag	9/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.650789073021921	2		442	524	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531042	187531043	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0060137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	258	538	0	ENST00000441802.2:c.9980_9981insG	p.Asp3327GlufsTer5	p.D3327Efs*5	ENST00000441802	NM_005245.3	3327	gat/gaGt	15/27	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.650789073021921	2		538	618	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184974	123184975	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	44	118	0	ENST00000218089.9:c.1021_1022insT	p.Gly341ValfsTer2	p.G341Vfs*2	ENST00000218089	NM_001042749.1	341	ggt/gTgt	12/35	1	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.650789073021921	1		118	72	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0060138-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	229	300	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.209793476691543	5	FACETS	1	0.975	1	1	0.975	1	CLONAL	4	TRUE	1	0.209793476691543	5		300	666	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0060138-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	86	471	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.895	0.79	1	0.895	0.79	1	CLONAL	1	TRUE	1	0.209793476691543	2		472	916	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987077	36987077	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0060138-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	82	617	0	ENST00000354822.5:c.612C>G	p.Tyr204Ter	p.Y204*	ENST00000354822	NM_001079668.2	204	taC/taG	3/3	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.209793476691543	2		617	769	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987097	36987097	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060138-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	86	603	0	ENST00000354822.5:c.592T>G	p.Phe198Val	p.F198V	ENST00000354822	NM_001079668.2	198	Ttc/Gtc	3/3	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.209793476691543	2		603	762	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249017	55249018	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCA	rs1554350381	NA	P-0060139-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	113	593	0	ENST00000275493.2:c.2317_2319dup	p.His773dup	p.H773dup	ENST00000275493	NM_005228.3	773	ccc/ccCCAc	20/28	1	2	FACETS	1	0.93	1	1	0.989	1	CLONAL	2	TRUE	1	0.2153697591194	2		593	507	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636722	2636722	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060139-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	60	664	0	ENST00000342085.4:c.1171T>A	p.Ser391Thr	p.S391T	ENST00000342085	NM_002613.4	391	Tcc/Acc	11/14	0.2153697591194	8	FACETS	0.95	0.816	1	0.136	0.116	0.157	CLONAL	1	TRUE	1	0.2153697591194	8		664	965	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544257	86544257	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060139-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	92	775	0	ENST00000262426.4:c.82C>A	p.Pro28Thr	p.P28T	ENST00000262426	NM_001451.2	28	Ccc/Acc	1/2	0.209093607820055	4	FACETS	0.983	0.876	1	0.656	0.584	0.731	CLONAL	2	TRUE	1	0.2153697591194	4		775	528	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274272	5274272	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060139-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	118	668	0	ENST00000357368.4:c.175G>T	p.Asp59Tyr	p.D59Y	ENST00000357368	NM_002850.3	59	Gac/Tac	3/38	1	2	FACETS	1	0.952	1	1	0.99	1	CLONAL	2	TRUE	1	0.2153697591194	2		668	508	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143033702	143033702	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060139-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	57	441	0	ENST00000262992.4:c.2269G>C	p.Ala757Pro	p.A757P	ENST00000262992	NM_001101669.1	757	Gct/Cct	20/24	1	2	FACETS	0.984	0.852	1	1	0.978	1	CLONAL	2	TRUE	1	0.2153697591194	2		441	269	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041693	47041693	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060139-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	111	651	0	ENST00000377604.3:c.1919del	p.Lys640ArgfsTer64	p.K640Rfs*64	ENST00000377604	NM_001204468.1	640	Aag/ag	17/24	1	2	FACETS	0.974	0.879	1	1	0.988	1	CLONAL	2	TRUE	1	0.2153697591194	2		651	529	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0060144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	116	385	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.743	0.67	0.82	0.743	0.67	0.82	SUBCLONAL	1	TRUE	1	0.424221469369136	2		385	736	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843510	3843510	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	107	691	0	ENST00000262367.5:c.1093C>G	p.His365Asp	p.H365D	ENST00000262367	NM_004380.2	365	Cat/Gat	4/31	0.362998337096299	3	FACETS	0.613	0.549	0.682	0.307	0.274	0.341	SUBCLONAL	1	TRUE	1	0.424221469369136	3		691	997	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044876	47044877	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0060144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	86	956	0	ENST00000377604.3:c.2206_2207dup	p.Ser736ArgfsTer67	p.S736Rfs*67	ENST00000377604	NM_001204468.1	734	-/GA	20/24	1	2	FACETS	0.49	0.433	0.552	0.49	0.433	0.552	SUBCLONAL	1	TRUE	1	0.424221469369136	2		956	827	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	43	475	0				ENST00000310581	NM_198253.2	-/1132			0.20625609253451	1	FACETS	0.491	0.409	0.582	0.491	0.409	0.582	SUBCLONAL	1	TRUE	0	0.20625609253451	1		475	762	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880257	37880257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	166	564	0	ENST00000269571.5:c.2301C>G	p.Ile767Met	p.I767M	ENST00000269571		767	atC/atG	19/27	0.20625609253451	2	FACETS	0.873	0.802	0.947	0.873	0.802	0.947	CLONAL	2	TRUE	0	0.20625609253451	2		564	922	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764146326	NA	P-0060145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	119	663	0	ENST00000269305.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000269305	NM_001126112.2	281	Gac/Aac	8/11	0.178845724044855	1	FACETS	0.956	0.861	1	0.956	0.861	1	CLONAL	1	TRUE	0	0.20625609253451	1		663	1083	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164509	36164509	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	82	712	0	ENST00000300305.3:c.1366G>A	p.Glu456Lys	p.E456K	ENST00000300305		456	Gag/Aag	8/8	1	2	FACETS	0.75	0.66	0.848	0.75	0.66	0.848	SUBCLONAL	1	TRUE	1	0.20625609253451	2		712	1060	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667422	241667422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756990249	NA	P-0060145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	46	532	0	ENST00000366560.3:c.1028G>A	p.Arg343Gln	p.R343Q	ENST00000366560	NM_000143.3	343	cGa/cAa	7/10	0.123698259080695	1	FACETS	0.461	0.387	0.544	0.461	0.387	0.544	INDETERMINATE	1	TRUE	0	0.20625609253451	1		532	867	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156122	99156122	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	127	632	0	ENST00000074304.5:c.802G>C	p.Glu268Gln	p.E268Q	ENST00000074304	NM_001134224.1	268	Gag/Cag	10/26	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.20625609253451	2		632	1058	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523735	41523735	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1186117620	NA	P-0060145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	115	583	0	ENST00000263253.7:c.1151C>T	p.Ser384Leu	p.S384L	ENST00000263253	NM_001429.3	384	tCa/tTa	4/31	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.20625609253451	2		583	1108	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194688	29194688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs919580482	NA	P-0060145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	126	687	0	ENST00000240100.2:c.1040C>T	p.Ser347Leu	p.S347L	ENST00000240100	NM_001394.6	347	tCg/tTg	4/4	0.140840529162187	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.20625609253451	1		687	993	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610065	43610065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3026759	NA	P-0060145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	71	815	0	ENST00000355710.3:c.2017G>A	p.Glu673Lys	p.E673K	ENST00000355710	NM_020975.4	673	Gag/Aag	11/20	0.140840529162187	1	FACETS	0.515	0.448	0.589	0.515	0.448	0.589	SUBCLONAL	1	TRUE	0	0.20625609253451	1		815	1198	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219148	133219148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	59	698	0	ENST00000320574.5:c.4896G>A	p.Met1632Ile	p.M1632I	ENST00000320574	NM_006231.2	1632	atG/atA	37/49	0.178845724044855	1	FACETS	0.509	0.436	0.588	0.509	0.436	0.588	SUBCLONAL	1	TRUE	0	0.20625609253451	1		698	1009	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28963935	28963935	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	81	560	0	ENST00000282397.4:c.1967G>C	p.Arg656Thr	p.R656T	ENST00000282397	NM_002019.4	656	aGa/aCa	13/30	1	2	FACETS	0.879	0.773	0.993	0.879	0.773	0.993	CLONAL	1	TRUE	1	0.20625609253451	2		560	894	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679422	29679422	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	62	442	0	ENST00000356175.3:c.7542G>C	p.Lys2514Asn	p.K2514N	ENST00000356175	NM_000267.3	2514	aaG/aaC	50/57	0.20625609253451	2	FACETS	0.716	0.617	0.824	0.358	0.308	0.412	SUBCLONAL	1	TRUE	0	0.20625609253451	2		442	840	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629057	14629057	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	73	534	0	ENST00000254322.2:c.105G>C	p.Lys35Asn	p.K35N	ENST00000254322	NM_006145.1	35	aaG/aaC	1/3	0.20625609253451	2	FACETS	0.817	0.713	0.93	0.409	0.356	0.465	CLONAL	1	TRUE	0	0.20625609253451	2		534	866	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138431140	138431140	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	55	314	0	ENST00000289153.2:c.1309C>G	p.Pro437Ala	p.P437A	ENST00000289153	NM_006219.2	437	Cct/Gct	8/22	NA	2	FACETS	0.884	0.756	1			1	INDETERMINATE	1	TRUE	NA	0.20625609253451	2		314	603	SUCCESS
ATR	545	MSKCC	GRCh37	3	142218528	142218528	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	75	418	0	ENST00000350721.4:c.5321G>C	p.Arg1774Thr	p.R1774T	ENST00000350721	NM_001184.3	1774	aGa/aCa	31/47	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.20625609253451	2		418	700	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295805	1295805	+	upstream_gene_variant	5'Flank	SNP	G	G	C	novel	NA	P-0060145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	65	855	0				ENST00000310581	NM_198253.2	-/1132			0.20625609253451	1	FACETS	0.488	0.421	0.561	0.488	0.421	0.561	SUBCLONAL	1	TRUE	0	0.20625609253451	1		855	1159	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449511	31449511	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	56	377	0	ENST00000344624.3:c.2698C>G	p.Pro900Ala	p.P900A	ENST00000344624		900	Cca/Gca	19/33	1	2	FACETS	0.841	0.719	0.973	0.841	0.719	0.973	CLONAL	1	TRUE	1	0.20625609253451	2		377	646	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673619	30673619	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	177	747	0	ENST00000376406.3:c.3341G>C	p.Arg1114Thr	p.R1114T	ENST00000376406	NM_014641.2	1114	aGa/aCa	10/15	1	2	FACETS	0.764	0.703	0.828	1	0.989	1	SUBCLONAL	2	TRUE	1	0.20625609253451	2		747	1123	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31239805	31239805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	207	886	0	ENST00000376228.5:c.44G>A	p.Gly15Glu	p.G15E	ENST00000376228	NM_002117.5	15	gGa/gAa	1/8	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.20625609253451	2		886	1396	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983005	149983005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	68	470	0	ENST00000253339.5:c.3253G>A	p.Asp1085Asn	p.D1085N	ENST00000253339		1085	Gat/Aat	7/7	1	2	FACETS	0.835	0.725	0.954	0.835	0.725	0.954	CLONAL	1	TRUE	1	0.20625609253451	2		470	790	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157891	27157891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	51	687	0	ENST00000380036.4:c.115G>A	p.Glu39Lys	p.E39K	ENST00000380036	NM_000459.3	39	Gaa/Aaa	2/23	0.203786232167982	1	FACETS	0.471	0.399	0.551	0.471	0.399	0.551	SUBCLONAL	1	TRUE	0	0.20625609253451	1		687	941	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771759	135771759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	127	742	0	ENST00000298552.3:c.3358G>A	p.Glu1120Lys	p.E1120K	ENST00000298552	NM_001162426.1	1120	Gaa/Aaa	23/23	0.203786232167982	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	0	0.20625609253451	1		742	1104	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0060147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	64	279	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.936	0.813	1	0.936	0.813	1	CLONAL	1	TRUE	1	0.31	2		279	441	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0060147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	70	450	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.814	0.71	0.925	0.814	0.71	0.925	CLONAL	1	TRUE	1	0.31	2		450	555	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0060147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	51	527	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.125992121813744	1	FACETS	0.463	0.393	0.54	0.463	0.393	0.54	INDETERMINATE	1	TRUE	0	0.31	1		528	601	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032401	10032401	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs78631453	NA	P-0060147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	50	507	1	ENST00000330684.3:c.422C>T	p.Thr141Met	p.T141M	ENST00000330684	NM_001134407.1	141	aCg/aTg	3/13	1	2	FACETS	0.633	0.537	0.738	0.633	0.537	0.738	SUBCLONAL	1	TRUE	1	0.31	2		508	510	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40460202	40460202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	85	549	0	ENST00000345506.4:c.1913G>A	p.Arg638His	p.R638H	ENST00000345506	NM_003152.3	638	cGc/cAc	17/20	1	2	FACETS	0.865	0.765	0.972	0.865	0.765	0.972	CLONAL	1	TRUE	1	0.31	2		549	634	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120062	70120062	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	66	628	0	ENST00000245479.2:c.1067del	p.Pro356ArgfsTer27	p.P356Rfs*27	ENST00000245479	NM_000346.3	355	gCc/gc	3/3	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.31	2		628	422	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0060147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	87	781	0	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	1	2	FACETS	0.923	0.818	1	0.923	0.818	1	CLONAL	1	TRUE	1	0.31	2		781	608	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006101	22006101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1425823622	NA	P-0060147-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	111	680	0	ENST00000276925.6:c.302G>A	p.Arg101Gln	p.R101Q	ENST00000276925	NM_004936.3	101	cGg/cAg	2/2	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.31	2		680	570	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469924	25469926	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0060148-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	99	621	0	ENST00000264709.3:c.1116_1118del	p.Leu373del	p.L373del	ENST00000264709	NM_175629.2	372	gtCCTg/gtg	9/23	0.242907068237687	3	FACETS	1	0.92	1	0.519	0.463	0.58	CLONAL	1	TRUE	1	0.242907068237687	3		621	880	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61323100	61323100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200813295	NA	P-0060148-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	48	869	0	ENST00000283752.5:c.964G>A	p.Gly322Ser	p.G322S	ENST00000283752	NM_006919.2	322	Ggt/Agt	8/8	0.242907068237687	1	FACETS	0.395	0.332	0.464	0.395	0.332	0.464	SUBCLONAL	1	TRUE	0	0.242907068237687	1		869	880	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15379742	15379742	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060148-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	49	536	0	ENST00000263377.2:c.397T>A	p.Phe133Ile	p.F133I	ENST00000263377	NM_058243.2	133	Ttt/Att	3/20	0.242907068237687	3	FACETS	0.625	0.528	0.732	0.312	0.264	0.366	SUBCLONAL	1	TRUE	1	0.242907068237687	3		536	724	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	98	475	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.861	0.772	0.955	0.861	0.772	0.955	CLONAL	1	TRUE	1	0.47824849687868	2		475	476	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913514	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	131	415	0	ENST00000288135.5:c.2466T>G	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaG	17/21	0.47824849687868	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.47824849687868	3		415	309	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31238925	31238925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141142418	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	11	10	1	ENST00000376228.5:c.544G>A	p.Ala182Thr	p.A182T	ENST00000376228	NM_002117.5	182	Gcc/Acc	3/8	1	2	FACETS	1	0.749	1	1	0.911	1	CLONAL	2	TRUE	1	0.47824849687868	2		11	23	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242662	46242662	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	50	331	0	ENST00000334344.6:c.1624C>T	p.Arg542Ter	p.R542*	ENST00000334344	NM_152641.2	542	Cga/Tga	13/21	1	2	FACETS	0.871	0.762	0.984	1	0.975	1	CLONAL	2	TRUE	1	0.47824849687868	2		331	120	SUCCESS
AR	367	MSKCC	GRCh37	X	66941766	66941766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	123	557	0	ENST00000374690.3:c.2410G>A	p.Glu804Lys	p.E804K	ENST00000374690	NM_000044.3	804	Gaa/Aaa	6/8	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.47824849687868	2		557	494	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42002918	42002918	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	147	402	0	ENST00000219905.7:c.2455C>T	p.Arg819Cys	p.R819C	ENST00000219905	NM_001164273.1	819	Cgt/Tgt	8/24	0.458709280167161	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.47824849687868	2		402	282	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857436	9857436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	58	713	0	ENST00000330684.3:c.3965G>A	p.Gly1322Glu	p.G1322E	ENST00000330684	NM_001134407.1	1322	gGa/gAa	13/13	0.294807201725978	1	FACETS	0.355	0.305	0.409	0.355	0.305	0.409	SUBCLONAL	1	TRUE	0	0.47824849687868	1		713	520	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124437	94124437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	31	358	0	ENST00000369303.4:c.146C>T	p.Ser49Phe	p.S49F	ENST00000369303	NM_004440.3	49	tCc/tTc	2/17	0.47824849687868	1	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	0	0.47824849687868	1		358	95	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396860	139396860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368396893	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	111	573	0	ENST00000277541.6:c.5248G>A	p.Val1750Met	p.V1750M	ENST00000277541	NM_017617.3	1750	Gtg/Atg	28/34	1	2	FACETS	0.905	0.817	0.997	0.905	0.817	0.997	CLONAL	1	TRUE	1	0.47824849687868	2		573	513	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508811	106508811	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	151	708	0	ENST00000359195.3:c.805G>A	p.Asp269Asn	p.D269N	ENST00000359195	NM_002649.2	269	Gat/Aat	2/11	0.475353988499615	1	FACETS	0.933	0.859	1	0.933	0.859	1	CLONAL	1	TRUE	0	0.47824849687868	1		708	515	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678602	88678602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243717189	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	134	594	0	ENST00000360948.2:c.934G>A	p.Glu312Lys	p.E312K	ENST00000360948	NM_001012338.2	312	Gag/Aag	9/19	0.458709280167161	2	FACETS	1	0.941	1	0.52	0.474	0.567	CLONAL	1	TRUE	0	0.47824849687868	2		594	539	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919024	50919024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868146189	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	142	685	0	ENST00000440232.2:c.2761C>T	p.Arg921Cys	p.R921C	ENST00000440232	NM_002691.3	921	Cgc/Tgc	22/27	1	2	FACETS	0.878	0.802	0.958	0.878	0.802	0.958	CLONAL	1	TRUE	1	0.47824849687868	2		685	676	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169486	27169486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	96	477	0	ENST00000380036.4:c.487C>T	p.His163Tyr	p.H163Y	ENST00000380036	NM_000459.3	163	Cat/Tat	4/23	1	2	FACETS	0.921	0.825	1	0.921	0.825	1	CLONAL	1	TRUE	1	0.47824849687868	2		477	436	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332868	70332868	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	120	673	0	ENST00000373644.4:c.773C>T	p.Pro258Leu	p.P258L	ENST00000373644	NM_030625.2	258	cCc/cTc	2/12	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.47824849687868	2		673	470	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026897	6026897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	53	255	0	ENST00000265849.7:c.1499C>T	p.Ser500Phe	p.S500F	ENST00000265849	NM_000535.5	500	tCc/tTc	11/15	1	2	FACETS	0.964	0.831	1	0.964	0.831	1	CLONAL	1	TRUE	1	0.47824849687868	2		255	230	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258577	16258577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1389712547	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	152	859	0	ENST00000375759.3:c.5842C>T	p.Pro1948Ser	p.P1948S	ENST00000375759	NM_015001.2	1948	Cct/Tct	11/15	1	2	FACETS	0.999	0.917	1	0.999	0.917	1	CLONAL	1	TRUE	1	0.47824849687868	2		859	636	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546376	46546376	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	74	531	0	ENST00000262741.5:c.153T>A	p.Asn51Lys	p.N51K	ENST00000262741	NM_003629.3	51	aaT/aaA	2/10	1	2	FACETS	0.967	0.854	1	0.967	0.854	1	CLONAL	1	TRUE	1	0.47824849687868	2		531	320	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150933536	150933536	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	123	584	0	ENST00000271640.5:c.2998A>C	p.Ser1000Arg	p.S1000R	ENST00000271640	NM_001145415.1	1000	Agc/Cgc	16/22	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.47824849687868	2		584	514	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226568857	226568858	+	missense_variant	Missense_Mutation	DNP	GT	GT	AG	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	83	585	1	ENST00000366794.5:c.1211_1212delinsCT	p.Asn404Thr	p.N404T	ENST00000366794	NM_001618.3	404	aAC/aCT	9/23	1	2	FACETS	0.722	0.639	0.81	0.722	0.639	0.81	SUBCLONAL	1	TRUE	1	0.47824849687868	2		586	481	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716158	243716158	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	67	443	0	ENST00000263826.5:c.1036T>C	p.Phe346Leu	p.F346L	ENST00000263826	NM_005465.4	346	Ttc/Ctc	10/13	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.47824849687868	2		443	265	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410720	32410720	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	116	599	0	ENST00000332351.3:c.1438A>G	p.Lys480Glu	p.K480E	ENST00000332351	NM_024426.4	480	Aag/Gag	10/10	1	2	FACETS	0.994	0.901	1	0.994	0.901	1	CLONAL	1	TRUE	1	0.47824849687868	2		599	488	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245456	46245456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	117	621	0	ENST00000334344.6:c.3550C>T	p.Pro1184Ser	p.P1184S	ENST00000334344	NM_152641.2	1184	Cct/Tct	15/21	1	2	FACETS	0.869	0.786	0.956	0.869	0.786	0.956	CLONAL	1	TRUE	1	0.47824849687868	2		621	563	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435270	49435271	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	132	710	0	ENST00000301067.7:c.6282_6283delinsTT	p.Arg2095Cys	p.R2095C	ENST00000301067	NM_003482.3	2094	gcCCgt/gcTTgt	31/54	1	2	FACETS	0.901	0.82	0.985	0.901	0.82	0.985	CLONAL	1	TRUE	1	0.47824849687868	2		710	613	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120699	115120699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1042037489	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	133	769	0	ENST00000257566.3:c.307C>T	p.Pro103Ser	p.P103S	ENST00000257566	NM_016569.3	103	Ccc/Tcc	1/8	1	2	FACETS	0.847	0.771	0.926	0.847	0.771	0.926	CLONAL	1	TRUE	1	0.47824849687868	2		769	657	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914233	32914233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358801	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	37	451	0	ENST00000380152.3:c.5741G>A	p.Ser1914Asn	p.S1914N	ENST00000380152		1914	aGc/aAc	11/27	1	2	FACETS	0.932	0.779	1	0.932	0.779	1	CLONAL	1	TRUE	1	0.47824849687868	2		451	166	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336123	73336123	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	90	571	0	ENST00000377767.4:c.2280T>G	p.Asn760Lys	p.N760K	ENST00000377767	NM_014953.3	760	aaT/aaG	17/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.47824849687868	2		571	323	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643291	38643291	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	158	519	0	ENST00000299084.4:c.761T>A	p.Leu254Ter	p.L254*	ENST00000299084	NM_152594.2	254	tTa/tAa	7/7	0.458709280167161	2	FACETS	0.955	0.889	1	0.955	0.889	1	CLONAL	2	TRUE	0	0.47824849687868	2		519	346	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021471	42021471	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	207	682	0	ENST00000219905.7:c.3767C>T	p.Ser1256Phe	p.S1256F	ENST00000219905	NM_001164273.1	1256	tCc/tTc	11/24	0.458709280167161	2	FACETS	0.949	0.892	1	0.949	0.892	1	CLONAL	2	TRUE	0	0.47824849687868	2		682	456	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041714	42041714	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	227	658	0	ENST00000219905.7:c.5909G>C	p.Arg1970Thr	p.R1970T	ENST00000219905	NM_001164273.1	1970	aGa/aCa	17/24	0.458709280167161	2	FACETS	0.942	0.887	0.997	0.942	0.887	0.997	CLONAL	2	TRUE	0	0.47824849687868	2		658	504	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508694	38508694	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	136	550	0	ENST00000254066.5:c.742G>C	p.Gly248Arg	p.G248R	ENST00000254066	NM_000964.3	248	Ggc/Cgc	6/9	1	2	FACETS	0.957	0.874	1	0.957	0.874	1	CLONAL	1	TRUE	1	0.47824849687868	2		550	594	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40872419	40872419	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	116	528	0	ENST00000428826.2:c.536T>C	p.Leu179Ser	p.L179S	ENST00000428826		179	tTg/tCg	7/21	1	2	FACETS	0.942	0.853	1	0.942	0.853	1	CLONAL	1	TRUE	1	0.47824849687868	2		528	515	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61323108	61323108	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	105	697	0	ENST00000283752.5:c.956G>A	p.Gly319Glu	p.G319E	ENST00000283752	NM_006919.2	319	gGg/gAg	8/8	1	2	FACETS	0.779	0.7	0.862	0.779	0.7	0.862	SUBCLONAL	1	TRUE	1	0.47824849687868	2		697	564	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726574	41726574	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	107	665	0	ENST00000301178.4:c.119A>G	p.Asn40Ser	p.N40S	ENST00000301178	NM_021913.4	40	aAc/aGc	2/20	1	2	FACETS	0.735	0.66	0.813	0.735	0.66	0.813	SUBCLONAL	1	TRUE	1	0.47824849687868	2		665	609	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46587867	46587867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs557184790	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	115	672	0	ENST00000263734.3:c.545C>T	p.Thr182Ile	p.T182I	ENST00000263734	NM_001430.4	182	aCt/aTt	5/16	1	2	FACETS	0.828	0.748	0.912	0.828	0.748	0.912	CLONAL	1	TRUE	1	0.47824849687868	2		672	581	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99179951	99179951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	128	683	0	ENST00000074304.5:c.1894C>T	p.Pro632Ser	p.P632S	ENST00000074304	NM_001134224.1	632	Ccg/Tcg	19/26	1	2	FACETS	0.944	0.859	1	0.944	0.859	1	CLONAL	1	TRUE	1	0.47824849687868	2		683	567	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54963238	54963238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	56	376	0	ENST00000312783.6:c.16G>A	p.Glu6Lys	p.E6K	ENST00000312783	NM_198436.1	6	Gaa/Aaa	3/10	1	2	FACETS	0.802	0.692	0.92	0.802	0.692	0.92	CLONAL	1	TRUE	1	0.47824849687868	2		376	292	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484430	57484430	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	139	605	0	ENST00000371085.3:c.611C>T	p.Thr204Ile	p.T204I	ENST00000371085	NM_000516.4	204	aCt/aTt	8/13	1	2	FACETS	0.999	0.913	1	0.999	0.913	1	CLONAL	1	TRUE	1	0.47824849687868	2		605	582	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268982	142268982	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	56	340	0	ENST00000350721.4:c.2968T>A	p.Phe990Ile	p.F990I	ENST00000350721	NM_001184.3	990	Ttt/Att	14/47	1	2	FACETS	0.887	0.767	1	0.887	0.767	1	CLONAL	1	TRUE	1	0.47824849687868	2		340	264	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796538	57796538	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	171	567	0	ENST00000309042.7:c.1514A>G	p.His505Arg	p.H505R	ENST00000309042	NM_005612.4	505	cAt/cGt	4/4	0.47824849687868	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.47824849687868	3		567	423	SUCCESS
APC	324	MSKCC	GRCh37	5	112175279	112175280	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	116	655	0	ENST00000257430.4:c.3988_3989delinsTT	p.Pro1330Phe	p.P1330F	ENST00000257430	NM_000038.5	1330	CCt/TTt	16/16	0.475353988499615	1	FACETS	0.907	0.824	0.993	0.907	0.824	0.993	CLONAL	1	TRUE	0	0.47824849687868	1		655	407	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456914	149456915	+	missense_variant	Missense_Mutation	DNP	GT	GT	AG	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	113	798	0	ENST00000286301.3:c.813_814delinsCT	p.Gln271_His272delinsHisTyr	p.Q271_H272delinsHY	ENST00000286301	NM_005211.3	271	caACat/caCTat	6/22	0.475353988499615	1	FACETS	0.751	0.679	0.825	0.751	0.679	0.825	SUBCLONAL	1	TRUE	0	0.47824849687868	1		798	479	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482877	140482877	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	112	735	0	ENST00000288602.6:c.1258C>T	p.Pro420Ser	p.P420S	ENST00000288602	NM_004333.4	420	Cca/Tca	10/18	1	2	FACETS	0.992	0.898	1	0.992	0.898	1	CLONAL	1	TRUE	1	0.47824849687868	2		735	472	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624407	140624421	+	inframe_deletion	In_Frame_Del	DEL	CGCCGGCGCCGGCGC	CGCCGGCGCCGGCGC	-	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	122	520	0	ENST00000288602.6:c.83_97del	p.Gly28_Gly32del	p.G28_G32del	ENST00000288602	NM_004333.4	28	gGCGCCGGCGCCGGCGcc/gcc	1/18	1	2	FACETS	0.957	0.869	1	0.957	0.869	1	CLONAL	1	TRUE	1	0.47824849687868	2		520	533	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187219	38187220	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	93	596	1	ENST00000317025.8:c.1257_1258delinsTT	p.Arg420Ter	p.R420*	ENST00000317025	NM_023034.1	419	acCCga/acTTga	6/24	0.475353988499615	1	FACETS	0.798	0.715	0.884	0.798	0.715	0.884	SUBCLONAL	1	TRUE	0	0.47824849687868	1		597	371	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518124	8518125	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	112	627	0	ENST00000356435.5:c.1266_1267delinsTA	p.Arg422_Asp423delinsSerAsn	p.R422_D423delinsSN	ENST00000356435		422	agGGat/agTAat	10/35	1	2	FACETS	0.844	0.762	0.93	0.844	0.762	0.93	CLONAL	1	TRUE	1	0.47824849687868	2		627	555	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518181	8518181	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	124	575	0	ENST00000356435.5:c.1210C>T	p.Pro404Ser	p.P404S	ENST00000356435		404	Ccc/Tcc	10/35	1	2	FACETS	0.957	0.869	1	0.957	0.869	1	CLONAL	1	TRUE	1	0.47824849687868	2		575	542	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197462	27197462	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	124	600	0	ENST00000380036.4:c.1774A>C	p.Lys592Gln	p.K592Q	ENST00000380036	NM_000459.3	592	Aaa/Caa	12/23	1	2	FACETS	0.986	0.896	1	0.986	0.896	1	CLONAL	1	TRUE	1	0.47824849687868	2		600	526	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409994	139409995	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	117	899	2	ENST00000277541.6:c.1843_1844delinsAA	p.Gly615Lys	p.G615K	ENST00000277541	NM_017617.3	615	GGg/AAg	11/34	1	2	FACETS	0.779	0.704	0.858	0.779	0.704	0.858	SUBCLONAL	1	TRUE	1	0.47824849687868	2		901	628	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933468	39933468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	146	752	0	ENST00000378444.4:c.1131G>A	p.Met377Ile	p.M377I	ENST00000378444	NM_001123385.1	377	atG/atA	4/15	1	2	FACETS	0.887	0.812	0.966	0.887	0.812	0.966	CLONAL	1	TRUE	1	0.47824849687868	2		752	688	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941863	44941863	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1165681830	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	49	330	0	ENST00000377967.4:c.3187A>G	p.Ser1063Gly	p.S1063G	ENST00000377967	NM_021140.2	1063	Agt/Ggt	21/29	1	2	FACETS	0.876	0.749	1	0.876	0.749	1	CLONAL	1	TRUE	1	0.47824849687868	2		330	234	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428989	47428990	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	116	676	0	ENST00000377045.4:c.1352_1353delinsTT	p.Ala451Val	p.A451V	ENST00000377045	NM_001654.4	451	gCC/gTT	13/16	1	2	FACETS	0.841	0.76	0.925	0.841	0.76	0.925	CLONAL	1	TRUE	1	0.47824849687868	2		676	577	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429012	47429013	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	109	695	1	ENST00000377045.4:c.1375_1376delinsAA	p.Gly459Lys	p.G459K	ENST00000377045	NM_001654.4	459	GGg/AAg	13/16	1	2	FACETS	0.779	0.702	0.861	0.779	0.702	0.861	SUBCLONAL	1	TRUE	1	0.47824849687868	2		696	585	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034393	123034393	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	49	316	0	ENST00000355640.3:c.1150T>C	p.Phe384Leu	p.F384L	ENST00000355640		384	Ttc/Ctc	6/7	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.47824849687868	2		316	196	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851943	63851944	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	G	novel	NA	P-0060149-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	131	646	0	ENST00000279873.7:c.2721_2722delinsG	p.Asp907GlufsTer2	p.D907Efs*2	ENST00000279873	NM_032199.2	907	gaTCtg/gaGtg	10/10	1	2	FACETS	0.857	0.78	0.938	0.857	0.78	0.938	CLONAL	1	TRUE	1	0.47824849687868	2		646	639	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0060149-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1432	90	699	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.986	0.871	1	0.986	0.871	1	CLONAL	1	TRUE	1	0.12	2		706	1522	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0060149-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	10	168	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	0.214079181571577	1	FACETS	0.593	0.401	0.836	0.593	0.401	0.836	SUBCLONAL	1	TRUE	0	0.12	1		168	264	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0060156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	306	388	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.340142478946268	5	FACETS	0.993	0.943	1	0.993	0.943	1	CLONAL	4	TRUE	1	0.340142478946268	5		388	684	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692794	89692794	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121909238	NA	P-0060156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	69	251	0	ENST00000371953.3:c.278A>G	p.His93Arg	p.H93R	ENST00000371953	NM_000314.4	93	cAt/cGt	5/9	0.340142478946268	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	2	TRUE	0	0.340142478946268	2		251	200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs1202793339	NA	P-0060156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	289	651	0	ENST00000269305.4:c.560-1G>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.297048221402085	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.340142478946268	2		651	830	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573991	7573992	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0060156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	97	434	0	ENST00000269305.4:c.1035dup	p.Glu346Ter	p.E346*	ENST00000269305	NM_001126112.2	345	-/T	10/11	0.297048221402085	2	FACETS	1	0.922	1	0.518	0.463	0.577	CLONAL	1	TRUE	0	0.340142478946268	2		434	550	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061111	38061138	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTCAGGGCCGCCCTTGGCGCCGCTGC	CTCTCAGGGCCGCCCTTGGCGCCGCTGC	-	novel	NA	P-0060156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	120	568	0	ENST00000250448.2:c.851_878del	p.Gly284AlafsTer28	p.G284Afs*28	ENST00000250448	NM_004496.3	284	gGCAGCGGCGCCAAGGGCGGCCCTGAGAGc/gc	2/2	0.340142478946268	3	FACETS	1	0.931	1	0.519	0.469	0.573	CLONAL	1	TRUE	1	0.340142478946268	3		568	795	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0060157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	103	497	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.300018140360776	3	FACETS	0.908	0.816	1	0.454	0.408	0.503	INDETERMINATE	1	TRUE	1	0.600743264466587	3		497	491	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0060157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	136	377	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.600743264466587	2	FACETS	0.967	0.903	1	0.967	0.903	1	CLONAL	2	TRUE	0	0.600743264466587	2		377	234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0060157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	330	433	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.600743264466587	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.600743264466587	2		434	548	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2185868	2185868	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	168	494	0	ENST00000398665.3:c.140A>T	p.Glu47Val	p.E47V	ENST00000398665	NM_032482.2	47	gAa/gTa	3/28	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.600743264466587	2		494	547	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864196	57864196	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs972690369	NA	P-0060157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	196	753	2	ENST00000228682.2:c.1673G>A	p.Arg558His	p.R558H	ENST00000228682	NM_005269.2	558	cGc/cAc	12/12	0.600743264466587	2	FACETS	0.878	0.815	0.943	0.439	0.407	0.472	CLONAL	1	TRUE	0	0.600743264466587	2		755	743	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	202	756	2	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	1	2	FACETS	0.982	0.914	1	0.982	0.914	1	CLONAL	1	TRUE	1	0.600743264466587	2		758	685	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139799	55139799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764214258	NA	P-0060157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	81	498	0	ENST00000257290.5:c.1460G>A	p.Arg487His	p.R487H	ENST00000257290	NM_006206.4	487	cGt/cAt	10/23	1	2	FACETS	0.497	0.438	0.559	0.497	0.438	0.559	SUBCLONAL	1	TRUE	1	0.600743264466587	2		498	543	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2214516	2214516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	177	683	0	ENST00000398665.3:c.1844C>T	p.Ser615Leu	p.S615L	ENST00000398665	NM_032482.2	615	tCg/tTg	19/28	1	2	FACETS	0.958	0.887	1	0.958	0.887	1	CLONAL	1	TRUE	1	0.600743264466587	2		683	615	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99180101	99180101	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0060157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	179	562	0	ENST00000074304.5:c.2043+1G>A		p.X681_splice	ENST00000074304	NM_001134224.1	681			0.300018140360776	3	FACETS	1	0.986	1	0.635	0.588	0.683	INDETERMINATE	1	TRUE	1	0.600743264466587	3		562	610	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962601	100962601	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs201384017	NA	P-0060157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	112	322	0	ENST00000325455.5:c.1796A>G	p.His599Arg	p.H599R	ENST00000325455	NM_001202474.3	599	cAc/cGc	3/8	0.596729044670155	2	FACETS	1	0.975	1	0.599	0.546	0.654	CLONAL	1	TRUE	0	0.600743264466587	2		322	311	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18972889	18972889	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	72	520	0	ENST00000262803.5:c.2528G>A	p.Arg843Gln	p.R843Q	ENST00000262803	NM_002911.3	843	cGg/cAg	18/24	1	2	FACETS	0.42	0.367	0.477	0.42	0.367	0.477	SUBCLONAL	1	TRUE	1	0.600743264466587	2		520	571	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868353	45868353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	206	627	0	ENST00000391945.4:c.424G>A	p.Val142Met	p.V142M	ENST00000391945	NM_000400.3	142	Gtg/Atg	6/23	0.600743264466587	3	FACETS	0.941	0.873	1	0.47	0.436	0.506	CLONAL	1	TRUE	1	0.600743264466587	3		627	948	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732963	30732963	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121918714	NA	P-0060157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	217	587	0	ENST00000295754.5:c.1576G>C	p.Glu526Gln	p.E526Q	ENST00000295754	NM_003242.5	526	Gag/Cag	7/7	0.600743264466587	2	FACETS	1	0.954	1	0.514	0.48	0.549	CLONAL	1	TRUE	0	0.600743264466587	2		587	703	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963142	38963142	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs200068996	NA	P-0060157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	119	353	0	ENST00000357387.3:c.1402C>T	p.Arg468Ter	p.R468*	ENST00000357387	NM_152756.3	468	Cga/Tga	17/38	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.600743264466587	2		353	352	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932104	39932104	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	81	667	0	ENST00000378444.4:c.2495G>C	p.Gly832Ala	p.G832A	ENST00000378444	NM_001123385.1	832	gGc/gCc	4/15	1	2	FACETS	0.439	0.387	0.495	0.439	0.387	0.495	SUBCLONAL	1	TRUE	1	0.600743264466587	2		667	614	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307985	11307985	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1257592579	NA	P-0060158-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	236	827	0	ENST00000361445.4:c.1007A>G	p.Tyr336Cys	p.Y336C	ENST00000361445	NM_004958.3	336	tAc/tGc	7/58	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.651246776464233	2		827	662	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115917	8115918	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0060158-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	275	987	0	ENST00000346208.3:c.1263_1264del	p.Met422AlafsTer84	p.M422Afs*84	ENST00000346208		421	ccGAtg/cctg	6/6	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.651246776464233	2		987	826	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570280	95570281	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs1555369632	NA	P-0060158-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	175	762	0	ENST00000393063.1:c.3452_3453del	p.Val1151GlufsTer12	p.V1151Efs*12	ENST00000393063	NM_030621.3	1151	gTG/g	22/28	1	2	FACETS	0.911	0.843	0.98	0.911	0.843	0.98	CLONAL	1	TRUE	1	0.651246776464233	2		762	590	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873389	151873390	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0060158-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	244	754	0	ENST00000262189.6:c.9148_9149insTG	p.Glu3050ValfsTer27	p.E3050Vfs*27	ENST00000262189	NM_170606.2	3050	gaa/gTGaa	38/59	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.651246776464233	2		754	645	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0060159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	115	499	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.933	0.852	1	0.933	0.852	1	CLONAL	1	TRUE	1	0.800669783102399	2		499	308	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665213	138665213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	142	517	0	ENST00000330315.3:c.352G>A	p.Glu118Lys	p.E118K	ENST00000330315	NM_023067.3	118	Gag/Aag	1/1	1	2	FACETS	0.999	0.923	1	0.999	0.923	1	CLONAL	1	TRUE	1	0.800669783102399	2		517	355	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540602	187540602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201352448	NA	P-0060159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	36	539	1	ENST00000441802.2:c.7138G>A	p.Val2380Ile	p.V2380I	ENST00000441802	NM_005245.3	2380	Gtt/Att	10/27	1	2	FACETS	0.159	0.13	0.191	0.159	0.13	0.191	SUBCLONAL	1	TRUE	1	0.800669783102399	2		540	566	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	207	232	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.800669783102399	1		232	272	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871992	45871992	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	160	405	0	ENST00000391945.4:c.256G>C	p.Glu86Gln	p.E86Q	ENST00000391945	NM_000400.3	86	Gag/Cag	5/23	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.800669783102399	2		405	385	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717609	89717609	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs876661024	NA	P-0060159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	10	346	0	ENST00000371953.3:c.635-1G>A		p.X212_splice	ENST00000371953	NM_000314.4	212			0.800669783102399	1	FACETS	0.065	0.043	0.091	0.065	0.043	0.091	SUBCLONAL	1	TRUE	0	0.800669783102399	1		346	232	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587119	189587119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765502786	NA	P-0060159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	168	361	0	ENST00000264731.3:c.1136G>A	p.Arg379His	p.R379H	ENST00000264731	NM_003722.4	379	cGt/cAt	9/14	1	2	FACETS	0.933	0.866	1	0.933	0.866	1	CLONAL	1	TRUE	1	0.800669783102399	2		361	450	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206581	108206581	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	171	368	0	ENST00000278616.4:c.8161G>T	p.Asp2721Tyr	p.D2721Y	ENST00000278616	NM_000051.3	2721	Gac/Tac	56/63	0.800669783102399	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.800669783102399	1		368	248	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397654	49397654	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	147	423	0	ENST00000418115.1:c.570C>A	p.Cys190Ter	p.C190*	ENST00000418115	NM_001664.2	190	tgC/tgA	5/5	1	2	FACETS	0.714	0.656	0.774	0.714	0.656	0.774	SUBCLONAL	1	TRUE	1	0.800669783102399	2		423	514	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162747	47162747	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	164	371	0	ENST00000409792.3:c.3379C>T	p.Gln1127Ter	p.Q1127*	ENST00000409792	NM_014159.6	1127	Caa/Taa	3/21	1	2	FACETS	0.966	0.897	1	0.966	0.897	1	CLONAL	1	TRUE	1	0.800669783102399	2		371	424	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894230	NA	P-0060159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	212	539	0	ENST00000451590.1:c.35G>T	p.Gly12Val	p.G12V	ENST00000451590	NM_001130442.1	12	gGc/gTc	2/5	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.800669783102399	2		539	512	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259351	16259351	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	43	631	0	ENST00000375759.3:c.6616C>A	p.Pro2206Thr	p.P2206T	ENST00000375759	NM_015001.2	2206	Cct/Act	11/15	1	2	FACETS	0.203	0.169	0.24	0.203	0.169	0.24	SUBCLONAL	1	TRUE	1	0.800669783102399	2		631	530	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57004472	57004472	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	117	484	0	ENST00000257254.3:c.7G>C	p.Glu3Gln	p.E3Q	ENST00000257254		3	Gaa/Caa	1/2	1	2	FACETS	0.706	0.642	0.773	0.706	0.642	0.773	SUBCLONAL	1	TRUE	1	0.800669783102399	2		484	414	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945378	71945378	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1289595378	NA	P-0060159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	186	548	0	ENST00000298229.2:c.2266A>G	p.Ile756Val	p.I756V	ENST00000298229	NM_001567.3	756	Att/Gtt	20/28	1	2	FACETS	0.956	0.891	1	0.956	0.891	1	CLONAL	1	TRUE	1	0.800669783102399	2		548	486	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245251	46245290	+	frameshift_variant	Frame_Shift_Del	DEL	TCCAGCTCAGCAGCTATTGGTTGGGCAGCAAAATGTTCAG	TCCAGCTCAGCAGCTATTGGTTGGGCAGCAAAATGTTCAG	AT	novel	NA	P-0060159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	72	553	1	ENST00000334344.6:c.3345_3384delinsAT	p.Pro1116PhefsTer31	p.P1116Ffs*31	ENST00000334344	NM_152641.2	1115	acTCCAGCTCAGCAGCTATTGGTTGGGCAGCAAAATGTTCAG/acAT	15/21	1	2	FACETS	0.318	0.278	0.361	0.318	0.278	0.361	SUBCLONAL	1	TRUE	1	0.800669783102399	2		554	566	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130205	2130205	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	153	589	0	ENST00000219476.3:c.3437C>G	p.Ala1146Gly	p.A1146G	ENST00000219476	NM_000548.3	1146	gCc/gGc	30/42	1	2	FACETS	0.681	0.626	0.738	0.681	0.626	0.738	SUBCLONAL	1	TRUE	1	0.800669783102399	2		589	561	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830857	3830858	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	GGAGCCATCGTTCATCA	novel	NA	P-0060159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	160	483	0	ENST00000262367.5:c.1682_1698dup	p.Asn567Ter	p.N567*	ENST00000262367	NM_004380.2	566	-/TGATGAACGATGGCTCC	8/31	1	2	FACETS	0.672	0.619	0.727	0.672	0.619	0.727	SUBCLONAL	1	TRUE	1	0.800669783102399	2		483	595	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213640	2213641	+	splice_donor_variant	Splice_Site	INS	-	-	ACTA	novel	NA	P-0060159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	133	531	0	ENST00000398665.3:c.1659+1_1659+2insACTA		p.X553_splice	ENST00000398665	NM_032482.2	553			1	2	FACETS	0.837	0.768	0.908	0.837	0.768	0.908	CLONAL	1	TRUE	1	0.800669783102399	2		531	397	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238958	5238963	+	inframe_deletion	In_Frame_Del	DEL	GGGGGT	GGGGGT	-	novel	NA	P-0060159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	148	552	0	ENST00000357368.4:c.1816_1821del	p.Thr606_Pro607del	p.T606_P607del	ENST00000357368	NM_002850.3	606	ACCCCC/-	13/38	1	2	FACETS	0.835	0.769	0.902	0.835	0.769	0.902	CLONAL	1	TRUE	1	0.800669783102399	2		552	443	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6270758	6270758	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	198	632	0	ENST00000252674.7:c.25G>T	p.Val9Leu	p.V9L	ENST00000252674	NM_005934.3	9	Gtg/Ttg	2/12	1	2	FACETS	0.799	0.744	0.855	0.799	0.744	0.855	SUBCLONAL	1	TRUE	1	0.800669783102399	2		632	619	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281580	15281580	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	27	580	0	ENST00000263388.2:c.4793A>G	p.Asp1598Gly	p.D1598G	ENST00000263388	NM_000435.2	1598	gAt/gGt	26/33	1	2	FACETS	0.152	0.12	0.188	0.152	0.12	0.188	SUBCLONAL	1	TRUE	1	0.800669783102399	2		580	444	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495243	212495243	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1453260317	NA	P-0060159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	228	405	0	ENST00000342788.4:c.2023G>A	p.Val675Ile	p.V675I	ENST00000342788	NM_005235.2	675	Gtt/Att	17/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.800669783102399	2		405	543	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309766	30309766	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1304898407	NA	P-0060159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	217	569	0	ENST00000307677.4:c.256G>A	p.Val86Ile	p.V86I	ENST00000307677	NM_138578.1	86	Gta/Ata	2/3	1	2	FACETS	0.975	0.914	1	0.975	0.914	1	CLONAL	1	TRUE	1	0.800669783102399	2		569	556	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245290	46245290	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	72	532	0	ENST00000334344.6:c.3384G>T	p.Gln1128His	p.Q1128H	ENST00000334344	NM_152641.2	1128	caG/caT	15/21	1	2	FACETS	0.334	0.292	0.379	0.334	0.292	0.379	SUBCLONAL	1	TRUE	1	0.800669783102399	2		532	539	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245250	46245287	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCAGCTCAGCAGCTATTGGTTGGGCAGCAAAATGTT	CTCCAGCTCAGCAGCTATTGGTTGGGCAGCAAAATGTT	-	novel	NA	P-0060159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	69	541	0	ENST00000334344.6:c.3345_3382del	p.Pro1116ValfsTer31	p.P1116Vfs*31	ENST00000334344	NM_152641.2	1115	aCTCCAGCTCAGCAGCTATTGGTTGGGCAGCAAAATGTT/a	15/21	1	2	FACETS	0.312	0.271	0.355	0.312	0.271	0.355	SUBCLONAL	1	TRUE	1	0.800669783102399	2		541	553	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0060160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	104	289	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.644255108924405	3	FACETS	0.788	0.717	0.86	0.788	0.717	0.86	SUBCLONAL	2	TRUE	1	0.644255108924405	3		289	271	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0060160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	40	66	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.906	0.769	1	0.906	0.769	1	CLONAL	1	TRUE	1	0.644255108924405	2		66	137	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0060160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	55	446	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.805	0.698	0.919	0.805	0.698	0.919	CLONAL	1	TRUE	1	0.644255108924405	2		446	212	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316237	11316237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748631718	NA	P-0060160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	145	598	0	ENST00000361445.4:c.517C>T	p.Arg173Cys	p.R173C	ENST00000361445	NM_004958.3	173	Cgt/Tgt	5/58	1	2	FACETS	0.856	0.785	0.929	0.856	0.785	0.929	CLONAL	1	TRUE	1	0.644255108924405	2		598	526	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959351	26959351	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	15	395	0	ENST00000381527.3:c.518A>G	p.Asp173Gly	p.D173G	ENST00000381527	NM_001260.1	173	gAc/gGc	6/13	1	2	FACETS	0.19	0.139	0.252	0.19	0.139	0.252	SUBCLONAL	1	TRUE	1	0.644255108924405	2		395	245	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007672	45007673	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0060160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	222	606	0	ENST00000558401.1:c.122dup	p.Asn41LysfsTer16	p.N41Kfs*16	ENST00000558401	NM_004048.2	40	tca/tcAa	2/4	0.596722090521251	2	FACETS	0.919	0.872	0.965	0.919	0.872	0.965	CLONAL	2	TRUE	0	0.644255108924405	2		606	375	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513352	41513352	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	114	735	1	ENST00000263253.7:c.256C>T	p.Arg86Ter	p.R86*	ENST00000263253	NM_001429.3	86	Cga/Tga	2/31	1	2	FACETS	0.817	0.741	0.897	0.817	0.741	0.897	CLONAL	1	TRUE	1	0.644255108924405	2		736	433	SUCCESS
APC	324	MSKCC	GRCh37	5	112175765	112175765	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691144	NA	P-0060160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	113	658	0	ENST00000257430.4:c.4474del	p.Ala1492ProfsTer15	p.A1492Pfs*15	ENST00000257430	NM_000038.5	1492	Gcc/cc	16/16	1	2	FACETS	0.899	0.817	0.985	0.899	0.817	0.985	CLONAL	1	TRUE	1	0.644255108924405	2		658	390	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782191	9782191	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs755934302	NA	P-0060160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	154	794	0	ENST00000377346.4:c.2214C>A	p.Ser738Arg	p.S738R	ENST00000377346	NM_005026.3	738	agC/agA	17/24	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.644255108924405	2		794	462	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141507	11141507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	132	765	0	ENST00000358026.2:c.3484G>A	p.Gly1162Ser	p.G1162S	ENST00000358026	NM_001128849.1	1162	Ggc/Agc	25/36	1	2	FACETS	0.709	0.646	0.775	0.709	0.646	0.775	SUBCLONAL	1	TRUE	1	0.644255108924405	2		765	578	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1623949	1623949	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0060160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	103	506	0	ENST00000344749.5:c.549+1G>A		p.X183_splice	ENST00000344749	NM_001136139.2	183			1	2	FACETS	0.824	0.743	0.908	0.824	0.743	0.908	CLONAL	1	TRUE	1	0.644255108924405	2		506	388	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11114048	11114048	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	130	627	0	ENST00000358026.2:c.1976A>G	p.Glu659Gly	p.E659G	ENST00000358026	NM_001128849.1	659	gAa/gGa	13/36	1	2	FACETS	0.947	0.867	1	0.947	0.867	1	CLONAL	1	TRUE	1	0.644255108924405	2		627	426	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211106	36211114	+	inframe_deletion	In_Frame_Del	DEL	GCCGTGGAG	GCCGTGGAG	-	rs767997887	NA	P-0060160-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	153	878	0	ENST00000222270.7:c.868_876del	p.Gly292_Gly294del	p.G292_G294del	ENST00000222270	NM_014727.1	286	aGCCGTGGAGgc/agc	3/37	0.644255108924405	4	FACETS	0.736	0.672	0.803	0.245	0.224	0.268	SUBCLONAL	1	TRUE	1	0.644255108924405	4		878	1061	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0060161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	86	392	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.508426166720513	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.560338566554322	1		392	195	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513282	44513287	+	inframe_deletion	In_Frame_Del	DEL	CCACCG	CCACCG	-	rs745888281	NA	P-0060161-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	42	581	3	ENST00000291552.4:c.648_653del	p.Gly222_Gly223del	p.G222_G223del	ENST00000291552	NM_006758.2	216	ggCGGTGGt/ggt	8/8	1	2	FACETS	0.728	0.614	0.851	0.728	0.614	0.851	SUBCLONAL	1	TRUE	1	0.560338566554322	2		584	206	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0060164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	143	393	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		393	311	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0060166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	981	575	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.856528860209597	5	FACETS	0.988	0.978	0.998	0.988	0.978	0.998	CLONAL	5	TRUE	0	0.866015575031509	5		575	1054	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942752	44942752	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1457797612	NA	P-0060166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	214	397	0	ENST00000377967.4:c.3332G>C	p.Arg1111Pro	p.R1111P	ENST00000377967	NM_021140.2	1111	cGt/cCt	23/29	0.851517075508165	2	FACETS	0.992	0.96	1	0.992	0.96	1	CLONAL	2	TRUE	0	0.866015575031509	2		397	249	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241433	105241433	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0060166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	22	645	0	ENST00000349310.3:c.547A>T	p.Lys183Ter	p.K183*	ENST00000349310	NM_001014432.1	183	Aag/Tag	7/15	0.830146720829408	2	FACETS	0.117	0.09	0.149	0.059	0.045	0.075	SUBCLONAL	1	TRUE	0	0.866015575031509	2		645	433	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725442	117725442	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0060166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	264	319	0	ENST00000368508.3:c.438+1G>T		p.X146_splice	ENST00000368508	NM_002944.2	146			0.530882416344809	4	FACETS	0.988	0.946	1			1	CLONAL	3	TRUE	NA	0.866015575031509	4		319	384	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5522562	5522562	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	26	325	0	ENST00000397747.3:c.16C>G	p.Leu6Val	p.L6V	ENST00000397747	NM_025239.3	6	Cta/Gta	2/7	0.687842592017039	2	FACETS	0.191	0.151	0.237	0.096	0.075	0.119	SUBCLONAL	1	TRUE	0	0.866015575031509	2		325	314	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034444	47034444	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	74	491	0	ENST00000377604.3:c.529G>T	p.Glu177Ter	p.E177*	ENST00000377604	NM_001204468.1	177	Gag/Tag	6/24	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.260784049368849	2		491	549	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602452	10602452	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	155	761	0	ENST00000171111.5:c.1126G>C	p.Ala376Pro	p.A376P	ENST00000171111	NM_203500.1	376	Gcc/Ccc	3/6	0.244361199344439	2	FACETS	0.853	0.783	0.926	0.853	0.783	0.926	CLONAL	2	TRUE	0	0.260784049368849	2		761	697	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0060167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	62	500	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	0.163188683738832	3	FACETS	1	0.952	1	0.612	0.53	0.701	CLONAL	1	TRUE	1	0.260784049368849	3		500	439	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434516	49434516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	85	783	0	ENST00000301067.7:c.7037G>A	p.Gly2346Asp	p.G2346D	ENST00000301067	NM_003482.3	2346	gGc/gAc	31/54	0.163188683738832	3	FACETS	0.947	0.837	1	0.474	0.418	0.533	CLONAL	1	TRUE	1	0.260784049368849	3		783	778	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003188	143003189	+	missense_variant	Missense_Mutation	DNP	TC	TC	CT	novel	NA	P-0060167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	24	351	0	ENST00000262992.4:c.2637_2638delinsAG	p.Met879_Arg880delinsIleGly	p.M879_R880delinsIG	ENST00000262992	NM_001101669.1	879	atGAga/atAGga	23/24	1	2	FACETS	0.687	0.54	0.856	0.687	0.54	0.856	SUBCLONAL	1	TRUE	1	0.260784049368849	2		351	268	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38315038	38315039	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	39	525	0	ENST00000425967.3:c.25dup	p.Arg9LysfsTer21	p.R9Kfs*21	ENST00000425967	NM_001174067.1	9	agg/aAgg	3/19	1	2	FACETS	0.672	0.557	0.8	0.672	0.557	0.8	SUBCLONAL	1	TRUE	1	0.260784049368849	2		525	445	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412051	63412051	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	97	708	0	ENST00000330258.3:c.1116G>T	p.Met372Ile	p.M372I	ENST00000330258	NM_152424.3	372	atG/atT	2/2	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.260784049368849	2		708	664	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218481	1218483	+	frameshift_variant	Frame_Shift_Del	DEL	ACG	ACG	TT	novel	NA	P-0060167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	89	499	0	ENST00000326873.7:c.356_358delinsTT	p.Asn119IlefsTer10	p.N119Ifs*10	ENST00000326873	NM_000455.4	119	aACGaa/aTTaa	2/10	0.244361199344439	2	FACETS	0.841	0.75	0.936	0.841	0.75	0.936	CLONAL	2	TRUE	0	0.260784049368849	2		499	406	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845617	68845617	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	13	465	0	ENST00000261769.5:c.863A>C	p.Asp288Ala	p.D288A	ENST00000261769	NM_004360.3	288	gAc/gCc	7/16	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		465	625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0060170-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	349	584	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.897968091560324	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.897968091560324	1		584	387	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594061	55594061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs891140054	NA	P-0060170-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	232	406	1	ENST00000288135.5:c.1847C>T	p.Ala616Val	p.A616V	ENST00000288135	NM_000222.2	616	gCg/gTg	12/21	0.799151570297531	1	FACETS	0.871	0.833	0.907	0.871	0.833	0.907	CLONAL	1	TRUE	0	0.897968091560324	1		407	327	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134654	2134654	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060170-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	139	647	0	ENST00000219476.3:c.4431G>T	p.Arg1477Ser	p.R1477S	ENST00000219476	NM_000548.3	1477	agG/agT	34/42	0.851519428098714	2	FACETS	0.506	0.462	0.552	0.253	0.231	0.276	SUBCLONAL	1	TRUE	0	0.897968091560324	2		647	612	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56367788	56367788	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060170-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	229	345	0	ENST00000348428.3:c.614A>G	p.Gln205Arg	p.Q205R	ENST00000348428	NM_006785.3	205	cAg/cGg	4/17	1	2	FACETS	0.988	0.931	1	0.988	0.931	1	CLONAL	1	TRUE	1	0.897968091560324	2		345	516	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2047312	2047329	+	inframe_deletion	In_Frame_Del	DEL	CCCGCAGCCGCGCAGCCG	CCCGCAGCCGCGCAGCCG	-	rs1246500736	NA	P-0060170-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	112	133	0	ENST00000349721.2:c.879_896del	p.Gln296_Ala301del	p.Q296_A301del	ENST00000349721	NM_003070.3	292	CCCGCAGCCGCGCAGCCG/-	5/34	0.826640797008909	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.897968091560324	1		133	128	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342048	70342048	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0060170-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	24	215	0	ENST00000374080.3:c.1102-2A>G		p.X368_splice	ENST00000374080		368			1	1	FACETS	0.088	0.069	0.111	0.088	0.069	0.111	SUBCLONAL	1	TRUE	0	0.897968091560324	1		215	334	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653154	29653154	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	GT	novel	NA	P-0060170-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	351	519	0	ENST00000356175.3:c.5089delinsGT	p.His1697ValfsTer5	p.H1697Vfs*5	ENST00000356175	NM_000267.3	1697	Cac/GTac	36/57	0.897968091560324	1	FACETS	0.993	0.964	1	0.993	0.964	1	CLONAL	1	TRUE	0	0.897968091560324	1		519	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0060174-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	47	484	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.1425437821811	3	FACETS	0.796	0.674	0.93	0.796	0.674	0.93	CLONAL	2	TRUE	1	0.178153515435726	3		484	361	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257633	19257633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060174-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	62	688	0	ENST00000162023.5:c.593C>T	p.Pro198Leu	p.P198L	ENST00000162023		198	cCc/cTc	10/13	0.178153515435726	3	FACETS	0.867	0.751	0.993	0.867	0.751	0.993	CLONAL	2	TRUE	1	0.178153515435726	3		688	437	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831203	3831203	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0060174-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	57	406	0	ENST00000262367.5:c.1676+2T>G		p.X559_splice	ENST00000262367	NM_004380.2	559			0.178153515435726	2	FACETS	0.899	0.775	1	0.899	0.775	1	CLONAL	2	TRUE	0	0.178153515435726	2		406	356	SUCCESS
ALK	238	MSKCC	GRCh37	2	29541171	29541171	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060174-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	18	538	0	ENST00000389048.3:c.1646A>G	p.Glu549Gly	p.E549G	ENST00000389048	NM_004304.4	549	gAg/gGg	8/29	0.178153515435726	3	FACETS	0.632	0.475	0.818	0.316	0.237	0.409	SUBCLONAL	1	TRUE	1	0.178153515435726	3		538	348	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566511	41566511	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060174-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	68	452	0	ENST00000263253.7:c.4388T>A	p.Leu1463Gln	p.L1463Q	ENST00000263253	NM_001429.3	1463	cTg/cAg	27/31	0.178153515435726	3	FACETS	0.945	0.825	1	0.945	0.825	1	CLONAL	2	TRUE	1	0.178153515435726	3		452	440	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945644	38945644	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060174-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	29	510	0	ENST00000357387.3:c.4582A>C	p.Ile1528Leu	p.I1528L	ENST00000357387	NM_152756.3	1528	Att/Ctt	34/38	0.178153515435726	3	FACETS	0.909	0.73	1	0.455	0.365	0.557	CLONAL	1	TRUE	1	0.178153515435726	3		510	390	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415024	109415024	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060174-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	22	456	0	ENST00000436639.2:c.253A>C	p.Ser85Arg	p.S85R	ENST00000436639	NM_014454.2	85	Agt/Cgt	1/10	0.0448234230391225	4	FACETS	0.772	0.598	0.975	0.386	0.299	0.488	INDETERMINATE	1	TRUE	2	0.178153515435726	4		456	377	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001203	150001203	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060174-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	24	522	0	ENST00000253339.5:c.2401C>A	p.Pro801Thr	p.P801T	ENST00000253339		801	Cca/Aca	4/7	0.0448234230391225	4	FACETS	0.86	0.674	1	0.43	0.337	0.538	INDETERMINATE	1	TRUE	2	0.178153515435726	4		522	369	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878772	151878772	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060174-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	48	599	0	ENST00000262189.6:c.6173G>C	p.Gly2058Ala	p.G2058A	ENST00000262189	NM_170606.2	2058	gGa/gCa	36/59	0.178153515435726	4	FACETS	1	0.946	1	0.428	0.362	0.501	CLONAL	1	TRUE	1	0.178153515435726	4		599	494	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0060177-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	65	61	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.317131997749931	2		61	347	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0060177-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	226	450	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.317131997749931	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.317131997749931	2		450	679	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0060177-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	117	534	0	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	1	2	FACETS	0.945	0.852	1	0.945	0.852	1	CLONAL	1	TRUE	1	0.317131997749931	2		534	781	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926888	112926888	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397507546	NA	P-0060177-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	96	459	0	ENST00000351677.2:c.1508G>C	p.Gly503Ala	p.G503A	ENST00000351677	NM_002834.3	503	gGg/gCg	13/16	1	2	FACETS	0.872	0.778	0.973	0.872	0.778	0.973	CLONAL	1	TRUE	1	0.317131997749931	2		459	694	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552143	29552144	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1555613558	NA	P-0060177-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	83	401	0	ENST00000356175.3:c.1882dup	p.Tyr628LeufsTer6	p.Y628Lfs*6	ENST00000356175	NM_000267.3	626	ctt/cTtt	17/57	1	2	FACETS	0.814	0.719	0.916	0.814	0.719	0.916	CLONAL	1	TRUE	1	0.317131997749931	2		401	643	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654592	29654594	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	novel	NA	P-0060177-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	124	517	0	ENST00000356175.3:c.5281_5283del	p.Ile1761del	p.I1761del	ENST00000356175	NM_000267.3	1761	ATT/-	37/57	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.317131997749931	2		517	731	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575102	48575102	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060177-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	122	443	0	ENST00000342988.3:c.296G>A	p.Trp99Ter	p.W99*	ENST00000342988	NM_005359.5	99	tGg/tAg	3/12	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.317131997749931	2		443	725	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060177-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	113	558	0	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	1	2	FACETS	0.869	0.782	0.962	0.869	0.782	0.962	CLONAL	1	TRUE	1	0.317131997749931	2		558	820	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725294	49725294	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060177-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	51	320	0	ENST00000449682.2:c.131G>T	p.Arg44Leu	p.R44L	ENST00000449682	NM_020998.3	44	cGg/cTg	2/18	1	2	FACETS	0.766	0.652	0.89	0.766	0.652	0.89	SUBCLONAL	1	TRUE	1	0.317131997749931	2		320	420	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747937	41747937	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138545772	NA	P-0060177-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	86	591	0	ENST00000226382.2:c.832G>A	p.Gly278Ser	p.G278S	ENST00000226382	NM_003924.3	278	Ggc/Agc	3/3	1	2	FACETS	0.805	0.712	0.904	0.805	0.712	0.904	CLONAL	1	TRUE	1	0.317131997749931	2		591	674	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155654	56155654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746479827	NA	P-0060177-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	133	563	1	ENST00000399503.3:c.746G>A	p.Arg249His	p.R249H	ENST00000399503	NM_005921.1	249	cGc/cAc	3/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.317131997749931	2		564	762	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031883	26031884	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs758780418	NA	P-0060177-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	117	474	0	ENST00000244661.2:c.405_406del	p.Arg135SerfsTer12	p.R135Sfs*12	ENST00000244661	NM_003537.3	135	agAGcg/agcg	1/1	1	2	FACETS	0.848	0.764	0.937	0.848	0.764	0.937	CLONAL	1	TRUE	1	0.317131997749931	2		474	870	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911107	29911107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45542135	NA	P-0060177-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	167	736	0	ENST00000376809.5:c.406G>A	p.Gly136Arg	p.G136R	ENST00000376809	NM_002116.7	136	Ggg/Agg	3/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.317131997749931	2		736	934	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468224	50468224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060177-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	133	674	0	ENST00000331340.3:c.1459C>T	p.Arg487Cys	p.R487C	ENST00000331340	NM_006060.4	487	Cgt/Tgt	8/8	1	2	FACETS	0.87	0.789	0.955	0.87	0.789	0.955	CLONAL	1	TRUE	1	0.317131997749931	2		674	964	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874092	151874093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060177-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	125	600	0	ENST00000262189.6:c.8445dup	p.Ser2816IlefsTer6	p.S2816Ifs*6	ENST00000262189	NM_170606.2	2815	-/A	38/59	1	2	FACETS	0.956	0.865	1	0.956	0.865	1	CLONAL	1	TRUE	1	0.317131997749931	2		600	825	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741719	145741719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781314533	NA	P-0060177-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	173	773	0	ENST00000428558.2:c.784C>T	p.Arg262Trp	p.R262W	ENST00000428558	NM_004260.3	262	Cgg/Tgg	5/22	0.317131997749931	2	FACETS	0.952	0.875	1	0.476	0.437	0.517	CLONAL	1	TRUE	0	0.317131997749931	2		773	1146	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	35	445	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.271	0.221	0.327	0.271	0.221	0.327	SUBCLONAL	1	TRUE	1	0.432928271809595	2		445	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138729528	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	25	545	0	ENST00000269305.4:c.523C>T	p.Arg175Cys	p.R175C	ENST00000269305	NM_001126112.2	175	Cgc/Tgc	5/11	1	2	FACETS	0.124	0.097	0.155	0.124	0.097	0.155	SUBCLONAL	1	TRUE	1	0.432928271809595	2		545	933	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	182	478	4	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.432928271809595	2		482	776	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	425	699	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.92	0.879	0.961	1	0.997	1	CLONAL	2	TRUE	1	0.432928271809595	2		706	1067	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	110	388	2	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.776	0.698	0.858	0.776	0.698	0.858	SUBCLONAL	1	TRUE	1	0.432928271809595	2		390	655	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	201	482	3	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.993	0.921	1	0.993	0.921	1	CLONAL	1	TRUE	1	0.432928271809595	2		485	935	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	226	586	0	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.432928271809595	2		586	961	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205092	38205092	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	86	381	2	ENST00000317025.8:c.598del	p.Ser200AlafsTer20	p.S200Afs*20	ENST00000317025	NM_023034.1	200	Agc/gc	2/24	1	2	FACETS	0.672	0.595	0.754	0.672	0.595	0.754	SUBCLONAL	1	TRUE	1	0.432928271809595	2		383	591	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	173	415	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.432928271809595	2		415	748	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	149	503	2	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.879	0.804	0.958	0.879	0.804	0.958	CLONAL	1	TRUE	1	0.432928271809595	2		505	783	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691872	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs79375991	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	313	422	13	ENST00000295754.5:c.383del	p.Lys128SerfsTer35	p.K128Sfs*35	ENST00000295754	NM_003242.5	125	gAa/ga	3/7	1	2	FACETS	0.934	0.886	0.983	1	0.996	1	CLONAL	2	TRUE	1	0.432928271809595	2		435	774	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	45	530	2	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.239	0.2	0.283	0.239	0.2	0.283	SUBCLONAL	1	TRUE	1	0.432928271809595	2		532	870	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	20	174	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.362	0.277	0.461	0.362	0.277	0.461	SUBCLONAL	1	TRUE	1	0.432928271809595	2		174	255	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	239	671	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.432928271809595	2		671	913	SUCCESS
MAD2L2	10459	MSKCC	GRCh37	1	11736959	11736959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151024263	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	186	453	0	ENST00000235310.3:c.278G>A	p.Arg93His	p.R93H	ENST00000235310		93	cGc/cAc	7/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.432928271809595	2		453	752	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023501	27023501	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	232	466	0	ENST00000324856.7:c.607del	p.His203ThrfsTer29	p.H203Tfs*29	ENST00000324856	NM_006015.4	203	Cac/ac	1/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.432928271809595	2		466	909	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099479	27099479	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	163	445	0	ENST00000324856.7:c.3715+1G>A		p.X1239_splice	ENST00000324856	NM_006015.4	1239			1	2	FACETS	0.988	0.909	1	0.988	0.909	1	CLONAL	1	TRUE	1	0.432928271809595	2		445	762	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805671	43805671	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	54	442	0	ENST00000372470.3:c.727A>G	p.Ile243Val	p.I243V	ENST00000372470	NM_005373.2	243	Atc/Gtc	5/12	1	2	FACETS	0.308	0.262	0.358	0.308	0.262	0.358	SUBCLONAL	1	TRUE	1	0.432928271809595	2		442	810	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458490	120458490	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	263	624	0	ENST00000256646.2:c.6855G>T	p.Gln2285His	p.Q2285H	ENST00000256646	NM_024408.3	2285	caG/caT	34/34	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.432928271809595	2		624	1064	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551409	150551409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	238	544	0	ENST00000369026.2:c.598G>A	p.Gly200Ser	p.G200S	ENST00000369026	NM_021960.4	200	Ggc/Agc	1/3	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.432928271809595	2		544	1038	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231488893	231488894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs567805129	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	128	390	0	ENST00000295050.7:c.1263dup	p.Ile422TyrfsTer11	p.I422Yfs*11	ENST00000295050	NM_032018.5	419	aat/aaTt	5/5	1	2	FACETS	0.949	0.863	1	0.949	0.863	1	CLONAL	1	TRUE	1	0.432928271809595	2		390	623	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128642	64128642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	178	437	0	ENST00000334205.4:c.499G>A	p.Val167Met	p.V167M	ENST00000334205	NM_003942.2	167	Gtg/Atg	5/17	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.432928271809595	2		437	754	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200671	67200671	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1474951609	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	265	583	0	ENST00000312629.5:c.782A>G	p.Asp261Gly	p.D261G	ENST00000312629	NM_003952.2	261	gAc/gGc	9/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.432928271809595	2		583	1093	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998396	100998396	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	121	426	0	ENST00000325455.5:c.1406C>T	p.Pro469Leu	p.P469L	ENST00000325455	NM_001202474.3	469	cCg/cTg	1/8	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.432928271809595	2		426	529	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445976	49445976	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371421459	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	276	691	0	ENST00000301067.7:c.1490C>T	p.Pro497Leu	p.P497L	ENST00000301067	NM_003482.3	497	cCg/cTg	10/54	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.432928271809595	2		691	1103	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447773	49447773	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	129	504	0	ENST00000301067.7:c.661del	p.Ala221LeufsTer40	p.A221Lfs*40	ENST00000301067	NM_003482.3	221	Gct/ct	5/54	1	2	FACETS	0.715	0.649	0.786	0.715	0.649	0.786	SUBCLONAL	1	TRUE	1	0.432928271809595	2		504	833	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563152	21563152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774128777	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	206	655	0	ENST00000382592.4:c.767C>T	p.Pro256Leu	p.P256L	ENST00000382592	NM_014572.2	256	cCg/cTg	4/8	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.432928271809595	2		655	920	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133898	41133898	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	179	562	0	ENST00000379561.5:c.1730del	p.Gly577AlafsTer5	p.G577Afs*5	ENST00000379561	NM_002015.3	577	gGc/gc	2/3	1	2	FACETS	0.891	0.822	0.963	0.891	0.822	0.963	CLONAL	1	TRUE	1	0.432928271809595	2		562	928	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030368	49030368	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	62	291	3	ENST00000267163.4:c.1848del	p.Gly617ValfsTer6	p.G617Vfs*6	ENST00000267163	NM_000321.2	615	Aaa/aa	19/27	1	2	FACETS	0.586	0.507	0.671	0.586	0.507	0.671	SUBCLONAL	1	TRUE	1	0.432928271809595	2		294	489	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046660	30046660	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	124	355	0	ENST00000331968.5:c.2523C>A	p.Asp841Glu	p.D841E	ENST00000331968	NM_002742.2	841	gaC/gaA	18/18	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.432928271809595	2		355	505	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871633	35871634	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	298	395	0	ENST00000216797.5:c.872_873del	p.Thr291ArgfsTer15	p.T291Rfs*15	ENST00000216797	NM_020529.2	291	aCA/a	5/6	0.379852173187878	3	FACETS	0.986	0.932	1	0.986	0.932	1	CLONAL	2	TRUE	1	0.432928271809595	3		395	849	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961493	41961493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771815727	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	190	442	0	ENST00000219905.7:c.401G>A	p.Arg134His	p.R134H	ENST00000219905	NM_001164273.1	134	cGt/cAt	2/24	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.432928271809595	2		442	739	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576198	88576198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768882070	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	179	459	0	ENST00000360948.2:c.1475C>T	p.Ser492Leu	p.S492L	ENST00000360948	NM_001012338.2	492	tCg/tTg	13/19	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.432928271809595	2		459	779	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354548	91354548	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1173538137	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	186	488	1	ENST00000355112.3:c.3988A>C	p.Thr1330Pro	p.T1330P	ENST00000355112	NM_000057.2	1330	Acc/Ccc	21/22	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.432928271809595	2		489	819	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121909	2121909	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760489473	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	194	478	0	ENST00000219476.3:c.2071C>T	p.Arg691Cys	p.R691C	ENST00000219476	NM_000548.3	691	Cgc/Tgc	19/42	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.432928271809595	2		478	766	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127616	2127616	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	244	616	0	ENST00000219476.3:c.2855C>A	p.Pro952His	p.P952H	ENST00000219476	NM_000548.3	952	cCc/cAc	26/42	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.432928271809595	2		616	1017	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779211	3779211	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783507	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	90	459	3	ENST00000262367.5:c.5837del	p.Pro1946HisfsTer30	p.P1946Hfs*30	ENST00000262367	NM_004380.2	1946	cCa/ca	31/31	1	2	FACETS	0.635	0.563	0.711	0.635	0.563	0.711	SUBCLONAL	1	TRUE	1	0.432928271809595	2		462	655	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128304	30128304	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	251	619	0	ENST00000263025.4:c.928A>T	p.Met310Leu	p.M310L	ENST00000263025	NM_002746.2	310	Atg/Ttg	7/9	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.432928271809595	2		619	970	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217239	7217239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763892022	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	201	420	0	ENST00000380728.2:c.466C>T	p.Pro156Ser	p.P156S	ENST00000380728		156	Ccc/Tcc	6/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.432928271809595	2		420	848	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989705	15989705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759220419	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	54	440	0	ENST00000268712.3:c.3068G>A	p.Arg1023Gln	p.R1023Q	ENST00000268712	NM_006311.3	1023	cGg/cAg	23/46	1	2	FACETS	0.291	0.248	0.339	0.291	0.248	0.339	SUBCLONAL	1	TRUE	1	0.432928271809595	2		440	856	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490386	29490386	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	162	366	0	ENST00000356175.3:c.471T>G	p.Ile157Met	p.I157M	ENST00000356175	NM_000267.3	157	atT/atG	4/57	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.432928271809595	2		366	627	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30326005	30326005	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	87	399	0	ENST00000322652.5:c.2208del	p.Lys736AsnfsTer8	p.K736Nfs*8	ENST00000322652	NM_015355.2	735	Aaa/aa	16/16	1	2	FACETS	0.852	0.757	0.952	0.852	0.757	0.952	CLONAL	1	TRUE	1	0.432928271809595	2		399	472	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40874872	40874874	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	135	314	0	ENST00000428826.2:c.426_428del	p.Glu142del	p.E142del	ENST00000428826		142	gaAGAt/gat	6/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.432928271809595	2		314	588	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2202757	2202757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1171294668	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	167	408	0	ENST00000398665.3:c.766C>T	p.Arg256Trp	p.R256W	ENST00000398665	NM_032482.2	256	Cgg/Tgg	9/28	1	2	FACETS	0.966	0.888	1	0.966	0.888	1	CLONAL	1	TRUE	1	0.432928271809595	2		408	799	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222475	2222475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200919682	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	194	489	0	ENST00000398665.3:c.3307G>A	p.Val1103Met	p.V1103M	ENST00000398665	NM_032482.2	1103	Gtg/Atg	24/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.432928271809595	2		489	815	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099215	4099215	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	190	459	0	ENST00000262948.5:c.903del	p.Arg303AlafsTer24	p.R303Afs*24	ENST00000262948	NM_030662.3	301	ccC/cc	7/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.432928271809595	2		459	745	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214430	5214430	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773377919	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	204	559	0	ENST00000357368.4:c.4556C>T	p.Thr1519Met	p.T1519M	ENST00000357368	NM_002850.3	1519	aCg/aTg	30/38	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.432928271809595	2		559	815	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953360	17953360	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	230	565	0	ENST00000458235.1:c.626C>T	p.Thr209Met	p.T209M	ENST00000458235	NM_000215.3	209	aCg/aTg	6/24	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.432928271809595	2		565	927	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224677	36224677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199585947	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	56	552	0	ENST00000222270.7:c.7063C>T	p.Arg2355Trp	p.R2355W	ENST00000222270	NM_014727.1	2355	Cgg/Tgg	30/37	1	2	FACETS	0.256	0.218	0.298	0.256	0.218	0.298	SUBCLONAL	1	TRUE	1	0.432928271809595	2		552	1010	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743997	41743997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	52	598	0	ENST00000301178.4:c.932G>A	p.Cys311Tyr	p.C311Y	ENST00000301178	NM_021913.4	311	tGc/tAc	7/20	1	2	FACETS	0.232	0.197	0.272	0.232	0.197	0.272	SUBCLONAL	1	TRUE	1	0.432928271809595	2		598	1034	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917123	50917123	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	186	495	0	ENST00000440232.2:c.2375T>G	p.Leu792Arg	p.L792R	ENST00000440232	NM_002691.3	792	cTg/cGg	19/27	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.432928271809595	2		495	836	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250273	39250273	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	167	385	0	ENST00000402219.2:c.1296G>T	p.Trp432Cys	p.W432C	ENST00000402219	NM_005633.3	432	tgG/tgT	10/23	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.432928271809595	2		385	600	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574065	46574065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	211	550	1	ENST00000263734.3:c.80G>A	p.Arg27Gln	p.R27Q	ENST00000263734	NM_001430.4	27	cGg/cAg	2/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.432928271809595	2		551	883	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46602856	46602856	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	195	515	0	ENST00000263734.3:c.914G>A	p.Gly305Asp	p.G305D	ENST00000263734	NM_001430.4	305	gGc/gAc	8/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.432928271809595	2		515	824	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872742	136872742	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	184	559	1	ENST00000241393.3:c.756G>A	p.Trp252Ter	p.W252*	ENST00000241393	NM_003467.2	252	tgG/tgA	2/2	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.432928271809595	2		560	832	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149973	202149973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1272714323	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	221	603	0	ENST00000358485.4:c.1414C>T	p.Arg472Ter	p.R472*	ENST00000358485	NM_001080125.1	472	Cga/Tga	8/9	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.432928271809595	2		603	904	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295773	212295773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1299031105	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	136	432	0	ENST00000342788.4:c.2540G>A	p.Arg847His	p.R847H	ENST00000342788	NM_005235.2	847	cGt/cAt	21/28	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.432928271809595	2		432	610	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21349261	21349261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750813513	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	234	597	0	ENST00000215739.8:c.1888C>T	p.Arg630Trp	p.R630W	ENST00000215739	NM_006767.3	630	Cgg/Tgg	16/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.432928271809595	2		597	927	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29279864	29279864	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	73	207	0	ENST00000544604.2:c.110T>C	p.Leu37Pro	p.L37P	ENST00000544604	NM_001206998.1	37	cTg/cCg	1/9	1	2	FACETS	0.932	0.82	1	0.932	0.82	1	CLONAL	1	TRUE	1	0.432928271809595	2		207	362	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067912	30067912	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	161	456	0	ENST00000338641.4:c.1097A>C	p.Glu366Ala	p.E366A	ENST00000338641	NM_000268.3	366	gAa/gCa	11/16	1	2	FACETS	0.884	0.812	0.96	0.884	0.812	0.96	CLONAL	1	TRUE	1	0.432928271809595	2		456	841	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181460	38181460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1216607510	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	186	432	1	ENST00000396334.3:c.473C>T	p.Ala158Val	p.A158V	ENST00000396334	NM_002468.4	158	gCg/gTg	2/5	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.432928271809595	2		433	810	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114584	73114585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	61	287	0	ENST00000356692.5:c.971dup	p.Asn324LysfsTer7	p.N324Kfs*7	ENST00000356692		322	aga/agAa	9/9	1	2	FACETS	0.742	0.643	0.848	0.742	0.643	0.848	SUBCLONAL	1	TRUE	1	0.432928271809595	2		287	380	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665096	138665096	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs758370933	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	153	370	0	ENST00000330315.3:c.469C>G	p.Pro157Ala	p.P157A	ENST00000330315	NM_023067.3	157	Ccc/Gcc	1/1	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.432928271809595	2		370	584	SUCCESS
ATR	545	MSKCC	GRCh37	3	142285073	142285073	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	127	342	0	ENST00000350721.4:c.182C>G	p.Ser61Cys	p.S61C	ENST00000350721	NM_001184.3	61	tCt/tGt	3/47	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.432928271809595	2		342	517	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998128	169998128	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs753143066	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	121	331	0	ENST00000295797.4:c.826del	p.Thr276GlnfsTer7	p.T276Qfs*7	ENST00000295797	NM_002740.5	273	ttA/tt	9/18	1	2	FACETS	0.974	0.883	1	0.974	0.883	1	CLONAL	1	TRUE	1	0.432928271809595	2		331	574	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191245	185191245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	261	551	0	ENST00000265026.3:c.2126G>A	p.Arg709Lys	p.R709K	ENST00000265026	NM_004721.4	709	aGa/aAa	11/14	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.432928271809595	2		551	938	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521123	187521123	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	109	482	0	ENST00000441802.2:c.12032T>C	p.Leu4011Pro	p.L4011P	ENST00000441802	NM_005245.3	4011	cTg/cCg	22/27	1	2	FACETS	0.67	0.601	0.742	0.67	0.601	0.742	SUBCLONAL	1	TRUE	1	0.432928271809595	2		482	752	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961088	79961088	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	70	428	0	ENST00000265081.6:c.485T>C	p.Val162Ala	p.V162A	ENST00000265081	NM_002439.4	162	gTt/gCt	3/24	1	2	FACETS	0.511	0.445	0.582	0.511	0.445	0.582	SUBCLONAL	1	TRUE	1	0.432928271809595	2		428	633	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672384	86672384	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	88	240	0	ENST00000274376.6:c.2184+2T>C		p.X728_splice	ENST00000274376	NM_002890.2	728			1	2	FACETS	0.994	0.886	1	0.994	0.886	1	CLONAL	1	TRUE	1	0.432928271809595	2		240	409	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519337	176519337	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	243	484	0	ENST00000292408.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000292408	NM_213647.1	248	cGg/cTg	7/18	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.432928271809595	2		484	911	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519459	176519459	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1216312811	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	229	572	0	ENST00000292408.4:c.865A>G	p.Ile289Val	p.I289V	ENST00000292408	NM_213647.1	289	Atc/Gtc	7/18	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.432928271809595	2		572	887	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721267	176721267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745572501	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	216	535	1	ENST00000439151.2:c.6898G>A	p.Ala2300Thr	p.A2300T	ENST00000439151	NM_022455.4	2300	Gct/Act	23/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.432928271809595	2		536	880	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911060	29911060	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs199474480	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	115	436	0	ENST00000376809.5:c.359A>G	p.Gln120Arg	p.Q120R	ENST00000376809	NM_002116.7	120	cAg/cGg	3/8	1	2	FACETS	0.694	0.626	0.767	0.694	0.626	0.767	SUBCLONAL	1	TRUE	1	0.432928271809595	2		436	765	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911140	29911140	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	196	369	0	ENST00000376809.5:c.439T>A	p.Tyr147Asn	p.Y147N	ENST00000376809	NM_002116.7	147	Tac/Aac	3/8	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.432928271809595	2		369	660	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323371	31323371	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	200	411	1	ENST00000412585.2:c.620-2A>G		p.X207_splice	ENST00000412585	NM_005514.6	207			0.422668742201058	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.432928271809595	1		412	625	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31939964	31939964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	234	539	0	ENST00000375333.2:c.191G>A	p.Arg64His	p.R64H	ENST00000375333	NM_032454.1	64	cGt/cAt	1/8	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.432928271809595	2		539	929	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33290643	33290643	+	5_prime_UTR_variant	5'UTR	SNP	G	G	C	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	123	195	0	ENST00000374542.5:c.-57C>G		p.*19*	ENST00000374542	NM_001141970.1	-/740		1/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.432928271809595	2		195	431	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553281	106553281	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	251	637	0	ENST00000369096.4:c.1251del	p.Tyr418ThrfsTer3	p.Y418Tfs*3	ENST00000369096	NM_001198.3	416	Ccc/cc	5/7	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.432928271809595	2		637	1029	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405953	157405954	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1554294674	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	223	565	0	ENST00000346085.5:c.2201dup	p.Ser736IlefsTer27	p.S736Ifs*27	ENST00000346085	NM_020732.3	732	ccg/ccGg	6/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.432928271809595	2		565	1004	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355311	81355311	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	112	343	0	ENST00000222390.5:c.1063C>T	p.Arg355Ter	p.R355*	ENST00000222390	NM_000601.4	355	Cga/Tga	9/18	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.432928271809595	2		343	512	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520087	106520087	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774448553	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	101	328	0	ENST00000359195.3:c.2515C>T	p.Arg839Cys	p.R839C	ENST00000359195	NM_002649.2	839	Cgc/Tgc	6/11	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.432928271809595	2		328	457	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124499021	124499021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	54	295	0	ENST00000357628.3:c.692G>A	p.Arg231Lys	p.R231K	ENST00000357628	NM_015450.2	231	aGa/aAa	9/19	1	2	FACETS	0.775	0.665	0.893	0.775	0.665	0.893	SUBCLONAL	1	TRUE	1	0.432928271809595	2		295	322	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148516765	148516765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	37	401	0	ENST00000320356.2:c.922C>T	p.Pro308Ser	p.P308S	ENST00000320356	NM_004456.4	308	Ccc/Tcc	9/20	1	2	FACETS	0.304	0.25	0.365	0.304	0.25	0.365	SUBCLONAL	1	TRUE	1	0.432928271809595	2		401	562	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958387	90958387	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	62	218	0	ENST00000265433.3:c.2051A>T	p.Asn684Ile	p.N684I	ENST00000265433	NM_002485.4	684	aAt/aTt	13/16	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.432928271809595	2		218	248	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2181665	2181665	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	76	210	0	ENST00000349721.2:c.4354del	p.Ile1452Ter	p.I1452*	ENST00000349721	NM_003070.3	1450	Aaa/aa	30/34	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.432928271809595	2		210	336	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436613	8436613	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	44	293	0	ENST00000356435.5:c.4065G>C	p.Leu1355Phe	p.L1355F	ENST00000356435		1355	ttG/ttC	24/35	1	2	FACETS	0.504	0.424	0.593	0.504	0.424	0.593	SUBCLONAL	1	TRUE	1	0.432928271809595	2		293	403	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486116	8486116	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	163	489	0	ENST00000356435.5:c.2701G>T	p.Val901Leu	p.V901L	ENST00000356435		901	Gtg/Ttg	17/35	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.432928271809595	2		489	725	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202933	27202933	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	33	405	0	ENST00000380036.4:c.2025G>T	p.Lys675Asn	p.K675N	ENST00000380036	NM_000459.3	675	aaG/aaT	13/23	0.432928271809595	1	FACETS	0.222	0.18	0.269	0.222	0.18	0.269	SUBCLONAL	1	TRUE	0	0.432928271809595	1		405	539	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231263	98231263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502291	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	118	601	1	ENST00000331920.6:c.2020G>A	p.Val674Met	p.V674M	ENST00000331920	NM_000264.3	674	Gtg/Atg	14/24	1	2	FACETS	0.516	0.464	0.57	0.516	0.464	0.57	SUBCLONAL	1	TRUE	1	0.432928271809595	2		602	1057	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932438	39932438	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	77	575	0	ENST00000378444.4:c.2161G>T	p.Gly721Trp	p.G721W	ENST00000378444	NM_001123385.1	721	Ggg/Tgg	4/15	1	2	FACETS	0.385	0.337	0.437	0.385	0.337	0.437	SUBCLONAL	1	TRUE	1	0.432928271809595	2		575	923	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247136	53247139	+	frameshift_variant	Frame_Shift_Del	DEL	CCTC	CCTC	-	novel	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	117	430	0	ENST00000375401.3:c.361_364del	p.Glu121LysfsTer16	p.E121Kfs*16	ENST00000375401	NM_004187.3	121	GAGGaa/aa	4/26	1	2	FACETS	0.773	0.698	0.853	0.773	0.698	0.853	SUBCLONAL	1	TRUE	1	0.432928271809595	2		430	699	SUCCESS
AR	367	MSKCC	GRCh37	X	66765290	66765290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777689173	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	178	549	0	ENST00000374690.3:c.302G>A	p.Arg101His	p.R101H	ENST00000374690	NM_000044.3	101	cGt/cAt	1/8	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.432928271809595	2		549	794	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099982	157099987	+	inframe_deletion	In_Frame_Del	DEL	GGCGGC	GGCGGC	-	rs587779747	NA	P-0060179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	131	631	0	ENST00000346085.5:c.939_944del	p.Gly318_Gly319del	p.G318_G319del	ENST00000346085	NM_020732.3	307	GGCGGC/-	1/20	1	2	FACETS	0.61	0.553	0.671	0.61	0.553	0.671	SUBCLONAL	1	TRUE	1	0.432928271809595	2		631	992	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	91	279	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.951	0.848	1	0.951	0.848	1	CLONAL	1	TRUE	1	0.432144255433386	2		279	443	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	176	372	2	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.432144255433386	2		374	771	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	69	343	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.432144255433386	1	FACETS	0.888	0.781	1	0.888	0.781	1	CLONAL	1	TRUE	0	0.432144255433386	1		343	282	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429978	78429978	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	128	322	1	ENST00000370768.2:c.901del	p.Ile301TyrfsTer22	p.I301Yfs*22	ENST00000370768	NM_003902.3	301	Ata/ta	11/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.432144255433386	2		323	560	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	231	518	2	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.957	0.892	1	0.957	0.892	1	CLONAL	1	TRUE	1	0.432144255433386	2		520	1117	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435291	110435291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	224	1233	0	ENST00000375856.3:c.3110C>T	p.Ala1037Val	p.A1037V	ENST00000375856	NM_003749.2	1037	gCc/gTc	1/2	1	2	FACETS	0.882	0.82	0.946	0.882	0.82	0.946	CLONAL	1	TRUE	1	0.432144255433386	2		1233	1175	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349641	89349641	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs772267579	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	165	584	5	ENST00000301030.4:c.3309del	p.Asp1104MetfsTer214	p.D1104Mfs*214	ENST00000301030	NM_001256183.1	1103	aaA/aa	9/13	1	2	FACETS	0.964	0.887	1	0.964	0.887	1	CLONAL	1	TRUE	1	0.432144255433386	2		589	792	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514302	69514302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1255340343	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	211	806	0	ENST00000294312.3:c.379C>T	p.Arg127Cys	p.R127C	ENST00000294312	NM_005117.2	127	Cgc/Tgc	3/3	1	2	FACETS	0.983	0.913	1	0.983	0.913	1	CLONAL	1	TRUE	1	0.432144255433386	2		806	993	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004242	29004242	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766441216	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	133	592	0	ENST00000282397.4:c.1051C>T	p.Arg351Trp	p.R351W	ENST00000282397	NM_002019.4	351	Cgg/Tgg	8/30	1	2	FACETS	0.726	0.659	0.796	0.726	0.659	0.796	SUBCLONAL	1	TRUE	1	0.432144255433386	2		592	848	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435612	110435612	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1240327417	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	174	914	0	ENST00000375856.3:c.2789G>A	p.Arg930His	p.R930H	ENST00000375856	NM_003749.2	930	cGc/cAc	1/2	1	2	FACETS	0.892	0.821	0.965	0.892	0.821	0.965	CLONAL	1	TRUE	1	0.432144255433386	2		914	903	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916726	178916726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772110575	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	68	308	0	ENST00000263967.3:c.113G>A	p.Arg38His	p.R38H	ENST00000263967	NM_006218.2	38	cGt/cAt	2/21	0.432144255433386	1	FACETS	0.86	0.755	0.97	0.86	0.755	0.97	CLONAL	1	TRUE	0	0.432144255433386	1		308	287	SUCCESS
APC	324	MSKCC	GRCh37	5	112173902	112173902	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1554084299	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	174	539	0	ENST00000257430.4:c.2612del	p.Gly871GlufsTer45	p.G871Efs*45	ENST00000257430	NM_000038.5	871	Gga/ga	16/16	1	2	FACETS	0.941	0.867	1	0.941	0.867	1	CLONAL	1	TRUE	1	0.432144255433386	2		539	856	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052626	42052626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	247	805	0	ENST00000219905.7:c.7297C>T	p.Arg2433Trp	p.R2433W	ENST00000219905	NM_001164273.1	2433	Cgg/Tgg	20/24	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.432144255433386	2		805	1090	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	364637	364637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774810442	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	201	844	0	ENST00000262320.3:c.925G>A	p.Gly309Ser	p.G309S	ENST00000262320	NM_003502.3	309	Ggc/Agc	3/11	1	2	FACETS	0.962	0.892	1	0.962	0.892	1	CLONAL	1	TRUE	1	0.432144255433386	2		844	967	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	145	524	4	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	1	2	FACETS	0.912	0.833	0.994	0.912	0.833	0.994	CLONAL	1	TRUE	1	0.432144255433386	2		528	736	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	232	1195	1	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	0.93	0.867	0.996	0.93	0.867	0.996	CLONAL	1	TRUE	1	0.432144255433386	2		1196	1154	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286254	66286255	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	49	283	0	ENST00000273854.3:c.1431dup	p.Gly478ArgfsTer26	p.G478Rfs*26	ENST00000273854	NM_004439.5	477	-/A	6/18	1	2	FACETS	0.646	0.549	0.752	0.646	0.549	0.752	SUBCLONAL	1	TRUE	1	0.432144255433386	2		283	351	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096314	2096314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767591879	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	193	840	1	ENST00000219066.1:c.193C>T	p.Arg65Cys	p.R65C	ENST00000219066	NM_002528.5	65	Cgt/Tgt	2/6	1	2	FACETS	0.939	0.869	1	0.939	0.869	1	CLONAL	1	TRUE	1	0.432144255433386	2		841	951	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43699735	43699735	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137879443	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	251	765	2	ENST00000382044.4:c.5780C>T	p.Thr1927Met	p.T1927M	ENST00000382044	NM_001141980.1	1927	aCg/aTg	28/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.432144255433386	2		767	1065	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24133959	24133959	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398122368	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	173	684	1	ENST00000263121.7:c.110G>A	p.Arg37His	p.R37H	ENST00000263121	NM_003073.3	37	cGt/cAt	2/9	1	2	FACETS	0.892	0.821	0.965	0.892	0.821	0.965	CLONAL	1	TRUE	1	0.432144255433386	2		685	898	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860074	57860075	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs759448855	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	158	902	1	ENST00000228682.2:c.821dup	p.Cys275LeufsTer32	p.C275Lfs*32	ENST00000228682	NM_005269.2	272	tgg/tGgg	8/12	1	2	FACETS	0.7	0.64	0.762	0.7	0.64	0.762	SUBCLONAL	1	TRUE	1	0.432144255433386	2		903	1045	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526312	189526312	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	244	1027	0	ENST00000264731.3:c.576G>A	p.Trp192Ter	p.W192*	ENST00000264731	NM_003722.4	192	tgG/tgA	4/14	1	2	FACETS	0.937	0.875	1	0.937	0.875	1	CLONAL	1	TRUE	1	0.432144255433386	2		1027	1205	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324717	31324717	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs41555918	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	34	157	0	ENST00000412585.2:c.91T>C	p.Tyr31His	p.Y31H	ENST00000412585	NM_005514.6	31	Tat/Cat	2/8	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.432144255433386	2		157	142	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272113	38272113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	193	756	0	ENST00000425967.3:c.2105C>T	p.Ala702Val	p.A702V	ENST00000425967	NM_001174067.1	702	gCa/gTa	16/19	1	2	FACETS	0.999	0.925	1	0.999	0.925	1	CLONAL	1	TRUE	1	0.432144255433386	2		756	894	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981832	63981832	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	217	1078	2	ENST00000398590.3:c.2340del	p.Thr781ProfsTer11	p.T781Pfs*11	ENST00000398590	NM_001177387.1	778	ggC/gg	12/14	1	2	FACETS	0.829	0.77	0.891	0.829	0.77	0.891	CLONAL	1	TRUE	1	0.432144255433386	2		1080	1211	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007298	143007298	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs199647396	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	45	244	1	ENST00000262992.4:c.2486C>T	p.Thr829Met	p.T829M	ENST00000262992	NM_001101669.1	829	aCg/aTg	22/24	1	2	FACETS	0.618	0.521	0.724	0.618	0.521	0.724	SUBCLONAL	1	TRUE	1	0.432144255433386	2		245	337	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446263	70446263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1282920941	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	209	805	0	ENST00000373644.4:c.5203G>A	p.Glu1735Lys	p.E1735K	ENST00000373644	NM_030625.2	1735	Gag/Aag	11/12	1	2	FACETS	0.929	0.862	0.999	0.929	0.862	0.999	CLONAL	1	TRUE	1	0.432144255433386	2		805	1041	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911540	114911540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	153	521	0	ENST00000543371.1:c.1058C>T	p.Pro353Leu	p.P353L	ENST00000543371	NM_001198531.1	353	cCt/cTt	10/14	1	2	FACETS	0.963	0.883	1	0.963	0.883	1	CLONAL	1	TRUE	1	0.432144255433386	2		521	735	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425109	49425109	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	219	1103	0	ENST00000301067.7:c.13379A>G	p.His4460Arg	p.H4460R	ENST00000301067	NM_003482.3	4460	cAt/cGt	39/54	1	2	FACETS	0.924	0.859	0.991	0.924	0.859	0.991	CLONAL	1	TRUE	1	0.432144255433386	2		1103	1097	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039420	49039420	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	167	425	0	ENST00000267163.4:c.2405G>T	p.Gly802Val	p.G802V	ENST00000267163	NM_000321.2	802	gGg/gTg	23/27	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.432144255433386	2		425	643	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988220	36988220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749580337	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	203	851	0	ENST00000354822.5:c.433G>A	p.Gly145Ser	p.G145S	ENST00000354822	NM_001079668.2	145	Ggc/Agc	2/3	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.432144255433386	2		851	864	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701105	29701105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771006452	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	206	700	0	ENST00000356175.3:c.8389G>A	p.Ala2797Thr	p.A2797T	ENST00000356175	NM_000267.3	2797	Gca/Aca	57/57	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.432144255433386	2		700	926	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511573	38511573	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	215	874	0	ENST00000254066.5:c.1071G>T	p.Glu357Asp	p.E357D	ENST00000254066	NM_000964.3	357	gaG/gaT	8/9	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.432144255433386	2		874	934	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224045	36224045	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	213	1072	0	ENST00000222270.7:c.6595C>T	p.Gln2199Ter	p.Q2199*	ENST00000222270	NM_014727.1	2199	Caa/Taa	28/37	1	2	FACETS	0.903	0.838	0.97	0.903	0.838	0.97	CLONAL	1	TRUE	1	0.432144255433386	2		1072	1092	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707965	47707965	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	98	327	0	ENST00000233146.2:c.2589T>G	p.Tyr863Ter	p.Y863*	ENST00000233146	NM_000251.2	863	taT/taG	15/16	1	2	FACETS	0.889	0.796	0.987	0.889	0.796	0.987	CLONAL	1	TRUE	1	0.432144255433386	2		327	510	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595963	52595963	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	181	613	0	ENST00000394830.3:c.3952G>T	p.Gly1318Cys	p.G1318C	ENST00000394830	NM_018313.4	1318	Ggc/Tgc	26/30	1	2	FACETS	0.91	0.839	0.983	0.91	0.839	0.983	CLONAL	1	TRUE	1	0.432144255433386	2		613	921	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444651	187444651	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772115541	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	215	862	0	ENST00000232014.4:c.1576C>T	p.Arg526Cys	p.R526C	ENST00000232014	NM_001130845.1	526	Cgc/Tgc	7/10	1	2	FACETS	0.988	0.918	1	0.988	0.918	1	CLONAL	1	TRUE	1	0.432144255433386	2		862	1007	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1296259	1296259	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	225	920	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.432144255433386	2		920	1008	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627187	86627187	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	163	459	0	ENST00000274376.6:c.562A>G	p.Arg188Gly	p.R188G	ENST00000274376	NM_002890.2	188	Aga/Gga	2/25	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.432144255433386	2		459	694	SUCCESS
APC	324	MSKCC	GRCh37	5	112175776	112175789	+	frameshift_variant	Frame_Shift_Del	DEL	TACTCCAGATGGAT	TACTCCAGATGGAT	-	novel	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	179	577	0	ENST00000257430.4:c.4486_4499del	p.Thr1496PhefsTer13	p.T1496Ffs*13	ENST00000257430	NM_000038.5	1495	agTACTCCAGATGGATtt/agtt	16/16	1	2	FACETS	0.896	0.826	0.968	0.896	0.826	0.968	CLONAL	1	TRUE	1	0.432144255433386	2		577	925	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542669	141542669	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777477236	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	206	775	0	ENST00000220592.5:c.2317C>T	p.Arg773Cys	p.R773C	ENST00000220592	NM_012154.3	773	Cgt/Tgt	18/19	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.432144255433386	2		775	913	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485313	8485313	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	73	232	0	ENST00000356435.5:c.3067A>T	p.Asn1023Tyr	p.N1023Y	ENST00000356435		1023	Aat/Tat	18/35	1	2	FACETS	0.936	0.824	1	0.936	0.824	1	CLONAL	1	TRUE	1	0.432144255433386	2		232	361	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855228	76855228	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060181-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	53	79	0	ENST00000373344.5:c.5759T>C	p.Met1920Thr	p.M1920T	ENST00000373344	NM_000489.3	1920	aTg/aCg	24/35	1	1	FACETS	0.782	0.687	0.878	1	0.974	1	SUBCLONAL	2	TRUE	0	0.432144255433386	1		79	123	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0060190-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	31	300	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.150978976415059	3	FACETS	0.558	0.451	0.679	0.279	0.225	0.34	INDETERMINATE	1	TRUE	1	0.31	3		300	414	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0060190-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	22	527	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.186	0.143	0.236	0.186	0.143	0.236	SUBCLONAL	1	TRUE	1	0.31	2		528	765	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602822	10602822	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	151	730	0	ENST00000171111.5:c.756G>T	p.Trp252Cys	p.W252C	ENST00000171111	NM_203500.1	252	tgG/tgT	3/6	0.696582452912896	1	FACETS	0.996	0.931	1	0.996	0.931	1	CLONAL	1	TRUE	0	0.699132150682793	1		730	282	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681707	78681707	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	8	485	0	ENST00000306801.3:c.415C>T	p.Arg139Cys	p.R139C	ENST00000306801	NM_020761.2	139	Cgc/Tgc	4/34	1	2	FACETS	0.067	0.042	0.098	0.067	0.042	0.098	SUBCLONAL	1	TRUE	1	0.699132150682793	2		485	343	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843676	156843676	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	169	878	0	ENST00000524377.1:c.1102G>T	p.Gly368Cys	p.G368C	ENST00000524377	NM_002529.3	368	Ggc/Tgc	8/17	0.344789146457534	5	FACETS	1	0.984	1	0.425	0.391	0.46	INDETERMINATE	1	TRUE	2	0.699132150682793	5		878	777	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180925	108180925	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	43	316	0	ENST00000278616.4:c.5801T>G	p.Leu1934Arg	p.L1934R	ENST00000278616	NM_000051.3	1934	cTg/cGg	39/63	0.699132150682793	2	FACETS	0.843	0.744	0.938	0.843	0.744	0.938	CLONAL	2	TRUE	0	0.699132150682793	2		316	73	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560533	65560533	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1435018573	NA	P-0060191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	73	442	0	ENST00000358664.4:c.64G>T	p.Ala22Ser	p.A22S	ENST00000358664	NM_002382.4	22	Gct/Tct	3/5	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.699132150682793	2		442	208	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532582	63532582	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	151	724	0	ENST00000307078.5:c.1997A>G	p.Asn666Ser	p.N666S	ENST00000307078	NM_004655.3	666	aAc/aGc	8/11	1	2	FACETS	0.887	0.817	0.959	0.887	0.817	0.959	CLONAL	1	TRUE	1	0.699132150682793	2		724	487	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178574	32178574	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	86	609	0	ENST00000375023.3:c.2820G>T	p.Gln940His	p.Q940H	ENST00000375023	NM_004557.3	940	caG/caT	18/30	1	2	FACETS	0.794	0.709	0.882	0.794	0.709	0.882	SUBCLONAL	1	TRUE	1	0.699132150682793	2		609	310	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481392	140481393	+	inframe_insertion	In_Frame_Ins	INS	-	-	TAGACTGTTCCAAATGATCCA	novel	NA	P-0060191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	11	335	0	ENST00000288602.6:c.1395_1415dup	p.Gly466_Tyr472dup	p.G466_Y472dup	ENST00000288602	NM_004333.4	466	tac/taTGGATCATTTGGAACAGTCTAc	11/18	1	2	FACETS	0.354	0.247	0.483	0.354	0.247	0.483	SUBCLONAL	1	TRUE	1	0.699132150682793	2		335	89	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	26	475	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.708	0.564	0.871	0.708	0.564	0.871	SUBCLONAL	1	FALSE	1	0.348017205832249	2		475	211	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	115	300	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.317402171200714	4	FACETS	1	0.963	1	0.746	0.678	0.817	CLONAL	2	FALSE	1	0.348017205832249	4		300	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	144	652	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.348017205832249	2		652	630	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058033	27058033	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	155	707	0	ENST00000324856.7:c.1741C>T	p.Gln581Ter	p.Q581*	ENST00000324856	NM_006015.4	581	Cag/Tag	3/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.348017205832249	2		707	739	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	80	814	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	1	2	FACETS	0.651	0.573	0.735	0.651	0.573	0.735	SUBCLONAL	1	FALSE	1	0.348017205832249	2		814	706	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091123	29091123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659827	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	22	315	0	ENST00000328354.6:c.1367C>T	p.Ser456Leu	p.S456L	ENST00000328354	NM_007194.3	456	tCa/tTa	12/15	1	2	FACETS	0.461	0.358	0.581	0.461	0.358	0.581	SUBCLONAL	1	FALSE	1	0.348017205832249	2		315	274	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546620	9546620	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764351685	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	68	601	0	ENST00000353224.5:c.1402G>A	p.Glu468Lys	p.E468K	ENST00000353224	NM_177990.2	468	Gag/Aag	5/10	0.348017205832249	2	FACETS	0.621	0.54	0.709	0.311	0.27	0.355	SUBCLONAL	1	FALSE	0	0.348017205832249	2		601	629	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458729	120458729	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	183	838	0	ENST00000256646.2:c.6616G>T	p.Glu2206Ter	p.E2206*	ENST00000256646	NM_024408.3	2206	Gaa/Taa	34/34	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.348017205832249	2		838	793	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652777	212652777	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	57	423	0	ENST00000342788.4:c.529C>T	p.Leu177Phe	p.L177F	ENST00000342788	NM_005235.2	177	Ctt/Ttt	4/28	0.248736852031597	2	FACETS	1	0.901	1	0.527	0.455	0.604	CLONAL	1	FALSE	0	0.348017205832249	2		423	311	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853195	68853195	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886039590	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	149	552	0	ENST00000261769.5:c.1578G>A	p.Trp526Ter	p.W526*	ENST00000261769	NM_004360.3	526	tgG/tgA	11/16	0.348017205832249	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	0	0.348017205832249	1		552	544	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416552	49416552	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	138	704	0	ENST00000301067.7:c.16159C>T	p.Gln5387Ter	p.Q5387*	ENST00000301067	NM_003482.3	5387	Cag/Tag	51/54	0.309962728496216	3	FACETS	0.767	0.7	0.836	0.767	0.7	0.836	SUBCLONAL	2	FALSE	1	0.348017205832249	3		704	607	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835952	151835952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	117	539	0	ENST00000262189.6:c.14572G>A	p.Glu4858Lys	p.E4858K	ENST00000262189	NM_170606.2	4858	Gaa/Aaa	58/59	0.241315519724945	4	FACETS	1	0.984	1	0.738	0.667	0.813	CLONAL	1	FALSE	2	0.348017205832249	4		539	614	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030213	180030213	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	47	753	0	ENST00000261937.6:c.4071C>A	p.Phe1357Leu	p.F1357L	ENST00000261937	NM_182925.4	1357	ttC/ttA	30/30	1	2	FACETS	0.543	0.458	0.637	0.543	0.458	0.637	SUBCLONAL	1	FALSE	1	0.348017205832249	2		753	497	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082599	16082599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	73	420	0	ENST00000281043.3:c.413G>A	p.Arg138His	p.R138H	ENST00000281043	NM_005378.4	138	cGc/cAc	2/3	0.309962728496216	3	FACETS	0.789	0.696	0.888	0.789	0.696	0.888	SUBCLONAL	2	FALSE	1	0.348017205832249	3		420	312	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857808	9857808	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	71	802	0	ENST00000330684.3:c.3593C>G	p.Ser1198Cys	p.S1198C	ENST00000330684	NM_001134407.1	1198	tCc/tGc	13/13	1	2	FACETS	0.567	0.495	0.646	0.567	0.495	0.646	SUBCLONAL	1	FALSE	1	0.348017205832249	2		802	719	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875031	151875031	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	93	408	0	ENST00000262189.6:c.7507C>T	p.Gln2503Ter	p.Q2503*	ENST00000262189	NM_170606.2	2503	Cag/Tag	38/59	0.241315519724945	4	FACETS	1	0.974	1	0.66	0.588	0.736	CLONAL	1	FALSE	2	0.348017205832249	4		408	546	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438033	438033	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	281	487	0	ENST00000399788.2:c.1936G>A	p.Glu646Lys	p.E646K	ENST00000399788	NM_001042603.1	646	Gaa/Aaa	14/28	0.185220800412954	3	FACETS	1	0.99	1			1	INDETERMINATE	2	FALSE	NA	0.348017205832249	3		487	783	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057775	27057775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	97	747	0	ENST00000324856.7:c.1483C>T	p.His495Tyr	p.H495Y	ENST00000324856	NM_006015.4	495	Cat/Tat	3/20	1	2	FACETS	0.687	0.612	0.767	0.687	0.612	0.767	SUBCLONAL	1	FALSE	1	0.348017205832249	2		747	811	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678029	58678029	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	47	744	0	ENST00000305921.3:c.254C>G	p.Ser85Trp	p.S85W	ENST00000305921	NM_003620.3	85	tCg/tGg	1/6	0.241315519724945	4	FACETS	0.549	0.462	0.645	0.275	0.231	0.323	SUBCLONAL	1	FALSE	2	0.348017205832249	4		744	663	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866415	56866415	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	111	504	0	ENST00000519728.1:c.662G>C	p.Arg221Thr	p.R221T	ENST00000519728	NM_002350.3	221	aGa/aCa	8/13	0.241315519724945	4	FACETS	1	0.981	1	0.707	0.637	0.781	CLONAL	1	FALSE	2	0.348017205832249	4		504	608	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045495	47045495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	68	753	0	ENST00000377604.3:c.2462G>A	p.Arg821His	p.R821H	ENST00000377604	NM_001204468.1	821	cGc/cAc	22/24	0.248736852031597	2	FACETS	0.744	0.648	0.848	0.372	0.324	0.424	SUBCLONAL	1	FALSE	0	0.348017205832249	2		753	525	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400947	72400947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	117	561	0	ENST00000357731.5:c.224C>T	p.Ser75Leu	p.S75L	ENST00000357731	NM_173808.2	75	tCa/tTa	2/7	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.348017205832249	2		561	608	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984425	201984425	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	64	638	0	ENST00000359651.3:c.1090G>T	p.Glu364Ter	p.E364*	ENST00000359651		364	Gaa/Taa	8/8	1	2	FACETS	0.623	0.54	0.714	0.623	0.54	0.714	SUBCLONAL	1	FALSE	1	0.348017205832249	2		638	590	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828165	243828165	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	15	267	0	ENST00000263826.5:c.193G>C	p.Glu65Gln	p.E65Q	ENST00000263826	NM_005465.4	65	Gaa/Caa	3/13	1	2	FACETS	0.302	0.221	0.401	0.302	0.221	0.401	SUBCLONAL	1	FALSE	1	0.348017205832249	2		267	285	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156698	2156698	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	37	810	0	ENST00000434045.2:c.224C>A	p.Ala75Asp	p.A75D	ENST00000434045	NM_001127598.1	75	gCc/gAc	3/5	1	2	FACETS	0.392	0.322	0.469	0.392	0.322	0.469	SUBCLONAL	1	FALSE	1	0.348017205832249	2		810	543	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205277	61205277	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	113	514	0	ENST00000301761.2:c.217G>C	p.Glu73Gln	p.E73Q	ENST00000301761	NM_017841.2	73	Gag/Cag	2/4	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.348017205832249	2		514	536	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416563	49416563	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	144	713	0	ENST00000301067.7:c.16148C>G	p.Ser5383Cys	p.S5383C	ENST00000301067	NM_003482.3	5383	tCc/tGc	51/54	0.309962728496216	3	FACETS	0.79	0.723	0.86	0.79	0.723	0.86	SUBCLONAL	2	FALSE	1	0.348017205832249	3		713	615	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641538	23641538	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	116	541	0	ENST00000261584.4:c.1937G>C	p.Arg646Thr	p.R646T	ENST00000261584	NM_024675.3	646	aGa/aCa	5/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.348017205832249	2		541	508	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673790	37673791	+	missense_variant	Missense_Mutation	DNP	CT	CT	TC	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	116	438	0	ENST00000447079.4:c.2944_2945delinsTC	p.Leu982Ser	p.L982S	ENST00000447079	NM_015083.1	982	CTa/TCa	10/14	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.348017205832249	2		438	595	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55674255	55674255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	76	432	0	ENST00000284073.2:c.481G>T	p.Glu161Ter	p.E161*	ENST00000284073	NM_138962.2	161	Gaa/Taa	8/14	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	FALSE	1	0.348017205832249	2		432	433	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821946	59821946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	19	277	0	ENST00000259008.2:c.2104G>A	p.Glu702Lys	p.E702K	ENST00000259008	NM_032043.2	702	Gaa/Aaa	15/20	0.241315519724945	4	FACETS	0.562	0.427	0.72	0.281	0.213	0.36	SUBCLONAL	1	FALSE	2	0.348017205832249	4		277	262	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78933959	78933959	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	103	737	0	ENST00000306801.3:c.3559G>A	p.Asp1187Asn	p.D1187N	ENST00000306801	NM_020761.2	1187	Gac/Aac	30/34	0.195033821085572	1	FACETS	0.914	0.821	1	0.914	0.821	1	INDETERMINATE	1	FALSE	0	0.348017205832249	1		737	535	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18964156	18964156	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	43	533	0	ENST00000262803.5:c.1153G>T	p.Asp385Tyr	p.D385Y	ENST00000262803	NM_002911.3	385	Gat/Tat	8/24	1	2	FACETS	0.618	0.518	0.728	0.618	0.518	0.728	SUBCLONAL	1	FALSE	1	0.348017205832249	2		533	400	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47601063	47601063	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	150	541	0	ENST00000263735.4:c.301G>C	p.Glu101Gln	p.E101Q	ENST00000263735	NM_002354.2	101	Gag/Cag	3/9	0.309962728496216	3	FACETS	1	0.983	1	0.651	0.596	0.709	CLONAL	1	FALSE	1	0.348017205832249	3		541	777	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346678	225346678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	65	342	0	ENST00000264414.4:c.1960G>A	p.Glu654Lys	p.E654K	ENST00000264414	NM_003590.4	654	Gaa/Aaa	14/16	0.248736852031597	2	FACETS	1	0.969	1	0.689	0.604	0.78	CLONAL	1	FALSE	0	0.348017205832249	2		342	271	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346768	225346768	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	104	383	0	ENST00000264414.4:c.1870G>C	p.Glu624Gln	p.E624Q	ENST00000264414	NM_003590.4	624	Gaa/Caa	14/16	0.248736852031597	2	FACETS	0.844	0.763	0.928	0.844	0.763	0.928	CLONAL	2	FALSE	0	0.348017205832249	2		383	354	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40738983	40738983	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	32	563	0	ENST00000373198.4:c.3301G>T	p.Val1101Phe	p.V1101F	ENST00000373198	NM_133170.3	1101	Gtc/Ttc	24/32	0.348017205832249	2	FACETS	0.36	0.291	0.437	0.18	0.145	0.219	SUBCLONAL	1	FALSE	0	0.348017205832249	2		563	511	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523629	41523629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	159	693	0	ENST00000263253.7:c.1045C>T	p.His349Tyr	p.H349Y	ENST00000263253	NM_001429.3	349	Cac/Tac	4/31	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.348017205832249	2		693	775	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652165	36652183	+	frameshift_variant	Frame_Shift_Del	DEL	GCACCTCACCTGCTCTGCT	GCACCTCACCTGCTCTGCT	-	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	62	769	0	ENST00000244741.5:c.290_308del	p.Thr97ArgfsTer45	p.T97Rfs*45	ENST00000244741	NM_000389.4	96	gGCACCTCACCTGCTCTGCTg/gg	2/3	0.348017205832249	3	FACETS	0.701	0.605	0.804	0.35	0.302	0.402	SUBCLONAL	1	FALSE	1	0.348017205832249	3		769	597	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92355095	92355095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	112	468	0	ENST00000265734.4:c.382C>T	p.Gln128Ter	p.Q128*	ENST00000265734	NM_001259.6	128	Cag/Tag	4/8	0.241315519724945	4	FACETS	1	0.98	1	0.683	0.616	0.754	CLONAL	1	FALSE	2	0.348017205832249	4		468	635	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2054661	2054661	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	125	445	0	ENST00000349721.2:c.1111G>C	p.Asp371His	p.D371H	ENST00000349721	NM_003070.3	371	Gat/Cat	6/34	0.192263962097428	3	FACETS	1	0.984	1	0.722	0.656	0.791	INDETERMINATE	1	FALSE	1	0.348017205832249	3		445	584	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456693	32456693	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	69	674	0	ENST00000332351.3:c.199C>T	p.Gln67Ter	p.Q67*	ENST00000332351	NM_024426.4	67	Cag/Tag	1/10	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	FALSE	1	0.348017205832249	2		674	379	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779172	135779172	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203631	NA	P-0060193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	119	1325	0	ENST00000298552.3:c.2074C>T	p.Arg692Ter	p.R692*	ENST00000298552	NM_001162426.1	692	Cga/Tga	17/23	0.489350211072299	2	FACETS	0.973	0.897	1	0.973	0.897	1	CLONAL	2	TRUE	0	0.489350211072299	2		1325	250	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0060193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	35	499	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.872	0.743	1	1	0.966	1	CLONAL	2	TRUE	1	0.489350211072299	2		499	82	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577537	7577538	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0060193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	167	1320	1	ENST00000269305.4:c.743_744delinsTT	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGG/cTT	7/11	NA	2	FACETS	0.91	0.861	0.957			1	INDETERMINATE	3	TRUE	NA	0.489350211072299	2		1321	250	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786887	135786887	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554817388	NA	P-0060193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	16	1136	0	ENST00000298552.3:c.982C>T	p.Gln328Ter	p.Q328*	ENST00000298552	NM_001162426.1	328	Cag/Tag	10/23	0.489350211072299	2	FACETS	0.237	0.175	0.311	0.118	0.087	0.156	SUBCLONAL	1	TRUE	0	0.489350211072299	2		1136	276	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983140	201983141	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0060193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	110	1512	0	ENST00000359651.3:c.991dup	p.Arg331ProfsTer140	p.R331Pfs*140	ENST00000359651		330	agc/agCc	7/8	0.425504015443293	5	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.489350211072299	5		1512	542	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534792	18534792	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	76	1142	0	ENST00000266497.5:c.1850A>G	p.Gln617Arg	p.Q617R	ENST00000266497		617	cAg/cGg	12/31	0.427082408910554	3	FACETS	1	0.963	1			1	CLONAL	1	TRUE	NA	0.489350211072299	3		1142	315	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415657	49415657	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0060193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	101	1195	0	ENST00000301067.7:c.16522-2A>G		p.X5508_splice	ENST00000301067	NM_003482.3	5508			0.493308146544673	3	FACETS	0.914	0.829	1	0.914	0.829	1	CLONAL	2	TRUE	1	0.489350211072299	3		1195	281	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435996	49435997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0060193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	68	1471	0	ENST00000301067.7:c.5984dup	p.Leu1996ThrfsTer4	p.L1996Tfs*4	ENST00000301067	NM_003482.3	1995	gga/ggGa	28/54	0.493308146544673	3	FACETS	1	0.952	1	0.588	0.516	0.665	CLONAL	1	TRUE	1	0.489350211072299	3		1471	294	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422005	47422005	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	240	1484	0	ENST00000404338.3:c.73G>T	p.Glu25Ter	p.E25*	ENST00000404338	NM_004491.4	25	Gag/Tag	1/6	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.489350211072299	2		1484	401	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196880	106196880	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	19	1194	0	ENST00000380013.4:c.5213C>G	p.Ser1738Cys	p.S1738C	ENST00000380013	NM_001127208.2	1738	tCt/tGt	11/11	0.174167260469733	4	FACETS	0.519	0.395	0.664	0.259	0.197	0.332	INDETERMINATE	1	TRUE	2	0.489350211072299	4		1194	223	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197895	123197896	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0060193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	46	424	0	ENST00000218089.9:c.2020dup	p.Gln674ProfsTer4	p.Q674Pfs*4	ENST00000218089	NM_001042749.1	673	-/C	20/35	0.492239924277063	2	FACETS	0.847	0.754	0.935			1	CLONAL	3	TRUE	NA	0.489350211072299	2		424	74	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73350199	73350199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	52	511	0	ENST00000377767.4:c.686C>T	p.Ser229Leu	p.S229L	ENST00000377767	NM_014953.3	229	tCa/tTa	5/21	0.316250407431543	3	FACETS	0.98	0.856	1	0.653	0.571	0.738	CLONAL	2	TRUE	0	0.489350211072299	3		511	135	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29099530	29099530	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	31	617	0	ENST00000328354.6:c.871T>G	p.Phe291Val	p.F291V	ENST00000328354	NM_007194.3	291	Ttt/Gtt	8/15	0.413411977831224	3	FACETS	1	0.927	1			1	CLONAL	1	TRUE	NA	0.489350211072299	3		617	124	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779172	135779172	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203631	NA	P-0060193-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	88	1325	0	ENST00000298552.3:c.2074C>T	p.Arg692Ter	p.R692*	ENST00000298552	NM_001162426.1	692	Cga/Tga	17/23	0.603608985302127	2	FACETS	0.959	0.88	1	0.959	0.88	1	CLONAL	2	TRUE	0	0.603608985302127	2		1325	152	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0060193-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	22	499	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.603608985302127	2		499	57	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577537	7577538	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0060193-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	110	1320	1	ENST00000269305.4:c.743_744delinsTT	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGG/cTT	7/11	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	2	TRUE	NA	0.603608985302127	2		1321	161	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786887	135786887	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554817388	NA	P-0060193-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	9	1136	0	ENST00000298552.3:c.982C>T	p.Gln328Ter	p.Q328*	ENST00000298552	NM_001162426.1	328	Cag/Tag	10/23	0.603608985302127	2	FACETS	0.134	0.088	0.192	0.067	0.044	0.096	SUBCLONAL	1	TRUE	0	0.603608985302127	2		1136	223	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983140	201983141	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0060193-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	95	1512	0	ENST00000359651.3:c.991dup	p.Arg331ProfsTer140	p.R331Pfs*140	ENST00000359651		330	agc/agCc	7/8	0.603608985302127	9	FACETS	1	0.963	1			1	CLONAL	2	TRUE	NA	0.603608985302127	9		1512	420	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534792	18534792	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060193-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	71	1142	0	ENST00000266497.5:c.1850A>G	p.Gln617Arg	p.Q617R	ENST00000266497		617	cAg/cGg	12/31	0.603608985302127	3	FACETS	1	0.959	1			1	CLONAL	1	TRUE	NA	0.603608985302127	3		1142	255	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415657	49415657	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0060193-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	92	1195	0	ENST00000301067.7:c.16522-2A>G		p.X5508_splice	ENST00000301067	NM_003482.3	5508			0.603608985302127	3	FACETS	0.898	0.814	0.983	0.898	0.814	0.983	CLONAL	2	TRUE	1	0.603608985302127	3		1195	221	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435996	49435997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0060193-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	54	1471	0	ENST00000301067.7:c.5984dup	p.Leu1996ThrfsTer4	p.L1996Tfs*4	ENST00000301067	NM_003482.3	1995	gga/ggGa	28/54	0.603608985302127	3	FACETS	1	0.912	1	0.537	0.464	0.614	CLONAL	1	TRUE	1	0.603608985302127	3		1471	217	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422005	47422005	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060193-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	206	1484	0	ENST00000404338.3:c.73G>T	p.Glu25Ter	p.E25*	ENST00000404338	NM_004491.4	25	Gag/Tag	1/6	0.603608985302127	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.603608985302127	3		1484	267	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196880	106196880	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060193-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	2	1194	0	ENST00000380013.4:c.5213C>G	p.Ser1738Cys	p.S1738C	ENST00000380013	NM_001127208.2	1738	tCt/tGt	11/11	0.205771033844156	3	FACETS	0.058	0.022	0.12	0.029	0.011	0.06	INDETERMINATE	1	TRUE	1	0.603608985302127	3		1194	149	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197895	123197896	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0060193-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	86	424	0	ENST00000218089.9:c.2020dup	p.Gln674ProfsTer4	p.Q674Pfs*4	ENST00000218089	NM_001042749.1	673	-/C	20/35	0.416674194450856	2	FACETS	1	0.968	1			1	CLONAL	2	TRUE	NA	0.603608985302127	2		424	130	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73350199	73350199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060193-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	69	511	0	ENST00000377767.4:c.686C>T	p.Ser229Leu	p.S229L	ENST00000377767	NM_014953.3	229	tCa/tTa	5/21	0.603608985302127	2	FACETS	0.969	0.879	1	0.969	0.879	1	CLONAL	2	TRUE	0	0.603608985302127	2		511	118	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29099530	29099530	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060193-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	58	617	0	ENST00000328354.6:c.871T>G	p.Phe291Val	p.F291V	ENST00000328354	NM_007194.3	291	Ttt/Gtt	8/15	NA	2	FACETS	0.775	0.688	0.863			1	INDETERMINATE	2	TRUE	NA	0.603608985302127	2		617	124	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	65	475	0				ENST00000310581	NM_198253.2	-/1132			0.269850009344654	3	FACETS	1	0.948	1	0.592	0.514	0.675	CLONAL	1	FALSE	1	0.269850009344654	3		475	462	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0060194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	62	356	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	FALSE	1	0.269850009344654	2		356	402	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164913	106164913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs898441677	NA	P-0060194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	46	640	0	ENST00000380013.4:c.3781C>T	p.Arg1261Cys	p.R1261C	ENST00000380013	NM_001127208.2	1261	Cgc/Tgc	6/11	1	2	FACETS	0.435	0.365	0.512	0.435	0.365	0.512	SUBCLONAL	1	FALSE	1	0.269850009344654	2		640	784	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469086	25469086	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	74	626	3	ENST00000264709.3:c.1372del	p.Arg458GlyfsTer193	p.R458Gfs*193	ENST00000264709	NM_175629.2	458	Cgg/gg	11/23	1	2	FACETS	0.648	0.566	0.737	0.648	0.566	0.737	SUBCLONAL	1	FALSE	1	0.269850009344654	2		629	846	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424627	47424627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	145	372	0	ENST00000404338.3:c.2695G>A	p.Asp899Asn	p.D899N	ENST00000404338	NM_004491.4	899	Gac/Aac	1/6	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.269850009344654	2		372	761	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0060195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	65	244	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.470502746662071	1	FACETS	0.78	0.683	0.882	0.78	0.683	0.882	SUBCLONAL	1	TRUE	0	0.470502746662071	1		244	271	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971203	21971204	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	252	625	0	ENST00000304494.5:c.154dup	p.Met52AsnfsTer68	p.M52Nfs*68	ENST00000304494	NM_000077.4	52	atg/aAtg	2/3	0.470502746662071	1	FACETS	0.937	0.879	0.997	0.937	0.879	0.997	CLONAL	1	TRUE	0	0.470502746662071	1		625	874	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778192	3778192	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	380	751	1	ENST00000262367.5:c.6856A>T	p.Asn2286Tyr	p.N2286Y	ENST00000262367	NM_004380.2	2286	Aac/Tac	31/31	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.470502746662071	2		752	1387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578447	7578460	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCATGGCGCGGA	GGCCATGGCGCGGA	-	novel	NA	P-0060195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	306	663	0	ENST00000269305.4:c.470_483del	p.Val157AspfsTer19	p.V157Dfs*19	ENST00000269305	NM_001126112.2	157	gTCCGCGCCATGGCC/g	5/11	0.470502746662071	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.470502746662071	1		663	972	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440910	56440914	+	frameshift_variant	Frame_Shift_Del	DEL	CAGTG	CAGTG	-	novel	NA	P-0060195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	332	621	0	ENST00000407977.2:c.423_427del	p.Thr142GlyfsTer6	p.T142Gfs*6	ENST00000407977		141	atCACTGag/atag	4/10	0.470502746662071	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.470502746662071	1		621	963	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534320	63534320	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0060195-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	385	807	0	ENST00000307078.5:c.1200+1G>T		p.X400_splice	ENST00000307078	NM_004655.3	400			0.470502746662071	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.470502746662071	1		807	1072	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0060196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	15	289	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.249754537565747	3	FACETS	0.643	0.473	0.844	0.322	0.236	0.422	SUBCLONAL	1	TRUE	1	0.38657750706897	3		289	144	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0060196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	21	388	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.635	0.493	0.799	0.635	0.493	0.799	SUBCLONAL	1	TRUE	1	0.38657750706897	2		388	171	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	13	554	0	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	0.163098567981374	3	FACETS	0.472	0.338	0.635	0.236	0.169	0.318	INDETERMINATE	1	TRUE	1	0.38657750706897	3		554	170	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021817	71021817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs797045586	NA	P-0060196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	23	441	0	ENST00000318789.4:c.1541G>A	p.Arg514His	p.R514H	ENST00000318789	NM_032682.5	514	cGt/cAt	18/21	1	2	FACETS	0.809	0.638	1	0.809	0.638	1	CLONAL	1	TRUE	1	0.38657750706897	2		441	147	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473722	67473722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs794727798	NA	P-0060196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	20	583	0	ENST00000327367.4:c.802C>T	p.Arg268Cys	p.R268C	ENST00000327367	NM_005902.3	268	Cgc/Tgc	6/9	0.206104361058667	2	FACETS	0.676	0.521	0.854	0.338	0.26	0.427	INDETERMINATE	1	TRUE	0	0.38657750706897	2		583	153	SUCCESS
APC	324	MSKCC	GRCh37	5	112174236	112174236	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	27	489	0	ENST00000257430.4:c.2945C>A	p.Ser982Ter	p.S982*	ENST00000257430	NM_000038.5	982	tCg/tAg	16/16	0.163098567981374	3	FACETS	1	0.92	1	0.651	0.526	0.789	INDETERMINATE	1	TRUE	1	0.38657750706897	3		489	128	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168975	11168975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329240441	NA	P-0060196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	11	439	0	ENST00000358026.2:c.4565C>T	p.Ser1522Leu	p.S1522L	ENST00000358026	NM_001128849.1	1522	tCg/tTg	32/36	1	2	FACETS	0.379	0.263	0.523	0.379	0.263	0.523	SUBCLONAL	1	TRUE	1	0.38657750706897	2		439	150	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230561605	230561605	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0060197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	147	759	0				ENST00000391860	NM_001258311.1	-/409			0.538594999523372	3	FACETS	1	0.98	1	0.608	0.557	0.66	CLONAL	1	TRUE	1	0.538594999523372	3		759	570	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692851	89692852	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0060197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	58	162	0	ENST00000371953.3:c.336_337dup	p.Ser113LysfsTer22	p.S113Kfs*22	ENST00000371953	NM_000314.4	112	cta/ctAAa	5/9	0.538594999523372	2	FACETS	0.905	0.805	1	0.905	0.805	1	CLONAL	2	TRUE	0	0.538594999523372	2		162	119	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881455	48881456	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	178	316	0	ENST00000267163.4:c.179dup	p.Leu60PhefsTer50	p.L60Ffs*50	ENST00000267163	NM_000321.2	59	-/T	2/27	0.538594999523372	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.538594999523372	2		316	313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0060197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	469	838	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.538594999523372	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.538594999523372	2		838	718	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320939	30320939	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	221	396	0	ENST00000322652.5:c.1349G>A	p.Cys450Tyr	p.C450Y	ENST00000322652	NM_015355.2	450	tGc/tAc	12/16	0.538594999523372	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.538594999523372	2		396	390	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629157	14629157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	134	632	0	ENST00000254322.2:c.5G>A	p.Gly2Asp	p.G2D	ENST00000254322	NM_006145.1	2	gGt/gAt	1/3	0.538594999523372	3	FACETS	0.998	0.909	1	0.499	0.454	0.545	CLONAL	1	TRUE	1	0.538594999523372	3		632	633	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167595	24167595	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	147	597	0	ENST00000263121.7:c.979G>T	p.Ala327Ser	p.A327S	ENST00000263121	NM_003073.3	327	Gcc/Tcc	7/9	0.538594999523372	2	FACETS	1	0.958	1	0.533	0.49	0.578	CLONAL	1	TRUE	0	0.538594999523372	2		597	512	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247373	153247373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	284	543	0	ENST00000281708.4:c.1429G>A	p.Gly477Ser	p.G477S	ENST00000281708	NM_033632.3	477	Ggt/Agt	10/12	0.538594999523372	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.538594999523372	2		543	481	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911112	29911112	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs41540615	NA	P-0060197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	375	799	0	ENST00000376809.5:c.411C>G	p.Tyr137Ter	p.Y137*	ENST00000376809	NM_002116.7	137	taC/taG	3/8	0.538594999523372	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.538594999523372	3		799	777	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31238100	31238100	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	221	497	0	ENST00000376228.5:c.782G>A	p.Gly261Glu	p.G261E	ENST00000376228	NM_002117.5	261	gGa/gAa	4/8	0.538594999523372	3	FACETS	0.864	0.817	0.91	1	0.992	1	CLONAL	3	TRUE	1	0.538594999523372	3		497	402	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341720	8341720	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	241	544	0	ENST00000356435.5:c.4920T>G	p.Asn1640Lys	p.N1640K	ENST00000356435		1640	aaT/aaG	29/35	0.170411328008833	3	FACETS	1	0.949	1	0.671	0.633	0.711	INDETERMINATE	2	TRUE	0	0.538594999523372	3		544	564	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225360597	225360598	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	G	novel	NA	P-0060197-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	186	353	0	ENST00000264414.4:c.1793_1794delinsC	p.Gln598ProfsTer2	p.Q598Pfs*2	ENST00000264414	NM_003590.4	598	cAG/cC	13/16	0.538594999523372	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.538594999523372	3		353	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0060204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	350	573	1	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	0.731356976150158	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.826842598288537	1		574	484	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47503744	47503746	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1387779417	NA	P-0060204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	801	854	2	ENST00000404338.3:c.4307_4309del	p.Phe1436del	p.F1436del	ENST00000404338	NM_004491.4	1433	ccCTTc/ccc	6/6	1	2	FACETS	0.927	0.908	0.946	1	0.998	1	CLONAL	2	TRUE	1	0.826842598288537	2		856	1045	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057874	27057874	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	451	933	0	ENST00000324856.7:c.1582C>T	p.Gln528Ter	p.Q528*	ENST00000324856	NM_006015.4	528	Cag/Tag	3/20	0.795980763244268	1	FACETS	0.991	0.959	1	0.991	0.959	1	CLONAL	1	TRUE	0	0.826842598288537	1		933	646	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073532	8073533	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0060204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	427	642	0	ENST00000377482.5:c.1126dup	p.Val376GlyfsTer9	p.V376Gfs*9	ENST00000377482	NM_018948.3	376	gtt/gGtt	4/4	0.82394522142245	1	FACETS	0.982	0.95	1	0.982	0.95	1	CLONAL	1	TRUE	0	0.826842598288537	1		642	617	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057868	27057868	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	456	929	0	ENST00000324856.7:c.1576C>T	p.Pro526Ser	p.P526S	ENST00000324856	NM_006015.4	526	Cca/Tca	3/20	0.795980763244268	1	FACETS	0.998	0.968	1	0.998	0.968	1	CLONAL	1	TRUE	0	0.826842598288537	1		929	648	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672260	86672265	+	inframe_deletion	In_Frame_Del	DEL	GAATGG	GAATGG	-	novel	NA	P-0060204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	297	597	0	ENST00000274376.6:c.2062_2067del	p.Glu688_Trp689del	p.E688_W689del	ENST00000274376	NM_002890.2	688	GAATGG/-	16/25	1	2	FACETS	0.966	0.914	1	0.966	0.914	1	CLONAL	1	TRUE	1	0.826842598288537	2		597	744	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401621	401621	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780902340	NA	P-0060204-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	478	883	0	ENST00000380956.4:c.943G>A	p.Val315Met	p.V315M	ENST00000380956	NM_001195286.1	315	Gtg/Atg	7/9	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.826842598288537	2		883	1127	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0060205-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	236	458	0	ENST00000269305.4:c.673-2A>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.788328643247796	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	FALSE	0	0.788328643247796	2		458	287	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141568583	141568583	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0060205-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	205	569	0	ENST00000220592.5:c.878+1G>A		p.X293_splice	ENST00000220592	NM_012154.3	293			0.746921413349675	5	FACETS	1	0.984	1	0.241	0.223	0.259	CLONAL	1	FALSE	0	0.788328643247796	5		569	942	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937619	17937619	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060205-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	175	567	0	ENST00000458235.1:c.3308G>T	p.Arg1103Leu	p.R1103L	ENST00000458235	NM_000215.3	1103	cGg/cTg	24/24	0.740490860166157	4	FACETS	1	0.96	1	0.531	0.49	0.574	CLONAL	1	FALSE	2	0.788328643247796	4		567	747	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116185	67116185	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060205-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	185	439	0	ENST00000412916.2:c.469G>C	p.Asp157His	p.D157H	ENST00000412916		157	Gac/Cac	5/6	0.319590468927112	6	FACETS	1	0.988	1	0.339	0.312	0.366	INDETERMINATE	1	FALSE	2	0.788328643247796	6		439	893	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725037	162725037	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060205-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	37	651	0	ENST00000367921.3:c.509C>A	p.Thr170Asn	p.T170N	ENST00000367921	NM_006182.2	170	aCc/aAc	6/18	0.693654030059086	3	FACETS	0.196	0.161	0.236	0.098	0.08	0.118	SUBCLONAL	1	FALSE	1	0.788328643247796	3		651	667	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252136	226252136	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs888157382	NA	P-0060205-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	47	161	0	ENST00000366813.1:c.84G>C	p.Lys28Asn	p.K28N	ENST00000366813		28	aaG/aaC	1/3	0.700571562803191	5	FACETS	0.982	0.835	1	0.246	0.208	0.286	CLONAL	1	FALSE	1	0.788328643247796	5		161	265	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231488944	231488944	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060205-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	225	456	0	ENST00000295050.7:c.1307A>G	p.Tyr436Cys	p.Y436C	ENST00000295050	NM_032018.5	436	tAt/tGt	5/5	0.700571562803191	5	FACETS	0.976	0.915	1	0.488	0.457	0.52	CLONAL	2	FALSE	1	0.788328643247796	5		456	638	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432944	432944	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768484697	NA	P-0060205-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	50	351	1	ENST00000399788.2:c.1972G>A	p.Val658Ile	p.V658I	ENST00000399788	NM_001042603.1	658	Gtc/Atc	15/28	0.640693041509158	6	FACETS	0.43	0.363	0.503			1	SUBCLONAL	1	FALSE	NA	0.788328643247796	6		352	761	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991955	72991955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1487650687	NA	P-0060205-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	111	615	0	ENST00000268489.5:c.2090C>T	p.Pro697Leu	p.P697L	ENST00000268489	NM_006885.3	697	cCg/cTg	2/10	0.319590468927112	6	FACETS	1	0.967	1	0.293	0.263	0.323	INDETERMINATE	1	FALSE	2	0.788328643247796	6		615	620	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674351	86674366	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTGAGGTAAGAATTTA	GTGAGGTAAGAATTTA	-	novel	NA	P-0060205-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	107	251	0	ENST00000274376.6:c.2483_2487+11del		p.X828_splice	ENST00000274376	NM_002890.2	828		18/25	0.788328643247796	2	FACETS	0.87	0.813	0.925	0.87	0.813	0.925	CLONAL	2	FALSE	0	0.788328643247796	2		251	156	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004907	150004907	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1372462435	NA	P-0060205-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	353	610	0	ENST00000253339.5:c.1318C>G	p.Pro440Ala	p.P440A	ENST00000253339		440	Cca/Gca	3/7	0.788328643247796	2	FACETS	0.98	0.949	1	0.98	0.949	1	CLONAL	2	FALSE	0	0.788328643247796	2		610	457	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864854	117864854	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060205-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	318	420	0	ENST00000297338.2:c.1255G>C	p.Glu419Gln	p.E419Q	ENST00000297338	NM_006265.2	419	Gaa/Caa	10/14	0.788328643247796	7	FACETS	1	0.99	1	0.593	0.56	0.626	CLONAL	2	FALSE	3	0.788328643247796	7		420	1011	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0060206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	117	300	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.423059945848355	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.423059945848355	2		300	265	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659675	NA	P-0060206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	214	461	0	ENST00000269305.4:c.764T>C	p.Ile255Thr	p.I255T	ENST00000269305	NM_001126112.2	255	aTc/aCc	7/11	0.423059945848355	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.423059945848355	2		461	458	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	10	381	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.423059945848355	1	FACETS	0.134	0.09	0.189	0.134	0.09	0.189	SUBCLONAL	1	TRUE	0	0.423059945848355	1		381	279	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591925	48591925	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	44	476	0	ENST00000342988.3:c.1088G>T	p.Cys363Phe	p.C363F	ENST00000342988	NM_005359.5	363	tGt/tTt	9/12	0.423059945848355	1	FACETS	0.497	0.418	0.583	0.497	0.418	0.583	SUBCLONAL	1	TRUE	0	0.423059945848355	1		476	330	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150923064	150923064	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	120	474	0	ENST00000271640.5:c.1711C>G	p.Leu571Val	p.L571V	ENST00000271640	NM_001145415.1	571	Ctt/Gtt	13/22	0.285931617036782	3	FACETS	1	0.979	1	0.639	0.579	0.701	CLONAL	1	TRUE	1	0.423059945848355	3		474	538	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649861	88649861	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	59	207	0	ENST00000372037.3:c.110C>A	p.Ser37Ter	p.S37*	ENST00000372037	NM_004329.2	37	tCa/tAa	4/13	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.423059945848355	2		207	234	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440705	56440706	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	265	562	0	ENST00000407977.2:c.512dup	p.Leu172AlafsTer16	p.L172Afs*16	ENST00000407977		171	aag/aaAg	5/10	0.423059945848355	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.423059945848355	2		562	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	174	590	1	ENST00000269305.4:c.403del	p.Cys135AlafsTer35	p.C135Afs*35	ENST00000269305	NM_001126112.2	135	Tgc/gc	5/11	0.648785575139062	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.648785575139062	1		591	341	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692948	89692951	+	frameshift_variant	Frame_Shift_Del	DEL	ATTT	ATTT	-	novel	NA	P-0060207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	100	326	0	ENST00000371953.3:c.432_435del	p.Lys144AsnfsTer2	p.K144Nfs*2	ENST00000371953	NM_000314.4	144	aaATTT/aa	5/9	0.256193037062399	1	FACETS	1	0.957	1	1	0.957	1	INDETERMINATE	1	TRUE	0	0.648785575139062	1		326	195	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274665	198274665	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	198	462	0	ENST00000335508.6:c.733C>G	p.Pro245Ala	p.P245A	ENST00000335508	NM_012433.2	245	Cct/Gct	7/25	0.531239723223108	3	FACETS	0.837	0.783	0.891	0.837	0.783	0.891	CLONAL	2	TRUE	1	0.648785575139062	3		462	483	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434545	121434545	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1343874863	NA	P-0060208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	135	631	0	ENST00000257555.6:c.1309G>A	p.Gly437Ser	p.G437S	ENST00000257555		437	Ggc/Agc	6/10	0.122326789373137	3	FACETS	1	0.969	1	1	0.989	1	INDETERMINATE	3	TRUE	1	0.24	3		631	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587780070	NA	P-0060209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	302	735	0	ENST00000269305.4:c.535C>A	p.His179Asn	p.H179N	ENST00000269305	NM_001126112.2	179	Cat/Aat	5/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	1	0.701523497512731	2		735	860	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725098	89725098	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	40	93	0	ENST00000371953.3:c.1081A>T	p.Ser361Cys	p.S361C	ENST00000371953	NM_000314.4	361	Agt/Tgt	9/9	1	2	FACETS	0.884	0.751	1	0.884	0.751	1	CLONAL	1	FALSE	1	0.701523497512731	2		93	129	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967661	90967661	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs863224713	NA	P-0060209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	141	354	0	ENST00000265433.3:c.1247T>C	p.Met416Thr	p.M416T	ENST00000265433	NM_002485.4	416	aTg/aCg	10/16	0.701523497512731	4	FACETS	0.969	0.884	1	0.323	0.294	0.353	CLONAL	1	FALSE	1	0.701523497512731	4		354	706	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651180	206651180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	270	688	0	ENST00000367120.3:c.790C>T	p.Pro264Ser	p.P264S	ENST00000367120	NM_014002.3	264	Ccc/Tcc	8/22	0.768637657761355	3	FACETS	1	0.967	1	0.521	0.49	0.554	CLONAL	1	TRUE	1	0.792964982557833	3		688	912	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434961	49434961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	439	646	0	ENST00000301067.7:c.6592C>T	p.Pro2198Ser	p.P2198S	ENST00000301067	NM_003482.3	2198	Ccc/Tcc	31/54	0.793263594182364	4	FACETS	1	0.967	1			1	CLONAL	2	TRUE	NA	0.792964982557833	4		646	982	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910459	32910459	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	171	317	0	ENST00000380152.3:c.1967C>G	p.Thr656Ser	p.T656S	ENST00000380152		656	aCt/aGt	11/27	0.726385168311854	4	FACETS	0.809	0.751	0.868	0.809	0.751	0.868	CLONAL	2	TRUE	2	0.792964982557833	4		317	478	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858648	9858648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	407	651	0	ENST00000330684.3:c.2753C>T	p.Pro918Leu	p.P918L	ENST00000330684	NM_001134407.1	918	cCc/cTc	13/13	0.792964982557833	2	FACETS	0.997	0.969	1	0.997	0.969	1	CLONAL	2	TRUE	0	0.792964982557833	2		651	515	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646797	23646797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	261	423	0	ENST00000261584.4:c.1070C>T	p.Ser357Phe	p.S357F	ENST00000261584	NM_024675.3	357	tCt/tTt	4/13	0.792964982557833	2	FACETS	0.946	0.91	0.98	0.946	0.91	0.98	CLONAL	2	TRUE	0	0.792964982557833	2		423	348	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992378	72992378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	486	608	0	ENST00000268489.5:c.1667C>T	p.Ser556Phe	p.S556F	ENST00000268489	NM_006885.3	556	tCt/tTt	2/10	0.792964982557833	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.792964982557833	2		608	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	1056	681	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.793263594182364	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	4	TRUE	0	0.792964982557833	4		681	1179	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1623954	1623954	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370431685	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	345	420	0	ENST00000344749.5:c.545C>T	p.Ser182Phe	p.S182F	ENST00000344749	NM_001136139.2	182	tCc/tTc	8/19	0.792964982557833	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.792964982557833	2		420	413	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231452	5231453	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	478	596	0	ENST00000357368.4:c.2023_2024delinsTT	p.Pro675Phe	p.P675F	ENST00000357368	NM_002850.3	675	CCc/TTc	14/38	0.792964982557833	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.792964982557833	2		596	569	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142914	7142914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	540	592	0	ENST00000302850.5:c.2455C>T	p.Arg819Cys	p.R819C	ENST00000302850	NM_000208.2	819	Cgc/Tgc	12/22	0.792964982557833	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.792964982557833	2		592	652	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389219	31389219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	241	495	0	ENST00000328111.2:c.2132C>T	p.Ser711Leu	p.S711L	ENST00000328111	NM_006892.3	711	tCa/tTa	19/23	0.726385168311854	4	FACETS	1	0.953	1	0.513	0.478	0.548	CLONAL	1	TRUE	2	0.792964982557833	4		495	1063	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721131	39721131	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	114	423	0	ENST00000361337.2:c.634C>T	p.Pro212Ser	p.P212S	ENST00000361337	NM_003286.2	212	Cct/Tct	9/21	0.726385168311854	4	FACETS	0.758	0.683	0.837	0.379	0.341	0.419	SUBCLONAL	1	TRUE	2	0.792964982557833	4		423	680	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748610	40748610	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	228	364	0	ENST00000373198.4:c.2906G>A	p.Gly969Glu	p.G969E	ENST00000373198	NM_133170.3	969	gGa/gAa	21/32	0.726385168311854	4	FACETS	0.838	0.786	0.891	0.838	0.786	0.891	CLONAL	2	TRUE	2	0.792964982557833	4		364	615	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770600	40770600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159844	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	386	506	0	ENST00000373198.4:c.2782G>A	p.Glu928Lys	p.E928K	ENST00000373198	NM_133170.3	928	Gag/Aag	19/32	0.726385168311854	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	2	0.792964982557833	4		506	871	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419939	41419939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	575	617	0	ENST00000373198.4:c.382G>A	p.Gly128Ser	p.G128S	ENST00000373198	NM_133170.3	128	Ggt/Agt	3/32	0.726385168311854	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.792964982557833	4		617	1278	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21341812	21341812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	511	558	0	ENST00000215739.8:c.340C>T	p.Pro114Ser	p.P114S	ENST00000215739	NM_006767.3	114	Cca/Tca	4/21	0.414359865754429	5	FACETS	1	0.995	1	0.817	0.785	0.85	INDETERMINATE	2	TRUE	2	0.792964982557833	5		558	1151	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29442812	29442812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	234	596	0	ENST00000544604.2:c.853C>T	p.Leu285Phe	p.L285F	ENST00000544604	NM_001206998.1	285	Ctc/Ttc	6/9	0.414359865754429	5	FACETS	1	0.966	1	0.352	0.328	0.378	INDETERMINATE	1	TRUE	2	0.792964982557833	5		596	1222	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458329	12458329	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1364613522	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	587	564	0	ENST00000287820.6:c.946C>T	p.Arg316Cys	p.R316C	ENST00000287820	NM_015869.4	316	Cgc/Tgc	6/7	0.768637657761355	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.792964982557833	3		564	973	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981675	63981675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767416994	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	276	647	0	ENST00000398590.3:c.2177C>T	p.Ser726Phe	p.S726F	ENST00000398590	NM_001177387.1	726	tCt/tTt	12/14	0.768637657761355	3	FACETS	1	0.972	1	0.528	0.496	0.56	CLONAL	1	TRUE	1	0.792964982557833	3		647	921	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803723	1803723	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	194	597	0	ENST00000260795.2:c.901G>A	p.Asp301Asn	p.D301N	ENST00000260795		301	Gac/Aac	6/17	1	2	FACETS	0.973	0.908	1	0.973	0.908	1	CLONAL	1	TRUE	1	0.792964982557833	2		597	503	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155278	55155278	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	343	484	0	ENST00000257290.5:c.2877A>T	p.Lys959Asn	p.K959N	ENST00000257290	NM_006206.4	959	aaA/aaT	21/23	0.793263594182364	4	FACETS	0.918	0.873	0.964	0.918	0.873	0.964	CLONAL	2	TRUE	2	0.792964982557833	4		484	845	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968556	55968556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	152	424	0	ENST00000263923.4:c.2107G>A	p.Asp703Asn	p.D703N	ENST00000263923	NM_002253.2	703	Gat/Aat	14/30	0.793263594182364	4	FACETS	1	0.923	1	0.503	0.461	0.547	CLONAL	1	TRUE	2	0.792964982557833	4		424	683	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973911	55973911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs941528100	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	462	526	0	ENST00000263923.4:c.1405G>A	p.Glu469Lys	p.E469K	ENST00000263923	NM_002253.2	469	Gag/Aag	10/30	0.793263594182364	4	FACETS	0.968	0.928	1	0.968	0.928	1	CLONAL	2	TRUE	2	0.792964982557833	4		526	1079	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295204	1295204	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs2735943	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	118	511	0				ENST00000310581	NM_198253.2	-/1132			0.793263594182364	4	FACETS	0.936	0.847	1	0.312	0.282	0.343	CLONAL	1	TRUE	1	0.792964982557833	4		511	570	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500492	149500492	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	227	571	0	ENST00000261799.4:c.2545C>T	p.Arg849Ter	p.R849*	ENST00000261799	NM_002609.3	849	Cga/Tga	18/23	0.756023708989473	4	FACETS	0.955	0.889	1	0.318	0.296	0.341	CLONAL	1	TRUE	1	0.792964982557833	4		571	1075	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800488	32800488	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	586	666	0	ENST00000374899.4:c.1059T>G	p.Cys353Trp	p.C353W	ENST00000374899	NM_018833.2	353	tgT/tgG	6/12	0.793263594182364	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.792964982557833	4		666	1250	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977609	2977609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	386	426	0	ENST00000396946.4:c.1075G>A	p.Glu359Lys	p.E359K	ENST00000396946	NM_032415.4	359	Gaa/Aaa	8/25	0.780118008404206	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.792964982557833	2		426	468	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467711	50467711	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	250	623	0	ENST00000331340.3:c.946A>C	p.Asn316His	p.N316H	ENST00000331340	NM_006060.4	316	Aac/Cac	8/8	0.780118008404206	2	FACETS	1	0.984	1	0.557	0.526	0.589	CLONAL	1	TRUE	0	0.792964982557833	2		623	566	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92404042	92404042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	137	415	0	ENST00000265734.4:c.337C>T	p.Pro113Ser	p.P113S	ENST00000265734	NM_001259.6	113	Cca/Tca	3/8	0.726385168311854	4	FACETS	0.994	0.908	1	0.497	0.454	0.543	CLONAL	1	TRUE	2	0.792964982557833	4		415	623	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205673	38205673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	304	470	0	ENST00000317025.8:c.17C>T	p.Ser6Phe	p.S6F	ENST00000317025	NM_023034.1	6	tCt/tTt	2/24	0.780118008404206	2	FACETS	0.961	0.928	0.992	0.961	0.928	0.992	CLONAL	2	TRUE	0	0.792964982557833	2		470	399	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863112	56863112	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	266	435	1	ENST00000519728.1:c.379G>A	p.Glu127Lys	p.E127K	ENST00000519728	NM_002350.3	127	Gaa/Aaa	5/13	0.780118008404206	2	FACETS	0.956	0.92	0.989	0.956	0.92	0.989	CLONAL	2	TRUE	0	0.792964982557833	2		436	351	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009400	69009400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	157	402	0	ENST00000288368.4:c.2517G>A	p.Met839Ile	p.M839I	ENST00000288368	NM_024870.2	839	atG/atA	22/40	0.793263594182364	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.792964982557833	1		402	223	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27192519	27192519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	216	401	0	ENST00000380036.4:c.1522G>A	p.Glu508Lys	p.E508K	ENST00000380036	NM_000459.3	508	Gaa/Aaa	11/23	0.768637657761355	3	FACETS	1	0.956	1	0.516	0.481	0.552	CLONAL	1	TRUE	1	0.792964982557833	3		401	737	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27209205	27209205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	257	393	0	ENST00000380036.4:c.2662C>T	p.Leu888Phe	p.L888F	ENST00000380036	NM_000459.3	888	Ctc/Ttc	16/23	0.768637657761355	3	FACETS	0.951	0.903	0.999	0.951	0.903	0.999	CLONAL	2	TRUE	1	0.792964982557833	3		393	476	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002653	37002653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	257	587	0	ENST00000358127.4:c.596G>A	p.Arg199Lys	p.R199K	ENST00000358127	NM_001280556.1	199	aGa/aAa	5/10	NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.792964982557833	2		587	642	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225959	53225959	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	251	642	0	ENST00000375401.3:c.2890C>T	p.Pro964Ser	p.P964S	ENST00000375401	NM_004187.3	964	Cct/Tct	19/26	0.494647021780228	5	FACETS	1	0.99	1			1	CLONAL	1	TRUE	NA	0.792964982557833	5		642	1077	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412125	63412125	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	467	607	0	ENST00000330258.3:c.1042G>T	p.Gly348Cys	p.G348C	ENST00000330258	NM_152424.3	348	Ggc/Tgc	2/2	0.494647021780228	5	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.792964982557833	5		607	1112	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939169	76939169	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	237	452	0	ENST00000373344.5:c.1579G>T	p.Asp527Tyr	p.D527Y	ENST00000373344	NM_000489.3	527	Gac/Tac	9/35	0.602887359701312	4	FACETS	0.859	0.807	0.911			1	CLONAL	2	TRUE	NA	0.792964982557833	4		452	624	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939496	76939496	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057523785	NA	P-0060210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	265	494	0	ENST00000373344.5:c.1252C>T	p.Arg418Ter	p.R418*	ENST00000373344	NM_000489.3	418	Cga/Tga	9/35	0.602887359701312	4	FACETS	0.981	0.927	1			1	CLONAL	2	TRUE	NA	0.792964982557833	4		494	611	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845844	72845844	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760400785	NA	P-0060211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	106	671	0	ENST00000268489.5:c.3623C>T	p.Ser1208Leu	p.S1208L	ENST00000268489	NM_006885.3	1208	tCg/tTg	6/10	0.403107770532466	2	FACETS	0.794	0.713	0.881	0.397	0.356	0.441	SUBCLONAL	1	TRUE	0	0.403107770532466	2		671	662	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266711	198266711	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	51	390	0	ENST00000335508.6:c.2221A>G	p.Lys741Glu	p.K741E	ENST00000335508	NM_012433.2	741	Aag/Gag	15/25	1	2	FACETS	0.652	0.556	0.757	0.652	0.556	0.757	SUBCLONAL	1	TRUE	1	0.403107770532466	2		390	388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577128	7577128	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	115	610	0	ENST00000269305.4:c.810T>A	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	ttT/ttA	8/11	0.403107770532466	1	FACETS	0.951	0.862	1	0.951	0.862	1	CLONAL	1	TRUE	0	0.403107770532466	1		610	479	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0060211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	130	334	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.359392229367314	2	FACETS	0.812	0.744	0.883	0.812	0.744	0.883	CLONAL	2	TRUE	0	0.403107770532466	2		334	397	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015012	37015012	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060211-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	134	599	0	ENST00000358127.4:c.392G>T	p.Ser131Ile	p.S131I	ENST00000358127	NM_001280556.1	131	aGc/aTc	3/10	0.403107770532466	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.403107770532466	1		599	496	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032794	30032794	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434259	NA	P-0060214-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	353	533	0	ENST00000338641.4:c.169C>T	p.Arg57Ter	p.R57*	ENST00000338641	NM_000268.3	57	Cga/Tga	2/16	0.748565704071377	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.748565704071377	1		533	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0060228-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	286	393	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.609861487673054	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.609861487673054	2		393	456	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0060228-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	198	356	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.451125063610195	4	FACETS	0.901	0.84	0.963	0.901	0.84	0.963	CLONAL	2	TRUE	2	0.609861487673054	4		356	580	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149246	119149246	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060228-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	133	473	0	ENST00000264033.4:c.1254C>A	p.Phe418Leu	p.F418L	ENST00000264033	NM_005188.3	418	ttC/ttA	9/16	0.609861487673054	3	FACETS	0.865	0.787	0.946	0.432	0.393	0.473	CLONAL	1	TRUE	1	0.609861487673054	3		473	658	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790072	40790072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753667	NA	P-0060228-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	583	489	1	ENST00000373198.4:c.2659G>A	p.Ala887Thr	p.A887T	ENST00000373198	NM_133170.3	887	Gcc/Acc	18/32	0.609861487673054	5	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	2	0.609861487673054	5		490	1082	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492797	56492798	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0060228-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	397	562	0	ENST00000407977.2:c.141dup	p.Ile48TyrfsTer27	p.I48Yfs*27	ENST00000407977		47	-/T	2/10	0.609861487673054	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.609861487673054	2		562	619	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032290	11032290	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0060228-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	276	532	0	ENST00000327064.4:c.1685-1G>A		p.X562_splice	ENST00000327064	NM_199141.1	562			0.48964180168883	4	FACETS	0.934	0.881	0.988	0.934	0.881	0.988	CLONAL	2	TRUE	2	0.609861487673054	4		532	780	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0060229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	66	487	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	0.738	0.64	0.844	0.738	0.64	0.844	SUBCLONAL	1	TRUE	1	0.271762032599896	2		487	658	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715678	30715678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039551	NA	P-0060229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	67	497	0	ENST00000295754.5:c.1336G>A	p.Asp446Asn	p.D446N	ENST00000295754	NM_003242.5	446	Gat/Aat	5/7	1	2	FACETS	0.72	0.625	0.823	0.72	0.625	0.823	SUBCLONAL	1	TRUE	1	0.271762032599896	2		497	685	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405959	70405959	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200333871	NA	P-0060229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	62	479	1	ENST00000373644.4:c.3473G>A	p.Arg1158Gln	p.R1158Q	ENST00000373644	NM_030625.2	1158	cGg/cAg	4/12	1	2	FACETS	0.658	0.568	0.757	0.658	0.568	0.757	SUBCLONAL	1	TRUE	1	0.271762032599896	2		480	693	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844150	68844151	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0060229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	118	448	0	ENST00000261769.5:c.738_739delinsAA	p.Met246_Glu247delinsIleLys	p.M246_E247delinsIK	ENST00000261769	NM_004360.3	246	atGGag/atAAag	6/16	0.189645132480323	2	FACETS	1	0.981	1	0.675	0.61	0.744	CLONAL	1	TRUE	0	0.271762032599896	2		448	643	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165692	185165692	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	114	414	0	ENST00000265026.3:c.967G>A	p.Glu323Lys	p.E323K	ENST00000265026	NM_004721.4	323	Gag/Aag	5/14	0.261133650421521	3	FACETS	1	0.983	1	0.725	0.654	0.8	CLONAL	1	TRUE	1	0.271762032599896	3		414	657	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981277	201981278	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0060230-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	63	585	0	ENST00000359651.3:c.358dup	p.Gln120ProfsTer15	p.Q120Pfs*15	ENST00000359651		119	gac/gaCc	2/8	0.423903356881231	1	FACETS	0.471	0.411	0.534	0.471	0.411	0.534	SUBCLONAL	1	TRUE	0	0.669546610964542	1		585	266	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920447	114920447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060230-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	114	379	0	ENST00000543371.1:c.1388G>A	p.Cys463Tyr	p.C463Y	ENST00000543371	NM_001198531.1	463	tGc/tAc	13/14	0.172799580034141	2	FACETS	1	0.962	1	0.549	0.501	0.598	INDETERMINATE	1	TRUE	0	0.669546610964542	2		379	310	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060230-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	117	454	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	0.177832369554555	2	FACETS	1	0.964	1	0.551	0.504	0.6	INDETERMINATE	1	TRUE	0	0.669546610964542	2		454	317	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482592	56482592	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060230-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	126	429	0	ENST00000267101.3:c.1049G>T	p.Gly350Val	p.G350V	ENST00000267101	NM_001982.3	350	gGa/gTa	9/28	0.177832369554555	2	FACETS	1	0.98	1	0.609	0.56	0.659	INDETERMINATE	1	TRUE	0	0.669546610964542	2		429	309	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51535061	51535061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200111039	NA	P-0060230-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	47	394	0	ENST00000260433.2:c.49G>A	p.Val17Met	p.V17M	ENST00000260433		17	Gtg/Atg	2/10	0.364483057307723	1	FACETS	0.401	0.341	0.465	0.401	0.341	0.465	INDETERMINATE	1	TRUE	0	0.669546610964542	1		394	233	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222322	2222322	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060230-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	96	559	0	ENST00000326181.6:c.606C>G	p.Ile202Met	p.I202M	ENST00000326181	NM_032271.2	202	atC/atG	8/21	0.364483057307723	1	FACETS	0.681	0.616	0.749	0.681	0.616	0.749	INDETERMINATE	1	TRUE	0	0.669546610964542	1		559	280	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577077	7577077	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs748891343	NA	P-0060230-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	62	564	0	ENST00000269305.4:c.861G>C	p.Glu287Asp	p.E287D	ENST00000269305	NM_001126112.2	287	gaG/gaC	8/11	0.669546610964542	3	FACETS	0.649	0.563	0.741			1	SUBCLONAL	1	TRUE	NA	0.669546610964542	3		564	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0060230-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	43	670	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.669546610964542	3	FACETS	0.546	0.459	0.642			1	SUBCLONAL	1	TRUE	NA	0.669546610964542	3		670	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577543	7577543	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060230-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	175	413	0	ENST00000269305.4:c.738G>C	p.Met246Ile	p.M246I	ENST00000269305	NM_001126112.2	246	atG/atC	7/11	0.669546610964542	3	FACETS	1	0.936	1			1	CLONAL	2	TRUE	NA	0.669546610964542	3		413	349	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762507	41762507	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060230-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	73	475	0	ENST00000301178.4:c.2187G>C	p.Lys729Asn	p.K729N	ENST00000301178	NM_021913.4	729	aaG/aaC	18/20	1	2	FACETS	0.796	0.704	0.893	0.796	0.704	0.893	SUBCLONAL	1	TRUE	1	0.669546610964542	2		475	274	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397710	49397710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060230-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	78	451	0	ENST00000418115.1:c.514G>A	p.Glu172Lys	p.E172K	ENST00000418115	NM_001664.2	172	Gaa/Aaa	5/5	0.318553309240433	2	FACETS	0.566	0.499	0.636	0.283	0.249	0.318	INDETERMINATE	1	TRUE	0	0.669546610964542	2		451	412	SUCCESS
ATR	545	MSKCC	GRCh37	3	142184047	142184047	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060230-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	131	230	0	ENST00000350721.4:c.6933G>C	p.Lys2311Asn	p.K2311N	ENST00000350721	NM_001184.3	2311	aaG/aaC	41/47	0.318553309240433	2	FACETS	1	0.987	1	0.694	0.641	0.747	INDETERMINATE	1	TRUE	0	0.669546610964542	2		230	282	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155421	106155421	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060230-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	63	411	0	ENST00000380013.4:c.322C>T	p.Gln108Ter	p.Q108*	ENST00000380013	NM_001127208.2	108	Cag/Tag	3/11	0.364483057307723	1	FACETS	0.438	0.382	0.497	0.438	0.382	0.497	INDETERMINATE	1	TRUE	0	0.669546610964542	1		411	286	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44920636	44920636	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060230-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	124	145	0	ENST00000377967.4:c.1397C>A	p.Ser466Ter	p.S466*	ENST00000377967	NM_021140.2	466	tCa/tAa	14/29	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.669546610964542	1		145	191	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338683	70338683	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060230-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	112	148	0	ENST00000374080.3:c.79C>G	p.Gln27Glu	p.Q27E	ENST00000374080		27	Cag/Gag	1/45	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.669546610964542	1		148	176	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400116	41400116	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060231-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	238	375	0	ENST00000373198.4:c.643G>T	p.Ala215Ser	p.A215S	ENST00000373198	NM_133170.3	215	Gct/Tct	5/32	0.791747588498168	9	FACETS	0.843	0.785	0.903	0.241	0.224	0.258	CLONAL	2	TRUE	2	0.791747588498168	9		375	1345	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579534	7579556	+	frameshift_variant	Frame_Shift_Del	DEL	TTCAATATCGTCCGGGGACAGCA	TTCAATATCGTCCGGGGACAGCA	-	novel	NA	P-0060231-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	275	622	0	ENST00000269305.4:c.131_153del	p.Met44ThrfsTer5	p.M44Tfs*5	ENST00000269305	NM_001126112.2	44	aTGCTGTCCCCGGACGATATTGAA/a	4/11	0.791747588498168	2	FACETS	0.995	0.961	1	0.995	0.961	1	CLONAL	2	TRUE	0	0.791747588498168	2		622	349	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178941905	178941905	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060231-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	236	345	0	ENST00000263967.3:c.2224C>T	p.Pro742Ser	p.P742S	ENST00000263967	NM_006218.2	742	Cca/Tca	15/21	0.689669467357798	4	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	2	0.791747588498168	4		345	530	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953574	38953574	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060231-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	60	292	0	ENST00000357387.3:c.2779C>A	p.Leu927Ile	p.L927I	ENST00000357387	NM_152756.3	927	Ctt/Att	28/38	0.791747588498168	4	FACETS	0.538	0.464	0.618	0.179	0.154	0.206	SUBCLONAL	1	TRUE	1	0.791747588498168	4		292	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0060232-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	364	484	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.823058663913861	1	FACETS	0.946	0.912	0.98	0.946	0.912	0.98	CLONAL	1	TRUE	0	0.823058663913861	1		484	550	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717642	89717642	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1085308049	NA	P-0060232-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	297	364	0	ENST00000371953.3:c.667A>T	p.Lys223Ter	p.K223*	ENST00000371953	NM_000314.4	223	Aag/Tag	7/9	0.823058663913861	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.823058663913861	1		364	393	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217165	66217165	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060232-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	60	389	0	ENST00000273854.3:c.2450C>G	p.Ser817Cys	p.S817C	ENST00000273854	NM_004439.5	817	tCt/tGt	14/18	1	2	FACETS	0.142	0.121	0.164	0.142	0.121	0.164	SUBCLONAL	1	TRUE	1	0.823058663913861	2		389	1028	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0060235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	145	569	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.192505728875007	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	FALSE	1	0.220470466800396	3		569	611	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0060235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	25	179	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	FALSE	1	0.220470466800396	2		179	189	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711248	114711252	+	frameshift_variant	Frame_Shift_Del	DEL	AGAGG	AGAGG	-	novel	NA	P-0060235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	79	268	0	ENST00000543371.1:c.263_267del	p.Lys88ThrfsTer7	p.K88Tfs*7	ENST00000543371	NM_001198531.1	88	aAGAGG/a	3/14	0.188729541615949	2	FACETS	0.779	0.688	0.876	0.779	0.688	0.876	SUBCLONAL	2	FALSE	0	0.220470466800396	2		268	460	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438209	49438209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	34	354	0	ENST00000301067.7:c.5060G>A	p.Arg1687His	p.R1687H	ENST00000301067	NM_003482.3	1687	cGc/cAc	20/54	0.192505728875007	3	FACETS	0.614	0.5	0.742	0.307	0.25	0.371	SUBCLONAL	1	FALSE	1	0.220470466800396	3		354	558	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964505	93964506	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0060235-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	30	250	0	ENST00000369303.4:c.2391_2392insT	p.Ile798TyrfsTer21	p.I798Yfs*21	ENST00000369303	NM_004440.3	797	-/T	14/17	0.220470466800396	7	FACETS	1	0.872	1	0.278	0.224	0.339	CLONAL	1	FALSE	3	0.220470466800396	7		250	380	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001303	29001303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201407326	NA	P-0060240-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	119	515	0	ENST00000282397.4:c.1429G>A	p.Glu477Lys	p.E477K	ENST00000282397	NM_002019.4	477	Gaa/Aaa	10/30	0.160653789122118	3	FACETS	1	0.947	1	0.356	0.322	0.391	INDETERMINATE	1	TRUE	0	0.482845914136838	3		515	573	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101895021	101895021	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060240-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	149	393	0	ENST00000374994.4:c.574G>T	p.Gly192Cys	p.G192C	ENST00000374994	NM_004612.2	192	Ggt/Tgt	3/9	0.482845914136838	2	FACETS	0.836	0.774	0.9	0.836	0.774	0.9	CLONAL	2	TRUE	0	0.482845914136838	2		393	369	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602412	10602412	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060240-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	47	786	0	ENST00000171111.5:c.1166A>T	p.Asp389Val	p.D389V	ENST00000171111	NM_203500.1	389	gAc/gTc	3/6	0.482845914136838	1	FACETS	0.273	0.23	0.321	0.273	0.23	0.321	SUBCLONAL	1	TRUE	0	0.482845914136838	1		786	540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0060241-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	64	569	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.0984188558825358	8	FACETS	0.88	0.762	1	0.44	0.381	0.505	CLONAL	3	FALSE	2	0.0984188558825358	8		569	638	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952100	178952100	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060241-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	32	476	0	ENST00000263967.3:c.3155C>A	p.Thr1052Lys	p.T1052K	ENST00000263967	NM_006218.2	1052	aCa/aAa	21/21	0.0984188558825358	7	FACETS	1	0.937	1	0.357	0.289	0.434	CLONAL	1	FALSE	3	0.0984188558825358	7		476	568	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2081904	2081904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060241-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	476	417	0	ENST00000349721.2:c.2257C>T	p.Leu753Phe	p.L753F	ENST00000349721	NM_003070.3	753	Ctt/Ttt	15/34	0.0984188558825358	27	FACETS	1	0.974	1	0.974	0.937	1	CLONAL	23	FALSE	3	0.0984188558825358	27		417	923	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833927	44833928	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0060241-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	24	116	0	ENST00000377967.4:c.352dup	p.Arg118LysfsTer8	p.R118Kfs*8	ENST00000377967	NM_021140.2	117	-/A	4/29	0.0984188558825358	6	FACETS	1	0.845	1			1	CLONAL	3	FALSE	NA	0.0984188558825358	6		116	179	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089725	27089725	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060242-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	284	562	0	ENST00000324856.7:c.2683del	p.Gln895LysfsTer24	p.Q895Kfs*24	ENST00000324856	NM_006015.4	894	aCc/ac	8/20	0.407452307037562	1	FACETS	0.792	0.752	0.832	0.792	0.752	0.832	INDETERMINATE	1	TRUE	0	0.764876215463313	1		562	579	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227674	36227674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060242-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	138	501	0	ENST00000222270.7:c.7243C>T	p.Arg2415Cys	p.R2415C	ENST00000222270	NM_014727.1	2415	Cgc/Tgc	31/37	0.452845626641704	3	FACETS	0.65	0.591	0.71	0.217	0.197	0.237	INDETERMINATE	1	TRUE	0	0.764876215463313	3		501	768	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157256637	157256637	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060242-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	123	393	0	ENST00000346085.5:c.1964C>T	p.Pro655Leu	p.P655L	ENST00000346085	NM_020732.3	655	cCt/cTt	5/20	0.386556445224777	2	FACETS	0.505	0.457	0.555	0.252	0.228	0.278	INDETERMINATE	1	TRUE	0	0.764876215463313	2		393	637	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019614	123019619	+	inframe_deletion	In_Frame_Del	DEL	TAATTT	TAATTT	-	novel	NA	P-0060242-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	104	344	0	ENST00000355640.3:c.103_108del	p.Asn35_Phe36del	p.N35_F36del	ENST00000355640		34	gcTAATTTt/gct	2/7	1	2	FACETS	0.468	0.42	0.519	0.468	0.42	0.519	SUBCLONAL	1	TRUE	1	0.764876215463313	2		344	581	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060243-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	144	671	1	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	0.261593350198045	5	FACETS	0.946	0.868	1	1	0.987	1	CLONAL	3	TRUE	3	0.261593350198045	5		672	540	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873640	35873640	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060243-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	105	526	0	ENST00000303115.3:c.596C>A	p.Ala199Glu	p.A199E	ENST00000303115	NM_002185.3	199	gCa/gAa	5/8	0.26549005408887	4	FACETS	0.959	0.868	1	1	0.983	1	CLONAL	3	TRUE	2	0.261593350198045	4		526	352	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070549	67070549	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060243-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	121	489	0	ENST00000412916.2:c.173del	p.Val58GlyfsTer31	p.V58Gfs*31	ENST00000412916		58	gTg/gg	3/6	0.26549005408887	1	FACETS	1	0.974	1	1	0.991	1	CLONAL	2	TRUE	0	0.261593350198045	1		489	345	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847266	68847267	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0060243-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	142	547	0	ENST00000261769.5:c.1191dup	p.Val398SerfsTer3	p.V398Sfs*3	ENST00000261769	NM_004360.3	396	-/A	9/16	0.26549005408887	1	FACETS	0.931	0.861	1	1	0.993	1	CLONAL	3	TRUE	0	0.261593350198045	1		547	338	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0060244-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	234	289	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.42447963327159	6	FACETS	1	0.969	1	0.83	0.784	0.876	CLONAL	4	TRUE	1	0.446632433015403	6		289	478	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622131	43622131	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060244-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	142	533	0	ENST00000355710.3:c.3148C>T	p.Arg1050Ter	p.R1050*	ENST00000355710	NM_020975.4	1050	Cga/Tga	19/20	1	2	FACETS	0.95	0.868	1	0.95	0.868	1	CLONAL	1	TRUE	1	0.446632433015403	2		533	669	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106469	27106469	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060244-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	203	678	0	ENST00000324856.7:c.6080del	p.Ala2027AspfsTer3	p.A2027Dfs*3	ENST00000324856	NM_006015.4	2027	gCa/ga	20/20	0.444441100629175	1	FACETS	0.902	0.838	0.967	0.902	0.838	0.967	CLONAL	1	TRUE	0	0.446632433015403	1		678	783	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28595715	28595715	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs367784435	NA	P-0060244-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	180	591	0	ENST00000253063.3:c.112C>G	p.Arg38Gly	p.R38G	ENST00000253063	NM_031459.4	38	Cgg/Ggg	2/10	0.444441100629175	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.446632433015403	1		591	605	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0060245-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	30	294	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	0.15561899140144	6	FACETS	1	0.939	1	0.478	0.389	0.576	INDETERMINATE	1	TRUE	3	0.502790938127538	6		294	167	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88428938	88428938	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060245-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	68	202	0	ENST00000360948.2:c.2162G>T	p.Cys721Phe	p.C721F	ENST00000360948	NM_001012338.2	721	tGt/tTt	17/19	0.15561899140144	6	FACETS	1	0.963	1	0.822	0.726	0.922	INDETERMINATE	2	TRUE	3	0.502790938127538	6		202	220	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441247	52441254	+	frameshift_variant	Frame_Shift_Del	DEL	GCACATAG	GCACATAG	A	novel	NA	P-0060245-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	163	729	0	ENST00000460680.1:c.516_523delinsT	p.Tyr173LeufsTer12	p.Y173Lfs*12	ENST00000460680	NM_004656.3	172	agCTATGTGCct/agTct	7/17	0.502790938127538	2	FACETS	0.888	0.827	0.95	0.888	0.827	0.95	CLONAL	2	TRUE	0	0.502790938127538	2		729	365	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0060246-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	136	289	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.380573287991005	5	FACETS	1	0.98	1	0.815	0.747	0.885	CLONAL	2	TRUE	2	0.410472352255645	5		289	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0060246-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	328	575	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.399951754707663	3	FACETS	0.941	0.897	0.986	0.941	0.897	0.986	CLONAL	3	TRUE	0	0.410472352255645	3		575	682	SUCCESS
APC	324	MSKCC	GRCh37	5	112175162	112175162	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561588104	NA	P-0060246-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	203	536	0	ENST00000257430.4:c.3871C>T	p.Gln1291Ter	p.Q1291*	ENST00000257430	NM_000038.5	1291	Cag/Tag	16/16	0.393762254304948	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.410472352255645	3		536	531	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912188	114912188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060246-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	164	400	0	ENST00000543371.1:c.1258C>T	p.Arg420Trp	p.R420W	ENST00000543371	NM_001198531.1	420	Cgg/Tgg	11/14	0.390238393230874	4	FACETS	0.997	0.921	1	0.997	0.921	1	CLONAL	2	TRUE	2	0.410472352255645	4		400	565	SUCCESS
APC	324	MSKCC	GRCh37	5	112175508	112175509	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0060246-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	104	521	0	ENST00000257430.4:c.4219_4220del	p.Ser1407Ter	p.S1407*	ENST00000257430	NM_000038.5	1406	cAG/c	16/16	0.393762254304948	3	FACETS	1	0.935	1	0.527	0.473	0.585	CLONAL	1	TRUE	1	0.410472352255645	3		521	579	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930399	39930399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1433397184	NA	P-0060246-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	215	565	0	ENST00000378444.4:c.3065G>A	p.Arg1022His	p.R1022H	ENST00000378444	NM_001123385.1	1022	cGc/cAc	6/15	0.410472352255645	5	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.410472352255645	5		565	698	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120004	70120005	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0060246-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	250	689	0	ENST00000245479.2:c.1008_1009dup	p.Ser337CysfsTer47	p.S337Cfs*47	ENST00000245479	NM_000346.3	336	atg/aTGtg	3/3	0.417302213364112	3	FACETS	0.851	0.803	0.899	1	0.991	1	CLONAL	3	TRUE	1	0.410472352255645	3		689	575	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0060247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	32	66	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.497	0.406	0.599	0.497	0.406	0.599	SUBCLONAL	1	TRUE	1	0.574454991178134	2		66	224	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0060247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	37	580	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	0.172	0.141	0.207	0.172	0.141	0.207	SUBCLONAL	1	TRUE	1	0.574454991178134	2		580	749	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0060247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	201	312	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.574454991178134	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.574454991178134	3		312	440	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0060247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	410	406	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.574454991178134	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.574454991178134	2		406	649	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982440	25982440	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	317	442	0	ENST00000435504.4:c.850C>T	p.Arg284Ter	p.R284*	ENST00000435504		284	Cga/Tga	9/13	0.490639816023531	2	FACETS	0.893	0.851	0.935	0.893	0.851	0.935	CLONAL	2	TRUE	0	0.574454991178134	2		442	618	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67626399	67626399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060247-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	21	471	0	ENST00000272342.5:c.322G>A	p.Asp108Asn	p.D108N	ENST00000272342	NM_019002.3	108	Gat/Aat	2/6	1	2	FACETS	0.213	0.163	0.27	0.213	0.163	0.27	SUBCLONAL	1	TRUE	1	0.574454991178134	2		471	344	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0060248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	17	388	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.632	0.47	0.826	0.632	0.47	0.826	SUBCLONAL	1	TRUE	1	0.11	2		388	489	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903731	41903731	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	24	755	0	ENST00000372991.4:c.826C>T	p.Gln276Ter	p.Q276*	ENST00000372991	NM_001760.3	276	Caa/Taa	5/5	1	2	FACETS	0.685	0.535	0.859	0.685	0.535	0.859	SUBCLONAL	1	TRUE	1	0.11	2		755	637	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948044	178948044	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060248-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	11	396	0	ENST00000263967.3:c.2816A>G	p.Asp939Gly	p.D939G	ENST00000263967	NM_006218.2	939	gAt/gGt	20/21	1	2	FACETS	0.441	0.303	0.613	0.441	0.303	0.613	SUBCLONAL	1	TRUE	1	0.11	2		396	454	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0060250-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	16	137	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.776	0.581	1	0.776	0.581	1	CLONAL	1	TRUE	1	0.408417311599996	2		137	101	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0060250-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	170	573	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.408417311599996	2		573	665	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0060250-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	55	312	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.408417311599996	2		312	212	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0060250-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	84	686	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	0.877	0.778	0.983	0.877	0.778	0.983	CLONAL	1	TRUE	1	0.408417311599996	2		686	469	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589153	67589155	+	inframe_deletion	In_Frame_Del	DEL	ATC	ATC	-	novel	NA	P-0060250-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	43	374	0	ENST00000274335.5:c.1142_1144del	p.Ile381del	p.I381del	ENST00000274335		381	ATC/-	9/15	1	2	FACETS	0.989	0.836	1	0.989	0.836	1	CLONAL	1	TRUE	1	0.408417311599996	2		374	213	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720677	89720677	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060250-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	30	110	0	ENST00000371953.3:c.828T>A	p.Asn276Lys	p.N276K	ENST00000371953	NM_000314.4	276	aaT/aaA	8/9	1	2	FACETS	0.907	0.756	1	1	0.96	1	CLONAL	2	TRUE	1	0.408417311599996	2		110	81	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101708	27101709	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0060250-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	111	543	0	ENST00000324856.7:c.4990_4991del	p.Ile1664TrpfsTer33	p.I1664Wfs*33	ENST00000324856	NM_006015.4	1664	ATt/t	18/20	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.408417311599996	2		543	513	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660522	67660523	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0060250-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	74	410	0	ENST00000264010.4:c.1425_1426del	p.Phe476SerfsTer2	p.F476Sfs*2	ENST00000264010	NM_006565.3	474	gcTGtg/gctg	8/12	1	2	FACETS	0.929	0.818	1	0.929	0.818	1	CLONAL	1	TRUE	1	0.408417311599996	2		410	390	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591244	67591263	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCAGGTGGTTGACTCAAAAA	TCAGGTGGTTGACTCAAAAA	-	novel	NA	P-0060250-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	78	485	0	ENST00000274335.5:c.1746-4_1761del		p.X582_splice	ENST00000274335		582		13/15	1	2	FACETS	0.895	0.79	1	0.895	0.79	1	CLONAL	1	TRUE	1	0.408417311599996	2		485	427	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483237	120483237	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	141	568	0	ENST00000256646.2:c.3124G>C	p.Asp1042His	p.D1042H	ENST00000256646	NM_024408.3	1042	Gat/Cat	19/34	1	2	FACETS	0.803	0.734	0.875	0.803	0.734	0.875	CLONAL	1	TRUE	1	0.558108447978304	2		568	629	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs770248150	NA	P-0060252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	67	390	0	ENST00000311936.3:c.351A>C	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaC	4/5	1	2	FACETS	0.767	0.672	0.868	0.767	0.672	0.868	SUBCLONAL	1	TRUE	1	0.558108447978304	2		390	313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	258	684	0	ENST00000269305.4:c.461del	p.Gly154AlafsTer16	p.G154Afs*16	ENST00000269305	NM_001126112.2	154	gGc/gc	5/11	0.558108447978304	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.558108447978304	1		684	592	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120291	70120292	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	384	686	0	ENST00000245479.2:c.1294dup	p.Tyr432LeufsTer146	p.Y432Lfs*146	ENST00000245479	NM_000346.3	431	-/T	3/3	0.558108447978304	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.558108447978304	2		686	675	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591933	48591933	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060500733	NA	P-0060252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	125	611	0	ENST00000342988.3:c.1096C>T	p.Gln366Ter	p.Q366*	ENST00000342988	NM_005359.5	366	Caa/Taa	9/12	0.558108447978304	1	FACETS	0.784	0.716	0.854	0.784	0.716	0.854	SUBCLONAL	1	TRUE	0	0.558108447978304	1		611	412	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913315	NA	P-0060252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	164	659	0	ENST00000326873.7:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000326873	NM_000455.4	194	Gac/Tac	4/10	0.558108447978304	1	FACETS	0.981	0.91	1	0.981	0.91	1	CLONAL	1	TRUE	0	0.558108447978304	1		659	432	SUCCESS
APC	324	MSKCC	GRCh37	5	112178756	112178756	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	166	645	0	ENST00000257430.4:c.7466del	p.Pro2489LeufsTer27	p.P2489Lfs*27	ENST00000257430	NM_000038.5	2489	Cct/ct	16/16	0.558108447978304	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.558108447978304	1		645	406	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0060252-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	230	577	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.558108447978304	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.558108447978304	1		577	424	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0060253-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	82	279	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.343653410322454	2		279	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0060253-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	121	584	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.343653410322454	1	FACETS	0.918	0.832	1	0.918	0.832	1	CLONAL	1	TRUE	0	0.343653410322454	1		584	635	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0060253-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	33	61	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.219237065014603	1	FACETS	0.692	0.567	0.83	0.692	0.567	0.83	SUBCLONAL	1	TRUE	0	0.343653410322454	1		61	230	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0060253-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	79	658	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.219237065014603	1	FACETS	0.546	0.48	0.617	0.546	0.48	0.617	SUBCLONAL	1	TRUE	0	0.343653410322454	1		658	697	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0060253-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	68	438	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.833	0.727	0.948	0.833	0.727	0.948	CLONAL	1	TRUE	1	0.343653410322454	2		438	475	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0060253-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	106	533	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.219237065014603	1	FACETS	0.758	0.68	0.84	0.758	0.68	0.84	SUBCLONAL	1	TRUE	0	0.343653410322454	1		533	674	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931673	39931673	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121434619	NA	P-0060253-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	126	504	0	ENST00000378444.4:c.2926C>T	p.Arg976Ter	p.R976*	ENST00000378444	NM_001123385.1	976	Cga/Tga	4/15	0.279980354032961	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.343653410322454	1		504	598	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186813	142186813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060253-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	30	360	0	ENST00000350721.4:c.6650G>A	p.Arg2217His	p.R2217H	ENST00000350721	NM_001184.3	2217	cGc/cAc	39/47	0.219237065014603	1	FACETS	0.419	0.338	0.511	0.419	0.338	0.511	SUBCLONAL	1	TRUE	0	0.343653410322454	1		360	345	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554289	63554289	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060253-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	139	600	0	ENST00000307078.5:c.450del	p.Lys150AsnfsTer8	p.K150Nfs*8	ENST00000307078	NM_004655.3	150	aaG/aa	2/11	0.279980354032961	1	FACETS	0.971	0.886	1	0.971	0.886	1	CLONAL	1	TRUE	0	0.343653410322454	1		600	690	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	271	475	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.98	0.927	1	1	0.995	1	CLONAL	2	TRUE	1	0.438738858638156	2		476	630	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	218	573	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.438738858638156	2		573	900	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	199	656	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.899	0.833	0.968	0.899	0.833	0.968	CLONAL	1	TRUE	1	0.438738858638156	2		657	1009	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	162	446	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.438738858638156	2		446	704	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	177	742	2	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.937	0.864	1	0.937	0.864	1	CLONAL	1	TRUE	1	0.438738858638156	2		744	861	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	213	503	0	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.974	0.905	1	0.974	0.905	1	CLONAL	1	TRUE	1	0.438738858638156	2		503	997	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589571	67589582	+	inframe_deletion	In_Frame_Del	DEL	TAGGGAAAAAAT	TAGGGAAAAAAT	-	novel	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	46	262	0	ENST00000274335.5:c.1336_1347del	p.Gly446_Leu449del	p.G446_L449del	ENST00000274335		445	gTAGGGAAAAAATta/gta	10/15	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.438738858638156	2		262	186	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	153	558	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	0.986	0.905	1	0.986	0.905	1	CLONAL	1	TRUE	1	0.438738858638156	2		558	707	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653782	89653782	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs886041877	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	46	357	0	ENST00000371953.3:c.80A>G	p.Tyr27Cys	p.Y27C	ENST00000371953	NM_000314.4	27	tAt/tGt	2/9	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.438738858638156	2		357	181	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510805	157510806	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1289067120	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	154	672	0	ENST00000346085.5:c.3586dup	p.Gln1196ProfsTer14	p.Q1196Pfs*14	ENST00000346085	NM_020732.3	1194	acc/aCcc	14/20	1	2	FACETS	0.908	0.832	0.987	0.908	0.832	0.987	CLONAL	1	TRUE	1	0.438738858638156	2		672	773	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717715	89717716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587782341	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	116	375	0	ENST00000371953.3:c.741dup	p.Pro248ThrfsTer5	p.P248Tfs*5	ENST00000371953	NM_000314.4	247	tta/ttAa	7/9	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.438738858638156	2		375	477	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	193	669	5	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.438738858638156	2		674	821	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156719	20156719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	103	397	0	ENST00000379607.5:c.38G>A	p.Arg13His	p.R13H	ENST00000379607	NM_001412.3	13	cGc/cAc	2/7	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.438738858638156	2		397	402	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027087	71027087	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	199	777	3	ENST00000318789.4:c.1240del	p.Leu414Ter	p.L414*	ENST00000318789	NM_032682.5	414	Ctg/tg	15/21	1	2	FACETS	0.971	0.9	1	0.971	0.9	1	CLONAL	1	TRUE	1	0.438738858638156	2		780	934	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230605	46230605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303729294	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	116	600	0	ENST00000334344.6:c.854G>A	p.Arg285Gln	p.R285Q	ENST00000334344	NM_152641.2	285	cGg/cAg	8/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.438738858638156	2		600	500	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	144	745	4	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.81	0.739	0.885	0.81	0.739	0.885	CLONAL	1	TRUE	1	0.438738858638156	2		749	810	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948483	71948484	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	206	903	0	ENST00000298229.2:c.3201dup	p.Ser1068GlnfsTer17	p.S1068Qfs*17	ENST00000298229	NM_001567.3	1065	-/C	26/28	1	2	FACETS	0.969	0.899	1	0.969	0.899	1	CLONAL	1	TRUE	1	0.438738858638156	2		903	969	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165456	47165456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217051214	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	189	710	0	ENST00000409792.3:c.670G>A	p.Ala224Thr	p.A224T	ENST00000409792	NM_014159.6	224	Gca/Aca	3/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.438738858638156	2		710	739	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379374	225379375	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1553523940	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	80	427	0	ENST00000264414.4:c.493_494del	p.Leu165IlefsTer37	p.L165Ifs*37	ENST00000264414	NM_003590.4	165	CTa/a	4/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.438738858638156	2		427	291	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914152	32914152	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507795	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	61	528	0	ENST00000380152.3:c.5660C>T	p.Thr1887Met	p.T1887M	ENST00000380152		1887	aCg/aTg	11/27	0.140092230810327	0	FACETS	0.58	0.505	0.66			1	INDETERMINATE	1	TRUE	0	0.438738858638156	0		528	269	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231475572	231475572	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	135	513	0	ENST00000295050.7:c.279C>A	p.Ser93Arg	p.S93R	ENST00000295050	NM_032018.5	93	agC/agA	2/5	0.438738858638156	3	FACETS	1	0.913	1	0.502	0.456	0.549	CLONAL	1	TRUE	1	0.438738858638156	3		513	748	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856463	111856464	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	186	771	1	ENST00000341259.2:c.519dup	p.Ala174ArgfsTer94	p.A174Rfs*94	ENST00000341259	NM_005475.2	172	acc/aCcc	2/8	1	2	FACETS	0.984	0.909	1	0.984	0.909	1	CLONAL	1	TRUE	1	0.438738858638156	2		772	862	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799275	88799275	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	43	619	0	ENST00000360948.2:c.110T>C	p.Val37Ala	p.V37A	ENST00000360948	NM_001012338.2	37	gTc/gCc	2/19	1	2	FACETS	0.26	0.217	0.308	0.26	0.217	0.308	SUBCLONAL	1	TRUE	1	0.438738858638156	2		619	754	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679633	33679634	+	missense_variant	Missense_Mutation	DNP	TG	TG	CA	novel	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	154	681	0	ENST00000308377.4:c.2447_2448inv	p.Ala816Val	p.A816V	ENST00000308377	NM_152270.3	816	gCA/gTG	5/5	1	2	FACETS	0.96	0.881	1	0.96	0.881	1	CLONAL	1	TRUE	1	0.438738858638156	2		681	731	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243013	41243013	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1567788422	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	180	476	0	ENST00000357654.3:c.4133T>C	p.Val1378Ala	p.V1378A	ENST00000357654	NM_007294.3	1378	gTc/gCc	11/23	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.438738858638156	2		476	658	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219929	36219929	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	206	780	0	ENST00000222270.7:c.4735del	p.Arg1579ValfsTer67	p.R1579Vfs*67	ENST00000222270	NM_014727.1	1577	gaC/ga	21/37	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.438738858638156	2		780	870	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912041	50912041	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	106	678	0	ENST00000440232.2:c.1776-1G>A		p.X592_splice	ENST00000440232	NM_002691.3	592			1	2	FACETS	0.593	0.531	0.659	0.593	0.531	0.659	SUBCLONAL	1	TRUE	1	0.438738858638156	2		678	815	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47596660	47596660	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867177667	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	191	437	0	ENST00000263735.4:c.16G>A	p.Val6Ile	p.V6I	ENST00000263735	NM_002354.2	6	Gtc/Atc	1/9	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.438738858638156	2		437	740	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270058	198270058	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	105	461	1	ENST00000335508.6:c.1378C>T	p.Pro460Ser	p.P460S	ENST00000335508	NM_012433.2	460	Cca/Tca	10/25	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.438738858638156	2		462	457	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757426	40757426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	152	600	0	ENST00000373198.4:c.2872C>T	p.His958Tyr	p.H958Y	ENST00000373198	NM_133170.3	958	Cac/Tac	20/32	0.271253973124443	0	FACETS	0.594	0.545	0.645			1	SUBCLONAL	1	TRUE	0	0.438738858638156	0		600	655	SUCCESS
REST	5978	MSKCC	GRCh37	4	57777291	57777291	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	134	660	0	ENST00000309042.7:c.487C>T	p.Pro163Ser	p.P163S	ENST00000309042	NM_005612.4	163	Cca/Tca	2/4	1	2	FACETS	0.834	0.759	0.913	0.834	0.759	0.913	CLONAL	1	TRUE	1	0.438738858638156	2		660	732	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982057	93982057	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	116	507	0	ENST00000369303.4:c.1408A>G	p.Asn470Asp	p.N470D	ENST00000369303	NM_004440.3	470	Aat/Gat	6/17	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.438738858638156	2		507	495	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949078	151949078	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	59	509	0	ENST00000262189.6:c.1567G>T	p.Glu523Ter	p.E523*	ENST00000262189	NM_170606.2	523	Gag/Tag	11/59	1	2	FACETS	0.658	0.568	0.755	0.658	0.568	0.755	SUBCLONAL	1	TRUE	1	0.438738858638156	2		509	409	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395120	139395120	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745809124	NA	P-0060254-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	199	771	2	ENST00000277541.6:c.5818C>T	p.Arg1940Cys	p.R1940C	ENST00000277541	NM_017617.3	1940	Cgc/Tgc	31/34	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.438738858638156	2		773	884	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	231	475	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.928	0.869	0.988	0.928	0.869	0.988	CLONAL	1	TRUE	1	0.68789241620235	2		475	724	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356248	66356248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202046693	NA	P-0060255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	350	772	0	ENST00000273854.3:c.1249C>T	p.Arg417Trp	p.R417W	ENST00000273854	NM_004439.5	417	Cgg/Tgg	5/18	1	2	FACETS	0.99	0.939	1	0.99	0.939	1	CLONAL	1	TRUE	1	0.68789241620235	2		772	1028	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs878854073	NA	P-0060255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	62	564	0	ENST00000269305.4:c.673-1G>A		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.688337618136459	1	FACETS	0.22	0.19	0.252	0.22	0.19	0.252	SUBCLONAL	1	TRUE	0	0.68789241620235	1		564	538	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021205	31021205	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	520	777	0	ENST00000375687.4:c.1204C>T	p.Arg402Ter	p.R402*	ENST00000375687	NM_015338.5	402	Cga/Tga	12/13	0.316598035473883	3	FACETS	0.821	0.788	0.854	0.821	0.788	0.854	INDETERMINATE	2	TRUE	1	0.68789241620235	3		777	1238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578270	7578270	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	428	825	0	ENST00000269305.4:c.579T>G	p.His193Gln	p.H193Q	ENST00000269305	NM_001126112.2	193	caT/caG	6/11	0.688337618136459	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.68789241620235	1		825	816	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645270	67645270	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	355	689	0	ENST00000264010.4:c.535G>T	p.Glu179Ter	p.E179*	ENST00000264010	NM_006565.3	179	Gaa/Taa	3/12	1	2	FACETS	0.95	0.902	1	0.95	0.902	1	CLONAL	1	TRUE	1	0.68789241620235	2		689	1086	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244538	41244538	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786202534	NA	P-0060255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	306	577	0	ENST00000357654.3:c.3010G>C	p.Glu1004Gln	p.E1004Q	ENST00000357654	NM_007294.3	1004	Gag/Cag	10/23	0.688337618136459	3	FACETS	1	0.977	1	0.534	0.503	0.565	CLONAL	1	TRUE	1	0.68789241620235	3		577	1120	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981812	201981812	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1196877377	NA	P-0060255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	427	755	2	ENST00000359651.3:c.523C>T	p.Gln175Ter	p.Q175*	ENST00000359651		175	Caa/Taa	4/8	0.357252153943194	1	FACETS	0.888	0.851	0.926	0.888	0.851	0.926	INDETERMINATE	1	TRUE	0	0.68789241620235	1		757	917	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061500	38061501	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	334	692	0	ENST00000250448.2:c.488dup	p.Arg164AlafsTer63	p.R164Afs*63	ENST00000250448	NM_004496.3	163	aag/aaAg	2/2	1	2	FACETS	0.994	0.942	1	0.994	0.942	1	CLONAL	1	TRUE	1	0.68789241620235	2		692	977	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831281	3831281	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	302	450	0	ENST00000262367.5:c.1600G>T	p.Gly534Ter	p.G534*	ENST00000262367	NM_004380.2	534	Gga/Tga	7/31	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.68789241620235	2		450	748	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645132	67645132	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	336	732	0	ENST00000264010.4:c.397G>C	p.Glu133Gln	p.E133Q	ENST00000264010	NM_006565.3	133	Gaa/Caa	3/12	1	2	FACETS	0.92	0.871	0.97	0.92	0.871	0.97	CLONAL	1	TRUE	1	0.68789241620235	2		732	1062	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244321	41244321	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs80357313	NA	P-0060255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	289	534	0	ENST00000357654.3:c.3227G>C	p.Arg1076Thr	p.R1076T	ENST00000357654	NM_007294.3	1076	aGa/aCa	10/23	0.688337618136459	3	FACETS	0.97	0.912	1	0.485	0.456	0.515	CLONAL	1	TRUE	1	0.68789241620235	3		534	1164	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62325742	62325742	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	275	571	0	ENST00000360203.5:c.3010C>G	p.Pro1004Ala	p.P1004A	ENST00000360203	NM_001283009.1	1004	Ccc/Gcc	31/35	0.316598035473883	3	FACETS	1	0.985	1	0.572	0.537	0.607	INDETERMINATE	1	TRUE	1	0.68789241620235	3		571	940	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627837	187627838	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0060255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	432	643	0	ENST00000441802.2:c.3144dup	p.Val1049CysfsTer12	p.V1049Cfs*12	ENST00000441802	NM_005245.3	1048	-/T	2/27	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.68789241620235	2		643	992	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974751	21974751	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1317637377	NA	P-0060255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	676	815	0	ENST00000304494.5:c.76G>C	p.Glu26Gln	p.E26Q	ENST00000304494	NM_000077.4	26	Gag/Cag	1/3	0.68789241620235	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.68789241620235	2		815	945	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974760	21974760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1131691186	NA	P-0060255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	662	831	0	ENST00000304494.5:c.67G>A	p.Gly23Ser	p.G23S	ENST00000304494	NM_000077.4	23	Ggt/Agt	1/3	0.68789241620235	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.68789241620235	2		831	941	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034438	47034438	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	258	517	0	ENST00000377604.3:c.523T>A	p.Phe175Ile	p.F175I	ENST00000377604	NM_001204468.1	175	Ttc/Atc	6/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.68789241620235	2		517	715	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356338	70356338	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060255-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	404	832	0	ENST00000374080.3:c.5237del	p.Pro1746GlnfsTer12	p.P1746Qfs*12	ENST00000374080		1745	Ccc/cc	37/45	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.68789241620235	2		832	1172	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0060256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	27	279	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.472	0.375	0.584	0.472	0.375	0.584	SUBCLONAL	1	TRUE	1	0.22	2		279	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0060256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	33	907	0	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			1	2	FACETS	0.297	0.24	0.361	0.297	0.24	0.361	SUBCLONAL	1	TRUE	1	0.22	2		907	1011	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141492	11141492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060256-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	35	764	0	ENST00000358026.2:c.3469C>T	p.Arg1157Trp	p.R1157W	ENST00000358026	NM_001128849.1	1157	Cgg/Tgg	25/36	1	2	FACETS	0.385	0.314	0.465	0.385	0.314	0.465	SUBCLONAL	1	TRUE	1	0.22	2		764	826	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0060258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	122	279	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.154277498731054	6	FACETS	0.871	0.795	0.949	0.871	0.795	0.949	INDETERMINATE	3	FALSE	3	0.490853015213265	6		279	377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0060258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	377	580	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.372089579524381	3	FACETS	1	0.993	1	0.813	0.777	0.849	CLONAL	2	FALSE	0	0.490853015213265	3		580	784	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731199	162731199	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	294	621	0	ENST00000367921.3:c.1054T>G	p.Phe352Val	p.F352V	ENST00000367921	NM_006182.2	352	Ttt/Gtt	9/18	0.438395146459642	3	FACETS	0.937	0.886	0.989	0.937	0.886	0.989	CLONAL	2	FALSE	1	0.490853015213265	3		621	796	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435567	18435567	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	180	480	0	ENST00000266497.5:c.552T>G	p.Ser184Arg	p.S184R	ENST00000266497		184	agT/agG	1/31	0.154277498731054	6	FACETS	0.886	0.822	0.951	0.886	0.822	0.951	INDETERMINATE	3	FALSE	3	0.490853015213265	6		480	547	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357108	89357108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs900210533	NA	P-0060258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	167	762	0	ENST00000301030.4:c.526G>A	p.Ala176Thr	p.A176T	ENST00000301030	NM_001256183.1	176	Gcc/Acc	6/13	0.154277498731054	6	FACETS	1	0.977	1	0.393	0.36	0.428	INDETERMINATE	1	FALSE	3	0.490853015213265	6		762	1143	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0060258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	286	530	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.447334587178331	3	FACETS	0.847	0.805	0.889	0.847	0.805	0.889	CLONAL	3	FALSE	0	0.490853015213265	3		530	571	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985473	2985473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	218	465	0	ENST00000396946.4:c.338G>A	p.Arg113Gln	p.R113Q	ENST00000396946	NM_032415.4	113	cGg/cAg	4/25	0.416434369691606	5	FACETS	0.995	0.928	1	0.663	0.619	0.709	CLONAL	2	FALSE	2	0.490853015213265	5		465	775	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786928	135786928	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373454700	NA	P-0060258-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	117	460	0	ENST00000298552.3:c.941C>T	p.Thr314Met	p.T314M	ENST00000298552	NM_001162426.1	314	aCg/aTg	10/23	0.154277498731054	6	FACETS	1	0.971	1	0.402	0.362	0.444	INDETERMINATE	1	FALSE	3	0.490853015213265	6		460	783	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0060259-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	121	527	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.281332285370508	2		528	677	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971175	21971182	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCGCCA	CTCCGCCA	-	novel	NA	P-0060259-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	99	630	0	ENST00000304494.5:c.176_183del	p.Val59AlafsTer58	p.V59Afs*58	ENST00000304494	NM_000077.4	59	gTGGCGGAG/g	2/3	0.274202124158846	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.281332285370508	1		630	445	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396502	30396502	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060259-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	62	520	0	ENST00000331968.5:c.217A>G	p.Ser73Gly	p.S73G	ENST00000331968	NM_002742.2	73	Agc/Ggc	1/18	1	2	FACETS	0.979	0.848	1	0.979	0.848	1	CLONAL	1	TRUE	1	0.281332285370508	2		520	450	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600515	10600516	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0060259-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	66	646	0	ENST00000171111.5:c.1339_1340del	p.Arg447GlyfsTer2	p.R447Gfs*2	ENST00000171111	NM_203500.1	447	CGg/g	4/6	0.274202124158846	1	FACETS	0.751	0.652	0.857	0.751	0.652	0.857	SUBCLONAL	1	TRUE	0	0.281332285370508	1		646	537	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0060260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	220	66	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.22126752358076	8	FACETS	0.967	0.917	1	1	0.991	1	CLONAL	9	FALSE	1	0.22126752358076	8		66	380	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0060260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	217	475	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	1	0.963	1	1	0.995	1	CLONAL	3	FALSE	1	0.22126752358076	2		475	627	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	325	471	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	1	0.97	1	1	0.997	1	CLONAL	3	FALSE	1	0.22126752358076	2		471	947	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179455	56179457	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	novel	NA	P-0060260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	175	441	0	ENST00000399503.3:c.3770_3772del	p.Cys1257del	p.C1257del	ENST00000399503	NM_005921.1	1256	tcTTGt/tct	15/20	1	2	FACETS	0.85	0.787	0.916	1	0.994	1	CLONAL	3	FALSE	1	0.22126752358076	2		441	620	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645413	215645414	+	missense_variant	Missense_Mutation	DNP	TG	TG	CC	novel	NA	P-0060260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	216	548	0	ENST00000260947.4:c.1184_1185delinsGG	p.Pro395Arg	p.P395R	ENST00000260947	NM_000465.2	395	cCA/cGG	4/11	1	2	FACETS	0.986	0.922	1	1	0.995	1	CLONAL	3	FALSE	1	0.22126752358076	2		548	660	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180580	56180581	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0060260-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	126	445	0	ENST00000399503.3:c.3911dup	p.Asn1305LysfsTer4	p.N1305Kfs*4	ENST00000399503	NM_005921.1	1303	-/C	16/20	1	2	FACETS	0.897	0.819	0.978	1	0.992	1	CLONAL	3	FALSE	1	0.22126752358076	2		445	423	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060261-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	47	475	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.324	0.274	0.38	0.324	0.274	0.38	SUBCLONAL	1	TRUE	1	0.63	2		475	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578412	7578414	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0060261-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	37	582	0	ENST00000269305.4:c.516_518del	p.Val173del	p.V173del	ENST00000269305	NM_001126112.2	172	gtTGTg/gtg	5/11	1	2	FACETS	0.18	0.148	0.216	0.18	0.148	0.216	SUBCLONAL	1	TRUE	1	0.63	2		582	653	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599916	10599916	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs946921406	NA	P-0060261-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	29	467	0	ENST00000171111.5:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000171111	NM_203500.1	554	Cga/Tga	5/6	1	2	FACETS	0.173	0.138	0.213	0.173	0.138	0.213	SUBCLONAL	1	TRUE	1	0.63	2		467	531	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897079	28897079	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060261-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	25	365	0	ENST00000282397.4:c.2801C>T	p.Ala934Val	p.A934V	ENST00000282397	NM_002019.4	934	gCa/gTa	21/30	1	2	FACETS	0.16	0.125	0.2	0.16	0.125	0.2	SUBCLONAL	1	TRUE	1	0.63	2		365	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0060263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	257	864	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.663572933269028	1	FACETS	0.987	0.935	1	0.987	0.935	1	CLONAL	1	TRUE	0	0.671662568080527	1		864	515	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736302	243736302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	382	477	0	ENST00000263826.5:c.745C>A	p.Arg249Ser	p.R249S	ENST00000263826	NM_005465.4	249	Cgt/Agt	8/13	0.671662568080527	4	FACETS	0.931	0.887	0.976	0.931	0.887	0.976	CLONAL	2	TRUE	2	0.671662568080527	4		477	1021	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778026	135778026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	212	513	0	ENST00000298552.3:c.2357G>T	p.Arg786Leu	p.R786L	ENST00000298552	NM_001162426.1	786	cGa/cTa	18/23	1	2	FACETS	0.993	0.927	1	0.993	0.927	1	CLONAL	1	TRUE	1	0.671662568080527	2		513	636	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260029	16260029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	107	707	0	ENST00000375759.3:c.7294C>T	p.Pro2432Ser	p.P2432S	ENST00000375759	NM_015001.2	2432	Ccc/Tcc	11/15	1	2	FACETS	0.389	0.348	0.432	0.389	0.348	0.432	SUBCLONAL	1	TRUE	1	0.671662568080527	2		707	819	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260156	16260156	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	106	655	0	ENST00000375759.3:c.7421C>G	p.Ser2474Cys	p.S2474C	ENST00000375759	NM_015001.2	2474	tCt/tGt	11/15	1	2	FACETS	0.37	0.331	0.411	0.37	0.331	0.411	SUBCLONAL	1	TRUE	1	0.671662568080527	2		655	854	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432197	121432208	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GTAAGGTCCACG	GTAAGGTCCACG	-	novel	NA	P-0060263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	177	576	0	ENST00000257555.6:c.949_955+5del		p.SKVHGdel	ENST00000257555		315	aGTAAGGTCCACGgt/agt	4/10	1	2	FACETS	0.849	0.786	0.914	0.849	0.786	0.914	CLONAL	1	TRUE	1	0.671662568080527	2		576	621	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375557	15375557	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	240	629	0	ENST00000263377.2:c.870G>C	p.Arg290Ser	p.R290S	ENST00000263377	NM_058243.2	290	agG/agC	6/20	1	2	FACETS	0.998	0.936	1	0.998	0.936	1	CLONAL	1	TRUE	1	0.671662568080527	2		629	716	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131234	202131234	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060263-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	68	507	0	ENST00000358485.4:c.202G>C	p.Asp68His	p.D68H	ENST00000358485	NM_001080125.1	68	Gat/Cat	2/9	1	2	FACETS	0.35	0.304	0.399	0.35	0.304	0.399	SUBCLONAL	1	TRUE	1	0.671662568080527	2		507	579	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756823	756823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060264-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	27	403	0	ENST00000314574.4:c.5G>A	p.Gly2Asp	p.G2D	ENST00000314574	NM_005433.3	2	gGc/gAc	2/12	1	2	FACETS	0.951	0.756	1	0.951	0.756	1	CLONAL	1	TRUE	1	0.12	2		403	473	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732969	30732969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893810	NA	P-0060264-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	44	563	0	ENST00000295754.5:c.1582C>T	p.Arg528Cys	p.R528C	ENST00000295754	NM_003242.5	528	Cgt/Tgt	7/7	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.12	2		563	689	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955550	48955550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913304	NA	P-0060279-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	59	293	0	ENST00000267163.4:c.1666C>T	p.Arg556Ter	p.R556*	ENST00000267163	NM_000321.2	556	Cga/Tga	17/27	0.199204992039811	3	FACETS	0.987	0.883	1	1	0.982	1	CLONAL	6	FALSE	0	0.199204992039811	3		293	110	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878186	48878186	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0060279-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	420	526	0	ENST00000267163.4:c.137+1G>C		p.X46_splice	ENST00000267163	NM_000321.2	46			0.199204992039811	3	FACETS	1	0.971	1	1	0.997	1	CLONAL	5	FALSE	0	0.199204992039811	3		526	911	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0060280-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	273	446	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.681091393633814	2	FACETS	0.995	0.953	1	0.995	0.953	1	CLONAL	2	TRUE	0	0.681091393633814	2		446	403	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347867	347867	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0060280-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	177	704	0	ENST00000262320.3:c.1639A>T	p.Lys547Ter	p.K547*	ENST00000262320	NM_003502.3	547	Aag/Tag	6/11	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.681091393633814	2		704	351	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667532	29667532	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060280-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	37	313	0	ENST00000356175.3:c.6868C>A	p.Leu2290Met	p.L2290M	ENST00000356175	NM_000267.3	2290	Ctg/Atg	46/57	0.593299798287721	3	FACETS	0.293	0.241	0.351	0.147	0.12	0.176	SUBCLONAL	1	TRUE	1	0.681091393633814	3		313	497	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036906	180036906	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060280-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	81	494	0	ENST00000261937.6:c.3806T>C	p.Val1269Ala	p.V1269A	ENST00000261937	NM_182925.4	1269	gTg/gCg	28/30	0.670883518692184	4	FACETS	0.728	0.643	0.82	0.243	0.214	0.274	SUBCLONAL	1	TRUE	1	0.681091393633814	4		494	549	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319929	8319929	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060280-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	187	375	0	ENST00000356435.5:c.5572A>T	p.Ser1858Cys	p.S1858C	ENST00000356435		1858	Agc/Tgc	34/35	0.493404124931322	4	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	2	0.681091393633814	4		375	442	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013719	170013719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388201066	NA	P-0060281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	42	275	0	ENST00000295797.4:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000295797	NM_002740.5	480	Cgc/Tgc	15/18	1	2	FACETS	0.827	0.707	0.953	0.827	0.707	0.953	CLONAL	1	TRUE	1	0.806040438257225	2		275	126	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	98	475	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.939	0.852	1	0.939	0.852	1	CLONAL	1	TRUE	1	0.806040438257225	2		475	259	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0060281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	218	665	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.959	0.899	1	0.959	0.899	1	CLONAL	1	TRUE	1	0.806040438257225	2		665	564	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022913	27022938	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGCCGCCGCCAGCAGCCTGGGCAA	CCCGCCGCCGCCAGCAGCCTGGGCAA	-	rs797045262	NA	P-0060281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	131	486	0	ENST00000324856.7:c.31_56del	p.Ser11AlafsTer91	p.S11Afs*91	ENST00000324856	NM_006015.4	7	CCCGCCGCCGCCAGCAGCCTGGGCAAc/c	1/20	1	2	FACETS	0.701	0.64	0.763	0.701	0.64	0.763	SUBCLONAL	1	TRUE	1	0.806040438257225	2		486	464	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858184	9858184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	227	621	0	ENST00000330684.3:c.3217G>A	p.Glu1073Lys	p.E1073K	ENST00000330684	NM_001134407.1	1073	Gaa/Aaa	13/13	1	2	FACETS	0.976	0.917	1	0.976	0.917	1	CLONAL	1	TRUE	1	0.806040438257225	2		621	577	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288486	15288486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	132	489	0	ENST00000263388.2:c.4253C>T	p.Ser1418Leu	p.S1418L	ENST00000263388	NM_000435.2	1418	tCg/tTg	24/33	1	2	FACETS	0.721	0.66	0.785	0.721	0.66	0.785	SUBCLONAL	1	TRUE	1	0.806040438257225	2		489	454	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858238	9858238	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs370107080	NA	P-0060281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	218	571	0	ENST00000330684.3:c.3163G>C	p.Glu1055Gln	p.E1055Q	ENST00000330684	NM_001134407.1	1055	Gag/Cag	13/13	1	2	FACETS	0.973	0.912	1	0.973	0.912	1	CLONAL	1	TRUE	1	0.806040438257225	2		571	556	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456456	89456456	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	143	408	0	ENST00000336596.2:c.1632G>A	p.Met544Ile	p.M544I	ENST00000336596	NM_005233.5	544	atG/atA	8/17	1	2	FACETS	0.868	0.799	0.938	0.868	0.799	0.938	CLONAL	1	TRUE	1	0.806040438257225	2		408	409	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022959	27022959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377110828	NA	P-0060281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	164	486	0	ENST00000324856.7:c.65C>T	p.Ser22Leu	p.S22L	ENST00000324856	NM_006015.4	22	tCg/tTg	1/20	1	2	FACETS	0.974	0.904	1	0.974	0.904	1	CLONAL	1	TRUE	1	0.806040438257225	2		486	418	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877124	89877124	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121907930	NA	P-0060281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	83	344	0	ENST00000389301.3:c.513G>A	p.Trp171Ter	p.W171*	ENST00000389301	NM_000135.2	171	tgG/tgA	5/43	1	2	FACETS	0.804	0.72	0.892	0.804	0.72	0.892	CLONAL	1	TRUE	1	0.806040438257225	2		344	256	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38793777	38793777	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	232	424	0	ENST00000348513.6:c.204G>T	p.Lys68Asn	p.K68N	ENST00000348513	NM_003079.4	68	aaG/aaT	5/11	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.806040438257225	2		424	571	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260637	10260637	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	131	385	0	ENST00000340748.4:c.2225G>A	p.Gly742Glu	p.G742E	ENST00000340748		742	gGg/gAg	24/40	1	2	FACETS	0.862	0.791	0.935	0.862	0.791	0.935	CLONAL	1	TRUE	1	0.806040438257225	2		385	377	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257988	19257988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	239	588	0	ENST00000162023.5:c.398C>T	p.Ala133Val	p.A133V	ENST00000162023		133	gCa/gTa	9/13	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.806040438257225	2		588	584	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572362	41572362	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	263	566	0	ENST00000263253.7:c.4891C>G	p.Leu1631Val	p.L1631V	ENST00000263253	NM_001429.3	1631	Ctc/Gtc	30/31	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.806040438257225	2		566	618	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945225	44945225	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0060281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	53	290	0	ENST00000377967.4:c.3548+1G>C		p.X1183_splice	ENST00000377967	NM_021140.2	1183			1	2	FACETS	0.967	0.846	1	0.967	0.846	1	CLONAL	1	TRUE	1	0.806040438257225	2		290	136	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44970653	44970656	+	frameshift_variant,stop_lost	Frame_Shift_Del	DEL	TTGA	TTGA	-	novel	NA	P-0060281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	89	302	0	ENST00000377967.4:c.4204_*1del		p.S*1401fs	ENST00000377967	NM_021140.2	1401	tcTTGA/tc	29/29	1	2	FACETS	0.99	0.895	1	0.99	0.895	1	CLONAL	1	TRUE	1	0.806040438257225	2		302	223	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182854	123182854	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0060281-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	38	228	0	ENST00000218089.9:c.820-1G>C		p.X274_splice	ENST00000218089	NM_001042749.1	274			1	2	FACETS	0.857	0.728	0.993	0.857	0.728	0.993	CLONAL	1	TRUE	1	0.806040438257225	2		228	110	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0060282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	34	289	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.874	0.715	1	0.874	0.715	1	CLONAL	1	TRUE	1	0.210159749684207	2		289	370	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0060282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	39	217	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.204684978313043	4	FACETS	1	0.93	1	0.622	0.517	0.739	CLONAL	1	TRUE	2	0.210159749684207	4		217	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0060282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	11	721	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	1	2	FACETS	0.252	0.173	0.351	0.252	0.173	0.351	SUBCLONAL	1	TRUE	1	0.210159749684207	2		721	415	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203621	108203621	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs769523686	NA	P-0060282-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	33	280	0	ENST00000278616.4:c.7921C>T	p.Gln2641Ter	p.Q2641*	ENST00000278616	NM_000051.3	2641	Cag/Tag	53/63	0.210159749684207	1	FACETS	0.822	0.67	0.992	0.822	0.67	0.992	CLONAL	1	TRUE	0	0.210159749684207	1		280	342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0060283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	254	671	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.556538269033141	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.556538269033141	2		671	442	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731475	47731475	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	106	569	0	ENST00000449228.1:c.317C>T	p.Pro106Leu	p.P106L	ENST00000449228	NM_001127240.2	106	cCt/cTt	2/4	0.556538269033141	4	FACETS	0.99	0.889	1	0.33	0.296	0.366	CLONAL	1	TRUE	1	0.556538269033141	4		569	599	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265880	41266334	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGT	TTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGT	-	novel	NA	P-0060283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	94	91	0	ENST00000349496.5:c.14-136_241+91del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.556538269033141	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	0	0.556538269033141	3		91	125	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356095	66356095	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	71	378	0	ENST00000273854.3:c.1402G>A	p.Ala468Thr	p.A468T	ENST00000273854	NM_004439.5	468	Gct/Act	5/18	0.556538269033141	3	FACETS	0.83	0.728	0.939	0.415	0.364	0.47	CLONAL	1	TRUE	1	0.556538269033141	3		378	393	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	132	475	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.436634250542623	2		475	599	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs104886003	NA	P-0060285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	52	277	0	ENST00000263967.3:c.1633G>C	p.Glu545Gln	p.E545Q	ENST00000263967	NM_006218.2	545	Gag/Cag	10/21	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.436634250542623	2		277	236	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549865	187549865	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs750386635	NA	P-0060285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	115	409	0	ENST00000441802.2:c.4376C>G	p.Ser1459Ter	p.S1459*	ENST00000441802	NM_005245.3	1459	tCa/tGa	8/27	1	2	FACETS	0.941	0.85	1	0.941	0.85	1	CLONAL	1	TRUE	1	0.436634250542623	2		409	560	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180870	106180870	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	100	434	0	ENST00000380013.4:c.3898T>G	p.Phe1300Val	p.F1300V	ENST00000380013	NM_001127208.2	1300	Ttt/Gtt	7/11	1	2	FACETS	0.889	0.797	0.986	0.889	0.797	0.986	CLONAL	1	TRUE	1	0.436634250542623	2		434	515	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324464	31324464	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1168937188	NA	P-0060285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	220	713	0	ENST00000412585.2:c.343+1G>A		p.X115_splice	ENST00000412585	NM_005514.6	115			1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.436634250542623	2		713	995	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203684	94203684	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	138	397	0	ENST00000323929.3:c.970G>C	p.Asp324His	p.D324H	ENST00000323929	NM_005591.3	324	Gat/Cat	9/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.436634250542623	2		397	538	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353815	68353815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	224	434	0	ENST00000487270.1:c.650G>A	p.Arg217Lys	p.R217K	ENST00000487270	NM_133509.3	217	aGa/aAa	7/11	0.436634250542623	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.436634250542623	2		434	498	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098948	178098949	+	inframe_insertion	In_Frame_Ins	INS	-	-	TACTCC	novel	NA	P-0060285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	145	429	0	ENST00000397062.3:c.91_96dup	p.Gly31_Val32dup	p.G31_V32dup	ENST00000397062	NM_006164.4	31	-/GGAGTA	2/5	1	2	FACETS	0.972	0.889	1	0.972	0.889	1	CLONAL	1	TRUE	1	0.436634250542623	2		429	683	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566494	41566499	+	inframe_deletion	In_Frame_Del	DEL	ACCCAA	ACCCAA	-	rs1555911316	NA	P-0060285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	160	462	0	ENST00000263253.7:c.4371_4376del	p.Ile1457_Lys1459delinsMet	p.I1457_K1459delinsM	ENST00000263253	NM_001429.3	1457	atACCCAAg/atg	27/31	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.436634250542623	2		462	671	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924762	49924762	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	221	619	0	ENST00000296474.3:c.4181C>T	p.Ser1394Leu	p.S1394L	ENST00000296474	NM_002447.2	1394	tCa/tTa	20/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.436634250542623	2		619	967	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253862	153253865	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	CTC	novel	NA	P-0060285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	57	314	0	ENST00000281708.4:c.868_871delinsGAG	p.Leu290GlufsTer52	p.L290Efs*52	ENST00000281708	NM_033632.3	290	CTCTat/GAGat	6/12	1	2	FACETS	0.711	0.613	0.818	0.711	0.613	0.818	SUBCLONAL	1	TRUE	1	0.436634250542623	2		314	367	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534536	140534536	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	129	525	0	ENST00000288602.6:c.377C>A	p.Ser126Tyr	p.S126Y	ENST00000288602	NM_004333.4	126	tCt/tAt	3/18	1	2	FACETS	0.833	0.757	0.914	0.833	0.757	0.914	CLONAL	1	TRUE	1	0.436634250542623	2		525	709	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534545	140534545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060285-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	132	516	0	ENST00000288602.6:c.368C>T	p.Ser123Phe	p.S123F	ENST00000288602	NM_004333.4	123	tCt/tTt	3/18	1	2	FACETS	0.842	0.766	0.922	0.842	0.766	0.922	CLONAL	1	TRUE	1	0.436634250542623	2		516	718	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	161	372	2	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.374682890603366	3	FACETS	1	0.984	1	0.649	0.596	0.704	CLONAL	1	TRUE	1	0.374682890603366	3		374	786	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	106	575	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	0.937	0.842	1	0.937	0.842	1	CLONAL	1	TRUE	1	0.374682890603366	2		575	604	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	149	298	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.842	0.768	0.918	0.842	0.768	0.918	CLONAL	1	TRUE	1	0.374682890603366	2		299	945	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	130	758	2	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	2	FACETS	0.738	0.669	0.811	0.738	0.669	0.811	SUBCLONAL	1	TRUE	1	0.374682890603366	2		760	940	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	372	699	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.968	1	1	0.997	1	CLONAL	2	TRUE	1	0.374682890603366	2		706	972	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	157	501	0	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.374682890603366	2		501	812	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	97	332	0	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.948	0.848	1	0.948	0.848	1	CLONAL	1	TRUE	1	0.374682890603366	2		332	546	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	90	388	2	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.823	0.731	0.92	0.823	0.731	0.92	CLONAL	1	TRUE	1	0.374682890603366	2		390	584	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681120	117681120	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs748436511	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	86	385	2	ENST00000368508.3:c.3500del	p.Leu1167Ter	p.L1167*	ENST00000368508	NM_002944.2	1167	tTa/ta	23/43	1	2	FACETS	0.766	0.679	0.86	0.766	0.679	0.86	SUBCLONAL	1	TRUE	1	0.374682890603366	2		387	599	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43733757	43733757	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	133	334	0	ENST00000382044.4:c.3065del	p.Asn1022MetfsTer20	p.N1022Mfs*20	ENST00000382044	NM_001141980.1	1022	aAt/at	15/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.374682890603366	2		334	609	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378266	225378266	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	66	308	0	ENST00000264414.4:c.629del	p.Leu210TrpfsTer16	p.L210Wfs*16	ENST00000264414	NM_003590.4	210	tTg/tg	5/16	1	2	FACETS	0.779	0.678	0.888	0.779	0.678	0.888	SUBCLONAL	1	TRUE	1	0.374682890603366	2		308	452	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130352	2130352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773951533	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	157	612	0	ENST00000219476.3:c.3584C>T	p.Ala1195Val	p.A1195V	ENST00000219476	NM_000548.3	1195	gCg/gTg	30/42	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.374682890603366	2		612	788	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393656	139393656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196509879	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	171	588	0	ENST00000277541.6:c.5990C>T	p.Thr1997Met	p.T1997M	ENST00000277541	NM_017617.3	1997	aCg/aTg	32/34	0.374682890603366	3	FACETS	1	0.937	1	0.512	0.47	0.555	CLONAL	1	TRUE	1	0.374682890603366	3		588	1059	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17743002	17743002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	153	489	2	ENST00000250003.3:c.910G>A	p.Ala304Thr	p.A304T	ENST00000250003	NM_002478.4	304	Gcc/Acc	3/3	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.374682890603366	2		491	655	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	87	366	1	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	0.374682890603366	2	FACETS	1	0.911	1	0.514	0.457	0.574	CLONAL	1	TRUE	0	0.374682890603366	2		367	452	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446283	70446284	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	146	573	0	ENST00000373644.4:c.5230dup	p.Arg1744LysfsTer26	p.R1744Kfs*26	ENST00000373644	NM_030625.2	1741	-/A	11/12	0.374682890603366	3	FACETS	0.913	0.832	0.997	0.456	0.416	0.499	CLONAL	1	TRUE	1	0.374682890603366	3		573	1014	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574571	41574571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1338889339	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	135	645	0	ENST00000263253.7:c.6856C>T	p.Pro2286Ser	p.P2286S	ENST00000263253	NM_001429.3	2286	Cca/Tca	31/31	1	2	FACETS	0.887	0.807	0.972	0.887	0.807	0.972	CLONAL	1	TRUE	1	0.374682890603366	2		645	812	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	150	595	7	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	0.946	0.865	1	0.946	0.865	1	CLONAL	1	TRUE	1	0.374682890603366	2		602	846	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	115	525	4	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	1	2	FACETS	0.904	0.816	0.997	0.904	0.816	0.997	CLONAL	1	TRUE	1	0.374682890603366	2		529	679	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012465	29012465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373801409	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	80	448	0	ENST00000282397.4:c.406G>A	p.Val136Ile	p.V136I	ENST00000282397	NM_002019.4	136	Gta/Ata	4/30	1	2	FACETS	0.798	0.704	0.899	0.798	0.704	0.899	SUBCLONAL	1	TRUE	1	0.374682890603366	2		448	535	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661664	227661664	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs761880048	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	158	669	13	ENST00000305123.5:c.1791del	p.His598ThrfsTer38	p.H598Tfs*38	ENST00000305123	NM_005544.2	597	ggG/gg	1/2	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.374682890603366	2		682	747	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	114	424	3	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	1	2	FACETS	0.926	0.835	1	0.926	0.835	1	CLONAL	1	TRUE	1	0.374682890603366	2		427	657	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483185	120483185	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	119	485	0	ENST00000256646.2:c.3176del	p.Asn1059ThrfsTer6	p.N1059Tfs*6	ENST00000256646	NM_024408.3	1059	aAc/ac	19/34	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.374682890603366	2		485	633	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969848	81969848	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568724894	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	133	507	0	ENST00000359376.3:c.2917G>A	p.Asp973Asn	p.D973N	ENST00000359376	NM_002661.3	973	Gac/Aac	27/33	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.374682890603366	2		507	690	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625120	69625120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782246758	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	121	456	0	ENST00000334134.2:c.673G>A	p.Val225Ile	p.V225I	ENST00000334134	NM_005247.2	225	Gtt/Att	3/3	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.374682890603366	2		456	604	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664761	138664761	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs797044528	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	93	440	0	ENST00000330315.3:c.804del	p.Gly269AlafsTer2	p.G269Afs*2	ENST00000330315	NM_023067.3	268	ccC/cc	1/1	1	2	FACETS	0.911	0.812	1	0.911	0.812	1	CLONAL	1	TRUE	1	0.374682890603366	2		440	545	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532654	63532654	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	112	533	2	ENST00000307078.5:c.1925del	p.Lys642ArgfsTer47	p.K642Rfs*47	ENST00000307078	NM_004655.3	642	aAg/ag	8/11	1	2	FACETS	0.843	0.759	0.932	0.843	0.759	0.932	CLONAL	1	TRUE	1	0.374682890603366	2		535	709	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	157	532	2	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.374682890603366	2		534	759	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66468014	66468014	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	54	267	0	ENST00000273854.3:c.255G>T	p.Glu85Asp	p.E85D	ENST00000273854	NM_004439.5	85	gaG/gaT	3/18	1	2	FACETS	0.814	0.699	0.94	0.814	0.699	0.94	CLONAL	1	TRUE	1	0.374682890603366	2		267	354	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806180	1806181	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760502257	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	136	616	2	ENST00000260795.2:c.1206dup	p.Lys403GlnfsTer93	p.K403Qfs*93	ENST00000260795		400	agc/agCc	8/17	1	2	FACETS	0.841	0.765	0.922	0.841	0.765	0.922	CLONAL	1	TRUE	1	0.374682890603366	2		618	863	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024758	31024758	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs754129466	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	154	591	0	ENST00000375687.4:c.4243C>T	p.Arg1415Ter	p.R1415*	ENST00000375687	NM_015338.5	1415	Cga/Tga	13/13	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.374682890603366	2		591	774	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432651	49432651	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs727503983	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	165	679	2	ENST00000301067.7:c.8488C>T	p.Arg2830Ter	p.R2830*	ENST00000301067	NM_003482.3	2830	Cga/Tga	34/54	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.374682890603366	2		681	838	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499362	89499363	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	155	479	1	ENST00000336596.2:c.2538dup	p.Met847HisfsTer26	p.M847Hfs*26	ENST00000336596	NM_005233.5	844	-/C	15/17	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.374682890603366	2		480	816	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042481	16042481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	62	286	0	ENST00000268712.3:c.1193G>A	p.Arg398Gln	p.R398Q	ENST00000268712	NM_006311.3	398	cGg/cAg	12/46	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.374682890603366	2		286	327	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874012	151874013	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	106	498	0	ENST00000262189.6:c.8525dup	p.Asn2842LysfsTer2	p.N2842Kfs*2	ENST00000262189	NM_170606.2	2842	aat/aaAt	38/59	1	2	FACETS	0.857	0.77	0.95	0.857	0.77	0.95	CLONAL	1	TRUE	1	0.374682890603366	2		498	660	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324132	31324132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41561215	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	72	160	0	ENST00000412585.2:c.431G>A	p.Gly144Asp	p.G144D	ENST00000412585	NM_005514.6	144	gGc/gAc	3/8	0.374682890603366	1	FACETS	0.831	0.741	0.923	1	0.981	1	CLONAL	2	TRUE	0	0.374682890603366	1		160	188	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219029	36219029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748191051	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	151	583	0	ENST00000222270.7:c.4528G>A	p.Ala1510Thr	p.A1510T	ENST00000222270	NM_014727.1	1510	Gcc/Acc	19/37	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.374682890603366	2		583	785	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223104	1223109	+	inframe_deletion	In_Frame_Del	DEL	GGACGA	GGACGA	-	rs762810203	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	161	593	1	ENST00000326873.7:c.1051_1056del	p.Glu351_Asp352del	p.E351_D352del	ENST00000326873	NM_000455.4	347	gcGGACGAg/gcg	8/10	1	2	FACETS	0.967	0.887	1	0.967	0.887	1	CLONAL	1	TRUE	1	0.374682890603366	2		594	889	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497902	25497902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1311728146	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	145	431	0	ENST00000264709.3:c.547C>T	p.Arg183Trp	p.R183W	ENST00000264709	NM_175629.2	183	Cgg/Tgg	6/23	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.374682890603366	2		431	662	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128028913	128028913	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	27	349	3	ENST00000285398.2:c.1944del	p.Met650TrpfsTer32	p.M650Wfs*32	ENST00000285398	NM_000122.1	648	aaA/aa	12/15	1	2	FACETS	0.27	0.214	0.334	0.27	0.214	0.334	SUBCLONAL	1	TRUE	1	0.374682890603366	2		352	534	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210874	36210874	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1002774016	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	161	713	0	ENST00000222270.7:c.625C>T	p.Arg209Trp	p.R209W	ENST00000222270	NM_014727.1	209	Cgg/Tgg	3/37	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.374682890603366	2		713	852	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15967447	15967452	+	inframe_deletion	In_Frame_Del	DEL	TCCCGT	TCCCGT	-	rs770726844	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	118	525	0	ENST00000268712.3:c.5151_5156del	p.Arg1720_Glu1721del	p.R1720_E1721del	ENST00000268712	NM_006311.3	1717	gaACGGGAg/gag	35/46	1	2	FACETS	0.798	0.72	0.881	0.798	0.72	0.881	SUBCLONAL	1	TRUE	1	0.374682890603366	2		525	789	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211545	98211545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370675945	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	150	491	2	ENST00000331920.6:c.3610G>A	p.Val1204Met	p.V1204M	ENST00000331920	NM_000264.3	1204	Gtg/Atg	22/24	0.374682890603366	3	FACETS	1	0.976	1	0.589	0.539	0.642	CLONAL	1	TRUE	1	0.374682890603366	3		493	807	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099947	157099947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	154	592	0	ENST00000346085.5:c.884G>A	p.Cys295Tyr	p.C295Y	ENST00000346085	NM_020732.3	295	tGc/tAc	1/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.374682890603366	2		592	687	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432665	29432665	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs543620241	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	118	450	0	ENST00000389048.3:c.3823C>T	p.Arg1275Ter	p.R1275*	ENST00000389048	NM_004304.4	1275	Cga/Tga	25/29	1	2	FACETS	0.963	0.871	1	0.963	0.871	1	CLONAL	1	TRUE	1	0.374682890603366	2		450	654	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31238184	31238184	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	20	92	0	ENST00000376228.5:c.698A>G	p.Tyr233Cys	p.Y233C	ENST00000376228	NM_002117.5	233	tAc/tGc	4/8	0.374682890603366	1	FACETS	0.885	0.689	1	0.885	0.689	1	CLONAL	1	TRUE	0	0.374682890603366	1		92	98	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149436861	149436861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs281860271	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	113	463	0	ENST00000286301.3:c.2308G>A	p.Ala770Thr	p.A770T	ENST00000286301	NM_005211.3	770	Gct/Act	17/22	1	2	FACETS	0.992	0.895	1	0.992	0.895	1	CLONAL	1	TRUE	1	0.374682890603366	2		463	608	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976674	55976674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201708587	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	87	453	2	ENST00000263923.4:c.1151C>T	p.Thr384Met	p.T384M	ENST00000263923	NM_002253.2	384	aCg/aTg	9/30	1	2	FACETS	0.797	0.706	0.893	0.797	0.706	0.893	SUBCLONAL	1	TRUE	1	0.374682890603366	2		455	583	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028092	69028092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1316821029	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	72	468	0	ENST00000288368.4:c.3251G>A	p.Arg1084Gln	p.R1084Q	ENST00000288368	NM_024870.2	1084	cGg/cAg	26/40	0.374682890603366	2	FACETS	0.754	0.66	0.854	0.377	0.33	0.427	SUBCLONAL	1	TRUE	0	0.374682890603366	2		468	510	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518304	8518304	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	138	387	0	ENST00000356435.5:c.1087T>C	p.Ser363Pro	p.S363P	ENST00000356435		363	Tct/Cct	10/35	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.374682890603366	2		387	565	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237737	16237737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs978129579	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	136	418	1	ENST00000375759.3:c.1184C>T	p.Ala395Val	p.A395V	ENST00000375759	NM_015001.2	395	gCa/gTa	5/15	1	2	FACETS	0.962	0.875	1	0.962	0.875	1	CLONAL	1	TRUE	1	0.374682890603366	2		419	755	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230459244	230459244	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	145	573	0	ENST00000391860.1:c.1157A>G	p.Tyr386Cys	p.Y386C	ENST00000391860	NM_001258311.1	386	tAc/tGc	7/7	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.374682890603366	2		573	772	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274672	123274672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	123	515	1	ENST00000358487.5:c.1246C>T	p.His416Tyr	p.H416Y	ENST00000358487	NM_000141.4	416	Cac/Tac	9/18	0.374682890603366	3	FACETS	0.859	0.777	0.947	0.43	0.388	0.474	CLONAL	1	TRUE	1	0.374682890603366	3		516	907	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50784950	50784950	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs78143971	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	105	342	0	ENST00000307179.4:c.2287C>T	p.Arg763Trp	p.R763W	ENST00000307179		763	Cgg/Tgg	15/20	1	2	FACETS	0.999	0.898	1	0.999	0.898	1	CLONAL	1	TRUE	1	0.374682890603366	2		342	561	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51535010	51535010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	63	466	0	ENST00000260433.2:c.100C>T	p.Leu34Phe	p.L34F	ENST00000260433		34	Ctt/Ttt	2/10	1	2	FACETS	0.521	0.45	0.598	0.521	0.45	0.598	SUBCLONAL	1	TRUE	1	0.374682890603366	2		466	645	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807808	3807808	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	135	412	0	ENST00000262367.5:c.3609+2T>C		p.X1203_splice	ENST00000262367	NM_004380.2	1203			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.374682890603366	2		412	650	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544659	86544659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	125	627	1	ENST00000262426.4:c.484G>A	p.Gly162Ser	p.G162S	ENST00000262426	NM_001451.2	162	Ggc/Agc	1/2	1	2	FACETS	0.881	0.798	0.969	0.881	0.798	0.969	CLONAL	1	TRUE	1	0.374682890603366	2		628	757	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348557	89348557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	144	558	1	ENST00000301030.4:c.4393C>T	p.His1465Tyr	p.H1465Y	ENST00000301030	NM_001256183.1	1465	Cac/Tac	9/13	1	2	FACETS	0.94	0.857	1	0.94	0.857	1	CLONAL	1	TRUE	1	0.374682890603366	2		559	818	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849423	89849423	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754123446	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	151	600	1	ENST00000389301.3:c.1558G>A	p.Asp520Asn	p.D520N	ENST00000389301	NM_000135.2	520	Gac/Aac	16/43	1	2	FACETS	0.915	0.836	0.997	0.915	0.836	0.997	CLONAL	1	TRUE	1	0.374682890603366	2		601	881	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575062	48575062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	107	362	0	ENST00000342988.3:c.256G>A	p.Gly86Ser	p.G86S	ENST00000342988	NM_005359.5	86	Ggt/Agt	3/12	1	2	FACETS	0.963	0.866	1	0.963	0.866	1	CLONAL	1	TRUE	1	0.374682890603366	2		362	593	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10283831	10283831	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769029526	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	146	413	0	ENST00000340748.4:c.655G>A	p.Ala219Thr	p.A219T	ENST00000340748		219	Gca/Aca	8/40	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.374682890603366	2		413	722	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106941	11106941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	175	653	0	ENST00000358026.2:c.1646G>A	p.Arg549His	p.R549H	ENST00000358026	NM_001128849.1	549	cGc/cAc	10/36	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.374682890603366	2		653	877	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11172464	11172464	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867536416	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	144	416	1	ENST00000358026.2:c.5012G>A	p.Arg1671His	p.R1671H	ENST00000358026	NM_001128849.1	1671	cGc/cAc	36/36	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.374682890603366	2		417	645	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469645	25469645	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	55	545	0	ENST00000264709.3:c.1123G>A	p.Val375Met	p.V375M	ENST00000264709	NM_175629.2	375	Gtg/Atg	10/23	1	2	FACETS	0.398	0.339	0.462	0.398	0.339	0.462	SUBCLONAL	1	TRUE	1	0.374682890603366	2		545	738	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795126	242795126	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	129	608	0	ENST00000334409.5:c.83del	p.Pro28GlnfsTer17	p.P28Qfs*17	ENST00000334409	NM_005018.2	28	cCa/ca	2/5	1	2	FACETS	0.981	0.891	1	0.981	0.891	1	CLONAL	1	TRUE	1	0.374682890603366	2		608	702	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569783	41569783	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	145	428	0	ENST00000263253.7:c.4774A>G	p.Lys1592Glu	p.K1592E	ENST00000263253	NM_001429.3	1592	Aaa/Gaa	29/31	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.374682890603366	2		428	651	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575592	55575592	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	78	266	0	ENST00000288135.5:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000288135	NM_000222.2	373	tAc/tGc	7/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.374682890603366	2		266	366	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144258384	144258385	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755581817	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	89	432	2	ENST00000262995.4:c.50dup	p.Glu18GlyfsTer34	p.E18Gfs*34	ENST00000262995	NM_207123.2	15	tcc/tCcc	1/11	1	2	FACETS	0.878	0.781	0.982	0.878	0.781	0.982	CLONAL	1	TRUE	1	0.374682890603366	2		434	541	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959905	38959905	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	106	414	0	ENST00000357387.3:c.2027T>G	p.Leu676Arg	p.L676R	ENST00000357387	NM_152756.3	676	cTg/cGg	21/38	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.374682890603366	2		414	493	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778123	27778123	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	195	785	0	ENST00000369163.2:c.272T>C	p.Met91Thr	p.M91T	ENST00000369163	NM_003536.2	91	aTg/aCg	1/1	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.374682890603366	2		785	990	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511340	157511340	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	117	464	0	ENST00000346085.5:c.3861del	p.Val1288CysfsTer9	p.V1288Cfs*9	ENST00000346085	NM_020732.3	1286	agA/ag	15/20	1	2	FACETS	0.982	0.887	1	0.982	0.887	1	CLONAL	1	TRUE	1	0.374682890603366	2		464	636	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268951	55268951	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	183	594	0	ENST00000275493.2:c.3017A>G	p.Asp1006Gly	p.D1006G	ENST00000275493	NM_005228.3	1006	gAc/gGc	25/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.374682890603366	2		594	844	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371773	116371774	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	102	336	0	ENST00000397752.3:c.1253_1254del	p.Thr418ArgfsTer10	p.T418Rfs*10	ENST00000397752	NM_000245.2	418	ACa/a	3/21	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.374682890603366	2		336	515	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38147995	38147995	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	91	386	0	ENST00000317025.8:c.3116del	p.Lys1039ArgfsTer13	p.K1039Rfs*13	ENST00000317025	NM_023034.1	1039	aAg/ag	17/24	0.374682890603366	2	FACETS	0.783	0.696	0.876	0.392	0.348	0.438	SUBCLONAL	1	TRUE	0	0.374682890603366	2		386	620	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141582970	141582970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	135	461	0	ENST00000220592.5:c.277G>A	p.Val93Met	p.V93M	ENST00000220592	NM_012154.3	93	Gtg/Atg	3/19	0.374682890603366	2	FACETS	1	0.924	1	0.508	0.462	0.556	CLONAL	1	TRUE	0	0.374682890603366	2		461	709	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97876923	97876923	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	99	357	0	ENST00000289081.3:c.1142A>G	p.Asp381Gly	p.D381G	ENST00000289081	NM_000136.2	381	gAc/gGc	12/15	0.374682890603366	3	FACETS	0.887	0.793	0.988	0.444	0.396	0.494	CLONAL	1	TRUE	1	0.374682890603366	3		357	707	SUCCESS
AR	367	MSKCC	GRCh37	X	66943598	66943598	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	104	491	0	ENST00000374690.3:c.2678C>T	p.Pro893Leu	p.P893L	ENST00000374690	NM_000044.3	893	cCg/cTg	8/8	1	2	FACETS	0.909	0.815	1	0.909	0.815	1	CLONAL	1	TRUE	1	0.374682890603366	2		491	611	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0060287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	154	584	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.335218704118201	2		584	775	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0060287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	153	460	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.335218704118201	2		461	674	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0060287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	182	583	0	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.335218704118201	2		583	901	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907621	76907621	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	84	198	0	ENST00000373344.5:c.4540C>T	p.Arg1514Ter	p.R1514*	ENST00000373344	NM_000489.3	1514	Cga/Tga	15/35	1	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.335218704118201	1		198	307	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100699	8100699	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	52	518	0	ENST00000346208.3:c.673T>A	p.Tyr225Asn	p.Y225N	ENST00000346208		225	Tac/Aac	3/6	1	2	FACETS	0.458	0.389	0.533	0.458	0.389	0.533	SUBCLONAL	1	TRUE	1	0.335218704118201	2		518	678	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0060288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	140	388	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.226793294314167	3	FACETS	1	0.984	1	0.673	0.615	0.734	INDETERMINATE	1	TRUE	1	0.39088846068594	3		388	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0060288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	67	541	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.513	0.446	0.587	0.513	0.446	0.587	SUBCLONAL	1	TRUE	1	0.39088846068594	2		541	668	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0060288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	163	645	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.39088846068594	2		645	806	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120983	115120983	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	59	554	0	ENST00000257566.3:c.23del	p.Pro8ArgfsTer23	p.P8Rfs*23	ENST00000257566	NM_016569.3	8	cCg/cg	1/8	1	2	FACETS	0.464	0.398	0.535	0.464	0.398	0.535	SUBCLONAL	1	TRUE	1	0.39088846068594	2		554	651	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437784	110437784	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	29	459	0	ENST00000375856.3:c.617G>C	p.Gly206Ala	p.G206A	ENST00000375856	NM_003749.2	206	gGt/gCt	1/2	1	2	FACETS	0.314	0.252	0.386	0.314	0.252	0.386	SUBCLONAL	1	TRUE	1	0.39088846068594	2		459	472	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0060289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	52	66	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.838	0.726	0.957	0.838	0.726	0.957	CLONAL	1	TRUE	1	0.700770605754789	2		66	177	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0060289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	192	487	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.700770605754789	1	FACETS	0.965	0.907	1	0.965	0.907	1	CLONAL	1	TRUE	0	0.700770605754789	1		487	369	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0060289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	117	88	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.700770605754789	2		88	324	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800962	243800962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	61	282	0	ENST00000263826.5:c.512G>A	p.Gly171Glu	p.G171E	ENST00000263826	NM_005465.4	171	gGa/gAa	5/13	1	2	FACETS	0.672	0.586	0.764	0.672	0.586	0.764	SUBCLONAL	1	TRUE	1	0.700770605754789	2		282	259	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052623	42052623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	305	484	0	ENST00000219905.7:c.7294G>A	p.Glu2432Lys	p.E2432K	ENST00000219905	NM_001164273.1	2432	Gag/Aag	20/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.700770605754789	2		484	845	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434740	99434740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	269	593	0	ENST00000268035.6:c.827G>A	p.Cys276Tyr	p.C276Y	ENST00000268035	NM_000875.3	276	tGt/tAt	3/21	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.700770605754789	2		593	764	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533339	29533339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1131691257	NA	P-0060289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	188	485	0	ENST00000356175.3:c.1342C>T	p.His448Tyr	p.H448Y	ENST00000356175	NM_000267.3	448	Cat/Tat	12/57	1	2	FACETS	0.979	0.911	1	0.979	0.911	1	CLONAL	1	TRUE	1	0.700770605754789	2		485	548	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185169174	185169174	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1198067962	NA	P-0060289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	159	352	0	ENST00000265026.3:c.1269C>G	p.Phe423Leu	p.F423L	ENST00000265026	NM_004721.4	423	ttC/ttG	7/14	1	2	FACETS	0.943	0.872	1	0.943	0.872	1	CLONAL	1	TRUE	1	0.700770605754789	2		352	481	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740698	58740698	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0060290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	325	812	0	ENST00000305921.3:c.1603A>T	p.Lys535Ter	p.K535*	ENST00000305921	NM_003620.3	535	Aaa/Taa	6/6	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.780617395543253	2		812	825	SUCCESS
APC	324	MSKCC	GRCh37	5	112128141	112128141	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs777848503	NA	P-0060290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	110	381	0	ENST00000257430.4:c.646-2A>T		p.X216_splice	ENST00000257430	NM_000038.5	216			1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.780617395543253	2		381	275	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0060290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	200	543	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	1	2	FACETS	0.985	0.921	1	0.985	0.921	1	CLONAL	1	TRUE	1	0.780617395543253	2		543	520	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538981	23538981	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	156	811	0	ENST00000380871.4:c.458A>G	p.Glu153Gly	p.E153G	ENST00000380871	NM_006167.3	153	gAa/gGa	2/2	0.560200140924118	1	FACETS	0.402	0.37	0.436	0.402	0.37	0.436	SUBCLONAL	1	TRUE	0	0.780617395543253	1		811	606	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0060290-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	118	279	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.447095992466964	3	FACETS	0.967	0.883	1	0.967	0.883	1	CLONAL	2	TRUE	1	0.447095992466964	3		279	334	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0060290-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	101	616	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.447095992466964	2		616	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578400	+	inframe_deletion	In_Frame_Del	DEL	GGTGGG	GGTGGG	-	novel	NA	P-0060290-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	300	924	0	ENST00000269305.4:c.530_535del	p.Pro177_His178del	p.P177_H178del	ENST00000269305	NM_001126112.2	177	cCCCACCat/cat	5/11	0.447095992466964	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.447095992466964	2		924	635	SUCCESS
APC	324	MSKCC	GRCh37	5	112175600	112175600	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0060290-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	175	818	0	ENST00000257430.4:c.4309A>T	p.Lys1437Ter	p.K1437*	ENST00000257430	NM_000038.5	1437	Aaa/Taa	16/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.447095992466964	2		818	650	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21639508	21639508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138278747	NA	P-0060290-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	144	477	0	ENST00000421138.2:c.406G>A	p.Val136Ile	p.V136I	ENST00000421138		136	Gtc/Atc	6/16	0.447095992466964	3	FACETS	0.816	0.749	0.884	0.816	0.749	0.884	CLONAL	2	TRUE	1	0.447095992466964	3		477	483	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420094	152420094	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138891155	NA	P-0060290-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	91	570	0	ENST00000206249.3:c.1781C>T	p.Thr594Met	p.T594M	ENST00000206249	NM_000125.3	594	aCg/aTg	8/8	1	2	FACETS	0.96	0.857	1	0.96	0.857	1	CLONAL	1	TRUE	1	0.447095992466964	2		570	424	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057302	30057302	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315496	NA	P-0060291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	139	535	0	ENST00000338641.4:c.784C>T	p.Arg262Ter	p.R262*	ENST00000338641	NM_000268.3	262	Cga/Tga	8/16	0.826258384764733	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.833130392713896	1		535	189	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416682	416682	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	211	519	0	ENST00000399788.2:c.3868G>C	p.Glu1290Gln	p.E1290Q	ENST00000399788	NM_001042603.1	1290	Gaa/Caa	23/28	0.833130392713896	3	FACETS	1	0.984	1	0.586	0.548	0.626	CLONAL	1	TRUE	1	0.833130392713896	3		519	612	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61725923	61725923	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	43	368	0	ENST00000401558.2:c.644A>G	p.Asn215Ser	p.N215S	ENST00000401558	NM_003400.3	215	aAt/aGt	9/25	0.833130392713896	4	FACETS	0.436	0.365	0.515	0.145	0.121	0.172	SUBCLONAL	1	TRUE	1	0.833130392713896	4		368	434	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649030	86649030	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	72	350	0	ENST00000274376.6:c.1310T>A	p.Leu437His	p.L437H	ENST00000274376	NM_002890.2	437	cTt/cAt	9/25	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.833130392713896	2		350	168	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579312	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	CG	novel	NA	P-0060291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	343	525	0	ENST00000269305.4:c.374_375dup	p.Tyr126ArgfsTer45	p.Y126Rfs*45	ENST00000269305	NM_001126112.2	125	-/CG		0.833130392713896	2	FACETS	0.983	0.955	1	0.983	0.955	1	CLONAL	2	TRUE	0	0.833130392713896	2		525	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0060292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	437	741	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.80472632538738	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.80472632538738	1		741	645	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682896	241682896	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs200496951	NA	P-0060292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	106	524	0	ENST00000366560.3:c.127C>G	p.Arg43Gly	p.R43G	ENST00000366560	NM_000143.3	43	Cga/Gga	1/10	1	2	FACETS	0.463	0.416	0.513	0.463	0.416	0.513	SUBCLONAL	1	TRUE	1	0.80472632538738	2		524	569	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245781	46245781	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060293-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	30	712	0	ENST00000334344.6:c.3875G>T	p.Ser1292Ile	p.S1292I	ENST00000334344	NM_152641.2	1292	aGt/aTt	15/21	1	2	FACETS	0.491	0.394	0.601	0.491	0.394	0.601	SUBCLONAL	1	TRUE	1	0.207287040114455	2		712	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0060294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	125	392	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.2004272411005	1	FACETS	1	0.961	1	1	0.991	1	CLONAL	2	TRUE	0	0.2004272411005	1		392	509	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0060294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	50	487	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.2004272411005	1	FACETS	0.909	0.772	1	0.909	0.772	1	CLONAL	1	TRUE	0	0.2004272411005	1		487	494	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912580	NA	P-0060294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	8	323	0	ENST00000342988.3:c.1157G>A	p.Gly386Asp	p.G386D	ENST00000342988	NM_005359.5	386	gGt/gAt	10/12	0.2004272411005	1	FACETS	0.191	0.122	0.281	0.191	0.122	0.281	SUBCLONAL	1	TRUE	0	0.2004272411005	1		323	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572991	7572991	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	223	573	0	ENST00000269305.4:c.1118del	p.Lys373ArgfsTer49	p.K373Rfs*49	ENST00000269305	NM_001126112.2	373	aAg/ag	11/11	0.2004272411005	1	FACETS	0.927	0.871	0.984	1	0.996	1	CLONAL	4	TRUE	0	0.2004272411005	1		573	540	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131271	202131271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060295-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	255	498	0	ENST00000358485.4:c.239C>T	p.Ser80Phe	p.S80F	ENST00000358485	NM_001080125.1	80	tCc/tTc	2/9	0.661583266933604	1	FACETS	0.968	0.916	1	0.968	0.916	1	CLONAL	1	TRUE	0	0.661583266933604	1		498	533	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541193	187541193	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060295-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	304	525	1	ENST00000441802.2:c.6547G>T	p.Glu2183Ter	p.E2183*	ENST00000441802	NM_005245.3	2183	Gaa/Taa	10/27	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.661583266933604	2		526	831	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230533	46230533	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	TAGGAG	novel	NA	P-0060295-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	150	399	0	ENST00000334344.6:c.782delinsTAGGAG	p.Ser261LeufsTer33	p.S261Lfs*33	ENST00000334344	NM_152641.2	261	tCa/tTAGGAGa	8/21	1	2	FACETS	0.814	0.748	0.883	0.814	0.748	0.883	CLONAL	1	TRUE	1	0.661583266933604	2		399	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0060296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	221	687	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.26363575799474	2	FACETS	0.759	0.708	0.813	0.759	0.708	0.813	SUBCLONAL	2	TRUE	0	0.3341575933341	2		687	871	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591894	48591894	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	170	559	0	ENST00000342988.3:c.1057T>G	p.Tyr353Asp	p.Y353D	ENST00000342988	NM_005359.5	353	Tac/Gac	9/12	0.3341575933341	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.3341575933341	1		559	665	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311644	15311644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1331168157	NA	P-0060296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	88	919	0	ENST00000263388.2:c.73C>T	p.Arg25Trp	p.R25W	ENST00000263388	NM_000435.2	25	Cgg/Tgg	1/33	0.24619039217568	2	FACETS	0.482	0.426	0.543	0.241	0.213	0.272	SUBCLONAL	1	TRUE	0	0.3341575933341	2		919	1093	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015073	27015073	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	160	454	0	ENST00000335756.4:c.175C>A	p.His59Asn	p.H59N	ENST00000335756	NM_001809.3	59	Cac/Aac	2/5	0.163655344720154	3	FACETS	0.776	0.713	0.842	0.776	0.713	0.842	INDETERMINATE	2	TRUE	1	0.3341575933341	3		454	720	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522240	157522240	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	144	764	0	ENST00000346085.5:c.4512G>C	p.Gln1504His	p.Q1504H	ENST00000346085	NM_020732.3	1504	caG/caC	18/20	1	2	FACETS	0.975	0.889	1	0.975	0.889	1	CLONAL	1	TRUE	1	0.3341575933341	2		764	884	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058497	69058497	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	44	376	0	ENST00000288368.4:c.4141T>G	p.Phe1381Val	p.F1381V	ENST00000288368	NM_024870.2	1381	Ttc/Gtc	34/40	0.304559263365124	4	FACETS	1	0.873	1	0.348	0.292	0.408	CLONAL	1	TRUE	1	0.3341575933341	4		376	337	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141570488	141570488	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	85	625	0	ENST00000220592.5:c.640A>G	p.Met214Val	p.M214V	ENST00000220592	NM_012154.3	214	Atg/Gtg	5/19	0.3341575933341	6	FACETS	0.758	0.668	0.855	0.253	0.222	0.285	SUBCLONAL	1	TRUE	3	0.3341575933341	6		625	1120	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974744	21974775	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTCCTCTACCCGACCCCGGGCCGCGGCCGT	ACCTCCTCTACCCGACCCCGGGCCGCGGCCGT	-	novel	NA	P-0060296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	143	787	0	ENST00000304494.5:c.52_83del	p.Thr18AlafsTer15	p.T18Afs*15	ENST00000304494	NM_000077.4	18	ACGGCCGCGGCCCGGGGTCGGGTAGAGGAGGTg/g	1/3	1	2	FACETS	0.884	0.805	0.967	0.884	0.805	0.967	CLONAL	1	TRUE	1	0.3341575933341	2		787	968	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594221	55594221	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913512	NA	P-0060297-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	291	383	0	ENST00000288135.5:c.1924A>G	p.Lys642Glu	p.K642E	ENST00000288135	NM_000222.2	642	Aaa/Gaa	13/21	0.472323798185135	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.483340864490163	2		383	511	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643391	38643392	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1424526290	NA	P-0060297-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	148	526	1	ENST00000299084.4:c.867dup	p.Ser290IlefsTer10	p.S290Ifs*10	ENST00000299084	NM_152594.2	287	-/A	7/7	0.483340864490163	1	FACETS	0.914	0.84	0.99	0.914	0.84	0.99	CLONAL	1	TRUE	0	0.483340864490163	1		527	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0060298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	216	575	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.256989298838306	2	FACETS	0.941	0.877	1	0.941	0.877	1	CLONAL	2	TRUE	0	0.27998792008417	2		575	820	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66522030	66522030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762014574	NA	P-0060298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	46	444	0	ENST00000358598.2:c.685G>A	p.Asp229Asn	p.D229N	ENST00000358598	NM_212471.2	229	Gac/Aac	7/11	1	2	FACETS	0.454	0.382	0.535	0.454	0.382	0.535	SUBCLONAL	1	TRUE	1	0.27998792008417	2		444	723	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375319	15375319	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	GG	novel	NA	P-0060298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	64	597	0	ENST00000263377.2:c.1108delinsCC	p.Ala370ProfsTer23	p.A370Pfs*23	ENST00000263377	NM_058243.2	370	Gcc/CCcc	6/20	1	2	FACETS	0.671	0.581	0.77	0.671	0.581	0.77	SUBCLONAL	1	TRUE	1	0.27998792008417	2		597	681	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432664	29432664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113994087	NA	P-0060299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	105	543	0	ENST00000389048.3:c.3824G>A	p.Arg1275Gln	p.R1275Q	ENST00000389048	NM_004304.4	1275	cGa/cAa	25/29	1	2	FACETS	0.397	0.356	0.44	0.397	0.356	0.44	SUBCLONAL	1	TRUE	1	0.810664205740552	2		543	653	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443695	29443695	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863225281	NA	P-0060299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	38	565	0	ENST00000389048.3:c.3522C>G	p.Phe1174Leu	p.F1174L	ENST00000389048	NM_004304.4	1174	ttC/ttG	23/29	1	2	FACETS	0.143	0.117	0.171	0.143	0.117	0.171	SUBCLONAL	1	TRUE	1	0.810664205740552	2		565	657	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445213	29445213	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519698	NA	P-0060299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	15	626	1	ENST00000389048.3:c.3512T>A	p.Ile1171Asn	p.I1171N	ENST00000389048	NM_004304.4	1171	aTc/aAc	22/29	1	2	FACETS	0.059	0.043	0.079	0.059	0.043	0.079	SUBCLONAL	1	TRUE	1	0.810664205740552	2		627	625	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0060300-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	145	499	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.67111973670586	2		499	394	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0060300-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	161	408	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.67111973670586	1	FACETS	0.938	0.874	1	0.938	0.874	1	CLONAL	1	TRUE	0	0.67111973670586	1		408	340	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508595	106508595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs182921583	NA	P-0060300-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	147	445	0	ENST00000359195.3:c.589G>A	p.Ala197Thr	p.A197T	ENST00000359195	NM_002649.2	197	Gcc/Acc	2/11	0.67111973670586	3	FACETS	0.88	0.805	0.957	0.44	0.402	0.479	CLONAL	1	TRUE	1	0.67111973670586	3		445	665	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088793	27088793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060300-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	159	445	0	ENST00000324856.7:c.2402G>A	p.Gly801Asp	p.G801D	ENST00000324856	NM_006015.4	801	gGt/gAt	7/20	1	2	FACETS	0.887	0.818	0.958	0.887	0.818	0.958	CLONAL	1	TRUE	1	0.67111973670586	2		445	534	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843518	156843518	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060300-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	193	567	0	ENST00000524377.1:c.944G>T	p.Trp315Leu	p.W315L	ENST00000524377	NM_002529.3	315	tGg/tTg	8/17	1	2	FACETS	0.928	0.863	0.994	0.928	0.863	0.994	CLONAL	1	TRUE	1	0.67111973670586	2		567	620	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820752	3820753	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060300-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	198	569	0	ENST00000262367.5:c.2698dup	p.Thr900AsnfsTer70	p.T900Nfs*70	ENST00000262367	NM_004380.2	900	acc/aAcc	14/31	1	2	FACETS	0.931	0.866	0.997	0.931	0.866	0.997	CLONAL	1	TRUE	1	0.67111973670586	2		569	634	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0060301-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	56	279	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.278023477782702	3	FACETS	1	0.961	1			1	CLONAL	1	TRUE	NA	0.28	3		279	336	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0060301-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	46	527	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.671	0.565	0.787	0.671	0.565	0.787	SUBCLONAL	1	TRUE	1	0.28	2		528	490	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0060301-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	14	160	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	1	2	FACETS	0.758	0.551	1	0.758	0.551	1	CLONAL	1	TRUE	1	0.28	2		160	132	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519927	NA	P-0060301-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	16	220	0	ENST00000263967.3:c.1625A>C	p.Glu542Ala	p.E542A	ENST00000263967	NM_006218.2	542	gAa/gCa	10/21	1	2	FACETS	0.752	0.559	0.979	0.752	0.559	0.979	CLONAL	1	TRUE	1	0.28	2		220	152	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245725	41245725	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs397508911	NA	P-0060301-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	54	362	1	ENST00000357654.3:c.1823del	p.Lys608ArgfsTer4	p.K608Rfs*4	ENST00000357654	NM_007294.3	608	aAg/ag	10/23	0.172704197951982	3	FACETS	0.912	0.78	1	0.456	0.39	0.529	CLONAL	1	TRUE	1	0.28	3		363	482	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008985	152009007	+	frameshift_variant	Frame_Shift_Del	DEL	TGCTTACACTTACACAAGATACT	TGCTTACACTTACACAAGATACT	-	novel	NA	P-0060301-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	47	348	0	ENST00000262189.6:c.615_637del	p.Val206ProfsTer6	p.V206Pfs*6	ENST00000262189	NM_170606.2	205	atAGTATCTTGTGTAAGTGTAAGCAcc/atcc	5/59	1	2	FACETS	0.803	0.679	0.94	0.803	0.679	0.94	CLONAL	1	TRUE	1	0.28	2		348	418	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0060303-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	118	388	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.225580026914604	3	FACETS	0.993	0.899	1	0.993	0.899	1	CLONAL	2	TRUE	1	0.225580026914604	3		388	586	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186742	108186742	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs532480170	NA	P-0060303-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	54	328	0	ENST00000278616.4:c.6100C>T	p.Arg2034Ter	p.R2034*	ENST00000278616	NM_000051.3	2034	Cga/Tga	42/63	0.225580026914604	1	FACETS	0.775	0.662	0.899	0.775	0.662	0.899	SUBCLONAL	1	TRUE	0	0.225580026914604	1		328	548	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023943	27023943	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060303-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	54	402	0	ENST00000324856.7:c.1049C>A	p.Ser350Ter	p.S350*	ENST00000324856	NM_006015.4	350	tCg/tAg	1/20	0.225580026914604	1	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	0	0.225580026914604	1		402	415	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027008	71027008	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0060303-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	74	452	0	ENST00000318789.4:c.1319C>G	p.Ser440Ter	p.S440*	ENST00000318789	NM_032682.5	440	tCa/tGa	15/21	0.225580026914604	1	FACETS	0.832	0.728	0.944	0.832	0.728	0.944	CLONAL	1	TRUE	0	0.225580026914604	1		452	700	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47088054	47088054	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060303-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	31	334	0	ENST00000409792.3:c.7021C>A	p.Pro2341Thr	p.P2341T	ENST00000409792	NM_014159.6	2341	Cca/Aca	16/21	0.225580026914604	1	FACETS	0.397	0.32	0.485	0.397	0.32	0.485	SUBCLONAL	1	TRUE	0	0.225580026914604	1		334	614	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875669	35875669	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060303-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	35	302	0	ENST00000303115.3:c.856C>A	p.Leu286Ile	p.L286I	ENST00000303115	NM_002185.3	286	Ctt/Att	7/8	1	2	FACETS	0.594	0.486	0.716	0.594	0.486	0.716	SUBCLONAL	1	TRUE	1	0.225580026914604	2		302	522	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877065	151877065	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060303-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	42	405	1	ENST00000262189.6:c.7296C>A	p.Phe2432Leu	p.F2432L	ENST00000262189	NM_170606.2	2432	ttC/ttA	37/59	0.225580026914604	1	FACETS	0.497	0.414	0.589	0.497	0.414	0.589	SUBCLONAL	1	TRUE	0	0.225580026914604	1		406	665	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0060304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	116	388	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.33741669763659	1	FACETS	0.94	0.851	1	0.94	0.851	1	CLONAL	1	TRUE	0	0.390369656195137	1		388	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0060304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	147	392	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.354513513045025	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.390369656195137	1		392	562	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928225	178928225	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	96	342	0	ENST00000263967.3:c.1411C>G	p.Pro471Ala	p.P471A	ENST00000263967	NM_006218.2	471	Cca/Gca	9/21	0.33741669763659	1	FACETS	0.892	0.799	0.989	0.892	0.799	0.989	CLONAL	1	TRUE	0	0.390369656195137	1		342	444	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027747	152027747	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	91	428	0	ENST00000262189.6:c.328C>T	p.Arg110Ter	p.R110*	ENST00000262189	NM_170606.2	110	Cga/Tga	3/59	0.354513513045025	1	FACETS	0.695	0.619	0.776	0.695	0.619	0.776	SUBCLONAL	1	TRUE	0	0.390369656195137	1		428	540	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907091	101907091	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	85	355	0	ENST00000374994.4:c.1051G>C	p.Asp351His	p.D351H	ENST00000374994	NM_004612.2	351	Gac/Cac	6/9	0.33741669763659	1	FACETS	0.769	0.682	0.86	0.769	0.682	0.86	SUBCLONAL	1	TRUE	0	0.390369656195137	1		355	456	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152248	99152248	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	79	341	0	ENST00000074304.5:c.327C>G	p.Ile109Met	p.I109M	ENST00000074304	NM_001134224.1	109	atC/atG	6/26	1	2	FACETS	0.664	0.584	0.749	0.664	0.584	0.749	SUBCLONAL	1	TRUE	1	0.390369656195137	2		341	610	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718687	190718687	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	153	277	0	ENST00000441310.2:c.845T>G	p.Leu282Arg	p.L282R	ENST00000441310	NM_000534.4	282	cTg/cGg	8/13	0.390369656195137	2	FACETS	0.935	0.865	1	0.935	0.865	1	CLONAL	2	TRUE	0	0.390369656195137	2		277	419	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287389	33287389	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs750390792	NA	P-0060304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	103	575	0	ENST00000374542.5:c.1708G>C	p.Glu570Gln	p.E570Q	ENST00000374542	NM_001141970.1	570	Gag/Cag	6/8	1	2	FACETS	0.624	0.558	0.694	0.624	0.558	0.694	SUBCLONAL	1	TRUE	1	0.390369656195137	2		575	846	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56882326	56882326	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	99	461	0	ENST00000519728.1:c.1024C>G	p.Pro342Ala	p.P342A	ENST00000519728	NM_002350.3	342	Cca/Gca	10/13	1	2	FACETS	0.785	0.702	0.874	0.785	0.702	0.874	SUBCLONAL	1	TRUE	1	0.390369656195137	2		461	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0060305-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	373	671	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.313071965780479	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.313071965780479	3		671	829	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275768	38275768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781310679	NA	P-0060305-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	106	647	0	ENST00000425967.3:c.1501C>T	p.Arg501Cys	p.R501C	ENST00000425967	NM_001174067.1	501	Cgc/Tgc	11/19	0.313071965780479	2	FACETS	1	0.953	1	0.553	0.497	0.613	CLONAL	1	TRUE	0	0.313071965780479	2		647	612	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372698	81372698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371502313	NA	P-0060305-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	77	453	0	ENST00000222390.5:c.836G>A	p.Arg279His	p.R279H	ENST00000222390	NM_000601.4	279	cGc/cAc	7/18	0.307092837205024	4	FACETS	1	0.887	1	0.505	0.444	0.572	CLONAL	1	TRUE	2	0.313071965780479	4		453	639	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29090046	29090046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1555913106	NA	P-0060305-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	17	127	0	ENST00000328354.6:c.1435G>T	p.Glu479Ter	p.E479*	ENST00000328354	NM_007194.3	479	Gaa/Taa	13/15	0.313071965780479	3	FACETS	0.748	0.561	0.967	0.374	0.28	0.484	CLONAL	1	TRUE	1	0.313071965780479	3		127	168	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400903	72400903	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060305-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	169	535	0	ENST00000357731.5:c.268C>T	p.Arg90Ter	p.R90*	ENST00000357731	NM_173808.2	90	Cga/Tga	2/7	0.313071965780479	3	FACETS	0.977	0.902	1	0.977	0.902	1	CLONAL	2	TRUE	1	0.313071965780479	3		535	639	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123572	108123572	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060305-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	74	319	0	ENST00000278616.4:c.1831A>G	p.Ile611Val	p.I611V	ENST00000278616	NM_000051.3	611	Att/Gtt	12/63	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.313071965780479	2		319	381	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647505	3647506	+	stop_gained	Nonsense_Mutation	DNP	GA	GA	TT	novel	NA	P-0060305-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	141	682	0	ENST00000294008.3:c.1557_1558delinsAA	p.Cys519_Pro520delinsTer	p.C519_P520delins*	ENST00000294008	NM_032444.2	519	tgTCct/tgAAct	7/15	0.313071965780479	3	FACETS	1	0.981	1	0.641	0.585	0.701	CLONAL	1	TRUE	1	0.313071965780479	3		682	812	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573151	41573151	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060305-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	210	664	0	ENST00000263253.7:c.5436G>C	p.Lys1812Asn	p.K1812N	ENST00000263253	NM_001429.3	1812	aaG/aaC	31/31	0.313071965780479	3	FACETS	0.948	0.882	1	0.948	0.882	1	CLONAL	2	TRUE	1	0.313071965780479	3		664	818	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573656	41573656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060305-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	240	778	0	ENST00000263253.7:c.5941G>A	p.Glu1981Lys	p.E1981K	ENST00000263253	NM_001429.3	1981	Gag/Aag	31/31	0.313071965780479	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.313071965780479	3		778	865	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448535	89448535	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060305-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	84	545	0	ENST00000336596.2:c.1499A>G	p.Lys500Arg	p.K500R	ENST00000336596	NM_005233.5	500	aAg/aGg	7/17	0.313071965780479	2	FACETS	0.997	0.883	1	0.499	0.441	0.56	CLONAL	1	TRUE	0	0.313071965780479	2		545	538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0060306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	366	652	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.785826360042748	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.785826360042748	1		652	555	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998498	100998498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	180	531	0	ENST00000325455.5:c.1304G>A	p.Gly435Glu	p.G435E	ENST00000325455	NM_001202474.3	435	gGg/gAg	1/8	1	2	FACETS	0.868	0.806	0.931	0.868	0.806	0.931	CLONAL	1	TRUE	1	0.785826360042748	2		531	528	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541542	29541542	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137854557	NA	P-0060306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	11	200	0	ENST00000356175.3:c.1466A>G	p.Tyr489Cys	p.Y489C	ENST00000356175	NM_000267.3	489	tAt/tGt	13/57	0.785826360042748	1	FACETS	0.221	0.154	0.3	0.221	0.154	0.3	SUBCLONAL	1	TRUE	0	0.785826360042748	1		200	77	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224170	39224170	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	144	217	0	ENST00000402219.2:c.2974G>C	p.Glu992Gln	p.E992Q	ENST00000402219	NM_005633.3	992	Gaa/Caa	19/23	0.485919760214652	4	FACETS	1	0.973	1	0.382	0.35	0.416	CLONAL	1	TRUE	1	0.785826360042748	4		217	571	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778879	76778879	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060306-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	124	336	0	ENST00000373344.5:c.6700G>A	p.Asp2234Asn	p.D2234N	ENST00000373344	NM_000489.3	2234	Gat/Aat	31/35	0.354754252587688	1	FACETS	0.414	0.377	0.452	0.414	0.377	0.452	INDETERMINATE	1	TRUE	0	0.785826360042748	1		336	463	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0060307-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	108	356	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.248958355757144	2	FACETS	0.874	0.79	0.961	0.874	0.79	0.961	CLONAL	2	TRUE	0	0.292207735601776	2		356	423	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0060307-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	31	499	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.815	1	1	0.815	1	CLONAL	1	TRUE	1	0.292207735601776	2		499	212	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0060307-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	48	447	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.292207735601776	1	FACETS	0.714	0.605	0.833	0.714	0.605	0.833	SUBCLONAL	1	TRUE	0	0.292207735601776	1		447	393	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150935531	150935531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060307-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	72	482	0	ENST00000271640.5:c.3373G>A	p.Ala1125Thr	p.A1125T	ENST00000271640	NM_001145415.1	1125	Gct/Act	19/22	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.292207735601776	2		482	491	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916831	48916831	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060307-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	37	276	0	ENST00000267163.4:c.361C>T	p.Gln121Ter	p.Q121*	ENST00000267163	NM_000321.2	121	Cag/Tag	3/27	1	2	FACETS	0.782	0.646	0.932	0.782	0.646	0.932	CLONAL	1	TRUE	1	0.292207735601776	2		276	324	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037966	49037966	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060307-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	33	231	0	ENST00000267163.4:c.2206C>T	p.Gln736Ter	p.Q736*	ENST00000267163	NM_000321.2	736	Cag/Tag	21/27	1	2	FACETS	0.733	0.599	0.884	0.733	0.599	0.884	SUBCLONAL	1	TRUE	1	0.292207735601776	2		231	308	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420258	88420258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550257984	NA	P-0060307-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	58	524	0	ENST00000360948.2:c.2428G>A	p.Glu810Lys	p.E810K	ENST00000360948	NM_001012338.2	810	Gaa/Aaa	19/19	0.292207735601776	1	FACETS	0.911	0.786	1	0.911	0.786	1	CLONAL	1	TRUE	0	0.292207735601776	1		524	372	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913503	NA	P-0060307-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	76	655	0	ENST00000330062.3:c.515G>T	p.Arg172Met	p.R172M	ENST00000330062	NM_002168.2	172	aGg/aTg	4/11	0.292207735601776	1	FACETS	0.897	0.789	1	0.897	0.789	1	CLONAL	1	TRUE	0	0.292207735601776	1		655	495	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61325851	61325851	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs543183353	NA	P-0060307-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	27	231	0	ENST00000283752.5:c.365C>T	p.Ala122Val	p.A122V	ENST00000283752	NM_006919.2	122	gCc/gTc	5/8	1	2	FACETS	0.988	0.793	1	0.988	0.793	1	CLONAL	1	TRUE	1	0.292207735601776	2		231	187	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73096341	73096341	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060307-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	23	174	0	ENST00000356692.5:c.121C>T	p.Gln41Ter	p.Q41*	ENST00000356692		41	Cag/Tag	3/9	1	2	FACETS	0.856	0.672	1	0.856	0.672	1	CLONAL	1	TRUE	1	0.292207735601776	2		174	184	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288921	33288921	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780621518	NA	P-0060307-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	38	467	0	ENST00000374542.5:c.631G>A	p.Asp211Asn	p.D211N	ENST00000374542	NM_001141970.1	211	Gat/Aat	3/8	1	2	FACETS	0.569	0.47	0.679	0.569	0.47	0.679	SUBCLONAL	1	TRUE	1	0.292207735601776	2		467	457	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6439807	6439807	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060307-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	110	430	0	ENST00000356142.4:c.333T>A	p.Asn111Lys	p.N111K	ENST00000356142	NM_018890.3	111	aaT/aaA	5/7	1	2	FACETS	0.789	0.713	0.869	1	0.985	1	SUBCLONAL	2	TRUE	1	0.292207735601776	2		430	477	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397695	116397695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060307-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	93	393	0	ENST00000397752.3:c.1969C>T	p.Pro657Ser	p.P657S	ENST00000397752	NM_000245.2	657	Cct/Tct	8/21	0.248958355757144	2	FACETS	0.915	0.821	1	0.915	0.821	1	CLONAL	2	TRUE	0	0.292207735601776	2		393	348	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900164	101900164	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060307-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	100	330	0	ENST00000374994.4:c.598A>G	p.Thr200Ala	p.T200A	ENST00000374994	NM_004612.2	200	Aca/Gca	4/9	0.261528809934334	2	FACETS	0.839	0.755	0.927	0.839	0.755	0.927	CLONAL	2	TRUE	0	0.292207735601776	2		330	408	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400980	139400980	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1397249771	NA	P-0060307-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	141	483	2	ENST00000277541.6:c.4013C>T	p.Ala1338Val	p.A1338V	ENST00000277541	NM_017617.3	1338	gCg/gTg	24/34	0.261528809934334	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.292207735601776	2		485	454	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797957	42797957	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060307-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	79	632	0	ENST00000575354.2:c.4012del	p.Leu1338Ter	p.L1338*	ENST00000575354	NM_015125.3	1337	Ccc/cc	16/20	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.292207735601776	2		632	517	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0060308-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	119	639	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.266965850474859	2		639	744	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462998	120462999	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0060308-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	117	442	0	ENST00000256646.2:c.5332_5333del	p.Ser1778ArgfsTer4	p.S1778Rfs*4	ENST00000256646	NM_024408.3	1778	TCa/a	30/34	1	2	FACETS	0.757	0.685	0.833	1	0.985	1	SUBCLONAL	2	TRUE	1	0.266965850474859	2		442	579	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120508153	120508159	+	frameshift_variant	Frame_Shift_Del	DEL	TCATCAA	TCATCAA	-	novel	NA	P-0060308-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	118	442	0	ENST00000256646.2:c.1598_1604del	p.Ile533ThrfsTer8	p.I533Tfs*8	ENST00000256646	NM_024408.3	533	aTTGATGAc/ac	10/34	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.266965850474859	2		442	676	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622418	28622418	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060308-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	123	359	0	ENST00000241453.7:c.1199G>C	p.Gly400Ala	p.G400A	ENST00000241453	NM_004119.2	400	gGa/gCa	9/24	0.151430116038999	4	FACETS	0.902	0.818	0.991			1	INDETERMINATE	2	TRUE	NA	0.266965850474859	4		359	647	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622524	28622524	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060308-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	106	334	0	ENST00000241453.7:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000241453	NM_004119.2	365	Gaa/Aaa	9/24	0.151430116038999	4	FACETS	0.776	0.697	0.86			1	INDETERMINATE	2	TRUE	NA	0.266965850474859	4		334	648	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622545	28622545	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060308-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	89	289	0	ENST00000241453.7:c.1072G>A	p.Asp358Asn	p.D358N	ENST00000241453	NM_004119.2	358	Gat/Aat	9/24	0.151430116038999	4	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.266965850474859	4		289	579	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622548	28622548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060308-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	84	282	0	ENST00000241453.7:c.1069G>A	p.Glu357Lys	p.E357K	ENST00000241453	NM_004119.2	357	Gaa/Aaa	9/24	0.151430116038999	4	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.266965850474859	4		282	581	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623777	28623777	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060308-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	88	418	0	ENST00000241453.7:c.877G>C	p.Glu293Gln	p.E293Q	ENST00000241453	NM_004119.2	293	Gag/Cag	7/24	0.151430116038999	4	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.266965850474859	4		418	662	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623792	28623792	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060308-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	84	427	0	ENST00000241453.7:c.862G>C	p.Glu288Gln	p.E288Q	ENST00000241453	NM_004119.2	288	Gaa/Caa	7/24	0.151430116038999	4	FACETS	1	0.956	1			1	INDETERMINATE	1	TRUE	NA	0.266965850474859	4		427	679	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578464	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060308-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	77	589	0	ENST00000269305.4:c.466C>A	p.Arg156Ser	p.R156S	ENST00000269305	NM_001126112.2	156	Cgc/Agc	5/11	1	2	FACETS	0.726	0.636	0.822	0.726	0.636	0.822	SUBCLONAL	1	TRUE	1	0.266965850474859	2		589	795	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0060308-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	79	574	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	1	2	FACETS	0.737	0.647	0.834	0.737	0.647	0.834	SUBCLONAL	1	TRUE	1	0.266965850474859	2		574	803	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396452	139396452	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0060308-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	159	669	0	ENST00000277541.6:c.5472+1G>A		p.X1824_splice	ENST00000277541	NM_017617.3	1824			1	2	FACETS	0.83	0.762	0.9	1	0.99	1	CLONAL	2	TRUE	1	0.266965850474859	2		669	718	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413171	139413171	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060308-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	114	575	0	ENST00000277541.6:c.971T>G	p.Val324Gly	p.V324G	ENST00000277541	NM_017617.3	324	gTc/gGc	6/34	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.266965850474859	2		575	713	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410754	63410754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060308-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	26	299	0	ENST00000330258.3:c.2413C>T	p.Pro805Ser	p.P805S	ENST00000330258	NM_152424.3	805	Ccc/Tcc	2/2	1	1	FACETS	0.41	0.324	0.508	0.41	0.324	0.508	SUBCLONAL	1	TRUE	0	0.266965850474859	1		299	412	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0060309-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	10	445	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.537	0.363	0.755	0.537	0.363	0.755	SUBCLONAL	1	TRUE	1	0.18	2		445	207	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730137	41730137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764280388	NA	P-0060309-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	29	314	0	ENST00000242208.4:c.392C>T	p.Thr131Ile	p.T131I	ENST00000242208	NM_002192.2	131	aCa/aTa	3/3	1	2	FACETS	0.876	0.703	1	0.876	0.703	1	CLONAL	1	TRUE	1	0.18	2		314	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0060364-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	25	446	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		446	785	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266092	41266097	+	inframe_deletion	In_Frame_Del	DEL	ACCTGG	ACCTGG	-	novel	NA	P-0060364-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	23	596	3	ENST00000349496.5:c.91_96del	p.Leu31_Asp32del	p.L31_D32del	ENST00000349496	NM_001904.3	30	tACCTGGac/tac	3/15	0.125064394382921	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		599	736	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696431	47696431	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519969	NA	P-0060365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	194	517	0	ENST00000347630.2:c.392G>C	p.Trp131Ser	p.W131S	ENST00000347630	NM_001007230.1	131	tGg/tCg	6/11	1	2	FACETS	0.96	0.89	1	0.96	0.89	1	CLONAL	1	TRUE	1	0.530510909680713	2		517	762	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117731	70117731	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1182522222	NA	P-0060365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	298	864	0	ENST00000245479.2:c.199G>A	p.Asp67Asn	p.D67N	ENST00000245479	NM_000346.3	67	Gac/Aac	1/3	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.530510909680713	2		864	950	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44935974	44935974	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060365-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	94	124	0	ENST00000377967.4:c.2735del	p.Ser912ThrfsTer25	p.S912Tfs*25	ENST00000377967	NM_021140.2	912	aGc/ac	18/29	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.530510909680713	1		124	187	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0060366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	401	671	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.55048195148141	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.55048195148141	2		671	718	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911579	134911579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs959853730	NA	P-0060366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	170	709	0	ENST00000398015.3:c.2044C>T	p.Arg682Cys	p.R682C	ENST00000398015	NM_004441.4	682	Cgc/Tgc	11/16	0.55048195148141	5	FACETS	0.941	0.864	1	0.235	0.216	0.256	CLONAL	1	TRUE	1	0.55048195148141	5		709	1198	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104673	193104673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	85	300	0	ENST00000367435.3:c.377G>A	p.Arg126Gln	p.R126Q	ENST00000367435	NM_024529.4	126	cGa/cAa	5/17	0.55048195148141	4	FACETS	0.893	0.792	1	0.298	0.264	0.334	CLONAL	1	TRUE	1	0.55048195148141	4		300	536	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656888	45656888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566695508	NA	P-0060366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	200	736	0	ENST00000407780.3:c.268G>A	p.Gly90Ser	p.G90S	ENST00000407780	NM_001283052.1	90	Ggc/Agc	3/7	0.55048195148141	3	FACETS	0.843	0.78	0.908	0.281	0.26	0.303	CLONAL	1	TRUE	0	0.55048195148141	3		736	1099	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7218326	7218326	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	138	611	0	ENST00000380728.2:c.46A>T	p.Arg16Trp	p.R16W	ENST00000380728		16	Agg/Tgg	2/11	0.55048195148141	2	FACETS	1	0.941	1	0.517	0.473	0.562	CLONAL	1	TRUE	0	0.55048195148141	2		611	485	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402843	20402843	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	120	522	0	ENST00000346618.3:c.380G>T	p.Gly127Val	p.G127V	ENST00000346618	NM_001949.4	127	gGc/gTc	1/7	0.539230839653104	3	FACETS	1	0.962	1	0.371	0.336	0.407	CLONAL	1	TRUE	0	0.55048195148141	3		522	500	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288366	33288366	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	204	733	0	ENST00000374542.5:c.1042G>C	p.Val348Leu	p.V348L	ENST00000374542	NM_001141970.1	348	Gtt/Ctt	4/8	0.55048195148141	3	FACETS	1	0.95	1	0.343	0.318	0.369	CLONAL	1	TRUE	0	0.55048195148141	3		733	918	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677948	117677948	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060366-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	127	436	0	ENST00000368508.3:c.3985T>C	p.Cys1329Arg	p.C1329R	ENST00000368508	NM_002944.2	1329	Tgt/Cgt	25/43	0.55048195148141	3	FACETS	0.986	0.896	1	0.329	0.298	0.36	CLONAL	1	TRUE	0	0.55048195148141	3		436	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577529	7577529	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs730882027	NA	P-0060367-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	536	695	0	ENST00000269305.4:c.752T>G	p.Ile251Ser	p.I251S	ENST00000269305	NM_001126112.2	251	aTc/aGc	7/11	0.927947275525281	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.927947275525281	1		695	614	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420174	88420174	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060367-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	506	703	0	ENST00000360948.2:c.2512C>G	p.Leu838Val	p.L838V	ENST00000360948	NM_001012338.2	838	Ctt/Gtt	19/19	0.490160412261642	1	FACETS	0.399	0.382	0.417	0.399	0.382	0.417	INDETERMINATE	1	TRUE	0	0.927947275525281	1		703	1465	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420235	88420235	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs869209165	NA	P-0060367-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	525	782	0	ENST00000360948.2:c.2451C>G	p.Ile817Met	p.I817M	ENST00000360948	NM_001012338.2	817	atC/atG	19/19	0.490160412261642	1	FACETS	0.392	0.375	0.409	0.392	0.375	0.409	INDETERMINATE	1	TRUE	0	0.927947275525281	1		782	1547	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0060368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	136	460	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.916	0.842	0.993	1	0.99	1	CLONAL	2	TRUE	1	0.375761062616785	2		461	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0060368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	289	587	1	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	0.37521880783672	0	FACETS	0.936	0.892	0.979			1	CLONAL	2	TRUE	0	0.375761062616785	0		588	513	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672996	30672996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	93	772	0	ENST00000376406.3:c.3964C>T	p.Pro1322Ser	p.P1322S	ENST00000376406	NM_014641.2	1322	Cct/Tct	10/15	1	2	FACETS	0.522	0.463	0.585	0.522	0.463	0.585	SUBCLONAL	1	TRUE	1	0.375761062616785	2		772	949	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978725	70978725	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	28	363	0	ENST00000276594.2:c.928C>A	p.His310Asn	p.H310N	ENST00000276594	NM_024504.3	310	Cat/Aat	5/8	1	2	FACETS	0.467	0.374	0.573	0.467	0.374	0.573	SUBCLONAL	1	TRUE	1	0.375761062616785	2		363	319	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918887	76918888	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCTTT	novel	NA	P-0060368-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	50	188	0	ENST00000373344.5:c.4099_4103dup	p.Arg1369LysfsTer8	p.R1369Kfs*8	ENST00000373344	NM_000489.3	1368	ggc/ggAAAGGc	12/35	1	1	FACETS	1	0.961	1	1	0.982	1	CLONAL	2	TRUE	0	0.375761062616785	1		188	89	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934264	48934264	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0060369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	26	124	0	ENST00000267163.4:c.718+1G>A		p.X240_splice	ENST00000267163	NM_000321.2	240			0.612357980917979	1	FACETS	0.921	0.76	1	0.921	0.76	1	CLONAL	1	TRUE	0	0.612357980917979	1		124	64	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403120	116403120	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371939364	NA	P-0060369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	123	494	0	ENST00000397752.3:c.2381C>G	p.Ser794Cys	p.S794C	ENST00000397752	NM_000245.2	794	tCt/tGt	11/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.612357980917979	2		494	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7590689	7590746	+	splice_donor_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	GCTTACCCAATCCAGGGAAGCGTGTCACCGTCGTGGAAAGCACGCTCCCAGCCCGAAC	GCTTACCCAATCCAGGGAAGCGTGTCACCGTCGTGGAAAGCACGCTCCCAGCCCGAAC	AT	novel	NA	P-0060369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	360	799	2	ENST00000269305.4:c.-80_-29+6delinsAT		p.X27_splice	ENST00000269305	NM_001126112.2	27		1/11	0.612357980917979	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.612357980917979	1		801	738	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221995	98221995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060369-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	168	660	0	ENST00000331920.6:c.2774C>T	p.Ala925Val	p.A925V	ENST00000331920	NM_000264.3	925	gCt/gTt	17/24	0.612357980917979	1	FACETS	0.594	0.548	0.642	0.594	0.548	0.642	SUBCLONAL	1	TRUE	0	0.612357980917979	1		660	641	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578390	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0060370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	160	779	0	ENST00000269305.4:c.539_540dup	p.Arg181SerfsTer67	p.R181Sfs*67	ENST00000269305	NM_001126112.2	180	-/AG	5/11	0.293338931281008	1	FACETS	0.968	0.887	1	0.968	0.887	1	CLONAL	1	TRUE	0	0.293338931281008	1		779	962	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711017	114711017	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	71	344	0	ENST00000543371.1:c.241G>T	p.Glu81Ter	p.E81*	ENST00000543371	NM_001198531.1	81	Gaa/Taa	2/14	1	2	FACETS	0.885	0.773	1	0.885	0.773	1	CLONAL	1	TRUE	1	0.293338931281008	2		344	547	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0060370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	83	312	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.240255230144013	3	FACETS	0.966	0.86	1	0.644	0.573	0.718	CLONAL	2	TRUE	0	0.293338931281008	3		312	336	SUCCESS
APC	324	MSKCC	GRCh37	5	112174782	112174782	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060370-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	91	275	0	ENST00000257430.4:c.3491del	p.Ile1164LysfsTer18	p.I1164Kfs*18	ENST00000257430	NM_000038.5	1164	aTa/aa	16/16	0.240255230144013	3	FACETS	0.859	0.773	0.948	0.859	0.773	0.948	CLONAL	3	TRUE	0	0.293338931281008	3		275	276	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	156	475	0				ENST00000310581	NM_198253.2	-/1132			0.421148405485267	3	FACETS	1	0.924	1	0.505	0.462	0.55	CLONAL	1	TRUE	1	0.421148405485267	3		475	888	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	592	698	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.421148405485267	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	0	0.421148405485267	3		698	1122	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	430	547	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.421148405485267	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.421148405485267	3		547	753	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259355	89259355	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	105	467	0	ENST00000336596.2:c.499G>A	p.Glu167Lys	p.E167K	ENST00000336596	NM_005233.5	167	Gag/Aag	3/17	0.393908986931158	3	FACETS	1	0.912	1	0.508	0.456	0.563	CLONAL	1	TRUE	1	0.421148405485267	3		467	594	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599221	28599221	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	70	652	1	ENST00000253063.3:c.667G>T	p.Asp223Tyr	p.D223Y	ENST00000253063	NM_031459.4	223	Gat/Tat	5/10	0.144508852696675	5	FACETS	0.499	0.433	0.57			1	INDETERMINATE	1	TRUE	NA	0.421148405485267	5		653	1088	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342969	70342969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	340	263	0	ENST00000374080.3:c.1510G>A	p.Val504Met	p.V504M	ENST00000374080		504	Gtg/Atg	11/45	0.367352049932501	2	FACETS	1	0.982	1			1	CLONAL	3	TRUE	NA	0.421148405485267	2		263	519	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859891	151859891	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	159	535	0	ENST00000262189.6:c.10771C>T	p.Gln3591Ter	p.Q3591*	ENST00000262189	NM_170606.2	3591	Cag/Tag	43/59	0.393908986931158	3	FACETS	1	0.982	1	0.624	0.573	0.677	CLONAL	1	TRUE	1	0.421148405485267	3		535	732	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255464	16255464	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	80	539	0	ENST00000375759.3:c.2729C>A	p.Ser910Tyr	p.S910Y	ENST00000375759	NM_015001.2	910	tCt/tAt	11/15	0.150167736478097	5	FACETS	0.727	0.639	0.822	0.242	0.213	0.274	INDETERMINATE	1	TRUE	2	0.421148405485267	5		539	853	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228399	228399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	64	418	0	ENST00000264932.6:c.721G>A	p.Asp241Asn	p.D241N	ENST00000264932	NM_004168.2	241	Gac/Aac	6/15	0.421148405485267	3	FACETS	0.469	0.405	0.539	0.235	0.202	0.27	SUBCLONAL	1	TRUE	1	0.421148405485267	3		418	784	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016164	31016164	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1285138418	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	148	434	0	ENST00000375687.4:c.410C>G	p.Ser137Cys	p.S137C	ENST00000375687	NM_015338.5	137	tCt/tGt	6/13	0.421148405485267	5	FACETS	0.99	0.902	1	0.33	0.3	0.361	CLONAL	1	TRUE	2	0.421148405485267	5		434	1159	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73995382	73995382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	62	572	0	ENST00000318443.5:c.688G>A	p.Asp230Asn	p.D230N	ENST00000318443	NM_001024736.1	230	Gat/Aat	4/10	1	2	FACETS	0.369	0.318	0.425	0.369	0.318	0.425	SUBCLONAL	1	TRUE	1	0.421148405485267	2		572	797	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383317	31383317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772079891	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	369	639	0	ENST00000328111.2:c.1229G>A	p.Arg410Gln	p.R410Q	ENST00000328111	NM_006892.3	410	cGa/cAa	11/23	0.421148405485267	5	FACETS	0.951	0.901	1	0.634	0.6	0.669	CLONAL	2	TRUE	2	0.421148405485267	5		639	1503	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879508	151879508	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	153	597	0	ENST00000262189.6:c.5437C>T	p.Gln1813Ter	p.Q1813*	ENST00000262189	NM_170606.2	1813	Cag/Tag	36/59	0.393908986931158	3	FACETS	1	0.932	1	0.51	0.467	0.556	CLONAL	1	TRUE	1	0.421148405485267	3		597	862	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42843808	42843808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772196502	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	54	446	0	ENST00000398585.3:c.1111C>T	p.His371Tyr	p.H371Y	ENST00000398585	NM_001135099.1	371	Cat/Tat	10/14	0.421148405485267	3	FACETS	0.369	0.314	0.43	0.185	0.157	0.215	SUBCLONAL	1	TRUE	1	0.421148405485267	3		446	841	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936949	48936949	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	126	213	0	ENST00000267163.4:c.719-2A>G		p.X240_splice	ENST00000267163	NM_000321.2	240			0.421148405485267	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.421148405485267	2		213	278	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877339	40877339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	240	464	0	ENST00000373198.4:c.2357C>T	p.Thr786Ile	p.T786I	ENST00000373198	NM_133170.3	786	aCc/aTc	15/32	0.150167736478097	5	FACETS	1	0.95	1	0.679	0.635	0.724	INDETERMINATE	2	TRUE	2	0.421148405485267	5		464	913	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256676	16256676	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	39	432	0	ENST00000375759.3:c.3941C>G	p.Ser1314Cys	p.S1314C	ENST00000375759	NM_015001.2	1314	tCt/tGt	11/15	0.150167736478097	5	FACETS	0.528	0.437	0.63	0.176	0.145	0.21	INDETERMINATE	1	TRUE	2	0.421148405485267	5		432	572	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257084	16257084	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	36	458	0	ENST00000375759.3:c.4349G>T	p.Arg1450Ile	p.R1450I	ENST00000375759	NM_015001.2	1450	aGa/aTa	11/15	0.150167736478097	5	FACETS	0.508	0.417	0.611	0.169	0.139	0.204	INDETERMINATE	1	TRUE	2	0.421148405485267	5		458	549	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258354	16258354	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	61	668	0	ENST00000375759.3:c.5619G>C	p.Glu1873Asp	p.E1873D	ENST00000375759	NM_015001.2	1873	gaG/gaC	11/15	0.150167736478097	5	FACETS	0.425	0.365	0.491	0.142	0.121	0.164	INDETERMINATE	1	TRUE	2	0.421148405485267	5		668	1112	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258716	16258716	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs760431541	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	70	716	0	ENST00000375759.3:c.5981G>T	p.Gly1994Val	p.G1994V	ENST00000375759	NM_015001.2	1994	gGa/gTa	11/15	0.150167736478097	5	FACETS	0.473	0.411	0.541	0.158	0.137	0.181	INDETERMINATE	1	TRUE	2	0.421148405485267	5		716	1147	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099893	27099894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	338	617	0	ENST00000324856.7:c.3773dup	p.Asp1258GlufsTer29	p.D1258Efs*29	ENST00000324856	NM_006015.4	1258	gac/gAac	15/20	0.144508852696675	5	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.421148405485267	5		617	1104	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599970	28599970	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	59	519	0	ENST00000253063.3:c.852G>C	p.Glu284Asp	p.E284D	ENST00000253063	NM_031459.4	284	gaG/gaC	6/10	0.144508852696675	5	FACETS	0.521	0.447	0.602			1	INDETERMINATE	1	TRUE	NA	0.421148405485267	5		519	878	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150935571	150935571	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	253	490	0	ENST00000271640.5:c.3413C>T	p.Ser1138Phe	p.S1138F	ENST00000271640	NM_001145415.1	1138	tCt/tTt	19/22	0.421148405485267	4	FACETS	0.791	0.74	0.844	0.791	0.74	0.844	SUBCLONAL	2	TRUE	2	0.421148405485267	4		490	1079	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150936084	150936084	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	268	566	0	ENST00000271640.5:c.3536C>G	p.Ser1179Ter	p.S1179*	ENST00000271640	NM_001145415.1	1179	tCa/tGa	20/22	0.421148405485267	4	FACETS	1	0.991	1	0.675	0.632	0.719	CLONAL	1	TRUE	2	0.421148405485267	4		566	1340	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150936835	150936835	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	224	511	0	ENST00000271640.5:c.3871C>T	p.Leu1291Phe	p.L1291F	ENST00000271640	NM_001145415.1	1291	Ctt/Ttt	22/22	0.421148405485267	4	FACETS	1	0.988	1	0.649	0.604	0.697	CLONAL	1	TRUE	2	0.421148405485267	4		511	1164	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658396	206658396	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1490955570	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	374	574	0	ENST00000367120.3:c.1490C>T	p.Ser497Phe	p.S497F	ENST00000367120	NM_014002.3	497	tCc/tTc	14/22	0.276841863540683	2	FACETS	0.987	0.941	1	0.987	0.941	1	CLONAL	2	TRUE	0	0.421148405485267	2		574	900	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852140	63852140	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	134	509	0	ENST00000279873.7:c.2918C>G	p.Ser973Ter	p.S973*	ENST00000279873	NM_032199.2	973	tCa/tGa	10/10	0.421148405485267	1	FACETS	0.832	0.758	0.908	0.832	0.758	0.908	CLONAL	1	TRUE	0	0.421148405485267	1		509	604	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	78128764	78128764	+	start_lost	Translation_Start_Site	SNP	C	C	A	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	139	545	0	ENST00000361507.4:c.3G>T	p.Met1?	p.M1?	ENST00000361507	NM_080491.2	1	atG/atT	1/10	0.367352049932501	4	FACETS	0.762	0.692	0.836			1	SUBCLONAL	1	TRUE	NA	0.421148405485267	4		545	1231	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434595	49434595	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	64	645	0	ENST00000301067.7:c.6958G>C	p.Glu2320Gln	p.E2320Q	ENST00000301067	NM_003482.3	2320	Gag/Cag	31/54	0.101260414785774	5	FACETS	0.527	0.455	0.606	0.132	0.113	0.152	INDETERMINATE	1	TRUE	1	0.421148405485267	5		645	941	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416780	121416780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	183	614	0	ENST00000257555.6:c.209C>T	p.Ser70Phe	p.S70F	ENST00000257555		70	tCc/tTc	1/10	0.101260414785774	5	FACETS	0.753	0.695	0.813	0.376	0.347	0.407	INDETERMINATE	2	TRUE	1	0.421148405485267	5		614	942	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28971174	28971174	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	41	363	0	ENST00000282397.4:c.1583G>C	p.Arg528Thr	p.R528T	ENST00000282397	NM_002019.4	528	aGa/aCa	12/30	1	2	FACETS	0.446	0.371	0.528	0.446	0.371	0.528	SUBCLONAL	1	TRUE	1	0.421148405485267	2		363	437	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337668	73337668	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	69	258	0	ENST00000377767.4:c.2048C>G	p.Ser683Cys	p.S683C	ENST00000377767	NM_014953.3	683	tCt/tGt	16/21	0.369823323320866	3	FACETS	1	0.906	1	0.521	0.456	0.59	CLONAL	1	TRUE	1	0.421148405485267	3		258	381	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518229	103518229	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	89	447	0	ENST00000355739.4:c.2167G>T	p.Asp723Tyr	p.D723Y	ENST00000355739	NM_000123.3	723	Gat/Tat	9/15	0.369823323320866	3	FACETS	0.648	0.574	0.728	0.324	0.287	0.364	SUBCLONAL	1	TRUE	1	0.421148405485267	3		447	789	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465376	99465376	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	46	366	0	ENST00000268035.6:c.2202-1G>C		p.X734_splice	ENST00000268035	NM_000875.3	734			1	2	FACETS	0.36	0.303	0.424	0.36	0.303	0.424	SUBCLONAL	1	TRUE	1	0.421148405485267	2		366	606	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857808	9857808	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	75	653	0	ENST00000330684.3:c.3593C>A	p.Ser1198Tyr	p.S1198Y	ENST00000330684	NM_001134407.1	1198	tCc/tAc	13/13	0.421148405485267	3	FACETS	0.394	0.344	0.449			1	SUBCLONAL	1	TRUE	NA	0.421148405485267	3		653	1093	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027539	48027539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372990379	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	66	423	0	ENST00000234420.5:c.2417C>T	p.Ser806Phe	p.S806F	ENST00000234420	NM_000179.2	806	tCc/tTc	4/10	0.240019057306799	4	FACETS	0.635	0.55	0.726	0.317	0.275	0.363	INDETERMINATE	1	TRUE	2	0.421148405485267	4		423	702	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202122988	202122988	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs377242086	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	67	515	0	ENST00000358485.4:c.34G>C	p.Glu12Gln	p.E12Q	ENST00000358485	NM_001080125.1	12	Gaa/Caa	1/9	1	2	FACETS	0.395	0.342	0.452	0.395	0.342	0.452	SUBCLONAL	1	TRUE	1	0.421148405485267	2		515	806	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727078	40727078	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	83	653	0	ENST00000373198.4:c.3886G>T	p.Glu1296Ter	p.E1296*	ENST00000373198	NM_133170.3	1296	Gag/Tag	28/32	0.150167736478097	5	FACETS	0.601	0.529	0.679	0.2	0.176	0.227	INDETERMINATE	1	TRUE	2	0.421148405485267	5		653	1070	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29383097	29383097	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	53	447	0	ENST00000544604.2:c.334G>C	p.Glu112Gln	p.E112Q	ENST00000544604	NM_001206998.1	112	Gaa/Caa	2/9	1	2	FACETS	0.381	0.324	0.443	0.381	0.324	0.443	SUBCLONAL	1	TRUE	1	0.421148405485267	2		447	661	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713279	30713279	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	58	577	0	ENST00000295754.5:c.604G>T	p.Glu202Ter	p.E202*	ENST00000295754	NM_003242.5	202	Gaa/Taa	4/7	0.393908986931158	3	FACETS	0.328	0.28	0.38	0.164	0.14	0.19	SUBCLONAL	1	TRUE	1	0.421148405485267	3		577	1017	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447250	187447250	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	57	684	0	ENST00000232014.4:c.943C>T	p.His315Tyr	p.H315Y	ENST00000232014	NM_001130845.1	315	Cat/Tat	5/10	0.393908986931158	3	FACETS	0.289	0.246	0.335	0.144	0.123	0.168	SUBCLONAL	1	TRUE	1	0.421148405485267	3		684	1135	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631171	176631171	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	66	489	0	ENST00000439151.2:c.1114C>G	p.Pro372Ala	p.P372A	ENST00000439151	NM_022455.4	372	Cct/Gct	4/23	0.421148405485267	2	FACETS	0.458	0.397	0.524	0.229	0.198	0.262	SUBCLONAL	1	TRUE	0	0.421148405485267	2		489	685	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056210	26056210	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	171	687	0	ENST00000343677.2:c.447G>C	p.Lys149Asn	p.K149N	ENST00000343677	NM_005319.3	149	aaG/aaC	1/1	0.420380645478675	3	FACETS	0.82	0.753	0.89	0.41	0.376	0.445	CLONAL	1	TRUE	1	0.421148405485267	3		687	1199	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815410	32815410	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs145691938	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	74	431	0	ENST00000354258.4:c.1963C>G	p.Leu655Val	p.L655V	ENST00000354258	NM_000593.5	655	Ctt/Gtt	9/11	0.420380645478675	3	FACETS	0.539	0.471	0.613	0.27	0.235	0.307	SUBCLONAL	1	TRUE	1	0.421148405485267	3		431	789	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677828	117677828	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	31	374	0	ENST00000368508.3:c.4105C>T	p.Gln1369Ter	p.Q1369*	ENST00000368508	NM_002944.2	1369	Cag/Tag	25/43	0.420380645478675	3	FACETS	0.319	0.257	0.39	0.16	0.128	0.195	SUBCLONAL	1	TRUE	1	0.421148405485267	3		374	558	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389256	8389256	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242339856	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	63	336	0	ENST00000356435.5:c.4362G>A	p.Met1454Ile	p.M1454I	ENST00000356435		1454	atG/atA	26/35	1	2	FACETS	0.699	0.606	0.799	0.699	0.606	0.799	SUBCLONAL	1	TRUE	1	0.421148405485267	2		336	428	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829782	76829782	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	19	127	0	ENST00000373344.5:c.6259G>C	p.Asp2087His	p.D2087H	ENST00000373344	NM_000489.3	2087	Gat/Cat	28/35	0.367352049932501	2	FACETS	0.389	0.296	0.498			1	SUBCLONAL	1	TRUE	NA	0.421148405485267	2		127	232	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918963	76918963	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	32	192	0	ENST00000373344.5:c.4028A>T	p.His1343Leu	p.H1343L	ENST00000373344	NM_000489.3	1343	cAc/cTc	12/35	0.367352049932501	2	FACETS	0.439	0.357	0.532			1	SUBCLONAL	1	TRUE	NA	0.421148405485267	2		192	346	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0060372-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	174	388	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.468582716795241	2		388	691	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0060376-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	200	865	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.388974930489072	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.388974930489072	1		865	773	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941484	71941484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762820798	NA	P-0060376-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	122	1018	1	ENST00000298229.2:c.1169G>A	p.Arg390His	p.R390H	ENST00000298229	NM_001567.3	390	cGc/cAc	10/28	1	2	FACETS	0.707	0.639	0.78	0.707	0.639	0.78	SUBCLONAL	1	TRUE	1	0.388974930489072	2		1019	887	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107137	27107137	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060376-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	224	839	0	ENST00000324856.7:c.6748G>T	p.Glu2250Ter	p.E2250*	ENST00000324856	NM_006015.4	2250	Gag/Tag	20/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.388974930489072	2		839	1014	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696644	47696644	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	237	505	0	ENST00000347630.2:c.304T>A	p.Phe102Ile	p.F102I	ENST00000347630	NM_001007230.1	102	Ttc/Atc	5/11	1	2	FACETS	1	0.96	1	1	0.995	1	CLONAL	2	TRUE	1	0.266955084252158	2		505	857	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239419	105239419	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1287	82	891	0	ENST00000349310.3:c.968A>C	p.Asp323Ala	p.D323A	ENST00000349310	NM_001014432.1	323	gAc/gCc	12/15	0.266955084252158	2	FACETS	0.449	0.394	0.508	0.224	0.197	0.254	SUBCLONAL	1	TRUE	0	0.266955084252158	2		891	1369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0060378-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	366	864	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.395582116443043	3	FACETS	1	0.99	1	0.745	0.711	0.779	CLONAL	2	TRUE	0	0.540291720529418	3		864	770	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112175	115112175	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060378-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	228	862	4	ENST00000257566.3:c.1565C>T	p.Pro522Leu	p.P522L	ENST00000257566	NM_016569.3	522	cCc/cTc	7/8	0.540291720529418	3	FACETS	0.841	0.789	0.895	0.561	0.526	0.597	CLONAL	2	TRUE	0	0.540291720529418	3		866	637	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0060379-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	101	279	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.864	0.777	0.956	0.864	0.777	0.956	CLONAL	1	TRUE	1	0.534772195947457	2		279	437	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0060379-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	131	438	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.518566414864599	1	FACETS	0.801	0.733	0.872	0.801	0.733	0.872	CLONAL	1	TRUE	0	0.534772195947457	1		438	448	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0060379-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	56	471	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.204	0.174	0.238	0.204	0.174	0.238	SUBCLONAL	1	TRUE	1	0.534772195947457	2		472	1025	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394805	45394805	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060379-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	175	531	1	ENST00000262160.6:c.544C>T	p.Arg182Ter	p.R182*	ENST00000262160	NM_005901.5	182	Cga/Tga	5/11	0.534772195947457	1	FACETS	0.927	0.861	0.996	0.927	0.861	0.996	CLONAL	1	TRUE	0	0.534772195947457	1		532	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578509	7578509	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519978	NA	P-0060379-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	81	970	0	ENST00000269305.4:c.421T>C	p.Cys141Arg	p.C141R	ENST00000269305	NM_001126112.2	141	Tgc/Cgc	5/11	0.534772195947457	1	FACETS	0.236	0.207	0.267	0.236	0.207	0.267	SUBCLONAL	1	TRUE	0	0.534772195947457	1		970	941	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0060379-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	218	876	0	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.534772195947457	1	FACETS	0.824	0.769	0.88	0.824	0.769	0.88	CLONAL	1	TRUE	0	0.534772195947457	1		876	725	SUCCESS
APC	324	MSKCC	GRCh37	5	112175541	112175544	+	frameshift_variant	Frame_Shift_Del	DEL	TTAT	TTAT	-	novel	NA	P-0060379-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	517	816	0	ENST00000257430.4:c.4250_4253del	p.Ile1417LysfsTer55	p.I1417Kfs*55	ENST00000257430	NM_000038.5	1417	aTTATa/aa	16/16	0.534772195947457	2	FACETS	0.998	0.962	1	0.998	0.962	1	CLONAL	2	TRUE	0	0.534772195947457	2		816	969	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0060380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	51	356	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.886	0.757	1	0.886	0.757	1	CLONAL	1	TRUE	1	0.355500476709958	2		356	324	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027306	48027306	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	85	553	0	ENST00000234420.5:c.2184A>T	p.Lys728Asn	p.K728N	ENST00000234420	NM_000179.2	728	aaA/aaT	4/10	1	2	FACETS	0.911	0.807	1	0.911	0.807	1	CLONAL	1	TRUE	1	0.355500476709958	2		553	525	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0060381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	112	541	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.222364073365094	2		541	910	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0060381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	57	484	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.772	0.662	0.893	0.772	0.662	0.893	SUBCLONAL	1	TRUE	1	0.222364073365094	2		484	664	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0060381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	24	179	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.222364073365094	1	FACETS	0.941	0.742	1	0.941	0.742	1	CLONAL	1	TRUE	0	0.222364073365094	1		179	204	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120511	94120511	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	49	599	0	ENST00000369303.4:c.540G>T	p.Lys180Asn	p.K180N	ENST00000369303	NM_004440.3	180	aaG/aaT	3/17	1	2	FACETS	0.642	0.543	0.752	0.642	0.543	0.752	SUBCLONAL	1	TRUE	1	0.222364073365094	2		599	686	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215422	5215422	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	137	897	0	ENST00000357368.4:c.4196C>A	p.Ser1399Tyr	p.S1399Y	ENST00000357368	NM_002850.3	1399	tCc/tAc	28/38	0.222364073365094	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.222364073365094	1		897	832	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612244	189612244	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	51	808	0	ENST00000264731.3:c.1996G>T	p.Asp666Tyr	p.D666Y	ENST00000264731	NM_003722.4	666	Gat/Tat	14/14	1	2	FACETS	0.575	0.487	0.672	0.575	0.487	0.672	SUBCLONAL	1	TRUE	1	0.222364073365094	2		808	798	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858097	152858097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs930788533	NA	P-0060381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	69	400	0	ENST00000406277.2:c.518G>A	p.Arg173Gln	p.R173Q	ENST00000406277	NM_152274.4	173	cGg/cAg	6/7	1	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.222364073365094	1		400	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0060382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	655	580	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.924237981764639	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.924237981764639	1		580	722	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861171	57861171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1608	273	751	0	ENST00000228682.2:c.968G>A	p.Arg323Gln	p.R323Q	ENST00000228682	NM_005269.2	323	cGg/cAg	9/12	0.721416141347185	5	FACETS	0.749	0.7	0.8			1	SUBCLONAL	1	TRUE	NA	0.924237981764639	5		751	1881	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134508	30134508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	96	564	0	ENST00000263025.4:c.23G>A	p.Gly8Glu	p.G8E	ENST00000263025	NM_002746.2	8	gGg/gAg	1/9	0.924237981764639	1	FACETS	0.508	0.462	0.554	0.508	0.462	0.554	SUBCLONAL	1	TRUE	0	0.924237981764639	1		564	220	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209305	133209305	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	471	847	0	ENST00000320574.5:c.6081G>C	p.Arg2027Ser	p.R2027S	ENST00000320574	NM_006231.2	2027	agG/agC	44/49	0.924237981764639	2	FACETS	0.849	0.827	0.871	0.849	0.827	0.871	CLONAL	2	TRUE	0	0.924237981764639	2		847	600	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47088089	47088089	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	49	411	0	ENST00000409792.3:c.6986A>G	p.Gln2329Arg	p.Q2329R	ENST00000409792	NM_014159.6	2329	cAg/cGg	16/21	0.924237981764639	2	FACETS	0.183	0.154	0.214	0.091	0.077	0.107	SUBCLONAL	1	TRUE	0	0.924237981764639	2		411	580	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933317	39933317	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060382-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	896	848	0	ENST00000378444.4:c.1282G>T	p.Glu428Ter	p.E428*	ENST00000378444	NM_001123385.1	428	Gag/Tag	4/15	0.849754010013737	4	FACETS	0.915	0.893	0.936	0.915	0.893	0.936	CLONAL	3	TRUE	1	0.924237981764639	4		848	1359	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0060383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	31	377	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.338323122582688	3	FACETS	0.771	0.633	0.921	0.771	0.633	0.921	CLONAL	2	TRUE	1	0.338323122582688	3		377	139	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0060383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	14	163	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.338323122582688	2	FACETS	0.92	0.712	1	1	0.897	1	CLONAL	3	TRUE	0	0.338323122582688	2		163	30	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221211	1221211	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0060383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	89	685	0	ENST00000326873.7:c.735-1G>T		p.X245_splice	ENST00000326873	NM_000455.4	245			0.338323122582688	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	0	0.338323122582688	3		685	178	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436410	49436410	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs756972898	NA	P-0060383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	55	811	0	ENST00000301067.7:c.5801A>G	p.Asn1934Ser	p.N1934S	ENST00000301067	NM_003482.3	1934	aAt/aGt	27/54	0.338323122582688	3	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	TRUE	1	0.338323122582688	3		811	175	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101046	27101053	+	frameshift_variant	Frame_Shift_Del	DEL	CTGAGCGC	CTGAGCGC	-	novel	NA	P-0060383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	47	751	0	ENST00000324856.7:c.4329_4336del	p.Glu1444ThrfsTer44	p.E1444Tfs*44	ENST00000324856	NM_006015.4	1443	aCTGAGCGC/a	18/20	0.338323122582688	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	2	TRUE	0	0.338323122582688	2		751	136	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933443	100933443	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	18	432	0	ENST00000325455.5:c.1947A>T	p.Arg649Ser	p.R649S	ENST00000325455	NM_001202474.3	649	agA/agT	4/8	0.338323122582688	3	FACETS	0.987	0.752	1	0.494	0.376	0.63	CLONAL	1	TRUE	1	0.338323122582688	3		432	126	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602391	10602391	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060383-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	100	876	0	ENST00000171111.5:c.1187A>G	p.Tyr396Cys	p.Y396C	ENST00000171111	NM_203500.1	396	tAc/tGc	3/6	0.338323122582688	3	FACETS	0.891	0.817	0.964	1	0.976	1	CLONAL	4	TRUE	0	0.338323122582688	3		876	194	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0060384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	75	445	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.643432888740137	3	FACETS	0.353	0.308	0.401	0.176	0.154	0.201	SUBCLONAL	1	TRUE	1	0.643432888740137	3		445	874	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240233	5240233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202189767	NA	P-0060384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	280	974	0	ENST00000357368.4:c.1681C>T	p.Arg561Trp	p.R561W	ENST00000357368	NM_002850.3	561	Cgg/Tgg	12/38	1	2	FACETS	0.992	0.935	1	0.992	0.935	1	CLONAL	1	TRUE	1	0.643432888740137	2		974	877	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0060384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	94	500	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.600544914482027	1	FACETS	0.674	0.607	0.743	0.674	0.607	0.743	SUBCLONAL	1	TRUE	0	0.643432888740137	1		500	294	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135691	64135691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151034403	NA	P-0060384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	281	1141	0	ENST00000334205.4:c.1159C>T	p.Arg387Trp	p.R387W	ENST00000334205	NM_003942.2	387	Cgg/Tgg	10/17	1	2	FACETS	0.996	0.938	1	0.996	0.938	1	CLONAL	1	TRUE	1	0.643432888740137	2		1141	877	SUCCESS
APC	324	MSKCC	GRCh37	5	112176863	112176863	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1270783041	NA	P-0060384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	86	516	0	ENST00000257430.4:c.5572C>T	p.Arg1858Ter	p.R1858*	ENST00000257430	NM_000038.5	1858	Cga/Tga	16/16	0.643432888740137	3	FACETS	0.462	0.409	0.52	0.231	0.204	0.26	SUBCLONAL	1	TRUE	1	0.643432888740137	3		516	764	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798379	42798379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749470261	NA	P-0060384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	164	705	0	ENST00000575354.2:c.4250G>A	p.Arg1417His	p.R1417H	ENST00000575354	NM_015125.3	1417	cGc/cAc	18/20	1	2	FACETS	0.488	0.448	0.531	0.488	0.448	0.531	SUBCLONAL	1	TRUE	1	0.643432888740137	2		705	1044	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495351	149495351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373655593	NA	P-0060384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	529	1027	0	ENST00000261799.4:c.3296C>T	p.Ala1099Val	p.A1099V	ENST00000261799	NM_002609.3	1099	gCg/gTg	23/23	0.223806649495654	3	FACETS	1	0.981	1	0.685	0.66	0.711	INDETERMINATE	2	TRUE	0	0.643432888740137	3		1027	1057	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782296	56782296	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760107958	NA	P-0060384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	288	947	0	ENST00000308159.5:c.137G>A	p.Arg46His	p.R46H	ENST00000308159	NM_014669.4	46	cGt/cAt	2/22	1	2	FACETS	0.952	0.897	1	0.952	0.897	1	CLONAL	1	TRUE	1	0.643432888740137	2		947	940	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402833	20402833	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1216519626	NA	P-0060384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	112	821	1	ENST00000346618.3:c.370A>G	p.Ser124Gly	p.S124G	ENST00000346618	NM_001949.4	124	Agc/Ggc	1/7	0.643432888740137	3	FACETS	0.549	0.493	0.608	0.275	0.246	0.304	SUBCLONAL	1	TRUE	1	0.643432888740137	3		822	838	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711895	89711895	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	12	518	0	ENST00000371953.3:c.513G>C	p.Gln171His	p.Q171H	ENST00000371953	NM_000314.4	171	caG/caC	6/9	0.600544914482027	1	FACETS	0.063	0.044	0.087	0.063	0.044	0.087	SUBCLONAL	1	TRUE	0	0.643432888740137	1		518	402	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227816	36227816	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190286476	NA	P-0060384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	316	1332	0	ENST00000222270.7:c.7301C>T	p.Ala2434Val	p.A2434V	ENST00000222270	NM_014727.1	2434	gCg/gTg	32/37	1	2	FACETS	0.928	0.876	0.98	0.928	0.876	0.98	CLONAL	1	TRUE	1	0.643432888740137	2		1332	1059	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247964	59247964	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	86	1367	0	ENST00000371222.2:c.779T>C	p.Met260Thr	p.M260T	ENST00000371222	NM_002228.3	260	aTg/aCg	1/1	1	2	FACETS	0.215	0.19	0.243	0.215	0.19	0.243	SUBCLONAL	1	TRUE	1	0.643432888740137	2		1367	1241	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47503744	47503746	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1387779417	NA	P-0060384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	276	854	2	ENST00000404338.3:c.4307_4309del	p.Phe1436del	p.F1436del	ENST00000404338	NM_004491.4	1433	ccCTTc/ccc	6/6	1	2	FACETS	0.825	0.775	0.876	0.825	0.775	0.876	CLONAL	1	TRUE	1	0.643432888740137	2		856	1040	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204636	108204636	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781994	NA	P-0060384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	13	184	0	ENST00000278616.4:c.7951C>T	p.Gln2651Ter	p.Q2651*	ENST00000278616	NM_000051.3	2651	Cag/Tag	54/63	0.411649426778266	1	FACETS	0.151	0.107	0.203	0.151	0.107	0.203	SUBCLONAL	1	TRUE	0	0.643432888740137	1		184	182	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216539	108216539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	99	458	0	ENST00000278616.4:c.8488G>T	p.Val2830Phe	p.V2830F	ENST00000278616	NM_000051.3	2830	Gtt/Ttt	58/63	0.411649426778266	1	FACETS	0.6	0.541	0.661	0.6	0.541	0.661	SUBCLONAL	1	TRUE	0	0.643432888740137	1		458	348	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859599	57859599	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1040509893	NA	P-0060384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	283	1298	0	ENST00000228682.2:c.653G>A	p.Arg218Gln	p.R218Q	ENST00000228682	NM_005269.2	218	cGg/cAg	7/12	1	2	FACETS	0.836	0.786	0.887	0.836	0.786	0.887	CLONAL	1	TRUE	1	0.643432888740137	2		1298	1052	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037971	49037971	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	38	148	0	ENST00000267163.4:c.2211G>C	p.Glu737Asp	p.E737D	ENST00000267163	NM_000321.2	737	gaG/gaC	21/27	0.643432888740137	1	FACETS	0.507	0.426	0.595	0.507	0.426	0.595	SUBCLONAL	1	TRUE	0	0.643432888740137	1		148	158	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441469	40441469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	262	990	0	ENST00000345506.4:c.40G>A	p.Ala14Thr	p.A14T	ENST00000345506	NM_003152.3	14	Gcg/Acg	3/20	1	2	FACETS	0.987	0.928	1	0.987	0.928	1	CLONAL	1	TRUE	1	0.643432888740137	2		990	825	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21348518	21348518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	204	1478	0	ENST00000215739.8:c.1575G>A	p.Met525Ile	p.M525I	ENST00000215739	NM_006767.3	525	atG/atA	14/21	0.633527567951312	1	FACETS	0.608	0.566	0.652	0.608	0.566	0.652	SUBCLONAL	1	TRUE	0	0.643432888740137	1		1478	707	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997853	149997854	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0060384-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	182	851	0	ENST00000253339.5:c.2613_2614del	p.Asp871GlufsTer6	p.D871Efs*6	ENST00000253339		871	gaTAgc/gagc	5/7	1	2	FACETS	0.611	0.564	0.66	0.611	0.564	0.66	SUBCLONAL	1	TRUE	1	0.643432888740137	2		851	926	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0060385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	242	1097	6	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.411498260511326	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.411498260511326	1		1103	857	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39317337	39317337	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	69	393	0	ENST00000373001.3:c.849A>T	p.Glu283Asp	p.E283D	ENST00000373001	NM_022157.3	283	gaA/gaT	5/7	1	2	FACETS	0.785	0.687	0.891	0.785	0.687	0.891	SUBCLONAL	1	TRUE	1	0.411498260511326	2		393	427	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233129	69233129	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	87	746	1	ENST00000462284.1:c.994C>A	p.Arg332Ser	p.R332S	ENST00000462284	NM_002392.5	332	Cgt/Agt	11/11	1	2	FACETS	0.649	0.574	0.728	0.649	0.574	0.728	SUBCLONAL	1	TRUE	1	0.411498260511326	2		747	652	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522557	67522559	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0060385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	35	605	0	ENST00000274335.5:c.60_62del	p.Glu20del	p.E20del	ENST00000274335		18	agAGAa/aga	1/15	0.411498260511326	1	FACETS	0.259	0.212	0.313	0.259	0.212	0.313	SUBCLONAL	1	TRUE	0	0.411498260511326	1		605	521	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841931	151841931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060385-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	190	827	0	ENST00000262189.6:c.14210C>T	p.Ser4737Leu	p.S4737L	ENST00000262189	NM_170606.2	4737	tCa/tTa	55/59	0.411498260511326	4	FACETS	1	0.976	1	0.38	0.35	0.411	CLONAL	1	TRUE	1	0.411498260511326	4		827	1144	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420312	88420312	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060386-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	257	781	0	ENST00000360948.2:c.2374C>G	p.Pro792Ala	p.P792A	ENST00000360948	NM_001012338.2	792	Ccc/Gcc	19/19	0.560353885867621	3	FACETS	1	0.969	1	0.528	0.494	0.564	CLONAL	1	TRUE	1	0.560353885867621	3		781	1111	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0060387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1291	124	569	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.626	0.564	0.692	0.626	0.564	0.692	SUBCLONAL	1	TRUE	1	0.28	2		569	1415	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0060387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	60	244	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.999	0.863	1	0.999	0.863	1	CLONAL	1	TRUE	1	0.28	2		244	429	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0060387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1304	78	415	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	0.27857540094202	3	FACETS	0.46	0.402	0.522	0.23	0.201	0.261	SUBCLONAL	1	TRUE	1	0.28	3		415	1382	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21973539	21974561	+	intron_variant	Intron	DEL	GTTGGCAAAATTTTAGAGATGCTAAGTTACCCATGTATTAATTACTTTTAAATCCTCCCCTAACTCCCTCACAAAACAGGAGTAGGGAGAGGAGAAACACCTCTGTTCAAAAATGAGGAATTGAAAACTCTTATCACAAATAAACTATATCAAGTAAGCTAAAGATAGTAAAAGAGCAAAAATGTTAGCAGATATTCCCAAAATGGTAACTACATATTACCTCTGGAATGATCACATGAATGTGGCTCATTATTTCCTAAGTTCCTACAGCAAACATATATTTATTTGCCCTACTCAGTTAAAAATAAACACAATATGTAGTTGCTTCTGAATAATTTTTCTCTCTCTCTTTCTCTCTTTCTTTCTTTCGACAAAGTCTCACTCTGTCACCCAGGCTGGAGTGAAGTGGCTCCATCTCGCTGTTCACTACAACCTCAGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAACCTCCCGAGTAGCTGGGATTACAGGCGCCTGCCACCACCCCCGGCTACTTTTTGTATTTTTAGTAGAGGCGAGGTTTCACCTGTTGGCCAGGCTGGTCTCGAACTCCCGACCTCAGGTGATTCCCCCCGCCTTGATCTCCCAAAGTGAAGGGATTACAAGGCGTGAGGCACCGCGCCCGGCCGCTTCTGAATAATTTCGATCAAAATTTATATTCGATATTTATTCCAACATACACCACAGATTTCCACTGATAATCCCTCCTAGTAAGAAAGATAAGCTCCATCCAGGTATCTGTGAATTGGAGGCTAAGTAGTCCCAGCACATCTTACATTTCTTTAAGACTCCCTTTTTATCCCAAACGTTCGTAAATTTTGTATCTGATAAAGAGCATACTTCCATCTAATACAAATATGTTCCCCCCTTCAGATCTTCTCAGCATTCGAGAGATCTGTACGCGCGTGGCTCCTCATTCCTCTTCCTTGGCTTCCCAAGCCCCCAGGGCGTCGCCAGGAGGAGGTCTGTGATTACAAACCCCTTCTGAAAACTCCCCAG	GTTGGCAAAATTTTAGAGATGCTAAGTTACCCATGTATTAATTACTTTTAAATCCTCCCCTAACTCCCTCACAAAACAGGAGTAGGGAGAGGAGAAACACCTCTGTTCAAAAATGAGGAATTGAAAACTCTTATCACAAATAAACTATATCAAGTAAGCTAAAGATAGTAAAAGAGCAAAAATGTTAGCAGATATTCCCAAAATGGTAACTACATATTACCTCTGGAATGATCACATGAATGTGGCTCATTATTTCCTAAGTTCCTACAGCAAACATATATTTATTTGCCCTACTCAGTTAAAAATAAACACAATATGTAGTTGCTTCTGAATAATTTTTCTCTCTCTCTTTCTCTCTTTCTTTCTTTCGACAAAGTCTCACTCTGTCACCCAGGCTGGAGTGAAGTGGCTCCATCTCGCTGTTCACTACAACCTCAGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAACCTCCCGAGTAGCTGGGATTACAGGCGCCTGCCACCACCCCCGGCTACTTTTTGTATTTTTAGTAGAGGCGAGGTTTCACCTGTTGGCCAGGCTGGTCTCGAACTCCCGACCTCAGGTGATTCCCCCCGCCTTGATCTCCCAAAGTGAAGGGATTACAAGGCGTGAGGCACCGCGCCCGGCCGCTTCTGAATAATTTCGATCAAAATTTATATTCGATATTTATTCCAACATACACCACAGATTTCCACTGATAATCCCTCCTAGTAAGAAAGATAAGCTCCATCCAGGTATCTGTGAATTGGAGGCTAAGTAGTCCCAGCACATCTTACATTTCTTTAAGACTCCCTTTTTATCCCAAACGTTCGTAAATTTTGTATCTGATAAAGAGCATACTTCCATCTAATACAAATATGTTCCCCCCTTCAGATCTTCTCAGCATTCGAGAGATCTGTACGCGCGTGGCTCCTCATTCCTCTTCCTTGGCTTCCCAAGCCCCCAGGGCGTCGCCAGGAGGAGGTCTGTGATTACAAACCCCTTCTGAAAACTCCCCAG	-	novel	NA	P-0060387-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	72	399	0	ENST00000304494.5:c.150+116_150+1138del		p.*50*	ENST00000304494	NM_000077.4	-/156			1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.28	2		399	471	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0060390-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	42	487	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	0.622	0.517	0.74	0.622	0.517	0.74	SUBCLONAL	1	TRUE	1	0.13	2		487	1038	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0060391-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	425	408	0	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	0.741622155679385	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.741622155679385	2		408	549	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978321	2978321	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs138920531	NA	P-0060391-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	95	770	0	ENST00000396946.4:c.1009C>T	p.Arg337Ter	p.R337*	ENST00000396946	NM_032415.4	337	Cga/Tga	7/25	0.741622155679385	2	FACETS	0.474	0.423	0.528	0.237	0.211	0.264	SUBCLONAL	1	TRUE	0	0.741622155679385	2		770	540	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194881	30194881	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0060391-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	48	121	0	ENST00000331968.5:c.265-1G>A		p.X89_splice	ENST00000331968	NM_002742.2	89			0.741622155679385	2	FACETS	0.492	0.419	0.571	0.246	0.209	0.286	SUBCLONAL	1	TRUE	0	0.741622155679385	2		121	263	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984433	72984433	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060391-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	298	508	0	ENST00000268489.5:c.3151A>T	p.Ser1051Cys	p.S1051C	ENST00000268489	NM_006885.3	1051	Agc/Tgc	3/10	0.741622155679385	2	FACETS	1	0.983	1	0.543	0.514	0.572	CLONAL	1	TRUE	0	0.741622155679385	2		508	740	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955139	55955139	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	rs1030650141	NA	P-0060391-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	34	227	0	ENST00000263923.4:c.3406T>A	p.Tyr1136Asn	p.Y1136N	ENST00000263923	NM_002253.2	1136	Tac/Aac	26/30	1	2	FACETS	0.22	0.179	0.265	0.22	0.179	0.265	SUBCLONAL	1	TRUE	1	0.741622155679385	2		227	417	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546874	9546874	+	frameshift_variant	Frame_Shift_Ins	INS	T	T	GG	novel	NA	P-0060391-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	250	537	0	ENST00000353224.5:c.1148delinsCC	p.Tyr383SerfsTer48	p.Y383Sfs*48	ENST00000353224	NM_177990.2	383	tAc/tCCc	5/10	0.721751151757588	3	FACETS	0.974	0.912	1	0.487	0.456	0.519	CLONAL	1	TRUE	1	0.741622155679385	3		537	949	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0060392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	302	741	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.712422766955073	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.712422766955073	1		741	543	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562580	21562581	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0060392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	21	759	0	ENST00000382592.4:c.1338dup	p.Val447ArgfsTer124	p.V447Rfs*124	ENST00000382592	NM_014572.2	446	-/C	4/8	0.712422766955073	1	FACETS	0.097	0.074	0.124	0.097	0.074	0.124	SUBCLONAL	1	TRUE	0	0.712422766955073	1		759	390	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033893	49033914	+	frameshift_variant	Frame_Shift_Del	DEL	AACATATCATCTGGACCCTTTT	AACATATCATCTGGACCCTTTT	-	novel	NA	P-0060392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	310	542	0	ENST00000267163.4:c.2030_2051del	p.Glu677AlafsTer12	p.E677Afs*12	ENST00000267163	NM_000321.2	677	gAACATATCATCTGGACCCTTTTc/gc	20/27	0.154674931048125	3	FACETS	0.913	0.879	0.945			1	INDETERMINATE	3	TRUE	NA	0.712422766955073	3		542	431	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140549981	140549981	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060392-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	50	173	0	ENST00000288602.6:c.170C>A	p.Thr57Lys	p.T57K	ENST00000288602	NM_004333.4	57	aCa/aAa	2/18	1	2	FACETS	0.821	0.709	0.939	0.821	0.709	0.939	CLONAL	1	TRUE	1	0.712422766955073	2		173	171	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0060394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	255	388	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.918	0.862	0.975	0.918	0.862	0.975	CLONAL	1	TRUE	1	0.691115151345189	2		388	804	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578266	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs942158624	NA	P-0060394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	488	700	0	ENST00000269305.4:c.583A>T	p.Ile195Phe	p.I195F	ENST00000269305	NM_001126112.2	195	Atc/Ttc	6/11	0.681989759466861	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.691115151345189	1		700	922	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858883	78858883	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3190	173	657	0	ENST00000306801.3:c.1918A>C	p.Ile640Leu	p.I640L	ENST00000306801	NM_020761.2	640	Atc/Ctc	17/34	0.691115151345189	6	FACETS	0.355	0.324	0.387			1	SUBCLONAL	1	TRUE	NA	0.691115151345189	6		657	3363	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252852	36252853	+	splice_donor_variant	Splice_Site	INS	-	-	CCT	novel	NA	P-0060394-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	311	411	0	ENST00000300305.3:c.507_508+1dup		p.X169_splice	ENST00000300305		169			1	2	FACETS	0.914	0.863	0.965	0.914	0.863	0.965	CLONAL	1	TRUE	1	0.691115151345189	2		411	985	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593652	55593653	+	inframe_insertion	In_Frame_Ins	INS	-	-	AACACAACTTCCTTATGATCACAAATGGGAGTTTCCCAGAAACAGGCTGAGTTT	novel	NA	P-0060395-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	55	620	0	ENST00000288135.5:c.1719_1772dup	p.Ser590_Phe591insLeuThrGlnLeuProTyrAspHisLysTrpGluPheProArgAsnArgLeuSer	p.S590_F591insLTQLPYDHKWEFPRNRLS	ENST00000288135	NM_000222.2	573	cca/ccAACACAACTTCCTTATGATCACAAATGGGAGTTTCCCAGAAACAGGCTGAGTTTa	11/21	1	2	FACETS	0.382	0.327	0.442	0.382	0.327	0.442	SUBCLONAL	1	TRUE	1	0.634528486860193	2		620	454	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	191	475	0				ENST00000310581	NM_198253.2	-/1132			0.235232795127323	3	FACETS	1	0.985	1	0.814	0.757	0.871	CLONAL	2	FALSE	0	0.313174820312098	3		475	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0060402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	496	569	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.256884705686365	4	FACETS	0.903	0.867	0.94	0.903	0.867	0.94	CLONAL	4	FALSE	0	0.313174820312098	4		569	1151	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052574	42052574	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	85	642	0	ENST00000219905.7:c.7245G>C	p.Gln2415His	p.Q2415H	ENST00000219905	NM_001164273.1	2415	caG/caC	20/24	0.202850040872592	3	FACETS	0.716	0.632	0.806	0.358	0.316	0.403	SUBCLONAL	1	FALSE	1	0.313174820312098	3		642	877	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636274	73636372	+	inframe_deletion	In_Frame_Del	DEL	TCCGGCCCCGACCCAGGCCCTCCCTGAGTTCACCAGTATATTCAGCTCACACCAGACCGCAGCTCCAGAGGTGAACAATATTTTCATCAAACAAGAACT	TCCGGCCCCGACCCAGGCCCTCCCTGAGTTCACCAGTATATTCAGCTCACACCAGACCGCAGCTCCAGAGGTGAACAATATTTTCATCAAACAAGAACT	-	novel	NA	P-0060402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	242	748	0	ENST00000377687.4:c.540_638del	p.Ala181_Pro213del	p.A181_P213del	ENST00000377687	NM_001730.3	179	ccTCCGGCCCCGACCCAGGCCCTCCCTGAGTTCACCAGTATATTCAGCTCACACCAGACCGCAGCTCCAGAGGTGAACAATATTTTCATCAAACAAGAACTt/cct	2/4	0.313174820312098	4	FACETS	1	0.992	1	0.485	0.451	0.519	CLONAL	1	FALSE	1	0.313174820312098	4		748	1396	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052646	42052646	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	84	665	0	ENST00000219905.7:c.7317G>C	p.Met2439Ile	p.M2439I	ENST00000219905	NM_001164273.1	2439	atG/atC	20/24	0.202850040872592	3	FACETS	0.752	0.663	0.847	0.376	0.331	0.424	SUBCLONAL	1	FALSE	1	0.313174820312098	3		665	825	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36208985	36208985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	124	277	0	ENST00000222270.7:c.65G>A	p.Gly22Asp	p.G22D	ENST00000222270	NM_014727.1	22	gGc/gAc	1/37	0.245700679800558	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	FALSE	1	0.313174820312098	3		277	419	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630618	187630619	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	165	550	0	ENST00000441802.2:c.363dup	p.Ala122SerfsTer3	p.A122Sfs*3	ENST00000441802	NM_005245.3	121	-/A	2/27	0.273331931592944	2	FACETS	0.908	0.839	0.98	0.908	0.839	0.98	CLONAL	2	FALSE	0	0.313174820312098	2		550	580	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459614	149459614	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0060402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	115	691	0	ENST00000286301.3:c.592+1G>A		p.X198_splice	ENST00000286301	NM_005211.3	198			0.235232795127323	3	FACETS	0.889	0.799	0.983	0.296	0.266	0.328	CLONAL	1	FALSE	0	0.313174820312098	3		691	956	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912286	29912286	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	209	766	0	ENST00000376809.5:c.907del	p.Gln303SerfsTer19	p.Q303Sfs*19	ENST00000376809	NM_002116.7	302	tCc/tc	5/8	0.245700679800558	3	FACETS	1	0.99	1	0.721	0.669	0.776	CLONAL	1	FALSE	1	0.313174820312098	3		766	1070	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850874	128850874	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764065797	NA	P-0060402-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	99	643	0	ENST00000249373.3:c.1721C>G	p.Ser574Cys	p.S574C	ENST00000249373	NM_005631.4	574	tCt/tGt	10/12	0.245700679800558	3	FACETS	0.813	0.725	0.908	0.407	0.362	0.454	CLONAL	1	FALSE	1	0.313174820312098	3		643	899	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762959	40762959	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs387906659	NA	P-0060403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	318	806	0	ENST00000392038.2:c.49G>A	p.Glu17Lys	p.E17K	ENST00000392038	NM_001626.4	17	Gaa/Aaa	3/14	0.232716739526227	5	FACETS	1	0.986	1	0.748	0.707	0.79	INDETERMINATE	2	TRUE	2	0.462750792741613	5		806	1037	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439883	52439883	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	393	792	0	ENST00000460680.1:c.829C>T	p.Gln277Ter	p.Q277*	ENST00000460680	NM_004656.3	277	Caa/Taa	10/17	0.462750792741613	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.462750792741613	2		792	805	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370942	55370942	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	298	834	0	ENST00000297316.4:c.244G>A	p.Glu82Lys	p.E82K	ENST00000297316	NM_022454.3	82	Gag/Aag	1/2	0.374784124654977	3	FACETS	0.959	0.906	1	0.959	0.906	1	CLONAL	2	TRUE	1	0.462750792741613	3		834	827	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504326	8504326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349236329	NA	P-0060403-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	116	663	0	ENST00000356435.5:c.1757C>T	p.Ala586Val	p.A586V	ENST00000356435		586	gCt/gTt	12/35	1	2	FACETS	0.675	0.608	0.745	0.675	0.608	0.745	SUBCLONAL	1	TRUE	1	0.462750792741613	2		663	743	SUCCESS
FH	2271	MSKCC	GRCh37	1	241661222	241661222	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1131691245	NA	P-0060404-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	191	411	0	ENST00000366560.3:c.1439C>G	p.Ser480Ter	p.S480*	ENST00000366560	NM_000143.3	480	tCa/tGa	10/10	0.686625430751167	1	FACETS	0.972	0.913	1	0.972	0.913	1	CLONAL	1	TRUE	0	0.686625430751167	1		411	376	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	401	760	5	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	1	0.991	1	1	0.997	1	CLONAL	2	TRUE	1	0.294709601132771	2		765	1172	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	101	388	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.294709601132771	2		388	599	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	453	877	12	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	1	0.982	1	1	0.997	1	CLONAL	2	TRUE	1	0.294709601132771	2		889	1455	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	636	699	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.886	0.854	0.919	1	0.998	1	CLONAL	3	TRUE	1	0.294709601132771	2		706	1623	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	69	332	0	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.294709601132771	2		332	403	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256126	16256126	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	336	700	0	ENST00000375759.3:c.3395del	p.Asn1132ThrfsTer22	p.N1132Tfs*22	ENST00000375759	NM_015001.2	1131	Aaa/aa	11/15	1	2	FACETS	0.883	0.838	0.928	1	0.997	1	CLONAL	3	TRUE	1	0.294709601132771	2		700	861	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257359	16257359	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	228	636	0	ENST00000375759.3:c.4624C>T	p.Arg1542Ter	p.R1542*	ENST00000375759	NM_015001.2	1542	Cga/Tga	11/15	1	2	FACETS	1	0.989	1	1	0.995	1	CLONAL	2	TRUE	1	0.294709601132771	2		636	626	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1344	89	486	0	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	1	2	FACETS	0.421	0.372	0.475	0.421	0.372	0.475	SUBCLONAL	1	TRUE	1	0.294709601132771	2		486	1433	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344833	65344833	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	61	559	0	ENST00000342505.4:c.206-2A>G		p.X69_splice	ENST00000342505	NM_002227.2	69			1	2	FACETS	0.559	0.481	0.643	0.559	0.481	0.643	SUBCLONAL	1	TRUE	1	0.294709601132771	2		559	741	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054921	176054921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138406127	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	65	277	0	ENST00000367669.3:c.1132C>T	p.Arg378Cys	p.R378C	ENST00000367669	NM_022457.5	378	Cgt/Tgt	10/20	1	2	FACETS	0.879	0.771	0.993	1	0.979	1	CLONAL	2	TRUE	1	0.294709601132771	2		277	251	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003485	57003485	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	C	C	T	rs764929700	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	412	926	0	ENST00000257254.3:c.994G>A	p.Ala332Thr	p.A332T	ENST00000257254		332	Gca/Aca	1/2	1	2	FACETS	1	0.987	1	1	0.997	1	CLONAL	2	TRUE	1	0.294709601132771	2		926	1268	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127752	64127752	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	74	702	0	ENST00000334205.4:c.245del	p.Thr82SerfsTer37	p.T82Sfs*37	ENST00000334205	NM_003942.2	82	aCg/ag	3/17	1	2	FACETS	0.491	0.428	0.559	0.491	0.428	0.559	SUBCLONAL	1	TRUE	1	0.294709601132771	2		702	1023	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94201025	94201025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780133	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	175	437	0	ENST00000323929.3:c.1052G>A	p.Arg351His	p.R351H	ENST00000323929	NM_005591.3	351	cGt/cAt	10/20	1	2	FACETS	0.91	0.847	0.974	1	0.994	1	CLONAL	3	TRUE	1	0.294709601132771	2		437	435	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307357	118307357	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555138529	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	32	346	2	ENST00000534358.1:c.134del	p.Pro45ArgfsTer105	p.P45Rfs*105	ENST00000534358	NM_005933.3	44	Ccc/cc	1/36	1	2	FACETS	0.447	0.362	0.543	0.447	0.362	0.543	SUBCLONAL	1	TRUE	1	0.294709601132771	2		348	486	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	60	527	2	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.788	0.679	0.905	0.788	0.679	0.905	CLONAL	1	TRUE	1	0.294709601132771	2		529	517	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422254	422254	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1448384274	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	40	571	0	ENST00000399788.2:c.3004C>T	p.Arg1002Ter	p.R1002*	ENST00000399788	NM_001042603.1	1002	Cga/Tga	20/28	1	2	FACETS	0.357	0.295	0.426	0.357	0.295	0.426	SUBCLONAL	1	TRUE	1	0.294709601132771	2		571	761	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383349	4383351	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	463	893	0	ENST00000261254.3:c.145_147del	p.Lys49del	p.K49del	ENST00000261254	NM_001759.3	48	cAGAag/cag	1/5	1	2	FACETS	1	0.993	1	1	0.997	1	CLONAL	2	TRUE	1	0.294709601132771	2		893	1310	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448461	49448461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748173147	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	569	858	1	ENST00000301067.7:c.250C>T	p.Arg84Cys	p.R84C	ENST00000301067	NM_003482.3	84	Cgc/Tgc	3/54	1	2	FACETS	0.879	0.844	0.913	1	0.998	1	CLONAL	3	TRUE	1	0.294709601132771	2		859	1465	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492779	50492779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1215265267	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	91	638	0	ENST00000394963.4:c.1544C>T	p.Thr515Ile	p.T515I	ENST00000394963	NM_003076.4	515	aCa/aTa	13/13	1	2	FACETS	0.547	0.485	0.615	0.547	0.485	0.615	SUBCLONAL	1	TRUE	1	0.294709601132771	2		638	1128	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865076	57865076	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462976482	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	108	841	0	ENST00000228682.2:c.2557del	p.Gln853SerfsTer93	p.Q853Sfs*93	ENST00000228682	NM_005269.2	851	taC/ta	12/12	1	2	FACETS	0.542	0.484	0.603	0.542	0.484	0.603	SUBCLONAL	1	TRUE	1	0.294709601132771	2		841	1353	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869486	102869486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755265524	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	354	650	0	ENST00000307046.8:c.155C>T	p.Thr52Met	p.T52M	ENST00000307046	NM_001111285.1	52	aCg/aTg	2/4	1	2	FACETS	0.952	0.901	1	1	0.996	1	CLONAL	2	TRUE	1	0.294709601132771	2		650	1262	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959432	26959432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	197	494	0	ENST00000381527.3:c.599G>A	p.Arg200Gln	p.R200Q	ENST00000381527	NM_001260.1	200	cGa/cAa	6/13	1	2	FACETS	0.898	0.84	0.958	1	0.995	1	CLONAL	3	TRUE	1	0.294709601132771	2		494	496	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004202	29004202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137862999	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	307	516	0	ENST00000282397.4:c.1091C>T	p.Ser364Leu	p.S364L	ENST00000282397	NM_002019.4	364	tCg/tTg	8/30	1	2	FACETS	0.857	0.812	0.904	1	0.996	1	CLONAL	3	TRUE	1	0.294709601132771	2		516	810	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355904	73355904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	484	747	0	ENST00000377767.4:c.67C>T	p.His23Tyr	p.H23Y	ENST00000377767	NM_014953.3	23	Cac/Tac	1/21	1	2	FACETS	0.904	0.866	0.942	1	0.998	1	CLONAL	3	TRUE	1	0.294709601132771	2		747	1211	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986737	36986737	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	88	878	0	ENST00000354822.5:c.952C>T	p.Gln318Ter	p.Q318*	ENST00000354822	NM_001079668.2	318	Cag/Tag	3/3	1	2	FACETS	0.585	0.517	0.658	0.585	0.517	0.658	SUBCLONAL	1	TRUE	1	0.294709601132771	2		878	1021	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060955	38060955	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	393	847	0	ENST00000250448.2:c.1034del	p.Gly345AlafsTer5	p.G345Afs*5	ENST00000250448	NM_004496.3	345	gGc/gc	2/2	1	2	FACETS	1	0.982	1	1	0.997	1	CLONAL	2	TRUE	1	0.294709601132771	2		847	1249	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42050032	42050032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	102	313	0	ENST00000219905.7:c.7186C>T	p.Arg2396Ter	p.R2396*	ENST00000219905	NM_001164273.1	2396	Cga/Tga	19/24	1	2	FACETS	1	0.974	1	1	0.99	1	CLONAL	2	TRUE	1	0.294709601132771	2		313	284	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43733757	43733757	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	37	334	0	ENST00000382044.4:c.3065del	p.Asn1022MetfsTer20	p.N1022Mfs*20	ENST00000382044	NM_001141980.1	1022	aAt/at	15/28	1	2	FACETS	0.517	0.425	0.619	0.517	0.425	0.619	SUBCLONAL	1	TRUE	1	0.294709601132771	2		334	486	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457615	67457615	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	610	925	1	ENST00000327367.4:c.425G>A	p.Arg142His	p.R142H	ENST00000327367	NM_005902.3	142	cGc/cAc	3/9	1	2	FACETS	0.911	0.877	0.945	1	0.998	1	CLONAL	3	TRUE	1	0.294709601132771	2		926	1515	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786719	3786719	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	121	719	0	ENST00000262367.5:c.4492C>T	p.Arg1498Ter	p.R1498*	ENST00000262367	NM_004380.2	1498	Cga/Tga	27/31	1	2	FACETS	0.725	0.654	0.801	0.725	0.654	0.801	SUBCLONAL	1	TRUE	1	0.294709601132771	2		719	1132	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900384	3900384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146887252	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	459	833	0	ENST00000262367.5:c.712G>A	p.Val238Met	p.V238M	ENST00000262367	NM_004380.2	238	Gtg/Atg	2/31	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	1	0.294709601132771	2		833	1349	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857251	9857252	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	248	811	0	ENST00000330684.3:c.4149dup	p.Ser1384LeufsTer15	p.S1384Lfs*15	ENST00000330684	NM_001134407.1	1383	-/C	13/13	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.294709601132771	2		811	1277	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129719	30129719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1379935159	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	604	760	0	ENST00000263025.4:c.494G>A	p.Arg165Gln	p.R165Q	ENST00000263025	NM_002746.2	165	cGa/cAa	3/9	1	2	FACETS	1	0.981	1	1	0.998	1	CLONAL	3	TRUE	1	0.294709601132771	2		760	1333	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	509	916	3	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	1	0.995	1	1	0.998	1	CLONAL	2	TRUE	1	0.294709601132771	2		919	1390	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984590	72984591	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	546	878	0	ENST00000268489.5:c.2993dup	p.Asn998LysfsTer49	p.N998Kfs*49	ENST00000268489	NM_006885.3	998	aac/aaAc	3/10	1	2	FACETS	0.854	0.819	0.888	1	0.998	1	CLONAL	3	TRUE	1	0.294709601132771	2		878	1447	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929516	81929516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760949449	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	511	489	0	ENST00000359376.3:c.1177G>A	p.Ala393Thr	p.A393T	ENST00000359376	NM_002661.3	393	Gcc/Acc	13/33	1	2	FACETS	0.902	0.866	0.939	1	0.998	1	CLONAL	3	TRUE	1	0.294709601132771	2		489	1281	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81973542	81973542	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	379	635	0	ENST00000359376.3:c.3359T>C	p.Val1120Ala	p.V1120A	ENST00000359376	NM_002661.3	1120	gTg/gCg	30/33	1	2	FACETS	1	0.969	1	1	0.997	1	CLONAL	3	TRUE	1	0.294709601132771	2		635	842	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346113	89346114	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs1555525296	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	168	531	0	ENST00000301030.4:c.6836_6837del	p.Val2279GlyfsTer16	p.V2279Gfs*16	ENST00000301030	NM_001256183.1	2279	gTG/g	9/13	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.294709601132771	2		531	764	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347172	89347173	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1290	122	954	0	ENST00000301030.4:c.5777dup	p.Glu1927GlyfsTer23	p.E1927Gfs*23	ENST00000301030	NM_001256183.1	1926	ccg/ccCg	9/13	1	2	FACETS	0.586	0.528	0.648	0.586	0.528	0.648	SUBCLONAL	1	TRUE	1	0.294709601132771	2		954	1412	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347713	89347713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561668093	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	648	948	2	ENST00000301030.4:c.5237C>T	p.Thr1746Met	p.T1746M	ENST00000301030	NM_001256183.1	1746	aCg/aTg	9/13	1	2	FACETS	0.91	0.878	0.944	1	0.998	1	CLONAL	3	TRUE	1	0.294709601132771	2		950	1610	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347788	89347788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1466820191	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	589	881	2	ENST00000301030.4:c.5162C>T	p.Thr1721Met	p.T1721M	ENST00000301030	NM_001256183.1	1721	aCg/aTg	9/13	1	2	FACETS	0.98	0.944	1	1	0.998	1	CLONAL	3	TRUE	1	0.294709601132771	2		883	1360	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8109821	8109821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766373871	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	470	682	0	ENST00000585124.1:c.674C>T	p.Ala225Val	p.A225V	ENST00000585124	NM_004217.3	225	gCg/gTg	7/9	1	2	FACETS	0.963	0.923	1	1	0.998	1	CLONAL	3	TRUE	1	0.294709601132771	2		682	1104	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012211	16012211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1391053845	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	144	413	0	ENST00000268712.3:c.2071C>T	p.Arg691Cys	p.R691C	ENST00000268712	NM_006311.3	691	Cgt/Tgt	19/46	1	2	FACETS	1	0.93	1	1	0.991	1	CLONAL	2	TRUE	1	0.294709601132771	2		413	482	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670055	29670055	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555535407	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	160	377	0	ENST00000356175.3:c.7028G>A	p.Arg2343Gln	p.R2343Q	ENST00000356175	NM_000267.3	2343	cGg/cAg	47/57	1	2	FACETS	0.878	0.815	0.943	1	0.994	1	CLONAL	3	TRUE	1	0.294709601132771	2		377	412	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37680973	37680973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764290780	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	394	762	0	ENST00000447079.4:c.3142C>T	p.Arg1048Ter	p.R1048*	ENST00000447079	NM_015083.1	1048	Cga/Tga	12/14	1	2	FACETS	1	0.985	1	1	0.997	1	CLONAL	2	TRUE	1	0.294709601132771	2		762	1230	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492796	56492798	+	inframe_deletion	In_Frame_Del	DEL	ATA	ATA	-	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	447	697	0	ENST00000407977.2:c.141_143del	p.Ile48del	p.I48del	ENST00000407977		47	atTATc/atc	2/10	1	2	FACETS	0.922	0.882	0.962	1	0.997	1	CLONAL	3	TRUE	1	0.294709601132771	2		697	1097	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395805	45395805	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	69	506	0	ENST00000262160.6:c.329C>A	p.Ser110Tyr	p.S110Y	ENST00000262160	NM_005901.5	110	tCt/tAt	4/11	1	2	FACETS	0.724	0.63	0.825	0.724	0.63	0.825	SUBCLONAL	1	TRUE	1	0.294709601132771	2		506	647	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220135	5220135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269111261	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	499	758	0	ENST00000357368.4:c.3580C>T	p.Arg1194Cys	p.R1194C	ENST00000357368	NM_002850.3	1194	Cgc/Tgc	22/38	1	2	FACETS	0.938	0.899	0.976	1	0.998	1	CLONAL	3	TRUE	1	0.294709601132771	2		758	1204	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221161	5221161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs575201235	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	590	910	0	ENST00000357368.4:c.3305G>A	p.Arg1102His	p.R1102H	ENST00000357368	NM_002850.3	1102	cGc/cAc	20/38	1	2	FACETS	0.902	0.868	0.937	1	0.998	1	CLONAL	3	TRUE	1	0.294709601132771	2		910	1479	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238958	5238958	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1229	89	775	0	ENST00000357368.4:c.1821del	p.Val608TrpfsTer30	p.V608Wfs*30	ENST00000357368	NM_002850.3	607	ccC/cc	13/38	1	2	FACETS	0.458	0.405	0.516	0.458	0.405	0.516	SUBCLONAL	1	TRUE	1	0.294709601132771	2		775	1318	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982398	10982398	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	309	346	1	ENST00000327064.4:c.20C>T	p.Ala7Val	p.A7V	ENST00000327064	NM_199141.1	7	gCg/gTg	1/16	1	2	FACETS	0.931	0.883	0.979	1	0.997	1	CLONAL	3	TRUE	1	0.294709601132771	2		347	751	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11022923	11022923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	545	752	0	ENST00000327064.4:c.622C>T	p.Arg208Trp	p.R208W	ENST00000327064	NM_199141.1	208	Cgg/Tgg	5/16	1	2	FACETS	0.93	0.894	0.967	1	0.998	1	CLONAL	3	TRUE	1	0.294709601132771	2		752	1325	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258532	19258532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754381519	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1353	102	939	0	ENST00000162023.5:c.368C>T	p.Pro123Leu	p.P123L	ENST00000162023		123	cCg/cTg	8/13	1	2	FACETS	0.476	0.424	0.532	0.476	0.424	0.532	SUBCLONAL	1	TRUE	1	0.294709601132771	2		939	1455	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223613	36223614	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs765758919	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1419	158	1089	2	ENST00000222270.7:c.6169dup	p.Arg2057ProfsTer3	p.R2057Pfs*3	ENST00000222270	NM_014727.1	2055	gcc/gCcc	28/37	1	2	FACETS	0.68	0.621	0.742	0.68	0.621	0.742	SUBCLONAL	1	TRUE	1	0.294709601132771	2		1091	1577	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752805	42752805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767131852	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	402	975	0	ENST00000222329.4:c.1459C>T	p.Arg487Cys	p.R487C	ENST00000222329	NM_006494.2	487	Cgc/Tgc	4/4	1	2	FACETS	1	0.973	1	1	0.997	1	CLONAL	2	TRUE	1	0.294709601132771	2		975	1320	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906366	50906366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762494977	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	431	864	1	ENST00000440232.2:c.1027C>T	p.Arg343Cys	p.R343C	ENST00000440232	NM_002691.3	343	Cgc/Tgc	9/27	1	2	FACETS	1	0.987	1	1	0.997	1	CLONAL	2	TRUE	1	0.294709601132771	2		865	1342	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919000	50919000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778012264	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	113	694	0	ENST00000440232.2:c.2737G>A	p.Gly913Arg	p.G913R	ENST00000440232	NM_002691.3	913	Ggg/Agg	22/27	1	2	FACETS	0.648	0.582	0.719	0.648	0.582	0.719	SUBCLONAL	1	TRUE	1	0.294709601132771	2		694	1183	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182542	99182542	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	92	789	0	ENST00000074304.5:c.2345T>C	p.Leu782Ser	p.L782S	ENST00000074304	NM_001134224.1	782	tTg/tCg	22/26	1	2	FACETS	0.483	0.428	0.543	0.483	0.428	0.543	SUBCLONAL	1	TRUE	1	0.294709601132771	2		789	1292	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182598	99182598	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253335546	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	134	840	0	ENST00000074304.5:c.2401G>A	p.Val801Met	p.V801M	ENST00000074304	NM_001134224.1	801	Gtg/Atg	22/26	1	2	FACETS	0.687	0.622	0.755	0.687	0.622	0.755	SUBCLONAL	1	TRUE	1	0.294709601132771	2		840	1324	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594062	158594062	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	205	517	0	ENST00000263640.3:c.1511A>G	p.Lys504Arg	p.K504R	ENST00000263640	NM_001105.4	504	aAa/aGa	11/11	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.294709601132771	2		517	579	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662055	227662055	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764398926	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	575	868	0	ENST00000305123.5:c.1400G>A	p.Cys467Tyr	p.C467Y	ENST00000305123	NM_005544.2	467	tGc/tAc	1/2	1	2	FACETS	0.959	0.923	0.996	1	0.998	1	CLONAL	3	TRUE	1	0.294709601132771	2		868	1356	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259367	36259367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	497	751	0	ENST00000300305.3:c.124C>T	p.Pro42Ser	p.P42S	ENST00000300305		42	Ccg/Tcg	3/8	1	2	FACETS	0.897	0.86	0.935	1	0.998	1	CLONAL	3	TRUE	1	0.294709601132771	2		751	1253	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145549	24145549	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1318	130	795	0	ENST00000263121.7:c.568C>T	p.Arg190Trp	p.R190W	ENST00000263121	NM_003073.3	190	Cgg/Tgg	5/9	1	2	FACETS	0.609	0.551	0.672	0.609	0.551	0.672	SUBCLONAL	1	TRUE	1	0.294709601132771	2		795	1448	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713612	30713612	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55751315	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	172	785	1	ENST00000295754.5:c.937C>T	p.Arg313Trp	p.R313W	ENST00000295754	NM_003242.5	313	Cgg/Tgg	4/7	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.294709601132771	2		786	1088	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934216	49934216	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1420723677	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	612	922	0	ENST00000296474.3:c.2291T>C	p.Phe764Ser	p.F764S	ENST00000296474	NM_002447.2	764	tTc/tCc	8/20	1	2	FACETS	0.96	0.925	0.995	1	0.998	1	CLONAL	3	TRUE	1	0.294709601132771	2		922	1442	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631641	119631641	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	116	476	0	ENST00000316626.5:c.625C>T	p.Arg209Ter	p.R209*	ENST00000316626		209	Cga/Tga	6/12	1	2	FACETS	0.935	0.849	1	1	0.989	1	CLONAL	2	TRUE	1	0.294709601132771	2		476	421	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851708	134851708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775424447	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	214	767	0	ENST00000398015.3:c.1114C>T	p.Arg372Cys	p.R372C	ENST00000398015	NM_004441.4	372	Cgc/Tgc	5/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.294709601132771	2		767	1348	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294282	1294282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751231538	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	506	856	0	ENST00000310581.5:c.719G>A	p.Arg240His	p.R240H	ENST00000310581	NM_198253.2	240	cGt/cAt	2/16	1	2	FACETS	0.957	0.919	0.996	1	0.998	1	CLONAL	3	TRUE	1	0.294709601132771	2		856	1196	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177584	56177584	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368201444	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	389	671	0	ENST00000399503.3:c.2557C>T	p.Arg853Cys	p.R853C	ENST00000399503	NM_005921.1	853	Cgt/Tgt	14/20	1	2	FACETS	0.857	0.816	0.898	1	0.997	1	CLONAL	3	TRUE	1	0.294709601132771	2		671	1027	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931452	131931452	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507178	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	337	530	12	ENST00000265335.6:c.2165del	p.Lys722ArgfsTer14	p.K722Rfs*14	ENST00000265335		719	ctA/ct	13/25	1	2	FACETS	0.958	0.911	1	1	0.997	1	CLONAL	3	TRUE	1	0.294709601132771	2		542	796	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456908	149456908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758675858	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	594	904	0	ENST00000286301.3:c.820G>A	p.Gly274Ser	p.G274S	ENST00000286301	NM_005211.3	274	Ggc/Agc	6/22	1	2	FACETS	1	0.995	1	1	0.998	1	CLONAL	2	TRUE	1	0.294709601132771	2		904	1625	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562218	176562218	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	102	729	0	ENST00000439151.2:c.118del	p.Ser40LeufsTer42	p.S40Lfs*42	ENST00000439151	NM_022455.4	38	aaT/aa	2/23	1	2	FACETS	0.642	0.572	0.716	0.642	0.572	0.716	SUBCLONAL	1	TRUE	1	0.294709601132771	2		729	1079	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707572	176707572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	275	612	1	ENST00000439151.2:c.5629C>T	p.Arg1877Cys	p.R1877C	ENST00000439151	NM_022455.4	1877	Cgt/Tgt	18/23	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.294709601132771	2		613	780	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225563	26225565	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1352	108	913	0	ENST00000360408.1:c.183_185del	p.Leu62del	p.L62del	ENST00000360408	NM_003532.2	61	CTT/-	1/1	1	2	FACETS	0.502	0.449	0.559	0.502	0.449	0.559	SUBCLONAL	1	TRUE	1	0.294709601132771	2		913	1460	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790908	89790910	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs746966684	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	320	835	0	ENST00000336032.3:c.301_303del	p.Lys101del	p.K101del	ENST00000336032	NM_006813.2	99	AAG/-	1/2	1	2	FACETS	0.98	0.926	1	1	0.996	1	CLONAL	2	TRUE	1	0.294709601132771	2		835	1108	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519505	137519506	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs780346130	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	259	714	5	ENST00000367739.4:c.1132_1133del	p.Ser378PhefsTer6	p.S378Ffs*6	ENST00000367739	NM_000416.2	378	AGt/t	7/7	0.294709601132771	1	FACETS	0.944	0.887	1	1	0.995	1	CLONAL	2	TRUE	0	0.294709601132771	1		719	794	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196029	138196029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150717698	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	377	734	0	ENST00000237289.4:c.343G>A	p.Val115Ile	p.V115I	ENST00000237289	NM_001270507.1	115	Gtt/Att	3/9	0.294709601132771	1	FACETS	0.921	0.875	0.968	1	0.996	1	CLONAL	2	TRUE	0	0.294709601132771	1		734	1184	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129338	152129338	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1361952517	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	421	767	1	ENST00000206249.3:c.296del	p.Pro99HisfsTer10	p.P99Hfs*10	ENST00000206249	NM_000125.3	97	ttC/tt	1/8	0.294709601132771	1	FACETS	1	0.989	1	1	0.997	1	CLONAL	2	TRUE	0	0.294709601132771	1		768	1104	SUCCESS
MET	4233	MSKCC	GRCh37	7	116422048	116422048	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	125	309	0	ENST00000397752.3:c.3529A>G	p.Thr1177Ala	p.T1177A	ENST00000397752	NM_000245.2	1177	Act/Gct	18/21	1	2	FACETS	1	0.981	1	1	0.992	1	CLONAL	2	TRUE	1	0.294709601132771	2		309	340	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930111	68930111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	352	542	0	ENST00000288368.4:c.172G>T	p.Ala58Ser	p.A58S	ENST00000288368	NM_024870.2	58	Gca/Tca	2/40	0.152698256833756	2	FACETS	1	0.991	1	1	0.996	1	INDETERMINATE	3	TRUE	0	0.294709601132771	2		542	696	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561430	141561430	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1673	104	930	0	ENST00000220592.5:c.1375del	p.Gln459SerfsTer9	p.Q459Sfs*9	ENST00000220592	NM_012154.3	459	Cag/ag	11/19	0.255300579848563	4	FACETS	0.514	0.458	0.574	0.171	0.152	0.192	SUBCLONAL	1	TRUE	1	0.294709601132771	4		930	1777	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5065000	5065000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200018153	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	122	466	0	ENST00000381652.3:c.1174G>A	p.Val392Met	p.V392M	ENST00000381652	NM_004972.3	392	Gtg/Atg	9/25	0.294709601132771	1	FACETS	0.972	0.889	1	1	0.99	1	CLONAL	2	TRUE	0	0.294709601132771	1		466	363	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753871	133753871	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	762	610	0	ENST00000318560.5:c.1340A>G	p.Gln447Arg	p.Q447R	ENST00000318560	NM_005157.4	447	cAg/cGg	8/11	0.294709601132771	5	FACETS	0.919	0.893	0.946	1	0.998	1	CLONAL	6	TRUE	1	0.294709601132771	5		610	1352	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360647	70360648	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAG	rs757160341	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	292	253	0	ENST00000374080.3:c.6226_6228dup	p.Gln2076dup	p.Q2076dup	ENST00000374080		2076	-/CAG	42/45	1	1	FACETS	0.925	0.878	0.971	1	0.996	1	CLONAL	3	TRUE	0	0.294709601132771	1		253	609	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152857987	152857987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146203325	NA	P-0060405-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	361	396	0	ENST00000406277.2:c.628G>A	p.Glu210Lys	p.E210K	ENST00000406277	NM_152274.4	210	Gag/Aag	6/7	1	1	FACETS	1	0.994	1	1	0.997	1	CLONAL	4	TRUE	0	0.294709601132771	1		396	470	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115628	108115628	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	46	420	0	ENST00000278616.4:c.776T>G	p.Leu259Arg	p.L259R	ENST00000278616	NM_000051.3	259	cTt/cGt	7/63	0.187440431617065	5	FACETS	1	0.874	1	0.347	0.293	0.407	INDETERMINATE	1	TRUE	2	0.339434036269916	5		420	393	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121599	2121599	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1319342312	NA	P-0060406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	89	722	0	ENST00000219476.3:c.1928A>G	p.Tyr643Cys	p.Y643C	ENST00000219476	NM_000548.3	643	tAc/tGc	18/42	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.339434036269916	2		722	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579531	7579543	+	frameshift_variant	Frame_Shift_Del	DEL	TTGTTCAATATCG	TTGTTCAATATCG	-	novel	NA	P-0060406-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	133	860	0	ENST00000269305.4:c.144_156del	p.Asp49GlyfsTer70	p.D49Gfs*70	ENST00000269305	NM_001126112.2	48	gaCGATATTGAACAA/ga	4/11	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.339434036269916	2		860	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0060408-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	131	758	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.370484129622206	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.370484129622206	1		758	485	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443576	29443576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750194005	NA	P-0060408-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	46	723	1	ENST00000389048.3:c.3641G>A	p.Arg1214His	p.R1214H	ENST00000389048	NM_004304.4	1214	cGc/cAc	23/29	0.370484129622206	1	FACETS	0.399	0.336	0.469	0.399	0.336	0.469	SUBCLONAL	1	TRUE	0	0.370484129622206	1		724	507	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024395	31024399	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAG	CAGAG	-	novel	NA	P-0060408-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	48	737	0	ENST00000375687.4:c.3882_3886del	p.Ser1295CysfsTer32	p.S1295Cfs*32	ENST00000375687	NM_015338.5	1294	CAGAGc/c	13/13	0.370484129622206	1	FACETS	0.376	0.317	0.44	0.376	0.317	0.44	SUBCLONAL	1	TRUE	0	0.370484129622206	1		737	562	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0060410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	724	580	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.545108469845725	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.545108469845725	2		580	1296	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208335	5208335	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148478353	NA	P-0060410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	594	775	0	ENST00000357368.4:c.5555C>T	p.Ser1852Leu	p.S1852L	ENST00000357368	NM_002850.3	1852	tCg/tTg	36/38	0.532886316467317	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.545108469845725	3		775	1385	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281281	15281281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776163983	NA	P-0060410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	616	998	0	ENST00000263388.2:c.4975G>A	p.Val1659Ile	p.V1659I	ENST00000263388	NM_000435.2	1659	Gtc/Atc	27/33	0.545108469845725	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.545108469845725	2		998	1094	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480543	50480543	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147034181	NA	P-0060410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	160	545	2	ENST00000394963.4:c.413G>A	p.Arg138His	p.R138H	ENST00000394963	NM_003076.4	138	cGt/cAt	4/13	1	2	FACETS	0.988	0.911	1	0.988	0.911	1	CLONAL	1	TRUE	1	0.545108469845725	2		547	594	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130337	11130337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs281875226	NA	P-0060410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	449	701	0	ENST00000358026.2:c.2576C>T	p.Thr859Met	p.T859M	ENST00000358026	NM_001128849.1	859	aCg/aTg	18/36	0.532886316467317	3	FACETS	0.93	0.89	0.971	0.93	0.89	0.971	CLONAL	2	TRUE	1	0.545108469845725	3		701	1127	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724319	117724319	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	205	655	0	ENST00000368508.3:c.560G>T	p.Arg187Met	p.R187M	ENST00000368508	NM_002944.2	187	aGg/aTg	6/43	1	2	FACETS	0.847	0.786	0.91	0.847	0.786	0.91	CLONAL	1	TRUE	1	0.545108469845725	2		655	888	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033223	69033245	+	frameshift_variant	Frame_Shift_Del	DEL	TCCTTGGAATCTTCCCAGCAGCG	TCCTTGGAATCTTCCCAGCAGCG	-	novel	NA	P-0060410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	58	546	0	ENST00000288368.4:c.3666_3688del	p.Trp1223AspfsTer11	p.W1223Dfs*11	ENST00000288368	NM_024870.2	1221	gaTCCTTGGAATCTTCCCAGCAGCGtc/gatc	30/40	0.545108469845725	3	FACETS	0.335	0.287	0.388	0.168	0.143	0.194	SUBCLONAL	1	TRUE	1	0.545108469845725	3		546	808	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223572	53223572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060410-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	502	432	0	ENST00000375401.3:c.3787G>A	p.Val1263Ile	p.V1263I	ENST00000375401	NM_004187.3	1263	Gta/Ata	23/26	0.478951952678337	2	FACETS	0.907	0.882	0.931			1	CLONAL	3	TRUE	NA	0.545108469845725	2		432	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0060411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	527	580	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.554699281962982	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.554699281962982	1		580	1202	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78422338	78422338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1244295456	NA	P-0060411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	372	647	3	ENST00000370768.2:c.1624G>A	p.Ala542Thr	p.A542T	ENST00000370768	NM_003902.3	542	Gct/Act	17/20	0.277937285302961	1	FACETS	0.934	0.888	0.98	0.934	0.888	0.98	INDETERMINATE	1	TRUE	0	0.554699281962982	1		650	1038	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597849	43597849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564490056	NA	P-0060411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	450	953	3	ENST00000355710.3:c.397C>T	p.Arg133Cys	p.R133C	ENST00000355710	NM_020975.4	133	Cgt/Tgt	3/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.554699281962982	2		956	1448	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614908	23614908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs180177137	NA	P-0060411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	252	609	4	ENST00000261584.4:c.3433G>A	p.Gly1145Ser	p.G1145S	ENST00000261584	NM_024675.3	1145	Ggt/Agt	13/13	1	2	FACETS	0.896	0.839	0.955	0.896	0.839	0.955	CLONAL	1	TRUE	1	0.554699281962982	2		613	1014	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215674142	215674164	+	frameshift_variant	Frame_Shift_Del	DEL	GAGCAGCGCAGCAGCTTCTCCAG	GAGCAGCGCAGCAGCTTCTCCAG	-	novel	NA	P-0060411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	290	597	3	ENST00000260947.4:c.130_152del	p.Leu44AlafsTer4	p.L44Afs*4	ENST00000260947	NM_000465.2	44	CTGGAGAAGCTGCTGCGCTGCTCg/g	1/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.554699281962982	2		600	986	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161907	47161907	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	111	563	8	ENST00000409792.3:c.4219del	p.Arg1407GlyfsTer5	p.R1407Gfs*5	ENST00000409792	NM_014159.6	1407	Agg/gg	3/21	0.185415475238936	2	FACETS	0.547	0.492	0.605	0.273	0.246	0.303	INDETERMINATE	1	TRUE	0	0.554699281962982	2		571	732	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845375	76845375	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	61	282	0	ENST00000373344.5:c.6146T>G	p.Leu2049Trp	p.L2049W	ENST00000373344	NM_000489.3	2049	tTg/tGg	27/35	1	2	FACETS	0.866	0.755	0.983	0.866	0.755	0.983	CLONAL	1	TRUE	1	0.554699281962982	2		282	254	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197875	123197875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776905490	NA	P-0060411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	39	223	1	ENST00000218089.9:c.1999C>T	p.Arg667Trp	p.R667W	ENST00000218089	NM_001042749.1	667	Cgg/Tgg	20/35	1	2	FACETS	0.717	0.601	0.844	0.717	0.601	0.844	SUBCLONAL	1	TRUE	1	0.554699281962982	2		224	196	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0060412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	86	599	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.452	0.398	0.509	0.452	0.398	0.509	SUBCLONAL	1	TRUE	1	0.360654365362124	2		599	1056	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0060412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	95	385	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.521	0.463	0.584	0.521	0.463	0.584	SUBCLONAL	1	TRUE	1	0.360654365362124	2		385	1011	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249028	55249028	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1275022697	NA	P-0060412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	78	836	0	ENST00000275493.2:c.2326C>T	p.Arg776Cys	p.R776C	ENST00000275493	NM_005228.3	776	Cgc/Tgc	20/28	1	2	FACETS	0.398	0.349	0.452	0.398	0.349	0.452	SUBCLONAL	1	TRUE	1	0.360654365362124	2		836	1086	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521926	157521926	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554235552	NA	P-0060412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	92	851	1	ENST00000346085.5:c.4198C>T	p.Gln1400Ter	p.Q1400*	ENST00000346085	NM_020732.3	1400	Cag/Tag	18/20	1	2	FACETS	0.434	0.384	0.487	0.434	0.384	0.487	SUBCLONAL	1	TRUE	1	0.360654365362124	2		852	1176	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851816	63851816	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200382682	NA	P-0060412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	70	774	0	ENST00000279873.7:c.2594C>T	p.Ser865Leu	p.S865L	ENST00000279873	NM_032199.2	865	tCg/tTg	10/10	1	2	FACETS	0.372	0.323	0.425	0.372	0.323	0.425	SUBCLONAL	1	TRUE	1	0.360654365362124	2		774	1044	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140500253	140500253	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	84	664	0	ENST00000288602.6:c.889C>T	p.His297Tyr	p.H297Y	ENST00000288602	NM_004333.4	297	Cac/Tac	7/18	1	2	FACETS	0.388	0.341	0.439	0.388	0.341	0.439	SUBCLONAL	1	TRUE	1	0.360654365362124	2		664	1200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0060415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	650	907	0	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.871457351155826	4	FACETS	1	0.996	1	1	0.996	1	CLONAL	4	FALSE	0	0.87064588650216	4		907	683	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922153	100922156	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ACTC	ACTC	-	novel	NA	P-0060415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	136	189	0	ENST00000325455.5:c.2356_2357+2del		p.X786_splice	ENST00000325455	NM_001202474.3	786		5/8	0.470614869038333	6	FACETS	0.952	0.88	1	0.952	0.88	1	INDETERMINATE	3	FALSE	3	0.87064588650216	6		189	300	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999084	100999085	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0060415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	224	645	0	ENST00000325455.5:c.716_717dup	p.Lys240AlafsTer62	p.K240Afs*62	ENST00000325455	NM_001202474.3	239	-/GC	1/8	0.470614869038333	6	FACETS	0.922	0.867	0.977	0.922	0.867	0.977	INDETERMINATE	3	FALSE	3	0.87064588650216	6		645	510	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019241	31019241	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	579	442	0	ENST00000375687.4:c.836A>G	p.His279Arg	p.H279R	ENST00000375687	NM_015338.5	279	cAc/cGc	9/13	0.871457351155826	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	FALSE	1	0.87064588650216	4		442	774	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2186198	2186198	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	229	417	0	ENST00000349721.2:c.4564G>C	p.Glu1522Gln	p.E1522Q	ENST00000349721	NM_003070.3	1522	Gag/Cag	32/34	0.87064588650216	6	FACETS	1	0.987	1	0.418	0.389	0.448	CLONAL	1	FALSE	3	0.87064588650216	6		417	1151	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720650	89720650	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1257124719	NA	P-0060479-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	16	138	0	ENST00000371953.3:c.802-1G>A		p.X268_splice	ENST00000371953	NM_000314.4	268			0.251530939425949	2	FACETS	0.963	0.74	1	0.963	0.74	1	CLONAL	2	TRUE	0	0.325702516329403	2		138	51	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431892	49431893	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0060479-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	203	695	1	ENST00000301067.7:c.9246_9247delinsTT	p.Glu3083Ter	p.E3083*	ENST00000301067	NM_003482.3	3082	cgGGag/cgTTag	34/54	0.325702516329403	5	FACETS	1	0.939	1			1	CLONAL	3	TRUE	NA	0.325702516329403	5		696	614	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577501	7577503	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0060479-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	102	438	0	ENST00000269305.4:c.778_780del	p.Ser261del	p.S261del	ENST00000269305	NM_001126112.2	260	TCC/-	7/11	0.184590776027508	5	FACETS	0.998	0.897	1	0.665	0.598	0.736	INDETERMINATE	2	TRUE	2	0.325702516329403	5		438	467	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610549	10610549	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060479-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	209	648	0	ENST00000171111.5:c.161A>G	p.Tyr54Cys	p.Y54C	ENST00000171111	NM_203500.1	54	tAc/tGc	2/6	0.325702516329403	6	FACETS	1	0.976	1	0.824	0.769	0.88	CLONAL	3	TRUE	2	0.325702516329403	6		648	643	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47502617	47502617	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060479-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	83	403	0	ENST00000404338.3:c.4093C>A	p.Pro1365Thr	p.P1365T	ENST00000404338	NM_004491.4	1365	Cca/Aca	5/6	0.26222611522706	2	FACETS	0.927	0.828	1	0.927	0.828	1	CLONAL	2	TRUE	0	0.325702516329403	2		403	275	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52649448	52649448	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060479-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	49	334	0	ENST00000394830.3:c.1843G>T	p.Glu615Ter	p.E615*	ENST00000394830	NM_018313.4	615	Gag/Tag	16/30	0.204984854109151	3	FACETS	0.941	0.809	1	0.627	0.539	0.721	CLONAL	2	TRUE	0	0.325702516329403	3		334	186	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873020	134873020	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060479-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	77	530	0	ENST00000398015.3:c.1324C>A	p.Gln442Lys	p.Q442K	ENST00000398015	NM_004441.4	442	Caa/Aaa	6/16	0.325702516329403	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.325702516329403	1		530	360	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461542	138461543	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060479-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	24	403	0	ENST00000289153.2:c.478dup	p.Ile160AsnfsTer22	p.I160Nfs*22	ENST00000289153	NM_006219.2	160	atc/aAtc	3/22	0.25876448704641	3	FACETS	0.888	0.701	1	0.296	0.233	0.367	CLONAL	1	TRUE	0	0.325702516329403	3		403	193	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631400	117631400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060479-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	19	334	0	ENST00000368508.3:c.6278C>T	p.Thr2093Ile	p.T2093I	ENST00000368508	NM_002944.2	2093	aCc/aTc	40/43	0.298940574030815	1	FACETS	0.565	0.431	0.72	0.565	0.431	0.72	SUBCLONAL	1	TRUE	0	0.325702516329403	1		334	173	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100364	157100364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060479-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	46	393	0	ENST00000346085.5:c.1301G>A	p.Gly434Asp	p.G434D	ENST00000346085	NM_020732.3	434	gGc/gAc	1/20	0.274678757344458	3	FACETS	0.907	0.767	1	0.454	0.383	0.531	CLONAL	1	TRUE	1	0.325702516329403	3		393	362	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977668	2977668	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0060479-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	71	398	0	ENST00000396946.4:c.1018-2A>G		p.X340_splice	ENST00000396946	NM_032415.4	340			0.274678757344458	3	FACETS	1	0.974	1	0.739	0.649	0.834	CLONAL	1	TRUE	1	0.325702516329403	3		398	343	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843774	151843775	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060479-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	39	436	0	ENST00000262189.6:c.13940dup	p.Ser4648ValfsTer2	p.S4648Vfs*2	ENST00000262189	NM_170606.2	4647	aag/aaAg	53/59	0.234719950186642	3	FACETS	0.767	0.637	0.911	0.384	0.318	0.456	CLONAL	1	TRUE	1	0.325702516329403	3		436	363	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848666	151848666	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060479-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	54	375	0	ENST00000262189.6:c.12527G>T	p.Gly4176Val	p.G4176V	ENST00000262189	NM_170606.2	4176	gGt/gTt	50/59	0.234719950186642	3	FACETS	0.846	0.731	0.968	0.846	0.731	0.968	CLONAL	2	TRUE	1	0.325702516329403	3		375	228	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974799	21974799	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060479-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	163	602	0	ENST00000304494.5:c.28G>T	p.Glu10Ter	p.E10*	ENST00000304494	NM_000077.4	10	Gag/Tag	1/3	0.259635624075265	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.325702516329403	2		602	446	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579472	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0060479-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	98	635	0	ENST00000269305.4:c.215_216del	p.Pro72ArgfsTer76	p.P72Rfs*76	ENST00000269305	NM_001126112.2	72	cCC/c	4/11	0.184590776027508	5	FACETS	0.806	0.721	0.895	0.537	0.48	0.597	INDETERMINATE	2	TRUE	2	0.325702516329403	5		635	556	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	96	475	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.5	2		475	289	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0060481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	194	356	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.778	0.726	0.83	1	0.992	1	SUBCLONAL	2	TRUE	1	0.5	2		356	499	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217380	123217380	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	59	90	0	ENST00000218089.9:c.3034C>T	p.Arg1012Ter	p.R1012*	ENST00000218089	NM_001042749.1	1012	Cga/Tga	29/35	1	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.5	1		90	138	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578219	7578220	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	344	752	0	ENST00000269305.4:c.629dup	p.Asn210LysfsTer6	p.N210Kfs*6	ENST00000269305	NM_001126112.2	210	aac/aaAc	6/11	0.212431980273546	3	FACETS	1	0.988	1	0.757	0.717	0.798	CLONAL	2	TRUE	0	0.313562924144043	3		752	1118	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492907	56492916	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGCCAGCT	GCAGCCAGCT	-	novel	NA	P-0060482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	152	619	0	ENST00000407977.2:c.23_32del	p.Gln8ProfsTer7	p.Q8Pfs*7	ENST00000407977		8	cAGCTGGCTGCc/cc	2/10	1	2	FACETS	0.895	0.817	0.977	0.895	0.817	0.977	CLONAL	1	TRUE	1	0.313562924144043	2		619	1083	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044967	47044967	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	215	902	1	ENST00000377604.3:c.2293C>T	p.Arg765Ter	p.R765*	ENST00000377604	NM_001204468.1	765	Cga/Tga	20/24	0.204240249539642	1	FACETS	0.927	0.86	0.996	0.927	0.86	0.996	CLONAL	1	TRUE	0	0.319969747194331	1		903	1218	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692900	89692900	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1114167645	NA	P-0060483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	132	267	0	ENST00000371953.3:c.384G>C	p.Lys128Asn	p.K128N	ENST00000371953	NM_000314.4	128	aaG/aaC	5/9	0.270365432866226	2	FACETS	0.814	0.743	0.887	0.814	0.743	0.887	CLONAL	2	TRUE	0	0.319969747194331	2		267	507	SUCCESS
APC	324	MSKCC	GRCh37	5	112175351	112175351	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	69	491	0	ENST00000257430.4:c.4063del	p.Ser1355LeufsTer60	p.S1355Lfs*60	ENST00000257430	NM_000038.5	1354	Ttt/tt	16/16	0.204240249539642	1	FACETS	0.448	0.389	0.512	0.448	0.389	0.512	SUBCLONAL	1	TRUE	0	0.319969747194331	1		491	809	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955906	55955906	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	72	428	0	ENST00000263923.4:c.3256A>G	p.Ser1086Gly	p.S1086G	ENST00000263923	NM_002253.2	1086	Agt/Ggt	24/30	0.204240249539642	1	FACETS	0.56	0.489	0.637	0.56	0.489	0.637	SUBCLONAL	1	TRUE	0	0.319969747194331	1		428	675	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530196	63530196	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	61	568	1	ENST00000307078.5:c.2239C>A	p.His747Asn	p.H747N	ENST00000307078	NM_004655.3	747	Cac/Aac	10/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.222989224735156	2		569	434	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541698	187541698	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0060484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	61	822	0	ENST00000441802.2:c.6042T>G	p.Tyr2014Ter	p.Y2014*	ENST00000441802	NM_005245.3	2014	taT/taG	10/27	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	FALSE	1	0.222989224735156	2		822	505	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0060485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	6	279	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.541	0.324	0.831	0.541	0.324	0.831	SUBCLONAL	1	FALSE	1	0.215440953661438	2		279	103	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0060485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	191	574	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.215440953661438	2		574	1224	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856070	151856070	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	40	712	0	ENST00000262189.6:c.11548C>T	p.Arg3850Ter	p.R3850*	ENST00000262189	NM_170606.2	3850	Cga/Tga	44/59	1	2	FACETS	0.675	0.56	0.803	0.675	0.56	0.803	SUBCLONAL	1	FALSE	1	0.215440953661438	2		712	550	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223532	2223532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	74	1149	0	ENST00000326181.6:c.1063C>T	p.Arg355Trp	p.R355W	ENST00000326181	NM_032271.2	355	Cgg/Tgg	11/21	NA	3	FACETS	0.685	0.598	0.78	0.342	0.299	0.39	INDETERMINATE	1	FALSE	1	0.215440953661438	3		1149	1111	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732925	30732925	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	107	814	0	ENST00000295754.5:c.1538T>G	p.Val513Gly	p.V513G	ENST00000295754	NM_003242.5	513	gTg/gGg	7/7	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.215440953661438	2		814	822	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845591	151845591	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	36	938	1	ENST00000262189.6:c.13421G>A	p.Cys4474Tyr	p.C4474Y	ENST00000262189	NM_170606.2	4474	tGc/tAc	52/59	1	2	FACETS	0.494	0.405	0.594	0.494	0.405	0.594	SUBCLONAL	1	FALSE	1	0.215440953661438	2		939	677	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044990	47044991	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0060485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	91	618	0	ENST00000377604.3:c.2319_2320dup	p.Leu774ArgfsTer29	p.L774Rfs*29	ENST00000377604	NM_001204468.1	772	-/GC	20/24	1	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	FALSE	0	0.215440953661438	1		618	733	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430822	47430822	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	111	604	0	ENST00000377045.4:c.1787C>T	p.Ala596Val	p.A596V	ENST00000377045	NM_001654.4	596	gCc/gTc	16/16	1	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	0	0.215440953661438	1		604	778	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0060490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	93	61	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.800447163006305	4	FACETS	1	0.97	1	0.408	0.366	0.452	CLONAL	1	TRUE	1	0.800447163006305	4		61	342	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0060490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	114	475	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.366	0.329	0.404	0.366	0.329	0.404	SUBCLONAL	1	TRUE	1	0.800447163006305	2		475	779	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344497	118344497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	152	639	0	ENST00000534358.1:c.2623G>A	p.Glu875Lys	p.E875K	ENST00000534358	NM_005933.3	875	Gag/Aag	3/36	1	2	FACETS	0.402	0.367	0.438	0.402	0.367	0.438	SUBCLONAL	1	TRUE	1	0.800447163006305	2		639	945	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878077	48878077	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060490-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	168	862	0	ENST00000267163.4:c.29C>T	p.Ala10Val	p.A10V	ENST00000267163	NM_000321.2	10	gCc/gTc	1/27	1	2	FACETS	0.401	0.367	0.435	0.401	0.367	0.435	SUBCLONAL	1	TRUE	1	0.800447163006305	2		862	1048	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	103	475	0				ENST00000310581	NM_198253.2	-/1132			0.420600530678536	10	FACETS	1	0.98	1	0.163	0.145	0.181	CLONAL	1	FALSE	1	0.420600530678536	10		475	898	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0060491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	90	66	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.369856360259026	5	FACETS	0.924	0.85	0.997	1	0.974	1	CLONAL	5	FALSE	1	0.420600530678536	5		66	151	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056291	27056292	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	303	746	0	ENST00000324856.7:c.1288dup	p.Tyr430LeufsTer193	p.Y430Lfs*193	ENST00000324856	NM_006015.4	429	-/T	2/20	0.158248855490066	3	FACETS	1	0.985	1	1	0.985	1	INDETERMINATE	2	FALSE	1	0.420600530678536	3		746	791	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039501	49039501	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0060491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	74	304	0	ENST00000267163.4:c.2486C>G	p.Ser829Ter	p.S829*	ENST00000267163	NM_000321.2	829	tCa/tGa	23/27	0.420600530678536	0	FACETS		NA	1			1	NA	3	FALSE	0	0.420600530678536	0		304	106	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019488	42019488	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	188	462	0	ENST00000219905.7:c.3541G>T	p.Glu1181Ter	p.E1181*	ENST00000219905	NM_001164273.1	1181	Gag/Tag	10/24	1	2	FACETS	1	0.939	1	1	0.994	1	CLONAL	2	FALSE	1	0.420600530678536	2		462	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0060491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	292	729	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	0.420600530678536	0	FACETS		NA	1			1	NA	3	FALSE	0	0.420600530678536	0		729	362	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965421	18965421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	110	501	0	ENST00000262803.5:c.1168G>A	p.Glu390Lys	p.E390K	ENST00000262803	NM_002911.3	390	Gag/Aag	9/24	0.420600530678536	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	0	0.420600530678536	1		501	352	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965767	18965767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	166	803	0	ENST00000262803.5:c.1345G>A	p.Glu449Lys	p.E449K	ENST00000262803	NM_002911.3	449	Gag/Aag	10/24	0.420600530678536	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	0	0.420600530678536	1		803	526	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0060491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	183	497	2	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	1	0.967	1	1	0.994	1	CLONAL	2	FALSE	1	0.420600530678536	2		499	412	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675553	30675553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	128	733	0	ENST00000376406.3:c.2803G>A	p.Glu935Lys	p.E935K	ENST00000376406	NM_014641.2	935	Gag/Aag	8/15	0.420600530678536	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	0	0.420600530678536	1		733	462	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345809	152345809	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0060491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	126	376	0	ENST00000359321.1:c.761C>G	p.Ser254Ter	p.S254*	ENST00000359321	NM_005431.1	254	tCa/tGa	3/3	1	2	FACETS	0.985	0.907	1	1	0.991	1	CLONAL	2	FALSE	1	0.420600530678536	2		376	304	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296067	15296067	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0060493-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	392	946	0	ENST00000263388.2:c.2296+1del		p.X766_splice	ENST00000263388	NM_000435.2	766			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		946	873	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0060494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	128	645	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.22	2		645	1140	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0060496-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	96	377	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.366210160711449	2		377	356	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226345	2226345	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060496-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	147	656	1	ENST00000326181.6:c.1958G>T	p.Arg653Leu	p.R653L	ENST00000326181	NM_032271.2	653	cGg/cTg	20/21	0.0671523792281421	3	FACETS	1	0.976	1	0.596	0.544	0.65	INDETERMINATE	1	TRUE	1	0.366210160711449	3		657	797	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091178	29091178	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs200050883	NA	P-0060496-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	21	154	0	ENST00000328354.6:c.1312G>T	p.Asp438Tyr	p.D438Y	ENST00000328354	NM_007194.3	438	Gat/Tat	12/15	1	2	FACETS	0.648	0.502	0.815	0.648	0.502	0.815	SUBCLONAL	1	TRUE	1	0.366210160711449	2		154	177	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456338	32456338	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060496-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	91	670	0	ENST00000332351.3:c.554C>A	p.Pro185His	p.P185H	ENST00000332351	NM_024426.4	185	cCc/cAc	1/10	1	2	FACETS	0.791	0.703	0.885	0.791	0.703	0.885	SUBCLONAL	1	TRUE	1	0.366210160711449	2		670	628	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518554	69518554	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060496-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	63	549	0	ENST00000294312.3:c.91G>T	p.Gly31Trp	p.G31W	ENST00000294312	NM_005117.2	31	Ggg/Tgg	1/3	1	2	FACETS	0.672	0.582	0.77	0.672	0.582	0.77	SUBCLONAL	1	TRUE	1	0.366210160711449	2		549	512	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211381	36211382	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0060496-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	65	564	0	ENST00000222270.7:c.1132_1133delinsTT	p.Gly378Leu	p.G378L	ENST00000222270	NM_014727.1	378	GGa/TTa	3/37	1	2	FACETS	0.516	0.447	0.591	0.516	0.447	0.591	SUBCLONAL	1	TRUE	1	0.366210160711449	2		564	688	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36024600	36024600	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs755567292	NA	P-0060496-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	136	516	0	ENST00000358208.4:c.589G>T	p.Ala197Ser	p.A197S	ENST00000358208		197	Gcc/Tcc	6/12	0.366210160711449	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.366210160711449	1		516	527	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448611	89448611	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060496-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	89	487	0	ENST00000336596.2:c.1575G>C	p.Glu525Asp	p.E525D	ENST00000336596	NM_005233.5	525	gaG/gaC	7/17	1	2	FACETS	0.774	0.687	0.867	0.774	0.687	0.867	SUBCLONAL	1	TRUE	1	0.366210160711449	2		487	628	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446962	187446962	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060496-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	121	650	0	ENST00000232014.4:c.1231C>G	p.Pro411Ala	p.P411A	ENST00000232014	NM_001130845.1	411	Cca/Gca	5/10	1	2	FACETS	0.858	0.776	0.945	0.858	0.776	0.945	CLONAL	1	TRUE	1	0.366210160711449	2		650	770	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045772	143045772	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060496-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	52	383	0	ENST00000262992.4:c.1862C>G	p.Thr621Arg	p.T621R	ENST00000262992	NM_001101669.1	621	aCg/aGg	17/24	1	2	FACETS	0.545	0.464	0.634	0.545	0.464	0.634	SUBCLONAL	1	TRUE	1	0.366210160711449	2		383	521	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981632	70981632	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060496-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	83	567	0	ENST00000276594.2:c.464C>A	p.Ala155Glu	p.A155E	ENST00000276594	NM_024504.3	155	gCg/gAg	2/8	1	2	FACETS	0.811	0.717	0.911	0.811	0.717	0.911	CLONAL	1	TRUE	1	0.366210160711449	2		567	559	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564650	139564650	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060496-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	128	520	0	ENST00000308874.7:c.439G>C	p.Gly147Arg	p.G147R	ENST00000308874		147	Ggc/Cgc	7/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.366210160711449	2		520	596	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412695	63412695	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0060496-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	137	465	0	ENST00000330258.3:c.472A>T	p.Lys158Ter	p.K158*	ENST00000330258	NM_152424.3	158	Aag/Tag	2/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.366210160711449	2		465	576	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504080	123504080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060496-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	65	311	0	ENST00000371139.4:c.256G>A	p.Ala86Thr	p.A86T	ENST00000371139	NM_001114937.2	86	Gca/Aca	3/4	1	2	FACETS	0.855	0.744	0.975	0.855	0.744	0.975	CLONAL	1	TRUE	1	0.366210160711449	2		311	415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579467	7579472	+	missense_variant	Missense_Mutation	ONP	CCACGG	CCACGG	AAACGC	novel	NA	P-0060496-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	156	693	0	ENST00000269305.4:c.215_220delinsGCGTTT	p.Pro72_Ala74delinsArgValSer	p.P72_A74delinsRVS	ENST00000269305	NM_001126112.2	72	cCCGTGGcc/cGCGTTTcc	4/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.366210160711449	2		693	764	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576870	7576870	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs876659384	NA	P-0060497-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	125	707	0	ENST00000269305.4:c.976G>T	p.Glu326Ter	p.E326*	ENST00000269305	NM_001126112.2	326	Gaa/Taa	9/11	0.54399437764017	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.54399437764017	1		707	274	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207081	1207081	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs137854584	NA	P-0060497-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	139	704	0	ENST00000326873.7:c.169G>T	p.Glu57Ter	p.E57*	ENST00000326873	NM_000455.4	57	Gaa/Taa	1/10	0.54399437764017	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.54399437764017	1		704	360	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948376	71948376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746017563	NA	P-0060497-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	142	866	1	ENST00000298229.2:c.3088C>T	p.Arg1030Trp	p.R1030W	ENST00000298229	NM_001567.3	1030	Cgg/Tgg	26/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.54399437764017	2		867	402	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514677	103514677	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060497-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	96	703	0	ENST00000355739.4:c.1178G>T	p.Arg393Ile	p.R393I	ENST00000355739	NM_000123.3	393	aGa/aTa	8/15	0.54399437764017	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.54399437764017	1		703	254	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789714	3789714	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060497-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	14	534	0	ENST00000262367.5:c.4145C>A	p.Ser1382Tyr	p.S1382Y	ENST00000262367	NM_004380.2	1382	tCt/tAt	25/31	0.54399437764017	1	FACETS	0.168	0.121	0.225	0.168	0.121	0.225	SUBCLONAL	1	TRUE	0	0.54399437764017	1		534	223	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346303	89346315	+	frameshift_variant	Frame_Shift_Del	DEL	GCCACGTCCAGCT	GCCACGTCCAGCT	-	novel	NA	P-0060497-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	47	764	0	ENST00000301030.4:c.6635_6647del	p.Lys2212IlefsTer2	p.K2212Ifs*2	ENST00000301030	NM_001256183.1	2212	aAGCTGGACGTGGCt/at	9/13	0.231192160932041	1	FACETS	0.464	0.394	0.54	0.464	0.394	0.54	INDETERMINATE	1	TRUE	0	0.54399437764017	1		764	271	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610234	10610242	+	inframe_deletion	In_Frame_Del	DEL	GCACCGTTC	GCACCGTTC	-	novel	NA	P-0060497-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	145	620	0	ENST00000171111.5:c.468_476del	p.Met156_Ala159delinsIle	p.M156_A159delinsI	ENST00000171111	NM_203500.1	156	atGAACGGTGCt/att	2/6	0.54399437764017	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.54399437764017	1		620	361	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217280	66217280	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060497-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	18	502	0	ENST00000273854.3:c.2335G>T	p.Gly779Cys	p.G779C	ENST00000273854	NM_004439.5	779	Ggc/Tgc	14/18	0.397708448860568	0	FACETS	0.181	0.136	0.232			1	SUBCLONAL	1	TRUE	0	0.54399437764017	0		502	167	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233719	233720	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0060497-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	37	223	0	ENST00000264932.6:c.1025_1026del	p.Val342GlyfsTer18	p.V342Gfs*18	ENST00000264932	NM_004168.2	341	gaTGtg/gatg	8/15	NA	2	FACETS	1	0.853	1			1	INDETERMINATE	1	TRUE	NA	0.54399437764017	2		223	134	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	43	475	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.957	0.802	1	0.957	0.802	1	CLONAL	1	TRUE	1	0.231656575884235	2		475	388	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0060499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	76	356	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.231656575884235	2		356	580	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0060499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	20	513	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.291	0.222	0.373	0.291	0.222	0.373	SUBCLONAL	1	TRUE	1	0.231656575884235	2		513	593	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0060499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	65	383	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.843	0.73	0.965	0.843	0.73	0.965	CLONAL	1	TRUE	1	0.231656575884235	2		383	666	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077427	30077427	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0060499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	56	598	0	ENST00000338641.4:c.1575-1G>A		p.X525_splice	ENST00000338641	NM_000268.3	525			0.231656575884235	1	FACETS	0.813	0.697	0.939	0.813	0.697	0.939	CLONAL	1	TRUE	0	0.231656575884235	1		598	526	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030553	47030553	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782480608	NA	P-0060499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	60	754	0	ENST00000377604.3:c.328G>A	p.Glu110Lys	p.E110K	ENST00000377604	NM_001204468.1	110	Gag/Aag	4/24	1	2	FACETS	0.784	0.675	0.903	0.784	0.675	0.903	CLONAL	1	TRUE	1	0.231656575884235	2		754	661	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737811	145737811	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	69	994	0	ENST00000428558.2:c.3019C>G	p.Leu1007Val	p.L1007V	ENST00000428558	NM_004260.3	1007	Ctc/Gtc	18/22	1	2	FACETS	0.785	0.683	0.896	0.785	0.683	0.896	SUBCLONAL	1	TRUE	1	0.231656575884235	2		994	759	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871120	12871120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1041108422	NA	P-0060499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	55	724	1	ENST00000228872.4:c.347C>T	p.Ala116Val	p.A116V	ENST00000228872	NM_004064.3	116	gCg/gTg	1/3	1	2	FACETS	0.761	0.65	0.882	0.761	0.65	0.882	SUBCLONAL	1	TRUE	1	0.231656575884235	2		725	624	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423671	47423671	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376565594	NA	P-0060499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	79	667	0	ENST00000404338.3:c.1739G>A	p.Arg580Gln	p.R580Q	ENST00000404338	NM_004491.4	580	cGg/cAg	1/6	1	2	FACETS	0.953	0.837	1	0.953	0.837	1	CLONAL	1	TRUE	1	0.231656575884235	2		667	716	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0060500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	30	279	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.84	0.679	1	0.84	0.679	1	CLONAL	1	TRUE	1	0.254142086613197	2		279	281	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907164	101907164	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	25	363	0	ENST00000374994.4:c.1124C>A	p.Thr375Lys	p.T375K	ENST00000374994	NM_004612.2	375	aCa/aAa	6/9	1	2	FACETS	0.778	0.615	0.963	0.778	0.615	0.963	CLONAL	1	TRUE	1	0.254142086613197	2		363	253	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828015	72828015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745989025	NA	P-0060500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	51	574	2	ENST00000268489.5:c.8566G>A	p.Asp2856Asn	p.D2856N	ENST00000268489	NM_006885.3	2856	Gac/Aac	9/10	0.254142086613197	1	FACETS	0.787	0.67	0.915	0.787	0.67	0.915	CLONAL	1	TRUE	0	0.254142086613197	1		576	445	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	896786	896786	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	73	613	0	ENST00000166345.3:c.265G>A	p.Asp89Asn	p.D89N	ENST00000166345	NM_004237.3	89	Gat/Aat	3/13	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.254142086613197	2		613	480	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844153	68844158	+	inframe_deletion	In_Frame_Del	DEL	GATTTT	GATTTT	-	novel	NA	P-0060500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	60	540	0	ENST00000261769.5:c.744_749del	p.Leu249_Ile250del	p.L249_I250del	ENST00000261769	NM_004360.3	247	gaGATTTTg/gag	6/16	0.254142086613197	1	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	0	0.254142086613197	1		540	403	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998970	11998970	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	45	412	0	ENST00000353533.5:c.472T>G	p.Cys158Gly	p.C158G	ENST00000353533	NM_003010.3	158	Tgc/Ggc	4/11	1	2	FACETS	0.937	0.789	1	0.937	0.789	1	CLONAL	1	TRUE	1	0.254142086613197	2		412	378	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589586	67589591	+	inframe_deletion	In_Frame_Del	DEL	ATGAAT	ATGAAT	-	novel	NA	P-0060501-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	23	338	0	ENST00000274335.5:c.1351_1356del	p.Glu451_Tyr452del	p.E451_Y452del	ENST00000274335		450	cATGAATat/cat	10/15	1	2	FACETS	0.654	0.509	0.82	0.654	0.509	0.82	SUBCLONAL	1	TRUE	1	0.20521896347675	2		338	343	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374245	138374245	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060501-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	32	490	0	ENST00000289153.2:c.3199G>T	p.Asp1067Tyr	p.D1067Y	ENST00000289153	NM_006219.2	1067	Gac/Tac	22/22	1	2	FACETS	0.551	0.446	0.67	0.551	0.446	0.67	SUBCLONAL	1	TRUE	1	0.20521896347675	2		490	566	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121909229	NA	P-0060501-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	60	375	0	ENST00000371953.3:c.389G>T	p.Arg130Leu	p.R130L	ENST00000371953	NM_000314.4	130	cGa/cTa	5/9	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.20521896347675	2		375	475	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370985	55370985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060501-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	99	563	0	ENST00000297316.4:c.287C>G	p.Ala96Gly	p.A96G	ENST00000297316	NM_022454.3	96	gCc/gGc	1/2	1	2	FACETS	0.771	0.689	0.857	1	0.982	1	SUBCLONAL	2	TRUE	1	0.20521896347675	2		563	626	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371722	55371722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060501-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	135	751	0	ENST00000297316.4:c.412C>T	p.Arg138Trp	p.R138W	ENST00000297316	NM_022454.3	138	Cgg/Tgg	2/2	1	2	FACETS	0.8	0.728	0.877	1	0.987	1	SUBCLONAL	2	TRUE	1	0.20521896347675	2		751	822	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0060501-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	87	389	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.20521896347675	2		389	568	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094382	27094383	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0060501-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	227	591	0	ENST00000324856.7:c.3091_3092del	p.Thr1031Ter	p.T1031*	ENST00000324856	NM_006015.4	1030	ttCAct/ttct	11/20	0.20521896347675	2	FACETS	0.906	0.846	0.967	1	0.99	1	CLONAL	3	TRUE	0	0.20521896347675	2		591	814	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211843	123211843	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060501-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	100	758	0	ENST00000218089.9:c.2710A>T	p.Met904Leu	p.M904L	ENST00000218089	NM_001042749.1	904	Atg/Ttg	27/35	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.20521896347675	2		758	666	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576926	7576927	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GC	GC	CT	novel	NA	P-0060502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	548	782	0	ENST00000269305.4:c.920-1_920delinsAG		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	0.804799608782355	3	FACETS	0.976	0.956	0.996	0.976	0.956	0.996	CLONAL	3	TRUE	0	0.804799608782355	3		782	652	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946319	2946319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373819371	NA	P-0060502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	175	688	2	ENST00000396946.4:c.3418G>A	p.Gly1140Ser	p.G1140S	ENST00000396946	NM_032415.4	1140	Ggc/Agc	25/25	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.804799608782355	NA		690	475	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946323	2946328	+	missense_variant	Missense_Mutation	ONP	CTTGTC	CTTGTC	TTTGTT	novel	NA	P-0060502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	176	705	0	ENST00000396946.4:c.3409_3414delinsAACAAA	p.Asp1137Asn	p.D1137N	ENST00000396946	NM_032415.4	1137	GACAAG/AACAAA	25/25	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.804799608782355	NA		705	488	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946352	2946352	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	182	654	0	ENST00000396946.4:c.3385G>C	p.Glu1129Gln	p.E1129Q	ENST00000396946	NM_032415.4	1129	Gag/Cag	25/25	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.804799608782355	NA		654	505	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946416	2946416	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	170	763	1	ENST00000396946.4:c.3321G>C	p.Glu1107Asp	p.E1107D	ENST00000396946	NM_032415.4	1107	gaG/gaC	25/25	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.804799608782355	NA		764	526	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946445	2946445	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	163	743	1	ENST00000396946.4:c.3292G>T	p.Glu1098Ter	p.E1098*	ENST00000396946	NM_032415.4	1098	Gag/Tag	25/25	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.804799608782355	NA		744	499	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214357	55214357	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	110	735	0	ENST00000275493.2:c.483C>A	p.Ser161Arg	p.S161R	ENST00000275493	NM_005228.3	161	agC/agA	4/28	0.512950716970614	4	FACETS	0.792	0.713	0.875	0.396	0.356	0.438	SUBCLONAL	1	TRUE	2	0.804799608782355	4		735	623	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875908	76875908	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	315	102	0	ENST00000373344.5:c.5227A>T	p.Arg1743Trp	p.R1743W	ENST00000373344	NM_000489.3	1743	Agg/Tgg	20/35	0.804330158673228	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.804799608782355	2		102	375	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0060503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	20	527	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		528	519	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0060503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	25	389	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.122703698373308	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		389	588	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612209	1612209	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs915880927	NA	P-0060503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	15	599	0	ENST00000344749.5:c.1810C>T	p.Arg604Ter	p.R604*	ENST00000344749	NM_001136139.2	604	Cga/Tga	18/19	0.232796596321773	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		599	291	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587781525	NA	P-0060504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	286	930	0	ENST00000269305.4:c.842A>G	p.Asp281Gly	p.D281G	ENST00000269305	NM_001126112.2	281	gAc/gGc	8/11	0.289672302811104	0	FACETS	0.782	0.742	0.822			1	SUBCLONAL	2	FALSE	0	0.372218415454629	0		930	617	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431115	49431115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	164	1301	0	ENST00000301067.7:c.10024del	p.Arg3342AlafsTer16	p.R3342Afs*16	ENST00000301067	NM_003482.3	3342	Cgc/gc	34/54	0.326812846179544	1	FACETS	0.864	0.794	0.937	0.864	0.794	0.937	CLONAL	1	FALSE	0	0.372218415454629	1		1301	830	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579315	7579315	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1555526478	NA	P-0060505-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	40	627	0	ENST00000269305.4:c.372C>A	p.Cys124Ter	p.C124*	ENST00000269305	NM_001126112.2	124	tgC/tgA	4/11	0.140478656910005	3	FACETS	0.489	0.405	0.582	0.163	0.135	0.194	INDETERMINATE	1	TRUE	0	0.311496150073052	3		627	607	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256056	16256056	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060505-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	104	736	0	ENST00000375759.3:c.3321T>G	p.Ile1107Met	p.I1107M	ENST00000375759	NM_015001.2	1107	atT/atG	11/15	0.299752835480486	3	FACETS	1	0.919	1	0.515	0.461	0.573	CLONAL	1	TRUE	1	0.311496150073052	3		736	749	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50769178	50769178	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060505-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	128	438	0	ENST00000307179.4:c.982G>T	p.Val328Leu	p.V328L	ENST00000307179		328	Gtg/Ttg	9/20	0.0969724504889273	4	FACETS	0.949	0.863	1	0.949	0.863	1	INDETERMINATE	2	TRUE	2	0.311496150073052	4		438	568	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627775	37627775	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs778359739	NA	P-0060505-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	199	706	0	ENST00000447079.4:c.1690C>G	p.Pro564Ala	p.P564A	ENST00000447079	NM_015083.1	564	Cca/Gca	2/14	0.140478656910005	3	FACETS	0.97	0.901	1	0.647	0.601	0.694	INDETERMINATE	2	TRUE	0	0.311496150073052	3		706	761	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0060507-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	383	279	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.415917726758941	5	FACETS	0.974	0.937	1	0.974	0.937	1	CLONAL	5	TRUE	0	0.415917726758941	5		279	614	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578412	7578412	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519747	NA	P-0060507-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	467	943	0	ENST00000269305.4:c.518T>A	p.Val173Glu	p.V173E	ENST00000269305	NM_001126112.2	173	gTg/gAg	5/11	0.415917726758941	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.415917726758941	2		943	1116	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948770	55948770	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368229220	NA	P-0060507-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	153	298	1	ENST00000263923.4:c.3695G>A	p.Arg1232Gln	p.R1232Q	ENST00000263923	NM_002253.2	1232	cGg/cAg	28/30	0.160687405218844	5	FACETS	1	0.947	1	0.693	0.637	0.751	INDETERMINATE	2	TRUE	2	0.415917726758941	5		299	575	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712616	43712616	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060507-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	319	648	0	ENST00000382044.4:c.4568T>C	p.Leu1523Pro	p.L1523P	ENST00000382044	NM_001141980.1	1523	cTc/cCc	21/28	0.138907910012919	6	FACETS	1	0.987	1	0.769	0.725	0.814	INDETERMINATE	2	TRUE	3	0.415917726758941	6		648	1218	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678430	88678430	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060507-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	280	688	0	ENST00000360948.2:c.1106C>G	p.Thr369Ser	p.T369S	ENST00000360948	NM_001012338.2	369	aCc/aGc	9/19	0.138907910012919	6	FACETS	1	0.982	1	0.742	0.697	0.788	INDETERMINATE	2	TRUE	3	0.415917726758941	6		688	1108	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353831	40353831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060507-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	390	749	0	ENST00000293328.3:c.2289G>A	p.Met763Ile	p.M763I	ENST00000293328	NM_012448.3	763	atG/atA	19/19	0.415917726758941	2	FACETS	0.932	0.888	0.976	0.932	0.888	0.976	CLONAL	2	TRUE	0	0.415917726758941	2		749	1006	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591928	48591928	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0060507-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	145	535	0	ENST00000342988.3:c.1091T>A	p.Leu364Ter	p.L364*	ENST00000342988	NM_005359.5	364	tTg/tAg	9/12	0.415917726758941	1	FACETS	0.984	0.903	1	0.984	0.903	1	CLONAL	1	TRUE	0	0.415917726758941	1		535	561	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510572	38510572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205678	NA	P-0060508-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	261	663	0	ENST00000254066.5:c.826C>T	p.Arg276Trp	p.R276W	ENST00000254066	NM_000964.3	276	Cgg/Tgg	7/9	1	2	FACETS	0.827	0.776	0.88	0.827	0.776	0.88	CLONAL	1	FALSE	1	0.66435415526391	2		663	950	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600446	10600446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060508-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	814	840	0	ENST00000171111.5:c.1409G>A	p.Arg470His	p.R470H	ENST00000171111	NM_203500.1	470	cGt/cAt	4/6	0.655709715990827	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	FALSE	0	0.66435415526391	2		840	1216	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674234	86674234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060508-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	126	415	0	ENST00000274376.6:c.2366G>A	p.Arg789Gln	p.R789Q	ENST00000274376	NM_002890.2	789	cGa/cAa	18/25	1	2	FACETS	0.794	0.723	0.867	0.794	0.723	0.867	SUBCLONAL	1	FALSE	1	0.66435415526391	2		415	478	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655272	45655272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764295138	NA	P-0060508-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	302	833	0	ENST00000407780.3:c.580C>T	p.Arg194Trp	p.R194W	ENST00000407780	NM_001283052.1	194	Cgg/Tgg	4/7	1	2	FACETS	0.856	0.807	0.906	0.856	0.807	0.906	CLONAL	1	FALSE	1	0.66435415526391	2		833	1062	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607203	189607203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060508-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4185	288	840	0	ENST00000264731.3:c.1582C>T	p.Pro528Ser	p.P528S	ENST00000264731	NM_003722.4	528	Cca/Tca	12/14	0.66435415526391	11	FACETS	0.773	0.722	0.827	0.077	0.072	0.083	SUBCLONAL	1	FALSE	1	0.66435415526391	11		840	4473	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0060510-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	24	479	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.64	0.5	0.802	0.64	0.5	0.802	SUBCLONAL	1	TRUE	1	0.15	2		479	500	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220644	1220644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1167609100	NA	P-0060510-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	37	976	0	ENST00000326873.7:c.662C>T	p.Pro221Leu	p.P221L	ENST00000326873	NM_000455.4	221	cCg/cTg	5/10	1	2	FACETS	0.554	0.455	0.666	0.554	0.455	0.666	SUBCLONAL	1	TRUE	1	0.15	2		976	890	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971170	21971170	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060510-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	64	939	0	ENST00000304494.5:c.188T>C	p.Leu63Pro	p.L63P	ENST00000304494	NM_000077.4	63	cTg/cCg	2/3	1	2	FACETS	0.985	0.851	1	0.985	0.851	1	CLONAL	1	TRUE	1	0.15	2		939	866	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974686	21974721	+	inframe_deletion	In_Frame_Del	DEL	CCTCCGACCGTAACTATTCGGTGCGTTGGGCAGCGC	CCTCCGACCGTAACTATTCGGTGCGTTGGGCAGCGC	-	novel	NA	P-0060510-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	46	911	0	ENST00000304494.5:c.106_141del	p.Ala36_Arg47del	p.A36_R47del	ENST00000304494	NM_000077.4	36	GCGCTGCCCAACGCACCGAATAGTTACGGTCGGAGG/-	1/3	1	2	FACETS	0.73	0.613	0.86	0.73	0.613	0.86	SUBCLONAL	1	TRUE	1	0.15	2		911	840	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0060511-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	454	736	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.842811926107703	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.84705511062159	2		736	524	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394771	45394771	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060511-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	54	412	0	ENST00000262160.6:c.578T>C	p.Leu193Pro	p.L193P	ENST00000262160	NM_005901.5	193	cTg/cCg	5/11	0.713694639927955	4	FACETS	1	0.919	1	0.363	0.314	0.416	CLONAL	1	TRUE	1	0.84705511062159	4		412	216	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106793	27106793	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	53	885	0	ENST00000324856.7:c.6404T>A	p.Ile2135Asn	p.I2135N	ENST00000324856	NM_006015.4	2135	aTt/aAt	20/20	0.158493863131728	3	FACETS	1	0.886	1	0.524	0.446	0.61	CLONAL	1	FALSE	1	0.158493863131728	3		885	689	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752960	128752960	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	136	758	0	ENST00000377970.2:c.1121A>G	p.His374Arg	p.H374R	ENST00000377970	NM_002467.4	374	cAc/cGc	3/3	0.158493863131728	3	FACETS	0.905	0.825	0.989	1	0.983	1	CLONAL	3	FALSE	1	0.158493863131728	3		758	682	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716081	52716081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	92	801	0	ENST00000322088.6:c.646G>A	p.Glu216Lys	p.E216K	ENST00000322088	NM_014225.5	216	Gag/Aag	5/15	0.158493863131728	5	FACETS	0.952	0.845	1	0.634	0.563	0.71	CLONAL	2	FALSE	2	0.158493863131728	5		801	755	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039389	49039389	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0060512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	14	558	0	ENST00000267163.4:c.2376del	p.Pro793LeufsTer17	p.P793Lfs*17	ENST00000267163	NM_000321.2	792	Ttt/tt	23/27	0.158493863131728	1	FACETS	0.894	0.655	1	1	0.907	1	CLONAL	2	FALSE	0	0.158493863131728	1		558	91	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279887	46279888	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAA	rs1255268332	NA	P-0060512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	61	683	0	ENST00000371998.3:c.3815_3816insACA	p.Gln1276dup	p.Q1276dup	ENST00000371998		1276	-/CAA	20/23	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	FALSE	1	0.158493863131728	2		683	703	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737918	145737918	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060512-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	109	935	0	ENST00000428558.2:c.2912C>G	p.Ala971Gly	p.A971G	ENST00000428558	NM_004260.3	971	gCc/gGc	18/22	0.158493863131728	3	FACETS	0.847	0.76	0.94	0.847	0.76	0.94	CLONAL	2	FALSE	1	0.158493863131728	3		935	876	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0060513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	47	388	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.354933459278438	2	FACETS	0.949	0.834	1	1	0.969	1	CLONAL	3	TRUE	0	0.354933459278438	2		388	93	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0060513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	11	349	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	0.354933459278438	1	FACETS	0.962	0.682	1	0.962	0.682	1	CLONAL	1	TRUE	0	0.354933459278438	1		349	53	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0060513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	128	584	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.354933459278438	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.354933459278438	1		584	573	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138295	2138295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45507199	NA	P-0060513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	149	887	2	ENST00000219476.3:c.5228G>A	p.Arg1743Gln	p.R1743Q	ENST00000219476	NM_000548.3	1743	cGg/cAg	41/42	0.204744678117265	2	FACETS	1	0.957	1	0.537	0.491	0.585	INDETERMINATE	1	TRUE	0	0.354933459278438	2		889	782	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	58	808	0	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	0.466	0.399	0.54	0.466	0.399	0.54	SUBCLONAL	1	TRUE	1	0.23	2		808	1082	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	122	298	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.23	2		299	935	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	127	699	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.879	0.794	0.969	0.879	0.794	0.969	CLONAL	1	TRUE	1	0.23	2		706	1256	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	86	803	1	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.23	2		804	715	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	19	684	1	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.725	0.551	0.927	0.725	0.551	0.927	CLONAL	1	TRUE	1	0.23	2		685	228	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	61	503	0	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.477	0.41	0.551	0.477	0.41	0.551	SUBCLONAL	1	TRUE	1	0.23	2		503	1112	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	82	447	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.109729267090903	0	FACETS	0.524	0.461	0.593			1	INDETERMINATE	1	TRUE	0	0.23	0		447	1047	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578213	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	41	694	0	ENST00000269305.4:c.636dup	p.Arg213SerfsTer3	p.R213Sfs*3	ENST00000269305	NM_001126112.2	212	-/T	6/11	1	2	FACETS	0.521	0.433	0.62	0.521	0.433	0.62	SUBCLONAL	1	TRUE	1	0.23	2		694	684	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843396	128843396	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61746143	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	73	702	0	ENST00000249373.3:c.503G>A	p.Arg168His	p.R168H	ENST00000249373	NM_005631.4	168	cGc/cAc	2/12	1	2	FACETS	0.789	0.689	0.897	0.789	0.689	0.897	SUBCLONAL	1	TRUE	1	0.23	2		702	805	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727909	41727909	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	91	667	0	ENST00000301178.4:c.538del	p.Leu180TrpfsTer18	p.L180Wfs*18	ENST00000301178	NM_021913.4	178	gtC/gt	4/20	0.249075460936589	4	FACETS	1	0.923	1	0.526	0.466	0.59	CLONAL	1	TRUE	2	0.23	4		667	925	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742547	145742547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1426829329	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	77	756	0	ENST00000428558.2:c.241del	p.His81IlefsTer2	p.H81Ifs*2	ENST00000428558	NM_004260.3	81	Cat/at	4/22	1	2	FACETS	0.544	0.476	0.618	0.544	0.476	0.618	SUBCLONAL	1	TRUE	1	0.23	2		756	1230	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272336	15272337	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs771517374	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1198	115	1015	4	ENST00000263388.2:c.6102dup	p.Gly2035ArgfsTer60	p.G2035Rfs*60	ENST00000263388	NM_000435.2	2034	-/C	33/33	0.249075460936589	4	FACETS	0.937	0.841	1	0.468	0.42	0.52	CLONAL	1	TRUE	2	0.23	4		1019	1313	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257144	19257144	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	35	574	0	ENST00000162023.5:c.819del	p.Thr274ProfsTer?	p.T274Pfs*?	ENST00000162023		273	ccC/cc	12/13	0.249075460936589	4	FACETS	0.735	0.602	0.886	0.368	0.301	0.443	SUBCLONAL	1	TRUE	2	0.23	4		574	509	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285059	15285059	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs367543285	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	161	806	0	ENST00000263388.2:c.4556T>C	p.Leu1519Pro	p.L1519P	ENST00000263388	NM_000435.2	1519	cTg/cCg	25/33	0.249075460936589	4	FACETS	1	0.983	1	0.643	0.588	0.701	CLONAL	1	TRUE	2	0.23	4		806	1338	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340356	8340356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs553232071	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	37	605	0	ENST00000356435.5:c.5240G>A	p.Arg1747His	p.R1747H	ENST00000356435		1747	cGt/cAt	31/35	0.109729267090903	0	FACETS	0.724	0.599	0.864			1	INDETERMINATE	1	TRUE	0	0.23	0		605	342	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793430	42793430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144065857	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	70	914	1	ENST00000575354.2:c.1232C>T	p.Ala411Val	p.A411V	ENST00000575354	NM_015125.3	411	gCg/gTg	8/20	0.249075460936589	4	FACETS	0.611	0.531	0.699	0.306	0.265	0.35	SUBCLONAL	1	TRUE	2	0.23	4		915	1225	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431874	49431874	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	63	1029	3	ENST00000301067.7:c.9265del	p.Val3089TrpfsTer30	p.V3089Wfs*30	ENST00000301067	NM_003482.3	3089	Gtg/tg	34/54	1	2	FACETS	0.473	0.407	0.545	0.473	0.407	0.545	SUBCLONAL	1	TRUE	1	0.23	2		1032	1158	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272238	15272238	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs760917811	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	102	884	0	ENST00000263388.2:c.6201del	p.Lys2069ArgfsTer16	p.K2069Rfs*16	ENST00000263388	NM_000435.2	2067	ccC/cc	33/33	0.249075460936589	4	FACETS	1	0.943	1	0.544	0.485	0.606	CLONAL	1	TRUE	2	0.23	4		884	1003	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267849	46267849	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	15	435	0	ENST00000371998.3:c.2615del	p.Asn872IlefsTer20	p.N872Ifs*20	ENST00000371998		870	gtA/gt	14/23	0.173102506554403	3	FACETS	1	0.891	1	0.742	0.55	0.965	CLONAL	1	TRUE	1	0.23	3		435	98	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870055	40870055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	10	400	0	ENST00000428826.2:c.962G>A	p.Arg321His	p.R321H	ENST00000428826		321	cGc/cAc	10/21	1	2	FACETS	1	0.823	1	1	0.823	1	CLONAL	1	TRUE	1	0.23	2		400	65	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299864	15299864	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1255	96	829	0	ENST00000263388.2:c.1314del	p.Cys440AlafsTer11	p.C440Afs*11	ENST00000263388	NM_000435.2	438	ggG/gg	8/33	0.249075460936589	4	FACETS	0.76	0.675	0.852	0.38	0.337	0.426	SUBCLONAL	1	TRUE	2	0.23	4		829	1351	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921136	50921136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs963136799	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	48	542	2	ENST00000440232.2:c.3256C>T	p.Arg1086Trp	p.R1086W	ENST00000440232	NM_002691.3	1086	Cgg/Tgg	27/27	0.249075460936589	4	FACETS	0.583	0.491	0.685	0.291	0.245	0.343	SUBCLONAL	1	TRUE	2	0.23	4		544	881	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149917	202149917	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	19	708	0	ENST00000358485.4:c.1358C>A	p.Pro453Gln	p.P453Q	ENST00000358485	NM_001080125.1	453	cCg/cAg	8/9	1	2	FACETS	0.53	0.402	0.68	0.53	0.402	0.68	SUBCLONAL	1	TRUE	1	0.23	2		708	312	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045909	47045909	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782208940	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	39	533	0	ENST00000377604.3:c.2704C>T	p.Arg902Trp	p.R902W	ENST00000377604	NM_001204468.1	902	Cgg/Tgg	24/24	0.3	2	FACETS	0.524	0.433	0.626	0.262	0.216	0.313	SUBCLONAL	1	TRUE	0	0.23	2		533	647	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103374	2103374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369594860	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	113	503	0	ENST00000219476.3:c.257C>T	p.Ala86Val	p.A86V	ENST00000219476	NM_000548.3	86	gCg/gTg	4/42	0.249075460936589	3	FACETS	1	0.954	1	0.553	0.497	0.613	CLONAL	1	TRUE	1	0.23	3		503	990	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150923861	150923864	+	frameshift_variant	Frame_Shift_Del	DEL	AACT	AACT	-	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	15	573	0	ENST00000271640.5:c.2239_2242del	p.Thr747SerfsTer23	p.T747Sfs*23	ENST00000271640	NM_001145415.1	745	cAACTa/ca	14/22	1	2	FACETS	0.535	0.391	0.707	0.535	0.391	0.707	SUBCLONAL	1	TRUE	1	0.23	2		573	244	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258786	16258786	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	50	862	0	ENST00000375759.3:c.6053del	p.Gly2018AlafsTer4	p.G2018Afs*4	ENST00000375759	NM_015001.2	2017	gtG/gt	11/15	1	2	FACETS	0.565	0.478	0.661	0.565	0.478	0.661	SUBCLONAL	1	TRUE	1	0.23	2		862	769	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647765	206647765	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	64	606	0	ENST00000367120.3:c.179G>T	p.Arg60Leu	p.R60L	ENST00000367120	NM_014002.3	60	cGg/cTg	4/22	1	2	FACETS	0.758	0.656	0.87	0.758	0.656	0.87	SUBCLONAL	1	TRUE	1	0.23	2		606	734	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205579	61205579	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	17	392	0	ENST00000301761.2:c.364G>A	p.Ala122Thr	p.A122T	ENST00000301761	NM_017841.2	122	Gcc/Acc	3/4	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.23	2		392	118	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238184	133238184	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	17	580	0	ENST00000320574.5:c.2793del	p.Phe931LeufsTer10	p.F931Lfs*10	ENST00000320574	NM_006231.2	931	ttT/tt	24/49	1	2	FACETS	0.475	0.354	0.619	0.475	0.354	0.619	SUBCLONAL	1	TRUE	1	0.23	2		580	311	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563414	21563414	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	127	818	1	ENST00000382592.4:c.505C>T	p.Arg169Trp	p.R169W	ENST00000382592	NM_014572.2	169	Cgg/Tgg	4/8	0.109729267090903	0	FACETS	0.767	0.694	0.846			1	INDETERMINATE	1	TRUE	0	0.23	0		819	1108	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778113	3778113	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1386	112	1014	2	ENST00000262367.5:c.6935A>G	p.Asn2312Ser	p.N2312S	ENST00000262367	NM_004380.2	2312	aAc/aGc	31/31	0.249075460936589	3	FACETS	0.725	0.649	0.806	0.362	0.324	0.403	SUBCLONAL	1	TRUE	1	0.23	3		1016	1498	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900351	3900351	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	72	749	0	ENST00000262367.5:c.745C>T	p.Gln249Ter	p.Q249*	ENST00000262367	NM_004380.2	249	Caa/Taa	2/31	0.249075460936589	3	FACETS	0.766	0.668	0.873	0.383	0.334	0.437	SUBCLONAL	1	TRUE	1	0.23	3		749	911	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896523	78896523	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	105	592	0	ENST00000306801.3:c.2521-1G>T		p.X841_splice	ENST00000306801	NM_020761.2	841			1	2	FACETS	0.89	0.796	0.99	0.89	0.796	0.99	CLONAL	1	TRUE	1	0.23	2		592	1026	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383266	42383266	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	62	852	0	ENST00000221972.3:c.286G>A	p.Val96Met	p.V96M	ENST00000221972	NM_021601.3	96	Gtg/Atg	2/5	0.249075460936589	4	FACETS	0.613	0.528	0.707	0.307	0.264	0.354	SUBCLONAL	1	TRUE	2	0.23	4		852	1081	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086185	16086185	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	28	652	0	ENST00000281043.3:c.1361T>C	p.Leu454Ser	p.L454S	ENST00000281043	NM_005378.4	454	tTg/tCg	3/3	1	2	FACETS	0.58	0.463	0.713	0.58	0.463	0.713	SUBCLONAL	1	TRUE	1	0.23	2		652	420	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29445547	29445550	+	frameshift_variant	Frame_Shift_Del	DEL	GCTT	GCTT	-	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	51	868	0	ENST00000544604.2:c.1382_1385del	p.Cys461SerfsTer108	p.C461Sfs*108	ENST00000544604	NM_001206998.1	460	GCTTgc/gc	8/9	1	2	FACETS	0.436	0.369	0.51	0.436	0.369	0.51	SUBCLONAL	1	TRUE	1	0.23	2		868	1018	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430587	181430587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1302	159	902	0	ENST00000325404.1:c.439G>A	p.Ala147Thr	p.A147T	ENST00000325404	NM_003106.3	147	Gcc/Acc	1/1	1	2	FACETS	0.946	0.865	1	0.946	0.865	1	CLONAL	1	TRUE	1	0.23	2		902	1461	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612116	189612116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	39	780	0	ENST00000264731.3:c.1868C>T	p.Ala623Val	p.A623V	ENST00000264731	NM_003722.4	623	gCc/gTc	14/14	1	2	FACETS	0.435	0.359	0.52	0.435	0.359	0.52	SUBCLONAL	1	TRUE	1	0.23	2		780	780	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594037	55594037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	36	463	0	ENST00000288135.5:c.1823C>T	p.Ala608Val	p.A608V	ENST00000288135	NM_000222.2	608	gCt/gTt	12/21	1	2	FACETS	0.984	0.812	1	0.984	0.812	1	CLONAL	1	TRUE	1	0.23	2		463	318	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324735	31324735	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1055758550	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	67	763	0	ENST00000412585.2:c.74-1G>A		p.X25_splice	ENST00000412585	NM_005514.6	25			1	2	FACETS	0.68	0.589	0.778	0.68	0.589	0.778	SUBCLONAL	1	TRUE	1	0.23	2		763	857	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969171	93969171	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	10	442	0	ENST00000369303.4:c.1825A>G	p.Ile609Val	p.I609V	ENST00000369303	NM_004440.3	609	Att/Gtt	10/17	1	2	FACETS	0.887	0.606	1	0.887	0.606	1	CLONAL	1	TRUE	1	0.23	2		442	98	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129471	152129471	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	105	661	2	ENST00000206249.3:c.424C>T	p.Arg142Cys	p.R142C	ENST00000206249	NM_000125.3	142	Cgc/Tgc	1/8	1	2	FACETS	0.966	0.864	1	0.966	0.864	1	CLONAL	1	TRUE	1	0.23	2		663	945	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983994	2983994	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	62	668	0	ENST00000396946.4:c.536G>T	p.Arg179Leu	p.R179L	ENST00000396946	NM_032415.4	179	cGg/cTg	5/25	1	2	FACETS	0.764	0.659	0.878	0.764	0.659	0.878	SUBCLONAL	1	TRUE	1	0.23	2		668	706	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104664	69104664	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	39	557	0	ENST00000288368.4:c.4508G>A	p.Cys1503Tyr	p.C1503Y	ENST00000288368	NM_024870.2	1503	tGc/tAc	37/40	1	2	FACETS	0.608	0.503	0.725	0.608	0.503	0.725	SUBCLONAL	1	TRUE	1	0.23	2		557	558	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342707	87342707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	30	519	0	ENST00000277120.3:c.992G>A	p.Cys331Tyr	p.C331Y	ENST00000277120		331	tGt/tAt	9/19	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.23	2		519	213	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035898	47035898	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	75	266	0	ENST00000377604.3:c.577-1G>A		p.X193_splice	ENST00000377604	NM_001204468.1	193			0.3	2	FACETS	0.921	0.813	1	0.921	0.813	1	CLONAL	2	TRUE	0	0.23	2		266	354	SUCCESS
AR	367	MSKCC	GRCh37	X	66765536	66765536	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	100	481	0	ENST00000374690.3:c.548A>T	p.Asp183Val	p.D183V	ENST00000374690	NM_000044.3	183	gAc/gTc	1/8	0.3	2	FACETS	0.953	0.856	1	0.953	0.856	1	CLONAL	2	TRUE	0	0.23	2		481	456	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060517-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	370	475	0				ENST00000310581	NM_198253.2	-/1132			0.438748922037566	3	FACETS	1	0.985	1	0.548	0.519	0.577	CLONAL	1	TRUE	1	0.712608448686456	3		475	1286	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534285	534285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894226	NA	P-0060517-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	485	744	0	ENST00000451590.1:c.38G>T	p.Gly13Val	p.G13V	ENST00000451590	NM_001130442.1	13	gGt/gTt	2/5	0.281264327132104	1	FACETS	0.741	0.71	0.772	0.741	0.71	0.772	INDETERMINATE	1	TRUE	0	0.712608448686456	1		744	1183	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493479	56493479	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060517-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	316	670	0	ENST00000267101.3:c.2887A>G	p.Asn963Asp	p.N963D	ENST00000267101	NM_001982.3	963	Aat/Gat	24/28	0.142895396214815	4	FACETS	0.959	0.909	1	0.959	0.909	1	INDETERMINATE	2	TRUE	2	0.712608448686456	4		670	792	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350153	89350153	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060517-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	395	757	0	ENST00000301030.4:c.2797T>A	p.Tyr933Asn	p.Y933N	ENST00000301030	NM_001256183.1	933	Tac/Aac	9/13	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.712608448686456	2		757	998	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132307	7132307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1423107716	NA	P-0060517-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	143	601	0	ENST00000302850.5:c.2704C>T	p.Arg902Cys	p.R902C	ENST00000302850	NM_000208.2	902	Cgc/Tgc	14/22	0.21994655775747	4	FACETS	0.549	0.499	0.602	0.274	0.249	0.301	INDETERMINATE	1	TRUE	2	0.712608448686456	4		601	1252	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354128	15354128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060517-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	68	496	0	ENST00000263377.2:c.2752C>T	p.Pro918Ser	p.P918S	ENST00000263377	NM_058243.2	918	Cca/Tca	14/20	0.21994655775747	4	FACETS	0.345	0.299	0.395	0.173	0.149	0.198	INDETERMINATE	1	TRUE	2	0.712608448686456	4		496	947	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37628938	37628938	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060517-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	280	462	0	ENST00000249071.6:c.128A>G	p.Asn43Ser	p.N43S	ENST00000249071	NM_002872.4	43	aAt/aGt	3/7	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.712608448686456	2		462	670	SUCCESS
APC	324	MSKCC	GRCh37	5	112178295	112178295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768295372	NA	P-0060517-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	98	548	0	ENST00000257430.4:c.7004G>A	p.Gly2335Glu	p.G2335E	ENST00000257430	NM_000038.5	2335	gGa/gAa	16/16	0.182052910312453	1	FACETS	0.588	0.531	0.647	0.588	0.531	0.647	INDETERMINATE	1	TRUE	0	0.712608448686456	1		548	301	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045688	26045688	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1350355423	NA	P-0060517-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	206	806	0	ENST00000540144.1:c.50C>T	p.Pro17Leu	p.P17L	ENST00000540144	NM_003531.2	17	cCg/cTg	1/1	1	2	FACETS	0.461	0.427	0.497	0.461	0.427	0.497	SUBCLONAL	1	TRUE	1	0.712608448686456	2		806	1254	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462457	92462457	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060517-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1373	168	660	0	ENST00000265734.4:c.181G>C	p.Glu61Gln	p.E61Q	ENST00000265734	NM_001259.6	61	Gag/Cag	2/8	0.712608448686456	3	FACETS	0.415	0.38	0.452	0.207	0.19	0.226	SUBCLONAL	1	TRUE	1	0.712608448686456	3		660	1541	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942845	44942846	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0060517-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	41	137	0	ENST00000377967.4:c.3427dup	p.Thr1143AsnfsTer8	p.T1143Nfs*8	ENST00000377967	NM_021140.2	1142	aga/agAa	23/29	0.462242421974675	2	FACETS	0.928	0.825	1			1	CLONAL	2	TRUE	NA	0.712608448686456	2		137	62	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040775	47040778	+	frameshift_variant	Frame_Shift_Del	DEL	AACC	AACC	-	novel	NA	P-0060517-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	355	399	0	ENST00000377604.3:c.1412_1415del	p.Thr471LysfsTer13	p.T471Kfs*13	ENST00000377604	NM_001204468.1	470	ggAACC/gg	13/24	0.462242421974675	2	FACETS	0.947	0.912	0.981			1	CLONAL	2	TRUE	NA	0.712608448686456	2		399	526	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066842	77066842	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs887262054	NA	P-0060522-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	81	566	0	ENST00000356341.3:c.643C>T	p.Arg215Trp	p.R215W	ENST00000356341	NM_002576.4	215	Cgg/Tgg	7/15	0.335525022736377	3	FACETS	0.886	0.781	0.998	0.443	0.39	0.499	CLONAL	1	TRUE	1	0.35185440190311	3		566	611	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755752	39755766	+	inframe_deletion	In_Frame_Del	DEL	TCCCCGTTGGTGCCT	TCCCCGTTGGTGCCT	-	novel	NA	P-0060522-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	79	621	0	ENST00000288319.7:c.999_1013del	p.Gly334_Glu338del	p.G334_E338del	ENST00000288319	NM_182918.3	333	gaAGGCACCAACGGGGAg/gag	10/10	1	2	FACETS	0.918	0.81	1	0.918	0.81	1	CLONAL	1	TRUE	1	0.35185440190311	2		621	489	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437853	52437853	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060522-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	212	666	0	ENST00000460680.1:c.1308A>C	p.Gln436His	p.Q436H	ENST00000460680	NM_004656.3	436	caA/caC	13/17	0.329060948288772	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	2	0.35185440190311	4		666	779	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859783	151859783	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060522-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	204	748	0	ENST00000262189.6:c.10879del	p.Ser3627GlnfsTer3	p.S3627Qfs*3	ENST00000262189	NM_170606.2	3627	Tca/ca	43/59	0.335525022736377	3	FACETS	0.933	0.868	0.999	0.933	0.868	0.999	CLONAL	2	TRUE	1	0.35185440190311	3		748	731	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	31	475	0				ENST00000310581	NM_198253.2	-/1132			0.470518091476317	1	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	0	0.477887059543462	1		475	88	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272123	15272123	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	29	738	0	ENST00000263388.2:c.6316del	p.Asp2106ThrfsTer43	p.D2106Tfs*43	ENST00000263388	NM_000435.2	2106	Gac/ac	33/33	0.271264783940633	2	FACETS	0.539	0.435	0.656	0.27	0.217	0.328	INDETERMINATE	1	TRUE	0	0.477887059543462	2		738	225	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796814	135796814	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060523-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	58	481	0	ENST00000298552.3:c.673G>T	p.Glu225Ter	p.E225*	ENST00000298552	NM_001162426.1	225	Gag/Tag	8/23	0.477887059543462	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.477887059543462	1		481	171	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231774	36231774	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1569061768	NA	P-0060524-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	47	841	0	ENST00000300305.3:c.610C>T	p.Arg204Ter	p.R204*	ENST00000300305		204	Cga/Tga	5/8	1	2	FACETS	0.195	0.164	0.23	0.195	0.164	0.23	SUBCLONAL	1	TRUE	1	0.579247955928354	2		841	833	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0060525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	208	497	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.389060651052192	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.413146431947926	3		497	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0060525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	253	433	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.299472136615604	3	FACETS	0.836	0.789	0.884	0.836	0.789	0.884	CLONAL	3	TRUE	0	0.413146431947926	3		434	589	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0060525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	186	701	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	0.413146431947926	2	FACETS	0.95	0.886	1	0.95	0.886	1	CLONAL	2	TRUE	0	0.413146431947926	2		701	474	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	360015	360015	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs752268532	NA	P-0060525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	114	559	0	ENST00000262320.3:c.1074G>C	p.Glu358Asp	p.E358D	ENST00000262320	NM_003502.3	358	gaG/gaC	4/11	0.413146431947926	2	FACETS	1	0.959	1	0.554	0.501	0.609	CLONAL	1	TRUE	0	0.413146431947926	2		559	498	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151164219	151164221	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	novel	NA	P-0060525-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	37	111	0	ENST00000262187.5:c.539_541del	p.Ser180del	p.S180del	ENST00000262187	NM_005614.3	180	tCATgc/tgc	8/8	0.413146431947926	3	FACETS	1	0.95	1	0.702	0.588	0.825	CLONAL	1	TRUE	1	0.413146431947926	3		111	154	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0060528-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	117	289	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.246359177373409	6	FACETS	1	0.96	1	0.447	0.404	0.493	CLONAL	2	TRUE	1	0.246359177373409	6		289	634	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0060530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	55	356	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.444370262344844	5	FACETS	0.57	0.486	0.661	0.19	0.162	0.221	SUBCLONAL	1	TRUE	2	0.443456799294985	5		356	725	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	272	731	0	ENST00000269305.4:c.472C>G	p.Arg158Gly	p.R158G	ENST00000269305	NM_001126112.2	158	Cgc/Ggc	5/11	0.387440732181691	2	FACETS	0.763	0.719	0.808	0.763	0.719	0.808	SUBCLONAL	2	TRUE	0	0.443456799294985	2		731	804	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242474	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGA	GAATTAAGA	-	rs121913436	NA	P-0060530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	156	417	0	ENST00000275493.2:c.2239_2247del	p.Leu747_Glu749del	p.L747_E749del	ENST00000275493	NM_005228.3	746	GAATTAAGA/-	19/28	0.443456799294985	6	FACETS	1	0.976	1	0.237	0.217	0.259	CLONAL	1	TRUE	1	0.443456799294985	6		417	1118	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961628	18961628	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060530-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	60	593	0	ENST00000262803.5:c.761C>A	p.Ala254Glu	p.A254E	ENST00000262803	NM_002911.3	254	gCa/gAa	5/24	0.387440732181691	2	FACETS	0.488	0.421	0.562	0.244	0.21	0.281	SUBCLONAL	1	TRUE	0	0.443456799294985	2		593	554	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs760043106	NA	P-0060531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	53	692	0	ENST00000269305.4:c.584T>A	p.Ile195Asn	p.I195N	ENST00000269305	NM_001126112.2	195	aTc/aAc	6/11	1	2	FACETS	0.567	0.482	0.662	0.567	0.482	0.662	SUBCLONAL	1	TRUE	1	0.17	2		692	1099	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564119	139564119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780712884	NA	P-0060531-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	55	529	0	ENST00000308874.7:c.259G>A	p.Ala87Thr	p.A87T	ENST00000308874		87	Gcg/Acg	5/10	1	2	FACETS	0.781	0.667	0.908	0.781	0.667	0.908	CLONAL	1	TRUE	1	0.17	2		529	828	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0060532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	179	499	0				ENST00000310581	NM_198253.2	-/1132			0.5039918469265	1	FACETS	0.765	0.716	0.813	0.765	0.716	0.813	SUBCLONAL	1	TRUE	0	0.778969522337942	1		499	367	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584530	187584530	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200633985	NA	P-0060532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	183	471	0	ENST00000441802.2:c.3503C>T	p.Ser1168Leu	p.S1168L	ENST00000441802	NM_005245.3	1168	tCg/tTg	3/27	0.503934963747873	1	FACETS	0.64	0.597	0.684	0.64	0.597	0.684	SUBCLONAL	1	TRUE	0	0.778969522337942	1		471	448	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0060532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	423	426	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.778969522337942	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.778969522337942	1		426	568	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086157	16086157	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	283	538	0	ENST00000281043.3:c.1333G>A	p.Glu445Lys	p.E445K	ENST00000281043	NM_005378.4	445	Gaa/Aaa	3/3	0.480373551954136	1	FACETS	0.746	0.707	0.784	0.746	0.707	0.784	SUBCLONAL	1	TRUE	0	0.778969522337942	1		538	595	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971121	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0060532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	270	580	0	ENST00000304494.5:c.237_238delinsTT	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	79	acCCga/acTTga	2/3	0.778969522337942	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.778969522337942	1		580	405	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560970	9560970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781706438	NA	P-0060532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	549	547	0	ENST00000353224.5:c.812C>T	p.Ser271Leu	p.S271L	ENST00000353224	NM_177990.2	271	tCg/tTg	4/10	0.778969522337942	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.778969522337942	3		547	973	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169269	99169269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	135	464	0	ENST00000074304.5:c.1199C>T	p.Ser400Phe	p.S400F	ENST00000074304	NM_001134224.1	400	tCc/tTc	15/26	0.5039918469265	1	FACETS	0.412	0.377	0.45	0.412	0.377	0.45	SUBCLONAL	1	TRUE	0	0.778969522337942	1		464	513	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211464	46211464	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs146524163	NA	P-0060532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	171	289	0	ENST00000334344.6:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000334344	NM_152641.2	144	Caa/Taa	5/21	0.412341530730722	1	FACETS	0.83	0.778	0.881	0.83	0.778	0.881	INDETERMINATE	1	TRUE	0	0.778969522337942	1		289	323	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970861	55970861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	134	455	0	ENST00000263923.4:c.1936G>A	p.Asp646Asn	p.D646N	ENST00000263923	NM_002253.2	646	Gac/Aac	13/30	0.503934963747873	1	FACETS	0.412	0.376	0.449	0.412	0.376	0.449	SUBCLONAL	1	TRUE	0	0.778969522337942	1		455	510	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434533	49434534	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0060532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	262	682	0	ENST00000301067.7:c.7019_7020delinsTT	p.Pro2340Leu	p.P2340L	ENST00000301067	NM_003482.3	2340	cCC/cTT	31/54	0.412341530730722	1	FACETS	0.681	0.643	0.719	0.681	0.643	0.719	INDETERMINATE	1	TRUE	0	0.778969522337942	1		682	603	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95573949	95573949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867444412	NA	P-0060532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	285	289	0	ENST00000393063.1:c.2800C>T	p.Pro934Ser	p.P934S	ENST00000393063	NM_030621.3	934	Cca/Tca	18/28	0.490344198302926	3	FACETS	0.903	0.858	0.948	0.903	0.858	0.948	CLONAL	2	TRUE	1	0.778969522337942	3		289	563	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294909	1294910	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0060532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	99	551	0	ENST00000310581.5:c.195_196delinsTT	p.Pro66Ser	p.P66S	ENST00000310581	NM_198253.2	65	ccCCcc/ccTTcc	1/16	0.5039918469265	1	FACETS	0.396	0.356	0.438	0.396	0.356	0.438	SUBCLONAL	1	TRUE	0	0.778969522337942	1		551	392	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484363	8484363	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	146	323	0	ENST00000356435.5:c.3169G>A	p.Gly1057Arg	p.G1057R	ENST00000356435		1057	Ggg/Agg	19/35	0.778969522337942	1	FACETS	0.832	0.776	0.888	0.832	0.776	0.888	CLONAL	1	TRUE	0	0.778969522337942	1		323	275	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205037	123205038	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0060532-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	81	169	0	ENST00000218089.9:c.2397_2398delinsTT	p.His800Tyr	p.H800Y	ENST00000218089	NM_001042749.1	799	agCCat/agTTat	25/35	0.778969522337942	0	FACETS		NA	1			1	NA	1	TRUE	NA	0.778969522337942	0		169	136	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913351	NA	P-0060533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	68	427	0	ENST00000288602.6:c.1397G>A	p.Gly466Glu	p.G466E	ENST00000288602	NM_004333.4	466	gGa/gAa	11/18	0.311102890103983	3	FACETS	0.942	0.821	1	0.314	0.273	0.358	CLONAL	1	TRUE	0	0.311102890103983	3		427	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574002	7574002	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs375338359	NA	P-0060533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	197	586	0	ENST00000269305.4:c.1025G>C	p.Arg342Pro	p.R342P	ENST00000269305	NM_001126112.2	342	cGa/cCa	10/11	0.311102890103983	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.311102890103983	2		586	528	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615730	1615730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372168347	NA	P-0060533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	263	818	0	ENST00000344749.5:c.1541C>T	p.Ser514Leu	p.S514L	ENST00000344749	NM_001136139.2	514	tCg/tTg	17/19	0.311102890103983	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.311102890103983	2		818	819	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22412959	22412959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	49	280	0	ENST00000344548.3:c.206C>T	p.Pro69Leu	p.P69L	ENST00000344548	NM_001039802.1	69	cCg/cTg	5/7	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.311102890103983	2		280	252	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212522479	212522479	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs978290380	NA	P-0060533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	85	588	0	ENST00000342788.4:c.1946G>T	p.Arg649Ile	p.R649I	ENST00000342788	NM_005235.2	649	aGa/aTa	16/28	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.311102890103983	2		588	543	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610322	10610322	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	263	1022	0	ENST00000171111.5:c.388C>T	p.Pro130Ser	p.P130S	ENST00000171111	NM_203500.1	130	Ccc/Tcc	2/6	0.311102890103983	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.311102890103983	2		1022	798	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196249	106196249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	99	772	0	ENST00000380013.4:c.4582C>T	p.Pro1528Ser	p.P1528S	ENST00000380013	NM_001127208.2	1528	Ccc/Tcc	11/11	1	2	FACETS	0.899	0.803	1	0.899	0.803	1	CLONAL	1	TRUE	1	0.311102890103983	2		772	708	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599873	28599873	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	56	545	0	ENST00000253063.3:c.755T>C	p.Phe252Ser	p.F252S	ENST00000253063	NM_031459.4	252	tTt/tCt	6/10	1	2	FACETS	0.711	0.61	0.822	0.711	0.61	0.822	SUBCLONAL	1	TRUE	1	0.311102890103983	2		545	506	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091458	193091458	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121434263	NA	P-0060533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	97	575	0	ENST00000367435.3:c.128G>A	p.Trp43Ter	p.W43*	ENST00000367435	NM_024529.4	43	tGg/tAg	1/17	1	2	FACETS	0.921	0.822	1	0.921	0.822	1	CLONAL	1	TRUE	1	0.311102890103983	2		575	677	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245758	46245758	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	310	708	0	ENST00000334344.6:c.3853del	p.Glu1285LysfsTer10	p.E1285Kfs*10	ENST00000334344	NM_152641.2	1284	aaG/aa	15/21	0.30637633465393	3	FACETS	0.972	0.921	1	1	0.994	1	CLONAL	3	TRUE	1	0.311102890103983	3		708	790	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663667	29663667	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660651	NA	P-0060533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	64	435	0	ENST00000356175.3:c.6099G>T	p.Met2033Ile	p.M2033I	ENST00000356175	NM_000267.3	2033	atG/atT	41/57	1	2	FACETS	0.994	0.864	1	0.994	0.864	1	CLONAL	1	TRUE	1	0.311102890103983	2		435	414	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067822	30067822	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	85	547	0	ENST00000338641.4:c.1007G>T	p.Arg336Leu	p.R336L	ENST00000338641	NM_000268.3	336	cGg/cTg	11/16	0.30637633465393	3	FACETS	0.94	0.831	1	0.47	0.415	0.528	CLONAL	1	TRUE	1	0.311102890103983	3		547	672	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266045	41266045	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	82	554	0	ENST00000349496.5:c.42G>T	p.Met14Ile	p.M14I	ENST00000349496	NM_001904.3	14	atG/atT	3/15	0.311102890103983	2	FACETS	0.873	0.77	0.982	0.436	0.385	0.491	CLONAL	1	TRUE	0	0.311102890103983	2		554	604	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55124972	55124972	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	74	487	0	ENST00000257290.5:c.37T>C	p.Cys13Arg	p.C13R	ENST00000257290	NM_006206.4	13	Tgt/Cgt	2/23	0.131298850981793	3	FACETS	0.922	0.808	1	0.307	0.269	0.349	INDETERMINATE	1	TRUE	0	0.311102890103983	3		487	596	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133594	55133594	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0060533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	185	646	0	ENST00000257290.5:c.898A>T	p.Lys300Ter	p.K300*	ENST00000257290	NM_006206.4	300	Aaa/Taa	6/23	0.131298850981793	3	FACETS	0.966	0.895	1	0.644	0.597	0.694	INDETERMINATE	2	TRUE	0	0.311102890103983	3		646	711	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514402	149514402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs771234317	NA	P-0060533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	106	683	0	ENST00000261799.4:c.542G>C	p.Gly181Ala	p.G181A	ENST00000261799	NM_002609.3	181	gGt/gCt	4/23	0.306803339949344	2	FACETS	0.962	0.863	1	0.481	0.431	0.534	CLONAL	1	TRUE	0	0.311102890103983	2		683	708	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974315	93974315	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060533-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	68	356	0	ENST00000369303.4:c.1739G>T	p.Arg580Ile	p.R580I	ENST00000369303	NM_004440.3	580	aGa/aTa	8/17	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.311102890103983	2		356	348	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0060534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	287	513	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	NA	2	FACETS	0.796	0.756	0.836			1	INDETERMINATE	2	TRUE	NA	0.6134966289371	2		513	588	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575209	48575209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767326	NA	P-0060534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	169	257	0	ENST00000342988.3:c.403C>T	p.Arg135Ter	p.R135*	ENST00000342988	NM_005359.5	135	Cga/Tga	3/12	0.6134966289371	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.6134966289371	1		257	349	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0060534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	181	377	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	0.328602800592503	3	FACETS	1	0.989	1	0.686	0.637	0.737	INDETERMINATE	1	TRUE	1	0.6134966289371	3		377	562	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735505	40735505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060534-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	100	492	0	ENST00000373198.4:c.3368C>T	p.Ala1123Val	p.A1123V	ENST00000373198	NM_133170.3	1123	gCc/gTc	25/32	0.235113793383025	1	FACETS	0.414	0.371	0.46	0.414	0.371	0.46	INDETERMINATE	1	TRUE	0	0.6134966289371	1		492	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0060543-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	323	621	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.431984258143132	3	FACETS	0.876	0.834	0.917	0.876	0.834	0.917	CLONAL	3	TRUE	0	0.460473327317856	3		621	657	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259516	+	missense_variant	Missense_Mutation	DNP	TG	TG	GT	rs1057519848	NA	P-0060543-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	232	554	0	ENST00000275493.2:c.2573_2574delinsGT	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTG/cGT	21/28	0.460473327317856	9	FACETS	0.945	0.879	1	0.27	0.251	0.29	CLONAL	2	TRUE	2	0.460473327317856	9		554	1392	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838311	156838311	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060543-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	287	737	0	ENST00000524377.1:c.590del	p.Lys197ArgfsTer42	p.K197Rfs*42	ENST00000524377	NM_002529.3	197	Aag/ag	6/17	0.40701085410413	5	FACETS	0.999	0.94	1	0.666	0.626	0.706	CLONAL	2	TRUE	2	0.460473327317856	5		737	1055	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858618	57858618	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060543-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	174	640	0	ENST00000228682.2:c.356G>T	p.Gly119Val	p.G119V	ENST00000228682	NM_005269.2	119	gGc/gTc	4/12	0.1466448775524	4	FACETS	0.768	0.708	0.829	0.768	0.708	0.829	INDETERMINATE	2	TRUE	2	0.460473327317856	4		640	719	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181015	32181015	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060543-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	131	488	0	ENST00000375023.3:c.2335G>A	p.Gly779Arg	p.G779R	ENST00000375023	NM_004557.3	779	Ggg/Agg	15/30	0.334138824975415	4	FACETS	1	0.984	1	0.702	0.639	0.767	CLONAL	1	TRUE	2	0.460473327317856	4		488	592	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771164	161771165	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0060543-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	182	494	0	ENST00000366898.1:c.1364dup	p.Val456ArgfsTer113	p.V456Rfs*113	ENST00000366898	NM_004562.2	455	cgc/cgGc	12/12	0.460473327317856	3	FACETS	0.837	0.777	0.899	0.837	0.777	0.899	CLONAL	2	TRUE	1	0.460473327317856	3		494	581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0060544-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	143	584	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.250560933553466	2		584	807	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0060544-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	87	791	0	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	1	2	FACETS	0.774	0.684	0.871	0.774	0.684	0.871	SUBCLONAL	1	TRUE	1	0.250560933553466	2		791	897	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851765	134851765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060544-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	98	768	0	ENST00000398015.3:c.1171G>A	p.Val391Ile	p.V391I	ENST00000398015	NM_004441.4	391	Gtc/Atc	5/16	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.250560933553466	2		768	763	SUCCESS
APC	324	MSKCC	GRCh37	5	112174471	112174475	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAC	AAAAC	-	rs587779352	NA	P-0060544-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	96	560	0	ENST00000257430.4:c.3183_3187del	p.Gln1062Ter	p.Q1062*	ENST00000257430	NM_000038.5	1060	atAAAACaa/ataa	16/16	0.217747334838486	2	FACETS	1	0.98	1	0.73	0.652	0.812	CLONAL	1	TRUE	0	0.250560933553466	2		560	525	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467841	50467841	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752909152	NA	P-0060544-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	70	709	0	ENST00000331340.3:c.1076C>T	p.Pro359Leu	p.P359L	ENST00000331340	NM_006060.4	359	cCg/cTg	8/8	0.13174988083616	3	FACETS	0.862	0.751	0.983	0.431	0.375	0.492	INDETERMINATE	1	TRUE	1	0.250560933553466	3		709	729	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114905788	114905788	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060544-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	37	491	0	ENST00000543371.1:c.807C>A	p.Tyr269Ter	p.Y269*	ENST00000543371	NM_001198531.1	269	taC/taA	8/14	1	2	FACETS	0.484	0.398	0.581	0.484	0.398	0.581	SUBCLONAL	1	TRUE	1	0.250560933553466	2		491	610	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0060545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	100	573	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.99	0.885	1	0.99	0.885	1	CLONAL	1	TRUE	1	0.31	2		573	652	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0060545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	30	343	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.958	0.778	1	0.958	0.778	1	CLONAL	1	TRUE	1	0.31	2		343	202	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0060545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	28	316	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.31	2		316	130	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0060545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	22	618	2	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	1	2	FACETS	0.24	0.185	0.305	0.24	0.185	0.305	SUBCLONAL	1	TRUE	1	0.31	2		620	591	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106649	27106649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	27	805	0	ENST00000324856.7:c.6260G>A	p.Gly2087Glu	p.G2087E	ENST00000324856	NM_006015.4	2087	gGa/gAa	20/20	1	2	FACETS	0.256	0.203	0.318	0.256	0.203	0.318	SUBCLONAL	1	TRUE	1	0.31	2		805	680	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692800	89692800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204856	NA	P-0060545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	23	323	0	ENST00000371953.3:c.284C>T	p.Pro95Leu	p.P95L	ENST00000371953	NM_000314.4	95	cCa/cTa	5/9	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.31	2		323	131	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251851	8251851	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781572416	NA	P-0060545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	75	756	0	ENST00000335790.3:c.226C>T	p.Arg76Cys	p.R76C	ENST00000335790	NM_002315.2	76	Cgc/Tgc	2/4	1	2	FACETS	0.817	0.717	0.925	0.817	0.717	0.925	CLONAL	1	TRUE	1	0.31	2		756	592	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845566	63845567	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0060545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	56	551	0	ENST00000279873.7:c.1307_1308dup	p.Lys437GlnfsTer43	p.K437Qfs*43	ENST00000279873	NM_032199.2	435	-/AC	9/10	1	2	FACETS	0.873	0.75	1	0.873	0.75	1	CLONAL	1	TRUE	1	0.31	2		551	414	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557639	95557639	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	73	561	0	ENST00000393063.1:c.5428G>T	p.Asp1810Tyr	p.D1810Y	ENST00000393063	NM_030621.3	1810	Gat/Tat	26/28	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.31	2		561	445	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574351	95574351	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	26	472	0	ENST00000393063.1:c.2516C>A	p.Ser839Tyr	p.S839Y	ENST00000393063	NM_030621.3	839	tCt/tAt	17/28	1	2	FACETS	0.717	0.57	0.883	0.717	0.57	0.883	SUBCLONAL	1	TRUE	1	0.31	2		472	234	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212488	36212488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060545-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	92	825	0	ENST00000222270.7:c.2239C>T	p.Gln747Ter	p.Q747*	ENST00000222270	NM_014727.1	747	Cag/Tag	3/37	1	2	FACETS	0.879	0.782	0.983	0.879	0.782	0.983	CLONAL	1	TRUE	1	0.31	2		825	675	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0060546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	141	499	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.7002495704068	2		499	351	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0060546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	442	465	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.608271776853327	4	FACETS	0.979	0.944	1			1	CLONAL	3	TRUE	NA	0.7002495704068	4		465	731	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288158	21288158	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	183	573	0	ENST00000354336.3:c.403C>T	p.Pro135Ser	p.P135S	ENST00000354336	NM_005207.3	135	Cct/Tct	2/3	1	2	FACETS	0.9	0.835	0.966	0.9	0.835	0.966	CLONAL	1	TRUE	1	0.7002495704068	2		573	581	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979378	93979378	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	112	450	0	ENST00000369303.4:c.1450G>A	p.Asp484Asn	p.D484N	ENST00000369303	NM_004440.3	484	Gat/Aat	7/17	1	2	FACETS	0.935	0.851	1	0.935	0.851	1	CLONAL	1	TRUE	1	0.7002495704068	2		450	342	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983275	149983275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	217	547	0	ENST00000253339.5:c.2983C>T	p.Arg995Cys	p.R995C	ENST00000253339		995	Cgc/Tgc	7/7	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.7002495704068	2		547	573	SUCCESS
BLM	641	MSKCC	GRCh37	15	91290720	91290720	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs139282091	NA	P-0060546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	138	380	0	ENST00000355112.3:c.98C>T	p.Ser33Leu	p.S33L	ENST00000355112	NM_000057.2	33	tCa/tTa	2/22	1	2	FACETS	0.961	0.883	1	0.961	0.883	1	CLONAL	1	TRUE	1	0.7002495704068	2		380	410	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212857	27212857	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs906836493	NA	P-0060546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	202	533	0	ENST00000380036.4:c.2839G>A	p.Asp947Asn	p.D947N	ENST00000380036	NM_000459.3	947	Gac/Aac	17/23	0.7002495704068	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.7002495704068	1		533	353	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873232	71873232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	196	570	0	ENST00000357731.5:c.962G>A	p.Gly321Glu	p.G321E	ENST00000357731	NM_173808.2	321	gGa/gAa	7/7	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.7002495704068	2		570	521	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092713	27092713	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs753300592	NA	P-0060546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	151	449	0	ENST00000324856.7:c.2734C>T	p.Pro912Ser	p.P912S	ENST00000324856	NM_006015.4	912	Ccg/Tcg	9/20	1	2	FACETS	0.969	0.894	1	0.969	0.894	1	CLONAL	1	TRUE	1	0.7002495704068	2		449	445	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93953163	93953163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	111	361	0	ENST00000369303.4:c.2978G>A	p.Gly993Glu	p.G993E	ENST00000369303	NM_004440.3	993	gGa/gAa	17/17	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.7002495704068	2		361	286	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651903	36651903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752557277	NA	P-0060546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	204	618	0	ENST00000244741.5:c.25C>T	p.Arg9Cys	p.R9C	ENST00000244741	NM_000389.4	9	Cgt/Tgt	2/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.7002495704068	2		618	522	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191451	185191451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060546-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	185	584	0	ENST00000265026.3:c.2332G>A	p.Glu778Lys	p.E778K	ENST00000265026	NM_004721.4	778	Gaa/Aaa	11/14	1	2	FACETS	0.999	0.929	1	0.999	0.929	1	CLONAL	1	TRUE	1	0.7002495704068	2		584	529	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0060547-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	87	479	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.858	0.759	0.965	0.858	0.759	0.965	CLONAL	1	TRUE	1	0.25	2		479	811	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060547-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	75	575	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.25	2		575	555	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0060547-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	37	383	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.476	0.391	0.571	0.476	0.391	0.571	SUBCLONAL	1	TRUE	1	0.25	2		383	622	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692911	89692911	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121909241	NA	P-0060547-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	43	344	0	ENST00000371953.3:c.395G>T	p.Gly132Val	p.G132V	ENST00000371953	NM_000314.4	132	gGt/gTt	5/9	0.299783473938635	3	FACETS	0.733	0.613	0.866	0.366	0.306	0.433	SUBCLONAL	1	TRUE	1	0.25	3		344	528	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725057	89725063	+	frameshift_variant	Frame_Shift_Del	DEL	TCACAAA	TCACAAA	-	novel	NA	P-0060547-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	66	183	0	ENST00000371953.3:c.1040_1046del	p.Phe347Ter	p.F347*	ENST00000371953	NM_000314.4	347	tTCACAAAa/ta	9/9	0.299783473938635	3	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	TRUE	1	0.25	3		183	277	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0060548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	108	621	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.216348593307976	2		621	855	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423601	88423601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	90	549	0	ENST00000360948.2:c.2234G>A	p.Arg745Gln	p.R745Q	ENST00000360948	NM_001012338.2	745	cGg/cAg	18/19	0.216348593307976	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.216348593307976	1		549	596	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129595	2129595	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	46	628	0	ENST00000219476.3:c.3322G>C	p.Ala1108Pro	p.A1108P	ENST00000219476	NM_000548.3	1108	Gcg/Ccg	29/42	1	2	FACETS	0.57	0.479	0.671	0.57	0.479	0.671	SUBCLONAL	1	TRUE	1	0.216348593307976	2		628	746	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589592	67589594	+	inframe_deletion	In_Frame_Del	DEL	ATA	ATA	-	novel	NA	P-0060548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	86	258	0	ENST00000274335.5:c.1356_1358del	p.Asn453del	p.N453del	ENST00000274335		452	tATAac/tac	10/15	0.156744879618534	2	FACETS	0.903	0.803	1	0.903	0.803	1	CLONAL	2	TRUE	0	0.216348593307976	2		258	440	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55269427	55269427	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0060548-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	122	734	0	ENST00000275493.2:c.3115-1G>A		p.X1039_splice	ENST00000275493	NM_005228.3	1039			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.216348593307976	2		734	903	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0060549-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	121	388	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.951	0.862	1	0.951	0.862	1	CLONAL	1	TRUE	1	0.447432423539451	2		388	569	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155725	56155726	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0060549-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	203	444	0	ENST00000399503.3:c.819_820del	p.Arg273SerfsTer27	p.R273Sfs*27	ENST00000399503	NM_005921.1	273	AGa/a	3/20	0.412747867763714	3	FACETS	0.85	0.792	0.91	0.85	0.792	0.91	CLONAL	2	TRUE	1	0.447432423539451	3		444	653	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061115	38061115	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1016447126	NA	P-0060549-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	183	600	0	ENST00000250448.2:c.874G>A	p.Glu292Lys	p.E292K	ENST00000250448	NM_004496.3	292	Gag/Aag	2/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.447432423539451	2		600	736	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061309	38061309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060549-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	178	711	0	ENST00000250448.2:c.680G>A	p.Cys227Tyr	p.C227Y	ENST00000250448	NM_004496.3	227	tGc/tAc	2/2	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.447432423539451	2		711	756	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061226	38061226	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060549-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	175	614	0	ENST00000250448.2:c.763G>C	p.Glu255Gln	p.E255Q	ENST00000250448	NM_004496.3	255	Gag/Cag	2/2	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.447432423539451	2		614	762	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874112	151874112	+	frameshift_variant	Frame_Shift_Ins	INS	T	T	GG	novel	NA	P-0060549-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	124	562	0	ENST00000262189.6:c.8426delinsCC	p.Lys2809ThrfsTer13	p.K2809Tfs*13	ENST00000262189	NM_170606.2	2809	aAa/aCCa	38/59	1	2	FACETS	0.967	0.878	1	0.967	0.878	1	CLONAL	1	TRUE	1	0.447432423539451	2		562	573	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060550-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	215	475	0				ENST00000310581	NM_198253.2	-/1132			0.178171982429534	1	FACETS	0.53	0.496	0.564	0.53	0.496	0.564	INDETERMINATE	1	TRUE	0	0.854495532187822	1		475	544	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0060550-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	122	174	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.854495532187822	2		174	267	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0060550-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	495	564	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	0.414167089962395	3	FACETS	0.879	0.846	0.911			1	INDETERMINATE	2	TRUE	NA	0.854495532187822	3		564	941	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729892	41729892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762543780	NA	P-0060550-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	315	598	0	ENST00000242208.4:c.637G>A	p.Ala213Thr	p.A213T	ENST00000242208	NM_002192.2	213	Gct/Act	3/3	0.178171982429534	1	FACETS	0.652	0.62	0.683	0.652	0.62	0.683	INDETERMINATE	1	TRUE	0	0.854495532187822	1		598	648	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165759	108165759	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060550-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	188	220	0	ENST00000278616.4:c.4882A>G	p.Met1628Val	p.M1628V	ENST00000278616	NM_000051.3	1628	Atg/Gtg	32/63	0.802763831275751	1	FACETS	0.94	0.895	0.984	0.94	0.895	0.984	CLONAL	1	TRUE	0	0.854495532187822	1		220	268	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981114	201981115	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0060550-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	315	605	1	ENST00000359651.3:c.194dup	p.Phe66ValfsTer26	p.F66Vfs*26	ENST00000359651		65	cag/cAag	2/8	0.337567930937796	3	FACETS	1	0.989	1	0.584	0.552	0.616	INDETERMINATE	1	TRUE	1	0.854495532187822	3		606	901	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981535	201981551	+	frameshift_variant	Frame_Shift_Del	DEL	TCCAGGAGGCCCTAGAC	TCCAGGAGGCCCTAGAC	-	novel	NA	P-0060550-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	431	520	1	ENST00000359651.3:c.449_465del	p.Phe150SerfsTer5	p.F150Sfs*5	ENST00000359651		150	tTCCAGGAGGCCCTAGAC/t	3/8	0.337567930937796	3	FACETS	0.825	0.791	0.858	0.825	0.791	0.858	INDETERMINATE	2	TRUE	1	0.854495532187822	3		521	873	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732904	44732913	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCGTCCCC	AGGCGTCCCC	-	novel	NA	P-0060550-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	219	502	0	ENST00000377967.4:c.107_116del	p.Glu36AlafsTer3	p.E36Afs*3	ENST00000377967	NM_021140.2	36	gAGGCGTCCCCc/gc	1/29	1	2	FACETS	0.895	0.839	0.951	0.895	0.839	0.951	CLONAL	1	TRUE	1	0.854495532187822	2		502	573	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966782	44966783	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0060550-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	164	249	0	ENST00000377967.4:c.4005+2dup		p.X1335_splice	ENST00000377967	NM_021140.2	1335			1	2	FACETS	0.979	0.911	1	0.979	0.911	1	CLONAL	1	TRUE	1	0.854495532187822	2		249	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs17849781	NA	P-0060551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	513	427	0	ENST00000269305.4:c.832C>G	p.Pro278Ala	p.P278A	ENST00000269305	NM_001126112.2	278	Cct/Gct	8/11	0.646982360630059	4	FACETS	1	0.99	1			1	CLONAL	4	TRUE	NA	0.644186861973975	4		427	638	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426638	47426638	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	108	504	0	ENST00000377045.4:c.883G>T	p.Gly295Trp	p.G295W	ENST00000377045	NM_001654.4	295	Ggg/Tgg	10/16	0.646982360630059	4	FACETS	0.882	0.793	0.976			1	CLONAL	1	TRUE	NA	0.644186861973975	4		504	625	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954022	32954023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs397507419	NA	P-0060551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	67	374	7	ENST00000380152.3:c.9097dup	p.Thr3033AsnfsTer11	p.T3033Nfs*11	ENST00000380152		3030	aca/acAa	23/27	0.646982360630059	2	FACETS	0.889	0.804	0.972	0.889	0.804	0.972	CLONAL	2	TRUE	0	0.644186861973975	2		381	117	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937172	36937172	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	128	529	0	ENST00000361632.4:c.1147G>T	p.Ala383Ser	p.A383S	ENST00000361632		383	Gcc/Tcc	9/16	0.379331231477345	5	FACETS	1	0.972	1	0.394	0.358	0.432	INDETERMINATE	1	TRUE	2	0.644186861973975	5		529	661	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739040	46739040	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs762177990	NA	P-0060551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	179	393	0	ENST00000371975.4:c.1389C>G	p.Ile463Met	p.I463M	ENST00000371975	NM_003579.3	463	atC/atG	13/18	0.379331231477345	5	FACETS	1	0.983	1	0.785	0.731	0.84	INDETERMINATE	2	TRUE	2	0.644186861973975	5		393	464	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461149	120461149	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	114	353	0	ENST00000256646.2:c.5809C>G	p.Leu1937Val	p.L1937V	ENST00000256646	NM_024408.3	1937	Cta/Gta	32/34	0.646982360630059	3	FACETS	1	0.939	1	0.523	0.474	0.575	CLONAL	1	TRUE	1	0.644186861973975	3		353	447	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293155	91293155	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1447056195	NA	P-0060551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	111	412	0	ENST00000355112.3:c.657T>G	p.Asp219Glu	p.D219E	ENST00000355112	NM_000057.2	219	gaT/gaG	3/22	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.644186861973975	2		412	339	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820775	3820776	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATCA	novel	NA	P-0060551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	124	512	0	ENST00000262367.5:c.2675_2676insTGAT	p.Ser893AspfsTer78	p.S893Dfs*78	ENST00000262367	NM_004380.2	892	gtg/gtTGATg	14/31	0.646982360630059	3	FACETS	0.969	0.881	1	0.485	0.44	0.531	CLONAL	1	TRUE	1	0.644186861973975	3		512	525	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50815232	50815232	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	186	419	0	ENST00000398568.2:c.1585C>A	p.Leu529Met	p.L529M	ENST00000398568	NM_001042412.1	529	Ctg/Atg	9/18	0.644186861973975	6	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.644186861973975	6		419	934	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984665	72984679	+	inframe_deletion	In_Frame_Del	DEL	CTCCGACAGGCTGCG	CTCCGACAGGCTGCG	-	novel	NA	P-0060551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	117	460	0	ENST00000268489.5:c.2905_2919del	p.Arg969_Glu973del	p.R969_E973del	ENST00000268489	NM_006885.3	969	CGCAGCCTGTCGGAG/-	3/10	0.418913522499872	1	FACETS	0.792	0.724	0.861	0.792	0.724	0.861	SUBCLONAL	1	TRUE	0	0.644186861973975	1		460	311	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096693	178096693	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	113	317	0	ENST00000397062.3:c.638T>A	p.Val213Asp	p.V213D	ENST00000397062	NM_006164.4	213	gTt/gAt	5/5	0.646982360630059	4	FACETS	0.765	0.695	0.838			1	SUBCLONAL	2	TRUE	NA	0.644186861973975	4		317	377	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319396	62319396	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	189	499	0	ENST00000360203.5:c.1588G>C	p.Asp530His	p.D530H	ENST00000360203	NM_001283009.1	530	Gac/Cac	18/35	0.644186861973975	6	FACETS	1	0.987	1	0.332	0.306	0.358	CLONAL	1	TRUE	2	0.644186861973975	6		499	1012	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215901	142215901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	48	317	0	ENST00000350721.4:c.5692G>A	p.Glu1898Lys	p.E1898K	ENST00000350721	NM_001184.3	1898	Gag/Aag	33/47	0.646982360630059	4	FACETS	0.581	0.492	0.678	0.194	0.164	0.226	SUBCLONAL	1	TRUE	1	0.644186861973975	4		317	422	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796094	57796094	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	71	369	0	ENST00000309042.7:c.1070G>C	p.Gly357Ala	p.G357A	ENST00000309042	NM_005612.4	357	gGg/gCg	4/4	0.644186861973975	7	FACETS	0.906	0.791	1	0.181	0.158	0.207	CLONAL	1	TRUE	2	0.644186861973975	7		369	635	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827195	170827195	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	13	274	0	ENST00000296930.5:c.567del	p.Ala190ArgfsTer3	p.A190Rfs*3	ENST00000296930	NM_002520.6	188	gAa/ga	7/11	0.646982360630059	3	FACETS	0.288	0.206	0.389	0.096	0.068	0.13	SUBCLONAL	1	TRUE	0	0.644186861973975	3		274	185	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670993	30670993	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	99	460	0	ENST00000376406.3:c.5753G>C	p.Gly1918Ala	p.G1918A	ENST00000376406	NM_014641.2	1918	gGt/gCt	12/15	0.437309197996253	3	FACETS	1	0.912	1	0.339	0.304	0.375	CLONAL	1	TRUE	0	0.644186861973975	3		460	400	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555212	106555212	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	105	449	0	ENST00000369096.4:c.2329C>G	p.Gln777Glu	p.Q777E	ENST00000369096	NM_001198.3	777	Caa/Gaa	7/7	1	2	FACETS	0.97	0.879	1	0.97	0.879	1	CLONAL	1	TRUE	1	0.644186861973975	2		449	336	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023133	150023133	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060551-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	87	345	0	ENST00000253339.5:c.130C>A	p.Pro44Thr	p.P44T	ENST00000253339		44	Cca/Aca	1/7	0.644186861973975	6	FACETS	1	0.964	1	0.242	0.214	0.271	CLONAL	1	TRUE	1	0.644186861973975	6		345	511	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0060552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	108	279	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.287928799640325	3	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	1	0.336337935573816	3		279	358	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0060552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	72	487	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.336337935573816	1	FACETS	0.8	0.702	0.906	0.8	0.702	0.906	CLONAL	1	TRUE	0	0.336337935573816	1		487	445	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0060552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	123	539	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	0.286306638933734	2	FACETS	0.858	0.783	0.937	0.858	0.783	0.937	CLONAL	2	TRUE	0	0.336337935573816	2		539	426	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276765	15276765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs550464740	NA	P-0060552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	63	689	0	ENST00000263388.2:c.5500C>T	p.Arg1834Trp	p.R1834W	ENST00000263388	NM_000435.2	1834	Cgg/Tgg	30/33	0.295374892789999	3	FACETS	0.865	0.749	0.99	0.432	0.374	0.495	CLONAL	1	TRUE	1	0.336337935573816	3		689	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0060552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	111	517	0	ENST00000269305.4:c.673-2A>C		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.286306638933734	2	FACETS	0.848	0.769	0.93	0.848	0.769	0.93	CLONAL	2	TRUE	0	0.336337935573816	2		517	389	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104356999	104356999	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	73	413	0	ENST00000369902.3:c.859G>T	p.Asp287Tyr	p.D287Y	ENST00000369902	NM_016169.3	287	Gac/Tac	7/12	0.0878570542518744	3	FACETS	1	0.968	1	0.66	0.581	0.745	INDETERMINATE	1	TRUE	1	0.336337935573816	3		413	384	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8246197	8246197	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	49	574	0	ENST00000335790.3:c.437A>C	p.Gln146Pro	p.Q146P	ENST00000335790	NM_002315.2	146	cAg/cCg	4/4	1	2	FACETS	0.638	0.54	0.744	0.638	0.54	0.744	SUBCLONAL	1	TRUE	1	0.336337935573816	2		574	457	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544242	86544242	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1567510586	NA	P-0060552-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	43	762	0	ENST00000262426.4:c.67G>C	p.Gly23Arg	p.G23R	ENST00000262426	NM_001451.2	23	Ggc/Cgc	1/2	0.287928799640325	3	FACETS	0.725	0.607	0.855	0.362	0.303	0.428	SUBCLONAL	1	TRUE	1	0.336337935573816	3		762	412	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0060553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	16	66	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.223960966067969	3	FACETS	0.413	0.306	0.538	0.138	0.102	0.18	INDETERMINATE	1	TRUE	0	0.624485975498178	3		66	163	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0060553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	11	61	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.223960966067969	3	FACETS	0.328	0.227	0.452	0.109	0.075	0.151	INDETERMINATE	1	TRUE	0	0.624485975498178	3		61	141	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800564	32800564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148663600	NA	P-0060553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	168	629	0	ENST00000374899.4:c.983C>T	p.Ala328Val	p.A328V	ENST00000374899	NM_018833.2	328	gCg/gTg	6/12	0.624485975498178	3	FACETS	0.811	0.745	0.879	0.405	0.372	0.44	CLONAL	1	TRUE	1	0.624485975498178	3		629	871	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581234	48581234	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767332	NA	P-0060553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	91	540	0	ENST00000342988.3:c.538C>T	p.Gln180Ter	p.Q180*	ENST00000342988	NM_005359.5	180	Caa/Taa	5/12	0.624485975498178	1	FACETS	0.411	0.366	0.458	0.411	0.366	0.458	SUBCLONAL	1	TRUE	0	0.624485975498178	1		540	488	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591928	48591928	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	36	585	0	ENST00000342988.3:c.1091T>C	p.Leu364Ser	p.L364S	ENST00000342988	NM_005359.5	364	tTg/tCg	9/12	0.624485975498178	1	FACETS	0.176	0.144	0.212	0.176	0.144	0.212	SUBCLONAL	1	TRUE	0	0.624485975498178	1		585	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	G	rs1131691039	NA	P-0060553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	544	760	0	ENST00000269305.4:c.919+1G>C		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.624485975498178	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.624485975498178	2		760	836	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953945	17953945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	174	671	0	ENST00000458235.1:c.457G>A	p.Gly153Ser	p.G153S	ENST00000458235	NM_000215.3	153	Ggc/Agc	5/24	0.52768730609114	3	FACETS	0.772	0.711	0.836	0.386	0.355	0.418	SUBCLONAL	1	TRUE	1	0.624485975498178	3		671	947	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950660	38950660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759204549	NA	P-0060553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	41	480	0	ENST00000357387.3:c.3290G>A	p.Arg1097His	p.R1097H	ENST00000357387	NM_152756.3	1097	cGt/cAt	31/38	0.406679491658623	3	FACETS	0.358	0.298	0.425	0.179	0.149	0.213	SUBCLONAL	1	TRUE	1	0.624485975498178	3		480	481	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522761	67522762	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0060553-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	149	607	0	ENST00000274335.5:c.260dup	p.Pro89AlafsTer17	p.P89Afs*17	ENST00000274335		86	-/C	1/15	0.181678490880684	2	FACETS	0.704	0.645	0.765	0.352	0.322	0.383	INDETERMINATE	1	TRUE	0	0.624485975498178	2		607	678	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	187	475	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.916	0.853	0.981	0.916	0.853	0.981	CLONAL	1	TRUE	1	0.784907538119558	2		475	520	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762959	40762959	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs387906659	NA	P-0060554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	111	806	0	ENST00000392038.2:c.49G>A	p.Glu17Lys	p.E17K	ENST00000392038	NM_001626.4	17	Gaa/Aaa	3/14	1	2	FACETS	0.441	0.396	0.487	0.441	0.396	0.487	SUBCLONAL	1	TRUE	1	0.784907538119558	2		806	642	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651987	36651988	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0060554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	350	757	0	ENST00000244741.5:c.110dup	p.Met38AsnfsTer10	p.M38Nfs*10	ENST00000244741	NM_000389.4	37	cta/cTta	2/3	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.784907538119558	2		757	849	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770065	56770065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752608224	NA	P-0060554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	289	651	0	ENST00000337432.4:c.61C>T	p.Pro21Ser	p.P21S	ENST00000337432	NM_058216.2	21	Cca/Tca	1/9	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.784907538119558	2		651	668	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776220	135776220	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs118203706	NA	P-0060554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	214	632	0	ENST00000298552.3:c.2507C>G	p.Ser836Ter	p.S836*	ENST00000298552	NM_001162426.1	836	tCa/tGa	20/23	0.784907538119558	1	FACETS	0.881	0.834	0.928	0.881	0.834	0.928	CLONAL	1	TRUE	0	0.784907538119558	1		632	376	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs149680468	NA	P-0060554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	16	665	0	ENST00000281708.4:c.1513C>A	p.Arg505Ser	p.R505S	ENST00000281708	NM_033632.3	505	Cgc/Agc	10/12	1	2	FACETS	0.055	0.04	0.073	0.055	0.04	0.073	SUBCLONAL	1	TRUE	1	0.784907538119558	2		665	747	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127167	22127167	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	225	491	0	ENST00000215832.6:c.961G>T	p.Asp321Tyr	p.D321Y	ENST00000215832	NM_002745.4	321	Gac/Tac	7/9	1	2	FACETS	0.937	0.878	0.996	0.937	0.878	0.996	CLONAL	1	TRUE	1	0.784907538119558	2		491	612	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254527	1254527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765787352	NA	P-0060554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	198	610	0	ENST00000310581.5:c.3251G>A	p.Arg1084Gln	p.R1084Q	ENST00000310581	NM_198253.2	1084	cGa/cAa	15/16	1	2	FACETS	0.904	0.844	0.966	0.904	0.844	0.966	CLONAL	1	TRUE	1	0.784907538119558	2		610	558	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498490	89498490	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	25	552	0	ENST00000336596.2:c.2462G>C	p.Gly821Ala	p.G821A	ENST00000336596	NM_005233.5	821	gGa/gCa	14/17	1	2	FACETS	0.127	0.1	0.159	0.127	0.1	0.159	SUBCLONAL	1	TRUE	1	0.784907538119558	2		552	500	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147214	61147214	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs757728369	NA	P-0060554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	31	191	0	ENST00000295025.8:c.892C>G	p.Leu298Val	p.L298V	ENST00000295025	NM_002908.2	298	Ctg/Gtg	8/11	1	2	FACETS	0.152	0.122	0.186	0.152	0.122	0.186	SUBCLONAL	1	TRUE	1	0.784907538119558	2		191	519	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506284	120506284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	300	711	0	ENST00000256646.2:c.1828G>A	p.Glu610Lys	p.E610K	ENST00000256646	NM_024408.3	610	Gaa/Aaa	11/34	1	2	FACETS	0.971	0.919	1	0.971	0.919	1	CLONAL	1	TRUE	1	0.784907538119558	2		711	787	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64126717	64126717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398692927	NA	P-0060554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	243	675	0	ENST00000334205.4:c.10G>A	p.Glu4Lys	p.E4K	ENST00000334205	NM_003942.2	4	Gag/Aag	1/17	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.784907538119558	2		675	599	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019386	42019386	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	32	504	0	ENST00000219905.7:c.3439G>C	p.Glu1147Gln	p.E1147Q	ENST00000219905	NM_001164273.1	1147	Gag/Cag	10/24	1	2	FACETS	0.158	0.128	0.193	0.158	0.128	0.193	SUBCLONAL	1	TRUE	1	0.784907538119558	2		504	515	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830764	3830764	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	55	643	0	ENST00000262367.5:c.1792C>G	p.Gln598Glu	p.Q598E	ENST00000262367	NM_004380.2	598	Cag/Gag	8/31	1	2	FACETS	0.246	0.21	0.286	0.246	0.21	0.286	SUBCLONAL	1	TRUE	1	0.784907538119558	2		643	569	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221634	22221634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	194	611	0	ENST00000215832.6:c.97G>A	p.Glu33Lys	p.E33K	ENST00000215832	NM_002745.4	33	Gag/Aag	1/9	1	2	FACETS	0.838	0.78	0.897	0.838	0.78	0.897	CLONAL	1	TRUE	1	0.784907538119558	2		611	590	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151181828	151181828	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	200	486	0	ENST00000262187.5:c.187G>C	p.Gly63Arg	p.G63R	ENST00000262187	NM_005614.3	63	Ggg/Cgg	3/8	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.784907538119558	2		486	495	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845100	151845123	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTGAACGGCAGACGTTACCTTTAG	GTGAACGGCAGACGTTACCTTTAG	-	novel	NA	P-0060554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	103	563	0	ENST00000262189.6:c.13889_13894+18del		p.X4630_splice	ENST00000262189	NM_170606.2	4630		52/59	1	2	FACETS	0.469	0.42	0.52	0.469	0.42	0.52	SUBCLONAL	1	TRUE	1	0.784907538119558	2		563	560	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874128	151874128	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	137	514	0	ENST00000262189.6:c.8410C>G	p.Leu2804Val	p.L2804V	ENST00000262189	NM_170606.2	2804	Ctg/Gtg	38/59	1	2	FACETS	0.879	0.808	0.952	0.879	0.808	0.952	CLONAL	1	TRUE	1	0.784907538119558	2		514	397	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933317	39933317	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060554-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	43	415	0	ENST00000378444.4:c.1282G>C	p.Glu428Gln	p.E428Q	ENST00000378444	NM_001123385.1	428	Gag/Cag	4/15	1	1	FACETS	0.171	0.143	0.202	0.171	0.143	0.202	SUBCLONAL	1	TRUE	0	0.784907538119558	1		415	390	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256229	16256229	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0060559-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	157	565	1	ENST00000375759.3:c.3494del	p.His1165ProfsTer22	p.H1165Pfs*22	ENST00000375759	NM_015001.2	1165	cAc/cc	11/15	0.808382137434238	1	FACETS	0.427	0.393	0.462	0.427	0.393	0.462	SUBCLONAL	1	TRUE	0	0.808382137434238	1		566	542	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577330	64577333	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	rs587776841	NA	P-0060559-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	298	572	0	ENST00000312049.6:c.249_252del	p.Ile85SerfsTer33	p.I85Sfs*33	ENST00000312049	NM_130799.2	83	ctGTCT/ct	2/10	0.808382137434238	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.808382137434238	1		572	430	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288947	33288947	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060559-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	420	522	0	ENST00000374542.5:c.605T>A	p.Ile202Asn	p.I202N	ENST00000374542	NM_001141970.1	202	aTc/aAc	3/8	0.808382137434238	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.808382137434238	1		522	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0060560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	106	454	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.236937411551481	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.236937411551481	1		454	556	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639204	3639204	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs758409623	NA	P-0060560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	53	604	0	ENST00000294008.3:c.4435C>T	p.Arg1479Ter	p.R1479*	ENST00000294008	NM_032444.2	1479	Cga/Tga	12/15	0.230432373146756	2	FACETS	0.605	0.515	0.705	0.303	0.257	0.353	SUBCLONAL	1	TRUE	0	0.236937411551481	2		604	739	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128321985	128321985	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	108	442	0	ENST00000265960.3:c.775T>A	p.Phe259Ile	p.F259I	ENST00000265960	NM_001006617.1	259	Ttc/Atc	6/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.236937411551481	2		442	629	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123499655	123499655	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060560-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	46	363	0	ENST00000371139.4:c.182C>T	p.Thr61Ile	p.T61I	ENST00000371139	NM_001114937.2	61	aCa/aTa	2/4	1	2	FACETS	0.781	0.658	0.917	0.781	0.658	0.917	CLONAL	1	TRUE	1	0.236937411551481	2		363	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0060561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	167	1097	6	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.489445773067826	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.489445773067826	1		1103	402	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0060561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	290	353	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.489445773067826	7	FACETS	0.988	0.936	1	0.988	0.936	1	CLONAL	4	TRUE	3	0.489445773067826	7		353	667	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467924	50467924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060561-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	110	553	0	ENST00000331340.3:c.1159G>A	p.Glu387Lys	p.E387K	ENST00000331340	NM_006060.4	387	Gag/Aag	8/8	0.489445773067826	7	FACETS	1	0.943	1	0.269	0.241	0.298	CLONAL	1	TRUE	3	0.489445773067826	7		553	930	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0060562-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	221	438	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.584732944085669	2		438	525	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0060563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	17	383	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.763	0.575	0.982	0.763	0.575	0.982	CLONAL	1	TRUE	1	0.342714738316063	2		383	130	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557362	187557362	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1223493108	NA	P-0060563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	25	428	0	ENST00000441802.2:c.4000C>T	p.Gln1334Ter	p.Q1334*	ENST00000441802	NM_005245.3	1334	Caa/Taa	6/27	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.342714738316063	2		428	133	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437901	52437901	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	28	499	0	ENST00000460680.1:c.1260del	p.Lys421ArgfsTer9	p.K421Rfs*9	ENST00000460680	NM_004656.3	420	ggG/gg	13/17	0.342714738316063	1	FACETS	0.801	0.647	0.973	0.801	0.647	0.973	CLONAL	1	TRUE	0	0.342714738316063	1		499	169	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628382	86628382	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	28	376	0	ENST00000274376.6:c.751G>T	p.Asp251Tyr	p.D251Y	ENST00000274376	NM_002890.2	251	Gac/Tac	3/25	0.288815249454451	3	FACETS	1	0.934	1	0.704	0.571	0.85	CLONAL	1	TRUE	1	0.342714738316063	3		376	136	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445276	29445276	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0060564-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	286	571	0	ENST00000389048.3:c.3451-2A>G		p.X1151_splice	ENST00000389048	NM_004304.4	1151			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		571	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0060565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	148	433	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.440406309739364	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.440406309739364	1		434	409	SUCCESS
APC	324	MSKCC	GRCh37	5	112154963	112154963	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660802	NA	P-0060565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	67	482	0	ENST00000257430.4:c.1234C>T	p.Gln412Ter	p.Q412*	ENST00000257430	NM_000038.5	412	Cag/Tag	10/16	1	2	FACETS	0.622	0.542	0.709	0.622	0.542	0.709	SUBCLONAL	1	TRUE	1	0.440406309739364	2		482	489	SUCCESS
APC	324	MSKCC	GRCh37	5	112164604	112164604	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554082118	NA	P-0060565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	98	428	0	ENST00000257430.4:c.1682del	p.Lys561ArgfsTer9	p.K561Rfs*9	ENST00000257430	NM_000038.5	560	Aaa/aa	14/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.440406309739364	2		428	352	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881681	111881684	+	frameshift_variant	Frame_Shift_Del	DEL	CTTG	CTTG	-	novel	NA	P-0060565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	143	505	0	ENST00000393256.3:c.360_363del	p.Cys121ArgfsTer13	p.C121Rfs*13	ENST00000393256	NM_006538.4	120	cCTTGc/cc	2/4	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.440406309739364	2		505	543	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537192	80537192	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	13	278	0	ENST00000286548.4:c.206A>T	p.Asp69Val	p.D69V	ENST00000286548	NM_002072.3	69	gAt/gTt	2/7	0.440406309739364	1	FACETS	0.218	0.155	0.295	0.218	0.155	0.295	SUBCLONAL	1	TRUE	0	0.440406309739364	1		278	211	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0060566-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	101	261	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.714441892148956	2		261	276	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443870	52443870	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060566-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	183	642	0	ENST00000460680.1:c.25G>T	p.Glu9Ter	p.E9*	ENST00000460680	NM_004656.3	9	Gag/Tag	1/17	0.714441892148956	1	FACETS	0.966	0.908	1	0.966	0.908	1	CLONAL	1	TRUE	0	0.714441892148956	1		642	341	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	110	475	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.356510852600897	2		475	465	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0060622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	101	445	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.969	0.868	1	0.969	0.868	1	CLONAL	1	TRUE	1	0.356510852600897	2		445	585	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249131	55249131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913431	NA	P-0060622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	171	620	0	ENST00000275493.2:c.2429G>A	p.Gly810Asp	p.G810D	ENST00000275493	NM_005228.3	810	gGc/gAc	20/28	0.356510852600897	3	FACETS	1	0.985	1	0.644	0.592	0.697	CLONAL	1	TRUE	1	0.356510852600897	3		620	878	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227927	55227927	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	83	461	0	ENST00000275493.2:c.1394G>T	p.Gly465Val	p.G465V	ENST00000275493	NM_005228.3	465	gGa/gTa	12/28	0.356510852600897	3	FACETS	0.836	0.738	0.941	0.418	0.369	0.471	CLONAL	1	TRUE	1	0.356510852600897	3		461	656	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589571	67589582	+	inframe_deletion	In_Frame_Del	DEL	TAGGGAAAAAAT	TAGGGAAAAAAT	-	novel	NA	P-0060622-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	67	262	0	ENST00000274335.5:c.1336_1347del	p.Gly446_Leu449del	p.G446_L449del	ENST00000274335		445	gTAGGGAAAAAATta/gta	10/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.356510852600897	2		262	284	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121472	108121472	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0060623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	34	458	0	ENST00000278616.4:c.1280T>A	p.Leu427Ter	p.L427*	ENST00000278616	NM_000051.3	427	tTa/tAa	10/63	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		458	668	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0060624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	206	473	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		473	638	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196158	108196158	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0060626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	241	270	0	ENST00000278616.4:c.6694G>T	p.Glu2232Ter	p.E2232*	ENST00000278616	NM_000051.3	2232	Gag/Tag	46/63	0.854738656350402	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.854738656350402	1		270	289	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59934593	59934593	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0060626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	202	230	0	ENST00000259008.2:c.206-1G>A		p.X69_splice	ENST00000259008	NM_032043.2	69			1	2	FACETS	0.953	0.892	1	0.953	0.892	1	CLONAL	1	TRUE	1	0.854738656350402	2		230	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0060627-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	215	610	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.377042976702833	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	0	0.377042976702833	2		610	568	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675589	30675589	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060627-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	81	703	0	ENST00000376406.3:c.2767G>T	p.Val923Leu	p.V923L	ENST00000376406	NM_014641.2	923	Gta/Tta	8/15	0.377042976702833	5	FACETS	0.783	0.689	0.885	0.261	0.229	0.295	SUBCLONAL	1	TRUE	2	0.377042976702833	5		703	859	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001145	150001145	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060627-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	129	513	0	ENST00000253339.5:c.2459A>G	p.His820Arg	p.H820R	ENST00000253339		820	cAt/cGt	4/7	0.336120284199414	3	FACETS	1	0.979	1	0.804	0.739	0.871	CLONAL	2	TRUE	0	0.377042976702833	3		513	337	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455081	50455081	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060627-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	131	453	0	ENST00000331340.3:c.628T>A	p.Tyr210Asn	p.Y210N	ENST00000331340	NM_006060.4	210	Tat/Aat	6/8	0.334148511395231	4	FACETS	0.957	0.873	1	0.957	0.873	1	CLONAL	2	TRUE	2	0.377042976702833	4		453	500	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992906	72992906	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060628-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	199	612	0	ENST00000268489.5:c.1139C>G	p.Pro380Arg	p.P380R	ENST00000268489	NM_006885.3	380	cCa/cGa	2/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.481335609643215	2		612	775	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7590139	7590779	+	splice_donor_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	TCTAGCGGAGCCGGGGGCTGCCTGGAAAGATCGCTCCAGGAAGGACAAAGGTCCGGAAGTTGTGGGACCTTAGCAGCTTGGGCTCCCCGGATCACCCCCAAATGATCATTTCGGAATGGAGCCCCAGTTTTCACTAGGATGCCATGGGCTCTAAAATATACAGCTATGAGTTCTCAATGTTTCGAGATCCAAAAGTCTCAGACCTCAATGCTTTGTGCATCTTTTATTTCAGGGATTCCCTACGCCCAGCACCGGGTGGATGTGCAAAGAAGTACGCTTTAGGCCGGCTCAAGGTTCCCCAAAGCTCCACTCCTCTGCCTAGGCGTTCAACTTTGAGTTCGGATGGTCCTAACATCCCCATCATCTACACCCAGGTCTCCCAACAATGCAACTCCTATGATGATCCCTCTAGCCAAGCTTCCATCCCACTCACCCCCAAACTCGCTAAGTCCCCACTGCCCCACCCCCAGCCCCAGCGATTTTCCCGAGCTGAAAATACACGGAGCCGAGAGCCCGTGACTCAGAGAGGACTCATCAAGTTCAGTCAGGAGCTTACCCAATCCAGGGAAGCGTGTCACCGTCGTGGAAAGCACGCTCCCAGCCCGAACGCAAAGTGTCCCCGGAGCCCAGCAGCTACCTGC	TCTAGCGGAGCCGGGGGCTGCCTGGAAAGATCGCTCCAGGAAGGACAAAGGTCCGGAAGTTGTGGGACCTTAGCAGCTTGGGCTCCCCGGATCACCCCCAAATGATCATTTCGGAATGGAGCCCCAGTTTTCACTAGGATGCCATGGGCTCTAAAATATACAGCTATGAGTTCTCAATGTTTCGAGATCCAAAAGTCTCAGACCTCAATGCTTTGTGCATCTTTTATTTCAGGGATTCCCTACGCCCAGCACCGGGTGGATGTGCAAAGAAGTACGCTTTAGGCCGGCTCAAGGTTCCCCAAAGCTCCACTCCTCTGCCTAGGCGTTCAACTTTGAGTTCGGATGGTCCTAACATCCCCATCATCTACACCCAGGTCTCCCAACAATGCAACTCCTATGATGATCCCTCTAGCCAAGCTTCCATCCCACTCACCCCCAAACTCGCTAAGTCCCCACTGCCCCACCCCCAGCCCCAGCGATTTTCCCGAGCTGAAAATACACGGAGCCGAGAGCCCGTGACTCAGAGAGGACTCATCAAGTTCAGTCAGGAGCTTACCCAATCCAGGGAAGCGTGTCACCGTCGTGGAAAGCACGCTCCCAGCCCGAACGCAAAGTGTCCCCGGAGCCCAGCAGCTACCTGC	-	novel	NA	P-0060628-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	158	664	0	ENST00000269305.4:c.-113_-29+556del		p.X38_splice	ENST00000269305	NM_001126112.2	38		1/11	0.460088388348114	1	FACETS	0.775	0.713	0.84	0.775	0.713	0.84	SUBCLONAL	1	TRUE	0	0.481335609643215	1		664	643	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	222	475	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.95	0.891	1	0.95	0.891	1	CLONAL	1	TRUE	1	0.803239857136704	2		475	582	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967049	25967052	+	frameshift_variant	Frame_Shift_Del	DEL	TCTG	TCTG	-	novel	NA	P-0060629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	89	628	0	ENST00000435504.4:c.2154_2157del	p.Asp718GlufsTer80	p.D718Efs*80	ENST00000435504		718	gaCAGA/ga	13/13	1	2	FACETS	0.24	0.212	0.27	0.24	0.212	0.27	SUBCLONAL	1	TRUE	1	0.803239857136704	2		628	923	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117632201	117632201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779401784	NA	P-0060629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	221	454	0	ENST00000368508.3:c.6215G>A	p.Arg2072Gln	p.R2072Q	ENST00000368508	NM_002944.2	2072	cGg/cAg	39/43	1	2	FACETS	0.967	0.907	1	0.967	0.907	1	CLONAL	1	TRUE	1	0.803239857136704	2		454	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576908	7576908	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	423	698	0	ENST00000269305.4:c.938del	p.Ser313ThrfsTer32	p.S313Tfs*32	ENST00000269305	NM_001126112.2	313	aGc/ac	9/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.803239857136704	2		698	1020	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579445	7579445	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0060629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	403	784	0	ENST00000269305.4:c.242del	p.Thr81AsnfsTer42	p.T81Nfs*42	ENST00000269305	NM_001126112.2	81	aCa/aa	4/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.803239857136704	2		784	950	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921591	39921591	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0060629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	57	229	0	ENST00000378444.4:c.4229C>G	p.Ser1410Ter	p.S1410*	ENST00000378444	NM_001123385.1	1410	tCa/tGa	10/15	1	1	FACETS	0.255	0.22	0.293	0.255	0.22	0.293	SUBCLONAL	1	TRUE	0	0.803239857136704	1		229	333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0060630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	38	810	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.259252550471371	1	FACETS	0.759	0.629	0.904	0.759	0.629	0.904	CLONAL	1	TRUE	0	0.259252550471371	1		810	336	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0060630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	38	356	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.922	0.765	1	0.922	0.765	1	CLONAL	1	TRUE	1	0.259252550471371	2		356	318	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0060630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	45	497	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.931	0.784	1	0.931	0.784	1	CLONAL	1	TRUE	1	0.259252550471371	2		497	373	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764312	39764312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751217612	NA	P-0060630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	36	476	2	ENST00000288319.7:c.800C>T	p.Thr267Met	p.T267M	ENST00000288319	NM_182918.3	267	aCg/aTg	7/10	1	2	FACETS	0.643	0.528	0.771	0.643	0.528	0.771	SUBCLONAL	1	TRUE	1	0.259252550471371	2		478	432	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359658	40359659	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0060630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	48	419	0	ENST00000293328.3:c.1994dup	p.Tyr665Ter	p.Y665*	ENST00000293328	NM_012448.3	665	tac/taAc	16/19	0.259252550471371	3	FACETS	0.994	0.842	1	0.497	0.421	0.58	CLONAL	1	TRUE	1	0.259252550471371	3		419	421	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794442	42794442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	39	629	0	ENST00000575354.2:c.1522C>T	p.Pro508Ser	p.P508S	ENST00000575354	NM_015125.3	508	Ccc/Tcc	10/20	1	2	FACETS	0.798	0.663	0.948	0.798	0.663	0.948	CLONAL	1	TRUE	1	0.259252550471371	2		629	377	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794971	242794971	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	38	588	0	ENST00000334409.5:c.238G>A	p.Ala80Thr	p.A80T	ENST00000334409	NM_005018.2	80	Gcc/Acc	2/5	1	2	FACETS	0.952	0.79	1	0.952	0.79	1	CLONAL	1	TRUE	1	0.259252550471371	2		588	308	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14026295	14026295	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	41	237	0	ENST00000405192.2:c.149T>A	p.Leu50Gln	p.L50Q	ENST00000405192	NM_001163147.1	50	cTa/cAa	4/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.259252550471371	2		237	217	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937470	76937470	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1557137763	NA	P-0060637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	13	384	0	ENST00000373344.5:c.3278G>T	p.Arg1093Met	p.R1093M	ENST00000373344	NM_000489.3	1093	aGg/aTg	9/35	1	2	FACETS	0.637	0.456	0.855	0.637	0.456	0.855	SUBCLONAL	1	TRUE	1	0.26	2		384	157	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609944	117609944	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs779954823	NA	P-0060637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	14	361	0	ENST00000368508.3:c.6755G>T	p.Cys2252Phe	p.C2252F	ENST00000368508	NM_002944.2	2252	tGt/tTt	43/43	1	2	FACETS	0.775	0.564	1	0.775	0.564	1	CLONAL	1	TRUE	1	0.26	2		361	139	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24133979	24133987	+	inframe_deletion	In_Frame_Del	DEL	TACAAGAGA	TACAAGAGA	-	novel	NA	P-0060637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	31	698	1	ENST00000263121.7:c.133_141del	p.Lys45_Tyr47del	p.K45_Y47del	ENST00000263121	NM_003073.3	44	TACAAGAGA/-	2/9	0.3	1	FACETS	0.443	0.358	0.54	0.443	0.358	0.54	SUBCLONAL	1	TRUE	0	0.26	1		699	468	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696432	47696432	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519968	NA	P-0060638-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	38	636	0	ENST00000347630.2:c.391T>G	p.Trp131Gly	p.W131G	ENST00000347630	NM_001007230.1	131	Tgg/Ggg	6/11	1	2	FACETS	0.951	0.785	1	0.951	0.785	1	CLONAL	1	TRUE	1	0.15	2		636	533	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061229	38061237	+	inframe_deletion	In_Frame_Del	DEL	ACATGTTGC	ACATGTTGC	-	novel	NA	P-0060638-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	25	961	0	ENST00000250448.2:c.752_760del	p.Gly251_Phe254delinsVal	p.G251_F254delinsV	ENST00000250448	NM_004496.3	251	gGCAACATGTtc/gtc	2/2	1	2	FACETS	0.32	0.25	0.4	0.32	0.25	0.4	SUBCLONAL	1	TRUE	1	0.15	2		961	1043	SUCCESS
AR	367	MSKCC	GRCh37	X	66931261	66931261	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060638-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	28	327	0	ENST00000374690.3:c.1903C>G	p.Leu635Val	p.L635V	ENST00000374690	NM_000044.3	635	Ctt/Gtt	4/8	0.3	2	FACETS	1	0.928	1	0.697	0.558	0.853	CLONAL	1	TRUE	0	0.15	2		327	268	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs587781433	NA	P-0060639-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	292	761	0	ENST00000269305.4:c.766A>C	p.Thr256Pro	p.T256P	ENST00000269305	NM_001126112.2	256	Aca/Cca	7/11	0.271679185439232	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.29	2		761	978	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645858	215645858	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060639-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	17	628	0	ENST00000260947.4:c.740C>G	p.Ser247Cys	p.S247C	ENST00000260947	NM_000465.2	247	tCt/tGt	4/11	1	2	FACETS	1	0.815	1	1	0.815	1	CLONAL	1	TRUE	1	0.29	2		628	107	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114905780	114905780	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060639-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	36	554	0	ENST00000543371.1:c.799C>G	p.Pro267Ala	p.P267A	ENST00000543371	NM_001198531.1	267	Cca/Gca	8/14	1	2	FACETS	0.739	0.609	0.884	0.739	0.609	0.884	SUBCLONAL	1	TRUE	1	0.29	2		554	336	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137190	64137191	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0060639-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1433	268	912	0	ENST00000334205.4:c.1623dup	p.Thr542HisfsTer95	p.T542Hfs*95	ENST00000334205	NM_003942.2	541	gac/gaCc	14/17	0.18244717258884	3	FACETS	1	0.988	1	0.622	0.581	0.664	CLONAL	1	TRUE	1	0.29	3		912	1701	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544760	86544760	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060639-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	197	901	0	ENST00000262426.4:c.585G>A	p.Met195Ile	p.M195I	ENST00000262426	NM_001451.2	195	atG/atA	1/2	0.29735503300662	1	FACETS	0.896	0.828	0.968	0.896	0.828	0.968	CLONAL	1	TRUE	0	0.29	1		901	1296	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103727	47103727	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060639-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	87	777	0	ENST00000409792.3:c.6219G>C	p.Glu2073Asp	p.E2073D	ENST00000409792	NM_014159.6	2073	gaG/gaC	14/21	0.283280941019681	2	FACETS	1	0.973	1	0.665	0.591	0.743	CLONAL	1	TRUE	0	0.29	2		777	451	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681909	30681909	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060639-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	191	785	0	ENST00000376406.3:c.188C>G	p.Ser63Cys	p.S63C	ENST00000376406	NM_014641.2	63	tCt/tGt	3/15	0.283280941019681	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.29	2		785	560	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0002218-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	344	484	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.503531672881656	15	FACETS	0.936	0.885	0.987	0.468	0.442	0.494	CLONAL	5	FALSE	5	0.503531672881656	15		484	1248	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0002218-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1546	217	611	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.503531672881656	15	FACETS	1	0.956	1	0.209	0.193	0.225	CLONAL	2	FALSE	5	0.503531672881656	15		612	1763	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121912651	NA	P-0002218-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	341	525	0	ENST00000269305.4:c.742C>G	p.Arg248Gly	p.R248G	ENST00000269305	NM_001126112.2	248	Cgg/Ggg	7/11	0.503531672881656	4	FACETS	0.952	0.914	0.988	0.952	0.914	0.988	CLONAL	4	FALSE	0	0.503531672881656	4		525	535	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941696	48941696	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002218-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	86	202	0	ENST00000267163.4:c.1010del	p.Leu337TrpfsTer12	p.L337Wfs*12	ENST00000267163	NM_000321.2	336	Ttt/tt	10/27	0.484669050953524	2	FACETS	0.894	0.81	0.979	0.894	0.81	0.979	CLONAL	2	FALSE	0	0.503531672881656	2		202	191	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873202	71873202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002218-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	111	543	0	ENST00000357731.5:c.992C>T	p.Ser331Phe	p.S331F	ENST00000357731	NM_173808.2	331	tCc/tTc	7/7	0.503531672881656	4	FACETS	1	0.919	1	0.256	0.23	0.283	CLONAL	1	FALSE	0	0.503531672881656	4		543	648	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652168	36652168	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002218-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	118	611	0	ENST00000244741.5:c.290C>T	p.Thr97Ile	p.T97I	ENST00000244741	NM_000389.4	97	aCc/aTc	2/3	0.503531672881656	4	FACETS	1	0.928	1	0.344	0.31	0.379	CLONAL	1	FALSE	1	0.503531672881656	4		611	683	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70412272	70412272	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002218-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	76	329	0	ENST00000373644.4:c.4382G>A	p.Gly1461Glu	p.G1461E	ENST00000373644	NM_030625.2	1461	gGa/gAa	6/12	0.503531672881656	6	FACETS	0.996	0.875	1	0.199	0.175	0.226	CLONAL	1	FALSE	1	0.503531672881656	6		329	608	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609618	81609618	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002218-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	288	719	0	ENST00000298171.2:c.1216A>T	p.Asn406Tyr	p.N406Y	ENST00000298171	NM_000369.2	406	Aac/Tac	10/10	0.503531672881656	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	FALSE	2	0.503531672881656	4		719	778	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0002982-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	108	323	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.517334014359375	3	FACETS	0.764	0.693	0.837	0.764	0.693	0.837	SUBCLONAL	2	TRUE	1	0.517334014359375	3		323	344	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557310	187557310	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002982-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	130	555	0	ENST00000441802.2:c.4052C>A	p.Pro1351Gln	p.P1351Q	ENST00000441802	NM_005245.3	1351	cCg/cAg	6/27	1	2	FACETS	0.938	0.855	1	0.938	0.855	1	CLONAL	1	TRUE	1	0.517334014359375	2		555	536	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370951	55370951	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002982-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	305	495	0	ENST00000297316.4:c.253C>G	p.Arg85Gly	p.R85G	ENST00000297316	NM_022454.3	85	Cgg/Ggg	1/2	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.517334014359375	2		495	879	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088681	27088682	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0003680-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	485	501	5	ENST00000324856.7:c.2296dup	p.Gln766ProfsTer51	p.Q766Pfs*51	ENST00000324856	NM_006015.4	764	tcc/tCcc	7/20	0.66262236383214	2	FACETS	0.986	0.955	1	0.986	0.955	1	CLONAL	2	TRUE	0	0.66262236383214	2		506	742	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975453	26975453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003680-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	203	462	0	ENST00000381527.3:c.1079C>T	p.Thr360Met	p.T360M	ENST00000381527	NM_001260.1	360	aCg/aTg	11/13	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.66262236383214	2		462	603	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0003680-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	276	738	0	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	1	2	FACETS	0.948	0.892	1	0.948	0.892	1	CLONAL	1	TRUE	1	0.66262236383214	2		738	879	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022967	31022968	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGGGA	novel	NA	P-0003680-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	245	620	1	ENST00000375687.4:c.2453_2457dup	p.Asp820TrpfsTer6	p.D820Wfs*6	ENST00000375687	NM_015338.5	818	gtg/gTGGGAtg	13/13	1	2	FACETS	0.919	0.861	0.977	0.919	0.861	0.977	CLONAL	1	TRUE	1	0.66262236383214	2		621	805	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0003680-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	266	585	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.983	0.925	1	0.983	0.925	1	CLONAL	1	TRUE	1	0.66262236383214	2		585	817	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434494	140434494	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1436193121	NA	P-0003680-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	226	442	1	ENST00000288602.6:c.2204G>A	p.Arg735Gln	p.R735Q	ENST00000288602	NM_004333.4	735	cGg/cAg	18/18	1	2	FACETS	0.966	0.904	1	0.966	0.904	1	CLONAL	1	TRUE	1	0.66262236383214	2		443	706	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005187-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	59	458	2	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.849	0.738	0.966	0.849	0.738	0.966	CLONAL	1	TRUE	1	0.562803789703186	2		460	247	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0005187-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	33	400	2	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.562803789703186	2		402	91	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005187-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	56	430	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.562803789703186	2		431	182	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0005187-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	28	429	4	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			0.310426145452409	1	FACETS	0.715	0.585	0.855	0.715	0.585	0.855	INDETERMINATE	1	TRUE	0	0.562803789703186	1		433	100	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0005187-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	76	428	0	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.916	0.811	1	0.916	0.811	1	CLONAL	1	TRUE	1	0.562803789703186	2		428	295	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0005187-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	51	595	0	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.813	0.699	0.935	0.813	0.699	0.935	CLONAL	1	TRUE	1	0.562803789703186	2		595	223	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0005187-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	41	314	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.562803789703186	2		314	133	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053574	37053574	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005187-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	32	294	0	ENST00000231790.2:c.661G>T	p.Gly221Ter	p.G221*	ENST00000231790	NM_000249.3	221	Gga/Tga	8/19	0.562803789703186	1	FACETS	0.997	0.838	1	0.997	0.838	1	CLONAL	1	TRUE	0	0.562803789703186	1		294	82	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411551	116411551	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0005187-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	80	260	0	ENST00000397752.3:c.2731-1G>C		p.X911_splice	ENST00000397752	NM_000245.2	911			0.562803789703186	9	FACETS	1	0.907	1	0.51	0.454	0.568	CLONAL	3	TRUE	3	0.562803789703186	9		260	276	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990723	7990723	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005187-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	40	304	0	ENST00000319144.4:c.38A>T	p.Asp13Val	p.D13V	ENST00000319144	NM_001139.2	13	gAc/gTc	1/15	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.562803789703186	2		304	117	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437784	52437803	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGTCCTTCTGGGACTCTT	GAGGTCCTTCTGGGACTCTT	-	novel	NA	P-0005187-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	60	385	0	ENST00000460680.1:c.1358_1377del	p.Lys453IlefsTer9	p.K453Ifs*9	ENST00000460680	NM_004656.3	453	aAAGAGTCCCAGAAGGACCTC/a	13/17	0.562803789703186	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.562803789703186	1		385	123	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163194	47163194	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005187-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	22	324	0	ENST00000409792.3:c.2932G>T	p.Glu978Ter	p.E978*	ENST00000409792	NM_014159.6	978	Gaa/Taa	3/21	0.562803789703186	1	FACETS	0.851	0.683	1	0.851	0.683	1	CLONAL	1	TRUE	0	0.562803789703186	1		324	66	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582134	189582135	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005187-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	31	403	0	ENST00000264731.3:c.699dup	p.Ala234SerfsTer2	p.A234Sfs*2	ENST00000264731	NM_003722.4	231	-/A	5/14	1	2	FACETS	0.383	0.31	0.464	0.383	0.31	0.464	SUBCLONAL	1	TRUE	1	0.562803789703186	2		403	288	SUCCESS
ATR	545	MSKCC	GRCh37	3	142232479	142232479	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005187-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	31	274	0	ENST00000350721.4:c.4505T>C	p.Val1502Ala	p.V1502A	ENST00000350721	NM_001184.3	1502	gTt/gCt	26/47	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.562803789703186	2		274	92	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681207	86681207	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1060503438	NA	P-0005187-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	31	189	0	ENST00000274376.6:c.2847+1G>A		p.X949_splice	ENST00000274376	NM_002890.2	949			0.51844828696901	3	FACETS	1	0.945	1	0.706	0.586	0.834	CLONAL	1	TRUE	1	0.562803789703186	3		189	100	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321215	65321215	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005187-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	18	390	0	ENST00000342505.4:c.1625G>A	p.Arg542His	p.R542H	ENST00000342505	NM_002227.2	542	cGc/cAc	11/25	1	2	FACETS	0.205	0.154	0.265	0.205	0.154	0.265	SUBCLONAL	1	TRUE	1	0.562803789703186	2		390	312	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3651005	3651005	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005187-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	24	289	0	ENST00000294008.3:c.1138G>T	p.Gly380Cys	p.G380C	ENST00000294008	NM_032444.2	380	Ggt/Tgt	5/15	1	2	FACETS	0.592	0.47	0.73	0.592	0.47	0.73	SUBCLONAL	1	TRUE	1	0.562803789703186	2		289	144	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60795887	60795887	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005187-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	16	411	0	ENST00000333681.4:c.691A>G	p.Thr231Ala	p.T231A	ENST00000333681		231	Acc/Gcc	3/3	0.328546716527827	3	FACETS	0.281	0.208	0.369	0.141	0.104	0.185	INDETERMINATE	1	TRUE	1	0.562803789703186	3		411	259	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7293878	7293878	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005187-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	14	660	0	ENST00000302850.5:c.25del	p.Ala9ArgfsTer56	p.A9Rfs*56	ENST00000302850	NM_000208.2	9	Gcg/cg	1/22	1	2	FACETS	0.224	0.162	0.299	0.224	0.162	0.299	SUBCLONAL	1	TRUE	1	0.562803789703186	2		660	222	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215570	36215570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005187-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	54	307	0	ENST00000222270.7:c.3367C>T	p.Arg1123Trp	p.R1123W	ENST00000222270	NM_014727.1	1123	Cgg/Tgg	9/37	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.562803789703186	2		307	152	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221690	22221690	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005187-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	26	391	0	ENST00000215832.6:c.41T>A	p.Val14Asp	p.V14D	ENST00000215832	NM_002745.4	14	gTc/gAc	1/9	1	2	FACETS	0.398	0.317	0.491	0.398	0.317	0.491	SUBCLONAL	1	TRUE	1	0.562803789703186	2		391	232	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361255	66361255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005187-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	33	342	0	ENST00000273854.3:c.917G>T	p.Arg306Ile	p.R306I	ENST00000273854	NM_004439.5	306	aGa/aTa	4/18	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.562803789703186	2		342	112	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630888	187630888	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005187-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	44	371	0	ENST00000441802.2:c.94C>A	p.Leu32Met	p.L32M	ENST00000441802	NM_005245.3	32	Ctg/Atg	2/27	1	2	FACETS	0.553	0.466	0.647	0.553	0.466	0.647	SUBCLONAL	1	TRUE	1	0.562803789703186	2		371	283	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554906	106554906	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005187-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	13	399	0	ENST00000369096.4:c.2023A>G	p.Lys675Glu	p.K675E	ENST00000369096	NM_001198.3	675	Aaa/Gaa	7/7	1	2	FACETS	0.189	0.135	0.256	0.189	0.135	0.256	SUBCLONAL	1	TRUE	1	0.562803789703186	2		399	244	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923427	36923427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005187-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	19	387	0	ENST00000358127.4:c.835G>A	p.Ala279Thr	p.A279T	ENST00000358127	NM_001280556.1	279	Gcc/Acc	7/10	1	2	FACETS	0.572	0.44	0.723	0.572	0.44	0.723	SUBCLONAL	1	TRUE	1	0.562803789703186	2		387	118	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760675	133760675	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005187-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	16	504	0	ENST00000318560.5:c.2998A>G	p.Thr1000Ala	p.T1000A	ENST00000318560	NM_005157.4	1000	Acc/Gcc	11/11	1	2	FACETS	0.334	0.248	0.436	0.334	0.248	0.436	SUBCLONAL	1	TRUE	1	0.562803789703186	2		504	170	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135804255	135804255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005187-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	55	475	0	ENST00000298552.3:c.5C>T	p.Ala2Val	p.A2V	ENST00000298552	NM_001162426.1	2	gCc/gTc	3/23	1	2	FACETS	0.832	0.719	0.951	0.832	0.719	0.951	CLONAL	1	TRUE	1	0.562803789703186	2		475	235	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0006479-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	103	185	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.589092464301	3	FACETS	0.967	0.883	1	0.967	0.883	1	CLONAL	2	TRUE	1	0.589092464301	3		185	234	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259420	16259420	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006479-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	249	489	0	ENST00000375759.3:c.6685G>T	p.Glu2229Ter	p.E2229*	ENST00000375759	NM_015001.2	2229	Gag/Tag	11/15	0.589092464301	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.589092464301	1		489	587	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111475	8111476	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006479-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	191	353	0	ENST00000346208.3:c.962dup	p.Thr322AspfsTer30	p.T322Dfs*30	ENST00000346208		321	cag/cAag	5/6	1	2	FACETS	0.926	0.86	0.995	0.926	0.86	0.995	CLONAL	1	TRUE	1	0.589092464301	2		353	700	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132912	64132912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200447389	NA	P-0006479-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	203	420	0	ENST00000334205.4:c.1046C>T	p.Pro349Leu	p.P349L	ENST00000334205	NM_003942.2	349	cCa/cTa	9/17	0.579129187055226	3	FACETS	0.899	0.834	0.967			1	CLONAL	1	TRUE	NA	0.589092464301	3		420	992	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123880896	123880896	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1161202109	NA	P-0006479-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	154	298	0	ENST00000330479.4:c.514C>G	p.Gln172Glu	p.Q172E	ENST00000330479	NM_020382.3	172	Caa/Gaa	5/9	1	2	FACETS	0.892	0.82	0.967	0.892	0.82	0.967	CLONAL	1	TRUE	1	0.589092464301	2		298	586	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941657	48941657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006479-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	44	132	0	ENST00000267163.4:c.967G>A	p.Glu323Lys	p.E323K	ENST00000267163	NM_000321.2	323	Gaa/Aaa	10/27	1	2	FACETS	0.807	0.686	0.937	0.807	0.686	0.937	CLONAL	1	TRUE	1	0.589092464301	2		132	185	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557688	95557688	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006479-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	140	278	0	ENST00000393063.1:c.5379G>C	p.Glu1793Asp	p.E1793D	ENST00000393063	NM_030621.3	1793	gaG/gaC	26/28	0.589092464301	3	FACETS	1	0.962	1	0.545	0.498	0.593	CLONAL	1	TRUE	1	0.589092464301	3		278	565	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50773816	50773816	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs779852315	NA	P-0006479-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	141	365	0	ENST00000307179.4:c.1357C>G	p.Pro453Ala	p.P453A	ENST00000307179		453	Cca/Gca	11/20	0.589092464301	1	FACETS	0.957	0.883	1	0.957	0.883	1	CLONAL	1	TRUE	0	0.589092464301	1		365	353	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100021	11100021	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006479-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	217	366	0	ENST00000358026.2:c.1147C>T	p.Gln383Ter	p.Q383*	ENST00000358026	NM_001128849.1	383	Cag/Tag	7/36	0.589092464301	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.589092464301	1		366	513	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727920	41727920	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138094666	NA	P-0006479-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	197	348	0	ENST00000301178.4:c.545C>T	p.Thr182Met	p.T182M	ENST00000301178	NM_021913.4	182	aCg/aTg	4/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.589092464301	2		348	644	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265618	152265618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006479-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	188	293	0	ENST00000206249.3:c.1071G>A	p.Met357Ile	p.M357I	ENST00000206249	NM_000125.3	357	atG/atA	4/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.589092464301	2		293	589	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0006479-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	184	291	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.513967451645123	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.589092464301	1		291	413	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412223	139412223	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006479-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	197	422	0	ENST00000277541.6:c.1422C>G	p.Phe474Leu	p.F474L	ENST00000277541	NM_017617.3	474	ttC/ttG	8/34	1	2	FACETS	0.915	0.85	0.982	0.915	0.85	0.982	CLONAL	1	TRUE	1	0.589092464301	2		422	731	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	116	228	0	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.951	0.867	1	0.951	0.867	1	CLONAL	1	TRUE	1	0.72	2		228	339	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	135	511	0	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	1	2	FACETS	0.775	0.709	0.843	0.775	0.709	0.843	SUBCLONAL	1	TRUE	1	0.72	2		511	484	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	110	408	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.79	0.716	0.866	0.79	0.716	0.866	SUBCLONAL	1	TRUE	1	0.72	2		408	387	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	124	336	1	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.728	0.663	0.796	0.728	0.663	0.796	SUBCLONAL	1	TRUE	1	0.72	2		337	473	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	200	308	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	0.955	0.909	0.999	1	0.995	1	CLONAL	2	TRUE	1	0.72	2		308	291	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	169	600	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.924	0.856	0.994	0.924	0.856	0.994	CLONAL	1	TRUE	1	0.72	2		600	508	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17743002	17743002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	21	490	1	ENST00000250003.3:c.910G>A	p.Ala304Thr	p.A304T	ENST00000250003	NM_002478.4	304	Gcc/Acc	3/3	1	2	FACETS	0.167	0.128	0.213	0.167	0.128	0.213	SUBCLONAL	1	TRUE	1	0.72	2		491	349	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680541	241680541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782207	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	100	292	0	ENST00000366560.3:c.208G>A	p.Ala70Thr	p.A70T	ENST00000366560	NM_000143.3	70	Gcc/Acc	2/10	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.72	2		292	261	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654642	67654642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	129	355	0	ENST00000264010.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000264010	NM_006565.3	377	Cgt/Tgt	6/12	1	2	FACETS	0.885	0.81	0.962	0.885	0.81	0.962	CLONAL	1	TRUE	1	0.72	2		355	405	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	177	514	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.72	2		514	418	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	118	421	9	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	1	2	FACETS	0.773	0.703	0.846	0.773	0.703	0.846	SUBCLONAL	1	TRUE	1	0.72	2		430	424	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563482	87563482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194954580	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	158	434	0	ENST00000277120.3:c.1870G>A	p.Val624Met	p.V624M	ENST00000277120		624	Gtg/Atg	16/19	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.72	2		434	433	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	179	478	9	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.72	2		487	471	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912188	114912188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	107	303	0	ENST00000543371.1:c.1258C>T	p.Arg420Trp	p.R420W	ENST00000543371	NM_001198531.1	420	Cgg/Tgg	11/14	1	2	FACETS	0.906	0.822	0.993	0.906	0.822	0.993	CLONAL	1	TRUE	1	0.72	2		303	328	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046958	128046958	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs772883177	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	66	395	6	ENST00000285398.2:c.777A>T	p.Glu259Asp	p.E259D	ENST00000285398	NM_000122.1	259	gaA/gaT	6/15	1	2	FACETS	0.417	0.363	0.475	0.417	0.363	0.475	SUBCLONAL	1	TRUE	1	0.72	2		401	440	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535336	66535336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349494063	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	36	468	0	ENST00000273854.3:c.125C>T	p.Thr42Met	p.T42M	ENST00000273854	NM_004439.5	42	aCg/aTg	1/18	1	2	FACETS	0.294	0.242	0.352	0.294	0.242	0.352	SUBCLONAL	1	TRUE	1	0.72	2		468	340	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46252810	46252810	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751452957	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	116	278	0	ENST00000371998.3:c.239G>A	p.Arg80His	p.R80H	ENST00000371998		80	cGt/cAt	4/23	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.72	2		278	295	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78914338	78914338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1484629953	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	170	386	0	ENST00000306801.3:c.2962C>T	p.Arg988Trp	p.R988W	ENST00000306801	NM_020761.2	988	Cgg/Tgg	25/34	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.72	2		386	424	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909464	50909464	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199576140	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	155	473	1	ENST00000440232.2:c.1268G>A	p.Arg423His	p.R423H	ENST00000440232	NM_002691.3	423	cGt/cAt	11/27	1	2	FACETS	0.93	0.859	1	0.93	0.859	1	CLONAL	1	TRUE	1	0.72	2		474	463	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56792470	56792470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	132	394	0	ENST00000308159.5:c.200G>A	p.Arg67Gln	p.R67Q	ENST00000308159	NM_014669.4	67	cGg/cAg	3/22	1	2	FACETS	0.914	0.838	0.993	0.914	0.838	0.993	CLONAL	1	TRUE	1	0.72	2		394	401	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426795	212426795	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	45	396	0	ENST00000342788.4:c.2320A>C	p.Ser774Arg	p.S774R	ENST00000342788	NM_005235.2	774	Agt/Cgt	20/28	1	2	FACETS	0.358	0.302	0.42	0.358	0.302	0.42	SUBCLONAL	1	TRUE	1	0.72	2		396	349	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800902	120800903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748469666	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	135	422	3	ENST00000257552.2:c.345dup	p.Leu116AlafsTer15	p.L116Afs*15	ENST00000257552	NM_002442.3	115	-/G	6/15	1	2	FACETS	0.821	0.751	0.892	0.821	0.751	0.892	CLONAL	1	TRUE	1	0.72	2		425	457	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475550	12475550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479145908	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	150	436	0	ENST00000287820.6:c.1424C>T	p.Thr475Met	p.T475M	ENST00000287820	NM_015869.4	475	aCg/aTg	7/7	1	2	FACETS	0.965	0.89	1	0.965	0.89	1	CLONAL	1	TRUE	1	0.72	2		436	432	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418670	49418670	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783698	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	148	415	0	ENST00000301067.7:c.15844C>T	p.Arg5282Ter	p.R5282*	ENST00000301067	NM_003482.3	5282	Cga/Tga	49/54	1	2	FACETS	0.882	0.812	0.954	0.882	0.812	0.954	CLONAL	1	TRUE	1	0.72	2		415	466	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562577	21562577	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395329857	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	118	400	2	ENST00000382592.4:c.1342C>T	p.Arg448Cys	p.R448C	ENST00000382592	NM_014572.2	448	Cgt/Tgt	4/8	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.72	2		402	322	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434732	49434732	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767236217	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	198	582	0	ENST00000301067.7:c.6821C>T	p.Ser2274Leu	p.S2274L	ENST00000301067	NM_003482.3	2274	tCg/tTg	31/54	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.72	2		582	523	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309141	137309141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767968089	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	135	492	0	ENST00000481739.1:c.748G>A	p.Val250Met	p.V250M	ENST00000481739	NM_002957.4	250	Gtg/Atg	5/10	1	2	FACETS	0.833	0.763	0.906	0.833	0.763	0.906	CLONAL	1	TRUE	1	0.72	2		492	450	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919936	50919936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763747258	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	132	489	0	ENST00000440232.2:c.3023G>A	p.Arg1008His	p.R1008H	ENST00000440232	NM_002691.3	1008	cGc/cAc	24/27	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.72	2		489	362	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273793	18273793	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs886041591	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	157	439	0	ENST00000222254.8:c.1126A>G	p.Lys376Glu	p.K376E	ENST00000222254	NM_005027.3	376	Aag/Gag	10/16	1	2	FACETS	0.876	0.808	0.945	0.876	0.808	0.945	CLONAL	1	TRUE	1	0.72	2		439	498	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605204	46605204	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1459319402	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	125	372	5	ENST00000263734.3:c.1421G>C	p.Ser474Thr	p.S474T	ENST00000263734	NM_001430.4	474	aGc/aCc	10/16	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.72	2		377	338	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281281	15281281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776163983	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	165	581	0	ENST00000263388.2:c.4975G>A	p.Val1659Ile	p.V1659I	ENST00000263388	NM_000435.2	1659	Gtc/Atc	27/33	1	2	FACETS	0.854	0.789	0.92	0.854	0.789	0.92	CLONAL	1	TRUE	1	0.72	2		581	537	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459840	149459840	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761316359	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	55	480	0	ENST00000286301.3:c.367G>A	p.Ala123Thr	p.A123T	ENST00000286301	NM_005211.3	123	Gca/Aca	4/22	1	2	FACETS	0.352	0.302	0.407	0.352	0.302	0.407	SUBCLONAL	1	TRUE	1	0.72	2		480	434	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944244	81944244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769887285	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	100	401	0	ENST00000359376.3:c.1853G>A	p.Arg618His	p.R618H	ENST00000359376	NM_002661.3	618	cGc/cAc	18/33	1	2	FACETS	0.644	0.579	0.713	0.644	0.579	0.713	SUBCLONAL	1	TRUE	1	0.72	2		401	431	SUCCESS
AR	367	MSKCC	GRCh37	X	66931429	66931429	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs978916227	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	132	497	0	ENST00000374690.3:c.2071G>A	p.Asp691Asn	p.D691N	ENST00000374690	NM_000044.3	691	Gac/Aac	4/8	1	2	FACETS	0.851	0.779	0.925	0.851	0.779	0.925	CLONAL	1	TRUE	1	0.72	2		497	431	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278406	39278406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775052125	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	90	246	0	ENST00000402219.2:c.743G>A	p.Arg248His	p.R248H	ENST00000402219	NM_005633.3	248	cGc/cAc	6/23	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.72	2		246	248	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610143	81610143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	35	506	1	ENST00000298171.2:c.1741G>A	p.Ala581Thr	p.A581T	ENST00000298171	NM_000369.2	581	Gca/Aca	10/10	1	2	FACETS	0.227	0.186	0.273	0.227	0.186	0.273	SUBCLONAL	1	TRUE	1	0.72	2		507	428	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105977	27105977	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	162	498	1	ENST00000324856.7:c.5588C>T	p.Thr1863Ile	p.T1863I	ENST00000324856	NM_006015.4	1863	aCa/aTa	20/20	1	2	FACETS	0.909	0.841	0.979	0.909	0.841	0.979	CLONAL	1	TRUE	1	0.72	2		499	495	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606403	93606403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs570398843	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	128	521	0	ENST00000375746.1:c.223G>A	p.Ala75Thr	p.A75T	ENST00000375746	NM_001174167.1	75	Gcc/Acc	2/14	1	2	FACETS	0.859	0.785	0.935	0.859	0.785	0.935	CLONAL	1	TRUE	1	0.72	2		521	414	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291542	15291542	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	61	436	0	ENST00000263388.2:c.3092G>A	p.Arg1031His	p.R1031H	ENST00000263388	NM_000435.2	1031	cGc/cAc	19/33	1	2	FACETS	0.446	0.386	0.51	0.446	0.386	0.51	SUBCLONAL	1	TRUE	1	0.72	2		436	380	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864451	151864451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs535118581	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	104	315	0	ENST00000262189.6:c.9530G>A	p.Arg3177His	p.R3177H	ENST00000262189	NM_170606.2	3177	cGt/cAt	42/59	1	2	FACETS	0.9	0.816	0.987	0.9	0.816	0.987	CLONAL	1	TRUE	1	0.72	2		315	321	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188944	11188944	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	157	382	0	ENST00000361445.4:c.5779del	p.Val1927Ter	p.V1927*	ENST00000361445	NM_004958.3	1927	Gtg/tg	41/58	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.72	2		382	435	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17354279	17354279	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1553177676	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	134	352	0	ENST00000375499.3:c.505C>T	p.Gln169Ter	p.Q169*	ENST00000375499	NM_003000.2	169	Cag/Tag	5/8	1	2	FACETS	0.964	0.886	1	0.964	0.886	1	CLONAL	1	TRUE	1	0.72	2		352	386	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28600631	28600631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	142	390	0	ENST00000253063.3:c.982C>T	p.Arg328Trp	p.R328W	ENST00000253063	NM_031459.4	328	Cgg/Tgg	7/10	1	2	FACETS	0.996	0.918	1	0.996	0.918	1	CLONAL	1	TRUE	1	0.72	2		390	396	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532600	46532600	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	137	335	0	ENST00000262741.5:c.478G>C	p.Val160Leu	p.V160L	ENST00000262741	NM_003629.3	160	Gtg/Ctg	4/10	1	2	FACETS	0.991	0.912	1	0.991	0.912	1	CLONAL	1	TRUE	1	0.72	2		335	384	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63661988	63661988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	29	434	0	ENST00000279873.7:c.92G>A	p.Gly31Asp	p.G31D	ENST00000279873	NM_032199.2	31	gGc/gAc	2/10	1	2	FACETS	0.182	0.146	0.224	0.182	0.146	0.224	SUBCLONAL	1	TRUE	1	0.72	2		434	442	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70432744	70432744	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	39	393	0	ENST00000373644.4:c.4766A>C	p.Lys1589Thr	p.K1589T	ENST00000373644	NM_030625.2	1589	aAg/aCg	8/12	1	2	FACETS	0.303	0.251	0.36	0.303	0.251	0.36	SUBCLONAL	1	TRUE	1	0.72	2		393	358	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456680	32456680	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	116	454	0	ENST00000332351.3:c.212C>A	p.Ser71Tyr	p.S71Y	ENST00000332351	NM_024426.4	71	tCc/tAc	1/10	1	2	FACETS	0.991	0.905	1	0.991	0.905	1	CLONAL	1	TRUE	1	0.72	2		454	325	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575506	64575506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143329068	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	159	539	0	ENST00000312049.6:c.511C>T	p.Arg171Trp	p.R171W	ENST00000312049	NM_130799.2	171	Cgg/Tgg	3/10	1	2	FACETS	0.966	0.894	1	0.966	0.894	1	CLONAL	1	TRUE	1	0.72	2		539	457	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202236	108202236	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	74	322	0	ENST00000278616.4:c.7581G>T	p.Met2527Ile	p.M2527I	ENST00000278616	NM_000051.3	2527	atG/atT	51/63	1	2	FACETS	0.878	0.781	0.98	0.878	0.781	0.98	CLONAL	1	TRUE	1	0.72	2		322	234	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913527	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	81	296	0	ENST00000311936.3:c.436G>C	p.Ala146Pro	p.A146P	ENST00000311936	NM_004985.3	146	Gca/Cca	4/5	1	2	FACETS	0.879	0.785	0.976	0.879	0.785	0.976	CLONAL	1	TRUE	1	0.72	2		296	256	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398212	25398212	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	19	226	0	ENST00000311936.3:c.107T>C	p.Ile36Thr	p.I36T	ENST00000311936	NM_004985.3	36	aTa/aCa	2/5	1	2	FACETS	0.265	0.202	0.339	0.265	0.202	0.339	SUBCLONAL	1	TRUE	1	0.72	2		226	199	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779346	3779346	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	72	494	0	ENST00000262367.5:c.5702A>G	p.Gln1901Arg	p.Q1901R	ENST00000262367	NM_004380.2	1901	cAg/cGg	31/31	1	2	FACETS	0.473	0.415	0.535	0.473	0.415	0.535	SUBCLONAL	1	TRUE	1	0.72	2		494	423	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646255	23646255	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	131	419	0	ENST00000261584.4:c.1612A>T	p.Ile538Phe	p.I538F	ENST00000261584	NM_024675.3	538	Att/Ttt	4/13	1	2	FACETS	0.809	0.739	0.88	0.809	0.739	0.88	CLONAL	1	TRUE	1	0.72	2		419	450	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857439	68857439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376854556	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	138	355	0	ENST00000261769.5:c.2074G>A	p.Ala692Thr	p.A692T	ENST00000261769	NM_004360.3	692	Gct/Act	13/16	1	2	FACETS	0.966	0.888	1	0.966	0.888	1	CLONAL	1	TRUE	1	0.72	2		355	397	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946282	81946282	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1468421212	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	140	416	0	ENST00000359376.3:c.2015G>A	p.Arg672Gln	p.R672Q	ENST00000359376	NM_002661.3	672	cGg/cAg	19/33	1	2	FACETS	0.926	0.851	1	0.926	0.851	1	CLONAL	1	TRUE	1	0.72	2		416	420	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560080	29560080	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	62	413	1	ENST00000356175.3:c.3557T>A	p.Ile1186Asn	p.I1186N	ENST00000356175	NM_000267.3	1186	aTc/aAc	27/57	1	2	FACETS	0.361	0.312	0.414	0.361	0.312	0.414	SUBCLONAL	1	TRUE	1	0.72	2		414	477	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654658	29654658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	25	409	0	ENST00000356175.3:c.5347G>A	p.Ala1783Thr	p.A1783T	ENST00000356175	NM_000267.3	1783	Gca/Aca	37/57	1	2	FACETS	0.14	0.11	0.175	0.14	0.11	0.175	SUBCLONAL	1	TRUE	1	0.72	2		409	495	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246844	10246844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1441106688	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	153	493	0	ENST00000340748.4:c.4561G>A	p.Gly1521Ser	p.G1521S	ENST00000340748		1521	Ggc/Agc	37/40	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.72	2		493	405	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297982	15297982	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764148985	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	127	483	0	ENST00000263388.2:c.1774C>T	p.Arg592Cys	p.R592C	ENST00000263388	NM_000435.2	592	Cgc/Tgc	11/33	1	2	FACETS	0.878	0.802	0.955	0.878	0.802	0.955	CLONAL	1	TRUE	1	0.72	2		483	402	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213298	36213298	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	62	439	0	ENST00000222270.7:c.2495C>A	p.Ala832Asp	p.A832D	ENST00000222270	NM_014727.1	832	gCt/gAt	4/37	1	2	FACETS	0.406	0.352	0.465	0.406	0.352	0.465	SUBCLONAL	1	TRUE	1	0.72	2		439	424	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868196	45868196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	149	480	0	ENST00000391945.4:c.494G>A	p.Gly165Glu	p.G165E	ENST00000391945	NM_000400.3	165	gGg/gAg	7/23	1	2	FACETS	0.956	0.882	1	0.956	0.882	1	CLONAL	1	TRUE	1	0.72	2		480	433	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470005	25470005	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1308281604	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	153	408	0	ENST00000264709.3:c.1037C>T	p.Pro346Leu	p.P346L	ENST00000264709	NM_175629.2	346	cCg/cTg	9/23	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.72	2		408	420	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033892	48034183	+	splice_acceptor_variant,coding_sequence_variant,3_prime_UTR_variant,intron_variant	Splice_Site	DEL	TTTTTTTTTTTTTTTTTAATTTTAAGGGAAGTTTGCCTGGCTAGTGAAAGGTCAACTGTAGATGCTGAAGCTGTCCATAAATTGCTGACTTTGATTAAGGAATTATAGACTGACTACATTGGAAGCTTTGAGTTGACTTCTGACAAAGGTGGTAAATTCAGACAACATTATGATCTAATAAACTTTATTTTTTAAAAATGACCATTTTTCCATTTTCTTTCTAGGAAATTAAACCCTTTTAATTCTTATCTACCTTCTACATAATGGTTATTGAATACTCCACAATATATTA	TTTTTTTTTTTTTTTTTAATTTTAAGGGAAGTTTGCCTGGCTAGTGAAAGGTCAACTGTAGATGCTGAAGCTGTCCATAAATTGCTGACTTTGATTAAGGAATTATAGACTGACTACATTGGAAGCTTTGAGTTGACTTCTGACAAAGGTGGTAAATTCAGACAACATTATGATCTAATAAACTTTATTTTTTAAAAATGACCATTTTTCCATTTTCTTTCTAGGAAATTAAACCCTTTTAATTCTTATCTACCTTCTACATAATGGTTATTGAATACTCCACAATATATTA	-	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	66	246	14	ENST00000234420.5:c.4002-26_*184del		p.X1334_splice	ENST00000234420	NM_000179.2	1334		10/10	1	2	FACETS	0.869	0.766	0.976	0.869	0.766	0.976	CLONAL	1	TRUE	1	0.72	2		260	211	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61720185	61720185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	95	269	0	ENST00000401558.2:c.1249C>T	p.Arg417Cys	p.R417C	ENST00000401558	NM_003400.3	417	Cgt/Tgt	13/25	1	2	FACETS	0.929	0.839	1	0.929	0.839	1	CLONAL	1	TRUE	1	0.72	2		269	284	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131212	202131212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	40	380	0	ENST00000358485.4:c.180G>A	p.Met60Ile	p.M60I	ENST00000358485	NM_001080125.1	60	atG/atA	2/9	1	2	FACETS	0.3	0.25	0.356	0.3	0.25	0.356	SUBCLONAL	1	TRUE	1	0.72	2		380	370	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215674148	215674148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	33	362	0	ENST00000260947.4:c.146G>A	p.Arg49His	p.R49H	ENST00000260947	NM_000465.2	49	cGc/cAc	1/11	1	2	FACETS	0.295	0.24	0.356	0.295	0.24	0.356	SUBCLONAL	1	TRUE	1	0.72	2		362	311	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21344726	21344726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1271199870	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	48	431	0	ENST00000215739.8:c.703G>A	p.Val235Met	p.V235M	ENST00000215739	NM_006767.3	235	Gtg/Atg	8/21	1	2	FACETS	0.294	0.249	0.344	0.294	0.249	0.344	SUBCLONAL	1	TRUE	1	0.72	2		431	453	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37622768	37622768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	152	408	0	ENST00000249071.6:c.524C>T	p.Ala175Val	p.A175V	ENST00000249071	NM_002872.4	175	gCc/gTc	6/7	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.72	2		408	395	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516911	187516911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	130	367	0	ENST00000441802.2:c.13070G>A	p.Ser4357Asn	p.S4357N	ENST00000441802	NM_005245.3	4357	aGt/aAt	26/27	1	2	FACETS	0.998	0.916	1	0.998	0.916	1	CLONAL	1	TRUE	1	0.72	2		367	362	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295650	1295650	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	174	587	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.72	2		587	432	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576754	67576754	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	81	308	0	ENST00000274335.5:c.837-1G>A		p.X279_splice	ENST00000274335		279			1	2	FACETS	0.941	0.843	1	0.941	0.843	1	CLONAL	1	TRUE	1	0.72	2		308	239	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502605	149502605	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	166	426	0	ENST00000261799.4:c.2183G>T	p.Ser728Ile	p.S728I	ENST00000261799	NM_002609.3	728	aGc/aTc	15/23	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.72	2		426	430	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021080	26021080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	107	569	0	ENST00000357647.3:c.363G>A	p.Met121Ile	p.M121I	ENST00000357647	NM_003529.2	121	atG/atA	1/1	0.295433111668563	2	FACETS	0.512	0.461	0.567	0.256	0.23	0.284	INDETERMINATE	1	TRUE	0	0.72	2		569	580	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911120	29911120	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs41557212	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	152	432	0	ENST00000376809.5:c.419A>C	p.Asp140Ala	p.D140A	ENST00000376809	NM_002116.7	140	gAc/gCc	3/8	0.295433111668563	2	FACETS	0.957	0.884	1	0.479	0.442	0.517	INDETERMINATE	1	TRUE	0	0.72	2		432	441	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818276	32818276	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777930194	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	54	373	0	ENST00000354258.4:c.1249C>T	p.Arg417Trp	p.R417W	ENST00000354258	NM_000593.5	417	Cgg/Tgg	5/11	1	2	FACETS	0.356	0.305	0.412	0.356	0.305	0.412	SUBCLONAL	1	TRUE	1	0.72	2		373	421	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334706	81334706	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	101	323	0	ENST00000222390.5:c.2010G>T	p.Glu670Asp	p.E670D	ENST00000222390	NM_000601.4	670	gaG/gaT	17/18	1	2	FACETS	0.951	0.862	1	0.951	0.862	1	CLONAL	1	TRUE	1	0.72	2		323	295	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002686	37002686	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	173	499	0	ENST00000358127.4:c.563C>T	p.Thr188Met	p.T188M	ENST00000358127	NM_001280556.1	188	aCg/aTg	5/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.72	2		499	415	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139563073	139563073	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	69	488	0	ENST00000308874.7:c.145T>C	p.Tyr49His	p.Y49H	ENST00000308874		49	Tac/Cac	4/10	1	2	FACETS	0.48	0.42	0.545	0.48	0.42	0.545	SUBCLONAL	1	TRUE	1	0.72	2		488	399	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1331520	1331520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773172070	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	100	342	0	ENST00000400841.2:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000400841		3	cGg/cAg	1/6	1	2	FACETS	0.803	0.724	0.885	0.803	0.724	0.885	CLONAL	1	TRUE	1	0.72	2		342	346	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039284	47039284	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	43	471	0	ENST00000377604.3:c.907A>C	p.Ile303Leu	p.I303L	ENST00000377604	NM_001204468.1	303	Att/Ctt	10/24	1	2	FACETS	0.269	0.225	0.318	0.269	0.225	0.318	SUBCLONAL	1	TRUE	1	0.72	2		471	444	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342717	70342717	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	132	368	0	ENST00000374080.3:c.1478G>T	p.Gly493Val	p.G493V	ENST00000374080		493	gGg/gTg	10/45	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.72	2		368	352	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349988	70349988	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006863-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	178	474	0	ENST00000374080.3:c.3971T>G	p.Ile1324Ser	p.I1324S	ENST00000374080		1324	aTt/aGt	28/45	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.72	2		474	456	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652146	36652146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008301-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	57	668	1	ENST00000244741.5:c.268G>A	p.Gly90Arg	p.G90R	ENST00000244741	NM_000389.4	90	Gga/Aga	2/3	1	2	FACETS	0.901	0.776	1	0.901	0.776	1	CLONAL	1	TRUE	1	0.343908380870335	2		669	368	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022774	31022790	+	frameshift_variant	Frame_Shift_Del	DEL	CACTGGGGACCAGCCAT	CACTGGGGACCAGCCAT	-	novel	NA	P-0008301-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	68	712	0	ENST00000375687.4:c.2259_2275del	p.Thr754ProfsTer14	p.T754Pfs*14	ENST00000375687	NM_015338.5	753	ccCACTGGGGACCAGCCATgc/ccgc	13/13	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.343908380870335	2		712	353	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696294	52696294	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0008301-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	62	507	0	ENST00000394830.3:c.385-2A>T		p.X129_splice	ENST00000394830	NM_018313.4	129			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.343908380870335	2		507	300	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295257	1295257	+	upstream_gene_variant	5'Flank	SNP	C	C	T	rs1405879643	NA	P-0008301-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	67	509	0				ENST00000310581	NM_198253.2	-/1132			0.343908380870335	3	FACETS	0.924	0.813	1	0.924	0.813	1	CLONAL	2	TRUE	1	0.343908380870335	3		509	247	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946287	2946287	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs969649975	NA	P-0008301-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	58	620	0	ENST00000396946.4:c.3450C>A	p.Asp1150Glu	p.D1150E	ENST00000396946	NM_032415.4	1150	gaC/gaA	25/25	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.343908380870335	2		620	327	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879214	151879214	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008301-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	39	666	0	ENST00000262189.6:c.5731G>T	p.Gly1911Cys	p.G1911C	ENST00000262189	NM_170606.2	1911	Ggc/Tgc	36/59	0.343908380870335	1	FACETS	0.549	0.456	0.652	0.549	0.456	0.652	SUBCLONAL	1	TRUE	0	0.343908380870335	1		666	342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579331	7579331	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009989-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	207	496	1	ENST00000269305.4:c.356C>G	p.Ala119Gly	p.A119G	ENST00000269305	NM_001126112.2	119	gCc/gGc	4/11	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.596399108693591	2		497	567	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216555	108216555	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009989-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	165	224	0	ENST00000278616.4:c.8504G>T	p.Cys2835Phe	p.C2835F	ENST00000278616	NM_000051.3	2835	tGc/tTc	58/63	0.128298710502505	4	FACETS	0.806	0.745	0.869	0.806	0.745	0.869	INDETERMINATE	2	TRUE	2	0.596399108693591	4		224	548	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217873	7217873	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009989-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	174	204	0	ENST00000380728.2:c.138del	p.Glu47AsnfsTer16	p.E47Nfs*16	ENST00000380728		46	gaA/ga	3/11	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.596399108693591	2		204	492	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108244	8108244	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009989-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	101	489	0	ENST00000585124.1:c.980T>C	p.Val327Ala	p.V327A	ENST00000585124	NM_004217.3	327	gTc/gCc	9/9	0.250471746425779	4	FACETS	0.711	0.636	0.792			1	INDETERMINATE	1	TRUE	NA	0.596399108693591	4		489	760	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439924	56439924	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009989-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	122	467	0	ENST00000407977.2:c.668G>T	p.Arg223Leu	p.R223L	ENST00000407977		223	cGc/cTc	6/10	1	2	FACETS	0.551	0.498	0.606	0.551	0.498	0.606	SUBCLONAL	1	TRUE	1	0.596399108693591	2		467	743	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249074	55249074	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009989-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	473	564	0	ENST00000275493.2:c.2372A>T	p.Gln791Leu	p.Q791L	ENST00000275493	NM_005228.3	791	cAg/cTg	20/28	0.596399108693591	3	FACETS	0.93	0.892	0.969	0.93	0.892	0.969	CLONAL	2	TRUE	1	0.596399108693591	3		564	1107	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010213-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	438	121	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.848912802275474	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	4	TRUE	0	0.84753970952123	4		121	465	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876425	35876425	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010213-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	169	702	0	ENST00000303115.3:c.1217T>G	p.Leu406Arg	p.L406R	ENST00000303115	NM_002185.3	406	cTt/cGt	8/8	0.84753970952123	7	FACETS	1	0.971	1	0.225	0.206	0.245	CLONAL	1	TRUE	2	0.84753970952123	7		702	1105	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340112	116340112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs780802614	NA	P-0010213-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	152	480	0	ENST00000397752.3:c.974C>A	p.Pro325His	p.P325H	ENST00000397752	NM_000245.2	325	cCt/cAt	2/21	0.491030059023114	3	FACETS	1	0.989	1	0.703	0.652	0.755	INDETERMINATE	1	TRUE	1	0.84753970952123	3		480	363	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037492	12037492	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010213-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	174	576	0	ENST00000396373.4:c.1123G>T	p.Gly375Ter	p.G375*	ENST00000396373	NM_001987.4	375	Gga/Tga	6/8	0.848912802275474	5	FACETS	1	0.984	1	0.25	0.23	0.27	CLONAL	1	TRUE	0	0.84753970952123	5		576	747	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623545	28623545	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010213-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	127	529	0	ENST00000241453.7:c.1012C>A	p.Gln338Lys	p.Q338K	ENST00000241453	NM_004119.2	338	Caa/Aaa	8/24	0.848912802275474	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.84753970952123	1		529	168	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28979946	28979946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764045713	NA	P-0010213-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	117	424	0	ENST00000282397.4:c.1522C>T	p.Arg508Cys	p.R508C	ENST00000282397	NM_002019.4	508	Cgc/Tgc	11/30	0.273061770375499	1	FACETS	0.666	0.614	0.718	0.666	0.614	0.718	INDETERMINATE	1	TRUE	0	0.84753970952123	1		424	239	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352598	68352598	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010213-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	147	367	0	ENST00000487270.1:c.465A>G	p.Ile155Met	p.I155M	ENST00000487270	NM_133509.3	155	atA/atG	6/11	0.836424326808704	3	FACETS	1	0.959	1	0.532	0.49	0.576	CLONAL	1	TRUE	1	0.84753970952123	3		367	464	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993600	72993600	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010213-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	220	768	0	ENST00000268489.5:c.445C>T	p.Gln149Ter	p.Q149*	ENST00000268489	NM_006885.3	149	Cag/Tag	2/10	0.396443953985553	3	FACETS	0.936	0.886	0.985	0.936	0.886	0.985	INDETERMINATE	2	TRUE	1	0.84753970952123	3		768	395	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376659	31376659	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0010213-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	103	429	0	ENST00000328111.2:c.655-1G>T		p.X219_splice	ENST00000328111	NM_006892.3	219			0.848912802275474	3	FACETS	1	0.928	1	0.515	0.466	0.566	CLONAL	1	TRUE	1	0.84753970952123	3		429	336	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740174	162740174	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010213-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	248	601	0	ENST00000367921.3:c.1377del	p.Ser460HisfsTer28	p.S460Hfs*28	ENST00000367921	NM_006182.2	459	tCc/tc	12/18	0.672289045689134	4	FACETS	0.943	0.89	0.997	0.943	0.89	0.997	CLONAL	2	TRUE	2	0.84753970952123	4		601	573	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937163	39937164	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0010213-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	95	504	0	ENST00000378444.4:c.19dup	p.Leu7ProfsTer29	p.L7Pfs*29	ENST00000378444	NM_001123385.1	7	ctg/cCtg	2/15	NA	2	FACETS	0.938	0.851	1			1	INDETERMINATE	1	TRUE	NA	0.84753970952123	2		504	239	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514974	148514974	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010213-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	72	529	0	ENST00000320356.2:c.1235C>T	p.Ser412Phe	p.S412F	ENST00000320356	NM_004456.4	412	tCc/tTc	10/20	0.491030059023114	3	FACETS	0.576	0.505	0.652	0.288	0.252	0.326	INDETERMINATE	1	TRUE	1	0.84753970952123	3		529	420	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202594	67202594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010213-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	70	800	0	ENST00000312629.5:c.1403C>T	p.Ser468Leu	p.S468L	ENST00000312629	NM_003952.2	468	tCa/tTa	15/15	0.836424326808704	3	FACETS	0.436	0.381	0.496	0.218	0.19	0.248	SUBCLONAL	1	TRUE	1	0.84753970952123	3		800	539	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376011	118376011	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010213-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	158	678	0	ENST00000534358.1:c.9404C>T	p.Thr3135Ile	p.T3135I	ENST00000534358	NM_005933.3	3135	aCc/aTc	27/36	0.837395357332813	3	FACETS	1	0.932	1	0.506	0.466	0.546	CLONAL	1	TRUE	1	0.84753970952123	3		678	525	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628657	21628657	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010213-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	367	495	0	ENST00000421138.2:c.1051G>T	p.Glu351Ter	p.E351*	ENST00000421138		351	Gaa/Taa	10/16	0.848912802275474	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.84753970952123	3		495	397	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046565	30046565	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010213-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	124	548	0	ENST00000331968.5:c.2618C>G	p.Ala873Gly	p.A873G	ENST00000331968	NM_002742.2	873	gCa/gGa	18/18	0.836424326808704	3	FACETS	1	0.93	1	0.511	0.466	0.557	CLONAL	1	TRUE	1	0.84753970952123	3		548	408	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37680959	37680960	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0010213-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	123	576	0	ENST00000447079.4:c.3128_3129delinsTT	p.Trp1043Phe	p.W1043F	ENST00000447079	NM_015083.1	1043	tGG/tTT	12/14	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.84753970952123	2		576	289	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40879651	40879651	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0010213-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	138	411	0	ENST00000428826.2:c.246+2T>C		p.X82_splice	ENST00000428826		82			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.84753970952123	2		411	274	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466813	57466813	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010213-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	43	192	0	ENST00000371085.3:c.32A>G	p.Asp11Gly	p.D11G	ENST00000371085	NM_000516.4	11	gAc/gGc	1/13	0.837395357332813	3	FACETS	0.87	0.74	1	0.435	0.37	0.505	CLONAL	1	TRUE	1	0.84753970952123	3		192	166	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172275	38172275	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010213-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	311	501	0	ENST00000317025.8:c.2132G>T	p.Gly711Val	p.G711V	ENST00000317025	NM_023034.1	711	gGt/gTt	12/24	0.848912802275474	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.84753970952123	3		501	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579464	7579465	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	A	novel	NA	P-0010213-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	500	789	0	ENST00000269305.4:c.222_223delinsT	p.Pro75LeufsTer48	p.P75Lfs*48	ENST00000269305	NM_001126112.2	74	gcCCct/gcTct	4/11	0.848912802275474	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.84753970952123	3		789	550	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0010599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	252	619	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.281907551621846	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	0	0.294144796754542	3		619	621	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0010599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	205	449	1	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	0.199921418053453	4	FACETS	0.919	0.857	0.983	1	0.99	1	CLONAL	3	TRUE	2	0.294144796754542	4		450	654	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211906	36211906	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	254	580	0	ENST00000222270.7:c.1659del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	553	Aaa/aa	3/37	0.294650419517162	5	FACETS	0.885	0.833	0.938	1	0.988	1	CLONAL	4	TRUE	2	0.294144796754542	5		580	703	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88428945	88428945	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	26	215	0	ENST00000360948.2:c.2155G>T	p.Asp719Tyr	p.D719Y	ENST00000360948	NM_001012338.2	719	Gat/Tat	17/19	0.294144796754542	5	FACETS	1	0.89	1	0.772	0.623	0.935	CLONAL	2	TRUE	2	0.294144796754542	5		215	110	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196085	108196085	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	47	401	0	ENST00000278616.4:c.6621A>C	p.Lys2207Asn	p.K2207N	ENST00000278616	NM_000051.3	2207	aaA/aaC	46/63	0.184742660739073	4	FACETS	0.755	0.641	0.878	0.503	0.427	0.585	SUBCLONAL	2	TRUE	1	0.294144796754542	4		401	274	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246525	46246525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	234	533	0	ENST00000334344.6:c.4619C>T	p.Thr1540Ile	p.T1540I	ENST00000334344	NM_152641.2	1540	aCa/aTa	15/21	0.294144796754542	6	FACETS	0.929	0.875	0.984	0.929	0.875	0.984	CLONAL	5	TRUE	1	0.294144796754542	6		533	544	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281764	49281764	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	108	575	0	ENST00000282018.3:c.811T>G	p.Leu271Val	p.L271V	ENST00000282018	NM_020377.2	271	Ttg/Gtg	1/1	0.169738119623024	4	FACETS	0.962	0.867	1	0.962	0.867	1	INDETERMINATE	2	TRUE	2	0.294144796754542	4		575	494	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492696	56492696	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	205	435	0	ENST00000407977.2:c.243del	p.Lys81AsnfsTer2	p.K81Nfs*2	ENST00000407977		81	aaA/aa	2/10	0.294144796754542	5	FACETS	1	0.954	1	1	0.954	1	CLONAL	5	TRUE	0	0.294144796754542	5		435	396	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681635	30681635	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	108	592	0	ENST00000376406.3:c.462G>T	p.Gln154His	p.Q154H	ENST00000376406	NM_014641.2	154	caG/caT	3/15	0.294144796754542	6	FACETS	0.753	0.676	0.835	0.502	0.451	0.557	SUBCLONAL	2	TRUE	3	0.294144796754542	6		592	774	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271271	38271271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776189467	NA	P-0010599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	232	693	0	ENST00000425967.3:c.2437G>A	p.Asp813Asn	p.D813N	ENST00000425967	NM_001174067.1	813	Gac/Aac	19/19	0.294144796754542	6	FACETS	0.972	0.908	1	0.729	0.681	0.778	CLONAL	3	TRUE	2	0.294144796754542	6		693	859	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099403	157099435	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAGCAACAGCAGCAG	CAGCAGCAGCAGCAGCAGCAGCAACAGCAGCAG	-	novel	NA	P-0014630-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	56	773	0	ENST00000346085.5:c.354_386del	p.Gln121_Gln131del	p.Q121_Q131del	ENST00000346085	NM_020732.3	114	CAGCAGCAGCAGCAGCAGCAGCAACAGCAGCAG/-	1/20	0.110510833547186	4	FACETS	0.706	0.605	0.817	0.353	0.302	0.409	INDETERMINATE	1	FALSE	2	0.342963409770703	4		773	621	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348892	89348892	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014630-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	75	698	0	ENST00000301030.4:c.4058C>A	p.Ser1353Tyr	p.S1353Y	ENST00000301030	NM_001256183.1	1353	tCc/tAc	9/13	0.342963409770703	3	FACETS	1	0.93	1	0.543	0.477	0.613	CLONAL	1	FALSE	1	0.342963409770703	3		698	472	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874969	151874970	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014630-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	39	425	0	ENST00000262189.6:c.7568dup	p.Arg2524Ter	p.R2524*	ENST00000262189	NM_170606.2	2523	cct/ccCt	38/59	0.342963409770703	2	FACETS	0.774	0.653	0.903	0.774	0.653	0.903	CLONAL	2	FALSE	0	0.342963409770703	2		425	147	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0015360-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	349	704	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.624597629234174	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.624399778000014	2		704	516	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133701	2133701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45517319	NA	P-0015360-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	177	469	0	ENST00000219476.3:c.3889G>A	p.Ala1297Thr	p.A1297T	ENST00000219476	NM_000548.3	1297	Gcc/Acc	33/42	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.624399778000014	2		469	515	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436097	56436097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015360-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	157	517	1	ENST00000407977.2:c.1040G>A	p.Gly347Asp	p.G347D	ENST00000407977		347	gGc/gAc	9/10	1	2	FACETS	0.818	0.752	0.886	0.818	0.752	0.886	CLONAL	1	TRUE	1	0.624399778000014	2		518	615	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056224	27056224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780917379	NA	P-0015360-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	418	439	0	ENST00000324856.7:c.1220C>T	p.Pro407Leu	p.P407L	ENST00000324856	NM_006015.4	407	cCt/cTt	2/20	NA	2	FACETS	1	0.978	1			1	INDETERMINATE	2	TRUE	NA	0.624399778000014	2		439	657	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615692	1615692	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015360-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	278	587	0	ENST00000344749.5:c.1579del	p.Arg527GlyfsTer16	p.R527Gfs*16	ENST00000344749	NM_001136139.2	527	Cgg/gg	17/19	0.624597629234174	2	FACETS	0.955	0.912	0.998	0.955	0.912	0.998	CLONAL	2	TRUE	0	0.624399778000014	2		587	466	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936098	71936098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015360-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	233	346	0	ENST00000298229.2:c.70C>T	p.Arg24Cys	p.R24C	ENST00000298229	NM_001567.3	24	Cgc/Tgc	1/28	0.624597629234174	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.624399778000014	3		346	447	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120872	115120872	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015360-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	267	437	0	ENST00000257566.3:c.134C>A	p.Thr45Lys	p.T45K	ENST00000257566	NM_016569.3	45	aCg/aAg	1/8	0.506963303114121	4	FACETS	0.985	0.929	1	0.985	0.929	1	CLONAL	2	TRUE	2	0.624399778000014	4		437	705	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610256	10610256	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015360-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	313	473	0	ENST00000171111.5:c.454G>T	p.Val152Phe	p.V152F	ENST00000171111	NM_203500.1	152	Gtc/Ttc	2/6	0.624597629234174	2	FACETS	0.962	0.921	1	0.962	0.921	1	CLONAL	2	TRUE	0	0.624399778000014	2		473	521	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390216	89390216	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015360-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	292	354	0	ENST00000336596.2:c.965G>C	p.Cys322Ser	p.C322S	ENST00000336596	NM_005233.5	322	tGt/tCt	4/17	0.558720603521598	3	FACETS	0.877	0.83	0.923	0.877	0.83	0.923	CLONAL	2	TRUE	1	0.624399778000014	3		354	700	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129287	152129287	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015360-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	154	386	0	ENST00000206249.3:c.240C>A	p.Tyr80Ter	p.Y80*	ENST00000206249	NM_000125.3	80	taC/taA	1/8	0.624597629234174	3	FACETS	0.927	0.851	1	0.464	0.425	0.504	CLONAL	1	TRUE	1	0.624399778000014	3		386	698	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981088	201981089	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015360-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	258	396	0	ENST00000359651.3:c.169dup	p.Ala57GlyfsTer35	p.A57Gfs*35	ENST00000359651		56	aag/aaGg	2/8	0.624597629234174	4	FACETS	0.922	0.868	0.977	0.922	0.868	0.977	CLONAL	2	TRUE	2	0.624399778000014	4		396	728	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711957	89711957	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015360-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	127	241	0	ENST00000371953.3:c.575C>A	p.Ala192Glu	p.A192E	ENST00000371953	NM_000314.4	192	gCa/gAa	6/9	0.624597629234174	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.624399778000014	1		241	262	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992468	72992468	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1309605420	NA	P-0015360-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	197	416	0	ENST00000268489.5:c.1577C>T	p.Ser526Leu	p.S526L	ENST00000268489	NM_006885.3	526	tCa/tTa	2/10	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.624399778000014	2		416	621	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346786	225346786	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015360-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	103	186	0	ENST00000264414.4:c.1852C>T	p.Gln618Ter	p.Q618*	ENST00000264414	NM_003590.4	618	Caa/Taa	14/16	0.624597629234174	3	FACETS	0.902	0.811	0.997	0.451	0.405	0.499	CLONAL	1	TRUE	1	0.624399778000014	3		186	480	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967875	93967875	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015360-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	347	323	0	ENST00000369303.4:c.2052C>A	p.Ser684Arg	p.S684R	ENST00000369303	NM_004440.3	684	agC/agA	11/17	0.624597629234174	3	FACETS	0.966	0.921	1	0.966	0.921	1	CLONAL	2	TRUE	1	0.624399778000014	3		323	755	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023202	27023202	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015360-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	300	386	0	ENST00000324856.7:c.308C>G	p.Ser103Trp	p.S103W	ENST00000324856	NM_006015.4	103	tCg/tGg	1/20	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.624399778000014	2		386	440	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429729	78429750	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTTAACTTTCTATCAAACCTGA	GTTAACTTTCTATCAAACCTGA	CT	novel	NA	P-0015360-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	265	257	1	ENST00000370768.2:c.1038_1041+18delinsAG		p.X346_splice	ENST00000370768	NM_003902.3	346		12/20	0.301174490894055	6	FACETS	0.843	0.794	0.893	0.632	0.595	0.67	INDETERMINATE	3	TRUE	2	0.624399778000014	6		258	755	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988281	36988281	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015360-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	268	379	0	ENST00000354822.5:c.372G>C	p.Met124Ile	p.M124I	ENST00000354822	NM_001079668.2	124	atG/atC	2/3	0.624597629234174	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.624399778000014	3		379	506	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574806	95574806	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015360-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	163	317	0	ENST00000393063.1:c.2291C>T	p.Pro764Leu	p.P764L	ENST00000393063	NM_030621.3	764	cCt/cTt	16/28	0.624597629234174	3	FACETS	1	0.927	1	0.504	0.464	0.545	CLONAL	1	TRUE	1	0.624399778000014	3		317	680	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064791	80064791	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015360-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	129	240	0	ENST00000265081.6:c.2222C>A	p.Ser741Tyr	p.S741Y	ENST00000265081	NM_002439.4	741	tCt/tAt	15/24	1	2	FACETS	0.972	0.889	1	0.972	0.889	1	CLONAL	1	TRUE	1	0.624399778000014	2		240	425	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2110403	2110403	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015360-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	167	331	0	ENST00000349721.2:c.3442T>A	p.Trp1148Arg	p.W1148R	ENST00000349721	NM_003070.3	1148	Tgg/Agg	24/34	0.624597629234174	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.624399778000014	1		331	356	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635160	87635160	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276608169	NA	P-0015360-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	311	348	0	ENST00000277120.3:c.2212C>T	p.Pro738Ser	p.P738S	ENST00000277120		738	Cca/Tca	18/19	0.624597629234174	2	FACETS	0.994	0.952	1	0.994	0.952	1	CLONAL	2	TRUE	0	0.624399778000014	2		348	501	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787749	135787749	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015360-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	547	304	0	ENST00000298552.3:c.833C>G	p.Ser278Cys	p.S278C	ENST00000298552	NM_001162426.1	278	tCt/tGt	9/23	0.624597629234174	4	FACETS	0.99	0.964	1			1	CLONAL	4	TRUE	NA	0.624399778000014	4		304	719	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016240-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	224	477	0				ENST00000310581	NM_198253.2	-/1132			0.348977405891374	9	FACETS	0.994	0.94	1	0.994	0.94	1	CLONAL	7	TRUE	2	0.348977405891374	9		477	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0016240-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	204	459	0	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.348977405891374	4	FACETS	0.923	0.868	0.979	0.923	0.868	0.979	CLONAL	4	TRUE	0	0.348977405891374	4		459	427	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47004894	47004894	+	intron_variant	Intron	SNP	G	G	C	novel	NA	P-0016240-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	155	742	0	ENST00000377604.3:c.-126+10G>C		p.*42*	ENST00000377604	NM_001204468.1	-/163			0.298555958160413	4	FACETS	0.897	0.824	0.973	0.897	0.824	0.973	CLONAL	2	TRUE	2	0.348977405891374	4		742	668	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213791	2214610	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCTTACTTCACCTTGGAGGCCACCAGCATGACCTCTCCCCCGCCCCATGTCCCCAGCTGGGTGTGAAGGCGCTGACCTACAACGACCTGATTCAAGCGCAGAAGGAGATCTCCGCCCATAACCAGCAGCTGCGGGAGCAGTCGGAGCAGCTGGAGCAGGACAACCGCGCGCTCCGCGGCCAGAGCTTGCAGCTGGTGGGTGCCGCGGCGCAAGGACAGGGACGTGGAACCAGAGGGGCCCTGCCTGGGCGGGTGTGTCCTCTGTGCGGGTGGGAGGCTCTGGAAGGCCCGCCTCTGTTGTGGGGTTTGTTCCCAGACGAATTGCGCCACCTGTGAAAGCTTGTCGAGCGCGTCACAGCAGGCAGGCCTGGGCCCCTCGGCTGGATGGTTTCTCAGCGGCCCTGGGTGTCATGGAGCCACACTCTGGCAGGCTCGAGGTGTGGGGTCATGCGAGCATCCCACCATCGTGGTGTGGGTGCTGGAGCTGCCTCATCTGTCCGTGGGGGGCCCCAGTCTCCGCGTGTTCCGCATCCTCAGCCTGCTATTCCAGAAACGGGGTCTGTGCCCTAAGCACACATGCTGTTGGCTGAGGCAGGCCCAGGGAACCCTGCCCTGAGAGTGTGGGGTGTGCTGGGCAGGCAGCCAGCCAGTCGCAACTGTCCCATCCCTATCCCCTCAGCTCAAGGCTCGCTGCGAGGAGCTGCAGCTGGACTGGGCCACGCTGTCGCTGGAGAAGCTGTTGAAGGAGAAGCAGGCCCTGAAGAGCCAGATCTCGGAGAAGCAGAGGCACTGCCTGGAGCTGCAGGTGGGCTGCGCGCGA	GGCTTACTTCACCTTGGAGGCCACCAGCATGACCTCTCCCCCGCCCCATGTCCCCAGCTGGGTGTGAAGGCGCTGACCTACAACGACCTGATTCAAGCGCAGAAGGAGATCTCCGCCCATAACCAGCAGCTGCGGGAGCAGTCGGAGCAGCTGGAGCAGGACAACCGCGCGCTCCGCGGCCAGAGCTTGCAGCTGGTGGGTGCCGCGGCGCAAGGACAGGGACGTGGAACCAGAGGGGCCCTGCCTGGGCGGGTGTGTCCTCTGTGCGGGTGGGAGGCTCTGGAAGGCCCGCCTCTGTTGTGGGGTTTGTTCCCAGACGAATTGCGCCACCTGTGAAAGCTTGTCGAGCGCGTCACAGCAGGCAGGCCTGGGCCCCTCGGCTGGATGGTTTCTCAGCGGCCCTGGGTGTCATGGAGCCACACTCTGGCAGGCTCGAGGTGTGGGGTCATGCGAGCATCCCACCATCGTGGTGTGGGTGCTGGAGCTGCCTCATCTGTCCGTGGGGGGCCCCAGTCTCCGCGTGTTCCGCATCCTCAGCCTGCTATTCCAGAAACGGGGTCTGTGCCCTAAGCACACATGCTGTTGGCTGAGGCAGGCCCAGGGAACCCTGCCCTGAGAGTGTGGGGTGTGCTGGGCAGGCAGCCAGCCAGTCGCAACTGTCCCATCCCTATCCCCTCAGCTCAAGGCTCGCTGCGAGGAGCTGCAGCTGGACTGGGCCACGCTGTCGCTGGAGAAGCTGTTGAAGGAGAAGCAGGCCCTGAAGAGCCAGATCTCGGAGAAGCAGAGGCACTGCCTGGAGCTGCAGGTGGGCTGCGCGCGA	-	novel	NA	P-0016240-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	56	391	0	ENST00000398665.3:c.1660-53_1923+19del		p.X554_splice	ENST00000398665	NM_032482.2	554		18-19/28	0.232708580661855	5	FACETS	1	0.965	1	0.478	0.411	0.55	CLONAL	1	TRUE	2	0.348977405891374	5		391	341	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288493	15288493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016240-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	78	378	0	ENST00000263388.2:c.4246G>T	p.Asp1416Tyr	p.D1416Y	ENST00000263388	NM_000435.2	1416	Gac/Tac	24/33	0.346782246278814	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	0	0.348977405891374	2		378	214	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151615	55151615	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016240-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	143	347	0	ENST00000257290.5:c.2401C>T	p.Gln801Ter	p.Q801*	ENST00000257290	NM_006206.4	801	Caa/Taa	17/23	0.342078344346242	3	FACETS	0.949	0.878	1	0.949	0.878	1	CLONAL	3	TRUE	0	0.348977405891374	3		347	338	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777657	9777657	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016240-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	182	603	0	ENST00000377346.4:c.993C>G	p.Ser331Arg	p.S331R	ENST00000377346	NM_005026.3	331	agC/agG	8/24	0.232708580661855	5	FACETS	0.916	0.851	0.984	0.916	0.851	0.984	CLONAL	3	TRUE	2	0.348977405891374	5		603	578	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117720	108117720	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876658322	NA	P-0016240-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	88	290	0	ENST00000278616.4:c.931A>G	p.Ile311Val	p.I311V	ENST00000278616	NM_000051.3	311	Att/Gtt	8/63	0.298555958160413	4	FACETS	0.874	0.78	0.974	0.874	0.78	0.974	CLONAL	2	TRUE	2	0.348977405891374	4		290	389	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63810652	63810652	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs753041204	NA	P-0016733-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	175	360	0	ENST00000279873.7:c.739A>G	p.Asn247Asp	p.N247D	ENST00000279873	NM_032199.2	247	Aat/Gat	5/10	1	2	FACETS	0.863	0.801	0.927	0.863	0.801	0.927	CLONAL	1	TRUE	1	0.766321503773525	2		360	529	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427700	72427700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016733-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	224	560	0	ENST00000477973.2:c.790G>A	p.Glu264Lys	p.E264K	ENST00000477973	NM_012234.5	264	Gaa/Aaa	4/4	1	2	FACETS	0.963	0.903	1	0.963	0.903	1	CLONAL	1	TRUE	1	0.766321503773525	2		560	607	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960216	151960216	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0016733-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	59	75	0	ENST00000262189.6:c.1185-1G>C		p.X395_splice	ENST00000262189	NM_170606.2	395			0.391672883171837	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.766321503773525	0		75	81	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631850	90631850	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016733-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	305	737	0	ENST00000330062.3:c.503T>C	p.Ile168Thr	p.I168T	ENST00000330062	NM_002168.2	168	aTc/aCc	4/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.766321503773525	2		737	710	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84406180	84406180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016733-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	173	406	0	ENST00000321945.7:c.46G>A	p.Gly16Ser	p.G16S	ENST00000321945	NM_139076.2	16	Ggc/Agc	1/9	1	2	FACETS	0.896	0.831	0.962	0.896	0.831	0.962	CLONAL	1	TRUE	1	0.766321503773525	2		406	504	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871632	35871633	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017240-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	56	370	0	ENST00000216797.5:c.873dup	p.Glu292ArgfsTer15	p.E292Rfs*15	ENST00000216797	NM_020529.2	291	-/A	5/6	1	2	FACETS	0.893	0.779	1	0.893	0.779	1	CLONAL	1	TRUE	1	0.685310175386353	2		370	183	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205747	108205747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565540761	NA	P-0017240-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	30	363	0	ENST00000278616.4:c.8062G>A	p.Ala2688Thr	p.A2688T	ENST00000278616	NM_000051.3	2688	Gca/Aca	55/63	1	2	FACETS	0.884	0.731	1	0.884	0.731	1	CLONAL	1	TRUE	1	0.685310175386353	2		363	99	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519239	187519239	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs780625419	NA	P-0017240-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	35	430	0	ENST00000441802.2:c.12144C>A	p.His4048Gln	p.H4048Q	ENST00000441802	NM_005245.3	4048	caC/caA	23/27	1	2	FACETS	0.73	0.608	0.86	0.73	0.608	0.86	SUBCLONAL	1	TRUE	1	0.685310175386353	2		430	140	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522656	176522656	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017240-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	110	653	0	ENST00000292408.4:c.1753T>G	p.Ser585Ala	p.S585A	ENST00000292408	NM_213647.1	585	Tcc/Gcc	13/18	1	2	FACETS	0.897	0.814	0.982	0.897	0.814	0.982	CLONAL	1	TRUE	1	0.685310175386353	2		653	358	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328385	137328385	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017240-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	48	457	0	ENST00000481739.1:c.1314C>G	p.Phe438Leu	p.F438L	ENST00000481739	NM_002957.4	438	ttC/ttG	10/10	1	2	FACETS	0.667	0.571	0.77	0.667	0.571	0.77	SUBCLONAL	1	TRUE	1	0.685310175386353	2		457	210	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981495	201981496	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	C	novel	NA	P-0017240-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	70	452	0	ENST00000359651.3:c.409_410delinsC	p.Ser137LeufsTer18	p.S137Lfs*18	ENST00000359651		137	AGt/Ct	3/8	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.685310175386353	2		452	200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0017913-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	302	604	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	0.98	0.927	1	0.98	0.927	1	CLONAL	1	TRUE	1	0.73926156512429	2		604	834	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0017913-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	321	532	0	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.73926156512429	2		532	852	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911593	114911593	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017913-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	253	570	0	ENST00000543371.1:c.1111G>C	p.Glu371Gln	p.E371Q	ENST00000543371	NM_001198531.1	371	Gag/Cag	10/14	1	2	FACETS	0.96	0.903	1	0.96	0.903	1	CLONAL	1	TRUE	1	0.73926156512429	2		570	713	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979283	40979283	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017913-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	215	599	0	ENST00000373198.4:c.1850G>T	p.Arg617Leu	p.R617L	ENST00000373198	NM_133170.3	617	cGg/cTg	11/32	0.34347857638536	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.73926156512429	0		599	556	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65349093	65349093	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017913-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	293	532	0	ENST00000342505.4:c.72del	p.Thr25LeufsTer3	p.T25Lfs*3	ENST00000342505	NM_002227.2	24	aaG/aa	3/25	0.727924663036809	1	FACETS	0.968	0.924	1	0.968	0.924	1	CLONAL	1	TRUE	0	0.73926156512429	1		532	516	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989443	85989443	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017913-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	134	329	0	ENST00000263360.6:c.1202G>A	p.Cys401Tyr	p.C401Y	ENST00000263360	NM_003797.3	401	tGt/tAt	12/12	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.73926156512429	2		329	355	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110515	4110515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017913-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	301	682	0	ENST00000262948.5:c.442G>A	p.Glu148Lys	p.E148K	ENST00000262948	NM_030662.3	148	Gaa/Aaa	3/11	1	2	FACETS	0.918	0.867	0.97	0.918	0.867	0.97	CLONAL	1	TRUE	1	0.73926156512429	2		682	887	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210481	5210481	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017913-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	267	664	0	ENST00000357368.4:c.5486G>T	p.Arg1829Leu	p.R1829L	ENST00000357368	NM_002850.3	1829	cGg/cTg	35/38	1	2	FACETS	0.903	0.85	0.957	0.903	0.85	0.957	CLONAL	1	TRUE	1	0.73926156512429	2		664	800	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182256	38182256	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017913-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	334	634	0	ENST00000396334.3:c.692G>T	p.Arg231Leu	p.R231L	ENST00000396334	NM_002468.4	231	cGg/cTg	4/5	0.727924663036809	1	FACETS	0.929	0.888	0.97	0.929	0.888	0.97	CLONAL	1	TRUE	0	0.73926156512429	1		634	613	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390206	89390206	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017913-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	196	529	0	ENST00000336596.2:c.955T>A	p.Ser319Thr	p.S319T	ENST00000336596	NM_005233.5	319	Tcc/Acc	4/17	0.73926156512429	1	FACETS	0.926	0.873	0.979	0.926	0.873	0.979	CLONAL	1	TRUE	0	0.73926156512429	1		529	361	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952316	38952316	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017913-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	171	488	0	ENST00000357387.3:c.3109A>T	p.Ser1037Cys	p.S1037C	ENST00000357387	NM_152756.3	1037	Agt/Tgt	30/38	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.73926156512429	2		488	459	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178535	56178535	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017913-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	178	500	0	ENST00000399503.3:c.3508G>C	p.Asp1170His	p.D1170H	ENST00000399503	NM_005921.1	1170	Gat/Cat	14/20	1	2	FACETS	0.955	0.888	1	0.955	0.888	1	CLONAL	1	TRUE	1	0.73926156512429	2		500	504	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515421	149515421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017913-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	244	615	0	ENST00000261799.4:c.61C>T	p.Leu21Phe	p.L21F	ENST00000261799	NM_002609.3	21	Ctc/Ttc	3/23	1	2	FACETS	0.951	0.894	1	0.951	0.894	1	CLONAL	1	TRUE	1	0.73926156512429	2		615	694	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176678794	176678794	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017913-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	648	630	0	ENST00000439151.2:c.4705G>T	p.Glu1569Ter	p.E1569*	ENST00000439151	NM_022455.4	1569	Gag/Tag	12/23	0.733197106404893	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.73926156512429	2		630	851	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813545	32813545	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0017913-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	197	420	0	ENST00000354258.4:c.2238C>G	p.Tyr746Ter	p.Y746*	ENST00000354258	NM_000593.5	746	taC/taG	11/11	0.721586001883485	1	FACETS	0.857	0.806	0.908	0.857	0.806	0.908	CLONAL	1	TRUE	0	0.73926156512429	1		420	392	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455145	50455145	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017913-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	200	469	0	ENST00000331340.3:c.692G>T	p.Gly231Val	p.G231V	ENST00000331340	NM_006060.4	231	gGc/gTc	6/8	0.393854797633738	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.73926156512429	0		469	462	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402552	139402552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017913-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	283	668	0	ENST00000277541.6:c.3365G>A	p.Cys1122Tyr	p.C1122Y	ENST00000277541	NM_017617.3	1122	tGt/tAt	21/34	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.73926156512429	2		668	745	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53244007	53244007	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017913-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	293	259	1	ENST00000375401.3:c.986T>A	p.Met329Lys	p.M329K	ENST00000375401	NM_004187.3	329	aTg/aAg	8/26	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.73926156512429	1		260	407	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150923057	150923057	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017913-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	250	584	0	ENST00000271640.5:c.1705del	p.Glu569ArgfsTer21	p.E569Rfs*21	ENST00000271640	NM_001145415.1	568	atG/at	13/22	1	2	FACETS	0.92	0.865	0.977	0.92	0.865	0.977	CLONAL	1	TRUE	1	0.73926156512429	2		584	735	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920627	96920627	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017913-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	99	551	0	ENST00000258439.3:c.353C>A	p.Pro118Gln	p.P118Q	ENST00000258439	NM_001193304.2	118	cCg/cAg	3/4	1	2	FACETS	0.334	0.298	0.373	0.334	0.298	0.373	SUBCLONAL	1	TRUE	1	0.73926156512429	2		551	801	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271411	26271411	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017913-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	963	913	0	ENST00000305910.3:c.202T>C	p.Phe68Leu	p.F68L	ENST00000305910	NM_003534.2	68	Ttc/Ctc	1/1	0.73926156512429	3	FACETS	0.876	0.857	0.894			1	CLONAL	3	TRUE	NA	0.73926156512429	3		913	1358	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334712	81334713	+	missense_variant	Missense_Mutation	DNP	TG	TG	GT	novel	NA	P-0017913-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	84	455	0	ENST00000222390.5:c.2003_2004delinsAC	p.Pro668His	p.P668H	ENST00000222390	NM_000601.4	668	cCA/cAC	17/18	0.73926156512429	1	FACETS	0.648	0.583	0.715	0.648	0.583	0.715	SUBCLONAL	1	TRUE	0	0.73926156512429	1		455	221	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435852	110435853	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCTGGCTGGGC	novel	NA	P-0018588-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1188	227	387	0	ENST00000375856.3:c.2538_2548dup	p.Ala850GlyfsTer20	p.A850Gfs*20	ENST00000375856	NM_003749.2	850	gcg/gGCCCAGCCAGGcg	1/2	0.869761990859677	4	FACETS	0.691	0.642	0.742			1	SUBCLONAL	1	TRUE	NA	0.8668758460499	4		387	1415	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646930	37646931	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0018588-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	280	280	0	ENST00000447079.4:c.2055_2056del	p.Pro686ArgfsTer13	p.P686Rfs*13	ENST00000447079	NM_015083.1	684	gaCTct/gact	3/14	0.869761990859677	3	FACETS	0.976	0.918	1			1	CLONAL	1	TRUE	NA	0.8668758460499	3		280	949	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676216	37676217	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0018588-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	477	267	0	ENST00000447079.4:c.2972_2973del	p.Ser991CysfsTer4	p.S991Cfs*4	ENST00000447079	NM_015083.1	991	TCt/t	11/14	0.869761990859677	3	FACETS	0.986	0.951	1			1	CLONAL	2	TRUE	NA	0.8668758460499	3		267	800	SUCCESS
AR	367	MSKCC	GRCh37	X	66943549	66943549	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519864	NA	P-0018588-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	443	144	0	ENST00000374690.3:c.2629T>C	p.Phe877Leu	p.F877L	ENST00000374690	NM_000044.3	877	Ttc/Ctc	8/8	0.8668758460499	3	FACETS	0.951	0.916	0.986			1	CLONAL	2	TRUE	NA	0.8668758460499	3		144	770	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21351063	21351063	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754243226	NA	P-0018588-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	353	395	0	ENST00000215739.8:c.2298G>A	p.Met766Ile	p.M766I	ENST00000215739	NM_006767.3	766	atG/atA	19/21	0.863609932181101	3	FACETS	0.995	0.943	1			1	CLONAL	1	TRUE	NA	0.8668758460499	3		395	1173	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0019020-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	331	351	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		351	357	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0019020-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	239	428	0	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		428	531	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560464	95560464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019020-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	103	492	0	ENST00000393063.1:c.5125G>A	p.Asp1709Asn	p.D1709N	ENST00000393063	NM_030621.3	1709	Gat/Aat	25/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		492	284	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557633	95557640	+	frameshift_variant	Frame_Shift_Del	DEL	AAATATCC	AAATATCC	-	novel	NA	P-0019020-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	154	240	0	ENST00000393063.1:c.5427_5434del	p.Asp1810Ter	p.D1810*	ENST00000393063	NM_030621.3	1809	ggGGATATTTtt/ggtt	26/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		240	303	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934510	9934510	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019020-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	17	267	0	ENST00000330684.3:c.1645T>A	p.Phe549Ile	p.F549I	ENST00000330684	NM_001134407.1	549	Ttt/Att	7/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		267	151	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	86	477	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.585535214648044	2		477	249	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0020065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	214	318	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.562958301286835	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.585535214648044	2		318	354	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449764	8449764	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	119	332	0	ENST00000356435.5:c.3949G>C	p.Asp1317His	p.D1317H	ENST00000356435		1317	Gac/Cac	23/35	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.585535214648044	2		332	365	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069599	69069599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	38	238	0	ENST00000288368.4:c.4274C>T	p.Ser1425Phe	p.S1425F	ENST00000288368	NM_024870.2	1425	tCt/tTt	35/40	0.41128704724994	2	FACETS	0.503	0.418	0.597	0.252	0.209	0.299	SUBCLONAL	1	TRUE	0	0.585535214648044	2		238	258	SUCCESS
REL	5966	MSKCC	GRCh37	2	61148994	61148994	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0020065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	110	424	0	ENST00000295025.8:c.1184C>G	p.Ser395Ter	p.S395*	ENST00000295025	NM_002908.2	395	tCa/tGa	11/11	0.231067750615142	5	FACETS	0.979	0.88	1	0.326	0.293	0.361	INDETERMINATE	1	TRUE	2	0.585535214648044	5		424	721	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344825	65344825	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	109	342	0	ENST00000342505.4:c.212C>T	p.Ser71Phe	p.S71F	ENST00000342505	NM_002227.2	71	tCt/tTt	4/25	1	2	FACETS	0.99	0.897	1	0.99	0.897	1	CLONAL	1	TRUE	1	0.585535214648044	2		342	376	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245849	46245849	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	199	461	0	ENST00000334344.6:c.3943G>T	p.Glu1315Ter	p.E1315*	ENST00000334344	NM_152641.2	1315	Gag/Tag	15/21	0.568575282955379	3	FACETS	0.961	0.901	1	0.961	0.901	1	CLONAL	2	TRUE	1	0.585535214648044	3		461	457	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480377	56480377	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759585997	NA	P-0020065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	139	365	0	ENST00000267101.3:c.484G>A	p.Asp162Asn	p.D162N	ENST00000267101	NM_001982.3	162	Gac/Aac	4/28	0.568575282955379	3	FACETS	1	0.958	1	0.539	0.493	0.588	CLONAL	1	TRUE	1	0.585535214648044	3		365	569	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609627	81609627	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149237353	NA	P-0020065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	165	524	0	ENST00000298171.2:c.1225G>A	p.Glu409Lys	p.E409K	ENST00000298171	NM_000369.2	409	Gaa/Aaa	10/10	0.250488195177219	2	FACETS	1	0.988	1	0.677	0.629	0.726	INDETERMINATE	1	TRUE	0	0.585535214648044	2		524	416	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354575	91354575	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	92	423	0	ENST00000355112.3:c.4015A>T	p.Met1339Leu	p.M1339L	ENST00000355112	NM_000057.2	1339	Atg/Ttg	21/22	1	2	FACETS	0.89	0.798	0.987	0.89	0.798	0.987	CLONAL	1	TRUE	1	0.585535214648044	2		423	353	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226056	2226056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	144	517	0	ENST00000326181.6:c.1753G>A	p.Asp585Asn	p.D585N	ENST00000326181	NM_032271.2	585	Gac/Aac	19/21	0.585535214648044	1	FACETS	0.925	0.854	0.998	0.925	0.854	0.998	CLONAL	1	TRUE	0	0.585535214648044	1		517	376	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976481	25976481	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs774776226	NA	P-0020065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	71	270	0	ENST00000435504.4:c.1064G>C	p.Arg355Thr	p.R355T	ENST00000435504		355	aGa/aCa	11/13	0.149537818035786	4	FACETS	1	0.97	1	0.45	0.396	0.506	INDETERMINATE	1	TRUE	1	0.585535214648044	4		270	285	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940141	49940141	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	170	515	0	ENST00000296474.3:c.902G>C	p.Arg301Thr	p.R301T	ENST00000296474	NM_002447.2	301	aGa/aCa	1/20	0.48058693274595	3	FACETS	0.812	0.754	0.872	0.812	0.754	0.872	CLONAL	2	TRUE	1	0.585535214648044	3		515	462	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456513	89456513	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	66	295	0	ENST00000336596.2:c.1689G>C	p.Leu563Phe	p.L563F	ENST00000336596	NM_005233.5	563	ttG/ttC	8/17	0.48058693274595	3	FACETS	0.801	0.699	0.91	0.4	0.349	0.455	CLONAL	1	TRUE	1	0.585535214648044	3		295	364	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266718	142266718	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	145	308	0	ENST00000350721.4:c.3206G>C	p.Arg1069Thr	p.R1069T	ENST00000350721	NM_001184.3	1069	aGa/aCa	16/47	0.48058693274595	3	FACETS	0.967	0.896	1	0.967	0.896	1	CLONAL	2	TRUE	1	0.585535214648044	3		308	331	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165623	118165623	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs773602227	NA	P-0020065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	120	478	0	ENST00000369448.3:c.133G>C	p.Glu45Gln	p.E45Q	ENST00000369448	NM_017709.3	45	Gag/Cag	2/2	1	2	FACETS	0.958	0.872	1	0.958	0.872	1	CLONAL	1	TRUE	1	0.585535214648044	2		478	428	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165816	118165816	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	115	473	0	ENST00000369448.3:c.326G>C	p.Arg109Thr	p.R109T	ENST00000369448	NM_017709.3	109	aGa/aCa	2/2	1	2	FACETS	0.947	0.859	1	0.947	0.859	1	CLONAL	1	TRUE	1	0.585535214648044	2		473	415	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176145127	176145127	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	99	286	0	ENST00000367669.3:c.484C>G	p.Gln162Glu	p.Q162E	ENST00000367669	NM_022457.5	162	Cag/Gag	3/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.585535214648044	2		286	295	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577361	64577361	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424266863	NA	P-0020065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	90	489	0	ENST00000312049.6:c.221G>A	p.Gly74Asp	p.G74D	ENST00000312049	NM_130799.2	74	gGc/gAc	2/10	0.243950263794139	3	FACETS	0.935	0.834	1	0.468	0.417	0.521	INDETERMINATE	1	TRUE	1	0.585535214648044	3		489	425	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158420	26158420	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	134	428	0	ENST00000289316.2:c.23C>A	p.Ala8Asp	p.A8D	ENST00000289316	NM_138720.2	8	gCt/gAt	1/2	0.265973123408222	5	FACETS	1	0.985	1	0.284	0.259	0.311	INDETERMINATE	1	TRUE	0	0.585535214648044	5		428	605	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508970	106508970	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	121	439	0	ENST00000359195.3:c.964G>C	p.Glu322Gln	p.E322Q	ENST00000359195	NM_002649.2	322	Gag/Cag	2/11	0.243950263794139	3	FACETS	0.909	0.824	0.998	0.454	0.412	0.499	INDETERMINATE	1	TRUE	1	0.585535214648044	3		439	588	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0026926-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	273	536	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.847247442659684	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.847247442659684	3		536	395	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026926-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	157	571	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.847247442659684	3	FACETS	1	0.982	1	0.598	0.553	0.644	CLONAL	1	TRUE	1	0.847247442659684	3		571	441	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111503	8111504	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAATGCCAATGGGGACCCT	novel	NA	P-0026926-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	142	498	0	ENST00000346208.3:c.991_1009dup	p.Val337GlufsTer21	p.V337Efs*21	ENST00000346208		330	agg/agGAATGCCAATGGGGACCCTg	5/6	0.812038594829804	4	FACETS	1	0.975	1	0.581	0.532	0.631	CLONAL	1	TRUE	2	0.847247442659684	4		498	533	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426771	212426771	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879060634	NA	P-0026926-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	127	554	0	ENST00000342788.4:c.2344C>T	p.Arg782Trp	p.R782W	ENST00000342788	NM_005235.2	782	Cgg/Tgg	20/28	0.847247442659684	4	FACETS	0.909	0.826	0.996	0.303	0.275	0.332	CLONAL	1	TRUE	1	0.847247442659684	4		554	609	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540068	187540068	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026926-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	119	468	0	ENST00000441802.2:c.7672A>T	p.Thr2558Ser	p.T2558S	ENST00000441802	NM_005245.3	2558	Acc/Tcc	10/27	0.740201956420684	4	FACETS	1	0.975	1	0.605	0.55	0.662	CLONAL	1	TRUE	2	0.847247442659684	4		468	429	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945198	32945198	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs80359117	NA	P-0026926-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	91	295	0	ENST00000380152.3:c.8593T>G	p.Leu2865Val	p.L2865V	ENST00000380152		2865	Tta/Gta	20/27	0.847247442659684	2	FACETS	1	0.941	1	0.524	0.476	0.573	CLONAL	1	TRUE	0	0.847247442659684	2		295	205	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038635	14038635	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs892310767	NA	P-0026926-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	121	344	0	ENST00000311895.7:c.1960T>G	p.Leu654Val	p.L654V	ENST00000311895	NM_005236.2	654	Tta/Gta	10/11	0.847247442659684	3	FACETS	1	0.969	1	0.566	0.517	0.617	CLONAL	1	TRUE	1	0.847247442659684	3		344	359	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024520	16024520	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026926-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	153	523	0	ENST00000268712.3:c.1698A>C	p.Gln566His	p.Q566H	ENST00000268712	NM_006311.3	566	caA/caC	16/46	0.847247442659684	3	FACETS	1	0.977	1	0.574	0.53	0.619	CLONAL	1	TRUE	1	0.847247442659684	3		523	448	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39751932	39751932	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026926-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	92	354	0	ENST00000361337.2:c.2293T>G	p.Phe765Val	p.F765V	ENST00000361337	NM_003286.2	765	Ttt/Gtt	21/21	0.847247442659684	8	FACETS	0.953	0.846	1			1	CLONAL	1	TRUE	NA	0.847247442659684	8		354	807	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851887	134851887	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026926-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	112	544	0	ENST00000398015.3:c.1293A>C	p.Gln431His	p.Q431H	ENST00000398015	NM_004441.4	431	caA/caC	5/16	0.847247442659684	3	FACETS	1	0.968	1	0.569	0.517	0.621	CLONAL	1	TRUE	1	0.847247442659684	3		544	331	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665126	138665126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026926-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	86	418	0	ENST00000330315.3:c.439C>T	p.Arg147Cys	p.R147C	ENST00000330315	NM_023067.3	147	Cgc/Tgc	1/1	0.847247442659684	3	FACETS	1	0.938	1	0.533	0.478	0.591	CLONAL	1	TRUE	1	0.847247442659684	3		418	271	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86676373	86676373	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026926-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	92	330	0	ENST00000274376.6:c.2651A>C	p.Lys884Thr	p.K884T	ENST00000274376	NM_002890.2	884	aAg/aCg	20/25	0.812038594829804	4	FACETS	0.953	0.852	1	0.476	0.426	0.53	CLONAL	1	TRUE	2	0.847247442659684	4		330	421	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220299	55220299	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026926-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	116	412	0	ENST00000275493.2:c.689A>T	p.Asp230Val	p.D230V	ENST00000275493	NM_005228.3	230	gAc/gTc	6/28	0.847247442659684	3	FACETS	1	0.979	1	0.621	0.567	0.676	CLONAL	1	TRUE	1	0.847247442659684	3		412	314	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37006519	37006519	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0026926-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	117	422	0	ENST00000358127.4:c.426A>C	p.Lys142Asn	p.K142N	ENST00000358127	NM_001280556.1	142	aaA/aaC	4/10	0.830094225182962	3	FACETS	1	0.972	1	0.578	0.528	0.63	CLONAL	1	TRUE	1	0.847247442659684	3		422	340	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410468	63410468	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026926-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	109	644	0	ENST00000330258.3:c.2699A>G	p.Glu900Gly	p.E900G	ENST00000330258	NM_152424.3	900	gAg/gGg	2/2	0.847247442659684	3	FACETS	0.9	0.814	0.989	0.45	0.407	0.495	CLONAL	1	TRUE	1	0.847247442659684	3		644	407	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0028059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	52	345	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.203494745111987	2	FACETS	0.84	0.733	0.95	0.84	0.733	0.95	INDETERMINATE	2	TRUE	0	0.445555413265572	2		345	139	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0028059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	50	467	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.512	0.435	0.597	0.512	0.435	0.597	SUBCLONAL	1	TRUE	1	0.445555413265572	2		467	438	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857460	68857460	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121964874	NA	P-0028059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	118	446	0	ENST00000261769.5:c.2095C>T	p.Gln699Ter	p.Q699*	ENST00000261769	NM_004360.3	699	Cag/Tag	13/16	0.35570156832635	0	FACETS	0.62	0.572	0.668			1	SUBCLONAL	2	TRUE	0	0.445555413265572	0		446	237	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230561434	230561435	+	5_prime_UTR_variant	5'UTR	INS	-	-	CGGGGCG	novel	NA	P-0028059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	71	916	0	ENST00000391860.1:c.-112_-106dup		p.*38*	ENST00000391860	NM_001258311.1	-/409		1/7	0.445555413265572	3	FACETS	0.792	0.701	0.888	0.792	0.701	0.888	SUBCLONAL	2	TRUE	1	0.445555413265572	3		916	246	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030136-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	113	477	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.78	0.704	0.86	0.78	0.704	0.86	SUBCLONAL	1	TRUE	1	0.510923124917724	2		477	567	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151316	202151316	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0030136-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	228	477	0	ENST00000358485.4:c.1616G>C	p.Ter539SerextTer88	p.*539Sext*88	ENST00000358485	NM_001080125.1	539	tGa/tCa	9/9	0.510886843739364	2	FACETS	0.949	0.896	1	0.949	0.896	1	CLONAL	2	TRUE	0	0.510923124917724	2		477	470	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566521	41566521	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030136-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	324	614	0	ENST00000263253.7:c.4398G>C	p.Trp1466Cys	p.W1466C	ENST00000263253	NM_001429.3	1466	tgG/tgC	27/31	0.488768207470514	2	FACETS	0.927	0.883	0.972	0.927	0.883	0.972	CLONAL	2	TRUE	0	0.510923124917724	2		614	684	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593508	48593508	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793725	NA	P-0030136-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	186	667	0	ENST00000342988.3:c.1259G>A	p.Arg420His	p.R420H	ENST00000342988	NM_005359.5	420	cGt/cAt	10/12	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.510923124917724	2		667	692	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857517	57857517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs890327478	NA	P-0030136-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	257	887	0	ENST00000228682.2:c.43G>A	p.Glu15Lys	p.E15K	ENST00000228682	NM_005269.2	15	Gag/Aag	2/12	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.510923124917724	2		887	992	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143318	30143345	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGGGCGTAGACACGGAAGAGCGAGGG	CCCGGGCGTAGACACGGAAGAGCGAGGG	-	novel	NA	P-0030136-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	132	874	0	ENST00000389048.3:c.181_208del	p.Pro61ThrfsTer11	p.P61Tfs*11	ENST00000389048	NM_004304.4	61	CCCTCGCTCTTCCGTGTCTACGCCCGGGac/ac	1/29	1	2	FACETS	0.764	0.695	0.837	0.764	0.695	0.837	SUBCLONAL	1	TRUE	1	0.510923124917724	2		874	676	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779184	3779184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030136-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	122	788	0	ENST00000262367.5:c.5864C>T	p.Ala1955Val	p.A1955V	ENST00000262367	NM_004380.2	1955	gCg/gTg	31/31	1	2	FACETS	0.758	0.687	0.833	0.758	0.687	0.833	SUBCLONAL	1	TRUE	1	0.510923124917724	2		788	630	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0030136-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	453	872	0	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	1	2	FACETS	0.763	0.73	0.797	1	0.996	1	SUBCLONAL	2	TRUE	1	0.510923124917724	2		872	1162	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259163	89259163	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030136-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	164	747	0	ENST00000336596.2:c.307C>A	p.Leu103Ile	p.L103I	ENST00000336596	NM_005233.5	103	Cta/Ata	3/17	1	2	FACETS	0.96	0.884	1	0.96	0.884	1	CLONAL	1	TRUE	1	0.510923124917724	2		747	669	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664816	138664816	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030136-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	127	591	0	ENST00000330315.3:c.749G>C	p.Gly250Ala	p.G250A	ENST00000330315	NM_023067.3	250	gGc/gCc	1/1	1	2	FACETS	0.917	0.835	1	0.917	0.835	1	CLONAL	1	TRUE	1	0.510923124917724	2		591	542	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911105	29911105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs41548812	NA	P-0030136-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	255	933	0	ENST00000376809.5:c.404G>C	p.Arg135Pro	p.R135P	ENST00000376809	NM_002116.7	135	cGc/cCc	3/8	1	2	FACETS	0.885	0.828	0.944	0.885	0.828	0.944	CLONAL	1	TRUE	1	0.510923124917724	2		933	1128	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0031619-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	154	613	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.3	4	FACETS	1	0.976	1	0.771	0.709	0.834	CLONAL	2	TRUE	1	0.31	4		614	563	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478161	138478161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031619-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	41	360	0	ENST00000289153.2:c.25C>T	p.Pro9Ser	p.P9S	ENST00000289153	NM_006219.2	9	Cct/Tct	1/22	0.142776793970637	3	FACETS	0.912	0.762	1	0.456	0.381	0.539	INDETERMINATE	1	TRUE	1	0.31	3		360	335	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428201	49428201	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031619-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	58	512	0	ENST00000301067.7:c.10499del	p.Gly3500GlufsTer2	p.G3500Efs*2	ENST00000301067	NM_003482.3	3500	gGa/ga	37/54	0.193428723952566	4	FACETS	0.783	0.672	0.904	0.392	0.336	0.452	CLONAL	1	TRUE	2	0.31	4		512	626	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434310	49434328	+	frameshift_variant	Frame_Shift_Del	DEL	GACTGGCAGGCACTCGGGA	GACTGGCAGGCACTCGGGA	-	novel	NA	P-0031619-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	87	526	0	ENST00000301067.7:c.7225_7243del	p.Ser2409LeufsTer11	p.S2409Lfs*11	ENST00000301067	NM_003482.3	2409	TCCCGAGTGCCTGCCAGTCct/ct	31/54	0.193428723952566	4	FACETS	1	0.962	1	0.601	0.532	0.674	CLONAL	1	TRUE	2	0.31	4		526	612	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0033093-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	484	688	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.66561071171381	2	FACETS	0.927	0.897	0.957	0.927	0.897	0.957	CLONAL	2	TRUE	0	0.697810598061827	2		688	748	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0033093-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	654	484	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.389196802901067	6	FACETS	0.967	0.942	0.991	0.806	0.785	0.826	INDETERMINATE	5	TRUE	0	0.697810598061827	6		484	929	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575209	48575209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767326	NA	P-0033093-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	161	314	0	ENST00000342988.3:c.403C>T	p.Arg135Ter	p.R135*	ENST00000342988	NM_005359.5	135	Cga/Tga	3/12	0.697810598061827	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.697810598061827	1		314	286	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989366	7989366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033093-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	62	646	0	ENST00000319144.4:c.320G>A	p.Gly107Asp	p.G107D	ENST00000319144	NM_001139.2	107	gGc/gAc	2/15	0.66561071171381	2	FACETS	0.259	0.223	0.298	0.129	0.111	0.149	SUBCLONAL	1	TRUE	0	0.697810598061827	2		646	687	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942662	48942662	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0033093-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	248	226	0	ENST00000267163.4:c.1050-1G>T		p.X350_splice	ENST00000267163	NM_000321.2	350			0.697810598061827	2	FACETS	0.993	0.95	1	0.993	0.95	1	CLONAL	2	TRUE	0	0.697810598061827	2		226	358	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236684	236684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033093-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	106	307	0	ENST00000264932.6:c.1402G>A	p.Ala468Thr	p.A468T	ENST00000264932	NM_004168.2	468	Gcc/Acc	10/15	0.69330288652537	5	FACETS	0.757	0.679	0.841	0.189	0.169	0.211	SUBCLONAL	1	TRUE	1	0.697810598061827	5		307	821	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243484	46243484	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033884-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	103	354	0	ENST00000334344.6:c.1837C>T	p.Gln613Ter	p.Q613*	ENST00000334344	NM_152641.2	613	Cag/Tag	14/21	0.701966540808998	3	FACETS	0.907	0.817	1	0.302	0.272	0.334	CLONAL	1	TRUE	0	0.701966540808998	3		354	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0033884-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	85	376	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.646088237267684	4	FACETS	0.896	0.795	1	0.299	0.265	0.335	CLONAL	1	TRUE	1	0.701966540808998	4		376	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578188	7578188	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201592	NA	P-0033884-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	317	407	0	ENST00000269305.4:c.661G>T	p.Glu221Ter	p.E221*	ENST00000269305	NM_001126112.2	221	Gag/Tag	6/11	0.646088237267684	4	FACETS	0.951	0.91	0.991	0.951	0.91	0.991	CLONAL	3	TRUE	1	0.701966540808998	4		407	539	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602284	10602302	+	frameshift_variant	Frame_Shift_Del	DEL	GGGAGCCGCCGACGGCATA	GGGAGCCGCCGACGGCATA	-	novel	NA	P-0033884-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	231	476	0	ENST00000171111.5:c.1276_1294del	p.Tyr426ThrfsTer26	p.Y426Tfs*26	ENST00000171111	NM_203500.1	426	TATGCCGTCGGCGGCTCCCac/ac	3/6	0.663551961058882	2	FACETS	0.979	0.936	1	0.979	0.936	1	CLONAL	2	TRUE	0	0.701966540808998	2		476	336	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40744858	40744865	+	frameshift_variant	Frame_Shift_Del	DEL	GTCTGGAA	GTCTGGAA	CTCT	novel	NA	P-0033884-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	157	438	1	ENST00000392038.2:c.655_662delinsAGAG	p.Phe219ArgfsTer9	p.F219Rfs*9	ENST00000392038	NM_001626.4	219	TTCCAGACc/AGAGc	8/14	0.663733660689705	2	FACETS	0.86	0.808	0.911	0.86	0.808	0.911	CLONAL	2	TRUE	0	0.701966540808998	2		439	260	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868196	45868196	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033884-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	205	467	0	ENST00000391945.4:c.494G>T	p.Gly165Val	p.G165V	ENST00000391945	NM_000400.3	165	gGg/gTg	7/23	0.663733660689705	2	FACETS	0.987	0.94	1	0.987	0.94	1	CLONAL	2	TRUE	0	0.701966540808998	2		467	296	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456429	89456429	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1257548456	NA	P-0033884-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	343	294	1	ENST00000336596.2:c.1605C>G	p.Ile535Met	p.I535M	ENST00000336596	NM_005233.5	535	atC/atG	8/17	0.701966540808998	3	FACETS	0.989	0.958	1	0.989	0.958	1	CLONAL	3	TRUE	0	0.701966540808998	3		295	445	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424216	47424216	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033884-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	92	417	0	ENST00000377045.4:c.221G>T	p.Trp74Leu	p.W74L	ENST00000377045	NM_001654.4	74	tGg/tTg	4/16	0.701966540808998	3	FACETS	0.874	0.782	0.972	0.437	0.391	0.486	CLONAL	1	TRUE	1	0.701966540808998	3		417	405	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179176	123179176	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033884-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	52	277	0	ENST00000218089.9:c.625G>T	p.Asp209Tyr	p.D209Y	ENST00000218089	NM_001042749.1	209	Gac/Tac	8/35	0.701966540808998	3	FACETS	0.672	0.575	0.776	0.336	0.287	0.388	SUBCLONAL	1	TRUE	1	0.701966540808998	3		277	298	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375906	118375906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033884-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	114	506	0	ENST00000534358.1:c.9299G>A	p.Gly3100Glu	p.G3100E	ENST00000534358	NM_005933.3	3100	gGa/gAa	27/36	0.701966540808998	3	FACETS	0.762	0.688	0.839	0.254	0.229	0.28	SUBCLONAL	1	TRUE	0	0.701966540808998	3		506	576	SUCCESS
REST	5978	MSKCC	GRCh37	4	57777678	57777678	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033884-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	99	297	0	ENST00000309042.7:c.874G>A	p.Val292Ile	p.V292I	ENST00000309042	NM_005612.4	292	Gtt/Att	2/4	1	2	FACETS	0.99	0.896	1	0.99	0.896	1	CLONAL	1	TRUE	1	0.701966540808998	2		297	285	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542150	187542151	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0033884-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	144	477	0	ENST00000441802.2:c.5589_5590delinsTT	p.Asn1864Tyr	p.N1864Y	ENST00000441802	NM_005245.3	1863	gcGAat/gcTTat	10/27	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.701966540808998	2		477	409	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393240	393240	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033884-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	73	452	0	ENST00000380956.4:c.88G>C	p.Asp30His	p.D30H	ENST00000380956	NM_001195286.1	30	Gac/Cac	2/9	0.583335134767871	6	FACETS	0.799	0.699	0.907	0.2	0.174	0.227	CLONAL	1	TRUE	2	0.701966540808998	6		452	626	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	456	556	0	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	0.823791230143531	1	FACETS	0.986	0.955	1	0.986	0.955	1	CLONAL	1	TRUE	0	0.823791230143531	1		556	660	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265352	16265352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	54	464	0	ENST00000375759.3:c.10844C>T	p.Pro3615Leu	p.P3615L	ENST00000375759	NM_015001.2	3615	cCc/cTc	14/15	0.823791230143531	1	FACETS	0.15	0.128	0.175	0.15	0.128	0.175	SUBCLONAL	1	TRUE	0	0.823791230143531	1		464	513	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101288	27101288	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	47	501	0	ENST00000324856.7:c.4570C>T	p.His1524Tyr	p.H1524Y	ENST00000324856	NM_006015.4	1524	Cat/Tat	18/20	0.823791230143531	1	FACETS	0.107	0.089	0.126	0.107	0.089	0.126	SUBCLONAL	1	TRUE	0	0.823791230143531	1		501	630	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344756	65344756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1272401704	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	46	399	0	ENST00000342505.4:c.281C>T	p.Thr94Ile	p.T94I	ENST00000342505	NM_002227.2	94	aCc/aTc	4/25	0.823791230143531	1	FACETS	0.144	0.121	0.169	0.144	0.121	0.169	SUBCLONAL	1	TRUE	0	0.823791230143531	1		399	457	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117712737	117712737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760388338	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	36	348	0	ENST00000369458.3:c.89G>A	p.Gly30Asp	p.G30D	ENST00000369458	NM_024626.3	30	gGt/gAt	2/6	0.823791230143531	1	FACETS	0.126	0.103	0.151	0.126	0.103	0.151	SUBCLONAL	1	TRUE	0	0.823791230143531	1		348	408	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161298223	161298223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	52	335	0	ENST00000367975.2:c.115G>A	p.Glu39Lys	p.E39K	ENST00000367975	NM_003001.3	39	Gag/Aag	3/6	1	2	FACETS	0.182	0.154	0.213	0.182	0.154	0.213	SUBCLONAL	1	TRUE	1	0.823791230143531	2		335	693	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230492860	230492860	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	51	522	0	ENST00000391860.1:c.194C>T	p.Ser65Phe	p.S65F	ENST00000391860	NM_001258311.1	65	tCc/tTc	2/7	1	2	FACETS	0.122	0.103	0.143	0.122	0.103	0.143	SUBCLONAL	1	TRUE	1	0.823791230143531	2		522	1013	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571952	64571953	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTTCAT	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	398	477	0	ENST00000312049.6:c.1681_1686dup	p.Met561_Lys562dup	p.M561_K562dup	ENST00000312049	NM_130799.2	561	-/ATGAAG	10/10	0.823791230143531	1	FACETS	0.895	0.862	0.927	0.895	0.862	0.927	CLONAL	1	TRUE	0	0.823791230143531	1		477	635	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942052	71942053	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1326136034	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	394	535	0	ENST00000298229.2:c.1322dup	p.Asn441LysfsTer25	p.N441Kfs*25	ENST00000298229	NM_001567.3	439	cca/ccAa	12/28	0.823791230143531	1	FACETS	0.952	0.918	0.985	0.952	0.918	0.985	CLONAL	1	TRUE	0	0.823791230143531	1		535	591	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112151	115112151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	95	539	0	ENST00000257566.3:c.1589C>T	p.Ala530Val	p.A530V	ENST00000257566	NM_016569.3	530	gCc/gTc	7/8	1	2	FACETS	0.218	0.193	0.245	0.218	0.193	0.245	SUBCLONAL	1	TRUE	1	0.823791230143531	2		539	1057	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194790	30194790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	73	363	0	ENST00000331968.5:c.355G>A	p.Ala119Thr	p.A119T	ENST00000331968	NM_002742.2	119	Gcg/Acg	2/18	1	2	FACETS	0.214	0.186	0.243	0.214	0.186	0.243	SUBCLONAL	1	TRUE	1	0.823791230143531	2		363	830	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	69061214	69061214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	26	239	0	ENST00000487270.1:c.1049G>A	p.Cys350Tyr	p.C350Y	ENST00000487270	NM_133509.3	350	tGc/tAc	11/11	1	2	FACETS	0.143	0.113	0.178	0.143	0.113	0.178	SUBCLONAL	1	TRUE	1	0.823791230143531	2		239	442	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675095	40675095	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	206	448	0	ENST00000249776.8:c.59C>A	p.Thr20Lys	p.T20K	ENST00000249776	NM_033286.3	20	aCa/aAa	1/9	1	2	FACETS	0.513	0.476	0.551	0.513	0.476	0.551	SUBCLONAL	1	TRUE	1	0.823791230143531	2		448	975	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43771689	43771689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs952691589	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	43	370	0	ENST00000382044.4:c.694C>T	p.Pro232Ser	p.P232S	ENST00000382044	NM_001141980.1	232	Ccc/Tcc	7/28	1	2	FACETS	0.126	0.105	0.15	0.126	0.105	0.15	SUBCLONAL	1	TRUE	1	0.823791230143531	2		370	826	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99491888	99491888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752140857	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	50	397	0	ENST00000268035.6:c.3673G>A	p.Val1225Ile	p.V1225I	ENST00000268035	NM_000875.3	1225	Gtc/Atc	20/21	1	2	FACETS	0.144	0.121	0.169	0.144	0.121	0.169	SUBCLONAL	1	TRUE	1	0.823791230143531	2		397	845	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646654	23646654	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	81	360	0	ENST00000261584.4:c.1213C>T	p.Pro405Ser	p.P405S	ENST00000261584	NM_024675.3	405	Cct/Tct	4/13	0.808981384494678	1	FACETS	0.253	0.223	0.284	0.253	0.223	0.284	SUBCLONAL	1	TRUE	0	0.823791230143531	1		360	458	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348442	89348442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	58	569	0	ENST00000301030.4:c.4508C>T	p.Ala1503Val	p.A1503V	ENST00000301030	NM_001256183.1	1503	gCc/gTc	9/13	0.783036501489155	2	FACETS	0.162	0.138	0.188	0.081	0.069	0.094	SUBCLONAL	1	TRUE	0	0.823791230143531	2		569	870	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882998	89882998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752776388	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	81	390	0	ENST00000389301.3:c.26C>T	p.Ser9Phe	p.S9F	ENST00000389301	NM_000135.2	9	tCc/tTc	1/43	0.783036501489155	2	FACETS	0.286	0.252	0.323	0.143	0.126	0.162	SUBCLONAL	1	TRUE	0	0.823791230143531	2		390	687	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359621	40359621	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	65	327	0	ENST00000293328.3:c.2032G>A	p.Val678Ile	p.V678I	ENST00000293328	NM_012448.3	678	Gta/Ata	16/19	1	2	FACETS	0.218	0.189	0.25	0.218	0.189	0.25	SUBCLONAL	1	TRUE	1	0.823791230143531	2		327	723	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40876363	40876363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	46	361	0	ENST00000428826.2:c.326C>T	p.Pro109Leu	p.P109L	ENST00000428826		109	cCc/cTc	5/21	1	2	FACETS	0.143	0.12	0.169	0.143	0.12	0.169	SUBCLONAL	1	TRUE	1	0.823791230143531	2		361	782	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244505	41244505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	45	353	0	ENST00000357654.3:c.3043G>A	p.Gly1015Arg	p.G1015R	ENST00000357654	NM_007294.3	1015	Gga/Aga	10/23	1	2	FACETS	0.157	0.131	0.186	0.157	0.131	0.186	SUBCLONAL	1	TRUE	1	0.823791230143531	2		353	696	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222533	2222533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	76	425	0	ENST00000398665.3:c.3365G>A	p.Gly1122Glu	p.G1122E	ENST00000398665	NM_032482.2	1122	gGg/gAg	24/28	1	2	FACETS	0.199	0.174	0.226	0.199	0.174	0.226	SUBCLONAL	1	TRUE	1	0.823791230143531	2		425	928	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355337	15355337	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	182	215	0	ENST00000263377.2:c.2286G>T	p.Gln762His	p.Q762H	ENST00000263377	NM_058243.2	762	caG/caT	13/20	1	2	FACETS	0.958	0.893	1	0.958	0.893	1	CLONAL	1	TRUE	1	0.823791230143531	2		215	461	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367792	15367792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	65	338	0	ENST00000263377.2:c.1534G>A	p.Ala512Thr	p.A512T	ENST00000263377	NM_058243.2	512	Gct/Act	8/20	1	2	FACETS	0.219	0.189	0.251	0.219	0.189	0.251	SUBCLONAL	1	TRUE	1	0.823791230143531	2		338	721	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937568	17937568	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	70	420	0	ENST00000458235.1:c.3359C>T	p.Ser1120Phe	p.S1120F	ENST00000458235	NM_000215.3	1120	tCc/tTc	24/24	1	2	FACETS	0.192	0.167	0.22	0.192	0.167	0.22	SUBCLONAL	1	TRUE	1	0.823791230143531	2		420	885	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937592	17937592	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	97	426	0	ENST00000458235.1:c.3335C>T	p.Ala1112Val	p.A1112V	ENST00000458235	NM_000215.3	1112	gCt/gTt	24/24	1	2	FACETS	0.25	0.222	0.28	0.25	0.222	0.28	SUBCLONAL	1	TRUE	1	0.823791230143531	2		426	942	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942568	17942568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	68	378	0	ENST00000458235.1:c.2720G>A	p.Ser907Asn	p.S907N	ENST00000458235	NM_000215.3	907	aGc/aAc	20/24	1	2	FACETS	0.237	0.205	0.27	0.237	0.205	0.27	SUBCLONAL	1	TRUE	1	0.823791230143531	2		378	698	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383644	42383644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148797987	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	159	424	0	ENST00000221972.3:c.419C>T	p.Thr140Ile	p.T140I	ENST00000221972	NM_021601.3	140	aCc/aTc	3/5	1	2	FACETS	0.432	0.396	0.47	0.432	0.396	0.47	SUBCLONAL	1	TRUE	1	0.823791230143531	2		424	894	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796489	42796489	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747682952	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	93	527	0	ENST00000575354.2:c.3046C>T	p.Pro1016Ser	p.P1016S	ENST00000575354	NM_015125.3	1016	Ccc/Tcc	13/20	1	2	FACETS	0.226	0.201	0.254	0.226	0.201	0.254	SUBCLONAL	1	TRUE	1	0.823791230143531	2		527	997	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910635	50910635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757100984	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	72	404	0	ENST00000440232.2:c.1738G>A	p.Asp580Asn	p.D580N	ENST00000440232	NM_002691.3	580	Gac/Aac	14/27	1	2	FACETS	0.214	0.187	0.245	0.214	0.187	0.245	SUBCLONAL	1	TRUE	1	0.823791230143531	2		404	815	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437172	220437172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199544141	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	30	467	0	ENST00000243786.2:c.76C>T	p.Arg26Trp	p.R26W	ENST00000243786	NM_002191.3	26	Cgg/Tgg	1/2	0.823791230143531	1	FACETS	0.083	0.066	0.102	0.083	0.066	0.102	SUBCLONAL	1	TRUE	0	0.823791230143531	1		467	518	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021532	31021532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	52	500	0	ENST00000375687.4:c.1531C>T	p.Pro511Ser	p.P511S	ENST00000375687	NM_015338.5	511	Cct/Tct	12/13	1	2	FACETS	0.127	0.107	0.149	0.127	0.107	0.149	SUBCLONAL	1	TRUE	1	0.823791230143531	2		500	993	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383238	31383238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150682895	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	120	487	0	ENST00000328111.2:c.1150G>A	p.Ala384Thr	p.A384T	ENST00000328111	NM_006892.3	384	Gct/Act	11/23	1	2	FACETS	0.29	0.262	0.321	0.29	0.262	0.321	SUBCLONAL	1	TRUE	1	0.823791230143531	2		487	1003	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934020	49934020	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	58	530	0	ENST00000296474.3:c.2392C>T	p.His798Tyr	p.H798Y	ENST00000296474	NM_002447.2	798	Cac/Tac	9/20	1	2	FACETS	0.141	0.12	0.163	0.141	0.12	0.163	SUBCLONAL	1	TRUE	1	0.823791230143531	2		530	1000	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851807	134851807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1406552743	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	91	562	0	ENST00000398015.3:c.1213G>A	p.Asp405Asn	p.D405N	ENST00000398015	NM_004441.4	405	Gac/Aac	5/16	1	2	FACETS	0.213	0.188	0.24	0.213	0.188	0.24	SUBCLONAL	1	TRUE	1	0.823791230143531	2		562	1037	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146641	185146641	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	204	407	0	ENST00000265026.3:c.272A>G	p.Asp91Gly	p.D91G	ENST00000265026	NM_004721.4	91	gAt/gGt	2/14	1	2	FACETS	0.54	0.5	0.58	0.54	0.5	0.58	SUBCLONAL	1	TRUE	1	0.823791230143531	2		407	918	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902607	1902607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770395467	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	43	484	0	ENST00000382891.5:c.226G>A	p.Ala76Thr	p.A76T	ENST00000382891	NM_133335.3	76	Gcc/Acc	2/22	0.45239132067165	1	FACETS	0.078	0.065	0.093	0.078	0.065	0.093	INDETERMINATE	1	TRUE	0	0.823791230143531	1		484	785	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55569954	55569954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138585275	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	39	297	1	ENST00000288135.5:c.821C>T	p.Thr274Met	p.T274M	ENST00000288135	NM_000222.2	274	aCg/aTg	5/21	1	2	FACETS	0.168	0.139	0.201	0.168	0.139	0.201	SUBCLONAL	1	TRUE	1	0.823791230143531	2		298	562	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1296025	1296025	+	upstream_gene_variant	5'Flank	SNP	A	A	G	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	90	578	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.208	0.184	0.234	0.208	0.184	0.234	SUBCLONAL	1	TRUE	1	0.823791230143531	2		578	1049	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659272	86659272	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	53	299	0	ENST00000274376.6:c.1561G>A	p.Asp521Asn	p.D521N	ENST00000274376	NM_002890.2	521	Gat/Aat	11/25	1	2	FACETS	0.263	0.224	0.306	0.263	0.224	0.306	SUBCLONAL	1	TRUE	1	0.823791230143531	2		299	489	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	35	417	0	ENST00000257430.4:c.4135G>A	p.Glu1379Lys	p.E1379K	ENST00000257430	NM_000038.5	1379	Gag/Aag	16/16	1	2	FACETS	0.098	0.079	0.119	0.098	0.079	0.119	SUBCLONAL	1	TRUE	1	0.823791230143531	2		417	869	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046665	180046665	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	110	622	0	ENST00000261937.6:c.2647G>A	p.Glu883Lys	p.E883K	ENST00000261937	NM_182925.4	883	Gag/Aag	18/30	1	2	FACETS	0.223	0.2	0.249	0.223	0.2	0.249	SUBCLONAL	1	TRUE	1	0.823791230143531	2		622	1195	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322997	31322997	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1206176477	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	88	545	0	ENST00000412585.2:c.899C>T	p.Pro300Leu	p.P300L	ENST00000412585	NM_005514.6	300	cCg/cTg	5/8	0.823791230143531	1	FACETS	0.204	0.18	0.229	0.204	0.18	0.229	SUBCLONAL	1	TRUE	0	0.823791230143531	1		545	617	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187527	32187527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	58	512	0	ENST00000375023.3:c.1352C>T	p.Ser451Phe	p.S451F	ENST00000375023	NM_004557.3	451	tCc/tTc	8/30	0.823791230143531	1	FACETS	0.135	0.116	0.156	0.135	0.116	0.156	SUBCLONAL	1	TRUE	0	0.823791230143531	1		512	613	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820946	32820946	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	39	509	0	ENST00000354258.4:c.648A>T	p.Lys216Asn	p.K216N	ENST00000354258	NM_000593.5	216	aaA/aaT	1/11	0.823791230143531	1	FACETS	0.087	0.071	0.104	0.087	0.071	0.104	SUBCLONAL	1	TRUE	0	0.823791230143531	1		509	642	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099506	157099506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	112	553	0	ENST00000346085.5:c.443C>T	p.Pro148Leu	p.P148L	ENST00000346085	NM_020732.3	148	cCt/cTt	1/20	0.823791230143531	1	FACETS	0.263	0.236	0.29	0.263	0.236	0.29	SUBCLONAL	1	TRUE	0	0.823791230143531	1		553	609	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913427	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	74	315	0	ENST00000275493.2:c.2236G>A	p.Glu746Lys	p.E746K	ENST00000275493	NM_005228.3	746	Gaa/Aaa	19/28	1	2	FACETS	0.277	0.242	0.315	0.277	0.242	0.315	SUBCLONAL	1	TRUE	1	0.823791230143531	2		315	648	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381502	81381502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	58	389	0	ENST00000222390.5:c.559C>T	p.Pro187Ser	p.P187S	ENST00000222390	NM_000601.4	187	Ccc/Tcc	5/18	1	2	FACETS	0.199	0.17	0.23	0.199	0.17	0.23	SUBCLONAL	1	TRUE	1	0.823791230143531	2		389	708	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2033051	2033051	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374114848	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	31	387	0	ENST00000349721.2:c.325C>T	p.Pro109Ser	p.P109S	ENST00000349721	NM_003070.3	109	Ccc/Tcc	3/34	0.823791230143531	1	FACETS	0.089	0.071	0.109	0.089	0.071	0.109	SUBCLONAL	1	TRUE	0	0.823791230143531	1		387	498	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080590	5080590	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	26	295	0	ENST00000381652.3:c.2341G>A	p.Ala781Thr	p.A781T	ENST00000381652	NM_004972.3	781	Gca/Aca	18/25	0.823791230143531	1	FACETS	0.113	0.089	0.14	0.113	0.089	0.14	SUBCLONAL	1	TRUE	0	0.823791230143531	1		295	329	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521327	8521327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	25	326	0	ENST00000356435.5:c.911C>T	p.Ala304Val	p.A304V	ENST00000356435		304	gCt/gTt	9/35	0.823791230143531	1	FACETS	0.095	0.075	0.119	0.095	0.075	0.119	SUBCLONAL	1	TRUE	0	0.823791230143531	1		326	375	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250008	110250008	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	179	461	0	ENST00000374672.4:c.667G>A	p.Gly223Ser	p.G223S	ENST00000374672	NM_004235.4	223	Ggc/Agc	3/5	1	2	FACETS	0.516	0.476	0.557	0.516	0.476	0.557	SUBCLONAL	1	TRUE	1	0.823791230143531	2		461	843	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760214	133760214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	76	422	0	ENST00000318560.5:c.2537C>T	p.Ala846Val	p.A846V	ENST00000318560	NM_005157.4	846	gCt/gTt	11/11	1	2	FACETS	0.219	0.192	0.249	0.219	0.192	0.249	SUBCLONAL	1	TRUE	1	0.823791230143531	2		422	841	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760700	133760700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	91	559	0	ENST00000318560.5:c.3023C>T	p.Thr1008Ile	p.T1008I	ENST00000318560	NM_005157.4	1008	aCc/aTc	11/11	1	2	FACETS	0.206	0.182	0.231	0.206	0.182	0.231	SUBCLONAL	1	TRUE	1	0.823791230143531	2		559	1075	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135777991	135777991	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	32	409	0	ENST00000298552.3:c.2391+1G>A		p.X797_splice	ENST00000298552	NM_001162426.1	797			1	2	FACETS	0.097	0.078	0.118	0.097	0.078	0.118	SUBCLONAL	1	TRUE	1	0.823791230143531	2		409	804	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293687	137293687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	180	461	0	ENST00000481739.1:c.238C>T	p.Pro80Ser	p.P80S	ENST00000481739	NM_002957.4	80	Ccc/Tcc	2/10	1	2	FACETS	0.532	0.491	0.574	0.532	0.491	0.574	SUBCLONAL	1	TRUE	1	0.823791230143531	2		461	822	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928852	44928852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750754452	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	61	331	1	ENST00000377967.4:c.1952C>T	p.Ser651Leu	p.S651L	ENST00000377967	NM_021140.2	651	tCg/tTg	17/29	0.823791230143531	1	FACETS	0.262	0.227	0.299	0.262	0.227	0.299	SUBCLONAL	1	TRUE	0	0.823791230143531	1		332	333	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411821	63411821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034730-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	35	561	0	ENST00000330258.3:c.1346C>T	p.Ala449Val	p.A449V	ENST00000330258	NM_152424.3	449	gCc/gTc	2/2	0.823791230143531	1	FACETS	0.073	0.06	0.089	0.073	0.06	0.089	SUBCLONAL	1	TRUE	0	0.823791230143531	1		561	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577098	7577098	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1567547687	NA	P-0036028-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	641	350	0	ENST00000269305.4:c.840A>C	p.Arg280Ser	p.R280S	ENST00000269305	NM_001126112.2	280	agA/agC	8/11	0.92049671655624	4	FACETS	1	0.996	1	1	0.996	1	CLONAL	4	TRUE	0	0.92049671655624	4		350	661	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166274	118166274	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036028-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	189	385	0	ENST00000369448.3:c.784G>C	p.Glu262Gln	p.E262Q	ENST00000369448	NM_017709.3	262	Gaa/Caa	2/2	0.92049671655624	3	FACETS	1	0.951	1	0.514	0.478	0.551	CLONAL	1	TRUE	1	0.92049671655624	3		385	583	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906903	32906903	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036028-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	149	295	0	ENST00000380152.3:c.1288G>C	p.Asp430His	p.D430H	ENST00000380152		430	Gac/Cac	10/27	0.92049671655624	2	FACETS	0.941	0.873	1	0.471	0.436	0.505	CLONAL	1	TRUE	0	0.92049671655624	2		295	344	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433771	149433771	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036028-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	159	389	0	ENST00000286301.3:c.2780C>G	p.Pro927Arg	p.P927R	ENST00000286301	NM_005211.3	927	cCg/cGg	22/22	0.92049671655624	2	FACETS	1	0.949	1	0.511	0.476	0.546	CLONAL	1	TRUE	0	0.92049671655624	2		389	338	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53244021	53244026	+	inframe_deletion	In_Frame_Del	DEL	TGACTC	TGACTC	-	novel	NA	P-0036028-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	74	259	0	ENST00000375401.3:c.967_972del	p.Glu323_Ser324del	p.E323_S324del	ENST00000375401	NM_004187.3	323	GAGTCA/-	8/26	0.214048852757319	5	FACETS	1	0.939	1	0.221	0.194	0.249	INDETERMINATE	1	TRUE	0	0.92049671655624	5		259	347	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026836	48026836	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064795256	NA	P-0036029-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	530	461	0	ENST00000234420.5:c.1714C>T	p.Gln572Ter	p.Q572*	ENST00000234420	NM_000179.2	572	Cag/Tag	4/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.911376608387719	2		461	1095	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351844	89351844	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1041612791	NA	P-0036029-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	11	490	0	ENST00000301030.4:c.1106A>G	p.Lys369Arg	p.K369R	ENST00000301030	NM_001256183.1	369	aAg/aGg	9/13	0.911376608387719	1	FACETS	0.026	0.018	0.037	0.026	0.018	0.037	SUBCLONAL	1	TRUE	0	0.911376608387719	1		490	502	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41209148	41209148	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs80357270	NA	P-0036029-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	204	414	0	ENST00000357654.3:c.5198A>G	p.Asp1733Gly	p.D1733G	ENST00000357654	NM_007294.3	1733	gAt/gGt	19/23	1	2	FACETS	0.472	0.438	0.508	0.472	0.438	0.508	SUBCLONAL	1	TRUE	1	0.911376608387719	2		414	948	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63976464	63976464	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036029-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	161	480	0	ENST00000398590.3:c.1611C>A	p.Asp537Glu	p.D537E	ENST00000398590	NM_001177387.1	537	gaC/gaA	11/14	1	2	FACETS	0.355	0.325	0.387	0.355	0.325	0.387	SUBCLONAL	1	TRUE	1	0.911376608387719	2		480	994	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63976471	63976485	+	inframe_deletion	In_Frame_Del	DEL	TGGAATCGACTTCGC	TGGAATCGACTTCGC	-	novel	NA	P-0036029-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	150	491	0	ENST00000398590.3:c.1620_1634del	p.Trp540_Arg544del	p.W540_R544del	ENST00000398590	NM_001177387.1	540	TGGAATCGACTTCGC/-	11/14	1	2	FACETS	0.326	0.297	0.356	0.326	0.297	0.356	SUBCLONAL	1	TRUE	1	0.911376608387719	2		491	1011	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037088-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	60	571	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.178806370572632	0	FACETS	0.434	0.374	0.5			1	INDETERMINATE	1	TRUE	0	0.312912761799518	0		571	607	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0037088-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	84	542	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	0.835	0.738	0.939	0.835	0.738	0.939	CLONAL	1	TRUE	1	0.312912761799518	2		542	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037088-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	118	571	0	ENST00000269305.4:c.376T>C	p.Tyr126His	p.Y126H	ENST00000269305	NM_001126112.2	126	Tac/Cac	5/11	0.312912761799518	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.312912761799518	1		571	578	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050394	176050394	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037088-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	31	350	0	ENST00000367669.3:c.1171G>T	p.Glu391Ter	p.E391*	ENST00000367669	NM_022457.5	391	Gaa/Taa	11/20	0.188718947608728	3	FACETS	0.513	0.414	0.624	0.256	0.207	0.312	SUBCLONAL	1	TRUE	1	0.312912761799518	3		350	447	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433276	49433276	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037088-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	58	653	0	ENST00000301067.7:c.8171C>A	p.Pro2724His	p.P2724H	ENST00000301067	NM_003482.3	2724	cCc/cAc	32/54	1	2	FACETS	0.527	0.452	0.609	0.527	0.452	0.609	SUBCLONAL	1	TRUE	1	0.312912761799518	2		653	704	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0038790-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	349	344	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.513817915655612	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.513817915655612	3		344	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0038790-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	364	592	1	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.507811889773287	3	FACETS	0.933	0.895	0.971	0.933	0.895	0.971	CLONAL	3	TRUE	0	0.513817915655612	3		593	636	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045024	47045024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038790-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	160	297	0	ENST00000377604.3:c.2350C>T	p.His784Tyr	p.H784Y	ENST00000377604	NM_001204468.1	784	Cac/Tac	20/24	1	1	FACETS	0.818	0.767	0.868	1	0.992	1	CLONAL	2	TRUE	0	0.513817915655612	1		297	283	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082695	16082695	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038790-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	27	273	0	ENST00000281043.3:c.509G>A	p.Arg170His	p.R170H	ENST00000281043	NM_005378.4	170	cGc/cAc	2/3	0.257453718577599	3	FACETS	0.706	0.567	0.863	0.353	0.283	0.432	INDETERMINATE	1	TRUE	1	0.513817915655612	3		273	187	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27098999	27098999	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038790-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	180	532	0	ENST00000324856.7:c.3415G>T	p.Gly1139Ter	p.G1139*	ENST00000324856	NM_006015.4	1139	Gga/Tga	13/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.513817915655612	2		532	621	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246387	46246387	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038790-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	472	524	0	ENST00000334344.6:c.4483del	p.His1495IlefsTer21	p.H1495Ifs*21	ENST00000334344	NM_152641.2	1494	tCc/tc	15/21	0.513817915655612	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	0	0.513817915655612	3		524	757	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610560	81610560	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038790-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	290	454	1	ENST00000298171.2:c.2158C>A	p.Gln720Lys	p.Q720K	ENST00000298171	NM_000369.2	720	Cag/Aag	10/10	0.513817915655612	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.513817915655612	3		455	702	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817493	39817493	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038790-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	136	488	0	ENST00000288319.7:c.70G>T	p.Gly24Ter	p.G24*	ENST00000288319	NM_182918.3	24	Gga/Tga	2/10	1	2	FACETS	0.975	0.891	1	0.975	0.891	1	CLONAL	1	TRUE	1	0.513817915655612	2		488	543	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177816	142177816	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs373093280	NA	P-0038790-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	319	332	0	ENST00000350721.4:c.7487A>G	p.Asn2496Ser	p.N2496S	ENST00000350721	NM_001184.3	2496	aAt/aGt	44/47	0.501431373411062	4	FACETS	0.974	0.928	1	0.974	0.928	1	CLONAL	3	TRUE	1	0.513817915655612	4		332	643	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6036983	6036983	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0038790-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	241	349	0	ENST00000265849.7:c.777T>A	p.Cys259Ter	p.C259*	ENST00000265849	NM_000535.5	259	tgT/tgA	7/15	0.383400362433165	4	FACETS	0.989	0.928	1	0.989	0.928	1	CLONAL	2	TRUE	2	0.513817915655612	4		349	718	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508617	106508617	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038790-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	253	469	0	ENST00000359195.3:c.611C>G	p.Ser204Cys	p.S204C	ENST00000359195	NM_002649.2	204	tCc/tGc	2/11	0.513817915655612	4	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	2	0.513817915655612	4		469	742	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340351	8340351	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038790-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	301	459	0	ENST00000356435.5:c.5245A>C	p.Met1749Leu	p.M1749L	ENST00000356435		1749	Atg/Ctg	31/35	0.513817915655612	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.513817915655612	2		459	561	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738186	133738186	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038790-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	264	355	0	ENST00000318560.5:c.586G>T	p.Ala196Ser	p.A196S	ENST00000318560	NM_005157.4	196	Gcc/Tcc	4/11	0.484476418564274	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.513817915655612	3		355	618	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671952	30671952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200530869	NA	P-0038865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	269	705	2	ENST00000376406.3:c.5008G>A	p.Val1670Ile	p.V1670I	ENST00000376406	NM_014641.2	1670	Gtc/Atc	10/15	0.8479771445935	3	FACETS	1	0.948	1	0.504	0.474	0.535	CLONAL	1	TRUE	1	0.900270510090648	3		707	859	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579551	7579552	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGCATCAAATCC	novel	NA	P-0038865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	447	701	0	ENST00000269305.4:c.135_136insGGATTTGATGCTG	p.Ser46GlyfsTer10	p.S46Gfs*10	ENST00000269305	NM_001126112.2	45	-/GGATTTGATGCTG	4/11	0.900270510090648	2	FACETS	0.8	0.775	0.823	0.8	0.775	0.823	SUBCLONAL	2	TRUE	0	0.900270510090648	2		701	621	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295535	1295535	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0038865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	239	859	0				ENST00000310581	NM_198253.2	-/1132			0.900270510090648	5	FACETS	0.998	0.93	1	0.333	0.31	0.356	CLONAL	1	TRUE	2	0.900270510090648	5		859	1251	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381457	81381457	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	192	408	0	ENST00000222390.5:c.604G>T	p.Asp202Tyr	p.D202Y	ENST00000222390	NM_000601.4	202	Gac/Tac	5/18	0.78697795090236	3	FACETS	0.927	0.861	0.995	0.464	0.43	0.498	CLONAL	1	TRUE	1	0.900270510090648	3		408	667	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0039314-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	41	344	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.862	0.719	1	0.862	0.719	1	CLONAL	1	TRUE	1	0.26	2		344	366	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948502	31948502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201134143	NA	P-0039314-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	26	238	0	ENST00000375333.2:c.985C>T	p.Arg329Trp	p.R329W	ENST00000375333	NM_032454.1	329	Cgg/Tgg	7/8	0.301220796126458	3	FACETS	0.638	0.506	0.791	0.319	0.253	0.396	SUBCLONAL	1	TRUE	1	0.26	3		238	354	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587409	29587409	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039314-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	38	333	0	ENST00000356175.3:c.4390G>A	p.Asp1464Asn	p.D1464N	ENST00000356175	NM_000267.3	1464	Gat/Aat	33/57	NA	2	FACETS	0.648	0.536	0.774			1	INDETERMINATE	1	TRUE	NA	0.26	2		333	451	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61310691	61310691	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039314-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	55	370	0	ENST00000341074.5:c.121G>C	p.Val41Leu	p.V41L	ENST00000341074	NM_002974.2	41	Gtc/Ctc	2/8	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.26	2		370	403	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61323000	61323000	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039314-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	137	565	0	ENST00000283752.5:c.1064C>T	p.Ser355Leu	p.S355L	ENST00000283752	NM_006919.2	355	tCa/tTa	8/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.26	2		565	797	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600476	10600477	+	missense_variant	Missense_Mutation	DNP	CT	CT	AG	novel	NA	P-0039314-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	196	610	0	ENST00000171111.5:c.1378_1379inv	p.Arg460Leu	p.R460L	ENST00000171111	NM_203500.1	460	AGg/CTg	4/6	0.249684303732321	2	FACETS	0.817	0.756	0.879	0.817	0.756	0.879	CLONAL	2	TRUE	0	0.26	2		610	923	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513288	44513288	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039314-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	152	584	0	ENST00000291552.4:c.647G>T	p.Gly216Val	p.G216V	ENST00000291552	NM_006758.2	216	gGc/gTc	8/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.26	2		584	911	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168618	32168618	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039314-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	89	520	0	ENST00000375023.3:c.4305T>A	p.His1435Gln	p.H1435Q	ENST00000375023	NM_004557.3	1435	caT/caA	23/30	0.301220796126458	3	FACETS	0.956	0.847	1	0.478	0.423	0.537	CLONAL	1	TRUE	1	0.26	3		520	809	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212734	27212734	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039314-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	86	511	0	ENST00000380036.4:c.2716C>A	p.Pro906Thr	p.P906T	ENST00000380036	NM_000459.3	906	Ccc/Acc	17/23	0.301220796126458	1	FACETS	0.996	0.882	1	0.996	0.882	1	CLONAL	1	TRUE	0	0.26	1		511	578	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057976	27057976	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039614-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	121	585	0	ENST00000324856.7:c.1684C>T	p.Gln562Ter	p.Q562*	ENST00000324856	NM_006015.4	562	Cag/Tag	3/20	0.665092279198688	3	FACETS	1	0.977	1			1	CLONAL	3	TRUE	NA	0.665092279198688	3		585	153	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259513	16259513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039614-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	56	610	0	ENST00000375759.3:c.6778G>A	p.Glu2260Lys	p.E2260K	ENST00000375759	NM_015001.2	2260	Gag/Aag	11/15	0.665092279198688	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	0	0.665092279198688	2		610	81	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104700	69104700	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149428879	NA	P-0039614-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	38	498	0	ENST00000288368.4:c.4544C>T	p.Ser1515Leu	p.S1515L	ENST00000288368	NM_024870.2	1515	tCg/tTg	37/40	0.461388638934715	4	FACETS	0.981	0.837	1	0.654	0.558	0.753	CLONAL	2	TRUE	1	0.665092279198688	4		498	97	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577508	7577509	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039614-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	49	384	0	ENST00000269305.4:c.772_773insC	p.Glu258AlafsTer6	p.E258Afs*6	ENST00000269305	NM_001126112.2	258	gaa/gCaa	7/11	0.665092279198688	2	FACETS	0.921	0.822	1	0.921	0.822	1	CLONAL	2	TRUE	0	0.665092279198688	2		384	80	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787769	135787769	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0039614-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	64	351	1	ENST00000298552.3:c.813T>G	p.Tyr271Ter	p.Y271*	ENST00000298552	NM_001162426.1	271	taT/taG	9/23	0.665092279198688	3	FACETS	1	0.928	1	1	0.928	1	CLONAL	3	TRUE	0	0.665092279198688	3		352	85	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259153	16259153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039614-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	41	559	0	ENST00000375759.3:c.6418G>A	p.Asp2140Asn	p.D2140N	ENST00000375759	NM_015001.2	2140	Gat/Aat	11/15	0.665092279198688	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	2	TRUE	0	0.665092279198688	2		559	60	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257983	16257983	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039614-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	88	523	0	ENST00000375759.3:c.5248G>C	p.Asp1750His	p.D1750H	ENST00000375759	NM_015001.2	1750	Gat/Cat	11/15	0.665092279198688	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.665092279198688	2		523	107	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791525	42791525	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039614-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	70	586	1	ENST00000575354.2:c.506G>A	p.Arg169His	p.R169H	ENST00000575354	NM_015125.3	169	cGt/cAt	4/20	0.665092279198688	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.665092279198688	4		587	148	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721486	49721486	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039614-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	19	343	0	ENST00000449682.2:c.2153T>G	p.Ile718Ser	p.I718S	ENST00000449682	NM_020998.3	718	aTt/aGt	18/18	0.662192365599476	5	FACETS	1	0.902	1	0.272	0.21	0.34	CLONAL	1	TRUE	0	0.665092279198688	5		343	84	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158735	26158735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039614-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	42	261	0	ENST00000289316.2:c.338C>T	p.Ser113Leu	p.S113L	ENST00000289316	NM_138720.2	113	tCg/tTg	1/2	0.665092279198688	2	FACETS	0.896	0.835	0.942	1	0.978	1	CLONAL	3	TRUE	0	0.665092279198688	2		261	47	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0039872-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	234	613	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.907329622317358	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.907329622317358	1		614	276	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0039872-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	198	844	17	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	0.387352149659617	1	FACETS	0.505	0.473	0.538	0.505	0.473	0.538	INDETERMINATE	1	TRUE	0	0.907329622317358	1		861	472	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463228	25463228	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039872-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	221	564	0	ENST00000264709.3:c.2265T>A	p.Phe755Leu	p.F755L	ENST00000264709	NM_175629.2	755	ttT/ttA	19/23	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.907329622317358	2		564	484	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427245	49427246	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0039872-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	225	728	0	ENST00000301067.7:c.11242_11243del	p.Leu3748ArgfsTer263	p.L3748Rfs*263	ENST00000301067	NM_003482.3	3748	CTa/a	39/54	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.907329622317358	2		728	477	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491283	2491283	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs776730987	NA	P-0041155-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	309	616	0	ENST00000355716.4:c.326G>C	p.Arg109Pro	p.R109P	ENST00000355716	NM_003820.2	109	cGg/cCg	4/8	1	2	FACETS	0.994	0.941	1	0.994	0.941	1	CLONAL	1	TRUE	1	0.708605220536227	2		616	877	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579325	7579326	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0041155-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	652	532	0	ENST00000269305.4:c.360_361dup	p.Ser121CysfsTer3	p.S121Cfs*3	ENST00000269305	NM_001126112.2	121	tct/tGTct	4/11	0.657057143821597	3	FACETS	0.902	0.879	0.925	0.902	0.879	0.925	CLONAL	3	TRUE	0	0.708605220536227	3		532	921	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216336	2216336	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041155-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	151	577	0	ENST00000398665.3:c.1980G>C	p.Lys660Asn	p.K660N	ENST00000398665	NM_032482.2	660	aaG/aaC	20/28	0.708605220536227	1	FACETS	0.398	0.364	0.433	0.398	0.364	0.433	SUBCLONAL	1	TRUE	0	0.708605220536227	1		577	692	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593669	55593669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041155-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1533	161	379	0	ENST00000288135.5:c.1735G>A	p.Asp579Asn	p.D579N	ENST00000288135	NM_000222.2	579	Gat/Aat	11/21	0.708605220536227	6	FACETS	0.648	0.592	0.708	0.13	0.118	0.142	SUBCLONAL	1	TRUE	1	0.708605220536227	6		379	1694	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0041452-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	46	344	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.395266158787415	2		344	214	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610608	52610609	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0041452-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	53	425	0	ENST00000394830.3:c.3564dup	p.Glu1189ArgfsTer6	p.E1189Rfs*6	ENST00000394830	NM_018313.4	1188	-/A	23/30	1	2	FACETS	0.982	0.845	1	0.982	0.845	1	CLONAL	1	TRUE	1	0.395266158787415	2		425	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578213	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs864309495	NA	P-0041452-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	73	684	0	ENST00000269305.4:c.636del	p.Arg213AspfsTer34	p.R213Dfs*34	ENST00000269305	NM_001126112.2	212	ttT/tt	6/11	0.395266158787415	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.395266158787415	1		684	265	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586250	48586250	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041452-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	46	373	0	ENST00000342988.3:c.919G>T	p.Glu307Ter	p.E307*	ENST00000342988	NM_005359.5	307	Gag/Tag	8/12	0.395266158787415	1	FACETS	0.968	0.826	1	0.968	0.826	1	CLONAL	1	TRUE	0	0.395266158787415	1		373	193	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351422	70351422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041452-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	61	310	0	ENST00000374080.3:c.4070G>A	p.Arg1357His	p.R1357H	ENST00000374080		1357	cGc/cAc	29/45	1	1	FACETS	0.924	0.822	1	1	0.981	1	CLONAL	2	TRUE	0	0.395266158787415	1		310	134	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924506	131924506	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041452-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	67	385	0	ENST00000265335.6:c.1179T>G	p.Ile393Met	p.I393M	ENST00000265335		393	atT/atG	8/25	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.395266158787415	2		385	284	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413956	139413956	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041452-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	75	535	0	ENST00000277541.6:c.804C>G	p.Asn268Lys	p.N268K	ENST00000277541	NM_017617.3	268	aaC/aaG	5/34	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.395266158787415	2		535	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782197	NA	P-0042249-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	93	881	0	ENST00000269305.4:c.434T>C	p.Leu145Pro	p.L145P	ENST00000269305	NM_001126112.2	145	cTg/cCg	5/11	1	2	FACETS	0.764	0.683	0.849	1	0.981	1	SUBCLONAL	2	TRUE	1	0.281171430372558	2		881	433	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592118	67592122	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTT	CTTTT	-	novel	NA	P-0042249-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	26	553	0	ENST00000274335.5:c.1937_1941del	p.Phe646CysfsTer6	p.F646Cfs*6	ENST00000274335		645	aCTTTT/a	14/15	0.281171430372558	1	FACETS	0.514	0.408	0.636	0.514	0.408	0.636	SUBCLONAL	1	TRUE	0	0.281171430372558	1		553	309	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970955	21970955	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042249-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	70	974	0	ENST00000304494.5:c.403G>A	p.Gly135Arg	p.G135R	ENST00000304494	NM_000077.4	135	Ggg/Agg	2/3	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.281171430372558	2		974	463	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351777	89351778	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0042249-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	14	687	0	ENST00000301030.4:c.1172dup	p.Tyr391Ter	p.Y391*	ENST00000301030	NM_001256183.1	391	tac/taAc	9/13	1	2	FACETS	0.255	0.183	0.342	0.255	0.183	0.342	SUBCLONAL	1	TRUE	1	0.281171430372558	2		687	391	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	170	485	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.772970871689085	4	FACETS	1	0.963	1	0.359	0.33	0.388	CLONAL	1	TRUE	1	0.772970871689085	4		485	725	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605102	46605102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540130771	NA	P-0042322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	277	556	0	ENST00000263734.3:c.1319C>T	p.Thr440Met	p.T440M	ENST00000263734	NM_001430.4	440	aCg/aTg	10/16	0.738078219154109	3	FACETS	0.972	0.925	1	0.972	0.925	1	CLONAL	2	TRUE	1	0.772970871689085	3		556	511	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912745	32912745	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	120	448	0	ENST00000380152.3:c.4253T>A	p.Ile1418Lys	p.I1418K	ENST00000380152		1418	aTa/aAa	11/27	0.768430639841429	2	FACETS	0.93	0.85	1	0.465	0.425	0.506	CLONAL	1	TRUE	0	0.772970871689085	2		448	334	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983963	15983964	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0042322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	354	440	0	ENST00000268712.3:c.3255_3256insC	p.Ile1086HisfsTer35	p.I1086Hfs*35	ENST00000268712	NM_006311.3	1085	-/C	24/46	0.768430639841429	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.772970871689085	2		440	445	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683531	29683531	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	248	398	0	ENST00000356175.3:c.7606C>T	p.Gln2536Ter	p.Q2536*	ENST00000356175	NM_000267.3	2536	Caa/Taa	51/57	0.768430639841429	2	FACETS	0.99	0.953	1	0.99	0.953	1	CLONAL	2	TRUE	0	0.772970871689085	2		398	324	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660688	227660688	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	345	668	0	ENST00000305123.5:c.2767T>G	p.Cys923Gly	p.C923G	ENST00000305123	NM_005544.2	923	Tgt/Ggt	1/2	0.772970871689085	3	FACETS	0.946	0.904	0.988	0.946	0.904	0.988	CLONAL	2	TRUE	1	0.772970871689085	3		668	654	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183346	56183346	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	247	380	0	ENST00000399503.3:c.4256A>T	p.Glu1419Val	p.E1419V	ENST00000399503	NM_005921.1	1419	gAg/gTg	18/20	0.768430639841429	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.772970871689085	2		380	309	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453135	140453136	+	missense_variant	Missense_Mutation	DNP	CA	CA	TT	rs121913377	NA	P-0042389-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	68	360	0	ENST00000288602.6:c.1799_1800delinsAA	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTG/gAA	15/18	1	2	FACETS	0.958	0.848	1	0.958	0.848	1	CLONAL	1	TRUE	1	0.71	2		360	200	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11018786	11018786	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762459878	NA	P-0042389-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	92	368	25	ENST00000327064.4:c.418C>T	p.Arg140Trp	p.R140W	ENST00000327064	NM_199141.1	140	Cgg/Tgg	3/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.71	2		393	230	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641898	12641898	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042389-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	62	447	0	ENST00000251849.4:c.851A>G	p.His284Arg	p.H284R	ENST00000251849	NM_002880.3	284	cAc/cGc	8/17	1	2	FACETS	0.944	0.831	1	0.944	0.831	1	CLONAL	1	TRUE	1	0.71	2		447	185	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435023	56435023	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042513-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	225	766	0	ENST00000407977.2:c.2114G>T	p.Gly705Val	p.G705V	ENST00000407977		705	gGc/gTc	9/10	1	2	FACETS	0.97	0.91	1	0.97	0.91	1	CLONAL	1	TRUE	1	0.76049394334488	2		766	610	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938358	76938358	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042513-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	194	416	0	ENST00000373344.5:c.2390C>A	p.Ser797Ter	p.S797*	ENST00000373344	NM_000489.3	797	tCa/tAa	9/35	0.255601404053954	1	FACETS	0.701	0.656	0.747	0.701	0.656	0.747	INDETERMINATE	1	TRUE	0	0.76049394334488	1		416	451	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263282	115263282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs138627779	NA	P-0042513-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	179	530	0	ENST00000438362.2:c.2068G>T	p.Asp690Tyr	p.D690Y	ENST00000438362	NM_001242891.1	690	Gat/Tat	17/20	1	2	FACETS	0.969	0.901	1	0.969	0.901	1	CLONAL	1	TRUE	1	0.76049394334488	2		530	486	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432366	49432366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042513-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	229	795	0	ENST00000301067.7:c.8773G>T	p.Ala2925Ser	p.A2925S	ENST00000301067	NM_003482.3	2925	Gcg/Tcg	34/54	0.76049394334488	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.76049394334488	1		795	354	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56809898	56809898	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042513-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	129	334	0	ENST00000337432.4:c.1019A>C	p.Gln340Pro	p.Q340P	ENST00000337432	NM_058216.2	340	cAa/cCa	8/9	1	2	FACETS	0.85	0.778	0.924	0.85	0.778	0.924	CLONAL	1	TRUE	1	0.76049394334488	2		334	399	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725067	47725067	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042513-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	188	738	0	ENST00000449228.1:c.677C>G	p.Ala226Gly	p.A226G	ENST00000449228	NM_001127240.2	226	gCc/gGc	4/4	0.76049394334488	1	FACETS	0.995	0.941	1	0.995	0.941	1	CLONAL	1	TRUE	0	0.76049394334488	1		738	308	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932448	39932448	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs375141085	NA	P-0042513-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	31	673	0	ENST00000378444.4:c.2151A>T	p.Gln717His	p.Q717H	ENST00000378444	NM_001123385.1	717	caA/caT	4/15	0.255601404053954	1	FACETS	0.101	0.081	0.124	0.101	0.081	0.124	INDETERMINATE	1	TRUE	0	0.76049394334488	1		673	498	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0043184-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	164	613	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.485763129638423	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.485763833248722	1		614	477	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0043184-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	260	480	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.485763833248722	2	FACETS	0.999	0.946	1	0.999	0.946	1	CLONAL	2	TRUE	0	0.485763833248722	2		480	536	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111562	8111562	+	splice_donor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0043184-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	133	407	0	ENST00000346208.3:c.1047+1del		p.X349_splice	ENST00000346208		349			0.485763833248722	3	FACETS	1	0.961	1	0.55	0.501	0.601	CLONAL	1	TRUE	1	0.485763833248722	3		407	619	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574494	41574494	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043184-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	157	607	0	ENST00000263253.7:c.6779A>G	p.Tyr2260Cys	p.Y2260C	ENST00000263253	NM_001429.3	2260	tAt/tGt	31/31	0.485763129638423	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.485763833248722	1		607	423	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933512	49933512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771786833	NA	P-0043184-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	145	698	4	ENST00000296474.3:c.2678G>A	p.Cys893Tyr	p.C893Y	ENST00000296474	NM_002447.2	893	tGt/tAt	11/20	0.485763129638423	1	FACETS	0.952	0.875	1	0.952	0.875	1	CLONAL	1	TRUE	0	0.485763833248722	1		702	475	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868897	117868897	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043184-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	81	363	0	ENST00000297338.2:c.802G>A	p.Asp268Asn	p.D268N	ENST00000297338	NM_006265.2	268	Gat/Aat	7/14	0.485763833248722	3	FACETS	0.982	0.87	1	0.491	0.435	0.551	CLONAL	1	TRUE	1	0.485763833248722	3		363	422	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144879	47144879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044303-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	122	209	0	ENST00000409792.3:c.4874G>A	p.Arg1625His	p.R1625H	ENST00000409792	NM_014159.6	1625	cGt/cAt	7/21	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.700266022729	2		209	324	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593605	55593610	+	inframe_deletion	In_Frame_Del	DEL	GAAGGT	GAAGGT	-	novel	NA	P-0044303-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	293	310	0	ENST00000288135.5:c.1671_1676del	p.Trp557_Val559delinsCys	p.W557_V559delinsC	ENST00000288135	NM_000222.2	557	tgGAAGGTt/tgt	11/21	0.700266022729	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.700266022729	2		310	386	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0044303-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	96	668	5	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	0.560927437606088	4	FACETS	0.797	0.711	0.887	0.398	0.355	0.444	SUBCLONAL	1	TRUE	2	0.700266022729	4		673	585	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044860-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	49	477	0				ENST00000310581	NM_198253.2	-/1132			0.571310133563997	5	FACETS	0.448	0.378	0.525	0.09	0.075	0.105	SUBCLONAL	1	TRUE	0	0.571310133563997	5		477	711	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044860-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	274	540	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.521094629519355	2	FACETS	0.887	0.842	0.931	0.887	0.842	0.931	CLONAL	2	TRUE	0	0.571310133563997	2		540	541	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802635	135802635	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203343	NA	P-0044860-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	281	375	0	ENST00000298552.3:c.163C>T	p.Gln55Ter	p.Q55*	ENST00000298552	NM_001162426.1	55	Cag/Tag	4/23	0.571310133563997	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.571310133563997	2		375	471	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459462	50459462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044860-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	239	374	0	ENST00000331340.3:c.751G>A	p.Glu251Lys	p.E251K	ENST00000331340	NM_006060.4	251	Gaa/Aaa	7/8	0.571310133563997	3	FACETS	0.974	0.918	1	0.974	0.918	1	CLONAL	2	TRUE	1	0.571310133563997	3		374	552	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741707	145741707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543009701	NA	P-0044860-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	196	587	0	ENST00000428558.2:c.796G>A	p.Glu266Lys	p.E266K	ENST00000428558	NM_004260.3	266	Gag/Aag	5/22	0.484129020644753	5	FACETS	1	0.982	1	0.299	0.276	0.322	CLONAL	1	TRUE	1	0.571310133563997	5		587	1066	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879888	37879888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044860-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	189	669	0	ENST00000269571.5:c.2183C>T	p.Ser728Phe	p.S728F	ENST00000269571		728	tCt/tTt	18/27	0.309749704325014	3	FACETS	1	0.98	1	0.582	0.539	0.626	INDETERMINATE	1	TRUE	1	0.571310133563997	3		669	731	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40490782	40490782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044860-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	148	287	0	ENST00000264657.5:c.517G>A	p.Asp173Asn	p.D173N	ENST00000264657	NM_139276.2	173	Gat/Aat	6/24	0.309749704325014	3	FACETS	0.755	0.696	0.816	0.755	0.696	0.816	INDETERMINATE	2	TRUE	1	0.571310133563997	3		287	441	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953357	17953357	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044860-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	125	466	0	ENST00000458235.1:c.629G>T	p.Arg210Leu	p.R210L	ENST00000458235	NM_000215.3	210	cGg/cTg	6/24	1	2	FACETS	0.88	0.801	0.963	0.88	0.801	0.963	CLONAL	1	TRUE	1	0.571310133563997	2		466	497	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307243	118307243	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555138451	NA	P-0044860-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	94	264	0	ENST00000534358.1:c.16C>T	p.Arg6Trp	p.R6W	ENST00000534358	NM_005933.3	6	Cgg/Tgg	1/36	0.309749704325014	3	FACETS	1	0.973	1	0.626	0.562	0.692	INDETERMINATE	1	TRUE	1	0.571310133563997	3		264	338	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982134	201982135	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044860-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	107	531	0	ENST00000359651.3:c.659dup	p.Asp220GlufsTer4	p.D220Efs*4	ENST00000359651		220	gat/gAat	5/8	0.207680517755947	3	FACETS	0.779	0.7	0.863	0.26	0.233	0.288	INDETERMINATE	1	TRUE	0	0.571310133563997	3		531	618	SUCCESS
ATR	545	MSKCC	GRCh37	3	142180806	142180806	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044860-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	91	269	0	ENST00000350721.4:c.7168C>G	p.Leu2390Val	p.L2390V	ENST00000350721	NM_001184.3	2390	Ctg/Gtg	42/47	0.571310133563997	4	FACETS	1	0.967	1			1	CLONAL	1	TRUE	NA	0.571310133563997	4		269	414	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447270	187447270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369445234	NA	P-0044860-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	74	505	0	ENST00000232014.4:c.923C>T	p.Ser308Leu	p.S308L	ENST00000232014	NM_001130845.1	308	tCg/tTg	5/10	0.282666308309877	4	FACETS	0.552	0.483	0.627	0.138	0.12	0.157	INDETERMINATE	1	TRUE	0	0.571310133563997	4		505	737	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781560	9781561	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0044860-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	55	460	0	ENST00000377346.4:c.1871dup	p.Tyr624Ter	p.Y624*	ENST00000377346	NM_005026.3	624	tac/tAac	15/24	0.205322959603649	3	FACETS	0.497	0.425	0.575	0.166	0.141	0.192	INDETERMINATE	1	TRUE	0	0.571310133563997	3		460	498	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102196028	102196028	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044860-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	73	412	0	ENST00000263464.3:c.788T>A	p.Phe263Tyr	p.F263Y	ENST00000263464	NM_001165.4	263	tTt/tAt	2/9	0.309749704325014	3	FACETS	0.52	0.455	0.59	0.26	0.227	0.295	INDETERMINATE	1	TRUE	1	0.571310133563997	3		412	632	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060728	38060728	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044860-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	208	623	0	ENST00000250448.2:c.1261G>T	p.Glu421Ter	p.E421*	ENST00000250448	NM_004496.3	421	Gaa/Taa	2/2	0.571310133563997	2	FACETS	1	0.973	1	0.543	0.506	0.58	CLONAL	1	TRUE	0	0.571310133563997	2		623	671	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942786	15942786	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044860-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	218	437	0	ENST00000268712.3:c.6916G>T	p.Glu2306Ter	p.E2306*	ENST00000268712	NM_006311.3	2306	Gag/Tag	44/46	0.521094629519355	2	FACETS	0.933	0.882	0.984	0.933	0.882	0.984	CLONAL	2	TRUE	0	0.571310133563997	2		437	409	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278102	15278102	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044860-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	135	486	0	ENST00000263388.2:c.5320G>T	p.Asp1774Tyr	p.D1774Y	ENST00000263388	NM_000435.2	1774	Gac/Tac	29/33	1	2	FACETS	0.987	0.903	1	0.987	0.903	1	CLONAL	1	TRUE	1	0.571310133563997	2		486	479	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948474	54948474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044860-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	165	357	0	ENST00000312783.6:c.844C>T	p.Pro282Ser	p.P282S	ENST00000312783	NM_198436.1	282	Cca/Tca	8/10	0.374989531583798	4	FACETS	0.763	0.704	0.824	0.763	0.704	0.824	SUBCLONAL	2	TRUE	2	0.571310133563997	4		357	595	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130688	29130688	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044860-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	73	443	0	ENST00000328354.6:c.22G>C	p.Glu8Gln	p.E8Q	ENST00000328354	NM_007194.3	8	Gag/Cag	2/15	0.264593034487499	2	FACETS	0.51	0.447	0.578	0.255	0.223	0.289	INDETERMINATE	1	TRUE	0	0.571310133563997	2		443	501	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502460	186502460	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044860-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	201	415	0	ENST00000323963.5:c.183G>C	p.Gln61His	p.Q61H	ENST00000323963		61	caG/caC	3/11	0.282666308309877	4	FACETS	0.86	0.801	0.92	0.43	0.4	0.46	INDETERMINATE	2	TRUE	0	0.571310133563997	4		415	643	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942734	44942748	+	inframe_deletion	In_Frame_Del	DEL	AACTTCCTGCTTTTG	AACTTCCTGCTTTTG	-	novel	NA	P-0044860-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	138	279	0	ENST00000377967.4:c.3314_3328del	p.Lys1105_Val1110delinsMet	p.K1105_V1110delinsM	ENST00000377967	NM_021140.2	1105	aAACTTCCTGCTTTTGtg/atg	23/29	0.571310133563997	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.571310133563997	1		279	288	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	205	967	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.804	0.747	0.864	1	0.992	1	CLONAL	2	FALSE	1	0.294591605871795	2		974	865	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	63	323	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.859	0.744	0.983	0.859	0.744	0.983	CLONAL	1	FALSE	1	0.294591605871795	2		323	498	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	14	738	0	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	1	2	FACETS	0.138	0.099	0.186	0.138	0.099	0.186	SUBCLONAL	1	FALSE	1	0.294591605871795	2		738	688	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374293	138374293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	74	456	0	ENST00000289153.2:c.3151G>A	p.Glu1051Lys	p.E1051K	ENST00000289153	NM_006219.2	1051	Gaa/Aaa	22/22	1	2	FACETS	0.773	0.677	0.877	0.773	0.677	0.877	SUBCLONAL	1	FALSE	1	0.294591605871795	2		456	650	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563311	21563311	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs77919685	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	75	763	0	ENST00000382592.4:c.608C>T	p.Ala203Val	p.A203V	ENST00000382592	NM_014572.2	203	gCg/gTg	4/8	1	2	FACETS	0.758	0.664	0.859	0.758	0.664	0.859	SUBCLONAL	1	FALSE	1	0.294591605871795	2		763	672	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	108	570	1	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	1	2	FACETS	0.87	0.78	0.965	0.87	0.78	0.965	CLONAL	1	FALSE	1	0.294591605871795	2		571	843	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	58	538	4	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.669	0.574	0.771	0.669	0.574	0.771	SUBCLONAL	1	FALSE	1	0.294591605871795	2		542	589	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	40	400	2	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.726	0.604	0.861	0.726	0.604	0.861	SUBCLONAL	1	FALSE	1	0.294591605871795	2		402	374	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	85	690	2	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.832	0.735	0.935	0.832	0.735	0.935	CLONAL	1	FALSE	1	0.294591605871795	2		692	694	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874637	35874637	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	56	445	1	ENST00000303115.3:c.799del	p.Arg267GlyfsTer28	p.R267Gfs*28	ENST00000303115	NM_002185.3	265	Aaa/aa	6/8	1	2	FACETS	0.641	0.549	0.742	0.641	0.549	0.742	SUBCLONAL	1	FALSE	1	0.294591605871795	2		446	593	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646981	23646981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	63	580	1	ENST00000261584.4:c.886del	p.Met296Ter	p.M296*	ENST00000261584	NM_024675.3	296	Atg/tg	4/13	1	2	FACETS	0.732	0.633	0.84	0.732	0.633	0.84	SUBCLONAL	1	FALSE	1	0.294591605871795	2		581	584	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361160	70361160	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs79912241	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	54	425	0	ENST00000374080.3:c.6348C>A	p.His2116Gln	p.H2116Q	ENST00000374080		2116	caC/caA	43/45	1	1	FACETS	0.49	0.418	0.569	0.49	0.418	0.569	SUBCLONAL	1	FALSE	0	0.294591605871795	1		425	638	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720803	89720804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs786204892	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	11	174	0	ENST00000371953.3:c.955dup	p.Thr319AsnfsTer6	p.T319Nfs*6	ENST00000371953	NM_000314.4	318	-/A	8/9	1	2	FACETS	0.522	0.362	0.719	0.522	0.362	0.719	SUBCLONAL	1	FALSE	1	0.294591605871795	2		174	143	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110203	3110203	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147528229	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	72	570	0	ENST00000078429.4:c.193G>A	p.Ala65Thr	p.A65T	ENST00000078429	NM_002067.2	65	Gcc/Acc	2/7	1	2	FACETS	0.837	0.732	0.95	0.837	0.732	0.95	CLONAL	1	FALSE	1	0.294591605871795	2		570	584	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020764	37020764	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	39	540	3	ENST00000358127.4:c.81del	p.Phe27LeufsTer2	p.F27Lfs*2	ENST00000358127	NM_001280556.1	27	ttT/tt	2/10	1	2	FACETS	0.374	0.309	0.447	0.374	0.309	0.447	SUBCLONAL	1	FALSE	1	0.294591605871795	2		543	708	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755426	39755427	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	85	694	1	ENST00000288319.7:c.1338dup	p.Ala447CysfsTer19	p.A447Cfs*19	ENST00000288319	NM_182918.3	446	-/T	10/10	1	2	FACETS	0.711	0.627	0.8	0.711	0.627	0.8	SUBCLONAL	1	FALSE	1	0.294591605871795	2		695	812	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354007	15354008	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	17	227	3	ENST00000263377.2:c.2872dup	p.Leu958ProfsTer135	p.L958Pfs*135	ENST00000263377	NM_058243.2	958	ctg/cCtg	14/20	1	2	FACETS	0.52	0.389	0.675	0.52	0.389	0.675	SUBCLONAL	1	FALSE	1	0.294591605871795	2		230	222	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	70	457	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	0.754	0.658	0.859	0.754	0.658	0.859	SUBCLONAL	1	FALSE	1	0.294591605871795	2		457	630	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	46	735	2	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	0.416	0.349	0.49	0.416	0.349	0.49	SUBCLONAL	1	FALSE	1	0.294591605871795	2		737	751	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434182	12434182	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776687	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	68	457	5	ENST00000287820.6:c.556del	p.Ser186ValfsTer47	p.S186Vfs*47	ENST00000287820	NM_015869.4	184	Aaa/aa	4/7	1	2	FACETS	0.679	0.59	0.775	0.679	0.59	0.775	SUBCLONAL	1	FALSE	1	0.294591605871795	2		462	680	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350772	89350775	+	frameshift_variant	Frame_Shift_Del	DEL	TTTG	TTTG	-	rs886039734	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	64	462	0	ENST00000301030.4:c.2175_2178del	p.Asn725LysfsTer23	p.N725Kfs*23	ENST00000301030	NM_001256183.1	725	aaCAAA/aa	9/13	1	2	FACETS	0.815	0.707	0.933	0.815	0.707	0.933	CLONAL	1	FALSE	1	0.294591605871795	2		462	533	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214398	36214398	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs868041281	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	62	550	6	ENST00000222270.7:c.3057del	p.Gly1020AlafsTer4	p.G1020Afs*4	ENST00000222270	NM_014727.1	1018	Aaa/aa	7/37	1	2	FACETS	0.753	0.651	0.864	0.753	0.651	0.864	SUBCLONAL	1	FALSE	1	0.294591605871795	2		556	559	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350105	89350105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368593056	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	90	751	0	ENST00000301030.4:c.2845C>T	p.Arg949Trp	p.R949W	ENST00000301030	NM_001256183.1	949	Cgg/Tgg	9/13	1	2	FACETS	0.715	0.634	0.803	0.715	0.634	0.803	SUBCLONAL	1	FALSE	1	0.294591605871795	2		751	854	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46587791	46587791	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	56	426	0	ENST00000263734.3:c.475del	p.Ser159AlafsTer12	p.S159Afs*12	ENST00000263734	NM_001430.4	157	Aaa/aa	5/16	1	2	FACETS	0.629	0.539	0.729	0.629	0.539	0.729	SUBCLONAL	1	FALSE	1	0.294591605871795	2		426	604	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925402	114925402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748822481	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	99	419	1	ENST00000543371.1:c.1485del	p.Ser496ProfsTer5	p.S496Pfs*5	ENST00000543371	NM_001198531.1	494	Ccc/cc	14/14	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.294591605871795	2		420	604	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220100	133220100	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	82	602	0	ENST00000320574.5:c.4337T>C	p.Val1446Ala	p.V1446A	ENST00000320574	NM_006231.2	1446	gTg/gCg	34/49	1	2	FACETS	0.867	0.765	0.977	0.867	0.765	0.977	CLONAL	1	FALSE	1	0.294591605871795	2		602	642	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192645	138192645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776714084	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	121	438	0	ENST00000237289.4:c.281C>T	p.Ala94Val	p.A94V	ENST00000237289	NM_001270507.1	94	gCg/gTg	2/9	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	FALSE	1	0.294591605871795	2		438	818	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092947	29092947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881688	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	49	374	0	ENST00000328354.6:c.1037G>A	p.Arg346His	p.R346H	ENST00000328354	NM_007194.3	346	cGt/cAt	10/15	1	2	FACETS	0.694	0.589	0.811	0.694	0.589	0.811	SUBCLONAL	1	FALSE	1	0.294591605871795	2		374	479	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808001	3808001	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	65	458	0	ENST00000262367.5:c.3418C>T	p.Arg1140Trp	p.R1140W	ENST00000262367	NM_004380.2	1140	Cgg/Tgg	18/31	1	2	FACETS	0.679	0.588	0.777	0.679	0.588	0.777	SUBCLONAL	1	FALSE	1	0.294591605871795	2		458	650	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1620979	1620979	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1329397192	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	78	747	3	ENST00000344749.5:c.1081del	p.Gln361ArgfsTer33	p.Q361Rfs*33	ENST00000344749	NM_001136139.2	361	Cag/ag	13/19	1	2	FACETS	0.636	0.558	0.721	0.636	0.558	0.721	SUBCLONAL	1	FALSE	1	0.294591605871795	2		750	832	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098009	178098009	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749353894	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	49	410	1	ENST00000397062.3:c.371C>T	p.Ala124Val	p.A124V	ENST00000397062	NM_006164.4	124	gCg/gTg	3/5	1	2	FACETS	0.61	0.517	0.714	0.61	0.517	0.714	SUBCLONAL	1	FALSE	1	0.294591605871795	2		411	545	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352576	89352576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762710349	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	43	461	0	ENST00000301030.4:c.763C>T	p.Arg255Trp	p.R255W	ENST00000301030	NM_001256183.1	255	Cgg/Tgg	8/13	1	2	FACETS	0.549	0.459	0.649	0.549	0.459	0.649	SUBCLONAL	1	FALSE	1	0.294591605871795	2		461	532	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11015633	11015634	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	91	528	0	ENST00000327064.4:c.235_236dup	p.Phe80SerfsTer46	p.F80Sfs*46	ENST00000327064	NM_199141.1	76	gat/gaTGt	2/16	1	2	FACETS	0.946	0.841	1	0.946	0.841	1	CLONAL	1	FALSE	1	0.294591605871795	2		528	653	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162429	47162429	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	68	566	0	ENST00000409792.3:c.3697del	p.Thr1233GlnfsTer3	p.T1233Qfs*3	ENST00000409792	NM_014159.6	1233	Aca/ca	3/21	1	2	FACETS	0.703	0.611	0.802	0.703	0.611	0.802	SUBCLONAL	1	FALSE	1	0.294591605871795	2		566	657	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022738	12022738	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772622167	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	107	819	0	ENST00000396373.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000396373	NM_001987.4	282	Cgg/Tgg	5/8	0.278366423487179	4	FACETS	1	0.938	1	0.533	0.477	0.592	CLONAL	1	FALSE	2	0.294591605871795	4		819	882	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244124	133244124	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794759	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	50	475	0	ENST00000320574.5:c.2284C>T	p.Arg762Trp	p.R762W	ENST00000320574	NM_006231.2	762	Cgg/Tgg	20/49	1	2	FACETS	0.58	0.492	0.678	0.58	0.492	0.678	SUBCLONAL	1	FALSE	1	0.294591605871795	2		475	585	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271507	15271507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771682246	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	46	645	0	ENST00000263388.2:c.6932C>T	p.Pro2311Leu	p.P2311L	ENST00000263388	NM_000435.2	2311	cCg/cTg	33/33	1	2	FACETS	0.52	0.437	0.611	0.52	0.437	0.611	SUBCLONAL	1	FALSE	1	0.294591605871795	2		645	601	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1936885	1936885	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1445291234	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	66	401	1	ENST00000382891.5:c.1576del	p.Arg526GlufsTer72	p.R526Efs*72	ENST00000382891	NM_133335.3	524	Aaa/aa	7/22	1	2	FACETS	0.722	0.626	0.825	0.722	0.626	0.825	SUBCLONAL	1	FALSE	1	0.294591605871795	2		402	621	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258735	16258735	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	102	711	2	ENST00000375759.3:c.6005del	p.Asn2002MetfsTer20	p.N2002Mfs*20	ENST00000375759	NM_015001.2	2000	ggA/gg	11/15	1	2	FACETS	0.782	0.698	0.871	0.782	0.698	0.871	SUBCLONAL	1	FALSE	1	0.294591605871795	2		713	886	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204515953	204515953	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	49	352	0	ENST00000367182.3:c.851T>G	p.Leu284Arg	p.L284R	ENST00000367182	NM_001278516.1	284	cTg/cGg	10/11	1	2	FACETS	0.682	0.578	0.796	0.682	0.578	0.796	SUBCLONAL	1	FALSE	1	0.294591605871795	2		352	488	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715673	18715673	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	54	431	0	ENST00000266497.5:c.3504A>T	p.Lys1168Asn	p.K1168N	ENST00000266497		1168	aaA/aaT	25/31	0.117736003652782	0	FACETS	0.495	0.423	0.574			1	INDETERMINATE	1	FALSE	0	0.294591605871795	0		431	522	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495604	56495604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142809206	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	99	669	0	ENST00000267101.3:c.3794G>A	p.Arg1265Gln	p.R1265Q	ENST00000267101	NM_001982.3	1265	cGg/cAg	28/28	0.100202674576897	4	FACETS	0.975	0.87	1	0.488	0.435	0.544	INDETERMINATE	1	FALSE	2	0.294591605871795	4		669	892	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482758	67482758	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	97	516	0	ENST00000327367.4:c.1162A>T	p.Thr388Ser	p.T388S	ENST00000327367	NM_005902.3	388	Act/Tct	9/9	1	2	FACETS	0.957	0.854	1	0.957	0.854	1	CLONAL	1	FALSE	1	0.294591605871795	2		516	688	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250839	99250839	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	98	595	0	ENST00000268035.6:c.143G>C	p.Arg48Pro	p.R48P	ENST00000268035	NM_000875.3	48	cGc/cCc	2/21	1	2	FACETS	0.94	0.839	1	0.94	0.839	1	CLONAL	1	FALSE	1	0.294591605871795	2		595	708	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134431	30134431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	70	588	0	ENST00000263025.4:c.100C>T	p.Gln34Ter	p.Q34*	ENST00000263025	NM_002746.2	34	Cag/Tag	1/9	1	2	FACETS	0.716	0.624	0.815	0.716	0.624	0.815	SUBCLONAL	1	FALSE	1	0.294591605871795	2		588	664	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828136	50828136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528100675	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	52	400	0	ENST00000398568.2:c.2474C>T	p.Pro825Leu	p.P825L	ENST00000398568	NM_001042412.1	825	cCg/cTg	17/18	1	2	FACETS	0.75	0.639	0.871	0.75	0.639	0.871	SUBCLONAL	1	FALSE	1	0.294591605871795	2		400	471	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618866	37618868	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs955200004	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	120	668	0	ENST00000447079.4:c.544_546del	p.Glu182del	p.E182del	ENST00000447079	NM_015083.1	181	aAGGag/aag	1/14	1	2	FACETS	0.85	0.766	0.938	0.85	0.766	0.938	CLONAL	1	FALSE	1	0.294591605871795	2		668	959	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184535	7184535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781007453	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	62	480	0	ENST00000302850.5:c.766C>T	p.Arg256Cys	p.R256C	ENST00000302850	NM_000208.2	256	Cgc/Tgc	3/22	1	2	FACETS	0.58	0.5	0.667	0.58	0.5	0.667	SUBCLONAL	1	FALSE	1	0.294591605871795	2		480	726	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250885	10250885	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	51	571	0	ENST00000340748.4:c.3595A>G	p.Met1199Val	p.M1199V	ENST00000340748		1199	Atg/Gtg	32/40	1	2	FACETS	0.666	0.566	0.775	0.666	0.566	0.775	SUBCLONAL	1	FALSE	1	0.294591605871795	2		571	520	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213533	36213533	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	68	673	0	ENST00000222270.7:c.2635C>A	p.Leu879Met	p.L879M	ENST00000222270	NM_014727.1	879	Ctg/Atg	5/37	1	2	FACETS	0.704	0.612	0.803	0.704	0.612	0.803	SUBCLONAL	1	FALSE	1	0.294591605871795	2		673	656	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716224	52716224	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	105	648	0	ENST00000322088.6:c.668T>C	p.Leu223Pro	p.L223P	ENST00000322088	NM_014225.5	223	cTg/cCg	6/15	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	FALSE	1	0.294591605871795	2		648	709	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566886	212566886	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	68	478	0	ENST00000342788.4:c.1295T>C	p.Leu432Pro	p.L432P	ENST00000342788	NM_005235.2	432	cTg/cCg	12/28	1	2	FACETS	0.623	0.541	0.712	0.623	0.541	0.712	SUBCLONAL	1	FALSE	1	0.294591605871795	2		478	741	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023506	31023506	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	82	674	0	ENST00000375687.4:c.2991G>C	p.Glu997Asp	p.E997D	ENST00000375687	NM_015338.5	997	gaG/gaC	13/13	1	2	FACETS	0.828	0.731	0.933	0.828	0.731	0.933	CLONAL	1	FALSE	1	0.294591605871795	2		674	672	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175836	24175836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	87	610	0	ENST00000263121.7:c.1064C>T	p.Thr355Ile	p.T355I	ENST00000263121	NM_003073.3	355	aCt/aTt	8/9	1	2	FACETS	0.824	0.729	0.925	0.824	0.729	0.925	CLONAL	1	FALSE	1	0.294591605871795	2		610	717	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374672	149374672	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	57	475	0	ENST00000360632.3:c.422A>G	p.Tyr141Cys	p.Y141C	ENST00000360632	NM_015472.4	141	tAc/tGc	2/7	1	2	FACETS	0.768	0.659	0.886	0.768	0.659	0.886	SUBCLONAL	1	FALSE	1	0.294591605871795	2		475	504	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250933	153250933	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	41	312	0	ENST00000281708.4:c.1127T>C	p.Leu376Pro	p.L376P	ENST00000281708	NM_033632.3	376	cTg/cCg	8/12	1	2	FACETS	0.87	0.727	1	0.87	0.727	1	CLONAL	1	FALSE	1	0.294591605871795	2		312	320	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589238	67589238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748784250	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	28	407	0	ENST00000274335.5:c.1226G>A	p.Arg409Gln	p.R409Q	ENST00000274335		409	cGg/cAg	9/15	1	2	FACETS	0.441	0.352	0.543	0.441	0.352	0.543	SUBCLONAL	1	FALSE	1	0.294591605871795	2		407	431	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047918	180047918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770591360	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	82	780	0	ENST00000261937.6:c.2257G>A	p.Ala753Thr	p.A753T	ENST00000261937	NM_182925.4	753	Gcc/Acc	15/30	1	2	FACETS	0.917	0.81	1	0.917	0.81	1	CLONAL	1	FALSE	1	0.294591605871795	2		780	607	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975415	13975415	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	107	544	0	ENST00000405192.2:c.472A>G	p.Thr158Ala	p.T158A	ENST00000405192	NM_001163147.1	158	Aca/Gca	7/12	1	2	FACETS	0.815	0.73	0.906	0.815	0.73	0.906	CLONAL	1	FALSE	1	0.294591605871795	2		544	891	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482918	140482918	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	116	624	0	ENST00000288602.6:c.1217T>C	p.Leu406Ser	p.L406S	ENST00000288602	NM_004333.4	406	tTa/tCa	10/18	1	2	FACETS	0.951	0.857	1	0.951	0.857	1	CLONAL	1	FALSE	1	0.294591605871795	2		624	828	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020741	37020741	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	96	518	0	ENST00000358127.4:c.104A>G	p.Asp35Gly	p.D35G	ENST00000358127	NM_001280556.1	35	gAt/gGt	2/10	1	2	FACETS	0.91	0.811	1	0.91	0.811	1	CLONAL	1	FALSE	1	0.294591605871795	2		518	716	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309058	137309058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139536056	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	63	605	0	ENST00000481739.1:c.665C>T	p.Ser222Leu	p.S222L	ENST00000481739	NM_002957.4	222	tCg/tTg	5/10	1	2	FACETS	0.651	0.563	0.747	0.651	0.563	0.747	SUBCLONAL	1	FALSE	1	0.294591605871795	2		605	657	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006840	47006840	+	5_prime_UTR_variant	5'UTR	SNP	T	T	C	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	90	304	0	ENST00000377604.3:c.-41T>C		p.*14*	ENST00000377604	NM_001204468.1	-/852		2/24	1	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	0	0.294591605871795	1		304	371	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240363	98240363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	56	497	0	ENST00000331920.6:c.1321C>T	p.Arg441Cys	p.R441C	ENST00000331920	NM_000264.3	441	Cgc/Tgc	9/24	1	2	FACETS	0.53	0.453	0.614	0.53	0.453	0.614	SUBCLONAL	1	FALSE	1	0.294591605871795	2		497	718	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560386	95560386	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	82	533	0	ENST00000393063.1:c.5203C>A	p.Leu1735Met	p.L1735M	ENST00000393063	NM_030621.3	1735	Ctg/Atg	25/28	1	2	FACETS	0.752	0.663	0.848	0.752	0.663	0.848	SUBCLONAL	1	FALSE	1	0.294591605871795	2		533	740	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50791212	50791212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	27	433	0	ENST00000307179.4:c.3284C>T	p.Ser1095Phe	p.S1095F	ENST00000307179		1095	tCt/tTt	20/20	1	2	FACETS	0.353	0.28	0.437	0.353	0.28	0.437	SUBCLONAL	1	FALSE	1	0.294591605871795	2		433	519	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476301	88476301	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	41	517	0	ENST00000360948.2:c.1831del	p.Asp611ThrfsTer10	p.D611Tfs*10	ENST00000360948	NM_001012338.2	611	Gac/ac	15/19	1	2	FACETS	0.424	0.352	0.505	0.424	0.352	0.505	SUBCLONAL	1	FALSE	1	0.294591605871795	2		517	656	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152198	11152200	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	59	546	0	ENST00000358026.2:c.4487_4489del	p.Lys1496del	p.K1496del	ENST00000358026	NM_001128849.1	1494	atGAAg/atg	31/36	1	2	FACETS	0.613	0.527	0.708	0.613	0.527	0.708	SUBCLONAL	1	FALSE	1	0.294591605871795	2		546	653	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21341825	21341825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769001939	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	92	569	0	ENST00000215739.8:c.353G>A	p.Arg118His	p.R118H	ENST00000215739	NM_006767.3	118	cGt/cAt	4/21	1	2	FACETS	0.89	0.791	0.995	0.89	0.791	0.995	CLONAL	1	FALSE	1	0.294591605871795	2		569	702	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29442873	29442873	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	75	483	0	ENST00000544604.2:c.912+2T>C		p.X304_splice	ENST00000544604	NM_001206998.1	304			1	2	FACETS	0.835	0.732	0.945	0.835	0.732	0.945	CLONAL	1	FALSE	1	0.294591605871795	2		483	610	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014077	70014077	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201351378	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	84	526	0	ENST00000394351.3:c.938G>A	p.Arg313Gln	p.R313Q	ENST00000394351	NM_000248.3	313	cGg/cAg	9/9	1	2	FACETS	0.881	0.779	0.991	0.881	0.779	0.991	CLONAL	1	FALSE	1	0.294591605871795	2		526	647	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910711	29910711	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	52	744	1	ENST00000376809.5:c.251G>T	p.Trp84Leu	p.W84L	ENST00000376809	NM_002116.7	84	tGg/tTg	2/8	1	2	FACETS	0.504	0.428	0.587	0.504	0.428	0.587	SUBCLONAL	1	FALSE	1	0.294591605871795	2		745	701	SUCCESS
MTAP	4507	MSKCC	GRCh37	9	21815504	21815504	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045253-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	22	257	0	ENST00000380172.4:c.106A>G	p.Thr36Ala	p.T36A	ENST00000380172	NM_002451.3	36	Act/Gct	2/8	1	2	FACETS	0.39	0.302	0.493	0.39	0.302	0.493	SUBCLONAL	1	FALSE	1	0.294591605871795	2		257	383	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0045332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	258	844	17	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.73380566513499	2		861	659	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0045332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	61	336	1	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.294	0.254	0.338	0.294	0.254	0.338	SUBCLONAL	1	TRUE	1	0.73380566513499	2		337	565	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0045332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	268	848	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.73380566513499	2		848	678	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136270	2136270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1371745883	NA	P-0045332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	226	792	0	ENST00000219476.3:c.4739G>A	p.Arg1580Gln	p.R1580Q	ENST00000219476	NM_000548.3	1580	cGg/cAg	37/42	1	2	FACETS	0.945	0.885	1	0.945	0.885	1	CLONAL	1	TRUE	1	0.73380566513499	2		792	652	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039484	49039484	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	111	330	0	ENST00000267163.4:c.2473del	p.Met825Ter	p.M825*	ENST00000267163	NM_000321.2	823	acA/ac	23/27	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.73380566513499	2		330	298	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821425	72821425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769841511	NA	P-0045332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	59	655	0	ENST00000268489.5:c.10750G>A	p.Ala3584Thr	p.A3584T	ENST00000268489	NM_006885.3	3584	Gca/Aca	10/10	1	2	FACETS	0.264	0.227	0.305	0.264	0.227	0.305	SUBCLONAL	1	TRUE	1	0.73380566513499	2		655	609	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285171	15285171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202085803	NA	P-0045332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	243	799	0	ENST00000263388.2:c.4444G>A	p.Gly1482Ser	p.G1482S	ENST00000263388	NM_000435.2	1482	Ggc/Agc	25/33	1	2	FACETS	0.942	0.885	1	0.942	0.885	1	CLONAL	1	TRUE	1	0.73380566513499	2		799	703	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155399	99155399	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1559033620	NA	P-0045332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	164	499	0	ENST00000074304.5:c.625C>T	p.Arg209Ter	p.R209*	ENST00000074304	NM_001134224.1	209	Cga/Tga	9/26	1	2	FACETS	0.945	0.875	1	0.945	0.875	1	CLONAL	1	TRUE	1	0.73380566513499	2		499	473	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656908	45656908	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	92	835	0	ENST00000407780.3:c.248G>A	p.Arg83Gln	p.R83Q	ENST00000407780	NM_001283052.1	83	cGa/cAa	3/7	1	2	FACETS	0.33	0.293	0.37	0.33	0.293	0.37	SUBCLONAL	1	TRUE	1	0.73380566513499	2		835	759	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210431	36210431	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs748888652	NA	P-0045332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	254	676	0	ENST00000222270.7:c.424C>T	p.Arg142Ter	p.R142*	ENST00000222270	NM_014727.1	142	Cga/Tga	2/37	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.73380566513499	2		676	660	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658625	206658625	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	56	698	0	ENST00000367120.3:c.1598A>G	p.Gln533Arg	p.Q533R	ENST00000367120	NM_014002.3	533	cAg/cGg	15/22	0.73380566513499	4	FACETS	0.24	0.204	0.279	0.08	0.068	0.093	SUBCLONAL	1	TRUE	1	0.73380566513499	4		698	1103	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720668	89720676	+	inframe_deletion	In_Frame_Del	DEL	TTGGGTAAA	TTGGGTAAA	-	novel	NA	P-0045332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	24	60	0	ENST00000371953.3:c.820_828del	p.Trp274_Asn276del	p.W274_N276del	ENST00000371953	NM_000314.4	273	ttTTGGGTAAAt/ttt	8/9	0.73380566513499	2	FACETS	1	0.919	1	0.617	0.509	0.728	CLONAL	1	TRUE	0	0.73380566513499	2		60	53	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039340	49039340	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0045332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	90	351	0	ENST00000267163.4:c.2326-1G>C		p.X776_splice	ENST00000267163	NM_000321.2	776			1	2	FACETS	0.846	0.76	0.935	0.846	0.76	0.935	CLONAL	1	TRUE	1	0.73380566513499	2		351	290	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184472	7184472	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	256	714	0	ENST00000302850.5:c.829G>A	p.Asp277Asn	p.D277N	ENST00000302850	NM_000208.2	277	Gac/Aac	3/22	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.73380566513499	2		714	646	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610511	10610511	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	244	804	1	ENST00000171111.5:c.199A>T	p.Met67Leu	p.M67L	ENST00000171111	NM_203500.1	67	Atg/Ttg	2/6	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.73380566513499	2		805	658	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703557	47703557	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	47	421	0	ENST00000233146.2:c.2057T>C	p.Val686Ala	p.V686A	ENST00000233146	NM_000251.2	686	gTa/gCa	13/16	1	2	FACETS	0.27	0.228	0.317	0.27	0.228	0.317	SUBCLONAL	1	TRUE	1	0.73380566513499	2		421	474	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193495	99193495	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763911653	NA	P-0045332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	245	757	0	ENST00000074304.5:c.2690G>A	p.Ser897Asn	p.S897N	ENST00000074304	NM_001134224.1	897	aGc/aAc	25/26	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.73380566513499	2		757	655	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170002295	170002295	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs746373616	NA	P-0045332-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	10	79	0	ENST00000295797.4:c.1114C>T	p.Arg372Ter	p.R372*	ENST00000295797	NM_002740.5	372	Cga/Tga	12/18	1	2	FACETS	0.379	0.26	0.522	0.379	0.26	0.522	SUBCLONAL	1	TRUE	1	0.73380566513499	2		79	72	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0045530-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	32	472	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.299607658326611	1	FACETS	0.636	0.519	0.768	0.636	0.519	0.768	SUBCLONAL	1	TRUE	0	0.32	1		472	264	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0045530-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	134	599	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.262152390193985	3	FACETS	1	0.923	1	0.673	0.616	0.733	CLONAL	2	TRUE	0	0.32	3		599	481	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984058	2984058	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045530-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	34	558	0	ENST00000396946.4:c.472del	p.Gln158SerfsTer9	p.Q158Sfs*9	ENST00000396946	NM_032415.4	158	Cag/ag	5/25	0.240343952951469	2	FACETS	0.483	0.394	0.583	0.241	0.197	0.292	SUBCLONAL	1	TRUE	0	0.32	2		558	440	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47599143	47599143	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045530-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	52	669	0	ENST00000430070.2:c.457T>G	p.Phe153Val	p.F153V	ENST00000430070	NM_018095.4	153	Ttt/Gtt	2/4	1	2	FACETS	0.585	0.497	0.68	0.585	0.497	0.68	SUBCLONAL	1	TRUE	1	0.32	2		669	556	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21643180	21643180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045530-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	22	407	0	ENST00000421138.2:c.347G>A	p.Gly116Glu	p.G116E	ENST00000421138		116	gGa/gAa	5/16	1	2	FACETS	0.606	0.471	0.761	0.606	0.471	0.761	SUBCLONAL	1	TRUE	1	0.32	2		407	227	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015865	112015865	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045530-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	26	404	0	ENST00000368678.4:c.1076T>A	p.Leu359Gln	p.L359Q	ENST00000368678		359	cTg/cAg	10/13	0.299607658326611	5	FACETS	0.585	0.463	0.726			1	SUBCLONAL	1	TRUE	NA	0.32	5		404	411	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195134	123195134	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0045530-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	24	408	0	ENST00000218089.9:c.1477A>T	p.Lys493Ter	p.K493*	ENST00000218089	NM_001042749.1	493	Aaa/Taa	16/35	1	2	FACETS	0.598	0.47	0.744	0.598	0.47	0.744	SUBCLONAL	1	TRUE	1	0.32	2		408	251	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195152	123195152	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045530-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	24	380	0	ENST00000218089.9:c.1495A>C	p.Asn499His	p.N499H	ENST00000218089	NM_001042749.1	499	Aat/Cat	16/35	1	2	FACETS	0.63	0.496	0.784	0.63	0.496	0.784	SUBCLONAL	1	TRUE	1	0.32	2		380	238	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907071	101907071	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	117	389	0	ENST00000374994.4:c.1031A>T	p.Asn344Ile	p.N344I	ENST00000374994	NM_004612.2	344	aAt/aTt	6/9	0.338921729814677	1	FACETS	0.999	0.904	1	0.999	0.904	1	CLONAL	1	TRUE	0	0.338921729814677	1		389	574	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0047468-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	578	723	0	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	0.446062863817493	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.446062863817493	2		723	1253	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966768	44966768	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047468-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	97	215	0	ENST00000377967.4:c.3992G>T	p.Cys1331Phe	p.C1331F	ENST00000377967	NM_021140.2	1331	tGt/tTt	27/29	1	1	FACETS	0.908	0.833	0.984	1	0.988	1	CLONAL	2	TRUE	0	0.446062863817493	1		215	186	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158357	108158357	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555095899	NA	P-0047468-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	95	405	0	ENST00000278616.4:c.4024G>A	p.Glu1342Lys	p.E1342K	ENST00000278616	NM_000051.3	1342	Gag/Aag	27/63	0.441284830119243	3	FACETS	0.935	0.835	1	0.468	0.417	0.521	CLONAL	1	TRUE	1	0.446062863817493	3		405	557	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487160	56487160	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047468-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	478	442	0	ENST00000267101.3:c.1306T>A	p.Leu436Met	p.L436M	ENST00000267101	NM_001982.3	436	Ttg/Atg	12/28	0.446062863817493	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	1	0.446062863817493	4		442	1006	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118613	17118614	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AT	novel	NA	P-0047468-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	353	460	0	ENST00000285071.4:c.1317_1318delinsAT	p.Glu440Ter	p.E440*	ENST00000285071	NM_144997.5	439	gtGGag/gtATag	12/14	0.446062863817493	2	FACETS	0.904	0.86	0.949	0.904	0.86	0.949	CLONAL	2	TRUE	0	0.446062863817493	2		460	875	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223162	5223162	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs771623625	NA	P-0047468-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	487	724	0	ENST00000357368.4:c.2641C>G	p.Leu881Val	p.L881V	ENST00000357368	NM_002850.3	881	Ctg/Gtg	18/38	0.446062863817493	2	FACETS	0.981	0.941	1	0.981	0.941	1	CLONAL	2	TRUE	0	0.446062863817493	2		724	1113	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399543	139399543	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047468-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	466	716	0	ENST00000277541.6:c.4600C>G	p.Gln1534Glu	p.Q1534E	ENST00000277541	NM_017617.3	1534	Cag/Gag	26/34	0.446062863817493	2	FACETS	0.974	0.933	1	0.974	0.933	1	CLONAL	2	TRUE	0	0.446062863817493	2		716	1073	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741456	39741456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770886088	NA	P-0047468-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	181	510	0	ENST00000361337.2:c.1343G>A	p.Arg448Gln	p.R448Q	ENST00000361337	NM_003286.2	448	cGg/cAg	14/21	0.441284830119243	3	FACETS	0.997	0.919	1	0.498	0.459	0.539	CLONAL	1	TRUE	1	0.446062863817493	3		510	996	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264537	1264537	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047468-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1617	180	610	0	ENST00000310581.5:c.2825T>C	p.Val942Ala	p.V942A	ENST00000310581	NM_198253.2	942	gTg/gCg	11/16	0.446062863817493	6	FACETS	0.85	0.78	0.923	0.212	0.195	0.231	CLONAL	1	TRUE	2	0.446062863817493	6		610	1797	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112035629	112035629	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047468-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	109	433	0	ENST00000368678.4:c.265G>T	p.Ala89Ser	p.A89S	ENST00000368678		89	Gcc/Tcc	4/13	1	2	FACETS	0.884	0.796	0.976	0.884	0.796	0.976	CLONAL	1	TRUE	1	0.446062863817493	2		433	553	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56402511	56402511	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047924-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	73	268	0	ENST00000348428.3:c.1553G>T	p.Arg518Ile	p.R518I	ENST00000348428	NM_006785.3	518	aGa/aTa	13/17	1	2	FACETS	0.975	0.865	1	0.975	0.865	1	CLONAL	1	TRUE	1	0.624221113589858	2		268	240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0048260-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	328	532	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.648159603382005	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.648159603382005	2		532	500	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026033	48026033	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1481054050	NA	P-0048260-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	441	801	0	ENST00000234420.5:c.911T>A	p.Val304Glu	p.V304E	ENST00000234420	NM_000179.2	304	gTg/gAg	4/10	0.648159603382005	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.648159603382005	2		801	649	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591243	67591393	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCAGGTGGTTGACTCAAAAAGGTGTTCGGCAAAAGAAGTTGAACGAGTGGTTGGGCAATGAAAACACTGAAGAGTAAGTAGTTACTAAAGATGGTGATAGCAGAAGATTTTTCTCATTTTAGGAAAATGCATGACTTGCTTTGTTTTTAG	TTCAGGTGGTTGACTCAAAAAGGTGTTCGGCAAAAGAAGTTGAACGAGTGGTTGGGCAATGAAAACACTGAAGAGTAAGTAGTTACTAAAGATGGTGATAGCAGAAGATTTTTCTCATTTTAGGAAAATGCATGACTTGCTTTGTTTTTAG	-	novel	NA	P-0048260-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	109	485	0	ENST00000274335.5:c.1746-5_1814+77del		p.X582_splice	ENST00000274335		582		13/15	0.648159603382005	2	FACETS	1	0.983	1	0.667	0.611	0.725	CLONAL	1	TRUE	0	0.648159603382005	2		485	252	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127409	17127409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752014050	NA	P-0048260-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	192	644	0	ENST00000285071.4:c.445G>A	p.Gly149Ser	p.G149S	ENST00000285071	NM_144997.5	149	Ggc/Agc	6/14	0.648159603382005	2	FACETS	1	0.964	1	0.527	0.491	0.564	CLONAL	1	TRUE	0	0.648159603382005	2		644	562	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808315	99808315	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048478-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	43	174	0	ENST00000280892.6:c.374A>C	p.Glu125Ala	p.E125A	ENST00000280892	NM_001130678.1	125	gAg/gCg	5/7	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.335770156129667	2		174	243	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64289191	64289191	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048478-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	60	245	0	ENST00000370651.3:c.359T>G	p.Ile120Ser	p.I120S	ENST00000370651	NM_003463.4	120	aTt/aGt	5/6	1	2	FACETS	0.893	0.773	1	0.893	0.773	1	CLONAL	1	TRUE	1	0.335770156129667	2		245	400	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626922	158626922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048478-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	21	308	0	ENST00000263640.3:c.748G>A	p.Glu250Lys	p.E250K	ENST00000263640	NM_001105.4	250	Gaa/Aaa	7/11	1	2	FACETS	0.314	0.241	0.4	0.314	0.241	0.4	SUBCLONAL	1	TRUE	1	0.335770156129667	2		308	398	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048662-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	259	477	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.871863963246071	2		477	459	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0048662-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	294	658	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	1	2	FACETS	0.896	0.847	0.944	0.896	0.847	0.944	CLONAL	1	TRUE	1	0.871863963246071	2		658	753	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892290	9892290	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1439688451	NA	P-0048662-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	381	688	0	ENST00000330684.3:c.2200G>C	p.Val734Leu	p.V734L	ENST00000330684	NM_001134407.1	734	Gtc/Ctc	11/13	NA	2	FACETS	0.904	0.861	0.947			1	INDETERMINATE	1	TRUE	NA	0.871863963246071	2		688	967	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934596	9934596	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048662-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	85	641	0	ENST00000330684.3:c.1559A>C	p.Glu520Ala	p.E520A	ENST00000330684	NM_001134407.1	520	gAa/gCa	7/13	NA	2	FACETS	0.237	0.209	0.268			1	INDETERMINATE	1	TRUE	NA	0.871863963246071	2		641	821	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048662-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	695	624	0	ENST00000269305.4:c.772G>C	p.Glu258Gln	p.E258Q	ENST00000269305	NM_001126112.2	258	Gaa/Caa	7/11	0.871863963246071	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.871863963246071	2		624	778	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067836	30067836	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315499	NA	P-0048662-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	442	588	0	ENST00000338641.4:c.1021C>T	p.Arg341Ter	p.R341*	ENST00000338641	NM_000268.3	341	Cga/Tga	11/16	0.871863963246071	1	FACETS	0.998	0.97	1	0.998	0.97	1	CLONAL	1	TRUE	0	0.871863963246071	1		588	573	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983955	2983955	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048662-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	272	656	0	ENST00000396946.4:c.575A>G	p.Asp192Gly	p.D192G	ENST00000396946	NM_032415.4	192	gAc/gGc	5/25	1	2	FACETS	0.889	0.839	0.939	0.889	0.839	0.939	CLONAL	1	TRUE	1	0.871863963246071	2		656	702	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93629445	93629445	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048662-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	312	452	0	ENST00000375746.1:c.879C>G	p.Ile293Met	p.I293M	ENST00000375746	NM_001174167.1	293	atC/atG	7/14	0.646154665861019	1	FACETS	0.864	0.83	0.898	0.864	0.83	0.898	CLONAL	1	TRUE	0	0.871863963246071	1		452	467	SUCCESS
AR	367	MSKCC	GRCh37	X	66765079	66765079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048662-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	228	700	0	ENST00000374690.3:c.91C>T	p.Arg31Cys	p.R31C	ENST00000374690	NM_000044.3	31	Cgc/Tgc	1/8	0.258344158878566	1	FACETS	0.373	0.349	0.399	0.373	0.349	0.399	INDETERMINATE	1	TRUE	0	0.871863963246071	1		700	790	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0048888-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	75	329	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.289578383875649	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	0	0.334273031665724	2		329	208	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65569055	65569055	+	start_lost	Translation_Start_Site	SNP	C	C	A	novel	NA	P-0048888-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	80	550	1	ENST00000358664.4:c.3G>T	p.Met1?	p.M1?	ENST00000358664	NM_002382.4	1	atG/atT	1/5	0.334273031665724	1	FACETS	0.949	0.84	1	0.949	0.84	1	CLONAL	1	TRUE	0	0.334273031665724	1		551	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572966	7572990	+	frameshift_variant	Frame_Shift_Del	DEL	TTTATGGCGGGAGGTAGACTGACCC	TTTATGGCGGGAGGTAGACTGACCC	-	novel	NA	P-0048888-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	71	668	0	ENST00000269305.4:c.1119_1143del	p.Gly374AsnfsTer40	p.G374Nfs*40	ENST00000269305	NM_001126112.2	373	aaGGGTCAGTCTACCTCCCGCCATAAA/aa	11/11	0.334273031665724	1	FACETS	0.929	0.815	1	0.929	0.815	1	CLONAL	1	TRUE	0	0.334273031665724	1		668	381	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971191	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCGC	GGGCGC	A	novel	NA	P-0048888-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	149	794	0	ENST00000304494.5:c.167_172delinsT	p.Ser56MetfsTer62	p.S56Mfs*62	ENST00000304494	NM_000077.4	56	aGCGCCCga/aTga	2/3	0.334273031665724	1	FACETS	0.788	0.726	0.852	1	0.989	1	SUBCLONAL	2	TRUE	0	0.334273031665724	1		794	471	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0049488-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	405	484	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.766124628839674	2	FACETS	0.932	0.909	0.954	0.932	0.909	0.954	CLONAL	2	TRUE	0	0.893996653113991	2		484	486	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0049488-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	312	480	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.82889132936178	3	FACETS	1	0.989	1	0.587	0.556	0.619	CLONAL	1	TRUE	1	0.893996653113991	3		480	860	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916759	48916759	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049488-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	203	255	0	ENST00000267163.4:c.289G>T	p.Glu97Ter	p.E97*	ENST00000267163	NM_000321.2	97	Gaa/Taa	3/27	0.893996653113991	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.893996653113991	3		255	216	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0049488-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	656	951	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.893996653113991	2	FACETS	0.98	0.963	0.996	0.98	0.963	0.996	CLONAL	2	TRUE	0	0.893996653113991	2		951	749	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518000	8518000	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049488-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	396	607	0	ENST00000356435.5:c.1391A>G	p.Asn464Ser	p.N464S	ENST00000356435		464	aAc/aGc	10/35	0.893996653113991	5	FACETS	0.988	0.941	1	0.658	0.627	0.69	CLONAL	2	TRUE	2	0.893996653113991	5		607	1050	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023215	1023215	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049488-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	291	628	0	ENST00000358495.3:c.1040C>G	p.Ser347Cys	p.S347C	ENST00000358495	NM_134424.2	347	tCt/tGt	11/12	0.183241662894242	1	FACETS	0.583	0.554	0.613	0.583	0.554	0.613	INDETERMINATE	1	TRUE	0	0.893996653113991	1		628	617	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0049640-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	73	808	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	1	2	FACETS	0.618	0.539	0.704	0.618	0.539	0.704	SUBCLONAL	1	FALSE	1	0.22034463064293	2		808	1072	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426543	49426543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760983900	NA	P-0049640-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	60	879	1	ENST00000301067.7:c.11945G>A	p.Arg3982Gln	p.R3982Q	ENST00000301067	NM_003482.3	3982	cGa/cAa	39/54	1	2	FACETS	0.487	0.418	0.563	0.487	0.418	0.563	SUBCLONAL	1	FALSE	1	0.22034463064293	2		880	1119	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370837	55370837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1470546998	NA	P-0049640-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	41	751	0	ENST00000297316.4:c.139G>A	p.Glu47Lys	p.E47K	ENST00000297316	NM_022454.3	47	Gag/Aag	1/2	1	2	FACETS	0.605	0.503	0.719	0.605	0.503	0.719	SUBCLONAL	1	FALSE	1	0.22034463064293	2		751	615	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276711	115276711	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049640-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	16	482	0	ENST00000438362.2:c.748G>C	p.Asp250His	p.D250H	ENST00000438362	NM_001242891.1	250	Gat/Cat	8/20	1	2	FACETS	0.517	0.382	0.678	0.517	0.382	0.678	SUBCLONAL	1	FALSE	1	0.22034463064293	2		482	281	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518319	187518319	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049640-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	43	593	0	ENST00000441802.2:c.12375G>C	p.Gln4125His	p.Q4125H	ENST00000441802	NM_005245.3	4125	caG/caC	25/27	0.170318243095182	0	FACETS	0.546	0.457	0.646			1	SUBCLONAL	1	FALSE	0	0.22034463064293	0		593	557	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426307	47426307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049640-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	47	866	0	ENST00000377045.4:c.724G>A	p.Asp242Asn	p.D242N	ENST00000377045	NM_001654.4	242	Gat/Aat	8/16	NA	2	FACETS	0.468	0.394	0.551			1	INDETERMINATE	1	FALSE	NA	0.22034463064293	2		866	911	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459278	120459278	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	178	504	0	ENST00000256646.2:c.6067T>C	p.Tyr2023His	p.Y2023H	ENST00000256646	NM_024408.3	2023	Tat/Cat	34/34	0.54653632184937	3	FACETS	0.984	0.91	1			1	CLONAL	1	TRUE	NA	0.704805882338578	3		504	694	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809273	243809273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780868494	NA	P-0049664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	126	494	1	ENST00000263826.5:c.351G>A	p.Met117Ile	p.M117I	ENST00000263826	NM_005465.4	117	atG/atA	4/13	1	2	FACETS	0.887	0.811	0.966	0.887	0.811	0.966	CLONAL	1	TRUE	1	0.704805882338578	2		495	403	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999249	100999249	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	371	1187	1	ENST00000325455.5:c.553C>A	p.Leu185Met	p.L185M	ENST00000325455	NM_001202474.3	185	Ctg/Atg	1/8	0.704805882338578	3	FACETS	1	0.963	1	0.51	0.483	0.537	CLONAL	1	TRUE	1	0.704805882338578	3		1188	1397	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643232	38643232	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs138553244	NA	P-0049664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	110	335	0	ENST00000299084.4:c.702C>G	p.Ile234Met	p.I234M	ENST00000299084	NM_152594.2	234	atC/atG	7/7	1	2	FACETS	0.991	0.902	1	0.991	0.902	1	CLONAL	1	TRUE	1	0.704805882338578	2		335	315	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679810	88679810	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	187	653	0	ENST00000360948.2:c.653A>G	p.Asn218Ser	p.N218S	ENST00000360948	NM_001012338.2	218	aAc/aGc	7/19	1	2	FACETS	0.814	0.755	0.874	0.814	0.755	0.874	CLONAL	1	TRUE	1	0.704805882338578	2		653	652	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041660	14041660	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	231	596	0	ENST00000311895.7:c.2207T>C	p.Leu736Ser	p.L736S	ENST00000311895	NM_005236.2	736	tTa/tCa	11/11	0.704805882338578	2	FACETS	1	0.968	1	0.524	0.492	0.557	CLONAL	1	TRUE	0	0.704805882338578	2		596	625	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831915	72831915	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	280	946	0	ENST00000268489.5:c.4666C>G	p.Gln1556Glu	p.Q1556E	ENST00000268489	NM_006885.3	1556	Caa/Gaa	9/10	0.704805882338578	2	FACETS	0.928	0.875	0.983	0.464	0.437	0.492	CLONAL	1	TRUE	0	0.704805882338578	2		946	856	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	811	1135	0	ENST00000269305.4:c.517G>C	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ctg	5/11	0.704805882338578	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.704805882338578	2		1135	1101	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979529	7979529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768784091	NA	P-0049664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	607	839	5	ENST00000319144.4:c.1496G>A	p.Arg499His	p.R499H	ENST00000319144	NM_001139.2	499	cGc/cAc	11/15	0.704805882338578	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.704805882338578	2		844	829	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687722	29687722	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0049664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	211	566	0	ENST00000356175.3:c.8314+1G>C		p.X2772_splice	ENST00000356175	NM_000267.3	2772			0.704805882338578	2	FACETS	1	0.98	1	0.556	0.521	0.592	CLONAL	1	TRUE	0	0.704805882338578	2		566	538	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593517	48593517	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	86	296	0	ENST00000342988.3:c.1268G>C	p.Gly423Ala	p.G423A	ENST00000342988	NM_005359.5	423	gGa/gCa	10/12	0.282858697327893	3	FACETS	1	0.96	1	0.383	0.343	0.425	INDETERMINATE	1	TRUE	0	0.704805882338578	3		296	287	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619835	1619835	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	459	1235	1	ENST00000344749.5:c.1111C>T	p.Arg371Ter	p.R371*	ENST00000344749	NM_001136139.2	371	Cga/Tga	14/19	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.704805882338578	2		1236	1204	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741237	40741237	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	367	992	0	ENST00000392038.2:c.1196A>T	p.Asp399Val	p.D399V	ENST00000392038	NM_001626.4	399	gAt/gTt	12/14	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.704805882338578	2		992	992	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753093	42753093	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	412	1260	1	ENST00000222329.4:c.1171G>T	p.Ala391Ser	p.A391S	ENST00000222329	NM_006494.2	391	Gct/Tct	4/4	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.704805882338578	2		1261	1125	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872969	136872969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767830104	NA	P-0049664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	160	492	0	ENST00000241393.3:c.529G>A	p.Val177Ile	p.V177I	ENST00000241393	NM_003467.2	177	Gtc/Atc	2/2	1	2	FACETS	0.989	0.915	1	0.989	0.915	1	CLONAL	1	TRUE	1	0.704805882338578	2		492	459	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375230	31375235	+	inframe_deletion	In_Frame_Del	DEL	TGGAGA	TGGAGA	-	novel	NA	P-0049664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1358	313	1013	0	ENST00000328111.2:c.633_638del	p.Gly212_Asp213del	p.G212_D213del	ENST00000328111	NM_006892.3	209	agTGGAGAt/agt	6/23	0.704805882338578	4	FACETS	0.906	0.852	0.962	0.302	0.284	0.321	CLONAL	1	TRUE	1	0.704805882338578	4		1013	1671	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827898	40827898	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1246	231	663	2	ENST00000373198.4:c.2530C>A	p.Gln844Lys	p.Q844K	ENST00000373198	NM_133170.3	844	Cag/Aag	17/32	0.704805882338578	4	FACETS	0.757	0.703	0.812	0.252	0.234	0.271	SUBCLONAL	1	TRUE	1	0.704805882338578	4		665	1477	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936579	49936579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	743	1105	0	ENST00000296474.3:c.1348G>A	p.Ala450Thr	p.A450T	ENST00000296474	NM_002447.2	450	Gca/Aca	2/20	0.704805882338578	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.704805882338578	2		1105	1031	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564530	86564530	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	325	939	0	ENST00000274376.6:c.266del	p.Gly89GlufsTer7	p.G89Efs*7	ENST00000274376	NM_002890.2	88	Ggg/gg	1/25	0.704805882338578	1	FACETS	0.959	0.915	1	0.959	0.915	1	CLONAL	1	TRUE	0	0.704805882338578	1		939	623	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043438	180043438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373876329	NA	P-0049664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	1123	965	1	ENST00000261937.6:c.3148G>A	p.Val1050Met	p.V1050M	ENST00000261937	NM_182925.4	1050	Gtg/Atg	23/30	0.704805882338578	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.704805882338578	3		966	1388	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288560	33288560	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	234	553	0	ENST00000374542.5:c.992A>T	p.Asp331Val	p.D331V	ENST00000374542	NM_001141970.1	331	gAt/gTt	3/8	0.704805882338578	3	FACETS	1	0.984	1	0.386	0.361	0.411	CLONAL	1	TRUE	0	0.704805882338578	3		553	776	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505488	157505488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	184	456	0	ENST00000346085.5:c.3469G>A	p.Glu1157Lys	p.E1157K	ENST00000346085	NM_020732.3	1157	Gaa/Aaa	13/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.704805882338578	2		456	464	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517988	8517988	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	137	532	0	ENST00000356435.5:c.1403A>C	p.Lys468Thr	p.K468T	ENST00000356435		468	aAa/aCa	10/35	0.320229100712645	1	FACETS	0.537	0.492	0.583	0.537	0.492	0.583	INDETERMINATE	1	TRUE	0	0.704805882338578	1		532	469	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317529	1317529	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	602	724	1	ENST00000400841.2:c.536A>C	p.Lys179Thr	p.K179T	ENST00000400841		179	aAg/aCg	5/6	0.627859728536366	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.704805882338578	1		725	825	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626623	100626623	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	146	420	0	ENST00000308731.7:c.307C>G	p.Gln103Glu	p.Q103E	ENST00000308731	NM_000061.2	103	Cag/Gag	4/19	0.694914202380815	2	FACETS	1	0.935	1	0.508	0.468	0.548	CLONAL	1	TRUE	0	0.704805882338578	2		420	408	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	15	477	0				ENST00000310581	NM_198253.2	-/1132			0.284411308233494	3	FACETS	0.535	0.391	0.706	0.267	0.195	0.353	SUBCLONAL	1	FALSE	1	0.284973599629576	3		477	225	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	38	333	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	1	2	FACETS	0.823	0.683	0.979	0.823	0.683	0.979	CLONAL	1	FALSE	1	0.284973599629576	2		333	324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	46	863	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	0.655	0.551	0.769	0.655	0.551	0.769	SUBCLONAL	1	FALSE	1	0.284973599629576	2		863	493	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059260	27059260	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	48	352	0	ENST00000324856.7:c.1897C>T	p.Gln633Ter	p.Q633*	ENST00000324856	NM_006015.4	633	Cag/Tag	4/20	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	FALSE	1	0.284973599629576	2		352	332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	45	481	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	1	2	FACETS	0.7	0.589	0.823	0.7	0.589	0.823	SUBCLONAL	1	FALSE	1	0.284973599629576	2		481	451	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376413	15376413	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs374747220	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	47	451	0	ENST00000263377.2:c.601C>G	p.Gln201Glu	p.Q201E	ENST00000263377	NM_058243.2	201	Caa/Gaa	5/20	1	2	FACETS	0.767	0.648	0.898	0.767	0.648	0.898	SUBCLONAL	1	FALSE	1	0.284973599629576	2		451	430	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856113	68856113	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782750	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	45	452	0	ENST00000261769.5:c.1921C>T	p.Gln641Ter	p.Q641*	ENST00000261769	NM_004360.3	641	Cag/Tag	12/16	1	2	FACETS	0.831	0.7	0.975	0.831	0.7	0.975	CLONAL	1	FALSE	1	0.284973599629576	2		452	380	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868209	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	32	457	1	ENST00000269571.5:c.929_930delinsAT	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCC/tAT	8/27	1	2	FACETS	0.507	0.411	0.615	0.507	0.411	0.615	SUBCLONAL	1	FALSE	1	0.284973599629576	2		458	443	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626737	28626737	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	25	423	0	ENST00000241453.7:c.559G>A	p.Glu187Lys	p.E187K	ENST00000241453	NM_004119.2	187	Gag/Aag	5/24	1	2	FACETS	0.41	0.322	0.511	0.41	0.322	0.511	SUBCLONAL	1	FALSE	1	0.284973599629576	2		423	428	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317926	8317926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	23	412	0	ENST00000356435.5:c.5687C>T	p.Ser1896Phe	p.S1896F	ENST00000356435		1896	tCc/tTc	35/35	1	2	FACETS	0.468	0.365	0.588	0.468	0.365	0.588	SUBCLONAL	1	FALSE	1	0.284973599629576	2		412	345	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532729	46532729	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756800675	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	31	421	0	ENST00000262741.5:c.349C>T	p.His117Tyr	p.H117Y	ENST00000262741	NM_003629.3	117	Cac/Tac	4/10	1	2	FACETS	0.7	0.567	0.849	0.7	0.567	0.849	SUBCLONAL	1	FALSE	1	0.284973599629576	2		421	311	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58711239	58711239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	27	328	0	ENST00000305921.3:c.727C>T	p.Arg243Cys	p.R243C	ENST00000305921	NM_003620.3	243	Cgt/Tgt	3/6	1	2	FACETS	0.6	0.478	0.739	0.6	0.478	0.739	SUBCLONAL	1	FALSE	1	0.284973599629576	2		328	316	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81534655	81534655	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	32	350	0	ENST00000298171.2:c.300G>C	p.Leu100Phe	p.L100F	ENST00000298171	NM_000369.2	100	ttG/ttC	3/10	1	2	FACETS	0.754	0.614	0.911	0.754	0.614	0.911	CLONAL	1	FALSE	1	0.284973599629576	2		350	298	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429360	78429360	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	31	447	0	ENST00000370768.2:c.1082G>C	p.Arg361Thr	p.R361T	ENST00000370768	NM_003902.3	361	aGa/aCa	13/20	1	2	FACETS	0.502	0.406	0.612	0.502	0.406	0.612	SUBCLONAL	1	FALSE	1	0.284973599629576	2		447	433	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262249	115262249	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	27	373	0	ENST00000438362.2:c.2305C>T	p.Leu769Phe	p.L769F	ENST00000438362	NM_001242891.1	769	Ctt/Ttt	18/20	1	2	FACETS	0.468	0.372	0.578	0.468	0.372	0.578	SUBCLONAL	1	FALSE	1	0.284973599629576	2		373	405	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165386	47165386	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	47	477	0	ENST00000409792.3:c.740C>G	p.Pro247Arg	p.P247R	ENST00000409792	NM_014159.6	247	cCa/cGa	3/21	1	2	FACETS	0.942	0.798	1	0.942	0.798	1	CLONAL	1	FALSE	1	0.284973599629576	2		477	350	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165630	47165630	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	54	676	0	ENST00000409792.3:c.496C>G	p.Pro166Ala	p.P166A	ENST00000409792	NM_014159.6	166	Cca/Gca	3/21	1	2	FACETS	0.682	0.582	0.791	0.682	0.582	0.791	SUBCLONAL	1	FALSE	1	0.284973599629576	2		676	556	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241975	72241975	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	34	325	0	ENST00000357731.5:c.415C>G	p.Pro139Ala	p.P139A	ENST00000357731	NM_173808.2	139	Cct/Gct	3/7	1	2	FACETS	0.858	0.704	1	0.858	0.704	1	CLONAL	1	FALSE	1	0.284973599629576	2		325	278	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444675	78444675	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	33	449	0	ENST00000370768.2:c.14C>G	p.Ser5Ter	p.S5*	ENST00000370768	NM_003902.3	5	tCa/tGa	1/20	1	2	FACETS	0.618	0.503	0.746	0.618	0.503	0.746	SUBCLONAL	1	FALSE	1	0.284973599629576	2		449	375	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375329	118375329	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	30	569	0	ENST00000534358.1:c.8722G>A	p.Glu2908Lys	p.E2908K	ENST00000534358	NM_005933.3	2908	Gaa/Aaa	27/36	1	2	FACETS	0.51	0.41	0.623	0.51	0.41	0.623	SUBCLONAL	1	FALSE	1	0.284973599629576	2		569	413	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479268	50479268	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	18	403	1	ENST00000394963.4:c.116G>C	p.Arg39Pro	p.R39P	ENST00000394963	NM_003076.4	39	cGa/cCa	1/13	1	2	FACETS	0.54	0.407	0.696	0.54	0.407	0.696	SUBCLONAL	1	FALSE	1	0.284973599629576	2		404	234	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28885748	28885748	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	20	309	0	ENST00000282397.4:c.3614C>G	p.Ser1205Ter	p.S1205*	ENST00000282397	NM_002019.4	1205	tCa/tGa	27/30	1	2	FACETS	0.518	0.396	0.66	0.518	0.396	0.66	SUBCLONAL	1	FALSE	1	0.284973599629576	2		309	271	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003090	42003090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1418511612	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	20	433	0	ENST00000219905.7:c.2627C>G	p.Ser876Cys	p.S876C	ENST00000219905	NM_001164273.1	876	tCt/tGt	8/24	1	2	FACETS	0.41	0.313	0.524	0.41	0.313	0.524	SUBCLONAL	1	FALSE	1	0.284973599629576	2		433	342	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639564	3639564	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	66	616	0	ENST00000294008.3:c.4075C>G	p.Pro1359Ala	p.P1359A	ENST00000294008	NM_032444.2	1359	Cca/Gca	12/15	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	FALSE	1	0.284973599629576	2		616	430	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627751	37627751	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	57	531	0	ENST00000447079.4:c.1666C>G	p.Pro556Ala	p.P556A	ENST00000447079	NM_015083.1	556	Cca/Gca	2/14	1	2	FACETS	0.883	0.759	1	0.883	0.759	1	CLONAL	1	FALSE	1	0.284973599629576	2		531	453	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627814	37627814	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	58	547	0	ENST00000447079.4:c.1729C>A	p.Pro577Thr	p.P577T	ENST00000447079	NM_015083.1	577	Cct/Act	2/14	1	2	FACETS	0.804	0.692	0.927	0.804	0.692	0.927	CLONAL	1	FALSE	1	0.284973599629576	2		547	506	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142925	30142925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	21	497	0	ENST00000389048.3:c.601G>A	p.Glu201Lys	p.E201K	ENST00000389048	NM_004304.4	201	Gag/Aag	1/29	1	2	FACETS	0.391	0.3	0.497	0.391	0.3	0.497	SUBCLONAL	1	FALSE	1	0.284973599629576	2		497	377	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026595	48026595	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	46	570	0	ENST00000234420.5:c.1473G>T	p.Met491Ile	p.M491I	ENST00000234420	NM_000179.2	491	atG/atT	4/10	1	2	FACETS	0.753	0.635	0.882	0.753	0.635	0.882	SUBCLONAL	1	FALSE	1	0.284973599629576	2		570	429	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630382	67630382	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	15	175	0	ENST00000272342.5:c.568G>C	p.Glu190Gln	p.E190Q	ENST00000272342	NM_019002.3	190	Gaa/Caa	5/6	1	2	FACETS	0.671	0.493	0.881	0.671	0.493	0.881	SUBCLONAL	1	FALSE	1	0.284973599629576	2		175	157	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719321	190719321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	14	334	0	ENST00000441310.2:c.1323G>A	p.Met441Ile	p.M441I	ENST00000441310	NM_000534.4	441	atG/atA	9/13	1	2	FACETS	0.42	0.303	0.561	0.42	0.303	0.561	SUBCLONAL	1	FALSE	1	0.284973599629576	2		334	234	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46255878	46255878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	11	220	0	ENST00000371998.3:c.490G>A	p.Glu164Lys	p.E164K	ENST00000371998		164	Gaa/Aaa	6/23	1	2	FACETS	0.411	0.284	0.568	0.411	0.284	0.568	SUBCLONAL	1	FALSE	1	0.284973599629576	2		220	188	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436417	52436417	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	38	436	0	ENST00000460680.1:c.2077G>T	p.Glu693Ter	p.E693*	ENST00000460680	NM_004656.3	693	Gag/Tag	17/17	1	2	FACETS	0.826	0.685	0.982	0.826	0.685	0.982	CLONAL	1	FALSE	1	0.284973599629576	2		436	323	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595820	52595820	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	69	461	0	ENST00000394830.3:c.4095G>T	p.Trp1365Cys	p.W1365C	ENST00000394830	NM_018313.4	1365	tgG/tgT	26/30	1	2	FACETS	0.992	0.866	1	0.992	0.866	1	CLONAL	1	FALSE	1	0.284973599629576	2		461	488	SUCCESS
ATR	545	MSKCC	GRCh37	3	142254029	142254029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	24	365	0	ENST00000350721.4:c.3838G>A	p.Asp1280Asn	p.D1280N	ENST00000350721	NM_001184.3	1280	Gat/Aat	21/47	1	2	FACETS	0.668	0.526	0.832	0.668	0.526	0.832	SUBCLONAL	1	FALSE	1	0.284973599629576	2		365	252	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968103	55968103	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	19	299	0	ENST00000263923.4:c.2227C>G	p.Leu743Val	p.L743V	ENST00000263923	NM_002253.2	743	Ctt/Gtt	15/30	1	2	FACETS	0.44	0.334	0.565	0.44	0.334	0.565	SUBCLONAL	1	FALSE	1	0.284973599629576	2		299	303	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397145	397145	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	63	554	0	ENST00000380956.4:c.530G>C	p.Ser177Thr	p.S177T	ENST00000380956	NM_001195286.1	177	aGc/aCc	5/9	1	2	FACETS	0.874	0.757	1	0.874	0.757	1	CLONAL	1	FALSE	1	0.284973599629576	2		554	506	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045882	26045882	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	55	666	0	ENST00000540144.1:c.244G>C	p.Asp82His	p.D82H	ENST00000540144	NM_003531.2	82	Gac/Cac	1/1	1	2	FACETS	0.668	0.571	0.774	0.668	0.571	0.774	SUBCLONAL	1	FALSE	1	0.284973599629576	2		666	578	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680017	30680017	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	42	580	0	ENST00000376406.3:c.1702G>C	p.Glu568Gln	p.E568Q	ENST00000376406	NM_014641.2	568	Gag/Cag	5/15	1	2	FACETS	0.627	0.524	0.742	0.627	0.524	0.742	SUBCLONAL	1	FALSE	1	0.284973599629576	2		580	470	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323162	31323162	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	71	654	0	ENST00000412585.2:c.827G>C	p.Gly276Ala	p.G276A	ENST00000412585	NM_005514.6	276	gGa/gCa	4/8	1	2	FACETS	0.899	0.786	1	0.899	0.786	1	CLONAL	1	FALSE	1	0.284973599629576	2		654	554	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099520	157099520	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1209401384	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	38	491	0	ENST00000346085.5:c.457G>A	p.Asp153Asn	p.D153N	ENST00000346085	NM_020732.3	153	Gac/Aac	1/20	1	2	FACETS	0.855	0.709	1	0.855	0.709	1	CLONAL	1	FALSE	1	0.284973599629576	2		491	312	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945385	151945385	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	12	234	0	ENST00000262189.6:c.2134G>C	p.Glu712Gln	p.E712Q	ENST00000262189	NM_170606.2	712	Gag/Cag	14/59	1	2	FACETS	0.533	0.376	0.725	0.533	0.376	0.725	SUBCLONAL	1	FALSE	1	0.284973599629576	2		234	158	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900305	101900305	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	34	368	0	ENST00000374994.4:c.739G>A	p.Glu247Lys	p.E247K	ENST00000374994	NM_004612.2	247	Gag/Aag	4/9	1	2	FACETS	0.732	0.599	0.88	0.732	0.599	0.88	SUBCLONAL	1	FALSE	1	0.284973599629576	2		368	326	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133729483	133729483	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	44	378	0	ENST00000318560.5:c.112G>C	p.Glu38Gln	p.E38Q	ENST00000318560	NM_005157.4	38	Gag/Cag	2/11	1	2	FACETS	0.651	0.546	0.768	0.651	0.546	0.768	SUBCLONAL	1	FALSE	1	0.284973599629576	2		378	474	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786055	135786055	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752575728	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	25	539	0	ENST00000298552.3:c.1166G>A	p.Gly389Glu	p.G389E	ENST00000298552	NM_001162426.1	389	gGa/gAa	12/23	1	2	FACETS	0.402	0.316	0.502	0.402	0.316	0.502	SUBCLONAL	1	FALSE	1	0.284973599629576	2		539	436	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874360	76874360	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050150-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	20	292	0	ENST00000373344.5:c.5362C>G	p.Gln1788Glu	p.Q1788E	ENST00000373344	NM_000489.3	1788	Cag/Gag	21/35	1	2	FACETS	0.662	0.508	0.841	0.662	0.508	0.841	SUBCLONAL	1	FALSE	1	0.284973599629576	2		292	212	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0050522-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	284	323	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.358222152130138	5	FACETS	0.85	0.805	0.894	0.85	0.805	0.894	INDETERMINATE	3	TRUE	2	0.774498808879857	5		323	622	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0050522-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	593	569	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.786426199800505	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.774498808879857	2		569	665	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004721	150004721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1034620976	NA	P-0050522-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	547	628	1	ENST00000253339.5:c.1504C>T	p.Arg502Cys	p.R502C	ENST00000253339		502	Cgt/Tgt	3/7	0.321245926100416	5	FACETS	0.903	0.876	0.931	0.723	0.7	0.745	INDETERMINATE	4	TRUE	0	0.774498808879857	5		629	845	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664864	138664893	+	inframe_deletion	In_Frame_Del	DEL	GCGGCTGCAGCCGCAGCTGCTGCAGCCGCT	GCGGCTGCAGCCGCAGCTGCTGCAGCCGCT	-	rs387906321	NA	P-0050522-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	16	357	1	ENST00000330315.3:c.672_701del	p.Ala225_Ala234del	p.A225_A234del	ENST00000330315	NM_023067.3	224	gcAGCGGCTGCAGCAGCTGCGGCTGCAGCCGCg/gcg	1/1	1	2	FACETS	0.135	0.099	0.178	0.135	0.099	0.178	SUBCLONAL	1	TRUE	1	0.774498808879857	2		358	306	SUCCESS
ATR	545	MSKCC	GRCh37	3	142172007	142172007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762196224	NA	P-0050522-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	126	409	0	ENST00000350721.4:c.7724C>T	p.Ala2575Val	p.A2575V	ENST00000350721	NM_001184.3	2575	gCg/gTg	46/47	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.774498808879857	2		409	320	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023327	33023336	+	frameshift_variant	Frame_Shift_Del	DEL	CCCAAGAAAT	CCCAAGAAAT	-	novel	NA	P-0050522-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	245	623	0	ENST00000300177.4:c.436_445del	p.Pro146SerfsTer4	p.P146Sfs*4	ENST00000300177	NM_001191322.1	146	CCCAAGAAATtc/tc	2/2	0.714270770502216	3	FACETS	1	0.982	1	0.563	0.527	0.599	CLONAL	1	TRUE	1	0.774498808879857	3		623	780	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437567	56437568	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACAGTTACGATGGGTGG	novel	NA	P-0050522-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	411	540	0	ENST00000407977.2:c.894_895insCCACCCATCGTAACTGT	p.Val299ProfsTer126	p.V299Pfs*126	ENST00000407977		298	-/CCACCCATCGTAACTGT	8/10	0.786426199800505	2	FACETS	0.827	0.797	0.856	0.827	0.797	0.856	CLONAL	2	TRUE	0	0.774498808879857	2		540	642	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646206	215646206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1163172447	NA	P-0050522-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	226	412	0	ENST00000260947.4:c.392G>A	p.Ser131Asn	p.S131N	ENST00000260947	NM_000465.2	131	aGt/aAt	4/11	0.171468243202367	3	FACETS	1	0.971	1	0.69	0.654	0.726	INDETERMINATE	2	TRUE	0	0.774498808879857	3		412	391	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796834	42796834	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050522-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	411	621	0	ENST00000575354.2:c.3292G>A	p.Gly1098Ser	p.G1098S	ENST00000575354	NM_015125.3	1098	Ggc/Agc	14/20	0.421581178259231	2	FACETS	0.861	0.832	0.89	0.861	0.832	0.89	INDETERMINATE	2	TRUE	0	0.774498808879857	2		621	616	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89176374	89176374	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050522-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	45	380	0	ENST00000336596.2:c.104C>A	p.Ser35Ter	p.S35*	ENST00000336596	NM_005233.5	35	tCa/tAa	2/17	1	2	FACETS	0.507	0.43	0.591	0.507	0.43	0.591	SUBCLONAL	1	TRUE	1	0.774498808879857	2		380	229	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103520468	103520468	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050522-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	20	308	0	ENST00000355739.4:c.2539G>T	p.Asp847Tyr	p.D847Y	ENST00000355739	NM_000123.3	847	Gac/Tac	12/15	0.171468243202367	3	FACETS	0.206	0.157	0.264	0.069	0.052	0.088	INDETERMINATE	1	TRUE	0	0.774498808879857	3		308	347	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646915	23646915	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1597097692	NA	P-0050522-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	24	580	0	ENST00000261584.4:c.952A>C	p.Ser318Arg	p.S318R	ENST00000261584	NM_024675.3	318	Agt/Cgt	4/13	0.786426199800505	2	FACETS	0.148	0.116	0.186	0.074	0.058	0.093	SUBCLONAL	1	TRUE	0	0.774498808879857	2		580	418	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544334	86544334	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050522-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	272	646	0	ENST00000262426.4:c.159C>A	p.Tyr53Ter	p.Y53*	ENST00000262426	NM_001451.2	53	taC/taA	1/2	0.786426199800505	2	FACETS	1	0.992	1	0.631	0.598	0.663	CLONAL	1	TRUE	0	0.774498808879857	2		646	557	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0051072-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	39	121	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.258531803957957	2		121	280	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0051072-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	92	503	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	1	2	FACETS	0.765	0.683	0.852	1	0.981	1	SUBCLONAL	2	TRUE	1	0.258531803957957	2		503	465	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974783	21974783	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658556	NA	P-0051072-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	91	718	0	ENST00000304494.5:c.44G>A	p.Trp15Ter	p.W15*	ENST00000304494	NM_000077.4	15	tGg/tAg	1/3	0.258531803957957	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.258531803957957	1		718	475	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426355	49426355	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051072-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	40	658	0	ENST00000301067.7:c.12133C>T	p.Gln4045Ter	p.Q4045*	ENST00000301067	NM_003482.3	4045	Cag/Tag	39/54	1	2	FACETS	0.619	0.514	0.736	0.619	0.514	0.736	SUBCLONAL	1	TRUE	1	0.258531803957957	2		658	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0052857-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	153	399	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.200086215010906	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.200086215010906	2		399	720	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024197	31024197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052857-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	57	517	0	ENST00000375687.4:c.3682G>A	p.Glu1228Lys	p.E1228K	ENST00000375687	NM_015338.5	1228	Gaa/Aaa	13/13	1	2	FACETS	0.763	0.653	0.883	0.763	0.653	0.883	SUBCLONAL	1	TRUE	1	0.200086215010906	2		517	747	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880219	37880220	+	missense_variant	Missense_Mutation	DNP	TT	TT	CC	rs121913469	NA	P-0052857-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	256	493	0	ENST00000269571.5:c.2263_2264delinsCC	p.Leu755Pro	p.L755P	ENST00000269571		755	TTg/CCg	19/27	0.200086215010906	5	FACETS	0.909	0.852	0.967	1	0.988	1	CLONAL	4	TRUE	2	0.200086215010906	5		493	915	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474026	29474026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147858673	NA	P-0052857-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	44	525	0	ENST00000389048.3:c.2149G>A	p.Glu717Lys	p.E717K	ENST00000389048	NM_004304.4	717	Gag/Aag	12/29	1	2	FACETS	0.529	0.442	0.625	0.529	0.442	0.625	SUBCLONAL	1	TRUE	1	0.200086215010906	2		525	832	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939507	71939507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373971775	NA	P-0052857-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	119	661	0	ENST00000298229.2:c.362G>A	p.Arg121Gln	p.R121Q	ENST00000298229	NM_001567.3	121	cGa/cAa	3/28	0.185350381242515	3	FACETS	1	0.973	1	0.618	0.556	0.683	CLONAL	1	TRUE	1	0.200086215010906	3		661	1059	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183258	56183258	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052857-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	65	413	0	ENST00000399503.3:c.4168G>T	p.Gly1390Ter	p.G1390*	ENST00000399503	NM_005921.1	1390	Gga/Tga	18/20	0.200086215010906	4	FACETS	0.958	0.829	1	0.479	0.414	0.549	CLONAL	1	TRUE	2	0.200086215010906	4		413	814	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508799	31508799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052857-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	123	397	0	ENST00000344624.3:c.1516G>A	p.Ala506Thr	p.A506T	ENST00000344624		506	Gca/Aca	7/33	0.200086215010906	4	FACETS	0.942	0.852	1	0.942	0.852	1	CLONAL	2	TRUE	2	0.200086215010906	4		397	783	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443583	29443583	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052857-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	99	446	0	ENST00000389048.3:c.3634C>G	p.Arg1212Gly	p.R1212G	ENST00000389048	NM_004304.4	1212	Cgc/Ggc	23/29	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.200086215010906	2		446	791	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099884	27099884	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052857-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	86	572	0	ENST00000324856.7:c.3763G>T	p.Gly1255Trp	p.G1255W	ENST00000324856	NM_006015.4	1255	Ggg/Tgg	15/20	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.200086215010906	2		572	813	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099869	27099869	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052857-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	90	530	0	ENST00000324856.7:c.3748C>T	p.Gln1250Ter	p.Q1250*	ENST00000324856	NM_006015.4	1250	Cag/Tag	15/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.200086215010906	2		530	766	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740174	162740174	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052857-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	69	519	1	ENST00000367921.3:c.1376C>A	p.Ser459Tyr	p.S459Y	ENST00000367921	NM_006182.2	459	tCc/tAc	12/18	0.200086215010906	3	FACETS	0.909	0.79	1	0.454	0.395	0.519	CLONAL	1	TRUE	1	0.200086215010906	3		520	835	SUCCESS
BLM	641	MSKCC	GRCh37	15	91298117	91298117	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052857-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	62	357	0	ENST00000355112.3:c.1036G>A	p.Glu346Lys	p.E346K	ENST00000355112	NM_000057.2	346	Gag/Aag	5/22	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.200086215010906	2		357	495	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170009677	170009677	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052857-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	37	264	0	ENST00000295797.4:c.1239C>G	p.Phe413Leu	p.F413L	ENST00000295797	NM_002740.5	413	ttC/ttG	13/18	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.200086215010906	2		264	299	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162475199	162475199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052857-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	55	376	0	ENST00000366898.1:c.542C>T	p.Ser181Phe	p.S181F	ENST00000366898	NM_004562.2	181	tCt/tTt	5/12	0.200086215010906	3	FACETS	1	0.908	1	0.542	0.463	0.628	CLONAL	1	TRUE	1	0.200086215010906	3		376	558	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048521	6048702	+	splice_donor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	CCACGCGCCTCGGCCATGTTCCCCCCATTTCCAGGGAGGTTGGAATGCCGTGGGTCTCAAAGAGGGCGCGCGAGAGGGGACACCGGAAGACTGCGAGCCCCGCTCACCTCGAGCTCTCAGCTCGCTCCATGGATGCAACACCCGATCCGCCTCGGGGACTGGGAAAGTTCCCTCCAGGGCTC	CCACGCGCCTCGGCCATGTTCCCCCCATTTCCAGGGAGGTTGGAATGCCGTGGGTCTCAAAGAGGGCGCGCGAGAGGGGACACCGGAAGACTGCGAGCCCCGCTCACCTCGAGCTCTCAGCTCGCTCCATGGATGCAACACCCGATCCGCCTCGGGGACTGGGAAAGTTCCCTCCAGGGCTC	-	novel	NA	P-0052857-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	174	570	0	ENST00000265849.7:c.-52_23+107del		p.X18_splice	ENST00000265849	NM_000535.5	18		1/15	0.200086215010906	6	FACETS	0.893	0.82	0.969	0.446	0.41	0.485	CLONAL	2	TRUE	2	0.200086215010906	6		570	1364	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482925	140482925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052857-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	129	549	1	ENST00000288602.6:c.1210G>A	p.Ala404Thr	p.A404T	ENST00000288602	NM_004333.4	404	Gcc/Acc	10/18	0.185350381242515	3	FACETS	0.876	0.794	0.961	0.876	0.794	0.961	CLONAL	2	TRUE	1	0.200086215010906	3		550	810	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504380	8504380	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1384063536	NA	P-0052857-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	39	374	0	ENST00000356435.5:c.1703C>T	p.Thr568Ile	p.T568I	ENST00000356435		568	aCa/aTa	12/35	0.200086215010906	4	FACETS	0.719	0.594	0.858	0.359	0.297	0.429	SUBCLONAL	1	TRUE	2	0.200086215010906	4		374	651	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829769	76829782	+	frameshift_variant	Frame_Shift_Del	DEL	GTAGTGGAACCATC	GTAGTGGAACCATC	A	novel	NA	P-0052857-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	55	188	0	ENST00000373344.5:c.6259_6272delinsT	p.Asp2087LeufsTer18	p.D2087Lfs*18	ENST00000373344	NM_000489.3	2087	GATGGTTCCACTACt/Tt	28/35	0.200086215010906	2	FACETS	1	0.905	1			1	CLONAL	3	TRUE	NA	0.200086215010906	2		188	175	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0052908-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	433	697	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.833441285088687	2	FACETS	0.97	0.947	0.991	0.97	0.947	0.991	CLONAL	2	TRUE	0	0.873679153513702	2		697	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882019	NA	P-0052908-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	1179	581	0	ENST00000269305.4:c.455del	p.Pro152ArgfsTer18	p.P152Rfs*18	ENST00000269305	NM_001126112.2	152	cCg/cg	5/11	0.873679153513702	5	FACETS	0.947	0.936	0.958			1	CLONAL	5	TRUE	NA	0.873679153513702	5		581	1317	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190795	106190795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1025708134	NA	P-0052908-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	364	317	0	ENST00000380013.4:c.4073G>A	p.Cys1358Tyr	p.C1358Y	ENST00000380013	NM_001127208.2	1358	tGc/tAc	9/11	0.841597297509707	2	FACETS	0.98	0.956	1	0.98	0.956	1	CLONAL	2	TRUE	0	0.873679153513702	2		317	425	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478641	57478726	+	splice_donor_variant,splice_acceptor_variant,intron_variant	Splice_Site	DEL	GTACGTGCTGGCTCCTTGTGCTGTCTGTCTTGTAGCGCCCTCCCAGCCAGTGCTGTTCCCTGACCGCTTTGCTAAATCATTTTCAG	GTACGTGCTGGCTCCTTGTGCTGTCTGTCTTGTAGCGCCCTCCCAGCCAGTGCTGTTCCCTGACCGCTTTGCTAAATCATTTTCAG	-	novel	NA	P-0052908-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	36	521	0	ENST00000371085.3:c.312+1_313-1del		p.X104_splice	ENST00000371085	NM_000516.4	104			0.304955147114908	3	FACETS	0.164	0.134	0.198	0.082	0.067	0.099	INDETERMINATE	1	TRUE	1	0.873679153513702	3		521	720	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	465682	465682	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052908-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	290	308	0	ENST00000399788.2:c.694A>G	p.Arg232Gly	p.R232G	ENST00000399788	NM_001042603.1	232	Aga/Gga	6/28	0.668891947843556	4	FACETS	0.945	0.896	0.995	0.945	0.896	0.995	CLONAL	2	TRUE	2	0.873679153513702	4		308	658	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424780	49424780	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0052908-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	439	521	0	ENST00000301067.7:c.13567A>T	p.Lys4523Ter	p.K4523*	ENST00000301067	NM_003482.3	4523	Aag/Tag	40/54	0.810113465373708	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.873679153513702	4		521	938	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785814	50785814	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052908-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	173	185	0	ENST00000398568.2:c.804C>G	p.Asp268Glu	p.D268E	ENST00000398568	NM_001042412.1	268	gaC/gaG	4/18	0.865627772740521	3	FACETS	0.912	0.857	0.967	0.912	0.857	0.967	CLONAL	2	TRUE	1	0.873679153513702	3		185	312	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984427	72984427	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052908-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	408	494	0	ENST00000268489.5:c.3157G>T	p.Glu1053Ter	p.E1053*	ENST00000268489	NM_006885.3	1053	Gag/Tag	3/10	0.865627772740521	3	FACETS	0.985	0.948	1	0.985	0.948	1	CLONAL	2	TRUE	1	0.873679153513702	3		494	681	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227037	2227037	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052908-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	243	475	0	ENST00000398665.3:c.4517G>T	p.Gly1506Val	p.G1506V	ENST00000398665	NM_032482.2	1506	gGc/gTc	27/28	0.427764598554494	4	FACETS	0.78	0.733	0.828	0.78	0.733	0.828	INDETERMINATE	2	TRUE	2	0.873679153513702	4		475	668	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225343033	225343033	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052908-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	248	348	0	ENST00000264414.4:c.2059G>T	p.Glu687Ter	p.E687*	ENST00000264414	NM_003590.4	687	Gag/Tag	15/16	0.436660337170995	5	FACETS	0.967	0.91	1	0.645	0.606	0.684	INDETERMINATE	2	TRUE	2	0.873679153513702	5		348	678	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074284	30074284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762588182	NA	P-0052908-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	345	410	0	ENST00000338641.4:c.1546C>T	p.Arg516Trp	p.R516W	ENST00000338641	NM_000268.3	516	Cgg/Tgg	14/16	0.481427821114035	5	FACETS	0.873	0.833	0.912	0.873	0.833	0.912	INDETERMINATE	3	TRUE	2	0.873679153513702	5		410	697	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39021158	39021158	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052908-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	236	271	0	ENST00000357387.3:c.178C>G	p.Leu60Val	p.L60V	ENST00000357387	NM_152756.3	60	Ctg/Gtg	3/38	0.873679153513702	7	FACETS	0.781	0.728	0.835	0.312	0.291	0.334	SUBCLONAL	2	TRUE	2	0.873679153513702	7		271	1102	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287622	33287622	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052908-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	426	459	0	ENST00000374542.5:c.1475G>T	p.Gly492Val	p.G492V	ENST00000374542	NM_001141970.1	492	gGa/gTa	6/8	0.813746754437735	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.873679153513702	3		459	675	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367288	50367288	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052908-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	295	483	0	ENST00000331340.3:c.95C>A	p.Pro32Gln	p.P32Q	ENST00000331340	NM_006060.4	32	cCg/cAg	3/8	0.633859731386764	1	FACETS	0.98	0.946	1	0.98	0.946	1	CLONAL	1	TRUE	0	0.873679153513702	1		483	388	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737421	145737421	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052908-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	380	594	0	ENST00000428558.2:c.3266T>A	p.Leu1089Gln	p.L1089Q	ENST00000428558	NM_004260.3	1089	cTg/cAg	20/22	0.873679153513702	5	FACETS	0.806	0.765	0.847	0.537	0.51	0.565	CLONAL	2	TRUE	2	0.873679153513702	5		594	1247	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690828	89690828	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052908-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	203	218	0	ENST00000371953.3:c.235del	p.Ala79ProfsTer20	p.A79Pfs*20	ENST00000371953	NM_000314.4	79	Gcc/cc	4/9	0.841597297509707	2	FACETS	0.915	0.879	0.948	0.915	0.879	0.948	CLONAL	2	TRUE	0	0.873679153513702	2		218	254	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610211	10610211	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052908-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	438	550	0	ENST00000171111.5:c.499G>C	p.Val167Leu	p.V167L	ENST00000171111	NM_203500.1	167	Gtt/Ctt	2/6	0.427764598554494	4	FACETS	1	0.992	1	1	0.992	1	INDETERMINATE	2	TRUE	2	0.873679153513702	4		550	835	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504410	186504411	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTTTA	novel	NA	P-0052908-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1492	122	280	0	ENST00000323963.5:c.749_753dup	p.Ile252PhefsTer22	p.I252Ffs*22	ENST00000323963		249	-/TTTTA	7/11	0.873679153513702	10	FACETS	0.778	0.7	0.86			1	SUBCLONAL	1	TRUE	NA	0.873679153513702	10		280	1614	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144666	55144666	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052908-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	366	345	0	ENST00000257290.5:c.2140G>T	p.Asp714Tyr	p.D714Y	ENST00000257290	NM_006206.4	714	Gat/Tat	15/23	0.841597297509707	2	FACETS	0.974	0.95	0.997	0.974	0.95	0.997	CLONAL	2	TRUE	0	0.873679153513702	2		345	430	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413111	63413111	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052908-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	359	209	0	ENST00000330258.3:c.56G>C	p.Ser19Thr	p.S19T	ENST00000330258	NM_152424.3	19	aGt/aCt	2/2	0.717919112202686	2	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.873679153513702	2		209	401	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218052	108218052	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1064794840	NA	P-0053166-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	142	170	0	ENST00000278616.4:c.8631G>C	p.Leu2877Phe	p.L2877F	ENST00000278616	NM_000051.3	2877	ttG/ttC	59/63	0.664161115400746	1	FACETS	0.998	0.928	1	0.998	0.928	1	CLONAL	1	TRUE	0	0.664257099397395	1		170	286	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156729	20156729	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs757280897	NA	P-0053166-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	158	191	0	ENST00000379607.5:c.28A>G	p.Lys10Glu	p.K10E	ENST00000379607	NM_001412.3	10	Aaa/Gaa	2/7	0.664257099397395	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.664257099397395	1		191	306	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892263	9892263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053166-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	220	464	0	ENST00000330684.3:c.2227G>A	p.Glu743Lys	p.E743K	ENST00000330684	NM_001134407.1	743	Gaa/Aaa	11/13	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.664257099397395	2		464	629	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061027	38061027	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053166-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	97	580	0	ENST00000250448.2:c.962A>G	p.Glu321Gly	p.E321G	ENST00000250448	NM_004496.3	321	gAg/gGg	2/2	1	2	FACETS	0.41	0.366	0.458	0.41	0.366	0.458	SUBCLONAL	1	TRUE	1	0.664257099397395	2		580	712	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0053228-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	115	355	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.93114828929592	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.93114828929592	3		355	167	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557546	21557546	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053228-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	215	484	0	ENST00000382592.4:c.2299C>A	p.Leu767Met	p.L767M	ENST00000382592	NM_014572.2	767	Ctg/Atg	5/8	0.522226670821974	4	FACETS	1	0.992	1	0.487	0.455	0.519	INDETERMINATE	1	TRUE	1	0.93114828929592	4		484	611	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162122	22162122	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053228-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	200	383	0	ENST00000215832.6:c.133A>C	p.Asn45His	p.N45H	ENST00000215832	NM_002745.4	45	Aat/Cat	2/9	0.93114828929592	4	FACETS	0.912	0.845	0.98	0.228	0.211	0.245	CLONAL	1	TRUE	0	0.93114828929592	4		383	910	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112919955	112919955	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053228-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	51	163	0	ENST00000351677.2:c.1170A>T	p.Glu390Asp	p.E390D	ENST00000351677	NM_002834.3	390	gaA/gaT	10/16	0.522226670821974	4	FACETS	1	0.955	1	0.422	0.365	0.482	INDETERMINATE	1	TRUE	1	0.93114828929592	4		163	167	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295520	1295520	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1397274276	NA	P-0053228-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	266	567	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.93114828929592	NA		567	453	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401371	139401371	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1230913341	NA	P-0053228-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	95	432	0	ENST00000277541.6:c.3698C>G	p.Ser1233Cys	p.S1233C	ENST00000277541	NM_017617.3	1233	tCc/tGc	23/34	0.93114828929592	2	FACETS	1	0.965	1	0.554	0.507	0.601	CLONAL	1	TRUE	0	0.93114828929592	2		432	184	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0054364-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	132	580	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	1	2	FACETS	0.422	0.382	0.464	0.422	0.382	0.464	SUBCLONAL	1	TRUE	1	0.571514193479536	2		580	1094	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101067	27101068	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054364-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	267	715	0	ENST00000324856.7:c.4354dup	p.Gln1452ProfsTer39	p.Q1452Pfs*39	ENST00000324856	NM_006015.4	1450	ggc/ggCc	18/20	0.571514193479536	1	FACETS	0.957	0.903	1	0.957	0.903	1	CLONAL	1	TRUE	0	0.571514193479536	1		715	697	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0054749-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	10	525	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		525	41	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054979-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	48	329	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.226473928256955	2		329	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0054979-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	67	428	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.226473928256955	2		428	460	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225768	26225768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054979-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	193	842	1	ENST00000360408.1:c.386G>A	p.Arg129His	p.R129H	ENST00000360408	NM_003532.2	129	cGc/cAc	1/1	0.226473928256955	3	FACETS	0.989	0.915	1	0.989	0.915	1	CLONAL	2	TRUE	1	0.226473928256955	3		843	959	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0055579-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	335	513	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.427545302404711	4	FACETS	1	0.974	1			1	CLONAL	4	TRUE	NA	0.423835151723001	4		513	551	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249002	55249003	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGTGGA	rs397517109	NA	P-0055579-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	617	437	4	ENST00000275493.2:c.2303_2311dup	p.Ser768_Asp770dup	p.S768_D770dup	ENST00000275493	NM_005228.3	768	gcc/gcCAGCGTGGAc	20/28	0.423835151723001	13	FACETS	0.949	0.918	0.98	0.777	0.751	0.802	CLONAL	9	TRUE	2	0.423835151723001	13		441	1135	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938110	76938110	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055579-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	63	213	0	ENST00000373344.5:c.2638G>A	p.Glu880Lys	p.E880K	ENST00000373344	NM_000489.3	880	Gaa/Aaa	9/35	0.423835151723001	3	FACETS	0.856	0.743	0.978			1	CLONAL	1	TRUE	NA	0.423835151723001	3		213	421	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1255441	1255441	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs770144114	NA	P-0055579-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	67	458	0	ENST00000310581.5:c.3118G>T	p.Ala1040Ser	p.A1040S	ENST00000310581	NM_198253.2	1040	Gcc/Tcc	14/16	0.423835151723001	6	FACETS	0.772	0.67	0.883	0.193	0.167	0.221	SUBCLONAL	1	TRUE	2	0.423835151723001	6		458	757	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640191	3640191	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055579-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	73	463	0	ENST00000294008.3:c.3448G>T	p.Glu1150Ter	p.E1150*	ENST00000294008	NM_032444.2	1150	Gag/Tag	12/15	0.423835151723001	5	FACETS	0.81	0.708	0.92	0.202	0.177	0.23	CLONAL	1	TRUE	1	0.423835151723001	5		463	696	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0055640-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	101	190	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.843	0.759	0.93	0.843	0.759	0.93	CLONAL	1	TRUE	1	0.619254694666114	2		190	387	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023723	27023726	+	frameshift_variant	Frame_Shift_Del	DEL	GGCG	GGCG	-	novel	NA	P-0055640-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	170	651	0	ENST00000324856.7:c.830_833del	p.Gly277AlafsTer85	p.G277Afs*85	ENST00000324856	NM_006015.4	277	GGCGgc/gc	1/20	0.120445498734073	4	FACETS	1	0.979	1	1	0.979	1	INDETERMINATE	2	TRUE	2	0.619254694666114	4		651	394	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099327	27099327	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055640-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	160	595	0	ENST00000324856.7:c.3565del	p.Asp1189MetfsTer17	p.D1189Mfs*17	ENST00000324856	NM_006015.4	1188	caG/ca	14/20	0.120445498734073	4	FACETS	1	0.982	1	1	0.982	1	INDETERMINATE	2	TRUE	2	0.619254694666114	4		595	358	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982100	201982102	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0055640-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	234	726	0	ENST00000359651.3:c.627_629del	p.Ser210del	p.S210del	ENST00000359651		208	caCTCc/cac	5/8	0.574703082962594	4	FACETS	0.793	0.742	0.845	0.528	0.494	0.563	SUBCLONAL	2	TRUE	1	0.619254694666114	4		726	772	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0055640-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	197	442	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.619254694666114	2	FACETS	0.991	0.965	1	1	0.995	1	CLONAL	3	TRUE	0	0.619254694666114	2		442	214	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670604	67670605	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGA	novel	NA	P-0055640-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	149	536	0	ENST00000264010.4:c.1850_1853dup	p.Leu619ArgfsTer6	p.L619Rfs*6	ENST00000264010	NM_006565.3	617	cca/cCAGAca	11/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.619254694666114	2		536	395	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831467	72831467	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055640-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	139	742	0	ENST00000268489.5:c.5114C>A	p.Ser1705Ter	p.S1705*	ENST00000268489	NM_006885.3	1705	tCa/tAa	9/10	1	2	FACETS	0.766	0.71	0.822	1	0.99	1	SUBCLONAL	2	TRUE	1	0.619254694666114	2		742	293	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510560	38510560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055640-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	166	492	0	ENST00000254066.5:c.814C>T	p.Arg272Trp	p.R272W	ENST00000254066	NM_000964.3	272	Cgg/Tgg	7/9	0.123334963860577	4	FACETS	1	0.98	1	1	0.98	1	INDETERMINATE	2	TRUE	2	0.619254694666114	4		492	380	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591131	67591135	+	frameshift_variant	Frame_Shift_Del	DEL	AGACG	AGACG	-	novel	NA	P-0055640-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	158	494	0	ENST00000274335.5:c.1727_1731del	p.Thr576ArgfsTer24	p.T576Rfs*24	ENST00000274335		575	aAGACG/a	12/15	0.561197029331492	1	FACETS	0.885	0.846	0.922	1	0.994	1	CLONAL	2	TRUE	0	0.619254694666114	1		494	199	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150022944	150022944	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055640-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	78	480	0	ENST00000253339.5:c.319C>T	p.Gln107Ter	p.Q107*	ENST00000253339		107	Caa/Taa	1/7	0.123334963860577	4	FACETS	0.853	0.761	0.949	0.853	0.761	0.949	INDETERMINATE	2	TRUE	2	0.619254694666114	4		480	239	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878785	151878785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055640-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	161	606	0	ENST00000262189.6:c.6160C>T	p.Gln2054Ter	p.Q2054*	ENST00000262189	NM_170606.2	2054	Cag/Tag	36/59	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.619254694666114	2		606	369	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891600	151891600	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055640-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	122	486	0	ENST00000262189.6:c.4432C>T	p.Gln1478Ter	p.Q1478*	ENST00000262189	NM_170606.2	1478	Cag/Tag	29/59	1	2	FACETS	0.776	0.716	0.836	1	0.989	1	SUBCLONAL	2	TRUE	1	0.619254694666114	2		486	254	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508977	106508978	+	missense_variant	Missense_Mutation	DNP	CA	CA	TG	novel	NA	P-0055640-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	117	708	0	ENST00000359195.3:c.971_972inv	p.Pro324Leu	p.P324L	ENST00000359195	NM_002649.2	324	cCA/cTG	2/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.619254694666114	2		708	271	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0056388-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	251	471	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.725906517802527	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.725906517802527	1		471	426	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8497250	8497250	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs72694737	NA	P-0056388-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	121	0	0	ENST00000356435.5:c.2341A>G	p.Thr781Ala	p.T781A	ENST00000356435		781	Act/Gct	15/35	0.196404320869072	2	FACETS	1	0.984	1	0.654	0.603	0.705	INDETERMINATE	1	TRUE	0	0.725906517802527	2		0	255	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222704	69222704	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056388-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	161	386	0	ENST00000462284.1:c.677C>A	p.Ser226Ter	p.S226*	ENST00000462284	NM_002392.5	226	tCg/tAg	8/11	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.725906517802527	2		386	439	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819770	170819772	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0056388-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	75	163	0	ENST00000296930.5:c.410_412del	p.Ser137del	p.S137del	ENST00000296930	NM_002520.6	137	AGT/-	5/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.725906517802527	2		163	194	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056466-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	267	477	0				ENST00000310581	NM_198253.2	-/1132			0.656165255901973	4	FACETS	1	0.991	1	0.804	0.762	0.846	CLONAL	2	TRUE	1	0.692682473146773	4		477	541	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0056466-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	78	185	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.205715237220893	4	FACETS	0.851	0.76	0.944	0.851	0.76	0.944	INDETERMINATE	2	TRUE	2	0.692682473146773	4		185	224	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0056466-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	309	566	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.692682473146773	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.692682473146773	1		566	472	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179050	123179050	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056466-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	107	271	0	ENST00000218089.9:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000218089	NM_001042749.1	167	Cag/Tag	8/35	0.692682473146773	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.692682473146773	1		271	185	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923342	9923342	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397514557	NA	P-0056466-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	88	353	0	ENST00000330684.3:c.1945C>G	p.Leu649Val	p.L649V	ENST00000330684	NM_001134407.1	649	Ctg/Gtg	9/13	0.205715237220893	4	FACETS	0.878	0.78	0.981	0.439	0.39	0.491	INDETERMINATE	1	TRUE	2	0.692682473146773	4		353	490	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757393	40757393	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs763353429	NA	P-0056466-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	208	423	0	ENST00000373198.4:c.2904+1G>A		p.X968_splice	ENST00000373198	NM_133170.3	968			NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.692682473146773	2		423	541	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920386	134920386	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056466-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	236	456	0	ENST00000398015.3:c.2201A>T	p.Tyr734Phe	p.Y734F	ENST00000398015	NM_004441.4	734	tAc/tTc	12/16	0.205715237220893	4	FACETS	0.929	0.873	0.986	0.929	0.873	0.986	INDETERMINATE	2	TRUE	2	0.692682473146773	4		456	621	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443695	29443695	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs863225281	NA	P-0056482-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	260	337	0	ENST00000389048.3:c.3522C>A	p.Phe1174Leu	p.F1174L	ENST00000389048	NM_004304.4	1174	ttC/ttA	23/29	0.663759328442441	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	2	0.663759328442441	4		337	641	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244820	41244820	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397509004	NA	P-0056482-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	155	370	0	ENST00000357654.3:c.2728C>G	p.Gln910Glu	p.Q910E	ENST00000357654	NM_007294.3	910	Caa/Gaa	10/23	0.663759328442441	4	FACETS	1	0.969	1	0.372	0.341	0.404	CLONAL	1	TRUE	1	0.663759328442441	4		370	696	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29197628	29197628	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056482-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	132	362	0	ENST00000240100.2:c.566del	p.Pro189HisfsTer38	p.P189Hfs*38	ENST00000240100	NM_001394.6	189	cCa/ca	2/4	0.663759328442441	3	FACETS	0.979	0.893	1	0.49	0.446	0.535	CLONAL	1	TRUE	1	0.663759328442441	3		362	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1060501197	NA	P-0056529-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	162	396	0	ENST00000269305.4:c.716del	p.Asn239ThrfsTer8	p.N239Tfs*8	ENST00000269305	NM_001126112.2	239	aAc/ac	7/11	0.461941260236687	3	FACETS	0.999	0.937	1	0.999	0.937	1	CLONAL	3	TRUE	0	0.461941260236687	3		396	288	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223257	41223257	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs80358096	NA	P-0056529-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	106	430	0	ENST00000357654.3:c.4676-2A>G		p.X1559_splice	ENST00000357654	NM_007294.3	1559			0.461941260236687	2	FACETS	0.937	0.856	1	0.937	0.856	1	CLONAL	2	TRUE	0	0.461941260236687	2		430	245	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027687	152027687	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056529-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	73	460	0	ENST00000262189.6:c.388A>T	p.Ser130Cys	p.S130C	ENST00000262189	NM_170606.2	130	Agt/Tgt	3/59	0.461941260236687	5	FACETS	1	0.955	1	0.239	0.209	0.27	CLONAL	1	TRUE	0	0.461941260236687	5		460	448	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859788	117859788	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056529-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	61	441	0	ENST00000297338.2:c.1847C>G	p.Pro616Arg	p.P616R	ENST00000297338	NM_006265.2	616	cCg/cGg	14/14	0.461941260236687	6	FACETS	1	0.896	1	0.261	0.225	0.3	CLONAL	1	TRUE	2	0.461941260236687	6		441	487	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0056583-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	64	536	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.282717638939101	2		536	447	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056583-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	60	648	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.282717638939101	2		648	407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863224683	NA	P-0056583-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	75	635	0	ENST00000269305.4:c.388C>G	p.Leu130Val	p.L130V	ENST00000269305	NM_001126112.2	130	Ctc/Gtc	5/11	0.280341777329301	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.282717638939101	1		635	436	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948079	178948079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056583-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	61	466	1	ENST00000263967.3:c.2851C>T	p.Arg951Cys	p.R951C	ENST00000263967	NM_006218.2	951	Cgt/Tgt	20/21	1	2	FACETS	0.981	0.848	1	0.981	0.848	1	CLONAL	1	TRUE	1	0.282717638939101	2		467	440	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888198	112888198	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121918453	NA	P-0056583-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	60	504	2	ENST00000351677.2:c.214G>C	p.Ala72Pro	p.A72P	ENST00000351677	NM_002834.3	72	Gcc/Ccc	3/16	1	2	FACETS	0.911	0.786	1	0.911	0.786	1	CLONAL	1	TRUE	1	0.282717638939101	2		506	466	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131397	17131397	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1282654875	NA	P-0056583-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	68	687	0	ENST00000285071.4:c.55C>G	p.Leu19Val	p.L19V	ENST00000285071	NM_144997.5	19	Ctc/Gtc	4/14	0.280341777329301	1	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	0	0.282717638939101	1		687	405	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231777	36231801	+	frameshift_variant	Frame_Shift_Del	DEL	GTTCTCGGGGCCCATCCACTGTGAT	GTTCTCGGGGCCCATCCACTGTGAT	-	novel	NA	P-0056583-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	95	764	0	ENST00000300305.3:c.583_607del	p.Ile195LeufsTer8	p.I195Lfs*8	ENST00000300305		195	ATCACAGTGGATGGGCCCCGAGAACct/ct	5/8	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.282717638939101	2		764	616	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068418	26068418	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056640-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	29	164	0	ENST00000435504.4:c.72C>A	p.Tyr24Ter	p.Y24*	ENST00000435504		24	taC/taA	2/13	1	2	FACETS	0.782	0.629	0.954	0.782	0.629	0.954	CLONAL	1	TRUE	1	0.259448462422553	2		164	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0056928-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	102	399	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.645854223946042	1	FACETS	0.839	0.763	0.916	0.839	0.763	0.916	CLONAL	1	TRUE	0	0.645854223946042	1		399	255	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274051	18274082	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCATTCCGCCACGTATCTCCAGGACCAGATTG	TCATTCCGCCACGTATCTCCAGGACCAGATTG	C	novel	NA	P-0056928-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	100	568	0	ENST00000222254.8:c.1291-22_1300delinsC		p.X431_splice	ENST00000222254	NM_005027.3	431		11/16	0.16841110745144	3	FACETS	0.808	0.725	0.896	0.404	0.362	0.448	INDETERMINATE	1	TRUE	1	0.645854223946042	3		568	507	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	170	525	0				ENST00000310581	NM_198253.2	-/1132			0.24728952436398	3	FACETS	0.87	0.803	0.94	1	0.986	1	CLONAL	3	TRUE	1	0.22	3		525	657	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	177	329	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.3	5	FACETS	1	0.942	1	1	0.942	1	CLONAL	4	TRUE	1	0.22	5		329	526	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092966	29092966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	54	388	0	ENST00000328354.6:c.1018G>A	p.Glu340Lys	p.E340K	ENST00000328354	NM_007194.3	340	Gaa/Aaa	10/15	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.22	2		388	448	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149817	202149817	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	68	618	0	ENST00000358485.4:c.1258C>T	p.Gln420Ter	p.Q420*	ENST00000358485	NM_001080125.1	420	Cag/Tag	8/9	1	2	FACETS	0.924	0.804	1	0.924	0.804	1	CLONAL	1	TRUE	1	0.22	2		618	669	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	41	296	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	0.289461611213259	3	FACETS	0.596	0.495	0.709	0.298	0.247	0.355	SUBCLONAL	1	TRUE	1	0.22	3		296	694	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112602	115112602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs865915137	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	144	590	0	ENST00000257566.3:c.1138G>A	p.Glu380Lys	p.E380K	ENST00000257566	NM_016569.3	380	Gag/Aag	7/8	0.289461611213259	3	FACETS	0.964	0.88	1	0.964	0.88	1	CLONAL	2	TRUE	1	0.22	3		590	754	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160488	108160488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730881369	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	21	467	0	ENST00000278616.4:c.4396C>T	p.Arg1466Ter	p.R1466*	ENST00000278616	NM_000051.3	1466	Cga/Tga	29/63	1	2	FACETS	0.471	0.362	0.599	0.471	0.362	0.599	SUBCLONAL	1	TRUE	1	0.22	2		467	405	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023219	27023232	+	frameshift_variant	Frame_Shift_Del	DEL	CCTAGGCCCGCCCT	CCTAGGCCCGCCCT	-	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	72	536	0	ENST00000324856.7:c.325_338del	p.Pro109GlufsTer3	p.P109Efs*3	ENST00000324856	NM_006015.4	109	CCTAGGCCCGCCCTg/g	1/20	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.22	2		536	633	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075655	8075655	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs772410037	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	71	450	0	ENST00000377482.5:c.25C>T	p.Gln9Ter	p.Q9*	ENST00000377482	NM_018948.3	9	Cag/Tag	2/4	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.22	2		450	623	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157149	106157149	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1205320001	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	45	561	0	ENST00000380013.4:c.2050C>T	p.Gln684Ter	p.Q684*	ENST00000380013	NM_001127208.2	684	Caa/Taa	3/11	1	2	FACETS	0.645	0.541	0.761	0.645	0.541	0.761	SUBCLONAL	1	TRUE	1	0.22	2		561	634	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117755	70117755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	178	640	0	ENST00000245479.2:c.223G>A	p.Glu75Lys	p.E75K	ENST00000245479	NM_000346.3	75	Gag/Aag	1/3	0.289461611213259	3	FACETS	0.986	0.909	1	0.986	0.909	1	CLONAL	2	TRUE	1	0.22	3		640	911	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619172	37619172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759485356	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	93	678	0	ENST00000447079.4:c.848C>T	p.Ser283Leu	p.S283L	ENST00000447079	NM_015083.1	283	tCg/tTg	1/14	0.098525454727586	3	FACETS	1	0.895	1	0.505	0.448	0.565	INDETERMINATE	1	TRUE	1	0.22	3		678	930	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242715	16242715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	48	506	0	ENST00000375759.3:c.1336G>A	p.Glu446Lys	p.E446K	ENST00000375759	NM_015001.2	446	Gaa/Aaa	6/15	1	2	FACETS	0.732	0.618	0.858	0.732	0.618	0.858	SUBCLONAL	1	TRUE	1	0.22	2		506	596	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129474	152129474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	71	475	0	ENST00000206249.3:c.427G>A	p.Glu143Lys	p.E143K	ENST00000206249	NM_000125.3	143	Gag/Aag	1/8	0.098525454727586	3	FACETS	1	0.965	1	0.657	0.574	0.747	INDETERMINATE	1	TRUE	1	0.22	3		475	545	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873585	151873585	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	137	590	0	ENST00000262189.6:c.8953C>T	p.Gln2985Ter	p.Q2985*	ENST00000262189	NM_170606.2	2985	Cag/Tag	38/59	0.289461611213259	3	FACETS	0.953	0.869	1	0.953	0.869	1	CLONAL	2	TRUE	1	0.22	3		590	725	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632297	215632297	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	103	442	0	ENST00000260947.4:c.1477C>T	p.Gln493Ter	p.Q493*	ENST00000260947	NM_000465.2	493	Caa/Taa	6/11	1	2	FACETS	0.835	0.749	0.925	1	0.985	1	CLONAL	2	TRUE	1	0.22	2		442	561	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112079	115112079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764962945	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	152	694	0	ENST00000257566.3:c.1661C>T	p.Ser554Leu	p.S554L	ENST00000257566	NM_016569.3	554	tCg/tTg	7/8	0.289461611213259	3	FACETS	0.862	0.788	0.939	0.862	0.788	0.939	CLONAL	2	TRUE	1	0.22	3		694	890	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061468	38061468	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	77	585	0	ENST00000250448.2:c.521C>T	p.Ser174Leu	p.S174L	ENST00000250448	NM_004496.3	174	tCg/tTg	2/2	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.22	2		585	589	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375527	118375527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	76	665	0	ENST00000534358.1:c.8920G>A	p.Glu2974Lys	p.E2974K	ENST00000534358	NM_005933.3	2974	Gaa/Aaa	27/36	1	2	FACETS	0.921	0.807	1	0.921	0.807	1	CLONAL	1	TRUE	1	0.22	2		665	750	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186666	11186679	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAATGGTCCTTACC	CAATGGTCCTTACC	-	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	38	439	0	ENST00000361445.4:c.6526_6526+13del		p.X2176_splice	ENST00000361445	NM_004958.3	2176		46/58	1	2	FACETS	0.605	0.499	0.724	0.605	0.499	0.724	SUBCLONAL	1	TRUE	1	0.22	2		439	571	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22408244	22408244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	46	359	0	ENST00000344548.3:c.135G>A	p.Met45Ile	p.M45I	ENST00000344548	NM_001039802.1	45	atG/atA	4/7	1	2	FACETS	0.895	0.755	1	0.895	0.755	1	CLONAL	1	TRUE	1	0.22	2		359	467	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818286	43818286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	73	629	0	ENST00000372470.3:c.1751C>T	p.Ser584Phe	p.S584F	ENST00000372470	NM_005373.2	584	tCc/tTc	12/12	1	2	FACETS	0.789	0.689	0.898	0.789	0.689	0.898	SUBCLONAL	1	TRUE	1	0.22	2		629	841	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601894	43601894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs77702891	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	38	640	0	ENST00000355710.3:c.938G>A	p.Arg313Gln	p.R313Q	ENST00000355710	NM_020975.4	313	cGg/cAg	5/20	1	2	FACETS	0.489	0.403	0.585	0.489	0.403	0.585	SUBCLONAL	1	TRUE	1	0.22	2		640	707	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143267	108143267	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	42	349	0	ENST00000278616.4:c.3086C>T	p.Thr1029Ile	p.T1029I	ENST00000278616	NM_000051.3	1029	aCa/aTa	21/63	1	2	FACETS	0.997	0.834	1	0.997	0.834	1	CLONAL	1	TRUE	1	0.22	2		349	383	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491597	56491597	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	105	467	0	ENST00000267101.3:c.2489T>C	p.Met830Thr	p.M830T	ENST00000267101	NM_001982.3	830	aTg/aCg	21/28	0.289461611213259	3	FACETS	0.83	0.745	0.92	0.83	0.745	0.92	CLONAL	2	TRUE	1	0.22	3		467	638	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778780	3778780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	60	707	0	ENST00000262367.5:c.6268C>T	p.Leu2090Phe	p.L2090F	ENST00000262367	NM_004380.2	2090	Ctc/Ttc	31/31	1	2	FACETS	0.711	0.611	0.82	0.711	0.611	0.82	SUBCLONAL	1	TRUE	1	0.22	2		707	767	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619250	37619250	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	116	628	0	ENST00000447079.4:c.926G>C	p.Arg309Pro	p.R309P	ENST00000447079	NM_015083.1	309	cGg/cCg	1/14	0.098525454727586	3	FACETS	1	0.975	1	0.632	0.569	0.699	INDETERMINATE	1	TRUE	1	0.22	3		628	926	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210571	5210571	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749866143	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	89	698	0	ENST00000357368.4:c.5396C>T	p.Ser1799Phe	p.S1799F	ENST00000357368	NM_002850.3	1799	tCt/tTt	35/38	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.22	2		698	756	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855835	45855835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	91	708	0	ENST00000391945.4:c.1975C>T	p.His659Tyr	p.H659Y	ENST00000391945	NM_000400.3	659	Cac/Tac	21/23	0.098525454727586	3	FACETS	1	0.937	1	0.542	0.481	0.608	INDETERMINATE	1	TRUE	1	0.22	3		708	847	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966195	25966195	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	65	620	0	ENST00000435504.4:c.3011G>C	p.Arg1004Thr	p.R1004T	ENST00000435504		1004	aGa/aCa	13/13	1	2	FACETS	0.701	0.606	0.804	0.701	0.606	0.804	SUBCLONAL	1	TRUE	1	0.22	2		620	843	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25990489	25990502	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCAAGCCTAGTA	CCCCAAGCCTAGTA	-	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	46	424	0	ENST00000435504.4:c.725_738del	p.Leu242Ter	p.L242*	ENST00000435504		242	tTACTAGGCTTGGGG/t	8/13	1	2	FACETS	0.772	0.649	0.907	0.772	0.649	0.907	CLONAL	1	TRUE	1	0.22	2		424	542	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12393098	12393098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	121	502	0	ENST00000287820.6:c.7G>A	p.Glu3Lys	p.E3K	ENST00000287820	NM_015869.4	3	Gaa/Aaa	1/7	0.3	3	FACETS	0.985	0.892	1	0.985	0.892	1	CLONAL	2	TRUE	1	0.22	3		502	620	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169999040	169999040	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	29	344	0	ENST00000295797.4:c.969G>C	p.Gln323His	p.Q323H	ENST00000295797	NM_002740.5	323	caG/caC	10/18	0.3	3	FACETS	0.778	0.625	0.953	0.389	0.312	0.477	CLONAL	1	TRUE	1	0.22	3		344	376	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196204	106196204	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	30	480	0	ENST00000380013.4:c.4538-1G>A		p.X1513_splice	ENST00000380013	NM_001127208.2	1513			1	2	FACETS	0.479	0.385	0.587	0.479	0.385	0.587	SUBCLONAL	1	TRUE	1	0.22	2		480	569	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196660	106196660	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	41	511	0	ENST00000380013.4:c.4993G>C	p.Asp1665His	p.D1665H	ENST00000380013	NM_001127208.2	1665	Gac/Cac	11/11	1	2	FACETS	0.561	0.466	0.667	0.561	0.466	0.667	SUBCLONAL	1	TRUE	1	0.22	2		511	664	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628873	187628873	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	40	604	0	ENST00000441802.2:c.2109C>G	p.Phe703Leu	p.F703L	ENST00000441802	NM_005245.3	703	ttC/ttG	2/27	1	2	FACETS	0.588	0.488	0.701	0.588	0.488	0.701	SUBCLONAL	1	TRUE	1	0.22	2		604	618	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462457	92462457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	37	497	0	ENST00000265734.4:c.181G>A	p.Glu61Lys	p.E61K	ENST00000265734	NM_001259.6	61	Gag/Aag	2/8	0.289461611213259	3	FACETS	0.569	0.468	0.683	0.285	0.234	0.342	SUBCLONAL	1	TRUE	1	0.22	3		497	656	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965410	68965410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	66	538	0	ENST00000288368.4:c.1022G>A	p.Cys341Tyr	p.C341Y	ENST00000288368	NM_024870.2	341	tGt/tAt	9/40	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.22	2		538	466	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636236	87636236	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	76	602	0	ENST00000277120.3:c.2401C>A	p.Leu801Met	p.L801M	ENST00000277120		801	Ctg/Atg	19/19	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.22	2		602	589	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918634	44918709	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AAATGCTACTTAAATGCAACTAGAAGCAAAAGTTGTAGTAATACCTCTGCACTTGCAGCACGAATTAAGTATTTAC	AAATGCTACTTAAATGCAACTAGAAGCAAAAGTTGTAGTAATACCTCTGCACTTGCAGCACGAATTAAGTATTTAC	-	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	46	249	0	ENST00000377967.4:c.1118_1193del	p.Lys373ArgfsTer41	p.K373Rfs*41	ENST00000377967	NM_021140.2	373	AAATGCTACTTAAATGCAACTAGAAGCAAAAGTTGTAGTAATACCTCTGCACTTGCAGCACGAATTAAGTATTTACag/ag	12/29	0.0968270578128609	2	FACETS	1	0.957	1			1	INDETERMINATE	1	TRUE	NA	0.22	2		249	295	SUCCESS
AR	367	MSKCC	GRCh37	X	66863127	66863127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	71	233	0	ENST00000374690.3:c.1646C>T	p.Pro549Leu	p.P549L	ENST00000374690	NM_000044.3	549	cCc/cTc	2/8	0.0968270578128609	2	FACETS	0.944	0.829	1			1	INDETERMINATE	2	TRUE	NA	0.22	2		233	342	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200084	123200149	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAATCGAAAATGGAGACATGCCTGAGCAGGTTTTTATTTATTTGCTAGTTACACATTTATCTTTGA	GAATCGAAAATGGAGACATGCCTGAGCAGGTTTTTATTTATTTGCTAGTTACACATTTATCTTTGA	-	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	18	184	0	ENST00000218089.9:c.2156_2184+37del		p.X719_splice	ENST00000218089	NM_001042749.1	719		22/35	0.0968270578128609	2	FACETS	1	0.819	1			1	INDETERMINATE	1	TRUE	NA	0.22	2		184	149	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31239000	31239000	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	36	362	0	ENST00000376228.5:c.469T>C	p.Trp157Arg	p.W157R	ENST00000376228	NM_002117.5	157	Tgg/Cgg	3/8	1	2	FACETS	0.974	0.803	1	0.974	0.803	1	CLONAL	1	TRUE	1	0.22	2		362	336	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424405	47424405	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	56	556	0	ENST00000404338.3:c.2473C>A	p.Pro825Thr	p.P825T	ENST00000404338	NM_004491.4	825	Cca/Aca	1/6	0.098525454727586	3	FACETS	0.75	0.642	0.87	0.375	0.321	0.435	INDETERMINATE	1	TRUE	1	0.22	3		556	753	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424985	47424985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759575115	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	64	590	0	ENST00000404338.3:c.3053G>A	p.Gly1018Glu	p.G1018E	ENST00000404338	NM_004491.4	1018	gGa/gAa	1/6	0.098525454727586	3	FACETS	0.907	0.785	1	0.454	0.392	0.52	INDETERMINATE	1	TRUE	1	0.22	3		590	712	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959137	2959137	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	53	591	0	ENST00000396946.4:c.2379G>C	p.Met793Ile	p.M793I	ENST00000396946	NM_032415.4	793	atG/atC	18/25	1	2	FACETS	0.711	0.605	0.827	0.711	0.605	0.827	SUBCLONAL	1	TRUE	1	0.22	2		591	678	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978321	2978321	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056993-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	27	573	0	ENST00000396946.4:c.1009C>G	p.Arg337Gly	p.R337G	ENST00000396946	NM_032415.4	337	Cga/Gga	7/25	1	2	FACETS	0.366	0.29	0.454	0.366	0.29	0.454	SUBCLONAL	1	TRUE	1	0.22	2		573	670	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0057059-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	23	688	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		688	322	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350618	89350618	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1433758363	NA	P-0057059-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	11	312	0	ENST00000301030.4:c.2332A>G	p.Lys778Glu	p.K778E	ENST00000301030	NM_001256183.1	778	Aag/Gag	9/13	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		312	185	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784112	9784112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057096-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	8	415	0	ENST00000377346.4:c.2680C>T	p.Arg894Trp	p.R894W	ENST00000377346	NM_005026.3	894	Cgg/Tgg	21/24	0.652786736733626	3	FACETS	0.096	0.061	0.141			1	SUBCLONAL	1	TRUE	NA	0.639032615267484	3		415	345	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573241	64573241	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057096-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	201	366	0	ENST00000312049.6:c.1051T>C	p.Tyr351His	p.Y351H	ENST00000312049	NM_130799.2	351	Tac/Cac	8/10	0.592889131534298	2	FACETS	0.936	0.886	0.985	0.936	0.886	0.985	CLONAL	2	TRUE	0	0.639032615267484	2		366	336	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0057364-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	12	344	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.287327732563792	5	FACETS	1	0.825	1	0.764	0.57	0.969	INDETERMINATE	2	FALSE	2	0.732597475676024	5		344	30	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222006	1222006	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0057364-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	89	495	0	ENST00000326873.7:c.920+1G>T		p.X307_splice	ENST00000326873	NM_000455.4	307			0.30840688576108	6	FACETS	0.96	0.88	1	0.64	0.587	0.692	INDETERMINATE	4	FALSE	0	0.732597475676024	6		495	156	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180273	38180273	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs779805093	NA	P-0057364-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	37	807	1	ENST00000396334.3:c.121C>T	p.Arg41Ter	p.R41*	ENST00000396334	NM_002468.4	41	Cga/Tga	1/5	0.293246695711216	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.732597475676024	0		808	162	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944843	31944843	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057364-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	21	627	0	ENST00000340398.3:c.258C>A	p.Ser86Arg	p.S86R	ENST00000340398	NM_001013699.2	86	agC/agA	1/1	0.287327732563792	5	FACETS	1	0.825	1	0.355	0.277	0.442	INDETERMINATE	1	FALSE	2	0.732597475676024	5		627	113	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106861	27106861	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	193	533	0	ENST00000324856.7:c.6472C>T	p.Arg2158Ter	p.R2158*	ENST00000324856	NM_006015.4	2158	Cga/Tga	20/20	0.457243149931953	1	FACETS	0.978	0.908	1	0.978	0.908	1	CLONAL	1	TRUE	0	0.457243149931953	1		533	666	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575427	64575427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	197	569	0	ENST00000312049.6:c.590C>T	p.Thr197Ile	p.T197I	ENST00000312049	NM_130799.2	197	aCc/aTc	3/10	0.457243149931953	1	FACETS	0.963	0.896	1	0.963	0.896	1	CLONAL	1	TRUE	0	0.457243149931953	1		569	690	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544720	86544720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758598952	NA	P-0057492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	128	431	0	ENST00000262426.4:c.545C>T	p.Pro182Leu	p.P182L	ENST00000262426	NM_001451.2	182	cCg/cTg	1/2	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.457243149931953	2		431	527	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21349261	21349261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750813513	NA	P-0057492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	132	521	1	ENST00000215739.8:c.1888C>T	p.Arg630Trp	p.R630W	ENST00000215739	NM_006767.3	630	Cgg/Tgg	16/21	0.457243149931953	1	FACETS	0.776	0.707	0.848	0.776	0.707	0.848	SUBCLONAL	1	TRUE	0	0.457243149931953	1		522	574	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0057563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	198	333	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	0.412119203083545	5	FACETS	1	0.955	1	0.69	0.641	0.74	CLONAL	2	FALSE	2	0.481879542056435	5		333	684	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	206	434	1	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	0.481879542056435	4	FACETS	0.877	0.817	0.94	0.877	0.817	0.94	CLONAL	2	FALSE	2	0.481879542056435	4		435	722	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647027	23647028	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	407	395	0	ENST00000261584.4:c.839dup	p.Asn280LysfsTer3	p.N280Kfs*3	ENST00000261584	NM_024675.3	280	aac/aaAc	4/13	0.481879542056435	4	FACETS	0.958	0.923	0.993	0.958	0.923	0.993	CLONAL	4	FALSE	0	0.481879542056435	4		395	653	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740459	58740459	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	94	386	0	ENST00000305921.3:c.1364A>C	p.Glu455Ala	p.E455A	ENST00000305921	NM_003620.3	455	gAg/gCg	6/6	0.193226778635717	6	FACETS	1	0.97	1	0.418	0.372	0.467	INDETERMINATE	1	FALSE	3	0.481879542056435	6		386	611	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147183	61147183	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	66	295	0	ENST00000295025.8:c.861del	p.Tyr287Ter	p.Y287*	ENST00000295025	NM_002908.2	287	taC/ta	8/11	0.193226778635717	6	FACETS	0.983	0.855	1	0.328	0.285	0.375	INDETERMINATE	1	FALSE	3	0.481879542056435	6		295	547	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505503	157505503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	232	387	1	ENST00000346085.5:c.3484C>T	p.Pro1162Ser	p.P1162S	ENST00000346085	NM_020732.3	1162	Ccc/Tcc	13/20	0.481879542056435	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	FALSE	1	0.481879542056435	3		388	526	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505509	157505524	+	frameshift_variant	Frame_Shift_Del	DEL	CCGGAAGTCTTCAGCA	CCGGAAGTCTTCAGCA	-	novel	NA	P-0057563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	202	395	0	ENST00000346085.5:c.3494_3509del	p.Glu1165GlyfsTer41	p.E1165Gfs*41	ENST00000346085	NM_020732.3	1164	CCGGAAGTCTTCAGCAcc/cc	13/20	0.481879542056435	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	FALSE	1	0.481879542056435	3		395	510	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545692	106545692	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	91	334	0	ENST00000359195.3:c.3169G>C	p.Val1057Leu	p.V1057L	ENST00000359195	NM_002649.2	1057	Gtg/Ctg	11/11	0.481879542056435	2	FACETS	0.981	0.877	1	0.491	0.438	0.545	CLONAL	1	FALSE	0	0.481879542056435	2		334	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0057852-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	226	650	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.684448174978107	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.684448174978107	3		650	274	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992580	72992580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201757720	NA	P-0057852-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	57	585	0	ENST00000268489.5:c.1465G>A	p.Glu489Lys	p.E489K	ENST00000268489	NM_006885.3	489	Gag/Aag	2/10	0.183296375761586	3	FACETS	1	0.965	1	0.441	0.386	0.498	INDETERMINATE	1	TRUE	0	0.684448174978107	3		585	169	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051093	13051093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451773406	NA	P-0057852-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	54	540	1	ENST00000316448.5:c.529C>T	p.Arg177Trp	p.R177W	ENST00000316448	NM_004343.3	177	Cgg/Tgg	5/9	0.58583087554454	3	FACETS	0.917	0.792	1	0.458	0.396	0.525	CLONAL	1	TRUE	1	0.684448174978107	3		541	231	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420163	49420180	+	inframe_deletion	In_Frame_Del	DEL	TCTGGTGAGGCAGCAGCT	TCTGGTGAGGCAGCAGCT	-	novel	NA	P-0057852-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	104	603	0	ENST00000301067.7:c.15569_15586del	p.Gln5190_Met5196delinsLeu	p.Q5190_M5196delinsL	ENST00000301067	NM_003482.3	5190	cAGCTGCTGCCTCACCAGAtg/ctg	48/54	0.661736626786617	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.684448174978107	2		603	141	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215917	41215917	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204269	NA	P-0057852-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	27	289	0	ENST00000357654.3:c.5126G>A	p.Gly1709Glu	p.G1709E	ENST00000357654	NM_007294.3	1709	gGa/gAa	17/23	0.684448174978107	2	FACETS	1	0.948	1	0.717	0.602	0.833	CLONAL	1	TRUE	0	0.684448174978107	2		289	55	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289683	15289683	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057852-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	55	647	0	ENST00000263388.2:c.3788C>G	p.Pro1263Arg	p.P1263R	ENST00000263388	NM_000435.2	1263	cCt/cGt	23/33	0.58583087554454	3	FACETS	0.817	0.705	0.937	0.409	0.352	0.469	CLONAL	1	TRUE	1	0.684448174978107	3		647	264	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723096	52723096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057852-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	19	494	0	ENST00000322088.6:c.1281G>A	p.Met427Ile	p.M427I	ENST00000322088	NM_014225.5	427	atG/atA	10/15	0.58583087554454	3	FACETS	0.373	0.284	0.476	0.186	0.142	0.238	SUBCLONAL	1	TRUE	1	0.684448174978107	3		494	200	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	907270	907270	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057852-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	45	340	0	ENST00000166345.3:c.634A>C	p.Ile212Leu	p.I212L	ENST00000166345	NM_004237.3	212	Ata/Cta	7/13	0.325653171782909	3	FACETS	1	0.933	1	0.726	0.64	0.811	INDETERMINATE	2	TRUE	0	0.684448174978107	3		340	81	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0057862-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	122	613	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.217352066146282	2	FACETS	0.818	0.742	0.896	0.818	0.742	0.896	CLONAL	2	TRUE	0	0.285331661474715	2		614	523	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429957	78429957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057862-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	115	387	0	ENST00000370768.2:c.922C>T	p.Arg308Cys	p.R308C	ENST00000370768	NM_003902.3	308	Cgc/Tgc	11/20	0.285331661474715	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.285331661474715	1		387	519	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175991	176175991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057862-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	39	435	0	ENST00000367669.3:c.124G>A	p.Val42Ile	p.V42I	ENST00000367669	NM_022457.5	42	Gtt/Att	1/20	0.285331661474715	1	FACETS	0.664	0.552	0.789	0.664	0.552	0.789	SUBCLONAL	1	TRUE	0	0.285331661474715	1		435	353	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343718	118343718	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057862-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	45	419	0	ENST00000534358.1:c.1844C>T	p.Pro615Leu	p.P615L	ENST00000534358	NM_005933.3	615	cCg/cTg	3/36	0.217352066146282	2	FACETS	0.706	0.593	0.829	0.353	0.296	0.415	SUBCLONAL	1	TRUE	0	0.285331661474715	2		419	447	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926888	112926888	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507546	NA	P-0057862-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	10	371	0	ENST00000351677.2:c.1508G>T	p.Gly503Val	p.G503V	ENST00000351677	NM_002834.3	503	gGg/gTg	13/16	0.285331661474715	1	FACETS	0.169	0.114	0.239	0.169	0.114	0.239	SUBCLONAL	1	TRUE	0	0.285331661474715	1		371	355	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549404	21549404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753026198	NA	P-0057862-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	97	541	0	ENST00000382592.4:c.2872C>T	p.Arg958Cys	p.R958C	ENST00000382592	NM_014572.2	958	Cgc/Tgc	8/8	0.285331661474715	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.285331661474715	1		541	432	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108822	2108822	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1213252028	NA	P-0057862-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	117	483	1	ENST00000219476.3:c.923G>A	p.Arg308Gln	p.R308Q	ENST00000219476	NM_000548.3	308	cGg/cAg	10/42	0.217352066146282	2	FACETS	0.934	0.848	1	0.934	0.848	1	CLONAL	2	TRUE	0	0.285331661474715	2		484	439	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991713	25991713	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs190136878	NA	P-0057862-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	50	341	0	ENST00000435504.4:c.529A>C	p.Lys177Gln	p.K177Q	ENST00000435504		177	Aag/Cag	7/13	0.285331661474715	1	FACETS	0.631	0.536	0.736	0.631	0.536	0.736	SUBCLONAL	1	TRUE	0	0.285331661474715	1		341	476	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027686	48027686	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs760558287	NA	P-0057862-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	85	339	0	ENST00000234420.5:c.2565del	p.Ile856LeufsTer12	p.I856Lfs*12	ENST00000234420	NM_000179.2	855	aTt/at	4/10	0.23065982668203	2	FACETS	1	0.977	1	0.72	0.639	0.804	CLONAL	1	TRUE	0	0.285331661474715	2		339	414	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164757	36164757	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057862-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	128	637	0	ENST00000300305.3:c.1118C>T	p.Ser373Leu	p.S373L	ENST00000300305		373	tCg/tTg	8/8	0.285331661474715	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.285331661474715	1		637	559	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277487	142277487	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057862-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	70	239	0	ENST00000350721.4:c.1864T>C	p.Cys622Arg	p.C622R	ENST00000350721	NM_001184.3	622	Tgt/Cgt	8/47	0.285331661474715	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.285331661474715	1		239	341	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124503636	124503636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554426994	NA	P-0057862-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	39	328	0	ENST00000357628.3:c.314C>T	p.Thr105Met	p.T105M	ENST00000357628	NM_015450.2	105	aCg/aTg	8/19	0.285331661474715	1	FACETS	0.524	0.434	0.624	0.524	0.434	0.624	SUBCLONAL	1	TRUE	0	0.285331661474715	1		328	447	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641218	23641218	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs180177110	NA	P-0121437-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	192	501	0	ENST00000261584.4:c.2257C>T	p.Arg753Ter	p.R753*	ENST00000261584	NM_024675.3	753	Cga/Tga	5/13	1	2	FACETS	0.896	0.832	0.961	0.896	0.832	0.961	CLONAL	1	NA	1	0.667798652684751	2		501	642	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380271	25380271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0121437-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	301	344	2	ENST00000311936.3:c.187G>A	p.Glu63Lys	p.E63K	ENST00000311936	NM_004985.3	63	Gag/Aag	3/5	0.667798652684751	4	FACETS	0.975	0.923	1	0.65	0.615	0.685	CLONAL	2	NA	1	0.667798652684751	4		346	771	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0058046-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	102	185	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.669836064053039	3	FACETS	1	0.944	1	0.534	0.481	0.588	CLONAL	1	TRUE	1	0.669836064053039	3		185	381	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466022	69466022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058046-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	504	685	0	ENST00000227507.2:c.860C>T	p.Pro287Leu	p.P287L	ENST00000227507	NM_053056.2	287	cCc/cTc	5/5	0.669836064053039	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.669836064053039	3		685	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0058046-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	194	403	0	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.669836064053039	2		403	458	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098966	178098966	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058046-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	252	369	0	ENST00000397062.3:c.79G>T	p.Asp27Tyr	p.D27Y	ENST00000397062	NM_006164.4	27	Gat/Tat	2/5	0.128525303911909	4	FACETS	0.886	0.833	0.94	0.886	0.833	0.94	INDETERMINATE	2	TRUE	2	0.669836064053039	4		369	709	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856356	45856356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058046-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	12	623	0	ENST00000391945.4:c.1816G>A	p.Glu606Lys	p.E606K	ENST00000391945	NM_000400.3	606	Gag/Aag	19/23	1	2	FACETS	0.075	0.052	0.103	0.075	0.052	0.103	SUBCLONAL	1	TRUE	1	0.669836064053039	2		623	480	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106031	27106032	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058046-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	257	616	0	ENST00000324856.7:c.5643dup	p.Val1882CysfsTer19	p.V1882Cfs*19	ENST00000324856	NM_006015.4	1881	cat/caTt	20/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.669836064053039	2		616	708	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425796	49425814	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTGCCGCTGCATGAGGA	AGCTGCCGCTGCATGAGGA	-	novel	NA	P-0058046-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	191	631	0	ENST00000301067.7:c.12674_12692del	p.Leu4225ArgfsTer47	p.L4225Rfs*47	ENST00000301067	NM_003482.3	4225	cTCCTCATGCAGCGGCAGCTg/cg	39/54	0.168366902580134	4	FACETS	0.917	0.855	0.981	0.917	0.855	0.981	INDETERMINATE	2	TRUE	2	0.669836064053039	4		631	519	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576848	7576877	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTACCTGAAGGGTGAAATATTCTCCATCC	AGTACCTGAAGGGTGAAATATTCTCCATCC	-	novel	NA	P-0058046-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	183	548	0	ENST00000269305.4:c.969_993+5del		p.X323_splice	ENST00000269305	NM_001126112.2	323		9/11	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.669836064053039	2		548	544	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1696842	1696842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs945313437	NA	P-0058046-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	13	299	0	ENST00000378625.1:c.4G>A	p.Glu2Lys	p.E2K	ENST00000378625	NM_001198994.1	2	Gaa/Aaa	2/14	0.669836064053039	1	FACETS	0.125	0.089	0.169	0.125	0.089	0.169	SUBCLONAL	1	TRUE	0	0.669836064053039	1		299	206	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339912	70339912	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058046-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	51	479	0	ENST00000374080.3:c.445T>A	p.Tyr149Asn	p.Y149N	ENST00000374080		149	Tac/Aac	4/45	0.669836064053039	1	FACETS	0.307	0.262	0.356	0.307	0.262	0.356	SUBCLONAL	1	TRUE	0	0.669836064053039	1		479	330	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948818	17948818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058291-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	105	654	0	ENST00000458235.1:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000458235	NM_000215.3	542	Gag/Aag	12/24	1	2	FACETS	0.693	0.62	0.771	0.693	0.62	0.771	SUBCLONAL	1	TRUE	1	0.346237037748791	2		654	875	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891277	101891277	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058291-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	95	444	0	ENST00000374994.4:c.238C>T	p.Arg80Ter	p.R80*	ENST00000374994	NM_004612.2	80	Cga/Tga	2/9	0.346237037748791	1	FACETS	0.895	0.8	0.996	0.895	0.8	0.996	CLONAL	1	TRUE	0	0.346237037748791	1		444	507	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259730	16259730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764509266	NA	P-0058291-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	129	740	0	ENST00000375759.3:c.6995G>A	p.Arg2332His	p.R2332H	ENST00000375759	NM_015001.2	2332	cGc/cAc	11/15	0.346237037748791	1	FACETS	0.864	0.785	0.948	0.864	0.785	0.948	CLONAL	1	TRUE	0	0.346237037748791	1		740	713	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726698	88726698	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375475747	NA	P-0058291-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	98	468	0	ENST00000360948.2:c.346C>T	p.Arg116Trp	p.R116W	ENST00000360948	NM_001012338.2	116	Cgg/Tgg	4/19	1	2	FACETS	0.882	0.788	0.982	0.882	0.788	0.982	CLONAL	1	TRUE	1	0.346237037748791	2		468	642	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986832	36986832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058291-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	74	644	0	ENST00000354822.5:c.857G>A	p.Arg286Gln	p.R286Q	ENST00000354822	NM_001079668.2	286	cGa/cAa	3/3	0.346237037748791	1	FACETS	0.633	0.555	0.718	0.633	0.555	0.718	SUBCLONAL	1	TRUE	0	0.346237037748791	1		644	558	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679291	29679291	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555536340	NA	P-0058291-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	95	435	0	ENST00000356175.3:c.7411C>T	p.Gln2471Ter	p.Q2471*	ENST00000356175	NM_000267.3	2471	Cag/Tag	50/57	0.346237037748791	1	FACETS	0.831	0.742	0.925	0.831	0.742	0.925	CLONAL	1	TRUE	0	0.346237037748791	1		435	546	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541681	120541685	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTT	AGCTT	-	novel	NA	P-0058291-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	124	760	0	ENST00000229340.5:c.172_176del	p.Lys58AlafsTer52	p.K58Afs*52	ENST00000229340	NM_006861.6	58	AAGCTg/g	3/6	1	2	FACETS	0.928	0.84	1	0.928	0.84	1	CLONAL	1	TRUE	1	0.346237037748791	2		760	772	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770827	59770827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876659013	NA	P-0058291-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	45	407	0	ENST00000259008.2:c.2539G>A	p.Asp847Asn	p.D847N	ENST00000259008	NM_032043.2	847	Gat/Aat	18/20	1	2	FACETS	0.718	0.605	0.842	0.718	0.605	0.842	SUBCLONAL	1	TRUE	1	0.346237037748791	2		407	362	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379701	17379701	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs775407791	NA	P-0058291-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	99	669	0	ENST00000359435.4:c.86C>G	p.Ser29Cys	p.S29C	ENST00000359435	NM_001033549.1	29	tCc/tGc	2/9	1	2	FACETS	0.725	0.647	0.808	0.725	0.647	0.808	SUBCLONAL	1	TRUE	1	0.346237037748791	2		669	789	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715381	61715381	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058291-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	49	328	0	ENST00000401558.2:c.2232G>T	p.Leu744Phe	p.L744F	ENST00000401558	NM_003400.3	744	ttG/ttT	19/25	1	2	FACETS	0.709	0.602	0.827	0.709	0.602	0.827	SUBCLONAL	1	TRUE	1	0.346237037748791	2		328	399	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098998	178099045	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCTATGTTTAAGACAAAAAAAGGAAGGAGAGAGCTCATGTTTTTTAA	TCCTATGTTTAAGACAAAAAAAGGAAGGAGAGAGCTCATGTTTTTTAA	-	novel	NA	P-0058291-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	54	393	0	ENST00000397062.3:c.46-46_47del		p.X16_splice	ENST00000397062	NM_006164.4	16		2/5	1	2	FACETS	0.572	0.489	0.664	0.572	0.489	0.664	SUBCLONAL	1	TRUE	1	0.346237037748791	2		393	545	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987055	69987055	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058291-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	179	605	0	ENST00000394351.3:c.116C>G	p.Thr39Ser	p.T39S	ENST00000394351	NM_000248.3	39	aCt/aGt	2/9	1	2	FACETS	0.751	0.695	0.81	1	0.99	1	SUBCLONAL	2	TRUE	1	0.346237037748791	2		605	688	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102901	71102901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749611196	NA	P-0058291-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	166	533	0	ENST00000318789.4:c.306G>A	p.Met102Ile	p.M102I	ENST00000318789	NM_032682.5	102	atG/atA	8/21	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.346237037748791	2		533	698	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509410	149509410	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058291-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	92	701	0	ENST00000261799.4:c.1489C>G	p.Leu497Val	p.L497V	ENST00000261799	NM_002609.3	497	Ctg/Gtg	10/23	0.346237037748791	1	FACETS	0.701	0.623	0.783	0.701	0.623	0.783	SUBCLONAL	1	TRUE	0	0.346237037748791	1		701	627	SUCCESS
MET	4233	MSKCC	GRCh37	7	116419003	116419003	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058291-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	73	421	0	ENST00000397752.3:c.3514G>T	p.Glu1172Ter	p.E1172*	ENST00000397752	NM_000245.2	1172	Gag/Tag	17/21	1	2	FACETS	0.852	0.747	0.965	0.852	0.747	0.965	CLONAL	1	TRUE	1	0.346237037748791	2		421	495	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90990452	90990452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554566610	NA	P-0058291-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	41	232	0	ENST00000265433.3:c.580G>A	p.Glu194Lys	p.E194K	ENST00000265433	NM_002485.4	194	Gaa/Aaa	5/16	0.319762523591331	3	FACETS	0.66	0.55	0.782	0.33	0.275	0.391	SUBCLONAL	1	TRUE	1	0.346237037748791	3		232	421	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604664	48604673	+	protein_altering_variant	In_Frame_Del	DEL	CGTCGCTTAT	CGTCGCTTAT	A	novel	NA	P-0058291-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	120	582	0	ENST00000342988.3:c.1486_1495delinsA	p.Arg496_Cys499delinsSer	p.R496_C499delinsS	ENST00000342988	NM_005359.5	496	CGTCGCTTATgc/Agc	12/12	0.346237037748791	1	FACETS	0.862	0.78	0.948	0.862	0.78	0.948	CLONAL	1	TRUE	0	0.346237037748791	1		582	665	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058309-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	17	477	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.552	0.412	0.718	0.552	0.412	0.718	SUBCLONAL	1	TRUE	1	0.238598330979591	2		477	258	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0058309-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	58	697	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.238598330979591	1	FACETS	0.923	0.794	1	0.923	0.794	1	CLONAL	1	TRUE	0	0.238598330979591	1		697	464	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514089	69514089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058309-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	52	702	0	ENST00000294312.3:c.592G>A	p.Asp198Asn	p.D198N	ENST00000294312	NM_005117.2	198	Gac/Aac	3/3	1	2	FACETS	0.96	0.819	1	0.96	0.819	1	CLONAL	1	TRUE	1	0.238598330979591	2		702	454	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410901	63410901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058309-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	60	666	0	ENST00000330258.3:c.2266G>A	p.Glu756Lys	p.E756K	ENST00000330258	NM_152424.3	756	Gaa/Aaa	2/2	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.238598330979591	2		666	483	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412376	139412376	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058309-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	125	679	0	ENST00000277541.6:c.1269C>G	p.Cys423Trp	p.C423W	ENST00000277541	NM_017617.3	423	tgC/tgG	8/34	0.235113292390449	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	0	0.238598330979591	2		679	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578264	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058309-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	45	757	0	ENST00000269305.4:c.585_586delinsTT	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	195	atCCga/atTTga	6/11	1	2	FACETS	0.633	0.531	0.746	0.633	0.531	0.746	SUBCLONAL	1	TRUE	1	0.238598330979591	2		757	596	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961751	55961751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058309-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	17	438	0	ENST00000263923.4:c.2810C>T	p.Pro937Leu	p.P937L	ENST00000263923	NM_002253.2	937	cCc/cTc	20/30	1	2	FACETS	0.491	0.366	0.64	0.491	0.366	0.64	SUBCLONAL	1	TRUE	1	0.238598330979591	2		438	290	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412859	63412859	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058309-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	57	714	0	ENST00000330258.3:c.308C>T	p.Ala103Val	p.A103V	ENST00000330258	NM_152424.3	103	gCc/gTc	2/2	1	2	FACETS	0.878	0.754	1	0.878	0.754	1	CLONAL	1	TRUE	1	0.238598330979591	2		714	544	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132935	64132935	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058309-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	40	656	0	ENST00000334205.4:c.1069C>T	p.Gln357Ter	p.Q357*	ENST00000334205	NM_003942.2	357	Cag/Tag	9/17	1	2	FACETS	0.755	0.628	0.897	0.755	0.628	0.897	SUBCLONAL	1	TRUE	1	0.238598330979591	2		656	444	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459202	120459203	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0058309-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	48	706	0	ENST00000256646.2:c.6141_6142dup	p.Asp2048GlyfsTer21	p.D2048Gfs*21	ENST00000256646	NM_024408.3	2048	gat/gGGat	34/34	1	2	FACETS	0.777	0.657	0.909	0.777	0.657	0.909	CLONAL	1	TRUE	1	0.238598330979591	2		706	518	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435158	49435158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770113503	NA	P-0058309-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	48	552	0	ENST00000301067.7:c.6395C>T	p.Pro2132Leu	p.P2132L	ENST00000301067	NM_003482.3	2132	cCc/cTc	31/54	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.238598330979591	2		552	388	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858489	57858489	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058309-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	45	619	0	ENST00000228682.2:c.227A>G	p.Lys76Arg	p.K76R	ENST00000228682	NM_005269.2	76	aAg/aGg	4/12	1	2	FACETS	0.76	0.639	0.895	0.76	0.639	0.895	SUBCLONAL	1	TRUE	1	0.238598330979591	2		619	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0058309-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	61	534	0	ENST00000269305.4:c.673-2del		p.X225_splice	ENST00000269305	NM_001126112.2	225			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.238598330979591	2		534	400	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556852	29556852	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0058309-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	31	255	0	ENST00000356175.3:c.2851-1G>A		p.X951_splice	ENST00000356175	NM_000267.3	951			1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.238598330979591	2		255	240	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215556	5215557	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058309-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	61	754	1	ENST00000357368.4:c.4146_4147delinsAA	p.Glu1383Lys	p.E1383K	ENST00000357368	NM_002850.3	1382	acGGag/acAAag	27/38	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.238598330979591	2		755	483	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097212	11097212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219033025	NA	P-0058309-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	49	693	0	ENST00000358026.2:c.703G>A	p.Gly235Ser	p.G235S	ENST00000358026	NM_001128849.1	235	Ggc/Agc	4/36	1	2	FACETS	0.859	0.728	1	0.859	0.728	1	CLONAL	1	TRUE	1	0.238598330979591	2		693	478	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251791	212251791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058309-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	56	684	0	ENST00000342788.4:c.3268G>A	p.Glu1090Lys	p.E1090K	ENST00000342788	NM_005235.2	1090	Gaa/Aaa	27/28	1	2	FACETS	0.853	0.731	0.987	0.853	0.731	0.987	CLONAL	1	TRUE	1	0.238598330979591	2		684	550	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566429	41566429	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058309-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	49	483	0	ENST00000263253.7:c.4306T>A	p.Trp1436Arg	p.W1436R	ENST00000263253	NM_001429.3	1436	Tgg/Agg	27/31	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.238598330979591	2		483	329	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628139	187628139	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs755629130	NA	P-0058309-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	39	722	0	ENST00000441802.2:c.2843G>A	p.Trp948Ter	p.W948*	ENST00000441802	NM_005245.3	948	tGg/tAg	2/27	1	2	FACETS	0.699	0.579	0.832	0.699	0.579	0.832	SUBCLONAL	1	TRUE	1	0.238598330979591	2		722	468	SUCCESS
APC	324	MSKCC	GRCh37	5	112176882	112176882	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1359257049	NA	P-0058309-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	42	574	0	ENST00000257430.4:c.5591C>T	p.Ser1864Phe	p.S1864F	ENST00000257430	NM_000038.5	1864	tCt/tTt	16/16	1	2	FACETS	0.762	0.636	0.901	0.762	0.636	0.901	CLONAL	1	TRUE	1	0.238598330979591	2		574	462	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902199	151902199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058309-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	26	291	0	ENST00000262189.6:c.3953G>A	p.Arg1318Lys	p.R1318K	ENST00000262189	NM_170606.2	1318	aGa/aAa	25/59	1	2	FACETS	0.778	0.618	0.961	0.778	0.618	0.961	CLONAL	1	TRUE	1	0.238598330979591	2		291	280	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009299	69009299	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1017780787	NA	P-0058309-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	43	458	0	ENST00000288368.4:c.2416G>A	p.Glu806Lys	p.E806K	ENST00000288368	NM_024870.2	806	Gag/Aag	22/40	1	2	FACETS	0.84	0.704	0.991	0.84	0.704	0.991	CLONAL	1	TRUE	1	0.238598330979591	2		458	429	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650377	48650377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058309-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	44	752	0	ENST00000376670.3:c.347C>T	p.Ser116Phe	p.S116F	ENST00000376670	NM_002049.3	116	tCt/tTt	3/6	1	2	FACETS	0.709	0.595	0.836	0.709	0.595	0.836	SUBCLONAL	1	TRUE	1	0.238598330979591	2		752	520	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340913	70340913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058309-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	40	676	0	ENST00000374080.3:c.646G>A	p.Gly216Ser	p.G216S	ENST00000374080		216	Ggt/Agt	5/45	1	2	FACETS	0.75	0.623	0.891	0.75	0.623	0.891	SUBCLONAL	1	TRUE	1	0.238598330979591	2		676	447	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939105	76939106	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058309-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	39	600	1	ENST00000373344.5:c.1642_1643delinsAA	p.Gly548Asn	p.G548N	ENST00000373344	NM_000489.3	548	GGc/AAc	9/35	1	2	FACETS	0.662	0.548	0.789	0.662	0.548	0.789	SUBCLONAL	1	TRUE	1	0.238598330979591	2		601	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577560	7577560	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	260	273	0	ENST00000269305.4:c.721del	p.Ser241ProfsTer6	p.S241Pfs*6	ENST00000269305	NM_001126112.2	241	Tcc/cc	7/11	0.70255382132321	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.70255382132321	2		273	364	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743865	40743865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758531464	NA	P-0058396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	462	246	0	ENST00000373198.4:c.3130G>A	p.Val1044Ile	p.V1044I	ENST00000373198	NM_133170.3	1044	Gtc/Atc	23/32	0.70255382132321	7	FACETS	0.903	0.866	0.94	0.903	0.866	0.94	CLONAL	4	TRUE	3	0.70255382132321	7		246	1004	SUCCESS
APC	324	MSKCC	GRCh37	5	112175225	112175225	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	121	287	0	ENST00000257430.4:c.3934G>T	p.Gly1312Ter	p.G1312*	ENST00000257430	NM_000038.5	1312	Gga/Tga	16/16	1	2	FACETS	0.996	0.91	1	0.996	0.91	1	CLONAL	1	TRUE	1	0.70255382132321	2		287	346	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939715	76939715	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149249195	NA	P-0058396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	73	281	0	ENST00000373344.5:c.1033G>A	p.Ala345Thr	p.A345T	ENST00000373344	NM_000489.3	345	Gca/Aca	9/35	1	2	FACETS	0.756	0.668	0.848	0.756	0.668	0.848	SUBCLONAL	1	TRUE	1	0.70255382132321	2		281	275	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053237	180053237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372947534	NA	P-0058396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	148	366	1	ENST00000261937.6:c.1132C>T	p.Arg378Cys	p.R378C	ENST00000261937	NM_182925.4	378	Cgc/Tgc	9/30	1	2	FACETS	0.98	0.904	1	0.98	0.904	1	CLONAL	1	TRUE	1	0.70255382132321	2		367	430	SUCCESS
APC	324	MSKCC	GRCh37	5	112170852	112170852	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	67	206	0	ENST00000257430.4:c.1948G>T	p.Glu650Ter	p.E650*	ENST00000257430	NM_000038.5	650	Gag/Tag	15/16	1	2	FACETS	0.84	0.741	0.944	0.84	0.741	0.944	CLONAL	1	TRUE	1	0.70255382132321	2		206	227	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197033	123197033	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1237531973	NA	P-0058396-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	99	184	0	ENST00000218089.9:c.1799A>G	p.Tyr600Cys	p.Y600C	ENST00000218089	NM_001042749.1	600	tAt/tGt	19/35	0.636344623729629	3	FACETS	0.92	0.841	0.999	0.92	0.841	0.999	CLONAL	2	TRUE	1	0.70255382132321	3		184	207	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936093	178936093	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913275	NA	P-0058423-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	24	247	0	ENST00000263967.3:c.1635G>T	p.Glu545Asp	p.E545D	ENST00000263967	NM_006218.2	545	gaG/gaT	10/21	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.471708059753352	2		247	92	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549568	5549568	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138254251	NA	P-0058423-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	89	511	0	ENST00000397747.3:c.595G>A	p.Val199Met	p.V199M	ENST00000397747	NM_025239.3	199	Gtg/Atg	4/7	1	2	FACETS	0.826	0.735	0.921	0.826	0.735	0.921	CLONAL	1	TRUE	1	0.471708059753352	2		511	457	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842705	68842705	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058479-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	155	525	0	ENST00000261769.5:c.641T>C	p.Leu214Pro	p.L214P	ENST00000261769	NM_004360.3	214	cTg/cCg	5/16	0.273170171081109	2	FACETS	0.977	0.899	1	0.977	0.899	1	CLONAL	2	TRUE	0	0.288553014337114	2		525	550	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641054	3641054	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143558209	NA	P-0058479-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	39	630	0	ENST00000294008.3:c.2585G>A	p.Arg862Gln	p.R862Q	ENST00000294008	NM_032444.2	862	cGa/cAa	12/15	1	2	FACETS	0.478	0.396	0.571	0.478	0.396	0.571	SUBCLONAL	1	TRUE	1	0.288553014337114	2		630	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0058479-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	105	687	0	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.288553014337114	2		687	614	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0058516-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	75	444	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.673550945541782	2		444	218	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0058516-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	25	232	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	0.825	0.667	0.997	0.825	0.667	0.997	CLONAL	1	TRUE	1	0.673550945541782	2		232	90	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0058593-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	69	754	1	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.136548600424831	3	FACETS	0.639	0.556	0.73			1	INDETERMINATE	1	FALSE	NA	0.317455844068391	3		755	788	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983148	149983148	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0058593-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	40	495	0	ENST00000253339.5:c.3110C>G	p.Ser1037Ter	p.S1037*	ENST00000253339		1037	tCa/tGa	7/7	1	2	FACETS	0.387	0.321	0.461	0.387	0.321	0.461	SUBCLONAL	1	FALSE	1	0.317455844068391	2		495	651	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953728	48953728	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1555286503	NA	P-0058593-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	12	178	0	ENST00000267163.4:c.1333-2A>G		p.X445_splice	ENST00000267163	NM_000321.2	445			1	2	FACETS	0.266	0.186	0.365	0.266	0.186	0.365	SUBCLONAL	1	FALSE	1	0.317455844068391	2		178	284	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681755	78681755	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058593-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	34	517	0	ENST00000306801.3:c.463G>T	p.Val155Leu	p.V155L	ENST00000306801	NM_020761.2	155	Gtg/Ttg	4/34	NA	2	FACETS	0.374	0.305	0.452			1	INDETERMINATE	1	FALSE	NA	0.317455844068391	2		517	573	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051244	13051244	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058593-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	60	664	0	ENST00000316448.5:c.680A>G	p.Asp227Gly	p.D227G	ENST00000316448	NM_004343.3	227	gAt/gGt	5/9	1	2	FACETS	0.454	0.39	0.524	0.454	0.39	0.524	SUBCLONAL	1	FALSE	1	0.317455844068391	2		664	832	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449755	8449755	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058593-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	90	458	0	ENST00000356435.5:c.3958G>T	p.Glu1320Ter	p.E1320*	ENST00000356435		1320	Gaa/Taa	23/35	0.317455844068391	3	FACETS	0.955	0.848	1	0.477	0.424	0.535	CLONAL	1	FALSE	1	0.317455844068391	3		458	688	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0058596-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	109	536	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.424072361405329	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.424072361405329	1		536	398	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247516	123247516	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519795	NA	P-0058596-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	137	442	0	ENST00000358487.5:c.1975A>G	p.Lys659Glu	p.K659E	ENST00000358487	NM_000141.4	659	Aag/Gag	14/18	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.424072361405329	2		442	495	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060782	38060784	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0058596-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	206	889	0	ENST00000250448.2:c.1205_1207del	p.Ile402del	p.I402del	ENST00000250448	NM_004496.3	402	aTCAac/aac	2/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.424072361405329	2		889	836	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057789	27057790	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058596-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	222	890	0	ENST00000324856.7:c.1498dup	p.Tyr500LeufsTer123	p.Y500Lfs*123	ENST00000324856	NM_006015.4	499	-/T	3/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.424072361405329	2		890	912	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573759	64573759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058596-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	179	788	0	ENST00000312049.6:c.994C>T	p.Arg332Cys	p.R332C	ENST00000312049	NM_130799.2	332	Cgc/Tgc	7/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.424072361405329	2		788	773	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170832399	170832399	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs776780244	NA	P-0058596-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	62	138	0	ENST00000296930.5:c.763A>G	p.Ile255Val	p.I255V	ENST00000296930	NM_002520.6	255	Ata/Gta	9/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.424072361405329	2		138	237	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132837	152132837	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058596-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	104	511	0	ENST00000262189.6:c.35del	p.Pro12ArgfsTer93	p.P12Rfs*93	ENST00000262189	NM_170606.2	12	cCg/cg	1/59	0.116607374371409	0	FACETS	0.734	0.662	0.808			1	INDETERMINATE	1	TRUE	0	0.424072361405329	0		511	385	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0058624-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	36	525	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.772	0.634	0.927	0.772	0.634	0.927	CLONAL	1	TRUE	1	0.18	2		525	518	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280292	1280292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201927653	NA	P-0058624-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	54	524	0	ENST00000310581.5:c.1931C>T	p.Thr644Met	p.T644M	ENST00000310581	NM_198253.2	644	aCg/aTg	4/16	1	2	FACETS	0.738	0.629	0.858	0.738	0.629	0.858	SUBCLONAL	1	TRUE	1	0.18	2		524	813	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56412972	56412984	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTCCCAAGCAT	TCTTCCCAAGCAT	-	novel	NA	P-0058624-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	59	360	0	ENST00000348428.3:c.1987_1999del	p.Leu663AlafsTer12	p.L663Afs*12	ENST00000348428	NM_006785.3	662	gaTCTTCCCAAGCAT/ga	16/17	1	2	FACETS	0.889	0.764	1	0.889	0.764	1	CLONAL	1	TRUE	1	0.18	2		360	737	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226095	226095	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1179470589	NA	P-0058624-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	35	264	0	ENST00000264932.6:c.554A>C	p.Gln185Pro	p.Q185P	ENST00000264932	NM_004168.2	185	cAg/cCg	5/15	1	2	FACETS	0.718	0.587	0.864	0.718	0.587	0.864	SUBCLONAL	1	TRUE	1	0.18	2		264	542	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39214712	39214712	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs56248239	NA	P-0058677-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	143	272	0	ENST00000402219.2:c.3412A>G	p.Ile1138Val	p.I1138V	ENST00000402219	NM_005633.3	1138	Ata/Gta	22/23	1	2	FACETS	0.985	0.905	1	0.985	0.905	1	CLONAL	1	TRUE	1	0.629818282680823	2		272	461	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657491	29657492	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0058677-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	139	314	0	ENST00000356175.3:c.5726_5727del	p.Cys1909TyrfsTer5	p.C1909Yfs*5	ENST00000356175	NM_000267.3	1908	gaGTgt/gagt	38/57	1	2	FACETS	0.943	0.865	1	0.943	0.865	1	CLONAL	1	TRUE	1	0.629818282680823	2		314	468	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267785	7267785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058677-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	158	472	0	ENST00000302850.5:c.223G>A	p.Asp75Asn	p.D75N	ENST00000302850	NM_000208.2	75	Gac/Aac	2/22	1	2	FACETS	0.848	0.78	0.917	0.848	0.78	0.917	CLONAL	1	TRUE	1	0.629818282680823	2		472	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0058721-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	327	745	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.489208254855157	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.519953698147522	2		745	619	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222163	53222163	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058721-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	34	673	0	ENST00000375401.3:c.4669C>T	p.Gln1557Ter	p.Q1557*	ENST00000375401	NM_004187.3	1557	Cag/Tag	26/26	0.16875228672045	4	FACETS	0.319	0.26	0.386	0.16	0.13	0.193	INDETERMINATE	1	TRUE	2	0.519953698147522	4		673	623	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916747	48916747	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690915	NA	P-0058721-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	25	319	0	ENST00000267163.4:c.277C>T	p.Gln93Ter	p.Q93*	ENST00000267163	NM_000321.2	93	Caa/Taa	3/27	0.519953698147522	1	FACETS	0.726	0.585	0.88	0.726	0.585	0.88	SUBCLONAL	1	TRUE	0	0.519953698147522	1		319	98	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938039	76938039	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058721-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	29	545	0	ENST00000373344.5:c.2709A>T	p.Glu903Asp	p.E903D	ENST00000373344	NM_000489.3	903	gaA/gaT	9/35	0.16875228672045	4	FACETS	0.344	0.275	0.422	0.172	0.137	0.211	INDETERMINATE	1	TRUE	2	0.519953698147522	4		545	493	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880219	37880229	+	protein_altering_variant	In_Frame_Del	DEL	TTGAGGGAAAA	TTGAGGGAAAA	GCCAAAGC	novel	NA	P-0058721-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	262	567	1	ENST00000269571.5:c.2263_2273delinsGCCAAAGC	p.Leu755_Asn758delinsAlaLysAla	p.L755_N758delinsAKA	ENST00000269571		755	TTGAGGGAAAAc/GCCAAAGCc	19/27	0.489208254855157	2	FACETS	0.984	0.934	1	0.984	0.934	1	CLONAL	2	TRUE	0	0.519953698147522	2		568	512	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0058723-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	11	329	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.342	0.235	0.476	0.342	0.235	0.476	SUBCLONAL	1	TRUE	1	0.14	2		329	460	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199630	11199630	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058723-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	32	431	0	ENST00000361445.4:c.4958G>A	p.Trp1653Ter	p.W1653*	ENST00000361445	NM_004958.3	1653	tGg/tAg	35/58	1	2	FACETS	0.733	0.593	0.891	0.733	0.593	0.891	SUBCLONAL	1	TRUE	1	0.14	2		431	624	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056290	27056290	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058723-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	39	518	0	ENST00000324856.7:c.1287del	p.Tyr430ThrfsTer3	p.Y430Tfs*3	ENST00000324856	NM_006015.4	429	cGg/cg	2/20	1	2	FACETS	0.776	0.641	0.927	0.776	0.641	0.927	CLONAL	1	TRUE	1	0.14	2		518	718	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482874	67482874	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	rs1555414506	NA	P-0058723-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	67	497	0	ENST00000327367.4:c.1278G>C	p.Ter426TyrextTer6	p.*426Yext*6	ENST00000327367	NM_005902.3	426	taG/taC	9/9	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.14	2		497	729	SUCCESS
PHF6	84295	MSKCC	GRCh37	X	133547590	133547590	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058723-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	34	344	0	ENST00000332070.3:c.488G>A	p.Arg163His	p.R163H	ENST00000332070	NM_032458.2	163	cGc/cAc	6/10	1	2	FACETS	0.864	0.705	1	0.864	0.705	1	CLONAL	1	TRUE	1	0.14	2		344	562	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936995	48936995	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778842	NA	P-0058734-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	94	358	0	ENST00000267163.4:c.763C>T	p.Arg255Ter	p.R255*	ENST00000267163	NM_000321.2	255	Cga/Tga	8/27	0.595412902919933	1	FACETS	0.999	0.948	1	1	0.991	1	CLONAL	2	TRUE	0	0.595412902919933	1		358	111	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0058763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	13	97	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	0.331671180408921	3	FACETS	1	0.771	1	0.538	0.389	0.712	CLONAL	1	FALSE	1	0.331671180408921	3		97	85	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	158	540	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.25258742867503	3	FACETS	1	0.98	1	0.786	0.726	0.847	CLONAL	2	FALSE	0	0.331671180408921	3		540	471	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287964	33287964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	188	591	0	ENST00000374542.5:c.1289C>T	p.Ala430Val	p.A430V	ENST00000374542	NM_001141970.1	430	gCc/gTc	5/8	0.331671180408921	5	FACETS	0.925	0.855	0.997	0.925	0.855	0.997	CLONAL	2	FALSE	3	0.331671180408921	5		591	918	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150923439	150923439	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	79	457	0	ENST00000271640.5:c.2086G>C	p.Glu696Gln	p.E696Q	ENST00000271640	NM_001145415.1	696	Gag/Cag	13/22	0.229261575563629	4	FACETS	1	0.955	1	0.59	0.519	0.665	CLONAL	1	FALSE	2	0.331671180408921	4		457	538	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150923523	150923523	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	70	482	0	ENST00000271640.5:c.2170G>C	p.Glu724Gln	p.E724Q	ENST00000271640	NM_001145415.1	724	Gaa/Caa	13/22	0.229261575563629	4	FACETS	0.986	0.861	1	0.493	0.43	0.561	CLONAL	1	FALSE	2	0.331671180408921	4		482	570	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70442602	70442602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	103	391	0	ENST00000373644.4:c.4924G>A	p.Glu1642Lys	p.E1642K	ENST00000373644	NM_030625.2	1642	Gaa/Aaa	10/12	0.331671180408921	5	FACETS	0.963	0.866	1			1	CLONAL	2	FALSE	NA	0.331671180408921	5		391	483	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624289	89624289	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	84	304	0	ENST00000371953.3:c.63C>G	p.Phe21Leu	p.F21L	ENST00000371953	NM_000314.4	21	ttC/ttG	1/9	0.331671180408921	2	FACETS	0.841	0.751	0.936	0.841	0.751	0.936	CLONAL	2	FALSE	0	0.331671180408921	2		304	301	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992468	72992469	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0058763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	145	550	0	ENST00000268489.5:c.1576_1577del	p.Ser526LysfsTer6	p.S526Kfs*6	ENST00000268489	NM_006885.3	526	TCa/a	2/10	0.331671180408921	2	FACETS	0.89	0.818	0.965	0.89	0.818	0.965	CLONAL	2	FALSE	0	0.331671180408921	2		550	491	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56402546	56402546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	31	250	0	ENST00000348428.3:c.1588G>A	p.Asp530Asn	p.D530N	ENST00000348428	NM_006785.3	530	Gat/Aat	13/17	1	2	FACETS	0.921	0.751	1	0.921	0.751	1	CLONAL	1	FALSE	1	0.331671180408921	2		250	203	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123499631	123499631	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	10	248	0	ENST00000371139.4:c.158C>A	p.Thr53Lys	p.T53K	ENST00000371139	NM_001114937.2	53	aCa/aAa	2/4	0.294436938126268	3	FACETS	0.399	0.271	0.561	0.2	0.135	0.281	SUBCLONAL	1	FALSE	1	0.331671180408921	3		248	176	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776984	135776984	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	50	422	0	ENST00000298552.3:c.2494del	p.Ser832ProfsTer17	p.S832Pfs*17	ENST00000298552	NM_001162426.1	832	Tcc/cc	19/23	0.214127209042665	1	FACETS	0.923	0.784	1	0.923	0.784	1	CLONAL	1	TRUE	0	0.214127209042665	1		422	452	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436361	52436381	+	frameshift_variant	Frame_Shift_Del	DEL	CTTGTGGAGCCGGCCGATGCT	CTTGTGGAGCCGGCCGATGCT	ATGCG	novel	NA	P-0058764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	53	638	1	ENST00000460680.1:c.2113_2133delinsCGCAT	p.Ser705ArgfsTer26	p.S705Rfs*26	ENST00000460680	NM_004656.3	705	AGCATCGGCCGGCTCCACAAG/CGCAT	17/17	0.214127209042665	1	FACETS	0.687	0.585	0.799	0.687	0.585	0.799	SUBCLONAL	1	TRUE	0	0.214127209042665	1		639	643	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0058788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	18	185	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.293797543502958	1	FACETS	0.813	0.613	1	0.813	0.613	1	CLONAL	1	TRUE	0	0.15	1		185	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0058788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	131	951	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.220983417323051	2	FACETS	1	0.959	1	1	0.988	1	CLONAL	3	TRUE	0	0.15	2		951	535	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622086	43622086	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	25	696	0	ENST00000355710.3:c.3103G>C	p.Glu1035Gln	p.E1035Q	ENST00000355710	NM_020975.4	1035	Gag/Cag	19/20	0.3	1	FACETS	0.702	0.553	0.875	0.702	0.553	0.875	SUBCLONAL	1	TRUE	0	0.15	1		696	439	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10789386	10789386	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	47	559	0	ENST00000361367.2:c.1720C>G	p.Leu574Val	p.L574V	ENST00000361367	NM_014633.3	574	Ctt/Gtt	14/25	0.3	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.15	1		559	446	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865789	57865789	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs769935841	NA	P-0058788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	29	802	0	ENST00000228682.2:c.3266G>C	p.Ser1089Thr	p.S1089T	ENST00000228682	NM_005269.2	1089	aGt/aCt	12/12	1	2	FACETS	0.925	0.742	1	0.925	0.742	1	CLONAL	1	TRUE	1	0.15	2		802	418	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120789156	120789156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1433178108	NA	P-0058788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	30	605	0	ENST00000257552.2:c.781G>A	p.Glu261Lys	p.E261K	ENST00000257552	NM_002442.3	261	Gag/Aag	11/15	0.3	1	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	0	0.15	1		605	321	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527973	103527973	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0058788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	37	616	0	ENST00000355739.4:c.3281C>G	p.Ser1094Ter	p.S1094*	ENST00000355739	NM_000123.3	1094	tCa/tGa	15/15	0.208664758385927	2	FACETS	1	0.826	1	0.501	0.413	0.601	CLONAL	1	TRUE	0	0.15	2		616	492	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3827617	3827617	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	32	422	0	ENST00000262367.5:c.2155C>G	p.Gln719Glu	p.Q719E	ENST00000262367	NM_004380.2	719	Caa/Gaa	11/31	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.15	2		422	350	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548909	29548909	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1135402820	NA	P-0058788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	41	290	0	ENST00000356175.3:c.1683G>A	p.Trp561Ter	p.W561*	ENST00000356175	NM_000267.3	561	tgG/tgA	15/57	0.220983417323051	2	FACETS	0.876	0.737	1	1	0.945	1	CLONAL	3	TRUE	0	0.15	2		290	208	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858859	78858859	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	33	782	0	ENST00000306801.3:c.1894G>A	p.Glu632Lys	p.E632K	ENST00000306801	NM_020761.2	632	Gag/Aag	17/34	0.220983417323051	2	FACETS	0.998	0.812	1	0.499	0.406	0.604	CLONAL	1	TRUE	0	0.15	2		782	441	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866381	42866381	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746151019	NA	P-0058788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	50	817	0	ENST00000398585.3:c.251C>T	p.Ser84Phe	p.S84F	ENST00000398585	NM_001135099.1	84	tCc/tTc	3/14	0.3	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.15	1		817	449	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437669	52437669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	37	861	1	ENST00000460680.1:c.1492G>A	p.Glu498Lys	p.E498K	ENST00000460680	NM_004656.3	498	Gag/Aag	13/17	0.293797543502958	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.15	1		862	395	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920436	134920436	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	38	702	0	ENST00000398015.3:c.2251C>G	p.Leu751Val	p.L751V	ENST00000398015	NM_004441.4	751	Ctg/Gtg	12/16	0.293797543502958	1	FACETS	1	0.84	1	1	0.84	1	CLONAL	1	TRUE	0	0.15	1		702	461	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512455	149512455	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	30	871	0	ENST00000261799.4:c.985G>C	p.Glu329Gln	p.E329Q	ENST00000261799	NM_002609.3	329	Gag/Cag	7/23	0.220983417323051	2	FACETS	0.794	0.638	0.97	0.397	0.319	0.485	CLONAL	1	TRUE	0	0.15	2		871	504	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43738986	43738986	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0058788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	21	784	0	ENST00000523873.1:c.3G>A	p.Met1?	p.M1?	ENST00000523873		1	atG/atA	1/8	0.293797543502958	1	FACETS	0.7	0.538	0.889	0.7	0.538	0.889	SUBCLONAL	1	TRUE	0	0.15	1		784	370	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520081	106520081	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	24	397	0	ENST00000359195.3:c.2509G>C	p.Asp837His	p.D837H	ENST00000359195	NM_002649.2	837	Gat/Cat	6/11	0.153610404921079	3	FACETS	0.896	0.702	1	0.448	0.351	0.56	CLONAL	1	TRUE	1	0.15	3		397	384	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27220069	27220069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs955187413	NA	P-0058788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	29	591	0	ENST00000380036.4:c.3126G>A	p.Met1042Ile	p.M1042I	ENST00000380036	NM_000459.3	1042	atG/atA	21/23	1	2	FACETS	0.873	0.7	1	0.873	0.7	1	CLONAL	1	TRUE	1	0.15	2		591	443	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15840928	15840928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	19	160	0	ENST00000307771.7:c.1012G>A	p.Glu338Lys	p.E338K	ENST00000307771	NM_005089.3	338	Gaa/Aaa	11/11	0.0811045832511694	2	FACETS	1	0.835	1			1	INDETERMINATE	2	TRUE	NA	0.15	2		160	114	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340946	70340946	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058788-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	43	409	0	ENST00000374080.3:c.679G>C	p.Glu227Gln	p.E227Q	ENST00000374080		227	Gag/Cag	5/45	0.0811045832511694	2	FACETS	1	0.895	1			1	INDETERMINATE	2	TRUE	NA	0.15	2		409	265	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574026	7574026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	148	458	0	ENST00000269305.4:c.1001G>T	p.Gly334Val	p.G334V	ENST00000269305	NM_001126112.2	334	gGg/gTg	10/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		458	617	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749994	162749994	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	186	557	0	ENST00000367921.3:c.2526C>G	p.Phe842Leu	p.F842L	ENST00000367921	NM_006182.2	842	ttC/ttG	18/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		557	963	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90992961	90992961	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs780470185	NA	P-0058792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	18	333	0	ENST00000265433.3:c.480+1G>A		p.X160_splice	ENST00000265433	NM_002485.4	160			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		333	155	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218440	36218440	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	321	527	0	ENST00000222270.7:c.4219G>T	p.Gly1407Trp	p.G1407W	ENST00000222270	NM_014727.1	1407	Ggg/Tgg	16/37	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		527	885	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51507372	51507372	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	26	509	0	ENST00000260433.2:c.916G>T	p.Ala306Ser	p.A306S	ENST00000260433		306	Gca/Tca	8/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		509	290	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727513	88727513	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs374069724	NA	P-0058792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	67	585	0	ENST00000360948.2:c.266G>T	p.Arg89Leu	p.R89L	ENST00000360948	NM_001012338.2	89	cGc/cTc	3/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		585	744	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592312	29592312	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	33	360	0	ENST00000356175.3:c.4727G>T	p.Gly1576Val	p.G1576V	ENST00000356175	NM_000267.3	1576	gGg/gTg	35/57	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		360	135	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119818	70119818	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	222	592	0	ENST00000245479.2:c.820G>C	p.Asp274His	p.D274H	ENST00000245479	NM_000346.3	274	Gac/Cac	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		592	776	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637933	39637933	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	44	488	0	ENST00000262039.4:c.2350G>T	p.Val784Leu	p.V784L	ENST00000262039	NM_002647.2	784	Gta/Tta	22/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		488	475	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61322997	61322998	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0058792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	78	634	0	ENST00000283752.5:c.1066_1067delinsAT	p.Pro356Ile	p.P356I	ENST00000283752	NM_006919.2	356	CCt/ATt	8/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		634	573	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308443	30308443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs778311875	NA	P-0058792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	222	570	0	ENST00000262643.3:c.457A>G	p.Met153Val	p.M153V	ENST00000262643	NM_001238.2	153	Atg/Gtg	6/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		570	662	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262405	39262405	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	15	475	0	ENST00000402219.2:c.1022G>T	p.Arg341Met	p.R341M	ENST00000402219	NM_005633.3	341	aGg/aTg	8/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		475	193	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160385	99160385	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	149	564	0	ENST00000074304.5:c.864G>T	p.Glu288Asp	p.E288D	ENST00000074304	NM_001134224.1	288	gaG/gaT	11/26	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		564	1100	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670633	134670633	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769719088	NA	P-0058792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	103	568	0	ENST00000398015.3:c.544G>A	p.Ala182Thr	p.A182T	ENST00000398015	NM_004441.4	182	Gcc/Acc	3/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		568	650	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456725	138456725	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	17	381	0	ENST00000289153.2:c.625G>T	p.Val209Leu	p.V209L	ENST00000289153	NM_006219.2	209	Gtg/Ttg	4/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		381	165	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188388	142188388	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	21	504	0	ENST00000350721.4:c.6343A>T	p.Met2115Leu	p.M2115L	ENST00000350721	NM_001184.3	2115	Atg/Ttg	38/47	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		504	178	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481648	20481648	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	98	538	0	ENST00000346618.3:c.718del	p.Gln240AsnfsTer24	p.Q240Nfs*24	ENST00000346618	NM_001949.4	239	gtC/gt	3/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		538	606	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250497	26250497	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	146	764	0	ENST00000446824.2:c.337A>T	p.Ile113Phe	p.I113F	ENST00000446824	NM_021018.2	113	Atc/Ttc	1/1	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		764	1285	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271518	26271518	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	90	763	0	ENST00000305910.3:c.95C>A	p.Ala32Asp	p.A32D	ENST00000305910	NM_003534.2	32	gCc/gAc	1/1	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		763	1120	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31939837	31939837	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs202228977	NA	P-0058792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	233	628	0	ENST00000375333.2:c.64T>C	p.Ser22Pro	p.S22P	ENST00000375333	NM_032454.1	22	Tcc/Ccc	1/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		628	1127	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223596	53223604	+	inframe_deletion	In_Frame_Del	DEL	GGCGCGGGC	GGCGCGGGC	-	novel	NA	P-0058792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	52	632	0	ENST00000375401.3:c.3755_3763del	p.Arg1252_Arg1254del	p.R1252_R1254del	ENST00000375401	NM_004187.3	1252	cGCCCGCGCCtg/ctg	23/26	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		632	782	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53241088	53241088	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	170	522	0	ENST00000375401.3:c.1123G>T	p.Glu375Ter	p.E375*	ENST00000375401	NM_004187.3	375	Gag/Tag	9/26	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		522	744	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350064	70350064	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058792-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	64	484	0	ENST00000374080.3:c.4047G>T	p.Gln1349His	p.Q1349H	ENST00000374080		1349	caG/caT	28/45	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		484	764	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	95	483	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.893	0.8	0.991	0.893	0.8	0.991	CLONAL	1	TRUE	1	0.492495006928753	2		483	432	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902658	1902658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761663126	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	155	499	0	ENST00000382891.5:c.277G>A	p.Ala93Thr	p.A93T	ENST00000382891	NM_133335.3	93	Gca/Aca	2/22	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.492495006928753	2		499	554	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692791	89692791	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1114167623	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	81	217	0	ENST00000371953.3:c.275A>G	p.Asp92Gly	p.D92G	ENST00000371953	NM_000314.4	92	gAc/gGc	5/9	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.492495006928753	2		217	240	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539951	187539951	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs777631605	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	128	472	0	ENST00000441802.2:c.7789C>T	p.Arg2597Ter	p.R2597*	ENST00000441802	NM_005245.3	2597	Cga/Tga	10/27	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.492495006928753	2		472	476	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	214	545	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.459881746335296	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.492495006928753	3		545	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	135	471	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.492495006928753	2		471	523	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074340	8074340	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	116	438	0	ENST00000377482.5:c.319G>T	p.Glu107Ter	p.E107*	ENST00000377482	NM_018948.3	107	Gaa/Taa	4/4	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.492495006928753	2		438	425	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075664	8075664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	98	335	0	ENST00000377482.5:c.16G>A	p.Val6Ile	p.V6I	ENST00000377482	NM_018948.3	6	Gtt/Att	2/4	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.492495006928753	2		335	374	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775962	9775962	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	66	375	0	ENST00000377346.4:c.426G>T	p.Lys142Asn	p.K142N	ENST00000377346	NM_005026.3	142	aaG/aaT	5/24	1	2	FACETS	0.873	0.764	0.989	0.873	0.764	0.989	CLONAL	1	TRUE	1	0.492495006928753	2		375	307	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182145	11182145	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	94	358	0	ENST00000361445.4:c.6701C>A	p.Ser2234Ter	p.S2234*	ENST00000361445	NM_004958.3	2234	tCg/tAg	48/58	1	2	FACETS	0.929	0.832	1	0.929	0.832	1	CLONAL	1	TRUE	1	0.492495006928753	2		358	411	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11204743	11204743	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	102	412	0	ENST00000361445.4:c.4834C>T	p.Arg1612Ter	p.R1612*	ENST00000361445	NM_004958.3	1612	Cga/Tga	34/58	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.492495006928753	2		412	409	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11210249	11210249	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs748220176	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	99	360	0	ENST00000361445.4:c.4504A>G	p.Thr1502Ala	p.T1502A	ENST00000361445	NM_004958.3	1502	Acc/Gcc	31/58	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.492495006928753	2		360	352	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272421	11272421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777142056	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	109	391	1	ENST00000361445.4:c.3509G>A	p.Arg1170His	p.R1170H	ENST00000361445	NM_004958.3	1170	cGc/cAc	23/58	1	2	FACETS	0.986	0.891	1	0.986	0.891	1	CLONAL	1	TRUE	1	0.492495006928753	2		392	449	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298590	11298590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs913197212	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	109	386	0	ENST00000361445.4:c.1871G>A	p.Arg624His	p.R624H	ENST00000361445	NM_004958.3	624	cGc/cAc	12/58	1	2	FACETS	0.988	0.893	1	0.988	0.893	1	CLONAL	1	TRUE	1	0.492495006928753	2		386	448	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262035	16262035	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	123	487	0	ENST00000375759.3:c.9300G>A	p.Met3100Ile	p.M3100I	ENST00000375759	NM_015001.2	3100	atG/atA	11/15	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.492495006928753	2		487	457	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092825	27092825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867253777	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	117	463	0	ENST00000324856.7:c.2846C>T	p.Ser949Phe	p.S949F	ENST00000324856	NM_006015.4	949	tCc/tTc	9/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.492495006928753	2		463	424	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804368	43804368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770877156	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	111	413	0	ENST00000372470.3:c.368G>A	p.Arg123Gln	p.R123Q	ENST00000372470	NM_005373.2	123	cGa/cAa	3/12	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.492495006928753	2		413	422	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805092	43805092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	121	471	0	ENST00000372470.3:c.542G>A	p.Gly181Asp	p.G181D	ENST00000372470	NM_005373.2	181	gGt/gAt	4/12	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.492495006928753	2		471	468	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797896	45797896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	104	519	0	ENST00000450313.1:c.875C>T	p.Pro292Leu	p.P292L	ENST00000450313	NM_012222.2	292	cCa/cTa	10/16	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.492495006928753	2		519	409	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439763	51439763	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	127	444	0	ENST00000262662.1:c.328G>A	p.Ala110Thr	p.A110T	ENST00000262662		110	Gct/Act	4/4	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.492495006928753	2		444	478	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247888	59247888	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	133	546	0	ENST00000371222.2:c.855A>C	p.Lys285Asn	p.K285N	ENST00000371222	NM_002228.3	285	aaA/aaC	1/1	1	2	FACETS	0.998	0.911	1	0.998	0.911	1	CLONAL	1	TRUE	1	0.492495006928753	2		546	541	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307182	65307182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	120	459	0	ENST00000342505.4:c.2506C>T	p.Pro836Ser	p.P836S	ENST00000342505	NM_002227.2	836	Cct/Tct	18/25	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.492495006928753	2		459	459	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400929	72400929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	94	362	0	ENST00000357731.5:c.242G>A	p.Gly81Glu	p.G81E	ENST00000357731	NM_173808.2	81	gGa/gAa	2/7	1	2	FACETS	0.957	0.857	1	0.957	0.857	1	CLONAL	1	TRUE	1	0.492495006928753	2		362	399	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429367	78429367	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	135	413	1	ENST00000370768.2:c.1075C>T	p.Arg359Ter	p.R359*	ENST00000370768	NM_003902.3	359	Cga/Tga	13/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.492495006928753	2		414	505	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430402	78430402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372081866	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	114	406	0	ENST00000370768.2:c.766C>T	p.Arg256Cys	p.R256C	ENST00000370768	NM_003902.3	256	Cgt/Tgt	10/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.492495006928753	2		406	422	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273009	115273009	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	99	421	0	ENST00000438362.2:c.1364G>T	p.Arg455Met	p.R455M	ENST00000438362	NM_001242891.1	455	aGg/aTg	12/20	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.492495006928753	2		421	393	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165657	118165657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs565811357	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	142	552	1	ENST00000369448.3:c.167G>A	p.Arg56His	p.R56H	ENST00000369448	NM_017709.3	56	cGc/cAc	2/2	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.492495006928753	2		553	512	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166139	118166139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766689047	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	130	546	0	ENST00000369448.3:c.649G>A	p.Gly217Arg	p.G217R	ENST00000369448	NM_017709.3	217	Ggg/Agg	2/2	1	2	FACETS	0.962	0.876	1	0.962	0.876	1	CLONAL	1	TRUE	1	0.492495006928753	2		546	549	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464914	120464914	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	108	388	0	ENST00000256646.2:c.5158G>T	p.Asp1720Tyr	p.D1720Y	ENST00000256646	NM_024408.3	1720	Gat/Tat	28/34	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.492495006928753	2		388	418	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464968	120464968	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	114	378	0	ENST00000256646.2:c.5104C>T	p.Arg1702Ter	p.R1702*	ENST00000256646	NM_024408.3	1702	Cga/Tga	28/34	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.492495006928753	2		378	441	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724490	162724490	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	203	490	0	ENST00000367921.3:c.262C>T	p.Gln88Ter	p.Q88*	ENST00000367921	NM_006182.2	88	Cag/Tag	5/18	0.459881746335296	3	FACETS	0.962	0.899	1	0.962	0.899	1	CLONAL	2	TRUE	1	0.492495006928753	3		490	534	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163310172	163310172	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	79	327	0	ENST00000271452.3:c.625A>C	p.Asn209His	p.N209H	ENST00000271452	NM_145697.2	209	Aat/Cat	9/14	0.459881746335296	3	FACETS	1	0.921	1	0.526	0.465	0.59	CLONAL	1	TRUE	1	0.492495006928753	3		327	380	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958525	175958525	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	173	331	0	ENST00000367669.3:c.1820T>G	p.Phe607Cys	p.F607C	ENST00000367669	NM_022457.5	607	tTt/tGt	16/20	0.459881746335296	3	FACETS	0.956	0.889	1	0.956	0.889	1	CLONAL	2	TRUE	1	0.492495006928753	3		331	458	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012395	176012395	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	216	316	0	ENST00000367669.3:c.1539G>T	p.Glu513Asp	p.E513D	ENST00000367669	NM_022457.5	513	gaG/gaT	14/20	0.459881746335296	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.492495006928753	3		316	485	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054983	176054983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs991566021	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	157	275	0	ENST00000367669.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000367669	NM_022457.5	357	cGa/cAa	10/20	0.459881746335296	3	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	1	0.492495006928753	3		275	389	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107230	193107230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	158	351	0	ENST00000367435.3:c.439C>T	p.Arg147Cys	p.R147C	ENST00000367435	NM_024529.4	147	Cgc/Tgc	6/17	0.459881746335296	3	FACETS	0.921	0.853	0.991	0.921	0.853	0.991	CLONAL	2	TRUE	1	0.492495006928753	3		351	434	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107244	193107244	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	160	364	0	ENST00000367435.3:c.453G>T	p.Glu151Asp	p.E151D	ENST00000367435	NM_024529.4	151	gaG/gaT	6/17	0.459881746335296	3	FACETS	0.888	0.822	0.956	0.888	0.822	0.956	CLONAL	2	TRUE	1	0.492495006928753	3		364	456	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111168	193111168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1452051467	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	203	490	0	ENST00000367435.3:c.701G>A	p.Arg234Gln	p.R234Q	ENST00000367435	NM_024529.4	234	cGa/cAa	7/17	0.459881746335296	3	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	1	0.492495006928753	3		490	509	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193205385	193205385	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	117	320	0	ENST00000367435.3:c.1317-1G>T		p.X439_splice	ENST00000367435	NM_024529.4	439			0.459881746335296	3	FACETS	1	0.972	1	0.595	0.539	0.653	CLONAL	1	TRUE	1	0.492495006928753	3		320	498	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549703	226549703	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	182	347	0	ENST00000366794.5:c.2930C>A	p.Ser977Tyr	p.S977Y	ENST00000366794	NM_001618.3	977	tCt/tAt	22/23	0.459881746335296	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.492495006928753	3		347	439	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612878	228612878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	144	616	0	ENST00000366696.1:c.149G>A	p.Arg50His	p.R50H	ENST00000366696	NM_003493.2	50	cGc/cAc	1/1	0.459881746335296	3	FACETS	0.994	0.908	1	0.497	0.454	0.542	CLONAL	1	TRUE	1	0.492495006928753	3		616	733	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230461161	230461161	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	182	338	0	ENST00000391860.1:c.929G>A	p.Gly310Glu	p.G310E	ENST00000391860	NM_001258311.1	310	gGa/gAa	6/7	0.459881746335296	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.492495006928753	3		338	413	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243675668	243675668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	75	308	0	ENST00000263826.5:c.1312G>A	p.Glu438Lys	p.E438K	ENST00000263826	NM_005465.4	438	Gaa/Aaa	12/13	0.459881746335296	3	FACETS	0.966	0.851	1	0.483	0.425	0.544	CLONAL	1	TRUE	1	0.492495006928753	3		308	393	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246518379	246518379	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773483378	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	207	338	0	ENST00000388985.4:c.182G>A	p.Arg61Gln	p.R61Q	ENST00000388985		61	cGa/cAa	2/12	0.459881746335296	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.492495006928753	3		338	499	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100283	8100283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	124	432	0	ENST00000346208.3:c.257G>A	p.Arg86His	p.R86H	ENST00000346208		86	cGc/cAc	3/6	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.492495006928753	2		432	430	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850620	63850620	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	107	391	0	ENST00000279873.7:c.1399-1G>T		p.X467_splice	ENST00000279873	NM_032199.2	467			1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.492495006928753	2		391	430	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851041	63851041	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	133	440	0	ENST00000279873.7:c.1819A>G	p.Asn607Asp	p.N607D	ENST00000279873	NM_032199.2	607	Aac/Gac	10/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.492495006928753	2		440	473	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851144	63851144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772420176	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	103	452	0	ENST00000279873.7:c.1922C>T	p.Ala641Val	p.A641V	ENST00000279873	NM_032199.2	641	gCg/gTg	10/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.492495006928753	2		452	393	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851851	63851851	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	152	529	0	ENST00000279873.7:c.2629G>T	p.Glu877Ter	p.E877*	ENST00000279873	NM_032199.2	877	Gaa/Taa	10/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.492495006928753	2		529	543	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333979	70333979	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	114	352	0	ENST00000373644.4:c.1884A>C	p.Lys628Asn	p.K628N	ENST00000373644	NM_030625.2	628	aaA/aaC	2/12	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.492495006928753	2		352	439	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404669	70404669	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564988139	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	97	458	0	ENST00000373644.4:c.2183C>T	p.Ala728Val	p.A728V	ENST00000373644	NM_030625.2	728	gCt/gTt	4/12	1	2	FACETS	0.903	0.81	1	0.903	0.81	1	CLONAL	1	TRUE	1	0.492495006928753	2		458	436	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405568	70405568	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	74	399	0	ENST00000373644.4:c.3082C>A	p.Leu1028Ile	p.L1028I	ENST00000373644	NM_030625.2	1028	Ctt/Att	4/12	1	2	FACETS	0.854	0.753	0.961	0.854	0.753	0.961	CLONAL	1	TRUE	1	0.492495006928753	2		399	352	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450609	70450609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759851979	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	124	392	0	ENST00000373644.4:c.5449G>A	p.Glu1817Lys	p.E1817K	ENST00000373644	NM_030625.2	1817	Gaa/Aaa	12/12	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.492495006928753	2		392	475	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649869	88649869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781556	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	65	195	0	ENST00000372037.3:c.118G>A	p.Asp40Asn	p.D40N	ENST00000372037	NM_004329.2	40	Gac/Aac	4/13	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.492495006928753	2		195	201	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685274	89685274	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	89	237	0	ENST00000371953.3:c.169T>G	p.Leu57Val	p.L57V	ENST00000371953	NM_000314.4	57	Ttg/Gtg	3/9	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.492495006928753	2		237	258	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692940	89692940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746152219	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	96	401	0	ENST00000371953.3:c.424C>T	p.Arg142Trp	p.R142W	ENST00000371953	NM_000314.4	142	Cgg/Tgg	5/9	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.492495006928753	2		401	378	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104268999	104268999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770989077	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	99	382	0	ENST00000369902.3:c.256G>A	p.Glu86Lys	p.E86K	ENST00000369902	NM_016169.3	86	Gag/Aag	2/12	1	2	FACETS	0.937	0.842	1	0.937	0.842	1	CLONAL	1	TRUE	1	0.492495006928753	2		382	429	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710655	114710655	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	120	455	0	ENST00000543371.1:c.140C>T	p.Ser47Phe	p.S47F	ENST00000543371	NM_001198531.1	47	tCt/tTt	1/14	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.492495006928753	2		455	470	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128974	64128974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1429343428	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	111	494	0	ENST00000334205.4:c.604G>A	p.Glu202Lys	p.E202K	ENST00000334205	NM_003942.2	202	Gag/Aag	6/17	1	2	FACETS	0.951	0.86	1	0.951	0.86	1	CLONAL	1	TRUE	1	0.492495006928753	2		494	474	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575571	64575571	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1444210255	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	115	467	0	ENST00000312049.6:c.446G>A	p.Gly149Asp	p.G149D	ENST00000312049	NM_130799.2	149	gGc/gAc	3/10	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.492495006928753	2		467	466	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625302	69625302	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782573423	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	98	423	1	ENST00000334134.2:c.491G>A	p.Arg164His	p.R164H	ENST00000334134	NM_005247.2	164	cGc/cAc	3/3	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.492495006928753	2		424	353	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625426	69625426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	99	356	0	ENST00000334134.2:c.367G>A	p.Glu123Lys	p.E123K	ENST00000334134	NM_005247.2	123	Gag/Aag	3/3	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.492495006928753	2		356	345	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77930365	77930365	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs775714252	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	98	387	0	ENST00000361507.4:c.1984A>G	p.Thr662Ala	p.T662A	ENST00000361507	NM_080491.2	662	Aca/Gca	10/10	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.492495006928753	2		387	383	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77932816	77932816	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	101	458	0	ENST00000361507.4:c.1668C>A	p.Phe556Leu	p.F556L	ENST00000361507	NM_080491.2	556	ttC/ttA	8/10	1	2	FACETS	0.89	0.799	0.985	0.89	0.799	0.985	CLONAL	1	TRUE	1	0.492495006928753	2		458	461	SUCCESS
EED	8726	MSKCC	GRCh37	11	85979586	85979586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408450238	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	77	252	0	ENST00000263360.6:c.949G>A	p.Asp317Asn	p.D317N	ENST00000263360	NM_003797.3	317	Gat/Aat	9/12	1	2	FACETS	0.85	0.751	0.954	0.85	0.751	0.954	CLONAL	1	TRUE	1	0.492495006928753	2		252	368	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190753	108190753	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587780635	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	63	242	0	ENST00000278616.4:c.6420C>A	p.Phe2140Leu	p.F2140L	ENST00000278616	NM_000051.3	2140	ttC/ttA	44/63	1	2	FACETS	0.907	0.792	1	0.907	0.792	1	CLONAL	1	TRUE	1	0.492495006928753	2		242	282	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203492	108203492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs138941496	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	62	290	0	ENST00000278616.4:c.7792C>T	p.Arg2598Ter	p.R2598*	ENST00000278616	NM_000051.3	2598	Cga/Tga	53/63	1	2	FACETS	0.954	0.832	1	0.954	0.832	1	CLONAL	1	TRUE	1	0.492495006928753	2		290	264	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307504	118307504	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	56	323	0	ENST00000534358.1:c.277T>A	p.Ser93Thr	p.S93T	ENST00000534358	NM_005933.3	93	Tct/Act	1/36	1	2	FACETS	0.972	0.842	1	0.972	0.842	1	CLONAL	1	TRUE	1	0.492495006928753	2		323	234	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118354927	118354927	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	102	305	0	ENST00000534358.1:c.4116G>T	p.Glu1372Asp	p.E1372D	ENST00000534358	NM_005933.3	1372	gaG/gaT	9/36	1	2	FACETS	0.963	0.867	1	0.963	0.867	1	CLONAL	1	TRUE	1	0.492495006928753	2		305	430	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374562	118374562	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs782497028	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	149	529	0	ENST00000534358.1:c.7955G>T	p.Ser2652Ile	p.S2652I	ENST00000534358	NM_005933.3	2652	aGc/aTc	27/36	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.492495006928753	2		529	581	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374685	118374685	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	120	522	0	ENST00000534358.1:c.8078C>A	p.Ser2693Tyr	p.S2693Y	ENST00000534358	NM_005933.3	2693	tCt/tAt	27/36	1	2	FACETS	0.952	0.864	1	0.952	0.864	1	CLONAL	1	TRUE	1	0.492495006928753	2		522	512	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376455	118376455	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781886946	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	141	505	0	ENST00000534358.1:c.9848G>A	p.Arg3283Gln	p.R3283Q	ENST00000534358	NM_005933.3	3283	cGa/cAa	27/36	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.492495006928753	2		505	531	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144687	119144687	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	105	367	0	ENST00000264033.4:c.700G>T	p.Asp234Tyr	p.D234Y	ENST00000264033	NM_005188.3	234	Gat/Tat	4/16	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.492495006928753	2		367	407	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416993	416993	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1343180176	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	135	509	0	ENST00000399788.2:c.3557A>G	p.Asn1186Ser	p.N1186S	ENST00000399788	NM_001042603.1	1186	aAc/aGc	23/28	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.492495006928753	2		509	522	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4388071	4388071	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	113	364	0	ENST00000261254.3:c.557C>A	p.Ala186Asp	p.A186D	ENST00000261254	NM_001759.3	186	gCt/gAt	3/5	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.492495006928753	2		364	413	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435061	18435061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603400	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	99	369	0	ENST00000266497.5:c.46G>A	p.Glu16Lys	p.E16K	ENST00000266497		16	Gaa/Aaa	1/31	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.492495006928753	2		369	392	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446936	18446936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	45	198	0	ENST00000266497.5:c.1021G>A	p.Glu341Lys	p.E341K	ENST00000266497		341	Gaa/Aaa	4/31	1	2	FACETS	0.662	0.56	0.773	0.662	0.56	0.773	SUBCLONAL	1	TRUE	1	0.492495006928753	2		198	276	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552618	18552618	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	95	373	0	ENST00000266497.5:c.2029T>G	p.Leu677Val	p.L677V	ENST00000266497		677	Tta/Gta	14/31	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.492495006928753	2		373	372	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716344	18716344	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778895247	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	81	376	1	ENST00000266497.5:c.3691G>A	p.Glu1231Lys	p.E1231K	ENST00000266497		1231	Gaa/Aaa	26/31	1	2	FACETS	0.843	0.748	0.945	0.843	0.748	0.945	CLONAL	1	TRUE	1	0.492495006928753	2		377	390	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378643	25378643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730880471	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	72	341	0	ENST00000311936.3:c.355G>A	p.Asp119Asn	p.D119N	ENST00000311936	NM_004985.3	119	Gat/Aat	4/5	1	2	FACETS	0.934	0.823	1	0.934	0.823	1	CLONAL	1	TRUE	1	0.492495006928753	2		341	313	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46215259	46215259	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	48	227	0	ENST00000334344.6:c.694G>T	p.Asp232Tyr	p.D232Y	ENST00000334344	NM_152641.2	232	Gac/Tac	6/21	1	2	FACETS	0.792	0.676	0.918	0.792	0.676	0.918	CLONAL	1	TRUE	1	0.492495006928753	2		227	246	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230405	46230405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1391481708	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	100	316	0	ENST00000334344.6:c.739C>T	p.Arg247Cys	p.R247C	ENST00000334344	NM_152641.2	247	Cgt/Tgt	7/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.492495006928753	2		316	356	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231316	46231316	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	94	319	0	ENST00000334344.6:c.1156G>T	p.Asp386Tyr	p.D386Y	ENST00000334344	NM_152641.2	386	Gat/Tat	10/21	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.492495006928753	2		319	364	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427369	49427370	+	stop_gained	Nonsense_Mutation	DNP	GA	GA	AC	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	85	473	0	ENST00000301067.7:c.11118_11119delinsGT	p.Arg3707Ter	p.R3707*	ENST00000301067	NM_003482.3	3706	ctTCga/ctGTga	39/54	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.492495006928753	2		473	345	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427983	49427983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866777837	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	91	388	0	ENST00000301067.7:c.10607G>A	p.Arg3536His	p.R3536H	ENST00000301067	NM_003482.3	3536	cGc/cAc	38/54	1	2	FACETS	0.838	0.748	0.933	0.838	0.748	0.933	CLONAL	1	TRUE	1	0.492495006928753	2		388	441	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436530	49436530	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	107	440	0	ENST00000301067.7:c.5776C>A	p.Leu1926Ile	p.L1926I	ENST00000301067	NM_003482.3	1926	Ctt/Att	26/54	1	2	FACETS	0.957	0.864	1	0.957	0.864	1	CLONAL	1	TRUE	1	0.492495006928753	2		440	454	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864605	57864605	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	119	481	0	ENST00000228682.2:c.2082G>T	p.Glu694Asp	p.E694D	ENST00000228682	NM_005269.2	694	gaG/gaT	12/12	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.492495006928753	2		481	442	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811782	102811782	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	125	498	0	ENST00000307046.8:c.403-1G>T		p.X135_splice	ENST00000307046	NM_001111285.1	135			1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.492495006928753	2		498	480	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891054	112891054	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	136	371	0	ENST00000351677.2:c.388G>T	p.Gly130Ter	p.G130*	ENST00000351677	NM_002834.3	130	Gga/Tga	4/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.492495006928753	2		371	436	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109969	115109969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	88	437	0	ENST00000257566.3:c.1909C>T	p.Arg637Trp	p.R637W	ENST00000257566	NM_016569.3	637	Cgg/Tgg	8/8	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.492495006928753	2		437	339	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117362	115117362	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	122	418	0	ENST00000257566.3:c.812A>T	p.Tyr271Phe	p.Y271F	ENST00000257566	NM_016569.3	271	tAc/tTc	4/8	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.492495006928753	2		418	447	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118938	115118938	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603321	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	116	373	0	ENST00000257566.3:c.403C>T	p.Pro135Ser	p.P135S	ENST00000257566	NM_016569.3	135	Cca/Tca	2/8	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.492495006928753	2		373	424	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120879	115120879	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs978439271	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	76	411	0	ENST00000257566.3:c.127G>A	p.Ala43Thr	p.A43T	ENST00000257566	NM_016569.3	43	Gcg/Acg	1/8	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.492495006928753	2		411	294	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244184	133244184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768004570	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	124	375	1	ENST00000320574.5:c.2224C>T	p.Arg742Cys	p.R742C	ENST00000320574	NM_006231.2	742	Cgt/Tgt	20/49	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.492495006928753	2		376	422	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249242	133249242	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854844	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	111	415	0	ENST00000320574.5:c.1657C>T	p.Arg553Cys	p.R553C	ENST00000320574	NM_006231.2	553	Cgc/Tgc	15/49	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.492495006928753	2		415	365	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249847	133249847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	111	358	0	ENST00000320574.5:c.1376C>T	p.Ser459Phe	p.S459F	ENST00000320574	NM_006231.2	459	tCt/tTt	14/49	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.492495006928753	2		358	377	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557912	21557912	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757472527	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	80	400	0	ENST00000382592.4:c.1933C>T	p.Arg645Trp	p.R645W	ENST00000382592	NM_014572.2	645	Cgg/Tgg	5/8	1	2	FACETS	0.764	0.676	0.858	0.764	0.676	0.858	SUBCLONAL	1	TRUE	1	0.492495006928753	2		400	425	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26970492	26970492	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	44	216	0	ENST00000381527.3:c.860+1G>A		p.X287_splice	ENST00000381527	NM_001260.1	287			1	2	FACETS	0.777	0.658	0.906	0.777	0.658	0.906	CLONAL	1	TRUE	1	0.492495006928753	2		216	230	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609673	28609673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	102	421	0	ENST00000241453.7:c.1556C>T	p.Ser519Phe	p.S519F	ENST00000241453	NM_004119.2	519	tCc/tTc	12/24	1	2	FACETS	0.998	0.899	1	0.998	0.899	1	CLONAL	1	TRUE	1	0.492495006928753	2		421	415	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623630	28623630	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	98	400	0	ENST00000241453.7:c.927G>T	p.Met309Ile	p.M309I	ENST00000241453	NM_004119.2	309	atG/atT	8/24	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.492495006928753	2		400	373	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626755	28626755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750445891	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	92	389	0	ENST00000241453.7:c.541G>A	p.Ala181Thr	p.A181T	ENST00000241453	NM_004119.2	181	Gcc/Acc	5/24	1	2	FACETS	0.83	0.741	0.924	0.83	0.741	0.924	CLONAL	1	TRUE	1	0.492495006928753	2		389	450	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964124	28964124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774943336	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	103	403	0	ENST00000282397.4:c.1778G>A	p.Arg593Gln	p.R593Q	ENST00000282397	NM_002019.4	593	cGg/cAg	13/30	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.492495006928753	2		403	394	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893318	32893318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507603	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	96	393	1	ENST00000380152.3:c.172G>A	p.Glu58Lys	p.E58K	ENST00000380152		58	Gaa/Aaa	3/27	1	2	FACETS	0.997	0.895	1	0.997	0.895	1	CLONAL	1	TRUE	1	0.492495006928753	2		394	391	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910477	32910477	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	83	353	0	ENST00000380152.3:c.1985C>A	p.Ser662Tyr	p.S662Y	ENST00000380152		662	tCt/tAt	11/27	1	2	FACETS	0.939	0.835	1	0.939	0.835	1	CLONAL	1	TRUE	1	0.492495006928753	2		353	359	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911247	32911247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs431825298	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	102	390	0	ENST00000380152.3:c.2755G>A	p.Glu919Lys	p.E919K	ENST00000380152		919	Gaa/Aaa	11/27	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.492495006928753	2		390	354	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915092	32915092	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs587781466	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	97	483	0	ENST00000380152.3:c.6600T>G	p.Phe2200Leu	p.F2200L	ENST00000380152		2200	ttT/ttG	11/27	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.492495006928753	2		483	363	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915177	32915177	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs730881548	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	100	447	0	ENST00000380152.3:c.6685G>T	p.Glu2229Ter	p.E2229*	ENST00000380152		2229	Gaa/Taa	11/27	1	2	FACETS	0.988	0.889	1	0.988	0.889	1	CLONAL	1	TRUE	1	0.492495006928753	2		447	411	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930610	32930610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358973	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	114	347	0	ENST00000380152.3:c.7481G>A	p.Arg2494Gln	p.R2494Q	ENST00000380152		2494	cGa/cAa	15/27	1	2	FACETS	0.96	0.87	1	0.96	0.87	1	CLONAL	1	TRUE	1	0.492495006928753	2		347	482	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133791	41133791	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	73	418	0	ENST00000379561.5:c.1837G>T	p.Asp613Tyr	p.D613Y	ENST00000379561	NM_002015.3	613	Gac/Tac	2/3	1	2	FACETS	0.896	0.789	1	0.896	0.789	1	CLONAL	1	TRUE	1	0.492495006928753	2		418	331	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134288	41134288	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1005190964	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	118	454	0	ENST00000379561.5:c.1340C>T	p.Ser447Leu	p.S447L	ENST00000379561	NM_002015.3	447	tCg/tTg	2/3	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.492495006928753	2		454	428	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134687	41134687	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760747458	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	116	447	1	ENST00000379561.5:c.941G>A	p.Arg314His	p.R314H	ENST00000379561	NM_002015.3	314	cGc/cAc	2/3	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.492495006928753	2		448	430	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030479	49030479	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	70	306	0	ENST00000267163.4:c.1954A>G	p.Lys652Glu	p.K652E	ENST00000267163	NM_000321.2	652	Aaa/Gaa	19/27	1	2	FACETS	0.9	0.791	1	0.9	0.791	1	CLONAL	1	TRUE	1	0.492495006928753	2		306	316	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039144	49039144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764520289	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	54	216	0	ENST00000267163.4:c.2222G>A	p.Arg741His	p.R741H	ENST00000267163	NM_000321.2	741	cGt/cAt	22/27	1	2	FACETS	0.937	0.809	1	0.937	0.809	1	CLONAL	1	TRUE	1	0.492495006928753	2		216	234	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49051498	49051498	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	58	246	0	ENST00000267163.4:c.2671C>A	p.Leu891Ile	p.L891I	ENST00000267163	NM_000321.2	891	Ctc/Atc	26/27	1	2	FACETS	0.969	0.842	1	0.969	0.842	1	CLONAL	1	TRUE	1	0.492495006928753	2		246	243	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281103	49281103	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	100	386	0	ENST00000282018.3:c.150C>A	p.Phe50Leu	p.F50L	ENST00000282018	NM_020377.2	50	ttC/ttA	1/1	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.492495006928753	2		386	369	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73348177	73348177	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	78	317	0	ENST00000377767.4:c.1008G>T	p.Glu336Asp	p.E336D	ENST00000377767	NM_014953.3	336	gaG/gaT	7/21	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.492495006928753	2		317	297	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355057	73355057	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs967179296	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	97	407	0	ENST00000377767.4:c.313G>A	p.Val105Ile	p.V105I	ENST00000377767	NM_014953.3	105	Gta/Ata	2/21	1	2	FACETS	0.954	0.856	1	0.954	0.856	1	CLONAL	1	TRUE	1	0.492495006928753	2		407	413	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514853	103514853	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	115	475	0	ENST00000355739.4:c.1354A>C	p.Asn452His	p.N452H	ENST00000355739	NM_000123.3	452	Aac/Cac	8/15	1	2	FACETS	0.896	0.811	0.986	0.896	0.811	0.986	CLONAL	1	TRUE	1	0.492495006928753	2		475	521	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434593	110434593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	86	442	0	ENST00000375856.3:c.3808C>T	p.Pro1270Ser	p.P1270S	ENST00000375856	NM_003749.2	1270	Ccg/Tcg	1/2	1	2	FACETS	0.891	0.793	0.994	0.891	0.793	0.994	CLONAL	1	TRUE	1	0.492495006928753	2		442	392	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435004	110435004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	88	430	1	ENST00000375856.3:c.3397G>A	p.Ala1133Thr	p.A1133T	ENST00000375856	NM_003749.2	1133	Gcc/Acc	1/2	1	2	FACETS	0.919	0.819	1	0.919	0.819	1	CLONAL	1	TRUE	1	0.492495006928753	2		431	389	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436306	110436306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	69	522	0	ENST00000375856.3:c.2095G>A	p.Ala699Thr	p.A699T	ENST00000375856	NM_003749.2	699	Gcc/Acc	1/2	1	2	FACETS	0.787	0.69	0.891	0.787	0.69	0.891	SUBCLONAL	1	TRUE	1	0.492495006928753	2		522	356	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436921	110436921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	90	458	0	ENST00000375856.3:c.1480G>A	p.Asp494Asn	p.D494N	ENST00000375856	NM_003749.2	494	Gac/Aac	1/2	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.492495006928753	2		458	324	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438223	110438223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	74	308	0	ENST00000375856.3:c.178G>A	p.Ala60Thr	p.A60T	ENST00000375856	NM_003749.2	60	Gcg/Acg	1/2	1	2	FACETS	0.976	0.862	1	0.976	0.862	1	CLONAL	1	TRUE	1	0.492495006928753	2		308	308	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068316	30068316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757547062	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	93	271	1	ENST00000331968.5:c.2083C>T	p.Arg695Trp	p.R695W	ENST00000331968	NM_002742.2	695	Cgg/Tgg	15/18	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.492495006928753	2		272	336	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061333	38061333	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	105	424	0	ENST00000250448.2:c.656G>A	p.Arg219His	p.R219H	ENST00000250448	NM_004496.3	219	cGc/cAc	2/2	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.492495006928753	2		424	386	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68878170	68878170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138522390	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	135	467	0	ENST00000487270.1:c.883G>A	p.Ala295Thr	p.A295T	ENST00000487270	NM_133509.3	295	Gca/Aca	9/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.492495006928753	2		467	441	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609351	81609351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	106	417	0	ENST00000298171.2:c.949G>A	p.Ala317Thr	p.A317T	ENST00000298171	NM_000369.2	317	Gcc/Acc	10/10	1	2	FACETS	0.952	0.859	1	0.952	0.859	1	CLONAL	1	TRUE	1	0.492495006928753	2		417	452	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610156	81610156	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	123	521	0	ENST00000298171.2:c.1754T>G	p.Phe585Cys	p.F585C	ENST00000298171	NM_000369.2	585	tTt/tGt	10/10	1	2	FACETS	0.968	0.88	1	0.968	0.88	1	CLONAL	1	TRUE	1	0.492495006928753	2		521	516	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570403	95570403	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	92	368	0	ENST00000393063.1:c.3330T>G	p.Ile1110Met	p.I1110M	ENST00000393063	NM_030621.3	1110	atT/atG	22/28	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.492495006928753	2		368	364	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95592924	95592924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755944755	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	41	289	0	ENST00000393063.1:c.896C>T	p.Ser299Leu	p.S299L	ENST00000393063	NM_030621.3	299	tCg/tTg	8/28	1	2	FACETS	0.721	0.605	0.847	0.721	0.605	0.847	SUBCLONAL	1	TRUE	1	0.492495006928753	2		289	231	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95592997	95592997	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1555375333	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	79	288	0	ENST00000393063.1:c.823G>T	p.Glu275Ter	p.E275*	ENST00000393063	NM_030621.3	275	Gaa/Taa	8/28	1	2	FACETS	0.999	0.887	1	0.999	0.887	1	CLONAL	1	TRUE	1	0.492495006928753	2		288	321	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95599767	95599767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	97	375	0	ENST00000393063.1:c.29G>A	p.Ser10Asn	p.S10N	ENST00000393063	NM_030621.3	10	aGc/aAc	3/28	1	2	FACETS	0.977	0.878	1	0.977	0.878	1	CLONAL	1	TRUE	1	0.492495006928753	2		375	403	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239232	105239232	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	116	475	0	ENST00000349310.3:c.1155G>T	p.Lys385Asn	p.K385N	ENST00000349310	NM_001014432.1	385	aaG/aaT	12/15	0.156072265087064	6	FACETS	0.982	0.89	1			1	INDETERMINATE	2	TRUE	NA	0.492495006928753	6		475	476	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40678613	40678613	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	146	338	0	ENST00000249776.8:c.355G>T	p.Glu119Ter	p.E119*	ENST00000249776	NM_033286.3	119	Gaa/Taa	3/9	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.492495006928753	2		338	509	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712760	43712760	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	120	464	0	ENST00000382044.4:c.4424C>T	p.Ala1475Val	p.A1475V	ENST00000382044	NM_001141980.1	1475	gCt/gTt	21/28	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.492495006928753	2		464	453	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713311	43713311	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	127	444	0	ENST00000382044.4:c.4162C>A	p.Leu1388Ile	p.L1388I	ENST00000382044	NM_001141980.1	1388	Ctt/Att	20/28	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.492495006928753	2		444	470	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738630	43738630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	102	390	0	ENST00000382044.4:c.2995C>T	p.Pro999Ser	p.P999S	ENST00000382044	NM_001141980.1	999	Cct/Tct	14/28	1	2	FACETS	0.948	0.853	1	0.948	0.853	1	CLONAL	1	TRUE	1	0.492495006928753	2		390	437	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762184	43762184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	105	465	0	ENST00000382044.4:c.1261G>A	p.Glu421Lys	p.E421K	ENST00000382044	NM_001141980.1	421	Gag/Aag	11/28	1	2	FACETS	0.976	0.88	1	0.976	0.88	1	CLONAL	1	TRUE	1	0.492495006928753	2		465	437	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473602	67473602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223735	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	82	330	0	ENST00000327367.4:c.682G>A	p.Glu228Lys	p.E228K	ENST00000327367	NM_005902.3	228	Gag/Aag	6/9	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.492495006928753	2		330	311	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483872	88483872	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	86	374	0	ENST00000360948.2:c.1698G>T	p.Lys566Asn	p.K566N	ENST00000360948	NM_001012338.2	566	aaG/aaT	14/19	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.492495006928753	2		374	346	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576177	88576177	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	91	363	0	ENST00000360948.2:c.1496A>C	p.Asp499Ala	p.D499A	ENST00000360948	NM_001012338.2	499	gAc/gCc	13/19	1	2	FACETS	0.938	0.839	1	0.938	0.839	1	CLONAL	1	TRUE	1	0.492495006928753	2		363	394	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690573	88690573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201576544	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	97	310	0	ENST00000360948.2:c.457C>T	p.Arg153Trp	p.R153W	ENST00000360948	NM_001012338.2	153	Cgg/Tgg	5/19	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.492495006928753	2		310	346	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690630	88690630	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	84	313	0	ENST00000360948.2:c.400C>A	p.Leu134Met	p.L134M	ENST00000360948	NM_001012338.2	134	Ctg/Atg	5/19	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.492495006928753	2		313	320	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304479	91304479	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	75	309	0	ENST00000355112.3:c.1876T>C	p.Tyr626His	p.Y626H	ENST00000355112	NM_000057.2	626	Tat/Cat	7/22	1	2	FACETS	0.967	0.855	1	0.967	0.855	1	CLONAL	1	TRUE	1	0.492495006928753	2		309	315	SUCCESS
BLM	641	MSKCC	GRCh37	15	91341538	91341538	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	80	305	0	ENST00000355112.3:c.3329C>T	p.Thr1110Ile	p.T1110I	ENST00000355112	NM_000057.2	1110	aCt/aTt	17/22	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.492495006928753	2		305	312	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250908	99250908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780055504	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	134	469	0	ENST00000268035.6:c.212G>A	p.Arg71His	p.R71H	ENST00000268035	NM_000875.3	71	cGc/cAc	2/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.492495006928753	2		469	456	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251057	99251057	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555434208	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	110	442	0	ENST00000268035.6:c.361G>A	p.Glu121Lys	p.E121K	ENST00000268035	NM_000875.3	121	Gag/Aag	2/21	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.492495006928753	2		442	424	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434566	99434566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773552392	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	89	434	0	ENST00000268035.6:c.653C>T	p.Thr218Met	p.T218M	ENST00000268035	NM_000875.3	218	aCg/aTg	3/21	1	2	FACETS	0.927	0.827	1	0.927	0.827	1	CLONAL	1	TRUE	1	0.492495006928753	2		434	390	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454583	99454583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543853218	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	132	384	0	ENST00000268035.6:c.1502C>T	p.Ser501Leu	p.S501L	ENST00000268035	NM_000875.3	501	tCg/tTg	7/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.492495006928753	2		384	460	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341245	341245	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1189783498	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	60	260	0	ENST00000262320.3:c.2239G>A	p.Ala747Thr	p.A747T	ENST00000262320	NM_003502.3	747	Gcg/Acg	9/11	1	2	FACETS	0.87	0.756	0.992	0.87	0.756	0.992	CLONAL	1	TRUE	1	0.492495006928753	2		260	280	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2224319	2224319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	98	420	0	ENST00000326181.6:c.1331C>T	p.Ala444Val	p.A444V	ENST00000326181	NM_032271.2	444	gCt/gTt	14/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.492495006928753	2		420	334	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639963	3639963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142008398	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	101	426	0	ENST00000294008.3:c.3676C>T	p.Arg1226Trp	p.R1226W	ENST00000294008	NM_032444.2	1226	Cgg/Tgg	12/15	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.492495006928753	2		426	371	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640124	3640124	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	76	412	0	ENST00000294008.3:c.3515C>A	p.Ser1172Tyr	p.S1172Y	ENST00000294008	NM_032444.2	1172	tCt/tAt	12/15	1	2	FACETS	0.73	0.643	0.822	0.73	0.643	0.822	SUBCLONAL	1	TRUE	1	0.492495006928753	2		412	423	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900633	3900633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780333650	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	125	502	0	ENST00000262367.5:c.463G>A	p.Ala155Thr	p.A155T	ENST00000262367	NM_004380.2	155	Gca/Aca	2/31	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.492495006928753	2		502	434	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862845	9862845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764289741	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	81	444	0	ENST00000330684.3:c.2458G>A	p.Val820Ile	p.V820I	ENST00000330684	NM_001134407.1	820	Gta/Ata	12/13	1	2	FACETS	0.956	0.849	1	0.956	0.849	1	CLONAL	1	TRUE	1	0.492495006928753	2		444	344	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934542	9934542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	101	397	0	ENST00000330684.3:c.1613C>T	p.Ser538Leu	p.S538L	ENST00000330684	NM_001134407.1	538	tCa/tTa	7/13	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.492495006928753	2		397	366	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031990	10031990	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	94	366	0	ENST00000330684.3:c.833C>A	p.Ser278Tyr	p.S278Y	ENST00000330684	NM_001134407.1	278	tCt/tAt	3/13	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.492495006928753	2		366	334	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029291	14029291	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	157	487	0	ENST00000311895.7:c.1502C>A	p.Pro501His	p.P501H	ENST00000311895	NM_005236.2	501	cCt/cAt	8/11	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.492495006928753	2		487	623	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129748	30129748	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	127	414	0	ENST00000263025.4:c.465G>T	p.Lys155Asn	p.K155N	ENST00000263025	NM_002746.2	155	aaG/aaT	3/9	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.492495006928753	2		414	438	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50784019	50784019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	108	407	0	ENST00000398568.2:c.410C>A	p.Ser137Tyr	p.S137Y	ENST00000398568	NM_001042412.1	137	tCt/tAt	3/18	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.492495006928753	2		407	419	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070558	67070558	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	119	332	0	ENST00000412916.2:c.182G>A	p.Gly61Glu	p.G61E	ENST00000412916		61	gGa/gAa	3/6	1	2	FACETS	0.944	0.856	1	0.944	0.856	1	CLONAL	1	TRUE	1	0.492495006928753	2		332	512	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857469	68857469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149127230	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	107	342	0	ENST00000261769.5:c.2104G>A	p.Glu702Lys	p.E702K	ENST00000261769	NM_004360.3	702	Gaa/Aaa	13/16	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.492495006928753	2		342	414	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821815	72821815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770453754	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	123	505	2	ENST00000268489.5:c.10360G>A	p.Asp3454Asn	p.D3454N	ENST00000268489	NM_006885.3	3454	Gac/Aac	10/10	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.492495006928753	2		507	469	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827608	72827608	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	82	387	0	ENST00000268489.5:c.8973G>T	p.Gln2991His	p.Q2991H	ENST00000268489	NM_006885.3	2991	caG/caT	9/10	1	2	FACETS	0.818	0.725	0.916	0.818	0.725	0.916	CLONAL	1	TRUE	1	0.492495006928753	2		387	407	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829676	72829676	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	113	447	0	ENST00000268489.5:c.6905A>T	p.Glu2302Val	p.E2302V	ENST00000268489	NM_006885.3	2302	gAg/gTg	9/10	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.492495006928753	2		447	428	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992163	72992163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564027629	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	125	475	1	ENST00000268489.5:c.1882G>A	p.Glu628Lys	p.E628K	ENST00000268489	NM_006885.3	628	Gag/Aag	2/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.492495006928753	2		476	408	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925108	81925108	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	98	309	0	ENST00000359376.3:c.899G>T	p.Ser300Ile	p.S300I	ENST00000359376	NM_002661.3	300	aGc/aTc	11/33	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.492495006928753	2		309	392	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86545050	86545050	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	71	375	0	ENST00000262426.4:c.875C>T	p.Pro292Leu	p.P292L	ENST00000262426	NM_001451.2	292	cCc/cTc	1/2	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.492495006928753	2		375	286	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86546589	86546589	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	86	408	0	ENST00000262426.4:c.1038C>A	p.Phe346Leu	p.F346L	ENST00000262426	NM_001451.2	346	ttC/ttA	2/2	1	2	FACETS	0.914	0.814	1	0.914	0.814	1	CLONAL	1	TRUE	1	0.492495006928753	2		408	382	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348836	89348836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146474985	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	201	560	0	ENST00000301030.4:c.4114G>A	p.Glu1372Lys	p.E1372K	ENST00000301030	NM_001256183.1	1372	Gag/Aag	9/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.492495006928753	2		560	695	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350738	89350738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139523271	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	123	419	0	ENST00000301030.4:c.2212C>T	p.Arg738Cys	p.R738C	ENST00000301030	NM_001256183.1	738	Cgt/Tgt	9/13	1	2	FACETS	0.968	0.88	1	0.968	0.88	1	CLONAL	1	TRUE	1	0.492495006928753	2		419	516	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217623	7217623	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	151	446	0	ENST00000380728.2:c.304C>T	p.Arg102Ter	p.R102*	ENST00000380728		102	Cga/Tga	4/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.492495006928753	2		446	532	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976582	7976582	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1456307325	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	98	368	0	ENST00000319144.4:c.1810A>G	p.Ile604Val	p.I604V	ENST00000319144	NM_001139.2	604	Att/Gtt	14/15	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.492495006928753	2		368	360	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004945	16004945	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	114	448	0	ENST00000268712.3:c.2309C>A	p.Pro770Gln	p.P770Q	ENST00000268712	NM_006311.3	770	cCa/cAa	20/46	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.492495006928753	2		448	457	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040686	16040686	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	60	282	0	ENST00000268712.3:c.1448A>C	p.Lys483Thr	p.K483T	ENST00000268712	NM_006311.3	483	aAa/aCa	14/46	1	2	FACETS	0.802	0.696	0.915	0.802	0.696	0.915	CLONAL	1	TRUE	1	0.492495006928753	2		282	304	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049724	16049724	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	126	356	0	ENST00000268712.3:c.1048C>T	p.Arg350Ter	p.R350*	ENST00000268712	NM_006311.3	350	Cga/Tga	10/46	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.492495006928753	2		356	478	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552212	29552212	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	78	280	0	ENST00000356175.3:c.1945G>T	p.Glu649Ter	p.E649*	ENST00000356175	NM_000267.3	649	Gaa/Taa	17/57	0.492495006928753	1	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	0	0.492495006928753	1		280	238	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321730	30321730	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	74	272	0	ENST00000322652.5:c.1585C>A	p.Leu529Ile	p.L529I	ENST00000322652	NM_015355.2	529	Ctt/Att	13/16	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.492495006928753	2		272	288	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38792658	38792658	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	131	365	0	ENST00000348513.6:c.358G>A	p.Glu120Lys	p.E120K	ENST00000348513	NM_003079.4	120	Gaa/Aaa	6/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.492495006928753	2		365	485	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354397	40354397	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	117	479	0	ENST00000293328.3:c.2198C>A	p.Ala733Asp	p.A733D	ENST00000293328	NM_012448.3	733	gCt/gAt	18/19	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.492495006928753	2		479	429	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40855768	40855768	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	85	338	0	ENST00000428826.2:c.2088T>G	p.Cys696Trp	p.C696W	ENST00000428826		696	tgT/tgG	19/21	1	2	FACETS	0.967	0.861	1	0.967	0.861	1	CLONAL	1	TRUE	1	0.492495006928753	2		338	357	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40879709	40879709	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs917590262	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	94	320	0	ENST00000428826.2:c.190C>T	p.Arg64Cys	p.R64C	ENST00000428826		64	Cgt/Tgt	4/21	1	2	FACETS	0.986	0.884	1	0.986	0.884	1	CLONAL	1	TRUE	1	0.492495006928753	2		320	387	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40880881	40880881	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	118	389	1	ENST00000428826.2:c.79C>T	p.Arg27Ter	p.R27*	ENST00000428826		27	Cga/Tga	3/21	1	2	FACETS	0.949	0.86	1	0.949	0.86	1	CLONAL	1	TRUE	1	0.492495006928753	2		390	505	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41209086	41209086	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs80357432	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	129	414	0	ENST00000357654.3:c.5260G>T	p.Glu1754Ter	p.E1754*	ENST00000357654	NM_007294.3	1754	Gaa/Taa	19/23	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.492495006928753	2		414	443	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245845	41245845	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	81	383	1	ENST00000357654.3:c.1703C>A	p.Pro568His	p.P568H	ENST00000357654	NM_007294.3	568	cCt/cAt	10/23	1	2	FACETS	0.962	0.854	1	0.962	0.854	1	CLONAL	1	TRUE	1	0.492495006928753	2		384	342	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246170	41246170	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	102	413	0	ENST00000357654.3:c.1378A>G	p.Ile460Val	p.I460V	ENST00000357654	NM_007294.3	460	Ata/Gta	10/23	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.492495006928753	2		413	373	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41276092	41276092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528902306	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	94	300	0	ENST00000357654.3:c.22G>A	p.Val8Ile	p.V8I	ENST00000357654	NM_007294.3	8	Gtt/Att	2/23	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.492495006928753	2		300	338	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805576	46805576	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	93	448	0	ENST00000290295.7:c.380T>C	p.Phe127Ser	p.F127S	ENST00000290295	NM_006361.5	127	tTt/tCt	1/2	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.492495006928753	2		448	326	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696645	47696645	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	112	366	0	ENST00000347630.2:c.303A>C	p.Lys101Asn	p.K101N	ENST00000347630	NM_001007230.1	101	aaA/aaC	5/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.492495006928753	2		366	416	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440904	56440904	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1458799446	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	107	468	1	ENST00000407977.2:c.433C>T	p.Arg145Ter	p.R145*	ENST00000407977		145	Cga/Tga	4/10	1	2	FACETS	0.99	0.894	1	0.99	0.894	1	CLONAL	1	TRUE	1	0.492495006928753	2		469	439	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772411	56772411	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	97	390	0	ENST00000337432.4:c.265G>T	p.Glu89Ter	p.E89*	ENST00000337432	NM_058216.2	89	Gaa/Taa	2/9	1	2	FACETS	0.982	0.882	1	0.982	0.882	1	CLONAL	1	TRUE	1	0.492495006928753	2		390	401	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58725327	58725327	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	54	388	0	ENST00000305921.3:c.901C>T	p.Leu301Phe	p.L301F	ENST00000305921	NM_003620.3	301	Ctt/Ttt	4/6	1	2	FACETS	0.528	0.452	0.611	0.528	0.452	0.611	SUBCLONAL	1	TRUE	1	0.492495006928753	2		388	415	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761384	59761384	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	111	450	0	ENST00000259008.2:c.3023T>C	p.Leu1008Ser	p.L1008S	ENST00000259008	NM_032043.2	1008	tTg/tCg	20/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.492495006928753	2		450	424	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857686	59857686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781321	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	100	320	0	ENST00000259008.2:c.1871C>T	p.Ser624Leu	p.S624L	ENST00000259008	NM_032043.2	624	tCg/tTg	13/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.492495006928753	2		320	363	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861649	59861649	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	79	295	0	ENST00000259008.2:c.1610T>G	p.Leu537Arg	p.L537R	ENST00000259008	NM_032043.2	537	cTt/cGt	11/20	1	2	FACETS	0.999	0.887	1	0.999	0.887	1	CLONAL	1	TRUE	1	0.492495006928753	2		295	321	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554452	63554452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	143	521	0	ENST00000307078.5:c.287G>A	p.Arg96Gln	p.R96Q	ENST00000307078	NM_004655.3	96	cGa/cAa	2/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.492495006928753	2		521	506	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519878	66519878	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	66	300	0	ENST00000358598.2:c.361G>T	p.Asp121Tyr	p.D121Y	ENST00000358598	NM_212471.2	121	Gat/Tat	4/11	1	2	FACETS	0.887	0.777	1	0.887	0.777	1	CLONAL	1	TRUE	1	0.492495006928753	2		300	302	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66523994	66523994	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	78	318	0	ENST00000358598.2:c.722G>T	p.Arg241Ile	p.R241I	ENST00000358598	NM_212471.2	241	aGa/aTa	8/11	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.492495006928753	2		318	294	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78704435	78704435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	122	432	0	ENST00000306801.3:c.583G>A	p.Asp195Asn	p.D195N	ENST00000306801	NM_020761.2	195	Gac/Aac	5/34	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.492495006928753	2		432	435	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727862	78727862	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781427409	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	109	365	0	ENST00000306801.3:c.707C>T	p.Ser236Leu	p.S236L	ENST00000306801	NM_020761.2	236	tCg/tTg	6/34	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.492495006928753	2		365	373	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78921030	78921030	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	131	352	0	ENST00000306801.3:c.3144T>G	p.Phe1048Leu	p.F1048L	ENST00000306801	NM_020761.2	1048	ttT/ttG	27/34	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.492495006928753	2		352	412	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78921082	78921082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1434467586	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	129	367	0	ENST00000306801.3:c.3196C>T	p.Arg1066Trp	p.R1066W	ENST00000306801	NM_020761.2	1066	Cgg/Tgg	27/34	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.492495006928753	2		367	404	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743085	743085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	96	329	0	ENST00000314574.4:c.893G>A	p.Gly298Glu	p.G298E	ENST00000314574	NM_005433.3	298	gGa/gAa	8/12	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.492495006928753	2		329	376	SUCCESS
YES1	7525	MSKCC	GRCh37	18	751708	751708	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	71	216	0	ENST00000314574.4:c.368A>C	p.Asn123Thr	p.N123T	ENST00000314574	NM_005433.3	123	aAt/aCt	3/12	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.492495006928753	2		216	269	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756611	756611	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	108	427	0	ENST00000314574.4:c.217G>T	p.Gly73Cys	p.G73C	ENST00000314574	NM_005433.3	73	Ggt/Tgt	2/12	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.492495006928753	2		427	433	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39618751	39618751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752104656	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	55	257	0	ENST00000262039.4:c.1975C>T	p.Arg659Trp	p.R659W	ENST00000262039	NM_002647.2	659	Cgg/Tgg	18/25	1	2	FACETS	0.837	0.722	0.959	0.837	0.722	0.959	CLONAL	1	TRUE	1	0.492495006928753	2		257	267	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422962	45422962	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	148	438	0	ENST00000262160.6:c.166G>T	p.Gly56Ter	p.G56*	ENST00000262160	NM_005901.5	56	Gga/Tga	2/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.492495006928753	2		438	501	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45423015	45423015	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	154	478	0	ENST00000262160.6:c.113A>G	p.Glu38Gly	p.E38G	ENST00000262160	NM_005901.5	38	gAa/gGa	2/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.492495006928753	2		478	583	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575206	48575206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	67	267	0	ENST00000342988.3:c.400G>A	p.Glu134Lys	p.E134K	ENST00000342988	NM_005359.5	134	Gaa/Aaa	3/12	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.492495006928753	2		267	272	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591858	48591858	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	136	450	0	ENST00000342988.3:c.1021G>T	p.Val341Phe	p.V341F	ENST00000342988	NM_005359.5	341	Gtt/Ttt	9/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.492495006928753	2		450	475	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414818	56414818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	92	434	0	ENST00000348428.3:c.2219C>T	p.Ser740Phe	p.S740F	ENST00000348428	NM_006785.3	740	tCt/tTt	17/17	1	2	FACETS	0.983	0.88	1	0.983	0.88	1	CLONAL	1	TRUE	1	0.492495006928753	2		434	380	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60795942	60795942	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	120	463	0	ENST00000333681.4:c.636C>A	p.Phe212Leu	p.F212L	ENST00000333681		212	ttC/ttA	3/3	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.492495006928753	2		463	461	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221306	1221306	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	103	404	1	ENST00000326873.7:c.829G>A	p.Asp277Asn	p.D277N	ENST00000326873	NM_000455.4	277	Gac/Aac	6/10	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.492495006928753	2		405	394	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2225428	2225428	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	100	351	0	ENST00000398665.3:c.3638C>A	p.Ser1213Tyr	p.S1213Y	ENST00000398665	NM_032482.2	1213	tCt/tAt	26/28	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.492495006928753	2		351	354	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210756	5210756	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	94	473	0	ENST00000357368.4:c.5295G>T	p.Trp1765Cys	p.W1765C	ENST00000357368	NM_002850.3	1765	tgG/tgT	34/38	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.492495006928753	2		473	328	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244386	5244386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1383575470	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	132	476	0	ENST00000357368.4:c.1096G>A	p.Glu366Lys	p.E366K	ENST00000357368	NM_002850.3	366	Gaa/Aaa	11/38	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.492495006928753	2		476	487	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267491	7267491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	140	434	0	ENST00000302850.5:c.517G>A	p.Val173Met	p.V173M	ENST00000302850	NM_000208.2	173	Gtg/Atg	2/22	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.492495006928753	2		434	503	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248598	10248598	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	81	403	0	ENST00000340748.4:c.4155G>T	p.Glu1385Asp	p.E1385D	ENST00000340748		1385	gaG/gaT	35/40	1	2	FACETS	0.924	0.82	1	0.924	0.82	1	CLONAL	1	TRUE	1	0.492495006928753	2		403	356	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030290	11030290	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	122	372	0	ENST00000327064.4:c.1040T>C	p.Ile347Thr	p.I347T	ENST00000327064	NM_199141.1	347	aTc/aCc	9/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.492495006928753	2		372	382	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101932	11101932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	139	415	0	ENST00000358026.2:c.1352G>A	p.Arg451His	p.R451H	ENST00000358026	NM_001128849.1	451	cGc/cAc	8/36	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.492495006928753	2		415	487	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11151989	11151989	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752264295	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	121	390	0	ENST00000358026.2:c.4273G>A	p.Glu1425Lys	p.E1425K	ENST00000358026	NM_001128849.1	1425	Gag/Aag	31/36	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.492495006928753	2		390	417	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627336	14627336	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	139	520	0	ENST00000254322.2:c.734A>C	p.Asn245Thr	p.N245T	ENST00000254322	NM_006145.1	245	aAt/aCt	2/3	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.492495006928753	2		520	556	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629028	14629028	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	83	388	0	ENST00000254322.2:c.134T>G	p.Phe45Cys	p.F45C	ENST00000254322	NM_006145.1	45	tTc/tGc	1/3	1	2	FACETS	0.977	0.869	1	0.977	0.869	1	CLONAL	1	TRUE	1	0.492495006928753	2		388	345	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285027	15285027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777398556	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	75	400	0	ENST00000263388.2:c.4588G>A	p.Asp1530Asn	p.D1530N	ENST00000263388	NM_000435.2	1530	Gac/Aac	25/33	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.492495006928753	2		400	276	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288819	15288819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1392500489	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	71	255	0	ENST00000263388.2:c.3920C>T	p.Thr1307Met	p.T1307M	ENST00000263388	NM_000435.2	1307	aCg/aTg	24/33	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.492495006928753	2		255	226	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292577	15292577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	117	338	0	ENST00000263388.2:c.2602G>A	p.Val868Met	p.V868M	ENST00000263388	NM_000435.2	868	Gtg/Atg	17/33	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.492495006928753	2		338	402	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297721	15297721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377689004	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	94	379	0	ENST00000263388.2:c.1919G>A	p.Arg640His	p.R640H	ENST00000263388	NM_000435.2	640	cGc/cAc	12/33	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.492495006928753	2		379	381	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384943	17384943	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1230353465	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	107	454	0	ENST00000359435.4:c.493G>A	p.Glu165Lys	p.E165K	ENST00000359435	NM_001033549.1	165	Gag/Aag	5/9	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.492495006928753	2		454	415	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17941329	17941329	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	97	382	0	ENST00000458235.1:c.3079A>G	p.Ser1027Gly	p.S1027G	ENST00000458235	NM_000215.3	1027	Agc/Ggc	22/24	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.492495006928753	2		382	389	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18963845	18963845	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	102	374	0	ENST00000262803.5:c.1022G>T	p.Arg341Ile	p.R341I	ENST00000262803	NM_002911.3	341	aGa/aTa	7/24	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.492495006928753	2		374	409	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303644	30303644	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778672861	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	94	423	0	ENST00000262643.3:c.72C>A	p.Phe24Leu	p.F24L	ENST00000262643	NM_001238.2	24	ttC/ttA	3/12	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.492495006928753	2		423	375	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210710	36210710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745637683	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	117	359	0	ENST00000222270.7:c.461G>A	p.Arg154His	p.R154H	ENST00000222270	NM_014727.1	154	cGc/cAc	3/37	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.492495006928753	2		359	400	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214807	36214807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	63	308	0	ENST00000222270.7:c.3233G>A	p.Arg1078His	p.R1078H	ENST00000222270	NM_014727.1	1078	cGc/cAc	8/37	1	2	FACETS	0.995	0.871	1	0.995	0.871	1	CLONAL	1	TRUE	1	0.492495006928753	2		308	257	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214849	36214849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775845065	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	92	348	0	ENST00000222270.7:c.3275C>T	p.Ser1092Leu	p.S1092L	ENST00000222270	NM_014727.1	1092	tCg/tTg	8/37	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.492495006928753	2		348	326	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216678	36216678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	88	431	0	ENST00000222270.7:c.3844C>T	p.Pro1282Ser	p.P1282S	ENST00000222270	NM_014727.1	1282	Ccc/Tcc	13/37	1	2	FACETS	0.971	0.867	1	0.971	0.867	1	CLONAL	1	TRUE	1	0.492495006928753	2		431	368	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218375	36218375	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	80	372	0	ENST00000222270.7:c.4154C>T	p.Ser1385Leu	p.S1385L	ENST00000222270	NM_014727.1	1385	tCg/tTg	16/37	1	2	FACETS	0.866	0.768	0.971	0.866	0.768	0.971	CLONAL	1	TRUE	1	0.492495006928753	2		372	375	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221323	36221323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	135	553	0	ENST00000222270.7:c.5157C>A	p.Phe1719Leu	p.F1719L	ENST00000222270	NM_014727.1	1719	ttC/ttA	24/37	1	2	FACETS	0.991	0.905	1	0.991	0.905	1	CLONAL	1	TRUE	1	0.492495006928753	2		553	553	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221672	36221672	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	92	485	0	ENST00000222270.7:c.5341C>A	p.Leu1781Met	p.L1781M	ENST00000222270	NM_014727.1	1781	Ctg/Atg	26/37	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.492495006928753	2		485	371	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222961	36222961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	107	488	0	ENST00000222270.7:c.5590C>T	p.Arg1864Ter	p.R1864*	ENST00000222270	NM_014727.1	1864	Cga/Tga	27/37	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.492495006928753	2		488	417	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758301	41758301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1352416510	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	86	323	0	ENST00000301178.4:c.1757C>T	p.Ala586Val	p.A586V	ENST00000301178	NM_021913.4	586	gCg/gTg	15/20	1	2	FACETS	0.936	0.834	1	0.936	0.834	1	CLONAL	1	TRUE	1	0.492495006928753	2		323	373	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753233	42753233	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377467874	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	94	552	0	ENST00000222329.4:c.1031G>A	p.Arg344His	p.R344H	ENST00000222329	NM_006494.2	344	cGc/cAc	4/4	1	2	FACETS	0.856	0.766	0.951	0.856	0.766	0.951	CLONAL	1	TRUE	1	0.492495006928753	2		552	446	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422257	47422257	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1324454897	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	105	445	0	ENST00000404338.3:c.325C>T	p.Arg109Ter	p.R109*	ENST00000404338	NM_004491.4	109	Cga/Tga	1/6	1	2	FACETS	0.98	0.884	1	0.98	0.884	1	CLONAL	1	TRUE	1	0.492495006928753	2		445	435	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910306	50910306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1341055535	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	95	375	1	ENST00000440232.2:c.1561C>T	p.Arg521Trp	p.R521W	ENST00000440232	NM_002691.3	521	Cgg/Tgg	13/27	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.492495006928753	2		376	347	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714594	52714594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	104	411	0	ENST00000322088.6:c.352G>A	p.Glu118Lys	p.E118K	ENST00000322088	NM_014225.5	118	Gag/Aag	4/15	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.492495006928753	2		411	393	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443627	29443627	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	120	443	0	ENST00000389048.3:c.3590A>C	p.Glu1197Ala	p.E1197A	ENST00000389048	NM_004304.4	1197	gAg/gCg	23/29	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.492495006928753	2		443	455	SUCCESS
ALK	238	MSKCC	GRCh37	2	29541237	29541237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	127	388	0	ENST00000389048.3:c.1580C>T	p.Pro527Leu	p.P527L	ENST00000389048	NM_004304.4	527	cCc/cTc	8/29	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.492495006928753	2		388	469	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754780	29754780	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs766100418	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	114	385	0	ENST00000389048.3:c.1154+1G>A		p.X385_splice	ENST00000389048	NM_004304.4	385			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.492495006928753	2		385	412	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754859	29754859	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	113	424	0	ENST00000389048.3:c.1076G>T	p.Gly359Val	p.G359V	ENST00000389048	NM_004304.4	359	gGa/gTa	4/29	1	2	FACETS	0.989	0.895	1	0.989	0.895	1	CLONAL	1	TRUE	1	0.492495006928753	2		424	464	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39237759	39237759	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	98	344	0	ENST00000402219.2:c.2476C>T	p.Arg826Ter	p.R826*	ENST00000402219	NM_005633.3	826	Cga/Tga	15/23	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.492495006928753	2		344	385	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607676	46607676	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	104	432	0	ENST00000263734.3:c.1865G>A	p.Gly622Asp	p.G622D	ENST00000263734	NM_001430.4	622	gGc/gAc	12/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.492495006928753	2		432	376	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672689	47672689	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	101	255	0	ENST00000233146.2:c.1279A>C	p.Lys427Gln	p.K427Q	ENST00000233146	NM_000251.2	427	Aaa/Caa	8/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.492495006928753	2		255	328	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702296	47702296	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1361816581	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	114	368	0	ENST00000233146.2:c.1892G>T	p.Arg631Ile	p.R631I	ENST00000233146	NM_000251.2	631	aGa/aTa	12/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.492495006928753	2		368	415	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705654	47705654	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	72	312	0	ENST00000233146.2:c.2454G>T	p.Lys818Asn	p.K818N	ENST00000233146	NM_000251.2	818	aaG/aaT	14/16	1	2	FACETS	0.848	0.746	0.956	0.848	0.746	0.956	CLONAL	1	TRUE	1	0.492495006928753	2		312	345	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707951	47707951	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63749830	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	95	347	0	ENST00000233146.2:c.2575G>T	p.Glu859Ter	p.E859*	ENST00000233146	NM_000251.2	859	Gaa/Taa	15/16	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.492495006928753	2		347	357	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023098	48023098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	111	407	0	ENST00000234420.5:c.523G>A	p.Ala175Thr	p.A175T	ENST00000234420	NM_000179.2	175	Gca/Aca	3/10	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.492495006928753	2		407	433	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026567	48026567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773226008	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	127	469	1	ENST00000234420.5:c.1445G>A	p.Arg482Gln	p.R482Q	ENST00000234420	NM_000179.2	482	cGa/cAa	4/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.492495006928753	2		470	444	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027678	48027678	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	102	392	0	ENST00000234420.5:c.2556G>T	p.Lys852Asn	p.K852N	ENST00000234420	NM_000179.2	852	aaG/aaT	4/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.492495006928753	2		392	386	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118840	61118840	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs201045327	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	98	397	0	ENST00000295025.8:c.33G>T	p.Glu11Asp	p.E11D	ENST00000295025	NM_002908.2	11	gaG/gaT	2/11	1	2	FACETS	0.856	0.767	0.949	0.856	0.767	0.949	CLONAL	1	TRUE	1	0.492495006928753	2		397	465	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719857	61719857	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	62	337	0	ENST00000401558.2:c.1411G>T	p.Asp471Tyr	p.D471Y	ENST00000401558	NM_003400.3	471	Gat/Tat	14/25	1	2	FACETS	0.836	0.728	0.952	0.836	0.728	0.952	CLONAL	1	TRUE	1	0.492495006928753	2		337	301	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631132	67631132	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	95	415	0	ENST00000272342.5:c.1318G>T	p.Asp440Tyr	p.D440Y	ENST00000272342	NM_019002.3	440	Gat/Tat	5/6	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.492495006928753	2		415	343	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919743	96919743	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753594901	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	83	417	2	ENST00000258439.3:c.520G>A	p.Ala174Thr	p.A174T	ENST00000258439	NM_001193304.2	174	Gcc/Acc	4/4	1	2	FACETS	0.96	0.854	1	0.96	0.854	1	CLONAL	1	TRUE	1	0.492495006928753	2		419	351	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99175946	99175946	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	98	314	0	ENST00000074304.5:c.1858G>T	p.Glu620Ter	p.E620*	ENST00000074304	NM_001134224.1	620	Gag/Tag	18/26	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.492495006928753	2		314	368	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185068	99185068	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143132498	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	84	365	0	ENST00000074304.5:c.2470G>A	p.Val824Met	p.V824M	ENST00000074304	NM_001134224.1	824	Gtg/Atg	23/26	1	2	FACETS	0.846	0.752	0.946	0.846	0.752	0.946	CLONAL	1	TRUE	1	0.492495006928753	2		365	403	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921785	111921785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758817904	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	108	382	0	ENST00000393256.3:c.574C>T	p.Arg192Cys	p.R192C	ENST00000393256	NM_006538.4	192	Cgc/Tgc	4/4	0.185945232014562	3	FACETS	1	0.98	1	0.668	0.604	0.735	INDETERMINATE	1	TRUE	1	0.492495006928753	3		382	409	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047078	128047078	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	111	357	0	ENST00000285398.2:c.658-1G>T		p.X220_splice	ENST00000285398	NM_000122.1	220			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.492495006928753	2		357	369	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630626	158630626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912678	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	101	396	0	ENST00000263640.3:c.617G>A	p.Arg206His	p.R206H	ENST00000263640	NM_001105.4	206	cGc/cAc	6/11	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.492495006928753	2		396	408	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660640	190660640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778185859	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	82	403	0	ENST00000441310.2:c.278G>A	p.Arg93His	p.R93H	ENST00000441310	NM_000534.4	93	cGt/cAt	3/13	1	2	FACETS	0.83	0.736	0.93	0.83	0.736	0.93	CLONAL	1	TRUE	1	0.492495006928753	2		403	401	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257052	198257052	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1352116876	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	87	308	1	ENST00000335508.6:c.3890G>A	p.Arg1297His	p.R1297H	ENST00000335508	NM_012433.2	1297	cGt/cAt	25/25	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.492495006928753	2		309	327	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198260920	198260920	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	89	383	0	ENST00000335508.6:c.3399G>T	p.Met1133Ile	p.M1133I	ENST00000335508	NM_012433.2	1133	atG/atT	23/25	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.492495006928753	2		383	334	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266166	198266166	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	91	344	0	ENST00000335508.6:c.2454C>A	p.Phe818Leu	p.F818L	ENST00000335508	NM_012433.2	818	ttC/ttA	17/25	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.492495006928753	2		344	326	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273266	198273266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	121	575	0	ENST00000335508.6:c.944G>A	p.Arg315Gln	p.R315Q	ENST00000335508	NM_012433.2	315	cGa/cAa	8/25	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.492495006928753	2		575	476	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274706	198274706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	95	342	0	ENST00000335508.6:c.692G>A	p.Arg231Lys	p.R231K	ENST00000335508	NM_012433.2	231	aGa/aAa	7/25	1	2	FACETS	0.984	0.883	1	0.984	0.883	1	CLONAL	1	TRUE	1	0.492495006928753	2		342	392	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131243	202131243	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	111	387	0	ENST00000358485.4:c.211G>T	p.Glu71Ter	p.E71*	ENST00000358485	NM_001080125.1	71	Gaa/Taa	2/9	1	2	FACETS	0.984	0.89	1	0.984	0.89	1	CLONAL	1	TRUE	1	0.492495006928753	2		387	458	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736158	204736158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs963824682	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	139	390	0	ENST00000302823.3:c.515C>T	p.Ser172Leu	p.S172L	ENST00000302823	NM_005214.4	172	tCg/tTg	3/4	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.492495006928753	2		390	483	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113208	209113208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	126	494	0	ENST00000345146.2:c.299G>A	p.Arg100Gln	p.R100Q	ENST00000345146	NM_005896.2	100	cGa/cAa	4/10	1	2	FACETS	0.951	0.865	1	0.951	0.865	1	CLONAL	1	TRUE	1	0.492495006928753	2		494	538	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593588	215593588	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs878854006	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	122	448	0	ENST00000260947.4:c.2146A>G	p.Thr716Ala	p.T716A	ENST00000260947	NM_000465.2	716	Acc/Gcc	11/11	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.492495006928753	2		448	490	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794793	242794793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759141096	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	74	375	0	ENST00000334409.5:c.416G>A	p.Arg139Gln	p.R139Q	ENST00000334409	NM_005018.2	139	cGg/cAg	2/5	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.492495006928753	2		375	282	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561352	9561352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773981325	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	123	328	0	ENST00000353224.5:c.430G>A	p.Glu144Lys	p.E144K	ENST00000353224	NM_177990.2	144	Gaa/Aaa	4/10	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.492495006928753	2		328	498	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016131	31016131	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	107	448	2	ENST00000375687.4:c.377C>A	p.Ser126Tyr	p.S126Y	ENST00000375687	NM_015338.5	126	tCt/tAt	6/13	1	2	FACETS	0.947	0.854	1	0.947	0.854	1	CLONAL	1	TRUE	1	0.492495006928753	2		450	459	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024342	31024342	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	128	425	0	ENST00000375687.4:c.3827C>A	p.Ser1276Tyr	p.S1276Y	ENST00000375687	NM_015338.5	1276	tCt/tAt	13/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.492495006928753	2		425	388	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376780	31376780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1422196524	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	86	385	2	ENST00000328111.2:c.775C>T	p.Arg259Trp	p.R259W	ENST00000328111	NM_006892.3	259	Cgg/Tgg	7/23	1	2	FACETS	0.995	0.888	1	0.995	0.888	1	CLONAL	1	TRUE	1	0.492495006928753	2		387	351	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389085	31389085	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	112	386	0	ENST00000328111.2:c.1998G>T	p.Glu666Asp	p.E666D	ENST00000328111	NM_006892.3	666	gaG/gaT	19/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.492495006928753	2		386	398	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012599	36012599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	57	349	0	ENST00000358208.4:c.43C>T	p.Arg15Cys	p.R15C	ENST00000358208		15	Cgc/Tgc	2/12	1	2	FACETS	0.877	0.759	1	0.877	0.759	1	CLONAL	1	TRUE	1	0.492495006928753	2		349	264	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101170	41101170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41279256	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	91	428	0	ENST00000373198.4:c.1186G>A	p.Val396Ile	p.V396I	ENST00000373198	NM_133170.3	396	Gta/Ata	8/32	1	2	FACETS	0.993	0.889	1	0.993	0.889	1	CLONAL	1	TRUE	1	0.492495006928753	2		428	372	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264072	46264072	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	96	312	0	ENST00000371998.3:c.1119G>T	p.Gln373His	p.Q373H	ENST00000371998		373	caG/caT	11/23	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.492495006928753	2		312	354	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948538	54948538	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	88	340	0	ENST00000312783.6:c.780G>T	p.Glu260Asp	p.E260D	ENST00000312783	NM_198436.1	260	gaG/gaT	8/10	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.492495006928753	2		340	335	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252871	36252871	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	116	333	0	ENST00000300305.3:c.491T>C	p.Val164Ala	p.V164A	ENST00000300305		164	gTc/gCc	4/8	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.492495006928753	2		333	443	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36265261	36265261	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	66	211	0	ENST00000300305.3:c.59-1G>T		p.X20_splice	ENST00000300305		20			1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.492495006928753	2		211	242	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288474	21288474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749456958	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	132	455	1	ENST00000354336.3:c.719C>T	p.Ala240Val	p.A240V	ENST00000354336	NM_005207.3	240	gCg/gTg	2/3	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.492495006928753	2		456	521	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21342366	21342366	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	94	373	0	ENST00000215739.8:c.468G>T	p.Lys156Asn	p.K156N	ENST00000215739	NM_006767.3	156	aaG/aaT	5/21	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.492495006928753	2		373	380	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21342407	21342407	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs781431741	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	71	342	0	ENST00000215739.8:c.509G>A	p.Arg170Gln	p.R170Q	ENST00000215739	NM_006767.3	170	cGg/cAg	5/21	1	2	FACETS	0.836	0.734	0.943	0.836	0.734	0.943	CLONAL	1	TRUE	1	0.492495006928753	2		342	345	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121252	29121252	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	87	399	0	ENST00000328354.6:c.423G>T	p.Lys141Asn	p.K141N	ENST00000328354	NM_007194.3	141	aaG/aaT	3/15	1	2	FACETS	0.913	0.814	1	0.913	0.814	1	CLONAL	1	TRUE	1	0.492495006928753	2		399	387	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130410	29130410	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1456691189	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	140	477	0	ENST00000328354.6:c.300G>T	p.Gln100His	p.Q100H	ENST00000328354	NM_007194.3	100	caG/caT	2/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.492495006928753	2		477	492	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536164	41536164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750740148	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	81	338	0	ENST00000263253.7:c.1781C>T	p.Thr594Met	p.T594M	ENST00000263253	NM_001429.3	594	aCg/aTg	9/31	1	2	FACETS	0.808	0.716	0.906	0.808	0.716	0.906	CLONAL	1	TRUE	1	0.492495006928753	2		338	407	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573881	41573881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752770043	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	123	527	1	ENST00000263253.7:c.6166C>T	p.Arg2056Trp	p.R2056W	ENST00000263253	NM_001429.3	2056	Cgg/Tgg	31/31	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.492495006928753	2		528	455	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183842	10183842	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	95	372	0	ENST00000256474.2:c.311G>A	p.Gly104Asp	p.G104D	ENST00000256474	NM_000551.3	104	gGc/gAc	1/3	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.492495006928753	2		372	327	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421274	12421274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149324518	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	159	457	0	ENST00000287820.6:c.154G>A	p.Val52Ile	p.V52I	ENST00000287820	NM_015869.4	52	Gta/Ata	2/7	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.492495006928753	2		457	561	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447395	12447395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	130	392	0	ENST00000287820.6:c.634C>T	p.Arg212Trp	p.R212W	ENST00000287820	NM_015869.4	212	Cgg/Tgg	5/7	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.492495006928753	2		392	458	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626703	12626703	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756160717	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	123	505	0	ENST00000251849.4:c.1586C>T	p.Ser529Leu	p.S529L	ENST00000251849	NM_002880.3	529	tCg/tTg	15/17	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.492495006928753	2		505	470	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627290	12627290	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	91	332	0	ENST00000251849.4:c.1426C>A	p.Leu476Ile	p.L476I	ENST00000251849	NM_002880.3	476	Ctc/Atc	14/17	1	2	FACETS	0.955	0.854	1	0.955	0.854	1	CLONAL	1	TRUE	1	0.492495006928753	2		332	387	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641297	12641297	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	87	300	0	ENST00000251849.4:c.1001G>T	p.Gly334Val	p.G334V	ENST00000251849	NM_002880.3	334	gGa/gTa	10/17	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.492495006928753	2		300	313	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37059010	37059010	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	83	377	0	ENST00000231790.2:c.804A>C	p.Glu268Asp	p.E268D	ENST00000231790	NM_000249.3	268	gaA/gaC	10/19	1	2	FACETS	0.82	0.728	0.918	0.82	0.728	0.918	CLONAL	1	TRUE	1	0.492495006928753	2		377	411	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070395	37070395	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	110	375	0	ENST00000231790.2:c.1530G>T	p.Gln510His	p.Q510H	ENST00000231790	NM_000249.3	510	caG/caT	13/19	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.492495006928753	2		375	421	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275649	41275649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	126	390	0	ENST00000349496.5:c.1544G>A	p.Arg515Gln	p.R515Q	ENST00000349496	NM_001904.3	515	cGa/cAa	10/15	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.492495006928753	2		390	495	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277839	41277839	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	100	376	0	ENST00000349496.5:c.1804-1G>T		p.X602_splice	ENST00000349496	NM_001904.3	602			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.492495006928753	2		376	374	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278106	41278106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	119	448	0	ENST00000349496.5:c.1982G>A	p.Arg661Gln	p.R661Q	ENST00000349496	NM_001904.3	661	cGa/cAa	13/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.492495006928753	2		448	439	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098948	47098948	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs967982470	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	128	432	0	ENST00000409792.3:c.6326G>A	p.Arg2109Gln	p.R2109Q	ENST00000409792	NM_014159.6	2109	cGa/cAa	15/21	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.492495006928753	2		432	451	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47108598	47108598	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	78	233	0	ENST00000409792.3:c.6071G>A	p.Arg2024Gln	p.R2024Q	ENST00000409792	NM_014159.6	2024	cGa/cAa	13/21	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.492495006928753	2		233	299	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139464	47139464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	141	308	0	ENST00000409792.3:c.5123G>A	p.Arg1708Gln	p.R1708Q	ENST00000409792	NM_014159.6	1708	cGa/cAa	9/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.492495006928753	2		308	508	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144907	47144907	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	81	325	0	ENST00000409792.3:c.4846G>T	p.Asp1616Tyr	p.D1616Y	ENST00000409792	NM_014159.6	1616	Gat/Tat	7/21	1	2	FACETS	0.976	0.867	1	0.976	0.867	1	CLONAL	1	TRUE	1	0.492495006928753	2		325	337	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162639	47162639	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	108	397	0	ENST00000409792.3:c.3487C>A	p.Pro1163Thr	p.P1163T	ENST00000409792	NM_014159.6	1163	Cct/Act	3/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.492495006928753	2		397	379	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165095	47165095	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760794263	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	92	403	0	ENST00000409792.3:c.1031G>A	p.Ser344Asn	p.S344N	ENST00000409792	NM_014159.6	344	aGc/aAc	3/21	1	2	FACETS	0.996	0.892	1	0.996	0.892	1	CLONAL	1	TRUE	1	0.492495006928753	2		403	375	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400006	49400006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	97	367	0	ENST00000418115.1:c.331C>T	p.Pro111Ser	p.P111S	ENST00000418115	NM_001664.2	111	Ccc/Tcc	4/5	1	2	FACETS	0.992	0.891	1	0.992	0.891	1	CLONAL	1	TRUE	1	0.492495006928753	2		367	397	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933408	49933408	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	108	501	0	ENST00000296474.3:c.2782G>T	p.Gly928Cys	p.G928C	ENST00000296474	NM_002447.2	928	Ggt/Tgt	11/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.492495006928753	2		501	389	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933993	49933993	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	99	414	0	ENST00000296474.3:c.2419C>A	p.Leu807Ile	p.L807I	ENST00000296474	NM_002447.2	807	Ctt/Att	9/20	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.492495006928753	2		414	394	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436392	52436392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	95	409	0	ENST00000460680.1:c.2102G>A	p.Arg701His	p.R701H	ENST00000460680	NM_004656.3	701	cGc/cAc	17/17	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.492495006928753	2		409	307	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443599	52443599	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	105	408	0	ENST00000460680.1:c.93G>T	p.Glu31Asp	p.E31D	ENST00000460680	NM_004656.3	31	gaG/gaT	3/17	1	2	FACETS	0.886	0.798	0.979	0.886	0.798	0.979	CLONAL	1	TRUE	1	0.492495006928753	2		408	481	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702632	52702632	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779102269	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	74	301	0	ENST00000394830.3:c.266C>A	p.Ser89Tyr	p.S89Y	ENST00000394830	NM_018313.4	89	tCt/tAt	4/30	1	2	FACETS	0.995	0.88	1	0.995	0.88	1	CLONAL	1	TRUE	1	0.492495006928753	2		301	302	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712529	52712529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	143	363	0	ENST00000394830.3:c.223G>A	p.Ala75Thr	p.A75T	ENST00000394830	NM_018313.4	75	Gca/Aca	3/30	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.492495006928753	2		363	479	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981197	63981197	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	128	474	0	ENST00000398590.3:c.1699C>T	p.Pro567Ser	p.P567S	ENST00000398590	NM_001177387.1	567	Ccc/Tcc	12/14	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.492495006928753	2		474	488	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981906	63981906	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	127	532	0	ENST00000398590.3:c.2408C>A	p.Ser803Tyr	p.S803Y	ENST00000398590	NM_001177387.1	803	tCt/tAt	12/14	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.492495006928753	2		532	490	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008512	70008512	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	138	451	0	ENST00000394351.3:c.799C>A	p.Leu267Ile	p.L267I	ENST00000394351	NM_000248.3	267	Ctt/Att	8/9	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.492495006928753	2		451	540	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015081	71015081	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	75	398	0	ENST00000318789.4:c.1849G>T	p.Glu617Ter	p.E617*	ENST00000318789	NM_032682.5	617	Gag/Tag	20/21	1	2	FACETS	0.699	0.615	0.788	0.699	0.615	0.788	SUBCLONAL	1	TRUE	1	0.492495006928753	2		398	436	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71050200	71050200	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	102	337	0	ENST00000318789.4:c.985A>G	p.Ser329Gly	p.S329G	ENST00000318789	NM_032682.5	329	Agt/Ggt	13/21	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.492495006928753	2		337	401	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73113297	73113297	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	75	271	0	ENST00000356692.5:c.638G>T	p.Ser213Ile	p.S213I	ENST00000356692		213	aGt/aTt	7/9	1	2	FACETS	0.917	0.81	1	0.917	0.81	1	CLONAL	1	TRUE	1	0.492495006928753	2		271	332	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114065	73114065	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	67	244	0	ENST00000356692.5:c.701A>T	p.Asp234Val	p.D234V	ENST00000356692		234	gAt/gTt	8/9	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.492495006928753	2		244	237	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391027	89391027	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	88	388	0	ENST00000336596.2:c.1093A>C	p.Lys365Gln	p.K365Q	ENST00000336596	NM_005233.5	365	Aaa/Caa	5/17	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.492495006928753	2		388	339	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462393	89462393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	66	314	0	ENST00000336596.2:c.1865C>T	p.Ser622Phe	p.S622F	ENST00000336596	NM_005233.5	622	tCc/tTc	10/17	1	2	FACETS	0.873	0.764	0.989	0.873	0.764	0.989	CLONAL	1	TRUE	1	0.492495006928753	2		314	307	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468445	89468445	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	71	386	0	ENST00000336596.2:c.1979C>T	p.Thr660Ile	p.T660I	ENST00000336596	NM_005233.5	660	aCa/aTa	11/17	1	2	FACETS	0.773	0.678	0.874	0.773	0.678	0.874	SUBCLONAL	1	TRUE	1	0.492495006928753	2		386	373	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498522	89498522	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	73	320	0	ENST00000336596.2:c.2494G>A	p.Asp832Asn	p.D832N	ENST00000336596	NM_005233.5	832	Gat/Aat	14/17	1	2	FACETS	0.912	0.804	1	0.912	0.804	1	CLONAL	1	TRUE	1	0.492495006928753	2		320	325	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119624613	119624613	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	102	348	1	ENST00000316626.5:c.802G>T	p.Glu268Ter	p.E268*	ENST00000316626		268	Gaa/Taa	7/12	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.492495006928753	2		349	332	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119721018	119721018	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	116	332	0	ENST00000316626.5:c.157G>T	p.Glu53Ter	p.E53*	ENST00000316626		53	Gaa/Taa	2/12	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.492495006928753	2		332	423	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967317	134967317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868241569	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	96	410	1	ENST00000398015.3:c.2656G>A	p.Ala886Thr	p.A886T	ENST00000398015	NM_004441.4	886	Gca/Aca	14/16	1	2	FACETS	0.87	0.779	0.966	0.87	0.779	0.966	CLONAL	1	TRUE	1	0.492495006928753	2		411	448	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374245	138374245	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	114	343	0	ENST00000289153.2:c.3199G>T	p.Asp1067Tyr	p.D1067Y	ENST00000289153	NM_006219.2	1067	Gac/Tac	22/22	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.492495006928753	2		343	402	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433362	138433362	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143122477	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	94	357	0	ENST00000289153.2:c.1250C>T	p.Thr417Met	p.T417M	ENST00000289153	NM_006219.2	417	aCg/aTg	7/22	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.492495006928753	2		357	356	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461453	138461453	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	94	319	0	ENST00000289153.2:c.568G>T	p.Asp190Tyr	p.D190Y	ENST00000289153	NM_006219.2	190	Gat/Tat	3/22	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.492495006928753	2		319	344	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474703	138474703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1467994756	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	83	337	1	ENST00000289153.2:c.290G>A	p.Arg97Gln	p.R97Q	ENST00000289153	NM_006219.2	97	cGa/cAa	2/22	1	2	FACETS	0.971	0.864	1	0.971	0.864	1	CLONAL	1	TRUE	1	0.492495006928753	2		338	347	SUCCESS
ATR	545	MSKCC	GRCh37	3	142184043	142184043	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	76	252	0	ENST00000350721.4:c.6937T>C	p.Ser2313Pro	p.S2313P	ENST00000350721	NM_001184.3	2313	Tct/Cct	41/47	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.492495006928753	2		252	298	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281340	142281340	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	97	432	0	ENST00000350721.4:c.904C>A	p.Leu302Ile	p.L302I	ENST00000350721	NM_001184.3	302	Cta/Ata	4/47	1	2	FACETS	0.963	0.865	1	0.963	0.865	1	CLONAL	1	TRUE	1	0.492495006928753	2		432	409	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916767	178916767	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	69	349	0	ENST00000263967.3:c.154G>T	p.Glu52Ter	p.E52*	ENST00000263967	NM_006218.2	52	Gaa/Taa	2/21	0.459881746335296	3	FACETS	0.818	0.715	0.928	0.409	0.357	0.464	CLONAL	1	TRUE	1	0.492495006928753	3		349	427	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919236	178919236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	148	278	1	ENST00000263967.3:c.721C>T	p.Leu241Phe	p.L241F	ENST00000263967	NM_006218.2	241	Ctc/Ttc	4/21	0.459881746335296	3	FACETS	0.861	0.794	0.93	0.861	0.794	0.93	CLONAL	2	TRUE	1	0.492495006928753	3		279	435	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937027	178937027	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	115	271	0	ENST00000263967.3:c.1708C>A	p.Leu570Met	p.L570M	ENST00000263967	NM_006218.2	570	Ctg/Atg	11/21	0.459881746335296	3	FACETS	0.933	0.852	1	0.933	0.852	1	CLONAL	2	TRUE	1	0.492495006928753	3		271	312	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178942502	178942502	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749840319	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	61	327	0	ENST00000263967.3:c.2309G>A	p.Arg770Gln	p.R770Q	ENST00000263967	NM_006218.2	770	cGa/cAa	16/21	0.459881746335296	3	FACETS	0.825	0.715	0.944	0.413	0.357	0.472	CLONAL	1	TRUE	1	0.492495006928753	3		327	374	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430162	181430162	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	73	224	0	ENST00000325404.1:c.14T>C	p.Met5Thr	p.M5T	ENST00000325404	NM_003106.3	5	aTg/aCg	1/1	0.459881746335296	3	FACETS	0.928	0.828	1	0.928	0.828	1	CLONAL	2	TRUE	1	0.492495006928753	3		224	199	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185200195	185200195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	221	373	0	ENST00000265026.3:c.2852C>T	p.Ser951Phe	p.S951F	ENST00000265026	NM_004721.4	951	tCt/tTt	14/14	0.459881746335296	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.492495006928753	3		373	494	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447384	187447384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780987785	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	244	570	1	ENST00000232014.4:c.809G>A	p.Arg270Gln	p.R270Q	ENST00000232014	NM_001130845.1	270	cGa/cAa	5/10	0.459881746335296	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.492495006928753	3		571	572	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587161	189587161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173679499	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	130	345	0	ENST00000264731.3:c.1178G>A	p.Arg393Gln	p.R393Q	ENST00000264731	NM_003722.4	393	cGa/cAa	9/14	0.459881746335296	3	FACETS	1	0.978	1	0.615	0.56	0.672	CLONAL	1	TRUE	1	0.492495006928753	3		345	535	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920289	1920289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146822227	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	104	421	0	ENST00000382891.5:c.1349G>A	p.Arg450Gln	p.R450Q	ENST00000382891	NM_133335.3	450	cGa/cAa	5/22	1	2	FACETS	0.92	0.828	1	0.92	0.828	1	CLONAL	1	TRUE	1	0.492495006928753	2		421	459	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1941428	1941428	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	113	360	0	ENST00000382891.5:c.1804C>T	p.Arg602Trp	p.R602W	ENST00000382891	NM_133335.3	602	Cgg/Tgg	9/22	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.492495006928753	2		360	445	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127539	55127539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	95	367	0	ENST00000257290.5:c.327G>T	p.Glu109Asp	p.E109D	ENST00000257290	NM_006206.4	109	gaG/gaT	3/23	1	2	FACETS	0.916	0.821	1	0.916	0.821	1	CLONAL	1	TRUE	1	0.492495006928753	2		367	421	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55130074	55130074	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	95	398	0	ENST00000257290.5:c.608T>G	p.Phe203Cys	p.F203C	ENST00000257290	NM_006206.4	203	tTt/tGt	4/23	1	2	FACETS	0.984	0.883	1	0.984	0.883	1	CLONAL	1	TRUE	1	0.492495006928753	2		398	392	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144623	55144623	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	129	411	0	ENST00000257290.5:c.2097G>T	p.Glu699Asp	p.E699D	ENST00000257290	NM_006206.4	699	gaG/gaT	15/23	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.492495006928753	2		411	445	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161380	55161380	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376544204	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	94	377	0	ENST00000257290.5:c.3211G>A	p.Asp1071Asn	p.D1071N	ENST00000257290	NM_006206.4	1071	Gac/Aac	23/23	1	2	FACETS	0.94	0.842	1	0.94	0.842	1	CLONAL	1	TRUE	1	0.492495006928753	2		377	406	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955584	55955584	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	76	340	0	ENST00000263923.4:c.3361G>T	p.Glu1121Ter	p.E1121*	ENST00000263923	NM_002253.2	1121	Gaa/Taa	25/30	1	2	FACETS	0.953	0.843	1	0.953	0.843	1	CLONAL	1	TRUE	1	0.492495006928753	2		340	324	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971117	55971117	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	86	351	0	ENST00000263923.4:c.1680G>T	p.Gln560His	p.Q560H	ENST00000263923	NM_002253.2	560	caG/caT	13/30	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.492495006928753	2		351	331	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976936	55976936	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	94	320	0	ENST00000263923.4:c.977-1G>T		p.X326_splice	ENST00000263923	NM_002253.2	326			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.492495006928753	2		320	321	SUCCESS
REST	5978	MSKCC	GRCh37	4	57798209	57798209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	105	425	0	ENST00000309042.7:c.3185G>A	p.Cys1062Tyr	p.C1062Y	ENST00000309042	NM_005612.4	1062	tGt/tAt	4/4	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.492495006928753	2		425	394	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231743	66231743	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	75	305	0	ENST00000273854.3:c.1957C>A	p.Pro653Thr	p.P653T	ENST00000273854	NM_004439.5	653	Cca/Aca	11/18	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.492495006928753	2		305	253	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233102	66233102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778292709	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	57	269	0	ENST00000273854.3:c.1897G>A	p.Glu633Lys	p.E633K	ENST00000273854	NM_004439.5	633	Gaa/Aaa	10/18	1	2	FACETS	0.726	0.626	0.832	0.726	0.626	0.832	SUBCLONAL	1	TRUE	1	0.492495006928753	2		269	319	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270111	66270111	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs539707153	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	99	338	0	ENST00000273854.3:c.1771G>A	p.Gly591Ser	p.G591S	ENST00000273854	NM_004439.5	591	Ggc/Agc	8/18	1	2	FACETS	0.985	0.886	1	0.985	0.886	1	CLONAL	1	TRUE	1	0.492495006928753	2		338	408	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356335	66356335	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	110	476	0	ENST00000273854.3:c.1162G>T	p.Asp388Tyr	p.D388Y	ENST00000273854	NM_004439.5	388	Gac/Tac	5/18	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.492495006928753	2		476	438	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155548	106155548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	128	451	0	ENST00000380013.4:c.449C>T	p.Ser150Phe	p.S150F	ENST00000380013	NM_001127208.2	150	tCt/tTt	3/11	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.492495006928753	2		451	495	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156312	106156312	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	178	556	0	ENST00000380013.4:c.1213C>T	p.Leu405Phe	p.L405F	ENST00000380013	NM_001127208.2	405	Ctt/Ttt	3/11	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.492495006928753	2		556	714	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193892	106193892	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1049545383	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	114	385	0	ENST00000380013.4:c.4354C>T	p.Arg1452Ter	p.R1452*	ENST00000380013	NM_001127208.2	1452	Cga/Tga	10/11	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.492495006928753	2		385	451	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029319	143029319	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	89	247	0	ENST00000262992.4:c.2301A>C	p.Glu767Asp	p.E767D	ENST00000262992	NM_001101669.1	767	gaA/gaC	21/24	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.492495006928753	2		247	288	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143326384	143326384	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	107	337	0	ENST00000262992.4:c.230G>T	p.Arg77Ile	p.R77I	ENST00000262992	NM_001101669.1	77	aGa/aTa	4/24	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.492495006928753	2		337	401	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144336667	144336667	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746261423	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	81	365	0	ENST00000262995.4:c.110G>A	p.Arg37His	p.R37H	ENST00000262995	NM_207123.2	37	cGt/cAt	2/11	1	2	FACETS	0.882	0.782	0.987	0.882	0.782	0.987	CLONAL	1	TRUE	1	0.492495006928753	2		365	373	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144359588	144359588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779671407	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	125	481	0	ENST00000262995.4:c.1030C>T	p.Arg344Trp	p.R344W	ENST00000262995	NM_207123.2	344	Cgg/Tgg	4/11	1	2	FACETS	0.918	0.834	1	0.918	0.834	1	CLONAL	1	TRUE	1	0.492495006928753	2		481	553	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516893	187516893	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	95	415	0	ENST00000441802.2:c.13088C>A	p.Ser4363Tyr	p.S4363Y	ENST00000441802	NM_005245.3	4363	tCt/tAt	26/27	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.492495006928753	2		415	385	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524525	187524525	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35670235	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	112	410	1	ENST00000441802.2:c.11155G>A	p.Val3719Met	p.V3719M	ENST00000441802	NM_005245.3	3719	Gtg/Atg	19/27	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.492495006928753	2		411	400	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541895	187541895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772868178	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	129	492	0	ENST00000441802.2:c.5845G>A	p.Glu1949Lys	p.E1949K	ENST00000441802	NM_005245.3	1949	Gag/Aag	10/27	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.492495006928753	2		492	517	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549821	187549821	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	128	406	0	ENST00000441802.2:c.4420G>T	p.Glu1474Ter	p.E1474*	ENST00000441802	NM_005245.3	1474	Gaa/Taa	8/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.492495006928753	2		406	425	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630237	187630237	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1333902122	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	130	547	0	ENST00000441802.2:c.745C>G	p.Gln249Glu	p.Q249E	ENST00000441802	NM_005245.3	249	Cag/Gag	2/27	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.492495006928753	2		547	493	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235381	235381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757251714	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	156	357	0	ENST00000264932.6:c.1187C>T	p.Thr396Met	p.T396M	ENST00000264932	NM_004168.2	396	aCg/aTg	9/15	NA	2	FACETS	0.806	0.747	0.866			1	INDETERMINATE	2	TRUE	NA	0.492495006928753	2		357	393	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	895030	895030	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	91	297	0	ENST00000166345.3:c.221C>A	p.Ser74Tyr	p.S74Y	ENST00000166345	NM_004237.3	74	tCt/tAt	2/13	NA	2	FACETS	0.882	0.788	0.981			1	INDETERMINATE	1	TRUE	NA	0.492495006928753	2		297	419	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278834	1278834	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	122	407	0	ENST00000310581.5:c.2208G>T	p.Gln736His	p.Q736H	ENST00000310581	NM_198253.2	736	caG/caT	6/16	NA	2	FACETS	1	0.913	1			1	INDETERMINATE	1	TRUE	NA	0.492495006928753	2		407	493	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293431	1293431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	111	332	0	ENST00000310581.5:c.1570C>T	p.Pro524Ser	p.P524S	ENST00000310581	NM_198253.2	524	Cca/Tca	2/16	0.14858861289065	4	FACETS	1	0.913	1			1	INDETERMINATE	2	TRUE	NA	0.492495006928753	4		332	335	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294403	1294403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1322987070	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	136	473	0	ENST00000310581.5:c.598G>A	p.Glu200Lys	p.E200K	ENST00000310581	NM_198253.2	200	Gaa/Aaa	2/16	0.14858861289065	4	FACETS	1	0.971	1			1	INDETERMINATE	2	TRUE	NA	0.492495006928753	4		473	369	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410888	31410888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771452865	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	137	377	0	ENST00000344624.3:c.3632C>T	p.Ala1211Val	p.A1211V	ENST00000344624		1211	gCg/gTg	28/33	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.492495006928753	2		377	483	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31421449	31421449	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	91	310	0	ENST00000344624.3:c.3455C>T	p.Ser1152Phe	p.S1152F	ENST00000344624		1152	tCc/tTc	27/33	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.492495006928753	2		310	350	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31429602	31429602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370990538	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	78	322	0	ENST00000344624.3:c.3196C>T	p.Arg1066Cys	p.R1066C	ENST00000344624		1066	Cgc/Tgc	24/33	1	2	FACETS	0.932	0.825	1	0.932	0.825	1	CLONAL	1	TRUE	1	0.492495006928753	2		322	340	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31451731	31451731	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	77	269	0	ENST00000344624.3:c.2591C>A	p.Pro864His	p.P864H	ENST00000344624		864	cCt/cAt	18/33	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.492495006928753	2		269	310	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35860997	35860997	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	82	374	0	ENST00000303115.3:c.126C>A	p.Cys42Ter	p.C42*	ENST00000303115	NM_002185.3	42	tgC/tgA	2/8	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.492495006928753	2		374	332	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867469	35867469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs191585195	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	89	366	0	ENST00000303115.3:c.283G>A	p.Glu95Lys	p.E95K	ENST00000303115	NM_002185.3	95	Gag/Aag	3/8	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.492495006928753	2		366	298	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871314	35871314	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs200751605	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	60	287	1	ENST00000303115.3:c.536C>T	p.Thr179Met	p.T179M	ENST00000303115	NM_002185.3	179	aCg/aTg	4/8	1	2	FACETS	0.899	0.782	1	0.899	0.782	1	CLONAL	1	TRUE	1	0.492495006928753	2		288	271	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945733	38945733	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	84	388	0	ENST00000357387.3:c.4493C>A	p.Ser1498Ter	p.S1498*	ENST00000357387	NM_152756.3	1498	tCa/tAa	34/38	1	2	FACETS	0.94	0.836	1	0.94	0.836	1	CLONAL	1	TRUE	1	0.492495006928753	2		388	363	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950304	38950304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs895560221	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	95	458	0	ENST00000357387.3:c.3646C>T	p.Arg1216Cys	p.R1216C	ENST00000357387	NM_152756.3	1216	Cgt/Tgt	31/38	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.492495006928753	2		458	365	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953634	38953634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146765449	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	49	257	0	ENST00000357387.3:c.2719C>T	p.Arg907Cys	p.R907C	ENST00000357387	NM_152756.3	907	Cgt/Tgt	28/38	1	2	FACETS	0.78	0.667	0.903	0.78	0.667	0.903	CLONAL	1	TRUE	1	0.492495006928753	2		257	255	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38954964	38954964	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	50	253	0	ENST00000357387.3:c.2610-1G>T		p.X870_splice	ENST00000357387	NM_152756.3	870			1	2	FACETS	0.981	0.843	1	0.981	0.843	1	CLONAL	1	TRUE	1	0.492495006928753	2		253	207	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38964897	38964897	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	31	329	0	ENST00000357387.3:c.1397G>T	p.Arg466Ile	p.R466I	ENST00000357387	NM_152756.3	466	aGa/aTa	16/38	1	2	FACETS	0.482	0.392	0.584	0.482	0.392	0.584	SUBCLONAL	1	TRUE	1	0.492495006928753	2		329	261	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39002706	39002706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	83	363	0	ENST00000357387.3:c.323G>A	p.Arg108Gln	p.R108Q	ENST00000357387	NM_152756.3	108	cGa/cAa	5/38	1	2	FACETS	0.803	0.712	0.899	0.803	0.712	0.899	CLONAL	1	TRUE	1	0.492495006928753	2		363	420	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179471	56179471	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	103	379	0	ENST00000399503.3:c.3784G>T	p.Asp1262Tyr	p.D1262Y	ENST00000399503	NM_005921.1	1262	Gat/Tat	15/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.492495006928753	2		379	385	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180609	56180609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	68	353	0	ENST00000399503.3:c.3938C>T	p.Thr1313Met	p.T1313M	ENST00000399503	NM_005921.1	1313	aCg/aTg	16/20	1	2	FACETS	0.942	0.828	1	0.942	0.828	1	CLONAL	1	TRUE	1	0.492495006928753	2		353	293	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750454	57750454	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	111	420	0	ENST00000274289.3:c.2014C>T	p.Arg672Ter	p.R672*	ENST00000274289	NM_006622.3	672	Cga/Tga	14/14	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.492495006928753	2		420	424	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588981	67588981	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	83	357	0	ENST00000274335.5:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000274335		358	Cga/Tga	8/15	1	2	FACETS	0.894	0.794	0.999	0.894	0.794	0.999	CLONAL	1	TRUE	1	0.492495006928753	2		357	377	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589618	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519838	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	53	169	0	ENST00000274335.5:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000274335		461	Cga/Tga	10/15	1	2	FACETS	0.783	0.673	0.901	0.783	0.673	0.901	CLONAL	1	TRUE	1	0.492495006928753	2		169	275	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064763	80064763	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	88	321	0	ENST00000265081.6:c.2194G>T	p.Glu732Ter	p.E732*	ENST00000265081	NM_002439.4	732	Gaa/Taa	15/24	1	2	FACETS	0.968	0.865	1	0.968	0.865	1	CLONAL	1	TRUE	1	0.492495006928753	2		321	369	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649000	86649000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755634472	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	71	295	0	ENST00000274376.6:c.1280G>A	p.Arg427Gln	p.R427Q	ENST00000274376	NM_002890.2	427	cGa/cAa	9/25	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.492495006928753	2		295	268	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672842	86672842	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	82	345	0	ENST00000274376.6:c.2329G>T	p.Glu777Ter	p.E777*	ENST00000274376	NM_002890.2	777	Gaa/Taa	17/25	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.492495006928753	2		345	306	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675668	86675668	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs983011713	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	69	251	0	ENST00000274376.6:c.2603+1G>A		p.X868_splice	ENST00000274376	NM_002890.2	868			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.492495006928753	2		251	236	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679577	86679577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	57	266	0	ENST00000274376.6:c.2738G>A	p.Arg913Gln	p.R913Q	ENST00000274376	NM_002890.2	913	cGg/cAg	21/25	1	2	FACETS	0.945	0.819	1	0.945	0.819	1	CLONAL	1	TRUE	1	0.492495006928753	2		266	245	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	97	421	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.492495006928753	2		421	361	SUCCESS
APC	324	MSKCC	GRCh37	5	112173741	112173741	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	79	396	0	ENST00000257430.4:c.2450G>A	p.Gly817Asp	p.G817D	ENST00000257430	NM_000038.5	817	gGc/gAc	16/16	1	2	FACETS	0.894	0.792	1	0.894	0.792	1	CLONAL	1	TRUE	1	0.492495006928753	2		396	359	SUCCESS
APC	324	MSKCC	GRCh37	5	112174110	112174110	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544709767	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	77	424	0	ENST00000257430.4:c.2819C>T	p.Ser940Leu	p.S940L	ENST00000257430	NM_000038.5	940	tCg/tTg	16/16	1	2	FACETS	0.904	0.799	1	0.904	0.799	1	CLONAL	1	TRUE	1	0.492495006928753	2		424	346	SUCCESS
APC	324	MSKCC	GRCh37	5	112174134	112174134	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	73	398	0	ENST00000257430.4:c.2843C>A	p.Ser948Tyr	p.S948Y	ENST00000257430	NM_000038.5	948	tCt/tAt	16/16	1	2	FACETS	0.89	0.785	1	0.89	0.785	1	CLONAL	1	TRUE	1	0.492495006928753	2		398	333	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267600319	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	120	624	0	ENST00000257430.4:c.4199C>T	p.Ser1400Leu	p.S1400L	ENST00000257430	NM_000038.5	1400	tCg/tTg	16/16	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.492495006928753	2		624	482	SUCCESS
APC	324	MSKCC	GRCh37	5	112177151	112177151	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	122	465	0	ENST00000257430.4:c.5860T>G	p.Phe1954Val	p.F1954V	ENST00000257430	NM_000038.5	1954	Ttt/Gtt	16/16	1	2	FACETS	0.989	0.899	1	0.989	0.899	1	CLONAL	1	TRUE	1	0.492495006928753	2		465	501	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923370	131923370	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1441715028	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	112	353	0	ENST00000265335.6:c.873G>T	p.Glu291Asp	p.E291D	ENST00000265335		291	gaG/gaT	6/25	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.492495006928753	2		353	396	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131945035	131945035	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	105	280	0	ENST00000265335.6:c.2983G>T	p.Glu995Ter	p.E995*	ENST00000265335		995	Gaa/Taa	19/25	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.492495006928753	2		280	366	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977877	131977877	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	65	348	0	ENST00000265335.6:c.3760A>C	p.Lys1254Gln	p.K1254Q	ENST00000265335		1254	Aaa/Caa	25/25	1	2	FACETS	0.731	0.637	0.832	0.731	0.637	0.832	SUBCLONAL	1	TRUE	1	0.492495006928753	2		348	361	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562906	176562906	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	57	468	0	ENST00000439151.2:c.802G>T	p.Glu268Ter	p.E268*	ENST00000439151	NM_022455.4	268	Gaa/Taa	2/23	0.45100875624056	1	FACETS	0.407	0.35	0.469	0.407	0.35	0.469	SUBCLONAL	1	TRUE	0	0.492495006928753	1		468	429	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687001	176687001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	45	407	0	ENST00000439151.2:c.4978C>T	p.Arg1660Cys	p.R1660C	ENST00000439151	NM_022455.4	1660	Cgc/Tgc	14/23	0.45100875624056	1	FACETS	0.348	0.293	0.409	0.348	0.293	0.409	SUBCLONAL	1	TRUE	0	0.492495006928753	1		407	396	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696681	176696681	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	60	400	2	ENST00000439151.2:c.5382C>A	p.Phe1794Leu	p.F1794L	ENST00000439151	NM_022455.4	1794	ttC/ttA	16/23	0.45100875624056	1	FACETS	0.455	0.393	0.521	0.455	0.393	0.521	SUBCLONAL	1	TRUE	0	0.492495006928753	1		402	404	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030221	180030221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143739828	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	101	376	1	ENST00000261937.6:c.4063G>A	p.Val1355Met	p.V1355M	ENST00000261937	NM_182925.4	1355	Gtg/Atg	30/30	0.45100875624056	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.492495006928753	1		377	291	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180037024	180037024	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	41	446	0	ENST00000261937.6:c.3688T>C	p.Tyr1230His	p.Y1230H	ENST00000261937	NM_182925.4	1230	Tat/Cat	28/30	0.45100875624056	1	FACETS	0.396	0.331	0.468	0.396	0.331	0.468	SUBCLONAL	1	TRUE	0	0.492495006928753	1		446	317	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048108	180048108	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	42	441	0	ENST00000261937.6:c.2165C>A	p.Ser722Tyr	p.S722Y	ENST00000261937	NM_182925.4	722	tCt/tAt	14/30	0.45100875624056	1	FACETS	0.429	0.359	0.505	0.429	0.359	0.505	SUBCLONAL	1	TRUE	0	0.492495006928753	1		441	300	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394897	394897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	115	407	0	ENST00000380956.4:c.293G>A	p.Arg98Gln	p.R98Q	ENST00000380956	NM_001195286.1	98	cGg/cAg	3/9	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.492495006928753	2		407	438	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395877	395877	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	119	399	0	ENST00000380956.4:c.434A>G	p.Gln145Arg	p.Q145R	ENST00000380956	NM_001195286.1	145	cAg/cGg	4/9	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.492495006928753	2		399	448	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20486919	20486919	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs376318599	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	73	262	0	ENST00000346618.3:c.885-1C>T		p.X295_splice	ENST00000346618	NM_001949.4	295			1	2	FACETS	0.907	0.799	1	0.907	0.799	1	CLONAL	1	TRUE	1	0.492495006928753	2		262	327	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20486949	20486949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188266138	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	97	287	0	ENST00000346618.3:c.914G>A	p.Arg305Gln	p.R305Q	ENST00000346618	NM_001949.4	305	cGa/cAa	5/7	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.492495006928753	2		287	353	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225407	26225407	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	136	496	0	ENST00000360408.1:c.25C>T	p.Arg9Cys	p.R9C	ENST00000360408	NM_003532.2	9	Cgt/Tgt	1/1	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.492495006928753	2		496	525	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271542	26271542	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	131	550	1	ENST00000305910.3:c.71A>C	p.Lys24Thr	p.K24T	ENST00000305910	NM_003534.2	24	aAg/aCg	1/1	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.492495006928753	2		551	487	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910572	29910572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45569434	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	11	174	2	ENST00000376809.5:c.112C>T	p.Arg38Trp	p.R38W	ENST00000376809	NM_002116.7	38	Cgg/Tgg	2/8	1	2	FACETS	0.251	0.173	0.347	0.251	0.173	0.347	SUBCLONAL	1	TRUE	1	0.492495006928753	2		176	178	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911231	29911231	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199474554	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	37	225	0	ENST00000376809.5:c.530C>T	p.Ala177Val	p.A177V	ENST00000376809	NM_002116.7	177	gCg/gTg	3/8	1	2	FACETS	0.637	0.529	0.756	0.637	0.529	0.756	SUBCLONAL	1	TRUE	1	0.492495006928753	2		225	236	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680388	30680388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748459364	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	111	437	0	ENST00000376406.3:c.1331G>A	p.Arg444Gln	p.R444Q	ENST00000376406	NM_014641.2	444	cGa/cAa	5/15	1	2	FACETS	0.961	0.869	1	0.961	0.869	1	CLONAL	1	TRUE	1	0.492495006928753	2		437	469	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170131	32170131	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	94	381	0	ENST00000375023.3:c.3477C>A	p.Cys1159Ter	p.C1159*	ENST00000375023	NM_004557.3	1159	tgC/tgA	21/30	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.492495006928753	2		381	349	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798105	32798105	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367718365	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	115	413	0	ENST00000374899.4:c.1574G>A	p.Gly525Glu	p.G525E	ENST00000374899	NM_018833.2	525	gGa/gAa	9/12	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.492495006928753	2		413	427	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798535	32798535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	130	457	0	ENST00000374899.4:c.1321G>A	p.Glu441Lys	p.E441K	ENST00000374899	NM_018833.2	441	Gag/Aag	8/12	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.492495006928753	2		457	441	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800476	32800476	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	114	507	0	ENST00000374899.4:c.1071G>T	p.Glu357Asp	p.E357D	ENST00000374899	NM_018833.2	357	gaG/gaT	6/12	1	2	FACETS	0.908	0.821	0.998	0.908	0.821	0.998	CLONAL	1	TRUE	1	0.492495006928753	2		507	510	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803528	32803528	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	120	354	1	ENST00000374899.4:c.631G>T	p.Gly211Ter	p.G211*	ENST00000374899	NM_018833.2	211	Gga/Tga	4/12	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.492495006928753	2		355	458	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37141739	37141739	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	103	396	0	ENST00000373509.5:c.814G>A	p.Ala272Thr	p.A272T	ENST00000373509	NM_002648.3	272	Gcc/Acc	6/6	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.492495006928753	2		396	361	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748479	43748479	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45533131	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	94	347	0	ENST00000523873.1:c.433C>T	p.Arg145Ter	p.R145*	ENST00000523873		145	Cga/Tga	6/8	1	2	FACETS	0.952	0.853	1	0.952	0.853	1	CLONAL	1	TRUE	1	0.492495006928753	2		347	401	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956553	93956553	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1035177735	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	100	407	0	ENST00000369303.4:c.2683C>T	p.Arg895Ter	p.R895*	ENST00000369303	NM_004440.3	895	Cga/Tga	15/17	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.492495006928753	2		407	365	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969104	93969104	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	95	409	0	ENST00000369303.4:c.1892C>T	p.Ser631Phe	p.S631F	ENST00000369303	NM_004440.3	631	tCc/tTc	10/17	1	2	FACETS	0.999	0.897	1	0.999	0.897	1	CLONAL	1	TRUE	1	0.492495006928753	2		409	386	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120360	94120360	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs749418654	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	127	486	0	ENST00000369303.4:c.691C>T	p.Arg231Ter	p.R231*	ENST00000369303	NM_004440.3	231	Cga/Tga	3/17	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.492495006928753	2		486	441	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609953	117609953	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	70	346	0	ENST00000368508.3:c.6746A>C	p.Asp2249Ala	p.D2249A	ENST00000368508	NM_002944.2	2249	gAt/gCt	43/43	1	2	FACETS	0.891	0.783	1	0.891	0.783	1	CLONAL	1	TRUE	1	0.492495006928753	2		346	319	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641102	117641102	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	114	488	0	ENST00000368508.3:c.5869G>T	p.Gly1957Ter	p.G1957*	ENST00000368508	NM_002944.2	1957	Gga/Tga	36/43	1	2	FACETS	0.953	0.862	1	0.953	0.862	1	CLONAL	1	TRUE	1	0.492495006928753	2		488	486	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117645533	117645533	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	87	446	0	ENST00000368508.3:c.5603T>C	p.Val1868Ala	p.V1868A	ENST00000368508	NM_002944.2	1868	gTt/gCt	34/43	1	2	FACETS	0.904	0.805	1	0.904	0.805	1	CLONAL	1	TRUE	1	0.492495006928753	2		446	391	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677978	117677978	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	78	415	0	ENST00000368508.3:c.3955A>C	p.Asn1319His	p.N1319H	ENST00000368508	NM_002944.2	1319	Aac/Cac	25/43	1	2	FACETS	0.91	0.806	1	0.91	0.806	1	CLONAL	1	TRUE	1	0.492495006928753	2		415	348	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681526	117681526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777135627	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	79	296	0	ENST00000368508.3:c.3424G>A	p.Val1142Ile	p.V1142I	ENST00000368508	NM_002944.2	1142	Gtt/Att	22/43	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.492495006928753	2		296	318	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715410	117715410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	92	339	0	ENST00000368508.3:c.1079G>A	p.Arg360Lys	p.R360K	ENST00000368508	NM_002944.2	360	aGa/aAa	10/43	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.492495006928753	2		339	303	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519403	137519403	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	75	393	0	ENST00000367739.4:c.1235T>G	p.Phe412Cys	p.F412C	ENST00000367739	NM_000416.2	412	tTt/tGt	7/7	1	2	FACETS	0.906	0.801	1	0.906	0.801	1	CLONAL	1	TRUE	1	0.492495006928753	2		393	336	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519412	137519412	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	86	388	0	ENST00000367739.4:c.1226G>T	p.Arg409Ile	p.R409I	ENST00000367739	NM_000416.2	409	aGa/aTa	7/7	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.492495006928753	2		388	349	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527420	137527420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1026353199	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	59	274	0	ENST00000367739.4:c.226G>A	p.Ala76Thr	p.A76T	ENST00000367739	NM_000416.2	76	Gcc/Acc	3/7	1	2	FACETS	0.929	0.807	1	0.929	0.807	1	CLONAL	1	TRUE	1	0.492495006928753	2		274	258	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004349	150004349	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	120	398	0	ENST00000253339.5:c.1876C>T	p.Arg626Ter	p.R626*	ENST00000253339		626	Cga/Tga	3/7	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.492495006928753	2		398	373	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382257	152382257	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	97	352	0	ENST00000206249.3:c.1367C>A	p.Ser456Tyr	p.S456Y	ENST00000206249	NM_000125.3	456	tCt/tAt	6/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.492495006928753	2		352	325	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522409	157522409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	134	511	0	ENST00000346085.5:c.4681C>T	p.Arg1561Cys	p.R1561C	ENST00000346085	NM_020732.3	1561	Cgc/Tgc	18/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.492495006928753	2		511	465	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954989	2954989	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	104	476	0	ENST00000396946.4:c.2721G>T	p.Glu907Asp	p.E907D	ENST00000396946	NM_032415.4	907	gaG/gaT	21/25	1	2	FACETS	0.916	0.825	1	0.916	0.825	1	CLONAL	1	TRUE	1	0.492495006928753	2		476	461	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987413	2987413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	105	353	0	ENST00000396946.4:c.16C>T	p.Pro6Ser	p.P6S	ENST00000396946	NM_032415.4	6	Cca/Tca	3/25	1	2	FACETS	0.974	0.878	1	0.974	0.878	1	CLONAL	1	TRUE	1	0.492495006928753	2		353	438	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940439	13940439	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	99	312	0	ENST00000405192.2:c.1067A>C	p.Lys356Thr	p.K356T	ENST00000405192	NM_001163147.1	356	aAa/aCa	11/12	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.492495006928753	2		312	358	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211104	55211104	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	109	410	0	ENST00000275493.2:c.347C>A	p.Ser116Tyr	p.S116Y	ENST00000275493	NM_005228.3	116	tCc/tAc	3/28	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.492495006928753	2		410	439	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224268	55224268	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	99	399	0	ENST00000275493.2:c.1049C>A	p.Ser350Tyr	p.S350Y	ENST00000275493	NM_005228.3	350	tCc/tAc	9/28	1	2	FACETS	0.96	0.862	1	0.96	0.862	1	CLONAL	1	TRUE	1	0.492495006928753	2		399	419	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259500	55259500	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	97	364	0	ENST00000275493.2:c.2558T>G	p.Ile853Ser	p.I853S	ENST00000275493	NM_005228.3	853	aTc/aGc	21/28	1	2	FACETS	0.968	0.869	1	0.968	0.869	1	CLONAL	1	TRUE	1	0.492495006928753	2		364	407	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334850	81334850	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	76	373	0	ENST00000222390.5:c.1866G>C	p.Leu622Phe	p.L622F	ENST00000222390	NM_000601.4	622	ttG/ttC	17/18	1	2	FACETS	0.924	0.817	1	0.924	0.817	1	CLONAL	1	TRUE	1	0.492495006928753	2		373	334	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508169	106508169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381484125	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	66	391	0	ENST00000359195.3:c.163G>A	p.Glu55Lys	p.E55K	ENST00000359195	NM_002649.2	55	Gaa/Aaa	2/11	1	2	FACETS	0.817	0.714	0.927	0.817	0.714	0.927	CLONAL	1	TRUE	1	0.492495006928753	2		391	328	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508824	106508824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226994105	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	124	420	0	ENST00000359195.3:c.818G>A	p.Arg273His	p.R273H	ENST00000359195	NM_002649.2	273	cGc/cAc	2/11	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.492495006928753	2		420	476	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513037	106513037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765837588	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	110	403	0	ENST00000359195.3:c.2051G>A	p.Arg684His	p.R684H	ENST00000359195	NM_002649.2	684	cGt/cAt	3/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.492495006928753	2		403	416	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398647	116398647	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	78	349	0	ENST00000397752.3:c.2237A>C	p.Glu746Ala	p.E746A	ENST00000397752	NM_000245.2	746	gAa/gCa	9/21	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.492495006928753	2		349	307	SUCCESS
MET	4233	MSKCC	GRCh37	7	116399512	116399512	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs773370210	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	93	428	0	ENST00000397752.3:c.2332A>C	p.Asn778His	p.N778H	ENST00000397752	NM_000245.2	778	Aat/Cat	10/21	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.492495006928753	2		428	359	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411683	116411683	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	150	495	0	ENST00000397752.3:c.2862G>A	p.Trp954Ter	p.W954*	ENST00000397752	NM_000245.2	954	tgG/tgA	13/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.492495006928753	2		495	554	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423453	116423453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	90	360	0	ENST00000397752.3:c.3728C>T	p.Ala1243Val	p.A1243V	ENST00000397752	NM_000245.2	1243	gCa/gTa	19/21	1	2	FACETS	0.889	0.794	0.99	0.889	0.794	0.99	CLONAL	1	TRUE	1	0.492495006928753	2		360	411	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435984	116435984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	163	447	1	ENST00000397752.3:c.3979C>T	p.Arg1327Cys	p.R1327C	ENST00000397752	NM_000245.2	1327	Cgc/Tgc	21/21	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.492495006928753	2		448	501	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124467350	124467350	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	55	305	0	ENST00000357628.3:c.1604T>G	p.Ile535Ser	p.I535S	ENST00000357628	NM_015450.2	535	aTt/aGt	17/19	1	2	FACETS	0.784	0.676	0.9	0.784	0.676	0.9	SUBCLONAL	1	TRUE	1	0.492495006928753	2		305	285	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124481063	124481063	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	73	267	1	ENST00000357628.3:c.1333C>A	p.Leu445Ile	p.L445I	ENST00000357628	NM_015450.2	445	Ctc/Atc	14/19	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.492495006928753	2		268	285	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124532351	124532351	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	59	285	0	ENST00000357628.3:c.93C>A	p.Phe31Leu	p.F31L	ENST00000357628	NM_015450.2	31	ttC/ttA	6/19	1	2	FACETS	0.85	0.737	0.97	0.85	0.737	0.97	CLONAL	1	TRUE	1	0.492495006928753	2		285	282	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845086	128845086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761395599	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	92	391	0	ENST00000249373.3:c.580G>A	p.Glu194Lys	p.E194K	ENST00000249373	NM_005631.4	194	Gaa/Aaa	3/12	1	2	FACETS	0.981	0.878	1	0.981	0.878	1	CLONAL	1	TRUE	1	0.492495006928753	2		391	381	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850320	128850320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	86	337	0	ENST00000249373.3:c.1583C>T	p.Thr528Ile	p.T528I	ENST00000249373	NM_005631.4	528	aCt/aTt	9/12	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.492495006928753	2		337	335	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508761	148508761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	93	276	0	ENST00000320356.2:c.1903G>T	p.Asp635Tyr	p.D635Y	ENST00000320356	NM_004456.4	635	Gat/Tat	16/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.492495006928753	2		276	324	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523717	148523717	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	94	272	0	ENST00000320356.2:c.736G>T	p.Glu246Ter	p.E246*	ENST00000320356	NM_004456.4	246	Gaa/Taa	8/20	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.492495006928753	2		272	371	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148544290	148544290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	85	336	0	ENST00000320356.2:c.101G>A	p.Arg34Gln	p.R34Q	ENST00000320356	NM_004456.4	34	cGa/cAa	2/20	1	2	FACETS	0.93	0.828	1	0.93	0.828	1	CLONAL	1	TRUE	1	0.492495006928753	2		336	371	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845580	151845580	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1287135873	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	117	475	0	ENST00000262189.6:c.13432C>T	p.Arg4478Ter	p.R4478*	ENST00000262189	NM_170606.2	4478	Cga/Tga	52/59	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.492495006928753	2		475	463	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875033	151875033	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	103	347	0	ENST00000262189.6:c.7505C>A	p.Pro2502His	p.P2502H	ENST00000262189	NM_170606.2	2502	cCt/cAt	38/59	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.492495006928753	2		347	377	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151882697	151882697	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	15	159	0	ENST00000262189.6:c.5028G>T	p.Lys1676Asn	p.K1676N	ENST00000262189	NM_170606.2	1676	aaG/aaT	34/59	1	2	FACETS	0.326	0.239	0.43	0.326	0.239	0.43	SUBCLONAL	1	TRUE	1	0.492495006928753	2		159	187	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538897	23538897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1200957711	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	124	377	0	ENST00000380871.4:c.542G>A	p.Arg181Gln	p.R181Q	ENST00000380871	NM_006167.3	181	cGa/cAa	2/2	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.492495006928753	2		377	414	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162925	38162925	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	133	397	0	ENST00000317025.8:c.2281G>T	p.Asp761Tyr	p.D761Y	ENST00000317025	NM_023034.1	761	Gat/Tat	13/24	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.492495006928753	2		397	494	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187315	38187315	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	111	432	0	ENST00000317025.8:c.1162G>T	p.Glu388Ter	p.E388*	ENST00000317025	NM_023034.1	388	Gaa/Taa	6/24	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.492495006928753	2		432	423	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205461	38205461	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs182796258	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	101	453	0	ENST00000317025.8:c.229A>G	p.Ile77Val	p.I77V	ENST00000317025	NM_023034.1	77	Atc/Gtc	2/24	1	2	FACETS	0.954	0.858	1	0.954	0.858	1	CLONAL	1	TRUE	1	0.492495006928753	2		453	430	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271703	38271703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1415925468	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	100	504	0	ENST00000425967.3:c.2246G>A	p.Arg749His	p.R749H	ENST00000425967	NM_001174067.1	749	cGc/cAc	17/19	1	2	FACETS	0.915	0.822	1	0.915	0.822	1	CLONAL	1	TRUE	1	0.492495006928753	2		504	444	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863042	56863042	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	78	356	0	ENST00000519728.1:c.309G>T	p.Lys103Asn	p.K103N	ENST00000519728	NM_002350.3	103	aaG/aaT	5/13	1	2	FACETS	0.897	0.794	1	0.897	0.794	1	CLONAL	1	TRUE	1	0.492495006928753	2		356	353	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863271	56863271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752739111	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	92	185	2	ENST00000519728.1:c.415G>A	p.Ala139Thr	p.A139T	ENST00000519728	NM_002350.3	139	Gca/Aca	6/13	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.492495006928753	2		187	373	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956771	68956771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774302685	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	129	401	0	ENST00000288368.4:c.889C>T	p.Arg297Cys	p.R297C	ENST00000288368	NM_024870.2	297	Cgt/Tgt	8/40	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.492495006928753	2		401	378	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978642	70978642	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	146	461	0	ENST00000276594.2:c.1011G>T	p.Gln337His	p.Q337H	ENST00000276594	NM_024504.3	337	caG/caT	5/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.492495006928753	2		461	512	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980478	70980478	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	103	390	0	ENST00000276594.2:c.899C>T	p.Ser300Phe	p.S300F	ENST00000276594	NM_024504.3	300	tCt/tTt	4/8	1	2	FACETS	0.923	0.831	1	0.923	0.831	1	CLONAL	1	TRUE	1	0.492495006928753	2		390	453	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981395	70981395	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	66	392	0	ENST00000276594.2:c.700+1G>T		p.X234_splice	ENST00000276594	NM_024504.3	234			1	2	FACETS	0.848	0.742	0.961	0.848	0.742	0.961	CLONAL	1	TRUE	1	0.492495006928753	2		392	316	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976658	90976658	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	63	316	0	ENST00000265433.3:c.974C>A	p.Pro325His	p.P325H	ENST00000265433	NM_002485.4	325	cCt/cAt	8/16	1	2	FACETS	0.856	0.746	0.972	0.856	0.746	0.972	CLONAL	1	TRUE	1	0.492495006928753	2		316	299	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859872	117859872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	90	384	0	ENST00000297338.2:c.1763C>T	p.Thr588Met	p.T588M	ENST00000297338	NM_006265.2	588	aCg/aTg	14/14	1	2	FACETS	0.988	0.883	1	0.988	0.883	1	CLONAL	1	TRUE	1	0.492495006928753	2		384	370	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864863	117864863	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	107	336	0	ENST00000297338.2:c.1246T>G	p.Phe416Val	p.F416V	ENST00000297338	NM_006265.2	416	Ttc/Gtc	10/14	1	2	FACETS	0.974	0.879	1	0.974	0.879	1	CLONAL	1	TRUE	1	0.492495006928753	2		336	446	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2086832	2086832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	93	596	0	ENST00000349721.2:c.2530C>T	p.Arg844Trp	p.R844W	ENST00000349721	NM_003070.3	844	Cgg/Tgg	18/34	0.413918410926449	0	FACETS	0.648	0.583	0.715			1	SUBCLONAL	1	TRUE	0	0.492495006928753	0		596	296	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2110274	2110274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs281875192	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	86	332	1	ENST00000349721.2:c.3313C>T	p.Arg1105Cys	p.R1105C	ENST00000349721	NM_003070.3	1105	Cgt/Tgt	24/34	0.413918410926449	0	FACETS	0.692	0.622	0.766			1	SUBCLONAL	1	TRUE	0	0.492495006928753	0		333	256	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2115967	2115967	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs281875189	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	118	362	0	ENST00000349721.2:c.3602C>T	p.Ala1201Val	p.A1201V	ENST00000349721	NM_003070.3	1201	gCg/gTg	25/34	0.413918410926449	0	FACETS	0.677	0.618	0.739			1	SUBCLONAL	1	TRUE	0	0.492495006928753	0		362	359	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050822	5050822	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	75	299	0	ENST00000381652.3:c.605A>C	p.Asn202Thr	p.N202T	ENST00000381652	NM_004972.3	202	aAc/aCc	6/25	0.413918410926449	0	FACETS	0.597	0.53	0.667			1	SUBCLONAL	1	TRUE	0	0.492495006928753	0		299	259	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484270	8484270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867884876	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	100	404	0	ENST00000356435.5:c.3262C>T	p.Arg1088Cys	p.R1088C	ENST00000356435		1088	Cgt/Tgt	19/35	0.413918410926449	0	FACETS	0.654	0.591	0.719			1	SUBCLONAL	1	TRUE	0	0.492495006928753	0		404	315	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633379	8633379	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	68	369	0	ENST00000356435.5:c.290A>C	p.Glu97Ala	p.E97A	ENST00000356435		97	gAa/gCa	3/35	0.413918410926449	0	FACETS	0.556	0.49	0.626			1	SUBCLONAL	1	TRUE	0	0.492495006928753	0		369	252	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27168543	27168543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	74	366	0	ENST00000380036.4:c.415G>A	p.Val139Met	p.V139M	ENST00000380036	NM_000459.3	139	Gtg/Atg	3/23	1	2	FACETS	0.93	0.821	1	0.93	0.821	1	CLONAL	1	TRUE	1	0.492495006928753	2		366	323	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197484	27197484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756064806	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	112	408	0	ENST00000380036.4:c.1796C>T	p.Ser599Leu	p.S599L	ENST00000380036	NM_000459.3	599	tCg/tTg	12/23	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.492495006928753	2		408	441	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27228298	27228298	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	74	255	0	ENST00000380036.4:c.3295C>T	p.Arg1099Ter	p.R1099*	ENST00000380036	NM_000459.3	1099	Cga/Tga	22/23	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.492495006928753	2		255	287	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015100	37015100	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	127	388	0	ENST00000358127.4:c.304T>C	p.Tyr102His	p.Y102H	ENST00000358127	NM_001280556.1	102	Tat/Cat	3/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.492495006928753	2		388	440	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285871	87285871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408094711	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	94	361	0	ENST00000277120.3:c.208G>A	p.Glu70Lys	p.E70K	ENST00000277120		70	Gaa/Aaa	2/19	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.492495006928753	2		361	346	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606304	93606304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	79	383	2	ENST00000375746.1:c.124C>T	p.Arg42Cys	p.R42C	ENST00000375746	NM_001174167.1	42	Cgc/Tgc	2/14	1	2	FACETS	0.969	0.86	1	0.969	0.86	1	CLONAL	1	TRUE	1	0.492495006928753	2		385	331	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93636573	93636573	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	78	335	0	ENST00000375746.1:c.1003G>T	p.Gly335Cys	p.G335C	ENST00000375746	NM_001174167.1	335	Ggc/Tgc	8/14	1	2	FACETS	0.827	0.731	0.929	0.827	0.731	0.929	CLONAL	1	TRUE	1	0.492495006928753	2		335	383	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93640003	93640003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	98	458	0	ENST00000375746.1:c.1332G>A	p.Trp444Ter	p.W444*	ENST00000375746	NM_001174167.1	444	tgG/tgA	10/14	1	2	FACETS	0.9	0.808	0.998	0.9	0.808	0.998	CLONAL	1	TRUE	1	0.492495006928753	2		458	442	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650147	93650147	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	109	323	0	ENST00000375746.1:c.1698C>A	p.Phe566Leu	p.F566L	ENST00000375746	NM_001174167.1	566	ttC/ttA	12/14	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.492495006928753	2		323	382	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93657854	93657854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	114	378	0	ENST00000375746.1:c.1880G>A	p.Arg627His	p.R627H	ENST00000375746	NM_001174167.1	627	cGc/cAc	14/14	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.492495006928753	2		378	455	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864063	97864063	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs185822330	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	107	371	0	ENST00000289081.3:c.1603C>T	p.Arg535Cys	p.R535C	ENST00000289081	NM_000136.2	535	Cgt/Tgt	15/15	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.492495006928753	2		371	431	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98002975	98002975	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	63	286	0	ENST00000289081.3:c.301G>T	p.Glu101Ter	p.E101*	ENST00000289081	NM_000136.2	101	Gaa/Taa	4/15	1	2	FACETS	0.98	0.857	1	0.98	0.857	1	CLONAL	1	TRUE	1	0.492495006928753	2		286	261	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98011412	98011412	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	71	329	0	ENST00000289081.3:c.162G>T	p.Glu54Asp	p.E54D	ENST00000289081	NM_000136.2	54	gaG/gaT	2/15	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.492495006928753	2		329	272	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900281	101900281	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	103	370	0	ENST00000374994.4:c.715G>T	p.Glu239Ter	p.E239*	ENST00000374994	NM_004612.2	239	Gaa/Taa	4/9	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.492495006928753	2		370	402	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250113	110250113	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	66	368	0	ENST00000374672.4:c.562G>A	p.Ala188Thr	p.A188T	ENST00000374672	NM_004235.4	188	Gcg/Acg	3/5	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.492495006928753	2		368	268	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250517	110250517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	66	286	0	ENST00000374672.4:c.158G>A	p.Arg53Gln	p.R53Q	ENST00000374672	NM_004235.4	53	cGa/cAa	3/5	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.492495006928753	2		286	226	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912146	127912146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564144380	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	78	366	0	ENST00000373547.4:c.724G>A	p.Glu242Lys	p.E242K	ENST00000373547	NM_002721.4	242	Gaa/Aaa	7/7	1	2	FACETS	0.905	0.801	1	0.905	0.801	1	CLONAL	1	TRUE	1	0.492495006928753	2		366	350	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915943	127915943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781486938	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	111	407	0	ENST00000373547.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000373547	NM_002721.4	180	Gaa/Aaa	6/7	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.492495006928753	2		407	397	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347973	128347973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757433296	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	87	342	0	ENST00000265960.3:c.532G>A	p.Asp178Asn	p.D178N	ENST00000265960	NM_001006617.1	178	Gat/Aat	5/12	1	2	FACETS	0.872	0.777	0.973	0.872	0.777	0.973	CLONAL	1	TRUE	1	0.492495006928753	2		342	405	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434811	128434811	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	104	395	0	ENST00000265960.3:c.43C>T	p.Arg15Ter	p.R15*	ENST00000265960	NM_001006617.1	15	Cga/Tga	2/12	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.492495006928753	2		395	386	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760487	133760487	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs770275661	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	105	410	0	ENST00000318560.5:c.2810T>C	p.Leu937Pro	p.L937P	ENST00000318560	NM_005157.4	937	cTg/cCg	11/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.492495006928753	2		410	362	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772900	135772900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780115763	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	105	427	0	ENST00000298552.3:c.2723G>A	p.Arg908Gln	p.R908Q	ENST00000298552	NM_001162426.1	908	cGg/cAg	21/23	1	2	FACETS	0.929	0.837	1	0.929	0.837	1	CLONAL	1	TRUE	1	0.492495006928753	2		427	459	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781196	135781196	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	103	444	0	ENST00000298552.3:c.1769C>A	p.Pro590His	p.P590H	ENST00000298552	NM_001162426.1	590	cCt/cAt	15/23	1	2	FACETS	0.917	0.825	1	0.917	0.825	1	CLONAL	1	TRUE	1	0.492495006928753	2		444	456	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400000	139400000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147841035	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	106	463	0	ENST00000277541.6:c.4348G>A	p.Glu1450Lys	p.E1450K	ENST00000277541	NM_017617.3	1450	Gag/Aag	25/34	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.492495006928753	2		463	406	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814697	139814697	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	91	409	0	ENST00000247668.2:c.690G>T	p.Glu230Asp	p.E230D	ENST00000247668	NM_021138.3	230	gaG/gaT	8/11	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.492495006928753	2		409	362	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815530	139815530	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528114067	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	106	387	0	ENST00000247668.2:c.1001C>T	p.Ala334Val	p.A334V	ENST00000247668	NM_021138.3	334	gCg/gTg	9/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.492495006928753	2		387	382	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15838385	15838385	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775221448	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	83	233	0	ENST00000307771.7:c.883C>T	p.Arg295Ter	p.R295*	ENST00000307771	NM_005089.3	295	Cga/Tga	10/11	1	2	FACETS	0.997	0.888	1	0.997	0.888	1	CLONAL	1	TRUE	1	0.492495006928753	2		233	338	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148647	20148647	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	67	251	0	ENST00000379607.5:c.416A>C	p.Glu139Ala	p.E139A	ENST00000379607	NM_001412.3	139	gAa/gCa	6/7	1	2	FACETS	0.989	0.869	1	0.989	0.869	1	CLONAL	1	TRUE	1	0.492495006928753	2		251	275	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911539	39911539	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	133	407	0	ENST00000378444.4:c.5091T>G	p.Phe1697Leu	p.F1697L	ENST00000378444	NM_001123385.1	1697	ttT/ttG	15/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.492495006928753	2		407	443	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921535	39921535	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	113	372	0	ENST00000378444.4:c.4285T>A	p.Ser1429Thr	p.S1429T	ENST00000378444	NM_001123385.1	1429	Tcc/Acc	10/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.492495006928753	2		372	404	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932135	39932135	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	131	422	0	ENST00000378444.4:c.2464T>G	p.Ser822Ala	p.S822A	ENST00000378444	NM_001123385.1	822	Tcc/Gcc	4/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.492495006928753	2		422	476	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932381	39932381	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	108	446	1	ENST00000378444.4:c.2218G>T	p.Glu740Ter	p.E740*	ENST00000378444	NM_001123385.1	740	Gag/Tag	4/15	1	2	FACETS	0.927	0.837	1	0.927	0.837	1	CLONAL	1	TRUE	1	0.492495006928753	2		447	473	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933587	39933587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	125	506	0	ENST00000378444.4:c.1012C>T	p.Arg338Trp	p.R338W	ENST00000378444	NM_001123385.1	338	Cgg/Tgg	4/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.492495006928753	2		506	458	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949998	44949998	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	77	331	0	ENST00000377967.4:c.3767A>G	p.Tyr1256Cys	p.Y1256C	ENST00000377967	NM_021140.2	1256	tAc/tGc	26/29	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.492495006928753	2		331	307	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969408	44969408	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	83	369	0	ENST00000377967.4:c.4090A>C	p.Lys1364Gln	p.K1364Q	ENST00000377967	NM_021140.2	1364	Aaa/Caa	28/29	1	2	FACETS	0.882	0.784	0.986	0.882	0.784	0.986	CLONAL	1	TRUE	1	0.492495006928753	2		369	382	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035980	47035980	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	101	382	0	ENST00000377604.3:c.658A>G	p.Asn220Asp	p.N220D	ENST00000377604	NM_001204468.1	220	Aat/Gat	7/24	1	2	FACETS	0.981	0.883	1	0.981	0.883	1	CLONAL	1	TRUE	1	0.492495006928753	2		382	418	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424451	47424451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	85	448	1	ENST00000377045.4:c.371G>A	p.Arg124His	p.R124H	ENST00000377045	NM_001654.4	124	cGt/cAt	5/16	1	2	FACETS	0.826	0.734	0.923	0.826	0.734	0.923	CLONAL	1	TRUE	1	0.492495006928753	2		449	418	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430355	47430355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763351013	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	106	442	0	ENST00000377045.4:c.1630C>T	p.Arg544Cys	p.R544C	ENST00000377045	NM_001654.4	544	Cgc/Tgc	15/16	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.492495006928753	2		442	408	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230800	53230800	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	111	439	0	ENST00000375401.3:c.1993G>T	p.Ala665Ser	p.A665S	ENST00000375401	NM_004187.3	665	Gct/Tct	14/26	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.492495006928753	2		439	378	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409762	63409762	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	59	277	0	ENST00000330258.3:c.3405G>T	p.Lys1135Asn	p.K1135N	ENST00000330258	NM_152424.3	1135	aaG/aaT	2/2	1	2	FACETS	0.94	0.817	1	0.94	0.817	1	CLONAL	1	TRUE	1	0.492495006928753	2		277	255	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410555	63410555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755281117	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	65	506	0	ENST00000330258.3:c.2612G>A	p.Arg871Gln	p.R871Q	ENST00000330258	NM_152424.3	871	cGa/cAa	2/2	1	2	FACETS	0.761	0.663	0.865	0.761	0.663	0.865	SUBCLONAL	1	TRUE	1	0.492495006928753	2		506	347	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411023	63411023	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	80	432	1	ENST00000330258.3:c.2144G>T	p.Ser715Ile	p.S715I	ENST00000330258	NM_152424.3	715	aGt/aTt	2/2	1	2	FACETS	0.89	0.789	0.997	0.89	0.789	0.997	CLONAL	1	TRUE	1	0.492495006928753	2		433	365	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411872	63411872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	124	583	0	ENST00000330258.3:c.1295G>A	p.Gly432Asp	p.G432D	ENST00000330258	NM_152424.3	432	gGc/gAc	2/2	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.492495006928753	2		583	457	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412064	63412064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	112	551	0	ENST00000330258.3:c.1103G>A	p.Gly368Asp	p.G368D	ENST00000330258	NM_152424.3	368	gGt/gAt	2/2	1	2	FACETS	0.88	0.795	0.969	0.88	0.795	0.969	CLONAL	1	TRUE	1	0.492495006928753	2		551	517	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412691	63412691	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	86	371	0	ENST00000330258.3:c.476T>G	p.Phe159Cys	p.F159C	ENST00000330258	NM_152424.3	159	tTt/tGt	2/2	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.492495006928753	2		371	314	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413055	63413055	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	94	454	0	ENST00000330258.3:c.112G>T	p.Glu38Ter	p.E38*	ENST00000330258	NM_152424.3	38	Gaa/Taa	2/2	1	2	FACETS	0.896	0.802	0.995	0.896	0.802	0.995	CLONAL	1	TRUE	1	0.492495006928753	2		454	426	SUCCESS
AR	367	MSKCC	GRCh37	X	66765140	66765140	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777787518	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	55	282	0	ENST00000374690.3:c.152G>A	p.Gly51Asp	p.G51D	ENST00000374690	NM_000044.3	51	gGc/gAc	1/8	1	2	FACETS	0.975	0.844	1	0.975	0.844	1	CLONAL	1	TRUE	1	0.492495006928753	2		282	229	SUCCESS
AR	367	MSKCC	GRCh37	X	66765382	66765382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770661499	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	95	439	0	ENST00000374690.3:c.394G>A	p.Val132Ile	p.V132I	ENST00000374690	NM_000044.3	132	Gtc/Atc	1/8	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.492495006928753	2		439	363	SUCCESS
AR	367	MSKCC	GRCh37	X	66766483	66766483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	73	309	1	ENST00000374690.3:c.1495G>A	p.Ala499Thr	p.A499T	ENST00000374690	NM_000044.3	499	Gca/Aca	1/8	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.492495006928753	2		310	288	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342433	70342433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs5981075	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	104	387	0	ENST00000374080.3:c.1324G>A	p.Asp442Asn	p.D442N	ENST00000374080		442	Gat/Aat	9/45	1	2	FACETS	0.956	0.861	1	0.956	0.861	1	CLONAL	1	TRUE	1	0.492495006928753	2		387	442	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343071	70343071	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	102	336	0	ENST00000374080.3:c.1612G>A	p.Ala538Thr	p.A538T	ENST00000374080		538	Gct/Act	11/45	1	2	FACETS	0.931	0.837	1	0.931	0.837	1	CLONAL	1	TRUE	1	0.492495006928753	2		336	445	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344654	70344654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	91	395	0	ENST00000374080.3:c.2015C>T	p.Ser672Phe	p.S672F	ENST00000374080		672	tCc/tTc	14/45	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.492495006928753	2		395	349	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345559	70345559	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	78	341	0	ENST00000374080.3:c.2418C>A	p.Phe806Leu	p.F806L	ENST00000374080		806	ttC/ttA	17/45	1	2	FACETS	0.943	0.835	1	0.943	0.835	1	CLONAL	1	TRUE	1	0.492495006928753	2		341	336	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345916	70345916	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	72	338	0	ENST00000374080.3:c.2453A>G	p.Asn818Ser	p.N818S	ENST00000374080		818	aAc/aGc	18/45	1	2	FACETS	0.848	0.746	0.956	0.848	0.746	0.956	CLONAL	1	TRUE	1	0.492495006928753	2		338	345	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354278	70354278	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	74	352	0	ENST00000374080.3:c.4689G>T	p.Glu1563Asp	p.E1563D	ENST00000374080		1563	gaG/gaT	34/45	1	2	FACETS	0.859	0.757	0.966	0.859	0.757	0.966	CLONAL	1	TRUE	1	0.492495006928753	2		352	350	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854954	76854954	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	57	391	0	ENST00000373344.5:c.5882G>T	p.Arg1961Ile	p.R1961I	ENST00000373344	NM_000489.3	1961	aGa/aTa	25/35	1	2	FACETS	0.645	0.556	0.741	0.645	0.556	0.741	SUBCLONAL	1	TRUE	1	0.492495006928753	2		391	359	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855216	76855216	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	48	351	0	ENST00000373344.5:c.5771C>A	p.Ser1924Tyr	p.S1924Y	ENST00000373344	NM_000489.3	1924	tCc/tAc	24/35	1	2	FACETS	0.665	0.566	0.773	0.665	0.566	0.773	SUBCLONAL	1	TRUE	1	0.492495006928753	2		351	293	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855227	76855227	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	45	336	0	ENST00000373344.5:c.5760G>T	p.Met1920Ile	p.M1920I	ENST00000373344	NM_000489.3	1920	atG/atT	24/35	1	2	FACETS	0.655	0.554	0.765	0.655	0.554	0.765	SUBCLONAL	1	TRUE	1	0.492495006928753	2		336	279	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855229	76855229	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs912772662	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	48	328	0	ENST00000373344.5:c.5758A>G	p.Met1920Val	p.M1920V	ENST00000373344	NM_000489.3	1920	Atg/Gtg	24/35	1	2	FACETS	0.701	0.597	0.814	0.701	0.597	0.814	SUBCLONAL	1	TRUE	1	0.492495006928753	2		328	278	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855243	76855243	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	50	336	0	ENST00000373344.5:c.5744C>A	p.Ser1915Tyr	p.S1915Y	ENST00000373344	NM_000489.3	1915	tCt/tAt	24/35	1	2	FACETS	0.744	0.636	0.86	0.744	0.636	0.86	SUBCLONAL	1	TRUE	1	0.492495006928753	2		336	273	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875925	76875925	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	66	357	0	ENST00000373344.5:c.5210C>A	p.Ser1737Tyr	p.S1737Y	ENST00000373344	NM_000489.3	1737	tCt/tAt	20/35	1	2	FACETS	0.84	0.735	0.952	0.84	0.735	0.952	CLONAL	1	TRUE	1	0.492495006928753	2		357	319	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888725	76888725	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	71	350	0	ENST00000373344.5:c.5104G>T	p.Glu1702Ter	p.E1702*	ENST00000373344	NM_000489.3	1702	Gaa/Taa	19/35	1	2	FACETS	0.887	0.78	1	0.887	0.78	1	CLONAL	1	TRUE	1	0.492495006928753	2		350	325	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891541	76891541	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	88	305	0	ENST00000373344.5:c.4564G>T	p.Glu1522Ter	p.E1522*	ENST00000373344	NM_000489.3	1522	Gaa/Taa	16/35	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.492495006928753	2		305	352	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937201	76937201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	104	440	0	ENST00000373344.5:c.3547G>A	p.Glu1183Lys	p.E1183K	ENST00000373344	NM_000489.3	1183	Gag/Aag	9/35	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.492495006928753	2		440	385	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937335	76937335	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	81	413	0	ENST00000373344.5:c.3413G>A	p.Arg1138Lys	p.R1138K	ENST00000373344	NM_000489.3	1138	aGa/aAa	9/35	1	2	FACETS	0.976	0.867	1	0.976	0.867	1	CLONAL	1	TRUE	1	0.492495006928753	2		413	337	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937464	76937464	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	88	399	0	ENST00000373344.5:c.3284A>C	p.Lys1095Thr	p.K1095T	ENST00000373344	NM_000489.3	1095	aAg/aCg	9/35	1	2	FACETS	0.916	0.817	1	0.916	0.817	1	CLONAL	1	TRUE	1	0.492495006928753	2		399	390	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938094	76938094	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	90	433	0	ENST00000373344.5:c.2654G>T	p.Arg885Ile	p.R885I	ENST00000373344	NM_000489.3	885	aGa/aTa	9/35	1	2	FACETS	0.848	0.756	0.945	0.848	0.756	0.945	CLONAL	1	TRUE	1	0.492495006928753	2		433	431	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939036	76939036	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	89	407	0	ENST00000373344.5:c.1712G>T	p.Arg571Ile	p.R571I	ENST00000373344	NM_000489.3	571	aGa/aTa	9/35	1	2	FACETS	0.844	0.753	0.941	0.844	0.753	0.941	CLONAL	1	TRUE	1	0.492495006928753	2		407	428	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939282	76939282	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1557141595	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	89	461	0	ENST00000373344.5:c.1466C>T	p.Thr489Ile	p.T489I	ENST00000373344	NM_000489.3	489	aCc/aTc	9/35	1	2	FACETS	0.869	0.775	0.968	0.869	0.775	0.968	CLONAL	1	TRUE	1	0.492495006928753	2		461	416	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939357	76939357	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	103	463	0	ENST00000373344.5:c.1391T>C	p.Leu464Pro	p.L464P	ENST00000373344	NM_000489.3	464	cTt/cCt	9/35	1	2	FACETS	0.93	0.837	1	0.93	0.837	1	CLONAL	1	TRUE	1	0.492495006928753	2		463	450	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76949351	76949351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	59	371	0	ENST00000373344.5:c.446G>A	p.Arg149Lys	p.R149K	ENST00000373344	NM_000489.3	149	aGa/aAa	6/35	1	2	FACETS	0.664	0.574	0.761	0.664	0.574	0.761	SUBCLONAL	1	TRUE	1	0.492495006928753	2		371	361	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952091	76952091	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	63	287	0	ENST00000373344.5:c.344A>C	p.Asp115Ala	p.D115A	ENST00000373344	NM_000489.3	115	gAt/gCt	5/35	1	2	FACETS	0.847	0.739	0.963	0.847	0.739	0.963	CLONAL	1	TRUE	1	0.492495006928753	2		287	302	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972659	76972659	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	77	307	0	ENST00000373344.5:c.82G>T	p.Glu28Ter	p.E28*	ENST00000373344	NM_000489.3	28	Gaa/Taa	2/35	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.492495006928753	2		307	300	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196981	123196981	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	52	321	0	ENST00000218089.9:c.1747G>T	p.Glu583Ter	p.E583*	ENST00000218089	NM_001042749.1	583	Gaa/Taa	19/35	1	2	FACETS	0.718	0.616	0.829	0.718	0.616	0.829	SUBCLONAL	1	TRUE	1	0.492495006928753	2		321	294	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197739	123197739	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	64	363	0	ENST00000218089.9:c.1863G>T	p.Glu621Asp	p.E621D	ENST00000218089	NM_001042749.1	621	gaG/gaT	20/35	1	2	FACETS	0.925	0.809	1	0.925	0.809	1	CLONAL	1	TRUE	1	0.492495006928753	2		363	281	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217393	123217393	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	81	305	0	ENST00000218089.9:c.3047G>T	p.Arg1016Ile	p.R1016I	ENST00000218089	NM_001042749.1	1016	aGa/aTa	29/35	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.492495006928753	2		305	287	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480575	123480575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	101	412	0	ENST00000371139.4:c.83G>A	p.Ser28Asn	p.S28N	ENST00000371139	NM_001114937.2	28	aGc/aAc	1/4	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.492495006928753	2		412	373	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480631	123480631	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	71	388	0	ENST00000371139.4:c.137+2T>C		p.X46_splice	ENST00000371139	NM_001114937.2	46			1	2	FACETS	0.915	0.806	1	0.915	0.806	1	CLONAL	1	TRUE	1	0.492495006928753	2		388	315	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123505234	123505234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1304562074	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	117	605	0	ENST00000371139.4:c.380C>T	p.Ala127Val	p.A127V	ENST00000371139	NM_001114937.2	127	gCc/gTc	4/4	1	2	FACETS	0.862	0.781	0.948	0.862	0.781	0.948	CLONAL	1	TRUE	1	0.492495006928753	2		605	551	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858120	152858120	+	synonymous_variant	Silent	SNP	G	G	A	rs782615471	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	72	411	0	ENST00000406277.2:c.495C>T	p.Ala165=	p.A165=	ENST00000406277	NM_152274.4	165	gcC/gcT	6/7	1	2	FACETS	0.86	0.757	0.97	0.86	0.757	0.97	CLONAL	1	TRUE	1	0.492495006928753	2		411	340	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519589	137519589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748947618	NA	P-0058900-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	110	420	0	ENST00000367739.4:c.1049C>T	p.Ser350Phe	p.S350F	ENST00000367739	NM_000416.2	350	tCt/tTt	7/7	1	2	FACETS	0.892	0.805	0.983	0.892	0.805	0.983	CLONAL	1	TRUE	1	0.492495006928753	2		420	501	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098800	178098800	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	65	450	0	ENST00000397062.3:c.245A>G	p.Glu82Gly	p.E82G	ENST00000397062	NM_006164.4	82	gAa/gGa	2/5	1	2	FACETS	0.382	0.331	0.439	0.382	0.331	0.439	SUBCLONAL	1	TRUE	1	0.421841683430338	2		450	806	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790165	40790165	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	71	583	0	ENST00000373198.4:c.2566G>A	p.Glu856Lys	p.E856K	ENST00000373198	NM_133170.3	856	Gag/Aag	18/32	0.133082859214964	5	FACETS	0.738	0.643	0.84	0.184	0.16	0.21	INDETERMINATE	1	TRUE	1	0.421841683430338	5		583	745	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691039	NA	P-0058921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	379	692	0	ENST00000269305.4:c.919+1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.421841683430338	2	FACETS	0.947	0.902	0.992	0.947	0.902	0.992	CLONAL	2	TRUE	0	0.421841683430338	2		692	949	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255007	16255007	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs72649638	NA	P-0058921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	78	576	0	ENST00000375759.3:c.2272C>T	p.Arg758Ter	p.R758*	ENST00000375759	NM_015001.2	758	Cga/Tga	11/15	0.269265004795057	1	FACETS	0.45	0.395	0.508	0.45	0.395	0.508	SUBCLONAL	1	TRUE	0	0.421841683430338	1		576	649	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759527	133759527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	182	754	1	ENST00000318560.5:c.1850G>A	p.Arg617His	p.R617H	ENST00000318560	NM_005157.4	617	cGc/cAc	11/11	1	2	FACETS	0.826	0.761	0.893	0.826	0.761	0.893	CLONAL	1	TRUE	1	0.421841683430338	2		755	1045	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370874	55370874	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	102	577	1	ENST00000297316.4:c.176C>T	p.Ala59Val	p.A59V	ENST00000297316	NM_022454.3	59	gCg/gTg	1/2	1	2	FACETS	0.657	0.588	0.731	0.657	0.588	0.731	SUBCLONAL	1	TRUE	1	0.421841683430338	2		578	736	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675562	86675562	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0058921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	72	157	0	ENST00000274376.6:c.2498C>G	p.Ser833Ter	p.S833*	ENST00000274376	NM_002890.2	833	tCa/tGa	19/25	0.408429921736563	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	0	0.421841683430338	1		157	260	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098919	178098942	+	inframe_deletion	In_Frame_Del	DEL	TCGCTGACTGAAGTCAAATACTTC	TCGCTGACTGAAGTCAAATACTTC	-	novel	NA	P-0058921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	143	384	0	ENST00000397062.3:c.103_126del	p.Glu35_Arg42del	p.E35_R42del	ENST00000397062	NM_006164.4	35	GAAGTATTTGACTTCAGTCAGCGA/-	2/5	1	2	FACETS	0.876	0.799	0.956	0.876	0.799	0.956	CLONAL	1	TRUE	1	0.421841683430338	2		384	774	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665747	241665747	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	55	363	0	ENST00000366560.3:c.1232T>C	p.Met411Thr	p.M411T	ENST00000366560	NM_000143.3	411	aTg/aCg	8/10	1	2	FACETS	0.421	0.36	0.489	0.421	0.36	0.489	SUBCLONAL	1	TRUE	1	0.421841683430338	2		363	619	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667501	241667501	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	33	334	0	ENST00000366560.3:c.949G>C	p.Ala317Pro	p.A317P	ENST00000366560	NM_000143.3	317	Gct/Cct	7/10	1	2	FACETS	0.297	0.241	0.36	0.297	0.241	0.36	SUBCLONAL	1	TRUE	1	0.421841683430338	2		334	527	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456439	32456459	+	inframe_deletion	In_Frame_Del	DEL	CGGCTCCGCGCCGCCCCAGCT	CGGCTCCGCGCCGCCCCAGCT	-	novel	NA	P-0058921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	71	593	0	ENST00000332351.3:c.433_453del	p.Ser145_Pro151del	p.S145_P151del	ENST00000332351	NM_024426.4	145	AGCTGGGGCGGCGCGGAGCCG/-	1/10	1	2	FACETS	0.508	0.443	0.579	0.508	0.443	0.579	SUBCLONAL	1	TRUE	1	0.421841683430338	2		593	662	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035299	42035299	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	193	539	0	ENST00000219905.7:c.5141C>G	p.Thr1714Ser	p.T1714S	ENST00000219905	NM_001164273.1	1714	aCt/aGt	15/24	NA	2	FACETS	0.965	0.893	1			1	INDETERMINATE	1	TRUE	NA	0.421841683430338	2		539	948	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241034	39241034	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	50	226	0	ENST00000402219.2:c.2037A>C	p.Lys679Asn	p.K679N	ENST00000402219	NM_005633.3	679	aaA/aaC	12/23	1	2	FACETS	0.541	0.46	0.63	0.541	0.46	0.63	SUBCLONAL	1	TRUE	1	0.421841683430338	2		226	438	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557319	187557329	+	frameshift_variant	Frame_Shift_Del	DEL	TTGGAGATCCA	TTGGAGATCCA	-	novel	NA	P-0058921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	97	535	0	ENST00000441802.2:c.4033_4043del	p.Trp1345AlafsTer11	p.W1345Afs*11	ENST00000441802	NM_005245.3	1345	TGGATCTCCAAg/g	6/27	0.206077280621033	1	FACETS	0.577	0.515	0.643	0.577	0.515	0.643	INDETERMINATE	1	TRUE	0	0.421841683430338	1		535	629	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056599	26056599	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1484542952	NA	P-0058921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	99	593	0	ENST00000343677.2:c.58G>A	p.Val20Ile	p.V20I	ENST00000343677	NM_005319.3	20	Gta/Ata	1/1	0.179500204029176	0	FACETS	0.454	0.406	0.505			1	INDETERMINATE	1	TRUE	0	0.421841683430338	0		593	598	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38139034	38139034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201914561	NA	P-0058921-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	119	321	0	ENST00000317025.8:c.3569G>A	p.Arg1190Gln	p.R1190Q	ENST00000317025	NM_023034.1	1190	cGa/cAa	20/24	1	2	FACETS	0.871	0.787	0.958	0.871	0.787	0.958	CLONAL	1	TRUE	1	0.421841683430338	2		321	648	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449875	29449875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150344432	NA	P-0058932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	35	938	0	ENST00000389048.3:c.2980G>A	p.Glu994Lys	p.E994K	ENST00000389048	NM_004304.4	994	Gaa/Aaa	18/29	0.255833730458586	2	FACETS	0.899	0.742	1	0.449	0.371	0.536	CLONAL	1	TRUE	0	0.349215711075457	2		938	223	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750607	128750607	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs61752959	NA	P-0058932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	12	774	3	ENST00000377970.2:c.144G>C	p.Gln48His	p.Q48H	ENST00000377970	NM_002467.4	48	caG/caC	2/3	0.349215711075457	5	FACETS	0.472	0.331	0.645	0.157	0.11	0.215	SUBCLONAL	1	TRUE	2	0.349215711075457	5		777	222	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163399	32163399	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058932-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	30	851	1	ENST00000375023.3:c.5827A>T	p.Arg1943Trp	p.R1943W	ENST00000375023	NM_004557.3	1943	Agg/Tgg	30/30	0.220026491082948	4	FACETS	0.694	0.56	0.846	0.347	0.28	0.423	SUBCLONAL	1	TRUE	2	0.349215711075457	4		852	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0058933-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	259	522	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.80408923732689	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.80408923732689	2		522	299	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0058933-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	215	412	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.786115702828926	4	FACETS	0.955	0.897	1	0.955	0.897	1	CLONAL	2	TRUE	2	0.80408923732689	4		412	505	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243484	46243484	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058933-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	317	354	0	ENST00000334344.6:c.1837C>T	p.Gln613Ter	p.Q613*	ENST00000334344	NM_152641.2	613	Cag/Tag	14/21	0.786115702828926	4	FACETS	0.981	0.932	1	0.981	0.932	1	CLONAL	2	TRUE	2	0.80408923732689	4		354	725	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222265	2222265	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369350082	NA	P-0058933-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	270	451	2	ENST00000398665.3:c.3097G>A	p.Gly1033Ser	p.G1033S	ENST00000398665	NM_032482.2	1033	Ggc/Agc	24/28	0.80408923732689	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.80408923732689	2		453	323	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244184	46244184	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058933-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	318	469	0	ENST00000334344.6:c.2278C>G	p.Gln760Glu	p.Q760E	ENST00000334344	NM_152641.2	760	Cag/Gag	15/21	0.786115702828926	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.80408923732689	4		469	657	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582127	189582127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058933-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	312	432	0	ENST00000264731.3:c.686C>G	p.Pro229Arg	p.P229R	ENST00000264731	NM_003722.4	229	cCt/cGt	5/14	0.757498811986725	5	FACETS	1	0.961	1	0.679	0.642	0.715	CLONAL	2	TRUE	2	0.80408923732689	5		432	841	SUCCESS
APC	324	MSKCC	GRCh37	5	112174175	112174175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554084565	NA	P-0058933-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	166	398	0	ENST00000257430.4:c.2884G>A	p.Asp962Asn	p.D962N	ENST00000257430	NM_000038.5	962	Gat/Aat	16/16	0.80408923732689	6	FACETS	1	0.965	1	0.274	0.251	0.297	CLONAL	1	TRUE	2	0.80408923732689	6		398	984	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971121	21971121	+	inframe_insertion	In_Frame_Ins	INS	G	G	AGTGAGA	novel	NA	P-0058933-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	86	486	0	ENST00000304494.5:c.237delinsTCTCACT	p.Leu78_Thr79dup	p.L78_T79dup	ENST00000304494	NM_000077.4	78	acC/acTCTCACT	2/3	0.80408923732689	1	FACETS	0.715	0.649	0.78	0.715	0.649	0.78	SUBCLONAL	1	TRUE	0	0.80408923732689	1		486	179	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	37	477	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.933	0.784	1	1	0.966	1	CLONAL	2	FALSE	1	0.287359703102128	2		477	138	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0058952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	81	547	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	1	2	FACETS	0.935	0.841	1	1	0.988	1	CLONAL	3	FALSE	1	0.287359703102128	2		547	201	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0058952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	40	185	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.94	1	1	0.975	1	CLONAL	2	FALSE	1	0.287359703102128	2		185	114	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539951	187539951	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs777631605	NA	P-0058952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	142	472	0	ENST00000441802.2:c.7789C>T	p.Arg2597Ter	p.R2597*	ENST00000441802	NM_005245.3	2597	Cga/Tga	10/27	1	2	FACETS	1	0.927	1	1	0.993	1	CLONAL	3	FALSE	1	0.287359703102128	2		472	329	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052632	42052632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779811318	NA	P-0058952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	151	617	0	ENST00000219905.7:c.7303C>T	p.Arg2435Trp	p.R2435W	ENST00000219905	NM_001164273.1	2435	Cgg/Tgg	20/24	1	2	FACETS	0.981	0.91	1	1	0.994	1	CLONAL	3	FALSE	1	0.287359703102128	2		617	357	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212365	36212365	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	141	905	0	ENST00000222270.7:c.2116C>T	p.Arg706Ter	p.R706*	ENST00000222270	NM_014727.1	706	Cga/Tga	3/37	1	2	FACETS	0.935	0.863	1	1	0.993	1	CLONAL	3	FALSE	1	0.287359703102128	2		905	350	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852397	63852397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	121	823	1	ENST00000279873.7:c.3175G>A	p.Gly1059Ser	p.G1059S	ENST00000279873	NM_032199.2	1059	Ggt/Agt	10/10	1	2	FACETS	0.861	0.788	0.935	1	0.992	1	CLONAL	3	FALSE	1	0.287359703102128	2		824	326	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727033	243727033	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	74	395	0	ENST00000263826.5:c.937C>G	p.Leu313Val	p.L313V	ENST00000263826	NM_005465.4	313	Ctg/Gtg	9/13	1	2	FACETS	0.97	0.869	1	1	0.987	1	CLONAL	3	FALSE	1	0.287359703102128	2		395	177	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227833	36227833	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	134	875	0	ENST00000222270.7:c.7318G>T	p.Glu2440Ter	p.E2440*	ENST00000222270	NM_014727.1	2440	Gag/Tag	32/37	1	2	FACETS	0.993	0.917	1	1	0.993	1	CLONAL	3	FALSE	1	0.287359703102128	2		875	313	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121052	29121052	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876659653	NA	P-0058952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	76	392	0	ENST00000328354.6:c.505T>A	p.Phe169Ile	p.F169I	ENST00000328354	NM_007194.3	169	Ttt/Att	4/15	1	2	FACETS	0.933	0.836	1	1	0.987	1	CLONAL	3	FALSE	1	0.287359703102128	2		392	189	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894230	NA	P-0058952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	141	771	0	ENST00000451590.1:c.35G>A	p.Gly12Asp	p.G12D	ENST00000451590	NM_001130442.1	12	gGc/gAc	2/5	1	2	FACETS	1	0.943	1	1	0.993	1	CLONAL	3	FALSE	1	0.287359703102128	2		771	320	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654618	67654618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	94	501	0	ENST00000264010.4:c.1105C>T	p.His369Tyr	p.H369Y	ENST00000264010	NM_006565.3	369	Cac/Tac	6/12	1	2	FACETS	0.839	0.758	0.922	1	0.989	1	CLONAL	3	FALSE	1	0.287359703102128	2		501	260	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37083760	37083760	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs63751244	NA	P-0058952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	67	303	0	ENST00000231790.2:c.1669G>A	p.Glu557Lys	p.E557K	ENST00000231790	NM_000249.3	557	Gaa/Aaa	15/19	0.160694294915353	4	FACETS	0.967	0.854	1	1	0.975	1	INDETERMINATE	3	FALSE	2	0.287359703102128	4		303	207	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629566	187629578	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAGCAGCTTTG	AAAAGCAGCTTTG	-	novel	NA	P-0058952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	162	760	0	ENST00000441802.2:c.1404_1416del	p.Tyr468Ter	p.Y468*	ENST00000441802	NM_005245.3	468	taCAAAGCTGCTTTT/ta	2/27	1	2	FACETS	0.928	0.862	0.995	1	0.994	1	CLONAL	3	FALSE	1	0.287359703102128	2		760	405	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752321	57752322	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0058952-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	86	372	0	ENST00000274289.3:c.1251dup	p.Glu418Ter	p.E418*	ENST00000274289	NM_006622.3	417	-/T	9/14	0.160694294915353	4	FACETS	0.988	0.887	1	1	0.981	1	INDETERMINATE	3	FALSE	2	0.287359703102128	4		372	260	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0058988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	286	609	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	0.84499984772709	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.84499984772709	1		609	370	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0058988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	87	299	0	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	0.84499984772709	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.84499984772709	1		299	108	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803802	43803802	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	251	590	0	ENST00000372470.3:c.112C>G	p.Leu38Val	p.L38V	ENST00000372470	NM_005373.2	38	Ctg/Gtg	2/12	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.84499984772709	2		590	551	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248637	8248637	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1565174484	NA	P-0058988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	279	701	0	ENST00000335790.3:c.250A>T	p.Thr84Ser	p.T84S	ENST00000335790	NM_002315.2	84	Acc/Tcc	3/4	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.84499984772709	2		701	577	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436542	49436542	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	251	595	0	ENST00000301067.7:c.5764C>T	p.Gln1922Ter	p.Q1922*	ENST00000301067	NM_003482.3	1922	Cag/Tag	26/54	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.84499984772709	2		595	549	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061333	38061333	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	214	553	0	ENST00000250448.2:c.656G>T	p.Arg219Leu	p.R219L	ENST00000250448	NM_004496.3	219	cGc/cTc	2/2	1	2	FACETS	0.941	0.883	1	0.941	0.883	1	CLONAL	1	TRUE	1	0.84499984772709	2		553	538	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73096338	73096341	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	ATTC	ATTC	-	novel	NA	P-0058988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	63	225	0	ENST00000356692.5:c.119_122del	p.Ile40SerfsTer16	p.I40Sfs*16	ENST00000356692		40	ATTCag/ag	3/9	0.84499984772709	1	FACETS	0.957	0.876	1	0.957	0.876	1	CLONAL	1	TRUE	0	0.84499984772709	1		225	90	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582453	119582453	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0058988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	189	418	0	ENST00000316626.5:c.949-1G>C		p.X317_splice	ENST00000316626		317			0.84499984772709	3	FACETS	1	0.976	1	0.553	0.514	0.593	CLONAL	1	TRUE	1	0.84499984772709	3		418	575	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672800	86672800	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	125	436	0	ENST00000274376.6:c.2287G>C	p.Glu763Gln	p.E763Q	ENST00000274376	NM_002890.2	763	Gaa/Caa	17/25	1	2	FACETS	0.957	0.88	1	0.957	0.88	1	CLONAL	1	TRUE	1	0.84499984772709	2		436	309	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776937	76776937	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058988-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	108	401	0	ENST00000373344.5:c.7015A>C	p.Thr2339Pro	p.T2339P	ENST00000373344	NM_000489.3	2339	Aca/Cca	33/35	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.84499984772709	2		401	228	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0059006-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	57	125	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.684716149393201	2	FACETS	0.979	0.889	1	0.979	0.889	1	CLONAL	2	TRUE	0	0.684716149393201	2		125	85	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0059006-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	321	547	0	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	0.684716149393201	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.684716149393201	1		547	490	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115977	8115978	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0059006-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	219	607	0	ENST00000346208.3:c.1323_1324del	p.Met442GlyfsTer64	p.M442Gfs*64	ENST00000346208		441	gcCAtg/gctg	6/6	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.684716149393201	2		607	633	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091344	193091344	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059006-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	49	539	0	ENST00000367435.3:c.14T>C	p.Leu5Pro	p.L5P	ENST00000367435	NM_024529.4	5	cTt/cCt	1/17	1	2	FACETS	0.277	0.235	0.324	0.277	0.235	0.324	SUBCLONAL	1	TRUE	1	0.684716149393201	2		539	516	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937497	178937497	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059006-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	80	184	0	ENST00000263967.3:c.1885T>A	p.Ser629Thr	p.S629T	ENST00000263967	NM_006218.2	629	Tct/Act	12/21	0.684716149393201	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.684716149393201	2		184	106	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0059009-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	209	293	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.338643431420391	3	FACETS	1	0.979	1	0.733	0.687	0.779	CLONAL	2	TRUE	0	0.485138898565466	3		293	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059009-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	275	759	0	ENST00000269305.4:c.472C>G	p.Arg158Gly	p.R158G	ENST00000269305	NM_001126112.2	158	Cgc/Ggc	5/11	0.34011772323406	2	FACETS	0.766	0.723	0.81	0.766	0.723	0.81	SUBCLONAL	2	TRUE	0	0.485138898565466	2		759	740	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922550	56922550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059009-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1238	331	583	0	ENST00000519728.1:c.1420G>A	p.Asp474Asn	p.D474N	ENST00000519728	NM_002350.3	474	Gac/Aac	13/13	0.485138898565466	8	FACETS	1	0.977	1	0.356	0.335	0.377	CLONAL	2	TRUE	2	0.485138898565466	8		583	1569	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981315	68981315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866864487	NA	P-0059009-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	132	291	0	ENST00000288368.4:c.1387C>T	p.Arg463Cys	p.R463C	ENST00000288368	NM_024870.2	463	Cgc/Tgc	12/40	0.485138898565466	8	FACETS	0.834	0.757	0.915	0.278	0.252	0.305	CLONAL	2	TRUE	2	0.485138898565466	8		291	801	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377327	118377327	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059009-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	391	609	0	ENST00000534358.1:c.10720G>T	p.Asp3574Tyr	p.D3574Y	ENST00000534358	NM_005933.3	3574	Gac/Tac	27/36	0.485138898565466	3	FACETS	1	0.994	1	0.811	0.776	0.847	CLONAL	2	TRUE	0	0.485138898565466	3		609	823	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105605	30105606	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0059009-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	274	576	0	ENST00000331968.5:c.1080_1081delinsTT	p.Met360_Glu361delinsIleTer	p.M360_E361delinsI*	ENST00000331968	NM_002742.2	360	atGGaa/atTTaa	7/18	0.485138898565466	3	FACETS	0.873	0.822	0.924	0.873	0.822	0.924	CLONAL	2	TRUE	1	0.485138898565466	3		576	804	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992881	72992881	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059009-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	110	581	0	ENST00000268489.5:c.1164G>T	p.Glu388Asp	p.E388D	ENST00000268489	NM_006885.3	388	gaG/gaT	2/10	1	2	FACETS	0.767	0.691	0.848	0.767	0.691	0.848	SUBCLONAL	1	TRUE	1	0.485138898565466	2		581	591	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376260	225376260	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059009-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	145	336	0	ENST00000264414.4:c.694G>A	p.Val232Ile	p.V232I	ENST00000264414	NM_003590.4	232	Gta/Ata	6/16	0.341121977855967	5	FACETS	0.848	0.777	0.922	0.565	0.517	0.615	CLONAL	2	TRUE	2	0.485138898565466	5		336	609	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957524	1957532	+	inframe_deletion	In_Frame_Del	DEL	GGGAAGAAG	GGGAAGAAG	-	novel	NA	P-0059009-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	213	517	1	ENST00000382891.5:c.2623_2631del	p.Gly875_Lys877del	p.G875_K877del	ENST00000382891	NM_133335.3	875	GGGAAGAAG/-	14/22	0.303547696910919	4	FACETS	0.85	0.792	0.91	0.85	0.792	0.91	CLONAL	2	TRUE	2	0.485138898565466	4		518	767	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540904	187540904	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059009-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	122	658	0	ENST00000441802.2:c.6836A>T	p.Asn2279Ile	p.N2279I	ENST00000441802	NM_005245.3	2279	aAc/aTc	10/27	0.338618375492945	3	FACETS	0.799	0.723	0.88	0.4	0.361	0.44	SUBCLONAL	1	TRUE	1	0.485138898565466	3		658	782	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81399221	81399221	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059009-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	89	599	0	ENST00000222390.5:c.67C>A	p.Pro23Thr	p.P23T	ENST00000222390	NM_000601.4	23	Ccc/Acc	1/18	0.338618375492945	3	FACETS	0.69	0.612	0.773	0.345	0.306	0.387	SUBCLONAL	1	TRUE	1	0.485138898565466	3		599	661	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970971	70970971	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059009-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1348	101	519	0	ENST00000276594.2:c.1290G>T	p.Arg430Ser	p.R430S	ENST00000276594	NM_024504.3	430	agG/agT	6/8	0.485138898565466	8	FACETS	0.706	0.628	0.789	0.118	0.104	0.132	SUBCLONAL	1	TRUE	2	0.485138898565466	8		519	1449	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874284	76874284	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059009-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	82	340	0	ENST00000373344.5:c.5438G>T	p.Gly1813Val	p.G1813V	ENST00000373344	NM_000489.3	1813	gGa/gTa	21/35	0.365814640602068	3	FACETS	0.873	0.773	0.98	0.437	0.386	0.49	CLONAL	1	TRUE	1	0.485138898565466	3		340	481	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938865	76938865	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059009-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	108	505	0	ENST00000373344.5:c.1883G>T	p.Gly628Val	p.G628V	ENST00000373344	NM_000489.3	628	gGa/gTa	9/35	0.365814640602068	3	FACETS	0.875	0.787	0.969	0.438	0.393	0.485	CLONAL	1	TRUE	1	0.485138898565466	3		505	632	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059012-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	77	121	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		121	273	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207203	1207203	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0059012-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	195	182	0	ENST00000326873.7:c.290+1G>T		p.X97_splice	ENST00000326873	NM_000455.4	97			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		182	463	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348782	11348782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059012-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	72	287	0	ENST00000332029.2:c.554C>T	p.Thr185Ile	p.T185I	ENST00000332029	NM_003745.1	185	aCc/aTc	2/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		287	579	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435238	18435238	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059012-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	227	574	0	ENST00000266497.5:c.223G>T	p.Gly75Trp	p.G75W	ENST00000266497		75	Ggg/Tgg	1/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		574	568	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176145102	176145102	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059012-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	32	362	0	ENST00000367669.3:c.509G>T	p.Cys170Phe	p.C170F	ENST00000367669	NM_022457.5	170	tGt/tTt	3/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		362	365	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333398	70333398	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs73276466	NA	P-0059012-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	115	475	0	ENST00000373644.4:c.1303G>T	p.Val435Phe	p.V435F	ENST00000373644	NM_030625.2	435	Gtt/Ttt	2/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		475	475	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544966	86544966	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059012-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	55	287	0	ENST00000262426.4:c.791C>A	p.Ser264Ter	p.S264*	ENST00000262426	NM_001451.2	264	tCg/tAg	1/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		287	434	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852020	128852020	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059012-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	104	446	0	ENST00000249373.3:c.2092C>G	p.Pro698Ala	p.P698A	ENST00000249373	NM_005631.4	698	Ccc/Gcc	12/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		446	502	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019976	123019976	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059012-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	46	379	1	ENST00000355640.3:c.464C>T	p.Pro155Leu	p.P155L	ENST00000355640		155	cCg/cTg	2/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		380	489	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0059016-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	141	395	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	1	2	FACETS	0.562	0.511	0.615	0.562	0.511	0.615	SUBCLONAL	1	TRUE	1	0.483683783076588	2		395	1038	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419921	152419924	+	missense_variant	Missense_Mutation	ONP	CTAT	CTAT	TCTC	novel	NA	P-0059016-T02-IM7	NA	A	A	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	122	334	0	ENST00000206249.3:c.1608_1611delinsTCTC	p.Tyr537Leu	p.Y537L	ENST00000206249	NM_000125.3	536	ctCTAT/ctTCTC	8/8	1	2	FACETS	0.57	0.515	0.628	0.57	0.515	0.628	SUBCLONAL	1	TRUE	1	0.483683783076588	2		334	885	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0059018-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	71	312	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.191899783737484	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	2	FALSE	0	0.22831657635765	2		312	302	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0059068-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	28	449	1	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.195	0.155	0.24	0.195	0.155	0.24	SUBCLONAL	1	TRUE	1	0.660087070527664	2		450	436	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445457	29445457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757580052	NA	P-0059068-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	24	403	0	ENST00000389048.3:c.3376G>A	p.Ala1126Thr	p.A1126T	ENST00000389048	NM_004304.4	1126	Gcc/Acc	21/29	1	2	FACETS	0.206	0.161	0.258	0.206	0.161	0.258	SUBCLONAL	1	TRUE	1	0.660087070527664	2		403	353	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041324	42041325	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0059068-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	48	436	0	ENST00000219905.7:c.5521dup	p.Arg1841ProfsTer10	p.R1841Pfs*10	ENST00000219905	NM_001164273.1	1840	atc/atCc	17/24	1	2	FACETS	0.285	0.24	0.333	0.285	0.24	0.333	SUBCLONAL	1	TRUE	1	0.660087070527664	2		436	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0059070-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	408	513	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.624865849474278	2	FACETS	0.983	0.947	1	0.983	0.947	1	CLONAL	2	TRUE	0	0.624865849474278	2		513	664	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0059070-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	159	403	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.944	0.871	1	0.944	0.871	1	CLONAL	1	TRUE	1	0.624865849474278	2		404	539	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042066	14042066	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059070-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	114	544	0	ENST00000311895.7:c.2613G>C	p.Lys871Asn	p.K871N	ENST00000311895	NM_005236.2	871	aaG/aaC	11/11	1	2	FACETS	0.472	0.425	0.522	0.472	0.425	0.522	SUBCLONAL	1	TRUE	1	0.624865849474278	2		544	773	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201875	67201875	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059070-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	110	637	0	ENST00000312629.5:c.1075G>C	p.Asp359His	p.D359H	ENST00000312629	NM_003952.2	359	Gat/Cat	13/15	1	2	FACETS	0.524	0.471	0.58	0.524	0.471	0.58	SUBCLONAL	1	TRUE	1	0.624865849474278	2		637	672	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719950	18719950	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059070-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	54	256	0	ENST00000266497.5:c.3847T>A	p.Tyr1283Asn	p.Y1283N	ENST00000266497		1283	Tac/Aac	27/31	0.304378671531582	3	FACETS	0.586	0.502	0.677	0.293	0.251	0.339	INDETERMINATE	1	TRUE	1	0.624865849474278	3		256	387	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391060	89391060	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059070-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	75	473	0	ENST00000336596.2:c.1126T>G	p.Cys376Gly	p.C376G	ENST00000336596	NM_005233.5	376	Tgc/Ggc	5/17	1	2	FACETS	0.408	0.357	0.462	0.408	0.357	0.462	SUBCLONAL	1	TRUE	1	0.624865849474278	2		473	589	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890086	76890086	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059070-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	157	281	0	ENST00000373344.5:c.4808A>G	p.Gln1603Arg	p.Q1603R	ENST00000373344	NM_000489.3	1603	cAg/cGg	17/35	0.624865849474278	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.624865849474278	1		281	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs878854073	NA	P-0059071-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	86	498	0	ENST00000269305.4:c.673-1G>A		p.X225_splice	ENST00000269305	NM_001126112.2	225			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		498	433	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157488217	157488217	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059072-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	173	523	0	ENST00000346085.5:c.2923T>G	p.Ser975Ala	p.S975A	ENST00000346085	NM_020732.3	975	Tcc/Gcc	10/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.754052493312512	2		523	440	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631839	90631839	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519906	NA	P-0059073-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	145	771	1	ENST00000330062.3:c.514A>G	p.Arg172Gly	p.R172G	ENST00000330062	NM_002168.2	172	Agg/Ggg	4/11	0.103599323440232	0	FACETS	0.345	0.316	0.375			1	INDETERMINATE	1	TRUE	0	0.614145153562265	0		772	528	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687312	37687312	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059073-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	57	607	0	ENST00000447079.4:c.4216G>T	p.Ala1406Ser	p.A1406S	ENST00000447079	NM_015083.1	1406	Gcc/Tcc	14/14	1	2	FACETS	0.411	0.353	0.474	0.411	0.353	0.474	SUBCLONAL	1	TRUE	1	0.614145153562265	2		607	452	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119000	70119000	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs772277252	NA	P-0059073-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	197	855	0	ENST00000245479.2:c.572A>C	p.Glu191Ala	p.E191A	ENST00000245479	NM_000346.3	191	gAg/gCg	2/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.614145153562265	2		855	567	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223992	36223992	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059073-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	174	722	0	ENST00000222270.7:c.6542C>T	p.Pro2181Leu	p.P2181L	ENST00000222270	NM_014727.1	2181	cCt/cTt	28/37	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.614145153562265	2		722	479	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437171	52437171	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059073-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	151	582	0	ENST00000460680.1:c.1873del	p.Glu625ArgfsTer12	p.E625Rfs*12	ENST00000460680	NM_004656.3	625	Gag/ag	14/17	0.614145153562265	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.614145153562265	1		582	320	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	147	477	0				ENST00000310581	NM_198253.2	-/1132			0.171576284671822	5	FACETS	0.958	0.879	1	0.638	0.586	0.693	INDETERMINATE	2	TRUE	2	0.489334251622301	5		477	544	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	54	458	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.366975195931017	4	FACETS	0.384	0.326	0.446	0.192	0.163	0.223	SUBCLONAL	1	TRUE	2	0.489334251622301	4		458	857	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	50	185	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.490096811149512	3	FACETS	1	0.942	1	0.6	0.515	0.691	CLONAL	1	TRUE	1	0.489334251622301	3		185	212	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651906	36651906	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	167	462	0	ENST00000244741.5:c.28C>T	p.Gln10Ter	p.Q10*	ENST00000244741	NM_000389.4	10	Cag/Tag	2/3	0.175450273391081	4	FACETS	1	0.988	1	0.708	0.652	0.766	INDETERMINATE	1	TRUE	2	0.489334251622301	4		462	718	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100436	8100436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1220437638	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	174	632	0	ENST00000346208.3:c.410C>T	p.Ser137Leu	p.S137L	ENST00000346208		137	tCg/tTg	3/6	0.339380158014474	3	FACETS	0.986	0.908	1	0.493	0.454	0.534	CLONAL	1	TRUE	1	0.489334251622301	3		632	898	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325170	123325170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371358242	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	72	406	0	ENST00000358487.5:c.158C>T	p.Ala53Val	p.A53V	ENST00000358487	NM_000141.4	53	gCg/gTg	3/18	0.272793854315799	1	FACETS	0.388	0.339	0.441	0.388	0.339	0.441	INDETERMINATE	1	TRUE	0	0.489334251622301	1		406	573	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017724	31017724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1005458245	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	36	323	0	ENST00000375687.4:c.586G>A	p.Asp196Asn	p.D196N	ENST00000375687	NM_015338.5	196	Gat/Aat	8/13	0.287501772181375	4	FACETS	0.395	0.324	0.475	0.197	0.162	0.238	INDETERMINATE	1	TRUE	2	0.489334251622301	4		323	555	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453149	140453149	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913361	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	200	254	0	ENST00000288602.6:c.1786G>C	p.Gly596Arg	p.G596R	ENST00000288602	NM_004333.4	596	Ggt/Cgt	15/18	0.436176704790549	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.489334251622301	3		254	488	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390302	56390302	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	29	259	0	ENST00000348428.3:c.1041G>C	p.Leu347Phe	p.L347F	ENST00000348428	NM_006785.3	347	ttG/ttC	10/17	0.339380158014474	3	FACETS	0.276	0.221	0.339	0.138	0.11	0.17	SUBCLONAL	1	TRUE	1	0.489334251622301	3		259	535	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999566	100999566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745363836	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	141	560	0	ENST00000325455.5:c.236C>T	p.Ser79Leu	p.S79L	ENST00000325455	NM_001202474.3	79	tCg/tTg	1/8	0.416997528214157	4	FACETS	0.889	0.81	0.973	0.445	0.405	0.487	CLONAL	1	TRUE	2	0.489334251622301	4		560	965	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380346	14380346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	158	412	0	ENST00000256196.4:c.71G>A	p.Gly24Asp	p.G24D	ENST00000256196		24	gGc/gAc	1/6	0.365506624593351	2	FACETS	1	0.99	1	0.749	0.693	0.806	CLONAL	1	TRUE	0	0.489334251622301	2		412	431	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446133	49446133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	325	610	0	ENST00000301067.7:c.1333G>A	p.Glu445Lys	p.E445K	ENST00000301067	NM_003482.3	445	Gag/Aag	10/54	0.215584257393591	5	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.489334251622301	5		610	1035	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	209	489	2	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	0.175450273391081	4	FACETS	0.767	0.714	0.823	0.767	0.714	0.823	INDETERMINATE	2	TRUE	2	0.489334251622301	4		491	829	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264401	46264401	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	62	398	0	ENST00000371998.3:c.1448C>T	p.Ser483Phe	p.S483F	ENST00000371998		483	tCt/tTt	11/23	0.287501772181375	4	FACETS	0.448	0.386	0.515	0.224	0.193	0.258	INDETERMINATE	1	TRUE	2	0.489334251622301	4		398	843	SUCCESS
MAD2L2	10459	MSKCC	GRCh37	1	11734846	11734846	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	22	273	0	ENST00000235310.3:c.622C>G	p.His208Asp	p.H208D	ENST00000235310		208	Cat/Gat	11/11	0.416340454913493	3	FACETS	0.258	0.199	0.326			1	SUBCLONAL	1	TRUE	NA	0.489334251622301	3		273	434	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106548	27106548	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	85	566	0	ENST00000324856.7:c.6159G>C	p.Leu2053Phe	p.L2053F	ENST00000324856	NM_006015.4	2053	ttG/ttC	20/20	1	2	FACETS	0.399	0.352	0.45	0.399	0.352	0.45	SUBCLONAL	1	TRUE	1	0.489334251622301	2		566	870	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107137	27107137	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	64	450	0	ENST00000324856.7:c.6748G>C	p.Glu2250Gln	p.E2250Q	ENST00000324856	NM_006015.4	2250	Gag/Cag	20/20	1	2	FACETS	0.368	0.318	0.423	0.368	0.318	0.423	SUBCLONAL	1	TRUE	1	0.489334251622301	2		450	710	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851870	63851870	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	71	487	0	ENST00000279873.7:c.2648A>C	p.Tyr883Ser	p.Y883S	ENST00000279873	NM_032199.2	883	tAt/tCt	10/10	0.339380158014474	3	FACETS	0.442	0.384	0.503	0.221	0.192	0.252	SUBCLONAL	1	TRUE	1	0.489334251622301	3		487	818	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47598965	47598965	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs371150449	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	57	408	0	ENST00000430070.2:c.635C>T	p.Ser212Leu	p.S212L	ENST00000430070	NM_018095.4	212	tCg/tTg	2/4	0.365506624593351	2	FACETS	0.313	0.267	0.362	0.156	0.133	0.181	SUBCLONAL	1	TRUE	0	0.489334251622301	2		408	745	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917683	94917683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	122	304	0	ENST00000536441.1:c.838G>A	p.Glu280Lys	p.E280K	ENST00000536441	NM_144665.3	280	Gag/Aag	6/10	0.416997528214157	4	FACETS	1	0.972	1	0.594	0.538	0.653	CLONAL	1	TRUE	2	0.489334251622301	4		304	625	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445278	49445278	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	390	632	0	ENST00000301067.7:c.2188G>T	p.Glu730Ter	p.E730*	ENST00000301067	NM_003482.3	730	Gag/Tag	10/54	0.215584257393591	5	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.489334251622301	5		632	1149	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431484	121431484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	69	427	0	ENST00000257555.6:c.688G>A	p.Glu230Lys	p.E230K	ENST00000257555		230	Gag/Aag	3/10	0.169256555749334	3	FACETS	0.489	0.425	0.558	0.244	0.212	0.279	INDETERMINATE	1	TRUE	1	0.489334251622301	3		427	718	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346397	89346397	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	48	513	0	ENST00000301030.4:c.6553G>C	p.Glu2185Gln	p.E2185Q	ENST00000301030	NM_001256183.1	2185	Gag/Cag	9/13	0.169256555749334	3	FACETS	0.373	0.314	0.437	0.186	0.157	0.219	INDETERMINATE	1	TRUE	1	0.489334251622301	3		513	655	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627830	37627830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	51	482	0	ENST00000447079.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000447079	NM_015083.1	582	tCa/tTa	2/14	0.366975195931017	4	FACETS	0.333	0.282	0.389	0.166	0.141	0.195	SUBCLONAL	1	TRUE	2	0.489334251622301	4		482	933	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40860003	40860003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	53	380	0	ENST00000428826.2:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000428826		545	Gag/Aag	15/21	0.366975195931017	4	FACETS	0.399	0.339	0.465	0.199	0.169	0.233	SUBCLONAL	1	TRUE	2	0.489334251622301	4		380	809	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223211	41223211	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	70	370	0	ENST00000357654.3:c.4720G>C	p.Asp1574His	p.D1574H	ENST00000357654	NM_007294.3	1574	Gac/Cac	15/23	0.366975195931017	4	FACETS	0.559	0.487	0.638	0.28	0.243	0.319	SUBCLONAL	1	TRUE	2	0.489334251622301	4		370	762	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39240622	39240622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	28	208	0	ENST00000402219.2:c.2146G>A	p.Glu716Lys	p.E716K	ENST00000402219	NM_005633.3	716	Gaa/Aaa	13/23	0.436176704790549	3	FACETS	0.423	0.338	0.519	0.211	0.169	0.26	SUBCLONAL	1	TRUE	1	0.489334251622301	3		208	337	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39240705	39240705	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	26	165	0	ENST00000402219.2:c.2064-1G>A		p.X688_splice	ENST00000402219	NM_005633.3	688			0.436176704790549	3	FACETS	0.401	0.317	0.496	0.2	0.158	0.248	SUBCLONAL	1	TRUE	1	0.489334251622301	3		165	330	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527576	41527576	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs769024926	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	67	355	0	ENST00000263253.7:c.1467G>T	p.Lys489Asn	p.K489N	ENST00000263253	NM_001429.3	489	aaG/aaT	6/31	0.169256555749334	3	FACETS	0.49	0.425	0.56	0.245	0.212	0.28	INDETERMINATE	1	TRUE	1	0.489334251622301	3		355	696	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527636	41527636	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs752280089	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	68	289	0	ENST00000263253.7:c.1527G>C	p.Met509Ile	p.M509I	ENST00000263253	NM_001429.3	509	atG/atC	6/31	0.169256555749334	3	FACETS	0.563	0.49	0.643	0.282	0.245	0.322	INDETERMINATE	1	TRUE	1	0.489334251622301	3		289	614	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531832	41531832	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	41	254	0	ENST00000263253.7:c.1544G>C	p.Gly515Ala	p.G515A	ENST00000263253	NM_001429.3	515	gGa/gCa	7/31	0.169256555749334	3	FACETS	0.467	0.389	0.553	0.233	0.194	0.277	INDETERMINATE	1	TRUE	1	0.489334251622301	3		254	447	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533746	41533746	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	53	279	0	ENST00000263253.7:c.1712G>A	p.Trp571Ter	p.W571*	ENST00000263253	NM_001429.3	571	tGg/tAg	8/31	0.169256555749334	3	FACETS	0.468	0.399	0.544	0.234	0.199	0.272	INDETERMINATE	1	TRUE	1	0.489334251622301	3		279	576	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281388	142281388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	146	358	0	ENST00000350721.4:c.856G>A	p.Asp286Asn	p.D286N	ENST00000350721	NM_001184.3	286	Gac/Aac	4/47	0.169256555749334	3	FACETS	1	0.988	1	0.73	0.67	0.791	INDETERMINATE	1	TRUE	1	0.489334251622301	3		358	509	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920348	1920348	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	55	320	0	ENST00000382891.5:c.1408G>T	p.Glu470Ter	p.E470*	ENST00000382891	NM_133335.3	470	Gag/Tag	5/22	0.193739928778342	3	FACETS	0.445	0.38	0.516	0.148	0.126	0.172	INDETERMINATE	1	TRUE	0	0.489334251622301	3		320	629	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630692	187630692	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	44	351	0	ENST00000441802.2:c.290G>A	p.Arg97Lys	p.R97K	ENST00000441802	NM_005245.3	97	aGa/aAa	2/27	0.193739928778342	3	FACETS	0.359	0.301	0.425	0.12	0.1	0.142	INDETERMINATE	1	TRUE	0	0.489334251622301	3		351	623	SUCCESS
APC	324	MSKCC	GRCh37	5	112179353	112179353	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	53	359	0	ENST00000257430.4:c.8062G>C	p.Glu2688Gln	p.E2688Q	ENST00000257430	NM_000038.5	2688	Gaa/Caa	16/16	0.115043668156494	5	FACETS	0.572	0.487	0.665	0.191	0.162	0.222	INDETERMINATE	1	TRUE	2	0.489334251622301	5		359	657	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672884	30672884	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	78	586	0	ENST00000376406.3:c.4076C>T	p.Ser1359Phe	p.S1359F	ENST00000376406	NM_014641.2	1359	tCt/tTt	10/15	0.175450273391081	4	FACETS	0.477	0.418	0.541	0.239	0.209	0.271	INDETERMINATE	1	TRUE	2	0.489334251622301	4		586	995	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339695	116339695	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	114	366	0	ENST00000397752.3:c.557del	p.Ser186TyrfsTer3	p.S186Yfs*3	ENST00000397752	NM_000245.2	186	tCa/ta	2/21	0.171576284671822	5	FACETS	1	0.939	1	0.353	0.318	0.39	INDETERMINATE	1	TRUE	2	0.489334251622301	5		366	763	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345962	152345962	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143856570	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	90	381	0	ENST00000359321.1:c.608C>T	p.Ser203Leu	p.S203L	ENST00000359321	NM_005431.1	203	tCg/tTg	3/3	0.436176704790549	3	FACETS	0.592	0.524	0.663	0.296	0.262	0.332	SUBCLONAL	1	TRUE	1	0.489334251622301	3		381	774	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238435	98238435	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	47	415	0	ENST00000331920.6:c.1609A>G	p.Thr537Ala	p.T537A	ENST00000331920	NM_000264.3	537	Acc/Gcc	12/24	0.489334251622301	2	FACETS	0.309	0.26	0.363	0.154	0.13	0.182	SUBCLONAL	1	TRUE	0	0.489334251622301	2		415	622	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855971	76855971	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	31	127	0	ENST00000373344.5:c.5629C>G	p.Gln1877Glu	p.Q1877E	ENST00000373344	NM_000489.3	1877	Cag/Gag	23/35	0.48149904108702	2	FACETS	0.401	0.325	0.487			1	SUBCLONAL	1	TRUE	NA	0.489334251622301	2		127	316	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611252	100611252	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059074-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	75	128	0	ENST00000308731.7:c.1354C>G	p.Leu452Val	p.L452V	ENST00000308731	NM_000061.2	452	Ctt/Gtt	15/19	0.48149904108702	2	FACETS	0.989	0.875	1			1	CLONAL	1	TRUE	NA	0.489334251622301	2		128	310	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0059075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	143	411	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	1	0.98	1	1	0.992	1	CLONAL	2	TRUE	1	0.239441750435397	2		411	490	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	156	573	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.978	1	1	0.993	1	CLONAL	2	TRUE	1	0.239441750435397	2		574	554	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645516	67645516	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	20	292	0	ENST00000264010.4:c.781G>A	p.Gly261Ser	p.G261S	ENST00000264010	NM_006565.3	261	Ggt/Agt	3/12	0.239441750435397	0	FACETS	0.652	0.501	0.826			1	SUBCLONAL	1	TRUE	0	0.239441750435397	0		292	195	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431445	49431445	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	175	563	0	ENST00000301067.7:c.9694G>T	p.Glu3232Ter	p.E3232*	ENST00000301067	NM_003482.3	3232	Gag/Tag	34/54	1	2	FACETS	0.858	0.795	0.923	1	0.994	1	CLONAL	3	TRUE	1	0.239441750435397	2		563	568	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711987	89711987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1085308053	NA	P-0059075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	121	256	0	ENST00000371953.3:c.605C>T	p.Thr202Ile	p.T202I	ENST00000371953	NM_000314.4	202	aCt/aTt	6/9	0.239441750435397	2	FACETS	0.986	0.917	1	1	0.992	1	CLONAL	5	TRUE	0	0.239441750435397	2		256	205	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243045	105243045	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	161	518	0	ENST00000349310.3:c.238T>G	p.Trp80Gly	p.W80G	ENST00000349310	NM_001014432.1	80	Tgg/Ggg	5/15	1	2	FACETS	0.909	0.84	0.98	1	0.994	1	CLONAL	3	TRUE	1	0.239441750435397	2		518	493	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591104	67591124	+	inframe_deletion	In_Frame_Del	DEL	TTAAACCAGACCTTATCCAGC	TTAAACCAGACCTTATCCAGC	-	novel	NA	P-0059075-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	114	357	0	ENST00000274335.5:c.1698_1718del	p.Ile566_Leu573delinsMet	p.I566_L573delinsM	ENST00000274335		566	aTTAAACCAGACCTTATCCAGCtg/atg	12/15	0.0923716910289447	4	FACETS	1	0.956	1	1	0.987	1	INDETERMINATE	3	TRUE	2	0.239441750435397	4		357	363	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0059076-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	100	525	0				ENST00000310581	NM_198253.2	-/1132			0.512992128613812	1	FACETS	0.979	0.887	1	0.979	0.887	1	CLONAL	1	TRUE	0	0.512992128613812	1		525	296	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0059076-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	288	390	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.510113821592013	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.512992128613812	2		390	503	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729163	66729163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516792	NA	P-0059076-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	157	562	0	ENST00000307102.5:c.371C>T	p.Pro124Leu	p.P124L	ENST00000307102	NM_002755.3	124	cCg/cTg	3/11	1	2	FACETS	0.97	0.892	1	0.97	0.892	1	CLONAL	1	TRUE	1	0.512992128613812	2		562	631	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685281	89685281	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060500116	NA	P-0059076-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	12	208	0	ENST00000371953.3:c.176C>G	p.Ser59Ter	p.S59*	ENST00000371953	NM_000314.4	59	tCa/tGa	3/9	0.512992128613812	1	FACETS	0.435	0.31	0.583	0.435	0.31	0.583	SUBCLONAL	1	TRUE	0	0.512992128613812	1		208	80	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411137	63411137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059076-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	131	554	0	ENST00000330258.3:c.2030C>T	p.Ser677Phe	p.S677F	ENST00000330258	NM_152424.3	677	tCc/tTc	2/2	0.16130304541644	1	FACETS	0.698	0.636	0.762	0.698	0.636	0.762	INDETERMINATE	1	TRUE	0	0.512992128613812	1		554	544	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309788	104309788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1280071055	NA	P-0059076-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	156	464	0	ENST00000369902.3:c.379G>A	p.Glu127Lys	p.E127K	ENST00000369902	NM_016169.3	127	Gaa/Aaa	3/12	0.512992128613812	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.512992128613812	1		464	443	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436709	110436710	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0059076-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	126	678	0	ENST00000375856.3:c.1691_1692delinsTT	p.Ala564Val	p.A564V	ENST00000375856	NM_003749.2	564	gCC/gTT	1/2	1	2	FACETS	0.901	0.82	0.986	0.901	0.82	0.986	CLONAL	1	TRUE	1	0.512992128613812	2		678	545	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682515	37682515	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059076-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	140	513	0	ENST00000447079.4:c.3706A>G	p.Ser1236Gly	p.S1236G	ENST00000447079	NM_015083.1	1236	Agt/Ggt	13/14	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.512992128613812	2		513	544	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909467	50909467	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059076-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	159	568	0	ENST00000440232.2:c.1271T>G	p.Val424Gly	p.V424G	ENST00000440232	NM_002691.3	424	gTg/gGg	11/27	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.512992128613812	2		568	611	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561010	9561010	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059076-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	174	554	0	ENST00000353224.5:c.772G>A	p.Gly258Arg	p.G258R	ENST00000353224	NM_177990.2	258	Gga/Aga	4/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.512992128613812	2		554	597	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264979	46264979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765672674	NA	P-0059076-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	145	534	0	ENST00000371998.3:c.1849G>A	p.Gly617Ser	p.G617S	ENST00000371998		617	Ggt/Agt	12/23	1	2	FACETS	0.96	0.879	1	0.96	0.879	1	CLONAL	1	TRUE	1	0.512992128613812	2		534	589	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059077-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	60	477	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.767	0.667	0.874	0.767	0.667	0.874	SUBCLONAL	1	TRUE	1	0.570767624252645	2		477	274	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0059077-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	118	323	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.570767624252645	2		323	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0059078-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	712	756	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.717814611754086	5	FACETS	1	0.996	1	1	0.996	1	CLONAL	5	FALSE	0	0.715302801025078	5		756	792	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259630	11260652	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTAAGAGGGTCTGTGTGACTTCAGCGATGTCTTGTGAGGTGAGGGCCAACTCGATGCTTCTGATGAGCTCATCCTGTTGATCTTCATTCAGTTCAGACCAGCAGGACACAAATGCAGCATTGAAGAGATCCCTGAAGGCAGAGAAGGTGGAAAATGGAGAGACCTCCCGTGCCTCTGCCTGCTGCCTCAAAGTCACACCTATCAATTCGCTTTTGGCATCACTGATTTTGGTTATACAAACCAGTGCTATACAGACCAGTGCTGTCCAAGAGAATTTTCCTGTCCAATATGGTAGCCAGTGATCACTAAAGCACTTGAACTGTGGCAAGTGTGGCCAAGGAACTGAATTTTACATTTTATTTATTTTTAATTAACCACATATGGCTAGTGTCTACTGAATTTTACACTGCAGGTACAGACATTGTGATATTCAGGGACTTGGGGGGCGAGTGGCAGGGCGGGGAGAAGAGCAGAGCAAAGTGACTTTTCTCCAAAGGAATATTTCTTGGCAGTTTTTGCATTATTTCTCTTCACTGGAGGAAATGGGAAATGAACAGTATAGGGACTTCTAACATAGAAGTTGGCATTAACAAATGCAGAAAATAATAATCATTAAATGATTCTTGGGATGTTTCTGGGACAATGTCTAAATTCTTAAGGTCAGAAATGTCAAAGGCAGCATCTGCAATTGCTTTCAAAATATAACCAGAATCCTTAGTTGGATGGTCATAAAAAATGACAACAGGACTAGAAGCATTAGCAAATAGGATCCAAATCCTTAAGTTCTAAAAGATTTTCTAAGCCAACAGTTGGGGCCTCACAAAGACATGGAACCAGAGGTTCCATTTCAAAGATTACTATGACCACTTTACATTACCACAGTACCACATGATGGACACATTTGCCATCCCTTACATCTAACATTAATTCTGTCCTCCCCACTGTTCTGGTGACTGTGCGGGGAAGGAAATGGGAAAAAACAGGATATACCTACAATGGATAGATTTAGCATTTGATGCCTCT	TTAAGAGGGTCTGTGTGACTTCAGCGATGTCTTGTGAGGTGAGGGCCAACTCGATGCTTCTGATGAGCTCATCCTGTTGATCTTCATTCAGTTCAGACCAGCAGGACACAAATGCAGCATTGAAGAGATCCCTGAAGGCAGAGAAGGTGGAAAATGGAGAGACCTCCCGTGCCTCTGCCTGCTGCCTCAAAGTCACACCTATCAATTCGCTTTTGGCATCACTGATTTTGGTTATACAAACCAGTGCTATACAGACCAGTGCTGTCCAAGAGAATTTTCCTGTCCAATATGGTAGCCAGTGATCACTAAAGCACTTGAACTGTGGCAAGTGTGGCCAAGGAACTGAATTTTACATTTTATTTATTTTTAATTAACCACATATGGCTAGTGTCTACTGAATTTTACACTGCAGGTACAGACATTGTGATATTCAGGGACTTGGGGGGCGAGTGGCAGGGCGGGGAGAAGAGCAGAGCAAAGTGACTTTTCTCCAAAGGAATATTTCTTGGCAGTTTTTGCATTATTTCTCTTCACTGGAGGAAATGGGAAATGAACAGTATAGGGACTTCTAACATAGAAGTTGGCATTAACAAATGCAGAAAATAATAATCATTAAATGATTCTTGGGATGTTTCTGGGACAATGTCTAAATTCTTAAGGTCAGAAATGTCAAAGGCAGCATCTGCAATTGCTTTCAAAATATAACCAGAATCCTTAGTTGGATGGTCATAAAAAATGACAACAGGACTAGAAGCATTAGCAAATAGGATCCAAATCCTTAAGTTCTAAAAGATTTTCTAAGCCAACAGTTGGGGCCTCACAAAGACATGGAACCAGAGGTTCCATTTCAAAGATTACTATGACCACTTTACATTACCACAGTACCACATGATGGACACATTTGCCATCCCTTACATCTAACATTAATTCTGTCCTCCCCACTGTTCTGGTGACTGTGCGGGGAAGGAAATGGGAAAAAACAGGATATACCTACAATGGATAGATTTAGCATTTGATGCCTCT	-	novel	NA	P-0059078-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	45	564	0	ENST00000361445.4:c.3945-891_4076del		p.X1315_splice	ENST00000361445	NM_004958.3	1315		27/58	0.652458036742275	4	FACETS	0.441	0.371	0.519	0.147	0.123	0.173	SUBCLONAL	1	FALSE	1	0.715302801025078	4		564	489	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400833	72400833	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059078-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	156	379	0	ENST00000357731.5:c.338A>T	p.Asp113Val	p.D113V	ENST00000357731	NM_173808.2	113	gAt/gTt	2/7	0.49960217425062	3	FACETS	1	0.949	1			1	CLONAL	2	FALSE	NA	0.715302801025078	3		379	291	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512271	120512271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059078-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	163	754	0	ENST00000256646.2:c.971G>A	p.Cys324Tyr	p.C324Y	ENST00000256646	NM_024408.3	324	tGt/tAt	6/34	0.634461921268942	5	FACETS	1	0.929	1	0.338	0.31	0.367	CLONAL	1	FALSE	2	0.715302801025078	5		754	932	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736297	243736297	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059078-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	343	475	0	ENST00000263826.5:c.750C>G	p.Phe250Leu	p.F250L	ENST00000263826	NM_005465.4	250	ttC/ttG	8/13	0.717814611754086	5	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	FALSE	2	0.715302801025078	5		475	624	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112745403	112745416	+	frameshift_variant	Frame_Shift_Del	DEL	ATTACGCTGGATGT	ATTACGCTGGATGT	-	novel	NA	P-0059078-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	98	298	0	ENST00000369452.4:c.722_735del	p.Ile241SerfsTer6	p.I241Sfs*6	ENST00000369452	NM_007373.3	241	ATTACGCTGGATGTa/a	3/9	0.654437491498879	4	FACETS	1	0.972	1	0.776	0.709	0.842	CLONAL	2	FALSE	1	0.715302801025078	4		298	202	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231485	46231485	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059078-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	142	312	0	ENST00000334344.6:c.1325G>A	p.Ser442Asn	p.S442N	ENST00000334344	NM_152641.2	442	aGc/aAc	10/21	0.562807519750098	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	FALSE	2	0.715302801025078	4		312	322	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792717	33792717	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059078-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	82	510	1	ENST00000498907.2:c.604G>C	p.Ala202Pro	p.A202P	ENST00000498907	NM_004364.3	202	Gcc/Ccc	1/1	0.715302801025078	8	FACETS	0.645	0.567	0.73	0.108	0.094	0.122	SUBCLONAL	1	FALSE	2	0.715302801025078	8		511	1118	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47492815	47492819	+	frameshift_variant	Frame_Shift_Ins	INS	CTGGC	CTGGC	TTTACAACCGTAA	novel	NA	P-0059078-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	103	520	1	ENST00000404338.3:c.3919_3923delinsTTTACAACCGTAA	p.Leu1307PhefsTer11	p.L1307Ffs*11	ENST00000404338	NM_004491.4	1307	CTGGCa/TTTACAACCGTAAa	4/6	0.715302801025078	5	FACETS	0.809	0.724	0.899	0.27	0.241	0.3	CLONAL	1	FALSE	2	0.715302801025078	5		521	738	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652305	36652305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200738687	NA	P-0059078-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	447	527	0	ENST00000244741.5:c.427C>T	p.Arg143Trp	p.R143W	ENST00000244741	NM_000389.4	143	Cgg/Tgg	2/3	0.715302801025078	5	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	FALSE	2	0.715302801025078	5		527	744	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391115	139391115	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059078-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	253	788	0	ENST00000277541.6:c.7076del	p.Leu2359ArgfsTer4	p.L2359Rfs*4	ENST00000277541	NM_017617.3	2359	cTg/cg	34/34	0.717814611754086	3	FACETS	0.978	0.927	1	0.978	0.927	1	CLONAL	2	FALSE	1	0.715302801025078	3		788	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0059079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	22	460	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.63	0.487	0.797	0.63	0.487	0.797	SUBCLONAL	1	TRUE	1	0.14	2		460	499	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562495	21562496	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGCGA	novel	NA	P-0059079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	9	485	0	ENST00000382592.4:c.1423_1424insTCGCCC	p.Ala474_Pro475insLeuAla	p.A474_P475insLA	ENST00000382592	NM_014572.2	475	ccc/cTCGCCCcc	4/8	1	2	FACETS	0.443	0.292	0.637	0.443	0.292	0.637	SUBCLONAL	1	TRUE	1	0.14	2		485	290	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438148	110438148	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	29	412	0	ENST00000375856.3:c.253A>G	p.Lys85Glu	p.K85E	ENST00000375856	NM_003749.2	85	Aag/Gag	1/2	1	2	FACETS	0.952	0.764	1	0.952	0.764	1	CLONAL	1	TRUE	1	0.14	2		412	435	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570323	95570323	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	27	460	0	ENST00000393063.1:c.3410C>A	p.Ala1137Asp	p.A1137D	ENST00000393063	NM_030621.3	1137	gCt/gAt	22/28	1	2	FACETS	0.84	0.668	1	0.84	0.668	1	CLONAL	1	TRUE	1	0.14	2		460	459	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528489	29528489	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764079291	NA	P-0059079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	24	322	1	ENST00000356175.3:c.1246C>T	p.Arg416Ter	p.R416*	ENST00000356175	NM_000267.3	416	Cga/Tga	11/57	1	2	FACETS	0.868	0.68	1	0.868	0.68	1	CLONAL	1	TRUE	1	0.14	2		323	395	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821793	59821793	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059079-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	26	286	0	ENST00000259008.2:c.2257G>T	p.Asp753Tyr	p.D753Y	ENST00000259008	NM_032043.2	753	Gat/Tat	15/20	1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	1	0.14	2		286	341	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0059082-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	94	284	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.979	0.879	1	0.979	0.879	1	CLONAL	1	TRUE	1	0.518798683431409	2		284	370	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0059082-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	51	289	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.518798683431409	2		289	187	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0059082-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	164	729	0	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.518798683431409	2		729	628	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023151	27023179	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	-	novel	NA	P-0059082-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	82	661	1	ENST00000324856.7:c.267_295del	p.Ser90ProfsTer11	p.S90Pfs*11	ENST00000324856	NM_006015.4	86	gGCGGAGCCGGCAGCGGCGGCGGGCCCGGC/g	1/20	1	2	FACETS	0.896	0.796	1	0.896	0.796	1	CLONAL	1	TRUE	1	0.518798683431409	2		662	353	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692910	89692910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059082-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	207	480	0	ENST00000371953.3:c.394G>A	p.Gly132Ser	p.G132S	ENST00000371953	NM_000314.4	132	Ggt/Agt	5/9	0.518798683431409	3	FACETS	0.944	0.893	0.994	0.944	0.893	0.994	CLONAL	3	TRUE	0	0.518798683431409	3		480	355	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0059082-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	24	243	1	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	1	2	FACETS	0.791	0.63	0.969	0.791	0.63	0.969	CLONAL	1	TRUE	1	0.518798683431409	2		244	117	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795028	45795028	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144616312	NA	P-0059082-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	124	731	0	ENST00000450313.1:c.1600C>T	p.Arg534Trp	p.R534W	ENST00000450313	NM_012222.2	534	Cgg/Tgg	16/16	1	2	FACETS	0.77	0.698	0.845	0.77	0.698	0.845	SUBCLONAL	1	TRUE	1	0.518798683431409	2		731	621	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146132	38146132	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059082-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	172	655	0	ENST00000317025.8:c.3374C>T	p.Pro1125Leu	p.P1125L	ENST00000317025	NM_023034.1	1125	cCg/cTg	19/24	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.518798683431409	2		655	558	SUCCESS
AR	367	MSKCC	GRCh37	X	66765986	66765986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059082-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	119	797	0	ENST00000374690.3:c.998C>T	p.Ala333Val	p.A333V	ENST00000374690	NM_000044.3	333	gCa/gTa	1/8	1	2	FACETS	0.956	0.868	1	0.956	0.868	1	CLONAL	1	TRUE	1	0.518798683431409	2		797	480	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916928	178916939	+	inframe_deletion	In_Frame_Del	DEL	AGGCAACCGTGA	AGGCAACCGTGA	-	novel	NA	P-0059083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	43	368	0	ENST00000263967.3:c.317_328del	p.Gly106_Glu109del	p.G106_E109del	ENST00000263967	NM_006218.2	105	gtAGGCAACCGTGAa/gta	2/21	0.105814662042607	3	FACETS	0.586	0.49	0.694	0.293	0.245	0.347	INDETERMINATE	1	TRUE	1	0.25	3		368	660	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424780	47424780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059083-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	51	548	0	ENST00000404338.3:c.2848G>A	p.Ala950Thr	p.A950T	ENST00000404338	NM_004491.4	950	Gct/Act	1/6	0.105814662042607	3	FACETS	0.55	0.466	0.642	0.275	0.233	0.321	INDETERMINATE	1	TRUE	1	0.25	3		548	835	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs786203436	NA	P-0059084-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	218	597	0	ENST00000269305.4:c.487T>G	p.Tyr163Asp	p.Y163D	ENST00000269305	NM_001126112.2	163	Tac/Gac	5/11	0.171134658415351	3	FACETS	1	0.977	1	0.736	0.686	0.787	CLONAL	2	TRUE	0	0.277597009574659	3		597	810	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212816	27212816	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059084-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	122	474	0	ENST00000380036.4:c.2798C>A	p.Ala933Glu	p.A933E	ENST00000380036	NM_000459.3	933	gCg/gAg	17/23	0.283678639036127	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.277597009574659	1		474	528	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059085-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	18	477	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	1	0.15	2		477	199	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418232	139418232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059085-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	38	802	0	ENST00000277541.6:c.340G>A	p.Gly114Arg	p.G114R	ENST00000277541	NM_017617.3	114	Ggg/Agg	3/34	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.15	2		802	383	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413009	49413009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519953	NA	P-0059085-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	20	518	0	ENST00000418115.1:c.14G>A	p.Arg5Gln	p.R5Q	ENST00000418115	NM_001664.2	5	cGg/cAg	2/5	1	2	FACETS	1	0.817	1	1	0.817	1	CLONAL	1	TRUE	1	0.15	2		518	247	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218425	36218425	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555730957	NA	P-0059085-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	26	711	0	ENST00000222270.7:c.4204C>T	p.Arg1402Ter	p.R1402*	ENST00000222270	NM_014727.1	1402	Cga/Tga	16/37	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.15	2		711	273	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244601	46244601	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0059085-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	29	787	0	ENST00000334344.6:c.2695A>T	p.Lys899Ter	p.K899*	ENST00000334344	NM_152641.2	899	Aaa/Taa	15/21	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.15	2		787	316	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26927915	26927916	+	stop_gained	Nonsense_Mutation	DNP	GA	GA	TT	novel	NA	P-0059085-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	20	431	1	ENST00000381527.3:c.354_355delinsTT	p.Lys118_Lys119delinsAsnTer	p.K118_K119delinsN*	ENST00000381527	NM_001260.1	118	aaGAag/aaTTag	4/13	1	2	FACETS	0.828	0.638	1	1	0.926	1	CLONAL	2	TRUE	1	0.15	2		432	161	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17129630	17129630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1327627870	NA	P-0059085-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	26	695	1	ENST00000285071.4:c.256C>T	p.Arg86Trp	p.R86W	ENST00000285071	NM_144997.5	86	Cgg/Tgg	5/14	1	2	FACETS	0.91	0.72	1	0.91	0.72	1	CLONAL	1	TRUE	1	0.15	2		696	381	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456436	89456436	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059085-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	17	471	0	ENST00000336596.2:c.1612G>C	p.Glu538Gln	p.E538Q	ENST00000336596	NM_005233.5	538	Gaa/Caa	8/17	1	2	FACETS	0.751	0.564	0.969	1	0.901	1	CLONAL	2	TRUE	1	0.15	2		471	151	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400113	139400113	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059085-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	39	929	0	ENST00000277541.6:c.4235A>G	p.Tyr1412Cys	p.Y1412C	ENST00000277541	NM_017617.3	1412	tAc/tGc	25/34	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.15	2		929	354	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0059086-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	44	125	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.310070926509861	2	FACETS	0.946	0.808	1	0.946	0.808	1	CLONAL	2	TRUE	0	0.310180289778434	2		125	150	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488657	212488657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374970657	NA	P-0059086-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	51	397	0	ENST00000342788.4:c.2192C>T	p.Thr731Met	p.T731M	ENST00000342788	NM_005235.2	731	aCg/aTg	18/28	1	2	FACETS	0.761	0.648	0.885	0.761	0.648	0.885	SUBCLONAL	1	TRUE	1	0.310180289778434	2		397	432	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183788	10183788	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059086-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	68	591	0	ENST00000256474.2:c.257C>A	p.Pro86His	p.P86H	ENST00000256474	NM_000551.3	86	cCc/cAc	1/3	0.310180289778434	1	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	0	0.310180289778434	1		591	350	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031946	26031946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059086-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	111	759	0	ENST00000244661.2:c.343G>A	p.Ala115Thr	p.A115T	ENST00000244661	NM_003537.3	115	Gct/Act	1/1	1	2	FACETS	0.984	0.886	1	0.984	0.886	1	CLONAL	1	TRUE	1	0.310180289778434	2		759	727	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs530941076	NA	P-0059087-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	188	645	0	ENST00000269305.4:c.658T>C	p.Tyr220His	p.Y220H	ENST00000269305	NM_001126112.2	220	Tat/Cat	6/11	0.553380024068513	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.553380024068513	1		645	483	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497653	125497653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059087-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	85	412	1	ENST00000428830.2:c.217C>T	p.His73Tyr	p.H73Y	ENST00000428830	NM_001114121.2	73	Cac/Tac	3/14	1	2	FACETS	0.853	0.76	0.951	0.853	0.76	0.951	CLONAL	1	TRUE	1	0.553380024068513	2		413	360	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257436	19257436	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059087-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	38	718	1	ENST00000162023.5:c.697C>A	p.Gln233Lys	p.Q233K	ENST00000162023		233	Cag/Aag	11/13	1	2	FACETS	0.2	0.164	0.239	0.2	0.164	0.239	SUBCLONAL	1	TRUE	1	0.553380024068513	2		719	688	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0059088-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	14	329	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.118295370322867	3	FACETS	0.401	0.289	0.538	0.201	0.144	0.269	INDETERMINATE	1	TRUE	1	0.21	3		329	367	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420339	49420339	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059088-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	115	604	0	ENST00000301067.7:c.15410A>G	p.Lys5137Arg	p.K5137R	ENST00000301067	NM_003482.3	5137	aAg/aGg	48/54	0.118295370322867	3	FACETS	1	0.983	1	0.728	0.656	0.805	INDETERMINATE	1	TRUE	1	0.21	3		604	831	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628950	187628950	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059088-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	39	552	0	ENST00000441802.2:c.2032G>C	p.Gly678Arg	p.G678R	ENST00000441802	NM_005245.3	678	Ggt/Cgt	2/27	1	2	FACETS	0.517	0.427	0.617	0.517	0.427	0.617	SUBCLONAL	1	TRUE	1	0.21	2		552	719	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210072	55210072	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059088-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	29	294	0	ENST00000275493.2:c.182T>A	p.Val61Asp	p.V61D	ENST00000275493	NM_005228.3	61	gTc/gAc	2/28	1	2	FACETS	0.52	0.416	0.639	0.52	0.416	0.639	SUBCLONAL	1	TRUE	1	0.21	2		294	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0059089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	201	522	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.553503639109123	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.553503639109123	1		522	455	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739031	40739031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358914349	NA	P-0059089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	68	539	0	ENST00000373198.4:c.3253G>A	p.Val1085Ile	p.V1085I	ENST00000373198	NM_133170.3	1085	Gtc/Atc	24/32	0.270184973648766	3	FACETS	0.458	0.398	0.523	0.229	0.199	0.262	INDETERMINATE	1	TRUE	1	0.553503639109123	3		539	685	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249457	153249457	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	108	422	0	ENST00000281708.4:c.1321C>G	p.Arg441Gly	p.R441G	ENST00000281708	NM_033632.3	441	Cgg/Ggg	9/12	0.44098595266364	1	FACETS	0.879	0.799	0.962	0.879	0.799	0.962	CLONAL	1	TRUE	0	0.553503639109123	1		422	321	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729122	66729122	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	66	501	0	ENST00000307102.5:c.330G>C	p.Gln110His	p.Q110H	ENST00000307102	NM_002755.3	110	caG/caC	3/11	1	2	FACETS	0.414	0.359	0.473	0.414	0.359	0.473	SUBCLONAL	1	TRUE	1	0.553503639109123	2		501	576	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523094	25523094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	112	534	0	ENST00000264709.3:c.91G>A	p.Glu31Lys	p.E31K	ENST00000264709	NM_175629.2	31	Gag/Aag	3/23	1	2	FACETS	0.658	0.593	0.726	0.658	0.593	0.726	SUBCLONAL	1	TRUE	1	0.553503639109123	2		534	615	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741217	145741217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867681178	NA	P-0059089-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	235	747	0	ENST00000428558.2:c.1189G>A	p.Val397Ile	p.V397I	ENST00000428558	NM_004260.3	397	Gtc/Atc	6/22	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.553503639109123	2		747	774	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0059090-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	175	390	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.348306232951223	6	FACETS	0.996	0.918	1			1	CLONAL	2	TRUE	NA	0.348306232951223	6		390	856	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0059090-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	113	697	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.348306232951223	2	FACETS	1	0.953	1	0.546	0.493	0.602	CLONAL	1	TRUE	0	0.348306232951223	2		697	594	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771348	68771356	+	inframe_deletion	In_Frame_Del	DEL	GCTGCTGCT	GCTGCTGCT	-	novel	NA	P-0059090-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	83	472	0	ENST00000261769.5:c.38_46del	p.Leu13_Leu15del	p.L13_L15del	ENST00000261769	NM_004360.3	10	gcGCTGCTGCTg/gcg	1/16	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.348306232951223	2		472	452	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731698	47731698	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059090-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	96	560	0	ENST00000449228.1:c.94A>G	p.Arg32Gly	p.R32G	ENST00000449228	NM_001127240.2	32	Agg/Ggg	2/4	0.264960828776552	3	FACETS	0.991	0.884	1	0.496	0.442	0.553	CLONAL	1	TRUE	1	0.348306232951223	3		560	653	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109309887	109309888	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0059090-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	69	245	0	ENST00000436639.2:c.1427_1428del	p.Tyr476Ter	p.Y476*	ENST00000436639	NM_014454.2	476	tAT/t	9/10	0.27646635085867	3	FACETS	1	0.971	1	0.468	0.411	0.53	CLONAL	1	TRUE	0	0.348306232951223	3		245	331	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165729	108165729	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs762083530	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	121	353	0	ENST00000278616.4:c.4852C>T	p.Arg1618Ter	p.R1618*	ENST00000278616	NM_000051.3	1618	Cga/Tga	32/63	1	2	FACETS	0.978	0.887	1	0.978	0.887	1	CLONAL	1	TRUE	1	0.447624629799922	2		353	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	381	471	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.956	1	1	0.997	1	CLONAL	2	TRUE	1	0.447624629799922	2		471	850	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589618	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519838	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	39	169	0	ENST00000274335.5:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000274335		461	Cga/Tga	10/15	1	2	FACETS	0.761	0.636	0.898	0.761	0.636	0.898	SUBCLONAL	1	TRUE	1	0.447624629799922	2		169	229	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267600319	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	167	624	0	ENST00000257430.4:c.4199C>T	p.Ser1400Leu	p.S1400L	ENST00000257430	NM_000038.5	1400	tCg/tTg	16/16	1	2	FACETS	0.994	0.915	1	0.994	0.915	1	CLONAL	1	TRUE	1	0.447624629799922	2		624	751	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	164	309	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	0.986	0.907	1	0.986	0.907	1	CLONAL	1	TRUE	1	0.447624629799922	2		309	743	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43766924	43766924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201580098	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	156	436	0	ENST00000382044.4:c.1127G>A	p.Arg376Gln	p.R376Q	ENST00000382044	NM_001141980.1	376	cGa/cAa	10/28	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.447624629799922	2		436	662	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1684391	1684391	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	225	779	0	ENST00000378625.1:c.1728G>T	p.Lys576Asn	p.K576N	ENST00000378625	NM_001198994.1	576	aaG/aaT	14/14	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.447624629799922	2		779	928	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733627	85733627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	154	495	0	ENST00000370580.1:c.385G>A	p.Ala129Thr	p.A129T	ENST00000370580	NM_003921.4	129	Gcc/Acc	3/3	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.447624629799922	2		495	661	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251266	115251266	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	144	365	0	ENST00000369535.4:c.460G>T	p.Asp154Tyr	p.D154Y	ENST00000369535	NM_002524.4	154	Gat/Tat	5/7	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.447624629799922	2		365	578	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282328	115282328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	102	337	0	ENST00000438362.2:c.322G>A	p.Asp108Asn	p.D108N	ENST00000438362	NM_001242891.1	108	Gac/Aac	3/20	1	2	FACETS	0.959	0.862	1	0.959	0.862	1	CLONAL	1	TRUE	1	0.447624629799922	2		337	475	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458062	120458062	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	222	838	0	ENST00000256646.2:c.7283C>A	p.Ser2428Ter	p.S2428*	ENST00000256646	NM_024408.3	2428	tCa/tAa	34/34	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.447624629799922	2		838	903	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120460374	120460374	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	156	529	0	ENST00000256646.2:c.5941C>A	p.Leu1981Ile	p.L1981I	ENST00000256646	NM_024408.3	1981	Ctt/Att	33/34	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.447624629799922	2		529	640	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150934621	150934621	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	94	241	0	ENST00000271640.5:c.3145A>C	p.Asn1049His	p.N1049H	ENST00000271640	NM_001145415.1	1049	Aac/Cac	17/22	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.447624629799922	2		241	371	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163295876	163295876	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	90	282	0	ENST00000271452.3:c.35C>A	p.Ala12Asp	p.A12D	ENST00000271452	NM_145697.2	12	gCt/gAt	2/14	1	2	FACETS	0.89	0.793	0.992	0.89	0.793	0.992	CLONAL	1	TRUE	1	0.447624629799922	2		282	452	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117008	193117008	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	91	237	1	ENST00000367435.3:c.741G>T	p.Lys247Asn	p.K247N	ENST00000367435	NM_024529.4	247	aaG/aaT	8/17	1	2	FACETS	0.937	0.836	1	0.937	0.836	1	CLONAL	1	TRUE	1	0.447624629799922	2		238	434	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809199	243809199	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	119	339	0	ENST00000263826.5:c.425G>T	p.Arg142Ile	p.R142I	ENST00000263826	NM_005465.4	142	aGa/aTa	4/13	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.447624629799922	2		339	509	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406670	70406670	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	135	439	0	ENST00000373644.4:c.4184T>G	p.Phe1395Cys	p.F1395C	ENST00000373644	NM_030625.2	1395	tTt/tGt	4/12	1	2	FACETS	0.948	0.865	1	0.948	0.865	1	CLONAL	1	TRUE	1	0.447624629799922	2		439	636	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406732	70406732	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768683199	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	139	426	0	ENST00000373644.4:c.4246G>T	p.Asp1416Tyr	p.D1416Y	ENST00000373644	NM_030625.2	1416	Gat/Tat	4/12	1	2	FACETS	0.978	0.893	1	0.978	0.893	1	CLONAL	1	TRUE	1	0.447624629799922	2		426	635	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624244	89624244	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	62	201	0	ENST00000371953.3:c.18A>C	p.Lys6Asn	p.K6N	ENST00000371953	NM_000314.4	6	aaA/aaC	1/9	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.447624629799922	2		201	242	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653824	89653824	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs794727244	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	64	173	0	ENST00000371953.3:c.122G>T	p.Arg41Ile	p.R41I	ENST00000371953	NM_000314.4	41	aGa/aTa	2/9	1	2	FACETS	0.934	0.816	1	0.934	0.816	1	CLONAL	1	TRUE	1	0.447624629799922	2		173	306	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104386990	104386990	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	116	481	1	ENST00000369902.3:c.1355C>A	p.Ser452Tyr	p.S452Y	ENST00000369902	NM_016169.3	452	tCt/tAt	11/12	1	2	FACETS	0.825	0.745	0.909	0.825	0.745	0.909	CLONAL	1	TRUE	1	0.447624629799922	2		482	628	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724138	112724138	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	119	354	0	ENST00000369452.4:c.22G>T	p.Glu8Ter	p.E8*	ENST00000369452	NM_007373.3	8	Gaa/Taa	2/9	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.447624629799922	2		354	475	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573758	64573758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	236	817	2	ENST00000312049.6:c.995G>A	p.Arg332His	p.R332H	ENST00000312049	NM_130799.2	332	cGc/cAc	7/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.447624629799922	2		819	971	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977204	85977204	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	55	119	0	ENST00000263360.6:c.806G>T	p.Arg269Ile	p.R269I	ENST00000263360	NM_003797.3	269	aGa/aTa	8/12	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.447624629799922	2		119	198	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988080	85988080	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	96	366	0	ENST00000263360.6:c.1025A>C	p.Lys342Thr	p.K342T	ENST00000263360	NM_003797.3	342	aAa/aCa	10/12	1	2	FACETS	0.823	0.736	0.916	0.823	0.736	0.916	CLONAL	1	TRUE	1	0.447624629799922	2		366	521	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918486	94918486	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	115	403	0	ENST00000536441.1:c.696C>A	p.Phe232Leu	p.F232L	ENST00000536441	NM_144665.3	232	ttC/ttA	5/10	1	2	FACETS	0.927	0.839	1	0.927	0.839	1	CLONAL	1	TRUE	1	0.447624629799922	2		403	554	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94922947	94922947	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	121	328	0	ENST00000536441.1:c.521T>C	p.Ile174Thr	p.I174T	ENST00000536441	NM_144665.3	174	aTt/aCt	4/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.447624629799922	2		328	502	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119720	108119720	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1555069657	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	102	293	0	ENST00000278616.4:c.1126G>T	p.Glu376Ter	p.E376*	ENST00000278616	NM_000051.3	376	Gaa/Taa	9/63	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.447624629799922	2		293	443	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123575	108123575	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs747242300	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	62	201	0	ENST00000278616.4:c.1834C>A	p.Leu612Ile	p.L612I	ENST00000278616	NM_000051.3	612	Ctt/Att	12/63	1	2	FACETS	0.824	0.717	0.94	0.824	0.717	0.94	CLONAL	1	TRUE	1	0.447624629799922	2		201	336	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143509	108143509	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1060501687	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	119	401	0	ENST00000278616.4:c.3214G>T	p.Glu1072Ter	p.E1072*	ENST00000278616	NM_000051.3	1072	Gaa/Taa	22/63	1	2	FACETS	0.992	0.899	1	0.992	0.899	1	CLONAL	1	TRUE	1	0.447624629799922	2		401	536	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180905	108180905	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	86	228	0	ENST00000278616.4:c.5781T>G	p.Ile1927Met	p.I1927M	ENST00000278616	NM_000051.3	1927	atT/atG	39/63	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.447624629799922	2		228	349	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348891	118348891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	136	436	0	ENST00000534358.1:c.3544C>T	p.Arg1182Cys	p.R1182C	ENST00000534358	NM_005933.3	1182	Cgc/Tgc	5/36	1	2	FACETS	0.993	0.906	1	0.993	0.906	1	CLONAL	1	TRUE	1	0.447624629799922	2		436	612	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377030	118377030	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	225	759	0	ENST00000534358.1:c.10423C>A	p.Leu3475Ile	p.L3475I	ENST00000534358	NM_005933.3	3475	Ctt/Att	27/36	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.447624629799922	2		759	956	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491370	18491370	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	61	170	0	ENST00000266497.5:c.1283A>C	p.Tyr428Ser	p.Y428S	ENST00000266497		428	tAt/tCt	8/31	1	2	FACETS	0.814	0.706	0.929	0.814	0.706	0.929	CLONAL	1	TRUE	1	0.447624629799922	2		170	335	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378706	25378706	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	69	180	0	ENST00000311936.3:c.292G>T	p.Glu98Ter	p.E98*	ENST00000311936	NM_004985.3	98	Gaa/Taa	4/5	1	2	FACETS	0.861	0.755	0.975	0.861	0.755	0.975	CLONAL	1	TRUE	1	0.447624629799922	2		180	358	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125024	46125024	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	118	445	0	ENST00000334344.6:c.211G>T	p.Glu71Ter	p.E71*	ENST00000334344	NM_152641.2	71	Gaa/Taa	3/21	1	2	FACETS	0.997	0.903	1	0.997	0.903	1	CLONAL	1	TRUE	1	0.447624629799922	2		445	529	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242627	46242627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757429134	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	69	221	0	ENST00000334344.6:c.1589C>T	p.Ala530Val	p.A530V	ENST00000334344	NM_152641.2	530	gCt/gTt	13/21	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.447624629799922	2		221	308	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245684	46245684	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	195	688	0	ENST00000334344.6:c.3778G>T	p.Glu1260Ter	p.E1260*	ENST00000334344	NM_152641.2	1260	Gaa/Taa	15/21	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.447624629799922	2		688	852	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246416	46246416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140500006	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	202	692	0	ENST00000334344.6:c.4510C>T	p.Arg1504Trp	p.R1504W	ENST00000334344	NM_152641.2	1504	Cgg/Tgg	15/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.447624629799922	2		692	831	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861837	57861837	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs759838377	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	208	797	0	ENST00000228682.2:c.1138C>T	p.Arg380Ter	p.R380*	ENST00000228682	NM_005269.2	380	Cga/Tga	10/12	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.447624629799922	2		797	925	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120795639	120795639	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	110	389	0	ENST00000257552.2:c.514C>A	p.His172Asn	p.H172N	ENST00000257552	NM_002442.3	172	Cat/Aat	8/15	1	2	FACETS	0.973	0.878	1	0.973	0.878	1	CLONAL	1	TRUE	1	0.447624629799922	2		389	505	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874087	123874087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	222	710	0	ENST00000330479.4:c.118C>T	p.Pro40Ser	p.P40S	ENST00000330479	NM_020382.3	40	Ccc/Tcc	2/9	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.447624629799922	2		710	828	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879626	123879626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376869233	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	149	451	2	ENST00000330479.4:c.322G>A	p.Ala108Thr	p.A108T	ENST00000330479	NM_020382.3	108	Gcc/Acc	4/9	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.447624629799922	2		453	595	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123888136	123888136	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	127	561	0	ENST00000330479.4:c.614G>T	p.Arg205Ile	p.R205I	ENST00000330479	NM_020382.3	205	aGa/aTa	6/9	1	2	FACETS	0.878	0.798	0.963	0.878	0.798	0.963	CLONAL	1	TRUE	1	0.447624629799922	2		561	646	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28886137	28886137	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1207529287	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	101	327	0	ENST00000282397.4:c.3485T>C	p.Val1162Ala	p.V1162A	ENST00000282397	NM_002019.4	1162	gTa/gCa	26/30	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.447624629799922	2		327	386	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28971168	28971168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	140	500	0	ENST00000282397.4:c.1589C>T	p.Ser530Phe	p.S530F	ENST00000282397	NM_002019.4	530	tCt/tTt	12/30	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.447624629799922	2		500	556	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913309	32913309	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	156	405	0	ENST00000380152.3:c.4817C>A	p.Ser1606Tyr	p.S1606Y	ENST00000380152		1606	tCt/tAt	11/27	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.447624629799922	2		405	596	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061408	38061408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	187	704	0	ENST00000250448.2:c.581G>A	p.Ser194Asn	p.S194N	ENST00000250448	NM_004496.3	194	aGc/aAc	2/2	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.447624629799922	2		704	785	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560494	65560494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	182	574	0	ENST00000358664.4:c.103C>T	p.Arg35Cys	p.R35C	ENST00000358664	NM_002382.4	35	Cgt/Tgt	3/5	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.447624629799922	2		574	724	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95556857	95556857	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	116	339	0	ENST00000393063.1:c.5747A>C	p.Gln1916Pro	p.Q1916P	ENST00000393063	NM_030621.3	1916	cAa/cCa	28/28	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.447624629799922	2		339	462	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562576	95562576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	192	768	0	ENST00000393063.1:c.4681G>A	p.Asp1561Asn	p.D1561N	ENST00000393063	NM_030621.3	1561	Gac/Aac	24/28	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.447624629799922	2		768	833	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590927	95590927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	149	533	0	ENST00000393063.1:c.982G>A	p.Glu328Lys	p.E328K	ENST00000393063	NM_030621.3	328	Gaa/Aaa	9/28	1	2	FACETS	0.995	0.912	1	0.995	0.912	1	CLONAL	1	TRUE	1	0.447624629799922	2		533	669	SUCCESS
SCG5	6447	MSKCC	GRCh37	15	32935881	32935881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532967380	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	176	607	1	ENST00000300175.4:c.88C>T	p.Arg30Trp	p.R30W	ENST00000300175	NM_001144757.1	30	Cgg/Tgg	2/6	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.447624629799922	2		608	744	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003131	42003131	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	211	568	1	ENST00000219905.7:c.2668T>C	p.Ser890Pro	p.S890P	ENST00000219905	NM_001164273.1	890	Tct/Cct	8/24	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.447624629799922	2		569	818	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021441	42021441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	185	584	0	ENST00000219905.7:c.3737G>A	p.Arg1246Gln	p.R1246Q	ENST00000219905	NM_001164273.1	1246	cGa/cAa	11/24	1	2	FACETS	0.962	0.889	1	0.962	0.889	1	CLONAL	1	TRUE	1	0.447624629799922	2		584	859	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724833	43724833	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	177	615	0	ENST00000382044.4:c.3234G>T	p.Glu1078Asp	p.E1078D	ENST00000382044	NM_001141980.1	1078	gaG/gaT	17/28	1	2	FACETS	0.997	0.92	1	0.997	0.92	1	CLONAL	1	TRUE	1	0.447624629799922	2		615	793	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748394	43748394	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	194	677	0	ENST00000382044.4:c.2412G>T	p.Glu804Asp	p.E804D	ENST00000382044	NM_001141980.1	804	gaG/gaT	12/28	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.447624629799922	2		677	835	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50773814	50773814	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	163	492	0	ENST00000307179.4:c.1355C>A	p.Ser452Tyr	p.S452Y	ENST00000307179		452	tCt/tAt	11/20	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.447624629799922	2		492	727	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358614	67358614	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	217	750	0	ENST00000327367.4:c.122A>C	p.Lys41Thr	p.K41T	ENST00000327367	NM_005902.3	41	aAa/aCa	1/9	1	2	FACETS	0.988	0.919	1	0.988	0.919	1	CLONAL	1	TRUE	1	0.447624629799922	2		750	981	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479703	67479703	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	169	590	0	ENST00000327367.4:c.1010G>A	p.Gly337Glu	p.G337E	ENST00000327367	NM_005902.3	337	gGa/gAa	8/9	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.447624629799922	2		590	673	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476305	88476305	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	127	561	0	ENST00000360948.2:c.1827T>A	p.Asp609Glu	p.D609E	ENST00000360948	NM_001012338.2	609	gaT/gaA	15/19	1	2	FACETS	0.905	0.822	0.992	0.905	0.822	0.992	CLONAL	1	TRUE	1	0.447624629799922	2		561	627	SUCCESS
BLM	641	MSKCC	GRCh37	15	91306287	91306287	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	121	373	0	ENST00000355112.3:c.1974T>G	p.Ile658Met	p.I658M	ENST00000355112	NM_000057.2	658	atT/atG	8/22	1	2	FACETS	0.934	0.846	1	0.934	0.846	1	CLONAL	1	TRUE	1	0.447624629799922	2		373	579	SUCCESS
BLM	641	MSKCC	GRCh37	15	91341563	91341563	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1351493073	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	67	172	0	ENST00000355112.3:c.3354C>A	p.Phe1118Leu	p.F1118L	ENST00000355112	NM_000057.2	1118	ttC/ttA	17/22	1	2	FACETS	0.899	0.787	1	0.899	0.787	1	CLONAL	1	TRUE	1	0.447624629799922	2		172	333	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656619	3656619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs913324001	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	212	780	1	ENST00000294008.3:c.616G>A	p.Ala206Thr	p.A206T	ENST00000294008	NM_032444.2	206	Gca/Aca	3/15	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.447624629799922	2		781	916	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828135	3828135	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	123	346	0	ENST00000262367.5:c.1990G>T	p.Glu664Ter	p.E664*	ENST00000262367	NM_004380.2	664	Gaa/Taa	10/31	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.447624629799922	2		346	503	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857926	9857926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	182	776	1	ENST00000330684.3:c.3475C>T	p.Arg1159Cys	p.R1159C	ENST00000330684	NM_001134407.1	1159	Cgc/Tgc	13/13	1	2	FACETS	0.965	0.891	1	0.965	0.891	1	CLONAL	1	TRUE	1	0.447624629799922	2		777	843	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858168	9858168	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	193	776	0	ENST00000330684.3:c.3233A>C	p.Lys1078Thr	p.K1078T	ENST00000330684	NM_001134407.1	1078	aAg/aCg	13/13	1	2	FACETS	0.958	0.887	1	0.958	0.887	1	CLONAL	1	TRUE	1	0.447624629799922	2		776	900	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923465	9923465	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	145	606	0	ENST00000330684.3:c.1822C>A	p.Leu608Ile	p.L608I	ENST00000330684	NM_001134407.1	608	Ctt/Att	9/13	1	2	FACETS	0.95	0.869	1	0.95	0.869	1	CLONAL	1	TRUE	1	0.447624629799922	2		606	682	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647241	23647241	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	181	420	0	ENST00000261584.4:c.626C>A	p.Ser209Tyr	p.S209Y	ENST00000261584	NM_024675.3	209	tCt/tAt	4/13	0.384535546975423	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.447624629799922	1		420	496	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865779	56865779	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	153	466	0	ENST00000308159.5:c.1111C>T	p.Leu371Phe	p.L371F	ENST00000308159	NM_014669.4	371	Ctc/Ttc	11/22	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.447624629799922	2		466	595	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822199	72822199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781682309	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	239	951	0	ENST00000268489.5:c.9976G>A	p.Ala3326Thr	p.A3326T	ENST00000268489	NM_006885.3	3326	Gcc/Acc	10/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.447624629799922	2		951	1037	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828699	72828699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762362472	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	173	755	0	ENST00000268489.5:c.7882G>A	p.Glu2628Lys	p.E2628K	ENST00000268489	NM_006885.3	2628	Gaa/Aaa	9/10	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.447624629799922	2		755	768	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831857	72831857	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	211	733	0	ENST00000268489.5:c.4724G>T	p.Arg1575Ile	p.R1575I	ENST00000268489	NM_006885.3	1575	aGa/aTa	9/10	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.447624629799922	2		733	935	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888069	81888069	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	137	471	0	ENST00000359376.3:c.214G>T	p.Glu72Ter	p.E72*	ENST00000359376	NM_002661.3	72	Gaa/Taa	3/33	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.447624629799922	2		471	588	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81904510	81904511	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	106	288	0	ENST00000359376.3:c.624dup	p.Leu209ThrfsTer4	p.L209Tfs*4	ENST00000359376	NM_002661.3	206	-/A	7/33	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.447624629799922	2		288	461	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349211	89349211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755642596	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	203	760	0	ENST00000301030.4:c.3739G>A	p.Ala1247Thr	p.A1247T	ENST00000301030	NM_001256183.1	1247	Gct/Act	9/13	1	2	FACETS	0.986	0.915	1	0.986	0.915	1	CLONAL	1	TRUE	1	0.447624629799922	2		760	920	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350695	89350695	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	132	472	0	ENST00000301030.4:c.2255C>A	p.Ser752Tyr	p.S752Y	ENST00000301030	NM_001256183.1	752	tCt/tAt	9/13	1	2	FACETS	0.903	0.822	0.988	0.903	0.822	0.988	CLONAL	1	TRUE	1	0.447624629799922	2		472	653	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508439	29508439	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	75	191	0	ENST00000356175.3:c.587-1G>T		p.X196_splice	ENST00000356175	NM_000267.3	196			1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.447624629799922	2		191	333	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679835	33679835	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	160	628	0	ENST00000308377.4:c.2246G>T	p.Arg749Ile	p.R749I	ENST00000308377	NM_152270.3	749	aGa/aTa	5/5	1	2	FACETS	0.993	0.913	1	0.993	0.913	1	CLONAL	1	TRUE	1	0.447624629799922	2		628	720	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619268	37619268	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	211	737	0	ENST00000447079.4:c.944G>T	p.Arg315Ile	p.R315I	ENST00000447079	NM_015083.1	315	aGa/aTa	1/14	1	2	FACETS	0.984	0.914	1	0.984	0.914	1	CLONAL	1	TRUE	1	0.447624629799922	2		737	958	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627651	37627651	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	222	743	0	ENST00000447079.4:c.1566A>C	p.Glu522Asp	p.E522D	ENST00000447079	NM_015083.1	522	gaA/gaC	2/14	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.447624629799922	2		743	855	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673781	37673781	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	172	577	0	ENST00000447079.4:c.2935C>T	p.Arg979Ter	p.R979*	ENST00000447079	NM_015083.1	979	Cga/Tga	10/14	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.447624629799922	2		577	733	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41201203	41201203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	133	511	0	ENST00000357654.3:c.5341G>A	p.Glu1781Lys	p.E1781K	ENST00000357654	NM_007294.3	1781	Gaa/Aaa	21/23	1	2	FACETS	0.891	0.811	0.975	0.891	0.811	0.975	CLONAL	1	TRUE	1	0.447624629799922	2		511	667	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223099	41223099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	184	689	0	ENST00000357654.3:c.4832C>T	p.Ala1611Val	p.A1611V	ENST00000357654	NM_007294.3	1611	gCc/gTc	15/23	1	2	FACETS	0.966	0.893	1	0.966	0.893	1	CLONAL	1	TRUE	1	0.447624629799922	2		689	851	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772510	56772510	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	144	490	0	ENST00000337432.4:c.364G>T	p.Glu122Ter	p.E122*	ENST00000337432	NM_058216.2	122	Gaa/Taa	2/9	1	2	FACETS	0.996	0.911	1	0.996	0.911	1	CLONAL	1	TRUE	1	0.447624629799922	2		490	646	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740472	58740472	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs763192608	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	152	577	0	ENST00000305921.3:c.1377G>T	p.Glu459Asp	p.E459D	ENST00000305921	NM_003620.3	459	gaG/gaT	6/6	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.447624629799922	2		577	659	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763428	59763428	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	146	453	0	ENST00000259008.2:c.2674C>A	p.Leu892Ile	p.L892I	ENST00000259008	NM_032043.2	892	Ctt/Att	19/20	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.447624629799922	2		453	630	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876606	59876606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782816	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	139	386	1	ENST00000259008.2:c.1195G>A	p.Glu399Lys	p.E399K	ENST00000259008	NM_032043.2	399	Gag/Aag	9/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.447624629799922	2		387	573	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885934	59885934	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	156	566	0	ENST00000259008.2:c.812T>C	p.Val271Ala	p.V271A	ENST00000259008	NM_032043.2	271	gTt/gCt	7/20	1	2	FACETS	0.951	0.873	1	0.951	0.873	1	CLONAL	1	TRUE	1	0.447624629799922	2		566	733	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368198	45368198	+	stop_lost	Nonstop_Mutation	SNP	T	T	G	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	133	564	0	ENST00000262160.6:c.1404A>C	p.Ter468TyrextTer8	p.*468Yext*8	ENST00000262160	NM_005901.5	468	taA/taC	11/11	0.447624629799922	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.447624629799922	1		564	456	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604668	48604668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	160	585	0	ENST00000342988.3:c.1490G>A	p.Arg497His	p.R497H	ENST00000342988	NM_005359.5	497	cGc/cAc	12/12	0.447624629799922	1	FACETS	0.96	0.885	1	0.96	0.885	1	CLONAL	1	TRUE	0	0.447624629799922	1		585	578	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604755	48604755	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	192	664	0	ENST00000342988.3:c.1577A>G	p.Glu526Gly	p.E526G	ENST00000342988	NM_005359.5	526	gAa/gGa	12/12	0.447624629799922	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.447624629799922	1		664	642	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632356	1632356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	150	792	0	ENST00000344749.5:c.194G>A	p.Ser65Asn	p.S65N	ENST00000344749	NM_001136139.2	65	aGc/aAc	4/19	0.447624629799922	1	FACETS	0.953	0.876	1	0.953	0.876	1	CLONAL	1	TRUE	0	0.447624629799922	1		792	546	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273502	5273502	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	191	680	0	ENST00000357368.4:c.330G>T	p.Gln110His	p.Q110H	ENST00000357368	NM_002850.3	110	caG/caT	4/38	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.447624629799922	2		680	816	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125344	7125344	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	203	839	1	ENST00000302850.5:c.3208G>T	p.Glu1070Ter	p.E1070*	ENST00000302850	NM_000208.2	1070	Gag/Tag	17/22	1	2	FACETS	0.948	0.879	1	0.948	0.879	1	CLONAL	1	TRUE	1	0.447624629799922	2		840	957	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265031	10265031	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	166	706	0	ENST00000340748.4:c.1909G>T	p.Glu637Ter	p.E637*	ENST00000340748		637	Gaa/Taa	21/40	1	2	FACETS	0.953	0.877	1	0.953	0.877	1	CLONAL	1	TRUE	1	0.447624629799922	2		706	778	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276316	15276316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372834264	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	183	684	0	ENST00000263388.2:c.5678G>A	p.Arg1893Gln	p.R1893Q	ENST00000263388	NM_000435.2	1893	cGa/cAa	31/33	1	2	FACETS	0.985	0.91	1	0.985	0.91	1	CLONAL	1	TRUE	1	0.447624629799922	2		684	830	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302801	15302801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756520455	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	218	886	0	ENST00000263388.2:c.649G>A	p.Asp217Asn	p.D217N	ENST00000263388	NM_000435.2	217	Gac/Aac	4/33	1	2	FACETS	0.995	0.926	1	0.995	0.926	1	CLONAL	1	TRUE	1	0.447624629799922	2		886	979	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378248	15378248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1186244524	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	163	549	0	ENST00000263377.2:c.538G>A	p.Gly180Arg	p.G180R	ENST00000263377	NM_058243.2	180	Gga/Aga	4/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.447624629799922	2		549	680	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17949172	17949172	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	200	746	0	ENST00000458235.1:c.1469G>T	p.Arg490Ile	p.R490I	ENST00000458235	NM_000215.3	490	aGa/aTa	11/24	1	2	FACETS	0.984	0.913	1	0.984	0.913	1	CLONAL	1	TRUE	1	0.447624629799922	2		746	908	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280096	18280096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149081991	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	187	694	0	ENST00000222254.8:c.2179G>A	p.Ala727Thr	p.A727T	ENST00000222254	NM_005027.3	727	Gcc/Acc	16/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.447624629799922	2		694	719	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971156	18971156	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	184	708	0	ENST00000262803.5:c.2209T>G	p.Phe737Val	p.F737V	ENST00000262803	NM_002911.3	737	Ttc/Gtc	16/24	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.447624629799922	2		708	756	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905151	50905151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137953986	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	227	890	0	ENST00000440232.2:c.433G>A	p.Ala145Thr	p.A145T	ENST00000440232	NM_002691.3	145	Gct/Act	4/27	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.447624629799922	2		890	986	SUCCESS
ALK	238	MSKCC	GRCh37	2	29430052	29430052	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	133	517	0	ENST00000389048.3:c.3923C>A	p.Ser1308Tyr	p.S1308Y	ENST00000389048	NM_004304.4	1308	tCt/tAt	26/29	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.447624629799922	2		517	550	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436905	29436905	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	159	561	0	ENST00000389048.3:c.3688G>T	p.Ala1230Ser	p.A1230S	ENST00000389048	NM_004304.4	1230	Gct/Tct	24/29	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.447624629799922	2		561	703	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213289	39213289	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	223	782	0	ENST00000402219.2:c.3678C>A	p.Phe1226Leu	p.F1226L	ENST00000402219	NM_005633.3	1226	ttC/ttA	23/23	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.447624629799922	2		782	953	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250104	39250104	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	119	430	0	ENST00000402219.2:c.1465C>T	p.Arg489Cys	p.R489C	ENST00000402219	NM_005633.3	489	Cgt/Tgt	10/23	1	2	FACETS	0.872	0.789	0.959	0.872	0.789	0.959	CLONAL	1	TRUE	1	0.447624629799922	2		430	610	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026015	48026015	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765237563	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	232	808	0	ENST00000234420.5:c.893G>A	p.Arg298Gln	p.R298Q	ENST00000234420	NM_000179.2	298	cGa/cAa	4/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.447624629799922	2		808	961	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033396	48033396	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	126	380	0	ENST00000234420.5:c.3700G>T	p.Glu1234Ter	p.E1234*	ENST00000234420	NM_000179.2	1234	Gaa/Taa	8/10	1	2	FACETS	0.902	0.819	0.989	0.902	0.819	0.989	CLONAL	1	TRUE	1	0.447624629799922	2		380	624	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	98	331	0	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	0.991	0.889	1	0.991	0.889	1	CLONAL	1	TRUE	1	0.447624629799922	2		331	442	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044487	128044487	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	160	685	0	ENST00000285398.2:c.1134C>A	p.Phe378Leu	p.F378L	ENST00000285398	NM_000122.1	378	ttC/ttA	8/15	1	2	FACETS	0.899	0.825	0.976	0.899	0.825	0.976	CLONAL	1	TRUE	1	0.447624629799922	2		685	795	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136289	202136289	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	137	438	0	ENST00000358485.4:c.533C>A	p.Ser178Tyr	p.S178Y	ENST00000358485	NM_001080125.1	178	tCt/tAt	3/9	0.445166508880774	3	FACETS	1	0.924	1	0.508	0.463	0.556	CLONAL	1	TRUE	1	0.447624629799922	3		438	737	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151289	202151289	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	129	426	0	ENST00000358485.4:c.1589G>T	p.Arg530Ile	p.R530I	ENST00000358485	NM_001080125.1	530	aGa/aTa	9/9	0.445166508880774	3	FACETS	0.966	0.877	1	0.483	0.438	0.53	CLONAL	1	TRUE	1	0.447624629799922	3		426	730	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288937	212288937	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	117	516	0	ENST00000342788.4:c.2809G>T	p.Glu937Ter	p.E937*	ENST00000342788	NM_005235.2	937	Gaa/Taa	23/28	0.445166508880774	3	FACETS	0.868	0.783	0.958	0.434	0.391	0.479	CLONAL	1	TRUE	1	0.447624629799922	3		516	737	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403212	213403212	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs751515664	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	137	656	0	ENST00000342788.4:c.43G>T	p.Val15Leu	p.V15L	ENST00000342788	NM_005235.2	15	Gtg/Ttg	1/28	0.445166508880774	3	FACETS	0.874	0.795	0.957	0.437	0.397	0.479	CLONAL	1	TRUE	1	0.447624629799922	3		656	857	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646066	215646066	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	135	607	0	ENST00000260947.4:c.532G>T	p.Asp178Tyr	p.D178Y	ENST00000260947	NM_000465.2	178	Gac/Tac	4/11	0.445166508880774	3	FACETS	0.872	0.792	0.955	0.436	0.396	0.478	CLONAL	1	TRUE	1	0.447624629799922	3		607	847	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422499	225422499	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	98	238	0	ENST00000264414.4:c.141G>T	p.Lys47Asn	p.K47N	ENST00000264414	NM_003590.4	47	aaG/aaT	2/16	0.445166508880774	3	FACETS	0.947	0.847	1	0.473	0.423	0.527	CLONAL	1	TRUE	1	0.447624629799922	3		238	566	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662211	227662211	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	248	837	0	ENST00000305123.5:c.1244C>T	p.Ser415Leu	p.S415L	ENST00000305123	NM_005544.2	415	tCg/tTg	1/2	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	1	TRUE	NA	0.447624629799922	2		837	1053	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546725	9546725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210292896	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	190	811	0	ENST00000353224.5:c.1297C>T	p.Arg433Trp	p.R433W	ENST00000353224	NM_177990.2	433	Cgg/Tgg	5/10	0.445166508880774	3	FACETS	0.935	0.863	1	0.468	0.431	0.505	CLONAL	1	TRUE	1	0.447624629799922	3		811	1111	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386343	31386343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	203	750	0	ENST00000328111.2:c.1568G>A	p.Ser523Asn	p.S523N	ENST00000328111	NM_006892.3	523	aGc/aAc	15/23	0.445166508880774	3	FACETS	1	0.972	1	0.548	0.508	0.59	CLONAL	1	TRUE	1	0.447624629799922	3		750	1012	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742622	39742622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	168	577	0	ENST00000361337.2:c.1465G>A	p.Ala489Thr	p.A489T	ENST00000361337	NM_003286.2	489	Gca/Aca	15/21	0.445166508880774	3	FACETS	1	0.924	1	0.503	0.462	0.545	CLONAL	1	TRUE	1	0.447624629799922	3		577	914	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252865	36252865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060499616	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	294	502	0	ENST00000300305.3:c.497G>A	p.Arg166Gln	p.R166Q	ENST00000300305		166	cGa/cAa	4/8	0.445166508880774	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.447624629799922	3		502	770	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252884	36252884	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	164	515	1	ENST00000300305.3:c.478G>T	p.Asp160Tyr	p.D160Y	ENST00000300305		160	Gac/Tac	4/8	0.445166508880774	3	FACETS	1	0.942	1	0.516	0.474	0.56	CLONAL	1	TRUE	1	0.447624629799922	3		516	869	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755606	39755606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	217	819	0	ENST00000288319.7:c.1159G>A	p.Ala387Thr	p.A387T	ENST00000288319	NM_182918.3	387	Gcc/Acc	10/10	0.445166508880774	3	FACETS	1	0.971	1	0.541	0.503	0.581	CLONAL	1	TRUE	1	0.447624629799922	3		819	1096	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	183	673	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	1	2	FACETS	0.921	0.85	0.994	0.921	0.85	0.994	CLONAL	1	TRUE	1	0.447624629799922	2		673	888	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275116	41275116	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	210	628	0	ENST00000349496.5:c.1282A>C	p.Thr428Pro	p.T428P	ENST00000349496	NM_001904.3	428	Act/Cct	9/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.447624629799922	2		628	833	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147540	47147540	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	186	701	0	ENST00000409792.3:c.4786T>G	p.Tyr1596Asp	p.Y1596D	ENST00000409792	NM_014159.6	1596	Tat/Gat	6/21	1	2	FACETS	0.909	0.84	0.981	0.909	0.84	0.981	CLONAL	1	TRUE	1	0.447624629799922	2		701	914	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164802	47164802	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	138	665	0	ENST00000409792.3:c.1324G>T	p.Glu442Ter	p.E442*	ENST00000409792	NM_014159.6	442	Gag/Tag	3/21	1	2	FACETS	0.841	0.767	0.919	0.841	0.767	0.919	CLONAL	1	TRUE	1	0.447624629799922	2		665	733	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924903	49924903	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	229	759	0	ENST00000296474.3:c.4040C>A	p.Ala1347Glu	p.A1347E	ENST00000296474	NM_002447.2	1347	gCa/gAa	20/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.447624629799922	2		759	919	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49929190	49929190	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs55856544	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	221	739	1	ENST00000296474.3:c.3352+1G>A		p.X1118_splice	ENST00000296474	NM_002447.2	1118			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.447624629799922	2		740	935	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610560	52610560	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	112	401	0	ENST00000394830.3:c.3613C>A	p.Leu1205Ile	p.L1205I	ENST00000394830	NM_018313.4	1205	Ctc/Atc	23/30	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.447624629799922	2		401	492	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637690	52637690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239654517	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	113	312	0	ENST00000394830.3:c.2626C>T	p.Arg876Cys	p.R876C	ENST00000394830	NM_018313.4	876	Cgt/Tgt	18/30	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.447624629799922	2		312	491	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468418	89468418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276606795	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	111	498	0	ENST00000336596.2:c.1952C>T	p.Ala651Val	p.A651V	ENST00000336596	NM_005233.5	651	gCc/gTc	11/17	1	2	FACETS	0.834	0.751	0.92	0.834	0.751	0.92	CLONAL	1	TRUE	1	0.447624629799922	2		498	595	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499433	89499433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	170	644	0	ENST00000336596.2:c.2603G>A	p.Arg868Lys	p.R868K	ENST00000336596	NM_005233.5	868	aGa/aAa	15/17	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.447624629799922	2		644	742	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202745	128202745	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	217	796	0	ENST00000341105.2:c.975G>A	p.Met325Ile	p.M325I	ENST00000341105	NM_032638.4	325	atG/atA	4/6	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.447624629799922	2		796	911	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205652	128205652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1179893883	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	151	623	0	ENST00000341105.2:c.223G>A	p.Ala75Thr	p.A75T	ENST00000341105	NM_032638.4	75	Gcg/Acg	2/6	1	2	FACETS	0.982	0.9	1	0.982	0.9	1	CLONAL	1	TRUE	1	0.447624629799922	2		623	687	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851670	134851670	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	162	700	0	ENST00000398015.3:c.1076T>C	p.Ile359Thr	p.I359T	ENST00000398015	NM_004441.4	359	aTc/aCc	5/16	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.447624629799922	2		700	715	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178199	142178199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746049210	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	104	406	0	ENST00000350721.4:c.7219C>T	p.Arg2407Cys	p.R2407C	ENST00000350721	NM_001184.3	2407	Cgc/Tgc	43/47	1	2	FACETS	0.815	0.732	0.903	0.815	0.732	0.903	CLONAL	1	TRUE	1	0.447624629799922	2		406	570	SUCCESS
ATR	545	MSKCC	GRCh37	3	142243002	142243002	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	124	439	0	ENST00000350721.4:c.3985G>T	p.Glu1329Ter	p.E1329*	ENST00000350721	NM_001184.3	1329	Gaa/Taa	22/47	1	2	FACETS	0.998	0.907	1	0.998	0.907	1	CLONAL	1	TRUE	1	0.447624629799922	2		439	555	SUCCESS
ATR	545	MSKCC	GRCh37	3	142253981	142253981	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	117	323	0	ENST00000350721.4:c.3886A>C	p.Asn1296His	p.N1296H	ENST00000350721	NM_001184.3	1296	Aat/Cat	21/47	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.447624629799922	2		323	494	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275366	142275366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	168	429	0	ENST00000350721.4:c.1937G>T	p.Arg646Ile	p.R646I	ENST00000350721	NM_001184.3	646	aGa/aTa	9/47	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.447624629799922	2		429	657	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917537	178917537	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	98	395	1	ENST00000263967.3:c.412G>T	p.Asp138Tyr	p.D138Y	ENST00000263967	NM_006218.2	138	Gac/Tac	3/21	1	2	FACETS	0.864	0.773	0.959	0.864	0.773	0.959	CLONAL	1	TRUE	1	0.447624629799922	2		396	507	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442757	187442757	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	190	760	1	ENST00000232014.4:c.1949G>A	p.Arg650Gln	p.R650Q	ENST00000232014	NM_001130845.1	650	cGa/cAa	9/10	1	2	FACETS	0.986	0.912	1	0.986	0.912	1	CLONAL	1	TRUE	1	0.447624629799922	2		761	861	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607168	189607168	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	216	857	1	ENST00000264731.3:c.1547T>C	p.Met516Thr	p.M516T	ENST00000264731	NM_003722.4	516	aTg/aCg	12/14	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.447624629799922	2		858	946	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612028	189612028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs900140738	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	178	685	0	ENST00000264731.3:c.1780C>T	p.Arg594Ter	p.R594*	ENST00000264731	NM_003722.4	594	Cga/Tga	14/14	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.447624629799922	2		685	756	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612176	189612176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	176	734	0	ENST00000264731.3:c.1928G>A	p.Arg643Gln	p.R643Q	ENST00000264731	NM_003722.4	643	cGa/cAa	14/14	1	2	FACETS	0.979	0.903	1	0.979	0.903	1	CLONAL	1	TRUE	1	0.447624629799922	2		734	803	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55124946	55124946	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138929755	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	145	528	0	ENST00000257290.5:c.11C>T	p.Ser4Phe	p.S4F	ENST00000257290	NM_006206.4	4	tCc/tTc	2/23	1	2	FACETS	0.977	0.894	1	0.977	0.894	1	CLONAL	1	TRUE	1	0.447624629799922	2		528	663	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55143649	55143649	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	134	611	0	ENST00000257290.5:c.1881G>T	p.Lys627Asn	p.K627N	ENST00000257290	NM_006206.4	627	aaG/aaT	13/23	1	2	FACETS	0.877	0.798	0.959	0.877	0.798	0.959	CLONAL	1	TRUE	1	0.447624629799922	2		611	683	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218795	66218795	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs774423059	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	86	229	0	ENST00000273854.3:c.2263T>C	p.Tyr755His	p.Y755H	ENST00000273854	NM_004439.5	755	Tat/Cat	13/18	1	2	FACETS	0.963	0.857	1	0.963	0.857	1	CLONAL	1	TRUE	1	0.447624629799922	2		229	399	SUCCESS
ALB	213	MSKCC	GRCh37	4	74275089	74275089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	91	325	0	ENST00000295897.4:c.500C>T	p.Ala167Val	p.A167V	ENST00000295897	NM_000477.5	167	gCc/gTc	5/15	1	2	FACETS	0.922	0.823	1	0.922	0.823	1	CLONAL	1	TRUE	1	0.447624629799922	2		325	441	SUCCESS
ALB	213	MSKCC	GRCh37	4	74279174	74279174	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774294755	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	131	500	0	ENST00000295897.4:c.881C>T	p.Ser294Leu	p.S294L	ENST00000295897	NM_000477.5	294	tCg/tTg	8/15	1	2	FACETS	0.966	0.879	1	0.966	0.879	1	CLONAL	1	TRUE	1	0.447624629799922	2		500	606	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197281	106197281	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	195	626	0	ENST00000380013.4:c.5614C>A	p.Leu1872Ile	p.L1872I	ENST00000380013	NM_001127208.2	1872	Ctc/Atc	11/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.447624629799922	2		626	805	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247367	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	153	586	0	ENST00000281708.4:c.1435C>T	p.Arg479Ter	p.R479*	ENST00000281708	NM_033632.3	479	Cga/Tga	10/12	1	2	FACETS	0.935	0.857	1	0.935	0.857	1	CLONAL	1	TRUE	1	0.447624629799922	2		586	731	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268087	153268087	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	144	468	0	ENST00000281708.4:c.721T>A	p.Phe241Ile	p.F241I	ENST00000281708	NM_033632.3	241	Ttt/Att	4/12	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.447624629799922	2		468	627	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268137	153268137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752114536	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	185	603	0	ENST00000281708.4:c.671G>A	p.Arg224Gln	p.R224Q	ENST00000281708	NM_033632.3	224	cGa/cAa	4/12	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.447624629799922	2		603	785	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510183	187510183	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765124620	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	227	706	1	ENST00000441802.2:c.13330G>A	p.Ala4444Thr	p.A4444T	ENST00000441802	NM_005245.3	4444	Gca/Aca	27/27	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.447624629799922	2		707	933	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534356	187534356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770029391	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	204	627	1	ENST00000441802.2:c.9370G>A	p.Glu3124Lys	p.E3124K	ENST00000441802	NM_005245.3	3124	Gaa/Aaa	13/27	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.447624629799922	2		628	845	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549725	187549725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199516712	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	180	612	0	ENST00000441802.2:c.4516C>T	p.Arg1506Cys	p.R1506C	ENST00000441802	NM_005245.3	1506	Cgt/Tgt	8/27	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.447624629799922	2		612	797	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31431755	31431755	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	139	500	0	ENST00000344624.3:c.3073G>A	p.Ala1025Thr	p.A1025T	ENST00000344624		1025	Gct/Act	23/33	1	2	FACETS	0.981	0.896	1	0.981	0.896	1	CLONAL	1	TRUE	1	0.447624629799922	2		500	633	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593331	67593331	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	209	676	0	ENST00000274335.5:c.2077G>T	p.Glu693Ter	p.E693*	ENST00000274335		693	Gaa/Taa	15/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.447624629799922	2		676	812	SUCCESS
APC	324	MSKCC	GRCh37	5	112155043	112155043	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	131	480	0	ENST00000257430.4:c.1312+2T>G		p.X438_splice	ENST00000257430	NM_000038.5	438			1	2	FACETS	0.947	0.862	1	0.947	0.862	1	CLONAL	1	TRUE	1	0.447624629799922	2		480	618	SUCCESS
APC	324	MSKCC	GRCh37	5	112170694	112170694	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	159	461	0	ENST00000257430.4:c.1790C>A	p.Ala597Glu	p.A597E	ENST00000257430	NM_000038.5	597	gCa/gAa	15/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.447624629799922	2		461	620	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	168	544	0	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.447624629799922	2		544	720	SUCCESS
APC	324	MSKCC	GRCh37	5	112176411	112176411	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	149	494	0	ENST00000257430.4:c.5120C>A	p.Ser1707Tyr	p.S1707Y	ENST00000257430	NM_000038.5	1707	tCt/tAt	16/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.447624629799922	2		494	602	SUCCESS
APC	324	MSKCC	GRCh37	5	112177472	112177472	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	125	517	0	ENST00000257430.4:c.6181G>T	p.Glu2061Ter	p.E2061*	ENST00000257430	NM_000038.5	2061	Gaa/Taa	16/16	1	2	FACETS	0.841	0.763	0.923	0.841	0.763	0.923	CLONAL	1	TRUE	1	0.447624629799922	2		517	664	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911514	131911514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143802516	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	132	377	1	ENST00000265335.6:c.259C>T	p.Arg87Cys	p.R87C	ENST00000265335		87	Cgt/Tgt	3/25	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.447624629799922	2		378	570	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562738	176562738	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	226	812	0	ENST00000439151.2:c.634G>A	p.Asp212Asn	p.D212N	ENST00000439151	NM_022455.4	212	Gac/Aac	2/23	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.447624629799922	2		812	1003	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562985	176562985	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	131	377	0	ENST00000439151.2:c.881A>C	p.Glu294Ala	p.E294A	ENST00000439151	NM_022455.4	294	gAa/gCa	2/23	1	2	FACETS	0.994	0.905	1	0.994	0.905	1	CLONAL	1	TRUE	1	0.447624629799922	2		377	589	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636645	176636645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	127	373	0	ENST00000439151.2:c.1245G>T	p.Gln415His	p.Q415H	ENST00000439151	NM_022455.4	415	caG/caT	5/23	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.447624629799922	2		373	553	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910685	29910685	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs199474408	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	259	1271	0	ENST00000376809.5:c.225G>A	p.Trp75Ter	p.W75*	ENST00000376809	NM_002116.7	75	tgG/tgA	2/8	0.447624629799922	1	FACETS	0.817	0.765	0.87	0.817	0.765	0.87	CLONAL	1	TRUE	0	0.447624629799922	1		1271	1100	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816896	32816896	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	108	451	0	ENST00000354258.4:c.1429-1G>A		p.X477_splice	ENST00000354258	NM_000593.5	477			0.447624629799922	1	FACETS	0.832	0.752	0.917	0.832	0.752	0.917	CLONAL	1	TRUE	0	0.447624629799922	1		451	450	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001395	150001395	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	131	476	0	ENST00000253339.5:c.2209C>T	p.Arg737Ter	p.R737*	ENST00000253339		737	Cga/Tga	4/7	0.447624629799922	1	FACETS	0.872	0.795	0.952	0.872	0.795	0.952	CLONAL	1	TRUE	0	0.447624629799922	1		476	521	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005662	150005662	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	152	608	0	ENST00000253339.5:c.563A>G	p.Gln188Arg	p.Q188R	ENST00000253339		188	cAg/cGg	3/7	0.447624629799922	1	FACETS	0.926	0.852	1	0.926	0.852	1	CLONAL	1	TRUE	0	0.447624629799922	1		608	569	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042253	6042253	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	160	511	0	ENST00000265849.7:c.368C>A	p.Ser123Tyr	p.S123Y	ENST00000265849	NM_000535.5	123	tCt/tAt	5/15	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.447624629799922	2		511	670	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739796	41739796	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	176	707	0	ENST00000242208.4:c.177G>T	p.Lys59Asn	p.K59N	ENST00000242208	NM_002192.2	59	aaG/aaT	2/3	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.447624629799922	2		707	762	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392173	81392173	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs758790721	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	61	148	0	ENST00000222390.5:c.104G>T	p.Arg35Ile	p.R35I	ENST00000222390	NM_000601.4	35	aGa/aTa	2/18	1	2	FACETS	0.915	0.795	1	0.915	0.795	1	CLONAL	1	TRUE	1	0.447624629799922	2		148	298	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859961	151859961	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	190	758	0	ENST00000262189.6:c.10701T>G	p.Ser3567Arg	p.S3567R	ENST00000262189	NM_170606.2	3567	agT/agG	43/59	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.447624629799922	2		758	808	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884466	151884466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1435892915	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	184	549	0	ENST00000262189.6:c.4889C>T	p.Ser1630Leu	p.S1630L	ENST00000262189	NM_170606.2	1630	tCg/tTg	33/59	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.447624629799922	2		549	773	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884921	151884921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760955374	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	149	548	0	ENST00000262189.6:c.4672C>T	p.Arg1558Trp	p.R1558W	ENST00000262189	NM_170606.2	1558	Cgg/Tgg	32/59	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.447624629799922	2		548	664	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194791	29194791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749288021	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	189	760	0	ENST00000240100.2:c.937C>T	p.Arg313Cys	p.R313C	ENST00000240100	NM_001394.6	313	Cgc/Tgc	4/4	1	2	FACETS	0.992	0.918	1	0.992	0.918	1	CLONAL	1	TRUE	1	0.447624629799922	2		760	851	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146156	38146156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	187	677	0	ENST00000317025.8:c.3350G>A	p.Arg1117Lys	p.R1117K	ENST00000317025	NM_023034.1	1117	aGa/aAa	19/24	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.447624629799922	2		677	787	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279359	38279359	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	163	799	0	ENST00000425967.3:c.1130C>A	p.Ser377Tyr	p.S377Y	ENST00000425967	NM_001174067.1	377	tCt/tAt	9/19	1	2	FACETS	0.876	0.805	0.951	0.876	0.805	0.951	CLONAL	1	TRUE	1	0.447624629799922	2		799	831	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950453	68950453	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	102	380	0	ENST00000288368.4:c.765T>G	p.Ile255Met	p.I255M	ENST00000288368	NM_024870.2	255	atT/atG	7/40	1	2	FACETS	0.875	0.785	0.969	0.875	0.785	0.969	CLONAL	1	TRUE	1	0.447624629799922	2		380	521	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009392	69009392	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	145	506	0	ENST00000288368.4:c.2509G>A	p.Glu837Lys	p.E837K	ENST00000288368	NM_024870.2	837	Gaa/Aaa	22/40	1	2	FACETS	0.977	0.894	1	0.977	0.894	1	CLONAL	1	TRUE	1	0.447624629799922	2		506	663	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020558	69020558	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753700	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	101	423	0	ENST00000288368.4:c.2930C>T	p.Ser977Leu	p.S977L	ENST00000288368	NM_024870.2	977	tCg/tTg	24/40	1	2	FACETS	0.883	0.792	0.979	0.883	0.792	0.979	CLONAL	1	TRUE	1	0.447624629799922	2		423	511	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965588	90965588	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781881	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	119	341	0	ENST00000265433.3:c.1729G>T	p.Asp577Tyr	p.D577Y	ENST00000265433	NM_002485.4	577	Gat/Tat	11/16	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.447624629799922	2		341	518	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117875450	117875450	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	60	457	0	ENST00000297338.2:c.193C>T	p.Arg65Ter	p.R65*	ENST00000297338	NM_006265.2	65	Cga/Tga	3/14	1	2	FACETS	0.492	0.424	0.566	0.492	0.424	0.566	SUBCLONAL	1	TRUE	1	0.447624629799922	2		457	545	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2084176	2084176	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	115	357	0	ENST00000349721.2:c.2506G>T	p.Asp836Tyr	p.D836Y	ENST00000349721	NM_003070.3	836	Gac/Tac	17/34	0.447624629799922	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.447624629799922	1		357	351	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050791	5050791	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	121	405	0	ENST00000381652.3:c.574G>T	p.Glu192Ter	p.E192*	ENST00000381652	NM_004972.3	192	Gaa/Taa	6/25	0.447624629799922	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.447624629799922	1		405	413	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5466819	5466819	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	123	474	0	ENST00000381577.3:c.840G>T	p.Lys280Asn	p.K280N	ENST00000381577	NM_014143.3	280	aaG/aaT	6/7	0.447624629799922	1	FACETS	0.841	0.765	0.921	0.841	0.765	0.921	CLONAL	1	TRUE	0	0.447624629799922	1		474	507	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465602	8465602	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	158	568	0	ENST00000356435.5:c.3578C>G	p.Ala1193Gly	p.A1193G	ENST00000356435		1193	gCc/gGc	21/35	0.447624629799922	1	FACETS	0.996	0.918	1	0.996	0.918	1	CLONAL	1	TRUE	0	0.447624629799922	1		568	550	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127951935	127951935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	148	671	0	ENST00000373547.4:c.63G>T	p.Glu21Asp	p.E21D	ENST00000373547	NM_002721.4	21	gaG/gaT	1/7	1	2	FACETS	0.953	0.872	1	0.953	0.872	1	CLONAL	1	TRUE	1	0.447624629799922	2		671	694	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781304	135781304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	200	827	0	ENST00000298552.3:c.1661C>T	p.Pro554Leu	p.P554L	ENST00000298552	NM_001162426.1	554	cCc/cTc	15/23	1	2	FACETS	0.981	0.91	1	0.981	0.91	1	CLONAL	1	TRUE	1	0.447624629799922	2		827	911	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139794113	139794113	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	160	519	0	ENST00000247668.2:c.256G>T	p.Glu86Ter	p.E86*	ENST00000247668	NM_021138.3	86	Gaa/Taa	3/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.447624629799922	2		519	668	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345290	70345290	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	181	338	0	ENST00000374080.3:c.2316G>T	p.Lys772Asn	p.K772N	ENST00000374080		772	aaG/aaT	16/45	1	1	FACETS	0.835	0.782	0.888	1	0.993	1	CLONAL	2	TRUE	0	0.447624629799922	1		338	376	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937553	76937553	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	140	166	0	ENST00000373344.5:c.3195G>T	p.Glu1065Asp	p.E1065D	ENST00000373344	NM_000489.3	1065	gaG/gaT	9/35	1	1	FACETS	0.858	0.797	0.919	1	0.991	1	CLONAL	2	TRUE	0	0.447624629799922	1		166	283	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938995	76938995	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs886044898	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	119	166	0	ENST00000373344.5:c.1753G>T	p.Glu585Ter	p.E585*	ENST00000373344	NM_000489.3	585	Gaa/Taa	9/35	1	1	FACETS	0.785	0.722	0.848	1	0.988	1	SUBCLONAL	2	TRUE	0	0.447624629799922	1		166	263	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182891	123182891	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	142	103	0	ENST00000218089.9:c.856A>C	p.Asn286His	p.N286H	ENST00000218089	NM_001042749.1	286	Aat/Cat	10/35	0.293476949552504	2	FACETS	0.92	0.862	0.975			1	CLONAL	3	TRUE	NA	0.447624629799922	2		103	230	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185222	123185222	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059091-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	148	94	0	ENST00000218089.9:c.1174A>C	p.Lys392Gln	p.K392Q	ENST00000218089	NM_001042749.1	392	Aaa/Caa	13/35	0.293476949552504	2	FACETS	0.938	0.882	0.993			1	CLONAL	3	TRUE	NA	0.447624629799922	2		94	235	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	114	477	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.898	0.814	0.987	0.898	0.814	0.987	CLONAL	1	TRUE	1	0.54	2		477	470	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0059099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	105	125	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.161704277513893	3	FACETS	1	0.982	1	0.706	0.639	0.775	INDETERMINATE	1	TRUE	1	0.54	3		125	350	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0059099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	202	468	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	0.3	2	FACETS	0.979	0.91	1			1	INDETERMINATE	1	TRUE	NA	0.54	2		468	764	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198453	108198453	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	163	340	0	ENST00000278616.4:c.7057C>A	p.Pro2353Thr	p.P2353T	ENST00000278616	NM_000051.3	2353	Cct/Act	48/63	1	2	FACETS	0.943	0.869	1	0.943	0.869	1	CLONAL	1	TRUE	1	0.54	2		340	640	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867571	45867571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	279	598	0	ENST00000391945.4:c.737C>T	p.Ser246Phe	p.S246F	ENST00000391945	NM_000400.3	246	tCc/tTc	9/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.54	2		598	942	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929235	44929235	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	195	215	0	ENST00000377967.4:c.2335C>T	p.Gln779Ter	p.Q779*	ENST00000377967	NM_021140.2	779	Cag/Tag	17/29	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.54	1		215	386	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0059099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	212	408	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	0.989	0.921	1	0.989	0.921	1	CLONAL	1	TRUE	1	0.54	2		408	794	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056181	27056181	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	198	379	0	ENST00000324856.7:c.1177C>T	p.Gln393Ter	p.Q393*	ENST00000324856	NM_006015.4	393	Cag/Tag	2/20	1	2	FACETS	0.992	0.922	1	0.992	0.922	1	CLONAL	1	TRUE	1	0.54	2		379	739	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973778	131973778	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	153	265	0	ENST00000265335.6:c.3481G>C	p.Glu1161Gln	p.E1161Q	ENST00000265335		1161	Gaa/Caa	23/25	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.54	2		265	507	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186681	11186681	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1024737469	NA	P-0059099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	186	353	0	ENST00000361445.4:c.6524T>C	p.Met2175Thr	p.M2175T	ENST00000361445	NM_004958.3	2175	aTg/aCg	46/58	1	2	FACETS	0.959	0.889	1	0.959	0.889	1	CLONAL	1	TRUE	1	0.54	2		353	718	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265477	198265477	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	180	329	0	ENST00000335508.6:c.2680G>A	p.Asp894Asn	p.D894N	ENST00000335508	NM_012433.2	894	Gat/Aat	18/25	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.54	2		329	623	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936176	71936176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	162	462	0	ENST00000298229.2:c.148G>A	p.Glu50Lys	p.E50K	ENST00000298229	NM_001567.3	50	Gag/Aag	1/28	1	2	FACETS	0.942	0.868	1	0.942	0.868	1	CLONAL	1	TRUE	1	0.54	2		462	637	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100088	157100088	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768271181	NA	P-0059099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	236	634	1	ENST00000346085.5:c.1025C>T	p.Ala342Val	p.A342V	ENST00000346085	NM_020732.3	342	gCg/gTg	1/20	1	2	FACETS	0.999	0.934	1	0.999	0.934	1	CLONAL	1	TRUE	1	0.54	2		635	875	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464935	120464935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	231	371	0	ENST00000256646.2:c.5137G>A	p.Glu1713Lys	p.E1713K	ENST00000256646	NM_024408.3	1713	Gaa/Aaa	28/34	0.3	1	FACETS	0.783	0.732	0.835	0.783	0.732	0.835	INDETERMINATE	1	TRUE	0	0.54	1		371	798	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981146	201981146	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	193	382	0	ENST00000359651.3:c.225G>A	p.Trp75Ter	p.W75*	ENST00000359651		75	tgG/tgA	2/8	1	2	FACETS	0.932	0.864	1	0.932	0.864	1	CLONAL	1	TRUE	1	0.54	2		382	767	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981162	201981162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	208	394	0	ENST00000359651.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000359651		81	Gag/Aag	2/8	1	2	FACETS	0.964	0.897	1	0.964	0.897	1	CLONAL	1	TRUE	1	0.54	2		394	799	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852755	63852755	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	201	373	0	ENST00000279873.7:c.3533A>C	p.Gln1178Pro	p.Q1178P	ENST00000279873	NM_032199.2	1178	cAg/cCg	10/10	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.54	2		373	728	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192582	94192582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564511708	NA	P-0059099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	127	217	0	ENST00000323929.3:c.1492G>A	p.Asp498Asn	p.D498N	ENST00000323929	NM_005591.3	498	Gat/Aat	13/20	1	2	FACETS	0.917	0.835	1	0.917	0.835	1	CLONAL	1	TRUE	1	0.54	2		217	513	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425263	49425263	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	249	525	0	ENST00000301067.7:c.13225G>C	p.Glu4409Gln	p.E4409Q	ENST00000301067	NM_003482.3	4409	Gag/Cag	39/54	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.54	2		525	859	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425449	49425449	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	285	605	0	ENST00000301067.7:c.13039C>T	p.Gln4347Ter	p.Q4347*	ENST00000301067	NM_003482.3	4347	Cag/Tag	39/54	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.54	2		605	1020	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748270	43748270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	211	441	0	ENST00000382044.4:c.2536G>A	p.Asp846Asn	p.D846N	ENST00000382044	NM_001141980.1	846	Gat/Aat	12/28	1	2	FACETS	0.936	0.871	1	0.936	0.871	1	CLONAL	1	TRUE	1	0.54	2		441	835	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661026	227661026	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	211	482	0	ENST00000305123.5:c.2429C>T	p.Ser810Phe	p.S810F	ENST00000305123	NM_005544.2	810	tCc/tTc	1/2	1	2	FACETS	0.966	0.899	1	0.966	0.899	1	CLONAL	1	TRUE	1	0.54	2		482	809	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121075	29121089	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	TCTATGTATGCAATG	TCTATGTATGCAATG	-	novel	NA	P-0059099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	172	257	0	ENST00000328354.6:c.468_482del	p.Tyr156_Glu161delinsTer	p.Y156_E161delins*	ENST00000328354	NM_007194.3	156	taCATTGCATACATAGAa/taa	4/15	1	2	FACETS	0.905	0.835	0.977	0.905	0.835	0.977	CLONAL	1	TRUE	1	0.54	2		257	704	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542789	187542790	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TATTTCACTCATTGGTGGACTGCCCTTA	novel	NA	P-0059099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	158	415	0	ENST00000441802.2:c.4923_4950dup	p.Thr1651Ter	p.T1651*	ENST00000441802	NM_005245.3	1650	-/TAAGGGCAGTCCACCAATGAGTGAAATA	10/27	0.3	2	FACETS	0.644	0.59	0.7			1	INDETERMINATE	1	TRUE	NA	0.54	2		415	909	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945643	151945643	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	155	244	0	ENST00000262189.6:c.1876G>T	p.Glu626Ter	p.E626*	ENST00000262189	NM_170606.2	626	Gaa/Taa	14/59	0.3	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.54	2		244	481	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760222	133760222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059099-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	159	438	0	ENST00000318560.5:c.2545G>A	p.Glu849Lys	p.E849K	ENST00000318560	NM_005157.4	849	Gag/Aag	11/11	1	2	FACETS	0.92	0.847	0.996	0.92	0.847	0.996	CLONAL	1	TRUE	1	0.54	2		438	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0059109-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	370	688	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.631288566947089	1	FACETS	0.992	0.947	1	0.992	0.947	1	CLONAL	1	TRUE	0	0.631288566947089	1		688	809	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956553	93956553	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1035177735	NA	P-0059109-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	125	407	0	ENST00000369303.4:c.2683C>T	p.Arg895Ter	p.R895*	ENST00000369303	NM_004440.3	895	Cga/Tga	15/17	0.631288566947089	1	FACETS	0.681	0.622	0.742	0.681	0.622	0.742	SUBCLONAL	1	TRUE	0	0.631288566947089	1		407	398	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115284229	115284240	+	inframe_deletion	In_Frame_Del	DEL	AGGAGGGGCTGC	AGGAGGGGCTGC	-	novel	NA	P-0059109-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	88	422	0	ENST00000438362.2:c.46_57del	p.Ala16_Pro19del	p.A16_P19del	ENST00000438362	NM_001242891.1	16	GCAGCCCCTCCT/-	2/20	1	2	FACETS	0.651	0.58	0.727	0.651	0.58	0.727	SUBCLONAL	1	TRUE	1	0.631288566947089	2		422	428	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562895	21562895	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059109-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	77	741	0	ENST00000382592.4:c.1024A>T	p.Ser342Cys	p.S342C	ENST00000382592	NM_014572.2	342	Agc/Tgc	4/8	0.631288566947089	1	FACETS	0.201	0.176	0.228	0.201	0.176	0.228	SUBCLONAL	1	TRUE	0	0.631288566947089	1		741	831	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911349	32911349	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059109-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	67	262	0	ENST00000380152.3:c.2857G>T	p.Glu953Ter	p.E953*	ENST00000380152		953	Gag/Tag	11/27	0.631288566947089	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.631288566947089	1		262	132	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70967541	70967549	+	inframe_deletion	In_Frame_Del	DEL	ACAATACAC	ACAATACAC	-	novel	NA	P-0059109-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	120	330	0	ENST00000276594.2:c.1474_1482del	p.Val492_Cys494del	p.V492_C494del	ENST00000276594	NM_024504.3	492	GTGTATTGT/-	7/8	0.631288566947089	1	FACETS	0.919	0.844	0.995	0.919	0.844	0.995	CLONAL	1	TRUE	0	0.631288566947089	1		330	283	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396830	139396830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059109-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	256	564	0	ENST00000277541.6:c.5278C>T	p.Arg1760Cys	p.R1760C	ENST00000277541	NM_017617.3	1760	Cgc/Tgc	28/34	0.631288566947089	1	FACETS	0.837	0.789	0.886	0.837	0.789	0.886	CLONAL	1	TRUE	0	0.631288566947089	1		564	663	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954165	48954312	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTTTTTAAATTATCTGTTTCAGGAAGAAGAACGATTATCCATTCAAAATTTTAGGTAAATTTTTTACTTTTAGTAAAAAATTTTTTTCTTTTTATAGAAGTAAGTATTTTATAATCTTTTTTTTTTTCCTTTAGCAAACTTCTGAA	TTTTTTTTAAATTATCTGTTTCAGGAAGAAGAACGATTATCCATTCAAAATTTTAGGTAAATTTTTTACTTTTAGTAAAAAATTTTTTTCTTTTTATAGAAGTAAGTATTTTATAATCTTTTTTTTTTTCCTTTAGCAAACTTCTGAA	-	novel	NA	P-0059110-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	46	87	0	ENST00000267163.4:c.1390-23_1434del		p.X464_splice	ENST00000267163	NM_000321.2	464		15-16/27	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		87	105	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0059125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	112	399	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.189359306031143	3	FACETS	1	0.953	1			1	CLONAL	2	TRUE	NA	0.25	3		399	464	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0059125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	74	848	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.25	2		848	465	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760979	133760979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	53	397	1	ENST00000318560.5:c.3302C>T	p.Pro1101Leu	p.P1101L	ENST00000318560	NM_005157.4	1101	cCg/cTg	11/11	1	2	FACETS	0.916	0.782	1	0.916	0.782	1	CLONAL	1	TRUE	1	0.25	2		398	463	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530198	212530198	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	32	357	0	ENST00000342788.4:c.1721C>A	p.Pro574His	p.P574H	ENST00000342788	NM_005235.2	574	cCt/cAt	15/28	1	2	FACETS	0.587	0.476	0.713	0.587	0.476	0.713	SUBCLONAL	1	TRUE	1	0.25	2		357	436	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719706	61719706	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	28	355	0	ENST00000401558.2:c.1562T>A	p.Ile521Lys	p.I521K	ENST00000401558	NM_003400.3	521	aTa/aAa	14/25	1	2	FACETS	0.433	0.345	0.534	0.433	0.345	0.534	SUBCLONAL	1	TRUE	1	0.25	2		355	517	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680497	30680497	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	41	409	0	ENST00000376406.3:c.1222G>C	p.Glu408Gln	p.E408Q	ENST00000376406	NM_014641.2	408	Gaa/Caa	5/15	1	2	FACETS	0.627	0.522	0.744	0.627	0.522	0.744	SUBCLONAL	1	TRUE	1	0.25	2		409	523	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554315	106554315	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	80	390	0	ENST00000369096.4:c.1843C>A	p.Leu615Ile	p.L615I	ENST00000369096	NM_001198.3	615	Ctc/Atc	6/7	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.25	2		390	540	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152009027	152009027	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059125-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	54	269	0	ENST00000262189.6:c.595del	p.Arg199AspfsTer7	p.R199Dfs*7	ENST00000262189	NM_170606.2	199	Cga/ga	5/59	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.25	2		269	377	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0059126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	34	185	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.928	0.766	1	0.928	0.766	1	CLONAL	1	TRUE	1	0.38768134848043	2		185	189	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0059126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	25	230	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.537	0.425	0.665	0.537	0.425	0.665	SUBCLONAL	1	TRUE	1	0.38768134848043	2		230	240	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087944	27087944	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0059126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	51	463	0	ENST00000324856.7:c.2231C>G	p.Ser744Ter	p.S744*	ENST00000324856	NM_006015.4	744	tCa/tGa	6/20	1	2	FACETS	0.598	0.509	0.695	0.598	0.509	0.695	SUBCLONAL	1	TRUE	1	0.38768134848043	2		463	440	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0059126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	20	121	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.524	0.402	0.665	0.524	0.402	0.665	SUBCLONAL	1	TRUE	1	0.38768134848043	2		121	197	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138729528	NA	P-0059126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	44	530	0	ENST00000269305.4:c.523C>T	p.Arg175Cys	p.R175C	ENST00000269305	NM_001126112.2	175	Cgc/Tgc	5/11	1	2	FACETS	0.483	0.405	0.569	0.483	0.405	0.569	SUBCLONAL	1	TRUE	1	0.38768134848043	2		530	470	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099397	27099397	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	34	463	0	ENST00000324856.7:c.3634C>T	p.Gln1212Ter	p.Q1212*	ENST00000324856	NM_006015.4	1212	Cag/Tag	14/20	1	2	FACETS	0.445	0.364	0.537	0.445	0.364	0.537	SUBCLONAL	1	TRUE	1	0.38768134848043	2		463	394	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161293455	161293455	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	44	273	0	ENST00000367975.2:c.72C>G	p.Ile24Met	p.I24M	ENST00000367975	NM_003001.3	24	atC/atG	2/6	0.38768134848043	3	FACETS	0.74	0.623	0.87	0.37	0.311	0.435	SUBCLONAL	1	TRUE	1	0.38768134848043	3		273	366	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717609	89717609	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs876661024	NA	P-0059126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	28	292	0	ENST00000371953.3:c.635-1G>A		p.X212_splice	ENST00000371953	NM_000314.4	212			1	2	FACETS	0.503	0.403	0.617	0.503	0.403	0.617	SUBCLONAL	1	TRUE	1	0.38768134848043	2		292	287	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636203	87636203	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	44	437	0	ENST00000277120.3:c.2368C>T	p.Arg790Ter	p.R790*	ENST00000277120		790	Cga/Tga	19/19	1	2	FACETS	0.522	0.438	0.614	0.522	0.438	0.614	SUBCLONAL	1	TRUE	1	0.38768134848043	2		437	435	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942694	48942694	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	28	142	0	ENST00000267163.4:c.1081A>G	p.Asn361Asp	p.N361D	ENST00000267163	NM_000321.2	361	Aac/Gac	11/27	1	2	FACETS	0.582	0.467	0.712	0.582	0.467	0.712	SUBCLONAL	1	TRUE	1	0.38768134848043	2		142	248	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149436893	149436893	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059126-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	27	466	0	ENST00000286301.3:c.2276C>G	p.Ser759Cys	p.S759C	ENST00000286301	NM_005211.3	759	tCc/tGc	17/22	1	2	FACETS	0.38	0.302	0.468	0.38	0.302	0.468	SUBCLONAL	1	TRUE	1	0.38768134848043	2		466	367	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061147	38061185	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	CCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCG	CCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCG	-	novel	NA	P-0059127-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	249	546	0	ENST00000250448.2:c.804_842del	p.Cys268_Gly281delinsTer	p.C268_G281delins*	ENST00000250448	NM_004496.3	268	tgCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGa/tga	2/2	0.552310533870574	3	FACETS	0.875	0.831	0.918	1	0.993	1	CLONAL	3	TRUE	1	0.544958084851137	3		546	443	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251518	10251520	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0059127-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	122	560	0	ENST00000340748.4:c.3412_3414del	p.Lys1138del	p.K1138del	ENST00000340748		1138	AAG/-	31/40	0.552310533870574	3	FACETS	1	0.962	1	0.556	0.505	0.61	CLONAL	1	TRUE	1	0.544958084851137	3		560	512	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0059128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	73	539	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.878	0.774	0.988	0.878	0.774	0.988	CLONAL	1	TRUE	1	0.500821500337796	2		539	332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0059128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	92	522	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.500442688754914	1	FACETS	0.934	0.84	1	0.934	0.84	1	CLONAL	1	TRUE	0	0.500821500337796	1		522	295	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0059128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	91	293	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.407493023659751	3	FACETS	0.916	0.827	1	0.916	0.827	1	CLONAL	2	TRUE	1	0.500821500337796	3		293	248	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0059128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	99	582	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.998	0.898	1	0.998	0.898	1	CLONAL	1	TRUE	1	0.500821500337796	2		582	396	SUCCESS
APC	324	MSKCC	GRCh37	5	112116538	112116538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs749479682	NA	P-0059128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	56	357	0	ENST00000257430.4:c.583C>T	p.Gln195Ter	p.Q195*	ENST00000257430	NM_000038.5	195	Caa/Taa	6/16	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.500821500337796	2		357	215	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178218	56178218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780012235	NA	P-0059128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	91	576	0	ENST00000399503.3:c.3191G>A	p.Arg1064Lys	p.R1064K	ENST00000399503	NM_005921.1	1064	aGa/aAa	14/20	1	2	FACETS	0.972	0.869	1	0.972	0.869	1	CLONAL	1	TRUE	1	0.500821500337796	2		576	374	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354212	15354212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201423321	NA	P-0059128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	74	600	3	ENST00000263377.2:c.2668G>A	p.Val890Met	p.V890M	ENST00000263377	NM_058243.2	890	Gtg/Atg	14/20	1	2	FACETS	0.869	0.767	0.978	0.869	0.767	0.978	CLONAL	1	TRUE	1	0.500821500337796	2		603	340	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953213	81953213	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	87	553	0	ENST00000359376.3:c.2179C>T	p.Arg727Ter	p.R727*	ENST00000359376	NM_002661.3	727	Cga/Tga	20/33	1	2	FACETS	0.886	0.79	0.988	0.886	0.79	0.988	CLONAL	1	TRUE	1	0.500821500337796	2		553	392	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146186	38146186	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1203258710	NA	P-0059128-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	131	509	0	ENST00000317025.8:c.3320C>T	p.Pro1107Leu	p.P1107L	ENST00000317025	NM_023034.1	1107	cCt/cTt	19/24	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.500821500337796	2		509	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0059129-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	161	674	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.381134432457435	2	FACETS	0.992	0.921	1	0.992	0.921	1	CLONAL	2	TRUE	0	0.400669314976424	2		674	405	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864769	68864769	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059129-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	55	390	0	ENST00000288368.4:c.140C>T	p.Ser47Leu	p.S47L	ENST00000288368	NM_024870.2	47	tCg/tTg	1/40	0.400669314976424	6	FACETS	0.907	0.776	1	0.227	0.194	0.263	CLONAL	1	TRUE	2	0.400669314976424	6		390	545	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404761	70404761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059129-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	60	426	0	ENST00000373644.4:c.2275G>A	p.Gly759Ser	p.G759S	ENST00000373644	NM_030625.2	759	Ggc/Agc	4/12	0.301823655134045	5	FACETS	1	0.948	1	0.402	0.347	0.46	CLONAL	1	TRUE	2	0.400669314976424	5		426	398	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913386	32913386	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059129-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	46	425	0	ENST00000380152.3:c.4894A>G	p.Ser1632Gly	p.S1632G	ENST00000380152		1632	Agt/Ggt	11/27	0.400669314976424	5	FACETS	0.711	0.599	0.835	0.237	0.199	0.279	SUBCLONAL	1	TRUE	2	0.400669314976424	5		425	517	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288153	21288153	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059129-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	80	486	0	ENST00000354336.3:c.398A>G	p.Asp133Gly	p.D133G	ENST00000354336	NM_005207.3	133	gAt/gGt	2/3	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.400669314976424	2		486	355	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	45	477	0				ENST00000310581	NM_198253.2	-/1132			0.222538369672189	3	FACETS	0.896	0.756	1	0.448	0.378	0.525	CLONAL	1	TRUE	1	0.3541954594446	3		477	334	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	96	284	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	0.159246857199345	4	FACETS	0.774	0.693	0.86	0.774	0.693	0.86	INDETERMINATE	2	TRUE	2	0.3541954594446	4		284	474	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866987936	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	82	535	0	ENST00000281708.4:c.1436G>C	p.Arg479Pro	p.R479P	ENST00000281708	NM_033632.3	479	cGa/cCa	10/12	0.222538369672189	3	FACETS	1	0.958	1	0.59	0.522	0.662	CLONAL	1	TRUE	1	0.3541954594446	3		535	462	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	142	687	0	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	0.265167295001415	2	FACETS	0.875	0.804	0.949	0.875	0.804	0.949	CLONAL	2	TRUE	0	0.3541954594446	2		687	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	148	689	0	ENST00000269305.4:c.404G>C	p.Cys135Ser	p.C135S	ENST00000269305	NM_001126112.2	135	tGc/tCc	5/11	0.25286610611056	2	FACETS	0.808	0.743	0.876	0.808	0.743	0.876	CLONAL	2	TRUE	0	0.3541954594446	2		689	517	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844172	68844172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	123	559	0	ENST00000261769.5:c.760G>A	p.Asp254Asn	p.D254N	ENST00000261769	NM_004360.3	254	Gat/Aat	6/16	0.245972105211931	5	FACETS	0.839	0.76	0.921	0.559	0.507	0.614	CLONAL	2	TRUE	2	0.3541954594446	5		559	634	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010560	48010560	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587779920	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	126	700	0	ENST00000234420.5:c.188C>G	p.Ser63Cys	p.S63C	ENST00000234420	NM_000179.2	63	tCc/tGc	1/10	0.3541954594446	3	FACETS	0.904	0.825	0.987	0.904	0.825	0.987	CLONAL	2	TRUE	1	0.3541954594446	3		700	463	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134955	41134955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	45	496	0	ENST00000379561.5:c.673C>T	p.Arg225Cys	p.R225C	ENST00000379561	NM_002015.3	225	Cgt/Tgt	2/3	0.3541954594446	3	FACETS	0.626	0.526	0.736	0.313	0.263	0.368	SUBCLONAL	1	TRUE	1	0.3541954594446	3		496	478	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332609	70332609	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1176805515	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	66	449	0	ENST00000373644.4:c.514C>G	p.Leu172Val	p.L172V	ENST00000373644	NM_030625.2	172	Cta/Gta	2/12	0.118653715254539	4	FACETS	1	0.955	1	0.611	0.532	0.696	INDETERMINATE	1	TRUE	2	0.3541954594446	4		449	413	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531867	41531867	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	48	470	0	ENST00000263253.7:c.1579C>G	p.Leu527Val	p.L527V	ENST00000263253	NM_001429.3	527	Ctt/Gtt	7/31	0.316833432243831	3	FACETS	0.776	0.658	0.906	0.388	0.329	0.453	CLONAL	1	TRUE	1	0.3541954594446	3		470	411	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992390	72992390	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs754146286	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	212	702	0	ENST00000268489.5:c.1655C>G	p.Ser552Cys	p.S552C	ENST00000268489	NM_006885.3	552	tCt/tGt	2/10	0.245972105211931	5	FACETS	1	0.986	1	0.808	0.753	0.865	CLONAL	2	TRUE	2	0.3541954594446	5		702	756	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519846	29519846	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	169	617	0	ENST00000389048.3:c.1725G>T	p.Lys575Asn	p.K575N	ENST00000389048	NM_004304.4	575	aaG/aaT	9/29	0.3541954594446	3	FACETS	0.883	0.815	0.953	0.883	0.815	0.953	CLONAL	2	TRUE	1	0.3541954594446	3		617	636	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005429	29005429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372354806	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	73	369	0	ENST00000282397.4:c.832G>A	p.Val278Ile	p.V278I	ENST00000282397	NM_002019.4	278	Gta/Ata	7/30	0.3541954594446	3	FACETS	1	0.965	1	0.64	0.563	0.722	CLONAL	1	TRUE	1	0.3541954594446	3		369	379	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609518	81609518	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs768939158	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	57	598	0	ENST00000298171.2:c.1120del	p.Gln374ArgfsTer38	p.Q374Rfs*38	ENST00000298171	NM_000369.2	372	aaC/aa	10/10	0.222538369672189	3	FACETS	0.639	0.548	0.738	0.319	0.274	0.369	SUBCLONAL	1	TRUE	1	0.3541954594446	3		598	593	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965421	18965421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	51	510	0	ENST00000262803.5:c.1168G>A	p.Glu390Lys	p.E390K	ENST00000262803	NM_002911.3	390	Gag/Aag	9/24	0.3541954594446	3	FACETS	0.811	0.691	0.942	0.405	0.345	0.471	CLONAL	1	TRUE	1	0.3541954594446	3		510	418	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536716	120536716	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	126	775	0	ENST00000229340.5:c.376G>C	p.Glu126Gln	p.E126Q	ENST00000229340	NM_006861.6	126	Gag/Cag	5/6	0.159246857199345	4	FACETS	1	0.984	1	0.724	0.657	0.795	INDETERMINATE	1	TRUE	2	0.3541954594446	4		775	665	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050770	5050770	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	77	421	0	ENST00000381652.3:c.553G>C	p.Asp185His	p.D185H	ENST00000381652	NM_004972.3	185	Gat/Cat	6/25	0.265167295001415	2	FACETS	1	0.965	1	0.623	0.551	0.699	CLONAL	1	TRUE	0	0.3541954594446	2		421	349	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178452	56178452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	68	539	0	ENST00000399503.3:c.3425C>T	p.Ser1142Leu	p.S1142L	ENST00000399503	NM_005921.1	1142	tCa/tTa	14/20	0.222538369672189	3	FACETS	1	0.954	1	0.599	0.524	0.68	CLONAL	1	TRUE	1	0.3541954594446	3		539	377	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150923439	150923439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	129	581	0	ENST00000271640.5:c.2086G>A	p.Glu696Lys	p.E696K	ENST00000271640	NM_001145415.1	696	Gag/Aag	13/22	0.159246857199345	4	FACETS	0.842	0.766	0.921	0.842	0.766	0.921	INDETERMINATE	2	TRUE	2	0.3541954594446	4		581	586	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782648	9782648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	66	551	0	ENST00000377346.4:c.2410G>A	p.Glu804Lys	p.E804K	ENST00000377346	NM_005026.3	804	Gag/Aag	19/24	0.3541954594446	3	FACETS	0.964	0.839	1	0.482	0.419	0.55	CLONAL	1	TRUE	1	0.3541954594446	3		551	455	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782657	9782657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	66	540	0	ENST00000377346.4:c.2419G>A	p.Asp807Asn	p.D807N	ENST00000377346	NM_005026.3	807	Gac/Aac	19/24	0.3541954594446	3	FACETS	1	0.874	1	0.502	0.437	0.572	CLONAL	1	TRUE	1	0.3541954594446	3		540	437	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743893	46743893	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	81	656	0	ENST00000371975.4:c.2183C>T	p.Ser728Phe	p.S728F	ENST00000371975	NM_003579.3	728	tCc/tTc	18/18	0.3541954594446	3	FACETS	0.899	0.793	1	0.449	0.396	0.506	CLONAL	1	TRUE	1	0.3541954594446	3		656	599	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958537	175958537	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	102	530	0	ENST00000367669.3:c.1808C>G	p.Ser603Cys	p.S603C	ENST00000367669	NM_022457.5	603	tCt/tGt	16/20	0.159246857199345	4	FACETS	0.924	0.832	1	0.924	0.832	1	INDETERMINATE	2	TRUE	2	0.3541954594446	4		530	422	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983049	201983049	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	130	720	0	ENST00000359651.3:c.898G>T	p.Glu300Ter	p.E300*	ENST00000359651		300	Gaa/Taa	7/8	0.159246857199345	4	FACETS	0.861	0.784	0.942	0.861	0.784	0.942	INDETERMINATE	2	TRUE	2	0.3541954594446	4		720	577	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446420	70446420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	127	714	0	ENST00000373644.4:c.5360C>T	p.Ser1787Leu	p.S1787L	ENST00000373644	NM_030625.2	1787	tCa/tTa	11/12	0.118653715254539	4	FACETS	0.807	0.733	0.884	0.807	0.733	0.884	INDETERMINATE	2	TRUE	2	0.3541954594446	4		714	602	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149316	119149316	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	68	572	0	ENST00000264033.4:c.1324C>G	p.Leu442Val	p.L442V	ENST00000264033	NM_005188.3	442	Ctg/Gtg	9/16	0.316833432243831	3	FACETS	0.757	0.659	0.863	0.379	0.329	0.432	SUBCLONAL	1	TRUE	1	0.3541954594446	3		572	597	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549092	21549092	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	62	652	0	ENST00000382592.4:c.3184G>T	p.Glu1062Ter	p.E1062*	ENST00000382592	NM_014572.2	1062	Gaa/Taa	8/8	0.14587465808119	3	FACETS	0.74	0.639	0.849			1	INDETERMINATE	1	TRUE	NA	0.3541954594446	3		652	557	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005287	29005287	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	67	430	0	ENST00000282397.4:c.974C>G	p.Ser325Ter	p.S325*	ENST00000282397	NM_002019.4	325	tCa/tGa	7/30	0.3541954594446	3	FACETS	1	0.956	1	0.608	0.531	0.691	CLONAL	1	TRUE	1	0.3541954594446	3		430	366	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972303	32972303	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	64	432	0	ENST00000380152.3:c.9653C>G	p.Ser3218Cys	p.S3218C	ENST00000380152		3218	tCt/tGt	27/27	0.3541954594446	3	FACETS	1	0.9	1	0.521	0.453	0.595	CLONAL	1	TRUE	1	0.3541954594446	3		432	408	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972329	32972329	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	73	458	0	ENST00000380152.3:c.9679C>T	p.Gln3227Ter	p.Q3227*	ENST00000380152		3227	Caa/Taa	27/27	0.3541954594446	3	FACETS	1	0.891	1	0.509	0.446	0.576	CLONAL	1	TRUE	1	0.3541954594446	3		458	477	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422064	81422064	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	63	627	0	ENST00000298171.2:c.40G>C	p.Asp14His	p.D14H	ENST00000298171	NM_000369.2	14	Gac/Cac	1/10	0.222538369672189	3	FACETS	0.801	0.693	0.917	0.4	0.346	0.459	CLONAL	1	TRUE	1	0.3541954594446	3		627	523	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89842219	89842219	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	118	424	0	ENST00000389301.3:c.1831G>C	p.Asp611His	p.D611H	ENST00000389301	NM_000135.2	611	Gat/Cat	21/43	0.245972105211931	5	FACETS	0.952	0.862	1	0.635	0.575	0.697	CLONAL	2	TRUE	2	0.3541954594446	5		424	536	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89865632	89865632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	114	645	0	ENST00000389301.3:c.835G>A	p.Asp279Asn	p.D279N	ENST00000389301	NM_000135.2	279	Gac/Aac	10/43	0.245972105211931	5	FACETS	0.756	0.682	0.834	0.504	0.454	0.556	SUBCLONAL	2	TRUE	2	0.3541954594446	5		645	652	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049817	16049817	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	96	421	0	ENST00000268712.3:c.955G>T	p.Glu319Ter	p.E319*	ENST00000268712	NM_006311.3	319	Gag/Tag	10/46	0.25286610611056	2	FACETS	0.783	0.705	0.865	0.783	0.705	0.865	SUBCLONAL	2	TRUE	0	0.3541954594446	2		421	346	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58700948	58700950	+	frameshift_variant	Frame_Shift_Ins	INS	TTC	TTC	ATTG	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	48	558	0	ENST00000305921.3:c.539_541delinsATTG	p.Ile180AsnfsTer13	p.I180Nfs*13	ENST00000305921	NM_003620.3	180	aTTCgg/aATTGgg	2/6	0.159246857199345	4	FACETS	0.595	0.502	0.697	0.297	0.251	0.349	INDETERMINATE	1	TRUE	2	0.3541954594446	4		558	617	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945418	17945418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1490273737	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	69	584	0	ENST00000458235.1:c.2312G>A	p.Arg771Gln	p.R771Q	ENST00000458235	NM_000215.3	771	cGa/cAa	17/24	0.3541954594446	3	FACETS	0.988	0.863	1	0.494	0.431	0.562	CLONAL	1	TRUE	1	0.3541954594446	3		584	464	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951092	17951092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	132	476	0	ENST00000458235.1:c.1201C>T	p.Leu401Phe	p.L401F	ENST00000458235	NM_000215.3	401	Ctc/Ttc	9/24	0.3541954594446	3	FACETS	0.997	0.912	1	0.997	0.912	1	CLONAL	2	TRUE	1	0.3541954594446	3		476	440	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954272	17954272	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	76	673	0	ENST00000458235.1:c.337G>C	p.Glu113Gln	p.E113Q	ENST00000458235	NM_000215.3	113	Gag/Cag	4/24	0.3541954594446	3	FACETS	0.892	0.784	1	0.446	0.392	0.505	CLONAL	1	TRUE	1	0.3541954594446	3		673	566	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303479	30303479	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	119	697	0	ENST00000262643.3:c.17G>A	p.Arg6Lys	p.R6K	ENST00000262643	NM_001238.2	6	aGg/aAg	2/12	0.3541954594446	3	FACETS	0.909	0.827	0.995	0.909	0.827	0.995	CLONAL	2	TRUE	1	0.3541954594446	3		697	435	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631205	67631205	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	30	440	0	ENST00000272342.5:c.1391C>A	p.Ser464Ter	p.S464*	ENST00000272342	NM_019002.3	464	tCa/tAa	5/6	0.3541954594446	3	FACETS	0.633	0.511	0.771	0.317	0.255	0.386	SUBCLONAL	1	TRUE	1	0.3541954594446	3		440	315	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387069	31387069	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	131	702	0	ENST00000328111.2:c.1694C>G	p.Pro565Arg	p.P565R	ENST00000328111	NM_006892.3	565	cCt/cGt	16/23	0.292698475647713	4	FACETS	1	0.985	1	0.361	0.328	0.396	CLONAL	1	TRUE	0	0.3541954594446	4		702	693	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389149	31389149	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	172	623	0	ENST00000328111.2:c.2062G>A	p.Asp688Asn	p.D688N	ENST00000328111	NM_006892.3	688	Gat/Aat	19/23	0.292698475647713	4	FACETS	0.933	0.861	1	0.466	0.43	0.504	CLONAL	2	TRUE	0	0.3541954594446	4		623	705	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091777	29091777	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	36	374	0	ENST00000328354.6:c.1180G>C	p.Glu394Gln	p.E394Q	ENST00000328354	NM_007194.3	394	Gaa/Caa	11/15	0.316833432243831	3	FACETS	0.764	0.63	0.914	0.382	0.315	0.457	CLONAL	1	TRUE	1	0.3541954594446	3		374	313	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437304	52437304	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1438648758	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	143	709	0	ENST00000460680.1:c.1740G>C	p.Lys580Asn	p.K580N	ENST00000460680	NM_004656.3	580	aaG/aaC	14/17	0.25286610611056	2	FACETS	0.839	0.771	0.91	0.839	0.771	0.91	CLONAL	2	TRUE	0	0.3541954594446	2		709	481	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437465	52437465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	137	737	0	ENST00000460680.1:c.1696G>A	p.Glu566Lys	p.E566K	ENST00000460680	NM_004656.3	566	Gag/Aag	13/17	0.25286610611056	2	FACETS	0.791	0.724	0.86	0.791	0.724	0.86	SUBCLONAL	2	TRUE	0	0.3541954594446	2		737	489	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437690	52437690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	139	729	0	ENST00000460680.1:c.1471G>A	p.Glu491Lys	p.E491K	ENST00000460680	NM_004656.3	491	Gag/Aag	13/17	0.25286610611056	2	FACETS	0.779	0.713	0.846	0.779	0.713	0.846	SUBCLONAL	2	TRUE	0	0.3541954594446	2		729	504	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437811	52437811	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	100	648	0	ENST00000460680.1:c.1350G>C	p.Glu450Asp	p.E450D	ENST00000460680	NM_004656.3	450	gaG/gaC	13/17	0.25286610611056	2	FACETS	1	0.979	1	0.684	0.615	0.756	CLONAL	1	TRUE	0	0.3541954594446	2		648	413	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35857089	35857089	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	83	491	0	ENST00000303115.3:c.10C>G	p.Leu4Val	p.L4V	ENST00000303115	NM_002185.3	4	Cta/Gta	1/8	0.222538369672189	3	FACETS	1	0.973	1	0.668	0.592	0.748	CLONAL	1	TRUE	1	0.3541954594446	3		491	413	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753972	57753972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	64	413	0	ENST00000274289.3:c.652G>A	p.Glu218Lys	p.E218K	ENST00000274289	NM_006622.3	218	Gaa/Aaa	5/14	0.222538369672189	3	FACETS	0.923	0.801	1	0.461	0.4	0.527	CLONAL	1	TRUE	1	0.3541954594446	3		413	461	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754253	57754253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	71	554	0	ENST00000274289.3:c.598G>A	p.Glu200Lys	p.E200K	ENST00000274289	NM_006622.3	200	Gaa/Aaa	4/14	0.222538369672189	3	FACETS	0.95	0.831	1	0.475	0.415	0.539	CLONAL	1	TRUE	1	0.3541954594446	3		554	497	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755669	57755669	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	73	722	1	ENST00000274289.3:c.118G>T	p.Glu40Ter	p.E40*	ENST00000274289	NM_006622.3	40	Gag/Tag	1/14	0.222538369672189	3	FACETS	0.957	0.839	1	0.479	0.419	0.542	CLONAL	1	TRUE	1	0.3541954594446	3		723	507	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80024721	80024721	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	46	328	0	ENST00000265081.6:c.1505C>G	p.Ser502Cys	p.S502C	ENST00000265081	NM_002439.4	502	tCt/tGt	10/24	1	2	FACETS	0.835	0.707	0.975	0.835	0.707	0.975	CLONAL	1	TRUE	1	0.3541954594446	2		328	311	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80063812	80063812	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	37	435	0	ENST00000265081.6:c.1957C>G	p.Gln653Glu	p.Q653E	ENST00000265081	NM_002439.4	653	Caa/Gaa	14/24	1	2	FACETS	0.661	0.547	0.788	0.661	0.547	0.788	SUBCLONAL	1	TRUE	1	0.3541954594446	2		435	316	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681485	30681485	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	239	603	0	ENST00000376406.3:c.527C>G	p.Ser176Cys	p.S176C	ENST00000376406	NM_014641.2	176	tCt/tGt	4/15	0.3541954594446	3	FACETS	0.869	0.818	0.922	0.869	0.818	0.922	CLONAL	3	TRUE	0	0.3541954594446	3		603	609	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080563	5080563	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	85	442	0	ENST00000381652.3:c.2314C>T	p.Leu772Phe	p.L772F	ENST00000381652	NM_004972.3	772	Ctt/Ttt	18/25	0.265167295001415	2	FACETS	0.795	0.71	0.883	0.795	0.71	0.883	SUBCLONAL	2	TRUE	0	0.3541954594446	2		442	302	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787831	135787831	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1554817691	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	105	376	0	ENST00000298552.3:c.751G>T	p.Glu251Ter	p.E251*	ENST00000298552	NM_001162426.1	251	Gaa/Taa	9/23	0.239890597877529	3	FACETS	1	0.95	1	0.716	0.649	0.785	CLONAL	2	TRUE	0	0.3541954594446	3		376	325	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922978	39922978	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	106	323	0	ENST00000378444.4:c.3730G>C	p.Glu1244Gln	p.E1244Q	ENST00000378444	NM_001123385.1	1244	Gag/Cag	8/15	0.14587465808119	2	FACETS	0.998	0.907	1			1	INDETERMINATE	2	TRUE	NA	0.3541954594446	2		323	300	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344017	70344017	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059131-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	46	260	0	ENST00000374080.3:c.1753C>T	p.Arg585Ter	p.R585*	ENST00000374080		585	Cga/Tga	13/45	0.14587465808119	2	FACETS	1	0.927	1			1	INDETERMINATE	1	TRUE	NA	0.3541954594446	2		260	225	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578522	7578522	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059140-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	237	678	0	ENST00000269305.4:c.408del	p.Gln136HisfsTer34	p.Q136Hfs*34	ENST00000269305	NM_001126112.2	136	caA/ca	5/11	0.376406673001905	3	FACETS	0.868	0.821	0.915	0.868	0.821	0.915	CLONAL	3	TRUE	0	0.495903634160754	3		678	458	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867354	45867354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755174338	NA	P-0059140-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	122	615	0	ENST00000391945.4:c.839G>A	p.Arg280His	p.R280H	ENST00000391945	NM_000400.3	280	cGc/cAc	10/23	0.500585844577443	2	FACETS	1	0.985	1	0.709	0.648	0.771	CLONAL	1	TRUE	0	0.495903634160754	2		615	347	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976157	18976157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358324082	NA	P-0059140-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	88	755	0	ENST00000262803.5:c.2917C>T	p.Pro973Ser	p.P973S	ENST00000262803	NM_002911.3	973	Cct/Tct	21/24	0.46284103024305	3	FACETS	1	0.946	1	0.366	0.326	0.409	CLONAL	1	TRUE	0	0.495903634160754	3		755	403	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755678	39755678	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059140-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	36	688	0	ENST00000288319.7:c.1087G>C	p.Asp363His	p.D363H	ENST00000288319	NM_182918.3	363	Gat/Cat	10/10	0.502696959794448	3	FACETS	0.322	0.264	0.387	0.161	0.132	0.194	SUBCLONAL	1	TRUE	1	0.495903634160754	3		688	563	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750558	41750558	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059140-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	22	572	0	ENST00000226382.2:c.70T>A	p.Ser24Thr	p.S24T	ENST00000226382	NM_003924.3	24	Tcg/Acg	1/3	0.385114855318397	1	FACETS	0.228	0.176	0.287	0.228	0.176	0.287	SUBCLONAL	1	TRUE	0	0.495903634160754	1		572	293	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185816	32185821	+	inframe_deletion	In_Frame_Del	DEL	TCCGCG	TCCGCG	-	novel	NA	P-0059140-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	37	486	0	ENST00000375023.3:c.1575_1580del	p.Ala526_Asp527del	p.A526_D527del	ENST00000375023	NM_004557.3	525	caCGCGGAt/cat	9/30	0.502696959794448	3	FACETS	0.436	0.359	0.522	0.218	0.179	0.261	SUBCLONAL	1	TRUE	1	0.495903634160754	3		486	427	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0059153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	68	329	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.952	0.831	1	0.952	0.831	1	CLONAL	1	TRUE	1	0.317371635306033	2		329	450	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453139	140453139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913375	NA	P-0059153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	94	342	0	ENST00000288602.6:c.1796C>T	p.Thr599Ile	p.T599I	ENST00000288602	NM_004333.4	599	aCa/aTa	15/18	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.317371635306033	2		342	568	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753170	42753170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753965187	NA	P-0059153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	111	763	0	ENST00000222329.4:c.1094C>T	p.Ser365Leu	p.S365L	ENST00000222329	NM_006494.2	365	tCg/tTg	4/4	1	2	FACETS	0.869	0.781	0.962	0.869	0.781	0.962	CLONAL	1	TRUE	1	0.317371635306033	2		763	805	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753155	42753155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	107	760	0	ENST00000222329.4:c.1109C>T	p.Ser370Phe	p.S370F	ENST00000222329	NM_006494.2	370	tCt/tTt	4/4	1	2	FACETS	0.852	0.764	0.946	0.852	0.764	0.946	CLONAL	1	TRUE	1	0.317371635306033	2		760	791	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881477	111881477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759304312	NA	P-0059153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	134	564	0	ENST00000393256.3:c.155G>A	p.Gly52Glu	p.G52E	ENST00000393256	NM_006538.4	52	gGg/gAg	2/4	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.317371635306033	2		564	684	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059145	47059146	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0059153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	127	450	1	ENST00000409792.3:c.7515dup	p.Lys2506Ter	p.K2506*	ENST00000409792	NM_014159.6	2505	-/T	20/21	0.317371635306033	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.317371635306033	1		451	531	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721504	49721504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1434724624	NA	P-0059153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	90	298	0	ENST00000449682.2:c.2135C>T	p.Ser712Phe	p.S712F	ENST00000449682	NM_020998.3	712	tCt/tTt	18/18	0.317371635306033	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.317371635306033	1		298	363	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040802	47040802	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0059153-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	133	304	0	ENST00000377604.3:c.1435+2T>G		p.X479_splice	ENST00000377604	NM_001204468.1	479			1	1	FACETS	0.833	0.764	0.905	1	0.989	1	CLONAL	2	TRUE	0	0.317371635306033	1		304	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579485	7579485	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs869312782	NA	P-0059154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	256	598	0	ENST00000269305.4:c.202G>T	p.Glu68Ter	p.E68*	ENST00000269305	NM_001126112.2	68	Gag/Tag	4/11	0.265566424221005	2	FACETS	0.9	0.844	0.957	0.9	0.844	0.957	CLONAL	2	TRUE	0	0.31	2		598	918	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115279379	115279379	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	56	233	0	ENST00000438362.2:c.638A>G	p.His213Arg	p.H213R	ENST00000438362	NM_001242891.1	213	cAt/cGt	6/20	0.302441725290961	1	FACETS	0.92	0.792	1	0.92	0.792	1	CLONAL	1	TRUE	0	0.31	1		233	332	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731065	162731065	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	170	479	0	ENST00000367921.3:c.920G>T	p.Arg307Leu	p.R307L	ENST00000367921	NM_006182.2	307	cGc/cTc	9/18	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.31	2		479	870	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919332	48919332	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	23	174	0	ENST00000267163.4:c.499del	p.Arg167GlyfsTer8	p.R167Gfs*8	ENST00000267163	NM_000321.2	166	gAa/ga	4/27	0.302441725290961	1	FACETS	0.552	0.432	0.69	0.552	0.432	0.69	SUBCLONAL	1	TRUE	0	0.31	1		174	227	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347933	89347933	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1482549571	NA	P-0059154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	131	547	0	ENST00000301030.4:c.5017G>C	p.Gly1673Arg	p.G1673R	ENST00000301030	NM_001256183.1	1673	Ggt/Cgt	9/13	0.2828631526466	2	FACETS	1	0.917	1	0.505	0.458	0.555	CLONAL	1	TRUE	0	0.31	2		547	836	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998937	11998937	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	66	304	0	ENST00000353533.5:c.439A>G	p.Met147Val	p.M147V	ENST00000353533	NM_003010.3	147	Atg/Gtg	4/11	0.206185168689918	3	FACETS	0.795	0.69	0.908	0.397	0.345	0.454	CLONAL	1	TRUE	1	0.31	3		304	619	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220475	1220475	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	139	651	0	ENST00000326873.7:c.568C>G	p.Leu190Val	p.L190V	ENST00000326873	NM_000455.4	190	Ctc/Gtc	4/10	0.302441725290961	1	FACETS	0.933	0.85	1	0.933	0.85	1	CLONAL	1	TRUE	0	0.31	1		651	812	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220485	1220485	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	135	657	0	ENST00000326873.7:c.578C>A	p.Ser193Tyr	p.S193Y	ENST00000326873	NM_000455.4	193	tCc/tAc	4/10	0.302441725290961	1	FACETS	0.911	0.828	0.998	0.911	0.828	0.998	CLONAL	1	TRUE	0	0.31	1		657	808	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141511	11141511	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	129	486	0	ENST00000358026.2:c.3488T>G	p.Leu1163Arg	p.L1163R	ENST00000358026	NM_001128849.1	1163	cTg/cGg	25/36	0.302441725290961	1	FACETS	0.95	0.863	1	0.95	0.863	1	CLONAL	1	TRUE	0	0.31	1		486	740	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6438327	6438327	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	73	283	0	ENST00000356142.4:c.260G>T	p.Arg87Leu	p.R87L	ENST00000356142	NM_018890.3	87	cGg/cTg	4/7	1	2	FACETS	0.871	0.763	0.987	0.871	0.763	0.987	CLONAL	1	TRUE	1	0.31	2		283	541	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511172	148511172	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	112	421	0	ENST00000320356.2:c.1730C>G	p.Pro577Arg	p.P577R	ENST00000320356	NM_004456.4	577	cCg/cGg	15/20	1	2	FACETS	0.857	0.77	0.949	0.857	0.77	0.949	CLONAL	1	TRUE	1	0.31	2		421	843	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345232	70345232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761529397	NA	P-0059154-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	113	471	0	ENST00000374080.3:c.2258G>A	p.Arg753Gln	p.R753Q	ENST00000374080		753	cGg/cAg	16/45	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.31	2		471	716	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	26	477	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.132	0.104	0.164	0.132	0.104	0.164	SUBCLONAL	1	TRUE	1	0.886292950634527	2		477	446	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31239830	31239830	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs878995294	NA	P-0059155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	62	774	0	ENST00000376228.5:c.19C>G	p.Arg7Gly	p.R7G	ENST00000376228	NM_002117.5	7	Cga/Gga	1/8	1	2	FACETS	0.188	0.162	0.216	0.188	0.162	0.216	SUBCLONAL	1	TRUE	1	0.886292950634527	2		774	745	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245876	46245886	+	frameshift_variant	Frame_Shift_Del	DEL	AATGGGCCATC	AATGGGCCATC	-	novel	NA	P-0059155-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	38	494	0	ENST00000334344.6:c.3971_3981del	p.Asn1324IlefsTer5	p.N1324Ifs*5	ENST00000334344	NM_152641.2	1324	AATGGGCCATCa/a	15/21	0.129618839611255	3	FACETS	0.208	0.171	0.249	0.104	0.085	0.125	INDETERMINATE	1	TRUE	1	0.886292950634527	3		494	595	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106547	27106547	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0059156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	173	828	0	ENST00000324856.7:c.6158T>A	p.Leu2053Ter	p.L2053*	ENST00000324856	NM_006015.4	2053	tTg/tAg	20/20	0.440255758103848	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	0	0.443575475420473	1		828	603	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163310114	163310248	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTTTTGAATCATTATAAAACGTGTTTGCTTTTTCCCTTAGATAGTGCTGCAAGAGGGAAATTCCCAAAAGAAGTCAAATATTTCAGAGAAAACCAAGCGTTTGGTAAACATCTTTTCTTTTCACTAGCATTTAAA	GTTTTGAATCATTATAAAACGTGTTTGCTTTTTCCCTTAGATAGTGCTGCAAGAGGGAAATTCCCAAAAGAAGTCAAATATTTCAGAGAAAACCAAGCGTTTGGTAAACATCTTTTCTTTTCACTAGCATTTAAA	-	novel	NA	P-0059156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	28	264	0	ENST00000271452.3:c.607-36_669+36del		p.X203_splice	ENST00000271452	NM_145697.2	203		9/14	1	2	FACETS	0.537	0.431	0.657	0.537	0.431	0.657	SUBCLONAL	1	FALSE	1	0.443575475420473	2		264	235	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983035	201983035	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	125	780	0	ENST00000359651.3:c.884G>T	p.Trp295Leu	p.W295L	ENST00000359651		295	tGg/tTg	7/8	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	1	0.443575475420473	2		780	525	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149334	119149334	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	121	624	0	ENST00000264033.4:c.1342G>T	p.Glu448Ter	p.E448*	ENST00000264033	NM_005188.3	448	Gag/Tag	9/16	1	2	FACETS	0.983	0.892	1	0.983	0.892	1	CLONAL	1	FALSE	1	0.443575475420473	2		624	555	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2089718	2090184	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,3_prime_UTR_variant,intron_variant	Splice_Site	DEL	GCCCTGCTCCAGACACGCGAGCACGGGTGTGTACGAACACATCCTTGTATGCGATTCCCAGGCTCTCTGCCCCCTCAGGGACAGACATCAGCCAGATCCCATCTGCAAACACACCAAAGCTTTATTCAACAGGCGTGGCTTCCTGAAGCGTAAAGCCACTTCACAGACGGTGGCCACAGCGGCACCTCGGCCAGAGCCATGCGGCCATCAGAGACCCTGGGCGGCCGGGCAGAGGGCTTGGTTGAGGCAGGCGTGGCAGCGAGGGTGCACAGGCAGACAGGTCTGCTGGCCGAAGCCCACCAAGAGTCCATTGATCTCGTGCCACAGCTCCCTGTGGGGGTGGGGGCTGGGTCAGTGCTGACAGAGGGCGGGCGGGGTGAGCTCTTCTCCCTAGGAAGCCCCCCACATACTCATACCTAGGCAGCCACTCCTCCAGGGCGGCGCGGGTCTCCTCTGGGGACTTGGTT	GCCCTGCTCCAGACACGCGAGCACGGGTGTGTACGAACACATCCTTGTATGCGATTCCCAGGCTCTCTGCCCCCTCAGGGACAGACATCAGCCAGATCCCATCTGCAAACACACCAAAGCTTTATTCAACAGGCGTGGCTTCCTGAAGCGTAAAGCCACTTCACAGACGGTGGCCACAGCGGCACCTCGGCCAGAGCCATGCGGCCATCAGAGACCCTGGGCGGCCGGGCAGAGGGCTTGGTTGAGGCAGGCGTGGCAGCGAGGGTGCACAGGCAGACAGGTCTGCTGGCCGAAGCCCACCAAGAGTCCATTGATCTCGTGCCACAGCTCCCTGTGGGGGTGGGGGCTGGGTCAGTGCTGACAGAGGGCGGGCGGGGTGAGCTCTTCTCCCTAGGAAGCCCCCCACATACTCATACCTAGGCAGCCACTCCTCCAGGGCGGCGCGGGTCTCCTCTGGGGACTTGGTT	-	novel	NA	P-0059156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	68	76	0				ENST00000219066	NM_002528.5	255		5-6/6	1	2	FACETS	0.964	0.88	1	1	0.987	1	CLONAL	3	FALSE	1	0.443575475420473	2		76	106	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891353	101891353	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059156-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	88	430	0	ENST00000374994.4:c.314A>C	p.His105Pro	p.H105P	ENST00000374994	NM_004612.2	105	cAt/cCt	2/9	0.443575475420473	1	FACETS	0.863	0.77	0.959	0.863	0.77	0.959	CLONAL	1	FALSE	0	0.443575475420473	1		430	358	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0059157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	15	185	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.181133729301717	3	FACETS	1	0.882	1	0.469	0.348	0.611	CLONAL	1	TRUE	0	0.241311410631244	3		185	99	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0059157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	148	929	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.241311410631244	2		929	899	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665213	138665213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	45	701	0	ENST00000330315.3:c.352G>A	p.Glu118Lys	p.E118K	ENST00000330315	NM_023067.3	118	Gag/Aag	1/1	0.213732329665572	4	FACETS	0.566	0.474	0.668			1	SUBCLONAL	1	TRUE	NA	0.241311410631244	4		701	818	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793881	NA	P-0059157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	74	697	1	ENST00000269305.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGg/gAg	8/11	1	2	FACETS	0.802	0.701	0.911	0.802	0.701	0.911	CLONAL	1	TRUE	1	0.241311410631244	2		698	765	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155681	56155681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	49	582	0	ENST00000399503.3:c.773C>T	p.Ser258Leu	p.S258L	ENST00000399503	NM_005921.1	258	tCa/tTa	3/20	1	2	FACETS	0.714	0.604	0.835	0.714	0.604	0.835	SUBCLONAL	1	TRUE	1	0.241311410631244	2		582	569	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931321	131931321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773761143	NA	P-0059157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	44	446	0	ENST00000265335.6:c.2026G>A	p.Glu676Lys	p.E676K	ENST00000265335		676	Gaa/Aaa	13/25	1	2	FACETS	0.833	0.699	0.98	0.833	0.699	0.98	CLONAL	1	TRUE	1	0.241311410631244	2		446	438	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023667	27023667	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	73	795	0	ENST00000324856.7:c.773C>G	p.Ser258Cys	p.S258C	ENST00000324856	NM_006015.4	258	tCc/tGc	1/20	1	2	FACETS	0.621	0.542	0.707	0.621	0.542	0.707	SUBCLONAL	1	TRUE	1	0.241311410631244	2		795	974	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940780	71940780	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1415696831	NA	P-0059157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	97	826	0	ENST00000298229.2:c.827C>G	p.Ser276Ter	p.S276*	ENST00000298229	NM_001567.3	276	tCa/tGa	7/28	0.241311410631244	1	FACETS	0.964	0.86	1	0.964	0.86	1	CLONAL	1	TRUE	0	0.241311410631244	1		826	733	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610620	81610620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	51	590	0	ENST00000298171.2:c.2218G>A	p.Glu740Lys	p.E740K	ENST00000298171	NM_000369.2	740	Gaa/Aaa	10/10	0.173281863237468	2	FACETS	0.695	0.59	0.811	0.348	0.295	0.406	SUBCLONAL	1	TRUE	0	0.241311410631244	2		590	608	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761057	59761057	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0059157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	30	469	0	ENST00000259008.2:c.3350C>G	p.Ser1117Ter	p.S1117*	ENST00000259008	NM_032043.2	1117	tCa/tGa	20/20	1	2	FACETS	0.775	0.625	0.943	0.775	0.625	0.943	CLONAL	1	TRUE	1	0.241311410631244	2		469	321	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561514	9561514	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059157-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	60	657	0	ENST00000353224.5:c.268G>C	p.Asp90His	p.D90H	ENST00000353224	NM_177990.2	90	Gac/Cac	4/10	1	2	FACETS	0.787	0.677	0.906	0.787	0.677	0.906	CLONAL	1	TRUE	1	0.241311410631244	2		657	632	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0059159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	300	306	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.634236164691931	2	FACETS	0.898	0.861	0.935	0.898	0.861	0.935	CLONAL	2	TRUE	0	0.721169516044972	2		307	463	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0059159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	196	148	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.63567021744059	4	FACETS	1	0.987	1	0.794	0.746	0.841	CLONAL	2	TRUE	1	0.721169516044972	4		148	393	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009359	69009359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755479314	NA	P-0059159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	62	382	0	ENST00000288368.4:c.2476G>A	p.Asp826Asn	p.D826N	ENST00000288368	NM_024870.2	826	Gac/Aac	22/40	0.192641879448284	3	FACETS	0.67	0.582	0.765	0.223	0.194	0.255	INDETERMINATE	1	TRUE	0	0.721169516044972	3		382	349	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222888	5222888	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	20	625	0	ENST00000357368.4:c.2915C>A	p.Ala972Asp	p.A972D	ENST00000357368	NM_002850.3	972	gCc/gAc	18/38	1	2	FACETS	0.149	0.113	0.191	0.149	0.113	0.191	SUBCLONAL	1	TRUE	1	0.721169516044972	2		625	372	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591175	67591610	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TATACATGAATAATTGGTGATTGCTACAATTCAGGATGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAAAAGGTGTTCGGCAAAAGAAGTTGAACGAGTGGTTGGGCAATGAAAACACTGAAGAGTAAGTAGTTACTAAAGATGGTGATAGCAGAAGATTTTTCTCATTTTAGGAAAATGCATGACTTGCTTTGTTTTTAGAACAAGTGAGGAATTTTACTGAGTTTGGAACATCTTGTAGGAGAAAATGTATAAACTCAGTGCCATTATCCAGAATTTTAAAAAAAGAAAGCTTAGCTAAGGAGGACTAGGATTTATTTTTACTCATAATGCTGTGAAACAACTCTCTGTGTCCATAATGATGTCCCTGAACATCTGAAAAATCCCAAAATATTTTTGGAACAGTCAGAGAAAAAAT	TATACATGAATAATTGGTGATTGCTACAATTCAGGATGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAAAAGGTGTTCGGCAAAAGAAGTTGAACGAGTGGTTGGGCAATGAAAACACTGAAGAGTAAGTAGTTACTAAAGATGGTGATAGCAGAAGATTTTTCTCATTTTAGGAAAATGCATGACTTGCTTTGTTTTTAGAACAAGTGAGGAATTTTACTGAGTTTGGAACATCTTGTAGGAGAAAATGTATAAACTCAGTGCCATTATCCAGAATTTTAAAAAAAGAAAGCTTAGCTAAGGAGGACTAGGATTTATTTTTACTCATAATGCTGTGAAACAACTCTCTGTGTCCATAATGATGTCCCTGAACATCTGAAAAATCCCAAAATATTTTTGGAACAGTCAGAGAAAAAAT	-	novel	NA	P-0059159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	52	344	0	ENST00000274335.5:c.1745+23_1814+294del		p.X582_splice	ENST00000274335		582		13/15	0.721169516044972	3	FACETS	0.525	0.448	0.608	0.262	0.224	0.304	SUBCLONAL	1	TRUE	1	0.721169516044972	3		344	374	SUCCESS
APC	324	MSKCC	GRCh37	5	112175237	112175237	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059159-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	317	435	0	ENST00000257430.4:c.3946del	p.Ala1316LeufsTer5	p.A1316Lfs*5	ENST00000257430	NM_000038.5	1316	Gct/ct	16/16	0.636874114109733	3	FACETS	0.852	0.819	0.884	0.852	0.819	0.884	CLONAL	3	TRUE	0	0.721169516044972	3		435	468	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0059161-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	95	91	0	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	0.492709618634481	3	FACETS	1	0.969	1	0.765	0.697	0.833	CLONAL	2	TRUE	0	0.512636902636568	3		91	203	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781354	3781354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059161-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	25	477	0	ENST00000262367.5:c.5011G>A	p.Ala1671Thr	p.A1671T	ENST00000262367	NM_004380.2	1671	Gcc/Acc	30/31	0.301452969551844	5	FACETS	0.369	0.29	0.46			1	INDETERMINATE	1	TRUE	NA	0.512636902636568	5		477	468	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170774	11170774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568565786	NA	P-0059161-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	31	497	0	ENST00000358026.2:c.4918C>T	p.Arg1640Trp	p.R1640W	ENST00000358026	NM_001128849.1	1640	Cgg/Tgg	35/36	0.4117830201375	4	FACETS	0.42	0.339	0.511	0.21	0.169	0.256	SUBCLONAL	1	TRUE	2	0.512636902636568	4		497	436	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410238	63410238	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059161-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	140	442	0	ENST00000330258.3:c.2929C>A	p.Pro977Thr	p.P977T	ENST00000330258	NM_152424.3	977	Ccc/Acc	2/2	0.229699959158775	5	FACETS	1	0.964	1	0.725	0.666	0.786	INDETERMINATE	2	TRUE	2	0.512636902636568	5		442	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578195	7578197	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0059163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	452	560	0	ENST00000269305.4:c.652_654del	p.Val218del	p.V218del	ENST00000269305	NM_001126112.2	218	GTG/-	6/11	0.837308577229284	2	FACETS	0.995	0.971	1	0.995	0.971	1	CLONAL	2	TRUE	0	0.833354926234871	2		560	545	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604181	189604181	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0059163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	357	411	0	ENST00000264731.3:c.1350-2A>T		p.X450_splice	ENST00000264731	NM_003722.4	450			0.837308577229284	3	FACETS	1	0.993	1	0.413	0.392	0.434	CLONAL	1	TRUE	0	0.833354926234871	3		411	980	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	42	483	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.19	2		483	402	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	29	582	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.617	0.494	0.757	0.617	0.494	0.757	SUBCLONAL	1	TRUE	1	0.19	2		582	495	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	38	545	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.19	2		545	386	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153609	55153609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501520	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	33	543	0	ENST00000257290.5:c.2575G>A	p.Val859Met	p.V859M	ENST00000257290	NM_006206.4	859	Gtg/Atg	19/23	1	2	FACETS	0.827	0.674	1	0.827	0.674	1	CLONAL	1	TRUE	1	0.19	2		543	420	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950099	38950099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757900166	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	41	689	0	ENST00000357387.3:c.3851C>T	p.Ser1284Leu	p.S1284L	ENST00000357387	NM_152756.3	1284	tCg/tTg	31/38	1	2	FACETS	0.841	0.7	0.998	0.841	0.7	0.998	CLONAL	1	TRUE	1	0.19	2		689	513	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	43	684	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.922	0.771	1	0.922	0.771	1	CLONAL	1	TRUE	1	0.19	2		684	491	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95592924	95592924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755944755	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	14	289	0	ENST00000393063.1:c.896C>T	p.Ser299Leu	p.S299L	ENST00000393063	NM_030621.3	299	tCg/tTg	8/28	1	2	FACETS	1	0.748	1	1	0.748	1	CLONAL	1	TRUE	1	0.19	2		289	143	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273266	198273266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	38	575	0	ENST00000335508.6:c.944G>A	p.Arg315Gln	p.R315Q	ENST00000335508	NM_012433.2	315	cGa/cAa	8/25	1	2	FACETS	0.781	0.645	0.933	0.781	0.645	0.933	CLONAL	1	TRUE	1	0.19	2		575	512	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2086832	2086832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	29	596	0	ENST00000349721.2:c.2530C>T	p.Arg844Trp	p.R844W	ENST00000349721	NM_003070.3	844	Cgg/Tgg	18/34	1	2	FACETS	0.781	0.627	0.956	0.781	0.627	0.956	CLONAL	1	TRUE	1	0.19	2		596	391	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16174607	16174607	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	30	501	0	ENST00000375759.3:c.45G>T	p.Glu15Asp	p.E15D	ENST00000375759	NM_015001.2	15	gaG/gaT	1/15	1	2	FACETS	0.951	0.768	1	0.951	0.768	1	CLONAL	1	TRUE	1	0.19	2		501	332	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202891	16202891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910179277	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	34	723	0	ENST00000375759.3:c.599G>A	p.Arg200Gln	p.R200Q	ENST00000375759	NM_015001.2	200	cGa/cAa	3/15	1	2	FACETS	0.655	0.535	0.792	0.655	0.535	0.792	SUBCLONAL	1	TRUE	1	0.19	2		723	546	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105551	27105551	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	30	589	0	ENST00000324856.7:c.5162G>A	p.Arg1721Gln	p.R1721Q	ENST00000324856	NM_006015.4	1721	cGa/cAa	20/20	1	2	FACETS	0.686	0.552	0.839	0.686	0.552	0.839	SUBCLONAL	1	TRUE	1	0.19	2		589	460	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506287	120506287	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	45	717	0	ENST00000256646.2:c.1825G>T	p.Asp609Tyr	p.D609Y	ENST00000256646	NM_024408.3	609	Gat/Tat	11/34	1	2	FACETS	0.89	0.748	1	0.89	0.748	1	CLONAL	1	TRUE	1	0.19	2		717	532	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163298676	163298676	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	26	453	0	ENST00000271452.3:c.316A>C	p.Thr106Pro	p.T106P	ENST00000271452	NM_145697.2	106	Act/Cct	5/14	1	2	FACETS	0.918	0.729	1	0.918	0.729	1	CLONAL	1	TRUE	1	0.19	2		453	298	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243708871	243708871	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	16	359	0	ENST00000263826.5:c.1192G>T	p.Glu398Ter	p.E398*	ENST00000263826	NM_005465.4	398	Gaa/Taa	11/13	1	2	FACETS	0.542	0.4	0.711	0.542	0.4	0.711	SUBCLONAL	1	TRUE	1	0.19	2		359	311	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615045	43615045	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	33	845	2	ENST00000355710.3:c.2459G>A	p.Arg820His	p.R820H	ENST00000355710	NM_020975.4	820	cGc/cAc	14/20	1	2	FACETS	0.744	0.605	0.9	0.744	0.605	0.9	SUBCLONAL	1	TRUE	1	0.19	2		847	467	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850642	63850642	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	23	556	0	ENST00000279873.7:c.1420G>T	p.Glu474Ter	p.E474*	ENST00000279873	NM_032199.2	474	Gaa/Taa	10/10	1	2	FACETS	0.567	0.441	0.713	0.567	0.441	0.713	SUBCLONAL	1	TRUE	1	0.19	2		556	427	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406125	70406125	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	31	586	0	ENST00000373644.4:c.3639T>G	p.Ile1213Met	p.I1213M	ENST00000373644	NM_030625.2	1213	atT/atG	4/12	1	2	FACETS	0.884	0.716	1	0.884	0.716	1	CLONAL	1	TRUE	1	0.19	2		586	369	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653793	89653793	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	15	304	0	ENST00000371953.3:c.91A>C	p.Asn31His	p.N31H	ENST00000371953	NM_000314.4	31	Aac/Cac	2/9	1	2	FACETS	0.708	0.518	0.935	0.708	0.518	0.935	CLONAL	1	TRUE	1	0.19	2		304	223	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	36	438	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.19	2		438	288	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279605	123279605	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	39	744	0	ENST00000358487.5:c.827T>G	p.Phe276Cys	p.F276C	ENST00000358487	NM_000141.4	276	tTt/tGt	7/18	1	2	FACETS	0.782	0.647	0.932	0.782	0.647	0.932	CLONAL	1	TRUE	1	0.19	2		744	525	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77936222	77936222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	32	514	0	ENST00000361507.4:c.1234C>T	p.Pro412Ser	p.P412S	ENST00000361507	NM_080491.2	412	Cca/Tca	5/10	1	2	FACETS	0.715	0.58	0.868	0.715	0.58	0.868	SUBCLONAL	1	TRUE	1	0.19	2		514	471	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94910992	94910992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	18	422	0	ENST00000536441.1:c.1138C>T	p.Arg380Trp	p.R380W	ENST00000536441	NM_144665.3	380	Cgg/Tgg	8/10	1	2	FACETS	0.619	0.466	0.801	0.619	0.466	0.801	SUBCLONAL	1	TRUE	1	0.19	2		422	306	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912674	100912674	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	24	357	0	ENST00000325455.5:c.2646+2T>C		p.X882_splice	ENST00000325455	NM_001202474.3	882			1	2	FACETS	0.856	0.672	1	0.856	0.672	1	CLONAL	1	TRUE	1	0.19	2		357	295	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115595	108115595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769166447	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	36	505	0	ENST00000278616.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000278616	NM_000051.3	248	cGa/cAa	7/63	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.19	2		505	339	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158403	108158403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730881390	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	32	450	0	ENST00000278616.4:c.4070C>A	p.Ser1357Tyr	p.S1357Y	ENST00000278616	NM_000051.3	1357	tCt/tAt	27/63	1	2	FACETS	1	0.834	1	1	0.834	1	CLONAL	1	TRUE	1	0.19	2		450	328	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173681	108173681	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	25	475	0	ENST00000278616.4:c.5421G>T	p.Lys1807Asn	p.K1807N	ENST00000278616	NM_000051.3	1807	aaG/aaT	36/63	1	2	FACETS	0.822	0.649	1	0.822	0.649	1	CLONAL	1	TRUE	1	0.19	2		475	320	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169179	119169179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150811339	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	30	721	0	ENST00000264033.4:c.2363G>A	p.Arg788Gln	p.R788Q	ENST00000264033	NM_005188.3	788	cGa/cAa	15/16	1	2	FACETS	0.635	0.511	0.777	0.635	0.511	0.777	SUBCLONAL	1	TRUE	1	0.19	2		721	497	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170436	119170436	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	41	613	0	ENST00000264033.4:c.2666A>C	p.Lys889Thr	p.K889T	ENST00000264033	NM_005188.3	889	aAa/aCa	16/16	1	2	FACETS	0.865	0.72	1	0.865	0.72	1	CLONAL	1	TRUE	1	0.19	2		613	499	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402122	402122	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	34	742	0	ENST00000399788.2:c.4669A>C	p.Lys1557Gln	p.K1557Q	ENST00000399788	NM_001042603.1	1557	Aaa/Caa	27/28	1	2	FACETS	0.726	0.592	0.876	0.726	0.592	0.876	SUBCLONAL	1	TRUE	1	0.19	2		742	493	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406212	406212	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	22	496	0	ENST00000399788.2:c.4229C>A	p.Ser1410Tyr	p.S1410Y	ENST00000399788	NM_001042603.1	1410	tCt/tAt	25/28	1	2	FACETS	0.638	0.494	0.806	0.638	0.494	0.806	SUBCLONAL	1	TRUE	1	0.19	2		496	363	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416137	416137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1449032009	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	39	613	0	ENST00000399788.2:c.4049G>A	p.Arg1350Gln	p.R1350Q	ENST00000399788	NM_001042603.1	1350	cGa/cAa	24/28	1	2	FACETS	0.873	0.724	1	0.873	0.724	1	CLONAL	1	TRUE	1	0.19	2		613	470	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11803069	11803069	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	24	389	0	ENST00000396373.4:c.8A>T	p.Glu3Val	p.E3V	ENST00000396373	NM_001987.4	3	gAg/gTg	1/8	1	2	FACETS	0.714	0.559	0.892	0.714	0.559	0.892	SUBCLONAL	1	TRUE	1	0.19	2		389	354	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534710	18534710	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764629808	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	27	553	0	ENST00000266497.5:c.1768C>A	p.Leu590Ile	p.L590I	ENST00000266497		590	Ctc/Atc	12/31	1	2	FACETS	0.685	0.544	0.846	0.685	0.544	0.846	SUBCLONAL	1	TRUE	1	0.19	2		553	415	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573894	18573894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759658584	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	19	331	0	ENST00000266497.5:c.2212C>T	p.Arg738Cys	p.R738C	ENST00000266497		738	Cgt/Tgt	15/31	1	2	FACETS	0.816	0.621	1	0.816	0.621	1	CLONAL	1	TRUE	1	0.19	2		331	245	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493449	56493449	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	23	602	0	ENST00000267101.3:c.2857A>C	p.Asn953His	p.N953H	ENST00000267101	NM_001982.3	953	Aac/Cac	24/28	1	2	FACETS	0.549	0.427	0.691	0.549	0.427	0.691	SUBCLONAL	1	TRUE	1	0.19	2		602	441	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212572	133212572	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	35	559	0	ENST00000320574.5:c.5717C>A	p.Ser1906Tyr	p.S1906Y	ENST00000320574	NM_006231.2	1906	tCt/tAt	42/49	1	2	FACETS	0.768	0.629	0.924	0.768	0.629	0.924	CLONAL	1	TRUE	1	0.19	2		559	480	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	30	309	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	0.684	0.55	0.835	0.684	0.55	0.835	SUBCLONAL	1	TRUE	1	0.19	2		309	462	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588594	28588594	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	33	499	0	ENST00000241453.7:c.2854G>T	p.Glu952Ter	p.E952*	ENST00000241453	NM_004119.2	952	Gaa/Taa	23/24	1	2	FACETS	0.871	0.709	1	0.871	0.709	1	CLONAL	1	TRUE	1	0.19	2		499	399	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601310	28601310	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	27	422	0	ENST00000241453.7:c.2122G>T	p.Glu708Ter	p.E708*	ENST00000241453	NM_004119.2	708	Gaa/Taa	17/24	1	2	FACETS	0.905	0.721	1	0.905	0.721	1	CLONAL	1	TRUE	1	0.19	2		422	314	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913424	32913424	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	28	509	0	ENST00000380152.3:c.4932A>C	p.Glu1644Asp	p.E1644D	ENST00000380152		1644	gaA/gaC	11/27	1	2	FACETS	0.833	0.666	1	0.833	0.666	1	CLONAL	1	TRUE	1	0.19	2		509	354	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918724	32918724	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	17	252	0	ENST00000380152.3:c.6871A>C	p.Asn2291His	p.N2291H	ENST00000380152		2291	Aat/Cat	12/27	1	2	FACETS	0.994	0.745	1	0.994	0.745	1	CLONAL	1	TRUE	1	0.19	2		252	180	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134274	41134274	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	50	722	0	ENST00000379561.5:c.1354A>G	p.Met452Val	p.M452V	ENST00000379561	NM_002015.3	452	Atg/Gtg	2/3	1	2	FACETS	0.937	0.794	1	0.937	0.794	1	CLONAL	1	TRUE	1	0.19	2		722	562	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49280999	49280999	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	40	579	0	ENST00000282018.3:c.46G>T	p.Glu16Ter	p.E16*	ENST00000282018	NM_020377.2	16	Gaa/Taa	1/1	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.19	2		579	386	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435798	110435798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1240854451	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	38	786	0	ENST00000375856.3:c.2603C>T	p.Ser868Leu	p.S868L	ENST00000375856	NM_003749.2	868	tCg/tTg	1/2	1	2	FACETS	0.866	0.716	1	0.866	0.716	1	CLONAL	1	TRUE	1	0.19	2		786	462	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436300	110436300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	50	947	1	ENST00000375856.3:c.2101G>A	p.Ala701Thr	p.A701T	ENST00000375856	NM_003749.2	701	Gcc/Acc	1/2	1	2	FACETS	0.841	0.712	0.982	0.841	0.712	0.982	CLONAL	1	TRUE	1	0.19	2		948	626	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557408	95557408	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	33	507	0	ENST00000393063.1:c.5566G>T	p.Glu1856Ter	p.E1856*	ENST00000393063	NM_030621.3	1856	Gaa/Taa	27/28	1	2	FACETS	0.931	0.759	1	0.931	0.759	1	CLONAL	1	TRUE	1	0.19	2		507	373	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40683726	40683726	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	25	505	0	ENST00000249776.8:c.718G>T	p.Glu240Ter	p.E240*	ENST00000249776	NM_033286.3	240	Gaa/Taa	7/9	1	2	FACETS	0.634	0.499	0.79	0.634	0.499	0.79	SUBCLONAL	1	TRUE	1	0.19	2		505	415	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762064	43762064	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	37	539	0	ENST00000382044.4:c.1381T>C	p.Phe461Leu	p.F461L	ENST00000382044	NM_001141980.1	461	Ttt/Ctt	11/28	1	2	FACETS	0.923	0.761	1	0.923	0.761	1	CLONAL	1	TRUE	1	0.19	2		539	422	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43766924	43766924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201580098	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	38	436	0	ENST00000382044.4:c.1127G>A	p.Arg376Gln	p.R376Q	ENST00000382044	NM_001141980.1	376	cGa/cAa	10/28	1	2	FACETS	0.978	0.809	1	0.978	0.809	1	CLONAL	1	TRUE	1	0.19	2		436	409	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50763871	50763871	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	28	477	0	ENST00000307179.4:c.728C>A	p.Ser243Tyr	p.S243Y	ENST00000307179		243	tCt/tAt	8/20	1	2	FACETS	0.735	0.587	0.904	0.735	0.587	0.904	CLONAL	1	TRUE	1	0.19	2		477	401	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3824598	3824598	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	51	606	0	ENST00000262367.5:c.2255A>G	p.Gln752Arg	p.Q752R	ENST00000262367	NM_004380.2	752	cAg/cGg	12/31	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.19	2		606	520	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50818241	50818241	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	21	363	0	ENST00000398568.2:c.1819T>G	p.Leu607Val	p.L607V	ENST00000398568	NM_001042412.1	607	Tta/Gta	11/18	1	2	FACETS	0.715	0.551	0.907	0.715	0.551	0.907	CLONAL	1	TRUE	1	0.19	2		363	309	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644754	67644754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779609208	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	49	680	0	ENST00000264010.4:c.19G>A	p.Glu7Lys	p.E7K	ENST00000264010	NM_006565.3	7	Gaa/Aaa	3/12	1	2	FACETS	0.891	0.754	1	0.891	0.754	1	CLONAL	1	TRUE	1	0.19	2		680	579	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350878	89350878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1336431815	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	45	510	0	ENST00000301030.4:c.2072G>A	p.Arg691His	p.R691H	ENST00000301030	NM_001256183.1	691	cGc/cAc	9/13	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.19	2		510	466	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89871793	89871793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779131886	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	37	478	0	ENST00000389301.3:c.604G>A	p.Asp202Asn	p.D202N	ENST00000389301	NM_000135.2	202	Gac/Aac	7/43	1	2	FACETS	0.966	0.798	1	0.966	0.798	1	CLONAL	1	TRUE	1	0.19	2		478	403	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979524	7979524	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	36	663	0	ENST00000319144.4:c.1501G>T	p.Asp501Tyr	p.D501Y	ENST00000319144	NM_001139.2	501	Gac/Tac	11/15	1	2	FACETS	0.777	0.638	0.932	0.777	0.638	0.932	CLONAL	1	TRUE	1	0.19	2		663	488	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553452	29553452	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1555613743	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	30	523	0	ENST00000356175.3:c.2002-1G>A		p.X668_splice	ENST00000356175	NM_000267.3	668			1	2	FACETS	0.761	0.613	0.929	0.761	0.613	0.929	CLONAL	1	TRUE	1	0.19	2		523	415	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657482	29657482	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	24	425	0	ENST00000356175.3:c.5715T>G	p.Phe1905Leu	p.F1905L	ENST00000356175	NM_000267.3	1905	ttT/ttG	38/57	1	2	FACETS	0.777	0.61	0.97	0.777	0.61	0.97	CLONAL	1	TRUE	1	0.19	2		425	325	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690438	33690438	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	29	708	0	ENST00000308377.4:c.389C>A	p.Ser130Tyr	p.S130Y	ENST00000308377	NM_152270.3	130	tCt/tAt	2/5	1	2	FACETS	0.587	0.47	0.721	0.587	0.47	0.721	SUBCLONAL	1	TRUE	1	0.19	2		708	520	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650879	37650879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs191899574	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	28	516	0	ENST00000447079.4:c.2351G>A	p.Arg784Gln	p.R784Q	ENST00000447079	NM_015083.1	784	cGa/cAa	5/14	1	2	FACETS	0.695	0.555	0.855	0.695	0.555	0.855	SUBCLONAL	1	TRUE	1	0.19	2		516	424	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883623	37883623	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1038581447	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	31	787	0	ENST00000269571.5:c.3235G>A	p.Glu1079Lys	p.E1079K	ENST00000269571		1079	Gaa/Aaa	26/27	1	2	FACETS	0.657	0.53	0.8	0.657	0.53	0.8	SUBCLONAL	1	TRUE	1	0.19	2		787	497	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47679279	47679279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1399168977	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	26	578	0	ENST00000347630.2:c.928G>A	p.Asp310Asn	p.D310N	ENST00000347630	NM_001007230.1	310	Gac/Aac	10/11	1	2	FACETS	0.611	0.483	0.758	0.611	0.483	0.758	SUBCLONAL	1	TRUE	1	0.19	2		578	448	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375016	45375016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226662382	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	37	564	0	ENST00000262160.6:c.827C>T	p.Ser276Leu	p.S276L	ENST00000262160	NM_005901.5	276	tCg/tTg	8/11	1	2	FACETS	1	0.829	1	1	0.829	1	CLONAL	1	TRUE	1	0.19	2		564	388	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395776	45395776	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	35	560	0	ENST00000262160.6:c.358C>T	p.Arg120Ter	p.R120*	ENST00000262160	NM_005901.5	120	Cga/Tga	4/11	1	2	FACETS	0.912	0.748	1	0.912	0.748	1	CLONAL	1	TRUE	1	0.19	2		560	404	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276647	15276647	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780169747	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	43	785	0	ENST00000263388.2:c.5618G>A	p.Arg1873His	p.R1873H	ENST00000263388	NM_000435.2	1873	cGc/cAc	30/33	1	2	FACETS	0.754	0.63	0.892	0.754	0.63	0.892	SUBCLONAL	1	TRUE	1	0.19	2		785	600	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289905	15289905	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	41	959	0	ENST00000263388.2:c.3649G>A	p.Ala1217Thr	p.A1217T	ENST00000263388	NM_000435.2	1217	Gca/Aca	22/33	1	2	FACETS	0.659	0.548	0.783	0.659	0.548	0.783	SUBCLONAL	1	TRUE	1	0.19	2		959	655	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210829	36210829	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	45	876	1	ENST00000222270.7:c.580A>G	p.Thr194Ala	p.T194A	ENST00000222270	NM_014727.1	194	Act/Gct	3/37	1	2	FACETS	0.83	0.696	0.977	0.83	0.696	0.977	CLONAL	1	TRUE	1	0.19	2		877	571	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220874	36220874	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568378349	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	32	634	0	ENST00000222270.7:c.4924G>A	p.Glu1642Lys	p.E1642K	ENST00000222270	NM_014727.1	1642	Gag/Aag	23/37	1	2	FACETS	0.689	0.558	0.837	0.689	0.558	0.837	SUBCLONAL	1	TRUE	1	0.19	2		634	489	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40771141	40771141	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	23	467	0	ENST00000392038.2:c.34C>T	p.Leu12Phe	p.L12F	ENST00000392038	NM_001626.4	12	Ctc/Ttc	2/14	1	2	FACETS	0.608	0.474	0.765	0.608	0.474	0.765	SUBCLONAL	1	TRUE	1	0.19	2		467	398	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383220	42383220	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs926961615	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	41	770	0	ENST00000221972.3:c.240C>A	p.Phe80Leu	p.F80L	ENST00000221972	NM_021601.3	80	ttC/ttA	2/5	1	2	FACETS	0.788	0.655	0.935	0.788	0.655	0.935	CLONAL	1	TRUE	1	0.19	2		770	548	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222489	39222489	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	25	609	0	ENST00000402219.2:c.3121C>T	p.Arg1041Cys	p.R1041C	ENST00000402219	NM_005633.3	1041	Cgt/Tgt	20/23	1	2	FACETS	0.612	0.482	0.762	0.612	0.482	0.762	SUBCLONAL	1	TRUE	1	0.19	2		609	430	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46587826	46587826	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	29	586	0	ENST00000263734.3:c.504C>A	p.Phe168Leu	p.F168L	ENST00000263734	NM_001430.4	168	ttC/ttA	5/16	1	2	FACETS	0.712	0.571	0.872	0.712	0.571	0.872	SUBCLONAL	1	TRUE	1	0.19	2		586	429	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690230	47690230	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63749947	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	36	441	0	ENST00000233146.2:c.1447G>T	p.Glu483Ter	p.E483*	ENST00000233146	NM_000251.2	483	Gaa/Taa	9/16	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.19	2		441	311	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630836	67630836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs547474628	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	27	612	0	ENST00000272342.5:c.1022G>A	p.Arg341Gln	p.R341Q	ENST00000272342	NM_019002.3	341	cGa/cAa	5/6	1	2	FACETS	0.746	0.593	0.92	0.746	0.593	0.92	CLONAL	1	TRUE	1	0.19	2		612	381	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631853	67631853	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	33	555	0	ENST00000272342.5:c.2039T>G	p.Phe680Cys	p.F680C	ENST00000272342	NM_019002.3	680	tTt/tGt	5/6	1	2	FACETS	1	0.826	1	1	0.826	1	CLONAL	1	TRUE	1	0.19	2		555	343	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131412	202131412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339962485	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	45	605	0	ENST00000358485.4:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000358485	NM_001080125.1	127	cGa/cAa	2/9	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.19	2		605	417	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37637655	37637655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1162764913	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	46	719	0	ENST00000249071.6:c.79G>A	p.Ala27Thr	p.A27T	ENST00000249071	NM_002872.4	27	Gcc/Acc	2/7	1	2	FACETS	0.972	0.819	1	0.972	0.819	1	CLONAL	1	TRUE	1	0.19	2		719	498	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042489	37042489	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	40	375	0	ENST00000231790.2:c.251A>C	p.Lys84Thr	p.K84T	ENST00000231790	NM_000249.3	84	aAa/aCa	3/19	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.19	2		375	292	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162695	47162695	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	30	517	0	ENST00000409792.3:c.3431C>A	p.Ser1144Tyr	p.S1144Y	ENST00000409792	NM_014159.6	1144	tCt/tAt	3/21	1	2	FACETS	0.797	0.643	0.973	0.797	0.643	0.973	CLONAL	1	TRUE	1	0.19	2		517	396	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390923	89390923	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1559654048	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	29	419	0	ENST00000336596.2:c.989G>T	p.Arg330Ile	p.R330I	ENST00000336596	NM_005233.5	330	aGa/aTa	5/17	1	2	FACETS	0.875	0.703	1	0.875	0.703	1	CLONAL	1	TRUE	1	0.19	2		419	349	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417933	138417933	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776210981	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	25	302	0	ENST00000289153.2:c.1586G>A	p.Arg529Gln	p.R529Q	ENST00000289153	NM_006219.2	529	cGa/cAa	11/22	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.19	2		302	234	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278103	142278103	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs756790263	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	27	388	0	ENST00000350721.4:c.1722T>G	p.Ile574Met	p.I574M	ENST00000350721	NM_001184.3	574	atT/atG	7/47	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.19	2		388	260	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981193	55981193	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	26	469	0	ENST00000263923.4:c.506G>T	p.Arg169Ile	p.R169I	ENST00000263923	NM_002253.2	169	aGa/aTa	5/30	1	2	FACETS	0.9	0.714	1	0.9	0.714	1	CLONAL	1	TRUE	1	0.19	2		469	304	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467635	66467635	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	40	585	0	ENST00000273854.3:c.634C>A	p.Leu212Ile	p.L212I	ENST00000273854	NM_004439.5	212	Ctt/Att	3/18	1	2	FACETS	0.961	0.799	1	0.961	0.799	1	CLONAL	1	TRUE	1	0.19	2		585	438	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467768	66467768	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	22	509	0	ENST00000273854.3:c.501G>T	p.Lys167Asn	p.K167N	ENST00000273854	NM_004439.5	167	aaG/aaT	3/18	1	2	FACETS	0.634	0.491	0.801	0.634	0.491	0.801	SUBCLONAL	1	TRUE	1	0.19	2		509	365	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467884	66467884	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	21	521	0	ENST00000273854.3:c.385G>T	p.Glu129Ter	p.E129*	ENST00000273854	NM_004439.5	129	Gaa/Taa	3/18	1	2	FACETS	0.571	0.439	0.726	0.571	0.439	0.726	SUBCLONAL	1	TRUE	1	0.19	2		521	387	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509140	66509140	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	16	343	0	ENST00000273854.3:c.187T>G	p.Leu63Val	p.L63V	ENST00000273854	NM_004439.5	63	Tta/Gta	2/18	1	2	FACETS	0.851	0.631	1	0.851	0.631	1	CLONAL	1	TRUE	1	0.19	2		343	198	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029259	143029259	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	12	263	0	ENST00000262992.4:c.2361G>T	p.Lys787Asn	p.K787N	ENST00000262992	NM_001101669.1	787	aaG/aaT	21/24	1	2	FACETS	0.596	0.419	0.814	0.596	0.419	0.814	SUBCLONAL	1	TRUE	1	0.19	2		263	212	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143226682	143226682	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	39	414	0	ENST00000262992.4:c.432C>A	p.Phe144Leu	p.F144L	ENST00000262992	NM_001101669.1	144	ttC/ttA	7/24	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.19	2		414	343	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540787	187540787	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	39	699	0	ENST00000441802.2:c.6953T>G	p.Ile2318Ser	p.I2318S	ENST00000441802	NM_005245.3	2318	aTc/aGc	10/27	1	2	FACETS	0.916	0.76	1	0.916	0.76	1	CLONAL	1	TRUE	1	0.19	2		699	448	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80021297	80021297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs963234468	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	24	414	0	ENST00000265081.6:c.1366G>A	p.Glu456Lys	p.E456K	ENST00000265081	NM_002439.4	456	Gaa/Aaa	9/24	1	2	FACETS	0.777	0.61	0.97	0.777	0.61	0.97	CLONAL	1	TRUE	1	0.19	2		414	325	SUCCESS
APC	324	MSKCC	GRCh37	5	112174328	112174328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	33	569	0	ENST00000257430.4:c.3037C>T	p.His1013Tyr	p.H1013Y	ENST00000257430	NM_000038.5	1013	Cat/Tat	16/16	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.19	2		569	301	SUCCESS
APC	324	MSKCC	GRCh37	5	112175799	112175799	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	38	566	0	ENST00000257430.4:c.4508C>A	p.Ser1503Ter	p.S1503*	ENST00000257430	NM_000038.5	1503	tCa/tAa	16/16	1	2	FACETS	0.932	0.771	1	0.932	0.771	1	CLONAL	1	TRUE	1	0.19	2		566	429	SUCCESS
APC	324	MSKCC	GRCh37	5	112177368	112177368	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	39	565	0	ENST00000257430.4:c.6077C>A	p.Ser2026Tyr	p.S2026Y	ENST00000257430	NM_000038.5	2026	tCt/tAt	16/16	1	2	FACETS	0.957	0.794	1	0.957	0.794	1	CLONAL	1	TRUE	1	0.19	2		565	429	SUCCESS
APC	324	MSKCC	GRCh37	5	112177901	112177901	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs752654519	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	32	523	0	ENST00000257430.4:c.6610C>T	p.Arg2204Ter	p.R2204*	ENST00000257430	NM_000038.5	2204	Cga/Tga	16/16	1	2	FACETS	0.877	0.712	1	0.877	0.712	1	CLONAL	1	TRUE	1	0.19	2		523	384	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793501	89793501	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	18	471	0	ENST00000336032.3:c.570G>T	p.Glu190Asp	p.E190D	ENST00000336032	NM_006813.2	190	gaG/gaT	2/2	1	2	FACETS	0.617	0.464	0.798	0.617	0.464	0.798	SUBCLONAL	1	TRUE	1	0.19	2		471	307	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322568	109322568	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	30	517	0	ENST00000436639.2:c.469T>G	p.Phe157Val	p.F157V	ENST00000436639	NM_014454.2	157	Ttc/Gtc	3/10	1	2	FACETS	0.897	0.724	1	0.897	0.724	1	CLONAL	1	TRUE	1	0.19	2		517	352	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622213	117622213	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	25	411	0	ENST00000368508.3:c.6657A>C	p.Arg2219Ser	p.R2219S	ENST00000368508	NM_002944.2	2219	agA/agC	42/43	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.19	2		411	251	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704548	117704548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	41	614	0	ENST00000368508.3:c.2428G>A	p.Glu810Lys	p.E810K	ENST00000368508	NM_002944.2	810	Gaa/Aaa	16/43	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.19	2		614	402	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026643	6026643	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs63750947	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	46	563	0	ENST00000265849.7:c.1753C>A	p.Leu585Ile	p.L585I	ENST00000265849	NM_000535.5	585	Ctt/Att	11/15	1	2	FACETS	0.982	0.827	1	0.982	0.827	1	CLONAL	1	TRUE	1	0.19	2		563	493	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381528	81381528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776090604	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	35	486	0	ENST00000222390.5:c.533G>A	p.Arg178Gln	p.R178Q	ENST00000222390	NM_000601.4	178	cGa/cAa	5/18	1	2	FACETS	0.899	0.737	1	0.899	0.737	1	CLONAL	1	TRUE	1	0.19	2		486	410	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381567	81381567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370760302	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	19	450	0	ENST00000222390.5:c.494C>T	p.Ser165Leu	p.S165L	ENST00000222390	NM_000601.4	165	tCg/tTg	5/18	1	2	FACETS	0.587	0.445	0.754	0.587	0.445	0.754	SUBCLONAL	1	TRUE	1	0.19	2		450	341	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339566	116339566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35469582	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	42	688	0	ENST00000397752.3:c.428G>A	p.Arg143Gln	p.R143Q	ENST00000397752	NM_000245.2	143	cGa/cAa	2/21	1	2	FACETS	0.933	0.779	1	0.933	0.779	1	CLONAL	1	TRUE	1	0.19	2		688	474	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900114	151900114	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	22	434	0	ENST00000262189.6:c.3997G>T	p.Glu1333Ter	p.E1333*	ENST00000262189	NM_170606.2	1333	Gaa/Taa	26/59	1	2	FACETS	0.836	0.649	1	0.836	0.649	1	CLONAL	1	TRUE	1	0.19	2		434	277	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945396	151945396	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	20	330	0	ENST00000262189.6:c.2123C>A	p.Ser708Ter	p.S708*	ENST00000262189	NM_170606.2	708	tCa/tAa	14/59	1	2	FACETS	0.948	0.728	1	0.948	0.728	1	CLONAL	1	TRUE	1	0.19	2		330	222	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955525	90955525	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730881864	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	22	436	0	ENST00000265433.3:c.2140C>T	p.Arg714Ter	p.R714*	ENST00000265433	NM_002485.4	714	Cga/Tga	14/16	1	2	FACETS	0.726	0.563	0.915	0.726	0.563	0.915	CLONAL	1	TRUE	1	0.19	2		436	319	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993708	90993708	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	34	260	0	ENST00000265433.3:c.215C>A	p.Ser72Tyr	p.S72Y	ENST00000265433	NM_002485.4	72	tCt/tAt	3/16	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.19	2		260	253	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5462858	5462858	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	34	512	0	ENST00000381577.3:c.419G>T	p.Arg140Ile	p.R140I	ENST00000381577	NM_014143.3	140	aGa/aTa	4/7	1	2	FACETS	0.947	0.774	1	0.947	0.774	1	CLONAL	1	TRUE	1	0.19	2		512	378	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465499	8465499	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	40	550	0	ENST00000356435.5:c.3681C>A	p.Phe1227Leu	p.F1227L	ENST00000356435		1227	ttC/ttA	21/35	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.19	2		550	334	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486071	8486071	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	26	680	1	ENST00000356435.5:c.2746G>T	p.Glu916Ter	p.E916*	ENST00000356435		916	Gaa/Taa	17/35	1	2	FACETS	0.59	0.466	0.732	0.59	0.466	0.732	SUBCLONAL	1	TRUE	1	0.19	2		681	464	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27109607	27109607	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	23	422	0	ENST00000380036.4:c.19T>G	p.Leu7Val	p.L7V	ENST00000380036	NM_000459.3	7	Tta/Gta	1/23	1	2	FACETS	0.7	0.545	0.878	0.7	0.545	0.878	SUBCLONAL	1	TRUE	1	0.19	2		422	346	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27168553	27168553	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	17	438	0	ENST00000380036.4:c.425C>A	p.Ser142Tyr	p.S142Y	ENST00000380036	NM_000459.3	142	tCt/tAt	3/23	1	2	FACETS	0.559	0.417	0.729	0.559	0.417	0.729	SUBCLONAL	1	TRUE	1	0.19	2		438	320	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133761036	133761036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1456042173	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	47	636	0	ENST00000318560.5:c.3359C>T	p.Ser1120Leu	p.S1120L	ENST00000318560	NM_005157.4	1120	tCg/tTg	11/11	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.19	2		636	467	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412375	139412375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1341448592	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	44	826	0	ENST00000277541.6:c.1270G>A	p.Glu424Lys	p.E424K	ENST00000277541	NM_017617.3	424	Gag/Aag	8/34	1	2	FACETS	0.862	0.723	1	0.862	0.723	1	CLONAL	1	TRUE	1	0.19	2		826	537	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941876	44941876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	29	405	0	ENST00000377967.4:c.3200C>T	p.Ser1067Leu	p.S1067L	ENST00000377967	NM_021140.2	1067	tCg/tTg	21/29	1	2	FACETS	1	0.808	1	1	0.808	1	CLONAL	1	TRUE	1	0.19	2		405	304	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413031	63413031	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	44	757	0	ENST00000330258.3:c.136T>C	p.Ser46Pro	p.S46P	ENST00000330258	NM_152424.3	46	Tca/Cca	2/2	1	2	FACETS	0.821	0.688	0.969	0.821	0.688	0.969	CLONAL	1	TRUE	1	0.19	2		757	564	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889176	76889176	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	24	397	0	ENST00000373344.5:c.4834C>A	p.Leu1612Ile	p.L1612I	ENST00000373344	NM_000489.3	1612	Ctt/Att	18/35	1	2	FACETS	0.851	0.668	1	0.851	0.668	1	CLONAL	1	TRUE	1	0.19	2		397	297	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938173	76938173	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	30	559	2	ENST00000373344.5:c.2575G>T	p.Gly859Ter	p.G859*	ENST00000373344	NM_000489.3	859	Gga/Tga	9/35	1	2	FACETS	0.791	0.638	0.966	0.791	0.638	0.966	CLONAL	1	TRUE	1	0.19	2		561	399	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939386	76939386	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	31	540	0	ENST00000373344.5:c.1362G>T	p.Lys454Asn	p.K454N	ENST00000373344	NM_000489.3	454	aaG/aaT	9/35	1	2	FACETS	0.818	0.662	0.995	0.818	0.662	0.995	CLONAL	1	TRUE	1	0.19	2		540	399	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939633	76939633	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	29	572	0	ENST00000373344.5:c.1115A>C	p.Lys372Thr	p.K372T	ENST00000373344	NM_000489.3	372	aAa/aCa	9/35	1	2	FACETS	0.757	0.608	0.928	0.757	0.608	0.928	CLONAL	1	TRUE	1	0.19	2		572	403	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020225	123020225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	43	344	1	ENST00000355640.3:c.713G>A	p.Arg238Gln	p.R238Q	ENST00000355640		238	cGa/cAa	2/7	1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	1	0.19	2		345	442	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034429	123034429	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	22	329	0	ENST00000355640.3:c.1186A>C	p.Lys396Gln	p.K396Q	ENST00000355640		396	Aaa/Caa	6/7	1	2	FACETS	0.842	0.654	1	0.842	0.654	1	CLONAL	1	TRUE	1	0.19	2		329	275	SUCCESS
PHF6	84295	MSKCC	GRCh37	X	133551289	133551289	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059180-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	16	425	0	ENST00000332070.3:c.925G>T	p.Asp309Tyr	p.D309Y	ENST00000332070	NM_032458.2	309	Gac/Tac	9/10	1	2	FACETS	0.69	0.511	0.905	0.69	0.511	0.905	SUBCLONAL	1	TRUE	1	0.19	2		425	244	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0059181-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	217	628	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.789	0.735	0.844	0.789	0.735	0.844	SUBCLONAL	1	TRUE	1	0.671048929148508	2		629	820	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0059181-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	93	245	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.915	0.823	1	0.915	0.823	1	CLONAL	1	TRUE	1	0.671048929148508	2		245	303	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922364	178922364	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059181-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	81	152	0	ENST00000263967.3:c.1133G>T	p.Cys378Phe	p.C378F	ENST00000263967	NM_006218.2	378	tGt/tTt	6/21	1	2	FACETS	0.936	0.836	1	0.936	0.836	1	CLONAL	1	TRUE	1	0.671048929148508	2		152	258	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0059181-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	141	579	0	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	1	2	FACETS	0.668	0.61	0.728	0.668	0.61	0.728	SUBCLONAL	1	TRUE	1	0.671048929148508	2		579	629	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720858	89720858	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1564568660	NA	P-0059181-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	152	101	0	ENST00000371953.3:c.1012del	p.Ser338LeufsTer6	p.S338Lfs*6	ENST00000371953	NM_000314.4	337	Ttt/tt	8/9	0.671048929148508	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.671048929148508	2		101	210	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189847	11189847	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059181-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	89	457	0	ENST00000361445.4:c.5662T>G	p.Phe1888Val	p.F1888V	ENST00000361445	NM_004958.3	1888	Ttc/Gtc	40/58	1	2	FACETS	0.441	0.392	0.494	0.441	0.392	0.494	SUBCLONAL	1	TRUE	1	0.671048929148508	2		457	601	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023463	27023481	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGCCTGGAGCCCTACGC	GGGGCCTGGAGCCCTACGC	-	novel	NA	P-0059181-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	134	599	0	ENST00000324856.7:c.575_593del	p.Leu192ProfsTer34	p.L192Pfs*34	ENST00000324856	NM_006015.4	190	gGGGGCCTGGAGCCCTACGCg/gg	1/20	1	2	FACETS	0.796	0.727	0.867	0.796	0.727	0.867	SUBCLONAL	1	TRUE	1	0.671048929148508	2		599	502	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099850	27099850	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059181-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	222	607	0	ENST00000324856.7:c.3729del	p.Phe1245SerfsTer24	p.F1245Sfs*24	ENST00000324856	NM_006015.4	1243	gaT/ga	15/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.671048929148508	2		607	603	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440663	56440663	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059181-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	120	665	0	ENST00000407977.2:c.555G>T	p.Arg185Ser	p.R185S	ENST00000407977		185	agG/agT	5/10	1	2	FACETS	0.567	0.513	0.623	0.567	0.513	0.623	SUBCLONAL	1	TRUE	1	0.671048929148508	2		665	631	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47503944	47503944	+	stop_lost	Nonstop_Mutation	SNP	G	G	T	novel	NA	P-0059181-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	184	546	0	ENST00000404338.3:c.4499G>T	p.Ter1500LeuextTer68	p.*1500Lext*68	ENST00000404338	NM_004491.4	1500	tGa/tTa	6/6	1	2	FACETS	0.983	0.913	1	0.983	0.913	1	CLONAL	1	TRUE	1	0.671048929148508	2		546	558	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	36	121	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.344024549079559	2		121	177	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0059182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	37	613	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.344024549079559	1	FACETS	0.821	0.682	0.973	0.821	0.682	0.973	CLONAL	1	TRUE	0	0.344024549079559	1		614	217	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0059182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	34	534	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.344024549079559	1	FACETS	0.765	0.63	0.914	0.765	0.63	0.914	CLONAL	1	TRUE	0	0.344024549079559	1		534	214	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589834	28589834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201923726	NA	P-0059182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	48	459	0	ENST00000241453.7:c.2546G>A	p.Arg849His	p.R849H	ENST00000241453	NM_004119.2	849	cGt/cAt	21/24	0.329963364290103	2	FACETS	0.856	0.737	0.982	0.856	0.737	0.982	CLONAL	2	TRUE	0	0.344024549079559	2		459	163	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473723	67473723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223740	NA	P-0059182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	54	636	0	ENST00000327367.4:c.803G>A	p.Arg268His	p.R268H	ENST00000327367	NM_005902.3	268	cGc/cAc	6/9	0.193785159225791	2	FACETS	0.751	0.65	0.858	0.751	0.65	0.858	INDETERMINATE	2	TRUE	0	0.344024549079559	2		636	209	SUCCESS
CBL	867	MSKCC	GRCh37	11	119168162	119168162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763213265	NA	P-0059182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	53	490	0	ENST00000264033.4:c.2222C>T	p.Ala741Val	p.A741V	ENST00000264033	NM_005188.3	741	gCg/gTg	14/16	0.16626734149222	2	FACETS	1	0.956	1	0.65	0.56	0.746	INDETERMINATE	1	TRUE	0	0.344024549079559	2		490	237	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120130	70120130	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	43	551	0	ENST00000245479.2:c.1132C>T	p.Gln378Ter	p.Q378*	ENST00000245479	NM_000346.3	378	Cag/Tag	3/3	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.344024549079559	2		551	191	SUCCESS
FH	2271	MSKCC	GRCh37	1	241672076	241672076	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	23	336	0	ENST00000366560.3:c.565G>T	p.Asp189Tyr	p.D189Y	ENST00000366560	NM_000143.3	189	Gat/Tat	5/10	1	2	FACETS	0.719	0.564	0.895	0.719	0.564	0.895	SUBCLONAL	1	TRUE	1	0.344024549079559	2		336	186	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627331	37627331	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059182-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	39	541	0	ENST00000447079.4:c.1246G>A	p.Asp416Asn	p.D416N	ENST00000447079	NM_015083.1	416	Gat/Aat	2/14	1	2	FACETS	0.957	0.799	1	0.957	0.799	1	CLONAL	1	TRUE	1	0.344024549079559	2		541	237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0059183-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	123	613	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.249975209680085	2		614	983	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0059183-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	62	185	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.145130466384228	3	FACETS	0.826	0.717	0.941			1	INDETERMINATE	2	TRUE	NA	0.249975209680085	3		185	338	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510620	38510620	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059183-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	99	450	0	ENST00000254066.5:c.874C>G	p.Leu292Val	p.L292V	ENST00000254066	NM_000964.3	292	Ctg/Gtg	7/9	1	2	FACETS	0.961	0.857	1	0.961	0.857	1	CLONAL	1	TRUE	1	0.249975209680085	2		450	824	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980924	40980924	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059183-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	104	423	0	ENST00000373198.4:c.1562T>A	p.Ile521Asn	p.I521N	ENST00000373198	NM_133170.3	521	aTc/aAc	10/32	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.249975209680085	2		423	789	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912010	56912010	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059183-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	54	296	0	ENST00000519728.1:c.1238A>T	p.Glu413Val	p.E413V	ENST00000519728	NM_002350.3	413	gAa/gTa	12/13	0.213754276891617	3	FACETS	0.767	0.654	0.89	0.383	0.327	0.445	SUBCLONAL	1	TRUE	1	0.249975209680085	3		296	634	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0059186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	57	483	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.505	0.433	0.583	0.505	0.433	0.583	SUBCLONAL	1	TRUE	1	0.421211786646059	2		483	536	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	84	121	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.421211786646059	3	FACETS	1	0.978	1	0.721	0.642	0.803	CLONAL	1	TRUE	1	0.421211786646059	3		121	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0059186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	295	657	1	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.248053142760297	4	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.421211786646059	4		658	802	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50138844	50138844	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	64	661	0	ENST00000246792.3:c.646G>T	p.Val216Phe	p.V216F	ENST00000246792	NM_006270.3	216	Gtc/Ttc	6/6	0.246989563288399	3	FACETS	0.525	0.454	0.602	0.262	0.227	0.301	INDETERMINATE	1	TRUE	1	0.421211786646059	3		661	701	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385257	41385257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293875597	NA	P-0059186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	221	535	0	ENST00000373198.4:c.704C>T	p.Thr235Met	p.T235M	ENST00000373198	NM_133170.3	235	aCg/aTg	6/32	0.368349118875192	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	2	0.421211786646059	4		535	724	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898764	134898764	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs185655852	NA	P-0059186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	51	556	0	ENST00000398015.3:c.1822C>T	p.Arg608Trp	p.R608W	ENST00000398015	NM_004441.4	608	Cgg/Tgg	10/16	0.421211786646059	3	FACETS	0.442	0.375	0.516	0.221	0.187	0.258	SUBCLONAL	1	TRUE	1	0.421211786646059	3		556	663	SUCCESS
APC	324	MSKCC	GRCh37	5	112175475	112175476	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0059186-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	79	490	0	ENST00000257430.4:c.4188dup	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1395	agt/agTt	16/16	1	2	FACETS	0.665	0.586	0.75	0.665	0.586	0.75	SUBCLONAL	1	TRUE	1	0.421211786646059	2		490	564	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372518	55372518	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059207-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	126	487	0	ENST00000297316.4:c.1208G>T	p.Ser403Ile	p.S403I	ENST00000297316	NM_022454.3	403	aGc/aTc	2/2	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.266330364087388	2		487	885	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs121913292	NA	P-0059207-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	170	353	0	ENST00000371953.3:c.389del	p.Arg130GlnfsTer4	p.R130Qfs*4	ENST00000371953	NM_000314.4	130	cGa/ca	5/9	0.266330364087388	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.266330364087388	2		353	598	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692879	89692879	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059207-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	32	238	0	ENST00000371953.3:c.364del	p.Ile122PhefsTer12	p.I122Ffs*12	ENST00000371953	NM_000314.4	121	gcA/gc	5/9	0.266330364087388	2	FACETS	0.613	0.498	0.743	0.307	0.249	0.372	SUBCLONAL	1	TRUE	0	0.266330364087388	2		238	392	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984866	72984866	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0059207-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	97	468	0	ENST00000268489.5:c.2720-2A>C		p.X907_splice	ENST00000268489	NM_006885.3	907			1	2	FACETS	0.866	0.771	0.967	0.866	0.771	0.967	CLONAL	1	TRUE	1	0.266330364087388	2		468	841	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589588	67589592	+	protein_altering_variant	In_Frame_Del	DEL	GAATA	GAATA	TG	novel	NA	P-0059207-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	60	245	0	ENST00000274335.5:c.1351_1355delinsTG	p.Glu451_Tyr452delinsCys	p.E451_Y452delinsC	ENST00000274335		451	GAATAt/TGt	10/15	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.266330364087388	2		245	360	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202708	16202708	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	302	225	0	ENST00000375759.3:c.416A>T	p.Asn139Ile	p.N139I	ENST00000375759	NM_015001.2	139	aAc/aTc	3/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.840124451674579	2		225	701	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247965	59247965	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	449	407	0	ENST00000371222.2:c.778A>T	p.Met260Leu	p.M260L	ENST00000371222	NM_002228.3	260	Atg/Ttg	1/1	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.840124451674579	2		407	988	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313268	65313268	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	349	306	0	ENST00000342505.4:c.1846A>T	p.Lys616Ter	p.K616*	ENST00000342505	NM_002227.2	616	Aag/Tag	13/25	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.840124451674579	2		306	823	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65348992	65348992	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	350	299	0	ENST00000342505.4:c.173A>T	p.Glu58Val	p.E58V	ENST00000342505	NM_002227.2	58	gAg/gTg	3/25	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.840124451674579	2		299	774	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166341	118166341	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	433	326	0	ENST00000369448.3:c.851A>C	p.Gln284Pro	p.Q284P	ENST00000369448	NM_017709.3	284	cAg/cCg	2/2	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.840124451674579	2		326	1022	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491055	120491055	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	375	294	0	ENST00000256646.2:c.2734A>G	p.Ile912Val	p.I912V	ENST00000256646	NM_024408.3	912	Att/Gtt	17/34	1	2	FACETS	0.995	0.949	1	0.995	0.949	1	CLONAL	1	TRUE	1	0.840124451674579	2		294	897	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512149	120512149	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	441	344	0	ENST00000256646.2:c.1093C>T	p.Pro365Ser	p.P365S	ENST00000256646	NM_024408.3	365	Cca/Tca	6/34	1	2	FACETS	0.995	0.952	1	0.995	0.952	1	CLONAL	1	TRUE	1	0.840124451674579	2		344	1055	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651643	206651643	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	402	346	1	ENST00000367120.3:c.953A>T	p.Gln318Leu	p.Q318L	ENST00000367120	NM_014002.3	318	cAg/cTg	9/22	1	2	FACETS	0.94	0.897	0.984	0.94	0.897	0.984	CLONAL	1	TRUE	1	0.840124451674579	2		347	1018	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858979	243858979	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	153	128	0	ENST00000263826.5:c.86T>A	p.Leu29Ter	p.L29*	ENST00000263826	NM_005465.4	29	tTg/tAg	2/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.840124451674579	2		128	350	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332573	70332573	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	279	214	0	ENST00000373644.4:c.478A>T	p.Met160Leu	p.M160L	ENST00000373644	NM_030625.2	160	Atg/Ttg	2/12	1	2	FACETS	0.987	0.933	1	0.987	0.933	1	CLONAL	1	TRUE	1	0.840124451674579	2		214	673	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426971	70426971	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	368	242	0	ENST00000373644.4:c.4631A>T	p.Tyr1544Phe	p.Y1544F	ENST00000373644	NM_030625.2	1544	tAc/tTc	7/12	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.840124451674579	2		242	845	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725042	89725042	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	124	117	0	ENST00000371953.3:c.1027-2A>T		p.X343_splice	ENST00000371953	NM_000314.4	343			0.840124451674579	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.840124451674579	1		117	162	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945634	71945634	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	330	287	0	ENST00000298229.2:c.2390A>T	p.Gln797Leu	p.Q797L	ENST00000298229	NM_001567.3	797	cAg/cTg	21/28	1	2	FACETS	0.976	0.927	1	0.976	0.927	1	CLONAL	1	TRUE	1	0.840124451674579	2		287	805	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180589	94180589	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	279	213	0	ENST00000323929.3:c.1579A>T	p.Arg527Ter	p.R527*	ENST00000323929	NM_005591.3	527	Aga/Tga	15/20	1	2	FACETS	0.974	0.921	1	0.974	0.921	1	CLONAL	1	TRUE	1	0.840124451674579	2		213	682	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352606	118352606	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	62	324	0	ENST00000534358.1:c.3811A>T	p.Ser1271Cys	p.S1271C	ENST00000534358	NM_005933.3	1271	Agt/Tgt	7/36	0.687930214314746	1	FACETS	0.14	0.121	0.162	0.14	0.121	0.162	SUBCLONAL	1	TRUE	0	0.840124451674579	1		324	610	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125499316	125499316	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	166	136	0	ENST00000428830.2:c.385A>T	p.Arg129Trp	p.R129W	ENST00000428830	NM_001114121.2	129	Agg/Tgg	5/14	1	2	FACETS	0.884	0.82	0.949	0.884	0.82	0.949	CLONAL	1	TRUE	1	0.840124451674579	2		136	447	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383334	4383334	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	359	355	0	ENST00000261254.3:c.128A>T	p.Tyr43Phe	p.Y43F	ENST00000261254	NM_001759.3	43	tAc/tTc	1/5	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.840124451674579	2		355	801	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650600	18650600	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	199	149	0	ENST00000266497.5:c.2811A>T	p.Gln937His	p.Q937H	ENST00000266497		937	caA/caT	20/31	0.840124451674579	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.840124451674579	1		149	257	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243818	46243818	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	214	162	0	ENST00000334344.6:c.1913del		p.X638_splice	ENST00000334344	NM_152641.2	638			1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.840124451674579	2		162	493	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245934	46245934	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	256	214	0	ENST00000334344.6:c.4028A>C	p.Gln1343Pro	p.Q1343P	ENST00000334344	NM_152641.2	1343	cAa/cCa	15/21	1	2	FACETS	0.967	0.912	1	0.967	0.912	1	CLONAL	1	TRUE	1	0.840124451674579	2		214	630	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431294	49431294	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	348	374	0	ENST00000301067.7:c.9845A>T	p.Gln3282Leu	p.Q3282L	ENST00000301067	NM_003482.3	3282	cAg/cTg	34/54	1	2	FACETS	0.922	0.876	0.968	0.922	0.876	0.968	CLONAL	1	TRUE	1	0.840124451674579	2		374	899	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444737	49444737	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	457	412	0	ENST00000301067.7:c.2729del	p.Pro910LeufsTer20	p.P910Lfs*20	ENST00000301067	NM_003482.3	910	cCt/ct	10/54	1	2	FACETS	0.992	0.95	1	0.992	0.95	1	CLONAL	1	TRUE	1	0.840124451674579	2		412	1097	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487286	56487286	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	390	281	0	ENST00000267101.3:c.1432A>T	p.Thr478Ser	p.T478S	ENST00000267101	NM_001982.3	478	Acg/Tcg	12/28	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.840124451674579	2		281	852	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495031	56495031	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	472	366	0	ENST00000267101.3:c.3388A>T	p.Ser1130Cys	p.S1130C	ENST00000267101	NM_001982.3	1130	Agc/Tgc	27/28	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.840124451674579	2		366	1110	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219407	133219407	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	327	304	0	ENST00000320574.5:c.4727A>T	p.Lys1576Met	p.K1576M	ENST00000320574	NM_006231.2	1576	aAg/aTg	36/49	1	2	FACETS	0.955	0.907	1	0.955	0.907	1	CLONAL	1	TRUE	1	0.840124451674579	2		304	815	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240717	133240717	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	360	349	0	ENST00000320574.5:c.2579A>T	p.Asp860Val	p.D860V	ENST00000320574	NM_006231.2	860	gAc/gTc	23/49	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.840124451674579	2		349	817	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245074	133245074	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	381	352	0	ENST00000320574.5:c.2041A>T	p.Ser681Cys	p.S681C	ENST00000320574	NM_006231.2	681	Agc/Tgc	19/49	1	2	FACETS	0.981	0.935	1	0.981	0.935	1	CLONAL	1	TRUE	1	0.840124451674579	2		352	925	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608285	28608285	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	513	201	0	ENST00000241453.7:c.1771T>A	p.Tyr591Asn	p.Y591N	ENST00000241453	NM_004119.2	591	Tac/Aac	14/24	0.840124451674579	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.840124451674579	2		201	602	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910524	32910524	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	322	152	0	ENST00000380152.3:c.2032A>T	p.Asn678Tyr	p.N678Y	ENST00000380152		678	Aat/Tat	11/27	0.840124451674579	2	FACETS	0.978	0.949	1	0.978	0.949	1	CLONAL	2	TRUE	0	0.840124451674579	2		152	392	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033822	49033822	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs587778867	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	454	159	0	ENST00000267163.4:c.1961-2A>T		p.X654_splice	ENST00000267163	NM_000321.2	654			0.840124451674579	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.840124451674579	2		159	537	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543297	65543297	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	376	294	0	ENST00000358664.4:c.380A>T	p.Lys127Met	p.K127M	ENST00000358664	NM_002382.4	127	aAg/aTg	5/5	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.840124451674579	2		294	840	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51504542	51504542	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	297	208	0	ENST00000260433.2:c.1238T>C	p.Phe413Ser	p.F413S	ENST00000260433		413	tTt/tCt	9/10	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.840124451674579	2		208	707	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472537	88472537	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	398	332	0	ENST00000360948.2:c.2018A>T	p.Gln673Leu	p.Q673L	ENST00000360948	NM_001012338.2	673	cAg/cTg	16/19	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.840124451674579	2		332	935	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991457	72991457	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	377	338	0	ENST00000268489.5:c.2588A>T	p.Gln863Leu	p.Q863L	ENST00000268489	NM_006885.3	863	cAa/cTa	2/10	1	2	FACETS	0.998	0.952	1	0.998	0.952	1	CLONAL	1	TRUE	1	0.840124451674579	2		338	899	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544360	86544360	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	330	360	0	ENST00000262426.4:c.185A>T	p.Gln62Leu	p.Q62L	ENST00000262426	NM_001451.2	62	cAg/cTg	1/2	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.840124451674579	2		360	747	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349181	89349181	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	441	305	1	ENST00000301030.4:c.3769A>T	p.Lys1257Ter	p.K1257*	ENST00000301030	NM_001256183.1	1257	Aaa/Taa	9/13	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.840124451674579	2		306	1005	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577098	7577098	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	427	306	0	ENST00000269305.4:c.840A>T	p.Arg280Ser	p.R280S	ENST00000269305	NM_001126112.2	280	agA/agT	8/11	0.840124451674579	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.840124451674579	1		306	559	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556482	29556482	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	241	149	0	ENST00000356175.3:c.2849A>T	p.Gln950Leu	p.Q950L	ENST00000356175	NM_000267.3	950	cAg/cTg	21/57	0.457214776425659	3	FACETS	1	0.988	1	0.606	0.569	0.644	INDETERMINATE	1	TRUE	1	0.840124451674579	3		149	672	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33689800	33689800	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	438	254	0	ENST00000308377.4:c.1027A>T	p.Thr343Ser	p.T343S	ENST00000308377	NM_152270.3	343	Aca/Tca	2/5	0.457214776425659	3	FACETS	0.779	0.747	0.812	0.779	0.747	0.812	INDETERMINATE	2	TRUE	1	0.840124451674579	3		254	950	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38792762	38792762	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	266	131	0	ENST00000348513.6:c.254A>T	p.Lys85Met	p.K85M	ENST00000348513	NM_003079.4	85	aAg/aTg	6/11	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.840124451674579	2		131	513	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456596	40456596	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	1047	380	0	ENST00000345506.4:c.1306A>T	p.Thr436Ser	p.T436S	ENST00000345506	NM_003152.3	436	Aca/Tca	12/20	0.626918165540331	4	FACETS	0.926	0.905	0.947	0.926	0.905	0.947	CLONAL	3	TRUE	1	0.840124451674579	4		380	1651	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223237	41223237	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	300	250	0	ENST00000357654.3:c.4694A>T	p.Glu1565Val	p.E1565V	ENST00000357654	NM_007294.3	1565	gAa/gTa	15/23	0.626918165540331	4	FACETS	1	0.973	1	0.353	0.332	0.374	CLONAL	1	TRUE	1	0.840124451674579	4		250	1242	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435236	56435236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1202	453	436	0	ENST00000407977.2:c.1901C>T	p.Pro634Leu	p.P634L	ENST00000407977		634	cCc/cTc	9/10	0.626918165540331	4	FACETS	1	0.993	1	0.4	0.381	0.419	CLONAL	1	TRUE	1	0.840124451674579	4		436	1655	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763424	59763424	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	483	178	0	ENST00000259008.2:c.2678A>T	p.Asn893Ile	p.N893I	ENST00000259008	NM_032043.2	893	aAt/aTt	19/20	0.626918165540331	4	FACETS	0.958	0.927	0.989	0.958	0.927	0.989	CLONAL	3	TRUE	1	0.840124451674579	4		178	736	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575104	48575104	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	299	228	0	ENST00000342988.3:c.298A>T	p.Arg100Trp	p.R100W	ENST00000342988	NM_005359.5	100	Agg/Tgg	3/12	0.184579089942408	2	FACETS	1	0.994	1	0.651	0.62	0.681	INDETERMINATE	1	TRUE	0	0.840124451674579	2		228	547	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61322899	61322899	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1377897057	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	222	129	0	ENST00000283752.5:c.1165T>A	p.Ser389Thr	p.S389T	ENST00000283752	NM_006919.2	389	Tcc/Acc	8/8	0.184579089942408	2	FACETS	1	0.992	1	0.652	0.617	0.687	INDETERMINATE	1	TRUE	0	0.840124451674579	2		129	405	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220463	1220463	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	334	383	0	ENST00000326873.7:c.556A>T	p.Thr186Ser	p.T186S	ENST00000326873	NM_000455.4	186	Acc/Tcc	4/10	1	2	FACETS	0.973	0.925	1	0.973	0.925	1	CLONAL	1	TRUE	1	0.840124451674579	2		383	817	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602256	10602256	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	332	305	0	ENST00000171111.5:c.1322A>T	p.Glu441Val	p.E441V	ENST00000171111	NM_203500.1	441	gAg/gTg	3/6	1	2	FACETS	0.914	0.867	0.961	0.914	0.867	0.961	CLONAL	1	TRUE	1	0.840124451674579	2		305	865	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945790	17945790	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	362	333	0	ENST00000458235.1:c.2070G>A	p.Trp690Ter	p.W690*	ENST00000458235	NM_000215.3	690	tgG/tgA	16/24	1	2	FACETS	0.989	0.942	1	0.989	0.942	1	CLONAL	1	TRUE	1	0.840124451674579	2		333	871	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971787	18971787	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	328	280	0	ENST00000262803.5:c.2453A>T	p.Tyr818Phe	p.Y818F	ENST00000262803	NM_002911.3	818	tAc/tTc	17/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.840124451674579	2		280	762	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212654	36212654	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	910	318	0	ENST00000222270.7:c.2405A>T	p.Gln802Leu	p.Q802L	ENST00000222270	NM_014727.1	802	cAg/cTg	3/37	0.840124451674579	3	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.840124451674579	3		318	1432	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224120	36224120	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	210	226	0	ENST00000222270.7:c.6670A>T	p.Ile2224Phe	p.I2224F	ENST00000222270	NM_014727.1	2224	Att/Ttt	28/37	0.840124451674579	3	FACETS	0.893	0.831	0.957			1	CLONAL	1	TRUE	NA	0.840124451674579	3		226	795	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794599	42794599	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	358	335	0	ENST00000575354.2:c.1679A>T	p.Gln560Leu	p.Q560L	ENST00000575354	NM_015125.3	560	cAg/cTg	10/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.840124451674579	2		335	833	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47503598	47503598	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	329	274	0	ENST00000404338.3:c.4153A>T	p.Asn1385Tyr	p.N1385Y	ENST00000404338	NM_004491.4	1385	Aac/Tac	6/6	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.840124451674579	2		274	738	SUCCESS
ALK	238	MSKCC	GRCh37	2	29448356	29448356	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	506	409	0	ENST00000389048.3:c.3143T>A	p.Leu1048Gln	p.L1048Q	ENST00000389048	NM_004304.4	1048	cTg/cAg	19/29	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.840124451674579	2		409	1115	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234330	39234330	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	120	103	0	ENST00000402219.2:c.2515A>T	p.Ile839Phe	p.I839F	ENST00000402219	NM_005633.3	839	Att/Ttt	16/23	1	2	FACETS	0.896	0.82	0.973	0.896	0.82	0.973	CLONAL	1	TRUE	1	0.840124451674579	2		103	319	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724097	61724097	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	252	151	0	ENST00000401558.2:c.805A>T	p.Thr269Ser	p.T269S	ENST00000401558	NM_003400.3	269	Act/Tct	10/25	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.840124451674579	2		151	597	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732682	204732682	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	350	229	0	ENST00000302823.3:c.17T>A	p.Phe6Tyr	p.F6Y	ENST00000302823	NM_005214.4	6	tTt/tAt	1/4	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.840124451674579	2		229	787	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488771	212488771	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	356	235	0	ENST00000342788.4:c.2080-2A>T		p.X694_splice	ENST00000342788	NM_005235.2	694			1	2	FACETS	0.954	0.908	1	0.954	0.908	1	CLONAL	1	TRUE	1	0.840124451674579	2		235	888	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439877	220439877	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	369	340	0	ENST00000243786.2:c.730T>A	p.Ser244Thr	p.S244T	ENST00000243786	NM_002191.3	244	Tct/Act	2/2	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.840124451674579	2		340	858	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225362568	225362568	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	139	157	0	ENST00000264414.4:c.1611-2A>T		p.X537_splice	ENST00000264414	NM_003590.4	537			1	2	FACETS	0.84	0.773	0.909	0.84	0.773	0.909	CLONAL	1	TRUE	1	0.840124451674579	2		157	394	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561068	9561068	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	304	328	0	ENST00000353224.5:c.714A>T	p.Arg238Ser	p.R238S	ENST00000353224	NM_177990.2	238	agA/agT	4/10	1	2	FACETS	0.92	0.871	0.969	0.92	0.871	0.969	CLONAL	1	TRUE	1	0.840124451674579	2		328	787	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561165	9561165	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	356	277	0	ENST00000353224.5:c.617T>A	p.Leu206Gln	p.L206Q	ENST00000353224	NM_177990.2	206	cTg/cAg	4/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.840124451674579	2		277	788	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016199	31016199	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	355	217	0	ENST00000375687.4:c.445A>T	p.Arg149Trp	p.R149W	ENST00000375687	NM_015338.5	149	Agg/Tgg	6/13	1	2	FACETS	0.961	0.915	1	0.961	0.915	1	CLONAL	1	TRUE	1	0.840124451674579	2		217	879	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31372570	31372570	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	373	247	0	ENST00000328111.2:c.211A>T	p.Thr71Ser	p.T71S	ENST00000328111	NM_006892.3	71	Aca/Tca	4/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.840124451674579	2		247	849	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735449	40735449	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	358	326	0	ENST00000373198.4:c.3424A>T	p.Arg1142Trp	p.R1142W	ENST00000373198	NM_133170.3	1142	Agg/Tgg	25/32	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.840124451674579	2		326	837	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46255863	46255863	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	173	63	0	ENST00000371998.3:c.475A>T	p.Asn159Tyr	p.N159Y	ENST00000371998		159	Aat/Tat	6/23	1	2	FACETS	0.976	0.909	1	0.976	0.909	1	CLONAL	1	TRUE	1	0.840124451674579	2		63	422	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42851172	42851172	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	304	171	0	ENST00000398585.3:c.721A>T	p.Ser241Cys	p.S241C	ENST00000398585	NM_001135099.1	241	Agc/Tgc	7/14	0.110838667633547	5	FACETS	1	0.98	1	0.711	0.673	0.749	INDETERMINATE	2	TRUE	2	0.840124451674579	5		171	767	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712615	52712615	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	311	166	0	ENST00000394830.3:c.139-2A>T		p.X47_splice	ENST00000394830	NM_018313.4	47			0.840124451674579	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.840124451674579	1		166	383	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987028	69987028	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	441	284	0	ENST00000394351.3:c.89A>T	p.Gln30Leu	p.Q30L	ENST00000394351	NM_000248.3	30	cAg/cTg	2/9	0.840124451674579	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.840124451674579	1		284	550	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456441	89456441	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	239	158	0	ENST00000336596.2:c.1617T>A	p.Ser539Arg	p.S539R	ENST00000336596	NM_005233.5	539	agT/agA	8/17	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.840124451674579	2		158	544	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169940512	169940512	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	329	272	0	ENST00000295797.4:c.55A>T	p.Ser19Cys	p.S19C	ENST00000295797	NM_002740.5	19	Agc/Tgc	1/18	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.840124451674579	2		272	764	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170020903	170020903	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	33	27	0	ENST00000295797.4:c.1779A>T	p.Glu593Asp	p.E593D	ENST00000295797	NM_002740.5	593	gaA/gaT	18/18	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.840124451674579	2		27	77	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955057	1955057	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	317	217	0	ENST00000382891.5:c.2144A>T	p.His715Leu	p.H715L	ENST00000382891	NM_133335.3	715	cAc/cTc	12/22	1	2	FACETS	0.95	0.902	1	0.95	0.902	1	CLONAL	1	TRUE	1	0.840124451674579	2		217	794	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750522	41750522	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	315	257	0	ENST00000226382.2:c.106T>A	p.Cys36Ser	p.C36S	ENST00000226382	NM_003924.3	36	Tgc/Agc	1/3	1	2	FACETS	0.874	0.828	0.921	0.874	0.828	0.921	CLONAL	1	TRUE	1	0.840124451674579	2		257	858	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158298	106158298	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	520	239	0	ENST00000380013.4:c.3199A>T	p.Arg1067Ter	p.R1067*	ENST00000380013	NM_001127208.2	1067	Aga/Tga	3/11	0.840124451674579	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.840124451674579	1		239	633	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630633	187630633	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	416	239	0	ENST00000441802.2:c.349A>T	p.Thr117Ser	p.T117S	ENST00000441802	NM_005245.3	117	Aca/Tca	2/27	0.840124451674579	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.840124451674579	1		239	516	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294199	1294199	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	328	359	0	ENST00000310581.5:c.802C>G	p.Arg268Gly	p.R268G	ENST00000310581	NM_198253.2	268	Cgt/Ggt	2/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.840124451674579	2		359	774	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569262	67569262	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	359	216	0	ENST00000274335.5:c.379A>T	p.Ile127Phe	p.I127F	ENST00000274335		127	Att/Ttt	2/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.840124451674579	2		216	846	SUCCESS
APC	324	MSKCC	GRCh37	5	112179428	112179428	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	404	236	0	ENST00000257430.4:c.8137A>T	p.Met2713Leu	p.M2713L	ENST00000257430	NM_000038.5	2713	Atg/Ttg	16/16	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.840124451674579	2		236	882	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940530	131940530	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	243	142	0	ENST00000265335.6:c.2557A>T	p.Ile853Leu	p.I853L	ENST00000265335		853	Ata/Tta	16/25	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.840124451674579	2		142	521	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131951804	131951804	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	193	90	0	ENST00000265335.6:c.3146A>T	p.Gln1049Leu	p.Q1049L	ENST00000265335		1049	cAg/cTg	20/25	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.840124451674579	2		90	419	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524591	176524591	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1436217943	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	464	414	0	ENST00000292408.4:c.2323T>A	p.Cys775Ser	p.C775S	ENST00000292408	NM_213647.1	775	Tgc/Agc	18/18	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.840124451674579	2		414	1063	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401634	401634	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	404	379	0	ENST00000380956.4:c.956T>A	p.Met319Lys	p.M319K	ENST00000380956	NM_001195286.1	319	aTg/aAg	7/9	0.840124451674579	3	FACETS	0.992	0.943	1	0.496	0.471	0.521	CLONAL	1	TRUE	1	0.840124451674579	3		379	1377	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821560	32821560	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs765553023	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	633	283	1	ENST00000354258.4:c.34T>A	p.Cys12Ser	p.C12S	ENST00000354258	NM_000593.5	12	Tgt/Agt	1/11	0.821934628335708	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.840124451674579	3		284	1050	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622155	117622155	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	160	133	0	ENST00000368508.3:c.6715A>G	p.Ile2239Val	p.I2239V	ENST00000368508	NM_002944.2	2239	Ata/Gta	42/43	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.840124451674579	2		133	340	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665423	117665423	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	207	125	0	ENST00000368508.3:c.4324A>G	p.Lys1442Glu	p.K1442E	ENST00000368508	NM_002944.2	1442	Aaa/Gaa	27/43	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.840124451674579	2		125	485	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951919	2951919	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	398	277	0	ENST00000396946.4:c.3031A>T	p.Arg1011Ter	p.R1011*	ENST00000396946	NM_032415.4	1011	Aga/Tga	23/25	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.840124451674579	2		277	915	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962948	2962948	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	381	310	0	ENST00000396946.4:c.1960A>T	p.Thr654Ser	p.T654S	ENST00000396946	NM_032415.4	654	Acc/Tcc	16/25	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.840124451674579	2		310	861	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268065	55268065	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	457	335	0	ENST00000275493.2:c.2905T>A	p.Ser969Thr	p.S969T	ENST00000275493	NM_005228.3	969	Tcc/Acc	24/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.840124451674579	2		335	1072	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846416	128846416	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	351	288	0	ENST00000249373.3:c.1252T>A	p.Phe418Ile	p.F418I	ENST00000249373	NM_005631.4	418	Ttc/Atc	6/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.840124451674579	2		288	808	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371891	55371891	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	292	363	0	ENST00000297316.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000297316	NM_022454.3	194	cTg/cGg	2/2	0.342924773232364	3	FACETS	1	0.992	1	0.638	0.603	0.673	INDETERMINATE	1	TRUE	1	0.840124451674579	3		363	774	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864571	56864571	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	312	178	0	ENST00000519728.1:c.534T>A	p.Asp178Glu	p.D178E	ENST00000519728	NM_002350.3	178	gaT/gaA	7/13	0.342924773232364	3	FACETS	0.829	0.789	0.869	0.829	0.789	0.869	INDETERMINATE	2	TRUE	1	0.840124451674579	3		178	636	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879429	56879429	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	331	229	0	ENST00000519728.1:c.946T>A	p.Tyr316Asn	p.Y316N	ENST00000519728	NM_002350.3	316	Tac/Aac	9/13	0.342924773232364	3	FACETS	1	0.989	1	0.583	0.552	0.614	INDETERMINATE	1	TRUE	1	0.840124451674579	3		229	960	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931863	68931863	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	227	188	0	ENST00000288368.4:c.293A>T	p.Glu98Val	p.E98V	ENST00000288368	NM_024870.2	98	gAa/gTa	3/40	0.342924773232364	3	FACETS	1	0.988	1	0.605	0.567	0.644	INDETERMINATE	1	TRUE	1	0.840124451674579	3		188	634	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2039860	2039860	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs62639302	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	530	338	0	ENST00000349721.2:c.750A>T	p.Gln250His	p.Q250H	ENST00000349721	NM_003070.3	250	caA/caT	4/34	0.464823047926407	1	FACETS	0.775	0.748	0.802	0.775	0.748	0.802	INDETERMINATE	1	TRUE	0	0.840124451674579	1		338	944	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2054619	2054619	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	347	191	0	ENST00000349721.2:c.1069A>T	p.Arg357Trp	p.R357W	ENST00000349721	NM_003070.3	357	Agg/Tgg	6/34	0.464823047926407	1	FACETS	0.804	0.77	0.837	0.804	0.77	0.837	INDETERMINATE	1	TRUE	0	0.840124451674579	1		191	596	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2060969	2060969	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	244	269	0	ENST00000349721.2:c.1675A>T	p.Arg559Trp	p.R559W	ENST00000349721	NM_003070.3	559	Agg/Tgg	9/34	0.464823047926407	1	FACETS	0.369	0.345	0.394	0.369	0.345	0.394	INDETERMINATE	1	TRUE	0	0.840124451674579	1		269	912	SUCCESS
MTAP	4507	MSKCC	GRCh37	9	21854865	21854865	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	377	231	0	ENST00000380172.4:c.686A>T	p.Glu229Val	p.E229V	ENST00000380172	NM_002451.3	229	gAa/gTa	6/8	0.464823047926407	1	FACETS	0.764	0.733	0.796	0.764	0.733	0.796	INDETERMINATE	1	TRUE	0	0.840124451674579	1		231	681	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923463	36923463	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	288	284	0	ENST00000358127.4:c.799A>T	p.Met267Leu	p.M267L	ENST00000358127	NM_001280556.1	267	Atg/Ttg	7/10	0.464823047926407	1	FACETS	0.686	0.651	0.72	0.686	0.651	0.72	INDETERMINATE	1	TRUE	0	0.840124451674579	1		284	580	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390977	139390977	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	474	433	0	ENST00000277541.6:c.7214A>T	p.Gln2405Leu	p.Q2405L	ENST00000277541	NM_017617.3	2405	cAg/cTg	34/34	0.464823047926407	1	FACETS	0.769	0.741	0.797	0.769	0.741	0.797	INDETERMINATE	1	TRUE	0	0.840124451674579	1		433	851	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139818378	139818378	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	333	260	0	ENST00000247668.2:c.1213A>T	p.Thr405Ser	p.T405S	ENST00000247668	NM_021138.3	405	Aca/Tca	10/11	0.464823047926407	1	FACETS	0.702	0.67	0.734	0.702	0.67	0.734	INDETERMINATE	1	TRUE	0	0.840124451674579	1		260	655	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934091	39934091	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	305	312	1	ENST00000378444.4:c.508A>T	p.Arg170Trp	p.R170W	ENST00000378444	NM_001123385.1	170	Agg/Tgg	4/15	0.292080617795125	1	FACETS	0.52	0.492	0.548	0.52	0.492	0.548	INDETERMINATE	1	TRUE	0	0.840124451674579	1		313	810	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942828	44942829	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	215	170	0	ENST00000377967.4:c.3408_3409insGT	p.Lys1137ValfsTer22	p.K1137Vfs*22	ENST00000377967	NM_021140.2	1136	-/GT	23/29	0.292080617795125	1	FACETS	0.617	0.58	0.655	0.617	0.58	0.655	INDETERMINATE	1	TRUE	0	0.840124451674579	1		170	481	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044899	47044899	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	416	338	0	ENST00000377604.3:c.2225A>T	p.Gln742Leu	p.Q742L	ENST00000377604	NM_001204468.1	742	cAg/cTg	20/24	0.292080617795125	1	FACETS	0.659	0.631	0.687	0.659	0.631	0.687	INDETERMINATE	1	TRUE	0	0.840124451674579	1		338	872	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422628	47422628	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	361	354	0	ENST00000377045.4:c.100A>T	p.Thr34Ser	p.T34S	ENST00000377045	NM_001654.4	34	Act/Tct	3/16	0.292080617795125	1	FACETS	0.644	0.614	0.674	0.644	0.614	0.674	INDETERMINATE	1	TRUE	0	0.840124451674579	1		354	774	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224252	53224252	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	301	332	0	ENST00000375401.3:c.3301-2A>T		p.X1101_splice	ENST00000375401	NM_004187.3	1101			0.292080617795125	1	FACETS	0.494	0.467	0.522	0.494	0.467	0.522	INDETERMINATE	1	TRUE	0	0.840124451674579	1		332	841	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226069	53226069	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	267	315	0	ENST00000375401.3:c.2780A>T	p.Gln927Leu	p.Q927L	ENST00000375401	NM_004187.3	927	cAg/cTg	19/26	0.292080617795125	1	FACETS	0.487	0.458	0.516	0.487	0.458	0.516	INDETERMINATE	1	TRUE	0	0.840124451674579	1		315	757	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53241068	53241068	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	346	255	0	ENST00000375401.3:c.1143A>T	p.Glu381Asp	p.E381D	ENST00000375401	NM_004187.3	381	gaA/gaT	9/26	0.292080617795125	1	FACETS	0.624	0.595	0.654	0.624	0.595	0.654	INDETERMINATE	1	TRUE	0	0.840124451674579	1		255	765	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411143	63411143	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	289	341	0	ENST00000330258.3:c.2024A>T	p.Gln675Leu	p.Q675L	ENST00000330258	NM_152424.3	675	cAg/cTg	2/2	0.292080617795125	1	FACETS	0.531	0.501	0.56	0.531	0.501	0.56	INDETERMINATE	1	TRUE	0	0.840124451674579	1		341	752	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339626	70339626	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	245	251	0	ENST00000374080.3:c.295A>T	p.Lys99Ter	p.K99*	ENST00000374080		99	Aag/Tag	3/45	0.292080617795125	1	FACETS	0.531	0.499	0.563	0.531	0.499	0.563	INDETERMINATE	1	TRUE	0	0.840124451674579	1		251	637	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76812976	76812976	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	183	170	0	ENST00000373344.5:c.6645A>T	p.Leu2215Phe	p.L2215F	ENST00000373344	NM_000489.3	2215	ttA/ttT	30/35	0.292080617795125	1	FACETS	0.564	0.526	0.602	0.564	0.526	0.602	INDETERMINATE	1	TRUE	0	0.840124451674579	1		170	448	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855000	76855000	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	224	156	0	ENST00000373344.5:c.5836A>T	p.Ser1946Cys	p.S1946C	ENST00000373344	NM_000489.3	1946	Agt/Tgt	25/35	0.292080617795125	1	FACETS	0.672	0.634	0.711	0.672	0.634	0.711	INDETERMINATE	1	TRUE	0	0.840124451674579	1		156	460	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937320	76937320	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	123	118	0	ENST00000373344.5:c.3428A>T	p.Lys1143Met	p.K1143M	ENST00000373344	NM_000489.3	1143	aAg/aTg	9/35	0.292080617795125	1	FACETS	0.487	0.445	0.529	0.487	0.445	0.529	INDETERMINATE	1	TRUE	0	0.840124451674579	1		118	349	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76949376	76949376	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059213-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	127	136	0	ENST00000373344.5:c.421T>A	p.Phe141Ile	p.F141I	ENST00000373344	NM_000489.3	141	Ttt/Att	6/35	0.292080617795125	1	FACETS	0.443	0.405	0.482	0.443	0.405	0.482	INDETERMINATE	1	TRUE	0	0.840124451674579	1		136	396	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0059239-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	29	412	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.350771199214634	1	FACETS	0.628	0.507	0.764	0.628	0.507	0.764	SUBCLONAL	1	TRUE	0	0.350771199214634	1		412	217	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059239-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	37	121	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.350771199214634	2		121	177	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746017	162746017	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059239-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	46	534	0	ENST00000367921.3:c.2140C>T	p.Arg714Ter	p.R714*	ENST00000367921	NM_006182.2	714	Cga/Tga	16/18	0.340164956754557	3	FACETS	0.826	0.698	0.968	0.413	0.349	0.484	CLONAL	1	TRUE	1	0.350771199214634	3		534	373	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207037	1207037	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059239-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	57	651	0	ENST00000326873.7:c.127del	p.Ala43ProfsTer8	p.A43Pfs*8	ENST00000326873	NM_000455.4	42	cGg/cg	1/10	0.350771199214634	1	FACETS	0.766	0.66	0.88	0.766	0.66	0.88	SUBCLONAL	1	TRUE	0	0.350771199214634	1		651	350	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575048	64575052	+	frameshift_variant	Frame_Shift_Del	DEL	CGAGT	CGAGT	-	novel	NA	P-0059239-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	55	588	0	ENST00000312049.6:c.755_759del	p.Asp252AlafsTer16	p.D252Afs*16	ENST00000312049	NM_130799.2	252	gACTCG/g	4/10	0.350771199214634	1	FACETS	0.686	0.589	0.791	0.686	0.589	0.791	SUBCLONAL	1	TRUE	0	0.350771199214634	1		588	377	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955548	48955570	+	frameshift_variant	Frame_Shift_Del	DEL	ATCGAATCATGGAATCCCTTGCA	ATCGAATCATGGAATCCCTTGCA	-	novel	NA	P-0059239-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	17	159	0	ENST00000267163.4:c.1664_1686del	p.His555LeufsTer9	p.H555Lfs*9	ENST00000267163	NM_000321.2	555	cATCGAATCATGGAATCCCTTGCA/c	17/27	0.350771199214634	1	FACETS	0.624	0.471	0.803	0.624	0.471	0.803	SUBCLONAL	1	TRUE	0	0.350771199214634	1		159	128	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577468	7577508	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCAGTGTGCAGGGTGGCAAGTGGCTCCTGACCTGGAGTCTT	CCAGTGTGCAGGGTGGCAAGTGGCTCCTGACCTGGAGTCTT	-	novel	NA	P-0059239-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	40	464	0	ENST00000269305.4:c.773_782+31del		p.X258_splice	ENST00000269305	NM_001126112.2	258		7/11	0.350771199214634	1	FACETS	0.712	0.596	0.841	0.712	0.596	0.841	SUBCLONAL	1	TRUE	0	0.350771199214634	1		464	264	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259309	89259309	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059239-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	32	438	0	ENST00000336596.2:c.455del	p.Phe152SerfsTer11	p.F152Sfs*11	ENST00000336596	NM_005233.5	151	agT/ag	3/17	1	2	FACETS	0.702	0.572	0.847	0.702	0.572	0.847	SUBCLONAL	1	TRUE	1	0.350771199214634	2		438	260	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059240-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	219	121	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.420829257803971	5	FACETS	0.956	0.896	1	0.956	0.896	1	CLONAL	3	TRUE	2	0.420829257803971	5		121	592	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912580	NA	P-0059240-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	101	409	0	ENST00000342988.3:c.1157G>A	p.Gly386Asp	p.G386D	ENST00000342988	NM_005359.5	386	gGt/gAt	10/12	0.420829257803971	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.420829257803971	1		409	354	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485824	8485824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs547908736	NA	P-0059240-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	179	402	0	ENST00000356435.5:c.2993C>T	p.Thr998Met	p.T998M	ENST00000356435		998	aCg/aTg	17/35	0.420829257803971	5	FACETS	0.825	0.761	0.891	0.55	0.507	0.594	CLONAL	2	TRUE	2	0.420829257803971	5		402	841	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578374	7578416	+	frameshift_variant	Frame_Shift_Del	DEL	CGCTATCTGAGCAGCGCTCATGGTGGGGGCAGCGCCTCACAAC	CGCTATCTGAGCAGCGCTCATGGTGGGGGCAGCGCCTCACAAC	-	novel	NA	P-0059240-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	297	661	0	ENST00000269305.4:c.514_556del	p.Val172MetfsTer61	p.V172Mfs*61	ENST00000269305	NM_001126112.2	172	GTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGat/at	5/11	0.420829257803971	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.420829257803971	2		661	684	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115956	8115956	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059244-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	297	597	0	ENST00000346208.3:c.1305del	p.Ser436ProfsTer39	p.S436Pfs*39	ENST00000346208		434	caC/ca	6/6	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.821036836420066	2		597	690	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820548	44820548	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059244-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	173	362	0	ENST00000377967.4:c.245del	p.Ser82PhefsTer2	p.S82Ffs*2	ENST00000377967	NM_021140.2	82	tCt/tt	3/29	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.821036836420066	2		362	408	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0059256-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	8127	635	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.689727796149216	34	FACETS	1	0.999	1	1	0.999	1	CLONAL	33	TRUE	1	0.689727796149216	34		635	8535	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126730	5126730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1437629509	NA	P-0059256-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	40	422	0	ENST00000381652.3:c.3338G>A	p.Arg1113His	p.R1113H	ENST00000381652	NM_004972.3	1113	cGc/cAc	25/25	0.691103280554857	2	FACETS	0.758	0.641	0.884	0.379	0.32	0.442	SUBCLONAL	1	TRUE	0	0.689727796149216	2		422	153	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0059256-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	974	882	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.691103280554857	4	FACETS	0.98	0.962	0.996	0.98	0.962	0.996	CLONAL	4	TRUE	0	0.689727796149216	4		882	1218	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268969	55268969	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059256-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	9926	775	49	ENST00000275493.2:c.3035A>T	p.Asp1012Val	p.D1012V	ENST00000275493	NM_005228.3	1012	gAt/gTt	25/28	0.689727796149216	34	FACETS	1	0.999	1	1	0.999	1	CLONAL	33	TRUE	1	0.689727796149216	34		824	10379	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475456	12475456	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059256-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	237	619	3	ENST00000287820.6:c.1330G>T	p.Ala444Ser	p.A444S	ENST00000287820	NM_015869.4	444	Gcc/Tcc	7/7	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.689727796149216	2		622	625	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778149	27778149	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059256-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1329	338	947	0	ENST00000369163.2:c.298T>A	p.Tyr100Asn	p.Y100N	ENST00000369163	NM_003536.2	100	Tac/Aac	1/1	0.671574476845585	4	FACETS	0.993	0.937	1	0.331	0.312	0.351	CLONAL	1	TRUE	1	0.689727796149216	4		947	1667	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578525	7578525	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519976	NA	P-0059257-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	99	664	0	ENST00000269305.4:c.405C>G	p.Cys135Trp	p.C135W	ENST00000269305	NM_001126112.2	135	tgC/tgG	5/11	0.0879902698045161	3	FACETS	1	0.979	1			1	INDETERMINATE	1	FALSE	NA	0.157930498593438	3		664	935	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005333	150005333	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059257-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	75	595	0	ENST00000253339.5:c.892G>T	p.Glu298Ter	p.E298*	ENST00000253339		298	Gag/Tag	3/7	0.157930498593438	1	FACETS	0.957	0.837	1	0.957	0.837	1	CLONAL	1	FALSE	0	0.157930498593438	1		595	914	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998189	169998189	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059257-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	51	368	0	ENST00000295797.4:c.880G>A	p.Glu294Lys	p.E294K	ENST00000295797	NM_002740.5	294	Gag/Aag	9/18	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	1	0.157930498593438	2		368	565	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434411	110434411	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059257-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	58	665	0	ENST00000375856.3:c.3990G>T	p.Leu1330Phe	p.L1330F	ENST00000375856	NM_003749.2	1330	ttG/ttT	1/2	0.157930498593438	1	FACETS	0.912	0.782	1	0.912	0.782	1	CLONAL	1	FALSE	0	0.157930498593438	1		665	742	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553350	41553350	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059257-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	51	457	0	ENST00000263253.7:c.3439G>T	p.Glu1147Ter	p.E1147*	ENST00000263253	NM_001429.3	1147	Gag/Tag	18/31	1	2	FACETS	0.799	0.678	0.934	0.799	0.678	0.934	CLONAL	1	FALSE	1	0.157930498593438	2		457	808	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505301	186505301	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059257-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	54	419	0	ENST00000323963.5:c.927G>C	p.Gln309His	p.Q309H	ENST00000323963		309	caG/caC	9/11	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	FALSE	1	0.157930498593438	2		419	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0059266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	253	613	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.636703843080356	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.636703843080356	2		614	362	SUCCESS
APC	324	MSKCC	GRCh37	5	112151291	112151291	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs876660765	NA	P-0059266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	46	141	0	ENST00000257430.4:c.933+1G>A		p.X311_splice	ENST00000257430	NM_000038.5	311			0.636703843080356	3	FACETS	1	0.901	1	0.535	0.457	0.618	CLONAL	1	TRUE	1	0.636703843080356	3		141	178	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0059266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	59	140	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.636703843080356	3	FACETS	0.82	0.723	0.919	0.82	0.723	0.919	CLONAL	2	TRUE	1	0.636703843080356	3		140	149	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913237	NA	P-0059266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	149	181	0	ENST00000369535.4:c.35G>T	p.Gly12Val	p.G12V	ENST00000369535	NM_002524.4	12	gGt/gTt	2/7	0.621523342476353	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.636703843080356	3		181	288	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196648	106196648	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	80	299	0	ENST00000380013.4:c.4981T>G	p.Tyr1661Asp	p.Y1661D	ENST00000380013	NM_001127208.2	1661	Tat/Gat	11/11	0.621523342476353	3	FACETS	1	0.928	1	0.529	0.47	0.591	CLONAL	1	TRUE	1	0.636703843080356	3		299	313	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976689	55976689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747477930	NA	P-0059266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	25	212	0	ENST00000263923.4:c.1136C>T	p.Ala379Val	p.A379V	ENST00000263923	NM_002253.2	379	gCg/gTg	9/30	0.621523342476353	3	FACETS	0.655	0.522	0.805	0.328	0.261	0.403	SUBCLONAL	1	TRUE	1	0.636703843080356	3		212	158	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437362	121437362	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059266-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	103	345	0	ENST00000257555.6:c.1700T>A	p.Val567Asp	p.V567D	ENST00000257555		567	gTc/gAc	9/10	0.621523342476353	3	FACETS	0.933	0.84	1	0.467	0.42	0.516	CLONAL	1	TRUE	1	0.636703843080356	3		345	457	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0059267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	230	390	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.734282516325479	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.821405844502229	3		390	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0059267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	286	318	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.821405844502229	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.821405844502229	2		318	326	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950303	38950303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561445386	NA	P-0059267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	221	253	0	ENST00000357387.3:c.3647G>A	p.Arg1216His	p.R1216H	ENST00000357387	NM_152756.3	1216	cGt/cAt	31/38	0.733655904573936	4	FACETS	0.994	0.935	1	0.994	0.935	1	CLONAL	2	TRUE	2	0.821405844502229	4		253	493	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562584	95562584	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059267-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	253	262	0	ENST00000393063.1:c.4673G>A	p.Ser1558Asn	p.S1558N	ENST00000393063	NM_030621.3	1558	aGc/aAc	24/28	0.821405844502229	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.821405844502229	3		262	380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0059268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	458	311	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.858002768062045	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.857150849136687	2		311	507	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069049	5069052	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs759468230	NA	P-0059268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	104	189	0	ENST00000381652.3:c.1356_1359del	p.Cys452Ter	p.C452*	ENST00000381652	NM_004972.3	452	TGTTtg/tg	11/25	0.858002768062045	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.857150849136687	1		189	128	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856023	111856023	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	176	280	0	ENST00000341259.2:c.74G>T	p.Gly25Val	p.G25V	ENST00000341259	NM_005475.2	25	gGc/gTc	2/8	0.858002768062045	2	FACETS	1	0.969	1	0.532	0.497	0.567	CLONAL	1	TRUE	0	0.857150849136687	2		280	386	SUCCESS
EED	8726	MSKCC	GRCh37	11	85979562	85979562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	139	165	0	ENST00000263360.6:c.925G>A	p.Val309Ile	p.V309I	ENST00000263360	NM_003797.3	309	Gtt/Att	9/12	0.858002768062045	2	FACETS	0.995	0.92	1	0.497	0.46	0.536	CLONAL	1	TRUE	0	0.857150849136687	2		165	326	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375161	118375163	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	novel	NA	P-0059268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	96	259	0	ENST00000534358.1:c.8556_8558del	p.Ile2852del	p.I2852del	ENST00000534358	NM_005933.3	2852	ATT/-	27/36	0.656775481419846	5	FACETS	0.691	0.615	0.771			1	SUBCLONAL	1	TRUE	NA	0.857150849136687	5		259	741	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608344	28608344	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	172	261	0	ENST00000241453.7:c.1712G>C	p.Arg571Thr	p.R571T	ENST00000241453	NM_004119.2	571	aGg/aCg	14/24	0.858002768062045	3	FACETS	1	0.969	1	0.542	0.502	0.583	CLONAL	1	TRUE	1	0.857150849136687	3		261	529	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918737	32918737	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555285151	NA	P-0059268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	86	126	0	ENST00000380152.3:c.6884G>C	p.Arg2295Thr	p.R2295T	ENST00000380152		2295	aGg/aCg	12/27	NA	2	FACETS	0.956	0.863	1			1	INDETERMINATE	1	TRUE	NA	0.857150849136687	2		126	210	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830797	3830797	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	172	231	0	ENST00000262367.5:c.1759G>C	p.Gly587Arg	p.G587R	ENST00000262367	NM_004380.2	587	Ggt/Cgt	8/31	0.858002768062045	3	FACETS	0.935	0.865	1	0.468	0.432	0.504	CLONAL	1	TRUE	1	0.857150849136687	3		231	613	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971292	15971293	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0059268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	192	268	0	ENST00000268712.3:c.4656_4657del	p.Gly1553GlnfsTer63	p.G1553Qfs*63	ENST00000268712	NM_006311.3	1552	agAGgc/aggc	32/46	0.858002768062045	2	FACETS	1	0.962	1	0.519	0.485	0.552	CLONAL	1	TRUE	0	0.857150849136687	2		268	432	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41258492	41258493	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0059268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	215	129	0	ENST00000357654.3:c.192dup	p.Lys65Ter	p.K65*	ENST00000357654	NM_007294.3	64	-/T	4/23	0.858002768062045	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.857150849136687	2		129	244	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056650	26056650	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	98	242	0	ENST00000343677.2:c.7G>C	p.Glu3Gln	p.E3Q	ENST00000343677	NM_005319.3	3	Gag/Cag	1/1	0.610967173959198	3	FACETS	0.672	0.602	0.746			1	SUBCLONAL	1	TRUE	NA	0.857150849136687	3		242	486	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981650	70981651	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0059268-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	162	310	0	ENST00000276594.2:c.445_446del	p.Leu149AsnfsTer13	p.L149Nfs*13	ENST00000276594	NM_024504.3	149	TTa/a	2/8	0.858002768062045	5	FACETS	0.956	0.877	1	0.239	0.219	0.26	CLONAL	1	TRUE	1	0.857150849136687	5		310	904	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	36	121	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.953	0.796	1	0.953	0.796	1	CLONAL	1	TRUE	1	0.500086412542204	2		121	151	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805011	43805011	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	31	280	0	ENST00000372470.3:c.461G>A	p.Trp154Ter	p.W154*	ENST00000372470	NM_005373.2	154	tGg/tAg	4/12	0.296459947648612	1	FACETS	0.352	0.286	0.427	0.352	0.286	0.427	INDETERMINATE	1	TRUE	0	0.500086412542204	1		280	264	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576098	88576098	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	60	246	0	ENST00000360948.2:c.1575G>T	p.Lys525Asn	p.K525N	ENST00000360948	NM_001012338.2	525	aaG/aaT	13/19	1	2	FACETS	0.919	0.8	1	0.919	0.8	1	CLONAL	1	TRUE	1	0.500086412542204	2		246	261	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207013	1207014	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0059269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	68	297	0	ENST00000326873.7:c.102dup	p.Ile35HisfsTer128	p.I35Hfs*128	ENST00000326873	NM_000455.4	34	gtc/gtCc	1/10	0.500086412542204	1	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	0	0.500086412542204	1		297	204	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451920	29451920	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	58	258	0	ENST00000389048.3:c.2645G>C	p.Gly882Ala	p.G882A	ENST00000389048	NM_004304.4	882	gGc/gCc	16/29	1	2	FACETS	0.966	0.84	1	0.966	0.84	1	CLONAL	1	TRUE	1	0.500086412542204	2		258	240	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372028	55372028	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	62	385	0	ENST00000297316.4:c.718C>A	p.Pro240Thr	p.P240T	ENST00000297316	NM_022454.3	240	Ccg/Acg	2/2	1	2	FACETS	0.915	0.798	1	0.915	0.798	1	CLONAL	1	TRUE	1	0.500086412542204	2		385	271	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390804	139390804	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059269-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	171	487	0	ENST00000277541.6:c.7387G>T	p.Ala2463Ser	p.A2463S	ENST00000277541	NM_017617.3	2463	Gcc/Tcc	34/34	0.500086412542204	2	FACETS	0.963	0.9	1	0.963	0.9	1	CLONAL	2	TRUE	0	0.500086412542204	2		487	355	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059271-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	23	121	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.636	0.497	0.796	0.636	0.497	0.796	SUBCLONAL	1	TRUE	1	0.284558836295389	2		121	254	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813315	102813315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761462868	NA	P-0059271-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	37	284	0	ENST00000307046.8:c.374G>A	p.Arg125His	p.R125H	ENST00000307046	NM_001111285.1	125	cGc/cAc	3/4	1	2	FACETS	0.403	0.331	0.484	0.403	0.331	0.484	SUBCLONAL	1	TRUE	1	0.284558836295389	2		284	645	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966791	18966791	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059271-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	35	243	0	ENST00000262803.5:c.1603del	p.His535ThrfsTer5	p.H535Tfs*5	ENST00000262803	NM_002911.3	534	atC/at	12/24	1	2	FACETS	0.41	0.335	0.494	0.41	0.335	0.494	SUBCLONAL	1	TRUE	1	0.284558836295389	2		243	600	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163720	32163720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253487294	NA	P-0059272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	34	319	0	ENST00000375023.3:c.5506G>A	p.Glu1836Lys	p.E1836K	ENST00000375023	NM_004557.3	1836	Gag/Aag	30/30	0.2153251736276	2	FACETS	0.636	0.52	0.766	0.318	0.26	0.383	SUBCLONAL	1	TRUE	0	0.271343651251691	2		319	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0059272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	64	261	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.271343651251691	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.271343651251691	1		261	353	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436088	49436088	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	84	337	0	ENST00000301067.7:c.5893G>T	p.Glu1965Ter	p.E1965*	ENST00000301067	NM_003482.3	1965	Gaa/Taa	28/54	0.260466720181205	3	FACETS	0.797	0.707	0.893	0.797	0.707	0.893	SUBCLONAL	2	TRUE	1	0.271343651251691	3		337	441	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433896	49433896	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	89	539	0	ENST00000301067.7:c.7657C>T	p.Gln2553Ter	p.Q2553*	ENST00000301067	NM_003482.3	2553	Cag/Tag	31/54	0.260466720181205	3	FACETS	1	0.944	1	0.552	0.489	0.619	CLONAL	1	TRUE	1	0.271343651251691	3		539	675	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435666	18435666	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	26	232	0	ENST00000266497.5:c.651G>A	p.Trp217Ter	p.W217*	ENST00000266497		217	tgG/tgA	1/31	1	2	FACETS	0.687	0.545	0.848	0.687	0.545	0.848	SUBCLONAL	1	TRUE	1	0.271343651251691	2		232	279	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55729496	55729496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747741239	NA	P-0059272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	88	307	0	ENST00000284073.2:c.764C>T	p.Ala255Val	p.A255V	ENST00000284073	NM_138962.2	255	gCg/gTg	11/14	0.266033612616886	2	FACETS	1	0.978	1	0.729	0.649	0.813	CLONAL	1	TRUE	0	0.271343651251691	2		307	445	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204511914	204511914	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	19	153	0	ENST00000367182.3:c.514G>A	p.Glu172Lys	p.E172K	ENST00000367182	NM_001278516.1	172	Gaa/Aaa	8/11	0.266033612616886	2	FACETS	0.625	0.476	0.8	0.313	0.238	0.4	SUBCLONAL	1	TRUE	0	0.271343651251691	2		153	224	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200595	67200595	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0059272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	120	381	0	ENST00000312629.5:c.708-2A>T		p.X236_splice	ENST00000312629	NM_003952.2	236			0.2153251736276	2	FACETS	0.841	0.763	0.922	0.841	0.763	0.922	CLONAL	2	TRUE	0	0.271343651251691	2		381	526	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433935	49433935	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	88	515	0	ENST00000301067.7:c.7618C>G	p.Gln2540Glu	p.Q2540E	ENST00000301067	NM_003482.3	2540	Cag/Gag	31/54	0.260466720181205	3	FACETS	1	0.952	1	0.568	0.504	0.637	CLONAL	1	TRUE	1	0.271343651251691	3		515	648	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434189	49434189	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	92	556	0	ENST00000301067.7:c.7364C>T	p.Ser2455Leu	p.S2455L	ENST00000301067	NM_003482.3	2455	tCa/tTa	31/54	0.260466720181205	3	FACETS	1	0.954	1	0.57	0.507	0.638	CLONAL	1	TRUE	1	0.271343651251691	3		556	675	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492347	56492347	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	88	271	0	ENST00000267101.3:c.2680G>T	p.Val894Phe	p.V894F	ENST00000267101	NM_001982.3	894	Gtc/Ttc	22/28	0.260466720181205	3	FACETS	0.89	0.793	0.992	0.89	0.793	0.992	CLONAL	2	TRUE	1	0.271343651251691	3		271	414	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860676	3860676	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	33	246	0	ENST00000262367.5:c.903G>C	p.Gln301His	p.Q301H	ENST00000262367	NM_004380.2	301	caG/caC	3/31	0.252473069329177	4	FACETS	0.801	0.653	0.968	0.267	0.217	0.323	CLONAL	1	TRUE	1	0.271343651251691	4		246	386	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973505	15973505	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1282845414	NA	P-0059272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	25	249	0	ENST00000268712.3:c.4487C>T	p.Ser1496Leu	p.S1496L	ENST00000268712	NM_006311.3	1496	tCa/tTa	31/46	0.271343651251691	1	FACETS	0.54	0.426	0.67	0.54	0.426	0.67	SUBCLONAL	1	TRUE	0	0.271343651251691	1		249	295	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25498371	25498371	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	20	190	0	ENST00000264709.3:c.490G>C	p.Glu164Gln	p.E164Q	ENST00000264709	NM_175629.2	164	Gag/Cag	5/23	0.271343651251691	3	FACETS	0.492	0.376	0.629	0.246	0.188	0.315	SUBCLONAL	1	TRUE	1	0.271343651251691	3		190	340	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259416	89259416	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	39	240	0	ENST00000336596.2:c.560G>C	p.Gly187Ala	p.G187A	ENST00000336596	NM_005233.5	187	gGt/gCt	3/17	NA	2	FACETS	0.821	0.682	0.975			1	INDETERMINATE	1	TRUE	NA	0.271343651251691	2		240	350	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215946	142215946	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	54	188	0	ENST00000350721.4:c.5647T>G	p.Trp1883Gly	p.W1883G	ENST00000350721	NM_001184.3	1883	Tgg/Ggg	33/47	0.266033612616886	2	FACETS	1	0.959	1	0.668	0.574	0.769	CLONAL	1	TRUE	0	0.271343651251691	2		188	298	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191392	185191392	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	46	381	0	ENST00000265026.3:c.2273C>A	p.Ser758Tyr	p.S758Y	ENST00000265026	NM_004721.4	758	tCc/tAc	11/14	0.256536201566356	4	FACETS	0.76	0.64	0.894	0.19	0.16	0.224	SUBCLONAL	1	TRUE	0	0.271343651251691	4		381	567	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31464408	31464408	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	37	177	0	ENST00000344624.3:c.2509G>C	p.Glu837Gln	p.E837Q	ENST00000344624		837	Gaa/Caa	17/33	0.260466720181205	3	FACETS	0.75	0.619	0.897	0.375	0.309	0.449	SUBCLONAL	1	TRUE	1	0.271343651251691	3		177	413	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206834	162206834	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	82	255	0	ENST00000366898.1:c.841C>A	p.Pro281Thr	p.P281T	ENST00000366898	NM_004562.2	281	Cct/Act	7/12	1	2	FACETS	0.808	0.717	0.904	1	0.981	1	CLONAL	2	TRUE	1	0.271343651251691	2		255	374	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896531	151896531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	21	164	0	ENST00000262189.6:c.4106G>A	p.Gly1369Glu	p.G1369E	ENST00000262189	NM_170606.2	1369	gGa/gAa	27/59	0.26664319453265	3	FACETS	0.803	0.62	1	0.401	0.31	0.507	CLONAL	1	TRUE	1	0.271343651251691	3		164	219	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482285	87482285	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	28	289	0	ENST00000277120.3:c.1572C>G	p.Ile524Met	p.I524M	ENST00000277120		524	atC/atG	14/19	0.266033612616886	2	FACETS	0.473	0.378	0.583	0.237	0.189	0.292	SUBCLONAL	1	TRUE	0	0.271343651251691	2		289	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555526101	NA	P-0059273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	282	290	0	ENST00000269305.4:c.497C>G	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tGa	5/11	0.374098381247572	3	FACETS	1	0.989	1	0.781	0.739	0.823	CLONAL	2	TRUE	0	0.448073056261287	3		290	658	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279130	142279130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	35	178	0	ENST00000350721.4:c.1516C>A	p.His506Asn	p.H506N	ENST00000350721	NM_001184.3	506	Cat/Aat	6/47	0.330371392942059	5	FACETS	1	0.944	1	0.463	0.383	0.551	CLONAL	1	TRUE	2	0.448073056261287	5		178	188	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962783	2962783	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	36	164	0	ENST00000396946.4:c.2125G>C	p.Gly709Arg	p.G709R	ENST00000396946	NM_032415.4	709	Ggc/Cgc	16/25	0.448073056261287	4	FACETS	0.508	0.417	0.61	0.169	0.139	0.204	SUBCLONAL	1	TRUE	1	0.448073056261287	4		164	458	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564110	139564110	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059273-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	53	262	0	ENST00000308874.7:c.250C>T	p.Pro84Ser	p.P84S	ENST00000308874		84	Cct/Tct	5/10	0.328499349492059	2	FACETS	0.686	0.587	0.792	0.343	0.293	0.396	SUBCLONAL	1	TRUE	0	0.448073056261287	2		262	345	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	121	228	0	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.979	0.89	1	0.979	0.89	1	CLONAL	1	TRUE	1	0.537615359300899	2		228	460	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	39	156	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.477	0.397	0.566	0.477	0.397	0.566	SUBCLONAL	1	TRUE	1	0.537615359300899	2		160	304	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	27	148	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.507	0.406	0.621	0.507	0.406	0.621	SUBCLONAL	1	TRUE	1	0.537615359300899	2		148	198	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	138	190	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.309114441852116	2	FACETS	1	0.931	1	0.509	0.466	0.554	INDETERMINATE	1	TRUE	0	0.537615359300899	2		190	504	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	62	298	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.318242004670925	1	FACETS	0.403	0.349	0.462	0.403	0.349	0.462	INDETERMINATE	1	TRUE	0	0.537615359300899	1		298	418	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	71	281	0	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.429	0.375	0.489	0.429	0.375	0.489	SUBCLONAL	1	TRUE	1	0.537615359300899	2		281	615	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863271	56863271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752739111	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	168	185	2	ENST00000519728.1:c.415G>A	p.Ala139Thr	p.A139T	ENST00000519728	NM_002350.3	139	Gca/Aca	6/13	0.537615359300899	3	FACETS	0.838	0.777	0.901	0.838	0.777	0.901	CLONAL	2	TRUE	1	0.537615359300899	3		187	473	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	35	115	0	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	0.587	0.484	0.699	0.587	0.484	0.699	SUBCLONAL	1	TRUE	1	0.537615359300899	2		115	222	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	115	291	1	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	1	2	FACETS	0.685	0.618	0.755	0.685	0.618	0.755	SUBCLONAL	1	TRUE	1	0.537615359300899	2		292	625	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744385	41744385	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	74	247	0	ENST00000301178.4:c.1010del	p.Pro337LeufsTer29	p.P337Lfs*29	ENST00000301178	NM_021913.4	335	ggC/gg	8/20	1	2	FACETS	0.581	0.51	0.657	0.581	0.51	0.657	SUBCLONAL	1	TRUE	1	0.537615359300899	2		247	474	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912149	114912149	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	61	185	0	ENST00000543371.1:c.1219C>T	p.Arg407Ter	p.R407*	ENST00000543371	NM_001198531.1	407	Cga/Tga	11/14	1	2	FACETS	0.515	0.445	0.59	0.515	0.445	0.59	SUBCLONAL	1	TRUE	1	0.537615359300899	2		185	441	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512401	38512402	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs745553450	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	60	248	1	ENST00000254066.5:c.1319dup	p.Pro441AlafsTer5	p.P441Afs*5	ENST00000254066	NM_000964.3	438	gcc/gCcc	9/9	1	2	FACETS	0.537	0.464	0.615	0.537	0.464	0.615	SUBCLONAL	1	TRUE	1	0.537615359300899	2		249	416	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123837	46123837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	65	220	0	ENST00000334344.6:c.109del	p.Ile37SerfsTer21	p.I37Sfs*21	ENST00000334344	NM_152641.2	35	Aaa/aa	2/21	1	2	FACETS	0.526	0.457	0.6	0.526	0.457	0.6	SUBCLONAL	1	TRUE	1	0.537615359300899	2		220	460	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971324	13971324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752431857	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	118	273	0	ENST00000405192.2:c.605C>T	p.Thr202Met	p.T202M	ENST00000405192	NM_001163147.1	202	aCg/aTg	8/12	1	2	FACETS	0.623	0.562	0.686	0.623	0.562	0.686	SUBCLONAL	1	TRUE	1	0.537615359300899	2		273	705	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173696	108173696	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	27	169	0	ENST00000278616.4:c.5441del	p.Leu1814TrpfsTer14	p.L1814Wfs*14	ENST00000278616	NM_000051.3	1812	gcT/gc	36/63	1	2	FACETS	0.391	0.312	0.48	0.391	0.312	0.48	SUBCLONAL	1	TRUE	1	0.537615359300899	2		169	257	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663406	67663406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775874494	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	83	205	1	ENST00000264010.4:c.1807C>T	p.Arg603Cys	p.R603C	ENST00000264010	NM_006565.3	603	Cgc/Tgc	10/12	1	2	FACETS	0.658	0.583	0.738	0.658	0.583	0.738	SUBCLONAL	1	TRUE	1	0.537615359300899	2		206	469	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256409	46256409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754382773	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	62	203	0	ENST00000371998.3:c.637G>A	p.Ala213Thr	p.A213T	ENST00000371998		213	Gcc/Acc	7/23	1	2	FACETS	0.51	0.442	0.584	0.51	0.442	0.584	SUBCLONAL	1	TRUE	1	0.537615359300899	2		203	452	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912075	50912077	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs398122386	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	32	333	0	ENST00000440232.2:c.1812_1814del	p.Ser605del	p.S605del	ENST00000440232	NM_002691.3	603	ttCTCc/ttc	15/27	1	2	FACETS	0.189	0.153	0.23	0.189	0.153	0.23	SUBCLONAL	1	TRUE	1	0.537615359300899	2		333	630	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231610	5231611	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	33	107	0	ENST00000357368.4:c.1865dup	p.Gln623SerfsTer4	p.Q623Sfs*4	ENST00000357368	NM_002850.3	622	cct/ccCt	14/38	1	2	FACETS	0.529	0.434	0.635	0.529	0.434	0.635	SUBCLONAL	1	TRUE	1	0.537615359300899	2		107	232	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944308	81944308	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	72	254	0	ENST00000359376.3:c.1921del	p.His641ThrfsTer11	p.H641Tfs*11	ENST00000359376	NM_002661.3	639	aaC/aa	18/33	1	2	FACETS	0.463	0.404	0.525	0.463	0.404	0.525	SUBCLONAL	1	TRUE	1	0.537615359300899	2		254	579	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089123	37089125	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs63751247	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	138	210	0	ENST00000231790.2:c.1852_1854del	p.Lys618del	p.K618del	ENST00000231790	NM_000249.3	615	ctGAAg/ctg	16/19	0.309114441852116	2	FACETS	1	0.975	1	0.581	0.533	0.63	INDETERMINATE	1	TRUE	0	0.537615359300899	2		210	442	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871130	12871131	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	26	260	0	ENST00000228872.4:c.361dup	p.Ala121GlyfsTer4	p.A121Gfs*4	ENST00000228872	NM_004064.3	119	-/G	1/3	1	2	FACETS	0.196	0.155	0.244	0.196	0.155	0.244	SUBCLONAL	1	TRUE	1	0.537615359300899	2		260	493	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216189	36216189	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	79	328	1	ENST00000222270.7:c.3602del	p.Pro1201ArgfsTer154	p.P1201Rfs*154	ENST00000222270	NM_014727.1	1199	ggC/gg	11/37	1	2	FACETS	0.481	0.423	0.543	0.481	0.423	0.543	SUBCLONAL	1	TRUE	1	0.537615359300899	2		329	611	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821381	72821382	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	35	232	1	ENST00000268489.5:c.10793dup	p.Pro3599SerfsTer67	p.P3599Sfs*67	ENST00000268489	NM_006885.3	3598	cct/ccCt	10/10	1	2	FACETS	0.298	0.244	0.359	0.298	0.244	0.359	SUBCLONAL	1	TRUE	1	0.537615359300899	2		233	437	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286238	66286238	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	53	178	0	ENST00000273854.3:c.1448del	p.Asn483ThrfsTer18	p.N483Tfs*18	ENST00000273854	NM_004439.5	483	aAc/ac	6/18	1	2	FACETS	0.628	0.539	0.725	0.628	0.539	0.725	SUBCLONAL	1	TRUE	1	0.537615359300899	2		178	314	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395746	45395746	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	84	252	0	ENST00000262160.6:c.388C>T	p.Arg130Ter	p.R130*	ENST00000262160	NM_005901.5	130	Cga/Tga	4/11	1	2	FACETS	0.651	0.577	0.73	0.651	0.577	0.73	SUBCLONAL	1	TRUE	1	0.537615359300899	2		252	480	SUCCESS
APC	324	MSKCC	GRCh37	5	112176350	112176350	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554086415	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	46	184	0	ENST00000257430.4:c.5059C>T	p.Arg1687Ter	p.R1687*	ENST00000257430	NM_000038.5	1687	Cga/Tga	16/16	1	2	FACETS	0.392	0.331	0.461	0.392	0.331	0.461	SUBCLONAL	1	TRUE	1	0.537615359300899	2		184	436	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604298	189604298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138832017	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	63	249	0	ENST00000264731.3:c.1465G>A	p.Ala489Thr	p.A489T	ENST00000264731	NM_003722.4	489	Gcc/Acc	11/14	1	2	FACETS	0.426	0.369	0.488	0.426	0.369	0.488	SUBCLONAL	1	TRUE	1	0.537615359300899	2		249	550	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086121	16086121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	80	235	0	ENST00000281043.3:c.1297C>T	p.Leu433Phe	p.L433F	ENST00000281043	NM_005378.4	433	Ctc/Ttc	3/3	1	2	FACETS	0.593	0.523	0.667	0.593	0.523	0.667	SUBCLONAL	1	TRUE	1	0.537615359300899	2		235	502	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471080	8471080	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	42	167	0	ENST00000356435.5:c.3419A>G	p.Tyr1140Cys	p.Y1140C	ENST00000356435		1140	tAc/tGc	20/35	1	2	FACETS	0.581	0.488	0.683	0.581	0.488	0.683	SUBCLONAL	1	TRUE	1	0.537615359300899	2		167	269	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541697	120541697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs984926660	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	79	239	0	ENST00000229340.5:c.160G>A	p.Gly54Arg	p.G54R	ENST00000229340	NM_006861.6	54	Ggg/Agg	3/6	1	2	FACETS	0.458	0.403	0.518	0.458	0.403	0.518	SUBCLONAL	1	TRUE	1	0.537615359300899	2		239	641	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45423105	45423105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1341462958	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	79	230	0	ENST00000262160.6:c.23C>T	p.Thr8Met	p.T8M	ENST00000262160	NM_005901.5	8	aCg/aTg	2/11	1	2	FACETS	0.54	0.476	0.609	0.54	0.476	0.609	SUBCLONAL	1	TRUE	1	0.537615359300899	2		230	544	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1685614	1685614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758300151	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	97	287	0	ENST00000378625.1:c.1412C>T	p.Ala471Val	p.A471V	ENST00000378625	NM_001198994.1	471	gCg/gTg	12/14	1	2	FACETS	0.545	0.486	0.608	0.545	0.486	0.608	SUBCLONAL	1	TRUE	1	0.537615359300899	2		287	662	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798487	45798487	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	107	305	0	ENST00000450313.1:c.524C>T	p.Ala175Val	p.A175V	ENST00000450313	NM_012222.2	175	gCt/gTt	7/16	1	2	FACETS	0.567	0.509	0.629	0.567	0.509	0.629	SUBCLONAL	1	TRUE	1	0.537615359300899	2		305	702	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47594943	47594943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747054418	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	82	272	0	ENST00000430070.2:c.1144G>A	p.Val382Met	p.V382M	ENST00000430070	NM_018095.4	382	Gtg/Atg	4/4	1	2	FACETS	0.474	0.418	0.534	0.474	0.418	0.534	SUBCLONAL	1	TRUE	1	0.537615359300899	2		272	644	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023686	1023686	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	80	225	0	ENST00000358495.3:c.878C>T	p.Ala293Val	p.A293V	ENST00000358495	NM_134424.2	293	gCc/gTc	10/12	1	2	FACETS	0.615	0.543	0.692	0.615	0.543	0.692	SUBCLONAL	1	TRUE	1	0.537615359300899	2		225	484	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039443	49039443	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	49	195	0	ENST00000267163.4:c.2428A>G	p.Lys810Glu	p.K810E	ENST00000267163	NM_000321.2	810	Aag/Gag	23/27	1	2	FACETS	0.445	0.377	0.518	0.445	0.377	0.518	SUBCLONAL	1	TRUE	1	0.537615359300899	2		195	410	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437296	110437296	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	24	63	0	ENST00000375856.3:c.1105G>T	p.Gly369Cys	p.G369C	ENST00000375856	NM_003749.2	369	Ggc/Tgc	1/2	1	2	FACETS	0.75	0.598	0.92	0.75	0.598	0.92	CLONAL	1	TRUE	1	0.537615359300899	2		63	119	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346830	91346831	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	44	162	0	ENST00000355112.3:c.3443dup	p.Leu1149AlafsTer4	p.L1149Afs*4	ENST00000355112	NM_000057.2	1146	-/A	18/22	1	2	FACETS	0.533	0.449	0.625	0.533	0.449	0.625	SUBCLONAL	1	TRUE	1	0.537615359300899	2		162	307	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106241	2106241	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555498571	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	59	146	0	ENST00000219476.3:c.644T>C	p.Ile215Thr	p.I215T	ENST00000219476	NM_000548.3	215	aTa/aCa	7/42	1	2	FACETS	0.634	0.549	0.727	0.634	0.549	0.727	SUBCLONAL	1	TRUE	1	0.537615359300899	2		146	346	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829188	72829188	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	101	328	0	ENST00000268489.5:c.7393A>G	p.Asn2465Asp	p.N2465D	ENST00000268489	NM_006885.3	2465	Aac/Gac	9/10	1	2	FACETS	0.6	0.537	0.667	0.6	0.537	0.667	SUBCLONAL	1	TRUE	1	0.537615359300899	2		328	626	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992075	72992075	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	79	289	0	ENST00000268489.5:c.1970G>A	p.Gly657Asp	p.G657D	ENST00000268489	NM_006885.3	657	gGc/gAc	2/10	1	2	FACETS	0.511	0.45	0.577	0.511	0.45	0.577	SUBCLONAL	1	TRUE	1	0.537615359300899	2		289	575	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16052817	16052817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	27	118	0	ENST00000268712.3:c.857G>A	p.Arg286Lys	p.R286K	ENST00000268712	NM_006311.3	286	aGg/aAg	9/46	1	2	FACETS	0.717	0.579	0.871	0.717	0.579	0.871	SUBCLONAL	1	TRUE	1	0.537615359300899	2		118	140	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63537661	63537661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202108391	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	70	164	0	ENST00000307078.5:c.971C>T	p.Pro324Leu	p.P324L	ENST00000307078	NM_004655.3	324	cCt/cTt	4/11	1	2	FACETS	0.553	0.483	0.628	0.553	0.483	0.628	SUBCLONAL	1	TRUE	1	0.537615359300899	2		164	471	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795250	42795250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	88	266	0	ENST00000575354.2:c.2330C>T	p.Ala777Val	p.A777V	ENST00000575354	NM_015125.3	777	gCt/gTt	10/20	1	2	FACETS	0.632	0.561	0.707	0.632	0.561	0.707	SUBCLONAL	1	TRUE	1	0.537615359300899	2		266	518	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855846	45855846	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	114	350	0	ENST00000391945.4:c.1964A>G	p.Asp655Gly	p.D655G	ENST00000391945	NM_000400.3	655	gAt/gGt	21/23	1	2	FACETS	0.591	0.532	0.653	0.591	0.532	0.653	SUBCLONAL	1	TRUE	1	0.537615359300899	2		350	718	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981798	63981798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369874836	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	97	367	1	ENST00000398590.3:c.2300C>T	p.Ala767Val	p.A767V	ENST00000398590	NM_001177387.1	767	gCg/gTg	12/14	1	2	FACETS	0.528	0.47	0.588	0.528	0.47	0.588	SUBCLONAL	1	TRUE	1	0.537615359300899	2		368	684	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156506	55156506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs267600189	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	58	189	0	ENST00000257290.5:c.2907C>A	p.Phe969Leu	p.F969L	ENST00000257290	NM_006206.4	969	ttC/ttA	22/23	1	2	FACETS	0.488	0.42	0.562	0.488	0.42	0.562	SUBCLONAL	1	TRUE	1	0.537615359300899	2		189	442	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293432	1293432	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1060503014	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	54	199	0	ENST00000310581.5:c.1569C>G	p.Ser523Arg	p.S523R	ENST00000310581	NM_198253.2	523	agC/agG	2/16	1	2	FACETS	0.482	0.412	0.557	0.482	0.412	0.557	SUBCLONAL	1	TRUE	1	0.537615359300899	2		199	417	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848652	151848652	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059274-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	45	176	0	ENST00000262189.6:c.12541A>G	p.Lys4181Glu	p.K4181E	ENST00000262189	NM_170606.2	4181	Aag/Gag	50/59	1	2	FACETS	0.5	0.421	0.586	0.5	0.421	0.586	SUBCLONAL	1	TRUE	1	0.537615359300899	2		176	335	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629912	187629913	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0059283-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	21	471	0	ENST00000441802.2:c.1069_1070insA	p.Ser357TyrfsTer12	p.S357Yfs*12	ENST00000441802	NM_005245.3	357	tct/tAct	2/27	1	2	FACETS	1	0.798	1	1	0.798	1	CLONAL	1	TRUE	1	0.14	2		471	289	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225556	2225556	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059284-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	26	536	0	ENST00000326181.6:c.1559A>G	p.Asn520Ser	p.N520S	ENST00000326181	NM_032271.2	520	aAc/aGc	17/21	0.136064937494306	0	FACETS	1	0.87	1			1	INDETERMINATE	1	TRUE	0	0.26	0		536	133	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0059286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	143	185	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.77	2		185	333	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0059286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	271	505	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.897	0.845	0.95	0.897	0.845	0.95	CLONAL	1	TRUE	1	0.77	2		505	785	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519886	NA	P-0059286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	329	454	0	ENST00000349496.5:c.97T>G	p.Ser33Ala	p.S33A	ENST00000349496	NM_001904.3	33	Tct/Gct	3/15	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.77	2		454	766	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994138	21994138	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	541	440	0	ENST00000579755.1:c.193G>A	p.Gly65Ser	p.G65S	ENST00000579755		65	Ggt/Agt	1/3	0.3		FACETS		0.963	1				INDETERMINATE	2	TRUE	0	0.77	2		440	711	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097641	27097641	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	258	486	2	ENST00000324856.7:c.3230C>A	p.Ala1077Glu	p.A1077E	ENST00000324856	NM_006015.4	1077	gCa/gAa	12/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.77	2		488	645	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342400	70342400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	260	454	0	ENST00000374080.3:c.1291C>T	p.Arg431Trp	p.R431W	ENST00000374080		431	Cgg/Tgg	9/45	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.77	2		454	671	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692899	89692909	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGACGAACT	AGGGACGAACT	-	novel	NA	P-0059286-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	282	283	0	ENST00000371953.3:c.383_393del	p.Lys128ArgfsTer48	p.K128Rfs*48	ENST00000371953	NM_000314.4	128	aAGGGACGAACT/a	5/9	0.3	2	FACETS	0.977	0.941	1	0.977	0.941	1	INDETERMINATE	2	TRUE	0	0.77	2		283	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0059287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	436	613	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.662519874453812	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	2	0.662519874453812	4		614	1092	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0059287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	417	599	0	ENST00000269305.4:c.672+1G>C		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.662519874453812	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.662519874453812	4		599	995	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0059288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	1118	704	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.930846341518487	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.930846341518487	2		704	1173	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944544	40944544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159842	NA	P-0059288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	183	377	0	ENST00000373198.4:c.1958G>A	p.Arg653Gln	p.R653Q	ENST00000373198	NM_133170.3	653	cGg/cAg	12/32	1	2	FACETS	0.491	0.454	0.53	0.491	0.454	0.53	SUBCLONAL	1	TRUE	1	0.930846341518487	2		377	801	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193967	106193967	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	253	261	0	ENST00000380013.4:c.4429G>C	p.Glu1477Gln	p.E1477Q	ENST00000380013	NM_001127208.2	1477	Gaa/Caa	10/11	0.930846341518487	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.930846341518487	1		261	287	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019658	123019658	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	137	254	0	ENST00000355640.3:c.146G>T	p.Arg49Leu	p.R49L	ENST00000355640		49	cGa/cTa	2/7	0.28012883752518	1	FACETS	0.356	0.326	0.387	0.356	0.326	0.387	INDETERMINATE	1	TRUE	0	0.930846341518487	1		254	442	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230473004	230473004	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	410	383	0	ENST00000391860.1:c.580C>T	p.Pro194Ser	p.P194S	ENST00000391860	NM_001258311.1	194	Cca/Tca	4/7	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.930846341518487	2		383	852	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575121	64575121	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	465	453	0	ENST00000312049.6:c.686G>T	p.Arg229Leu	p.R229L	ENST00000312049	NM_130799.2	229	cGc/cTc	4/10	1	2	FACETS	0.976	0.936	1	0.976	0.936	1	CLONAL	1	TRUE	1	0.930846341518487	2		453	1024	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77937627	77937627	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	362	295	0	ENST00000361507.4:c.1091C>A	p.Pro364His	p.P364H	ENST00000361507	NM_080491.2	364	cCt/cAt	4/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.930846341518487	2		295	756	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601284	28601284	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	161	175	0	ENST00000241453.7:c.2148G>C	p.Glu716Asp	p.E716D	ENST00000241453	NM_004119.2	716	gaG/gaC	17/24	0.930846341518487	1	FACETS	0.994	0.958	1	0.994	0.958	1	CLONAL	1	TRUE	0	0.930846341518487	1		175	186	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916743	48916743	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0059288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	134	53	0	ENST00000267163.4:c.273T>A	p.Tyr91Ter	p.Y91*	ENST00000267163	NM_000321.2	91	taT/taA	3/27	0.930846341518487	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.930846341518487	1		53	142	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944402	40944402	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	246	369	0	ENST00000373198.4:c.2100C>A	p.Ser700Arg	p.S700R	ENST00000373198	NM_133170.3	700	agC/agA	12/32	1	2	FACETS	0.934	0.881	0.987	0.934	0.881	0.987	CLONAL	1	TRUE	1	0.930846341518487	2		369	566	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038276	30038276	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0059288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	371	301	0	ENST00000338641.4:c.447+2T>G		p.X149_splice	ENST00000338641	NM_000268.3	149			0.930846341518487	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.930846341518487	1		301	403	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400047	139400047	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	616	506	0	ENST00000277541.6:c.4301del	p.Gly1434ValfsTer11	p.G1434Vfs*11	ENST00000277541	NM_017617.3	1434	gGt/gt	25/34	0.472889343820766	1	FACETS	0.636	0.615	0.656	0.636	0.615	0.656	INDETERMINATE	1	TRUE	0	0.930846341518487	1		506	1113	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932068	39932068	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	440	452	0	ENST00000378444.4:c.2531C>A	p.Pro844Gln	p.P844Q	ENST00000378444	NM_001123385.1	844	cCg/cAg	4/15	1	2	FACETS	0.785	0.75	0.821	0.785	0.75	0.821	SUBCLONAL	1	TRUE	1	0.930846341518487	2		452	1204	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223604	53223604	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	528	423	0	ENST00000375401.3:c.3755G>T	p.Arg1252Leu	p.R1252L	ENST00000375401	NM_004187.3	1252	cGc/cTc	23/26	0.414619553460097	1	FACETS	0.586	0.564	0.607	0.586	0.564	0.607	INDETERMINATE	1	TRUE	0	0.930846341518487	1		423	1035	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409931	63409931	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059288-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	381	521	0	ENST00000330258.3:c.3236del	p.Gly1079AlafsTer51	p.G1079Afs*51	ENST00000330258	NM_152424.3	1079	gGc/gc	2/2	0.414619553460097	1	FACETS	0.53	0.507	0.554	0.53	0.507	0.554	INDETERMINATE	1	TRUE	0	0.930846341518487	1		521	825	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0059289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	41	528	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.455	0.377	0.542	0.455	0.377	0.542	SUBCLONAL	1	TRUE	1	0.17	2		528	1060	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424174	47424174	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059289-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	47	393	0	ENST00000404338.3:c.2242G>T	p.Glu748Ter	p.E748*	ENST00000404338	NM_004491.4	748	Gaa/Taa	1/6	1	2	FACETS	0.736	0.62	0.866	0.736	0.62	0.866	SUBCLONAL	1	TRUE	1	0.17	2		393	751	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0059290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	160	329	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.494576312712614	5	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	2	0.494576312712614	5		329	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0059290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	425	613	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.491833622536016	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.494576312712614	3		614	673	SUCCESS
APC	324	MSKCC	GRCh37	5	112157627	112157628	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs1554080698	NA	P-0059290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	171	201	0	ENST00000257430.4:c.1354_1355del	p.Val452SerfsTer7	p.V452Sfs*7	ENST00000257430	NM_000038.5	449	gcTGtg/gctg	11/16	0.480486688755485	4	FACETS	1	0.973	1	0.802	0.752	0.852	CLONAL	3	TRUE	0	0.494576312712614	4		201	322	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907822	76907822	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	132	260	0	ENST00000373344.5:c.4339G>A	p.Glu1447Lys	p.E1447K	ENST00000373344	NM_000489.3	1447	Gag/Aag	15/35	0.494576312712614	6	FACETS	0.904	0.824	0.988	0.452	0.412	0.494	CLONAL	2	TRUE	2	0.494576312712614	6		260	587	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873640	35873640	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	180	298	0	ENST00000303115.3:c.596C>A	p.Ala199Glu	p.A199E	ENST00000303115	NM_002185.3	199	gCa/gAa	5/8	0.452499797994066	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.494576312712614	4		298	517	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751391	57751391	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	169	293	0	ENST00000274289.3:c.1600C>T	p.His534Tyr	p.H534Y	ENST00000274289	NM_006622.3	534	Cac/Tac	11/14	0.465309333435672	4	FACETS	0.867	0.801	0.935	0.434	0.4	0.468	CLONAL	2	TRUE	0	0.494576312712614	4		293	589	SUCCESS
APC	324	MSKCC	GRCh37	5	112157637	112157637	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1561546092	NA	P-0059290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	192	196	0	ENST00000257430.4:c.1357C>G	p.Leu453Val	p.L453V	ENST00000257430	NM_000038.5	453	Cta/Gta	11/16	0.480486688755485	4	FACETS	0.927	0.877	0.976	0.927	0.877	0.976	CLONAL	4	TRUE	0	0.494576312712614	4		196	313	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027684	152027684	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0059290-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	194	284	0	ENST00000262189.6:c.389+2T>C		p.X130_splice	ENST00000262189	NM_170606.2	130			0.452499797994066	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.494576312712614	4		284	542	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0059291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	31	329	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.101713407536859	4	FACETS	1	0.937	1	0.696	0.568	0.838	INDETERMINATE	1	TRUE	2	0.319313864672778	4		329	184	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0059291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	51	524	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	0.319313864672778	1	FACETS	0.991	0.849	1	0.991	0.849	1	CLONAL	1	TRUE	0	0.319313864672778	1		524	271	SUCCESS
APC	324	MSKCC	GRCh37	5	112175761	112175761	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	98	535	1	ENST00000257430.4:c.4473del	p.Phe1491LeufsTer16	p.F1491Lfs*16	ENST00000257430	NM_000038.5	1490	caT/ca	16/16	0.319313864672778	2	FACETS	0.959	0.865	1	0.959	0.865	1	CLONAL	2	TRUE	0	0.319313864672778	2		536	320	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395736	45395736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	56	516	0	ENST00000262160.6:c.398G>A	p.Arg133His	p.R133H	ENST00000262160	NM_005901.5	133	cGc/cAc	4/11	0.319313864672778	1	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	0	0.319313864672778	1		516	285	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729721	41729721	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	47	657	1	ENST00000242208.4:c.808A>G	p.Lys270Glu	p.K270E	ENST00000242208	NM_002192.2	270	Aaa/Gaa	3/3	1	2	FACETS	0.829	0.702	0.968	0.829	0.702	0.968	CLONAL	1	TRUE	1	0.319313864672778	2		658	355	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509200	106509200	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1399955792	NA	P-0059291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	50	622	0	ENST00000359195.3:c.1194A>T	p.Arg398Ser	p.R398S	ENST00000359195	NM_002649.2	398	agA/agT	2/11	1	2	FACETS	0.908	0.774	1	0.908	0.774	1	CLONAL	1	TRUE	1	0.319313864672778	2		622	345	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90995006	90995006	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059291-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	31	318	0	ENST00000265433.3:c.115C>T	p.Gln39Ter	p.Q39*	ENST00000265433	NM_002485.4	39	Cag/Tag	2/16	0.147215966815219	3	FACETS	1	0.829	1	0.509	0.415	0.615	INDETERMINATE	1	TRUE	1	0.319313864672778	3		318	221	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0059292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	54	293	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.995	0.87	1	0.995	0.87	1	CLONAL	1	TRUE	1	0.728600718587579	2		293	149	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0059292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	160	613	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.718754632836152	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.728600718587579	1		614	251	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216382	36216383	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0059292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	115	770	0	ENST00000222270.7:c.3648_3649dup	p.Phe1217CysfsTer139	p.F1217Cfs*139	ENST00000222270	NM_014727.1	1215	-/GT	12/37	1	2	FACETS	0.957	0.873	1	0.957	0.873	1	CLONAL	1	TRUE	1	0.728600718587579	2		770	330	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277844	41277844	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	82	560	0	ENST00000349496.5:c.1808T>G	p.Leu603Arg	p.L603R	ENST00000349496	NM_001904.3	603	cTt/cGt	12/15	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.728600718587579	2		560	225	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0059292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	109	600	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.872	0.792	0.955	0.872	0.792	0.955	CLONAL	1	TRUE	1	0.728600718587579	2		600	343	SUCCESS
APC	324	MSKCC	GRCh37	5	112175261	112175261	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	121	609	0	ENST00000257430.4:c.3971del	p.Pro1324GlnfsTer91	p.P1324Qfs*91	ENST00000257430	NM_000038.5	1324	Cca/ca	16/16	1	2	FACETS	0.966	0.883	1	0.966	0.883	1	CLONAL	1	TRUE	1	0.728600718587579	2		609	344	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223506	36223506	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059292-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	27	876	0	ENST00000222270.7:c.6056G>T	p.Gly2019Val	p.G2019V	ENST00000222270	NM_014727.1	2019	gGc/gTc	28/37	1	2	FACETS	0.193	0.153	0.239	0.193	0.153	0.239	SUBCLONAL	1	TRUE	1	0.728600718587579	2		876	384	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489582	56489582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56387488	NA	P-0059293-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	104	581	0	ENST00000267101.3:c.2047C>T	p.Arg683Trp	p.R683W	ENST00000267101	NM_001982.3	683	Cgg/Tgg	17/28	0.761222260329043	4	FACETS	1	0.972	1	0.603	0.544	0.663	CLONAL	1	TRUE	2	0.860831406389324	4		581	373	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933787	39933787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748212546	NA	P-0059293-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	10	740	0	ENST00000378444.4:c.812C>T	p.Ser271Leu	p.S271L	ENST00000378444	NM_001123385.1	271	tCg/tTg	4/15	0.779800003938621	1	FACETS	0.077	0.052	0.108	0.077	0.052	0.108	SUBCLONAL	1	TRUE	0	0.860831406389324	1		740	172	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436169	51436169	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059293-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	97	422	0	ENST00000262662.1:c.129G>T	p.Gln43His	p.Q43H	ENST00000262662		43	caG/caT	3/4	0.496094917536661	5	FACETS	1	0.957	1	0.377	0.337	0.418	INDETERMINATE	1	TRUE	2	0.860831406389324	5		422	457	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857812	89857812	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059293-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	85	509	0	ENST00000389301.3:c.1358A>T	p.Lys453Met	p.K453M	ENST00000389301	NM_000135.2	453	aAg/aTg	14/43	0.763717077806993	2	FACETS	0.89	0.801	0.98	0.445	0.4	0.49	CLONAL	1	TRUE	0	0.860831406389324	2		509	222	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579456	7579457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0059293-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	334	731	0	ENST00000269305.4:c.230dup	p.Ala78SerfsTer71	p.A78Sfs*71	ENST00000269305	NM_001126112.2	77	cca/ccCa	4/11	0.697108868592155	4	FACETS	1	0.995	1	0.87	0.844	0.894	CLONAL	3	TRUE	0	0.860831406389324	4		731	415	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899084	40899084	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059293-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	34	383	0	ENST00000373198.4:c.2186del	p.Gly729AlafsTer5	p.G729Afs*5	ENST00000373198	NM_133170.3	729	gGc/gc	14/32	0.860831406389324	4	FACETS	0.546	0.448	0.656	0.182	0.149	0.219	SUBCLONAL	1	TRUE	1	0.860831406389324	4		383	269	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0059294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	411	1512	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	0.771998255387427	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.771998255387427	1		1512	644	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246416	10246416	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059294-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	291	811	0	ENST00000340748.4:c.4721G>T	p.Arg1574Leu	p.R1574L	ENST00000340748		1574	cGg/cTg	38/40	0.771998255387427	4	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.771998255387427	4		811	1033	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0059296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	23	360	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.17	0.131	0.214	0.17	0.131	0.214	SUBCLONAL	1	TRUE	1	0.418955700519781	2		360	647	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951962	178951962	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	116	350	0	ENST00000263967.3:c.3017T>G	p.Leu1006Arg	p.L1006R	ENST00000263967	NM_006218.2	1006	cTt/cGt	21/21	1	2	FACETS	0.847	0.764	0.933	0.847	0.764	0.933	CLONAL	1	TRUE	1	0.418955700519781	2		350	654	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81954837	81954837	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	332	374	0	ENST00000359376.3:c.2270G>T	p.Arg757Ile	p.R757I	ENST00000359376	NM_002661.3	757	aGa/aTa	21/33	0.418955700519781	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.418955700519781	2		374	749	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411827	63411827	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769608759	NA	P-0059296-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	145	633	2	ENST00000330258.3:c.1340G>T	p.Gly447Val	p.G447V	ENST00000330258	NM_152424.3	447	gGc/gTc	2/2	1	2	FACETS	0.811	0.74	0.886	0.811	0.74	0.886	CLONAL	1	TRUE	1	0.418955700519781	2		635	853	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059297-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	112	477	0				ENST00000310581	NM_198253.2	-/1132			0.340185345503775	3	FACETS	0.902	0.818	0.989	0.902	0.818	0.989	CLONAL	2	TRUE	1	0.370886467797671	3		477	397	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577125	64577147	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGGGCTCCAACCTGTGATGAAG	CTGGGCTCCAACCTGTGATGAAG	-	novel	NA	P-0059297-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	150	288	0	ENST00000312049.6:c.435_445+12del		p.X145_splice	ENST00000312049	NM_130799.2	145		2/10	0.370886467797671	2	FACETS	0.825	0.76	0.893	0.825	0.76	0.893	CLONAL	2	TRUE	0	0.370886467797671	2		288	490	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564512	41564512	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555911075	NA	P-0059297-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	81	281	0	ENST00000263253.7:c.3934C>T	p.Arg1312Ter	p.R1312*	ENST00000263253	NM_001429.3	1312	Cga/Tga	24/31	0.340185345503775	3	FACETS	0.899	0.793	1	0.449	0.396	0.506	CLONAL	1	TRUE	1	0.370886467797671	3		281	576	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0059297-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	183	259	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	0.338952717815674	4	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	2	0.370886467797671	4		259	656	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	58	195	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.735	0.633	0.846	0.735	0.633	0.846	SUBCLONAL	1	TRUE	1	0.354686426717872	2		195	445	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	32	429	1	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	0.295	0.239	0.359	0.295	0.239	0.359	SUBCLONAL	1	TRUE	1	0.354686426717872	2		430	611	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	152	336	1	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.354686426717872	2		337	701	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186895	142186895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866304619	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	29	214	0	ENST00000350721.4:c.6568C>T	p.Arg2190Cys	p.R2190C	ENST00000350721	NM_001184.3	2190	Cgt/Tgt	39/47	1	2	FACETS	0.33	0.264	0.406	0.33	0.264	0.406	SUBCLONAL	1	TRUE	1	0.354686426717872	2		214	495	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561352	9561352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773981325	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	42	328	0	ENST00000353224.5:c.430G>A	p.Glu144Lys	p.E144K	ENST00000353224	NM_177990.2	144	Gaa/Aaa	4/10	1	2	FACETS	0.349	0.29	0.414	0.349	0.29	0.414	SUBCLONAL	1	TRUE	1	0.354686426717872	2		328	679	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242662	46242662	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	85	195	0	ENST00000334344.6:c.1624C>T	p.Arg542Ter	p.R542*	ENST00000334344	NM_152641.2	542	Cga/Tga	13/21	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.354686426717872	2		195	460	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245898	16245898	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	28	177	0	ENST00000375759.3:c.1522-1G>A		p.X508_splice	ENST00000375759	NM_015001.2	508			1	2	FACETS	0.363	0.29	0.447	0.363	0.29	0.447	SUBCLONAL	1	TRUE	1	0.354686426717872	2		177	435	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258227	16258227	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1022665445	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	124	415	0	ENST00000375759.3:c.5492C>T	p.Ala1831Val	p.A1831V	ENST00000375759	NM_015001.2	1831	gCt/gTt	11/15	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.354686426717872	2		415	655	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264055	16264055	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	41	425	0	ENST00000375759.3:c.10424A>G	p.His3475Arg	p.H3475R	ENST00000375759	NM_015001.2	3475	cAc/cGc	12/15	1	2	FACETS	0.303	0.251	0.361	0.303	0.251	0.361	SUBCLONAL	1	TRUE	1	0.354686426717872	2		425	763	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100312	27100312	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	96	433	0	ENST00000324856.7:c.4024C>T	p.Gln1342Ter	p.Q1342*	ENST00000324856	NM_006015.4	1342	Cag/Tag	17/20	1	2	FACETS	0.73	0.65	0.814	0.73	0.65	0.814	SUBCLONAL	1	TRUE	1	0.354686426717872	2		433	742	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106078	27106078	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	49	394	0	ENST00000324856.7:c.5693del	p.Pro1898HisfsTer25	p.P1898Hfs*25	ENST00000324856	NM_006015.4	1897	Ccc/cc	20/20	1	2	FACETS	0.399	0.337	0.468	0.399	0.337	0.468	SUBCLONAL	1	TRUE	1	0.354686426717872	2		394	692	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78425896	78425896	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	97	316	0	ENST00000370768.2:c.1549T>A	p.Trp517Arg	p.W517R	ENST00000370768	NM_003902.3	517	Tgg/Agg	16/20	1	2	FACETS	0.836	0.746	0.932	0.836	0.746	0.932	CLONAL	1	TRUE	1	0.354686426717872	2		316	654	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733513	85733513	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs387906350	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	53	360	0	ENST00000370580.1:c.499del	p.Ser167LeufsTer6	p.S167Lfs*6	ENST00000370580	NM_003921.4	167	Tct/ct	3/3	1	2	FACETS	0.451	0.384	0.525	0.451	0.384	0.525	SUBCLONAL	1	TRUE	1	0.354686426717872	2		360	662	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256535	115256535	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	90	264	0	ENST00000369535.4:c.176C>A	p.Ala59Asp	p.A59D	ENST00000369535	NM_002524.4	59	gCt/gAt	3/7	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.354686426717872	2		264	504	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480582	120480582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368918146	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	95	270	0	ENST00000256646.2:c.3235G>A	p.Val1079Ile	p.V1079I	ENST00000256646	NM_024408.3	1079	Gtt/Att	20/34	1	2	FACETS	0.938	0.837	1	0.938	0.837	1	CLONAL	1	TRUE	1	0.354686426717872	2		270	571	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193205391	193205391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778432682	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	52	274	0	ENST00000367435.3:c.1322G>A	p.Arg441His	p.R441H	ENST00000367435	NM_024529.4	441	cGc/cAc	15/17	1	2	FACETS	0.465	0.395	0.541	0.465	0.395	0.541	SUBCLONAL	1	TRUE	1	0.354686426717872	2		274	631	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601840	43601840	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758159521	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	29	327	0	ENST00000355710.3:c.884C>T	p.Thr295Met	p.T295M	ENST00000355710	NM_020975.4	295	aCg/aTg	5/20	1	2	FACETS	0.334	0.268	0.411	0.334	0.268	0.411	SUBCLONAL	1	TRUE	1	0.354686426717872	2		327	489	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999337	100999337	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	53	443	0	ENST00000325455.5:c.465del	p.Ala156ProfsTer10	p.A156Pfs*10	ENST00000325455	NM_001202474.3	155	ccC/cc	1/8	1	2	FACETS	0.407	0.346	0.473	0.407	0.346	0.473	SUBCLONAL	1	TRUE	1	0.354686426717872	2		443	735	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409060	4409060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781695497	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	58	250	0	ENST00000261254.3:c.755C>T	p.Ala252Val	p.A252V	ENST00000261254	NM_001759.3	252	gCg/gTg	5/5	1	2	FACETS	0.621	0.533	0.715	0.621	0.533	0.715	SUBCLONAL	1	TRUE	1	0.354686426717872	2		250	527	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380277	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913238	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	107	215	0	ENST00000311936.3:c.181C>G	p.Gln61Glu	p.Q61E	ENST00000311936	NM_004985.3	61	Caa/Gaa	3/5	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.354686426717872	2		215	521	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380295	25380295	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	98	215	0	ENST00000311936.3:c.163A>T	p.Ile55Phe	p.I55F	ENST00000311936	NM_004985.3	55	Att/Ttt	3/5	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.354686426717872	2		215	480	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856181	111856181	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754838420	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	100	422	0	ENST00000341259.2:c.232G>A	p.Glu78Lys	p.E78K	ENST00000341259	NM_005475.2	78	Gag/Aag	2/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.354686426717872	2		422	494	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885463	111885463	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	48	374	0	ENST00000341259.2:c.1240C>A	p.Leu414Met	p.L414M	ENST00000341259	NM_005475.2	414	Ctg/Atg	7/8	1	2	FACETS	0.463	0.391	0.543	0.463	0.391	0.543	SUBCLONAL	1	TRUE	1	0.354686426717872	2		374	584	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218401	133218401	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1565936216	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	63	329	0	ENST00000320574.5:c.5210A>G	p.Asn1737Ser	p.N1737S	ENST00000320574	NM_006231.2	1737	aAc/aGc	39/49	1	2	FACETS	0.732	0.635	0.838	0.732	0.635	0.838	SUBCLONAL	1	TRUE	1	0.354686426717872	2		329	485	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563252	21563252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	45	548	0	ENST00000382592.4:c.667G>A	p.Gly223Arg	p.G223R	ENST00000382592	NM_014572.2	223	Ggg/Agg	4/8	1	2	FACETS	0.399	0.334	0.47	0.399	0.334	0.47	SUBCLONAL	1	TRUE	1	0.354686426717872	2		548	636	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954198	32954198	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs80359173	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	43	269	0	ENST00000380152.3:c.9172A>G	p.Ser3058Gly	p.S3058G	ENST00000380152		3058	Agc/Ggc	24/27	1	2	FACETS	0.405	0.339	0.48	0.405	0.339	0.48	SUBCLONAL	1	TRUE	1	0.354686426717872	2		269	598	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240066	41240066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	35	130	0	ENST00000379561.5:c.284C>T	p.Ala95Val	p.A95V	ENST00000379561	NM_002015.3	95	gCg/gTg	1/3	1	2	FACETS	0.707	0.582	0.846	0.707	0.582	0.846	SUBCLONAL	1	TRUE	1	0.354686426717872	2		130	279	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504585	103504585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747957305	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	59	255	1	ENST00000355739.4:c.206G>A	p.Arg69Gln	p.R69Q	ENST00000355739	NM_000123.3	69	cGa/cAa	2/15	1	2	FACETS	0.544	0.467	0.627	0.544	0.467	0.627	SUBCLONAL	1	TRUE	1	0.354686426717872	2		256	612	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528053	103528053	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	63	290	0	ENST00000355739.4:c.3361G>T	p.Glu1121Ter	p.E1121*	ENST00000355739	NM_000123.3	1121	Gag/Tag	15/15	1	2	FACETS	0.622	0.538	0.713	0.622	0.538	0.713	SUBCLONAL	1	TRUE	1	0.354686426717872	2		290	571	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574059	95574059	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	22	179	0	ENST00000393063.1:c.2690T>C	p.Met897Thr	p.M897T	ENST00000393063	NM_030621.3	897	aTg/aCg	18/28	1	2	FACETS	0.284	0.219	0.359	0.284	0.219	0.359	SUBCLONAL	1	TRUE	1	0.354686426717872	2		179	437	SUCCESS
SCG5	6447	MSKCC	GRCh37	15	32988754	32988755	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	25	220	0	ENST00000300175.4:c.585dup	p.Val196CysfsTer12	p.V196Cfs*12	ENST00000300175	NM_001144757.1	195	gtt/gTtt	6/6	1	2	FACETS	0.313	0.246	0.391	0.313	0.246	0.391	SUBCLONAL	1	TRUE	1	0.354686426717872	2		220	450	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591587	38591587	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057517941	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	84	175	0	ENST00000299084.4:c.46C>T	p.Arg16Ter	p.R16*	ENST00000299084	NM_152594.2	16	Cga/Tga	2/7	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.354686426717872	2		175	437	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50733660	50733661	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	69	203	0	ENST00000307179.4:c.226dup	p.Arg76LysfsTer3	p.R76Kfs*3	ENST00000307179		73	-/A	3/20	1	2	FACETS	0.799	0.697	0.908	0.799	0.697	0.908	CLONAL	1	TRUE	1	0.354686426717872	2		203	487	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680791	88680791	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	25	251	0	ENST00000360948.2:c.466C>T	p.Gln156Ter	p.Q156*	ENST00000360948	NM_001012338.2	156	Cag/Tag	6/19	1	2	FACETS	0.324	0.255	0.404	0.324	0.255	0.404	SUBCLONAL	1	TRUE	1	0.354686426717872	2		251	435	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396164	396164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753904293	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	43	288	0	ENST00000262320.3:c.862G>A	p.Glu288Lys	p.E288K	ENST00000262320	NM_003502.3	288	Gaa/Aaa	2/11	1	2	FACETS	0.508	0.425	0.6	0.508	0.425	0.6	SUBCLONAL	1	TRUE	1	0.354686426717872	2		288	477	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094737	2094737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750992242	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	92	360	0	ENST00000219066.1:c.443C>T	p.Ala148Val	p.A148V	ENST00000219066	NM_002528.5	148	gCg/gTg	3/6	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.354686426717872	2		360	506	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2218089	2218089	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	29	451	0	ENST00000326181.6:c.151A>C	p.Ser51Arg	p.S51R	ENST00000326181	NM_032271.2	51	Agc/Cgc	4/21	1	2	FACETS	0.285	0.228	0.351	0.285	0.228	0.351	SUBCLONAL	1	TRUE	1	0.354686426717872	2		451	573	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222552	2222552	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	69	372	1	ENST00000326181.6:c.746C>A	p.Ala249Asp	p.A249D	ENST00000326181	NM_032271.2	249	gCc/gAc	9/21	1	2	FACETS	0.796	0.694	0.904	0.796	0.694	0.904	CLONAL	1	TRUE	1	0.354686426717872	2		373	489	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900321	3900321	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750216784	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	43	307	1	ENST00000262367.5:c.775G>A	p.Ala259Thr	p.A259T	ENST00000262367	NM_004380.2	259	Gca/Aca	2/31	1	2	FACETS	0.433	0.362	0.512	0.433	0.362	0.512	SUBCLONAL	1	TRUE	1	0.354686426717872	2		308	560	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983992	7983992	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769882996	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	53	354	0	ENST00000319144.4:c.634G>A	p.Val212Ile	p.V212I	ENST00000319144	NM_001139.2	212	Gtc/Atc	5/15	1	2	FACETS	0.567	0.484	0.659	0.567	0.484	0.659	SUBCLONAL	1	TRUE	1	0.354686426717872	2		354	527	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989352	7989352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	26	383	0	ENST00000319144.4:c.334G>A	p.Ala112Thr	p.A112T	ENST00000319144	NM_001139.2	112	Gca/Aca	2/15	1	2	FACETS	0.333	0.263	0.414	0.333	0.263	0.414	SUBCLONAL	1	TRUE	1	0.354686426717872	2		383	440	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120115	70120115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	231	368	0	ENST00000245479.2:c.1121del	p.Pro374ArgfsTer9	p.P374Rfs*9	ENST00000245479	NM_000346.3	373	Ccc/cc	3/3	0.354686426717872	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.354686426717872	2		368	545	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899251	78899251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200161901	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	66	353	0	ENST00000306801.3:c.2890G>A	p.Ala964Thr	p.A964T	ENST00000306801	NM_020761.2	964	Gcc/Acc	24/34	0.354686426717872	2	FACETS	0.621	0.539	0.71	0.311	0.269	0.355	SUBCLONAL	1	TRUE	0	0.354686426717872	2		353	599	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220126	5220126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781134304	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	46	436	0	ENST00000357368.4:c.3589C>T	p.Arg1197Trp	p.R1197W	ENST00000357368	NM_002850.3	1197	Cgg/Tgg	22/38	1	2	FACETS	0.464	0.39	0.546	0.464	0.39	0.546	SUBCLONAL	1	TRUE	1	0.354686426717872	2		436	559	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7152900	7152900	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	83	315	0	ENST00000302850.5:c.2068G>A	p.Glu690Lys	p.E690K	ENST00000302850	NM_000208.2	690	Gag/Aag	10/22	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.354686426717872	2		315	433	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251856	10251856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	93	259	0	ENST00000340748.4:c.3271G>A	p.Ala1091Thr	p.A1091T	ENST00000340748		1091	Gca/Aca	30/40	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.354686426717872	2		259	498	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222943	36222943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750345473	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	113	476	0	ENST00000222270.7:c.5572C>T	p.Arg1858Cys	p.R1858C	ENST00000222270	NM_014727.1	1858	Cgt/Tgt	27/37	1	2	FACETS	0.932	0.839	1	0.932	0.839	1	CLONAL	1	TRUE	1	0.354686426717872	2		476	684	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223667	36223667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	108	493	0	ENST00000222270.7:c.6217G>A	p.Glu2073Lys	p.E2073K	ENST00000222270	NM_014727.1	2073	Gag/Aag	28/37	1	2	FACETS	0.917	0.824	1	0.917	0.824	1	CLONAL	1	TRUE	1	0.354686426717872	2		493	664	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423175	47423175	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	37	327	0	ENST00000404338.3:c.1243C>A	p.Leu415Ile	p.L415I	ENST00000404338	NM_004491.4	415	Cta/Ata	1/6	1	2	FACETS	0.348	0.286	0.417	0.348	0.286	0.417	SUBCLONAL	1	TRUE	1	0.354686426717872	2		327	600	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470906	25470906	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	52	383	0	ENST00000264709.3:c.855G>T	p.Glu285Asp	p.E285D	ENST00000264709	NM_175629.2	285	gaG/gaT	7/23	1	2	FACETS	0.534	0.454	0.621	0.534	0.454	0.621	SUBCLONAL	1	TRUE	1	0.354686426717872	2		383	549	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051157	128051157	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	48	328	0	ENST00000285398.2:c.166T>C	p.Tyr56His	p.Y56H	ENST00000285398	NM_000122.1	56	Tat/Cat	2/15	1	2	FACETS	0.469	0.396	0.55	0.469	0.396	0.55	SUBCLONAL	1	TRUE	1	0.354686426717872	2		328	577	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149680	202149680	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	78	362	0	ENST00000358485.4:c.1121T>C	p.Leu374Pro	p.L374P	ENST00000358485	NM_001080125.1	374	cTc/cCc	8/9	1	2	FACETS	0.721	0.634	0.814	0.721	0.634	0.814	SUBCLONAL	1	TRUE	1	0.354686426717872	2		362	610	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36014523	36014523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	136	298	0	ENST00000358208.4:c.296C>T	p.Thr99Met	p.T99M	ENST00000358208		99	aCg/aTg	3/12	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.354686426717872	2		298	526	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29099518	29099518	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	30	228	0	ENST00000328354.6:c.883G>T	p.Glu295Ter	p.E295*	ENST00000328354	NM_007194.3	295	Gaa/Taa	8/15	1	2	FACETS	0.359	0.289	0.439	0.359	0.289	0.439	SUBCLONAL	1	TRUE	1	0.354686426717872	2		228	471	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161712	47161712	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	119	251	0	ENST00000409792.3:c.4414T>A	p.Tyr1472Asn	p.Y1472N	ENST00000409792	NM_014159.6	1472	Tac/Aac	3/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.354686426717872	2		251	555	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801217	1801217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886042775	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	73	339	1	ENST00000260795.2:c.346C>T	p.Arg116Cys	p.R116C	ENST00000260795		116	Cgc/Tgc	2/17	1	2	FACETS	0.769	0.674	0.872	0.769	0.674	0.872	SUBCLONAL	1	TRUE	1	0.354686426717872	2		340	535	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130097	143130097	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	27	182	0	ENST00000262992.4:c.919A>G	p.Met307Val	p.M307V	ENST00000262992	NM_001101669.1	307	Atg/Gtg	11/24	1	2	FACETS	0.337	0.267	0.416	0.337	0.267	0.416	SUBCLONAL	1	TRUE	1	0.354686426717872	2		182	452	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524960	187524960	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767643023	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	46	346	0	ENST00000441802.2:c.10720G>A	p.Val3574Met	p.V3574M	ENST00000441802	NM_005245.3	3574	Gtg/Atg	19/27	1	2	FACETS	0.437	0.368	0.515	0.437	0.368	0.515	SUBCLONAL	1	TRUE	1	0.354686426717872	2		346	593	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183268	56183268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	98	276	0	ENST00000399503.3:c.4178C>T	p.Ala1393Val	p.A1393V	ENST00000399503	NM_005921.1	1393	gCc/gTc	18/20	1	2	FACETS	0.975	0.872	1	0.975	0.872	1	CLONAL	1	TRUE	1	0.354686426717872	2		276	567	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	71	178	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.74	0.647	0.84	0.74	0.647	0.84	SUBCLONAL	1	TRUE	1	0.354686426717872	2		178	541	SUCCESS
APC	324	MSKCC	GRCh37	5	112175921	112175921	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	105	306	0	ENST00000257430.4:c.4630G>T	p.Glu1544Ter	p.E1544*	ENST00000257430	NM_000038.5	1544	Gaa/Taa	16/16	1	2	FACETS	0.921	0.826	1	0.921	0.826	1	CLONAL	1	TRUE	1	0.354686426717872	2		306	643	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324581	31324581	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs151341152	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	107	355	0	ENST00000412585.2:c.227T>C	p.Ile76Thr	p.I76T	ENST00000412585	NM_005514.6	76	aTa/aCa	2/8	0.259340634501151	2	FACETS	1	0.919	1	0.512	0.46	0.567	CLONAL	1	TRUE	0	0.354686426717872	2		355	589	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790671	89790671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	64	429	0	ENST00000336032.3:c.58C>T	p.Pro20Ser	p.P20S	ENST00000336032	NM_006813.2	20	Ccg/Tcg	1/2	1	2	FACETS	0.484	0.419	0.556	0.484	0.419	0.556	SUBCLONAL	1	TRUE	1	0.354686426717872	2		429	745	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317311	87317312	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	54	294	0	ENST00000277120.3:c.341dup	p.Asn114LysfsTer19	p.N114Kfs*19	ENST00000277120		112	-/A	4/19	1	2	FACETS	0.507	0.433	0.589	0.507	0.433	0.589	SUBCLONAL	1	TRUE	1	0.354686426717872	2		294	600	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93636954	93636954	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	34	325	0	ENST00000375746.1:c.1004G>C	p.Gly335Ala	p.G335A	ENST00000375746	NM_001174167.1	335	gGc/gCc	9/14	1	2	FACETS	0.367	0.299	0.444	0.367	0.299	0.444	SUBCLONAL	1	TRUE	1	0.354686426717872	2		325	522	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410015	139410015	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	49	496	0	ENST00000277541.6:c.1823C>A	p.Ser608Tyr	p.S608Y	ENST00000277541	NM_017617.3	608	tCc/tAc	11/34	1	2	FACETS	0.434	0.367	0.508	0.434	0.367	0.508	SUBCLONAL	1	TRUE	1	0.354686426717872	2		496	637	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929149	44929149	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs756545808	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	40	271	0	ENST00000377967.4:c.2249A>G	p.His750Arg	p.H750R	ENST00000377967	NM_021140.2	750	cAt/cGt	17/29	1	2	FACETS	0.488	0.406	0.58	0.488	0.406	0.58	SUBCLONAL	1	TRUE	1	0.354686426717872	2		271	462	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030658	47030658	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs782679832	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	61	276	0	ENST00000377604.3:c.432+1G>A		p.X144_splice	ENST00000377604	NM_001204468.1	144			1	2	FACETS	0.955	0.829	1	0.955	0.829	1	CLONAL	1	TRUE	1	0.354686426717872	2		276	360	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650778	48650778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104894809	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	28	447	0	ENST00000376670.3:c.647G>A	p.Arg216Gln	p.R216Q	ENST00000376670	NM_002049.3	216	cGg/cAg	4/6	1	2	FACETS	0.291	0.232	0.359	0.291	0.232	0.359	SUBCLONAL	1	TRUE	1	0.354686426717872	2		447	542	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410914	63410915	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	81	331	0	ENST00000330258.3:c.2252dup	p.Glu752Ter	p.E752*	ENST00000330258	NM_152424.3	751	cct/ccCt	2/2	1	2	FACETS	0.785	0.692	0.884	0.785	0.692	0.884	SUBCLONAL	1	TRUE	1	0.354686426717872	2		331	582	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345912	70345912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863223702	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	27	280	0	ENST00000374080.3:c.2449C>T	p.Arg817Cys	p.R817C	ENST00000374080		817	Cgc/Tgc	18/45	1	2	FACETS	0.308	0.244	0.381	0.308	0.244	0.381	SUBCLONAL	1	TRUE	1	0.354686426717872	2		280	495	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533790	63533790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059298-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	140	477	0	ENST00000307078.5:c.1364C>T	p.Pro455Leu	p.P455L	ENST00000307078	NM_004655.3	455	cCa/cTa	6/11	0.354686426717872	2	FACETS	1	0.976	1	0.594	0.543	0.649	CLONAL	1	TRUE	0	0.354686426717872	2		477	664	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	181	477	0				ENST00000310581	NM_198253.2	-/1132			0.281876271336529	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.288526470229586	4		477	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0059299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	78	285	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	0.232437053782626	3	FACETS	0.829	0.728	0.938	0.415	0.364	0.469	CLONAL	1	TRUE	1	0.288526470229586	3		285	746	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0059299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	151	609	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	0.232437053782626	3	FACETS	0.782	0.716	0.851	0.782	0.716	0.851	SUBCLONAL	2	TRUE	1	0.288526470229586	3		609	766	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306713	41306713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	89	287	0	ENST00000373198.4:c.946G>A	p.Gly316Arg	p.G316R	ENST00000373198	NM_133170.3	316	Ggg/Agg	7/32	0.257062658454069	0	FACETS	0.735	0.653	0.823			1	SUBCLONAL	1	TRUE	0	0.288526470229586	0		287	597	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45377687	45377687	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	44	151	0	ENST00000262160.6:c.742G>C	p.Glu248Gln	p.E248Q	ENST00000262160	NM_005901.5	248	Gaa/Caa	7/11	0.232437053782626	3	FACETS	0.814	0.683	0.958	0.407	0.341	0.479	CLONAL	1	TRUE	1	0.288526470229586	3		151	429	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427369	49427369	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1565779294	NA	P-0059299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	140	390	0	ENST00000301067.7:c.11119C>T	p.Arg3707Ter	p.R3707*	ENST00000301067	NM_003482.3	3707	Cga/Tga	39/54	0.232437053782626	3	FACETS	1	0.984	1	0.68	0.619	0.743	CLONAL	1	TRUE	1	0.288526470229586	3		390	817	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606901	43606901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773576143	NA	P-0059299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	114	429	0	ENST00000355710.3:c.1510G>A	p.Val504Met	p.V504M	ENST00000355710	NM_020975.4	504	Gtg/Atg	7/20	1	2	FACETS	0.967	0.871	1	0.967	0.871	1	CLONAL	1	TRUE	1	0.288526470229586	2		429	817	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420727	49420727	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	79	423	0	ENST00000301067.7:c.15022G>T	p.Glu5008Ter	p.E5008*	ENST00000301067	NM_003482.3	5008	Gaa/Taa	48/54	0.232437053782626	3	FACETS	0.732	0.643	0.828	0.366	0.321	0.414	SUBCLONAL	1	TRUE	1	0.288526470229586	3		423	856	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274070	10274070	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	102	392	0	ENST00000330684.3:c.199G>A	p.Val67Met	p.V67M	ENST00000330684	NM_001134407.1	67	Gtg/Atg	2/13	1	2	FACETS	0.902	0.806	1	0.902	0.806	1	CLONAL	1	TRUE	1	0.288526470229586	2		392	784	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509080	66509080	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0059299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	35	150	0	ENST00000273854.3:c.246+1G>T		p.X82_splice	ENST00000273854	NM_004439.5	82			0.188325357901866	1	FACETS	0.564	0.463	0.677	0.564	0.463	0.677	SUBCLONAL	1	TRUE	0	0.288526470229586	1		150	368	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755590	57755590	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	150	378	0	ENST00000274289.3:c.197G>T	p.Gly66Val	p.G66V	ENST00000274289	NM_006622.3	66	gGg/gTg	1/14	0.176647841180955	2	FACETS	1	0.979	1	0.609	0.556	0.664	CLONAL	1	TRUE	0	0.288526470229586	2		378	854	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032042	26032042	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059299-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	133	468	0	ENST00000244661.2:c.247C>A	p.Leu83Ile	p.L83I	ENST00000244661	NM_003537.3	83	Ctt/Att	1/1	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.288526470229586	2		468	913	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0059300-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	60	329	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.906	0.79	1	0.906	0.79	1	CLONAL	1	TRUE	1	0.536150375566257	2		329	247	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0059300-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	56	185	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.881	0.764	1	0.881	0.764	1	CLONAL	1	TRUE	1	0.536150375566257	2		185	237	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604665	48604665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660045	NA	P-0059300-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	173	301	0	ENST00000342988.3:c.1487G>A	p.Arg496His	p.R496H	ENST00000342988	NM_005359.5	496	cGt/cAt	12/12	0.536150375566257	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.536150375566257	1		301	439	SUCCESS
APC	324	MSKCC	GRCh37	5	112175411	112175411	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059300-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	397	345	0	ENST00000257430.4:c.4120G>T	p.Glu1374Ter	p.E1374*	ENST00000257430	NM_000038.5	1374	Gaa/Taa	16/16	0.534765300089806	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.536150375566257	2		345	716	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237751	16237751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762701924	NA	P-0059300-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	122	252	0	ENST00000375759.3:c.1198C>T	p.Leu400Phe	p.L400F	ENST00000375759	NM_015001.2	400	Ctt/Ttt	5/15	0.536150375566257	1	FACETS	0.797	0.726	0.87	0.797	0.726	0.87	SUBCLONAL	1	TRUE	0	0.536150375566257	1		252	418	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477155	67477155	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059300-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	64	405	0	ENST00000327367.4:c.962A>T	p.Asn321Ile	p.N321I	ENST00000327367	NM_005902.3	321	aAc/aTc	7/9	0.536150375566257	1	FACETS	0.289	0.25	0.332	0.289	0.25	0.332	SUBCLONAL	1	TRUE	0	0.536150375566257	1		405	604	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395704	45395704	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0059300-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	141	297	0	ENST00000262160.6:c.430A>T	p.Lys144Ter	p.K144*	ENST00000262160	NM_005901.5	144	Aag/Tag	4/11	0.536150375566257	1	FACETS	0.97	0.893	1	0.97	0.893	1	CLONAL	1	TRUE	0	0.536150375566257	1		297	397	SUCCESS
APC	324	MSKCC	GRCh37	5	112175537	112175537	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059300-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	424	361	0	ENST00000257430.4:c.4246G>T	p.Gly1416Cys	p.G1416C	ENST00000257430	NM_000038.5	1416	Ggc/Tgc	16/16	0.534765300089806	2	FACETS	0.97	0.931	1	0.97	0.931	1	CLONAL	2	TRUE	0	0.536150375566257	2		361	815	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225747	26225747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766913987	NA	P-0059300-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	231	472	0	ENST00000360408.1:c.365C>T	p.Pro122Leu	p.P122L	ENST00000360408	NM_003532.2	122	cCt/cTt	1/1	1	2	FACETS	0.883	0.824	0.944	0.883	0.824	0.944	CLONAL	1	TRUE	1	0.536150375566257	2		472	976	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0059301-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	50	525	0				ENST00000310581	NM_198253.2	-/1132			0.474207275591533	1	FACETS	1	0.92	1	1	0.985	1	CLONAL	5	FALSE	0	0.216045952954807	1		525	80	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0059301-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	183	403	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.188659282563434	3	FACETS	1	0.98	1	1	0.994	1	CLONAL	4	FALSE	1	0.216045952954807	3		404	419	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412675	139412675	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059301-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	135	393	0	ENST00000277541.6:c.1169A>G	p.Asn390Ser	p.N390S	ENST00000277541	NM_017617.3	390	aAc/aGc	7/34	0.216045952954807	7	FACETS	1	0.961	1	0.821	0.749	0.896	CLONAL	3	FALSE	3	0.216045952954807	7		393	586	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0059302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	289	306	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.536722298361953	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.536722298361953	2		307	485	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864386	151864386	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059302-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	115	197	0	ENST00000262189.6:c.9595G>A	p.Glu3199Lys	p.E3199K	ENST00000262189	NM_170606.2	3199	Gaa/Aaa	42/59	0.536722298361953	3	FACETS	1	0.966	1	0.572	0.518	0.628	CLONAL	1	TRUE	1	0.536722298361953	3		197	475	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0059303-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	715	318	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.922363413070326	3	FACETS	0.995	0.983	1	0.995	0.983	1	CLONAL	3	TRUE	0	0.922363413070326	3		318	759	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030368	49030368	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059303-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	382	243	1	ENST00000267163.4:c.1848del	p.Gly617ValfsTer6	p.G617Vfs*6	ENST00000267163	NM_000321.2	615	Aaa/aa	19/27	0.922363413070326	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.922363413070326	2		244	412	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287398	38287398	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778531708	NA	P-0059303-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	335	467	0	ENST00000425967.3:c.259C>T	p.Arg87Cys	p.R87C	ENST00000425967	NM_001174067.1	87	Cgc/Tgc	4/19	1	2	FACETS	0.975	0.928	1	0.975	0.928	1	CLONAL	1	TRUE	1	0.922363413070326	2		467	745	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584452	187584452	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0059303-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	209	207	0	ENST00000441802.2:c.3580+1G>T		p.X1194_splice	ENST00000441802	NM_005245.3	1194			0.922363413070326	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.922363413070326	1		207	240	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400155	41400156	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0059303-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	403	262	0	ENST00000373198.4:c.603_604delinsTT	p.Glu202Ter	p.E202*	ENST00000373198	NM_133170.3	201	gtGGag/gtTTag	5/32	0.896471624058287	3	FACETS	0.951	0.915	0.987	0.951	0.915	0.987	CLONAL	2	TRUE	1	0.922363413070326	3		262	671	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407491	407491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059303-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	208	265	0	ENST00000380956.4:c.1249G>A	p.Ala417Thr	p.A417T	ENST00000380956	NM_001195286.1	417	Gct/Act	9/9	0.896471624058287	3	FACETS	1	0.941	1	0.505	0.471	0.54	CLONAL	1	TRUE	1	0.922363413070326	3		265	653	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510809	157510809	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059303-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	326	361	0	ENST00000346085.5:c.3584C>A	p.Pro1195His	p.P1195H	ENST00000346085	NM_020732.3	1195	cCc/cAc	14/20	0.896471624058287	3	FACETS	0.994	0.94	1	0.497	0.47	0.525	CLONAL	1	TRUE	1	0.922363413070326	3		361	1039	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0059304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	14	458	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.469	0.339	0.628	0.469	0.339	0.628	SUBCLONAL	1	TRUE	1	0.21	2		458	284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0059304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	46	360	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	1	2	FACETS	0.565	0.474	0.665	0.565	0.474	0.665	SUBCLONAL	1	TRUE	1	0.21	2		360	776	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042265	42042265	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059304-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	41	358	0	ENST00000219905.7:c.6460del	p.Leu2154TyrfsTer25	p.L2154Yfs*25	ENST00000219905	NM_001164273.1	2154	Cta/ta	17/24	1	2	FACETS	0.608	0.505	0.723	0.608	0.505	0.723	SUBCLONAL	1	TRUE	1	0.21	2		358	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0059308-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	143	407	0	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	0.27134503554616	9	FACETS	1	0.947	1			1	CLONAL	6	FALSE	NA	0.27134503554616	9		407	333	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842705	68842705	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059308-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	58	525	0	ENST00000261769.5:c.641T>C	p.Leu214Pro	p.L214P	ENST00000261769	NM_004360.3	214	cTg/cCg	5/16	0.27134503554616	3	FACETS	1	0.949	1	1	0.982	1	CLONAL	5	FALSE	0	0.27134503554616	3		525	90	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137528167	137528167	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs777965499	NA	P-0059308-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	19	188	0	ENST00000367739.4:c.133A>G	p.Ile45Val	p.I45V	ENST00000367739	NM_000416.2	45	Atc/Gtc	2/7	0.231041394051443	5	FACETS	1	0.864	1	0.782	0.607	0.978	CLONAL	2	FALSE	2	0.27134503554616	5		188	84	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784579	43784579	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	224	495	0	ENST00000382044.4:c.95C>G	p.Pro32Arg	p.P32R	ENST00000382044	NM_001141980.1	32	cCt/cGt	2/28	0.57788038876652	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	2	0.575227258508295	4		495	600	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577024	7577048	+	frameshift_variant	Frame_Shift_Del	DEL	TTAGTGCTCCCTGGGGGCAGCTCGT	TTAGTGCTCCCTGGGGGCAGCTCGT	-	novel	NA	P-0059310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	227	689	0	ENST00000269305.4:c.890_914del	p.His297ArgfsTer40	p.H297Rfs*40	ENST00000269305	NM_001126112.2	297	cACGAGCTGCCCCCAGGGAGCACTAAg/cg	8/11	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	2	TRUE	NA	0.575227258508295	2		689	378	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226417	41226417	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	422	541	0	ENST00000357654.3:c.4606G>T	p.Glu1536Ter	p.E1536*	ENST00000357654	NM_007294.3	1536	Gag/Tag	14/23	0.506712108355174	5	FACETS	1	0.991	1			1	CLONAL	5	TRUE	NA	0.575227258508295	5		541	526	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17389621	17389654	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACAGCCCTTCACTGACCCCCGCCTCCCCGGCAGG	ACAGCCCTTCACTGACCCCCGCCTCCCCGGCAGG	-	novel	NA	P-0059310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	157	492	0	ENST00000359435.4:c.787-32_788del		p.X263_splice	ENST00000359435	NM_001033549.1	263		9/9	0.57788038876652	4	FACETS	1	0.925	1	1	0.925	1	CLONAL	2	TRUE	2	0.575227258508295	4		492	430	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017165	31017165	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	148	450	0	ENST00000375687.4:c.496G>T	p.Gly166Trp	p.G166W	ENST00000375687	NM_015338.5	166	Ggg/Tgg	7/13	0.498678879283248	4	FACETS	0.887	0.817	0.959	0.887	0.817	0.959	CLONAL	2	TRUE	2	0.575227258508295	4		450	457	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72873592	72873982	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTTGTTCCTGACTCTTTTCCAAAAAGGCCATCATTTTTGAATATTTGTCAGTCCACCAAGGATTATACTTCAAAATCTGTTCAATCGCCTCATCTTCAAAAAAGTCAGCTCTAGGAAAAAACATTGAAAGAACTTACTATACAGGATTTCACTGGCTTTTACTTTTTAACATTTTATCTTAACTCATATTTGTACTAGAAATACAGATTTTAATTCAAAGTACATTTCAAGGAAAGACTGAACACTATATTTACTTTCTTTGTAGTTACTAACCACAAACATAAGTTATTTACCATAAAACAAAAGTAAGTATCTGCCTAAAGGGATATATAACATTGCTGATCTCTTTTTTTTTTTTTTTTAACTTTTTTTAAAAGAGATGGGTCTCAC	TCTTGTTCCTGACTCTTTTCCAAAAAGGCCATCATTTTTGAATATTTGTCAGTCCACCAAGGATTATACTTCAAAATCTGTTCAATCGCCTCATCTTCAAAAAAGTCAGCTCTAGGAAAAAACATTGAAAGAACTTACTATACAGGATTTCACTGGCTTTTACTTTTTAACATTTTATCTTAACTCATATTTGTACTAGAAATACAGATTTTAATTCAAAGTACATTTCAAGGAAAGACTGAACACTATATTTACTTTCTTTGTAGTTACTAACCACAAACATAAGTTATTTACCATAAAACAAAAGTAAGTATCTGCCTAAAGGGATATATAACATTGCTGATCTCTTTTTTTTTTTTTTTTAACTTTTTTTAAAAGAGATGGGTCTCAC	-	novel	NA	P-0059310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	36	412	0	ENST00000325599.8:c.600-280_710del		p.X200_splice	ENST00000325599	NM_018130.2	200		6/11	0.57788038876652	4	FACETS	0.666	0.55	0.796			1	SUBCLONAL	1	TRUE	NA	0.575227258508295	4		412	296	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141582944	141582944	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059310-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	96	532	0	ENST00000220592.5:c.303C>A	p.Tyr101Ter	p.Y101*	ENST00000220592	NM_012154.3	101	taC/taA	3/19	0.575227258508295	8	FACETS	0.904	0.804	1	0.151	0.134	0.169	CLONAL	1	TRUE	2	0.575227258508295	8		532	1006	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0059311-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	152	542	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	0.227777390009353	4	FACETS	0.891	0.821	0.963	0.891	0.821	0.963	CLONAL	3	FALSE	1	0.299028535529512	4		542	494	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211743	5211743	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059311-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	77	666	0	ENST00000357368.4:c.5092A>C	p.Ile1698Leu	p.I1698L	ENST00000357368	NM_002850.3	1698	Atc/Ctc	33/38	0.299028535529512	5	FACETS	0.935	0.825	1	0.623	0.55	0.701	CLONAL	2	FALSE	2	0.299028535529512	5		666	399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs786202525	NA	P-0059312-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	108	651	0	ENST00000269305.4:c.532del	p.His178ThrfsTer69	p.H178Tfs*69	ENST00000269305	NM_001126112.2	178	Cac/ac	5/11	0.459790836453149	1	FACETS	0.538	0.484	0.596	0.538	0.484	0.596	SUBCLONAL	1	TRUE	0	0.459790836453149	1		651	672	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0059312-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	105	404	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.459790836453149	1	FACETS	0.928	0.839	1	0.928	0.839	1	CLONAL	1	TRUE	0	0.459790836453149	1		404	379	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239510	123239510	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059312-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	99	636	0	ENST00000358487.5:c.2327T>C	p.Leu776Pro	p.L776P	ENST00000358487	NM_000141.4	776	cTc/cCc	18/18	0.459790836453149	1	FACETS	0.59	0.528	0.656	0.59	0.528	0.656	SUBCLONAL	1	TRUE	0	0.459790836453149	1		636	562	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0059314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	184	540	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.918	0.852	0.987	0.918	0.852	0.987	CLONAL	1	TRUE	1	0.619271765471657	2		540	647	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880956	134880956	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1296	166	569	0	ENST00000398015.3:c.1519C>T	p.Arg507Cys	p.R507C	ENST00000398015	NM_004441.4	507	Cgt/Tgt	7/16	0.619271765471657	7	FACETS	0.934	0.856	1	0.156	0.142	0.17	CLONAL	1	TRUE	1	0.619271765471657	7		569	1462	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417852	138417852	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059314-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	848	417	0	ENST00000289153.2:c.1667A>G	p.Asp556Gly	p.D556G	ENST00000289153	NM_006219.2	556	gAt/gGt	11/22	0.619271765471657	7	FACETS	0.983	0.961	1	0.983	0.961	1	CLONAL	6	TRUE	1	0.619271765471657	7		417	1183	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0059315-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	178	536	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.701150359762781	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.701150359762781	2		536	244	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0059315-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	56	306	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.913	0.797	1	0.913	0.797	1	CLONAL	1	TRUE	1	0.701150359762781	2		306	175	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0059315-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	14	241	0	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	0.701150359762781	1	FACETS	0.309	0.227	0.404	0.309	0.227	0.404	SUBCLONAL	1	TRUE	0	0.701150359762781	1		241	84	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911606	134911606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767340477	NA	P-0059315-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	143	571	0	ENST00000398015.3:c.2071C>T	p.Arg691Trp	p.R691W	ENST00000398015	NM_004441.4	691	Cgg/Tgg	11/16	0.701150359762781	2	FACETS	1	0.971	1	0.554	0.511	0.598	CLONAL	1	TRUE	0	0.701150359762781	2		571	368	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970818	79970818	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs766534747	NA	P-0059315-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	37	380	0	ENST00000265081.6:c.1044C>G	p.Ile348Met	p.I348M	ENST00000265081	NM_002439.4	348	atC/atG	7/24	1	2	FACETS	0.77	0.647	0.902	0.77	0.647	0.902	CLONAL	1	TRUE	1	0.701150359762781	2		380	137	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094284	27094294	+	frameshift_variant	Frame_Shift_Del	DEL	TCCAGTTCTTC	TCCAGTTCTTC	-	novel	NA	P-0059315-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	207	536	0	ENST00000324856.7:c.2993_3003del	p.Ser998TyrfsTer5	p.S998Yfs*5	ENST00000324856	NM_006015.4	998	TCCAGTTCTTCt/t	11/20	NA	2	FACETS	0.946	0.9	0.991			1	INDETERMINATE	2	TRUE	NA	0.701150359762781	2		536	312	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534308	534308	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059315-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	122	522	0	ENST00000451590.1:c.15G>T	p.Lys5Asn	p.K5N	ENST00000451590	NM_001130442.1	5	aaG/aaT	2/5	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.701150359762781	2		522	347	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354980	70354980	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059315-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	173	636	0	ENST00000374080.3:c.4902G>C	p.Lys1634Asn	p.K1634N	ENST00000374080		1634	aaG/aaC	36/45	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.701150359762781	2		636	468	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575484	64575484	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059316-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	355	563	0	ENST00000312049.6:c.533del	p.Ser178LeufsTer7	p.S178Lfs*7	ENST00000312049	NM_130799.2	178	tCt/tt	3/10	0.828503854729872	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.828503854729872	1		563	473	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939403	76939404	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0059316-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	120	211	0	ENST00000373344.5:c.1344dup	p.Pro449ThrfsTer15	p.P449Tfs*15	ENST00000373344	NM_000489.3	448	-/A	9/35	1	1	FACETS	0.964	0.904	1	0.964	0.904	1	CLONAL	1	TRUE	0	0.828503854729872	1		211	176	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	51	477	0				ENST00000310581	NM_198253.2	-/1132			NA	3	FACETS	1	0.892	1			1	INDETERMINATE	2	TRUE	NA	0.324936520259738	3		477	176	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24133968	24133968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	44	386	0	ENST00000263121.7:c.119G>A	p.Arg40Gln	p.R40Q	ENST00000263121	NM_003073.3	40	cGa/cAa	2/9	0.185752849738906	2	FACETS	0.689	0.579	0.81	0.345	0.289	0.405	INDETERMINATE	1	TRUE	0	0.324936520259738	2		386	393	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877387	28877387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747687298	NA	P-0059317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	129	396	0	ENST00000282397.4:c.3934G>A	p.Ala1312Thr	p.A1312T	ENST00000282397	NM_002019.4	1312	Gct/Act	30/30	0.324936520259738	3	FACETS	0.845	0.77	0.924	0.845	0.77	0.924	CLONAL	2	TRUE	1	0.324936520259738	3		396	546	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624844	9624844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	60	375	0	ENST00000353224.5:c.133G>A	p.Asp45Asn	p.D45N	ENST00000353224	NM_177990.2	45	Gat/Aat	3/10	0.324936520259738	3	FACETS	0.904	0.78	1	0.452	0.39	0.519	CLONAL	1	TRUE	1	0.324936520259738	3		375	475	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61722711	61722711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059317-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	119	372	0	ENST00000401558.2:c.926C>T	p.Ser309Leu	p.S309L	ENST00000401558	NM_003400.3	309	tCa/tTa	11/25	0.324936520259738	3	FACETS	0.948	0.862	1	0.948	0.862	1	CLONAL	2	TRUE	1	0.324936520259738	3		372	449	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877387	28877387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747687298	NA	P-0059317-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	19	396	0	ENST00000282397.4:c.3934G>A	p.Ala1312Thr	p.A1312T	ENST00000282397	NM_002019.4	1312	Gct/Act	30/30	1	2	FACETS	0.424	0.321	0.546	0.424	0.321	0.546	SUBCLONAL	1	TRUE	1	0.24	2		396	373	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221642	36221642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471498012	NA	P-0059318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	31	640	0	ENST00000222270.7:c.5311C>T	p.Arg1771Trp	p.R1771W	ENST00000222270	NM_014727.1	1771	Cgg/Tgg	26/37	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	FALSE	1	0.266098443552797	2		640	205	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16203122	16203122	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	24	592	0	ENST00000375759.3:c.830G>T	p.Arg277Ile	p.R277I	ENST00000375759	NM_015001.2	277	aGa/aTa	3/15	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	FALSE	1	0.266098443552797	2		592	155	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115815	8115853	+	inframe_deletion	In_Frame_Del	DEL	GAACAGCTCGTTTAACCCGGCCGCCCTCTCCAGACACAT	GAACAGCTCGTTTAACCCGGCCGCCCTCTCCAGACACAT	-	novel	NA	P-0059318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	27	550	0	ENST00000346208.3:c.1162_1200del	p.Asn388_Met400del	p.N388_M400del	ENST00000346208		387	aaGAACAGCTCGTTTAACCCGGCCGCCCTCTCCAGACACATg/aag	6/6	1	2	FACETS	0.688	0.548	0.847	0.688	0.548	0.847	SUBCLONAL	1	FALSE	1	0.266098443552797	2		550	295	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589615	69589615	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	35	1090	0	ENST00000168712.1:c.238A>G	p.Ile80Val	p.I80V	ENST00000168712	NM_002007.2	80	Atc/Gtc	1/3	0.234375163867291	1	FACETS	0.653	0.537	0.784	0.653	0.537	0.784	SUBCLONAL	1	FALSE	0	0.266098443552797	1		1090	349	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923662	131923662	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	11	438	0	ENST00000265335.6:c.932A>C	p.His311Pro	p.H311P	ENST00000265335		311	cAc/cCc	7/25	1	2	FACETS	0.719	0.5	0.986	0.719	0.5	0.986	CLONAL	1	FALSE	1	0.266098443552797	2		438	115	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722156	176722156	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	15	761	0	ENST00000439151.2:c.7787G>A	p.Ser2596Asn	p.S2596N	ENST00000439151	NM_022455.4	2596	aGt/aAt	23/23	1	2	FACETS	0.43	0.314	0.57	0.43	0.314	0.57	SUBCLONAL	1	FALSE	1	0.266098443552797	2		761	262	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374979	45374980	+	stop_gained,inframe_insertion	Nonsense_Mutation	INS	-	-	TAC	novel	NA	P-0059318-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	10	493	0	ENST00000262160.6:c.863_864insGTA	p.Glu288_Thr289insTer	p.E288_T289ins*	ENST00000262160	NM_005901.5	288	gaa/gaGTAa	8/11	0.234375163867291	1	FACETS	0.497	0.338	0.695	0.497	0.338	0.695	SUBCLONAL	1	FALSE	0	0.266098443552797	1		493	131	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879794	37879794	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059318-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	198	900	0	ENST00000269571.5:c.2089G>T	p.Val697Leu	p.V697L	ENST00000269571		697	Gtg/Ttg	18/27	0.479263213814454	6	FACETS	1	0.982	1	0.3	0.277	0.325	CLONAL	1	TRUE	2	0.479263213814454	6		900	1347	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221642	36221642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471498012	NA	P-0059318-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	139	640	0	ENST00000222270.7:c.5311C>T	p.Arg1771Trp	p.R1771W	ENST00000222270	NM_014727.1	1771	Cgg/Tgg	26/37	0.480245867458384	3	FACETS	1	0.969	1	0.567	0.518	0.619	CLONAL	1	TRUE	1	0.479263213814454	3		640	634	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64289970	64289970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754493391	NA	P-0059318-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	94	342	0	ENST00000370651.3:c.413G>A	p.Arg138His	p.R138H	ENST00000370651	NM_003463.4	138	cGt/cAt	6/6	0.480245867458384	0	FACETS	0.757	0.683	0.832			1	SUBCLONAL	1	TRUE	0	0.479263213814454	0		342	270	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16203122	16203122	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059318-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	141	592	0	ENST00000375759.3:c.830G>T	p.Arg277Ile	p.R277I	ENST00000375759	NM_015001.2	277	aGa/aTa	3/15	0.00574295055334506	4	FACETS	0.829	0.759	0.901	0.829	0.759	0.901	INDETERMINATE	2	TRUE	2	0.479263213814454	4		592	525	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115815	8115853	+	inframe_deletion	In_Frame_Del	DEL	GAACAGCTCGTTTAACCCGGCCGCCCTCTCCAGACACAT	GAACAGCTCGTTTAACCCGGCCGCCCTCTCCAGACACAT	-	novel	NA	P-0059318-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	149	550	0	ENST00000346208.3:c.1162_1200del	p.Asn388_Met400del	p.N388_M400del	ENST00000346208		387	aaGAACAGCTCGTTTAACCCGGCCGCCCTCTCCAGACACATg/aag	6/6	NA	2	FACETS	0.925	0.848	1			1	INDETERMINATE	1	TRUE	NA	0.479263213814454	2		550	672	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589615	69589615	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059318-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	127	1090	0	ENST00000168712.1:c.238A>G	p.Ile80Val	p.I80V	ENST00000168712	NM_002007.2	80	Atc/Gtc	1/3	0.479263213814454	8	FACETS	0.942	0.85	1	0.157	0.141	0.174	CLONAL	1	TRUE	2	0.479263213814454	8		1090	1372	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923662	131923662	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059318-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	106	438	0	ENST00000265335.6:c.932A>C	p.His311Pro	p.H311P	ENST00000265335		311	cAc/cCc	7/25	0.480245867458384	4	FACETS	1	0.98	1	0.682	0.614	0.753	CLONAL	1	TRUE	2	0.479263213814454	4		438	480	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722156	176722156	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059318-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	139	761	0	ENST00000439151.2:c.7787G>A	p.Ser2596Asn	p.S2596N	ENST00000439151	NM_022455.4	2596	aGt/aAt	23/23	0.480245867458384	4	FACETS	1	0.946	1	0.526	0.479	0.576	CLONAL	1	TRUE	2	0.479263213814454	4		761	815	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885710	23885710	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059318-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	60	620	0	ENST00000374561.5:c.208C>G	p.Leu70Val	p.L70V	ENST00000374561	NM_002167.4	70	Cta/Gta	1/3	0.00574295055334506	4	FACETS	0.579	0.498	0.667	0.289	0.249	0.334	INDETERMINATE	1	TRUE	2	0.479263213814454	4		620	640	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865704	57865704	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059318-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	244	632	0	ENST00000228682.2:c.3181C>A	p.Pro1061Thr	p.P1061T	ENST00000228682	NM_005269.2	1061	Cct/Act	12/12	0.479263213814454	5	FACETS	1	0.94	1	0.502	0.47	0.535	CLONAL	2	TRUE	1	0.479263213814454	5		632	872	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701787	43701873	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACAGCAAGTTGGCTCTTATCATTGCCACTATATTAGGTTACACAAAGAAACTCCTCACCTGGGCTTCATTGAAATCTTCAAGGATAT	ACAGCAAGTTGGCTCTTATCATTGCCACTATATTAGGTTACACAAAGAAACTCCTCACCTGGGCTTCATTGAAATCTTCAAGGATAT	-	novel	NA	P-0059318-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	39	244	0	ENST00000382044.4:c.5372_5400+58del		p.X1791_splice	ENST00000382044	NM_001141980.1	1791		25/28	1	2	FACETS	0.736	0.616	0.868	0.736	0.616	0.868	SUBCLONAL	1	TRUE	1	0.479263213814454	2		244	221	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026014	14026014	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059318-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	82	340	0	ENST00000311895.7:c.974G>T	p.Gly325Val	p.G325V	ENST00000311895	NM_005236.2	325	gGt/gTt	6/11	0.479263213814454	5	FACETS	1	0.927	1	0.356	0.314	0.4	CLONAL	1	TRUE	2	0.479263213814454	5		340	551	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783863	50783863	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059318-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	113	425	0	ENST00000398568.2:c.254A>G	p.Asp85Gly	p.D85G	ENST00000398568	NM_001042412.1	85	gAt/gGt	3/18	0.480245867458384	2	FACETS	1	0.971	1	0.588	0.533	0.645	CLONAL	1	TRUE	0	0.479263213814454	2		425	401	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821539	72821539	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059318-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	65	460	0	ENST00000268489.5:c.10636C>T	p.Gln3546Ter	p.Q3546*	ENST00000268489	NM_006885.3	3546	Caa/Taa	10/10	0.480245867458384	2	FACETS	0.803	0.7	0.912	0.401	0.35	0.456	CLONAL	1	TRUE	0	0.479263213814454	2		460	338	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391123	89391123	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059318-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	89	537	0	ENST00000336596.2:c.1189A>G	p.Thr397Ala	p.T397A	ENST00000336596	NM_005233.5	397	Aca/Gca	5/17	0.317676229227025	3	FACETS	0.848	0.754	0.948	0.424	0.377	0.474	CLONAL	1	TRUE	1	0.479263213814454	3		537	543	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197728	66197728	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059318-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	31	465	0	ENST00000273854.3:c.2971T>A	p.Tyr991Asn	p.Y991N	ENST00000273854	NM_004439.5	991	Tac/Aac	17/18	1	2	FACETS	0.267	0.215	0.325	0.267	0.215	0.325	SUBCLONAL	1	TRUE	1	0.479263213814454	2		465	485	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709137	117709137	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059318-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	90	502	0	ENST00000368508.3:c.1820A>C	p.Asn607Thr	p.N607T	ENST00000368508	NM_002944.2	607	aAc/aCc	13/43	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.479263213814454	2		502	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0059320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	112	503	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	1	2	FACETS	0.611	0.549	0.677	0.611	0.549	0.677	SUBCLONAL	1	TRUE	1	0.4	2		503	916	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47679240	47679240	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059320-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	73	359	0	ENST00000347630.2:c.967del	p.Asp323IlefsTer49	p.D323Ifs*49	ENST00000347630	NM_001007230.1	323	Gat/at	10/11	1	2	FACETS	0.522	0.456	0.593	0.522	0.456	0.593	SUBCLONAL	1	TRUE	1	0.4	2		359	699	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0059321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	299	409	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.735501387121596	2	FACETS	0.954	0.918	0.989	0.954	0.918	0.989	CLONAL	2	TRUE	0	0.747987827621734	2		409	419	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55228007	55228007	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	449	424	1	ENST00000275493.2:c.1474A>C	p.Ser492Arg	p.S492R	ENST00000275493	NM_005228.3	492	Agc/Cgc	12/28	0.747987827621734	4	FACETS	0.85	0.812	0.888	0.566	0.541	0.592	CLONAL	2	TRUE	1	0.747987827621734	4		425	1235	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549395	21549395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143631255	NA	P-0059321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	569	646	0	ENST00000382592.4:c.2881C>T	p.Arg961Trp	p.R961W	ENST00000382592	NM_014572.2	961	Cgg/Tgg	8/8	0.565644072297615	3	FACETS	0.979	0.945	1			1	CLONAL	2	TRUE	NA	0.747987827621734	3		646	1068	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579433	7579433	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1064793279	NA	P-0059321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	733	732	1	ENST00000269305.4:c.254del	p.Pro85LeufsTer38	p.P85Lfs*38	ENST00000269305	NM_001126112.2	85	cCt/ct	4/11	0.747987827621734	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.747987827621734	2		733	972	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982392	201982392	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0059321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	357	680	0	ENST00000359651.3:c.771C>G	p.Tyr257Ter	p.Y257*	ENST00000359651		257	taC/taG	6/8	0.617244983753302	4	FACETS	1	0.981	1	0.36	0.341	0.381	CLONAL	1	TRUE	1	0.747987827621734	4		680	1543	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827439	72827439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	407	571	0	ENST00000268489.5:c.9142C>T	p.His3048Tyr	p.H3048Y	ENST00000268489	NM_006885.3	3048	Cat/Tat	9/10	0.199509491301765	3	FACETS	0.958	0.919	0.998			1	INDETERMINATE	2	TRUE	NA	0.747987827621734	3		571	780	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533606	63533606	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	378	710	0	ENST00000307078.5:c.1548C>G	p.His516Gln	p.H516Q	ENST00000307078	NM_004655.3	516	caC/caG	6/11	0.475934509918935	3	FACETS	1	0.993	1	0.421	0.4	0.442	CLONAL	1	TRUE	0	0.747987827621734	3		710	1100	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284912	15284912	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	50	582	0	ENST00000263388.2:c.4703G>T	p.Arg1568Leu	p.R1568L	ENST00000263388	NM_000435.2	1568	cGg/cTg	25/33	0.355055920388696	3	FACETS	0.213	0.18	0.25	0.071	0.06	0.084	INDETERMINATE	1	TRUE	0	0.747987827621734	3		582	861	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046357	180046357	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs771222400	NA	P-0059321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	44	513	0	ENST00000261937.6:c.2657C>A	p.Thr886Lys	p.T886K	ENST00000261937	NM_182925.4	886	aCg/aAg	19/30	0.735501387121596	2	FACETS	0.219	0.183	0.258	0.109	0.091	0.129	SUBCLONAL	1	TRUE	0	0.747987827621734	2		513	538	SUCCESS
AR	367	MSKCC	GRCh37	X	66765328	66765328	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059321-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	192	338	0	ENST00000374690.3:c.340C>A	p.Gln114Lys	p.Q114K	ENST00000374690	NM_000044.3	114	Cag/Aag	1/8	0.509093101216225	2	FACETS	0.878	0.817	0.94			1	CLONAL	1	TRUE	NA	0.747987827621734	2		338	585	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109671	115109672	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0059322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	271	513	0	ENST00000257566.3:c.2205_2206dup	p.Asp736GlyfsTer154	p.D736Gfs*154	ENST00000257566	NM_016569.3	736	gac/gGGac	8/8	0.540787606554831	2	FACETS	0.896	0.852	0.939	0.896	0.852	0.939	CLONAL	2	TRUE	0	0.617426495157143	2		513	490	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855998	68856005	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTGAGA	CTGTGAGA	-	novel	NA	P-0059322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	156	561	0	ENST00000261769.5:c.1806_1813del	p.Phe602LeufsTer12	p.F602Lfs*12	ENST00000261769	NM_004360.3	602	ttCTGTGAGAgg/ttgg	12/16	0.577981889830281	1	FACETS	0.809	0.748	0.871	0.809	0.748	0.871	CLONAL	1	TRUE	0	0.617426495157143	1		561	432	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149608	202149608	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	51	560	0	ENST00000358485.4:c.1051del	p.Ile351SerfsTer5	p.I351Sfs*5	ENST00000358485	NM_001080125.1	350	cAa/ca	8/9	1	2	FACETS	0.297	0.252	0.347	0.297	0.252	0.347	SUBCLONAL	1	TRUE	1	0.617426495157143	2		560	556	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968169	68968173	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAG	AAGAG	-	novel	NA	P-0059322-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	122	405	0	ENST00000288368.4:c.1200_1204del	p.Arg401ThrfsTer6	p.R401Tfs*6	ENST00000288368	NM_024870.2	400	AAGAGa/a	10/40	0.339384285917899	1	FACETS	0.66	0.601	0.72	0.66	0.601	0.72	INDETERMINATE	1	TRUE	0	0.617426495157143	1		405	414	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507318	8507318	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	170	497	0	ENST00000356435.5:c.1660G>T	p.Gly554Trp	p.G554W	ENST00000356435		554	Ggg/Tgg	11/35	0.353178444635258	3	FACETS	0.997	0.924	1	0.997	0.924	1	CLONAL	2	TRUE	1	0.408122027937168	3		497	503	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497533	125497533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	137	395	0	ENST00000428830.2:c.97G>A	p.Glu33Lys	p.E33K	ENST00000428830	NM_001114121.2	33	Gaa/Aaa	3/14	0.417391984219818	3	FACETS	0.991	0.91	1	0.991	0.91	1	CLONAL	2	TRUE	1	0.408122027937168	3		395	408	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074297	8074297	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	94	579	0	ENST00000377482.5:c.362A>G	p.Asn121Ser	p.N121S	ENST00000377482	NM_018948.3	121	aAt/aGt	4/4	0.408122027937168	5	FACETS	0.976	0.868	1	0.244	0.217	0.273	CLONAL	1	TRUE	1	0.408122027937168	5		579	761	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150900412	150900412	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	79	534	0	ENST00000271640.5:c.222G>C	p.Glu74Asp	p.E74D	ENST00000271640	NM_001145415.1	74	gaG/gaC	2/22	0.165003497245927	5	FACETS	1	0.967	1			1	INDETERMINATE	1	TRUE	NA	0.408122027937168	5		534	489	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675328	241675328	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0059323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	285	385	0	ENST00000366560.3:c.494T>G	p.Leu165Ter	p.L165*	ENST00000366560	NM_000143.3	165	tTa/tGa	4/10	0.408122027937168	5	FACETS	1	0.98	1	1	0.98	1	CLONAL	4	TRUE	1	0.408122027937168	5		385	533	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316059	14316059	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	55	196	0	ENST00000256196.4:c.366G>C	p.Met122Ile	p.M122I	ENST00000256196		122	atG/atC	4/6	0.336947550105791	3	FACETS	0.954	0.832	1	0.954	0.832	1	CLONAL	2	TRUE	1	0.408122027937168	3		196	170	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18439859	18439859	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0059323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	90	353	0	ENST00000266497.5:c.757A>T	p.Lys253Ter	p.K253*	ENST00000266497		253	Aaa/Taa	2/31	0.123581138680047	3	FACETS	0.84	0.754	0.931			1	INDETERMINATE	2	TRUE	NA	0.408122027937168	3		353	316	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244605	46244605	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs781284991	NA	P-0059323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	101	544	0	ENST00000334344.6:c.2699C>G	p.Pro900Arg	p.P900R	ENST00000334344	NM_152641.2	900	cCt/cGt	15/21	0.414644722080694	4	FACETS	0.937	0.837	1	0.468	0.418	0.521	CLONAL	1	TRUE	2	0.408122027937168	4		544	744	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911229	32911230	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACTTGACTTGT	novel	NA	P-0059323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	42	401	0	ENST00000380152.3:c.2738_2748dup	p.Val917ThrfsTer2	p.V917Tfs*2	ENST00000380152		913	gac/gACTTGACTTGTac	11/27	0.157795428693163	3	FACETS	0.749	0.627	0.882	0.374	0.313	0.441	INDETERMINATE	1	TRUE	1	0.408122027937168	3		401	331	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913011	32913011	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	97	537	0	ENST00000380152.3:c.4519C>T	p.Gln1507Ter	p.Q1507*	ENST00000380152		1507	Cag/Tag	11/27	0.157795428693163	3	FACETS	1	0.978	1	0.685	0.614	0.759	INDETERMINATE	1	TRUE	1	0.408122027937168	3		537	418	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2107156	2107167	+	inframe_deletion	In_Frame_Del	DEL	CATGTGCCACCT	CATGTGCCACCT	-	novel	NA	P-0059323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	63	553	0	ENST00000219476.3:c.829_840del	p.Cys277_Met280del	p.C277_M280del	ENST00000219476	NM_000548.3	275	aaCATGTGCCACCTc/aac	9/42	0.342488598674589	4	FACETS	0.782	0.677	0.896	0.391	0.338	0.448	SUBCLONAL	1	TRUE	2	0.408122027937168	4		553	556	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2214477	2214477	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	139	557	0	ENST00000398665.3:c.1805C>T	p.Ala602Val	p.A602V	ENST00000398665	NM_032482.2	602	gCt/gTt	19/28	0.169404795821754	4	FACETS	0.861	0.787	0.937	0.861	0.787	0.937	INDETERMINATE	2	TRUE	2	0.408122027937168	4		557	557	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211627	5211627	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	135	459	0	ENST00000357368.4:c.5208C>G	p.Ile1736Met	p.I1736M	ENST00000357368	NM_002850.3	1736	atC/atG	33/38	0.169404795821754	4	FACETS	0.904	0.827	0.985	0.904	0.827	0.985	INDETERMINATE	2	TRUE	2	0.408122027937168	4		459	515	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546769	9546769	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	215	645	0	ENST00000353224.5:c.1253C>A	p.Ser418Tyr	p.S418Y	ENST00000353224	NM_177990.2	418	tCc/tAc	5/10	0.342488598674589	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.408122027937168	4		645	676	SUCCESS
APC	324	MSKCC	GRCh37	5	112173687	112173840	+	frameshift_variant	Frame_Shift_Del	DEL	ATGTTTTTGACACCAATCGACATGATGATAATAGGTCAGACAATTTTAATACTGGCAACATGACTGTCCTTTCACCATATTTGAATACTACAGTGTTACCCAGCTCCTCTTCATCAAGAGGAAGCTTAGATAGTTCTCGTTCTGAAAAAGATAG	ATGTTTTTGACACCAATCGACATGATGATAATAGGTCAGACAATTTTAATACTGGCAACATGACTGTCCTTTCACCATATTTGAATACTACAGTGTTACCCAGCTCCTCTTCATCAAGAGGAAGCTTAGATAGTTCTCGTTCTGAAAAAGATAG	-	novel	NA	P-0059323-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	76	552	0	ENST00000257430.4:c.2397_2550del	p.Tyr799Ter	p.Y799*	ENST00000257430	NM_000038.5	799	tATGTTTTTGACACCAATCGACATGATGATAATAGGTCAGACAATTTTAATACTGGCAACATGACTGTCCTTTCACCATATTTGAATACTACAGTGTTACCCAGCTCCTCTTCATCAAGAGGAAGCTTAGATAGTTCTCGTTCTGAAAAAGATAGa/ta	16/16	0.408122027937168	7	FACETS	0.976	0.855	1	0.244	0.213	0.277	CLONAL	1	TRUE	3	0.408122027937168	7		552	771	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061249	38061249	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	83	529	0	ENST00000250448.2:c.740A>G	p.His247Arg	p.H247R	ENST00000250448	NM_004496.3	247	cAc/cGc	2/2	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.682378676668716	2		529	226	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	78128663	78128816	+	splice_donor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	CGCCCCTGGGCGGCCGCGCCCGCACTCACATAGCGCCTCAACTTCTTCTCGGGAGGCGATTTCCTCAGCCAGCCGGTGCACACCACGTCGCCGCCGCCGCTCATGCTGCCGGCCTGGAGCCCCCCGCCGGGTCGCGCGGACGAGGGCGCGGGCT	CGCCCCTGGGCGGCCGCGCCCGCACTCACATAGCGCCTCAACTTCTTCTCGGGAGGCGATTTCCTCAGCCAGCCGGTGCACACCACGTCGCCGCCGCCGCTCATGCTGCCGGCCTGGAGCCCCCCGCCGGGTCGCGCGGACGAGGGCGCGGGCT	-	novel	NA	P-0059324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	21	646	0	ENST00000361507.4:c.-50_75+29del		p.X17_splice	ENST00000361507	NM_080491.2	17		1/10	1	2	FACETS	0.239	0.184	0.302	0.239	0.184	0.302	SUBCLONAL	1	TRUE	1	0.682378676668716	2		646	258	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47108599	47108599	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	31	250	0	ENST00000409792.3:c.6070C>G	p.Arg2024Gly	p.R2024G	ENST00000409792	NM_014159.6	2024	Cga/Gga	13/21	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.682378676668716	2		250	88	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125230	47125231	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0059324-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	12	374	1	ENST00000409792.3:c.6039_6040delinsTT	p.Asp2014Tyr	p.D2014Y	ENST00000409792	NM_014159.6	2013	ctGGac/ctTTac	12/21	1	2	FACETS	0.239	0.168	0.325	0.239	0.168	0.325	SUBCLONAL	1	TRUE	1	0.682378676668716	2		375	147	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	32	477	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	FALSE	1	0.851418030401267	2		477	72	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0059325-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	58	403	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.879	0.773	0.989	0.879	0.773	0.989	CLONAL	1	FALSE	1	0.851418030401267	2		404	155	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059325-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	83	477	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.895	0.804	0.988	0.895	0.804	0.988	CLONAL	1	TRUE	1	0.835792649247921	2		477	222	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0059325-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	211	403	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.996	0.934	1	0.996	0.934	1	CLONAL	1	TRUE	1	0.835792649247921	2		404	507	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902164	50902164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3218773	NA	P-0059325-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	24	558	0	ENST00000440232.2:c.56G>A	p.Arg19His	p.R19H	ENST00000440232	NM_002691.3	19	cGt/cAt	2/27	0.835792649247921	1	FACETS	0.153	0.12	0.191	0.153	0.12	0.191	SUBCLONAL	1	TRUE	0	0.835792649247921	1		558	218	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467169	25467169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772310511	NA	P-0059325-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	35	705	0	ENST00000264709.3:c.1706C>T	p.Pro569Leu	p.P569L	ENST00000264709	NM_175629.2	569	cCg/cTg	15/23	1	2	FACETS	0.183	0.15	0.221	0.183	0.15	0.221	SUBCLONAL	1	TRUE	1	0.835792649247921	2		705	457	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66521899	66521899	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs369011860	NA	P-0059325-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	36	355	0	ENST00000358598.2:c.554A>G	p.Tyr185Cys	p.Y185C	ENST00000358598	NM_212471.2	185	tAt/tGt	7/11	1	2	FACETS	0.18	0.148	0.217	0.18	0.148	0.217	SUBCLONAL	1	TRUE	1	0.835792649247921	2		355	478	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413067	139413067	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059325-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	80	585	0	ENST00000277541.6:c.1075T>A	p.Cys359Ser	p.C359S	ENST00000277541	NM_017617.3	359	Tgc/Agc	6/34	0.118805419357177	4	FACETS	0.792	0.7	0.889	0.396	0.35	0.445	INDETERMINATE	1	TRUE	2	0.835792649247921	4		585	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579321	7579322	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs587780067	NA	P-0059326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	149	453	0	ENST00000269305.4:c.365_366del	p.Val122AspfsTer26	p.V122Dfs*26	ENST00000269305	NM_001126112.2	122	gTG/g	4/11	NA	2	FACETS	0.867	0.804	0.93			1	INDETERMINATE	2	TRUE	NA	0.507081346931008	2		453	339	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1686006	1686006	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1474315493	NA	P-0059326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	74	466	0	ENST00000378625.1:c.1255G>A	p.Gly419Arg	p.G419R	ENST00000378625	NM_001198994.1	419	Ggg/Agg	10/14	0.387019347137954	3	FACETS	0.837	0.736	0.946	0.419	0.368	0.473	CLONAL	1	TRUE	1	0.507081346931008	3		466	437	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584689	187584689	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	82	371	0	ENST00000441802.2:c.3344G>T	p.Gly1115Val	p.G1115V	ENST00000441802	NM_005245.3	1115	gGt/gTt	3/27	0.479929155773138	3	FACETS	0.915	0.811	1	0.458	0.405	0.513	CLONAL	1	TRUE	1	0.507081346931008	3		371	443	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38975693	38975693	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	124	374	0	ENST00000357387.3:c.835G>C	p.Ala279Pro	p.A279P	ENST00000357387	NM_152756.3	279	Gca/Cca	10/38	0.421164866618683	4	FACETS	0.806	0.735	0.881	0.806	0.735	0.881	CLONAL	2	TRUE	2	0.507081346931008	4		374	457	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273157	55273157	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059326-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	122	495	0	ENST00000275493.2:c.3480A>C	p.Lys1160Asn	p.K1160N	ENST00000275493	NM_005228.3	1160	aaA/aaC	28/28	0.479929155773138	3	FACETS	1	0.981	1	0.657	0.598	0.719	CLONAL	1	TRUE	1	0.507081346931008	3		495	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	36	513	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	1	2	FACETS	0.875	0.719	1	0.875	0.719	1	CLONAL	1	TRUE	1	0.16	2		513	514	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	41	449	1	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.16	2		450	477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	43	471	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.16	2		471	493	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	16	284	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.565	0.417	0.743	0.565	0.417	0.743	SUBCLONAL	1	TRUE	1	0.16	2		284	354	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139464	47139464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	24	308	0	ENST00000409792.3:c.5123G>A	p.Arg1708Gln	p.R1708Q	ENST00000409792	NM_014159.6	1708	cGa/cAa	9/21	1	2	FACETS	0.665	0.52	0.833	0.665	0.52	0.833	SUBCLONAL	1	TRUE	1	0.16	2		308	451	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	24	309	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	0.815	0.639	1	0.815	0.639	1	CLONAL	1	TRUE	1	0.16	2		309	368	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020225	123020225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	30	344	1	ENST00000355640.3:c.713G>A	p.Arg238Gln	p.R238Q	ENST00000355640		238	cGa/cAa	2/7	1	2	FACETS	0.889	0.716	1	0.889	0.716	1	CLONAL	1	TRUE	1	0.16	2		345	422	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778812	76778812	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	33	296	0	ENST00000373344.5:c.6767C>A	p.Ser2256Tyr	p.S2256Y	ENST00000373344	NM_000489.3	2256	tCt/tAt	31/35	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.16	2		296	375	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141631	202141631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs17860424	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	40	363	0	ENST00000358485.4:c.919C>T	p.Arg307Trp	p.R307W	ENST00000358485	NM_001080125.1	307	Cgg/Tgg	7/9	1	2	FACETS	0.982	0.816	1	0.982	0.816	1	CLONAL	1	TRUE	1	0.16	2		363	509	SUCCESS
APC	324	MSKCC	GRCh37	5	112178000	112178000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768922431	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	23	365	0	ENST00000257430.4:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000257430	NM_000038.5	2237	Cga/Tga	16/16	1	2	FACETS	0.635	0.494	0.799	0.635	0.494	0.799	SUBCLONAL	1	TRUE	1	0.16	2		365	453	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812335	212812335	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	24	329	0	ENST00000342788.4:c.241C>T	p.Arg81Ter	p.R81*	ENST00000342788	NM_005235.2	81	Cga/Tga	3/28	1	2	FACETS	0.792	0.62	0.99	0.792	0.62	0.99	CLONAL	1	TRUE	1	0.16	2		329	379	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059183	27059183	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	25	287	0	ENST00000324856.7:c.1820C>A	p.Ser607Ter	p.S607*	ENST00000324856	NM_006015.4	607	tCa/tAa	4/20	1	2	FACETS	1	0.83	1	1	0.83	1	CLONAL	1	TRUE	1	0.16	2		287	295	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211461	46211461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	15	205	0	ENST00000334344.6:c.427C>T	p.Arg143Cys	p.R143C	ENST00000334344	NM_152641.2	143	Cgt/Tgt	5/21	1	2	FACETS	0.848	0.621	1	0.848	0.621	1	CLONAL	1	TRUE	1	0.16	2		205	221	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260177	149260177	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	33	341	0	ENST00000360632.3:c.716G>T	p.Arg239Ile	p.R239I	ENST00000360632	NM_015472.4	239	aGa/aTa	4/7	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.16	2		341	371	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221243	1221243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	33	413	0	ENST00000326873.7:c.766G>A	p.Glu256Lys	p.E256K	ENST00000326873	NM_000455.4	256	Gaa/Aaa	6/10	1	2	FACETS	0.771	0.627	0.934	0.771	0.627	0.934	CLONAL	1	TRUE	1	0.16	2		413	535	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119595322	119595322	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	26	254	0	ENST00000316626.5:c.847G>T	p.Glu283Ter	p.E283*	ENST00000316626		283	Gaa/Taa	8/12	1	2	FACETS	0.827	0.655	1	0.827	0.655	1	CLONAL	1	TRUE	1	0.16	2		254	393	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937070	48937070	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	24	179	0	ENST00000267163.4:c.838G>T	p.Glu280Ter	p.E280*	ENST00000267163	NM_000321.2	280	Gaa/Taa	8/27	1	2	FACETS	1	0.828	1	1	0.828	1	CLONAL	1	TRUE	1	0.16	2		179	282	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433394	49433394	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783727	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	23	521	0	ENST00000301067.7:c.8053C>T	p.Arg2685Ter	p.R2685*	ENST00000301067	NM_003482.3	2685	Cga/Tga	32/54	1	2	FACETS	0.73	0.568	0.917	0.73	0.568	0.917	CLONAL	1	TRUE	1	0.16	2		521	394	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176490	123176490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	20	172	0	ENST00000218089.9:c.457G>A	p.Asp153Asn	p.D153N	ENST00000218089	NM_001042749.1	153	Gat/Aat	7/35	1	2	FACETS	0.868	0.664	1	0.868	0.664	1	CLONAL	1	TRUE	1	0.16	2		172	288	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118806	115118806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754023417	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	40	431	0	ENST00000257566.3:c.535G>A	p.Glu179Lys	p.E179K	ENST00000257566	NM_016569.3	179	Gaa/Aaa	2/8	1	2	FACETS	0.829	0.688	0.987	0.829	0.688	0.987	CLONAL	1	TRUE	1	0.16	2		431	603	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685303	89685303	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	16	81	0	ENST00000371953.3:c.198G>T	p.Lys66Asn	p.K66N	ENST00000371953	NM_000314.4	66	aaG/aaT	3/9	1	2	FACETS	1	0.78	1	1	0.78	1	CLONAL	1	TRUE	1	0.16	2		81	189	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46736432	46736432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764014400	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	22	317	1	ENST00000371975.4:c.1144C>T	p.Arg382Trp	p.R382W	ENST00000371975	NM_003579.3	382	Cgg/Tgg	10/18	1	2	FACETS	0.702	0.543	0.886	0.702	0.543	0.886	SUBCLONAL	1	TRUE	1	0.16	2		318	392	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8246251	8246251	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	20	386	0	ENST00000335790.3:c.383A>C	p.Lys128Thr	p.K128T	ENST00000335790	NM_002315.2	128	aAa/aCa	4/4	1	2	FACETS	0.712	0.544	0.91	0.712	0.544	0.91	CLONAL	1	TRUE	1	0.16	2		386	351	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	37	429	0	ENST00000267101.3:c.2783A>C	p.Glu928Ala	p.E928A	ENST00000267101	NM_001982.3	928	gAg/gCg	23/28	1	2	FACETS	0.936	0.771	1	0.936	0.771	1	CLONAL	1	TRUE	1	0.16	2		429	494	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041986	42041986	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	28	348	0	ENST00000219905.7:c.6181G>A	p.Asp2061Asn	p.D2061N	ENST00000219905	NM_001164273.1	2061	Gat/Aat	17/24	1	2	FACETS	0.794	0.634	0.977	0.794	0.634	0.977	CLONAL	1	TRUE	1	0.16	2		348	441	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646978	37646978	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	30	285	0	ENST00000447079.4:c.2100G>T	p.Lys700Asn	p.K700N	ENST00000447079	NM_015083.1	700	aaG/aaT	3/14	1	2	FACETS	0.812	0.653	0.992	0.812	0.653	0.992	CLONAL	1	TRUE	1	0.16	2		285	462	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424921	47424921	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	28	403	0	ENST00000404338.3:c.2989C>T	p.Arg997Ter	p.R997*	ENST00000404338	NM_004491.4	997	Cga/Tga	1/6	1	2	FACETS	0.774	0.618	0.953	0.774	0.618	0.953	CLONAL	1	TRUE	1	0.16	2		403	452	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631601	67631601	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	34	322	0	ENST00000272342.5:c.1787T>C	p.Leu596Ser	p.L596S	ENST00000272342	NM_019002.3	596	tTa/tCa	5/6	1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	1	0.16	2		322	408	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288991	212288991	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	27	277	0	ENST00000342788.4:c.2755A>G	p.Lys919Glu	p.K919E	ENST00000342788	NM_005235.2	919	Aaa/Gaa	23/28	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.16	2		277	311	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63976477	63976477	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs940227869	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	26	351	1	ENST00000398590.3:c.1624C>T	p.Arg542Ter	p.R542*	ENST00000398590	NM_001177387.1	542	Cga/Tga	11/14	1	2	FACETS	0.862	0.683	1	0.862	0.683	1	CLONAL	1	TRUE	1	0.16	2		352	377	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270159	66270159	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	30	326	0	ENST00000273854.3:c.1723A>C	p.Ile575Leu	p.I575L	ENST00000273854	NM_004439.5	575	Att/Ctt	8/18	1	2	FACETS	1	0.806	1	1	0.806	1	CLONAL	1	TRUE	1	0.16	2		326	375	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177928	56177928	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	29	471	0	ENST00000399503.3:c.2901G>T	p.Leu967Phe	p.L967F	ENST00000399503	NM_005921.1	967	ttG/ttT	14/20	1	2	FACETS	0.735	0.589	0.902	0.735	0.589	0.902	CLONAL	1	TRUE	1	0.16	2		471	493	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862915	117862915	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	17	231	0	ENST00000297338.2:c.1562T>G	p.Leu521Arg	p.L521R	ENST00000297338	NM_006265.2	521	cTt/cGt	12/14	1	2	FACETS	0.644	0.48	0.839	0.644	0.48	0.839	SUBCLONAL	1	TRUE	1	0.16	2		231	330	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2119506	2119506	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs759746608	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	29	299	0	ENST00000349721.2:c.3733C>T	p.Arg1245Ter	p.R1245*	ENST00000349721	NM_003070.3	1245	Cga/Tga	26/34	1	2	FACETS	1	0.821	1	1	0.821	1	CLONAL	1	TRUE	1	0.16	2		299	354	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072505	5072505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	22	209	0	ENST00000381652.3:c.1655G>A	p.Gly552Asp	p.G552D	ENST00000381652	NM_004972.3	552	gGc/gAc	13/25	1	2	FACETS	0.76	0.588	0.959	0.76	0.588	0.959	CLONAL	1	TRUE	1	0.16	2		209	362	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27168576	27168576	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs753021890	NA	P-0059327-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	21	210	0	ENST00000380036.4:c.448G>T	p.Glu150Ter	p.E150*	ENST00000380036	NM_000459.3	150	Gaa/Taa	3/23	1	2	FACETS	0.742	0.57	0.941	0.742	0.57	0.941	CLONAL	1	TRUE	1	0.16	2		210	354	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	69	477	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.864	0.754	0.981	0.864	0.754	0.981	CLONAL	1	TRUE	1	0.34	2		477	470	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987033	36987033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	89	428	0	ENST00000354822.5:c.656C>T	p.Pro219Leu	p.P219L	ENST00000354822	NM_001079668.2	219	cCg/cTg	3/3	1	2	FACETS	0.947	0.841	1	0.947	0.841	1	CLONAL	1	TRUE	1	0.34	2		428	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0059328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	207	572	0	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	0.279609000154254	2	FACETS	0.792	0.737	0.848	0.792	0.737	0.848	SUBCLONAL	2	TRUE	0	0.34	2		572	769	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983114	111983114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	175	515	0	ENST00000368678.4:c.1433G>A	p.Arg478Gln	p.R478Q	ENST00000368678		478	cGa/cAa	13/13	0.3	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.34	1		515	692	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6439797	6439797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	67	387	0	ENST00000356142.4:c.323C>T	p.Ser108Leu	p.S108L	ENST00000356142	NM_018890.3	108	tCa/tTa	5/7	1	2	FACETS	0.619	0.537	0.707	0.619	0.537	0.707	SUBCLONAL	1	TRUE	1	0.34	2		387	637	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802635	135802635	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203343	NA	P-0059328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	156	375	0	ENST00000298552.3:c.163C>T	p.Gln55Ter	p.Q55*	ENST00000298552	NM_001162426.1	55	Cag/Tag	4/23	0.279609000154254	2	FACETS	0.798	0.734	0.864	0.798	0.734	0.864	SUBCLONAL	2	TRUE	0	0.34	2		375	575	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061257	38061257	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	143	563	0	ENST00000250448.2:c.732G>A	p.Trp244Ter	p.W244*	ENST00000250448	NM_004496.3	244	tgG/tgA	2/2	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.34	2		563	811	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057901	27057901	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	200	580	0	ENST00000324856.7:c.1609C>T	p.Gln537Ter	p.Q537*	ENST00000324856	NM_006015.4	537	Cag/Tag	3/20	0.179534600501836	3	FACETS	0.765	0.709	0.822	0.765	0.709	0.822	INDETERMINATE	2	TRUE	1	0.34	3		580	900	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93973596	93973596	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	42	252	0	ENST00000369303.4:c.1780G>T	p.Glu594Ter	p.E594*	ENST00000369303	NM_004440.3	594	Gaa/Taa	9/17	0.3	1	FACETS	0.74	0.622	0.87	0.74	0.622	0.87	SUBCLONAL	1	TRUE	0	0.34	1		252	277	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8246207	8246207	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750816256	NA	P-0059328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	73	444	0	ENST00000335790.3:c.427G>A	p.Glu143Lys	p.E143K	ENST00000335790	NM_002315.2	143	Gag/Aag	4/4	0.16587492121116	1	FACETS	0.646	0.565	0.732	0.646	0.565	0.732	INDETERMINATE	1	TRUE	0	0.34	1		444	552	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741816	17741816	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1263455250	NA	P-0059328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	54	412	0	ENST00000250003.3:c.487C>G	p.Leu163Val	p.L163V	ENST00000250003	NM_002478.4	163	Ctg/Gtg	1/3	0.16587492121116	1	FACETS	0.594	0.508	0.687	0.594	0.508	0.687	INDETERMINATE	1	TRUE	0	0.34	1		412	444	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118361946	118361946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	40	378	0	ENST00000534358.1:c.4732G>T	p.Asp1578Tyr	p.D1578Y	ENST00000534358	NM_005933.3	1578	Gat/Tat	14/36	0.151229845325274	4	FACETS	0.448	0.371	0.535	0.149	0.123	0.179	INDETERMINATE	1	TRUE	1	0.34	4		378	703	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33446176	33446176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	128	391	0	ENST00000345365.6:c.98C>T	p.Ser33Phe	p.S33F	ENST00000345365	NM_002878.3	33	tCt/tTt	2/10	0.179534600501836	3	FACETS	1	0.982	1	0.671	0.61	0.736	INDETERMINATE	1	TRUE	1	0.34	3		391	656	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41267787	41267787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	53	302	0	ENST00000357654.3:c.90G>T	p.Leu30Phe	p.L30F	ENST00000357654	NM_007294.3	30	ttG/ttT	3/23	0.179534600501836	3	FACETS	0.672	0.573	0.78	0.336	0.286	0.39	INDETERMINATE	1	TRUE	1	0.34	3		302	543	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626403	12626403	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	154	473	0	ENST00000251849.4:c.1746G>C	p.Lys582Asn	p.K582N	ENST00000251849	NM_002880.3	582	aaG/aaC	16/17	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.34	2		473	826	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162447	47162447	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	174	406	0	ENST00000409792.3:c.3679G>C	p.Asp1227His	p.D1227H	ENST00000409792	NM_014159.6	1227	Gat/Cat	3/21	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.34	2		406	707	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163175	47163175	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	154	411	0	ENST00000409792.3:c.2951G>C	p.Arg984Thr	p.R984T	ENST00000409792	NM_014159.6	984	aGa/aCa	3/21	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.34	2		411	652	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63967905	63967905	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	67	470	0	ENST00000398590.3:c.796G>C	p.Asp266His	p.D266H	ENST00000398590	NM_001177387.1	266	Gat/Cat	7/14	1	2	FACETS	0.558	0.484	0.638	0.558	0.484	0.638	SUBCLONAL	1	TRUE	1	0.34	2		470	706	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138409933	138409933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	101	356	0	ENST00000289153.2:c.1945G>A	p.Glu649Lys	p.E649K	ENST00000289153	NM_006219.2	649	Gag/Aag	13/22	0.153747246205266	4	FACETS	1	0.973	1	0.633	0.566	0.703	INDETERMINATE	1	TRUE	2	0.34	4		356	629	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542166	141542166	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	123	355	0	ENST00000220592.5:c.2557C>G	p.Leu853Val	p.L853V	ENST00000220592	NM_012154.3	853	Ctg/Gtg	19/19	0.3	4	FACETS	1	0.965	1	0.571	0.516	0.629	CLONAL	1	TRUE	2	0.34	4		355	849	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44948997	44948997	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059328-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	93	141	0	ENST00000377967.4:c.3558G>C	p.Leu1186Phe	p.L1186F	ENST00000377967	NM_021140.2	1186	ttG/ttC	25/29	0.23162121980645	2	FACETS	1	0.963	1			1	CLONAL	2	TRUE	NA	0.34	2		141	241	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519922	NA	P-0059334-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	190	454	0	ENST00000397062.3:c.235G>A	p.Glu79Lys	p.E79K	ENST00000397062	NM_006164.4	79	Gag/Aag	2/5	0.237427723618443	4	FACETS	1	0.935	1	1	0.935	1	INDETERMINATE	2	TRUE	2	0.420260452191397	4		454	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0059334-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	225	418	0	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	0.420260452191397	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.420260452191397	2		418	525	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986889	36986889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059334-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	125	595	0	ENST00000354822.5:c.800G>A	p.Gly267Glu	p.G267E	ENST00000354822	NM_001079668.2	267	gGg/gAg	3/3	1	2	FACETS	0.897	0.814	0.985	0.897	0.814	0.985	CLONAL	1	TRUE	1	0.420260452191397	2		595	663	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506683	103506683	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059334-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	53	369	0	ENST00000355739.4:c.426C>A	p.Asp142Glu	p.D142E	ENST00000355739	NM_000123.3	142	gaC/gaA	4/15	1	2	FACETS	0.589	0.503	0.683	0.589	0.503	0.683	SUBCLONAL	1	TRUE	1	0.420260452191397	2		369	428	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434482	110434483	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0059334-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	105	500	0	ENST00000375856.3:c.3918dup	p.Gly1307ArgfsTer18	p.G1307Rfs*18	ENST00000375856	NM_003749.2	1306	-/C	1/2	1	2	FACETS	0.934	0.84	1	0.934	0.84	1	CLONAL	1	TRUE	1	0.420260452191397	2		500	535	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679193	88679193	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059334-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	161	402	0	ENST00000360948.2:c.844C>G	p.Leu282Val	p.L282V	ENST00000360948	NM_001012338.2	282	Ctg/Gtg	8/19	0.420260452191397	3	FACETS	0.756	0.697	0.818	0.756	0.697	0.818	SUBCLONAL	2	TRUE	1	0.420260452191397	3		402	613	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2114420	2114420	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1309168496	NA	P-0059334-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	325	505	0	ENST00000219476.3:c.1591A>G	p.Ile531Val	p.I531V	ENST00000219476	NM_000548.3	531	Atc/Gtc	15/42	0.397448975271299	3	FACETS	0.941	0.897	0.985	0.941	0.897	0.985	CLONAL	3	TRUE	0	0.420260452191397	3		505	663	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587526	29587526	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059334-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	160	340	0	ENST00000356175.3:c.4507A>T	p.Ser1503Cys	p.S1503C	ENST00000356175	NM_000267.3	1503	Agc/Tgc	33/57	0.420260452191397	2	FACETS	0.92	0.853	0.988	0.92	0.853	0.988	CLONAL	2	TRUE	0	0.420260452191397	2		340	414	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170752	7170752	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059334-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	250	424	0	ENST00000302850.5:c.1279T>A	p.Phe427Ile	p.F427I	ENST00000302850	NM_000208.2	427	Ttc/Atc	6/22	0.420260452191397	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.420260452191397	2		424	537	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724085	61724085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059334-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	152	408	0	ENST00000401558.2:c.817G>A	p.Gly273Ser	p.G273S	ENST00000401558	NM_003400.3	273	Ggt/Agt	10/25	0.420260452191397	6	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.420260452191397	6		408	899	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422513	225422513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059334-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	130	326	0	ENST00000264414.4:c.127G>A	p.Glu43Lys	p.E43K	ENST00000264414	NM_003590.4	43	Gaa/Aaa	2/16	0.420260452191397	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.420260452191397	1		326	327	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670533	134670533	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059334-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	117	480	0	ENST00000398015.3:c.444G>T	p.Gln148His	p.Q148H	ENST00000398015	NM_004441.4	148	caG/caT	3/16	0.420260452191397	4	FACETS	0.937	0.844	1	0.468	0.422	0.518	CLONAL	1	TRUE	2	0.420260452191397	4		480	844	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670829	134670829	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059334-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	255	518	0	ENST00000398015.3:c.740T>C	p.Met247Thr	p.M247T	ENST00000398015	NM_004441.4	247	aTg/aCg	3/16	0.420260452191397	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	2	0.420260452191397	4		518	826	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561752	55561752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059334-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	292	456	0	ENST00000288135.5:c.142G>A	p.Val48Ile	p.V48I	ENST00000288135	NM_000222.2	48	Gtc/Atc	2/21	0.420260452191397	5	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	3	0.420260452191397	5		456	962	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956196	55956196	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059334-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	217	400	0	ENST00000263923.4:c.3119A>G	p.Asn1040Ser	p.N1040S	ENST00000263923	NM_002253.2	1040	aAc/aGc	23/30	0.420260452191397	5	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	3	0.420260452191397	5		400	721	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818426	170818426	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059334-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	39	208	0	ENST00000296930.5:c.256A>G	p.Thr86Ala	p.T86A	ENST00000296930	NM_002520.6	86	Acg/Gcg	3/11	0.190671869055649	5	FACETS	0.89	0.74	1	0.297	0.246	0.352	INDETERMINATE	1	TRUE	2	0.420260452191397	5		208	340	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665245	117665245	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059334-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	86	334	0	ENST00000368508.3:c.4502C>G	p.Ser1501Cys	p.S1501C	ENST00000368508	NM_002944.2	1501	tCt/tGt	27/43	0.139612735307254	1	FACETS	0.895	0.798	0.998	0.895	0.798	0.998	INDETERMINATE	1	TRUE	0	0.420260452191397	1		334	361	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521292	8521292	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059334-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	170	329	0	ENST00000356435.5:c.946C>A	p.Gln316Lys	p.Q316K	ENST00000356435		316	Cag/Aag	9/35	0.420260452191397	2	FACETS	0.977	0.909	1	0.977	0.909	1	CLONAL	2	TRUE	0	0.420260452191397	2		329	414	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059356-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	77	477	0				ENST00000310581	NM_198253.2	-/1132			0.34043560694313	3	FACETS	1	0.972	1	0.653	0.581	0.727	INDETERMINATE	1	TRUE	1	0.637754509265646	3		477	244	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0059356-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	370	522	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.591390362790094	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	0	0.637754509265646	3		522	506	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027160	49027160	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0059356-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	92	313	0	ENST00000267163.4:c.1727C>G	p.Ser576Ter	p.S576*	ENST00000267163	NM_000321.2	576	tCa/tGa	18/27	0.612117445763728	2	FACETS	0.919	0.845	0.991	0.919	0.845	0.991	CLONAL	2	TRUE	0	0.637754509265646	2		313	157	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782335	9782335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059356-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	91	628	1	ENST00000377346.4:c.2268G>A	p.Met756Ile	p.M756I	ENST00000377346	NM_005026.3	756	atG/atA	18/24	1	2	FACETS	0.751	0.672	0.834	0.751	0.672	0.834	SUBCLONAL	1	TRUE	1	0.637754509265646	2		629	380	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099340	27099340	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059356-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	112	531	0	ENST00000324856.7:c.3577G>A	p.Asp1193Asn	p.D1193N	ENST00000324856	NM_006015.4	1193	Gat/Aat	14/20	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.637754509265646	2		531	335	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982361	201982361	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755079997	NA	P-0059356-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	128	670	0	ENST00000359651.3:c.740G>A	p.Arg247Gln	p.R247Q	ENST00000359651		247	cGa/cAa	6/8	0.34043560694313	3	FACETS	0.842	0.765	0.922	0.421	0.382	0.461	INDETERMINATE	1	TRUE	1	0.637754509265646	3		670	629	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231474184	231474184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059356-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	115	529	0	ENST00000295050.7:c.55G>A	p.Glu19Lys	p.E19K	ENST00000295050	NM_032018.5	19	Gag/Aag	1/5	0.34043560694313	3	FACETS	0.991	0.898	1	0.495	0.449	0.544	INDETERMINATE	1	TRUE	1	0.637754509265646	3		529	480	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50821720	50821720	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059356-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	27	161	0	ENST00000398568.2:c.2056C>G	p.Leu686Val	p.L686V	ENST00000398568	NM_001042412.1	686	Ctg/Gtg	13/18	0.637754509265646	1	FACETS	0.824	0.681	0.973	0.824	0.681	0.973	CLONAL	1	TRUE	0	0.637754509265646	1		161	70	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55674285	55674285	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059356-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	80	393	0	ENST00000284073.2:c.511C>A	p.His171Asn	p.H171N	ENST00000284073	NM_138962.2	171	Cat/Aat	8/14	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.637754509265646	NA		393	397	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774181	56774181	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059356-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	163	497	0	ENST00000337432.4:c.532C>G	p.Gln178Glu	p.Q178E	ENST00000337432	NM_058216.2	178	Cag/Gag	3/9	0.602759605416726	3	FACETS	0.885	0.823	0.947	0.885	0.823	0.947	CLONAL	2	TRUE	1	0.637754509265646	3		497	381	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279352	18279352	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059356-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	63	552	0	ENST00000222254.8:c.1804G>A	p.Glu602Lys	p.E602K	ENST00000222254	NM_005027.3	602	Gag/Aag	14/16	0.297539116997853	3	FACETS	0.524	0.454	0.6	0.175	0.151	0.2	INDETERMINATE	1	TRUE	0	0.637754509265646	3		552	497	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52663014	52663014	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1474605653	NA	P-0059356-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	29	295	0	ENST00000394830.3:c.1339C>T	p.His447Tyr	p.H447Y	ENST00000394830	NM_018313.4	447	Cat/Tat	13/30	0.301728486800066	2	FACETS	0.37	0.298	0.451	0.185	0.149	0.226	INDETERMINATE	1	TRUE	0	0.637754509265646	2		295	246	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277572	142277572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059356-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	52	277	1	ENST00000350721.4:c.1779G>A	p.Met593Ile	p.M593I	ENST00000350721	NM_001184.3	593	atG/atA	8/47	1	2	FACETS	0.792	0.683	0.907	0.792	0.683	0.907	CLONAL	1	TRUE	1	0.637754509265646	2		278	206	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245452	153245452	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059356-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	38	444	0	ENST00000281708.4:c.1739A>G	p.His580Arg	p.H580R	ENST00000281708	NM_033632.3	580	cAc/cGc	11/12	0.413088227960374	1	FACETS	0.364	0.303	0.431	0.364	0.303	0.431	SUBCLONAL	1	TRUE	0	0.637754509265646	1		444	223	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245522	153245522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059356-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	53	400	0	ENST00000281708.4:c.1669G>A	p.Gly557Arg	p.G557R	ENST00000281708	NM_033632.3	557	Gga/Aga	11/12	0.413088227960374	1	FACETS	0.64	0.555	0.729	0.64	0.555	0.729	SUBCLONAL	1	TRUE	0	0.637754509265646	1		400	177	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045663	26045663	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059356-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	106	599	0	ENST00000540144.1:c.25C>G	p.Arg9Gly	p.R9G	ENST00000540144	NM_003531.2	9	Cgc/Ggc	1/1	0.118380930731606	3	FACETS	0.755	0.678	0.835	0.252	0.226	0.279	INDETERMINATE	1	TRUE	0	0.637754509265646	3		599	581	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679755	30679755	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059356-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	128	624	0	ENST00000376406.3:c.1964T>C	p.Leu655Pro	p.L655P	ENST00000376406	NM_014641.2	655	cTa/cCa	5/15	0.118380930731606	3	FACETS	1	0.92	1	0.337	0.306	0.368	INDETERMINATE	1	TRUE	0	0.637754509265646	3		624	524	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527778	157527778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059356-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	97	558	0	ENST00000346085.5:c.5503G>A	p.Glu1835Lys	p.E1835K	ENST00000346085	NM_020732.3	1835	Gag/Aag	20/20	0.118380930731606	3	FACETS	0.896	0.803	0.993	0.299	0.267	0.331	INDETERMINATE	1	TRUE	0	0.637754509265646	3		558	448	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0059356-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	107	243	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.2292416410155	4	FACETS	1	0.974	1	0.585	0.535	0.634	INDETERMINATE	2	TRUE	0	0.637754509265646	4		243	235	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534882	5534882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059356-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	150	572	0	ENST00000397747.3:c.193G>A	p.Asp65Asn	p.D65N	ENST00000397747	NM_025239.3	65	Gat/Aat	3/7	0.413088227960374	1	FACETS	0.828	0.766	0.891	0.828	0.766	0.891	CLONAL	1	TRUE	0	0.637754509265646	1		572	387	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139440180	139440180	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059356-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	161	890	0	ENST00000277541.6:c.59G>A	p.Arg20Gln	p.R20Q	ENST00000277541	NM_017617.3	20	cGa/cAa	1/34	0.269688176026248	2	FACETS	1	0.973	1	0.555	0.513	0.597	INDETERMINATE	1	TRUE	0	0.637754509265646	2		890	455	SUCCESS
AR	367	MSKCC	GRCh37	X	66765025	66765025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1335991486	NA	P-0059356-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	209	246	0	ENST00000374690.3:c.37C>T	p.Arg13Trp	p.R13W	ENST00000374690	NM_000044.3	13	Cgg/Tgg	1/8	0.628618155417773	2	FACETS	1	0.987	1			1	CLONAL	2	TRUE	NA	0.637754509265646	2		246	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0059357-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	165	613	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.277728660191772	2	FACETS	0.759	0.701	0.82	0.759	0.701	0.82	SUBCLONAL	2	TRUE	0	0.366999663515878	2		614	592	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361078	70361107	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGCAGCAGCAGCAACAGCAACAGCAGCAGC	AGCAGCAGCAGCAACAGCAACAGCAGCAGC	-	rs773480549	NA	P-0059357-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	26	588	0	ENST00000374080.3:c.6300_6329del		p.X2100_splice	ENST00000374080		2100		43/45	0.366999663515878	1	FACETS	0.259	0.205	0.322	0.259	0.205	0.322	SUBCLONAL	1	TRUE	0	0.366999663515878	1		588	446	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050980	49050980	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0059357-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	91	373	0	ENST00000267163.4:c.2663+1G>T		p.X888_splice	ENST00000267163	NM_000321.2	888			0.366999663515878	2	FACETS	0.855	0.769	0.944	0.855	0.769	0.944	CLONAL	2	TRUE	0	0.366999663515878	2		373	290	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944702	206944702	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059357-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	49	391	0	ENST00000423557.1:c.224A>C	p.Lys75Thr	p.K75T	ENST00000423557	NM_000572.2	75	aAg/aCg	2/5	1	2	FACETS	0.647	0.549	0.754	0.647	0.549	0.754	SUBCLONAL	1	TRUE	1	0.366999663515878	2		391	413	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440474	49440474	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059357-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	142	610	0	ENST00000301067.7:c.4336G>C	p.Asp1446His	p.D1446H	ENST00000301067	NM_003482.3	1446	Gat/Cat	15/54	0.190749598679678	3	FACETS	0.83	0.76	0.902	0.553	0.506	0.601	INDETERMINATE	2	TRUE	0	0.366999663515878	3		610	552	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472502	88472502	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059357-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	62	664	0	ENST00000360948.2:c.2053T>G	p.Cys685Gly	p.C685G	ENST00000360948	NM_001012338.2	685	Tgc/Ggc	16/19	0.323926025583584	3	FACETS	0.806	0.697	0.924	0.269	0.232	0.308	CLONAL	1	TRUE	0	0.366999663515878	3		664	496	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353731	15353731	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059357-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	53	437	0	ENST00000263377.2:c.3149A>C	p.Lys1050Thr	p.K1050T	ENST00000263377	NM_058243.2	1050	aAg/aCg	14/20	0.256200209023987	3	FACETS	0.7	0.598	0.813	0.35	0.299	0.407	SUBCLONAL	1	TRUE	1	0.366999663515878	3		437	488	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059358-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	111	121	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.46306989090781	2	FACETS	1	0.969	1	0.584	0.529	0.641	CLONAL	1	TRUE	0	0.464958153193384	2		121	409	SUCCESS
APC	324	MSKCC	GRCh37	5	112151291	112151291	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs876660765	NA	P-0059358-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	88	141	0	ENST00000257430.4:c.933+1G>A		p.X311_splice	ENST00000257430	NM_000038.5	311			1	2	FACETS	0.932	0.831	1	0.932	0.831	1	CLONAL	1	TRUE	1	0.464958153193384	2		141	406	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117728	70117728	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059358-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	334	715	0	ENST00000245479.2:c.196G>T	p.Glu66Ter	p.E66*	ENST00000245479	NM_000346.3	66	Gag/Tag	1/3	0.464958153193384	3	FACETS	0.989	0.939	1	0.989	0.939	1	CLONAL	2	TRUE	1	0.464958153193384	3		715	895	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579554	7579554	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059358-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	144	587	0	ENST00000269305.4:c.133del	p.Leu45CysfsTer78	p.L45Cfs*78	ENST00000269305	NM_001126112.2	45	Ctg/tg	4/11	0.464958153193384	1	FACETS	0.921	0.845	1	0.921	0.845	1	CLONAL	1	TRUE	0	0.464958153193384	1		587	516	SUCCESS
APC	324	MSKCC	GRCh37	5	112174886	112174886	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0059358-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	151	434	0	ENST00000257430.4:c.3595A>T	p.Lys1199Ter	p.K1199*	ENST00000257430	NM_000038.5	1199	Aag/Tag	16/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.464958153193384	2		434	592	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0059360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	104	148	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.193301891384465	3	FACETS	0.849	0.77	0.931	0.566	0.513	0.621	INDETERMINATE	2	TRUE	0	0.490489460525496	3		148	311	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0059360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	128	600	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.35620220403379	3	FACETS	1	0.982	1	0.659	0.601	0.72	CLONAL	1	TRUE	1	0.490489460525496	3		600	493	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0059360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	42	514	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.35620220403379	3	FACETS	0.493	0.411	0.582	0.246	0.205	0.291	SUBCLONAL	1	TRUE	1	0.490489460525496	3		514	433	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440951	56440951	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	49	603	1	ENST00000407977.2:c.386C>A	p.Ala129Glu	p.A129E	ENST00000407977		129	gCg/gAg	4/10	1	2	FACETS	0.495	0.42	0.577	0.495	0.42	0.577	SUBCLONAL	1	TRUE	1	0.490489460525496	2		604	404	SUCCESS
APC	324	MSKCC	GRCh37	5	112174362	112174362	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	88	413	0	ENST00000257430.4:c.3071C>A	p.Pro1024Gln	p.P1024Q	ENST00000257430	NM_000038.5	1024	cCa/cAa	16/16	0.35620220403379	3	FACETS	1	0.977	1	0.687	0.615	0.763	CLONAL	1	TRUE	1	0.490489460525496	3		413	325	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374389	81374389	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059360-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	108	353	0	ENST00000222390.5:c.673C>A	p.His225Asn	p.H225N	ENST00000222390	NM_000601.4	225	Cat/Aat	6/18	0.234547559236254	4	FACETS	0.892	0.808	0.979	0.892	0.808	0.979	INDETERMINATE	2	TRUE	2	0.490489460525496	4		353	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579348	7579349	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0059361-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	162	660	0	ENST00000269305.4:c.338_339insAT	p.Phe113LeufsTer11	p.F113Lfs*11	ENST00000269305	NM_001126112.2	113	ttc/ttATc	4/11	0.504330983912214	1	FACETS	0.971	0.897	1	0.971	0.897	1	CLONAL	1	TRUE	0	0.504330983912214	1		660	495	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460516	8460516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748838568	NA	P-0059361-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	134	552	0	ENST00000356435.5:c.3770C>T	p.Pro1257Leu	p.P1257L	ENST00000356435		1257	cCg/cTg	22/35	1	2	FACETS	0.949	0.866	1	0.949	0.866	1	CLONAL	1	TRUE	1	0.504330983912214	2		552	560	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0059362-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	42	539	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.279981186737523	1	FACETS	0.604	0.505	0.714	0.604	0.505	0.714	SUBCLONAL	1	TRUE	0	0.279981186737523	1		539	427	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0059362-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	53	329	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.279981186737523	2		329	292	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0059362-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	76	396	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.279981186737523	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.279981186737523	1		396	414	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0059362-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	28	299	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.279981186737523	1	FACETS	0.915	0.737	1	0.915	0.737	1	CLONAL	1	TRUE	0	0.279981186737523	1		299	188	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064376	30064376	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1365006505	NA	P-0059362-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	71	308	0	ENST00000338641.4:c.940G>A	p.Asp314Asn	p.D314N	ENST00000338641	NM_000268.3	314	Gat/Aat	10/16	0.279981186737523	1	FACETS	0.989	0.866	1	0.989	0.866	1	CLONAL	1	TRUE	0	0.279981186737523	1		308	441	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091740	29091740	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200649225	NA	P-0059362-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	15	101	1	ENST00000328354.6:c.1217G>A	p.Arg406His	p.R406H	ENST00000328354	NM_007194.3	406	cGt/cAt	11/15	0.279981186737523	1	FACETS	0.731	0.539	0.957	0.731	0.539	0.957	CLONAL	1	TRUE	0	0.279981186737523	1		102	126	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066760	30066760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059362-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	24	318	0	ENST00000331968.5:c.2371G>A	p.Asp791Asn	p.D791N	ENST00000331968	NM_002742.2	791	Gac/Aac	16/18	1	2	FACETS	0.539	0.423	0.673	0.539	0.423	0.673	SUBCLONAL	1	TRUE	1	0.279981186737523	2		318	318	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911555	114911555	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059362-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	62	326	0	ENST00000543371.1:c.1073T>A	p.Met358Lys	p.M358K	ENST00000543371	NM_001198531.1	358	aTg/aAg	10/14	0.279981186737523	1	FACETS	0.947	0.822	1	0.947	0.822	1	CLONAL	1	TRUE	0	0.279981186737523	1		326	402	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212192	36212192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059362-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	37	287	0	ENST00000222270.7:c.1943G>A	p.Arg648Gln	p.R648Q	ENST00000222270	NM_014727.1	648	cGg/cAg	3/37	1	2	FACETS	0.74	0.612	0.884	0.74	0.612	0.884	SUBCLONAL	1	TRUE	1	0.279981186737523	2		287	357	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97887454	97887454	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059362-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	69	329	0	ENST00000289081.3:c.910G>A	p.Glu304Lys	p.E304K	ENST00000289081	NM_000136.2	304	Gaa/Aaa	10/15	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.279981186737523	2		329	450	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231743	66231743	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059363-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	16	305	0	ENST00000273854.3:c.1957C>A	p.Pro653Thr	p.P653T	ENST00000273854	NM_004439.5	653	Cca/Aca	11/18	1	2	FACETS	0.662	0.489	0.869	0.662	0.489	0.869	SUBCLONAL	1	TRUE	1	0.167869051578153	2		305	288	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156654	2156654	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059363-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	61	741	0	ENST00000434045.2:c.268G>T	p.Gly90Cys	p.G90C	ENST00000434045	NM_001127598.1	90	Ggc/Tgc	3/5	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.167869051578153	2		741	568	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205157	61205157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144867876	NA	P-0059363-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	40	472	0	ENST00000301761.2:c.97C>T	p.Arg33Cys	p.R33C	ENST00000301761	NM_017841.2	33	Cgc/Tgc	2/4	1	2	FACETS	1	0.837	1	1	0.837	1	CLONAL	1	TRUE	1	0.167869051578153	2		472	473	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246629	46246629	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059363-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	72	474	0	ENST00000334344.6:c.4723C>T	p.Gln1575Ter	p.Q1575*	ENST00000334344	NM_152641.2	1575	Cag/Tag	15/21	0.167869051578153	2	FACETS	0.922	0.808	1	0.922	0.808	1	CLONAL	2	TRUE	0	0.167869051578153	2		474	465	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41021734	41021734	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1249471221	NA	P-0059363-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	30	475	0	ENST00000267868.3:c.676G>A	p.Ala226Thr	p.A226T	ENST00000267868	NM_002875.4	226	Gcc/Acc	8/10	1	2	FACETS	0.818	0.659	0.999	0.818	0.659	0.999	CLONAL	1	TRUE	1	0.167869051578153	2		475	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780071	NA	P-0059363-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	75	731	0	ENST00000269305.4:c.580C>T	p.Leu194Phe	p.L194F	ENST00000269305	NM_001126112.2	194	Ctt/Ttt	6/11	1	2	FACETS	0.757	0.664	0.857	1	0.975	1	SUBCLONAL	2	TRUE	1	0.167869051578153	2		731	590	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602341	10602341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1178941219	NA	P-0059363-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	77	763	1	ENST00000171111.5:c.1237C>T	p.Arg413Cys	p.R413C	ENST00000171111	NM_203500.1	413	Cgt/Tgt	3/6	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.167869051578153	2		764	643	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295801	212295801	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1423325504	NA	P-0059363-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	44	468	0	ENST00000342788.4:c.2512C>T	p.Arg838Ter	p.R838*	ENST00000342788	NM_005235.2	838	Cga/Tga	21/28	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.167869051578153	2		468	482	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169988208	169988208	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0059363-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	39	380	0	ENST00000295797.4:c.451-1G>A		p.X151_splice	ENST00000295797	NM_002740.5	151			1	2	FACETS	0.88	0.729	1	0.88	0.729	1	CLONAL	1	TRUE	1	0.167869051578153	2		380	528	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169988252	169988252	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059363-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	34	458	0	ENST00000295797.4:c.494G>C	p.Gly165Ala	p.G165A	ENST00000295797	NM_002740.5	165	gGa/gCa	6/18	1	2	FACETS	0.681	0.555	0.823	0.681	0.555	0.823	SUBCLONAL	1	TRUE	1	0.167869051578153	2		458	595	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504989	186504989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059363-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	38	430	0	ENST00000323963.5:c.845C>T	p.Thr282Met	p.T282M	ENST00000323963		282	aCg/aTg	8/11	1	2	FACETS	0.876	0.723	1	0.876	0.723	1	CLONAL	1	TRUE	1	0.167869051578153	2		430	517	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279527	1279527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767382450	NA	P-0059363-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	102	557	0	ENST00000310581.5:c.2009C>T	p.Ala670Val	p.A670V	ENST00000310581	NM_198253.2	670	gCg/gTg	5/16	0.167869051578153	3	FACETS	0.856	0.768	0.948	1	0.975	1	CLONAL	3	TRUE	1	0.167869051578153	3		557	513	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31529147	31529147	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059363-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	111	481	0	ENST00000344624.3:c.20G>A	p.Cys7Tyr	p.C7Y	ENST00000344624		7	tGt/tAt	1/33	0.167869051578153	3	FACETS	0.866	0.781	0.955	1	0.978	1	CLONAL	3	TRUE	1	0.167869051578153	3		481	552	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509120	106509120	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1158677193	NA	P-0059363-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	35	691	0	ENST00000359195.3:c.1114G>A	p.Val372Ile	p.V372I	ENST00000359195	NM_002649.2	372	Gtc/Atc	2/11	1	2	FACETS	0.73	0.597	0.88	0.73	0.597	0.88	SUBCLONAL	1	TRUE	1	0.167869051578153	2		691	571	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559300	141559300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059363-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	53	671	0	ENST00000220592.5:c.1501G>A	p.Val501Met	p.V501M	ENST00000220592	NM_012154.3	501	Gtg/Atg	12/19	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.167869051578153	2		671	613	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841225	15841225	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745810533	NA	P-0059363-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	54	422	0	ENST00000307771.7:c.1309C>T	p.Arg437Trp	p.R437W	ENST00000307771	NM_005089.3	437	Cgg/Tgg	11/11	1	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.167869051578153	1		422	398	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183794	10183794	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	108	606	0	ENST00000256474.2:c.263G>T	p.Trp88Leu	p.W88L	ENST00000256474	NM_000551.3	88	tGg/tTg	1/3	0.507027542642294	1	FACETS	0.935	0.849	1	0.935	0.849	1	CLONAL	1	TRUE	0	0.507027542642294	1		606	340	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595815	52595816	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0059371-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	131	618	0	ENST00000394830.3:c.4099_4100del	p.Asn1367SerfsTer2	p.N1367Sfs*2	ENST00000394830	NM_018313.4	1367	AAt/t	26/30	0.507027542642294	1	FACETS	0.871	0.796	0.948	0.871	0.796	0.948	CLONAL	1	TRUE	0	0.507027542642294	1		618	443	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059372-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	104	477	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.310913801070261	2		477	526	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891137	101891137	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1554698880	NA	P-0059372-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	87	450	0	ENST00000374994.4:c.98C>T	p.Ala33Val	p.A33V	ENST00000374994	NM_004612.2	33	gCg/gTg	2/9	0.310913801070261	1	FACETS	0.934	0.83	1	0.934	0.83	1	CLONAL	1	TRUE	0	0.310913801070261	1		450	506	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254717	46254717	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059372-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	54	475	0	ENST00000334344.6:c.4907G>A	p.Trp1636Ter	p.W1636*	ENST00000334344	NM_152641.2	1636	tGg/tAg	16/21	0.310913801070261	1	FACETS	0.653	0.559	0.756	0.653	0.559	0.756	SUBCLONAL	1	TRUE	0	0.310913801070261	1		475	449	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741482	145741482	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1022453211	NA	P-0059372-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	90	889	0	ENST00000428558.2:c.1021A>G	p.Ile341Val	p.I341V	ENST00000428558	NM_004260.3	341	Atc/Gtc	5/22	NA	2	FACETS	0.638	0.565	0.716			1	INDETERMINATE	1	TRUE	NA	0.310913801070261	2		889	908	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0059373-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	129	471	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.308219180938853	3	FACETS	0.976	0.897	1	0.976	0.897	1	CLONAL	3	TRUE	0	0.308219180938853	3		471	330	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610033	43610033	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059373-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	38	755	0	ENST00000355710.3:c.1985A>C	p.Lys662Thr	p.K662T	ENST00000355710	NM_020975.4	662	aAg/aCg	11/20	0.19649434990979	3	FACETS	1	0.922	1	0.598	0.498	0.708	CLONAL	1	TRUE	1	0.308219180938853	3		755	238	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15967388	15967388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776176516	NA	P-0059373-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	15	487	0	ENST00000268712.3:c.5215C>T	p.Arg1739Trp	p.R1739W	ENST00000268712	NM_006311.3	1739	Cgg/Tgg	35/46	0.308219180938853	3	FACETS	0.407	0.297	0.539	0.136	0.099	0.18	SUBCLONAL	1	TRUE	0	0.308219180938853	3		487	276	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260104	16260104	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059373-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	18	723	0	ENST00000375759.3:c.7369G>A	p.Asp2457Asn	p.D2457N	ENST00000375759	NM_015001.2	2457	Gac/Aac	11/15	0.281367627259228	3	FACETS	0.4	0.301	0.518	0.2	0.15	0.259	SUBCLONAL	1	TRUE	1	0.308219180938853	3		723	337	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	532722	532722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564787942	NA	P-0059373-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	17	491	0	ENST00000451590.1:c.484G>A	p.Glu162Lys	p.E162K	ENST00000451590	NM_001130442.1	162	Gag/Aag	5/5	0.281367627259228	3	FACETS	0.535	0.4	0.695	0.267	0.2	0.348	SUBCLONAL	1	TRUE	1	0.308219180938853	3		491	238	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790141	40790141	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059373-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	51	590	0	ENST00000373198.4:c.2590A>G	p.Ile864Val	p.I864V	ENST00000373198	NM_133170.3	864	Atc/Gtc	18/32	0.308219180938853	3	FACETS	1	0.955	1	0.659	0.563	0.761	CLONAL	1	TRUE	1	0.308219180938853	3		590	290	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157192757	157192757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1207706014	NA	P-0059373-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	27	355	0	ENST00000346085.5:c.1747G>A	p.Asp583Asn	p.D583N	ENST00000346085	NM_020732.3	583	Gat/Aat	3/20	1	2	FACETS	0.889	0.713	1	0.889	0.713	1	CLONAL	1	TRUE	1	0.308219180938853	2		355	197	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0059374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	50	458	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.0684107360956556	3	FACETS	0.98	0.833	1	0.49	0.416	0.571	INDETERMINATE	1	TRUE	1	0.266481502628481	3		458	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0059374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	76	460	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.249811708499711	1	FACETS	0.993	0.873	1	0.993	0.873	1	CLONAL	1	TRUE	0	0.266481502628481	1		460	498	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591894	48591941	+	inframe_deletion	In_Frame_Del	DEL	TACGTGGACCCTTCTGGAGGAGATCGCTTTTGTTTGGGTCAACTCTCC	TACGTGGACCCTTCTGGAGGAGATCGCTTTTGTTTGGGTCAACTCTCC	-	novel	NA	P-0059374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	63	561	0	ENST00000342988.3:c.1057_1104del	p.Tyr353_Ser368del	p.Y353_S368del	ENST00000342988	NM_005359.5	353	TACGTGGACCCTTCTGGAGGAGATCGCTTTTGTTTGGGTCAACTCTCC/-	9/12	0.266481502628481	1	FACETS	0.69	0.597	0.791	0.69	0.597	0.791	SUBCLONAL	1	TRUE	0	0.266481502628481	1		561	594	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578359	212578359	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	55	339	0	ENST00000342788.4:c.898G>C	p.Asp300His	p.D300H	ENST00000342788	NM_005235.2	300	Gat/Cat	8/28	1	2	FACETS	0.873	0.748	1	0.873	0.748	1	CLONAL	1	TRUE	1	0.266481502628481	2		339	473	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361132	66361132	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059374-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	57	465	0	ENST00000273854.3:c.1040C>T	p.Ser347Phe	p.S347F	ENST00000273854	NM_004439.5	347	tCt/tTt	4/18	0.266481502628481	1	FACETS	0.742	0.637	0.856	0.742	0.637	0.856	SUBCLONAL	1	TRUE	0	0.266481502628481	1		465	500	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059375-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	60	477	0				ENST00000310581	NM_198253.2	-/1132			0.150630024982789	4	FACETS	0.91	0.791	1	0.91	0.791	1	INDETERMINATE	2	TRUE	2	0.308197873259766	4		477	280	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0059375-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	116	323	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.190611478524603	3	FACETS	1	0.931	1	0.686	0.623	0.752	CLONAL	2	TRUE	0	0.308197873259766	3		323	422	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956771	68956771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774302685	NA	P-0059375-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	152	401	0	ENST00000288368.4:c.889C>T	p.Arg297Cys	p.R297C	ENST00000288368	NM_024870.2	297	Cgt/Tgt	8/40	0.308197873259766	5	FACETS	1	0.97	1	0.748	0.686	0.812	CLONAL	2	TRUE	2	0.308197873259766	5		401	643	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28931588	NA	P-0059375-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	112	505	0	ENST00000349496.5:c.94G>C	p.Asp32His	p.D32H	ENST00000349496	NM_001904.3	32	Gac/Cac	3/15	0.150630024982789	4	FACETS	1	0.983	1	0.75	0.676	0.828	INDETERMINATE	1	TRUE	2	0.308197873259766	4		505	634	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	461373	461373	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059375-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	100	290	0	ENST00000399788.2:c.1147C>T	p.His383Tyr	p.H383Y	ENST00000399788	NM_001042603.1	383	Cat/Tat	9/28	0.150630024982789	4	FACETS	1	0.932	1	1	0.932	1	INDETERMINATE	2	TRUE	2	0.308197873259766	4		290	406	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242662	46242662	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059375-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	67	195	0	ENST00000334344.6:c.1624C>T	p.Arg542Ter	p.R542*	ENST00000334344	NM_152641.2	542	Cga/Tga	13/21	0.150630024982789	4	FACETS	0.951	0.834	1	0.951	0.834	1	INDETERMINATE	2	TRUE	2	0.308197873259766	4		195	299	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188847	32188847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059375-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	76	656	0	ENST00000375023.3:c.707G>A	p.Gly236Glu	p.G236E	ENST00000375023	NM_004557.3	236	gGa/gAa	4/30	0.184539543628529	3	FACETS	1	0.938	1	0.554	0.487	0.626	INDETERMINATE	1	TRUE	1	0.308197873259766	3		656	514	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646827	37646827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532472038	NA	P-0059375-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	91	333	0	ENST00000447079.4:c.1949C>T	p.Pro650Leu	p.P650L	ENST00000447079	NM_015083.1	650	cCt/cTt	3/14	0.150630024982789	4	FACETS	0.845	0.754	0.942	0.845	0.754	0.942	INDETERMINATE	2	TRUE	2	0.308197873259766	4		333	457	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532630	46532630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs903957905	NA	P-0059375-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	41	419	0	ENST00000262741.5:c.448C>T	p.Pro150Ser	p.P150S	ENST00000262741	NM_003629.3	150	Ccc/Tcc	4/10	0.177980146082614	2	FACETS	0.68	0.568	0.805	0.34	0.284	0.403	INDETERMINATE	1	TRUE	0	0.308197873259766	2		419	391	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211464	46211482	+	frameshift_variant	Frame_Shift_Del	DEL	CAAAGTTATGGGCTGTCCA	CAAAGTTATGGGCTGTCCA	-	novel	NA	P-0059375-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	63	329	0	ENST00000334344.6:c.430_448del	p.Gln144TrpfsTer65	p.Q144Wfs*65	ENST00000334344	NM_152641.2	144	CAAAGTTATGGGCTGTCCAtg/tg	5/21	0.150630024982789	4	FACETS	1	0.971	1	0.743	0.646	0.847	INDETERMINATE	1	TRUE	2	0.308197873259766	4		329	360	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29002026	29002026	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868043212	NA	P-0059375-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	67	346	0	ENST00000282397.4:c.1139C>T	p.Ser380Phe	p.S380F	ENST00000282397	NM_002019.4	380	tCt/tTt	9/30	0.184539543628529	3	FACETS	1	0.961	1	0.638	0.557	0.725	INDETERMINATE	1	TRUE	1	0.308197873259766	3		346	393	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068386	26068386	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059375-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	38	150	0	ENST00000435504.4:c.104T>C	p.Leu35Pro	p.L35P	ENST00000435504		35	cTt/cCt	2/13	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.308197873259766	2		150	230	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639067	176639067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059375-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	60	535	0	ENST00000439151.2:c.3667C>T	p.His1223Tyr	p.H1223Y	ENST00000439151	NM_022455.4	1223	Cat/Tat	5/23	0.150630024982789	4	FACETS	0.717	0.617	0.827	0.359	0.308	0.414	INDETERMINATE	1	TRUE	2	0.308197873259766	4		535	710	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982059	93982059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059375-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	100	421	0	ENST00000369303.4:c.1406C>T	p.Pro469Leu	p.P469L	ENST00000369303	NM_004440.3	469	cCc/cTc	6/17	0.177980146082614	2	FACETS	0.763	0.686	0.844	0.763	0.686	0.844	INDETERMINATE	2	TRUE	0	0.308197873259766	2		421	425	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100172	157100172	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059375-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	92	511	1	ENST00000346085.5:c.1109C>T	p.Ser370Phe	p.S370F	ENST00000346085	NM_020732.3	370	tCc/tTc	1/20	0.177980146082614	2	FACETS	0.916	0.822	1	0.916	0.822	1	INDETERMINATE	2	TRUE	0	0.308197873259766	2		512	326	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931800	68931800	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059375-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	131	321	0	ENST00000288368.4:c.230T>A	p.Ile77Asn	p.I77N	ENST00000288368	NM_024870.2	77	aTt/aAt	3/40	0.308197873259766	5	FACETS	0.895	0.818	0.975	0.895	0.818	0.975	CLONAL	3	TRUE	2	0.308197873259766	5		321	463	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0059376-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	115	536	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.172535190639262	4	FACETS	1	0.984	1	0.73	0.66	0.803	INDETERMINATE	1	TRUE	2	0.424221293432772	4		536	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0059376-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	237	311	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.390957002024616	2	FACETS	0.84	0.789	0.893	0.84	0.789	0.893	CLONAL	2	TRUE	0	0.424221293432772	2		311	665	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556364	29556365	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0059376-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	171	485	0	ENST00000356175.3:c.2733dup	p.Gln912SerfsTer7	p.Q912Sfs*7	ENST00000356175	NM_000267.3	911	ctt/cTtt	21/57	0.390957002024616	2	FACETS	0.84	0.779	0.902	0.84	0.779	0.902	CLONAL	2	TRUE	0	0.424221293432772	2		485	480	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144336635	144336635	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059376-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	45	344	0	ENST00000262995.4:c.78G>C	p.Trp26Cys	p.W26C	ENST00000262995	NM_207123.2	26	tgG/tgC	2/11	0.424221293432772	2	FACETS	0.536	0.451	0.629	0.268	0.225	0.315	SUBCLONAL	1	TRUE	0	0.424221293432772	2		344	396	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144336708	144336708	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059376-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	47	352	0	ENST00000262995.4:c.151G>A	p.Asp51Asn	p.D51N	ENST00000262995	NM_207123.2	51	Gat/Aat	2/11	0.424221293432772	2	FACETS	0.535	0.452	0.626	0.268	0.226	0.313	SUBCLONAL	1	TRUE	0	0.424221293432772	2		352	414	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	103	623	2	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.24	2		625	606	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	100	556	2	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.791	0.709	0.877	1	0.983	1	SUBCLONAL	2	TRUE	1	0.24	2		558	527	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	142	573	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.813	0.742	0.887	1	0.988	1	CLONAL	2	TRUE	1	0.24	2		574	728	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465976	69465976	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	117	781	1	ENST00000227507.2:c.814G>T	p.Glu272Ter	p.E272*	ENST00000227507	NM_053056.2	272	Gag/Tag	5/5	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.24	2		782	683	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	99	680	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.24	2		680	583	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692980	89692980	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060500126	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	44	482	1	ENST00000371953.3:c.464A>G	p.Tyr155Cys	p.Y155C	ENST00000371953	NM_000314.4	155	tAt/tGt	5/9	1	2	FACETS	0.826	0.699	0.963	1	0.966	1	CLONAL	2	TRUE	1	0.24	2		483	222	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422384	47422384	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	76	487	0	ENST00000377045.4:c.23del	p.Pro8LeufsTer26	p.P8Lfs*26	ENST00000377045	NM_001654.4	6	ggC/gg	2/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.24	2		487	469	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926893	112926893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	80	486	0	ENST00000351677.2:c.1513G>A	p.Val505Ile	p.V505I	ENST00000351677	NM_002834.3	505	Gtc/Atc	13/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.24	2		486	491	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916726	178916726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772110575	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	30	396	0	ENST00000263967.3:c.113G>A	p.Arg38His	p.R38H	ENST00000263967	NM_006218.2	38	cGt/cAt	2/21	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.24	2		396	208	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519927	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	24	227	0	ENST00000263967.3:c.1625A>T	p.Glu542Val	p.E542V	ENST00000263967	NM_006218.2	542	gAa/gTa	10/21	1	2	FACETS	0.885	0.706	1	1	0.944	1	CLONAL	2	TRUE	1	0.24	2		227	113	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905324	50905324	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	152	874	1	ENST00000440232.2:c.537del	p.Arg180GlyfsTer3	p.R180Gfs*3	ENST00000440232	NM_002691.3	178	Ggg/gg	5/27	0.24986707243561	3	FACETS	0.879	0.805	0.957	0.586	0.536	0.638	CLONAL	2	TRUE	0	0.24	3		875	807	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521525	46521525	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	56	379	0	ENST00000262741.5:c.883del	p.Met295Ter	p.M295*	ENST00000262741	NM_003629.3	295	Atg/tg	7/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.24	2		379	360	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478902	56478902	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	118	579	0	ENST00000267101.3:c.358A>G	p.Met120Val	p.M120V	ENST00000267101	NM_001982.3	120	Atg/Gtg	3/28	1	2	FACETS	0.765	0.691	0.842	1	0.985	1	SUBCLONAL	2	TRUE	1	0.24	2		579	643	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204992	128204992	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	87	747	1	ENST00000341105.2:c.449del	p.Gly150GlufsTer68	p.G150Efs*68	ENST00000341105	NM_032638.4	150	gGa/ga	3/6	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.24	2		748	560	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374828	149374828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	81	508	0	ENST00000360632.3:c.266C>T	p.Ser89Leu	p.S89L	ENST00000360632	NM_015472.4	89	tCg/tTg	2/7	1	2	FACETS	0.776	0.687	0.871	1	0.979	1	SUBCLONAL	2	TRUE	1	0.24	2		508	435	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	30	403	0	ENST00000371953.3:c.511C>A	p.Gln171Lys	p.Q171K	ENST00000371953	NM_000314.4	171	Cag/Aag	6/9	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.24	2		403	213	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428670	49428670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	123	625	0	ENST00000301067.7:c.10280C>T	p.Ala3427Val	p.A3427V	ENST00000301067	NM_003482.3	3427	gCc/gTc	35/54	1	2	FACETS	0.85	0.771	0.933	1	0.988	1	CLONAL	2	TRUE	1	0.24	2		625	603	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107012	27107013	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCAGCAGAGCCAGG	novel	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	101	809	0	ENST00000324856.7:c.6629_6642dup	p.Leu2215ArgfsTer21	p.L2215Rfs*21	ENST00000324856	NM_006015.4	2208	ttc/ttCCAGCAGAGCCAGGc	20/20	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.24	2		809	763	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711895	89711895	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	31	402	0	ENST00000371953.3:c.513G>T	p.Gln171His	p.Q171H	ENST00000371953	NM_000314.4	171	caG/caT	6/9	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.24	2		402	214	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43767817	43767818	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	130	638	0	ENST00000382044.4:c.1030_1031del	p.Leu344AlafsTer29	p.L344Afs*29	ENST00000382044	NM_001141980.1	344	CTg/g	9/28	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.24	2		638	731	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250842	99250842	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	123	621	0	ENST00000268035.6:c.146T>C	p.Leu49Pro	p.L49P	ENST00000268035	NM_000875.3	49	cTg/cCg	2/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.24	2		621	695	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434795	99434795	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	118	642	0	ENST00000268035.6:c.882G>T	p.Glu294Asp	p.E294D	ENST00000268035	NM_000875.3	294	gaG/gaT	3/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.24	2		642	687	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351844	89351844	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	90	583	2	ENST00000301030.4:c.1106del	p.Lys369ArgfsTer58	p.K369Rfs*58	ENST00000301030	NM_001256183.1	369	aAg/ag	9/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.24	2		585	550	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55607082	55607082	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	57	333	0	ENST00000284073.2:c.451A>G	p.Arg151Gly	p.R151G	ENST00000284073	NM_138962.2	151	Aga/Gga	7/14	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.24	2		333	373	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223510	36223510	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	130	892	0	ENST00000222270.7:c.6064del	p.Asp2022ThrfsTer18	p.D2022Tfs*18	ENST00000222270	NM_014727.1	2020	ccG/cc	28/37	0.110051785146198	4	FACETS	0.938	0.852	1	0.938	0.852	1	INDETERMINATE	2	TRUE	2	0.24	4		892	716	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383062	42383062	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	41	214	0	ENST00000221972.3:c.82C>T	p.Pro28Ser	p.P28S	ENST00000221972	NM_021601.3	28	Cct/Tct	2/5	0.110051785146198	4	FACETS	0.976	0.821	1	0.976	0.821	1	INDETERMINATE	2	TRUE	2	0.24	4		214	217	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705534	47705534	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs63750618	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	19	504	0	ENST00000233146.2:c.2334C>A	p.Cys778Ter	p.C778*	ENST00000233146	NM_000251.2	778	tgC/tgA	14/16	1	2	FACETS	0.501	0.38	0.644	0.501	0.38	0.644	SUBCLONAL	1	TRUE	1	0.24	2		504	316	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661378	227661378	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	37	706	1	ENST00000305123.5:c.2077A>G	p.Thr693Ala	p.T693A	ENST00000305123	NM_005544.2	693	Acc/Gcc	1/2	1	2	FACETS	0.478	0.393	0.574	0.478	0.393	0.574	SUBCLONAL	1	TRUE	1	0.24	2		707	645	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247468	71247468	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1382312066	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	114	573	0	ENST00000318789.4:c.65G>A	p.Gly22Asp	p.G22D	ENST00000318789	NM_032682.5	22	gGc/gAc	6/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.24	2		573	656	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144573	55144573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	57	469	0	ENST00000257290.5:c.2047G>A	p.Val683Ile	p.V683I	ENST00000257290	NM_006206.4	683	Gtc/Atc	15/23	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.24	2		469	350	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170814986	170814987	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	36	190	0	ENST00000296930.5:c.35dup	p.Arg13GlufsTer10	p.R13Efs*10	ENST00000296930	NM_002520.6	12	ctg/cTtg	1/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.24	2		190	218	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020991	26020991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463045135	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	44	860	0	ENST00000357647.3:c.274G>A	p.Ala92Thr	p.A92T	ENST00000357647	NM_003529.2	92	Gct/Act	1/1	1	2	FACETS	0.449	0.375	0.532	0.449	0.375	0.532	SUBCLONAL	1	TRUE	1	0.24	2		860	816	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874166	151874167	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATAC	novel	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	41	503	0	ENST00000262189.6:c.8368_8371dup	p.Ser2791CysfsTer4	p.S2791Cfs*4	ENST00000262189	NM_170606.2	2791	tct/tGTATct	38/59	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.24	2		503	317	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2110278	2110278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	52	494	0	ENST00000349721.2:c.3317C>T	p.Ala1106Val	p.A1106V	ENST00000349721	NM_003070.3	1106	gCt/gTt	24/34	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.24	2		494	399	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933388	39933388	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	132	715	0	ENST00000378444.4:c.1211A>T	p.Gln404Leu	p.Q404L	ENST00000378444	NM_001123385.1	404	cAg/cTg	4/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.24	2		715	795	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424403	47424403	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	90	720	0	ENST00000377045.4:c.323G>A	p.Ser108Asn	p.S108N	ENST00000377045	NM_001654.4	108	aGc/aAc	5/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.24	2		720	631	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347199	70347199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772101551	NA	P-0059377-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	84	648	0	ENST00000374080.3:c.2863G>A	p.Val955Met	p.V955M	ENST00000374080		955	Gtg/Atg	21/45	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.24	2		648	591	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0059378-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	81	635	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.260915617814425	2		635	422	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934641	9934641	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059378-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	57	525	0	ENST00000330684.3:c.1514C>T	p.Ala505Val	p.A505V	ENST00000330684	NM_001134407.1	505	gCa/gTa	7/13	0.145872550438232	5	FACETS	1	0.938	1	0.39	0.335	0.451	INDETERMINATE	1	TRUE	2	0.260915617814425	5		525	519	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413049	139413049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064795070	NA	P-0059379-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	11	640	0	ENST00000277541.6:c.1093C>T	p.Arg365Cys	p.R365C	ENST00000277541	NM_017617.3	365	Cgc/Tgc	6/34	0.256038147135962	2	FACETS	0.168	0.115	0.234	0.084	0.057	0.117	SUBCLONAL	1	TRUE	0	0.31	2		640	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057520006	NA	P-0059379-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	157	687	0	ENST00000269305.4:c.821T>A	p.Val274Asp	p.V274D	ENST00000269305	NM_001126112.2	274	gTt/gAt	8/11	0.256549328686448	2	FACETS	0.985	0.909	1	0.985	0.909	1	CLONAL	2	TRUE	0	0.31	2		687	514	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11273524	11273524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059379-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	50	584	0	ENST00000361445.4:c.3217C>T	p.Gln1073Ter	p.Q1073*	ENST00000361445	NM_004958.3	1073	Cag/Tag	21/58	0.299211448783405	5	FACETS	0.661	0.56	0.773	0.22	0.186	0.258	SUBCLONAL	1	TRUE	2	0.31	5		584	715	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226574114	226574114	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059379-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	104	518	0	ENST00000366794.5:c.747G>T	p.Lys249Asn	p.K249N	ENST00000366794	NM_001618.3	249	aaG/aaT	6/23	0.196704777890466	4	FACETS	0.821	0.738	0.909	0.821	0.738	0.909	CLONAL	2	TRUE	2	0.31	4		518	535	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347393	91347417	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAGGTAGACTTTATGGAAACAGAA	AAAGGTAGACTTTATGGAAACAGAA	-	novel	NA	P-0059379-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	25	422	0	ENST00000355112.3:c.3559-2_3581del		p.X1187_splice	ENST00000355112	NM_000057.2	1187		19/22	1	2	FACETS	0.477	0.376	0.593	0.477	0.376	0.593	SUBCLONAL	1	TRUE	1	0.31	2		422	338	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795234	42795234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059379-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	56	802	0	ENST00000575354.2:c.2314G>A	p.Ala772Thr	p.A772T	ENST00000575354	NM_015125.3	772	Gcc/Acc	10/20	0.198742620654803	3	FACETS	0.76	0.651	0.879	0.38	0.325	0.44	SUBCLONAL	1	TRUE	1	0.31	3		802	549	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46275845	46275845	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059379-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	118	598	0	ENST00000371998.3:c.3281C>G	p.Ala1094Gly	p.A1094G	ENST00000371998		1094	gCt/gGt	18/23	0.196704777890466	4	FACETS	0.847	0.766	0.931	0.847	0.766	0.931	CLONAL	2	TRUE	2	0.31	4		598	589	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609824	117609824	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059379-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	79	596	0	ENST00000368508.3:c.6875T>C	p.Leu2292Pro	p.L2292P	ENST00000368508	NM_002944.2	2292	cTa/cCa	43/43	0.242626515464769	3	FACETS	1	0.905	1	0.515	0.454	0.582	CLONAL	1	TRUE	1	0.31	3		596	571	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0059380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	154	704	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.421700755300506	1	FACETS	0.874	0.806	0.944	0.874	0.806	0.944	CLONAL	1	TRUE	0	0.526680651555625	1		704	493	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041881	42041881	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	69	572	0	ENST00000219905.7:c.6076G>T	p.Glu2026Ter	p.E2026*	ENST00000219905	NM_001164273.1	2026	Gaa/Taa	17/24	1	2	FACETS	0.814	0.714	0.919	0.814	0.714	0.919	CLONAL	1	TRUE	1	0.526680651555625	2		572	322	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144359177	144359177	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059380-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	47	382	0	ENST00000262995.4:c.619A>G	p.Thr207Ala	p.T207A	ENST00000262995	NM_207123.2	207	Acc/Gcc	4/11	0.193722787308473	1	FACETS	0.635	0.542	0.735	0.635	0.542	0.735	INDETERMINATE	1	TRUE	0	0.526680651555625	1		382	207	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0059381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	179	570	0	ENST00000349496.5:c.101G>A	p.Gly34Glu	p.G34E	ENST00000349496	NM_001904.3	34	gGa/gAa	3/15	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.617628448316713	2		570	568	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0059381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	119	525	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.617628448316713	2		525	332	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0059381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	118	323	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.617628448316713	2		323	382	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940657	131940657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	114	398	1	ENST00000265335.6:c.2684C>T	p.Ser895Phe	p.S895F	ENST00000265335		895	tCc/tTc	16/25	1	2	FACETS	0.89	0.807	0.975	0.89	0.807	0.975	CLONAL	1	TRUE	1	0.617628448316713	2		399	415	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468158	50468158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	147	675	0	ENST00000331340.3:c.1393G>A	p.Glu465Lys	p.E465K	ENST00000331340	NM_006060.4	465	Gaa/Aaa	8/8	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.617628448316713	2		675	462	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125499310	125499313	+	frameshift_variant	Frame_Shift_Del	DEL	ACTC	ACTC	-	novel	NA	P-0059381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	118	409	0	ENST00000428830.2:c.381_384del	p.His128GlyfsTer36	p.H128Gfs*36	ENST00000428830	NM_001114121.2	127	ACTCac/ac	5/14	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.617628448316713	2		409	379	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872668	136872668	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	178	639	0	ENST00000241393.3:c.830A>G	p.Glu277Gly	p.E277G	ENST00000241393	NM_003467.2	277	gAg/gGg	2/2	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.617628448316713	2		639	538	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845662	151845663	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0059381-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	30	627	0	ENST00000262189.6:c.13349_13350del	p.Val4450GlyfsTer22	p.V4450Gfs*22	ENST00000262189	NM_170606.2	4450	gTG/g	52/59	1	2	FACETS	0.18	0.144	0.22	0.18	0.144	0.22	SUBCLONAL	1	TRUE	1	0.617628448316713	2		627	540	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059407-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	92	477	0				ENST00000310581	NM_198253.2	-/1132			0.423475417606482	1	FACETS	0.984	0.882	1	0.984	0.882	1	CLONAL	1	TRUE	0	0.423475417606482	1		477	348	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188204	10188204	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059407-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	98	434	0	ENST00000256474.2:c.349del	p.Trp117GlyfsTer42	p.W117Gfs*42	ENST00000256474	NM_000551.3	116	cTt/ct	2/3	0.423475417606482	1	FACETS	0.95	0.854	1	0.95	0.854	1	CLONAL	1	TRUE	0	0.423475417606482	1		434	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578476	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0059407-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	149	760	0	ENST00000269305.4:c.454_455del	p.Pro152AlafsTer28	p.P152Afs*28	ENST00000269305	NM_001126112.2	152	CCg/g	5/11	0.423475417606482	1	FACETS	0.869	0.797	0.945	0.869	0.797	0.945	CLONAL	1	TRUE	0	0.423475417606482	1		760	638	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50788143	50788143	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059407-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	83	352	0	ENST00000307179.4:c.2757del	p.Glu919AspfsTer38	p.E919Dfs*38	ENST00000307179		919	gaG/ga	17/20	1	2	FACETS	0.933	0.828	1	0.933	0.828	1	CLONAL	1	TRUE	1	0.423475417606482	2		352	420	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61717812	61717812	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059407-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	96	479	0	ENST00000401558.2:c.1987C>T	p.Gln663Ter	p.Q663*	ENST00000401558	NM_003400.3	663	Caa/Taa	17/25	1	2	FACETS	0.922	0.824	1	0.922	0.824	1	CLONAL	1	TRUE	1	0.423475417606482	2		479	492	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164980	47164980	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059407-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	86	492	0	ENST00000409792.3:c.1146del	p.Lys382AsnfsTer102	p.K382Nfs*102	ENST00000409792	NM_014159.6	382	aaA/aa	3/21	0.423475417606482	1	FACETS	0.823	0.733	0.918	0.823	0.733	0.918	CLONAL	1	TRUE	0	0.423475417606482	1		492	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0059408-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	228	614	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.216837210026586	3	FACETS	0.989	0.924	1	0.989	0.924	1	CLONAL	3	TRUE	0	0.216837210026586	3		614	786	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859427	57859427	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151317566	NA	P-0059408-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	60	663	0	ENST00000228682.2:c.572G>A	p.Arg191Gln	p.R191Q	ENST00000228682	NM_005269.2	191	cGg/cAg	6/12	0.102095798810699	4	FACETS	0.866	0.744	0.998	0.433	0.372	0.499	INDETERMINATE	1	TRUE	2	0.216837210026586	4		663	778	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400784	72400784	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059408-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	41	474	0	ENST00000357731.5:c.387G>T	p.Met129Ile	p.M129I	ENST00000357731	NM_173808.2	129	atG/atT	2/7	0.113427203007834	3	FACETS	0.665	0.553	0.791	0.333	0.276	0.396	INDETERMINATE	1	TRUE	1	0.216837210026586	3		474	630	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400808	72400808	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059408-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	40	499	2	ENST00000357731.5:c.363G>T	p.Gln121His	p.Q121H	ENST00000357731	NM_173808.2	121	caG/caT	2/7	0.113427203007834	3	FACETS	0.62	0.514	0.738	0.31	0.257	0.369	INDETERMINATE	1	TRUE	1	0.216837210026586	3		501	660	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676315	37676315	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059408-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	254	579	0	ENST00000447079.4:c.3070G>T	p.Glu1024Ter	p.E1024*	ENST00000447079	NM_015083.1	1024	Gaa/Taa	11/14	0.18792539851116	2	FACETS	0.973	0.913	1	1	0.993	1	CLONAL	3	TRUE	0	0.216837210026586	2		579	803	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306772	41306772	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059408-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	72	622	0	ENST00000373198.4:c.887A>G	p.Glu296Gly	p.E296G	ENST00000373198	NM_133170.3	296	gAg/gGg	7/32	0.113427203007834	3	FACETS	0.975	0.851	1	0.487	0.425	0.555	INDETERMINATE	1	TRUE	1	0.216837210026586	3		622	755	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372095	55372095	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059408-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	77	838	0	ENST00000297316.4:c.785C>T	p.Pro262Leu	p.P262L	ENST00000297316	NM_022454.3	262	cCc/cTc	2/2	0.191040453929689	3	FACETS	0.909	0.797	1	0.455	0.398	0.515	CLONAL	1	TRUE	1	0.216837210026586	3		838	866	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059409-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	58	121	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.199804609105713	0	FACETS	0.985	0.852	1			1	CLONAL	1	TRUE	0	0.27525401607478	0		121	310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0059409-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	182	503	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.27525401607478	1	FACETS	0.782	0.724	0.843	1	0.991	1	SUBCLONAL	2	TRUE	0	0.27525401607478	1		503	729	SUCCESS
APC	324	MSKCC	GRCh37	5	112175524	112175524	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059409-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	136	607	0	ENST00000257430.4:c.4233del	p.Ser1411ArgfsTer4	p.S1411Rfs*4	ENST00000257430	NM_000038.5	1411	agT/ag	16/16	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.27525401607478	2		607	692	SUCCESS
APC	324	MSKCC	GRCh37	5	112170820	112170821	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs397515732	NA	P-0059409-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	105	431	0	ENST00000257430.4:c.1917dup	p.Arg640ThrfsTer11	p.R640Tfs*11	ENST00000257430	NM_000038.5	639	tta/ttAa	15/16	1	2	FACETS	0.91	0.821	1	1	0.987	1	CLONAL	2	TRUE	1	0.27525401607478	2		431	419	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0059411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	266	458	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.616917565640046	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.616917565640046	2		458	426	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0059411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	887	784	2	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.0871872991640892	3	FACETS	0.927	0.905	0.949			1	INDETERMINATE	3	TRUE	NA	0.616917565640046	3		786	1353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs967461896	NA	P-0059411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	372	868	0	ENST00000269305.4:c.526T>C	p.Cys176Arg	p.C176R	ENST00000269305	NM_001126112.2	176	Tgc/Cgc	5/11	0.616917565640046	1	FACETS	0.941	0.897	0.986	0.941	0.897	0.986	CLONAL	1	TRUE	0	0.616917565640046	1		868	886	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784056	120784056	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	159	831	0	ENST00000257552.2:c.929C>A	p.Thr310Asn	p.T310N	ENST00000257552	NM_002442.3	310	aCc/aAc	13/15	0.616917565640046	2	FACETS	0.374	0.341	0.408	0.187	0.17	0.204	SUBCLONAL	1	TRUE	0	0.616917565640046	2		831	1379	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502194	157502256	+	inframe_deletion	In_Frame_Del	DEL	ACCTCACCTTCATGGAAGAGAGAGGCTCTCCTGTCTCAAGTCTGCCTGCCGTGGGCAAGAAGC	ACCTCACCTTCATGGAAGAGAGAGGCTCTCCTGTCTCAAGTCTGCCTGCCGTGGGCAAGAAGC	-	novel	NA	P-0059411-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	143	684	0	ENST00000346085.5:c.3227_3289del	p.Tyr1076_Pro1097delinsSer	p.Y1076_P1097delinsS	ENST00000346085	NM_020732.3	1076	tACCTCACCTTCATGGAAGAGAGAGGCTCTCCTGTCTCAAGTCTGCCTGCCGTGGGCAAGAAGCcc/tcc	12/20	0.616917565640046	1	FACETS	0.396	0.361	0.433	0.396	0.361	0.433	SUBCLONAL	1	TRUE	0	0.616917565640046	1		684	809	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	81	121	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.215038252498688	4	FACETS	1	0.919	1	1	0.919	1	CLONAL	3	TRUE	1	0.215038252498688	4		121	294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579536	7579536	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059412-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	37	895	0	ENST00000269305.4:c.151del	p.Glu51AsnfsTer72	p.E51Nfs*72	ENST00000269305	NM_001126112.2	51	Gaa/aa	4/11	0.215038252498688	1	FACETS	0.903	0.747	1	0.903	0.747	1	CLONAL	1	TRUE	0	0.215038252498688	1		895	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0059413-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	161	522	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.969	0.893	1	0.969	0.893	1	CLONAL	1	TRUE	1	0.530760668047852	2		522	626	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0059413-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	218	470	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.530760668047852	2		470	731	SUCCESS
APC	324	MSKCC	GRCh37	5	112174106	112174106	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0059413-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	118	388	2	ENST00000257430.4:c.2815A>T	p.Lys939Ter	p.K939*	ENST00000257430	NM_000038.5	939	Aag/Tag	16/16	0.529811850304415	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.530760668047852	1		390	324	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557165	29557338	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTATTGTTTTCAAACTTACATTTAATTCGTTTTACTTGATGACTAAAGTATTTAGAATGCCTTCTCTTTTGTCTATATCTGATAATTTTTTTATTGTTTCTATGTCTATATAGGTATGTTCGTGTGCTTGGGAATATGGTCCATGCAATTCAAATAAAAACGAAACTGTGTCAA	TTATTGTTTTCAAACTTACATTTAATTCGTTTTACTTGATGACTAAAGTATTTAGAATGCCTTCTCTTTTGTCTATATCTGATAATTTTTTTATTGTTTCTATGTCTATATAGGTATGTTCGTGTGCTTGGGAATATGGTCCATGCAATTCAAATAAAAACGAAACTGTGTCAA	-	novel	NA	P-0059413-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	81	130	0	ENST00000356175.3:c.2991-110_3054del		p.X997_splice	ENST00000356175	NM_000267.3	997		23/57	0.530760668047852	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	0	0.530760668047852	2		130	146	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927454	49927454	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059413-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	207	500	4	ENST00000296474.3:c.3850G>A	p.Gly1284Ser	p.G1284S	ENST00000296474	NM_002447.2	1284	Ggt/Agt	19/20	0.529811850304415	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.530760668047852	1		504	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579527	7579528	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0059414-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	54	803	0	ENST00000269305.4:c.159dup	p.Phe54ValfsTer3	p.F54Vfs*3	ENST00000269305	NM_001126112.2	53	-/G	4/11	0.320248850274406	1	FACETS	0.385	0.328	0.448	0.385	0.328	0.448	SUBCLONAL	1	TRUE	0	0.320248850274406	1		803	735	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839896	27839896	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059414-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	178	875	0	ENST00000328488.2:c.198del	p.Pro67LeufsTer24	p.P67Lfs*24	ENST00000328488	NM_003533.2	66	ctA/ct	1/1	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.320248850274406	2		875	1002	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714427	117714428	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0059414-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	92	403	0	ENST00000368508.3:c.1220_1221dup	p.Ile408LeufsTer21	p.I408Lfs*21	ENST00000368508	NM_002944.2	407	-/CT	11/43	0.320248850274406	1	FACETS	0.928	0.827	1	0.928	0.827	1	CLONAL	1	TRUE	0	0.320248850274406	1		403	520	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527700	157527715	+	frameshift_variant	Frame_Shift_Del	DEL	GTGCAGGAGTTCAATA	GTGCAGGAGTTCAATA	-	novel	NA	P-0059414-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	137	633	0	ENST00000346085.5:c.5428_5443del	p.Gln1810AlafsTer36	p.Q1810Afs*36	ENST00000346085	NM_020732.3	1809	GTGCAGGAGTTCAATAgt/gt	20/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.320248850274406	2		633	789	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579527	7579528	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0059414-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	207	803	0	ENST00000269305.4:c.159dup	p.Phe54ValfsTer3	p.F54Vfs*3	ENST00000269305	NM_001126112.2	53	-/G	4/11	0.387719818035817	3	FACETS	1	0.975	1	0.716	0.672	0.762	CLONAL	2	TRUE	0	0.496811895388865	3		803	484	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839896	27839896	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059414-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	346	875	0	ENST00000328488.2:c.198del	p.Pro67LeufsTer24	p.P67Lfs*24	ENST00000328488	NM_003533.2	66	ctA/ct	1/1	0.496811895388865	5	FACETS	1	0.989	1	0.772	0.732	0.813	CLONAL	2	TRUE	2	0.496811895388865	5		875	1050	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714427	117714428	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0059414-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	105	403	0	ENST00000368508.3:c.1220_1221dup	p.Ile408LeufsTer21	p.I408Lfs*21	ENST00000368508	NM_002944.2	407	-/CT	11/43	0.500038786166981	1	FACETS	0.913	0.846	0.979	1	0.99	1	CLONAL	2	TRUE	0	0.496811895388865	1		403	174	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527700	157527715	+	frameshift_variant	Frame_Shift_Del	DEL	GTGCAGGAGTTCAATA	GTGCAGGAGTTCAATA	-	novel	NA	P-0059414-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	216	633	0	ENST00000346085.5:c.5428_5443del	p.Gln1810AlafsTer36	p.Q1810Afs*36	ENST00000346085	NM_020732.3	1809	GTGCAGGAGTTCAATAgt/gt	20/20	0.484085057153892	4	FACETS	0.963	0.899	1	0.963	0.899	1	CLONAL	2	TRUE	2	0.496811895388865	4		633	676	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	71	967	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.53456929309082	2	FACETS	0.278	0.242	0.318	0.139	0.121	0.159	SUBCLONAL	1	TRUE	0	0.53456929309082	2		974	954	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	131	156	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.961	0.877	1	0.961	0.877	1	CLONAL	1	TRUE	1	0.53456929309082	2		160	510	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444659	78444659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs908264837	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	192	647	0	ENST00000370768.2:c.30del	p.Ser11LeufsTer43	p.S11Lfs*43	ENST00000370768	NM_003902.3	10	ccC/cc	1/20	1	2	FACETS	0.867	0.803	0.933	0.867	0.803	0.933	CLONAL	1	TRUE	1	0.53456929309082	2		647	829	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	208	628	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.819	0.761	0.88	0.819	0.761	0.88	CLONAL	1	TRUE	1	0.53456929309082	2		629	950	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	229	783	5	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.958	0.895	1	0.958	0.895	1	CLONAL	1	TRUE	1	0.53456929309082	2		788	894	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489535	56489535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1403278713	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	199	646	0	ENST00000267101.3:c.2000G>A	p.Arg667His	p.R667H	ENST00000267101	NM_001982.3	667	cGt/cAt	17/28	1	2	FACETS	0.901	0.836	0.968	0.901	0.836	0.968	CLONAL	1	TRUE	1	0.53456929309082	2		646	826	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	24	163	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.655	0.52	0.807	0.655	0.52	0.807	SUBCLONAL	1	TRUE	1	0.53456929309082	2		163	137	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	53	428	0	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.247	0.21	0.288	0.247	0.21	0.288	SUBCLONAL	1	TRUE	1	0.53456929309082	2		428	802	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	433	684	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.53456929309082	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.53456929309082	2		684	781	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652117	36652117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs114149607	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	174	769	0	ENST00000244741.5:c.239C>T	p.Thr80Met	p.T80M	ENST00000244741	NM_000389.4	80	aCg/aTg	2/3	1	2	FACETS	0.807	0.744	0.872	0.807	0.744	0.872	CLONAL	1	TRUE	1	0.53456929309082	2		769	807	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	193	644	0	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	1	2	FACETS	0.989	0.918	1	0.989	0.918	1	CLONAL	1	TRUE	1	0.53456929309082	2		644	730	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	173	587	3	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.53456929309082	2		590	647	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772951	135772951	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs118203724	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	138	453	0	ENST00000298552.3:c.2672del	p.Asn891ThrfsTer40	p.N891Tfs*40	ENST00000298552	NM_001162426.1	891	aAc/ac	21/23	1	2	FACETS	0.929	0.849	1	0.929	0.849	1	CLONAL	1	TRUE	1	0.53456929309082	2		453	556	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	153	479	1	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.53456929309082	2		480	489	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	52	580	0	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	0.271	0.23	0.317	0.271	0.23	0.317	SUBCLONAL	1	TRUE	1	0.53456929309082	2		580	717	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661663	227661664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761880048	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	147	739	11	ENST00000305123.5:c.1791dup	p.His598AlafsTer13	p.H598Afs*13	ENST00000305123	NM_005544.2	597	-/G	1/2	1	2	FACETS	0.778	0.712	0.847	0.778	0.712	0.847	SUBCLONAL	1	TRUE	1	0.53456929309082	2		750	707	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186895	142186895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866304619	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	103	214	0	ENST00000350721.4:c.6568C>T	p.Arg2190Cys	p.R2190C	ENST00000350721	NM_001184.3	2190	Cgt/Tgt	39/47	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.53456929309082	2		214	381	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027087	71027087	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	45	749	1	ENST00000318789.4:c.1240del	p.Leu414Ter	p.L414*	ENST00000318789	NM_032682.5	414	Ctg/tg	15/21	1	2	FACETS	0.208	0.174	0.245	0.208	0.174	0.245	SUBCLONAL	1	TRUE	1	0.53456929309082	2		750	811	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591135	67591136	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	127	477	0	ENST00000274335.5:c.1732_1733del	p.Asp578ProfsTer23	p.D578Pfs*23	ENST00000274335		576	acGAga/acga	12/15	1	2	FACETS	0.845	0.769	0.925	0.845	0.769	0.925	CLONAL	1	TRUE	1	0.53456929309082	2		477	562	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797261	135797261	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	114	485	0	ENST00000298552.3:c.608del	p.Leu203CysfsTer7	p.L203Cfs*7	ENST00000298552	NM_001162426.1	203	tTg/tg	7/23	1	2	FACETS	0.713	0.644	0.786	0.713	0.644	0.786	SUBCLONAL	1	TRUE	1	0.53456929309082	2		485	598	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909698	50909698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	217	701	0	ENST00000440232.2:c.1418C>T	p.Thr473Met	p.T473M	ENST00000440232	NM_002691.3	473	aCg/aTg	12/27	1	2	FACETS	0.928	0.864	0.994	0.928	0.864	0.994	CLONAL	1	TRUE	1	0.53456929309082	2		701	875	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37045935	37045935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750781	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	156	488	0	ENST00000231790.2:c.350C>T	p.Thr117Met	p.T117M	ENST00000231790	NM_000249.3	117	aCg/aTg	4/19	1	2	FACETS	0.976	0.898	1	0.976	0.898	1	CLONAL	1	TRUE	1	0.53456929309082	2		488	598	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717730	89717730	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121909239	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	126	406	0	ENST00000371953.3:c.755A>G	p.Asp252Gly	p.D252G	ENST00000371953	NM_000314.4	252	gAt/gGt	7/9	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.53456929309082	2		406	442	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	169	844	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.732	0.673	0.793	0.732	0.673	0.793	SUBCLONAL	1	TRUE	1	0.53456929309082	2		846	864	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300040	137300040	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	183	565	0	ENST00000481739.1:c.331del	p.Leu111TrpfsTer57	p.L111Wfs*57	ENST00000481739	NM_002957.4	109	Ccc/cc	3/10	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.53456929309082	2		565	667	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564511	86564511	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	222	706	0	ENST00000274376.6:c.248del	p.Gly83GlufsTer4	p.G83Efs*4	ENST00000274376	NM_002890.2	81	ctG/ct	1/25	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.53456929309082	2		706	721	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274740	142274741	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	86	347	0	ENST00000350721.4:c.2319_2320del	p.Lys773AsnfsTer3	p.K773Nfs*3	ENST00000350721	NM_001184.3	773	aaAAta/aata	10/47	1	2	FACETS	0.849	0.756	0.947	0.849	0.756	0.947	CLONAL	1	TRUE	1	0.53456929309082	2		347	379	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453399	40453399	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs759027671	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	239	644	2	ENST00000345506.4:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000345506	NM_003152.3	366	Ccc/cc	10/20	0.53456929309082	2	FACETS	0.949	0.887	1	0.475	0.443	0.507	CLONAL	1	TRUE	0	0.53456929309082	2		646	942	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512491	149512491	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759481106	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	203	734	1	ENST00000261799.4:c.949C>T	p.Arg317Trp	p.R317W	ENST00000261799	NM_002609.3	317	Cgg/Tgg	7/23	1	2	FACETS	0.979	0.91	1	0.979	0.91	1	CLONAL	1	TRUE	1	0.53456929309082	2		735	776	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55704619	55704619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567945640	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	167	508	0	ENST00000284073.2:c.682C>T	p.Arg228Cys	p.R228C	ENST00000284073	NM_138962.2	228	Cgt/Tgt	10/14	0.53456929309082	2	FACETS	1	0.944	1	0.514	0.474	0.555	CLONAL	1	TRUE	0	0.53456929309082	2		508	608	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427469	49427472	+	frameshift_variant	Frame_Shift_Del	DEL	AAGG	AAGG	-	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	234	795	0	ENST00000301067.7:c.11016_11019del	p.Phe3672LeufsTer76	p.F3672Lfs*76	ENST00000301067	NM_003482.3	3672	ttCCTT/tt	39/54	1	2	FACETS	0.991	0.926	1	0.991	0.926	1	CLONAL	1	TRUE	1	0.53456929309082	2		795	883	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3634827	3634827	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs543847606	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	249	580	0	ENST00000294008.3:c.4682C>T	p.Thr1561Met	p.T1561M	ENST00000294008	NM_032444.2	1561	aCg/aTg	13/15	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.53456929309082	2		580	919	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885995	59885995	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752309409	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	146	559	0	ENST00000259008.2:c.751C>T	p.Arg251Cys	p.R251C	ENST00000259008	NM_032043.2	251	Cgc/Tgc	7/20	0.53456929309082	2	FACETS	0.858	0.785	0.933	0.429	0.392	0.467	CLONAL	1	TRUE	0	0.53456929309082	2		559	637	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252376	133252376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759414746	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	166	510	0	ENST00000320574.5:c.1051G>A	p.Val351Ile	p.V351I	ENST00000320574	NM_006231.2	351	Gtc/Atc	11/49	1	2	FACETS	0.992	0.915	1	0.992	0.915	1	CLONAL	1	TRUE	1	0.53456929309082	2		510	626	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617532	158617532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	224	642	0	ENST00000263640.3:c.1124G>A	p.Arg375His	p.R375H	ENST00000263640	NM_001105.4	375	cGt/cAt	9/11	1	2	FACETS	0.985	0.919	1	0.985	0.919	1	CLONAL	1	TRUE	1	0.53456929309082	2		642	851	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025530	1025530	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377410286	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	209	649	0	ENST00000358495.3:c.845C>T	p.Pro282Leu	p.P282L	ENST00000358495	NM_134424.2	282	cCg/cTg	9/12	1	2	FACETS	0.964	0.897	1	0.964	0.897	1	CLONAL	1	TRUE	1	0.53456929309082	2		649	811	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188126	11188126	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	222	641	0	ENST00000361445.4:c.5968G>A	p.Ala1990Thr	p.A1990T	ENST00000361445	NM_004958.3	1990	Gca/Aca	43/58	1	2	FACETS	0.994	0.927	1	0.994	0.927	1	CLONAL	1	TRUE	1	0.53456929309082	2		641	836	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90645597	90645597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	127	440	0	ENST00000330062.3:c.26G>A	p.Arg9His	p.R9H	ENST00000330062	NM_002168.2	9	cGc/cAc	1/11	1	2	FACETS	0.98	0.893	1	0.98	0.893	1	CLONAL	1	TRUE	1	0.53456929309082	2		440	485	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267524	7267524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	189	622	2	ENST00000302850.5:c.484C>T	p.Arg162Cys	p.R162C	ENST00000302850	NM_000208.2	162	Cgt/Tgt	2/22	1	2	FACETS	0.934	0.865	1	0.934	0.865	1	CLONAL	1	TRUE	1	0.53456929309082	2		624	757	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437638	52437638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553644908	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	248	715	0	ENST00000460680.1:c.1523G>A	p.Arg508His	p.R508H	ENST00000460680	NM_004656.3	508	cGc/cAc	13/17	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.53456929309082	2		715	856	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822005	72822005	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	177	740	1	ENST00000268489.5:c.10170del	p.Val3391CysfsTer94	p.V3391Cfs*94	ENST00000268489	NM_006885.3	3390	aaA/aa	10/10	1	2	FACETS	0.813	0.75	0.878	0.813	0.75	0.878	CLONAL	1	TRUE	1	0.53456929309082	2		741	815	SUCCESS
APC	324	MSKCC	GRCh37	5	112175504	112175504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761966904	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	151	646	0	ENST00000257430.4:c.4213G>A	p.Val1405Ile	p.V1405I	ENST00000257430	NM_000038.5	1405	Gtt/Att	16/16	1	2	FACETS	0.885	0.812	0.962	0.885	0.812	0.962	CLONAL	1	TRUE	1	0.53456929309082	2		646	638	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900946	114900946	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	194	567	0	ENST00000543371.1:c.556A>G	p.Asn186Asp	p.N186D	ENST00000543371	NM_001198531.1	186	Aac/Gac	6/14	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.53456929309082	2		567	702	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942728	44942728	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	124	362	0	ENST00000377967.4:c.3308T>C	p.Leu1103Pro	p.L1103P	ENST00000377967	NM_021140.2	1103	cTg/cCg	23/29	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.53456929309082	2		362	463	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912440	50912440	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	205	608	0	ENST00000440232.2:c.1954C>T	p.Arg652Trp	p.R652W	ENST00000440232	NM_002691.3	652	Cgg/Tgg	16/27	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.53456929309082	2		608	714	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553478	29553478	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781807	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	277	604	1	ENST00000356175.3:c.2033del	p.Pro678ArgfsTer10	p.P678Rfs*10	ENST00000356175	NM_000267.3	676	aCc/ac	18/57	0.53456929309082	2	FACETS	0.811	0.767	0.855	0.811	0.767	0.855	CLONAL	2	TRUE	0	0.53456929309082	2		605	639	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1685019	1685019	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375840869	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	168	650	0	ENST00000378625.1:c.1606C>T	p.Arg536Cys	p.R536C	ENST00000378625	NM_001198994.1	536	Cgc/Tgc	13/14	1	2	FACETS	0.96	0.885	1	0.96	0.885	1	CLONAL	1	TRUE	1	0.53456929309082	2		650	655	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1749278	1749279	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	127	448	0	ENST00000378609.4:c.93_94del	p.Gln32AspfsTer46	p.Q32Dfs*46	ENST00000378609	NM_002074.3	31	tcTCag/tcag	4/12	1	2	FACETS	0.903	0.822	0.988	0.903	0.822	0.988	CLONAL	1	TRUE	1	0.53456929309082	2		448	526	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759906	63759906	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	175	610	0	ENST00000279873.7:c.559T>C	p.Tyr187His	p.Y187H	ENST00000279873	NM_032199.2	187	Tac/Cac	4/10	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.53456929309082	2		610	651	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852088	63852088	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs952373984	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	217	693	0	ENST00000279873.7:c.2866C>T	p.Arg956Trp	p.R956W	ENST00000279873	NM_032199.2	956	Cgg/Tgg	10/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.53456929309082	2		693	717	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10776589	10776589	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	167	586	0	ENST00000361367.2:c.229G>T	p.Asp77Tyr	p.D77Y	ENST00000361367	NM_014633.3	77	Gac/Tac	3/25	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.53456929309082	2		586	584	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47594585	47594585	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	264	714	1	ENST00000430070.2:c.1502del	p.Lys501ArgfsTer16	p.K501Rfs*16	ENST00000430070	NM_018095.4	501	aAg/ag	4/4	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.53456929309082	2		715	891	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127691	64127691	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	203	595	0	ENST00000334205.4:c.184T>C	p.Tyr62His	p.Y62H	ENST00000334205	NM_003942.2	62	Tac/Cac	3/17	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.53456929309082	2		595	729	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946159	71946159	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	201	634	0	ENST00000298229.2:c.2416-1G>A		p.X806_splice	ENST00000298229	NM_001567.3	806			1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.53456929309082	2		634	748	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949324	71949324	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1339673499	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	202	768	0	ENST00000298229.2:c.3704A>G	p.Asp1235Gly	p.D1235G	ENST00000298229	NM_001567.3	1235	gAc/gGc	28/28	1	2	FACETS	0.846	0.785	0.91	0.846	0.785	0.91	CLONAL	1	TRUE	1	0.53456929309082	2		768	893	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498256	498257	+	frameshift_variant,start_lost,start_retained_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	142	438	0	ENST00000399788.2:c.1dup	p.Met1?	p.M1?	ENST00000399788	NM_001042603.1	1	atg/aAtg	1/28	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.53456929309082	2		438	519	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257765	133257765	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	160	616	0	ENST00000320574.5:c.163G>T	p.Glu55Ter	p.E55*	ENST00000320574	NM_006231.2	55	Gag/Tag	2/49	1	2	FACETS	0.842	0.774	0.913	0.842	0.774	0.913	CLONAL	1	TRUE	1	0.53456929309082	2		616	711	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434403	110434403	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	185	598	0	ENST00000375856.3:c.3998C>T	p.Ala1333Val	p.A1333V	ENST00000375856	NM_003749.2	1333	gCc/gTc	1/2	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.53456929309082	2		598	662	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819682	81819682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372502550	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	211	681	0	ENST00000359376.3:c.88G>A	p.Val30Met	p.V30M	ENST00000359376	NM_002661.3	30	Gtg/Atg	2/33	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.53456929309082	2		681	789	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86545002	86545002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199658264	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	162	602	0	ENST00000262426.4:c.827C>T	p.Ala276Val	p.A276V	ENST00000262426	NM_001451.2	276	gCg/gTg	1/2	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.53456929309082	2		602	560	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348157	89348157	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	239	694	0	ENST00000301030.4:c.4793A>G	p.His1598Arg	p.H1598R	ENST00000301030	NM_001256183.1	1598	cAc/cGc	9/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.53456929309082	2		694	846	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351770	89351770	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	209	588	0	ENST00000301030.4:c.1180A>C	p.Asn394His	p.N394H	ENST00000301030	NM_001256183.1	394	Aat/Cat	9/13	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.53456929309082	2		588	751	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41258512	41258512	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	111	308	2	ENST00000357654.3:c.173C>A	p.Pro58His	p.P58H	ENST00000357654	NM_007294.3	58	cCt/cAt	4/23	0.53456929309082	2	FACETS	0.942	0.852	1	0.471	0.426	0.518	CLONAL	1	TRUE	0	0.53456929309082	2		310	441	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41267776	41267776	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	134	364	0	ENST00000357654.3:c.101C>A	p.Pro34His	p.P34H	ENST00000357654	NM_007294.3	34	cCt/cAt	3/23	0.53456929309082	2	FACETS	0.985	0.9	1	0.492	0.45	0.537	CLONAL	1	TRUE	0	0.53456929309082	2		364	509	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222299	2222299	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	212	743	0	ENST00000398665.3:c.3131G>T	p.Arg1044Met	p.R1044M	ENST00000398665	NM_032482.2	1044	aGg/aTg	24/28	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.53456929309082	2		743	783	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097240	11097240	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	173	692	0	ENST00000358026.2:c.731C>A	p.Pro244Gln	p.P244Q	ENST00000358026	NM_001128849.1	244	cCg/cAg	4/36	1	2	FACETS	0.882	0.814	0.953	0.882	0.814	0.953	CLONAL	1	TRUE	1	0.53456929309082	2		692	734	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353962	15353962	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	72	231	0	ENST00000263377.2:c.2918A>C	p.Gln973Pro	p.Q973P	ENST00000263377	NM_058243.2	973	cAg/cCg	14/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.53456929309082	2		231	240	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256793	19256793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1008837361	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	35	532	0	ENST00000162023.5:c.920G>A	p.Arg307His	p.R307H	ENST00000162023		307	cGc/cAc	13/13	1	2	FACETS	0.207	0.168	0.249	0.207	0.168	0.249	SUBCLONAL	1	TRUE	1	0.53456929309082	2		532	634	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36208924	36208924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	157	339	0	ENST00000222270.7:c.4G>A	p.Ala2Thr	p.A2T	ENST00000222270	NM_014727.1	2	Gcg/Acg	1/37	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.53456929309082	2		339	453	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234182	39234182	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	79	353	1	ENST00000402219.2:c.2663A>G	p.His888Arg	p.H888R	ENST00000402219	NM_005633.3	888	cAc/cGc	16/23	0.53456929309082	2	FACETS	0.83	0.735	0.93	0.415	0.367	0.465	CLONAL	1	TRUE	0	0.53456929309082	2		354	356	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705581	47705582	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	286	548	0	ENST00000233146.2:c.2382dup	p.Pro795ThrfsTer4	p.P795Tfs*4	ENST00000233146	NM_000251.2	794	ata/atAa	14/16	0.53456929309082	2	FACETS	0.929	0.882	0.975	0.929	0.882	0.975	CLONAL	2	TRUE	0	0.53456929309082	2		548	576	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185200165	185200165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779071892	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	163	481	0	ENST00000265026.3:c.2822C>T	p.Ser941Leu	p.S941L	ENST00000265026	NM_004721.4	941	tCg/tTg	14/14	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.53456929309082	2		481	609	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196520	106196520	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	131	678	0	ENST00000380013.4:c.4853A>G	p.Tyr1618Cys	p.Y1618C	ENST00000380013	NM_001127208.2	1618	tAc/tGc	11/11	1	2	FACETS	0.777	0.707	0.85	0.777	0.707	0.85	SUBCLONAL	1	TRUE	1	0.53456929309082	2		678	631	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526964	31526964	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	199	549	0	ENST00000344624.3:c.76G>T	p.Gly26Ter	p.G26*	ENST00000344624		26	Gga/Tga	2/33	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.53456929309082	2		549	704	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80083422	80083422	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	156	540	0	ENST00000265081.6:c.2474T>C	p.Val825Ala	p.V825A	ENST00000265081	NM_002439.4	825	gTg/gCg	18/24	1	2	FACETS	0.993	0.913	1	0.993	0.913	1	CLONAL	1	TRUE	1	0.53456929309082	2		540	588	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674251	86674251	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	140	462	0	ENST00000274376.6:c.2383A>C	p.Ser795Arg	p.S795R	ENST00000274376	NM_002890.2	795	Agc/Cgc	18/25	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.53456929309082	2		462	504	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815851	32815851	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149070070	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	178	597	1	ENST00000354258.4:c.1765C>T	p.Arg589Cys	p.R589C	ENST00000354258	NM_000593.5	589	Cgc/Tgc	8/11	1	2	FACETS	0.987	0.913	1	0.987	0.913	1	CLONAL	1	TRUE	1	0.53456929309082	2		598	675	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56882353	56882353	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	151	541	0	ENST00000519728.1:c.1050+1G>A		p.X350_splice	ENST00000519728	NM_002350.3	350			1	2	FACETS	0.875	0.802	0.95	0.875	0.802	0.95	CLONAL	1	TRUE	1	0.53456929309082	2		541	646	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27183574	27183574	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	157	513	0	ENST00000380036.4:c.1148T>C	p.Met383Thr	p.M383T	ENST00000380036	NM_000459.3	383	aTg/aCg	8/23	1	2	FACETS	0.966	0.889	1	0.966	0.889	1	CLONAL	1	TRUE	1	0.53456929309082	2		513	608	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338701	70338701	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	138	446	0	ENST00000374080.3:c.97G>T	p.Glu33Ter	p.E33*	ENST00000374080		33	Gag/Tag	1/45	1	2	FACETS	0.859	0.785	0.937	0.859	0.785	0.937	CLONAL	1	TRUE	1	0.53456929309082	2		446	601	SUCCESS
BTK	695	MSKCC	GRCh37	X	100624987	100624988	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0059416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	35	383	0	ENST00000308731.7:c.389dup	p.Asn130LysfsTer8	p.N130Kfs*8	ENST00000308731	NM_000061.2	130	aac/aaAc	5/19	1	2	FACETS	0.269	0.22	0.324	0.269	0.22	0.324	SUBCLONAL	1	TRUE	1	0.53456929309082	2		383	487	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0059417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	84	458	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.89	0.798	0.986	0.89	0.798	0.986	CLONAL	1	TRUE	1	0.734315895027481	2		458	257	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0059417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	104	299	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.734315895027481	2	FACETS	0.957	0.895	1	0.957	0.895	1	CLONAL	2	TRUE	0	0.734315895027481	2		299	148	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161492	2161492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753098162	NA	P-0059417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	113	753	0	ENST00000434045.2:c.35C>T	p.Ala12Val	p.A12V	ENST00000434045	NM_001127598.1	12	gCc/gTc	2/5	1	2	FACETS	0.865	0.786	0.945	0.865	0.786	0.945	CLONAL	1	TRUE	1	0.734315895027481	2		753	356	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038452	180038452	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs744282	NA	P-0059417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	189	698	0	ENST00000261937.6:c.3565C>T	p.Arg1189Cys	p.R1189C	ENST00000261937	NM_182925.4	1189	Cgc/Tgc	27/30	0.734315895027481	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.734315895027481	1		698	264	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057982	27057982	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	176	837	0	ENST00000324856.7:c.1690del	p.Gln564AsnfsTer55	p.Q564Nfs*55	ENST00000324856	NM_006015.4	564	Caa/aa	3/20	1	2	FACETS	0.898	0.833	0.964	0.898	0.833	0.964	CLONAL	1	TRUE	1	0.734315895027481	2		837	534	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636645	73636645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	283	863	0	ENST00000377687.4:c.908C>T	p.Ser303Leu	p.S303L	ENST00000377687	NM_001730.3	303	tCa/tTa	2/4	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.734315895027481	2		863	662	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40447680	40447680	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	168	688	0	ENST00000345506.4:c.419A>G	p.Lys140Arg	p.K140R	ENST00000345506	NM_003152.3	140	aAg/aGg	6/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.734315895027481	2		688	444	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164734	36164738	+	frameshift_variant	Frame_Shift_Del	DEL	GGTAG	GGTAG	-	novel	NA	P-0059417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	167	914	0	ENST00000300305.3:c.1137_1141del	p.Tyr380AlafsTer218	p.Y380Afs*218	ENST00000300305		379	acCTACCtg/actg	8/8	0.387671186960977	1	FACETS	0.982	0.923	1	0.982	0.923	1	INDETERMINATE	1	TRUE	0	0.734315895027481	1		914	293	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096198	71096198	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	197	648	0	ENST00000318789.4:c.559C>T	p.Gln187Ter	p.Q187*	ENST00000318789	NM_032682.5	187	Cag/Tag	10/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.734315895027481	2		648	458	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591096	67591097	+	inframe_insertion	In_Frame_Ins	INS	-	-	AACAGCATTAAACCAGACCTT	novel	NA	P-0059417-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	171	613	0	ENST00000274335.5:c.1691_1711dup	p.Asn564_Leu570dup	p.N564_L570dup	ENST00000274335		564	-/AACAGCATTAAACCAGACCTT	12/15	0.734315895027481	2	FACETS	1	0.983	1	0.585	0.545	0.626	CLONAL	1	TRUE	0	0.734315895027481	2		613	398	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0059421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	18	329	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.682	0.513	0.882	0.682	0.513	0.882	SUBCLONAL	1	TRUE	1	0.16	2		329	330	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220070	36220070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	49	535	0	ENST00000222270.7:c.4790G>A	p.Arg1597Gln	p.R1597Q	ENST00000222270	NM_014727.1	1597	cGg/cAg	22/37	1	2	FACETS	0.999	0.845	1	0.999	0.845	1	CLONAL	1	TRUE	1	0.16	2		535	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0059421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	55	613	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.16	2		614	564	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575061	48575061	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059421-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	23	315	0	ENST00000342988.3:c.255del	p.Gly86ValfsTer8	p.G86Vfs*8	ENST00000342988	NM_005359.5	85	gcT/gc	3/12	1	2	FACETS	0.803	0.626	1	0.803	0.626	1	CLONAL	1	TRUE	1	0.16	2		315	358	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0059422-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	117	455	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	0.956	0.87	1	0.956	0.87	1	CLONAL	1	TRUE	1	0.642515502466158	2		455	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0059423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	184	524	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	0.764518859672052	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.764518859672052	1		524	246	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022989	33022990	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0059423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	27	394	0	ENST00000300177.4:c.104dup	p.Pro36AlafsTer8	p.P36Afs*8	ENST00000300177	NM_001191322.1	33	atc/atCc	2/2	0.764518859672052	1	FACETS	0.194	0.155	0.238	0.194	0.155	0.238	SUBCLONAL	1	TRUE	0	0.764518859672052	1		394	225	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119829	108119829	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	178	216	0	ENST00000278616.4:c.1235G>T	p.Trp412Leu	p.W412L	ENST00000278616	NM_000051.3	412	tGg/tTg	9/63	0.764518859672052	2	FACETS	0.999	0.955	1	0.999	0.955	1	CLONAL	2	TRUE	0	0.764518859672052	2		216	233	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752916	42752916	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	155	564	0	ENST00000222329.4:c.1348G>T	p.Asp450Tyr	p.D450Y	ENST00000222329	NM_006494.2	450	Gac/Tac	4/4	0.143381867491593	4	FACETS	1	0.988	1	0.706	0.65	0.762	INDETERMINATE	1	TRUE	2	0.764518859672052	4		564	507	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925336	131925337	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0059423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	69	209	0	ENST00000265335.6:c.1262_1263del	p.Lys421ArgfsTer10	p.K421Rfs*10	ENST00000265335		420	gAA/g	9/25	0.524204717339572	3	FACETS	1	0.887	1	0.335	0.296	0.377	CLONAL	1	TRUE	0	0.764518859672052	3		209	248	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250527	26250527	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059423-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	153	654	0	ENST00000446824.2:c.307G>C	p.Gly103Arg	p.G103R	ENST00000446824	NM_021018.2	103	Ggg/Cgg	1/1	0.199254424216433	2	FACETS	0.801	0.738	0.865	0.4	0.369	0.433	INDETERMINATE	1	TRUE	0	0.764518859672052	2		654	500	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710623	117710623	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763487146	NA	P-0059424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	177	762	0	ENST00000368508.3:c.1649C>T	p.Ser550Leu	p.S550L	ENST00000368508	NM_002944.2	550	tCa/tTa	12/43	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.842266386066197	2		762	411	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945049	31945049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059424-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	165	823	0	ENST00000340398.3:c.52C>T	p.Arg18Cys	p.R18C	ENST00000340398	NM_001013699.2	18	Cgc/Tgc	1/1	1	2	FACETS	0.935	0.868	1	0.935	0.868	1	CLONAL	1	TRUE	1	0.842266386066197	2		823	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0059426-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	384	593	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.515647154101115	3	FACETS	1	0.989	1			1	CLONAL	3	TRUE	NA	0.772828670619376	3		593	449	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0059426-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	198	403	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.772828670619376	2		404	456	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413070	139413072	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0059426-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	12	619	0	ENST00000277541.6:c.1070_1072del	p.Phe357del	p.F357del	ENST00000277541	NM_017617.3	357	tTCTac/tac	6/34	1	2	FACETS	0.078	0.054	0.107	0.078	0.054	0.107	SUBCLONAL	1	TRUE	1	0.772828670619376	2		619	400	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918950	76918951	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0059426-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	154	221	0	ENST00000373344.5:c.4040_4041del	p.Val1347GlufsTer2	p.V1347Efs*2	ENST00000373344	NM_000489.3	1347	gTG/g	12/35	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.772828670619376	1		221	214	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705445	47705445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63751477	NA	P-0059426-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	73	399	0	ENST00000233146.2:c.2245G>A	p.Glu749Lys	p.E749K	ENST00000233146	NM_000251.2	749	Gaa/Aaa	14/16	1	2	FACETS	0.475	0.417	0.536	0.475	0.417	0.536	SUBCLONAL	1	TRUE	1	0.772828670619376	2		399	398	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064769	80064769	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770330684	NA	P-0059426-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	76	377	0	ENST00000265081.6:c.2200C>T	p.Arg734Ter	p.R734*	ENST00000265081	NM_002439.4	734	Cga/Tga	15/24	1	2	FACETS	0.456	0.402	0.515	0.456	0.402	0.515	SUBCLONAL	1	TRUE	1	0.772828670619376	2		377	431	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217229	7217239	+	frameshift_variant	Frame_Shift_Del	DEL	AGCACTTGGGG	AGCACTTGGGG	-	novel	NA	P-0059426-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	101	605	0	ENST00000380728.2:c.466_476del	p.Pro156TyrfsTer46	p.P156Yfs*46	ENST00000380728		156	CCCCAAGTGCTt/t	6/11	0.515647154101115	3	FACETS	0.875	0.788	0.967			1	CLONAL	1	TRUE	NA	0.772828670619376	3		605	414	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031761	11031761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059426-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	177	711	0	ENST00000327064.4:c.1573G>A	p.Ala525Thr	p.A525T	ENST00000327064	NM_199141.1	525	Gcc/Acc	14/16	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.772828670619376	2		711	410	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302349	15302349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1412202114	NA	P-0059426-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	59	643	0	ENST00000263388.2:c.922G>A	p.Gly308Ser	p.G308S	ENST00000263388	NM_000435.2	308	Ggc/Agc	6/33	0.350855189165515	1	FACETS	0.26	0.225	0.299	0.26	0.225	0.299	INDETERMINATE	1	TRUE	0	0.772828670619376	1		643	360	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023123	48023126	+	frameshift_variant	Frame_Shift_Del	DEL	TAAA	TAAA	-	rs1023534466	NA	P-0059426-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	89	558	0	ENST00000234420.5:c.552_555del	p.Asn184LysfsTer26	p.N184Kfs*26	ENST00000234420	NM_000179.2	183	tTAAAt/tt	3/10	1	2	FACETS	0.579	0.516	0.644	0.579	0.516	0.644	SUBCLONAL	1	TRUE	1	0.772828670619376	2		558	398	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638084	176638084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059426-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	92	554	1	ENST00000439151.2:c.2684G>A	p.Ser895Asn	p.S895N	ENST00000439151	NM_022455.4	895	aGt/aAt	5/23	1	2	FACETS	0.549	0.49	0.61	0.549	0.49	0.61	SUBCLONAL	1	TRUE	1	0.772828670619376	2		555	434	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721583	176721583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059426-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	94	743	0	ENST00000439151.2:c.7214G>A	p.Arg2405Lys	p.R2405K	ENST00000439151	NM_022455.4	2405	aGg/aAg	23/23	1	2	FACETS	0.457	0.408	0.51	0.457	0.408	0.51	SUBCLONAL	1	TRUE	1	0.772828670619376	2		743	532	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622204	162622204	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059426-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	95	606	0	ENST00000366898.1:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000366898	NM_004562.2	165	Cag/Tag	4/12	1	2	FACETS	0.542	0.484	0.602	0.542	0.484	0.602	SUBCLONAL	1	TRUE	1	0.772828670619376	2		606	454	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46587791	46587791	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	31	426	0	ENST00000263734.3:c.475del	p.Ser159AlafsTer12	p.S159Afs*12	ENST00000263734	NM_001430.4	157	Aaa/aa	5/16	0.319174585035089	1	FACETS	0.635	0.516	0.769	0.635	0.516	0.769	SUBCLONAL	1	TRUE	0	0.319174585035089	1		426	257	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193153	11193153	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	102	534	0	ENST00000361445.4:c.5348A>G	p.Asp1783Gly	p.D1783G	ENST00000361445	NM_004958.3	1783	gAc/gGc	38/58	1	2	FACETS	0.813	0.733	0.897	1	0.985	1	CLONAL	2	TRUE	1	0.319174585035089	2		534	393	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805695	43805695	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs757014193	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	24	556	0	ENST00000372470.3:c.751T>C	p.Ser251Pro	p.S251P	ENST00000372470	NM_005373.2	251	Tcc/Ccc	5/12	1	2	FACETS	0.424	0.332	0.53	0.424	0.332	0.53	SUBCLONAL	1	TRUE	1	0.319174585035089	2		556	355	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830752	156830752	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	55	406	0	ENST00000524377.1:c.26A>C	p.Gln9Pro	p.Q9P	ENST00000524377	NM_002529.3	9	cAg/cCg	1/17	0.319174585035089	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.319174585035089	1		406	237	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306640	163306640	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	29	169	0	ENST00000271452.3:c.435+2T>A		p.X145_splice	ENST00000271452	NM_145697.2	145			1	2	FACETS	1	0.835	1	1	0.835	1	CLONAL	1	TRUE	1	0.319174585035089	2		169	176	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104690	193104690	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs780017801	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	54	252	0	ENST00000367435.3:c.394T>G	p.Leu132Val	p.L132V	ENST00000367435	NM_024529.4	132	Tta/Gta	5/17	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.319174585035089	2		252	263	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982406	201982406	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	124	624	0	ENST00000359651.3:c.785A>G	p.Glu262Gly	p.E262G	ENST00000359651		262	gAg/gGg	6/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.319174585035089	2		624	525	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406645	70406645	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs754614889	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	58	361	0	ENST00000373644.4:c.4159A>G	p.Thr1387Ala	p.T1387A	ENST00000373644	NM_030625.2	1387	Aca/Gca	4/12	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.319174585035089	2		361	271	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325021	123325021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	133	556	0	ENST00000358487.5:c.307G>A	p.Gly103Ser	p.G103S	ENST00000358487	NM_000141.4	103	Ggc/Agc	3/18	0.319174585035089	1	FACETS	0.773	0.707	0.841	1	0.988	1	SUBCLONAL	2	TRUE	0	0.319174585035089	1		556	453	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571942	64571942	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	119	660	0	ENST00000312049.6:c.1697T>C	p.Val566Ala	p.V566A	ENST00000312049	NM_130799.2	566	gTg/gCg	10/10	0.232448682943048	3	FACETS	0.848	0.769	0.93	0.848	0.769	0.93	CLONAL	2	TRUE	1	0.319174585035089	3		660	510	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	76	527	0	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.319174585035089	2		527	453	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244376	46244376	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	36	435	0	ENST00000334344.6:c.2470A>G	p.Thr824Ala	p.T824A	ENST00000334344	NM_152641.2	824	Aca/Gca	15/21	1	2	FACETS	0.47	0.386	0.564	0.47	0.386	0.564	SUBCLONAL	1	TRUE	1	0.319174585035089	2		435	480	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891154	112891154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	40	458	0	ENST00000351677.2:c.488G>A	p.Gly163Asp	p.G163D	ENST00000351677	NM_002834.3	163	gGc/gAc	4/16	1	2	FACETS	0.668	0.556	0.793	0.668	0.556	0.793	SUBCLONAL	1	TRUE	1	0.319174585035089	2		458	375	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434424	110434424	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1594388745	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	141	579	0	ENST00000375856.3:c.3977T>C	p.Leu1326Ser	p.L1326S	ENST00000375856	NM_003749.2	1326	tTg/tCg	1/2	1	2	FACETS	0.783	0.717	0.852	1	0.988	1	SUBCLONAL	2	TRUE	1	0.319174585035089	2		579	564	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986718	36986718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1268490942	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	34	634	1	ENST00000354822.5:c.971C>T	p.Ala324Val	p.A324V	ENST00000354822	NM_001079668.2	324	gCg/gTg	3/3	0.165194674326832	3	FACETS	0.879	0.721	1	0.44	0.36	0.528	INDETERMINATE	1	TRUE	1	0.319174585035089	3		635	281	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005460	42005460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	175	607	0	ENST00000219905.7:c.3196C>T	p.Arg1066Cys	p.R1066C	ENST00000219905	NM_001164273.1	1066	Cgc/Tgc	9/24	1	2	FACETS	0.881	0.816	0.949	1	0.992	1	CLONAL	2	TRUE	1	0.319174585035089	2		607	622	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040841	42040841	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	17	397	0	ENST00000219905.7:c.5219C>T	p.Ala1740Val	p.A1740V	ENST00000219905	NM_001164273.1	1740	gCt/gTt	16/24	1	2	FACETS	0.334	0.249	0.435	0.334	0.249	0.435	SUBCLONAL	1	TRUE	1	0.319174585035089	2		397	319	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701933	43701933	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	64	275	0	ENST00000382044.4:c.5312del	p.Leu1771TrpfsTer39	p.L1771Wfs*39	ENST00000382044	NM_001141980.1	1771	tTg/tg	25/28	1	2	FACETS	0.783	0.686	0.886	1	0.975	1	SUBCLONAL	2	TRUE	1	0.319174585035089	2		275	256	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701940	43701940	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	66	223	0	ENST00000382044.4:c.5306-1G>A		p.X1769_splice	ENST00000382044	NM_001141980.1	1769			1	2	FACETS	0.936	0.824	1	1	0.981	1	CLONAL	2	TRUE	1	0.319174585035089	2		223	221	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	237	519	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	1	2	FACETS	0.855	0.8	0.912	1	0.994	1	CLONAL	2	TRUE	1	0.319174585035089	2		519	868	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	78	353	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.319174585035089	2		353	424	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727451	66727451	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519729	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	58	418	0	ENST00000307102.5:c.167A>C	p.Gln56Pro	p.Q56P	ENST00000307102	NM_002755.3	56	cAg/cCg	2/11	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.319174585035089	2		418	342	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727536	66727536	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	32	430	0	ENST00000307102.5:c.252G>T	p.Lys84Asn	p.K84N	ENST00000307102	NM_002755.3	84	aaG/aaT	2/11	1	2	FACETS	0.611	0.497	0.74	0.611	0.497	0.74	SUBCLONAL	1	TRUE	1	0.319174585035089	2		430	328	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476323	88476323	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	61	491	1	ENST00000360948.2:c.1809C>A	p.Phe603Leu	p.F603L	ENST00000360948	NM_001012338.2	603	ttC/ttA	15/19	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.319174585035089	2		492	318	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862857	9862857	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	32	526	0	ENST00000330684.3:c.2446A>G	p.Asn816Asp	p.N816D	ENST00000330684	NM_001134407.1	816	Aac/Gac	12/13	0.138662741306865	0	FACETS	0.428	0.348	0.518			1	INDETERMINATE	1	TRUE	0	0.319174585035089	0		526	319	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041519	14041519	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161291089	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	61	377	0	ENST00000311895.7:c.2066G>A	p.Arg689His	p.R689H	ENST00000311895	NM_005236.2	689	cGt/cAt	11/11	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.319174585035089	2		377	335	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822379	72822380	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	158	866	0	ENST00000268489.5:c.9795dup	p.Thr3266HisfsTer165	p.T3266Hfs*165	ENST00000268489	NM_006885.3	3265	-/C	10/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.319174585035089	2		866	667	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827915	72827915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753622432	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	90	618	0	ENST00000268489.5:c.8666G>A	p.Arg2889Gln	p.R2889Q	ENST00000268489	NM_006885.3	2889	cGg/cAg	9/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.319174585035089	2		618	384	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831215	72831215	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	100	658	0	ENST00000268489.5:c.5366A>G	p.Gln1789Arg	p.Q1789R	ENST00000268489	NM_006885.3	1789	cAa/cGa	9/10	1	2	FACETS	0.777	0.699	0.859	1	0.984	1	SUBCLONAL	2	TRUE	1	0.319174585035089	2		658	403	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346865	89346865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199785661	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	61	617	1	ENST00000301030.4:c.6085G>A	p.Val2029Ile	p.V2029I	ENST00000301030	NM_001256183.1	2029	Gtc/Atc	9/13	0.183630101230121	0	FACETS	0.891	0.775	1			1	INDETERMINATE	1	TRUE	0	0.319174585035089	0		618	292	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17125941	17125941	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367843558	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	75	576	0	ENST00000285071.4:c.653G>A	p.Arg218His	p.R218H	ENST00000285071	NM_144997.5	218	cGt/cAt	7/14	1	2	FACETS	0.758	0.67	0.851	1	0.977	1	SUBCLONAL	2	TRUE	1	0.319174585035089	2		576	310	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654857	29654857	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786202112	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	48	357	0	ENST00000356175.3:c.5546G>A	p.Arg1849Gln	p.R1849Q	ENST00000356175	NM_000267.3	1849	cGg/cAg	37/57	1	2	FACETS	0.983	0.836	1	0.983	0.836	1	CLONAL	1	TRUE	1	0.319174585035089	2		357	306	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687472	37687472	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	27	666	1	ENST00000447079.4:c.4382del	p.Gly1461AlafsTer38	p.G1461Afs*38	ENST00000447079	NM_015083.1	1459	tGg/tg	14/14	1	2	FACETS	0.363	0.288	0.449	0.363	0.288	0.449	SUBCLONAL	1	TRUE	1	0.319174585035089	2		667	466	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533887	63533887	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	71	700	0	ENST00000307078.5:c.1267del	p.Leu423SerfsTer35	p.L423Sfs*35	ENST00000307078	NM_004655.3	423	Ctc/tc	6/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.319174585035089	2		700	324	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4094479	4094479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768826287	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	59	518	1	ENST00000262948.5:c.1064C>T	p.Ala355Val	p.A355V	ENST00000262948	NM_030662.3	355	gCg/gTg	10/11	0.230038578186002	0	FACETS	0.961	0.835	1			1	CLONAL	1	TRUE	0	0.319174585035089	0		519	262	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222730	5222731	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs756013055	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	53	563	0	ENST00000357368.4:c.3072dup	p.Val1025ArgfsTer34	p.V1025Rfs*34	ENST00000357368	NM_002850.3	1024	-/C	18/38	0.230038578186002	0	FACETS	0.677	0.58	0.782			1	SUBCLONAL	1	TRUE	0	0.319174585035089	0		563	334	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602518	10602518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	112	766	0	ENST00000171111.5:c.1060C>T	p.Arg354Trp	p.R354W	ENST00000171111	NM_203500.1	354	Cgg/Tgg	3/6	0.138662741306865	0	FACETS	1	0.933	1			1	INDETERMINATE	1	TRUE	0	0.319174585035089	0		766	460	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101878	11101878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	19	695	0	ENST00000358026.2:c.1298C>T	p.Ala433Val	p.A433V	ENST00000358026	NM_001128849.1	433	gCc/gTc	8/36	0.138662741306865	0	FACETS	0.215	0.163	0.277			1	INDETERMINATE	1	TRUE	0	0.319174585035089	0		695	377	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290273	15290273	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	30	634	0	ENST00000263388.2:c.3362A>G	p.Asp1121Gly	p.D1121G	ENST00000263388	NM_000435.2	1121	gAc/gGc	21/33	1	2	FACETS	0.39	0.314	0.477	0.39	0.314	0.477	SUBCLONAL	1	TRUE	1	0.319174585035089	2		634	482	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375552	15375552	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	37	667	0	ENST00000263377.2:c.875C>A	p.Ala292Glu	p.A292E	ENST00000263377	NM_058243.2	292	gCa/gAa	6/20	1	2	FACETS	0.487	0.401	0.583	0.487	0.401	0.583	SUBCLONAL	1	TRUE	1	0.319174585035089	2		667	476	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965467	18965467	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	66	424	0	ENST00000262803.5:c.1214T>C	p.Val405Ala	p.V405A	ENST00000262803	NM_002911.3	405	gTg/gCg	9/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.319174585035089	2		424	307	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223133	36223133	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	81	819	0	ENST00000222270.7:c.5683A>T	p.Thr1895Ser	p.T1895S	ENST00000222270	NM_014727.1	1895	Acc/Tcc	28/37	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.319174585035089	2		819	389	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223761	36223761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747697534	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	95	769	1	ENST00000222270.7:c.6311G>A	p.Arg2104Gln	p.R2104Q	ENST00000222270	NM_014727.1	2104	cGg/cAg	28/37	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.319174585035089	2		770	442	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	51	429	4	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			0.319174585035089	1	FACETS	0.901	0.771	1	0.901	0.771	1	CLONAL	1	TRUE	0	0.319174585035089	1		433	298	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468148	25468148	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751419033	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	88	593	0	ENST00000264709.3:c.1528G>A	p.Val510Ile	p.V510I	ENST00000264709	NM_175629.2	510	Gtt/Att	13/23	1	2	FACETS	0.753	0.673	0.838	1	0.98	1	SUBCLONAL	2	TRUE	1	0.319174585035089	2		593	366	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436862	29436862	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1553392309	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	16	437	0	ENST00000389048.3:c.3731A>G	p.His1244Arg	p.H1244R	ENST00000389048	NM_004304.4	1244	cAc/cGc	24/29	1	2	FACETS	0.373	0.275	0.489	0.373	0.275	0.489	SUBCLONAL	1	TRUE	1	0.319174585035089	2		437	269	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250368	39250368	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	52	201	0	ENST00000402219.2:c.1203-2A>T		p.X401_splice	ENST00000402219	NM_005633.3	401			0.319174585035089	1	FACETS	0.913	0.795	1	1	0.976	1	CLONAL	2	TRUE	0	0.319174585035089	1		201	150	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637398	47637398	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	72	371	0	ENST00000233146.2:c.533del	p.Phe178SerfsTer36	p.F178Sfs*36	ENST00000233146	NM_000251.2	178	Ttc/tc	3/16	0.319174585035089	1	FACETS	0.957	0.853	1	1	0.983	1	CLONAL	2	TRUE	0	0.319174585035089	1		371	198	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026204	48026204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750440	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	64	386	0	ENST00000234420.5:c.1082G>A	p.Arg361His	p.R361H	ENST00000234420	NM_000179.2	361	cGc/cAc	4/10	0.319174585035089	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.319174585035089	1		386	286	SUCCESS
REL	5966	MSKCC	GRCh37	2	61121652	61121652	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	26	301	0	ENST00000295025.8:c.274G>A	p.Glu92Lys	p.E92K	ENST00000295025	NM_002908.2	92	Gaa/Aaa	3/11	1	2	FACETS	0.652	0.518	0.804	0.652	0.518	0.804	SUBCLONAL	1	TRUE	1	0.319174585035089	2		301	250	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149922	202149922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	49	542	0	ENST00000358485.4:c.1363G>A	p.Glu455Lys	p.E455K	ENST00000358485	NM_001080125.1	455	Gag/Aag	8/9	1	2	FACETS	0.83	0.705	0.966	0.83	0.705	0.966	CLONAL	1	TRUE	1	0.319174585035089	2		542	370	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150030	202150030	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs931648756	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	72	481	0	ENST00000358485.4:c.1471C>T	p.Arg491Ter	p.R491*	ENST00000358485	NM_001080125.1	491	Cga/Tga	8/9	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.319174585035089	2		481	345	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	72	281	0	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.319174585035089	2		281	391	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31372571	31372571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752527055	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	30	414	0	ENST00000328111.2:c.212C>T	p.Thr71Ile	p.T71I	ENST00000328111	NM_006892.3	71	aCa/aTa	4/23	1	2	FACETS	0.593	0.479	0.722	0.593	0.479	0.722	SUBCLONAL	1	TRUE	1	0.319174585035089	2		414	317	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400112	41400112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	20	433	0	ENST00000373198.4:c.647G>A	p.Gly216Asp	p.G216D	ENST00000373198	NM_133170.3	216	gGt/gAt	5/32	0.319174585035089	1	FACETS	0.355	0.271	0.452	0.355	0.271	0.452	SUBCLONAL	1	TRUE	0	0.319174585035089	1		433	297	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817345	39817345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	46	500	0	ENST00000288319.7:c.218G>A	p.Ser73Asn	p.S73N	ENST00000288319	NM_182918.3	73	aGc/aAc	2/10	1	2	FACETS	0.884	0.748	1	0.884	0.748	1	CLONAL	1	TRUE	1	0.319174585035089	2		500	326	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655272	45655272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764295138	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	93	606	0	ENST00000407780.3:c.580C>T	p.Arg194Trp	p.R194W	ENST00000407780	NM_001283052.1	194	Cgg/Tgg	4/7	1	2	FACETS	0.763	0.683	0.846	1	0.982	1	SUBCLONAL	2	TRUE	1	0.319174585035089	2		606	382	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143131	24143131	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	53	525	0	ENST00000263121.7:c.363G>T	p.Arg121Ser	p.R121S	ENST00000263121	NM_003073.3	121	agG/agT	4/9	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.319174585035089	2		525	285	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095882	29095882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148053495	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	69	348	0	ENST00000328354.6:c.952C>T	p.Arg318Cys	p.R318C	ENST00000328354	NM_007194.3	318	Cgc/Tgc	9/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.319174585035089	2		348	344	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645742	12645742	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	89	442	0	ENST00000251849.4:c.727T>C	p.Ser243Pro	p.S243P	ENST00000251849	NM_002880.3	243	Tcc/Ccc	7/17	0.165194674326832	3	FACETS	1	0.978	1	0.711	0.633	0.793	INDETERMINATE	1	TRUE	1	0.319174585035089	3		442	455	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163278	47163278	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372092336	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	61	305	0	ENST00000409792.3:c.2848C>T	p.Arg950Cys	p.R950C	ENST00000409792	NM_014159.6	950	Cgt/Tgt	3/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.319174585035089	2		305	279	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63898393	63898393	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1187351635	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	136	446	0	ENST00000398590.3:c.119C>A	p.Pro40Gln	p.P40Q	ENST00000398590	NM_001177387.1	40	cCg/cAg	3/14	0.232448682943048	3	FACETS	0.881	0.804	0.96	0.881	0.804	0.96	CLONAL	2	TRUE	1	0.319174585035089	3		446	561	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037150	71037150	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	180	441	0	ENST00000318789.4:c.1141C>T	p.Gln381Ter	p.Q381*	ENST00000318789	NM_032682.5	381	Cag/Tag	14/21	0.232448682943048	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.319174585035089	3		441	610	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665552	138665552	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1457137582	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	25	377	0	ENST00000330315.3:c.13T>C	p.Tyr5His	p.Y5H	ENST00000330315	NM_023067.3	5	Tac/Cac	1/1	1	2	FACETS	0.856	0.68	1	0.856	0.68	1	CLONAL	1	TRUE	1	0.319174585035089	2		377	183	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	45	284	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.881	0.744	1	0.881	0.744	1	CLONAL	1	TRUE	1	0.319174585035089	2		284	320	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503787	186503789	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs1560084666	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	97	302	0	ENST00000323963.5:c.470_472del	p.Val157del	p.V157del	ENST00000323963		155	aTTGtt/att	5/11	1	2	FACETS	0.754	0.677	0.835	1	0.982	1	SUBCLONAL	2	TRUE	1	0.319174585035089	2		302	403	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	52	779	1	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	0.230038578186002	0	FACETS	0.546	0.466	0.634			1	SUBCLONAL	1	TRUE	0	0.319174585035089	0		780	406	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045841	143045841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	97	411	2	ENST00000262992.4:c.1793C>T	p.Ala598Val	p.A598V	ENST00000262992	NM_001101669.1	598	gCc/gTc	17/24	1	2	FACETS	0.766	0.687	0.847	1	0.983	1	SUBCLONAL	2	TRUE	1	0.319174585035089	2		413	397	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539018	187539018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374444088	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	28	504	0	ENST00000441802.2:c.8722G>A	p.Val2908Ile	p.V2908I	ENST00000441802	NM_005245.3	2908	Gtc/Atc	10/27	1	2	FACETS	0.396	0.316	0.488	0.396	0.316	0.488	SUBCLONAL	1	TRUE	1	0.319174585035089	2		504	443	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539965	187539965	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs368192179	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	86	423	0	ENST00000441802.2:c.7775A>G	p.Asn2592Ser	p.N2592S	ENST00000441802	NM_005245.3	2592	aAt/aGt	10/27	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.319174585035089	2		423	369	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628049	187628049	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	36	472	0	ENST00000441802.2:c.2933A>G	p.Lys978Arg	p.K978R	ENST00000441802	NM_005245.3	978	aAa/aGa	2/27	1	2	FACETS	0.538	0.443	0.646	0.538	0.443	0.646	SUBCLONAL	1	TRUE	1	0.319174585035089	2		472	419	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31451740	31451740	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	32	243	0	ENST00000344624.3:c.2582T>C	p.Met861Thr	p.M861T	ENST00000344624		861	aTg/aCg	18/33	0.165194674326832	3	FACETS	0.802	0.661	0.956	0.802	0.661	0.956	INDETERMINATE	2	TRUE	1	0.319174585035089	3		243	145	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753051	57753051	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1460803067	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	93	430	0	ENST00000274289.3:c.965G>A	p.Arg322His	p.R322H	ENST00000274289	NM_006622.3	322	cGt/cAt	7/14	0.165194674326832	3	FACETS	0.764	0.683	0.85	0.764	0.683	0.85	INDETERMINATE	2	TRUE	1	0.319174585035089	3		430	442	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056416	26056416	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	231	527	0	ENST00000343677.2:c.241A>G	p.Lys81Glu	p.K81E	ENST00000343677	NM_005319.3	81	Aaa/Gaa	1/1	0.319174585035089	6	FACETS	1	0.96	1	0.776	0.726	0.827	CLONAL	3	TRUE	2	0.319174585035089	6		527	764	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910714	29910714	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	199	791	1	ENST00000376809.5:c.254A>G	p.Asp85Gly	p.D85G	ENST00000376809	NM_002116.7	85	gAc/gGc	2/8	0.153134435660632	2	FACETS	0.773	0.717	0.83	0.773	0.717	0.83	INDETERMINATE	2	TRUE	0	0.319174585035089	2		792	807	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681453	30681453	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	62	372	0	ENST00000376406.3:c.559A>G	p.Thr187Ala	p.T187A	ENST00000376406	NM_014641.2	187	Aca/Gca	4/15	0.319174585035089	3	FACETS	1	0.949	1	0.601	0.521	0.686	CLONAL	1	TRUE	1	0.319174585035089	3		372	375	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165344	32165344	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	77	549	0	ENST00000375023.3:c.4784T>C	p.Val1595Ala	p.V1595A	ENST00000375023	NM_004557.3	1595	gTt/gCt	27/30	0.319174585035089	3	FACETS	1	0.951	1	0.579	0.51	0.653	CLONAL	1	TRUE	1	0.319174585035089	3		549	483	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771192	161771192	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	69	517	0	ENST00000366898.1:c.1337G>A	p.Cys446Tyr	p.C446Y	ENST00000366898	NM_004562.2	446	tGc/tAc	12/12	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.319174585035089	2		517	391	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781212	161781212	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	45	496	0	ENST00000366898.1:c.1193C>A	p.Ala398Asp	p.A398D	ENST00000366898	NM_004562.2	398	gCc/gAc	11/12	1	2	FACETS	0.847	0.714	0.992	0.847	0.714	0.992	CLONAL	1	TRUE	1	0.319174585035089	2		496	333	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229237	55229237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	65	720	0	ENST00000275493.2:c.1544G>A	p.Cys515Tyr	p.C515Y	ENST00000275493	NM_005228.3	515	tGc/tAc	13/28	0.319174585035089	3	FACETS	0.865	0.751	0.989	0.433	0.375	0.495	CLONAL	1	TRUE	1	0.319174585035089	3		720	546	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509310	106509310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	45	485	0	ENST00000359195.3:c.1304G>A	p.Cys435Tyr	p.C435Y	ENST00000359195	NM_002649.2	435	tGc/tAc	2/11	0.303279399821376	4	FACETS	0.828	0.697	0.974	0.276	0.232	0.325	CLONAL	1	TRUE	1	0.319174585035089	4		485	449	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	80	599	1	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	0.303279399821376	4	FACETS	0.812	0.719	0.912	0.542	0.479	0.608	CLONAL	2	TRUE	1	0.319174585035089	4		600	407	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	86	680	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	0.303279399821376	4	FACETS	1	0.972	1	0.443	0.393	0.497	CLONAL	1	TRUE	1	0.319174585035089	4		680	535	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878464	151878464	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	199	530	0	ENST00000262189.6:c.6481C>T	p.Gln2161Ter	p.Q2161*	ENST00000262189	NM_170606.2	2161	Caa/Taa	36/59	0.303279399821376	4	FACETS	0.976	0.91	1	0.976	0.91	1	CLONAL	3	TRUE	1	0.319174585035089	4		530	562	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38184266	38184266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	26	258	0	ENST00000317025.8:c.1690G>A	p.Ala564Thr	p.A564T	ENST00000317025	NM_023034.1	564	Gca/Aca	7/24	1	2	FACETS	0.765	0.609	0.941	0.765	0.609	0.941	CLONAL	1	TRUE	1	0.319174585035089	2		258	213	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738410	145738410	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1268491409	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	169	711	0	ENST00000428558.2:c.2575A>G	p.Arg859Gly	p.R859G	ENST00000428558	NM_004260.3	859	Agg/Ggg	16/22	1	2	FACETS	1	0.949	1	1	0.993	1	CLONAL	2	TRUE	1	0.319174585035089	2		711	514	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341258	8341258	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	77	285	2	ENST00000356435.5:c.4958G>A	p.Ser1653Asn	p.S1653N	ENST00000356435		1653	aGc/aAc	30/35	1	2	FACETS	0.884	0.785	0.987	1	0.982	1	CLONAL	2	TRUE	1	0.319174585035089	2		287	273	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27190548	27190548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	45	363	0	ENST00000380036.4:c.1349C>T	p.Ala450Val	p.A450V	ENST00000380036	NM_000459.3	450	gCc/gTc	10/23	1	2	FACETS	0.732	0.617	0.859	0.732	0.617	0.859	SUBCLONAL	1	TRUE	1	0.319174585035089	2		363	385	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342722	87342722	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	94	430	0	ENST00000277120.3:c.1007T>C	p.Val336Ala	p.V336A	ENST00000277120		336	gTt/gCt	9/19	1	2	FACETS	0.807	0.724	0.894	1	0.984	1	CLONAL	2	TRUE	1	0.319174585035089	2		430	365	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407503	139407503	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	16	371	0	ENST00000277541.6:c.2437T>C	p.Tyr813His	p.Y813H	ENST00000277541	NM_017617.3	813	Tac/Cac	15/34	0.314891397950377	0	FACETS	0.315	0.233	0.412			1	SUBCLONAL	1	TRUE	0	0.319174585035089	0		371	217	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939814	76939814	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	64	152	0	ENST00000373344.5:c.934A>G	p.Thr312Ala	p.T312A	ENST00000373344	NM_000489.3	312	Aca/Gca	9/35	1	1	FACETS	1	0.964	1	1	0.985	1	CLONAL	2	TRUE	0	0.319174585035089	1		152	139	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0059427-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	106	783	5	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.832	0.752	0.916	1	0.986	1	CLONAL	2	TRUE	1	0.319174585035089	2		788	399	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0059428-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	72	458	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.230727455504865	2	FACETS	1	0.952	1	0.575	0.509	0.645	INDETERMINATE	1	FALSE	0	0.492637296720477	2		458	254	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059428-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	78	648	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.372239360174267	1	FACETS	0.951	0.847	1	0.951	0.847	1	CLONAL	1	FALSE	0	0.492637296720477	1		648	251	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0059428-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	54	100	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	FALSE	1	0.492637296720477	2		100	209	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0059428-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	174	566	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.142452882909166	4	FACETS	1	0.976	1			1	INDETERMINATE	3	FALSE	NA	0.492637296720477	4		566	325	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216444	36216444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059428-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	125	639	0	ENST00000222270.7:c.3707C>T	p.Pro1236Leu	p.P1236L	ENST00000222270	NM_014727.1	1236	cCc/cTc	12/37	0.256566568637189	4	FACETS	0.956	0.874	1	0.478	0.437	0.521	INDETERMINATE	2	FALSE	0	0.492637296720477	4		639	396	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62322163	62322163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457469809	NA	P-0059428-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	20	461	0	ENST00000360203.5:c.2419C>T	p.Pro807Ser	p.P807S	ENST00000360203	NM_001283009.1	807	Cca/Tca	27/35	1	2	FACETS	0.446	0.343	0.565	0.446	0.343	0.565	SUBCLONAL	1	FALSE	1	0.492637296720477	2		461	182	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446252	29446252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773142324	NA	P-0059428-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	20	599	0	ENST00000544604.2:c.2083C>T	p.Pro695Ser	p.P695S	ENST00000544604	NM_001206998.1	695	Cct/Tct	8/9	0.492637296720477	1	FACETS	0.352	0.27	0.445	0.352	0.27	0.445	SUBCLONAL	1	FALSE	0	0.492637296720477	1		599	174	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967336	134967336	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059428-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	25	519	0	ENST00000398015.3:c.2675C>A	p.Ala892Glu	p.A892E	ENST00000398015	NM_004441.4	892	gCa/gAa	14/16	1	2	FACETS	0.486	0.385	0.6	0.486	0.385	0.6	SUBCLONAL	1	FALSE	1	0.492637296720477	2		519	209	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77961269	77961269	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059430-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3019	609	531	0	ENST00000361507.4:c.554C>T	p.Ser185Phe	p.S185F	ENST00000361507	NM_080491.2	185	tCc/tTc	3/10	0.477709048865947	26	FACETS	0.946	0.905	0.988			1	CLONAL	5	FALSE	NA	0.477709048865947	26		531	3628	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77961417	77961417	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059430-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2560	520	499	0	ENST00000361507.4:c.406C>T	p.His136Tyr	p.H136Y	ENST00000361507	NM_080491.2	136	Cat/Tat	3/10	0.477709048865947	26	FACETS	0.952	0.907	0.998			1	CLONAL	5	FALSE	NA	0.477709048865947	26		499	3080	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551362	141551362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059430-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	144	553	0	ENST00000220592.5:c.1935G>A	p.Met645Ile	p.M645I	ENST00000220592	NM_012154.3	645	atG/atA	15/19	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.477709048865947	2		553	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0059433-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	226	471	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.647779242412954	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.647779242412954	1		471	362	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845583	68845583	+	splice_region_variant,intron_variant	Splice_Region	DEL	C	C	-	novel	NA	P-0059433-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	108	433	0	ENST00000261769.5:c.833-3del		p.X278_splice	ENST00000261769	NM_004360.3	278			0.647779242412954	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.647779242412954	1		433	198	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815382	32815382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059433-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	33	574	0	ENST00000354258.4:c.1991C>T	p.Thr664Ile	p.T664I	ENST00000354258	NM_000593.5	664	aCc/aTc	9/11	1	2	FACETS	0.249	0.202	0.301	0.249	0.202	0.301	SUBCLONAL	1	TRUE	1	0.647779242412954	2		574	410	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254597	1254597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1418488828	NA	P-0059434-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	122	405	0	ENST00000310581.5:c.3181G>A	p.Ala1061Thr	p.A1061T	ENST00000310581	NM_198253.2	1061	Gcc/Acc	15/16	0.920018051585836	3	FACETS	1	0.941	1	0.519	0.474	0.566	CLONAL	1	TRUE	1	0.923067515890897	3		405	372	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593589	55593594	+	inframe_deletion	In_Frame_Del	DEL	TGTATG	TGTATG	-	novel	NA	P-0059434-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	181	444	0	ENST00000288135.5:c.1655_1660del	p.Met552_Glu554delinsLys	p.M552_E554delinsK	ENST00000288135	NM_000222.2	552	aTGTATGaa/aaa	11/21	1	2	FACETS	0.988	0.924	1	0.988	0.924	1	CLONAL	1	TRUE	1	0.923067515890897	2		444	397	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0059435-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	121	471	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	NA	2	FACETS	1	0.945	1			1	INDETERMINATE	1	TRUE	NA	0.387115977106768	2		471	589	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0059435-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	165	612	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.387115977106768	2		612	843	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448379	56448387	+	inframe_deletion	In_Frame_Del	DEL	GGTACAGCG	GGTACAGCG	-	novel	NA	P-0059435-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	140	530	0	ENST00000407977.2:c.260_268del	p.Pro87_Tyr89del	p.P87_Y89del	ENST00000407977		87	cCGCTGTACCtg/ctg	3/10	1	2	FACETS	0.981	0.895	1	0.981	0.895	1	CLONAL	1	TRUE	1	0.387115977106768	2		530	737	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164198	32164198	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs769112107	NA	P-0059435-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	97	392	0	ENST00000375023.3:c.5201G>T	p.Gly1734Val	p.G1734V	ENST00000375023	NM_004557.3	1734	gGg/gTg	29/30	1	2	FACETS	0.858	0.767	0.955	0.858	0.767	0.955	CLONAL	1	TRUE	1	0.387115977106768	2		392	584	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593593	55593610	+	inframe_deletion	In_Frame_Del	DEL	TGAAGTACAGTGGAAGGT	TGAAGTACAGTGGAAGGT	-	novel	NA	P-0059436-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	204	393	0	ENST00000288135.5:c.1661_1678del	p.Glu554_Val559del	p.E554_V559del	ENST00000288135	NM_000222.2	553	taTGAAGTACAGTGGAAGGTt/tat	11/21	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.905863540025692	2		393	441	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	46	121	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.177288914471898	4	FACETS	1	0.931	1	1	0.931	1	CLONAL	3	FALSE	1	0.223013074770852	4		121	147	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0059439-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	48	613	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.223013074770852	2	FACETS	1	0.873	1	1	0.968	1	CLONAL	3	FALSE	0	0.223013074770852	2		614	142	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059440-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	118	477	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.801	0.726	0.88	0.801	0.726	0.88	CLONAL	1	TRUE	1	0.567449299691023	2		477	519	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0059440-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	268	863	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.567449299691023	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.567449299691023	1		863	670	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050906	49050906	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059440-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	178	420	0	ENST00000267163.4:c.2590G>T	p.Glu864Ter	p.E864*	ENST00000267163	NM_000321.2	864	Gaa/Taa	25/27	0.567449299691023	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.567449299691023	1		420	426	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855787	45855787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059440-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	204	650	0	ENST00000391945.4:c.2023G>A	p.Gly675Ser	p.G675S	ENST00000391945	NM_000400.3	675	Ggc/Agc	21/23	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.567449299691023	2		650	705	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971266	15971278	+	frameshift_variant	Frame_Shift_Del	DEL	CCGATAAACCTCG	CCGATAAACCTCG	-	novel	NA	P-0059442-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	88	526	0	ENST00000268712.3:c.4671_4683del	p.Glu1558AlafsTer53	p.E1558Afs*53	ENST00000268712	NM_006311.3	1557	ggCGAGGTTTATCGG/gg	32/46	0.210379511152261	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	0	0.210379511152261	1		526	566	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380269	25380270	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCCTCTTGACCTGCTGTGTCGAGAATA	novel	NA	P-0059443-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	41	451	0	ENST00000311936.3:c.162_188dup	p.Asp54_Glu62dup	p.D54_E62dup	ENST00000311936	NM_004985.3	54	gag/gaTATTCTCGACACAGCAGGTCAAGAGGAg	3/5	0.222666772568444	8	FACETS	1	0.932	1			1	CLONAL	1	TRUE	NA	0.222666772568444	8		451	492	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690426	33690426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376084054	NA	P-0059443-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	84	647	0	ENST00000308377.4:c.401G>A	p.Arg134His	p.R134H	ENST00000308377	NM_152270.3	134	cGt/cAt	2/5	0.180738125426512	5	FACETS	0.877	0.776	0.985			1	CLONAL	2	TRUE	NA	0.222666772568444	5		647	574	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3094783	3094783	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059443-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	49	716	0	ENST00000078429.4:c.134T>C	p.Leu45Pro	p.L45P	ENST00000078429	NM_002067.2	45	cTc/cCc	1/7	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.222666772568444	2		716	304	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222819	53222819	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0059443-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	39	651	0	ENST00000375401.3:c.4118-1G>T		p.X1373_splice	ENST00000375401	NM_004187.3	1373			0.222884058540977	0	FACETS	0.667	0.559	0.786			1	SUBCLONAL	2	TRUE	0	0.222666772568444	0		651	204	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248208	59248208	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	423	623	0	ENST00000371222.2:c.535G>T	p.Gly179Cys	p.G179C	ENST00000371222	NM_002228.3	179	Ggc/Tgc	1/1	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.767506086572213	2		623	1067	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954351	48954351	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	231	267	0	ENST00000267163.4:c.1472T>G	p.Leu491Arg	p.L491R	ENST00000267163	NM_000321.2	491	cTt/cGt	16/27	0.552711434954147	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.767506086572213	1		267	345	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577096	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0059444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	433	570	0	ENST00000269305.4:c.842_843del	p.Asp281AlafsTer24	p.D281Afs*24	ENST00000269305	NM_001126112.2	281	gAC/g	8/11	0.767506086572213	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.767506086572213	1		570	673	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075122	16075122	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	266	398	0	ENST00000268712.3:c.430A>G	p.Lys144Glu	p.K144E	ENST00000268712	NM_006311.3	144	Aag/Gag	4/46	0.767506086572213	1	FACETS	0.998	0.953	1	0.998	0.953	1	CLONAL	1	TRUE	0	0.767506086572213	1		398	428	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562746	29562746	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs199474742	NA	P-0059444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	306	437	0	ENST00000356175.3:c.3826C>G	p.Arg1276Gly	p.R1276G	ENST00000356175	NM_000267.3	1276	Cga/Gga	28/57	0.767506086572213	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.767506086572213	1		437	444	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467140	25467140	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1472	402	652	0	ENST00000264709.3:c.1735G>C	p.Asp579His	p.D579H	ENST00000264709	NM_175629.2	579	Gac/Cac	15/23	0.73854842964314	4	FACETS	0.988	0.937	1	0.494	0.468	0.521	CLONAL	1	TRUE	2	0.767506086572213	4		652	1874	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947085	178947085	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	220	399	0	ENST00000263967.3:c.2521A>G	p.Ile841Val	p.I841V	ENST00000263967	NM_006218.2	841	Atc/Gtc	18/21	0.749891478065974	4	FACETS	1	0.975	1	0.274	0.255	0.294	CLONAL	1	TRUE	0	0.767506086572213	4		399	923	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139758	55139767	+	frameshift_variant	Frame_Shift_Del	DEL	CACGGAGATC	CACGGAGATC	-	novel	NA	P-0059444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3834	332	476	0	ENST00000257290.5:c.1422_1431del	p.Glu475ProfsTer11	p.E475Pfs*11	ENST00000257290	NM_006206.4	473	atCACGGAGATC/at	10/23	0.767506086572213	12	FACETS	1	0.943	1			1	CLONAL	1	TRUE	NA	0.767506086572213	12		476	4166	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31238951	31238951	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059444-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	132	369	0	ENST00000376228.5:c.518C>A	p.Ala173Glu	p.A173E	ENST00000376228	NM_002117.5	173	gCg/gAg	3/8	0.767506086572213	1	FACETS	0.33	0.3	0.361	0.33	0.3	0.361	SUBCLONAL	1	TRUE	0	0.767506086572213	1		369	643	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	203	228	0	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.872	0.814	0.931	0.872	0.814	0.931	CLONAL	1	TRUE	1	0.8	2		228	582	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	350	844	17	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.8	2		861	862	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	35	97	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.398	0.328	0.474	0.398	0.328	0.474	SUBCLONAL	1	TRUE	1	0.8	2		97	220	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	643	298	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.926	0.903	0.948	1	0.998	1	CLONAL	2	TRUE	1	0.8	2		298	868	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	344	577	2	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.994	0.945	1	0.994	0.945	1	CLONAL	1	TRUE	1	0.8	2		579	865	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65323437	65323437	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1240783724	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	280	590	0	ENST00000342505.4:c.1360C>T	p.Arg454Trp	p.R454W	ENST00000342505	NM_002227.2	454	Cgg/Tgg	10/25	1	2	FACETS	0.916	0.865	0.968	0.916	0.865	0.968	CLONAL	1	TRUE	1	0.8	2		590	764	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954272	32954273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359752	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	159	208	0	ENST00000380152.3:c.9253dup	p.Thr3085AsnfsTer26	p.T3085Nfs*26	ENST00000380152		3082	-/A	24/27	1	2	FACETS	0.806	0.745	0.87	0.806	0.745	0.87	CLONAL	1	TRUE	1	0.8	2		208	493	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611219	100611219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781792640	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	179	201	0	ENST00000308731.7:c.1387G>A	p.Val463Ile	p.V463I	ENST00000308731	NM_000061.2	463	Gtc/Atc	15/19	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.8	1		201	247	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	351	709	2	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.875	0.83	0.92	0.875	0.83	0.92	CLONAL	1	TRUE	1	0.8	2		711	1003	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217302	11217302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	296	466	0	ENST00000361445.4:c.4376C>T	p.Ala1459Val	p.A1459V	ENST00000361445	NM_004958.3	1459	gCc/gTc	30/58	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.8	2		466	680	SUCCESS
APC	324	MSKCC	GRCh37	5	112111408	112111411	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	-	rs387906231	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	78	44	0	ENST00000257430.4:c.509_512del	p.Asp170ValfsTer4	p.D170Vfs*4	ENST00000257430	NM_000038.5	169	ATAGat/at	5/16	1	2	FACETS	0.942	0.844	1	0.942	0.844	1	CLONAL	1	TRUE	1	0.8	2		44	207	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	276	532	2	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.872	0.822	0.923	0.872	0.822	0.923	CLONAL	1	TRUE	1	0.8	2		534	791	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524624	103524624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377353991	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	241	348	0	ENST00000355739.4:c.2755C>T	p.Arg919Trp	p.R919W	ENST00000355739	NM_000123.3	919	Cgg/Tgg	13/15	1	2	FACETS	0.967	0.91	1	0.967	0.91	1	CLONAL	1	TRUE	1	0.8	2		348	623	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166770	32166770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs947409717	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	304	530	0	ENST00000375023.3:c.4468C>T	p.Arg1490Trp	p.R1490W	ENST00000375023	NM_004557.3	1490	Cgg/Tgg	24/30	1	2	FACETS	0.984	0.933	1	0.984	0.933	1	CLONAL	1	TRUE	1	0.8	2		530	772	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508725	106508725	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	287	587	1	ENST00000359195.3:c.723del	p.Gly242AlafsTer17	p.G242Afs*17	ENST00000359195	NM_002649.2	240	aCc/ac	2/11	1	2	FACETS	0.915	0.864	0.967	0.915	0.864	0.967	CLONAL	1	TRUE	1	0.8	2		588	784	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937878	36937878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3918018	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	342	697	0	ENST00000361632.4:c.958G>A	p.Asp320Asn	p.D320N	ENST00000361632		320	Gac/Aac	7/16	1	2	FACETS	0.97	0.922	1	0.97	0.922	1	CLONAL	1	TRUE	1	0.8	2		697	881	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238417	98238417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137903539	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	287	520	0	ENST00000331920.6:c.1627C>T	p.Arg543Cys	p.R543C	ENST00000331920	NM_000264.3	543	Cgc/Tgc	12/24	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.8	2		520	702	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856209	111856209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	286	529	1	ENST00000341259.2:c.260G>A	p.Arg87His	p.R87H	ENST00000341259	NM_005475.2	87	cGc/cAc	2/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.8	2		530	686	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1962801	1962801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772470710	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	316	500	0	ENST00000382891.5:c.3295G>A	p.Glu1099Lys	p.E1099K	ENST00000382891	NM_133335.3	1099	Gag/Aag	18/22	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.8	2		500	764	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176504	142176504	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1196005889	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	213	279	0	ENST00000350721.4:c.7597C>T	p.Arg2533Ter	p.R2533*	ENST00000350721	NM_001184.3	2533	Cga/Tga	45/47	1	2	FACETS	0.992	0.929	1	0.992	0.929	1	CLONAL	1	TRUE	1	0.8	2		279	537	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	372	595	0	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.877	0.833	0.92	0.877	0.833	0.92	CLONAL	1	TRUE	1	0.8	2		595	1061	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132999	30132999	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749612527	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	226	465	0	ENST00000331968.5:c.602G>A	p.Arg201Gln	p.R201Q	ENST00000331968	NM_002742.2	201	cGg/cAg	4/18	1	2	FACETS	0.964	0.905	1	0.964	0.905	1	CLONAL	1	TRUE	1	0.8	2		465	586	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133538	55133538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770343276	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	258	505	2	ENST00000257290.5:c.842C>T	p.Thr281Met	p.T281M	ENST00000257290	NM_006206.4	281	aCg/aTg	6/23	1	2	FACETS	0.982	0.926	1	0.982	0.926	1	CLONAL	1	TRUE	1	0.8	2		507	657	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795734	42795734	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	369	655	0	ENST00000575354.2:c.2726del	p.Pro909ArgfsTer15	p.P909Rfs*15	ENST00000575354	NM_015125.3	908	gCc/gc	11/20	1	2	FACETS	0.95	0.904	0.997	0.95	0.904	0.997	CLONAL	1	TRUE	1	0.8	2		655	971	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574619	41574620	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	354	670	0	ENST00000263253.7:c.6910_6911del	p.Ser2304GlnfsTer74	p.S2304Qfs*74	ENST00000263253	NM_001429.3	2302	TCt/t	31/31	1	2	FACETS	0.888	0.843	0.933	0.888	0.843	0.933	CLONAL	1	TRUE	1	0.8	2		670	997	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624404	140624409	+	inframe_deletion	In_Frame_Del	DEL	CGGCGC	CGGCGC	-	rs397507458	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	155	408	0	ENST00000288602.6:c.95_100del	p.Gly32_Ala33del	p.G32_A33del	ENST00000288602	NM_004333.4	32	gGCGCCGcg/gcg	1/18	1	2	FACETS	0.747	0.688	0.807	0.747	0.688	0.807	SUBCLONAL	1	TRUE	1	0.8	2		408	519	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395793	45395793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1404495202	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	219	340	1	ENST00000262160.6:c.341G>A	p.Arg114His	p.R114H	ENST00000262160	NM_005901.5	114	cGt/cAt	4/11	1	2	FACETS	0.923	0.865	0.983	0.923	0.865	0.983	CLONAL	1	TRUE	1	0.8	2		341	593	SUCCESS
APC	324	MSKCC	GRCh37	5	112174424	112174424	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	227	316	0	ENST00000257430.4:c.3133C>T	p.Gln1045Ter	p.Q1045*	ENST00000257430	NM_000038.5	1045	Cag/Tag	16/16	1	2	FACETS	0.98	0.92	1	0.98	0.92	1	CLONAL	1	TRUE	1	0.8	2		316	579	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040627	47040627	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	301	189	0	ENST00000377604.3:c.1262G>T	p.Gly421Val	p.G421V	ENST00000377604	NM_001204468.1	421	gGg/gTg	13/24	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.8	1		189	358	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905567	50905567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760077781	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	406	772	1	ENST00000440232.2:c.695G>A	p.Arg232His	p.R232H	ENST00000440232	NM_002691.3	232	cGt/cAt	6/27	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.8	2		773	941	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137065	64137065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767134558	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	297	528	0	ENST00000334205.4:c.1576G>A	p.Val526Met	p.V526M	ENST00000334205	NM_003942.2	526	Gtg/Atg	13/17	1	2	FACETS	0.961	0.909	1	0.961	0.909	1	CLONAL	1	TRUE	1	0.8	2		528	773	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110129	8110129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746973523	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	298	548	0	ENST00000585124.1:c.476G>A	p.Arg159His	p.R159H	ENST00000585124	NM_004217.3	159	cGc/cAc	6/9	1	2	FACETS	0.943	0.892	0.995	0.943	0.892	0.995	CLONAL	1	TRUE	1	0.8	2		548	790	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273533	5273533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	264	541	0	ENST00000357368.4:c.299G>A	p.Arg100Gln	p.R100Q	ENST00000357368	NM_002850.3	100	cGg/cAg	4/38	1	2	FACETS	0.931	0.877	0.985	0.931	0.877	0.985	CLONAL	1	TRUE	1	0.8	2		541	709	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849884	156849884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770727871	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	259	511	0	ENST00000524377.1:c.2140G>A	p.Gly714Ser	p.G714S	ENST00000524377	NM_002529.3	714	Ggc/Agc	16/17	1	2	FACETS	0.941	0.887	0.996	0.941	0.887	0.996	CLONAL	1	TRUE	1	0.8	2		511	688	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911249	29911249	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs199474560	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	242	368	0	ENST00000376809.5:c.548A>G	p.Tyr183Cys	p.Y183C	ENST00000376809	NM_002116.7	183	tAc/tGc	3/8	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.8	2		368	509	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775630	9775630	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	306	515	0	ENST00000377346.4:c.173T>C	p.Leu58Pro	p.L58P	ENST00000377346	NM_005026.3	58	cTc/cCc	4/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.8	2		515	696	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444621	78444621	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	407	602	0	ENST00000370768.2:c.68G>A	p.Gly23Asp	p.G23D	ENST00000370768	NM_003902.3	23	gGt/gAt	1/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.8	2		602	989	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983052	201983052	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	346	592	0	ENST00000359651.3:c.901G>T	p.Gly301Cys	p.G301C	ENST00000359651		301	Ggc/Tgc	7/8	1	2	FACETS	0.976	0.928	1	0.976	0.928	1	CLONAL	1	TRUE	1	0.8	2		592	886	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851423	63851423	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	317	500	1	ENST00000279873.7:c.2201A>C	p.Gln734Pro	p.Q734P	ENST00000279873	NM_032199.2	734	cAg/cCg	10/10	1	2	FACETS	0.996	0.944	1	0.996	0.944	1	CLONAL	1	TRUE	1	0.8	2		501	796	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180552	94180552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	244	361	0	ENST00000323929.3:c.1616C>T	p.Ala539Val	p.A539V	ENST00000323929	NM_005591.3	539	gCc/gTc	15/20	1	2	FACETS	0.968	0.911	1	0.968	0.911	1	CLONAL	1	TRUE	1	0.8	2		361	630	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344442	118344442	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs782432998	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	353	539	0	ENST00000534358.1:c.2568G>T	p.Glu856Asp	p.E856D	ENST00000534358	NM_005933.3	856	gaG/gaT	3/36	1	2	FACETS	0.937	0.89	0.984	0.937	0.89	0.984	CLONAL	1	TRUE	1	0.8	2		539	942	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240035	41240035	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1238982941	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	78	211	0	ENST00000379561.5:c.315del	p.Leu106CysfsTer227	p.L106Cfs*227	ENST00000379561	NM_002015.3	105	ggG/gg	1/3	1	2	FACETS	0.882	0.789	0.979	0.882	0.789	0.979	CLONAL	1	TRUE	1	0.8	2		211	221	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117674	70117674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	388	681	1	ENST00000245479.2:c.142C>T	p.Pro48Ser	p.P48S	ENST00000245479	NM_000346.3	48	Ccc/Tcc	1/3	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.8	2		682	934	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302923	15302923	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	334	640	0	ENST00000263388.2:c.527A>G	p.Asn176Ser	p.N176S	ENST00000263388	NM_000435.2	176	aAc/aGc	4/33	1	2	FACETS	0.978	0.928	1	0.978	0.928	1	CLONAL	1	TRUE	1	0.8	2		640	854	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955119	17955119	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	301	593	0	ENST00000458235.1:c.108del	p.Gln39SerfsTer108	p.Q39Sfs*108	ENST00000458235	NM_000215.3	36	ggG/gg	2/24	1	2	FACETS	0.972	0.92	1	0.972	0.92	1	CLONAL	1	TRUE	1	0.8	2		593	774	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216708	36216708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758227116	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	302	560	0	ENST00000222270.7:c.3874C>T	p.Arg1292Trp	p.R1292W	ENST00000222270	NM_014727.1	1292	Cgg/Tgg	13/37	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.8	2		560	752	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422684	47422684	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1298488368	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	252	415	0	ENST00000404338.3:c.752G>A	p.Arg251Gln	p.R251Q	ENST00000404338	NM_004491.4	251	cGg/cAg	1/6	1	2	FACETS	0.952	0.896	1	0.952	0.896	1	CLONAL	1	TRUE	1	0.8	2		415	662	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690201	47690201	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	188	119	0	ENST00000233146.2:c.1418C>A	p.Ser473Ter	p.S473*	ENST00000233146	NM_000251.2	473	tCa/tAa	9/16	1	2	FACETS	0.979	0.914	1	0.979	0.914	1	CLONAL	1	TRUE	1	0.8	2		119	480	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321687	62321687	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369014080	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	303	549	0	ENST00000360203.5:c.2306G>A	p.Arg769His	p.R769H	ENST00000360203	NM_001283009.1	769	cGt/cAt	26/35	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.8	2		549	738	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691872	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs79375991	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	482	384	15	ENST00000295754.5:c.383del	p.Lys128SerfsTer35	p.K128Sfs*35	ENST00000295754	NM_003242.5	125	gAa/ga	3/7	1	2	FACETS	0.816	0.79	0.842	1	0.997	1	CLONAL	2	TRUE	1	0.8	2		399	738	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138592	55138592	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	92	413	0	ENST00000257290.5:c.1269T>A	p.Asp423Glu	p.D423E	ENST00000257290	NM_006206.4	423	gaT/gaA	9/23	1	2	FACETS	0.369	0.328	0.412	0.369	0.328	0.412	SUBCLONAL	1	TRUE	1	0.8	2		413	624	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527692	157527692	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	281	527	0	ENST00000346085.5:c.5417T>C	p.Leu1806Ser	p.L1806S	ENST00000346085	NM_020732.3	1806	tTg/tCg	20/20	0.147264645846689	1	FACETS	0.584	0.551	0.617	0.584	0.551	0.617	INDETERMINATE	1	TRUE	0	0.8	1		527	722	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213563	27213563	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867553064	NA	P-0059448-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	210	322	0	ENST00000380036.4:c.2959C>T	p.Arg987Ter	p.R987*	ENST00000380036	NM_000459.3	987	Cga/Tga	18/23	1	2	FACETS	0.887	0.829	0.946	0.887	0.829	0.946	CLONAL	1	TRUE	1	0.8	2		322	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0059449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	208	613	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.415332715193042	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.415332715193042	1		614	655	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0059449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	51	100	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.415332715193042	2		100	207	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0059449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	84	513	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.7	0.619	0.786	0.7	0.619	0.786	SUBCLONAL	1	TRUE	1	0.415332715193042	2		513	578	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0059449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	78	506	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	1	2	FACETS	0.698	0.615	0.788	0.698	0.615	0.788	SUBCLONAL	1	TRUE	1	0.415332715193042	2		506	538	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23635370	23635370	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45624036	NA	P-0059449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	47	212	0	ENST00000261584.4:c.2794G>A	p.Val932Met	p.V932M	ENST00000261584	NM_024675.3	932	Gtg/Atg	8/13	NA	2	FACETS	0.803	0.682	0.934			1	INDETERMINATE	1	TRUE	NA	0.415332715193042	2		212	282	SUCCESS
APC	324	MSKCC	GRCh37	5	112116538	112116538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs749479682	NA	P-0059449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	78	357	0	ENST00000257430.4:c.583C>T	p.Gln195Ter	p.Q195*	ENST00000257430	NM_000038.5	195	Caa/Taa	6/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.415332715193042	2		357	292	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309749	65309749	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059449-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	95	532	0	ENST00000342505.4:c.2401G>A	p.Glu801Lys	p.E801K	ENST00000342505	NM_002227.2	801	Gag/Aag	17/25	1	2	FACETS	0.79	0.705	0.88	0.79	0.705	0.88	SUBCLONAL	1	TRUE	1	0.415332715193042	2		532	579	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0059450-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	103	569	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.324811858455657	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	0	0.324811858455657	1		569	527	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459531	50459531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059450-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	64	302	0	ENST00000331340.3:c.820C>T	p.Arg274Cys	p.R274C	ENST00000331340	NM_006060.4	274	Cgt/Tgt	7/8	1	2	FACETS	0.916	0.796	1	0.916	0.796	1	CLONAL	1	TRUE	1	0.324811858455657	2		302	430	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220673	1220673	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059450-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	67	532	0	ENST00000326873.7:c.692del	p.Phe231SerfsTer56	p.F231Sfs*56	ENST00000326873	NM_000455.4	231	Ttc/tc	5/10	0.324811858455657	1	FACETS	0.778	0.678	0.886	0.778	0.678	0.886	SUBCLONAL	1	TRUE	0	0.324811858455657	1		532	444	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14317323	14317323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782189872	NA	P-0059450-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	46	171	0	ENST00000256196.4:c.187C>T	p.Arg63Trp	p.R63W	ENST00000256196		63	Cgg/Tgg	2/6	0.324811858455657	1	FACETS	0.909	0.771	1	0.909	0.771	1	CLONAL	1	TRUE	0	0.324811858455657	1		171	261	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339014	225339015	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0059450-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	47	188	0	ENST00000264414.4:c.2254_2255del	p.Glu752IlefsTer7	p.E752Ifs*7	ENST00000264414	NM_003590.4	752	GAa/a	16/16	1	2	FACETS	0.768	0.649	0.897	0.768	0.649	0.897	SUBCLONAL	1	TRUE	1	0.324811858455657	2		188	377	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815540	139815540	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1190945071	NA	P-0059450-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	189	516	0	ENST00000247668.2:c.1011C>G	p.Asp337Glu	p.D337E	ENST00000247668	NM_021138.3	337	gaC/gaG	9/11	0.324806418757791	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.324811858455657	2		516	534	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0059451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	51	185	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.49704436290522	2		185	201	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0059451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	66	428	0	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	1	2	FACETS	0.479	0.415	0.547	0.479	0.415	0.547	SUBCLONAL	1	TRUE	1	0.49704436290522	2		428	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579417	7579427	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGGGGGCTG	GGAGGGGGCTG	-	rs1567556165	NA	P-0059451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	45	734	0	ENST00000269305.4:c.260_270del	p.Pro87LeufsTer58	p.P87Lfs*58	ENST00000269305	NM_001126112.2	87	cCAGCCCCCTCC/c	4/11	0.49704436290522	1	FACETS	0.204	0.171	0.241	0.204	0.171	0.241	SUBCLONAL	1	TRUE	0	0.49704436290522	1		734	667	SUCCESS
APC	324	MSKCC	GRCh37	5	112175488	112175488	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	173	540	0	ENST00000257430.4:c.4198del	p.Ser1400ArgfsTer15	p.S1400Rfs*15	ENST00000257430	NM_000038.5	1399	cgT/cg	16/16	0.49704436290522	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.49704436290522	1		540	507	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38173476	38173476	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs372612316	NA	P-0059451-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	139	409	0	ENST00000317025.8:c.1940A>G	p.Tyr647Cys	p.Y647C	ENST00000317025	NM_023034.1	647	tAc/tGc	10/24	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.49704436290522	2		409	530	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0059452-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	69	367	2	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	0.200159963639497	3	FACETS	1	0.904	1	0.684	0.604	0.768	CLONAL	2	TRUE	0	0.330486468814876	3		369	237	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612693	228612693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059452-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	51	736	2	ENST00000366696.1:c.334G>A	p.Val112Ile	p.V112I	ENST00000366696	NM_003493.2	112	Gtc/Atc	1/1	0.327959520431663	4	FACETS	0.836	0.711	0.973	0.279	0.237	0.325	CLONAL	1	TRUE	1	0.330486468814876	4		738	491	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856136	111856136	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059452-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	21	567	0	ENST00000341259.2:c.187G>C	p.Val63Leu	p.V63L	ENST00000341259	NM_005475.2	63	Gtg/Ctg	2/8	0.330486468814876	4	FACETS	0.482	0.37	0.612	0.161	0.123	0.204	SUBCLONAL	1	TRUE	1	0.330486468814876	4		567	351	SUCCESS
APC	324	MSKCC	GRCh37	5	112174112	112174112	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	81	554	0	ENST00000257430.4:c.2821G>T	p.Glu941Ter	p.E941*	ENST00000257430	NM_000038.5	941	Gaa/Taa	16/16	0.305532799286306	1	FACETS	0.756	0.673	0.843	1	0.979	1	SUBCLONAL	2	TRUE	0	0.305532799286306	1		554	297	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750430	133750430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	40	708	2	ENST00000318560.5:c.1261G>A	p.Asp421Asn	p.D421N	ENST00000318560	NM_005157.4	421	Gac/Aac	7/11	1	2	FACETS	0.471	0.391	0.561	0.471	0.391	0.561	SUBCLONAL	1	TRUE	1	0.305532799286306	2		710	556	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911922	32911922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1274123258	NA	P-0059455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	76	518	0	ENST00000380152.3:c.3430G>A	p.Val1144Met	p.V1144M	ENST00000380152		1144	Gtg/Atg	11/27	0.198795135717755	4	FACETS	0.92	0.813	1	0.92	0.813	1	CLONAL	2	TRUE	2	0.305532799286306	4		518	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577083	7577084	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0059455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	120	830	0	ENST00000269305.4:c.854_855insT	p.Glu285AspfsTer21	p.E285Dfs*21	ENST00000269305	NM_001126112.2	285	gag/gaTg	8/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.305532799286306	2		830	550	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793163	33793163	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	56	775	0	ENST00000498907.2:c.158G>C	p.Gly53Ala	p.G53A	ENST00000498907	NM_004364.3	53	gGc/gCc	1/1	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.305532799286306	2		775	332	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503819	186503819	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059455-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	33	543	0	ENST00000323963.5:c.496A>G	p.Met166Val	p.M166V	ENST00000323963		166	Atg/Gtg	5/11	1	2	FACETS	0.704	0.575	0.848	0.704	0.575	0.848	SUBCLONAL	1	TRUE	1	0.305532799286306	2		543	307	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0059456-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	142	525	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		525	369	SUCCESS
AR	367	MSKCC	GRCh37	X	66765080	66765080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059456-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	222	603	0	ENST00000374690.3:c.92G>A	p.Arg31His	p.R31H	ENST00000374690	NM_000044.3	31	cGc/cAc	1/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		603	572	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0059456-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3711	15939	813	1	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		814	19650	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223567	55223567	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059456-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14181	1857	618	0	ENST00000275493.2:c.934G>T	p.Gly312Trp	p.G312W	ENST00000275493	NM_005228.3	312	Ggg/Tgg	8/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		618	16038	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0059457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	405	674	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.665449138186896	2		674	1062	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717699	89717709	+	frameshift_variant	Frame_Shift_Del	DEL	GAGTTCCCTCA	GAGTTCCCTCA	-	novel	NA	P-0059457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	227	377	0	ENST00000371953.3:c.725_735del	p.Glu242AlafsTer7	p.E242Afs*7	ENST00000371953	NM_000314.4	242	GAGTTCCCTCAg/g	7/9	0.668376795616669	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.665449138186896	1		377	313	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437698	49437698	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	666	700	0	ENST00000301067.7:c.5272G>C	p.Gly1758Arg	p.G1758R	ENST00000301067	NM_003482.3	1758	Ggg/Cgg	22/54	0.370625564516806	3	FACETS	0.854	0.83	0.878	0.854	0.83	0.878	INDETERMINATE	3	TRUE	0	0.665449138186896	3		700	1041	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845839	72845839	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	331	639	0	ENST00000268489.5:c.3628C>T	p.Arg1210Ter	p.R1210*	ENST00000268489	NM_006885.3	1210	Cga/Tga	6/10	0.668376795616669	2	FACETS	1	0.994	1	0.669	0.636	0.701	CLONAL	1	TRUE	0	0.665449138186896	2		639	744	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0059457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	290	517	0	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.665449138186896	2		517	749	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584497	39584497	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	308	520	0	ENST00000262039.4:c.1162G>T	p.Asp388Tyr	p.D388Y	ENST00000262039	NM_002647.2	388	Gat/Tat	10/25	0.414364400459626	4	FACETS	0.771	0.728	0.815			1	SUBCLONAL	2	TRUE	NA	0.665449138186896	4		520	1000	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612270	1612270	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	304	608	0	ENST00000344749.5:c.1749G>T	p.Gln583His	p.Q583H	ENST00000344749	NM_001136139.2	583	caG/caT	18/19	0.590660821682508	1	FACETS	0.885	0.84	0.93	0.885	0.84	0.93	CLONAL	1	TRUE	0	0.665449138186896	1		608	689	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568504	41568504	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	112	301	0	ENST00000263253.7:c.4454A>T	p.Asp1485Val	p.D1485V	ENST00000263253	NM_001429.3	1485	gAt/gTt	28/31	0.401670465600243	2	FACETS	0.895	0.831	0.958	0.895	0.831	0.958	CLONAL	2	TRUE	0	0.665449138186896	2		301	188	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602664	55602664	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs1057519713	NA	P-0059457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	211	355	0	ENST00000288135.5:c.2485G>C	p.Ala829Pro	p.A829P	ENST00000288135	NM_000222.2	829	Gct/Cct	18/21	0.668376795616669	4	FACETS	0.943	0.883	1	0.471	0.441	0.502	CLONAL	2	TRUE	0	0.665449138186896	4		355	560	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940403	31940404	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0059457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	462	639	0	ENST00000375333.2:c.443_444del	p.Ala148GlyfsTer15	p.A148Gfs*15	ENST00000375333	NM_032454.1	146	GCg/g	3/8	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.665449138186896	2		639	1239	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207710	29207710	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	625	595	0	ENST00000240100.2:c.86G>C	p.Gly29Ala	p.G29A	ENST00000240100	NM_001394.6	29	gGc/gCc	1/4	0.442973798746222	2	FACETS	0.876	0.849	0.903	0.876	0.849	0.903	CLONAL	2	TRUE	0	0.665449138186896	2		595	1072	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028022	69028022	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	46	376	0	ENST00000288368.4:c.3181G>T	p.Glu1061Ter	p.E1061*	ENST00000288368	NM_024870.2	1061	Gaa/Taa	26/40	0.590660821682508	1	FACETS	0.721	0.622	0.823	0.721	0.622	0.823	SUBCLONAL	1	TRUE	0	0.665449138186896	1		376	128	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974721	21974721	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	1397	694	0	ENST00000304494.5:c.106del	p.Ala36ArgfsTer17	p.A36Rfs*17	ENST00000304494	NM_000077.4	36	Gcg/cg	1/3	0.668376795616669	3	FACETS	1	0.998	1	1	0.998	1	CLONAL	3	TRUE	0	0.665449138186896	3		694	1709	SUCCESS
AR	367	MSKCC	GRCh37	X	66765932	66765932	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1364038551	NA	P-0059457-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	135	345	0	ENST00000374690.3:c.944G>T	p.Gly315Val	p.G315V	ENST00000374690	NM_000044.3	315	gGt/gTt	1/8	0.668376795616669	2	FACETS	0.616	0.561	0.673			1	SUBCLONAL	1	TRUE	NA	0.665449138186896	2		345	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0059458-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	359	522	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.824479379977556	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.824479379977556	2		522	427	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589559	67589591	+	inframe_deletion	In_Frame_Del	DEL	ATATTGAAGCTGTAGGGAAAAAATTACATGAAT	ATATTGAAGCTGTAGGGAAAAAATTACATGAAT	-	novel	NA	P-0059458-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	124	154	0	ENST00000274335.5:c.1325_1357del	p.Ile442_Tyr452del	p.I442_Y452del	ENST00000274335		441	aATATTGAAGCTGTAGGGAAAAAATTACATGAATat/aat	10/15	0.824479379977556	2	FACETS	0.958	0.909	1	0.958	0.909	1	CLONAL	2	TRUE	0	0.824479379977556	2		154	157	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481429	40481446	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TCACAATTGGCTCGGCCC	TCACAATTGGCTCGGCCC	-	novel	NA	P-0059458-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	207	450	0	ENST00000264657.5:c.1263_1280del	p.Gly422_Asp427del	p.G422_D427del	ENST00000264657	NM_139276.2	421	ggGGGCCGAGCCAATTGTGAt/ggt	14/24	0.814337016011682	2	FACETS	0.903	0.864	0.94	0.903	0.864	0.94	CLONAL	2	TRUE	0	0.824479379977556	2		450	278	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249263	10249263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059458-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	58	451	0	ENST00000340748.4:c.3919G>A	p.Ala1307Thr	p.A1307T	ENST00000340748		1307	Gcc/Acc	34/40	1	2	FACETS	0.373	0.322	0.429	0.373	0.322	0.429	SUBCLONAL	1	TRUE	1	0.824479379977556	2		451	377	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961109	55961109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374755237	NA	P-0059459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	37	365	2	ENST00000263923.4:c.2831G>A	p.Arg944Gln	p.R944Q	ENST00000263923	NM_002253.2	944	cGa/cAa	21/30	1	2	FACETS	0.515	0.425	0.615	0.515	0.425	0.615	SUBCLONAL	1	TRUE	1	0.378072980137896	2		367	380	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143191873	143191873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	338	489	0	ENST00000262992.4:c.558G>T	p.Met186Ile	p.M186I	ENST00000262992	NM_001101669.1	186	atG/atT	8/24	0.378072980137896	5	FACETS	0.876	0.833	0.919	0.876	0.833	0.919	CLONAL	4	TRUE	1	0.378072980137896	5		489	800	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092823	27092823	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0059459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	62	487	0	ENST00000324856.7:c.2844T>A	p.Tyr948Ter	p.Y948*	ENST00000324856	NM_006015.4	948	taT/taA	9/20	1	2	FACETS	0.806	0.699	0.921	0.806	0.699	0.921	CLONAL	1	TRUE	1	0.378072980137896	2		487	407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578450	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0059459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	217	785	0	ENST00000269305.4:c.480_481delinsTT	p.Met160_Ala161delinsIleSer	p.M160_A161delinsIS	ENST00000269305	NM_001126112.2	160	atGGcc/atTTcc	5/11	0.247237675410101	2	FACETS	1	0.991	1	0.712	0.664	0.762	CLONAL	1	TRUE	0	0.378072980137896	2		785	806	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628717	21628717	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	17	433	0	ENST00000421138.2:c.991A>T	p.Thr331Ser	p.T331S	ENST00000421138		331	Acg/Tcg	10/16	0.378072980137896	1	FACETS	0.496	0.373	0.64	0.496	0.373	0.64	SUBCLONAL	1	TRUE	0	0.378072980137896	1		433	147	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042208	42042208	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	78	529	0	ENST00000219905.7:c.6404del	p.Lys2135ArgfsTer44	p.K2135Rfs*44	ENST00000219905	NM_001164273.1	2135	Aag/ag	17/24	0.247237675410101	2	FACETS	0.784	0.698	0.874	0.784	0.698	0.874	SUBCLONAL	2	TRUE	0	0.378072980137896	2		529	263	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656655	3656655	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	130	585	0	ENST00000294008.3:c.580A>T	p.Thr194Ser	p.T194S	ENST00000294008	NM_032444.2	194	Aca/Tca	3/15	1	2	FACETS	0.881	0.799	0.966	0.881	0.799	0.966	CLONAL	1	TRUE	1	0.378072980137896	2		585	781	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991359	72991359	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	85	487	0	ENST00000268489.5:c.2686G>T	p.Ala896Ser	p.A896S	ENST00000268489	NM_006885.3	896	Gcc/Tcc	2/10	1	2	FACETS	0.706	0.624	0.793	0.706	0.624	0.793	SUBCLONAL	1	TRUE	1	0.378072980137896	2		487	637	SUCCESS
SERPINB4	6318	MSKCC	GRCh37	18	61305006	61305006	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	32	346	0	ENST00000341074.5:c.1120A>T	p.Arg374Trp	p.R374W	ENST00000341074	NM_002974.2	374	Agg/Tgg	8/8	0.340238399466639	1	FACETS	0.663	0.542	0.797	0.663	0.542	0.797	SUBCLONAL	1	TRUE	0	0.378072980137896	1		346	207	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968301	18968301	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	134	540	0	ENST00000262803.5:c.2141A>C	p.Asn714Thr	p.N714T	ENST00000262803	NM_002911.3	714	aAc/aCc	15/24	0.264218298148764	2	FACETS	1	0.981	1	0.641	0.585	0.699	CLONAL	1	TRUE	0	0.378072980137896	2		540	553	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795437	39795437	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	172	548	1	ENST00000288319.7:c.283G>T	p.Gly95Cys	p.G95C	ENST00000288319	NM_182918.3	95	Ggc/Tgc	3/10	0.247237675410101	2	FACETS	1	0.987	1	0.672	0.62	0.725	CLONAL	1	TRUE	0	0.378072980137896	2		549	677	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970998	55970998	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	69	495	0	ENST00000263923.4:c.1799C>A	p.Thr600Lys	p.T600K	ENST00000263923	NM_002253.2	600	aCa/aAa	13/30	1	2	FACETS	0.717	0.626	0.816	0.717	0.626	0.816	SUBCLONAL	1	TRUE	1	0.378072980137896	2		495	509	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931820	68931820	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	61	392	0	ENST00000288368.4:c.250C>G	p.His84Asp	p.H84D	ENST00000288368	NM_024870.2	84	Cat/Gat	3/40	0.253458101103081	4	FACETS	1	0.962	1	0.664	0.576	0.758	CLONAL	1	TRUE	2	0.378072980137896	4		392	335	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123022477	123022477	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059459-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	34	360	0	ENST00000355640.3:c.886G>T	p.Asp296Tyr	p.D296Y	ENST00000355640		296	Gat/Tat	3/7	0.378072980137896	1	FACETS	0.843	0.697	1	0.843	0.697	1	CLONAL	1	TRUE	0	0.378072980137896	1		360	173	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0059460-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	95	539	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.965	0.861	1	0.965	0.861	1	CLONAL	1	TRUE	1	0.349087030766242	2		539	564	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059460-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	74	121	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.349087030766242	2		121	350	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0059460-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	90	369	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.349087030766242	2		369	503	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958789	55958789	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059460-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	87	347	0	ENST00000263923.4:c.3064C>T	p.Arg1022Ter	p.R1022*	ENST00000263923	NM_002253.2	1022	Cga/Tga	22/30	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.349087030766242	2		347	438	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759863	133759863	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768245401	NA	P-0059460-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	125	562	1	ENST00000318560.5:c.2186C>T	p.Thr729Met	p.T729M	ENST00000318560	NM_005157.4	729	aCg/aTg	11/11	0.346635219646087	3	FACETS	1	0.963	1	0.562	0.508	0.617	CLONAL	1	TRUE	1	0.349087030766242	3		563	749	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446164	70446164	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059460-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	96	463	0	ENST00000373644.4:c.5104G>T	p.Asp1702Tyr	p.D1702Y	ENST00000373644	NM_030625.2	1702	Gat/Tat	11/12	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.349087030766242	2		463	534	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4388038	4388038	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059460-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	105	550	0	ENST00000261254.3:c.524C>A	p.Ser175Tyr	p.S175Y	ENST00000261254	NM_001759.3	175	tCt/tAt	3/5	1	2	FACETS	0.944	0.848	1	0.944	0.848	1	CLONAL	1	TRUE	1	0.349087030766242	2		550	637	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117908	70117908	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059460-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	143	649	0	ENST00000245479.2:c.376C>T	p.Gln126Ter	p.Q126*	ENST00000245479	NM_000346.3	126	Cag/Tag	1/3	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.349087030766242	2		649	629	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117919	70117934	+	frameshift_variant	Frame_Shift_Del	DEL	CTTGCACAACGCCGAG	CTTGCACAACGCCGAG	-	novel	NA	P-0059460-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	126	650	0	ENST00000245479.2:c.389_404del	p.Leu130SerfsTer12	p.L130Sfs*12	ENST00000245479	NM_000346.3	129	caCTTGCACAACGCCGAG/ca	1/3	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.349087030766242	2		650	636	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591854	48591854	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059460-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	120	542	0	ENST00000342988.3:c.1017T>A	p.Phe339Leu	p.F339L	ENST00000342988	NM_005359.5	339	ttT/ttA	9/12	0.349087030766242	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.349087030766242	1		542	537	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979240	93979240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059460-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	79	521	0	ENST00000369303.4:c.1588C>T	p.Leu530Phe	p.L530F	ENST00000369303	NM_004440.3	530	Ctt/Ttt	7/17	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.349087030766242	2		521	420	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879904	44879904	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059460-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	85	180	0	ENST00000377967.4:c.493C>G	p.Arg165Gly	p.R165G	ENST00000377967	NM_021140.2	165	Cga/Gga	6/29	1	1	FACETS	0.914	0.823	1	1	0.985	1	CLONAL	2	TRUE	0	0.349087030766242	1		180	220	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528073	157528094	+	protein_altering_variant	In_Frame_Del	DEL	CCATCGCGCACTGGCAGGACTC	CCATCGCGCACTGGCAGGACTC	A	novel	NA	P-0059460-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	126	678	0	ENST00000346085.5:c.5798_5819delinsA	p.Thr1933_Ser1940delinsLys	p.T1933_S1940delinsK	ENST00000346085	NM_020732.3	1933	aCCATCGCGCACTGGCAGGACTCg/aAg	20/20	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.349087030766242	2		678	722	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0059461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	94	386	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	0.280886925165764	3	FACETS	0.552	0.491	0.617	0.184	0.163	0.206	INDETERMINATE	1	TRUE	0	0.667854188065357	3		386	680	SUCCESS
APC	324	MSKCC	GRCh37	5	112173926	112173926	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060503287	NA	P-0059461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	390	393	0	ENST00000257430.4:c.2635C>T	p.Gln879Ter	p.Q879*	ENST00000257430	NM_000038.5	879	Cag/Tag	16/16	0.667854188065357	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.667854188065357	2		393	567	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933574	39933574	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	118	303	0	ENST00000378444.4:c.1025G>A	p.Arg342Gln	p.R342Q	ENST00000378444	NM_001123385.1	342	cGa/cAa	4/15	0.666573652149596	2	FACETS	0.461	0.416	0.508			1	SUBCLONAL	1	TRUE	NA	0.667854188065357	2		303	767	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013720	170013720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	132	210	9	ENST00000295797.4:c.1439G>A	p.Arg480His	p.R480H	ENST00000295797	NM_002740.5	480	cGc/cAc	15/18	0.280886925165764	3	FACETS	1	0.96	1	0.7	0.65	0.75	INDETERMINATE	2	TRUE	0	0.667854188065357	3		219	251	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792754	33792755	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGC	rs746430067	NA	P-0059461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	118	379	0	ENST00000498907.2:c.564_566dup	p.Pro189dup	p.P189dup	ENST00000498907	NM_004364.3	189	ccc/ccGCCc	1/1	1	2	FACETS	0.726	0.658	0.796	0.726	0.658	0.796	SUBCLONAL	1	TRUE	1	0.667854188065357	2		379	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577561	7577568	+	frameshift_variant	Frame_Shift_Del	DEL	ACTGTTAC	ACTGTTAC	-	novel	NA	P-0059461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	189	374	0	ENST00000269305.4:c.713_720del	p.Cys238PhefsTer23	p.C238Ffs*23	ENST00000269305	NM_001126112.2	238	tGTAACAGT/t	7/11	0.667854188065357	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.667854188065357	1		374	351	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658439	117658439	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	43	331	0	ENST00000368508.3:c.5144A>T	p.Asn1715Ile	p.N1715I	ENST00000368508	NM_002944.2	1715	aAt/aTt	31/43	1	2	FACETS	0.404	0.339	0.475	0.404	0.339	0.475	SUBCLONAL	1	TRUE	1	0.667854188065357	2		331	319	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610310	10610315	+	stop_gained	Nonsense_Mutation	ONP	CCATGA	CCATGA	AAATGC	novel	NA	P-0059461-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	83	539	0	ENST00000171111.5:c.395_400delinsGCATTT	p.Val132_Glu134delinsGlyIleTer	p.V132_E134delinsGI*	ENST00000171111	NM_203500.1	132	gTCATGGag/gGCATTTag	2/6	1	2	FACETS	0.4	0.353	0.45	0.4	0.353	0.45	SUBCLONAL	1	TRUE	1	0.667854188065357	2		539	622	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36934783	36934783	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059462-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	337	584	0	ENST00000361632.4:c.1550A>G	p.His517Arg	p.H517R	ENST00000361632		517	cAt/cGt	11/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.5900296360232	2		584	1047	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0059462-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	357	563	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.592990904911329	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.5900296360232	1		563	762	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6222445	6222445	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059462-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	265	746	0	ENST00000252674.7:c.797C>A	p.Thr266Lys	p.T266K	ENST00000252674	NM_005934.3	266	aCg/aAg	6/12	0.592990904911329	1	FACETS	0.918	0.866	0.971	0.918	0.866	0.971	CLONAL	1	TRUE	0	0.5900296360232	1		746	690	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589632	67589643	+	inframe_deletion	In_Frame_Del	DEL	ATTATATGAAGA	ATTATATGAAGA	-	novel	NA	P-0059462-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	164	305	0	ENST00000274335.5:c.1397_1408del	p.Leu466_Glu469del	p.L466_E469del	ENST00000274335		465	agATTATATGAAGAa/aga	10/15	0.592990904911329	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.5900296360232	1		305	387	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0059463-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	1422	635	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.196654727391236	23	FACETS	0.976	0.958	0.994	1	0.993	1	CLONAL	21	TRUE	3	0.196654727391236	23		635	2162	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574000	7574000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059463-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	105	415	0	ENST00000269305.4:c.1027G>T	p.Glu343Ter	p.E343*	ENST00000269305	NM_001126112.2	343	Gag/Tag	10/11	0.196317212281884	2	FACETS	0.921	0.827	1	0.921	0.827	1	CLONAL	2	TRUE	0	0.196654727391236	2		415	580	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528621	89528621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780470195	NA	P-0059463-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	43	334	0	ENST00000336596.2:c.2921C>T	p.Thr974Met	p.T974M	ENST00000336596	NM_005233.5	974	aCg/aTg	17/17	0.196654727391236	2	FACETS	0.729	0.609	0.862	0.364	0.304	0.431	SUBCLONAL	1	TRUE	0	0.196654727391236	2		334	600	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872053	35872053	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059463-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	80	511	0	ENST00000216797.5:c.560T>G	p.Leu187Arg	p.L187R	ENST00000216797	NM_020529.2	187	cTa/cGa	4/6	0.196654727391236	6	FACETS	1	0.942	1			1	CLONAL	1	TRUE	NA	0.196654727391236	6		511	1008	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041348	47041348	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0059463-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	70	342	0	ENST00000377604.3:c.1694-2A>G		p.X565_splice	ENST00000377604	NM_001204468.1	565			1	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.196654727391236	1		342	481	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0059464-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	52	484	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.160697783190568	4	FACETS	0.776	0.662	0.902	0.776	0.662	0.902	CLONAL	2	TRUE	2	0.17	4		484	461	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0059464-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	48	412	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.160697783190568	3	FACETS	0.784	0.664	0.914	0.784	0.664	0.914	CLONAL	2	TRUE	1	0.17	3		412	391	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913399	NA	P-0059464-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	48	547	0	ENST00000349496.5:c.100G>C	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Cga	3/15	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.17	2		547	491	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604750	48604750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059464-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	27	584	0	ENST00000342988.3:c.1572G>T	p.Trp524Cys	p.W524C	ENST00000342988	NM_005359.5	524	tgG/tgT	12/12	1	2	FACETS	0.682	0.541	0.842	0.682	0.541	0.842	SUBCLONAL	1	TRUE	1	0.17	2		584	466	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971169	21971176	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCAGCT	CAGCAGCT	-	novel	NA	P-0059464-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	31	669	0	ENST00000304494.5:c.182_189del	p.Glu61AlafsTer56	p.E61Afs*56	ENST00000304494	NM_000077.4	61	gAGCTGCTG/g	2/3	1	2	FACETS	0.866	0.7	1	0.866	0.7	1	CLONAL	1	TRUE	1	0.17	2		669	421	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115111972	115111972	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059465-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	243	513	0	ENST00000257566.3:c.1768C>T	p.Gln590Ter	p.Q590*	ENST00000257566	NM_016569.3	590	Cag/Tag	7/8	0.212631562085539	5	FACETS	0.988	0.937	1	1	0.996	1	CLONAL	7	TRUE	2	0.212631562085539	5		513	436	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005888	69005888	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059465-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	117	377	0	ENST00000288368.4:c.2299G>A	p.Asp767Asn	p.D767N	ENST00000288368	NM_024870.2	767	Gac/Aac	21/40	0.212631562085539	7	FACETS	1	0.954	1	0.466	0.422	0.512	CLONAL	3	TRUE	0	0.212631562085539	7		377	517	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571996	64571996	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059465-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	236	535	0	ENST00000312049.6:c.1643del	p.Gly548ValfsTer11	p.G548Vfs*11	ENST00000312049	NM_130799.2	548	gGt/gt	10/10	0.215764535021277	1	FACETS	0.937	0.894	0.978	1	0.996	1	CLONAL	6	TRUE	0	0.212631562085539	1		535	353	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984753	11984754	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0059465-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	102	246	0	ENST00000353533.5:c.301dup	p.Asp101GlyfsTer31	p.D101Gfs*31	ENST00000353533	NM_003010.3	100	gag/gaGg	3/11	0.215764535021277	0	FACETS	0.94	0.883	0.991			1	CLONAL	6	TRUE	0	0.212631562085539	0		246	134	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467828	50467828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1040607869	NA	P-0059473-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	209	618	0	ENST00000331340.3:c.1063G>A	p.Ala355Thr	p.A355T	ENST00000331340	NM_006060.4	355	Gcg/Acg	8/8	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.66	2		618	629	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051658	30051658	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555993345	NA	P-0059475-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	144	369	0	ENST00000338641.4:c.592C>T	p.Arg198Ter	p.R198*	ENST00000338641	NM_000268.3	198	Cga/Tga	6/16	0.3	0	FACETS		NA	1			1	NA	4	TRUE	0	0.35	0		369	175	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs17849781	NA	P-0059476-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	27	691	0	ENST00000269305.4:c.832C>A	p.Pro278Thr	p.P278T	ENST00000269305	NM_001126112.2	278	Cct/Act	8/11	0.184076206215847	1	FACETS	0.879	0.701	1	0.879	0.701	1	CLONAL	1	TRUE	0	0.184076206215847	1		691	303	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578541	7578541	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1131691013	NA	P-0059477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	222	501	0	ENST00000269305.4:c.389T>C	p.Leu130Pro	p.L130P	ENST00000269305	NM_001126112.2	130	cTc/cCc	5/11	0.20494114803468	3	FACETS	0.984	0.918	1	0.984	0.918	1	CLONAL	3	TRUE	0	0.20494114803468	3		501	809	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061098	38061098	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	95	585	0	ENST00000250448.2:c.891del	p.Ser298LeufsTer23	p.S298Lfs*23	ENST00000250448	NM_004496.3	297	ccC/cc	2/2	0.20494114803468	3	FACETS	1	0.96	1	0.391	0.347	0.437	CLONAL	1	TRUE	0	0.20494114803468	3		585	872	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216590	108216590	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	43	336	0	ENST00000278616.4:c.8539G>C	p.Glu2847Gln	p.E2847Q	ENST00000278616	NM_000051.3	2847	Gag/Cag	58/63	1	2	FACETS	0.846	0.708	0.999	0.846	0.708	0.999	CLONAL	1	TRUE	1	0.20494114803468	2		336	496	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441851	49441851	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	69	416	0	ENST00000301067.7:c.4133A>G	p.Asp1378Gly	p.D1378G	ENST00000301067	NM_003482.3	1378	gAc/gGc	14/54	0.20494114803468	5	FACETS	1	0.877	1	0.337	0.292	0.385	CLONAL	1	TRUE	2	0.20494114803468	5		416	872	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81922810	81922810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	127	385	0	ENST00000359376.3:c.799G>A	p.Glu267Lys	p.E267K	ENST00000359376	NM_002661.3	267	Gag/Aag	10/33	0.152933319256653	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	2	0.20494114803468	4		385	686	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380451	31380451	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	170	599	0	ENST00000328111.2:c.941G>T	p.Gly314Val	p.G314V	ENST00000328111	NM_006892.3	314	gGc/gTc	9/23	0.20494114803468	5	FACETS	1	0.964	1	0.723	0.664	0.784	CLONAL	2	TRUE	2	0.20494114803468	5		599	1000	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651359	52651359	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	61	399	0	ENST00000394830.3:c.1737A>C	p.Lys579Asn	p.K579N	ENST00000394830	NM_018313.4	579	aaA/aaC	15/30	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.20494114803468	2		399	558	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542708	187542708	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	70	440	0	ENST00000441802.2:c.5032G>T	p.Glu1678Ter	p.E1678*	ENST00000441802	NM_005245.3	1678	Gaa/Taa	10/27	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.20494114803468	2		440	649	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31486614	31486617	+	frameshift_variant	Frame_Shift_Del	DEL	TCAA	TCAA	-	novel	NA	P-0059477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	37	344	0	ENST00000344624.3:c.1895_1898del	p.Ile632LysfsTer3	p.I632Kfs*3	ENST00000344624		632	aTTGAa/aa	11/33	0.20494114803468	3	FACETS	0.644	0.53	0.773	0.322	0.265	0.387	SUBCLONAL	1	TRUE	1	0.20494114803468	3		344	618	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0059478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	91	323	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.430216801155789	5	FACETS	1	0.938	1	0.71	0.636	0.786	CLONAL	2	TRUE	2	0.430216801155789	5		323	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577595	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0059478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	108	532	0	ENST00000269305.4:c.686_687del	p.Cys229TyrfsTer10	p.C229Yfs*10	ENST00000269305	NM_001126112.2	229	tGT/t	7/11	0.421697614294304	2	FACETS	0.866	0.788	0.945	0.866	0.788	0.945	CLONAL	2	TRUE	0	0.430216801155789	2		532	290	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301888	65301888	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	66	391	0	ENST00000342505.4:c.3151G>C	p.Glu1051Gln	p.E1051Q	ENST00000342505	NM_002227.2	1051	Gaa/Caa	23/25	0.421697614294304	2	FACETS	0.919	0.816	1	0.919	0.816	1	CLONAL	2	TRUE	0	0.430216801155789	2		391	167	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429361	78429361	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1158364154	NA	P-0059478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	172	475	0	ENST00000370768.2:c.1081A>G	p.Arg361Gly	p.R361G	ENST00000370768	NM_003902.3	361	Aga/Gga	13/20	0.407764490431525	4	FACETS	1	0.98	1			1	CLONAL	2	TRUE	NA	0.430216801155789	4		475	494	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741370	17741370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	142	576	0	ENST00000250003.3:c.41C>T	p.Thr14Met	p.T14M	ENST00000250003	NM_002478.4	14	aCg/aTg	1/3	0.430216801155789	6	FACETS	0.942	0.861	1	0.471	0.43	0.513	CLONAL	2	TRUE	2	0.430216801155789	6		576	652	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118361941	118361946	+	inframe_deletion	In_Frame_Del	DEL	ATGATG	ATGATG	-	novel	NA	P-0059478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	137	436	0	ENST00000534358.1:c.4734_4739del	p.Asp1579_Asp1580del	p.D1579_D1580del	ENST00000534358	NM_005933.3	1576	tATGATGat/tat	14/36	0.430216801155789	4	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	2	0.430216801155789	4		436	438	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	430214	430214	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	98	480	0	ENST00000399788.2:c.2488G>T	p.Val830Phe	p.V830F	ENST00000399788	NM_001042603.1	830	Gtc/Ttc	18/28	0.430216801155789	7	FACETS	1	0.979	1	0.287	0.256	0.32	CLONAL	1	TRUE	2	0.430216801155789	7		480	659	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856239	111856239	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	33	598	0	ENST00000341259.2:c.290C>A	p.Pro97Gln	p.P97Q	ENST00000341259	NM_005475.2	97	cCa/cAa	2/8	0.430216801155789	4	FACETS	0.515	0.419	0.623	0.258	0.209	0.312	SUBCLONAL	1	TRUE	2	0.430216801155789	4		598	426	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536676	120536676	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	218	696	0	ENST00000229340.5:c.416C>A	p.Ala139Asp	p.A139D	ENST00000229340	NM_006861.6	139	gCc/gAc	5/6	0.430216801155789	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.430216801155789	4		696	629	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132612	67132612	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0059478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	72	409	0	ENST00000412916.2:c.496-1G>C		p.X166_splice	ENST00000412916		166			0.430216801155789	4	FACETS	1	0.967	1	0.658	0.578	0.742	CLONAL	1	TRUE	2	0.430216801155789	4		409	364	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31025059	31025059	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	158	575	0	ENST00000375687.4:c.4544T>A	p.Met1515Lys	p.M1515K	ENST00000375687	NM_015338.5	1515	aTg/aAg	13/13	0.430216801155789	7	FACETS	0.802	0.735	0.873	0.321	0.294	0.35	CLONAL	2	TRUE	2	0.430216801155789	7		575	950	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505326	186505326	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	90	428	0	ENST00000323963.5:c.952G>A	p.Glu318Lys	p.E318K	ENST00000323963		318	Gaa/Aaa	9/11	0.421697614294304	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.430216801155789	2		428	198	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230840	66230840	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	103	421	0	ENST00000273854.3:c.2131G>A	p.Val711Ile	p.V711I	ENST00000273854	NM_004439.5	711	Gta/Ata	12/18	0.430216801155789	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.430216801155789	4		421	296	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117746720	117746720	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	86	377	0	ENST00000368508.3:c.100C>A	p.Leu34Ile	p.L34I	ENST00000368508	NM_002944.2	34	Cta/Ata	1/43	0.428866921711395	2	FACETS	0.98	0.886	1	0.98	0.886	1	CLONAL	2	TRUE	0	0.430216801155789	2		377	204	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74868220	74868220	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059479-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	57	126	0	ENST00000284811.8:c.74A>T	p.Asp25Val	p.D25V	ENST00000284811		25	gAt/gTt	3/4	0.637821149823023	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.637821149823023	1		126	109	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0059480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	91	329	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.904	0.81	1	0.904	0.81	1	CLONAL	1	TRUE	1	0.583805399719512	2		329	345	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0059480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	167	613	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.583805399719512	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.583805399719512	1		614	383	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106263	27106264	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0059480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	318	750	0	ENST00000324856.7:c.5877_5878dup	p.His1960ProfsTer56	p.H1960Pfs*56	ENST00000324856	NM_006015.4	1958	-/CC	20/20	0.583805399719512	2	FACETS	0.973	0.93	1	0.973	0.93	1	CLONAL	2	TRUE	0	0.583805399719512	2		750	560	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230572	46230572	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	135	552	0	ENST00000334344.6:c.821G>T	p.Arg274Leu	p.R274L	ENST00000334344	NM_152641.2	274	cGa/cTa	8/21	1	2	FACETS	0.916	0.837	0.997	0.916	0.837	0.997	CLONAL	1	TRUE	1	0.583805399719512	2		552	505	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440327	187440327	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	263	585	0	ENST00000232014.4:c.2040G>T	p.Lys680Asn	p.K680N	ENST00000232014	NM_001130845.1	680	aaG/aaT	10/10	0.583805399719512	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.583805399719512	3		585	569	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938514	44938514	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059480-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	117	221	0	ENST00000377967.4:c.3062G>A	p.Trp1021Ter	p.W1021*	ENST00000377967	NM_021140.2	1021	tGg/tAg	20/29	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.583805399719512	1		221	200	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	50	477	0				ENST00000310581	NM_198253.2	-/1132			0.823185929966883	6	FACETS	1	0.938	1	0.298	0.254	0.345	CLONAL	1	TRUE	2	0.823185929966883	6		477	270	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0059481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	341	522	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.823185929966883	4	FACETS	1	0.988	1	1	0.997	1	CLONAL	4	TRUE	2	0.823185929966883	4		522	373	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131895051	131895051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370769989	NA	P-0059481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	99	217	0	ENST00000265335.6:c.205G>A	p.Asp69Asn	p.D69N	ENST00000265335		69	Gat/Aat	2/25	0.820893385017541	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	TRUE	0	0.823185929966883	3		217	110	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731065	162731065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747307320	NA	P-0059481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	83	581	0	ENST00000367921.3:c.920G>A	p.Arg307His	p.R307H	ENST00000367921	NM_006182.2	307	cGc/cAc	9/18	0.823185929966883	6	FACETS	0.999	0.884	1	0.2	0.176	0.225	CLONAL	1	TRUE	1	0.823185929966883	6		581	534	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881513	48881513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	223	408	0	ENST00000267163.4:c.235G>T	p.Glu79Ter	p.E79*	ENST00000267163	NM_000321.2	79	Gag/Tag	2/27	0.823185929966883	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.823185929966883	3		408	241	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858570	9858570	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064797025	NA	P-0059481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	85	635	0	ENST00000330684.3:c.2831C>T	p.Ser944Leu	p.S944L	ENST00000330684	NM_001134407.1	944	tCa/tTa	13/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.823185929966883	2		635	167	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797351	135797351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777484049	NA	P-0059481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	73	520	0	ENST00000298552.3:c.518C>T	p.Ala173Val	p.A173V	ENST00000298552	NM_001162426.1	173	gCg/gTg	7/23	0.822587560818489	4	FACETS	0.948	0.835	1	0.237	0.208	0.267	CLONAL	1	TRUE	0	0.823185929966883	4		520	341	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68758616	68758616	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	119	567	0	ENST00000487270.1:c.772C>G	p.Gln258Glu	p.Q258E	ENST00000487270	NM_133509.3	258	Cag/Gag	8/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.823185929966883	2		567	254	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68758652	68758652	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	121	584	0	ENST00000487270.1:c.808C>T	p.Gln270Ter	p.Q270*	ENST00000487270	NM_133509.3	270	Cag/Tag	8/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.823185929966883	2		584	253	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554240	63554240	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	81	643	0	ENST00000307078.5:c.499G>T	p.Asp167Tyr	p.D167Y	ENST00000307078	NM_004655.3	167	Gat/Tat	2/11	0.823185929966883	5	FACETS	0.794	0.701	0.893	0.265	0.233	0.298	SUBCLONAL	1	TRUE	2	0.823185929966883	5		643	554	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285243	212285243	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	68	492	0	ENST00000342788.4:c.3058G>C	p.Glu1020Gln	p.E1020Q	ENST00000342788	NM_005235.2	1020	Gag/Cag	25/28	0.823185929966883	3	FACETS	0.997	0.879	1	0.498	0.439	0.56	CLONAL	1	TRUE	1	0.823185929966883	3		492	234	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713612	30713612	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55751315	NA	P-0059481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	93	634	3	ENST00000295754.5:c.937C>T	p.Arg313Trp	p.R313W	ENST00000295754	NM_003242.5	313	Cgg/Tgg	4/7	0.823185929966883	4	FACETS	1	0.955	1	0.56	0.502	0.621	CLONAL	1	TRUE	2	0.823185929966883	4		637	368	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220488	123220488	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	43	487	0	ENST00000218089.9:c.3145C>A	p.Leu1049Ile	p.L1049I	ENST00000218089	NM_001042749.1	1049	Cta/Ata	30/35	0.823185929966883	3	FACETS	0.641	0.541	0.75	0.321	0.27	0.375	SUBCLONAL	1	TRUE	1	0.823185929966883	3		487	230	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059481-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	139	477	0				ENST00000310581	NM_198253.2	-/1132			0.611922412829792	6	FACETS	0.941	0.861	1	0.47	0.43	0.512	CLONAL	2	TRUE	2	0.611922412829792	6		477	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0059481-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	626	522	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.61964926458372	4	FACETS	1	0.996	1	1	0.998	1	CLONAL	4	TRUE	2	0.611922412829792	4		522	756	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131895051	131895051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370769989	NA	P-0059481-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	103	217	0	ENST00000265335.6:c.205G>A	p.Asp69Asn	p.D69N	ENST00000265335		69	Gat/Aat	2/25	0.61964926458372	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	0	0.611922412829792	2		217	168	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731065	162731065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747307320	NA	P-0059481-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	147	581	0	ENST00000367921.3:c.920G>A	p.Arg307His	p.R307H	ENST00000367921	NM_006182.2	307	cGc/cAc	9/18	0.611922412829792	6	FACETS	1	0.965	1	0.222	0.202	0.243	CLONAL	1	TRUE	1	0.611922412829792	6		581	963	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881513	48881513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059481-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	191	408	0	ENST00000267163.4:c.235G>T	p.Glu79Ter	p.E79*	ENST00000267163	NM_000321.2	79	Gag/Tag	2/27	0.618121326482706	2	FACETS	0.997	0.943	1	0.997	0.943	1	CLONAL	2	TRUE	0	0.611922412829792	2		408	313	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858570	9858570	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064797025	NA	P-0059481-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	160	635	0	ENST00000330684.3:c.2831C>T	p.Ser944Leu	p.S944L	ENST00000330684	NM_001134407.1	944	tCa/tTa	13/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.611922412829792	2		635	456	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797351	135797351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777484049	NA	P-0059481-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	134	520	0	ENST00000298552.3:c.518C>T	p.Ala173Val	p.A173V	ENST00000298552	NM_001162426.1	173	gCg/gTg	7/23	0.61964926458372	3	FACETS	0.898	0.818	0.981	0.299	0.272	0.327	CLONAL	1	TRUE	0	0.611922412829792	3		520	637	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68758616	68758616	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059481-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	153	567	0	ENST00000487270.1:c.772C>G	p.Gln258Glu	p.Q258E	ENST00000487270	NM_133509.3	258	Cag/Gag	8/11	1	2	FACETS	0.996	0.918	1	0.996	0.918	1	CLONAL	1	TRUE	1	0.611922412829792	2		567	502	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68758652	68758652	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059481-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	171	584	0	ENST00000487270.1:c.808C>T	p.Gln270Ter	p.Q270*	ENST00000487270	NM_133509.3	270	Cag/Tag	8/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.611922412829792	2		584	534	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554240	63554240	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059481-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	158	643	0	ENST00000307078.5:c.499G>T	p.Asp167Tyr	p.D167Y	ENST00000307078	NM_004655.3	167	Gat/Tat	2/11	0.611922412829792	6	FACETS	0.987	0.902	1	0.247	0.225	0.269	CLONAL	1	TRUE	2	0.611922412829792	6		643	1164	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285243	212285243	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059481-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	68	492	0	ENST00000342788.4:c.3058G>C	p.Glu1020Gln	p.E1020Q	ENST00000342788	NM_005235.2	1020	Gag/Cag	25/28	0.365066194889833	3	FACETS	0.574	0.5	0.653	0.191	0.166	0.218	INDETERMINATE	1	TRUE	0	0.611922412829792	3		492	506	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713612	30713612	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55751315	NA	P-0059481-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	143	634	3	ENST00000295754.5:c.937C>T	p.Arg313Trp	p.R313W	ENST00000295754	NM_003242.5	313	Cgg/Tgg	4/7	0.61964926458372	4	FACETS	0.999	0.912	1	0.5	0.456	0.545	CLONAL	1	TRUE	2	0.611922412829792	4		637	754	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220488	123220488	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059481-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	91	487	0	ENST00000218089.9:c.3145C>A	p.Leu1049Ile	p.L1049I	ENST00000218089	NM_001042749.1	1049	Cta/Ata	30/35	0.61964926458372	3	FACETS	0.673	0.599	0.752	0.337	0.299	0.376	SUBCLONAL	1	TRUE	1	0.611922412829792	3		487	577	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0059483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	89	788	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.965	0.857	1	0.965	0.857	1	CLONAL	1	TRUE	1	0.31	2		788	595	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692920	89692921	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs398123323	NA	P-0059483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	36	570	0	ENST00000371953.3:c.405dup	p.Cys136MetfsTer44	p.C136Mfs*44	ENST00000371953	NM_000314.4	135	ata/atAa	5/9	1	2	FACETS	0.767	0.632	0.916	0.767	0.632	0.916	CLONAL	1	TRUE	1	0.31	2		570	303	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690811	89690811	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	41	267	0	ENST00000371953.3:c.220del	p.Arg74AspfsTer25	p.R74Dfs*25	ENST00000371953	NM_000314.4	73	gAa/ga	4/9	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.31	2		267	231	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928072	178928107	+	inframe_deletion	In_Frame_Del	DEL	TGGATTAGAAGATTTGCTGAACCCTATTGGTGTTAC	TGGATTAGAAGATTTGCTGAACCCTATTGGTGTTAC	-	novel	NA	P-0059483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	46	442	0	ENST00000263967.3:c.1355_1390del	p.Leu452_Gly463del	p.L452_G463del	ENST00000263967	NM_006218.2	450	caTGGATTAGAAGATTTGCTGAACCCTATTGGTGTTACt/cat	8/21	1	2	FACETS	0.951	0.805	1	0.951	0.805	1	CLONAL	1	TRUE	1	0.31	2		442	312	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106144	27106145	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTAGCACCTTGACCGAGGATGGA	novel	NA	P-0059483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	69	822	0	ENST00000324856.7:c.5756_5778dup	p.Ala1927LeufsTer4	p.A1927Lfs*4	ENST00000324856	NM_006015.4	1919	tct/tCTAGCACCTTGACCGAGGATGGAct	20/20	1	2	FACETS	0.752	0.655	0.856	0.752	0.655	0.856	SUBCLONAL	1	TRUE	1	0.31	2		822	592	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339222	70339222	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0059483-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	58	473	0	ENST00000374080.3:c.100del		p.X34_splice	ENST00000374080		34			1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.31	2		473	343	SUCCESS
MET	4233	MSKCC	GRCh37	7	116417463	116417463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913244	NA	P-0059484-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	95	422	0	ENST00000397752.3:c.3280C>T	p.His1094Tyr	p.H1094Y	ENST00000397752	NM_000245.2	1094	Cat/Tat	16/21	0.458280202629165	3	FACETS	0.878	0.794	0.964	0.878	0.794	0.964	CLONAL	2	TRUE	1	0.518116763998731	3		422	263	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0059491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	46	525	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.23129959367831	2		525	300	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0059491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	50	546	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.891	0.757	1	0.891	0.757	1	CLONAL	1	TRUE	1	0.23129959367831	2		546	485	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565530	41565530	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	43	281	0	ENST00000263253.7:c.4196A>G	p.Asp1399Gly	p.D1399G	ENST00000263253	NM_001429.3	1399	gAt/gGt	26/31	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.23129959367831	2		281	285	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088734	27088735	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0059491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	53	651	0	ENST00000324856.7:c.2348_2349del	p.Thr783ArgfsTer33	p.T783Rfs*33	ENST00000324856	NM_006015.4	781	atACac/atac	7/20	1	2	FACETS	0.866	0.739	1	0.866	0.739	1	CLONAL	1	TRUE	1	0.23129959367831	2		651	529	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711983	89711983	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554900638	NA	P-0059491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	65	288	0	ENST00000371953.3:c.601G>T	p.Glu201Ter	p.E201*	ENST00000371953	NM_000314.4	201	Gaa/Taa	6/9	0.23129959367831	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	0	0.23129959367831	2		288	260	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595920	52595920	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	60	700	0	ENST00000394830.3:c.3995G>T	p.Ser1332Ile	p.S1332I	ENST00000394830	NM_018313.4	1332	aGt/aTt	26/30	1	2	FACETS	0.99	0.854	1	0.99	0.854	1	CLONAL	1	TRUE	1	0.23129959367831	2		700	524	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197369	26197369	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	72	1000	0	ENST00000356476.2:c.110A>T	p.Lys37Met	p.K37M	ENST00000356476		37	aAg/aTg	1/1	1	2	FACETS	0.902	0.788	1	0.902	0.788	1	CLONAL	1	TRUE	1	0.23129959367831	2		1000	690	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0059492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	127	323	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.412292610783565	2	FACETS	0.917	0.842	0.994	0.917	0.842	0.994	CLONAL	2	TRUE	0	0.417108350435813	2		323	332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0059492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	247	593	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.412292610783565	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.417108350435813	2		593	530	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492817	56492817	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	218	583	0	ENST00000407977.2:c.122del	p.Ser41Ter	p.S41*	ENST00000407977		41	tCa/ta	2/10	0.412292610783565	2	FACETS	0.959	0.9	1	0.959	0.9	1	CLONAL	2	TRUE	0	0.417108350435813	2		583	545	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0059493-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	133	355	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.376031224978911	6	FACETS	0.939	0.865	1	0.704	0.649	0.76	INDETERMINATE	3	TRUE	2	0.704417938152121	6		355	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577095	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519984	NA	P-0059493-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	133	653	0	ENST00000269305.4:c.843C>A	p.Asp281Glu	p.D281E	ENST00000269305	NM_001126112.2	281	gaC/gaA	8/11	0.58469039175793	2	FACETS	0.87	0.814	0.925	0.87	0.814	0.925	CLONAL	2	TRUE	0	0.704417938152121	2		653	217	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129616	47129616	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059493-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	99	401	0	ENST00000409792.3:c.5264T>G	p.Leu1755Arg	p.L1755R	ENST00000409792	NM_014159.6	1755	cTg/cGg	10/21	0.476130792066649	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.704417938152121	4		401	220	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47088112	47088112	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0059493-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	70	348	0	ENST00000409792.3:c.6964-1G>C		p.X2322_splice	ENST00000409792	NM_014159.6	2322			0.476130792066649	4	FACETS	0.76	0.672	0.85	0.76	0.672	0.85	SUBCLONAL	2	TRUE	2	0.704417938152121	4		348	223	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559864	29559864	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs371544233	NA	P-0059493-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	114	495	0	ENST00000356175.3:c.3461A>T	p.Asn1154Ile	p.N1154I	ENST00000356175	NM_000267.3	1154	aAt/aTt	26/57	0.527446173142372	4	FACETS	0.913	0.834	0.994	0.913	0.834	0.994	CLONAL	2	TRUE	2	0.704417938152121	4		495	302	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665721	29665721	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs1060500266	NA	P-0059493-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	80	333	0	ENST00000356175.3:c.6757-1G>C		p.X2253_splice	ENST00000356175	NM_000267.3	2253			0.527446173142372	4	FACETS	1	0.907	1	1	0.907	1	CLONAL	2	TRUE	2	0.704417938152121	4		333	192	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593583	55593595	+	protein_altering_variant,splice_region_variant	In_Frame_Del	DEL	AACCCATGTATGA	AACCCATGTATGA	T	novel	NA	P-0059495-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	93	525	0	ENST00000288135.5:c.1649_1661delinsT	p.Lys550_Glu554delinsIle	p.K550_E554delinsI	ENST00000288135	NM_000222.2	550	aAACCCATGTATGAa/aTa	11/21	1	2	FACETS	0.708	0.638	0.781	0.708	0.638	0.781	SUBCLONAL	1	TRUE	1	0.927844281493547	2		525	283	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011207	12011207	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059495-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	56	378	0	ENST00000353533.5:c.614T>C	p.Leu205Ser	p.L205S	ENST00000353533	NM_003010.3	205	tTa/tCa	5/11	0.89826775458318	1	FACETS	0.789	0.717	0.857	0.789	0.717	0.857	SUBCLONAL	1	TRUE	0	0.927844281493547	1		378	82	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463210	25463217	+	frameshift_variant	Frame_Shift_Del	DEL	CATGGCCA	CATGGCCA	-	novel	NA	P-0059495-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	111	786	0	ENST00000264709.3:c.2276_2283del	p.Val759GlyfsTer3	p.V759Gfs*3	ENST00000264709	NM_175629.2	759	gTGGCCATG/g	19/23	0.370076351487121	1	FACETS	0.58	0.534	0.627	0.58	0.534	0.627	INDETERMINATE	1	TRUE	0	0.927844281493547	1		786	221	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970865	79970865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059496-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	113	352	0	ENST00000265081.6:c.1091C>T	p.Ser364Phe	p.S364F	ENST00000265081	NM_002439.4	364	tCt/tTt	7/24	0.460329920111229	4	FACETS	1	0.911	1	0.668	0.607	0.73	CLONAL	2	TRUE	1	0.465896570084991	4		352	355	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0059497-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	290	563	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		563	431	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0059497-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	65	460	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		460	354	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506191	103506191	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs760467381	NA	P-0059497-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	21	406	0	ENST00000355739.4:c.349C>G	p.Gln117Glu	p.Q117E	ENST00000355739	NM_000123.3	117	Caa/Gaa	3/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		406	371	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0059498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	75	536	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.249984116310214	2		536	549	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0059498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	97	585	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.249984116310214	2		585	712	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0059498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	136	415	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	0.249984116310214	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.249984116310214	2		415	488	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100198	27100198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	129	908	1	ENST00000324856.7:c.3994C>T	p.Gln1332Ter	p.Q1332*	ENST00000324856	NM_006015.4	1332	Cag/Tag	16/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.249984116310214	2		909	877	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176329	24176329	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1568963596	NA	P-0059498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	55	466	0	ENST00000263121.7:c.1120C>T	p.Arg374Trp	p.R374W	ENST00000263121	NM_003073.3	374	Cgg/Tgg	9/9	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.249984116310214	2		466	379	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845615	63845618	+	frameshift_variant	Frame_Shift_Del	DEL	AAGA	AAGA	-	novel	NA	P-0059498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	109	584	0	ENST00000279873.7:c.1360_1363del	p.Glu454LysfsTer24	p.E454Kfs*24	ENST00000279873	NM_032199.2	452	AAGAaa/aa	9/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.249984116310214	2		584	772	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0059499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	164	613	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.321979170567428	2	FACETS	0.853	0.793	0.914	1	0.987	1	CLONAL	3	TRUE	0	0.321979170567428	2		614	398	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630855	187630855	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560660262	NA	P-0059499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	35	655	1	ENST00000441802.2:c.127G>A	p.Val43Met	p.V43M	ENST00000441802	NM_005245.3	43	Gtg/Atg	2/27	0.321979170567428	5	FACETS	0.562	0.459	0.677	0.187	0.153	0.226	SUBCLONAL	1	TRUE	2	0.321979170567428	5		656	574	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349643	70349643	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	41	842	0	ENST00000374080.3:c.3805T>A	p.Ser1269Thr	p.S1269T	ENST00000374080		1269	Tct/Act	27/45	1	2	FACETS	0.612	0.51	0.725	0.612	0.51	0.725	SUBCLONAL	1	TRUE	1	0.321979170567428	2		842	416	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176719126	176719126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761103348	NA	P-0059499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	33	669	0	ENST00000439151.2:c.6430G>A	p.Ala2144Thr	p.A2144T	ENST00000439151	NM_022455.4	2144	Gca/Aca	22/23	0.308707107063902	2	FACETS	0.582	0.475	0.703	0.291	0.237	0.352	SUBCLONAL	1	TRUE	0	0.321979170567428	2		669	352	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522109	157522109	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554235709	NA	P-0059499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	77	837	0	ENST00000346085.5:c.4381C>T	p.Gln1461Ter	p.Q1461*	ENST00000346085	NM_020732.3	1461	Cag/Tag	18/20	0.267450675831821	4	FACETS	1	0.965	1	0.425	0.374	0.48	CLONAL	1	TRUE	1	0.321979170567428	4		837	496	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47598971	47598973	+	missense_variant	Missense_Mutation	TNP	ATA	ATA	CTT	novel	NA	P-0059499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	34	710	0	ENST00000430070.2:c.627_629delinsAAG	p.Asp209_Ile210delinsGluSer	p.D209_I210delinsES	ENST00000430070	NM_018095.4	209	gaTATc/gaAAGc	2/4	0.321979170567428	3	FACETS	0.538	0.439	0.649	0.269	0.219	0.325	SUBCLONAL	1	TRUE	1	0.321979170567428	3		710	456	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	89	121	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.214000526961786	4	FACETS	0.977	0.872	1	0.977	0.872	1	CLONAL	2	TRUE	2	0.282805542415049	4		121	413	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220444	1220444	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131690939	NA	P-0059502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	144	751	0	ENST00000326873.7:c.540del	p.Asn181ThrfsTer106	p.N181Tfs*106	ENST00000326873	NM_000455.4	179	ccG/cc	4/10	0.282805542415049	2	FACETS	0.952	0.873	1	0.952	0.873	1	CLONAL	2	TRUE	0	0.282805542415049	2		751	535	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236085	108236085	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	160	639	0	ENST00000278616.4:c.9021A>T	p.Glu3007Asp	p.E3007D	ENST00000278616	NM_000051.3	3007	gaA/gaT	63/63	0.214000526961786	4	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	2	0.282805542415049	4		639	694	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1962781	1962781	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	134	587	0	ENST00000382891.5:c.3275A>G	p.Tyr1092Cys	p.Y1092C	ENST00000382891	NM_133335.3	1092	tAc/tGc	18/22	0.214000526961786	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	2	0.282805542415049	4		587	556	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172517	108172517	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs876660175	NA	P-0059502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	67	348	0	ENST00000278616.4:c.5319+1G>T		p.X1773_splice	ENST00000278616	NM_000051.3	1773			0.214000526961786	4	FACETS	1	0.971	1	0.725	0.633	0.825	CLONAL	1	TRUE	2	0.282805542415049	4		348	419	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031919	10031920	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0059502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	121	658	2	ENST00000330684.3:c.903_904delinsTT	p.Ala302Ser	p.A302S	ENST00000330684	NM_001134407.1	301	acCGct/acTTct	3/13	0.214000526961786	4	FACETS	0.951	0.862	1	0.951	0.862	1	CLONAL	2	TRUE	2	0.282805542415049	4		660	577	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839802	27839802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059502-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	100	918	0	ENST00000328488.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000328488	NM_003533.2	98	Gag/Aag	1/1	0.141482871336217	4	FACETS	1	0.969	1	0.615	0.549	0.684	INDETERMINATE	1	TRUE	2	0.282805542415049	4		918	738	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0059505-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	578	697	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.683784016865786	4	FACETS	0.951	0.92	0.981			1	CLONAL	3	TRUE	NA	0.683784016865786	4		697	998	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164543	36164543	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059505-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	168	868	0	ENST00000300305.3:c.1332del	p.Ser445AlafsTer149	p.S445Afs*149	ENST00000300305		444	ccC/cc	8/8	1	2	FACETS	0.83	0.767	0.895	0.83	0.767	0.895	CLONAL	1	TRUE	1	0.683784016865786	2		868	592	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862208	68862208	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0059505-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	184	636	0	ENST00000261769.5:c.2295+1G>T		p.X765_splice	ENST00000261769	NM_004360.3	765			0.683784016865786	1	FACETS	0.955	0.895	1	0.955	0.895	1	CLONAL	1	TRUE	0	0.683784016865786	1		636	371	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	53	477	0				ENST00000310581	NM_198253.2	-/1132			0.133467988428341	3	FACETS	0.925	0.81	1	0.617	0.54	0.697	INDETERMINATE	2	TRUE	0	0.523721870983721	3		477	138	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0059506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	92	522	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.402891842785259	4	FACETS	0.797	0.715	0.882			1	SUBCLONAL	2	TRUE	NA	0.523721870983721	4		522	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0059506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	143	863	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.402891842785259	4	FACETS	1	0.933	1			1	CLONAL	2	TRUE	NA	0.523721870983721	4		863	410	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294665	1294665	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	41	691	3	ENST00000310581.5:c.336del	p.Glu113ArgfsTer15	p.E113Rfs*15	ENST00000310581	NM_198253.2	112	ccC/cc	2/16	0.133467988428341	3	FACETS	1	0.905	1	0.368	0.31	0.43	INDETERMINATE	1	TRUE	0	0.523721870983721	3		694	179	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917510	178917510	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	89	306	0	ENST00000263967.3:c.385G>C	p.Asp129His	p.D129H	ENST00000263967	NM_006218.2	129	Gat/Cat	3/21	0.31995082972815	4	FACETS	0.812	0.727	0.9	0.812	0.727	0.9	CLONAL	2	TRUE	2	0.523721870983721	4		306	319	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002870	69002870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867044170	NA	P-0059506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	82	446	0	ENST00000288368.4:c.2170G>A	p.Gly724Arg	p.G724R	ENST00000288368	NM_024870.2	724	Gga/Aga	20/40	0.133467988428341	3	FACETS	0.769	0.687	0.853	0.513	0.458	0.569	INDETERMINATE	2	TRUE	0	0.523721870983721	3		446	257	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023783	27023783	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	136	803	0	ENST00000324856.7:c.889C>T	p.Gln297Ter	p.Q297*	ENST00000324856	NM_006015.4	297	Caa/Taa	1/20	0.523721870983721	3	FACETS	0.926	0.864	0.986	0.926	0.864	0.986	CLONAL	3	TRUE	0	0.523721870983721	3		803	236	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082957	16082957	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	32	506	0	ENST00000281043.3:c.772del	p.Asp258ThrfsTer3	p.D258Tfs*3	ENST00000281043	NM_005378.4	257	gaG/ga	2/3	0.523721870983721	3	FACETS	0.573	0.467	0.692	0.287	0.233	0.346	SUBCLONAL	1	TRUE	1	0.523721870983721	3		506	269	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741464	39741464	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	123	592	0	ENST00000361337.2:c.1351A>C	p.Lys451Gln	p.K451Q	ENST00000361337	NM_003286.2	451	Aaa/Caa	14/21	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.523721870983721	2		592	374	SUCCESS
APC	324	MSKCC	GRCh37	5	112174893	112174893	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs730881247	NA	P-0059506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	119	442	0	ENST00000257430.4:c.3602C>G	p.Ser1201Ter	p.S1201*	ENST00000257430	NM_000038.5	1201	tCa/tGa	16/16	0.448393996765673	2	FACETS	1	0.986	1	0.724	0.662	0.786	CLONAL	1	TRUE	0	0.523721870983721	2		442	314	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380138	116380138	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059507-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	31	487	0	ENST00000397752.3:c.1527G>C	p.Lys509Asn	p.K509N	ENST00000397752	NM_000245.2	509	aaG/aaC	4/21	1	2	FACETS	0.24	0.193	0.292	0.24	0.193	0.292	SUBCLONAL	1	TRUE	1	0.542060054133888	2		487	477	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0059508-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	91	525	0				ENST00000310581	NM_198253.2	-/1132			0.211258527887597	0	FACETS	0.809	0.737	0.882			1	CLONAL	4	FALSE	0	0.229251961039866	0		525	189	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106000	27106001	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0059508-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	67	692	0	ENST00000324856.7:c.5612dup	p.His1871GlnfsTer30	p.H1871Qfs*30	ENST00000324856	NM_006015.4	1871	cac/cAac	20/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.229251961039866	2		692	464	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164760	47164760	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059508-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	65	544	0	ENST00000409792.3:c.1366C>T	p.Arg456Ter	p.R456*	ENST00000409792	NM_014159.6	456	Cga/Tga	3/21	1	2	FACETS	0.808	0.704	0.918	1	0.975	1	CLONAL	2	FALSE	1	0.229251961039866	2		544	351	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254677	16254677	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059508-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	24	538	1	ENST00000375759.3:c.1942C>T	p.Arg648Trp	p.R648W	ENST00000375759	NM_015001.2	648	Cgg/Tgg	11/15	1	2	FACETS	0.58	0.454	0.725	0.58	0.454	0.725	SUBCLONAL	1	FALSE	1	0.229251961039866	2		539	361	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023203	33023203	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059508-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	155	674	0	ENST00000300177.4:c.312C>A	p.His104Gln	p.H104Q	ENST00000300177	NM_001191322.1	104	caC/caA	2/2	0.161608409537024	1	FACETS	0.905	0.836	0.975	1	0.993	1	CLONAL	3	FALSE	0	0.229251961039866	1		674	441	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870786	12870786	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059508-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	106	507	0	ENST00000228872.4:c.13del	p.Arg5GlufsTer37	p.R5Efs*37	ENST00000228872	NM_004064.3	5	Cga/ga	1/3	1	2	FACETS	0.876	0.788	0.968	1	0.986	1	CLONAL	2	FALSE	1	0.229251961039866	2		507	528	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572334	41572334	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059508-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	60	625	0	ENST00000263253.7:c.4863C>A	p.Cys1621Ter	p.C1621*	ENST00000263253	NM_001429.3	1621	tgC/tgA	30/31	0.161608409537024	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	0	0.229251961039866	1		625	368	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913233	NA	P-0059509-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	897	654	0	ENST00000451590.1:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000451590	NM_001130442.1	61	cAg/cTg	3/5	0.717063792575908	6	FACETS	1	0.987	1			1	CLONAL	4	TRUE	NA	0.82961420127449	6		654	1413	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624297	89624297	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059509-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	9	370	0	ENST00000371953.3:c.71A>T	p.Asp24Val	p.D24V	ENST00000371953	NM_000314.4	24	gAc/gTc	1/9	0.822073985174623	2	FACETS	0.059	0.038	0.085	0.029	0.019	0.043	SUBCLONAL	1	TRUE	0	0.82961420127449	2		370	370	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268224	153268224	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0059509-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	108	331	0	ENST00000281708.4:c.585-1G>A		p.X195_splice	ENST00000281708	NM_033632.3	195			0.822073985174623	2	FACETS	0.553	0.499	0.61	0.276	0.249	0.305	SUBCLONAL	1	TRUE	0	0.82961420127449	2		331	471	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526079	66526079	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059509-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	101	540	0	ENST00000358598.2:c.910C>T	p.Gln304Ter	p.Q304*	ENST00000358598	NM_212471.2	304	Caa/Taa	10/11	0.822073985174623	2	FACETS	0.413	0.37	0.459	0.207	0.185	0.23	SUBCLONAL	1	TRUE	0	0.82961420127449	2		540	589	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150936218	150936218	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs111660370	NA	P-0059509-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	448	585	0	ENST00000271640.5:c.3669+1G>A		p.X1223_splice	ENST00000271640	NM_001145415.1	1223			0.822073985174623	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.82961420127449	2		585	532	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933632	39933633	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0059509-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	488	694	0	ENST00000378444.4:c.966dup	p.Ser323GlnfsTer58	p.S323Qfs*58	ENST00000378444	NM_001123385.1	322	-/C	4/15	0.822073985174623	2	FACETS	0.931	0.906	0.954	0.931	0.906	0.954	CLONAL	2	TRUE	0	0.82961420127449	2		694	632	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059510-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	79	477	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.827	0.737	0.92	0.827	0.737	0.92	CLONAL	1	TRUE	1	0.755488658314599	2		477	253	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720803	89720804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs786204892	NA	P-0059510-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	32	174	0	ENST00000371953.3:c.955dup	p.Thr319AsnfsTer6	p.T319Nfs*6	ENST00000371953	NM_000314.4	318	-/A	8/9	0.755488658314599	1	FACETS	0.787	0.669	0.906	0.787	0.669	0.906	CLONAL	1	TRUE	0	0.755488658314599	1		174	67	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293719	1293719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1400139919	NA	P-0059510-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	78	788	0	ENST00000310581.5:c.1282C>T	p.Arg428Trp	p.R428W	ENST00000310581	NM_198253.2	428	Cgg/Tgg	2/16	1	2	FACETS	0.411	0.362	0.464	0.411	0.362	0.464	SUBCLONAL	1	TRUE	1	0.755488658314599	2		788	502	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818312	43818312	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0059510-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	288	748	0	ENST00000372470.3:c.1777A>T	p.Arg593Ter	p.R593*	ENST00000372470	NM_005373.2	593	Aga/Tga	12/12	0.38561139205134	3	FACETS	0.886	0.841	0.93	0.886	0.841	0.93	INDETERMINATE	2	TRUE	1	0.755488658314599	3		748	593	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81914522	81914522	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059510-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	142	418	0	ENST00000359376.3:c.656A>G	p.Asp219Gly	p.D219G	ENST00000359376	NM_002661.3	219	gAt/gGt	8/33	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.755488658314599	2		418	339	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946759	17946759	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059510-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	156	600	1	ENST00000458235.1:c.1888C>G	p.Gln630Glu	p.Q630E	ENST00000458235	NM_000215.3	630	Cag/Gag	14/24	0.3805843225143	3	FACETS	1	0.967	1	0.364	0.335	0.394	INDETERMINATE	1	TRUE	0	0.755488658314599	3		601	521	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961017	18961017	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059510-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	145	598	0	ENST00000262803.5:c.595G>T	p.Ala199Ser	p.A199S	ENST00000262803	NM_002911.3	199	Gcc/Tcc	4/24	0.3805843225143	3	FACETS	0.926	0.849	1	0.309	0.283	0.336	INDETERMINATE	1	TRUE	0	0.755488658314599	3		598	571	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976483	18976483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059510-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	78	730	0	ENST00000262803.5:c.3133G>A	p.Ala1045Thr	p.A1045T	ENST00000262803	NM_002911.3	1045	Gcg/Acg	22/24	0.3805843225143	3	FACETS	0.538	0.473	0.607	0.179	0.157	0.203	INDETERMINATE	1	TRUE	0	0.755488658314599	3		730	529	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439175	52439175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1192490528	NA	P-0059510-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	194	656	0	ENST00000460680.1:c.1067G>A	p.Arg356Gln	p.R356Q	ENST00000460680	NM_004656.3	356	cGg/cAg	11/17	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.755488658314599	2		656	490	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004264	150004264	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059510-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	79	409	0	ENST00000253339.5:c.1961A>T	p.His654Leu	p.H654L	ENST00000253339		654	cAt/cTt	3/7	1	2	FACETS	0.497	0.439	0.558	0.497	0.439	0.558	SUBCLONAL	1	TRUE	1	0.755488658314599	2		409	421	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426672	47426672	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059510-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	98	737	0	ENST00000377045.4:c.917C>A	p.Pro306Gln	p.P306Q	ENST00000377045	NM_001654.4	306	cCa/cAa	10/16	1	2	FACETS	0.49	0.439	0.545	0.49	0.439	0.545	SUBCLONAL	1	TRUE	1	0.755488658314599	2		737	529	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0059511-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	40	329	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.73	0.606	0.867	0.73	0.606	0.867	SUBCLONAL	1	TRUE	1	0.228357816738721	2		329	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0059511-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	128	698	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.228357816738721	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.228357816738721	1		698	893	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0059526-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	485	306	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.698125539621402	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.698125539621402	2		307	664	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584513	48584514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs377767334	NA	P-0059526-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	204	491	1	ENST00000342988.3:c.692dup	p.Ser232GlnfsTer3	p.S232Qfs*3	ENST00000342988	NM_005359.5	229	ctg/ctGg	6/12	0.6923204063057	1	FACETS	0.923	0.869	0.978	0.923	0.869	0.978	CLONAL	1	TRUE	0	0.698125539621402	1		492	412	SUCCESS
APC	324	MSKCC	GRCh37	5	112102972	112102973	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0059526-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	207	480	0	ENST00000257430.4:c.308dup	p.Ser104IlefsTer35	p.S104Ifs*35	ENST00000257430	NM_000038.5	103	gta/gTta	4/16	0.6923204063057	1	FACETS	0.97	0.914	1	0.97	0.914	1	CLONAL	1	TRUE	0	0.698125539621402	1		480	398	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242442	55242443	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTAAAATTCCCGTCGCTA	novel	NA	P-0059526-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	340	392	0	ENST00000275493.2:c.2214_2231dup	p.Ile740_Lys745dup	p.I740_K745dup	ENST00000275493	NM_005228.3	740	gtt/gTTAAAATTCCCGTCGCTAtt	19/28	0.698125539621402	4	FACETS	0.947	0.9	0.995	0.632	0.6	0.664	CLONAL	2	TRUE	1	0.698125539621402	4		392	873	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63531746	63531746	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059526-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	74	447	0	ENST00000307078.5:c.2235A>C	p.Glu745Asp	p.E745D	ENST00000307078	NM_004655.3	745	gaA/gaC	9/11	0.681090601431584	4	FACETS	0.408	0.356	0.464	0.204	0.178	0.232	SUBCLONAL	1	TRUE	2	0.698125539621402	4		447	883	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213917	66213917	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059526-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	162	343	0	ENST00000273854.3:c.2513G>T	p.Gly838Val	p.G838V	ENST00000273854	NM_004439.5	838	gGa/gTa	15/18	0.672824514238723	3	FACETS	0.901	0.829	0.976			1	CLONAL	1	TRUE	NA	0.698125539621402	3		343	695	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149511557	149511557	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1462400450	NA	P-0059526-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	208	553	0	ENST00000261799.4:c.1228C>T	p.Gln410Ter	p.Q410*	ENST00000261799	NM_002609.3	410	Cag/Tag	8/23	0.698125539621402	2	FACETS	0.983	0.918	1	0.492	0.459	0.525	CLONAL	1	TRUE	0	0.698125539621402	2		553	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882019	NA	P-0059533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	314	530	0	ENST00000269305.4:c.455dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	ccg/ccCg	5/11	0.673261112019795	2	FACETS	0.976	0.937	1	0.976	0.937	1	CLONAL	2	TRUE	0	0.673261112019795	2		530	478	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0059533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	253	293	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.673261112019795	5	FACETS	0.993	0.941	1	0.993	0.941	1	CLONAL	3	TRUE	2	0.673261112019795	5		293	507	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375486	15375486	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	185	505	0	ENST00000263377.2:c.941A>G	p.Lys314Arg	p.K314R	ENST00000263377	NM_058243.2	314	aAg/aGg	6/20	0.64030923093827	3	FACETS	1	0.981	1	0.586	0.543	0.629	CLONAL	1	TRUE	1	0.673261112019795	3		505	627	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792812	33792812	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	187	281	0	ENST00000498907.2:c.509C>G	p.Ala170Gly	p.A170G	ENST00000498907	NM_004364.3	170	gCc/gGc	1/1	0.503341130197975	6	FACETS	1	0.977	1	0.744	0.691	0.798	CLONAL	2	TRUE	3	0.673261112019795	6		281	584	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032109	26032109	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	188	624	0	ENST00000244661.2:c.180G>C	p.Glu60Asp	p.E60D	ENST00000244661	NM_003537.3	60	gaG/gaC	1/1	0.597420141819161	4	FACETS	0.934	0.863	1	0.467	0.431	0.505	CLONAL	1	TRUE	2	0.673261112019795	4		624	1000	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240698	55240698	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	448	525	0	ENST00000275493.2:c.1942A>T	p.Thr648Ser	p.T648S	ENST00000275493	NM_005228.3	648	Act/Tct	17/28	0.673261112019795	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.673261112019795	3		525	574	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781245	135781246	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CTGGCATTCCCTGTCTCCCGCAGGGCTTTCATCAGCA	novel	NA	P-0059533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	157	553	0	ENST00000298552.3:c.1683_1719dup	p.Thr574CysfsTer2	p.T574Cfs*2	ENST00000298552	NM_001162426.1	573	-/TGCTGATGAAAGCCCTGCGGGAGACAGGGAATGCCAG	15/23	0.497797733278094	4	FACETS	0.972	0.891	1	0.486	0.445	0.528	CLONAL	1	TRUE	2	0.673261112019795	4		553	803	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754638	57754638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059535-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	72	247	0	ENST00000274289.3:c.409C>T	p.Leu137Phe	p.L137F	ENST00000274289	NM_006622.3	137	Ctt/Ttt	3/14	0.483956477788493	2	FACETS	1	0.908	1	0.517	0.456	0.581	CLONAL	1	TRUE	0	0.483956477788493	2		247	288	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059535-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	145	121	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.483956477788493	6	FACETS	1	0.976	1	0.78	0.716	0.846	CLONAL	2	TRUE	3	0.483956477788493	6		121	504	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111747	56111747	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059535-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	90	397	0	ENST00000399503.3:c.347C>A	p.Ala116Asp	p.A116D	ENST00000399503	NM_005921.1	116	gCc/gAc	1/20	0.483956477788493	2	FACETS	1	0.947	1	0.547	0.49	0.607	CLONAL	1	TRUE	0	0.483956477788493	2		397	340	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176684114	176684114	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059535-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	309	415	0	ENST00000439151.2:c.4928G>A	p.Cys1643Tyr	p.C1643Y	ENST00000439151	NM_022455.4	1643	tGt/tAt	13/23	0.483956477788493	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.483956477788493	2		415	580	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0059570-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	304	511	20	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.390850796957036	3	FACETS	0.994	0.946	1	0.994	0.946	1	CLONAL	3	TRUE	0	0.407814553516478	3		531	602	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0059570-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	215	505	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.407814553516478	2	FACETS	0.997	0.935	1	0.997	0.935	1	CLONAL	2	TRUE	0	0.407814553516478	2		505	529	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456425	89456425	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059570-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	46	285	3	ENST00000336596.2:c.1601C>G	p.Ser534Cys	p.S534C	ENST00000336596	NM_005233.5	534	tCc/tGc	8/17	0.378661720733966	4	FACETS	1	0.942	1	0.623	0.528	0.725	CLONAL	1	TRUE	2	0.407814553516478	4		288	255	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891448	76891448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059570-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	37	247	3	ENST00000373344.5:c.4657C>T	p.His1553Tyr	p.H1553Y	ENST00000373344	NM_000489.3	1553	Cat/Tat	16/35	0.310149982681699	1	FACETS	0.772	0.644	0.913	0.772	0.644	0.913	CLONAL	1	TRUE	0	0.407814553516478	1		250	187	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	104	329	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.585173194158292	2		329	342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	252	593	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.585173194158292	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.585173194158292	1		593	590	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	285	697	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.585173194158292	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.585173194158292	1		697	656	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	135	380	1	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.585173194158292	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.585173194158292	1		381	324	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508533	106508533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773456619	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	95	554	0	ENST00000359195.3:c.527C>T	p.Thr176Met	p.T176M	ENST00000359195	NM_002649.2	176	aCg/aTg	2/11	0.335796618516449	1	FACETS	0.345	0.307	0.386	0.345	0.307	0.386	INDETERMINATE	1	TRUE	0	0.585173194158292	1		554	665	SUCCESS
REL	5966	MSKCC	GRCh37	2	61128146	61128146	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	108	237	0	ENST00000295025.8:c.322C>T	p.Arg108Ter	p.R108*	ENST00000295025	NM_002908.2	108	Cga/Tga	4/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.585173194158292	2		237	331	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964405	93964405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	30	395	0	ENST00000369303.4:c.2492C>T	p.Ser831Phe	p.S831F	ENST00000369303	NM_004440.3	831	tCt/tTt	14/17	1	2	FACETS	0.25	0.201	0.306	0.25	0.201	0.306	SUBCLONAL	1	TRUE	1	0.585173194158292	2		395	410	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821959	72821960	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762108866	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	146	755	4	ENST00000268489.5:c.10215dup	p.Gly3406ArgfsTer25	p.G3406Rfs*25	ENST00000268489	NM_006885.3	3405	-/C	10/10	1	2	FACETS	0.52	0.474	0.568	0.52	0.474	0.568	SUBCLONAL	1	TRUE	1	0.585173194158292	2		759	960	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573200	41573200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	287	718	0	ENST00000263253.7:c.5485C>T	p.Arg1829Cys	p.R1829C	ENST00000263253	NM_001429.3	1829	Cgc/Tgc	31/31	0.585173194158292	1	FACETS	0.997	0.944	1	0.997	0.944	1	CLONAL	1	TRUE	0	0.585173194158292	1		718	696	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999449	100999450	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs777896116	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	195	781	0	ENST00000325455.5:c.352_353del	p.Leu118ValfsTer65	p.L118Vfs*65	ENST00000325455	NM_001202474.3	118	CTg/g	1/8	1	2	FACETS	0.756	0.701	0.814	0.756	0.701	0.814	SUBCLONAL	1	TRUE	1	0.585173194158292	2		781	881	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481601	20481601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	151	541	0	ENST00000346618.3:c.670G>A	p.Val224Ile	p.V224I	ENST00000346618	NM_001949.4	224	Gtt/Att	3/7	0.585173194158292	1	FACETS	0.698	0.642	0.756	0.698	0.642	0.756	SUBCLONAL	1	TRUE	0	0.585173194158292	1		541	523	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031750	36031750	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879255268	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	255	702	0	ENST00000358208.4:c.1579G>A	p.Glu527Lys	p.E527K	ENST00000358208		527	Gag/Aag	12/12	1	2	FACETS	0.916	0.859	0.976	0.916	0.859	0.976	CLONAL	1	TRUE	1	0.585173194158292	2		702	951	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289925	15289925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35031555	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	154	857	1	ENST00000263388.2:c.3629G>A	p.Arg1210His	p.R1210H	ENST00000263388	NM_000435.2	1210	cGc/cAc	22/33	0.335796618516449	1	FACETS	0.388	0.355	0.423	0.388	0.355	0.423	INDETERMINATE	1	TRUE	0	0.585173194158292	1		858	959	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254851	16254851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748777153	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	216	595	0	ENST00000375759.3:c.2116C>T	p.Arg706Cys	p.R706C	ENST00000375759	NM_015001.2	706	Cgt/Tgt	11/15	1	2	FACETS	0.996	0.93	1	0.996	0.93	1	CLONAL	1	TRUE	1	0.585173194158292	2		595	741	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395147	139395147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	305	760	1	ENST00000277541.6:c.5791G>A	p.Ala1931Thr	p.A1931T	ENST00000277541	NM_017617.3	1931	Gcc/Acc	31/34	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.585173194158292	2		761	1037	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162688917	162688917	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	155	381	0	ENST00000367921.3:c.64A>G	p.Lys22Glu	p.K22E	ENST00000367921	NM_006182.2	22	Aaa/Gaa	3/18	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.585173194158292	2		381	524	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795341	39795341	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1028107759	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	246	544	0	ENST00000288319.7:c.379G>A	p.Val127Met	p.V127M	ENST00000288319	NM_182918.3	127	Gtg/Atg	3/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.585173194158292	2		544	796	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499034	149499034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs921756253	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	184	590	0	ENST00000261799.4:c.2794G>A	p.Glu932Lys	p.E932K	ENST00000261799	NM_002609.3	932	Gag/Aag	20/23	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.585173194158292	2		590	605	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883554	37883554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs574436396	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	234	638	0	ENST00000269571.5:c.3166G>A	p.Gly1056Ser	p.G1056S	ENST00000269571		1056	Ggt/Agt	26/27	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.585173194158292	2		638	771	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450655	70450655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771857626	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	215	591	0	ENST00000373644.4:c.5495C>T	p.Ser1832Leu	p.S1832L	ENST00000373644	NM_030625.2	1832	tCg/tTg	12/12	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.585173194158292	2		591	722	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110213	3110213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	65	692	0	ENST00000078429.4:c.203C>T	p.Ser68Leu	p.S68L	ENST00000078429	NM_002067.2	68	tCg/tTg	2/7	0.335796618516449	1	FACETS	0.226	0.195	0.259	0.226	0.195	0.259	INDETERMINATE	1	TRUE	0	0.585173194158292	1		692	695	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341313	89341313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773189154	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	83	199	0	ENST00000301030.4:c.7622C>T	p.Ala2541Val	p.A2541V	ENST00000301030	NM_001256183.1	2541	gCg/gTg	11/13	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.585173194158292	2		199	272	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060665	38060665	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	400	862	2	ENST00000250448.2:c.1324G>A	p.Ala442Thr	p.A442T	ENST00000250448	NM_004496.3	442	Gcc/Acc	2/2	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.585173194158292	2		864	1295	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046378	69046378	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375506738	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	208	518	0	ENST00000288368.4:c.3851C>T	p.Ala1284Val	p.A1284V	ENST00000288368	NM_024870.2	1284	gCg/gTg	32/40	1	2	FACETS	0.929	0.865	0.995	0.929	0.865	0.995	CLONAL	1	TRUE	1	0.585173194158292	2		518	765	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866342	37866342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770976272	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	224	563	0	ENST00000269571.5:c.647C>T	p.Thr216Met	p.T216M	ENST00000269571		216	aCg/aTg	6/27	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.585173194158292	2		563	743	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37882896	37882896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1377136060	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	202	610	0	ENST00000269571.5:c.2954G>A	p.Arg985His	p.R985H	ENST00000269571		985	cGc/cAc	24/27	1	2	FACETS	0.866	0.805	0.93	0.866	0.805	0.93	CLONAL	1	TRUE	1	0.585173194158292	2		610	797	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563152	21563152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774128777	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	266	756	0	ENST00000382592.4:c.767C>T	p.Pro256Leu	p.P256L	ENST00000382592	NM_014572.2	256	cCg/cTg	4/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.585173194158292	2		756	863	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941429	71941429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754156985	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	229	756	0	ENST00000298229.2:c.1114C>T	p.Arg372Cys	p.R372C	ENST00000298229	NM_001567.3	372	Cgt/Tgt	10/28	1	2	FACETS	0.785	0.732	0.84	0.785	0.732	0.84	SUBCLONAL	1	TRUE	1	0.585173194158292	2		756	997	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719271	61719271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	157	481	0	ENST00000401558.2:c.1786C>T	p.Arg596Cys	p.R596C	ENST00000401558	NM_003400.3	596	Cgc/Tgc	16/25	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.585173194158292	2		481	532	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753390	42753390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776319250	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	141	875	2	ENST00000222329.4:c.874G>A	p.Gly292Arg	p.G292R	ENST00000222329	NM_006494.2	292	Ggg/Agg	4/4	0.335796618516449	1	FACETS	0.349	0.317	0.382	0.349	0.317	0.382	INDETERMINATE	1	TRUE	0	0.585173194158292	1		877	978	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485765	57485765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs893327176	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	206	537	0	ENST00000371085.3:c.1066C>T	p.Arg356Cys	p.R356C	ENST00000371085	NM_000516.4	356	Cgt/Tgt	13/13	1	2	FACETS	0.994	0.926	1	0.994	0.926	1	CLONAL	1	TRUE	1	0.585173194158292	2		537	708	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948527	71948527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749369759	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	86	794	1	ENST00000298229.2:c.3239G>A	p.Arg1080His	p.R1080H	ENST00000298229	NM_001567.3	1080	cGt/cAt	26/28	1	2	FACETS	0.287	0.253	0.323	0.287	0.253	0.323	SUBCLONAL	1	TRUE	1	0.585173194158292	2		795	1025	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128053	30128053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1246728652	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	258	679	0	ENST00000263025.4:c.1076G>A	p.Arg359Gln	p.R359Q	ENST00000263025	NM_002746.2	359	cGg/cAg	8/9	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.585173194158292	2		679	871	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38954955	38954955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111974076	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	84	322	0	ENST00000357387.3:c.2618G>A	p.Arg873His	p.R873H	ENST00000357387	NM_152756.3	873	cGt/cAt	27/38	1	2	FACETS	0.911	0.813	1	0.911	0.813	1	CLONAL	1	TRUE	1	0.585173194158292	2		322	315	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512308	38512308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	181	516	0	ENST00000254066.5:c.1219C>T	p.Pro407Ser	p.P407S	ENST00000254066	NM_000964.3	407	Ccg/Tcg	9/9	1	2	FACETS	0.911	0.843	0.981	0.911	0.843	0.981	CLONAL	1	TRUE	1	0.585173194158292	2		516	679	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965427	18965427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	213	454	0	ENST00000262803.5:c.1174G>A	p.Ala392Thr	p.A392T	ENST00000262803	NM_002911.3	392	Gcc/Acc	9/24	0.335796618516449	1	FACETS	0.928	0.869	0.988	0.928	0.869	0.988	INDETERMINATE	1	TRUE	0	0.585173194158292	1		454	555	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638884	176638884	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765811504	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	239	590	0	ENST00000439151.2:c.3484C>T	p.Arg1162Cys	p.R1162C	ENST00000439151	NM_022455.4	1162	Cgt/Tgt	5/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.585173194158292	2		590	754	SUCCESS
APC	324	MSKCC	GRCh37	5	112116551	112116551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748193367	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	68	390	0	ENST00000257430.4:c.596C>T	p.Ala199Val	p.A199V	ENST00000257430	NM_000038.5	199	gCg/gTg	6/16	0.280976138083571	1	FACETS	0.452	0.395	0.512	0.452	0.395	0.512	INDETERMINATE	1	TRUE	0	0.585173194158292	1		390	364	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272237	15272237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs189252435	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	263	702	2	ENST00000263388.2:c.6202G>A	p.Gly2068Arg	p.G2068R	ENST00000263388	NM_000435.2	2068	Ggg/Agg	33/33	0.335796618516449	1	FACETS	0.862	0.811	0.913	0.862	0.811	0.913	INDETERMINATE	1	TRUE	0	0.585173194158292	1		704	738	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389096	31389096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	202	548	0	ENST00000328111.2:c.2009G>A	p.Arg670Gln	p.R670Q	ENST00000328111	NM_006892.3	670	cGg/cAg	19/23	1	2	FACETS	0.948	0.882	1	0.948	0.882	1	CLONAL	1	TRUE	1	0.585173194158292	2		548	728	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243776975	243776975	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	68	313	0	ENST00000263826.5:c.694G>A	p.Glu232Lys	p.E232K	ENST00000263826	NM_005465.4	232	Gag/Aag	7/13	1	2	FACETS	0.68	0.595	0.77	0.68	0.595	0.77	SUBCLONAL	1	TRUE	1	0.585173194158292	2		313	342	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69458700	69458700	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	257	605	0	ENST00000227507.2:c.515A>C	p.Glu172Ala	p.E172A	ENST00000227507	NM_053056.2	172	gAg/gCg	3/5	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.585173194158292	2		605	753	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226551	2226551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	366	858	1	ENST00000398665.3:c.4031C>T	p.Ala1344Val	p.A1344V	ENST00000398665	NM_032482.2	1344	gCg/gTg	27/28	0.335796618516449	1	FACETS	0.888	0.844	0.932	0.888	0.844	0.932	INDETERMINATE	1	TRUE	0	0.585173194158292	1		859	997	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439770	220439770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761632829	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	318	837	0	ENST00000243786.2:c.623G>A	p.Arg208Gln	p.R208Q	ENST00000243786	NM_002191.3	208	cGg/cAg	2/2	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.585173194158292	2		837	1081	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657059	45657059	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371610323	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	61	513	0	ENST00000407780.3:c.97G>A	p.Val33Met	p.V33M	ENST00000407780	NM_001283052.1	33	Gtg/Atg	3/7	1	2	FACETS	0.299	0.257	0.345	0.299	0.257	0.345	SUBCLONAL	1	TRUE	1	0.585173194158292	2		513	697	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803399	1803399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs946840147	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	81	884	1	ENST00000260795.2:c.668G>A	p.Arg223His	p.R223H	ENST00000260795		223	cGc/cAc	5/17	1	2	FACETS	0.259	0.227	0.293	0.259	0.227	0.293	SUBCLONAL	1	TRUE	1	0.585173194158292	2		885	1069	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750610	41750610	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	117	500	0	ENST00000226382.2:c.18T>A	p.Tyr6Ter	p.Y6*	ENST00000226382	NM_003924.3	6	taT/taA	1/3	1	2	FACETS	0.818	0.741	0.898	0.818	0.741	0.898	CLONAL	1	TRUE	1	0.585173194158292	2		500	489	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5065041	5065041	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1471795147	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	130	404	1	ENST00000381652.3:c.1214+1G>A		p.X405_splice	ENST00000381652	NM_004972.3	405			0.585173194158292	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.585173194158292	1		405	294	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894953	101894953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	133	499	0	ENST00000374994.4:c.506C>T	p.Pro169Leu	p.P169L	ENST00000374994	NM_004612.2	169	cCt/cTt	3/9	1	2	FACETS	0.816	0.744	0.891	0.816	0.744	0.891	CLONAL	1	TRUE	1	0.585173194158292	2		499	557	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133761032	133761032	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	237	624	0	ENST00000318560.5:c.3355A>T	p.Ser1119Cys	p.S1119C	ENST00000318560	NM_005157.4	1119	Agt/Tgt	11/11	1	2	FACETS	0.979	0.917	1	0.979	0.917	1	CLONAL	1	TRUE	1	0.585173194158292	2		624	827	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941879	44941879	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	129	159	0	ENST00000377967.4:c.3203C>A	p.Ser1068Ter	p.S1068*	ENST00000377967	NM_021140.2	1068	tCa/tAa	21/29	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.585173194158292	1		159	243	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222480	53222480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437945152	NA	P-0059571-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	328	363	0	ENST00000375401.3:c.4352G>A	p.Arg1451Gln	p.R1451Q	ENST00000375401	NM_004187.3	1451	cGg/cAg	26/26	1	1	FACETS	0.788	0.757	0.819	1	0.996	1	SUBCLONAL	2	TRUE	0	0.585173194158292	1		363	503	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722761	49722761	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs62262682	NA	P-0059573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	16	25	0	ENST00000449682.2:c.1478G>T	p.Arg493Leu	p.R493L	ENST00000449682	NM_020998.3	493	cGt/cTt	13/18	0.818082214550371	2	FACETS	1	0.924	1	0.724	0.586	0.855	CLONAL	1	TRUE	0	0.818082214550371	2		25	27	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883197	37883197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	257	524	0	ENST00000269571.5:c.3100G>A	p.Asp1034Asn	p.D1034N	ENST00000269571		1034	Gac/Aac	25/27	1	2	FACETS	0.942	0.888	0.997	0.942	0.888	0.997	CLONAL	1	TRUE	1	0.818082214550371	2		524	667	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435563	56435563	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1329146787	NA	P-0059573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	307	536	0	ENST00000407977.2:c.1574G>T	p.Ser525Ile	p.S525I	ENST00000407977		525	aGt/aTt	9/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.818082214550371	2		536	738	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027544	48027545	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0059573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	189	383	0	ENST00000234420.5:c.2424dup	p.Val809CysfsTer11	p.V809Cfs*11	ENST00000234420	NM_000179.2	808	gtt/gTtt	4/10	1	2	FACETS	0.911	0.85	0.974	0.911	0.85	0.974	CLONAL	1	TRUE	1	0.818082214550371	2		383	507	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441280	52441281	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0059573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	733	651	0	ENST00000460680.1:c.489dup	p.Thr164AspfsTer19	p.T164Dfs*19	ENST00000460680	NM_004656.3	163	-/G	7/17	0.818082214550371	2	FACETS	0.979	0.959	0.998	0.979	0.959	0.998	CLONAL	2	TRUE	0	0.818082214550371	2		651	915	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38949833	38949833	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	332	389	0	ENST00000357387.3:c.4117T>G	p.Ser1373Ala	p.S1373A	ENST00000357387	NM_152756.3	1373	Tcc/Gcc	31/38	0.818082214550371	3	FACETS	0.942	0.9	0.983	0.942	0.9	0.983	CLONAL	2	TRUE	1	0.818082214550371	3		389	607	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637219	176637219	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	301	495	0	ENST00000439151.2:c.1819A>C	p.Asn607His	p.N607H	ENST00000439151	NM_022455.4	607	Aat/Cat	5/23	0.779722280011121	4	FACETS	0.953	0.896	1	0.318	0.298	0.338	CLONAL	1	TRUE	1	0.818082214550371	4		495	1404	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710813	117710813	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059573-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	323	482	0	ENST00000368508.3:c.1459T>C	p.Ser487Pro	p.S487P	ENST00000368508	NM_002944.2	487	Tcc/Ccc	12/43	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.818082214550371	2		482	697	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692979	89692979	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123325	NA	P-0059574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	174	400	0	ENST00000371953.3:c.463T>C	p.Tyr155His	p.Y155H	ENST00000371953	NM_000314.4	155	Tat/Cat	5/9	0.587390563995628	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.6	1		400	400	SUCCESS
APC	324	MSKCC	GRCh37	5	112175246	112175246	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1057517558	NA	P-0059574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	252	514	0	ENST00000257430.4:c.3956del	p.Pro1319LeufsTer2	p.P1319Lfs*2	ENST00000257430	NM_000038.5	1319	Cct/ct	16/16	1	2	FACETS	0.964	0.904	1	0.964	0.904	1	CLONAL	1	TRUE	1	0.6	2		514	871	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0059574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	183	428	0	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	0.587390563995628	1	FACETS	0.97	0.906	1	0.97	0.906	1	CLONAL	1	TRUE	0	0.6	1		428	440	SUCCESS
APC	324	MSKCC	GRCh37	5	112174412	112174412	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	156	464	0	ENST00000257430.4:c.3121C>T	p.Gln1041Ter	p.Q1041*	ENST00000257430	NM_000038.5	1041	Caa/Taa	16/16	1	2	FACETS	0.985	0.908	1	0.985	0.908	1	CLONAL	1	TRUE	1	0.6	2		464	528	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604665	48604665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660045	NA	P-0059574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	217	301	0	ENST00000342988.3:c.1487G>A	p.Arg496His	p.R496H	ENST00000342988	NM_005359.5	496	cGt/cAt	12/12	0.587390563995628	1	FACETS	0.961	0.902	1	0.961	0.902	1	CLONAL	1	TRUE	0	0.6	1		301	527	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0059574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	153	341	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	1	2	FACETS	0.924	0.85	1	0.924	0.85	1	CLONAL	1	TRUE	1	0.6	2		341	552	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375008	45375008	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	155	460	0	ENST00000262160.6:c.835del	p.Tyr279IlefsTer4	p.Y279Ifs*4	ENST00000262160	NM_005901.5	279	Tat/at	8/11	0.587390563995628	1	FACETS	0.828	0.765	0.892	0.828	0.765	0.892	CLONAL	1	TRUE	0	0.6	1		460	437	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27016023	27016023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	207	467	0	ENST00000335756.4:c.299C>T	p.Ala100Val	p.A100V	ENST00000335756	NM_001809.3	100	gCa/gTa	4/5	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.6	2		467	681	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99812422	99812422	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	152	350	0	ENST00000280892.6:c.247A>T	p.Ile83Phe	p.I83F	ENST00000280892	NM_001130678.1	83	Atc/Ttc	3/7	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.6	2		350	470	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	173	477	0				ENST00000310581	NM_198253.2	-/1132			0.850961820506636	6	FACETS	1	0.988	1	0.358	0.329	0.387	CLONAL	1	FALSE	2	0.850961820506636	6		477	768	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0059576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	620	619	2	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.850961820506636	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	FALSE	0	0.850961820506636	3		621	670	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027160	49027160	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0059576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	40	313	0	ENST00000267163.4:c.1727C>G	p.Ser576Ter	p.S576*	ENST00000267163	NM_000321.2	576	tCa/tGa	18/27	0.470302179955059	6	FACETS	1	0.887	1	0.525	0.447	0.607	INDETERMINATE	2	FALSE	2	0.850961820506636	6		313	121	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027133	49027133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853292	NA	P-0059576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	72	178	0	ENST00000267163.4:c.1700C>T	p.Ser567Leu	p.S567L	ENST00000267163	NM_000321.2	567	tCa/tTa	18/27	0.470302179955059	6	FACETS	0.969	0.883	1	0.969	0.883	1	INDETERMINATE	4	FALSE	2	0.850961820506636	6		178	118	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	540	482	0	ENST00000267101.3:c.273G>C	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atC	3/28	0.850961820506636	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	4	FALSE	0	0.850961820506636	4		482	578	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435229	49435230	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0059576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	491	666	1	ENST00000301067.7:c.6323dup	p.Gln2109AlafsTer46	p.Q2109Afs*46	ENST00000301067	NM_003482.3	2108	ccg/ccCg	31/54	0.689630372581261	5	FACETS	1	0.996	1			1	CLONAL	4	FALSE	NA	0.850961820506636	5		667	592	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639012	3639012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190668825	NA	P-0059576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	373	581	2	ENST00000294008.3:c.4627G>A	p.Glu1543Lys	p.E1543K	ENST00000294008	NM_032444.2	1543	Gag/Aag	12/15	0.850961820506636	5	FACETS	0.957	0.917	0.997	0.957	0.917	0.997	CLONAL	3	FALSE	2	0.850961820506636	5		583	695	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755356	39755356	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	482	636	0	ENST00000288319.7:c.1409A>G	p.His470Arg	p.H470R	ENST00000288319	NM_182918.3	470	cAt/cGt	10/10	0.712123492474497	6	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	FALSE	3	0.850961820506636	6		636	992	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268084	153268084	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	237	392	0	ENST00000281708.4:c.724C>G	p.Gln242Glu	p.Q242E	ENST00000281708	NM_033632.3	242	Cag/Gag	4/12	0.696367881346553	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	FALSE	2	0.850961820506636	4		392	450	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1253917	1253917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	282	683	2	ENST00000310581.5:c.3325G>A	p.Gly1109Arg	p.G1109R	ENST00000310581	NM_198253.2	1109	Ggg/Agg	16/16	0.850961820506636	6	FACETS	0.85	0.799	0.902	0.425	0.399	0.451	CLONAL	2	FALSE	2	0.850961820506636	6		685	1053	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969935	161969935	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	121	435	0	ENST00000366898.1:c.1034C>A	p.Pro345His	p.P345H	ENST00000366898	NM_004562.2	345	cCt/cAt	9/12	0.696367881346553	4	FACETS	1	0.97	1	0.577	0.525	0.632	CLONAL	1	FALSE	2	0.850961820506636	4		435	456	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993616	90993616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059576-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	35	204	0	ENST00000265433.3:c.307G>A	p.Gly103Arg	p.G103R	ENST00000265433	NM_002485.4	103	Gga/Aga	3/16	0.712123492474497	6	FACETS	0.751	0.625	0.887	0.501	0.417	0.591	SUBCLONAL	2	FALSE	3	0.850961820506636	6		204	148	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059576-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	187	477	0				ENST00000310581	NM_198253.2	-/1132			0.108218177535639	5	FACETS	0.863	0.801	0.926	0.431	0.4	0.463	INDETERMINATE	2	TRUE	1	0.753047073470098	5		477	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0059576-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	782	619	2	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.714101859610437	3	FACETS	0.912	0.892	0.931	0.912	0.892	0.931	CLONAL	3	TRUE	0	0.753047073470098	3		621	1045	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027160	49027160	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0059576-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	178	313	0	ENST00000267163.4:c.1727C>G	p.Ser576Ter	p.S576*	ENST00000267163	NM_000321.2	576	tCa/tGa	18/27	0.381635148217403	6	FACETS	1	0.935	1	0.505	0.467	0.543	INDETERMINATE	2	TRUE	2	0.753047073470098	6		313	587	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027133	49027133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853292	NA	P-0059576-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	248	178	0	ENST00000267163.4:c.1700C>T	p.Ser567Leu	p.S567L	ENST00000267163	NM_000321.2	567	tCa/tTa	18/27	0.381635148217403	6	FACETS	0.905	0.859	0.951	0.905	0.859	0.951	INDETERMINATE	4	TRUE	2	0.753047073470098	6		178	456	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059576-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	694	482	0	ENST00000267101.3:c.273G>C	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atC	3/28	0.714101859610437	3	FACETS	0.98	0.96	0.999	0.98	0.96	0.999	CLONAL	3	TRUE	0	0.753047073470098	3		482	863	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435229	49435230	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0059576-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	538	666	1	ENST00000301067.7:c.6323dup	p.Gln2109AlafsTer46	p.Q2109Afs*46	ENST00000301067	NM_003482.3	2108	ccg/ccCg	31/54	0.714101859610437	3	FACETS	1	0.996	1	0.82	0.795	0.844	CLONAL	2	TRUE	0	0.753047073470098	3		667	800	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639012	3639012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190668825	NA	P-0059576-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	865	581	2	ENST00000294008.3:c.4627G>A	p.Glu1543Lys	p.E1543K	ENST00000294008	NM_032444.2	1543	Gag/Aag	12/15	0.605066419519395	4	FACETS	0.93	0.906	0.954	0.93	0.906	0.954	CLONAL	3	TRUE	1	0.753047073470098	4		583	1444	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755356	39755356	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059576-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	474	636	0	ENST00000288319.7:c.1409A>G	p.His470Arg	p.H470R	ENST00000288319	NM_182918.3	470	cAt/cGt	10/10	0.446506195737391	3	FACETS	0.857	0.823	0.891	0.857	0.823	0.891	INDETERMINATE	2	TRUE	1	0.753047073470098	3		636	1011	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268084	153268084	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059576-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	411	392	0	ENST00000281708.4:c.724C>G	p.Gln242Glu	p.Q242E	ENST00000281708	NM_033632.3	242	Cag/Gag	4/12	0.700527992937541	3	FACETS	0.925	0.887	0.963	0.925	0.887	0.963	CLONAL	2	TRUE	1	0.753047073470098	3		392	812	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1253917	1253917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059576-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	293	683	2	ENST00000310581.5:c.3325G>A	p.Gly1109Arg	p.G1109R	ENST00000310581	NM_198253.2	1109	Ggg/Agg	16/16	0.108218177535639	5	FACETS	0.926	0.874	0.979	0.463	0.437	0.49	INDETERMINATE	2	TRUE	1	0.753047073470098	5		685	895	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969935	161969935	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059576-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	209	435	0	ENST00000366898.1:c.1034C>A	p.Pro345His	p.P345H	ENST00000366898	NM_004562.2	345	cCt/cAt	9/12	0.37127917512794	2	FACETS	0.955	0.893	1	0.478	0.446	0.51	INDETERMINATE	1	TRUE	0	0.753047073470098	2		435	581	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993616	90993616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059576-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	65	204	0	ENST00000265433.3:c.307G>A	p.Gly103Arg	p.G103R	ENST00000265433	NM_002485.4	103	Gga/Aga	3/16	0.466240982617411	4	FACETS	0.563	0.488	0.643	0.188	0.162	0.215	SUBCLONAL	1	TRUE	1	0.753047073470098	4		204	538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0059577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	382	688	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.584871771140268	2	FACETS	0.943	0.907	0.978	0.943	0.907	0.978	CLONAL	2	TRUE	0	0.658568382580721	2		688	615	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414400	6414400	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	15	262	0	ENST00000356142.4:c.34G>A	p.Gly12Arg	p.G12R	ENST00000356142	NM_018890.3	12	Gga/Aga	1/7	0.505381635722593	4	FACETS	0.223	0.162	0.296			1	SUBCLONAL	1	TRUE	NA	0.658568382580721	4		262	339	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242647	16242647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777234386	NA	P-0059577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	120	378	0	ENST00000375759.3:c.1268G>A	p.Arg423His	p.R423H	ENST00000375759	NM_015001.2	423	cGc/cAc	6/15	1	2	FACETS	0.851	0.775	0.931	0.851	0.775	0.931	CLONAL	1	TRUE	1	0.658568382580721	2		378	428	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100597	8100597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	194	710	0	ENST00000346208.3:c.571C>T	p.Pro191Ser	p.P191S	ENST00000346208		191	Ccc/Tcc	3/6	0.658568382580721	3	FACETS	0.912	0.845	0.981	0.456	0.422	0.491	CLONAL	1	TRUE	1	0.658568382580721	3		710	859	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437504	49437504	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	178	588	0	ENST00000301067.7:c.5381T>C	p.Val1794Ala	p.V1794A	ENST00000301067	NM_003482.3	1794	gTg/gCg	23/54	0.658568382580721	3	FACETS	0.894	0.825	0.965	0.298	0.275	0.322	CLONAL	1	TRUE	0	0.658568382580721	3		588	804	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49280997	49280997	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0059577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	124	459	0	ENST00000282018.3:c.44C>G	p.Ser15Ter	p.S15*	ENST00000282018	NM_020377.2	15	tCa/tGa	1/1	0.62967318427488	3	FACETS	0.97	0.882	1	0.323	0.294	0.354	CLONAL	1	TRUE	0	0.658568382580721	3		459	516	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131895051	131895051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370769989	NA	P-0059578-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	8	217	0	ENST00000265335.6:c.205G>A	p.Asp69Asn	p.D69N	ENST00000265335		69	Gat/Aat	2/25	1	2	FACETS	0.159	0.102	0.234	0.159	0.102	0.234	SUBCLONAL	1	TRUE	1	0.314667682097601	2		217	319	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191448	185191448	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1012339817	NA	P-0059578-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	41	469	0	ENST00000265026.3:c.2329G>A	p.Glu777Lys	p.E777K	ENST00000265026	NM_004721.4	777	Gaa/Aaa	11/14	1	2	FACETS	0.337	0.28	0.401	0.337	0.28	0.401	SUBCLONAL	1	TRUE	1	0.314667682097601	2		469	773	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120465	94120465	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059578-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	52	452	0	ENST00000369303.4:c.586G>T	p.Val196Phe	p.V196F	ENST00000369303	NM_004440.3	196	Gtt/Ttt	3/17	0.314667682097601	1	FACETS	0.584	0.497	0.678	0.584	0.497	0.678	SUBCLONAL	1	TRUE	0	0.314667682097601	1		452	477	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451210	70451210	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059578-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	33	527	0	ENST00000373644.4:c.6050C>T	p.Ser2017Leu	p.S2017L	ENST00000373644	NM_030625.2	2017	tCg/tTg	12/12	0.188338822735047	1	FACETS	0.269	0.218	0.327	0.269	0.218	0.327	INDETERMINATE	1	TRUE	0	0.314667682097601	1		527	656	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753351	42753353	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0059578-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	71	720	0	ENST00000222329.4:c.911_913del	p.Ser304del	p.S304del	ENST00000222329	NM_006494.2	304	tCCTtc/ttc	4/4	1	2	FACETS	0.485	0.422	0.554	0.485	0.422	0.554	SUBCLONAL	1	TRUE	1	0.314667682097601	2		720	930	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948097	178948097	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059578-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	95	344	0	ENST00000263967.3:c.2869A>C	p.Thr957Pro	p.T957P	ENST00000263967	NM_006218.2	957	Aca/Cca	20/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.314667682097601	2		344	543	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573454	55573454	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0059578-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	62	307	0	ENST00000288135.5:c.1115+1G>A		p.X372_splice	ENST00000288135	NM_000222.2	372			1	2	FACETS	0.993	0.861	1	0.993	0.861	1	CLONAL	1	TRUE	1	0.314667682097601	2		307	397	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0059579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	325	333	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	0.634808519624446	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.634808519624446	3		333	621	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104712	193104712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	15	241	0	ENST00000367435.3:c.416G>A	p.Arg139Gln	p.R139Q	ENST00000367435	NM_024529.4	139	cGa/cAa	5/17	1	2	FACETS	0.163	0.119	0.216	0.163	0.119	0.216	SUBCLONAL	1	TRUE	1	0.634808519624446	2		241	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0059579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	221	460	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.634808519624446	1	FACETS	0.923	0.867	0.979	0.923	0.867	0.979	CLONAL	1	TRUE	0	0.634808519624446	1		460	515	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664915	138664915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs797044527	NA	P-0059579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	77	360	0	ENST00000330315.3:c.650C>T	p.Ser217Phe	p.S217F	ENST00000330315	NM_023067.3	217	tCc/tTc	1/1	1	2	FACETS	0.423	0.371	0.478	0.423	0.371	0.478	SUBCLONAL	1	TRUE	1	0.634808519624446	2		360	574	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672218	86672218	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	136	276	0	ENST00000274376.6:c.2020C>G	p.Arg674Gly	p.R674G	ENST00000274376	NM_002890.2	674	Cgc/Ggc	16/25	1	2	FACETS	0.948	0.869	1	0.948	0.869	1	CLONAL	1	TRUE	1	0.634808519624446	2		276	452	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187812	11187812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	131	341	0	ENST00000361445.4:c.6085G>A	p.Glu2029Lys	p.E2029K	ENST00000361445	NM_004958.3	2029	Gaa/Aaa	44/58	0.2861007956238	1	FACETS	0.432	0.393	0.473	0.432	0.393	0.473	INDETERMINATE	1	TRUE	0	0.634808519624446	1		341	652	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121593	2121593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	54	406	2	ENST00000219476.3:c.1922G>A	p.Ser641Asn	p.S641N	ENST00000219476	NM_000548.3	641	aGc/aAc	18/42	0.634808519624446	1	FACETS	0.173	0.147	0.202	0.173	0.147	0.202	SUBCLONAL	1	TRUE	0	0.634808519624446	1		408	670	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47503709	47503709	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	271	455	0	ENST00000404338.3:c.4264C>T	p.Gln1422Ter	p.Q1422*	ENST00000404338	NM_004491.4	1422	Cag/Tag	6/6	1	2	FACETS	0.972	0.915	1	0.972	0.915	1	CLONAL	1	TRUE	1	0.634808519624446	2		455	878	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0059580-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	231	306	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.374582297967434	2	FACETS	0.99	0.929	1	0.99	0.929	1	CLONAL	2	TRUE	0	0.374582297967434	2		307	623	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059580-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	79	121	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.374582297967434	2	FACETS	0.921	0.824	1	0.921	0.824	1	CLONAL	2	TRUE	0	0.374582297967434	2		121	229	SUCCESS
APC	324	MSKCC	GRCh37	5	112175273	112175273	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123121	NA	P-0059580-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	221	400	0	ENST00000257430.4:c.3982C>T	p.Gln1328Ter	p.Q1328*	ENST00000257430	NM_000038.5	1328	Cag/Tag	16/16	0.374582297967434	2	FACETS	0.969	0.908	1	0.969	0.908	1	CLONAL	2	TRUE	0	0.374582297967434	2		400	609	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178663	32178663	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144069425	NA	P-0059580-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	250	460	0	ENST00000375023.3:c.2731G>A	p.Gly911Ser	p.G911S	ENST00000375023	NM_004557.3	911	Ggc/Agc	18/30	0.273488052996237	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.374582297967434	4		460	835	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510904	157510904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554232979	NA	P-0059580-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	229	419	0	ENST00000346085.5:c.3679C>T	p.Gln1227Ter	p.Q1227*	ENST00000346085	NM_020732.3	1227	Caa/Taa	14/20	0.273488052996237	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.374582297967434	4		419	789	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116254	209116254	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059580-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	64	312	0	ENST00000345146.2:c.22G>T	p.Gly8Cys	p.G8C	ENST00000345146	NM_005896.2	8	Ggt/Tgt	3/10	0.142954217945301	4	FACETS	1	0.951	1	0.601	0.522	0.685	INDETERMINATE	1	TRUE	2	0.374582297967434	4		312	391	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920410	114920410	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059580-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	192	344	0	ENST00000543371.1:c.1351T>A	p.Phe451Ile	p.F451I	ENST00000543371	NM_001198531.1	451	Ttc/Atc	13/14	0.374582297967434	2	FACETS	0.956	0.891	1	0.956	0.891	1	CLONAL	2	TRUE	0	0.374582297967434	2		344	536	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0059583-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	210	458	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.459485571108058	2	FACETS	1	0.99	1	0.666	0.622	0.712	CLONAL	1	TRUE	0	0.485578153802676	2		458	649	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691039	NA	P-0059583-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	306	739	0	ENST00000269305.4:c.919+1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.459485571108058	2	FACETS	0.913	0.867	0.96	0.913	0.867	0.96	CLONAL	2	TRUE	0	0.485578153802676	2		739	690	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965575	93965575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059583-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	42	512	0	ENST00000369303.4:c.2353G>A	p.Asp785Asn	p.D785N	ENST00000369303	NM_004440.3	785	Gat/Aat	13/17	1	2	FACETS	0.437	0.365	0.516	0.437	0.365	0.516	SUBCLONAL	1	TRUE	1	0.485578153802676	2		512	396	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050274	13050274	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059583-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	81	634	0	ENST00000316448.5:c.226G>C	p.Ala76Pro	p.A76P	ENST00000316448	NM_004343.3	76	Gct/Cct	3/9	NA	2	FACETS	0.442	0.389	0.499			1	INDETERMINATE	1	TRUE	NA	0.485578153802676	2		634	755	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0059584-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	10	125	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.478	0.324	0.67	0.478	0.324	0.67	SUBCLONAL	1	TRUE	1	0.26	2		125	161	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0059584-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	54	582	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.996	0.853	1	0.996	0.853	1	CLONAL	1	TRUE	1	0.26	2		582	417	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059584-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	42	559	1	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	0.191937812868383	1	FACETS	0.734	0.614	0.866	0.734	0.614	0.866	SUBCLONAL	1	TRUE	0	0.26	1		560	383	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812205	43812205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866559375	NA	P-0059584-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	45	566	2	ENST00000372470.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000372470	NM_005373.2	357	cGa/cAa	7/12	1	2	FACETS	0.778	0.654	0.914	0.778	0.654	0.914	CLONAL	1	TRUE	1	0.26	2		568	445	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602691	55602691	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059584-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	36	417	0	ENST00000288135.5:c.2512C>A	p.Pro838Thr	p.P838T	ENST00000288135	NM_000222.2	838	Cct/Act	18/21	1	2	FACETS	0.81	0.667	0.969	0.81	0.667	0.969	CLONAL	1	TRUE	1	0.26	2		417	342	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0059584-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	23	148	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.592	0.462	0.742	0.592	0.462	0.742	SUBCLONAL	1	TRUE	1	0.26	2		148	299	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174395	11174395	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1085307113	NA	P-0059584-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	36	448	0	ENST00000361445.4:c.7280T>C	p.Leu2427Pro	p.L2427P	ENST00000361445	NM_004958.3	2427	cTg/cCg	53/58	1	2	FACETS	0.989	0.817	1	0.989	0.817	1	CLONAL	1	TRUE	1	0.26	2		448	280	SUCCESS
APC	324	MSKCC	GRCh37	5	112162845	112162845	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0059584-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	21	405	0	ENST00000257430.4:c.1449T>A	p.Cys483Ter	p.C483*	ENST00000257430	NM_000038.5	483	tgT/tgA	12/16	0.191937812868383	3	FACETS	0.64	0.494	0.811	0.32	0.247	0.406	SUBCLONAL	1	TRUE	1	0.26	3		405	285	SUCCESS
APC	324	MSKCC	GRCh37	5	112175768	112175768	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059584-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	57	521	0	ENST00000257430.4:c.4477del	p.Thr1493ArgfsTer14	p.T1493Rfs*14	ENST00000257430	NM_000038.5	1493	Acg/cg	16/16	0.191937812868383	3	FACETS	1	0.935	1	0.577	0.497	0.665	CLONAL	1	TRUE	1	0.26	3		521	429	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0059585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	97	536	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.309768188682182	2		536	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0059585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	83	522	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.293227353052082	1	FACETS	0.854	0.756	0.96	0.854	0.756	0.96	CLONAL	1	TRUE	0	0.309768188682182	1		522	530	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0059585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	68	483	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.818	0.712	0.931	0.818	0.712	0.931	CLONAL	1	TRUE	1	0.309768188682182	2		483	537	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	106	676	0	ENST00000346208.3:c.878T>A	p.Met293Lys	p.M293K	ENST00000346208		293	aTg/aAg	4/6	1	2	FACETS	0.961	0.862	1	0.961	0.862	1	CLONAL	1	TRUE	1	0.309768188682182	2		676	712	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267359	198267359	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs377023736	NA	P-0059585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	77	586	0	ENST00000335508.6:c.1998G>T	p.Lys666Asn	p.K666N	ENST00000335508	NM_012433.2	666	aaG/aaT	14/25	1	2	FACETS	0.798	0.701	0.902	0.798	0.701	0.902	CLONAL	1	TRUE	1	0.309768188682182	2		586	623	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181857	56181857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	53	440	0	ENST00000399503.3:c.4081C>T	p.His1361Tyr	p.H1361Y	ENST00000399503	NM_005921.1	1361	Cat/Tat	17/20	1	2	FACETS	0.943	0.807	1	0.943	0.807	1	CLONAL	1	TRUE	1	0.309768188682182	2		440	363	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168785	56168785	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	74	550	1	ENST00000399503.3:c.1639C>T	p.Gln547Ter	p.Q547*	ENST00000399503	NM_005921.1	547	Cag/Tag	9/20	1	2	FACETS	0.957	0.84	1	0.957	0.84	1	CLONAL	1	TRUE	1	0.309768188682182	2		551	499	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830365	72830371	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGATG	GGTGATG	-	novel	NA	P-0059585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	117	764	0	ENST00000268489.5:c.6210_6216del	p.Ile2071HisfsTer28	p.I2071Hfs*28	ENST00000268489	NM_006885.3	2070	ccCATCACC/cc	9/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.309768188682182	2		764	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0059586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	166	601	0	ENST00000269305.4:c.673-1G>C		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.662287138682658	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.662287138682658	1		601	305	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622084	1622084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748395369	NA	P-0059586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	165	781	0	ENST00000344749.5:c.791C>T	p.Thr264Met	p.T264M	ENST00000344749	NM_001136139.2	264	aCg/aTg	10/19	0.662287138682658	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.662287138682658	1		781	303	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598198	28598198	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	272	658	0	ENST00000253063.3:c.170G>T	p.Gly57Val	p.G57V	ENST00000253063	NM_031459.4	57	gGg/gTg	3/10	0.371073931110187	3	FACETS	0.905	0.857	0.954	0.905	0.857	0.954	INDETERMINATE	2	TRUE	1	0.662287138682658	3		658	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691039	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	101	739	0	ENST00000269305.4:c.919+1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			1	2	FACETS	0.935	0.833	1	0.935	0.833	1	CLONAL	1	TRUE	1	0.201245545800343	2		739	1074	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	112	697	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.201245545800343	2		697	990	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494647	2494647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	90	704	0	ENST00000355716.4:c.787G>A	p.Asp263Asn	p.D263N	ENST00000355716	NM_003820.2	263	Gac/Aac	8/8	1	2	FACETS	0.94	0.832	1	0.94	0.832	1	CLONAL	1	TRUE	1	0.201245545800343	2		704	952	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074378	8074379	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	77	612	0	ENST00000377482.5:c.280_281delinsTT	p.Pro94Phe	p.P94F	ENST00000377482	NM_018948.3	94	CCt/TTt	4/4	1	2	FACETS	0.935	0.82	1	0.935	0.82	1	CLONAL	1	TRUE	1	0.201245545800343	2		612	818	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257189	16257189	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	45	549	0	ENST00000375759.3:c.4454C>T	p.Ser1485Phe	p.S1485F	ENST00000375759	NM_015001.2	1485	tCt/tTt	11/15	1	2	FACETS	0.67	0.562	0.791	0.67	0.562	0.791	SUBCLONAL	1	TRUE	1	0.201245545800343	2		549	667	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809769	36809769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	73	634	0	ENST00000373129.3:c.836C>T	p.Pro279Leu	p.P279L	ENST00000373129	NM_032017.1	279	cCg/cTg	9/12	1	2	FACETS	0.955	0.834	1	0.955	0.834	1	CLONAL	1	TRUE	1	0.201245545800343	2		634	760	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076812	72076812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	66	540	0	ENST00000357731.5:c.685G>A	p.Glu229Lys	p.E229K	ENST00000357731	NM_173808.2	229	Gaa/Aaa	5/7	1	2	FACETS	0.923	0.8	1	0.923	0.8	1	CLONAL	1	TRUE	1	0.201245545800343	2		540	711	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429951	78429951	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	42	530	0	ENST00000370768.2:c.928C>T	p.Gln310Ter	p.Q310*	ENST00000370768	NM_003902.3	310	Cag/Tag	11/20	1	2	FACETS	0.745	0.622	0.883	0.745	0.622	0.883	SUBCLONAL	1	TRUE	1	0.201245545800343	2		530	560	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464917	120464918	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	62	585	0	ENST00000256646.2:c.5154_5155delinsTT	p.Arg1719Ter	p.R1719*	ENST00000256646	NM_024408.3	1718	cgCCga/cgTTga	28/34	1	2	FACETS	0.792	0.683	0.911	0.792	0.683	0.911	CLONAL	1	TRUE	1	0.201245545800343	2		585	778	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870379	155870380	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	62	561	0	ENST00000368323.3:c.459_460delinsTT	p.Arg154Ter	p.R154*	ENST00000368323	NM_006912.5	153	gcCCga/gcTTga	6/6	1	2	FACETS	0.796	0.686	0.916	0.796	0.686	0.916	CLONAL	1	TRUE	1	0.201245545800343	2		561	774	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845329	156845329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1273	157	1157	0	ENST00000524377.1:c.1372C>T	p.Pro458Ser	p.P458S	ENST00000524377	NM_002529.3	458	Cca/Tca	12/17	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.201245545800343	2		1157	1430	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104264001	104264001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	118	570	0	ENST00000369902.3:c.92C>T	p.Pro31Leu	p.P31L	ENST00000369902	NM_016169.3	31	cCc/cTc	1/12	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.201245545800343	2		570	1036	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413533	32413533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	96	486	0	ENST00000332351.3:c.1417C>T	p.His473Tyr	p.H473Y	ENST00000332351	NM_024426.4	473	Cat/Tat	9/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.201245545800343	2		486	666	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456732	32456732	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	135	677	0	ENST00000332351.3:c.160C>T	p.Gln54Ter	p.Q54*	ENST00000332351	NM_024426.4	54	Cag/Tag	1/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.201245545800343	2		677	902	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939500	71939501	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	106	859	1	ENST00000298229.2:c.355_356delinsAA	p.Gly119Asn	p.G119N	ENST00000298229	NM_001567.3	119	GGt/AAt	3/28	1	2	FACETS	0.985	0.881	1	0.985	0.881	1	CLONAL	1	TRUE	1	0.201245545800343	2		860	1070	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981673	101981673	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs906963349	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	159	684	0	ENST00000282441.5:c.94G>A	p.Gly32Arg	p.G32R	ENST00000282441	NM_001130145.2	32	Gga/Aga	1/9	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.201245545800343	2		684	1085	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121777	108121778	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	52	534	0	ENST00000278616.4:c.1585_1586delinsAA	p.Gly529Lys	p.G529K	ENST00000278616	NM_000051.3	529	GGg/AAg	10/63	1	2	FACETS	0.82	0.698	0.955	0.82	0.698	0.955	CLONAL	1	TRUE	1	0.201245545800343	2		534	630	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493501	56493501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774326613	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	103	634	0	ENST00000267101.3:c.2909G>A	p.Arg970Gln	p.R970Q	ENST00000267101	NM_001982.3	970	cGa/cAa	24/28	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.201245545800343	2		634	953	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557815	21557815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	81	630	0	ENST00000382592.4:c.2030G>A	p.Gly677Asp	p.G677D	ENST00000382592	NM_014572.2	677	gGt/gAt	5/8	0.201245545800343	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	0	0.201245545800343	1		630	702	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562627	21562627	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754998895	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	70	492	0	ENST00000382592.4:c.1292C>T	p.Thr431Ile	p.T431I	ENST00000382592	NM_014572.2	431	aCc/aTc	4/8	0.201245545800343	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.201245545800343	1		492	586	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599046	28599046	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	45	374	0	ENST00000241453.7:c.2242G>A	p.Asp748Asn	p.D748N	ENST00000241453	NM_004119.2	748	Gac/Aac	18/24	0.201245545800343	1	FACETS	0.824	0.693	0.969	0.824	0.693	0.969	CLONAL	1	TRUE	0	0.201245545800343	1		374	488	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907522	32907522	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs431825288	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	41	390	0	ENST00000380152.3:c.1907C>T	p.Ser636Leu	p.S636L	ENST00000380152		636	tCa/tTa	10/27	0.201245545800343	1	FACETS	0.864	0.721	1	0.864	0.721	1	CLONAL	1	TRUE	0	0.201245545800343	1		390	424	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81558876	81558876	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	56	459	0	ENST00000298171.2:c.469G>A	p.Glu157Lys	p.E157K	ENST00000298171	NM_000369.2	157	Gaa/Aaa	6/10	1	2	FACETS	0.89	0.762	1	0.89	0.762	1	CLONAL	1	TRUE	1	0.201245545800343	2		459	625	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582119	95582119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753796042	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	80	555	0	ENST00000393063.1:c.1792G>A	p.Glu598Lys	p.E598K	ENST00000393063	NM_030621.3	598	Gag/Aag	12/28	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.201245545800343	2		555	740	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678461	88678461	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	102	698	0	ENST00000360948.2:c.1075T>G	p.Ser359Ala	p.S359A	ENST00000360948	NM_001012338.2	359	Tcc/Gcc	9/19	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.201245545800343	2		698	838	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110688	2110688	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	91	595	0	ENST00000219476.3:c.993del	p.Asn331LysfsTer32	p.N331Kfs*32	ENST00000219476	NM_000548.3	331	aaC/aa	11/42	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.201245545800343	NA		595	820	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134540	2134541	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	118	891	0	ENST00000219476.3:c.4317_4318delinsTT	p.Gln1440Ter	p.Q1440*	ENST00000219476	NM_000548.3	1439	ggCCag/ggTTag	34/42	0.201245545800343	1	FACETS	0.987	0.888	1	0.987	0.888	1	CLONAL	1	TRUE	0	0.201245545800343	1		891	1069	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639732	3639732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759828401	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	110	705	0	ENST00000294008.3:c.3907G>A	p.Glu1303Lys	p.E1303K	ENST00000294008	NM_032444.2	1303	Gaa/Aaa	12/15	0.201245545800343	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.201245545800343	1		705	947	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640287	3640287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1460013656	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	75	644	0	ENST00000294008.3:c.3352C>T	p.Pro1118Ser	p.P1118S	ENST00000294008	NM_032444.2	1118	Cca/Tca	12/15	0.201245545800343	1	FACETS	0.897	0.786	1	0.897	0.786	1	CLONAL	1	TRUE	0	0.201245545800343	1		644	747	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070617	67070617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	76	540	0	ENST00000412916.2:c.241C>T	p.Pro81Ser	p.P81S	ENST00000412916		81	Cct/Tct	3/6	1	2	FACETS	0.914	0.801	1	0.914	0.801	1	CLONAL	1	TRUE	1	0.201245545800343	2		540	826	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984793	72984793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	80	686	1	ENST00000268489.5:c.2791G>A	p.Gly931Ser	p.G931S	ENST00000268489	NM_006885.3	931	Ggc/Agc	3/10	1	2	FACETS	0.876	0.769	0.99	0.876	0.769	0.99	CLONAL	1	TRUE	1	0.201245545800343	2		687	908	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577540	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	rs1555525498	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	83	559	0	ENST00000269305.4:c.741_742delinsTT	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	247	aaCCgg/aaTTgg	7/11	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.201245545800343	2		559	765	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578476	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	117	833	0	ENST00000269305.4:c.454_455delinsTT	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	CCg/TTg	5/11	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.201245545800343	2		833	1110	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690706	33690706	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	69	621	0	ENST00000308377.4:c.121C>T	p.Gln41Ter	p.Q41*	ENST00000308377	NM_152270.3	41	Caa/Taa	2/5	1	2	FACETS	0.868	0.755	0.991	0.868	0.755	0.991	CLONAL	1	TRUE	1	0.201245545800343	2		621	790	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868300	37868300	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	93	640	0	ENST00000269571.5:c.1021G>A	p.Val341Met	p.V341M	ENST00000269571		341	Gtg/Atg	8/27	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.201245545800343	2		640	836	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435541	56435542	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	88	743	0	ENST00000407977.2:c.1595_1596delinsTT	p.Ser532Phe	p.S532F	ENST00000407977		532	tCC/tTT	9/10	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.201245545800343	2		743	851	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876514	59876515	+	missense_variant	Missense_Mutation	DNP	AT	AT	TA	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	57	447	0	ENST00000259008.2:c.1286_1287delinsTA	p.Asn429Ile	p.N429I	ENST00000259008	NM_032043.2	429	aAT/aTA	9/20	1	2	FACETS	0.896	0.768	1	0.896	0.768	1	CLONAL	1	TRUE	1	0.201245545800343	2		447	632	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625656	1625656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	101	615	0	ENST00000344749.5:c.418C>T	p.Pro140Ser	p.P140S	ENST00000344749	NM_001136139.2	140	Cct/Tct	7/19	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.201245545800343	2		615	918	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265096	5265096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	98	672	0	ENST00000357368.4:c.491C>T	p.Pro164Leu	p.P164L	ENST00000357368	NM_002850.3	164	cCt/cTt	5/38	1	2	FACETS	0.998	0.889	1	0.998	0.889	1	CLONAL	1	TRUE	1	0.201245545800343	2		672	976	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6222145	6222145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	95	704	0	ENST00000252674.7:c.1097C>T	p.Ser366Phe	p.S366F	ENST00000252674	NM_005934.3	366	tCc/tTc	6/12	1	2	FACETS	0.994	0.883	1	0.994	0.883	1	CLONAL	1	TRUE	1	0.201245545800343	2		704	950	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214867	36214867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	107	616	0	ENST00000222270.7:c.3293G>A	p.Gly1098Glu	p.G1098E	ENST00000222270	NM_014727.1	1098	gGg/gAg	8/37	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.201245545800343	2		616	865	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753172	42753173	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	122	969	0	ENST00000222329.4:c.1091_1092delinsTT	p.Ala364Val	p.A364V	ENST00000222329	NM_006494.2	364	gCC/gTT	4/4	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.201245545800343	2		969	1192	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795001	42795001	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs373041068	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	92	811	0	ENST00000575354.2:c.2081C>G	p.Ser694Cys	p.S694C	ENST00000575354	NM_015125.3	694	tCt/tGt	10/20	1	2	FACETS	0.863	0.765	0.969	0.863	0.765	0.969	CLONAL	1	TRUE	1	0.201245545800343	2		811	1059	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423881	47423881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	96	626	0	ENST00000404338.3:c.1949C>T	p.Ser650Phe	p.S650F	ENST00000404338	NM_004491.4	650	tCt/tTt	1/6	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.201245545800343	2		626	803	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424533	47424534	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	77	587	2	ENST00000404338.3:c.2601_2602delinsAA	p.Ala868Thr	p.A868T	ENST00000404338	NM_004491.4	867	ttGGct/ttAAct	1/6	1	2	FACETS	0.937	0.821	1	0.937	0.821	1	CLONAL	1	TRUE	1	0.201245545800343	2		589	817	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725004	47725004	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	112	772	0	ENST00000449228.1:c.740C>T	p.Pro247Leu	p.P247L	ENST00000449228	NM_001127240.2	247	cCt/cTt	4/4	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.201245545800343	2		772	1003	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085696	16085697	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	60	613	0	ENST00000281043.3:c.872_873delinsTT	p.Thr291Ile	p.T291I	ENST00000281043	NM_005378.4	291	aCC/aTT	3/3	1	2	FACETS	0.818	0.704	0.943	0.818	0.704	0.943	CLONAL	1	TRUE	1	0.201245545800343	2		613	729	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241064	39241065	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	32	362	0	ENST00000402219.2:c.2006_2007delinsTT	p.Pro669Leu	p.P669L	ENST00000402219	NM_005633.3	669	cCC/cTT	12/23	1	2	FACETS	0.681	0.552	0.827	0.681	0.552	0.827	SUBCLONAL	1	TRUE	1	0.201245545800343	2		362	467	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149212	61149212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	73	623	0	ENST00000295025.8:c.1402G>A	p.Asp468Asn	p.D468N	ENST00000295025	NM_002908.2	468	Gac/Aac	11/11	1	2	FACETS	0.862	0.752	0.98	0.862	0.752	0.98	CLONAL	1	TRUE	1	0.201245545800343	2		623	842	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488718	212488718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267599191	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	69	694	0	ENST00000342788.4:c.2131C>T	p.Arg711Cys	p.R711C	ENST00000342788	NM_005235.2	711	Cgt/Tgt	18/28	1	2	FACETS	0.831	0.723	0.949	0.831	0.723	0.949	CLONAL	1	TRUE	1	0.201245545800343	2		694	825	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537918	212537918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146197533	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	80	526	0	ENST00000342788.4:c.1687G>A	p.Glu563Lys	p.E563K	ENST00000342788	NM_005235.2	563	Gaa/Aaa	14/28	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.201245545800343	2		526	752	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661733	227661734	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	87	755	0	ENST00000305123.5:c.1721_1722delinsTT	p.Ser574Phe	p.S574F	ENST00000305123	NM_005544.2	574	tCC/tTT	1/2	1	2	FACETS	0.907	0.802	1	0.907	0.802	1	CLONAL	1	TRUE	1	0.201245545800343	2		755	953	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022387	31022388	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	102	801	1	ENST00000375687.4:c.1872_1873delinsTT	p.Arg625Ter	p.R625*	ENST00000375687	NM_015338.5	624	gtCCga/gtTTga	13/13	1	2	FACETS	0.983	0.877	1	0.983	0.877	1	CLONAL	1	TRUE	1	0.201245545800343	2		802	1031	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143262	24143262	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	97	839	0	ENST00000263121.7:c.494C>T	p.Pro165Leu	p.P165L	ENST00000263121	NM_003073.3	165	cCc/cTc	4/9	1	2	FACETS	0.892	0.793	0.997	0.892	0.793	0.997	CLONAL	1	TRUE	1	0.201245545800343	2		839	1081	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026856	71026857	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	40	465	0	ENST00000318789.4:c.1365_1366delinsTT	p.Gln456Ter	p.Q456*	ENST00000318789	NM_032682.5	455	aaCCaa/aaTTaa	16/21	1	2	FACETS	0.832	0.691	0.988	0.832	0.691	0.988	CLONAL	1	TRUE	1	0.201245545800343	2		465	478	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199903	128199903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777726701	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	128	814	0	ENST00000341105.2:c.1402G>A	p.Gly468Ser	p.G468S	ENST00000341105	NM_032638.4	468	Ggc/Agc	6/6	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.201245545800343	2		814	1146	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670300	134670300	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	69	634	0	ENST00000398015.3:c.211T>G	p.Trp71Gly	p.W71G	ENST00000398015	NM_004441.4	71	Tgg/Ggg	3/16	1	2	FACETS	0.859	0.747	0.981	0.859	0.747	0.981	CLONAL	1	TRUE	1	0.201245545800343	2		634	798	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880891	134880891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200172177	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	65	563	0	ENST00000398015.3:c.1454G>A	p.Arg485Lys	p.R485K	ENST00000398015	NM_004441.4	485	aGg/aAg	7/16	1	2	FACETS	0.919	0.796	1	0.919	0.796	1	CLONAL	1	TRUE	1	0.201245545800343	2		563	703	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967309	134967310	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	79	675	0	ENST00000398015.3:c.2648_2649delinsAA	p.Arg883Gln	p.R883Q	ENST00000398015	NM_004441.4	883	cGG/cAA	14/16	1	2	FACETS	0.953	0.837	1	0.953	0.837	1	CLONAL	1	TRUE	1	0.201245545800343	2		675	824	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182679031	182679031	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	16	274	0	ENST00000292782.4:c.503C>T	p.Pro168Leu	p.P168L	ENST00000292782	NM_020640.2	168	cCa/cTa	4/7	1	2	FACETS	0.548	0.405	0.72	0.548	0.405	0.72	SUBCLONAL	1	TRUE	1	0.201245545800343	2		274	290	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803160	1803161	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	120	848	1	ENST00000260795.2:c.512_513delinsTT	p.Thr171Ile	p.T171I	ENST00000260795		171	aCC/aTT	4/17	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.201245545800343	2		849	1109	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127498	55127499	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	99	609	2	ENST00000257290.5:c.286_287delinsAA	p.Gly96Lys	p.G96K	ENST00000257290	NM_006206.4	96	GGg/AAg	3/23	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.201245545800343	2		611	882	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796030	57796030	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	56	520	0	ENST00000309042.7:c.1006C>T	p.Gln336Ter	p.Q336*	ENST00000309042	NM_005612.4	336	Cag/Tag	4/4	1	2	FACETS	0.903	0.774	1	0.903	0.774	1	CLONAL	1	TRUE	1	0.201245545800343	2		520	616	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524477	187524478	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	70	571	0	ENST00000441802.2:c.11202_11203delinsTT	p.Gln3735Ter	p.Q3735*	ENST00000441802	NM_005245.3	3734	ttCCag/ttTTag	19/27	1	2	FACETS	0.875	0.762	0.998	0.875	0.762	0.998	CLONAL	1	TRUE	1	0.201245545800343	2		571	795	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629753	187630251	+	frameshift_variant	Frame_Shift_Del	DEL	TTAGCTTTTCCAGGTGTACTTTTAAAAACATACCTCAAATGGGAATAAGCAGGAATGGCCTTTACCATGACCACAGGTGTGTTGGGAGGAGCAAATTCACTTATTTCTGCTCTGTAAACATCCTTTTCAAACTTGACTGGCCCGGCTTTGAACTGTGGAGAAGTCACGTGAATGACTTTAACAGAAGAGAACTGGGGCGGAGTTCCTTTATCTTTAGCCTGTAGTGTGAGATTGTAGCCGAAAGGATGACTGTCCCAATCAATGCCACCGATGGCTTTGACTTTATACTCCTTACTCCCTGGAAAGGACCTCACTGTTCTAAACTGCTGGAGAAGGTCACCTGCCACGATGCTTAAAGATGCTATGTCACCATTGGCACCCTGATCGCAGTCATCCACTGTCACAATTGCATATGCTGGGTCCCTGTCCAGTTCTGATGGTGACAATGTCACTGCTGTTATCACCGGAGCACATTCATTGGCCTGTTCGATGTGCACCG	TTAGCTTTTCCAGGTGTACTTTTAAAAACATACCTCAAATGGGAATAAGCAGGAATGGCCTTTACCATGACCACAGGTGTGTTGGGAGGAGCAAATTCACTTATTTCTGCTCTGTAAACATCCTTTTCAAACTTGACTGGCCCGGCTTTGAACTGTGGAGAAGTCACGTGAATGACTTTAACAGAAGAGAACTGGGGCGGAGTTCCTTTATCTTTAGCCTGTAGTGTGAGATTGTAGCCGAAAGGATGACTGTCCCAATCAATGCCACCGATGGCTTTGACTTTATACTCCTTACTCCCTGGAAAGGACCTCACTGTTCTAAACTGCTGGAGAAGGTCACCTGCCACGATGCTTAAAGATGCTATGTCACCATTGGCACCCTGATCGCAGTCATCCACTGTCACAATTGCATATGCTGGGTCCCTGTCCAGTTCTGATGGTGACAATGTCACTGCTGTTATCACCGGAGCACATTCATTGGCCTGTTCGATGTGCACCG	-	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	59	467	0	ENST00000441802.2:c.731_1229del	p.Thr244AsnfsTer4	p.T244Nfs*4	ENST00000441802	NM_005245.3	244	aCGGTGCACATCGAACAGGCCAATGAATGTGCTCCGGTGATAACAGCAGTGACATTGTCACCATCAGAACTGGACAGGGACCCAGCATATGCAATTGTGACAGTGGATGACTGCGATCAGGGTGCCAATGGTGACATAGCATCTTTAAGCATCGTGGCAGGTGACCTTCTCCAGCAGTTTAGAACAGTGAGGTCCTTTCCAGGGAGTAAGGAGTATAAAGTCAAAGCCATCGGTGGCATTGATTGGGACAGTCATCCTTTCGGCTACAATCTCACACTACAGGCTAAAGATAAAGGAACTCCGCCCCAGTTCTCTTCTGTTAAAGTCATTCACGTGACTTCTCCACAGTTCAAAGCCGGGCCAGTCAAGTTTGAAAAGGATGTTTACAGAGCAGAAATAAGTGAATTTGCTCCTCCCAACACACCTGTGGTCATGGTAAAGGCCATTCCTGCTTATTCCCATTTGAGGTATGTTTTTAAAAGTACACCTGGAAAAGCTAAa/aa	2/27	1	2	FACETS	0.909	0.782	1	0.909	0.782	1	CLONAL	1	TRUE	1	0.201245545800343	2		467	645	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	240485	240485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	17	130	0	ENST00000264932.6:c.1445C>T	p.Pro482Leu	p.P482L	ENST00000264932	NM_004168.2	482	cCt/cTt	11/15	1	2	FACETS	1	0.827	1	1	0.827	1	CLONAL	1	TRUE	1	0.201245545800343	2		130	149	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294043	1294043	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1368428332	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	73	831	0	ENST00000310581.5:c.958C>T	p.Pro320Ser	p.P320S	ENST00000310581	NM_198253.2	320	Cct/Tct	2/16	1	2	FACETS	0.728	0.635	0.829	0.728	0.635	0.829	SUBCLONAL	1	TRUE	1	0.201245545800343	2		831	996	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	91	573	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.201245545800343	2		573	771	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1296225	1296225	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	109	704	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.201245545800343	2		704	942	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064787	80064787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs931950562	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	26	348	0	ENST00000265081.6:c.2218C>T	p.Pro740Ser	p.P740S	ENST00000265081	NM_002439.4	740	Cct/Tct	15/24	1	2	FACETS	0.81	0.642	1	0.81	0.642	1	CLONAL	1	TRUE	1	0.201245545800343	2		348	319	SUCCESS
APC	324	MSKCC	GRCh37	5	112128185	112128185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779805	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	36	409	0	ENST00000257430.4:c.688C>T	p.Arg230Cys	p.R230C	ENST00000257430	NM_000038.5	230	Cgt/Tgt	7/16	1	2	FACETS	0.747	0.614	0.897	0.747	0.614	0.897	SUBCLONAL	1	TRUE	1	0.201245545800343	2		409	479	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512482	149512483	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	77	734	0	ENST00000261799.4:c.957_958delinsAA	p.Gly320Arg	p.G320R	ENST00000261799	NM_002609.3	319	ctGGga/ctAAga	7/23	1	2	FACETS	0.748	0.655	0.849	0.748	0.655	0.849	SUBCLONAL	1	TRUE	1	0.201245545800343	2		734	1023	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197373	26197373	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1437	207	969	0	ENST00000356476.2:c.106G>T	p.Val36Leu	p.V36L	ENST00000356476		36	Gtg/Ttg	1/1	0.170017793114517	4	FACETS	0.752	0.695	0.811	0.752	0.695	0.811	SUBCLONAL	2	TRUE	2	0.201245545800343	4		969	1644	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271495	26271495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1375	238	956	0	ENST00000305910.3:c.118C>T	p.His40Tyr	p.H40Y	ENST00000305910	NM_003534.2	40	Cat/Tat	1/1	0.170017793114517	4	FACETS	0.881	0.819	0.945	0.881	0.819	0.945	CLONAL	2	TRUE	2	0.201245545800343	4		956	1613	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120330	94120330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465849290	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	65	603	0	ENST00000369303.4:c.721G>A	p.Glu241Lys	p.E241K	ENST00000369303	NM_004440.3	241	Gaa/Aaa	3/17	1	2	FACETS	0.759	0.657	0.871	0.759	0.657	0.871	SUBCLONAL	1	TRUE	1	0.201245545800343	2		603	851	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983017	149983018	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	46	522	0	ENST00000253339.5:c.3240_3241delinsTT	p.Arg1081Ter	p.R1081*	ENST00000253339		1080	ttCCga/ttTTga	7/7	0.201245545800343	1	FACETS	0.877	0.739	1	0.877	0.739	1	CLONAL	1	TRUE	0	0.201245545800343	1		522	469	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959029	2959029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	94	619	0	ENST00000396946.4:c.2487G>A	p.Met829Ile	p.M829I	ENST00000396946	NM_032415.4	829	atG/atA	18/25	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.201245545800343	2		619	815	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509694	106509694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779178136	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	89	655	0	ENST00000359195.3:c.1688C>T	p.Pro563Leu	p.P563L	ENST00000359195	NM_002649.2	563	cCa/cTa	2/11	1	2	FACETS	0.962	0.852	1	0.962	0.852	1	CLONAL	1	TRUE	1	0.201245545800343	2		655	919	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902223	151902223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	32	252	0	ENST00000262189.6:c.3929C>T	p.Ser1310Phe	p.S1310F	ENST00000262189	NM_170606.2	1310	tCt/tTt	25/59	1	2	FACETS	1	0.824	1	1	0.824	1	CLONAL	1	TRUE	1	0.201245545800343	2		252	314	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538820	23538820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753524833	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	91	575	0	ENST00000380871.4:c.619C>T	p.Arg207Trp	p.R207W	ENST00000380871	NM_006167.3	207	Cgg/Tgg	2/2	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.201245545800343	2		575	760	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028073	69028073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	51	458	0	ENST00000288368.4:c.3232G>A	p.Gly1078Arg	p.G1078R	ENST00000288368	NM_024870.2	1078	Gga/Aga	26/40	1	2	FACETS	0.913	0.776	1	0.913	0.776	1	CLONAL	1	TRUE	1	0.201245545800343	2		458	555	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738434	145738434	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	110	819	0	ENST00000428558.2:c.2551C>T	p.Pro851Ser	p.P851S	ENST00000428558	NM_004260.3	851	Cca/Tca	16/22	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.201245545800343	2		819	977	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500779	8500780	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	82	594	0	ENST00000356435.5:c.2102_2103delinsTT	p.Ser701Phe	p.S701F	ENST00000356435		701	tCC/tTT	13/35	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.201245545800343	2		594	736	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971116	21971116	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	145	855	0	ENST00000304494.5:c.242C>A	p.Pro81His	p.P81H	ENST00000304494	NM_000077.4	81	cCc/cAc	2/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.201245545800343	2		855	1127	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570361	87570362	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	79	778	1	ENST00000277120.3:c.2101_2102delinsAA	p.Gly701Lys	p.G701K	ENST00000277120		701	GGg/AAg	17/19	1	2	FACETS	0.786	0.689	0.89	0.786	0.689	0.89	SUBCLONAL	1	TRUE	1	0.201245545800343	2		779	999	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212172	98212172	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	64	613	0	ENST00000331920.6:c.3500G>A	p.Gly1167Glu	p.G1167E	ENST00000331920	NM_000264.3	1167	gGg/gAg	21/24	1	2	FACETS	0.874	0.756	1	0.874	0.756	1	CLONAL	1	TRUE	1	0.201245545800343	2		613	728	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900288	101900288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111854391	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	86	480	0	ENST00000374994.4:c.722C>T	p.Ser241Leu	p.S241L	ENST00000374994	NM_004612.2	241	tCg/tTg	4/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.201245545800343	2		480	666	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396852	139396869	+	inframe_deletion	In_Frame_Del	DEL	GCAGCCCACGAAGAACAG	GCAGCCCACGAAGAACAG	-	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	77	611	0	ENST00000277541.6:c.5239_5256del	p.Leu1747_Cys1752del	p.L1747_C1752del	ENST00000277541	NM_017617.3	1747	CTGTTCTTCGTGGGCTGC/-	28/34	1	2	FACETS	0.96	0.842	1	0.96	0.842	1	CLONAL	1	TRUE	1	0.201245545800343	2		611	797	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400167	139400167	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329672903	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	95	779	0	ENST00000277541.6:c.4181G>A	p.Gly1394Asp	p.G1394D	ENST00000277541	NM_017617.3	1394	gGc/gAc	25/34	1	2	FACETS	0.882	0.784	0.988	0.882	0.784	0.988	CLONAL	1	TRUE	1	0.201245545800343	2		779	1070	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404272	139404274	+	frameshift_variant	Frame_Shift_Del	DEL	GTG	GTG	TA	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	109	801	1	ENST00000277541.6:c.2880_2882delinsTA	p.Thr961ArgfsTer218	p.T961Rfs*218	ENST00000277541	NM_017617.3	960	tgCACg/tgTAg	18/34	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.201245545800343	2		802	1041	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417542	139417542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	101	814	0	ENST00000277541.6:c.502C>T	p.Pro168Ser	p.P168S	ENST00000277541	NM_017617.3	168	Ccc/Tcc	4/34	1	2	FACETS	0.98	0.874	1	0.98	0.874	1	CLONAL	1	TRUE	1	0.201245545800343	2		814	1024	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417601	139417601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	81	741	0	ENST00000277541.6:c.443C>T	p.Pro148Leu	p.P148L	ENST00000277541	NM_017617.3	148	cCc/cTc	4/34	1	2	FACETS	0.855	0.752	0.967	0.855	0.752	0.967	CLONAL	1	TRUE	1	0.201245545800343	2		741	941	SUCCESS
AR	367	MSKCC	GRCh37	X	66765261	66765262	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	85	370	0	ENST00000374690.3:c.273_274delinsAA	p.Gly92Ser	p.G92S	ENST00000374690	NM_000044.3	91	caGGgt/caAAgt	1/8	1	1	FACETS	0.813	0.722	0.911	1	0.981	1	CLONAL	2	TRUE	0	0.201245545800343	1		370	467	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524477	187524477	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	70	569	0	ENST00000441802.2:c.11203C>T	p.Gln3735Ter	p.Q3735*	ENST00000441802	NM_005245.3	3735	Cag/Tag	19/27	1	2	FACETS	0.877	0.764	1	0.877	0.764	1	CLONAL	1	TRUE	1	0.201245545800343	2		569	793	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0059589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	322	688	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.661198736144715	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.661198736144715	1		688	611	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0059589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	97	323	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.661198736144715	3	FACETS	0.923	0.828	1	0.461	0.414	0.512	CLONAL	1	TRUE	1	0.661198736144715	3		323	423	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462644	29462644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745499366	NA	P-0059589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	330	564	0	ENST00000389048.3:c.2257C>T	p.Arg753Trp	p.R753W	ENST00000389048	NM_004304.4	753	Cgg/Tgg	13/29	0.661198736144715	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.661198736144715	1		564	627	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448324	56448325	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGAC	novel	NA	P-0059589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	343	522	0	ENST00000407977.2:c.319_322dup	p.Lys108SerfsTer18	p.K108Sfs*18	ENST00000407977		108	aag/aGTCAag	3/10	0.661198736144715	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.661198736144715	1		522	681	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989685	68989685	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	141	371	0	ENST00000288368.4:c.1623C>A	p.Asp541Glu	p.D541E	ENST00000288368	NM_024870.2	541	gaC/gaA	15/40	1	2	FACETS	0.923	0.848	1	0.923	0.848	1	CLONAL	1	TRUE	1	0.661198736144715	2		371	462	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798761	135798761	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059590-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	210	427	0	ENST00000298552.3:c.482T>A	p.Leu161Gln	p.L161Q	ENST00000298552	NM_001162426.1	161	cTg/cAg	6/23	0.499835899597466	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.499835899597466	2		427	366	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604640	43604640	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	36	705	0	ENST00000355710.3:c.1225T>G	p.Ser409Ala	p.S409A	ENST00000355710	NM_020975.4	409	Tcc/Gcc	6/20	0.566807232984047	3	FACETS	0.25	0.204	0.301	0.125	0.102	0.151	SUBCLONAL	1	TRUE	1	0.566807232984047	3		705	653	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845609	63845609	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	287	624	0	ENST00000279873.7:c.1351del	p.Ser451AlafsTer28	p.S451Afs*28	ENST00000279873	NM_032199.2	450	Aaa/aa	9/10	0.566807232984047	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.566807232984047	3		624	622	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0059591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	82	140	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	0.566807232984047	3	FACETS	0.872	0.797	0.945	0.872	0.797	0.945	CLONAL	3	TRUE	0	0.566807232984047	3		140	142	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	151	588	0	ENST00000397062.3:c.246A>T	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaT	2/5	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.566807232984047	2		588	480	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0059591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	107	546	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.808	0.729	0.892	0.808	0.729	0.892	CLONAL	1	TRUE	1	0.566807232984047	2		546	467	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461456	138461456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	96	394	0	ENST00000289153.2:c.565G>A	p.Glu189Lys	p.E189K	ENST00000289153	NM_006219.2	189	Gaa/Aaa	3/22	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.566807232984047	2		394	333	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589217	67589222	+	inframe_deletion	In_Frame_Del	DEL	TTGAAT	TTGAAT	-	novel	NA	P-0059591-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	56	416	0	ENST00000274335.5:c.1206_1211del	p.Glu403_Leu404del	p.E403_L404del	ENST00000274335		402	gTTGAATta/gta	9/15	1	2	FACETS	0.784	0.679	0.897	0.784	0.679	0.897	SUBCLONAL	1	TRUE	1	0.566807232984047	2		416	252	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0059595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	70	405	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.483719458235129	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.483719458235129	1		405	149	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061160	38061161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCGCCG	novel	NA	P-0059595-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	52	459	0	ENST00000250448.2:c.822_828dup	p.Gly277ArgfsTer18	p.G277Rfs*18	ENST00000250448	NM_004496.3	276	-/CGGCGGC	2/2	1	2	FACETS	0.973	0.838	1	0.973	0.838	1	CLONAL	1	TRUE	1	0.483719458235129	2		459	221	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059596-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	72	477	0				ENST00000310581	NM_198253.2	-/1132			0.577712355945582	3	FACETS	0.783	0.7	0.869	0.783	0.7	0.869	SUBCLONAL	2	TRUE	1	0.675575862461842	3		477	182	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0059596-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	342	929	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.589088898563505	4	FACETS	0.968	0.938	0.997	1	0.997	1	CLONAL	4	TRUE	2	0.675575862461842	4		929	438	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651906	36651906	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059596-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	181	462	0	ENST00000244741.5:c.28C>T	p.Gln10Ter	p.Q10*	ENST00000244741	NM_000389.4	10	Cag/Tag	2/3	0.577712355945582	3	FACETS	0.985	0.923	1	0.985	0.923	1	CLONAL	2	TRUE	1	0.675575862461842	3		462	364	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542861	187542861	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1340793072	NA	P-0059596-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	149	430	0	ENST00000441802.2:c.4879C>T	p.Arg1627Ter	p.R1627*	ENST00000441802	NM_005245.3	1627	Cga/Tga	10/27	0.589088898563505	4	FACETS	0.91	0.841	0.981	0.91	0.841	0.981	CLONAL	2	TRUE	2	0.675575862461842	4		430	406	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584769	187584769	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0059596-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	177	388	0	ENST00000441802.2:c.3266-2A>T		p.X1089_splice	ENST00000441802	NM_005245.3	1089			0.589088898563505	4	FACETS	0.965	0.898	1	0.965	0.898	1	CLONAL	2	TRUE	2	0.675575862461842	4		388	455	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2998140	2998140	+	start_lost	Translation_Start_Site	SNP	T	T	C	rs770444970	NA	P-0059596-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	72	383	0	ENST00000396946.4:c.1A>G	p.Met1?	p.M1?	ENST00000396946	NM_032415.4	1	Atg/Gtg	2/25	0.55081802671481	4	FACETS	1	0.932	1	0.543	0.478	0.612	CLONAL	1	TRUE	2	0.675575862461842	4		383	329	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	32	477	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.834	1	1	0.834	1	CLONAL	1	TRUE	1	0.64	2		477	100	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0059597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	52	323	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.64	2		323	161	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577518	7577518	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519995	NA	P-0059597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	54	396	0	ENST00000269305.4:c.763A>T	p.Ile255Phe	p.I255F	ENST00000269305	NM_001126112.2	255	Atc/Ttc	7/11	1	2	FACETS	0.541	0.465	0.623	0.541	0.465	0.623	SUBCLONAL	1	TRUE	1	0.64	2		396	312	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200943	108200943	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1555122944	NA	P-0059597-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	52	388	0	ENST00000278616.4:c.7310A>G	p.Tyr2437Cys	p.Y2437C	ENST00000278616	NM_000051.3	2437	tAc/tGc	50/63	1	2	FACETS	0.888	0.768	1	0.888	0.768	1	CLONAL	1	TRUE	1	0.64	2		388	183	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0059598-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	41	329	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.792	0.672	0.92	0.792	0.672	0.92	CLONAL	1	TRUE	1	0.708841012220966	2		329	146	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0059598-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	40	345	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.757	0.641	0.882	0.757	0.641	0.882	SUBCLONAL	1	TRUE	1	0.708841012220966	2		345	149	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604785	48604785	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059598-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	160	413	0	ENST00000342988.3:c.1607T>C	p.Leu536Pro	p.L536P	ENST00000342988	NM_005359.5	536	cTa/cCa	12/12	0.708841012220966	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.708841012220966	1		413	257	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877391	40877391	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372713520	NA	P-0059598-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	233	417	0	ENST00000373198.4:c.2305G>A	p.Val769Met	p.V769M	ENST00000373198	NM_133170.3	769	Gtg/Atg	15/32	0.708841012220966	3	FACETS	0.907	0.856	0.958	0.907	0.856	0.958	CLONAL	2	TRUE	1	0.708841012220966	3		417	491	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115681	108115681	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs876660933	NA	P-0059598-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	90	373	0	ENST00000278616.4:c.829G>T	p.Glu277Ter	p.E277*	ENST00000278616	NM_000051.3	277	Gaa/Taa	7/63	0.688241965621059	2	FACETS	0.819	0.752	0.885	0.819	0.752	0.885	CLONAL	2	TRUE	0	0.708841012220966	2		373	155	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266049	41266557	+	splice_donor_variant,splice_acceptor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	CCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCAT	CCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCAT	-	novel	NA	P-0059598-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	154	461	0	ENST00000349496.5:c.48_356del		p.X16_splice	ENST00000349496	NM_001904.3	16	CCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCAT/-	3-4/15	0.684624913583111	2	FACETS	1	0.99	1	0.712	0.664	0.76	CLONAL	1	TRUE	0	0.708841012220966	2		461	305	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0059599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	56	525	0				ENST00000310581	NM_198253.2	-/1132			0.0353222008119238	3	FACETS	0.882	0.767	1	0.882	0.767	1	INDETERMINATE	2	TRUE	1	0.377141312541479	3		525	200	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41905044	41905044	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059599-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	70	449	0	ENST00000372991.4:c.503T>A	p.Leu168His	p.L168H	ENST00000372991	NM_001760.3	168	cTc/cAc	3/5	0.377141312541479	1	FACETS	0.896	0.787	1	0.896	0.787	1	CLONAL	1	TRUE	0	0.377141312541479	1		449	336	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	173	477	0				ENST00000310581	NM_198253.2	-/1132			0.264082174890277	4	FACETS	1	0.981	1	0.791	0.731	0.854	CLONAL	2	TRUE	1	0.290683578688101	4		477	647	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363243	40363243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	45	762	0	ENST00000397332.2:c.986C>T	p.Ser329Leu	p.S329L	ENST00000397332	NM_001033082.2	329	tCg/tTg	3/3	1	2	FACETS	0.445	0.373	0.526	0.445	0.373	0.526	SUBCLONAL	1	TRUE	1	0.290683578688101	2		762	695	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73633525	73633554	+	inframe_deletion	In_Frame_Del	DEL	GCCGCAGGACGAGCCGGTGTTCGCGCAGCT	GCCGCAGGACGAGCCGGTGTTCGCGCAGCT	-	novel	NA	P-0059614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	62	434	0	ENST00000377687.4:c.60_89del	p.Pro21_Leu30del	p.P21_L30del	ENST00000377687	NM_001730.3	20	gcGCCGCAGGACGAGCCGGTGTTCGCGCAGCTc/gcc	1/4	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.290683578688101	2		434	409	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56882302	56882302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1327427054	NA	P-0059614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	59	540	0	ENST00000519728.1:c.1000G>A	p.Asp334Asn	p.D334N	ENST00000519728	NM_002350.3	334	Gat/Aat	10/13	1	2	FACETS	0.643	0.553	0.742	0.643	0.553	0.742	SUBCLONAL	1	TRUE	1	0.290683578688101	2		540	631	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056376	26056378	+	frameshift_variant	Frame_Shift_Del	DEL	ACC	ACC	G	novel	NA	P-0059614-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	40	635	0	ENST00000343677.2:c.279_281delinsC	p.Val94AlafsTer12	p.V94Afs*12	ENST00000343677	NM_005319.3	93	ctGGTg/ctCg	1/1	1	2	FACETS	0.355	0.294	0.424	0.355	0.294	0.424	SUBCLONAL	1	TRUE	1	0.290683578688101	2		635	775	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0059615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	100	344	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.43655220042557	4	FACETS	0.916	0.835	0.997	1	0.983	1	CLONAL	3	FALSE	2	0.475098302569822	4		344	226	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0059615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	27	381	1	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.449836246782455	3	FACETS	1	0.816	1	0.506	0.408	0.614	CLONAL	1	FALSE	1	0.475098302569822	3		382	139	SUCCESS
APC	324	MSKCC	GRCh37	5	112175761	112175761	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	64	535	1	ENST00000257430.4:c.4473del	p.Phe1491LeufsTer16	p.F1491Lfs*16	ENST00000257430	NM_000038.5	1490	caT/ca	16/16	0.395208406524547	4	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	FALSE	2	0.475098302569822	4		536	179	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555525585	NA	P-0059615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	142	513	0	ENST00000269305.4:c.673-2A>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.475098302569822	2	FACETS	0.902	0.847	0.954	1	0.99	1	CLONAL	3	FALSE	0	0.475098302569822	2		513	221	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508424	106508424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751449393	NA	P-0059615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	108	600	0	ENST00000359195.3:c.418C>T	p.Arg140Trp	p.R140W	ENST00000359195	NM_002649.2	140	Cgg/Tgg	2/11	0.475098302569822	6	FACETS	0.888	0.806	0.972	0.888	0.806	0.972	CLONAL	3	FALSE	3	0.475098302569822	6		600	333	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911575	114911575	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	101	530	0	ENST00000543371.1:c.1093A>G	p.Arg365Gly	p.R365G	ENST00000543371	NM_001198531.1	365	Aga/Gga	10/14	0.176189377054659	3	FACETS	1	0.974	1	0.787	0.718	0.855	INDETERMINATE	2	FALSE	0	0.475098302569822	3		530	223	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245373	153245373	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	46	306	0	ENST00000281708.4:c.1818G>T	p.Trp606Cys	p.W606C	ENST00000281708	NM_033632.3	606	tgG/tgT	11/12	0.449836246782455	3	FACETS	0.943	0.815	1	0.943	0.815	1	CLONAL	2	FALSE	1	0.475098302569822	3		306	127	SUCCESS
APC	324	MSKCC	GRCh37	5	112173645	112173645	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	TC	novel	NA	P-0059615-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	51	404	0	ENST00000257430.4:c.2354delinsTC	p.His785LeufsTer3	p.H785Lfs*3	ENST00000257430	NM_000038.5	785	cAt/cTCt	16/16	0.395208406524547	4	FACETS	1	0.89	1	1	0.89	1	CLONAL	2	FALSE	2	0.475098302569822	4		404	154	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	157	477	0				ENST00000310581	NM_198253.2	-/1132			0.348236196733815	3	FACETS	0.854	0.791	0.919	0.854	0.791	0.919	CLONAL	3	TRUE	0	0.348236196733815	3		477	413	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820936	3820936	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	126	388	0	ENST00000262367.5:c.2515C>T	p.Gln839Ter	p.Q839*	ENST00000262367	NM_004380.2	839	Cag/Tag	14/31	0.143439264046524	3	FACETS	0.9	0.82	0.983	0.9	0.82	0.983	INDETERMINATE	2	TRUE	1	0.348236196733815	3		388	472	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570468	39570468	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs267605182	NA	P-0059623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	14	244	0	ENST00000262039.4:c.664C>T	p.Arg222Ter	p.R222*	ENST00000262039	NM_002647.2	222	Cga/Tga	6/25	1	2	FACETS	0.345	0.249	0.461	0.345	0.249	0.461	SUBCLONAL	1	TRUE	1	0.348236196733815	2		244	233	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624450	21624451	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0059623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	42	405	0	ENST00000421138.2:c.1578dup	p.Leu527ThrfsTer14	p.L527Tfs*14	ENST00000421138		526	-/A	14/16	0.130550708795757	4	FACETS	0.593	0.495	0.703	0.297	0.247	0.352	INDETERMINATE	1	TRUE	2	0.348236196733815	4		405	548	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532651	63532651	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	44	468	0	ENST00000307078.5:c.1928C>G	p.Ala643Gly	p.A643G	ENST00000307078	NM_004655.3	643	gCc/gGc	8/11	0.199812399222534	5	FACETS	0.627	0.525	0.74	0.209	0.175	0.247	INDETERMINATE	1	TRUE	2	0.348236196733815	5		468	614	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097239	11097239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	101	450	1	ENST00000358026.2:c.730C>T	p.Pro244Ser	p.P244S	ENST00000358026	NM_001128849.1	244	Ccg/Tcg	4/36	0.143439264046524	3	FACETS	1	0.979	1	0.684	0.614	0.758	INDETERMINATE	1	TRUE	1	0.348236196733815	3		451	498	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349650	15349655	+	inframe_deletion	In_Frame_Del	DEL	GGCGGC	GGCGGC	-	novel	NA	P-0059623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	33	544	0	ENST00000263377.2:c.3919_3924del	p.Ala1307_Ala1308del	p.A1307_A1308del	ENST00000263377	NM_058243.2	1307	GCCGCC/-	19/20	0.143439264046524	3	FACETS	0.382	0.31	0.464	0.191	0.155	0.232	INDETERMINATE	1	TRUE	1	0.348236196733815	3		544	582	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144387298	144387298	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs765263787	NA	P-0059623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	28	335	0	ENST00000262995.4:c.1936A>G	p.Met646Val	p.M646V	ENST00000262995	NM_207123.2	646	Atg/Gtg	10/11	1	2	FACETS	0.353	0.281	0.434	0.353	0.281	0.434	SUBCLONAL	1	TRUE	1	0.348236196733815	2		335	456	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411251	63411251	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs779876963	NA	P-0059623-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	15	326	0	ENST00000330258.3:c.1916A>G	p.Gln639Arg	p.Q639R	ENST00000330258	NM_152424.3	639	cAa/cGa	2/2	1	1	FACETS	0.244	0.178	0.324	0.244	0.178	0.324	SUBCLONAL	1	TRUE	0	0.348236196733815	1		326	291	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162099	47162099	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	62	493	0	ENST00000409792.3:c.4027C>T	p.Gln1343Ter	p.Q1343*	ENST00000409792	NM_014159.6	1343	Caa/Taa	3/21	0.410614427680369	1	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	0	0.410614427680369	1		493	239	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718277	117718277	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1298952570	NA	P-0059624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	49	353	0	ENST00000368508.3:c.580C>T	p.Pro194Ser	p.P194S	ENST00000368508	NM_002944.2	194	Cct/Tct	7/43	1	2	FACETS	0.855	0.73	0.992	0.855	0.73	0.992	CLONAL	1	TRUE	1	0.410614427680369	2		353	279	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950413	68950413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	41	411	0	ENST00000288368.4:c.725C>T	p.Thr242Ile	p.T242I	ENST00000288368	NM_024870.2	242	aCc/aTc	7/40	1	2	FACETS	0.783	0.657	0.921	0.783	0.657	0.921	CLONAL	1	TRUE	1	0.410614427680369	2		411	255	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18943047	18943047	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	130	773	0	ENST00000262803.5:c.29C>G	p.Ser10Trp	p.S10W	ENST00000262803	NM_002911.3	10	tCg/tGg	1/24	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.410614427680369	2		773	573	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637679	52637679	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	46	352	0	ENST00000394830.3:c.2637del	p.Cys880AlafsTer35	p.C880Afs*35	ENST00000394830	NM_018313.4	879	ctC/ct	18/30	0.410614427680369	1	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	0	0.410614427680369	1		352	175	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934240	39934240	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059624-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	93	237	0	ENST00000378444.4:c.359del	p.Pro120GlnfsTer41	p.P120Qfs*41	ENST00000378444	NM_001123385.1	120	cCa/ca	4/15	1	1	FACETS	0.753	0.682	0.826	1	0.983	1	SUBCLONAL	2	TRUE	0	0.410614427680369	1		237	239	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0059625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	86	329	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.756249616664236	4	FACETS	0.941	0.85	1	0.941	0.85	1	CLONAL	2	FALSE	2	0.763664918984709	4		329	211	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578204	7578204	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520001	NA	P-0059625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	329	448	0	ENST00000269305.4:c.645T>G	p.Ser215Arg	p.S215R	ENST00000269305	NM_001126112.2	215	agT/agG	6/11	0.763664918984709	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	FALSE	0	0.763664918984709	2		448	420	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592122	67592122	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	223	295	0	ENST00000274335.5:c.1938T>G	p.Phe646Leu	p.F646L	ENST00000274335		646	ttT/ttG	14/15	0.763664918984709	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	FALSE	0	0.763664918984709	2		295	270	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438018	49438018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs111266743	NA	P-0059625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	285	446	0	ENST00000301067.7:c.5153C>T	p.Ala1718Val	p.A1718V	ENST00000301067	NM_003482.3	1718	gCg/gTg	21/54	0.756249616664236	4	FACETS	0.974	0.922	1	0.974	0.922	1	CLONAL	2	FALSE	2	0.763664918984709	4		446	676	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144049	11144051	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0059625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	115	461	0	ENST00000358026.2:c.3634_3636del	p.Glu1212del	p.E1212del	ENST00000358026	NM_001128849.1	1210	gtGGAg/gtg	26/36	0.756249616664236	4	FACETS	0.749	0.675	0.827	0.375	0.337	0.414	SUBCLONAL	1	FALSE	2	0.763664918984709	4		461	709	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6029461	6029461	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059625-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	92	203	0	ENST00000265849.7:c.1114del	p.Val372SerfsTer13	p.V372Sfs*13	ENST00000265849	NM_000535.5	372	Gtc/tc	10/15	0.358617347478952	5	FACETS	1	0.949	1	0.718	0.649	0.788	INDETERMINATE	2	FALSE	2	0.763664918984709	5		203	240	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0059625-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	61	329	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.240537893553813	4	FACETS	1	0.907	1			1	INDETERMINATE	2	TRUE	NA	0.507006017679881	4		329	175	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578204	7578204	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520001	NA	P-0059625-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	183	448	0	ENST00000269305.4:c.645T>G	p.Ser215Arg	p.S215R	ENST00000269305	NM_001126112.2	215	agT/agG	6/11	0.495050665980675	2	FACETS	0.889	0.831	0.947	0.889	0.831	0.947	CLONAL	2	TRUE	0	0.507006017679881	2		448	406	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592122	67592122	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059625-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	136	295	0	ENST00000274335.5:c.1938T>G	p.Phe646Leu	p.F646L	ENST00000274335		646	ttT/ttG	14/15	0.488377432892333	2	FACETS	0.897	0.83	0.965	0.897	0.83	0.965	CLONAL	2	TRUE	0	0.507006017679881	2		295	299	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438018	49438018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs111266743	NA	P-0059625-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	92	446	0	ENST00000301067.7:c.5153C>T	p.Ala1718Val	p.A1718V	ENST00000301067	NM_003482.3	1718	gCg/gTg	21/54	0.507006017679881	4	FACETS	0.935	0.832	1	0.312	0.277	0.348	CLONAL	1	TRUE	1	0.507006017679881	4		446	585	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923327	9923327	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059625-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	62	204	0	ENST00000330684.3:c.1960A>C	p.Ile654Leu	p.I654L	ENST00000330684	NM_001134407.1	654	Atc/Ctc	9/13	0.479387231650981	1	FACETS	0.956	0.841	1	0.956	0.841	1	CLONAL	1	TRUE	0	0.507006017679881	1		204	191	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0059626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	253	393	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.539825413915083	2	FACETS	0.913	0.864	0.961	0.913	0.864	0.961	CLONAL	2	TRUE	0	0.543428542002725	2		393	510	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932963	39932963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	292	295	0	ENST00000378444.4:c.1636C>T	p.Arg546Cys	p.R546C	ENST00000378444	NM_001123385.1	546	Cgc/Tgc	4/15	0.464523334878165	2	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.543428542002725	2		295	451	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659807	88659807	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691178	NA	P-0059626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	72	219	0	ENST00000372037.3:c.454C>T	p.Arg152Ter	p.R152*	ENST00000372037	NM_004329.2	152	Cga/Tga	7/13	0.543428542002725	3	FACETS	0.838	0.758	0.917	0.838	0.758	0.917	CLONAL	3	TRUE	0	0.543428542002725	3		219	134	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343311	118344234	+	inframe_deletion	In_Frame_Del	DEL	TAGTAGCCCCAGTGTTGATACCTCCACAGACTCTCAGGCTTCTGAGGAGATTCAGGTACTTCCTGAGGAGCGGAGCGATACCCCTGAAGTTCATCCTCCACTGCCCATTTCCCAGTCCCCAGAAAATGAGAGTAATGATAGGAGAAGCAGAAGGTATTCAGTGTCGGAGAGAAGTTTTGGATCTAGAACGACGAAAAAATTATCAACTCTACAAAGTGCCCCCCAGCAGCAGACCTCCTCGTCTCCACCTCCACCTCTGCTGACTCCACCGCCACCACTGCAGCCAGCCTCCAGTATCTCTGACCACACACCTTGGCTTATGCCTCCAACAATCCCCTTAGCATCACCATTTTTGCCTGCTTCCACTGCTCCTATGCAAGGGAAGCGAAAATCTATTTTGCGAGAACCGACATTTAGGTGGACTTCTTTAAAGCATTCTAGGTCAGAGCCACAATACTTTTCCTCAGCAAAGTATGCCAAAGAAGGTCTTATTCGCAAACCAATATTTGATAATTTCCGACCCCCTCCACTAACTCCCGAGGACGTTGGCTTTGCATCTGGTTTTTCTGCATCTGGTACCGCTGCTTCAGCCCGATTGTTTTCGCCACTCCATTCTGGAACAAGGTTTGATATGCACAAAAGGAGCCCTCTTCTGAGAGCTCCAAGATTTACTCCAAGTGAGGCTCACTCTAGAATATTTGAGTCTGTAACCTTGCCTAGTAATCGAACTTCTGCTGGAACATCTTCTTCAGGAGTATCCAATAGAAAAAGGAAAAGAAAAGTGTTTAGTCCTATTCGATCTGAACCAAGATCTCCTTCTCACTCCATGAGGACAAGAAGTGGAAGGCTTAGTAGTTCTGAGCTCTCACCTCTCACCCCCCCGTCTTCTGTCTCTTCCTCGTTAAGCATTTCTGTTAGTCCTCT	TAGTAGCCCCAGTGTTGATACCTCCACAGACTCTCAGGCTTCTGAGGAGATTCAGGTACTTCCTGAGGAGCGGAGCGATACCCCTGAAGTTCATCCTCCACTGCCCATTTCCCAGTCCCCAGAAAATGAGAGTAATGATAGGAGAAGCAGAAGGTATTCAGTGTCGGAGAGAAGTTTTGGATCTAGAACGACGAAAAAATTATCAACTCTACAAAGTGCCCCCCAGCAGCAGACCTCCTCGTCTCCACCTCCACCTCTGCTGACTCCACCGCCACCACTGCAGCCAGCCTCCAGTATCTCTGACCACACACCTTGGCTTATGCCTCCAACAATCCCCTTAGCATCACCATTTTTGCCTGCTTCCACTGCTCCTATGCAAGGGAAGCGAAAATCTATTTTGCGAGAACCGACATTTAGGTGGACTTCTTTAAAGCATTCTAGGTCAGAGCCACAATACTTTTCCTCAGCAAAGTATGCCAAAGAAGGTCTTATTCGCAAACCAATATTTGATAATTTCCGACCCCCTCCACTAACTCCCGAGGACGTTGGCTTTGCATCTGGTTTTTCTGCATCTGGTACCGCTGCTTCAGCCCGATTGTTTTCGCCACTCCATTCTGGAACAAGGTTTGATATGCACAAAAGGAGCCCTCTTCTGAGAGCTCCAAGATTTACTCCAAGTGAGGCTCACTCTAGAATATTTGAGTCTGTAACCTTGCCTAGTAATCGAACTTCTGCTGGAACATCTTCTTCAGGAGTATCCAATAGAAAAAGGAAAAGAAAAGTGTTTAGTCCTATTCGATCTGAACCAAGATCTCCTTCTCACTCCATGAGGACAAGAAGTGGAAGGCTTAGTAGTTCTGAGCTCTCACCTCTCACCCCCCCGTCTTCTGTCTCTTCCTCGTTAAGCATTTCTGTTAGTCCTCT	-	novel	NA	P-0059626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	84	455	0	ENST00000534358.1:c.1438_2361del	p.Ser480_Leu787del	p.S480_L787del	ENST00000534358	NM_005933.3	479	tcTAGTAGCCCCAGTGTTGATACCTCCACAGACTCTCAGGCTTCTGAGGAGATTCAGGTACTTCCTGAGGAGCGGAGCGATACCCCTGAAGTTCATCCTCCACTGCCCATTTCCCAGTCCCCAGAAAATGAGAGTAATGATAGGAGAAGCAGAAGGTATTCAGTGTCGGAGAGAAGTTTTGGATCTAGAACGACGAAAAAATTATCAACTCTACAAAGTGCCCCCCAGCAGCAGACCTCCTCGTCTCCACCTCCACCTCTGCTGACTCCACCGCCACCACTGCAGCCAGCCTCCAGTATCTCTGACCACACACCTTGGCTTATGCCTCCAACAATCCCCTTAGCATCACCATTTTTGCCTGCTTCCACTGCTCCTATGCAAGGGAAGCGAAAATCTATTTTGCGAGAACCGACATTTAGGTGGACTTCTTTAAAGCATTCTAGGTCAGAGCCACAATACTTTTCCTCAGCAAAGTATGCCAAAGAAGGTCTTATTCGCAAACCAATATTTGATAATTTCCGACCCCCTCCACTAACTCCCGAGGACGTTGGCTTTGCATCTGGTTTTTCTGCATCTGGTACCGCTGCTTCAGCCCGATTGTTTTCGCCACTCCATTCTGGAACAAGGTTTGATATGCACAAAAGGAGCCCTCTTCTGAGAGCTCCAAGATTTACTCCAAGTGAGGCTCACTCTAGAATATTTGAGTCTGTAACCTTGCCTAGTAATCGAACTTCTGCTGGAACATCTTCTTCAGGAGTATCCAATAGAAAAAGGAAAAGAAAAGTGTTTAGTCCTATTCGATCTGAACCAAGATCTCCTTCTCACTCCATGAGGACAAGAAGTGGAAGGCTTAGTAGTTCTGAGCTCTCACCTCTCACCCCCCCGTCTTCTGTCTCTTCCTCGTTAAGCATTTCTGTTAGTCCTCTt/tct	3/36	0.510655615109093	3	FACETS	0.674	0.596	0.758	0.225	0.198	0.253	SUBCLONAL	1	TRUE	0	0.543428542002725	3		455	583	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30047517	30047517	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	32	229	0	ENST00000331968.5:c.2484C>A	p.Tyr828Ter	p.Y828*	ENST00000331968	NM_002742.2	828	taC/taA	17/18	0.22430751479244	6	FACETS	1	0.93	1	0.436	0.357	0.523	INDETERMINATE	1	TRUE	3	0.543428542002725	6		229	188	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783788	50783788	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	140	396	0	ENST00000398568.2:c.179T>C	p.Ile60Thr	p.I60T	ENST00000398568	NM_001042412.1	60	aTt/aCt	3/18	0.543428542002725	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.543428542002725	3		396	286	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541563	29541563	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	19	128	0	ENST00000356175.3:c.1487T>G	p.Met496Arg	p.M496R	ENST00000356175	NM_000267.3	496	aTg/aGg	13/57	0.232982352948765	4	FACETS	1	0.899	1	0.666	0.517	0.832	INDETERMINATE	1	TRUE	2	0.543428542002725	4		128	81	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145537	61145537	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	36	228	0	ENST00000295025.8:c.649G>C	p.Glu217Gln	p.E217Q	ENST00000295025	NM_002908.2	217	Gaa/Caa	7/11	0.543428542002725	3	FACETS	0.648	0.536	0.773	0.324	0.268	0.387	SUBCLONAL	1	TRUE	1	0.543428542002725	3		228	260	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31435924	31435924	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs747793683	NA	P-0059626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	50	299	0	ENST00000344624.3:c.2990C>A	p.Ala997Glu	p.A997E	ENST00000344624		997	gCa/gAa	22/33	0.540343805260598	3	FACETS	0.711	0.606	0.825	0.356	0.303	0.413	SUBCLONAL	1	TRUE	1	0.543428542002725	3		299	329	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672857	86672857	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059626-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	65	328	0	ENST00000274376.6:c.2344G>T	p.Asp782Tyr	p.D782Y	ENST00000274376	NM_002890.2	782	Gat/Tat	17/25	0.512019671875456	2	FACETS	0.913	0.818	1	0.913	0.818	1	CLONAL	2	TRUE	0	0.543428542002725	2		328	131	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409950	63409950	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059627-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	109	447	1	ENST00000330258.3:c.3217C>A	p.Pro1073Thr	p.P1073T	ENST00000330258	NM_152424.3	1073	Cca/Aca	2/2	1	2	FACETS	0.598	0.54	0.659	0.598	0.54	0.659	SUBCLONAL	1	TRUE	1	0.799477374280246	2		448	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059628-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	132	355	0	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	0.208236210365935	2	FACETS	0.823	0.75	0.899	0.823	0.75	0.899	CLONAL	2	TRUE	0	0.272814756571899	2		355	588	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858337	9858337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560057284	NA	P-0059628-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	136	429	0	ENST00000330684.3:c.3064C>T	p.Arg1022Cys	p.R1022C	ENST00000330684	NM_001134407.1	1022	Cgc/Tgc	13/13	0.157978809812518	4	FACETS	0.845	0.769	0.924	0.845	0.769	0.924	INDETERMINATE	2	TRUE	2	0.272814756571899	4		429	751	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241894	72241894	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059628-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	42	292	0	ENST00000357731.5:c.496C>A	p.Pro166Thr	p.P166T	ENST00000357731	NM_173808.2	166	Cca/Aca	3/7	1	2	FACETS	0.804	0.673	0.949	0.804	0.673	0.949	CLONAL	1	TRUE	1	0.272814756571899	2		292	383	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992239	11992239	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0059628-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	95	300	0	ENST00000396373.4:c.328+1G>T		p.X110_splice	ENST00000396373	NM_001987.4	110			0.157978809812518	4	FACETS	0.81	0.723	0.902	0.81	0.723	0.902	INDETERMINATE	2	TRUE	2	0.272814756571899	4		300	547	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	92	477	0				ENST00000310581	NM_198253.2	-/1132			0.629123790635891	3	FACETS	0.712	0.635	0.795	0.356	0.317	0.398	SUBCLONAL	1	TRUE	1	0.646072435820238	3		477	529	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	237	615	0	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.646072435820238	2		615	734	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36824381	36824382	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACTGCACTAT	novel	NA	P-0059629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	146	507	0	ENST00000373129.3:c.145_154dup	p.Cys52TyrfsTer13	p.C52Yfs*13	ENST00000373129	NM_032017.1	52	tgt/tATAGTGCAGTgt	4/12	1	2	FACETS	0.781	0.716	0.848	0.781	0.716	0.848	SUBCLONAL	1	TRUE	1	0.646072435820238	2		507	579	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325228	39325228	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	177	600	0	ENST00000373001.3:c.91G>C	p.Glu31Gln	p.E31Q	ENST00000373001	NM_022157.3	31	Gag/Cag	1/7	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.646072435820238	2		600	537	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432620	78432620	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	92	359	0	ENST00000370768.2:c.363A>T	p.Glu121Asp	p.E121D	ENST00000370768	NM_003902.3	121	gaA/gaT	6/20	1	2	FACETS	0.863	0.775	0.955	0.863	0.775	0.955	CLONAL	1	TRUE	1	0.646072435820238	2		359	330	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115801	8115818	+	inframe_deletion	In_Frame_Del	DEL	GAGGACTTCCCCAAGAAC	GAGGACTTCCCCAAGAAC	-	novel	NA	P-0059629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	220	581	0	ENST00000346208.3:c.1147_1164del	p.Glu383_Asn388del	p.E383_N388del	ENST00000346208		383	GAGGACTTCCCCAAGAAC/-	6/6	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.646072435820238	2		581	680	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160489	108160489	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	14	278	0	ENST00000278616.4:c.4397G>C	p.Arg1466Pro	p.R1466P	ENST00000278616	NM_000051.3	1466	cGa/cCa	29/63	1	2	FACETS	0.113	0.081	0.153	0.113	0.081	0.153	SUBCLONAL	1	TRUE	1	0.646072435820238	2		278	382	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307522	118307540	+	frameshift_variant	Frame_Shift_Del	DEL	GCCTCTTCAGGGCCGGCCC	GCCTCTTCAGGGCCGGCCC	-	novel	NA	P-0059629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	157	528	0	ENST00000534358.1:c.295_313del	p.Ala99CysfsTer45	p.A99Cfs*45	ENST00000534358	NM_005933.3	99	GCCTCTTCAGGGCCGGCCCtg/tg	1/36	1	2	FACETS	0.996	0.919	1	0.996	0.919	1	CLONAL	1	TRUE	1	0.646072435820238	2		528	488	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649203	23649203	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	103	364	0	ENST00000261584.4:c.179A>T	p.Gln60Leu	p.Q60L	ENST00000261584	NM_024675.3	60	cAg/cTg	3/13	1	2	FACETS	0.781	0.704	0.862	0.781	0.704	0.862	SUBCLONAL	1	TRUE	1	0.646072435820238	2		364	408	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0059629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	338	487	0	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	0.646072435820238	3	FACETS	0.997	0.951	1	0.997	0.951	1	CLONAL	2	TRUE	1	0.646072435820238	3		487	694	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272384	15272384	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	238	644	0	ENST00000263388.2:c.6055G>T	p.Asp2019Tyr	p.D2019Y	ENST00000263388	NM_000435.2	2019	Gac/Tac	33/33	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.646072435820238	2		644	715	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281331	15281331	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751362166	NA	P-0059629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	208	715	0	ENST00000263388.2:c.4925C>T	p.Pro1642Leu	p.P1642L	ENST00000263388	NM_000435.2	1642	cCg/cTg	27/33	1	2	FACETS	0.989	0.923	1	0.989	0.923	1	CLONAL	1	TRUE	1	0.646072435820238	2		715	651	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871990	45871990	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	159	438	0	ENST00000391945.4:c.258G>C	p.Glu86Asp	p.E86D	ENST00000391945	NM_000400.3	86	gaG/gaC	5/23	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.646072435820238	2		438	463	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128018850	128018850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375990467	NA	P-0059629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	167	488	0	ENST00000285398.2:c.2018C>T	p.Ser673Leu	p.S673L	ENST00000285398	NM_000122.1	673	tCa/tTa	13/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.646072435820238	2		488	467	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46266509	46266509	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	94	306	0	ENST00000371998.3:c.2494C>T	p.Gln832Ter	p.Q832*	ENST00000371998		832	Caa/Taa	13/23	1	2	FACETS	0.98	0.883	1	0.98	0.883	1	CLONAL	1	TRUE	1	0.646072435820238	2		306	297	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21340139	21340139	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	149	381	0	ENST00000215739.8:c.273G>T	p.Met91Ile	p.M91I	ENST00000215739	NM_006767.3	91	atG/atT	3/21	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.646072435820238	2		381	447	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21349296	21349296	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	206	636	0	ENST00000215739.8:c.1923G>T	p.Leu641Phe	p.L641F	ENST00000215739	NM_006767.3	641	ttG/ttT	16/21	1	2	FACETS	0.977	0.911	1	0.977	0.911	1	CLONAL	1	TRUE	1	0.646072435820238	2		636	653	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442621	52442627	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCTGGG	GGCTGGG	C	novel	NA	P-0059629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	156	551	0	ENST00000460680.1:c.123-5_124delinsG		p.X41_splice	ENST00000460680	NM_004656.3	41		4/17	0.646072435820238	1	FACETS	0.854	0.792	0.916	0.854	0.792	0.916	CLONAL	1	TRUE	0	0.646072435820238	1		551	383	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63898847	63898847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	149	497	0	ENST00000398590.3:c.340G>A	p.Glu114Lys	p.E114K	ENST00000398590	NM_001177387.1	114	Gaa/Aaa	4/14	0.646072435820238	1	FACETS	0.805	0.744	0.867	0.805	0.744	0.867	CLONAL	1	TRUE	0	0.646072435820238	1		497	388	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665150	138665150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	152	504	0	ENST00000330315.3:c.415G>A	p.Glu139Lys	p.E139K	ENST00000330315	NM_023067.3	139	Gag/Aag	1/1	0.629123790635891	3	FACETS	1	0.962	1	0.54	0.496	0.586	CLONAL	1	TRUE	1	0.646072435820238	3		504	576	SUCCESS
ATR	545	MSKCC	GRCh37	3	142297500	142297500	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	103	367	0	ENST00000350721.4:c.47G>T	p.Arg16Leu	p.R16L	ENST00000350721	NM_001184.3	16	cGg/cTg	1/47	0.629123790635891	3	FACETS	0.944	0.85	1	0.472	0.425	0.522	CLONAL	1	TRUE	1	0.646072435820238	3		367	447	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542846	187542846	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	124	420	0	ENST00000441802.2:c.4894G>A	p.Glu1632Lys	p.E1632K	ENST00000441802	NM_005245.3	1632	Gag/Aag	10/27	1	2	FACETS	0.863	0.786	0.942	0.863	0.786	0.942	CLONAL	1	TRUE	1	0.646072435820238	2		420	445	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131976476	131976476	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	191	545	0	ENST00000265335.6:c.3731C>G	p.Ser1244Cys	p.S1244C	ENST00000265335		1244	tCt/tGt	24/25	0.646072435820238	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.646072435820238	1		545	361	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488390	20488390	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1243212211	NA	P-0059629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	143	490	0	ENST00000346618.3:c.1046A>G	p.Tyr349Cys	p.Y349C	ENST00000346618	NM_001949.4	349	tAc/tGc	6/7	1	2	FACETS	0.917	0.842	0.994	0.917	0.842	0.994	CLONAL	1	TRUE	1	0.646072435820238	2		490	483	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178706	32178706	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	160	444	0	ENST00000375023.3:c.2688C>G	p.Asp896Glu	p.D896E	ENST00000375023	NM_004557.3	896	gaC/gaG	18/30	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.646072435820238	2		444	485	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790830	89790830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	207	660	0	ENST00000336032.3:c.217C>T	p.Arg73Cys	p.R73C	ENST00000336032	NM_006813.2	73	Cgc/Tgc	1/2	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.646072435820238	2		660	637	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519191	137519191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	110	372	0	ENST00000367739.4:c.1447G>A	p.Glu483Lys	p.E483K	ENST00000367739	NM_000416.2	483	Gaa/Aaa	7/7	0.646072435820238	1	FACETS	0.93	0.852	1	0.93	0.852	1	CLONAL	1	TRUE	0	0.646072435820238	1		372	248	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849927	151849927	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	211	500	0	ENST00000262189.6:c.12389A>G	p.His4130Arg	p.H4130R	ENST00000262189	NM_170606.2	4130	cAc/cGc	49/59	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.646072435820238	2		500	631	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008888	152008888	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	121	347	0	ENST00000262189.6:c.734C>T	p.Ser245Phe	p.S245F	ENST00000262189	NM_170606.2	245	tCt/tTt	5/59	1	2	FACETS	0.956	0.871	1	0.956	0.871	1	CLONAL	1	TRUE	1	0.646072435820238	2		347	392	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635188	87635188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	175	457	1	ENST00000277120.3:c.2240C>T	p.Thr747Met	p.T747M	ENST00000277120		747	aCg/aTg	18/19	0.646072435820238	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.646072435820238	1		458	348	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197822	123197822	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	72	147	0	ENST00000218089.9:c.1946G>C	p.Arg649Thr	p.R649T	ENST00000218089	NM_001042749.1	649	aGa/aCa	20/35	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.646072435820238	1		147	110	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215311	123215311	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059629-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	91	125	0	ENST00000218089.9:c.2857C>T	p.Arg953Ter	p.R953*	ENST00000218089	NM_001042749.1	953	Cga/Tga	28/35	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.646072435820238	1		125	150	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	55	477	0				ENST00000310581	NM_198253.2	-/1132			0.245751938763928	3	FACETS	1	0.96	1	0.677	0.582	0.781	CLONAL	1	TRUE	1	0.245751938763928	3		477	371	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040642	16040642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	20	335	0	ENST00000268712.3:c.1492C>T	p.Arg498Cys	p.R498C	ENST00000268712	NM_006311.3	498	Cgc/Tgc	14/46	0.230515098433885	2	FACETS	0.684	0.524	0.87	0.342	0.262	0.435	SUBCLONAL	1	TRUE	0	0.245751938763928	2		335	238	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758858	41758858	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746561913	NA	P-0059630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	47	471	0	ENST00000301178.4:c.1912G>A	p.Gly638Arg	p.G638R	ENST00000301178	NM_021913.4	638	Ggg/Agg	16/20	0.245751938763928	5	FACETS	0.871	0.734	1	0.29	0.244	0.341	CLONAL	1	TRUE	2	0.245751938763928	5		471	601	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477806	140477806	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs180177039	NA	P-0059630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	54	306	0	ENST00000288602.6:c.1502A>T	p.Glu501Val	p.E501V	ENST00000288602	NM_004333.4	501	gAa/gTa	12/18	0.245751938763928	3	FACETS	0.842	0.724	0.969	0.842	0.724	0.969	CLONAL	2	TRUE	1	0.245751938763928	3		306	293	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913233	NA	P-0059630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	106	654	0	ENST00000451590.1:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000451590	NM_001130442.1	61	cAg/cTg	3/5	0.245751938763928	2	FACETS	1	0.983	1	0.749	0.673	0.829	CLONAL	1	TRUE	0	0.245751938763928	2		654	576	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176328	24176328	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059630-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	36	332	0	ENST00000263121.7:c.1119G>T	p.Arg373Ser	p.R373S	ENST00000263121	NM_003073.3	373	agG/agT	9/9	0.245751938763928	3	FACETS	0.866	0.713	1	0.433	0.356	0.519	CLONAL	1	TRUE	1	0.245751938763928	3		332	380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0059631-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	311	545	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.299310386316253	3	FACETS	1	0.988	1	0.756	0.717	0.796	CLONAL	2	TRUE	0	0.425241736921607	3		545	782	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467826	66467826	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059631-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	100	402	0	ENST00000273854.3:c.443A>C	p.Lys148Thr	p.K148T	ENST00000273854	NM_004439.5	148	aAg/aCg	3/18	0.40822116069398	1	FACETS	0.693	0.621	0.77	0.693	0.621	0.77	SUBCLONAL	1	TRUE	0	0.425241736921607	1		402	534	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332798	65332798	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059631-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	97	341	0	ENST00000342505.4:c.741C>A	p.Phe247Leu	p.F247L	ENST00000342505	NM_002227.2	247	ttC/ttA	7/25	1	2	FACETS	0.753	0.672	0.838	0.753	0.672	0.838	SUBCLONAL	1	TRUE	1	0.425241736921607	2		341	606	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342847	118342847	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs781840795	NA	P-0059631-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	108	449	0	ENST00000534358.1:c.973G>C	p.Glu325Gln	p.E325Q	ENST00000534358	NM_005933.3	325	Gaa/Caa	3/36	NA	2	FACETS	0.894	0.805	0.988			1	INDETERMINATE	1	TRUE	NA	0.425241736921607	2		449	568	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914979	32914979	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398122559	NA	P-0059631-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	89	326	0	ENST00000380152.3:c.6487C>T	p.Gln2163Ter	p.Q2163*	ENST00000380152		2163	Caa/Taa	11/27	0.40822116069398	1	FACETS	0.808	0.721	0.9	0.808	0.721	0.9	CLONAL	1	TRUE	0	0.425241736921607	1		326	408	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892166	9892166	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059631-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	115	432	0	ENST00000330684.3:c.2324T>C	p.Ile775Thr	p.I775T	ENST00000330684	NM_001134407.1	775	aTc/aCc	11/13	0.40822116069398	1	FACETS	0.928	0.841	1	0.928	0.841	1	CLONAL	1	TRUE	0	0.425241736921607	1		432	459	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562635	29562638	+	frameshift_variant	Frame_Shift_Del	DEL	CTAG	CTAG	-	novel	NA	P-0059631-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	83	299	0	ENST00000356175.3:c.3717_3720del	p.Ala1240GlufsTer25	p.A1240Efs*25	ENST00000356175	NM_000267.3	1239	CTAGct/ct	28/57	0.40822116069398	1	FACETS	0.899	0.8	1	0.899	0.8	1	CLONAL	1	TRUE	0	0.425241736921607	1		299	342	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0059632-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	91	344	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.176699379392672	5	FACETS	1	0.953	1	0.74	0.664	0.82	INDETERMINATE	2	TRUE	2	0.403483852436081	5		344	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0059632-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	168	341	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.403483852436081	2	FACETS	0.991	0.922	1	0.991	0.922	1	CLONAL	2	TRUE	0	0.403483852436081	2		341	420	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0059632-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	166	355	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	0.403483852436081	2	FACETS	0.975	0.906	1	0.975	0.906	1	CLONAL	2	TRUE	0	0.403483852436081	2		355	422	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16235970	16235970	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059632-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	116	270	0	ENST00000375759.3:c.1036T>C	p.Ser346Pro	p.S346P	ENST00000375759	NM_015001.2	346	Tct/Cct	4/15	0.291820974884989	3	FACETS	0.862	0.783	0.943	0.862	0.783	0.943	CLONAL	2	TRUE	1	0.403483852436081	3		270	401	SUCCESS
APC	324	MSKCC	GRCh37	5	112173572	112173573	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0059632-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	40	314	0	ENST00000257430.4:c.2282_2283dup	p.Ala762LysfsTer4	p.A762Kfs*4	ENST00000257430	NM_000038.5	761	gaa/gAAaa	16/16	0.403483852436081	2	FACETS	0.565	0.47	0.669	0.282	0.235	0.335	SUBCLONAL	1	TRUE	0	0.403483852436081	2		314	351	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157406027	157406028	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0059632-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	166	327	0	ENST00000346085.5:c.2270dup	p.Ser758LysfsTer5	p.S758Kfs*5	ENST00000346085	NM_020732.3	757	gca/gCca	6/20	0.403483852436081	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	2	TRUE	0	0.403483852436081	2		327	410	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964482	70964482	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059632-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	113	373	0	ENST00000276594.2:c.1546C>A	p.Pro516Thr	p.P516T	ENST00000276594	NM_024504.3	516	Ccc/Acc	8/8	0.403483852436081	3	FACETS	0.962	0.866	1	0.481	0.433	0.531	CLONAL	1	TRUE	1	0.403483852436081	3		373	700	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	87	477	0				ENST00000310581	NM_198253.2	-/1132			0.165398458554973	3	FACETS	0.87	0.775	0.971	1	0.972	1	CLONAL	3	TRUE	1	0.170172119559184	3		477	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0059633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	88	351	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.160361967503136	2	FACETS	0.876	0.778	0.982	0.876	0.778	0.982	CLONAL	2	TRUE	0	0.170172119559184	2		351	590	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874034	123874034	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs186822980	NA	P-0059633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	188	406	0	ENST00000330479.4:c.65T>C	p.Val22Ala	p.V22A	ENST00000330479	NM_020382.3	22	gTg/gCg	2/9	0.113845643098351	4	FACETS	1	0.971	1	1	0.992	1	CLONAL	3	TRUE	2	0.170172119559184	4		406	788	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0059637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	77	329	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.465973822313953	3	FACETS	0.882	0.777	0.994	0.441	0.388	0.497	CLONAL	1	TRUE	1	0.466140916330746	3		329	462	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0059637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	239	668	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	0.955	0.891	1	0.955	0.891	1	CLONAL	1	TRUE	1	0.466140916330746	2		668	1074	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0059637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	234	628	2	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.466140916330746	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.466140916330746	1		630	735	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812331	212812331	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059638-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	75	414	0	ENST00000342788.4:c.245A>T	p.Glu82Val	p.E82V	ENST00000342788	NM_005235.2	82	gAa/gTa	3/28	1	2	FACETS	0.37	0.325	0.418	0.37	0.325	0.418	SUBCLONAL	1	TRUE	1	0.873636394170452	2		414	464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0059639-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	46	513	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	1	2	FACETS	0.728	0.612	0.858	0.728	0.612	0.858	SUBCLONAL	1	TRUE	1	0.17	2		513	743	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs869025608	NA	P-0059639-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	50	351	0	ENST00000307102.5:c.171G>C	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaC	2/11	1	2	FACETS	0.831	0.704	0.971	0.831	0.704	0.971	CLONAL	1	TRUE	1	0.17	2		351	708	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645974	215645975	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs587780033	NA	P-0059639-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	28	423	0	ENST00000260947.4:c.623dup	p.Lys209GlufsTer5	p.K209Efs*5	ENST00000260947	NM_000465.2	208	aag/aaAg	4/11	1	2	FACETS	0.658	0.524	0.81	0.658	0.524	0.81	SUBCLONAL	1	TRUE	1	0.17	2		423	501	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037144	71037144	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0059639-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	53	369	0	ENST00000318789.4:c.1146+1G>A		p.X382_splice	ENST00000318789	NM_032682.5	382			1	2	FACETS	0.784	0.667	0.913	0.784	0.667	0.913	CLONAL	1	TRUE	1	0.17	2		369	795	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448494	49448494	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059639-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	73	482	0	ENST00000301067.7:c.217G>T	p.Glu73Ter	p.E73*	ENST00000301067	NM_003482.3	73	Gag/Tag	3/54	1	2	FACETS	0.967	0.844	1	0.967	0.844	1	CLONAL	1	TRUE	1	0.17	2		482	888	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209381	133209381	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1247397969	NA	P-0059640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	141	539	0	ENST00000320574.5:c.6005C>T	p.Ala2002Val	p.A2002V	ENST00000320574	NM_006231.2	2002	gCg/gTg	44/49	0.274856016799879	3	FACETS	0.905	0.829	0.983	0.905	0.829	0.983	CLONAL	2	TRUE	1	0.351734491302294	3		539	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576887	7576891	+	stop_gained	Nonsense_Mutation	ONP	TTCTT	TTCTT	CTCTA	novel	NA	P-0059640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	302	633	0	ENST00000269305.4:c.955_959delinsTAGAG	p.Lys319_Lys320delinsTer	p.K319_K320delins*	ENST00000269305	NM_001126112.2	319	AAGAAg/TAGAGg	9/11	0.351734491302294	3	FACETS	0.928	0.88	0.977	0.928	0.88	0.977	CLONAL	3	TRUE	0	0.351734491302294	3		633	725	SUCCESS
APC	324	MSKCC	GRCh37	5	112175235	112175235	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	222	437	0	ENST00000257430.4:c.3944C>A	p.Ser1315Ter	p.S1315*	ENST00000257430	NM_000038.5	1315	tCa/tAa	16/16	0.351734491302294	3	FACETS	0.846	0.793	0.899	0.846	0.793	0.899	CLONAL	3	TRUE	0	0.351734491302294	3		437	585	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0059641-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	175	582	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.969	0.895	1	0.969	0.895	1	CLONAL	1	TRUE	1	0.504395546760434	2		582	716	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0059641-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	211	565	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.504395546760434	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.504395546760434	1		565	591	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310820	123310820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747502397	NA	P-0059641-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	175	473	0	ENST00000358487.5:c.608G>A	p.Arg203His	p.R203H	ENST00000358487	NM_000141.4	203	cGc/cAc	5/18	1	2	FACETS	0.993	0.917	1	0.993	0.917	1	CLONAL	1	TRUE	1	0.504395546760434	2		473	699	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022802	31022802	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059641-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	789	608	0	ENST00000375687.4:c.2290del	p.Leu764TyrfsTer8	p.L764Yfs*8	ENST00000375687	NM_015338.5	763	Ccc/cc	13/13	0.504395546760434	6	FACETS	0.953	0.924	0.983	0.953	0.924	0.983	CLONAL	4	TRUE	2	0.504395546760434	6		608	1648	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650368	48650368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782208453	NA	P-0059641-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	177	676	0	ENST00000376670.3:c.338G>A	p.Arg113His	p.R113H	ENST00000376670	NM_002049.3	113	cGc/cAc	3/6	0.504395546760434	3	FACETS	0.813	0.748	0.881	0.406	0.374	0.441	CLONAL	1	TRUE	1	0.504395546760434	3		676	1081	SUCCESS
APC	324	MSKCC	GRCh37	5	112175398	112175399	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0059641-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	175	545	0	ENST00000257430.4:c.4111dup	p.Ser1371LysfsTer4	p.S1371Kfs*4	ENST00000257430	NM_000038.5	1369	-/A	16/16	0.504395546760434	1	FACETS	0.996	0.924	1	0.996	0.924	1	CLONAL	1	TRUE	0	0.504395546760434	1		545	521	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380282	25380282	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059641-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	160	443	0	ENST00000311936.3:c.176C>G	p.Ala59Gly	p.A59G	ENST00000311936	NM_004985.3	59	gCa/gGa	3/5	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.504395546760434	2		443	625	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0059642-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	161	472	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.620860244798018	2		472	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0059642-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	382	593	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.620860244798018	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.620860244798018	3		593	743	SUCCESS
APC	324	MSKCC	GRCh37	5	112175724	112175724	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059642-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	185	593	0	ENST00000257430.4:c.4435del	p.Val1479SerfsTer28	p.V1479Sfs*28	ENST00000257430	NM_000038.5	1478	aGg/ag	16/16	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.620860244798018	2		593	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0059643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	152	720	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.323683131694701	2	FACETS	0.815	0.749	0.884	0.815	0.749	0.884	CLONAL	2	TRUE	0	0.323683131694701	2		720	576	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190656564	190656564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370084230	NA	P-0059643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	78	389	0	ENST00000441310.2:c.29G>A	p.Arg10Gln	p.R10Q	ENST00000441310	NM_000534.4	10	cGa/cAa	2/13	0.198536717357403	5	FACETS	1	0.933	1	0.364	0.319	0.411	CLONAL	1	TRUE	2	0.323683131694701	5		389	656	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47503913	47503913	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	204	505	0	ENST00000404338.3:c.4470del	p.Ser1491ProfsTer308	p.S1491Pfs*308	ENST00000404338	NM_004491.4	1490	Ccc/cc	6/6	0.211094914671986	3	FACETS	0.855	0.799	0.912	1	0.989	1	CLONAL	3	TRUE	1	0.323683131694701	3		505	571	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425389	47425399	+	frameshift_variant	Frame_Shift_Del	DEL	AGCAAGCCAGT	AGCAAGCCAGT	G	novel	NA	P-0059643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	97	644	0	ENST00000404338.3:c.3457_3467delinsG	p.Ser1153GlyfsTer67	p.S1153Gfs*67	ENST00000404338	NM_004491.4	1153	AGCAAGCCAGTg/Gg	1/6	0.211094914671986	3	FACETS	1	0.927	1	0.525	0.468	0.585	CLONAL	1	TRUE	1	0.323683131694701	3		644	663	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747342068	NA	P-0059644-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	630	541	0	ENST00000269305.4:c.394A>G	p.Lys132Glu	p.K132E	ENST00000269305	NM_001126112.2	132	Aag/Gag	5/11	0.496538231036113	3	FACETS	0.995	0.965	1	0.995	0.965	1	CLONAL	3	TRUE	0	0.506170981102181	3		541	1045	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851717	134851717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150028142	NA	P-0059644-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	79	589	0	ENST00000398015.3:c.1123G>A	p.Asp375Asn	p.D375N	ENST00000398015	NM_004441.4	375	Gac/Aac	5/16	0.326599759166218	1	FACETS	0.415	0.365	0.468	0.415	0.365	0.468	SUBCLONAL	1	TRUE	0	0.506170981102181	1		589	562	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468364	89468364	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059644-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	41	386	0	ENST00000336596.2:c.1898G>T	p.Gly633Val	p.G633V	ENST00000336596	NM_005233.5	633	gGa/gTa	11/17	0.326599759166218	1	FACETS	0.346	0.288	0.409	0.346	0.288	0.409	SUBCLONAL	1	TRUE	0	0.506170981102181	1		386	350	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495199	212495199	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059644-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	41	415	0	ENST00000342788.4:c.2067C>A	p.Phe689Leu	p.F689L	ENST00000342788	NM_005235.2	689	ttC/ttA	17/28	0.338172905065582	1	FACETS	0.324	0.27	0.384	0.324	0.27	0.384	SUBCLONAL	1	TRUE	0	0.506170981102181	1		415	373	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852772	63852772	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059644-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	47	417	0	ENST00000279873.7:c.3550C>T	p.Pro1184Ser	p.P1184S	ENST00000279873	NM_032199.2	1184	Ccc/Tcc	10/10	1	2	FACETS	0.25	0.21	0.294	0.25	0.21	0.294	SUBCLONAL	1	TRUE	1	0.506170981102181	2		417	743	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029514	16029514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059644-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	274	453	0	ENST00000268712.3:c.1516G>A	p.Ala506Thr	p.A506T	ENST00000268712	NM_006311.3	506	Gct/Act	15/46	0.506170981102181	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.506170981102181	2		453	511	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400106	41400106	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059644-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	336	432	0	ENST00000373198.4:c.653A>C	p.Lys218Thr	p.K218T	ENST00000373198	NM_133170.3	218	aAg/aCg	5/32	0.409946181180648	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.506170981102181	3		432	778	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098804	47098804	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059644-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	220	617	0	ENST00000409792.3:c.6470A>G	p.Tyr2157Cys	p.Y2157C	ENST00000409792	NM_014159.6	2157	tAt/tGt	15/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.506170981102181	2		617	812	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155665	106155665	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059644-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	49	517	0	ENST00000380013.4:c.566G>T	p.Ser189Ile	p.S189I	ENST00000380013	NM_001127208.2	189	aGt/aTt	3/11	0.474112312630532	2	FACETS	0.298	0.252	0.349	0.149	0.126	0.175	SUBCLONAL	1	TRUE	0	0.506170981102181	2		517	650	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545713	106545713	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059644-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	32	469	0	ENST00000359195.3:c.3190G>T	p.Ala1064Ser	p.A1064S	ENST00000359195	NM_002649.2	1064	Gct/Tct	11/11	1	2	FACETS	0.245	0.198	0.298	0.245	0.198	0.298	SUBCLONAL	1	TRUE	1	0.506170981102181	2		469	516	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249870	110249870	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059644-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	371	576	0	ENST00000374672.4:c.805G>T	p.Gly269Trp	p.G269W	ENST00000374672	NM_004235.4	269	Ggg/Tgg	3/5	0.40415730915074	2	FACETS	0.948	0.906	0.991	0.948	0.906	0.991	CLONAL	2	TRUE	0	0.506170981102181	2		576	773	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411135	63411135	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059644-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	57	289	0	ENST00000330258.3:c.2032C>T	p.His678Tyr	p.H678Y	ENST00000330258	NM_152424.3	678	Cac/Tac	2/2	0.439658125455217	2	FACETS	0.429	0.368	0.495			1	SUBCLONAL	1	TRUE	NA	0.506170981102181	2		289	525	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0059645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	85	399	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.261709234389195	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.261709234389195	1		399	504	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	37	174	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	0.672	0.554	0.803	0.672	0.554	0.803	SUBCLONAL	1	TRUE	1	0.261709234389195	2		174	421	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	53	121	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.869	0.742	1	0.869	0.742	1	CLONAL	1	TRUE	1	0.261709234389195	2		121	466	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0059645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	83	516	0	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	1	2	FACETS	0.985	0.87	1	0.985	0.87	1	CLONAL	1	TRUE	1	0.261709234389195	2		516	644	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0059645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	77	369	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.261709234389195	2		369	505	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604655	48604655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	75	520	0	ENST00000342988.3:c.1477G>A	p.Asp493Asn	p.D493N	ENST00000342988	NM_005359.5	493	Gat/Aat	12/12	0.261709234389195	1	FACETS	0.832	0.729	0.942	0.832	0.729	0.942	CLONAL	1	TRUE	0	0.261709234389195	1		520	599	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251882	153251882	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0059645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	60	279	0	ENST00000281708.4:c.1122+2T>C		p.X374_splice	ENST00000281708	NM_033632.3	374			1	2	FACETS	0.953	0.823	1	0.953	0.823	1	CLONAL	1	TRUE	1	0.261709234389195	2		279	481	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0059646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	108	688	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.265248780023779	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.307941145080517	1		688	544	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	39	121	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.718	0.596	0.852	0.718	0.596	0.852	SUBCLONAL	1	TRUE	1	0.307941145080517	2		121	353	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	144	477	0				ENST00000310581	NM_198253.2	-/1132			0.47132460436671	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	0	0.469608879828365	2		477	303	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866444	37866444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	235	795	0	ENST00000269571.5:c.749C>T	p.Ser250Phe	p.S250F	ENST00000269571		250	tCt/tTt	6/27	0.465406183301371	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.469608879828365	2		795	480	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0059647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	213	658	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.465406183301371	2	FACETS	0.982	0.923	1	0.982	0.923	1	CLONAL	2	TRUE	0	0.469608879828365	2		658	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0059647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	292	596	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.24126616933088	3	FACETS	0.843	0.801	0.886			1	INDETERMINATE	3	TRUE	NA	0.469608879828365	3		596	607	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480320	56480320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	138	480	0	ENST00000267101.3:c.427C>A	p.Leu143Met	p.L143M	ENST00000267101	NM_001982.3	143	Ctg/Atg	4/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.469608879828365	2		480	494	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947585	48947585	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0059647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	58	132	0	ENST00000267163.4:c.1172C>G	p.Ser391Ter	p.S391*	ENST00000267163	NM_000321.2	391	tCa/tGa	12/27	0.47132460436671	2	FACETS	0.758	0.665	0.854	0.758	0.665	0.854	SUBCLONAL	2	TRUE	0	0.469608879828365	2		132	163	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4102403	4102403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457335620	NA	P-0059647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	90	693	2	ENST00000262948.5:c.499G>A	p.Glu167Lys	p.E167K	ENST00000262948	NM_030662.3	167	Gag/Aag	4/11	1	2	FACETS	0.852	0.759	0.949	0.852	0.759	0.949	CLONAL	1	TRUE	1	0.469608879828365	2		695	450	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004984	150004984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	154	555	0	ENST00000253339.5:c.1241G>A	p.Arg414Lys	p.R414K	ENST00000253339		414	aGa/aAa	3/7	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.469608879828365	2		555	581	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023249	27023249	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	130	599	0	ENST00000324856.7:c.355G>T	p.Glu119Ter	p.E119*	ENST00000324856	NM_006015.4	119	Gag/Tag	1/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.469608879828365	2		599	405	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27016077	27016077	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194974108	NA	P-0059647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	112	543	0	ENST00000335756.4:c.353G>A	p.Arg118Gln	p.R118Q	ENST00000335756	NM_001809.3	118	cGa/cAa	4/5	0.398933796810914	3	FACETS	1	0.947	1	0.536	0.484	0.591	CLONAL	1	TRUE	1	0.469608879828365	3		543	549	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319959	8319959	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	226	436	0	ENST00000356435.5:c.5542G>T	p.Val1848Phe	p.V1848F	ENST00000356435		1848	Gtt/Ttt	34/35	0.398933796810914	3	FACETS	0.904	0.847	0.963	0.904	0.847	0.963	CLONAL	2	TRUE	1	0.469608879828365	3		436	657	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420121	49420121	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	146	715	1	ENST00000301067.7:c.15628T>A	p.Tyr5210Asn	p.Y5210N	ENST00000301067	NM_003482.3	5210	Tac/Aac	48/54	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.469608879828365	2		716	555	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123880918	123880918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148212570	NA	P-0059647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	109	493	0	ENST00000330479.4:c.536G>A	p.Arg179His	p.R179H	ENST00000330479	NM_020382.3	179	cGc/cAc	5/9	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.469608879828365	2		493	436	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37863384	37863384	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	256	848	0	ENST00000269571.5:c.215C>A	p.Ser72Tyr	p.S72Y	ENST00000269571		72	tCc/tAc	2/27	0.465406183301371	2	FACETS	0.991	0.937	1	0.991	0.937	1	CLONAL	2	TRUE	0	0.469608879828365	2		848	550	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289332	33289332	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	106	496	0	ENST00000374542.5:c.220T>C	p.Cys74Arg	p.C74R	ENST00000374542	NM_001141970.1	74	Tgt/Cgt	3/8	1	2	FACETS	0.981	0.885	1	0.981	0.885	1	CLONAL	1	TRUE	1	0.469608879828365	2		496	460	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346870	70346870	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1221964452	NA	P-0059647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	77	573	0	ENST00000374080.3:c.2737G>T	p.Asp913Tyr	p.D913Y	ENST00000374080		913	Gat/Tat	20/45	1	2	FACETS	0.682	0.6	0.769	0.682	0.6	0.769	SUBCLONAL	1	TRUE	1	0.469608879828365	2		573	481	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0059648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	144	323	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.396571209186161	3	FACETS	0.963	0.889	1	0.963	0.889	1	CLONAL	2	TRUE	1	0.498310516202079	3		323	375	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0059648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	288	600	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.498310516202079	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.498310516202079	1		600	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0059648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	240	503	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.498310516202079	2	FACETS	0.923	0.871	0.975	0.923	0.871	0.975	CLONAL	2	TRUE	0	0.498310516202079	2		503	522	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0059648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	165	383	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	0.497434181057083	3	FACETS	0.905	0.839	0.973	0.905	0.839	0.973	CLONAL	2	TRUE	1	0.498310516202079	3		383	457	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877366	28877366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1392528455	NA	P-0059648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	563	432	0	ENST00000282397.4:c.3955G>A	p.Ala1319Thr	p.A1319T	ENST00000282397	NM_002019.4	1319	Gcg/Acg	30/30	0.498310516202079	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	1	0.498310516202079	4		432	1009	SUCCESS
AR	367	MSKCC	GRCh37	X	66766106	66766106	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	204	651	0	ENST00000374690.3:c.1118G>T	p.Gly373Val	p.G373V	ENST00000374690	NM_000044.3	373	gGa/gTa	1/8	0.25053632320687	3	FACETS	1	0.989	1	0.66	0.613	0.708	INDETERMINATE	1	TRUE	1	0.498310516202079	3		651	775	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043387	180043387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760757893	NA	P-0059648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	59	620	0	ENST00000261937.6:c.3199G>A	p.Asp1067Asn	p.D1067N	ENST00000261937	NM_182925.4	1067	Gac/Aac	23/30	0.498310516202079	1	FACETS	0.294	0.252	0.339	0.294	0.252	0.339	SUBCLONAL	1	TRUE	0	0.498310516202079	1		620	605	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620114	21620114	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	560	495	0	ENST00000382592.4:c.52C>T	p.Arg18Ter	p.R18*	ENST00000382592	NM_014572.2	18	Cga/Tga	2/8	0.498310516202079	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	1	0.498310516202079	4		495	973	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	166	121	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.537690883553455	6	FACETS	0.932	0.865	1	0.699	0.649	0.751	CLONAL	3	TRUE	2	0.57745067452201	6		121	443	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0059649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	149	747	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	0.57745067452201	3	FACETS	0.991	0.908	1	0.496	0.454	0.539	CLONAL	1	TRUE	1	0.57745067452201	3		747	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0059649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	202	407	0	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	0.57745067452201	3	FACETS	0.905	0.847	0.964	0.905	0.847	0.964	CLONAL	2	TRUE	1	0.57745067452201	3		407	498	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576887	7576891	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTT	TTCTT	-	novel	NA	P-0059649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	150	793	0	ENST00000269305.4:c.955_959del	p.Lys319GlufsTer16	p.K319Efs*16	ENST00000269305	NM_001126112.2	319	AAGAAg/g	9/11	0.57745067452201	3	FACETS	1	0.935	1	0.512	0.469	0.556	CLONAL	1	TRUE	1	0.57745067452201	3		793	654	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262102	10262102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	298	783	1	ENST00000340748.4:c.2189G>A	p.Arg730His	p.R730H	ENST00000340748		730	cGc/cAc	23/40	0.57745067452201	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.57745067452201	3		784	625	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624271	89624272	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs786204883	NA	P-0059649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	64	271	0	ENST00000371953.3:c.46dup	p.Tyr16LeufsTer28	p.Y16Lfs*28	ENST00000371953	NM_000314.4	15	-/T	1/9	0.57745067452201	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.57745067452201	1		271	152	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215951	41215951	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	114	497	0	ENST00000357654.3:c.5092del	p.Glu1698AsnfsTer4	p.E1698Nfs*4	ENST00000357654	NM_007294.3	1698	Gaa/aa	17/23	0.57745067452201	3	FACETS	1	0.947	1	0.533	0.483	0.586	CLONAL	1	TRUE	1	0.57745067452201	3		497	477	SUCCESS
APC	324	MSKCC	GRCh37	5	112173783	112173784	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0059649-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	219	590	0	ENST00000257430.4:c.2493dup	p.Pro832ThrfsTer12	p.P832Tfs*12	ENST00000257430	NM_000038.5	831	tta/ttAa	16/16	0.57745067452201	3	FACETS	0.924	0.868	0.981	0.924	0.868	0.981	CLONAL	2	TRUE	1	0.57745067452201	3		590	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577507	7577507	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	315	501	6	ENST00000269305.4:c.774del	p.Asp259ThrfsTer86	p.D259Tfs*86	ENST00000269305	NM_001126112.2	258	gaA/ga	7/11	0.376541154002236	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	0	0.376541154002236	3		507	630	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0059651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	155	547	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.235680835615407	3	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	FALSE	1	0.235680835615407	3		547	708	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576919	7576919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	199	741	0	ENST00000269305.4:c.927del	p.Asn310ThrfsTer35	p.N310Tfs*35	ENST00000269305	NM_001126112.2	309	ccC/cc	9/11	0.162918779448589	2	FACETS	0.886	0.821	0.953	0.886	0.821	0.953	CLONAL	2	FALSE	0	0.235680835615407	2		741	953	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028850	47028850	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	64	327	0	ENST00000377604.3:c.154G>T	p.Glu52Ter	p.E52*	ENST00000377604	NM_001204468.1	52	Gag/Tag	3/24	1	1	FACETS	0.82	0.717	0.931	1	0.976	1	CLONAL	2	FALSE	0	0.235680835615407	1		327	292	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190615	11190615	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	95	699	0	ENST00000361445.4:c.5584C>G	p.Pro1862Ala	p.P1862A	ENST00000361445	NM_004958.3	1862	Cca/Gca	39/58	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	FALSE	1	0.235680835615407	2		699	804	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740230	46740230	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	35	531	0	ENST00000371975.4:c.1710G>T	p.Met570Ile	p.M570I	ENST00000371975	NM_003579.3	570	atG/atT	16/18	1	2	FACETS	0.477	0.39	0.575	0.477	0.39	0.575	SUBCLONAL	1	FALSE	1	0.235680835615407	2		531	623	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149238774	149238774	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059651-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	105	530	0	ENST00000360632.3:c.1021G>A	p.Glu341Lys	p.E341K	ENST00000360632	NM_015472.4	341	Gaa/Aaa	7/7	0.231011522932304	4	FACETS	1	0.975	1			1	CLONAL	1	FALSE	NA	0.235680835615407	4		530	845	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0059653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	86	329	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		329	398	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	116	477	0				ENST00000310581	NM_198253.2	-/1132			0.11530775106406	6	FACETS	0.916	0.83	1	0.611	0.553	0.671	INDETERMINATE	2	TRUE	3	0.483524930386651	6		477	515	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936983	48936983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690863	NA	P-0059654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	263	464	0	ENST00000267163.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000267163	NM_000321.2	251	Cga/Tga	8/27	0.263777997022024	3	FACETS	0.893	0.841	0.947	0.893	0.841	0.947	INDETERMINATE	2	TRUE	1	0.483524930386651	3		464	756	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0059654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	193	844	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.483524930386651	1	FACETS	0.979	0.911	1	0.979	0.911	1	CLONAL	1	TRUE	0	0.483524930386651	1		844	618	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102067	27102067	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0059654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	151	624	1	ENST00000324856.7:c.4994-1G>A		p.X1665_splice	ENST00000324856	NM_006015.4	1665			1	2	FACETS	0.954	0.875	1	0.954	0.875	1	CLONAL	1	TRUE	1	0.483524930386651	2		625	655	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881523	48881523	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	154	418	0	ENST00000267163.4:c.245C>A	p.Ser82Ter	p.S82*	ENST00000267163	NM_000321.2	82	tCa/tAa	2/27	0.263777997022024	3	FACETS	1	0.987	1	0.698	0.642	0.755	INDETERMINATE	1	TRUE	1	0.483524930386651	3		418	567	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352533	89352533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771447879	NA	P-0059654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	165	660	0	ENST00000301030.4:c.806C>T	p.Thr269Met	p.T269M	ENST00000301030	NM_001256183.1	269	aCg/aTg	8/13	0.403255732277525	3	FACETS	1	0.928	1	0.505	0.464	0.548	CLONAL	1	TRUE	1	0.483524930386651	3		660	839	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64289204	64289204	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	233	445	0	ENST00000370651.3:c.372G>A	p.Met124Ile	p.M124I	ENST00000370651	NM_003463.4	124	atG/atA	5/6	0.483524930386651	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.483524930386651	2		445	465	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644924	67644924	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	387	751	0	ENST00000264010.4:c.190del	p.Glu64AsnfsTer10	p.E64Nfs*10	ENST00000264010	NM_006565.3	63	atG/at	3/12	0.403255732277525	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.483524930386651	3		751	980	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552216	29552217	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0059654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	245	514	0	ENST00000356175.3:c.1950dup	p.Leu651ThrfsTer19	p.L651Tfs*19	ENST00000356175	NM_000267.3	650	tta/ttAa	17/57	NA	2	FACETS	1	0.957	1			1	INDETERMINATE	2	TRUE	NA	0.483524930386651	2		514	500	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858138	40858138	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	207	587	0	ENST00000428826.2:c.1726C>G	p.Leu576Val	p.L576V	ENST00000428826		576	Ctg/Gtg	16/21	0.483524930386651	3	FACETS	1	0.976	1	0.557	0.517	0.599	CLONAL	1	TRUE	1	0.483524930386651	3		587	954	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163837	32163837	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1311339180	NA	P-0059654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	65	620	0	ENST00000375023.3:c.5389G>C	p.Asp1797His	p.D1797H	ENST00000375023	NM_004557.3	1797	Gac/Cac	30/30	0.483524930386651	3	FACETS	0.594	0.515	0.679	0.198	0.171	0.227	SUBCLONAL	1	TRUE	0	0.483524930386651	3		620	562	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969968	161969968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746215864	NA	P-0059654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	172	547	0	ENST00000366898.1:c.1001G>A	p.Arg334His	p.R334H	ENST00000366898	NM_004562.2	334	cGc/cAc	9/12	0.483524930386651	2	FACETS	1	0.985	1	0.624	0.577	0.672	CLONAL	1	TRUE	0	0.483524930386651	2		547	570	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940373	13940373	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	150	405	0	ENST00000405192.2:c.1133T>C	p.Ile378Thr	p.I378T	ENST00000405192	NM_001163147.1	378	aTt/aCt	11/12	0.216241028527872	5	FACETS	0.832	0.763	0.904	0.555	0.509	0.603	INDETERMINATE	2	TRUE	2	0.483524930386651	5		405	643	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195192	123195192	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0059654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	161	223	0	ENST00000218089.9:c.1534+1G>A		p.X512_splice	ENST00000218089	NM_001042749.1	512			0.0920150152127729	2	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.483524930386651	2		223	283	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0059655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	205	967	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.962	0.897	1	0.962	0.897	1	CLONAL	1	TRUE	1	0.658527301297021	2		974	647	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444659	78444659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs908264837	NA	P-0059655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	176	647	0	ENST00000370768.2:c.30del	p.Ser11LeufsTer43	p.S11Lfs*43	ENST00000370768	NM_003902.3	10	ccC/cc	1/20	1	2	FACETS	0.918	0.851	0.988	0.918	0.851	0.988	CLONAL	1	TRUE	1	0.658527301297021	2		647	582	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0059655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	188	844	17	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.658527301297021	2		861	525	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045888	47045888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782671192	NA	P-0059655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	235	866	0	ENST00000377604.3:c.2683C>T	p.Arg895Trp	p.R895W	ENST00000377604	NM_001204468.1	895	Cgg/Tgg	24/24	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.658527301297021	2		866	690	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0059655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	180	628	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.812	0.752	0.875	0.812	0.752	0.875	CLONAL	1	TRUE	1	0.658527301297021	2		629	673	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0059655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	42	298	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.274	0.228	0.324	0.274	0.228	0.324	SUBCLONAL	1	TRUE	1	0.658527301297021	2		298	466	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs1057519842	NA	P-0059655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	103	506	0	ENST00000274335.5:c.1727_1729del	p.Thr576del	p.T576del	ENST00000274335		575	aaGACg/aag	12/15	1	2	FACETS	0.77	0.695	0.85	0.77	0.695	0.85	SUBCLONAL	1	TRUE	1	0.658527301297021	2		506	406	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047132	77047132	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	151	548	0	ENST00000356341.3:c.1412G>A	p.Arg471Lys	p.R471K	ENST00000356341	NM_002576.4	471	aGa/aAa	13/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.658527301297021	2		548	414	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890149	76890150	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0059655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	135	454	0	ENST00000373344.5:c.4744dup	p.Thr1582AsnfsTer19	p.T1582Nfs*19	ENST00000373344	NM_000489.3	1582	aca/aAca	17/35	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.658527301297021	2		454	392	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100727	8100728	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs771019738	NA	P-0059655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	32	745	1	ENST00000346208.3:c.708dup	p.Ser237GlnfsTer66	p.S237Qfs*66	ENST00000346208		234	ttc/ttCc	3/6	1	2	FACETS	0.19	0.154	0.231	0.19	0.154	0.231	SUBCLONAL	1	TRUE	1	0.658527301297021	2		746	511	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720711	89720712	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0059655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	27	102	0	ENST00000371953.3:c.867dup	p.Val290SerfsTer8	p.V290Sfs*8	ENST00000371953	NM_000314.4	288	gaa/gAaa	8/9	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.658527301297021	2		102	76	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38960546	38960546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1230911017	NA	P-0059655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	140	509	0	ENST00000357387.3:c.1805C>T	p.Thr602Met	p.T602M	ENST00000357387	NM_152756.3	602	aCg/aTg	20/38	1	2	FACETS	0.804	0.736	0.874	0.804	0.736	0.874	CLONAL	1	TRUE	1	0.658527301297021	2		509	529	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380350	14380350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	110	570	0	ENST00000256196.4:c.67G>A	p.Gly23Ser	p.G23S	ENST00000256196		23	Ggc/Agc	1/6	1	2	FACETS	0.955	0.867	1	0.955	0.867	1	CLONAL	1	TRUE	1	0.658527301297021	2		570	350	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741552	17741552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	103	576	3	ENST00000250003.3:c.223G>A	p.Ala75Thr	p.A75T	ENST00000250003	NM_002478.4	75	Gca/Aca	1/3	1	2	FACETS	0.705	0.634	0.778	0.705	0.634	0.778	SUBCLONAL	1	TRUE	1	0.658527301297021	2		579	444	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598336	28598336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769442139	NA	P-0059655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	217	712	0	ENST00000253063.3:c.308C>T	p.Thr103Met	p.T103M	ENST00000253063	NM_031459.4	103	aCg/aTg	3/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.658527301297021	2		712	594	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821594	72821599	+	inframe_deletion	In_Frame_Del	DEL	GCCGCC	GCCGCC	-	rs374416547	NA	P-0059655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	25	668	2	ENST00000268489.5:c.10576_10581del	p.Gly3526_Gly3527del	p.G3526_G3527del	ENST00000268489	NM_006885.3	3526	GGCGGC/-	10/10	1	2	FACETS	0.225	0.177	0.28	0.225	0.177	0.28	SUBCLONAL	1	TRUE	1	0.658527301297021	2		670	338	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216506	36216506	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs956016804	NA	P-0059655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	134	754	0	ENST00000222270.7:c.3769C>T	p.Arg1257Cys	p.R1257C	ENST00000222270	NM_014727.1	1257	Cgc/Tgc	12/37	1	2	FACETS	0.74	0.675	0.807	0.74	0.675	0.807	SUBCLONAL	1	TRUE	1	0.658527301297021	2		754	550	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817460	39817460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774083516	NA	P-0059655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	115	599	0	ENST00000288319.7:c.103G>A	p.Ala35Thr	p.A35T	ENST00000288319	NM_182918.3	35	Gcg/Acg	2/10	1	2	FACETS	0.667	0.603	0.733	0.667	0.603	0.733	SUBCLONAL	1	TRUE	1	0.658527301297021	2		599	524	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348161	89348161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	103	640	0	ENST00000301030.4:c.4789C>T	p.Arg1597Cys	p.R1597C	ENST00000301030	NM_001256183.1	1597	Cgc/Tgc	9/13	1	2	FACETS	0.598	0.537	0.662	0.598	0.537	0.662	SUBCLONAL	1	TRUE	1	0.658527301297021	2		640	523	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902289	151902289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1345303559	NA	P-0059655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	22	94	0	ENST00000262189.6:c.3863G>A	p.Arg1288Gln	p.R1288Q	ENST00000262189	NM_170606.2	1288	cGg/cAg	25/59	1	2	FACETS	0.928	0.742	1	0.928	0.742	1	CLONAL	1	TRUE	1	0.658527301297021	2		94	72	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363058	40363058	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	146	535	0	ENST00000397332.2:c.1171C>A	p.Leu391Ile	p.L391I	ENST00000397332	NM_001033082.2	391	Ctc/Atc	3/3	1	2	FACETS	0.958	0.881	1	0.958	0.881	1	CLONAL	1	TRUE	1	0.658527301297021	2		535	463	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231474164	231474166	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0059655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	37	537	0	ENST00000295050.7:c.40_42del	p.Glu14del	p.E14del	ENST00000295050	NM_032018.5	12	cAGGag/cag	1/5	0.658527301297021	5	FACETS	0.384	0.316	0.46	0.128	0.105	0.154	SUBCLONAL	1	TRUE	2	0.658527301297021	5		537	582	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949374	71949374	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	181	700	0	ENST00000298229.2:c.3754G>T	p.Asp1252Tyr	p.D1252Y	ENST00000298229	NM_001567.3	1252	Gac/Tac	28/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.658527301297021	2		700	501	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793376	18793376	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	107	474	0	ENST00000266497.5:c.4073G>T	p.Gly1358Val	p.G1358V	ENST00000266497		1358	gGc/gTc	30/31	1	2	FACETS	0.926	0.839	1	0.926	0.839	1	CLONAL	1	TRUE	1	0.658527301297021	2		474	351	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112275	115112275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	125	649	0	ENST00000257566.3:c.1465G>A	p.Ala489Thr	p.A489T	ENST00000257566	NM_016569.3	489	Gcc/Acc	7/8	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.658527301297021	2		649	352	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018196	48018197	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TACAGTTTTTTGA	novel	NA	P-0059655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	133	564	0	ENST00000234420.5:c.393_405dup	p.Asp136ThrfsTer4	p.D136Tfs*4	ENST00000234420	NM_000179.2	131	gta/gTACAGTTTTTTGAta	2/10	1	2	FACETS	0.683	0.623	0.747	0.683	0.623	0.747	SUBCLONAL	1	TRUE	1	0.658527301297021	2		564	591	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176538	56176538	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	104	449	0	ENST00000399503.3:c.2089del	p.Arg697AlafsTer28	p.R697Afs*28	ENST00000399503	NM_005921.1	696	agC/ag	12/20	1	2	FACETS	0.769	0.693	0.847	0.769	0.693	0.847	SUBCLONAL	1	TRUE	1	0.658527301297021	2		449	411	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158089	27158089	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	197	672	0	ENST00000380036.4:c.313C>T	p.Arg105Ter	p.R105*	ENST00000380036	NM_000459.3	105	Cga/Tga	2/23	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.658527301297021	2		672	565	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045682	47045682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782323783	NA	P-0059655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	129	803	2	ENST00000377604.3:c.2563G>A	p.Gly855Arg	p.G855R	ENST00000377604	NM_001204468.1	855	Ggg/Agg	23/24	1	2	FACETS	0.758	0.691	0.828	0.758	0.691	0.828	SUBCLONAL	1	TRUE	1	0.658527301297021	2		805	517	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28929495	NA	P-0059656-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	129	619	0	ENST00000275493.2:c.2155G>A	p.Gly719Ser	p.G719S	ENST00000275493	NM_005228.3	719	Ggc/Agc	18/28	0.341838081052149	3	FACETS	0.875	0.801	0.952	0.875	0.801	0.952	CLONAL	2	TRUE	1	0.442346364534114	3		619	407	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298003	15298003	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752404540	NA	P-0059656-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	28	791	0	ENST00000263388.2:c.1753G>A	p.Glu585Lys	p.E585K	ENST00000263388	NM_000435.2	585	Gaa/Aaa	11/33	0.349328596787043	4	FACETS	0.461	0.368	0.567	0.231	0.184	0.284	SUBCLONAL	1	TRUE	2	0.442346364534114	4		791	396	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0059656-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	129	730	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.341838081052149	3	FACETS	0.873	0.799	0.949	0.873	0.799	0.949	CLONAL	2	TRUE	1	0.442346364534114	3		730	408	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219164	133219164	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1274894982	NA	P-0059656-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	93	761	0	ENST00000320574.5:c.4880A>G	p.His1627Arg	p.H1627R	ENST00000320574	NM_006231.2	1627	cAt/cGt	37/49	0.442346364534114	3	FACETS	1	0.975	1	0.652	0.583	0.723	CLONAL	1	TRUE	1	0.442346364534114	3		761	394	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493805	56493805	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1565861449	NA	P-0059656-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	70	768	0	ENST00000267101.3:c.3121C>T	p.Pro1041Ser	p.P1041S	ENST00000267101	NM_001982.3	1041	Cca/Tca	25/28	0.325742879151469	5	FACETS	0.801	0.698	0.913	0.267	0.232	0.305	CLONAL	1	TRUE	2	0.442346364534114	5		768	657	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729558	41729558	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059656-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	22	804	0	ENST00000242208.4:c.971A>G	p.Lys324Arg	p.K324R	ENST00000242208	NM_002192.2	324	aAa/aGa	3/3	0.341838081052149	3	FACETS	0.291	0.225	0.368	0.146	0.112	0.184	SUBCLONAL	1	TRUE	1	0.442346364534114	3		804	417	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593606	55593623	+	inframe_deletion	In_Frame_Del	DEL	AAGGTTGTTGAGGAGATA	AAGGTTGTTGAGGAGATA	-	novel	NA	P-0059657-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	326	364	0	ENST00000288135.5:c.1674_1691del	p.Lys558_Ile563del	p.K558_I563del	ENST00000288135	NM_000222.2	558	AAGGTTGTTGAGGAGATA/-	11/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.842502278049183	2		364	733	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29422372	29422396	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCGCTTCGACGAGCAGGTAACCGGC	CCGCTTCGACGAGCAGGTAACCGGC	-	novel	NA	P-0059658-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	101	468	0	ENST00000356175.3:c.48_60+12del		p.X16_splice	ENST00000356175	NM_000267.3	16		1/57	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		468	188	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0059659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	380	517	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.363365772492033	5	FACETS	0.944	0.905	0.982	0.944	0.905	0.982	CLONAL	5	TRUE	0	0.363365772492033	5		517	685	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41242984	41242984	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs876660601	NA	P-0059659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	166	462	0	ENST00000357654.3:c.4162C>T	p.Gln1388Ter	p.Q1388*	ENST00000357654	NM_007294.3	1388	Cag/Tag	11/23	0.297920526515702	3	FACETS	1	0.98	1	0.777	0.721	0.835	CLONAL	2	TRUE	0	0.363365772492033	3		462	463	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321001	137321001	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343863109	NA	P-0059659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	139	379	0	ENST00000481739.1:c.958G>A	p.Val320Met	p.V320M	ENST00000481739	NM_002957.4	320	Gtg/Atg	7/10	0.303575822922108	4	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	2	0.363365772492033	4		379	498	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31423036	31423036	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	122	401	0	ENST00000344624.3:c.3277A>C	p.Thr1093Pro	p.T1093P	ENST00000344624		1093	Act/Cct	26/33	0.24388791097643	4	FACETS	0.976	0.888	1	0.976	0.888	1	CLONAL	2	TRUE	2	0.363365772492033	4		401	469	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020820	112020820	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	84	430	0	ENST00000368678.4:c.751C>T	p.Pro251Ser	p.P251S	ENST00000368678		251	Cca/Tca	8/13	0.303575822922108	4	FACETS	1	0.919	1	0.524	0.464	0.589	CLONAL	1	TRUE	2	0.363365772492033	4		430	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0059660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	54	593	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.31818370492509	1	FACETS	0.909	0.781	1	0.909	0.781	1	CLONAL	1	FALSE	0	0.318941053745615	1		593	313	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120132	70120133	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0059660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	57	889	0	ENST00000245479.2:c.1137_1138dup	p.His380ArgfsTer4	p.H380Rfs*4	ENST00000245479	NM_000346.3	378	-/GC	3/3	0.31818370492509	1	FACETS	0.846	0.73	0.972	0.846	0.73	0.972	CLONAL	1	FALSE	0	0.318941053745615	1		889	355	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357156	70357156	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059660-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	45	851	0	ENST00000374080.3:c.5671T>C	p.Ser1891Pro	p.S1891P	ENST00000374080		1891	Tcc/Ccc	39/45	1	2	FACETS	0.722	0.608	0.847	0.722	0.608	0.847	SUBCLONAL	1	FALSE	1	0.318941053745615	2		851	391	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554900	187554900	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	56	554	0	ENST00000441802.2:c.4261C>A	p.Gln1421Lys	p.Q1421K	ENST00000441802	NM_005245.3	1421	Cag/Aag	7/27	0.368312507954497	6	FACETS	0.56	0.479	0.648	0.14	0.119	0.162	INDETERMINATE	1	FALSE	2	0.703122520132662	6		554	685	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356412	66356412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763166233	NA	P-0059661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	142	521	0	ENST00000273854.3:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000273854	NM_004439.5	362	cGg/cAg	5/18	0.336495688532013	5	FACETS	0.928	0.853	1	0.619	0.569	0.671	INDETERMINATE	2	FALSE	2	0.703122520132662	5		521	447	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919268	48919268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	40	391	0	ENST00000267163.4:c.433G>A	p.Asp145Asn	p.D145N	ENST00000267163	NM_000321.2	145	Gat/Aat	4/27	0.303450247738312	3	FACETS	0.589	0.493	0.695	0.196	0.164	0.232	INDETERMINATE	1	FALSE	0	0.703122520132662	3		391	261	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683441	182683441	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	27	406	0	ENST00000292782.4:c.104G>A	p.Trp35Ter	p.W35*	ENST00000292782	NM_020640.2	35	tGg/tAg	2/7	0.710659757474787	4	FACETS	0.264	0.21	0.327	0.132	0.105	0.164	SUBCLONAL	1	FALSE	2	0.703122520132662	4		406	495	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673605	30673605	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1616	87	747	0	ENST00000376406.3:c.3355C>G	p.Pro1119Ala	p.P1119A	ENST00000376406	NM_014641.2	1119	Cca/Gca	10/15	0.703122520132662	9	FACETS	0.503	0.443	0.568	0.072	0.063	0.082	SUBCLONAL	1	FALSE	2	0.703122520132662	9		747	1703	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0059664-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	13	536	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	FALSE	1	0.356359247939525	2		536	50	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346157	89346158	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs878855327	NA	P-0059665-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	8	691	1	ENST00000301030.4:c.6792dup	p.Ala2265ArgfsTer8	p.A2265Rfs*8	ENST00000301030	NM_001256183.1	2264	-/C	9/13	1	2	FACETS	0.238	0.153	0.35	0.238	0.153	0.35	SUBCLONAL	1	FALSE	1	0.2059638539077	2		692	326	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0059666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	48	458	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.247638716142911	3	FACETS	1	0.954	1	0.68	0.576	0.794	CLONAL	1	TRUE	1	0.19	3		458	407	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604701	48604701	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	54	524	0	ENST00000342988.3:c.1523G>T	p.Gly508Val	p.G508V	ENST00000342988	NM_005359.5	508	gGc/gTc	12/12	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.19	2		524	562	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589812	69589812	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1158890592	NA	P-0059666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	30	943	0	ENST00000168712.1:c.41C>T	p.Ala14Val	p.A14V	ENST00000168712	NM_002007.2	14	gCg/gTg	1/3	1	2	FACETS	0.856	0.69	1	0.856	0.69	1	CLONAL	1	TRUE	1	0.19	2		943	369	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368258	45368258	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	41	467	0	ENST00000262160.6:c.1344G>A	p.Trp448Ter	p.W448*	ENST00000262160	NM_005901.5	448	tgG/tgA	11/11	1	2	FACETS	1	0.835	1	1	0.835	1	CLONAL	1	TRUE	1	0.19	2		467	431	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99204042	99204042	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529481819	NA	P-0059666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	45	363	0	ENST00000074304.5:c.2905G>A	p.Glu969Lys	p.E969K	ENST00000074304	NM_001134224.1	969	Gaa/Aaa	26/26	1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	1	0.19	2		363	470	SUCCESS
APC	324	MSKCC	GRCh37	5	112176024	112176025	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TATTATTT	novel	NA	P-0059666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	30	586	0	ENST00000257430.4:c.4734_4741dup	p.Ser1581LeufsTer72	p.S1581Lfs*72	ENST00000257430	NM_000038.5	1578	tgt/tgTATTATTTt	16/16	1	2	FACETS	0.655	0.527	0.801	0.655	0.527	0.801	SUBCLONAL	1	TRUE	1	0.19	2		586	482	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0059667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	86	525	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.261800322712614	2		525	455	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22408266	22408266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	70	297	0	ENST00000344548.3:c.157C>T	p.Leu53Phe	p.L53F	ENST00000344548	NM_001039802.1	53	Ctt/Ttt	4/7	0.261800322712614	3	FACETS	1	0.887	1	0.509	0.444	0.579	CLONAL	1	TRUE	1	0.261800322712614	3		297	594	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118370592	118370592	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	67	344	0	ENST00000534358.1:c.6122C>T	p.Ser2041Phe	p.S2041F	ENST00000534358	NM_005933.3	2041	tCc/tTc	24/36	0.176752909519488	2	FACETS	0.838	0.728	0.956	0.419	0.364	0.478	CLONAL	1	TRUE	0	0.261800322712614	2		344	611	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446354	29446354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1157412359	NA	P-0059667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	86	439	0	ENST00000544604.2:c.2185G>A	p.Gly729Ser	p.G729S	ENST00000544604	NM_001206998.1	729	Ggc/Agc	8/9	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.261800322712614	2		439	548	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103681	47103681	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs183768442	NA	P-0059667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	123	545	0	ENST00000409792.3:c.6265G>A	p.Glu2089Lys	p.E2089K	ENST00000409792	NM_014159.6	2089	Gag/Aag	14/21	0.206414723058515	4	FACETS	1	0.979	1	0.657	0.593	0.724	CLONAL	1	TRUE	2	0.261800322712614	4		545	903	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	172	121	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.429047042478378	3	FACETS	0.957	0.887	1	0.957	0.887	1	CLONAL	2	TRUE	1	0.429047042478378	3		121	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0059668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	151	545	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.429047042478378	1	FACETS	0.996	0.916	1	0.996	0.916	1	CLONAL	1	TRUE	0	0.429047042478378	1		545	555	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521481	8521481	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760428875	NA	P-0059668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	114	429	0	ENST00000356435.5:c.757G>A	p.Val253Ile	p.V253I	ENST00000356435		253	Gtt/Att	9/35	0.429047042478378	1	FACETS	0.934	0.846	1	0.934	0.846	1	CLONAL	1	TRUE	0	0.429047042478378	1		429	447	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252129	226252149	+	inframe_deletion	In_Frame_Del	DEL	CTCGCAAGAGTGCGCCCTCTA	CTCGCAAGAGTGCGCCCTCTA	-	novel	NA	P-0059668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	117	107	0	ENST00000366813.1:c.79_99del	p.Arg27_Thr33del	p.R27_T33del	ENST00000366813		26	gCTCGCAAGAGTGCGCCCTCTAct/gct	1/3	0.197161827544435	5	FACETS	0.996	0.912	1	0.996	0.912	1	INDETERMINATE	3	TRUE	2	0.429047042478378	5		107	300	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946352	71946352	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	110	563	0	ENST00000298229.2:c.2516T>G	p.Val839Gly	p.V839G	ENST00000298229	NM_001567.3	839	gTt/gGt	23/28	1	2	FACETS	0.877	0.79	0.968	0.877	0.79	0.968	CLONAL	1	TRUE	1	0.429047042478378	2		563	585	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480377	56480377	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	126	425	0	ENST00000267101.3:c.484G>T	p.Asp162Tyr	p.D162Y	ENST00000267101	NM_001982.3	162	Gac/Tac	4/28	1	2	FACETS	0.921	0.836	1	0.921	0.836	1	CLONAL	1	TRUE	1	0.429047042478378	2		425	638	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440922	56441662	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGAGGACAGCACTGGCTCCTCGCTCACCCGCCATCCGAGCCTGCAGAGGCACACAGTAGAGGTTGGGCTGAGGTCAGGGAAGGACAGAGCCCACCCACAGGCTAGCCTCACCCCTCACACATCTATCCCTTCCTAGGATTATGCCCACAGCACATCTTTGCACACTCACATCTACCTATGCAAGGGGTCACTGGGTCTAAGATCTCCTCTTCTGCCTCCTGAGCTCACTCAGGTCCCCACTGCCTTCAAGGGATAATATCTAGCTTTTCCTTTTGTAATGGAACAAACCCTTAAGGGGGGTTTACAGGGTGCCAGGTGGTGGACCTGGCTCTAGGATGAAAGACAAATAAGACACAGCTCCTGCCCTCAGGGTACAATCAGCCTGCCTTCACTAAGAGGTATGAGCACGAAGAGTAGGAGGGACCTGCACCCCTTAGAAGGAGAAGAGAGAGGAAGAAGGGGACAGCAGAGAAGTAGAGCTCTCCTTCAGAGGGAGCTGGGCTTTCCAGGGCCCAGTCCTGCCTGCAGGGCATCTCCCCAGCTCAGGCAAAGGTCTAAGAGCCTGGGACGCCACTCTCACGCAAGGCCACCATCACAAAGCCCCTGTCTCAGCTCATCTCATGGGCTCCCTCTCCTTGCCACACTCTACTTTGCCAAGTCTTTCTCTGGCTCCAATTCAAGGACTTAGAGGAGTCCTTGTCCAGTGGTTTATCCTTTCGTCCCCTCCCTTAGGGTGGCATT	AGAGGACAGCACTGGCTCCTCGCTCACCCGCCATCCGAGCCTGCAGAGGCACACAGTAGAGGTTGGGCTGAGGTCAGGGAAGGACAGAGCCCACCCACAGGCTAGCCTCACCCCTCACACATCTATCCCTTCCTAGGATTATGCCCACAGCACATCTTTGCACACTCACATCTACCTATGCAAGGGGTCACTGGGTCTAAGATCTCCTCTTCTGCCTCCTGAGCTCACTCAGGTCCCCACTGCCTTCAAGGGATAATATCTAGCTTTTCCTTTTGTAATGGAACAAACCCTTAAGGGGGGTTTACAGGGTGCCAGGTGGTGGACCTGGCTCTAGGATGAAAGACAAATAAGACACAGCTCCTGCCCTCAGGGTACAATCAGCCTGCCTTCACTAAGAGGTATGAGCACGAAGAGTAGGAGGGACCTGCACCCCTTAGAAGGAGAAGAGAGAGGAAGAAGGGGACAGCAGAGAAGTAGAGCTCTCCTTCAGAGGGAGCTGGGCTTTCCAGGGCCCAGTCCTGCCTGCAGGGCATCTCCCCAGCTCAGGCAAAGGTCTAAGAGCCTGGGACGCCACTCTCACGCAAGGCCACCATCACAAAGCCCCTGTCTCAGCTCATCTCATGGGCTCCCTCTCCTTGCCACACTCTACTTTGCCAAGTCTTTCTCTGGCTCCAATTCAAGGACTTAGAGGAGTCCTTGTCCAGTGGTTTATCCTTTCGTCCCCTCCCTTAGGGTGGCATT	-	novel	NA	P-0059668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	83	523	0	ENST00000407977.2:c.376-701_415del		p.X126_splice	ENST00000407977		126		4/10	1	2	FACETS	0.722	0.638	0.811	0.722	0.638	0.811	SUBCLONAL	1	TRUE	1	0.429047042478378	2		523	536	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039529	180039529	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	71	423	0	ENST00000261937.6:c.3514C>A	p.Leu1172Met	p.L1172M	ENST00000261937	NM_182925.4	1172	Ctg/Atg	26/30	0.155170753109454	2	FACETS	0.638	0.557	0.724	0.319	0.278	0.362	INDETERMINATE	1	TRUE	0	0.429047042478378	2		423	519	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955059	93955059	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	60	317	0	ENST00000369303.4:c.2839G>T	p.Ala947Ser	p.A947S	ENST00000369303	NM_004440.3	947	Gct/Tct	16/17	1	2	FACETS	0.684	0.591	0.784	0.684	0.591	0.784	SUBCLONAL	1	TRUE	1	0.429047042478378	2		317	409	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936053	44936056	+	frameshift_variant	Frame_Shift_Del	DEL	ACCT	ACCT	-	novel	NA	P-0059668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	83	178	0	ENST00000377967.4:c.2816_2819del	p.Pro939HisfsTer30	p.P939Hfs*30	ENST00000377967	NM_021140.2	938	ccACCT/cc	18/29	1	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.429047042478378	1		178	215	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450138	32450138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777166391	NA	P-0059669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	274	692	0	ENST00000332351.3:c.674C>T	p.Thr225Met	p.T225M	ENST00000332351	NM_024426.4	225	aCg/aTg	2/10	0.419264710198701	2	FACETS	0.894	0.844	0.944	0.894	0.844	0.944	CLONAL	2	TRUE	0	0.444982652400662	2		692	689	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441469	52441469	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1559590768	NA	P-0059669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	152	749	0	ENST00000460680.1:c.383G>A	p.Gly128Glu	p.G128E	ENST00000460680	NM_004656.3	128	gGa/gAa	6/17	0.431106635546121	1	FACETS	0.761	0.698	0.827	0.761	0.698	0.827	SUBCLONAL	1	TRUE	0	0.444982652400662	1		749	698	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443406	187443406	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	149	650	0	ENST00000232014.4:c.1720T>C	p.Tyr574His	p.Y574H	ENST00000232014	NM_001130845.1	574	Tat/Cat	8/10	1	2	FACETS	0.954	0.874	1	0.954	0.874	1	CLONAL	1	TRUE	1	0.444982652400662	2		650	702	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245539	153245539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1001597080	NA	P-0059669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	98	516	0	ENST00000281708.4:c.1652G>A	p.Gly551Asp	p.G551D	ENST00000281708	NM_033632.3	551	gGt/gAt	11/12	0.444982652400662	1	FACETS	0.78	0.7	0.864	0.78	0.7	0.864	SUBCLONAL	1	TRUE	0	0.444982652400662	1		516	439	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207444	29207444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	124	492	0	ENST00000240100.2:c.352C>T	p.Leu118Phe	p.L118F	ENST00000240100	NM_001394.6	118	Ctc/Ttc	1/4	0.38591924563702	3	FACETS	0.976	0.884	1	0.488	0.442	0.537	CLONAL	1	TRUE	1	0.444982652400662	3		492	698	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0059670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	36	344	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.702	0.579	0.839	0.702	0.579	0.839	SUBCLONAL	1	TRUE	1	0.325595562509293	2		344	315	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50776547	50776547	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759699181	NA	P-0059670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	23	325	0	ENST00000307179.4:c.1879G>A	p.Glu627Lys	p.E627K	ENST00000307179		627	Gaa/Aaa	12/20	1	2	FACETS	0.44	0.343	0.552	0.44	0.343	0.552	SUBCLONAL	1	TRUE	1	0.325595562509293	2		325	321	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220382	1220382	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	66	553	0	ENST00000326873.7:c.475C>T	p.Gln159Ter	p.Q159*	ENST00000326873	NM_000455.4	159	Cag/Tag	4/10	0.325595562509293	1	FACETS	0.743	0.646	0.846	0.743	0.646	0.846	SUBCLONAL	1	TRUE	0	0.325595562509293	1		553	457	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723110	52723110	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	50	489	0	ENST00000322088.6:c.1295G>T	p.Gly432Val	p.G432V	ENST00000322088	NM_014225.5	432	gGa/gTa	10/15	1	2	FACETS	0.832	0.709	0.967	0.832	0.709	0.967	CLONAL	1	TRUE	1	0.325595562509293	2		489	369	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613112	52613112	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	71	504	0	ENST00000394830.3:c.3416T>G	p.Val1139Gly	p.V1139G	ENST00000394830	NM_018313.4	1139	gTc/gGc	22/30	0.325595562509293	1	FACETS	0.692	0.604	0.785	0.692	0.604	0.785	SUBCLONAL	1	TRUE	0	0.325595562509293	1		504	528	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156348	106156348	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	73	613	0	ENST00000380013.4:c.1249C>T	p.Gln417Ter	p.Q417*	ENST00000380013	NM_001127208.2	417	Cag/Tag	3/11	1	2	FACETS	0.768	0.672	0.871	0.768	0.672	0.871	SUBCLONAL	1	TRUE	1	0.325595562509293	2		613	584	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0059672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	106	403	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.677750715902227	2		404	237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0059672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	309	650	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.677750715902227	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.677750715902227	2		650	370	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624242	89624243	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs121913290	NA	P-0059672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	42	93	0	ENST00000371953.3:c.17_18del	p.Lys6ArgfsTer4	p.K6Rfs*4	ENST00000371953	NM_000314.4	6	AAa/a	1/9	0.677750715902227	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.677750715902227	1		93	73	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955043	17955043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs199602590	NA	P-0059672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	162	315	0	ENST00000458235.1:c.184G>A	p.Gly62Ser	p.G62S	ENST00000458235	NM_000215.3	62	Ggc/Agc	2/24	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.677750715902227	2		315	398	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473600	67473600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	179	236	0	ENST00000327367.4:c.680G>A	p.Cys227Tyr	p.C227Y	ENST00000327367	NM_005902.3	227	tGc/tAc	6/9	1	2	FACETS	0.755	0.708	0.801	1	0.992	1	SUBCLONAL	2	TRUE	1	0.677750715902227	2		236	350	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143044523	143044523	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	31	140	0	ENST00000262992.4:c.1939C>A	p.Leu647Met	p.L647M	ENST00000262992	NM_001101669.1	647	Ctg/Atg	18/24	1	2	FACETS	0.487	0.397	0.586	0.487	0.397	0.586	SUBCLONAL	1	TRUE	1	0.677750715902227	2		140	188	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	35	477	0				ENST00000310581	NM_198253.2	-/1132			0.223210345382792	1	FACETS	0.861	0.713	1	0.861	0.713	1	CLONAL	1	TRUE	0	0.352649308455022	1		477	190	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0059673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	23	344	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.776	0.621	0.946	1	0.935	1	CLONAL	2	TRUE	1	0.352649308455022	2		344	84	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246491	46246491	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	44	264	0	ENST00000334344.6:c.4585G>T	p.Gly1529Ter	p.G1529*	ENST00000334344	NM_152641.2	1529	Gga/Tga	15/21	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.352649308455022	2		264	234	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041355	47041355	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	36	332	0	ENST00000377604.3:c.1701del	p.Asp568ThrfsTer136	p.D568Tfs*136	ENST00000377604	NM_001204468.1	567	Ccc/cc	16/24	0.352649308455022	1	FACETS	0.559	0.461	0.667	0.559	0.461	0.667	SUBCLONAL	1	TRUE	0	0.352649308455022	1		332	301	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579855	7579856	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0059673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	51	255	0	ENST00000269305.4:c.57_58del	p.Ser20ArgfsTer8	p.S20Rfs*8	ENST00000269305	NM_001126112.2	19	ttTTca/ttca	2/11	0.223210345382792	1	FACETS	0.851	0.728	0.983	0.851	0.728	0.983	CLONAL	1	TRUE	0	0.352649308455022	1		255	280	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191513	10191513	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1131690962	NA	P-0059674-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	90	267	0	ENST00000256474.2:c.506T>C	p.Leu169Pro	p.L169P	ENST00000256474	NM_000551.3	169	cTa/cCa	3/3	0.391072360444808	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	0	0.391072360444808	1		267	310	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637711	52637711	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059674-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	23	149	0	ENST00000394830.3:c.2605C>T	p.Gln869Ter	p.Q869*	ENST00000394830	NM_018313.4	869	Cag/Tag	18/30	0.391072360444808	1	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	FALSE	0	0.391072360444808	1		149	89	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56839486	56839486	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059674-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	87	240	0	ENST00000308159.5:c.431T>G	p.Ile144Ser	p.I144S	ENST00000308159	NM_014669.4	144	aTt/aGt	5/22	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.391072360444808	2		240	385	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566546	41566546	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059674-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	59	205	0	ENST00000263253.7:c.4423G>T	p.Val1475Leu	p.V1475L	ENST00000263253	NM_001429.3	1475	Gta/Tta	27/31	1	2	FACETS	0.937	0.811	1	0.937	0.811	1	CLONAL	1	FALSE	1	0.391072360444808	2		205	322	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0059675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	19	329	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.871	0.664	1	0.871	0.664	1	CLONAL	1	TRUE	1	0.217088840967958	2		329	201	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129655	11129655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	17	317	0	ENST00000358026.2:c.2461G>A	p.Glu821Lys	p.E821K	ENST00000358026	NM_001128849.1	821	Gag/Aag	17/36	1	2	FACETS	0.358	0.266	0.468	0.358	0.266	0.468	SUBCLONAL	1	TRUE	1	0.217088840967958	2		317	437	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442569	52442569	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	29	275	0	ENST00000460680.1:c.176G>C	p.Arg59Pro	p.R59P	ENST00000460680	NM_004656.3	59	cGg/cCg	4/17	1	2	FACETS	0.592	0.475	0.726	0.592	0.475	0.726	SUBCLONAL	1	TRUE	1	0.217088840967958	2		275	451	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125395	47125395	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	23	275	0	ENST00000409792.3:c.5875G>T	p.Glu1959Ter	p.E1959*	ENST00000409792	NM_014159.6	1959	Gaa/Taa	12/21	1	2	FACETS	0.597	0.465	0.75	0.597	0.465	0.75	SUBCLONAL	1	TRUE	1	0.217088840967958	2		275	355	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222979	1222990	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGCAGCTGGTTC	TGCAGCTGGTTC	-	novel	NA	P-0059675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	52	294	0	ENST00000326873.7:c.921-5_927del		p.X307_splice	ENST00000326873	NM_000455.4	307		8/10	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.217088840967958	2		294	420	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442074	52442074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	38	308	0	ENST00000460680.1:c.275C>T	p.Ala92Val	p.A92V	ENST00000460680	NM_004656.3	92	gCa/gTa	5/17	1	2	FACETS	0.756	0.625	0.903	0.756	0.625	0.903	CLONAL	1	TRUE	1	0.217088840967958	2		308	463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0059676-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	80	593	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.217381196346252	3	FACETS	1	0.95	1	0.751	0.667	0.84	CLONAL	2	TRUE	0	0.244466812841293	3		593	326	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0059676-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	133	315	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.217381196346252	3	FACETS	0.923	0.845	1	0.923	0.845	1	CLONAL	3	TRUE	0	0.244466812841293	3		315	441	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520273	176520273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759709290	NA	P-0059676-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	39	278	0	ENST00000292408.4:c.1192C>T	p.Arg398Trp	p.R398W	ENST00000292408	NM_213647.1	398	Cgg/Tgg	9/18	1	2	FACETS	0.985	0.819	1	0.985	0.819	1	CLONAL	1	TRUE	1	0.244466812841293	2		278	324	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158089	106158089	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775382692	NA	P-0059676-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	44	268	0	ENST00000380013.4:c.2990C>T	p.Pro997Leu	p.P997L	ENST00000380013	NM_001127208.2	997	cCa/cTa	3/11	1	2	FACETS	0.889	0.747	1	0.889	0.747	1	CLONAL	1	TRUE	1	0.244466812841293	2		268	405	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426748	121426748	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059676-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	100	303	0	ENST00000257555.6:c.439C>T	p.His147Tyr	p.H147Y	ENST00000257555		147	Cac/Tac	2/10	0.244466812841293	3	FACETS	1	0.913	1	1	0.913	1	CLONAL	2	TRUE	1	0.244466812841293	3		303	451	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2161812	2161812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059676-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	92	209	0	ENST00000349721.2:c.4108C>T	p.Arg1370Cys	p.R1370C	ENST00000349721	NM_003070.3	1370	Cgc/Tgc	28/34	0.217381196346252	3	FACETS	0.929	0.835	1	0.929	0.835	1	CLONAL	3	TRUE	0	0.244466812841293	3		209	303	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267597	7267597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059677-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	23	285	1	ENST00000302850.5:c.411G>A	p.Met137Ile	p.M137I	ENST00000302850	NM_000208.2	137	atG/atA	2/22	1	2	FACETS	0.675	0.526	0.848	0.675	0.526	0.848	SUBCLONAL	1	TRUE	1	0.180210836450348	2		286	378	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428410	49428411	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1284500089	NA	P-0059677-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	65	336	0	ENST00000301067.7:c.10394dup	p.Pro3466ThrfsTer2	p.P3466Tfs*2	ENST00000301067	NM_003482.3	3465	gga/ggGa	36/54	0.144960146022312	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.180210836450348	2		336	308	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1690564	1690564	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1283393461	NA	P-0059677-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	21	318	0	ENST00000378625.1:c.551G>A	p.Gly184Glu	p.G184E	ENST00000378625	NM_001198994.1	184	gGa/gAa	5/14	1	2	FACETS	0.715	0.55	0.907	0.715	0.55	0.907	CLONAL	1	TRUE	1	0.180210836450348	2		318	326	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937174	36937174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059677-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	59	372	0	ENST00000361632.4:c.1145G>A	p.Gly382Glu	p.G382E	ENST00000361632		382	gGg/gAg	9/16	1	2	FACETS	0.848	0.733	0.973	1	0.974	1	CLONAL	2	TRUE	1	0.180210836450348	2		372	386	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281878	49281878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059677-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	17	292	0	ENST00000282018.3:c.925G>A	p.Gly309Arg	p.G309R	ENST00000282018	NM_020377.2	309	Ggg/Agg	1/1	0.0512849331644247	3	FACETS	0.623	0.464	0.812	0.312	0.232	0.406	INDETERMINATE	1	TRUE	1	0.180210836450348	3		292	330	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6230643	6230643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059677-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	25	333	0	ENST00000252674.7:c.358G>A	p.Glu120Lys	p.E120K	ENST00000252674	NM_005934.3	120	Gag/Aag	4/12	1	2	FACETS	0.841	0.663	1	0.841	0.663	1	CLONAL	1	TRUE	1	0.180210836450348	2		333	330	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73113251	73113251	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059677-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	11	187	0	ENST00000356692.5:c.592G>A	p.Asp198Asn	p.D198N	ENST00000356692		198	Gac/Aac	7/9	1	2	FACETS	0.601	0.415	0.832	0.601	0.415	0.832	SUBCLONAL	1	TRUE	1	0.180210836450348	2		187	203	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878964	151878964	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059677-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	19	330	0	ENST00000262189.6:c.5981del	p.Thr1994MetfsTer6	p.T1994Mfs*6	ENST00000262189	NM_170606.2	1994	aCt/at	36/59	1	2	FACETS	0.787	0.598	1	0.787	0.598	1	CLONAL	1	TRUE	1	0.180210836450348	2		330	268	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891305	101891305	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059677-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	30	215	0	ENST00000374994.4:c.266C>G	p.Ser89Cys	p.S89C	ENST00000374994	NM_004612.2	89	tCt/tGt	2/9	0.144960146022312	2	FACETS	1	0.884	1	0.568	0.459	0.691	CLONAL	1	TRUE	0	0.180210836450348	2		215	293	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748290	41748290	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	68	264	0	ENST00000226382.2:c.479C>T	p.Ala160Val	p.A160V	ENST00000226382	NM_003924.3	160	gCg/gTg	3/3	0.262390304134128	1	FACETS	0.755	0.664	0.85	0.755	0.664	0.85	INDETERMINATE	1	TRUE	0	0.516250856610663	1		264	259	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420856	49420856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200747934	NA	P-0059678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	49	300	0	ENST00000301067.7:c.14893G>A	p.Ala4965Thr	p.A4965T	ENST00000301067	NM_003482.3	4965	Gcc/Acc	48/54	0.516250856610663	1	FACETS	0.575	0.491	0.665	0.575	0.491	0.665	SUBCLONAL	1	TRUE	0	0.516250856610663	1		300	245	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982070	38982070	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059678-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	16	212	0	ENST00000357387.3:c.652T>C	p.Cys218Arg	p.C218R	ENST00000357387	NM_152756.3	218	Tgc/Cgc	8/38	0.440697301575233	3	FACETS	0.353	0.261	0.462	0.176	0.13	0.231	SUBCLONAL	1	TRUE	1	0.516250856610663	3		212	221	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645291	67645291	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059680-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	54	308	0	ENST00000264010.4:c.556C>T	p.Gln186Ter	p.Q186*	ENST00000264010	NM_006565.3	186	Cag/Tag	3/12	1	2	FACETS	0.92	0.788	1	0.92	0.788	1	CLONAL	1	TRUE	1	0.288335337605895	2		308	407	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842396	68842435	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAGAGACTGGGTTATTCCTCCCATCAGCTGCCCAGAAA	AAGAGAGACTGGGTTATTCCTCCCATCAGCTGCCCAGAAA	-	novel	NA	P-0059680-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	46	261	0	ENST00000261769.5:c.458_497del	p.Lys153MetfsTer49	p.K153Mfs*49	ENST00000261769	NM_004360.3	153	AAGAGAGACTGGGTTATTCCTCCCATCAGCTGCCCAGAAAat/at	4/16	0.288335337605895	1	FACETS	0.889	0.753	1	0.889	0.753	1	CLONAL	1	TRUE	0	0.288335337605895	1		261	307	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648387	30648407	+	inframe_deletion	In_Frame_Del	DEL	GCTGCTCAGGGGCCTGTGGCC	GCTGCTCAGGGGCCTGTGGCC	-	novel	NA	P-0059680-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	76	268	0	ENST00000295754.5:c.17_37del	p.Leu6_Leu12del	p.L6_L12del	ENST00000295754	NM_003242.5	4	ggGCTGCTCAGGGGCCTGTGGCCg/ggg	1/7	0.288335337605895	2	FACETS	0.931	0.826	1	0.931	0.826	1	CLONAL	2	TRUE	0	0.288335337605895	2		268	283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577518	7577518	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519995	NA	P-0059681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	140	396	0	ENST00000269305.4:c.763A>T	p.Ile255Phe	p.I255F	ENST00000269305	NM_001126112.2	255	Atc/Ttc	7/11	0.473748120220207	2	FACETS	0.926	0.858	0.993	0.926	0.858	0.993	CLONAL	2	TRUE	0	0.507596047061605	2		396	298	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357714	70357714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1009330609	NA	P-0059681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	43	210	0	ENST00000374080.3:c.5965C>T	p.Arg1989Cys	p.R1989C	ENST00000374080		1989	Cgc/Tgc	41/45	0.380907095293971	2	FACETS	0.541	0.455	0.636			1	SUBCLONAL	1	TRUE	NA	0.507596047061605	2		210	313	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	40	121	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.818	0.688	0.959	1	0.962	1	CLONAL	2	TRUE	1	0.262843885477908	2		121	186	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578240	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0059682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	84	264	0	ENST00000269305.4:c.608_609dup	p.Glu204TrpfsTer44	p.E204Wfs*44	ENST00000269305	NM_001126112.2	203	-/TG	6/11	0.252077855834002	2	FACETS	0.795	0.706	0.889	0.795	0.706	0.889	SUBCLONAL	2	TRUE	0	0.262843885477908	2		264	402	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581234	48581234	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767332	NA	P-0059682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	24	168	0	ENST00000342988.3:c.538C>T	p.Gln180Ter	p.Q180*	ENST00000342988	NM_005359.5	180	Caa/Taa	5/12	0.262843885477908	1	FACETS	0.475	0.372	0.593	0.475	0.372	0.593	SUBCLONAL	1	TRUE	0	0.262843885477908	1		168	334	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436185	56436185	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0059682-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	74	183	0	ENST00000407977.2:c.953-1G>T		p.X318_splice	ENST00000407977		318			0.252077855834002	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.262843885477908	2		183	242	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	81	525	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.600844331996889	2		525	220	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	48	480	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.624	0.532	0.724	0.624	0.532	0.724	SUBCLONAL	1	TRUE	1	0.600844331996889	2		480	256	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	65	296	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	1	2	FACETS	0.759	0.664	0.86	0.759	0.664	0.86	SUBCLONAL	1	TRUE	1	0.600844331996889	2		296	285	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871992	45871992	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	69	227	0	ENST00000391945.4:c.256G>C	p.Glu86Gln	p.E86Q	ENST00000391945	NM_000400.3	86	Gag/Cag	5/23	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.600844331996889	2		227	214	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	343	293	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	0.529399007053969	4	FACETS	0.886	0.852	0.918	1	0.994	1	CLONAL	4	TRUE	1	0.600844331996889	4		293	516	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864656	37864656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs950730453	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	132	361	0	ENST00000269571.5:c.308G>A	p.Arg103Gln	p.R103Q	ENST00000269571		103	cGa/cAa	3/27	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.600844331996889	2		361	389	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882319	89882319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	97	273	0	ENST00000389301.3:c.155G>A	p.Arg52Gln	p.R52Q	ENST00000389301	NM_000135.2	52	cGa/cAa	2/43	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.600844331996889	2		273	283	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652120	36652130	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCCCGGCGA	GGCCCCGGCGA	-	novel	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	95	385	0	ENST00000244741.5:c.246_256del	p.Arg83GlyfsTer2	p.R83Gfs*2	ENST00000244741	NM_000389.4	81	gGGCCCCGGCGA/g	2/3	1	2	FACETS	0.917	0.824	1	0.917	0.824	1	CLONAL	1	TRUE	1	0.600844331996889	2		385	345	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	68	294	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			1	2	FACETS	0.8	0.703	0.903	0.8	0.703	0.903	CLONAL	1	TRUE	1	0.600844331996889	2		294	283	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158326	108158326	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	32	170	0	ENST00000278616.4:c.3994-1G>C		p.X1332_splice	ENST00000278616	NM_000051.3	1332			1	2	FACETS	0.826	0.683	0.981	0.826	0.683	0.981	CLONAL	1	TRUE	1	0.600844331996889	2		170	129	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052983	180052983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1221447329	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	95	409	1	ENST00000261937.6:c.1307C>T	p.Ser436Leu	p.S436L	ENST00000261937	NM_182925.4	436	tCg/tTg	10/30	1	2	FACETS	0.941	0.846	1	0.941	0.846	1	CLONAL	1	TRUE	1	0.600844331996889	2		410	336	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420292	49420292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761700549	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	76	380	0	ENST00000301067.7:c.15457C>T	p.Arg5153Trp	p.R5153W	ENST00000301067	NM_003482.3	5153	Cgg/Tgg	48/54	1	2	FACETS	0.796	0.704	0.892	0.796	0.704	0.892	SUBCLONAL	1	TRUE	1	0.600844331996889	2		380	318	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157824	106157824	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs754287180	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	76	252	0	ENST00000380013.4:c.2725C>T	p.Gln909Ter	p.Q909*	ENST00000380013	NM_001127208.2	909	Caa/Taa	3/11	1	2	FACETS	0.917	0.813	1	0.917	0.813	1	CLONAL	1	TRUE	1	0.600844331996889	2		252	276	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651527	52651527	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	49	206	0	ENST00000394830.3:c.1569G>A	p.Met523Ile	p.M523I	ENST00000394830	NM_018313.4	523	atG/atA	15/30	1	2	FACETS	0.82	0.704	0.944	0.82	0.704	0.944	CLONAL	1	TRUE	1	0.600844331996889	2		206	199	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932248	36932248	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	94	428	1	ENST00000361632.4:c.2221C>T	p.Gln741Ter	p.Q741*	ENST00000361632		741	Caa/Taa	16/16	1	2	FACETS	0.832	0.746	0.922	0.832	0.746	0.922	CLONAL	1	TRUE	1	0.600844331996889	2		429	376	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628101	187628101	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	95	307	0	ENST00000441802.2:c.2881C>T	p.Gln961Ter	p.Q961*	ENST00000441802	NM_005245.3	961	Cag/Tag	2/27	1	2	FACETS	0.95	0.854	1	0.95	0.854	1	CLONAL	1	TRUE	1	0.600844331996889	2		307	333	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	83	365	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	0.675	0.599	0.756	0.675	0.599	0.756	SUBCLONAL	1	TRUE	1	0.600844331996889	2		365	409	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132097	176132097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	29	149	0	ENST00000367669.3:c.670G>A	p.Asp224Asn	p.D224N	ENST00000367669	NM_022457.5	224	Gat/Aat	5/20	1	2	FACETS	0.743	0.606	0.892	0.743	0.606	0.892	SUBCLONAL	1	TRUE	1	0.600844331996889	2		149	130	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710670	114710670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	86	286	0	ENST00000543371.1:c.155C>T	p.Ser52Leu	p.S52L	ENST00000543371	NM_001198531.1	52	tCa/tTa	1/14	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.600844331996889	2		286	286	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211495	46211496	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCT	novel	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	33	157	0	ENST00000334344.6:c.464_465insTGCC	p.Asn156AlafsTer3	p.N156Afs*3	ENST00000334344	NM_152641.2	154	tcg/tcGCCTg	5/21	1	2	FACETS	0.796	0.659	0.944	0.796	0.659	0.944	CLONAL	1	TRUE	1	0.600844331996889	2		157	138	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426746	49426746	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	109	411	0	ENST00000301067.7:c.11742del	p.Gln3914HisfsTer65	p.Q3914Hfs*65	ENST00000301067	NM_003482.3	3914	caG/ca	39/54	1	2	FACETS	0.965	0.875	1	0.965	0.875	1	CLONAL	1	TRUE	1	0.600844331996889	2		411	376	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885937	111885937	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	74	377	0	ENST00000341259.2:c.1559C>T	p.Ser520Leu	p.S520L	ENST00000341259	NM_005475.2	520	tCa/tTa	8/8	1	2	FACETS	0.714	0.629	0.804	0.714	0.629	0.804	SUBCLONAL	1	TRUE	1	0.600844331996889	2		377	345	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124346	2124346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	83	356	0	ENST00000219476.3:c.2501C>T	p.Ser834Leu	p.S834L	ENST00000219476	NM_000548.3	834	tCa/tTa	22/42	1	2	FACETS	0.94	0.839	1	0.94	0.839	1	CLONAL	1	TRUE	1	0.600844331996889	2		356	294	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041993	14041993	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	69	288	0	ENST00000311895.7:c.2540G>T	p.Gly847Val	p.G847V	ENST00000311895	NM_005236.2	847	gGt/gTt	11/11	1	2	FACETS	0.806	0.709	0.909	0.806	0.709	0.909	CLONAL	1	TRUE	1	0.600844331996889	2		288	285	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701036	29701036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1475978079	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	58	250	1	ENST00000356175.3:c.8320G>A	p.Asp2774Asn	p.D2774N	ENST00000356175	NM_000267.3	2774	Gac/Aac	57/57	1	2	FACETS	0.906	0.79	1	0.906	0.79	1	CLONAL	1	TRUE	1	0.600844331996889	2		251	213	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591795	48591795	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	28	213	0	ENST00000342988.3:c.958C>T	p.Pro320Ser	p.P320S	ENST00000342988	NM_005359.5	320	Cct/Tct	9/12	1	2	FACETS	0.507	0.408	0.617	0.507	0.408	0.617	SUBCLONAL	1	TRUE	1	0.600844331996889	2		213	184	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37045950	37045950	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	35	225	0	ENST00000231790.2:c.365G>A	p.Gly122Glu	p.G122E	ENST00000231790	NM_000249.3	122	gGa/gAa	4/19	1	2	FACETS	0.613	0.508	0.729	0.613	0.508	0.729	SUBCLONAL	1	TRUE	1	0.600844331996889	2		225	190	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169981184	169981184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	51	151	0	ENST00000295797.4:c.331G>A	p.Glu111Lys	p.E111K	ENST00000295797	NM_002740.5	111	Gaa/Aaa	4/18	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.600844331996889	2		151	167	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446932	187446932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	100	356	0	ENST00000232014.4:c.1261G>A	p.Glu421Lys	p.E421K	ENST00000232014	NM_001130845.1	421	Gag/Aag	5/10	1	2	FACETS	0.885	0.797	0.977	0.885	0.797	0.977	CLONAL	1	TRUE	1	0.600844331996889	2		356	376	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540037	187540037	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	69	263	0	ENST00000441802.2:c.7703T>A	p.Leu2568Ter	p.L2568*	ENST00000441802	NM_005245.3	2568	tTa/tAa	10/27	1	2	FACETS	0.89	0.785	1	0.89	0.785	1	CLONAL	1	TRUE	1	0.600844331996889	2		263	258	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250542	26250542	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	115	438	0	ENST00000446824.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000446824	NM_021018.2	98	Gag/Aag	1/1	1	2	FACETS	0.987	0.897	1	0.987	0.897	1	CLONAL	1	TRUE	1	0.600844331996889	2		438	388	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109309770	109309770	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	40	185	0	ENST00000436639.2:c.1545G>A	p.Trp515Ter	p.W515*	ENST00000436639	NM_014454.2	515	tgG/tgA	9/10	1	2	FACETS	0.679	0.571	0.797	0.679	0.571	0.797	SUBCLONAL	1	TRUE	1	0.600844331996889	2		185	196	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519358	137519358	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	57	255	0	ENST00000367739.4:c.1280A>G	p.Asp427Gly	p.D427G	ENST00000367739	NM_000416.2	427	gAc/gGc	7/7	1	2	FACETS	0.973	0.848	1	0.973	0.848	1	CLONAL	1	TRUE	1	0.600844331996889	2		255	195	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997709	149997709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	71	254	0	ENST00000253339.5:c.2758G>A	p.Glu920Lys	p.E920K	ENST00000253339		920	Gaa/Aaa	5/7	1	2	FACETS	0.957	0.846	1	0.957	0.846	1	CLONAL	1	TRUE	1	0.600844331996889	2		254	247	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005387	150005387	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	99	364	0	ENST00000253339.5:c.838A>G	p.Asn280Asp	p.N280D	ENST00000253339		280	Aac/Gac	3/7	1	2	FACETS	0.908	0.818	1	0.908	0.818	1	CLONAL	1	TRUE	1	0.600844331996889	2		364	363	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270475	98270475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	57	222	0	ENST00000331920.6:c.169G>A	p.Asp57Asn	p.D57N	ENST00000331920	NM_000264.3	57	Gac/Aac	1/24	1	2	FACETS	0.724	0.627	0.828	0.724	0.627	0.828	SUBCLONAL	1	TRUE	1	0.600844331996889	2		222	262	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424651	47424651	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs779536112	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	254	330	0	ENST00000377045.4:c.459G>T	p.Gln153His	p.Q153H	ENST00000377045	NM_001654.4	153	caG/caT	6/16	0.529399007053969	4	FACETS	0.998	0.949	1	0.998	0.949	1	CLONAL	3	TRUE	1	0.600844331996889	4		330	452	SUCCESS
AR	367	MSKCC	GRCh37	X	66765690	66765690	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	119	425	0	ENST00000374690.3:c.702C>A	p.Asp234Glu	p.D234E	ENST00000374690	NM_000044.3	234	gaC/gaA	1/8	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.600844331996889	2		425	385	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0059704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	35	634	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.377524733650539	2		634	134	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246293	46246293	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	32	686	0	ENST00000334344.6:c.4387C>T	p.Gln1463Ter	p.Q1463*	ENST00000334344	NM_152641.2	1463	Caa/Taa	15/21	0.27952986073912	3	FACETS	1	0.863	1	0.693	0.578	0.814	CLONAL	2	TRUE	0	0.377524733650539	3		686	97	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143326415	143326415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773384747	NA	P-0059704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	26	558	0	ENST00000262992.4:c.199G>A	p.Val67Ile	p.V67I	ENST00000262992	NM_001101669.1	67	Gta/Ata	4/24	0.377524733650539	1	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	0	0.377524733650539	1		558	103	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099060	27099072	+	frameshift_variant	Frame_Shift_Del	DEL	ACTTAAAGCCACC	ACTTAAAGCCACC	-	novel	NA	P-0059704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	18	885	0	ENST00000324856.7:c.3477_3489del	p.Asp1159GlufsTer17	p.D1159Efs*17	ENST00000324856	NM_006015.4	1159	gACTTAAAGCCACCa/ga	13/20	1	2	FACETS	0.437	0.33	0.564	0.437	0.33	0.564	SUBCLONAL	1	TRUE	1	0.377524733650539	2		885	218	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856392	111856392	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs868066223	NA	P-0059704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	59	788	0	ENST00000341259.2:c.443G>T	p.Arg148Leu	p.R148L	ENST00000341259	NM_005475.2	148	cGc/cTc	2/8	0.377524733650539	3	FACETS	1	0.915	1	1	0.915	1	CLONAL	2	TRUE	1	0.377524733650539	3		788	176	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126117	2126117	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	10	699	0	ENST00000219476.3:c.2688G>T	p.Trp896Cys	p.W896C	ENST00000219476	NM_000548.3	896	tgG/tgT	24/42	1	2	FACETS	0.27	0.183	0.38	0.27	0.183	0.38	SUBCLONAL	1	TRUE	1	0.377524733650539	2		699	196	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797182	42797182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	30	977	0	ENST00000575354.2:c.3544G>A	p.Ala1182Thr	p.A1182T	ENST00000575354	NM_015125.3	1182	Gca/Aca	15/20	1	2	FACETS	0.688	0.557	0.834	0.688	0.557	0.834	SUBCLONAL	1	TRUE	1	0.377524733650539	2		977	231	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37637681	37637681	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1317148335	NA	P-0059704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	20	841	2	ENST00000249071.6:c.53G>A	p.Cys18Tyr	p.C18Y	ENST00000249071	NM_002872.4	18	tGc/tAc	2/7	1	2	FACETS	0.731	0.564	0.922	0.731	0.564	0.922	CLONAL	1	TRUE	1	0.377524733650539	2		843	145	SUCCESS
ALB	213	MSKCC	GRCh37	4	74270058	74270058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1022250698	NA	P-0059704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	12	473	0	ENST00000295897.4:c.14C>T	p.Thr5Ile	p.T5I	ENST00000295897	NM_000477.5	5	aCc/aTc	1/15	0.377524733650539	1	FACETS	0.973	0.704	1	0.973	0.704	1	CLONAL	1	TRUE	0	0.377524733650539	1		473	53	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401694	401694	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	49	915	0	ENST00000380956.4:c.1016C>T	p.Pro339Leu	p.P339L	ENST00000380956	NM_001195286.1	339	cCc/cTc	7/9	0.165139548747706	4	FACETS	0.995	0.843	1	0.497	0.421	0.581	CLONAL	1	FALSE	2	0.243027787659478	4		915	504	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183802	10183802	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	37	781	0	ENST00000256474.2:c.272del	p.Phe91SerfsTer68	p.F91Sfs*68	ENST00000256474	NM_000551.3	91	Ttc/tc	1/3	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	FALSE	1	0.243027787659478	2		781	294	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682391	52682392	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	A	novel	NA	P-0059705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	25	480	0	ENST00000394830.3:c.781_782delinsT	p.Thr261PhefsTer22	p.T261Ffs*22	ENST00000394830	NM_018313.4	261	ACt/Tt	8/30	1	2	FACETS	0.748	0.591	0.928	0.748	0.591	0.928	CLONAL	1	FALSE	1	0.243027787659478	2		480	275	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971105	21971105	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	316	681	0	ENST00000304494.5:c.253G>C	p.Ala85Pro	p.A85P	ENST00000304494	NM_000077.4	85	Gct/Cct	2/3	0.42664328114629	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.42664328114629	2		681	612	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736165	204736166	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0059706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	102	531	1	ENST00000302823.3:c.529dup	p.Tyr177LeufsTer2	p.Y177Lfs*2	ENST00000302823	NM_005214.4	174	-/T	3/4	0.378880983835061	4	FACETS	0.905	0.809	1	0.302	0.269	0.336	CLONAL	1	TRUE	1	0.42664328114629	4		532	754	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576851	7576851	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0059706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	273	609	0	ENST00000269305.4:c.993+2T>C		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.373696001501991	2	FACETS	0.983	0.929	1	0.983	0.929	1	CLONAL	2	TRUE	0	0.42664328114629	2		609	651	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436603	8436603	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	153	341	0	ENST00000356435.5:c.4075C>A	p.Gln1359Lys	p.Q1359K	ENST00000356435		1359	Cag/Aag	24/35	0.42664328114629	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.42664328114629	2		341	333	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245873	41245873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	83	459	0	ENST00000357654.3:c.1675G>T	p.Gly559Cys	p.G559C	ENST00000357654	NM_007294.3	559	Ggt/Tgt	10/23	0.422862574406695	3	FACETS	1	0.917	1	0.521	0.462	0.584	CLONAL	1	TRUE	1	0.42664328114629	3		459	453	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576240	88576240	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	163	616	0	ENST00000360948.2:c.1433C>A	p.Ala478Asp	p.A478D	ENST00000360948	NM_001012338.2	478	gCc/gAc	13/19	0.416357558187893	2	FACETS	0.794	0.735	0.855	0.794	0.735	0.855	SUBCLONAL	2	TRUE	0	0.42664328114629	2		616	481	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599867	10599867	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0059706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	266	624	0	ENST00000171111.5:c.1708+1G>T		p.X570_splice	ENST00000171111	NM_203500.1	570			0.416357558187893	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.42664328114629	2		624	601	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097855	8097855	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	210	646	0	ENST00000346208.3:c.237C>A	p.His79Gln	p.H79Q	ENST00000346208		79	caC/caA	2/6	0.383576817508489	3	FACETS	0.987	0.923	1	0.987	0.923	1	CLONAL	2	TRUE	1	0.42664328114629	3		646	605	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117745	108117745	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	73	358	0	ENST00000278616.4:c.956T>C	p.Leu319Pro	p.L319P	ENST00000278616	NM_000051.3	319	cTa/cCa	8/63	1	2	FACETS	0.983	0.866	1	0.983	0.866	1	CLONAL	1	TRUE	1	0.42664328114629	2		358	348	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153482	108153482	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	80	349	0	ENST00000278616.4:c.3622G>C	p.Asp1208His	p.D1208H	ENST00000278616	NM_000051.3	1208	Gac/Cac	25/63	1	2	FACETS	0.893	0.79	1	0.893	0.79	1	CLONAL	1	TRUE	1	0.42664328114629	2		349	420	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	461428	461428	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	98	387	0	ENST00000399788.2:c.1092G>T	p.Gln364His	p.Q364H	ENST00000399788	NM_001042603.1	364	caG/caT	9/28	0.422862574406695	3	FACETS	0.999	0.894	1	0.499	0.447	0.555	CLONAL	1	TRUE	1	0.42664328114629	3		387	558	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491401	18491401	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	124	397	0	ENST00000266497.5:c.1314C>A	p.Cys438Ter	p.C438*	ENST00000266497		438	tgC/tgA	8/31	0.422862574406695	3	FACETS	0.818	0.746	0.893	0.818	0.746	0.893	CLONAL	2	TRUE	1	0.42664328114629	3		397	431	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117322	115117322	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0059706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	162	466	0	ENST00000257566.3:c.852C>G	p.Tyr284Ter	p.Y284*	ENST00000257566	NM_016569.3	284	taC/taG	4/8	0.422862574406695	3	FACETS	0.891	0.823	0.961	0.891	0.823	0.961	CLONAL	2	TRUE	1	0.42664328114629	3		466	517	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347071	347071	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	113	541	0	ENST00000262320.3:c.1940G>T	p.Arg647Leu	p.R647L	ENST00000262320	NM_003502.3	647	cGc/cTc	7/11	0.42664328114629	3	FACETS	1	0.942	1	0.531	0.479	0.586	CLONAL	1	TRUE	1	0.42664328114629	3		541	605	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627434	37627434	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	263	643	0	ENST00000447079.4:c.1349G>T	p.Ser450Ile	p.S450I	ENST00000447079	NM_015083.1	450	aGt/aTt	2/14	0.422862574406695	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.42664328114629	3		643	719	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144062	11144062	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	246	656	0	ENST00000358026.2:c.3643C>G	p.Leu1215Val	p.L1215V	ENST00000358026	NM_001128849.1	1215	Cta/Gta	26/36	0.416357558187893	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.42664328114629	2		656	539	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723088	52723088	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	226	609	0	ENST00000322088.6:c.1273G>A	p.Glu425Lys	p.E425K	ENST00000322088	NM_014225.5	425	Gag/Aag	10/15	0.416357558187893	2	FACETS	0.943	0.885	1	0.943	0.885	1	CLONAL	2	TRUE	0	0.42664328114629	2		609	562	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116164	209116164	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	247	465	0	ENST00000345146.2:c.112G>T	p.Asp38Tyr	p.D38Y	ENST00000345146	NM_005896.2	38	Gat/Tat	3/10	0.378880983835061	4	FACETS	0.888	0.836	0.941	0.888	0.836	0.941	CLONAL	3	TRUE	1	0.42664328114629	4		465	620	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265219	46265219	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	260	634	0	ENST00000371998.3:c.2089G>C	p.Glu697Gln	p.E697Q	ENST00000371998		697	Gag/Cag	12/23	0.359718216268476	2	FACETS	0.923	0.871	0.977	0.923	0.871	0.977	CLONAL	2	TRUE	0	0.42664328114629	2		634	660	SUCCESS
ATR	545	MSKCC	GRCh37	3	142180811	142180811	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	175	368	0	ENST00000350721.4:c.7163C>T	p.Pro2388Leu	p.P2388L	ENST00000350721	NM_001184.3	2388	cCt/cTt	42/47	0.35799510357563	3	FACETS	0.88	0.822	0.938	0.88	0.822	0.938	CLONAL	3	TRUE	0	0.42664328114629	3		368	377	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1272328	1272328	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs483352771	NA	P-0059706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	183	565	0	ENST00000310581.5:c.2354C>A	p.Pro785Gln	p.P785Q	ENST00000310581	NM_198253.2	785	cCg/cAg	7/16	0.243847152043561	5	FACETS	1	0.981	1	0.778	0.722	0.835	INDETERMINATE	2	TRUE	2	0.42664328114629	5		565	603	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031887	26031887	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	135	624	0	ENST00000244661.2:c.402A>C	p.Glu134Asp	p.E134D	ENST00000244661	NM_003537.3	134	gaA/gaC	1/1	0.42664328114629	3	FACETS	0.963	0.876	1	0.482	0.438	0.528	CLONAL	1	TRUE	1	0.42664328114629	3		624	797	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335740	81335740	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	175	394	0	ENST00000222390.5:c.1620C>A	p.Asp540Glu	p.D540E	ENST00000222390	NM_000601.4	540	gaC/gaA	15/18	0.35799510357563	3	FACETS	0.86	0.803	0.917	0.86	0.803	0.917	CLONAL	3	TRUE	0	0.42664328114629	3		394	386	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939505	68939505	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	148	390	0	ENST00000288368.4:c.490G>T	p.Gly164Ter	p.G164*	ENST00000288368	NM_024870.2	164	Gga/Tga	5/40	0.42664328114629	2	FACETS	0.933	0.863	1	0.933	0.863	1	CLONAL	2	TRUE	0	0.42664328114629	2		390	372	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912815	100912815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1000609240	NA	P-0059707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	77	413	0	ENST00000325455.5:c.2507G>A	p.Arg836Gln	p.R836Q	ENST00000325455	NM_001202474.3	836	cGa/cAa	7/8	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.43040231743973	2		413	337	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497359	149497359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397509382	NA	P-0059707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	127	624	0	ENST00000261799.4:c.2959C>T	p.Arg987Trp	p.R987W	ENST00000261799	NM_002609.3	987	Cgg/Tgg	22/23	0.160539367609608	4	FACETS	0.779	0.709	0.852	0.519	0.472	0.568	INDETERMINATE	2	TRUE	1	0.43040231743973	4		624	542	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186829	108186829	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	85	512	0	ENST00000278616.4:c.6187G>T	p.Gly2063Ter	p.G2063*	ENST00000278616	NM_000051.3	2063	Gga/Tga	42/63	1	2	FACETS	0.932	0.828	1	0.932	0.828	1	CLONAL	1	TRUE	1	0.43040231743973	2		512	424	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861725	59861725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	48	403	0	ENST00000259008.2:c.1534G>A	p.Glu512Lys	p.E512K	ENST00000259008	NM_032043.2	512	Gag/Aag	11/20	1	2	FACETS	0.811	0.691	0.942	0.811	0.691	0.942	CLONAL	1	TRUE	1	0.43040231743973	2		403	275	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188277	10188277	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	114	453	0	ENST00000256474.2:c.420del	p.Asn141MetfsTer18	p.N141Mfs*18	ENST00000256474	NM_000551.3	140	ctC/ct	2/3	0.43040231743973	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.43040231743973	1		453	318	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443748	52443761	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GGGTGAAGAGGCCT	GGGTGAAGAGGCCT	-	novel	NA	P-0059707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	100	841	0	ENST00000460680.1:c.38-2_49del		p.X13_splice	ENST00000460680	NM_004656.3	13		2/17	0.43040231743973	1	FACETS	0.898	0.808	0.993	0.898	0.808	0.993	CLONAL	1	TRUE	0	0.43040231743973	1		841	406	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588152	67588152	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	58	464	0	ENST00000274335.5:c.982T>G	p.Leu328Val	p.L328V	ENST00000274335		328	Tta/Gta	7/15	1	2	FACETS	0.783	0.677	0.898	0.783	0.677	0.898	SUBCLONAL	1	TRUE	1	0.43040231743973	2		464	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0059708-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	529	882	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.263432632779615	6	FACETS	0.934	0.899	0.969	0.934	0.899	0.969	CLONAL	6	TRUE	0	0.263432632779615	6		882	1094	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150923415	150923415	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059708-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	39	628	0	ENST00000271640.5:c.2062G>C	p.Asp688His	p.D688H	ENST00000271640	NM_001145415.1	688	Gat/Cat	13/22	1	2	FACETS	0.533	0.441	0.636	0.533	0.441	0.636	SUBCLONAL	1	TRUE	1	0.263432632779615	2		628	555	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308417	30308417	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059708-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	95	619	0	ENST00000262643.3:c.431T>G	p.Met144Arg	p.M144R	ENST00000262643	NM_001238.2	144	aTg/aGg	6/12	0.126343012774185	3	FACETS	1	0.956	1	0.572	0.509	0.638	INDETERMINATE	1	TRUE	1	0.263432632779615	3		619	714	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485757	57485757	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059708-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	135	617	0	ENST00000371085.3:c.1058G>C	p.Gly353Ala	p.G353A	ENST00000371085	NM_000516.4	353	gGa/gCa	13/13	0.0995510840409994	4	FACETS	0.885	0.805	0.968	0.885	0.805	0.968	INDETERMINATE	2	TRUE	2	0.263432632779615	4		617	732	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805550	32805550	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059708-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	148	804	0	ENST00000374899.4:c.461C>G	p.Ala154Gly	p.A154G	ENST00000374899	NM_018833.2	154	gCc/gGc	2/12	0.0995510840409994	4	FACETS	0.777	0.709	0.848	0.777	0.709	0.848	INDETERMINATE	2	TRUE	2	0.263432632779615	4		804	914	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0059709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	11	688	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.633038944287932	1	FACETS	0.079	0.054	0.111	0.079	0.054	0.111	SUBCLONAL	1	TRUE	0	0.633038944287932	1		688	299	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781504	NA	P-0059709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	97	810	0	ENST00000269305.4:c.314G>T	p.Gly105Val	p.G105V	ENST00000269305	NM_001126112.2	105	gGc/gTc	4/11	0.633038944287932	1	FACETS	0.708	0.639	0.779	0.708	0.639	0.779	SUBCLONAL	1	TRUE	0	0.633038944287932	1		810	296	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946227	81946227	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1295648437	NA	P-0059709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	125	729	0	ENST00000359376.3:c.1960G>A	p.Gly654Arg	p.G654R	ENST00000359376	NM_002661.3	654	Gga/Aga	19/33	1	2	FACETS	0.83	0.756	0.907	0.83	0.756	0.907	CLONAL	1	TRUE	1	0.633038944287932	2		729	476	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888695	76888695	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	95	192	0	ENST00000373344.5:c.5134G>A	p.Gly1712Ser	p.G1712S	ENST00000373344	NM_000489.3	1712	Ggc/Agc	19/35	0.21729789648407	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.633038944287932	2		192	231	SUCCESS
ALB	213	MSKCC	GRCh37	4	74270123	74270123	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs141733599	NA	P-0059709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	178	473	0	ENST00000295897.4:c.79C>T	p.His27Tyr	p.H27Y	ENST00000295897	NM_000477.5	27	Cac/Tac	1/15	0.215661472239085	4	FACETS	0.773	0.716	0.831	0.773	0.716	0.831	INDETERMINATE	2	TRUE	2	0.633038944287932	4		473	594	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0059710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	165	593	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.260558473182872	3	FACETS	1	0.941	1	0.677	0.628	0.727	INDETERMINATE	2	TRUE	0	0.450203742876938	3		593	442	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609305	39609305	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	138	320	0	ENST00000262039.4:c.1607G>C	p.Arg536Thr	p.R536T	ENST00000262039	NM_002647.2	536	aGa/aCa	15/25	0.233958479684783	4	FACETS	0.983	0.902	1	0.492	0.451	0.534	INDETERMINATE	2	TRUE	0	0.450203742876938	4		320	452	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268925	115268925	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	206	355	0	ENST00000438362.2:c.1685C>G	p.Ser562Cys	p.S562C	ENST00000438362	NM_001242891.1	562	tCc/tGc	14/20	0.291800096388616	5	FACETS	0.93	0.876	0.985	0.744	0.701	0.788	CLONAL	4	TRUE	0	0.450203742876938	5		355	412	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246274	46246274	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	113	410	0	ENST00000334344.6:c.4368G>C	p.Leu1456Phe	p.L1456F	ENST00000334344	NM_152641.2	1456	ttG/ttC	15/21	0.444421035721782	4	FACETS	1	0.981	1	0.687	0.62	0.756	CLONAL	1	TRUE	2	0.450203742876938	4		410	530	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864799	57864799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	229	574	0	ENST00000228682.2:c.2276C>A	p.Thr759Asn	p.T759N	ENST00000228682	NM_005269.2	759	aCc/aAc	12/12	0.444421035721782	4	FACETS	0.839	0.783	0.897	0.839	0.783	0.897	CLONAL	2	TRUE	2	0.450203742876938	4		574	879	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39618766	39618766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	49	237	0	ENST00000262039.4:c.1990G>A	p.Asp664Asn	p.D664N	ENST00000262039	NM_002647.2	664	Gac/Aac	18/25	0.233958479684783	4	FACETS	1	0.961	1	0.352	0.301	0.407	INDETERMINATE	1	TRUE	0	0.450203742876938	4		237	224	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55991415	55991415	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	201	488	0	ENST00000263923.4:c.46G>T	p.Glu16Ter	p.E16*	ENST00000263923	NM_002253.2	16	Gag/Tag	1/30	0.260558473182872	3	FACETS	0.838	0.78	0.897	0.558	0.52	0.598	INDETERMINATE	2	TRUE	0	0.450203742876938	3		488	653	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0059711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	32	185	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.368742400825179	3	FACETS	1	0.944	1	0.454	0.38	0.532	INDETERMINATE	1	TRUE	0	0.707322903365365	3		185	90	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237691	16237691	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	43	558	0	ENST00000375759.3:c.1138C>G	p.Leu380Val	p.L380V	ENST00000375759	NM_015001.2	380	Ctg/Gtg	5/15	0.256104143250574	3	FACETS	0.762	0.644	0.89	0.254	0.214	0.297	INDETERMINATE	1	TRUE	0	0.707322903365365	3		558	216	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099442	27099442	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs875989849	NA	P-0059711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	69	638	2	ENST00000324856.7:c.3679G>T	p.Glu1227Ter	p.E1227*	ENST00000324856	NM_006015.4	1227	Gag/Tag	14/20	0.256104143250574	3	FACETS	1	0.973	1	0.459	0.407	0.512	INDETERMINATE	1	TRUE	0	0.707322903365365	3		640	192	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625269	69625269	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	27	762	0	ENST00000334134.2:c.524C>A	p.Ser175Tyr	p.S175Y	ENST00000334134	NM_005247.2	175	tCc/tAc	3/3	0.327827206142018	1	FACETS	0.536	0.438	0.642	0.536	0.438	0.642	INDETERMINATE	1	TRUE	0	0.707322903365365	1		762	92	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124644	108124644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659808	NA	P-0059711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	20	516	0	ENST00000278616.4:c.2002G>A	p.Glu668Lys	p.E668K	ENST00000278616	NM_000051.3	668	Gaa/Aaa	13/63	0.707322903365365	1	FACETS	0.831	0.672	0.993	0.831	0.672	0.993	CLONAL	1	TRUE	0	0.707322903365365	1		516	44	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287412	46287412	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0059711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	54	449	0	ENST00000334344.6:c.5272-1G>C		p.X1758_splice	ENST00000334344	NM_152641.2	1758			0.444423012281517	3	FACETS	0.847	0.746	0.949	0.847	0.746	0.949	CLONAL	2	TRUE	1	0.707322903365365	3		449	122	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046497	30046497	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	44	633	0	ENST00000331968.5:c.2686G>A	p.Glu896Lys	p.E896K	ENST00000331968	NM_002742.2	896	Gag/Aag	18/18	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.707322903365365	2		633	93	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51520125	51520125	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	32	378	0	ENST00000260433.2:c.302C>T	p.Ser101Leu	p.S101L	ENST00000260433		101	tCa/tTa	4/10	1	2	FACETS	0.943	0.787	1	0.943	0.787	1	CLONAL	1	TRUE	1	0.707322903365365	2		378	96	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451468	187451468	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	29	554	0	ENST00000232014.4:c.14C>T	p.Ala5Val	p.A5V	ENST00000232014	NM_001130845.1	5	gCt/gTt	3/10	0.368742400825179	3	FACETS	0.649	0.526	0.786	0.216	0.175	0.262	INDETERMINATE	1	TRUE	0	0.707322903365365	3		554	171	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247367	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747241612	NA	P-0059711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	52	533	0	ENST00000281708.4:c.1435C>G	p.Arg479Gly	p.R479G	ENST00000281708	NM_033632.3	479	Cga/Gga	10/12	0.403259035214253	1	FACETS	1	0.916	1	1	0.916	1	INDETERMINATE	1	TRUE	0	0.707322903365365	1		533	92	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170832320	170832320	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	43	169	0	ENST00000296930.5:c.684C>G	p.Phe228Leu	p.F228L	ENST00000296930	NM_002520.6	228	ttC/ttG	9/11	0.483772312166444	3	FACETS	1	0.964	1	0.735	0.633	0.84	CLONAL	1	TRUE	1	0.707322903365365	3		169	112	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707784	176707784	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	89	605	2	ENST00000439151.2:c.5841C>A	p.Phe1947Leu	p.F1947L	ENST00000439151	NM_022455.4	1947	ttC/ttA	18/23	0.315258528727976	1	FACETS	1	0.985	1	1	0.985	1	INDETERMINATE	1	TRUE	0	0.707322903365365	1		607	125	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056505	26056505	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs549427826	NA	P-0059711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	124	694	0	ENST00000343677.2:c.152C>T	p.Ser51Phe	p.S51F	ENST00000343677	NM_005319.3	51	tCt/tTt	1/1	0.659796404034799	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.707322903365365	1		694	208	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002884	69002884	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	27	512	0	ENST00000288368.4:c.2184C>A	p.Ser728Arg	p.S728R	ENST00000288368	NM_024870.2	728	agC/agA	20/40	0.707322903365365	1	FACETS	0.641	0.527	0.761	0.641	0.527	0.761	SUBCLONAL	1	TRUE	0	0.707322903365365	1		512	77	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750945	128750945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	55	660	0	ENST00000377970.2:c.482C>T	p.Ser161Leu	p.S161L	ENST00000377970	NM_002467.4	161	tCa/tTa	2/3	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.707322903365365	2		660	138	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2056717	2056717	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	44	600	0	ENST00000349721.2:c.1219G>C	p.Glu407Gln	p.E407Q	ENST00000349721	NM_003070.3	407	Gag/Cag	7/34	0.315258528727976	1	FACETS	0.718	0.62	0.819	0.718	0.62	0.819	INDETERMINATE	1	TRUE	0	0.707322903365365	1		600	112	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499727	8499727	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	11	664	0	ENST00000356435.5:c.2242C>T	p.Gln748Ter	p.Q748*	ENST00000356435		748	Cag/Tag	14/35	0.707322903365365	1	FACETS	0.353	0.249	0.474	0.353	0.249	0.474	SUBCLONAL	1	TRUE	0	0.707322903365365	1		664	57	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636710	8636710	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	22	543	0	ENST00000356435.5:c.199C>T	p.Gln67Ter	p.Q67*	ENST00000356435		67	Cag/Tag	2/35	0.707322903365365	1	FACETS	0.406	0.321	0.501	0.406	0.321	0.501	SUBCLONAL	1	TRUE	0	0.707322903365365	1		543	99	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395093	139395093	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059711-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	33	789	0	ENST00000277541.6:c.5845G>C	p.Glu1949Gln	p.E1949Q	ENST00000277541	NM_017617.3	1949	Gag/Cag	31/34	0.256104143250574	3	FACETS	0.902	0.747	1	0.301	0.249	0.357	INDETERMINATE	1	TRUE	0	0.707322903365365	3		789	140	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450366	50450366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	121	560	1	ENST00000331340.3:c.550C>T	p.Arg184Trp	p.R184W	ENST00000331340	NM_006060.4	184	Cgg/Tgg	5/8	0.477795859449471	3	FACETS	0.957	0.866	1	0.478	0.433	0.526	CLONAL	1	TRUE	1	0.477795859449471	3		561	656	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223422	53223422	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	109	267	0	ENST00000375401.3:c.3937C>T	p.Gln1313Ter	p.Q1313*	ENST00000375401	NM_004187.3	1313	Caa/Taa	23/26	1	1	FACETS	0.811	0.747	0.876	1	0.988	1	CLONAL	2	TRUE	0	0.477795859449471	1		267	214	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981308	201981308	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0059712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	128	523	0	ENST00000359651.3:c.385+2T>C		p.X129_splice	ENST00000359651		129			1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.477795859449471	2		523	501	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348511	56348511	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	160	482	0	ENST00000348428.3:c.319A>C	p.Ser107Arg	p.S107R	ENST00000348428	NM_006785.3	107	Agt/Cgt	2/17	0.477795859449471	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.477795859449471	1		482	489	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47601078	47601087	+	frameshift_variant	Frame_Shift_Del	DEL	AAGGCCAAGC	AAGGCCAAGC	-	novel	NA	P-0059712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	126	469	0	ENST00000263735.4:c.317_326del	p.Lys106SerfsTer11	p.K106Sfs*11	ENST00000263735	NM_002354.2	106	AAGGCCAAGCag/ag	3/9	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.477795859449471	2		469	486	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183864	10183864	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	111	506	0	ENST00000256474.2:c.333del	p.Tyr112ThrfsTer47	p.Y112Tfs*47	ENST00000256474	NM_000551.3	111	agC/ag	1/3	0.477795859449471	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.477795859449471	1		506	350	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139561	47139561	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	96	408	0	ENST00000409792.3:c.5026C>T	p.Gln1676Ter	p.Q1676*	ENST00000409792	NM_014159.6	1676	Cag/Tag	9/21	0.477795859449471	1	FACETS	0.788	0.708	0.873	0.788	0.708	0.873	SUBCLONAL	1	TRUE	0	0.477795859449471	1		408	388	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696160	52696166	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTGCC	CTGTGCC	-	novel	NA	P-0059712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	114	453	0	ENST00000394830.3:c.511_517del	p.Gly171Ter	p.G171*	ENST00000394830	NM_018313.4	171	GGCACAGtg/tg	5/30	0.477795859449471	1	FACETS	0.851	0.771	0.933	0.851	0.771	0.933	CLONAL	1	TRUE	0	0.477795859449471	1		453	427	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6038777	6038777	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059712-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	102	467	0	ENST00000265849.7:c.667A>C	p.Ile223Leu	p.I223L	ENST00000265849	NM_000535.5	223	Ata/Cta	6/15	0.477795859449471	3	FACETS	0.828	0.741	0.919	0.414	0.37	0.46	CLONAL	1	TRUE	1	0.477795859449471	3		467	639	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0059713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	499	390	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.528882705585705	4	FACETS	0.917	0.887	0.946	0.917	0.887	0.946	CLONAL	3	TRUE	1	0.857921743927914	4		390	786	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723585	49723585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059713-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	16	82	0	ENST00000449682.2:c.1057G>A	p.Glu353Lys	p.E353K	ENST00000449682	NM_020998.3	353	Gag/Aag	9/18	1	2	FACETS	0.932	0.726	1	0.932	0.726	1	CLONAL	1	TRUE	1	0.857921743927914	2		82	40	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0059716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	140	525	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.560041913600633	2		525	367	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717735	89717739	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGT	AAAGT	-	rs606231169	NA	P-0059716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	291	331	0	ENST00000371953.3:c.761_765del	p.Lys254ArgfsTer42	p.K254Rfs*42	ENST00000371953	NM_000314.4	254	AAAGTa/a	7/9	0.560041913600633	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.560041913600633	2		331	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577157	7577157	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0059716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	218	549	0	ENST00000269305.4:c.783-2A>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	0.889	0.838	0.939	1	0.994	1	CLONAL	2	TRUE	1	0.560041913600633	2		549	438	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520259	176520260	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0059716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	145	747	0	ENST00000292408.4:c.1179_1180dup	p.Ala394GlyfsTer58	p.A394Gfs*58	ENST00000292408	NM_213647.1	393	cag/caGGg	9/18	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.560041913600633	2		747	491	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829772	76829772	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059716-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	22	167	0	ENST00000373344.5:c.6269C>A	p.Thr2090Asn	p.T2090N	ENST00000373344	NM_000489.3	2090	aCt/aAt	28/35	1	1	FACETS	0.161	0.124	0.203	0.161	0.124	0.203	SUBCLONAL	1	TRUE	0	0.560041913600633	1		167	352	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	76	458	2	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.596	0.522	0.676	0.596	0.522	0.676	SUBCLONAL	1	TRUE	1	0.32	2		460	797	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	53	613	0	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.357	0.303	0.416	0.357	0.303	0.416	SUBCLONAL	1	TRUE	1	0.32	2		613	929	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	59	156	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.904	0.78	1	0.904	0.78	1	CLONAL	1	TRUE	1	0.32	2		160	408	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	65	580	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	1	2	FACETS	0.469	0.406	0.538	0.469	0.406	0.538	SUBCLONAL	1	TRUE	1	0.32	2		580	866	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	45	269	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.82	0.692	0.961	0.82	0.692	0.961	CLONAL	1	TRUE	1	0.32	2		269	343	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11015633	11015634	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	57	528	0	ENST00000327064.4:c.235_236dup	p.Phe80SerfsTer46	p.F80Sfs*46	ENST00000327064	NM_199141.1	76	gat/gaTGt	2/16	1	2	FACETS	0.481	0.412	0.557	0.481	0.412	0.557	SUBCLONAL	1	TRUE	1	0.32	2		528	740	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	147	628	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.32	2		629	864	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903766	41903766	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	68	575	0	ENST00000372991.4:c.791G>A	p.Ser264Asn	p.S264N	ENST00000372991	NM_001760.3	264	aGc/aAc	5/5	1	2	FACETS	0.526	0.457	0.601	0.526	0.457	0.601	SUBCLONAL	1	TRUE	1	0.32	2		575	808	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	114	430	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.917	0.826	1	0.917	0.826	1	CLONAL	1	TRUE	1	0.32	2		431	777	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855966	68855966	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35187787	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	105	586	0	ENST00000261769.5:c.1774G>A	p.Ala592Thr	p.A592T	ENST00000261769	NM_004360.3	592	Gcc/Acc	12/16	1	2	FACETS	0.883	0.792	0.981	0.883	0.792	0.981	CLONAL	1	TRUE	1	0.32	2		586	743	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	42	408	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.0856173687807732	0	FACETS	0.232	0.193	0.276			1	INDETERMINATE	1	TRUE	0	0.32	0		408	770	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	161	496	0	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.32	2		496	736	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211462	46211462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	54	328	0	ENST00000334344.6:c.428G>A	p.Arg143His	p.R143H	ENST00000334344	NM_152641.2	143	cGt/cAt	5/21	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.32	2		328	319	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088788	27088788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	40	545	2	ENST00000324856.7:c.2402del	p.Gly801ValfsTer32	p.G801Vfs*32	ENST00000324856	NM_006015.4	799	caG/ca	7/20	1	2	FACETS	0.353	0.292	0.421	0.353	0.292	0.421	SUBCLONAL	1	TRUE	1	0.32	2		547	708	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	42	593	3	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	0.358	0.298	0.425	0.358	0.298	0.425	SUBCLONAL	1	TRUE	1	0.32	2		596	733	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859815	117859815	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	113	384	0	ENST00000297338.2:c.1820A>G	p.Gln607Arg	p.Q607R	ENST00000297338	NM_006265.2	607	cAa/cGa	14/14	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.32	2		384	690	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692983	89692983	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	70	384	0	ENST00000371953.3:c.467G>T	p.Gly156Val	p.G156V	ENST00000371953	NM_000314.4	156	gGg/gTg	5/9	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.32	2		384	420	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748660	43748661	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	48	580	0	ENST00000382044.4:c.2145dup	p.Glu716ArgfsTer9	p.E716Rfs*9	ENST00000382044	NM_001141980.1	715	-/A	12/28	1	2	FACETS	0.446	0.376	0.524	0.446	0.376	0.524	SUBCLONAL	1	TRUE	1	0.32	2		580	672	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141568583	141568583	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	50	548	0	ENST00000220592.5:c.878+1G>A		p.X293_splice	ENST00000220592	NM_012154.3	293			1	2	FACETS	0.386	0.327	0.452	0.386	0.327	0.452	SUBCLONAL	1	TRUE	1	0.32	2		548	809	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021386	42021386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529502058	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	41	437	0	ENST00000219905.7:c.3682G>A	p.Val1228Ile	p.V1228I	ENST00000219905	NM_001164273.1	1228	Gtc/Atc	11/24	1	2	FACETS	0.401	0.333	0.477	0.401	0.333	0.477	SUBCLONAL	1	TRUE	1	0.32	2		437	639	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443569	52443569	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	36	508	0	ENST00000460680.1:c.122+1del		p.X41_splice	ENST00000460680	NM_004656.3	41			1	2	FACETS	0.288	0.236	0.347	0.288	0.236	0.347	SUBCLONAL	1	TRUE	1	0.32	2		508	781	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589563	67589586	+	inframe_deletion	In_Frame_Del	DEL	TGAAGCTGTAGGGAAAAAATTACA	TGAAGCTGTAGGGAAAAAATTACA	-	novel	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	37	271	0	ENST00000274335.5:c.1330_1353del	p.Ala444_Glu451del	p.A444_E451del	ENST00000274335		442	atTGAAGCTGTAGGGAAAAAATTACAt/att	10/15	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.32	2		271	186	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850619	63850619	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	138	428	0	ENST00000279873.7:c.1399-2A>G		p.X467_splice	ENST00000279873	NM_032199.2	467			1	2	FACETS	0.77	0.704	0.839	1	0.988	1	SUBCLONAL	2	TRUE	1	0.32	2		428	560	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465976	69465976	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	139	781	1	ENST00000227507.2:c.814G>T	p.Glu272Ter	p.E272*	ENST00000227507	NM_053056.2	272	Gag/Tag	5/5	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.32	2		782	723	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426784	49426784	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	48	668	1	ENST00000301067.7:c.11704C>T	p.Gln3902Ter	p.Q3902*	ENST00000301067	NM_003482.3	3902	Cag/Tag	39/54	1	2	FACETS	0.328	0.276	0.385	0.328	0.276	0.385	SUBCLONAL	1	TRUE	1	0.32	2		669	916	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027523	48027523	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265121267	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	42	487	0	ENST00000234420.5:c.2401G>A	p.Val801Met	p.V801M	ENST00000234420	NM_000179.2	801	Gtg/Atg	4/10	1	2	FACETS	0.446	0.371	0.528	0.446	0.371	0.528	SUBCLONAL	1	TRUE	1	0.32	2		487	589	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285675	46285675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1201192337	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	46	430	0	ENST00000334344.6:c.5035C>T	p.Arg1679Trp	p.R1679W	ENST00000334344	NM_152641.2	1679	Cgg/Tgg	17/21	1	2	FACETS	0.365	0.306	0.431	0.365	0.306	0.431	SUBCLONAL	1	TRUE	1	0.32	2		430	787	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281045	49281045	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200483129	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	86	437	1	ENST00000282018.3:c.92G>A	p.Cys31Tyr	p.C31Y	ENST00000282018	NM_020377.2	31	tGc/tAc	1/1	1	2	FACETS	0.933	0.827	1	0.933	0.827	1	CLONAL	1	TRUE	1	0.32	2		438	576	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310553	65310553	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	117	571	0	ENST00000342505.4:c.2135A>G	p.His712Arg	p.H712R	ENST00000342505	NM_002227.2	712	cAt/cGt	16/25	1	2	FACETS	0.95	0.857	1	0.95	0.857	1	CLONAL	1	TRUE	1	0.32	2		571	770	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47599130	47599130	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs952989581	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	136	577	0	ENST00000430070.2:c.470C>T	p.Thr157Ile	p.T157I	ENST00000430070	NM_018095.4	157	aCa/aTa	2/4	1	2	FACETS	0.94	0.855	1	0.94	0.855	1	CLONAL	1	TRUE	1	0.32	2		577	904	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830491	72830491	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	42	603	1	ENST00000268489.5:c.6090C>A	p.Tyr2030Ter	p.Y2030*	ENST00000268489	NM_006885.3	2030	taC/taA	9/10	1	2	FACETS	0.363	0.302	0.431	0.363	0.302	0.431	SUBCLONAL	1	TRUE	1	0.32	2		604	723	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143993	11143993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568509370	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	107	558	0	ENST00000358026.2:c.3574C>T	p.Arg1192Cys	p.R1192C	ENST00000358026	NM_001128849.1	1192	Cgc/Tgc	26/36	1	2	FACETS	0.826	0.74	0.916	0.826	0.74	0.916	CLONAL	1	TRUE	1	0.32	2		558	810	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727894	41727894	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	95	435	0	ENST00000301178.4:c.519G>A	p.Trp173Ter	p.W173*	ENST00000301178	NM_021913.4	173	tgG/tgA	4/20	1	2	FACETS	0.931	0.83	1	0.931	0.83	1	CLONAL	1	TRUE	1	0.32	2		435	638	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645936	215645936	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	37	523	0	ENST00000260947.4:c.662A>T	p.Glu221Val	p.E221V	ENST00000260947	NM_000465.2	221	gAg/gTg	4/11	1	2	FACETS	0.391	0.321	0.469	0.391	0.321	0.469	SUBCLONAL	1	TRUE	1	0.32	2		523	592	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326487	62326487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs6062495	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	107	653	0	ENST00000360203.5:c.3412C>T	p.Arg1138Trp	p.R1138W	ENST00000360203	NM_001283009.1	1138	Cgg/Tgg	33/35	1	2	FACETS	0.895	0.803	0.993	0.895	0.803	0.993	CLONAL	1	TRUE	1	0.32	2		653	747	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902505	1902505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	111	504	0	ENST00000382891.5:c.124C>T	p.Arg42Cys	p.R42C	ENST00000382891	NM_133335.3	42	Cgc/Tgc	2/22	1	2	FACETS	0.848	0.762	0.939	0.848	0.762	0.939	CLONAL	1	TRUE	1	0.32	2		504	818	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748081	41748081	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	15	340	0	ENST00000226382.2:c.688G>A	p.Gly230Arg	p.G230R	ENST00000226382	NM_003924.3	230	Ggg/Agg	3/3	1	2	FACETS	0.324	0.237	0.43	0.324	0.237	0.43	SUBCLONAL	1	TRUE	1	0.32	2		340	289	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218782	66218782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	26	320	0	ENST00000273854.3:c.2276G>A	p.Gly759Asp	p.G759D	ENST00000273854	NM_004439.5	759	gGc/gAc	13/18	1	2	FACETS	0.466	0.369	0.577	0.466	0.369	0.577	SUBCLONAL	1	TRUE	1	0.32	2		320	349	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628854	187628854	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	93	567	0	ENST00000441802.2:c.2128A>G	p.Asn710Asp	p.N710D	ENST00000441802	NM_005245.3	710	Aat/Gat	2/27	1	2	FACETS	0.753	0.669	0.842	0.753	0.669	0.842	SUBCLONAL	1	TRUE	1	0.32	2		567	772	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591145	67591153	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TACTTGATG	TACTTGATG	-	novel	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	113	407	0	ENST00000274335.5:c.1740_1745+3del		p.X580_splice	ENST00000274335		580		12/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.32	2		407	524	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039591	180039591	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	90	453	0	ENST00000261937.6:c.3452G>A	p.Cys1151Tyr	p.C1151Y	ENST00000261937	NM_182925.4	1151	tGc/tAc	26/30	1	2	FACETS	0.857	0.761	0.96	0.857	0.761	0.96	CLONAL	1	TRUE	1	0.32	2		453	656	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436155	116436155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758486336	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	101	453	0	ENST00000397752.3:c.4150G>A	p.Ala1384Thr	p.A1384T	ENST00000397752	NM_000245.2	1384	Gcc/Acc	21/21	1	2	FACETS	0.942	0.843	1	0.942	0.843	1	CLONAL	1	TRUE	1	0.32	2		453	670	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132787	152132787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059717-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	99	384	0	ENST00000262189.6:c.85C>T	p.Pro29Ser	p.P29S	ENST00000262189	NM_170606.2	29	Ccc/Tcc	1/59	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.32	2		384	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577560	7577560	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520002	NA	P-0059718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	179	501	0	ENST00000269305.4:c.721T>C	p.Ser241Pro	p.S241P	ENST00000269305	NM_001126112.2	241	Tcc/Ccc	7/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.48514867729025	2		501	517	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56857680	56857680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35563991	NA	P-0059718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	160	546	0	ENST00000308159.5:c.716C>T	p.Thr239Met	p.T239M	ENST00000308159	NM_014669.4	239	aCg/aTg	8/22	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.48514867729025	2		546	580	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827361	72827361	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	74	646	1	ENST00000268489.5:c.9220C>T	p.Gln3074Ter	p.Q3074*	ENST00000268489	NM_006885.3	3074	Cag/Tag	9/10	1	2	FACETS	0.476	0.416	0.54	0.476	0.416	0.54	SUBCLONAL	1	TRUE	1	0.48514867729025	2		647	641	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041037	112041037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761032788	NA	P-0059718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	242	556	2	ENST00000368678.4:c.218C>T	p.Thr73Met	p.T73M	ENST00000368678		73	aCg/aTg	3/13	0.358171209692217	3	FACETS	0.769	0.72	0.819	0.769	0.72	0.819	SUBCLONAL	2	TRUE	1	0.48514867729025	3		558	806	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099479	27099479	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0059718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	237	503	0	ENST00000324856.7:c.3715+1G>T		p.X1239_splice	ENST00000324856	NM_006015.4	1239			0.41197007859254	2	FACETS	0.814	0.766	0.863	0.814	0.766	0.863	CLONAL	2	TRUE	0	0.48514867729025	2		503	600	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574043	46574043	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1394833849	NA	P-0059718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	151	610	1	ENST00000263734.3:c.58C>T	p.Arg20Trp	p.R20W	ENST00000263734	NM_001430.4	20	Cgg/Tgg	2/16	0.155885938420578	3	FACETS	1	0.936	1	0.513	0.469	0.558	INDETERMINATE	1	TRUE	1	0.48514867729025	3		611	754	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436860	110436860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059718-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	94	726	0	ENST00000375856.3:c.1541G>A	p.Cys514Tyr	p.C514Y	ENST00000375856	NM_003749.2	514	tGc/tAc	1/2	0.48514867729025	3	FACETS	0.586	0.521	0.656	0.293	0.26	0.328	SUBCLONAL	1	TRUE	1	0.48514867729025	3		726	821	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0059719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	189	863	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.329981748536463	0	FACETS	0.904	0.848	0.961			1	CLONAL	2	FALSE	0	0.344391732210874	0		863	398	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12393124	12393125	+	missense_variant	Missense_Mutation	DNP	CC	CC	GG	novel	NA	P-0059719-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	61	365	0	ENST00000287820.6:c.33_34inv	p.Asp11_Pro12delinsGluAla	p.D11_P12delinsEA	ENST00000287820	NM_015869.4	11	gaCCca/gaGGca	1/7	0.303605116379545	1	FACETS	0.79	0.685	0.904	0.79	0.685	0.904	CLONAL	1	FALSE	0	0.344391732210874	1		365	371	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0059747-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	356	390	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.572629556225532	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.588207883233575	2		390	604	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354348	354348	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059747-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	110	459	0	ENST00000262320.3:c.1210G>T	p.Glu404Ter	p.E404*	ENST00000262320	NM_003502.3	404	Gag/Tag	5/11	0.588207883233575	1	FACETS	0.767	0.697	0.84	0.767	0.697	0.84	SUBCLONAL	1	TRUE	0	0.588207883233575	1		459	344	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347981	347982	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0059747-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	60	759	0	ENST00000262320.3:c.1524dup	p.Ala509CysfsTer82	p.A509Cfs*82	ENST00000262320	NM_003502.3	508	-/T	6/11	0.588207883233575	1	FACETS	0.276	0.238	0.318	0.276	0.238	0.318	SUBCLONAL	1	TRUE	0	0.588207883233575	1		759	521	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631007	67631007	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059747-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	210	539	0	ENST00000272342.5:c.1193A>G	p.Asp398Gly	p.D398G	ENST00000272342	NM_019002.3	398	gAc/gGc	5/6	0.527633800215087	4	FACETS	0.978	0.907	1	0.489	0.453	0.526	CLONAL	1	TRUE	2	0.588207883233575	4		539	1159	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0059748-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	31	668	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		668	713	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0059750-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	8	536	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.754075854366363	1	FACETS	0.033	0.021	0.05	0.033	0.021	0.05	SUBCLONAL	1	TRUE	0	0.754075854366363	1		536	395	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573142	64573142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059750-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	329	527	0	ENST00000312049.6:c.1150G>T	p.Glu384Ter	p.E384*	ENST00000312049	NM_130799.2	384	Gag/Tag	8/10	0.754075854366363	1	FACETS	0.983	0.942	1	0.983	0.942	1	CLONAL	1	TRUE	0	0.754075854366363	1		527	553	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509612	106509612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	89	662	0	ENST00000359195.3:c.1606C>T	p.Pro536Ser	p.P536S	ENST00000359195	NM_002649.2	536	Cct/Tct	2/11	0.32574028567286	3	FACETS	1	0.945	1	0.553	0.491	0.618	CLONAL	1	TRUE	1	0.336575465441508	3		662	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579419	7579419	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	179	804	0	ENST00000269305.4:c.268del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	90	Tcc/cc	4/11	0.210501024383672	3	FACETS	1	0.984	1			1	CLONAL	2	TRUE	NA	0.336575465441508	3		804	517	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707641	176707641	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059751-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	71	494	0	ENST00000439151.2:c.5698A>C	p.Thr1900Pro	p.T1900P	ENST00000439151	NM_022455.4	1900	Act/Cct	18/23	0.32574028567286	3	FACETS	0.833	0.727	0.946	0.416	0.363	0.473	CLONAL	1	TRUE	1	0.336575465441508	3		494	592	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	517	593	1	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.677451529783765	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.677451529783765	1		594	908	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1274	244	967	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.280989111655693	3	FACETS	0.635	0.592	0.68	0.212	0.197	0.227	INDETERMINATE	1	TRUE	0	0.677451529783765	3		974	1518	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	141	156	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.677451529783765	1	FACETS	0.773	0.714	0.834	0.773	0.714	0.834	SUBCLONAL	1	TRUE	0	0.677451529783765	1		160	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	771	470	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.668699204204595	2	FACETS	0.914	0.89	0.938	0.914	0.89	0.938	CLONAL	2	TRUE	0	0.677451529783765	2		470	1245	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099988	27099988	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	865	722	0	ENST00000324856.7:c.3866+1G>A		p.X1289_splice	ENST00000324856	NM_006015.4	1289			0.668699204204595	2	FACETS	0.981	0.957	1	0.981	0.957	1	CLONAL	2	TRUE	0	0.677451529783765	2		722	1302	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46725746	46725746	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759738884	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	672	560	0	ENST00000371975.4:c.382G>A	p.Ala128Thr	p.A128T	ENST00000371975	NM_003579.3	128	Gct/Act	5/18	0.668699204204595	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.677451529783765	2		560	982	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65300295	65300295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	260	447	0	ENST00000342505.4:c.3415C>T	p.Arg1139Trp	p.R1139W	ENST00000342505	NM_002227.2	1139	Cgg/Tgg	25/25	0.636911206835859	2	FACETS	0.89	0.849	0.932	0.89	0.849	0.932	CLONAL	2	TRUE	0	0.677451529783765	2		447	431	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150936140	150936140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	892	603	0	ENST00000271640.5:c.3592C>T	p.Arg1198Cys	p.R1198C	ENST00000271640	NM_001145415.1	1198	Cgc/Tgc	20/22	0.65392534843501	3	FACETS	1	0.998	1	0.825	0.804	0.845	CLONAL	2	TRUE	0	0.677451529783765	3		603	1425	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446318	70446318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1429461725	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	172	644	0	ENST00000373644.4:c.5258G>A	p.Arg1753His	p.R1753H	ENST00000373644	NM_030625.2	1753	cGt/cAt	11/12	0.331118036113849	1	FACETS	0.349	0.321	0.379	0.349	0.321	0.379	INDETERMINATE	1	TRUE	0	0.677451529783765	1		644	961	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88677065	88677065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765530074	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	78	325	1	ENST00000372037.3:c.850C>T	p.Arg284Cys	p.R284C	ENST00000372037	NM_004329.2	284	Cgc/Tgc	9/13	0.331118036113849	1	FACETS	0.415	0.367	0.466	0.415	0.367	0.466	INDETERMINATE	1	TRUE	0	0.677451529783765	1		326	367	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631102	69631102	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121917704	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	205	602	0	ENST00000334134.2:c.310C>T	p.Arg104Ter	p.R104*	ENST00000334134	NM_005247.2	104	Cga/Tga	2/3	0.303260361740177	2	FACETS	0.559	0.518	0.601	0.279	0.259	0.301	INDETERMINATE	1	TRUE	0	0.677451529783765	2		602	1083	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	441055	441055	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778756065	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	474	547	0	ENST00000399788.2:c.1703G>A	p.Arg568His	p.R568H	ENST00000399788	NM_001042603.1	568	cGt/cAt	13/28	0.342495614403259	4	FACETS	0.882	0.843	0.921	0.882	0.843	0.921	INDETERMINATE	2	TRUE	2	0.677451529783765	4		547	1331	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46215214	46215214	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1433103583	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	32	213	0	ENST00000334344.6:c.652del	p.Ser218ProfsTer74	p.S218Pfs*74	ENST00000334344	NM_152641.2	217	Ttt/tt	6/21	0.427077952691829	3	FACETS	0.536	0.437	0.646	0.268	0.218	0.323	SUBCLONAL	1	TRUE	1	0.677451529783765	3		213	236	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860174	57860174	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	125	445	0	ENST00000228682.2:c.912+2T>C		p.X304_splice	ENST00000228682	NM_005269.2	304			0.427077952691829	3	FACETS	0.495	0.447	0.545	0.247	0.223	0.273	SUBCLONAL	1	TRUE	1	0.677451529783765	3		445	999	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434351	121434351	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	176	577	0	ENST00000257555.6:c.1115C>A	p.Ala372Glu	p.A372E	ENST00000257555		372	gCa/gAa	6/10	0.427077952691829	3	FACETS	0.582	0.535	0.631	0.291	0.267	0.316	SUBCLONAL	1	TRUE	1	0.677451529783765	3		577	1195	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435129	110435129	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	182	712	2	ENST00000375856.3:c.3272del	p.Pro1091ArgfsTer15	p.P1091Rfs*15	ENST00000375856	NM_003749.2	1091	cCg/cg	1/2	1	2	FACETS	0.427	0.393	0.463	0.427	0.393	0.463	SUBCLONAL	1	TRUE	1	0.677451529783765	2		714	1257	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435263	110435263	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1182	173	750	1	ENST00000375856.3:c.3138del	p.Ala1047ProfsTer59	p.A1047Pfs*59	ENST00000375856	NM_003749.2	1046	ccC/cc	1/2	1	2	FACETS	0.377	0.346	0.41	0.377	0.346	0.41	SUBCLONAL	1	TRUE	1	0.677451529783765	2		751	1355	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643608	38643608	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	109	505	0	ENST00000299084.4:c.1081del	p.Arg361AspfsTer45	p.R361Dfs*45	ENST00000299084	NM_152594.2	360	Aaa/aa	7/7	0.179010348522086	5	FACETS	0.799	0.717	0.886	0.266	0.239	0.296	INDETERMINATE	1	TRUE	2	0.677451529783765	5		505	812	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226309	2226309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1192	215	708	0	ENST00000326181.6:c.1922G>A	p.Arg641His	p.R641H	ENST00000326181	NM_032271.2	641	cGt/cAt	20/21	0.152117119729914	3	FACETS	0.604	0.56	0.65	0.201	0.186	0.217	INDETERMINATE	1	TRUE	0	0.677451529783765	3		708	1407	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822586	72822586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	332	722	4	ENST00000268489.5:c.9589del	p.Gln3197SerfsTer44	p.Q3197Sfs*44	ENST00000268489	NM_006885.3	3197	Cag/ag	10/10	0.152117119729914	3	FACETS	0.869	0.82	0.92	0.29	0.273	0.307	INDETERMINATE	1	TRUE	0	0.677451529783765	3		726	1510	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822729	72822729	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	508	643	0	ENST00000268489.5:c.9446C>A	p.Pro3149Gln	p.P3149Q	ENST00000268489	NM_006885.3	3149	cCg/cAg	10/10	0.152117119729914	3	FACETS	0.875	0.841	0.91	0.583	0.56	0.607	INDETERMINATE	2	TRUE	0	0.677451529783765	3		643	1147	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984742	72984742	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1337540676	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	288	556	0	ENST00000268489.5:c.2842G>A	p.Ala948Thr	p.A948T	ENST00000268489	NM_006885.3	948	Gcc/Acc	3/10	0.152117119729914	3	FACETS	0.926	0.87	0.984	0.309	0.29	0.328	INDETERMINATE	1	TRUE	0	0.677451529783765	3		556	1229	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969848	81969848	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568724894	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	163	554	1	ENST00000359376.3:c.2917G>A	p.Asp973Asn	p.D973N	ENST00000359376	NM_002661.3	973	Gac/Aac	27/33	0.152117119729914	3	FACETS	0.558	0.511	0.607	0.186	0.17	0.203	INDETERMINATE	1	TRUE	0	0.677451529783765	3		555	1155	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544519	86544519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	501	602	0	ENST00000262426.4:c.344G>A	p.Arg115Gln	p.R115Q	ENST00000262426	NM_001451.2	115	cGg/cAg	1/2	0.152117119729914	3	FACETS	0.826	0.793	0.86	0.551	0.528	0.574	INDETERMINATE	2	TRUE	0	0.677451529783765	3		602	1198	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349641	89349641	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs772267579	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	210	497	4	ENST00000301030.4:c.3309del	p.Asp1104MetfsTer214	p.D1104Mfs*214	ENST00000301030	NM_001256183.1	1103	aaA/aa	9/13	0.152117119729914	3	FACETS	0.98	0.911	1	0.327	0.303	0.351	INDETERMINATE	1	TRUE	0	0.677451529783765	3		501	847	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881064	37881064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	234	647	0	ENST00000269571.5:c.2393C>T	p.Thr798Ile	p.T798I	ENST00000269571		798	aCa/aTa	20/27	0.280989111655693	3	FACETS	0.641	0.596	0.687	0.214	0.198	0.229	INDETERMINATE	1	TRUE	0	0.677451529783765	3		647	1443	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448387	56448387	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764750571	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	763	624	0	ENST00000407977.2:c.260C>T	p.Pro87Leu	p.P87L	ENST00000407977		87	cCg/cTg	3/10	0.280989111655693	3	FACETS	1	0.994	1	0.719	0.697	0.74	INDETERMINATE	2	TRUE	0	0.677451529783765	3		624	1399	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110622	4110622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	369	672	3	ENST00000262948.5:c.335G>A	p.Arg112Gln	p.R112Q	ENST00000262948	NM_030662.3	112	cGg/cAg	3/11	0.398683881408809	1	FACETS	0.725	0.689	0.761	0.725	0.689	0.761	INDETERMINATE	1	TRUE	0	0.677451529783765	1		675	994	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222990	5222990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	280	625	0	ENST00000357368.4:c.2813C>T	p.Ala938Val	p.A938V	ENST00000357368	NM_002850.3	938	gCc/gTc	18/38	0.398683881408809	1	FACETS	0.715	0.675	0.756	0.715	0.675	0.756	INDETERMINATE	1	TRUE	0	0.677451529783765	1		625	764	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349718	15349718	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	297	638	0	ENST00000263377.2:c.3856C>G	p.Gln1286Glu	p.Q1286E	ENST00000263377	NM_058243.2	1286	Cag/Gag	19/20	0.398683881408809	1	FACETS	0.637	0.601	0.674	0.637	0.601	0.674	INDETERMINATE	1	TRUE	0	0.677451529783765	1		638	910	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965767	18965767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	192	621	0	ENST00000262803.5:c.1345G>A	p.Glu449Lys	p.E449K	ENST00000262803	NM_002911.3	449	Gag/Aag	10/24	0.398683881408809	1	FACETS	0.406	0.375	0.437	0.406	0.375	0.437	INDETERMINATE	1	TRUE	0	0.677451529783765	1		621	924	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260057	19260057	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1254581471	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	147	575	0	ENST00000162023.5:c.236G>A	p.Arg79His	p.R79H	ENST00000162023		79	cGc/cAc	7/13	0.398683881408809	1	FACETS	0.323	0.294	0.353	0.323	0.294	0.353	INDETERMINATE	1	TRUE	0	0.677451529783765	1		575	889	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1273	176	511	0	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	0.350953848739345	3	FACETS	0.48	0.441	0.521	0.24	0.22	0.261	INDETERMINATE	1	TRUE	1	0.677451529783765	3		511	1449	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214821	36214821	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	307	479	0	ENST00000222270.7:c.3247C>T	p.Arg1083Ter	p.R1083*	ENST00000222270	NM_014727.1	1083	Cga/Tga	8/37	0.350953848739345	3	FACETS	1	0.984	1	0.559	0.527	0.591	INDETERMINATE	1	TRUE	1	0.677451529783765	3		479	1086	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224532	36224532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759167832	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	216	687	1	ENST00000222270.7:c.6994C>T	p.Arg2332Cys	p.R2332C	ENST00000222270	NM_014727.1	2332	Cgt/Tgt	29/37	0.350953848739345	3	FACETS	0.627	0.582	0.675	0.314	0.291	0.338	INDETERMINATE	1	TRUE	1	0.677451529783765	3		688	1361	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224678	36224678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752822802	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	400	720	0	ENST00000222270.7:c.7064G>A	p.Arg2355Gln	p.R2355Q	ENST00000222270	NM_014727.1	2355	cGg/cAg	30/37	0.350953848739345	3	FACETS	1	0.985	1	0.545	0.518	0.573	INDETERMINATE	1	TRUE	1	0.677451529783765	3		720	1450	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	162	528	5	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	0.350953848739345	3	FACETS	0.557	0.51	0.607	0.279	0.255	0.304	INDETERMINATE	1	TRUE	1	0.677451529783765	3		533	1149	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797754	42797754	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1215	221	693	0	ENST00000575354.2:c.3806T>C	p.Phe1269Ser	p.F1269S	ENST00000575354	NM_015125.3	1269	tTc/tCc	16/20	0.350953848739345	3	FACETS	0.608	0.564	0.654	0.304	0.282	0.327	INDETERMINATE	1	TRUE	1	0.677451529783765	3		693	1436	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716328	52716328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1343613316	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	328	559	0	ENST00000322088.6:c.772C>T	p.Arg258Cys	p.R258C	ENST00000322088	NM_014225.5	258	Cgc/Tgc	6/15	0.350953848739345	3	FACETS	1	0.969	1	0.519	0.49	0.549	INDETERMINATE	1	TRUE	1	0.677451529783765	3		559	1248	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	686	605	9	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	0.668699204204595	2	FACETS	0.941	0.915	0.967	0.941	0.915	0.967	CLONAL	2	TRUE	0	0.677451529783765	2		614	1076	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251595	212251595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1044752647	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	203	623	1	ENST00000342788.4:c.3464G>A	p.Arg1155Gln	p.R1155Q	ENST00000342788	NM_005235.2	1155	cGa/cAa	27/28	0.381260693569448	3	FACETS	0.647	0.599	0.697	0.216	0.199	0.233	INDETERMINATE	1	TRUE	0	0.677451529783765	3		624	1240	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750723	39750723	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	272	296	0	ENST00000361337.2:c.2123G>A	p.Arg708Gln	p.R708Q	ENST00000361337	NM_003286.2	708	cGa/cAa	20/21	0.392871958597019	2	FACETS	0.765	0.726	0.803	0.765	0.726	0.803	INDETERMINATE	2	TRUE	0	0.677451529783765	2		296	525	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279790	46279790	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776910504	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	604	607	0	ENST00000371998.3:c.3716G>A	p.Arg1239Gln	p.R1239Q	ENST00000371998		1239	cGa/cAa	20/23	0.392871958597019	2	FACETS	0.779	0.753	0.805	0.779	0.753	0.805	INDETERMINATE	2	TRUE	0	0.677451529783765	2		607	1144	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755608	39755608	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	171	607	0	ENST00000288319.7:c.1157A>G	p.Tyr386Cys	p.Y386C	ENST00000288319	NM_182918.3	386	tAc/tGc	10/10	1	2	FACETS	0.472	0.433	0.512	0.472	0.433	0.512	SUBCLONAL	1	TRUE	1	0.677451529783765	2		607	1070	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077556	30077556	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1179425098	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	296	490	0	ENST00000338641.4:c.1703G>A	p.Arg568Lys	p.R568K	ENST00000338641	NM_000268.3	568	aGg/aAg	15/16	0.247449914444967	1	FACETS	0.699	0.66	0.738	0.699	0.66	0.738	INDETERMINATE	1	TRUE	0	0.677451529783765	1		490	827	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165282	47165283	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	75	483	1	ENST00000409792.3:c.843dup	p.Glu282ArgfsTer9	p.E282Rfs*9	ENST00000409792	NM_014159.6	281	-/A	3/21	0.325580518877065	2	FACETS	0.427	0.374	0.483	0.213	0.187	0.242	INDETERMINATE	1	TRUE	0	0.677451529783765	2		484	519	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981832	63981832	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	164	635	1	ENST00000398590.3:c.2340del	p.Thr781ProfsTer11	p.T781Pfs*11	ENST00000398590	NM_001177387.1	778	ggC/gg	12/14	0.325580518877065	2	FACETS	0.418	0.383	0.455	0.209	0.191	0.228	INDETERMINATE	1	TRUE	0	0.677451529783765	2		636	1159	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873094	134873094	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	154	484	1	ENST00000398015.3:c.1398C>A	p.Asp466Glu	p.D466E	ENST00000398015	NM_004441.4	466	gaC/gaA	6/16	0.325580518877065	2	FACETS	0.492	0.45	0.536	0.246	0.225	0.268	INDETERMINATE	1	TRUE	0	0.677451529783765	2		485	924	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455573	189455573	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	81	519	0	ENST00000264731.3:c.107A>G	p.Tyr36Cys	p.Y36C	ENST00000264731	NM_003722.4	36	tAc/tGc	2/14	0.325580518877065	2	FACETS	0.573	0.508	0.643	0.287	0.254	0.322	INDETERMINATE	1	TRUE	0	0.677451529783765	2		519	417	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961447	1961447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771867435	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	501	523	2	ENST00000382891.5:c.3235G>A	p.Ala1079Thr	p.A1079T	ENST00000382891	NM_133335.3	1079	Gcc/Acc	17/22	0.303260361740177	2	FACETS	1	0.996	1	0.702	0.674	0.729	INDETERMINATE	1	TRUE	0	0.677451529783765	2		525	1054	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295584	1295584	+	upstream_gene_variant	5'Flank	SNP	T	T	C	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1217	193	677	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.404	0.372	0.437	0.404	0.372	0.437	SUBCLONAL	1	TRUE	1	0.677451529783765	2		677	1410	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522741	67522741	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	415	567	1	ENST00000274335.5:c.244del	p.Ile82SerfsTer32	p.I82Sfs*32	ENST00000274335		80	Aaa/aa	1/15	0.677451529783765	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.677451529783765	1		568	756	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149450025	149450025	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs760090380	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	144	563	1	ENST00000286301.3:c.1192C>A	p.Leu398Ile	p.L398I	ENST00000286301	NM_005211.3	398	Ctt/Att	8/22	0.677451529783765	1	FACETS	0.364	0.332	0.398	0.364	0.332	0.398	SUBCLONAL	1	TRUE	0	0.677451529783765	1		564	772	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225789	26225789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	255	576	0	ENST00000360408.1:c.407C>T	p.Ala136Val	p.A136V	ENST00000360408	NM_003532.2	136	gCg/gTg	1/1	1	2	FACETS	0.688	0.644	0.734	0.688	0.644	0.734	SUBCLONAL	1	TRUE	1	0.677451529783765	2		576	1094	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89791130	89791130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	213	401	0	ENST00000336032.3:c.517G>T	p.Gly173Cys	p.G173C	ENST00000336032	NM_006813.2	173	Ggc/Tgc	1/2	0.398683881408809	1	FACETS	0.683	0.638	0.728	0.683	0.638	0.728	INDETERMINATE	1	TRUE	0	0.677451529783765	1		401	609	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519505	137519506	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs780346130	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	219	558	12	ENST00000367739.4:c.1132_1133del	p.Ser378PhefsTer6	p.S378Ffs*6	ENST00000367739	NM_000416.2	378	AGt/t	7/7	0.398683881408809	1	FACETS	0.614	0.574	0.656	0.614	0.574	0.656	INDETERMINATE	1	TRUE	0	0.677451529783765	1		570	696	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884798	151884798	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	82	419	0	ENST00000262189.6:c.4793+2T>C		p.X1598_splice	ENST00000262189	NM_170606.2	1598			0.152117119729914	3	FACETS	0.502	0.442	0.565	0.167	0.147	0.189	INDETERMINATE	1	TRUE	0	0.677451529783765	3		419	646	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572658	141572658	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1467557787	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	262	578	0	ENST00000220592.5:c.412G>A	p.Val138Met	p.V138M	ENST00000220592	NM_012154.3	138	Gtg/Atg	4/19	0.57592920845273	2	FACETS	0.67	0.628	0.714	0.335	0.314	0.357	SUBCLONAL	1	TRUE	0	0.677451529783765	2		578	1154	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2084104	2084104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	300	441	0	ENST00000349721.2:c.2434C>T	p.Arg812Cys	p.R812C	ENST00000349721	NM_003070.3	812	Cgc/Tgc	17/34	0.677451529783765	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.677451529783765	1		441	509	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089711	5089711	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	115	401	0	ENST00000381652.3:c.2609C>A	p.Pro870His	p.P870H	ENST00000381652	NM_004972.3	870	cCt/cAt	20/25	0.677451529783765	1	FACETS	0.447	0.405	0.492	0.447	0.405	0.492	SUBCLONAL	1	TRUE	0	0.677451529783765	1		401	502	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971053	21971053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137854598	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	550	577	0	ENST00000304494.5:c.305C>T	p.Ala102Val	p.A102V	ENST00000304494	NM_000077.4	102	gCg/gTg	2/3	0.677451529783765	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.677451529783765	1		577	923	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904985	101904985	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	217	405	0	ENST00000374994.4:c.973G>T	p.Gly325Ter	p.G325*	ENST00000374994	NM_004612.2	325	Gga/Tga	5/9	0.677451529783765	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.677451529783765	1		405	365	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417436	139417436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182763411	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	609	667	0	ENST00000277541.6:c.608G>A	p.Arg203His	p.R203H	ENST00000277541	NM_017617.3	203	cGc/cAc	4/34	0.677451529783765	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.677451529783765	1		667	1011	SUCCESS
AR	367	MSKCC	GRCh37	X	66943588	66943588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886041133	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	261	505	0	ENST00000374690.3:c.2668G>A	p.Val890Met	p.V890M	ENST00000374690	NM_000044.3	890	Gtg/Atg	8/8	0.442616941174662	1	FACETS	0.725	0.683	0.767	0.725	0.683	0.767	SUBCLONAL	1	TRUE	0	0.677451529783765	1		505	703	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829749	76829749	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059752-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	36	476	0	ENST00000373344.5:c.6292T>C	p.Trp2098Arg	p.W2098R	ENST00000373344	NM_000489.3	2098	Tgg/Cgg	28/35	0.599283798713035	1	FACETS	0.298	0.246	0.355	0.298	0.246	0.355	SUBCLONAL	1	TRUE	0	0.677451529783765	1		476	236	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0059753-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	296	560	0	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	0.858084842489029	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.858084842489029	1		560	375	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636827	2636827	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059753-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	362	668	0	ENST00000342085.4:c.1276C>A	p.Leu426Met	p.L426M	ENST00000342085	NM_002613.4	426	Ctg/Atg	11/14	1	2	FACETS	0.995	0.948	1	0.995	0.948	1	CLONAL	1	TRUE	1	0.858084842489029	2		668	848	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548785	29549013	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAAAATAAGTACTCCAGTGTTATGTTTACCAAAAATGTTTGAGTGAGTCTTCTCTTTGTCTTTCTCTTTTTTAAAAAATTCAGGCTCTGCTGGTTCTTCATCAGTTAGATAGCATTGATTTGTGGAATCCTGATGCTCCTGTAGAAACATTTTGGGAGATTAGGTATATGTACTTTTATTTTTTAAATTCAACTTTTAAATTTTATTTTGTATTTTTGTCTTGAAATAT	TAAAATAAGTACTCCAGTGTTATGTTTACCAAAAATGTTTGAGTGAGTCTTCTCTTTGTCTTTCTCTTTTTTAAAAAATTCAGGCTCTGCTGGTTCTTCATCAGTTAGATAGCATTGATTTGTGGAATCCTGATGCTCCTGTAGAAACATTTTGGGAGATTAGGTATATGTACTTTTATTTTTTAAATTCAACTTTTAAATTTTATTTTGTATTTTTGTCTTGAAATAT	-	novel	NA	P-0059753-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	34	219	0	ENST00000356175.3:c.1642-80_1721+69del		p.X548_splice	ENST00000356175	NM_000267.3	548		15/57	0.858084842489029	1	FACETS	0.905	0.797	1	0.905	0.797	1	CLONAL	1	TRUE	0	0.858084842489029	1		219	50	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115070	3115070	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059753-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	282	661	0	ENST00000078429.4:c.605G>A	p.Arg202Gln	p.R202Q	ENST00000078429	NM_002067.2	202	cGg/cAg	4/7	0.85730333724137	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.858084842489029	1		661	350	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0059754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	127	125	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.601259992930669	2		125	351	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952006	178952006	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	228	536	0	ENST00000263967.3:c.3061T>C	p.Tyr1021His	p.Y1021H	ENST00000263967	NM_006218.2	1021	Tac/Cac	21/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.601259992930669	2		536	708	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061267	38061267	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	258	700	0	ENST00000250448.2:c.722G>C	p.Gly241Ala	p.G241A	ENST00000250448	NM_004496.3	241	gGc/gCc	2/2	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.601259992930669	2		700	837	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263719	16263720	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCAG	novel	NA	P-0059754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	138	741	0	ENST00000375759.3:c.10091_10094dup	p.Pro3367CysfsTer49	p.P3367Cfs*49	ENST00000375759	NM_015001.2	3363	gcc/gcCCAGc	12/15	0.367188822059565	1	FACETS	0.404	0.368	0.443	0.404	0.368	0.443	SUBCLONAL	1	TRUE	0	0.601259992930669	1		741	794	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665858	241665858	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059754-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	100	445	0	ENST00000366560.3:c.1121C>G	p.Pro374Arg	p.P374R	ENST00000366560	NM_000143.3	374	cCt/cGt	8/10	0.601259992930669	4	FACETS	0.529	0.472	0.591	0.176	0.157	0.197	SUBCLONAL	1	TRUE	1	0.601259992930669	4		445	1006	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468308	50468308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1270036178	NA	P-0059755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	49	559	0	ENST00000331340.3:c.1543C>T	p.Arg515Cys	p.R515C	ENST00000331340	NM_006060.4	515	Cgc/Tgc	8/8	1	2	FACETS	0.561	0.475	0.656	0.561	0.475	0.656	SUBCLONAL	1	TRUE	1	0.306014203832744	2		559	571	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374175	118374175	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	129	705	0	ENST00000534358.1:c.7568T>C	p.Val2523Ala	p.V2523A	ENST00000534358	NM_005933.3	2523	gTc/gCc	27/36	0.306014203832744	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.306014203832744	1		705	667	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856640	111856640	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs899111445	NA	P-0059755-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	67	547	0	ENST00000341259.2:c.691G>T	p.Asp231Tyr	p.D231Y	ENST00000341259	NM_005475.2	231	Gat/Tat	2/8	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.306014203832744	2		547	403	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0059756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	115	329	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.625024367736145	3	FACETS	0.912	0.838	0.986	0.912	0.838	0.986	CLONAL	2	TRUE	1	0.681981908625002	3		329	248	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0059756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	378	569	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.642020766817484	2	FACETS	0.951	0.916	0.985	0.951	0.916	0.985	CLONAL	2	TRUE	0	0.681981908625002	2		569	583	SUCCESS
APC	324	MSKCC	GRCh37	5	112175198	112175198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	80	454	0	ENST00000257430.4:c.3907C>T	p.Gln1303Ter	p.Q1303*	ENST00000257430	NM_000038.5	1303	Caa/Taa	16/16	1	2	FACETS	0.969	0.867	1	0.969	0.867	1	CLONAL	1	TRUE	1	0.681981908625002	2		454	242	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671760	30671760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs75355880	NA	P-0059756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	356	572	0	ENST00000376406.3:c.5200G>A	p.Ala1734Thr	p.A1734T	ENST00000376406	NM_014641.2	1734	Gca/Aca	10/15	0.6454218717177	3	FACETS	0.938	0.896	0.981	0.938	0.896	0.981	CLONAL	2	TRUE	1	0.681981908625002	3		572	746	SUCCESS
APC	324	MSKCC	GRCh37	5	112128203	112128203	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554074786	NA	P-0059756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	45	318	1	ENST00000257430.4:c.706C>T	p.Gln236Ter	p.Q236*	ENST00000257430	NM_000038.5	236	Cag/Tag	7/16	1	2	FACETS	0.647	0.55	0.751	0.647	0.55	0.751	SUBCLONAL	1	TRUE	1	0.681981908625002	2		319	204	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347216	89347216	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	401	664	0	ENST00000301030.4:c.5734G>T	p.Asp1912Tyr	p.D1912Y	ENST00000301030	NM_001256183.1	1912	Gac/Tac	9/13	0.648595475572198	2	FACETS	0.951	0.917	0.985	0.951	0.917	0.985	CLONAL	2	TRUE	0	0.681981908625002	2		664	618	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535367	66535367	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	17	462	0	ENST00000273854.3:c.94T>A	p.Tyr32Asn	p.Y32N	ENST00000273854	NM_004439.5	32	Tac/Aac	1/18	0.566664183081857	1	FACETS	0.12	0.089	0.156	0.12	0.089	0.156	SUBCLONAL	1	TRUE	0	0.681981908625002	1		462	274	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372217	55372217	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	675	608	0	ENST00000297316.4:c.907C>G	p.Pro303Ala	p.P303A	ENST00000297316	NM_022454.3	303	Ccc/Gcc	2/2	0.630397692174416	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	4	TRUE	0	0.681981908625002	4		608	799	SUCCESS
MTAP	4507	MSKCC	GRCh37	9	21816722	21816722	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059756-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	18	292	0	ENST00000380172.4:c.130G>A	p.Ala44Thr	p.A44T	ENST00000380172	NM_002451.3	44	Gcc/Acc	3/8	0.356176819020632	5	FACETS	0.479	0.361	0.617	0.16	0.12	0.206	INDETERMINATE	1	TRUE	2	0.681981908625002	5		292	223	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059759-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	22	121	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	1	0.14	2		121	275	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0059760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	119	536	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.377362034247662	4	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	2	0.392146885095909	4		536	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0059760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	69	396	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.373190381281076	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.392146885095909	1		396	257	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129884	55129884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs574683248	NA	P-0059760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	47	392	0	ENST00000257290.5:c.418G>A	p.Val140Met	p.V140M	ENST00000257290	NM_006206.4	140	Gtg/Atg	4/23	0.392146885095909	3	FACETS	0.846	0.717	0.987	0.423	0.358	0.494	CLONAL	1	TRUE	1	0.392146885095909	3		392	339	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014170	70014170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769488988	NA	P-0059760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	71	482	0	ENST00000394351.3:c.1031C>T	p.Thr344Met	p.T344M	ENST00000394351	NM_000248.3	344	aCg/aTg	9/9	0.188124826549555	4	FACETS	1	0.941	1	0.376	0.329	0.426	INDETERMINATE	1	TRUE	1	0.392146885095909	4		482	447	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169999684	169999684	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1232048013	NA	P-0059760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	18	151	0	ENST00000295797.4:c.995T>C	p.Ile332Thr	p.I332T	ENST00000295797	NM_002740.5	332	aTa/aCa	11/18	0.377362034247662	4	FACETS	0.983	0.748	1	0.492	0.374	0.628	CLONAL	1	TRUE	2	0.392146885095909	4		151	130	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059762-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	92	571	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.581532702397603	1	FACETS	0.812	0.731	0.895	0.812	0.731	0.895	CLONAL	1	TRUE	0	0.585289128741028	1		571	274	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934574	NA	P-0059762-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	243	507	0	ENST00000269305.4:c.844C>G	p.Arg282Gly	p.R282G	ENST00000269305	NM_001126112.2	282	Cgg/Ggg	8/11	0.550341117601659	2	FACETS	0.968	0.919	1	0.968	0.919	1	CLONAL	2	TRUE	0	0.585289128741028	2		507	429	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	106	121	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.267305265058602	4	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	2	0.28	4		121	462	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	258	500	0	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	0.30186150427593	3	FACETS	0.883	0.83	0.937	1	0.991	1	CLONAL	3	TRUE	1	0.28	3		500	793	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579310	7579310	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1555526469	NA	P-0059763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	155	416	0	ENST00000269305.4:c.375+2T>C		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.30186150427593	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.28	2		416	494	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426118	47426118	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	113	494	0	ENST00000377045.4:c.638C>T	p.Thr213Met	p.T213M	ENST00000377045	NM_001654.4	213	aCg/aTg	7/16	0.30186150427593	3	FACETS	1	0.971	1	0.608	0.547	0.672	CLONAL	1	TRUE	1	0.28	3		494	757	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858920	243858920	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	45	348	0	ENST00000263826.5:c.145T>C	p.Tyr49His	p.Y49H	ENST00000263826	NM_005465.4	49	Tat/Cat	2/13	0.30186150427593	1	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	0	0.28	1		348	261	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57004316	57004316	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	G	G	A	rs200201854	NA	P-0059763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	100	518	0	ENST00000257254.3:c.163C>T	p.Arg55Trp	p.R55W	ENST00000257254		55	Cgg/Tgg	1/2	0.30186150427593	2	FACETS	1	0.946	1	0.545	0.487	0.607	CLONAL	1	TRUE	0	0.28	2		518	655	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487275	56487275	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	82	411	0	ENST00000267101.3:c.1421T>G	p.Leu474Arg	p.L474R	ENST00000267101	NM_001982.3	474	cTt/cGt	12/28	0.30186150427593	3	FACETS	1	0.896	1	0.508	0.448	0.573	CLONAL	1	TRUE	1	0.28	3		411	657	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384819	17384819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533740745	NA	P-0059763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	93	440	0	ENST00000359435.4:c.451G>A	p.Asp151Asn	p.D151N	ENST00000359435	NM_001033549.1	151	Gat/Aat	4/9	0.30186150427593	3	FACETS	1	0.896	1	0.504	0.448	0.564	CLONAL	1	TRUE	1	0.28	3		440	751	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868336	45868336	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	61	474	0	ENST00000391945.4:c.441G>T	p.Gln147His	p.Q147H	ENST00000391945	NM_000400.3	147	caG/caT	6/23	0.279005838378932	3	FACETS	0.683	0.588	0.787	0.342	0.294	0.394	SUBCLONAL	1	TRUE	1	0.28	3		474	727	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031941	26031941	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059763-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	155	612	0	ENST00000244661.2:c.348G>C	p.Lys116Asn	p.K116N	ENST00000244661	NM_003537.3	116	aaG/aaC	1/1	0.15426743598262	5	FACETS	0.821	0.751	0.894	0.41	0.375	0.447	INDETERMINATE	2	TRUE	1	0.28	5		612	958	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21347167	21347167	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747430075	NA	P-0059764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	148	463	0	ENST00000215739.8:c.1234C>T	p.Arg412Cys	p.R412C	ENST00000215739	NM_006767.3	412	Cgc/Tgc	11/21	1	2	FACETS	0.987	0.915	1	0.987	0.915	1	CLONAL	1	TRUE	1	0.890060667525915	2		463	337	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067100	143067100	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059764-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	212	466	0	ENST00000262992.4:c.1613T>A	p.Met538Lys	p.M538K	ENST00000262992	NM_001101669.1	538	aTg/aAg	16/24	0.890060667525915	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.890060667525915	2		466	227	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424484	49424484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754146878	NA	P-0059764-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	42	483	0	ENST00000301067.7:c.13739G>A	p.Gly4580Asp	p.G4580D	ENST00000301067	NM_003482.3	4580	gGc/gAc	41/54	0.0925207940678625	10	FACETS	1	0.899	1	0.879	0.738	1	CLONAL	4	TRUE	5	0.0925207940678625	10		483	283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0059765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	204	593	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.434346989871562	3	FACETS	0.987	0.931	1	0.987	0.931	1	CLONAL	3	TRUE	0	0.434346989871562	3		593	386	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145412	61145412	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	47	312	0	ENST00000295025.8:c.622T>C	p.Cys208Arg	p.C208R	ENST00000295025	NM_002908.2	208	Tgt/Cgt	6/11	0.434346989871562	3	FACETS	0.828	0.702	0.966	0.414	0.351	0.483	CLONAL	1	TRUE	1	0.434346989871562	3		312	318	SUCCESS
REST	5978	MSKCC	GRCh37	4	57797464	57797464	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	86	578	0	ENST00000309042.7:c.2440C>G	p.Pro814Ala	p.P814A	ENST00000309042	NM_005612.4	814	Cct/Gct	4/4	0.331865493827576	3	FACETS	0.941	0.835	1	0.471	0.417	0.527	CLONAL	1	TRUE	1	0.434346989871562	3		578	512	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501583	149501589	+	frameshift_variant	Frame_Shift_Del	DEL	TCCCCGG	TCCCCGG	-	novel	NA	P-0059765-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	53	415	0	ENST00000261799.4:c.2198_2204del	p.Thr733ArgfsTer9	p.T733Rfs*9	ENST00000261799	NM_002609.3	733	aCCGGGGAg/ag	16/23	0.379558490684422	4	FACETS	0.768	0.656	0.89			1	SUBCLONAL	1	TRUE	NA	0.434346989871562	4		415	456	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692891	89692891	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059769-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	31	238	1	ENST00000371953.3:c.375A>T	p.Lys125Asn	p.K125N	ENST00000371953	NM_000314.4	125	aaA/aaT	5/9	0.346478697906014	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.346478697906014	1		239	127	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712760	43712760	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1466285699	NA	P-0059769-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	74	536	0	ENST00000382044.4:c.4424C>G	p.Ala1475Gly	p.A1475G	ENST00000382044	NM_001141980.1	1475	gCt/gGt	21/28	1	2	FACETS	0.929	0.816	1	0.929	0.816	1	CLONAL	1	TRUE	1	0.346478697906014	2		536	460	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636978	176636978	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059769-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	21	517	0	ENST00000439151.2:c.1578G>C	p.Arg526Ser	p.R526S	ENST00000439151	NM_022455.4	526	agG/agC	5/23	1	2	FACETS	0.327	0.251	0.415	0.327	0.251	0.415	SUBCLONAL	1	TRUE	1	0.346478697906014	2		517	371	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0059770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	204	668	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.666608268424682	2		668	586	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441459	52441461	+	inframe_deletion	In_Frame_Del	DEL	AAT	AAT	-	novel	NA	P-0059770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	187	450	0	ENST00000460680.1:c.391_393del	p.Ile131del	p.I131del	ENST00000460680	NM_004656.3	131	ATT/-	6/17	0.666608268424682	1	FACETS	0.954	0.894	1	0.954	0.894	1	CLONAL	1	TRUE	0	0.666608268424682	1		450	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	143	522	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.941	1	1	0.993	1	CLONAL	3	TRUE	1	0.232376622723574	2		522	400	SUCCESS
MAD2L2	10459	MSKCC	GRCh37	1	11737631	11737631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377687352	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	104	361	0	ENST00000235310.3:c.200C>T	p.Thr67Met	p.T67M	ENST00000235310		67	aCg/aTg	6/11	1	2	FACETS	0.878	0.794	0.964	1	0.99	1	CLONAL	3	TRUE	1	0.232376622723574	2		361	340	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097703	27097704	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	49	490	0	ENST00000324856.7:c.3292_3293del	p.Gln1098ValfsTer6	p.Q1098Vfs*6	ENST00000324856	NM_006015.4	1098	CAg/g	12/20	1	2	FACETS	0.999	0.848	1	0.999	0.848	1	CLONAL	1	TRUE	1	0.232376622723574	2		490	422	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937066	36937066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564880597	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	114	471	0	ENST00000361632.4:c.1253G>A	p.Arg418His	p.R418H	ENST00000361632		418	cGt/cAt	9/16	1	2	FACETS	0.965	0.879	1	1	0.991	1	CLONAL	3	TRUE	1	0.232376622723574	2		471	339	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444659	78444659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs908264837	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	61	647	0	ENST00000370768.2:c.30del	p.Ser11LeufsTer43	p.S11Lfs*43	ENST00000370768	NM_003902.3	10	ccC/cc	1/20	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.232376622723574	2		647	485	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268950	115268950	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs750855257	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	121	382	0	ENST00000438362.2:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000438362	NM_001242891.1	554	Cga/Tga	14/20	1	2	FACETS	0.995	0.909	1	1	0.992	1	CLONAL	3	TRUE	1	0.232376622723574	2		382	349	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165561	118165561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	175	532	0	ENST00000369448.3:c.71G>A	p.Arg24Gln	p.R24Q	ENST00000369448	NM_017709.3	24	cGg/cAg	2/2	1	2	FACETS	1	0.98	1	1	0.995	1	CLONAL	3	TRUE	1	0.232376622723574	2		532	442	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841451	156841451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	167	577	0	ENST00000524377.1:c.754G>A	p.Ala252Thr	p.A252T	ENST00000524377	NM_002529.3	252	Gcc/Acc	7/17	1	2	FACETS	1	0.963	1	1	0.994	1	CLONAL	3	TRUE	1	0.232376622723574	2		577	452	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692791	89692791	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1114167623	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	72	217	0	ENST00000371953.3:c.275A>G	p.Asp92Gly	p.D92G	ENST00000371953	NM_000314.4	92	gAc/gGc	5/9	1	2	FACETS	1	0.942	1	1	0.987	1	CLONAL	3	TRUE	1	0.232376622723574	2		217	190	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	72	269	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.943	0.838	1	1	0.986	1	CLONAL	3	TRUE	1	0.232376622723574	2		269	219	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316391	14316391	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	80	358	0	ENST00000256196.4:c.214C>A	p.Gln72Lys	p.Q72K	ENST00000256196		72	Caa/Aaa	3/6	1	2	FACETS	0.883	0.788	0.982	1	0.987	1	CLONAL	3	TRUE	1	0.232376622723574	2		358	260	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943741	71943742	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	141	547	0	ENST00000298229.2:c.1789_1790del	p.Leu597AlafsTer32	p.L597Afs*32	ENST00000298229	NM_001567.3	595	aTC/a	15/28	1	2	FACETS	0.913	0.839	0.989	1	0.993	1	CLONAL	3	TRUE	1	0.232376622723574	2		547	443	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77961222	77961222	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1465572548	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	129	466	0	ENST00000361507.4:c.601C>T	p.Arg201Ter	p.R201*	ENST00000361507	NM_080491.2	201	Cga/Tga	3/10	1	2	FACETS	0.947	0.867	1	1	0.992	1	CLONAL	3	TRUE	1	0.232376622723574	2		466	391	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165729	108165729	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs762083530	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	127	353	0	ENST00000278616.4:c.4852C>T	p.Arg1618Ter	p.R1618*	ENST00000278616	NM_000051.3	1618	Cga/Tga	32/63	1	2	FACETS	0.949	0.875	1	1	0.993	1	CLONAL	4	TRUE	1	0.232376622723574	2		353	288	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420289	49420289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768551828	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	144	463	0	ENST00000301067.7:c.15460C>T	p.Arg5154Trp	p.R5154W	ENST00000301067	NM_003482.3	5154	Cgg/Tgg	48/54	1	2	FACETS	0.93	0.856	1	1	0.993	1	CLONAL	3	TRUE	1	0.232376622723574	2		463	444	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433722	49433722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572359740	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	155	610	0	ENST00000301067.7:c.7831C>T	p.Arg2611Cys	p.R2611C	ENST00000301067	NM_003482.3	2611	Cgc/Tgc	31/54	1	2	FACETS	1	0.972	1	1	0.994	1	CLONAL	3	TRUE	1	0.232376622723574	2		610	403	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487277	56487277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035001455	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	136	475	0	ENST00000267101.3:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000267101	NM_001982.3	475	Cgg/Tgg	12/28	1	2	FACETS	1	0.94	1	1	0.993	1	CLONAL	3	TRUE	1	0.232376622723574	2		475	380	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863318	57863319	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs757280991	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	104	497	0	ENST00000228682.2:c.1418dup	p.Ser474GlnfsTer3	p.S474Qfs*3	ENST00000228682	NM_005269.2	471	-/G	11/12	1	2	FACETS	0.86	0.778	0.945	1	0.99	1	CLONAL	3	TRUE	1	0.232376622723574	2		497	347	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961418	41961418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	116	427	0	ENST00000219905.7:c.326G>A	p.Arg109His	p.R109H	ENST00000219905	NM_001164273.1	109	cGt/cAt	2/24	1	2	FACETS	0.945	0.862	1	1	0.991	1	CLONAL	3	TRUE	1	0.232376622723574	2		427	352	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707977	43707977	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	126	435	0	ENST00000382044.4:c.4904G>A	p.Arg1635His	p.R1635H	ENST00000382044	NM_001141980.1	1635	cGc/cAc	23/28	1	2	FACETS	0.99	0.907	1	1	0.992	1	CLONAL	3	TRUE	1	0.232376622723574	2		435	365	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341260	341260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374579262	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	98	336	0	ENST00000262320.3:c.2224G>A	p.Val742Ile	p.V742I	ENST00000262320	NM_003502.3	742	Gtc/Atc	9/11	0.232376622723574	1	FACETS	1	0.959	1	1	0.991	1	CLONAL	3	TRUE	0	0.232376622723574	1		336	227	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124202	2124202	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs796053511	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	111	442	0	ENST00000219476.3:c.2357G>A	p.Arg786His	p.R786H	ENST00000219476	NM_000548.3	786	cGc/cAc	22/42	0.232376622723574	1	FACETS	1	0.937	1	1	0.992	1	CLONAL	3	TRUE	0	0.232376622723574	1		442	273	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56792469	56792469	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1431901735	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	135	419	0	ENST00000308159.5:c.199C>T	p.Arg67Trp	p.R67W	ENST00000308159	NM_014669.4	67	Cgg/Tgg	3/22	0.232376622723574	1	FACETS	0.989	0.911	1	1	0.993	1	CLONAL	3	TRUE	0	0.232376622723574	1		419	346	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654643	67654643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs968244943	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	162	444	0	ENST00000264010.4:c.1130G>A	p.Arg377His	p.R377H	ENST00000264010	NM_006565.3	377	cGt/cAt	6/12	0.232376622723574	1	FACETS	0.954	0.891	1	1	0.994	1	CLONAL	4	TRUE	0	0.232376622723574	1		444	323	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993348	72993348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759852645	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	134	544	0	ENST00000268489.5:c.697G>A	p.Val233Met	p.V233M	ENST00000268489	NM_006885.3	233	Gtg/Atg	2/10	0.232376622723574	1	FACETS	1	0.978	1	1	0.992	1	CLONAL	2	TRUE	0	0.232376622723574	1		544	424	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819740	81819740	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1231997442	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	175	471	0	ENST00000359376.3:c.146C>T	p.Thr49Met	p.T49M	ENST00000359376	NM_002661.3	49	aCg/aTg	2/33	0.232376622723574	1	FACETS	0.895	0.836	0.953	1	0.995	1	CLONAL	4	TRUE	0	0.232376622723574	1		471	372	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	45	756	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.708	0.595	0.834	0.708	0.595	0.834	SUBCLONAL	1	TRUE	1	0.232376622723574	2		756	547	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	20	613	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.378	0.288	0.484	0.378	0.288	0.484	SUBCLONAL	1	TRUE	1	0.232376622723574	2		614	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	161	470	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	1	2	FACETS	1	0.951	1	1	0.994	1	CLONAL	3	TRUE	1	0.232376622723574	2		470	446	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602494	10602494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	141	510	0	ENST00000171111.5:c.1084C>T	p.Arg362Trp	p.R362W	ENST00000171111	NM_203500.1	362	Cgg/Tgg	3/6	1	2	FACETS	0.975	0.897	1	1	0.993	1	CLONAL	3	TRUE	1	0.232376622723574	2		510	415	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602767	10602767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	192	506	0	ENST00000171111.5:c.811G>A	p.Val271Met	p.V271M	ENST00000171111	NM_203500.1	271	Gtg/Atg	3/6	1	2	FACETS	0.92	0.861	0.98	1	0.995	1	CLONAL	4	TRUE	1	0.232376622723574	2		506	449	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276271	15276271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757787552	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	138	520	0	ENST00000263388.2:c.5723C>T	p.Thr1908Met	p.T1908M	ENST00000263388	NM_000435.2	1908	aCg/aTg	31/33	1	2	FACETS	0.954	0.877	1	1	0.993	1	CLONAL	3	TRUE	1	0.232376622723574	2		520	415	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384974	17384974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765161255	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	117	460	0	ENST00000359435.4:c.524C>T	p.Thr175Met	p.T175M	ENST00000359435	NM_001033549.1	175	aCg/aTg	5/9	1	2	FACETS	0.94	0.857	1	1	0.991	1	CLONAL	3	TRUE	1	0.232376622723574	2		460	357	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211355	36211357	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs201152143	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	153	605	2	ENST00000222270.7:c.1117_1119del	p.Glu373del	p.E373del	ENST00000222270	NM_014727.1	369	aAAGaa/aaa	3/37	1	2	FACETS	0.986	0.911	1	1	0.993	1	CLONAL	3	TRUE	1	0.232376622723574	2		607	445	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213941	36213941	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749133342	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	130	529	0	ENST00000222270.7:c.2767C>T	p.Arg923Trp	p.R923W	ENST00000222270	NM_014727.1	923	Cgg/Tgg	6/37	1	2	FACETS	0.981	0.9	1	1	0.992	1	CLONAL	3	TRUE	1	0.232376622723574	2		529	380	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218638	36218638	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749126437	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	161	481	0	ENST00000222270.7:c.4342G>A	p.Gly1448Ser	p.G1448S	ENST00000222270	NM_014727.1	1448	Ggc/Agc	17/37	1	2	FACETS	0.881	0.819	0.945	1	0.994	1	CLONAL	4	TRUE	1	0.232376622723574	2		481	393	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791715	42791715	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157030312	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	192	564	1	ENST00000575354.2:c.601C>T	p.Arg201Trp	p.R201W	ENST00000575354	NM_015125.3	201	Cgg/Tgg	5/20	1	2	FACETS	1	0.976	1	1	0.995	1	CLONAL	3	TRUE	1	0.232376622723574	2		565	502	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	165	551	0	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	0.888	0.825	0.951	1	0.994	1	CLONAL	4	TRUE	1	0.232376622723574	2		551	400	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47643434	47643434	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs12476364	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	103	357	0	ENST00000233146.2:c.943-1G>A		p.X315_splice	ENST00000233146	NM_000251.2	315			1	2	FACETS	1	0.964	1	1	0.991	1	CLONAL	3	TRUE	1	0.232376622723574	2		357	264	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656973	47656973	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	121	328	0	ENST00000233146.2:c.1170del	p.Ala391ProfsTer21	p.A391Pfs*21	ENST00000233146	NM_000251.2	390	cTt/ct	7/16	1	2	FACETS	1	0.941	1	1	0.992	1	CLONAL	3	TRUE	1	0.232376622723574	2		328	335	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661390	227661390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141094678	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	30	542	1	ENST00000305123.5:c.2065G>A	p.Val689Ile	p.V689I	ENST00000305123	NM_005544.2	689	Gtc/Atc	1/2	1	2	FACETS	0.746	0.602	0.91	0.746	0.602	0.91	CLONAL	1	TRUE	1	0.232376622723574	2		543	346	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022317	31022317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778606251	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	164	491	0	ENST00000375687.4:c.1802C>T	p.Thr601Met	p.T601M	ENST00000375687	NM_015338.5	601	aCg/aTg	13/13	1	2	FACETS	1	0.943	1	1	0.994	1	CLONAL	3	TRUE	1	0.232376622723574	2		491	461	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	148	844	17	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	1	0.967	1	1	0.994	1	CLONAL	3	TRUE	1	0.232376622723574	2		861	392	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46251043	46251043	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1013161408	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	86	295	0	ENST00000371998.3:c.52C>T	p.Arg18Cys	p.R18C	ENST00000371998		18	Cgc/Tgc	3/23	1	2	FACETS	0.894	0.801	0.99	1	0.988	1	CLONAL	3	TRUE	1	0.232376622723574	2		295	276	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62322253	62322253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753435220	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	127	366	0	ENST00000360203.5:c.2509G>A	p.Ala837Thr	p.A837T	ENST00000360203	NM_001283009.1	837	Gcc/Acc	27/35	1	2	FACETS	1	0.97	1	1	0.993	1	CLONAL	3	TRUE	1	0.232376622723574	2		366	325	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548243	41548243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775368605	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	151	355	0	ENST00000263253.7:c.3031G>A	p.Glu1011Lys	p.E1011K	ENST00000263253	NM_001429.3	1011	Gaa/Aaa	16/31	0.232376622723574	1	FACETS	1	0.963	1	1	0.994	1	CLONAL	3	TRUE	0	0.232376622723574	1		355	360	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519886	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	62	435	0	ENST00000349496.5:c.97T>C	p.Ser33Pro	p.S33P	ENST00000349496	NM_001904.3	33	Tct/Cct	3/15	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.232376622723574	2		435	428	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651370	52651370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs965565832	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	129	430	0	ENST00000394830.3:c.1726C>T	p.Arg576Cys	p.R576C	ENST00000394830	NM_018313.4	576	Cgc/Tgc	15/30	1	2	FACETS	1	0.955	1	1	0.993	1	CLONAL	3	TRUE	1	0.232376622723574	2		430	349	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682400	52682400	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	42	296	0	ENST00000394830.3:c.773del	p.Asn258MetfsTer25	p.N258Mfs*25	ENST00000394830	NM_018313.4	258	aAt/at	8/30	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.232376622723574	2		296	292	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027093	71027093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200629338	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	185	563	0	ENST00000318789.4:c.1234G>A	p.Ala412Thr	p.A412T	ENST00000318789	NM_032682.5	412	Gcc/Acc	15/21	1	2	FACETS	1	0.964	1	1	0.995	1	CLONAL	3	TRUE	1	0.232376622723574	2		563	503	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	13	97	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	1	0.795	1	1	0.795	1	CLONAL	1	TRUE	1	0.232376622723574	2		97	99	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217169	66217169	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	143	411	0	ENST00000273854.3:c.2446G>T	p.Val816Leu	p.V816L	ENST00000273854	NM_004439.5	816	Gtg/Ttg	14/18	1	2	FACETS	1	0.975	1	1	0.993	1	CLONAL	3	TRUE	1	0.232376622723574	2		411	362	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114277	143114277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs76891221	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	127	357	0	ENST00000262992.4:c.1144C>T	p.Arg382Trp	p.R382W	ENST00000262992	NM_001101669.1	382	Cgg/Tgg	13/24	1	2	FACETS	1	0.974	1	1	0.993	1	CLONAL	3	TRUE	1	0.232376622723574	2		357	317	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249457	153249457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	118	379	0	ENST00000281708.4:c.1321C>T	p.Arg441Trp	p.R441W	ENST00000281708	NM_033632.3	441	Cgg/Tgg	9/12	1	2	FACETS	1	0.958	1	1	0.992	1	CLONAL	3	TRUE	1	0.232376622723574	2		379	314	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295958	1295958	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	47	646	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.911	0.77	1	0.911	0.77	1	CLONAL	1	TRUE	1	0.232376622723574	2		646	444	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178095	56178095	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374455781	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	121	442	0	ENST00000399503.3:c.3068G>A	p.Arg1023His	p.R1023H	ENST00000399503	NM_005921.1	1023	cGc/cAc	14/20	1	2	FACETS	0.931	0.85	1	1	0.992	1	CLONAL	3	TRUE	1	0.232376622723574	2		442	373	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158576	26158576	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs779562726	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	18	408	0	ENST00000289316.2:c.179T>C	p.Met60Thr	p.M60T	ENST00000289316	NM_138720.2	60	aTg/aCg	1/2	1	2	FACETS	0.472	0.355	0.611	0.472	0.355	0.611	SUBCLONAL	1	TRUE	1	0.232376622723574	2		408	328	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672176	30672176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779031191	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	204	754	0	ENST00000376406.3:c.4784G>A	p.Arg1595Gln	p.R1595Q	ENST00000376406	NM_014641.2	1595	cGg/cAg	10/15	1	2	FACETS	0.969	0.904	1	1	0.995	1	CLONAL	3	TRUE	1	0.232376622723574	2		754	604	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800444	32800444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758423176	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	154	561	0	ENST00000374899.4:c.1103G>A	p.Arg368Gln	p.R368Q	ENST00000374899	NM_018833.2	368	cGg/cAg	6/12	1	2	FACETS	1	0.923	1	1	0.994	1	CLONAL	3	TRUE	1	0.232376622723574	2		561	442	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552984	106552984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	176	607	0	ENST00000369096.4:c.949G>A	p.Gly317Arg	p.G317R	ENST00000369096	NM_001198.3	317	Ggg/Agg	5/7	1	2	FACETS	1	0.967	1	1	0.994	1	CLONAL	3	TRUE	1	0.232376622723574	2		607	473	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100138	157100138	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1289468231	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	87	499	0	ENST00000346085.5:c.1079del	p.Gly360AlafsTer9	p.G360Afs*9	ENST00000346085	NM_020732.3	359	Ggg/gg	1/20	1	2	FACETS	0.867	0.777	0.96	1	0.988	1	CLONAL	3	TRUE	1	0.232376622723574	2		499	288	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760592	133760592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2229067	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	74	538	0	ENST00000318560.5:c.2915C>T	p.Ser972Leu	p.S972L	ENST00000318560	NM_005157.4	972	tCg/tTg	11/11	1	2	FACETS	0.753	0.662	0.85	1	0.976	1	SUBCLONAL	2	TRUE	1	0.232376622723574	2		538	423	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328444	137328444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780219731	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	129	439	0	ENST00000481739.1:c.1373C>T	p.Pro458Leu	p.P458L	ENST00000481739	NM_002957.4	458	cCg/cTg	10/10	1	2	FACETS	1	0.946	1	1	0.993	1	CLONAL	3	TRUE	1	0.232376622723574	2		439	356	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401291	139401291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751169922	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	164	508	0	ENST00000277541.6:c.3778G>A	p.Val1260Met	p.V1260M	ENST00000277541	NM_017617.3	1260	Gtg/Atg	23/34	1	2	FACETS	1	0.974	1	1	0.994	1	CLONAL	3	TRUE	1	0.232376622723574	2		508	425	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932891	39932891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748813798	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	191	603	0	ENST00000378444.4:c.1708G>A	p.Ala570Thr	p.A570T	ENST00000378444	NM_001123385.1	570	Gca/Aca	4/15	1	2	FACETS	1	0.977	1	1	0.995	1	CLONAL	3	TRUE	1	0.232376622723574	2		603	497	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028833	47028833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782523524	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	127	501	0	ENST00000377604.3:c.137G>A	p.Arg46His	p.R46H	ENST00000377604	NM_001204468.1	46	cGc/cAc	3/24	1	2	FACETS	1	0.929	1	1	0.992	1	CLONAL	3	TRUE	1	0.232376622723574	2		501	359	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411266	63411266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778813513	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	165	548	0	ENST00000330258.3:c.1901G>A	p.Arg634His	p.R634H	ENST00000330258	NM_152424.3	634	cGt/cAt	2/2	1	2	FACETS	1	0.931	1	1	0.994	1	CLONAL	3	TRUE	1	0.232376622723574	2		548	471	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350030	70350030	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059771-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	126	481	0	ENST00000374080.3:c.4013A>C	p.Asn1338Thr	p.N1338T	ENST00000374080		1338	aAc/aCc	28/45	1	2	FACETS	0.946	0.866	1	1	0.992	1	CLONAL	3	TRUE	1	0.232376622723574	2		481	382	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0059772-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	45	556	2	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.272254377286302	1	FACETS	0.858	0.724	1	0.858	0.724	1	CLONAL	1	TRUE	0	0.272254377286302	1		558	333	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0059772-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	107	360	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.272254377286302	2	FACETS	0.912	0.823	1	0.912	0.823	1	CLONAL	2	TRUE	0	0.272254377286302	2		360	431	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0059772-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	70	411	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.272254377286302	2		411	509	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278343	39278343	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059772-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	27	408	0	ENST00000402219.2:c.806T>A	p.Met269Lys	p.M269K	ENST00000402219	NM_005633.3	269	aTg/aAg	6/23	0.220340671585367	3	FACETS	0.811	0.647	0.997	0.405	0.323	0.499	CLONAL	1	TRUE	1	0.272254377286302	3		408	278	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0059772-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	36	396	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	1	2	FACETS	0.787	0.649	0.941	0.787	0.649	0.941	CLONAL	1	TRUE	1	0.272254377286302	2		396	336	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100175	27100176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0059772-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	51	672	0	ENST00000324856.7:c.3976_3977dup	p.Gln1327ArgfsTer155	p.Q1327Rfs*155	ENST00000324856	NM_006015.4	1324	tac/taCCc	16/20	1	2	FACETS	0.682	0.58	0.795	0.682	0.58	0.795	SUBCLONAL	1	TRUE	1	0.272254377286302	2		672	549	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857425	9857425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1268143219	NA	P-0059773-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	50	499	0	ENST00000330684.3:c.3976G>A	p.Gly1326Ser	p.G1326S	ENST00000330684	NM_001134407.1	1326	Ggc/Agc	13/13	0.751206464280214	6	FACETS	0.454	0.385	0.532			1	SUBCLONAL	1	FALSE	NA	0.751206464280214	6		499	733	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239981	98239981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142791675	NA	P-0059773-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	77	348	0	ENST00000331920.6:c.1351G>A	p.Ala451Thr	p.A451T	ENST00000331920	NM_000264.3	451	Gcc/Acc	10/24	0.755586904237159	5	FACETS	0.903	0.795	1	0.301	0.265	0.34	CLONAL	1	FALSE	2	0.751206464280214	5		348	483	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426141	49426142	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0059773-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	41	528	1	ENST00000301067.7:c.12346dup	p.His4116ProfsTer11	p.H4116Pfs*11	ENST00000301067	NM_003482.3	4116	cat/cCat	39/54	0.75473550515028	3	FACETS	0.405	0.338	0.479			1	SUBCLONAL	1	FALSE	NA	0.751206464280214	3		529	371	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795295	42795295	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059773-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	33	426	0	ENST00000575354.2:c.2375C>A	p.Ala792Glu	p.A792E	ENST00000575354	NM_015125.3	792	gCg/gAg	10/20	0.755586904237159	3	FACETS	0.371	0.302	0.447	0.185	0.151	0.224	SUBCLONAL	1	FALSE	1	0.751206464280214	3		426	326	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539036	23539036	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059773-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	72	549	0	ENST00000380871.4:c.403C>A	p.Gln135Lys	p.Q135K	ENST00000380871	NM_006167.3	135	Cag/Aag	2/2	0.27576187619083	2	FACETS	0.549	0.483	0.62	0.275	0.241	0.31	INDETERMINATE	1	FALSE	0	0.751206464280214	2		549	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0059774-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	211	604	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		604	445	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916929	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059774-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	25	273	0	ENST00000263967.3:c.316G>T	p.Gly106Cys	p.G106C	ENST00000263967	NM_006218.2	106	Ggc/Tgc	2/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		273	111	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155400	99155400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs965243879	NA	P-0059774-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	79	411	0	ENST00000074304.5:c.626G>A	p.Arg209Gln	p.R209Q	ENST00000074304	NM_001134224.1	209	cGa/cAa	9/26	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		411	321	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94963972	94963972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059774-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	101	332	0	ENST00000536441.1:c.53C>T	p.Thr18Ile	p.T18I	ENST00000536441	NM_144665.3	18	aCc/aTc	1/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		332	460	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102094475	102094476	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTTA	novel	NA	P-0059774-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	35	333	0	ENST00000282441.5:c.1156_1159dup	p.Asn387ThrfsTer2	p.N387Tfs*2	ENST00000282441	NM_001130145.2	385	-/CTTA	7/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		333	215	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636650	73636650	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059774-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	141	589	1	ENST00000377687.4:c.913C>A	p.Pro305Thr	p.P305T	ENST00000377687	NM_001730.3	305	Cca/Aca	2/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		590	635	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66522027	66522027	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059774-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	62	431	0	ENST00000358598.2:c.682C>G	p.Arg228Gly	p.R228G	ENST00000358598	NM_212471.2	228	Cga/Gga	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		431	236	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965214	25965214	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1559497398	NA	P-0059774-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	125	533	0	ENST00000435504.4:c.3992T>C	p.Ile1331Thr	p.I1331T	ENST00000435504		1331	aTc/aCc	13/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		533	448	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022659	36022659	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1416349077	NA	P-0059774-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	101	438	0	ENST00000358208.4:c.532C>T	p.Arg178Ter	p.R178*	ENST00000358208		178	Cga/Tga	5/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		438	398	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253852	153253862	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAGCACATA	GAAAGCACATA	-	novel	NA	P-0059774-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	24	240	0	ENST00000281708.4:c.871_881del	p.Tyr291IlefsTer22	p.Y291Ifs*22	ENST00000281708	NM_033632.3	291	TATGTGCTTTCa/a	6/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		240	108	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0059775-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	23	457	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.57	0.443	0.718	0.57	0.443	0.718	SUBCLONAL	1	TRUE	1	0.16	2		457	504	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248150	110248150	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059775-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	39	404	0	ENST00000374672.4:c.1322A>G	p.Asp441Gly	p.D441G	ENST00000374672	NM_004235.4	441	gAt/gGt	5/5	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.16	2		404	433	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946337	2946337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759681668	NA	P-0059775-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	27	419	0	ENST00000396946.4:c.3400G>A	p.Val1134Ile	p.V1134I	ENST00000396946	NM_032415.4	1134	Gtt/Att	25/25	1	2	FACETS	0.717	0.569	0.886	0.717	0.569	0.886	SUBCLONAL	1	TRUE	1	0.16	2		419	471	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444689	49444689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200825022	NA	P-0059775-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	39	601	0	ENST00000301067.7:c.2777C>T	p.Ser926Leu	p.S926L	ENST00000301067	NM_003482.3	926	tCg/tTg	10/54	1	2	FACETS	0.756	0.625	0.902	0.756	0.625	0.902	CLONAL	1	TRUE	1	0.16	2		601	645	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0059775-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	33	306	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.16	2		306	368	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657161	215657192	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACACAATTACTTTAAAATAATTAAAAAAAAAA	ACACAATTACTTTAAAATAATTAAAAAAAAAA	-	novel	NA	P-0059775-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	19	394	0	ENST00000260947.4:c.216-23_224del		p.X72_splice	ENST00000260947	NM_000465.2	72		3/11	1	2	FACETS	0.642	0.486	0.825	0.642	0.486	0.825	SUBCLONAL	1	TRUE	1	0.16	2		394	370	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441771	49441771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	85	371	0	ENST00000301067.7:c.4213C>T	p.His1405Tyr	p.H1405Y	ENST00000301067	NM_003482.3	1405	Cac/Tac	14/54	NA	2	FACETS	0.796	0.709	0.889			1	INDETERMINATE	1	TRUE	NA	0.560210334742876	2		371	381	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456361	40456361	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs763602853	NA	P-0059776-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	99	455	0	ENST00000345506.4:c.1171G>A	p.Glu391Lys	p.E391K	ENST00000345506	NM_003152.3	391	Gag/Aag	11/20	0.560210334742876	2	FACETS	1	0.969	1	0.589	0.533	0.647	CLONAL	1	TRUE	0	0.560210334742876	2		455	300	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0059777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	79	329	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.53595619718312	2		329	242	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	32	327	0	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	0.338	0.275	0.41	0.338	0.275	0.41	SUBCLONAL	1	TRUE	1	0.53595619718312	2		327	353	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560514	65560514	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	86	265	0	ENST00000358664.4:c.83A>G	p.His28Arg	p.H28R	ENST00000358664	NM_002382.4	28	cAt/cGt	3/5	1	2	FACETS	0.975	0.871	1	0.975	0.871	1	CLONAL	1	TRUE	1	0.53595619718312	2		265	329	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919231	178919231	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	85	222	0	ENST00000263967.3:c.716T>G	p.Leu239Arg	p.L239R	ENST00000263967	NM_006218.2	239	cTa/cGa	4/21	1	2	FACETS	0.976	0.871	1	0.976	0.871	1	CLONAL	1	TRUE	1	0.53595619718312	2		222	325	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0059777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	21	336	3	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	0.53595619718312	2	FACETS	0.207	0.159	0.264	0.104	0.079	0.132	SUBCLONAL	1	TRUE	0	0.53595619718312	2		339	378	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023769	27023769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	17	293	0	ENST00000324856.7:c.879del	p.Thr294ProfsTer69	p.T294Pfs*69	ENST00000324856	NM_006015.4	292	aCc/ac	1/20	1	2	FACETS	0.304	0.227	0.394	0.304	0.227	0.394	SUBCLONAL	1	TRUE	1	0.53595619718312	2		293	209	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182867	123182867	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	81	194	0	ENST00000218089.9:c.832C>G	p.Gln278Glu	p.Q278E	ENST00000218089	NM_001042749.1	278	Caa/Gaa	10/35	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.53595619718312	2		194	287	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101751	71101751	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	54	308	0	ENST00000318789.4:c.447del	p.Lys149AsnfsTer57	p.K149Nfs*57	ENST00000318789	NM_032682.5	149	aaA/aa	9/21	1	2	FACETS	0.598	0.513	0.69	0.598	0.513	0.69	SUBCLONAL	1	TRUE	1	0.53595619718312	2		308	337	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591247	67591247	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0059777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	101	290	0	ENST00000274335.5:c.1746-1G>C		p.X582_splice	ENST00000274335		582			1	2	FACETS	0.952	0.857	1	0.952	0.857	1	CLONAL	1	TRUE	1	0.53595619718312	2		290	396	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372446	55372447	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0059777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	104	401	0	ENST00000297316.4:c.1138dup	p.Gln380ProfsTer4	p.Q380Pfs*4	ENST00000297316	NM_022454.3	379	tac/taCc	2/2	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.53595619718312	2		401	355	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878058	48878058	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1226865525	NA	P-0059777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	35	317	0	ENST00000267163.4:c.13del	p.Thr5ProfsTer60	p.T5Pfs*60	ENST00000267163	NM_000321.2	4	Aaa/aa	1/27	1	2	FACETS	0.48	0.395	0.575	0.48	0.395	0.575	SUBCLONAL	1	TRUE	1	0.53595619718312	2		317	272	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540496	187540496	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs367553275	NA	P-0059777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	44	379	0	ENST00000441802.2:c.7244A>G	p.Tyr2415Cys	p.Y2415C	ENST00000441802	NM_005245.3	2415	tAt/tGt	10/27	1	2	FACETS	0.385	0.323	0.453	0.385	0.323	0.453	SUBCLONAL	1	TRUE	1	0.53595619718312	2		379	427	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56832443	56832443	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371252223	NA	P-0059777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	34	222	0	ENST00000308159.5:c.353G>A	p.Arg118Gln	p.R118Q	ENST00000308159	NM_014669.4	118	cGg/cAg	4/22	1	2	FACETS	0.416	0.341	0.5	0.416	0.341	0.5	SUBCLONAL	1	TRUE	1	0.53595619718312	2		222	305	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662312	67662312	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	108	341	0	ENST00000264010.4:c.1558G>T	p.Glu520Ter	p.E520*	ENST00000264010	NM_006565.3	520	Gag/Tag	9/12	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.53595619718312	2		341	397	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088802	27088803	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0059777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	76	280	0	ENST00000324856.7:c.2414dup	p.Gln806ThrfsTer11	p.Q806Tfs*11	ENST00000324856	NM_006015.4	804	ggc/ggCc	7/20	1	2	FACETS	0.827	0.731	0.929	0.827	0.731	0.929	CLONAL	1	TRUE	1	0.53595619718312	2		280	343	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0059777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	42	331	1	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.412	0.345	0.487	0.412	0.345	0.487	SUBCLONAL	1	TRUE	1	0.53595619718312	2		332	380	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163315466	163315466	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0059777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	18	280	0	ENST00000271452.3:c.808-2A>G		p.X270_splice	ENST00000271452	NM_145697.2	270			1	2	FACETS	0.237	0.178	0.306	0.237	0.178	0.306	SUBCLONAL	1	TRUE	1	0.53595619718312	2		280	284	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690818	89690818	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1564828960	NA	P-0059777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	126	171	0	ENST00000371953.3:c.226del	p.Tyr76MetfsTer23	p.Y76Mfs*23	ENST00000371953	NM_000314.4	75	caT/ca	4/9	0.53595619718312	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.53595619718312	2		171	223	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749107	43749107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	51	360	0	ENST00000382044.4:c.1699G>A	p.Ala567Thr	p.A567T	ENST00000382044	NM_001141980.1	567	Gct/Act	12/28	1	2	FACETS	0.487	0.415	0.565	0.487	0.415	0.565	SUBCLONAL	1	TRUE	1	0.53595619718312	2		360	391	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436043	56436043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	41	415	0	ENST00000407977.2:c.1094C>T	p.Ala365Val	p.A365V	ENST00000407977		365	gCa/gTa	9/10	1	2	FACETS	0.477	0.398	0.563	0.477	0.398	0.563	SUBCLONAL	1	TRUE	1	0.53595619718312	2		415	321	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141533	11141534	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0059777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	32	348	0	ENST00000358026.2:c.3512_3513del	p.Val1171AspfsTer4	p.V1171Dfs*4	ENST00000358026	NM_001128849.1	1170	acTGtg/actg	25/36	1	2	FACETS	0.347	0.282	0.421	0.347	0.282	0.421	SUBCLONAL	1	TRUE	1	0.53595619718312	2		348	344	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31424571	31424571	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	27	264	0	ENST00000344624.3:c.3224G>T	p.Arg1075Leu	p.R1075L	ENST00000344624		1075	cGc/cTc	25/33	1	2	FACETS	0.319	0.254	0.393	0.319	0.254	0.393	SUBCLONAL	1	TRUE	1	0.53595619718312	2		264	316	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	146	477	0				ENST00000310581	NM_198253.2	-/1132			0.464158503388515	5	FACETS	0.946	0.881	1	0.946	0.881	1	CLONAL	4	TRUE	1	0.464158503388515	5		477	282	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0059778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	119	479	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	0.464158503388515	2	FACETS	1	0.968	1	0.571	0.519	0.625	CLONAL	1	TRUE	0	0.464158503388515	2		479	449	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395665	31395665	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1182001726	NA	P-0059778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	97	503	0	ENST00000328111.2:c.2518C>T	p.Arg840Ter	p.R840*	ENST00000328111	NM_006892.3	840	Cga/Tga	23/23	0.145283167426044	6	FACETS	1	0.98	1	0.48	0.429	0.534	INDETERMINATE	1	TRUE	3	0.464158503388515	6		503	560	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324070	31324070	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs151341262	NA	P-0059778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	185	414	0	ENST00000412585.2:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000412585	NM_005514.6	165	Cag/Tag	3/8	0.464158503388515	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.464158503388515	2		414	331	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543749	29543749	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs780995980	NA	P-0059778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	116	486	0	ENST00000389048.3:c.1415-1G>A		p.X472_splice	ENST00000389048	NM_004304.4	472			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.464158503388515	2		486	381	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38949852	38949852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	480	463	0	ENST00000357387.3:c.4098G>A	p.Met1366Ile	p.M1366I	ENST00000357387	NM_152756.3	1366	atG/atA	31/38	0.464158503388515	5	FACETS	0.903	0.872	0.933	1	0.994	1	CLONAL	5	TRUE	1	0.464158503388515	5		463	777	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602713	10602713	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059780-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	92	569	1	ENST00000171111.5:c.865G>T	p.Glu289Ter	p.E289*	ENST00000171111	NM_203500.1	289	Gag/Tag	3/6	1	2	FACETS	0.988	0.881	1	0.988	0.881	1	CLONAL	1	TRUE	1	0.366683168554385	2		570	508	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059781-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	114	477	0				ENST00000310581	NM_198253.2	-/1132			0.895266546471514	5	FACETS	0.875	0.797	0.955	0.583	0.531	0.637	CLONAL	2	TRUE	2	0.895266546471514	5		477	341	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955538	48955538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913303	NA	P-0059781-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	254	344	0	ENST00000267163.4:c.1654C>T	p.Arg552Ter	p.R552*	ENST00000267163	NM_000321.2	552	Cga/Tga	17/27	0.895266546471514	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.895266546471514	2		344	271	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0059781-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	615	483	0	ENST00000269305.4:c.375+1G>T		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.895266546471514	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.895266546471514	3		483	659	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929191	44929191	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs772552174	NA	P-0059781-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	203	233	0	ENST00000377967.4:c.2291A>G	p.His764Arg	p.H764R	ENST00000377967	NM_021140.2	764	cAt/cGt	17/29	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.895266546471514	1		233	215	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844408	156844408	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059781-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	399	805	0	ENST00000524377.1:c.1241C>A	p.Thr414Lys	p.T414K	ENST00000524377	NM_002529.3	414	aCa/aAa	10/17	0.49620963835921	3	FACETS	1	0.992	1	0.594	0.565	0.622	INDETERMINATE	1	TRUE	1	0.895266546471514	3		805	1087	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295130	91295130	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059781-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	132	378	0	ENST00000355112.3:c.913C>G	p.Pro305Ala	p.P305A	ENST00000355112	NM_000057.2	305	Cca/Gca	4/22	0.895266546471514	2	FACETS	1	0.93	1	0.503	0.465	0.542	CLONAL	1	TRUE	0	0.895266546471514	2		378	293	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730803	40730803	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059781-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	187	537	0	ENST00000373198.4:c.3732C>G	p.Asp1244Glu	p.D1244E	ENST00000373198	NM_133170.3	1244	gaC/gaG	27/32	0.895266546471514	3	FACETS	0.966	0.897	1	0.483	0.448	0.519	CLONAL	1	TRUE	1	0.895266546471514	3		537	626	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31495464	31495464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059782-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	26	410	0	ENST00000344624.3:c.1684C>T	p.Arg562Cys	p.R562C	ENST00000344624		562	Cgt/Tgt	9/33	1	2	FACETS	0.345	0.272	0.428	0.345	0.272	0.428	SUBCLONAL	1	TRUE	1	0.312263211830231	2		410	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0059783-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	44	306	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.279430457049587	1	FACETS	0.826	0.704	0.956	1	0.967	1	CLONAL	2	FALSE	0	0.279430457049587	1		307	164	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678619	88678619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148888023	NA	P-0059783-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	54	525	0	ENST00000360948.2:c.917G>A	p.Arg306His	p.R306H	ENST00000360948	NM_001012338.2	306	cGt/cAt	9/19	0.186755764245671	4	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	FALSE	2	0.279430457049587	4		525	212	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604707	48604707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059783-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	78	499	0	ENST00000342988.3:c.1529G>A	p.Gly510Glu	p.G510E	ENST00000342988	NM_005359.5	510	gGa/gAa	12/12	0.279430457049587	2	FACETS	0.979	0.87	1	0.979	0.87	1	CLONAL	2	FALSE	0	0.279430457049587	2		499	285	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110556	4110556	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs727504370	NA	P-0059783-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	52	616	0	ENST00000262948.5:c.401A>G	p.Tyr134Cys	p.Y134C	ENST00000262948	NM_030662.3	134	tAc/tGc	3/11	0.253272234358485	0	FACETS	1	0.931	1			1	CLONAL	1	FALSE	0	0.279430457049587	0		616	235	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0059783-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	77	458	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.279430457049587	6	FACETS	1	0.957	1	0.787	0.695	0.884	CLONAL	2	FALSE	3	0.279430457049587	6		458	364	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860036	152860036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1240480716	NA	P-0059783-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	42	548	0	ENST00000406277.2:c.392G>A	p.Arg131His	p.R131H	ENST00000406277	NM_152274.4	131	cGc/cAc	5/7	1		FACETS		0.819	1				CLONAL	2	FALSE	1	0.279430457049587	2		548	156	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0059784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	12	525	0				ENST00000310581	NM_198253.2	-/1132			0.211884371444162	0	FACETS	0.783	0.565	1			1	CLONAL	2	FALSE	0	0.211884371444162	0		525	57	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0059784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	78	390	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.211884371444162	3	FACETS	0.994	0.884	1	1	0.978	1	CLONAL	3	FALSE	1	0.211884371444162	3		390	273	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271315	1271315	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369810792	NA	P-0059784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	18	399	0	ENST00000310581.5:c.2387C>T	p.Ser796Phe	p.S796F	ENST00000310581	NM_198253.2	796	tCc/tTc	8/16	0.211884371444162	0	FACETS	1	0.874	1			1	CLONAL	1	FALSE	0	0.211884371444162	0		399	107	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437756	49437756	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	45	639	0	ENST00000301067.7:c.5214G>T	p.Glu1738Asp	p.E1738D	ENST00000301067	NM_003482.3	1738	gaG/gaT	22/54	0.109104325486251	4	FACETS	1	0.927	1	1	0.927	1	INDETERMINATE	2	FALSE	2	0.211884371444162	4		639	222	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439636	51439637	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0059784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	40	469	0	ENST00000262662.1:c.201_202delinsTT	p.Arg68Ter	p.R68*	ENST00000262662		67	gaCCga/gaTTga	4/4	0.211884371444162	3	FACETS	1	0.859	1	0.518	0.431	0.615	CLONAL	1	FALSE	1	0.211884371444162	3		469	403	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059170	42059170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368218967	NA	P-0059784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	40	630	0	ENST00000219905.7:c.8890C>T	p.Pro2964Ser	p.P2964S	ENST00000219905	NM_001164273.1	2964	Ccc/Tcc	24/24	0.211884371444162	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	FALSE	0	0.211884371444162	1		630	257	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312906	30312906	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	20	529	0	ENST00000262643.3:c.709C>T	p.Leu237Phe	p.L237F	ENST00000262643	NM_001238.2	237	Ctt/Ttt	9/12	0.137881803711951	0	FACETS	0.87	0.67	1			1	CLONAL	1	FALSE	0	0.211884371444162	0		529	171	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216120	36216120	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0059784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	17	498	0	ENST00000222270.7:c.3529-1G>A		p.X1177_splice	ENST00000222270	NM_014727.1	1177			0.137881803711951	0	FACETS	0.639	0.478	0.828			1	SUBCLONAL	1	FALSE	0	0.211884371444162	0		498	198	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812248	212812248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1372768089	NA	P-0059784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	25	437	0	ENST00000342788.4:c.328C>T	p.Leu110Phe	p.L110F	ENST00000342788	NM_005235.2	110	Ctt/Ttt	3/28	0.137881803711951	0	FACETS	0.894	0.709	1			1	CLONAL	1	FALSE	0	0.211884371444162	0		437	208	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293784	1293784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059784-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	25	621	0	ENST00000310581.5:c.1217G>A	p.Gly406Glu	p.G406E	ENST00000310581	NM_198253.2	406	gGg/gAg	2/16	0.211884371444162	0	FACETS	0.721	0.576	0.882			1	SUBCLONAL	2	FALSE	0	0.211884371444162	0		621	129	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0059785-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	224	613	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.498103397506967	2	FACETS	0.984	0.928	1	0.984	0.928	1	CLONAL	2	TRUE	0	0.498103397506967	2		614	457	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243416	46243419	+	frameshift_variant	Frame_Shift_Del	DEL	GGCA	GGCA	-	novel	NA	P-0059785-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	86	294	0	ENST00000334344.6:c.1773_1776del	p.Gln591HisfsTer6	p.Q591Hfs*6	ENST00000334344	NM_152641.2	590	gGGCAg/gg	14/21	0.497112540296958	2	FACETS	0.855	0.773	0.938	0.855	0.773	0.938	CLONAL	2	TRUE	0	0.498103397506967	2		294	202	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109792	115109807	+	frameshift_variant	Frame_Shift_Del	DEL	AGCGGCTGTTGAGTTC	AGCGGCTGTTGAGTTC	-	novel	NA	P-0059785-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	202	489	2	ENST00000257566.3:c.2071_2086del	p.Glu691ProfsTer193	p.E691Pfs*193	ENST00000257566	NM_016569.3	691	GAACTCAACAGCCGCTcc/cc	8/8	0.497112540296958	2	FACETS	0.984	0.926	1	0.984	0.926	1	CLONAL	2	TRUE	0	0.498103397506967	2		491	412	SUCCESS
APC	324	MSKCC	GRCh37	5	112175729	112175747	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGTTCTTCCAGATGCTG	CAGGTTCTTCCAGATGCTG	-	novel	NA	P-0059785-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	125	465	0	ENST00000257430.4:c.4438_4456del	p.Gln1480IlefsTer21	p.Q1480Ifs*21	ENST00000257430	NM_000038.5	1480	CAGGTTCTTCCAGATGCTGat/at	16/16	0.498103397506967	2	FACETS	0.82	0.754	0.888	0.82	0.754	0.888	CLONAL	2	TRUE	0	0.498103397506967	2		465	306	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339722	70339722	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059785-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	158	165	0	ENST00000374080.3:c.391A>G	p.Lys131Glu	p.K131E	ENST00000374080		131	Aaa/Gaa	3/45	0.407722254253811	2	FACETS	0.889	0.839	0.936			1	CLONAL	3	TRUE	NA	0.498103397506967	2		165	238	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059786-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	15	477	0				ENST00000310581	NM_198253.2	-/1132			0.124057000414802	3	FACETS	0.39	0.285	0.516	0.195	0.142	0.258	INDETERMINATE	1	TRUE	1	0.341280578974356	3		477	264	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0059786-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	65	697	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	0.762	0.662	0.87	0.762	0.662	0.87	SUBCLONAL	1	TRUE	1	0.341280578974356	2		697	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0059786-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	72	511	20	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.747	0.653	0.848	0.747	0.653	0.848	SUBCLONAL	1	TRUE	1	0.341280578974356	2		531	565	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21553928	21553928	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059786-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	19	354	0	ENST00000382592.4:c.2674C>G	p.Gln892Glu	p.Q892E	ENST00000382592	NM_014572.2	892	Caa/Gaa	7/8	1	2	FACETS	0.321	0.243	0.413	0.321	0.243	0.413	SUBCLONAL	1	TRUE	1	0.341280578974356	2		354	347	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39763623	39763623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059786-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	24	388	0	ENST00000288319.7:c.829C>T	p.Pro277Ser	p.P277S	ENST00000288319	NM_182918.3	277	Cct/Tct	8/10	1	2	FACETS	0.332	0.26	0.416	0.332	0.26	0.416	SUBCLONAL	1	TRUE	1	0.341280578974356	2		388	423	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663346	227663346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024227751	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	82	580	0	ENST00000305123.5:c.109G>A	p.Glu37Lys	p.E37K	ENST00000305123	NM_005544.2	37	Gag/Aag	1/2	1	2	FACETS	0.954	0.847	1	0.954	0.847	1	CLONAL	1	TRUE	1	0.49	2		580	351	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	42	477	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.888	0.751	1	0.888	0.751	1	CLONAL	1	TRUE	1	0.49	2		477	193	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129655	11129655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	31	317	0	ENST00000358026.2:c.2461G>A	p.Glu821Lys	p.E821K	ENST00000358026	NM_001128849.1	821	Gag/Aag	17/36	1	2	FACETS	0.225	0.181	0.274	0.225	0.181	0.274	SUBCLONAL	1	TRUE	1	0.49	2		317	563	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	78	185	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.49	2		185	270	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056260	27056261	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCAGCCATACGGGTCCCAGACCCCGCAGC	novel	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	27	611	0	ENST00000324856.7:c.1258_1286dup	p.Tyr430SerfsTer13	p.Y430Sfs*13	ENST00000324856	NM_006015.4	419	ggg/ggGCAGCCATACGGGTCCCAGACCCCGCAGCg	2/20	1	2	FACETS	0.217	0.172	0.269	0.217	0.172	0.269	SUBCLONAL	1	TRUE	1	0.49	2		611	508	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983074	201983074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	32	650	0	ENST00000359651.3:c.923C>T	p.Ser308Phe	p.S308F	ENST00000359651		308	tCc/tTc	7/8	1	2	FACETS	0.268	0.217	0.325	0.268	0.217	0.325	SUBCLONAL	1	TRUE	1	0.49	2		650	488	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230561393	230561393	+	5_prime_UTR_variant	5'UTR	SNP	C	C	T	novel	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	51	873	0	ENST00000391860.1:c.-64G>A		p.*22*	ENST00000391860	NM_001258311.1	-/409		1/7	1	2	FACETS	0.504	0.429	0.586	0.504	0.429	0.586	SUBCLONAL	1	TRUE	1	0.49	2		873	413	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998588	100998588	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1258502528	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	39	633	1	ENST00000325455.5:c.1214T>C	p.Leu405Pro	p.L405P	ENST00000325455	NM_001202474.3	405	cTt/cCt	1/8	1	2	FACETS	0.463	0.384	0.55	0.463	0.384	0.55	SUBCLONAL	1	TRUE	1	0.49	2		634	344	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374366	118374366	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	148	624	0	ENST00000534358.1:c.7759C>T	p.Gln2587Ter	p.Q2587*	ENST00000534358	NM_005933.3	2587	Caa/Taa	27/36	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.49	2		624	519	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123829	46123829	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	59	537	1	ENST00000334344.6:c.95C>A	p.Ser32Ter	p.S32*	ENST00000334344	NM_152641.2	32	tCg/tAg	2/21	1	2	FACETS	0.507	0.437	0.583	0.507	0.437	0.583	SUBCLONAL	1	TRUE	1	0.49	2		538	475	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205334	46205334	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	20	348	0	ENST00000334344.6:c.418G>C	p.Asp140His	p.D140H	ENST00000334344	NM_152641.2	140	Gat/Cat	4/21	1	2	FACETS	0.224	0.17	0.286	0.224	0.17	0.286	SUBCLONAL	1	TRUE	1	0.49	2		348	365	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	97	484	1	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.49	2		485	386	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495462	56495462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	70	671	0	ENST00000267101.3:c.3652G>A	p.Glu1218Lys	p.E1218K	ENST00000267101	NM_001982.3	1218	Gag/Aag	28/28	1	2	FACETS	0.58	0.506	0.658	0.58	0.506	0.658	SUBCLONAL	1	TRUE	1	0.49	2		671	493	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110013	115110013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	107	610	0	ENST00000257566.3:c.1865C>T	p.Ser622Leu	p.S622L	ENST00000257566	NM_016569.3	622	tCg/tTg	8/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.49	2		610	381	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120796850	120796850	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	42	422	0	ENST00000257552.2:c.409G>T	p.Asp137Tyr	p.D137Y	ENST00000257552	NM_002442.3	137	Gac/Tac	7/15	1	2	FACETS	0.506	0.423	0.596	0.506	0.423	0.596	SUBCLONAL	1	TRUE	1	0.49	2		422	339	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623768	28623782	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTACCTCCTCGAGTG	TTACCTCCTCGAGTG	-	novel	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	89	538	0	ENST00000241453.7:c.872_882+4del		p.X291_splice	ENST00000241453	NM_004119.2	291		7/24	1	2	FACETS	0.953	0.851	1	0.953	0.851	1	CLONAL	1	TRUE	1	0.49	2		538	381	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033877	49033877	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	128	414	0	ENST00000267163.4:c.2014G>A	p.Glu672Lys	p.E672K	ENST00000267163	NM_000321.2	672	Gag/Aag	20/27	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.49	2		414	467	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73636303	73636346	+	frameshift_variant	Frame_Shift_Del	DEL	TCACCAGTATATTCAGCTCACACCAGACCGCAGCTCCAGAGGTG	TCACCAGTATATTCAGCTCACACCAGACCGCAGCTCCAGAGGTG	-	novel	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	53	684	0	ENST00000377687.4:c.566_609del	p.Phe189Ter	p.F189*	ENST00000377687	NM_001730.3	189	tTCACCAGTATATTCAGCTCACACCAGACCGCAGCTCCAGAGGTG/t	2/4	1	2	FACETS	0.344	0.293	0.4	0.344	0.293	0.4	SUBCLONAL	1	TRUE	1	0.49	2		684	629	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990351	81990351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	69	566	0	ENST00000359376.3:c.3622G>A	p.Glu1208Lys	p.E1208K	ENST00000359376	NM_002661.3	1208	Gaa/Aaa	32/33	1	2	FACETS	0.588	0.513	0.668	0.588	0.513	0.668	SUBCLONAL	1	TRUE	1	0.49	2		566	479	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619264	37619264	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	125	614	0	ENST00000447079.4:c.940G>A	p.Glu314Lys	p.E314K	ENST00000447079	NM_015083.1	314	Gaa/Aaa	1/14	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.49	2		614	454	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879903	37879903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	15	766	0	ENST00000269571.5:c.2198C>T	p.Thr733Ile	p.T733I	ENST00000269571		733	aCa/aTa	18/27	1	2	FACETS	0.11	0.08	0.147	0.11	0.08	0.147	SUBCLONAL	1	TRUE	1	0.49	2		766	557	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78519547	78519547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	40	515	0	ENST00000306801.3:c.118G>A	p.Glu40Lys	p.E40K	ENST00000306801	NM_020761.2	40	Gaa/Aaa	1/34	1	2	FACETS	0.353	0.293	0.419	0.353	0.293	0.419	SUBCLONAL	1	TRUE	1	0.49	2		515	463	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272301	18272301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	56	694	0	ENST00000222254.8:c.811G>A	p.Asp271Asn	p.D271N	ENST00000222254	NM_005027.3	271	Gac/Aac	6/16	1	2	FACETS	0.619	0.533	0.713	0.619	0.533	0.713	SUBCLONAL	1	TRUE	1	0.49	2		694	369	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726597	41726606	+	frameshift_variant	Frame_Shift_Del	DEL	CGGGGACTCA	CGGGGACTCA	-	novel	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	47	575	0	ENST00000301178.4:c.146_155del	p.Gly49AlafsTer46	p.G49Afs*46	ENST00000301178	NM_021913.4	48	CGGGGACTCAcg/cg	2/20	1	2	FACETS	0.464	0.392	0.544	0.464	0.392	0.544	SUBCLONAL	1	TRUE	1	0.49	2		575	413	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796286	42796289	+	frameshift_variant	Frame_Shift_Del	DEL	CCGC	CCGC	-	novel	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	119	659	0	ENST00000575354.2:c.2937_2940del	p.Pro980Ter	p.P980*	ENST00000575354	NM_015125.3	979	CCGCcc/cc	12/20	1	2	FACETS	0.981	0.89	1	0.981	0.89	1	CLONAL	1	TRUE	1	0.49	2		659	495	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871992	45871992	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	90	227	0	ENST00000391945.4:c.256G>C	p.Glu86Gln	p.E86Q	ENST00000391945	NM_000400.3	86	Gag/Cag	5/23	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.49	2		227	352	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422356	47422356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	95	569	0	ENST00000404338.3:c.424G>A	p.Glu142Lys	p.E142K	ENST00000404338	NM_004491.4	142	Gag/Aag	1/6	1	2	FACETS	0.753	0.673	0.838	0.753	0.673	0.838	SUBCLONAL	1	TRUE	1	0.49	2		569	515	SUCCESS
ALK	238	MSKCC	GRCh37	2	29541195	29541195	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	51	484	0	ENST00000389048.3:c.1622C>G	p.Ala541Gly	p.A541G	ENST00000389048	NM_004304.4	541	gCa/gGa	8/29	1	2	FACETS	0.485	0.413	0.564	0.485	0.413	0.564	SUBCLONAL	1	TRUE	1	0.49	2		484	429	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67626363	67626363	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775269026	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	37	345	0	ENST00000272342.5:c.286C>T	p.Pro96Ser	p.P96S	ENST00000272342	NM_019002.3	96	Cct/Tct	2/6	1	2	FACETS	0.327	0.269	0.391	0.327	0.269	0.391	SUBCLONAL	1	TRUE	1	0.49	2		345	462	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24135828	24135828	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	134	556	0	ENST00000263121.7:c.315G>C	p.Glu105Asp	p.E105D	ENST00000263121	NM_003073.3	105	gaG/gaC	3/9	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.49	2		556	542	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	55	190	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.454	0.388	0.525	0.454	0.388	0.525	SUBCLONAL	1	TRUE	1	0.49	2		190	495	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940739	49940739	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	67	767	0	ENST00000296474.3:c.304C>T	p.Gln102Ter	p.Q102*	ENST00000296474	NM_002447.2	102	Cag/Tag	1/20	1	2	FACETS	0.591	0.514	0.673	0.591	0.514	0.673	SUBCLONAL	1	TRUE	1	0.49	2		767	463	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440373	52440373	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	79	633	0	ENST00000460680.1:c.679C>A	p.Arg227Ser	p.R227S	ENST00000460680	NM_004656.3	227	Cgc/Agc	9/17	1	2	FACETS	0.651	0.574	0.734	0.651	0.574	0.734	SUBCLONAL	1	TRUE	1	0.49	2		633	495	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	17	789	0	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	0.175	0.13	0.229	0.175	0.13	0.229	SUBCLONAL	1	TRUE	1	0.49	2		789	396	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807889	1807889	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs78311289	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	95	949	0	ENST00000260795.2:c.1948A>G	p.Lys650Glu	p.K650E	ENST00000260795		650	Aag/Gag	13/17	1	2	FACETS	0.577	0.514	0.644	0.577	0.514	0.644	SUBCLONAL	1	TRUE	1	0.49	2		949	672	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540074	187540074	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs921535768	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	111	506	0	ENST00000441802.2:c.7666C>T	p.Arg2556Ter	p.R2556*	ENST00000441802	NM_005245.3	2556	Cga/Tga	10/27	1	2	FACETS	0.97	0.877	1	0.97	0.877	1	CLONAL	1	TRUE	1	0.49	2		506	467	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181845	56181845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	49	342	0	ENST00000399503.3:c.4069C>T	p.Leu1357Phe	p.L1357F	ENST00000399503	NM_005921.1	1357	Ctt/Ttt	17/20	1	2	FACETS	0.583	0.496	0.678	0.583	0.496	0.678	SUBCLONAL	1	TRUE	1	0.49	2		342	343	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637048	176637048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	51	581	0	ENST00000439151.2:c.1648G>A	p.Glu550Lys	p.E550K	ENST00000439151	NM_022455.4	550	Gaa/Aaa	5/23	1	2	FACETS	0.465	0.395	0.54	0.465	0.395	0.54	SUBCLONAL	1	TRUE	1	0.49	2		581	448	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197187	26197187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	121	876	0	ENST00000356476.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000356476		98	Gag/Aag	1/1	1	2	FACETS	0.634	0.573	0.699	0.634	0.573	0.699	SUBCLONAL	1	TRUE	1	0.49	2		876	779	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652129	36652129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34916193	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	85	678	0	ENST00000244741.5:c.251G>A	p.Arg84Gln	p.R84Q	ENST00000244741	NM_000389.4	84	cGa/cAa	2/3	1	2	FACETS	0.705	0.625	0.79	0.705	0.625	0.79	SUBCLONAL	1	TRUE	1	0.49	2		678	492	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100467	157100473	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCC	GGCGGCC	-	novel	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	20	274	0	ENST00000346085.5:c.1405_1411del	p.Ala469ArgfsTer31	p.A469Rfs*31	ENST00000346085	NM_020732.3	468	caGGCGGCC/ca	1/20	1	2	FACETS	0.459	0.353	0.581	0.459	0.353	0.581	SUBCLONAL	1	TRUE	1	0.49	2		274	178	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874308	151874308	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	26	501	0	ENST00000262189.6:c.8230A>T	p.Asn2744Tyr	p.N2744Y	ENST00000262189	NM_170606.2	2744	Aac/Tac	38/59	1	2	FACETS	0.271	0.215	0.337	0.271	0.215	0.337	SUBCLONAL	1	TRUE	1	0.49	2		501	391	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922743	44922759	+	frameshift_variant	Frame_Shift_Del	DEL	CAAACTCAGTCTCTGGC	CAAACTCAGTCTCTGGC	-	novel	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	137	297	0	ENST00000377967.4:c.1606_1622del	p.Asn536AlafsTer11	p.N536Afs*11	ENST00000377967	NM_021140.2	535	aCAAACTCAGTCTCTGGC/a	16/29	1	1	FACETS	0.828	0.771	0.885	1	0.991	1	CLONAL	2	TRUE	0	0.49	1		297	255	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936039	44936039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059787-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	25	164	0	ENST00000377967.4:c.2800G>A	p.Asp934Asn	p.D934N	ENST00000377967	NM_021140.2	934	Gac/Aac	18/29	1	1	FACETS	0.342	0.271	0.424	0.342	0.271	0.424	SUBCLONAL	1	TRUE	0	0.49	1		164	225	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747342068	NA	P-0059788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	234	541	0	ENST00000269305.4:c.394A>G	p.Lys132Glu	p.K132E	ENST00000269305	NM_001126112.2	132	Aag/Gag	5/11	0.388468688500483	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.388468688500483	2		541	571	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589592	67589594	+	inframe_deletion	In_Frame_Del	DEL	ATA	ATA	-	novel	NA	P-0059788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	227	323	0	ENST00000274335.5:c.1356_1358del	p.Asn453del	p.N453del	ENST00000274335		452	tATAac/tac	10/15	0.388468688500483	3	FACETS	1	0.987	1	0.798	0.749	0.848	CLONAL	2	TRUE	0	0.388468688500483	3		323	583	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374356	81374356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	103	321	0	ENST00000222390.5:c.706G>A	p.Asp236Asn	p.D236N	ENST00000222390	NM_000601.4	236	Gat/Aat	6/18	0.382284036781577	5	FACETS	1	0.916	1	0.257	0.229	0.286	CLONAL	1	TRUE	1	0.388468688500483	5		321	817	SUCCESS
EED	8726	MSKCC	GRCh37	11	85967429	85967429	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	50	343	0	ENST00000263360.6:c.427G>C	p.Ala143Pro	p.A143P	ENST00000263360	NM_003797.3	143	Gct/Cct	5/12	1	2	FACETS	0.439	0.372	0.512	0.439	0.372	0.512	SUBCLONAL	1	TRUE	1	0.388468688500483	2		343	587	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244248	46244248	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	369	594	0	ENST00000334344.6:c.2342G>C	p.Gly781Ala	p.G781A	ENST00000334344	NM_152641.2	781	gGa/gCa	15/21	0.388468688500483	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.388468688500483	3		594	1052	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900579	3900579	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	467	593	0	ENST00000262367.5:c.517C>T	p.Pro173Ser	p.P173S	ENST00000262367	NM_004380.2	173	Cct/Tct	2/31	0.388468688500483	5	FACETS	1	0.991	1	0.844	0.809	0.88	CLONAL	3	TRUE	1	0.388468688500483	5		593	1127	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832251	72832251	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	625	549	0	ENST00000268489.5:c.4330C>G	p.Leu1444Val	p.L1444V	ENST00000268489	NM_006885.3	1444	Ctg/Gtg	9/10	0.388468688500483	6	FACETS	1	0.993	1	0.876	0.846	0.907	CLONAL	4	TRUE	1	0.388468688500483	6		549	1305	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873961	151873961	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059788-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	399	532	0	ENST00000262189.6:c.8577C>G	p.His2859Gln	p.H2859Q	ENST00000262189	NM_170606.2	2859	caC/caG	38/59	0.388468688500483	4	FACETS	0.934	0.891	0.978	0.934	0.891	0.978	CLONAL	3	TRUE	1	0.388468688500483	4		532	1018	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10273392	10273392	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059790-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	86	335	0	ENST00000340748.4:c.911C>G	p.Pro304Arg	p.P304R	ENST00000340748		304	cCt/cGt	12/40	1	2	FACETS	0.931	0.834	1	0.931	0.834	1	CLONAL	1	TRUE	1	0.657352402645791	2		335	281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0059793-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	470	522	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.359162523344552	5	FACETS	0.906	0.873	0.939	0.906	0.873	0.939	CLONAL	5	TRUE	0	0.403056041689465	5		522	826	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553591	106553591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376600972	NA	P-0059793-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	177	633	1	ENST00000369096.4:c.1556C>T	p.Ala519Val	p.A519V	ENST00000369096	NM_001198.3	519	gCg/gTg	5/7	0.403056041689465	3	FACETS	1	0.967	1	0.547	0.503	0.592	CLONAL	1	TRUE	1	0.403056041689465	3		634	965	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223093	5223093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269321557	NA	P-0059793-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	59	633	0	ENST00000357368.4:c.2710C>T	p.Arg904Trp	p.R904W	ENST00000357368	NM_002850.3	904	Cgg/Tgg	18/38	0.403056041689465	3	FACETS	0.524	0.45	0.605	0.262	0.225	0.303	SUBCLONAL	1	TRUE	1	0.403056041689465	3		633	671	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100919	27100919	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059793-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	251	548	0	ENST00000324856.7:c.4201C>T	p.Gln1401Ter	p.Q1401*	ENST00000324856	NM_006015.4	1401	Cag/Tag	18/20	0.403056041689465	2	FACETS	0.892	0.839	0.946	0.892	0.839	0.946	CLONAL	2	TRUE	0	0.403056041689465	2		548	698	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484207	8484207	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773612496	NA	P-0059793-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	76	408	0	ENST00000356435.5:c.3325C>T	p.Arg1109Cys	p.R1109C	ENST00000356435		1109	Cgt/Tgt	19/35	0.403056041689465	0	FACETS	0.654	0.578	0.735			1	SUBCLONAL	1	TRUE	0	0.403056041689465	0		408	344	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056505	26056505	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs549427826	NA	P-0059793-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	568	595	0	ENST00000343677.2:c.152C>G	p.Ser51Cys	p.S51C	ENST00000343677	NM_005319.3	51	tCt/tGt	1/1	0.403056041689465	5	FACETS	0.952	0.918	0.987	0.952	0.918	0.987	CLONAL	4	TRUE	1	0.403056041689465	5		595	1187	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0059794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	16	329	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.977	0.722	1	0.977	0.722	1	CLONAL	1	TRUE	1	0.13	2		329	252	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0059794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	17	195	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.828	0.617	1	0.828	0.617	1	CLONAL	1	TRUE	1	0.13	2		195	316	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0059794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	14	545	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.477	0.343	0.64	0.477	0.343	0.64	SUBCLONAL	1	TRUE	1	0.13	2		545	452	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203565	108203565	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766351395	NA	P-0059794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	22	397	0	ENST00000278616.4:c.7865C>T	p.Ala2622Val	p.A2622V	ENST00000278616	NM_000051.3	2622	gCa/gTa	53/63	1	2	FACETS	1	0.826	1	1	0.826	1	CLONAL	1	TRUE	1	0.13	2		397	314	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662274	67662275	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0059794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	38	544	0	ENST00000264010.4:c.1521dup	p.Arg508GlufsTer23	p.R508Efs*23	ENST00000264010	NM_006565.3	507	gag/gaGg	9/12	1	2	FACETS	1	0.829	1	1	0.829	1	CLONAL	1	TRUE	1	0.13	2		544	582	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591239	67591270	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTTTTTCAGGTGGTTGACTCAAAAAGGTGTTC	GTTTTTCAGGTGGTTGACTCAAAAAGGTGTTC	-	novel	NA	P-0059794-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	19	463	0	ENST00000274335.5:c.1746-8_1769del		p.X582_splice	ENST00000274335		582		13/15	1	2	FACETS	0.625	0.473	0.804	0.625	0.473	0.804	SUBCLONAL	1	TRUE	1	0.13	2		463	468	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	347	648	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.705820207894457	5	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	2	0.704223579422898	5		648	650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs530941076	NA	P-0059808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	487	581	0	ENST00000269305.4:c.658T>A	p.Tyr220Asn	p.Y220N	ENST00000269305	NM_001126112.2	220	Tat/Aat	6/11	0.685315012702625	3	FACETS	0.96	0.934	0.986	0.96	0.934	0.986	CLONAL	3	TRUE	0	0.704223579422898	3		581	649	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	193	489	0	ENST00000281708.4:c.1514G>C	p.Arg505Pro	p.R505P	ENST00000281708	NM_033632.3	505	cGc/cCc	10/12	0.361513928261427	4	FACETS	0.789	0.734	0.845	0.789	0.734	0.845	INDETERMINATE	2	TRUE	2	0.704223579422898	4		489	592	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551367	150551367	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	267	588	0	ENST00000369026.2:c.640C>G	p.Arg214Gly	p.R214G	ENST00000369026	NM_021960.4	214	Cga/Gga	1/3	0.705820207894457	3	FACETS	1	0.983	1	0.56	0.526	0.594	CLONAL	1	TRUE	1	0.704223579422898	3		588	916	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551815	150551815	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	176	529	0	ENST00000369026.2:c.192C>A	p.Ser64Arg	p.S64R	ENST00000369026	NM_021960.4	64	agC/agA	1/3	0.705820207894457	3	FACETS	0.992	0.917	1	0.496	0.458	0.535	CLONAL	1	TRUE	1	0.704223579422898	3		529	681	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821027	32821027	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	157	634	0	ENST00000354258.4:c.567G>C	p.Arg189Ser	p.R189S	ENST00000354258	NM_000593.5	189	agG/agC	1/11	0.704223579422898	5	FACETS	1	0.941	1	0.345	0.315	0.375	CLONAL	1	TRUE	2	0.704223579422898	5		634	887	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133710889	133710889	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	110	338	0	ENST00000318560.5:c.56C>G	p.Ser19Trp	p.S19W	ENST00000318560	NM_005157.4	19	tCg/tGg	1/11	0.705820207894457	4	FACETS	0.857	0.772	0.947	0.429	0.386	0.474	CLONAL	1	TRUE	2	0.704223579422898	4		338	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0059809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	225	599	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.583480039722933	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.583480039722933	1		599	470	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359593	40359593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	33	338	0	ENST00000293328.3:c.2060C>T	p.Pro687Leu	p.P687L	ENST00000293328	NM_012448.3	687	cCc/cTc	16/19	0.452870727771307	5	FACETS	0.37	0.301	0.449	0.123	0.1	0.15	SUBCLONAL	1	TRUE	2	0.583480039722933	5		338	573	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245407	153245407	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	205	382	1	ENST00000281708.4:c.1784T>A	p.Val595Asp	p.V595D	ENST00000281708	NM_033632.3	595	gTc/gAc	11/12	0.583480039722933	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.583480039722933	1		383	396	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679153	117679153	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	248	374	0	ENST00000368508.3:c.3668T>C	p.Val1223Ala	p.V1223A	ENST00000368508	NM_002944.2	1223	gTt/gCt	24/43	0.583480039722933	2	FACETS	0.975	0.926	1	0.975	0.926	1	CLONAL	2	TRUE	0	0.583480039722933	2		374	436	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975498	13975498	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059809-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	64	467	0	ENST00000405192.2:c.389T>A	p.Val130Glu	p.V130E	ENST00000405192	NM_001163147.1	130	gTg/gAg	7/12	1	2	FACETS	0.407	0.353	0.466	0.407	0.353	0.466	SUBCLONAL	1	TRUE	1	0.583480039722933	2		467	539	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0059810-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	40	429	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	0.914	0.758	1	0.914	0.758	1	CLONAL	1	TRUE	1	0.14	2		429	625	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0059811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	101	525	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.710095538036435	2		525	262	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0059811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	141	344	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.988	0.909	1	0.988	0.909	1	CLONAL	1	TRUE	1	0.710095538036435	2		344	402	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138321	2138321	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45517414	NA	P-0059811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	38	657	0	ENST00000219476.3:c.5254C>T	p.Gln1752Ter	p.Q1752*	ENST00000219476	NM_000548.3	1752	Cag/Tag	41/42	0.702186763723152	1	FACETS	0.203	0.168	0.242	0.203	0.168	0.242	SUBCLONAL	1	TRUE	0	0.710095538036435	1		657	340	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156623	2156623	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	149	635	0	ENST00000434045.2:c.299T>C	p.Val100Ala	p.V100A	ENST00000434045	NM_001127598.1	100	gTc/gCc	3/5	0.702186763723152	1	FACETS	0.93	0.867	0.993	0.93	0.867	0.993	CLONAL	1	TRUE	0	0.710095538036435	1		635	291	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117231	7117231	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	32	592	0	ENST00000302850.5:c.3985C>G	p.Leu1329Val	p.L1329V	ENST00000302850	NM_000208.2	1329	Ctg/Gtg	22/22	0.516434806611696	1	FACETS	0.114	0.092	0.139	0.114	0.092	0.139	SUBCLONAL	1	TRUE	0	0.710095538036435	1		592	509	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891374	101891375	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AACT	novel	NA	P-0059811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	50	367	0	ENST00000374994.4:c.337_340dup	p.Thr114AsnfsTer49	p.T114Nfs*49	ENST00000374994	NM_004612.2	112	cca/ccAACTa	2/9	0.710095538036435	1	FACETS	0.236	0.2	0.275	0.236	0.2	0.275	SUBCLONAL	1	TRUE	0	0.710095538036435	1		367	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0059812-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	306	399	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.379117205183314	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.379117205183314	2		399	717	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135046	11135046	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059812-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	157	446	2	ENST00000358026.2:c.3013C>T	p.Arg1005Ter	p.R1005*	ENST00000358026	NM_001128849.1	1005	Cga/Tga	21/36	0.266006640920608	2	FACETS	1	0.987	1	0.694	0.638	0.751	CLONAL	1	TRUE	0	0.379117205183314	2		448	597	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	311	967	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.985	0.93	1	1	0.996	1	CLONAL	3	TRUE	1	0.20923518567532	2		974	1006	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	68	228	0	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.20923518567532	2		228	447	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	65	156	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.977	0.86	1	1	0.985	1	CLONAL	3	TRUE	1	0.20923518567532	2		160	212	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	98	580	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.20923518567532	2		580	797	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254905	16254905	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs949668986	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	124	595	0	ENST00000375759.3:c.2170C>T	p.Arg724Ter	p.R724*	ENST00000375759	NM_015001.2	724	Cga/Tga	11/15	1	2	FACETS	0.763	0.69	0.839	1	0.985	1	SUBCLONAL	2	TRUE	1	0.20923518567532	2		595	777	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101099	27101099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	117	641	0	ENST00000324856.7:c.4381C>T	p.Arg1461Ter	p.R1461*	ENST00000324856	NM_006015.4	1461	Cga/Tga	18/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.20923518567532	2		641	843	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	135	573	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.20923518567532	2		574	961	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247893	59247893	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	126	695	0	ENST00000371222.2:c.850del	p.Val284Ter	p.V284*	ENST00000371222	NM_002228.3	284	Gtg/tg	1/1	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.20923518567532	2		695	1019	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466362	120466363	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	41	672	0	ENST00000256646.2:c.4756dup	p.Glu1586GlyfsTer10	p.E1586Gfs*10	ENST00000256646	NM_024408.3	1586	gaa/gGaa	26/34	1	2	FACETS	0.599	0.498	0.712	0.599	0.498	0.712	SUBCLONAL	1	TRUE	1	0.20923518567532	2		672	654	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466378	120466378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779822957	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	74	666	1	ENST00000256646.2:c.4741C>T	p.Arg1581Trp	p.R1581W	ENST00000256646	NM_024408.3	1581	Cgg/Tgg	26/34	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.20923518567532	2		667	706	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150921896	150921896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	79	543	0	ENST00000271640.5:c.1475C>T	p.Thr492Met	p.T492M	ENST00000271640	NM_001145415.1	492	aCg/aTg	12/22	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.20923518567532	2		543	699	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150931707	150931707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	86	549	1	ENST00000271640.5:c.2384G>A	p.Arg795Gln	p.R795Q	ENST00000271640	NM_001145415.1	795	cGg/cAg	15/22	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.20923518567532	2		550	612	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880486	155880486	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	108	497	0	ENST00000368323.3:c.67A>G	p.Lys23Glu	p.K23E	ENST00000368323	NM_006912.5	23	Aaa/Gaa	2/6	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.20923518567532	2		497	759	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746114	162746114	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771259035	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	73	516	0	ENST00000367921.3:c.2237G>A	p.Arg746Gln	p.R746Q	ENST00000367921	NM_006182.2	746	cGg/cAg	16/18	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.20923518567532	2		516	651	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736238	243736238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	39	348	0	ENST00000263826.5:c.809G>A	p.Arg270His	p.R270H	ENST00000263826	NM_005465.4	270	cGt/cAt	8/13	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.20923518567532	2		348	323	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88679173	88679174	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	26	183	0	ENST00000372037.3:c.1118dup	p.Asn373LysfsTer8	p.N373Kfs*8	ENST00000372037	NM_004329.2	371	-/A	10/13	1	2	FACETS	0.786	0.63	0.962	1	0.939	1	CLONAL	2	TRUE	1	0.20923518567532	2		183	158	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154380	2154380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1191719522	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	116	738	0	ENST00000434045.2:c.548G>A	p.Arg183His	p.R183H	ENST00000434045	NM_001127598.1	183	cGc/cAc	5/5	0.202105814671596	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.20923518567532	1		738	745	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003536	57003536	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	G	G	A	rs137997556	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	115	798	0	ENST00000257254.3:c.943C>T	p.Arg315Cys	p.R315C	ENST00000257254		315	Cgc/Tgc	1/2	0.202105814671596	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.20923518567532	1		798	834	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128998	64128998	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141880979	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	142	861	0	ENST00000334205.4:c.628C>T	p.Arg210Cys	p.R210C	ENST00000334205	NM_003942.2	210	Cgt/Tgt	6/17	0.202885398953844	3	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.20923518567532	3		861	1071	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132875	64132875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746182941	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	113	718	0	ENST00000334205.4:c.1009C>T	p.Arg337Trp	p.R337W	ENST00000334205	NM_003942.2	337	Cgg/Tgg	9/17	0.202885398953844	3	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.20923518567532	3		718	830	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625143	69625143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	77	617	0	ENST00000334134.2:c.650C>T	p.Pro217Leu	p.P217L	ENST00000334134	NM_005247.2	217	cCg/cTg	3/3	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.20923518567532	2		617	577	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236186	108236187	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	66	571	0	ENST00000278616.4:c.9126dup	p.Lys3043GlnfsTer20	p.K3043Qfs*20	ENST00000278616	NM_000051.3	3041	gac/gaCc	63/63	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.20923518567532	2		571	469	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118353167	118353167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	40	359	0	ENST00000534358.1:c.4043C>T	p.Ala1348Val	p.A1348V	ENST00000534358	NM_005933.3	1348	gCt/gTt	8/36	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.20923518567532	2		359	294	SUCCESS
CBL	867	MSKCC	GRCh37	11	119146717	119146717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	61	501	0	ENST00000264033.4:c.880C>T	p.Arg294Trp	p.R294W	ENST00000264033	NM_005188.3	294	Cgg/Tgg	6/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.20923518567532	2		501	438	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149355	119149356	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATG	rs397507494	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	51	544	0	ENST00000264033.4:c.1380_1382dup	p.Asp460dup	p.D460dup	ENST00000264033	NM_005188.3	460	tat/tATGat	9/16	1	2	FACETS	0.929	0.789	1	0.929	0.789	1	CLONAL	1	TRUE	1	0.20923518567532	2		544	525	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170256	119170256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374672276	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	94	623	0	ENST00000264033.4:c.2486G>A	p.Arg829Gln	p.R829Q	ENST00000264033	NM_005188.3	829	cGg/cAg	16/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.20923518567532	2		623	728	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383293	4383293	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	115	716	0	ENST00000261254.3:c.87C>A	p.Asn29Lys	p.N29K	ENST00000261254	NM_001759.3	29	aaC/aaA	1/5	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.20923518567532	2		716	895	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944983	31944983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1175067252	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	128	809	0	ENST00000340398.3:c.118C>T	p.Arg40Cys	p.R40C	ENST00000340398	NM_001013699.2	40	Cgc/Tgc	1/1	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.20923518567532	2		809	948	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432632	49432632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886202729	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	130	756	0	ENST00000301067.7:c.8507G>A	p.Arg2836His	p.R2836H	ENST00000301067	NM_003482.3	2836	cGc/cAc	34/54	0.173331154324017	3	FACETS	0.759	0.688	0.834	0.759	0.688	0.834	SUBCLONAL	2	TRUE	1	0.20923518567532	3		756	904	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438061	49438061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	111	713	0	ENST00000301067.7:c.5110C>T	p.Arg1704Trp	p.R1704W	ENST00000301067	NM_003482.3	1704	Cgg/Tgg	21/54	0.173331154324017	3	FACETS	1	0.979	1	0.683	0.613	0.757	CLONAL	1	TRUE	1	0.20923518567532	3		713	858	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481811	56481811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767905298	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	114	583	0	ENST00000267101.3:c.739C>T	p.Arg247Trp	p.R247W	ENST00000267101	NM_001982.3	247	Cgg/Tgg	7/28	0.173331154324017	3	FACETS	0.781	0.703	0.863	0.781	0.703	0.863	SUBCLONAL	2	TRUE	1	0.20923518567532	3		583	771	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426820	121426820	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520291	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	122	625	0	ENST00000257555.6:c.511C>T	p.Arg171Ter	p.R171*	ENST00000257555		171	Cga/Tga	2/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.20923518567532	2		625	807	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21565492	21565492	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753428765	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	101	697	0	ENST00000382592.4:c.394G>A	p.Ala132Thr	p.A132T	ENST00000382592	NM_014572.2	132	Gcc/Acc	3/8	0.153010358049907	0	FACETS	0.958	0.856	1			1	CLONAL	1	TRUE	0	0.20923518567532	0		697	797	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28979940	28979940	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	32	304	0	ENST00000282397.4:c.1528G>A	p.Ala510Thr	p.A510T	ENST00000282397	NM_002019.4	510	Gca/Aca	11/30	0.153010358049907	0	FACETS	1	0.896	1			1	CLONAL	1	TRUE	0	0.20923518567532	0		304	211	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972803	32972803	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507261	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	30	424	0	ENST00000380152.3:c.10153C>T	p.Arg3385Cys	p.R3385C	ENST00000380152		3385	Cgt/Tgt	27/27	1	2	FACETS	0.905	0.73	1	0.905	0.73	1	CLONAL	1	TRUE	1	0.20923518567532	2		424	317	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068881	30068881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1042493523	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	18	269	0	ENST00000331968.5:c.2048C>T	p.Thr683Met	p.T683M	ENST00000331968	NM_002742.2	683	aCg/aTg	14/18	1	2	FACETS	1	0.83	1	1	0.83	1	CLONAL	1	TRUE	1	0.20923518567532	2		269	153	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422176	81422176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758059665	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	81	637	0	ENST00000298171.2:c.152C>T	p.Pro51Leu	p.P51L	ENST00000298171	NM_000369.2	51	cCg/cTg	1/10	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.20923518567532	2		637	738	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557422	95557422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1426678586	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	42	374	0	ENST00000393063.1:c.5552G>A	p.Arg1851His	p.R1851H	ENST00000393063	NM_030621.3	1851	cGt/cAt	27/28	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.20923518567532	2		374	270	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035256	42035256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374543045	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	81	687	0	ENST00000219905.7:c.5098G>A	p.Val1700Met	p.V1700M	ENST00000219905	NM_001164273.1	1700	Gtg/Atg	15/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.20923518567532	2		687	574	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052603	42052603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	98	553	0	ENST00000219905.7:c.7274G>A	p.Arg2425His	p.R2425H	ENST00000219905	NM_001164273.1	2425	cGc/cAc	20/24	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.20923518567532	2		553	705	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052635	42052635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	100	555	0	ENST00000219905.7:c.7306C>T	p.Arg2436Cys	p.R2436C	ENST00000219905	NM_001164273.1	2436	Cgt/Tgt	20/24	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.20923518567532	2		555	734	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007825	45007825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	61	512	0	ENST00000558401.1:c.276del	p.Thr93LeufsTer10	p.T93Lfs*10	ENST00000558401	NM_004048.2	91	aCc/ac	2/4	1	2	FACETS	0.817	0.708	0.933	1	0.974	1	CLONAL	2	TRUE	1	0.20923518567532	2		512	357	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007855	45007856	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	61	508	0	ENST00000558401.1:c.305_306del	p.Val102GlufsTer12	p.V102Efs*12	ENST00000558401	NM_004048.2	101	cGT/c	2/4	1	2	FACETS	0.773	0.67	0.884	1	0.972	1	SUBCLONAL	2	TRUE	1	0.20923518567532	2		508	377	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628529	90628529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1220662107	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	104	628	0	ENST00000330062.3:c.1058G>A	p.Arg353His	p.R353H	ENST00000330062	NM_002168.2	353	cGc/cAc	8/11	0.20923518567532	2	FACETS	1	0.961	1	0.577	0.516	0.642	CLONAL	1	TRUE	0	0.20923518567532	2		628	861	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434581	99434581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1461059080	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	217	689	0	ENST00000268035.6:c.668C>T	p.Ala223Val	p.A223V	ENST00000268035	NM_000875.3	223	gCg/gTg	3/21	0.20923518567532	2	FACETS	0.835	0.778	0.894	1	0.987	1	CLONAL	3	TRUE	0	0.20923518567532	2		689	828	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396233	396234	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769619638	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	105	683	0	ENST00000262320.3:c.792dup	p.Gly265ArgfsTer20	p.G265Rfs*20	ENST00000262320	NM_003502.3	264	-/C	2/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.20923518567532	2		683	832	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639657	3639657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1394177026	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	136	897	0	ENST00000294008.3:c.3982G>A	p.Val1328Ile	p.V1328I	ENST00000294008	NM_032444.2	1328	Gtc/Atc	12/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.20923518567532	2		897	1025	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639789	3639789	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373107728	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	93	747	0	ENST00000294008.3:c.3850G>A	p.Val1284Met	p.V1284M	ENST00000294008	NM_032444.2	1284	Gtg/Atg	12/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.20923518567532	2		747	742	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779157	3779157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867327595	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	106	682	0	ENST00000262367.5:c.5891G>A	p.Arg1964His	p.R1964H	ENST00000262367	NM_004380.2	1964	cGt/cAt	31/31	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.20923518567532	2		682	693	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781218	3781218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	135	698	0	ENST00000262367.5:c.5147C>T	p.Thr1716Met	p.T1716M	ENST00000262367	NM_004380.2	1716	aCg/aTg	30/31	1	2	FACETS	0.756	0.687	0.828	1	0.986	1	SUBCLONAL	2	TRUE	1	0.20923518567532	2		698	854	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862737	9862737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201072838	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	64	610	0	ENST00000330684.3:c.2566C>T	p.Arg856Trp	p.R856W	ENST00000330684	NM_001134407.1	856	Cgg/Tgg	12/13	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.20923518567532	2		610	570	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14021901	14021901	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	22	206	0	ENST00000311895.7:c.601A>C	p.Asn201His	p.N201H	ENST00000311895	NM_005236.2	201	Aac/Cac	4/11	1	2	FACETS	0.891	0.701	1	1	0.939	1	CLONAL	2	TRUE	1	0.20923518567532	2		206	118	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847301	68847301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138135866	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	83	558	0	ENST00000261769.5:c.1223C>T	p.Ala408Val	p.A408V	ENST00000261769	NM_004360.3	408	gCg/gTg	9/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.20923518567532	2		558	569	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946287	81946287	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1271283443	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	108	599	0	ENST00000359376.3:c.2020C>T	p.Arg674Ter	p.R674*	ENST00000359376	NM_002661.3	674	Cga/Tga	19/33	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.20923518567532	2		599	734	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349484	89349484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs964523960	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	122	667	0	ENST00000301030.4:c.3466C>T	p.Arg1156Trp	p.R1156W	ENST00000301030	NM_001256183.1	1156	Cgg/Tgg	9/13	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.20923518567532	2		667	842	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667607	29667607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781428	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	51	431	1	ENST00000356175.3:c.6943G>A	p.Ala2315Thr	p.A2315T	ENST00000356175	NM_000267.3	2315	Gca/Aca	46/57	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.20923518567532	2		432	449	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679779	33679779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs546044791	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	68	647	0	ENST00000308377.4:c.2302G>A	p.Glu768Lys	p.E768K	ENST00000308377	NM_152270.3	768	Gaa/Aaa	5/5	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.20923518567532	2		647	607	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760967	59760967	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	25	198	0	ENST00000259008.2:c.3440del	p.Asn1147MetfsTer3	p.N1147Mfs*3	ENST00000259008	NM_032043.2	1147	aAt/at	20/20	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.20923518567532	2		198	169	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220604	1220604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555738372	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	131	695	0	ENST00000326873.7:c.622G>A	p.Asp208Asn	p.D208N	ENST00000326873	NM_000455.4	208	Gac/Aac	5/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.20923518567532	2		695	844	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2189740	2189740	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	105	629	0	ENST00000398665.3:c.210C>G	p.Ser70Arg	p.S70R	ENST00000398665	NM_032482.2	70	agC/agG	4/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.20923518567532	2		629	797	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101829	11101829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	94	659	0	ENST00000358026.2:c.1249C>T	p.Arg417Cys	p.R417C	ENST00000358026	NM_001128849.1	417	Cgc/Tgc	8/36	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.20923518567532	2		659	758	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271747	15271747	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs773656789	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	120	882	0	ENST00000263388.2:c.6692del	p.Pro2231GlnfsTer15	p.P2231Qfs*15	ENST00000263388	NM_000435.2	2231	cCa/ca	33/33	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.20923518567532	2		882	877	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299953	15299953	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1349902555	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	117	704	0	ENST00000263388.2:c.1225G>A	p.Val409Met	p.V409M	ENST00000263388	NM_000435.2	409	Gtg/Atg	8/33	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.20923518567532	2		704	860	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260114	19260114	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757104393	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	134	664	0	ENST00000162023.5:c.179C>T	p.Thr60Met	p.T60M	ENST00000162023		60	aCg/aTg	7/13	NA	2	FACETS	0.763	0.693	0.837			1	INDETERMINATE	2	TRUE	NA	0.20923518567532	2		664	839	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213358	36213359	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	97	669	0	ENST00000222270.7:c.2561_2562del	p.Glu854AlafsTer34	p.E854Afs*34	ENST00000222270	NM_014727.1	852	aAG/a	4/37	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.20923518567532	2		669	771	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213573	36213573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1236115722	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	111	678	0	ENST00000222270.7:c.2675G>A	p.Arg892His	p.R892H	ENST00000222270	NM_014727.1	892	cGc/cAc	5/37	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.20923518567532	2		678	783	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40771132	40771132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781407242	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	57	465	0	ENST00000392038.2:c.43C>T	p.Arg15Cys	p.R15C	ENST00000392038	NM_001626.4	15	Cgt/Tgt	2/14	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.20923518567532	2		465	492	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	154	429	1	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	0.787	0.72	0.858	1	0.989	1	SUBCLONAL	2	TRUE	1	0.20923518567532	2		430	935	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422932	47422932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	73	603	0	ENST00000404338.3:c.1000G>A	p.Glu334Lys	p.E334K	ENST00000404338	NM_004491.4	334	Gag/Aag	1/6	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.20923518567532	2		603	632	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47503775	47503775	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	123	823	0	ENST00000404338.3:c.4335del	p.Gly1446AlafsTer353	p.G1446Afs*353	ENST00000404338	NM_004491.4	1444	Ccc/cc	6/6	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.20923518567532	2		823	975	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905911	50905911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199545019	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	101	732	0	ENST00000440232.2:c.883G>A	p.Val295Met	p.V295M	ENST00000440232	NM_002691.3	295	Gtg/Atg	8/27	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.20923518567532	2		732	791	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46611698	46611698	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770192015	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	82	658	0	ENST00000263734.3:c.2512G>A	p.Glu838Lys	p.E838K	ENST00000263734	NM_001430.4	838	Gaa/Aaa	16/16	0.20923518567532	2	FACETS	1	0.901	1	0.512	0.451	0.578	CLONAL	1	TRUE	0	0.20923518567532	2		658	765	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67631688	67631688	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	17	175	0	ENST00000272342.5:c.1874A>T	p.Asp625Val	p.D625V	ENST00000272342	NM_019002.3	625	gAc/gTc	5/6	0.20923518567532	2	FACETS	1	0.903	1	0.745	0.564	0.955	CLONAL	1	TRUE	0	0.20923518567532	2		175	109	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096022	178096022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs184287392	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	91	591	0	ENST00000397062.3:c.1309C>T	p.Arg437Trp	p.R437W	ENST00000397062	NM_006164.4	437	Cgg/Tgg	5/5	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.20923518567532	2		591	629	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379426	225379426	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	18	177	0	ENST00000264414.4:c.442C>T	p.Arg148Ter	p.R148*	ENST00000264414	NM_003590.4	148	Cga/Tga	4/16	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.20923518567532	2		177	134	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022296	31022297	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	90	706	0	ENST00000375687.4:c.1786dup	p.Arg596ProfsTer23	p.R596Pfs*23	ENST00000375687	NM_015338.5	594	tgc/tgCc	13/13	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.20923518567532	2		706	768	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31372649	31372649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200902224	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	103	525	0	ENST00000328111.2:c.290G>A	p.Arg97His	p.R97H	ENST00000328111	NM_006892.3	97	cGt/cAt	4/23	1	2	FACETS	0.785	0.704	0.871	1	0.983	1	SUBCLONAL	2	TRUE	1	0.20923518567532	2		525	627	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728813	39728813	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	97	500	0	ENST00000361337.2:c.1093G>A	p.Gly365Ser	p.G365S	ENST00000361337	NM_003286.2	365	Ggc/Agc	12/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.20923518567532	2		500	646	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101119	41101119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755381090	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	90	645	0	ENST00000373198.4:c.1237G>A	p.Ala413Thr	p.A413T	ENST00000373198	NM_133170.3	413	Gcg/Acg	8/32	0.20923518567532	0	FACETS	0.979	0.869	1			1	CLONAL	1	TRUE	0	0.20923518567532	0		645	695	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279760	46279760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757419594	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	61	562	0	ENST00000371998.3:c.3686G>A	p.Arg1229His	p.R1229H	ENST00000371998		1229	cGc/cAc	20/23	1	2	FACETS	0.934	0.806	1	0.934	0.806	1	CLONAL	1	TRUE	1	0.20923518567532	2		562	624	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755554	39755554	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	95	788	1	ENST00000288319.7:c.1211del	p.Pro404ArgfsTer25	p.P404Rfs*25	ENST00000288319	NM_182918.3	404	cCg/cg	10/10	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.20923518567532	2		789	843	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30090756	30090756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145446060	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	60	457	0	ENST00000338641.4:c.1753G>A	p.Ala585Thr	p.A585T	ENST00000338641	NM_000268.3	585	Gcc/Acc	16/16	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.20923518567532	2		457	537	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127713	47127713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376246790	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	81	526	0	ENST00000409792.3:c.5369G>A	p.Arg1790Gln	p.R1790Q	ENST00000409792	NM_014159.6	1790	cGg/cAg	11/21	0.173331154324017	3	FACETS	1	0.969	1	0.658	0.58	0.742	CLONAL	1	TRUE	1	0.20923518567532	3		526	650	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723381	49723381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1440228604	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	112	617	0	ENST00000449682.2:c.1162G>A	p.Ala388Thr	p.A388T	ENST00000449682	NM_020998.3	388	Gca/Aca	10/18	0.173331154324017	3	FACETS	0.842	0.758	0.931	0.842	0.758	0.931	CLONAL	2	TRUE	1	0.20923518567532	3		617	702	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940127	49940127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs553617101	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	122	684	0	ENST00000296474.3:c.916C>T	p.Arg306Cys	p.R306C	ENST00000296474	NM_002447.2	306	Cgc/Tgc	1/20	0.173331154324017	3	FACETS	1	0.983	1	0.714	0.645	0.787	CLONAL	1	TRUE	1	0.20923518567532	3		684	902	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981237	63981237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs183231074	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	119	759	1	ENST00000398590.3:c.1739G>A	p.Arg580Gln	p.R580Q	ENST00000398590	NM_001177387.1	580	cGg/cAg	12/14	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.20923518567532	2		760	886	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	22	288	0	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.20923518567532	2		288	171	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806228	1806228	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868356240	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	101	724	0	ENST00000260795.2:c.1247G>A	p.Arg416His	p.R416H	ENST00000260795		416	cGc/cAc	8/17	0.20923518567532	0	FACETS	1	0.974	1			1	CLONAL	1	TRUE	0	0.20923518567532	0		724	595	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153609	55153609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501520	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	52	543	0	ENST00000257290.5:c.2575G>A	p.Val859Met	p.V859M	ENST00000257290	NM_006206.4	859	Gtg/Atg	19/23	0.202105814671596	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.20923518567532	1		543	410	SUCCESS
REST	5978	MSKCC	GRCh37	4	57777225	57777225	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	82	613	0	ENST00000309042.7:c.425del	p.Pro142LeufsTer94	p.P142Lfs*94	ENST00000309042	NM_005612.4	141	Ccc/cc	2/4	0.202105814671596	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.20923518567532	1		613	622	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294258	1294258	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	77	787	0	ENST00000310581.5:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000310581	NM_198253.2	248	cGg/cAg	2/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.20923518567532	2		787	591	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950099	38950099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757900166	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	46	689	0	ENST00000357387.3:c.3851C>T	p.Ser1284Leu	p.S1284L	ENST00000357387	NM_152756.3	1284	tCg/tTg	31/38	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.20923518567532	2		689	389	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751937	57751937	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs552180691	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	71	507	0	ENST00000274289.3:c.1300G>A	p.Ala434Thr	p.A434T	ENST00000274289	NM_006622.3	434	Gca/Aca	10/14	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.20923518567532	2		507	585	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505026	149505026	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	103	574	0	ENST00000261799.4:c.1789C>T	p.Arg597Trp	p.R597W	ENST00000261799	NM_002609.3	597	Cgg/Tgg	12/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.20923518567532	2		574	729	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637525	176637525	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1461402096	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	50	505	0	ENST00000439151.2:c.2125A>G	p.Thr709Ala	p.T709A	ENST00000439151	NM_022455.4	709	Aca/Gca	5/23	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.20923518567532	2		505	326	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553435	106553435	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs77256382	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	99	637	0	ENST00000369096.4:c.1400C>T	p.Pro467Leu	p.P467L	ENST00000369096	NM_001198.3	467	cCg/cTg	5/7	0.202105814671596	1	FACETS	0.988	0.881	1	0.988	0.881	1	CLONAL	1	TRUE	0	0.20923518567532	1		637	858	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199967	138199967	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1430533454	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	114	732	0	ENST00000237289.4:c.1385C>T	p.Pro462Leu	p.P462L	ENST00000237289	NM_001270507.1	462	cCg/cTg	7/9	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.20923518567532	2		732	871	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129060	152129060	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	83	646	0	ENST00000206249.3:c.13C>A	p.Leu5Ile	p.L5I	ENST00000206249	NM_000125.3	5	Ctc/Atc	1/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.20923518567532	2		646	576	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374361	81374361	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1476385169	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	27	352	0	ENST00000222390.5:c.701G>A	p.Arg234His	p.R234H	ENST00000222390	NM_000601.4	234	cGc/cAc	6/18	1	2	FACETS	1	0.831	1	1	0.831	1	CLONAL	1	TRUE	1	0.20923518567532	2		352	247	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415058	116415058	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1319458719	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	101	577	0	ENST00000397752.3:c.3152T>C	p.Val1051Ala	p.V1051A	ENST00000397752	NM_000245.2	1051	gTc/gCc	15/21	1	2	FACETS	0.874	0.784	0.97	1	0.985	1	CLONAL	2	TRUE	1	0.20923518567532	2		577	552	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845229	151845229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	105	652	0	ENST00000262189.6:c.13783C>T	p.Arg4595Cys	p.R4595C	ENST00000262189	NM_170606.2	4595	Cgc/Tgc	52/59	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.20923518567532	2		652	765	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863054	56863054	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1266824391	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	79	326	0	ENST00000519728.1:c.327del	p.Glu110LysfsTer15	p.E110Kfs*15	ENST00000519728	NM_002350.3	107	acA/ac	5/13	0.19878311756842	4	FACETS	0.972	0.863	1	1	0.977	1	CLONAL	3	TRUE	2	0.20923518567532	4		326	313	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74858992	74858992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	38	152	0	ENST00000284811.8:c.212C>T	p.Ser71Leu	p.S71L	ENST00000284811		71	tCg/tTg	4/4	0.19878311756842	4	FACETS	0.877	0.735	1	1	0.943	1	CLONAL	3	TRUE	2	0.20923518567532	4		152	167	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566003	141566003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	81	535	0	ENST00000220592.5:c.1261G>A	p.Gly421Arg	p.G421R	ENST00000220592	NM_012154.3	421	Ggg/Agg	10/19	0.19878311756842	4	FACETS	1	0.963	1	0.622	0.547	0.702	CLONAL	1	TRUE	2	0.20923518567532	4		535	753	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739866	145739866	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755425093	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	259	695	0	ENST00000428558.2:c.1664C>T	p.Ser555Leu	p.S555L	ENST00000428558	NM_004260.3	555	tCg/tTg	10/22	0.19878311756842	4	FACETS	0.97	0.909	1	1	0.992	1	CLONAL	3	TRUE	2	0.20923518567532	4		695	1029	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742465	145742465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750502685	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	109	613	0	ENST00000428558.2:c.323G>A	p.Arg108Gln	p.R108Q	ENST00000428558	NM_004260.3	108	cGg/cAg	4/22	0.19878311756842	4	FACETS	1	0.97	1	0.61	0.546	0.677	CLONAL	1	TRUE	2	0.20923518567532	4		613	1033	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2047456	2047456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760227940	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	62	510	0	ENST00000349721.2:c.1018G>A	p.Val340Met	p.V340M	ENST00000349721	NM_003070.3	340	Gtg/Atg	5/34	0.202105814671596	1	FACETS	0.887	0.766	1	0.887	0.766	1	CLONAL	1	TRUE	0	0.20923518567532	1		510	598	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22008918	22008918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	90	627	0	ENST00000276925.6:c.35del	p.Gly12AlafsTer15	p.G12Afs*15	ENST00000276925	NM_004936.3	12	gGc/gc	1/2	0.202105814671596	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.20923518567532	1		627	729	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	72	611	6	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	0.202105814671596	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	0	0.20923518567532	1		617	587	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128268597	128268597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	89	489	0	ENST00000265960.3:c.1058G>A	p.Arg353His	p.R353H	ENST00000265960	NM_001006617.1	353	cGc/cAc	8/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.20923518567532	2		489	624	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390765	139390765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763785541	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	139	827	1	ENST00000277541.6:c.7426G>A	p.Val2476Met	p.V2476M	ENST00000277541	NM_017617.3	2476	Gtg/Atg	34/34	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.20923518567532	2		828	953	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390944	139390945	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTG	rs762336270	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	114	962	0	ENST00000277541.6:c.7244_7246dup	p.Pro2415dup	p.P2415dup	ENST00000277541	NM_017617.3	2415	cag/cCACag	34/34	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.20923518567532	2		962	1029	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395174	139395174	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	113	825	0	ENST00000277541.6:c.5764A>G	p.Asn1922Asp	p.N1922D	ENST00000277541	NM_017617.3	1922	Aac/Gac	31/34	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.20923518567532	2		825	862	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396919	139396919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375897519	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	89	521	1	ENST00000277541.6:c.5189C>T	p.Pro1730Leu	p.P1730L	ENST00000277541	NM_017617.3	1730	cCg/cTg	28/34	1	2	FACETS	0.762	0.677	0.853	1	0.98	1	SUBCLONAL	2	TRUE	1	0.20923518567532	2		522	558	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399162	139399162	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs998433493	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	89	550	0	ENST00000277541.6:c.4981C>T	p.Arg1661Trp	p.R1661W	ENST00000277541	NM_017617.3	1661	Cgg/Tgg	26/34	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.20923518567532	2		550	653	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030576	47030576	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs782706875	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	100	648	1	ENST00000377604.3:c.351G>T	p.Glu117Asp	p.E117D	ENST00000377604	NM_001204468.1	117	gaG/gaT	4/24	1	2	FACETS	0.775	0.693	0.861	1	0.982	1	SUBCLONAL	2	TRUE	1	0.20923518567532	2		649	617	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426493	47426493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1046676785	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	164	811	0	ENST00000377045.4:c.836G>A	p.Arg279His	p.R279H	ENST00000377045	NM_001654.4	279	cGc/cAc	9/16	1	2	FACETS	0.879	0.807	0.954	1	0.991	1	CLONAL	2	TRUE	1	0.20923518567532	2		811	892	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341238	70341238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754407926	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	116	733	0	ENST00000374080.3:c.797G>A	p.Arg266His	p.R266H	ENST00000374080		266	cGc/cAc	6/45	0.153010358049907	0	FACETS	1	0.97	1			1	CLONAL	1	TRUE	0	0.20923518567532	0		733	733	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224793	123224793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	19	386	0	ENST00000218089.9:c.3557G>A	p.Arg1186Gln	p.R1186Q	ENST00000218089	NM_001042749.1	1186	cGa/cAa	32/35	0.153010358049907	0	FACETS	0.504	0.382	0.647			1	SUBCLONAL	1	TRUE	0	0.20923518567532	0		386	285	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	214	371	0	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.707367205376791	2		371	597	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0059814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	207	496	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.961	0.897	1	0.961	0.897	1	CLONAL	1	TRUE	1	0.707367205376791	2		496	609	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223523	36223523	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368364777	NA	P-0059814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	380	731	0	ENST00000222270.7:c.6073G>A	p.Glu2025Lys	p.E2025K	ENST00000222270	NM_014727.1	2025	Gag/Aag	28/37	1	2	FACETS	0.978	0.93	1	0.978	0.93	1	CLONAL	1	TRUE	1	0.707367205376791	2		731	1099	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346347	73346347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	164	348	0	ENST00000377767.4:c.1453G>A	p.Asp485Asn	p.D485N	ENST00000377767	NM_014953.3	485	Gat/Aat	10/21	0.707367205376791	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.707367205376791	1		348	267	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988270	36988270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	114	541	0	ENST00000354822.5:c.383C>T	p.Pro128Leu	p.P128L	ENST00000354822	NM_001079668.2	128	cCg/cTg	2/3	1	2	FACETS	0.462	0.416	0.51	0.462	0.416	0.51	SUBCLONAL	1	TRUE	1	0.707367205376791	2		541	698	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3795318	3795318	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	285	484	0	ENST00000262367.5:c.3874C>T	p.Gln1292Ter	p.Q1292*	ENST00000262367	NM_004380.2	1292	Cag/Tag	22/31	1	2	FACETS	0.995	0.939	1	0.995	0.939	1	CLONAL	1	TRUE	1	0.707367205376791	2		484	810	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101111	4101111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	150	338	0	ENST00000262948.5:c.611C>T	p.Ser204Phe	p.S204F	ENST00000262948	NM_030662.3	204	tCt/tTt	6/11	1	2	FACETS	0.862	0.793	0.933	0.862	0.793	0.933	CLONAL	1	TRUE	1	0.707367205376791	2		338	492	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794896	242794896	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	309	563	0	ENST00000334409.5:c.313G>C	p.Asp105His	p.D105H	ENST00000334409	NM_005018.2	105	Gac/Cac	2/5	NA	2	FACETS	1	0.961	1			1	INDETERMINATE	1	TRUE	NA	0.707367205376791	2		563	857	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62322231	62322231	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	252	463	0	ENST00000360203.5:c.2487G>C	p.Gln829His	p.Q829H	ENST00000360203	NM_001283009.1	829	caG/caC	27/35	0.337251262504897	3	FACETS	1	0.977	1	0.361	0.338	0.385	INDETERMINATE	1	TRUE	0	0.707367205376791	3		463	890	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286181	66286181	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	145	375	0	ENST00000273854.3:c.1505A>G	p.Tyr502Cys	p.Y502C	ENST00000273854	NM_004439.5	502	tAt/tGt	6/18	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.707367205376791	2		375	331	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590391	67590391	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	139	293	0	ENST00000274335.5:c.1453G>T	p.Glu485Ter	p.E485*	ENST00000274335		485	Gaa/Taa	11/15	1	2	FACETS	0.873	0.802	0.947	0.873	0.802	0.947	CLONAL	1	TRUE	1	0.707367205376791	2		293	450	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371969	55371969	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	282	637	0	ENST00000297316.4:c.659C>G	p.Pro220Arg	p.P220R	ENST00000297316	NM_022454.3	220	cCc/cGc	2/2	1	2	FACETS	0.953	0.898	1	0.953	0.898	1	CLONAL	1	TRUE	1	0.707367205376791	2		637	837	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566317	141566317	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	302	544	0	ENST00000220592.5:c.1095C>G	p.Ile365Met	p.I365M	ENST00000220592	NM_012154.3	365	atC/atG	9/19	1	2	FACETS	0.999	0.944	1	0.999	0.944	1	CLONAL	1	TRUE	1	0.707367205376791	2		544	855	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039340	49039340	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0059815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1	424	324	0	ENST00000267163.4:c.2326-1del		p.X776_splice	ENST00000267163	NM_000321.2	776			0.968464899558058	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.968464899558058	2		324	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782082	NA	P-0059815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4	535	444	0	ENST00000269305.4:c.745A>T	p.Arg249Trp	p.R249W	ENST00000269305	NM_001126112.2	249	Agg/Tgg	7/11	0.968464899558058	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.968464899558058	1		444	539	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481426	140481426	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	206	259	0	ENST00000288602.6:c.1382A>C	p.Gln461Pro	p.Q461P	ENST00000288602	NM_004333.4	461	cAa/cCa	11/18	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.968464899558058	2		259	386	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595269	141595269	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753287384	NA	P-0059815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	358	392	0	ENST00000220592.5:c.164A>G	p.Tyr55Cys	p.Y55C	ENST00000220592	NM_012154.3	55	tAt/tGt	2/19	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.968464899558058	2		392	709	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137313582	137313582	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	265	623	0	ENST00000481739.1:c.841G>T	p.Glu281Ter	p.E281*	ENST00000481739	NM_002957.4	281	Gag/Tag	6/10	0.478269754350823	1	FACETS	0.319	0.3	0.339	0.319	0.3	0.339	INDETERMINATE	1	TRUE	0	0.968464899558058	1		623	884	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395155	139395155	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	575	636	0	ENST00000277541.6:c.5783G>A	p.Gly1928Asp	p.G1928D	ENST00000277541	NM_017617.3	1928	gGc/gAc	31/34	0.478269754350823	1	FACETS	0.671	0.65	0.691	0.671	0.65	0.691	INDETERMINATE	1	TRUE	0	0.968464899558058	1		636	913	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0059870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	133	344	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.42989289238956	2		344	560	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243776981	243776981	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	158	374	0	ENST00000263826.5:c.688G>T	p.Gly230Trp	p.G230W	ENST00000263826	NM_005465.4	230	Ggg/Tgg	7/13	0.196532607321865	3	FACETS	0.851	0.784	0.919	0.851	0.784	0.919	INDETERMINATE	2	TRUE	1	0.42989289238956	3		374	525	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625399	69625399	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs372402801	NA	P-0059870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	107	730	0	ENST00000334134.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000334134	NM_005247.2	132	Cgg/Ggg	3/3	1	2	FACETS	0.523	0.469	0.582	0.523	0.469	0.582	SUBCLONAL	1	TRUE	1	0.42989289238956	2		730	951	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409162	4409162	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	99	599	0	ENST00000261254.3:c.857A>T	p.Asp286Val	p.D286V	ENST00000261254	NM_001759.3	286	gAt/gTt	5/5	1	2	FACETS	0.476	0.424	0.531	0.476	0.424	0.531	SUBCLONAL	1	TRUE	1	0.42989289238956	2		599	968	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446410	49446410	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	232	677	0	ENST00000301067.7:c.1195G>T	p.Gly399Trp	p.G399W	ENST00000301067	NM_003482.3	399	Ggg/Tgg	9/54	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.42989289238956	2		677	1063	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584413	39584413	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	190	535	0	ENST00000262039.4:c.1078G>T	p.Val360Leu	p.V360L	ENST00000262039	NM_002647.2	360	Gta/Tta	10/25	0.42989289238956	1	FACETS	0.948	0.879	1	0.948	0.879	1	CLONAL	1	TRUE	0	0.42989289238956	1		535	732	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985790	60985790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	65	618	0	ENST00000333681.4:c.110C>T	p.Ala37Val	p.A37V	ENST00000333681		37	gCc/gTc	2/3	0.42989289238956	1	FACETS	0.301	0.26	0.345	0.301	0.26	0.345	SUBCLONAL	1	TRUE	0	0.42989289238956	1		618	789	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276798	15276798	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	243	739	0	ENST00000263388.2:c.5467G>C	p.Asp1823His	p.D1823H	ENST00000263388	NM_000435.2	1823	Gac/Cac	30/33	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.42989289238956	2		739	1128	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39657718	39657718	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	160	459	0	ENST00000361337.2:c.11A>G	p.Asp4Gly	p.D4G	ENST00000361337	NM_003286.2	4	gAc/gGc	1/21	0.218256713889058	1	FACETS	0.856	0.787	0.927	0.856	0.787	0.927	INDETERMINATE	1	TRUE	0	0.42989289238956	1		459	683	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927080	131927080	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059870-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	120	466	0	ENST00000265335.6:c.1617G>C	p.Glu539Asp	p.E539D	ENST00000265335		539	gaG/gaC	10/25	1	2	FACETS	0.945	0.856	1	0.945	0.856	1	CLONAL	1	TRUE	1	0.42989289238956	2		466	591	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0059871-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	177	635	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.458544630112963	2		635	759	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085681	16085681	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762164859	NA	P-0059871-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	109	473	0	ENST00000281043.3:c.857G>A	p.Arg286His	p.R286H	ENST00000281043	NM_005378.4	286	cGt/cAt	3/3	0.252186920841549	1	FACETS	0.584	0.526	0.646	0.584	0.526	0.646	INDETERMINATE	1	TRUE	0	0.458544630112963	1		473	627	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374998	149374998	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059871-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	104	586	0	ENST00000360632.3:c.96C>A	p.Phe32Leu	p.F32L	ENST00000360632	NM_015472.4	32	ttC/ttA	2/7	0.242891387720614	1	FACETS	0.493	0.442	0.548	0.493	0.442	0.548	INDETERMINATE	1	TRUE	0	0.458544630112963	1		586	709	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0059872-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	25	664	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		664	1123	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	32	536	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.374	0.303	0.455	0.374	0.303	0.455	SUBCLONAL	1	TRUE	1	0.30588181000764	2		536	559	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	135	766	3	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	0.889	0.807	0.975	0.889	0.807	0.975	CLONAL	1	TRUE	1	0.30588181000764	2		769	993	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729153	66729153	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519856	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	139	695	0	ENST00000307102.5:c.361T>A	p.Cys121Ser	p.C121S	ENST00000307102	NM_002755.3	121	Tgc/Agc	3/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.30588181000764	2		695	827	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	279	967	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.974	0.917	1	1	0.995	1	CLONAL	2	TRUE	1	0.30588181000764	2		974	936	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	138	458	2	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.30588181000764	2		460	865	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578215	28578216	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	71	561	0	ENST00000241453.7:c.2955_2956del	p.Pro986AlafsTer27	p.P986Afs*27	ENST00000241453	NM_004119.2	985	tcTCcg/tccg	24/24	1	2	FACETS	0.681	0.594	0.775	0.681	0.594	0.775	SUBCLONAL	1	TRUE	1	0.30588181000764	2		561	682	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100728	8100728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs771019738	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	48	696	0	ENST00000346208.3:c.708del	p.Ser237AlafsTer28	p.S237Afs*28	ENST00000346208		234	ttC/tt	3/6	1	2	FACETS	0.436	0.367	0.512	0.436	0.367	0.512	SUBCLONAL	1	TRUE	1	0.30588181000764	2		696	720	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974758	21974759	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	69	676	0	ENST00000304494.5:c.68dup	p.Arg24SerfsTer20	p.R24Sfs*20	ENST00000304494	NM_000077.4	23	ggt/ggGt	1/3	1	2	FACETS	0.71	0.619	0.81	0.71	0.619	0.81	SUBCLONAL	1	TRUE	1	0.30588181000764	2		676	635	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	115	613	0	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.89	0.801	0.984	0.89	0.801	0.984	CLONAL	1	TRUE	1	0.30588181000764	2		613	845	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	61	723	0	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.535	0.46	0.616	0.535	0.46	0.616	SUBCLONAL	1	TRUE	1	0.30588181000764	2		723	746	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435153	110435153	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776792996	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	97	733	0	ENST00000375856.3:c.3248C>T	p.Pro1083Leu	p.P1083L	ENST00000375856	NM_003749.2	1083	cCg/cTg	1/2	1	2	FACETS	0.941	0.84	1	0.941	0.84	1	CLONAL	1	TRUE	1	0.30588181000764	2		733	674	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781157	135781157	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	107	744	0	ENST00000298552.3:c.1808del	p.Pro603ArgfsTer26	p.P603Rfs*26	ENST00000298552	NM_001162426.1	603	cCg/cg	15/23	1	2	FACETS	0.843	0.756	0.936	0.843	0.756	0.936	CLONAL	1	TRUE	1	0.30588181000764	2		744	830	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	53	623	2	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	0.454	0.386	0.528	0.454	0.386	0.528	SUBCLONAL	1	TRUE	1	0.30588181000764	2		625	764	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687471	37687472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs760014508	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	93	671	1	ENST00000447079.4:c.4382dup	p.Thr1463AsnfsTer50	p.T1463Nfs*50	ENST00000447079	NM_015083.1	1459	tgg/tGgg	14/14	1	2	FACETS	0.757	0.673	0.848	0.757	0.673	0.848	SUBCLONAL	1	TRUE	1	0.30588181000764	2		672	803	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	89	228	0	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.302929107072906	1	FACETS	0.984	0.875	1	0.984	0.875	1	CLONAL	1	TRUE	0	0.30588181000764	1		228	501	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508995	106508995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs62001906	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	109	626	1	ENST00000359195.3:c.989C>T	p.Thr330Met	p.T330M	ENST00000359195	NM_002649.2	330	aCg/aTg	2/11	1	2	FACETS	0.917	0.824	1	0.917	0.824	1	CLONAL	1	TRUE	1	0.30588181000764	2		627	777	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806180	1806181	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760502257	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	108	809	1	ENST00000260795.2:c.1206dup	p.Lys403GlnfsTer93	p.K403Qfs*93	ENST00000260795		400	agc/agCc	8/17	1	2	FACETS	0.861	0.772	0.955	0.861	0.772	0.955	CLONAL	1	TRUE	1	0.30588181000764	2		810	820	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348996	11348996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750257680	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	103	577	0	ENST00000332029.2:c.340G>A	p.Ala114Thr	p.A114T	ENST00000332029	NM_003745.1	114	Gcc/Acc	2/2	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.30588181000764	2		577	624	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217557	142217557	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1268253442	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	57	412	0	ENST00000350721.4:c.5440del	p.Arg1814GlufsTer10	p.R1814Efs*10	ENST00000350721	NM_001184.3	1814	Aga/ga	32/47	1	2	FACETS	0.877	0.754	1	0.877	0.754	1	CLONAL	1	TRUE	1	0.30588181000764	2		412	425	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439919	56439919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	127	615	2	ENST00000407977.2:c.673del	p.Arg225AlafsTer194	p.R225Afs*194	ENST00000407977		225	Cgc/gc	6/10	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.30588181000764	2		617	830	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350062	81350062	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs759145490	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	49	330	0	ENST00000222390.5:c.1270C>T	p.Arg424Cys	p.R424C	ENST00000222390	NM_000601.4	424	Cgt/Tgt	10/18	1	2	FACETS	0.974	0.829	1	0.974	0.829	1	CLONAL	1	TRUE	1	0.30588181000764	2		330	329	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749490	41749490	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	70	494	0	ENST00000226382.2:c.305G>A	p.Arg102His	p.R102H	ENST00000226382	NM_003924.3	102	cGc/cAc	2/3	1	2	FACETS	0.822	0.717	0.934	0.822	0.717	0.934	CLONAL	1	TRUE	1	0.30588181000764	2		494	557	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	119	156	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.30588181000764	2		160	527	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841231	15841236	+	inframe_deletion	In_Frame_Del	DEL	AGCCGG	AGCCGG	-	rs752736259	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	93	888	1	ENST00000307771.7:c.1338_1343del	p.Ser447_Arg448del	p.S447_R448del	ENST00000307771	NM_005089.3	439	AGCCGG/-	11/11	1	2	FACETS	0.666	0.591	0.746	0.666	0.591	0.746	SUBCLONAL	1	TRUE	1	0.30588181000764	2		889	913	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902658	1902658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761663126	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	60	499	0	ENST00000382891.5:c.277G>A	p.Ala93Thr	p.A93T	ENST00000382891	NM_133335.3	93	Gca/Aca	2/22	1	2	FACETS	0.452	0.388	0.522	0.452	0.388	0.522	SUBCLONAL	1	TRUE	1	0.30588181000764	2		499	868	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936277	78936277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1476697249	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	79	581	0	ENST00000306801.3:c.3709C>T	p.Arg1237Cys	p.R1237C	ENST00000306801	NM_020761.2	1237	Cgc/Tgc	32/34	1	2	FACETS	0.864	0.76	0.975	0.864	0.76	0.975	CLONAL	1	TRUE	1	0.30588181000764	2		581	598	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121531	108121531	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779815	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	94	534	0	ENST00000278616.4:c.1339C>T	p.Arg447Ter	p.R447*	ENST00000278616	NM_000051.3	447	Cga/Tga	10/63	1	2	FACETS	0.92	0.819	1	0.92	0.819	1	CLONAL	1	TRUE	1	0.30588181000764	2		534	668	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562756	21562756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs12867400	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	89	700	0	ENST00000382592.4:c.1163C>T	p.Ala388Val	p.A388V	ENST00000382592	NM_014572.2	388	gCg/gTg	4/8	1	2	FACETS	0.807	0.715	0.905	0.807	0.715	0.905	CLONAL	1	TRUE	1	0.30588181000764	2		700	721	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911107	29911107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45542135	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	111	485	0	ENST00000376809.5:c.406G>A	p.Gly136Arg	p.G136R	ENST00000376809	NM_002116.7	136	Ggg/Agg	3/8	1	2	FACETS	0.799	0.723	0.879	1	0.986	1	SUBCLONAL	2	TRUE	1	0.30588181000764	2		485	454	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361098	70361103	+	inframe_deletion	In_Frame_Del	DEL	CAGCAG	CAGCAG	-	rs766775649	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	55	714	2	ENST00000374080.3:c.6303_6308del	p.Gln2114_Gln2115del	p.Q2114_Q2115del	ENST00000374080		2096	CAGCAG/-	43/45	1	2	FACETS	0.397	0.338	0.461	0.397	0.338	0.461	SUBCLONAL	1	TRUE	1	0.30588181000764	2		716	906	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276974	123276974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918504	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	89	599	0	ENST00000358487.5:c.943G>A	p.Ala315Thr	p.A315T	ENST00000358487	NM_000141.4	315	Gcc/Acc	8/18	0.302929107072906	1	FACETS	0.754	0.669	0.844	0.754	0.669	0.844	SUBCLONAL	1	TRUE	0	0.30588181000764	1		599	654	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641768	23641768	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1060502759	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	67	340	0	ENST00000261584.4:c.1707del	p.Glu570ArgfsTer29	p.E570Rfs*29	ENST00000261584	NM_024675.3	569	aaA/aa	5/13	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.30588181000764	2		340	389	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265385	10265385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397509392	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	137	768	0	ENST00000340748.4:c.1661C>T	p.Ala554Val	p.A554V	ENST00000340748		554	gCg/gTg	20/40	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.30588181000764	2		768	891	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435455	56435455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs553934414	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	160	763	0	ENST00000407977.2:c.1682G>A	p.Arg561Gln	p.R561Q	ENST00000407977		561	cGg/cAg	9/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.30588181000764	2		763	833	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836295	151836295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	118	569	0	ENST00000262189.6:c.14510C>T	p.Ala4837Val	p.A4837V	ENST00000262189	NM_170606.2	4837	gCg/gTg	57/59	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.30588181000764	2		569	699	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340270	116340270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749738523	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	32	510	0	ENST00000397752.3:c.1132G>A	p.Val378Ile	p.V378I	ENST00000397752	NM_000245.2	378	Gtc/Atc	2/21	1	2	FACETS	0.336	0.272	0.409	0.336	0.272	0.409	SUBCLONAL	1	TRUE	1	0.30588181000764	2		510	622	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665110	182665110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1361986556	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	26	277	0	ENST00000292782.4:c.616C>T	p.Arg206Ter	p.R206*	ENST00000292782	NM_020640.2	206	Cga/Tga	6/7	1	2	FACETS	0.538	0.426	0.665	0.538	0.426	0.665	SUBCLONAL	1	TRUE	1	0.30588181000764	2		277	316	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50483697	50483697	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	56	342	0	ENST00000394963.4:c.802G>A	p.Asp268Asn	p.D268N	ENST00000394963	NM_003076.4	268	Gat/Aat	7/13	1	2	FACETS	0.734	0.629	0.848	0.734	0.629	0.848	SUBCLONAL	1	TRUE	1	0.30588181000764	2		342	499	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852590	63852590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	97	573	0	ENST00000279873.7:c.3368C>T	p.Ser1123Leu	p.S1123L	ENST00000279873	NM_032199.2	1123	tCg/tTg	10/10	1	2	FACETS	0.902	0.805	1	0.902	0.805	1	CLONAL	1	TRUE	1	0.30588181000764	2		573	703	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421834	49421834	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs117904191	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	120	821	0	ENST00000301067.7:c.14473C>T	p.Arg4825Trp	p.R4825W	ENST00000301067	NM_003482.3	4825	Cgg/Tgg	46/54	1	2	FACETS	0.794	0.716	0.877	0.794	0.716	0.877	SUBCLONAL	1	TRUE	1	0.30588181000764	2		821	988	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260325	10260325	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757300501	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	122	693	0	ENST00000340748.4:c.2342C>T	p.Ala781Val	p.A781V	ENST00000340748		781	gCg/gTg	25/40	1	2	FACETS	0.982	0.888	1	0.982	0.888	1	CLONAL	1	TRUE	1	0.30588181000764	2		693	812	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864646	68864646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	65	385	0	ENST00000288368.4:c.17G>A	p.Arg6His	p.R6H	ENST00000288368	NM_024870.2	6	cGc/cAc	1/40	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.30588181000764	2		385	376	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096344	2096344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1210160367	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	111	643	1	ENST00000219066.1:c.163G>A	p.Val55Met	p.V55M	ENST00000219066	NM_002528.5	55	Gtg/Atg	2/6	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.30588181000764	2		644	707	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186774	142186774	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	41	326	0	ENST00000350721.4:c.6687+2T>C		p.X2229_splice	ENST00000350721	NM_001184.3	2229			1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.30588181000764	2		326	216	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81971470	81971470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	110	659	0	ENST00000359376.3:c.3160G>A	p.Glu1054Lys	p.E1054K	ENST00000359376	NM_002661.3	1054	Gag/Aag	28/33	1	2	FACETS	0.96	0.863	1	0.96	0.863	1	CLONAL	1	TRUE	1	0.30588181000764	2		659	749	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	109	586	2	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	0.30588181000764	2	FACETS	1	0.928	1	0.52	0.467	0.576	CLONAL	1	TRUE	0	0.30588181000764	2		588	685	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201870	67201870	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	129	718	0	ENST00000312629.5:c.1070A>G	p.Gln357Arg	p.Q357R	ENST00000312629	NM_003952.2	357	cAg/cGg	13/15	1	2	FACETS	0.997	0.904	1	0.997	0.904	1	CLONAL	1	TRUE	1	0.30588181000764	2		718	846	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117785	108117787	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs753330963	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	39	325	0	ENST00000278616.4:c.999_1001del	p.Ser334del	p.S334del	ENST00000278616	NM_000051.3	332	taTTCt/tat	8/63	1	2	FACETS	0.879	0.732	1	0.879	0.732	1	CLONAL	1	TRUE	1	0.30588181000764	2		325	290	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945013	31945013	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs879142499	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	128	754	0	ENST00000340398.3:c.88A>G	p.Thr30Ala	p.T30A	ENST00000340398	NM_001013699.2	30	Acc/Gcc	1/1	1	2	FACETS	0.865	0.783	0.951	0.865	0.783	0.951	CLONAL	1	TRUE	1	0.30588181000764	2		754	968	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643276	38643276	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	37	466	0	ENST00000299084.4:c.746A>G	p.Asn249Ser	p.N249S	ENST00000299084	NM_152594.2	249	aAc/aGc	7/7	1	2	FACETS	0.463	0.381	0.555	0.463	0.381	0.555	SUBCLONAL	1	TRUE	1	0.30588181000764	2		466	522	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714123	43714124	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	120	754	0	ENST00000382044.4:c.4029_4030del	p.Gly1344GlufsTer25	p.G1344Efs*25	ENST00000382044	NM_001141980.1	1343	agAGgg/aggg	19/28	1	2	FACETS	0.906	0.818	0.999	0.906	0.818	0.999	CLONAL	1	TRUE	1	0.30588181000764	2		754	866	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56792499	56792499	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	115	544	0	ENST00000308159.5:c.229C>T	p.Arg77Ter	p.R77*	ENST00000308159	NM_014669.4	77	Cga/Tga	3/22	1	2	FACETS	0.965	0.87	1	0.965	0.87	1	CLONAL	1	TRUE	1	0.30588181000764	2		544	779	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346574	89346574	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763901180	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	86	804	0	ENST00000301030.4:c.6376G>A	p.Gly2126Ser	p.G2126S	ENST00000301030	NM_001256183.1	2126	Ggc/Agc	9/13	1	2	FACETS	0.785	0.695	0.883	0.785	0.695	0.883	SUBCLONAL	1	TRUE	1	0.30588181000764	2		804	716	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308441	30308441	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	73	555	0	ENST00000262643.3:c.455T>C	p.Leu152Ser	p.L152S	ENST00000262643	NM_001238.2	152	tTa/tCa	6/12	1	2	FACETS	0.722	0.631	0.82	0.722	0.631	0.82	SUBCLONAL	1	TRUE	1	0.30588181000764	2		555	661	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868371	45868371	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	124	660	0	ENST00000391945.4:c.406A>G	p.Ser136Gly	p.S136G	ENST00000391945	NM_000400.3	136	Agc/Ggc	6/23	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.30588181000764	2		660	765	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474001	29474001	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	93	607	0	ENST00000389048.3:c.2174T>A	p.Ile725Asn	p.I725N	ENST00000389048	NM_004304.4	725	aTc/aAc	12/29	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.30588181000764	2		607	592	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248726	212248727	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	87	526	0	ENST00000342788.4:c.3540dup	p.Gln1181SerfsTer5	p.Q1181Sfs*5	ENST00000342788	NM_005235.2	1180	-/T	28/28	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.30588181000764	2		526	560	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661399	227661399	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	65	694	0	ENST00000305123.5:c.2056A>C	p.Ser686Arg	p.S686R	ENST00000305123	NM_005544.2	686	Agc/Cgc	1/2	1	2	FACETS	0.558	0.483	0.64	0.558	0.483	0.64	SUBCLONAL	1	TRUE	1	0.30588181000764	2		694	761	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31451701	31451701	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	84	424	0	ENST00000344624.3:c.2621A>G	p.Gln874Arg	p.Q874R	ENST00000344624		874	cAa/cGa	18/33	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.30588181000764	2		424	494	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192437	138192437	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	34	566	0	ENST00000237289.4:c.73A>G	p.Thr25Ala	p.T25A	ENST00000237289	NM_001270507.1	25	Act/Gct	2/9	1	2	FACETS	0.347	0.282	0.42	0.347	0.282	0.42	SUBCLONAL	1	TRUE	1	0.30588181000764	2		566	641	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381573	81381573	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	47	386	0	ENST00000222390.5:c.488del	p.Leu163CysfsTer50	p.L163Cfs*50	ENST00000222390	NM_000601.4	163	tTg/tg	5/18	1	2	FACETS	0.601	0.507	0.705	0.601	0.507	0.705	SUBCLONAL	1	TRUE	1	0.30588181000764	2		386	511	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960164	151960164	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	26	251	0	ENST00000262189.6:c.1236del	p.Tyr413IlefsTer10	p.Y413Ifs*10	ENST00000262189	NM_170606.2	412	ggG/gg	9/59	1	2	FACETS	0.659	0.524	0.813	0.659	0.524	0.813	SUBCLONAL	1	TRUE	1	0.30588181000764	2		251	258	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869653	117869653	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1462000579	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	72	431	0	ENST00000297338.2:c.541G>A	p.Asp181Asn	p.D181N	ENST00000297338	NM_006265.2	181	Gac/Aac	6/14	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.30588181000764	2		431	393	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400156	139400156	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	105	816	0	ENST00000277541.6:c.4192T>G	p.Tyr1398Asp	p.Y1398D	ENST00000277541	NM_017617.3	1398	Tac/Gac	25/34	1	2	FACETS	0.915	0.82	1	0.915	0.82	1	CLONAL	1	TRUE	1	0.30588181000764	2		816	750	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858134	152858134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1393228949	NA	P-0059873-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	127	714	0	ENST00000406277.2:c.481C>T	p.Arg161Trp	p.R161W	ENST00000406277	NM_152274.4	161	Cgg/Tgg	6/7	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.30588181000764	2		714	750	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042169	6042169	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	35	473	0	ENST00000265849.7:c.452G>T	p.Arg151Leu	p.R151L	ENST00000265849	NM_000535.5	151	cGc/cTc	5/15	1	2	FACETS	0.53	0.435	0.636	0.53	0.435	0.636	SUBCLONAL	1	FALSE	1	0.382910880522025	2		473	345	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900244	101900246	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs863223829	NA	P-0059874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	51	385	0	ENST00000374994.4:c.683_685del	p.Glu228del	p.E228del	ENST00000374994	NM_004612.2	226	ggAGAa/gga	4/9	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	FALSE	1	0.382910880522025	2		385	231	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847399	68847399	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0059874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	47	420	0	ENST00000261769.5:c.1320+1G>A		p.X440_splice	ENST00000261769	NM_004360.3	440			0.158440525091293	3	FACETS	1	0.917	1	0.56	0.476	0.651	INDETERMINATE	1	FALSE	1	0.382910880522025	3		420	261	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772297	68772330	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCCGCGTCCTGGGCAGAGGTGAGGGCGCGCTGCC	GCCGCGTCCTGGGCAGAGGTGAGGGCGCGCTGCC	-	novel	NA	P-0059874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	55	466	0	ENST00000261769.5:c.147_163+17del		p.X49_splice	ENST00000261769	NM_004360.3	49		2/16	0.158440525091293	3	FACETS	1	0.892	1	0.522	0.449	0.601	INDETERMINATE	1	FALSE	1	0.382910880522025	3		466	328	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953360	17953360	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	28	491	0	ENST00000458235.1:c.626C>G	p.Thr209Arg	p.T209R	ENST00000458235	NM_000215.3	209	aCg/aGg	6/24	1	2	FACETS	0.483	0.386	0.592	0.483	0.386	0.592	SUBCLONAL	1	FALSE	1	0.382910880522025	2		491	303	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447405	12447405	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	88	433	0	ENST00000287820.6:c.644A>G	p.Gln215Arg	p.Q215R	ENST00000287820	NM_015869.4	215	cAg/cGg	5/7	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.382910880522025	2		433	370	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439144	52439145	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0059874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	57	487	0	ENST00000460680.1:c.1097dup	p.Tyr366Ter	p.Y366*	ENST00000460680	NM_004656.3	366	tat/taAt	11/17	0.374807853506688	1	FACETS	0.875	0.758	1	0.875	0.758	1	CLONAL	1	FALSE	0	0.382910880522025	1		487	275	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874446	151874446	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059874-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	28	417	0	ENST00000262189.6:c.8092G>T	p.Glu2698Ter	p.E2698*	ENST00000262189	NM_170606.2	2698	Gaa/Taa	38/59	1	2	FACETS	0.707	0.568	0.862	0.707	0.568	0.862	SUBCLONAL	1	FALSE	1	0.382910880522025	2		417	207	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721673	176721673	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059875-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	46	733	0	ENST00000439151.2:c.7304A>C	p.Lys2435Thr	p.K2435T	ENST00000439151	NM_022455.4	2435	aAa/aCa	23/23	1	2	FACETS	0.84	0.719	0.97	1	0.978	1	CLONAL	3	FALSE	1	0.208597472551123	2		733	175	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0059876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	126	525	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.45	2		525	532	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913355	NA	P-0059876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	124	369	0	ENST00000288602.6:c.1406G>A	p.Gly469Glu	p.G469E	ENST00000288602	NM_004333.4	469	gGa/gAa	11/18	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.45	2		369	522	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057691	27057691	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	176	659	0	ENST00000324856.7:c.1399C>T	p.Gln467Ter	p.Q467*	ENST00000324856	NM_006015.4	467	Cag/Tag	3/20	1	2	FACETS	0.855	0.788	0.925	0.855	0.788	0.925	CLONAL	1	TRUE	1	0.45	2		659	915	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856356	45856356	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	161	578	0	ENST00000391945.4:c.1816G>C	p.Glu606Gln	p.E606Q	ENST00000391945	NM_000400.3	606	Gag/Cag	19/23	1	2	FACETS	0.912	0.837	0.989	0.912	0.837	0.989	CLONAL	1	TRUE	1	0.45	2		578	785	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253826	153253826	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	97	381	0	ENST00000281708.4:c.907C>T	p.Gln303Ter	p.Q303*	ENST00000281708	NM_033632.3	303	Caa/Taa	6/12	1	2	FACETS	0.921	0.825	1	0.921	0.825	1	CLONAL	1	TRUE	1	0.45	2		381	468	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819954	170819968	+	inframe_deletion	In_Frame_Del	DEL	GATGATGATGAAGAG	GATGATGATGAAGAG	-	rs764077801	NA	P-0059876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	43	359	0	ENST00000296930.5:c.511_524+1del		p.DDDEEdel	ENST00000296930	NM_002520.6	166	GATGATGATGAAGAG/-	6/11	1	2	FACETS	0.433	0.363	0.512	0.433	0.363	0.512	SUBCLONAL	1	TRUE	1	0.45	2		359	441	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137522040	137522041	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0059876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	47	191	0	ENST00000367739.4:c.838dup	p.Ser280LysfsTer22	p.S280Kfs*22	ENST00000367739	NM_000416.2	280	agc/aAgc	6/7	1	2	FACETS	0.76	0.645	0.884	0.76	0.645	0.884	SUBCLONAL	1	TRUE	1	0.45	2		191	275	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982987	201982987	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	182	662	0	ENST00000359651.3:c.836T>C	p.Ile279Thr	p.I279T	ENST00000359651		279	aTc/aCc	7/8	1	2	FACETS	0.947	0.875	1	0.947	0.875	1	CLONAL	1	TRUE	1	0.45	2		662	854	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675551	86675551	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0059876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	70	266	0	ENST00000274376.6:c.2488-1G>T		p.X830_splice	ENST00000274376	NM_002890.2	830			1	2	FACETS	0.902	0.792	1	0.902	0.792	1	CLONAL	1	TRUE	1	0.45	2		266	345	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475277	40475277	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0059876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	140	526	0	ENST00000264657.5:c.1748+1G>T		p.X583_splice	ENST00000264657	NM_139276.2	583			1	2	FACETS	0.845	0.771	0.923	0.845	0.771	0.923	CLONAL	1	TRUE	1	0.45	2		526	736	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336251	73336251	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	110	387	0	ENST00000377767.4:c.2152G>A	p.Ala718Thr	p.A718T	ENST00000377767	NM_014953.3	718	Gcc/Acc	17/21	1	2	FACETS	0.982	0.886	1	0.982	0.886	1	CLONAL	1	TRUE	1	0.45	2		387	498	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129655	11129655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	165	317	0	ENST00000358026.2:c.2461G>A	p.Glu821Lys	p.E821K	ENST00000358026	NM_001128849.1	821	Gag/Aag	17/36	1	2	FACETS	0.906	0.833	0.983	0.906	0.833	0.983	CLONAL	1	TRUE	1	0.45	2		317	809	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78425907	78425907	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	164	660	0	ENST00000370768.2:c.1538C>A	p.Ala513Glu	p.A513E	ENST00000370768	NM_003902.3	513	gCa/gAa	16/20	1	2	FACETS	0.848	0.778	0.92	0.848	0.778	0.92	CLONAL	1	TRUE	1	0.45	2		660	860	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175942	176175942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs964768927	NA	P-0059876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	164	559	0	ENST00000367669.3:c.173C>T	p.Ser58Leu	p.S58L	ENST00000367669	NM_022457.5	58	tCg/tTg	1/20	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.45	2		559	712	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983017	201983017	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	206	672	0	ENST00000359651.3:c.866A>C	p.Asn289Thr	p.N289T	ENST00000359651		289	aAc/aCc	7/8	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.45	2		672	852	SUCCESS
KLF5	688	MSKCC	GRCh37	13	73649902	73649902	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	152	588	0	ENST00000377687.4:c.1252G>C	p.Asp418His	p.D418H	ENST00000377687	NM_001730.3	418	Gat/Cat	4/4	1	2	FACETS	0.919	0.842	0.999	0.919	0.842	0.999	CLONAL	1	TRUE	1	0.45	2		588	735	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618426	37618427	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0059876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	167	615	0	ENST00000447079.4:c.103_104del	p.Arg35SerfsTer11	p.R35Sfs*11	ENST00000447079	NM_015083.1	34	gaGCgt/gagt	1/14	1	2	FACETS	0.891	0.819	0.966	0.891	0.819	0.966	CLONAL	1	TRUE	1	0.45	2		615	833	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271363	18271363	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	214	506	0	ENST00000222254.8:c.405T>G	p.Ile135Met	p.I135M	ENST00000222254	NM_005027.3	135	atT/atG	3/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.45	2		506	837	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728790	190728790	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	103	400	0	ENST00000441310.2:c.2178G>C	p.Leu726Phe	p.L726F	ENST00000441310	NM_000534.4	726	ttG/ttC	10/13	1	2	FACETS	0.763	0.684	0.846	0.763	0.684	0.846	SUBCLONAL	1	TRUE	1	0.45	2		400	600	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799919	72799919	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	107	475	0	ENST00000325599.8:c.1250T>C	p.Leu417Ser	p.L417S	ENST00000325599	NM_018130.2	417	tTa/tCa	11/11	1	2	FACETS	0.795	0.715	0.88	0.795	0.715	0.88	SUBCLONAL	1	TRUE	1	0.45	2		475	598	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205819	128205819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	163	584	1	ENST00000341105.2:c.56C>T	p.Ala19Val	p.A19V	ENST00000341105	NM_032638.4	19	gCg/gTg	2/6	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.45	2		585	723	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998118	169998118	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	119	430	0	ENST00000295797.4:c.809T>G	p.Leu270Trp	p.L270W	ENST00000295797	NM_002740.5	270	tTg/tGg	9/18	1	2	FACETS	0.96	0.87	1	0.96	0.87	1	CLONAL	1	TRUE	1	0.45	2		430	551	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156316	106156316	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	218	699	0	ENST00000380013.4:c.1217T>G	p.Leu406Arg	p.L406R	ENST00000380013	NM_001127208.2	406	cTt/cGt	3/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.45	2		699	939	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539566	187539566	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	175	570	0	ENST00000441802.2:c.8174T>C	p.Ile2725Thr	p.I2725T	ENST00000441802	NM_005245.3	2725	aTc/aCc	10/27	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.45	2		570	717	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569787	67569788	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACAGAACAC	novel	NA	P-0059876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	108	459	0	ENST00000274335.5:c.450_458dup	p.Thr152_Gln153insHisArgThr	p.T152_Q153insHRT	ENST00000274335		150	tac/tACAGAACACac	3/15	1	2	FACETS	0.693	0.622	0.767	0.693	0.622	0.767	SUBCLONAL	1	TRUE	1	0.45	2		459	693	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652060	36652064	+	frameshift_variant	Frame_Shift_Del	DEL	GTGAC	GTGAC	-	novel	NA	P-0059876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	196	719	0	ENST00000244741.5:c.182_186del	p.Gly61ValfsTer26	p.G61Vfs*26	ENST00000244741	NM_000389.4	61	gGTGAC/g	2/3	1	2	FACETS	0.889	0.823	0.957	0.889	0.823	0.957	CLONAL	1	TRUE	1	0.45	2		719	980	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200476	138200476	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	162	507	0	ENST00000237289.4:c.1894A>G	p.Arg632Gly	p.R632G	ENST00000237289	NM_001270507.1	632	Aga/Gga	7/9	1	2	FACETS	0.921	0.846	0.999	0.921	0.846	0.999	CLONAL	1	TRUE	1	0.45	2		507	782	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403195	116403195	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	113	469	0	ENST00000397752.3:c.2456C>G	p.Ala819Gly	p.A819G	ENST00000397752	NM_000245.2	819	gCc/gGc	11/21	1	2	FACETS	0.813	0.733	0.897	0.813	0.733	0.897	CLONAL	1	TRUE	1	0.45	2		469	618	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399993	139399993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	192	651	0	ENST00000277541.6:c.4355C>T	p.Pro1452Leu	p.P1452L	ENST00000277541	NM_017617.3	1452	cCc/cTc	25/34	1	2	FACETS	0.91	0.842	0.98	0.91	0.842	0.98	CLONAL	1	TRUE	1	0.45	2		651	938	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945141	44945161	+	inframe_deletion	In_Frame_Del	DEL	TAACATAAATATTGGCCCAGG	TAACATAAATATTGGCCCAGG	-	novel	NA	P-0059876-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	95	216	0	ENST00000377967.4:c.3466_3486del	p.Asn1156_Gly1162del	p.N1156_G1162del	ENST00000377967	NM_021140.2	1155	gtTAACATAAATATTGGCCCAGGt/gtt	24/29	1	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.45	1		216	259	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	85	121	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.24	2		121	655	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608039	28608039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762198688	NA	P-0059879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	68	501	1	ENST00000241453.7:c.1927G>A	p.Val643Ile	p.V643I	ENST00000241453	NM_004119.2	643	Gtc/Atc	15/24	1	2	FACETS	0.648	0.563	0.741	0.648	0.563	0.741	SUBCLONAL	1	TRUE	1	0.24	2		502	874	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589559	67589591	+	inframe_deletion	In_Frame_Del	DEL	ATATTGAAGCTGTAGGGAAAAAATTACATGAAT	ATATTGAAGCTGTAGGGAAAAAATTACATGAAT	-	novel	NA	P-0059879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	14	154	0	ENST00000274335.5:c.1325_1357del	p.Ile442_Tyr452del	p.I442_Y452del	ENST00000274335		441	aATATTGAAGCTGTAGGGAAAAAATTACATGAATat/aat	10/15	1	2	FACETS	0.891	0.648	1	0.891	0.648	1	CLONAL	1	TRUE	1	0.24	2		154	131	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711891	89711891	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	71	396	0	ENST00000371953.3:c.509del	p.Ser170IlefsTer13	p.S170Ifs*13	ENST00000371953	NM_000314.4	170	aGt/at	6/9	0.203209254170855	3	FACETS	1	0.907	1	0.523	0.457	0.595	CLONAL	1	TRUE	1	0.24	3		396	633	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717691	89717701	+	frameshift_variant	Frame_Shift_Del	DEL	TGTACTTTGAG	TGTACTTTGAG	-	novel	NA	P-0059879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	137	440	0	ENST00000371953.3:c.717_727del	p.Met239IlefsTer10	p.M239Ifs*10	ENST00000371953	NM_000314.4	239	aTGTACTTTGAG/a	7/9	0.203209254170855	3	FACETS	0.827	0.753	0.905	0.827	0.753	0.905	CLONAL	2	TRUE	1	0.24	3		440	773	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0059880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	319	525	0				ENST00000310581	NM_198253.2	-/1132			0.834156695247263	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.834156695247263	3		525	514	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0059880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	242	345	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.834156695247263	3	FACETS	0.977	0.928	1	0.977	0.928	1	CLONAL	2	TRUE	1	0.834156695247263	3		345	421	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100175	27100176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0059880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	560	857	0	ENST00000324856.7:c.3977dup	p.Gln1327AlafsTer11	p.Q1327Afs*11	ENST00000324856	NM_006015.4	1324	tac/taCc	16/20	0.834156695247263	3	FACETS	0.903	0.872	0.935	0.903	0.872	0.935	CLONAL	2	TRUE	1	0.834156695247263	3		857	1053	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0059880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	522	788	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.834156695247263	3	FACETS	0.99	0.956	1	0.99	0.956	1	CLONAL	2	TRUE	1	0.834156695247263	3		788	896	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263850	133263850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	163	558	0	ENST00000320574.5:c.52G>A	p.Glu18Lys	p.E18K	ENST00000320574	NM_006231.2	18	Gag/Aag	1/49	0.700419170951519	4	FACETS	0.996	0.916	1	0.498	0.458	0.539	CLONAL	1	TRUE	2	0.834156695247263	4		558	720	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098816	178098816	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	282	568	0	ENST00000397062.3:c.229G>C	p.Asp77His	p.D77H	ENST00000397062	NM_006164.4	77	Gat/Cat	2/5	0.834156695247263	3	FACETS	1	0.984	1	0.559	0.527	0.592	CLONAL	1	TRUE	1	0.834156695247263	3		568	857	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770065	56770065	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs752608224	NA	P-0059880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	251	637	0	ENST00000337432.4:c.61C>G	p.Pro21Ala	p.P21A	ENST00000337432	NM_058216.2	21	Cca/Gca	1/9	0.834156695247263	3	FACETS	1	0.985	1	0.572	0.537	0.607	CLONAL	1	TRUE	1	0.834156695247263	3		637	746	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437325	220437325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	258	695	0	ENST00000243786.2:c.229G>A	p.Glu77Lys	p.E77K	ENST00000243786	NM_002191.3	77	Gag/Aag	1/2	0.834156695247263	3	FACETS	1	0.972	1	0.529	0.496	0.562	CLONAL	1	TRUE	1	0.834156695247263	3		695	829	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692918	89692918	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	151	511	0	ENST00000371953.3:c.402G>A	p.Met134Ile	p.M134I	ENST00000371953	NM_000314.4	134	atG/atA	5/9	0.834156695247263	3	FACETS	0.788	0.723	0.856	0.394	0.361	0.428	SUBCLONAL	1	TRUE	1	0.834156695247263	3		511	651	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732437	74732437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	269	813	0	ENST00000359995.5:c.472C>T	p.Arg158Trp	p.R158W	ENST00000359995	NM_001195427.1	158	Cgg/Tgg	2/3	0.834156695247263	3	FACETS	1	0.949	1	0.506	0.475	0.537	CLONAL	1	TRUE	1	0.834156695247263	3		813	904	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245954	16245954	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	216	605	0	ENST00000375759.3:c.1577C>T	p.Ser526Leu	p.S526L	ENST00000375759	NM_015001.2	526	tCg/tTg	8/15	0.33924434883027	5	FACETS	0.818	0.763	0.873	0.545	0.509	0.582	INDETERMINATE	2	TRUE	2	0.834156695247263	5		605	713	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599300	28599300	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	256	708	0	ENST00000253063.3:c.746C>G	p.Ser249Cys	p.S249C	ENST00000253063	NM_031459.4	249	tCt/tGt	5/10	0.834156695247263	3	FACETS	1	0.978	1	0.542	0.509	0.576	CLONAL	1	TRUE	1	0.834156695247263	3		708	802	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254732	16254732	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	196	611	0	ENST00000375759.3:c.1997G>T	p.Gly666Val	p.G666V	ENST00000375759	NM_015001.2	666	gGa/gTa	11/15	0.33924434883027	5	FACETS	1	0.991	1	0.495	0.46	0.532	INDETERMINATE	1	TRUE	2	0.834156695247263	5		611	712	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259243	16259243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	301	872	0	ENST00000375759.3:c.6508G>A	p.Glu2170Lys	p.E2170K	ENST00000375759	NM_015001.2	2170	Gag/Aag	11/15	0.33924434883027	5	FACETS	0.867	0.818	0.916	0.578	0.545	0.611	INDETERMINATE	2	TRUE	2	0.834156695247263	5		872	937	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439847	51439847	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1297989432	NA	P-0059880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	268	700	0	ENST00000262662.1:c.412G>A	p.Asp138Asn	p.D138N	ENST00000262662		138	Gac/Aac	4/4	0.834156695247263	3	FACETS	0.949	0.891	1	0.474	0.445	0.504	CLONAL	1	TRUE	1	0.834156695247263	3		700	960	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741855	162741855	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	244	756	0	ENST00000367921.3:c.1546G>C	p.Glu516Gln	p.E516Q	ENST00000367921	NM_006182.2	516	Gag/Cag	13/18	0.834156695247263	3	FACETS	0.954	0.893	1	0.477	0.446	0.508	CLONAL	1	TRUE	1	0.834156695247263	3		756	869	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518777	204518777	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	178	485	0	ENST00000367182.3:c.1440G>C	p.Glu480Asp	p.E480D	ENST00000367182	NM_001278516.1	480	gaG/gaC	11/11	0.834156695247263	3	FACETS	1	0.928	1	0.501	0.464	0.539	CLONAL	1	TRUE	1	0.834156695247263	3		485	604	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394639	394639	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	223	685	0	ENST00000399788.2:c.5056C>A	p.Leu1686Ile	p.L1686I	ENST00000399788	NM_001042603.1	1686	Ctt/Att	28/28	0.834156695247263	4	FACETS	0.995	0.926	1	0.497	0.463	0.533	CLONAL	1	TRUE	2	0.834156695247263	4		685	986	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893231	32893231	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	147	386	0	ENST00000380152.3:c.85C>A	p.Leu29Ile	p.L29I	ENST00000380152		29	Ctt/Att	3/27	1	2	FACETS	0.937	0.867	1	0.937	0.867	1	CLONAL	1	TRUE	1	0.834156695247263	2		386	376	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95599662	95599662	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	163	408	0	ENST00000393063.1:c.134G>C	p.Arg45Thr	p.R45T	ENST00000393063	NM_030621.3	45	aGa/aCa	3/28	0.834156695247263	3	FACETS	1	0.959	1	0.352	0.325	0.38	CLONAL	1	TRUE	0	0.834156695247263	3		408	524	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40678690	40678690	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	190	594	0	ENST00000249776.8:c.432G>T	p.Glu144Asp	p.E144D	ENST00000249776	NM_033286.3	144	gaG/gaT	3/9	1	2	FACETS	0.992	0.928	1	0.992	0.928	1	CLONAL	1	TRUE	1	0.834156695247263	2		594	459	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222352	2222352	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	223	781	0	ENST00000326181.6:c.636C>A	p.Phe212Leu	p.F212L	ENST00000326181	NM_032271.2	212	ttC/ttA	8/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.834156695247263	2		781	511	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785530	50785530	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	177	522	0	ENST00000398568.2:c.520C>G	p.Gln174Glu	p.Q174E	ENST00000398568	NM_001042412.1	174	Caa/Gaa	4/18	1	2	FACETS	0.89	0.827	0.953	0.89	0.827	0.953	CLONAL	1	TRUE	1	0.834156695247263	2		522	477	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351493	89351493	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0059880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	250	756	0	ENST00000301030.4:c.1457C>G	p.Ser486Ter	p.S486*	ENST00000301030	NM_001256183.1	486	tCa/tGa	9/13	1	2	FACETS	0.961	0.905	1	0.961	0.905	1	CLONAL	1	TRUE	1	0.834156695247263	2		756	624	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130100	143130100	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	150	429	0	ENST00000262992.4:c.916C>T	p.Gln306Ter	p.Q306*	ENST00000262992	NM_001101669.1	306	Caa/Taa	11/24	1	2	FACETS	0.937	0.866	1	0.937	0.866	1	CLONAL	1	TRUE	1	0.834156695247263	2		429	384	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144361421	144361421	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	259	709	0	ENST00000262995.4:c.1471C>T	p.Pro491Ser	p.P491S	ENST00000262995	NM_207123.2	491	Cct/Tct	6/11	1	2	FACETS	0.966	0.911	1	0.966	0.911	1	CLONAL	1	TRUE	1	0.834156695247263	2		709	643	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935637	13935637	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	232	633	0	ENST00000405192.2:c.1219C>T	p.Gln407Ter	p.Q407*	ENST00000405192	NM_001163147.1	407	Cag/Tag	12/12	0.834156695247263	4	FACETS	0.955	0.891	1	0.478	0.445	0.511	CLONAL	1	TRUE	2	0.834156695247263	4		633	1068	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851523	151851523	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs564716850	NA	P-0059880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	223	562	0	ENST00000262189.6:c.11968G>C	p.Asp3990His	p.D3990H	ENST00000262189	NM_170606.2	3990	Gat/Cat	47/59	0.834156695247263	4	FACETS	1	0.946	1	0.509	0.474	0.545	CLONAL	1	TRUE	2	0.834156695247263	4		562	963	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878044	151878044	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	314	750	0	ENST00000262189.6:c.6901C>T	p.Gln2301Ter	p.Q2301*	ENST00000262189	NM_170606.2	2301	Cag/Tag	36/59	0.834156695247263	4	FACETS	1	0.984	1	0.556	0.524	0.589	CLONAL	1	TRUE	2	0.834156695247263	4		750	1241	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	506	121	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.663276180469517	4	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.732516892655844	4		121	1076	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578217	7578217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	394	734	1	ENST00000269305.4:c.632C>T	p.Thr211Ile	p.T211I	ENST00000269305	NM_001126112.2	211	aCt/aTt	6/11	0.732516892655844	1	FACETS	0.991	0.952	1	0.991	0.952	1	CLONAL	1	TRUE	0	0.732516892655844	1		735	688	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739038	145739038	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1421	131	762	0	ENST00000428558.2:c.2117A>G	p.Tyr706Cys	p.Y706C	ENST00000428558	NM_004260.3	706	tAc/tGc	13/22	0.732516892655844	3	FACETS	0.315	0.284	0.347	0.157	0.142	0.174	SUBCLONAL	1	TRUE	1	0.732516892655844	3		762	1552	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354369	354369	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	34	559	0	ENST00000262320.3:c.1189G>T	p.Glu397Ter	p.E397*	ENST00000262320	NM_003502.3	397	Gag/Tag	5/11	0.732516892655844	1	FACETS	0.104	0.085	0.126	0.104	0.085	0.126	SUBCLONAL	1	TRUE	0	0.732516892655844	1		559	564	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726988	61727044	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GATAAAAGTTGGCCAATGTTTGGGCCATTCTTGTTTCAGTATCTAAAACAAGACATG	GATAAAAGTTGGCCAATGTTTGGGCCATTCTTGTTTCAGTATCTAAAACAAGACATG	CAT	novel	NA	P-0059881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	201	430	2	ENST00000401558.2:c.409-15_450delinsATG		p.X137_splice	ENST00000401558	NM_003400.3	137		7/25	1	2	FACETS	0.924	0.862	0.987	0.924	0.862	0.987	CLONAL	1	TRUE	1	0.732516892655844	2		432	594	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161671	47161671	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0059881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	154	288	0	ENST00000409792.3:c.4454+1G>T		p.X1485_splice	ENST00000409792	NM_014159.6	1485			0.732516892655844	1	FACETS	0.998	0.936	1	0.998	0.936	1	CLONAL	1	TRUE	0	0.732516892655844	1		288	267	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	49	477	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.612	0.519	0.715	0.612	0.519	0.715	SUBCLONAL	1	TRUE	1	0.32534885803557	2		477	492	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21348482	21348482	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	162	1013	0	ENST00000215739.8:c.1539C>G	p.Ile513Met	p.I513M	ENST00000215739	NM_006767.3	513	atC/atG	14/21	0.32534885803557	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.32534885803557	1		1013	832	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441469	52441469	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	147	974	0	ENST00000460680.1:c.383G>T	p.Gly128Val	p.G128V	ENST00000460680	NM_004656.3	128	gGa/gTa	6/17	1	2	FACETS	0.886	0.808	0.968	0.886	0.808	0.968	CLONAL	1	TRUE	1	0.32534885803557	2		974	1020	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443577	52443577	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	129	760	0	ENST00000460680.1:c.115del	p.Cys39ValfsTer33	p.C39Vfs*33	ENST00000460680	NM_004656.3	39	Tgt/gt	3/17	1	2	FACETS	0.924	0.838	1	0.924	0.838	1	CLONAL	1	TRUE	1	0.32534885803557	2		760	858	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0059884-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	574	688	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.347972336883132	5	FACETS	1	0.967	1	1	0.967	1	CLONAL	5	TRUE	0	0.347972336883132	5		688	1004	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179110	123179110	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059884-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	43	421	0	ENST00000218089.9:c.559C>A	p.Gln187Lys	p.Q187K	ENST00000218089	NM_001042749.1	187	Caa/Aaa	8/35	0.161620867296316	3	FACETS	0.756	0.634	0.89	0.252	0.211	0.297	INDETERMINATE	1	TRUE	0	0.347972336883132	3		421	384	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739328	46739346	+	frameshift_variant	Frame_Shift_Del	DEL	GTGACCCGAAGCCGTAGCA	GTGACCCGAAGCCGTAGCA	-	novel	NA	P-0059884-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	83	739	0	ENST00000371975.4:c.1524_1542del	p.Arg509LysfsTer2	p.R509Kfs*2	ENST00000371975	NM_003579.3	507	GTGACCCGAAGCCGTAGCAgt/gt	14/18	0.289407450180992	4	FACETS	0.874	0.771	0.984	0.437	0.385	0.492	CLONAL	1	TRUE	2	0.347972336883132	4		739	736	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608294	28608294	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059884-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	61	612	0	ENST00000241453.7:c.1762G>T	p.Glu588Ter	p.E588*	ENST00000241453	NM_004119.2	588	Gag/Tag	14/24	0.332500102712844	3	FACETS	0.771	0.665	0.885	0.257	0.221	0.295	SUBCLONAL	1	TRUE	0	0.347972336883132	3		612	534	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50815308	50815308	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772603046	NA	P-0059884-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	73	597	0	ENST00000398568.2:c.1661G>A	p.Arg554His	p.R554H	ENST00000398568	NM_001042412.1	554	cGc/cAc	9/18	0.327620392126	3	FACETS	0.776	0.678	0.881	0.388	0.339	0.441	SUBCLONAL	1	TRUE	1	0.347972336883132	3		597	635	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727901	41727901	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059884-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	72	628	0	ENST00000301178.4:c.526G>T	p.Asp176Tyr	p.D176Y	ENST00000301178	NM_021913.4	176	Gat/Tat	4/20	NA	2	FACETS	0.775	0.678	0.879			1	INDETERMINATE	1	TRUE	NA	0.347972336883132	2		628	534	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124511018	124511018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200145895	NA	P-0059884-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	23	294	0	ENST00000357628.3:c.202G>A	p.Ala68Thr	p.A68T	ENST00000357628	NM_015450.2	68	Gcc/Acc	7/19	0.347972336883132	3	FACETS	0.497	0.388	0.624	0.249	0.194	0.312	SUBCLONAL	1	TRUE	1	0.347972336883132	3		294	312	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0059885-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	87	398	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.977	0.866	1	0.977	0.866	1	CLONAL	1	FALSE	1	0.312515594067671	2		398	570	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427537	49427537	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059885-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	99	674	0	ENST00000301067.7:c.10951C>T	p.Gln3651Ter	p.Q3651*	ENST00000301067	NM_003482.3	3651	Caa/Taa	39/54	1	2	FACETS	0.849	0.758	0.946	0.849	0.758	0.946	CLONAL	1	FALSE	1	0.312515594067671	2		674	746	SUCCESS
APC	324	MSKCC	GRCh37	5	112178010	112178010	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059885-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	82	528	0	ENST00000257430.4:c.6719C>G	p.Ser2240Cys	p.S2240C	ENST00000257430	NM_000038.5	2240	tCc/tGc	16/16	1	2	FACETS	0.746	0.658	0.841	0.746	0.658	0.841	SUBCLONAL	1	FALSE	1	0.312515594067671	2		528	703	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123234428	123234428	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059885-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	34	134	0	ENST00000218089.9:c.3788T>G	p.Leu1263Arg	p.L1263R	ENST00000218089	NM_001042749.1	1263	cTt/cGt	35/35	1	1	FACETS	1	0.908	1	1	0.97	1	CLONAL	2	FALSE	0	0.312515594067671	1		134	83	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77933206	77933206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559388025	NA	P-0059886-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	84	551	0	ENST00000361507.4:c.1603G>A	p.Val535Ile	p.V535I	ENST00000361507	NM_080491.2	535	Gtc/Atc	7/10	0.438416484822026	4	FACETS	0.574	0.506	0.647	0.287	0.253	0.324	SUBCLONAL	1	TRUE	2	0.535716109910325	4		551	839	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033845	49033845	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750578651	NA	P-0059886-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	82	488	0	ENST00000267163.4:c.1982G>A	p.Arg661Gln	p.R661Q	ENST00000267163	NM_000321.2	661	cGg/cAg	20/27	0.535716109910325	4	FACETS	0.594	0.523	0.67	0.148	0.13	0.168	SUBCLONAL	1	TRUE	0	0.535716109910325	4		488	792	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0059886-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	387	731	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.440049651670032	2	FACETS	0.933	0.893	0.973	0.933	0.893	0.973	CLONAL	2	TRUE	0	0.535716109910325	2		731	774	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732562	190732562	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059886-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	93	367	0	ENST00000441310.2:c.2380A>G	p.Lys794Glu	p.K794E	ENST00000441310	NM_000534.4	794	Aaa/Gaa	11/13	0.438416484822026	4	FACETS	1	0.978	1	0.685	0.614	0.761	CLONAL	1	TRUE	2	0.535716109910325	4		367	389	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0059886-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	197	472	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	NA	2	FACETS	0.76	0.711	0.81			1	INDETERMINATE	2	TRUE	NA	0.535716109910325	2		472	484	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359893	87359893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059886-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	240	504	0	ENST00000277120.3:c.1201G>A	p.Gly401Arg	p.G401R	ENST00000277120		401	Gga/Aga	11/19	0.468665474930369	3	FACETS	0.892	0.838	0.946	0.892	0.838	0.946	CLONAL	2	TRUE	1	0.535716109910325	3		504	637	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610247	10610247	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	132	731	0	ENST00000171111.5:c.463G>T	p.Val155Phe	p.V155F	ENST00000171111	NM_203500.1	155	Gtc/Ttc	2/6	0.433271994708998	0	FACETS	0.598	0.545	0.653			1	SUBCLONAL	1	TRUE	0	0.4467295600402	0		731	547	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336625	81336625	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs527951814	NA	P-0059890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	67	349	0	ENST00000222390.5:c.1597C>T	p.Arg533Ter	p.R533*	ENST00000222390	NM_000601.4	533	Cga/Tga	14/18	0.316817624212916	3	FACETS	0.627	0.545	0.716	0.314	0.272	0.358	SUBCLONAL	1	TRUE	1	0.4467295600402	3		349	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1131691023	NA	P-0059890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	195	776	0	ENST00000269305.4:c.470T>A	p.Val157Asp	p.V157D	ENST00000269305	NM_001126112.2	157	gTc/gAc	5/11	0.4467295600402	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.4467295600402	1		776	625	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917805	29917805	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	50	663	0	ENST00000389048.3:c.863G>A	p.Trp288Ter	p.W288*	ENST00000389048	NM_004304.4	288	tGg/tAg	3/29	1	2	FACETS	0.368	0.311	0.43	0.368	0.311	0.43	SUBCLONAL	1	TRUE	1	0.4467295600402	2		663	609	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411993	63411993	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	191	869	0	ENST00000330258.3:c.1174G>T	p.Glu392Ter	p.E392*	ENST00000330258	NM_152424.3	392	Gag/Tag	2/2	0.4467295600402	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.4467295600402	1		869	609	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89842183	89842183	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	35	574	0	ENST00000389301.3:c.1867C>T	p.Gln623Ter	p.Q623*	ENST00000389301	NM_000135.2	623	Cag/Tag	21/43	1	2	FACETS	0.265	0.217	0.32	0.265	0.217	0.32	SUBCLONAL	1	TRUE	1	0.4467295600402	2		574	591	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748056	72748056	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs756289443	NA	P-0059890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	124	729	0	ENST00000357731.5:c.122C>G	p.Pro41Arg	p.P41R	ENST00000357731	NM_173808.2	41	cCc/cGc	1/7	1	2	FACETS	0.773	0.7	0.85	0.773	0.7	0.85	SUBCLONAL	1	TRUE	1	0.4467295600402	2		729	718	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165812	118165812	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	229	738	0	ENST00000369448.3:c.322G>T	p.Val108Phe	p.V108F	ENST00000369448	NM_017709.3	108	Gtt/Ttt	2/2	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.4467295600402	2		738	871	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012862	176012863	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0059890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	107	372	0	ENST00000367669.3:c.1513_1514del	p.Arg505ValfsTer8	p.R505Vfs*8	ENST00000367669	NM_022457.5	505	AGg/g	13/20	1	2	FACETS	0.889	0.8	0.982	0.889	0.8	0.982	CLONAL	1	TRUE	1	0.4467295600402	2		372	539	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828170	243828170	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	79	293	0	ENST00000263826.5:c.188A>T	p.Lys63Ile	p.K63I	ENST00000263826	NM_005465.4	63	aAa/aTa	3/13	1	2	FACETS	0.741	0.654	0.835	0.741	0.654	0.835	SUBCLONAL	1	TRUE	1	0.4467295600402	2		293	477	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597940	43597940	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs149403911	NA	P-0059890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	189	851	0	ENST00000355710.3:c.488G>T	p.Arg163Leu	p.R163L	ENST00000355710	NM_020975.4	163	cGg/cTg	3/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.4467295600402	2		851	708	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913180	32913180	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs864622546	NA	P-0059890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	122	618	0	ENST00000380152.3:c.4688G>T	p.Trp1563Leu	p.W1563L	ENST00000380152		1563	tGg/tTg	11/27	0.4467295600402	1	FACETS	0.724	0.656	0.795	0.724	0.656	0.795	SUBCLONAL	1	TRUE	0	0.4467295600402	1		618	586	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514693	103514693	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	86	757	0	ENST00000355739.4:c.1194C>A	p.Asp398Glu	p.D398E	ENST00000355739	NM_000123.3	398	gaC/gaA	8/15	0.4467295600402	1	FACETS	0.417	0.369	0.469	0.417	0.369	0.469	SUBCLONAL	1	TRUE	0	0.4467295600402	1		757	717	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51507938	51507938	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764710550	NA	P-0059890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	52	403	0	ENST00000260433.2:c.820G>A	p.Glu274Lys	p.E274K	ENST00000260433		274	Gaa/Aaa	7/10	1	2	FACETS	0.479	0.408	0.557	0.479	0.408	0.557	SUBCLONAL	1	TRUE	1	0.4467295600402	2		403	486	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56866294	56866294	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	29	509	0	ENST00000308159.5:c.1339G>T	p.Asp447Tyr	p.D447Y	ENST00000308159	NM_014669.4	447	Gac/Tac	12/22	1	2	FACETS	0.242	0.194	0.298	0.242	0.194	0.298	SUBCLONAL	1	TRUE	1	0.4467295600402	2		509	536	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663484	29663484	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	86	537	0	ENST00000356175.3:c.6077C>T	p.Ser2026Leu	p.S2026L	ENST00000356175	NM_000267.3	2026	tCa/tTa	40/57	1	2	FACETS	0.655	0.58	0.735	0.655	0.58	0.735	SUBCLONAL	1	TRUE	1	0.4467295600402	2		537	588	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428353	33428353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	116	587	0	ENST00000345365.6:c.770G>A	p.Ser257Asn	p.S257N	ENST00000345365	NM_002878.3	257	aGc/aAc	9/10	1	2	FACETS	0.897	0.811	0.987	0.897	0.811	0.987	CLONAL	1	TRUE	1	0.4467295600402	2		587	579	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117919	70117919	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	164	836	1	ENST00000245479.2:c.387C>A	p.His129Gln	p.H129Q	ENST00000245479	NM_000346.3	129	caC/caA	1/3	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.4467295600402	2		837	528	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39542598	39542598	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0059890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	175	570	0	ENST00000262039.4:c.401+1G>A		p.X134_splice	ENST00000262039	NM_002647.2	134			0.179939779789937	3	FACETS	1	0.988	1	0.695	0.642	0.749	INDETERMINATE	1	TRUE	1	0.4467295600402	3		570	690	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223212	36223212	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	365	1050	0	ENST00000222270.7:c.5762C>A	p.Pro1921His	p.P1921H	ENST00000222270	NM_014727.1	1921	cCc/cAc	28/37	0.365309004118299	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.4467295600402	2		1050	772	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543797	212543797	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	161	548	0	ENST00000342788.4:c.1602G>T	p.Glu534Asp	p.E534D	ENST00000342788	NM_005235.2	534	gaG/gaT	13/28	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.4467295600402	2		548	675	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280768	41280768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	188	688	2	ENST00000349496.5:c.2281G>A	p.Asp761Asn	p.D761N	ENST00000349496	NM_001904.3	761	Gac/Aac	15/15	0.4467295600402	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.4467295600402	1		690	561	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138431093	138431093	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	34	359	0	ENST00000289153.2:c.1356G>T	p.Leu452Phe	p.L452F	ENST00000289153	NM_006219.2	452	ttG/ttT	8/22	0.4467295600402	3	FACETS	0.276	0.224	0.334	0.138	0.112	0.167	SUBCLONAL	1	TRUE	1	0.4467295600402	3		359	675	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149452973	149452974	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0059890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	138	629	0	ENST00000286301.3:c.972_973delinsTT	p.Met324_Val325delinsIleLeu	p.M324_V325delinsIL	ENST00000286301	NM_005211.3	324	atGGtg/atTTtg	7/22	0.4467295600402	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.4467295600402	1		629	456	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985579	2985579	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	192	563	0	ENST00000396946.4:c.232G>T	p.Asp78Tyr	p.D78Y	ENST00000396946	NM_032415.4	78	Gac/Tac	4/25	0.394151224510517	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.4467295600402	1		563	604	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012286	152012286	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1365230259	NA	P-0059890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	93	518	0	ENST00000262189.6:c.527A>G	p.Asn176Ser	p.N176S	ENST00000262189	NM_170606.2	176	aAc/aGc	4/59	0.316817624212916	3	FACETS	0.755	0.671	0.843	0.377	0.335	0.422	SUBCLONAL	1	TRUE	1	0.4467295600402	3		518	675	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020415	69020415	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	65	568	0	ENST00000288368.4:c.2787C>A	p.His929Gln	p.H929Q	ENST00000288368	NM_024870.2	929	caC/caA	24/40	0.394151224510517	1	FACETS	0.382	0.331	0.437	0.382	0.331	0.437	SUBCLONAL	1	TRUE	0	0.4467295600402	1		568	592	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123026	5123026	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	104	533	0	ENST00000381652.3:c.3082G>T	p.Glu1028Ter	p.E1028*	ENST00000381652	NM_004972.3	1028	Gag/Tag	23/25	1	2	FACETS	0.74	0.664	0.821	0.74	0.664	0.821	SUBCLONAL	1	TRUE	1	0.4467295600402	2		533	629	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223899	53223899	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059890-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	139	753	0	ENST00000375401.3:c.3460G>T	p.Glu1154Ter	p.E1154*	ENST00000375401	NM_004187.3	1154	Gaa/Taa	23/26	0.4467295600402	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.4467295600402	1		753	477	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0059892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	2489	484	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.248086330952889	36	FACETS	1	0.994	1	0.98	0.968	0.992	CLONAL	32	TRUE	3	0.248086330952889	36		484	3237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0059892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	189	285	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	0.248086330952889	2	FACETS	0.996	0.923	1	0.996	0.923	1	CLONAL	2	TRUE	0	0.248086330952889	2		285	765	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424840	47424841	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1365296949	NA	P-0059892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	131	603	0	ENST00000404338.3:c.2914dup	p.Arg972ProfsTer40	p.R972Pfs*40	ENST00000404338	NM_004491.4	970	tcc/tCcc	1/6	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.248086330952889	2		603	1030	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100975	41100975	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	336	667	0	ENST00000373198.4:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000373198	NM_133170.3	461	Cga/Tga	8/32	0.248086330952889	2	FACETS	0.872	0.825	0.918	1	0.993	1	CLONAL	3	TRUE	0	0.248086330952889	2		667	1036	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613155	52613155	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	195	512	0	ENST00000394830.3:c.3373C>T	p.Gln1125Ter	p.Q1125*	ENST00000394830	NM_018313.4	1125	Cag/Tag	22/30	0.248086330952889	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.248086330952889	2		512	738	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484363	8484363	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	86	376	0	ENST00000356435.5:c.3169G>T	p.Gly1057Trp	p.G1057W	ENST00000356435		1057	Ggg/Tgg	19/35	1	2	FACETS	0.762	0.677	0.852	1	0.98	1	SUBCLONAL	2	TRUE	1	0.248086330952889	2		376	455	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499771	8499771	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs748340591	NA	P-0059892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	197	494	0	ENST00000356435.5:c.2198G>T	p.Arg733Leu	p.R733L	ENST00000356435		733	cGc/cTc	14/35	1	2	FACETS	0.869	0.805	0.935	1	0.992	1	CLONAL	2	TRUE	1	0.248086330952889	2		494	914	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045133	47045134	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0059892-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	98	627	0	ENST00000377604.3:c.2376dup	p.Arg793AlafsTer16	p.R793Afs*16	ENST00000377604	NM_001204468.1	792	cgg/cGgg	21/24	0.248086330952889	1	FACETS	0.784	0.698	0.875	0.784	0.698	0.875	SUBCLONAL	1	TRUE	0	0.248086330952889	1		627	883	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0059893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	267	306	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.483658635337233	2	FACETS	0.993	0.941	1	0.993	0.941	1	CLONAL	2	TRUE	0	0.483658635337233	2		307	556	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920422	114920422	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	107	461	0	ENST00000543371.1:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000543371	NM_001198531.1	455	Cga/Tga	13/14	0.483658635337233	3	FACETS	0.974	0.877	1	0.487	0.438	0.539	CLONAL	1	TRUE	1	0.483658635337233	3		461	564	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913558	32913559	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359479	NA	P-0059893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	58	336	0	ENST00000380152.3:c.5073dup	p.Trp1692MetfsTer3	p.W1692Mfs*3	ENST00000380152		1689	gca/gcAa	11/27	0.483658635337233	6	FACETS	0.792	0.68	0.914	0.158	0.136	0.183	CLONAL	1	TRUE	1	0.483658635337233	6		336	596	SUCCESS
APC	324	MSKCC	GRCh37	5	112170652	112170652	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	125	316	0	ENST00000257430.4:c.1748C>A	p.Ser583Ter	p.S583*	ENST00000257430	NM_000038.5	583	tCa/tAa	15/16	0.479406191926607	3	FACETS	0.936	0.858	1	0.936	0.858	1	CLONAL	2	TRUE	1	0.483658635337233	3		316	343	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607771	46607771	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375135104	NA	P-0059893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	151	605	0	ENST00000263734.3:c.1960G>A	p.Val654Ile	p.V654I	ENST00000263734	NM_001430.4	654	Gtc/Atc	12/16	0.479406191926607	3	FACETS	1	0.939	1	0.516	0.472	0.561	CLONAL	1	TRUE	1	0.483658635337233	3		605	752	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151927393	151927393	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs773059152	NA	P-0059893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	24	33	0	ENST00000262189.6:c.2783A>G	p.Asp928Gly	p.D928G	ENST00000262189	NM_170606.2	928	gAt/gGt	17/59	0.483658635337233	5	FACETS	0.931	0.776	1	1	0.926	1	CLONAL	4	TRUE	2	0.483658635337233	5		33	46	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0059894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	96	125	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.291872957942511	5	FACETS	1	0.974	1	0.825	0.745	0.908	CLONAL	2	FALSE	2	0.441397439371364	5		125	292	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0059894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	274	593	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.33813145945386	3	FACETS	1	0.991	1	0.821	0.778	0.866	CLONAL	2	FALSE	0	0.441397439371364	3		593	615	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743844	40743844	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	176	365	0	ENST00000373198.4:c.3151C>T	p.Gln1051Ter	p.Q1051*	ENST00000373198	NM_133170.3	1051	Cag/Tag	23/32	0.338065132405697	5	FACETS	1	0.977	1			1	CLONAL	2	FALSE	NA	0.441397439371364	5		365	583	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523279	9523279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763590647	NA	P-0059894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	120	535	0	ENST00000353224.5:c.1958G>A	p.Arg653Gln	p.R653Q	ENST00000353224	NM_177990.2	653	cGg/cAg	9/10	0.291872957942511	5	FACETS	1	0.978	1	0.431	0.389	0.475	CLONAL	1	FALSE	2	0.441397439371364	5		535	699	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828162	3828162	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	35	268	0	ENST00000262367.5:c.1963G>C	p.Ala655Pro	p.A655P	ENST00000262367	NM_004380.2	655	Gca/Cca	10/31	0.095004384093893	5	FACETS	0.753	0.618	0.904			1	INDETERMINATE	1	FALSE	NA	0.441397439371364	5		268	350	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449558	187449558	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	256	533	0	ENST00000232014.4:c.322A>C	p.Thr108Pro	p.T108P	ENST00000232014	NM_001130845.1	108	Acg/Ccg	4/10	0.291872957942511	5	FACETS	1	0.987	1	0.784	0.736	0.833	CLONAL	2	FALSE	2	0.441397439371364	5		533	820	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675706	30675706	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	41	498	0	ENST00000376406.3:c.2650G>C	p.Glu884Gln	p.E884Q	ENST00000376406	NM_014641.2	884	Gaa/Caa	8/15	0.317719786470934	3	FACETS	0.345	0.287	0.411	0.115	0.095	0.137	SUBCLONAL	1	FALSE	0	0.441397439371364	3		498	657	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478928	56478928	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	35	586	0	ENST00000267101.3:c.384C>G	p.Ser128Arg	p.S128R	ENST00000267101	NM_001982.3	128	agC/agG	3/28	1	2	FACETS	0.687	0.562	0.829	0.687	0.562	0.829	SUBCLONAL	1	FALSE	1	0.167501129182683	2		586	608	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448390	56448390	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	91	718	0	ENST00000407977.2:c.257A>T	p.His86Leu	p.H86L	ENST00000407977		86	cAc/cTc	3/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.167501129182683	2		718	794	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772548	56772548	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059895-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	68	376	0	ENST00000337432.4:c.402A>T	p.Leu134Phe	p.L134F	ENST00000337432	NM_058216.2	134	ttA/ttT	2/9	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.167501129182683	2		376	557	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	104	477	0				ENST00000310581	NM_198253.2	-/1132			0.402540268999161	4	FACETS	1	0.983	1	0.749	0.674	0.827	CLONAL	1	TRUE	2	0.452310567518011	4		477	446	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087961	27087961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	216	586	0	ENST00000324856.7:c.2248C>T	p.Arg750Ter	p.R750*	ENST00000324856	NM_006015.4	750	Cga/Tga	6/20	0.208129583447254	5	FACETS	1	0.987	1	0.817	0.764	0.872	INDETERMINATE	2	TRUE	2	0.452310567518011	5		586	654	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400077	41400077	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs765578477	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	195	476	0	ENST00000373198.4:c.682C>T	p.Gln228Ter	p.Q228*	ENST00000373198	NM_133170.3	228	Cag/Tag	5/32	0.268113387583101	4	FACETS	1	0.971	1			1	INDETERMINATE	2	TRUE	NA	0.452310567518011	4		476	581	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7174716	7174716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373995681	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	203	669	0	ENST00000302850.5:c.1001C>T	p.Pro334Leu	p.P334L	ENST00000302850	NM_000208.2	334	cCc/cTc	4/22	0.352796016820453	4	FACETS	0.932	0.868	0.999	0.932	0.868	0.999	CLONAL	2	TRUE	2	0.452310567518011	4		669	699	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955046	93955046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141581954	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	138	354	0	ENST00000369303.4:c.2852C>T	p.Ser951Phe	p.S951F	ENST00000369303	NM_004440.3	951	tCc/tTc	16/17	0.415630053619383	2	FACETS	0.969	0.896	1	0.969	0.896	1	CLONAL	2	TRUE	0	0.452310567518011	2		354	315	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052602	42052602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	274	602	0	ENST00000219905.7:c.7273C>T	p.Arg2425Cys	p.R2425C	ENST00000219905	NM_001164273.1	2425	Cgc/Tgc	20/24	0.296475515542886	5	FACETS	1	0.99	1	0.819	0.771	0.867	CLONAL	2	TRUE	2	0.452310567518011	5		602	828	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969953	81969953	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	223	642	0	ENST00000359376.3:c.3022C>T	p.Gln1008Ter	p.Q1008*	ENST00000359376	NM_002661.3	1008	Cag/Tag	27/33	0.415630053619383	2	FACETS	0.965	0.908	1	0.965	0.908	1	CLONAL	2	TRUE	0	0.452310567518011	2		642	511	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255076	16255076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1283954838	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	269	720	0	ENST00000375759.3:c.2341C>T	p.Arg781Cys	p.R781C	ENST00000375759	NM_015001.2	781	Cgt/Tgt	11/15	0.208129583447254	5	FACETS	1	0.989	1	0.817	0.769	0.865	INDETERMINATE	2	TRUE	2	0.452310567518011	5		720	815	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372152	55372152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	211	774	0	ENST00000297316.4:c.842C>T	p.Pro281Leu	p.P281L	ENST00000297316	NM_022454.3	281	cCc/cTc	2/2	0.352796016820453	4	FACETS	0.921	0.858	0.985	0.921	0.858	0.985	CLONAL	2	TRUE	2	0.452310567518011	4		774	736	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965718	93965718	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1327213322	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	182	547	0	ENST00000369303.4:c.2210G>A	p.Gly737Glu	p.G737E	ENST00000369303	NM_004440.3	737	gGa/gAa	13/17	0.415630053619383	2	FACETS	0.925	0.863	0.987	0.925	0.863	0.987	CLONAL	2	TRUE	0	0.452310567518011	2		547	435	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426978	49426978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	263	749	0	ENST00000301067.7:c.11510C>T	p.Ser3837Phe	p.S3837F	ENST00000301067	NM_003482.3	3837	tCc/tTc	39/54	0.452310567518011	6	FACETS	1	0.97	1			1	CLONAL	2	TRUE	NA	0.452310567518011	6		749	1048	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341701	8341701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766088715	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	154	549	0	ENST00000356435.5:c.4939G>A	p.Glu1647Lys	p.E1647K	ENST00000356435		1647	Gaa/Aaa	29/35	0.415630053619383	2	FACETS	0.769	0.71	0.829	0.769	0.71	0.829	SUBCLONAL	2	TRUE	0	0.452310567518011	2		549	443	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472664	88472664	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs56300182	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	188	589	0	ENST00000360948.2:c.1891G>A	p.Ala631Thr	p.A631T	ENST00000360948	NM_001012338.2	631	Gcc/Acc	16/19	0.208129583447254	5	FACETS	1	0.981	1	0.775	0.72	0.831	INDETERMINATE	2	TRUE	2	0.452310567518011	5		589	600	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026115	71026115	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs797045584	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	250	445	0	ENST00000318789.4:c.1507C>T	p.Arg503Ter	p.R503*	ENST00000318789	NM_032682.5	503	Cga/Tga	17/21	0.452911714531946	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.452310567518011	4		445	730	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445178	49445178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771291128	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	567	967	0	ENST00000301067.7:c.2288C>T	p.Pro763Leu	p.P763L	ENST00000301067	NM_003482.3	763	cCg/cTg	10/54	0.452310567518011	6	FACETS	0.976	0.94	1			1	CLONAL	4	TRUE	NA	0.452310567518011	6		967	1223	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129916	69129916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243836474	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	219	643	0	ENST00000288368.4:c.4670G>A	p.Arg1557His	p.R1557H	ENST00000288368	NM_024870.2	1557	cGt/cAt	38/40	0.352796016820453	4	FACETS	0.948	0.885	1	0.948	0.885	1	CLONAL	2	TRUE	2	0.452310567518011	4		643	742	SUCCESS
ATM	472	MSKCC	GRCh37	11	108100051	108100051	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	104	346	0	ENST00000278616.4:c.331+1G>T		p.X111_splice	ENST00000278616	NM_000051.3	111			0.289427465052081	2	FACETS	1	0.981	1	0.684	0.619	0.752	CLONAL	1	TRUE	0	0.452310567518011	2		346	336	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263974	16263974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745984704	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	284	820	0	ENST00000375759.3:c.10343C>T	p.Pro3448Leu	p.P3448L	ENST00000375759	NM_015001.2	3448	cCc/cTc	12/15	0.208129583447254	5	FACETS	1	0.99	1	0.818	0.771	0.866	INDETERMINATE	2	TRUE	2	0.452310567518011	5		820	859	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244598	46244598	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	261	679	0	ENST00000334344.6:c.2692C>T	p.Pro898Ser	p.P898S	ENST00000334344	NM_152641.2	898	Cca/Tca	15/21	0.452310567518011	6	FACETS	0.959	0.898	1			1	CLONAL	2	TRUE	NA	0.452310567518011	6		679	1146	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108754	2108754	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	178	589	0	ENST00000219476.3:c.855C>A	p.Tyr285Ter	p.Y285*	ENST00000219476	NM_000548.3	285	taC/taA	10/42	0.296475515542886	5	FACETS	0.91	0.841	0.981	0.607	0.56	0.654	CLONAL	2	TRUE	2	0.452310567518011	5		589	726	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553642	29553644	+	frameshift_variant	Frame_Shift_Del	DEL	CTC	CTC	TT	novel	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	175	645	0	ENST00000356175.3:c.2191_2193delinsTT	p.Leu731PhefsTer17	p.L731Ffs*17	ENST00000356175	NM_000267.3	731	CTC/TT	18/57	0.296475515542886	5	FACETS	0.884	0.816	0.954	0.589	0.544	0.636	CLONAL	2	TRUE	2	0.452310567518011	5		645	735	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654766	29654767	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	268	750	0	ENST00000356175.3:c.5455_5456delinsTT	p.Pro1819Phe	p.P1819F	ENST00000356175	NM_000267.3	1819	CCc/TTc	37/57	0.296475515542886	5	FACETS	1	0.983	1	0.746	0.701	0.792	CLONAL	2	TRUE	2	0.452310567518011	5		750	889	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575206	48575206	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs748395067	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	294	322	0	ENST00000342988.3:c.400G>C	p.Glu134Gln	p.E134Q	ENST00000342988	NM_005359.5	134	Gaa/Caa	3/12	0.451259383356385	4	FACETS	0.937	0.894	0.978	0.937	0.894	0.978	CLONAL	4	TRUE	0	0.452310567518011	4		322	504	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39283913	39283913	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	165	383	0	ENST00000402219.2:c.440A>T	p.Asn147Ile	p.N147I	ENST00000402219	NM_005633.3	147	aAt/aTt	4/23	0.452911714531946	4	FACETS	1	0.933	1	1	0.933	1	CLONAL	2	TRUE	2	0.452310567518011	4		383	525	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62293295	62293295	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs769533935	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	178	466	0	ENST00000360203.5:c.394C>T	p.Arg132Trp	p.R132W	ENST00000360203	NM_001283009.1	132	Cgg/Tgg	4/35	0.296475515542886	5	FACETS	1	0.973	1	0.735	0.681	0.791	CLONAL	2	TRUE	2	0.452310567518011	5		466	599	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322926	31322926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61759954	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	180	684	0	ENST00000412585.2:c.970G>A	p.Gly324Arg	p.G324R	ENST00000412585	NM_005514.6	324	Gga/Aga	5/8	0.452911714531946	3	FACETS	1	0.988	1	0.451	0.417	0.487	CLONAL	1	TRUE	0	0.452310567518011	3		684	721	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662428	117662428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201532881	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	209	577	0	ENST00000368508.3:c.4949C>T	p.Pro1650Leu	p.P1650L	ENST00000368508	NM_002944.2	1650	cCt/cTt	30/43	0.415630053619383	2	FACETS	0.917	0.86	0.975	0.917	0.86	0.975	CLONAL	2	TRUE	0	0.452310567518011	2		577	504	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686297	117686297	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	209	453	0	ENST00000368508.3:c.3044A>T	p.Asn1015Ile	p.N1015I	ENST00000368508	NM_002944.2	1015	aAt/aTt	20/43	0.415630053619383	2	FACETS	0.926	0.868	0.984	0.926	0.868	0.984	CLONAL	2	TRUE	0	0.452310567518011	2		453	499	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161990440	161990440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	178	560	0	ENST00000366898.1:c.880C>T	p.Pro294Ser	p.P294S	ENST00000366898	NM_004562.2	294	Ccc/Tcc	8/12	0.415630053619383	2	FACETS	0.903	0.841	0.965	0.903	0.841	0.965	CLONAL	2	TRUE	0	0.452310567518011	2		560	436	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891555	151891555	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	123	461	0	ENST00000262189.6:c.4477A>G	p.Ser1493Gly	p.S1493G	ENST00000262189	NM_170606.2	1493	Agt/Ggt	29/59	0.452310567518011	5	FACETS	1	0.974	1	0.407	0.368	0.448	CLONAL	1	TRUE	2	0.452310567518011	5		461	748	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964370	70964370	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	123	451	0	ENST00000276594.2:c.1658A>T	p.Lys553Ile	p.K553I	ENST00000276594	NM_024504.3	553	aAa/aTa	8/8	0.352796016820453	4	FACETS	1	0.985	1	0.729	0.662	0.799	CLONAL	1	TRUE	2	0.452310567518011	4		451	542	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74868172	74868172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1563677151	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	123	303	0	ENST00000284811.8:c.122C>T	p.Thr41Met	p.T41M	ENST00000284811		41	aCg/aTg	3/4	0.352796016820453	4	FACETS	1	0.933	1	1	0.933	1	CLONAL	2	TRUE	2	0.452310567518011	4		303	385	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389396	8389396	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	22	407	0	ENST00000356435.5:c.4222A>T	p.Ser1408Cys	p.S1408C	ENST00000356435		1408	Agt/Tgt	26/35	0.415630053619383	2	FACETS	0.271	0.21	0.342	0.135	0.105	0.171	SUBCLONAL	1	TRUE	0	0.452310567518011	2		407	359	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485953	8485953	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763256154	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	212	699	0	ENST00000356435.5:c.2864C>T	p.Thr955Ile	p.T955I	ENST00000356435		955	aCc/aTc	17/35	0.415630053619383	2	FACETS	0.941	0.883	1	0.941	0.883	1	CLONAL	2	TRUE	0	0.452310567518011	2		699	498	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231109	98231110	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	183	668	0	ENST00000331920.6:c.2173_2174delinsTT	p.Pro725Phe	p.P725F	ENST00000331920	NM_000264.3	725	CCc/TTc	14/24	0.415630053619383	2	FACETS	0.817	0.761	0.875	0.817	0.761	0.875	CLONAL	2	TRUE	0	0.452310567518011	2		668	495	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933708	39933708	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	245	380	0	ENST00000378444.4:c.891T>G	p.Asn297Lys	p.N297K	ENST00000378444	NM_001123385.1	297	aaT/aaG	4/15	0.393559001018648	2	FACETS	0.919	0.876	0.961			1	CLONAL	3	TRUE	NA	0.452310567518011	2		380	393	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650532	48650532	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	288	461	0	ENST00000376670.3:c.502T>C	p.Phe168Leu	p.F168L	ENST00000376670	NM_002049.3	168	Ttt/Ctt	3/6	0.393559001018648	2	FACETS	0.96	0.92	1			1	CLONAL	3	TRUE	NA	0.452310567518011	2		461	442	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860139	152860139	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0059896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	160	222	0	ENST00000406277.2:c.291-2A>T		p.X97_splice	ENST00000406277	NM_152274.4	97			0.286912399048653		FACETS		0.824	0.929				CLONAL	3	TRUE	NA	0.452310567518011	2		222	269	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578232	7578232	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059901-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	321	781	2	ENST00000269305.4:c.617del	p.Leu206TrpfsTer41	p.L206Wfs*41	ENST00000269305	NM_001126112.2	206	tTg/tg	6/11	0.748597896380188	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.748597896380188	1		783	508	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089754	27089754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059901-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	178	742	0	ENST00000324856.7:c.2710G>A	p.Ala904Thr	p.A904T	ENST00000324856	NM_006015.4	904	Gct/Act	8/20	0.402762993564684	1	FACETS	0.461	0.427	0.497	0.461	0.427	0.497	INDETERMINATE	1	TRUE	0	0.748597896380188	1		742	645	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs17849781	NA	P-0059902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	43	482	0	ENST00000269305.4:c.832C>G	p.Pro278Ala	p.P278A	ENST00000269305	NM_001126112.2	278	Cct/Gct	8/11	1	2	FACETS	0.818	0.683	0.969	0.818	0.683	0.969	CLONAL	1	TRUE	1	0.14	2		482	751	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534494	187534494	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs779324710	NA	P-0059902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	32	346	0	ENST00000441802.2:c.9232G>A	p.Glu3078Lys	p.E3078K	ENST00000441802	NM_005245.3	3078	Gaa/Aaa	13/27	1	2	FACETS	0.818	0.662	0.994	0.818	0.662	0.994	CLONAL	1	TRUE	1	0.14	2		346	559	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939352	76939352	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	45	321	0	ENST00000373344.5:c.1396A>G	p.Arg466Gly	p.R466G	ENST00000373344	NM_000489.3	466	Aga/Gga	9/35	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.14	2		321	609	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	27	477	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.833	0.671	1	0.833	0.671	1	CLONAL	1	TRUE	1	0.46	2		477	141	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0059903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	56	323	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.46	2		323	191	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0059903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	90	480	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.109285717759983	3	FACETS	1	0.966	1	0.602	0.537	0.67	INDETERMINATE	1	TRUE	1	0.46	3		480	400	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29439416	29439416	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	119	486	0	ENST00000544604.2:c.631C>T	p.Arg211Ter	p.R211*	ENST00000544604	NM_001206998.1	211	Cga/Tga	4/9	1	2	FACETS	0.993	0.901	1	0.993	0.901	1	CLONAL	1	TRUE	1	0.46	2		486	521	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038731	47038739	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGCCCCT	GCTGCCCCT	C	novel	NA	P-0059903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	94	587	0	ENST00000377604.3:c.738_746delinsC	p.Lys246AsnfsTer52	p.K246Nfs*52	ENST00000377604	NM_001204468.1	246	aaGCTGCCCCTc/aaCc	9/24	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.46	2		587	398	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	82	121	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.164162036236541	2	FACETS	1	0.968	1	0.614	0.549	0.681	INDETERMINATE	1	TRUE	0	0.526096784499184	2		121	254	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	224	434	0	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	0.526096784499184	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.526096784499184	1		434	554	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532653	63532654	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1301294410	NA	P-0059904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	169	482	0	ENST00000307078.5:c.1925dup	p.Ala643GlyfsTer64	p.A643Gfs*64	ENST00000307078	NM_004655.3	642	aag/aaAg	8/11	0.526096784499184	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.526096784499184	1		482	464	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951085	17951085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	194	340	0	ENST00000458235.1:c.1208G>A	p.Arg403His	p.R403H	ENST00000458235	NM_000215.3	403	cGc/cAc	9/24	0.151515986519557	4	FACETS	0.846	0.786	0.908	0.846	0.786	0.908	INDETERMINATE	2	TRUE	2	0.526096784499184	4		340	665	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793386	242793386	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs756100729	NA	P-0059904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	210	515	0	ENST00000334409.5:c.691C>T	p.Arg231Ter	p.R231*	ENST00000334409	NM_005018.2	231	Cga/Tga	5/5	NA	2	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.526096784499184	2		515	731	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998516	100998516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749208871	NA	P-0059904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	182	545	0	ENST00000325455.5:c.1286C>T	p.Ala429Val	p.A429V	ENST00000325455	NM_001202474.3	429	gCg/gTg	1/8	0.180702666229046	2	FACETS	1	0.976	1	0.559	0.518	0.601	INDETERMINATE	1	TRUE	0	0.526096784499184	2		545	619	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs80338963	NA	P-0059904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	180	422	0	ENST00000342988.3:c.1081C>G	p.Arg361Gly	p.R361G	ENST00000342988	NM_005359.5	361	Cgc/Ggc	9/12	0.526096784499184	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.526096784499184	1		422	405	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256529	16256529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749587229	NA	P-0059904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	37	532	0	ENST00000375759.3:c.3794G>A	p.Arg1265Gln	p.R1265Q	ENST00000375759	NM_015001.2	1265	cGa/cAa	11/15	1	2	FACETS	0.212	0.174	0.255	0.212	0.174	0.255	SUBCLONAL	1	TRUE	1	0.526096784499184	2		532	663	SUCCESS
EED	8726	MSKCC	GRCh37	11	85961344	85961344	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138343311	NA	P-0059904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	27	277	0	ENST00000263360.6:c.121G>A	p.Ala41Thr	p.A41T	ENST00000263360	NM_003797.3	41	Gct/Act	2/12	0.180702666229046	2	FACETS	0.287	0.228	0.354	0.143	0.114	0.177	INDETERMINATE	1	TRUE	0	0.526096784499184	2		277	358	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652803	212652803	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200302763	NA	P-0059904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	79	342	0	ENST00000342788.4:c.503G>A	p.Arg168Gln	p.R168Q	ENST00000342788	NM_005235.2	168	cGg/cAg	4/28	0.102798421947666	3	FACETS	1	0.974	1	0.677	0.603	0.756	INDETERMINATE	1	TRUE	1	0.526096784499184	3		342	280	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141580	202141580	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0059904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	46	376	0	ENST00000358485.4:c.868A>T	p.Lys290Ter	p.K290*	ENST00000358485	NM_001080125.1	290	Aaa/Taa	7/9	0.151515986519557	4	FACETS	0.428	0.36	0.504	0.214	0.18	0.252	INDETERMINATE	1	TRUE	2	0.526096784499184	4		376	623	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183797	10183797	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs5030807	NA	P-0059905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	97	357	0	ENST00000256474.2:c.266T>A	p.Leu89His	p.L89H	ENST00000256474	NM_000551.3	89	cTc/cAc	1/3	0.358460589663214	1	FACETS	0.792	0.708	0.881	0.792	0.708	0.881	SUBCLONAL	1	TRUE	0	0.358460589663214	1		357	561	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245912954	245912954	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	46	248	0	ENST00000388985.4:c.1198A>C	p.Met400Leu	p.M400L	ENST00000388985		400	Atg/Ctg	12/12	1	2	FACETS	0.882	0.747	1	0.882	0.747	1	CLONAL	1	TRUE	1	0.358460589663214	2		248	291	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95598899	95598899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	33	249	0	ENST00000393063.1:c.260G>A	p.Gly87Glu	p.G87E	ENST00000393063	NM_030621.3	87	gGa/gAa	4/28	0.294493234852939	1	FACETS	0.889	0.733	1	0.889	0.733	1	CLONAL	1	TRUE	0	0.358460589663214	1		249	170	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56872889	56872889	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	36	259	0	ENST00000308159.5:c.2044A>T	p.Asn682Tyr	p.N682Y	ENST00000308159	NM_014669.4	682	Aat/Tat	19/22	1	2	FACETS	0.81	0.67	0.965	0.81	0.67	0.965	CLONAL	1	TRUE	1	0.358460589663214	2		259	248	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443575	52443583	+	inframe_deletion	In_Frame_Del	DEL	ACATTTGCT	ACATTTGCT	-	novel	NA	P-0059905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	103	345	0	ENST00000460680.1:c.109_117del	p.Ser37_Cys39del	p.S37_C39del	ENST00000460680	NM_004656.3	37	AGCAAATGT/-	3/17	0.358460589663214	1	FACETS	0.734	0.657	0.814	0.734	0.657	0.814	SUBCLONAL	1	TRUE	0	0.358460589663214	1		345	643	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401619	401619	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	130	519	1	ENST00000380956.4:c.941G>A	p.Gly314Asp	p.G314D	ENST00000380956	NM_001195286.1	314	gGc/gAc	7/9	1	2	FACETS	0.776	0.703	0.853	0.776	0.703	0.853	SUBCLONAL	1	TRUE	1	0.358460589663214	2		520	935	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000076	30000077	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0059906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	117	504	0	ENST00000338641.4:c.90dup	p.Ala31ArgfsTer18	p.A31Rfs*18	ENST00000338641	NM_000268.3	30	gac/gaCc	1/16	0.506096626053674	1	FACETS	0.792	0.719	0.868	0.792	0.719	0.868	SUBCLONAL	1	TRUE	0	0.506096626053674	1		504	436	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186501410	186501410	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	124	353	0	ENST00000323963.5:c.11G>C	p.Gly4Ala	p.G4A	ENST00000323963		4	gGc/gCc	1/11	1	2	FACETS	0.86	0.781	0.942	0.86	0.781	0.942	CLONAL	1	TRUE	1	0.506096626053674	2		353	570	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0059907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	10	195	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.369	0.249	0.518	0.369	0.249	0.518	SUBCLONAL	1	TRUE	1	0.27	2		195	201	SUCCESS
APC	324	MSKCC	GRCh37	5	112137073	112137073	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	12	271	1	ENST00000257430.4:c.827A>G	p.Asn276Ser	p.N276S	ENST00000257430	NM_000038.5	276	aAt/aGt	8/16	1	2	FACETS	0.48	0.338	0.655	0.48	0.338	0.655	SUBCLONAL	1	TRUE	1	0.27	2		272	185	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0059908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	85	345	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.236721798854116	3	FACETS	0.881	0.782	0.986	0.881	0.782	0.986	CLONAL	2	TRUE	1	0.236721798854116	3		345	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0059908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	124	556	0	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	0.236721798854116	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.236721798854116	1		556	791	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261290	16261290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	121	600	0	ENST00000375759.3:c.8555C>T	p.Ser2852Phe	p.S2852F	ENST00000375759	NM_015001.2	2852	tCc/tTc	11/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.236721798854116	2		600	927	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670086	29670086	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	49	244	0	ENST00000356175.3:c.7059G>A	p.Met2353Ile	p.M2353I	ENST00000356175	NM_000267.3	2353	atG/atA	47/57	NA	2	FACETS	0.914	0.775	1			1	INDETERMINATE	1	TRUE	NA	0.236721798854116	2		244	453	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62311234	62311234	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	67	517	0	ENST00000360203.5:c.1070T>A	p.Ile357Asn	p.I357N	ENST00000360203	NM_001283009.1	357	aTc/aAc	13/35	0.179565796539021	4	FACETS	0.758	0.657	0.869	0.379	0.328	0.435	SUBCLONAL	1	TRUE	2	0.236721798854116	4		517	923	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775942	9775942	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	59	486	0	ENST00000377346.4:c.406G>A	p.Val136Met	p.V136M	ENST00000377346	NM_005026.3	136	Gtg/Atg	5/24	0.38645964669104	1	FACETS	0.398	0.344	0.456	0.398	0.344	0.456	SUBCLONAL	1	TRUE	0	0.590084718121367	1		486	354	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936934	48936954	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTTACCACTTTTACAGAAAC	ATTTACCACTTTTACAGAAAC	-	novel	NA	P-0060000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	137	239	0	ENST00000267163.4:c.719-16_723del		p.X240_splice	ENST00000267163	NM_000321.2	240		8/27	0.590084718121367	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.590084718121367	1		239	306	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0060001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	148	445	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.392995061632066	1	FACETS	0.964	0.892	1	0.964	0.892	1	CLONAL	1	TRUE	0	0.587758986245921	1		445	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579415	7579415	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	338	577	0	ENST00000269305.4:c.272G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tGg/tAg	4/11	0.587758986245921	2	FACETS	0.985	0.943	1	0.985	0.943	1	CLONAL	2	TRUE	0	0.587758986245921	2		577	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0060002-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	308	688	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.418966985169116	2	FACETS	0.798	0.756	0.84	0.798	0.756	0.84	SUBCLONAL	2	TRUE	0	0.504689920877807	2		688	765	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739853	46739853	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1312637312	NA	P-0060002-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	246	457	0	ENST00000371975.4:c.1654C>T	p.Arg552Ter	p.R552*	ENST00000371975	NM_003579.3	552	Cga/Tga	15/18	0.293216814223805	3	FACETS	0.752	0.705	0.8	0.752	0.705	0.8	INDETERMINATE	2	TRUE	1	0.504689920877807	3		457	812	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0060010-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	208	399	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.277649407903666	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.277649407903666	3		399	684	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0060010-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	101	539	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.277649407903666	3	FACETS	1	0.948	1	0.549	0.491	0.612	CLONAL	1	TRUE	1	0.277649407903666	3		539	754	SUCCESS
APC	324	MSKCC	GRCh37	5	112174086	112174086	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs878853432	NA	P-0060010-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	154	417	0	ENST00000257430.4:c.2795C>G	p.Ser932Ter	p.S932*	ENST00000257430	NM_000038.5	932	tCa/tGa	16/16	0.277649407903666	3	FACETS	0.862	0.79	0.936	0.862	0.79	0.936	CLONAL	2	TRUE	1	0.277649407903666	3		417	733	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006827	47006827	+	5_prime_UTR_variant	5'UTR	SNP	C	C	T	novel	NA	P-0060010-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	356	261	1	ENST00000377604.3:c.-54C>T		p.*18*	ENST00000377604	NM_001204468.1	-/852		2/24	0.277649407903666	3	FACETS	0.962	0.923	1			1	CLONAL	5	TRUE	NA	0.277649407903666	3		262	607	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92247472	92247472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060010-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	303	539	0	ENST00000265734.4:c.748C>T	p.Pro250Ser	p.P250S	ENST00000265734	NM_001259.6	250	Ccc/Tcc	7/8	0.277649407903666	5	FACETS	0.96	0.905	1	0.96	0.905	1	CLONAL	3	TRUE	2	0.277649407903666	5		539	1074	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403494	139403494	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060010-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	91	575	0	ENST00000277541.6:c.2999A>G	p.Asp1000Gly	p.D1000G	ENST00000277541	NM_017617.3	1000	gAc/gGc	19/34	0.256883228696058	4	FACETS	0.773	0.684	0.868	0.386	0.342	0.434	SUBCLONAL	1	TRUE	2	0.277649407903666	4		575	1084	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0060011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	30	355	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.827	0.666	1	0.827	0.666	1	CLONAL	1	TRUE	1	0.17	2		355	427	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596017	43596017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	44	520	0	ENST00000355710.3:c.184G>A	p.Glu62Lys	p.E62K	ENST00000355710	NM_020975.4	62	Gag/Aag	2/20	1	2	FACETS	0.798	0.668	0.942	0.798	0.668	0.942	CLONAL	1	TRUE	1	0.17	2		520	649	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416853	416853	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	61	591	0	ENST00000399788.2:c.3697C>T	p.Leu1233Phe	p.L1233F	ENST00000399788	NM_001042603.1	1233	Ctt/Ttt	23/28	1	2	FACETS	0.884	0.761	1	0.884	0.761	1	CLONAL	1	TRUE	1	0.17	2		591	812	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444289	49444289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs961754523	NA	P-0060011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	49	616	0	ENST00000301067.7:c.3082C>T	p.Leu1028Phe	p.L1028F	ENST00000301067	NM_003482.3	1028	Ctt/Ttt	11/54	1	2	FACETS	0.692	0.584	0.811	0.692	0.584	0.811	SUBCLONAL	1	TRUE	1	0.17	2		616	833	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61328312	61328312	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	22	359	0	ENST00000283752.5:c.139G>A	p.Asp47Asn	p.D47N	ENST00000283752	NM_006919.2	47	Gac/Aac	2/8	1	2	FACETS	0.612	0.473	0.774	0.612	0.473	0.774	SUBCLONAL	1	TRUE	1	0.17	2		359	423	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221457	36221457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	46	595	0	ENST00000222270.7:c.5216C>T	p.Ser1739Phe	p.S1739F	ENST00000222270	NM_014727.1	1739	tCc/tTc	25/37	1	2	FACETS	0.649	0.545	0.765	0.649	0.545	0.765	SUBCLONAL	1	TRUE	1	0.17	2		595	834	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0060011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	46	570	0	ENST00000349496.5:c.101G>A	p.Gly34Glu	p.G34E	ENST00000349496	NM_001904.3	34	gGa/gAa	3/15	1	2	FACETS	0.781	0.656	0.919	0.781	0.656	0.919	CLONAL	1	TRUE	1	0.17	2		570	693	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266163	41266163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	42	432	0	ENST00000349496.5:c.160G>A	p.Glu54Lys	p.E54K	ENST00000349496	NM_001904.3	54	Gaa/Aaa	3/15	1	2	FACETS	0.772	0.643	0.916	0.772	0.643	0.916	CLONAL	1	TRUE	1	0.17	2		432	640	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590654	189590654	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	44	397	0	ENST00000264731.3:c.1219G>A	p.Gly407Ser	p.G407S	ENST00000264731	NM_003722.4	407	Ggc/Agc	10/14	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.17	2		397	507	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803104	1803104	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0060011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	33	523	0	ENST00000260795.2:c.456C>G	p.Tyr152Ter	p.Y152*	ENST00000260795		152	taC/taG	4/17	1	2	FACETS	0.629	0.511	0.763	0.629	0.511	0.763	SUBCLONAL	1	TRUE	1	0.17	2		523	617	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141119	55141119	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	31	417	0	ENST00000257290.5:c.1765C>T	p.Pro589Ser	p.P589S	ENST00000257290	NM_006206.4	589	Cca/Tca	12/23	1	2	FACETS	0.682	0.55	0.831	0.682	0.55	0.831	SUBCLONAL	1	TRUE	1	0.17	2		417	535	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144359225	144359225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	28	367	0	ENST00000262995.4:c.667C>T	p.Pro223Ser	p.P223S	ENST00000262995	NM_207123.2	223	Cct/Tct	4/11	1	2	FACETS	0.732	0.584	0.901	0.732	0.584	0.901	CLONAL	1	TRUE	1	0.17	2		367	450	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293662	1293662	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1304418053	NA	P-0060011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	57	578	0	ENST00000310581.5:c.1339C>T	p.Arg447Cys	p.R447C	ENST00000310581	NM_198253.2	447	Cgc/Tgc	2/16	1	2	FACETS	0.955	0.818	1	0.955	0.818	1	CLONAL	1	TRUE	1	0.17	2		578	702	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0060011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	32	525	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.983	0.798	1	0.983	0.798	1	CLONAL	1	TRUE	1	0.17	2		525	383	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223550	55223550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	43	496	0	ENST00000275493.2:c.917C>T	p.Ser306Leu	p.S306L	ENST00000275493	NM_005228.3	306	tCg/tTg	8/28	1	2	FACETS	0.746	0.623	0.883	0.746	0.623	0.883	SUBCLONAL	1	TRUE	1	0.17	2		496	678	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169504	27169504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866968099	NA	P-0060011-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	38	439	0	ENST00000380036.4:c.505G>A	p.Glu169Lys	p.E169K	ENST00000380036	NM_000459.3	169	Gaa/Aaa	4/23	0.146982986018653	1	FACETS	0.755	0.623	0.902	0.755	0.623	0.902	CLONAL	1	TRUE	0	0.17	1		439	542	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974769	21974770	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCCGT	rs1563892769	NA	P-0060013-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	520	551	0	ENST00000304494.5:c.52_57dup	p.Thr18_Ala19dup	p.T18_A19dup	ENST00000304494	NM_000077.4	18	-/ACGGCC	1/3	0.63897785262709	2	FACETS	0.931	0.9	0.961	0.931	0.9	0.961	CLONAL	2	TRUE	0	0.653535971521586	2		551	855	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0060013-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	322	380	0	ENST00000269305.4:c.673-2A>C		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.644611448153515	2	FACETS	0.938	0.899	0.977	0.938	0.899	0.977	CLONAL	2	TRUE	0	0.653535971521586	2		380	525	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0060013-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	192	329	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.235416064268686	3	FACETS	0.898	0.841	0.956	0.898	0.841	0.956	INDETERMINATE	2	TRUE	1	0.653535971521586	3		329	434	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434555	49434555	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs377504041	NA	P-0060013-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	67	584	0	ENST00000301067.7:c.6998C>A	p.Pro2333His	p.P2333H	ENST00000301067	NM_003482.3	2333	cCt/cAt	31/54	1	2	FACETS	0.259	0.225	0.297	0.259	0.225	0.297	SUBCLONAL	1	TRUE	1	0.653535971521586	2		584	791	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833952	44833953	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0060013-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	121	90	0	ENST00000377967.4:c.377dup	p.Tyr126Ter	p.Y126*	ENST00000377967	NM_021140.2	126	tac/tAac	4/29	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.653535971521586	1		90	173	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216397	2216397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1386157480	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	170	760	0	ENST00000398665.3:c.2041C>T	p.Arg681Cys	p.R681C	ENST00000398665	NM_032482.2	681	Cgc/Tgc	20/28	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.502305087116479	2		760	664	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641144	117641144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866970127	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	189	805	0	ENST00000368508.3:c.5827G>A	p.Glu1943Lys	p.E1943K	ENST00000368508	NM_002944.2	1943	Gaa/Aaa	36/43	0.502305087116479	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.502305087116479	1		805	510	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522569	106522569	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746783339	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	84	359	0	ENST00000359195.3:c.2546G>A	p.Arg849Gln	p.R849Q	ENST00000359195	NM_002649.2	849	cGa/cAa	7/11	1	2	FACETS	0.906	0.806	1	0.906	0.806	1	CLONAL	1	TRUE	1	0.502305087116479	2		359	369	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280068	66280068	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	197	625	0	ENST00000273854.3:c.1621C>T	p.Arg541Ter	p.R541*	ENST00000273854	NM_004439.5	541	Cga/Tga	7/18	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.502305087116479	2		625	681	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381466	81381466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	145	575	0	ENST00000222390.5:c.595G>A	p.Glu199Lys	p.E199K	ENST00000222390	NM_000601.4	199	Gaa/Aaa	5/18	1	2	FACETS	0.992	0.909	1	0.992	0.909	1	CLONAL	1	TRUE	1	0.502305087116479	2		575	582	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367239	50367239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1045233686	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	121	597	0	ENST00000331340.3:c.46G>A	p.Glu16Lys	p.E16K	ENST00000331340	NM_006060.4	16	Gaa/Aaa	3/8	0.502305087116479	1	FACETS	0.64	0.58	0.702	0.64	0.58	0.702	SUBCLONAL	1	TRUE	0	0.502305087116479	1		597	564	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500867	149500867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774032065	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	236	601	0	ENST00000261799.4:c.2363G>A	p.Arg788Gln	p.R788Q	ENST00000261799	NM_002609.3	788	cGa/cAa	17/23	0.502305087116479	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.502305087116479	1		601	478	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295230	+	upstream_gene_variant	5'Flank	TNP	GGG	GGG	AGA	novel	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	78	607	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.868	0.768	0.973	0.868	0.768	0.973	CLONAL	1	TRUE	1	0.502305087116479	2		607	358	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352727	70352727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1488661030	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	108	431	0	ENST00000374080.3:c.4448C>T	p.Ser1483Leu	p.S1483L	ENST00000374080		1483	tCg/tTg	32/45	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.502305087116479	2		431	421	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518554	69518554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	111	579	0	ENST00000294312.3:c.91G>A	p.Gly31Arg	p.G31R	ENST00000294312	NM_005117.2	31	Ggg/Agg	1/3	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.502305087116479	2		579	438	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427545	49427545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758858726	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	172	768	0	ENST00000301067.7:c.10943C>T	p.Pro3648Leu	p.P3648L	ENST00000301067	NM_003482.3	3648	cCg/cTg	39/54	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.502305087116479	2		768	641	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331730	68331730	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	54	246	0	ENST00000487270.1:c.326C>T	p.Pro109Leu	p.P109L	ENST00000487270	NM_133509.3	109	cCa/cTa	5/11	1	2	FACETS	0.96	0.83	1	0.96	0.83	1	CLONAL	1	TRUE	1	0.502305087116479	2		246	224	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686229	117686229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	127	586	0	ENST00000368508.3:c.3112G>A	p.Glu1038Lys	p.E1038K	ENST00000368508	NM_002944.2	1038	Gaa/Aaa	20/43	0.502305087116479	1	FACETS	0.93	0.851	1	0.93	0.851	1	CLONAL	1	TRUE	0	0.502305087116479	1		586	407	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520237	9520237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1345841620	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	132	557	0	ENST00000353224.5:c.2032G>A	p.Asp678Asn	p.D678N	ENST00000353224	NM_177990.2	678	Gac/Aac	10/10	1	2	FACETS	0.932	0.85	1	0.932	0.85	1	CLONAL	1	TRUE	1	0.502305087116479	2		557	564	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754823	29754823	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	173	752	0	ENST00000389048.3:c.1112C>T	p.Ala371Val	p.A371V	ENST00000389048	NM_004304.4	371	gCt/gTt	4/29	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.502305087116479	2		752	665	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307426	118307426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	75	420	0	ENST00000534358.1:c.199G>A	p.Ala67Thr	p.A67T	ENST00000534358	NM_005933.3	67	Gcg/Acg	1/36	0.502305087116479	1	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	0	0.502305087116479	1		420	223	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422658	49422658	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	173	687	0	ENST00000301067.7:c.14335G>A	p.Gly4779Arg	p.G4779R	ENST00000301067	NM_003482.3	4779	Gga/Aga	45/54	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.502305087116479	2		687	659	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436074	49436075	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	128	649	1	ENST00000301067.7:c.5906_5907delinsTT	p.Pro1969Leu	p.P1969L	ENST00000301067	NM_003482.3	1969	cCC/cTT	28/54	1	2	FACETS	0.927	0.843	1	0.927	0.843	1	CLONAL	1	TRUE	1	0.502305087116479	2		650	550	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912777	32912777	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs80358665	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	164	566	0	ENST00000380152.3:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000380152		1429	Cag/Tag	11/27	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.502305087116479	2		566	577	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239266	105239266	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	176	803	0	ENST00000349310.3:c.1121C>T	p.Pro374Leu	p.P374L	ENST00000349310	NM_001014432.1	374	cCc/cTc	12/15	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.502305087116479	2		803	688	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923481	9923482	+	missense_variant	Missense_Mutation	DNP	TC	TC	GT	novel	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	124	628	0	ENST00000330684.3:c.1805_1806delinsAC	p.Gly602Asp	p.G602D	ENST00000330684	NM_001134407.1	602	gGA/gAC	9/13	1	2	FACETS	0.93	0.845	1	0.93	0.845	1	CLONAL	1	TRUE	1	0.502305087116479	2		628	531	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969942	81969942	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	168	724	0	ENST00000359376.3:c.3011T>G	p.Leu1004Arg	p.L1004R	ENST00000359376	NM_002661.3	1004	cTg/cGg	27/33	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.502305087116479	2		724	663	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15970088	15971110	+	intron_variant	Intron	DEL	GATAAAATATTTCCCACAGTTACTTTCCTATTATTATGAAATGTAAATAACCCTTAGAATTCTTACTTTTAAAATTTAGCATACTGATAATGAAAAATTCTTCTCTAAGGACCAAAGTGAGGCACAAGTATTCTGTGTCCTAATTTGCACCTGAAGGATACTTATTAAGCAAAGAGTTTATTTAGGCCAGAGAAGAGGTCTCAGCAGAAAACACATGTGTGACTGGGCTCAGCCAATAGCGGCAAGGAAGAGCAAGGACTGCACCCTGGGAGGACAAGGTGCAGCCGGTGGTCCTGCAGATTATAACAGCCCAGCCAAGCCTCTCTGTACCAACCGATGTGACTGCTCCTCTCCCCTCCCTGTGTAAAACACAATGCCCTCTGCCCAGCAGACTGCTCTCTAGAAACCTGCACATCTGCACCTATCAGATTCTGTCTACCAATGTCAGTGGTGTTCTGAAGTTTCTTCCAGCTGTACTTGTTACTAGAATTATGTAACTTAATGACATAATTTGTAAATCAAGGAAGAATGAAGAGTGGTTTCTCTGAAAACTAACAGCTTTGGAAAGAGTTGATACAGAAGTTGAATCAGGTGCGGACTAGACAACTTCAAAGGCTGGAAAAAAAATCTAGAAGGATTCTGTATTTAGATTGCTTGGAAGTGTCTTTACTTGGAAGTTCTAGCTTTACTTAAAAAAAAGAATTTCTTTTATATAAGACAGTGAGACTTAATCACTTGTTTATGAAAAAGCCTTGGCATTAGATCAGAGTTCTGGTAAATGAACGTCTATTTATGCTGTAAGTTAACATGTTTAGGTATGCCTCTGTCATTTTAAAATAATTATTCACATTAATCCACTTTTTCAACTAGTTTCACCAAGTGCCATCAGATAAGAGAGCTTTTCATATACTATTCTTTTTAGTTCTTTACCGGGTGCTGATAAGATTTTATTTCTTGATCTGGGTGCTGGTAACATGGGAGAATTTAGTTTGTGAAAATTCACTGAGCTGTACATTAATGATA	GATAAAATATTTCCCACAGTTACTTTCCTATTATTATGAAATGTAAATAACCCTTAGAATTCTTACTTTTAAAATTTAGCATACTGATAATGAAAAATTCTTCTCTAAGGACCAAAGTGAGGCACAAGTATTCTGTGTCCTAATTTGCACCTGAAGGATACTTATTAAGCAAAGAGTTTATTTAGGCCAGAGAAGAGGTCTCAGCAGAAAACACATGTGTGACTGGGCTCAGCCAATAGCGGCAAGGAAGAGCAAGGACTGCACCCTGGGAGGACAAGGTGCAGCCGGTGGTCCTGCAGATTATAACAGCCCAGCCAAGCCTCTCTGTACCAACCGATGTGACTGCTCCTCTCCCCTCCCTGTGTAAAACACAATGCCCTCTGCCCAGCAGACTGCTCTCTAGAAACCTGCACATCTGCACCTATCAGATTCTGTCTACCAATGTCAGTGGTGTTCTGAAGTTTCTTCCAGCTGTACTTGTTACTAGAATTATGTAACTTAATGACATAATTTGTAAATCAAGGAAGAATGAAGAGTGGTTTCTCTGAAAACTAACAGCTTTGGAAAGAGTTGATACAGAAGTTGAATCAGGTGCGGACTAGACAACTTCAAAGGCTGGAAAAAAAATCTAGAAGGATTCTGTATTTAGATTGCTTGGAAGTGTCTTTACTTGGAAGTTCTAGCTTTACTTAAAAAAAAGAATTTCTTTTATATAAGACAGTGAGACTTAATCACTTGTTTATGAAAAAGCCTTGGCATTAGATCAGAGTTCTGGTAAATGAACGTCTATTTATGCTGTAAGTTAACATGTTTAGGTATGCCTCTGTCATTTTAAAATAATTATTCACATTAATCCACTTTTTCAACTAGTTTCACCAAGTGCCATCAGATAAGAGAGCTTTTCATATACTATTCTTTTTAGTTCTTTACCGGGTGCTGATAAGATTTTATTTCTTGATCTGGGTGCTGGTAACATGGGAGAATTTAGTTTGTGAAAATTCACTGAGCTGTACATTAATGATA	-	novel	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	0	109	0	0	ENST00000268712.3:c.4741+100_4742-1078del		p.*1581*	ENST00000268712	NM_006311.3	-/2440			1	2	FACETS		NA	1	1	0.993	1	NA	4	TRUE	1	0.502305087116479	2		0	109	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562683	29562683	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060500308	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	115	547	0	ENST00000356175.3:c.3763C>T	p.Gln1255Ter	p.Q1255*	ENST00000356175	NM_000267.3	1255	Caa/Taa	28/57	0.502305087116479	1	FACETS	0.822	0.746	0.901	0.822	0.746	0.901	CLONAL	1	TRUE	0	0.502305087116479	1		547	417	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690205	33690205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	126	677	0	ENST00000308377.4:c.622C>T	p.Pro208Ser	p.P208S	ENST00000308377	NM_152270.3	208	Cct/Tct	2/5	0.502305087116479	1	FACETS	0.846	0.772	0.923	0.846	0.772	0.923	CLONAL	1	TRUE	0	0.502305087116479	1		677	444	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791573	42791574	+	missense_variant	Missense_Mutation	DNP	CT	CT	TC	novel	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	167	884	0	ENST00000575354.2:c.554_555delinsTC	p.Ser185Phe	p.S185F	ENST00000575354	NM_015125.3	185	tCT/tTC	4/20	1	2	FACETS	0.976	0.9	1	0.976	0.9	1	CLONAL	1	TRUE	1	0.502305087116479	2		884	681	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871992	45871992	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	138	496	0	ENST00000391945.4:c.256G>A	p.Glu86Lys	p.E86K	ENST00000391945	NM_000400.3	86	Gag/Aag	5/23	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.502305087116479	2		496	507	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085719	16085719	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	33	568	0	ENST00000281043.3:c.895A>C	p.Ile299Leu	p.I299L	ENST00000281043	NM_005378.4	299	Atc/Ctc	3/3	1	2	FACETS	0.221	0.179	0.269	0.221	0.179	0.269	SUBCLONAL	1	TRUE	1	0.502305087116479	2		568	594	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754936	29754937	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	35	697	1	ENST00000389048.3:c.998_999delinsAA	p.Ile333Lys	p.I333K	ENST00000389048	NM_004304.4	333	aTC/aAA	4/29	1	2	FACETS	0.216	0.177	0.261	0.216	0.177	0.261	SUBCLONAL	1	TRUE	1	0.502305087116479	2		698	644	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147583	61147583	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	62	320	0	ENST00000295025.8:c.988A>T	p.Thr330Ser	p.T330S	ENST00000295025	NM_002908.2	330	Acc/Tcc	9/11	1	2	FACETS	0.904	0.789	1	0.904	0.789	1	CLONAL	1	TRUE	1	0.502305087116479	2		320	273	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326882	62326882	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537878959	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	183	778	1	ENST00000360203.5:c.3701C>T	p.Pro1234Leu	p.P1234L	ENST00000360203	NM_001283009.1	1234	cCg/cTg	34/35	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.502305087116479	2		779	726	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447273	187447273	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779829722	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	197	762	0	ENST00000232014.4:c.920C>T	p.Ser307Phe	p.S307F	ENST00000232014	NM_001130845.1	307	tCc/tTc	5/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.502305087116479	2		762	724	SUCCESS
ALB	213	MSKCC	GRCh37	4	74285972	74285972	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	94	357	0	ENST00000295897.4:c.1787G>A	p.Gly596Asp	p.G596D	ENST00000295897	NM_000477.5	596	gGt/gAt	14/15	1	2	FACETS	0.97	0.869	1	0.97	0.869	1	CLONAL	1	TRUE	1	0.502305087116479	2		357	386	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188295	32188295	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777684671	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	175	923	0	ENST00000375023.3:c.1046G>A	p.Gly349Asp	p.G349D	ENST00000375023	NM_004557.3	349	gGc/gAc	6/30	0.502305087116479	3	FACETS	0.911	0.839	0.986	0.455	0.419	0.493	CLONAL	1	TRUE	1	0.502305087116479	3		923	957	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877211	151877211	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs781570710	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	129	531	1	ENST00000262189.6:c.7150C>T	p.Arg2384Trp	p.R2384W	ENST00000262189	NM_170606.2	2384	Cgg/Tgg	37/59	1	2	FACETS	0.866	0.788	0.948	0.866	0.788	0.948	CLONAL	1	TRUE	1	0.502305087116479	2		532	593	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518285	8518285	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	114	591	1	ENST00000356435.5:c.1106A>T	p.Glu369Val	p.E369V	ENST00000356435		369	gAa/gTa	10/35	1	2	FACETS	0.94	0.851	1	0.94	0.851	1	CLONAL	1	TRUE	1	0.502305087116479	2		592	483	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8733789	8733789	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1249636201	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	130	624	0	ENST00000356435.5:c.55G>A	p.Asp19Asn	p.D19N	ENST00000356435		19	Gat/Aat	1/35	1	2	FACETS	0.959	0.874	1	0.959	0.874	1	CLONAL	1	TRUE	1	0.502305087116479	2		624	540	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937167	39937167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	187	599	0	ENST00000378444.4:c.16C>T	p.Pro6Ser	p.P6S	ENST00000378444	NM_001123385.1	6	Ccc/Tcc	2/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.502305087116479	2		599	610	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651660	48651660	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	182	789	0	ENST00000376670.3:c.826G>A	p.Asp276Asn	p.D276N	ENST00000376670	NM_002049.3	276	Gat/Aat	5/6	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.502305087116479	2		789	686	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341643	70341643	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	188	749	0	ENST00000374080.3:c.1078T>G	p.Phe360Val	p.F360V	ENST00000374080		360	Ttt/Gtt	7/45	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.502305087116479	2		749	654	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351974	70351974	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	188	683	0	ENST00000374080.3:c.4171C>T	p.Gln1391Ter	p.Q1391*	ENST00000374080		1391	Caa/Taa	30/45	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.502305087116479	2		683	696	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123040951	123040951	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	28	105	0	ENST00000355640.3:c.1414A>G	p.Lys472Glu	p.K472E	ENST00000355640		472	Aaa/Gaa	7/7	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.502305087116479	2		105	96	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2161840	2161842	+	frameshift_variant	Frame_Shift_Del	DEL	ATC	ATC	GT	novel	NA	P-0060014-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	171	697	1	ENST00000349721.2:c.4136_4138delinsGT	p.Asn1379SerfsTer5	p.N1379Sfs*5	ENST00000349721	NM_003070.3	1379	aATCcc/aGTcc	28/34	1	2	FACETS	0.987	0.911	1	0.987	0.911	1	CLONAL	1	TRUE	1	0.502305087116479	2		698	690	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs199469672	NA	P-0060021-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	13	378	0	ENST00000374080.3:c.131G>C	p.Gly44Ala	p.G44A	ENST00000374080		44	gGt/gCt	2/45	1	2	FACETS	0.196	0.139	0.266	0.196	0.139	0.266	SUBCLONAL	1	TRUE	1	0.28564491973899	2		378	465	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699360	47699360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060021-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	65	368	0	ENST00000347630.2:c.148G>A	p.Glu50Lys	p.E50K	ENST00000347630	NM_001007230.1	50	Gaa/Aaa	4/11	0.28564491973899	1	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	0	0.28564491973899	1		368	383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0060021-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	123	553	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	0.28564491973899	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.28564491973899	1		553	587	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118823	115118823	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060021-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	49	498	0	ENST00000257566.3:c.518C>G	p.Ala173Gly	p.A173G	ENST00000257566	NM_016569.3	173	gCt/gGt	2/8	1	2	FACETS	0.536	0.453	0.627	0.536	0.453	0.627	SUBCLONAL	1	TRUE	1	0.28564491973899	2		498	640	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163298055	163298055	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	59	300	0	ENST00000271452.3:c.236T>C	p.Met79Thr	p.M79T	ENST00000271452	NM_145697.2	79	aTg/aCg	4/14	0.63193389898094	5	FACETS	1	0.931	1	0.28	0.243	0.321	CLONAL	1	TRUE	1	0.673241815575504	5		300	314	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163310188	163310188	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0060033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	60	303	0	ENST00000271452.3:c.641C>G	p.Ser214Ter	p.S214*	ENST00000271452	NM_145697.2	214	tCa/tGa	9/14	0.63193389898094	5	FACETS	0.923	0.799	1	0.231	0.199	0.265	CLONAL	1	TRUE	1	0.673241815575504	5		303	388	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50763849	50763849	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	81	318	0	ENST00000307179.4:c.706G>A	p.Glu236Lys	p.E236K	ENST00000307179		236	Gaa/Aaa	8/20	0.673241815575504	3	FACETS	1	0.948	1	0.555	0.494	0.618	CLONAL	1	TRUE	1	0.673241815575504	3		318	290	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379718	17379718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1193352612	NA	P-0060033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	116	596	0	ENST00000359435.4:c.103G>A	p.Glu35Lys	p.E35K	ENST00000359435	NM_001033549.1	35	Gag/Aag	2/9	0.673241815575504	3	FACETS	1	0.919	1	0.507	0.46	0.557	CLONAL	1	TRUE	1	0.673241815575504	3		596	454	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663346	227663346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024227751	NA	P-0060033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	96	580	0	ENST00000305123.5:c.109G>A	p.Glu37Lys	p.E37K	ENST00000305123	NM_005544.2	37	Gag/Aag	1/2	0.673241815575504	3	FACETS	0.916	0.822	1	0.458	0.411	0.508	CLONAL	1	TRUE	1	0.673241815575504	3		580	416	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735503	40735503	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1352	92	534	0	ENST00000373198.4:c.3370G>T	p.Glu1124Ter	p.E1124*	ENST00000373198	NM_133170.3	1124	Gag/Tag	25/32	0.673241815575504	10	FACETS	0.699	0.618	0.786			1	SUBCLONAL	1	TRUE	NA	0.673241815575504	10		534	1444	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902508	1902508	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1165866735	NA	P-0060033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	128	539	0	ENST00000382891.5:c.127G>A	p.Glu43Lys	p.E43K	ENST00000382891	NM_133335.3	43	Gag/Aag	2/22	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.673241815575504	2		539	372	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156711	55156711	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0060033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	106	577	0	ENST00000257290.5:c.3112A>T	p.Asn1038Tyr	p.N1038Y	ENST00000257290	NM_006206.4	1038	Aac/Tac	22/23	0.673241815575504	3	FACETS	0.983	0.888	1	0.492	0.444	0.542	CLONAL	1	TRUE	1	0.673241815575504	3		577	428	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565840	55565840	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	72	336	0	ENST00000288135.5:c.664C>T	p.Leu222Phe	p.L222F	ENST00000288135	NM_000222.2	222	Ctt/Ttt	4/21	0.673241815575504	3	FACETS	1	0.942	1	0.554	0.49	0.621	CLONAL	1	TRUE	1	0.673241815575504	3		336	258	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0060033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	116	477	0				ENST00000310581	NM_198253.2	-/1132			0.596563626316472	4	FACETS	0.89	0.812	0.969	0.89	0.812	0.969	CLONAL	2	TRUE	2	0.673241815575504	4		477	324	SUCCESS
APC	324	MSKCC	GRCh37	5	112173828	112173828	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	75	394	0	ENST00000257430.4:c.2537C>T	p.Ser846Phe	p.S846F	ENST00000257430	NM_000038.5	846	tCt/tTt	16/16	1	2	FACETS	0.982	0.874	1	0.982	0.874	1	CLONAL	1	TRUE	1	0.673241815575504	2		394	227	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402831	139402831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	125	493	0	ENST00000277541.6:c.3178G>A	p.Val1060Met	p.V1060M	ENST00000277541	NM_017617.3	1060	Gtg/Atg	20/34	0.673241815575504	3	FACETS	1	0.98	1	0.631	0.577	0.688	CLONAL	1	TRUE	1	0.673241815575504	3		493	393	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0060055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	41	355	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.549601386394944	2		355	125	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0060055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	46	525	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.549601386394944	2		525	135	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804214	43804214	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	65	567	0	ENST00000372470.3:c.214G>A	p.Glu72Lys	p.E72K	ENST00000372470	NM_005373.2	72	Gag/Aag	3/12	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.549601386394944	2		567	204	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636727	8636727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159852	NA	P-0060055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	41	440	0	ENST00000356435.5:c.182G>A	p.Gly61Glu	p.G61E	ENST00000356435		61	gGa/gAa	2/35	0.131262980855035	0	FACETS	0.525	0.447	0.607			1	INDETERMINATE	1	TRUE	0	0.549601386394944	0		440	128	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796989	78796989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	62	485	0	ENST00000306801.3:c.1102C>T	p.Pro368Ser	p.P368S	ENST00000306801	NM_020761.2	368	Ccg/Tcg	9/34	0.549601386394944	3	FACETS	0.965	0.841	1	0.483	0.42	0.549	CLONAL	1	TRUE	1	0.549601386394944	3		485	298	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36945037	36945037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200059719	NA	P-0060055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	46	523	1	ENST00000361632.4:c.61G>A	p.Gly21Arg	p.G21R	ENST00000361632		21	Gga/Aga	2/16	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.549601386394944	2		524	167	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12393128	12393128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	24	469	0	ENST00000287820.6:c.37G>A	p.Glu13Lys	p.E13K	ENST00000287820	NM_015869.4	13	Gaa/Aaa	1/7	1	2	FACETS	0.716	0.57	0.879	0.716	0.57	0.879	SUBCLONAL	1	TRUE	1	0.549601386394944	2		469	122	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988659	41988659	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	28	520	0	ENST00000219905.7:c.1451C>T	p.Ser484Phe	p.S484F	ENST00000219905	NM_001164273.1	484	tCt/tTt	3/24	0.347040428382009	1	FACETS	0.632	0.514	0.76	0.632	0.514	0.76	SUBCLONAL	1	TRUE	0	0.549601386394944	1		520	117	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262510	16262510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs551660149	NA	P-0060055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	53	430	0	ENST00000375759.3:c.9775C>T	p.Pro3259Ser	p.P3259S	ENST00000375759	NM_015001.2	3259	Cct/Tct	11/15	0.549601386394944	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.549601386394944	1		430	128	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165957	118165957	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	67	599	0	ENST00000369448.3:c.467C>T	p.Ser156Phe	p.S156F	ENST00000369448	NM_017709.3	156	tCc/tTc	2/2	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.549601386394944	2		599	210	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462776	69462776	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0060055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	37	512	0	ENST00000227507.2:c.589T>C	p.Ser197Pro	p.S197P	ENST00000227507	NM_053056.2	197	Tcc/Ccc	4/5	1	2	FACETS	0.783	0.654	0.923	0.783	0.654	0.923	CLONAL	1	TRUE	1	0.549601386394944	2		512	172	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77961428	77961428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1456163372	NA	P-0060055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	52	484	0	ENST00000361507.4:c.395C>T	p.Ser132Phe	p.S132F	ENST00000361507	NM_080491.2	132	tCc/tTc	3/10	1	2	FACETS	0.88	0.759	1	0.88	0.759	1	CLONAL	1	TRUE	1	0.549601386394944	2		484	215	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680634	88680634	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0060055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	39	393	0	ENST00000360948.2:c.622+1G>A		p.X208_splice	ENST00000360948	NM_001012338.2	208			0.151830155487323	0	FACETS	0.444	0.374	0.518			1	INDETERMINATE	1	TRUE	0	0.549601386394944	0		393	144	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857547	9857547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs367543132	NA	P-0060055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	36	566	0	ENST00000330684.3:c.3854G>T	p.Arg1285Met	p.R1285M	ENST00000330684	NM_001134407.1	1285	aGg/aTg	13/13	1	2	FACETS	0.891	0.745	1	0.891	0.745	1	CLONAL	1	TRUE	1	0.549601386394944	2		566	147	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817544	39817544	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	30	450	0	ENST00000288319.7:c.19G>A	p.Glu7Lys	p.E7K	ENST00000288319	NM_182918.3	7	Gaa/Aaa	2/10	0.21442474590175	0	FACETS	0.443	0.364	0.528			1	INDETERMINATE	1	TRUE	0	0.549601386394944	0		450	111	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729980	30729980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	39	449	0	ENST00000295754.5:c.1501C>T	p.Pro501Ser	p.P501S	ENST00000295754	NM_003242.5	501	Ccc/Tcc	6/7	1	2	FACETS	0.83	0.698	0.973	0.83	0.698	0.973	CLONAL	1	TRUE	1	0.549601386394944	2		449	171	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934249	49934249	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1575439776	NA	P-0060055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	43	622	1	ENST00000296474.3:c.2258T>G	p.Val753Gly	p.V753G	ENST00000296474	NM_002447.2	753	gTg/gGg	8/20	1	2	FACETS	0.915	0.778	1	0.915	0.778	1	CLONAL	1	TRUE	1	0.549601386394944	2		623	171	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149290654	149290654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs981487444	NA	P-0060055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	56	381	0	ENST00000360632.3:c.565C>T	p.Leu189Phe	p.L189F	ENST00000360632	NM_015472.4	189	Ctc/Ttc	3/7	1	2	FACETS	0.989	0.86	1	0.989	0.86	1	CLONAL	1	TRUE	1	0.549601386394944	2		381	206	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750545	41750545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	31	505	0	ENST00000226382.2:c.83C>T	p.Ser28Leu	p.S28L	ENST00000226382	NM_003924.3	28	tCa/tTa	1/3	1	2	FACETS	0.684	0.559	0.821	0.684	0.559	0.821	SUBCLONAL	1	TRUE	1	0.549601386394944	2		505	165	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876365	35876365	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201790771	NA	P-0060055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	43	576	0	ENST00000303115.3:c.1157G>A	p.Arg386Lys	p.R386K	ENST00000303115	NM_002185.3	386	aGg/aAg	8/8	1	2	FACETS	0.943	0.802	1	0.943	0.802	1	CLONAL	1	TRUE	1	0.549601386394944	2		576	166	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694653	176694653	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0060055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	38	498	0	ENST00000439151.2:c.5237A>G	p.Asn1746Ser	p.N1746S	ENST00000439151	NM_022455.4	1746	aAt/aGt	15/23	1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	TRUE	1	0.549601386394944	2		498	138	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168963	32168963	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138132429	NA	P-0060055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	62	698	0	ENST00000375023.3:c.4070C>G	p.Pro1357Arg	p.P1357R	ENST00000375023	NM_004557.3	1357	cCc/cGc	22/30	0.549601386394944	3	FACETS	1	0.898	1	0.517	0.451	0.588	CLONAL	1	TRUE	1	0.549601386394944	3		698	278	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	130	525	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.965	0.881	1	0.965	0.881	1	CLONAL	1	TRUE	1	0.568337319882643	2		525	474	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	143	438	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	0.85	0.778	0.925	0.85	0.778	0.925	CLONAL	1	TRUE	1	0.568337319882643	2		438	592	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100362	8100362	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	246	846	0	ENST00000346208.3:c.336G>A	p.Trp112Ter	p.W112*	ENST00000346208		112	tgG/tgA	3/6	1	2	FACETS	0.935	0.875	0.996	0.935	0.875	0.996	CLONAL	1	TRUE	1	0.568337319882643	2		846	926	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624300	89624300	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs786204912	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	122	430	0	ENST00000371953.3:c.74T>A	p.Leu25Ter	p.L25*	ENST00000371953	NM_000314.4	25	tTg/tAg	1/9	0.568337319882643	1	FACETS	0.815	0.744	0.888	0.815	0.744	0.888	CLONAL	1	TRUE	0	0.568337319882643	1		430	377	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624305	89624306	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	TG	TG	CT	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	125	449	1	ENST00000371953.3:c.79_79+1delinsCT		p.X27_splice	ENST00000371953	NM_000314.4	27		1/9	0.568337319882643	1	FACETS	0.816	0.746	0.888	0.816	0.746	0.888	CLONAL	1	TRUE	0	0.568337319882643	1		450	386	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717750	89717750	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	126	375	0	ENST00000371953.3:c.775C>T	p.His259Tyr	p.H259Y	ENST00000371953	NM_000314.4	259	Cac/Tac	7/9	0.568337319882643	1	FACETS	0.986	0.905	1	0.986	0.905	1	CLONAL	1	TRUE	0	0.568337319882643	1		375	322	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112767404	112767404	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	118	427	0	ENST00000369452.4:c.1277C>T	p.Ser426Phe	p.S426F	ENST00000369452	NM_007373.3	426	tCt/tTt	6/9	0.568337319882643	1	FACETS	0.872	0.796	0.95	0.872	0.796	0.95	CLONAL	1	TRUE	0	0.568337319882643	1		427	341	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239448	123239448	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	169	631	0	ENST00000358487.5:c.2389del	p.Val797PhefsTer19	p.V797Ffs*19	ENST00000358487	NM_000141.4	797	Gtt/tt	18/18	0.568337319882643	1	FACETS	0.914	0.848	0.981	0.914	0.848	0.981	CLONAL	1	TRUE	0	0.568337319882643	1		631	466	SUCCESS
CTR9	9646	MSKCC	GRCh37	11	10785346	10785346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	184	533	0	ENST00000361367.2:c.1114C>T	p.Pro372Ser	p.P372S	ENST00000361367	NM_014633.3	372	Cct/Tct	9/25	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.568337319882643	2		533	625	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933481	100933481	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs1209629034	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	99	399	0	ENST00000325455.5:c.1909C>T	p.Arg637Ter	p.R637*	ENST00000325455	NM_001202474.3	637	Cga/Tga	4/8	1	2	FACETS	0.864	0.777	0.956	0.864	0.777	0.956	CLONAL	1	TRUE	1	0.568337319882643	2		399	403	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492303	56492303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	166	542	0	ENST00000267101.3:c.2636C>T	p.Ala879Val	p.A879V	ENST00000267101	NM_001982.3	879	gCc/gTc	22/28	1	2	FACETS	0.966	0.891	1	0.966	0.891	1	CLONAL	1	TRUE	1	0.568337319882643	2		542	605	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495786	56495786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	153	547	0	ENST00000267101.3:c.3976C>T	p.Pro1326Ser	p.P1326S	ENST00000267101	NM_001982.3	1326	Cct/Tct	28/28	1	2	FACETS	0.874	0.803	0.948	0.874	0.803	0.948	CLONAL	1	TRUE	1	0.568337319882643	2		547	616	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865053	57865053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745312143	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	255	785	0	ENST00000228682.2:c.2530C>T	p.Pro844Ser	p.P844S	ENST00000228682	NM_005269.2	844	Cca/Tca	12/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.568337319882643	2		785	845	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109828	115109828	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	219	663	0	ENST00000257566.3:c.2050G>T	p.Val684Leu	p.V684L	ENST00000257566	NM_016569.3	684	Gtg/Ttg	8/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.568337319882643	2		663	682	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608024	28608024	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	196	509	0	ENST00000241453.7:c.1942G>A	p.Glu648Lys	p.E648K	ENST00000241453	NM_004119.2	648	Gaa/Aaa	15/24	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.568337319882643	2		509	666	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28885761	28885761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	147	515	0	ENST00000282397.4:c.3601C>T	p.Pro1201Ser	p.P1201S	ENST00000282397	NM_002019.4	1201	Ccg/Tcg	27/30	1	2	FACETS	0.937	0.86	1	0.937	0.86	1	CLONAL	1	TRUE	1	0.568337319882643	2		515	552	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239607	105239607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	201	749	0	ENST00000349310.3:c.938C>T	p.Pro313Leu	p.P313L	ENST00000349310	NM_001014432.1	313	cCt/cTt	11/15	1	2	FACETS	0.972	0.903	1	0.972	0.903	1	CLONAL	1	TRUE	1	0.568337319882643	2		749	728	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675119	40675119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766760890	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	236	613	0	ENST00000249776.8:c.83C>T	p.Pro28Leu	p.P28L	ENST00000249776	NM_033286.3	28	cCg/cTg	1/9	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.568337319882643	2		613	803	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998934	11998934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	134	431	0	ENST00000353533.5:c.436C>T	p.Leu146Phe	p.L146F	ENST00000353533	NM_003010.3	146	Ctt/Ttt	4/11	1	2	FACETS	0.947	0.866	1	0.947	0.866	1	CLONAL	1	TRUE	1	0.568337319882643	2		431	498	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560226	29560226	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555615109	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	182	521	0	ENST00000356175.3:c.3703C>T	p.Gln1235Ter	p.Q1235*	ENST00000356175	NM_000267.3	1235	Cag/Tag	27/57	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.568337319882643	2		521	564	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652904	29652904	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	164	522	0	ENST00000356175.3:c.4839T>A	p.Tyr1613Ter	p.Y1613*	ENST00000356175	NM_000267.3	1613	taT/taA	36/57	1	2	FACETS	0.968	0.893	1	0.968	0.893	1	CLONAL	1	TRUE	1	0.568337319882643	2		522	596	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690027	33690027	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	192	584	0	ENST00000308377.4:c.800C>T	p.Pro267Leu	p.P267L	ENST00000308377	NM_152270.3	267	cCt/cTt	2/5	1	2	FACETS	0.916	0.849	0.984	0.916	0.849	0.984	CLONAL	1	TRUE	1	0.568337319882643	2		584	738	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59870990	59870990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	149	428	0	ENST00000259008.2:c.1441G>A	p.Gly481Ser	p.G481S	ENST00000259008	NM_032043.2	481	Ggt/Agt	10/20	1	2	FACETS	0.966	0.887	1	0.966	0.887	1	CLONAL	1	TRUE	1	0.568337319882643	2		428	543	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7120670	7120670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	209	550	0	ENST00000302850.5:c.3620C>T	p.Ser1207Phe	p.S1207F	ENST00000302850	NM_000208.2	1207	tCc/tTc	20/22	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.568337319882643	2		550	682	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967041	18967041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	172	548	0	ENST00000262803.5:c.1756G>A	p.Glu586Lys	p.E586K	ENST00000262803	NM_002911.3	586	Gag/Aag	13/24	1	2	FACETS	0.952	0.879	1	0.952	0.879	1	CLONAL	1	TRUE	1	0.568337319882643	2		548	636	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224124	36224124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276663757	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	196	424	0	ENST00000222270.7:c.6674C>T	p.Ser2225Phe	p.S2225F	ENST00000222270	NM_014727.1	2225	tCc/tTc	28/37	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.568337319882643	2		424	522	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61729447	61729447	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	88	329	0	ENST00000401558.2:c.302-2A>G		p.X101_splice	ENST00000401558	NM_003400.3	101			1	2	FACETS	0.772	0.688	0.861	0.772	0.688	0.861	SUBCLONAL	1	TRUE	1	0.568337319882643	2		329	401	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209110124	209110124	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766372640	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	178	451	0	ENST00000345146.2:c.439C>T	p.Pro147Ser	p.P147S	ENST00000345146	NM_005896.2	147	Cct/Tct	5/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.568337319882643	2		451	611	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248669	212248669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	184	651	0	ENST00000342788.4:c.3598G>A	p.Asp1200Asn	p.D1200N	ENST00000342788	NM_005235.2	1200	Gat/Aat	28/28	1	2	FACETS	0.995	0.922	1	0.995	0.922	1	CLONAL	1	TRUE	1	0.568337319882643	2		651	651	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376694	31376694	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	121	527	1	ENST00000328111.2:c.689G>A	p.Trp230Ter	p.W230*	ENST00000328111	NM_006892.3	230	tGg/tAg	7/23	1	2	FACETS	0.752	0.682	0.826	0.752	0.682	0.826	SUBCLONAL	1	TRUE	1	0.568337319882643	2		528	566	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730876	40730876	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372862828	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	206	651	0	ENST00000373198.4:c.3659G>A	p.Arg1220Gln	p.R1220Q	ENST00000373198	NM_133170.3	1220	cGg/cAg	27/32	0.455102791861908	1	FACETS	0.778	0.725	0.832	0.778	0.725	0.832	SUBCLONAL	1	TRUE	0	0.568337319882643	1		651	667	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757435	40757435	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238347113	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	176	632	0	ENST00000373198.4:c.2863G>A	p.Gly955Arg	p.G955R	ENST00000373198	NM_133170.3	955	Gga/Aga	20/32	0.455102791861908	1	FACETS	0.778	0.721	0.836	0.778	0.721	0.836	SUBCLONAL	1	TRUE	0	0.568337319882643	1		632	570	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29106029	29106029	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	73	235	0	ENST00000328354.6:c.811G>T	p.Glu271Ter	p.E271*	ENST00000328354	NM_007194.3	271	Gaa/Taa	7/15	0.247166220326695	1	FACETS	0.748	0.663	0.836	0.748	0.663	0.836	INDETERMINATE	1	TRUE	0	0.568337319882643	1		235	246	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47061331	47061331	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	205	577	0	ENST00000409792.3:c.7351-1G>A		p.X2451_splice	ENST00000409792	NM_014159.6	2451			1	2	FACETS	0.982	0.913	1	0.982	0.913	1	CLONAL	1	TRUE	1	0.568337319882643	2		577	735	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933662	49933662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	210	743	0	ENST00000296474.3:c.2615C>T	p.Pro872Leu	p.P872L	ENST00000296474	NM_002447.2	872	cCa/cTa	10/20	1	2	FACETS	0.888	0.826	0.952	0.888	0.826	0.952	CLONAL	1	TRUE	1	0.568337319882643	2		743	832	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807551	1807551	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	194	772	0	ENST00000260795.2:c.1720G>A	p.Gly574Ser	p.G574S	ENST00000260795		574	Ggc/Agc	12/17	1	2	FACETS	0.936	0.869	1	0.936	0.869	1	CLONAL	1	TRUE	1	0.568337319882643	2		772	729	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35857117	35857117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	154	512	0	ENST00000303115.3:c.38C>T	p.Ser13Phe	p.S13F	ENST00000303115	NM_002185.3	13	tCt/tTt	1/8	1	2	FACETS	0.963	0.886	1	0.963	0.886	1	CLONAL	1	TRUE	1	0.568337319882643	2		512	563	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874636	35874636	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	185	554	0	ENST00000303115.3:c.792G>A	p.Trp264Ter	p.W264*	ENST00000303115	NM_002185.3	264	tgG/tgA	6/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.568337319882643	2		554	626	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673379	30673379	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1152	232	753	0	ENST00000376406.3:c.3581C>T	p.Ser1194Phe	p.S1194F	ENST00000376406	NM_014641.2	1194	tCc/tTc	10/15	0.55901730941188	4	FACETS	0.925	0.861	0.992	0.308	0.287	0.331	CLONAL	1	TRUE	1	0.568337319882643	4		753	1384	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124443	94124443	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	129	378	0	ENST00000369303.4:c.140G>A	p.Trp47Ter	p.W47*	ENST00000369303	NM_004440.3	47	tGg/tAg	2/17	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.568337319882643	2		378	448	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109319730	109319730	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	151	454	2	ENST00000436639.2:c.958G>A	p.Ala320Thr	p.A320T	ENST00000436639	NM_014454.2	320	Gca/Aca	5/10	1	2	FACETS	0.932	0.857	1	0.932	0.857	1	CLONAL	1	TRUE	1	0.568337319882643	2		456	570	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662453	117662453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	165	556	0	ENST00000368508.3:c.4924G>A	p.Glu1642Lys	p.E1642K	ENST00000368508	NM_002944.2	1642	Gaa/Aaa	30/43	1	2	FACETS	0.999	0.923	1	0.999	0.923	1	CLONAL	1	TRUE	1	0.568337319882643	2		556	581	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117730760	117730760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	127	440	0	ENST00000368508.3:c.274G>A	p.Glu92Lys	p.E92K	ENST00000368508	NM_002944.2	92	Gaa/Aaa	4/43	1	2	FACETS	0.859	0.783	0.94	0.859	0.783	0.94	CLONAL	1	TRUE	1	0.568337319882643	2		440	520	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117737457	117737457	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	95	336	0	ENST00000368508.3:c.192G>A	p.Trp64Ter	p.W64*	ENST00000368508	NM_002944.2	64	tgG/tgA	3/43	1	2	FACETS	0.866	0.777	0.959	0.866	0.777	0.959	CLONAL	1	TRUE	1	0.568337319882643	2		336	386	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162475133	162475133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	176	520	0	ENST00000366898.1:c.608G>A	p.Gly203Glu	p.G203E	ENST00000366898	NM_004562.2	203	gGg/gAg	5/12	1	2	FACETS	0.993	0.919	1	0.993	0.919	1	CLONAL	1	TRUE	1	0.568337319882643	2		520	624	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984153	2984153	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	144	592	0	ENST00000396946.4:c.377G>A	p.Gly126Asp	p.G126D	ENST00000396946	NM_032415.4	126	gGc/gAc	5/25	NA	2	FACETS	0.91	0.834	0.989			1	INDETERMINATE	1	TRUE	NA	0.568337319882643	2		592	557	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913355	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	131	369	0	ENST00000288602.6:c.1406G>A	p.Gly469Glu	p.G469E	ENST00000288602	NM_004333.4	469	gGa/gAa	11/18	1	2	FACETS	0.931	0.85	1	0.931	0.85	1	CLONAL	1	TRUE	1	0.568337319882643	2		369	495	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949697	151949697	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	196	569	0	ENST00000262189.6:c.1403C>T	p.Pro468Leu	p.P468L	ENST00000262189	NM_170606.2	468	cCc/cTc	10/59	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.568337319882643	2		569	682	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864641	56864641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	154	442	0	ENST00000519728.1:c.604C>T	p.Pro202Ser	p.P202S	ENST00000519728	NM_002350.3	202	Ccc/Tcc	7/13	0.568337319882643	3	FACETS	0.982	0.9	1	0.491	0.45	0.533	CLONAL	1	TRUE	1	0.568337319882643	3		442	709	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965481	68965481	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	193	563	0	ENST00000288368.4:c.1093G>A	p.Gly365Ser	p.G365S	ENST00000288368	NM_024870.2	365	Ggt/Agt	9/40	0.568337319882643	3	FACETS	1	0.935	1	0.505	0.468	0.544	CLONAL	1	TRUE	1	0.568337319882643	3		563	863	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981367	68981367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	197	356	0	ENST00000288368.4:c.1439C>T	p.Ser480Leu	p.S480L	ENST00000288368	NM_024870.2	480	tCa/tTa	12/40	0.568337319882643	3	FACETS	0.875	0.817	0.933	0.875	0.817	0.933	CLONAL	2	TRUE	1	0.568337319882643	3		356	509	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2077718	2077718	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199989401	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	184	599	1	ENST00000349721.2:c.2126C>T	p.Ser709Leu	p.S709L	ENST00000349721	NM_003070.3	709	tCg/tTg	14/34	1	2	FACETS	0.98	0.908	1	0.98	0.908	1	CLONAL	1	TRUE	1	0.568337319882643	2		600	661	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404630	8404630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs954240920	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	119	407	0	ENST00000356435.5:c.4117G>A	p.Glu1373Lys	p.E1373K	ENST00000356435		1373	Gaa/Aaa	25/35	1	2	FACETS	0.969	0.882	1	0.969	0.882	1	CLONAL	1	TRUE	1	0.568337319882643	2		407	432	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504362	8504362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	150	537	0	ENST00000356435.5:c.1721G>A	p.Gly574Glu	p.G574E	ENST00000356435		574	gGa/gAa	12/35	1	2	FACETS	0.99	0.911	1	0.99	0.911	1	CLONAL	1	TRUE	1	0.568337319882643	2		537	533	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	204	593	1	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.568337319882643	2		594	697	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390779	139390779	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771318379	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	258	796	0	ENST00000277541.6:c.7412C>T	p.Ser2471Leu	p.S2471L	ENST00000277541	NM_017617.3	2471	tCg/tTg	34/34	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.568337319882643	2		796	829	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399444	139399444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1333725995	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	221	714	0	ENST00000277541.6:c.4699G>A	p.Glu1567Lys	p.E1567K	ENST00000277541	NM_017617.3	1567	Gag/Aag	26/34	1	2	FACETS	0.998	0.932	1	0.998	0.932	1	CLONAL	1	TRUE	1	0.568337319882643	2		714	779	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814253	76814253	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060056-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	125	375	0	ENST00000373344.5:c.6391C>T	p.Arg2131Ter	p.R2131*	ENST00000373344	NM_000489.3	2131	Cga/Tga	29/35	1	2	FACETS	0.94	0.856	1	0.94	0.856	1	CLONAL	1	TRUE	1	0.568337319882643	2		375	468	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0060058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	322	536	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.683247102221547	5	FACETS	1	0.964	1	1	0.964	1	CLONAL	3	TRUE	2	0.683247102221547	5		536	628	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205228	NA	P-0060058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	268	750	0	ENST00000322088.6:c.536C>T	p.Pro179Leu	p.P179L	ENST00000322088	NM_014225.5	179	cCc/cTc	5/15	0.656837801764776	3	FACETS	0.953	0.904	1	0.953	0.904	1	CLONAL	2	TRUE	1	0.683247102221547	3		750	552	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059204	27059219	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCCCCCTCAATGAC	CAGCCCCCTCAATGAC	-	novel	NA	P-0060058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	188	482	0	ENST00000324856.7:c.1842_1857del	p.Ala615ProfsTer9	p.A615Pfs*9	ENST00000324856	NM_006015.4	614	tCAGCCCCCTCAATGACc/tc	4/20	0.656837801764776	3	FACETS	0.916	0.858	0.974	0.916	0.858	0.974	CLONAL	2	TRUE	1	0.683247102221547	3		482	403	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124633	108124633	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0060058-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	87	538	0	ENST00000278616.4:c.1991C>G	p.Thr664Ser	p.T664S	ENST00000278616	NM_000051.3	664	aCc/aGc	13/63	0.656837801764776	3	FACETS	0.957	0.854	1	0.479	0.427	0.533	CLONAL	1	TRUE	1	0.683247102221547	3		538	357	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0060059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	222	306	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.458424886864245	1	FACETS	0.979	0.915	1	0.979	0.915	1	CLONAL	1	TRUE	0	0.466525909116254	1		307	745	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288969	212288969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148791072	NA	P-0060059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	63	535	0	ENST00000342788.4:c.2777C>T	p.Thr926Met	p.T926M	ENST00000342788	NM_005235.2	926	aCg/aTg	23/28	1	2	FACETS	0.355	0.307	0.409	0.355	0.307	0.409	SUBCLONAL	1	TRUE	1	0.466525909116254	2		535	760	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729871	39729871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	180	622	0	ENST00000361337.2:c.1186C>T	p.Pro396Ser	p.P396S	ENST00000361337	NM_003286.2	396	Cct/Tct	13/21	0.466525909116254	3	FACETS	0.905	0.833	0.979	0.452	0.416	0.49	CLONAL	1	TRUE	1	0.466525909116254	3		622	1052	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120247	70120247	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886043831	NA	P-0060059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	246	723	0	ENST00000245479.2:c.1249C>T	p.Gln417Ter	p.Q417*	ENST00000245479	NM_000346.3	417	Cag/Tag	3/3	1	2	FACETS	0.98	0.916	1	0.98	0.916	1	CLONAL	1	TRUE	1	0.466525909116254	2		723	1076	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135300	2135300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745895675	NA	P-0060059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	213	541	0	ENST00000219476.3:c.4639G>A	p.Val1547Ile	p.V1547I	ENST00000219476	NM_000548.3	1547	Gtc/Atc	36/42	1	2	FACETS	0.981	0.912	1	0.981	0.912	1	CLONAL	1	TRUE	1	0.466525909116254	2		541	931	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166398	7166398	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767160876	NA	P-0060059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	62	594	0	ENST00000302850.5:c.1628C>T	p.Thr543Met	p.T543M	ENST00000302850	NM_000208.2	543	aCg/aTg	8/22	1	2	FACETS	0.301	0.259	0.346	0.301	0.259	0.346	SUBCLONAL	1	TRUE	1	0.466525909116254	2		594	884	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015660	27015660	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	231	612	0	ENST00000335756.4:c.247G>C	p.Asp83His	p.D83H	ENST00000335756	NM_001809.3	83	Gac/Cac	3/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.466525909116254	2		612	871	SUCCESS
APC	324	MSKCC	GRCh37	5	112175441	112175442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTAGCAGATGTACTTCTGTCAGTTCACTTGATAGTTTTGAGAGTCGTTCGATTGCC	novel	NA	P-0060059-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	81	522	0	ENST00000257430.4:c.4151_4206dup	p.Ser1403LeufsTer31	p.S1403Lfs*31	ENST00000257430	NM_000038.5	1384	ttt/tTTAGCAGATGTACTTCTGTCAGTTCACTTGATAGTTTTGAGAGTCGTTCGATTGCCtt	16/16	0.466525909116254	1	FACETS	0.332	0.292	0.376	0.332	0.292	0.376	SUBCLONAL	1	TRUE	0	0.466525909116254	1		522	801	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0060061-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	22	547	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	1	2	FACETS	0.266	0.206	0.337	0.266	0.206	0.337	SUBCLONAL	1	TRUE	1	0.361540993258066	2		547	457	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295230	1295230	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs796516131	NA	P-0060061-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	48	551	0				ENST00000310581	NM_198253.2	-/1132			0.176947933449055	4	FACETS	0.783	0.662	0.915	0.391	0.331	0.458	INDETERMINATE	1	TRUE	2	0.361540993258066	4		551	462	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427522	49427522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201283589	NA	P-0060061-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	40	641	1	ENST00000301067.7:c.10966C>T	p.Arg3656Cys	p.R3656C	ENST00000301067	NM_003482.3	3656	Cgc/Tgc	39/54	0.126345307073336	3	FACETS	0.436	0.362	0.52	0.218	0.181	0.26	INDETERMINATE	1	TRUE	1	0.361540993258066	3		642	599	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911920	94911920	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0060061-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	24	463	2	ENST00000536441.1:c.1010A>T	p.Asp337Val	p.D337V	ENST00000536441	NM_144665.3	337	gAc/gTc	7/10	0.286065276926075	3	FACETS	0.332	0.26	0.416	0.166	0.13	0.208	SUBCLONAL	1	TRUE	1	0.361540993258066	3		465	472	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0060062-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	75	209	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.559354601724121	4	FACETS	0.786	0.697	0.879	0.786	0.697	0.879	SUBCLONAL	2	TRUE	2	0.559354601724121	4		209	266	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508514	106508514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1406220505	NA	P-0060062-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	77	574	0	ENST00000359195.3:c.508G>A	p.Asp170Asn	p.D170N	ENST00000359195	NM_002649.2	170	Gac/Aac	2/11	0.506940262858726	4	FACETS	0.63	0.553	0.713	0.315	0.276	0.357	SUBCLONAL	1	TRUE	2	0.559354601724121	4		574	681	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762439	41762439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371618406	NA	P-0060062-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	159	724	0	ENST00000301178.4:c.2119C>T	p.Arg707Cys	p.R707C	ENST00000301178	NM_021913.4	707	Cgt/Tgt	18/20	0.552380600831555	4	FACETS	0.954	0.874	1	0.318	0.291	0.346	CLONAL	1	TRUE	1	0.559354601724121	4		724	929	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674240	86674240	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060062-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	251	480	0	ENST00000274376.6:c.2372C>T	p.Thr791Ile	p.T791I	ENST00000274376	NM_002890.2	791	aCa/aTa	18/25	0.559354601724121	4	FACETS	0.887	0.833	0.942	0.887	0.833	0.942	CLONAL	2	TRUE	2	0.559354601724121	4		480	789	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731140	162731140	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752360996	NA	P-0060062-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	357	769	0	ENST00000367921.3:c.995G>A	p.Arg332Gln	p.R332Q	ENST00000367921	NM_006182.2	332	cGg/cAg	9/18	0.559354601724121	6	FACETS	0.979	0.927	1	0.49	0.463	0.517	CLONAL	2	TRUE	2	0.559354601724121	6		769	1381	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880219	37880227	+	inframe_deletion	In_Frame_Del	DEL	TTGAGGGAA	TTGAGGGAA	-	novel	NA	P-0060062-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	341	591	0	ENST00000269571.5:c.2263_2271del	p.Leu755_Glu757del	p.L755_E757del	ENST00000269571		755	TTGAGGGAA/-	19/27	0.559354601724121	3	FACETS	0.986	0.939	1	0.986	0.939	1	CLONAL	2	TRUE	1	0.559354601724121	3		591	791	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268144	153268144	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs920052554	NA	P-0060063-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	511	587	0	ENST00000281708.4:c.664C>T	p.Arg222Ter	p.R222*	ENST00000281708	NM_033632.3	222	Cga/Tga	4/12	0.679702461612195	3	FACETS	0.999	0.973	1	0.999	0.973	1	CLONAL	3	TRUE	0	0.681210626962963	3		587	671	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0060063-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	298	483	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.669720483538524	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.681210626962963	2		483	430	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573545	48573545	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060063-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	276	509	0	ENST00000342988.3:c.129G>T	p.Leu43Phe	p.L43F	ENST00000342988	NM_005359.5	43	ttG/ttT	2/12	0.680759024640686	2	FACETS	0.965	0.924	1	0.965	0.924	1	CLONAL	2	TRUE	0	0.681210626962963	2		509	420	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228979	36228979	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555734923	NA	P-0060063-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	449	659	0	ENST00000222270.7:c.7759C>T	p.Arg2587Ter	p.R2587*	ENST00000222270	NM_014727.1	2587	Cga/Tga	36/37	0.593296534133462	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.681210626962963	4		659	1082	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220070	36220070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0060063-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	185	535	0	ENST00000222270.7:c.4790G>A	p.Arg1597Gln	p.R1597Q	ENST00000222270	NM_014727.1	1597	cGg/cAg	22/37	0.593296534133462	4	FACETS	0.882	0.814	0.953	0.441	0.407	0.477	CLONAL	1	TRUE	2	0.681210626962963	4		535	1035	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359677	40359677	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0060063-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	452	437	0	ENST00000293328.3:c.1976G>A	p.Arg659His	p.R659H	ENST00000293328	NM_012448.3	659	cGc/cAc	16/19	0.681210626962963	4	FACETS	0.986	0.951	1	0.986	0.951	1	CLONAL	3	TRUE	1	0.681210626962963	4		437	754	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1941429	1941429	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1418871757	NA	P-0060063-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	185	447	0	ENST00000382891.5:c.1805G>A	p.Arg602Gln	p.R602Q	ENST00000382891	NM_133335.3	602	cGg/cAg	9/22	0.679702461612195	3	FACETS	1	0.976	1	0.374	0.347	0.402	CLONAL	1	TRUE	0	0.681210626962963	3		447	649	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163913	152163913	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0060063-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	256	477	0	ENST00000206249.3:c.634A>C	p.Ser212Arg	p.S212R	ENST00000206249	NM_000125.3	212	Agt/Cgt	2/8	0.55711149472216	4	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	2	0.681210626962963	4		477	630	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971115	21971133	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTCGGGTGAGAGTGGCG	GGGTCGGGTGAGAGTGGCG	-	rs730881674	NA	P-0060064-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	68	752	0	ENST00000304494.5:c.225_243del	p.Ala76CysfsTer64	p.A76Cfs*64	ENST00000304494	NM_000077.4	75	ccCGCCACTCTCACCCGACCC/cc	2/3	0.263072309017551	1	FACETS	0.653	0.567	0.745	0.653	0.567	0.745	SUBCLONAL	1	TRUE	0	0.263072309017551	1		752	688	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782620	NA	P-0060064-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	156	746	0	ENST00000269305.4:c.427G>A	p.Val143Met	p.V143M	ENST00000269305	NM_001126112.2	143	Gtg/Atg	5/11	0.263072309017551	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.263072309017551	1		746	786	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73113184	73113184	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0060064-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	27	402	0	ENST00000356692.5:c.525G>T	p.Arg175Ser	p.R175S	ENST00000356692		175	agG/agT	7/9	1	2	FACETS	0.492	0.391	0.608	0.492	0.391	0.608	SUBCLONAL	1	TRUE	1	0.263072309017551	2		402	417	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918337	44918337	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060064-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	39	245	0	ENST00000377967.4:c.962G>A	p.Trp321Ter	p.W321*	ENST00000377967	NM_021140.2	321	tGg/tAg	11/29	0.159455082626965	0	FACETS	1	0.936	1			1	CLONAL	1	TRUE	NA	0.263072309017551	0		245	175	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0060065-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	23	515	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.46	0.356	0.58	0.46	0.356	0.58	SUBCLONAL	1	TRUE	1	0.13	2		515	770	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0060065-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	14	174	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	0.457	0.329	0.614	0.457	0.329	0.614	SUBCLONAL	1	TRUE	1	0.13	2		174	471	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845593	68845604	+	inframe_deletion	In_Frame_Del	DEL	CTGTGATGGAGG	CTGTGATGGAGG	-	novel	NA	P-0060065-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	50	442	0	ENST00000261769.5:c.839_850del	p.Ser280_Val284delinsPhe	p.S280_V284delinsF	ENST00000261769	NM_004360.3	280	tCTGTGATGGAGGtc/ttc	7/16	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.13	2		442	667	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530162	63530162	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0060065-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	40	475	0	ENST00000307078.5:c.2273C>G	p.Ala758Gly	p.A758G	ENST00000307078	NM_004655.3	758	gCg/gGg	10/11	1	2	FACETS	0.824	0.683	0.982	0.824	0.683	0.982	CLONAL	1	TRUE	1	0.13	2		475	747	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120336	70120337	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0060065-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	49	639	0	ENST00000245479.2:c.1340dup	p.Asn447LysfsTer131	p.N447Kfs*131	ENST00000245479	NM_000346.3	446	-/A	3/3	1	2	FACETS	0.902	0.762	1	0.902	0.762	1	CLONAL	1	TRUE	1	0.13	2		639	836	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0002413-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	66	253	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.777	0.678	0.884	0.777	0.678	0.884	SUBCLONAL	1	TRUE	1	0.441125154195033	2		253	385	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0002413-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	118	391	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.441125154195033	2		391	531	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0002413-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	398	245	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.441125154195033	3	FACETS	0.933	0.888	0.979	0.933	0.888	0.979	CLONAL	2	TRUE	1	0.441125154195033	3		245	1180	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0002413-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	220	444	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.441125154195033	2		444	932	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160588	56160588	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002413-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	179	287	0	ENST00000399503.3:c.862C>T	p.Arg288Ter	p.R288*	ENST00000399503	NM_005921.1	288	Cga/Tga	4/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.441125154195033	2		287	692	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120185	70120185	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002413-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	286	194	0	ENST00000245479.2:c.1187A>T	p.His396Leu	p.H396L	ENST00000245479	NM_000346.3	396	cAc/cTc	3/3	0.437214259629911	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	TRUE	0	0.441125154195033	3		194	508	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120196	70120196	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002413-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	297	213	0	ENST00000245479.2:c.1198G>T	p.Glu400Ter	p.E400*	ENST00000245479	NM_000346.3	400	Gag/Tag	3/3	0.437214259629911	3	FACETS	0.992	0.946	1	0.992	0.946	1	CLONAL	3	TRUE	0	0.441125154195033	3		213	552	SUCCESS
APC	324	MSKCC	GRCh37	5	112173603	112173603	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs878853426	NA	P-0002413-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	198	388	0	ENST00000257430.4:c.2314del	p.Thr772LeufsTer5	p.T772Lfs*5	ENST00000257430	NM_000038.5	771	gAa/ga	16/16	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.441125154195033	2		388	804	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0003848-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	434	738	0				ENST00000310581	NM_198253.2	-/1132			0.666070119685336	3	FACETS	0.997	0.957	1	0.997	0.957	1	CLONAL	2	TRUE	1	0.666070119685336	3		738	871	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0003848-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	471	885	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.666070119685336	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.666070119685336	1		885	736	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631934	90631934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913502	NA	P-0003848-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	25	507	0	ENST00000330062.3:c.419G>A	p.Arg140Gln	p.R140Q	ENST00000330062	NM_002168.2	140	cGg/cAg	4/11	0.379678334415591	1	FACETS	0.071	0.055	0.089	0.071	0.055	0.089	INDETERMINATE	1	TRUE	0	0.666070119685336	1		507	706	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5073770	5073770	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs77375493	NA	P-0003848-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	37	277	1	ENST00000381652.3:c.1849G>T	p.Val617Phe	p.V617F	ENST00000381652	NM_004972.3	617	Gtc/Ttc	14/25	0.666070119685336	1	FACETS	0.268	0.221	0.319	0.268	0.221	0.319	SUBCLONAL	1	TRUE	0	0.666070119685336	1		278	277	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732959	74732959	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs751713049	NA	P-0003848-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	20	434	0	ENST00000359995.5:c.284C>A	p.Pro95His	p.P95H	ENST00000359995	NM_001195427.1	95	cCc/cAc	1/3	0.379678334415591	1	FACETS	0.061	0.046	0.079	0.061	0.046	0.079	INDETERMINATE	1	TRUE	0	0.666070119685336	1		434	652	SUCCESS
ATM	472	MSKCC	GRCh37	11	108183190	108183191	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003848-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	156	262	0	ENST00000278616.4:c.5977dup	p.Ser1993LysfsTer2	p.S1993Kfs*2	ENST00000278616	NM_000051.3	1991	gaa/gAaa	40/63	0.666070119685336	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.666070119685336	1		262	275	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970905	21970905	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003848-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	272	438	0	ENST00000304494.5:c.453del	p.Ser152GlnfsTer41	p.S152Qfs*41	ENST00000304494	NM_000077.4	151	ccC/cc	2/3	0.666070119685336	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.666070119685336	1		438	520	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984410	201984415	+	inframe_deletion	In_Frame_Del	DEL	AGCGGC	AGCGGC	-	novel	NA	P-0003848-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	70	388	0	ENST00000359651.3:c.1075_1080del	p.Ser359_Gly360del	p.S359_G360del	ENST00000359651		359	AGCGGC/-	8/8	1	2	FACETS	0.271	0.236	0.31	0.271	0.236	0.31	SUBCLONAL	1	TRUE	1	0.666070119685336	2		388	775	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982748	7982748	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003848-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	255	430	0	ENST00000319144.4:c.1037G>C	p.Gly346Ala	p.G346A	ENST00000319144	NM_001139.2	346	gGa/gCa	8/15	0.666070119685336	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.666070119685336	1		430	467	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922797	44922798	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0003848-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	282	432	0	ENST00000377967.4:c.1662_1663del	p.Gln555AlafsTer25	p.Q555Afs*25	ENST00000377967	NM_021140.2	553	gTC/g	16/29	0.569935794413701	1	FACETS	0.984	0.934	1	0.984	0.934	1	CLONAL	1	TRUE	0	0.666070119685336	1		432	574	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211886	123211886	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003848-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	175	523	0	ENST00000218089.9:c.2755del	p.Ile920PhefsTer11	p.I920Ffs*11	ENST00000218089	NM_001042749.1	918	aCc/ac	27/35	0.569935794413701	1	FACETS	0.857	0.799	0.915	0.857	0.799	0.915	CLONAL	1	TRUE	0	0.666070119685336	1		523	409	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0004249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	289	366	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.208687906079279	1	FACETS	0.66	0.624	0.697	0.66	0.624	0.697	INDETERMINATE	1	TRUE	0	0.728755353174405	1		366	764	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276788	15276788	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	268	403	0	ENST00000263388.2:c.5477G>T	p.Cys1826Phe	p.C1826F	ENST00000263388	NM_000435.2	1826	tGc/tTc	30/33	0.666820028682809	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.728755353174405	1		403	430	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873695	35873695	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	235	393	0	ENST00000303115.3:c.651G>C	p.Trp217Cys	p.W217C	ENST00000303115	NM_002185.3	217	tgG/tgC	5/8	1	2	FACETS	0.977	0.917	1	0.977	0.917	1	CLONAL	1	TRUE	1	0.728755353174405	2		393	660	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604494	43604494	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762472027	NA	P-0004249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	212	408	0	ENST00000355710.3:c.1079G>A	p.Arg360Gln	p.R360Q	ENST00000355710	NM_020975.4	360	cGg/cAg	6/20	NA	2	FACETS	0.97	0.907	1			1	INDETERMINATE	1	TRUE	NA	0.728755353174405	2		408	600	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94163109	94163109	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	374	486	0	ENST00000323929.3:c.2038G>A	p.Val680Ile	p.V680I	ENST00000323929	NM_005591.3	680	Gta/Ata	19/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.728755353174405	2		486	938	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18762517	18762517	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	256	436	0	ENST00000266497.5:c.4013A>G	p.Tyr1338Cys	p.Y1338C	ENST00000266497		1338	tAc/tGc	29/31	0.208687906079279	1	FACETS	0.63	0.593	0.668	0.63	0.593	0.668	INDETERMINATE	1	TRUE	0	0.728755353174405	1		436	709	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589808	28589808	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568745490	NA	P-0004249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	236	430	0	ENST00000241453.7:c.2572G>A	p.Glu858Lys	p.E858K	ENST00000241453	NM_004119.2	858	Gaa/Aaa	21/24	0.717603703402237	3	FACETS	0.958	0.896	1	0.479	0.448	0.512	CLONAL	1	TRUE	1	0.728755353174405	3		430	922	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586250	48586250	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	280	340	0	ENST00000342988.3:c.919G>T	p.Glu307Ter	p.E307*	ENST00000342988	NM_005359.5	307	Gag/Tag	8/12	0.728755353174405	1	FACETS	0.987	0.94	1	0.987	0.94	1	CLONAL	1	TRUE	0	0.728755353174405	1		340	495	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115421	115115422	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTTTTGCAAAAGGGTTGTTGTCTATTTTTAACTGGGTTAT	novel	NA	P-0004249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	151	483	0	ENST00000257566.3:c.865_904dup	p.Gly302AspfsTer38	p.G302Dfs*38	ENST00000257566	NM_016569.3	302	ggt/gATAACCCAGTTAAAAATAGACAACAACCCTTTTGCAAAAGgt	5/8	1	2	FACETS	0.358	0.326	0.391	0.358	0.326	0.391	SUBCLONAL	1	TRUE	1	0.728755353174405	2		483	1158	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578220	7578221	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TTCTGTCATCCAAATACTCCACACG	novel	NA	P-0004249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	267	476	0	ENST00000269305.4:c.604_628dup	p.Asn210ThrfsTer7	p.N210Tfs*7	ENST00000269305	NM_001126112.2	210	aac/aCGTGTGGAGTATTTGGATGACAGAAac	6/11	0.727219901520525	1	FACETS	0.64	0.603	0.677	0.64	0.603	0.677	SUBCLONAL	1	TRUE	0	0.728755353174405	1		476	728	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	69	391	2	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	0.198125352532023	0	FACETS	1	0.932	1			1	CLONAL	2	FALSE	0	0.197613429580887	0		393	258	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	125	544	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.198125352532023	1	FACETS	0.886	0.808	0.966	1	0.992	1	CLONAL	3	FALSE	0	0.197613429580887	1		548	429	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	134	516	0	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	1	0.964	1	1	0.993	1	CLONAL	3	FALSE	1	0.197613429580887	2		516	414	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	211	372	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	1	2	FACETS	0.9	0.838	0.964	1	0.995	1	CLONAL	3	FALSE	1	0.197613429580887	2		372	791	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	144	505	5	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	NA	2	FACETS	0.915	0.839	0.993			1	INDETERMINATE	3	FALSE	NA	0.197613429580887	2		510	531	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497346	149497346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs75748462	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	141	495	0	ENST00000261799.4:c.2972G>A	p.Arg991His	p.R991H	ENST00000261799	NM_002609.3	991	cGc/cAc	22/23	1	2	FACETS	1	0.976	1	1	0.992	1	CLONAL	2	FALSE	1	0.197613429580887	2		495	600	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419930	41419930	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	119	609	0	ENST00000373198.4:c.391del	p.Gln131LysfsTer17	p.Q131Kfs*17	ENST00000373198	NM_133170.3	131	Caa/aa	3/32	0.198125352532023	0	FACETS	0.972	0.882	1			1	CLONAL	2	FALSE	0	0.197613429580887	0		609	497	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	183	614	1	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	1	2	FACETS	0.986	0.915	1	1	0.994	1	CLONAL	3	FALSE	1	0.197613429580887	2		615	626	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216560	2216560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777525091	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	245	625	0	ENST00000398665.3:c.2204C>T	p.Thr735Met	p.T735M	ENST00000398665	NM_032482.2	735	aCg/aTg	20/28	0.198125352532023	0	FACETS	0.821	0.781	0.86			1	CLONAL	6	FALSE	0	0.197613429580887	0		625	404	SUCCESS
APC	324	MSKCC	GRCh37	5	112175166	112175166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371113837	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	112	300	0	ENST00000257430.4:c.3875C>T	p.Thr1292Met	p.T1292M	ENST00000257430	NM_000038.5	1292	aCg/aTg	16/16	1	2	FACETS	0.915	0.829	1	1	0.991	1	CLONAL	3	FALSE	1	0.197613429580887	2		300	413	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857935	89857935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11646374	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	125	493	0	ENST00000389301.3:c.1235C>T	p.Ala412Val	p.A412V	ENST00000389301	NM_000135.2	412	gCg/gTg	14/43	0.198125352532023	1	FACETS	0.854	0.779	0.932	1	0.991	1	CLONAL	3	FALSE	0	0.197613429580887	1		493	445	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923252	78923252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	65	561	2	ENST00000306801.3:c.3275C>T	p.Ala1092Val	p.A1092V	ENST00000306801	NM_020761.2	1092	gCc/gTc	28/34	0.196316789548606	0	FACETS	0.863	0.754	0.978			1	CLONAL	2	FALSE	0	0.197613429580887	0		563	306	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	60	453	0	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	1	0.934	1	1	0.981	1	CLONAL	2	FALSE	1	0.197613429580887	2		453	271	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440943	56440943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786205215	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	159	572	0	ENST00000407977.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000407977		132	Cga/Tga	4/10	0.198125352532023	1	FACETS	1	0.982	1	1	0.993	1	CLONAL	2	FALSE	0	0.197613429580887	1		572	592	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346884	73346884	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	347	537	3	ENST00000377767.4:c.1333del	p.Ser445HisfsTer20	p.S445Hfs*20	ENST00000377767	NM_014953.3	445	Tca/ca	9/21	0.197613429580887	6	FACETS	1	0.983	1	1	0.994	1	CLONAL	5	FALSE	2	0.197613429580887	6		540	912	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	121	610	1	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	0.198125352532023	1	FACETS	1	0.967	1	1	0.99	1	CLONAL	2	FALSE	0	0.197613429580887	1		611	485	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37061889	37061889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793519	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	150	590	2	ENST00000231790.2:c.973C>T	p.Arg325Trp	p.R325W	ENST00000231790	NM_000249.3	325	Cgg/Tgg	11/19	1	2	FACETS	1	0.982	1	1	0.993	1	CLONAL	2	FALSE	1	0.197613429580887	2		592	608	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446284	70446284	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	151	669	6	ENST00000373644.4:c.5230del	p.Arg1744GlufsTer18	p.R1744Efs*18	ENST00000373644	NM_030625.2	1742	Aaa/aa	11/12	0.197613429580887	1	FACETS	1	0.927	1	1	0.991	1	CLONAL	2	FALSE	0	0.197613429580887	1		675	680	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274794	123274794	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913478	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	143	496	0	ENST00000358487.5:c.1124A>G	p.Tyr375Cys	p.Y375C	ENST00000358487	NM_000141.4	375	tAc/tGc	9/18	0.197613429580887	1	FACETS	1	0.977	1	1	0.992	1	CLONAL	2	FALSE	0	0.197613429580887	1		496	548	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794441	42794441	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	104	617	2	ENST00000575354.2:c.1526del	p.Pro509HisfsTer14	p.P509Hfs*14	ENST00000575354	NM_015125.3	507	cgC/cg	10/20	0.198125352532023	1	FACETS	1	0.95	1	1	0.989	1	CLONAL	2	FALSE	0	0.197613429580887	1		619	436	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106194030	106194030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1298652864	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	213	552	0	ENST00000380013.4:c.4492C>T	p.Arg1498Cys	p.R1498C	ENST00000380013	NM_001127208.2	1498	Cgt/Tgt	10/11	1	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	2	FALSE	1	0.197613429580887	2		552	896	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	43	317	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	NA	2	FACETS	1	0.917	1			1	INDETERMINATE	3	FALSE	NA	0.197613429580887	2		317	131	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157488293	157488293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750810656	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	151	337	0	ENST00000346085.5:c.2999C>T	p.Ala1000Val	p.A1000V	ENST00000346085	NM_020732.3	1000	gCg/gTg	10/20	1	2	FACETS	1	0.934	1	1	0.993	1	CLONAL	3	FALSE	1	0.197613429580887	2		337	501	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796882	42796883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761345552	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	102	525	6	ENST00000575354.2:c.3347dup	p.Ser1117LysfsTer34	p.S1117Kfs*34	ENST00000575354	NM_015125.3	1114	gcc/gCcc	14/20	0.198125352532023	1	FACETS	1	0.951	1	1	0.988	1	CLONAL	2	FALSE	0	0.197613429580887	1		531	425	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777635	9777635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773473376	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	103	497	0	ENST00000377346.4:c.971G>A	p.Arg324His	p.R324H	ENST00000377346	NM_005026.3	324	cGc/cAc	8/24	0.198125352532023	0	FACETS	0.934	0.84	1			1	CLONAL	2	FALSE	0	0.197613429580887	0		497	448	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105938	27105938	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs750044693	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	98	371	0	ENST00000324856.7:c.5549A>G	p.Asp1850Gly	p.D1850G	ENST00000324856	NM_006015.4	1850	gAc/gGc	20/20	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	2	FALSE	NA	0.197613429580887	2		371	420	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945758	206945758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	118	393	0	ENST00000423557.1:c.23G>A	p.Cys8Tyr	p.C8Y	ENST00000423557	NM_000572.2	8	tGt/tAt	1/5	1	2	FACETS	1	0.966	1	1	0.99	1	CLONAL	2	FALSE	1	0.197613429580887	2		393	522	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989523	212989523	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	186	653	0	ENST00000342788.4:c.188T>C	p.Leu63Pro	p.L63P	ENST00000342788	NM_005235.2	63	cTg/cCg	2/28	1	2	FACETS	0.869	0.805	0.935	1	0.994	1	CLONAL	3	FALSE	1	0.197613429580887	2		653	722	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928301	178928301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	135	499	0	ENST00000263967.3:c.1487C>T	p.Ala496Val	p.A496V	ENST00000263967	NM_006218.2	496	gCc/gTc	9/21	1	2	FACETS	1	0.939	1	1	0.991	1	CLONAL	2	FALSE	1	0.197613429580887	2		499	658	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430444	181430444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	150	614	0	ENST00000325404.1:c.296C>T	p.Ala99Val	p.A99V	ENST00000325404	NM_003106.3	99	gCg/gTg	1/1	1	2	FACETS	0.852	0.782	0.924	1	0.993	1	CLONAL	3	FALSE	1	0.197613429580887	2		614	594	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1266594	1266594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	112	589	0	ENST00000310581.5:c.2639C>T	p.Ala880Val	p.A880V	ENST00000310581	NM_198253.2	880	gCg/gTg	10/16	0.198125352532023	0	FACETS	0.775	0.703	0.85			1	SUBCLONAL	3	FALSE	0	0.197613429580887	0		589	391	SUCCESS
APC	324	MSKCC	GRCh37	5	112128203	112128203	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554074786	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	218	584	1	ENST00000257430.4:c.706C>T	p.Gln236Ter	p.Q236*	ENST00000257430	NM_000038.5	236	Cag/Tag	7/16	1	2	FACETS	0.872	0.813	0.934	1	0.995	1	CLONAL	3	FALSE	1	0.197613429580887	2		585	843	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401501	401501	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771669183	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	71	460	0	ENST00000380956.4:c.823C>T	p.Arg275Trp	p.R275W	ENST00000380956	NM_001195286.1	275	Cgg/Tgg	7/9	NA	2	FACETS	0.984	0.864	1			1	INDETERMINATE	2	FALSE	NA	0.197613429580887	2		460	365	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158714	26158714	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	53	104	0	ENST00000289316.2:c.317A>G	p.Glu106Gly	p.E106G	ENST00000289316	NM_138720.2	106	gAg/gGg	1/2	0.197613429580887	5	FACETS	0.999	0.862	1	0.999	0.862	1	CLONAL	3	FALSE	2	0.197613429580887	5		104	232	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710608	117710608	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	216	570	0	ENST00000368508.3:c.1664A>G	p.His555Arg	p.H555R	ENST00000368508	NM_002944.2	555	cAc/cGc	12/43	NA	2	FACETS	0.922	0.86	0.987			1	INDETERMINATE	3	FALSE	NA	0.197613429580887	2		570	790	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873383	151873383	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	167	576	0	ENST00000262189.6:c.9155C>T	p.Pro3052Leu	p.P3052L	ENST00000262189	NM_170606.2	3052	cCt/cTt	38/59	0.197613429580887	1	FACETS	1	0.983	1	1	0.993	1	CLONAL	2	FALSE	0	0.197613429580887	1		576	617	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371972	55371972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	54	207	0	ENST00000297316.4:c.662C>T	p.Thr221Met	p.T221M	ENST00000297316	NM_022454.3	221	aCg/aTg	2/2	1	2	FACETS	0.836	0.723	0.956	1	0.981	1	CLONAL	3	FALSE	1	0.197613429580887	2		207	218	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570292	87570292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463968979	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	130	489	0	ENST00000277120.3:c.2032G>A	p.Ala678Thr	p.A678T	ENST00000277120		678	Gcg/Acg	17/19	0.198125352532023	1	FACETS	1	0.975	1	1	0.991	1	CLONAL	2	FALSE	0	0.197613429580887	1		489	499	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760520	133760520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1240583398	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	76	528	0	ENST00000318560.5:c.2843C>T	p.Pro948Leu	p.P948L	ENST00000318560	NM_005157.4	948	cCc/cTc	11/11	0.198125352532023	0	FACETS	1	0.915	1			1	CLONAL	2	FALSE	0	0.197613429580887	0		528	297	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771818	135771818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	183	692	0	ENST00000298552.3:c.3299G>A	p.Ser1100Asn	p.S1100N	ENST00000298552	NM_001162426.1	1100	aGc/aAc	23/23	0.198125352532023	0	FACETS	0.83	0.77	0.891			1	CLONAL	3	FALSE	0	0.197613429580887	0		692	597	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925366	114925366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	168	693	0	ENST00000543371.1:c.1444C>A	p.Pro482Thr	p.P482T	ENST00000543371	NM_001198531.1	482	Cca/Aca	14/14	0.197613429580887	1	FACETS	1	0.983	1	1	0.993	1	CLONAL	2	FALSE	0	0.197613429580887	1		693	627	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575134	64575134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057521110	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	100	467	0	ENST00000312049.6:c.673G>A	p.Gly225Arg	p.G225R	ENST00000312049	NM_130799.2	225	Gga/Aga	4/10	1	2	FACETS	1	0.973	1	1	0.989	1	CLONAL	2	FALSE	1	0.197613429580887	2		467	405	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77064603	77064603	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767363828	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	154	578	0	ENST00000356341.3:c.814C>T	p.Arg272Trp	p.R272W	ENST00000356341	NM_002576.4	272	Cgg/Tgg	8/15	1	2	FACETS	0.854	0.785	0.926	1	0.993	1	CLONAL	3	FALSE	1	0.197613429580887	2		578	608	SUCCESS
EED	8726	MSKCC	GRCh37	11	85961377	85961377	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772993565	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	171	485	0	ENST00000263360.6:c.154C>T	p.Arg52Cys	p.R52C	ENST00000263360	NM_003797.3	52	Cgc/Tgc	2/12	1	2	FACETS	1	0.968	1	1	0.993	1	CLONAL	2	FALSE	1	0.197613429580887	2		485	791	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195289	102195289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs186307109	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	268	813	1	ENST00000263464.3:c.49G>A	p.Ala17Thr	p.A17T	ENST00000263464	NM_001165.4	17	Gcc/Acc	2/9	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	FALSE	1	0.197613429580887	2		814	1100	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195395	102195395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762397304	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	238	765	0	ENST00000263464.3:c.155G>A	p.Arg52His	p.R52H	ENST00000263464	NM_001165.4	52	cGt/cAt	2/9	1	2	FACETS	0.88	0.823	0.939	1	0.995	1	CLONAL	3	FALSE	1	0.197613429580887	2		765	912	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445338	49445338	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	107	374	1	ENST00000301067.7:c.2128C>A	p.Pro710Thr	p.P710T	ENST00000301067	NM_003482.3	710	Cca/Aca	10/54	1	2	FACETS	0.942	0.853	1	1	0.991	1	CLONAL	3	FALSE	1	0.197613429580887	2		375	383	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987168	36987168	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1160967358	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	70	287	0	ENST00000354822.5:c.521G>A	p.Gly174Asp	p.G174D	ENST00000354822	NM_001079668.2	174	gGc/gAc	3/3	1	2	FACETS	0.898	0.792	1	1	0.985	1	CLONAL	3	FALSE	1	0.197613429580887	2		287	263	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243083	105243083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1396308032	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	107	599	0	ENST00000349310.3:c.200G>A	p.Arg67Gln	p.R67Q	ENST00000349310	NM_001014432.1	67	cGg/cAg	5/15	0.198125352532023	1	FACETS	0.954	0.865	1	1	0.991	1	CLONAL	3	FALSE	0	0.197613429580887	1		599	341	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988331	41988331	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139403711	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	216	819	0	ENST00000219905.7:c.1123G>A	p.Gly375Arg	p.G375R	ENST00000219905	NM_001164273.1	375	Gga/Aga	3/24	0.198125352532023	0	FACETS	1	0.975	1			1	CLONAL	2	FALSE	0	0.197613429580887	0		819	800	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026059	14026059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753728949	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	142	372	0	ENST00000311895.7:c.1019G>A	p.Arg340Gln	p.R340Q	ENST00000311895	NM_005236.2	340	cGa/cAa	6/11	0.196316789548606	0	FACETS	1	0.935	1			1	CLONAL	2	FALSE	0	0.197613429580887	0		372	563	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865783	56865783	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148421556	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	228	744	3	ENST00000308159.5:c.1115G>A	p.Arg372Gln	p.R372Q	ENST00000308159	NM_014669.4	372	cGg/cAg	11/22	0.196316789548606	0	FACETS	0.77	0.719	0.821			1	SUBCLONAL	3	FALSE	0	0.197613429580887	0		747	802	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992222	72992222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	129	754	0	ENST00000268489.5:c.1823G>A	p.Ser608Asn	p.S608N	ENST00000268489	NM_006885.3	608	aGc/aAc	2/10	0.196316789548606	0	FACETS	0.935	0.852	1			1	CLONAL	2	FALSE	0	0.197613429580887	0		754	560	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969933	81969933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752209691	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	165	718	3	ENST00000359376.3:c.3002G>A	p.Arg1001His	p.R1001H	ENST00000359376	NM_002661.3	1001	cGc/cAc	27/33	0.198125352532023	0	FACETS	0.748	0.69	0.808			1	SUBCLONAL	3	FALSE	0	0.197613429580887	0		721	597	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89839744	89839744	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs965355095	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	159	658	1	ENST00000389301.3:c.1949T>C	p.Leu650Pro	p.L650P	ENST00000389301	NM_000135.2	650	cTg/cCg	22/43	0.198125352532023	1	FACETS	1	0.978	1	1	0.993	1	CLONAL	2	FALSE	0	0.197613429580887	1		659	618	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489825	40489825	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	202	654	1	ENST00000264657.5:c.601C>T	p.Gln201Ter	p.Q201*	ENST00000264657	NM_139276.2	201	Cag/Tag	7/24	0.198125352532023	1	FACETS	1	0.977	1	1	0.994	1	CLONAL	2	FALSE	0	0.197613429580887	1		655	822	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435828	56435828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs995358248	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	133	443	0	ENST00000407977.2:c.1309C>T	p.Arg437Trp	p.R437W	ENST00000407977		437	Cgg/Tgg	9/10	0.198125352532023	1	FACETS	0.947	0.868	1	1	0.992	1	CLONAL	3	FALSE	0	0.197613429580887	1		443	427	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216740	2216740	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285057389	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	138	355	0	ENST00000398665.3:c.2384C>T	p.Pro795Leu	p.P795L	ENST00000398665	NM_032482.2	795	cCg/cTg	20/28	0.198125352532023	0	FACETS	0.966	0.903	1			1	CLONAL	5	FALSE	0	0.197613429580887	0		355	232	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245810	5245810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	147	551	0	ENST00000357368.4:c.965C>T	p.Ala322Val	p.A322V	ENST00000357368	NM_002850.3	322	gCg/gTg	10/38	0.198125352532023	0	FACETS	0.963	0.895	1			1	CLONAL	4	FALSE	0	0.197613429580887	0		551	310	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125379	7125379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778982272	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	245	758	1	ENST00000302850.5:c.3173C>T	p.Thr1058Met	p.T1058M	ENST00000302850	NM_000208.2	1058	aCg/aTg	17/22	0.198125352532023	0	FACETS	0.867	0.822	0.912			1	CLONAL	5	FALSE	0	0.197613429580887	0		759	459	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291058	10291058	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	87	427	0	ENST00000340748.4:c.413C>T	p.Pro138Leu	p.P138L	ENST00000340748		138	cCc/cTc	4/40	0.198125352532023	0	FACETS	0.95	0.847	1			1	CLONAL	2	FALSE	0	0.197613429580887	0		427	372	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279645	18279645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	130	536	2	ENST00000222254.8:c.1918C>T	p.Arg640Trp	p.R640W	ENST00000222254	NM_005027.3	640	Cgg/Tgg	15/16	0.198125352532023	1	FACETS	1	0.953	1	1	0.991	1	CLONAL	2	FALSE	0	0.197613429580887	1		538	554	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793502	42793502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755293924	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	147	641	1	ENST00000575354.2:c.1304C>T	p.Thr435Met	p.T435M	ENST00000575354	NM_015125.3	435	aCg/aTg	8/20	0.198125352532023	1	FACETS	0.855	0.785	0.927	1	0.993	1	CLONAL	3	FALSE	0	0.197613429580887	1		642	523	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855573	45855573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746618110	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	86	562	3	ENST00000391945.4:c.2084G>A	p.Arg695His	p.R695H	ENST00000391945	NM_000400.3	695	cGc/cAc	22/23	0.198125352532023	1	FACETS	1	0.936	1	1	0.986	1	CLONAL	2	FALSE	0	0.197613429580887	1		565	366	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909524	50909524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	175	712	0	ENST00000440232.2:c.1328G>A	p.Arg443Gln	p.R443Q	ENST00000440232	NM_002691.3	443	cGg/cAg	11/27	0.198125352532023	0	FACETS	0.869	0.806	0.934			1	CLONAL	3	FALSE	0	0.197613429580887	0		712	545	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017802	31017802	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780662350	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	115	593	0	ENST00000375687.4:c.664G>A	p.Glu222Lys	p.E222K	ENST00000375687	NM_015338.5	222	Gag/Aag	8/13	1	2	FACETS	0.836	0.758	0.918	1	0.991	1	CLONAL	3	FALSE	1	0.197613429580887	2		593	464	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650388	48650388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	150	382	0	ENST00000376670.3:c.358G>A	p.Ala120Thr	p.A120T	ENST00000376670	NM_002049.3	120	Gcc/Acc	3/6	0.198125352532023	0	FACETS	0.892	0.834	0.95			1	CLONAL	5	FALSE	NA	0.197613429580887	0		382	273	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123499636	123499636	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs111033623	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	177	330	0	ENST00000371139.4:c.163C>T	p.Arg55Ter	p.R55*	ENST00000371139	NM_001114937.2	55	Cga/Tga	2/4	1	1	FACETS	1	0.975	1	1	0.995	1	CLONAL	4	FALSE	0	0.197613429580887	1		330	372	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652118	36652118	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	146	536	0	ENST00000244741.5:c.243del	p.Arg83GlyfsTer65	p.R83Gfs*65	ENST00000244741	NM_000389.4	80	acG/ac	2/3	0.197613429580887	5	FACETS	0.877	0.805	0.952			1	CLONAL	4	FALSE	NA	0.197613429580887	5		536	546	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373950	118373951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	145	710	0	ENST00000534358.1:c.7349dup	p.Leu2450PhefsTer10	p.L2450Ffs*10	ENST00000534358	NM_005933.3	2448	tct/tcTt	27/36	0.198125352532023	1	FACETS	0.991	0.907	1	1	0.991	1	CLONAL	2	FALSE	0	0.197613429580887	1		710	667	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940552	49940553	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	125	746	0	ENST00000296474.3:c.490_491del	p.Phe164LeufsTer5	p.F164Lfs*5	ENST00000296474	NM_002447.2	164	TTc/c	1/20	0.198125352532023	1	FACETS	1	0.978	1	1	0.991	1	CLONAL	2	FALSE	0	0.197613429580887	1		746	463	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914422	32914422	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	281	877	1	ENST00000380152.3:c.5934del	p.Phe1978LeufsTer26	p.F1978Lfs*26	ENST00000380152		1977	aTt/at	11/27	0.198125352532023	3	FACETS	1	0.986	1	0.78	0.732	0.83	CLONAL	2	FALSE	0	0.197613429580887	3		878	1335	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972893	32972893	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	136	386	0	ENST00000380152.3:c.10248del	p.Lys3416AsnfsTer11	p.K3416Nfs*11	ENST00000380152		3415	Aaa/aa	27/27	0.198125352532023	3	FACETS	1	0.914	1	0.67	0.609	0.733	CLONAL	2	FALSE	0	0.197613429580887	3		386	753	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270530	98270530	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs751977093	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	49	306	1	ENST00000331920.6:c.114del	p.Leu39CysfsTer41	p.L39Cfs*41	ENST00000331920	NM_000264.3	38	ggG/gg	1/24	0.197053235289298	3	FACETS	0.886	0.76	1			1	CLONAL	3	FALSE	NA	0.197613429580887	3		307	205	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063358	67063359	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	101	411	0	ENST00000412916.2:c.54dup	p.Arg19Ter	p.R19*	ENST00000412916		16	-/T	1/6	0.196316789548606	0	FACETS	1	0.949	1			1	CLONAL	2	FALSE	0	0.197613429580887	0		411	378	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532709	187532710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	167	664	0	ENST00000441802.2:c.9683dup	p.Val3229CysfsTer3	p.V3229Cfs*3	ENST00000441802	NM_005245.3	3228	cct/ccCt	14/27	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	2	FALSE	NA	0.197613429580887	2		664	688	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165216	32165216	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767972771	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	128	492	1	ENST00000375023.3:c.4912del	p.Leu1638CysfsTer68	p.L1638Cfs*68	ENST00000375023	NM_004557.3	1638	Ctg/tg	27/30	0.197613429580887	5	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	FALSE	2	0.197613429580887	5		493	480	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829895	72829895	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	164	821	1	ENST00000268489.5:c.6686del	p.Pro2229LeufsTer26	p.P2229Lfs*26	ENST00000268489	NM_006885.3	2229	cCt/ct	9/10	0.196316789548606	0	FACETS	0.979	0.902	1			1	CLONAL	2	FALSE	0	0.197613429580887	0		822	680	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375459	40375459	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	215	1201	0	ENST00000293328.3:c.491del	p.Lys164SerfsTer17	p.K164Sfs*17	ENST00000293328	NM_012448.3	164	aAg/ag	5/19	0.198125352532023	1	FACETS	1	0.977	1	1	0.994	1	CLONAL	2	FALSE	0	0.197613429580887	1		1201	881	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931452	131931453	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	104	293	0	ENST00000265335.6:c.2164_2165del	p.Lys722GlyfsTer5	p.K722Gfs*5	ENST00000265335		719	ctAAaa/ctaa	13/25	1	2	FACETS	1	0.904	1	1	0.988	1	CLONAL	2	FALSE	1	0.197613429580887	2		293	523	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261245	16261246	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	90	349	0	ENST00000375759.3:c.8516dup	p.Ala2840GlyfsTer7	p.A2840Gfs*7	ENST00000375759	NM_015001.2	2837	atc/atCc	11/15	NA	2	FACETS	1	0.948	1			1	INDETERMINATE	2	FALSE	NA	0.197613429580887	2		349	413	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005187-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	38	302	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.666	0.553	0.79	0.666	0.553	0.79	SUBCLONAL	1	TRUE	1	0.407629655284771	2		302	280	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587777893	NA	P-0005187-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	95	255	0	ENST00000361445.4:c.5930C>A	p.Thr1977Lys	p.T1977K	ENST00000361445	NM_004958.3	1977	aCa/aAa	43/58	1	2	FACETS	0.967	0.865	1	0.967	0.865	1	CLONAL	1	TRUE	1	0.407629655284771	2		255	482	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411551	116411551	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0005187-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	53	156	0	ENST00000397752.3:c.2731-1G>C		p.X911_splice	ENST00000397752	NM_000245.2	911			0.378691545946804	3	FACETS	0.954	0.818	1	0.477	0.409	0.551	CLONAL	1	TRUE	1	0.407629655284771	3		156	328	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681207	86681207	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1060503438	NA	P-0005187-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	37	125	0	ENST00000274376.6:c.2847+1G>A		p.X949_splice	ENST00000274376	NM_002890.2	949			1	2	FACETS	0.796	0.661	0.944	0.796	0.661	0.944	CLONAL	1	TRUE	1	0.407629655284771	2		125	228	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643672	52643672	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005187-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	86	269	0	ENST00000394830.3:c.2224G>T	p.Glu742Ter	p.E742*	ENST00000394830	NM_018313.4	742	Gag/Tag	17/30	0.407629655284771	1	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	0	0.407629655284771	1		269	336	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0005298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	168	259	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.504518290169213	3	FACETS	0.852	0.783	0.923	0.426	0.391	0.462	CLONAL	1	FALSE	1	0.571829343127026	3		259	887	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0005298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	206	408	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.915	0.851	0.981	0.915	0.851	0.981	CLONAL	1	FALSE	1	0.571829343127026	2		408	787	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692884	89692884	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121909222	NA	P-0005298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	316	188	1	ENST00000371953.3:c.368A>G	p.His123Arg	p.H123R	ENST00000371953	NM_000314.4	123	cAc/cGc	5/9	0.566631433217936	2	FACETS	0.948	0.905	0.991	0.948	0.905	0.991	CLONAL	2	FALSE	0	0.571829343127026	2		189	583	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411492	63411492	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	358	391	0	ENST00000330258.3:c.1675G>T	p.Glu559Ter	p.E559*	ENST00000330258	NM_152424.3	559	Gaa/Taa	2/2	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	FALSE	0	0.571829343127026	1		391	666	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603046	48603077	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGGCGGCTACTGCACAAGCTGCAGCAGCTG	GCAGGCGGCTACTGCACAAGCTGCAGCAGCTG	-	novel	NA	P-0005298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	214	337	0	ENST00000342988.3:c.1347_1378del	p.Gln449HisfsTer34	p.Q449Hfs*34	ENST00000342988	NM_005359.5	449	caGCAGGCGGCTACTGCACAAGCTGCAGCAGCTGcc/cacc	11/12	0.571829343127026	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	0	0.571829343127026	1		337	525	SUCCESS
APC	324	MSKCC	GRCh37	5	112175779	112175780	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0005298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	162	314	0	ENST00000257430.4:c.4490dup	p.Asp1498ArgfsTer16	p.D1498Rfs*16	ENST00000257430	NM_000038.5	1496	-/C	16/16	1	2	FACETS	0.907	0.835	0.98	0.907	0.835	0.98	CLONAL	1	FALSE	1	0.571829343127026	2		314	625	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933593	39933594	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0005298-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	131	196	0	ENST00000378444.4:c.1005dup	p.Ser336LeufsTer45	p.S336Lfs*45	ENST00000378444	NM_001123385.1	335	-/C	4/15	1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	0	0.571829343127026	1		196	278	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	16	302	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.826	1	1	0.826	1	CLONAL	1	TRUE	1	0.26	2		302	108	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	49	452	0	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	1	2	FACETS	0.743	0.63	0.868	0.743	0.63	0.868	SUBCLONAL	1	TRUE	1	0.26	2		452	507	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872957	35872957	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	43	268	0	ENST00000216797.5:c.275A>C	p.Glu92Ala	p.E92A	ENST00000216797	NM_020529.2	92	gAa/gCa	2/6	1	2	FACETS	0.675	0.565	0.797	0.675	0.565	0.797	SUBCLONAL	1	TRUE	1	0.26	2		268	490	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5206796	5206796	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	42	325	0	ENST00000357368.4:c.5836T>C	p.Tyr1946His	p.Y1946H	ENST00000357368	NM_002850.3	1946	Tat/Cat	38/38	1	2	FACETS	0.641	0.535	0.759	0.641	0.535	0.759	SUBCLONAL	1	TRUE	1	0.26	2		325	504	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98222004	98222004	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	33	239	0	ENST00000331920.6:c.2765A>T	p.Tyr922Phe	p.Y922F	ENST00000331920	NM_000264.3	922	tAc/tTc	17/24	1	2	FACETS	0.628	0.512	0.76	0.628	0.512	0.76	SUBCLONAL	1	TRUE	1	0.26	2		239	404	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833914	44833930	+	frameshift_variant	Frame_Shift_Del	DEL	TATCTGCATACCAGAGG	TATCTGCATACCAGAGG	-	novel	NA	P-0005586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	47	145	0	ENST00000377967.4:c.340_356del	p.Ser114LeufsTer6	p.S114Lfs*6	ENST00000377967	NM_021140.2	113	tTATCTGCATACCAGAGG/t	4/29	1	1	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	0	0.26	1		145	301	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0005762-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	501	1110	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.868980230825721	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.868980230825721	1		1111	640	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907131	32907131	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005762-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1616	671	552	0	ENST00000380152.3:c.1516T>G	p.Phe506Val	p.F506V	ENST00000380152		506	Ttc/Gtc	10/27	0.864415093605102	3	FACETS	0.969	0.931	1	0.484	0.465	0.503	CLONAL	1	TRUE	1	0.868980230825721	3		552	2287	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0006764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	10	256	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	NA	2	FACETS	0.206	0.139	0.292			1	INDETERMINATE	1	FALSE	NA	0.262875744309331	2		256	369	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555687605	NA	P-0006764-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	15	527	0	ENST00000342988.3:c.1610A>G	p.Asp537Gly	p.D537G	ENST00000342988	NM_005359.5	537	gAc/gGc	12/12	1	2	FACETS	0.391	0.285	0.518	0.391	0.285	0.518	SUBCLONAL	1	FALSE	1	0.262875744309331	2		527	292	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	117	366	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.414819447414195	1	FACETS	0.89	0.807	0.977	0.89	0.807	0.977	CLONAL	1	TRUE	0	0.421032507541323	1		366	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747342068	NA	P-0007683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	165	347	0	ENST00000269305.4:c.394A>G	p.Lys132Glu	p.K132E	ENST00000269305	NM_001126112.2	132	Aag/Gag	5/11	0.414819447414195	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.421032507541323	1		347	578	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0007683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	225	387	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.412682781382407	2	FACETS	0.925	0.868	0.982	0.925	0.868	0.982	CLONAL	2	TRUE	0	0.421032507541323	2		387	578	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137779	64137779	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	129	502	0	ENST00000334205.4:c.1880A>G	p.Lys627Arg	p.K627R	ENST00000334205	NM_003942.2	627	aAa/aGa	15/17	0.250822499201115	1	FACETS	0.57	0.517	0.627	0.57	0.517	0.627	INDETERMINATE	1	TRUE	0	0.421032507541323	1		502	848	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0007809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	316	265	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA	2	FACETS	0.969	0.921	1			1	INDETERMINATE	1	TRUE	NA	0.922723456559822	2		265	707	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0007809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	315	696	3	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.971	0.923	1	0.971	0.923	1	CLONAL	1	TRUE	1	0.922723456559822	2		699	703	SUCCESS
APC	324	MSKCC	GRCh37	5	112175198	112175198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	206	156	0	ENST00000257430.4:c.3907C>T	p.Gln1303Ter	p.Q1303*	ENST00000257430	NM_000038.5	1303	Caa/Taa	16/16	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.922723456559822	2		156	445	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972695	25972695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1249025549	NA	P-0007809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	496	318	0	ENST00000435504.4:c.1730C>T	p.Ala577Val	p.A577V	ENST00000435504		577	gCc/gTc	12/13	0.922723456559822	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.922723456559822	1		318	569	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143440	30143440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	117	62	0	ENST00000389048.3:c.86C>T	p.Ala29Val	p.A29V	ENST00000389048	NM_004304.4	29	gCg/gTg	1/29	0.922723456559822	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.922723456559822	1		62	126	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280061	66280061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1254027522	NA	P-0007809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	419	322	0	ENST00000273854.3:c.1628G>A	p.Arg543His	p.R543H	ENST00000273854	NM_004439.5	543	cGt/cAt	7/18	0.922723456559822	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.922723456559822	1		322	458	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129141	152129141	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	364	326	0	ENST00000206249.3:c.94A>C	p.Lys32Gln	p.K32Q	ENST00000206249	NM_000125.3	32	Aag/Cag	1/8	1	2	FACETS	0.9	0.857	0.943	0.9	0.857	0.943	CLONAL	1	TRUE	1	0.922723456559822	2		326	877	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346641	81346641	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	296	286	0	ENST00000222390.5:c.1312A>G	p.Asn438Asp	p.N438D	ENST00000222390	NM_000601.4	438	Aat/Gat	11/18	0.922723456559822	3	FACETS	0.845	0.795	0.895	0.422	0.397	0.448	CLONAL	1	TRUE	1	0.922723456559822	3		286	1110	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830502	72830502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756766481	NA	P-0007809-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	497	401	2	ENST00000268489.5:c.6079G>A	p.Asp2027Asn	p.D2027N	ENST00000268489	NM_006885.3	2027	Gat/Aat	9/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.922723456559822	2		403	1053	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591892	48591892	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	109	396	0	ENST00000342988.3:c.1055G>T	p.Gly352Val	p.G352V	ENST00000342988	NM_005359.5	352	gGa/gTa	9/12	0.257659765319179	2	FACETS	1	0.973	1	0.611	0.552	0.673	CLONAL	1	TRUE	0	0.392130691622488	2		396	455	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794439	242794439	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	140	1132	2	ENST00000334409.5:c.503C>A	p.Thr168Asn	p.T168N	ENST00000334409	NM_005018.2	168	aCc/aAc	3/5	0.151427103111871	3	FACETS	0.792	0.719	0.867			1	INDETERMINATE	1	TRUE	NA	0.392130691622488	3		1134	1079	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821214	72821214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1044596115	NA	P-0008332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	160	604	1	ENST00000268489.5:c.10961C>T	p.Ser3654Leu	p.S3654L	ENST00000268489	NM_006885.3	3654	tCg/tTg	10/10	0.257512955116577	2	FACETS	1	0.986	1	0.67	0.617	0.725	CLONAL	1	TRUE	0	0.392130691622488	2		605	609	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023864	31023864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1172005201	NA	P-0008332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	64	526	0	ENST00000375687.4:c.3349C>T	p.Pro1117Ser	p.P1117S	ENST00000375687	NM_015338.5	1117	Ccc/Tcc	13/13	0.157534421959561	5	FACETS	0.883	0.765	1	0.294	0.255	0.337	INDETERMINATE	1	TRUE	2	0.392130691622488	5		526	587	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197187	26197187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	63	425	0	ENST00000356476.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000356476		98	Gag/Aag	1/1	0.392130691622488	3	FACETS	0.672	0.581	0.77	0.336	0.29	0.385	SUBCLONAL	1	TRUE	1	0.392130691622488	3		425	572	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434148	12434148	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	52	295	0	ENST00000287820.6:c.516C>G	p.Ile172Met	p.I172M	ENST00000287820	NM_015869.4	172	atC/atG	4/7	0.294187580145115	3	FACETS	0.682	0.581	0.792	0.227	0.193	0.264	SUBCLONAL	1	TRUE	0	0.392130691622488	3		295	465	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122785	7122785	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0008332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	69	534	0	ENST00000302850.5:c.3370-1G>C		p.X1124_splice	ENST00000302850	NM_000208.2	1124			1	2	FACETS	0.755	0.659	0.858	0.755	0.659	0.858	SUBCLONAL	1	TRUE	1	0.392130691622488	2		534	466	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782141	9782141	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	81	581	0	ENST00000377346.4:c.2164G>A	p.Glu722Lys	p.E722K	ENST00000377346	NM_005026.3	722	Gag/Aag	17/24	0.255301889867479	4	FACETS	0.877	0.773	0.988			1	CLONAL	1	TRUE	NA	0.392130691622488	4		581	656	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999795	100999795	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	46	592	0	ENST00000325455.5:c.7G>C	p.Glu3Gln	p.E3Q	ENST00000325455	NM_001202474.3	3	Gag/Cag	1/8	0.392130691622488	3	FACETS	0.51	0.429	0.6	0.17	0.143	0.2	SUBCLONAL	1	TRUE	0	0.392130691622488	3		592	550	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438020	438020	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	41	258	0	ENST00000399788.2:c.1949G>A	p.Arg650Lys	p.R650K	ENST00000399788	NM_001042603.1	650	aGa/aAa	14/28	NA	2	FACETS	0.636	0.531	0.751			1	INDETERMINATE	1	TRUE	NA	0.392130691622488	2		258	329	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829209	72829209	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	88	687	0	ENST00000268489.5:c.7372G>C	p.Glu2458Gln	p.E2458Q	ENST00000268489	NM_006885.3	2458	Gag/Cag	9/10	0.257512955116577	2	FACETS	0.769	0.682	0.861	0.384	0.341	0.431	SUBCLONAL	1	TRUE	0	0.392130691622488	2		687	584	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832221	72832221	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	51	413	0	ENST00000268489.5:c.4360G>T	p.Glu1454Ter	p.E1454*	ENST00000268489	NM_006885.3	1454	Gag/Tag	9/10	0.257512955116577	2	FACETS	0.618	0.526	0.718	0.309	0.263	0.359	SUBCLONAL	1	TRUE	0	0.392130691622488	2		413	421	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158400	106158400	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs762575727	NA	P-0008332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	24	194	0	ENST00000380013.4:c.3301C>G	p.Leu1101Val	p.L1101V	ENST00000380013	NM_001127208.2	1101	Ctc/Gtc	3/11	0.341598442894716	4	FACETS	0.59	0.463	0.735	0.295	0.231	0.368	SUBCLONAL	1	TRUE	2	0.392130691622488	4		194	289	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161783	56161783	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	45	254	0	ENST00000399503.3:c.1280C>G	p.Ser427Cys	p.S427C	ENST00000399503	NM_005921.1	427	tCt/tGt	6/20	0.30387458927322	5	FACETS	0.668	0.561	0.786	0.223	0.187	0.262	SUBCLONAL	1	TRUE	2	0.392130691622488	5		254	546	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981621	70981621	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	88	821	0	ENST00000276594.2:c.475C>G	p.Leu159Val	p.L159V	ENST00000276594	NM_024504.3	159	Ctg/Gtg	2/8	0.33631090323133	4	FACETS	0.589	0.521	0.663			1	SUBCLONAL	1	TRUE	NA	0.392130691622488	4		821	1060	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0008540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	76	773	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	0.775	0.684	0.872	0.775	0.684	0.872	SUBCLONAL	1	TRUE	1	0.520069780316375	2		773	377	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0008540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	212	245	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.829	0.778	0.88	1	0.993	1	CLONAL	2	TRUE	1	0.520069780316375	2		245	492	SUCCESS
APC	324	MSKCC	GRCh37	5	112175246	112175246	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1057517558	NA	P-0008540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	55	733	1	ENST00000257430.4:c.3956del	p.Pro1319LeufsTer2	p.P1319Lfs*2	ENST00000257430	NM_000038.5	1319	Cct/ct	16/16	1	2	FACETS	0.81	0.7	0.929	0.81	0.7	0.929	CLONAL	1	TRUE	1	0.520069780316375	2		734	261	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564764	86564764	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	77	1269	3	ENST00000274376.6:c.496G>T	p.Glu166Ter	p.E166*	ENST00000274376	NM_002890.2	166	Gag/Tag	1/25	1	2	FACETS	0.626	0.551	0.706	0.626	0.551	0.706	SUBCLONAL	1	TRUE	1	0.520069780316375	2		1272	473	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220049	133220049	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	66	960	3	ENST00000320574.5:c.4388T>C	p.Phe1463Ser	p.F1463S	ENST00000320574	NM_006231.2	1463	tTt/tCt	34/49	1	2	FACETS	0.758	0.662	0.86	0.758	0.662	0.86	SUBCLONAL	1	TRUE	1	0.520069780316375	2		963	335	SUCCESS
APC	324	MSKCC	GRCh37	5	112154980	112154980	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	94	966	0	ENST00000257430.4:c.1251del	p.Cys417TrpfsTer37	p.C417Wfs*37	ENST00000257430	NM_000038.5	417	tgT/tg	10/16	1	2	FACETS	0.849	0.759	0.942	0.849	0.759	0.942	CLONAL	1	TRUE	1	0.520069780316375	2		966	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577069	7577075	+	frameshift_variant	Frame_Shift_Del	DEL	CGGAGAT	CGGAGAT	-	novel	NA	P-0008540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	112	976	0	ENST00000269305.4:c.863_869del	p.Asn288ThrfsTer55	p.N288Tfs*55	ENST00000269305	NM_001126112.2	288	aATCTCCGc/ac	8/11	1	2	FACETS	0.79	0.713	0.871	0.79	0.713	0.871	SUBCLONAL	1	TRUE	1	0.520069780316375	2		976	545	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0009261-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	1486	452	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.69549531397889	9	FACETS	1	0.996	1			1	CLONAL	7	TRUE	NA	0.69549531397889	9		452	2029	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009261-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	363	1066	1	ENST00000269305.4:c.380C>A	p.Ser127Tyr	p.S127Y	ENST00000269305	NM_001126112.2	127	tCc/tAc	5/11	0.69549531397889	2	FACETS	0.968	0.933	1	0.968	0.933	1	CLONAL	2	TRUE	0	0.69549531397889	2		1067	539	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009261-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	1378	1028	1	ENST00000269571.5:c.829G>T	p.Asp277Tyr	p.D277Y	ENST00000269571		277	Gac/Tac	7/27	0.69549531397889	9	FACETS	1	0.99	1			1	CLONAL	7	TRUE	NA	0.69549531397889	9		1029	1924	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224496	224496	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009261-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	35	209	0	ENST00000264932.6:c.172G>C	p.Val58Leu	p.V58L	ENST00000264932	NM_004168.2	58	Gtg/Ctg	3/15	NA	2	FACETS	0.658	0.547	0.778			1	INDETERMINATE	1	TRUE	NA	0.69549531397889	2		209	153	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864368	162864368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009261-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	235	691	0	ENST00000366898.1:c.145G>A	p.Glu49Lys	p.E49K	ENST00000366898	NM_004562.2	49	Gag/Aag	2/12	0.69549531397889	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.69549531397889	3		691	450	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534564	140534564	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009261-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	136	527	0	ENST00000288602.6:c.349A>T	p.Met117Leu	p.M117L	ENST00000288602	NM_004333.4	117	Atg/Ttg	3/18	NA	2	FACETS	1	0.953	1			1	INDETERMINATE	1	TRUE	NA	0.69549531397889	2		527	372	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953228	81953228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369760877	NA	P-0009261-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	111	556	1	ENST00000359376.3:c.2194C>T	p.Arg732Cys	p.R732C	ENST00000359376	NM_002661.3	732	Cgc/Tgc	20/33	0.62252042454939	3	FACETS	0.896	0.81	0.987			1	CLONAL	1	TRUE	NA	0.69549531397889	3		557	480	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967262	38967262	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0009261-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	74	324	0	ENST00000357387.3:c.1218+1G>T		p.X406_splice	ENST00000357387	NM_152756.3	406			0.69549531397889	3	FACETS	0.986	0.872	1	0.493	0.436	0.553	CLONAL	1	TRUE	1	0.69549531397889	3		324	291	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165062	47165062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009261-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	97	469	1	ENST00000409792.3:c.1064C>T	p.Ser355Leu	p.S355L	ENST00000409792	NM_014159.6	355	tCa/tTa	3/21	0.69549531397889	2	FACETS	0.936	0.845	1	0.468	0.422	0.515	CLONAL	1	TRUE	0	0.69549531397889	2		470	298	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138092	64138092	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009261-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	189	1142	0	ENST00000334205.4:c.2015C>A	p.Ser672Ter	p.S672*	ENST00000334205	NM_003942.2	672	tCg/tAg	16/17	0.233184213854443	2	FACETS	0.683	0.632	0.735	0.341	0.316	0.368	INDETERMINATE	1	TRUE	0	0.69549531397889	2		1142	796	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246476	10246476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009261-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	181	1301	1	ENST00000340748.4:c.4661C>T	p.Ala1554Val	p.A1554V	ENST00000340748		1554	gCc/gTc	38/40	0.69549531397889	2	FACETS	0.946	0.879	1	0.473	0.439	0.508	CLONAL	1	TRUE	0	0.69549531397889	2		1302	550	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	257	190	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.625087486948334	4	FACETS	0.953	0.897	1	0.953	0.897	1	CLONAL	2	TRUE	2	0.625087486948334	4		190	701	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435780	56435780	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	206	223	0	ENST00000407977.2:c.1357G>T	p.Glu453Ter	p.E453*	ENST00000407977		453	Gaa/Taa	9/10	0.625972360579741	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.625087486948334	3		223	381	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437577	52437578	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0009760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	601	745	0	ENST00000460680.1:c.1583_1584insA	p.Lys529GlnfsTer8	p.K529Qfs*8	ENST00000460680	NM_004656.3	528	tcc/tcAc	13/17	0.625972360579741	2	FACETS	0.996	0.966	1	0.996	0.966	1	CLONAL	2	TRUE	0	0.625087486948334	2		745	965	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928065	178928088	+	inframe_deletion	In_Frame_Del	DEL	TACCTCATGGATTAGAAGATTTGC	TACCTCATGGATTAGAAGATTTGC	-	novel	NA	P-0009760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	145	351	0	ENST00000263967.3:c.1344_1367del	p.Pro449_Leu456del	p.P449_L456del	ENST00000263967	NM_006218.2	448	gTACCTCATGGATTAGAAGATTTGCtg/gtg	8/21	0.625087486948334	4	FACETS	1	0.975	1	0.584	0.535	0.636	CLONAL	1	TRUE	2	0.625087486948334	4		351	645	SUCCESS
APC	324	MSKCC	GRCh37	5	112175908	112175909	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1554086015	NA	P-0009760-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	232	339	0	ENST00000257430.4:c.4619_4620del	p.Glu1540AlafsTer3	p.E1540Afs*3	ENST00000257430	NM_000038.5	1539	tcAGag/tcag	16/16	NA	2	FACETS	0.99	0.942	1			1	INDETERMINATE	2	TRUE	NA	0.625087486948334	2		339	375	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0009903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	118	318	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.374785916390804	1	FACETS	0.399	0.361	0.439	0.399	0.361	0.439	INDETERMINATE	1	TRUE	0	0.693424495227311	1		318	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0009903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	174	563	0	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	0.674972451962735	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.693424495227311	1		563	273	SUCCESS
APC	324	MSKCC	GRCh37	5	112175021	112175021	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs79122263	NA	P-0009903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	103	459	0	ENST00000257430.4:c.3730C>T	p.Gln1244Ter	p.Q1244*	ENST00000257430	NM_000038.5	1244	Caa/Taa	16/16	0.374785916390804	1	FACETS	0.656	0.595	0.718	0.656	0.595	0.718	INDETERMINATE	1	TRUE	0	0.693424495227311	1		459	296	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143235903	143235903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	194	465	0	ENST00000262992.4:c.385G>A	p.Val129Ile	p.V129I	ENST00000262992	NM_001101669.1	129	Gtc/Atc	6/24	0.374785916390804	1	FACETS	0.877	0.822	0.931	0.877	0.822	0.931	INDETERMINATE	1	TRUE	0	0.693424495227311	1		465	417	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925329	114925329	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009903-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	125	803	0	ENST00000543371.1:c.1407C>G	p.Cys469Trp	p.C469W	ENST00000543371	NM_001198531.1	469	tgC/tgG	14/14	0.287657021122251	1	FACETS	0.37	0.335	0.406	0.37	0.335	0.406	INDETERMINATE	1	TRUE	0	0.693424495227311	1		803	637	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0010009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	101	311	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.237110616741949	2		311	749	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0010009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	163	464	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.154264968070987	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.237110616741949	1		464	1125	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829404	72829404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200268844	NA	P-0010009-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1804	166	669	3	ENST00000268489.5:c.7177G>A	p.Ala2393Thr	p.A2393T	ENST00000268489	NM_006885.3	2393	Gcc/Acc	9/10	0.154264968070987	1	FACETS	0.626	0.573	0.683	0.626	0.573	0.683	SUBCLONAL	1	TRUE	0	0.237110616741949	1		672	1970	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0010147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	121	307	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.737	0.674	0.801	0.737	0.674	0.801	SUBCLONAL	1	TRUE	1	0.954878121298136	2		307	344	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411246	63411246	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	814	594	1	ENST00000330258.3:c.1921C>T	p.Arg641Ter	p.R641*	ENST00000330258	NM_152424.3	641	Cga/Tga	2/2	0.677063437204827	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	2	0.954878121298136	4		595	1589	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0010147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	1012	482	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.910666839719813	3	FACETS	0.986	0.977	0.994	0.986	0.977	0.994	CLONAL	3	TRUE	0	0.954878121298136	3		483	1059	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0010147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	472	261	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	0.866825562126312	3	FACETS	0.991	0.958	1	0.991	0.958	1	CLONAL	2	TRUE	1	0.954878121298136	3		261	737	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384651	31384651	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	766	563	1	ENST00000328111.2:c.1359del	p.Leu454SerfsTer136	p.L454Sfs*136	ENST00000328111	NM_006892.3	451	gaG/ga	13/23	0.887071160930961	4	FACETS	0.862	0.834	0.891	0.862	0.834	0.891	CLONAL	2	TRUE	2	0.954878121298136	4		564	1819	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045839	180045839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140041761	NA	P-0010147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	383	435	0	ENST00000261937.6:c.2932G>A	p.Asp978Asn	p.D978N	ENST00000261937	NM_182925.4	978	Gac/Aac	21/30	1	2	FACETS	0.993	0.949	1	0.993	0.949	1	CLONAL	1	TRUE	1	0.954878121298136	2		435	808	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840041	27840041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1462	564	601	1	ENST00000328488.2:c.53G>A	p.Arg18His	p.R18H	ENST00000328488	NM_003533.2	18	cGc/cAc	1/1	0.775386246568374	4	FACETS	1	0.992	1	0.57	0.546	0.595	CLONAL	1	TRUE	2	0.954878121298136	4		602	2026	SUCCESS
APC	324	MSKCC	GRCh37	5	112175542	112175543	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	194	392	0	ENST00000257430.4:c.4252dup	p.Ile1418AsnfsTer5	p.I1418Nfs*5	ENST00000257430	NM_000038.5	1417	-/A	16/16	1	2	FACETS	0.921	0.863	0.98	0.921	0.863	0.98	CLONAL	1	TRUE	1	0.954878121298136	2		392	441	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261677	16261677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745687072	NA	P-0010367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	145	216	0	ENST00000375759.3:c.8942C>T	p.Thr2981Met	p.T2981M	ENST00000375759	NM_015001.2	2981	aCg/aTg	11/15	0.480115652186558	3	FACETS	0.848	0.782	0.915	0.848	0.782	0.915	CLONAL	2	TRUE	1	0.544064185680654	3		216	400	SUCCESS
APC	324	MSKCC	GRCh37	5	112174577	112174577	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587783029	NA	P-0010367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	172	501	0	ENST00000257430.4:c.3286C>T	p.Gln1096Ter	p.Q1096*	ENST00000257430	NM_000038.5	1096	Cag/Tag	16/16	1	2	FACETS	0.905	0.835	0.977	0.905	0.835	0.977	CLONAL	1	TRUE	1	0.544064185680654	2		501	699	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0010367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	125	303	0	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.544064185680654	2		303	454	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285670	46285670	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	160	406	0	ENST00000334344.6:c.5030G>T	p.Arg1677Leu	p.R1677L	ENST00000334344	NM_152641.2	1677	cGa/cTa	17/21	1	2	FACETS	0.949	0.873	1	0.949	0.873	1	CLONAL	1	TRUE	1	0.544064185680654	2		406	620	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0010367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	122	323	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.544064185680654	1	FACETS	0.855	0.78	0.931	0.855	0.78	0.931	CLONAL	1	TRUE	0	0.544064185680654	1		323	382	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029511	16029511	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	200	628	3	ENST00000268712.3:c.1519C>T	p.Arg507Ter	p.R507*	ENST00000268712	NM_006311.3	507	Cga/Tga	15/46	0.544064185680654	1	FACETS	0.877	0.818	0.938	0.877	0.818	0.938	CLONAL	1	TRUE	0	0.544064185680654	1		631	610	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727129	40727129	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010367-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	140	483	0	ENST00000373198.4:c.3835T>C	p.Phe1279Leu	p.F1279L	ENST00000373198	NM_133170.3	1279	Ttc/Ctc	28/32	0.482260034443354	4	FACETS	0.702	0.638	0.77	0.351	0.319	0.385	SUBCLONAL	1	TRUE	2	0.544064185680654	4		483	1132	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0010497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	94	1110	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.215493874971244	2	FACETS	0.956	0.855	1	0.956	0.855	1	CLONAL	2	TRUE	0	0.218014996408598	2		1111	451	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0010497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	22	187	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.215493874971244	2	FACETS	1	0.815	1	0.526	0.409	0.659	CLONAL	1	TRUE	0	0.218014996408598	2		188	192	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645697	215645697	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	52	382	0	ENST00000260947.4:c.901G>A	p.Glu301Lys	p.E301K	ENST00000260947	NM_000465.2	301	Gag/Aag	4/11	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.218014996408598	2		382	461	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663346	227663346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024227751	NA	P-0010497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	27	188	0	ENST00000305123.5:c.109G>A	p.Glu37Lys	p.E37K	ENST00000305123	NM_005544.2	37	Gag/Aag	1/2	1	2	FACETS	0.744	0.592	0.917	0.744	0.592	0.917	CLONAL	1	TRUE	1	0.218014996408598	2		188	333	SUCCESS
ATR	545	MSKCC	GRCh37	3	142286928	142286928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751709684	NA	P-0010497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	144	371	0	ENST00000350721.4:c.128G>A	p.Arg43Gln	p.R43Q	ENST00000350721	NM_001184.3	43	cGg/cAg	2/47	0.215493874971244	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.218014996408598	2		371	609	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404581	70404582	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0010497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	57	463	0	ENST00000373644.4:c.2095_2096delinsAT	p.Glu699Ile	p.E699I	ENST00000373644	NM_030625.2	699	GAa/ATa	4/12	0.215493874971244	2	FACETS	0.817	0.7	0.945	0.409	0.35	0.473	CLONAL	1	TRUE	0	0.218014996408598	2		463	640	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561190	9561190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762286985	NA	P-0010497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	76	438	0	ENST00000353224.5:c.592G>A	p.Asp198Asn	p.D198N	ENST00000353224	NM_177990.2	198	Gat/Aat	4/10	0.129556728212217	4	FACETS	1	0.886	1	0.506	0.443	0.574	INDETERMINATE	1	TRUE	2	0.218014996408598	4		438	839	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317529	1317529	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	95	485	0	ENST00000400841.2:c.536A>C	p.Lys179Thr	p.K179T	ENST00000400841		179	aAg/aCg	5/6	0.196896324790854	3	FACETS	0.795	0.706	0.891	0.398	0.353	0.446	SUBCLONAL	1	TRUE	1	0.218014996408598	3		485	1215	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253861	153253862	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	49	216	0	ENST00000281708.4:c.871dup	p.Tyr291LeufsTer26	p.Y291Lfs*26	ENST00000281708	NM_033632.3	291	tat/tTat	6/12	0.218014996408598	2	FACETS	0.895	0.765	1	0.895	0.765	1	CLONAL	2	TRUE	0	0.218014996408598	2		216	251	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	433	366	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.796726358610377	4	FACETS	0.976	0.935	1	0.976	0.935	1	CLONAL	2	TRUE	2	0.801062587191125	4		366	997	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0012680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	1082	400	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.801062587191125	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.801062587191125	3		400	1236	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172331	7172331	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758151117	NA	P-0012680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	315	467	1	ENST00000302850.5:c.1238G>A	p.Arg413His	p.R413H	ENST00000302850	NM_000208.2	413	cGt/cAt	5/22	0.801062587191125	3	FACETS	0.94	0.887	0.994	0.47	0.443	0.497	CLONAL	1	TRUE	1	0.801062587191125	3		468	1172	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622230	162622230	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	543	510	0	ENST00000366898.1:c.467G>T	p.Arg156Ile	p.R156I	ENST00000366898	NM_004562.2	156	aGa/aTa	4/12	0.719217499631587	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.801062587191125	4		510	1204	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650282	12650282	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	680	570	0	ENST00000251849.4:c.564T>G	p.Ser188Arg	p.S188R	ENST00000251849	NM_002880.3	188	agT/agG	5/17	0.801062587191125	3	FACETS	0.953	0.923	0.982	0.953	0.923	0.982	CLONAL	2	TRUE	1	0.801062587191125	3		570	1248	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362519	118362519	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	352	469	0	ENST00000534358.1:c.4880G>C	p.Cys1627Ser	p.C1627S	ENST00000534358	NM_005933.3	1627	tGt/tCt	15/36	0.801062587191125	3	FACETS	0.948	0.897	0.999	0.474	0.448	0.5	CLONAL	1	TRUE	1	0.801062587191125	3		469	1299	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870831	12870831	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	284	168	0	ENST00000228872.4:c.58C>T	p.Gln20Ter	p.Q20*	ENST00000228872	NM_004064.3	20	Cag/Tag	1/3	0.796726358610377	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	2	0.801062587191125	4		168	631	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287412	46287412	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0012680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	204	361	2	ENST00000334344.6:c.5272-1G>T		p.X1758_splice	ENST00000334344	NM_152641.2	1758			0.796726358610377	4	FACETS	1	0.935	1	0.504	0.468	0.542	CLONAL	1	TRUE	2	0.801062587191125	4		363	910	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188307	32188308	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0012680-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	676	640	0	ENST00000375023.3:c.1033_1034del	p.Ser345TrpfsTer8	p.S345Wfs*8	ENST00000375023	NM_004557.3	345	AGt/t	6/30	0.796726358610377	4	FACETS	0.858	0.827	0.889	0.858	0.827	0.889	CLONAL	2	TRUE	2	0.801062587191125	4		640	1771	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0013897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	169	427	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.492913184879773	2		427	675	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0013897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	400	245	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.493625190538248	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.492913184879773	3		245	940	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535427	66535427	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1472517358	NA	P-0013897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	62	232	0	ENST00000273854.3:c.34C>T	p.Arg12Trp	p.R12W	ENST00000273854	NM_004439.5	12	Cgg/Tgg	1/18	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.492913184879773	2		232	188	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0013897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	197	992	3	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	1	2	FACETS	0.875	0.811	0.942	0.875	0.811	0.942	CLONAL	1	TRUE	1	0.492913184879773	2		995	913	SUCCESS
APC	324	MSKCC	GRCh37	5	112175235	112175235	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0013897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	213	307	0	ENST00000257430.4:c.3944C>G	p.Ser1315Ter	p.S1315*	ENST00000257430	NM_000038.5	1315	tCa/tGa	16/16	0.492913184879773	2	FACETS	0.969	0.912	1	0.969	0.912	1	CLONAL	2	TRUE	0	0.492913184879773	2		307	446	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591127	67591129	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0013897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	95	397	1	ENST00000274335.5:c.1721_1723del	p.Arg574del	p.R574del	ENST00000274335		574	AGA/-	12/15	0.492913184879773	2	FACETS	0.783	0.7	0.871	0.392	0.35	0.436	SUBCLONAL	1	TRUE	0	0.492913184879773	2		398	492	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729880	30729881	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0013897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	72	238	0	ENST00000295754.5:c.1403_1404del	p.Lys468ArgfsTer3	p.K468Rfs*3	ENST00000295754	NM_003242.5	467	gtAAaa/gtaa	6/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.492913184879773	2		238	203	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222726	5222726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779918003	NA	P-0013897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	36	217	0	ENST00000357368.4:c.3077G>A	p.Arg1026His	p.R1026H	ENST00000357368	NM_002850.3	1026	cGc/cAc	18/38	0.410158201352594	1	FACETS	0.786	0.658	0.924	0.786	0.658	0.924	CLONAL	1	TRUE	0	0.492913184879773	1		217	140	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518737	176518737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753812223	NA	P-0013897-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	132	511	0	ENST00000292408.4:c.655C>T	p.Arg219Cys	p.R219C	ENST00000292408	NM_213647.1	219	Cgc/Tgc	6/18	0.492913184879773	2	FACETS	1	0.973	1	0.577	0.528	0.629	CLONAL	1	TRUE	0	0.492913184879773	2		511	464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0014416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	44	1110	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.323816053655501	1	FACETS	0.418	0.35	0.493	0.418	0.35	0.493	SUBCLONAL	1	TRUE	0	0.334688426654678	1		1111	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0014416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	292	630	1	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.323816053655501	1	FACETS	0.883	0.834	0.932	1	0.995	1	CLONAL	2	TRUE	0	0.334688426654678	1		631	823	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0014416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	261	225	0	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	0.334688426654678	4	FACETS	0.957	0.906	1	0.957	0.906	1	CLONAL	4	TRUE	0	0.334688426654678	4		225	544	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0014416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	55	286	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.334688426654678	4	FACETS	0.541	0.461	0.628	0.135	0.115	0.157	SUBCLONAL	1	TRUE	0	0.334688426654678	4		286	811	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554307	29554307	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1590	137	552	0	ENST00000356175.3:c.2323G>C	p.Glu775Gln	p.E775Q	ENST00000356175	NM_000267.3	775	Gag/Cag	19/57	0.334688426654678	5	FACETS	0.712	0.645	0.783	0.237	0.215	0.261	SUBCLONAL	1	TRUE	2	0.334688426654678	5		552	1727	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546560	9546560	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771840400	NA	P-0014416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	42	323	0	ENST00000353224.5:c.1462C>T	p.Arg488Ter	p.R488*	ENST00000353224	NM_177990.2	488	Cga/Tga	5/10	NA	2	FACETS	0.399	0.332	0.473			1	INDETERMINATE	1	TRUE	NA	0.334688426654678	2		323	629	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249440	153249440	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	148	422	0	ENST00000281708.4:c.1338G>T	p.Trp446Cys	p.W446C	ENST00000281708	NM_033632.3	446	tgG/tgT	9/12	0.334688426654678	3	FACETS	1	0.946	1	0.525	0.479	0.574	CLONAL	1	TRUE	1	0.334688426654678	3		422	983	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69011937	69011937	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	177	514	0	ENST00000288368.4:c.2574A>C	p.Lys858Asn	p.K858N	ENST00000288368	NM_024870.2	858	aaA/aaC	23/40	0.153828352914871	4	FACETS	1	0.963	1	0.54	0.496	0.586	INDETERMINATE	1	TRUE	2	0.334688426654678	4		514	1307	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285809	87285809	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1371476425	NA	P-0014416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	33	434	1	ENST00000277120.3:c.146C>T	p.Ser49Phe	p.S49F	ENST00000277120		49	tCt/tTt	2/19	0.153828352914871	4	FACETS	0.402	0.327	0.488	0.201	0.163	0.244	INDETERMINATE	1	TRUE	2	0.334688426654678	4		435	654	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804206	46804209	+	protein_altering_variant	In_Frame_Del	DEL	GCGG	GCGG	A	novel	NA	P-0014416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	132	489	0	ENST00000290295.7:c.798_801delinsT	p.Arg268del	p.R268del	ENST00000290295	NM_006361.5	266	aaCCGC/aaT	2/2	0.334688426654678	5	FACETS	0.921	0.834	1	0.307	0.278	0.338	CLONAL	1	TRUE	2	0.334688426654678	5		489	1286	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	432	190	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.717070680526878	3	FACETS	0.961	0.922	0.999	0.961	0.922	0.999	CLONAL	2	TRUE	1	0.717070680526878	3		190	852	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16203108	16203108	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	151	503	0	ENST00000375759.3:c.816C>A	p.Ser272Arg	p.S272R	ENST00000375759	NM_015001.2	272	agC/agA	3/15	0.548448437326561	4	FACETS	0.687	0.627	0.75			1	SUBCLONAL	1	TRUE	NA	0.717070680526878	4		503	1053	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578206	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs886039484	NA	P-0014754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	671	805	0	ENST00000269305.4:c.643A>G	p.Ser215Gly	p.S215G	ENST00000269305	NM_001126112.2	215	Agt/Ggt	6/11	0.715816904466607	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.717070680526878	2		805	902	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646173	215646173	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0014754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	167	449	0	ENST00000260947.4:c.425C>G	p.Ser142Ter	p.S142*	ENST00000260947	NM_000465.2	142	tCa/tGa	4/11	0.717070680526878	3	FACETS	0.92	0.848	0.994	0.46	0.424	0.497	CLONAL	1	TRUE	1	0.717070680526878	3		449	688	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797242	32797242	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771932254	NA	P-0014754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1482	274	701	1	ENST00000374899.4:c.1867C>T	p.Arg623Ter	p.R623*	ENST00000374899	NM_018833.2	623	Cga/Tga	11/12	0.561321203563531	6	FACETS	1	0.969	1	0.353	0.33	0.377	CLONAL	1	TRUE	3	0.717070680526878	6		702	1756	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0014774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	210	1110	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.765	0.711	0.822	1	0.991	1	SUBCLONAL	2	TRUE	1	0.29	2		1111	946	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873066	134873066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762457030	NA	P-0014774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	161	533	1	ENST00000398015.3:c.1370C>T	p.Pro457Leu	p.P457L	ENST00000398015	NM_004441.4	457	cCg/cTg	6/16	1	2	FACETS	0.971	0.889	1	0.971	0.889	1	CLONAL	1	TRUE	1	0.29	2		534	1143	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350062	81350062	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs759145490	NA	P-0014774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	81	291	0	ENST00000222390.5:c.1270C>T	p.Arg424Cys	p.R424C	ENST00000222390	NM_000601.4	424	Cgt/Tgt	10/18	1	2	FACETS	0.75	0.66	0.846	0.75	0.66	0.846	SUBCLONAL	1	TRUE	1	0.29	2		291	745	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306713	41306713	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1357	81	526	0	ENST00000373198.4:c.946G>C	p.Gly316Arg	p.G316R	ENST00000373198	NM_133170.3	316	Ggg/Cgg	7/32	0.288099810738082	5	FACETS	0.557	0.489	0.632	0.139	0.122	0.158	SUBCLONAL	1	TRUE	1	0.29	5		526	1438	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595892	52595892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	80	539	2	ENST00000394830.3:c.4023G>A	p.Met1341Ile	p.M1341I	ENST00000394830	NM_018313.4	1341	atG/atA	26/30	0.178425136793497	1	FACETS	0.454	0.398	0.514	0.454	0.398	0.514	SUBCLONAL	1	TRUE	0	0.29	1		541	1040	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481477	140481477	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1328	145	640	2	ENST00000288602.6:c.1331G>A	p.Arg444Gln	p.R444Q	ENST00000288602	NM_004333.4	444	cGg/cAg	11/18	1	2	FACETS	0.679	0.617	0.744	0.679	0.617	0.744	SUBCLONAL	1	TRUE	1	0.29	2		642	1473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0014908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	333	328	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.741969502648092	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	FALSE	0	0.755555971923938	2		328	433	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0014908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	97	584	1	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	0.128360111602325	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.755555971923938	0		585	252	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143044	30143044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	35	956	5	ENST00000389048.3:c.482C>T	p.Ala161Val	p.A161V	ENST00000389048	NM_004304.4	161	gCg/gTg	1/29	0.128360111602325	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.755555971923938	0		961	388	SUCCESS
APC	324	MSKCC	GRCh37	5	112175475	112175476	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTTTGAGA	novel	NA	P-0014908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	16	325	0	ENST00000257430.4:c.4185_4192dup	p.Ser1398IlefsTer20	p.S1398Ifs*20	ENST00000257430	NM_000038.5	1395	agt/agTTTTGAGAt	16/16	0.128360111602325	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.755555971923938	0		325	128	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845970	156845970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	35	720	1	ENST00000524377.1:c.1600C>T	p.Pro534Ser	p.P534S	ENST00000524377	NM_002529.3	534	Cct/Tct	13/17	0.737027342141345	3	FACETS	0.275	0.225	0.331	0.092	0.075	0.111	SUBCLONAL	1	FALSE	0	0.755555971923938	3		721	464	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100732	8100732	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs148835259	NA	P-0014908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	114	789	0	ENST00000346208.3:c.706C>G	p.Pro236Ala	p.P236A	ENST00000346208		236	Ccc/Gcc	3/6	0.241814967124157	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.755555971923938	0		789	345	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256167	133256167	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1060500782	NA	P-0014908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	22	569	0	ENST00000320574.5:c.494A>C	p.Lys165Thr	p.K165T	ENST00000320574	NM_006231.2	165	aAa/aCa	6/49	0.128360111602325	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.755555971923938	0		569	309	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438148	56438148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	534	949	1	ENST00000407977.2:c.845G>A	p.Gly282Glu	p.G282E	ENST00000407977		282	gGg/gAg	7/10	0.755555971923938	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	FALSE	0	0.755555971923938	2		950	635	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144027	11144027	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	198	778	1	ENST00000358026.2:c.3608G>T	p.Arg1203Leu	p.R1203L	ENST00000358026	NM_001128849.1	1203	cGc/cTc	26/36	0.279560394574268	1	FACETS	0.606	0.566	0.647	0.606	0.566	0.647	INDETERMINATE	1	FALSE	0	0.755555971923938	1		779	538	SUCCESS
APC	324	MSKCC	GRCh37	5	112174172	112174173	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATGATAGTTT	novel	NA	P-0014908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	34	442	0	ENST00000257430.4:c.2883_2892dup	p.Asn965Ter	p.N965*	ENST00000257430	NM_000038.5	961	aat/aATGATAGTTTat	16/16	0.128360111602325	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.755555971923938	0		442	141	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0016969-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	113	695	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.24437099211213	2	FACETS	0.797	0.72	0.877	0.797	0.72	0.877	SUBCLONAL	2	TRUE	0	0.278672038143779	2		695	509	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016969-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	65	459	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	0.958	0.832	1	0.958	0.832	1	CLONAL	1	TRUE	1	0.278672038143779	2		459	487	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661621	227661621	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016969-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	34	527	0	ENST00000305123.5:c.1834T>C	p.Tyr612His	p.Y612H	ENST00000305123	NM_005544.2	612	Tac/Cac	1/2	0.268747756605248	1	FACETS	0.431	0.352	0.521	0.431	0.352	0.521	SUBCLONAL	1	TRUE	0	0.278672038143779	1		527	487	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928071	178928097	+	inframe_deletion	In_Frame_Del	DEL	ATGGATTAGAAGATTTGCTGAACCCTA	ATGGATTAGAAGATTTGCTGAACCCTA	-	novel	NA	P-0016969-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	105	307	0	ENST00000263967.3:c.1349_1375del	p.His450_Ile459delinsLeu	p.H450_I459delinsL	ENST00000263967	NM_006218.2	450	cATGGATTAGAAGATTTGCTGAACCCTAtt/ctt	8/21	0.219632996396846	3	FACETS	1	0.911	1	0.673	0.607	0.742	CLONAL	2	TRUE	0	0.278672038143779	3		307	425	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30954194	30954194	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016969-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	33	308	0	ENST00000375687.4:c.68del	p.Asn23ThrfsTer7	p.N23Tfs*7	ENST00000375687	NM_015338.5	22	gAa/ga	2/13	0.232192501668078	3	FACETS	0.694	0.565	0.838	0.347	0.282	0.419	SUBCLONAL	1	TRUE	1	0.278672038143779	3		308	389	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976805	2976805	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016969-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	55	433	0	ENST00000396946.4:c.1207T>A	p.Tyr403Asn	p.Y403N	ENST00000396946	NM_032415.4	403	Tac/Aac	9/25	0.278672038143779	5	FACETS	0.812	0.694	0.942	0.162	0.138	0.189	CLONAL	1	TRUE	0	0.278672038143779	5		433	689	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	289	302	0				ENST00000310581	NM_198253.2	-/1132			0.707810863597258	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.925861213146135	4		302	563	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0017163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	236	427	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.925861213146135	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.925861213146135	3		427	370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0017163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	629	609	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.925861213146135	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.925861213146135	3		609	654	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156720	20156720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	89	172	0	ENST00000379607.5:c.37C>T	p.Arg13Cys	p.R13C	ENST00000379607	NM_001412.3	13	Cgc/Tgc	2/7	0.841327070765459	2	FACETS	0.933	0.886	0.973			1	CLONAL	2	TRUE	NA	0.925861213146135	2		172	103	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123836	46123836	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	154	594	0	ENST00000334344.6:c.102T>A	p.Phe34Leu	p.F34L	ENST00000334344	NM_152641.2	34	ttT/ttA	2/21	0.205177480864416	4	FACETS	1	0.987	1	0.339	0.312	0.366	INDETERMINATE	1	TRUE	0	0.925861213146135	4		594	473	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051011	180051011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146167161	NA	P-0017163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	533	603	0	ENST00000261937.6:c.1472C>T	p.Ala491Val	p.A491V	ENST00000261937	NM_182925.4	491	gCg/gTg	11/30	0.915307661930425	3	FACETS	0.985	0.971	0.998	0.985	0.971	0.998	CLONAL	3	TRUE	0	0.925861213146135	3		603	570	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305412	65305412	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	606	568	0	ENST00000342505.4:c.2716G>T	p.Ala906Ser	p.A906S	ENST00000342505	NM_002227.2	906	Gct/Tct	20/25	0.924456724072217	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	1	0.925861213146135	4		568	825	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410667	32410667	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	388	491	0	ENST00000332351.3:c.1491T>A	p.Asp497Glu	p.D497E	ENST00000332351	NM_024426.4	497	gaT/gaA	10/10	0.464881380906847	6	FACETS	0.991	0.948	1	0.991	0.948	1	INDETERMINATE	3	TRUE	3	0.925861213146135	6		491	804	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480477	89480477	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1411035734	NA	P-0017163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	339	454	0	ENST00000336596.2:c.2314G>C	p.Glu772Gln	p.E772Q	ENST00000336596	NM_005233.5	772	Gag/Cag	13/17	0.906714662311175	2	FACETS	0.969	0.947	0.988	0.969	0.947	0.988	CLONAL	2	TRUE	0	0.925861213146135	2		454	378	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845934	72845934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759043061	NA	P-0017163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	172	492	0	ENST00000268489.5:c.3533C>T	p.Ser1178Leu	p.S1178L	ENST00000268489	NM_006885.3	1178	tCg/tTg	6/10	0.914246825404047	5	FACETS	1	0.932	1	0.203	0.186	0.22	CLONAL	1	TRUE	0	0.925861213146135	5		492	876	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622272	162622369	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTGATCTACCTGCTGGAGAAGAAAAAGCAGAAGAAGTGGCTAATAATGCTGCATCTAAATTGAGACAAGAAACTCTTTAAAAGCTTGTTAGAGGCAA	ATTGATCTACCTGCTGGAGAAGAAAAAGCAGAAGAAGTGGCTAATAATGCTGCATCTAAATTGAGACAAGAAACTCTTTAAAAGCTTGTTAGAGGCAA	-	novel	NA	P-0017163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	103	470	0	ENST00000366898.1:c.413-85_425del		p.X138_splice	ENST00000366898	NM_004562.2	138		4/12	0.925861213146135	3	FACETS	0.62	0.557	0.687	0.207	0.185	0.229	SUBCLONAL	1	TRUE	0	0.925861213146135	3		470	525	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0018241-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	138	192	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.328371046910561	4	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	2	0.389890896745262	4		192	480	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435202	18435203	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0018241-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	105	399	0	ENST00000266497.5:c.187_188insC	p.Phe63SerfsTer18	p.F63Sfs*18	ENST00000266497		63	ttt/tCtt	1/31	0.328371046910561	4	FACETS	1	0.945	1	0.541	0.485	0.6	CLONAL	1	TRUE	2	0.389890896745262	4		399	692	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435641	110435641	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018241-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	77	367	0	ENST00000375856.3:c.2760C>G	p.Ile920Met	p.I920M	ENST00000375856	NM_003749.2	920	atC/atG	1/2	0.345367816418303	4	FACETS	0.93	0.818	1	0.465	0.409	0.526	CLONAL	1	TRUE	2	0.389890896745262	4		367	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0018241-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	188	350	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.365424503120133	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.389890896745262	2		350	452	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525485	137525485	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018241-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	79	256	0	ENST00000367739.4:c.530G>C	p.Arg177Thr	p.R177T	ENST00000367739	NM_000416.2	177	aGa/aCa	4/7	0.384823592041664	3	FACETS	1	0.888	1	0.503	0.444	0.567	CLONAL	1	TRUE	1	0.389890896745262	3		256	481	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213507	27213507	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018241-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	86	286	0	ENST00000380036.4:c.2903G>C	p.Arg968Thr	p.R968T	ENST00000380036	NM_000459.3	968	aGa/aCa	18/23	0.389890896745262	5	FACETS	1	0.954	1	0.385	0.34	0.432	CLONAL	1	TRUE	2	0.389890896745262	5		286	606	SUCCESS
AR	367	MSKCC	GRCh37	X	66766199	66766199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035114992	NA	P-0018241-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	16	234	0	ENST00000374690.3:c.1211C>T	p.Ala404Val	p.A404V	ENST00000374690	NM_000044.3	404	gCg/gTg	1/8	0.377864213950658	2	FACETS	0.274	0.202	0.361			1	SUBCLONAL	1	TRUE	NA	0.389890896745262	2		234	299	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0018281-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	28	378	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	0.234	0.187	0.289	0.234	0.187	0.289	SUBCLONAL	1	TRUE	1	0.469460133566078	2		378	509	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	75	963	1				ENST00000310581	NM_198253.2	-/1132			0.335157506482745	1	FACETS	0.676	0.593	0.765	0.676	0.593	0.765	SUBCLONAL	1	TRUE	0	0.335157506482745	1		964	551	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089562	27089562	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	202	968	0	ENST00000324856.7:c.2518C>T	p.Gln840Ter	p.Q840*	ENST00000324856	NM_006015.4	840	Caa/Taa	8/20	0.19645990060914	1	FACETS	1	0.989	1	1	0.989	1	INDETERMINATE	1	TRUE	0	0.335157506482745	1		968	751	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937001	48937001	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	27	508	1	ENST00000267163.4:c.769C>T	p.Gln257Ter	p.Q257*	ENST00000267163	NM_000321.2	257	Cag/Tag	8/27	0.335157506482745	1	FACETS	0.322	0.255	0.397	0.322	0.255	0.397	SUBCLONAL	1	TRUE	0	0.335157506482745	1		509	417	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872213	45872213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	81	967	3	ENST00000391945.4:c.221C>T	p.Ser74Leu	p.S74L	ENST00000391945	NM_000400.3	74	tCa/tTa	4/23	0.247468591531165	1	FACETS	0.629	0.554	0.709	0.629	0.554	0.709	SUBCLONAL	1	TRUE	0	0.335157506482745	1		970	640	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	102	130	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	1	1	FACETS	1	0.934	1	1	0.989	1	CLONAL	2	TRUE	0	0.335157506482745	1		130	246	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799020	42799020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1025458986	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1182	172	1804	1	ENST00000575354.2:c.4504C>T	p.Pro1502Ser	p.P1502S	ENST00000575354	NM_015125.3	1502	Ccc/Tcc	20/20	0.247468591531165	1	FACETS	0.631	0.579	0.686	0.631	0.579	0.686	SUBCLONAL	1	TRUE	0	0.335157506482745	1		1805	1354	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380271	25380271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	66	571	0	ENST00000311936.3:c.187G>A	p.Glu63Lys	p.E63K	ENST00000311936	NM_004985.3	63	Gag/Aag	3/5	1	2	FACETS	0.791	0.688	0.902	0.791	0.688	0.902	CLONAL	1	TRUE	1	0.335157506482745	2		571	498	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431631	6431631	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	135	888	0	ENST00000356142.4:c.184G>A	p.Glu62Lys	p.E62K	ENST00000356142	NM_018890.3	62	Gaa/Aaa	3/7	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.335157506482745	2		888	646	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237610	16237610	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	32	226	0	ENST00000375759.3:c.1057G>C	p.Asp353His	p.D353H	ENST00000375759	NM_015001.2	353	Gat/Cat	5/15	1	2	FACETS	0.984	0.806	1	0.984	0.806	1	CLONAL	1	TRUE	1	0.335157506482745	2		226	194	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094347	27094347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	51	503	0	ENST00000324856.7:c.3055G>A	p.Glu1019Lys	p.E1019K	ENST00000324856	NM_006015.4	1019	Gag/Aag	11/20	0.19645990060914	1	FACETS	0.609	0.519	0.708	0.609	0.519	0.708	INDETERMINATE	1	TRUE	0	0.335157506482745	1		503	416	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432578	78432578	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	21	438	0	ENST00000370768.2:c.405G>C	p.Gln135His	p.Q135H	ENST00000370768	NM_003902.3	135	caG/caC	6/20	1	2	FACETS	0.377	0.29	0.479	0.377	0.29	0.479	SUBCLONAL	1	TRUE	1	0.335157506482745	2		438	332	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830860	156830860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	104	1316	0	ENST00000524377.1:c.134C>T	p.Ser45Phe	p.S45F	ENST00000524377	NM_002529.3	45	tCc/tTc	1/17	0.273736427909439	3	FACETS	0.677	0.604	0.754	0.226	0.201	0.252	SUBCLONAL	1	TRUE	0	0.335157506482745	3		1316	1071	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226553657	226553657	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1320424324	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	114	325	0	ENST00000366794.5:c.2503G>A	p.Asp835Asn	p.D835N	ENST00000366794	NM_001618.3	835	Gat/Aat	18/23	0.273736427909439	3	FACETS	0.843	0.769	0.919	0.843	0.769	0.919	CLONAL	3	TRUE	0	0.335157506482745	3		325	314	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406480	70406480	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	85	866	2	ENST00000373644.4:c.3994C>T	p.Gln1332Ter	p.Q1332*	ENST00000373644	NM_030625.2	1332	Cag/Tag	4/12	0.247468591531165	1	FACETS	0.589	0.52	0.662	0.589	0.52	0.662	SUBCLONAL	1	TRUE	0	0.335157506482745	1		868	717	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692819	89692819	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	15	255	0	ENST00000371953.3:c.303C>G	p.Ile101Met	p.I101M	ENST00000371953	NM_000314.4	101	atC/atG	5/9	0.247468591531165	1	FACETS	0.353	0.258	0.466	0.353	0.258	0.466	SUBCLONAL	1	TRUE	0	0.335157506482745	1		255	211	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742921	17742921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769178698	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	102	1099	0	ENST00000250003.3:c.829G>A	p.Glu277Lys	p.E277K	ENST00000250003	NM_002478.4	277	Gag/Aag	3/3	0.247468591531165	1	FACETS	0.744	0.666	0.827	0.744	0.666	0.827	SUBCLONAL	1	TRUE	0	0.335157506482745	1		1099	681	SUCCESS
EED	8726	MSKCC	GRCh37	11	85956284	85956284	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1250649508	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	27	242	0	ENST00000263360.6:c.13G>A	p.Glu5Lys	p.E5K	ENST00000263360	NM_003797.3	5	Gaa/Aaa	1/12	0.247468591531165	1	FACETS	0.571	0.456	0.7	0.571	0.456	0.7	SUBCLONAL	1	TRUE	0	0.335157506482745	1		242	235	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374012	118374012	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	34	290	0	ENST00000534358.1:c.7405G>A	p.Asp2469Asn	p.D2469N	ENST00000534358	NM_005933.3	2469	Gat/Aat	27/36	0.247468591531165	1	FACETS	0.889	0.734	1	0.889	0.734	1	CLONAL	1	TRUE	0	0.335157506482745	1		290	190	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390745	118390745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	67	342	1	ENST00000534358.1:c.11395G>A	p.Glu3799Lys	p.E3799K	ENST00000534358	NM_005933.3	3799	Gaa/Aaa	33/36	0.247468591531165	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.335157506482745	1		343	269	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120554416	120554416	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	74	343	0	ENST00000229340.5:c.39C>G	p.Ile13Met	p.I13M	ENST00000229340	NM_006861.6	13	atC/atG	1/6	1	2	FACETS	0.783	0.693	0.878	1	0.978	1	SUBCLONAL	2	TRUE	1	0.335157506482745	2		343	282	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911598	32911598	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	23	244	0	ENST00000380152.3:c.3106G>C	p.Glu1036Gln	p.E1036Q	ENST00000380152		1036	Gaa/Caa	11/27	0.294969989225587	4	FACETS	0.786	0.615	0.983			1	CLONAL	1	TRUE	NA	0.335157506482745	4		244	233	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912225	32912225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	35	360	0	ENST00000380152.3:c.3733G>A	p.Glu1245Lys	p.E1245K	ENST00000380152		1245	Gag/Aag	11/27	0.294969989225587	4	FACETS	0.65	0.533	0.782			1	SUBCLONAL	1	TRUE	NA	0.335157506482745	4		360	429	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871597	35871597	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	20	264	0	ENST00000216797.5:c.906+3G>A		p.X302_splice	ENST00000216797	NM_020529.2	302			0.247468591531165	1	FACETS	0.464	0.356	0.59	0.464	0.356	0.59	SUBCLONAL	1	TRUE	0	0.335157506482745	1		264	214	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675520	40675520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	93	686	0	ENST00000249776.8:c.301G>A	p.Ala101Thr	p.A101T	ENST00000249776	NM_033286.3	101	Gca/Aca	2/9	0.247468591531165	1	FACETS	0.802	0.715	0.895	0.802	0.715	0.895	CLONAL	1	TRUE	0	0.335157506482745	1		686	576	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457287	67457287	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	137	869	0	ENST00000327367.4:c.261C>G	p.Ile87Met	p.I87M	ENST00000327367	NM_005902.3	87	atC/atG	2/9	0.247468591531165	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.335157506482745	1		869	615	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295106	91295106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	14	215	0	ENST00000355112.3:c.889G>A	p.Asp297Asn	p.D297N	ENST00000355112	NM_000057.2	297	Gat/Aat	4/22	0.247468591531165	1	FACETS	0.416	0.302	0.554	0.416	0.302	0.554	SUBCLONAL	1	TRUE	0	0.335157506482745	1		215	167	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644823	67644823	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	54	519	0	ENST00000264010.4:c.88G>A	p.Glu30Lys	p.E30K	ENST00000264010	NM_006565.3	30	Gaa/Aaa	3/12	0.335157506482745	2	FACETS	0.713	0.61	0.825	0.356	0.305	0.413	SUBCLONAL	1	TRUE	0	0.335157506482745	2		519	452	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341251	89341251	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	79	813	0	ENST00000301030.4:c.7684G>A	p.Glu2562Lys	p.E2562K	ENST00000301030	NM_001256183.1	2562	Gag/Aag	11/13	NA	2	FACETS	0.725	0.638	0.819			1	INDETERMINATE	1	TRUE	NA	0.335157506482745	2		813	650	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217917	7217917	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	38	241	0	ENST00000380728.2:c.95-1G>A		p.X32_splice	ENST00000380728		32			0.335157506482745	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.335157506482745	1		241	155	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40384156	40384156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	27	533	0	ENST00000293328.3:c.-10-1G>C		p.X4_splice	ENST00000293328	NM_012448.3	4			1	2	FACETS	0.326	0.259	0.404	0.326	0.259	0.404	SUBCLONAL	1	TRUE	1	0.335157506482745	2		533	494	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678029	58678029	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567962294	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	95	459	0	ENST00000305921.3:c.254C>T	p.Ser85Leu	p.S85L	ENST00000305921	NM_003620.3	85	tCg/tTg	1/6	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.335157506482745	2		459	430	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119972	70119972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1348433812	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	126	573	0	ENST00000245479.2:c.974C>T	p.Ala325Val	p.A325V	ENST00000245479	NM_000346.3	325	gCg/gTg	3/3	1	2	FACETS	0.777	0.708	0.849	1	0.987	1	SUBCLONAL	2	TRUE	1	0.335157506482745	2		573	484	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732502	74732502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	36	194	0	ENST00000359995.5:c.407C>T	p.Ser136Phe	p.S136F	ENST00000359995	NM_001195427.1	136	tCc/tTc	2/3	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.335157506482745	2		194	186	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78519590	78519590	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	51	307	2	ENST00000306801.3:c.161G>A	p.Arg54Gln	p.R54Q	ENST00000306801	NM_020761.2	54	cGg/cAg	1/34	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.335157506482745	2		309	274	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4123815	4123815	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	84	979	0	ENST00000262948.5:c.58G>T	p.Glu20Ter	p.E20*	ENST00000262948	NM_030662.3	20	Gag/Tag	1/11	0.247468591531165	1	FACETS	0.595	0.525	0.67	0.595	0.525	0.67	SUBCLONAL	1	TRUE	0	0.335157506482745	1		979	701	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917131	50917131	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	163	1046	0	ENST00000440232.2:c.2383G>C	p.Glu795Gln	p.E795Q	ENST00000440232	NM_002691.3	795	Gag/Cag	19/27	0.247468591531165	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.335157506482745	1		1046	718	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143108	30143108	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	116	1383	0	ENST00000389048.3:c.418C>T	p.Gln140Ter	p.Q140*	ENST00000389048	NM_004304.4	140	Cag/Tag	1/29	0.325264569743023	2	FACETS	0.597	0.537	0.662	0.299	0.268	0.331	SUBCLONAL	1	TRUE	0	0.335157506482745	2		1383	1159	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285805	198285805	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	332	742	0	ENST00000335508.6:c.248G>C	p.Gly83Ala	p.G83A	ENST00000335508	NM_012433.2	83	gGa/gCa	3/25	0.335157506482745	4	FACETS	1	0.99	1			1	CLONAL	3	TRUE	NA	0.335157506482745	4		742	771	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113257	209113257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	32	409	0	ENST00000345146.2:c.250G>A	p.Glu84Lys	p.E84K	ENST00000345146	NM_005896.2	84	Gag/Aag	4/10	1	2	FACETS	0.516	0.419	0.625	0.516	0.419	0.625	SUBCLONAL	1	TRUE	1	0.335157506482745	2		409	370	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012684	36012684	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	42	291	1	ENST00000358208.4:c.128C>T	p.Ser43Leu	p.S43L	ENST00000358208		43	tCg/tTg	2/12	0.247468591531165	1	FACETS	0.712	0.597	0.838	0.712	0.597	0.838	SUBCLONAL	1	TRUE	0	0.335157506482745	1		292	293	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279766	46279766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	149	749	0	ENST00000371998.3:c.3692G>A	p.Arg1231Lys	p.R1231K	ENST00000371998		1231	aGa/aAa	20/23	0.247468591531165	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.335157506482745	1		749	515	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035172	30035172	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	42	508	0	ENST00000338641.4:c.334G>C	p.Glu112Gln	p.E112Q	ENST00000338641	NM_000268.3	112	Gag/Cag	3/16	0.335157506482745	1	FACETS	0.589	0.493	0.695	0.589	0.493	0.695	SUBCLONAL	1	TRUE	0	0.335157506482745	1		508	354	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568524	41568524	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	20	315	0	ENST00000263253.7:c.4474G>T	p.Glu1492Ter	p.E1492*	ENST00000263253	NM_001429.3	1492	Gaa/Taa	28/31	0.335157506482745	1	FACETS	0.574	0.442	0.727	0.574	0.442	0.727	SUBCLONAL	1	TRUE	0	0.335157506482745	1		315	173	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568605	41568605	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	30	387	0	ENST00000263253.7:c.4555G>C	p.Glu1519Gln	p.E1519Q	ENST00000263253	NM_001429.3	1519	Gaa/Caa	28/31	0.335157506482745	1	FACETS	0.753	0.611	0.91	0.753	0.611	0.91	CLONAL	1	TRUE	0	0.335157506482745	1		387	198	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37059008	37059008	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs748423430	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	29	467	0	ENST00000231790.2:c.802G>C	p.Glu268Gln	p.E268Q	ENST00000231790	NM_000249.3	268	Gaa/Caa	10/19	0.153747263286648	3	FACETS	0.504	0.404	0.617	0.252	0.202	0.309	INDETERMINATE	1	TRUE	1	0.335157506482745	3		467	401	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181396	38181396	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	73	472	0	ENST00000396334.3:c.409G>T	p.Glu137Ter	p.E137*	ENST00000396334	NM_002468.4	137	Gag/Tag	2/5	0.153747263286648	3	FACETS	1	0.955	1	0.597	0.524	0.675	INDETERMINATE	1	TRUE	1	0.335157506482745	3		472	426	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037219	71037219	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	61	348	0	ENST00000318789.4:c.1072G>C	p.Asp358His	p.D358H	ENST00000318789	NM_032682.5	358	Gac/Cac	14/21	0.247468591531165	1	FACETS	0.866	0.751	0.989	0.866	0.751	0.989	CLONAL	1	TRUE	0	0.335157506482745	1		348	350	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390135	89390135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	24	257	0	ENST00000336596.2:c.884C>T	p.Ser295Phe	p.S295F	ENST00000336596	NM_005233.5	295	tCt/tTt	4/17	0.247468591531165	1	FACETS	0.469	0.369	0.584	0.469	0.369	0.584	SUBCLONAL	1	TRUE	0	0.335157506482745	1		257	254	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198035	185198035	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1384908531	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	21	354	0	ENST00000265026.3:c.2517C>G	p.Ile839Met	p.I839M	ENST00000265026	NM_004721.4	839	atC/atG	13/14	0.153747263286648	3	FACETS	0.491	0.378	0.622	0.245	0.189	0.311	INDETERMINATE	1	TRUE	1	0.335157506482745	3		354	298	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958791	55958791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	37	691	0	ENST00000263923.4:c.3062C>T	p.Ser1021Leu	p.S1021L	ENST00000263923	NM_002253.2	1021	tCg/tTg	22/30	1	2	FACETS	0.449	0.369	0.538	0.449	0.369	0.538	SUBCLONAL	1	TRUE	1	0.335157506482745	2		691	492	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958823	55958870	+	protein_altering_variant	In_Frame_Del	DEL	GAAGCTGTAACAGATGAGATGCTCCAAGGTCAGGAAGTCCTTATACAG	GAAGCTGTAACAGATGAGATGCTCCAAGGTCAGGAAGTCCTTATACAG	ATACAA	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	30	689	2	ENST00000263923.4:c.2983_3030delinsTTGTAT	p.Lys997_Phe1010del	p.K997_F1010del	ENST00000263923	NM_002253.2	995	CTGTATAAGGACTTCCTGACCTTGGAGCATCTCATCTGTTACAGCTTC/TTGTAT	22/30	1	2	FACETS	0.359	0.288	0.439	0.359	0.288	0.439	SUBCLONAL	1	TRUE	1	0.335157506482745	2		691	499	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197085	26197085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	19	353	0	ENST00000356476.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000356476		132	Cgt/Tgt	1/1	0.153747263286648	3	FACETS	0.411	0.312	0.528	0.206	0.156	0.264	INDETERMINATE	1	TRUE	1	0.335157506482745	3		353	322	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250440	26250440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	45	352	0	ENST00000446824.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000446824	NM_021018.2	132	Cgc/Tgc	1/1	0.153747263286648	3	FACETS	0.974	0.822	1	0.487	0.411	0.57	INDETERMINATE	1	TRUE	1	0.335157506482745	3		352	322	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839778	27839778	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	98	487	0	ENST00000328488.2:c.316G>A	p.Glu106Lys	p.E106K	ENST00000328488	NM_003533.2	106	Gag/Aag	1/1	0.153747263286648	3	FACETS	0.764	0.685	0.846	0.764	0.685	0.846	INDETERMINATE	2	TRUE	1	0.335157506482745	3		487	447	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839889	27839889	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	67	541	0	ENST00000328488.2:c.205C>G	p.Gln69Glu	p.Q69E	ENST00000328488	NM_003533.2	69	Cag/Gag	1/1	0.153747263286648	3	FACETS	0.891	0.775	1	0.445	0.387	0.508	INDETERMINATE	1	TRUE	1	0.335157506482745	3		541	524	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816480	32816480	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	90	1029	0	ENST00000354258.4:c.1695C>G	p.Phe565Leu	p.F565L	ENST00000354258	NM_000593.5	565	ttC/ttG	7/11	1	2	FACETS	0.519	0.459	0.583	0.519	0.459	0.583	SUBCLONAL	1	TRUE	1	0.335157506482745	2		1029	1035	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820190	32820190	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757711839	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	136	786	0	ENST00000354258.4:c.868C>T	p.Leu290Phe	p.L290F	ENST00000354258	NM_000593.5	290	Ctc/Ttc	2/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.335157506482745	2		786	621	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199864	138199864	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	67	577	0	ENST00000237289.4:c.1282G>C	p.Glu428Gln	p.E428Q	ENST00000237289	NM_001270507.1	428	Gag/Cag	7/9	0.247468591531165	1	FACETS	0.695	0.605	0.791	0.695	0.605	0.791	SUBCLONAL	1	TRUE	0	0.335157506482745	1		577	479	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150424	157150424	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	73	686	0	ENST00000346085.5:c.1606C>T	p.His536Tyr	p.H536Y	ENST00000346085	NM_020732.3	536	Cat/Tat	2/20	0.247468591531165	1	FACETS	0.628	0.55	0.713	0.628	0.55	0.713	SUBCLONAL	1	TRUE	0	0.335157506482745	1		686	577	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522635	106522635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	46	309	0	ENST00000359195.3:c.2612C>T	p.Ser871Leu	p.S871L	ENST00000359195	NM_002649.2	871	tCa/tTa	7/11	0.335157506482745	3	FACETS	1	0.936	1	0.602	0.511	0.702	CLONAL	1	TRUE	1	0.335157506482745	3		309	266	SUCCESS
MET	4233	MSKCC	GRCh37	7	116414509	116414509	+	intron_variant	Intron	SNP	G	G	C	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	62	542	0	ENST00000397752.3:c.3029-426G>C		p.*1010*	ENST00000397752	NM_000245.2	-/1390			0.335157506482745	3	FACETS	0.88	0.761	1	0.44	0.38	0.504	CLONAL	1	TRUE	1	0.335157506482745	3		542	491	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853131	151853131	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	86	366	0	ENST00000262189.6:c.11824C>G	p.Leu3942Val	p.L3942V	ENST00000262189	NM_170606.2	3942	Cta/Gta	46/59	0.335157506482745	3	FACETS	0.808	0.72	0.9	0.808	0.72	0.9	CLONAL	2	TRUE	1	0.335157506482745	3		366	371	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205058	38205058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142206759	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	45	437	0	ENST00000317025.8:c.632G>A	p.Arg211His	p.R211H	ENST00000317025	NM_023034.1	211	cGc/cAc	2/24	0.335157506482745	7	FACETS	0.685	0.574	0.808			1	SUBCLONAL	1	TRUE	NA	0.335157506482745	7		437	721	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239692	53239692	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	110	475	0	ENST00000375401.3:c.1650G>T	p.Lys550Asn	p.K550N	ENST00000375401	NM_004187.3	550	aaG/aaT	12/26	1	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.335157506482745	1		475	448	SUCCESS
BLM	641	MSKCC	GRCh37	15	91337480	91337480	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs764965627	NA	P-0019007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	28	187	0	ENST00000355112.3:c.3103G>C	p.Glu1035Gln	p.E1035Q	ENST00000355112	NM_000057.2	1035	Gaa/Caa	16/22	0.247468591531165	1	FACETS	0.959	0.777	1	0.959	0.777	1	CLONAL	1	TRUE	0	0.335157506482745	1		187	145	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	409	302	0				ENST00000310581	NM_198253.2	-/1132			0.244684468694275	11	FACETS	1	0.965	1	1	0.965	1	CLONAL	9	FALSE	2	0.244684468694275	11		302	776	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179050	123179050	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	43	548	0	ENST00000218089.9:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000218089	NM_001042749.1	167	Cag/Tag	8/35	0.100484999654753	3	FACETS	1	0.948	1			1	INDETERMINATE	1	FALSE	NA	0.244684468694275	3		548	294	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436941	110436941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	54	201	1	ENST00000375856.3:c.1460C>T	p.Ser487Phe	p.S487F	ENST00000375856	NM_003749.2	487	tCc/tTc	1/2	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	1	0.244684468694275	2		202	365	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89874760	89874760	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	47	460	0	ENST00000389301.3:c.538G>C	p.Glu180Gln	p.E180Q	ENST00000389301	NM_000135.2	180	Gaa/Caa	6/43	0.244684468694275	5	FACETS	0.898	0.757	1	0.299	0.252	0.351	CLONAL	1	FALSE	2	0.244684468694275	5		460	585	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917611	151917611	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs938655561	NA	P-0020252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	76	503	0	ENST00000262189.6:c.3709C>T	p.Arg1237Ter	p.R1237*	ENST00000262189	NM_170606.2	1237	Cga/Tga	23/59	0.244684468694275	6	FACETS	1	0.926	1	0.795	0.704	0.89	CLONAL	3	FALSE	2	0.244684468694275	6		503	291	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911143	32911143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777421358	NA	P-0020252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	12	311	0	ENST00000380152.3:c.2651C>T	p.Ser884Leu	p.S884L	ENST00000380152		884	tCa/tTa	11/27	1	2	FACETS	1	0.753	1	1	0.753	1	CLONAL	1	FALSE	1	0.244684468694275	2		311	92	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205167	61205167	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	124	500	0	ENST00000301761.2:c.107G>C	p.Arg36Thr	p.R36T	ENST00000301761	NM_017841.2	36	aGa/aCa	2/4	0.244684468694275	5	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	FALSE	3	0.244684468694275	5		500	671	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426583	49426583	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	224	811	0	ENST00000301067.7:c.11905C>T	p.Gln3969Ter	p.Q3969*	ENST00000301067	NM_003482.3	3969	Cag/Tag	39/54	0.244684468694275	6	FACETS	1	0.986	1	0.812	0.756	0.871	CLONAL	2	FALSE	3	0.244684468694275	6		811	1119	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828647	72828647	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	147	652	0	ENST00000268489.5:c.7934G>T	p.Arg2645Ile	p.R2645I	ENST00000268489	NM_006885.3	2645	aGa/aTa	9/10	0.244684468694275	6	FACETS	1	0.973	1	0.771	0.704	0.84	CLONAL	2	FALSE	3	0.244684468694275	6		652	774	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829248	72829248	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	239	715	0	ENST00000268489.5:c.7333G>T	p.Glu2445Ter	p.E2445*	ENST00000268489	NM_006885.3	2445	Gaa/Taa	9/10	0.244684468694275	6	FACETS	0.848	0.791	0.907	0.848	0.791	0.907	CLONAL	3	FALSE	3	0.244684468694275	6		715	1144	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829616	72829616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745878919	NA	P-0020252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	112	558	0	ENST00000268489.5:c.6965G>A	p.Arg2322Gln	p.R2322Q	ENST00000268489	NM_006885.3	2322	cGa/cAa	9/10	0.244684468694275	6	FACETS	1	0.963	1	0.76	0.685	0.839	CLONAL	2	FALSE	3	0.244684468694275	6		558	598	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829773	72829773	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	141	693	1	ENST00000268489.5:c.6808G>A	p.Asp2270Asn	p.D2270N	ENST00000268489	NM_006885.3	2270	Gat/Aat	9/10	0.244684468694275	6	FACETS	1	0.975	1	0.789	0.72	0.861	CLONAL	2	FALSE	3	0.244684468694275	6		694	725	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793295	242793295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	213	867	0	ENST00000334409.5:c.782C>T	p.Ser261Phe	p.S261F	ENST00000334409	NM_005018.2	261	tCc/tTc	5/5	0.165799119300252	5	FACETS	1	0.983	1	0.786	0.73	0.844	CLONAL	2	FALSE	2	0.244684468694275	5		867	1009	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36024625	36024625	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	235	803	0	ENST00000358208.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000358208		205	tAc/tGc	6/12	0.244684468694275	5	FACETS	1	0.985	1	0.792	0.739	0.847	CLONAL	2	FALSE	2	0.244684468694275	5		803	1105	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279744	46279744	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	113	361	0	ENST00000371998.3:c.3670C>T	p.Gln1224Ter	p.Q1224*	ENST00000371998		1224	Caa/Taa	20/23	0.244684468694275	5	FACETS	1	0.949	1	0.721	0.65	0.795	CLONAL	2	FALSE	2	0.244684468694275	5		361	584	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117739663	117739663	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	27	285	0	ENST00000368508.3:c.130C>G	p.Gln44Glu	p.Q44E	ENST00000368508	NM_002944.2	44	Cag/Gag	2/43	1	2	FACETS	0.721	0.575	0.888	0.721	0.575	0.888	SUBCLONAL	1	FALSE	1	0.244684468694275	2		285	306	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462494	92462494	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs748860173	NA	P-0020252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	84	482	0	ENST00000265734.4:c.144G>C	p.Gln48His	p.Q48H	ENST00000265734	NM_001259.6	48	caG/caC	2/8	0.244684468694275	6	FACETS	0.926	0.816	1	0.232	0.204	0.262	CLONAL	1	FALSE	2	0.244684468694275	6		482	1104	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	598	302	0				ENST00000310581	NM_198253.2	-/1132			0.44096241060481	5	FACETS	0.919	0.883	0.955	0.689	0.662	0.716	CLONAL	3	FALSE	1	0.44096241060481	5		302	1635	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0022070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	34	259	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.44463011965325	0	FACETS	0.712	0.595	0.839			1	SUBCLONAL	1	FALSE	0	0.44096241060481	0		259	121	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747129	40747129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	24	818	0	ENST00000373198.4:c.2953G>A	p.Glu985Lys	p.E985K	ENST00000373198	NM_133170.3	985	Gag/Aag	22/32	0.343947443858625	3	FACETS	0.404	0.316	0.504	0.202	0.158	0.252	SUBCLONAL	1	FALSE	1	0.44096241060481	3		818	329	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258970	153258970	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	12	653	0	ENST00000281708.4:c.845C>A	p.Ser282Ter	p.S282*	ENST00000281708	NM_033632.3	282	tCa/tAa	5/12	0.44463011965325	0	FACETS	0.166	0.117	0.227			1	SUBCLONAL	1	FALSE	0	0.44096241060481	0		653	183	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622184	162622184	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	28	640	0	ENST00000366898.1:c.513G>T	p.Gln171His	p.Q171H	ENST00000366898	NM_004562.2	171	caG/caT	4/12	0.343947443858625	3	FACETS	0.548	0.439	0.671	0.274	0.219	0.336	SUBCLONAL	1	FALSE	1	0.44096241060481	3		640	283	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158611	26158611	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	157	512	0	ENST00000289316.2:c.214G>C	p.Glu72Gln	p.E72Q	ENST00000289316	NM_138720.2	72	Gag/Cag	1/2	0.44463011965325	3	FACETS	0.814	0.75	0.879	0.814	0.75	0.879	CLONAL	2	FALSE	1	0.44096241060481	3		512	534	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736450	85736450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	21	879	0	ENST00000370580.1:c.197G>A	p.Gly66Glu	p.G66E	ENST00000370580	NM_003921.4	66	gGa/gAa	2/3	0.161744758752085	5	FACETS	0.646	0.498	0.817	0.215	0.166	0.273	INDETERMINATE	1	FALSE	2	0.44096241060481	5		879	245	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551711	150551715	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAA	AAGAA	-	novel	NA	P-0022070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	62	415	0	ENST00000369026.2:c.292_296del	p.Phe98ArgfsTer10	p.F98Rfs*10	ENST00000369026	NM_021960.4	98	TTCTTc/c	1/3	0.44463011965325	4	FACETS	0.429	0.369	0.495	0.215	0.184	0.248	SUBCLONAL	1	FALSE	2	0.44096241060481	4		415	944	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202530	67202530	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1760	305	1056	0	ENST00000312629.5:c.1339C>G	p.Leu447Val	p.L447V	ENST00000312629	NM_003952.2	447	Cta/Gta	15/15	0.23338002965107	3	FACETS	0.818	0.767	0.87	0.273	0.255	0.29	INDETERMINATE	1	FALSE	0	0.44096241060481	3		1056	2065	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233195	69233195	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	44	509	0	ENST00000462284.1:c.1060G>A	p.Glu354Lys	p.E354K	ENST00000462284	NM_002392.5	354	Gaa/Aaa	11/11	0.36468472382848	3	FACETS	0.786	0.662	0.921	0.393	0.331	0.461	CLONAL	1	FALSE	1	0.44096241060481	3		509	310	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046641	42046642	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0022070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	22	314	0	ENST00000219905.7:c.7018_7019del	p.Val2340ArgfsTer4	p.V2340Rfs*4	ENST00000219905	NM_001164273.1	2339	TGt/t	18/24	0.343947443858625	3	FACETS	0.68	0.531	0.851	0.34	0.265	0.426	SUBCLONAL	1	FALSE	1	0.44096241060481	3		314	179	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650701	67650701	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	186	1011	0	ENST00000264010.4:c.1006G>A	p.Glu336Lys	p.E336K	ENST00000264010	NM_006565.3	336	Gaa/Aaa	5/12	0.161744758752085	5	FACETS	1	0.962	1	0.705	0.653	0.758	INDETERMINATE	2	FALSE	2	0.44096241060481	5		1011	663	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944527	40944528	+	missense_variant	Missense_Mutation	DNP	CG	CG	TA	novel	NA	P-0022070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	64	943	4	ENST00000373198.4:c.1974_1975delinsTA	p.Asp659Asn	p.D659N	ENST00000373198	NM_133170.3	658	ctCGat/ctTAat	12/32	0.343947443858625	3	FACETS	0.665	0.576	0.761	0.332	0.288	0.381	SUBCLONAL	1	FALSE	1	0.44096241060481	3		947	533	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280209	142280209	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	42	778	0	ENST00000350721.4:c.1225G>C	p.Glu409Gln	p.E409Q	ENST00000350721	NM_001184.3	409	Gag/Cag	5/47	0.282087615799156	3	FACETS	0.468	0.39	0.554	0.156	0.13	0.185	SUBCLONAL	1	FALSE	0	0.44096241060481	3		778	497	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324159	31324160	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0022070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1369	451	981	0	ENST00000412585.2:c.403dup	p.Arg135ProfsTer4	p.R135Pfs*4	ENST00000412585	NM_005514.6	135	cgc/cCgc	3/8	0.30683586894803	2	FACETS	1	0.989	1	0.562	0.535	0.59	CLONAL	1	FALSE	0	0.44096241060481	2		981	1820	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265562	152265562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	88	800	2	ENST00000206249.3:c.1015G>A	p.Glu339Lys	p.E339K	ENST00000206249	NM_000125.3	339	Gaa/Aaa	4/8	0.343947443858625	3	FACETS	1	0.946	1	0.551	0.49	0.615	CLONAL	1	FALSE	1	0.44096241060481	3		802	442	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265573	152265573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	81	791	1	ENST00000206249.3:c.1026G>A	p.Met342Ile	p.M342I	ENST00000206249	NM_000125.3	342	atG/atA	4/8	0.343947443858625	3	FACETS	1	0.918	1	0.523	0.462	0.586	CLONAL	1	FALSE	1	0.44096241060481	3		792	429	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922795	44922813	+	frameshift_variant	Frame_Shift_Del	DEL	CGTCTCTCAGCCTGGAGTC	CGTCTCTCAGCCTGGAGTC	-	novel	NA	P-0022070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	28	380	0	ENST00000377967.4:c.1660_1678del	p.Ser554LeufsTer33	p.S554Lfs*33	ENST00000377967	NM_021140.2	552	agCGTCTCTCAGCCTGGAGTC/ag	16/29	0.426346141273694	2	FACETS	0.852	0.69	1			1	CLONAL	1	FALSE	NA	0.44096241060481	2		380	149	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022194-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	37	302	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.998	0.853	1	0.998	0.853	1	CLONAL	1	TRUE	1	0.832965117230553	2		302	89	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0022194-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	179	387	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.832965117230553	4	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	2	0.832965117230553	4		387	387	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451522	70451522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022194-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	164	731	0	ENST00000373644.4:c.6362C>T	p.Ser2121Phe	p.S2121F	ENST00000373644	NM_030625.2	2121	tCc/tTc	12/12	0.832965117230553	3	FACETS	1	0.925	1	0.501	0.462	0.54	CLONAL	1	TRUE	1	0.832965117230553	3		731	557	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416646	29416646	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544926207	NA	P-0022194-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	100	403	1	ENST00000389048.3:c.4307G>A	p.Arg1436His	p.R1436H	ENST00000389048	NM_004304.4	1436	cGc/cAc	29/29	0.50018357916037	4	FACETS	1	0.922	1	0.515	0.463	0.57	CLONAL	1	TRUE	2	0.832965117230553	4		404	427	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022194-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	333	817	5	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	0.832965117230553	4	FACETS	0.977	0.93	1	0.977	0.93	1	CLONAL	2	TRUE	2	0.832965117230553	4		822	750	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450885	70450885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022194-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	108	568	1	ENST00000373644.4:c.5725C>T	p.Pro1909Ser	p.P1909S	ENST00000373644	NM_030625.2	1909	Cct/Tct	12/12	0.832965117230553	3	FACETS	0.967	0.875	1	0.483	0.437	0.531	CLONAL	1	TRUE	1	0.832965117230553	3		569	380	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450901	70450901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022194-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	99	579	1	ENST00000373644.4:c.5741C>T	p.Ser1914Phe	p.S1914F	ENST00000373644	NM_030625.2	1914	tCt/tTt	12/12	0.832965117230553	3	FACETS	0.903	0.813	0.997	0.451	0.406	0.499	CLONAL	1	TRUE	1	0.832965117230553	3		580	373	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427746	49427746	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022194-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	344	674	0	ENST00000301067.7:c.10742T>G	p.Val3581Gly	p.V3581G	ENST00000301067	NM_003482.3	3581	gTc/gGc	39/54	0.832965117230553	4	FACETS	0.931	0.895	0.967	0.931	0.895	0.967	CLONAL	3	TRUE	1	0.832965117230553	4		674	542	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879598	37879599	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCG	novel	NA	P-0022194-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	263	676	0	ENST00000269571.5:c.1973_1974insCCG	p.Val658_Val659insArg	p.V658_V659insR	ENST00000269571		658	gtg/gtCCGg	17/27	0.832965117230553	3	FACETS	0.934	0.888	0.98	0.934	0.888	0.98	CLONAL	2	TRUE	1	0.832965117230553	3		676	479	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843243	128843243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173715127	NA	P-0022194-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	246	592	1	ENST00000249373.3:c.350G>A	p.Arg117His	p.R117H	ENST00000249373	NM_005631.4	117	cGc/cAc	2/12	0.832965117230553	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.832965117230553	4		593	512	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798755	135798755	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0022194-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	223	273	0	ENST00000298552.3:c.488C>G	p.Ser163Ter	p.S163*	ENST00000298552	NM_001162426.1	163	tCa/tGa	6/23	0.832965117230553	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.832965117230553	3		273	244	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803114	1803114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022194-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	108	533	0	ENST00000260795.2:c.466C>T	p.Pro156Ser	p.P156S	ENST00000260795		156	Ccc/Tcc	4/17	0.741494870640642	3	FACETS	1	0.939	1	0.523	0.474	0.574	CLONAL	1	TRUE	1	0.832965117230553	3		533	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579366	7579366	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0022283-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	420	533	0	ENST00000269305.4:c.321C>G	p.Tyr107Ter	p.Y107*	ENST00000269305	NM_001126112.2	107	taC/taG	4/11	0.709498027091202	3	FACETS	0.89	0.867	0.911	0.89	0.867	0.911	CLONAL	3	TRUE	0	0.892092106865458	3		533	510	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222982	1222982	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs727504172	NA	P-0022283-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	496	455	0	ENST00000326873.7:c.921-2A>T		p.X307_splice	ENST00000326873	NM_000455.4	307			0.864740805424081	3	FACETS	0.919	0.9	0.938	0.919	0.9	0.938	CLONAL	3	TRUE	0	0.892092106865458	3		455	583	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0022283-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	111	333	0	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	0.824678146910452	3	FACETS	0.897	0.813	0.985	0.449	0.406	0.493	CLONAL	1	TRUE	1	0.892092106865458	3		333	401	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248397	59248397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022283-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	486	592	0	ENST00000371222.2:c.346C>T	p.Arg116Cys	p.R116C	ENST00000371222	NM_002228.3	116	Cgc/Tgc	1/1	0.824678146910452	3	FACETS	0.895	0.863	0.928	0.895	0.863	0.928	CLONAL	2	TRUE	1	0.892092106865458	3		592	880	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870945	12870977	+	inframe_deletion	In_Frame_Del	DEL	CGCAAGTGGAATTTCGATTTTCAGAATCACAAA	CGCAAGTGGAATTTCGATTTTCAGAATCACAAA	-	novel	NA	P-0022283-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	482	526	0	ENST00000228872.4:c.173_205del	p.Arg58_Lys68del	p.R58_K68del	ENST00000228872	NM_004064.3	58	CGCAAGTGGAATTTCGATTTTCAGAATCACAAA/-	1/3	0.75167752151868	3	FACETS	0.86	0.838	0.88	0.86	0.838	0.88	CLONAL	3	TRUE	0	0.892092106865458	3		526	606	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003734	45003748	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	TTCGGGCCGAGATGT	TTCGGGCCGAGATGT	-	novel	NA	P-0022283-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	350	428	0	ENST00000558401.1:c.-11_4del		p.*4*	ENST00000558401	NM_004048.2	?-2/119		1/4	0.776685898195324	2	FACETS	0.88	0.853	0.905	0.88	0.853	0.905	CLONAL	2	TRUE	0	0.892092106865458	2		428	446	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714651	52714651	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022283-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	314	549	0	ENST00000322088.6:c.409G>T	p.Gly137Cys	p.G137C	ENST00000322088	NM_014225.5	137	Ggc/Tgc	4/15	0.696878375605674	4	FACETS	0.791	0.749	0.833	0.791	0.749	0.833	SUBCLONAL	2	TRUE	2	0.892092106865458	4		549	842	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010475	48010475	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022283-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	331	442	0	ENST00000234420.5:c.103G>T	p.Ala35Ser	p.A35S	ENST00000234420	NM_000179.2	35	Gcc/Tcc	1/10	0.824678146910452	3	FACETS	0.827	0.789	0.865	0.827	0.789	0.865	CLONAL	2	TRUE	1	0.892092106865458	3		442	649	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415121	116415121	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022283-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	386	464	0	ENST00000397752.3:c.3215G>T	p.Gly1072Val	p.G1072V	ENST00000397752	NM_000245.2	1072	gGg/gTg	15/21	0.892092106865458	4	FACETS	0.926	0.884	0.968	0.926	0.884	0.968	CLONAL	2	TRUE	2	0.892092106865458	4		464	884	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759407	133759407	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022283-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	149	402	0	ENST00000318560.5:c.1730G>T	p.Arg577Leu	p.R577L	ENST00000318560	NM_005157.4	577	cGa/cTa	11/11	0.616158685676408	3	FACETS	0.888	0.816	0.963	0.444	0.408	0.482	CLONAL	1	TRUE	1	0.892092106865458	3		402	544	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608322	100608322	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022283-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	158	423	0	ENST00000308731.7:c.1768A>C	p.Ile590Leu	p.I590L	ENST00000308731	NM_000061.2	590	Att/Ctt	18/19	0.892092106865458	4	FACETS	0.746	0.684	0.812	0.373	0.342	0.406	SUBCLONAL	1	TRUE	2	0.892092106865458	4		423	898	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023147	27023147	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022283-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	159	386	0	ENST00000324856.7:c.253G>A	p.Gly85Ser	p.G85S	ENST00000324856	NM_006015.4	85	Ggc/Agc	1/20	0.824678146910452	3	FACETS	0.819	0.754	0.887	0.41	0.377	0.444	CLONAL	1	TRUE	1	0.892092106865458	3		386	629	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551754	150551754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022283-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1382	200	510	0	ENST00000369026.2:c.253G>A	p.Glu85Lys	p.E85K	ENST00000369026	NM_021960.4	85	Gag/Aag	1/3	0.892092106865458	7	FACETS	0.916	0.845	0.989			1	CLONAL	1	TRUE	NA	0.892092106865458	7		510	1582	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180599	94180599	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022283-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	265	328	0	ENST00000323929.3:c.1569G>T	p.Met523Ile	p.M523I	ENST00000323929	NM_005591.3	523	atG/atT	15/20	0.616158685676408	3	FACETS	0.809	0.767	0.851	0.809	0.767	0.851	CLONAL	2	TRUE	1	0.892092106865458	3		328	531	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020565	69020565	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022283-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	46	312	0	ENST00000288368.4:c.2937A>C	p.Gln979His	p.Q979H	ENST00000288368	NM_024870.2	979	caA/caC	24/40	0.892092106865458	6	FACETS	0.329	0.276	0.388	0.082	0.069	0.097	SUBCLONAL	1	TRUE	2	0.892092106865458	6		312	873	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0022806-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	140	265	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.337929451570671	4	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	2	0.359826980629648	4		265	503	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054254	30054254	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1555994854	NA	P-0022806-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	177	403	0	ENST00000338641.4:c.675+1G>A		p.X225_splice	ENST00000338641	NM_000268.3	225			0.348385332168451	0	FACETS	0.631	0.586	0.677			1	SUBCLONAL	2	TRUE	0	0.359826980629648	0		403	499	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896455	28896455	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022806-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	193	259	0	ENST00000282397.4:c.2995C>A	p.Leu999Met	p.L999M	ENST00000282397	NM_002019.4	999	Ctg/Atg	22/30	0.227011147372887	1	FACETS	0.928	0.867	0.989	1	0.993	1	CLONAL	2	TRUE	0	0.359826980629648	1		259	474	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641155	23641155	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs757892044	NA	P-0022806-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	226	371	0	ENST00000261584.4:c.2320A>G	p.Lys774Glu	p.K774E	ENST00000261584	NM_024675.3	774	Aaa/Gaa	5/13	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.359826980629648	2		371	887	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219391	1219391	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022806-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	267	1367	0	ENST00000326873.7:c.443T>C	p.Phe148Ser	p.F148S	ENST00000326873	NM_000455.4	148	tTc/tCc	3/10	0.364536435383818	0	FACETS	0.712	0.672	0.753			1	SUBCLONAL	2	TRUE	0	0.359826980629648	0		1367	667	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2206758	2206758	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022806-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	218	1143	0	ENST00000398665.3:c.818C>A	p.Ala273Glu	p.A273E	ENST00000398665	NM_032482.2	273	gCa/gAa	10/28	0.364536435383818	0	FACETS	0.637	0.596	0.678			1	SUBCLONAL	2	TRUE	0	0.359826980629648	0		1143	609	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226504	2226504	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022806-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	248	1518	0	ENST00000398665.3:c.3984A>T	p.Leu1328Phe	p.L1328F	ENST00000398665	NM_032482.2	1328	ttA/ttT	27/28	0.364536435383818	0	FACETS	0.599	0.563	0.637			1	SUBCLONAL	2	TRUE	0	0.359826980629648	0		1518	736	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298005	15298005	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022806-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	239	1037	0	ENST00000263388.2:c.1751A>G	p.Asp584Gly	p.D584G	ENST00000263388	NM_000435.2	584	gAc/gGc	11/33	0.288553871588414	0	FACETS	0.658	0.618	0.699			1	SUBCLONAL	2	TRUE	0	0.359826980629648	0		1037	646	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752648	42752648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022806-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	223	1006	0	ENST00000222329.4:c.1616C>T	p.Ala539Val	p.A539V	ENST00000222329	NM_006494.2	539	gCc/gTc	4/4	0.338067841284401	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.359826980629648	1		1006	821	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156038	99156038	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022806-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	221	428	0	ENST00000074304.5:c.718G>A	p.Gly240Ser	p.G240S	ENST00000074304	NM_001134224.1	240	Ggt/Agt	10/26	0.364536435383818	3	FACETS	0.96	0.896	1	0.96	0.896	1	CLONAL	2	TRUE	1	0.359826980629648	3		428	755	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55524211	55524211	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022806-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	158	267	0	ENST00000288135.5:c.30T>A	p.Phe10Leu	p.F10L	ENST00000288135	NM_000222.2	10	ttT/ttA	1/21	0.337929451570671	4	FACETS	0.972	0.895	1	0.972	0.895	1	CLONAL	2	TRUE	2	0.359826980629648	4		267	614	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964343	55964343	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022806-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	136	270	0	ENST00000263923.4:c.2470G>T	p.Ala824Ser	p.A824S	ENST00000263923	NM_002253.2	824	Gcc/Tcc	17/30	0.337929451570671	4	FACETS	0.798	0.728	0.872	0.798	0.728	0.872	SUBCLONAL	2	TRUE	2	0.359826980629648	4		270	644	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168977	11168977	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs758517117	NA	P-0022806-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	122	790	0	ENST00000358026.2:c.4567C>T	p.Arg1523Ter	p.R1523*	ENST00000358026	NM_001128849.1	1523	Cga/Tga	32/36	0.288553871588414	0	FACETS	0.789	0.716	0.866			1	SUBCLONAL	1	TRUE	0	0.359826980629648	0		790	550	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945072	151945072	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022806-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	30	121	0	ENST00000262189.6:c.2447A>C	p.Tyr816Ser	p.Y816S	ENST00000262189	NM_170606.2	816	tAc/tCc	14/59	0.337929451570671	4	FACETS	0.711	0.574	0.866	0.355	0.287	0.433	SUBCLONAL	1	TRUE	2	0.359826980629648	4		121	319	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026203-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	56	302	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.681	0.591	0.776	0.681	0.591	0.776	SUBCLONAL	1	TRUE	1	0.761872042680826	2		302	216	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACAACCCCC	rs397517115	NA	P-0026203-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4105	4707	430	0	ENST00000275493.2:c.2311_2319dup	p.Asn771_His773dup	p.N771_H773dup	ENST00000275493	NM_005228.3	771	gac/gACAACCCCCac	20/28	0.761872042680826	33	FACETS	0.998	0.986	1	0.561	0.554	0.568	CLONAL	18	TRUE	1	0.761872042680826	33		430	8812	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0026203-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	82	259	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.97	0.871	1	0.97	0.871	1	CLONAL	1	TRUE	1	0.761872042680826	2		259	222	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862720	9862720	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026203-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	173	357	0	ENST00000330684.3:c.2583C>G	p.Phe861Leu	p.F861L	ENST00000330684	NM_001134407.1	861	ttC/ttG	12/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.761872042680826	2		357	416	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225732	26225732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026203-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	303	582	0	ENST00000360408.1:c.350G>A	p.Arg117His	p.R117H	ENST00000360408	NM_003532.2	117	cGc/cAc	1/1	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.761872042680826	2		582	767	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0026308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	1388	661	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.3	11	FACETS	0.979	0.96	0.997			1	CLONAL	13	TRUE	NA	0.2	11		661	2073	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763098116	NA	P-0026308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	61	778	13	ENST00000269305.4:c.830G>A	p.Cys277Tyr	p.C277Y	ENST00000269305	NM_001126112.2	277	tGt/tAt	8/11	1	2	FACETS	0.729	0.627	0.84	0.729	0.627	0.84	SUBCLONAL	1	TRUE	1	0.2	2		791	837	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs863224451	NA	P-0026308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	81	806	0	ENST00000269305.4:c.824G>C	p.Cys275Ser	p.C275S	ENST00000269305	NM_001126112.2	275	tGt/tCt	8/11	1	2	FACETS	0.974	0.857	1	0.974	0.857	1	CLONAL	1	TRUE	1	0.2	2		806	832	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799269	45799269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553130580	NA	P-0026308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	36	456	2	ENST00000450313.1:c.164C>T	p.Ala55Val	p.A55V	ENST00000450313	NM_012222.2	55	gCa/gTa	3/16	1	2	FACETS	0.579	0.475	0.696	0.579	0.475	0.696	SUBCLONAL	1	TRUE	1	0.2	2		458	622	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044879	47044879	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	99	682	1	ENST00000377604.3:c.2205del	p.Ser736ValfsTer66	p.S736Vfs*66	ENST00000377604	NM_001204468.1	735	gaG/ga	20/24	1	1	FACETS	0.769	0.688	0.855	1	0.982	1	SUBCLONAL	2	TRUE	0	0.2	1		683	579	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0028513-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	668	308	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.879456134065663	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.879895432946146	3		308	721	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78865523	78865523	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028513-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	412	397	0	ENST00000306801.3:c.1987C>G	p.Leu663Val	p.L663V	ENST00000306801	NM_020761.2	663	Ctg/Gtg	18/34	0.879895432946146	2	FACETS	1	0.993	1	0.58	0.556	0.604	CLONAL	1	TRUE	0	0.879895432946146	2		397	807	SUCCESS
APC	324	MSKCC	GRCh37	5	112176974	112176974	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028513-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	122	515	0	ENST00000257430.4:c.5683A>G	p.Thr1895Ala	p.T1895A	ENST00000257430	NM_000038.5	1895	Acc/Gcc	16/16	1	2	FACETS	0.48	0.435	0.527	0.48	0.435	0.527	SUBCLONAL	1	TRUE	1	0.879895432946146	2		515	578	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564098	139564098	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028513-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	260	459	0	ENST00000308874.7:c.238G>T	p.Ala80Ser	p.A80S	ENST00000308874		80	Gcc/Tcc	5/10	0.879456134065663	3	FACETS	1	0.95	1	0.338	0.317	0.359	CLONAL	1	TRUE	0	0.879895432946146	3		459	840	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345274	70345274	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028513-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	251	419	0	ENST00000374080.3:c.2300C>A	p.Ala767Asp	p.A767D	ENST00000374080		767	gCc/gAc	16/45	0.879895432946146	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.879895432946146	1		419	304	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0028944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	360	265	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.812700373446861	6	FACETS	0.94	0.908	0.97	0.94	0.908	0.97	CLONAL	5	TRUE	1	0.812700373446861	6		265	495	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945129	32945129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80359104	NA	P-0028944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	110	444	0	ENST00000380152.3:c.8524C>T	p.Arg2842Cys	p.R2842C	ENST00000380152		2842	Cgc/Tgc	20/27	0.812700373446861	3	FACETS	1	0.977	1	0.616	0.561	0.673	CLONAL	1	TRUE	1	0.812700373446861	3		444	309	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739594	41739594	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	57	309	0	ENST00000242208.4:c.379G>T	p.Ala127Ser	p.A127S	ENST00000242208	NM_002192.2	127	Gcc/Tcc	2/3	0.473937468138672	5	FACETS	0.778	0.678	0.884	0.519	0.452	0.589	INDETERMINATE	2	TRUE	2	0.812700373446861	5		309	200	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101631	27101631	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	95	828	0	ENST00000324856.7:c.4913del	p.Asp1638ValfsTer16	p.D1638Vfs*16	ENST00000324856	NM_006015.4	1638	gAt/gt	18/20	1	2	FACETS	0.899	0.813	0.987	0.899	0.813	0.987	CLONAL	1	TRUE	1	0.812700373446861	2		828	260	SUCCESS
RET	5979	MSKCC	GRCh37	10	43602018	43602018	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0028944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	80	648	0	ENST00000355710.3:c.1062T>A	p.Tyr354Ter	p.Y354*	ENST00000355710	NM_020975.4	354	taT/taA	5/20	0.812700373446861	5	FACETS	0.94	0.83	1	0.235	0.207	0.264	CLONAL	1	TRUE	1	0.812700373446861	5		648	465	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205835	108205835	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	200	526	0	ENST00000278616.4:c.8150A>C	p.Lys2717Thr	p.K2717T	ENST00000278616	NM_000051.3	2717	aAg/aCg	55/63	0.812700373446861	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.812700373446861	2		526	245	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263869	133263870	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0028944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	107	589	0	ENST00000320574.5:c.32_33del	p.Ala11GlyfsTer12	p.A11Gfs*12	ENST00000320574	NM_006231.2	11	gCG/g	1/49	0.652512710441582	4	FACETS	1	0.959	1	0.373	0.336	0.411	CLONAL	1	TRUE	1	0.812700373446861	4		589	427	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609706	81609706	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	322	838	0	ENST00000298171.2:c.1304T>C	p.Val435Ala	p.V435A	ENST00000298171	NM_000369.2	435	gTc/gCc	10/10	0.812700373446861	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	1	0.812700373446861	4		838	430	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867572	78867572	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	127	709	0	ENST00000306801.3:c.2308G>T	p.Gly770Cys	p.G770C	ENST00000306801	NM_020761.2	770	Ggc/Tgc	20/34	1	2	FACETS	0.977	0.898	1	0.977	0.898	1	CLONAL	1	TRUE	1	0.812700373446861	2		709	320	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221298	1221308	+	frameshift_variant	Frame_Shift_Del	DEL	TCCCGGGCGAC	TCCCGGGCGAC	-	novel	NA	P-0028944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	230	775	0	ENST00000326873.7:c.822_832del	p.Ile274MetfsTer7	p.I274Mfs*7	ENST00000326873	NM_000455.4	274	aTCCCGGGCGAC/a	6/10	0.812700373446861	3	FACETS	0.938	0.904	0.968	0.938	0.904	0.968	CLONAL	3	TRUE	0	0.812700373446861	3		775	283	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390204	89390204	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	168	598	0	ENST00000336596.2:c.953C>A	p.Pro318Gln	p.P318Q	ENST00000336596	NM_005233.5	318	cCa/cAa	4/17	0.812700373446861	3	FACETS	1	0.99	1	0.727	0.676	0.778	CLONAL	1	TRUE	1	0.812700373446861	3		598	400	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540161	187540161	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	96	633	0	ENST00000441802.2:c.7579G>C	p.Val2527Leu	p.V2527L	ENST00000441802	NM_005245.3	2527	Gtt/Ctt	10/27	1	2	FACETS	0.968	0.878	1	0.968	0.878	1	CLONAL	1	TRUE	1	0.812700373446861	2		633	244	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589225	67589225	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	167	487	0	ENST00000274335.5:c.1213A>G	p.Ile405Val	p.I405V	ENST00000274335		405	Ata/Gta	9/15	0.812700373446861	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.812700373446861	3		487	258	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346551	81346551	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	132	500	0	ENST00000222390.5:c.1402C>A	p.Arg468Ser	p.R468S	ENST00000222390	NM_000601.4	468	Cgt/Agt	11/18	0.812700373446861	3	FACETS	0.976	0.909	1	0.976	0.909	1	CLONAL	2	TRUE	1	0.812700373446861	3		500	234	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1686033	1686033	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028944-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	95	707	0	ENST00000378625.1:c.1228C>T	p.Gln410Ter	p.Q410*	ENST00000378625	NM_001198994.1	410	Cag/Tag	10/14	0.812700373446861	3	FACETS	1	0.94	1	0.53	0.478	0.585	CLONAL	1	TRUE	1	0.812700373446861	3		707	310	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029409-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	352	547	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.73672526128128	3	FACETS	1	0.981	1			1	CLONAL	2	TRUE	NA	0.798747003982448	3		547	593	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717769	89717770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029409-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	238	217	0	ENST00000371953.3:c.800dup	p.Asp268GlyfsTer30	p.D268Gfs*30	ENST00000371953	NM_000314.4	265	cta/ctAa	7/9	0.73672526128128	3	FACETS	0.927	0.893	0.958			1	CLONAL	3	TRUE	NA	0.798747003982448	3		217	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0029409-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	187	593	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.798747003982448	3	FACETS	0.987	0.915	1	0.329	0.305	0.354	CLONAL	1	TRUE	0	0.798747003982448	3		593	664	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541970	187541970	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs189271562	NA	P-0029409-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	152	499	0	ENST00000441802.2:c.5770G>A	p.Gly1924Arg	p.G1924R	ENST00000441802	NM_005245.3	1924	Ggg/Agg	10/27	0.798747003982448	2	FACETS	0.959	0.887	1	0.479	0.443	0.516	CLONAL	1	TRUE	0	0.798747003982448	2		499	397	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048735	180048735	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029409-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	528	496	0	ENST00000261937.6:c.1827C>G	p.Asp609Glu	p.D609E	ENST00000261937	NM_182925.4	609	gaC/gaG	13/30	0.756669370208495	5	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	TRUE	2	0.798747003982448	5		496	955	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872048	35872048	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029409-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	200	454	0	ENST00000216797.5:c.565T>G	p.Leu189Val	p.L189V	ENST00000216797	NM_020529.2	189	Tta/Gta	4/6	0.798747003982448	4	FACETS	1	0.959	1	0.349	0.324	0.376	CLONAL	1	TRUE	1	0.798747003982448	4		454	860	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672840	86672840	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029409-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	97	330	0	ENST00000274376.6:c.2327G>A	p.Arg776Lys	p.R776K	ENST00000274376	NM_002890.2	776	aGa/aAa	17/25	0.798747003982448	2	FACETS	0.975	0.885	1	0.488	0.442	0.534	CLONAL	1	TRUE	0	0.798747003982448	2		330	249	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985525	2985525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029409-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	143	390	0	ENST00000396946.4:c.286G>A	p.Glu96Lys	p.E96K	ENST00000396946	NM_032415.4	96	Gaa/Aaa	4/25	0.776054470864945	5	FACETS	0.989	0.902	1	0.247	0.225	0.27	CLONAL	1	TRUE	1	0.798747003982448	5		390	796	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38137056	38137056	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0029409-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	101	279	0	ENST00000317025.8:c.3760+2T>G		p.X1254_splice	ENST00000317025	NM_023034.1	1254			0.798747003982448	8	FACETS	0.878	0.783	0.979	0.146	0.13	0.164	CLONAL	1	TRUE	2	0.798747003982448	8		279	978	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342158	70342158	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029409-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	158	457	0	ENST00000374080.3:c.1210C>G	p.Leu404Val	p.L404V	ENST00000374080		404	Ctg/Gtg	8/45	0.756669370208495	5	FACETS	0.965	0.884	1	0.322	0.294	0.35	CLONAL	1	TRUE	2	0.798747003982448	5		457	901	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437379	110437379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030151-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	11	308	0	ENST00000375856.3:c.1022G>A	p.Arg341His	p.R341H	ENST00000375856	NM_003749.2	341	cGc/cAc	1/2	0.591243263070237	2	FACETS	0.204	0.141	0.283	0.102	0.07	0.142	SUBCLONAL	1	TRUE	0	0.591243263070237	2		308	182	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47595150	47595156	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGTGG	GCCGTGG	-	novel	NA	P-0030151-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	38	480	0	ENST00000430070.2:c.931_937del	p.Pro311AlafsTer57	p.P311Afs*57	ENST00000430070	NM_018095.4	311	CCACGGCgc/gc	4/4	0.591243263070237	3	FACETS	0.378	0.312	0.451	0.189	0.156	0.226	SUBCLONAL	1	TRUE	1	0.591243263070237	3		480	441	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0030527-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	110	280	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.343542625131815	5	FACETS	0.888	0.813	0.965	0.888	0.813	0.965	INDETERMINATE	3	FALSE	2	0.597478912411735	5		280	262	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0030527-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	139	327	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.596428111036929	2	FACETS	0.977	0.914	1	0.977	0.914	1	CLONAL	2	FALSE	0	0.597478912411735	2		327	238	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808971	3808971	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030527-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	66	412	0	ENST00000262367.5:c.3253T>C	p.Phe1085Leu	p.F1085L	ENST00000262367	NM_004380.2	1085	Ttt/Ctt	17/31	0.343542625131815	5	FACETS	0.79	0.694	0.893	0.527	0.462	0.595	INDETERMINATE	2	FALSE	2	0.597478912411735	5		412	265	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650710	67650710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243010179	NA	P-0030527-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	20	518	0	ENST00000264010.4:c.1015C>T	p.Arg339Trp	p.R339W	ENST00000264010	NM_006565.3	339	Cgg/Tgg	5/12	0.597478912411735	3	FACETS	0.295	0.225	0.376	0.147	0.112	0.188	SUBCLONAL	1	FALSE	1	0.597478912411735	3		518	295	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654615	67654615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030527-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	88	431	0	ENST00000264010.4:c.1102C>T	p.Arg368Cys	p.R368C	ENST00000264010	NM_006565.3	368	Cgt/Tgt	6/12	0.597478912411735	3	FACETS	0.956	0.867	1	0.956	0.867	1	CLONAL	2	FALSE	1	0.597478912411735	3		431	200	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39774506	39774506	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030527-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	30	450	0	ENST00000288319.7:c.646C>T	p.Pro216Ser	p.P216S	ENST00000288319	NM_182918.3	216	Cca/Tca	5/10	0.102620071772936	4	FACETS	0.733	0.594	0.887	0.366	0.297	0.444	INDETERMINATE	1	FALSE	2	0.597478912411735	4		450	219	SUCCESS
APC	324	MSKCC	GRCh37	5	112175594	112175594	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030527-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	143	655	0	ENST00000257430.4:c.4303del	p.Arg1435GlufsTer38	p.R1435Efs*38	ENST00000257430	NM_000038.5	1435	Aga/ga	16/16	0.343542625131815	5	FACETS	0.885	0.812	0.96	0.59	0.541	0.64	INDETERMINATE	2	FALSE	2	0.597478912411735	5		655	513	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671543	30671543	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030527-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	102	607	0	ENST00000376406.3:c.5417A>C	p.Lys1806Thr	p.K1806T	ENST00000376406	NM_014641.2	1806	aAg/aCg	10/15	0.597478912411735	4	FACETS	1	0.928	1	0.521	0.468	0.578	CLONAL	1	FALSE	2	0.597478912411735	4		607	523	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0031534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	96	425	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.488028427967091	4	FACETS	0.987	0.881	1	0.494	0.44	0.55	CLONAL	1	FALSE	2	0.488028427967091	4		425	593	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0031534-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	98	425	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.472976602920639	4	FACETS	1	0.907	1	0.508	0.454	0.565	CLONAL	1	TRUE	2	0.498499740313475	4		425	580	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398255	25398255	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913236	NA	P-0031920-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	82	335	0	ENST00000311936.3:c.64C>A	p.Gln22Lys	p.Q22K	ENST00000311936	NM_004985.3	22	Cag/Aag	2/5	1	2	FACETS	0.895	0.806	0.985	0.895	0.806	0.985	CLONAL	1	TRUE	1	0.916706648444614	2		335	200	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248189	59248189	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774994834	NA	P-0031920-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	26	91	0	ENST00000371222.2:c.554G>A	p.Gly185Asp	p.G185D	ENST00000371222	NM_002228.3	185	gGc/gAc	1/1	0.916706648444614	3	FACETS	1	0.907	1	0.591	0.485	0.702	CLONAL	1	TRUE	1	0.916706648444614	3		91	70	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028668	12028674	+	frameshift_variant	Frame_Shift_Del	DEL	TGGAGTT	TGGAGTT	-	novel	NA	P-0031920-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	80	322	0	ENST00000353533.5:c.874_880del	p.Ser292GlyfsTer24	p.S292Gfs*24	ENST00000353533	NM_003010.3	291	TGGAGTTtg/tg	8/11	0.916706648444614	1	FACETS	0.837	0.775	0.894	0.837	0.775	0.894	CLONAL	1	TRUE	0	0.916706648444614	1		322	113	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972723	25972723	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031920-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	125	378	0	ENST00000435504.4:c.1702A>G	p.Arg568Gly	p.R568G	ENST00000435504		568	Agg/Ggg	12/13	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.916706648444614	2		378	267	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226361	2226361	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	583	889	0	ENST00000398665.3:c.3841G>T	p.Glu1281Ter	p.E1281*	ENST00000398665	NM_032482.2	1281	Gag/Tag	27/28	0.944832871467584	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.944832871467584	2		889	605	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	398	723	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	NA	2	FACETS	1	0.997	1			1	INDETERMINATE	2	TRUE	NA	0.944832871467584	2		723	408	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386450	31386450	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	271	564	0	ENST00000328111.2:c.1674+1G>C		p.X558_splice	ENST00000328111	NM_006892.3	558			0.944832871467584	5	FACETS	0.995	0.932	1	0.249	0.233	0.266	CLONAL	1	TRUE	1	0.944832871467584	5		564	1393	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100403	8100403	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	237	811	1	ENST00000346208.3:c.377C>A	p.Ser126Tyr	p.S126Y	ENST00000346208		126	tCc/tAc	3/6	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.944832871467584	2		812	464	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670880	134670880	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	183	285	0	ENST00000398015.3:c.791G>T	p.Ser264Ile	p.S264I	ENST00000398015	NM_004441.4	264	aGc/aTc	3/16	0.528079923180732	4	FACETS	1	0.988	1	0.442	0.41	0.475	INDETERMINATE	1	TRUE	1	0.944832871467584	4		285	568	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100507	8100507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1158297550	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	243	781	0	ENST00000346208.3:c.481G>A	p.Val161Ile	p.V161I	ENST00000346208		161	Gtc/Atc	3/6	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.944832871467584	2		781	485	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741657	17741657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	86	373	1	ENST00000250003.3:c.328C>T	p.Arg110Cys	p.R110C	ENST00000250003	NM_002478.4	110	Cgc/Tgc	1/3	0.882470745594176	3	FACETS	0.84	0.751	0.934	0.28	0.25	0.312	CLONAL	1	TRUE	0	0.944832871467584	3		374	319	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507321	8507321	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750349056	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	348	358	0	ENST00000356435.5:c.1657G>A	p.Asp553Asn	p.D553N	ENST00000356435		553	Gat/Aat	11/35	0.944832871467584	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.944832871467584	2		358	362	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187817	11187817	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	452	502	0	ENST00000361445.4:c.6080G>T	p.Trp2027Leu	p.W2027L	ENST00000361445	NM_004958.3	2027	tGg/tTg	44/58	0.944832871467584	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.944832871467584	3		502	695	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316145	11316145	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	451	604	0	ENST00000361445.4:c.609G>C	p.Gln203His	p.Q203H	ENST00000361445	NM_004958.3	203	caG/caC	5/58	0.944832871467584	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.944832871467584	3		604	676	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175996765	175996765	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	138	400	0	ENST00000367669.3:c.1672G>T	p.Val558Leu	p.V558L	ENST00000367669	NM_022457.5	558	Gtg/Ttg	15/20	0.692903350376807	3	FACETS	1	0.921	1	0.501	0.46	0.544	CLONAL	1	TRUE	1	0.944832871467584	3		400	429	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192687	94192710	+	inframe_deletion	In_Frame_Del	DEL	CCACAAATTCTTGTACTGCTTCAC	CCACAAATTCTTGTACTGCTTCAC	-	novel	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	360	488	0	ENST00000323929.3:c.1364_1387del	p.Gly455_Val462del	p.G455_V462del	ENST00000323929	NM_005591.3	455	gGTGAAGCAGTACAAGAATTTGTGGac/gac	13/20	0.944832871467584	3	FACETS	0.899	0.862	0.936	0.899	0.862	0.936	CLONAL	2	TRUE	1	0.944832871467584	3		488	624	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204761	94204761	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	193	376	0	ENST00000323929.3:c.824C>A	p.Ser275Tyr	p.S275Y	ENST00000323929	NM_005591.3	275	tCc/tAc	8/20	0.944832871467584	3	FACETS	1	0.97	1	0.537	0.5	0.575	CLONAL	1	TRUE	1	0.944832871467584	3		376	560	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497576	125497576	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	91	264	0	ENST00000428830.2:c.140A>G	p.Asp47Gly	p.D47G	ENST00000428830	NM_001114121.2	47	gAc/gGc	3/14	0.944832871467584	3	FACETS	1	0.968	1	0.586	0.529	0.644	CLONAL	1	TRUE	1	0.944832871467584	3		264	242	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337660	73337660	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1175752033	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	154	199	0	ENST00000377767.4:c.2056G>C	p.Ala686Pro	p.A686P	ENST00000377767	NM_014953.3	686	Gct/Cct	16/21	0.944832871467584	3	FACETS	0.913	0.856	0.968	0.913	0.856	0.968	CLONAL	2	TRUE	1	0.944832871467584	3		199	263	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544683	65544684	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	517	673	0	ENST00000358664.4:c.242_243del	p.His81ProfsTer5	p.H81Pfs*5	ENST00000358664	NM_002382.4	81	cAC/c	4/5	0.944832871467584	2	FACETS	0.96	0.944	0.975	0.96	0.944	0.975	CLONAL	2	TRUE	0	0.944832871467584	2		673	570	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43772156	43772156	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	252	660	0	ENST00000382044.4:c.559G>C	p.Glu187Gln	p.E187Q	ENST00000382044	NM_001141980.1	187	Gag/Cag	6/28	0.944832871467584	2	FACETS	1	0.972	1	0.521	0.493	0.549	CLONAL	1	TRUE	0	0.944832871467584	2		660	512	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614983	23614983	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs876658773	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	278	273	1	ENST00000261584.4:c.3358G>T	p.Glu1120Ter	p.E1120*	ENST00000261584	NM_024675.3	1120	Gaa/Taa	13/13	0.944832871467584	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.944832871467584	2		274	286	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56867141	56867141	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	409	531	0	ENST00000308159.5:c.1360A>T	p.Thr454Ser	p.T454S	ENST00000308159	NM_014669.4	454	Acg/Tcg	13/22	0.944832871467584	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.944832871467584	2		531	416	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435602	56435602	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	258	611	0	ENST00000407977.2:c.1535G>T	p.Ser512Ile	p.S512I	ENST00000407977		512	aGc/aTc	9/10	0.944832871467584	3	FACETS	0.995	0.935	1	0.498	0.467	0.529	CLONAL	1	TRUE	1	0.944832871467584	3		611	808	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18964065	18964065	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	402	507	0	ENST00000262803.5:c.1062G>T	p.Met354Ile	p.M354I	ENST00000262803	NM_002911.3	354	atG/atT	8/24	0.944832871467584	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.944832871467584	2		507	419	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794361	242794361	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200312345	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	153	789	1	ENST00000334409.5:c.581G>A	p.Arg194Gln	p.R194Q	ENST00000334409	NM_005018.2	194	cGg/cAg	3/5	0.211074346054752	5	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.944832871467584	5		790	531	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52649469	52649469	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	152	463	0	ENST00000394830.3:c.1822T>G	p.Tyr608Asp	p.Y608D	ENST00000394830	NM_018313.4	608	Tat/Gat	16/30	1	2	FACETS	0.914	0.848	0.981	0.914	0.848	0.981	CLONAL	1	TRUE	1	0.944832871467584	2		463	352	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137522018	137522018	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	99	200	0	ENST00000367739.4:c.861G>C	p.Leu287Phe	p.L287F	ENST00000367739	NM_000416.2	287	ttG/ttC	6/7	0.944832871467584	2	FACETS	0.97	0.933	1	0.97	0.933	1	CLONAL	2	TRUE	0	0.944832871467584	2		200	108	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69103970	69103970	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	210	500	1	ENST00000288368.4:c.4360G>T	p.Asp1454Tyr	p.D1454Y	ENST00000288368	NM_024870.2	1454	Gac/Tac	36/40	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.944832871467584	2		501	439	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133748425	133748425	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	287	322	0	ENST00000318560.5:c.1085+1G>T		p.X362_splice	ENST00000318560	NM_005157.4	362			0.944832871467584	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.944832871467584	2		322	293	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617573	100617574	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	226	320	0	ENST00000308731.7:c.495_496delinsAA	p.Cys165_Gln166delinsTer	p.C165_Q166delins*	ENST00000308731	NM_000061.2	165	tgCCaa/tgAAaa	6/19	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.944832871467584	1		320	234	SUCCESS
FH	2271	MSKCC	GRCh37	1	241676920	241676920	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	86	335	0	ENST00000366560.3:c.361A>G	p.Met121Val	p.M121V	ENST00000366560	NM_000143.3	121	Atg/Gtg	3/10	0.692903350376807	3	FACETS	0.761	0.679	0.848	0.381	0.339	0.424	SUBCLONAL	1	TRUE	1	0.944832871467584	3		335	352	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55693391	55693391	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	231	688	0	ENST00000284073.2:c.598G>T	p.Ala200Ser	p.A200S	ENST00000284073	NM_138962.2	200	Gcc/Tcc	9/14	0.944832871467584	3	FACETS	0.988	0.925	1	0.494	0.462	0.526	CLONAL	1	TRUE	1	0.944832871467584	3		688	729	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827927	40827927	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs536150112	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	261	551	0	ENST00000373198.4:c.2501G>T	p.Arg834Leu	p.R834L	ENST00000373198	NM_133170.3	834	cGc/cTc	17/32	0.656536578591314	5	FACETS	1	0.988	1	0.305	0.286	0.326	CLONAL	1	TRUE	1	0.944832871467584	5		551	1093	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37628870	37628870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748613308	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	363	684	0	ENST00000249071.6:c.196C>T	p.Arg66Cys	p.R66C	ENST00000249071	NM_002872.4	66	Cgt/Tgt	3/7	0.944832871467584	2	FACETS	1	0.961	1	0.504	0.481	0.527	CLONAL	1	TRUE	0	0.944832871467584	2		684	763	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438568	52438568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	231	487	0	ENST00000460680.1:c.1151G>A	p.Ser384Asn	p.S384N	ENST00000460680	NM_004656.3	384	aGc/aAc	12/17	1	2	FACETS	0.974	0.918	1	0.974	0.918	1	CLONAL	1	TRUE	1	0.944832871467584	2		487	502	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143326387	143326387	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	164	378	0	ENST00000262992.4:c.227C>T	p.Thr76Ile	p.T76I	ENST00000262992	NM_001101669.1	76	aCa/aTa	4/24	0.944832871467584	2	FACETS	1	0.967	1	0.528	0.493	0.562	CLONAL	1	TRUE	0	0.944832871467584	2		378	329	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974719	21974721	+	frameshift_variant	Frame_Shift_Del	DEL	CGC	CGC	GG	novel	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	408	353	1	ENST00000304494.5:c.106_108delinsCC	p.Ala36ProfsTer17	p.A36Pfs*17	ENST00000304494	NM_000077.4	36	GCG/CC	1/3	0.944832871467584	2	FACETS	0.968	0.95	0.984	0.968	0.95	0.984	CLONAL	2	TRUE	0	0.944832871467584	2		354	446	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561218	9561218	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs753745102	NA	P-0032183-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	96	503	0	ENST00000353224.5:c.564G>C	p.Leu188Phe	p.L188F	ENST00000353224	NM_177990.2	188	ttG/ttC	4/10	1	2	FACETS	0.484	0.434	0.537	0.484	0.434	0.537	SUBCLONAL	1	TRUE	1	0.944832871467584	2		503	420	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0033566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	94	403	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.377077186005724	4	FACETS	1	0.921	1	1	0.921	1	CLONAL	4	FALSE	0	0.377077186005724	4		403	171	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0033566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	49	441	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.323749106792031	4	FACETS	0.939	0.817	1	0.705	0.613	0.799	CLONAL	3	FALSE	0	0.377077186005724	4		441	127	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933406	100933406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150584881	NA	P-0033566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	16	461	0	ENST00000325455.5:c.1984G>A	p.Val662Ile	p.V662I	ENST00000325455	NM_001202474.3	662	Gtt/Att	4/8	0.377077186005724	3	FACETS	0.72	0.537	0.936	0.36	0.268	0.468	CLONAL	1	FALSE	1	0.377077186005724	3		461	140	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610002	81610002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150602845	NA	P-0033566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	12	340	0	ENST00000298171.2:c.1600C>T	p.Arg534Cys	p.R534C	ENST00000298171	NM_000369.2	534	Cgc/Tgc	10/10	0.260754380110574	3	FACETS	0.565	0.399	0.766	0.282	0.199	0.383	SUBCLONAL	1	FALSE	1	0.377077186005724	3		340	134	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0033566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	70	462	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.377077186005724	2	FACETS	0.987	0.879	1	0.987	0.879	1	CLONAL	2	FALSE	0	0.377077186005724	2		462	188	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39709868	39709870	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs748165145	NA	P-0033566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	19	198	0	ENST00000361337.2:c.504_506del	p.Glu169del	p.E169del	ENST00000361337	NM_003286.2	165	ctAGAa/cta	7/21	0.377077186005724	6	FACETS	0.982	0.75	1	0.246	0.187	0.313	CLONAL	1	FALSE	2	0.377077186005724	6		198	180	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779184	3779184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	64	503	1	ENST00000262367.5:c.5864C>T	p.Ala1955Val	p.A1955V	ENST00000262367	NM_004380.2	1955	gCg/gTg	31/31	0.377077186005724	4	FACETS	0.962	0.853	1	1	0.975	1	CLONAL	3	FALSE	2	0.377077186005724	4		504	162	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094272	193094272	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs121434265	NA	P-0033566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	33	400	0	ENST00000367435.3:c.162C>G	p.Tyr54Ter	p.Y54*	ENST00000367435	NM_024529.4	54	taC/taG	2/17	0.367228413520236	3	FACETS	1	0.825	1	0.502	0.412	0.602	CLONAL	1	FALSE	1	0.377077186005724	3		400	207	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411510	63411510	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	53	782	1	ENST00000330258.3:c.1657del	p.Ala553GlnfsTer9	p.A553Qfs*9	ENST00000330258	NM_152424.3	553	Gca/ca	2/2	0.377077186005724	3	FACETS	0.852	0.738	0.974	0.852	0.738	0.974	CLONAL	2	FALSE	1	0.377077186005724	3		783	196	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872097	76872097	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0033566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	29	416	0	ENST00000373344.5:c.5550C>G	p.Tyr1850Ter	p.Y1850*	ENST00000373344	NM_000489.3	1850	taC/taG	22/35	0.377077186005724	3	FACETS	1	0.857	1	0.535	0.433	0.647	CLONAL	1	FALSE	1	0.377077186005724	3		416	171	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0033598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	63	408	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.39055074878392	1	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	0	0.40425084111143	1		408	245	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0033598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	101	297	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.400653210534248	1	FACETS	0.923	0.83	1	0.923	0.83	1	CLONAL	1	TRUE	0	0.40425084111143	1		297	432	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446729	49446729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376475904	NA	P-0033598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	109	454	2	ENST00000301067.7:c.1081G>A	p.Val361Ile	p.V361I	ENST00000301067	NM_003482.3	361	Gtt/Att	8/54	0.400653210534248	1	FACETS	0.973	0.88	1	0.973	0.88	1	CLONAL	1	TRUE	0	0.40425084111143	1		456	442	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745999	745999	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	104	484	0	ENST00000314574.4:c.523C>T	p.Pro175Ser	p.P175S	ENST00000314574	NM_005433.3	175	Cct/Tct	5/12	1	2	FACETS	0.993	0.893	1	0.993	0.893	1	CLONAL	1	TRUE	1	0.40425084111143	2		484	518	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220391	1220392	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACGGCC	novel	NA	P-0033598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	262	665	0	ENST00000326873.7:c.485_490dup	p.Gly163_Leu164insHisGly	p.G163_L164insHG	ENST00000326873	NM_000455.4	162	gac/gACGGCCac	4/10	0.40425084111143	2	FACETS	0.906	0.854	0.96	0.906	0.854	0.96	CLONAL	2	TRUE	0	0.40425084111143	2		665	715	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375269	15375275	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCAGT	GCCCAGT	-	novel	NA	P-0033598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	54	653	0	ENST00000263377.2:c.1152_1158del	p.Leu385TyrfsTer14	p.L385Yfs*14	ENST00000263377	NM_058243.2	384	gcACTGGGC/gc	6/20	0.40425084111143	2	FACETS	0.359	0.305	0.417	0.179	0.152	0.209	SUBCLONAL	1	TRUE	0	0.40425084111143	2		653	745	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42384977	42384977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782624281	NA	P-0033598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	238	540	0	ENST00000221972.3:c.611G>A	p.Arg204Gln	p.R204Q	ENST00000221972	NM_021601.3	204	cGg/cAg	5/5	0.389452221913831	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	1	0.40425084111143	3		540	704	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611814	100611814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	122	542	1	ENST00000308731.7:c.1307C>T	p.Ser436Phe	p.S436F	ENST00000308731	NM_000061.2	436	tCc/tTc	14/19	1	2	FACETS	0.9	0.814	0.989	0.9	0.814	0.989	CLONAL	1	TRUE	1	0.40425084111143	2		543	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0033623-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	14	632	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.914678788557355	1	FACETS	0.045	0.032	0.06	0.045	0.032	0.06	SUBCLONAL	1	TRUE	0	0.914678788557355	1		632	371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912655	NA	P-0033623-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	9	404	0	ENST00000269305.4:c.725G>C	p.Cys242Ser	p.C242S	ENST00000269305	NM_001126112.2	242	tGc/tCc	7/11	0.914678788557355	1	FACETS	0.037	0.024	0.053	0.037	0.024	0.053	SUBCLONAL	1	TRUE	0	0.914678788557355	1		404	291	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876660825	NA	P-0033623-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	28	695	0	ENST00000269305.4:c.569C>G	p.Pro190Arg	p.P190R	ENST00000269305	NM_001126112.2	190	cCt/cGt	6/11	0.914678788557355	1	FACETS	0.081	0.064	0.1	0.081	0.064	0.1	SUBCLONAL	1	TRUE	0	0.914678788557355	1		695	412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0033800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	167	328	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.323519668713086	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.323519668713086	1		328	725	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17349180	17349180	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138996609	NA	P-0033800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	78	564	0	ENST00000375499.3:c.688C>T	p.Arg230Cys	p.R230C	ENST00000375499	NM_003000.2	230	Cgc/Tgc	7/8	1	2	FACETS	0.748	0.657	0.845	0.748	0.657	0.845	SUBCLONAL	1	TRUE	1	0.323519668713086	2		564	645	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121935	2121947	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTGAGTGGGGCC	GGTGAGTGGGGCC	-	novel	NA	P-0033800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	123	709	0	ENST00000219476.3:c.2097+2_2097+14del		p.X699_splice	ENST00000219476	NM_000548.3	699		19/42	0.323519668713086	1	FACETS	0.951	0.862	1	0.951	0.862	1	CLONAL	1	TRUE	0	0.323519668713086	1		709	670	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525611	137525611	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	49	537	0	ENST00000367739.4:c.404G>C	p.Arg135Thr	p.R135T	ENST00000367739	NM_000416.2	135	aGa/aCa	4/7	1	2	FACETS	0.489	0.414	0.573	0.489	0.414	0.573	SUBCLONAL	1	TRUE	1	0.323519668713086	2		537	619	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0033815-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	85	661	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.198301037392412	3	FACETS	1	0.915	1	1	0.915	1	CLONAL	2	TRUE	1	0.13	3		661	668	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0033815-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	41	724	0	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	1	2	FACETS	0.787	0.654	0.937	0.787	0.654	0.937	CLONAL	1	TRUE	1	0.13	2		724	801	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984856	72984856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033815-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	35	495	0	ENST00000268489.5:c.2728G>A	p.Glu910Lys	p.E910K	ENST00000268489	NM_006885.3	910	Gag/Aag	3/10	1	2	FACETS	0.99	0.81	1	0.99	0.81	1	CLONAL	1	TRUE	1	0.13	2		495	544	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1040454	1040454	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs769802409	NA	P-0033815-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	45	609	0	ENST00000358495.3:c.118C>G	p.Gln40Glu	p.Q40E	ENST00000358495	NM_134424.2	40	Cag/Gag	3/12	1	2	FACETS	0.951	0.797	1	0.951	0.797	1	CLONAL	1	TRUE	1	0.13	2		609	728	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	59	190	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.727	0.624	0.839	0.727	0.624	0.839	SUBCLONAL	1	TRUE	1	0.2	2		190	812	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0033938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	61	259	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.2	2		259	599	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538904	187538904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	55	473	0	ENST00000441802.2:c.8836G>A	p.Asp2946Asn	p.D2946N	ENST00000441802	NM_005245.3	2946	Gat/Aat	10/27	1	2	FACETS	0.921	0.788	1	0.921	0.788	1	CLONAL	1	TRUE	1	0.2	2		473	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578476	7578476	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	101	909	6	ENST00000269305.4:c.454C>A	p.Pro152Thr	p.P152T	ENST00000269305	NM_001126112.2	152	Ccg/Acg	5/11	0.251657846620518	1	FACETS	0.758	0.675	0.846	0.758	0.675	0.846	SUBCLONAL	1	TRUE	0	0.2	1		915	1200	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539435	187539435	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	57	557	0	ENST00000441802.2:c.8305G>A	p.Glu2769Lys	p.E2769K	ENST00000441802	NM_005245.3	2769	Gag/Aag	10/27	1	2	FACETS	0.78	0.668	0.902	0.78	0.668	0.902	CLONAL	1	TRUE	1	0.2	2		557	731	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539741	187539741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1423289460	NA	P-0033938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	64	556	0	ENST00000441802.2:c.7999G>A	p.Glu2667Lys	p.E2667K	ENST00000441802	NM_005245.3	2667	Gaa/Aaa	10/27	1	2	FACETS	0.86	0.744	0.987	0.86	0.744	0.987	CLONAL	1	TRUE	1	0.2	2		556	744	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435936	56435936	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	130	504	0	ENST00000407977.2:c.1201G>T	p.Glu401Ter	p.E401*	ENST00000407977		401	Gag/Tag	9/10	0.172899464460443	2	FACETS	0.874	0.793	0.958	0.874	0.793	0.958	CLONAL	2	TRUE	0	0.2	2		504	744	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251785	212251785	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	52	390	0	ENST00000342788.4:c.3274C>A	p.Pro1092Thr	p.P1092T	ENST00000342788	NM_005235.2	1092	Cct/Act	27/28	NA	2	FACETS	0.877	0.746	1			1	INDETERMINATE	1	TRUE	NA	0.2	2		390	593	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538291	187538291	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	77	725	0	ENST00000441802.2:c.8943G>C	p.Lys2981Asn	p.K2981N	ENST00000441802	NM_005245.3	2981	aaG/aaC	11/27	1	2	FACETS	0.849	0.744	0.963	0.849	0.744	0.963	CLONAL	1	TRUE	1	0.2	2		725	907	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538898	187538898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	50	460	0	ENST00000441802.2:c.8842G>A	p.Glu2948Lys	p.E2948K	ENST00000441802	NM_005245.3	2948	Gaa/Aaa	10/27	1	2	FACETS	0.898	0.761	1	0.898	0.761	1	CLONAL	1	TRUE	1	0.2	2		460	557	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539378	187539378	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	55	579	0	ENST00000441802.2:c.8362G>C	p.Glu2788Gln	p.E2788Q	ENST00000441802	NM_005245.3	2788	Gag/Cag	10/27	1	2	FACETS	0.795	0.679	0.922	0.795	0.679	0.922	CLONAL	1	TRUE	1	0.2	2		579	692	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539495	187539495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	81	549	0	ENST00000441802.2:c.8245G>A	p.Glu2749Lys	p.E2749K	ENST00000441802	NM_005245.3	2749	Gag/Aag	10/27	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.2	2		549	740	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539747	187539747	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	68	539	0	ENST00000441802.2:c.7993G>C	p.Glu2665Gln	p.E2665Q	ENST00000441802	NM_005245.3	2665	Gaa/Caa	10/27	1	2	FACETS	0.93	0.808	1	0.93	0.808	1	CLONAL	1	TRUE	1	0.2	2		539	731	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539810	187539810	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	67	584	0	ENST00000441802.2:c.7930G>T	p.Glu2644Ter	p.E2644*	ENST00000441802	NM_005245.3	2644	Gag/Tag	10/27	1	2	FACETS	0.933	0.81	1	0.933	0.81	1	CLONAL	1	TRUE	1	0.2	2		584	718	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539975	187539975	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	76	542	0	ENST00000441802.2:c.7765G>A	p.Asp2589Asn	p.D2589N	ENST00000441802	NM_005245.3	2589	Gac/Aac	10/27	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.2	2		542	734	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540019	187540019	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	75	564	0	ENST00000441802.2:c.7721G>C	p.Gly2574Ala	p.G2574A	ENST00000441802	NM_005245.3	2574	gGa/gCa	10/27	1	2	FACETS	0.959	0.839	1	0.959	0.839	1	CLONAL	1	TRUE	1	0.2	2		564	782	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540749	187540749	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	59	507	0	ENST00000441802.2:c.6991G>C	p.Asp2331His	p.D2331H	ENST00000441802	NM_005245.3	2331	Gat/Cat	10/27	1	2	FACETS	0.883	0.759	1	0.883	0.759	1	CLONAL	1	TRUE	1	0.2	2		507	668	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540872	187540872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	56	447	0	ENST00000441802.2:c.6868G>A	p.Val2290Met	p.V2290M	ENST00000441802	NM_005245.3	2290	Gtg/Atg	10/27	1	2	FACETS	0.984	0.843	1	0.984	0.843	1	CLONAL	1	TRUE	1	0.2	2		447	569	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541076	187541076	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	50	480	0	ENST00000441802.2:c.6664G>C	p.Asp2222His	p.D2222H	ENST00000441802	NM_005245.3	2222	Gac/Cac	10/27	1	2	FACETS	0.754	0.639	0.881	0.754	0.639	0.881	SUBCLONAL	1	TRUE	1	0.2	2		480	663	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541405	187541405	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	50	519	0	ENST00000441802.2:c.6335G>C	p.Arg2112Thr	p.R2112T	ENST00000441802	NM_005245.3	2112	aGa/aCa	10/27	1	2	FACETS	0.693	0.587	0.811	0.693	0.587	0.811	SUBCLONAL	1	TRUE	1	0.2	2		519	721	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541421	187541421	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	48	528	0	ENST00000441802.2:c.6319G>A	p.Asp2107Asn	p.D2107N	ENST00000441802	NM_005245.3	2107	Gac/Aac	10/27	1	2	FACETS	0.688	0.58	0.807	0.688	0.58	0.807	SUBCLONAL	1	TRUE	1	0.2	2		528	698	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043376	6043376	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	14	95	0	ENST00000265849.7:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000265849	NM_000535.5	100	Cag/Tag	4/15	1	2	FACETS	0.966	0.702	1	0.966	0.702	1	CLONAL	1	TRUE	1	0.2	2		95	145	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932540	39932541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	96	897	0	ENST00000378444.4:c.2058dup	p.Pro687ThrfsTer53	p.P687Tfs*53	ENST00000378444	NM_001123385.1	686	-/A	4/15	0.172899464460443	2	FACETS	0.783	0.695	0.877	0.392	0.347	0.439	SUBCLONAL	1	TRUE	0	0.2	2		897	1226	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0034233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	166	245	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.231833050821026	3	FACETS	0.842	0.775	0.912	0.561	0.516	0.608	CLONAL	2	FALSE	0	0.297729719792713	3		245	761	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685315	89685315	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1554897280	NA	P-0034233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	69	282	0	ENST00000371953.3:c.209+1G>A		p.X70_splice	ENST00000371953	NM_000314.4	70			0.207590460626268	2	FACETS	0.788	0.687	0.898	0.394	0.343	0.449	SUBCLONAL	1	FALSE	0	0.297729719792713	2		282	588	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852158	128852158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141955434	NA	P-0034233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	84	502	0	ENST00000249373.3:c.2230C>T	p.Pro744Ser	p.P744S	ENST00000249373	NM_005631.4	744	Cct/Tct	12/12	0.240095126172099	5	FACETS	0.935	0.824	1	0.312	0.274	0.352	CLONAL	1	FALSE	2	0.297729719792713	5		502	873	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578463	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371524413	NA	P-0034233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	204	486	0	ENST00000269305.4:c.467G>C	p.Arg156Pro	p.R156P	ENST00000269305	NM_001126112.2	156	cGc/cCc	5/11	0.293404136610751	2	FACETS	0.99	0.922	1	0.99	0.922	1	CLONAL	2	FALSE	0	0.297729719792713	2		486	692	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294576	1294576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	127	299	0	ENST00000310581.5:c.425G>A	p.Arg142His	p.R142H	ENST00000310581	NM_198253.2	142	cGc/cAc	2/16	1	2	FACETS	1	0.968	1	1	0.991	1	CLONAL	2	FALSE	1	0.297729719792713	2		299	382	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511702	66511702	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	99	231	0	ENST00000358598.2:c.162T>G	p.Phe54Leu	p.F54L	ENST00000358598	NM_212471.2	54	ttT/ttG	2/11	0.293404136610751	2	FACETS	1	0.98	1	0.718	0.644	0.796	CLONAL	1	FALSE	0	0.297729719792713	2		231	463	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976857	55976857	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	50	440	0	ENST00000263923.4:c.1055C>A	p.Ala352Glu	p.A352E	ENST00000263923	NM_002253.2	352	gCg/gAg	8/30	1	2	FACETS	0.509	0.431	0.595	0.509	0.431	0.595	SUBCLONAL	1	FALSE	1	0.297729719792713	2		440	660	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781518	135781518	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	83	216	0	ENST00000298552.3:c.1447T>C	p.Ser483Pro	p.S483P	ENST00000298552	NM_001162426.1	483	Tct/Cct	15/23	0.297729719792713	3	FACETS	0.821	0.729	0.918	0.821	0.729	0.918	CLONAL	2	FALSE	1	0.297729719792713	3		216	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0034272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	218	804	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.719222606828067	1	FACETS	0.985	0.932	1	0.985	0.932	1	CLONAL	1	TRUE	0	0.719222606828067	1		804	394	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191760	123191760	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034272-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	98	340	0	ENST00000218089.9:c.1349G>T	p.Arg450Ile	p.R450I	ENST00000218089	NM_001042749.1	450	aGa/aTa	15/35	1	2	FACETS	0.849	0.766	0.935	0.849	0.766	0.935	CLONAL	1	TRUE	1	0.719222606828067	2		340	321	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034502-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	22	259	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.181244526566212	2	FACETS	1	0.898	1	0.647	0.505	0.81	CLONAL	1	TRUE	0	0.184769832424541	2		259	184	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0034502-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	273	287	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.184769832424541	8	FACETS	0.966	0.913	1	1	0.986	1	CLONAL	7	TRUE	2	0.184769832424541	8		287	679	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519988	NA	P-0034502-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	134	533	0	ENST00000269305.4:c.808T>G	p.Phe270Val	p.F270V	ENST00000269305	NM_001126112.2	270	Ttt/Gtt	8/11	0.171654411205116	4	FACETS	1	0.924	1	1	0.924	1	CLONAL	3	TRUE	1	0.184769832424541	4		533	565	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249092	55249092	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034502-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	66	557	0	ENST00000275493.2:c.2390G>C	p.Cys797Ser	p.C797S	ENST00000275493	NM_005228.3	797	tGc/tCc	20/28	0.184769832424541	8	FACETS	1	0.922	1	0.183	0.158	0.21	CLONAL	1	TRUE	2	0.184769832424541	8		557	1013	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692792	89692792	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034502-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	64	216	0	ENST00000371953.3:c.277del	p.His93IlefsTer6	p.H93Ifs*6	ENST00000371953	NM_000314.4	92	gaC/ga	5/9	0.171654411205116	4	FACETS	1	0.912	1	1	0.912	1	CLONAL	3	TRUE	1	0.184769832424541	4		216	260	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458686	120458686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886041979	NA	P-0034502-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	62	689	0	ENST00000256646.2:c.6659C>T	p.Ser2220Leu	p.S2220L	ENST00000256646	NM_024408.3	2220	tCa/tTa	34/34	0.184769832424541	5	FACETS	0.896	0.771	1	0.299	0.257	0.344	CLONAL	1	TRUE	2	0.184769832424541	5		689	957	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203436	NA	P-0034568-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	11	463	0	ENST00000269305.4:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269305	NM_001126112.2	163	Tac/Cac	5/11	1	2	FACETS	0.547	0.376	0.762	0.547	0.376	0.762	SUBCLONAL	1	TRUE	1	0.1	2		463	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0034568-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	12	323	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	1	2	FACETS	0.784	0.55	1	0.784	0.55	1	CLONAL	1	TRUE	1	0.1	2		323	306	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431721	49431722	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0034568-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	18	524	0	ENST00000301067.7:c.9417dup	p.Lys3140GlnfsTer36	p.K3140Qfs*36	ENST00000301067	NM_003482.3	3139	-/C	34/54	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.1	2		524	300	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81979830	81979830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772932697	NA	P-0034568-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	31	417	0	ENST00000359376.3:c.3532G>A	p.Ala1178Thr	p.A1178T	ENST00000359376	NM_002661.3	1178	Gct/Act	31/33	0.100769029772944	0	FACETS	1	0.836	1			1	CLONAL	1	TRUE	0	0.1	0		417	537	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0034866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	157	265	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.266878161902028	3	FACETS	0.951	0.882	1	0.634	0.588	0.681	INDETERMINATE	2	TRUE	0	0.535177181201362	3		265	391	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	162	259	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.268428464384365	3	FACETS	0.929	0.862	0.997	0.929	0.862	0.997	INDETERMINATE	2	TRUE	1	0.535177181201362	3		259	413	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0034866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	151	508	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.256844895871332	2	FACETS	1	0.989	1	0.739	0.684	0.795	INDETERMINATE	1	TRUE	0	0.535177181201362	2		508	382	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916143	9916143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762659685	NA	P-0034866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	69	308	0	ENST00000330684.3:c.2146G>A	p.Ala716Thr	p.A716T	ENST00000330684	NM_001134407.1	716	Gcc/Acc	10/13	0.332185725371131	3	FACETS	0.739	0.646	0.84	0.37	0.323	0.42	SUBCLONAL	1	TRUE	1	0.535177181201362	3		308	442	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0034866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	108	173	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.451602728929879	3	FACETS	0.958	0.889	1	0.958	0.889	1	CLONAL	3	TRUE	0	0.535177181201362	3		173	178	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524631	187524631	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	71	473	0	ENST00000441802.2:c.11049G>T	p.Leu3683Phe	p.L3683F	ENST00000441802	NM_005245.3	3683	ttG/ttT	19/27	0.256844895871332	2	FACETS	0.467	0.408	0.531	0.234	0.204	0.266	INDETERMINATE	1	TRUE	0	0.535177181201362	2		473	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0034866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	189	392	0	ENST00000269305.4:c.560-2A>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.514271810481532	2	FACETS	0.978	0.92	1	0.978	0.92	1	CLONAL	2	TRUE	0	0.535177181201362	2		392	361	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349528	89349528	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	62	497	1	ENST00000301030.4:c.3422G>A	p.Ser1141Asn	p.S1141N	ENST00000301030	NM_001256183.1	1141	aGc/aAc	9/13	0.332185725371131	3	FACETS	0.49	0.423	0.563	0.245	0.211	0.282	SUBCLONAL	1	TRUE	1	0.535177181201362	3		498	599	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933368	39933368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	139	518	0	ENST00000378444.4:c.1231C>T	p.Arg411Trp	p.R411W	ENST00000378444	NM_001123385.1	411	Cgg/Tgg	4/15	1	2	FACETS	0.936	0.856	1	0.936	0.856	1	CLONAL	1	TRUE	1	0.535177181201362	2		518	555	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411856	116411880	+	intron_variant	Intron	DEL	CCATGATAGCCGTCTTTAACAAGCT	CCATGATAGCCGTCTTTAACAAGCT	-	novel	NA	P-0035162-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4	61	567	0	ENST00000397752.3:c.2888-46_2888-22del		p.*963*	ENST00000397752	NM_000245.2	-/1390			0.398136866707841	20	FACETS	0.982	0.938	1	1	0.981	1	CLONAL	22	TRUE	0	0.398136866707841	20		567	65	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423413	116423413	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035162-T06-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	11	326	0	ENST00000397752.3:c.3688T>A	p.Tyr1230Asn	p.Y1230N	ENST00000397752	NM_000245.2	1230	Tat/Aat	19/21	0.398136866707841	20	FACETS	0.918	0.655	1	0.275	0.196	0.366	CLONAL	6	TRUE	0	0.398136866707841	20		326	46	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	184	338	0	ENST00000206249.3:c.1607T>A	p.Leu536His	p.L536H	ENST00000206249	NM_000125.3	536	cTc/cAc	8/8	0.640227855988887	6	FACETS	0.882	0.816	0.95	0.353	0.326	0.38	CLONAL	2	TRUE	1	0.669268096531969	6		338	729	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912717	100912717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1181450031	NA	P-0035163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	76	266	0	ENST00000325455.5:c.2605C>T	p.Arg869Cys	p.R869C	ENST00000325455	NM_001202474.3	869	Cgt/Tgt	7/8	0.635546558420182	3	FACETS	1	0.945	1	0.37	0.328	0.414	CLONAL	1	TRUE	0	0.669268096531969	3		266	273	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641058	23641058	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45464991	NA	P-0035163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	126	390	1	ENST00000261584.4:c.2417C>T	p.Pro806Leu	p.P806L	ENST00000261584	NM_024675.3	806	cCg/cTg	5/13	0.232549216276112	5	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.669268096531969	5		391	524	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120675	115120676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0035163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	71	354	0	ENST00000257566.3:c.330dup	p.Glu111ArgfsTer27	p.E111Rfs*27	ENST00000257566	NM_016569.3	110	-/A	1/8	0.669268096531969	3	FACETS	0.726	0.637	0.821	0.363	0.318	0.411	SUBCLONAL	1	TRUE	1	0.669268096531969	3		354	390	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115944	8115945	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0035163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	127	398	1	ENST00000346208.3:c.1292dup	p.Pro432ThrfsTer75	p.P432Tfs*75	ENST00000346208		430	-/G	6/6	0.608671283424169	5	FACETS	1	0.969	1	0.289	0.262	0.317	CLONAL	1	TRUE	1	0.669268096531969	5		399	659	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366959	15366959	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	126	405	0	ENST00000263377.2:c.1667A>G	p.Glu556Gly	p.E556G	ENST00000263377	NM_058243.2	556	gAa/gGa	9/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.669268096531969	2		405	340	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425878	49425878	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	178	401	0	ENST00000301067.7:c.12610G>T	p.Val4204Phe	p.V4204F	ENST00000301067	NM_003482.3	4204	Gtc/Ttc	39/54	0.232549216276112	5	FACETS	1	0.947	1			1	INDETERMINATE	2	TRUE	NA	0.669268096531969	5		401	521	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533743	63533743	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs544255284	NA	P-0035163-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1273	168	493	0	ENST00000307078.5:c.1411C>T	p.His471Tyr	p.H471Y	ENST00000307078	NM_004655.3	471	Cac/Tac	6/11	0.669268096531969	9	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.669268096531969	9		493	1441	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0035324-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	127	564	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.292231498157337	20	FACETS	0.974	0.917	1	0.974	0.917	1	CLONAL	18	TRUE	2	0.292231498157337	20		564	180	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0035324-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	10	566	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.155525086387049	3	FACETS	0.817	0.569	1	0.545	0.379	0.739	INDETERMINATE	2	TRUE	0	0.292231498157337	3		566	48	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259439	55259439	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs397517126	NA	P-0035324-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	117	408	0	ENST00000275493.2:c.2497T>G	p.Leu833Val	p.L833V	ENST00000275493	NM_005228.3	833	Ttg/Gtg	21/28	0.292231498157337	20	FACETS	0.988	0.925	1	0.933	0.874	0.99	CLONAL	17	TRUE	2	0.292231498157337	20		408	173	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612157	189612157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035324-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	15	563	1	ENST00000264731.3:c.1909C>T	p.Arg637Cys	p.R637C	ENST00000264731	NM_003722.4	637	Cgt/Tgt	14/14	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.292231498157337	NA		564	83	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0035329-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	50	1110	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.16	2		1111	558	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829003	72830025	+	inframe_deletion	In_Frame_Del	DEL	CTGAGGAGGTAGGTTTGCGAGCTGTTGAGGAGTTGATGTGTGGAGGGGCTTGAGGGGCAGGTGGGAGAGCTGGGAAGGACTGGGGCTCGACTGGGGTAAGGGGCACTGTGGAGGGGGCGCTTGTGGAGGAGGCTGTGGCAACGAAGGCAGGGACACCAGCTGGGGGAGCTTCTGCTGGGGAGTGTTGGTCTTCTGCTCGGGCTGCTCTTGCTGCTGCAGCTCTGGCTTTGGTTGTCCTTGCTTTTCTTGGGTTTGGTTTGGCTGTGCACTGGGAGCTTCCGCCAGCTTTGGTTTCTCATCGCCTGCCTCTGTTTTTGAATTGAAGGTGGCCAGTTCCTCAGCCTCCGCTGTAAGCTGCAAGAAAGCGGAGGAAGCTGTATTATTGGCTGATGGTGCTGGGGCGCTGTAAGCCTGTGAGGGCATCGGGGTACTGCAGGATGAGCTGGTAGGCGTCAGGATTTCCATGGCATCCATGGAATCCTCATTTTGGCTGTCGTCCTGCCCCTCCTCATCCTCATCCTTGTAACACAGCTTCTTCTGGTGCTTGATGAGATCAAAGATGCGCTGAAACACCAGGCTACATTTTTTGCACTGGTAGTTCAAGTTGCTTGTTCGAATGTATCTATCATTTGTAAGCTCACGCCGCTCTCCATCTTTGCCCTCTCCCTGATTCTCATAATTCTTCCTGGCCTTCTGTCGGGCATTCTGAAACCACACCACTATCACTCGGGTTGGAAGGTTCAGTAAATTAGAGAGTTGCTCAAATTCATCATCCTTTGGGTAAGCATTGGCATCGAAGAAGTCCTGTAAGACCCTCAGCTGGTAGTCCGTAAACCTTGTTCTTGAAGACCTCTTGCTTCCCCAGTACTCCTGCTTTGGAGGTTCCGGCGAAGGGGGCCGGGAGTCAATCTTGAGCTCCTCCAGGCTGGTGATAGGAGGATTACTGAAGTTGTAAGGGGAGTCCTTGTTACGCTGCCTCTCTTTGAAGAGAGTGTTCCTGAACCAGTGCTTGATCACTTTCTG	CTGAGGAGGTAGGTTTGCGAGCTGTTGAGGAGTTGATGTGTGGAGGGGCTTGAGGGGCAGGTGGGAGAGCTGGGAAGGACTGGGGCTCGACTGGGGTAAGGGGCACTGTGGAGGGGGCGCTTGTGGAGGAGGCTGTGGCAACGAAGGCAGGGACACCAGCTGGGGGAGCTTCTGCTGGGGAGTGTTGGTCTTCTGCTCGGGCTGCTCTTGCTGCTGCAGCTCTGGCTTTGGTTGTCCTTGCTTTTCTTGGGTTTGGTTTGGCTGTGCACTGGGAGCTTCCGCCAGCTTTGGTTTCTCATCGCCTGCCTCTGTTTTTGAATTGAAGGTGGCCAGTTCCTCAGCCTCCGCTGTAAGCTGCAAGAAAGCGGAGGAAGCTGTATTATTGGCTGATGGTGCTGGGGCGCTGTAAGCCTGTGAGGGCATCGGGGTACTGCAGGATGAGCTGGTAGGCGTCAGGATTTCCATGGCATCCATGGAATCCTCATTTTGGCTGTCGTCCTGCCCCTCCTCATCCTCATCCTTGTAACACAGCTTCTTCTGGTGCTTGATGAGATCAAAGATGCGCTGAAACACCAGGCTACATTTTTTGCACTGGTAGTTCAAGTTGCTTGTTCGAATGTATCTATCATTTGTAAGCTCACGCCGCTCTCCATCTTTGCCCTCTCCCTGATTCTCATAATTCTTCCTGGCCTTCTGTCGGGCATTCTGAAACCACACCACTATCACTCGGGTTGGAAGGTTCAGTAAATTAGAGAGTTGCTCAAATTCATCATCCTTTGGGTAAGCATTGGCATCGAAGAAGTCCTGTAAGACCCTCAGCTGGTAGTCCGTAAACCTTGTTCTTGAAGACCTCTTGCTTCCCCAGTACTCCTGCTTTGGAGGTTCCGGCGAAGGGGGCCGGGAGTCAATCTTGAGCTCCTCCAGGCTGGTGATAGGAGGATTACTGAAGTTGTAAGGGGAGTCCTTGTTACGCTGCCTCTCTTTGAAGAGAGTGTTCCTGAACCAGTGCTTGATCACTTTCTG	-	novel	NA	P-0035329-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	31	509	0	ENST00000268489.5:c.6557_7579del	p.Gln2186_Gln2526del	p.Q2186_Q2526del	ENST00000268489	NM_006885.3	2186	CAGAAAGTGATCAAGCACTGGTTCAGGAACACTCTCTTCAAAGAGAGGCAGCGTAACAAGGACTCCCCTTACAACTTCAGTAATCCTCCTATCACCAGCCTGGAGGAGCTCAAGATTGACTCCCGGCCCCCTTCGCCGGAACCTCCAAAGCAGGAGTACTGGGGAAGCAAGAGGTCTTCAAGAACAAGGTTTACGGACTACCAGCTGAGGGTCTTACAGGACTTCTTCGATGCCAATGCTTACCCAAAGGATGATGAATTTGAGCAACTCTCTAATTTACTGAACCTTCCAACCCGAGTGATAGTGGTGTGGTTTCAGAATGCCCGACAGAAGGCCAGGAAGAATTATGAGAATCAGGGAGAGGGCAAAGATGGAGAGCGGCGTGAGCTTACAAATGATAGATACATTCGAACAAGCAACTTGAACTACCAGTGCAAAAAATGTAGCCTGGTGTTTCAGCGCATCTTTGATCTCATCAAGCACCAGAAGAAGCTGTGTTACAAGGATGAGGATGAGGAGGGGCAGGACGACAGCCAAAATGAGGATTCCATGGATGCCATGGAAATCCTGACGCCTACCAGCTCATCCTGCAGTACCCCGATGCCCTCACAGGCTTACAGCGCCCCAGCACCATCAGCCAATAATACAGCTTCCTCCGCTTTCTTGCAGCTTACAGCGGAGGCTGAGGAACTGGCCACCTTCAATTCAAAAACAGAGGCAGGCGATGAGAAACCAAAGCTGGCGGAAGCTCCCAGTGCACAGCCAAACCAAACCCAAGAAAAGCAAGGACAACCAAAGCCAGAGCTGCAGCAGCAAGAGCAGCCCGAGCAGAAGACCAACACTCCCCAGCAGAAGCTCCCCCAGCTGGTGTCCCTGCCTTCGTTGCCACAGCCTCCTCCACAAGCGCCCCCTCCACAGTGCCCCTTACCCCAGTCGAGCCCCAGTCCTTCCCAGCTCTCCCACCTGCCCCTCAAGCCCCTCCACACATCAACTCCTCAACAGCTCGCAAACCTACCTCCTCAG/-	9/10	1	2	FACETS	0.735	0.594	0.896	0.735	0.594	0.896	SUBCLONAL	1	TRUE	1	0.16	2		509	527	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0035549-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	52	280	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.375112324167618	3	FACETS	1	0.908	1	0.541	0.463	0.625	CLONAL	1	TRUE	1	0.375821063118191	3		280	304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0035549-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	162	400	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.375821063118191	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.375821063118191	2		400	422	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035549-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	147	410	1	ENST00000257430.4:c.4199C>A	p.Ser1400Ter	p.S1400*	ENST00000257430	NM_000038.5	1400	tCg/tAg	16/16	0.375112324167618	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.375821063118191	3		411	431	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332607	153332607	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035549-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	181	507	0	ENST00000281708.4:c.349G>T	p.Glu117Ter	p.E117*	ENST00000281708	NM_033632.3	117	Gag/Tag	2/12	0.375821063118191	2	FACETS	0.942	0.876	1	0.942	0.876	1	CLONAL	2	TRUE	0	0.375821063118191	2		507	511	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450048	32450048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444869026	NA	P-0035549-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	76	403	0	ENST00000332351.3:c.764C>T	p.Ser255Leu	p.S255L	ENST00000332351	NM_024426.4	255	tCg/tTg	2/10	0.375112324167618	3	FACETS	1	0.908	1	0.519	0.456	0.585	CLONAL	1	TRUE	1	0.375821063118191	3		403	463	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967567	26967567	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035549-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	197	335	0	ENST00000381527.3:c.710G>A	p.Arg237Gln	p.R237Q	ENST00000381527	NM_001260.1	237	cGa/cAa	7/13	0.375821063118191	13	FACETS	1	0.942	1	0.407	0.377	0.438	CLONAL	4	TRUE	3	0.375821063118191	13		335	790	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633551	69633551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035549-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	73	414	0	ENST00000334134.2:c.151G>A	p.Ala51Thr	p.A51T	ENST00000334134	NM_005247.2	51	Gcc/Acc	1/3	0.375112324167618	3	FACETS	1	0.948	1	0.574	0.504	0.648	CLONAL	1	TRUE	1	0.375821063118191	3		414	402	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619850	21619850	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035549-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	70	332	0	ENST00000382592.4:c.316G>T	p.Glu106Ter	p.E106*	ENST00000382592	NM_014572.2	106	Gaa/Taa	2/8	0.375821063118191	6	FACETS	1	0.876	1			1	CLONAL	1	TRUE	NA	0.375821063118191	6		332	649	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606075	81606076	+	missense_variant	Missense_Mutation	DNP	CT	CT	AA	novel	NA	P-0035549-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	64	404	0	ENST00000298171.2:c.745_746delinsAA	p.Leu249Lys	p.L249K	ENST00000298171	NM_000369.2	249	CTg/AAg	9/10	0.375112324167618	3	FACETS	0.948	0.823	1	0.474	0.411	0.541	CLONAL	1	TRUE	1	0.375821063118191	3		404	427	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476284	88476285	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0035549-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	49	356	0	ENST00000360948.2:c.1847_1848delinsAT	p.Val616Asp	p.V616D	ENST00000360948	NM_001012338.2	616	gTC/gAT	15/19	NA	2	FACETS	0.969	0.827	1			1	INDETERMINATE	1	TRUE	NA	0.375821063118191	2		356	269	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687072	37687075	+	frameshift_variant	Frame_Shift_Del	DEL	ATGG	ATGG	-	novel	NA	P-0035549-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	89	392	0	ENST00000447079.4:c.3977_3980del	p.Met1326SerfsTer36	p.M1326Sfs*36	ENST00000447079	NM_015083.1	1326	ATGGag/ag	14/14	0.372386580271919	3	FACETS	1	0.893	1			1	CLONAL	1	TRUE	NA	0.375821063118191	3		392	560	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212252710	212252710	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035549-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	39	274	0	ENST00000342788.4:c.3143T>G	p.Ile1048Ser	p.I1048S	ENST00000342788	NM_005235.2	1048	aTt/aGt	26/28	0.375112324167618	3	FACETS	0.862	0.718	1	0.431	0.359	0.511	CLONAL	1	TRUE	1	0.375821063118191	3		274	286	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796121	57796121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035549-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	70	332	0	ENST00000309042.7:c.1097G>A	p.Cys366Tyr	p.C366Y	ENST00000309042	NM_005612.4	366	tGt/tAt	4/4	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.375821063118191	2		332	363	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654844	29654844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035846-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	77	368	0	ENST00000356175.3:c.5533G>A	p.Asp1845Asn	p.D1845N	ENST00000356175	NM_000267.3	1845	Gac/Aac	37/57	1	2	FACETS	0.997	0.886	1	0.997	0.886	1	CLONAL	1	TRUE	1	0.568041604838028	2		368	272	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058033	27058033	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036446-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	246	530	0	ENST00000324856.7:c.1741C>T	p.Gln581Ter	p.Q581*	ENST00000324856	NM_006015.4	581	Cag/Tag	3/20	0.543019992798518	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.706454663006339	1		530	421	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247367	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747241612	NA	P-0036446-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	138	390	0	ENST00000281708.4:c.1435C>G	p.Arg479Gly	p.R479G	ENST00000281708	NM_033632.3	479	Cga/Gga	10/12	0.329806021552199	1	FACETS	0.71	0.654	0.766	0.71	0.654	0.766	INDETERMINATE	1	TRUE	0	0.706454663006339	1		390	356	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120178	70120178	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057518216	NA	P-0036446-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	384	450	0	ENST00000245479.2:c.1180C>T	p.Arg394Ter	p.R394*	ENST00000245479	NM_000346.3	394	Cga/Tga	3/3	0.706454663006339	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.706454663006339	2		450	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578289	7578300	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTAAGAGCAAT	CCTAAGAGCAAT	-	novel	NA	P-0036446-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	296	583	0	ENST00000269305.4:c.560-11_560del		p.X187_splice	ENST00000269305	NM_001126112.2	187		6/11	0.706454663006339	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.706454663006339	1		583	460	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928072	178928086	+	inframe_deletion	In_Frame_Del	DEL	TGGATTAGAAGATTT	TGGATTAGAAGATTT	-	novel	NA	P-0036446-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	205	318	0	ENST00000263967.3:c.1350_1364del	p.His450_Leu455delinsGln	p.H450_L455delinsQ	ENST00000263967	NM_006218.2	450	caTGGATTAGAAGATTTg/cag	8/21	0.706454663006339	4	FACETS	0.9	0.85	0.949	0.9	0.85	0.949	CLONAL	3	TRUE	1	0.706454663006339	4		318	367	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967949	93967949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780064217	NA	P-0036446-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	47	324	0	ENST00000369303.4:c.1978G>A	p.Val660Ile	p.V660I	ENST00000369303	NM_004440.3	660	Gtt/Att	11/17	0.200291187004965	2	FACETS	0.561	0.478	0.651	0.281	0.239	0.326	INDETERMINATE	1	TRUE	0	0.706454663006339	2		324	237	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920657	127920657	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036446-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	74	228	0	ENST00000373547.4:c.242A>C	p.Asp81Ala	p.D81A	ENST00000373547	NM_002721.4	81	gAt/gCt	4/7	0.317901688765693	1	FACETS	0.869	0.782	0.955	0.869	0.782	0.955	INDETERMINATE	1	TRUE	0	0.706454663006339	1		228	156	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	133	738	0				ENST00000310581	NM_198253.2	-/1132			0.174678297263752	4	FACETS	0.839	0.78	0.899	1	0.985	1	INDETERMINATE	3	TRUE	2	0.7070556209082	4		738	255	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262592	16262592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	121	353	0	ENST00000375759.3:c.9857C>A	p.Pro3286His	p.P3286H	ENST00000375759	NM_015001.2	3286	cCt/cAt	11/15	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.7070556209082	2		353	337	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023748	27023748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	46	342	0	ENST00000324856.7:c.854G>A	p.Gly285Glu	p.G285E	ENST00000324856	NM_006015.4	285	gGa/gAa	1/20	1	2	FACETS	0.735	0.629	0.849	0.735	0.629	0.849	SUBCLONAL	1	TRUE	1	0.7070556209082	2		342	177	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101423	27101423	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	79	202	0	ENST00000324856.7:c.4705C>T	p.Pro1569Ser	p.P1569S	ENST00000324856	NM_006015.4	1569	Cca/Tca	18/20	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.7070556209082	2		202	216	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935268	36935268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	133	327	0	ENST00000361632.4:c.1459G>A	p.Gly487Arg	p.G487R	ENST00000361632		487	Ggg/Agg	10/16	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.7070556209082	2		327	348	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166271	118166271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	142	449	0	ENST00000369448.3:c.781G>A	p.Glu261Lys	p.E261K	ENST00000369448	NM_017709.3	261	Gaa/Aaa	2/2	1	2	FACETS	0.846	0.776	0.917	0.846	0.776	0.917	CLONAL	1	TRUE	1	0.7070556209082	2		449	475	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849128	156849128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	131	382	0	ENST00000524377.1:c.2020G>A	p.Asp674Asn	p.D674N	ENST00000524377	NM_002529.3	674	Gat/Aat	15/17	0.638933955674331	3	FACETS	1	0.926	1	0.508	0.463	0.554	CLONAL	1	TRUE	1	0.7070556209082	3		382	494	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104377181	104377182	+	missense_variant	Missense_Mutation	DNP	TA	TA	CT	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	145	417	1	ENST00000369902.3:c.1292_1293delinsCT	p.Leu431Ser	p.L431S	ENST00000369902	NM_016169.3	431	tTA/tCT	10/12	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.7070556209082	2		418	372	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256135	123256135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141929882	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	118	336	0	ENST00000358487.5:c.1774C>T	p.Arg592Cys	p.R592C	ENST00000358487	NM_000141.4	592	Cgt/Tgt	13/18	0.638933955674331	3	FACETS	0.814	0.737	0.895	0.407	0.368	0.448	CLONAL	1	TRUE	1	0.7070556209082	3		336	555	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324081	123324081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	97	185	0	ENST00000358487.5:c.389C>T	p.Ser130Phe	p.S130F	ENST00000358487	NM_000141.4	130	tCc/tTc	4/18	0.638933955674331	3	FACETS	0.985	0.885	1	0.493	0.442	0.545	CLONAL	1	TRUE	1	0.7070556209082	3		185	377	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57004307	57004307	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	G	G	A	rs370702287	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	137	391	0	ENST00000257254.3:c.172C>T	p.Arg58Trp	p.R58W	ENST00000257254		58	Cgg/Tgg	1/2	1	2	FACETS	0.934	0.858	1	0.934	0.858	1	CLONAL	1	TRUE	1	0.7070556209082	2		391	415	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141997	108141997	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780619	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	122	295	0	ENST00000278616.4:c.2941C>T	p.Arg981Cys	p.R981C	ENST00000278616	NM_000051.3	981	Cgt/Tgt	20/63	0.7070556209082	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.7070556209082	1		295	213	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103398	119103398	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	126	266	0	ENST00000264033.4:c.436C>T	p.Gln146Ter	p.Q146*	ENST00000264033	NM_005188.3	146	Cag/Tag	2/16	0.7070556209082	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.7070556209082	1		266	225	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417041	417041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	127	398	0	ENST00000399788.2:c.3509C>T	p.Ala1170Val	p.A1170V	ENST00000399788	NM_001042603.1	1170	gCc/gTc	23/28	0.166980714434997	2	FACETS	0.859	0.785	0.936	0.43	0.392	0.468	INDETERMINATE	1	TRUE	0	0.7070556209082	2		398	418	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431735	49431735	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	83	383	0	ENST00000301067.7:c.9404C>T	p.Thr3135Ile	p.T3135I	ENST00000301067	NM_003482.3	3135	aCc/aTc	34/54	0.166980714434997	2	FACETS	0.729	0.649	0.813	0.365	0.324	0.407	INDETERMINATE	1	TRUE	0	0.7070556209082	2		383	322	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112892368	112892368	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	130	203	0	ENST00000351677.2:c.526G>A	p.Glu176Lys	p.E176K	ENST00000351677	NM_002834.3	176	Gaa/Aaa	5/16	0.166980714434997	2	FACETS	1	0.985	1	0.654	0.605	0.704	INDETERMINATE	1	TRUE	0	0.7070556209082	2		203	281	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112910803	112910803	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	73	231	0	ENST00000351677.2:c.812A>T	p.Gln271Leu	p.Q271L	ENST00000351677	NM_002834.3	271	cAa/cTa	7/16	0.166980714434997	2	FACETS	0.73	0.645	0.819	0.365	0.322	0.41	INDETERMINATE	1	TRUE	0	0.7070556209082	2		231	283	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601256	28601256	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	93	308	0	ENST00000241453.7:c.2176T>C	p.Tyr726His	p.Y726H	ENST00000241453	NM_004119.2	726	Tac/Cac	17/24	0.25218046754955	1	FACETS	0.558	0.501	0.616	0.558	0.501	0.616	INDETERMINATE	1	TRUE	0	0.7070556209082	1		308	305	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964022	28964022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	153	336	0	ENST00000282397.4:c.1880C>T	p.Ser627Phe	p.S627F	ENST00000282397	NM_002019.4	627	tCc/tTc	13/30	0.25218046754955	1	FACETS	0.694	0.642	0.747	0.694	0.642	0.747	INDETERMINATE	1	TRUE	0	0.7070556209082	1		336	403	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005419	29005419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55687105	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	124	356	0	ENST00000282397.4:c.842G>A	p.Arg281Gln	p.R281Q	ENST00000282397	NM_002019.4	281	cGa/cAa	7/30	0.25218046754955	1	FACETS	0.625	0.571	0.679	0.625	0.571	0.679	INDETERMINATE	1	TRUE	0	0.7070556209082	1		356	363	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012452	29012452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	134	304	0	ENST00000282397.4:c.419G>A	p.Ser140Asn	p.S140N	ENST00000282397	NM_002019.4	140	aGt/aAt	4/30	0.25218046754955	1	FACETS	0.734	0.676	0.792	0.734	0.676	0.792	INDETERMINATE	1	TRUE	0	0.7070556209082	1		304	334	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944632	32944632	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	76	294	0	ENST00000380152.3:c.8425T>C	p.Phe2809Leu	p.F2809L	ENST00000380152		2809	Ttc/Ctc	19/27	0.25218046754955	1	FACETS	0.473	0.419	0.53	0.473	0.419	0.53	INDETERMINATE	1	TRUE	0	0.7070556209082	1		294	294	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336134	73336134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	92	339	0	ENST00000377767.4:c.2269G>A	p.Gly757Arg	p.G757R	ENST00000377767	NM_014953.3	757	Gga/Aga	17/21	0.25218046754955	1	FACETS	0.599	0.539	0.66	0.599	0.539	0.66	INDETERMINATE	1	TRUE	0	0.7070556209082	1		339	281	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569948	95569948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	137	411	0	ENST00000393063.1:c.3785C>T	p.Pro1262Leu	p.P1262L	ENST00000393063	NM_030621.3	1262	cCt/cTt	22/28	0.166980714434997	2	FACETS	0.754	0.69	0.821	0.377	0.345	0.411	INDETERMINATE	1	TRUE	0	0.7070556209082	2		411	514	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041734	42041734	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	162	400	0	ENST00000219905.7:c.5929C>T	p.Gln1977Ter	p.Q1977*	ENST00000219905	NM_001164273.1	1977	Cag/Tag	17/24	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.7070556209082	2		400	413	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052602	42052602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	145	343	0	ENST00000219905.7:c.7273C>T	p.Arg2425Cys	p.R2425C	ENST00000219905	NM_001164273.1	2425	Cgc/Tgc	20/24	1	2	FACETS	0.905	0.833	0.98	0.905	0.833	0.98	CLONAL	1	TRUE	1	0.7070556209082	2		343	453	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713311	43713311	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	172	355	0	ENST00000382044.4:c.4162C>G	p.Leu1388Val	p.L1388V	ENST00000382044	NM_001141980.1	1388	Ctt/Gtt	20/28	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.7070556209082	2		355	468	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472652	88472652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	164	268	0	ENST00000360948.2:c.1903G>A	p.Asp635Asn	p.D635N	ENST00000360948	NM_001012338.2	635	Gat/Aat	16/19	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.7070556209082	2		268	395	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476280	88476280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	98	282	0	ENST00000360948.2:c.1852G>A	p.Glu618Lys	p.E618K	ENST00000360948	NM_001012338.2	618	Gaa/Aaa	15/19	1	2	FACETS	0.85	0.767	0.937	0.85	0.767	0.937	CLONAL	1	TRUE	1	0.7070556209082	2		282	326	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396431	396431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	150	385	0	ENST00000262320.3:c.595C>T	p.Pro199Ser	p.P199S	ENST00000262320	NM_003502.3	199	Ccc/Tcc	2/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.7070556209082	2		385	340	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632744	23632744	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	107	284	0	ENST00000261584.4:c.3052G>T	p.Glu1018Ter	p.E1018*	ENST00000261584	NM_024675.3	1018	Gag/Tag	10/13	1	2	FACETS	0.867	0.786	0.951	0.867	0.786	0.951	CLONAL	1	TRUE	1	0.7070556209082	2		284	349	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671678	67671679	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	101	407	0	ENST00000264010.4:c.2087_2088delinsTT	p.Pro696Leu	p.P696L	ENST00000264010	NM_006565.3	696	cCC/cTT	12/12	0.25218046754955	1	FACETS	0.528	0.476	0.581	0.528	0.476	0.581	INDETERMINATE	1	TRUE	0	0.7070556209082	1		407	350	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346081	89346081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	42	104	0	ENST00000301030.4:c.6869C>T	p.Pro2290Leu	p.P2290L	ENST00000301030	NM_001256183.1	2290	cCc/cTc	9/13	0.25218046754955	1	FACETS	0.753	0.649	0.859	0.753	0.649	0.859	INDETERMINATE	1	TRUE	0	0.7070556209082	1		104	102	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350869	89350869	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	108	288	0	ENST00000301030.4:c.2081T>G	p.Phe694Cys	p.F694C	ENST00000301030	NM_001256183.1	694	tTt/tGt	9/13	0.25218046754955	1	FACETS	0.65	0.591	0.71	0.65	0.591	0.71	INDETERMINATE	1	TRUE	0	0.7070556209082	1		288	304	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958242	11958242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1261150954	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	67	143	0	ENST00000353533.5:c.152C>T	p.Pro51Leu	p.P51L	ENST00000353533	NM_003010.3	51	cCa/cTa	2/11	0.166980714434997	2	FACETS	0.828	0.729	0.93	0.414	0.364	0.465	INDETERMINATE	1	TRUE	0	0.7070556209082	2		143	229	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554601	29554602	+	missense_variant	Missense_Mutation	DNP	AA	AA	GT	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	82	242	0	ENST00000356175.3:c.2386_2387delinsGT	p.Lys796Val	p.K796V	ENST00000356175	NM_000267.3	796	AAa/GTa	20/57	0.166980714434997	2	FACETS	0.789	0.703	0.878	0.394	0.351	0.439	INDETERMINATE	1	TRUE	0	0.7070556209082	2		242	294	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576001	29576001	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	105	244	0	ENST00000356175.3:c.3975-1G>A		p.X1325_splice	ENST00000356175	NM_000267.3	1325			0.166980714434997	2	FACETS	0.754	0.681	0.83	0.377	0.34	0.415	INDETERMINATE	1	TRUE	0	0.7070556209082	2		244	394	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653151	29653151	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	195	383	0	ENST00000356175.3:c.5086G>T	p.Glu1696Ter	p.E1696*	ENST00000356175	NM_000267.3	1696	Gag/Tag	36/57	0.166980714434997	2	FACETS	1	0.984	1	0.586	0.548	0.624	INDETERMINATE	1	TRUE	0	0.7070556209082	2		383	471	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33681060	33681060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780673919	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	145	267	0	ENST00000308377.4:c.1217G>A	p.Arg406Gln	p.R406Q	ENST00000308377	NM_152270.3	406	cGa/cAa	4/5	0.166980714434997	2	FACETS	1	0.983	1	0.607	0.562	0.652	INDETERMINATE	1	TRUE	0	0.7070556209082	2		267	338	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690521	33690521	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	140	362	0	ENST00000308377.4:c.306T>G	p.Cys102Trp	p.C102W	ENST00000308377	NM_152270.3	102	tgT/tgG	2/5	0.166980714434997	2	FACETS	1	0.983	1	0.615	0.569	0.662	INDETERMINATE	1	TRUE	0	0.7070556209082	2		362	322	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864574	37864574	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	143	300	0	ENST00000269571.5:c.226G>A	p.Asp76Asn	p.D76N	ENST00000269571		76	Gat/Aat	3/27	0.166980714434997	2	FACETS	1	0.98	1	0.588	0.544	0.633	INDETERMINATE	1	TRUE	0	0.7070556209082	2		300	344	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857681	59857681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	113	245	0	ENST00000259008.2:c.1876G>A	p.Glu626Lys	p.E626K	ENST00000259008	NM_032043.2	626	Gaa/Aaa	13/20	0.166980714434997	2	FACETS	0.862	0.783	0.943	0.431	0.391	0.472	INDETERMINATE	1	TRUE	0	0.7070556209082	2		245	371	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222899	36222899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	109	389	0	ENST00000222270.7:c.5528C>T	p.Pro1843Leu	p.P1843L	ENST00000222270	NM_014727.1	1843	cCt/cTt	27/37	1	2	FACETS	0.976	0.888	1	0.976	0.888	1	CLONAL	1	TRUE	1	0.7070556209082	2		389	316	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792107	42792107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1382074611	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	126	257	0	ENST00000575354.2:c.911G>A	p.Gly304Asp	p.G304D	ENST00000575354	NM_015125.3	304	gGc/gAc	6/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.7070556209082	2		257	315	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965017	25965017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	89	358	0	ENST00000435504.4:c.4189C>T	p.Pro1397Ser	p.P1397S	ENST00000435504		1397	Cct/Tct	13/13	1	2	FACETS	0.836	0.75	0.926	0.836	0.75	0.926	CLONAL	1	TRUE	1	0.7070556209082	2		358	301	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185035	99185035	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	161	253	0	ENST00000074304.5:c.2437T>C	p.Phe813Leu	p.F813L	ENST00000074304	NM_001134224.1	813	Ttt/Ctt	23/26	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.7070556209082	2		253	398	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538275	9538275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	196	347	0	ENST00000353224.5:c.1723C>T	p.Leu575Phe	p.L575F	ENST00000353224	NM_177990.2	575	Ctc/Ttc	7/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.7070556209082	2		347	476	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31015959	31015959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	153	336	0	ENST00000375687.4:c.281C>T	p.Pro94Leu	p.P94L	ENST00000375687	NM_015338.5	94	cCa/cTa	5/13	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.7070556209082	2		336	376	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739115	40739115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	104	283	0	ENST00000373198.4:c.3169G>A	p.Glu1057Lys	p.E1057K	ENST00000373198	NM_133170.3	1057	Gag/Aag	24/32	1	2	FACETS	0.85	0.769	0.934	0.85	0.769	0.934	CLONAL	1	TRUE	1	0.7070556209082	2		283	346	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827900	40827900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767977370	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	159	287	0	ENST00000373198.4:c.2528C>T	p.Ser843Phe	p.S843F	ENST00000373198	NM_133170.3	843	tCt/tTt	17/32	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.7070556209082	2		287	414	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817438	39817438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748243137	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	147	350	0	ENST00000288319.7:c.125G>A	p.Gly42Glu	p.G42E	ENST00000288319	NM_182918.3	42	gGa/gAa	2/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.7070556209082	2		350	355	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852517	42852517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	92	304	0	ENST00000398585.3:c.569G>A	p.Gly190Glu	p.G190E	ENST00000398585	NM_001135099.1	190	gGa/gAa	6/14	1	2	FACETS	0.975	0.879	1	0.975	0.879	1	CLONAL	1	TRUE	1	0.7070556209082	2		304	267	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655440	45655440	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	113	294	0	ENST00000407780.3:c.412T>G	p.Phe138Val	p.F138V	ENST00000407780	NM_001283052.1	138	Ttc/Gtc	4/7	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.7070556209082	2		294	293	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035181	30035181	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	115	302	0	ENST00000338641.4:c.343C>T	p.Gln115Ter	p.Q115*	ENST00000338641	NM_000268.3	115	Caa/Taa	3/16	0.25218046754955	1	FACETS	0.619	0.564	0.675	0.619	0.564	0.675	INDETERMINATE	1	TRUE	0	0.7070556209082	1		302	340	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259116	89259117	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	137	354	0	ENST00000336596.2:c.260_261delinsAT	p.Val87Asp	p.V87D	ENST00000336596	NM_005233.5	87	gTC/gAT	3/17	0.638933955674331	3	FACETS	0.886	0.809	0.966	0.443	0.404	0.483	CLONAL	1	TRUE	1	0.7070556209082	3		354	592	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456447	189456447	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	271	305	0	ENST00000264731.3:c.208C>T	p.Gln70Ter	p.Q70*	ENST00000264731	NM_003722.4	70	Cag/Tag	3/14	0.7070556209082	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.7070556209082	2		305	373	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133586	55133586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501507	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	141	359	0	ENST00000257290.5:c.890G>A	p.Arg297Lys	p.R297K	ENST00000257290	NM_006206.4	297	aGg/aAg	6/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.7070556209082	2		359	341	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156489	55156489	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1290364180	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	83	293	0	ENST00000257290.5:c.2890A>G	p.Lys964Glu	p.K964E	ENST00000257290	NM_006206.4	964	Aaa/Gaa	22/23	1	2	FACETS	0.866	0.775	0.962	0.866	0.775	0.962	CLONAL	1	TRUE	1	0.7070556209082	2		293	271	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157485	106157485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747398674	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	122	241	0	ENST00000380013.4:c.2386G>A	p.Glu796Lys	p.E796K	ENST00000380013	NM_001127208.2	796	Gag/Aag	3/11	1	2	FACETS	0.956	0.874	1	0.956	0.874	1	CLONAL	1	TRUE	1	0.7070556209082	2		241	361	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541439	187541439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1246955615	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	153	368	0	ENST00000441802.2:c.6301C>T	p.Arg2101Cys	p.R2101C	ENST00000441802	NM_005245.3	2101	Cgc/Tgc	10/27	0.241739645507968	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.7070556209082	0		368	357	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295230	1295230	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs796516131	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	114	236	0				ENST00000310581	NM_198253.2	-/1132			0.174678297263752	4	FACETS	1	0.917	1	1	0.917	1	INDETERMINATE	2	TRUE	2	0.7070556209082	4		236	275	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435618	149435618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	189	296	1	ENST00000286301.3:c.2525G>A	p.Gly842Asp	p.G842D	ENST00000286301	NM_005211.3	842	gGc/gAc	19/22	0.174678297263752	4	FACETS	0.927	0.865	0.991	0.927	0.865	0.991	INDETERMINATE	2	TRUE	2	0.7070556209082	4		297	492	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500491	149500491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770930584	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	195	314	0	ENST00000261799.4:c.2546G>A	p.Arg849Gln	p.R849Q	ENST00000261799	NM_002609.3	849	cGa/cAa	18/23	0.174678297263752	4	FACETS	0.951	0.889	1	0.951	0.889	1	INDETERMINATE	2	TRUE	2	0.7070556209082	4		314	495	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250700	26250700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	223	500	0	ENST00000446824.2:c.134G>A	p.Gly45Asp	p.G45D	ENST00000446824	NM_021018.2	45	gGt/gAt	1/1	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.7070556209082	2		500	510	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797788	32797788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370090254	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	133	318	0	ENST00000374899.4:c.1714G>A	p.Glu572Lys	p.E572K	ENST00000374899	NM_018833.2	572	Gaa/Aaa	10/12	0.580014819119414	3	FACETS	1	0.979	1	0.612	0.561	0.665	CLONAL	1	TRUE	1	0.7070556209082	3		318	416	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956552	93956552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754119070	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	106	307	0	ENST00000369303.4:c.2684G>A	p.Arg895Gln	p.R895Q	ENST00000369303	NM_004440.3	895	cGa/cAa	15/17	0.25218046754955	1	FACETS	0.657	0.597	0.718	0.657	0.597	0.718	INDETERMINATE	1	TRUE	0	0.7070556209082	1		307	295	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068097	94068097	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	139	311	0	ENST00000369303.4:c.865C>T	p.Gln289Ter	p.Q289*	ENST00000369303	NM_004440.3	289	Caa/Taa	4/17	0.25218046754955	1	FACETS	0.741	0.684	0.799	0.741	0.684	0.799	INDETERMINATE	1	TRUE	0	0.7070556209082	1		311	343	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725567	117725567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767519397	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	137	254	0	ENST00000368508.3:c.314C>T	p.Pro105Leu	p.P105L	ENST00000368508	NM_002944.2	105	cCc/cTc	5/43	0.25218046754955	1	FACETS	0.728	0.671	0.786	0.728	0.671	0.786	INDETERMINATE	1	TRUE	0	0.7070556209082	1		254	344	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6037030	6037030	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1562671039	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	218	233	0	ENST00000265849.7:c.730C>T	p.Gln244Ter	p.Q244*	ENST00000265849	NM_000535.5	244	Cag/Tag	7/15	0.609094191945704	4	FACETS	0.928	0.87	0.987	0.928	0.87	0.987	CLONAL	2	TRUE	2	0.7070556209082	4		233	567	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220344	55220344	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	179	196	0	ENST00000275493.2:c.734A>G	p.Glu245Gly	p.E245G	ENST00000275493	NM_005228.3	245	gAg/gGg	6/28	0.549275749031328	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	2	0.7070556209082	4		196	412	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55232974	55232974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1249099747	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	164	273	0	ENST00000275493.2:c.1724G>A	p.Gly575Glu	p.G575E	ENST00000275493	NM_005228.3	575	gGa/gAa	15/28	0.549275749031328	4	FACETS	0.876	0.812	0.941	0.876	0.812	0.941	CLONAL	2	TRUE	2	0.7070556209082	4		273	452	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359032	81359032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	499	255	0	ENST00000222390.5:c.929G>A	p.Gly310Glu	p.G310E	ENST00000222390	NM_000601.4	310	gGa/gAa	8/18	0.7070556209082	6	FACETS	0.926	0.892	0.959	0.926	0.892	0.959	CLONAL	4	TRUE	2	0.7070556209082	6		255	920	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945093	151945093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746147314	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	19	198	0	ENST00000262189.6:c.2426G>A	p.Gly809Glu	p.G809E	ENST00000262189	NM_170606.2	809	gGa/gAa	14/59	0.7070556209082	5	FACETS	0.477	0.363	0.611	0.159	0.121	0.204	SUBCLONAL	1	TRUE	2	0.7070556209082	5		198	232	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879289	56879289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	189	316	0	ENST00000519728.1:c.806G>A	p.Ser269Asn	p.S269N	ENST00000519728	NM_002350.3	269	aGt/aAt	9/13	0.23379230900631	5	FACETS	1	0.977	1	0.739	0.689	0.79	INDETERMINATE	2	TRUE	2	0.7070556209082	5		316	497	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069575	69069575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	180	203	0	ENST00000288368.4:c.4250G>A	p.Gly1417Glu	p.G1417E	ENST00000288368	NM_024870.2	1417	gGa/gAa	35/40	0.23379230900631	5	FACETS	1	0.985	1	0.804	0.75	0.859	INDETERMINATE	2	TRUE	2	0.7070556209082	5		203	435	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2029083	2029083	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	338	352	0	ENST00000349721.2:c.61C>T	p.Pro21Ser	p.P21S	ENST00000349721	NM_003070.3	21	Cct/Tct	2/34	0.7070556209082	2	FACETS	0.998	0.962	1	0.998	0.962	1	CLONAL	2	TRUE	0	0.7070556209082	2		352	479	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2039699	2039699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	253	404	1	ENST00000349721.2:c.589C>T	p.Pro197Ser	p.P197S	ENST00000349721	NM_003070.3	197	Ccc/Tcc	4/34	0.7070556209082	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.7070556209082	2		405	342	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5055750	5055750	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs771912975	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	173	249	0	ENST00000381652.3:c.1018C>T	p.Arg340Ter	p.R340*	ENST00000381652	NM_004972.3	340	Cga/Tga	8/25	0.7070556209082	2	FACETS	0.995	0.945	1	0.995	0.945	1	CLONAL	2	TRUE	0	0.7070556209082	2		249	246	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524946	8524946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567730036	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	230	222	0	ENST00000356435.5:c.658C>T	p.Pro220Ser	p.P220S	ENST00000356435		220	Cct/Tct	7/35	0.7070556209082	2	FACETS	0.998	0.955	1	0.998	0.955	1	CLONAL	2	TRUE	0	0.7070556209082	2		222	326	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27228284	27228284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	201	224	0	ENST00000380036.4:c.3281G>A	p.Arg1094Lys	p.R1094K	ENST00000380036	NM_000459.3	1094	aGa/aAa	22/23	0.7070556209082	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.7070556209082	2		224	256	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317533	1317533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199794164	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	61	230	0	ENST00000400841.2:c.532G>A	p.Glu178Lys	p.E178K	ENST00000400841		178	Gag/Aag	5/6	1	1	FACETS	0.549	0.481	0.621	0.549	0.481	0.621	SUBCLONAL	1	TRUE	0	0.7070556209082	1		230	203	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913538	39913538	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	109	140	0	ENST00000378444.4:c.4790C>T	p.Thr1597Ile	p.T1597I	ENST00000378444	NM_001123385.1	1597	aCt/aTt	13/15	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.7070556209082	1		140	146	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223368	53223368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	140	155	0	ENST00000375401.3:c.3991C>T	p.Pro1331Ser	p.P1331S	ENST00000375401	NM_004187.3	1331	Cct/Tct	23/26	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.7070556209082	1		155	187	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938304	76938304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	104	163	2	ENST00000373344.5:c.2444C>T	p.Ser815Phe	p.S815F	ENST00000373344	NM_000489.3	815	tCt/tTt	9/35	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.7070556209082	1		165	147	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55231508	55231508	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3423	420	536	0	ENST00000275493.2:c.1714A>G	p.Thr572Ala	p.T572A	ENST00000275493	NM_005228.3	572	Aca/Gca	14/28	0.726331191791456	7	FACETS	0.847	0.802	0.895	0.141	0.133	0.15	CLONAL	1	TRUE	1	0.726331191791456	7		536	3843	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933824	36933824	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	435	756	0	ENST00000361632.4:c.1577-2A>T		p.X526_splice	ENST00000361632		526			0.512079052723577	3	FACETS	0.987	0.939	1			1	CLONAL	1	TRUE	NA	0.726331191791456	3		756	1654	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18439800	18439800	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	359	334	0	ENST00000266497.5:c.698A>T	p.Gln233Leu	p.Q233L	ENST00000266497		233	cAg/cTg	2/31	0.726331191791456	3	FACETS	0.989	0.947	1	0.989	0.947	1	CLONAL	2	TRUE	1	0.726331191791456	3		334	681	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433955	49433955	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1263	892	979	0	ENST00000301067.7:c.7598C>G	p.Pro2533Arg	p.P2533R	ENST00000301067	NM_003482.3	2533	cCc/cGc	31/54	0.503940682975497	4	FACETS	0.984	0.954	1	0.984	0.954	1	CLONAL	2	TRUE	2	0.726331191791456	4		979	2155	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115443	115115443	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	781	529	0	ENST00000257566.3:c.883G>A	p.Asp295Asn	p.D295N	ENST00000257566	NM_016569.3	295	Gac/Aac	5/8	0.726331191791456	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.726331191791456	3		529	1411	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118767	115118767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768160499	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	942	656	2	ENST00000257566.3:c.574G>A	p.Ala192Thr	p.A192T	ENST00000257566	NM_016569.3	192	Gct/Act	2/8	0.726331191791456	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.726331191791456	3		658	1716	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118925	115118925	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	140	359	0	ENST00000257566.3:c.416G>C	p.Arg139Thr	p.R139T	ENST00000257566	NM_016569.3	139	aGa/aCa	2/8	0.726331191791456	3	FACETS	0.838	0.766	0.914	0.419	0.383	0.457	CLONAL	1	TRUE	1	0.726331191791456	3		359	627	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422071	81422071	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	1770	627	0	ENST00000298171.2:c.47C>A	p.Pro16His	p.P16H	ENST00000298171	NM_000369.2	16	cCc/cAc	1/10	0.726331191791456	6	FACETS	1	0.997	1	1	0.997	1	CLONAL	5	TRUE	1	0.726331191791456	6		627	2307	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961517	41961517	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	351	593	0	ENST00000219905.7:c.425G>T	p.Trp142Leu	p.W142L	ENST00000219905	NM_001164273.1	142	tGg/tTg	2/24	0.726331191791456	3	FACETS	1	0.952	1	0.503	0.476	0.531	CLONAL	1	TRUE	1	0.726331191791456	3		593	1309	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578541	7578541	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	826	890	0	ENST00000269305.4:c.389T>G	p.Leu130Arg	p.L130R	ENST00000269305	NM_001126112.2	130	cTc/cGc	5/11	0.726331191791456	2	FACETS	0.99	0.968	1	0.99	0.968	1	CLONAL	2	TRUE	0	0.726331191791456	2		890	1149	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245112	41245112	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1512	1100	743	0	ENST00000357654.3:c.2436G>T	p.Lys812Asn	p.K812N	ENST00000357654	NM_007294.3	812	aaG/aaT	10/23	0.503940682975497	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.726331191791456	4		743	2612	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745856	745945	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCTGGGTGAAAAATAAATACTTTCACTATATCTTTCTCAAAATACTGCCCCAAGAAATTTTATACTTATACTAATATAACAATATTCAT	ACCTGGGTGAAAAATAAATACTTTCACTATATCTTTCTCAAAATACTGCCCCAAGAAATTTTATACTTATACTAATATAACAATATTCAT	-	novel	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2246	201	497	0	ENST00000314574.4:c.574+3_576del		p.X192_splice	ENST00000314574	NM_005433.3	192		6/12	0.726331191791456	4	FACETS	0.39	0.36	0.423			1	SUBCLONAL	1	TRUE	NA	0.726331191791456	4		497	2447	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221084	5221084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371881792	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	372	735	0	ENST00000357368.4:c.3382G>A	p.Val1128Ile	p.V1128I	ENST00000357368	NM_002850.3	1128	Gtc/Atc	20/38	0.726331191791456	2	FACETS	0.948	0.901	0.996	0.474	0.45	0.498	CLONAL	1	TRUE	0	0.726331191791456	2		735	1080	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134261	11134262	+	missense_variant	Missense_Mutation	DNP	TG	TG	CT	novel	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	1159	664	0	ENST00000358026.2:c.2927_2928delinsCT	p.Leu976Ser	p.L976S	ENST00000358026	NM_001128849.1	976	tTG/tCT	20/36	0.726331191791456	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.726331191791456	3		664	1423	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298045	15298045	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	1115	1004	1	ENST00000263388.2:c.1711G>T	p.Ala571Ser	p.A571S	ENST00000263388	NM_000435.2	571	Gct/Tct	11/33	0.726331191791456	3	FACETS	0.935	0.918	0.952	0.935	0.918	0.952	CLONAL	3	TRUE	0	0.726331191791456	3		1005	1492	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463508	25463509	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	277	677	1	ENST00000264709.3:c.2173_2173+1delinsTT		p.X725_splice	ENST00000264709	NM_175629.2	725		18/23	0.726331191791456	3	FACETS	0.838	0.787	0.892	0.419	0.393	0.446	CLONAL	1	TRUE	1	0.726331191791456	3		678	1240	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972641	25972641	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	691	485	0	ENST00000435504.4:c.1784A>T	p.Gln595Leu	p.Q595L	ENST00000435504		595	cAg/cTg	12/13	0.726331191791456	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.726331191791456	3		485	1284	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142942	30142942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1442742511	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1262	422	790	0	ENST00000389048.3:c.584C>T	p.Ala195Val	p.A195V	ENST00000389048	NM_004304.4	195	gCg/gTg	1/29	0.726331191791456	3	FACETS	0.941	0.894	0.988	0.47	0.447	0.494	CLONAL	1	TRUE	1	0.726331191791456	3		790	1684	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730919	40730919	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1987	847	619	0	ENST00000373198.4:c.3616C>T	p.Pro1206Ser	p.P1206S	ENST00000373198	NM_133170.3	1206	Ccc/Tcc	27/32	0.726331191791456	5	FACETS	0.86	0.83	0.89	0.573	0.553	0.593	CLONAL	2	TRUE	2	0.726331191791456	5		619	2834	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866303	42866303	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1283	319	792	1	ENST00000398585.3:c.329C>T	p.Ser110Phe	p.S110F	ENST00000398585	NM_001135099.1	110	tCc/tTc	3/14	0.376299517325913	5	FACETS	1	0.986	1	0.382	0.359	0.405	INDETERMINATE	1	TRUE	2	0.726331191791456	5		793	1602	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175889	24176325	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTACCCCTGGCCCTGTGGTCCTGGGCTCTGCCCACAGGCACCTGGCTTTCCAGGCAGAGGCAGGGCCATTGCCTTTCCCAGTCTCCCATGGTCTCTGAGACAGAGTACCTCTAGTGCTGCTAGAGGCAGGCAGGCTTCTGGGTGATAAGGCCCCATCCAAACGCCAGGGTATGTTTCCCTGCATGGAACAAACATAATTCCTCAGGCTGAGGGTCTGACCACAGCCCAGATCCAGGTTTTGGGGTCCCTGGAGTGATGAGCAGGGCCTGAGTGGCAGACAGGCGAGGCTGAGAGAAGGCTGGGTCTGACCCTGCTGGGGGCCCACATCCTGCCTCTGTTCCCACCCCTACACTTGGCTGCCCTGTAGAGCCTTGGGAAGGGCAGCGCCCAGGCTGGGAGCTGGCCCCGACTCATTGCCCTCCCCACTCCTCTTCC	AGGTACCCCTGGCCCTGTGGTCCTGGGCTCTGCCCACAGGCACCTGGCTTTCCAGGCAGAGGCAGGGCCATTGCCTTTCCCAGTCTCCCATGGTCTCTGAGACAGAGTACCTCTAGTGCTGCTAGAGGCAGGCAGGCTTCTGGGTGATAAGGCCCCATCCAAACGCCAGGGTATGTTTCCCTGCATGGAACAAACATAATTCCTCAGGCTGAGGGTCTGACCACAGCCCAGATCCAGGTTTTGGGGTCCCTGGAGTGATGAGCAGGGCCTGAGTGGCAGACAGGCGAGGCTGAGAGAAGGCTGGGTCTGACCCTGCTGGGGGCCCACATCCTGCCTCTGTTCCCACCCCTACACTTGGCTGCCCTGTAGAGCCTTGGGAAGGGCAGCGCCCAGGCTGGGAGCTGGCCCCGACTCATTGCCCTCCCCACTCCTCTTCC	-	novel	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1197	407	544	0	ENST00000263121.7:c.1118+2_1119del		p.X373_splice	ENST00000263121	NM_003073.3	373		8/9	0.726331191791456	3	FACETS	0.952	0.904	1	0.476	0.452	0.501	CLONAL	1	TRUE	1	0.726331191791456	3		544	1604	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41521941	41521941	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	532	659	0	ENST00000263253.7:c.803G>T	p.Ser268Ile	p.S268I	ENST00000263253	NM_001429.3	268	aGt/aTt	3/31	0.52295649767128	4	FACETS	0.981	0.942	1			1	CLONAL	2	TRUE	NA	0.726331191791456	4		659	1289	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670852	134670852	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	597	501	0	ENST00000398015.3:c.763T>A	p.Cys255Ser	p.C255S	ENST00000398015	NM_004441.4	255	Tgc/Agc	3/16	0.503940682975497	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.726331191791456	4		501	1365	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549739	187549739	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	362	449	0	ENST00000441802.2:c.4502G>T	p.Ser1501Ile	p.S1501I	ENST00000441802	NM_005245.3	1501	aGt/aTt	8/27	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.726331191791456	2		449	979	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629371	187629371	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	538	702	0	ENST00000441802.2:c.1611G>T	p.Arg537Ser	p.R537S	ENST00000441802	NM_005245.3	537	agG/agT	2/27	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.726331191791456	2		702	1390	SUCCESS
APC	324	MSKCC	GRCh37	5	112170733	112170733	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs756090401	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	567	643	0	ENST00000257430.4:c.1829A>G	p.Asp610Gly	p.D610G	ENST00000257430	NM_000038.5	610	gAt/gGt	15/16	0.726331191791456	2	FACETS	0.961	0.934	0.988	0.961	0.934	0.988	CLONAL	2	TRUE	0	0.726331191791456	2		643	812	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512494	149512494	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs41287112	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	690	571	0	ENST00000261799.4:c.946G>T	p.Val316Leu	p.V316L	ENST00000261799	NM_002609.3	316	Gtg/Ttg	7/23	0.726331191791456	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.726331191791456	2		571	906	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058749	180058749	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	708	774	0	ENST00000261937.6:c.88C>A	p.Pro30Thr	p.P30T	ENST00000261937	NM_182925.4	30	Ccg/Acg	2/30	0.726331191791456	2	FACETS	0.939	0.915	0.963	0.939	0.915	0.963	CLONAL	2	TRUE	0	0.726331191791456	2		774	1038	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679980	30679980	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	681	598	0	ENST00000376406.3:c.1739A>G	p.Asp580Gly	p.D580G	ENST00000376406	NM_014641.2	580	gAt/gGt	5/15	0.376299517325913	5	FACETS	0.855	0.826	0.885	0.855	0.826	0.885	INDETERMINATE	3	TRUE	2	0.726331191791456	5		598	1527	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680438	30680438	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	752	666	1	ENST00000376406.3:c.1281G>T	p.Trp427Cys	p.W427C	ENST00000376406	NM_014641.2	427	tgG/tgT	5/15	0.376299517325913	5	FACETS	1	0.996	1	0.823	0.796	0.85	INDETERMINATE	2	TRUE	2	0.726331191791456	5		667	1752	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248993	55248993	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	2344	767	0	ENST00000275493.2:c.2291A>T	p.Tyr764Phe	p.Y764F	ENST00000275493	NM_005228.3	764	tAc/tTc	20/28	0.726331191791456	7	FACETS	1	0.997	1	1	0.997	1	CLONAL	6	TRUE	1	0.726331191791456	7		767	2944	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392150	81392150	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	553	325	0	ENST00000222390.5:c.127A>T	p.Lys43Ter	p.K43*	ENST00000222390	NM_000601.4	43	Aaa/Taa	2/18	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.726331191791456	2		325	742	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372148	55372148	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	378	276	0	ENST00000297316.4:c.838G>T	p.Gly280Cys	p.G280C	ENST00000297316	NM_022454.3	280	Ggt/Tgt	2/2	0.112961502579805	5	FACETS	1	0.992	1			1	INDETERMINATE	4	TRUE	NA	0.726331191791456	5		276	502	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942864	68942864	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	1626	640	0	ENST00000288368.4:c.676G>C	p.Glu226Gln	p.E226Q	ENST00000288368	NM_024870.2	226	Gaa/Caa	6/40	0.726331191791456	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	4	TRUE	0	0.726331191791456	4		640	1921	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949988	44949988	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	230	201	0	ENST00000377967.4:c.3757G>T	p.Val1253Leu	p.V1253L	ENST00000377967	NM_021140.2	1253	Gtg/Ttg	26/29	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.726331191791456	1		201	335	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340819	70340819	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0037338-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	468	296	0	ENST00000374080.3:c.554-2A>G		p.X185_splice	ENST00000374080		185			0.52295649767128	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.726331191791456	2		296	552	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0038791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	218	418	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.649979735347835	3	FACETS	0.885	0.832	0.938	0.885	0.832	0.938	CLONAL	2	TRUE	1	0.664322635841743	3		418	494	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968156	55968156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	117	307	0	ENST00000263923.4:c.2174G>A	p.Arg725His	p.R725H	ENST00000263923	NM_002253.2	725	cGc/cAc	15/30	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.664322635841743	2		307	307	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273944	10273944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	144	453	0	ENST00000330684.3:c.325G>A	p.Val109Ile	p.V109I	ENST00000330684	NM_001134407.1	109	Gta/Ata	2/13	0.664322635841743	3	FACETS	1	0.968	1	0.555	0.509	0.603	CLONAL	1	TRUE	1	0.664322635841743	3		453	520	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899063	40899063	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1405822046	NA	P-0038791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	53	270	0	ENST00000373198.4:c.2207G>A	p.Gly736Glu	p.G736E	ENST00000373198	NM_133170.3	736	gGg/gAg	14/32	0.535040805478745	6	FACETS	0.609	0.519	0.708	0.152	0.129	0.177	SUBCLONAL	1	TRUE	2	0.664322635841743	6		270	610	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412698	63412698	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	87	446	0	ENST00000330258.3:c.469G>C	p.Glu157Gln	p.E157Q	ENST00000330258	NM_152424.3	157	Gag/Cag	2/2	0.664322635841743	3	FACETS	0.967	0.862	1	0.483	0.431	0.538	CLONAL	1	TRUE	1	0.664322635841743	3		446	361	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087952	27087958	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCAAG	GCCCAAG	-	novel	NA	P-0038791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	223	413	0	ENST00000324856.7:c.2239_2245del	p.Ala747IlefsTer84	p.A747Ifs*84	ENST00000324856	NM_006015.4	747	GCCCAAGat/at	6/20	0.664322635841743	2	FACETS	0.843	0.799	0.888	0.843	0.799	0.888	CLONAL	2	TRUE	0	0.664322635841743	2		413	398	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210048	55210048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759219499	NA	P-0038791-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	129	319	0	ENST00000275493.2:c.158G>A	p.Arg53Lys	p.R53K	ENST00000275493	NM_005228.3	53	aGg/aAg	2/28	0.659665726126701	3	FACETS	0.958	0.873	1	0.479	0.436	0.524	CLONAL	1	TRUE	1	0.664322635841743	3		319	540	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039386-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	90	302	0				ENST00000310581	NM_198253.2	-/1132			0.613577410436901	4	FACETS	0.947	0.843	1	0.316	0.281	0.353	CLONAL	1	TRUE	1	0.613577410436901	4		302	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0039386-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	277	537	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.580845830403589	3	FACETS	0.912	0.863	0.961	0.912	0.863	0.961	CLONAL	2	TRUE	1	0.613577410436901	3		537	647	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0039386-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	51	253	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.15953545138371	3	FACETS	1	0.955	1	0.635	0.549	0.726	INDETERMINATE	1	TRUE	1	0.613577410436901	3		253	171	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0039386-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	191	669	0	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	0.580845830403589	3	FACETS	1	0.962	1	0.529	0.49	0.569	CLONAL	1	TRUE	1	0.613577410436901	3		669	769	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106593	27106593	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039386-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	261	688	0	ENST00000324856.7:c.6207del	p.Gln2070SerfsTer65	p.Q2070Sfs*65	ENST00000324856	NM_006015.4	2068	tcG/tc	20/20	0.186102494906798	3	FACETS	0.967	0.914	1	0.644	0.609	0.68	INDETERMINATE	2	TRUE	0	0.613577410436901	3		688	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578223	7578223	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039386-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	299	539	0	ENST00000269305.4:c.626G>C	p.Arg209Thr	p.R209T	ENST00000269305	NM_001126112.2	209	aGa/aCa	6/11	0.580845830403589	3	FACETS	0.894	0.848	0.941	0.894	0.848	0.941	CLONAL	2	TRUE	1	0.613577410436901	3		539	712	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120611957	120611957	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039386-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	19	68	0	ENST00000256646.2:c.64C>A	p.Pro22Thr	p.P22T	ENST00000256646	NM_024408.3	22	Ccc/Acc	1/34	NA	2	FACETS	1	0.821	1			1	INDETERMINATE	1	TRUE	NA	0.613577410436901	2		68	59	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366466	118366466	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0039386-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	142	405	0	ENST00000534358.1:c.5415T>A	p.Tyr1805Ter	p.Y1805*	ENST00000534358	NM_005933.3	1805	taT/taA	19/36	0.15953545138371	3	FACETS	1	0.988	1	0.725	0.667	0.785	INDETERMINATE	1	TRUE	1	0.613577410436901	3		405	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039386-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	290	571	0	ENST00000269305.4:c.880G>C	p.Glu294Gln	p.E294Q	ENST00000269305	NM_001126112.2	294	Gag/Cag	8/11	0.580845830403589	3	FACETS	0.867	0.821	0.914	0.867	0.821	0.914	CLONAL	2	TRUE	1	0.613577410436901	3		571	712	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577599	7577599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039386-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	226	436	0	ENST00000269305.4:c.682G>A	p.Asp228Asn	p.D228N	ENST00000269305	NM_001126112.2	228	Gac/Aac	7/11	0.580845830403589	3	FACETS	0.883	0.83	0.937	0.883	0.83	0.937	CLONAL	2	TRUE	1	0.613577410436901	3		436	545	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873460	45873460	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039386-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	139	436	0	ENST00000391945.4:c.36C>A	p.Phe12Leu	p.F12L	ENST00000391945	NM_000400.3	12	ttC/ttA	2/23	0.187366430845384	2	FACETS	1	0.985	1	0.649	0.599	0.7	INDETERMINATE	1	TRUE	0	0.613577410436901	2		436	349	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170872	99170872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039386-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	200	528	0	ENST00000074304.5:c.1501G>A	p.Asp501Asn	p.D501N	ENST00000074304	NM_001134224.1	501	Gac/Aac	16/26	0.613577410436901	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.613577410436901	1		528	420	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933111	39933111	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039386-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	225	280	0	ENST00000378444.4:c.1488C>G	p.Ile496Met	p.I496M	ENST00000378444	NM_001123385.1	496	atC/atG	4/15	0.613577410436901	2	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.613577410436901	2		280	326	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972617	76972617	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039386-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	89	139	0	ENST00000373344.5:c.124C>G	p.Gln42Glu	p.Q42E	ENST00000373344	NM_000489.3	42	Caa/Gaa	2/35	0.613577410436901	2	FACETS	1	0.968	1			1	CLONAL	2	TRUE	NA	0.613577410436901	2		139	133	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690073	33690073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039386-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	124	456	0	ENST00000308377.4:c.754G>A	p.Asp252Asn	p.D252N	ENST00000308377	NM_152270.3	252	Gat/Aat	2/5	0.580845830403589	3	FACETS	1	0.963	1	0.555	0.505	0.607	CLONAL	1	TRUE	1	0.613577410436901	3		456	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0040320-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	478	368	0	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.597853378335426	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.615191685931435	2		368	735	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943388	17943388	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040320-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	82	391	0	ENST00000458235.1:c.2620A>G	p.Ile874Val	p.I874V	ENST00000458235	NM_000215.3	874	Atc/Gtc	19/24	0.567132712108629	4	FACETS	0.408	0.358	0.461	0.136	0.119	0.154	SUBCLONAL	1	TRUE	1	0.615191685931435	4		391	1056	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215918	142215918	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040320-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	58	295	0	ENST00000350721.4:c.5675A>C	p.Asn1892Thr	p.N1892T	ENST00000350721	NM_001184.3	1892	aAt/aCt	33/47	1	2	FACETS	0.403	0.347	0.464	0.403	0.347	0.464	SUBCLONAL	1	TRUE	1	0.615191685931435	2		295	468	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0040383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	140	258	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.580575494606164	2		258	464	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0040383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	127	425	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.923	0.842	1	0.923	0.842	1	CLONAL	1	TRUE	1	0.580575494606164	2		425	474	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0040383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	78	408	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.878	0.779	0.982	0.878	0.779	0.982	CLONAL	1	TRUE	1	0.580575494606164	2		408	306	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713870	30713870	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1023568316	NA	P-0040383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	470	830	0	ENST00000295754.5:c.1195G>C	p.Gly399Arg	p.G399R	ENST00000295754	NM_003242.5	399	Ggg/Cgg	4/7	0.580575494606164	2	FACETS	0.971	0.935	1	0.971	0.935	1	CLONAL	2	TRUE	0	0.580575494606164	2		830	834	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967215	134967215	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	175	819	0	ENST00000398015.3:c.2554G>T	p.Ala852Ser	p.A852S	ENST00000398015	NM_004441.4	852	Gct/Tct	14/16	1	2	FACETS	0.925	0.855	0.997	0.925	0.855	0.997	CLONAL	1	TRUE	1	0.580575494606164	2		819	652	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	103	488	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	0.959	0.866	1	0.959	0.866	1	CLONAL	1	TRUE	1	0.580575494606164	2		488	370	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157822	106157822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	94	279	0	ENST00000380013.4:c.2723G>A	p.Gly908Asp	p.G908D	ENST00000380013	NM_001127208.2	908	gGt/gAt	3/11	1	2	FACETS	0.993	0.893	1	0.993	0.893	1	CLONAL	1	TRUE	1	0.580575494606164	2		279	326	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876485	59876485	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753214212	NA	P-0040383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	142	314	0	ENST00000259008.2:c.1316G>A	p.Arg439Gln	p.R439Q	ENST00000259008	NM_032043.2	439	cGa/cAa	9/20	1	2	FACETS	0.928	0.851	1	0.928	0.851	1	CLONAL	1	TRUE	1	0.580575494606164	2		314	527	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55991403	55991403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	309	1184	2	ENST00000263923.4:c.58G>A	p.Ala20Thr	p.A20T	ENST00000263923	NM_002253.2	20	Gcc/Acc	1/30	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.580575494606164	2		1186	933	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389318	8389318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	151	438	0	ENST00000356435.5:c.4300G>A	p.Glu1434Lys	p.E1434K	ENST00000356435		1434	Gaa/Aaa	26/35	1	2	FACETS	0.911	0.837	0.988	0.911	0.837	0.988	CLONAL	1	TRUE	1	0.580575494606164	2		438	571	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844393	156844395	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs768558242	NA	P-0040383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	287	1281	0	ENST00000524377.1:c.1231_1233del	p.Lys411del	p.K411del	ENST00000524377	NM_002529.3	409	gAGAag/gag	10/17	0.434072698533	1	FACETS	0.775	0.731	0.821	0.775	0.731	0.821	SUBCLONAL	1	TRUE	0	0.580575494606164	1		1281	905	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993366	72993366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140855443	NA	P-0040383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	280	1182	1	ENST00000268489.5:c.679G>A	p.Val227Ile	p.V227I	ENST00000268489	NM_006885.3	227	Gtc/Atc	2/10	1	2	FACETS	0.961	0.904	1	0.961	0.904	1	CLONAL	1	TRUE	1	0.580575494606164	2		1183	1004	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218864	133218864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1235110857	NA	P-0040383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	254	1053	0	ENST00000320574.5:c.5072G>A	p.Arg1691His	p.R1691H	ENST00000320574	NM_006231.2	1691	cGc/cAc	38/49	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.580575494606164	2		1053	847	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120611974	120611974	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1553217924	NA	P-0040383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	10	112	0	ENST00000256646.2:c.47G>A	p.Trp16Ter	p.W16*	ENST00000256646	NM_024408.3	16	tGg/tAg	1/34	0.434072698533	1	FACETS	0.445	0.308	0.607	0.445	0.308	0.607	SUBCLONAL	1	TRUE	0	0.580575494606164	1		112	55	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215552	5215552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs114166264	NA	P-0040383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	223	1174	1	ENST00000357368.4:c.4151G>A	p.Arg1384Gln	p.R1384Q	ENST00000357368	NM_002850.3	1384	cGg/cAg	27/38	1	2	FACETS	0.898	0.838	0.961	0.898	0.838	0.961	CLONAL	1	TRUE	1	0.580575494606164	2		1175	855	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202123071	202123072	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	143	583	2	ENST00000358485.4:c.117_118delinsAA	p.Glu40Lys	p.E40K	ENST00000358485	NM_001080125.1	39	tcGGag/tcAAag	1/9	1	2	FACETS	0.849	0.778	0.924	0.849	0.778	0.924	CLONAL	1	TRUE	1	0.580575494606164	2		585	580	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374244	138374244	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	177	481	0	ENST00000289153.2:c.3200A>C	p.Asp1067Ala	p.D1067A	ENST00000289153	NM_006219.2	1067	gAc/gCc	22/22	1	2	FACETS	0.91	0.842	0.981	0.91	0.842	0.981	CLONAL	1	TRUE	1	0.580575494606164	2		481	670	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46733198	46733198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778893165	NA	P-0040383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	155	711	0	ENST00000371975.4:c.959G>A	p.Arg320Gln	p.R320Q	ENST00000371975	NM_003579.3	320	cGg/cAg	9/18	0.434072698533	1	FACETS	0.49	0.449	0.532	0.49	0.449	0.532	SUBCLONAL	1	TRUE	0	0.580575494606164	1		711	774	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219960	36219960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1228449559	NA	P-0040383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	176	1046	1	ENST00000222270.7:c.4762G>A	p.Gly1588Arg	p.G1588R	ENST00000222270	NM_014727.1	1588	Ggg/Agg	21/37	0.472172098564698	3	FACETS	0.837	0.771	0.905	0.418	0.385	0.453	CLONAL	1	TRUE	1	0.580575494606164	3		1047	935	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021118	31021118	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1427299519	NA	P-0040821-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	52	640	1	ENST00000375687.4:c.1117C>T	p.Gln373Ter	p.Q373*	ENST00000375687	NM_015338.5	373	Cag/Tag	12/13	1	2	FACETS	0.461	0.391	0.537	0.461	0.391	0.537	SUBCLONAL	1	FALSE	1	0.31566309228596	2		641	715	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912839	32912839	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1060502450	NA	P-0040821-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	43	277	0	ENST00000380152.3:c.4347C>A	p.Phe1449Leu	p.F1449L	ENST00000380152		1449	ttC/ttA	11/27	0.31566309228596	1	FACETS	0.706	0.593	0.83	0.706	0.593	0.83	SUBCLONAL	1	FALSE	0	0.31566309228596	1		277	325	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041118-T07-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	20	805	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	1	2	FACETS	0.345	0.263	0.443	0.345	0.263	0.443	SUBCLONAL	1	TRUE	1	0.15	2		805	772	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577557	7577557	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519982	NA	P-0041595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	320	697	0	ENST00000269305.4:c.724T>G	p.Cys242Gly	p.C242G	ENST00000269305	NM_001126112.2	242	Tgc/Ggc	7/11	0.757990386238721	1	FACETS	0.991	0.949	1	0.991	0.949	1	CLONAL	1	TRUE	0	0.757990386238721	1		697	529	SUCCESS
APC	324	MSKCC	GRCh37	5	112173847	112173848	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0041595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	144	384	0	ENST00000257430.4:c.2563_2564dup	p.Arg856AsnfsTer6	p.R856Nfs*6	ENST00000257430	NM_000038.5	852	-/GA	16/16	1	2	FACETS	0.888	0.817	0.96	0.888	0.817	0.96	CLONAL	1	TRUE	1	0.757990386238721	2		384	428	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0041595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	90	431	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.848	0.763	0.937	0.848	0.763	0.937	CLONAL	1	TRUE	1	0.757990386238721	2		431	280	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242849	142242849	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	156	477	0	ENST00000350721.4:c.4138G>T	p.Asp1380Tyr	p.D1380Y	ENST00000350721	NM_001184.3	1380	Gat/Tat	22/47	1	2	FACETS	0.744	0.685	0.805	0.744	0.685	0.805	SUBCLONAL	1	TRUE	1	0.757990386238721	2		477	553	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012701	36012701	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	397	159	0	ENST00000358208.4:c.145G>A	p.Gly49Ser	p.G49S	ENST00000358208		49	Ggc/Agc	2/12	0.757990386238721	6	FACETS	0.879	0.842	0.915	0.879	0.842	0.915	CLONAL	4	TRUE	2	0.757990386238721	6		159	750	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750575	57750575	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	158	429	0	ENST00000274289.3:c.1893A>C	p.Lys631Asn	p.K631N	ENST00000274289	NM_006622.3	631	aaA/aaC	14/14	1	2	FACETS	0.92	0.851	0.991	0.92	0.851	0.991	CLONAL	1	TRUE	1	0.757990386238721	2		429	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0045235-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	151	531	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	0.536252966389458	2	FACETS	0.937	0.875	0.998	0.937	0.875	0.998	CLONAL	2	TRUE	0	0.579892391445767	2		531	278	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145437	58145437	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1555201381	NA	P-0045235-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	53	560	0	ENST00000257904.6:c.64A>C	p.Lys22Gln	p.K22Q	ENST00000257904	NM_000075.3	22	Aag/Cag	2/8	0.515395719378841	2	FACETS	0.68	0.584	0.782	0.34	0.292	0.391	SUBCLONAL	1	TRUE	0	0.579892391445767	2		560	269	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991701	72991715	+	inframe_deletion	In_Frame_Del	DEL	CCGCCGCCGCAGCCA	CCGCCGCCGCAGCCA	-	rs750272637	NA	P-0045235-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	22	609	0	ENST00000268489.5:c.2330_2344del	p.Val777_Ala781del	p.V777_A781del	ENST00000268489	NM_006885.3	777	gTGGCTGCGGCGGCGGcg/gcg	2/10	1	2	FACETS	0.345	0.268	0.433	0.345	0.268	0.433	SUBCLONAL	1	TRUE	1	0.579892391445767	2		609	220	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249281	133249281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770307281	NA	P-0045235-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	49	545	0	ENST00000320574.5:c.1618G>A	p.Val540Ile	p.V540I	ENST00000320574	NM_006231.2	540	Gtc/Atc	15/49	0.579892391445767	1	FACETS	0.515	0.44	0.595	0.515	0.44	0.595	SUBCLONAL	1	TRUE	0	0.579892391445767	1		545	233	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917681	178917681	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045235-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	26	256	0	ENST00000263967.3:c.556G>C	p.Asp186His	p.D186H	ENST00000263967	NM_006218.2	186	Gat/Cat	3/21	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.579892391445767	2		256	78	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852099	63852106	+	frameshift_variant	Frame_Shift_Del	DEL	CATGACCA	CATGACCA	-	novel	NA	P-0045235-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	16	534	0	ENST00000279873.7:c.2877_2884del	p.Met960ValfsTer4	p.M960Vfs*4	ENST00000279873	NM_032199.2	959	ccCATGACCAtg/cctg	10/10	0.579892391445767	1	FACETS	0.17	0.126	0.223	0.17	0.126	0.223	SUBCLONAL	1	TRUE	0	0.579892391445767	1		534	230	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945013	31945013	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045235-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	42	658	0	ENST00000340398.3:c.88del	p.Thr30ProfsTer7	p.T30Pfs*7	ENST00000340398	NM_001013699.2	30	Acc/cc	1/1	0.290230692148524	3	FACETS	0.494	0.413	0.584	0.247	0.206	0.292	INDETERMINATE	1	TRUE	1	0.579892391445767	3		658	378	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960129	151960129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1449933432	NA	P-0045235-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	11	294	0	ENST00000262189.6:c.1271C>T	p.Ser424Leu	p.S424L	ENST00000262189	NM_170606.2	424	tCa/tTa	9/59	0.579892391445767	3	FACETS	0.259	0.179	0.358	0.129	0.089	0.179	SUBCLONAL	1	TRUE	1	0.579892391445767	3		294	189	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0045909-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	1132	1096	2	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.254649337263414	5	FACETS	0.915	0.898	0.931			1	INDETERMINATE	5	TRUE	NA	0.638240123408644	5		1098	1518	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199873	128199873	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780263343	NA	P-0045909-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	225	734	0	ENST00000341105.2:c.1432G>A	p.Ala478Thr	p.A478T	ENST00000341105	NM_032638.4	478	Gcc/Acc	6/6	0.49832132610163	4	FACETS	0.967	0.9	1	0.484	0.45	0.519	CLONAL	1	TRUE	2	0.638240123408644	4		734	1194	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81891957	81891957	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768646306	NA	P-0045909-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	155	471	0	ENST00000359376.3:c.427G>A	p.Glu143Lys	p.E143K	ENST00000359376	NM_002661.3	143	Gag/Aag	4/33	0.638240123408644	3	FACETS	0.963	0.885	1	0.482	0.442	0.523	CLONAL	1	TRUE	1	0.638240123408644	3		471	665	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660789	227660789	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045909-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	194	816	0	ENST00000305123.5:c.2666A>G	p.Glu889Gly	p.E889G	ENST00000305123	NM_005544.2	889	gAg/gGg	1/2	0.556769642422821	3	FACETS	1	0.948	1	0.513	0.476	0.552	CLONAL	1	TRUE	1	0.638240123408644	3		816	781	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877356	28877356	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1411750922	NA	P-0045909-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1711	245	577	0	ENST00000282397.4:c.3965C>T	p.Ser1322Phe	p.S1322F	ENST00000282397	NM_002019.4	1322	tCc/tTc	30/30	0.638240123408644	5	FACETS	0.768	0.715	0.824	0.192	0.178	0.206	SUBCLONAL	1	TRUE	1	0.638240123408644	5		577	1956	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885856	111885856	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045909-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	318	921	0	ENST00000341259.2:c.1478G>A	p.Gly493Asp	p.G493D	ENST00000341259	NM_005475.2	493	gGt/gAt	8/8	0.631428375847117	3	FACETS	0.981	0.925	1	0.327	0.308	0.347	CLONAL	1	TRUE	0	0.638240123408644	3		921	1340	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046211-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	154	302	0				ENST00000310581	NM_198253.2	-/1132			0.519318097041523	3	FACETS	0.857	0.792	0.923	0.857	0.792	0.923	CLONAL	2	TRUE	1	0.519318097041523	3		302	436	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652147	36652148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046211-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	140	411	0	ENST00000244741.5:c.270dup	p.Gly91ArgfsTer38	p.G91Rfs*38	ENST00000244741	NM_000389.4	90	gga/ggAa	2/3	1	2	FACETS	0.881	0.805	0.96	0.881	0.805	0.96	CLONAL	1	TRUE	1	0.519318097041523	2		411	612	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29107942	29107942	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs749366698	NA	P-0046211-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	79	280	0	ENST00000328354.6:c.747G>T	p.Lys249Asn	p.K249N	ENST00000328354	NM_007194.3	249	aaG/aaT	6/15	1	2	FACETS	0.988	0.877	1	0.988	0.877	1	CLONAL	1	TRUE	1	0.519318097041523	2		280	308	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046211-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	122	302	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.948	0.866	1	0.948	0.866	1	CLONAL	1	TRUE	1	0.671708062649784	2		302	383	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652147	36652148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046211-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	210	411	0	ENST00000244741.5:c.270dup	p.Gly91ArgfsTer38	p.G91Rfs*38	ENST00000244741	NM_000389.4	90	gga/ggAa	2/3	1	2	FACETS	0.887	0.827	0.949	0.887	0.827	0.949	CLONAL	1	TRUE	1	0.671708062649784	2		411	705	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29107942	29107942	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs749366698	NA	P-0046211-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	83	280	0	ENST00000328354.6:c.747G>T	p.Lys249Asn	p.K249N	ENST00000328354	NM_007194.3	249	aaG/aaT	6/15	1	2	FACETS	0.838	0.748	0.932	0.838	0.748	0.932	CLONAL	1	TRUE	1	0.671708062649784	2		280	295	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130354	2130354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046211-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	36	538	0	ENST00000219476.3:c.3586G>A	p.Glu1196Lys	p.E1196K	ENST00000219476	NM_000548.3	1196	Gag/Aag	30/42	1	2	FACETS	0.15	0.122	0.181	0.15	0.122	0.181	SUBCLONAL	1	TRUE	1	0.671708062649784	2		538	716	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0047181-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	171	265	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.568501565670362	2		265	439	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054395	42054396	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047181-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	69	298	1	ENST00000219905.7:c.7585dup	p.Arg2529LysfsTer9	p.R2529Kfs*9	ENST00000219905	NM_001164273.1	2527	caa/cAaa	22/24	1	2	FACETS	0.855	0.752	0.963	0.855	0.752	0.963	CLONAL	1	TRUE	1	0.568501565670362	2		299	284	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207118	1207118	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047181-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	534	845	0	ENST00000326873.7:c.206C>A	p.Ser69Ter	p.S69*	ENST00000326873	NM_000455.4	69	tCg/tAg	1/10	NA	2	FACETS	0.94	0.907	0.973			1	INDETERMINATE	2	TRUE	NA	0.568501565670362	2		845	999	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274541	198274541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047181-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	200	570	0	ENST00000335508.6:c.857C>T	p.Ser286Phe	p.S286F	ENST00000335508	NM_012433.2	286	tCc/tTc	7/25	1	2	FACETS	0.922	0.857	0.99	0.922	0.857	0.99	CLONAL	1	TRUE	1	0.568501565670362	2		570	763	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259196	89259196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047181-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	106	380	0	ENST00000336596.2:c.340G>A	p.Gly114Arg	p.G114R	ENST00000336596	NM_005233.5	114	Gga/Aga	3/17	1	2	FACETS	0.951	0.86	1	0.951	0.86	1	CLONAL	1	TRUE	1	0.568501565670362	2		380	392	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227925	123227925	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047181-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	100	362	0	ENST00000218089.9:c.3636G>C	p.Met1212Ile	p.M1212I	ENST00000218089	NM_001042749.1	1212	atG/atC	33/35	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.568501565670362	2		362	350	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047863-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	62	366	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.25	2		366	376	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0047863-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	28	253	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.665	0.532	0.816	0.665	0.532	0.816	SUBCLONAL	1	TRUE	1	0.25	2		253	337	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0047863-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	25	391	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.873	0.691	1	0.873	0.691	1	CLONAL	1	TRUE	1	0.25	2		391	229	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0047863-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	58	197	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.222030510712114	2	FACETS	0.789	0.683	0.903	0.789	0.683	0.903	CLONAL	2	TRUE	0	0.25	2		197	294	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662817	227662817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1273995645	NA	P-0047863-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	81	588	0	ENST00000305123.5:c.638G>A	p.Arg213His	p.R213H	ENST00000305123	NM_005544.2	213	cGc/cAc	1/2	0.181735777164887	1	FACETS	0.818	0.721	0.923	0.818	0.721	0.923	CLONAL	1	TRUE	0	0.25	1		588	693	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117757	70117758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0047863-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	96	591	0	ENST00000245479.2:c.227_228dup	p.Val77ArgfsTer34	p.V77Rfs*34	ENST00000245479	NM_000346.3	75	-/GC	1/3	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.25	2		591	686	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131084	55131084	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0047863-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	30	294	0	ENST00000257290.5:c.629-2A>T		p.X210_splice	ENST00000257290	NM_006206.4	210			1	2	FACETS	0.682	0.55	0.831	0.682	0.55	0.831	SUBCLONAL	1	TRUE	1	0.25	2		294	352	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039888	47039900	+	frameshift_variant	Frame_Shift_Del	DEL	CAGTGGGCCATCT	CAGTGGGCCATCT	-	novel	NA	P-0047863-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	78	288	0	ENST00000377604.3:c.1233_1245del	p.Gln411HisfsTer70	p.Q411Hfs*70	ENST00000377604	NM_001204468.1	411	CAGTGGGCCATCTca/ca	12/24	1	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.25	1		288	388	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	132	544	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.789	0.715	0.867	1	0.987	1	SUBCLONAL	2	TRUE	1	0.17	2		548	984	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157485	106157485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747398674	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	21	241	0	ENST00000380013.4:c.2386G>A	p.Glu796Lys	p.E796K	ENST00000380013	NM_001127208.2	796	Gag/Aag	3/11	1	2	FACETS	0.681	0.523	0.864	0.681	0.523	0.864	SUBCLONAL	1	TRUE	1	0.17	2		241	363	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004345	150004345	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	33	325	0	ENST00000253339.5:c.1880G>T	p.Arg627Met	p.R627M	ENST00000253339		627	aGg/aTg	3/7	1	2	FACETS	0.697	0.566	0.845	0.697	0.566	0.845	SUBCLONAL	1	TRUE	1	0.17	2		325	557	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63810661	63810661	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	38	184	2	ENST00000279873.7:c.748G>T	p.Gly250Cys	p.G250C	ENST00000279873	NM_032199.2	250	Ggc/Tgc	5/10	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.17	2		186	343	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354008	15354008	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	20	236	0	ENST00000263377.2:c.2872del	p.Leu958CysfsTer110	p.L958Cfs*110	ENST00000263377	NM_058243.2	958	Ctg/tg	14/20	1	2	FACETS	0.674	0.515	0.861	0.674	0.515	0.861	SUBCLONAL	1	TRUE	1	0.17	2		236	349	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747879	41747879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	47	461	0	ENST00000226382.2:c.890C>T	p.Ser297Leu	p.S297L	ENST00000226382	NM_003924.3	297	tCg/tTg	3/3	1	2	FACETS	0.762	0.641	0.895	0.762	0.641	0.895	SUBCLONAL	1	TRUE	1	0.17	2		461	726	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998600	100998600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	60	578	0	ENST00000325455.5:c.1202C>T	p.Pro401Leu	p.P401L	ENST00000325455	NM_001202474.3	401	cCg/cTg	1/8	1	2	FACETS	0.874	0.751	1	0.874	0.751	1	CLONAL	1	TRUE	1	0.17	2		578	808	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347484	91347484	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	50	467	0	ENST00000355112.3:c.3651del	p.Lys1217AsnfsTer62	p.K1217Nfs*62	ENST00000355112	NM_000057.2	1216	Aaa/aa	19/22	1	2	FACETS	0.953	0.808	1	0.953	0.808	1	CLONAL	1	TRUE	1	0.17	2		467	617	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084145	47084146	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	56	469	0	ENST00000409792.3:c.7143dup	p.Ser2382LeufsTer47	p.S2382Lfs*47	ENST00000409792	NM_014159.6	2381	-/C	17/21	1	2	FACETS	0.941	0.805	1	0.941	0.805	1	CLONAL	1	TRUE	1	0.17	2		469	700	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638885	176638885	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	75	467	1	ENST00000439151.2:c.3485G>A	p.Arg1162His	p.R1162H	ENST00000439151	NM_022455.4	1162	cGt/cAt	5/23	1	2	FACETS	0.924	0.808	1	0.924	0.808	1	CLONAL	1	TRUE	1	0.17	2		468	955	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082313	16082314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs780080562	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1204	68	793	4	ENST00000281043.3:c.134dup	p.Glu47GlyfsTer8	p.E47Gfs*8	ENST00000281043	NM_005378.4	43	acc/aCcc	2/3	1	2	FACETS	0.629	0.545	0.721	0.629	0.545	0.721	SUBCLONAL	1	TRUE	1	0.17	2		797	1272	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467747	50467747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	68	514	3	ENST00000331340.3:c.982C>T	p.Arg328Cys	p.R328C	ENST00000331340	NM_006060.4	328	Cgc/Tgc	8/8	1	2	FACETS	0.985	0.856	1	0.985	0.856	1	CLONAL	1	TRUE	1	0.17	2		517	812	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842042	3842042	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783464	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	46	332	0	ENST00000262367.5:c.1270C>T	p.Arg424Ter	p.R424*	ENST00000262367	NM_004380.2	424	Cga/Tga	5/31	1	2	FACETS	0.935	0.786	1	0.935	0.786	1	CLONAL	1	TRUE	1	0.17	2		332	579	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498235	498235	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	19	189	2	ENST00000399788.2:c.23del	p.Gly8AlafsTer58	p.G8Afs*58	ENST00000399788	NM_001042603.1	8	gGc/gc	1/28	1	2	FACETS	0.681	0.517	0.875	0.681	0.517	0.875	SUBCLONAL	1	TRUE	1	0.17	2		191	328	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979986	7979987	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs746723399	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	62	671	2	ENST00000319144.4:c.1350dup	p.Leu451AlafsTer27	p.L451Afs*27	ENST00000319144	NM_001139.2	450	-/G	10/15	1	2	FACETS	0.695	0.599	0.801	0.695	0.599	0.801	SUBCLONAL	1	TRUE	1	0.17	2		673	1049	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212230	5212230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367918810	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	67	572	0	ENST00000357368.4:c.4801G>A	p.Val1601Ile	p.V1601I	ENST00000357368	NM_002850.3	1601	Gtc/Atc	32/38	1	2	FACETS	0.842	0.73	0.964	0.842	0.73	0.964	CLONAL	1	TRUE	1	0.17	2		572	936	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138382756	138382756	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	42	352	1	ENST00000289153.2:c.2788del	p.Thr930LeufsTer62	p.T930Lfs*62	ENST00000289153	NM_006219.2	930	Act/ct	19/22	1	2	FACETS	0.809	0.674	0.959	0.809	0.674	0.959	CLONAL	1	TRUE	1	0.17	2		353	611	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421039	49421039	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123721	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	67	458	0	ENST00000301067.7:c.14710C>T	p.Arg4904Ter	p.R4904*	ENST00000301067	NM_003482.3	4904	Cga/Tga	48/54	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.17	2		458	779	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996149	73996149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1202	92	858	0	ENST00000318443.5:c.883C>T	p.His295Tyr	p.H295Y	ENST00000318443	NM_001024736.1	295	Cac/Tac	5/10	1	2	FACETS	0.836	0.741	0.94	0.836	0.741	0.94	CLONAL	1	TRUE	1	0.17	2		858	1294	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023715	27023716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	44	373	0	ENST00000324856.7:c.827dup	p.Gly277ArgfsTer123	p.G277Rfs*123	ENST00000324856	NM_006015.4	274	atg/atGg	1/20	1	2	FACETS	0.835	0.699	0.986	0.835	0.699	0.986	CLONAL	1	TRUE	1	0.17	2		373	620	SUCCESS
APC	324	MSKCC	GRCh37	5	112178865	112178865	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762034315	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	58	254	0	ENST00000257430.4:c.7574G>A	p.Arg2525His	p.R2525H	ENST00000257430	NM_000038.5	2525	cGc/cAc	16/16	1	2	FACETS	0.836	0.721	0.961	1	0.973	1	CLONAL	2	TRUE	1	0.17	2		254	408	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819704	81819704	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	55	532	0	ENST00000359376.3:c.114del	p.Glu39SerfsTer7	p.E39Sfs*7	ENST00000359376	NM_002661.3	37	aCc/ac	2/33	1	2	FACETS	0.715	0.61	0.831	0.715	0.61	0.831	SUBCLONAL	1	TRUE	1	0.17	2		532	905	SUCCESS
AR	367	MSKCC	GRCh37	X	66765076	66765076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761416673	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	91	645	0	ENST00000374690.3:c.88G>A	p.Val30Met	p.V30M	ENST00000374690	NM_000044.3	30	Gtg/Atg	1/8	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.17	2		645	984	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120528	70120528	+	stop_lost	Nonstop_Mutation	SNP	A	A	C	novel	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	72	805	0	ENST00000245479.2:c.1530A>C	p.Ter510CysextTer49	p.*510Cext*49	ENST00000245479	NM_000346.3	510	tgA/tgC	3/3	1	2	FACETS	0.673	0.586	0.768	0.673	0.586	0.768	SUBCLONAL	1	TRUE	1	0.17	2		805	1258	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643738	38643738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772476060	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	78	578	0	ENST00000299084.4:c.1208G>A	p.Arg403Gln	p.R403Q	ENST00000299084	NM_152594.2	403	cGa/cAa	7/7	1	2	FACETS	0.897	0.786	1	0.897	0.786	1	CLONAL	1	TRUE	1	0.17	2		578	1023	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16248759	16248759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775761539	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	19	268	0	ENST00000375759.3:c.1765C>T	p.Arg589Trp	p.R589W	ENST00000375759	NM_015001.2	589	Cgg/Tgg	10/15	1	2	FACETS	0.624	0.473	0.803	0.624	0.473	0.803	SUBCLONAL	1	TRUE	1	0.17	2		268	358	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101511	27101511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748573855	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	78	732	2	ENST00000324856.7:c.4793G>A	p.Arg1598His	p.R1598H	ENST00000324856	NM_006015.4	1598	cGc/cAc	18/20	1	2	FACETS	0.787	0.689	0.893	0.787	0.689	0.893	SUBCLONAL	1	TRUE	1	0.17	2		734	1166	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012725	36012725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1432190943	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	15	90	0	ENST00000358208.4:c.169G>A	p.Ala57Thr	p.A57T	ENST00000358208		57	Gcg/Acg	2/12	1	2	FACETS	0.891	0.653	1	0.891	0.653	1	CLONAL	1	TRUE	1	0.17	2		90	198	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650824	12650824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773801570	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	22	300	0	ENST00000251849.4:c.331C>T	p.Arg111Cys	p.R111C	ENST00000251849	NM_002880.3	111	Cgc/Tgc	4/17	1	2	FACETS	0.588	0.455	0.744	0.588	0.455	0.744	SUBCLONAL	1	TRUE	1	0.17	2		300	440	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782301	9782301	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	85	540	0	ENST00000377346.4:c.2235-1G>A		p.X745_splice	ENST00000377346	NM_005026.3	745			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.17	2		540	853	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262588	16262588	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	58	411	1	ENST00000375759.3:c.9853C>A	p.Pro3285Thr	p.P3285T	ENST00000375759	NM_015001.2	3285	Cct/Act	11/15	1	2	FACETS	0.982	0.842	1	0.982	0.842	1	CLONAL	1	TRUE	1	0.17	2		412	695	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458644	120458644	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	61	519	2	ENST00000256646.2:c.6701G>A	p.Gly2234Asp	p.G2234D	ENST00000256646	NM_024408.3	2234	gGc/gAc	34/34	1	2	FACETS	0.938	0.808	1	0.938	0.808	1	CLONAL	1	TRUE	1	0.17	2		521	765	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998652	100998652	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	69	666	1	ENST00000325455.5:c.1150G>T	p.Ala384Ser	p.A384S	ENST00000325455	NM_001202474.3	384	Gct/Tct	1/8	1	2	FACETS	0.824	0.716	0.942	0.824	0.716	0.942	CLONAL	1	TRUE	1	0.17	2		667	985	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961796	41961796	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	36	345	0	ENST00000219905.7:c.704C>T	p.Ala235Val	p.A235V	ENST00000219905	NM_001164273.1	235	gCa/gTa	2/24	1	2	FACETS	0.849	0.697	1	0.849	0.697	1	CLONAL	1	TRUE	1	0.17	2		345	499	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246142	41246142	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	50	569	0	ENST00000357654.3:c.1406C>T	p.Ala469Val	p.A469V	ENST00000357654	NM_007294.3	469	gCa/gTa	10/23	1	2	FACETS	0.75	0.635	0.878	0.75	0.635	0.878	SUBCLONAL	1	TRUE	1	0.17	2		569	784	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125793	47125793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	28	290	0	ENST00000409792.3:c.5477G>A	p.Arg1826His	p.R1826H	ENST00000409792	NM_014159.6	1826	cGc/cAc	12/21	1	2	FACETS	0.735	0.587	0.905	0.735	0.587	0.905	CLONAL	1	TRUE	1	0.17	2		290	448	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595935	52595935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	69	501	0	ENST00000394830.3:c.3980G>A	p.Arg1327Gln	p.R1327Q	ENST00000394830	NM_018313.4	1327	cGg/cAg	26/30	1	2	FACETS	0.876	0.761	1	0.876	0.761	1	CLONAL	1	TRUE	1	0.17	2		501	927	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156388	106156388	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	26	266	0	ENST00000380013.4:c.1289T>C	p.Val430Ala	p.V430A	ENST00000380013	NM_001127208.2	430	gTt/gCt	3/11	1	2	FACETS	0.752	0.595	0.932	0.752	0.595	0.932	CLONAL	1	TRUE	1	0.17	2		266	407	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047667	180047667	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	71	653	0	ENST00000261937.6:c.2348G>A	p.Gly783Asp	p.G783D	ENST00000261937	NM_182925.4	783	gGc/gAc	16/30	1	2	FACETS	0.768	0.668	0.877	0.768	0.668	0.877	SUBCLONAL	1	TRUE	1	0.17	2		653	1087	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224296	55224297	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	42	402	0	ENST00000275493.2:c.1082dup	p.Asn361LysfsTer17	p.N361Kfs*17	ENST00000275493	NM_005228.3	359	-/A	9/28	1	2	FACETS	0.709	0.59	0.841	0.709	0.59	0.841	SUBCLONAL	1	TRUE	1	0.17	2		402	697	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38173443	38173443	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	40	396	0	ENST00000317025.8:c.1973T>C	p.Leu658Pro	p.L658P	ENST00000317025	NM_023034.1	658	cTg/cCg	10/24	1	2	FACETS	0.72	0.597	0.857	0.72	0.597	0.857	SUBCLONAL	1	TRUE	1	0.17	2		396	654	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738281	145738281	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761231404	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	79	715	1	ENST00000428558.2:c.2704C>T	p.Arg902Trp	p.R902W	ENST00000428558	NM_004260.3	902	Cgg/Tgg	16/22	1	2	FACETS	0.798	0.7	0.905	0.798	0.7	0.905	CLONAL	1	TRUE	1	0.17	2		716	1164	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815509	139815509	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1323086155	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	68	566	0	ENST00000247668.2:c.980G>A	p.Ser327Asn	p.S327N	ENST00000247668	NM_021138.3	327	aGc/aAc	9/11	0.20466705215749	3	FACETS	0.822	0.713	0.941	0.411	0.356	0.471	CLONAL	1	TRUE	1	0.17	3		566	1056	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410050	63410050	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049078-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	74	526	0	ENST00000330258.3:c.3117G>T	p.Gln1039His	p.Q1039H	ENST00000330258	NM_152424.3	1039	caG/caT	2/2	1	2	FACETS	0.993	0.867	1	0.993	0.867	1	CLONAL	1	TRUE	1	0.17	2		526	877	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049097-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	20	302	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.357	0.272	0.457	0.357	0.272	0.457	SUBCLONAL	1	TRUE	1	0.269881153647101	2		302	415	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983460	90983460	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34767364	NA	P-0049097-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	46	366	0	ENST00000265433.3:c.643C>T	p.Arg215Trp	p.R215W	ENST00000265433	NM_002485.4	215	Cgg/Tgg	6/16	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.269881153647101	2		366	331	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032401	10032401	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs78631453	NA	P-0049097-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	39	565	0	ENST00000330684.3:c.422C>T	p.Thr141Met	p.T141M	ENST00000330684	NM_001134407.1	141	aCg/aTg	3/13	1	2	FACETS	0.598	0.496	0.713	0.598	0.496	0.713	SUBCLONAL	1	TRUE	1	0.269881153647101	2		565	483	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129903	69129903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752113779	NA	P-0049097-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	57	623	0	ENST00000288368.4:c.4657G>A	p.Gly1553Arg	p.G1553R	ENST00000288368	NM_024870.2	1553	Gga/Aga	38/40	1	2	FACETS	0.657	0.563	0.76	0.657	0.563	0.76	SUBCLONAL	1	TRUE	1	0.269881153647101	2		623	643	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528124	29528124	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049097-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	29	393	0	ENST00000356175.3:c.1132G>A	p.Asp378Asn	p.D378N	ENST00000356175	NM_000267.3	378	Gac/Aac	10/57	1	2	FACETS	0.823	0.663	1	0.823	0.663	1	CLONAL	1	TRUE	1	0.269881153647101	2		393	261	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528428	29528428	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs876660782	NA	P-0049097-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	37	363	0	ENST00000356175.3:c.1186-1G>C		p.X396_splice	ENST00000356175	NM_000267.3	396			1	2	FACETS	0.979	0.811	1	0.979	0.811	1	CLONAL	1	TRUE	1	0.269881153647101	2		363	280	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0049219-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	41	738	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.37	2		738	221	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0049219-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	86	425	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.37	2		425	336	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0049539-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	78	259	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.737360969856592	4	FACETS	0.965	0.883	1	0.724	0.662	0.783	CLONAL	3	TRUE	0	0.737360969856592	4		259	127	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579355	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049539-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	94	842	3	ENST00000269305.4:c.332del	p.Leu111ArgfsTer12	p.L111Rfs*12	ENST00000269305	NM_001126112.2	111	cTg/cg	4/11	0.737360969856592	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.737360969856592	2		845	124	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874286	155874286	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs868208063	NA	P-0049539-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	23	455	0	ENST00000368323.3:c.245T>G	p.Phe82Cys	p.F82C	ENST00000368323	NM_006912.5	82	tTt/tGt	5/6	0.461071081003926	5	FACETS	1	0.914	1	0.442	0.352	0.542	CLONAL	1	TRUE	2	0.737360969856592	5		455	99	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279932	18279932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1423694208	NA	P-0049539-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	28	710	0	ENST00000222254.8:c.2015G>A	p.Arg672His	p.R672H	ENST00000222254	NM_005027.3	672	cGc/cAc	16/16	0.737360969856592	8	FACETS	1	0.932	1	0.235	0.189	0.286	CLONAL	1	TRUE	2	0.737360969856592	8		710	173	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220126	5220126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781134304	NA	P-0049539-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	30	664	5	ENST00000357368.4:c.3589C>T	p.Arg1197Trp	p.R1197W	ENST00000357368	NM_002850.3	1197	Cgg/Tgg	22/38	0.713847404702929	2	FACETS	0.992	0.875	1	0.992	0.875	1	CLONAL	2	TRUE	0	0.737360969856592	2		669	41	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69103973	69103973	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049539-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	69	478	0	ENST00000288368.4:c.4363A>G	p.Lys1455Glu	p.K1455E	ENST00000288368	NM_024870.2	1455	Aag/Gag	36/40	0.737360969856592	6	FACETS	1	0.897	1	0.406	0.359	0.456	CLONAL	2	TRUE	1	0.737360969856592	6		478	228	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222441	53222441	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049539-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	21	1024	0	ENST00000375401.3:c.4391A>C	p.Asp1464Ala	p.D1464A	ENST00000375401	NM_004187.3	1464	gAt/gCt	26/26	0.663075550325156	3	FACETS	0.847	0.666	1	0.424	0.333	0.525	CLONAL	1	TRUE	1	0.737360969856592	3		1024	92	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813686	50813686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747968461	NA	P-0049539-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	31	671	2	ENST00000398568.2:c.1240C>T	p.His414Tyr	p.H414Y	ENST00000398568	NM_001042412.1	414	Cac/Tac	8/18	0.723006492647204	2	FACETS	0.955	0.797	1	0.478	0.398	0.561	CLONAL	1	TRUE	0	0.737360969856592	2		673	88	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015351	176015351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049539-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	10	256	0	ENST00000367669.3:c.1387C>T	p.Pro463Ser	p.P463S	ENST00000367669	NM_022457.5	463	Cct/Tct	12/20	0.461071081003926	5	FACETS	0.376	0.255	0.527	0.125	0.085	0.176	SUBCLONAL	1	TRUE	2	0.737360969856592	5		256	152	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287455	38287455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773442656	NA	P-0049539-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	28	676	0	ENST00000425967.3:c.202G>A	p.Gly68Arg	p.G68R	ENST00000425967	NM_001174067.1	68	Gga/Aga	4/19	0.737360969856592	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.737360969856592	1		676	44	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733513	85733513	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs387906350	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	121	373	3	ENST00000370580.1:c.499del	p.Ser167LeufsTer6	p.S167Lfs*6	ENST00000370580	NM_003921.4	167	Tct/ct	3/3	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.526647397099178	2		376	420	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	113	453	0	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.795	0.718	0.875	0.795	0.718	0.875	SUBCLONAL	1	TRUE	1	0.526647397099178	2		453	540	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570292	87570292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463968979	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	156	489	0	ENST00000277120.3:c.2032G>A	p.Ala678Thr	p.A678T	ENST00000277120		678	Gcg/Acg	17/19	0.15729885132825	0	FACETS	0.614	0.567	0.662			1	INDETERMINATE	1	TRUE	0	0.526647397099178	0		489	457	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	187	370	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	0.276968815698171	3	FACETS	0.908	0.847	0.971	0.908	0.847	0.971	INDETERMINATE	2	TRUE	1	0.526647397099178	3		370	494	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	119	417	0	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	1	2	FACETS	0.84	0.761	0.922	0.84	0.761	0.922	CLONAL	1	TRUE	1	0.526647397099178	2		417	538	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612175	189612175	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1560311554	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	143	400	0	ENST00000264731.3:c.1927C>T	p.Arg643Ter	p.R643*	ENST00000264731	NM_003722.4	643	Cga/Tga	14/14	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.526647397099178	2		400	515	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857910	9857910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	106	440	0	ENST00000330684.3:c.3491C>T	p.Thr1164Met	p.T1164M	ENST00000330684	NM_001134407.1	1164	aCg/aTg	13/13	0.398438582876021	1	FACETS	0.862	0.781	0.946	0.862	0.781	0.946	CLONAL	1	TRUE	0	0.526647397099178	1		440	344	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670606	30670606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1371318631	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	149	412	0	ENST00000376406.3:c.5914G>A	p.Asp1972Asn	p.D1972N	ENST00000376406	NM_014641.2	1972	Gac/Aac	13/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.526647397099178	2		412	489	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023769	27023769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	137	405	0	ENST00000324856.7:c.879del	p.Thr294ProfsTer69	p.T294Pfs*69	ENST00000324856	NM_006015.4	292	aCc/ac	1/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.526647397099178	2		405	486	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284979	15284979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774475688	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	128	459	0	ENST00000263388.2:c.4636C>T	p.Arg1546Cys	p.R1546C	ENST00000263388	NM_000435.2	1546	Cgc/Tgc	25/33	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.526647397099178	2		459	486	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	138	401	0	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	0.398438582876021	1	FACETS	0.837	0.768	0.909	0.837	0.768	0.909	CLONAL	1	TRUE	0	0.526647397099178	1		401	461	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026984	71026984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763413735	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	125	457	0	ENST00000318789.4:c.1343C>T	p.Ser448Leu	p.S448L	ENST00000318789	NM_032682.5	448	tCg/tTg	15/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.526647397099178	2		457	439	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442808	99442809	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	132	373	0	ENST00000268035.6:c.1211dup	p.Asn404LysfsTer66	p.N404Kfs*66	ENST00000268035	NM_000875.3	402	cta/ctAa	5/21	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.526647397099178	2		373	437	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536193	41536193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	102	292	0	ENST00000263253.7:c.1810C>T	p.Arg604Trp	p.R604W	ENST00000263253	NM_001429.3	604	Cgg/Tgg	9/31	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.526647397099178	2		292	358	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470498	25470498	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747448117	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	139	401	0	ENST00000264709.3:c.976C>T	p.Arg326Cys	p.R326C	ENST00000264709	NM_175629.2	326	Cgc/Tgc	8/23	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.526647397099178	2		401	501	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972525	32972525	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56121817	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	105	439	0	ENST00000380152.3:c.9875C>T	p.Pro3292Leu	p.P3292L	ENST00000380152		3292	cCg/cTg	27/27	1	2	FACETS	0.943	0.85	1	0.943	0.85	1	CLONAL	1	TRUE	1	0.526647397099178	2		439	423	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494170	140494170	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	112	409	0	ENST00000288602.6:c.1078C>T	p.Arg360Ter	p.R360*	ENST00000288602	NM_004333.4	360	Cga/Tga	8/18	1	2	FACETS	0.915	0.828	1	0.915	0.828	1	CLONAL	1	TRUE	1	0.526647397099178	2		409	465	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217240	11217240	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148486930	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	134	341	0	ENST00000361445.4:c.4438C>T	p.Arg1480Cys	p.R1480C	ENST00000361445	NM_004958.3	1480	Cgc/Tgc	30/58	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.526647397099178	2		341	488	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191118	185191118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564401067	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	143	494	0	ENST00000265026.3:c.1999G>A	p.Ala667Thr	p.A667T	ENST00000265026	NM_004721.4	667	Gcc/Acc	11/14	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.526647397099178	2		494	528	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	280	530	4	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	0.15729885132825	0	FACETS	0.874	0.829	0.918			1	INDETERMINATE	1	TRUE	0	0.526647397099178	0		534	576	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433388	49433388	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555191598	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	129	494	0	ENST00000301067.7:c.8059C>T	p.Arg2687Ter	p.R2687*	ENST00000301067	NM_003482.3	2687	Cga/Tga	32/54	1	2	FACETS	0.982	0.895	1	0.982	0.895	1	CLONAL	1	TRUE	1	0.526647397099178	2		494	499	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431874	49431874	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	132	559	0	ENST00000301067.7:c.9265del	p.Val3089TrpfsTer30	p.V3089Wfs*30	ENST00000301067	NM_003482.3	3089	Gtg/tg	34/54	1	2	FACETS	0.824	0.751	0.901	0.824	0.751	0.901	CLONAL	1	TRUE	1	0.526647397099178	2		559	608	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671005	30671005	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1344945241	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	188	453	1	ENST00000376406.3:c.5741del	p.Gly1914GlufsTer57	p.G1914Efs*57	ENST00000376406	NM_014641.2	1914	gGa/ga	12/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.526647397099178	2		454	648	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81891943	81891943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771121259	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	54	359	0	ENST00000359376.3:c.413C>T	p.Thr138Met	p.T138M	ENST00000359376	NM_002661.3	138	aCg/aTg	4/33	0.398438582876021	1	FACETS	0.466	0.4	0.538	0.466	0.4	0.538	SUBCLONAL	1	TRUE	0	0.526647397099178	1		359	324	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290030	15290030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752282553	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	189	542	0	ENST00000263388.2:c.3524G>A	p.Arg1175Gln	p.R1175Q	ENST00000263388	NM_000435.2	1175	cGg/cAg	22/33	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.526647397099178	2		542	640	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658535	206658535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1281179215	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	158	452	0	ENST00000367120.3:c.1508C>T	p.Ala503Val	p.A503V	ENST00000367120	NM_014002.3	503	gCg/gTg	15/22	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.526647397099178	2		452	539	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006463	12006463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	139	444	0	ENST00000396373.4:c.431C>T	p.Pro144Leu	p.P144L	ENST00000396373	NM_001987.4	144	cCg/cTg	4/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.526647397099178	2		444	497	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562552	21562552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	100	387	0	ENST00000382592.4:c.1367C>T	p.Thr456Met	p.T456M	ENST00000382592	NM_014572.2	456	aCg/aTg	4/8	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.526647397099178	2		387	331	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849994	151849994	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	96	372	1	ENST00000262189.6:c.12322C>T	p.Arg4108Ter	p.R4108*	ENST00000262189	NM_170606.2	4108	Cga/Tga	49/59	1	2	FACETS	0.791	0.708	0.878	0.791	0.708	0.878	SUBCLONAL	1	TRUE	1	0.526647397099178	2		373	461	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028642	42028642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367727094	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	132	420	0	ENST00000219905.7:c.4180C>T	p.Arg1394Cys	p.R1394C	ENST00000219905	NM_001164273.1	1394	Cgt/Tgt	13/24	1	2	FACETS	0.939	0.856	1	0.939	0.856	1	CLONAL	1	TRUE	1	0.526647397099178	2		420	534	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707900	47707900	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	92	290	2	ENST00000233146.2:c.2524G>T	p.Glu842Ter	p.E842*	ENST00000233146	NM_000251.2	842	Gag/Tag	15/16	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.526647397099178	2		292	303	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46597034	46597034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767899036	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	97	278	0	ENST00000263734.3:c.848C>T	p.Ala283Val	p.A283V	ENST00000263734	NM_001430.4	283	gCg/gTg	7/16	1	2	FACETS	0.964	0.867	1	0.964	0.867	1	CLONAL	1	TRUE	1	0.526647397099178	2		278	382	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502194	157502194	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	133	354	0	ENST00000346085.5:c.3227A>G	p.Tyr1076Cys	p.Y1076C	ENST00000346085	NM_020732.3	1076	tAc/tGc	12/20	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.526647397099178	2		354	481	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604707	48604707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs377767371	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	136	417	0	ENST00000342988.3:c.1529G>T	p.Gly510Val	p.G510V	ENST00000342988	NM_005359.5	510	gGa/gTa	12/12	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.526647397099178	2		417	471	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367315	50367315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751092583	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	87	418	0	ENST00000331340.3:c.122C>T	p.Ser41Leu	p.S41L	ENST00000331340	NM_006060.4	41	tCg/tTg	3/8	0.15729885132825	0	FACETS	0.387	0.345	0.432			1	INDETERMINATE	1	TRUE	0	0.526647397099178	0		418	404	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854949	76854949	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	52	175	0	ENST00000373344.5:c.5887C>T	p.Arg1963Trp	p.R1963W	ENST00000373344	NM_000489.3	1963	Cgg/Tgg	25/35	1	1	FACETS	0.898	0.808	0.984	1	0.98	1	CLONAL	2	TRUE	0	0.526647397099178	1		175	81	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217225	11217225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	146	317	0	ENST00000361445.4:c.4453G>A	p.Glu1485Lys	p.E1485K	ENST00000361445	NM_004958.3	1485	Gag/Aag	30/58	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.526647397099178	2		317	507	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216310	2216310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780465036	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	153	409	0	ENST00000398665.3:c.1954C>T	p.Arg652Trp	p.R652W	ENST00000398665	NM_032482.2	652	Cgg/Tgg	20/28	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.526647397099178	2		409	505	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596063	43596063	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs570176656	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	172	394	0	ENST00000355710.3:c.230G>A	p.Arg77His	p.R77H	ENST00000355710	NM_020975.4	77	cGc/cAc	2/20	0.276968815698171	3	FACETS	0.87	0.808	0.934	0.87	0.808	0.934	INDETERMINATE	2	TRUE	1	0.526647397099178	3		394	474	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224219	36224219	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	49	277	0	ENST00000222270.7:c.6773del	p.Pro2258LeufsTer3	p.P2258Lfs*3	ENST00000222270	NM_014727.1	2257	Ccc/cc	28/37	1	2	FACETS	0.583	0.496	0.678	0.583	0.496	0.678	SUBCLONAL	1	TRUE	1	0.526647397099178	2		277	319	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598946	28598946	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1003343893	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	143	449	0	ENST00000253063.3:c.506G>T	p.Arg169Leu	p.R169L	ENST00000253063	NM_031459.4	169	cGg/cTg	4/10	1	2	FACETS	0.882	0.807	0.96	0.882	0.807	0.96	CLONAL	1	TRUE	1	0.526647397099178	2		449	616	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11301671	11301671	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	108	345	0	ENST00000361445.4:c.1480G>T	p.Gly494Trp	p.G494W	ENST00000361445	NM_004958.3	494	Ggg/Tgg	10/58	1	2	FACETS	0.952	0.86	1	0.952	0.86	1	CLONAL	1	TRUE	1	0.526647397099178	2		345	431	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518658	204518658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	111	362	0	ENST00000367182.3:c.1321G>A	p.Glu441Lys	p.E441K	ENST00000367182	NM_001278516.1	441	Gag/Aag	11/11	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.526647397099178	2		362	415	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109992	115109992	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	147	418	0	ENST00000257566.3:c.1886T>C	p.Leu629Pro	p.L629P	ENST00000257566	NM_016569.3	629	cTc/cCc	8/8	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.526647397099178	2		418	438	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544660	65544660	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	153	429	0	ENST00000358664.4:c.266A>G	p.Lys89Arg	p.K89R	ENST00000358664	NM_002382.4	89	aAg/aGg	4/5	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.526647397099178	2		429	540	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781372	3781372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	131	452	0	ENST00000262367.5:c.4993G>A	p.Asp1665Asn	p.D1665N	ENST00000262367	NM_004380.2	1665	Gac/Aac	30/31	0.398438582876021	1	FACETS	0.875	0.801	0.951	0.875	0.801	0.951	CLONAL	1	TRUE	0	0.526647397099178	1		452	419	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796993	78796993	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376501662	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	133	366	0	ENST00000306801.3:c.1106G>A	p.Arg369His	p.R369H	ENST00000306801	NM_020761.2	369	cGt/cAt	9/34	1	2	FACETS	0.996	0.91	1	0.996	0.91	1	CLONAL	1	TRUE	1	0.526647397099178	2		366	507	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4094473	4094473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201110543	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	136	298	0	ENST00000262948.5:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000262948	NM_030662.3	357	cGg/cAg	10/11	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.526647397099178	2		298	500	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224087	36224087	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	141	399	0	ENST00000222270.7:c.6641del	p.Pro2214GlnfsTer2	p.P2214Qfs*2	ENST00000222270	NM_014727.1	2213	Ccc/cc	28/37	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.526647397099178	2		399	467	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023499	31023499	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	127	445	0	ENST00000375687.4:c.2984A>G	p.His995Arg	p.H995R	ENST00000375687	NM_015338.5	995	cAc/cGc	13/13	1	2	FACETS	0.924	0.841	1	0.924	0.841	1	CLONAL	1	TRUE	1	0.526647397099178	2		445	522	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798402	32798402	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	140	405	0	ENST00000374899.4:c.1454T>C	p.Val485Ala	p.V485A	ENST00000374899	NM_018833.2	485	gTg/gCg	8/12	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.526647397099178	2		405	512	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399408	139399409	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAC	novel	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	154	515	0	ENST00000277541.6:c.4732_4734dup	p.Val1578dup	p.V1578dup	ENST00000277541	NM_017617.3	1578	-/GTG	26/34	1	2	FACETS	0.901	0.827	0.978	0.901	0.827	0.978	CLONAL	1	TRUE	1	0.526647397099178	2		515	649	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814897	139814897	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	150	419	0	ENST00000247668.2:c.890C>T	p.Ala297Val	p.A297V	ENST00000247668	NM_021138.3	297	gCc/gTc	8/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.526647397099178	2		419	538	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938603	76938603	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	72	173	0	ENST00000373344.5:c.2145A>T	p.Lys715Asn	p.K715N	ENST00000373344	NM_000489.3	715	aaA/aaT	9/35	1	1	FACETS	0.819	0.744	0.891	1	0.984	1	CLONAL	2	TRUE	0	0.526647397099178	1		173	123	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166547	118166547	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs74114325	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	138	412	0	ENST00000369448.3:c.1057G>A	p.Val353Ile	p.V353I	ENST00000369448	NM_017709.3	353	Gtc/Atc	2/2	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.526647397099178	2		412	515	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231488894	231488894	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	85	292	1	ENST00000295050.7:c.1263del	p.Phe421LeufsTer7	p.F421Lfs*7	ENST00000295050	NM_032018.5	419	aaT/aa	5/5	1	2	FACETS	0.999	0.892	1	0.999	0.892	1	CLONAL	1	TRUE	1	0.526647397099178	2		293	323	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534318	534318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1447218022	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	115	402	0	ENST00000451590.1:c.5C>T	p.Thr2Met	p.T2M	ENST00000451590	NM_001130442.1	2	aCg/aTg	2/5	1	2	FACETS	0.914	0.828	1	0.914	0.828	1	CLONAL	1	TRUE	1	0.526647397099178	2		402	478	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21344720	21344720	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs535425465	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	132	406	0	ENST00000215739.8:c.697G>A	p.Val233Met	p.V233M	ENST00000215739	NM_006767.3	233	Gtg/Atg	8/21	1	2	FACETS	0.999	0.912	1	0.999	0.912	1	CLONAL	1	TRUE	1	0.526647397099178	2		406	502	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839867	27839867	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334849705	NA	P-0049585-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	208	583	0	ENST00000328488.2:c.227C>T	p.Ala76Val	p.A76V	ENST00000328488	NM_003533.2	76	gCa/gTa	1/1	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.526647397099178	2		583	725	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714131	43714131	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049825-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	189	451	0	ENST00000382044.4:c.4022C>A	p.Pro1341Gln	p.P1341Q	ENST00000382044	NM_001141980.1	1341	cCa/cAa	19/28	0.346891183605021	4	FACETS	0.842	0.786	0.899	1	0.988	1	CLONAL	3	TRUE	2	0.454232135274161	4		451	479	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733142	74733142	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049825-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	57	526	0	ENST00000359995.5:c.101T>C	p.Phe34Ser	p.F34S	ENST00000359995	NM_001195427.1	34	tTc/tCc	1/3	0.454232135274161	7	FACETS	1	0.862	1	0.201	0.172	0.232	CLONAL	1	TRUE	2	0.454232135274161	7		526	534	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752700	42752700	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049825-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	66	472	0	ENST00000222329.4:c.1564G>T	p.Gly522Trp	p.G522W	ENST00000222329	NM_006494.2	522	Ggg/Tgg	4/4	0.454232135274161	3	FACETS	1	0.947	1	0.579	0.506	0.656	CLONAL	1	TRUE	1	0.454232135274161	3		472	308	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226042	53226042	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049825-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	117	507	0	ENST00000375401.3:c.2807G>T	p.Arg936Leu	p.R936L	ENST00000375401	NM_004187.3	936	cGc/cTc	19/26	0.327242200125436	4	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	2	0.454232135274161	4		507	350	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049866-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	52	302	0				ENST00000310581	NM_198253.2	-/1132			0.258737865263976	3	FACETS	0.922	0.786	1	0.461	0.393	0.536	CLONAL	1	TRUE	1	0.273937456820225	3		302	468	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0049866-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	34	374	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.467	0.38	0.564	0.467	0.38	0.564	SUBCLONAL	1	TRUE	1	0.273937456820225	2		374	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049866-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	75	582	0	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	0.273937456820225	1	FACETS	0.895	0.786	1	0.895	0.786	1	CLONAL	1	TRUE	0	0.273937456820225	1		582	528	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182032	38182032	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049866-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	43	722	0	ENST00000396334.3:c.656C>G	p.Ser219Cys	p.S219C	ENST00000396334	NM_002468.4	219	tCt/tGt	3/5	1	2	FACETS	0.501	0.418	0.593	0.501	0.418	0.593	SUBCLONAL	1	TRUE	1	0.273937456820225	2		722	627	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121909	2121909	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760489473	NA	P-0049866-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	83	685	2	ENST00000219476.3:c.2071C>T	p.Arg691Cys	p.R691C	ENST00000219476	NM_000548.3	691	Cgc/Tgc	19/42	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.273937456820225	2		687	545	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942703	44942703	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0049866-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	53	331	0	ENST00000377967.4:c.3285-2A>T		p.X1095_splice	ENST00000377967	NM_021140.2	1095			0.273937456820225	1	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	0	0.273937456820225	1		331	328	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982157	201982157	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049866-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	79	643	0	ENST00000359651.3:c.684del	p.Ser229AlafsTer25	p.S229Afs*25	ENST00000359651		227	ttC/tt	5/8	0.142295087550609	3	FACETS	1	0.903	1	0.515	0.453	0.581	INDETERMINATE	1	TRUE	1	0.273937456820225	3		643	637	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524812	187524812	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs184690159	NA	P-0049866-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	132	632	1	ENST00000441802.2:c.10868C>T	p.Thr3623Met	p.T3623M	ENST00000441802	NM_005245.3	3623	aCg/aTg	19/27	0.218488447564666	2	FACETS	0.941	0.859	1	0.941	0.859	1	CLONAL	2	TRUE	0	0.273937456820225	2		633	512	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981085	201981086	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0049866-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	93	548	0	ENST00000359651.3:c.165_166insGG	p.Lys56GlyfsTer100	p.K56Gfs*100	ENST00000359651		55	gag/gaGGg	2/8	0.142295087550609	3	FACETS	1	0.978	1	0.711	0.634	0.793	INDETERMINATE	1	TRUE	1	0.273937456820225	3		548	543	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545842	41545842	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0049866-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	90	638	0	ENST00000263253.7:c.2457T>A	p.Cys819Ter	p.C819*	ENST00000263253	NM_001429.3	819	tgT/tgA	14/31	0.142295087550609	3	FACETS	1	0.948	1	0.558	0.496	0.625	INDETERMINATE	1	TRUE	1	0.273937456820225	3		638	669	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286922	33286922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049866-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	116	779	0	ENST00000374542.5:c.2015C>T	p.Pro672Leu	p.P672L	ENST00000374542	NM_001141970.1	672	cCc/cTc	7/8	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.273937456820225	2		779	784	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448523	89448523	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049866-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	63	496	0	ENST00000336596.2:c.1487T>G	p.Ile496Ser	p.I496S	ENST00000336596	NM_005233.5	496	aTc/aGc	7/17	1	2	FACETS	0.814	0.704	0.933	0.814	0.704	0.933	CLONAL	1	TRUE	1	0.273937456820225	2		496	565	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207789	102207789	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049866-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	28	143	0	ENST00000263464.3:c.1771T>A	p.Cys591Ser	p.C591S	ENST00000263464	NM_001165.4	591	Tgt/Agt	9/9	1	2	FACETS	0.507	0.405	0.624	0.507	0.405	0.624	SUBCLONAL	1	TRUE	1	0.273937456820225	2		143	403	SUCCESS
MTAP	4507	MSKCC	GRCh37	9	21818188	21818188	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1312488107	NA	P-0049866-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	77	424	0	ENST00000380172.4:c.334C>G	p.Gln112Glu	p.Q112E	ENST00000380172	NM_002451.3	112	Cag/Gag	4/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.273937456820225	2		424	403	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050200-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	88	302	0				ENST00000310581	NM_198253.2	-/1132			0.388762931677398	3	FACETS	0.907	0.813	1	0.907	0.813	1	CLONAL	2	TRUE	1	0.388762931677398	3		302	298	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796547	42796547	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050200-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	78	521	0	ENST00000575354.2:c.3104C>A	p.Thr1035Lys	p.T1035K	ENST00000575354	NM_015125.3	1035	aCg/aAg	13/20	0.388762931677398	3	FACETS	1	0.904	1	0.514	0.453	0.579	CLONAL	1	TRUE	1	0.388762931677398	3		521	466	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526750	31526750	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050200-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	64	460	0	ENST00000344624.3:c.290C>G	p.Pro97Arg	p.P97R	ENST00000344624		97	cCa/cGa	2/33	0.388762931677398	3	FACETS	0.917	0.796	1	0.458	0.398	0.523	CLONAL	1	TRUE	1	0.388762931677398	3		460	429	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786910	135786910	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0050200-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	184	379	0	ENST00000298552.3:c.959T>A	p.Leu320Ter	p.L320*	ENST00000298552	NM_001162426.1	320	tTa/tAa	10/23	0.388762931677398	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.388762931677398	2		379	412	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	103	302	0				ENST00000310581	NM_198253.2	-/1132			0.162499522463706	3	FACETS	0.852	0.765	0.944	1	0.975	1	CLONAL	3	TRUE	1	0.162499522463706	3		302	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0050559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	53	895	2	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	1	2	FACETS	0.59	0.501	0.689	0.59	0.501	0.689	SUBCLONAL	1	TRUE	1	0.162499522463706	2		897	1105	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094325	27094325	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	47	709	0	ENST00000324856.7:c.3033G>C	p.Leu1011Phe	p.L1011F	ENST00000324856	NM_006015.4	1011	ttG/ttC	11/20	1	2	FACETS	0.643	0.541	0.757	0.643	0.541	0.757	SUBCLONAL	1	TRUE	1	0.162499522463706	2		709	899	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105761	27105761	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	60	618	0	ENST00000324856.7:c.5372C>A	p.Ser1791Ter	p.S1791*	ENST00000324856	NM_006015.4	1791	tCa/tAa	20/20	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.162499522463706	2		618	720	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623709	43623709	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	111	687	0	ENST00000355710.3:c.3337G>C	p.Asp1113His	p.D1113H	ENST00000355710	NM_020975.4	1113	Gat/Cat	20/20	0.162499522463706	2	FACETS	0.753	0.676	0.835	0.753	0.676	0.835	SUBCLONAL	2	TRUE	0	0.162499522463706	2		687	907	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720653	89720654	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	32	333	0	ENST00000371953.3:c.808dup	p.Met270AsnfsTer28	p.M270Nfs*28	ENST00000371953	NM_000314.4	268	-/A	8/9	0.162499522463706	2	FACETS	1	0.884	1	0.563	0.457	0.681	CLONAL	1	TRUE	0	0.162499522463706	2		333	350	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102198800	102198800	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	35	490	0	ENST00000263464.3:c.971G>C	p.Arg324Thr	p.R324T	ENST00000263464	NM_001165.4	324	aGa/aCa	4/9	1	2	FACETS	0.836	0.685	1	0.836	0.685	1	CLONAL	1	TRUE	1	0.162499522463706	2		490	515	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050564	49050895	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCAGAGTAGGCAGTTGCTGGAGGAAGAATGTGAGCTGCATGGGAAAAGACAGGAGGATTTACAAAGAGTGGGTGTTTAATTGGGGATGGAATTAGGTAGTTATTCTGATTTTTAGATTTTTCATATCTTTTATTTGGTCCAATGAAGCAGAAAATTTAAATGAAGTTATTACCTTTGCCTGATTTTTGACACACCTCAAACTATAACTTGAGGTTGCTAACTATGAAACACTGGCATTTAATGATTTAAAGTAAAGAATTCTGTAATTTGTAGACTTCTGAGAAGTTCCAGAAAATAAATCAGATGGTATGTAACAGCGACCGTGTGCTCAA	GCAGAGTAGGCAGTTGCTGGAGGAAGAATGTGAGCTGCATGGGAAAAGACAGGAGGATTTACAAAGAGTGGGTGTTTAATTGGGGATGGAATTAGGTAGTTATTCTGATTTTTAGATTTTTCATATCTTTTATTTGGTCCAATGAAGCAGAAAATTTAAATGAAGTTATTACCTTTGCCTGATTTTTGACACACCTCAAACTATAACTTGAGGTTGCTAACTATGAAACACTGGCATTTAATGATTTAAAGTAAAGAATTCTGTAATTTGTAGACTTCTGAGAAGTTCCAGAAAATAAATCAGATGGTATGTAACAGCGACCGTGTGCTCAA	-	novel	NA	P-0050559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	25	18	0	ENST00000267163.4:c.2521-273_2579del		p.X841_splice	ENST00000267163	NM_000321.2	841		25/27	1	2	FACETS	0.95	0.82	1	1	0.971	1	CLONAL	9	TRUE	1	0.162499522463706	2		18	36	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0050559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	103	915	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.162499522463706	2		915	1245	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967196	25967196	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	60	611	0	ENST00000435504.4:c.2010G>C	p.Gln670His	p.Q670H	ENST00000435504		670	caG/caC	13/13	1	2	FACETS	0.991	0.853	1	0.991	0.853	1	CLONAL	1	TRUE	1	0.162499522463706	2		611	745	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141685	202141685	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	45	499	0	ENST00000358485.4:c.973G>C	p.Asp325His	p.D325H	ENST00000358485	NM_001080125.1	325	Gat/Cat	7/9	1	2	FACETS	0.925	0.776	1	0.925	0.776	1	CLONAL	1	TRUE	1	0.162499522463706	2		499	599	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513379	41513379	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1290523966	NA	P-0050559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	90	830	0	ENST00000263253.7:c.283A>G	p.Met95Val	p.M95V	ENST00000263253	NM_001429.3	95	Atg/Gtg	2/31	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.162499522463706	2		830	1080	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542656	187542656	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0050559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	43	738	0	ENST00000441802.2:c.5084C>G	p.Ser1695Ter	p.S1695*	ENST00000441802	NM_005245.3	1695	tCa/tGa	10/27	1	2	FACETS	0.715	0.597	0.847	0.715	0.597	0.847	SUBCLONAL	1	TRUE	1	0.162499522463706	2		738	740	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670698	86670698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	26	418	0	ENST00000274376.6:c.1976G>A	p.Ser659Asn	p.S659N	ENST00000274376	NM_002890.2	659	aGt/aAt	15/25	1	2	FACETS	0.775	0.613	0.961	0.775	0.613	0.961	CLONAL	1	TRUE	1	0.162499522463706	2		418	413	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038877	47038877	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0050559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	128	459	0	ENST00000377604.3:c.884C>G	p.Ser295Ter	p.S295*	ENST00000377604	NM_001204468.1	295	tCa/tGa	9/24	1	1	FACETS	1	0.974	1	1	0.991	1	CLONAL	2	TRUE	0	0.162499522463706	1		459	608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0050578-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	262	914	1	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.409181432541515	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.409181432541515	3		915	674	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518437	204518437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201947927	NA	P-0050578-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	428	807	0	ENST00000367182.3:c.1100C>T	p.Ser367Leu	p.S367L	ENST00000367182	NM_001278516.1	367	tCg/tTg	11/11	0.409181432541515	5	FACETS	0.917	0.883	0.951	0.917	0.883	0.951	CLONAL	5	TRUE	0	0.409181432541515	5		807	736	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40742005	40742005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050578-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	111	1082	0	ENST00000392038.2:c.967G>A	p.Glu323Lys	p.E323K	ENST00000392038	NM_001626.4	323	Gag/Aag	11/14	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.409181432541515	2		1082	517	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40742002	40742005	+	missense_variant	Missense_Mutation	ONP	CCTC	CCTC	TCTT	novel	NA	P-0050578-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	116	1070	0	ENST00000392038.2:c.967_970delinsAAGA	p.Glu323_Asp324delinsLysAsn	p.E323_D324delinsKN	ENST00000392038	NM_001626.4	323	GAGGac/AAGAac	11/14	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.409181432541515	2		1070	518	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182126	99182126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050578-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	90	729	0	ENST00000074304.5:c.2191G>A	p.Asp731Asn	p.D731N	ENST00000074304	NM_001134224.1	731	Gac/Aac	21/26	0.392225947018415	3	FACETS	1	0.933	1	0.533	0.475	0.595	CLONAL	1	TRUE	1	0.409181432541515	3		729	497	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77937957	77937957	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050578-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	116	936	0	ENST00000361507.4:c.761del	p.Pro254ArgfsTer58	p.P254Rfs*58	ENST00000361507	NM_080491.2	254	cCg/cg	4/10	0.409181432541515	5	FACETS	0.741	0.666	0.821			1	SUBCLONAL	1	TRUE	NA	0.409181432541515	5		936	1235	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134454	41134454	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050578-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	220	746	0	ENST00000379561.5:c.1174C>T	p.Gln392Ter	p.Q392*	ENST00000379561	NM_002015.3	392	Cag/Tag	2/3	0.409181432541515	2	FACETS	0.957	0.897	1	0.957	0.897	1	CLONAL	2	TRUE	0	0.409181432541515	2		746	562	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351689	89351689	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050578-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	116	866	0	ENST00000301030.4:c.1261G>T	p.Gly421Trp	p.G421W	ENST00000301030	NM_001256183.1	421	Ggg/Tgg	9/13	0.409181432541515	3	FACETS	0.997	0.9	1	0.499	0.45	0.55	CLONAL	1	TRUE	1	0.409181432541515	3		866	685	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16021245	16021245	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050578-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	52	535	0	ENST00000268712.3:c.2012G>T	p.Arg671Met	p.R671M	ENST00000268712	NM_006311.3	671	aGg/aTg	18/46	0.409181432541515	3	FACETS	0.785	0.67	0.91	0.393	0.335	0.455	CLONAL	1	TRUE	1	0.409181432541515	3		535	390	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265360	46265361	+	missense_variant	Missense_Mutation	DNP	AG	AG	GT	novel	NA	P-0050578-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	92	753	0	ENST00000371998.3:c.2230_2231delinsGT	p.Arg744Val	p.R744V	ENST00000371998		744	AGg/GTg	12/23	0.392225947018415	3	FACETS	1	0.924	1	0.523	0.466	0.583	CLONAL	1	TRUE	1	0.409181432541515	3		753	518	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091831	29091831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050578-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	49	312	0	ENST00000328354.6:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000328354	NM_007194.3	376	Gga/Aga	11/15	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.409181432541515	2		312	222	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	79	302	0				ENST00000310581	NM_198253.2	-/1132			0.163208674475504	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	1	0.234225543451878	3		302	331	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0050757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	86	374	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.163208674475504	3	FACETS	0.988	0.879	1	0.988	0.879	1	CLONAL	2	TRUE	1	0.234225543451878	3		374	415	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092809	27092809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	118	461	0	ENST00000324856.7:c.2830C>T	p.Gln944Ter	p.Q944*	ENST00000324856	NM_006015.4	944	Cag/Tag	9/20	0.233117105085086	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.234225543451878	2		461	445	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868663	37868663	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1275492389	NA	P-0050757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	94	566	0	ENST00000269571.5:c.1110C>G	p.Ile370Met	p.I370M	ENST00000269571		370	atC/atG	9/27	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.234225543451878	2		566	588	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0050757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	93	449	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.234225543451878	2		449	545	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263850	133263850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	66	467	0	ENST00000320574.5:c.52G>A	p.Glu18Lys	p.E18K	ENST00000320574	NM_006231.2	18	Gag/Aag	1/49	NA	2	FACETS	0.851	0.744	0.966			1	INDETERMINATE	2	TRUE	NA	0.234225543451878	2		467	331	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414399	6414399	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	42	327	0	ENST00000356142.4:c.33C>A	p.Asp11Glu	p.D11E	ENST00000356142	NM_018890.3	11	gaC/gaA	1/7	0.212784883935789	3	FACETS	1	0.926	1	0.598	0.501	0.705	CLONAL	1	TRUE	1	0.234225543451878	3		327	335	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987067	36987067	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	103	513	1	ENST00000354822.5:c.622C>T	p.Arg208Ter	p.R208*	ENST00000354822	NM_001079668.2	208	Cga/Tga	3/3	1	2	FACETS	0.997	0.898	1	1	0.988	1	CLONAL	2	TRUE	1	0.234225543451878	2		514	441	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087548	27087548	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	162	579	0	ENST00000324856.7:c.2122C>T	p.Gln708Ter	p.Q708*	ENST00000324856	NM_006015.4	708	Cag/Tag	5/20	0.233117105085086	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.234225543451878	2		579	620	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587782272	NA	P-0050757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	61	398	0	ENST00000269305.4:c.994-1G>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.234225543451878	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.234225543451878	1		398	339	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927381	245927381	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1260469748	NA	P-0050757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	38	464	0	ENST00000388985.4:c.1147C>G	p.Gln383Glu	p.Q383E	ENST00000388985		383	Caa/Gaa	11/12	1	2	FACETS	0.704	0.582	0.84	0.704	0.582	0.84	SUBCLONAL	1	TRUE	1	0.234225543451878	2		464	461	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211928	36211928	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0050757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	88	569	0	ENST00000222270.7:c.1679C>G	p.Ser560Ter	p.S560*	ENST00000222270	NM_014727.1	560	tCa/tGa	3/37	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.234225543451878	2		569	543	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89824998	89824998	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501883	NA	P-0050757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	47	517	0	ENST00000389301.3:c.2968G>A	p.Asp990Asn	p.D990N	ENST00000389301	NM_000135.2	990	Gat/Aat	30/43	1	2	FACETS	0.694	0.585	0.815	0.694	0.585	0.815	SUBCLONAL	1	TRUE	1	0.234225543451878	2		517	578	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308324	30308324	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	36	497	0	ENST00000262643.3:c.338G>C	p.Arg113Thr	p.R113T	ENST00000262643	NM_001238.2	113	aGa/aCa	6/12	1	2	FACETS	0.685	0.563	0.821	0.685	0.563	0.821	SUBCLONAL	1	TRUE	1	0.234225543451878	2		497	449	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44894227	44894228	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	43	261	0	ENST00000377967.4:c.619dup	p.Ile207AsnfsTer10	p.I207Nfs*10	ENST00000377967	NM_021140.2	206	gaa/gAaa	7/29	0.234225543451878	3	FACETS	0.844	0.718	0.978	1	0.946	1	CLONAL	3	TRUE	1	0.234225543451878	3		261	162	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870853	12870853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500190	NA	P-0050757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	33	493	0	ENST00000228872.4:c.80C>T	p.Ser27Leu	p.S27L	ENST00000228872	NM_004064.3	27	tCg/tTg	1/3	1	2	FACETS	0.551	0.448	0.668	0.551	0.448	0.668	SUBCLONAL	1	TRUE	1	0.234225543451878	2		493	511	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662386	117662386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	53	490	0	ENST00000368508.3:c.4991C>T	p.Ser1664Phe	p.S1664F	ENST00000368508	NM_002944.2	1664	tCc/tTc	30/43	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.234225543451878	2		490	327	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266845	18266845	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	33	498	0	ENST00000222254.8:c.156G>T	p.Gln52His	p.Q52H	ENST00000222254	NM_005027.3	52	caG/caT	2/16	1	2	FACETS	0.617	0.502	0.746	0.617	0.502	0.746	SUBCLONAL	1	TRUE	1	0.234225543451878	2		498	457	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195769	102195769	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	73	476	0	ENST00000263464.3:c.529C>T	p.Gln177Ter	p.Q177*	ENST00000263464	NM_001165.4	177	Cag/Tag	2/9	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.234225543451878	2		476	497	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380680	118380680	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	42	356	0	ENST00000534358.1:c.10918G>T	p.Glu3640Ter	p.E3640*	ENST00000534358	NM_005933.3	3640	Gaa/Taa	30/36	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.234225543451878	2		356	324	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233162	69233162	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	62	436	0	ENST00000462284.1:c.1027G>C	p.Asp343His	p.D343H	ENST00000462284	NM_002392.5	343	Gat/Cat	11/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.234225543451878	2		436	439	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423592	88423592	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	49	465	0	ENST00000360948.2:c.2243C>G	p.Thr748Ser	p.T748S	ENST00000360948	NM_001012338.2	748	aCt/aGt	18/19	0.222109922870686	1	FACETS	0.836	0.709	0.975	0.836	0.709	0.975	CLONAL	1	TRUE	0	0.234225543451878	1		465	442	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224384	36224384	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs868232650	NA	P-0050757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	104	750	0	ENST00000222270.7:c.6934C>G	p.Gln2312Glu	p.Q2312E	ENST00000222270	NM_014727.1	2312	Cag/Gag	28/37	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.234225543451878	2		750	633	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791166	42791166	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	78	582	0	ENST00000575354.2:c.226G>A	p.Glu76Lys	p.E76K	ENST00000575354	NM_015125.3	76	Gag/Aag	3/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.234225543451878	2		582	522	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791252	42791252	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1256325889	NA	P-0050757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	63	576	0	ENST00000575354.2:c.312G>C	p.Glu104Asp	p.E104D	ENST00000575354	NM_015125.3	104	gaG/gaC	3/20	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.234225543451878	2		576	491	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792055	42792055	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	102	524	0	ENST00000575354.2:c.859G>A	p.Gly287Arg	p.G287R	ENST00000575354	NM_015125.3	287	Ggg/Agg	6/20	1	2	FACETS	0.799	0.717	0.886	1	0.984	1	SUBCLONAL	2	TRUE	1	0.234225543451878	2		524	545	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792078	42792078	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	112	511	0	ENST00000575354.2:c.882G>C	p.Glu294Asp	p.E294D	ENST00000575354	NM_015125.3	294	gaG/gaC	6/20	1	2	FACETS	0.842	0.76	0.928	1	0.986	1	CLONAL	2	TRUE	1	0.234225543451878	2		511	568	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715419	117715419	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	16	321	0	ENST00000368508.3:c.1070C>G	p.Ser357Cys	p.S357C	ENST00000368508	NM_002944.2	357	tCt/tGt	10/43	1	2	FACETS	0.644	0.477	0.843	0.644	0.477	0.843	SUBCLONAL	1	TRUE	1	0.234225543451878	2		321	212	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397729	116397729	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	52	404	0	ENST00000397752.3:c.2003C>G	p.Pro668Arg	p.P668R	ENST00000397752	NM_000245.2	668	cCt/cGt	8/21	1	2	FACETS	0.776	0.666	0.896	1	0.968	1	SUBCLONAL	2	TRUE	1	0.234225543451878	2		404	286	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879415	151879415	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	73	527	0	ENST00000262189.6:c.5530G>C	p.Asp1844His	p.D1844H	ENST00000262189	NM_170606.2	1844	Gat/Cat	36/59	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.234225543451878	2		527	573	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772733	135772733	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0050757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	88	494	0	ENST00000298552.3:c.2814-1G>C		p.X938_splice	ENST00000298552	NM_001162426.1	938			0.234225543451878	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.234225543451878	1		494	456	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84388618	84388618	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	10	188	0	ENST00000321945.7:c.670G>C	p.Glu224Gln	p.E224Q	ENST00000321945	NM_139076.2	224	Gag/Cag	7/9	0.222109922870686	1	FACETS	0.698	0.476	0.972	0.698	0.476	0.972	SUBCLONAL	1	TRUE	0	0.234225543451878	1		188	108	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231065	53231065	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050757-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	43	555	0	ENST00000375401.3:c.1837G>A	p.Glu613Lys	p.E613K	ENST00000375401	NM_004187.3	613	Gag/Aag	13/26	1	2	FACETS	0.657	0.549	0.777	0.657	0.549	0.777	SUBCLONAL	1	TRUE	1	0.234225543451878	2		555	559	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	85	302	0				ENST00000310581	NM_198253.2	-/1132			0.215511695985747	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	3	TRUE	1	0.222102194998991	4		302	275	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	132	374	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.222102194998991	5	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	3	0.222102194998991	5		374	658	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092809	27092809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	192	461	0	ENST00000324856.7:c.2830C>T	p.Gln944Ter	p.Q944*	ENST00000324856	NM_006015.4	944	Cag/Tag	9/20	0.194605448292851	4	FACETS	0.982	0.915	1	1	0.989	1	CLONAL	4	TRUE	1	0.222102194998991	4		461	538	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868663	37868663	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1275492389	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	136	566	0	ENST00000269571.5:c.1110C>G	p.Ile370Met	p.I370M	ENST00000269571		370	atC/atG	9/27	0.222102194998991	5	FACETS	1	0.959	1	0.728	0.662	0.796	CLONAL	2	TRUE	2	0.222102194998991	5		566	748	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	140	449	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.222102194998991	5	FACETS	0.966	0.883	1	0.966	0.883	1	CLONAL	3	TRUE	2	0.222102194998991	5		449	580	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263850	133263850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	66	467	0	ENST00000320574.5:c.52G>A	p.Glu18Lys	p.E18K	ENST00000320574	NM_006231.2	18	Gag/Aag	1/49	0.0781655561228942	3	FACETS	0.943	0.824	1			1	INDETERMINATE	2	TRUE	NA	0.222102194998991	3		467	350	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414399	6414399	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	54	327	0	ENST00000356142.4:c.33C>A	p.Asp11Glu	p.D11E	ENST00000356142	NM_018890.3	11	gaC/gaA	1/7	0.222102194998991	6	FACETS	0.931	0.798	1	0.621	0.532	0.717	CLONAL	2	TRUE	3	0.222102194998991	6		327	377	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987067	36987067	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	83	513	1	ENST00000354822.5:c.622C>T	p.Arg208Ter	p.R208*	ENST00000354822	NM_001079668.2	208	Cga/Tga	3/3	0.222102194998991	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	1	0.222102194998991	3		514	367	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087548	27087548	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	223	579	0	ENST00000324856.7:c.2122C>T	p.Gln708Ter	p.Q708*	ENST00000324856	NM_006015.4	708	Cag/Tag	5/20	0.194605448292851	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	1	0.222102194998991	4		579	720	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587782272	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	118	398	0	ENST00000269305.4:c.994-1G>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.161623753046991	3	FACETS	1	0.975	1	0.813	0.738	0.892	CLONAL	2	TRUE	0	0.222102194998991	3		398	484	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927381	245927381	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1260469748	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	47	464	0	ENST00000388985.4:c.1147C>G	p.Gln383Glu	p.Q383E	ENST00000388985		383	Caa/Gaa	11/12	0.222102194998991	3	FACETS	0.835	0.704	0.98	0.418	0.352	0.49	CLONAL	1	TRUE	1	0.222102194998991	3		464	563	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408885	41408885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868295248	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	59	435	0	ENST00000373198.4:c.541G>A	p.Glu181Lys	p.E181K	ENST00000373198	NM_133170.3	181	Gag/Aag	4/32	0.222102194998991	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.222102194998991	1		435	388	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211928	36211928	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	39	569	0	ENST00000222270.7:c.1679C>G	p.Ser560Ter	p.S560*	ENST00000222270	NM_014727.1	560	tCa/tGa	3/37	0.222102194998991	3	FACETS	0.81	0.671	0.964	0.405	0.335	0.482	CLONAL	1	TRUE	1	0.222102194998991	3		569	482	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89824998	89824998	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501883	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	46	517	0	ENST00000389301.3:c.2968G>A	p.Asp990Asn	p.D990N	ENST00000389301	NM_000135.2	990	Gat/Aat	30/43	0.222102194998991	3	FACETS	0.803	0.676	0.944	0.402	0.338	0.472	CLONAL	1	TRUE	1	0.222102194998991	3		517	573	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308324	30308324	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	111	497	0	ENST00000262643.3:c.338G>C	p.Arg113Thr	p.R113T	ENST00000262643	NM_001238.2	113	aGa/aCa	6/12	0.222102194998991	3	FACETS	0.976	0.88	1	0.976	0.88	1	CLONAL	2	TRUE	1	0.222102194998991	3		497	569	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44894227	44894228	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	104	261	0	ENST00000377967.4:c.619dup	p.Ile207AsnfsTer10	p.I207Nfs*10	ENST00000377967	NM_021140.2	206	gaa/gAaa	7/29	0.222102194998991	5	FACETS	1	0.918	1			1	CLONAL	3	TRUE	NA	0.222102194998991	5		261	408	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870853	12870853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500190	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	64	493	0	ENST00000228872.4:c.80C>T	p.Ser27Leu	p.S27L	ENST00000228872	NM_004064.3	27	tCg/tTg	1/3	0.157875182593638	4	FACETS	1	0.924	1	0.55	0.476	0.631	CLONAL	1	TRUE	2	0.222102194998991	4		493	640	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662386	117662386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	107	490	0	ENST00000368508.3:c.4991C>T	p.Ser1664Phe	p.S1664F	ENST00000368508	NM_002944.2	1664	tCc/tTc	30/43	0.157875182593638	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	2	0.222102194998991	4		490	521	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266845	18266845	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	79	498	0	ENST00000222254.8:c.156G>T	p.Gln52His	p.Q52H	ENST00000222254	NM_005027.3	52	caG/caT	2/16	0.222102194998991	3	FACETS	0.88	0.777	0.99	0.88	0.777	0.99	CLONAL	2	TRUE	1	0.222102194998991	3		498	449	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195769	102195769	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	143	476	0	ENST00000263464.3:c.529C>T	p.Gln177Ter	p.Q177*	ENST00000263464	NM_001165.4	177	Cag/Tag	2/9	0.222102194998991	5	FACETS	1	0.97	1	0.76	0.694	0.829	CLONAL	2	TRUE	2	0.222102194998991	5		476	753	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380680	118380680	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	107	356	0	ENST00000534358.1:c.10918G>T	p.Glu3640Ter	p.E3640*	ENST00000534358	NM_005933.3	3640	Gaa/Taa	30/36	0.222102194998991	5	FACETS	1	0.974	1	0.831	0.749	0.918	CLONAL	2	TRUE	2	0.222102194998991	5		356	515	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233162	69233162	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	111	436	0	ENST00000462284.1:c.1027G>C	p.Asp343His	p.D343H	ENST00000462284	NM_002392.5	343	Gat/Cat	11/11	0.202156134298836	4	FACETS	0.962	0.866	1	0.962	0.866	1	CLONAL	2	TRUE	2	0.222102194998991	4		436	635	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423592	88423592	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	49	465	0	ENST00000360948.2:c.2243C>G	p.Thr748Ser	p.T748S	ENST00000360948	NM_001012338.2	748	aCt/aGt	18/19	0.222102194998991	1	FACETS	0.973	0.826	1	0.973	0.826	1	CLONAL	1	TRUE	0	0.222102194998991	1		465	403	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224384	36224384	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs868232650	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	58	750	0	ENST00000222270.7:c.6934C>G	p.Gln2312Glu	p.Q2312E	ENST00000222270	NM_014727.1	2312	Cag/Gag	28/37	0.222102194998991	3	FACETS	0.994	0.854	1	0.497	0.427	0.573	CLONAL	1	TRUE	1	0.222102194998991	3		750	584	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791166	42791166	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	59	582	0	ENST00000575354.2:c.226G>A	p.Glu76Lys	p.E76K	ENST00000575354	NM_015125.3	76	Gag/Aag	3/20	0.222102194998991	3	FACETS	1	0.885	1	0.516	0.444	0.595	CLONAL	1	TRUE	1	0.222102194998991	3		582	572	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791252	42791252	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1256325889	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	52	576	0	ENST00000575354.2:c.312G>C	p.Glu104Asp	p.E104D	ENST00000575354	NM_015125.3	104	gaG/gaC	3/20	0.222102194998991	3	FACETS	1	0.888	1	0.526	0.448	0.611	CLONAL	1	TRUE	1	0.222102194998991	3		576	495	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792055	42792055	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	54	524	0	ENST00000575354.2:c.859G>A	p.Gly287Arg	p.G287R	ENST00000575354	NM_015125.3	287	Ggg/Agg	6/20	0.222102194998991	3	FACETS	1	0.918	1	0.556	0.475	0.644	CLONAL	1	TRUE	1	0.222102194998991	3		524	486	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792078	42792078	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	69	511	0	ENST00000575354.2:c.882G>C	p.Glu294Asp	p.E294D	ENST00000575354	NM_015125.3	294	gaG/gaC	6/20	0.222102194998991	3	FACETS	1	0.97	1	0.703	0.614	0.799	CLONAL	1	TRUE	1	0.222102194998991	3		511	491	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715419	117715419	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	65	321	0	ENST00000368508.3:c.1070C>G	p.Ser357Cys	p.S357C	ENST00000368508	NM_002944.2	357	tCt/tGt	10/43	0.157875182593638	4	FACETS	0.795	0.691	0.907	0.795	0.691	0.907	CLONAL	2	TRUE	2	0.222102194998991	4		321	450	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397729	116397729	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	106	404	0	ENST00000397752.3:c.2003C>G	p.Pro668Arg	p.P668R	ENST00000397752	NM_000245.2	668	cCt/cGt	8/21	0.202156134298836	4	FACETS	1	0.925	1	1	0.925	1	CLONAL	2	TRUE	2	0.222102194998991	4		404	564	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879415	151879415	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	141	527	0	ENST00000262189.6:c.5530G>C	p.Asp1844His	p.D1844H	ENST00000262189	NM_170606.2	1844	Gat/Cat	36/59	0.202156134298836	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.222102194998991	4		527	638	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772733	135772733	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	126	494	0	ENST00000298552.3:c.2814-1G>C		p.X938_splice	ENST00000298552	NM_001162426.1	938			0.217303474662319	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.222102194998991	2		494	506	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84388618	84388618	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	41	188	0	ENST00000321945.7:c.670G>C	p.Glu224Gln	p.E224Q	ENST00000321945	NM_139076.2	224	Gag/Cag	7/9	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.222102194998991	2		188	349	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231065	53231065	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	53	555	0	ENST00000375401.3:c.1837G>A	p.Glu613Lys	p.E613K	ENST00000375401	NM_004187.3	613	Gag/Aag	13/26	0.222102194998991	3	FACETS	1	0.866	1	0.508	0.433	0.59	CLONAL	1	TRUE	1	0.222102194998991	3		555	522	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41267787	41267787	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	32	229	0	ENST00000357654.3:c.90G>C	p.Leu30Phe	p.L30F	ENST00000357654	NM_007294.3	30	ttG/ttC	3/23	0.222102194998991	5	FACETS	0.871	0.707	1	0.29	0.235	0.353	CLONAL	1	TRUE	2	0.222102194998991	5		229	441	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235320	235320	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050757-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	45	343	0	ENST00000264932.6:c.1126C>G	p.Leu376Val	p.L376V	ENST00000264932	NM_004168.2	376	Ctg/Gtg	9/15	0.215511695985747	4	FACETS	0.986	0.829	1	0.329	0.276	0.387	CLONAL	1	TRUE	1	0.222102194998991	4		343	502	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0051006-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	33	452	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.752478984283612	2		452	72	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984412	201984413	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0051006-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	26	616	0	ENST00000359651.3:c.1079dup	p.Trp361LeufsTer110	p.W361Lfs*110	ENST00000359651		359	-/G	8/8	1	2	FACETS	0.934	0.81	1	1	0.965	1	CLONAL	2	TRUE	1	0.752478984283612	2		616	37	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093424	30093424	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051006-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	13	455	0	ENST00000331968.5:c.1839C>G	p.Ile613Met	p.I613M	ENST00000331968	NM_002742.2	613	atC/atG	13/18	1	2	FACETS	1	0.765	1	1	0.765	1	CLONAL	1	TRUE	1	0.752478984283612	2		455	34	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0051008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	23	259	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.17	0.132	0.214	0.17	0.132	0.214	SUBCLONAL	1	TRUE	1	0.766637159599337	2		259	353	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444310	49444310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	296	732	0	ENST00000301067.7:c.3061C>T	p.Pro1021Ser	p.P1021S	ENST00000301067	NM_003482.3	1021	Cct/Tct	11/54	1	2	FACETS	0.976	0.923	1	0.976	0.923	1	CLONAL	1	TRUE	1	0.766637159599337	2		732	791	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495462	56495462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	248	637	1	ENST00000267101.3:c.3652G>A	p.Glu1218Lys	p.E1218K	ENST00000267101	NM_001982.3	1218	Gag/Aag	28/28	1	2	FACETS	0.958	0.901	1	0.958	0.901	1	CLONAL	1	TRUE	1	0.766637159599337	2		638	675	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120535131	120535131	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	36	499	0	ENST00000229340.5:c.524A>G	p.Asn175Ser	p.N175S	ENST00000229340	NM_006861.6	175	aAc/aGc	6/6	1	2	FACETS	0.163	0.133	0.196	0.163	0.133	0.196	SUBCLONAL	1	TRUE	1	0.766637159599337	2		499	577	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223043	5223044	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0051008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	240	648	0	ENST00000357368.4:c.2759dup	p.Leu921ProfsTer62	p.L921Pfs*62	ENST00000357368	NM_002850.3	920	gtc/gtTc	18/38	1	2	FACETS	0.943	0.886	1	0.943	0.886	1	CLONAL	1	TRUE	1	0.766637159599337	2		648	664	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0051008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	668	885	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.766641440914949	3	FACETS	0.89	0.868	0.911			1	CLONAL	3	TRUE	NA	0.766637159599337	3		885	903	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805540	1805540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	797	587	0	ENST00000260795.2:c.1052C>T	p.Ser351Phe	p.S351F	ENST00000260795		351	tCt/tTt	7/17	0.766641440914949	3	FACETS	0.925	0.906	0.944			1	CLONAL	3	TRUE	NA	0.766637159599337	3		587	1036	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806618	1806618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	889	699	0	ENST00000260795.2:c.1334C>T	p.Ser445Leu	p.S445L	ENST00000260795		445	tCa/tTa	9/17	0.766641440914949	3	FACETS	0.916	0.898	0.934			1	CLONAL	3	TRUE	NA	0.766637159599337	3		699	1167	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449745	8449745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1172700321	NA	P-0051008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	57	396	1	ENST00000356435.5:c.3968G>A	p.Arg1323His	p.R1323H	ENST00000356435		1323	cGc/cAc	23/35	0.598475613752595	1	FACETS	0.246	0.211	0.283	0.246	0.211	0.283	SUBCLONAL	1	TRUE	0	0.766637159599337	1		397	373	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760412	133760412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1168825454	NA	P-0051008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	252	572	0	ENST00000318560.5:c.2735G>A	p.Gly912Glu	p.G912E	ENST00000318560	NM_005157.4	912	gGa/gAa	11/11	0.766637159599337	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.766637159599337	1		572	388	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760976	133760976	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	253	631	0	ENST00000318560.5:c.3299G>A	p.Cys1100Tyr	p.C1100Y	ENST00000318560	NM_005157.4	1100	tGc/tAc	11/11	0.766637159599337	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.766637159599337	1		631	404	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786039	135786039	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	200	581	0	ENST00000298552.3:c.1182del	p.Pro395LeufsTer45	p.P395Lfs*45	ENST00000298552	NM_001162426.1	394	tcT/tc	12/23	0.766637159599337	1	FACETS	0.757	0.711	0.804	0.757	0.711	0.804	SUBCLONAL	1	TRUE	0	0.766637159599337	1		581	425	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222203	53222204	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0051008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	172	279	0	ENST00000375401.3:c.4628_4629insTT	p.Thr1544Ter	p.T1544*	ENST00000375401	NM_004187.3	1543	ctg/ctTTg	26/26	1	1	FACETS	0.948	0.892	1	0.948	0.892	1	CLONAL	1	TRUE	0	0.766637159599337	1		279	292	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0051132-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	106	555	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.654157909694003	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.654157909694003	1		555	212	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363898	118363898	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1038015863	NA	P-0051132-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	20	284	0	ENST00000534358.1:c.5131C>A	p.Leu1711Ile	p.L1711I	ENST00000534358	NM_005933.3	1711	Cta/Ata	16/36	0.630171933604574	2	FACETS	0.185	0.141	0.237	0.093	0.07	0.119	SUBCLONAL	1	TRUE	0	0.654157909694003	2		284	330	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483135	29483136	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AACA	novel	NA	P-0051132-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	29	279	0	ENST00000356175.3:c.197_200dup	p.Asn67LysfsTer11	p.N67Kfs*11	ENST00000356175	NM_000267.3	65	-/AACA	2/57	0.5169318274984	2	FACETS	0.288	0.231	0.352	0.144	0.115	0.176	SUBCLONAL	1	TRUE	0	0.654157909694003	2		279	308	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250274	39250274	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051132-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	151	449	0	ENST00000402219.2:c.1295G>T	p.Trp432Leu	p.W432L	ENST00000402219	NM_005633.3	432	tGg/tTg	10/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.654157909694003	2		449	436	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181469	38181469	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051132-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	71	479	0	ENST00000396334.3:c.482C>G	p.Thr161Ser	p.T161S	ENST00000396334	NM_002468.4	161	aCc/aGc	2/5	1	2	FACETS	0.662	0.582	0.747	0.662	0.582	0.747	SUBCLONAL	1	TRUE	1	0.654157909694003	2		479	328	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680385	30680385	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051132-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	94	467	0	ENST00000376406.3:c.1334G>A	p.Ser445Asn	p.S445N	ENST00000376406	NM_014641.2	445	aGc/aAc	5/15	1	2	FACETS	0.821	0.737	0.909	0.821	0.737	0.909	CLONAL	1	TRUE	1	0.654157909694003	2		467	350	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0051294-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	8	400	0	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	0.115674996329334	4	FACETS	1	0.776	1	0.625	0.416	0.876	INDETERMINATE	1	TRUE	2	0.508098919273258	4		400	38	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251839	212251839	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051294-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	14	248	0	ENST00000342788.4:c.3220G>A	p.Glu1074Lys	p.E1074K	ENST00000342788	NM_005235.2	1074	Gaa/Aaa	27/28	0.369176100203963	1	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	0	0.508098919273258	1		248	28	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458878	120458878	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051294-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	13	576	0	ENST00000256646.2:c.6467C>G	p.Ser2156Cys	p.S2156C	ENST00000256646	NM_024408.3	2156	tCt/tGt	34/34	0.264084219138615	6	FACETS	0.882	0.658	1			1	INDETERMINATE	3	TRUE	NA	0.508098919273258	6		576	39	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256735	16256735	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051294-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	15	410	0	ENST00000375759.3:c.4000G>T	p.Glu1334Ter	p.E1334*	ENST00000375759	NM_015001.2	1334	Gaa/Taa	11/15	1	2	FACETS	0.82	0.635	1	1	0.919	1	CLONAL	2	TRUE	1	0.508098919273258	2		410	36	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425263	49425263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051294-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	15	686	2	ENST00000301067.7:c.13225G>A	p.Glu4409Lys	p.E4409K	ENST00000301067	NM_003482.3	4409	Gag/Aag	39/54	NA	2	FACETS	1	0.877	1			1	INDETERMINATE	1	TRUE	NA	0.508098919273258	2		688	46	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249332	133249332	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1275423655	NA	P-0051294-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	10	689	1	ENST00000320574.5:c.1567G>C	p.Glu523Gln	p.E523Q	ENST00000320574	NM_006231.2	523	Gag/Cag	15/49	0.508098919273258	5	FACETS	1	0.815	1	0.428	0.297	0.584	CLONAL	1	TRUE	2	0.508098919273258	5		690	54	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350954	89350954	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs747922528	NA	P-0051294-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4	16	743	0	ENST00000301030.4:c.1996C>T	p.Gln666Ter	p.Q666*	ENST00000301030	NM_001256183.1	666	Cag/Tag	9/13	0.508098919273258	2	FACETS	1	0.885	1	1	0.944	1	CLONAL	3	TRUE	0	0.508098919273258	2		743	20	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946451	2946451	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051294-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	12	604	0	ENST00000396946.4:c.3286G>C	p.Glu1096Gln	p.E1096Q	ENST00000396946	NM_032415.4	1096	Gag/Cag	25/25	0.115674996329334	4	FACETS	0.913	0.691	1	1	0.881	1	INDETERMINATE	3	TRUE	2	0.508098919273258	4		604	26	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0051577-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	43	372	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.21	2		372	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051577-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	79	472	2	ENST00000269305.4:c.772G>C	p.Glu258Gln	p.E258Q	ENST00000269305	NM_001126112.2	258	Gaa/Caa	7/11	1	2	FACETS	0.821	0.725	0.924	1	0.98	1	CLONAL	2	TRUE	1	0.21	2		474	458	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259315	16259315	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs756634501	NA	P-0051577-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	54	712	0	ENST00000375759.3:c.6580G>T	p.Ala2194Ser	p.A2194S	ENST00000375759	NM_015001.2	2194	Gca/Tca	11/15	1	2	FACETS	0.861	0.735	1	0.861	0.735	1	CLONAL	1	TRUE	1	0.21	2		712	597	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262221	115262221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051673-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	102	319	0	ENST00000438362.2:c.2333C>T	p.Ala778Val	p.A778V	ENST00000438362	NM_001242891.1	778	gCc/gTc	18/20	0.340364174723199	1	FACETS	0.366	0.328	0.407	0.366	0.328	0.407	INDETERMINATE	1	TRUE	0	0.622311259131454	1		319	617	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246594	46246594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051673-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	113	403	0	ENST00000334344.6:c.4688G>A	p.Ser1563Asn	p.S1563N	ENST00000334344	NM_152641.2	1563	aGc/aAc	15/21	0.464359668553529	3	FACETS	0.541	0.486	0.599	0.271	0.243	0.3	SUBCLONAL	1	TRUE	1	0.622311259131454	3		403	880	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149556	202149556	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051673-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	113	482	0	ENST00000358485.4:c.997T>G	p.Phe333Val	p.F333V	ENST00000358485	NM_001080125.1	333	Ttt/Gtt	8/9	0.375549752451946	3	FACETS	0.544	0.489	0.602	0.181	0.163	0.201	SUBCLONAL	1	TRUE	0	0.622311259131454	3		482	876	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191513	10191513	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1205346910	NA	P-0051673-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	310	471	0	ENST00000256474.2:c.506del	p.Leu169GlnfsTer33	p.L169Qfs*33	ENST00000256474	NM_000551.3	169	cTa/ca	3/3	0.622311259131454	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.622311259131454	1		471	628	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47088076	47088076	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051673-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	251	391	0	ENST00000409792.3:c.6999del	p.Gln2334AsnfsTer19	p.Q2334Nfs*19	ENST00000409792	NM_014159.6	2333	ggG/gg	16/21	0.622311259131454	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.622311259131454	1		391	534	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441216	52441216	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553645794	NA	P-0051673-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	287	574	0	ENST00000460680.1:c.554G>A	p.Gly185Glu	p.G185E	ENST00000460680	NM_004656.3	185	gGg/gAg	7/17	0.622311259131454	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.622311259131454	1		574	589	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0052153-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	294	425	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.848663345234918	2		425	676	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999410	100999410	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052425-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	77	774	0	ENST00000325455.5:c.392C>G	p.Pro131Arg	p.P131R	ENST00000325455	NM_001202474.3	131	cCt/cGt	1/8	0.455385876218501	1	FACETS	0.103	0.089	0.117	0.103	0.089	0.117	INDETERMINATE	1	TRUE	0	0.786479702463585	1		774	1159	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912664	NA	P-0052425-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	458	512	0	ENST00000269305.4:c.1010G>C	p.Arg337Pro	p.R337P	ENST00000269305	NM_001126112.2	337	cGc/cCc	10/11	0.786479702463585	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.786479702463585	1		512	673	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249011	55249012	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAACCCAGG	novel	NA	P-0052425-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	648	706	0	ENST00000275493.2:c.2315_2316insAGGCAACCC	p.Pro772_His773insGlyAsnPro	p.P772_H773insGNP	ENST00000275493	NM_005228.3	770	gac/gaCAACCCAGGc	20/28	0.190685864174673	3	FACETS	0.804	0.776	0.832	0.536	0.517	0.555	INDETERMINATE	2	TRUE	0	0.786479702463585	3		706	1428	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0052445-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	46	190	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.1415478690061	2		190	476	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0052445-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	52	250	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.123548062727098	2	FACETS	1	0.962	1	0.73	0.622	0.849	CLONAL	1	FALSE	0	0.1415478690061	2		250	503	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0052445-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	55	330	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	0.123548062727098	2	FACETS	0.795	0.68	0.919	0.795	0.68	0.919	CLONAL	2	FALSE	0	0.1415478690061	2		330	489	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257336	16257336	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0052445-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	44	626	0	ENST00000375759.3:c.4601C>G	p.Ser1534Ter	p.S1534*	ENST00000375759	NM_015001.2	1534	tCa/tGa	11/15	0.1415478690061	1	FACETS	0.724	0.605	0.856	0.724	0.605	0.856	SUBCLONAL	1	FALSE	0	0.1415478690061	1		626	798	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274223	10274223	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052445-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	85	489	0	ENST00000330684.3:c.46C>G	p.Leu16Val	p.L16V	ENST00000330684	NM_001134407.1	16	Ctg/Gtg	2/13	0.1415478690061	3	FACETS	0.869	0.768	0.977	0.869	0.768	0.977	CLONAL	2	FALSE	1	0.1415478690061	3		489	740	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174899	56174900	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052445-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	42	482	0	ENST00000399503.3:c.2059dup	p.Ile687AsnfsTer10	p.I687Nfs*10	ENST00000399503	NM_005921.1	686	-/A	11/20	1	2	FACETS	0.795	0.662	0.944	0.795	0.662	0.944	CLONAL	1	FALSE	1	0.1415478690061	2		482	746	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180536	56180537	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052445-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	35	332	0	ENST00000399503.3:c.3867dup	p.Ala1290SerfsTer19	p.A1290Sfs*19	ENST00000399503	NM_005921.1	1289	gaa/gAaa	16/20	1	2	FACETS	0.808	0.661	0.974	0.808	0.661	0.974	CLONAL	1	FALSE	1	0.1415478690061	2		332	612	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672333	86672346	+	frameshift_variant	Frame_Shift_Del	DEL	ACTCTATGGAAAAA	ACTCTATGGAAAAA	-	novel	NA	P-0052445-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	55	436	0	ENST00000274376.6:c.2136_2149del	p.Ser713HisfsTer8	p.S713Hfs*8	ENST00000274376	NM_002890.2	712	tACTCTATGGAAAAA/t	16/25	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	1	0.1415478690061	2		436	671	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502252	186502252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052445-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	47	580	0	ENST00000323963.5:c.61G>A	p.Asp21Asn	p.D21N	ENST00000323963		21	Gat/Aat	2/11	0.123548062727098	2	FACETS	0.823	0.692	0.968	0.411	0.346	0.484	CLONAL	1	FALSE	0	0.1415478690061	2		580	807	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0052722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	94	265	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.321765048905644	4	FACETS	0.983	0.888	1	0.737	0.666	0.81	CLONAL	3	TRUE	0	0.321765048905644	4		265	262	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220370	1220370	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0052722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	181	413	0	ENST00000326873.7:c.465-2A>T		p.X155_splice	ENST00000326873	NM_000455.4	155			0.321765048905644	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.321765048905644	2		413	536	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041519	14041519	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161291089	NA	P-0052722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	99	308	1	ENST00000311895.7:c.2066G>A	p.Arg689His	p.R689H	ENST00000311895	NM_005236.2	689	cGt/cAt	11/11	0.321765048905644	6	FACETS	0.828	0.74	0.92			1	CLONAL	2	TRUE	NA	0.321765048905644	6		309	611	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39746916	39746916	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	65	181	0	ENST00000361337.2:c.1930A>G	p.Met644Val	p.M644V	ENST00000361337	NM_003286.2	644	Atg/Gtg	18/21	0.27082046051977	3	FACETS	0.895	0.785	1	0.895	0.785	1	CLONAL	2	TRUE	1	0.321765048905644	3		181	262	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69143600	69143600	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	124	274	0	ENST00000288368.4:c.4808C>A	p.Ala1603Asp	p.A1603D	ENST00000288368	NM_024870.2	1603	gCt/gAt	40/40	0.321765048905644	4	FACETS	1	0.973	1			1	CLONAL	2	TRUE	NA	0.321765048905644	4		274	433	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225449677	225449677	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	52	275	0	ENST00000264414.4:c.50G>A	p.Arg17Gln	p.R17Q	ENST00000264414	NM_003590.4	17	cGg/cAg	1/16	0.281562435791578	4	FACETS	0.861	0.734	1	0.431	0.367	0.501	CLONAL	1	TRUE	2	0.321765048905644	4		275	496	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985543	2985543	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	78	327	0	ENST00000396946.4:c.268G>C	p.Val90Leu	p.V90L	ENST00000396946	NM_032415.4	90	Gtc/Ctc	4/25	0.281562435791578	4	FACETS	1	0.94	1	0.555	0.488	0.627	CLONAL	1	TRUE	2	0.321765048905644	4		327	577	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381522	81381522	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	106	311	0	ENST00000222390.5:c.539C>A	p.Pro180His	p.P180H	ENST00000222390	NM_000601.4	180	cCt/cAt	5/18	0.291300522966904	5	FACETS	0.927	0.834	1			1	CLONAL	2	TRUE	NA	0.321765048905644	5		311	527	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319867	8319867	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	80	313	0	ENST00000356435.5:c.5634G>T	p.Met1878Ile	p.M1878I	ENST00000356435		1878	atG/atT	34/35	0.321765048905644	2	FACETS	0.834	0.742	0.931	0.834	0.742	0.931	CLONAL	2	TRUE	0	0.321765048905644	2		313	298	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0052862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	97	374	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.432907696756364	5	FACETS	1	0.958	1	0.747	0.673	0.823	CLONAL	2	TRUE	2	0.432907696756364	5		374	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577093	7577093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882008	NA	P-0052862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	305	651	0	ENST00000269305.4:c.845G>A	p.Arg282Gln	p.R282Q	ENST00000269305	NM_001126112.2	282	cGg/cAg	8/11	0.432907696756364	2	FACETS	0.998	0.947	1	0.998	0.947	1	CLONAL	2	TRUE	0	0.432907696756364	2		651	706	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894230	NA	P-0052862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	371	600	0	ENST00000451590.1:c.35G>A	p.Gly12Asp	p.G12D	ENST00000451590	NM_001130442.1	12	gGc/gAc	2/5	0.432907696756364	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.432907696756364	2		600	721	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627281	86627281	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1554044823	NA	P-0052862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	102	353	0	ENST00000274376.6:c.656C>G	p.Ser219Ter	p.S219*	ENST00000274376	NM_002890.2	219	tCa/tGa	2/25	0.432907696756364	2	FACETS	0.994	0.907	1	0.994	0.907	1	CLONAL	2	TRUE	0	0.432907696756364	2		353	237	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433896	49433896	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	477	940	0	ENST00000301067.7:c.7657C>T	p.Gln2553Ter	p.Q2553*	ENST00000301067	NM_003482.3	2553	Cag/Tag	31/54	0.406780108055374	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.432907696756364	3		940	1216	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244235	153244235	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0052862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	137	324	0	ENST00000281708.4:c.1922C>G	p.Ser641Ter	p.S641*	ENST00000281708	NM_033632.3	641	tCa/tGa	12/12	0.432907696756364	2	FACETS	0.998	0.923	1	0.998	0.923	1	CLONAL	2	TRUE	0	0.432907696756364	2		324	317	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104353437	104353437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	323	701	1	ENST00000369902.3:c.642G>A	p.Trp214Ter	p.W214*	ENST00000369902	NM_016169.3	214	tgG/tgA	5/12	0.432907696756364	2	FACETS	0.987	0.938	1	0.987	0.938	1	CLONAL	2	TRUE	0	0.432907696756364	2		702	756	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84403331	84403331	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776427276	NA	P-0052862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	95	354	0	ENST00000321945.7:c.154G>A	p.Asp52Asn	p.D52N	ENST00000321945	NM_139076.2	52	Gat/Aat	2/9	0.432907696756364	2	FACETS	0.896	0.812	0.982	0.896	0.812	0.982	CLONAL	2	TRUE	0	0.432907696756364	2		354	245	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953950	131953950	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	60	240	0	ENST00000265335.6:c.3353A>G	p.Asn1118Ser	p.N1118S	ENST00000265335		1118	aAc/aGc	21/25	0.432907696756364	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	0	0.432907696756364	2		240	127	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0053158-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	327	605	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.999	0.946	1	0.999	0.946	1	CLONAL	1	TRUE	1	0.659752019221588	2		605	992	SUCCESS
APC	324	MSKCC	GRCh37	5	112174466	112174466	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053158-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	142	250	0	ENST00000257430.4:c.3175G>T	p.Glu1059Ter	p.E1059*	ENST00000257430	NM_000038.5	1059	Gaa/Taa	16/16	0.338816111858577	1	FACETS	0.885	0.819	0.951	0.885	0.819	0.951	INDETERMINATE	1	TRUE	0	0.659752019221588	1		250	326	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562962	95562962	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747593690	NA	P-0053158-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	107	405	0	ENST00000393063.1:c.4295C>T	p.Pro1432Leu	p.P1432L	ENST00000393063	NM_030621.3	1432	cCg/cTg	24/28	0.388548983596857	1	FACETS	0.399	0.359	0.441	0.399	0.359	0.441	INDETERMINATE	1	TRUE	0	0.659752019221588	1		405	545	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114917819	114917819	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053158-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	404	564	0	ENST00000543371.1:c.1309G>T	p.Glu437Ter	p.E437*	ENST00000543371	NM_001198531.1	437	Gag/Tag	12/14	0.302626099357782	2	FACETS	1	0.996	1	0.73	0.699	0.761	INDETERMINATE	1	TRUE	0	0.659752019221588	2		564	839	SUCCESS
APC	324	MSKCC	GRCh37	5	112175281	112175282	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053158-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	66	267	0	ENST00000257430.4:c.3991dup	p.Arg1331LysfsTer11	p.R1331Kfs*11	ENST00000257430	NM_000038.5	1330	-/A	16/16	0.338816111858577	1	FACETS	0.438	0.383	0.497	0.438	0.383	0.497	INDETERMINATE	1	TRUE	0	0.659752019221588	1		267	306	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405962	49405962	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053609-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	41	246	0	ENST00000418115.1:c.176A>G	p.Asp59Gly	p.D59G	ENST00000418115	NM_001664.2	59	gAc/gGc	3/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		246	574	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0053609-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	63	287	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		287	527	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235838	108235838	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053609-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	32	424	0	ENST00000278616.4:c.8880G>T	p.Trp2960Cys	p.W2960C	ENST00000278616	NM_000051.3	2960	tgG/tgT	62/63	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		424	532	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0054088-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	292	187	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.991	0.941	1	0.991	0.941	1	CLONAL	1	TRUE	1	0.95009940586748	2		188	620	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0054088-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	359	662	1	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.95009940586748	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.95009940586748	1		663	376	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0054088-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	234	403	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.845	0.794	0.896	0.845	0.794	0.896	CLONAL	1	TRUE	1	0.95009940586748	2		403	583	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032069	26032069	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054088-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	148	494	0	ENST00000244661.2:c.220G>C	p.Glu74Gln	p.E74Q	ENST00000244661	NM_003537.3	74	Gaa/Caa	1/1	0.185866523206333	1	FACETS	0.303	0.278	0.329	0.303	0.278	0.329	INDETERMINATE	1	TRUE	0	0.95009940586748	1		494	539	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0054088-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	22	375	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.95009940586748	1	FACETS	0.028	0.021	0.036	0.028	0.021	0.036	SUBCLONAL	1	TRUE	0	0.95009940586748	1		375	868	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054088-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3555	205	507	0	ENST00000425967.3:c.1731C>G	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaG	13/19	0.95009940586748	12	FACETS	0.66	0.608	0.715			1	SUBCLONAL	1	TRUE	NA	0.95009940586748	12		507	3760	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117782	108117782	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054088-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	215	334	0	ENST00000278616.4:c.993G>C	p.Lys331Asn	p.K331N	ENST00000278616	NM_000051.3	331	aaG/aaC	8/63	0.95009940586748	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.95009940586748	1		334	225	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440867	52440867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054088-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	416	715	1	ENST00000460680.1:c.637C>T	p.Arg213Cys	p.R213C	ENST00000460680	NM_004656.3	213	Cgt/Tgt	8/17	0.95009940586748	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.95009940586748	1		716	441	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900243	101900243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054088-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	252	394	0	ENST00000374994.4:c.677G>A	p.Gly226Glu	p.G226E	ENST00000374994	NM_004612.2	226	gGa/gAa	4/9	1	2	FACETS	0.984	0.931	1	0.984	0.931	1	CLONAL	1	TRUE	1	0.95009940586748	2		394	539	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028022	69028022	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054088-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	82	497	0	ENST00000288368.4:c.3181G>C	p.Glu1061Gln	p.E1061Q	ENST00000288368	NM_024870.2	1061	Gaa/Caa	26/40	0.936632968853942	5	FACETS	0.452	0.398	0.511	0.113	0.099	0.128	SUBCLONAL	1	TRUE	1	0.95009940586748	5		497	926	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0054487-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	15	425	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.791	1	1	0.791	1	CLONAL	1	TRUE	1	0.408061997756273	2		425	69	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781476	3781476	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0054487-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	6	0	0	ENST00000262367.5:c.4891-2A>G		p.X1631_splice	ENST00000262367	NM_004380.2	1631			1	2	FACETS	0.291	0.174	0.447	0.291	0.174	0.447	SUBCLONAL	1	TRUE	1	0.408061997756273	2		0	101	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205108	123205109	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054487-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	16	209	0	ENST00000218089.9:c.2469dup	p.Glu824Ter	p.E824*	ENST00000218089	NM_001042749.1	823	tct/tcTt	25/35	1	1	FACETS	1	0.778	1	1	0.778	1	CLONAL	1	TRUE	0	0.408061997756273	1		209	61	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0054728-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	388	259	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.205829107653294	8	FACETS	0.946	0.903	0.99			1	CLONAL	7	TRUE	NA	0.205829107653294	8		259	921	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974769	21974770	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCCGT	rs1563892769	NA	P-0054728-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	13	208	0	ENST00000304494.5:c.52_57dup	p.Thr18_Ala19dup	p.T18_A19dup	ENST00000304494	NM_000077.4	18	-/ACGGCC	1/3	0.205829107653294	1	FACETS	0.47	0.335	0.635	0.47	0.335	0.635	SUBCLONAL	1	TRUE	0	0.205829107653294	1		208	241	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574000	7574000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054728-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	193	455	0	ENST00000269305.4:c.1027G>T	p.Glu343Ter	p.E343*	ENST00000269305	NM_001126112.2	343	Gag/Tag	10/11	0.205829107653294	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.205829107653294	2		455	890	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392035	81392035	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054728-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	18	335	0	ENST00000222390.5:c.242C>A	p.Pro81Gln	p.P81Q	ENST00000222390	NM_000601.4	81	cCa/cAa	2/18	1	2	FACETS	0.51	0.383	0.66	0.51	0.383	0.66	SUBCLONAL	1	TRUE	1	0.205829107653294	2		335	343	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105858	27105877	+	frameshift_variant	Frame_Shift_Del	DEL	TGTGGTGGACTGCTCAGATA	TGTGGTGGACTGCTCAGATA	-	novel	NA	P-0054728-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	90	634	0	ENST00000324856.7:c.5469_5488del	p.Phe1823LeufsTer9	p.F1823Lfs*9	ENST00000324856	NM_006015.4	1823	ttTGTGGTGGACTGCTCAGATAag/ttag	20/20	0.205829107653294	2	FACETS	1	0.975	1	0.686	0.61	0.768	CLONAL	1	TRUE	0	0.205829107653294	2		634	637	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058638	72058638	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054728-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	88	392	0	ENST00000357731.5:c.802C>A	p.Gln268Lys	p.Q268K	ENST00000357731	NM_173808.2	268	Caa/Aaa	6/7	0.205829107653294	2	FACETS	0.969	0.863	1	0.969	0.863	1	CLONAL	2	TRUE	0	0.205829107653294	2		392	441	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120460366	120460366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054728-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	115	475	0	ENST00000256646.2:c.5949G>T	p.Trp1983Cys	p.W1983C	ENST00000256646	NM_024408.3	1983	tgG/tgT	33/34	0.205829107653294	2	FACETS	0.853	0.77	0.941	0.853	0.77	0.941	CLONAL	2	TRUE	0	0.205829107653294	2		475	655	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163298065	163298065	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054728-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	35	558	0	ENST00000271452.3:c.246del	p.Leu83TyrfsTer6	p.L83Yfs*6	ENST00000271452	NM_145697.2	82	ttC/tt	4/14	1	2	FACETS	0.568	0.464	0.685	0.568	0.464	0.685	SUBCLONAL	1	TRUE	1	0.205829107653294	2		558	599	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123622	46123622	+	frameshift_variant,start_lost	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054728-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	33	278	0	ENST00000334344.6:c.4del	p.Ala2?	p.A2?	ENST00000334344	NM_152641.2	1	atG/at	1/21	1	2	FACETS	0.993	0.811	1	0.993	0.811	1	CLONAL	1	TRUE	1	0.205829107653294	2		278	323	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753261	42753261	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054728-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	72	876	1	ENST00000222329.4:c.1003C>T	p.Pro335Ser	p.P335S	ENST00000222329	NM_006494.2	335	Cct/Tct	4/4	1	2	FACETS	0.786	0.685	0.895	0.786	0.685	0.895	SUBCLONAL	1	TRUE	1	0.205829107653294	2		877	890	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023981	31023981	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054728-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	73	678	0	ENST00000375687.4:c.3466G>T	p.Gly1156Ter	p.G1156*	ENST00000375687	NM_015338.5	1156	Gga/Tga	13/13	0.105009068142734	3	FACETS	1	0.907	1	0.523	0.457	0.595	INDETERMINATE	1	TRUE	1	0.205829107653294	3		678	748	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967276	134967276	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs534330476	NA	P-0054728-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	91	644	0	ENST00000398015.3:c.2615C>A	p.Ala872Glu	p.A872E	ENST00000398015	NM_004441.4	872	gCg/gAg	14/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.205829107653294	2		644	723	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127525	55127525	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054728-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	33	456	0	ENST00000257290.5:c.313A>T	p.Thr105Ser	p.T105S	ENST00000257290	NM_006206.4	105	Act/Tct	3/23	1	2	FACETS	0.612	0.497	0.741	0.612	0.497	0.741	SUBCLONAL	1	TRUE	1	0.205829107653294	2		456	524	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230873	66230873	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0054728-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	40	435	0	ENST00000273854.3:c.2098A>T	p.Arg700Ter	p.R700*	ENST00000273854	NM_004439.5	700	Aga/Tga	12/18	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.205829107653294	2		435	380	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038460	180038460	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1400346855	NA	P-0054728-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	113	758	0	ENST00000261937.6:c.3557T>C	p.Met1186Thr	p.M1186T	ENST00000261937	NM_182925.4	1186	aTg/aCg	27/30	0.191389142874207	0	FACETS	0.688	0.62	0.759			1	SUBCLONAL	2	TRUE	0	0.205829107653294	0		758	634	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417436	139417445	+	frameshift_variant	Frame_Shift_Del	DEL	CGGTAGGAGC	CGGTAGGAGC	-	novel	NA	P-0054728-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	94	734	0	ENST00000277541.6:c.599_608del	p.Gly200AlafsTer74	p.G200Afs*74	ENST00000277541	NM_017617.3	200	gGCTCCTACCGc/gc	4/34	0.205829107653294	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.205829107653294	1		734	701	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0054790-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	32	425	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.202503721653849	2	FACETS	0.835	0.686	0.998	0.417	0.343	0.499	INDETERMINATE	1	FALSE	0	0.476247903969673	2		425	161	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214591	5214591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770889503	NA	P-0054790-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	8	459	0	ENST00000357368.4:c.4475G>A	p.Arg1492Gln	p.R1492Q	ENST00000357368	NM_002850.3	1492	cGg/cAg	29/38	0.20272521525	3	FACETS	0.132	0.084	0.194	0.066	0.042	0.097	INDETERMINATE	1	FALSE	1	0.476247903969673	3		459	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0054877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	249	328	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.605792062599751	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.605792062599751	1		328	563	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0054877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	79	307	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.354510480408244	1	FACETS	0.742	0.662	0.825	0.742	0.662	0.825	INDETERMINATE	1	TRUE	0	0.605792062599751	1		307	245	SUCCESS
APC	324	MSKCC	GRCh37	5	112175433	112175434	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0054877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	47	331	0	ENST00000257430.4:c.4143_4144del	p.Leu1382HisfsTer3	p.L1382Hfs*3	ENST00000257430	NM_000038.5	1381	cCA/c	16/16	0.354510480408244	1	FACETS	0.381	0.323	0.444	0.381	0.323	0.444	INDETERMINATE	1	TRUE	0	0.605792062599751	1		331	284	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741637	17741637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	149	525	1	ENST00000250003.3:c.308G>A	p.Arg103His	p.R103H	ENST00000250003	NM_002478.4	103	cGc/cAc	1/3	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.605792062599751	2		526	424	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518586	204518586	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	49	314	0	ENST00000367182.3:c.1249C>T	p.Leu417Phe	p.L417F	ENST00000367182	NM_001278516.1	417	Ctt/Ttt	11/11	0.307523633085894	1	FACETS	0.455	0.388	0.526	0.455	0.388	0.526	INDETERMINATE	1	TRUE	0	0.605792062599751	1		314	248	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987066	36987066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1325836054	NA	P-0054877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	138	1076	0	ENST00000354822.5:c.623G>A	p.Arg208Gln	p.R208Q	ENST00000354822	NM_001079668.2	208	cGa/cAa	3/3	0.605792062599751	1	FACETS	0.588	0.538	0.64	0.588	0.538	0.64	SUBCLONAL	1	TRUE	0	0.605792062599751	1		1076	540	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139837	55139837	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	111	738	1	ENST00000257290.5:c.1498C>T	p.Arg500Ter	p.R500*	ENST00000257290	NM_006206.4	500	Cga/Tga	10/23	0.43334174880384	1	FACETS	0.44	0.396	0.486	0.44	0.396	0.486	SUBCLONAL	1	TRUE	0	0.605792062599751	1		739	581	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0054896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	57	341	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.310744728866604	3	FACETS	1	0.966	1	0.711	0.615	0.815	CLONAL	1	TRUE	1	0.310744728866604	3		341	298	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0054896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	20	280	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.287691704064837	3	FACETS	0.808	0.622	1	0.404	0.311	0.512	CLONAL	1	TRUE	1	0.310744728866604	3		280	184	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0054896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	145	1063	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	0.310744728866604	2	FACETS	0.913	0.838	0.99	0.913	0.838	0.99	CLONAL	2	TRUE	0	0.310744728866604	2		1063	511	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268766	41268766	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	27	353	0	ENST00000349496.5:c.1004A>T	p.Lys335Ile	p.K335I	ENST00000349496	NM_001904.3	335	aAa/aTa	7/15	1	2	FACETS	0.882	0.707	1	0.882	0.707	1	CLONAL	1	TRUE	1	0.310744728866604	2		353	197	SUCCESS
APC	324	MSKCC	GRCh37	5	112175912	112175912	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201801	NA	P-0054896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	16	224	0	ENST00000257430.4:c.4621C>T	p.Gln1541Ter	p.Q1541*	ENST00000257430	NM_000038.5	1541	Cag/Tag	16/16	0.287691704064837	3	FACETS	1	0.859	1	0.62	0.465	0.798	CLONAL	1	TRUE	1	0.310744728866604	3		224	96	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732604	190732604	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs759191350	NA	P-0054896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	67	492	1	ENST00000441310.2:c.2422C>G	p.Leu808Val	p.L808V	ENST00000441310	NM_000534.4	808	Ctg/Gtg	11/13	0.287691704064837	3	FACETS	0.796	0.697	0.901	0.796	0.697	0.901	CLONAL	2	TRUE	1	0.310744728866604	3		493	313	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0054915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	111	253	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.989	0.898	1	0.989	0.898	1	CLONAL	1	TRUE	1	0.600222651345801	2		253	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1555525367	NA	P-0054915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	169	753	1	ENST00000269305.4:c.783-1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.5883065656637	1	FACETS	0.957	0.89	1	0.957	0.89	1	CLONAL	1	TRUE	0	0.600222651345801	1		754	412	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164884	106164884	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1339287432	NA	P-0054915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	139	544	0	ENST00000380013.4:c.3752C>T	p.Thr1251Met	p.T1251M	ENST00000380013	NM_001127208.2	1251	aCg/aTg	6/11	1	2	FACETS	0.949	0.87	1	0.949	0.87	1	CLONAL	1	TRUE	1	0.600222651345801	2		544	488	SUCCESS
APC	324	MSKCC	GRCh37	5	112128141	112128141	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0054915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	184	390	1	ENST00000257430.4:c.646-2A>C		p.X216_splice	ENST00000257430	NM_000038.5	216			0.600222651345801	2	FACETS	0.976	0.921	1	0.976	0.921	1	CLONAL	2	TRUE	0	0.600222651345801	2		391	314	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	88	366	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.484996356495654	3	FACETS	1	0.971	1	0.624	0.559	0.691	CLONAL	1	TRUE	1	0.622949202088907	3		366	297	SUCCESS
APC	324	MSKCC	GRCh37	5	112174885	112174886	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs864622106	NA	P-0054927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	54	270	0	ENST00000257430.4:c.3595_3596del	p.Lys1199GlufsTer8	p.K1199Efs*8	ENST00000257430	NM_000038.5	1198	tcAAag/tcag	16/16	0.622949202088907	1	FACETS	0.884	0.776	0.996	0.884	0.776	0.996	CLONAL	1	TRUE	0	0.622949202088907	1		270	135	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578232	7578232	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0054927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	516	749	0	ENST00000269305.4:c.617T>A	p.Leu206Ter	p.L206*	ENST00000269305	NM_001126112.2	206	tTg/tAg	6/11	0.622949202088907	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.622949202088907	1		749	881	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341701	8341701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766088715	NA	P-0054927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	109	486	0	ENST00000356435.5:c.4939G>A	p.Glu1647Lys	p.E1647K	ENST00000356435		1647	Gaa/Aaa	29/35	1	2	FACETS	0.854	0.772	0.938	0.854	0.772	0.938	CLONAL	1	TRUE	1	0.622949202088907	2		486	410	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221354	36221354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766608261	NA	P-0054927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1982	357	840	0	ENST00000222270.7:c.5188G>A	p.Val1730Met	p.V1730M	ENST00000222270	NM_014727.1	1730	Gtg/Atg	24/37	0.622949202088907	6	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.622949202088907	6		840	2339	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247816	59247816	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	386	819	0	ENST00000371222.2:c.927del	p.Lys309AsnfsTer5	p.K309Nfs*5	ENST00000371222	NM_002228.3	309	aaA/aa	1/1	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.622949202088907	2		819	1205	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243675653	243675653	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	43	309	0	ENST00000263826.5:c.1327A>G	p.Thr443Ala	p.T443A	ENST00000263826	NM_005465.4	443	Act/Gct	12/13	1	2	FACETS	0.803	0.682	0.932	0.803	0.682	0.932	CLONAL	1	TRUE	1	0.622949202088907	2		309	172	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94908714	94908714	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	111	591	0	ENST00000536441.1:c.1340C>G	p.Thr447Ser	p.T447S	ENST00000536441	NM_144665.3	447	aCt/aGt	9/10	0.412957953317388	1	FACETS	0.912	0.834	0.991	0.912	0.834	0.991	CLONAL	1	TRUE	0	0.622949202088907	1		591	269	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2107180	2107180	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0054927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	276	663	0	ENST00000219476.3:c.848+1G>T		p.X283_splice	ENST00000219476	NM_000548.3	283			1	2	FACETS	0.929	0.874	0.985	0.929	0.874	0.985	CLONAL	1	TRUE	1	0.622949202088907	2		663	954	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14628976	14628976	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	159	492	0	ENST00000254322.2:c.186G>C	p.Glu62Asp	p.E62D	ENST00000254322	NM_006145.1	62	gaG/gaC	1/3	NA	2	FACETS	0.475	0.434	0.517			1	INDETERMINATE	1	TRUE	NA	0.622949202088907	2		492	1075	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629105	14629105	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	117	339	0	ENST00000254322.2:c.57G>C	p.Glu19Asp	p.E19D	ENST00000254322	NM_006145.1	19	gaG/gaC	1/3	NA	2	FACETS	0.52	0.469	0.573			1	INDETERMINATE	1	TRUE	NA	0.622949202088907	2		339	723	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629141	14629141	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs779624471	NA	P-0054927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	128	413	0	ENST00000254322.2:c.21G>C	p.Gln7His	p.Q7H	ENST00000254322	NM_006145.1	7	caG/caC	1/3	NA	2	FACETS	0.519	0.47	0.57			1	INDETERMINATE	1	TRUE	NA	0.622949202088907	2		413	792	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657058	45657070	+	frameshift_variant	Frame_Shift_Del	DEL	ACGTCGCTGCCTA	ACGTCGCTGCCTA	-	novel	NA	P-0054927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	87	412	0	ENST00000407780.3:c.86_98del	p.Val29GlyfsTer15	p.V29Gfs*15	ENST00000407780	NM_001283052.1	29	gTAGGCAGCGACGTg/gg	3/7	1	2	FACETS	0.428	0.379	0.481	0.428	0.379	0.481	SUBCLONAL	1	TRUE	1	0.622949202088907	2		412	652	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294139	1294139	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1399684203	NA	P-0054927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	324	618	1	ENST00000310581.5:c.862G>A	p.Ala288Thr	p.A288T	ENST00000310581	NM_198253.2	288	Gcg/Acg	2/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.622949202088907	2		619	983	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0054937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	573	804	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.659790146789216	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.767314262817121	1		804	851	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602590	10602590	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	381	739	0	ENST00000171111.5:c.988A>G	p.Thr330Ala	p.T330A	ENST00000171111	NM_203500.1	330	Acc/Gcc	3/6	1	2	FACETS	0.959	0.912	1	0.959	0.912	1	CLONAL	1	TRUE	1	0.767314262817121	2		739	1036	SUCCESS
APC	324	MSKCC	GRCh37	5	112175485	112175485	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	180	410	0	ENST00000257430.4:c.4194del	p.Arg1399ValfsTer16	p.R1399Vfs*16	ENST00000257430	NM_000038.5	1398	agT/ag	16/16	0.767314262817121	1	FACETS	0.939	0.885	0.992	0.939	0.885	0.992	CLONAL	1	TRUE	0	0.767314262817121	1		410	308	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0054939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	149	425	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.23035512627161	5	FACETS	0.876	0.806	0.948	1	0.977	1	CLONAL	4	TRUE	2	0.23035512627161	5		425	497	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456893	149456893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3829986	NA	P-0054939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	186	882	0	ENST00000286301.3:c.835G>A	p.Val279Met	p.V279M	ENST00000286301	NM_005211.3	279	Gtg/Atg	6/22	0.229712044218195	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.23035512627161	3		882	843	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578260	7578260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204041	NA	P-0054939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	174	899	1	ENST00000269305.4:c.589G>A	p.Val197Met	p.V197M	ENST00000269305	NM_001126112.2	197	Gtg/Atg	6/11	0.23035512627161	2	FACETS	0.989	0.912	1	0.989	0.912	1	CLONAL	2	TRUE	0	0.23035512627161	2		900	764	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492772	56492773	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	196	804	0	ENST00000407977.2:c.166dup	p.Asp56GlyfsTer19	p.D56Gfs*19	ENST00000407977		56	gac/gGac	2/10	0.23035512627161	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.23035512627161	2		804	726	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100436	102100436	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	81	573	0	ENST00000282441.5:c.1280A>T	p.Asp427Val	p.D427V	ENST00000282441	NM_001130145.2	427	gAt/gTt	9/9	0.229712044218195	3	FACETS	1	0.967	1	0.644	0.568	0.726	CLONAL	1	TRUE	1	0.23035512627161	3		573	609	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0055008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	28	327	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.459500271319232	2	FACETS	1	0.933	1	0.664	0.547	0.789	CLONAL	1	TRUE	0	0.495927211682416	2		327	85	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106861	27106861	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	9	243	0	ENST00000324856.7:c.6472C>T	p.Arg2158Ter	p.R2158*	ENST00000324856	NM_006015.4	2158	Cga/Tga	20/20	0.495927211682416	3	FACETS	0.102	0.067	0.148	0.034	0.022	0.05	SUBCLONAL	1	TRUE	0	0.495927211682416	3		243	442	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355957	73355957	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	179	292	0	ENST00000377767.4:c.14del	p.Lys5ArgfsTer4	p.K5Rfs*4	ENST00000377767	NM_014953.3	5	aAg/ag	1/21	0.495927211682416	5	FACETS	0.778	0.718	0.84	0.389	0.359	0.42	SUBCLONAL	2	TRUE	1	0.495927211682416	5		292	809	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577131	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCTGT	novel	NA	P-0055008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	166	302	0	ENST00000269305.4:c.803_807dup	p.Phe270ThrfsTer77	p.F270Tfs*77	ENST00000269305	NM_001126112.2	269	-/ACAGC	8/11	0.314043117758718	3	FACETS	0.976	0.906	1	0.651	0.604	0.698	CLONAL	2	TRUE	0	0.495927211682416	3		302	428	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15818015	15818017	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0055008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	44	73	0	ENST00000307771.7:c.147_149del	p.Glu49del	p.E49del	ENST00000307771	NM_005089.3	48	GAG/-	3/11	0.495927211682416	4	FACETS	1	0.948	1			1	CLONAL	3	TRUE	NA	0.495927211682416	4		73	77	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0055063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	35	425	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.12	2		425	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0055063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	44	632	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.735	0.614	0.87	0.735	0.614	0.87	SUBCLONAL	1	TRUE	1	0.12	2		632	998	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0055063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	27	410	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.775	0.615	0.959	0.775	0.615	0.959	CLONAL	1	TRUE	1	0.12	2		410	581	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450243	50450243	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757521297	NA	P-0055063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	34	482	0	ENST00000331340.3:c.427C>T	p.Arg143Trp	p.R143W	ENST00000331340	NM_006060.4	143	Cgg/Tgg	5/8	1	2	FACETS	0.979	0.798	1	0.979	0.798	1	CLONAL	1	TRUE	1	0.12	2		482	579	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0055081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	286	1110	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.698186487569969	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.698186487569969	1		1111	484	SUCCESS
APC	324	MSKCC	GRCh37	5	112175429	112175430	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0055081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	72	383	0	ENST00000257430.4:c.4142dup	p.Leu1382ThrfsTer4	p.L1382Tfs*4	ENST00000257430	NM_000038.5	1380	acc/aCcc	16/16	0.351932447544297	1	FACETS	0.439	0.387	0.494	0.439	0.387	0.494	INDETERMINATE	1	TRUE	0	0.698186487569969	1		383	306	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120461	70120461	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	158	1098	0	ENST00000245479.2:c.1464del	p.Ile489SerfsTer34	p.I489Sfs*34	ENST00000245479	NM_000346.3	488	tCc/tc	3/3	0.351932447544297	1	FACETS	0.389	0.356	0.422	0.389	0.356	0.422	INDETERMINATE	1	TRUE	0	0.698186487569969	1		1098	758	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435691	18435691	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	62	238	0	ENST00000266497.5:c.676G>T	p.Glu226Ter	p.E226*	ENST00000266497		226	Gag/Tag	1/31	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.698186487569969	2		238	175	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251755	212251755	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	51	511	0	ENST00000342788.4:c.3304T>G	p.Phe1102Val	p.F1102V	ENST00000342788	NM_005235.2	1102	Ttt/Gtt	27/28	1	2	FACETS	0.339	0.288	0.394	0.339	0.288	0.394	SUBCLONAL	1	TRUE	1	0.698186487569969	2		511	431	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24158957	24158957	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	91	740	0	ENST00000263121.7:c.629A>C	p.Glu210Ala	p.E210A	ENST00000263121	NM_003073.3	210	gAg/gCg	6/9	0.351932447544297	1	FACETS	0.363	0.323	0.404	0.363	0.323	0.404	INDETERMINATE	1	TRUE	0	0.698186487569969	1		740	468	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505636	186505723	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGATCTACCTACCAATCGTGAAAACTATATTCACAGGTGAGAAGCCAGCATCTTGGCTGTATTGAAAAAAATTCATACGTTTTTCTAC	TGATCTACCTACCAATCGTGAAAACTATATTCACAGGTGAGAAGCCAGCATCTTGGCTGTATTGAAAAAAATTCATACGTTTTTCTAC	-	novel	NA	P-0055081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	105	432	0	ENST00000323963.5:c.1046_1079+54del		p.X349_splice	ENST00000323963		349		10/11	1	2	FACETS	0.934	0.847	1	0.934	0.847	1	CLONAL	1	TRUE	1	0.698186487569969	2		432	322	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467826	66467875	+	frameshift_variant	Frame_Shift_Del	DEL	TTACAGGTCCCCAGTCCTCCAGGAAGGCTGTTGCAGTCCCGCAGGGTAAA	TTACAGGTCCCCAGTCCTCCAGGAAGGCTGTTGCAGTCCCGCAGGGTAAA	-	novel	NA	P-0055081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	45	478	0	ENST00000273854.3:c.394_443del	p.Phe132GlyfsTer4	p.F132Gfs*4	ENST00000273854	NM_004439.5	132	TTTACCCTGCGGGACTGCAACAGCCTTCCTGGAGGACTGGGGACCTGTAAg/g	3/18	0.351932447544297	1	FACETS	0.295	0.249	0.346	0.295	0.249	0.346	INDETERMINATE	1	TRUE	0	0.698186487569969	1		478	284	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	69	425	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.357837185271751	2		425	365	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693003	89693003	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs786204900	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	42	395	0	ENST00000371953.3:c.491del	p.Lys164ArgfsTer3	p.K164Rfs*3	ENST00000371953	NM_000314.4	163	Aaa/aa	5/9	1	2	FACETS	0.755	0.633	0.889	0.755	0.633	0.889	SUBCLONAL	1	TRUE	1	0.357837185271751	2		395	311	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	69	468	1	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.588	0.512	0.67	0.588	0.512	0.67	SUBCLONAL	1	TRUE	1	0.357837185271751	2		469	656	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	51	156	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.796	0.679	0.923	0.796	0.679	0.923	CLONAL	1	TRUE	1	0.357837185271751	2		157	358	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	99	478	4	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.749	0.668	0.834	0.749	0.668	0.834	SUBCLONAL	1	TRUE	1	0.357837185271751	2		482	739	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913252	39913253	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs797044647	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	135	587	0	ENST00000378444.4:c.4862dup	p.Gly1622ArgfsTer7	p.G1622Rfs*7	ENST00000378444	NM_001123385.1	1621	cca/ccCa	14/15	1	2	FACETS	0.993	0.903	1	0.993	0.903	1	CLONAL	1	TRUE	1	0.357837185271751	2		587	760	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	26	98	0	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	2	FACETS	0.515	0.409	0.637	0.515	0.409	0.637	SUBCLONAL	1	TRUE	1	0.357837185271751	2		98	282	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023559	27023560	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	31	431	1	ENST00000324856.7:c.671dup	p.Pro225AlafsTer175	p.P225Afs*175	ENST00000324856	NM_006015.4	222	tac/taCc	1/20	1	2	FACETS	0.312	0.251	0.38	0.312	0.251	0.38	SUBCLONAL	1	TRUE	1	0.357837185271751	2		432	556	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266849	18266849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201370957	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	40	439	2	ENST00000222254.8:c.160G>A	p.Val54Met	p.V54M	ENST00000222254	NM_005027.3	54	Gtg/Atg	2/16	1	2	FACETS	0.344	0.285	0.41	0.344	0.285	0.41	SUBCLONAL	1	TRUE	1	0.357837185271751	2		441	650	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391119	139391119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780869345	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	171	854	0	ENST00000277541.6:c.7072G>A	p.Ala2358Thr	p.A2358T	ENST00000277541	NM_017617.3	2358	Gcc/Acc	34/34	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.357837185271751	2		854	941	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956964	2956964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395288944	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	143	651	0	ENST00000396946.4:c.2663G>A	p.Arg888His	p.R888H	ENST00000396946	NM_032415.4	888	cGt/cAt	20/25	1	2	FACETS	0.889	0.81	0.972	0.889	0.81	0.972	CLONAL	1	TRUE	1	0.357837185271751	2		651	899	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777898	3777898	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	78	928	1	ENST00000262367.5:c.7150del	p.His2384ThrfsTer12	p.H2384Tfs*12	ENST00000262367	NM_004380.2	2384	Cac/ac	31/31	1	2	FACETS	0.376	0.329	0.427	0.376	0.329	0.427	SUBCLONAL	1	TRUE	1	0.357837185271751	2		929	1158	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440912	56440912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	288	695	0	ENST00000407977.2:c.425C>T	p.Thr142Ile	p.T142I	ENST00000407977		142	aCt/aTt	4/10	0.357837185271751	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.357837185271751	2		695	785	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518020	187518020	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755404071	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	127	552	0	ENST00000441802.2:c.12674C>T	p.Thr4225Met	p.T4225M	ENST00000441802	NM_005245.3	4225	aCg/aTg	25/27	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.357837185271751	2		552	668	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505443	157505443	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554231830	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	48	513	0	ENST00000346085.5:c.3428del	p.Lys1143SerfsTer68	p.K1143Sfs*68	ENST00000346085	NM_020732.3	1142	Aaa/aa	13/20	1	2	FACETS	0.35	0.295	0.411	0.35	0.295	0.411	SUBCLONAL	1	TRUE	1	0.357837185271751	2		513	767	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885939	111885939	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	136	605	0	ENST00000341259.2:c.1566del	p.Glu523SerfsTer25	p.E523Sfs*25	ENST00000341259	NM_005475.2	521	Ccc/cc	8/8	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.357837185271751	2		605	742	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713414	40713414	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	117	811	0	ENST00000373198.4:c.4101del	p.Ser1368ProfsTer31	p.S1368Pfs*31	ENST00000373198	NM_133170.3	1367	ccC/cc	30/32	1	2	FACETS	0.762	0.687	0.842	0.762	0.687	0.842	SUBCLONAL	1	TRUE	1	0.357837185271751	2		811	858	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348561	56348561	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	73	337	0	ENST00000348428.3:c.374del	p.Pro125GlnfsTer3	p.P125Qfs*3	ENST00000348428	NM_006785.3	123	agC/ag	2/17	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.357837185271751	2		337	368	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486050	29486050	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1438566555	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	44	316	0	ENST00000356175.3:c.233del	p.Asn78IlefsTer7	p.N78Ifs*7	ENST00000356175	NM_000267.3	76	gAa/ga	3/57	1	2	FACETS	0.863	0.728	1	0.863	0.728	1	CLONAL	1	TRUE	1	0.357837185271751	2		316	285	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	221	549	5	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.357837185271751	2		554	862	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324892	31324892	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs765875917	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	59	422	0	ENST00000412585.2:c.44del	p.Ala15GlyfsTer5	p.A15Gfs*5	ENST00000412585	NM_005514.6	15	gCg/gg	1/8	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.357837185271751	2		422	257	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910533	29910533	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	22	262	0	ENST00000376809.5:c.74-1G>T		p.X25_splice	ENST00000376809	NM_002116.7	25			0.357837185271751	1	FACETS	0.37	0.287	0.466	0.37	0.287	0.466	SUBCLONAL	1	TRUE	0	0.357837185271751	1		262	273	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405962	49405962	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	124	246	0	ENST00000418115.1:c.176A>G	p.Asp59Gly	p.D59G	ENST00000418115	NM_001664.2	59	gAc/gGc	3/5	1	2	FACETS	0.916	0.829	1	0.916	0.829	1	CLONAL	1	TRUE	1	0.357837185271751	2		246	757	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976482	7976482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	132	648	0	ENST00000319144.4:c.1910G>A	p.Arg637Gln	p.R637Q	ENST00000319144	NM_001139.2	637	cGa/cAa	14/15	1	2	FACETS	0.968	0.88	1	0.968	0.88	1	CLONAL	1	TRUE	1	0.357837185271751	2		648	762	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097688	27097688	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	75	586	0	ENST00000324856.7:c.3281del	p.Lys1094SerfsTer67	p.K1094Sfs*67	ENST00000324856	NM_006015.4	1093	Aaa/aa	12/20	1	2	FACETS	0.559	0.489	0.634	0.559	0.489	0.634	SUBCLONAL	1	TRUE	1	0.357837185271751	2		586	750	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815802	32815802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	110	673	0	ENST00000354258.4:c.1814G>A	p.Ser605Asn	p.S605N	ENST00000354258	NM_000593.5	605	aGc/aAc	8/11	1	2	FACETS	0.684	0.614	0.758	0.684	0.614	0.758	SUBCLONAL	1	TRUE	1	0.357837185271751	2		673	899	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821048	32821048	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	71	900	5	ENST00000354258.4:c.546del	p.Ser184ProfsTer54	p.S184Pfs*54	ENST00000354258	NM_000593.5	182	ccC/cc	1/11	1	2	FACETS	0.374	0.325	0.428	0.374	0.325	0.428	SUBCLONAL	1	TRUE	1	0.357837185271751	2		905	1060	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56801430	56801430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881932	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	83	498	1	ENST00000337432.4:c.934C>T	p.Arg312Trp	p.R312W	ENST00000337432	NM_058216.2	312	Cgg/Tgg	7/9	0.357837185271751	2	FACETS	0.926	0.82	1	0.463	0.41	0.52	CLONAL	1	TRUE	0	0.357837185271751	2		499	501	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249911	110249911	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	120	621	0	ENST00000374672.4:c.764C>A	p.Pro255His	p.P255H	ENST00000374672	NM_004235.4	255	cCt/cAt	3/5	1	2	FACETS	0.96	0.868	1	0.96	0.868	1	CLONAL	1	TRUE	1	0.357837185271751	2		621	699	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133898	41133898	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	89	406	0	ENST00000379561.5:c.1730del	p.Gly577AlafsTer5	p.G577Afs*5	ENST00000379561	NM_002015.3	577	gGc/gc	2/3	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.357837185271751	2		406	484	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753149	42753151	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs199960550	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	133	792	7	ENST00000222329.4:c.1113_1115del	p.Ser373del	p.S373del	ENST00000222329	NM_006494.2	371	tcTTCc/tcc	4/4	1	2	FACETS	0.855	0.777	0.938	0.855	0.777	0.938	CLONAL	1	TRUE	1	0.357837185271751	2		799	869	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468397	89468398	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1467832547	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	52	276	1	ENST00000336596.2:c.1938dup	p.Glu647ArgfsTer7	p.E647Rfs*7	ENST00000336596	NM_005233.5	644	tca/tcAa	11/17	1	2	FACETS	0.905	0.775	1	0.905	0.775	1	CLONAL	1	TRUE	1	0.357837185271751	2		277	321	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129222	152129222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	72	752	1	ENST00000206249.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000206249	NM_000125.3	59	Gcc/Acc	1/8	1	2	FACETS	0.436	0.379	0.496	0.436	0.379	0.496	SUBCLONAL	1	TRUE	1	0.357837185271751	2		753	924	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347191	89347191	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	123	672	0	ENST00000301030.4:c.5759C>T	p.Thr1920Met	p.T1920M	ENST00000301030	NM_001256183.1	1920	aCg/aTg	9/13	1	2	FACETS	0.839	0.759	0.924	0.839	0.759	0.924	CLONAL	1	TRUE	1	0.357837185271751	2		672	819	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458005	120458005	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	140	592	0	ENST00000256646.2:c.7340del	p.Gly2447ValfsTer43	p.G2447Vfs*43	ENST00000256646	NM_024408.3	2447	gGt/gt	34/34	1	2	FACETS	0.957	0.872	1	0.957	0.872	1	CLONAL	1	TRUE	1	0.357837185271751	2		592	818	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685497	29685497	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1417908560	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	32	292	0	ENST00000356175.3:c.7908-1G>T		p.X2636_splice	ENST00000356175	NM_000267.3	2636			1	2	FACETS	0.715	0.584	0.863	0.715	0.584	0.863	SUBCLONAL	1	TRUE	1	0.357837185271751	2		292	250	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443806	49443806	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556879323	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	117	841	0	ENST00000301067.7:c.3565C>T	p.Arg1189Cys	p.R1189C	ENST00000301067	NM_003482.3	1189	Cgt/Tgt	11/54	1	2	FACETS	0.604	0.544	0.669	0.604	0.544	0.669	SUBCLONAL	1	TRUE	1	0.357837185271751	2		841	1082	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950349	17950349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755309429	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	195	797	0	ENST00000458235.1:c.1378G>A	p.Gly460Arg	p.G460R	ENST00000458235	NM_000215.3	460	Ggg/Agg	10/24	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.357837185271751	2		797	1023	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323268	31323268	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1322740343	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	28	297	0	ENST00000412585.2:c.721T>C	p.Trp241Arg	p.W241R	ENST00000412585	NM_005514.6	241	Tgg/Cgg	4/8	1	2	FACETS	0.378	0.302	0.465	0.378	0.302	0.465	SUBCLONAL	1	TRUE	1	0.357837185271751	2		297	414	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436060	49436060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777415982	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	48	645	2	ENST00000301067.7:c.5921C>T	p.Thr1974Met	p.T1974M	ENST00000301067	NM_003482.3	1974	aCg/aTg	28/54	1	2	FACETS	0.388	0.327	0.455	0.388	0.327	0.455	SUBCLONAL	1	TRUE	1	0.357837185271751	2		647	692	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128419995	128419995	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1238730432	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	104	229	0	ENST00000265960.3:c.433C>T	p.Arg145Cys	p.R145C	ENST00000265960	NM_001006617.1	145	Cgc/Tgc	4/12	1	2	FACETS	0.788	0.705	0.875	0.788	0.705	0.875	SUBCLONAL	1	TRUE	1	0.357837185271751	2		229	738	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760966	59760967	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs753683450	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	55	567	0	ENST00000259008.2:c.3440dup	p.Asn1147LysfsTer2	p.N1147Kfs*2	ENST00000259008	NM_032043.2	1147	aat/aaAt	20/20	0.357837185271751	2	FACETS	0.561	0.48	0.65	0.28	0.24	0.325	SUBCLONAL	1	TRUE	0	0.357837185271751	2		567	548	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744384	41744385	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1450387909	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	161	736	0	ENST00000301178.4:c.1010dup	p.Glu338Ter	p.E338*	ENST00000301178	NM_021913.4	335	ggc/ggCc	8/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.357837185271751	2		736	799	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971057	21971057	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894094	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	42	423	0	ENST00000304494.5:c.301G>A	p.Gly101Arg	p.G101R	ENST00000304494	NM_000077.4	101	Ggg/Agg	2/3	1	2	FACETS	0.404	0.337	0.479	0.404	0.337	0.479	SUBCLONAL	1	TRUE	1	0.357837185271751	2		423	581	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934234	39934234	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs369585835	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	197	763	0	ENST00000378444.4:c.365T>C	p.Met122Thr	p.M122T	ENST00000378444	NM_001123385.1	122	aTg/aCg	4/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.357837185271751	2		763	944	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420203	49420204	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	95	752	0	ENST00000301067.7:c.15545dup	p.Leu5183ProfsTer16	p.L5183Pfs*16	ENST00000301067	NM_003482.3	5182	ggc/ggGc	48/54	1	2	FACETS	0.58	0.516	0.649	0.58	0.516	0.649	SUBCLONAL	1	TRUE	1	0.357837185271751	2		752	915	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313250	30313250	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	37	613	1	ENST00000262643.3:c.944A>G	p.Lys315Arg	p.K315R	ENST00000262643	NM_001238.2	315	aAg/aGg	10/12	1	2	FACETS	0.288	0.237	0.347	0.288	0.237	0.347	SUBCLONAL	1	TRUE	1	0.357837185271751	2		614	717	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858254	59858254	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs780020495	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	31	569	1	ENST00000259008.2:c.1741C>T	p.Arg581Ter	p.R581*	ENST00000259008	NM_032043.2	581	Cga/Tga	12/20	0.357837185271751	2	FACETS	0.287	0.231	0.35	0.143	0.115	0.175	SUBCLONAL	1	TRUE	0	0.357837185271751	2		570	604	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943770	71943770	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	49	770	0	ENST00000298229.2:c.1815del	p.Phe605LeufsTer16	p.F605Lfs*16	ENST00000298229	NM_001567.3	605	Ttt/tt	15/28	1	2	FACETS	0.281	0.236	0.329	0.281	0.236	0.329	SUBCLONAL	1	TRUE	1	0.357837185271751	2		770	976	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437499	49437499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs186948725	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	169	713	3	ENST00000301067.7:c.5386C>T	p.Arg1796Trp	p.R1796W	ENST00000301067	NM_003482.3	1796	Cgg/Tgg	23/54	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.357837185271751	2		716	906	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059307	42059307	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	100	407	0	ENST00000219905.7:c.9027G>T	p.Lys3009Asn	p.K3009N	ENST00000219905	NM_001164273.1	3009	aaG/aaT	24/24	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.357837185271751	2		407	506	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639765	3639765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1418445974	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	141	916	0	ENST00000294008.3:c.3874C>T	p.Pro1292Ser	p.P1292S	ENST00000294008	NM_032444.2	1292	Ccc/Tcc	12/15	1	2	FACETS	0.765	0.696	0.838	0.765	0.696	0.838	SUBCLONAL	1	TRUE	1	0.357837185271751	2		916	1030	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348245	89348245	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	188	815	3	ENST00000301030.4:c.4705A>G	p.Arg1569Gly	p.R1569G	ENST00000301030	NM_001256183.1	1569	Agg/Ggg	9/13	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.357837185271751	2		818	1046	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322671	30322671	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	95	649	0	ENST00000322652.5:c.1684A>G	p.Asn562Asp	p.N562D	ENST00000322652	NM_015355.2	562	Aat/Gat	14/16	1	2	FACETS	0.873	0.779	0.974	0.873	0.779	0.974	CLONAL	1	TRUE	1	0.357837185271751	2		649	608	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45423012	45423012	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	103	407	2	ENST00000262160.6:c.116del	p.Lys39SerfsTer7	p.K39Sfs*7	ENST00000262160	NM_005901.5	39	aAg/ag	2/11	1	2	FACETS	0.969	0.869	1	0.969	0.869	1	CLONAL	1	TRUE	1	0.357837185271751	2		409	594	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752972	42752972	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	180	835	0	ENST00000222329.4:c.1292C>A	p.Ser431Ter	p.S431*	ENST00000222329	NM_006494.2	431	tCg/tAg	4/4	1	2	FACETS	0.989	0.912	1	0.989	0.912	1	CLONAL	1	TRUE	1	0.357837185271751	2		835	1017	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912892	50912892	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	122	757	0	ENST00000440232.2:c.2123T>C	p.Val708Ala	p.V708A	ENST00000440232	NM_002691.3	708	gTg/gCg	17/27	1	2	FACETS	0.807	0.729	0.889	0.807	0.729	0.889	CLONAL	1	TRUE	1	0.357837185271751	2		757	845	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422475	225422475	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	84	421	0	ENST00000264414.4:c.165G>T	p.Glu55Asp	p.E55D	ENST00000264414	NM_003590.4	55	gaG/gaT	2/16	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.357837185271751	2		421	444	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024631	31024632	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	122	612	0	ENST00000375687.4:c.4118_4119del	p.Phe1373CysfsTer6	p.F1373Cfs*6	ENST00000375687	NM_015338.5	1372	acTTtt/actt	13/13	1	2	FACETS	0.924	0.836	1	0.924	0.836	1	CLONAL	1	TRUE	1	0.357837185271751	2		612	738	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626122	12626123	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	31	399	0	ENST00000251849.4:c.1837_1838del	p.Leu613ThrfsTer19	p.L613Tfs*19	ENST00000251849	NM_002880.3	613	CTa/a	17/17	1	2	FACETS	0.331	0.267	0.404	0.331	0.267	0.404	SUBCLONAL	1	TRUE	1	0.357837185271751	2		399	523	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670539	134670540	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	149	747	0	ENST00000398015.3:c.453dup	p.Gly152TrpfsTer109	p.G152Wfs*109	ENST00000398015	NM_004441.4	150	-/T	3/16	1	2	FACETS	0.976	0.892	1	0.976	0.892	1	CLONAL	1	TRUE	1	0.357837185271751	2		747	853	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281731	142281731	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	47	619	0	ENST00000350721.4:c.513G>A	p.Trp171Ter	p.W171*	ENST00000350721	NM_001184.3	171	tgG/tgA	4/47	1	2	FACETS	0.494	0.416	0.579	0.494	0.416	0.579	SUBCLONAL	1	TRUE	1	0.357837185271751	2		619	532	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912291	29912291	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	80	608	0	ENST00000376809.5:c.912del	p.Thr305ProfsTer17	p.T305Pfs*17	ENST00000376809	NM_002116.7	304	Ccc/cc	5/8	0.357837185271751	1	FACETS	0.561	0.493	0.633	0.561	0.493	0.633	SUBCLONAL	1	TRUE	0	0.357837185271751	1		608	655	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323279	31323279	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	30	213	0	ENST00000412585.2:c.710T>C	p.Ile237Thr	p.I237T	ENST00000412585	NM_005514.6	237	aTc/aCc	4/8	1	2	FACETS	0.572	0.462	0.696	0.572	0.462	0.696	SUBCLONAL	1	TRUE	1	0.357837185271751	2		213	293	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820949	32820949	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	59	865	0	ENST00000354258.4:c.645del	p.His215GlnfsTer23	p.H215Qfs*23	ENST00000354258	NM_000593.5	215	caC/ca	1/11	1	2	FACETS	0.316	0.27	0.365	0.316	0.27	0.365	SUBCLONAL	1	TRUE	1	0.357837185271751	2		865	1045	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821191	32821191	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	135	794	0	ENST00000354258.4:c.403del	p.Val135SerfsTer22	p.V135Sfs*22	ENST00000354258	NM_000593.5	135	Gtc/tc	1/11	1	2	FACETS	0.762	0.692	0.836	0.762	0.692	0.836	SUBCLONAL	1	TRUE	1	0.357837185271751	2		794	990	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851863	128851863	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	64	758	0	ENST00000249373.3:c.1937-2A>G		p.X646_splice	ENST00000249373	NM_005631.4	646			1	2	FACETS	0.435	0.376	0.5	0.435	0.376	0.5	SUBCLONAL	1	TRUE	1	0.357837185271751	2		758	822	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141545652	141545652	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	196	735	1	ENST00000220592.5:c.2186A>C	p.Asn729Thr	p.N729T	ENST00000220592	NM_012154.3	729	aAc/aCc	17/19	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.357837185271751	2		736	990	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080244	5080244	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	24	245	0	ENST00000381652.3:c.2147T>C	p.Ile716Thr	p.I716T	ENST00000381652	NM_004972.3	716	aTa/aCa	17/25	1	2	FACETS	0.636	0.501	0.789	0.636	0.501	0.789	SUBCLONAL	1	TRUE	1	0.357837185271751	2		245	211	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0055089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	174	192	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.949	0.878	1	0.949	0.878	1	CLONAL	1	TRUE	1	0.592301072606476	2		192	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0055089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	370	803	0	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	0.592301072606476	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.592301072606476	1		803	781	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278094	41278094	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	178	473	0	ENST00000349496.5:c.1970C>A	p.Ala657Asp	p.A657D	ENST00000349496	NM_001904.3	657	gCt/gAt	13/15	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.592301072606476	2		473	582	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950475	68950475	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371711855	NA	P-0055089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	157	603	0	ENST00000288368.4:c.787C>T	p.Arg263Trp	p.R263W	ENST00000288368	NM_024870.2	263	Cgg/Tgg	7/40	1	2	FACETS	0.873	0.803	0.946	0.873	0.803	0.946	CLONAL	1	TRUE	1	0.592301072606476	2		603	607	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266046	41266665	+	splice_donor_variant,splice_acceptor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	GAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCAAGATGATGCAGAACTTGCCACACGTGCAATCCCT	GAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCAAGATGATGCAGAACTTGCCACACGTGCAATCCCT	-	novel	NA	P-0055089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	85	367	0	ENST00000349496.5:c.47_466del		p.X16_splice	ENST00000349496	NM_001904.3	16	GAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCAAGATGATGCAGAACTTGCCACACGTGCAATCCCT/-	3-4/15	1	2	FACETS	0.703	0.625	0.786	0.703	0.625	0.786	SUBCLONAL	1	TRUE	1	0.592301072606476	2		367	408	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266217	41266217	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	94	470	0	ENST00000349496.5:c.214C>T	p.Gln72Ter	p.Q72*	ENST00000349496	NM_001904.3	72	Cag/Tag	3/15	1	2	FACETS	0.678	0.606	0.754	0.678	0.606	0.754	SUBCLONAL	1	TRUE	1	0.592301072606476	2		470	468	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105578	27105578	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	233	682	0	ENST00000324856.7:c.5192del	p.Leu1731Ter	p.L1731*	ENST00000324856	NM_006015.4	1730	aTt/at	20/20	0.592301072606476	1	FACETS	0.918	0.863	0.975	0.918	0.863	0.975	CLONAL	1	TRUE	0	0.592301072606476	1		682	603	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604610	55604610	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	224	703	0	ENST00000288135.5:c.2818G>A	p.Ala940Thr	p.A940T	ENST00000288135	NM_000222.2	940	Gca/Aca	21/21	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.592301072606476	2		703	744	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177798	56177798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	175	439	0	ENST00000399503.3:c.2771C>T	p.Ser924Leu	p.S924L	ENST00000399503	NM_005921.1	924	tCa/tTa	14/20	0.592301072606476	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.592301072606476	1		439	346	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751420	57751420	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	191	538	1	ENST00000274289.3:c.1571C>A	p.Thr524Asn	p.T524N	ENST00000274289	NM_006622.3	524	aCc/aAc	11/14	0.592301072606476	1	FACETS	0.987	0.922	1	0.987	0.922	1	CLONAL	1	TRUE	0	0.592301072606476	1		539	460	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0055091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	74	425	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.356711895555057	2		425	404	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0055091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	44	315	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.356711895555057	2		315	215	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560460	95560460	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	115	580	0	ENST00000393063.1:c.5129C>T	p.Ala1710Val	p.A1710V	ENST00000393063	NM_030621.3	1710	gCg/gTg	25/28	1	2	FACETS	0.88	0.793	0.971	0.88	0.793	0.971	CLONAL	1	TRUE	1	0.356711895555057	2		580	733	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578217	7578218	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0055091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	146	835	0	ENST00000269305.4:c.631_632del	p.Thr211PhefsTer4	p.T211Ffs*4	ENST00000269305	NM_001126112.2	211	ACt/t	6/11	0.356711895555057	1	FACETS	0.92	0.841	1	0.92	0.841	1	CLONAL	1	TRUE	0	0.356711895555057	1		835	731	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400765	72400765	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	42	301	0	ENST00000357731.5:c.406C>A	p.Gln136Lys	p.Q136K	ENST00000357731	NM_173808.2	136	Caa/Aaa	2/7	1	2	FACETS	0.859	0.722	1	0.859	0.722	1	CLONAL	1	TRUE	1	0.356711895555057	2		301	274	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0055116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	53	870	2	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	0.203730509158939	1	FACETS	0.799	0.681	0.928	0.799	0.681	0.928	CLONAL	1	TRUE	0	0.203730509158939	1		872	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0055116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	14	400	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.203730509158939	1	FACETS	0.185	0.132	0.248	0.185	0.132	0.248	SUBCLONAL	1	TRUE	0	0.203730509158939	1		400	669	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0055116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	54	555	1	ENST00000311936.3:c.180_181delinsAA	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggAAaa	3/5	1	2	FACETS	0.841	0.718	0.977	0.841	0.718	0.977	CLONAL	1	TRUE	1	0.203730509158939	2		556	630	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38137094	38137094	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1351115556	NA	P-0055116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	69	634	1	ENST00000317025.8:c.3724C>T	p.Arg1242Ter	p.R1242*	ENST00000317025	NM_023034.1	1242	Cga/Tga	21/24	1	2	FACETS	0.839	0.73	0.958	0.839	0.73	0.958	CLONAL	1	TRUE	1	0.203730509158939	2		635	807	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438069	49438069	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	39	728	0	ENST00000301067.7:c.5102T>C	p.Val1701Ala	p.V1701A	ENST00000301067	NM_003482.3	1701	gTg/gCg	21/54	1	2	FACETS	0.618	0.511	0.737	0.618	0.511	0.737	SUBCLONAL	1	TRUE	1	0.203730509158939	2		728	620	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442546	49442546	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	25	368	0	ENST00000301067.7:c.4027G>C	p.Asp1343His	p.D1343H	ENST00000301067	NM_003482.3	1343	Gac/Cac	13/54	1	2	FACETS	0.609	0.479	0.758	0.609	0.479	0.758	SUBCLONAL	1	TRUE	1	0.203730509158939	2		368	403	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435863	56435863	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0055116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	44	572	0	ENST00000407977.2:c.1274C>G	p.Ser425Ter	p.S425*	ENST00000407977		425	tCa/tGa	9/10	0.203730509158939	1	FACETS	0.926	0.778	1	0.926	0.778	1	CLONAL	1	TRUE	0	0.203730509158939	1		572	419	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872446	136872446	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	18	218	0	ENST00000241393.3:c.1052C>G	p.Ser351Cys	p.S351C	ENST00000241393	NM_003467.2	351	tCc/tGc	2/2	1	2	FACETS	0.647	0.487	0.836	0.647	0.487	0.836	SUBCLONAL	1	TRUE	1	0.203730509158939	2		218	273	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931285	131931285	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	42	359	0	ENST00000265335.6:c.1990G>C	p.Ala664Pro	p.A664P	ENST00000265335		664	Gca/Cca	13/25	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.203730509158939	2		359	374	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372392	55372392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	44	839	1	ENST00000297316.4:c.1082C>T	p.Thr361Met	p.T361M	ENST00000297316	NM_022454.3	361	aCg/aTg	2/2	1	2	FACETS	0.749	0.627	0.883	0.749	0.627	0.883	SUBCLONAL	1	TRUE	1	0.203730509158939	2		840	577	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139794068	139794069	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0055116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	66	663	1	ENST00000247668.2:c.211_212delinsTT	p.Ala71Phe	p.A71F	ENST00000247668	NM_021138.3	71	GCc/TTc	3/11	0.178468926189966	1	FACETS	0.664	0.574	0.76	0.664	0.574	0.76	SUBCLONAL	1	TRUE	0	0.203730509158939	1		664	877	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0055126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	481	1110	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.87929587743586	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.891411018066987	1		1111	591	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650681	18650681	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	74	276	0	ENST00000266497.5:c.2892A>C	p.Gln964His	p.Q964H	ENST00000266497		964	caA/caC	20/31	0.273986429483843	1	FACETS	0.253	0.222	0.285	0.253	0.222	0.285	INDETERMINATE	1	TRUE	0	0.891411018066987	1		276	364	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78797019	78797019	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	107	488	0	ENST00000306801.3:c.1132A>C	p.Met378Leu	p.M378L	ENST00000306801	NM_020761.2	378	Atg/Ctg	9/34	1	2	FACETS	0.351	0.315	0.389	0.351	0.315	0.389	SUBCLONAL	1	TRUE	1	0.891411018066987	2		488	684	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279605	18279605	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	463	729	0	ENST00000222254.8:c.1878G>C	p.Lys626Asn	p.K626N	ENST00000222254	NM_005027.3	626	aaG/aaC	15/16	0.444767929396815	1	FACETS	0.678	0.653	0.704	0.678	0.653	0.704	INDETERMINATE	1	TRUE	0	0.891411018066987	1		729	849	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212194	36212194	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	416	698	1	ENST00000222270.7:c.1945G>T	p.Ala649Ser	p.A649S	ENST00000222270	NM_014727.1	649	Gcc/Tcc	3/37	0.444767929396815	1	FACETS	0.675	0.648	0.702	0.675	0.648	0.702	INDETERMINATE	1	TRUE	0	0.891411018066987	1		699	766	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856356	45856356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	230	790	0	ENST00000391945.4:c.1816G>A	p.Glu606Lys	p.E606K	ENST00000391945	NM_000400.3	606	Gag/Aag	19/23	0.444767929396815	1	FACETS	0.338	0.316	0.361	0.338	0.316	0.361	INDETERMINATE	1	TRUE	0	0.891411018066987	1		790	846	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565796	55565796	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	284	431	0	ENST00000288135.5:c.620C>A	p.Ala207Asp	p.A207D	ENST00000288135	NM_000222.2	207	gCc/gAc	4/21	1	2	FACETS	0.964	0.913	1	0.964	0.913	1	CLONAL	1	TRUE	1	0.891411018066987	2		431	661	SUCCESS
APC	324	MSKCC	GRCh37	5	112174310	112174310	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0055126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	249	266	0	ENST00000257430.4:c.3019A>T	p.Lys1007Ter	p.K1007*	ENST00000257430	NM_000038.5	1007	Aaa/Taa	16/16	0.860328386388003	2	FACETS	0.994	0.967	1	0.994	0.967	1	CLONAL	2	TRUE	0	0.891411018066987	2		266	281	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	71	374	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.901	0.791	1	0.901	0.791	1	CLONAL	1	TRUE	1	0.436625211211377	2		374	361	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429978	78429978	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	84	344	0	ENST00000370768.2:c.901del	p.Ile301TyrfsTer22	p.I301Yfs*22	ENST00000370768	NM_003902.3	301	Ata/ta	11/20	1	2	FACETS	0.936	0.832	1	0.936	0.832	1	CLONAL	1	TRUE	1	0.436625211211377	2		344	411	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	155	659	0	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.436625211211377	2		659	695	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395204	139395204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375978224	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	288	1355	2	ENST00000277541.6:c.5734G>A	p.Asp1912Asn	p.D1912N	ENST00000277541	NM_017617.3	1912	Gac/Aac	31/34	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.436625211211377	2		1357	1311	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288967	212288967	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs537458255	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	56	531	1	ENST00000342788.4:c.2779C>T	p.Arg927Ter	p.R927*	ENST00000342788	NM_005235.2	927	Cga/Tga	23/28	1	2	FACETS	0.626	0.537	0.721	0.626	0.537	0.721	SUBCLONAL	1	TRUE	1	0.436625211211377	2		532	410	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	183	328	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.436625211211377	2	FACETS	0.899	0.838	0.961	0.899	0.838	0.961	CLONAL	2	TRUE	0	0.436625211211377	2		328	466	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	148	758	1	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.841	0.769	0.917	0.841	0.769	0.917	CLONAL	1	TRUE	1	0.436625211211377	2		759	806	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926884	112926884	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	144	700	0	ENST00000351677.2:c.1504T>C	p.Ser502Pro	p.S502P	ENST00000351677	NM_002834.3	502	Tca/Cca	13/16	1	2	FACETS	0.964	0.882	1	0.964	0.882	1	CLONAL	1	TRUE	1	0.436625211211377	2		700	684	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	119	341	1	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.98	0.888	1	0.98	0.888	1	CLONAL	1	TRUE	1	0.436625211211377	2		342	556	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557909	187557909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564430066	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	157	501	1	ENST00000441802.2:c.3802C>T	p.Arg1268Trp	p.R1268W	ENST00000441802	NM_005245.3	1268	Cgg/Tgg	5/27	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.436625211211377	2		502	664	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049853	16049853	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	65	272	0	ENST00000268712.3:c.919del	p.Ile307SerfsTer19	p.I307Sfs*19	ENST00000268712	NM_006311.3	307	Atc/tc	10/46	1	2	FACETS	0.908	0.793	1	0.908	0.793	1	CLONAL	1	TRUE	1	0.436625211211377	2		272	328	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934243	49934243	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1407832113	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	185	458	1	ENST00000296474.3:c.2264del	p.Gly755ValfsTer19	p.G755Vfs*19	ENST00000296474	NM_002447.2	755	gGt/gt	8/20	1	2	FACETS	0.904	0.835	0.976	0.904	0.835	0.976	CLONAL	1	TRUE	1	0.436625211211377	2		459	937	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646084	215646085	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs746325928	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	105	614	1	ENST00000260947.4:c.513dup	p.Asp172ArgfsTer10	p.D172Rfs*10	ENST00000260947	NM_000465.2	171	-/A	4/11	1	2	FACETS	0.815	0.732	0.903	0.815	0.732	0.903	CLONAL	1	TRUE	1	0.436625211211377	2		615	590	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350311	89350311	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	233	880	1	ENST00000301030.4:c.2639C>T	p.Thr880Met	p.T880M	ENST00000301030	NM_001256183.1	880	aCg/aTg	9/13	1	2	FACETS	0.987	0.92	1	0.987	0.92	1	CLONAL	1	TRUE	1	0.436625211211377	2		881	1081	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941109	36941109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761404285	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	188	877	2	ENST00000361632.4:c.230G>A	p.Arg77His	p.R77H	ENST00000361632		77	cGt/cAt	3/16	1	2	FACETS	0.985	0.911	1	0.985	0.911	1	CLONAL	1	TRUE	1	0.436625211211377	2		879	874	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	182	886	5	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	1	2	FACETS	0.915	0.845	0.988	0.915	0.845	0.988	CLONAL	1	TRUE	1	0.436625211211377	2		891	911	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	261	520	1	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.936	0.876	0.999	0.936	0.876	0.999	CLONAL	1	TRUE	1	0.436625211211377	2		521	1277	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047888	180047888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	228	1239	1	ENST00000261937.6:c.2287G>A	p.Val763Met	p.V763M	ENST00000261937	NM_182925.4	763	Gtg/Atg	15/30	1	2	FACETS	0.903	0.841	0.968	0.903	0.841	0.968	CLONAL	1	TRUE	1	0.436625211211377	2		1240	1156	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262102	10262102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	193	705	2	ENST00000340748.4:c.2189G>A	p.Arg730His	p.R730H	ENST00000340748		730	cGc/cAc	23/40	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.436625211211377	2		707	825	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	132	709	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	0.797	0.724	0.873	0.797	0.724	0.873	SUBCLONAL	1	TRUE	1	0.436625211211377	2		709	759	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399315	139399315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369467132	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	253	1091	1	ENST00000277541.6:c.4828G>A	p.Ala1610Thr	p.A1610T	ENST00000277541	NM_017617.3	1610	Gca/Aca	26/34	1	2	FACETS	0.97	0.907	1	0.97	0.907	1	CLONAL	1	TRUE	1	0.436625211211377	2		1092	1195	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	184	902	3	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.926	0.855	1	0.926	0.855	1	CLONAL	1	TRUE	1	0.436625211211377	2		905	910	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989706	68989706	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	98	510	0	ENST00000288368.4:c.1642+2T>C		p.X548_splice	ENST00000288368	NM_024870.2	548			1	2	FACETS	0.821	0.734	0.912	0.821	0.734	0.912	CLONAL	1	TRUE	1	0.436625211211377	2		510	547	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146944	38146945	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	147	704	0	ENST00000317025.8:c.3197dup	p.Asn1066LysfsTer14	p.N1066Kfs*14	ENST00000317025	NM_023034.1	1066	aac/aaAc	18/24	1	2	FACETS	0.827	0.756	0.902	0.827	0.756	0.902	CLONAL	1	TRUE	1	0.436625211211377	2		704	814	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595382	141595382	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	190	903	1	ENST00000220592.5:c.51del	p.Ile18SerfsTer121	p.I18Sfs*121	ENST00000220592	NM_012154.3	17	ccC/cc	2/19	1	2	FACETS	0.91	0.842	0.982	0.91	0.842	0.982	CLONAL	1	TRUE	1	0.436625211211377	2		904	956	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117191	7117191	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	185	819	2	ENST00000302850.5:c.4025del	p.Gly1342AlafsTer23	p.G1342Afs*23	ENST00000302850	NM_000208.2	1342	gGc/gc	22/22	1	2	FACETS	0.956	0.884	1	0.956	0.884	1	CLONAL	1	TRUE	1	0.436625211211377	2		821	886	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136260	202136262	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs763516126	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	118	512	0	ENST00000358485.4:c.509_511del	p.Glu170del	p.E170del	ENST00000358485	NM_001080125.1	168	tcAGAa/tca	3/9	1	2	FACETS	0.952	0.862	1	0.952	0.862	1	CLONAL	1	TRUE	1	0.436625211211377	2		512	568	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268420	142268420	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	54	353	0	ENST00000350721.4:c.3072T>G	p.Asn1024Lys	p.N1024K	ENST00000350721	NM_001184.3	1024	aaT/aaG	15/47	1	2	FACETS	0.819	0.704	0.943	0.819	0.704	0.943	CLONAL	1	TRUE	1	0.436625211211377	2		353	302	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156092	99156092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1247349502	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	116	744	0	ENST00000074304.5:c.772G>A	p.Val258Met	p.V258M	ENST00000074304	NM_001134224.1	258	Gtg/Atg	10/26	1	2	FACETS	0.677	0.61	0.748	0.677	0.61	0.748	SUBCLONAL	1	TRUE	1	0.436625211211377	2		744	785	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123889485	123889485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	56	306	0	ENST00000330479.4:c.712C>T	p.Arg238Trp	p.R238W	ENST00000330479	NM_020382.3	238	Cgg/Tgg	7/9	1	2	FACETS	0.777	0.67	0.893	0.777	0.67	0.893	SUBCLONAL	1	TRUE	1	0.436625211211377	2		306	330	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64288881	64288881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369392023	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	117	598	0	ENST00000370651.3:c.277C>T	p.Arg93Cys	p.R93C	ENST00000370651	NM_003463.4	93	Cgt/Tgt	4/6	1	2	FACETS	0.765	0.69	0.843	0.765	0.69	0.843	SUBCLONAL	1	TRUE	1	0.436625211211377	2		598	701	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800903	120800903	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748469666	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	182	894	1	ENST00000257552.2:c.345del	p.Leu116CysfsTer3	p.L116Cfs*3	ENST00000257552	NM_002442.3	115	ggG/gg	6/15	1	2	FACETS	0.862	0.795	0.932	0.862	0.795	0.932	CLONAL	1	TRUE	1	0.436625211211377	2		895	967	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510570	38510570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757750800	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	141	652	0	ENST00000254066.5:c.824C>T	p.Thr275Met	p.T275M	ENST00000254066	NM_000964.3	275	aCg/aTg	7/9	1	2	FACETS	0.917	0.837	1	0.917	0.837	1	CLONAL	1	TRUE	1	0.436625211211377	2		652	704	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40747868	40747868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752597471	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	189	926	3	ENST00000392038.2:c.550C>T	p.Arg184Trp	p.R184W	ENST00000392038	NM_001626.4	184	Cgg/Tgg	6/14	1	2	FACETS	0.927	0.857	1	0.927	0.857	1	CLONAL	1	TRUE	1	0.436625211211377	2		929	934	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324464	31324464	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1168937188	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	51	117	0	ENST00000412585.2:c.343+1G>A		p.X115_splice	ENST00000412585	NM_005514.6	115			0.436625211211377	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	0	0.436625211211377	2		117	108	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074276	8074276	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	118	598	0	ENST00000377482.5:c.383del	p.Pro128LeufsTer3	p.P128Lfs*3	ENST00000377482	NM_018948.3	128	cCt/ct	4/4	1	2	FACETS	0.995	0.902	1	0.995	0.902	1	CLONAL	1	TRUE	1	0.436625211211377	2		598	543	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264699	11264699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	129	821	0	ENST00000361445.4:c.3863G>A	p.Ser1288Asn	p.S1288N	ENST00000361445	NM_004958.3	1288	aGc/aAc	26/58	1	2	FACETS	0.662	0.599	0.727	0.662	0.599	0.727	SUBCLONAL	1	TRUE	1	0.436625211211377	2		821	893	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101052	27101052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769572233	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	193	886	0	ENST00000324856.7:c.4334G>A	p.Arg1445His	p.R1445H	ENST00000324856	NM_006015.4	1445	cGc/cAc	18/20	1	2	FACETS	0.961	0.889	1	0.961	0.889	1	CLONAL	1	TRUE	1	0.436625211211377	2		886	920	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498202	498202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	114	505	0	ENST00000399788.2:c.56G>A	p.Cys19Tyr	p.C19Y	ENST00000399788	NM_001042603.1	19	tGc/tAc	1/28	1	2	FACETS	0.911	0.823	1	0.911	0.823	1	CLONAL	1	TRUE	1	0.436625211211377	2		505	573	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555718	21555718	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	168	900	1	ENST00000382592.4:c.2552G>T	p.Gly851Val	p.G851V	ENST00000382592	NM_014572.2	851	gGg/gTg	6/8	1	2	FACETS	0.894	0.822	0.969	0.894	0.822	0.969	CLONAL	1	TRUE	1	0.436625211211377	2		901	861	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061826	38061826	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	213	981	0	ENST00000250448.2:c.163A>G	p.Thr55Ala	p.T55A	ENST00000250448	NM_004496.3	55	Acg/Gcg	2/2	1	2	FACETS	0.927	0.861	0.996	0.927	0.861	0.996	CLONAL	1	TRUE	1	0.436625211211377	2		981	1052	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133175	30133175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771152806	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	123	569	0	ENST00000263025.4:c.323G>A	p.Arg108Gln	p.R108Q	ENST00000263025	NM_002746.2	108	cGg/cAg	2/9	1	2	FACETS	0.863	0.782	0.948	0.863	0.782	0.948	CLONAL	1	TRUE	1	0.436625211211377	2		569	653	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976137	7976137	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	210	806	1	ENST00000319144.4:c.2058del	p.Tyr687ThrfsTer8	p.Y687Tfs*8	ENST00000319144	NM_001139.2	686	ccC/cc	15/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.436625211211377	2		807	867	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619203	37619203	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	144	706	0	ENST00000447079.4:c.882del	p.Tyr295ThrfsTer43	p.Y295Tfs*43	ENST00000447079	NM_015083.1	293	agC/ag	1/14	1	2	FACETS	0.888	0.811	0.968	0.888	0.811	0.968	CLONAL	1	TRUE	1	0.436625211211377	2		706	743	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621896	1621896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	272	1193	0	ENST00000344749.5:c.896C>T	p.Ala299Val	p.A299V	ENST00000344749	NM_001136139.2	299	gCc/gTc	11/19	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.436625211211377	2		1193	1225	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082465	16082465	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	200	1042	0	ENST00000281043.3:c.279G>T	p.Glu93Asp	p.E93D	ENST00000281043	NM_005378.4	93	gaG/gaT	2/3	1	2	FACETS	0.953	0.883	1	0.953	0.883	1	CLONAL	1	TRUE	1	0.436625211211377	2		1042	961	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248468	212248468	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	104	451	0	ENST00000342788.4:c.3799T>G	p.Phe1267Val	p.F1267V	ENST00000342788	NM_005235.2	1267	Ttt/Gtt	28/28	1	2	FACETS	0.99	0.891	1	0.99	0.891	1	CLONAL	1	TRUE	1	0.436625211211377	2		451	481	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543658	9543658	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368217948	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	156	434	0	ENST00000353224.5:c.1496G>A	p.Arg499Gln	p.R499Q	ENST00000353224	NM_177990.2	499	cGg/cAg	6/10	0.267261998629044	2	FACETS	0.759	0.7	0.818	0.759	0.7	0.818	SUBCLONAL	2	TRUE	0	0.436625211211377	2		434	471	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755546	57755546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	154	785	0	ENST00000274289.3:c.241C>T	p.Arg81Cys	p.R81C	ENST00000274289	NM_006622.3	81	Cgc/Tgc	1/14	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.436625211211377	2		785	705	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057035	180057035	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753792784	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	240	1171	2	ENST00000261937.6:c.584C>T	p.Thr195Met	p.T195M	ENST00000261937	NM_182925.4	195	aCg/aTg	5/30	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.436625211211377	2		1173	1074	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286844	33286844	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	157	765	0	ENST00000374542.5:c.2093T>C	p.Leu698Pro	p.L698P	ENST00000374542	NM_001141970.1	698	cTc/cCc	7/8	1	2	FACETS	0.844	0.774	0.918	0.844	0.774	0.918	CLONAL	1	TRUE	1	0.436625211211377	2		765	852	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891244	101891244	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	83	431	0	ENST00000374994.4:c.205A>G	p.Ser69Gly	p.S69G	ENST00000374994	NM_004612.2	69	Agc/Ggc	2/9	1	2	FACETS	0.678	0.599	0.762	0.678	0.599	0.762	SUBCLONAL	1	TRUE	1	0.436625211211377	2		431	561	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759764	133759764	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	185	872	0	ENST00000318560.5:c.2087G>A	p.Ser696Asn	p.S696N	ENST00000318560	NM_005157.4	696	aGc/aAc	11/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.436625211211377	2		872	812	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0055210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	52	366	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.64	0.549	0.738	0.64	0.549	0.738	SUBCLONAL	1	TRUE	1	0.593365067864643	2		366	274	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0055210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	258	875	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.593365067864643	1	FACETS	0.917	0.864	0.97	0.917	0.864	0.97	CLONAL	1	TRUE	0	0.593365067864643	1		875	667	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0055210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	94	406	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.100268863123159	5	FACETS	0.827	0.742	0.916	0.414	0.371	0.458	INDETERMINATE	2	TRUE	1	0.593365067864643	5		406	362	SUCCESS
APC	324	MSKCC	GRCh37	5	112175749	112175750	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0055210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	57	287	0	ENST00000257430.4:c.4459dup	p.Thr1487AsnfsTer27	p.T1487Nfs*27	ENST00000257430	NM_000038.5	1486	-/A	16/16	1	2	FACETS	0.694	0.6	0.794	0.694	0.6	0.794	SUBCLONAL	1	TRUE	1	0.593365067864643	2		287	277	SUCCESS
APC	324	MSKCC	GRCh37	5	112174214	112174214	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0055210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	51	302	0	ENST00000257430.4:c.2923A>T	p.Lys975Ter	p.K975*	ENST00000257430	NM_000038.5	975	Aaa/Taa	16/16	1	2	FACETS	0.654	0.56	0.754	0.654	0.56	0.754	SUBCLONAL	1	TRUE	1	0.593365067864643	2		302	263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0055260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	637	545	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.762313723293163	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.762313723293163	2		545	797	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913255	NA	P-0055260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	428	775	0	ENST00000369535.4:c.183A>C	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caC	3/7	0.328378544268067	4	FACETS	0.845	0.812	0.877			1	INDETERMINATE	3	TRUE	NA	0.762313723293163	4		775	781	SUCCESS
APC	324	MSKCC	GRCh37	5	112173696	112173697	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0055260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	118	486	0	ENST00000257430.4:c.2406dup	p.Thr803HisfsTer5	p.T803Hfs*5	ENST00000257430	NM_000038.5	802	gac/gaCc	16/16	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.762313723293163	2		486	309	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0055260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	132	740	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.909	0.834	0.986	0.909	0.834	0.986	CLONAL	1	TRUE	1	0.762313723293163	2		740	381	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407557	407557	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	150	600	0	ENST00000380956.4:c.1315G>T	p.Asp439Tyr	p.D439Y	ENST00000380956	NM_001195286.1	439	Gat/Tat	9/9	1	2	FACETS	0.969	0.896	1	0.969	0.896	1	CLONAL	1	TRUE	1	0.762313723293163	2		600	406	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411246	63411246	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	384	594	1	ENST00000330258.3:c.1921C>T	p.Arg641Ter	p.R641*	ENST00000330258	NM_152424.3	641	Cga/Tga	2/2	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.762313723293163	1		595	453	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339940	70339940	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	232	409	0	ENST00000374080.3:c.473G>T	p.Trp158Leu	p.W158L	ENST00000374080		158	tGg/tTg	4/45	0.741565117859983	2	FACETS	1	0.965	1			1	CLONAL	1	TRUE	NA	0.762313723293163	2		409	586	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	44	578	5	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.21	0.175	0.249	0.21	0.175	0.249	SUBCLONAL	1	TRUE	1	0.542952709411271	2		583	772	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	238	391	2	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.542952709411271	2		393	759	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	518	544	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.978	1	1	0.998	1	CLONAL	2	TRUE	1	0.542952709411271	2		548	937	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882050	36882050	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs780753361	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	266	882	1	ENST00000358127.4:c.963del	p.Ala322LeufsTer11	p.A322Lfs*11	ENST00000358127	NM_001280556.1	321	ccC/cc	8/10	1	2	FACETS	0.918	0.861	0.977	0.918	0.861	0.977	CLONAL	1	TRUE	1	0.542952709411271	2		883	1067	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	68	98	0	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	2	FACETS	0.798	0.7	0.902	0.798	0.7	0.902	CLONAL	1	TRUE	1	0.542952709411271	2		98	314	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	150	328	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.542952709411271	2	FACETS	1	0.978	1	0.584	0.538	0.632	CLONAL	1	TRUE	0	0.542952709411271	2		328	473	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	187	341	1	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.542952709411271	2		342	505	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	68	520	1	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.215	0.186	0.247	0.215	0.186	0.247	SUBCLONAL	1	TRUE	1	0.542952709411271	2		521	1164	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161907	47161907	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	109	374	1	ENST00000409792.3:c.4219del	p.Arg1407GlyfsTer5	p.R1407Gfs*5	ENST00000409792	NM_014159.6	1407	Agg/gg	3/21	0.542952709411271	2	FACETS	0.979	0.886	1	0.49	0.443	0.538	CLONAL	1	TRUE	0	0.542952709411271	2		375	410	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	220	570	0	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	2	FACETS	0.755	0.702	0.81	0.755	0.702	0.81	SUBCLONAL	1	TRUE	1	0.542952709411271	2		570	1073	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505471	25505471	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771499883	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	49	764	0	ENST00000264709.3:c.287G>A	p.Arg96Gln	p.R96Q	ENST00000264709	NM_175629.2	96	cGg/cAg	4/23	1	2	FACETS	0.214	0.18	0.251	0.214	0.18	0.251	SUBCLONAL	1	TRUE	1	0.542952709411271	2		764	843	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819294	3819294	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753380	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	48	637	1	ENST00000262367.5:c.2941G>A	p.Ala981Thr	p.A981T	ENST00000262367	NM_004380.2	981	Gca/Aca	15/31	1	2	FACETS	0.199	0.168	0.235	0.199	0.168	0.235	SUBCLONAL	1	TRUE	1	0.542952709411271	2		638	887	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	19	469	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.542952709411271	1	FACETS	0.191	0.145	0.245	0.191	0.145	0.245	SUBCLONAL	1	TRUE	0	0.542952709411271	1		469	267	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097621	27097622	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	168	496	0	ENST00000324856.7:c.3216dup	p.Trp1073MetfsTer32	p.W1073Mfs*32	ENST00000324856	NM_006015.4	1070	-/A	12/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.542952709411271	2		496	570	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120232	70120232	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	250	716	0	ENST00000245479.2:c.1234C>T	p.Gln412Ter	p.Q412*	ENST00000245479	NM_000346.3	412	Cag/Tag	3/3	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.542952709411271	2		716	868	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256769	19256769	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	218	786	2	ENST00000162023.5:c.944del	p.Pro315GlnfsTer?	p.P315Qfs*?	ENST00000162023		315	cCa/ca	13/13	1	2	FACETS	0.87	0.81	0.932	0.87	0.81	0.932	CLONAL	1	TRUE	1	0.542952709411271	2		788	923	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578214	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs864309495	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	278	710	0	ENST00000269305.4:c.635_636del	p.Phe212SerfsTer3	p.F212Sfs*3	ENST00000269305	NM_001126112.2	212	tTT/t	6/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.542952709411271	2		710	902	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	88	386	3	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.756	0.673	0.843	0.756	0.673	0.843	SUBCLONAL	1	TRUE	1	0.542952709411271	2		389	429	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085942	16085942	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	229	566	1	ENST00000281043.3:c.1118G>A	p.Arg373Gln	p.R373Q	ENST00000281043	NM_005378.4	373	cGa/cAa	3/3	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.542952709411271	2		567	685	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435984	116435984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	181	610	1	ENST00000397752.3:c.3979C>T	p.Arg1327Cys	p.R1327C	ENST00000397752	NM_000245.2	1327	Cgc/Tgc	21/21	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.542952709411271	2		611	629	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852608	63852608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	136	537	0	ENST00000279873.7:c.3386G>A	p.Gly1129Glu	p.G1129E	ENST00000279873	NM_032199.2	1129	gGa/gAa	10/10	1	2	FACETS	0.841	0.767	0.917	0.841	0.767	0.917	CLONAL	1	TRUE	1	0.542952709411271	2		537	596	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	191	675	2	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.542952709411271	2		677	686	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937659	17937659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144968714	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	312	792	1	ENST00000458235.1:c.3268G>A	p.Ala1090Thr	p.A1090T	ENST00000458235	NM_000215.3	1090	Gcc/Acc	24/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.542952709411271	2		793	1035	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100728	8100728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs771019738	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	287	831	6	ENST00000346208.3:c.708del	p.Ser237AlafsTer28	p.S237Afs*28	ENST00000346208		234	ttC/tt	3/6	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.542952709411271	2		837	915	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268379	142268380	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1559984993	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	45	394	2	ENST00000350721.4:c.3112dup	p.Ser1038PhefsTer11	p.S1038Ffs*11	ENST00000350721	NM_001184.3	1038	tct/tTct	15/47	1	2	FACETS	0.817	0.694	0.948	0.817	0.694	0.948	CLONAL	1	TRUE	1	0.542952709411271	2		396	203	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	299	516	0	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.956	0.9	1	0.956	0.9	1	CLONAL	1	TRUE	1	0.542952709411271	2		516	1152	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579463	7579463	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	313	910	1	ENST00000269305.4:c.224del	p.Pro75LeufsTer48	p.P75Lfs*48	ENST00000269305	NM_001126112.2	75	cCt/ct	4/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.542952709411271	2		911	1043	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752960	128752960	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	157	503	0	ENST00000377970.2:c.1121A>G	p.His374Arg	p.H374R	ENST00000377970	NM_002467.4	374	cAc/cGc	3/3	1	2	FACETS	0.975	0.898	1	0.975	0.898	1	CLONAL	1	TRUE	1	0.542952709411271	2		503	593	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	180	501	0	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.542952709411271	2		501	587	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	335	650	11	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	0.869	0.828	0.91	1	0.996	1	CLONAL	2	TRUE	1	0.542952709411271	2		661	710	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	658	824	6	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	1	0.994	1	1	0.998	1	CLONAL	2	TRUE	1	0.542952709411271	2		830	1116	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646085	215646085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	109	468	3	ENST00000260947.4:c.513del	p.Asp172MetfsTer40	p.D172Mfs*40	ENST00000260947	NM_000465.2	171	aaA/aa	4/11	1	2	FACETS	0.875	0.79	0.963	0.875	0.79	0.963	CLONAL	1	TRUE	1	0.542952709411271	2		471	459	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772715	135772715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	157	529	0	ENST00000298552.3:c.2831C>T	p.Ala944Val	p.A944V	ENST00000298552	NM_001162426.1	944	gCa/gTa	22/23	1	2	FACETS	0.999	0.92	1	0.999	0.92	1	CLONAL	1	TRUE	1	0.542952709411271	2		529	579	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	182	486	4	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.542952709411271	2		490	578	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831357	72831358	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTG	rs34918837	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	78	401	2	ENST00000268489.5:c.5221_5223dup	p.Gln1741dup	p.Q1741dup	ENST00000268489	NM_006885.3	1741	-/CAA	9/10	1	2	FACETS	0.597	0.526	0.673	0.597	0.526	0.673	SUBCLONAL	1	TRUE	1	0.542952709411271	2		403	481	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317160	11317160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	285	724	2	ENST00000361445.4:c.334C>T	p.Arg112Trp	p.R112W	ENST00000361445	NM_004958.3	112	Cgg/Tgg	4/58	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.542952709411271	2		726	919	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073804	8073804	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1557463619	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	102	357	0	ENST00000377482.5:c.855del	p.Arg286GlufsTer9	p.R286Efs*9	ENST00000377482	NM_018948.3	285	ccC/cc	4/4	1	2	FACETS	0.971	0.875	1	0.971	0.875	1	CLONAL	1	TRUE	1	0.542952709411271	2		357	387	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835781	68835781	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060501215	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	217	598	1	ENST00000261769.5:c.377del	p.Pro126ArgfsTer89	p.P126Rfs*89	ENST00000261769	NM_004360.3	124	cgC/cg	3/16	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.542952709411271	2		599	763	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567646	226567647	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1159330096	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	220	475	0	ENST00000366794.5:c.1519dup	p.Ser507LysfsTer14	p.S507Kfs*14	ENST00000366794	NM_001618.3	507	agc/aAgc	10/23	1	2	FACETS	0.935	0.871	1	0.935	0.871	1	CLONAL	1	TRUE	1	0.542952709411271	2		475	867	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512401	38512402	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs745553450	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	212	736	3	ENST00000254066.5:c.1319dup	p.Pro441AlafsTer5	p.P441Afs*5	ENST00000254066	NM_000964.3	438	gcc/gCcc	9/9	1	2	FACETS	0.969	0.902	1	0.969	0.902	1	CLONAL	1	TRUE	1	0.542952709411271	2		739	806	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733513	85733513	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs387906350	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	96	373	3	ENST00000370580.1:c.499del	p.Ser167LeufsTer6	p.S167Lfs*6	ENST00000370580	NM_003921.4	167	Tct/ct	3/3	1	2	FACETS	0.824	0.739	0.914	0.824	0.739	0.914	CLONAL	1	TRUE	1	0.542952709411271	2		376	429	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287294	46287294	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	28	550	0	ENST00000334344.6:c.5239G>T	p.Gly1747Ter	p.G1747*	ENST00000334344	NM_152641.2	1747	Gga/Tga	19/21	1	2	FACETS	0.188	0.15	0.232	0.188	0.15	0.232	SUBCLONAL	1	TRUE	1	0.542952709411271	2		550	548	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639588	47639588	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63749897	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	66	311	0	ENST00000233146.2:c.687del	p.Ala230LeufsTer16	p.A230Lfs*16	ENST00000233146	NM_000251.2	227	agA/ag	4/16	1	2	FACETS	0.904	0.793	1	0.904	0.793	1	CLONAL	1	TRUE	1	0.542952709411271	2		311	269	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97873817	97873817	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	72	829	2	ENST00000289081.3:c.1257del	p.Thr420ArgfsTer27	p.T420Rfs*27	ENST00000289081	NM_000136.2	419	ccC/cc	13/15	1	2	FACETS	0.26	0.226	0.296	0.26	0.226	0.296	SUBCLONAL	1	TRUE	1	0.542952709411271	2		831	1022	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630605	187630605	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	155	598	0	ENST00000441802.2:c.377del	p.Asn126IlefsTer20	p.N126Ifs*20	ENST00000441802	NM_005245.3	126	aAt/at	2/27	1	2	FACETS	0.912	0.838	0.989	0.912	0.838	0.989	CLONAL	1	TRUE	1	0.542952709411271	2		598	626	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043349	6043349	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781716	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	12	183	1	ENST00000265849.7:c.325del	p.Glu109LysfsTer3	p.E109Kfs*3	ENST00000265849	NM_000535.5	109	Gaa/aa	4/15	1	2	FACETS	0.244	0.172	0.333	0.244	0.172	0.333	SUBCLONAL	1	TRUE	1	0.542952709411271	2		184	181	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259729	16259729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758740337	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	191	532	0	ENST00000375759.3:c.6994C>T	p.Arg2332Cys	p.R2332C	ENST00000375759	NM_015001.2	2332	Cgc/Tgc	11/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.542952709411271	2		532	632	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822586	72822586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	177	685	4	ENST00000268489.5:c.9589del	p.Gln3197SerfsTer44	p.Q3197Sfs*44	ENST00000268489	NM_006885.3	3197	Cag/ag	10/10	1	2	FACETS	0.878	0.81	0.947	0.878	0.81	0.947	CLONAL	1	TRUE	1	0.542952709411271	2		689	743	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804358	46804358	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139475791	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	215	676	1	ENST00000290295.7:c.649C>T	p.Arg217Cys	p.R217C	ENST00000290295	NM_006361.5	217	Cgc/Tgc	2/2	1	2	FACETS	0.98	0.913	1	0.98	0.913	1	CLONAL	1	TRUE	1	0.542952709411271	2		677	808	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497824	25497824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	239	815	0	ENST00000264709.3:c.625C>T	p.Arg209Cys	p.R209C	ENST00000264709	NM_175629.2	209	Cgc/Tgc	6/23	1	2	FACETS	0.939	0.877	1	0.939	0.877	1	CLONAL	1	TRUE	1	0.542952709411271	2		815	938	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16052795	16052795	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	37	354	0	ENST00000268712.3:c.879del	p.Phe293LeufsTer33	p.F293Lfs*33	ENST00000268712	NM_006311.3	293	ttT/tt	9/46	1	2	FACETS	0.847	0.708	0.996	0.847	0.708	0.996	CLONAL	1	TRUE	1	0.542952709411271	2		354	161	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15821896	15821896	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	57	328	1	ENST00000307771.7:c.294del	p.Lys98AsnfsTer10	p.K98Nfs*10	ENST00000307771	NM_005089.3	97	Aaa/aa	4/11	NA	2	FACETS	0.808	0.7	0.923			1	INDETERMINATE	1	TRUE	NA	0.542952709411271	2		329	260	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	222	196	2	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.956	1	1	0.995	1	CLONAL	2	TRUE	1	0.542952709411271	2		198	404	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194905	29194905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375453930	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	320	836	0	ENST00000240100.2:c.823C>T	p.Arg275Cys	p.R275C	ENST00000240100	NM_001394.6	275	Cgc/Tgc	4/4	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.542952709411271	2		836	1021	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240613	133240613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201115064	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	171	602	3	ENST00000320574.5:c.2683G>A	p.Ala895Thr	p.A895T	ENST00000320574	NM_006231.2	895	Gcc/Acc	23/49	1	2	FACETS	0.942	0.869	1	0.942	0.869	1	CLONAL	1	TRUE	1	0.542952709411271	2		605	669	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351595	89351595	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	213	736	2	ENST00000301030.4:c.1355del	p.Asn452IlefsTer3	p.N452Ifs*3	ENST00000301030	NM_001256183.1	452	aAt/at	9/13	1	2	FACETS	0.873	0.812	0.936	0.873	0.812	0.936	CLONAL	1	TRUE	1	0.542952709411271	2		738	899	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782074	66782075	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	115	299	0	ENST00000307102.5:c.1047_1048del	p.Arg349SerfsTer16	p.R349Sfs*16	ENST00000307102	NM_002755.3	347	gcAGag/gcag	10/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.542952709411271	2		299	397	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248285	59248285	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	69	225	1	ENST00000371222.2:c.458del	p.Gly153AlafsTer29	p.G153Afs*29	ENST00000371222	NM_002228.3	153	gGc/gc	1/1	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.542952709411271	2		226	210	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134575	2134575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142848358	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	313	1056	3	ENST00000219476.3:c.4352G>A	p.Arg1451His	p.R1451H	ENST00000219476	NM_000548.3	1451	cGc/cAc	34/42	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.542952709411271	2		1059	1038	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	138	415	14	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	1	2	FACETS	0.895	0.83	0.96	1	0.991	1	CLONAL	2	TRUE	1	0.542952709411271	2		429	284	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399158	139399158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774808496	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	268	833	0	ENST00000277541.6:c.4985G>A	p.Arg1662Gln	p.R1662Q	ENST00000277541	NM_017617.3	1662	cGg/cAg	26/34	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.542952709411271	2		833	928	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218451	36218451	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs34078597	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	282	916	1	ENST00000222270.7:c.4235del	p.Gly1412AlafsTer10	p.G1412Afs*10	ENST00000222270	NM_014727.1	1410	caG/ca	16/37	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.542952709411271	2		917	909	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752805	42752805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767131852	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	350	983	0	ENST00000222329.4:c.1459C>T	p.Arg487Cys	p.R487C	ENST00000222329	NM_006494.2	487	Cgc/Tgc	4/4	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.542952709411271	2		983	1093	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371824	55371824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	144	209	0	ENST00000297316.4:c.514G>A	p.Gly172Ser	p.G172S	ENST00000297316	NM_022454.3	172	Ggc/Agc	2/2	1	2	FACETS	0.884	0.821	0.947	1	0.991	1	CLONAL	2	TRUE	1	0.542952709411271	2		209	300	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277149	38277149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752627281	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	231	677	1	ENST00000425967.3:c.1279G>A	p.Val427Ile	p.V427I	ENST00000425967	NM_001174067.1	427	Gtc/Atc	10/19	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.542952709411271	2		678	792	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224678	36224678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752822802	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	267	857	0	ENST00000222270.7:c.7064G>A	p.Arg2355Gln	p.R2355Q	ENST00000222270	NM_014727.1	2355	cGg/cAg	30/37	1	2	FACETS	0.92	0.863	0.979	0.92	0.863	0.979	CLONAL	1	TRUE	1	0.542952709411271	2		857	1069	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164464	36164464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	165	495	0	ENST00000300305.3:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000300305		471	Cgc/Tgc	8/8	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.542952709411271	2		495	564	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986730	36986730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	36	101	0	ENST00000354822.5:c.959C>T	p.Ala320Val	p.A320V	ENST00000354822	NM_001079668.2	320	gCg/gTg	3/3	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.542952709411271	2		101	127	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245525	46245525	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	80	359	0	ENST00000334344.6:c.3619C>T	p.Gln1207Ter	p.Q1207*	ENST00000334344	NM_152641.2	1207	Cag/Tag	15/21	1	2	FACETS	0.746	0.66	0.837	0.746	0.66	0.837	SUBCLONAL	1	TRUE	1	0.542952709411271	2		359	395	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741892	145741892	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs757780731	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	305	891	0	ENST00000428558.2:c.611C>G	p.Ala204Gly	p.A204G	ENST00000428558	NM_004260.3	204	gCc/gGc	5/22	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.542952709411271	2		891	940	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434863	49434864	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	299	913	1	ENST00000301067.7:c.6689dup	p.Pro2231ThrfsTer12	p.P2231Tfs*12	ENST00000301067	NM_003482.3	2230	cca/ccCa	31/54	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.542952709411271	2		914	1016	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106162508	106162508	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	53	235	0	ENST00000380013.4:c.3426del	p.Asp1143MetfsTer9	p.D1143Mfs*9	ENST00000380013	NM_001127208.2	1141	gAa/ga	4/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.542952709411271	2		235	158	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986723	36986723	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1465370806	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	36	82	0	ENST00000354822.5:c.966C>G	p.His322Gln	p.H322Q	ENST00000354822	NM_001079668.2	322	caC/caG	3/3	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.542952709411271	2		82	109	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151871274	151871274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	112	492	0	ENST00000262189.6:c.9316G>A	p.Gly3106Ser	p.G3106S	ENST00000262189	NM_170606.2	3106	Ggt/Agt	39/59	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.542952709411271	2		492	359	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295788	212295788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1412193732	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	71	521	1	ENST00000342788.4:c.2525G>A	p.Arg842Gln	p.R842Q	ENST00000342788	NM_005235.2	842	cGg/cAg	21/28	1	2	FACETS	0.765	0.672	0.863	0.765	0.672	0.863	SUBCLONAL	1	TRUE	1	0.542952709411271	2		522	342	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118662	11118662	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1486794288	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	267	759	1	ENST00000358026.2:c.2086G>A	p.Asp696Asn	p.D696N	ENST00000358026	NM_001128849.1	696	Gat/Aat	14/36	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.542952709411271	2		760	879	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843323	128843323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	309	961	0	ENST00000249373.3:c.430C>T	p.Arg144Cys	p.R144C	ENST00000249373	NM_005631.4	144	Cgt/Tgt	2/12	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.542952709411271	2		961	1009	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94926668	94926668	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1407767283	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	16	447	0	ENST00000536441.1:c.97T>C	p.Ser33Pro	p.S33P	ENST00000536441	NM_144665.3	33	Tct/Cct	2/10	1	2	FACETS	0.198	0.146	0.261	0.198	0.146	0.261	SUBCLONAL	1	TRUE	1	0.542952709411271	2		447	297	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437565	52437565	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	239	776	1	ENST00000460680.1:c.1596del	p.Phe532LeufsTer39	p.F532Lfs*39	ENST00000460680	NM_004656.3	532	ttT/tt	13/17	0.542952709411271	2	FACETS	0.937	0.875	1	0.468	0.437	0.5	CLONAL	1	TRUE	0	0.542952709411271	2		777	940	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002852	69002852	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	60	301	0	ENST00000288368.4:c.2152T>C	p.Cys718Arg	p.C718R	ENST00000288368	NM_024870.2	718	Tgc/Cgc	20/40	1	2	FACETS	0.611	0.528	0.699	0.611	0.528	0.699	SUBCLONAL	1	TRUE	1	0.542952709411271	2		301	362	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618427	37618427	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750600272	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	168	493	0	ENST00000447079.4:c.103C>T	p.Arg35Cys	p.R35C	ENST00000447079	NM_015083.1	35	Cgt/Tgt	1/14	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.542952709411271	2		493	587	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397141	397141	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs756699452	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	202	512	0	ENST00000380956.4:c.526C>T	p.Arg176Ter	p.R176*	ENST00000380956	NM_001195286.1	176	Cga/Tga	5/9	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.542952709411271	2		512	634	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670055	29670055	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555535407	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	55	386	0	ENST00000356175.3:c.7028G>A	p.Arg2343Gln	p.R2343Q	ENST00000356175	NM_000267.3	2343	cGg/cAg	47/57	1	2	FACETS	0.9	0.78	1	0.9	0.78	1	CLONAL	1	TRUE	1	0.542952709411271	2		386	225	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229255	36229255	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	273	878	0	ENST00000222270.7:c.7945C>T	p.Arg2649Cys	p.R2649C	ENST00000222270	NM_014727.1	2649	Cgc/Tgc	37/37	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.542952709411271	2		878	874	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644661	134644661	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376895227	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	149	471	2	ENST00000398015.3:c.62C>T	p.Thr21Met	p.T21M	ENST00000398015	NM_004441.4	21	aCg/aTg	2/16	1	2	FACETS	0.987	0.907	1	0.987	0.907	1	CLONAL	1	TRUE	1	0.542952709411271	2		473	556	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261827	16261827	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	201	709	0	ENST00000375759.3:c.9092C>A	p.Pro3031His	p.P3031H	ENST00000375759	NM_015001.2	3031	cCc/cAc	11/15	1	2	FACETS	0.96	0.892	1	0.96	0.892	1	CLONAL	1	TRUE	1	0.542952709411271	2		709	771	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322656	39322656	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	90	560	0	ENST00000373001.3:c.336C>A	p.Phe112Leu	p.F112L	ENST00000373001	NM_022157.3	112	ttC/ttA	2/7	1	2	FACETS	0.866	0.774	0.962	0.866	0.774	0.962	CLONAL	1	TRUE	1	0.542952709411271	2		560	383	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166208	118166209	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	143	414	0	ENST00000369448.3:c.720_721del	p.Gly241ArgfsTer42	p.G241Rfs*42	ENST00000369448	NM_017709.3	240	AGa/a	2/2	1	2	FACETS	0.954	0.874	1	0.954	0.874	1	CLONAL	1	TRUE	1	0.542952709411271	2		414	552	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551728	150551728	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	152	420	0	ENST00000369026.2:c.279del	p.Ala94ArgfsTer150	p.A94Rfs*150	ENST00000369026	NM_021960.4	93	ccC/cc	1/3	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.542952709411271	2		420	446	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741873	162741873	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	201	506	0	ENST00000367921.3:c.1564G>A	p.Ala522Thr	p.A522T	ENST00000367921	NM_006182.2	522	Gca/Aca	13/18	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.542952709411271	2		506	631	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680616	241680616	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	52	282	0	ENST00000366560.3:c.133G>A	p.Ala45Thr	p.A45T	ENST00000366560	NM_000143.3	45	Gca/Aca	2/10	1	2	FACETS	0.808	0.695	0.929	0.808	0.695	0.929	CLONAL	1	TRUE	1	0.542952709411271	2		282	237	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446348	70446348	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	177	564	0	ENST00000373644.4:c.5288C>T	p.Thr1763Ile	p.T1763I	ENST00000373644	NM_030625.2	1763	aCa/aTa	11/12	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.542952709411271	2		564	649	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248625	8248625	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	246	828	0	ENST00000335790.3:c.262T>G	p.Cys88Gly	p.C88G	ENST00000335790	NM_002315.2	88	Tgt/Ggt	3/4	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.542952709411271	2		828	790	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207729	102207729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	74	389	0	ENST00000263464.3:c.1711C>T	p.Pro571Ser	p.P571S	ENST00000263464	NM_001165.4	571	Cct/Tct	9/9	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.542952709411271	2		389	193	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307289	118307289	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	38	91	0	ENST00000534358.1:c.62G>C	p.Gly21Ala	p.G21A	ENST00000534358	NM_005933.3	21	gGc/gCc	1/36	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.542952709411271	2		91	120	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118365463	118365463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555043470	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	36	314	0	ENST00000534358.1:c.5344C>T	p.Pro1782Ser	p.P1782S	ENST00000534358	NM_005933.3	1782	Cca/Tca	18/36	0.142732373702402	3	FACETS	0.947	0.788	1			1	INDETERMINATE	1	TRUE	NA	0.542952709411271	3		314	178	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944766	31944766	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	24	314	0	ENST00000340398.3:c.335T>A	p.Ile112Asn	p.I112N	ENST00000340398	NM_001013699.2	112	aTc/aAc	1/1	1	2	FACETS	0.227	0.177	0.284	0.227	0.177	0.284	SUBCLONAL	1	TRUE	1	0.542952709411271	2		314	390	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245211	46245211	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	190	546	0	ENST00000334344.6:c.3305C>T	p.Ala1102Val	p.A1102V	ENST00000334344	NM_152641.2	1102	gCc/gTc	15/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.542952709411271	2		546	649	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285880	46285880	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	67	396	0	ENST00000334344.6:c.5147+1G>T		p.X1716_splice	ENST00000334344	NM_152641.2	1716			1	2	FACETS	0.786	0.688	0.89	0.786	0.688	0.89	SUBCLONAL	1	TRUE	1	0.542952709411271	2		396	314	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73351563	73351563	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	104	212	0	ENST00000377767.4:c.649G>A	p.Glu217Lys	p.E217K	ENST00000377767	NM_014953.3	217	Gaa/Aaa	4/21	1	2	FACETS	0.836	0.765	0.909	1	0.988	1	CLONAL	2	TRUE	1	0.542952709411271	2		212	229	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436401	110436401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs76110593	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	477	804	0	ENST00000375856.3:c.2000G>A	p.Ser667Asn	p.S667N	ENST00000375856	NM_003749.2	667	aGc/aAc	1/2	0.468692907057872	3	FACETS	1	0.977	1			1	CLONAL	2	TRUE	NA	0.542952709411271	3		804	1089	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590650	95590652	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	54	318	0	ENST00000393063.1:c.1257_1259del	p.Asp419del	p.D419del	ENST00000393063	NM_030621.3	419	gaTGAg/gag	9/28	1	2	FACETS	0.786	0.678	0.902	0.786	0.678	0.902	CLONAL	1	TRUE	1	0.542952709411271	2		318	253	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465564	99465564	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	195	586	0	ENST00000268035.6:c.2389A>G	p.Thr797Ala	p.T797A	ENST00000268035	NM_000875.3	797	Aca/Gca	11/21	1	2	FACETS	0.953	0.884	1	0.953	0.884	1	CLONAL	1	TRUE	1	0.542952709411271	2		586	754	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348767	11348767	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	144	418	0	ENST00000332029.2:c.569A>G	p.Asn190Ser	p.N190S	ENST00000332029	NM_003745.1	190	aAc/aGc	2/2	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.542952709411271	2		418	515	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56832428	56832428	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	79	400	2	ENST00000308159.5:c.338C>T	p.Ala113Val	p.A113V	ENST00000308159	NM_014669.4	113	gCc/gTc	4/22	1	2	FACETS	0.822	0.728	0.921	0.822	0.728	0.921	CLONAL	1	TRUE	1	0.542952709411271	2		402	354	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349735	89349735	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	222	721	0	ENST00000301030.4:c.3215A>G	p.Lys1072Arg	p.K1072R	ENST00000301030	NM_001256183.1	1072	aAa/aGa	9/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.542952709411271	2		721	728	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965522	15965522	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	103	370	0	ENST00000268712.3:c.5284A>G	p.Arg1762Gly	p.R1762G	ENST00000268712	NM_006311.3	1762	Aga/Gga	36/46	1	2	FACETS	0.878	0.791	0.97	0.878	0.791	0.97	CLONAL	1	TRUE	1	0.542952709411271	2		370	432	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38506115	38506115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	225	727	2	ENST00000254066.5:c.407C>T	p.Thr136Ile	p.T136I	ENST00000254066	NM_000964.3	136	aCc/aTc	4/9	1	2	FACETS	0.877	0.817	0.939	0.877	0.817	0.939	CLONAL	1	TRUE	1	0.542952709411271	2		729	945	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40854893	40854893	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	140	497	0	ENST00000428826.2:c.2183+2T>C		p.X728_splice	ENST00000428826		728			1	2	FACETS	0.816	0.745	0.89	0.816	0.745	0.89	CLONAL	1	TRUE	1	0.542952709411271	2		497	632	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870532	40870532	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	248	643	0	ENST00000428826.2:c.871C>A	p.Leu291Met	p.L291M	ENST00000428826		291	Ctg/Atg	9/21	1	2	FACETS	0.951	0.89	1	0.951	0.89	1	CLONAL	1	TRUE	1	0.542952709411271	2		643	961	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41209133	41209133	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs886040279	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	183	571	0	ENST00000357654.3:c.5213del	p.Gly1738GlufsTer27	p.G1738Efs*27	ENST00000357654	NM_007294.3	1738	gGa/ga	19/23	1	2	FACETS	0.956	0.885	1	0.956	0.885	1	CLONAL	1	TRUE	1	0.542952709411271	2		571	705	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119945	70119945	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	176	570	0	ENST00000245479.2:c.947del	p.Thr316ArgfsTer67	p.T316Rfs*67	ENST00000245479	NM_000346.3	316	aCg/ag	3/3	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.542952709411271	2		570	598	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110533	4110533	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	277	707	0	ENST00000262948.5:c.424del	p.Glu142ArgfsTer18	p.E142Rfs*18	ENST00000262948	NM_030662.3	142	Gag/ag	3/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.542952709411271	2		707	843	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610099	10610099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370296794	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	231	786	1	ENST00000171111.5:c.611G>A	p.Arg204Gln	p.R204Q	ENST00000171111	NM_203500.1	204	cGg/cAg	2/6	1	2	FACETS	0.851	0.794	0.91	0.851	0.794	0.91	CLONAL	1	TRUE	1	0.542952709411271	2		787	1000	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17941392	17941392	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	253	694	1	ENST00000458235.1:c.3016C>T	p.Arg1006Cys	p.R1006C	ENST00000458235	NM_000215.3	1006	Cgc/Tgc	22/24	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.542952709411271	2		695	838	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974379	18974379	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	204	667	1	ENST00000262803.5:c.2733G>A	p.Met911Ile	p.M911I	ENST00000262803	NM_002911.3	911	atG/atA	19/24	1	2	FACETS	0.99	0.921	1	0.99	0.921	1	CLONAL	1	TRUE	1	0.542952709411271	2		668	759	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40747946	40747946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	219	699	1	ENST00000392038.2:c.472C>A	p.Leu158Ile	p.L158I	ENST00000392038	NM_001626.4	158	Ctt/Att	6/14	1	2	FACETS	0.832	0.774	0.891	0.832	0.774	0.891	CLONAL	1	TRUE	1	0.542952709411271	2		700	970	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867339	45867339	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	274	964	0	ENST00000391945.4:c.854A>G	p.Tyr285Cys	p.Y285C	ENST00000391945	NM_000400.3	285	tAc/tGc	10/23	1	2	FACETS	0.949	0.891	1	0.949	0.891	1	CLONAL	1	TRUE	1	0.542952709411271	2		964	1064	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50143325	50143325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	73	106	0	ENST00000246792.3:c.31C>T	p.Arg11Trp	p.R11W	ENST00000246792	NM_006270.3	11	Cgg/Tgg	1/6	1	2	FACETS	0.786	0.705	0.869	1	0.981	1	SUBCLONAL	2	TRUE	1	0.542952709411271	2		106	171	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082882	16082882	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	45	146	0	ENST00000281043.3:c.700del	p.Val234SerfsTer27	p.V234Sfs*27	ENST00000281043	NM_005378.4	232	ccG/cc	2/3	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.542952709411271	2		146	149	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026218	48026218	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	105	410	0	ENST00000234420.5:c.1096T>C	p.Tyr366His	p.Y366H	ENST00000234420	NM_000179.2	366	Tat/Cat	4/10	1	2	FACETS	0.895	0.807	0.987	0.895	0.807	0.987	CLONAL	1	TRUE	1	0.542952709411271	2		410	432	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026820	48026821	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	92	439	0	ENST00000234420.5:c.1699_1700del	p.Lys567ValfsTer9	p.K567Vfs*9	ENST00000234420	NM_000179.2	566	ggAAag/ggag	4/10	1	2	FACETS	0.873	0.782	0.97	0.873	0.782	0.97	CLONAL	1	TRUE	1	0.542952709411271	2		439	388	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030797	48030797	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587781544	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	55	330	1	ENST00000234420.5:c.3416del	p.Gly1139AlafsTer6	p.G1139Afs*6	ENST00000234420	NM_000179.2	1137	atG/at	5/10	1	2	FACETS	0.767	0.662	0.88	0.767	0.662	0.88	SUBCLONAL	1	TRUE	1	0.542952709411271	2		331	264	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095537	178095540	+	frameshift_variant	Frame_Shift_Del	DEL	CTTA	CTTA	-	rs748937667	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	51	298	0	ENST00000397062.3:c.1791_1794del	p.Ser597ArgfsTer14	p.S597Rfs*14	ENST00000397062	NM_006164.4	597	agTAAG/ag	5/5	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.542952709411271	2		298	187	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735321	204735321	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	98	287	0	ENST00000302823.3:c.122C>A	p.Ala41Asp	p.A41D	ENST00000302823	NM_005214.4	41	gCc/gAc	2/4	1	2	FACETS	0.926	0.832	1	0.926	0.832	1	CLONAL	1	TRUE	1	0.542952709411271	2		287	390	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576848	212576848	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	24	392	0	ENST00000342788.4:c.1051A>G	p.Ser351Gly	p.S351G	ENST00000342788	NM_005235.2	351	Agt/Ggt	9/28	1	2	FACETS	0.384	0.302	0.478	0.384	0.302	0.478	SUBCLONAL	1	TRUE	1	0.542952709411271	2		392	230	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663271	227663271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	259	684	0	ENST00000305123.5:c.184C>T	p.Arg62Cys	p.R62C	ENST00000305123	NM_005544.2	62	Cgc/Tgc	1/2	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.542952709411271	2		684	761	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523292	9523292	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	196	533	0	ENST00000353224.5:c.1945del	p.Leu649SerfsTer15	p.L649Sfs*15	ENST00000353224	NM_177990.2	649	Ctc/tc	9/10	1	2	FACETS	0.968	0.899	1	0.968	0.899	1	CLONAL	1	TRUE	1	0.542952709411271	2		533	746	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268687	46268687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	174	536	0	ENST00000371998.3:c.2972T>C	p.Met991Thr	p.M991T	ENST00000371998		991	aTg/aCg	16/23	1	2	FACETS	0.925	0.854	0.998	0.925	0.854	0.998	CLONAL	1	TRUE	1	0.542952709411271	2		536	693	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171734	36171734	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	145	458	0	ENST00000300305.3:c.831del	p.Pro278ArgfsTer33	p.P278Rfs*33	ENST00000300305		277	ccA/cc	7/8	1	2	FACETS	0.978	0.897	1	0.978	0.897	1	CLONAL	1	TRUE	1	0.542952709411271	2		458	546	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12647769	12647769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	67	368	0	ENST00000251849.4:c.611G>A	p.Ser204Asn	p.S204N	ENST00000251849	NM_002880.3	204	aGt/aAt	6/17	0.542952709411271	2	FACETS	0.634	0.554	0.721	0.317	0.277	0.361	SUBCLONAL	1	TRUE	0	0.542952709411271	2		368	389	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715616	30715616	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1553630438	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	93	254	0	ENST00000295754.5:c.1274T>C	p.Met425Thr	p.M425T	ENST00000295754	NM_003242.5	425	aTg/aCg	5/7	0.542952709411271	2	FACETS	1	0.968	1	0.595	0.536	0.656	CLONAL	1	TRUE	0	0.542952709411271	2		254	288	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067452	37067452	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	408	593	0	ENST00000231790.2:c.1363del	p.Thr455LeufsTer36	p.T455Lfs*36	ENST00000231790	NM_000249.3	455	Act/ct	12/19	0.542952709411271	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.542952709411271	2		593	650	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278164	41278165	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	130	474	0	ENST00000349496.5:c.2046_2047del	p.Phe683GlnfsTer9	p.F683Qfs*9	ENST00000349496	NM_001904.3	680	agCTct/agct	13/15	0.542952709411271	2	FACETS	0.828	0.754	0.906	0.414	0.377	0.453	CLONAL	1	TRUE	0	0.542952709411271	2		474	578	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164819	47164819	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	112	340	0	ENST00000409792.3:c.1307G>T	p.Arg436Met	p.R436M	ENST00000409792	NM_014159.6	436	aGg/aTg	3/21	0.542952709411271	2	FACETS	0.944	0.855	1	0.472	0.427	0.519	CLONAL	1	TRUE	0	0.542952709411271	2		340	437	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217599	142217599	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	59	445	1	ENST00000350721.4:c.5398T>C	p.Trp1800Arg	p.W1800R	ENST00000350721	NM_001184.3	1800	Tgg/Cgg	32/47	1	2	FACETS	0.793	0.689	0.905	0.793	0.689	0.905	CLONAL	1	TRUE	1	0.542952709411271	2		446	274	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806249	1806249	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	209	712	0	ENST00000260795.2:c.1266+2T>C		p.X422_splice	ENST00000260795		422			1	2	FACETS	0.937	0.871	1	0.937	0.871	1	CLONAL	1	TRUE	1	0.542952709411271	2		712	822	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55597585	55597585	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	18	349	0	ENST00000288135.5:c.2233G>T	p.Gly745Cys	p.G745C	ENST00000288135	NM_000222.2	745	Ggc/Tgc	15/21	1	2	FACETS	0.186	0.14	0.241	0.186	0.14	0.241	SUBCLONAL	1	TRUE	1	0.542952709411271	2		349	356	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	223658	223658	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	121	416	0	ENST00000264932.6:c.125G>T	p.Arg42Met	p.R42M	ENST00000264932	NM_004168.2	42	aGg/aTg	2/15	1	2	FACETS	0.832	0.755	0.912	0.832	0.755	0.912	CLONAL	1	TRUE	1	0.542952709411271	2		416	536	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526637	31526637	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	265	642	2	ENST00000344624.3:c.403G>A	p.Ala135Thr	p.A135T	ENST00000344624		135	Gca/Aca	2/33	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.542952709411271	2		644	842	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963030	38963030	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1561464882	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	14	297	0	ENST00000357387.3:c.1514A>G	p.His505Arg	p.H505R	ENST00000357387	NM_152756.3	505	cAc/cGc	17/38	1	2	FACETS	0.273	0.197	0.364	0.273	0.197	0.364	SUBCLONAL	1	TRUE	1	0.542952709411271	2		297	189	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433789	149433789	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs113928549	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	43	829	0	ENST00000286301.3:c.2764-2A>G		p.X922_splice	ENST00000286301	NM_005211.3	922			1	2	FACETS	0.187	0.156	0.222	0.187	0.156	0.222	SUBCLONAL	1	TRUE	1	0.542952709411271	2		829	847	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271549	26271549	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	161	561	0	ENST00000305910.3:c.64G>A	p.Ala22Thr	p.A22T	ENST00000305910	NM_003534.2	22	Gcc/Acc	1/1	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.542952709411271	2		561	581	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680224	30680224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	252	777	0	ENST00000376406.3:c.1495G>A	p.Val499Met	p.V499M	ENST00000376406	NM_014641.2	499	Gtg/Atg	5/15	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.542952709411271	2		777	706	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287482	33287482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	182	675	2	ENST00000374542.5:c.1615G>A	p.Ala539Thr	p.A539T	ENST00000374542	NM_001141970.1	539	Gcc/Acc	6/8	1	2	FACETS	0.849	0.784	0.915	0.849	0.784	0.915	CLONAL	1	TRUE	1	0.542952709411271	2		677	790	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92247441	92247441	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	23	291	0	ENST00000265734.4:c.779A>G	p.Gln260Arg	p.Q260R	ENST00000265734	NM_001259.6	260	cAa/cGa	7/8	1	2	FACETS	0.209	0.162	0.263	0.209	0.162	0.263	SUBCLONAL	1	TRUE	1	0.542952709411271	2		291	406	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435790	116435790	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1263785859	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	178	582	0	ENST00000397752.3:c.3880G>A	p.Val1294Ile	p.V1294I	ENST00000397752	NM_000245.2	1294	Gtt/Att	20/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.542952709411271	2		582	603	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853377	151853377	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	160	496	0	ENST00000262189.6:c.11725C>A	p.Pro3909Thr	p.P3909T	ENST00000262189	NM_170606.2	3909	Cct/Act	45/59	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.542952709411271	2		496	546	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133879	38133879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	260	749	0	ENST00000317025.8:c.4007G>A	p.Cys1336Tyr	p.C1336Y	ENST00000317025	NM_023034.1	1336	tGt/tAt	23/24	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.542952709411271	2		749	823	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38139082	38139082	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	55	406	0	ENST00000317025.8:c.3521A>G	p.Tyr1174Cys	p.Y1174C	ENST00000317025	NM_023034.1	1174	tAc/tGc	20/24	1	2	FACETS	0.75	0.647	0.861	0.75	0.647	0.861	SUBCLONAL	1	TRUE	1	0.542952709411271	2		406	270	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274872	38274872	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	191	659	1	ENST00000425967.3:c.1708G>T	p.Gly570Trp	p.G570W	ENST00000425967	NM_001174067.1	570	Ggg/Tgg	13/19	1	2	FACETS	0.904	0.838	0.973	0.904	0.838	0.973	CLONAL	1	TRUE	1	0.542952709411271	2		660	778	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891293	101891293	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	108	549	0	ENST00000374994.4:c.254T>C	p.Val85Ala	p.V85A	ENST00000374994	NM_004612.2	85	gTa/gCa	2/9	1	2	FACETS	0.831	0.749	0.916	0.831	0.749	0.916	CLONAL	1	TRUE	1	0.542952709411271	2		549	479	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399351	139399351	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	279	1020	1	ENST00000277541.6:c.4792C>A	p.Arg1598Ser	p.R1598S	ENST00000277541	NM_017617.3	1598	Cgc/Agc	26/34	1	2	FACETS	0.943	0.886	1	0.943	0.886	1	CLONAL	1	TRUE	1	0.542952709411271	2		1021	1090	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405678	139405678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	265	946	2	ENST00000277541.6:c.2513G>A	p.Cys838Tyr	p.C838Y	ENST00000277541	NM_017617.3	838	tGc/tAc	16/34	1	2	FACETS	0.92	0.863	0.979	0.92	0.863	0.979	CLONAL	1	TRUE	1	0.542952709411271	2		948	1061	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413175	139413175	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	293	935	0	ENST00000277541.6:c.967T>C	p.Cys323Arg	p.C323R	ENST00000277541	NM_017617.3	323	Tgt/Cgt	6/34	1	2	FACETS	0.962	0.905	1	0.962	0.905	1	CLONAL	1	TRUE	1	0.542952709411271	2		935	1122	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317466	1317466	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	279	727	0	ENST00000400841.2:c.599del	p.Pro200GlnfsTer7	p.P200Qfs*7	ENST00000400841		200	cCa/ca	5/6	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.542952709411271	2		727	843	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430792	47430792	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	345	784	0	ENST00000377045.4:c.1757T>C	p.Leu586Ser	p.L586S	ENST00000377045	NM_001654.4	586	tTg/tCg	16/16	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.542952709411271	2		784	992	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245093	53245093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	242	781	1	ENST00000375401.3:c.847G>A	p.Val283Met	p.V283M	ENST00000375401	NM_004187.3	283	Gtg/Atg	7/26	1	2	FACETS	0.977	0.914	1	0.977	0.914	1	CLONAL	1	TRUE	1	0.542952709411271	2		782	912	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74868165	74868165	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	27	132	0	ENST00000284811.8:c.129del	p.Ala44ProfsTer3	p.A44Pfs*3	ENST00000284811		43	aaA/aa	3/4	1	2	FACETS	0.985	0.802	1	0.985	0.802	1	CLONAL	1	TRUE	1	0.542952709411271	2		132	101	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0055288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	2061	661	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.876041878861977	19	FACETS	1	0.997	1	1	0.997	1	CLONAL	17	TRUE	2	0.876041878861977	19		661	2304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs967461896	NA	P-0055288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	138	840	0	ENST00000269305.4:c.526T>C	p.Cys176Arg	p.C176R	ENST00000269305	NM_001126112.2	176	Tgc/Cgc	5/11	0.83485589877787	2	FACETS	0.943	0.901	0.981	0.943	0.901	0.981	CLONAL	2	TRUE	0	0.876041878861977	2		840	167	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155899	106155899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767332628	NA	P-0055288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	85	463	0	ENST00000380013.4:c.800C>T	p.Pro267Leu	p.P267L	ENST00000380013	NM_001127208.2	267	cCa/cTa	3/11	0.52029938200765	3	FACETS	1	0.971	1	0.612	0.551	0.675	INDETERMINATE	1	TRUE	1	0.876041878861977	3		463	228	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0055331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	266	341	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.629170760090288	2	FACETS	0.844	0.815	0.871	1	0.995	1	CLONAL	3	FALSE	0	0.629170760090288	2		341	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0055331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	512	545	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.629170760090288	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	FALSE	0	0.629170760090288	1		545	750	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0055331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	123	740	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	1	0.629170760090288	2		740	373	SUCCESS
APC	324	MSKCC	GRCh37	5	112154942	112154942	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779780	NA	P-0055331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	356	1101	0	ENST00000257430.4:c.1213C>T	p.Arg405Ter	p.R405*	ENST00000257430	NM_000038.5	405	Cga/Tga	10/16	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	1	0.629170760090288	2		1101	934	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467677	66467677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1343594860	NA	P-0055331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	56	415	3	ENST00000273854.3:c.592G>A	p.Glu198Lys	p.E198K	ENST00000273854	NM_004439.5	198	Gag/Aag	3/18	0.129271596742333	0	FACETS	0.178	0.153	0.205			1	INDETERMINATE	1	FALSE	0	0.629170760090288	0		418	371	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119776	70119776	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	462	910	1	ENST00000245479.2:c.779del	p.Pro260GlnfsTer19	p.P260Qfs*19	ENST00000245479	NM_000346.3	260	Cca/ca	3/3	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	FALSE	1	0.629170760090288	2		911	1103	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120511	70120511	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	467	1423	1	ENST00000245479.2:c.1513C>T	p.Gln505Ter	p.Q505*	ENST00000245479	NM_000346.3	505	Cag/Tag	3/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.629170760090288	2		1424	1440	SUCCESS
APC	324	MSKCC	GRCh37	5	112173644	112173648	+	frameshift_variant	Frame_Shift_Del	DEL	CATCG	CATCG	-	novel	NA	P-0055331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	116	362	0	ENST00000257430.4:c.2353_2357del	p.His785Ter	p.H785*	ENST00000257430	NM_000038.5	785	CATCGt/t	16/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	1	0.629170760090288	2		362	348	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978873	13978873	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0055331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	144	359	0	ENST00000405192.2:c.236-2A>C		p.X79_splice	ENST00000405192	NM_001163147.1	79			0.629170760090288	3	FACETS	1	0.97	1	0.561	0.515	0.61	CLONAL	1	FALSE	1	0.629170760090288	3		359	536	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0055362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	111	366	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.257091626994006	3	FACETS	1	0.983	1	0.669	0.612	0.728	INDETERMINATE	1	TRUE	1	0.849877956164543	3		366	278	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691039	NA	P-0055362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	256	683	0	ENST00000269305.4:c.919+1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.849877956164543	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.849877956164543	1		683	322	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591925	48591925	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	147	353	0	ENST00000342988.3:c.1088G>T	p.Cys363Phe	p.C363F	ENST00000342988	NM_005359.5	363	tGt/tTt	9/12	0.849877956164543	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.849877956164543	1		353	176	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920413	114920413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767830105	NA	P-0055362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	170	436	0	ENST00000543371.1:c.1354G>A	p.Gly452Arg	p.G452R	ENST00000543371	NM_001198531.1	452	Ggg/Agg	13/14	0.202664914915532	4	FACETS	0.889	0.828	0.952	0.889	0.828	0.952	INDETERMINATE	2	TRUE	2	0.849877956164543	4		436	416	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781862	3781862	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1274540523	NA	P-0055362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	301	553	1	ENST00000262367.5:c.4805G>A	p.Arg1602His	p.R1602H	ENST00000262367	NM_004380.2	1602	cGc/cAc	29/31	0.322884228670647	3	FACETS	0.881	0.839	0.922	0.881	0.839	0.922	INDETERMINATE	2	TRUE	1	0.849877956164543	3		554	573	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508787	31508787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370207689	NA	P-0055362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	199	580	0	ENST00000344624.3:c.1528C>T	p.Arg510Cys	p.R510C	ENST00000344624		510	Cgc/Tgc	7/33	0.257091626994006	3	FACETS	1	0.992	1	0.738	0.692	0.785	INDETERMINATE	1	TRUE	1	0.849877956164543	3		580	452	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856448	111856448	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1445323886	NA	P-0055362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	120	310	1	ENST00000341259.2:c.499G>A	p.Gly167Arg	p.G167R	ENST00000341259	NM_005475.2	167	Gga/Aga	2/8	0.257091626994006	3	FACETS	1	0.983	1	0.651	0.597	0.707	INDETERMINATE	1	TRUE	1	0.849877956164543	3		311	309	SUCCESS
APC	324	MSKCC	GRCh37	5	112175599	112175599	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	193	196	0	ENST00000257430.4:c.4308del	p.Ser1436ArgfsTer37	p.S1436Rfs*37	ENST00000257430	NM_000038.5	1436	agT/ag	16/16	0.840299527004578	2	FACETS	0.987	0.952	1	0.987	0.952	1	CLONAL	2	TRUE	0	0.849877956164543	2		196	230	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122404	17122405	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0055362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	248	665	1	ENST00000285071.4:c.990_991insAC	p.Ser331ThrfsTer23	p.S331Tfs*23	ENST00000285071	NM_144997.5	330	-/AC	9/14	0.849877956164543	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.849877956164543	1		666	317	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291101	10291101	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	193	673	0	ENST00000340748.4:c.370G>C	p.Asp124His	p.D124H	ENST00000340748		124	Gat/Cat	4/40	0.322884228670647	3	FACETS	1	0.981	1	0.574	0.534	0.614	INDETERMINATE	1	TRUE	1	0.849877956164543	3		673	564	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42861500	42861501	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	AATCA	novel	NA	P-0055362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	148	447	0	ENST00000398585.3:c.369_370insTGATT	p.Ile124Ter	p.I124*	ENST00000398585	NM_001135099.1	123	-/TGATT	4/14	0.257091626994006	3	FACETS	1	0.978	1	0.584	0.538	0.631	INDETERMINATE	1	TRUE	1	0.849877956164543	3		447	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0055456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	91	1110	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.325	0.288	0.366	0.325	0.288	0.366	SUBCLONAL	1	TRUE	1	0.518266660051812	2		1111	1079	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0055456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	196	411	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.312514863054791	1	FACETS	0.822	0.764	0.881	0.822	0.764	0.881	CLONAL	1	TRUE	0	0.518266660051812	1		411	682	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0055456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	20	576	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.127	0.096	0.163	0.127	0.096	0.163	SUBCLONAL	1	TRUE	1	0.518266660051812	2		576	610	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117870	70117870	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	38	608	0	ENST00000245479.2:c.338T>C	p.Met113Thr	p.M113T	ENST00000245479	NM_000346.3	113	aTg/aCg	1/3	1	2	FACETS	0.213	0.175	0.255	0.213	0.175	0.255	SUBCLONAL	1	TRUE	1	0.518266660051812	2		608	690	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	85	244	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.518266660051812	2		244	282	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112919929	112919929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1214510641	NA	P-0055456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	28	283	0	ENST00000351677.2:c.1144G>A	p.Val382Ile	p.V382I	ENST00000351677	NM_002834.3	382	Gtc/Atc	10/16	1	2	FACETS	0.301	0.24	0.37	0.301	0.24	0.37	SUBCLONAL	1	TRUE	1	0.518266660051812	2		283	359	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120535147	120535147	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771876856	NA	P-0055456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	70	604	1	ENST00000229340.5:c.508C>T	p.Arg170Ter	p.R170*	ENST00000229340	NM_006861.6	170	Cga/Tga	6/6	1	2	FACETS	0.332	0.289	0.379	0.332	0.289	0.379	SUBCLONAL	1	TRUE	1	0.518266660051812	2		605	813	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89846290	89846290	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778754162	NA	P-0055456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	69	777	0	ENST00000389301.3:c.1702G>A	p.Val568Ile	p.V568I	ENST00000389301	NM_000135.2	568	Gtc/Atc	18/43	1	2	FACETS	0.285	0.247	0.326	0.285	0.247	0.326	SUBCLONAL	1	TRUE	1	0.518266660051812	2		777	935	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56338949	56338949	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	11	24	0	ENST00000348428.3:c.74C>T	p.Pro25Leu	p.P25L	ENST00000348428	NM_006785.3	25	cCg/cTg	1/17	1	2	FACETS	0.624	0.439	0.845	0.624	0.439	0.845	SUBCLONAL	1	TRUE	1	0.518266660051812	2		24	68	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146978	38146991	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTGTGCTTTCAA	CTTTGTGCTTTCAA	-	novel	NA	P-0055456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	65	599	0	ENST00000317025.8:c.3151_3164del	p.Leu1051ArgfsTer3	p.L1051Rfs*3	ENST00000317025	NM_023034.1	1051	TTGAAAGCACAAAGa/a	18/24	1	2	FACETS	0.284	0.245	0.326	0.284	0.245	0.326	SUBCLONAL	1	TRUE	1	0.518266660051812	2		599	884	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224460	53224460	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	252	486	0	ENST00000375401.3:c.3253del	p.Ala1085ProfsTer62	p.A1085Pfs*62	ENST00000375401	NM_004187.3	1085	Gcc/cc	21/26	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.518266660051812	1		486	562	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0055470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	104	190	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.560884520874751	4	FACETS	0.885	0.811	0.96	0.885	0.811	0.96	CLONAL	3	TRUE	1	0.560884520874751	4		190	218	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646594	23646594	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576081828	NA	P-0055470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	37	548	0	ENST00000261584.4:c.1273G>A	p.Val425Met	p.V425M	ENST00000261584	NM_024675.3	425	Gtg/Atg	4/13	1	2	FACETS	0.857	0.717	1	0.857	0.717	1	CLONAL	1	TRUE	1	0.560884520874751	2		548	154	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691936	30691938	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	novel	NA	P-0055470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	27	310	0	ENST00000295754.5:c.442_444del	p.Ile148del	p.I148del	ENST00000295754	NM_003242.5	146	aaCATc/aac	3/7	0.560884520874751	1	FACETS	0.835	0.684	0.995	0.835	0.684	0.995	CLONAL	1	TRUE	0	0.560884520874751	1		310	83	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176104158	176104158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	28	343	0	ENST00000367669.3:c.956C>T	p.Ser319Phe	p.S319F	ENST00000367669	NM_022457.5	319	tCt/tTt	8/20	0.560884520874751	3	FACETS	0.68	0.548	0.828	0.34	0.274	0.414	SUBCLONAL	1	TRUE	1	0.560884520874751	3		343	188	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16021323	16021323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	33	273	0	ENST00000268712.3:c.1934G>T	p.Arg645Leu	p.R645L	ENST00000268712	NM_006311.3	645	cGt/cTt	18/46	0.159846375719696	1	FACETS	0.73	0.608	0.861	0.73	0.608	0.861	INDETERMINATE	1	TRUE	0	0.560884520874751	1		273	116	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266059	41266235	+	inframe_deletion	In_Frame_Del	DEL	AAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAAC	AAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAAC	-	novel	NA	P-0055470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	12	366	0	ENST00000349496.5:c.59_235del	p.Ala20_Gln78del	p.A20_Q78del	ENST00000349496	NM_001904.3	19	aAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACaa/aaa	3/15	0.560884520874751	1	FACETS	0.261	0.184	0.353	0.261	0.184	0.353	SUBCLONAL	1	TRUE	0	0.560884520874751	1		366	118	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0055530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	82	311	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.302870187556546	3	FACETS	0.818	0.722	0.921	0.409	0.361	0.461	CLONAL	1	TRUE	1	0.383491374325938	3		311	623	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0055530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	141	219	0	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	0.383491374325938	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.383491374325938	2		219	348	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120244	70120244	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	353	597	0	ENST00000245479.2:c.1246C>T	p.Gln416Ter	p.Q416*	ENST00000245479	NM_000346.3	416	Caa/Taa	3/3	0.383491374325938	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.383491374325938	2		597	867	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500661	99500661	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370843278	NA	P-0055530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	108	471	1	ENST00000268035.6:c.4094C>T	p.Ser1365Leu	p.S1365L	ENST00000268035	NM_000875.3	1365	tCg/tTg	21/21	1	2	FACETS	0.953	0.858	1	0.953	0.858	1	CLONAL	1	TRUE	1	0.383491374325938	2		472	591	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748194	41748194	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	133	516	0	ENST00000226382.2:c.575C>A	p.Pro192Gln	p.P192Q	ENST00000226382	NM_003924.3	192	cCg/cAg	3/3	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.383491374325938	2		516	661	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680043	30680043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	206	622	0	ENST00000376406.3:c.1676C>T	p.Pro559Leu	p.P559L	ENST00000376406	NM_014641.2	559	cCa/cTa	5/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.383491374325938	2		622	983	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979544	2979544	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766516628	NA	P-0055530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	110	380	0	ENST00000396946.4:c.703C>T	p.Arg235Trp	p.R235W	ENST00000396946	NM_032415.4	235	Cgg/Tgg	6/25	0.302870187556546	3	FACETS	0.934	0.84	1	0.467	0.42	0.517	CLONAL	1	TRUE	1	0.383491374325938	3		380	732	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087494	27087494	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	189	680	0	ENST00000324856.7:c.2069del	p.Pro690LeufsTer52	p.P690Lfs*52	ENST00000324856	NM_006015.4	690	Cct/ct	5/20	1	2	FACETS	0.982	0.907	1	0.982	0.907	1	CLONAL	1	TRUE	1	0.383491374325938	2		680	1004	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101090	27101090	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	233	720	1	ENST00000324856.7:c.4372C>T	p.Gln1458Ter	p.Q1458*	ENST00000324856	NM_006015.4	1458	Cag/Tag	18/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.383491374325938	2		721	1093	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46240721	46240722	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0055530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	73	273	0	ENST00000334344.6:c.1580+2dup		p.X527_splice	ENST00000334344	NM_152641.2	527			1	2	FACETS	0.986	0.867	1	0.986	0.867	1	CLONAL	1	TRUE	1	0.383491374325938	2		273	386	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5225822	5225822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202087387	NA	P-0055530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	168	665	1	ENST00000357368.4:c.2410G>A	p.Ala804Thr	p.A804T	ENST00000357368	NM_002850.3	804	Gcg/Acg	17/38	1	2	FACETS	0.94	0.864	1	0.94	0.864	1	CLONAL	1	TRUE	1	0.383491374325938	2		666	932	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251627	212251627	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	119	467	1	ENST00000342788.4:c.3432G>T	p.Glu1144Asp	p.E1144D	ENST00000342788	NM_005235.2	1144	gaG/gaT	27/28	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.383491374325938	2		468	614	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637453	176637453	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	278	400	0	ENST00000439151.2:c.2053A>C	p.Lys685Gln	p.K685Q	ENST00000439151	NM_022455.4	685	Aag/Cag	5/23	0.383491374325938	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.383491374325938	2		400	665	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188775	32188775	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	189	736	0	ENST00000375023.3:c.779A>G	p.His260Arg	p.H260R	ENST00000375023	NM_004557.3	260	cAc/cGc	4/30	1	2	FACETS	0.995	0.919	1	0.995	0.919	1	CLONAL	1	TRUE	1	0.383491374325938	2		736	991	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0055546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	132	190	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.349528183386627	3	FACETS	0.872	0.796	0.95	0.872	0.796	0.95	CLONAL	2	TRUE	1	0.349528183386627	3		190	509	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0055546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	122	712	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.349528183386627	2		712	645	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0055546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	72	187	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.349528183386627	2		188	362	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0055546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	35	265	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.693	0.57	0.83	0.693	0.57	0.83	SUBCLONAL	1	TRUE	1	0.349528183386627	2		265	289	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0055546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	37	431	0				ENST00000310581	NM_198253.2	-/1132			0.137193640255345	1	FACETS	0.805	0.669	0.954	0.805	0.669	0.954	INDETERMINATE	1	TRUE	0	0.349528183386627	1		431	217	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137087	64137087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	80	317	0	ENST00000334205.4:c.1598C>T	p.Pro533Leu	p.P533L	ENST00000334205	NM_003942.2	533	cCg/cTg	13/17	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.349528183386627	2		317	381	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385262	4385262	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	103	560	0	ENST00000261254.3:c.287C>T	p.Ser96Phe	p.S96F	ENST00000261254	NM_001759.3	96	tCc/tTc	2/5	0.349528183386627	3	FACETS	0.993	0.89	1	0.497	0.445	0.552	CLONAL	1	TRUE	1	0.349528183386627	3		560	697	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046512	30046512	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	96	613	1	ENST00000331968.5:c.2671C>A	p.His891Asn	p.H891N	ENST00000331968	NM_002742.2	891	Cac/Aac	18/18	1	2	FACETS	0.957	0.855	1	0.957	0.855	1	CLONAL	1	TRUE	1	0.349528183386627	2		614	574	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934821	9934821	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	51	479	0	ENST00000330684.3:c.1469A>C	p.Asn490Thr	p.N490T	ENST00000330684	NM_001134407.1	490	aAc/aCc	6/13	1	2	FACETS	0.671	0.571	0.78	0.671	0.571	0.78	SUBCLONAL	1	TRUE	1	0.349528183386627	2		479	435	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118865	70118865	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	104	546	0	ENST00000245479.2:c.437T>C	p.Leu146Pro	p.L146P	ENST00000245479	NM_000346.3	146	cTg/cCg	2/3	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.349528183386627	2		546	537	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645381	215645381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780014	NA	P-0055546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	74	571	0	ENST00000260947.4:c.1217G>A	p.Arg406Gln	p.R406Q	ENST00000260947	NM_000465.2	406	cGa/cAa	4/11	1	2	FACETS	0.88	0.773	0.995	0.88	0.773	0.995	CLONAL	1	TRUE	1	0.349528183386627	2		571	481	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520171	9520171	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	42	461	0	ENST00000353224.5:c.2098T>G	p.Leu700Val	p.L700V	ENST00000353224	NM_177990.2	700	Tta/Gta	10/10	0.349528183386627	3	FACETS	0.526	0.438	0.623	0.263	0.219	0.312	SUBCLONAL	1	TRUE	1	0.349528183386627	3		461	537	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266043	41266623	+	splice_acceptor_variant,splice_donor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	ATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATT	ATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATT	-	novel	NA	P-0055546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	43	338	0	ENST00000349496.5:c.41_421del		p.X14_splice	ENST00000349496	NM_001904.3	14	ATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATT/-	3-4/15	1	2	FACETS	0.776	0.652	0.912	0.776	0.652	0.912	CLONAL	1	TRUE	1	0.349528183386627	2		338	317	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670859	134670859	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	68	443	0	ENST00000398015.3:c.770C>A	p.Pro257His	p.P257H	ENST00000398015	NM_004441.4	257	cCt/cAt	3/16	1	2	FACETS	0.903	0.788	1	0.903	0.788	1	CLONAL	1	TRUE	1	0.349528183386627	2		443	431	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403621	138403621	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	26	398	0	ENST00000289153.2:c.2161A>C	p.Thr721Pro	p.T721P	ENST00000289153	NM_006219.2	721	Act/Cct	15/22	1	2	FACETS	0.33	0.261	0.41	0.33	0.261	0.41	SUBCLONAL	1	TRUE	1	0.349528183386627	2		398	451	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446883	187446883	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	84	694	0	ENST00000232014.4:c.1310A>C	p.Asp437Ala	p.D437A	ENST00000232014	NM_001130845.1	437	gAc/gCc	5/10	1	2	FACETS	0.713	0.63	0.802	0.713	0.63	0.802	SUBCLONAL	1	TRUE	1	0.349528183386627	2		694	674	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0055715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	394	190	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.532431100742996	4	FACETS	0.901	0.862	0.939	0.901	0.862	0.939	CLONAL	3	TRUE	1	0.572514261945589	4		190	801	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0055715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	486	545	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.572514261945589	2	FACETS	0.873	0.84	0.907	0.873	0.84	0.907	CLONAL	2	TRUE	0	0.572514261945589	2		545	972	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0055715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	323	469	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.273991018927551	4	FACETS	1	0.981	1			1	INDETERMINATE	3	TRUE	NA	0.572514261945589	4		469	566	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279237	142279237	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1445735789	NA	P-0055715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	332	481	0	ENST00000350721.4:c.1409C>G	p.Ala470Gly	p.A470G	ENST00000350721	NM_001184.3	470	gCt/gGt	6/47	0.572514261945589	2	FACETS	0.986	0.944	1	0.986	0.944	1	CLONAL	2	TRUE	0	0.572514261945589	2		481	588	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630764	187630764	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	209	687	0	ENST00000441802.2:c.218A>G	p.Lys73Arg	p.K73R	ENST00000441802	NM_005245.3	73	aAa/aGa	2/27	0.200527575612025	0	FACETS	0.422	0.393	0.452			1	INDETERMINATE	1	TRUE	0	0.572514261945589	0		687	739	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739743	41739743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	176	693	1	ENST00000242208.4:c.230C>T	p.Pro77Leu	p.P77L	ENST00000242208	NM_002192.2	77	cCg/cTg	2/3	0.437949693726981	4	FACETS	0.73	0.67	0.792	0.365	0.335	0.396	SUBCLONAL	1	TRUE	2	0.572514261945589	4		694	1325	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0055813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	54	319	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	0.220887816770786	3	FACETS	0.939	0.803	1	0.47	0.401	0.544	CLONAL	1	TRUE	1	0.272180768731404	3		319	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579529	7579529	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658483	NA	P-0055813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	140	777	1	ENST00000269305.4:c.158G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tGg/tAg	4/11	0.258554897455647	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.272180768731404	1		778	872	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0055813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	85	265	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.272180768731404	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.272180768731404	1		265	438	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	54	348	0	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	1	2	FACETS	0.859	0.735	0.994	0.859	0.735	0.994	CLONAL	1	TRUE	1	0.272180768731404	2		348	462	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0055813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	53	696	3	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.793	0.677	0.92	0.793	0.677	0.92	CLONAL	1	TRUE	1	0.272180768731404	2		699	491	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42870072	42870072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	84	645	0	ENST00000398585.3:c.100G>A	p.Asp34Asn	p.D34N	ENST00000398585	NM_001135099.1	34	Gat/Aat	2/14	0.229280360813311	3	FACETS	0.761	0.671	0.859	0.381	0.335	0.43	SUBCLONAL	1	TRUE	1	0.272180768731404	3		645	921	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928439	69928439	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	124	678	1	ENST00000352241.4:c.259C>T	p.Gln87Ter	p.Q87*	ENST00000352241	NM_198159.2	87	Caa/Taa	2/10	0.272180768731404	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.272180768731404	1		679	763	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851558	128851558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201898555	NA	P-0055813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	97	777	0	ENST00000249373.3:c.1883G>A	p.Arg628Gln	p.R628Q	ENST00000249373	NM_005631.4	628	cGg/cAg	11/12	0.220887816770786	3	FACETS	0.811	0.721	0.906	0.405	0.36	0.453	CLONAL	1	TRUE	1	0.272180768731404	3		777	999	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0055836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	121	947	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.30484881784841	1	FACETS	0.884	0.799	0.974	0.884	0.799	0.974	CLONAL	1	TRUE	0	0.31	1		947	746	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593387	48593387	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0055836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	83	379	0	ENST00000342988.3:c.1140-2A>T		p.X380_splice	ENST00000342988	NM_005359.5	380			0.30484881784841	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.31	1		379	372	SUCCESS
APC	324	MSKCC	GRCh37	5	112162945	112162945	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1114167599	NA	P-0055836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	27	346	1	ENST00000257430.4:c.1548+1G>A		p.X516_splice	ENST00000257430	NM_000038.5	516			0.30484881784841	1	FACETS	0.643	0.514	0.788	0.643	0.514	0.788	SUBCLONAL	1	TRUE	0	0.31	1		347	229	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120291	70120292	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	177	879	0	ENST00000245479.2:c.1294dup	p.Tyr432LeufsTer146	p.Y432Lfs*146	ENST00000245479	NM_000346.3	431	-/T	3/3	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.31	2		879	967	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912172	114912172	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	126	656	0	ENST00000543371.1:c.1242C>A	p.Tyr414Ter	p.Y414*	ENST00000543371	NM_001198531.1	414	taC/taA	11/14	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.31	2		656	763	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748161	43748161	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	90	651	0	ENST00000382044.4:c.2645C>A	p.Ser882Ter	p.S882*	ENST00000382044	NM_001141980.1	882	tCa/tAa	12/28	1	2	FACETS	0.859	0.762	0.962	0.859	0.762	0.962	CLONAL	1	TRUE	1	0.31	2		651	676	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356095	66356095	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	64	534	0	ENST00000273854.3:c.1402G>T	p.Ala468Ser	p.A468S	ENST00000273854	NM_004439.5	468	Gct/Tct	5/18	1	2	FACETS	0.818	0.709	0.935	0.818	0.709	0.935	CLONAL	1	TRUE	1	0.31	2		534	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0055880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	181	1110	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.251848398942401	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.251848398942401	1		1111	864	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0055880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	79	696	3	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.196146997424512	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.251848398942401	1		699	430	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041026	112041026	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746134687	NA	P-0055880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	59	462	1	ENST00000368678.4:c.229C>T	p.Arg77Cys	p.R77C	ENST00000368678		77	Cgt/Tgt	3/13	1	2	FACETS	0.696	0.598	0.803	0.696	0.598	0.803	SUBCLONAL	1	TRUE	1	0.251848398942401	2		463	673	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281176	49281176	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758137158	NA	P-0055880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1361	92	820	1	ENST00000282018.3:c.223G>A	p.Val75Ile	p.V75I	ENST00000282018	NM_020377.2	75	Gtt/Att	1/1	0.251848398942401	4	FACETS	0.629	0.557	0.708	0.21	0.185	0.236	SUBCLONAL	1	TRUE	1	0.251848398942401	4		821	1453	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014141	70014141	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	45	607	0	ENST00000394351.3:c.1002C>G	p.Asp334Glu	p.D334E	ENST00000394351	NM_000248.3	334	gaC/gaG	9/9	0.152734685320828	3	FACETS	0.447	0.374	0.528	0.224	0.187	0.264	SUBCLONAL	1	TRUE	1	0.251848398942401	3		607	900	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137528202	137528202	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	74	263	0	ENST00000367739.4:c.98C>G	p.Thr33Ser	p.T33S	ENST00000367739	NM_000416.2	33	aCt/aGt	2/7	0.742091362665788	4	FACETS	0.851	0.749	0.959	0.425	0.374	0.48	CLONAL	1	TRUE	2	0.809200459949802	4		263	389	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898755	134898755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs546798910	NA	P-0055901-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	76	581	0	ENST00000398015.3:c.1813G>A	p.Glu605Lys	p.E605K	ENST00000398015	NM_004441.4	605	Gaa/Aaa	10/16	1	2	FACETS	0.805	0.708	0.908	1	0.978	1	CLONAL	2	FALSE	1	0.203996022854682	2		581	463	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427930	49427930	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055901-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	38	681	0	ENST00000301067.7:c.10660C>G	p.Arg3554Gly	p.R3554G	ENST00000301067	NM_003482.3	3554	Cgt/Ggt	38/54	1	2	FACETS	0.837	0.692	0.999	0.837	0.692	0.999	CLONAL	1	FALSE	1	0.203996022854682	2		681	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578206	+	protein_altering_variant	In_Frame_Ins	INS	-	-	ACACCACAG	novel	NA	P-0055901-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	70	735	0	ENST00000269305.4:c.643_644insCTGTGGTGT	p.Ser215delinsThrValValCys	p.S215delinsTVVC	ENST00000269305	NM_001126112.2	215	agt/aCTGTGGTGTgt	6/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.203996022854682	2		735	530	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0055974-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	368	285	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.448078570116158	7	FACETS	1	0.974	1	1	0.974	1	CLONAL	5	TRUE	2	0.448078570116158	7		285	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577523	7577523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055974-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	282	388	0	ENST00000269305.4:c.758C>T	p.Thr253Ile	p.T253I	ENST00000269305	NM_001126112.2	253	aCc/aTc	7/11	0.41186074142454	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.448078570116158	3		388	724	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791286	42791286	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs61741480	NA	P-0055974-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	261	391	0	ENST00000575354.2:c.346G>T	p.Val116Leu	p.V116L	ENST00000575354	NM_015125.3	116	Gtg/Ttg	3/20	0.382221427924631	4	FACETS	0.996	0.936	1	0.996	0.936	1	CLONAL	2	TRUE	2	0.448078570116158	4		391	847	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998382	100998382	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055974-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	236	333	0	ENST00000325455.5:c.1420C>A	p.Pro474Thr	p.P474T	ENST00000325455	NM_001202474.3	474	Ccg/Acg	1/8	0.382221427924631	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.448078570116158	4		333	683	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101064	4101064	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs727504363	NA	P-0055974-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	130	207	0	ENST00000262948.5:c.658A>G	p.Ile220Val	p.I220V	ENST00000262948	NM_030662.3	220	Atc/Gtc	6/11	0.448078570116158	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	0	0.448078570116158	2		207	289	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259388	89259388	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055974-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	108	401	0	ENST00000336596.2:c.532G>T	p.Gly178Ter	p.G178*	ENST00000336596	NM_005233.5	178	Gga/Tga	3/17	0.41186074142454	3	FACETS	0.925	0.832	1	0.462	0.415	0.512	CLONAL	1	TRUE	1	0.448078570116158	3		401	638	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231111	142231111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055974-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	67	252	0	ENST00000350721.4:c.4843G>A	p.Asp1615Asn	p.D1615N	ENST00000350721	NM_001184.3	1615	Gac/Aac	27/47	0.41186074142454	3	FACETS	0.911	0.795	1	0.455	0.397	0.518	CLONAL	1	TRUE	1	0.448078570116158	3		252	402	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450319	50450320	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0055974-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	179	407	0	ENST00000331340.3:c.503_504delinsAA	p.Ser168Ter	p.S168*	ENST00000331340	NM_006060.4	168	tCC/tAA	5/8	0.333676940731208	6	FACETS	0.843	0.777	0.911	0.421	0.388	0.456	CLONAL	2	TRUE	2	0.448078570116158	6		407	899	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375964	8375964	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs144763077	NA	P-0055974-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	122	365	0	ENST00000356435.5:c.4633G>T	p.Asp1545Tyr	p.D1545Y	ENST00000356435		1545	Gat/Tat	28/35	0.361638418679535	3	FACETS	1	0.972	1	0.591	0.536	0.648	CLONAL	1	TRUE	1	0.448078570116158	3		365	564	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002710	37002710	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055974-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	295	420	0	ENST00000358127.4:c.539C>A	p.Ser180Tyr	p.S180Y	ENST00000358127	NM_001280556.1	180	tCc/tAc	5/10	0.41186074142454	3	FACETS	0.995	0.94	1	0.995	0.94	1	CLONAL	2	TRUE	1	0.448078570116158	3		420	810	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039668	47039668	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055974-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	133	400	0	ENST00000377604.3:c.1120G>C	p.Gly374Arg	p.G374R	ENST00000377604	NM_001204468.1	374	Ggc/Cgc	11/24	1	2	FACETS	0.936	0.853	1	0.936	0.853	1	CLONAL	1	TRUE	1	0.448078570116158	2		400	634	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412245	63412245	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055974-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	176	567	0	ENST00000330258.3:c.922C>G	p.Pro308Ala	p.P308A	ENST00000330258	NM_152424.3	308	Cca/Gca	2/2	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.448078570116158	2		567	762	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230461056	230461056	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055974-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	145	309	0	ENST00000391860.1:c.1034A>T	p.Lys345Met	p.K345M	ENST00000391860	NM_001258311.1	345	aAg/aTg	6/7	0.371991612399344	5	FACETS	0.855	0.782	0.93	0.57	0.521	0.62	CLONAL	2	TRUE	2	0.448078570116158	5		309	633	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690125	33690125	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0055974-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	122	454	0	ENST00000308377.4:c.702C>G	p.Tyr234Ter	p.Y234*	ENST00000308377	NM_152270.3	234	taC/taG	2/5	0.41186074142454	3	FACETS	1	0.953	1	0.541	0.49	0.594	CLONAL	1	TRUE	1	0.448078570116158	3		454	616	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132565	11132568	+	frameshift_variant	Frame_Shift_Del	DEL	CCTG	CCTG	-	novel	NA	P-0055974-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	341	470	0	ENST00000358026.2:c.2782_2785del	p.Leu928CysfsTer21	p.L928Cfs*21	ENST00000358026	NM_001128849.1	927	ttCCTG/tt	19/36	0.448078570116158	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.448078570116158	2		470	715	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161990442	161990442	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055974-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	79	356	0	ENST00000366898.1:c.878G>T	p.Cys293Phe	p.C293F	ENST00000366898	NM_004562.2	293	tGt/tTt	8/12	0.41186074142454	3	FACETS	0.783	0.69	0.883	0.392	0.345	0.442	SUBCLONAL	1	TRUE	1	0.448078570116158	3		356	551	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124537219	124537219	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055974-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	89	130	0	ENST00000357628.3:c.9G>T	p.Leu3Phe	p.L3F	ENST00000357628	NM_015450.2	3	ttG/ttT	5/19	0.333676940731208	6	FACETS	1	0.929	1	0.778	0.702	0.857	CLONAL	3	TRUE	2	0.448078570116158	6		130	242	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0055990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	232	405	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.604154896089986	1	FACETS	0.993	0.934	1	0.993	0.934	1	CLONAL	1	TRUE	0	0.604154896089986	1		405	540	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0055990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	190	425	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.382780913466001	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.604154896089986	4		425	447	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106036	8106036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	224	454	0	ENST00000346208.3:c.856G>A	p.Ala286Thr	p.A286T	ENST00000346208		286	Gcc/Acc	4/6	0.306955957616425	3	FACETS	1	0.988	1	0.629	0.588	0.672	INDETERMINATE	1	TRUE	1	0.604154896089986	3		454	767	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8525018	8525018	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1329822805	NA	P-0055990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	73	195	0	ENST00000356435.5:c.586C>T	p.Gln196Ter	p.Q196*	ENST00000356435		196	Cag/Tag	7/35	0.110679376098186	3	FACETS	0.915	0.806	1	0.305	0.268	0.344	INDETERMINATE	1	TRUE	0	0.604154896089986	3		195	344	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340429	8340429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	270	422	0	ENST00000356435.5:c.5167G>A	p.Glu1723Lys	p.E1723K	ENST00000356435		1723	Gag/Aag	31/35	0.110679376098186	3	FACETS	0.807	0.761	0.854	0.538	0.507	0.569	INDETERMINATE	2	TRUE	0	0.604154896089986	3		422	721	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711961	89711962	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	159	307	0	ENST00000371953.3:c.581dup	p.Leu194PhefsTer8	p.L194Ffs*8	ENST00000371953	NM_000314.4	193	-/T	6/9	0.533767575367368	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.604154896089986	1		307	290	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339874	70339874	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	78	438	0	ENST00000374080.3:c.407T>G	p.Phe136Cys	p.F136C	ENST00000374080		136	tTc/tGc	4/45	0.499557878561584	1	FACETS	0.383	0.337	0.431	0.383	0.337	0.431	SUBCLONAL	1	TRUE	0	0.604154896089986	1		438	471	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0055998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	107	366	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.250861024118116	3	FACETS	1	0.967	1	1	0.987	1	CLONAL	3	TRUE	1	0.250861024118116	3		366	283	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0055998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	109	740	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.962	0.876	1	1	0.991	1	CLONAL	3	TRUE	1	0.250861024118116	2		740	301	SUCCESS
APC	324	MSKCC	GRCh37	5	112163677	112163677	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0055998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	73	273	0	ENST00000257430.4:c.1600A>T	p.Lys534Ter	p.K534*	ENST00000257430	NM_000038.5	534	Aaa/Taa	13/16	1	2	FACETS	1	0.914	1	1	0.987	1	CLONAL	3	TRUE	1	0.250861024118116	2		273	189	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577144	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs879253942	NA	P-0055998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	84	622	0	ENST00000269305.4:c.794T>C	p.Leu265Pro	p.L265P	ENST00000269305	NM_001126112.2	265	cTg/cCg	8/11	1	2	FACETS	0.907	0.801	1	0.907	0.801	1	CLONAL	1	TRUE	1	0.250861024118116	2		622	738	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411576	63411576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	295	487	0	ENST00000330258.3:c.1591C>T	p.Arg531Ter	p.R531*	ENST00000330258	NM_152424.3	531	Cga/Tga	2/2	0.132782988315469	2	FACETS	1	0.992	1			1	INDETERMINATE	6	TRUE	NA	0.250861024118116	2		487	362	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55130043	55130043	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774431464	NA	P-0055998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	37	661	0	ENST00000257290.5:c.577G>A	p.Val193Ile	p.V193I	ENST00000257290	NM_006206.4	193	Gtc/Atc	4/23	1	2	FACETS	0.502	0.413	0.602	0.502	0.413	0.602	SUBCLONAL	1	TRUE	1	0.250861024118116	2		661	588	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911625	114911625	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	208	569	0	ENST00000543371.1:c.1143C>A	p.Asn381Lys	p.N381K	ENST00000543371	NM_001198531.1	381	aaC/aaA	10/14	1	2	FACETS	1	0.979	1	1	0.994	1	CLONAL	2	TRUE	1	0.250861024118116	2		569	736	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0056001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	661	891	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.748264509211847	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.748264509211847	1		891	1056	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0056001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	183	366	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.748264509211847	1	FACETS	0.997	0.941	1	0.997	0.941	1	CLONAL	1	TRUE	0	0.748264509211847	1		366	307	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0056001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	155	318	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.829	0.764	0.895	0.829	0.764	0.895	CLONAL	1	TRUE	1	0.748264509211847	2		318	500	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0056001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	461	344	2	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	0.748264509211847	1	FACETS	0.872	0.839	0.906	0.872	0.839	0.906	CLONAL	1	TRUE	0	0.748264509211847	1		346	884	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0056001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	201	372	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	1	2	FACETS	0.959	0.896	1	0.959	0.896	1	CLONAL	1	TRUE	1	0.748264509211847	2		372	560	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248584	212248584	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0056001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	435	532	0	ENST00000342788.4:c.3683C>G	p.Ser1228Ter	p.S1228*	ENST00000342788	NM_005235.2	1228	tCa/tGa	28/28	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.748264509211847	2		532	1139	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044522	47044522	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	558	400	4	ENST00000377604.3:c.2020del	p.Gln674SerfsTer30	p.Q674Sfs*30	ENST00000377604	NM_001204468.1	673	ttC/tt	18/24	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.748264509211847	1		404	793	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0056008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	165	190	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.456040290521411	3	FACETS	0.985	0.914	1	0.985	0.914	1	CLONAL	2	TRUE	1	0.456040290521411	3		190	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0056008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	274	493	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.456040290521411	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.456040290521411	1		493	839	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0056008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	86	444	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	0.809	0.719	0.905	0.809	0.719	0.905	CLONAL	1	TRUE	1	0.456040290521411	2		444	466	SUCCESS
APC	324	MSKCC	GRCh37	5	112174043	112174043	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	91	306	0	ENST00000257430.4:c.2752G>T	p.Glu918Ter	p.E918*	ENST00000257430	NM_000038.5	918	Gag/Tag	16/16	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.456040290521411	2		306	380	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002701	37002701	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	130	617	0	ENST00000358127.4:c.548G>C	p.Gly183Ala	p.G183A	ENST00000358127	NM_001280556.1	183	gGc/gCc	5/10	0.196667157914996	2	FACETS	0.62	0.561	0.681	0.31	0.28	0.341	INDETERMINATE	1	TRUE	0	0.456040290521411	2		617	920	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238957	5238957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760549393	NA	P-0056008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	41	584	0	ENST00000357368.4:c.1822G>A	p.Val608Met	p.V608M	ENST00000357368	NM_002850.3	608	Gtg/Atg	13/38	0.324387692498738	2	FACETS	0.259	0.215	0.308	0.13	0.107	0.154	SUBCLONAL	1	TRUE	0	0.456040290521411	2		584	694	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0056085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	167	545	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.376762379845912	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.376762379845912	1		545	715	SUCCESS
APC	324	MSKCC	GRCh37	5	112175328	112175328	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0056088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	159	338	0	ENST00000257430.4:c.4037C>G	p.Ser1346Ter	p.S1346*	ENST00000257430	NM_000038.5	1346	tCa/tGa	16/16	0.432743241494684	2	FACETS	0.969	0.901	1	0.969	0.901	1	CLONAL	2	TRUE	0	0.432743241494684	2		338	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577520	7577520	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	384	773	0	ENST00000269305.4:c.761T>A	p.Ile254Asn	p.I254N	ENST00000269305	NM_001126112.2	254	aTc/aAc	7/11	0.432743241494684	2	FACETS	0.982	0.937	1	0.982	0.937	1	CLONAL	2	TRUE	0	0.432743241494684	2		773	904	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055982	180055982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147644625	NA	P-0056088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	74	829	0	ENST00000261937.6:c.1003G>A	p.Val335Ile	p.V335I	ENST00000261937	NM_182925.4	335	Gtc/Atc	8/30	0.427695873653059	3	FACETS	0.399	0.348	0.455	0.133	0.116	0.152	SUBCLONAL	1	TRUE	0	0.432743241494684	3		829	1042	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190860	106190860	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	141	557	0	ENST00000380013.4:c.4138C>A	p.His1380Asn	p.H1380N	ENST00000380013	NM_001127208.2	1380	Cat/Aat	9/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.432743241494684	2		557	616	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587181	212587181	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	102	599	0	ENST00000342788.4:c.820C>A	p.Gln274Lys	p.Q274K	ENST00000342788	NM_005235.2	274	Caa/Aaa	7/28	0.404986780332477	3	FACETS	0.62	0.553	0.691	0.31	0.276	0.346	SUBCLONAL	1	TRUE	1	0.432743241494684	3		599	925	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553227	106553227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	297	780	0	ENST00000369096.4:c.1192C>T	p.Leu398Phe	p.L398F	ENST00000369096	NM_001198.3	398	Ctc/Ttc	5/7	0.230577358409924	2	FACETS	0.772	0.729	0.816	0.772	0.729	0.816	INDETERMINATE	2	TRUE	0	0.432743241494684	2		780	889	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443613	29443613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519783	NA	P-0056097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	49	859	0	ENST00000389048.3:c.3604G>A	p.Gly1202Arg	p.G1202R	ENST00000389048	NM_004304.4	1202	Gga/Aga	23/29	0.747125836259569	2	FACETS	0.745	0.642	0.855	0.373	0.321	0.428	SUBCLONAL	1	TRUE	0	0.747125836259569	2		859	176	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788631	3788631	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	78	439	0	ENST00000262367.5:c.4323del	p.Pro1442HisfsTer17	p.P1442Hfs*17	ENST00000262367	NM_004380.2	1441	cgG/cg	26/31	0.747125836259569	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.747125836259569	3		439	122	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950397	17950397	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	54	949	0	ENST00000458235.1:c.1330A>C	p.Ser444Arg	p.S444R	ENST00000458235	NM_000215.3	444	Agc/Cgc	10/24	0.676583515253366	3	FACETS	0.928	0.803	1	0.464	0.401	0.531	CLONAL	1	TRUE	1	0.747125836259569	3		949	214	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228803	36228803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	56	1001	0	ENST00000222270.7:c.7702C>T	p.His2568Tyr	p.H2568Y	ENST00000222270	NM_014727.1	2568	Cac/Tac	35/37	0.676583515253366	3	FACETS	0.962	0.836	1	0.481	0.418	0.548	CLONAL	1	TRUE	1	0.747125836259569	3		1001	214	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0056107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	55	374	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.865	0.742	0.999	0.865	0.742	0.999	CLONAL	1	TRUE	1	0.31	2		374	410	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259760	16259760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747967254	NA	P-0056107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	86	473	0	ENST00000375759.3:c.7025G>A	p.Arg2342Gln	p.R2342Q	ENST00000375759	NM_015001.2	2342	cGa/cAa	11/15	1	2	FACETS	0.963	0.854	1	0.963	0.854	1	CLONAL	1	TRUE	1	0.31	2		473	576	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628554	90628554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	80	828	0	ENST00000330062.3:c.1033G>A	p.Glu345Lys	p.E345K	ENST00000330062	NM_002168.2	345	Gag/Aag	8/11	1	2	FACETS	0.505	0.443	0.572	0.505	0.443	0.572	SUBCLONAL	1	TRUE	1	0.31	2		828	1022	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842334	68842334	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	99	361	0	ENST00000261769.5:c.397del	p.Ser133LeufsTer82	p.S133Lfs*82	ENST00000261769	NM_004360.3	132	gTt/gt	4/16	0.299554041481056	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.31	1		361	410	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937706	36937706	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	58	732	0	ENST00000361632.4:c.1032G>C	p.Gln344His	p.Q344H	ENST00000361632		344	caG/caC	8/16	1	2	FACETS	0.431	0.369	0.499	0.431	0.369	0.499	SUBCLONAL	1	TRUE	1	0.31	2		732	868	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416854	121416854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555210473	NA	P-0056107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	65	848	0	ENST00000257555.6:c.283G>A	p.Glu95Lys	p.E95K	ENST00000257555		95	Gag/Aag	1/10	0.299554041481056	1	FACETS	0.378	0.327	0.434	0.378	0.327	0.434	SUBCLONAL	1	TRUE	0	0.31	1		848	937	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16001811	16001811	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0056107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	27	318	0	ENST00000268712.3:c.2691-1G>A		p.X897_splice	ENST00000268712	NM_006311.3	897			0.299554041481056	1	FACETS	0.399	0.317	0.492	0.399	0.317	0.492	SUBCLONAL	1	TRUE	0	0.31	1		318	369	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687415	37687415	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	66	452	1	ENST00000447079.4:c.4319A>G	p.Tyr1440Cys	p.Y1440C	ENST00000447079	NM_015083.1	1440	tAt/tGt	14/14	1	2	FACETS	0.751	0.652	0.858	0.751	0.652	0.858	SUBCLONAL	1	TRUE	1	0.31	2		453	567	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0056133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	207	366	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.489577498237397	4	FACETS	0.955	0.892	1	0.955	0.892	1	CLONAL	2	TRUE	2	0.562177837509515	4		366	602	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0056133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	153	327	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.562177837509515	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.562177837509515	3		327	340	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0056133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	88	318	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.562177837509515	3	FACETS	0.848	0.754	0.947	0.424	0.377	0.474	CLONAL	1	TRUE	1	0.562177837509515	3		318	473	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052635	42052635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	141	341	1	ENST00000219905.7:c.7306C>T	p.Arg2436Cys	p.R2436C	ENST00000219905	NM_001164273.1	2436	Cgt/Tgt	20/24	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.562177837509515	2		342	490	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214636	5214636	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532712500	NA	P-0056133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	225	693	1	ENST00000357368.4:c.4430G>A	p.Arg1477His	p.R1477H	ENST00000357368	NM_002850.3	1477	cGt/cAt	29/38	0.562177837509515	3	FACETS	0.976	0.908	1	0.488	0.454	0.523	CLONAL	1	TRUE	1	0.562177837509515	3		694	1051	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612929	228612929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200220156	NA	P-0056133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	383	543	0	ENST00000366696.1:c.98C>T	p.Thr33Ile	p.T33I	ENST00000366696	NM_003493.2	33	aCt/aTt	1/1	0.489577498237397	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.562177837509515	4		543	1005	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	181	196	2	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.763	0.706	0.821	1	0.99	1	SUBCLONAL	2	TRUE	1	0.35	2		198	678	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	78	359	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	1	2	FACETS	0.445	0.39	0.504	0.445	0.39	0.504	SUBCLONAL	1	TRUE	1	0.35	2		359	1002	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931452	131931453	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	82	293	0	ENST00000265335.6:c.2164_2165del	p.Lys722GlyfsTer5	p.K722Gfs*5	ENST00000265335		719	ctAAaa/ctaa	13/25	1	2	FACETS	0.693	0.611	0.781	0.693	0.611	0.781	SUBCLONAL	1	TRUE	1	0.35	2		293	676	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	38	347	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	0.476	0.393	0.569	0.476	0.393	0.569	SUBCLONAL	1	TRUE	1	0.35	2		347	456	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355374	15355374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781044333	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	60	732	2	ENST00000263377.2:c.2249C>T	p.Pro750Leu	p.P750L	ENST00000263377	NM_058243.2	750	cCg/cTg	13/20	1	2	FACETS	0.407	0.35	0.47	0.407	0.35	0.47	SUBCLONAL	1	TRUE	1	0.35	2		734	842	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	40	430	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	1	2	FACETS	0.535	0.445	0.636	0.535	0.445	0.636	SUBCLONAL	1	TRUE	1	0.35	2		430	427	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	92	387	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	1	2	FACETS	0.833	0.741	0.931	0.833	0.741	0.931	CLONAL	1	TRUE	1	0.35	2		387	631	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	74	268	0	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.35	2		268	397	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752965	128752965	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	149	524	0	ENST00000377970.2:c.1126G>C	p.Val376Leu	p.V376L	ENST00000377970	NM_002467.4	376	Gtc/Ctc	3/3	0.297837753060334	3	FACETS	1	0.971	1	0.572	0.523	0.624	CLONAL	1	TRUE	1	0.35	3		524	874	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	191	415	1	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.35	2		416	1046	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101272	4101272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370799450	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	201	865	0	ENST00000262948.5:c.535C>T	p.Arg179Trp	p.R179W	ENST00000262948	NM_030662.3	179	Cgg/Tgg	5/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.35	2		865	1023	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913407	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	203	462	0	ENST00000349496.5:c.133T>G	p.Ser45Ala	p.S45A	ENST00000349496	NM_001904.3	45	Tct/Gct	3/15	0.297837753060334	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.35	2		462	521	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007332	143007332	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	86	429	1	ENST00000262992.4:c.2452del	p.Arg818GlufsTer4	p.R818Efs*4	ENST00000262992	NM_001101669.1	818	Aga/ga	22/24	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.35	2		430	464	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432040	121432040	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771108132	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	241	1180	2	ENST00000257555.6:c.787C>T	p.Arg263Cys	p.R263C	ENST00000257555		263	Cgt/Tgt	4/10	0.297837753060334	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.35	1		1182	1104	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741573	17741573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285231710	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	103	277	0	ENST00000250003.3:c.244C>T	p.Arg82Cys	p.R82C	ENST00000250003	NM_002478.4	82	Cgc/Tgc	1/3	1	2	FACETS	0.831	0.751	0.915	1	0.986	1	CLONAL	2	TRUE	1	0.35	2		277	354	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	109	746	1	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	0.874	0.785	0.967	0.874	0.785	0.967	CLONAL	1	TRUE	1	0.35	2		747	713	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188237	142188237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	21	410	0	ENST00000350721.4:c.6494C>T	p.Ala2165Val	p.A2165V	ENST00000350721	NM_001184.3	2165	gCc/gTc	38/47	1	2	FACETS	0.337	0.259	0.428	0.337	0.259	0.428	SUBCLONAL	1	TRUE	1	0.35	2		410	356	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007825	45007825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	38	347	0	ENST00000558401.1:c.276del	p.Thr93LeufsTer10	p.T93Lfs*10	ENST00000558401	NM_004048.2	91	aCc/ac	2/4	1	2	FACETS	0.417	0.344	0.498	0.417	0.344	0.498	SUBCLONAL	1	TRUE	1	0.35	2		347	521	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920422	114920422	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	173	649	0	ENST00000543371.1:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000543371	NM_001198531.1	455	Cga/Tga	13/14	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.35	2		649	863	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103754	47103755	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	rs749901643	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	58	677	0	ENST00000409792.3:c.6190_6191dup	p.Asp2064GlufsTer84	p.D2064Efs*84	ENST00000409792	NM_014159.6	2064	gac/gaGAc	14/21	0.297837753060334	2	FACETS	0.369	0.316	0.427	0.184	0.158	0.214	SUBCLONAL	1	TRUE	0	0.35	2		677	899	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903755	114903755	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	150	666	1	ENST00000543371.1:c.763del	p.His255IlefsTer3	p.H255Ifs*3	ENST00000543371	NM_001198531.1	253	atC/at	7/14	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.35	2		667	793	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728564	190728565	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	63	512	0	ENST00000441310.2:c.1958dup	p.Ile654AspfsTer21	p.I654Dfs*21	ENST00000441310	NM_000534.4	651	aga/agAa	10/13	1	2	FACETS	0.703	0.609	0.805	0.703	0.609	0.805	SUBCLONAL	1	TRUE	1	0.35	2		512	512	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050364	13050364	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	156	815	0	ENST00000316448.5:c.320del	p.Gly107AlafsTer4	p.G107Afs*4	ENST00000316448	NM_004343.3	106	Ggg/gg	3/9	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.35	2		815	884	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029453	16029454	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	79	549	1	ENST00000268712.3:c.1576_1577del	p.Glu526LysfsTer9	p.E526Kfs*9	ENST00000268712	NM_006311.3	526	GAa/a	15/46	1	2	FACETS	0.766	0.675	0.865	0.766	0.675	0.865	SUBCLONAL	1	TRUE	1	0.35	2		550	589	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435777	56435777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1055597951	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	130	933	0	ENST00000407977.2:c.1360C>T	p.Arg454Cys	p.R454C	ENST00000407977		454	Cgc/Tgc	9/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.35	2		933	650	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631917	90631918	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs747216375	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	73	907	7	ENST00000330062.3:c.435dup	p.Thr146AspfsTer126	p.T146Dfs*126	ENST00000330062	NM_002168.2	145	-/G	4/11	1	2	FACETS	0.409	0.357	0.466	0.409	0.357	0.466	SUBCLONAL	1	TRUE	1	0.35	2		914	1019	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	158	310	0	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.35	2		310	817	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870972	12870973	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	102	536	0	ENST00000228872.4:c.201_202del	p.His67GlnfsTer57	p.H67Qfs*57	ENST00000228872	NM_004064.3	67	CAc/c	1/3	0.297837753060334	1	FACETS	0.873	0.783	0.967	0.873	0.783	0.967	CLONAL	1	TRUE	0	0.35	1		536	551	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275291	41275291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750554859	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	118	605	0	ENST00000349496.5:c.1457G>A	p.Arg486His	p.R486H	ENST00000349496	NM_001904.3	486	cGc/cAc	9/15	0.297837753060334	2	FACETS	1	0.955	1	0.547	0.495	0.602	CLONAL	1	TRUE	0	0.35	2		605	616	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911141	29911141	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	116	866	0	ENST00000376809.5:c.440A>G	p.Tyr147Cys	p.Y147C	ENST00000376809	NM_002116.7	147	tAc/tGc	3/8	1	2	FACETS	0.835	0.752	0.922	0.835	0.752	0.922	CLONAL	1	TRUE	1	0.35	2		866	794	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	333	973	6	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	0.297837753060334	3	FACETS	0.841	0.794	0.889	0.841	0.794	0.889	CLONAL	2	TRUE	1	0.35	3		979	1329	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24133968	24133968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	108	450	0	ENST00000263121.7:c.119G>A	p.Arg40Gln	p.R40Q	ENST00000263121	NM_003073.3	40	cGa/cAa	2/9	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.35	2		450	488	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652125	36652125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374965936	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	174	1010	0	ENST00000244741.5:c.247C>T	p.Arg83Trp	p.R83W	ENST00000244741	NM_000389.4	83	Cgg/Tgg	2/3	1	2	FACETS	0.954	0.878	1	0.954	0.878	1	CLONAL	1	TRUE	1	0.35	2		1010	1042	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	87	510	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	NA	3	FACETS	0.512	0.452	0.577	0.256	0.226	0.289	INDETERMINATE	1	TRUE	1	0.35	3		510	1140	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111191	193111191	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	33	361	0	ENST00000367435.3:c.724G>T	p.Gly242Ter	p.G242*	ENST00000367435	NM_024529.4	242	Gga/Tga	7/17	1	2	FACETS	0.629	0.513	0.757	0.629	0.513	0.757	SUBCLONAL	1	TRUE	1	0.35	2		361	300	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38139044	38139044	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	120	619	0	ENST00000317025.8:c.3559C>T	p.Arg1187Ter	p.R1187*	ENST00000317025	NM_023034.1	1187	Cga/Tga	20/24	0.297837753060334	3	FACETS	1	0.962	1	0.564	0.51	0.621	CLONAL	1	TRUE	1	0.35	3		619	714	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37665993	37665993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	92	681	0	ENST00000447079.4:c.2645G>A	p.Arg882Gln	p.R882Q	ENST00000447079	NM_015083.1	882	cGg/cAg	7/14	1	2	FACETS	0.637	0.565	0.714	0.637	0.565	0.714	SUBCLONAL	1	TRUE	1	0.35	2		681	825	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434562	49434562	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	100	1073	0	ENST00000301067.7:c.6991del	p.Leu2331Ter	p.L2331*	ENST00000301067	NM_003482.3	2331	Ctg/tg	31/54	NA	3	FACETS	0.678	0.605	0.757	0.339	0.302	0.379	INDETERMINATE	1	TRUE	1	0.35	3		1073	990	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953633	32953633	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359732	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	68	401	1	ENST00000380152.3:c.8940del	p.Glu2981LysfsTer7	p.E2981Kfs*7	ENST00000380152		2978	tcA/tc	22/27	1	2	FACETS	0.82	0.715	0.933	0.82	0.715	0.933	CLONAL	1	TRUE	1	0.35	2		402	474	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214713	36214714	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	123	871	4	ENST00000222270.7:c.3145dup	p.Ala1049GlyfsTer39	p.A1049Gfs*39	ENST00000222270	NM_014727.1	1047	cgg/cGgg	8/37	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.35	2		875	677	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291364	11291364	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1375320238	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	111	563	2	ENST00000361445.4:c.2642G>A	p.Arg881His	p.R881H	ENST00000361445	NM_004958.3	881	cGc/cAc	17/58	1	2	FACETS	0.985	0.887	1	0.985	0.887	1	CLONAL	1	TRUE	1	0.35	2		565	644	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965809	25965809	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1285225904	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	166	799	1	ENST00000435504.4:c.3397C>T	p.Arg1133Trp	p.R1133W	ENST00000435504		1133	Cgg/Tgg	13/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.35	2		800	894	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522740	67522741	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	22	327	0	ENST00000274335.5:c.244dup	p.Ile82AsnfsTer24	p.I82Nfs*24	ENST00000274335		79	-/A	1/15	1	2	FACETS	0.333	0.258	0.421	0.333	0.258	0.421	SUBCLONAL	1	TRUE	1	0.35	2		327	377	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428251	33428251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150134822	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	146	705	1	ENST00000345365.6:c.872G>A	p.Arg291His	p.R291H	ENST00000345365	NM_002878.3	291	cGc/cAc	9/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.35	2		706	758	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852254	63852254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	155	794	0	ENST00000279873.7:c.3032C>T	p.Pro1011Leu	p.P1011L	ENST00000279873	NM_032199.2	1011	cCg/cTg	10/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.35	2		794	743	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309085	137309085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777558913	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	201	1093	0	ENST00000481739.1:c.692C>T	p.Pro231Leu	p.P231L	ENST00000481739	NM_002957.4	231	cCg/cTg	5/10	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.35	2		1093	1122	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434186	49434186	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370115365	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	224	1200	0	ENST00000301067.7:c.7367G>A	p.Arg2456His	p.R2456H	ENST00000301067	NM_003482.3	2456	cGc/cAc	31/54	NA	3	FACETS	1	0.989	1	0.658	0.612	0.706	INDETERMINATE	1	TRUE	1	0.35	3		1200	1143	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342361	70342361	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	160	730	0	ENST00000374080.3:c.1252C>T	p.Arg418Cys	p.R418C	ENST00000374080		418	Cgt/Tgt	9/45	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.35	2		730	818	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155366	47155366	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs750924110	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	99	413	0	ENST00000409792.3:c.4715C>T	p.Ser1572Leu	p.S1572L	ENST00000409792	NM_014159.6	1572	tCg/tTg	5/21	0.297837753060334	2	FACETS	1	0.95	1	0.55	0.493	0.611	CLONAL	1	TRUE	0	0.35	2		413	514	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918180	50918180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	50	1076	3	ENST00000440232.2:c.2497C>T	p.Arg833Cys	p.R833C	ENST00000440232	NM_002691.3	833	Cgc/Tgc	20/27	1	2	FACETS	0.345	0.292	0.404	0.345	0.292	0.404	SUBCLONAL	1	TRUE	1	0.35	2		1079	828	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247487	53247487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146232504	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	131	767	1	ENST00000375401.3:c.322C>T	p.Arg108Trp	p.R108W	ENST00000375401	NM_004187.3	108	Cgg/Tgg	3/26	1	2	FACETS	0.924	0.839	1	0.924	0.839	1	CLONAL	1	TRUE	1	0.35	2		768	810	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491718	120491718	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	58	393	0	ENST00000256646.2:c.2511T>A	p.Cys837Ter	p.C837*	ENST00000256646	NM_024408.3	837	tgT/tgA	16/34	1	2	FACETS	0.71	0.611	0.817	0.71	0.611	0.817	SUBCLONAL	1	TRUE	1	0.35	2		393	467	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514052	69514052	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	183	840	2	ENST00000294312.3:c.629G>T	p.Arg210Met	p.R210M	ENST00000294312	NM_005117.2	210	aGg/aTg	3/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.35	2		842	881	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946481	71946481	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	173	884	0	ENST00000298229.2:c.2645G>A	p.Arg882His	p.R882H	ENST00000298229	NM_001567.3	882	cGt/cAt	23/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.35	2		884	883	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487322	56487322	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775042280	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	110	532	0	ENST00000267101.3:c.1468C>T	p.Arg490Cys	p.R490C	ENST00000267101	NM_001982.3	490	Cgc/Tgc	12/28	NA	3	FACETS	1	0.977	1	0.646	0.582	0.713	INDETERMINATE	1	TRUE	1	0.35	3		532	572	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201519	133201519	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	193	1053	0	ENST00000320574.5:c.6719G>T	p.Gly2240Val	p.G2240V	ENST00000320574	NM_006231.2	2240	gGa/gTa	48/49	0.297837753060334	1	FACETS	0.888	0.821	0.957	0.888	0.821	0.957	CLONAL	1	TRUE	0	0.35	1		1053	1025	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727514	88727514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770278704	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	136	734	2	ENST00000360948.2:c.265C>T	p.Arg89Cys	p.R89C	ENST00000360948	NM_001012338.2	89	Cgc/Tgc	3/19	1	2	FACETS	0.951	0.865	1	0.951	0.865	1	CLONAL	1	TRUE	1	0.35	2		736	817	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935651	15935651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	121	509	0	ENST00000268712.3:c.7282C>T	p.Leu2428Phe	p.L2428F	ENST00000268712	NM_006311.3	2428	Ctc/Ttc	46/46	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.35	2		509	636	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462577	40462577	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	168	852	1	ENST00000345506.4:c.2275G>T	p.Asp759Tyr	p.D759Y	ENST00000345506	NM_003152.3	759	Gat/Tat	20/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.35	2		853	910	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619160	1619160	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1349192826	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	204	992	0	ENST00000344749.5:c.1400G>A	p.Ser467Asn	p.S467N	ENST00000344749	NM_001136139.2	467	aGc/aAc	16/19	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.35	2		992	1121	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222958	5222958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781437725	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	80	555	0	ENST00000357368.4:c.2845C>T	p.Arg949Cys	p.R949C	ENST00000357368	NM_002850.3	949	Cgc/Tgc	18/38	1	2	FACETS	0.636	0.559	0.718	0.636	0.559	0.718	SUBCLONAL	1	TRUE	1	0.35	2		555	719	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945454	17945454	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	182	969	0	ENST00000458235.1:c.2276G>T	p.Cys759Phe	p.C759F	ENST00000458235	NM_000215.3	759	tGc/tTc	17/24	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.35	2		969	973	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976401	25976401	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	87	537	0	ENST00000435504.4:c.1142+2T>C		p.X381_splice	ENST00000435504		381			1	2	FACETS	0.986	0.876	1	0.986	0.876	1	CLONAL	1	TRUE	1	0.35	2		537	504	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143051	30143051	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367875912	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	94	1005	0	ENST00000389048.3:c.475G>A	p.Gly159Arg	p.G159R	ENST00000389048	NM_004304.4	159	Ggg/Agg	1/29	1	2	FACETS	0.514	0.456	0.576	0.514	0.456	0.576	SUBCLONAL	1	TRUE	1	0.35	2		1005	1045	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39239439	39239439	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	38	600	0	ENST00000402219.2:c.2218A>G	p.Lys740Glu	p.K740E	ENST00000402219	NM_005633.3	740	Aaa/Gaa	14/23	1	2	FACETS	0.362	0.298	0.433	0.362	0.298	0.433	SUBCLONAL	1	TRUE	1	0.35	2		600	600	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098927	178098927	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	72	513	0	ENST00000397062.3:c.118A>G	p.Ser40Gly	p.S40G	ENST00000397062	NM_006164.4	40	Agt/Ggt	2/5	1	2	FACETS	0.825	0.722	0.935	0.825	0.722	0.935	CLONAL	1	TRUE	1	0.35	2		513	499	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141599	202141599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	52	448	0	ENST00000358485.4:c.887T>C	p.Leu296Pro	p.L296P	ENST00000358485	NM_001080125.1	296	cTg/cCg	7/9	1	2	FACETS	0.486	0.413	0.565	0.486	0.413	0.565	SUBCLONAL	1	TRUE	1	0.35	2		448	612	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248719	212248719	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	97	559	0	ENST00000342788.4:c.3548T>C	p.Leu1183Ser	p.L1183S	ENST00000342788	NM_005235.2	1183	tTg/tCg	28/28	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.35	2		559	476	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439701	220439702	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	100	1246	1	ENST00000243786.2:c.562_563del	p.Leu188AlafsTer22	p.L188Afs*22	ENST00000243786	NM_002191.3	185	gCT/g	2/2	1	2	FACETS	0.538	0.479	0.601	0.538	0.479	0.601	SUBCLONAL	1	TRUE	1	0.35	2		1247	1062	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031152	36031152	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	178	774	1	ENST00000358208.4:c.1271G>T	p.Gly424Val	p.G424V	ENST00000358208		424	gGt/gTt	11/12	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.35	2		775	775	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713220	30713222	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	95	484	0	ENST00000295754.5:c.553_555del	p.Ile185del	p.I185del	ENST00000295754	NM_003242.5	182	gTCAtc/gtc	4/7	0.297837753060334	2	FACETS	0.944	0.843	1	0.472	0.421	0.526	CLONAL	1	TRUE	0	0.35	2		484	575	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539149	187539149	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	115	610	0	ENST00000441802.2:c.8591T>C	p.Met2864Thr	p.M2864T	ENST00000441802	NM_005245.3	2864	aTg/aCg	10/27	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.35	2		610	569	SUCCESS
APC	324	MSKCC	GRCh37	5	112154880	112154880	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	55	866	1	ENST00000257430.4:c.1151G>A	p.Ser384Asn	p.S384N	ENST00000257430	NM_000038.5	384	aGt/aAt	10/16	1	2	FACETS	0.395	0.337	0.459	0.395	0.337	0.459	SUBCLONAL	1	TRUE	1	0.35	2		867	795	SUCCESS
APC	324	MSKCC	GRCh37	5	112170862	112170862	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1060503318	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	106	527	0	ENST00000257430.4:c.1958G>T	p.Arg653Met	p.R653M	ENST00000257430	NM_000038.5	653	aGg/aTg	15/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.35	2		527	486	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480092	20480092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	82	474	0	ENST00000346618.3:c.409G>A	p.Glu137Lys	p.E137K	ENST00000346618	NM_001949.4	137	Gag/Aag	2/7	1	2	FACETS	0.943	0.834	1	0.943	0.834	1	CLONAL	1	TRUE	1	0.35	2		474	497	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112025220	112025220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	129	639	1	ENST00000368678.4:c.529G>A	p.Glu177Lys	p.E177K	ENST00000368678		177	Gag/Aag	6/13	1	2	FACETS	0.882	0.799	0.968	0.882	0.799	0.968	CLONAL	1	TRUE	1	0.35	2		640	836	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949040	151949040	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	48	569	0	ENST00000262189.6:c.1605A>G	p.Ile535Met	p.I535M	ENST00000262189	NM_170606.2	535	atA/atG	11/59	1	2	FACETS	0.442	0.373	0.518	0.442	0.373	0.518	SUBCLONAL	1	TRUE	1	0.35	2		569	621	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90949256	90949256	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	rs1554554233	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	22	315	0	ENST00000265433.3:c.2232del	p.Phe744LeufsTer7	p.F744Lfs*7	ENST00000265433	NM_002485.4	744	ttT/tt	15/16	0.297837753060334	3	FACETS	0.591	0.459	0.743	0.295	0.229	0.372	SUBCLONAL	1	TRUE	1	0.35	3		315	250	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772940	135772940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576476807	NA	P-0056136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	56	595	1	ENST00000298552.3:c.2683G>A	p.Val895Ile	p.V895I	ENST00000298552	NM_001162426.1	895	Gtt/Att	21/23	1	2	FACETS	0.438	0.374	0.508	0.438	0.374	0.508	SUBCLONAL	1	TRUE	1	0.35	2		596	731	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188308	10188308	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056157-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	116	233	0	ENST00000256474.2:c.451A>T	p.Ile151Phe	p.I151F	ENST00000256474	NM_000551.3	151	Atc/Ttc	2/3	0.616383055561217	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.61770349369305	1		233	259	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643965	52643965	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056157-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	44	124	0	ENST00000394830.3:c.1931del	p.Lys644ArgfsTer12	p.K644Rfs*12	ENST00000394830	NM_018313.4	644	aAg/ag	17/30	0.616383055561217	1	FACETS	0.92	0.796	1	0.92	0.796	1	CLONAL	1	TRUE	0	0.61770349369305	1		124	107	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554863	187554863	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056157-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	174	329	0	ENST00000441802.2:c.4298A>G	p.Asp1433Gly	p.D1433G	ENST00000441802	NM_005245.3	1433	gAt/gGt	7/27	1	2	FACETS	0.978	0.906	1	0.978	0.906	1	CLONAL	1	TRUE	1	0.61770349369305	2		329	576	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79974872	79974872	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056157-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	180	732	0	ENST00000265081.6:c.1300G>T	p.Glu434Ter	p.E434*	ENST00000265081	NM_002439.4	434	Gag/Tag	8/24	1	2	FACETS	0.927	0.858	0.997	0.927	0.858	0.997	CLONAL	1	TRUE	1	0.61770349369305	2		732	629	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099128	157099128	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056157-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	162	851	0	ENST00000346085.5:c.65A>C	p.Glu22Ala	p.E22A	ENST00000346085	NM_020732.3	22	gAg/gCg	1/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.61770349369305	2		851	506	SUCCESS
APC	324	MSKCC	GRCh37	5	112175198	112175198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	68	156	0	ENST00000257430.4:c.3907C>T	p.Gln1303Ter	p.Q1303*	ENST00000257430	NM_000038.5	1303	Caa/Taa	16/16	0.303535328359092	4	FACETS	1	0.913	1	1	0.913	1	CLONAL	2	TRUE	2	0.473741140960138	4		156	204	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710666	114710666	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	211	373	1	ENST00000543371.1:c.151G>T	p.Glu51Ter	p.E51*	ENST00000543371	NM_001198531.1	51	Gaa/Taa	1/14	0.227375361942996	5	FACETS	1	0.976	1	0.732	0.683	0.782	INDETERMINATE	2	TRUE	2	0.473741140960138	5		374	694	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577572	7577572	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882004	NA	P-0056211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	282	506	0	ENST00000269305.4:c.709A>G	p.Met237Val	p.M237V	ENST00000269305	NM_001126112.2	237	Atg/Gtg	7/11	0.272371709552508	3	FACETS	1	0.985	1	0.736	0.696	0.776	INDETERMINATE	2	TRUE	0	0.473741140960138	3		506	667	SUCCESS
APC	324	MSKCC	GRCh37	5	112175067	112175068	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	41	173	0	ENST00000257430.4:c.3777dup	p.Gln1260ThrfsTer16	p.Q1260Tfs*16	ENST00000257430	NM_000038.5	1259	ata/atAa	16/16	0.303535328359092	4	FACETS	1	0.956	1	0.717	0.605	0.837	CLONAL	1	TRUE	2	0.473741140960138	4		173	178	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026420	6026420	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	125	292	0	ENST00000265849.7:c.1976C>A	p.Ala659Glu	p.A659E	ENST00000265849	NM_000535.5	659	gCa/gAa	11/15	0.319902555380393	5	FACETS	1	0.92	1	0.673	0.614	0.735	CLONAL	2	TRUE	2	0.473741140960138	5		292	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0056246-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	38	856	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.16	2		856	451	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101136	27101145	+	frameshift_variant	Frame_Shift_Del	DEL	AGCAAAACAT	AGCAAAACAT	-	novel	NA	P-0056246-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	24	538	0	ENST00000324856.7:c.4418_4427del	p.Gln1473ArgfsTer5	p.Q1473Rfs*5	ENST00000324856	NM_006015.4	1473	cAGCAAAACATg/cg	18/20	1	2	FACETS	0.676	0.529	0.846	0.676	0.529	0.846	SUBCLONAL	1	TRUE	1	0.16	2		538	444	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357181	70357181	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056246-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	18	259	0	ENST00000374080.3:c.5696G>T	p.Arg1899Leu	p.R1899L	ENST00000374080		1899	cGg/cTg	39/45	1	1	FACETS	0.945	0.714	1	0.945	0.714	1	CLONAL	1	TRUE	0	0.16	1		259	219	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0056274-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	291	192	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.820407367646664	2		192	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0056274-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	272	879	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.820407367646664	2		879	617	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758858	41758858	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746561913	NA	P-0056274-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	198	722	0	ENST00000301178.4:c.1912G>A	p.Gly638Arg	p.G638R	ENST00000301178	NM_021913.4	638	Ggg/Agg	16/20	0.645112987106405	4	FACETS	1	0.958	1	0.524	0.486	0.563	CLONAL	1	TRUE	2	0.820407367646664	4		722	839	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87322773	87322773	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056274-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	212	415	0	ENST00000277120.3:c.374A>G	p.Asn125Ser	p.N125S	ENST00000277120		125	aAc/aGc	5/19	0.820407367646664	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.820407367646664	3		415	339	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903682	114903682	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056274-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	188	558	0	ENST00000543371.1:c.686G>T	p.Gly229Val	p.G229V	ENST00000543371	NM_001198531.1	229	gGa/gTa	7/14	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.820407367646664	2		558	434	SUCCESS
APC	324	MSKCC	GRCh37	5	112164656	112164656	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0056274-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	155	488	0	ENST00000257430.4:c.1730T>G	p.Leu577Ter	p.L577*	ENST00000257430	NM_000038.5	577	tTa/tGa	14/16	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.820407367646664	2		488	375	SUCCESS
APC	324	MSKCC	GRCh37	5	112175775	112175775	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056274-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	218	727	0	ENST00000257430.4:c.4484del	p.Ser1495IlefsTer12	p.S1495Ifs*12	ENST00000257430	NM_000038.5	1495	aGt/at	16/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.820407367646664	2		727	504	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937011	76937011	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0056291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	34	169	0	ENST00000373344.5:c.3736+1G>T		p.X1246_splice	ENST00000373344	NM_000489.3	1246			1	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.565123082208566	1		169	62	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366766	40366776	+	frameshift_variant	Frame_Shift_Del	DEL	GCGAGCCGGTC	GCGAGCCGGTC	-	novel	NA	P-0056291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	124	373	0	ENST00000397332.2:c.421_431del	p.Asp141SerfsTer54	p.D141Sfs*54	ENST00000397332	NM_001033082.2	141	GACCGGCTCGCt/t	2/3	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.565123082208566	2		373	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577513	7577514	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTGATGATG	novel	NA	P-0056291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	228	616	0	ENST00000269305.4:c.759_767dup	p.Ile254_Thr256dup	p.I254_T256dup	ENST00000269305	NM_001126112.2	254	aca/acCATCATCACa	7/11	0.565123082208566	1	FACETS	0.815	0.763	0.869	0.815	0.763	0.869	CLONAL	1	TRUE	0	0.565123082208566	1		616	710	SUCCESS
APC	324	MSKCC	GRCh37	5	112175322	112175323	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	147	275	0	ENST00000257430.4:c.4032dup	p.Glu1345ArgfsTer9	p.E1345Rfs*9	ENST00000257430	NM_000038.5	1344	tca/tcAa	16/16	0.544596541341309	2	FACETS	0.922	0.86	0.985	0.922	0.86	0.985	CLONAL	2	TRUE	0	0.565123082208566	2		275	282	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845134	128845134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1247135717	NA	P-0056291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	272	864	2	ENST00000249373.3:c.628G>A	p.Val210Met	p.V210M	ENST00000249373	NM_005631.4	210	Gtg/Atg	3/12	1	2	FACETS	0.918	0.862	0.975	0.918	0.862	0.975	CLONAL	1	TRUE	1	0.565123082208566	2		866	1049	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	142	341	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.947	1	1	0.994	1	CLONAL	4	TRUE	1	0.213141230620319	2		341	324	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	172	1032	7	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.901	0.837	0.965	1	0.995	1	CLONAL	4	TRUE	1	0.213141230620319	2		1039	448	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	130	609	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.975	1	1	0.993	1	CLONAL	3	TRUE	1	0.213141230620319	2		609	352	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	90	408	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	1	0.919	1	1	0.99	1	CLONAL	4	TRUE	1	0.213141230620319	2		408	208	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	197	478	4	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	0.213141230620319	0	FACETS	0.816	0.775	0.856			1	CLONAL	6	TRUE	0	0.213141230620319	0		482	297	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	146	341	1	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.213141230620319	2	FACETS	1	0.969	1	1	0.993	1	CLONAL	4	TRUE	0	0.213141230620319	2		342	317	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	171	650	11	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	1	0.977	1	1	0.994	1	CLONAL	3	TRUE	1	0.213141230620319	2		661	475	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	135	486	4	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	1	0.924	1	1	0.993	1	CLONAL	3	TRUE	1	0.213141230620319	2		490	419	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	123	552	1	ENST00000263967.3:c.3012G>A	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atA	21/21	1	2	FACETS	0.928	0.852	1	1	0.993	1	CLONAL	4	TRUE	1	0.213141230620319	2		553	311	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220615	2220615	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	rs774508592	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	191	778	0	ENST00000326181.6:c.237del	p.Ile80SerfsTer48	p.I80Sfs*48	ENST00000326181	NM_032271.2	78	Ccc/cc	5/21	1	2	FACETS	0.968	0.904	1	1	0.995	1	CLONAL	4	TRUE	1	0.213141230620319	2		778	463	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880257	37880257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	156	643	0	ENST00000269571.5:c.2301C>G	p.Ile767Met	p.I767M	ENST00000269571		767	atC/atG	19/27	1	2	FACETS	0.913	0.846	0.981	1	0.994	1	CLONAL	4	TRUE	1	0.213141230620319	2		643	401	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	147	505	5	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.993	0.914	1	1	0.993	1	CLONAL	3	TRUE	1	0.213141230620319	2		510	463	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	126	723	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.966	0.888	1	1	0.993	1	CLONAL	4	TRUE	1	0.213141230620319	2		723	306	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170432	119170432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	153	609	2	ENST00000264033.4:c.2662G>A	p.Ala888Thr	p.A888T	ENST00000264033	NM_005188.3	888	Gcc/Acc	16/16	1	2	FACETS	0.902	0.835	0.97	1	0.994	1	CLONAL	4	TRUE	1	0.213141230620319	2		611	398	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	187	869	2	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	0.213141230620319	1	FACETS	1	0.978	1	1	0.995	1	CLONAL	3	TRUE	0	0.213141230620319	1		871	470	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541475	187541475	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs76613365	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	136	568	2	ENST00000441802.2:c.6265G>A	p.Val2089Ile	p.V2089I	ENST00000441802	NM_005245.3	2089	Gtt/Att	10/27	1	2	FACETS	0.904	0.833	0.976	1	0.993	1	CLONAL	4	TRUE	1	0.213141230620319	2		570	353	SUCCESS
APC	324	MSKCC	GRCh37	5	112175101	112175101	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs587783033	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	75	251	0	ENST00000257430.4:c.3814del	p.Ser1272GlnfsTer16	p.S1272Qfs*16	ENST00000257430	NM_000038.5	1270	tgT/tg	16/16	1	2	FACETS	0.977	0.877	1	1	0.988	1	CLONAL	4	TRUE	1	0.213141230620319	2		251	180	SUCCESS
APC	324	MSKCC	GRCh37	5	112164664	112164664	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1060503259	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	73	309	3	ENST00000257430.4:c.1742del	p.Lys581ArgfsTer9	p.K581Rfs*9	ENST00000257430	NM_000038.5	580	Aaa/aa	14/16	1	2	FACETS	1	0.925	1	1	0.987	1	CLONAL	3	TRUE	1	0.213141230620319	2		312	217	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942053	71942053	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	233	925	3	ENST00000298229.2:c.1322del	p.Asn441ThrfsTer2	p.N441Tfs*2	ENST00000298229	NM_001567.3	439	ccA/cc	12/28	1	2	FACETS	1	0.967	1	1	0.996	1	CLONAL	4	TRUE	1	0.213141230620319	2		928	526	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891299	101891299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	133	621	2	ENST00000374994.4:c.260C>T	p.Ala87Val	p.A87V	ENST00000374994	NM_004612.2	87	gCa/gTa	2/9	0.213141230620319	1	FACETS	1	0.945	1	1	0.993	1	CLONAL	3	TRUE	0	0.213141230620319	1		623	359	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912052	50912052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773180520	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	213	1040	0	ENST00000440232.2:c.1786G>A	p.Val596Ile	p.V596I	ENST00000440232	NM_002691.3	596	Gtc/Atc	15/27	1	2	FACETS	1	0.969	1	1	0.996	1	CLONAL	4	TRUE	1	0.213141230620319	2		1040	477	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379758	17379758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754145226	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	262	1188	2	ENST00000359435.4:c.143G>A	p.Arg48His	p.R48H	ENST00000359435	NM_001033549.1	48	cGc/cAc	2/9	1	2	FACETS	0.962	0.908	1	1	0.996	1	CLONAL	4	TRUE	1	0.213141230620319	2		1190	639	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867536	45867536	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767916267	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	29	1188	1	ENST00000391945.4:c.772C>T	p.Arg258Trp	p.R258W	ENST00000391945	NM_000400.3	258	Cgg/Tgg	9/23	1	2	FACETS	0.515	0.413	0.633	0.515	0.413	0.633	SUBCLONAL	1	TRUE	1	0.213141230620319	2		1189	528	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339110	65339111	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	125	636	3	ENST00000342505.4:c.425dup	p.Ile143AspfsTer9	p.I143Dfs*9	ENST00000342505	NM_002227.2	142	aag/aaAg	5/25	1	2	FACETS	0.97	0.886	1	1	0.992	1	CLONAL	3	TRUE	1	0.213141230620319	2		639	403	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402834	20402836	+	inframe_deletion	In_Frame_Del	DEL	GCG	GCG	-	rs746263274	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	19	36	0	ENST00000346618.3:c.385_387del	p.Gly129del	p.G129del	ENST00000346618	NM_001949.4	124	aGCGgc/agc	1/7	0.0709751919634731	4	FACETS	1	0.84	1	1	0.929	1	INDETERMINATE	3	TRUE	2	0.213141230620319	4		36	66	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435129	110435129	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	108	722	1	ENST00000375856.3:c.3272del	p.Pro1091ArgfsTer15	p.P1091Rfs*15	ENST00000375856	NM_003749.2	1091	cCg/cg	1/2	0.213141230620319	1	FACETS	1	0.967	1	1	0.99	1	CLONAL	2	TRUE	0	0.213141230620319	1		723	391	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448297	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	T	novel	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	238	939	4	ENST00000407977.2:c.349_350delinsA	p.Arg117ThrfsTer41	p.R117Tfs*41	ENST00000407977		117	CGc/Ac	3/10	1	2	FACETS	0.903	0.849	0.958	1	0.996	1	CLONAL	4	TRUE	1	0.213141230620319	2		943	618	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858437	27858437	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	210	757	0	ENST00000359303.2:c.134G>A	p.Gly45Asp	p.G45D	ENST00000359303	NM_003535.2	45	gGc/gAc	1/1	0.0709751919634731	4	FACETS	1	0.981	1	1	0.995	1	INDETERMINATE	4	TRUE	2	0.213141230620319	4		757	533	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562430	21562430	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	148	561	0	ENST00000382592.4:c.1489G>A	p.Ala497Thr	p.A497T	ENST00000382592	NM_014572.2	497	Gca/Aca	4/8	0.213141230620319	0	FACETS	0.942	0.878	1			1	CLONAL	4	TRUE	0	0.213141230620319	0		561	290	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281565	198281565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147879907	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	232	721	2	ENST00000335508.6:c.566C>T	p.Ala189Val	p.A189V	ENST00000335508	NM_012433.2	189	gCg/gTg	6/25	1	2	FACETS	1	0.957	1	1	0.996	1	CLONAL	4	TRUE	1	0.213141230620319	2		723	534	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946307	2946307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370705908	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	210	1083	1	ENST00000396946.4:c.3430C>T	p.Arg1144Cys	p.R1144C	ENST00000396946	NM_032415.4	1144	Cgc/Tgc	25/25	0.213141230620319	4	FACETS	1	0.95	1			1	CLONAL	5	TRUE	NA	0.213141230620319	4		1084	472	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128201187	128201189	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs769571755	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	181	922	0	ENST00000265960.3:c.1546_1548del	p.Glu516del	p.E516del	ENST00000265960	NM_001006617.1	516	GAG/-	12/12	0.213141230620319	1	FACETS	1	0.982	1	1	0.995	1	CLONAL	3	TRUE	0	0.213141230620319	1		922	439	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638711	176638712	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs797045812	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	33	923	0	ENST00000439151.2:c.3316dup	p.Ser1106PhefsTer2	p.S1106Ffs*2	ENST00000439151	NM_022455.4	1104	cat/caTt	5/23	1	2	FACETS	0.619	0.504	0.75	0.619	0.504	0.75	SUBCLONAL	1	TRUE	1	0.213141230620319	2		923	500	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112745506	112745506	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	88	540	0	ENST00000369452.4:c.824A>T	p.Asp275Val	p.D275V	ENST00000369452	NM_007373.3	275	gAc/gTc	3/9	0.213141230620319	2	FACETS	0.93	0.834	1	1	0.978	1	CLONAL	3	TRUE	0	0.213141230620319	2		540	296	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434353	49434354	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	184	1093	0	ENST00000301067.7:c.7199dup	p.Arg2401SerfsTer33	p.R2401Sfs*33	ENST00000301067	NM_003482.3	2400	cct/ccCt	31/54	1	2	FACETS	1	0.949	1	1	0.995	1	CLONAL	3	TRUE	1	0.213141230620319	2		1093	561	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209096	133209096	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	105	591	0	ENST00000320574.5:c.6137-2A>G		p.X2046_splice	ENST00000320574	NM_006231.2	2046			1	2	FACETS	1	0.965	1	1	0.991	1	CLONAL	3	TRUE	1	0.213141230620319	2		591	291	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986676	36986676	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	16	32	0	ENST00000354822.5:c.1013G>T	p.Ser338Ile	p.S338I	ENST00000354822	NM_001079668.2	338	aGc/aTc	3/3	1	2	FACETS	1	0.815	1	1	0.95	1	CLONAL	4	TRUE	1	0.213141230620319	2		32	36	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42002912	42002912	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	126	478	0	ENST00000219905.7:c.2453del	p.Asn818IlefsTer10	p.N818Ifs*10	ENST00000219905	NM_001164273.1	817	Aaa/aa	8/24	1	2	FACETS	1	0.926	1	1	0.993	1	CLONAL	4	TRUE	1	0.213141230620319	2		478	294	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438223	56438223	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	220	1045	0	ENST00000407977.2:c.770del	p.Gly257ValfsTer162	p.G257Vfs*162	ENST00000407977		257	gGt/gt	7/10	1	2	FACETS	0.887	0.831	0.943	1	0.996	1	CLONAL	4	TRUE	1	0.213141230620319	2		1045	582	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029205	26029205	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	106	375	0	ENST00000435504.4:c.145G>T	p.Gly49Trp	p.G49W	ENST00000435504		49	Ggg/Tgg	4/13	1	2	FACETS	0.908	0.833	0.983	1	0.992	1	CLONAL	5	TRUE	1	0.213141230620319	2		375	219	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128030445	128030445	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	172	724	0	ENST00000285398.2:c.1823C>A	p.Ser608Tyr	p.S608Y	ENST00000285398	NM_000122.1	608	tCc/tAc	11/15	1	2	FACETS	0.949	0.884	1	1	0.995	1	CLONAL	4	TRUE	1	0.213141230620319	2		724	425	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732934	30732934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149847376	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	151	481	1	ENST00000295754.5:c.1547C>T	p.Thr516Met	p.T516M	ENST00000295754	NM_003242.5	516	aCg/aTg	7/7	1	2	FACETS	0.886	0.819	0.954	1	0.994	1	CLONAL	4	TRUE	1	0.213141230620319	2		482	400	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275146	41275146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	128	529	0	ENST00000349496.5:c.1312G>A	p.Val438Ile	p.V438I	ENST00000349496	NM_001904.3	438	Gtc/Atc	9/15	1	2	FACETS	1	0.965	1	1	0.993	1	CLONAL	3	TRUE	1	0.213141230620319	2		529	365	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161957	47161957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	153	495	0	ENST00000409792.3:c.4169C>T	p.Ser1390Leu	p.S1390L	ENST00000409792	NM_014159.6	1390	tCa/tTa	3/21	1	2	FACETS	1	0.977	1	1	0.994	1	CLONAL	4	TRUE	1	0.213141230620319	2		495	322	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198258	185198258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201522676	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	204	724	0	ENST00000265026.3:c.2740C>T	p.Arg914Cys	p.R914C	ENST00000265026	NM_004721.4	914	Cgc/Tgc	13/14	1	2	FACETS	0.933	0.873	0.993	1	0.995	1	CLONAL	4	TRUE	1	0.213141230620319	2		724	513	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852134	128852134	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs771690738	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	106	1237	0	ENST00000249373.3:c.2206C>A	p.Pro736Thr	p.P736T	ENST00000249373	NM_005631.4	736	Cca/Aca	12/12	1	2	FACETS	0.874	0.786	0.967	1	0.986	1	CLONAL	2	TRUE	1	0.213141230620319	2		1237	569	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967562	90967562	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1563531108	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	23	482	0	ENST00000265433.3:c.1346A>G	p.Gln449Arg	p.Q449R	ENST00000265433	NM_002485.4	449	cAg/cGg	10/16	1	2	FACETS	0.705	0.55	0.884	0.705	0.55	0.884	SUBCLONAL	1	TRUE	1	0.213141230620319	2		482	306	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019868	123019868	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	203	787	0	ENST00000355640.3:c.356A>G	p.Asn119Ser	p.N119S	ENST00000355640		119	aAc/aGc	2/7	0.213141230620319	0	FACETS	0.782	0.733	0.832			1	SUBCLONAL	4	TRUE	0	0.213141230620319	0		787	479	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185002	123185002	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	60	406	0	ENST00000218089.9:c.1049C>A	p.Ala350Asp	p.A350D	ENST00000218089	NM_001042749.1	350	gCt/gAt	12/35	0.213141230620319	0	FACETS	0.834	0.733	0.94			1	CLONAL	3	TRUE	0	0.213141230620319	0		406	177	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0056317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	122	190	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.270340071769585	3	FACETS	0.874	0.798	0.953	0.874	0.798	0.953	CLONAL	3	TRUE	0	0.27	3		190	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0056317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	375	405	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.246552690165178	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.27	3		405	966	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0056317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	88	259	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.264848134444402	3	FACETS	0.894	0.796	0.996	0.894	0.796	0.996	CLONAL	2	TRUE	1	0.27	3		259	414	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0056317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	86	387	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.264848134444402	3	FACETS	0.908	0.809	1	0.908	0.809	1	CLONAL	2	TRUE	1	0.27	3		387	398	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711340	114711340	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	56	324	0	ENST00000543371.1:c.355G>T	p.Gly119Ter	p.G119*	ENST00000543371	NM_001198531.1	119	Gga/Tga	3/14	0.233972016325871	4	FACETS	1	0.912	1	0.363	0.311	0.419	CLONAL	1	TRUE	1	0.27	4		324	484	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678383	88678383	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	134	963	0	ENST00000360948.2:c.1153G>C	p.Gly385Arg	p.G385R	ENST00000360948	NM_001012338.2	385	Ggc/Cgc	9/19	0.233972016325871	4	FACETS	1	0.946	1	0.354	0.321	0.39	CLONAL	1	TRUE	1	0.27	4		963	1186	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645993	215645993	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1018602332	NA	P-0056317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	40	502	0	ENST00000260947.4:c.605C>G	p.Ser202Cys	p.S202C	ENST00000260947	NM_000465.2	202	tCt/tGt	4/11	0.270340071769585	3	FACETS	0.684	0.568	0.813	0.228	0.189	0.271	SUBCLONAL	1	TRUE	0	0.27	3		502	492	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	95	425	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.35393230714526	2		425	428	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	38	408	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.35393230714526	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	0	0.35393230714526	1		408	159	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	69	374	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.35393230714526	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.35393230714526	1		374	275	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	145	196	2	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.35393230714526	2		198	692	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	137	349	0	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.35393230714526	2		349	591	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	87	386	4	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.35393230714526	2		390	451	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	112	277	3	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.35393230714526	2		280	477	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	145	333	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.773	0.709	0.839	1	0.989	1	SUBCLONAL	2	TRUE	1	0.35393230714526	2		333	530	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120031	70120031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	27	460	0	ENST00000245479.2:c.1037del	p.Pro346ArgfsTer37	p.P346Rfs*37	ENST00000245479	NM_000346.3	345	Ccc/cc	3/3	1	2	FACETS	0.803	0.655	0.963	1	0.947	1	CLONAL	2	TRUE	1	0.35393230714526	2		460	95	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149973	202149973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1272714323	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	265	535	1	ENST00000358485.4:c.1414C>T	p.Arg472Ter	p.R472*	ENST00000358485	NM_001080125.1	472	Cga/Tga	8/9	0.185437602574602	3	FACETS	1	0.965	1	1	0.965	1	INDETERMINATE	2	TRUE	1	0.35393230714526	3		536	849	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937603	76937603	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	54	274	0	ENST00000373344.5:c.3145del	p.Ile1049Ter	p.I1049*	ENST00000373344	NM_000489.3	1049	Ata/ta	9/35	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.35393230714526	2		274	301	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981315	68981315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866864487	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	48	166	0	ENST00000288368.4:c.1387C>T	p.Arg463Cys	p.R463C	ENST00000288368	NM_024870.2	463	Cgc/Tgc	12/40	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.35393230714526	2		166	267	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214398	36214398	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs868041281	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	204	308	1	ENST00000222270.7:c.3057del	p.Gly1020AlafsTer4	p.G1020Afs*4	ENST00000222270	NM_014727.1	1018	Aaa/aa	7/37	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.35393230714526	2		309	816	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101068	27101068	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	187	681	1	ENST00000324856.7:c.4354del	p.Gln1452ArgfsTer29	p.Q1452Rfs*29	ENST00000324856	NM_006015.4	1450	ggC/gg	18/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.35393230714526	2		682	901	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982123	93982123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769773179	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	74	272	0	ENST00000369303.4:c.1342G>A	p.Gly448Arg	p.G448R	ENST00000369303	NM_004440.3	448	Gga/Aga	6/17	1	2	FACETS	0.923	0.811	1	0.923	0.811	1	CLONAL	1	TRUE	1	0.35393230714526	2		272	453	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701087	29701087	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	145	336	3	ENST00000356175.3:c.8371C>T	p.Arg2791Ter	p.R2791*	ENST00000356175	NM_000267.3	2791	Cga/Tga	57/57	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.35393230714526	2		339	594	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576486	67576487	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	85	282	0	ENST00000274335.5:c.770dup	p.Asn257LysfsTer10	p.N257Kfs*10	ENST00000274335		255	-/A	5/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.35393230714526	2		282	373	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042041	42042041	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	139	409	0	ENST00000219905.7:c.6240del	p.Val2081TrpfsTer21	p.V2081Wfs*21	ENST00000219905	NM_001164273.1	2079	gAa/ga	17/24	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.35393230714526	2		409	537	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255118	16255118	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	124	300	0	ENST00000375759.3:c.2383C>T	p.Arg795Ter	p.R795*	ENST00000375759	NM_015001.2	795	Cga/Tga	11/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.35393230714526	2		300	490	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026132	71026132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751543308	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	127	316	0	ENST00000318789.4:c.1490G>A	p.Arg497Gln	p.R497Q	ENST00000318789	NM_032682.5	497	cGa/cAa	17/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.35393230714526	2		316	554	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524540	176524540	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148143006	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	251	861	0	ENST00000292408.4:c.2272C>T	p.Arg758Cys	p.R758C	ENST00000292408	NM_213647.1	758	Cgc/Tgc	18/18	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.35393230714526	2		861	1074	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680406	30680406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764942978	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	55	516	0	ENST00000376406.3:c.1313G>A	p.Arg438His	p.R438H	ENST00000376406	NM_014641.2	438	cGt/cAt	5/15	0.353220069278966	2	FACETS	0.449	0.383	0.521	0.225	0.191	0.261	SUBCLONAL	1	TRUE	0	0.35393230714526	2		516	692	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324094	31324094	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs151341247	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	80	253	1	ENST00000412585.2:c.469T>C	p.Trp157Arg	p.W157R	ENST00000412585	NM_005514.6	157	Tgg/Cgg	3/8	0.353220069278966	2	FACETS	0.807	0.719	0.899	0.807	0.719	0.899	CLONAL	2	TRUE	0	0.35393230714526	2		254	280	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259007	153259007	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	48	196	0	ENST00000281708.4:c.808C>T	p.Gln270Ter	p.Q270*	ENST00000281708	NM_033632.3	270	Caa/Taa	5/12	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.35393230714526	2		196	243	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615014	43615014	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	149	709	0	ENST00000355710.3:c.2428G>T	p.Gly810Cys	p.G810C	ENST00000355710	NM_020975.4	810	Ggc/Tgc	14/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.35393230714526	2		709	705	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740131	162740131	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	107	340	0	ENST00000367921.3:c.1333C>A	p.Leu445Ile	p.L445I	ENST00000367921	NM_006182.2	445	Ctt/Att	12/18	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.35393230714526	2		340	503	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511631	38511631	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	131	583	0	ENST00000254066.5:c.1129A>G	p.Met377Val	p.M377V	ENST00000254066	NM_000964.3	377	Atg/Gtg	8/9	1	2	FACETS	0.963	0.874	1	0.963	0.874	1	CLONAL	1	TRUE	1	0.35393230714526	2		583	769	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183857	10183857	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	168	594	0	ENST00000256474.2:c.326T>C	p.Ile109Thr	p.I109T	ENST00000256474	NM_000551.3	109	aTc/aCc	1/3	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.35393230714526	2		594	693	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156696	106156696	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	97	313	0	ENST00000380013.4:c.1597A>T	p.Met533Leu	p.M533L	ENST00000380013	NM_001127208.2	533	Atg/Ttg	3/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.35393230714526	2		313	411	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659279	86659279	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	51	182	0	ENST00000274376.6:c.1568G>A	p.Ser523Asn	p.S523N	ENST00000274376	NM_002890.2	523	aGt/aAt	11/25	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.35393230714526	2		182	231	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030347	180030347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	237	790	0	ENST00000261937.6:c.3937C>T	p.Pro1313Ser	p.P1313S	ENST00000261937	NM_182925.4	1313	Cct/Tct	30/30	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.35393230714526	2		790	965	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225453	26225454	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	165	342	0	ENST00000360408.1:c.71_72del	p.Lys24SerfsTer99	p.K24Sfs*99	ENST00000360408	NM_003532.2	24	aAG/a	1/1	0.353220069278966	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.35393230714526	2		342	418	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793865	89793866	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	104	309	0	ENST00000336032.3:c.934_935del	p.Arg312GlyfsTer27	p.R312Gfs*27	ENST00000336032	NM_006813.2	312	AGg/g	2/2	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.35393230714526	2		309	450	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525606	137525606	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	21	378	0	ENST00000367739.4:c.409del	p.Glu137ArgfsTer6	p.E137Rfs*6	ENST00000367739	NM_000416.2	137	Gag/ag	4/7	1	2	FACETS	0.287	0.22	0.365	0.287	0.22	0.365	SUBCLONAL	1	TRUE	1	0.35393230714526	2		378	414	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339149	116339150	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	49	210	0	ENST00000397752.3:c.11_12insA	p.Ala5ArgfsTer23	p.A5Rfs*23	ENST00000397752	NM_000245.2	4	ccc/ccAc	2/21	1	2	FACETS	0.939	0.8	1	0.939	0.8	1	CLONAL	1	TRUE	1	0.35393230714526	2		210	295	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403178	116403178	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	138	424	0	ENST00000397752.3:c.2443del	p.Leu815Ter	p.L815*	ENST00000397752	NM_000245.2	813	ctC/ct	11/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.35393230714526	2		424	592	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	117	609	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.325185212961811	2		609	485	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	137	277	3	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	0.266564660969986	3	FACETS	0.919	0.84	1	0.919	0.84	1	CLONAL	2	TRUE	1	0.325185212961811	3		280	533	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319406	11319406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149221273	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	83	679	0	ENST00000361445.4:c.61G>A	p.Val21Ile	p.V21I	ENST00000361445	NM_004958.3	21	Gtc/Atc	2/58	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.325185212961811	2		679	505	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17350532	17350532	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	61	535	0	ENST00000375499.3:c.578G>T	p.Ser193Ile	p.S193I	ENST00000375499	NM_003000.2	193	aGc/aTc	6/8	1	2	FACETS	0.866	0.75	0.993	0.866	0.75	0.993	CLONAL	1	TRUE	1	0.325185212961811	2		535	433	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258114	123258114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	39	329	0	ENST00000358487.5:c.1567G>A	p.Ala523Thr	p.A523T	ENST00000358487	NM_000141.4	523	Gcc/Acc	12/18	1	2	FACETS	0.923	0.769	1	0.923	0.769	1	CLONAL	1	TRUE	1	0.325185212961811	2		329	260	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362639	118362639	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782779521	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	48	468	0	ENST00000534358.1:c.5000G>A	p.Arg1667Gln	p.R1667Q	ENST00000534358	NM_005933.3	1667	cGg/cAg	15/36	1	2	FACETS	0.744	0.63	0.868	0.744	0.63	0.868	SUBCLONAL	1	TRUE	1	0.325185212961811	2		468	397	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871798	12871799	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	75	543	0	ENST00000228872.4:c.517_518del	p.Asn173CysfsTer31	p.N173Cfs*31	ENST00000228872	NM_004064.3	172	gAA/g	2/3	1	2	FACETS	0.945	0.831	1	0.945	0.831	1	CLONAL	1	TRUE	1	0.325185212961811	2		543	488	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs770248150	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	51	394	0	ENST00000311936.3:c.351A>C	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaC	4/5	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.325185212961811	2		394	285	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425562	49425562	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	74	790	1	ENST00000301067.7:c.12926C>A	p.Pro4309His	p.P4309H	ENST00000301067	NM_003482.3	4309	cCt/cAt	39/54	1	2	FACETS	0.899	0.789	1	0.899	0.789	1	CLONAL	1	TRUE	1	0.325185212961811	2		791	506	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434004	49434005	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750341925	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	63	767	2	ENST00000301067.7:c.7548dup	p.Asn2517GlnfsTer138	p.N2517Qfs*138	ENST00000301067	NM_003482.3	2516	-/C	31/54	1	2	FACETS	0.943	0.818	1	0.943	0.818	1	CLONAL	1	TRUE	1	0.325185212961811	2		769	411	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446993	49446993	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	71	592	0	ENST00000301067.7:c.951C>A	p.Cys317Ter	p.C317*	ENST00000301067	NM_003482.3	317	tgC/tgA	7/54	1	2	FACETS	0.829	0.724	0.941	0.829	0.724	0.941	CLONAL	1	TRUE	1	0.325185212961811	2		592	527	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914340	32914343	+	frameshift_variant	Frame_Shift_Del	DEL	GTTA	GTTA	-	rs80359543	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	46	438	0	ENST00000380152.3:c.5851_5854del	p.Ser1951TrpfsTer11	p.S1951Wfs*11	ENST00000380152		1950	GTTAgt/gt	11/27	1	2	FACETS	0.873	0.739	1	0.873	0.739	1	CLONAL	1	TRUE	1	0.325185212961811	2		438	324	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43730536	43730536	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	64	490	0	ENST00000382044.4:c.3177del	p.Thr1060ProfsTer36	p.T1060Pfs*36	ENST00000382044	NM_001141980.1	1059	ccC/cc	16/28	1	2	FACETS	0.918	0.797	1	0.918	0.797	1	CLONAL	1	TRUE	1	0.325185212961811	2		490	429	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50763861	50763861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	55	463	0	ENST00000307179.4:c.718C>T	p.Pro240Ser	p.P240S	ENST00000307179		240	Cca/Tca	8/20	1	2	FACETS	0.992	0.853	1	0.992	0.853	1	CLONAL	1	TRUE	1	0.325185212961811	2		463	341	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117594	70117594	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	69	773	4	ENST00000245479.2:c.66del	p.Ser23AlafsTer38	p.S23Afs*38	ENST00000245479	NM_000346.3	21	gCc/gc	1/3	1	2	FACETS	0.952	0.831	1	0.952	0.831	1	CLONAL	1	TRUE	1	0.325185212961811	2		777	446	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290919	15290919	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	61	709	1	ENST00000263388.2:c.3291del	p.Thr1098ProfsTer174	p.T1098Pfs*174	ENST00000263388	NM_000435.2	1097	ggG/gg	20/33	1	2	FACETS	0.814	0.704	0.933	0.814	0.704	0.933	CLONAL	1	TRUE	1	0.325185212961811	2		710	461	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296358	15296358	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	68	806	0	ENST00000263388.2:c.2084del	p.Pro695ArgfsTer165	p.P695Rfs*165	ENST00000263388	NM_000435.2	695	cCg/cg	13/33	1	2	FACETS	0.884	0.771	1	0.884	0.771	1	CLONAL	1	TRUE	1	0.325185212961811	2		806	473	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955111	17955112	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755706305	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	40	629	1	ENST00000458235.1:c.115dup	p.Gln39ProfsTer13	p.Q39Pfs*13	ENST00000458235	NM_000215.3	39	cag/cCag	2/24	1	2	FACETS	0.642	0.535	0.762	0.642	0.535	0.762	SUBCLONAL	1	TRUE	1	0.325185212961811	2		630	383	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955130	17955130	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs565783591	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	73	604	0	ENST00000458235.1:c.97C>T	p.Arg33Trp	p.R33W	ENST00000458235	NM_000215.3	33	Cgg/Tgg	2/24	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.325185212961811	2		604	366	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	49	688	0	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	1	2	FACETS	0.628	0.532	0.733	0.628	0.532	0.733	SUBCLONAL	1	TRUE	1	0.325185212961811	2		688	480	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18963076	18963076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196281615	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	64	559	0	ENST00000262803.5:c.943G>A	p.Asp315Asn	p.D315N	ENST00000262803	NM_002911.3	315	Gac/Aac	6/24	1	2	FACETS	0.991	0.862	1	0.991	0.862	1	CLONAL	1	TRUE	1	0.325185212961811	2		559	397	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211057	36211057	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	74	720	0	ENST00000222270.7:c.808G>T	p.Glu270Ter	p.E270*	ENST00000222270	NM_014727.1	270	Gag/Tag	3/37	1	2	FACETS	0.936	0.822	1	0.936	0.822	1	CLONAL	1	TRUE	1	0.325185212961811	2		720	486	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231773	36231773	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1569061762	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	79	734	0	ENST00000300305.3:c.611G>A	p.Arg204Gln	p.R204Q	ENST00000300305		204	cGa/cAa	5/8	1	2	FACETS	0.8	0.705	0.903	0.8	0.705	0.903	CLONAL	1	TRUE	1	0.325185212961811	2		734	607	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37056036	37056036	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs267607789	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	102	331	0	ENST00000231790.2:c.790+1G>A		p.X264_splice	ENST00000231790	NM_000249.3	264			0.323079301401342	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.325185212961811	2		331	295	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070348	37070349	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs63750855	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	65	547	1	ENST00000231790.2:c.1489dup	p.Arg497ProfsTer6	p.R497Pfs*6	ENST00000231790	NM_000249.3	495	acc/aCcc	13/19	0.323079301401342	2	FACETS	0.888	0.772	1	0.444	0.386	0.507	CLONAL	1	TRUE	0	0.325185212961811	2		548	450	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49929190	49929190	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs55856544	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	157	628	0	ENST00000296474.3:c.3352+1G>A		p.X1118_splice	ENST00000296474	NM_002447.2	1118			0.323079301401342	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.325185212961811	2		628	421	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63938072	63938072	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1156529426	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	46	426	0	ENST00000398590.3:c.412T>C	p.Phe138Leu	p.F138L	ENST00000398590	NM_001177387.1	138	Ttc/Ctc	5/14	1	2	FACETS	0.775	0.655	0.907	0.775	0.655	0.907	CLONAL	1	TRUE	1	0.325185212961811	2		426	365	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1253886	1253886	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1308414404	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	46	642	0	ENST00000310581.5:c.3356C>T	p.Ala1119Val	p.A1119V	ENST00000310581	NM_198253.2	1119	gCc/gTc	16/16	1	2	FACETS	0.754	0.637	0.883	0.754	0.637	0.883	SUBCLONAL	1	TRUE	1	0.325185212961811	2		642	375	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295098	1295098	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1166646936	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	52	784	0	ENST00000310581.5:c.7C>T	p.Arg3Cys	p.R3C	ENST00000310581	NM_198253.2	3	Cgc/Tgc	1/16	1	2	FACETS	0.99	0.848	1	0.99	0.848	1	CLONAL	1	TRUE	1	0.325185212961811	2		784	323	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522741	67522741	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	49	582	2	ENST00000274335.5:c.244del	p.Ile82SerfsTer32	p.I82Sfs*32	ENST00000274335		80	Aaa/aa	1/15	1	2	FACETS	0.647	0.548	0.755	0.647	0.548	0.755	SUBCLONAL	1	TRUE	1	0.325185212961811	2		584	466	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	66	319	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.325185212961811	2		319	357	SUCCESS
APC	324	MSKCC	GRCh37	5	112176026	112176038	+	frameshift_variant	Frame_Shift_Del	DEL	ATTATTTCTGCCA	ATTATTTCTGCCA	-	novel	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	60	579	0	ENST00000257430.4:c.4735_4747del	p.Ile1579CysfsTer67	p.I1579Cfs*67	ENST00000257430	NM_000038.5	1579	ATTATTTCTGCCAtg/tg	16/16	1	2	FACETS	0.714	0.616	0.82	0.714	0.616	0.82	SUBCLONAL	1	TRUE	1	0.325185212961811	2		579	517	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048787	180048787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	73	715	1	ENST00000261937.6:c.1775G>A	p.Arg592His	p.R592H	ENST00000261937	NM_182925.4	592	cGc/cAc	13/30	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.325185212961811	2		716	395	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911249	29911249	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs199474560	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	28	345	0	ENST00000376809.5:c.548A>G	p.Tyr183Cys	p.Y183C	ENST00000376809	NM_002116.7	183	tAc/tGc	3/8	1	2	FACETS	0.733	0.589	0.895	0.733	0.589	0.895	SUBCLONAL	1	TRUE	1	0.325185212961811	2		345	235	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64290026	64290026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	52	478	0	ENST00000370651.3:c.469C>T	p.Arg157Trp	p.R157W	ENST00000370651	NM_003463.4	157	Cgg/Tgg	6/6	1	2	FACETS	0.848	0.725	0.983	0.848	0.725	0.983	CLONAL	1	TRUE	1	0.325185212961811	2		478	377	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273044	55273044	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	66	685	0	ENST00000275493.2:c.3367C>A	p.Pro1123Thr	p.P1123T	ENST00000275493	NM_005228.3	1123	Cca/Aca	28/28	1	2	FACETS	0.875	0.761	0.997	0.875	0.761	0.997	CLONAL	1	TRUE	1	0.325185212961811	2		685	464	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511221	148511221	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1268069858	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	57	430	0	ENST00000320356.2:c.1681C>T	p.Arg561Cys	p.R561C	ENST00000320356	NM_004456.4	561	Cgc/Tgc	15/20	0.325185212961811	3	FACETS	0.906	0.779	1	0.453	0.389	0.522	CLONAL	1	TRUE	1	0.325185212961811	3		430	450	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874418	151874419	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	42	601	0	ENST00000262189.6:c.8119dup	p.Val2707GlyfsTer2	p.V2707Gfs*2	ENST00000262189	NM_170606.2	2707	gtt/gGtt	38/59	0.325185212961811	3	FACETS	0.636	0.531	0.753	0.318	0.265	0.377	SUBCLONAL	1	TRUE	1	0.325185212961811	3		601	472	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879231	151879231	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	77	651	0	ENST00000262189.6:c.5714C>A	p.Pro1905His	p.P1905H	ENST00000262189	NM_170606.2	1905	cCt/cAt	36/59	0.325185212961811	3	FACETS	1	0.914	1	0.524	0.461	0.592	CLONAL	1	TRUE	1	0.325185212961811	3		651	525	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132814	152132815	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	35	506	0	ENST00000262189.6:c.57dup	p.Glu20ArgfsTer39	p.E20Rfs*39	ENST00000262189	NM_170606.2	19	-/C	1/59	0.325185212961811	3	FACETS	0.797	0.655	0.955	0.399	0.327	0.478	CLONAL	1	TRUE	1	0.325185212961811	3		506	314	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971132	21971132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774633329	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	88	782	0	ENST00000304494.5:c.226G>A	p.Ala76Thr	p.A76T	ENST00000304494	NM_000077.4	76	Gcc/Acc	2/3	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.325185212961811	2		782	422	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570334	87570334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	82	713	0	ENST00000277120.3:c.2074G>A	p.Asp692Asn	p.D692N	ENST00000277120		692	Gat/Aat	17/19	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.325185212961811	2		713	465	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426304	47426304	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	86	847	0	ENST00000377045.4:c.721A>G	p.Thr241Ala	p.T241A	ENST00000377045	NM_001654.4	241	Act/Gct	8/16	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.325185212961811	2		847	529	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	51	620	0	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	1	2	FACETS	0.899	0.767	1	0.899	0.767	1	CLONAL	1	TRUE	1	0.325185212961811	2		620	349	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354209	70354209	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056681-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	42	432	1	ENST00000374080.3:c.4625del	p.Gly1542AlafsTer45	p.G1542Afs*45	ENST00000374080		1540	gtG/gt	34/45	1	2	FACETS	0.81	0.679	0.954	0.81	0.679	0.954	CLONAL	1	TRUE	1	0.325185212961811	2		433	319	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0056711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	102	366	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.372195194807995	3	FACETS	0.874	0.789	0.963	0.874	0.789	0.963	CLONAL	2	TRUE	1	0.383039411143958	3		366	363	SUCCESS
APC	324	MSKCC	GRCh37	5	112175182	112175182	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	70	140	0	ENST00000257430.4:c.3892del	p.Ser1298LeufsTer7	p.S1298Lfs*7	ENST00000257430	NM_000038.5	1297	gaT/ga	16/16	0.308864017168926	3	FACETS	0.974	0.875	1	1	0.979	1	CLONAL	3	TRUE	1	0.383039411143958	3		140	149	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440372	52440372	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	131	477	0	ENST00000460680.1:c.680G>C	p.Arg227Pro	p.R227P	ENST00000460680	NM_004656.3	227	cGc/cCc	9/17	0.115664705438883	3	FACETS	0.856	0.782	0.933	0.571	0.521	0.622	INDETERMINATE	2	TRUE	0	0.383039411143958	3		477	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578255	7578255	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	218	545	0	ENST00000269305.4:c.594del	p.Gly199GlufsTer48	p.G199Efs*48	ENST00000269305	NM_001126112.2	198	gaA/ga	6/11	0.383039411143958	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.383039411143958	2		545	492	SUCCESS
APC	324	MSKCC	GRCh37	5	112177149	112177150	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0056711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	33	199	0	ENST00000257430.4:c.5858_5859insG	p.Asn1953LysfsTer5	p.N1953Kfs*5	ENST00000257430	NM_000038.5	1953	aat/aaGt	16/16	0.308864017168926	3	FACETS	0.72	0.589	0.867	0.36	0.294	0.434	SUBCLONAL	1	TRUE	1	0.383039411143958	3		199	285	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577144	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs879253942	NA	P-0056931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	406	622	0	ENST00000269305.4:c.794T>C	p.Leu265Pro	p.L265P	ENST00000269305	NM_001126112.2	265	cTg/cCg	8/11	0.556782219877937	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.556782219877937	2		622	725	SUCCESS
APC	324	MSKCC	GRCh37	5	112176601	112176601	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	107	227	0	ENST00000257430.4:c.5310G>C	p.Lys1770Asn	p.K1770N	ENST00000257430	NM_000038.5	1770	aaG/aaC	16/16	0.556782219877937	1	FACETS	0.998	0.909	1	0.998	0.909	1	CLONAL	1	TRUE	0	0.556782219877937	1		227	278	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250250	133250250	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs483352909	NA	P-0056931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	137	775	0	ENST00000320574.5:c.1270C>G	p.Leu424Val	p.L424V	ENST00000320574	NM_006231.2	424	Ctc/Gtc	13/49	0.552302901029033	2	FACETS	0.719	0.656	0.786	0.36	0.328	0.393	SUBCLONAL	1	TRUE	0	0.556782219877937	2		775	684	SUCCESS
APC	324	MSKCC	GRCh37	5	112174438	112174438	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs863225340	NA	P-0056931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	122	245	0	ENST00000257430.4:c.3147G>A	p.Trp1049Ter	p.W1049*	ENST00000257430	NM_000038.5	1049	tgG/tgA	16/16	0.556782219877937	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.556782219877937	1		245	251	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428194	72428194	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0056931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	53	410	0	ENST00000477973.2:c.698C>G	p.Ser233Ter	p.S233*	ENST00000477973	NM_012234.5	233	tCa/tGa	3/4	0.531897452310704	2	FACETS	0.363	0.309	0.421	0.181	0.154	0.211	SUBCLONAL	1	TRUE	0	0.556782219877937	2		410	525	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162426	47162426	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	136	403	0	ENST00000409792.3:c.3700G>T	p.Glu1234Ter	p.E1234*	ENST00000409792	NM_014159.6	1234	Gaa/Taa	3/21	0.531897452310704	2	FACETS	1	0.972	1	0.569	0.522	0.618	CLONAL	1	TRUE	0	0.556782219877937	2		403	429	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	108	211	0	ENST00000257430.4:c.3916G>C	p.Glu1306Gln	p.E1306Q	ENST00000257430	NM_000038.5	1306	Gaa/Caa	16/16	0.556782219877937	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.556782219877937	1		211	245	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955601	55955601	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	72	418	0	ENST00000263923.4:c.3344T>A	p.Phe1115Tyr	p.F1115Y	ENST00000263923	NM_002253.2	1115	tTt/tAt	25/30	0.531897452310704	2	FACETS	0.515	0.451	0.584	0.258	0.225	0.292	SUBCLONAL	1	TRUE	0	0.556782219877937	2		418	502	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575504	67575505	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0056931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	270	398	0	ENST00000274335.5:c.577_578del	p.Leu193ThrfsTer12	p.L193Tfs*12	ENST00000274335		193	TTa/a	4/15	0.313657072962198	5	FACETS	1	0.99	1	0.819	0.773	0.867	INDETERMINATE	2	TRUE	2	0.556782219877937	5		398	724	SUCCESS
APC	324	MSKCC	GRCh37	5	112173548	112173548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	138	276	0	ENST00000257430.4:c.2257C>T	p.His753Tyr	p.H753Y	ENST00000257430	NM_000038.5	753	Cat/Tat	16/16	0.556782219877937	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.556782219877937	1		276	302	SUCCESS
APC	324	MSKCC	GRCh37	5	112174937	112174937	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	101	214	0	ENST00000257430.4:c.3646G>A	p.Glu1216Lys	p.E1216K	ENST00000257430	NM_000038.5	1216	Gag/Aag	16/16	0.556782219877937	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.556782219877937	1		214	226	SUCCESS
APC	324	MSKCC	GRCh37	5	112175109	112175109	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	88	172	0	ENST00000257430.4:c.3818G>A	p.Arg1273Lys	p.R1273K	ENST00000257430	NM_000038.5	1273	aGa/aAa	16/16	0.556782219877937	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.556782219877937	1		172	173	SUCCESS
APC	324	MSKCC	GRCh37	5	112175984	112175984	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	108	225	0	ENST00000257430.4:c.4693G>C	p.Asp1565His	p.D1565H	ENST00000257430	NM_000038.5	1565	Gat/Cat	16/16	0.556782219877937	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.556782219877937	1		225	234	SUCCESS
APC	324	MSKCC	GRCh37	5	112176368	112176368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	156	277	0	ENST00000257430.4:c.5077G>A	p.Glu1693Lys	p.E1693K	ENST00000257430	NM_000038.5	1693	Gaa/Aaa	16/16	0.556782219877937	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.556782219877937	1		277	317	SUCCESS
APC	324	MSKCC	GRCh37	5	112176408	112176408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	135	275	0	ENST00000257430.4:c.5117C>T	p.Ser1706Leu	p.S1706L	ENST00000257430	NM_000038.5	1706	tCa/tTa	16/16	0.556782219877937	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.556782219877937	1		275	287	SUCCESS
APC	324	MSKCC	GRCh37	5	112177217	112177217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	123	298	0	ENST00000257430.4:c.5926G>A	p.Asp1976Asn	p.D1976N	ENST00000257430	NM_000038.5	1976	Gac/Aac	16/16	0.556782219877937	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.556782219877937	1		298	271	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52621416	52621423	+	frameshift_variant	Frame_Shift_Ins	INS	CTTTGTTG	CTTTGTTG	TAATAGTAA	novel	NA	P-0056931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	157	479	2	ENST00000394830.3:c.2994_3001delinsTTACTATTA	p.Asn999TyrfsTer6	p.N999Yfs*6	ENST00000394830	NM_018313.4	998	taCAACAAAGtt/taTTACTATTAtt	20/30	0.531897452310704	2	FACETS	1	0.957	1	0.528	0.487	0.571	CLONAL	1	TRUE	0	0.556782219877937	2		481	534	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0056942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	102	190	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.346770760509816	1	FACETS	0.769	0.689	0.854	0.769	0.689	0.854	SUBCLONAL	1	TRUE	0	0.346770760509816	1		190	632	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0056942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	181	545	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.346770760509816	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.346770760509816	1		545	828	SUCCESS
APC	324	MSKCC	GRCh37	5	112163696	112163697	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1131691555	NA	P-0056942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	75	276	0	ENST00000257430.4:c.1620dup	p.Gln541ThrfsTer19	p.Q541Tfs*19	ENST00000257430	NM_000038.5	540	tta/ttAa	13/16	0.148382097406383	3	FACETS	1	0.96	1	0.609	0.536	0.686	INDETERMINATE	1	TRUE	1	0.346770760509816	3		276	417	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667524	241667524	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756528378	NA	P-0056942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	71	259	0	ENST00000366560.3:c.926C>T	p.Pro309Leu	p.P309L	ENST00000366560	NM_000143.3	309	cCg/cTg	7/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.346770760509816	2		259	298	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42870081	42870081	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	63	730	0	ENST00000398585.3:c.91G>C	p.Asp31His	p.D31H	ENST00000398585	NM_001135099.1	31	Gat/Cat	2/14	1	2	FACETS	0.429	0.37	0.494	0.429	0.37	0.494	SUBCLONAL	1	TRUE	1	0.346770760509816	2		730	846	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910736	32910736	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1555282563	NA	P-0056942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	45	458	0	ENST00000380152.3:c.2244C>G	p.Tyr748Ter	p.Y748*	ENST00000380152		748	taC/taG	11/27	0.219074138312967	5	FACETS	0.527	0.442	0.622	0.176	0.147	0.208	SUBCLONAL	1	TRUE	2	0.346770760509816	5		458	748	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55143554	55143554	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0056942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	38	360	1	ENST00000257290.5:c.1787-1G>T		p.X596_splice	ENST00000257290	NM_006206.4	596			0.346770760509816	1	FACETS	0.372	0.307	0.445	0.372	0.307	0.445	SUBCLONAL	1	TRUE	0	0.346770760509816	1		361	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0056962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	169	891	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.479278732640316	1	FACETS	0.848	0.783	0.916	0.848	0.783	0.916	CLONAL	1	TRUE	0	0.479278732640316	1		891	632	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0056962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	101	366	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.908	0.816	1	0.908	0.816	1	CLONAL	1	TRUE	1	0.479278732640316	2		366	464	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0056962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	216	712	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.998	0.929	1	0.998	0.929	1	CLONAL	1	TRUE	1	0.479278732640316	2		712	903	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981315	68981315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866864487	NA	P-0056962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	44	166	0	ENST00000288368.4:c.1387C>T	p.Arg463Cys	p.R463C	ENST00000288368	NM_024870.2	463	Cgc/Tgc	12/40	1	2	FACETS	0.678	0.572	0.793	0.678	0.572	0.793	SUBCLONAL	1	TRUE	1	0.479278732640316	2		166	271	SUCCESS
APC	324	MSKCC	GRCh37	5	112163698	112163698	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854572	NA	P-0056962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	14	265	0	ENST00000257430.4:c.1621C>T	p.Gln541Ter	p.Q541*	ENST00000257430	NM_000038.5	541	Cag/Tag	13/16	0.207681986102951	3	FACETS	0.26	0.187	0.347	0.087	0.062	0.116	INDETERMINATE	1	TRUE	0	0.479278732640316	3		265	279	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274928	41274928	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	95	431	2	ENST00000349496.5:c.1178C>A	p.Thr393Asn	p.T393N	ENST00000349496	NM_001904.3	393	aCt/aAt	8/15	1	2	FACETS	0.901	0.807	1	0.901	0.807	1	CLONAL	1	TRUE	1	0.479278732640316	2		433	440	SUCCESS
APC	324	MSKCC	GRCh37	5	112175582	112175583	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0056962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	161	431	0	ENST00000257430.4:c.4292dup	p.Met1431IlefsTer7	p.M1431Ifs*7	ENST00000257430	NM_000038.5	1431	atg/aTtg	16/16	0.207681986102951	3	FACETS	0.875	0.809	0.942	0.583	0.539	0.628	INDETERMINATE	2	TRUE	0	0.479278732640316	3		431	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0057055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	34	1110	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.866	0.706	1	0.866	0.706	1	CLONAL	1	TRUE	1	0.12	2		1111	654	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0057055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	18	192	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.804	0.604	1	0.804	0.604	1	CLONAL	1	TRUE	1	0.12	2		192	373	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0057055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	22	410	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.828	0.64	1	0.828	0.64	1	CLONAL	1	TRUE	1	0.12	2		410	443	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100944	27100944	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	27	458	0	ENST00000324856.7:c.4226A>C	p.Gln1409Pro	p.Q1409P	ENST00000324856	NM_006015.4	1409	cAg/cCg	18/20	1	2	FACETS	0.833	0.662	1	0.833	0.662	1	CLONAL	1	TRUE	1	0.12	2		458	540	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163773	72163773	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	23	338	0	ENST00000357731.5:c.585G>C	p.Arg195Ser	p.R195S	ENST00000357731	NM_173808.2	195	agG/agC	4/7	1	2	FACETS	0.881	0.686	1	0.881	0.686	1	CLONAL	1	TRUE	1	0.12	2		338	435	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	60	738	0				ENST00000310581	NM_198253.2	-/1132			0.38810361448256	1	FACETS	0.725	0.637	0.817	0.725	0.637	0.817	SUBCLONAL	1	TRUE	0	0.636976489757082	1		738	177	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	151	533	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	1	2	FACETS	0.893	0.821	0.967	0.893	0.821	0.967	CLONAL	1	TRUE	1	0.636976489757082	2		533	531	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131301	202131301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748087575	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	121	524	0	ENST00000358485.4:c.269C>T	p.Pro90Leu	p.P90L	ENST00000358485	NM_001080125.1	90	cCg/cTg	2/9	0.406225483311625	1	FACETS	0.632	0.575	0.69	0.632	0.575	0.69	SUBCLONAL	1	TRUE	0	0.636976489757082	1		524	410	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691101	18691101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1327878312	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	64	428	0	ENST00000266497.5:c.3212C>T	p.Pro1071Leu	p.P1071L	ENST00000266497		1071	cCt/cTt	23/31	0.264799349309228	2	FACETS	0.45	0.39	0.514	0.225	0.195	0.257	INDETERMINATE	1	TRUE	0	0.636976489757082	2		428	447	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421541	32421541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	112	527	0	ENST00000332351.3:c.1051G>A	p.Gly351Arg	p.G351R	ENST00000332351	NM_024426.4	351	Gga/Aga	6/10	0.148753696744656	0	FACETS	0.306	0.277	0.336			1	INDETERMINATE	1	TRUE	0	0.636976489757082	0		527	417	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399857	139399857	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	303	420	0	ENST00000277541.6:c.4491G>A	p.Trp1497Ter	p.W1497*	ENST00000277541	NM_017617.3	1497	tgG/tgA	25/34	0.544469022604921	3	FACETS	0.905	0.868	0.941	0.905	0.868	0.941	CLONAL	3	TRUE	0	0.636976489757082	3		420	462	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857638	9857638	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555482232	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	113	585	0	ENST00000330684.3:c.3763C>T	p.Gln1255Ter	p.Q1255*	ENST00000330684	NM_001134407.1	1255	Cag/Tag	13/13	1	2	FACETS	0.941	0.855	1	0.941	0.855	1	CLONAL	1	TRUE	1	0.636976489757082	2		585	377	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857368	9857368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	128	550	0	ENST00000330684.3:c.4033C>T	p.Pro1345Ser	p.P1345S	ENST00000330684	NM_001134407.1	1345	Ccc/Tcc	13/13	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.636976489757082	2		550	361	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964429	55964429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747827262	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	146	417	0	ENST00000263923.4:c.2384G>A	p.Gly795Glu	p.G795E	ENST00000263923	NM_002253.2	795	gGg/gAg	17/30	0.313403179850146	2	FACETS	1	0.986	1	0.657	0.608	0.706	INDETERMINATE	1	TRUE	0	0.636976489757082	2		417	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577540	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	rs1555525498	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	110	370	0	ENST00000269305.4:c.741_742delinsTT	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	247	aaCCgg/aaTTgg	7/11	1	2	FACETS	0.847	0.767	0.93	0.847	0.767	0.93	CLONAL	1	TRUE	1	0.636976489757082	2		370	408	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243708849	243708849	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	73	304	0	ENST00000263826.5:c.1214T>C	p.Phe405Ser	p.F405S	ENST00000263826	NM_005465.4	405	tTc/tCc	11/13	0.311806789018644	1	FACETS	0.374	0.328	0.423	0.374	0.328	0.423	INDETERMINATE	1	TRUE	0	0.636976489757082	1		304	418	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359593	40359593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	136	298	0	ENST00000293328.3:c.2060C>T	p.Pro687Leu	p.P687L	ENST00000293328	NM_012448.3	687	cCc/cTc	16/19	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.636976489757082	2		298	417	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609791	81609791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	134	636	0	ENST00000298171.2:c.1389G>A	p.Met463Ile	p.M463I	ENST00000298171	NM_000369.2	463	atG/atA	10/10	1	2	FACETS	0.871	0.797	0.948	0.871	0.797	0.948	CLONAL	1	TRUE	1	0.636976489757082	2		636	483	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193214	11193214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	155	442	0	ENST00000361445.4:c.5287G>A	p.Gly1763Ser	p.G1763S	ENST00000361445	NM_004958.3	1763	Ggc/Agc	38/58	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.636976489757082	2		442	360	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748789	43748790	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	145	535	0	ENST00000382044.4:c.2016_2017delinsTT	p.Pro673Ser	p.P673S	ENST00000382044	NM_001141980.1	672	atCCct/atTTct	12/28	0.406225483311625	1	FACETS	0.749	0.691	0.81	0.749	0.691	0.81	SUBCLONAL	1	TRUE	0	0.636976489757082	1		535	414	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46543186	46543187	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	70	330	1	ENST00000262741.5:c.314_314+1delinsAA		p.X105_splice	ENST00000262741	NM_003629.3	105		3/10	0.311806789018644	1	FACETS	0.376	0.329	0.427	0.376	0.329	0.427	INDETERMINATE	1	TRUE	0	0.636976489757082	1		331	398	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637664	23637664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766315705	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	116	396	0	ENST00000261584.4:c.2641G>A	p.Gly881Ser	p.G881S	ENST00000261584	NM_024675.3	881	Ggt/Agt	7/13	1	2	FACETS	0.824	0.748	0.903	0.824	0.748	0.903	CLONAL	1	TRUE	1	0.636976489757082	2		396	442	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249393	153249393	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	251	476	0	ENST00000281708.4:c.1385C>T	p.Ser462Phe	p.S462F	ENST00000281708	NM_033632.3	462	tCc/tTc	9/12	0.313403179850146	2	FACETS	0.799	0.757	0.841	0.799	0.757	0.841	INDETERMINATE	2	TRUE	0	0.636976489757082	2		476	493	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291551	15291551	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	56	498	0	ENST00000263388.2:c.3083G>A	p.Trp1028Ter	p.W1028*	ENST00000263388	NM_000435.2	1028	tGg/tAg	19/33	0.311806789018644	1	FACETS	0.385	0.332	0.443	0.385	0.332	0.443	INDETERMINATE	1	TRUE	0	0.636976489757082	1		498	311	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875711	56875711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	111	464	0	ENST00000308159.5:c.2315C>T	p.Ser772Phe	p.S772F	ENST00000308159	NM_014669.4	772	tCc/tTc	21/22	1	2	FACETS	0.781	0.707	0.859	0.781	0.707	0.859	SUBCLONAL	1	TRUE	1	0.636976489757082	2		464	446	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435364	110435364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	182	654	0	ENST00000375856.3:c.3037C>T	p.Pro1013Ser	p.P1013S	ENST00000375856	NM_003749.2	1013	Ccg/Tcg	1/2	0.38810361448256	1	FACETS	0.936	0.875	0.998	0.936	0.875	0.998	CLONAL	1	TRUE	0	0.636976489757082	1		654	416	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703508	47703508	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1558519495	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	57	399	0	ENST00000233146.2:c.2008C>T	p.Pro670Ser	p.P670S	ENST00000233146	NM_000251.2	670	Ccc/Tcc	13/16	0.406225483311625	1	FACETS	0.404	0.349	0.463	0.404	0.349	0.463	SUBCLONAL	1	TRUE	0	0.636976489757082	1		399	302	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801170	1801170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778352	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	62	461	0	ENST00000260795.2:c.299C>T	p.Ser100Phe	p.S100F	ENST00000260795		100	tCc/tTc	2/17	0.313403179850146	2	FACETS	0.493	0.427	0.563	0.246	0.213	0.282	INDETERMINATE	1	TRUE	0	0.636976489757082	2		461	395	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209333	98209333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	257	533	0	ENST00000331920.6:c.4205C>T	p.Pro1402Leu	p.P1402L	ENST00000331920	NM_000264.3	1402	cCt/cTt	23/24	0.627370342297162	2	FACETS	0.982	0.937	1	0.982	0.937	1	CLONAL	2	TRUE	0	0.636976489757082	2		533	411	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020405	69020405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	221	443	0	ENST00000288368.4:c.2777C>T	p.Ser926Phe	p.S926F	ENST00000288368	NM_024870.2	926	tCc/tTc	24/40	0.492486338418638	3	FACETS	0.847	0.795	0.899	0.847	0.795	0.899	CLONAL	2	TRUE	1	0.636976489757082	3		443	540	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797411	45797411	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	176	750	0	ENST00000450313.1:c.1108G>A	p.Glu370Lys	p.E370K	ENST00000450313	NM_012222.2	370	Gag/Aag	12/16	0.311806789018644	1	FACETS	0.819	0.762	0.877	0.819	0.762	0.877	INDETERMINATE	1	TRUE	0	0.636976489757082	1		750	460	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280136	115280136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	82	395	0	ENST00000438362.2:c.496C>T	p.Pro166Ser	p.P166S	ENST00000438362	NM_001242891.1	166	Ccg/Tcg	5/20	0.311806789018644	1	FACETS	0.395	0.35	0.443	0.395	0.35	0.443	INDETERMINATE	1	TRUE	0	0.636976489757082	1		395	444	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956224	175956224	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	131	316	0	ENST00000367669.3:c.1988C>T	p.Ser663Phe	p.S663F	ENST00000367669	NM_022457.5	663	tCt/tTt	18/20	0.311806789018644	1	FACETS	0.863	0.794	0.932	0.863	0.794	0.932	INDETERMINATE	1	TRUE	0	0.636976489757082	1		316	325	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944142	71944143	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	87	497	0	ENST00000298229.2:c.1975_1976delinsTT	p.Pro659Phe	p.P659F	ENST00000298229	NM_001567.3	659	CCc/TTc	17/28	1	2	FACETS	0.736	0.657	0.82	0.736	0.657	0.82	SUBCLONAL	1	TRUE	1	0.636976489757082	2		497	371	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77937667	77937667	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408895583	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	60	422	0	ENST00000361507.4:c.1051C>T	p.Pro351Ser	p.P351S	ENST00000361507	NM_080491.2	351	Ccc/Tcc	4/10	1	2	FACETS	0.659	0.572	0.751	0.659	0.572	0.751	SUBCLONAL	1	TRUE	1	0.636976489757082	2		422	286	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922299	100922299	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	131	342	0	ENST00000325455.5:c.2213G>A	p.Gly738Asp	p.G738D	ENST00000325455	NM_001202474.3	738	gGt/gAt	5/8	1	2	FACETS	0.998	0.914	1	0.998	0.914	1	CLONAL	1	TRUE	1	0.636976489757082	2		342	412	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205235	46205235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1462618917	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	175	387	0	ENST00000334344.6:c.319G>A	p.Gly107Arg	p.G107R	ENST00000334344	NM_152641.2	107	Ggg/Agg	4/21	0.264799349309228	2	FACETS	1	0.991	1	0.714	0.666	0.761	INDETERMINATE	1	TRUE	0	0.636976489757082	2		387	385	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123889508	123889509	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	27	47	0	ENST00000330479.4:c.735_736delinsTT	p.His246Tyr	p.H246Y	ENST00000330479	NM_020382.3	245	taCCac/taTTac	7/9	0.313403179850146	2	FACETS	0.8	0.673	0.926	0.8	0.673	0.926	INDETERMINATE	2	TRUE	0	0.636976489757082	2		47	53	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95597930	95597936	+	frameshift_variant	Frame_Shift_Del	DEL	ATCTGAA	ATCTGAA	-	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	126	347	0	ENST00000393063.1:c.348_354del	p.Asp118ArgfsTer8	p.D118Rfs*8	ENST00000393063	NM_030621.3	116	caTTCAGAT/ca	5/28	1	2	FACETS	0.916	0.836	0.998	0.916	0.836	0.998	CLONAL	1	TRUE	1	0.636976489757082	2		347	432	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643498	38643498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	59	450	0	ENST00000299084.4:c.968C>T	p.Ser323Leu	p.S323L	ENST00000299084	NM_152594.2	323	tCa/tTa	7/7	0.406225483311625	1	FACETS	0.322	0.278	0.37	0.322	0.278	0.37	SUBCLONAL	1	TRUE	0	0.636976489757082	1		450	392	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51507285	51507285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	51	340	0	ENST00000260433.2:c.1003G>A	p.Glu335Lys	p.E335K	ENST00000260433		335	Gaa/Aaa	8/10	0.406225483311625	1	FACETS	0.301	0.257	0.35	0.301	0.257	0.35	SUBCLONAL	1	TRUE	0	0.636976489757082	1		340	362	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500614	99500614	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	95	501	0	ENST00000268035.6:c.4047G>A	p.Met1349Ile	p.M1349I	ENST00000268035	NM_000875.3	1349	atG/atA	21/21	0.406225483311625	1	FACETS	0.643	0.579	0.71	0.643	0.579	0.71	SUBCLONAL	1	TRUE	0	0.636976489757082	1		501	316	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633134	3633134	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	105	475	0	ENST00000294008.3:c.5117C>T	p.Ser1706Phe	p.S1706F	ENST00000294008	NM_032444.2	1706	tCt/tTt	14/15	1	2	FACETS	0.934	0.845	1	0.934	0.845	1	CLONAL	1	TRUE	1	0.636976489757082	2		475	353	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349036	11349037	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	89	483	0	ENST00000332029.2:c.299_300delinsTT	p.Thr100Ile	p.T100I	ENST00000332029	NM_003745.1	100	aCC/aTT	2/2	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.636976489757082	2		483	275	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646911	23646911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200144401	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	152	452	0	ENST00000261584.4:c.956C>T	p.Ser319Phe	p.S319F	ENST00000261584	NM_024675.3	319	tCt/tTt	4/13	1	2	FACETS	0.93	0.856	1	0.93	0.856	1	CLONAL	1	TRUE	1	0.636976489757082	2		452	513	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510689	38510689	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	126	435	0	ENST00000254066.5:c.943C>T	p.Gln315Ter	p.Q315*	ENST00000254066	NM_000964.3	315	Cag/Tag	7/9	1	2	FACETS	0.883	0.806	0.963	0.883	0.806	0.963	CLONAL	1	TRUE	1	0.636976489757082	2		435	448	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936340	78936340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751407036	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	107	415	1	ENST00000306801.3:c.3772G>A	p.Ala1258Thr	p.A1258T	ENST00000306801	NM_020761.2	1258	Gcc/Acc	32/34	1	2	FACETS	0.968	0.878	1	0.968	0.878	1	CLONAL	1	TRUE	1	0.636976489757082	2		416	347	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985533	60985533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	80	626	0	ENST00000333681.4:c.367C>T	p.Pro123Ser	p.P123S	ENST00000333681		123	Ccc/Tcc	2/3	0.406225483311625	1	FACETS	0.45	0.399	0.505	0.45	0.399	0.505	SUBCLONAL	1	TRUE	0	0.636976489757082	1		626	380	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1620979	1620980	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	49	512	1	ENST00000344749.5:c.1080_1081delinsTT	p.Gln361Ter	p.Q361*	ENST00000344749	NM_001136139.2	360	ccCCag/ccTTag	13/19	0.336193595834757	1	FACETS	0.254	0.215	0.296	0.254	0.215	0.296	INDETERMINATE	1	TRUE	0	0.636976489757082	1		513	413	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2220123	2220123	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	130	367	0	ENST00000398665.3:c.2708C>T	p.Pro903Leu	p.P903L	ENST00000398665	NM_032482.2	903	cCc/cTc	23/28	0.336193595834757	1	FACETS	0.828	0.761	0.896	0.828	0.761	0.896	INDETERMINATE	1	TRUE	0	0.636976489757082	1		367	336	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384825	17384825	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1189656970	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	64	502	0	ENST00000359435.4:c.457A>G	p.Thr153Ala	p.T153A	ENST00000359435	NM_001033549.1	153	Acg/Gcg	4/9	0.311806789018644	1	FACETS	0.342	0.297	0.391	0.342	0.297	0.391	INDETERMINATE	1	TRUE	0	0.636976489757082	1		502	400	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948853	17948853	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	125	448	0	ENST00000458235.1:c.1589G>A	p.Gly530Glu	p.G530E	ENST00000458235	NM_000215.3	530	gGg/gAg	12/24	0.311806789018644	1	FACETS	0.741	0.678	0.805	0.741	0.678	0.805	INDETERMINATE	1	TRUE	0	0.636976489757082	1		448	361	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727911	41727911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201959501	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	50	384	0	ENST00000301178.4:c.536C>T	p.Pro179Leu	p.P179L	ENST00000301178	NM_021913.4	179	cCc/cTc	4/20	0.311806789018644	1	FACETS	0.39	0.334	0.452	0.39	0.334	0.452	INDETERMINATE	1	TRUE	0	0.636976489757082	1		384	274	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044581	128044581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	55	424	0	ENST00000285398.2:c.1040C>T	p.Ser347Phe	p.S347F	ENST00000285398	NM_000122.1	347	tCc/tTc	8/15	0.406225483311625	1	FACETS	0.382	0.329	0.44	0.382	0.329	0.44	SUBCLONAL	1	TRUE	0	0.636976489757082	1		424	308	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873224	136873224	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	121	578	0	ENST00000241393.3:c.274C>T	p.Pro92Ser	p.P92S	ENST00000241393	NM_003467.2	92	Ccc/Tcc	2/2	0.406225483311625	1	FACETS	0.625	0.57	0.683	0.625	0.57	0.683	SUBCLONAL	1	TRUE	0	0.636976489757082	1		578	414	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485818	57485819	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	213	468	0	ENST00000371085.3:c.1119_1120delinsTT	p.Arg374Cys	p.R374C	ENST00000371085	NM_000516.4	373	cgCCgt/cgTTgt	13/13	0.193208572408411	3	FACETS	0.868	0.814	0.922	0.579	0.543	0.615	INDETERMINATE	2	TRUE	0	0.636976489757082	3		468	508	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545142	41545142	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	75	418	0	ENST00000263253.7:c.2342C>T	p.Pro781Leu	p.P781L	ENST00000263253	NM_001429.3	781	cCt/cTt	13/31	0.371275741896307	1	FACETS	0.386	0.339	0.435	0.386	0.339	0.435	INDETERMINATE	1	TRUE	0	0.636976489757082	1		418	416	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280148	142280149	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	121	347	0	ENST00000350721.4:c.1285_1286delinsTT	p.Pro429Phe	p.P429F	ENST00000350721	NM_001184.3	429	CCc/TTc	5/47	0.311806789018644	1	FACETS	0.755	0.69	0.821	0.755	0.69	0.821	INDETERMINATE	1	TRUE	0	0.636976489757082	1		347	343	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169953136	169953136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	158	405	0	ENST00000295797.4:c.220G>A	p.Glu74Lys	p.E74K	ENST00000295797	NM_002740.5	74	Gaa/Aaa	2/18	0.181149492053506	3	FACETS	1	0.988	1	0.702	0.649	0.756	INDETERMINATE	1	TRUE	1	0.636976489757082	3		405	466	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748116	41748116	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	98	423	0	ENST00000226382.2:c.653C>T	p.Pro218Leu	p.P218L	ENST00000226382	NM_003924.3	218	cCc/cTc	3/3	0.313403179850146	2	FACETS	1	0.984	1	0.726	0.662	0.79	INDETERMINATE	1	TRUE	0	0.636976489757082	2		423	212	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796226	57796226	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	219	498	0	ENST00000309042.7:c.1202A>C	p.Lys401Thr	p.K401T	ENST00000309042	NM_005612.4	401	aAg/aCg	4/4	0.313403179850146	2	FACETS	1	0.991	1	0.679	0.638	0.721	INDETERMINATE	1	TRUE	0	0.636976489757082	2		498	506	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99809047	99809047	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	63	309	0	ENST00000280892.6:c.338T>A	p.Leu113His	p.L113H	ENST00000280892	NM_001130678.1	113	cTt/cAt	4/7	0.313403179850146	2	FACETS	0.467	0.405	0.533	0.233	0.202	0.267	INDETERMINATE	1	TRUE	0	0.636976489757082	2		309	424	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557197	187557197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	59	509	0	ENST00000441802.2:c.4165C>T	p.Leu1389Phe	p.L1389F	ENST00000441802	NM_005245.3	1389	Ctt/Ttt	6/27	0.313403179850146	2	FACETS	0.375	0.323	0.432	0.188	0.161	0.216	INDETERMINATE	1	TRUE	0	0.636976489757082	2		509	494	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294906	1294906	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	43	411	2	ENST00000310581.5:c.199G>A	p.Ala67Thr	p.A67T	ENST00000310581	NM_198253.2	67	Gcc/Acc	1/16	0.38810361448256	1	FACETS	0.458	0.387	0.534	0.458	0.387	0.534	SUBCLONAL	1	TRUE	0	0.636976489757082	1		413	201	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295747	1295747	+	upstream_gene_variant	5'Flank	SNP	C	C	T	rs1268654095	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	53	624	0				ENST00000310581	NM_198253.2	-/1132			0.38810361448256	1	FACETS	0.333	0.285	0.384	0.333	0.285	0.384	SUBCLONAL	1	TRUE	0	0.636976489757082	1		624	341	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80057366	80057366	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	56	413	0	ENST00000265081.6:c.1765G>A	p.Glu589Lys	p.E589K	ENST00000265081	NM_002439.4	589	Gaa/Aaa	13/24	0.38810361448256	1	FACETS	0.317	0.272	0.365	0.317	0.272	0.365	SUBCLONAL	1	TRUE	0	0.636976489757082	1		413	378	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671002	30671002	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	218	570	0	ENST00000376406.3:c.5744G>T	p.Ser1915Ile	p.S1915I	ENST00000376406	NM_014641.2	1915	aGt/aTt	12/15	0.282759750160512	6	FACETS	1	0.95	1	0.511	0.476	0.546	INDETERMINATE	2	TRUE	2	0.636976489757082	6		570	762	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288576	33288576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	168	488	0	ENST00000374542.5:c.976G>A	p.Glu326Lys	p.E326K	ENST00000374542	NM_001141970.1	326	Gag/Aag	3/8	0.282759750160512	6	FACETS	0.899	0.829	0.972	0.45	0.414	0.486	INDETERMINATE	2	TRUE	2	0.636976489757082	6		488	667	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94129041	94129041	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	174	466	0	ENST00000369303.4:c.19T>G	p.Tyr7Asp	p.Y7D	ENST00000369303	NM_004440.3	7	Tac/Gac	1/17	0.636976489757082	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.636976489757082	1		466	347	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508107	106508107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	41	495	0	ENST00000359195.3:c.101C>T	p.Ser34Phe	p.S34F	ENST00000359195	NM_002649.2	34	tCc/tTc	2/11	0.218632636896735	3	FACETS	0.461	0.385	0.546	0.154	0.128	0.182	INDETERMINATE	1	TRUE	0	0.636976489757082	3		495	368	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878990	151878991	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	241	588	0	ENST00000262189.6:c.5954_5955delinsTT	p.Ser1985Phe	p.S1985F	ENST00000262189	NM_170606.2	1985	tCC/tTT	36/59	0.218632636896735	3	FACETS	0.907	0.855	0.959	0.605	0.57	0.64	INDETERMINATE	2	TRUE	0	0.636976489757082	3		588	550	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345753	152345753	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	126	358	0	ENST00000359321.1:c.817G>T	p.Gly273Ter	p.G273*	ENST00000359321	NM_005431.1	273	Gga/Tga	3/3	0.218632636896735	3	FACETS	1	0.943	1	0.349	0.318	0.382	INDETERMINATE	1	TRUE	0	0.636976489757082	3		358	498	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371842	55371842	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267607082	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	38	533	0	ENST00000297316.4:c.532G>A	p.Gly178Ser	p.G178S	ENST00000297316	NM_022454.3	178	Ggc/Agc	2/2	0.492486338418638	3	FACETS	0.521	0.432	0.619	0.26	0.216	0.31	SUBCLONAL	1	TRUE	1	0.636976489757082	3		533	302	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020396	69020396	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	211	431	0	ENST00000288368.4:c.2768C>G	p.Ser923Cys	p.S923C	ENST00000288368	NM_024870.2	923	tCt/tGt	24/40	0.492486338418638	3	FACETS	0.855	0.801	0.909	0.855	0.801	0.909	CLONAL	2	TRUE	1	0.636976489757082	3		431	511	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559294	141559294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	74	539	0	ENST00000220592.5:c.1507C>T	p.Pro503Ser	p.P503S	ENST00000220592	NM_012154.3	503	Ccc/Tcc	12/19	0.228823556232236	5	FACETS	0.816	0.715	0.924			1	INDETERMINATE	1	TRUE	NA	0.636976489757082	5		539	557	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133729472	133729472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1165776027	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	354	355	0	ENST00000318560.5:c.101C>T	p.Ala34Val	p.A34V	ENST00000318560	NM_005157.4	34	gCa/gTa	2/11	0.544469022604921	3	FACETS	0.943	0.909	0.976	0.943	0.909	0.976	CLONAL	3	TRUE	0	0.636976489757082	3		355	518	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429394	47429394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	44	229	0	ENST00000377045.4:c.1522C>T	p.Pro508Ser	p.P508S	ENST00000377045	NM_001654.4	508	Cct/Tct	14/16	1	1	FACETS	0.615	0.526	0.711	0.615	0.526	0.711	SUBCLONAL	1	TRUE	0	0.636976489757082	1		229	153	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292548	15292550	+	frameshift_variant	Frame_Shift_Del	DEL	AGG	AGG	GA	novel	NA	P-0057066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	92	479	0	ENST00000263388.2:c.2629_2631delinsTC	p.Pro877SerfsTer16	p.P877Sfs*16	ENST00000263388	NM_000435.2	877	CCT/TC	17/33	0.311806789018644	1	FACETS	0.597	0.535	0.661	0.597	0.535	0.661	INDETERMINATE	1	TRUE	0	0.636976489757082	1		479	330	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106099	27106099	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057067-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	270	479	0	ENST00000324856.7:c.5710G>T	p.Glu1904Ter	p.E1904*	ENST00000324856	NM_006015.4	1904	Gaa/Taa	20/20	NA	2	FACETS	0.958	0.906	1			1	INDETERMINATE	1	TRUE	NA	0.888941901356197	2		479	634	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACT	novel	NA	P-0057067-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	361	440	0	ENST00000275493.2:c.2310_2311insTAC	p.Asp770_Asn771insTyr	p.D770_N771insY	ENST00000275493	NM_005228.3	770	gac/gACTac	20/28	0.501074630794646	6	FACETS	0.922	0.879	0.965	0.922	0.879	0.965	INDETERMINATE	3	TRUE	3	0.888941901356197	6		440	816	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0057067-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	206	308	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.688022143712672	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.888941901356197	1		308	248	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233750	233750	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs746165168	NA	P-0057067-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	153	289	0	ENST00000264932.6:c.1054C>T	p.Arg352Ter	p.R352*	ENST00000264932	NM_004168.2	352	Cga/Tga	8/15	0.379314835051189	1	FACETS	0.625	0.582	0.667	0.625	0.582	0.667	INDETERMINATE	1	TRUE	0	0.888941901356197	1		289	306	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591900	48591900	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057067-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	216	390	0	ENST00000342988.3:c.1063G>T	p.Asp355Tyr	p.D355Y	ENST00000342988	NM_005359.5	355	Gac/Tac	9/12	0.888941901356197	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.888941901356197	1		390	269	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444304	49444304	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057067-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	284	536	0	ENST00000301067.7:c.3067C>T	p.Gln1023Ter	p.Q1023*	ENST00000301067	NM_003482.3	1023	Cag/Tag	11/54	0.888941901356197	2	FACETS	1	0.977	1	0.525	0.498	0.553	CLONAL	1	TRUE	0	0.888941901356197	2		536	608	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770600	40770600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159844	NA	P-0057067-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	135	363	0	ENST00000373198.4:c.2782G>A	p.Glu928Lys	p.E928K	ENST00000373198	NM_133170.3	928	Gag/Aag	19/32	0.872805701677325	1	FACETS	0.541	0.499	0.583	0.541	0.499	0.583	SUBCLONAL	1	TRUE	0	0.888941901356197	1		363	312	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622099	43622099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs79853121	NA	P-0057067-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	145	379	0	ENST00000355710.3:c.3116C>T	p.Pro1039Leu	p.P1039L	ENST00000355710	NM_020975.4	1039	cCg/cTg	19/20	0.320184465762781	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.888941901356197	0		379	329	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437315	52437315	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0057067-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	174	402	0	ENST00000460680.1:c.1730-1G>C		p.X577_splice	ENST00000460680	NM_004656.3	577			0.8838258932748	1	FACETS	0.998	0.956	1	0.998	0.956	1	CLONAL	1	TRUE	0	0.888941901356197	1		402	218	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971110	55971110	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057067-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	159	329	0	ENST00000263923.4:c.1687G>A	p.Glu563Lys	p.E563K	ENST00000263923	NM_002253.2	563	Gag/Aag	13/30	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.888941901356197	2		329	348	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725466	162725466	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs889257496	NA	P-0057067-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	165	359	0	ENST00000367921.3:c.578C>G	p.Ser193Cys	p.S193C	ENST00000367921	NM_006182.2	193	tCt/tGt	7/18	1	2	FACETS	0.952	0.886	1	0.952	0.886	1	CLONAL	1	TRUE	1	0.888941901356197	2		359	390	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067911	30067911	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057067-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	223	384	0	ENST00000338641.4:c.1096G>T	p.Glu366Ter	p.E366*	ENST00000338641	NM_000268.3	366	Gaa/Taa	11/16	0.888941901356197	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.888941901356197	1		384	268	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31239788	31239788	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057067-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	242	396	0	ENST00000376228.5:c.61G>C	p.Glu21Gln	p.E21Q	ENST00000376228	NM_002117.5	21	Gag/Cag	1/8	1	2	FACETS	0.787	0.753	0.819	1	0.995	1	SUBCLONAL	2	TRUE	1	0.888941901356197	2		396	346	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782336	56782336	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057067-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	166	308	0	ENST00000308159.5:c.177G>T	p.Lys59Asn	p.K59N	ENST00000308159	NM_014669.4	59	aaG/aaT	2/22	1	2	FACETS	0.953	0.887	1	0.953	0.887	1	CLONAL	1	TRUE	1	0.888941901356197	2		308	392	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132438	11132438	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057067-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	203	544	0	ENST00000358026.2:c.2654G>C	p.Arg885Pro	p.R885P	ENST00000358026	NM_001128849.1	885	cGc/cCc	19/36	0.868518516285068	3	FACETS	0.916	0.853	0.982	0.458	0.426	0.491	CLONAL	1	TRUE	1	0.888941901356197	3		544	720	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130649	29130649	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587782323	NA	P-0057067-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	194	421	0	ENST00000328354.6:c.61C>A	p.Pro21Thr	p.P21T	ENST00000328354	NM_007194.3	21	Ccc/Acc	2/15	0.888941901356197	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.888941901356197	1		421	224	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130666	29130666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057067-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	193	385	0	ENST00000328354.6:c.44G>A	p.Ser15Asn	p.S15N	ENST00000328354	NM_007194.3	15	aGc/aAc	2/15	0.888941901356197	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.888941901356197	1		385	217	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1253868	1253868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1291687212	NA	P-0057067-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	135	418	0	ENST00000310581.5:c.3374C>T	p.Ser1125Leu	p.S1125L	ENST00000310581	NM_198253.2	1125	tCa/tTa	16/16	0.379314835051189	1	FACETS	0.586	0.542	0.63	0.586	0.542	0.63	INDETERMINATE	1	TRUE	0	0.888941901356197	1		418	288	SUCCESS
APC	324	MSKCC	GRCh37	5	112179502	112179502	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1366190280	NA	P-0057067-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	205	409	0	ENST00000257430.4:c.8211G>C	p.Glu2737Asp	p.E2737D	ENST00000257430	NM_000038.5	2737	gaG/gaC	16/16	1	2	FACETS	0.896	0.838	0.954	0.896	0.838	0.954	CLONAL	1	TRUE	1	0.888941901356197	2		409	515	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056523	26056523	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774567285	NA	P-0057067-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	260	422	0	ENST00000343677.2:c.134C>T	p.Thr45Ile	p.T45I	ENST00000343677	NM_005319.3	45	aCc/aTc	1/1	0.206013440566257	4	FACETS	0.932	0.88	0.983	0.621	0.587	0.656	INDETERMINATE	2	TRUE	1	0.888941901356197	4		422	593	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0057113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	17	265	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.529	0.393	0.691	0.529	0.393	0.691	SUBCLONAL	1	TRUE	1	0.12	2		265	536	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045551	47045551	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	24	427	0	ENST00000377604.3:c.2519del	p.Gly840AlafsTer7	p.G840Afs*7	ENST00000377604	NM_001204468.1	840	Ggc/gc	22/24	1	1	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	TRUE	0	0.12	1		427	342	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	139	190	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.972	1	1	0.992	1	CLONAL	2	TRUE	1	0.204066228260715	2		190	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0057199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	333	1110	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.204066228260715	1	FACETS	0.874	0.827	0.922	1	0.997	1	CLONAL	3	TRUE	0	0.204066228260715	1		1111	1118	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154748	2154748	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs369122420	NA	P-0057199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	242	889	0	ENST00000434045.2:c.473C>T	p.Pro158Leu	p.P158L	ENST00000434045	NM_001127598.1	158	cCg/cTg	4/5	0.204066228260715	1	FACETS	0.979	0.914	1	1	0.994	1	CLONAL	2	TRUE	0	0.204066228260715	1		889	1088	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50788270	50788270	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	91	560	0	ENST00000398568.2:c.848T>C	p.Val283Ala	p.V283A	ENST00000398568	NM_001042412.1	283	gTg/gCg	5/18	0.204066228260715	1	FACETS	0.896	0.794	1	0.896	0.794	1	CLONAL	1	TRUE	0	0.204066228260715	1		560	894	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505365	157505365	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	39	358	0	ENST00000346085.5:c.3346G>A	p.Val1116Ile	p.V1116I	ENST00000346085	NM_020732.3	1116	Gtt/Att	13/20	0.204066228260715	0	FACETS	0.54	0.447	0.645			1	SUBCLONAL	1	TRUE	0	0.204066228260715	0		358	563	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624296	89624296	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1554890405	NA	P-0057247-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	181	269	0	ENST00000371953.3:c.70del	p.Asp24ThrfsTer2	p.D24Tfs*2	ENST00000371953	NM_000314.4	24	Gac/ac	1/9	0.581283492364699	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.581283492364699	1		269	401	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591611	38591611	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434313	NA	P-0057247-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	149	295	0	ENST00000299084.4:c.70C>T	p.Arg24Ter	p.R24*	ENST00000299084	NM_152594.2	24	Cga/Tga	2/7	1	2	FACETS	0.967	0.889	1	0.967	0.889	1	CLONAL	1	TRUE	1	0.581283492364699	2		295	530	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295182	1295183	+	upstream_gene_variant	5'Flank	INS	-	-	GGGCGGGGCCGCGGAAAGGAAG	novel	NA	P-0057247-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	70	488	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.374	0.326	0.426	0.374	0.326	0.426	SUBCLONAL	1	TRUE	1	0.581283492364699	2		488	644	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057973	27057973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	128	526	0	ENST00000324856.7:c.1681C>T	p.Gln561Ter	p.Q561*	ENST00000324856	NM_006015.4	561	Cag/Tag	3/20	1	2	FACETS	0.826	0.749	0.907	0.826	0.749	0.907	CLONAL	1	TRUE	1	0.406606806379406	2		526	762	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188305	10188305	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs794727253	NA	P-0057287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	51	305	0	ENST00000256474.2:c.449del	p.Asn150IlefsTer9	p.N150Ifs*9	ENST00000256474	NM_000551.3	150	Aat/at	2/3	0.406606806379406	1	FACETS	0.819	0.703	0.944	0.819	0.703	0.944	CLONAL	1	TRUE	0	0.406606806379406	1		305	244	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058686	47058686	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	71	320	0	ENST00000409792.3:c.7592del	p.Glu2531GlyfsTer6	p.E2531Gfs*6	ENST00000409792	NM_014159.6	2531	gAg/gg	21/21	0.406606806379406	1	FACETS	0.88	0.775	0.992	0.88	0.775	0.992	CLONAL	1	TRUE	0	0.406606806379406	1		320	316	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242747	66242747	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057287-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	122	326	0	ENST00000273854.3:c.1825C>A	p.Leu609Met	p.L609M	ENST00000273854	NM_004439.5	609	Ctg/Atg	9/18	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.406606806379406	2		326	599	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8109838	8109838	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057389-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	258	573	0	ENST00000585124.1:c.657C>A	p.Phe219Leu	p.F219L	ENST00000585124	NM_004217.3	219	ttC/ttA	7/9	0.811346144025012	2	FACETS	0.918	0.865	0.972	0.459	0.432	0.486	CLONAL	1	TRUE	0	0.826599085399311	2		573	680	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912844	50912844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057389-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	312	734	0	ENST00000440232.2:c.2075C>T	p.Ala692Val	p.A692V	ENST00000440232	NM_002691.3	692	gCg/gTg	17/27	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.826599085399311	2		734	726	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467556	66467556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147719164	NA	P-0057389-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	34	607	1	ENST00000273854.3:c.713G>A	p.Arg238Gln	p.R238Q	ENST00000273854	NM_004439.5	238	cGa/cAa	3/18	1	2	FACETS	0.154	0.125	0.186	0.154	0.125	0.186	SUBCLONAL	1	TRUE	1	0.826599085399311	2		608	534	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101910017	101910017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057389-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	81	399	0	ENST00000374994.4:c.1337G>A	p.Cys446Tyr	p.C446Y	ENST00000374994	NM_004612.2	446	tGt/tAt	8/9	0.797862503480924	2	FACETS	0.933	0.872	0.989	0.933	0.872	0.989	CLONAL	2	TRUE	0	0.826599085399311	2		399	105	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	88	738	0				ENST00000310581	NM_198253.2	-/1132			0.232642078614257	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.236573201136305	3		738	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	52	308	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.232642078614257	3	FACETS	1	0.888	1	0.525	0.448	0.61	CLONAL	1	TRUE	1	0.236573201136305	3		308	468	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	146	488	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.222416900345889	3	FACETS	0.959	0.881	1	0.959	0.881	1	CLONAL	3	TRUE	0	0.236573201136305	3		488	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	99	895	2	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	0.232642078614257	3	FACETS	0.91	0.816	1	0.91	0.816	1	CLONAL	2	TRUE	1	0.236573201136305	3		897	514	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535490	187535490	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	40	337	0	ENST00000441802.2:c.9084T>A	p.Tyr3028Ter	p.Y3028*	ENST00000441802	NM_005245.3	3028	taT/taA	12/27	0.236573201136305	3	FACETS	1	0.923	1	0.598	0.499	0.708	CLONAL	1	TRUE	1	0.236573201136305	3		337	316	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244787	46244787	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	58	489	0	ENST00000334344.6:c.2881C>T	p.Gln961Ter	p.Q961*	ENST00000334344	NM_152641.2	961	Cag/Tag	15/21	0.232642078614257	3	FACETS	0.999	0.859	1	0.499	0.429	0.576	CLONAL	1	TRUE	1	0.236573201136305	3		489	549	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543748	29543748	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	91	432	0	ENST00000389048.3:c.1415G>A	p.Arg472Gln	p.R472Q	ENST00000389048	NM_004304.4	472	cGg/cAg	7/29	0.188471857639885	4	FACETS	0.913	0.813	1	0.913	0.813	1	CLONAL	2	TRUE	2	0.236573201136305	4		432	521	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248683	212248683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	41	430	0	ENST00000342788.4:c.3584C>T	p.Pro1195Leu	p.P1195L	ENST00000342788	NM_005235.2	1195	cCa/cTa	28/28	0.232642078614257	3	FACETS	0.881	0.734	1	0.44	0.367	0.522	CLONAL	1	TRUE	1	0.236573201136305	3		430	440	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626668	100626668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	54	135	0	ENST00000308731.7:c.262G>A	p.Glu88Lys	p.E88K	ENST00000308731	NM_000061.2	88	Gaa/Aaa	4/19	0.236573201136305	2	FACETS	1	0.948	1			1	CLONAL	2	TRUE	NA	0.236573201136305	2		135	191	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412675	139412675	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	229	504	0	ENST00000277541.6:c.1169A>G	p.Asn390Ser	p.N390S	ENST00000277541	NM_017617.3	390	aAc/aGc	7/34	0.236573201136305	4	FACETS	0.989	0.929	1	0.989	0.929	1	CLONAL	4	TRUE	0	0.236573201136305	4		504	605	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035169	30035169	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	123	315	0	ENST00000338641.4:c.331C>T	p.Gln111Ter	p.Q111*	ENST00000338641	NM_000268.3	111	Cag/Tag	3/16	0.236573201136305	3	FACETS	0.969	0.884	1	0.969	0.884	1	CLONAL	3	TRUE	0	0.236573201136305	3		315	400	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281334	142281334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754292203	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	23	380	0	ENST00000350721.4:c.910C>T	p.Pro304Ser	p.P304S	ENST00000350721	NM_001184.3	304	Ccc/Tcc	4/47	0.236573201136305	3	FACETS	0.75	0.585	0.94	0.375	0.292	0.47	CLONAL	1	TRUE	1	0.236573201136305	3		380	290	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374358	81374358	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	59	249	0	ENST00000222390.5:c.704G>T	p.Trp235Leu	p.W235L	ENST00000222390	NM_000601.4	235	tGg/tTg	6/18	0.221204021159128	4	FACETS	0.91	0.787	1	0.91	0.787	1	CLONAL	2	TRUE	2	0.236573201136305	4		249	339	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606536	93606536	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	141	434	0	ENST00000375746.1:c.356C>T	p.Pro119Leu	p.P119L	ENST00000375746	NM_001174167.1	119	cCc/cTc	2/14	0.219664371055797	4	FACETS	1	0.922	1	1	0.922	1	CLONAL	3	TRUE	1	0.236573201136305	4		434	489	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957132	81957132	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1567534502	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	44	361	0	ENST00000359376.3:c.2350C>T	p.Arg784Ter	p.R784*	ENST00000359376	NM_002661.3	784	Cga/Tga	22/33	0.236573201136305	3	FACETS	1	0.868	1	0.519	0.436	0.61	CLONAL	1	TRUE	1	0.236573201136305	3		361	401	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120509	94120509	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	65	360	0	ENST00000369303.4:c.542G>A	p.Gly181Glu	p.G181E	ENST00000369303	NM_004440.3	181	gGa/gAa	3/17	0.236573201136305	3	FACETS	0.774	0.674	0.881	0.774	0.674	0.881	SUBCLONAL	2	TRUE	1	0.236573201136305	3		360	397	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264414	16264415	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	102	419	0	ENST00000375759.3:c.10617_10618delinsTT	p.Leu3540Phe	p.L3540F	ENST00000375759	NM_015001.2	3539	ccCCtt/ccTTtt	13/15	0.232642078614257	3	FACETS	1	0.922	1	1	0.922	1	CLONAL	2	TRUE	1	0.236573201136305	3		419	468	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115284242	115284242	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	42	383	0	ENST00000438362.2:c.44C>G	p.Pro15Arg	p.P15R	ENST00000438362	NM_001242891.1	15	cCt/cGt	2/20	0.232642078614257	3	FACETS	1	0.841	1	0.503	0.42	0.594	CLONAL	1	TRUE	1	0.236573201136305	3		383	395	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471808	120471808	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	62	430	0	ENST00000256646.2:c.3683A>G	p.Asp1228Gly	p.D1228G	ENST00000256646	NM_024408.3	1228	gAc/gGc	23/34	0.232642078614257	3	FACETS	1	0.957	1	0.637	0.552	0.73	CLONAL	1	TRUE	1	0.236573201136305	3		430	460	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510738	120510738	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	48	388	0	ENST00000256646.2:c.1226G>A	p.Gly409Glu	p.G409E	ENST00000256646	NM_024408.3	409	gGg/gAg	7/34	0.232642078614257	3	FACETS	0.906	0.766	1	0.453	0.383	0.53	CLONAL	1	TRUE	1	0.236573201136305	3		388	501	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446855	18446855	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	16	168	0	ENST00000266497.5:c.940C>G	p.Leu314Val	p.L314V	ENST00000266497		314	Cta/Gta	4/31	0.232642078614257	3	FACETS	1	0.76	1	0.511	0.38	0.665	CLONAL	1	TRUE	1	0.236573201136305	3		168	148	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287506	46287506	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	41	224	0	ENST00000334344.6:c.5363+2T>G		p.X1788_splice	ENST00000334344	NM_152641.2	1788			0.232642078614257	3	FACETS	0.999	0.842	1	0.999	0.842	1	CLONAL	2	TRUE	1	0.236573201136305	3		224	194	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865253	57865253	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	87	404	0	ENST00000228682.2:c.2730G>A	p.Trp910Ter	p.W910*	ENST00000228682	NM_005269.2	910	tgG/tgA	12/12	0.232642078614257	3	FACETS	0.914	0.813	1	0.914	0.813	1	CLONAL	2	TRUE	1	0.236573201136305	3		404	450	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592671	28592671	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	102	362	0	ENST00000241453.7:c.2474T>G	p.Val825Gly	p.V825G	ENST00000241453	NM_004119.2	825	gTg/gGg	20/24	0.216403854689792	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.236573201136305	2		362	352	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022930	33022931	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	104	320	0	ENST00000300177.4:c.39_40delinsTT	p.Leu14Phe	p.L14F	ENST00000300177	NM_001191322.1	13	ctCCtc/ctTTtc	2/2	0.236573201136305	3	FACETS	1	0.968	1	0.788	0.71	0.869	CLONAL	2	TRUE	0	0.236573201136305	3		320	416	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830888	72830888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753973363	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	47	536	0	ENST00000268489.5:c.5693G>A	p.Gly1898Glu	p.G1898E	ENST00000268489	NM_006885.3	1898	gGg/gAg	9/10	0.236573201136305	3	FACETS	0.802	0.676	0.941	0.401	0.338	0.471	CLONAL	1	TRUE	1	0.236573201136305	3		536	554	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588746	29588746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	83	275	0	ENST00000356175.3:c.4532G>A	p.Gly1511Glu	p.G1511E	ENST00000356175	NM_000267.3	1511	gGa/gAa	34/57	0.232642078614257	3	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	1	0.236573201136305	3		275	362	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532450	63532451	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	38	392	0	ENST00000307078.5:c.2128_2129delinsTT	p.Pro710Phe	p.P710F	ENST00000307078	NM_004655.3	710	CCc/TTc	8/11	0.232642078614257	3	FACETS	0.885	0.732	1	0.442	0.366	0.528	CLONAL	1	TRUE	1	0.236573201136305	3		392	406	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249253	10249253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	47	407	0	ENST00000340748.4:c.3929G>A	p.Arg1310Lys	p.R1310K	ENST00000340748		1310	aGg/aAg	34/40	1	2	FACETS	0.953	0.805	1	0.953	0.805	1	CLONAL	1	TRUE	1	0.236573201136305	2		407	417	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155289	185155289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	61	321	1	ENST00000265026.3:c.530G>A	p.Gly177Glu	p.G177E	ENST00000265026	NM_004721.4	177	gGa/gAa	3/14	0.236573201136305	3	FACETS	1	0.95	1	0.61	0.527	0.699	CLONAL	1	TRUE	1	0.236573201136305	3		322	473	SUCCESS
ALB	213	MSKCC	GRCh37	4	74270051	74270051	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	32	276	0	ENST00000295897.4:c.7T>G	p.Trp3Gly	p.W3G	ENST00000295897	NM_000477.5	3	Tgg/Ggg	1/15	0.236573201136305	3	FACETS	0.922	0.75	1	0.461	0.375	0.558	CLONAL	1	TRUE	1	0.236573201136305	3		276	328	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156282	106156282	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	51	537	0	ENST00000380013.4:c.1183A>C	p.Thr395Pro	p.T395P	ENST00000380013	NM_001127208.2	395	Act/Cct	3/11	0.236573201136305	3	FACETS	0.891	0.757	1	0.446	0.378	0.519	CLONAL	1	TRUE	1	0.236573201136305	3		537	541	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80040424	80040424	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	40	220	0	ENST00000265081.6:c.1753C>T	p.Leu585Phe	p.L585F	ENST00000265081	NM_002439.4	585	Ctt/Ttt	12/24	0.232642078614257	3	FACETS	0.871	0.731	1	0.871	0.731	1	CLONAL	2	TRUE	1	0.236573201136305	3		220	217	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956624	93956624	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	91	339	0	ENST00000369303.4:c.2612A>T	p.Asp871Val	p.D871V	ENST00000369303	NM_004440.3	871	gAt/gTt	15/17	0.236573201136305	3	FACETS	0.952	0.849	1	0.952	0.849	1	CLONAL	2	TRUE	1	0.236573201136305	3		339	452	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686889	117686889	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	25	250	0	ENST00000368508.3:c.2828C>T	p.Thr943Ile	p.T943I	ENST00000368508	NM_002944.2	943	aCc/aTc	19/43	1	2	FACETS	1	0.812	1	1	0.812	1	CLONAL	1	TRUE	1	0.236573201136305	2		250	206	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738696	145738697	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	135	563	0	ENST00000428558.2:c.2367_2368delinsAA	p.Gly790Arg	p.G790R	ENST00000428558	NM_004260.3	789	ctGGgg/ctAAgg	15/22	0.221204021159128	4	FACETS	1	0.919	1	1	0.919	1	CLONAL	2	TRUE	2	0.236573201136305	4		563	699	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413927	139413927	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	239	386	0	ENST00000277541.6:c.833C>T	p.Thr278Ile	p.T278I	ENST00000277541	NM_017617.3	278	aCc/aTc	5/34	0.236573201136305	4	FACETS	0.939	0.886	0.993	1	0.988	1	CLONAL	5	TRUE	0	0.236573201136305	4		386	532	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532450	63532450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057399-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	36	392	0	ENST00000307078.5:c.2129C>T	p.Pro710Leu	p.P710L	ENST00000307078	NM_004655.3	710	cCc/cTc	8/11	0.232642078614257	3	FACETS	0.845	0.695	1	0.422	0.347	0.506	CLONAL	1	TRUE	1	0.236573201136305	3		392	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0057442-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	332	773	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	NA	2	FACETS	0.922	0.887	0.957			1	INDETERMINATE	3	TRUE	NA	0.479155547283666	2		773	501	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033903	49033909	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGACC	CTGGACC	-	novel	NA	P-0057442-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	100	257	0	ENST00000267163.4:c.2042_2048del	p.Trp681PhefsTer13	p.W681Ffs*13	ENST00000267163	NM_000321.2	680	atCTGGACC/at	20/27	0.479155547283666	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.479155547283666	2		257	176	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1685042	1685042	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057442-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	146	444	0	ENST00000378625.1:c.1583A>G	p.Asp528Gly	p.D528G	ENST00000378625	NM_001198994.1	528	gAt/gGt	13/14	0.146398442642345	5	FACETS	1	0.977	1	0.778	0.716	0.841	INDETERMINATE	2	TRUE	2	0.479155547283666	5		444	449	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999377	100999377	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057442-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	76	564	0	ENST00000325455.5:c.425T>G	p.Leu142Arg	p.L142R	ENST00000325455	NM_001202474.3	142	cTg/cGg	1/8	0.190490877478926	2	FACETS	0.958	0.848	1	0.479	0.424	0.538	INDETERMINATE	1	TRUE	0	0.479155547283666	2		564	331	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994607	73994607	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs766904389	NA	P-0057442-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	95	470	0	ENST00000318443.5:c.91G>T	p.Val31Phe	p.V31F	ENST00000318443	NM_001024736.1	31	Gtc/Ttc	3/10	0.193741180219633	2	FACETS	0.924	0.828	1	0.462	0.414	0.513	INDETERMINATE	1	TRUE	0	0.479155547283666	2		470	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	103	328	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.237502283930643	2	FACETS	0.929	0.835	1	0.929	0.835	1	CLONAL	2	FALSE	0	0.237502283930643	2		328	467	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	60	302	0				ENST00000310581	NM_198253.2	-/1132			0.237502283930643	6	FACETS	0.796	0.687	0.914	0.398	0.343	0.457	CLONAL	2	FALSE	2	0.237502283930643	6		302	468	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347770	347770	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	53	488	0	ENST00000262320.3:c.1736C>G	p.Ser579Ter	p.S579*	ENST00000262320	NM_003502.3	579	tCa/tGa	6/11	1	2	FACETS	0.82	0.7	0.953	0.82	0.7	0.953	CLONAL	1	FALSE	1	0.237502283930643	2		488	544	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587118	189587118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761885185	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	47	294	0	ENST00000264731.3:c.1135C>T	p.Arg379Cys	p.R379C	ENST00000264731	NM_003722.4	379	Cgt/Tgt	9/14	0.193602167682183	3	FACETS	1	0.854	1	0.505	0.427	0.592	CLONAL	1	FALSE	1	0.237502283930643	3		294	438	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533703	63533703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	158	599	0	ENST00000307078.5:c.1451G>A	p.Gly484Asp	p.G484D	ENST00000307078	NM_004655.3	484	gGt/gAt	6/11	0.237502283930643	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	FALSE	0	0.237502283930643	2		599	644	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692901	89692901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786204929	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	40	233	0	ENST00000371953.3:c.385G>A	p.Gly129Arg	p.G129R	ENST00000371953	NM_000314.4	129	Gga/Aga	5/9	1	2	FACETS	0.913	0.76	1	0.913	0.76	1	CLONAL	1	FALSE	1	0.237502283930643	2		233	369	SUCCESS
APC	324	MSKCC	GRCh37	5	112116491	112116491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	64	206	0	ENST00000257430.4:c.536C>T	p.Ser179Phe	p.S179F	ENST00000257430	NM_000038.5	179	tCc/tTc	6/16	0.208146084290856	2	FACETS	0.983	0.86	1	0.983	0.86	1	CLONAL	2	FALSE	0	0.237502283930643	2		206	274	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332864	70332864	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	88	441	0	ENST00000373644.4:c.769A>G	p.Thr257Ala	p.T257A	ENST00000373644	NM_030625.2	257	Acc/Gcc	2/12	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.237502283930643	2		441	652	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226980	2226980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	49	503	0	ENST00000398665.3:c.4460C>T	p.Ser1487Phe	p.S1487F	ENST00000398665	NM_032482.2	1487	tCc/tTc	27/28	1	2	FACETS	0.738	0.625	0.863	0.738	0.625	0.863	SUBCLONAL	1	FALSE	1	0.237502283930643	2		503	559	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923440	9923440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	86	411	0	ENST00000330684.3:c.1847C>T	p.Ser616Phe	p.S616F	ENST00000330684	NM_001134407.1	616	tCc/tTc	9/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.237502283930643	2		411	534	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721099	61721099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458439158	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	64	392	0	ENST00000401558.2:c.1175C>T	p.Pro392Leu	p.P392L	ENST00000401558	NM_003400.3	392	cCg/cTg	12/25	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	FALSE	1	0.237502283930643	2		392	512	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426751	49426751	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	59	566	0	ENST00000301067.7:c.11737C>T	p.Gln3913Ter	p.Q3913*	ENST00000301067	NM_003482.3	3913	Cag/Tag	39/54	1	2	FACETS	0.657	0.564	0.759	0.657	0.564	0.759	SUBCLONAL	1	FALSE	1	0.237502283930643	2		566	756	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221270	1221270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	98	516	0	ENST00000326873.7:c.793G>A	p.Glu265Lys	p.E265K	ENST00000326873	NM_000455.4	265	Gag/Aag	6/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.237502283930643	2		516	635	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194832	30194832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1434470951	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	57	393	0	ENST00000331968.5:c.313C>T	p.Arg105Cys	p.R105C	ENST00000331968	NM_002742.2	105	Cgc/Tgc	2/18	1	2	FACETS	0.907	0.779	1	0.907	0.779	1	CLONAL	1	FALSE	1	0.237502283930643	2		393	529	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324214	31324214	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs281864614	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	55	462	0	ENST00000412585.2:c.349C>G	p.His117Asp	p.H117D	ENST00000412585	NM_005514.6	117	Cac/Gac	3/8	0.193602167682183	3	FACETS	0.998	0.855	1	0.499	0.427	0.578	CLONAL	1	FALSE	1	0.237502283930643	3		462	519	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457279	67457279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	40	597	0	ENST00000327367.4:c.253C>T	p.His85Tyr	p.H85Y	ENST00000327367	NM_005902.3	85	Cat/Tat	2/9	1	2	FACETS	0.488	0.404	0.582	0.488	0.404	0.582	SUBCLONAL	1	FALSE	1	0.237502283930643	2		597	690	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223707	36223707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1468457510	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	60	582	0	ENST00000222270.7:c.6257C>T	p.Ser2086Leu	p.S2086L	ENST00000222270	NM_014727.1	2086	tCg/tTg	28/37	1	2	FACETS	0.82	0.706	0.944	0.82	0.706	0.944	CLONAL	1	FALSE	1	0.237502283930643	2		582	616	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794089	42794089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	57	366	0	ENST00000575354.2:c.1450C>T	p.Pro484Ser	p.P484S	ENST00000575354	NM_015125.3	484	Cca/Tca	9/20	0.205644532205872	3	FACETS	1	0.865	1			1	CLONAL	1	FALSE	NA	0.237502283930643	3		366	533	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139762	55139762	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	75	437	0	ENST00000257290.5:c.1423G>A	p.Glu475Lys	p.E475K	ENST00000257290	NM_006206.4	475	Gag/Aag	10/23	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.237502283930643	2		437	482	SUCCESS
ALK	238	MSKCC	GRCh37	2	29420510	29420510	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758127441	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	85	373	0	ENST00000389048.3:c.3971C>T	p.Ser1324Phe	p.S1324F	ENST00000389048	NM_004304.4	1324	tCt/tTt	27/29	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.237502283930643	2		373	528	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779271	3779271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370704436	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	53	427	0	ENST00000262367.5:c.5777G>A	p.Arg1926Gln	p.R1926Q	ENST00000262367	NM_004380.2	1926	cGg/cAg	31/31	1	2	FACETS	0.894	0.763	1	0.894	0.763	1	CLONAL	1	FALSE	1	0.237502283930643	2		427	499	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467670	66467670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	88	351	0	ENST00000273854.3:c.599G>A	p.Arg200Lys	p.R200K	ENST00000273854	NM_004439.5	200	aGa/aAa	3/18	1	2	FACETS	0.769	0.684	0.859	1	0.98	1	SUBCLONAL	2	FALSE	1	0.237502283930643	2		351	482	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519492	176519492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	111	496	0	ENST00000292408.4:c.898C>T	p.Pro300Ser	p.P300S	ENST00000292408	NM_213647.1	300	Ccc/Tcc	7/18	0.208146084290856	2	FACETS	0.956	0.864	1	0.956	0.864	1	CLONAL	2	FALSE	0	0.237502283930643	2		496	489	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149498309	149498309	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	103	364	0	ENST00000261799.4:c.2904+1G>A		p.X968_splice	ENST00000261799	NM_002609.3	968			0.208146084290856	2	FACETS	0.929	0.835	1	0.929	0.835	1	CLONAL	2	FALSE	0	0.237502283930643	2		364	467	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126567	2126567	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1378325757	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	54	399	0	ENST00000219476.3:c.2818C>T	p.Leu940Phe	p.L940F	ENST00000219476	NM_000548.3	940	Ctc/Ttc	25/42	1	2	FACETS	0.813	0.695	0.943	0.813	0.695	0.943	CLONAL	1	FALSE	1	0.237502283930643	2		399	559	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447781	49447781	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	55	455	0	ENST00000301067.7:c.653G>A	p.Ser218Asn	p.S218N	ENST00000301067	NM_003482.3	218	aGt/aAt	5/54	1	2	FACETS	0.848	0.726	0.982	0.848	0.726	0.982	CLONAL	1	FALSE	1	0.237502283930643	2		455	546	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412689	139412690	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	106	522	0	ENST00000277541.6:c.1154_1155delinsTT	p.Ser385Phe	p.S385F	ENST00000277541	NM_017617.3	385	tCC/tTT	7/34	1	2	FACETS	0.787	0.708	0.871	1	0.984	1	SUBCLONAL	2	FALSE	1	0.237502283930643	2		522	567	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234276	39234276	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	44	266	0	ENST00000402219.2:c.2569G>C	p.Glu857Gln	p.E857Q	ENST00000402219	NM_005633.3	857	Gag/Cag	16/23	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	FALSE	1	0.237502283930643	2		266	364	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494635	2494635	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	76	432	0	ENST00000355716.4:c.775C>G	p.Gln259Glu	p.Q259E	ENST00000355716	NM_003820.2	259	Cag/Gag	8/8	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	1	0.237502283930643	2		432	588	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254846	16254846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	55	453	0	ENST00000375759.3:c.2111G>A	p.Arg704Lys	p.R704K	ENST00000375759	NM_015001.2	704	aGa/aAa	11/15	1	2	FACETS	0.715	0.611	0.829	0.715	0.611	0.829	SUBCLONAL	1	FALSE	1	0.237502283930643	2		453	648	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699408	117699408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	74	417	0	ENST00000369458.3:c.233G>A	p.Gly78Asp	p.G78D	ENST00000369458	NM_024626.3	78	gGc/gAc	3/6	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	1	0.237502283930643	2		417	581	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61213435	61213435	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	127	407	0	ENST00000301761.2:c.393A>G	p.Ile131Met	p.I131M	ENST00000301761	NM_017841.2	131	atA/atG	4/4	0.193602167682183	3	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	FALSE	1	0.237502283930643	3		407	575	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124737	108124737	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1060501539	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	39	302	0	ENST00000278616.4:c.2095G>C	p.Glu699Gln	p.E699Q	ENST00000278616	NM_000051.3	699	Gaa/Caa	13/63	0.193602167682183	3	FACETS	0.824	0.683	0.981	0.412	0.341	0.491	CLONAL	1	FALSE	1	0.237502283930643	3		302	446	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435057	49435058	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	97	444	0	ENST00000301067.7:c.6495_6496delinsTT	p.Gln2166Ter	p.Q2166*	ENST00000301067	NM_003482.3	2165	ccCCag/ccTTag	31/54	1	2	FACETS	0.792	0.708	0.88	1	0.983	1	SUBCLONAL	2	FALSE	1	0.237502283930643	2		444	516	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885967	111885967	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779973889	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	45	512	0	ENST00000341259.2:c.1589C>T	p.Pro530Leu	p.P530L	ENST00000341259	NM_005475.2	530	cCt/cTt	8/8	1	2	FACETS	0.565	0.474	0.666	0.565	0.474	0.666	SUBCLONAL	1	FALSE	1	0.237502283930643	2		512	671	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784071	120784071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	116	577	0	ENST00000257552.2:c.914G>A	p.Gly305Glu	p.G305E	ENST00000257552	NM_002442.3	305	gGg/gAg	13/15	1	2	FACETS	0.903	0.817	0.993	1	0.988	1	CLONAL	2	FALSE	1	0.237502283930643	2		577	541	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907177	32907177	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	55	364	0	ENST00000380152.3:c.1562C>T	p.Ser521Leu	p.S521L	ENST00000380152		521	tCa/tTa	10/27	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	FALSE	1	0.237502283930643	2		364	437	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911964	32911964	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555283258	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	38	423	0	ENST00000380152.3:c.3472G>A	p.Glu1158Lys	p.E1158K	ENST00000380152		1158	Gaa/Aaa	11/27	1	2	FACETS	0.658	0.544	0.786	0.658	0.544	0.786	SUBCLONAL	1	FALSE	1	0.237502283930643	2		423	486	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134081	41134081	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	143	543	0	ENST00000379561.5:c.1547T>C	p.Met516Thr	p.M516T	ENST00000379561	NM_002015.3	516	aTg/aCg	2/3	0.237502283930643	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	FALSE	0	0.237502283930643	2		543	590	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037906	49037934	+	frameshift_variant	Frame_Shift_Del	DEL	AATATAGACCTTAAATTCAAAATCATTGT	AATATAGACCTTAAATTCAAAATCATTGT	-	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	47	232	0	ENST00000267163.4:c.2148_2176del	p.Ile717SerfsTer24	p.I717Sfs*24	ENST00000267163	NM_000321.2	716	AATATAGACCTTAAATTCAAAATCATTGTa/a	21/27	0.237502283930643	2	FACETS	1	0.96	1	0.728	0.618	0.846	CLONAL	1	FALSE	0	0.237502283930643	2		232	272	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38064126	38064126	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	70	699	0	ENST00000250448.2:c.52T>A	p.Tyr18Asn	p.Y18N	ENST00000250448	NM_004496.3	18	Tac/Aac	1/2	1	2	FACETS	0.813	0.708	0.927	0.813	0.708	0.927	CLONAL	1	FALSE	1	0.237502283930643	2		699	725	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640271	3640271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	34	443	0	ENST00000294008.3:c.3368C>T	p.Ser1123Phe	p.S1123F	ENST00000294008	NM_032444.2	1123	tCt/tTt	12/15	1	2	FACETS	0.486	0.396	0.588	0.486	0.396	0.588	SUBCLONAL	1	FALSE	1	0.237502283930643	2		443	589	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857971	9857971	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	44	500	0	ENST00000330684.3:c.3430A>T	p.Asn1144Tyr	p.N1144Y	ENST00000330684	NM_001134407.1	1144	Aac/Tac	13/13	1	2	FACETS	0.617	0.516	0.728	0.617	0.516	0.728	SUBCLONAL	1	FALSE	1	0.237502283930643	2		500	601	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875744	56875744	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	32	326	0	ENST00000308159.5:c.2348C>T	p.Ser783Phe	p.S783F	ENST00000308159	NM_014669.4	783	tCt/tTt	21/22	1	2	FACETS	0.519	0.421	0.631	0.519	0.421	0.631	SUBCLONAL	1	FALSE	1	0.237502283930643	2		326	519	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992117	72992117	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	137	493	0	ENST00000268489.5:c.1928C>T	p.Pro643Leu	p.P643L	ENST00000268489	NM_006885.3	643	cCc/cTc	2/10	1	2	FACETS	0.904	0.825	0.987	1	0.99	1	CLONAL	2	FALSE	1	0.237502283930643	2		493	638	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347671	89347671	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	110	562	0	ENST00000301030.4:c.5279T>G	p.Phe1760Cys	p.F1760C	ENST00000301030	NM_001256183.1	1760	tTt/tGt	9/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.237502283930643	2		562	665	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849420	89849420	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768419751	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	127	509	0	ENST00000389301.3:c.1561C>T	p.Leu521Phe	p.L521F	ENST00000389301	NM_000135.2	521	Ctc/Ttc	16/43	1	2	FACETS	0.846	0.768	0.927	1	0.988	1	CLONAL	2	FALSE	1	0.237502283930643	2		509	632	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322620	30322620	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	53	322	0	ENST00000322652.5:c.1633G>C	p.Glu545Gln	p.E545Q	ENST00000322652	NM_015355.2	545	Gaa/Caa	14/16	0.237502283930643	2	FACETS	1	0.876	1	0.514	0.439	0.596	CLONAL	1	FALSE	0	0.237502283930643	2		322	434	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40368093	40368093	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	150	382	0	ENST00000293328.3:c.1412A>T	p.His471Leu	p.H471L	ENST00000293328	NM_012448.3	471	cAt/cTt	12/19	0.237502283930643	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	FALSE	0	0.237502283930643	2		382	553	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39537545	39537545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	50	356	0	ENST00000262039.4:c.79G>A	p.Glu27Lys	p.E27K	ENST00000262039	NM_002647.2	27	Gaa/Aaa	2/25	0.208146084290856	2	FACETS	1	0.922	1	0.567	0.483	0.66	CLONAL	1	FALSE	0	0.237502283930643	2		356	371	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968202	18968202	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	79	376	0	ENST00000262803.5:c.2042C>G	p.Ser681Ter	p.S681*	ENST00000262803	NM_002911.3	681	tCa/tGa	15/24	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.237502283930643	2		376	445	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256676	19256676	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	45	493	0	ENST00000162023.5:c.1037C>T	p.Ser346Phe	p.S346F	ENST00000162023		346	tCc/tTc	13/13	1	2	FACETS	0.711	0.597	0.837	0.711	0.597	0.837	SUBCLONAL	1	FALSE	1	0.237502283930643	2		493	533	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795083	42795084	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	56	499	0	ENST00000575354.2:c.2163_2164delinsTT	p.Pro722Ser	p.P722S	ENST00000575354	NM_015125.3	721	tcCCcg/tcTTcg	10/20	0.205644532205872	3	FACETS	0.859	0.736	0.994			1	CLONAL	1	FALSE	NA	0.237502283930643	3		499	614	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921185	50921185	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	37	389	0	ENST00000440232.2:c.3305C>T	p.Pro1102Leu	p.P1102L	ENST00000440232	NM_002691.3	1102	cCt/cTt	27/27	0.193602167682183	3	FACETS	0.737	0.607	0.882	0.368	0.303	0.441	SUBCLONAL	1	FALSE	1	0.237502283930643	3		389	473	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607403	46607403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	91	503	0	ENST00000263734.3:c.1592C>T	p.Pro531Leu	p.P531L	ENST00000263734	NM_001430.4	531	cCc/cTc	12/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.237502283930643	2		503	540	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573358	41573358	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	89	557	0	ENST00000263253.7:c.5643T>A	p.Asn1881Lys	p.N1881K	ENST00000263253	NM_001429.3	1881	aaT/aaA	31/31	0.166460954042309	3	FACETS	1	0.973	1	0.67	0.594	0.75	CLONAL	1	FALSE	1	0.237502283930643	3		557	626	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573663	41573663	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1419768039	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	76	530	0	ENST00000263253.7:c.5948G>A	p.Gly1983Glu	p.G1983E	ENST00000263253	NM_001429.3	1983	gGg/gAg	31/31	0.166460954042309	3	FACETS	1	0.965	1	0.643	0.564	0.727	CLONAL	1	FALSE	1	0.237502283930643	3		530	557	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202849	128202849	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	136	491	0	ENST00000341105.2:c.872-1G>A		p.X291_splice	ENST00000341105	NM_032638.4	291			0.193602167682183	3	FACETS	1	0.913	1	1	0.913	1	CLONAL	2	FALSE	1	0.237502283930643	3		491	640	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268344	142268344	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	35	240	0	ENST00000350721.4:c.3148G>C	p.Glu1050Gln	p.E1050Q	ENST00000350721	NM_001184.3	1050	Gaa/Caa	15/47	0.193602167682183	3	FACETS	1	0.882	1	0.548	0.45	0.656	CLONAL	1	FALSE	1	0.237502283930643	3		240	301	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447703	187447703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	68	544	0	ENST00000232014.4:c.490G>A	p.Glu164Lys	p.E164K	ENST00000232014	NM_001130845.1	164	Gag/Aag	5/10	0.193602167682183	3	FACETS	0.974	0.847	1	0.487	0.423	0.556	CLONAL	1	FALSE	1	0.237502283930643	3		544	658	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197321	106197321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	39	401	0	ENST00000380013.4:c.5654C>T	p.Pro1885Leu	p.P1885L	ENST00000380013	NM_001127208.2	1885	cCt/cTt	11/11	1	2	FACETS	0.702	0.581	0.836	0.702	0.581	0.836	SUBCLONAL	1	FALSE	1	0.237502283930643	2		401	468	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549842	187549842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	77	373	0	ENST00000441802.2:c.4399G>A	p.Glu1467Lys	p.E1467K	ENST00000441802	NM_005245.3	1467	Gaa/Aaa	8/27	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.237502283930643	2		373	459	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629283	187629283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	93	471	0	ENST00000441802.2:c.1699C>T	p.Pro567Ser	p.P567S	ENST00000441802	NM_005245.3	567	Cct/Tct	2/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.237502283930643	2		471	547	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35857125	35857125	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	66	336	0	ENST00000303115.3:c.46C>T	p.Gln16Ter	p.Q16*	ENST00000303115	NM_002185.3	16	Caa/Taa	1/8	0.237502283930643	6	FACETS	1	0.92	1	0.271	0.235	0.311	CLONAL	1	FALSE	2	0.237502283930643	6		336	755	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036966	180036966	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	95	500	0	ENST00000261937.6:c.3746C>T	p.Ser1249Phe	p.S1249F	ENST00000261937	NM_182925.4	1249	tCc/tTc	28/30	0.208146084290856	2	FACETS	1	0.98	1	0.745	0.665	0.829	CLONAL	1	FALSE	0	0.237502283930643	2		500	537	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680433	30680433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	136	465	0	ENST00000376406.3:c.1286G>A	p.Arg429Lys	p.R429K	ENST00000376406	NM_014641.2	429	aGa/aAa	5/15	0.193602167682183	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	FALSE	1	0.237502283930643	3		465	601	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181543	32181544	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	64	394	0	ENST00000375023.3:c.2241_2242delinsTT	p.Pro748Ser	p.P748S	ENST00000375023	NM_004557.3	747	agCCct/agTTct	14/30	0.193602167682183	3	FACETS	1	0.912	1	0.535	0.463	0.612	CLONAL	1	FALSE	1	0.237502283930643	3		394	564	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005420	150005421	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	79	486	0	ENST00000253339.5:c.804_805delinsAA	p.Trp268_Glu269delinsTer	p.W268_E269delins*	ENST00000253339		268	tgGGaa/tgAAaa	3/7	0.237502283930643	2	FACETS	1	0.92	1	0.53	0.466	0.598	CLONAL	1	FALSE	0	0.237502283930643	2		486	628	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873468	151873468	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	70	530	0	ENST00000262189.6:c.9070A>T	p.Ser3024Cys	p.S3024C	ENST00000262189	NM_170606.2	3024	Agc/Tgc	38/59	1	2	FACETS	0.946	0.825	1	0.946	0.825	1	CLONAL	1	FALSE	1	0.237502283930643	2		530	623	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27192573	27192573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746958138	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	131	359	0	ENST00000380036.4:c.1576G>A	p.Gly526Arg	p.G526R	ENST00000380036	NM_000459.3	526	Ggg/Agg	11/23	0.193602167682183	3	FACETS	0.973	0.886	1	0.973	0.886	1	CLONAL	2	FALSE	1	0.237502283930643	3		359	634	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221996	98221996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	43	407	0	ENST00000331920.6:c.2773G>A	p.Ala925Thr	p.A925T	ENST00000331920	NM_000264.3	925	Gct/Act	17/24	1	2	FACETS	0.676	0.565	0.798	0.676	0.565	0.798	SUBCLONAL	1	FALSE	1	0.237502283930643	2		407	536	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760808	133760808	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	43	467	0	ENST00000318560.5:c.3131C>T	p.Ser1044Phe	p.S1044F	ENST00000318560	NM_005157.4	1044	tCt/tTt	11/11	1	2	FACETS	0.827	0.692	0.975	0.827	0.692	0.975	CLONAL	1	FALSE	1	0.237502283930643	2		467	438	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763876	76763877	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	88	188	0	ENST00000373344.5:c.7431_7432delinsTT	p.Pro2478Ser	p.P2478S	ENST00000373344	NM_000489.3	2477	ccCCca/ccTTca	35/35	0.237502283930643	2	FACETS	0.902	0.81	0.997			1	CLONAL	3	FALSE	NA	0.237502283930643	2		188	274	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176493	123176493	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	37	125	0	ENST00000218089.9:c.460G>T	p.Glu154Ter	p.E154*	ENST00000218089	NM_001042749.1	154	Gag/Tag	7/35	0.237502283930643	2	FACETS	1	0.933	1			1	CLONAL	1	FALSE	NA	0.237502283930643	2		125	245	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005420	150005420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	74	486	0	ENST00000253339.5:c.805G>A	p.Glu269Lys	p.E269K	ENST00000253339		269	Gaa/Aaa	3/7	0.237502283930643	2	FACETS	0.999	0.875	1	0.499	0.437	0.566	CLONAL	1	FALSE	0	0.237502283930643	2		486	624	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230468604	230468604	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	124	457	3	ENST00000391860.1:c.914C>A	p.Ser305Tyr	p.S305Y	ENST00000391860	NM_001258311.1	305	tCc/tAc	5/7	0.237502283930643	3	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	FALSE	1	0.237502283930643	3		460	562	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534285	534285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894226	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	124	455	0	ENST00000451590.1:c.38G>A	p.Gly13Asp	p.G13D	ENST00000451590	NM_001130442.1	13	gGt/gAt	2/5	0.237502283930643	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	FALSE	0	0.237502283930643	2		455	487	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514403	103514403	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs760722074	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	44	316	0	ENST00000355739.4:c.904G>C	p.Glu302Gln	p.E302Q	ENST00000355739	NM_000123.3	302	Gaa/Caa	8/15	0.237502283930643	2	FACETS	0.884	0.743	1	0.442	0.371	0.521	CLONAL	1	FALSE	0	0.237502283930643	2		316	419	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437904	110437904	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1435175514	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	20	225	0	ENST00000375856.3:c.497C>G	p.Ser166Cys	p.S166C	ENST00000375856	NM_003749.2	166	tCc/tGc	1/2	0.237502283930643	2	FACETS	0.846	0.65	1	0.423	0.325	0.537	CLONAL	1	FALSE	0	0.237502283930643	2		225	199	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50763955	50763955	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	75	322	0	ENST00000307179.4:c.812G>C	p.Gly271Ala	p.G271A	ENST00000307179		271	gGa/gCa	8/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.237502283930643	2		322	447	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587492	29587492	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	65	330	0	ENST00000356175.3:c.4473G>A	p.Trp1491Ter	p.W1491*	ENST00000356175	NM_000267.3	1491	tgG/tgA	33/57	0.237502283930643	2	FACETS	1	0.94	1	0.574	0.498	0.655	CLONAL	1	FALSE	0	0.237502283930643	2		330	477	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679291	29679291	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555536340	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	54	378	0	ENST00000356175.3:c.7411C>T	p.Gln2471Ter	p.Q2471*	ENST00000356175	NM_000267.3	2471	Cag/Tag	50/57	0.237502283930643	2	FACETS	1	0.911	1	0.544	0.466	0.629	CLONAL	1	FALSE	0	0.237502283930643	2		378	418	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144808	11144808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1206010353	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	62	461	0	ENST00000358026.2:c.3883G>A	p.Glu1295Lys	p.E1295K	ENST00000358026	NM_001128849.1	1295	Gag/Aag	28/36	1	2	FACETS	0.944	0.816	1	0.944	0.816	1	CLONAL	1	FALSE	1	0.237502283930643	2		461	553	SUCCESS
ALB	213	MSKCC	GRCh37	4	74283887	74283887	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	31	370	0	ENST00000295897.4:c.1511C>T	p.Ser504Phe	p.S504F	ENST00000295897	NM_000477.5	504	tCc/tTc	12/15	1	2	FACETS	0.537	0.434	0.655	0.537	0.434	0.655	SUBCLONAL	1	FALSE	1	0.237502283930643	2		370	486	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251488	251488	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	10	35	0	ENST00000264932.6:c.1699G>C	p.Glu567Gln	p.E567Q	ENST00000264932	NM_004168.2	567	Gag/Cag	13/15	0.237502283930643	6	FACETS	0.851	0.585	1	0.425	0.292	0.587	CLONAL	2	FALSE	2	0.237502283930643	6		35	73	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295510	1295510	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0057533-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	43	599	0				ENST00000310581	NM_198253.2	-/1132			0.237502283930643	6	FACETS	0.635	0.53	0.753	0.159	0.132	0.189	SUBCLONAL	1	FALSE	2	0.237502283930643	6		599	841	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0057675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	147	375	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.533994990890891	2		375	543	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107135	27107135	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0057675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	176	545	0	ENST00000324856.7:c.6746C>G	p.Ser2249Ter	p.S2249*	ENST00000324856	NM_006015.4	2249	tCa/tGa	20/20	1	2	FACETS	0.842	0.777	0.909	0.842	0.777	0.909	CLONAL	1	TRUE	1	0.533994990890891	2		545	783	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984428	201984428	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	202	477	0	ENST00000359651.3:c.1093G>C	p.Glu365Gln	p.E365Q	ENST00000359651		365	Gag/Cag	8/8	0.533994990890891	4	FACETS	1	0.964	1	0.355	0.328	0.382	CLONAL	1	TRUE	1	0.533994990890891	4		477	1090	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26927934	26927934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	76	319	0	ENST00000381527.3:c.373C>T	p.Arg125Trp	p.R125W	ENST00000381527	NM_001260.1	125	Cgg/Tgg	4/13	1	2	FACETS	0.915	0.81	1	0.915	0.81	1	CLONAL	1	TRUE	1	0.533994990890891	2		319	311	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771873	135771873	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	176	507	0	ENST00000298552.3:c.3244C>A	p.Pro1082Thr	p.P1082T	ENST00000298552	NM_001162426.1	1082	Ccc/Acc	23/23	1	2	FACETS	0.96	0.887	1	0.96	0.887	1	CLONAL	1	TRUE	1	0.533994990890891	2		507	687	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740362	46740362	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	174	427	0	ENST00000371975.4:c.1842G>C	p.Lys614Asn	p.K614N	ENST00000371975	NM_003579.3	614	aaG/aaC	16/18	1	2	FACETS	0.976	0.901	1	0.976	0.901	1	CLONAL	1	TRUE	1	0.533994990890891	2		427	668	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150549859	150549859	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	168	386	0	ENST00000369026.2:c.1045A>G	p.Ile349Val	p.I349V	ENST00000369026	NM_021960.4	349	Ata/Gta	3/3	0.533994990890891	4	FACETS	0.977	0.897	1	0.326	0.299	0.354	CLONAL	1	TRUE	1	0.533994990890891	4		386	988	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230561668	230561668	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0057675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	80	162	0				ENST00000391860	NM_001258311.1	-/409			0.533994990890891	4	FACETS	1	0.97	1	0.43	0.381	0.482	CLONAL	1	TRUE	1	0.533994990890891	4		162	356	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100624	8100624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764299422	NA	P-0057675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	196	589	0	ENST00000346208.3:c.598C>T	p.His200Tyr	p.H200Y	ENST00000346208		200	Cac/Tac	3/6	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.533994990890891	2		589	670	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115382	115115383	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	novel	NA	P-0057675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	132	305	0	ENST00000257566.3:c.941+2dup		p.X314_splice	ENST00000257566	NM_016569.3	314			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.533994990890891	2		305	447	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562165	21562165	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	135	533	0	ENST00000382592.4:c.1754G>C	p.Arg585Thr	p.R585T	ENST00000382592	NM_014572.2	585	aGa/aCa	4/8	1	2	FACETS	0.688	0.626	0.753	0.688	0.626	0.753	SUBCLONAL	1	TRUE	1	0.533994990890891	2		533	735	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862080	68862080	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	169	407	0	ENST00000261769.5:c.2168del	p.Leu723ArgfsTer47	p.L723Rfs*47	ENST00000261769	NM_004360.3	723	cTg/cg	14/16	0.533994990890891	1	FACETS	0.981	0.91	1	0.981	0.91	1	CLONAL	1	TRUE	0	0.533994990890891	1		407	473	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422248	47422248	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	140	454	0	ENST00000404338.3:c.316C>T	p.Gln106Ter	p.Q106*	ENST00000404338	NM_004491.4	106	Caa/Taa	1/6	1	2	FACETS	0.973	0.891	1	0.973	0.891	1	CLONAL	1	TRUE	1	0.533994990890891	2		454	539	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162506	47162506	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	130	411	0	ENST00000409792.3:c.3620C>G	p.Ser1207Cys	p.S1207C	ENST00000409792	NM_014159.6	1207	tCt/tGt	3/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.533994990890891	2		411	467	SUCCESS
ALB	213	MSKCC	GRCh37	4	74283298	74283298	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	106	342	0	ENST00000295897.4:c.1340T>A	p.Leu447His	p.L447H	ENST00000295897	NM_000477.5	447	cTt/cAt	11/15	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.533994990890891	2		342	324	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265533	152265533	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	153	407	0	ENST00000206249.3:c.986C>G	p.Ser329Cys	p.S329C	ENST00000206249	NM_000125.3	329	tCc/tGc	4/8	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.533994990890891	2		407	527	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874116	151874116	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	116	470	0	ENST00000262189.6:c.8422G>C	p.Asp2808His	p.D2808H	ENST00000262189	NM_170606.2	2808	Gat/Cat	38/59	1	2	FACETS	0.972	0.882	1	0.972	0.882	1	CLONAL	1	TRUE	1	0.533994990890891	2		470	447	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285954	38285954	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0057675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	120	412	0	ENST00000425967.3:c.458-1G>A		p.X153_splice	ENST00000425967	NM_001174067.1	153			0.533994990890891	6	FACETS	0.771	0.695	0.853			1	SUBCLONAL	1	TRUE	NA	0.533994990890891	6		412	1205	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410844	63410844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	134	437	0	ENST00000330258.3:c.2323G>A	p.Glu775Lys	p.E775K	ENST00000330258	NM_152424.3	775	Gag/Aag	2/2	0.327338642491096	1	FACETS	0.736	0.672	0.801	0.736	0.672	0.801	SUBCLONAL	1	TRUE	0	0.533994990890891	1		437	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0057796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	186	773	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.618916442163904	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.618916442163904	1		773	386	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175857	24175859	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs875989800	NA	P-0057796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	109	673	0	ENST00000263121.7:c.1091_1093del	p.Lys364del	p.K364del	ENST00000263121	NM_003073.3	362	gAGAag/gag	8/9	0.219233193951301	1	FACETS	0.595	0.538	0.654	0.595	0.538	0.654	INDETERMINATE	1	TRUE	0	0.618916442163904	1		673	409	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121877	2121877	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756536921	NA	P-0057796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	208	1250	0	ENST00000219476.3:c.2039G>A	p.Arg680Gln	p.R680Q	ENST00000219476	NM_000548.3	680	cGg/cAg	19/42	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.618916442163904	2		1250	548	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243704	41243704	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs397509113	NA	P-0057796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	90	528	0	ENST00000357654.3:c.3844del	p.Glu1282AsnfsTer25	p.E1282Nfs*25	ENST00000357654	NM_007294.3	1282	Gaa/aa	10/23	0.618916442163904	1	FACETS	0.952	0.863	1	0.952	0.863	1	CLONAL	1	TRUE	0	0.618916442163904	1		528	211	SUCCESS
ATR	545	MSKCC	GRCh37	3	142203992	142203994	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0057796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	47	332	0	ENST00000350721.4:c.6209_6211del	p.Leu2070del	p.L2070del	ENST00000350721	NM_001184.3	2070	cTTCat/cat	36/47	1	2	FACETS	0.804	0.688	0.927	0.804	0.688	0.927	CLONAL	1	TRUE	1	0.618916442163904	2		332	189	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0057859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	45	259	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.96	0.826	1	0.96	0.826	1	CLONAL	1	TRUE	1	0.6890859600393	2		259	136	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0057859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	38	165	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.6890859600393	2		165	106	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057705	27057705	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	62	588	0	ENST00000324856.7:c.1413C>A	p.Tyr471Ter	p.Y471*	ENST00000324856	NM_006015.4	471	taC/taA	3/20	1	2	FACETS	0.266	0.229	0.306	0.266	0.229	0.306	SUBCLONAL	1	TRUE	1	0.6890859600393	2		588	676	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021828	71021828	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0057859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	86	316	0	ENST00000318789.4:c.1531-1G>A		p.X511_splice	ENST00000318789	NM_032682.5	511			0.6890859600393	1	FACETS	0.798	0.721	0.876	0.798	0.721	0.876	SUBCLONAL	1	TRUE	0	0.6890859600393	1		316	205	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344082	118344086	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAA	GAAAA	-	novel	NA	P-0057859-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	145	475	0	ENST00000534358.1:c.2214_2218del	p.Arg738SerfsTer3	p.R738Sfs*3	ENST00000534358	NM_005933.3	736	agGAAAAga/agga	3/36	0.6890859600393	1	FACETS	0.887	0.823	0.951	0.887	0.823	0.951	CLONAL	1	TRUE	0	0.6890859600393	1		475	311	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578418	7578418	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057860-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	248	550	0	ENST00000269305.4:c.512A>G	p.Glu171Gly	p.E171G	ENST00000269305	NM_001126112.2	171	gAg/gGg	5/11	0.590957753845442	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.578649249889333	1		550	439	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0057860-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	35	425	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.590957753845442	3	FACETS	0.502	0.412	0.601	0.251	0.206	0.301	SUBCLONAL	1	TRUE	1	0.578649249889333	3		425	311	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7119467	7119467	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057860-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	81	443	0	ENST00000302850.5:c.3787G>C	p.Glu1263Gln	p.E1263Q	ENST00000302850	NM_000208.2	1263	Gag/Cag	21/22	0.237301528377801	2	FACETS	0.707	0.626	0.792	0.353	0.313	0.396	INDETERMINATE	1	TRUE	0	0.578649249889333	2		443	396	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242481	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAGCAA	TTAAGAGAAGCAA	C	rs397509368	NA	P-0057860-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	221	373	0	ENST00000275493.2:c.2239_2251delinsC	p.Leu747_Thr751delinsPro	p.L747_T751delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGCAAca/Cca	19/28	0.590957753845442	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.578649249889333	3		373	430	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518088	176518088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057860-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	198	480	0	ENST00000292408.4:c.586C>T	p.Arg196Cys	p.R196C	ENST00000292408	NM_213647.1	196	Cgc/Tgc	5/18	0.393680097076753	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.578649249889333	1		480	403	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752739	42752739	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057860-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	37	526	0	ENST00000222329.4:c.1525G>A	p.Glu509Lys	p.E509K	ENST00000222329	NM_006494.2	509	Gag/Aag	4/4	1	2	FACETS	0.238	0.196	0.286	0.238	0.196	0.286	SUBCLONAL	1	TRUE	1	0.578649249889333	2		526	537	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752793	42752793	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057860-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	52	554	0	ENST00000222329.4:c.1471G>C	p.Asp491His	p.D491H	ENST00000222329	NM_006494.2	491	Gac/Cac	4/4	1	2	FACETS	0.288	0.245	0.336	0.288	0.245	0.336	SUBCLONAL	1	TRUE	1	0.578649249889333	2		554	623	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754622	42754622	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057860-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	47	491	0	ENST00000222329.4:c.118G>C	p.Glu40Gln	p.E40Q	ENST00000222329	NM_006494.2	40	Gag/Cag	2/4	1	2	FACETS	0.269	0.227	0.317	0.269	0.227	0.317	SUBCLONAL	1	TRUE	1	0.578649249889333	2		491	603	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155408	185155408	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057860-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	127	491	0	ENST00000265026.3:c.649A>T	p.Ile217Phe	p.I217F	ENST00000265026	NM_004721.4	217	Atc/Ttc	3/14	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.578649249889333	2		491	329	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11168301	11168301	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057864-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	155	504	0	ENST00000361445.4:c.7571A>T	p.Gln2524Leu	p.Q2524L	ENST00000361445	NM_004958.3	2524	cAa/cTa	57/58	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.565108377151236	2		504	541	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263995	16263995	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057864-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	143	862	0	ENST00000375759.3:c.10364A>G	p.Gln3455Arg	p.Q3455R	ENST00000375759	NM_015001.2	3455	cAg/cGg	12/15	1	2	FACETS	0.708	0.646	0.772	0.708	0.646	0.772	SUBCLONAL	1	TRUE	1	0.565108377151236	2		862	715	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0058013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	85	190	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.196815165814435	3	FACETS	1	0.978	1	0.747	0.661	0.838	CLONAL	1	TRUE	1	0.21	3		190	599	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0058013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	39	319	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	1	0.831	1	1	0.831	1	CLONAL	1	TRUE	1	0.21	2		319	371	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468436	89468436	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	21	267	0	ENST00000336596.2:c.1970T>C	p.Val657Ala	p.V657A	ENST00000336596	NM_005233.5	657	gTt/gCt	11/17	1	2	FACETS	0.499	0.383	0.634	0.499	0.383	0.634	SUBCLONAL	1	TRUE	1	0.21	2		267	401	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285796	198285796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	49	407	0	ENST00000335508.6:c.257C>T	p.Ala86Val	p.A86V	ENST00000335508	NM_012433.2	86	gCc/gTc	3/25	1	2	FACETS	0.734	0.621	0.859	0.734	0.621	0.859	SUBCLONAL	1	TRUE	1	0.21	2		407	636	SUCCESS
APC	324	MSKCC	GRCh37	5	112175582	112175583	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0058013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	48	368	0	ENST00000257430.4:c.4292_4293dup	p.Pro1432CysfsTer42	p.P1432Cfs*42	ENST00000257430	NM_000038.5	1431	atg/aTGtg	16/16	1	2	FACETS	0.977	0.827	1	0.977	0.827	1	CLONAL	1	TRUE	1	0.21	2		368	468	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0058026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	64	696	3	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.382773757589007	2		699	329	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555525585	NA	P-0058026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	156	460	0	ENST00000269305.4:c.673-2A>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.330363845215092	1	FACETS	0.777	0.719	0.837	1	0.99	1	SUBCLONAL	2	TRUE	0	0.382773757589007	1		460	424	SUCCESS
APC	324	MSKCC	GRCh37	5	112137082	112137082	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0058026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	38	189	0	ENST00000257430.4:c.834+2T>G		p.X278_splice	ENST00000257430	NM_000038.5	278			1	2	FACETS	0.841	0.701	0.996	0.841	0.701	0.996	CLONAL	1	TRUE	1	0.382773757589007	2		189	236	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97873865	97873865	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	292	650	0	ENST00000289081.3:c.1209G>A	p.Trp403Ter	p.W403*	ENST00000289081	NM_000136.2	403	tgG/tgA	13/15	0.263820324387261	2	FACETS	0.986	0.932	1	0.986	0.932	1	CLONAL	2	TRUE	0	0.382773757589007	2		650	774	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0058030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	102	327	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.399649949127714	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	0	0.47435204578165	2		327	211	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115600	108115600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772821016	NA	P-0058030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	69	378	0	ENST00000278616.4:c.748C>T	p.Arg250Ter	p.R250*	ENST00000278616	NM_000051.3	250	Cga/Tga	7/63	1	2	FACETS	0.903	0.793	1	0.903	0.793	1	CLONAL	1	TRUE	1	0.47435204578165	2		378	322	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907719	76907719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	101	476	2	ENST00000373344.5:c.4442G>A	p.Arg1481Gln	p.R1481Q	ENST00000373344	NM_000489.3	1481	cGg/cAg	15/35	1	2	FACETS	0.724	0.649	0.804	0.724	0.649	0.804	SUBCLONAL	1	TRUE	1	0.47435204578165	2		478	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0058030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	372	820	0	ENST00000269305.4:c.376-1G>T		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.47435204578165	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.47435204578165	1		820	873	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0058065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	346	412	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.463074195050509	2	FACETS	0.995	0.949	1	0.995	0.949	1	CLONAL	2	TRUE	0	0.487119843015378	2		412	714	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	400	548	0	ENST00000304494.5:c.322G>C	p.Asp108His	p.D108H	ENST00000304494	NM_000077.4	108	Gat/Cat	2/3	0.463074195050509	2	FACETS	0.9	0.86	0.941	0.9	0.86	0.941	CLONAL	2	TRUE	0	0.487119843015378	2		548	912	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482281	87482281	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	98	470	0	ENST00000277120.3:c.1568A>C	p.Lys523Thr	p.K523T	ENST00000277120		523	aAg/aCg	14/19	0.394385764891477	3	FACETS	0.708	0.632	0.789	0.354	0.316	0.395	SUBCLONAL	1	TRUE	1	0.487119843015378	3		470	707	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467383	66467383	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	193	423	0	ENST00000273854.3:c.886G>A	p.Glu296Lys	p.E296K	ENST00000273854	NM_004439.5	296	Gaa/Aaa	3/18	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.487119843015378	2		423	732	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288850	11288850	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	176	472	0	ENST00000361445.4:c.2905A>T	p.Thr969Ser	p.T969S	ENST00000361445	NM_004958.3	969	Acc/Tcc	19/58	0.464884179502667	3	FACETS	0.926	0.853	1	0.463	0.426	0.502	CLONAL	1	TRUE	1	0.487119843015378	3		472	970	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500425	99500425	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	397	568	0	ENST00000268035.6:c.3858G>T	p.Lys1286Asn	p.K1286N	ENST00000268035	NM_000875.3	1286	aaG/aaT	21/21	0.463074195050509	2	FACETS	0.978	0.936	1	0.978	0.936	1	CLONAL	2	TRUE	0	0.487119843015378	2		568	833	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639608	3639608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	237	655	0	ENST00000294008.3:c.4031C>T	p.Ser1344Phe	p.S1344F	ENST00000294008	NM_032444.2	1344	tCc/tTc	12/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.487119843015378	2		655	923	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576001	29576001	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1060500370	NA	P-0058065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	202	299	0	ENST00000356175.3:c.3975-1G>T		p.X1325_splice	ENST00000356175	NM_000267.3	1325			0.463074195050509	2	FACETS	0.964	0.906	1	0.964	0.906	1	CLONAL	2	TRUE	0	0.487119843015378	2		299	430	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274903	142274903	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	54	388	0	ENST00000350721.4:c.2157C>A	p.His719Gln	p.H719Q	ENST00000350721	NM_001184.3	719	caC/caA	10/47	0.487119843015378	3	FACETS	0.709	0.607	0.819	0.354	0.303	0.41	SUBCLONAL	1	TRUE	1	0.487119843015378	3		388	389	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	917217	917217	+	stop_lost	Nonstop_Mutation	SNP	G	G	T	novel	NA	P-0058065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	292	431	0	ENST00000166345.3:c.1298G>T	p.Ter433LeuextTer38	p.*433Lext*38	ENST00000166345	NM_004237.3	433	tGa/tTa	13/13	0.287321167794433	5	FACETS	1	0.953	1	0.675	0.636	0.716	INDETERMINATE	2	TRUE	2	0.487119843015378	5		431	1024	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282556	1282556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	124	472	0	ENST00000310581.5:c.1757G>A	p.Ser586Asn	p.S586N	ENST00000310581	NM_198253.2	586	aGc/aAc	3/16	0.287321167794433	5	FACETS	0.849	0.767	0.936	0.283	0.255	0.312	INDETERMINATE	1	TRUE	2	0.487119843015378	5		472	1038	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495430	149495430	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	402	612	0	ENST00000261799.4:c.3217del	p.Glu1073SerfsTer59	p.E1073Sfs*59	ENST00000261799	NM_002609.3	1073	Gag/ag	23/23	0.463074195050509	2	FACETS	0.925	0.885	0.966	0.925	0.885	0.966	CLONAL	2	TRUE	0	0.487119843015378	2		612	892	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519568	137519568	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1257969756	NA	P-0058065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	327	415	0	ENST00000367739.4:c.1070C>G	p.Thr357Ser	p.T357S	ENST00000367739	NM_000416.2	357	aCt/aGt	7/7	0.464884179502667	3	FACETS	0.983	0.933	1	0.983	0.933	1	CLONAL	2	TRUE	1	0.487119843015378	3		415	849	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240702	55240702	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1198	69	538	0	ENST00000275493.2:c.1946G>T	p.Gly649Val	p.G649V	ENST00000275493	NM_005228.3	649	gGg/gTg	17/28	0.366019778677101	4	FACETS	0.333	0.288	0.381	0.166	0.144	0.191	SUBCLONAL	1	TRUE	2	0.487119843015378	4		538	1267	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124499156	124499156	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058065-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	43	307	0	ENST00000357628.3:c.557G>T	p.Gly186Val	p.G186V	ENST00000357628	NM_015450.2	186	gGc/gTc	9/19	1	2	FACETS	0.761	0.642	0.89	0.761	0.642	0.89	SUBCLONAL	1	TRUE	1	0.487119843015378	2		307	232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0058107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	470	427	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.560240383655801	2	FACETS	0.994	0.957	1	0.994	0.957	1	CLONAL	2	TRUE	0	0.560240383655801	2		427	844	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0058107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	171	224	3	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	0.558875911333937	2	FACETS	0.981	0.921	1	0.981	0.921	1	CLONAL	2	TRUE	0	0.560240383655801	2		227	311	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185796	32185796	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs8192591	NA	P-0058107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	508	703	0	ENST00000375023.3:c.1600G>A	p.Gly534Ser	p.G534S	ENST00000375023	NM_004557.3	534	Ggc/Agc	9/30	0.560240383655801	3	FACETS	0.988	0.949	1	0.988	0.949	1	CLONAL	2	TRUE	1	0.560240383655801	3		703	1175	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245521	153245521	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	382	352	0	ENST00000281708.4:c.1670G>T	p.Gly557Val	p.G557V	ENST00000281708	NM_033632.3	557	gGa/gTa	11/12	0.560240383655801	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	0	0.560240383655801	3		352	569	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118886	70118889	+	frameshift_variant	Frame_Shift_Del	DEL	CCTT	CCTT	-	novel	NA	P-0058107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	527	736	1	ENST00000245479.2:c.459_462del	p.Phe154TrpfsTer28	p.F154Wfs*28	ENST00000245479	NM_000346.3	153	cCCTTc/cc	2/3	0.178097171973642	6	FACETS	0.891	0.854	0.929	0.891	0.854	0.929	INDETERMINATE	3	TRUE	3	0.560240383655801	6		737	1492	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280815	41280815	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	274	390	0	ENST00000349496.5:c.2328G>A	p.Trp776Ter	p.W776*	ENST00000349496	NM_001904.3	776	tgG/tgA	15/15	0.560240383655801	3	FACETS	0.969	0.917	1	0.969	0.917	1	CLONAL	2	TRUE	1	0.560240383655801	3		390	646	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412386	63412387	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1569192251	NA	P-0058107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	868	431	0	ENST00000330258.3:c.780dup	p.Pro261ThrfsTer17	p.P261Tfs*17	ENST00000330258	NM_152424.3	260	-/A	2/2	0.560240383655801	3	FACETS	1	0.994	1			1	CLONAL	3	TRUE	NA	0.560240383655801	3		431	1259	SUCCESS
APC	324	MSKCC	GRCh37	5	112173583	112173594	+	frameshift_variant	Frame_Shift_Del	DEL	AGATGCTCAGCA	AGATGCTCAGCA	C	novel	NA	P-0058107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	159	283	0	ENST00000257430.4:c.2292_2303delinsC	p.Leu764PhefsTer7	p.L764Ffs*7	ENST00000257430	NM_000038.5	764	ttAGATGCTCAGCAc/ttCc	16/16	0.558875911333937	2	FACETS	0.992	0.93	1	0.992	0.93	1	CLONAL	2	TRUE	0	0.560240383655801	2		283	286	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047299	180047299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058228-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	141	502	0	ENST00000261937.6:c.2416G>A	p.Ala806Thr	p.A806T	ENST00000261937	NM_182925.4	806	Gca/Aca	17/30	1	2	FACETS	0.884	0.807	0.965	0.884	0.807	0.965	CLONAL	1	TRUE	1	0.449705037374589	2		502	709	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578261	7578262	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	A	novel	NA	P-0058228-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	139	546	0	ENST00000269305.4:c.587_588delinsT	p.Arg196LeufsTer51	p.R196Lfs*51	ENST00000269305	NM_001126112.2	196	cGA/cT	6/11	0.449705037374589	1	FACETS	0.822	0.751	0.895	0.822	0.751	0.895	CLONAL	1	TRUE	0	0.449705037374589	1		546	583	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333404	70333404	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058228-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	138	479	0	ENST00000373644.4:c.1309C>G	p.Pro437Ala	p.P437A	ENST00000373644	NM_030625.2	437	Cca/Gca	2/12	0.449705037374589	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.449705037374589	1		479	460	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624248	89624249	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCGT	novel	NA	P-0058228-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	40	122	0	ENST00000371953.3:c.24_27dup	p.Ser10ArgfsTer2	p.S10Rfs*2	ENST00000371953	NM_000314.4	8	atc/aTCGTtc	1/9	0.449705037374589	1	FACETS	0.901	0.762	1	0.901	0.762	1	CLONAL	1	TRUE	0	0.449705037374589	1		122	153	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086045	16086045	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058228-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	140	491	0	ENST00000281043.3:c.1221del	p.His407GlnfsTer6	p.H407Qfs*6	ENST00000281043	NM_005378.4	407	caC/ca	3/3	1	2	FACETS	0.968	0.884	1	0.968	0.884	1	CLONAL	1	TRUE	1	0.449705037374589	2		491	643	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589602	67589603	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTTCAAGAAAAAAGTCGAGAATATGAT	novel	NA	P-0058228-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	32	138	0	ENST00000274335.5:c.1366_1392dup	p.Phe456_Asp464dup	p.F456_D464dup	ENST00000274335		456	-/TTTCAAGAAAAAAGTCGAGAATATGAT	10/15	1	2	FACETS	0.531	0.433	0.641	0.531	0.433	0.641	SUBCLONAL	1	TRUE	1	0.449705037374589	2		138	268	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398852	398852	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058228-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	124	498	0	ENST00000380956.4:c.662A>T	p.Tyr221Phe	p.Y221F	ENST00000380956	NM_001195286.1	221	tAt/tTt	6/9	1	2	FACETS	0.951	0.863	1	0.951	0.863	1	CLONAL	1	TRUE	1	0.449705037374589	2		498	580	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0058229-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	16	405	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.467085023496804	1	FACETS	0.108	0.079	0.143	0.108	0.079	0.143	SUBCLONAL	1	TRUE	0	0.467085023496804	1		405	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0058229-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	198	493	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.467085023496804	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.467085023496804	1		493	510	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105920	27105920	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058229-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	361	542	0	ENST00000324856.7:c.5531G>A	p.Trp1844Ter	p.W1844*	ENST00000324856	NM_006015.4	1844	tGg/tAg	20/20	0.467085023496804	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.467085023496804	2		542	714	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987325	2987325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058229-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	74	397	0	ENST00000396946.4:c.104G>A	p.Arg35His	p.R35H	ENST00000396946	NM_032415.4	35	cGc/cAc	3/25	NA	2	FACETS	0.543	0.476	0.616			1	INDETERMINATE	1	TRUE	NA	0.467085023496804	2		397	583	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544518	86544518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058229-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	101	515	0	ENST00000262426.4:c.343C>T	p.Arg115Trp	p.R115W	ENST00000262426	NM_001451.2	115	Cgg/Tgg	1/2	0.163352948803444	0	FACETS	0.443	0.397	0.492			1	INDETERMINATE	1	TRUE	0	0.467085023496804	0		515	520	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61709615	61709615	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058229-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	21	166	0	ENST00000401558.2:c.2872A>G	p.Ile958Val	p.I958V	ENST00000401558	NM_003400.3	958	Ata/Gta	23/25	1	2	FACETS	0.345	0.265	0.436	0.345	0.265	0.436	SUBCLONAL	1	TRUE	1	0.467085023496804	2		166	261	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502265	157502281	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTTCCGACTCTACGT	CTGTTCCGACTCTACGT	-	novel	NA	P-0058229-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	62	481	0	ENST00000346085.5:c.3301_3317del	p.Phe1101ArgfsTer11	p.F1101Rfs*11	ENST00000346085	NM_020732.3	1100	CTGTTCCGACTCTACGTc/c	12/20	0.156850454716487	2	FACETS	0.426	0.368	0.49	0.213	0.184	0.245	INDETERMINATE	1	TRUE	0	0.467085023496804	2		481	623	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277238	38277238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909641	NA	P-0058229-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	171	503	0	ENST00000425967.3:c.1190C>T	p.Pro397Leu	p.P397L	ENST00000425967	NM_001174067.1	397	cCg/cTg	10/19	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.467085023496804	2		503	611	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2123912	2123912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058229-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	28	441	0	ENST00000349721.2:c.3956C>T	p.Ala1319Val	p.A1319V	ENST00000349721	NM_003070.3	1319	gCc/gTc	27/34	0.467085023496804	1	FACETS	0.178	0.142	0.22	0.178	0.142	0.22	SUBCLONAL	1	TRUE	0	0.467085023496804	1		441	516	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0058233-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	94	190	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.697143800522039	3	FACETS	0.812	0.737	0.888	0.812	0.737	0.888	CLONAL	2	TRUE	1	0.697143800522039	3		190	224	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574000	7574000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058233-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	216	455	0	ENST00000269305.4:c.1027G>T	p.Glu343Ter	p.E343*	ENST00000269305	NM_001126112.2	343	Gag/Tag	10/11	0.673077433135632	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.697143800522039	2		455	309	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0058233-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	278	488	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.67968934478396	2	FACETS	0.97	0.93	1	0.97	0.93	1	CLONAL	2	TRUE	0	0.697143800522039	2		488	411	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440445	49440445	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058233-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	254	514	0	ENST00000301067.7:c.4365del	p.Cys1456AlafsTer50	p.C1456Afs*50	ENST00000301067	NM_003482.3	1455	taC/ta	15/54	0.697143800522039	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.697143800522039	3		514	459	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265521	152265521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058233-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	235	399	0	ENST00000206249.3:c.974C>T	p.Pro325Leu	p.P325L	ENST00000206249	NM_000125.3	325	cCg/cTg	4/8	0.388985796038799	5	FACETS	0.966	0.913	1	0.966	0.913	1	INDETERMINATE	3	TRUE	2	0.697143800522039	5		399	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0058277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	125	1110	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.779	0.712	0.848	1	0.987	1	SUBCLONAL	2	TRUE	1	0.42	2		1111	382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0058277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	133	449	0	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	1	2	FACETS	0.861	0.791	0.932	1	0.99	1	CLONAL	2	TRUE	1	0.42	2		449	368	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0058277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	79	356	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.42	2		356	330	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849205	76849209	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAG	AAGAG	-	novel	NA	P-0058277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	79	217	0	ENST00000373344.5:c.6067_6071del	p.Leu2023Ter	p.L2023*	ENST00000373344	NM_000489.3	2023	CTCTTt/t	26/35	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.42	2		217	253	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185049	123185049	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058277-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	25	125	0	ENST00000218089.9:c.1096C>A	p.Leu366Ile	p.L366I	ENST00000218089	NM_001042749.1	366	Ctt/Att	12/35	1	2	FACETS	0.661	0.525	0.815	0.661	0.525	0.815	SUBCLONAL	1	TRUE	1	0.42	2		125	180	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994234	21994234	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1287464120	NA	P-0058289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1403	202	754	0	ENST00000579755.1:c.97G>T	p.Glu33Ter	p.E33*	ENST00000579755		33	Gag/Tag	1/3	0.326050370076148		FACETS		0.701	0.819				SUBCLONAL	1	TRUE	0	0.331851705208516	2		754	1605	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293074	91293075	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	63	305	0	ENST00000355112.3:c.582dup	p.Lys195Ter	p.K195*	ENST00000355112	NM_000057.2	192	-/T	3/22	0.170014211108967	2	FACETS	0.542	0.468	0.623	0.271	0.234	0.312	INDETERMINATE	1	TRUE	0	0.331851705208516	2		305	700	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624291	89624291	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	105	431	0	ENST00000371953.3:c.65A>C	p.Asp22Ala	p.D22A	ENST00000371953	NM_000314.4	22	gAc/gCc	1/9	1	2	FACETS	0.753	0.674	0.837	0.753	0.674	0.837	SUBCLONAL	1	TRUE	1	0.331851705208516	2		431	840	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78797005	78797005	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1387655925	NA	P-0058289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	67	503	0	ENST00000306801.3:c.1118C>T	p.Thr373Met	p.T373M	ENST00000306801	NM_020761.2	373	aCg/aTg	9/34	0.331851705208516	4	FACETS	0.472	0.409	0.541			1	SUBCLONAL	1	TRUE	NA	0.331851705208516	4		503	1139	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117499	4117499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	41	431	0	ENST00000262948.5:c.221G>A	p.Arg74Lys	p.R74K	ENST00000262948	NM_030662.3	74	aGg/aAg	2/11	0.170014211108967	2	FACETS	0.322	0.267	0.384	0.161	0.133	0.192	INDETERMINATE	1	TRUE	0	0.331851705208516	2		431	767	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40864892	40864892	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1384718881	NA	P-0058289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	38	328	0	ENST00000373198.4:c.2376T>G	p.Asn792Lys	p.N792K	ENST00000373198	NM_133170.3	792	aaT/aaG	16/32	0.183475479409046	3	FACETS	0.519	0.429	0.621	0.26	0.214	0.311	INDETERMINATE	1	TRUE	1	0.331851705208516	3		328	514	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0058293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	269	265	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.245239646652815	14	FACETS	1	0.968	1			1	CLONAL	12	TRUE	NA	0.245239646652815	14		265	444	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519920	NA	P-0058293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	53	348	0	ENST00000397062.3:c.85G>C	p.Asp29His	p.D29H	ENST00000397062	NM_006164.4	29	Gat/Cat	2/5	0.215629786238235	3	FACETS	1	0.908	1	1	0.908	1	CLONAL	2	TRUE	1	0.245239646652815	3		348	227	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16247440	16247440	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	74	370	0	ENST00000375759.3:c.1711G>C	p.Glu571Gln	p.E571Q	ENST00000375759	NM_015001.2	571	Gag/Cag	9/15	0.0970286025420708	4	FACETS	0.921	0.81	1	0.921	0.81	1	INDETERMINATE	2	TRUE	2	0.245239646652815	4		370	408	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202638	108202638	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	42	304	0	ENST00000278616.4:c.7662T>A	p.His2554Gln	p.H2554Q	ENST00000278616	NM_000051.3	2554	caT/caA	52/63	0.206393063853662	3	FACETS	0.92	0.776	1	0.92	0.776	1	CLONAL	2	TRUE	1	0.245239646652815	3		304	209	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94178989	94178989	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	36	234	0	ENST00000323929.3:c.1854G>T	p.Met618Ile	p.M618I	ENST00000323929	NM_005591.3	618	atG/atT	16/20	0.206393063853662	3	FACETS	0.953	0.793	1	0.953	0.793	1	CLONAL	2	TRUE	1	0.245239646652815	3		234	173	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102098199	102098199	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0058293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	76	288	0	ENST00000282441.5:c.1164-1G>T		p.X388_splice	ENST00000282441	NM_001130145.2	388			0.206393063853662	3	FACETS	0.939	0.835	1	1	0.976	1	CLONAL	3	TRUE	1	0.245239646652815	3		288	247	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42843885	42843885	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	19	365	0	ENST00000398585.3:c.1034G>T	p.Trp345Leu	p.W345L	ENST00000398585	NM_001135099.1	345	tGg/tTg	10/14	0.206393063853662	3	FACETS	0.596	0.452	0.764	0.298	0.226	0.382	SUBCLONAL	1	TRUE	1	0.245239646652815	3		365	292	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513338	106513338	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	69	357	0	ENST00000359195.3:c.2242G>T	p.Asp748Tyr	p.D748Y	ENST00000359195	NM_002649.2	748	Gat/Tat	4/11	0.245239646652815	5	FACETS	1	0.931	1	0.729	0.639	0.825	CLONAL	2	TRUE	2	0.245239646652815	5		357	352	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978728	70978728	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	32	319	0	ENST00000276594.2:c.925G>T	p.Gly309Cys	p.G309C	ENST00000276594	NM_024504.3	309	Ggt/Tgt	5/8	0.245239646652815	5	FACETS	0.793	0.648	0.955	0.529	0.432	0.637	CLONAL	2	TRUE	2	0.245239646652815	5		319	225	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245367	53245367	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058293-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	44	342	0	ENST00000375401.3:c.670G>T	p.Glu224Ter	p.E224*	ENST00000375401	NM_004187.3	224	Gag/Tag	6/26	0.245239646652815	2	FACETS	0.842	0.714	0.981	0.842	0.714	0.981	CLONAL	2	TRUE	0	0.245239646652815	2		342	213	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0058295-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	129	362	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.3221021302801	3	FACETS	0.841	0.767	0.917	0.841	0.767	0.917	CLONAL	2	TRUE	1	0.387097801080602	3		362	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0058295-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	97	464	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.387097801080602	2		464	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0058302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	303	556	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.693238609282383	1	FACETS	0.977	0.931	1	0.977	0.931	1	CLONAL	1	TRUE	0	0.693708386945908	1		556	584	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981360	68981360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1474820456	NA	P-0058302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	75	279	0	ENST00000288368.4:c.1432G>A	p.Val478Met	p.V478M	ENST00000288368	NM_024870.2	478	Gtg/Atg	12/40	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.693708386945908	2		279	207	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795022	45795022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746159001	NA	P-0058302-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	335	635	0	ENST00000450313.1:c.1606C>T	p.His536Tyr	p.H536Y	ENST00000450313	NM_012222.2	536	Cac/Tac	16/16	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.693708386945908	2		635	948	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0058303-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	673	190	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.749949730576022	16	FACETS	1	0.99	1			1	CLONAL	7	TRUE	NA	0.749949730576022	16		190	1507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0058303-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	126	427	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.736763296473265	3	FACETS	0.922	0.84	1	0.461	0.42	0.504	CLONAL	1	TRUE	1	0.749949730576022	3		427	501	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057520007	NA	P-0058303-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	353	540	0	ENST00000269305.4:c.614A>T	p.Tyr205Phe	p.Y205F	ENST00000269305	NM_001126112.2	205	tAt/tTt	6/11	0.736763296473265	3	FACETS	0.993	0.95	1	0.993	0.95	1	CLONAL	2	TRUE	1	0.749949730576022	3		540	652	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253762	30253762	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058303-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	133	433	0	ENST00000307677.4:c.692G>T	p.Ser231Ile	p.S231I	ENST00000307677	NM_138578.1	231	aGt/aTt	3/3	0.736763296473265	3	FACETS	0.977	0.893	1	0.489	0.446	0.533	CLONAL	1	TRUE	1	0.749949730576022	3		433	499	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280292	1280292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201927653	NA	P-0058303-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	145	518	0	ENST00000310581.5:c.1931C>T	p.Thr644Met	p.T644M	ENST00000310581	NM_198253.2	644	aCg/aTg	4/16	0.749949730576022	7	FACETS	0.924	0.841	1	0.231	0.21	0.253	CLONAL	1	TRUE	3	0.749949730576022	7		518	1203	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332868	152332868	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058303-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	214	416	0	ENST00000206249.3:c.1174G>T	p.Val392Phe	p.V392F	ENST00000206249	NM_000125.3	392	Gtc/Ttc	5/8	0.749949730576022	2	FACETS	0.971	0.928	1	0.971	0.928	1	CLONAL	2	TRUE	0	0.749949730576022	2		416	294	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925688	114925688	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058303-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	143	442	0	ENST00000543371.1:c.1766C>G	p.Thr589Ser	p.T589S	ENST00000543371	NM_001198531.1	589	aCc/aGc	14/14	0.749949730576022	2	FACETS	1	0.958	1	0.528	0.488	0.569	CLONAL	1	TRUE	0	0.749949730576022	2		442	361	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625190	69625191	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0058303-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	230	503	0	ENST00000334134.2:c.602_603delinsAG	p.Pro201Gln	p.P201Q	ENST00000334134	NM_005247.2	201	cCC/cAG	3/3	0.469530947511212	6	FACETS	0.858	0.805	0.911	0.858	0.805	0.911	CLONAL	3	TRUE	3	0.749949730576022	6		503	596	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346024	73346024	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058303-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	222	289	0	ENST00000377767.4:c.1514A>T	p.His505Leu	p.H505L	ENST00000377767	NM_014953.3	505	cAt/cTt	11/21	0.749949730576022	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.749949730576022	2		289	274	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046556	30046556	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs774699925	NA	P-0058303-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	597	412	0	ENST00000331968.5:c.2627A>T	p.Gln876Leu	p.Q876L	ENST00000331968	NM_002742.2	876	cAg/cTg	18/18	0.749949730576022	6	FACETS	1	0.989	1	1	0.989	1	CLONAL	4	TRUE	2	0.749949730576022	6		412	957	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755666	39755666	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058303-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	293	462	0	ENST00000288319.7:c.1099C>A	p.Arg367Ser	p.R367S	ENST00000288319	NM_182918.3	367	Cgc/Agc	10/10	0.749949730576022	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.749949730576022	2		462	381	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5070016	5070016	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058303-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	102	266	0	ENST00000381652.3:c.1605G>T	p.Met535Ile	p.M535I	ENST00000381652	NM_004972.3	535	atG/atT	12/25	0.749949730576022	2	FACETS	1	0.966	1	0.562	0.512	0.613	CLONAL	1	TRUE	0	0.749949730576022	2		266	242	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	69	302	0				ENST00000310581	NM_198253.2	-/1132			0.211862925726949	0	FACETS	0.801	0.717	0.886			1	INDETERMINATE	1	FALSE	0	0.529731035651209	0		302	153	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0058395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	252	187	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.225107402393603	3	FACETS	1	0.965	1	1	0.965	1	INDETERMINATE	2	FALSE	1	0.529731035651209	3		188	584	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912079	127912079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	8	273	1	ENST00000373547.4:c.791G>A	p.Arg264His	p.R264H	ENST00000373547	NM_002721.4	264	cGt/cAt	7/7	1	2	FACETS	0.078	0.049	0.115	0.078	0.049	0.115	SUBCLONAL	1	FALSE	1	0.529731035651209	2		274	389	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910459	32910459	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660857	NA	P-0058395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	82	266	0	ENST00000380152.3:c.1967C>T	p.Thr656Ile	p.T656I	ENST00000380152		656	aCt/aTt	11/27	0.156585507023471	4	FACETS	1	0.968	1	0.628	0.557	0.703	INDETERMINATE	1	FALSE	2	0.529731035651209	4		266	377	SUCCESS
BLM	641	MSKCC	GRCh37	15	91341493	91341493	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	98	333	0	ENST00000355112.3:c.3284A>C	p.Gln1095Pro	p.Q1095P	ENST00000355112	NM_000057.2	1095	cAa/cCa	17/22	0.458116186971145	1	FACETS	0.81	0.73	0.893	0.81	0.73	0.893	CLONAL	1	FALSE	0	0.529731035651209	1		333	336	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37092127	37092127	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1196350669	NA	P-0058395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	83	331	0	ENST00000231790.2:c.2254G>C	p.Val752Leu	p.V752L	ENST00000231790	NM_000249.3	752	Gtc/Ctc	19/19	0.156585507023471	4	FACETS	1	0.955	1	0.576	0.511	0.645	INDETERMINATE	1	FALSE	2	0.529731035651209	4		331	416	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547248	106547248	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	85	317	0	ENST00000369096.4:c.485T>G	p.Val162Gly	p.V162G	ENST00000369096	NM_001198.3	162	gTg/gGg	4/7	0.482666381713929	1	FACETS	0.761	0.68	0.846	0.761	0.68	0.846	SUBCLONAL	1	FALSE	0	0.529731035651209	1		317	310	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462547	92462547	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	134	672	0	ENST00000265734.4:c.91C>G	p.Arg31Gly	p.R31G	ENST00000265734	NM_001259.6	31	Cgc/Ggc	2/8	0.225107402393603	3	FACETS	1	0.976	1	0.596	0.544	0.65	INDETERMINATE	1	FALSE	1	0.529731035651209	3		672	537	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156607	55156607	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	549	615	0	ENST00000257290.5:c.3008G>A	p.Trp1003Ter	p.W1003*	ENST00000257290	NM_006206.4	1003	tGg/tAg	22/23	0.748855005270645	4	FACETS	1	0.987	1	0.705	0.678	0.731	CLONAL	2	TRUE	1	0.748855005270645	4		615	1213	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866441	42866441	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770444484	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	407	1017	1	ENST00000398585.3:c.191C>T	p.Pro64Leu	p.P64L	ENST00000398585	NM_001135099.1	64	cCc/cTc	3/14	0.743458338230976	3	FACETS	1	0.984	1	0.538	0.511	0.565	CLONAL	1	TRUE	1	0.748855005270645	3		1018	1389	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938967	76938967	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782774889	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	495	419	0	ENST00000373344.5:c.1781C>T	p.Ser594Phe	p.S594F	ENST00000373344	NM_000489.3	594	tCc/tTc	9/35	0.642609937347067	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	2	0.748855005270645	4		419	1054	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819177	3819177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	70	568	0	ENST00000262367.5:c.3058G>A	p.Glu1020Lys	p.E1020K	ENST00000262367	NM_004380.2	1020	Gag/Aag	15/31	0.748855005270645	2	FACETS	0.302	0.263	0.344	0.151	0.131	0.172	SUBCLONAL	1	TRUE	0	0.748855005270645	2		568	620	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531880	41531880	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	171	419	0	ENST00000263253.7:c.1592C>G	p.Ser531Ter	p.S531*	ENST00000263253	NM_001429.3	531	tCa/tGa	7/31	0.748855005270645	3	FACETS	1	0.924	1	0.5	0.462	0.539	CLONAL	1	TRUE	1	0.748855005270645	3		419	628	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876235	35876235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866784625	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	240	572	0	ENST00000303115.3:c.1027G>A	p.Asp343Asn	p.D343N	ENST00000303115	NM_002185.3	343	Gat/Aat	8/8	0.748855005270645	2	FACETS	1	0.985	1	0.567	0.534	0.601	CLONAL	1	TRUE	0	0.748855005270645	2		572	565	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934194	48934194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	189	208	0	ENST00000267163.4:c.649C>T	p.Gln217Ter	p.Q217*	ENST00000267163	NM_000321.2	217	Cag/Tag	7/27	0.748855005270645	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.748855005270645	2		208	247	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538302	9538302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	202	486	0	ENST00000353224.5:c.1696C>T	p.His566Tyr	p.H566Y	ENST00000353224	NM_177990.2	566	Cac/Tac	7/10	0.748855005270645	3	FACETS	0.982	0.913	1	0.491	0.456	0.527	CLONAL	1	TRUE	1	0.748855005270645	3		486	755	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601881	43601881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	384	813	0	ENST00000355710.3:c.925G>A	p.Glu309Lys	p.E309K	ENST00000355710	NM_020975.4	309	Gag/Aag	5/20	0.748855005270645	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.748855005270645	1		813	562	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099852	27099852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	565	710	0	ENST00000324856.7:c.3731C>T	p.Pro1244Leu	p.P1244L	ENST00000324856	NM_006015.4	1244	cCc/cTc	15/20	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.748855005270645	2		710	699	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003303	42003303	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	241	499	0	ENST00000219905.7:c.2840C>G	p.Ser947Ter	p.S947*	ENST00000219905	NM_001164273.1	947	tCa/tGa	8/24	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.748855005270645	2		499	623	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412544	80412544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	129	316	0	ENST00000286548.4:c.497G>A	p.Arg166His	p.R166H	ENST00000286548	NM_002072.3	166	cGc/cAc	4/7	0.642609937347067	4	FACETS	0.883	0.802	0.968	0.442	0.401	0.484	CLONAL	1	TRUE	2	0.748855005270645	4		316	682	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	142	436	1				ENST00000310581	NM_198253.2	-/1132			0.748855005270645	2	FACETS	0.967	0.892	1	0.484	0.446	0.523	CLONAL	1	TRUE	0	0.748855005270645	2		437	392	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554352	106554352	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	421	426	0	ENST00000369096.4:c.1880G>A	p.Gly627Glu	p.G627E	ENST00000369096	NM_001198.3	627	gGa/gAa	6/7	0.748855005270645	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.748855005270645	3		426	741	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149440464	149440464	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371692872	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	330	741	0	ENST00000286301.3:c.1930G>A	p.Glu644Lys	p.E644K	ENST00000286301	NM_005211.3	644	Gag/Aag	14/22	0.748855005270645	2	FACETS	1	0.98	1	0.53	0.503	0.558	CLONAL	1	TRUE	0	0.748855005270645	2		741	831	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099209	157099209	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	284	665	0	ENST00000346085.5:c.146C>G	p.Ser49Cys	p.S49C	ENST00000346085	NM_020732.3	49	tCt/tGt	1/20	0.748855005270645	3	FACETS	1	0.986	1	0.572	0.538	0.606	CLONAL	1	TRUE	1	0.748855005270645	3		665	912	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211154	36211154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	436	980	1	ENST00000222270.7:c.905C>T	p.Pro302Leu	p.P302L	ENST00000222270	NM_014727.1	302	cCc/cTc	3/37	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.748855005270645	2		981	1086	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644460	18644460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	99	270	0	ENST00000266497.5:c.2638C>T	p.Pro880Ser	p.P880S	ENST00000266497		880	Cct/Tct	18/31	0.748855005270645	3	FACETS	0.966	0.87	1	0.483	0.435	0.534	CLONAL	1	TRUE	1	0.748855005270645	3		270	376	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424972	49424972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748519188	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	355	802	0	ENST00000301067.7:c.13516C>T	p.Pro4506Ser	p.P4506S	ENST00000301067	NM_003482.3	4506	Ccc/Tcc	39/54	0.748855005270645	3	FACETS	1	0.987	1	0.559	0.529	0.589	CLONAL	1	TRUE	1	0.748855005270645	3		802	1166	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449496	149449496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	628	762	0	ENST00000286301.3:c.1450G>A	p.Glu484Lys	p.E484K	ENST00000286301	NM_005211.3	484	Gag/Aag	10/22	0.748855005270645	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.748855005270645	2		762	766	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185028	32185028	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140082058	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	303	817	1	ENST00000375023.3:c.1640G>A	p.Arg547Gln	p.R547Q	ENST00000375023	NM_004557.3	547	cGa/cAa	10/30	0.748855005270645	3	FACETS	0.953	0.898	1	0.477	0.449	0.505	CLONAL	1	TRUE	1	0.748855005270645	3		818	1167	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140449109	140449109	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	122	334	0	ENST00000288602.6:c.1970C>G	p.Ser657Ter	p.S657*	ENST00000288602	NM_004333.4	657	tCa/tGa	16/18	0.748855005270645	3	FACETS	0.961	0.874	1	0.481	0.437	0.526	CLONAL	1	TRUE	1	0.748855005270645	3		334	466	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612087	43612087	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	267	733	0	ENST00000355710.3:c.2192G>A	p.Gly731Glu	p.G731E	ENST00000355710	NM_020975.4	731	gGa/gAa	12/20	0.748855005270645	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.748855005270645	1		733	413	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31493367	31493367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	143	306	0	ENST00000344624.3:c.1789C>T	p.His597Tyr	p.H597Y	ENST00000344624		597	Cac/Tac	10/33	0.748855005270645	2	FACETS	0.955	0.88	1	0.477	0.44	0.516	CLONAL	1	TRUE	0	0.748855005270645	2		306	400	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164407	47164407	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	37	201	0	ENST00000409792.3:c.1719C>A	p.Phe573Leu	p.F573L	ENST00000409792	NM_014159.6	573	ttC/ttA	3/21	0.748855005270645	3	FACETS	0.352	0.29	0.421	0.176	0.145	0.211	SUBCLONAL	1	TRUE	1	0.748855005270645	3		201	386	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834541	156834542	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1328	352	912	2	ENST00000524377.1:c.309_310delinsTT	p.Arg104Cys	p.R104C	ENST00000524377	NM_002529.3	103	ctCCgt/ctTTgt	3/17	0.71889717384537	4	FACETS	0.979	0.924	1	0.489	0.462	0.517	CLONAL	1	TRUE	2	0.748855005270645	4		914	1680	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713612	52713612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	232	559	0	ENST00000394830.3:c.116C>T	p.Ser39Phe	p.S39F	ENST00000394830	NM_018313.4	39	tCc/tTc	2/30	0.748855005270645	3	FACETS	1	0.972	1	0.535	0.5	0.571	CLONAL	1	TRUE	1	0.748855005270645	3		559	796	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577101	7577102	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	667	786	1	ENST00000269305.4:c.836_837delinsAA	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGG/gAA	8/11	0.748855005270645	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.748855005270645	2		787	804	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179121	123179121	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	191	430	0	ENST00000218089.9:c.570C>G	p.Ile190Met	p.I190M	ENST00000218089	NM_001042749.1	190	atC/atG	8/35	0.642609937347067	4	FACETS	1	0.965	1	0.534	0.494	0.575	CLONAL	1	TRUE	2	0.748855005270645	4		430	835	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117730754	117730754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373938735	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	472	559	0	ENST00000368508.3:c.280G>A	p.Glu94Lys	p.E94K	ENST00000368508	NM_002944.2	94	Gaa/Aaa	4/43	0.748855005270645	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.748855005270645	3		559	837	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6037039	6037039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	192	294	0	ENST00000265849.7:c.721C>T	p.Pro241Ser	p.P241S	ENST00000265849	NM_000535.5	241	Cct/Tct	7/15	0.71889717384537	4	FACETS	1	0.986	1	0.633	0.588	0.68	CLONAL	1	TRUE	2	0.748855005270645	4		294	708	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53254068	53254068	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	280	625	0	ENST00000375401.3:c.4G>T	p.Glu2Ter	p.E2*	ENST00000375401	NM_004187.3	2	Gag/Tag	1/26	0.748855005270645	3	FACETS	1	0.979	1	0.542	0.51	0.575	CLONAL	1	TRUE	1	0.748855005270645	3		625	948	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784908	9784908	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	753	896	0	ENST00000377346.4:c.2911G>C	p.Gly971Arg	p.G971R	ENST00000377346	NM_005026.3	971	Ggg/Cgg	23/24	0.748855005270645	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.748855005270645	3		896	1345	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937063	36937063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	256	686	0	ENST00000361632.4:c.1256C>T	p.Pro419Leu	p.P419L	ENST00000361632		419	cCc/cTc	9/16	0.748855005270645	3	FACETS	0.946	0.887	1	0.473	0.443	0.504	CLONAL	1	TRUE	1	0.748855005270645	3		686	993	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78425925	78425925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	169	445	0	ENST00000370768.2:c.1520C>T	p.Pro507Leu	p.P507L	ENST00000370768	NM_003902.3	507	cCc/cTc	16/20	0.748855005270645	3	FACETS	0.949	0.875	1	0.474	0.437	0.512	CLONAL	1	TRUE	1	0.748855005270645	3		445	654	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846237	156846237	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	736	885	0	ENST00000524377.1:c.1678G>C	p.Glu560Gln	p.E560Q	ENST00000524377	NM_002529.3	560	Gag/Cag	14/17	0.71889717384537	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.748855005270645	4		885	1672	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983009	201983010	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1282	317	840	0	ENST00000359651.3:c.858_859delinsAA	p.Glu287Lys	p.E287K	ENST00000359651		286	ccGGag/ccAAag	7/8	0.71889717384537	4	FACETS	0.926	0.871	0.982	0.463	0.435	0.491	CLONAL	1	TRUE	2	0.748855005270645	4		840	1599	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555979	226555979	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	246	558	0	ENST00000366794.5:c.2198C>G	p.Ser733Ter	p.S733*	ENST00000366794	NM_001618.3	733	tCa/tGa	16/23	0.71889717384537	4	FACETS	1	0.956	1	0.515	0.481	0.55	CLONAL	1	TRUE	2	0.748855005270645	4		558	1116	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741936	17741936	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	146	397	0	ENST00000250003.3:c.607C>G	p.Arg203Gly	p.R203G	ENST00000250003	NM_002478.4	203	Cgc/Ggc	1/3	0.748855005270645	2	FACETS	1	0.938	1	0.509	0.47	0.549	CLONAL	1	TRUE	0	0.748855005270645	2		397	383	SUCCESS
EED	8726	MSKCC	GRCh37	11	85966286	85966286	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	101	198	0	ENST00000263360.6:c.383C>G	p.Ser128Ter	p.S128*	ENST00000263360	NM_003797.3	128	tCa/tGa	4/12	0.748855005270645	2	FACETS	1	0.911	1	0.501	0.455	0.549	CLONAL	1	TRUE	0	0.748855005270645	2		198	269	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435767	49435767	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	561	681	0	ENST00000301067.7:c.6116C>G	p.Ser2039Ter	p.S2039*	ENST00000301067	NM_003482.3	2039	tCa/tGa	29/54	0.748855005270645	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.748855005270645	3		681	1008	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50488233	50488233	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	220	544	0	ENST00000394963.4:c.1147G>C	p.Asp383His	p.D383H	ENST00000394963	NM_003076.4	383	Gat/Cat	10/13	0.748855005270645	3	FACETS	0.98	0.914	1	0.49	0.457	0.524	CLONAL	1	TRUE	1	0.748855005270645	3		544	824	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794811	120794811	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	416	996	0	ENST00000257552.2:c.546G>C	p.Lys182Asn	p.K182N	ENST00000257552	NM_002442.3	182	aaG/aaC	9/15	0.748855005270645	3	FACETS	1	0.989	1	0.566	0.538	0.593	CLONAL	1	TRUE	1	0.748855005270645	3		996	1350	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38641622	38641622	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	115	315	0	ENST00000299084.4:c.583-1G>C		p.X195_splice	ENST00000299084	NM_152594.2	195			1	2	FACETS	0.991	0.905	1	0.991	0.905	1	CLONAL	1	TRUE	1	0.748855005270645	2		315	310	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003000	42003000	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	264	484	0	ENST00000219905.7:c.2537C>G	p.Ser846Cys	p.S846C	ENST00000219905	NM_001164273.1	846	tCt/tGt	8/24	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.748855005270645	2		484	660	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714100	43714101	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	297	864	1	ENST00000382044.4:c.4052_4053delinsTT	p.Pro1351Leu	p.P1351L	ENST00000382044	NM_001141980.1	1351	cCC/cTT	19/28	1	2	FACETS	0.943	0.891	0.996	0.943	0.891	0.996	CLONAL	1	TRUE	1	0.748855005270645	2		865	841	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303927	91303927	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	242	581	0	ENST00000355112.3:c.1324G>C	p.Asp442His	p.D442H	ENST00000355112	NM_000057.2	442	Gat/Cat	7/22	0.748855005270645	3	FACETS	0.931	0.871	0.993	0.466	0.435	0.497	CLONAL	1	TRUE	1	0.748855005270645	3		581	954	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858180	9858180	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867432846	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	306	665	0	ENST00000330684.3:c.3221C>T	p.Pro1074Leu	p.P1074L	ENST00000330684	NM_001134407.1	1074	cCt/cTt	13/13	0.748855005270645	2	FACETS	1	0.991	1	0.596	0.565	0.626	CLONAL	1	TRUE	0	0.748855005270645	2		665	686	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23652466	23652466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377085677	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	326	878	0	ENST00000261584.4:c.13C>T	p.Pro5Ser	p.P5S	ENST00000261584	NM_024675.3	5	Ccc/Tcc	1/13	0.748855005270645	2	FACETS	1	0.977	1	0.525	0.498	0.552	CLONAL	1	TRUE	0	0.748855005270645	2		878	829	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81954803	81954803	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	356	385	0	ENST00000359376.3:c.2236G>A	p.Glu746Lys	p.E746K	ENST00000359376	NM_002661.3	746	Gaa/Aaa	21/33	0.748855005270645	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.748855005270645	2		385	437	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980503	7980503	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	263	537	0	ENST00000319144.4:c.1080G>C	p.Gln360His	p.Q360H	ENST00000319144	NM_001139.2	360	caG/caC	9/15	0.748855005270645	2	FACETS	1	0.98	1	0.542	0.511	0.573	CLONAL	1	TRUE	0	0.748855005270645	2		537	648	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618450	37618450	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	241	506	0	ENST00000447079.4:c.126C>G	p.His42Gln	p.H42Q	ENST00000447079	NM_015083.1	42	caC/caG	1/14	0.748855005270645	2	FACETS	1	0.979	1	0.542	0.51	0.574	CLONAL	1	TRUE	0	0.748855005270645	2		506	594	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627850	37627850	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	542	611	0	ENST00000447079.4:c.1765C>G	p.His589Asp	p.H589D	ENST00000447079	NM_015083.1	589	Cac/Gac	2/14	0.748855005270645	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.748855005270645	2		611	692	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120442	70120442	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	411	954	0	ENST00000245479.2:c.1444G>C	p.Asp482His	p.D482H	ENST00000245479	NM_000346.3	482	Gac/Cac	3/3	0.748855005270645	2	FACETS	1	0.99	1	0.558	0.533	0.583	CLONAL	1	TRUE	0	0.748855005270645	2		954	984	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229341	5229341	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	371	808	2	ENST00000357368.4:c.2362G>A	p.Asp788Asn	p.D788N	ENST00000357368	NM_002850.3	788	Gac/Aac	16/38	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.748855005270645	2		810	949	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262130	10262130	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	304	699	0	ENST00000340748.4:c.2161G>A	p.Gly721Arg	p.G721R	ENST00000340748		721	Ggg/Agg	23/40	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.748855005270645	2		699	810	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265699	10265699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	229	560	1	ENST00000340748.4:c.1478C>T	p.Pro493Leu	p.P493L	ENST00000340748		493	cCc/cTc	19/40	1	2	FACETS	0.96	0.9	1	0.96	0.9	1	CLONAL	1	TRUE	1	0.748855005270645	2		561	637	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270547	10270548	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	354	845	1	ENST00000340748.4:c.1092_1093delinsTT	p.Leu365Phe	p.L365F	ENST00000340748		364	gaCCtc/gaTTtc	15/40	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.748855005270645	2		846	905	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291458	10291458	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	214	526	0	ENST00000340748.4:c.221C>T	p.Ser74Phe	p.S74F	ENST00000340748		74	tCc/tTc	3/40	1	2	FACETS	0.961	0.899	1	0.961	0.899	1	CLONAL	1	TRUE	1	0.748855005270645	2		526	595	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355275	15355276	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	249	377	1	ENST00000263377.2:c.2347_2348delinsTT	p.Pro783Phe	p.P783F	ENST00000263377	NM_058243.2	783	CCc/TTc	13/20	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.748855005270645	2		378	531	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221681	36221681	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	413	999	0	ENST00000222270.7:c.5350C>G	p.Arg1784Gly	p.R1784G	ENST00000222270	NM_014727.1	1784	Cgg/Ggg	26/37	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.748855005270645	2		999	1015	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222266	39222266	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	184	390	0	ENST00000402219.2:c.3344C>G	p.Ser1115Ter	p.S1115*	ENST00000402219	NM_005633.3	1115	tCa/tGa	20/23	0.748855005270645	3	FACETS	1	0.961	1	0.527	0.488	0.567	CLONAL	1	TRUE	1	0.748855005270645	3		390	641	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607544	46607544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776284833	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	414	973	2	ENST00000263734.3:c.1733C>T	p.Ala578Val	p.A578V	ENST00000263734	NM_001430.4	578	gCc/gTc	12/16	0.748855005270645	3	FACETS	1	0.983	1	0.535	0.509	0.562	CLONAL	1	TRUE	1	0.748855005270645	3		975	1420	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023151	31023152	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1260	230	605	0	ENST00000375687.4:c.2637dup	p.Thr880TyrfsTer2	p.T880Yfs*2	ENST00000375687	NM_015338.5	879	gat/gaTt	13/13	0.748855005270645	5	FACETS	0.875	0.814	0.94	0.219	0.203	0.235	CLONAL	1	TRUE	1	0.748855005270645	5		605	1490	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744037	39744038	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	91	285	0	ENST00000361337.2:c.1665_1666delinsAA	p.Met555_Glu556delinsIleLys	p.M555_E556delinsIK	ENST00000361337	NM_003286.2	555	atGGag/atAAag	16/21	0.748855005270645	5	FACETS	0.717	0.636	0.803	0.179	0.159	0.201	SUBCLONAL	1	TRUE	1	0.748855005270645	5		285	720	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46271112	46271112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs6018612	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	164	448	0	ENST00000371998.3:c.3236C>T	p.Pro1079Leu	p.P1079L	ENST00000371998		1079	cCt/cTt	17/23	0.748855005270645	5	FACETS	0.853	0.782	0.928	0.213	0.195	0.232	CLONAL	1	TRUE	1	0.748855005270645	5		448	1090	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143248	24143248	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	308	797	0	ENST00000263121.7:c.480G>C	p.Lys160Asn	p.K160N	ENST00000263121	NM_003073.3	160	aaG/aaC	4/9	0.748855005270645	3	FACETS	0.895	0.843	0.949	0.448	0.421	0.475	CLONAL	1	TRUE	1	0.748855005270645	3		797	1263	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37081704	37081704	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1575594284	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	209	496	0	ENST00000231790.2:c.1586C>T	p.Ser529Phe	p.S529F	ENST00000231790	NM_000249.3	529	tCc/tTc	14/19	0.748855005270645	3	FACETS	0.925	0.861	0.992	0.463	0.43	0.496	CLONAL	1	TRUE	1	0.748855005270645	3		496	829	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623173	52623173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	270	520	2	ENST00000394830.3:c.2878G>A	p.Val960Ile	p.V960I	ENST00000394830	NM_018313.4	960	Gtt/Att	19/30	0.748855005270645	3	FACETS	1	0.961	1	0.515	0.484	0.547	CLONAL	1	TRUE	1	0.748855005270645	3		522	962	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799917	72799917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	162	436	0	ENST00000325599.8:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000325599	NM_018130.2	418	Gaa/Aaa	11/11	0.748855005270645	3	FACETS	0.908	0.836	0.983	0.454	0.418	0.492	CLONAL	1	TRUE	1	0.748855005270645	3		436	655	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274980	142274980	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	196	228	0	ENST00000350721.4:c.2080G>A	p.Asp694Asn	p.D694N	ENST00000350721	NM_001184.3	694	Gat/Aat	10/47	0.748855005270645	3	FACETS	0.972	0.916	1	0.972	0.916	1	CLONAL	2	TRUE	1	0.748855005270645	3		228	370	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155410	106155410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	193	394	0	ENST00000380013.4:c.311C>T	p.Ser104Phe	p.S104F	ENST00000380013	NM_001127208.2	104	tCt/tTt	3/11	0.748855005270645	4	FACETS	1	0.97	1	0.363	0.336	0.391	CLONAL	1	TRUE	1	0.748855005270645	4		394	828	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557981	187557981	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	175	436	0	ENST00000441802.2:c.3730C>G	p.Gln1244Glu	p.Q1244E	ENST00000441802	NM_005245.3	1244	Cag/Gag	5/27	0.727203502820465	4	FACETS	1	0.94	1	0.341	0.314	0.369	CLONAL	1	TRUE	1	0.748855005270645	4		436	799	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673780	176673780	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	186	355	0	ENST00000439151.2:c.4480G>C	p.Glu1494Gln	p.E1494Q	ENST00000439151	NM_022455.4	1494	Gag/Cag	10/23	0.748855005270645	2	FACETS	1	0.982	1	0.57	0.532	0.608	CLONAL	1	TRUE	0	0.748855005270645	2		355	436	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041035	112041035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	249	626	2	ENST00000368678.4:c.220G>A	p.Gly74Arg	p.G74R	ENST00000368678		74	Ggg/Agg	3/13	0.748855005270645	3	FACETS	1	0.97	1	0.528	0.495	0.563	CLONAL	1	TRUE	1	0.748855005270645	3		628	865	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630078	117630078	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	95	244	0	ENST00000368508.3:c.6448C>G	p.Leu2150Val	p.L2150V	ENST00000368508	NM_002944.2	2150	Ctg/Gtg	41/43	0.748855005270645	3	FACETS	0.945	0.848	1	0.473	0.424	0.523	CLONAL	1	TRUE	1	0.748855005270645	3		244	369	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706860	117706860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1175898010	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	180	389	0	ENST00000368508.3:c.2290G>A	p.Gly764Arg	p.G764R	ENST00000368508	NM_002944.2	764	Gga/Aga	15/43	0.748855005270645	3	FACETS	1	0.968	1	0.539	0.499	0.58	CLONAL	1	TRUE	1	0.748855005270645	3		389	613	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519266	137519266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	189	389	1	ENST00000367739.4:c.1372G>A	p.Asp458Asn	p.D458N	ENST00000367739	NM_000416.2	458	Gat/Aat	7/7	0.748855005270645	3	FACETS	1	0.965	1	0.532	0.494	0.571	CLONAL	1	TRUE	1	0.748855005270645	3		390	652	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439724	140439724	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	178	351	0	ENST00000288602.6:c.2015G>C	p.Gly672Ala	p.G672A	ENST00000288602	NM_004333.4	672	gGa/gCa	17/18	0.748855005270645	3	FACETS	1	0.974	1	0.554	0.513	0.596	CLONAL	1	TRUE	1	0.748855005270645	3		351	590	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894808	101894808	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	143	338	0	ENST00000374994.4:c.361C>T	p.Leu121Phe	p.L121F	ENST00000374994	NM_004612.2	121	Ctt/Ttt	3/9	0.642609937347067	4	FACETS	0.969	0.886	1	0.485	0.443	0.529	CLONAL	1	TRUE	2	0.748855005270645	4		338	689	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412379	139412380	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	649	858	0	ENST00000277541.6:c.1265_1266delinsTT	p.Pro422Leu	p.P422L	ENST00000277541	NM_017617.3	422	cCC/cTT	8/34	0.748855005270645	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.748855005270645	4		858	1499	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045910	47045910	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	342	854	0	ENST00000377604.3:c.2705G>C	p.Arg902Pro	p.R902P	ENST00000377604	NM_001204468.1	902	cGg/cCg	24/24	0.748855005270645	3	FACETS	1	0.967	1	0.515	0.487	0.543	CLONAL	1	TRUE	1	0.748855005270645	3		854	1220	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349589	70349589	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1162	305	731	0	ENST00000374080.3:c.3751G>C	p.Glu1251Gln	p.E1251Q	ENST00000374080		1251	Gag/Cag	27/45	0.642609937347067	4	FACETS	0.971	0.913	1	0.486	0.456	0.516	CLONAL	1	TRUE	2	0.748855005270645	4		731	1467	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70355038	70355038	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1313	332	770	1	ENST00000374080.3:c.4960C>T	p.Gln1654Ter	p.Q1654*	ENST00000374080		1654	Cag/Tag	36/45	0.642609937347067	4	FACETS	0.943	0.889	0.998	0.471	0.444	0.499	CLONAL	1	TRUE	2	0.748855005270645	4		771	1645	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244917	46244919	+	stop_gained	Nonsense_Mutation	TNP	GTC	GTC	TTT	novel	NA	P-0058402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	477	544	0	ENST00000334344.6:c.3011_3013delinsTTT	p.Ser1004_Gln1005delinsIleTer	p.S1004_Q1005delinsI*	ENST00000334344	NM_152641.2	1004	aGTCaa/aTTTaa	15/21	0.748855005270645	3	FACETS	0.988	0.951	1	0.988	0.951	1	CLONAL	2	TRUE	1	0.748855005270645	3		544	886	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003747	45003747	+	start_lost	Translation_Start_Site	SNP	G	G	T	novel	NA	P-0058415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	72	444	0	ENST00000558401.1:c.3G>T	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	atG/atT	1/4	0.594507801246994	1	FACETS	0.484	0.425	0.546	0.484	0.425	0.546	SUBCLONAL	1	TRUE	0	0.594507801246994	1		444	352	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567556006	NA	P-0058415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	421	672	0	ENST00000269305.4:c.298del	p.Gln100ArgfsTer23	p.Q100Rfs*23	ENST00000269305	NM_001126112.2	100	Cag/ag	4/11	0.588309852094918	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.594507801246994	2		672	681	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754067	42754067	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058415-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	295	494	0	ENST00000222329.4:c.285C>G	p.His95Gln	p.H95Q	ENST00000222329	NM_006494.2	95	caC/caG	3/4	0.543903835176478	5	FACETS	0.885	0.833	0.937	0.442	0.416	0.469	CLONAL	2	TRUE	1	0.594507801246994	5		494	1061	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349224	70349224	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	65	466	0	ENST00000374080.3:c.3636G>T	p.Gln1212His	p.Q1212H	ENST00000374080		1212	caG/caT	26/45	1	2	FACETS	0.564	0.489	0.646	0.564	0.489	0.646	SUBCLONAL	1	TRUE	1	0.34038556770833	2		466	677	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445865	49445865	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs946192879	NA	P-0058416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	74	587	0	ENST00000301067.7:c.1601C>T	p.Thr534Met	p.T534M	ENST00000301067	NM_003482.3	534	aCg/aTg	10/54	1	2	FACETS	0.49	0.428	0.557	0.49	0.428	0.557	SUBCLONAL	1	TRUE	1	0.34038556770833	2		587	888	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614839	23614839	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	43	386	0	ENST00000261584.4:c.3502G>A	p.Asp1168Asn	p.D1168N	ENST00000261584	NM_024675.3	1168	Gac/Aac	13/13	1	2	FACETS	0.439	0.367	0.52	0.439	0.367	0.52	SUBCLONAL	1	TRUE	1	0.34038556770833	2		386	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578199	7578200	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCAC	novel	NA	P-0058416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	117	461	0	ENST00000269305.4:c.646_649dup	p.Val217GlyfsTer6	p.V217Gfs*6	ENST00000269305	NM_001126112.2	217	gtg/gGTGGtg	6/11	0.320808525307597	1	FACETS	0.87	0.786	0.958	0.87	0.786	0.958	CLONAL	1	TRUE	0	0.34038556770833	1		461	656	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151270	202151270	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	104	413	0	ENST00000358485.4:c.1570C>G	p.Gln524Glu	p.Q524E	ENST00000358485	NM_001080125.1	524	Cag/Gag	9/9	0.160091727705928	2	FACETS	1	0.952	1	0.551	0.494	0.61	INDETERMINATE	1	TRUE	0	0.34038556770833	2		413	555	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193924	106193924	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	106	409	0	ENST00000380013.4:c.4386G>C	p.Lys1462Asn	p.K1462N	ENST00000380013	NM_001127208.2	1462	aaG/aaC	10/11	0.160091727705928	2	FACETS	1	0.955	1	0.555	0.499	0.614	INDETERMINATE	1	TRUE	0	0.34038556770833	2		409	561	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937993	76937993	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058416-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	42	412	0	ENST00000373344.5:c.2755G>T	p.Asp919Tyr	p.D919Y	ENST00000373344	NM_000489.3	919	Gat/Tat	9/35	1	2	FACETS	0.433	0.361	0.513	0.433	0.361	0.513	SUBCLONAL	1	TRUE	1	0.34038556770833	2		412	570	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	803	738	0				ENST00000310581	NM_198253.2	-/1132			0.426398609208958	8	FACETS	1	0.99	1	1	0.997	1	CLONAL	7	TRUE	2	0.426398609208958	8		738	1195	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983076	201983076	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	216	803	0	ENST00000359651.3:c.925G>C	p.Glu309Gln	p.E309Q	ENST00000359651		309	Gag/Cag	7/8	0.141397651821759	3	FACETS	1	0.958	1	0.348	0.323	0.375	INDETERMINATE	1	TRUE	0	0.426398609208958	3		803	1176	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206664990	206664990	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	120	685	0	ENST00000367120.3:c.1743C>A	p.Phe581Leu	p.F581L	ENST00000367120	NM_014002.3	581	ttC/ttA	18/22	0.141397651821759	3	FACETS	0.605	0.545	0.669	0.202	0.181	0.223	INDETERMINATE	1	TRUE	0	0.426398609208958	3		685	1128	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206665023	206665023	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	101	688	0	ENST00000367120.3:c.1776C>A	p.Phe592Leu	p.F592L	ENST00000367120	NM_014002.3	592	ttC/ttA	18/22	0.141397651821759	3	FACETS	0.513	0.457	0.572	0.171	0.152	0.191	INDETERMINATE	1	TRUE	0	0.426398609208958	3		688	1121	SUCCESS
FH	2271	MSKCC	GRCh37	1	241683007	241683007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	55	546	0	ENST00000366560.3:c.16C>T	p.Arg6Trp	p.R6W	ENST00000366560	NM_000143.3	6	Cgg/Tgg	1/10	0.141397651821759	3	FACETS	0.31	0.264	0.36	0.103	0.088	0.12	INDETERMINATE	1	TRUE	0	0.426398609208958	3		546	1011	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	71	244	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.529	0.461	0.601	0.529	0.461	0.601	SUBCLONAL	1	TRUE	1	0.426398609208958	2		244	630	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717612	89717612	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	168	464	1	ENST00000371953.3:c.638del	p.Pro213LeufsTer8	p.P213Lfs*8	ENST00000371953	NM_000314.4	213	Cct/ct	7/9	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.426398609208958	2		465	535	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741423	17741423	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	185	896	0	ENST00000250003.3:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000250003	NM_002478.4	32	Gac/Tac	1/3	0.212707561216473	2	FACETS	0.701	0.646	0.759	0.35	0.323	0.38	INDETERMINATE	1	TRUE	0	0.426398609208958	2		896	1238	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905387	11905387	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	58	410	0	ENST00000396373.4:c.37G>A	p.Glu13Lys	p.E13K	ENST00000396373	NM_001987.4	13	Gaa/Aaa	2/8	0.426398609208958	2	FACETS	0.419	0.359	0.484	0.209	0.179	0.242	SUBCLONAL	1	TRUE	0	0.426398609208958	2		410	650	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435896	49435896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1417	81	907	0	ENST00000301067.7:c.6085C>T	p.Pro2029Ser	p.P2029S	ENST00000301067	NM_003482.3	2029	Cct/Tct	28/54	0.426398609208958	3	FACETS	0.308	0.27	0.349	0.154	0.135	0.175	SUBCLONAL	1	TRUE	1	0.426398609208958	3		907	1498	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487162	56487162	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs2229045	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	269	573	0	ENST00000267101.3:c.1308G>C	p.Leu436Phe	p.L436F	ENST00000267101	NM_001982.3	436	ttG/ttC	12/28	0.426398609208958	3	FACETS	0.805	0.756	0.855	0.805	0.756	0.855	CLONAL	2	TRUE	1	0.426398609208958	3		573	951	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487277	56487277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035001455	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	338	653	0	ENST00000267101.3:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000267101	NM_001982.3	475	Cgg/Tgg	12/28	0.426398609208958	3	FACETS	0.859	0.813	0.906	0.859	0.813	0.906	CLONAL	2	TRUE	1	0.426398609208958	3		653	1119	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489566	56489566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	311	611	0	ENST00000267101.3:c.2031G>A	p.Met677Ile	p.M677I	ENST00000267101	NM_001982.3	677	atG/atA	17/28	0.426398609208958	3	FACETS	0.809	0.763	0.856	0.809	0.763	0.856	CLONAL	2	TRUE	1	0.426398609208958	3		611	1094	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915249	32915249	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555284846	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	72	563	0	ENST00000380152.3:c.6757C>G	p.Leu2253Val	p.L2253V	ENST00000380152		2253	Ctt/Gtt	11/27	0.332549477923748	2	FACETS	0.478	0.417	0.544	0.239	0.208	0.272	SUBCLONAL	1	TRUE	0	0.426398609208958	2		563	706	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304435	91304435	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	86	369	0	ENST00000355112.3:c.1832C>T	p.Ser611Leu	p.S611L	ENST00000355112	NM_000057.2	611	tCa/tTa	7/22	0.212707561216473	2	FACETS	0.76	0.674	0.851	0.38	0.337	0.426	INDETERMINATE	1	TRUE	0	0.426398609208958	2		369	531	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823921	3823921	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1371	79	784	0	ENST00000262367.5:c.2294C>G	p.Ser765Cys	p.S765C	ENST00000262367	NM_004380.2	765	tCt/tGt	13/31	0.426398609208958	3	FACETS	0.31	0.271	0.352	0.103	0.09	0.118	SUBCLONAL	1	TRUE	0	0.426398609208958	3		784	1450	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50827573	50827573	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	91	402	0	ENST00000398568.2:c.2458C>T	p.Gln820Ter	p.Q820*	ENST00000398568	NM_001042412.1	820	Caa/Taa	16/18	0.368287778919578	1	FACETS	0.665	0.592	0.742	0.665	0.592	0.742	SUBCLONAL	1	TRUE	0	0.426398609208958	1		402	505	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063380	67063380	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1376636053	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	95	382	0	ENST00000412916.2:c.70G>A	p.Glu24Lys	p.E24K	ENST00000412916		24	Gag/Aag	1/6	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.426398609208958	NA		382	799	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934382	81934382	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	100	627	0	ENST00000359376.3:c.1359C>G	p.Ile453Met	p.I453M	ENST00000359376	NM_002661.3	453	atC/atG	14/33	0.280475815852716	5	FACETS	0.594	0.529	0.664	0.119	0.105	0.133	SUBCLONAL	1	TRUE	0	0.426398609208958	5		627	1294	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935636	15935636	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532511938	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	77	456	0	ENST00000268712.3:c.7297G>A	p.Glu2433Lys	p.E2433K	ENST00000268712	NM_006311.3	2433	Gag/Aag	46/46	1	2	FACETS	0.52	0.456	0.588	0.52	0.456	0.588	SUBCLONAL	1	TRUE	1	0.426398609208958	2		456	695	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15952175	15952175	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	98	663	0	ENST00000268712.3:c.6520G>C	p.Glu2174Gln	p.E2174Q	ENST00000268712	NM_006311.3	2174	Gag/Cag	41/46	1	2	FACETS	0.432	0.384	0.483	0.432	0.384	0.483	SUBCLONAL	1	TRUE	1	0.426398609208958	2		663	1065	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684020	29684020	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774781617	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	181	594	0	ENST00000356175.3:c.7718G>A	p.Arg2573His	p.R2573H	ENST00000356175	NM_000267.3	2573	cGt/cAt	52/57	0.426398609208958	3	FACETS	0.893	0.823	0.967	0.447	0.411	0.484	CLONAL	1	TRUE	1	0.426398609208958	3		594	1153	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649024	37649026	+	frameshift_variant	Frame_Shift_Del	DEL	GAG	GAG	AA	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	74	500	1	ENST00000447079.4:c.2129_2131delinsAA	p.Gly710GlufsTer43	p.G710Efs*43	ENST00000447079	NM_015083.1	710	gGAGaa/gAAaa	4/14	0.426398609208958	3	FACETS	0.469	0.409	0.533	0.234	0.204	0.267	SUBCLONAL	1	TRUE	1	0.426398609208958	3		501	898	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649041	37649041	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	69	397	0	ENST00000447079.4:c.2146G>C	p.Glu716Gln	p.E716Q	ENST00000447079	NM_015083.1	716	Gaa/Caa	4/14	0.426398609208958	3	FACETS	0.555	0.483	0.634	0.278	0.241	0.317	SUBCLONAL	1	TRUE	1	0.426398609208958	3		397	707	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687212	37687212	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1266	122	794	0	ENST00000447079.4:c.4116G>C	p.Lys1372Asn	p.K1372N	ENST00000447079	NM_015083.1	1372	aaG/aaC	14/14	0.426398609208958	3	FACETS	0.5	0.45	0.553	0.25	0.225	0.277	SUBCLONAL	1	TRUE	1	0.426398609208958	3		794	1388	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678001	58678001	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	52	198	0	ENST00000305921.3:c.226C>G	p.Arg76Gly	p.R76G	ENST00000305921	NM_003620.3	76	Cgc/Ggc	1/6	0.426398609208958	3	FACETS	0.779	0.665	0.902	0.389	0.332	0.451	CLONAL	1	TRUE	1	0.426398609208958	3		198	380	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936301	78936301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1602	99	954	0	ENST00000306801.3:c.3733G>A	p.Glu1245Lys	p.E1245K	ENST00000306801	NM_020761.2	1245	Gag/Aag	32/34	0.426398609208958	3	FACETS	0.331	0.294	0.371	0.166	0.147	0.186	SUBCLONAL	1	TRUE	1	0.426398609208958	3		954	1701	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208389	5208389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771526918	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	126	718	0	ENST00000357368.4:c.5501G>A	p.Arg1834Gln	p.R1834Q	ENST00000357368	NM_002850.3	1834	cGg/cAg	36/38	1	2	FACETS	0.565	0.511	0.623	0.565	0.511	0.623	SUBCLONAL	1	TRUE	1	0.426398609208958	2		718	1046	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220114	5220114	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1204949982	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	110	863	2	ENST00000357368.4:c.3601C>T	p.Gln1201Ter	p.Q1201*	ENST00000357368	NM_002850.3	1201	Cag/Tag	22/38	1	2	FACETS	0.443	0.397	0.492	0.443	0.397	0.492	SUBCLONAL	1	TRUE	1	0.426398609208958	2		865	1165	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054686	13054686	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	114	600	0	ENST00000316448.5:c.1213G>C	p.Glu405Gln	p.E405Q	ENST00000316448	NM_004343.3	405	Gag/Cag	9/9	0.324083471205995	3	FACETS	0.637	0.573	0.706			1	SUBCLONAL	1	TRUE	NA	0.426398609208958	3		600	1018	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50138849	50138849	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1837	105	1121	1	ENST00000246792.3:c.641C>T	p.Pro214Leu	p.P214L	ENST00000246792	NM_006270.3	214	cCc/cTc	6/6	0.116776843722313	5	FACETS	0.416	0.37	0.464	0.139	0.123	0.155	INDETERMINATE	1	TRUE	2	0.426398609208958	5		1122	1942	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537966	212537966	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	103	484	0	ENST00000342788.4:c.1639G>C	p.Glu547Gln	p.E547Q	ENST00000342788	NM_005235.2	547	Gag/Cag	14/28	1	2	FACETS	0.724	0.649	0.804	0.724	0.649	0.804	SUBCLONAL	1	TRUE	1	0.426398609208958	2		484	667	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440021	220440021	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	299	1126	0	ENST00000243786.2:c.874C>G	p.His292Asp	p.H292D	ENST00000243786	NM_002191.3	292	Cat/Gat	2/2	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.426398609208958	2		1126	1392	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017724	31017724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1005458245	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1365	153	801	1	ENST00000375687.4:c.586G>A	p.Asp196Asn	p.D196N	ENST00000375687	NM_015338.5	196	Gat/Aat	8/13	0.426398609208958	4	FACETS	0.674	0.615	0.737	0.225	0.205	0.246	SUBCLONAL	1	TRUE	1	0.426398609208958	4		802	1518	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023870	31023870	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1463	207	814	0	ENST00000375687.4:c.3355G>C	p.Glu1119Gln	p.E1119Q	ENST00000375687	NM_015338.5	1119	Gag/Cag	13/13	0.426398609208958	4	FACETS	0.829	0.767	0.895	0.276	0.255	0.299	CLONAL	1	TRUE	1	0.426398609208958	4		814	1670	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024021	31024021	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1650	91	799	0	ENST00000375687.4:c.3506C>G	p.Ser1169Cys	p.S1169C	ENST00000375687	NM_015338.5	1169	tCt/tGt	13/13	0.426398609208958	4	FACETS	0.35	0.309	0.394	0.117	0.103	0.132	SUBCLONAL	1	TRUE	1	0.426398609208958	4		799	1741	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067878	30067878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	203	708	0	ENST00000338641.4:c.1063G>A	p.Glu355Lys	p.E355K	ENST00000338641	NM_000268.3	355	Gag/Aag	11/16	1	2	FACETS	0.907	0.84	0.976	0.907	0.84	0.976	CLONAL	1	TRUE	1	0.426398609208958	2		708	1050	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537106	41537106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	115	393	0	ENST00000263253.7:c.1933G>A	p.Glu645Lys	p.E645K	ENST00000263253	NM_001429.3	645	Gaa/Aaa	10/31	1	2	FACETS	0.806	0.727	0.889	0.806	0.727	0.889	CLONAL	1	TRUE	1	0.426398609208958	2		393	669	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572505	41572505	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1253	258	1076	0	ENST00000263253.7:c.5034G>C	p.Glu1678Asp	p.E1678D	ENST00000263253	NM_001429.3	1678	gaG/gaC	30/31	1	2	FACETS	0.801	0.748	0.856	0.801	0.748	0.856	CLONAL	1	TRUE	1	0.426398609208958	2		1076	1511	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573790	41573790	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	257	963	0	ENST00000263253.7:c.6075G>C	p.Leu2025Phe	p.L2025F	ENST00000263253	NM_001429.3	2025	ttG/ttC	31/31	1	2	FACETS	0.9	0.841	0.961	0.9	0.841	0.961	CLONAL	1	TRUE	1	0.426398609208958	2		963	1339	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574171	41574171	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	187	762	0	ENST00000263253.7:c.6456G>C	p.Gln2152His	p.Q2152H	ENST00000263253	NM_001429.3	2152	caG/caC	31/31	1	2	FACETS	0.872	0.805	0.941	0.872	0.805	0.941	CLONAL	1	TRUE	1	0.426398609208958	2		762	1006	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851565	134851565	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	117	633	0	ENST00000398015.3:c.971C>G	p.Ser324Ter	p.S324*	ENST00000398015	NM_004441.4	324	tCa/tGa	5/16	0.310503498990401	4	FACETS	0.666	0.598	0.737	0.166	0.149	0.185	SUBCLONAL	1	TRUE	0	0.426398609208958	4		633	1176	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665358	138665358	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1261	554	912	0	ENST00000330315.3:c.207G>C	p.Glu69Asp	p.E69D	ENST00000330315	NM_023067.3	69	gaG/gaC	1/1	0.310503498990401	4	FACETS	1	0.973	1	0.511	0.489	0.532	CLONAL	2	TRUE	0	0.426398609208958	4		912	1815	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665080	182665080	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4624	1087	372	0	ENST00000292782.4:c.646C>A	p.Leu216Ile	p.L216I	ENST00000292782	NM_020640.2	216	Ctt/Att	6/7	0.426398609208958	44	FACETS	0.987	0.955	1			1	CLONAL	9	TRUE	NA	0.426398609208958	44		372	5711	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447327	187447327	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776120197	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1324	224	847	1	ENST00000232014.4:c.866G>A	p.Arg289Gln	p.R289Q	ENST00000232014	NM_001130845.1	289	cGa/cAa	5/10	0.426398609208958	3	FACETS	0.823	0.764	0.885			1	CLONAL	1	TRUE	NA	0.426398609208958	3		848	1548	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961244	1961244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	85	614	0	ENST00000382891.5:c.3032C>T	p.Ser1011Leu	p.S1011L	ENST00000382891	NM_133335.3	1011	tCa/tTa	17/22	0.229830856760729	3	FACETS	0.486	0.428	0.548	0.243	0.214	0.274	INDETERMINATE	1	TRUE	1	0.426398609208958	3		614	996	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383669	84383669	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	186	664	0	ENST00000321945.7:c.1183G>C	p.Glu395Gln	p.E395Q	ENST00000321945	NM_139076.2	395	Gaa/Caa	9/9	0.229830856760729	3	FACETS	1	0.933	1	0.506	0.467	0.547	INDETERMINATE	1	TRUE	1	0.426398609208958	3		664	1046	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156087	106156087	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	58	342	0	ENST00000380013.4:c.988G>C	p.Glu330Gln	p.E330Q	ENST00000380013	NM_001127208.2	330	Gag/Cag	3/11	0.229830856760729	3	FACETS	0.556	0.477	0.641	0.278	0.238	0.321	INDETERMINATE	1	TRUE	1	0.426398609208958	3		342	594	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158407	106158407	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	83	277	0	ENST00000380013.4:c.3308A>C	p.Asn1103Thr	p.N1103T	ENST00000380013	NM_001127208.2	1103	aAt/aCt	3/11	0.229830856760729	3	FACETS	1	0.899	1	0.508	0.45	0.57	INDETERMINATE	1	TRUE	1	0.426398609208958	3		277	465	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067017	143067017	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	83	507	0	ENST00000262992.4:c.1696G>C	p.Asp566His	p.D566H	ENST00000262992	NM_001101669.1	566	Gat/Cat	16/24	0.229830856760729	3	FACETS	0.559	0.492	0.631	0.279	0.246	0.316	INDETERMINATE	1	TRUE	1	0.426398609208958	3		507	845	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541007	187541007	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	109	479	0	ENST00000441802.2:c.6733G>C	p.Glu2245Gln	p.E2245Q	ENST00000441802	NM_005245.3	2245	Gag/Cag	10/27	0.229830856760729	3	FACETS	0.849	0.762	0.94	0.424	0.381	0.47	INDETERMINATE	1	TRUE	1	0.426398609208958	3		479	731	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409179	31409179	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1815	143	598	0	ENST00000344624.3:c.3838G>A	p.Asp1280Asn	p.D1280N	ENST00000344624		1280	Gac/Aac	30/33	0.426398609208958	8	FACETS	0.781	0.708	0.857	0.13	0.118	0.143	SUBCLONAL	1	TRUE	2	0.426398609208958	8		598	1958	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449414	31449414	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1814	182	514	0	ENST00000344624.3:c.2795T>C	p.Val932Ala	p.V932A	ENST00000344624		932	gTt/gCt	19/33	0.426398609208958	8	FACETS	0.975	0.895	1	0.162	0.149	0.177	CLONAL	1	TRUE	2	0.426398609208958	8		514	1996	SUCCESS
APC	324	MSKCC	GRCh37	5	112177968	112177968	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1246580689	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	110	469	1	ENST00000257430.4:c.6677G>A	p.Arg2226Gln	p.R2226Q	ENST00000257430	NM_000038.5	2226	cGa/cAa	16/16	0.212707561216473	2	FACETS	0.857	0.772	0.947	0.429	0.386	0.474	INDETERMINATE	1	TRUE	0	0.426398609208958	2		470	602	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638683	176638683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	179	694	1	ENST00000439151.2:c.3283G>A	p.Gly1095Ser	p.G1095S	ENST00000439151	NM_022455.4	1095	Ggc/Agc	5/23	0.426398609208958	3	FACETS	0.777	0.714	0.842	0.388	0.357	0.421	SUBCLONAL	1	TRUE	1	0.426398609208958	3		695	1311	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696721	176696721	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	130	475	0	ENST00000439151.2:c.5422C>T	p.His1808Tyr	p.H1808Y	ENST00000439151	NM_022455.4	1808	Cac/Tac	16/23	0.426398609208958	3	FACETS	0.844	0.765	0.926	0.422	0.382	0.463	CLONAL	1	TRUE	1	0.426398609208958	3		475	877	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158595	26158595	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769305558	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	254	576	0	ENST00000289316.2:c.198C>A	p.Phe66Leu	p.F66L	ENST00000289316	NM_138720.2	66	ttC/ttA	1/2	0.426398609208958	4	FACETS	0.761	0.712	0.811	0.761	0.712	0.811	SUBCLONAL	2	TRUE	2	0.426398609208958	4		576	1117	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652020	36652020	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1407742055	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	823	1109	1	ENST00000244741.5:c.142C>T	p.Arg48Ter	p.R48*	ENST00000244741	NM_000389.4	48	Cga/Tga	2/3	0.260989679369121	3	FACETS	0.934	0.906	0.962			1	CLONAL	3	TRUE	NA	0.426398609208958	3		1110	1671	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005453	150005453	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	64	655	0	ENST00000253339.5:c.772C>G	p.Pro258Ala	p.P258A	ENST00000253339		258	Cca/Gca	3/7	1	2	FACETS	0.36	0.311	0.414	0.36	0.311	0.414	SUBCLONAL	1	TRUE	1	0.426398609208958	2		655	834	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016336	150016336	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	77	441	1	ENST00000253339.5:c.370C>T	p.Gln124Ter	p.Q124*	ENST00000253339		124	Cag/Tag	2/7	1	2	FACETS	0.626	0.55	0.707	0.626	0.55	0.707	SUBCLONAL	1	TRUE	1	0.426398609208958	2		442	577	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372774	81372774	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	97	423	0	ENST00000222390.5:c.760G>T	p.Gly254Cys	p.G254C	ENST00000222390	NM_000601.4	254	Ggc/Tgc	7/18	0.373794157101885	3	FACETS	0.698	0.622	0.779	0.233	0.207	0.26	SUBCLONAL	1	TRUE	0	0.426398609208958	3		423	791	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845571	128845571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1156577972	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	82	851	0	ENST00000249373.3:c.868C>T	p.Arg290Cys	p.R290C	ENST00000249373	NM_005631.4	290	Cgc/Tgc	4/12	0.212707561216473	2	FACETS	0.367	0.322	0.415	0.184	0.161	0.208	INDETERMINATE	1	TRUE	0	0.426398609208958	2		851	1048	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38135882	38135882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	171	645	0	ENST00000317025.8:c.3809G>A	p.Arg1270Lys	p.R1270K	ENST00000317025	NM_023034.1	1270	aGa/aAa	22/24	1	2	FACETS	0.893	0.822	0.968	0.893	0.822	0.968	CLONAL	1	TRUE	1	0.426398609208958	2		645	898	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38135901	38135901	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	157	584	0	ENST00000317025.8:c.3790G>C	p.Asp1264His	p.D1264H	ENST00000317025	NM_023034.1	1264	Gat/Cat	22/24	1	2	FACETS	0.918	0.842	0.998	0.918	0.842	0.998	CLONAL	1	TRUE	1	0.426398609208958	2		584	802	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38283688	38283688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	202	747	0	ENST00000425967.3:c.790G>A	p.Glu264Lys	p.E264K	ENST00000425967	NM_001174067.1	264	Gag/Aag	7/19	1	2	FACETS	0.956	0.886	1	0.956	0.886	1	CLONAL	1	TRUE	1	0.426398609208958	2		747	991	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572724	141572724	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	119	650	0	ENST00000220592.5:c.346G>A	p.Glu116Lys	p.E116K	ENST00000220592	NM_012154.3	116	Gag/Aag	4/19	0.327537338266285	3	FACETS	0.548	0.493	0.607	0.274	0.246	0.304	SUBCLONAL	1	TRUE	1	0.426398609208958	3		650	1235	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738304	145738304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1206178457	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1567	209	1206	0	ENST00000428558.2:c.2681G>A	p.Arg894Lys	p.R894K	ENST00000428558	NM_004260.3	894	aGa/aAa	16/22	0.327537338266285	3	FACETS	0.67	0.619	0.723	0.335	0.309	0.362	SUBCLONAL	1	TRUE	1	0.426398609208958	3		1206	1776	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128206794	128206794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	92	514	1	ENST00000265960.3:c.1429G>A	p.Glu477Lys	p.E477K	ENST00000265960	NM_001006617.1	477	Gaa/Aaa	11/12	1	2	FACETS	0.524	0.465	0.587	0.524	0.465	0.587	SUBCLONAL	1	TRUE	1	0.426398609208958	2		515	824	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781365	135781365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs796053458	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	132	828	0	ENST00000298552.3:c.1600G>A	p.Glu534Lys	p.E534K	ENST00000298552	NM_001162426.1	534	Gag/Aag	15/23	1	2	FACETS	0.569	0.515	0.625	0.569	0.515	0.625	SUBCLONAL	1	TRUE	1	0.426398609208958	2		828	1089	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787825	135787825	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	110	437	0	ENST00000298552.3:c.757C>G	p.His253Asp	p.H253D	ENST00000298552	NM_001162426.1	253	Cat/Gat	9/23	1	2	FACETS	0.824	0.742	0.911	0.824	0.742	0.911	CLONAL	1	TRUE	1	0.426398609208958	2		437	626	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929065	44929065	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	90	343	0	ENST00000377967.4:c.2165G>C	p.Gly722Ala	p.G722A	ENST00000377967	NM_021140.2	722	gGa/gCa	17/29	0.426398609208958	2	FACETS	0.601	0.533	0.674			1	SUBCLONAL	1	TRUE	NA	0.426398609208958	2		343	702	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226259052	226259052	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	30	88	0	ENST00000366813.1:c.283G>C	p.Glu95Gln	p.E95Q	ENST00000366813		95	Gag/Cag	3/3	0.141397651821759	3	FACETS	1	0.916	1	0.409	0.335	0.491	INDETERMINATE	1	TRUE	0	0.426398609208958	3		88	139	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058460-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	80	302	0				ENST00000310581	NM_198253.2	-/1132			0.204053761233826	1	FACETS	0.526	0.47	0.585	0.526	0.47	0.585	INDETERMINATE	1	TRUE	0	0.756323750634077	1		302	250	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0058460-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	332	425	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.394799737947899	3	FACETS	0.915	0.873	0.957	0.915	0.873	0.957	INDETERMINATE	2	TRUE	1	0.756323750634077	3		425	661	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690570	88690570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058460-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	62	349	0	ENST00000360948.2:c.460G>A	p.Glu154Lys	p.E154K	ENST00000360948	NM_001012338.2	154	Gaa/Aaa	5/19	1	2	FACETS	0.359	0.31	0.411	0.359	0.31	0.411	SUBCLONAL	1	TRUE	1	0.756323750634077	2		349	457	SUCCESS
BLM	641	MSKCC	GRCh37	15	91352370	91352370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058460-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	95	329	0	ENST00000355112.3:c.3755C>T	p.Ser1252Phe	p.S1252F	ENST00000355112	NM_000057.2	1252	tCt/tTt	20/22	1	2	FACETS	0.552	0.494	0.613	0.552	0.494	0.613	SUBCLONAL	1	TRUE	1	0.756323750634077	2		329	455	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866441	42866441	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770444484	NA	P-0058460-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	222	1017	1	ENST00000398585.3:c.191C>T	p.Pro64Leu	p.P64L	ENST00000398585	NM_001135099.1	64	cCc/cTc	3/14	0.484302955063585	1	FACETS	0.742	0.698	0.786	0.742	0.698	0.786	SUBCLONAL	1	TRUE	0	0.756323750634077	1		1018	492	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932677	49932677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754028685	NA	P-0058460-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	111	534	0	ENST00000296474.3:c.3194C>T	p.Ala1065Val	p.A1065V	ENST00000296474	NM_002447.2	1065	gCg/gTg	14/20	0.419179986662296	3	FACETS	0.614	0.553	0.679	0.307	0.276	0.34	INDETERMINATE	1	TRUE	1	0.756323750634077	3		534	659	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444310	50444311	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058460-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	198	539	0	ENST00000331340.3:c.240_241delinsAA	p.Asp81Asn	p.D81N	ENST00000331340	NM_006060.4	80	gaGGat/gaAAat	4/8	0.183155690935212	2	FACETS	0.799	0.744	0.856	0.4	0.372	0.428	INDETERMINATE	1	TRUE	0	0.756323750634077	2		539	655	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0058462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	13	265	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		265	622	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0058464-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	246	593	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.441119846134462	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.441119846134462	2		593	553	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375990	8375990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142960593	NA	P-0058464-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	32	381	0	ENST00000356435.5:c.4607G>A	p.Arg1536His	p.R1536H	ENST00000356435		1536	cGt/cAt	28/35	0.441119846134462	3	FACETS	0.287	0.232	0.35	0.096	0.077	0.117	SUBCLONAL	1	TRUE	0	0.441119846134462	3		381	616	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285296	212285296	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058464-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	24	352	0	ENST00000342788.4:c.3005A>C	p.Lys1002Thr	p.K1002T	ENST00000342788	NM_005235.2	1002	aAg/aCg	25/28	0.110009062340835	5	FACETS	0.37	0.289	0.463	0.123	0.096	0.155	INDETERMINATE	1	TRUE	2	0.441119846134462	5		352	489	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426718	49426718	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886041106	NA	P-0058464-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	302	652	1	ENST00000301067.7:c.11770C>T	p.Gln3924Ter	p.Q3924*	ENST00000301067	NM_003482.3	3924	Cag/Tag	39/54	0.441119846134462	3	FACETS	0.953	0.901	1	0.953	0.901	1	CLONAL	2	TRUE	1	0.441119846134462	3		653	877	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145705	61145705	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058464-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	179	370	0	ENST00000295025.8:c.817G>A	p.Glu273Lys	p.E273K	ENST00000295025	NM_002908.2	273	Gaa/Aaa	7/11	0.269975106870104	3	FACETS	0.845	0.784	0.908	0.845	0.784	0.908	CLONAL	2	TRUE	1	0.441119846134462	3		370	586	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347159	89347159	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058464-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	119	567	0	ENST00000301030.4:c.5791C>A	p.Leu1931Met	p.L1931M	ENST00000301030	NM_001256183.1	1931	Ctg/Atg	9/13	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.441119846134462	2		567	482	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797256	32797256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058464-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	219	491	0	ENST00000374899.4:c.1853C>T	p.Ala618Val	p.A618V	ENST00000374899	NM_018833.2	618	gCc/gTc	11/12	0.229894683262614	2	FACETS	0.911	0.855	0.968	0.911	0.855	0.968	INDETERMINATE	2	TRUE	0	0.441119846134462	2		491	545	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974692	21974693	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0058464-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	372	503	0	ENST00000304494.5:c.133_134dup	p.Arg46ValfsTer8	p.R46Vfs*8	ENST00000304494	NM_000077.4	45	ggt/ggGGt	1/3	0.441119846134462	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.441119846134462	3		503	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0058481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	268	328	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.441015839673264	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.459868133593668	1		328	770	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953038	2953038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747530675	NA	P-0058481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	431	594	2	ENST00000396946.4:c.2902G>A	p.Ala968Thr	p.A968T	ENST00000396946	NM_032415.4	968	Gcc/Acc	22/25	0.460145996579675	3	FACETS	0.996	0.951	1	0.996	0.951	1	CLONAL	2	TRUE	1	0.459868133593668	3		596	1157	SUCCESS
APC	324	MSKCC	GRCh37	5	112175162	112175162	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561588104	NA	P-0058481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	182	573	2	ENST00000257430.4:c.3871C>T	p.Gln1291Ter	p.Q1291*	ENST00000257430	NM_000038.5	1291	Cag/Tag	16/16	0.459868133593668	1	FACETS	0.958	0.888	1	0.958	0.888	1	CLONAL	1	TRUE	0	0.459868133593668	1		575	636	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268138	153268138	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1406877044	NA	P-0058481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	360	487	0	ENST00000281708.4:c.670C>T	p.Arg224Ter	p.R224*	ENST00000281708	NM_033632.3	224	Cga/Tga	4/12	1	2	FACETS	0.895	0.852	0.938	1	0.996	1	CLONAL	2	TRUE	1	0.459868133593668	2		487	875	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78831645	78831645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572833876	NA	P-0058481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	182	556	0	ENST00000306801.3:c.1454G>A	p.Arg485Gln	p.R485Q	ENST00000306801	NM_020761.2	485	cGa/cAa	13/34	1	2	FACETS	0.869	0.802	0.938	0.869	0.802	0.938	CLONAL	1	TRUE	1	0.459868133593668	2		556	911	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420598	49420598	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	96	694	0	ENST00000301067.7:c.15151A>G	p.Asn5051Asp	p.N5051D	ENST00000301067	NM_003482.3	5051	Aac/Gac	48/54	1	2	FACETS	0.376	0.334	0.422	0.376	0.334	0.422	SUBCLONAL	1	TRUE	1	0.459868133593668	2		694	1109	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514784	103514784	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	112	633	0	ENST00000355739.4:c.1285G>T	p.Asp429Tyr	p.D429Y	ENST00000355739	NM_000123.3	429	Gat/Tat	8/15	0.240785345081358	1	FACETS	0.416	0.373	0.461	0.416	0.373	0.461	INDETERMINATE	1	TRUE	0	0.459868133593668	1		633	902	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533631	63533631	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	55	699	0	ENST00000307078.5:c.1523A>C	p.Lys508Thr	p.K508T	ENST00000307078	NM_004655.3	508	aAg/aCg	6/11	0.240785345081358	1	FACETS	0.177	0.15	0.206	0.177	0.15	0.206	INDETERMINATE	1	TRUE	0	0.459868133593668	1		699	1042	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396230	139396230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1313068805	NA	P-0058481-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	93	650	0	ENST00000277541.6:c.5608G>A	p.Asp1870Asn	p.D1870N	ENST00000277541	NM_017617.3	1870	Gac/Aac	30/34	1	2	FACETS	0.402	0.357	0.451	0.402	0.357	0.451	SUBCLONAL	1	TRUE	1	0.459868133593668	2		650	1005	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214364	36214364	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	270	799	0	ENST00000222270.7:c.3018C>G	p.Asp1006Glu	p.D1006E	ENST00000222270	NM_014727.1	1006	gaC/gaG	7/37	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.911238371434267	2		799	588	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	1126	302	0				ENST00000310581	NM_198253.2	-/1132			0.763907170850042	7	FACETS	0.997	0.98	1	0.997	0.98	1	CLONAL	6	TRUE	1	0.763907170850042	7		302	1434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579408	7579430	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGGGCCAGGAGGGGGCTGGTG	CAGGGGCCAGGAGGGGGCTGGTG	-	rs886041861	NA	P-0058486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	590	1035	0	ENST00000269305.4:c.257_279del	p.Ala86ValfsTer55	p.A86Vfs*55	ENST00000269305	NM_001126112.2	86	gCACCAGCCCCCTCCTGGCCCCTG/g	4/11	0.763907170850042	2	FACETS	0.9	0.875	0.925	0.9	0.875	0.925	CLONAL	2	TRUE	0	0.763907170850042	2		1035	858	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008424	71008424	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	123	692	0	ENST00000318789.4:c.2008G>A	p.Glu670Lys	p.E670K	ENST00000318789	NM_032682.5	670	Gaa/Aaa	21/21	0.364905343163225	2	FACETS	0.652	0.593	0.714	0.326	0.296	0.357	INDETERMINATE	1	TRUE	0	0.763907170850042	2		692	494	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41560064	41560064	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	91	536	0	ENST00000263253.7:c.3736G>T	p.Glu1246Ter	p.E1246*	ENST00000263253	NM_001429.3	1246	Gaa/Taa	22/31	0.462094305603733	1	FACETS	0.422	0.378	0.468	0.422	0.378	0.468	SUBCLONAL	1	TRUE	0	0.763907170850042	1		536	349	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518644	204518644	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	85	666	0	ENST00000367182.3:c.1307C>T	p.Pro436Leu	p.P436L	ENST00000367182	NM_001278516.1	436	cCa/cTa	11/11	0.417369699170111	2	FACETS	0.347	0.307	0.39	0.174	0.153	0.195	INDETERMINATE	1	TRUE	0	0.763907170850042	2		666	641	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562665	95562665	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	113	837	0	ENST00000393063.1:c.4592C>T	p.Ser1531Leu	p.S1531L	ENST00000393063	NM_030621.3	1531	tCa/tTa	24/28	NA	2	FACETS	0.418	0.377	0.463			1	INDETERMINATE	1	TRUE	NA	0.763907170850042	2		837	707	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39576601	39576601	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0058486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	28	280	0	ENST00000262039.4:c.892-1G>C		p.X298_splice	ENST00000262039	NM_002647.2	298			0.64884669266225	3	FACETS	0.4	0.321	0.49	0.2	0.16	0.245	SUBCLONAL	1	TRUE	1	0.763907170850042	3		280	253	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6227098	6227098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1445603115	NA	P-0058486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	143	953	1	ENST00000252674.7:c.436G>A	p.Glu146Lys	p.E146K	ENST00000252674	NM_005934.3	146	Gaa/Aaa	5/12	0.719813354757011	3	FACETS	0.457	0.415	0.5	0.228	0.207	0.25	SUBCLONAL	1	TRUE	1	0.763907170850042	3		954	1133	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990433	69990433	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	71	438	0	ENST00000394351.3:c.392A>G	p.Asn131Ser	p.N131S	ENST00000394351	NM_000248.3	131	aAt/aGt	4/9	0.364905343163225	2	FACETS	0.639	0.563	0.719	0.319	0.281	0.36	INDETERMINATE	1	TRUE	0	0.763907170850042	2		438	291	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047220	180047220	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	127	976	0	ENST00000261937.6:c.2495C>T	p.Ser832Phe	p.S832F	ENST00000261937	NM_182925.4	832	tCc/tTc	17/30	0.763907170850042	1	FACETS	0.342	0.31	0.375	0.342	0.31	0.375	SUBCLONAL	1	TRUE	0	0.763907170850042	1		976	601	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635165	87635165	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058486-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	98	709	0	ENST00000277120.3:c.2217G>C	p.Glu739Asp	p.E739D	ENST00000277120		739	gaG/gaC	18/19	1	2	FACETS	0.413	0.368	0.459	0.413	0.368	0.459	SUBCLONAL	1	TRUE	1	0.763907170850042	2		709	622	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0058488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	119	425	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.699278998888402	3	FACETS	0.961	0.887	1	0.961	0.887	1	CLONAL	2	TRUE	1	0.699278998888402	3		425	239	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259244	89259244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	103	622	0	ENST00000336596.2:c.388G>A	p.Asp130Asn	p.D130N	ENST00000336596	NM_005233.5	130	Gat/Aat	3/17	1	2	FACETS	0.966	0.876	1	0.966	0.876	1	CLONAL	1	TRUE	1	0.699278998888402	2		622	305	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551427	141551427	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196970558	NA	P-0058488-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	229	704	0	ENST00000220592.5:c.1870C>T	p.Arg624Cys	p.R624C	ENST00000220592	NM_012154.3	624	Cgc/Tgc	15/19	0.699278998888402	3	FACETS	0.962	0.898	1	0.481	0.449	0.514	CLONAL	1	TRUE	1	0.699278998888402	3		704	919	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	717	805	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.751505262083369	4	FACETS	0.993	0.976	1	0.993	0.976	1	CLONAL	4	TRUE	0	0.75161649156552	4		805	841	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831656	72831656	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	204	830	0	ENST00000268489.5:c.4925G>C	p.Ser1642Thr	p.S1642T	ENST00000268489	NM_006885.3	1642	aGc/aCc	9/10	0.751505262083369	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.75161649156552	1		830	326	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116272	209116272	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs751591193	NA	P-0058489-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	76	307	0	ENST00000345146.2:c.4T>C	p.Ser2Pro	p.S2P	ENST00000345146	NM_005896.2	2	Tcc/Ccc	3/10	0.751505262083369	3	FACETS	1	0.925	1	0.527	0.468	0.589	CLONAL	1	TRUE	1	0.75161649156552	3		307	264	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs786202525	NA	P-0058491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	356	836	10	ENST00000269305.4:c.532del	p.His178ThrfsTer69	p.H178Tfs*69	ENST00000269305	NM_001126112.2	178	Cac/ac	5/11	0.39820772885596	3	FACETS	0.882	0.843	0.921	0.882	0.843	0.921	CLONAL	3	TRUE	0	0.471576008879768	3		846	705	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163767	72163767	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	17	393	2	ENST00000357731.5:c.591G>T	p.Gln197His	p.Q197H	ENST00000357731	NM_173808.2	197	caG/caT	4/7	NA	2	FACETS	0.68	0.515	0.871			1	INDETERMINATE	1	TRUE	NA	0.471576008879768	2		395	106	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944895	31944895	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	221	313	4	ENST00000340398.3:c.206G>T	p.Arg69Met	p.R69M	ENST00000340398	NM_001013699.2	69	aGg/aTg	1/1	0.47685297180358	3	FACETS	0.993	0.94	1	1	0.994	1	CLONAL	3	TRUE	1	0.471576008879768	3		317	389	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811619	102811619	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	148	671	5	ENST00000307046.8:c.565T>A	p.Cys189Ser	p.C189S	ENST00000307046	NM_001111285.1	189	Tgc/Agc	4/4	0.475413327417749	3	FACETS	0.875	0.807	0.946	0.875	0.807	0.946	CLONAL	2	TRUE	1	0.471576008879768	3		676	443	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934207	48934208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTCCTTGACTATTTTATTAAACTCTCACCTCCCATGTTGCTCAAA	novel	NA	P-0058491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	25	333	2	ENST00000267163.4:c.663_708dup	p.Glu237CysfsTer3	p.E237Cfs*3	ENST00000267163	NM_000321.2	221	tgt/tgTGTCCTTGACTATTTTATTAAACTCTCACCTCCCATGTTGCTCAAAt	7/27	0.47685297180358	2	FACETS	0.876	0.702	1	0.438	0.351	0.535	CLONAL	1	TRUE	0	0.471576008879768	2		335	121	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745954	745954	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs771329396	NA	P-0058491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	51	344	0	ENST00000314574.4:c.568A>G	p.Thr190Ala	p.T190A	ENST00000314574	NM_005433.3	190	Act/Gct	5/12	0.168273825328799	5	FACETS	0.919	0.801	1	0.919	0.801	1	INDETERMINATE	3	TRUE	2	0.471576008879768	5		344	134	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748336	41748336	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058491-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	221	653	2	ENST00000226382.2:c.433T>C	p.Trp145Arg	p.W145R	ENST00000226382	NM_003924.3	145	Tgg/Cgg	3/3	0.377129835251846	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.471576008879768	3		655	553	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0058492-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	111	425	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.921	1	1	0.989	1	CLONAL	2	TRUE	1	0.21	2		425	517	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0058494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	145	366	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.754200442412414	4	FACETS	1	0.986	1	0.831	0.775	0.887	CLONAL	2	TRUE	1	0.756406967347173	4		366	270	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267360	198267360	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs374250186	NA	P-0058494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	216	537	0	ENST00000335508.6:c.1997A>T	p.Lys666Met	p.K666M	ENST00000335508	NM_012433.2	666	aAg/aTg	14/25	0.493693840442603	5	FACETS	0.947	0.893	1	0.947	0.893	1	CLONAL	3	TRUE	2	0.756406967347173	5		537	429	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476745	140476745	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs878854675	NA	P-0058494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	40	409	0	ENST00000288602.6:c.1661T>C	p.Ile554Thr	p.I554T	ENST00000288602	NM_004333.4	554	aTa/aCa	13/18	0.625536116681425	5	FACETS	0.656	0.547	0.777	0.219	0.182	0.259	SUBCLONAL	1	TRUE	2	0.756406967347173	5		409	344	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968239	2968239	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	164	726	0	ENST00000396946.4:c.1747C>A	p.His583Asn	p.H583N	ENST00000396946	NM_032415.4	583	Cat/Aat	13/25	0.756406967347173	3	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.756406967347173	3		726	433	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346668	81346668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	103	470	0	ENST00000222390.5:c.1285G>A	p.Glu429Lys	p.E429K	ENST00000222390	NM_000601.4	429	Gaa/Aaa	11/18	0.625536116681425	5	FACETS	1	0.982	1	0.483	0.436	0.533	CLONAL	1	TRUE	2	0.756406967347173	5		470	401	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274264	10274264	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	121	708	0	ENST00000330684.3:c.5G>T	p.Gly2Val	p.G2V	ENST00000330684	NM_001134407.1	2	gGc/gTc	2/13	0.218707424734707	5	FACETS	1	0.974	1	0.772	0.708	0.836	INDETERMINATE	2	TRUE	2	0.756406967347173	5		708	295	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653035	29653035	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	389	659	0	ENST00000356175.3:c.4970A>T	p.Tyr1657Phe	p.Y1657F	ENST00000356175	NM_000267.3	1657	tAt/tTt	36/57	0.657302622652448	6	FACETS	1	0.974	1	1	0.974	1	CLONAL	4	TRUE	2	0.756406967347173	6		659	636	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946158	55946159	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0058494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	77	725	1	ENST00000263923.4:c.4020_4021delinsAA	p.Gln1341Lys	p.Q1341K	ENST00000263923	NM_002253.2	1340	gcCCag/gcAAag	30/30	0.658366704577065	3	FACETS	0.926	0.821	1	0.463	0.41	0.518	CLONAL	1	TRUE	1	0.756406967347173	3		726	303	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143181718	143181718	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0058494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	74	258	2	ENST00000262992.4:c.616-1G>T		p.X206_splice	ENST00000262992	NM_001101669.1	206			0.513034527366881	3	FACETS	0.822	0.739	0.906	0.822	0.739	0.906	CLONAL	2	TRUE	1	0.756406967347173	3		260	164	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295351	1295351	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0058494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	161	973	0				ENST00000310581	NM_198253.2	-/1132			0.371624283338206	5	FACETS	1	0.965	1	0.713	0.661	0.766	INDETERMINATE	2	TRUE	2	0.756406967347173	5		973	425	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503836	149503836	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	151	714	0	ENST00000261799.4:c.2000T>A	p.Leu667Gln	p.L667Q	ENST00000261799	NM_002609.3	667	cTg/cAg	14/23	0.437196096358162	4	FACETS	0.872	0.806	0.939	0.872	0.806	0.939	INDETERMINATE	2	TRUE	2	0.756406967347173	4		714	402	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721268	176721268	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371532898	NA	P-0058494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	188	821	0	ENST00000439151.2:c.6899C>G	p.Ala2300Gly	p.A2300G	ENST00000439151	NM_022455.4	2300	gCt/gGt	23/23	0.493693840442603	5	FACETS	1	0.987	1	0.819	0.766	0.872	CLONAL	2	TRUE	2	0.756406967347173	5		821	432	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225493	26225493	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	91	1001	0	ENST00000360408.1:c.111G>T	p.Lys37Asn	p.K37N	ENST00000360408	NM_003532.2	37	aaG/aaT	1/1	0.756406967347173	6	FACETS	0.726	0.644	0.814	0.181	0.161	0.204	SUBCLONAL	1	TRUE	2	0.756406967347173	6		1001	833	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157454311	157454311	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150249745	NA	P-0058494-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	47	609	0	ENST00000346085.5:c.2521G>A	p.Gly841Ser	p.G841S	ENST00000346085	NM_020732.3	841	Ggt/Agt	8/20	0.647655522398872	2	FACETS	0.522	0.445	0.606	0.261	0.222	0.303	SUBCLONAL	1	TRUE	0	0.756406967347173	2		609	238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0058495-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	110	1110	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.14	2		1111	1131	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413009	49413009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519953	NA	P-0058495-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	53	729	1	ENST00000418115.1:c.14G>A	p.Arg5Gln	p.R5Q	ENST00000418115	NM_001664.2	5	cGg/cAg	2/5	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.14	2		730	741	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222152	2222152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768663974	NA	P-0058495-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	72	1238	0	ENST00000398665.3:c.2984G>A	p.Arg995Gln	p.R995Q	ENST00000398665	NM_032482.2	995	cGg/cAg	24/28	1	2	FACETS	0.859	0.747	0.979	0.859	0.747	0.979	CLONAL	1	TRUE	1	0.14	2		1238	1198	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	98	302	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.876	0.791	0.965	0.876	0.791	0.965	CLONAL	1	TRUE	1	0.710115706057522	2		302	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0058498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	246	580	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.710115706057522	2		580	626	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836623	89836623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137913973	NA	P-0058498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	214	708	0	ENST00000389301.3:c.2267G>A	p.Arg756His	p.R756H	ENST00000389301	NM_000135.2	756	cGt/cAt	25/43	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.710115706057522	2		708	545	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589552	69589552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	32	1189	1	ENST00000168712.1:c.301G>A	p.Asp101Asn	p.D101N	ENST00000168712	NM_002007.2	101	Gac/Aac	1/3	0.710115706057522	1	FACETS	0.132	0.107	0.161	0.132	0.107	0.161	SUBCLONAL	1	TRUE	0	0.710115706057522	1		1190	440	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240707	55240707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1562783502	NA	P-0058498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23772	1285	816	0	ENST00000275493.2:c.1951G>A	p.Val651Met	p.V651M	ENST00000275493	NM_005228.3	651	Gtg/Atg	17/28	0.710115706057522	51	FACETS	0.886	0.857	0.915	0.053	0.051	0.055	CLONAL	3	TRUE	1	0.710115706057522	51		816	25057	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692916	89692916	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	199	462	0	ENST00000371953.3:c.400A>G	p.Met134Val	p.M134V	ENST00000371953	NM_000314.4	134	Atg/Gtg	5/9	0.710115706057522	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.710115706057522	1		462	344	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573187	41573187	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	296	832	0	ENST00000263253.7:c.5472G>T	p.Gln1824His	p.Q1824H	ENST00000263253	NM_001429.3	1824	caG/caT	31/31	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.710115706057522	2		832	761	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395922	395922	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1472591082	NA	P-0058498-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	191	655	0	ENST00000380956.4:c.479C>T	p.Ser160Leu	p.S160L	ENST00000380956	NM_001195286.1	160	tCg/tTg	4/9	1	2	FACETS	0.929	0.865	0.995	0.929	0.865	0.995	CLONAL	1	TRUE	1	0.710115706057522	2		655	579	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0058499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	248	545	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.851035110102002	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.893279772461991	1		545	300	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	144	302	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.908	0.84	0.978	0.908	0.84	0.978	CLONAL	1	TRUE	1	0.893279772461991	2		302	355	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508563	106508563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757016725	NA	P-0058499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	208	559	0	ENST00000359195.3:c.557C>T	p.Ala186Val	p.A186V	ENST00000359195	NM_002649.2	186	gCg/gTg	2/11	0.852391055355176	4	FACETS	0.883	0.819	0.948	0.441	0.409	0.474	CLONAL	1	TRUE	2	0.893279772461991	4		559	999	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711928	89711931	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	rs1564837868	NA	P-0058499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	139	353	0	ENST00000371953.3:c.548_551del	p.Lys183IlefsTer15	p.K183Ifs*15	ENST00000371953	NM_000314.4	182	ttAAAG/tt	6/9	0.893279772461991	1	FACETS	0.951	0.904	0.996	0.951	0.904	0.996	CLONAL	1	TRUE	0	0.893279772461991	1		353	181	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691103	18691103	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	128	328	0	ENST00000266497.5:c.3214T>C	p.Phe1072Leu	p.F1072L	ENST00000266497		1072	Ttc/Ctc	23/31	NA	2	FACETS	0.91	0.837	0.984			1	INDETERMINATE	1	TRUE	NA	0.893279772461991	2		328	315	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858225	9858225	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs772497745	NA	P-0058499-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	52	606	0	ENST00000330684.3:c.3176C>G	p.Ser1059Cys	p.S1059C	ENST00000330684	NM_001134407.1	1059	tCt/tGt	13/13	0.229426484222649	1	FACETS	0.102	0.086	0.119	0.102	0.086	0.119	INDETERMINATE	1	TRUE	0	0.893279772461991	1		606	631	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0058500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	129	696	3	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.937	0.857	1	0.937	0.857	1	CLONAL	1	TRUE	1	0.656905858431836	2		699	419	SUCCESS
APC	324	MSKCC	GRCh37	5	112175162	112175162	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561588104	NA	P-0058500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	74	573	2	ENST00000257430.4:c.3871C>T	p.Gln1291Ter	p.Q1291*	ENST00000257430	NM_000038.5	1291	Cag/Tag	16/16	1	2	FACETS	0.813	0.72	0.911	0.813	0.72	0.911	CLONAL	1	TRUE	1	0.656905858431836	2		575	277	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0058500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	409	768	16	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.643252598890982	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.656905858431836	2		784	618	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170799	11170799	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878854234	NA	P-0058500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	188	698	8	ENST00000358026.2:c.4943C>T	p.Pro1648Leu	p.P1648L	ENST00000358026	NM_001128849.1	1648	cCg/cTg	35/36	0.572951440160137	3	FACETS	1	0.99	1	0.469	0.437	0.503	CLONAL	1	TRUE	0	0.656905858431836	3		706	540	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456525	189456525	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058500-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	120	601	1	ENST00000264731.3:c.286A>C	p.Ile96Leu	p.I96L	ENST00000264731	NM_003722.4	96	Atc/Ctc	3/14	0.656905858431836	3	FACETS	0.862	0.781	0.947	0.431	0.39	0.474	CLONAL	1	TRUE	1	0.656905858431836	3		602	563	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0058501-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	167	697	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.235288367820636	4	FACETS	1	0.979	1	0.786	0.724	0.851	CLONAL	2	TRUE	1	0.252184915883303	4		699	703	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098352	108098352	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs730881359	NA	P-0058501-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	69	352	0	ENST00000278616.4:c.1A>G	p.Met1?	p.M1?	ENST00000278616	NM_000051.3	1	Atg/Gtg	2/63	0.252184915883303	2	FACETS	0.8	0.701	0.905	0.8	0.701	0.905	CLONAL	2	TRUE	0	0.252184915883303	2		352	342	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302287	15302287	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058501-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	39	764	0	ENST00000263388.2:c.984del	p.Cys329AlafsTer43	p.C329Afs*43	ENST00000263388	NM_000435.2	328	acC/ac	6/33	1	2	FACETS	0.424	0.35	0.506	0.424	0.35	0.506	SUBCLONAL	1	TRUE	1	0.252184915883303	2		764	730	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422911	47422911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199897795	NA	P-0058501-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	77	741	0	ENST00000404338.3:c.979C>T	p.Arg327Cys	p.R327C	ENST00000404338	NM_004491.4	327	Cgc/Tgc	1/6	0.132946025504665	4	FACETS	0.982	0.861	1	0.491	0.43	0.556	INDETERMINATE	1	TRUE	2	0.252184915883303	4		741	779	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0058503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	221	738	0				ENST00000310581	NM_198253.2	-/1132			0.34382803966806	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.34382803966806	2		738	516	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0058503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	827	471	1	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.34382803966806	13	FACETS	0.971	0.949	0.994			1	CLONAL	12	TRUE	NA	0.34382803966806	13		472	1193	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331729	68331729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	30	220	0	ENST00000487270.1:c.325C>T	p.Pro109Ser	p.P109S	ENST00000487270	NM_133509.3	109	Cca/Tca	5/11	1	2	FACETS	0.954	0.776	1	0.954	0.776	1	CLONAL	1	TRUE	1	0.34382803966806	2		220	183	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274897	41274897	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	106	631	0	ENST00000349496.5:c.1147T>C	p.Trp383Arg	p.W383R	ENST00000349496	NM_001904.3	383	Tgg/Cgg	8/15	1	2	FACETS	0.976	0.876	1	0.976	0.876	1	CLONAL	1	TRUE	1	0.34382803966806	2		631	632	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259533	55259533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	94	673	0	ENST00000275493.2:c.2591C>T	p.Ala864Val	p.A864V	ENST00000275493	NM_005228.3	864	gCg/gTg	21/28	0.34382803966806	3	FACETS	0.964	0.858	1	0.482	0.429	0.538	CLONAL	1	TRUE	1	0.34382803966806	3		673	665	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472664	88472664	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs56300182	NA	P-0058503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	66	741	0	ENST00000360948.2:c.1891G>A	p.Ala631Thr	p.A631T	ENST00000360948	NM_001012338.2	631	Gcc/Acc	16/19	0.304865488037354	3	FACETS	0.728	0.632	0.832	0.364	0.316	0.416	SUBCLONAL	1	TRUE	1	0.34382803966806	3		741	618	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007353	143007353	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	61	329	0	ENST00000262992.4:c.2431C>T	p.Gln811Ter	p.Q811*	ENST00000262992	NM_001101669.1	811	Caa/Taa	22/24	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.34382803966806	2		329	306	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133188	30133188	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	108	683	0	ENST00000263025.4:c.310C>T	p.Arg104Ter	p.R104*	ENST00000263025	NM_002746.2	104	Cga/Tga	2/9	1	2	FACETS	0.935	0.84	1	0.935	0.84	1	CLONAL	1	TRUE	1	0.34382803966806	2		683	672	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456393	32456393	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	201	863	0	ENST00000332351.3:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000332351	NM_024426.4	167	Cag/Tag	1/10	0.34382803966806	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.34382803966806	2		863	558	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915094	32915094	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	132	460	0	ENST00000380152.3:c.6602C>A	p.Ser2201Tyr	p.S2201Y	ENST00000380152		2201	tCt/tAt	11/27	0.34382803966806	9	FACETS	0.824	0.747	0.906	0.236	0.213	0.259	CLONAL	2	TRUE	2	0.34382803966806	9		460	1026	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795448	39795448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1255036573	NA	P-0058503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	79	759	0	ENST00000288319.7:c.272G>A	p.Gly91Glu	p.G91E	ENST00000288319	NM_182918.3	91	gGg/gAg	3/10	0.304865488037354	3	FACETS	0.739	0.649	0.835	0.369	0.324	0.418	SUBCLONAL	1	TRUE	1	0.34382803966806	3		759	729	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866333	42866333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1296163361	NA	P-0058503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	247	894	0	ENST00000398585.3:c.299C>T	p.Pro100Leu	p.P100L	ENST00000398585	NM_001135099.1	100	cCc/cTc	3/14	0.304865488037354	3	FACETS	0.932	0.873	0.993	0.932	0.873	0.993	CLONAL	2	TRUE	1	0.34382803966806	3		894	903	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680050	30680051	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0058503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	115	864	0	ENST00000376406.3:c.1668dup	p.Gly557TrpfsTer22	p.G557Wfs*22	ENST00000376406	NM_014641.2	556	-/T	5/15	0.34382803966806	3	FACETS	0.817	0.734	0.904	0.408	0.367	0.452	CLONAL	1	TRUE	1	0.34382803966806	3		864	960	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224474	55224474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058503-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	72	597	0	ENST00000275493.2:c.1156C>T	p.Pro386Ser	p.P386S	ENST00000275493	NM_005228.3	386	Cct/Tct	10/28	0.34382803966806	3	FACETS	0.793	0.693	0.901	0.396	0.346	0.451	CLONAL	1	TRUE	1	0.34382803966806	3		597	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578435	7578435	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	361	938	0	ENST00000269305.4:c.495del	p.Gln165HisfsTer5	p.Q165Hfs*5	ENST00000269305	NM_001126112.2	165	caG/ca	5/11	0.455168130071816	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.450607164681874	2		938	721	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794494	242794494	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	141	749	0	ENST00000334409.5:c.448G>A	p.Glu150Lys	p.E150K	ENST00000334409	NM_005018.2	150	Gaa/Aaa	3/5	NA	2	FACETS	1	0.962	1			1	INDETERMINATE	1	TRUE	NA	0.450607164681874	2		749	573	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825216	50825529	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTTTCCTAATCACTAGGAGAACTTTCCAGTCTAAAAACTAAGCAAAATAAATCATTTATAAGGTCTTGTGCCTGAGCACATTTAATTATTTTATCCAAATCATTTATTTCTCTCTGTTGTTCTGACTATCCAAAGCTACACCATCAATTTTATGGTTTTTCTGTTCTCAAATACTGCTGGGACAACTTAACATTTTGATTTAAGCATTTGATAAATAGGTTGTATGTATTTTTTTCTCTGCGTGTTTTTAGATCAGCAGGTCAAAAGGTACAAGATTGTTACTTCTATCAAATTTTTATGGAAAAAAATGAG	TTTTTTCCTAATCACTAGGAGAACTTTCCAGTCTAAAAACTAAGCAAAATAAATCATTTATAAGGTCTTGTGCCTGAGCACATTTAATTATTTTATCCAAATCATTTATTTCTCTCTGTTGTTCTGACTATCCAAAGCTACACCATCAATTTTATGGTTTTTCTGTTCTCAAATACTGCTGGGACAACTTAACATTTTGATTTAAGCATTTGATAAATAGGTTGTATGTATTTTTTTCTCTGCGTGTTTTTAGATCAGCAGGTCAAAAGGTACAAGATTGTTACTTCTATCAAATTTTTATGGAAAAAAATGAG	-	novel	NA	P-0058504-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	12	29	0	ENST00000398568.2:c.2100-253_2160del		p.X700_splice	ENST00000398568	NM_001042412.1	700		14/18	0.455168130071816	1	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	0	0.450607164681874	1		29	32	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273788	18273788	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058505-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	219	801	0	ENST00000222254.8:c.1121A>G	p.Asn374Ser	p.N374S	ENST00000222254	NM_005027.3	374	aAc/aGc	10/16	0.725270232410921	3	FACETS	1	0.966	1	0.528	0.493	0.565	CLONAL	1	TRUE	1	0.725270232410921	3		801	779	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902442	1902442	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058505-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	188	642	0	ENST00000382891.5:c.61A>T	p.Met21Leu	p.M21L	ENST00000382891	NM_133335.3	21	Atg/Ttg	2/22	0.725270232410921	5	FACETS	1	0.987	1	0.261	0.241	0.282	CLONAL	1	TRUE	0	0.725270232410921	5		642	829	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0058506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	264	885	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.710097439488217	2		885	730	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39318047	39318047	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	69	295	0	ENST00000373001.3:c.755C>T	p.Ser252Leu	p.S252L	ENST00000373001	NM_022157.3	252	tCa/tTa	4/7	1	2	FACETS	0.497	0.435	0.564	0.497	0.435	0.564	SUBCLONAL	1	TRUE	1	0.710097439488217	2		295	391	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400939	72400939	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs369949208	NA	P-0058506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	39	614	0	ENST00000357731.5:c.232A>C	p.Ile78Leu	p.I78L	ENST00000357731	NM_173808.2	78	Att/Ctt	2/7	1	2	FACETS	0.146	0.12	0.174	0.146	0.12	0.174	SUBCLONAL	1	TRUE	1	0.710097439488217	2		614	754	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230461123	230461123	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	223	587	0	ENST00000391860.1:c.967C>T	p.Pro323Ser	p.P323S	ENST00000391860	NM_001258311.1	323	Ccc/Tcc	6/7	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.710097439488217	2		587	594	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604666	43604667	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	80	824	1	ENST00000355710.3:c.1251_1252delinsTT	p.Arg418Ter	p.R418*	ENST00000355710	NM_020975.4	417	cgCCga/cgTTga	6/20	1	2	FACETS	0.309	0.272	0.349	0.309	0.272	0.349	SUBCLONAL	1	TRUE	1	0.710097439488217	2		825	729	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039420	49039420	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	76	549	0	ENST00000267163.4:c.2405G>A	p.Gly802Glu	p.G802E	ENST00000267163	NM_000321.2	802	gGg/gAg	23/27	0.533180846543367	1	FACETS	0.273	0.24	0.309	0.273	0.24	0.309	SUBCLONAL	1	TRUE	0	0.710097439488217	1		549	505	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779015	3779016	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	331	893	0	ENST00000262367.5:c.6032_6033delinsTT	p.Pro2011Leu	p.P2011L	ENST00000262367	NM_004380.2	2011	cCC/cTT	31/31	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.710097439488217	2		893	902	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50815178	50815178	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	265	589	0	ENST00000398568.2:c.1531A>G	p.Thr511Ala	p.T511A	ENST00000398568	NM_001042412.1	511	Acg/Gcg	9/18	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.710097439488217	2		589	662	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0058506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	666	877	0	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	0.710097439488217	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.710097439488217	2		877	861	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943499	17943500	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AT	novel	NA	P-0058506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	248	850	0	ENST00000458235.1:c.2508_2509delinsAT	p.Glu837Ter	p.E837*	ENST00000458235	NM_000215.3	836	gtGGag/gtATag	19/24	1	2	FACETS	0.846	0.793	0.9	0.846	0.793	0.9	CLONAL	1	TRUE	1	0.710097439488217	2		850	826	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67626366	67626366	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	195	421	0	ENST00000272342.5:c.289A>C	p.Asn97His	p.N97H	ENST00000272342	NM_019002.3	97	Aat/Cat	2/6	1	2	FACETS	0.915	0.852	0.98	0.915	0.852	0.98	CLONAL	1	TRUE	1	0.710097439488217	2		421	600	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735572	204735573	+	missense_variant	Missense_Mutation	DNP	GG	GG	AC	novel	NA	P-0058506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	233	777	0	ENST00000302823.3:c.373_374delinsAC	p.Gly125Thr	p.G125T	ENST00000302823	NM_005214.4	125	GGa/ACa	2/4	1	2	FACETS	0.898	0.841	0.956	0.898	0.841	0.956	CLONAL	1	TRUE	1	0.710097439488217	2		777	731	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125739	47125739	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	252	529	0	ENST00000409792.3:c.5531C>T	p.Ser1844Phe	p.S1844F	ENST00000409792	NM_014159.6	1844	tCt/tTt	12/21	0.710097439488217	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.710097439488217	1		529	396	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437770	52437770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	282	754	0	ENST00000460680.1:c.1391C>T	p.Ser464Phe	p.S464F	ENST00000460680	NM_004656.3	464	tCc/tTc	13/17	0.710097439488217	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.710097439488217	1		754	482	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69998252	69998253	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	217	634	0	ENST00000394351.3:c.492_493delinsTT	p.Pro165Ser	p.P165S	ENST00000394351	NM_000248.3	164	ccCCca/ccTTca	5/9	0.710097439488217	1	FACETS	0.993	0.939	1	0.993	0.939	1	CLONAL	1	TRUE	0	0.710097439488217	1		634	397	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670335	134670336	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	223	668	0	ENST00000398015.3:c.246_247delinsTT	p.His83Tyr	p.H83Y	ENST00000398015	NM_004441.4	82	gcCCat/gcTTat	3/16	0.710097439488217	3	FACETS	0.877	0.816	0.939	0.438	0.408	0.47	CLONAL	1	TRUE	1	0.710097439488217	3		668	971	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444680	187444680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	507	668	0	ENST00000232014.4:c.1547G>A	p.Gly516Glu	p.G516E	ENST00000232014	NM_001130845.1	516	gGg/gAg	7/10	0.689513100853922	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.710097439488217	3		668	937	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156048	106156048	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1434577007	NA	P-0058506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	265	686	0	ENST00000380013.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000380013	NM_001127208.2	317	Cag/Tag	3/11	1	2	FACETS	0.994	0.936	1	0.994	0.936	1	CLONAL	1	TRUE	1	0.710097439488217	2		686	751	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439311	149439311	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	249	754	0	ENST00000286301.3:c.2084G>A	p.Gly695Glu	p.G695E	ENST00000286301	NM_005211.3	695	gGa/gAa	15/22	1	2	FACETS	0.986	0.927	1	0.986	0.927	1	CLONAL	1	TRUE	1	0.710097439488217	2		754	711	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675426	30675427	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	314	860	1	ENST00000376406.3:c.2929_2930delinsTT	p.Pro977Leu	p.P977L	ENST00000376406	NM_014641.2	977	CCg/TTg	8/15	0.689513100853922	3	FACETS	1	0.951	1	0.504	0.475	0.534	CLONAL	1	TRUE	1	0.710097439488217	3		861	1188	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987337	2987337	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	125	665	0	ENST00000396946.4:c.92A>C	p.His31Pro	p.H31P	ENST00000396946	NM_032415.4	31	cAc/cCc	3/25	1	2	FACETS	0.521	0.472	0.572	0.521	0.472	0.572	SUBCLONAL	1	TRUE	1	0.710097439488217	2		665	676	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450324	50450324	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	284	823	0	ENST00000331340.3:c.508G>A	p.Glu170Lys	p.E170K	ENST00000331340	NM_006060.4	170	Gag/Aag	5/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.710097439488217	2		823	742	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615610	100615610	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058506-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	19	370	0	ENST00000308731.7:c.722A>C	p.Tyr241Ser	p.Y241S	ENST00000308731	NM_000061.2	241	tAt/tCt	8/19	1	1	FACETS	0.093	0.07	0.12	0.093	0.07	0.12	SUBCLONAL	1	TRUE	0	0.710097439488217	1		370	372	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727451	66727451	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519729	NA	P-0058507-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	19	665	0	ENST00000307102.5:c.167A>C	p.Gln56Pro	p.Q56P	ENST00000307102	NM_002755.3	56	cAg/cCg	2/11	0.268273851410653	3	FACETS	0.168	0.126	0.217	0.084	0.063	0.109	SUBCLONAL	1	TRUE	1	0.394069884003138	3		665	689	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227017	2227017	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs370187220	NA	P-0058507-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	178	890	0	ENST00000398665.3:c.4497C>G	p.Ser1499Arg	p.S1499R	ENST00000398665	NM_032482.2	1499	agC/agG	27/28	0.268273851410653	3	FACETS	1	0.99	1	0.744	0.687	0.802	CLONAL	1	TRUE	1	0.394069884003138	3		890	727	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596029	43596029	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058507-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	71	805	0	ENST00000355710.3:c.196T>G	p.Phe66Val	p.F66V	ENST00000355710	NM_020975.4	66	Ttc/Gtc	2/20	0.25154512594025	4	FACETS	0.677	0.59	0.771	0.339	0.295	0.386	SUBCLONAL	1	TRUE	2	0.394069884003138	4		805	742	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779190	3779190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058507-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	44	753	0	ENST00000262367.5:c.5858C>T	p.Pro1953Leu	p.P1953L	ENST00000262367	NM_004380.2	1953	cCt/cTt	31/31	0.27311580118293	5	FACETS	0.479	0.4	0.566	0.16	0.133	0.189	SUBCLONAL	1	TRUE	2	0.394069884003138	5		753	742	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660757	227660757	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058507-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	99	897	0	ENST00000305123.5:c.2698G>A	p.Glu900Lys	p.E900K	ENST00000305123	NM_005544.2	900	Gaa/Aaa	1/2	0.25154512594025	4	FACETS	0.735	0.655	0.821	0.367	0.327	0.411	SUBCLONAL	1	TRUE	2	0.394069884003138	4		897	953	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69032520	69032520	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058507-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	79	465	0	ENST00000288368.4:c.3594A>C	p.Gln1198His	p.Q1198H	ENST00000288368	NM_024870.2	1198	caA/caC	29/40	0.268059234923635	6	FACETS	0.897	0.788	1	0.224	0.197	0.254	CLONAL	1	TRUE	2	0.394069884003138	6		465	799	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410318	63410318	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058507-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	206	485	0	ENST00000330258.3:c.2849C>G	p.Thr950Ser	p.T950S	ENST00000330258	NM_152424.3	950	aCt/aGt	2/2	0.394069884003138	2	FACETS	1	0.971	1			1	CLONAL	2	TRUE	NA	0.394069884003138	2		485	493	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058508-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	194	302	0				ENST00000310581	NM_198253.2	-/1132			0.300476326977088	5	FACETS	0.787	0.73	0.846	0.525	0.486	0.564	INDETERMINATE	2	TRUE	2	0.63192948059234	5		302	760	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0058508-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	447	856	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	NA	2	FACETS	0.903	0.87	0.937			1	INDETERMINATE	2	TRUE	NA	0.63192948059234	2		856	783	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857686	59857686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781321	NA	P-0058508-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	78	372	0	ENST00000259008.2:c.1871C>T	p.Ser624Leu	p.S624L	ENST00000259008	NM_032043.2	624	tCg/tTg	13/20	0.29806154110421	2	FACETS	0.477	0.42	0.538	0.238	0.21	0.269	INDETERMINATE	1	TRUE	0	0.63192948059234	2		372	518	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456556	40456556	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058508-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	137	786	0	ENST00000345506.4:c.1266G>C	p.Lys422Asn	p.K422N	ENST00000345506	NM_003152.3	422	aaG/aaC	12/20	0.29806154110421	2	FACETS	0.506	0.46	0.554	0.253	0.23	0.277	INDETERMINATE	1	TRUE	0	0.63192948059234	2		786	857	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902211	50902211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs554554906	NA	P-0058508-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	143	758	0	ENST00000440232.2:c.103G>A	p.Glu35Lys	p.E35K	ENST00000440232	NM_002691.3	35	Gag/Aag	2/27	0.63192948059234	3	FACETS	0.61	0.555	0.667	0.305	0.277	0.334	SUBCLONAL	1	TRUE	1	0.63192948059234	3		758	977	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288887	212288887	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058508-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	259	470	0	ENST00000342788.4:c.2859G>A	p.Met953Ile	p.M953I	ENST00000342788	NM_005235.2	953	atG/atA	23/28	0.613384138475516	2	FACETS	0.881	0.838	0.925	0.881	0.838	0.925	CLONAL	2	TRUE	0	0.63192948059234	2		470	465	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193817	106193817	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058508-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	220	576	0	ENST00000380013.4:c.4279G>C	p.Asp1427His	p.D1427H	ENST00000380013	NM_001127208.2	1427	Gat/Cat	10/11	0.398592795106203	1	FACETS	0.8	0.75	0.852	0.8	0.75	0.852	SUBCLONAL	1	TRUE	0	0.63192948059234	1		576	595	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945417	151945417	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058508-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	92	355	0	ENST00000262189.6:c.2102C>T	p.Ser701Phe	p.S701F	ENST00000262189	NM_170606.2	701	tCc/tTc	14/59	0.63192948059234	3	FACETS	0.606	0.539	0.678	0.303	0.269	0.339	SUBCLONAL	1	TRUE	1	0.63192948059234	3		355	632	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089699	5089699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1351324295	NA	P-0058508-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	94	390	0	ENST00000381652.3:c.2597G>A	p.Cys866Tyr	p.C866Y	ENST00000381652	NM_004972.3	866	tGc/tAc	20/25	0.63192948059234	2	FACETS	0.544	0.485	0.606	0.272	0.242	0.303	SUBCLONAL	1	TRUE	0	0.63192948059234	2		390	547	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781101	135781102	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0058508-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	429	683	0	ENST00000298552.3:c.1863_1864del	p.Ile621MetfsTer4	p.I621Mfs*4	ENST00000298552	NM_001162426.1	621	atCAgg/atgg	15/23	NA	2	FACETS	0.912	0.878	0.947			1	INDETERMINATE	2	TRUE	NA	0.63192948059234	2		683	744	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44920636	44920636	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0058508-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	187	182	0	ENST00000377967.4:c.1397C>G	p.Ser466Ter	p.S466*	ENST00000377967	NM_021140.2	466	tCa/tGa	14/29	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.63192948059234	1		182	279	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0058509-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	114	265	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.210016186853657	2	FACETS	1	0.986	1	0.73	0.667	0.793	INDETERMINATE	1	TRUE	0	0.536970904359068	2		265	291	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0058509-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	154	431	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.369312678169865	1	FACETS	0.671	0.617	0.728	0.671	0.617	0.728	SUBCLONAL	1	TRUE	0	0.536970904359068	1		431	625	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735470	40735470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761910971	NA	P-0058509-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	359	773	0	ENST00000373198.4:c.3403G>A	p.Val1135Met	p.V1135M	ENST00000373198	NM_133170.3	1135	Gtg/Atg	25/32	0.165494187156851	5	FACETS	1	0.98	1	0.71	0.674	0.748	INDETERMINATE	2	TRUE	2	0.536970904359068	5		773	1133	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579344	7579345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0058509-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	269	810	0	ENST00000269305.4:c.342dup	p.His115AlafsTer34	p.H115Afs*34	ENST00000269305	NM_001126112.2	114	-/G	4/11	0.536970904359068	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.536970904359068	1		810	682	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665870	241665870	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1553340894	NA	P-0058509-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	84	497	0	ENST00000366560.3:c.1109G>A	p.Gly370Asp	p.G370D	ENST00000366560	NM_000143.3	370	gGc/gAc	8/10	0.358537541381309	1	FACETS	0.451	0.4	0.507	0.451	0.4	0.507	SUBCLONAL	1	TRUE	0	0.536970904359068	1		497	507	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114917746	114917778	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	GCAGTAATTCCCTGTGTTTCATCTCTTCATCTA	GCAGTAATTCCCTGTGTTTCATCTCTTCATCTA	-	novel	NA	P-0058509-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	143	380	0	ENST00000543371.1:c.1270-33_1270-1del		p.X424_splice	ENST00000543371	NM_001198531.1	424			0.369312678169865	1	FACETS	0.888	0.816	0.961	0.888	0.816	0.961	CLONAL	1	TRUE	0	0.536970904359068	1		380	439	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988135	85988135	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058509-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	87	480	0	ENST00000263360.6:c.1080G>T	p.Gln360His	p.Q360H	ENST00000263360	NM_003797.3	360	caG/caT	10/12	1	2	FACETS	0.939	0.839	1	0.939	0.839	1	CLONAL	1	TRUE	1	0.536970904359068	2		480	345	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557561	95557562	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATA	novel	NA	P-0058509-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	91	726	0	ENST00000393063.1:c.5503_5505dup	p.Tyr1835dup	p.Y1835dup	ENST00000393063	NM_030621.3	1835	-/TAT	26/28	0.458725965478263	1	FACETS	0.417	0.37	0.466	0.417	0.37	0.466	SUBCLONAL	1	TRUE	0	0.536970904359068	1		726	595	SUCCESS
APC	324	MSKCC	GRCh37	5	112137001	112137001	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058509-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	49	486	0	ENST00000257430.4:c.756del	p.Gly253AlafsTer40	p.G253Afs*40	ENST00000257430	NM_000038.5	252	aCc/ac	8/16	0.369312678169865	1	FACETS	0.286	0.243	0.335	0.286	0.243	0.335	SUBCLONAL	1	TRUE	0	0.536970904359068	1		486	466	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0058520-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	132	256	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.222537437382798	6	FACETS	1	0.963	1	0.87	0.798	0.944	CLONAL	4	TRUE	1	0.222537437382798	6		256	394	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604784	48604784	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058520-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	54	534	1	ENST00000342988.3:c.1606C>A	p.Leu536Ile	p.L536I	ENST00000342988	NM_005359.5	536	Cta/Ata	12/12	0.222537437382798	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.222537437382798	1		535	359	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249462	110249462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058520-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	87	705	0	ENST00000374672.4:c.1111C>T	p.Pro371Ser	p.P371S	ENST00000374672	NM_004235.4	371	Ccc/Tcc	4/5	1	2	FACETS	0.765	0.679	0.856	1	0.98	1	SUBCLONAL	2	TRUE	1	0.222537437382798	2		705	511	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0058530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	121	190	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.218380938601288	3	FACETS	0.946	0.856	1	0.946	0.856	1	CLONAL	2	TRUE	1	0.218380938601288	3		190	650	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0058530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	46	187	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.779	0.655	0.915	0.779	0.655	0.915	CLONAL	1	TRUE	1	0.218380938601288	2		188	541	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0058530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	47	740	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.926	0.782	1	0.926	0.782	1	CLONAL	1	TRUE	1	0.218380938601288	2		740	465	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473723	67473723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223740	NA	P-0058530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	78	746	1	ENST00000327367.4:c.803G>A	p.Arg268His	p.R268H	ENST00000327367	NM_005902.3	268	cGc/cAc	6/9	1	2	FACETS	0.73	0.64	0.828	0.73	0.64	0.828	SUBCLONAL	1	TRUE	1	0.218380938601288	2		747	978	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473722	67473722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs794727798	NA	P-0058530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	117	741	1	ENST00000327367.4:c.802C>T	p.Arg268Cys	p.R268C	ENST00000327367	NM_005902.3	268	Cgc/Tgc	6/9	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.218380938601288	2		742	970	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750945	128750945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	96	557	0	ENST00000377970.2:c.482C>T	p.Ser161Leu	p.S161L	ENST00000377970	NM_002467.4	161	tCa/tTa	2/3	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.218380938601288	2		557	840	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923604	39923604	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	206	439	0	ENST00000378444.4:c.3487C>T	p.Arg1163Ter	p.R1163*	ENST00000378444	NM_001123385.1	1163	Cga/Tga	7/15	0.200201789642189	2	FACETS	0.881	0.82	0.943			1	CLONAL	3	TRUE	NA	0.218380938601288	2		439	714	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8284885	8284885	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	42	540	3	ENST00000335790.3:c.25G>A	p.Gly9Ser	p.G9S	ENST00000335790	NM_002315.2	9	Ggc/Agc	1/4	1	2	FACETS	0.465	0.386	0.552	0.465	0.386	0.552	SUBCLONAL	1	TRUE	1	0.218380938601288	2		543	828	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210724	36210725	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0058530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	75	1024	0	ENST00000222270.7:c.481dup	p.Leu161ProfsTer23	p.L161Pfs*23	ENST00000222270	NM_014727.1	159	acc/aCcc	3/37	1	2	FACETS	0.564	0.492	0.642	0.564	0.492	0.642	SUBCLONAL	1	TRUE	1	0.218380938601288	2		1024	1218	SUCCESS
APC	324	MSKCC	GRCh37	5	112174094	112174098	+	frameshift_variant	Frame_Shift_Del	DEL	TACAA	TACAA	-	novel	NA	P-0058530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	38	268	0	ENST00000257430.4:c.2804_2808del	p.Tyr935PhefsTer3	p.Y935Ffs*3	ENST00000257430	NM_000038.5	935	TACAAt/t	16/16	1	2	FACETS	0.758	0.627	0.905	0.758	0.627	0.905	CLONAL	1	TRUE	1	0.218380938601288	2		268	459	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069177	5069177	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	33	397	0	ENST00000381652.3:c.1482G>C	p.Gln494His	p.Q494H	ENST00000381652	NM_004972.3	494	caG/caC	11/25	1	2	FACETS	0.67	0.545	0.811	0.67	0.545	0.811	SUBCLONAL	1	TRUE	1	0.218380938601288	2		397	451	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371710	45371715	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CCGGTA	CCGGTA	TGTAT	novel	NA	P-0058530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	78	277	0	ENST00000262160.6:c.1276_1280+1delinsATACA		p.X426_splice	ENST00000262160	NM_005901.5	426		10/11	0.180629374650505	2	FACETS	1	0.974	1	0.707	0.623	0.797	CLONAL	1	TRUE	0	0.218380938601288	2		277	505	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046641	42046642	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	51	314	0	ENST00000219905.7:c.7018_7019del	p.Val2340ArgfsTer4	p.V2340Rfs*4	ENST00000219905	NM_001164273.1	2339	TGt/t	18/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		314	500	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276860	15276861	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs753725730	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	100	909	8	ENST00000263388.2:c.5404dup	p.Ala1802GlyfsTer8	p.A1802Gfs*8	ENST00000263388	NM_000435.2	1802	gct/gGct	30/33	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		917	1210	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	86	478	4	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		482	1006	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268144	153268144	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs920052554	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	85	384	0	ENST00000281708.4:c.664C>T	p.Arg222Ter	p.R222*	ENST00000281708	NM_033632.3	222	Cga/Tga	4/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		384	787	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293661	1293661	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1427	134	1528	1	ENST00000310581.5:c.1340G>A	p.Arg447His	p.R447H	ENST00000310581	NM_198253.2	447	cGc/cAc	2/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1529	1561	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629103	86629103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753769946	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	29	207	0	ENST00000274376.6:c.848G>A	p.Arg283His	p.R283H	ENST00000274376	NM_002890.2	283	cGt/cAt	4/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		207	326	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197563	106197563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745668941	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	61	328	0	ENST00000380013.4:c.5896C>T	p.Arg1966Cys	p.R1966C	ENST00000380013	NM_001127208.2	1966	Cgt/Tgt	11/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		328	574	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	54	407	5	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		412	567	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829040	128829042	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	rs570242755	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	13	66	0	ENST00000249373.3:c.67_69del	p.Leu23del	p.L23del	ENST00000249373	NM_005631.4	16	ggGCTg/ggg	1/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		66	155	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427588	72427588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	45	361	0	ENST00000477973.2:c.902G>A	p.Arg301His	p.R301H	ENST00000477973	NM_012234.5	301	cGt/cAt	4/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		361	592	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467589	66467589	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772693559	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	44	332	0	ENST00000273854.3:c.680G>A	p.Arg227His	p.R227H	ENST00000273854	NM_004439.5	227	cGt/cAt	3/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		332	526	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265479	152265479	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766779326	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	82	646	1	ENST00000206249.3:c.932C>T	p.Thr311Met	p.T311M	ENST00000206249	NM_000125.3	311	aCg/aTg	4/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		647	928	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440643	56440643	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	129	809	1	ENST00000407977.2:c.575del	p.Pro192ArgfsTer11	p.P192Rfs*11	ENST00000407977		192	cCg/cg	5/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		810	1159	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2202758	2202758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1197029182	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	83	710	1	ENST00000398665.3:c.767G>A	p.Arg256Gln	p.R256Q	ENST00000398665	NM_032482.2	256	cGg/cAg	9/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		711	1040	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	99	495	4	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		499	1152	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863054	56863054	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1266824391	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	78	512	0	ENST00000519728.1:c.327del	p.Glu110LysfsTer15	p.E110Kfs*15	ENST00000519728	NM_002350.3	107	acA/ac	5/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		512	876	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527817	157527817	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	58	558	2	ENST00000346085.5:c.5547del	p.Leu1850Ter	p.L1850*	ENST00000346085	NM_020732.3	1848	Ccc/cc	20/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		560	697	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646980	23646981	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	92	711	2	ENST00000261584.4:c.886dup	p.Met296AsnfsTer7	p.M296Nfs*7	ENST00000261584	NM_024675.3	296	atg/aAtg	4/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		713	1037	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426973	49426973	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1565778024	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	121	938	1	ENST00000301067.7:c.11515del	p.Gln3839SerfsTer42	p.Q3839Sfs*42	ENST00000301067	NM_003482.3	3839	Cag/ag	39/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		939	1155	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748899	41748899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750167315	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	124	851	0	ENST00000301178.4:c.1424G>A	p.Arg475Gln	p.R475Q	ENST00000301178	NM_021913.4	475	cGa/cAa	11/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		851	1133	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857958	9857958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140536516	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	71	699	0	ENST00000330684.3:c.3443C>T	p.Pro1148Leu	p.P1148L	ENST00000330684	NM_001134407.1	1148	cCg/cTg	13/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		699	886	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103525619	103525619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs574826021	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	49	304	0	ENST00000355739.4:c.2890C>T	p.Arg964Trp	p.R964W	ENST00000355739	NM_000123.3	964	Cgg/Tgg	14/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		304	543	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988304	41988304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs563448726	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	107	562	0	ENST00000219905.7:c.1096C>T	p.Arg366Cys	p.R366C	ENST00000219905	NM_001164273.1	366	Cgt/Tgt	3/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		562	998	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045137	47045137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556782140	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	96	431	0	ENST00000377604.3:c.2378G>A	p.Arg793Gln	p.R793Q	ENST00000377604	NM_001204468.1	793	cGa/cAa	21/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		431	543	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50488225	50488225	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	73	556	0	ENST00000394963.4:c.1139A>G	p.Asp380Gly	p.D380G	ENST00000394963	NM_003076.4	380	gAc/gGc	10/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		556	830	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481363	56481363	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	120	873	3	ENST00000267101.3:c.555del	p.Cys186ValfsTer20	p.C186Vfs*20	ENST00000267101	NM_001982.3	184	Ccc/cc	5/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		876	1203	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19261516	19261516	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	112	881	0	ENST00000162023.5:c.29G>T	p.Arg10Leu	p.R10L	ENST00000162023		10	cGc/cTc	6/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		881	1220	SUCCESS
REL	5966	MSKCC	GRCh37	2	61144060	61144060	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	72	453	0	ENST00000295025.8:c.443T>C	p.Val148Ala	p.V148A	ENST00000295025	NM_002908.2	148	gTg/gCg	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		453	779	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264984	46264985	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	45	434	0	ENST00000371998.3:c.1860dup	p.Leu621IlefsTer10	p.L621Ifs*10	ENST00000371998		618	-/A	12/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		434	651	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164754	36164754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1177469638	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1423	162	1267	1	ENST00000300305.3:c.1121C>T	p.Ala374Val	p.A374V	ENST00000300305		374	gCc/gTc	8/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1268	1585	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174829	56174830	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	58	299	0	ENST00000399503.3:c.1992_1993del	p.Thr665SerfsTer31	p.T665Sfs*31	ENST00000399503	NM_005921.1	663	gTA/g	11/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		299	585	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415144	109415147	+	frameshift_variant	Frame_Shift_Del	DEL	TTTC	TTTC	-	rs1308319847	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1470	137	919	0	ENST00000436639.2:c.130_133del	p.Glu44HisfsTer18	p.E44Hfs*18	ENST00000436639	NM_014454.2	44	GAAAca/ca	1/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		919	1607	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951853	2951853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200858011	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	217	992	1	ENST00000396946.4:c.3097G>A	p.Ala1033Thr	p.A1033T	ENST00000396946	NM_032415.4	1033	Gcg/Acg	23/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		993	1366	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730281	133730281	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	94	612	0	ENST00000318560.5:c.347T>A	p.Ile116Asn	p.I116N	ENST00000318560	NM_005157.4	116	aTc/aAc	3/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		612	929	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889130	76889130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058589-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	190	207	2	ENST00000373344.5:c.4880C>A	p.Pro1627His	p.P1627H	ENST00000373344	NM_000489.3	1627	cCt/cAt	18/35	1	1	FACETS	0.794	0.753	0.833	1	0.994	1	SUBCLONAL	2	TRUE	0	0.59159383861062	1		209	285	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0058595-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	9	265	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.582	0.384	0.834	0.582	0.384	0.834	SUBCLONAL	1	TRUE	1	0.13	2		265	238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577083	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0058595-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	11	437	0	ENST00000269305.4:c.855_856delinsTT	p.Glu285_Glu286delinsAspTer	p.E285_E286delinsD*	ENST00000269305	NM_001126112.2	285	gaGGaa/gaTTaa	8/11	1	2	FACETS	0.364	0.25	0.507	0.364	0.25	0.507	SUBCLONAL	1	TRUE	1	0.13	2		437	465	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218282	133218282	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058595-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	22	354	0	ENST00000320574.5:c.5329A>T	p.Ser1777Cys	p.S1777C	ENST00000320574	NM_006231.2	1777	Agt/Tgt	39/49	1	2	FACETS	0.855	0.662	1	0.855	0.662	1	CLONAL	1	TRUE	1	0.13	2		354	396	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722237	49722237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157230035	NA	P-0058595-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	11	271	0	ENST00000449682.2:c.1703G>A	p.Arg568Gln	p.R568Q	ENST00000449682	NM_020998.3	568	cGg/cAg	15/18	1	2	FACETS	0.795	0.549	1	0.795	0.549	1	CLONAL	1	TRUE	1	0.13	2		271	213	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081511	143081511	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058595-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	17	301	0	ENST00000262992.4:c.1563G>C	p.Trp521Cys	p.W521C	ENST00000262992	NM_001101669.1	521	tgG/tgC	15/24	1	2	FACETS	0.924	0.69	1	0.924	0.69	1	CLONAL	1	TRUE	1	0.13	2		301	283	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410868	63410868	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058595-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	20	212	0	ENST00000330258.3:c.2299G>T	p.Val767Leu	p.V767L	ENST00000330258	NM_152424.3	767	Gtg/Ttg	2/2	1	1	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	0	0.13	1		212	221	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0058597-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	349	564	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.421830242697751	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	1	0.426499225957193	4		564	733	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0058597-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	436	492	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.421830242697751	4	FACETS	0.993	0.951	1	0.993	0.951	1	CLONAL	3	TRUE	1	0.426499225957193	4		492	979	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418409	139418409	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058597-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	144	516	0	ENST00000277541.6:c.163C>T	p.Pro55Ser	p.P55S	ENST00000277541	NM_017617.3	55	Ccg/Tcg	3/34	0.426499225957193	1	FACETS	0.997	0.914	1	0.997	0.914	1	CLONAL	1	TRUE	0	0.426499225957193	1		516	533	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933401	39933401	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058597-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	87	666	0	ENST00000378444.4:c.1198G>T	p.Gly400Cys	p.G400C	ENST00000378444	NM_001123385.1	400	Ggc/Tgc	4/15	0.258768564903367	1	FACETS	0.448	0.396	0.503	0.448	0.396	0.503	SUBCLONAL	1	TRUE	0	0.426499225957193	1		666	717	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0058598-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	48	256	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.147518621269573	4	FACETS	1	0.956	1	0.684	0.582	0.796	INDETERMINATE	1	FALSE	2	0.3	4		256	304	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867540	35867541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs869312857	NA	P-0058598-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	56	252	0	ENST00000303115.3:c.361dup	p.Ile121AsnfsTer8	p.I121Nfs*8	ENST00000303115	NM_002185.3	118	-/A	3/8	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.3	2		252	302	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528621	89528621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780470195	NA	P-0058598-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	60	465	0	ENST00000336596.2:c.2921C>T	p.Thr974Met	p.T974M	ENST00000336596	NM_005233.5	974	aCg/aTg	17/17	0.15369670193297	3	FACETS	1	0.967	1	0.712	0.617	0.814	INDETERMINATE	1	FALSE	1	0.3	3		465	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577119	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0058598-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	98	623	0	ENST00000269305.4:c.819dup	p.Val274CysfsTer32	p.V274Cfs*32	ENST00000269305	NM_001126112.2	273	-/T	8/11	0.238222463800323	2	FACETS	0.811	0.728	0.897	0.811	0.728	0.897	CLONAL	2	FALSE	0	0.3	2		623	403	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246105	46246105	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs545415503	NA	P-0058598-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	82	383	0	ENST00000334344.6:c.4199A>T	p.Asp1400Val	p.D1400V	ENST00000334344	NM_152641.2	1400	gAt/gTt	15/21	0.147518621269573	4	FACETS	0.877	0.778	0.983	0.877	0.778	0.983	INDETERMINATE	2	FALSE	2	0.3	4		383	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0058599-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	41	328	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.294752747665486	1	FACETS	0.7	0.586	0.826	0.7	0.586	0.826	SUBCLONAL	1	TRUE	0	0.336958558140349	1		328	289	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0058606-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	109	374	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.414689420444118	1	FACETS	0.839	0.766	0.913	0.839	0.766	0.913	CLONAL	1	TRUE	0	0.641790391858299	1		374	275	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0058606-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	68	428	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	0.414689420444118	1	FACETS	0.746	0.661	0.833	0.746	0.661	0.833	SUBCLONAL	1	TRUE	0	0.641790391858299	1		428	193	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0058612-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	337	552	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.431615842853692	3	FACETS	0.986	0.942	1	0.986	0.942	1	CLONAL	3	TRUE	0	0.431615842853692	3		552	642	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111458	8111458	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058612-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	36	377	0	ENST00000346208.3:c.944C>A	p.Thr315Lys	p.T315K	ENST00000346208		315	aCg/aAg	5/6	0.381466551348431	3	FACETS	0.454	0.373	0.544	0.227	0.186	0.272	SUBCLONAL	1	TRUE	1	0.431615842853692	3		377	447	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257338	16257338	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1167704638	NA	P-0058612-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	94	388	0	ENST00000375759.3:c.4603A>G	p.Ile1535Val	p.I1535V	ENST00000375759	NM_015001.2	1535	Atc/Gtc	11/15	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.431615842853692	2		388	419	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729309	41729309	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058612-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	69	312	0	ENST00000242208.4:c.1220G>T	p.Gly407Val	p.G407V	ENST00000242208	NM_002192.2	407	gGt/gTt	3/3	0.381466551348431	3	FACETS	0.854	0.746	0.97	0.427	0.373	0.485	CLONAL	1	TRUE	1	0.431615842853692	3		312	455	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739078	40739078	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058612-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	171	382	0	ENST00000373198.4:c.3206G>T	p.Trp1069Leu	p.W1069L	ENST00000373198	NM_133170.3	1069	tGg/tTg	24/32	0.406278309909303	4	FACETS	0.955	0.883	1	0.955	0.883	1	CLONAL	2	TRUE	2	0.431615842853692	4		382	594	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153652	55153652	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058612-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	75	346	0	ENST00000257290.5:c.2618C>A	p.Thr873Asn	p.T873N	ENST00000257290	NM_006206.4	873	aCc/aAc	19/23	0.381466551348431	3	FACETS	0.917	0.806	1	0.458	0.403	0.518	CLONAL	1	TRUE	1	0.431615842853692	3		346	461	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551366	150551366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058612-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	231	460	0	ENST00000369026.2:c.641G>T	p.Arg214Leu	p.R214L	ENST00000369026	NM_021960.4	214	cGa/cTa	1/3	0.431615842853692	6	FACETS	0.887	0.826	0.95	0.444	0.413	0.475	CLONAL	2	TRUE	2	0.431615842853692	6		460	1124	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306550	163306550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058612-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	67	195	0	ENST00000271452.3:c.347G>T	p.Arg116Leu	p.R116L	ENST00000271452	NM_145697.2	116	cGg/cTg	6/14	0.431615842853692	6	FACETS	0.803	0.702	0.912	0.402	0.351	0.456	CLONAL	2	TRUE	2	0.431615842853692	6		195	360	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3634774	3634774	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058612-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	166	387	0	ENST00000294008.3:c.4735G>T	p.Asp1579Tyr	p.D1579Y	ENST00000294008	NM_032444.2	1579	Gat/Tat	13/15	0.406278309909303	4	FACETS	0.922	0.851	0.995	0.922	0.851	0.995	CLONAL	2	TRUE	2	0.431615842853692	4		387	597	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014033	14014033	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058612-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	152	318	0	ENST00000311895.7:c.11G>T	p.Gly4Val	p.G4V	ENST00000311895	NM_005236.2	4	gGg/gTg	1/11	0.406278309909303	4	FACETS	0.937	0.862	1	0.937	0.862	1	CLONAL	2	TRUE	2	0.431615842853692	4		318	538	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576050	29576050	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058612-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	104	386	0	ENST00000356175.3:c.4023G>C	p.Gln1341His	p.Q1341H	ENST00000356175	NM_000267.3	1341	caG/caC	30/57	0.431615842853692	5	FACETS	1	0.976	1	0.437	0.392	0.484	CLONAL	1	TRUE	2	0.431615842853692	5		386	606	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576057	29576057	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1555617328	NA	P-0058612-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	110	399	0	ENST00000356175.3:c.4030G>T	p.Glu1344Ter	p.E1344*	ENST00000356175	NM_000267.3	1344	Gaa/Taa	30/57	0.431615842853692	5	FACETS	1	0.979	1	0.45	0.405	0.498	CLONAL	1	TRUE	2	0.431615842853692	5		399	622	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39647475	39647475	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058612-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	112	351	0	ENST00000262039.4:c.2647C>T	p.Gln883Ter	p.Q883*	ENST00000262039	NM_002647.2	883	Cag/Tag	24/25	0.331496410372633	3	FACETS	0.807	0.732	0.885	0.807	0.732	0.885	CLONAL	2	TRUE	1	0.431615842853692	3		351	391	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097115	11097115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058612-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	243	455	0	ENST00000358026.2:c.607del	p.Ala203ArgfsTer100	p.A203Rfs*100	ENST00000358026	NM_001128849.1	202	atG/at	4/36	0.416076365829928	2	FACETS	0.967	0.911	1	0.967	0.911	1	CLONAL	2	TRUE	0	0.431615842853692	2		455	582	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42381449	42381449	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058612-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	181	491	0	ENST00000221972.3:c.75C>A	p.Tyr25Ter	p.Y25*	ENST00000221972	NM_021601.3	25	taC/taA	1/5	0.431615842853692	6	FACETS	0.881	0.813	0.951	0.44	0.406	0.476	CLONAL	2	TRUE	2	0.431615842853692	6		491	887	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47492836	47492836	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058612-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	151	389	0	ENST00000404338.3:c.3940G>T	p.Val1314Leu	p.V1314L	ENST00000404338	NM_004491.4	1314	Gtg/Ttg	4/6	0.406278309909303	4	FACETS	0.853	0.784	0.925	0.853	0.784	0.925	CLONAL	2	TRUE	2	0.431615842853692	4		389	587	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979303	40979303	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058612-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	171	360	0	ENST00000373198.4:c.1830G>T	p.Met610Ile	p.M610I	ENST00000373198	NM_133170.3	610	atG/atT	11/32	0.406278309909303	4	FACETS	0.976	0.903	1	0.976	0.903	1	CLONAL	2	TRUE	2	0.431615842853692	4		360	581	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119595357	119595357	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0058612-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	50	263	0	ENST00000316626.5:c.814-2A>G		p.X272_splice	ENST00000316626		272			0.431615842853692	5	FACETS	0.858	0.729	0.999	0.214	0.182	0.25	CLONAL	1	TRUE	1	0.431615842853692	5		263	445	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169981209	169981209	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058612-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	242	224	0	ENST00000295797.4:c.356G>T	p.Gly119Val	p.G119V	ENST00000295797	NM_002740.5	119	gGa/gTa	4/18	0.431615842853692	6	FACETS	0.963	0.914	1	0.963	0.914	1	CLONAL	5	TRUE	1	0.431615842853692	6		224	434	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157311	106157311	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058612-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	85	459	0	ENST00000380013.4:c.2212C>G	p.Leu738Val	p.L738V	ENST00000380013	NM_001127208.2	738	Ctc/Gtc	3/11	0.381466551348431	3	FACETS	0.939	0.832	1	0.469	0.416	0.526	CLONAL	1	TRUE	1	0.431615842853692	3		459	510	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293568	1293568	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058612-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	238	439	0	ENST00000310581.5:c.1433G>T	p.Trp478Leu	p.W478L	ENST00000310581	NM_198253.2	478	tGg/tTg	2/16	0.376690500251327	5	FACETS	0.847	0.794	0.901	0.847	0.794	0.901	CLONAL	3	TRUE	2	0.431615842853692	5		439	715	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295547	1295547	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215810	NA	P-0058612-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	127	519	0				ENST00000310581	NM_198253.2	-/1132			0.376690500251327	5	FACETS	1	0.947	1	0.356	0.322	0.392	CLONAL	1	TRUE	2	0.431615842853692	5		519	908	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295651	1295651	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0058612-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	129	528	0				ENST00000310581	NM_198253.2	-/1132			0.376690500251327	5	FACETS	1	0.936	1	0.348	0.315	0.383	CLONAL	1	TRUE	2	0.431615842853692	5		528	944	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876520	35876520	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058612-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	76	420	0	ENST00000303115.3:c.1312C>A	p.Leu438Ile	p.L438I	ENST00000303115	NM_002185.3	438	Ctt/Att	8/8	0.376690500251327	5	FACETS	0.862	0.756	0.976	0.287	0.252	0.326	CLONAL	1	TRUE	2	0.431615842853692	5		420	673	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675185	176675185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058612-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	234	334	0	ENST00000439151.2:c.4501G>A	p.Glu1501Lys	p.E1501K	ENST00000439151	NM_022455.4	1501	Gaa/Aaa	11/23	0.406225042772442	4	FACETS	0.989	0.932	1	0.989	0.932	1	CLONAL	3	TRUE	1	0.431615842853692	4		334	523	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979326	93979326	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058612-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	178	325	0	ENST00000369303.4:c.1502C>A	p.Ser501Tyr	p.S501Y	ENST00000369303	NM_004440.3	501	tCc/tAc	7/17	0.396419504224238	3	FACETS	0.969	0.909	1	0.969	0.909	1	CLONAL	3	TRUE	0	0.431615842853692	3		325	345	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519351	137519351	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058612-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	241	347	0	ENST00000367739.4:c.1287A>T	p.Glu429Asp	p.E429D	ENST00000367739	NM_000416.2	429	gaA/gaT	7/7	0.396419504224238	3	FACETS	0.922	0.871	0.972	0.922	0.871	0.972	CLONAL	3	TRUE	0	0.431615842853692	3		347	491	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964473	70964473	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058612-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	107	440	0	ENST00000276594.2:c.1555T>C	p.Cys519Arg	p.C519R	ENST00000276594	NM_024504.3	519	Tgc/Cgc	8/8	0.381466551348431	3	FACETS	1	0.939	1	0.531	0.477	0.587	CLONAL	1	TRUE	1	0.431615842853692	3		440	568	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117875369	117875369	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058612-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	108	291	0	ENST00000297338.2:c.274G>T	p.Gly92Cys	p.G92C	ENST00000297338	NM_006265.2	92	Ggt/Tgt	3/14	0.381466551348431	3	FACETS	0.89	0.807	0.975	0.89	0.807	0.975	CLONAL	2	TRUE	1	0.431615842853692	3		291	342	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2104034	2104034	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058612-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	56	365	0	ENST00000349721.2:c.3157G>A	p.Glu1053Lys	p.E1053K	ENST00000349721	NM_003070.3	1053	Gag/Aag	23/34	0.394693949909131	2	FACETS	0.75	0.646	0.863	0.375	0.323	0.432	SUBCLONAL	1	TRUE	0	0.431615842853692	2		365	346	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460418	8460418	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058612-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	106	280	0	ENST00000356435.5:c.3868T>A	p.Tyr1290Asn	p.Y1290N	ENST00000356435		1290	Tat/Aat	22/35	0.394693949909131	2	FACETS	0.896	0.817	0.978	0.896	0.817	0.978	CLONAL	2	TRUE	0	0.431615842853692	2		280	274	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890149	76890149	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058612-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	102	159	0	ENST00000373344.5:c.4745C>A	p.Thr1582Lys	p.T1582K	ENST00000373344	NM_000489.3	1582	aCa/aAa	17/35	0.208653432862145	2	FACETS	1	0.97	1			1	INDETERMINATE	2	TRUE	NA	0.431615842853692	2		159	208	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0058614-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	55	265	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.2	2		265	407	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589761	69589761	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058614-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	37	828	0	ENST00000168712.1:c.92del	p.Ala31AspfsTer96	p.A31Dfs*96	ENST00000168712	NM_002007.2	31	gCa/ga	1/3	1	2	FACETS	0.565	0.464	0.678	0.565	0.464	0.678	SUBCLONAL	1	TRUE	1	0.2	2		828	655	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21348891	21348891	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058614-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	41	598	0	ENST00000215739.8:c.1660G>C	p.Ala554Pro	p.A554P	ENST00000215739	NM_006767.3	554	Gca/Cca	15/21	1	2	FACETS	0.711	0.591	0.844	0.711	0.591	0.844	SUBCLONAL	1	TRUE	1	0.2	2		598	577	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729528	41729528	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058614-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	40	515	0	ENST00000242208.4:c.1001G>C	p.Gly334Ala	p.G334A	ENST00000242208	NM_002192.2	334	gGc/gCc	3/3	1	2	FACETS	0.598	0.496	0.712	0.598	0.496	0.712	SUBCLONAL	1	TRUE	1	0.2	2		515	669	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482820	140482820	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0058614-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	99	482	0	ENST00000288602.6:c.1314+1G>T		p.X438_splice	ENST00000288602	NM_004333.4	438			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.2	2		482	711	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034444	47034444	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058614-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	29	414	0	ENST00000377604.3:c.529G>T	p.Glu177Ter	p.E177*	ENST00000377604	NM_001204468.1	177	Gag/Tag	6/24	1	2	FACETS	0.647	0.519	0.794	0.647	0.519	0.794	SUBCLONAL	1	TRUE	1	0.2	2		414	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0058615-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	137	328	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.490344703213003	1	FACETS	0.935	0.858	1	0.935	0.858	1	CLONAL	1	TRUE	0	0.490344703213003	1		328	451	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408885	41408885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868295248	NA	P-0058615-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	121	435	0	ENST00000373198.4:c.541G>A	p.Glu181Lys	p.E181K	ENST00000373198	NM_133170.3	181	Gag/Aag	4/32	1	2	FACETS	0.839	0.761	0.922	0.839	0.761	0.922	CLONAL	1	TRUE	1	0.490344703213003	2		435	588	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522551	176522551	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058615-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	188	712	0	ENST00000292408.4:c.1648G>C	p.Val550Leu	p.V550L	ENST00000292408	NM_213647.1	550	Gtg/Ctg	13/18	1	2	FACETS	0.937	0.868	1	0.937	0.868	1	CLONAL	1	TRUE	1	0.490344703213003	2		712	818	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374915	149374915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772542532	NA	P-0058615-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	165	568	0	ENST00000360632.3:c.179C>T	p.Ser60Leu	p.S60L	ENST00000360632	NM_015472.4	60	tCg/tTg	2/7	1	2	FACETS	0.963	0.887	1	0.963	0.887	1	CLONAL	1	TRUE	1	0.490344703213003	2		568	699	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456648	32456648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752686863	NA	P-0058615-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	121	489	1	ENST00000332351.3:c.244G>A	p.Ala82Thr	p.A82T	ENST00000332351	NM_024426.4	82	Gcc/Acc	1/10	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.490344703213003	2		490	471	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38960627	38960627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376491170	NA	P-0058615-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	108	342	0	ENST00000357387.3:c.1724G>A	p.Arg575Gln	p.R575Q	ENST00000357387	NM_152756.3	575	cGa/cAa	20/38	1	2	FACETS	0.769	0.692	0.85	0.769	0.692	0.85	SUBCLONAL	1	TRUE	1	0.490344703213003	2		342	573	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155416	185155416	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058615-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	120	418	0	ENST00000265026.3:c.657C>G	p.Phe219Leu	p.F219L	ENST00000265026	NM_004721.4	219	ttC/ttG	3/14	1	2	FACETS	0.945	0.857	1	0.945	0.857	1	CLONAL	1	TRUE	1	0.490344703213003	2		418	518	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214068	36214068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058615-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	167	608	0	ENST00000222270.7:c.2894G>A	p.Arg965Gln	p.R965Q	ENST00000222270	NM_014727.1	965	cGa/cAa	6/37	1	2	FACETS	0.902	0.831	0.977	0.902	0.831	0.977	CLONAL	1	TRUE	1	0.490344703213003	2		608	755	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845616	68845616	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058615-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	161	426	0	ENST00000261769.5:c.862G>C	p.Asp288His	p.D288H	ENST00000261769	NM_004360.3	288	Gac/Cac	7/16	0.490344703213003	1	FACETS	0.93	0.858	1	0.93	0.858	1	CLONAL	1	TRUE	0	0.490344703213003	1		426	533	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023214	27023214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1473846356	NA	P-0058615-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	120	500	0	ENST00000324856.7:c.320C>T	p.Ala107Val	p.A107V	ENST00000324856	NM_006015.4	107	gCg/gTg	1/20	1	2	FACETS	0.92	0.834	1	0.92	0.834	1	CLONAL	1	TRUE	1	0.490344703213003	2		500	532	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36824405	36824405	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058615-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	120	455	0	ENST00000373129.3:c.131C>A	p.Ser44Ter	p.S44*	ENST00000373129	NM_032017.1	44	tCa/tAa	4/12	0.490344703213003	1	FACETS	0.736	0.668	0.807	0.736	0.668	0.807	SUBCLONAL	1	TRUE	0	0.490344703213003	1		455	502	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150917513	150917513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058615-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	166	561	0	ENST00000271640.5:c.1069G>T	p.Glu357Ter	p.E357*	ENST00000271640	NM_001145415.1	357	Gag/Tag	9/22	1	2	FACETS	0.874	0.804	0.946	0.874	0.804	0.946	CLONAL	1	TRUE	1	0.490344703213003	2		561	775	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111433	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	G	novel	NA	P-0058615-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	153	505	0	ENST00000346208.3:c.922-3C>G		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.972	0.892	1	0.972	0.892	1	CLONAL	1	TRUE	1	0.490344703213003	2		505	642	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	430265	430265	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058615-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	119	426	0	ENST00000399788.2:c.2437G>C	p.Asp813His	p.D813H	ENST00000399788	NM_001042603.1	813	Gat/Cat	18/28	1	2	FACETS	0.906	0.821	0.994	0.906	0.821	0.994	CLONAL	1	TRUE	1	0.490344703213003	2		426	536	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445091	49445091	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058615-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	180	650	0	ENST00000301067.7:c.2375C>G	p.Ala792Gly	p.A792G	ENST00000301067	NM_003482.3	792	gCt/gGt	10/54	1	2	FACETS	0.92	0.85	0.993	0.92	0.85	0.993	CLONAL	1	TRUE	1	0.490344703213003	2		650	798	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865229	40865229	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058615-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	130	380	0	ENST00000428826.2:c.1202C>T	p.Ser401Leu	p.S401L	ENST00000428826		401	tCa/tTa	11/21	0.490344703213003	1	FACETS	0.895	0.818	0.975	0.895	0.818	0.975	CLONAL	1	TRUE	0	0.490344703213003	1		380	447	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760886	59760886	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786202662	NA	P-0058615-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	89	390	0	ENST00000259008.2:c.3521G>C	p.Arg1174Thr	p.R1174T	ENST00000259008	NM_032043.2	1174	aGa/aCa	20/20	0.45280547559409	5	FACETS	1	0.895	1	0.202	0.179	0.226	CLONAL	1	TRUE	0	0.490344703213003	5		390	625	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7128953	7128953	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0058615-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	81	416	0	ENST00000302850.5:c.2855C>G	p.Ser952Ter	p.S952*	ENST00000302850	NM_000208.2	952	tCa/tGa	15/22	1	2	FACETS	0.697	0.616	0.783	0.697	0.616	0.783	SUBCLONAL	1	TRUE	1	0.490344703213003	2		416	474	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291044	15291044	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058615-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	162	630	0	ENST00000263388.2:c.3166C>T	p.Gln1056Ter	p.Q1056*	ENST00000263388	NM_000435.2	1056	Cag/Tag	20/33	1	2	FACETS	0.916	0.843	0.993	0.916	0.843	0.993	CLONAL	1	TRUE	1	0.490344703213003	2		630	721	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023297	31023297	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058615-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	157	504	0	ENST00000375687.4:c.2782G>C	p.Glu928Gln	p.E928Q	ENST00000375687	NM_015338.5	928	Gag/Cag	13/13	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.490344703213003	2		504	635	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024034	31024034	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058615-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	150	596	0	ENST00000375687.4:c.3519G>C	p.Leu1173Phe	p.L1173F	ENST00000375687	NM_015338.5	1173	ttG/ttC	13/13	1	2	FACETS	0.8	0.732	0.871	0.8	0.732	0.871	SUBCLONAL	1	TRUE	1	0.490344703213003	2		596	765	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796797	57796815	+	frameshift_variant	Frame_Shift_Del	DEL	AAGCAGTAAGCCTCCTCAG	AAGCAGTAAGCCTCCTCAG	-	novel	NA	P-0058615-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	102	586	0	ENST00000309042.7:c.1776_1794del	p.Ser592ArgfsTer119	p.S592Rfs*119	ENST00000309042	NM_005612.4	591	aaAAGCAGTAAGCCTCCTCAG/aa	4/4	0.490344703213003	1	FACETS	0.729	0.656	0.805	0.729	0.656	0.805	SUBCLONAL	1	TRUE	0	0.490344703213003	1		586	431	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332681	153332681	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0058615-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	163	546	0	ENST00000281708.4:c.275C>G	p.Ser92Ter	p.S92*	ENST00000281708	NM_033632.3	92	tCa/tGa	2/12	0.446980621692977	2	FACETS	0.895	0.823	0.97	0.447	0.411	0.485	CLONAL	1	TRUE	0	0.490344703213003	2		546	743	SUCCESS
APC	324	MSKCC	GRCh37	5	112173313	112173313	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058615-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	88	427	0	ENST00000257430.4:c.2022G>C	p.Leu674Phe	p.L674F	ENST00000257430	NM_000038.5	674	ttG/ttC	16/16	1	2	FACETS	0.794	0.707	0.887	0.794	0.707	0.887	SUBCLONAL	1	TRUE	1	0.490344703213003	2		427	452	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459791	149459791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569441099	NA	P-0058615-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	158	618	0	ENST00000286301.3:c.416C>T	p.Ser139Leu	p.S139L	ENST00000286301	NM_005211.3	139	tCg/tTg	4/22	1	2	FACETS	0.888	0.815	0.963	0.888	0.815	0.963	CLONAL	1	TRUE	1	0.490344703213003	2		618	726	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288703	33288703	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058615-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	167	544	0	ENST00000374542.5:c.849C>A	p.Phe283Leu	p.F283L	ENST00000374542	NM_001141970.1	283	ttC/ttA	3/8	1	2	FACETS	0.911	0.838	0.986	0.911	0.838	0.986	CLONAL	1	TRUE	1	0.490344703213003	2		544	748	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	32	192	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.828	1	1	0.828	1	CLONAL	1	TRUE	1	0.336668900356567	2		192	188	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	52	608	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.772	0.659	0.895	0.772	0.659	0.895	SUBCLONAL	1	TRUE	1	0.336668900356567	2		609	400	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	22	697	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.434	0.337	0.547	0.434	0.337	0.547	SUBCLONAL	1	TRUE	1	0.336668900356567	2		699	301	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	58	544	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.84	0.724	0.966	0.84	0.724	0.966	CLONAL	1	TRUE	1	0.336668900356567	2		548	410	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	27	250	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.336668900356567	2		250	134	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	58	478	4	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.971	0.838	1	0.971	0.838	1	CLONAL	1	TRUE	1	0.336668900356567	2		482	355	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	69	520	1	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.94	0.822	1	0.94	0.822	1	CLONAL	1	TRUE	1	0.336668900356567	2		521	436	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	52	196	2	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.336668900356567	2		198	214	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270530	98270530	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs751977093	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	34	306	1	ENST00000331920.6:c.114del	p.Leu39CysfsTer41	p.L39Cfs*41	ENST00000331920	NM_000264.3	38	ggG/gg	1/24	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.336668900356567	2		307	171	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005482	42005482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775446234	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	72	519	0	ENST00000219905.7:c.3218G>A	p.Arg1073Gln	p.R1073Q	ENST00000219905	NM_001164273.1	1073	cGa/cAa	9/24	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.336668900356567	2		519	417	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256768	19256769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1202792889	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	30	432	0	ENST00000162023.5:c.944dup	p.Val316SerfsTer6	p.V316Sfs*6	ENST00000162023		315	cca/ccCa	13/13	1	2	FACETS	0.568	0.458	0.691	0.568	0.458	0.691	SUBCLONAL	1	TRUE	1	0.336668900356567	2		432	314	SUCCESS
APC	324	MSKCC	GRCh37	5	112174490	112174493	+	frameshift_variant	Frame_Shift_Del	DEL	CAAT	CAAT	-	rs587779353	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	46	301	0	ENST00000257430.4:c.3202_3205del	p.Ser1068GlyfsTer57	p.S1068Gfs*57	ENST00000257430	NM_000038.5	1067	CAATca/ca	16/16	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.336668900356567	2		301	266	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851693	134851693	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1042789	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	52	413	0	ENST00000398015.3:c.1099C>T	p.Arg367Cys	p.R367C	ENST00000398015	NM_004441.4	367	Cgc/Tgc	5/16	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.336668900356567	2		413	256	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154242	2154242	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755455183	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	48	600	2	ENST00000434045.2:c.686del	p.Pro229GlnfsTer27	p.P229Qfs*27	ENST00000434045	NM_001127598.1	229	cCa/ca	5/5	1	2	FACETS	0.957	0.814	1	0.957	0.814	1	CLONAL	1	TRUE	1	0.336668900356567	2		602	298	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911535	101911535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113605875	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	35	313	0	ENST00000374994.4:c.1460G>A	p.Arg487Gln	p.R487Q	ENST00000374994	NM_004612.2	487	cGg/cAg	9/9	1	2	FACETS	0.751	0.618	0.898	0.751	0.618	0.898	SUBCLONAL	1	TRUE	1	0.336668900356567	2		313	277	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	75	501	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.336668900356567	2		501	430	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141632	202141632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764461240	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	55	367	0	ENST00000358485.4:c.920G>A	p.Arg307Gln	p.R307Q	ENST00000358485	NM_001080125.1	307	cGg/cAg	7/9	1	2	FACETS	0.92	0.791	1	0.92	0.791	1	CLONAL	1	TRUE	1	0.336668900356567	2		367	355	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637690	52637690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239654517	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	45	217	0	ENST00000394830.3:c.2626C>T	p.Arg876Cys	p.R876C	ENST00000394830	NM_018313.4	876	Cgt/Tgt	18/30	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.336668900356567	2		217	190	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169116	32169116	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1263727065	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	58	483	3	ENST00000375023.3:c.3917del	p.Pro1306GlnfsTer3	p.P1306Qfs*3	ENST00000375023	NM_004557.3	1306	cCa/ca	22/30	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.336668900356567	2		486	312	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510806	157510806	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	47	379	0	ENST00000346085.5:c.3586del	p.Gln1196SerfsTer15	p.Q1196Sfs*15	ENST00000346085	NM_020732.3	1194	aCc/ac	14/20	1	2	FACETS	0.901	0.764	1	0.901	0.764	1	CLONAL	1	TRUE	1	0.336668900356567	2		379	310	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2492096	2492097	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs772088410	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	40	391	0	ENST00000355716.4:c.500dup	p.Thr169AspfsTer65	p.T169Dfs*65	ENST00000355716	NM_003820.2	165	tgc/tgCc	5/8	1	2	FACETS	0.88	0.736	1	0.88	0.736	1	CLONAL	1	TRUE	1	0.336668900356567	2		391	270	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955112	17955112	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755706305	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	46	426	1	ENST00000458235.1:c.115del	p.Gln39SerfsTer108	p.Q39Sfs*108	ENST00000458235	NM_000215.3	39	Cag/ag	2/24	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.336668900356567	2		427	270	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416952	416953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs771545848	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	61	437	5	ENST00000399788.2:c.3597dup	p.Gly1200ArgfsTer7	p.G1200Rfs*7	ENST00000399788	NM_001042603.1	1199	-/A	23/28	1	2	FACETS	0.924	0.801	1	0.924	0.801	1	CLONAL	1	TRUE	1	0.336668900356567	2		442	392	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911288	29911288	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs45552635	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	39	477	1	ENST00000376809.5:c.587T>C	p.Leu196Pro	p.L196P	ENST00000376809	NM_002116.7	196	cTg/cCg	3/8	1	2	FACETS	0.715	0.595	0.848	0.715	0.595	0.848	SUBCLONAL	1	TRUE	1	0.336668900356567	2		478	324	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627217	37627217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370304179	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	66	338	0	ENST00000447079.4:c.1132C>T	p.Arg378Cys	p.R378C	ENST00000447079	NM_015083.1	378	Cgc/Tgc	2/14	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.336668900356567	2		338	342	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032574	12032574	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	42	339	0	ENST00000353533.5:c.1013del	p.Pro338ArgfsTer25	p.P338Rfs*25	ENST00000353533	NM_003010.3	337	tCc/tc	9/11	1	2	FACETS	0.875	0.735	1	0.875	0.735	1	CLONAL	1	TRUE	1	0.336668900356567	2		339	285	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857958	9857958	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs140536516	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	46	458	0	ENST00000330684.3:c.3443C>A	p.Pro1148Gln	p.P1148Q	ENST00000330684	NM_001134407.1	1148	cCg/cAg	13/13	1	2	FACETS	0.813	0.688	0.951	0.813	0.688	0.951	CLONAL	1	TRUE	1	0.336668900356567	2		458	336	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947452	38947452	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1406752443	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	31	412	0	ENST00000357387.3:c.4228C>T	p.Arg1410Trp	p.R1410W	ENST00000357387	NM_152756.3	1410	Cgg/Tgg	32/38	1	2	FACETS	0.572	0.463	0.694	0.572	0.463	0.694	SUBCLONAL	1	TRUE	1	0.336668900356567	2		412	322	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984407	201984407	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	140	393	0	ENST00000359651.3:c.1072T>C	p.Ser358Pro	p.S358P	ENST00000359651		358	Tca/Cca	8/8	0.336668900356567	2	FACETS	0.84	0.777	0.904	1	0.984	1	CLONAL	3	TRUE	0	0.336668900356567	2		393	330	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710625	114710626	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	61	365	0	ENST00000543371.1:c.115_116dup	p.Asp40GlyfsTer3	p.D40Gfs*3	ENST00000543371	NM_001198531.1	37	gca/gcAGa	1/14	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.336668900356567	2		365	322	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178656	108178656	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587781730	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	41	268	0	ENST00000278616.4:c.5712del	p.Lys1904AsnfsTer13	p.K1904Nfs*13	ENST00000278616	NM_000051.3	1903	Aaa/aa	38/63	1	2	FACETS	0.982	0.824	1	0.982	0.824	1	CLONAL	1	TRUE	1	0.336668900356567	2		268	248	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434467	110434467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772356858	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	44	405	0	ENST00000375856.3:c.3934G>A	p.Gly1312Ser	p.G1312S	ENST00000375856	NM_003749.2	1312	Ggt/Agt	1/2	1	2	FACETS	0.914	0.771	1	0.914	0.771	1	CLONAL	1	TRUE	1	0.336668900356567	2		405	286	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961510	41961510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs189815293	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	38	362	0	ENST00000219905.7:c.418C>T	p.Arg140Cys	p.R140C	ENST00000219905	NM_001164273.1	140	Cgt/Tgt	2/24	1	2	FACETS	0.781	0.649	0.928	0.781	0.649	0.928	CLONAL	1	TRUE	1	0.336668900356567	2		362	289	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669522	88669522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568926009	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	33	269	0	ENST00000360948.2:c.1376G>A	p.Arg459Gln	p.R459Q	ENST00000360948	NM_001012338.2	459	cGg/cAg	12/19	1	2	FACETS	0.817	0.669	0.981	0.817	0.669	0.981	CLONAL	1	TRUE	1	0.336668900356567	2		269	240	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467842	99467842	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760639369	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	43	451	0	ENST00000268035.6:c.2711G>A	p.Arg904Gln	p.R904Q	ENST00000268035	NM_000875.3	904	cGg/cAg	13/21	1	2	FACETS	0.791	0.664	0.93	0.791	0.664	0.93	CLONAL	1	TRUE	1	0.336668900356567	2		451	323	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830199	72830199	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	45	502	0	ENST00000268489.5:c.6382C>A	p.Leu2128Met	p.L2128M	ENST00000268489	NM_006885.3	2128	Ctg/Atg	9/10	1	2	FACETS	0.951	0.805	1	0.951	0.805	1	CLONAL	1	TRUE	1	0.336668900356567	2		502	281	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559168	29559168	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	35	218	0	ENST00000356175.3:c.3275G>C	p.Gly1092Ala	p.G1092A	ENST00000356175	NM_000267.3	1092	gGt/gCt	25/57	1	2	FACETS	0.967	0.799	1	0.967	0.799	1	CLONAL	1	TRUE	1	0.336668900356567	2		218	215	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29686010	29686010	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757391670	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	33	235	0	ENST00000356175.3:c.8074C>T	p.Arg2692Trp	p.R2692W	ENST00000356175	NM_000267.3	2692	Cgg/Tgg	55/57	1	2	FACETS	0.929	0.763	1	0.929	0.763	1	CLONAL	1	TRUE	1	0.336668900356567	2		235	211	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226796	2226796	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1358779949	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	62	522	0	ENST00000398665.3:c.4276C>A	p.Leu1426Ile	p.L1426I	ENST00000398665	NM_032482.2	1426	Ctc/Atc	27/28	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.336668900356567	2		522	351	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7128929	7128929	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	48	338	0	ENST00000302850.5:c.2879G>C	p.Gly960Ala	p.G960A	ENST00000302850	NM_000208.2	960	gGc/gCc	15/22	1	2	FACETS	0.96	0.817	1	0.96	0.817	1	CLONAL	1	TRUE	1	0.336668900356567	2		338	297	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132512	11132512	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	13	485	0	ENST00000358026.2:c.2728A>T	p.Thr910Ser	p.T910S	ENST00000358026	NM_001128849.1	910	Acg/Tcg	19/36	1	2	FACETS	0.208	0.147	0.282	0.208	0.147	0.282	SUBCLONAL	1	TRUE	1	0.336668900356567	2		485	372	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350002	15350002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	64	438	0	ENST00000263377.2:c.3650C>T	p.Ala1217Val	p.A1217V	ENST00000263377	NM_058243.2	1217	gCc/gTc	18/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.336668900356567	2		438	316	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754461	41754461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777326148	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	63	426	0	ENST00000301178.4:c.1580G>A	p.Arg527Gln	p.R527Q	ENST00000301178	NM_021913.4	527	cGg/cAg	13/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.336668900356567	2		426	313	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383633	42383633	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	45	396	0	ENST00000221972.3:c.412del	p.Glu138ArgfsTer54	p.E138Rfs*54	ENST00000221972	NM_021601.3	136	atG/at	3/5	1	2	FACETS	0.958	0.81	1	0.958	0.81	1	CLONAL	1	TRUE	1	0.336668900356567	2		396	279	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082451	16082451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	54	413	0	ENST00000281043.3:c.265G>A	p.Gly89Ser	p.G89S	ENST00000281043	NM_005378.4	89	Ggc/Agc	2/3	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.336668900356567	2		413	261	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142865	30142865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	49	453	0	ENST00000389048.3:c.661G>A	p.Gly221Arg	p.G221R	ENST00000389048	NM_004304.4	221	Ggg/Agg	1/29	1	2	FACETS	0.936	0.797	1	0.936	0.797	1	CLONAL	1	TRUE	1	0.336668900356567	2		453	311	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637505	47637506	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	49	357	0	ENST00000233146.2:c.641_642del	p.Arg214ThrfsTer17	p.R214Tfs*17	ENST00000233146	NM_000251.2	213	ctGAga/ctga	3/16	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.336668900356567	2		357	289	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513494	41513494	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	46	470	0	ENST00000263253.7:c.398C>T	p.Ser133Phe	p.S133F	ENST00000263253	NM_001429.3	133	tCt/tTt	2/31	1	2	FACETS	0.781	0.66	0.913	0.781	0.66	0.913	CLONAL	1	TRUE	1	0.336668900356567	2		470	350	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430430	181430431	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	49	522	0	ENST00000325404.1:c.284dup	p.Arg96AlafsTer14	p.R96Afs*14	ENST00000325404	NM_003106.3	94	-/A	1/1	1	2	FACETS	0.958	0.816	1	0.958	0.816	1	CLONAL	1	TRUE	1	0.336668900356567	2		522	304	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032176	26032176	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1561919109	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	81	598	3	ENST00000244661.2:c.113del	p.Lys38SerfsTer25	p.K38Sfs*25	ENST00000244661	NM_003537.3	38	aAg/ag	1/1	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.336668900356567	2		601	455	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911281	29911282	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	37	446	0	ENST00000376809.5:c.581_582del	p.Arg194IlefsTer26	p.R194Ifs*26	ENST00000376809	NM_002116.7	194	AGa/a	3/8	1	2	FACETS	0.702	0.581	0.837	0.702	0.581	0.837	SUBCLONAL	1	TRUE	1	0.336668900356567	2		446	313	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911318	29911318	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs199474584	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	29	669	2	ENST00000376809.5:c.617C>T	p.Thr206Met	p.T206M	ENST00000376809	NM_002116.7	206	aCg/aTg	3/8	1	2	FACETS	0.397	0.318	0.487	0.397	0.318	0.487	SUBCLONAL	1	TRUE	1	0.336668900356567	2		671	434	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967236	93967236	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058616-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	18	203	0	ENST00000369303.4:c.2116C>G	p.Pro706Ala	p.P706A	ENST00000369303	NM_004440.3	706	Cca/Gca	12/17	1	2	FACETS	0.786	0.598	1	0.786	0.598	1	CLONAL	1	TRUE	1	0.336668900356567	2		203	136	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0058621-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	146	428	0	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	0.275393079752953	3	FACETS	1	0.976	1	0.778	0.714	0.843	CLONAL	2	TRUE	0	0.283489370248029	3		428	504	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124268	2124268	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0058621-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	49	380	1	ENST00000219476.3:c.2423T>A	p.Leu808Ter	p.L808*	ENST00000219476	NM_000548.3	808	tTg/tAg	22/42	0.218990378601005	3	FACETS	0.858	0.727	1	0.286	0.242	0.334	CLONAL	1	TRUE	0	0.283489370248029	3		381	460	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587126	212587126	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058621-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	56	292	0	ENST00000342788.4:c.875A>C	p.Lys292Thr	p.K292T	ENST00000342788	NM_005235.2	292	aAa/aCa	7/28	0.237375903242004	2	FACETS	0.998	0.858	1	0.499	0.429	0.575	CLONAL	1	TRUE	0	0.283489370248029	2		292	396	SUCCESS
APC	324	MSKCC	GRCh37	5	112163677	112163677	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0058633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	115	273	0	ENST00000257430.4:c.1600A>T	p.Lys534Ter	p.K534*	ENST00000257430	NM_000038.5	534	Aaa/Taa	13/16	0.443161469457506	1	FACETS	0.771	0.708	0.835	1	0.987	1	SUBCLONAL	2	FALSE	0	0.443161469457506	1		273	262	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970916	21970916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3731249	NA	P-0058633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	78	475	0	ENST00000304494.5:c.442G>A	p.Ala148Thr	p.A148T	ENST00000304494	NM_000077.4	148	Gcg/Acg	2/3	0.123332277570198	4	FACETS	1	0.9	1	0.512	0.451	0.577	INDETERMINATE	1	FALSE	2	0.443161469457506	4		475	496	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467922	50467922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	83	437	0	ENST00000331340.3:c.1157G>A	p.Arg386His	p.R386H	ENST00000331340	NM_006060.4	386	cGc/cAc	8/8	0.443161469457506	5	FACETS	0.913	0.806	1	0.304	0.268	0.343	CLONAL	1	FALSE	2	0.443161469457506	5		437	683	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920424	114920425	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0058633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	194	362	0	ENST00000543371.1:c.1366_1367del	p.Gln456AspfsTer20	p.Q456Dfs*20	ENST00000543371	NM_001198531.1	455	cgACag/cgag	13/14	0.139858348214467	5	FACETS	0.996	0.93	1	0.747	0.698	0.797	INDETERMINATE	3	FALSE	1	0.443161469457506	5		362	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576893	7576894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCTGGGGA	novel	NA	P-0058633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	258	485	0	ENST00000269305.4:c.945_952dup	p.Pro318LeufsTer30	p.P318Lfs*30	ENST00000269305	NM_001126112.2	318	cca/cTCCCCAGCca	9/11	0.443161469457506	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	FALSE	0	0.443161469457506	2		485	559	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231617	5231617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	68	126	0	ENST00000357368.4:c.1859C>T	p.Ala620Val	p.A620V	ENST00000357368	NM_002850.3	620	gCc/gTc	14/38	0.101717787872131	6	FACETS	0.98	0.868	1	0.98	0.868	1	INDETERMINATE	3	FALSE	3	0.443161469457506	6		126	197	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056655	26056655	+	start_lost	Translation_Start_Site	SNP	A	A	T	novel	NA	P-0058633-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	72	359	0	ENST00000343677.2:c.2T>A	p.Met1?	p.M1?	ENST00000343677	NM_005319.3	1	aTg/aAg	1/1	0.139858348214467	5	FACETS	1	0.972	1	0.35	0.307	0.396	INDETERMINATE	1	FALSE	1	0.443161469457506	5		359	386	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0058635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	115	366	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.3	3	FACETS	0.905	0.825	0.988	1	0.99	1	CLONAL	5	TRUE	1	0.16	3		366	343	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974744	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAGCAGCGCCCGCA	CCTCCAGCAGCGCCCGCA	-	novel	NA	P-0058635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	23	451	0	ENST00000304494.5:c.83_100del	p.Val28_Glu33del	p.V28_E33del	ENST00000304494	NM_000077.4	28	gTGCGGGCGCTGCTGGAGGcg/gcg	1/3	1	2	FACETS	1	0.833	1	1	0.833	1	CLONAL	1	TRUE	1	0.16	2		451	266	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579316	7579317	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0058635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	16	357	0	ENST00000269305.4:c.369_370dup	p.Cys124PhefsTer47	p.C124Ffs*47	ENST00000269305	NM_001126112.2	124	tgc/tTTgc	4/11	0.3	1	FACETS	0.702	0.519	0.921	0.702	0.519	0.921	CLONAL	1	TRUE	0	0.16	1		357	262	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437618	52437618	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs765929006	NA	P-0058635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	21	533	0	ENST00000460680.1:c.1543A>C	p.Asn515His	p.N515H	ENST00000460680	NM_004656.3	515	Aac/Cac	13/17	1	2	FACETS	0.899	0.693	1	0.899	0.693	1	CLONAL	1	TRUE	1	0.16	2		533	292	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748004	72748005	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	AA	AA	CC	novel	NA	P-0058635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	21	343	0	ENST00000357731.5:c.173_174delinsGG	p.Leu58Arg	p.L58R	ENST00000357731	NM_173808.2	58	cTT/cGG	1/7	1	2	FACETS	0.731	0.562	0.928	0.731	0.562	0.928	CLONAL	1	TRUE	1	0.16	2		343	359	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864544	57864544	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058635-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	20	501	0	ENST00000228682.2:c.2021A>C	p.Gln674Pro	p.Q674P	ENST00000228682	NM_005269.2	674	cAg/cCg	12/12	1	2	FACETS	0.772	0.59	0.985	0.772	0.59	0.985	CLONAL	1	TRUE	1	0.16	2		501	324	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0058636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	70	206	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.39507093729325	2		206	335	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204864	NA	P-0058636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	62	230	0	ENST00000371953.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000371953	NM_000314.4	171	Cag/Tag	6/9	1	2	FACETS	0.918	0.798	1	0.918	0.798	1	CLONAL	1	TRUE	1	0.39507093729325	2		230	342	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375967	8375967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	42	260	0	ENST00000356435.5:c.4630C>T	p.Pro1544Ser	p.P1544S	ENST00000356435		1544	Ccc/Tcc	28/35	1	2	FACETS	0.561	0.469	0.662	0.561	0.469	0.662	SUBCLONAL	1	TRUE	1	0.39507093729325	2		260	379	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966955	25966955	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	141	442	0	ENST00000435504.4:c.2251C>T	p.Gln751Ter	p.Q751*	ENST00000435504		751	Cag/Tag	13/13	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.39507093729325	2		442	622	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910755	29910755	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs41542015	NA	P-0058636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	149	456	0	ENST00000376809.5:c.295C>T	p.Arg99Ter	p.R99*	ENST00000376809	NM_002116.7	99	Cga/Tga	2/8	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.39507093729325	2		456	726	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144863	58144863	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs34386532	NA	P-0058636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	134	460	0	ENST00000257904.6:c.365G>A	p.Arg122His	p.R122H	ENST00000257904	NM_000075.3	122	cGc/cAc	4/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.39507093729325	2		460	630	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387420	17387420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757371052	NA	P-0058636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	116	396	0	ENST00000359435.4:c.686C>T	p.Thr229Met	p.T229M	ENST00000359435	NM_001033549.1	229	aCg/aTg	7/9	1	2	FACETS	0.96	0.867	1	0.96	0.867	1	CLONAL	1	TRUE	1	0.39507093729325	2		396	612	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217654	7217654	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	98	346	0	ENST00000380728.2:c.273G>C	p.Lys91Asn	p.K91N	ENST00000380728		91	aaG/aaC	4/11	1	2	FACETS	0.902	0.807	1	0.902	0.807	1	CLONAL	1	TRUE	1	0.39507093729325	2		346	550	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150923415	150923415	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	78	315	0	ENST00000271640.5:c.2062G>A	p.Asp688Asn	p.D688N	ENST00000271640	NM_001145415.1	688	Gat/Aat	13/22	1	2	FACETS	0.92	0.812	1	0.92	0.812	1	CLONAL	1	TRUE	1	0.39507093729325	2		315	429	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257233	133257233	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	91	275	0	ENST00000320574.5:c.245T>C	p.Val82Ala	p.V82A	ENST00000320574	NM_006231.2	82	gTg/gCg	3/49	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.39507093729325	2		275	383	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021712	31021712	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058636-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	69	325	0	ENST00000375687.4:c.1713del	p.Ile572SerfsTer131	p.I572Sfs*131	ENST00000375687	NM_015338.5	571	Ccc/cc	12/13	1	2	FACETS	0.722	0.63	0.82	0.722	0.63	0.82	SUBCLONAL	1	TRUE	1	0.39507093729325	2		325	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0058637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	204	328	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.778141630746006	2		328	524	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	354	302	0				ENST00000310581	NM_198253.2	-/1132			0.75914159532554	4	FACETS	0.984	0.947	1	0.984	0.947	1	CLONAL	3	TRUE	1	0.778141630746006	4		302	548	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105551	27105551	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	237	376	0	ENST00000324856.7:c.5162G>C	p.Arg1721Pro	p.R1721P	ENST00000324856	NM_006015.4	1721	cGa/cCa	20/20	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.778141630746006	2		376	467	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150936725	150936725	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	232	330	0	ENST00000271640.5:c.3761G>A	p.Arg1254Lys	p.R1254K	ENST00000271640	NM_001145415.1	1254	aGa/aAa	22/22	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.778141630746006	2		330	574	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111437	8111437	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	212	315	0	ENST00000346208.3:c.923C>T	p.Ser308Phe	p.S308F	ENST00000346208		308	tCt/tTt	5/6	1	2	FACETS	0.928	0.868	0.989	0.928	0.868	0.989	CLONAL	1	TRUE	1	0.778141630746006	2		315	587	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63816885	63816885	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	162	240	0	ENST00000279873.7:c.856G>C	p.Glu286Gln	p.E286Q	ENST00000279873	NM_032199.2	286	Gag/Cag	6/10	1	2	FACETS	0.938	0.869	1	0.938	0.869	1	CLONAL	1	TRUE	1	0.778141630746006	2		240	444	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195928	102195928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770838087	NA	P-0058637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	102	345	0	ENST00000263464.3:c.688C>T	p.Pro230Ser	p.P230S	ENST00000263464	NM_001165.4	230	Ccc/Tcc	2/9	1	2	FACETS	0.639	0.576	0.706	0.639	0.576	0.706	SUBCLONAL	1	TRUE	1	0.778141630746006	2		345	410	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32932056	32932056	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	175	304	0	ENST00000380152.3:c.7795G>C	p.Glu2599Gln	p.E2599Q	ENST00000380152		2599	Gaa/Caa	16/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.778141630746006	2		304	398	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951120	48951120	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	121	216	0	ENST00000267163.4:c.1282G>T	p.Glu428Ter	p.E428*	ENST00000267163	NM_000321.2	428	Gag/Tag	13/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.778141630746006	2		216	263	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955394	48955394	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886043247	NA	P-0058637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	87	213	0	ENST00000267163.4:c.1510C>T	p.Gln504Ter	p.Q504*	ENST00000267163	NM_000321.2	504	Cag/Tag	17/27	1	2	FACETS	0.877	0.788	0.969	0.877	0.788	0.969	CLONAL	1	TRUE	1	0.778141630746006	2		213	255	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988856	41988856	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	145	375	0	ENST00000219905.7:c.1648C>G	p.Gln550Glu	p.Q550E	ENST00000219905	NM_001164273.1	550	Cag/Gag	3/24	1	2	FACETS	0.991	0.916	1	0.991	0.916	1	CLONAL	1	TRUE	1	0.778141630746006	2		375	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514495	NA	P-0058637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	264	415	0	ENST00000269305.4:c.542G>A	p.Arg181His	p.R181H	ENST00000269305	NM_001126112.2	181	cGc/cAc	5/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.778141630746006	2		415	632	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456507	189456507	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	184	323	0	ENST00000264731.3:c.268G>C	p.Glu90Gln	p.E90Q	ENST00000264731	NM_003722.4	90	Gag/Cag	3/14	1	2	FACETS	0.987	0.92	1	0.987	0.92	1	CLONAL	1	TRUE	1	0.778141630746006	2		323	479	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057000	180057000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762995809	NA	P-0058637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	222	422	0	ENST00000261937.6:c.619G>A	p.Glu207Lys	p.E207K	ENST00000261937	NM_182925.4	207	Gag/Aag	5/30	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.778141630746006	2		422	472	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845722	151845722	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058637-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	231	392	0	ENST00000262189.6:c.13290G>C	p.Leu4430Phe	p.L4430F	ENST00000262189	NM_170606.2	4430	ttG/ttC	52/59	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.778141630746006	2		392	536	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0058638-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	73	297	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.513152069744888	2	FACETS	0.938	0.845	1	0.938	0.845	1	CLONAL	2	TRUE	0	0.51543529716303	2		297	151	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225060	NA	P-0058638-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	56	294	0	ENST00000263967.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000263967	NM_006218.2	104	cCa/cTa	2/21	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.51543529716303	2		294	206	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0058638-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	96	345	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.51543529716303	2		345	299	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023855	27023855	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058638-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	57	464	0	ENST00000324856.7:c.961C>T	p.Gln321Ter	p.Q321*	ENST00000324856	NM_006015.4	321	Cag/Tag	1/20	1	2	FACETS	0.871	0.755	0.995	0.871	0.755	0.995	CLONAL	1	TRUE	1	0.51543529716303	2		464	254	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522600	176522600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058638-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	91	548	1	ENST00000292408.4:c.1697G>A	p.Arg566His	p.R566H	ENST00000292408	NM_213647.1	566	cGc/cAc	13/18	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.51543529716303	2		549	327	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054334	42054336	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0058638-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	31	277	0	ENST00000219905.7:c.7523_7525del	p.Glu2508del	p.E2508del	ENST00000219905	NM_001164273.1	2506	acAGAa/aca	22/24	1	2	FACETS	0.691	0.565	0.831	0.691	0.565	0.831	SUBCLONAL	1	TRUE	1	0.51543529716303	2		277	174	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589596	67589598	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0058638-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	32	233	0	ENST00000274335.5:c.1359_1361del	p.Thr454del	p.T454del	ENST00000274335		453	aaCACt/aat	10/15	1	2	FACETS	0.705	0.579	0.845	0.705	0.579	0.845	SUBCLONAL	1	TRUE	1	0.51543529716303	2		233	176	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670612	67670613	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	A	novel	NA	P-0058638-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	67	330	0	ENST00000264010.4:c.1857_1858delinsA	p.Asp620ThrfsTer11	p.D620Tfs*11	ENST00000264010	NM_006565.3	619	ctGGac/ctAac	11/12	1	2	FACETS	0.977	0.859	1	0.977	0.859	1	CLONAL	1	TRUE	1	0.51543529716303	2		330	266	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578504	7578540	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTG	AGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTG	-	novel	NA	P-0058639-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	258	465	0	ENST00000269305.4:c.390_426del	p.Asn131CysfsTer27	p.N131Cfs*27	ENST00000269305	NM_001126112.2	130	ctCAACAAGATGTTTTGCCAACTGGCCAAGACCTGCCCT/ct	5/11	0.475519842951924	3	FACETS	1	0.986	1	0.756	0.715	0.798	CLONAL	2	TRUE	0	0.491859690097332	3		465	576	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937512	178937512	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058639-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	23	135	0	ENST00000263967.3:c.1900C>A	p.Gln634Lys	p.Q634K	ENST00000263967	NM_006218.2	634	Cag/Aag	12/21	0.443912373989781	5	FACETS	0.945	0.743	1	0.315	0.247	0.392	CLONAL	1	TRUE	2	0.491859690097332	5		135	172	SUCCESS
MET	4233	MSKCC	GRCh37	7	116422101	116422101	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0058639-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	78	261	0	ENST00000397752.3:c.3582T>A	p.Tyr1194Ter	p.Y1194*	ENST00000397752	NM_000245.2	1194	taT/taA	18/21	0.491859690097332	6	FACETS	1	0.946	1	0.378	0.332	0.427	CLONAL	1	TRUE	3	0.491859690097332	6		261	555	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0058640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	65	251	0	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	0.509950182339834	1	FACETS	0.913	0.805	1	0.913	0.805	1	CLONAL	1	TRUE	0	0.509950182339834	1		251	208	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685268	89685268	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0058640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	102	269	0	ENST00000371953.3:c.165-2A>C		p.X55_splice	ENST00000371953	NM_000314.4	55			0.509950182339834	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.509950182339834	1		269	262	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147512	47147512	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	213	713	0	ENST00000409792.3:c.4814A>G	p.Tyr1605Cys	p.Y1605C	ENST00000409792	NM_014159.6	1605	tAt/tGt	6/21	0.509950182339834	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.509950182339834	1		713	594	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111557	8111557	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	140	387	0	ENST00000346208.3:c.1043A>G	p.His348Arg	p.H348R	ENST00000346208		348	cAc/cGc	5/6	0.509950182339834	1	FACETS	0.986	0.906	1	0.986	0.906	1	CLONAL	1	TRUE	0	0.509950182339834	1		387	415	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42049966	42050011	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAATCCTGTCTTTATCCAGGTCCTGTACTCACATCTCTGCAGATG	AAAATCCTGTCTTTATCCAGGTCCTGTACTCACATCTCTGCAGATG	-	novel	NA	P-0058640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	62	236	0	ENST00000219905.7:c.7140-16_7169del		p.X2380_splice	ENST00000219905	NM_001164273.1	2380		19/24	1	2	FACETS	0.853	0.744	0.97	0.853	0.744	0.97	CLONAL	1	TRUE	1	0.509950182339834	2		236	285	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183824	10183828	+	frameshift_variant	Frame_Shift_Del	DEL	ACCCA	ACCCA	-	novel	NA	P-0058640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	131	460	0	ENST00000256474.2:c.295_299del	p.Pro99AlafsTer31	p.P99Afs*31	ENST00000256474	NM_000551.3	98	tACCCA/t	1/3	0.509950182339834	1	FACETS	0.801	0.731	0.873	0.801	0.731	0.873	CLONAL	1	TRUE	0	0.509950182339834	1		460	478	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80150073	80150073	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	136	436	0	ENST00000265081.6:c.2940del	p.Thr981ArgfsTer21	p.T981Rfs*21	ENST00000265081	NM_002439.4	980	Ggg/gg	21/24	1	2	FACETS	0.98	0.896	1	0.98	0.896	1	CLONAL	1	TRUE	1	0.509950182339834	2		436	544	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100481	157100481	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058640-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	72	235	0	ENST00000346085.5:c.1418del	p.Met473ArgfsTer29	p.M473Rfs*29	ENST00000346085	NM_020732.3	473	aTg/ag	1/20	1	2	FACETS	0.935	0.825	1	0.935	0.825	1	CLONAL	1	TRUE	1	0.509950182339834	2		235	302	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0058642-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	337	518	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.734469163475051	2	FACETS	1	0.996	1	0.739	0.707	0.771	CLONAL	1	TRUE	0	0.748821008218589	2		518	609	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0058642-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	194	555	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.707014374015353	1	FACETS	0.965	0.911	1	0.965	0.911	1	CLONAL	1	TRUE	0	0.748821008218589	1		555	336	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50481257	50481257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058642-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	74	424	0	ENST00000394963.4:c.643C>T	p.Leu215Phe	p.L215F	ENST00000394963	NM_003076.4	215	Ctc/Ttc	5/13	0.360755038123825	1	FACETS	0.356	0.314	0.401	0.356	0.314	0.401	INDETERMINATE	1	TRUE	0	0.748821008218589	1		424	347	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339062	65339070	+	inframe_deletion	In_Frame_Del	DEL	CAGATACTC	CAGATACTC	-	novel	NA	P-0058643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	63	321	0	ENST00000342505.4:c.466_474del	p.Glu156_Leu158del	p.E156_L158del	ENST00000342505	NM_002227.2	156	GAGTATCTG/-	5/25	1	2	FACETS	0.869	0.752	0.996	0.869	0.752	0.996	CLONAL	1	FALSE	1	0.254731036806109	2		321	569	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112764367	112764367	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	21	129	0	ENST00000369452.4:c.976C>G	p.Leu326Val	p.L326V	ENST00000369452	NM_007373.3	326	Ctt/Gtt	5/9	0.208717863659897	2	FACETS	0.681	0.526	0.861	0.341	0.263	0.431	SUBCLONAL	1	FALSE	0	0.254731036806109	2		129	242	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908221	28908221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	34	186	0	ENST00000282397.4:c.2534C>T	p.Ser845Leu	p.S845L	ENST00000282397	NM_002019.4	845	tCa/tTa	18/30	0.254731036806109	1	FACETS	0.523	0.427	0.632	0.523	0.427	0.632	SUBCLONAL	1	FALSE	0	0.254731036806109	1		186	445	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32890645	32890645	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	32	171	0	ENST00000380152.3:c.48G>C	p.Lys16Asn	p.K16N	ENST00000380152		16	aaG/aaC	2/27	0.254731036806109	1	FACETS	0.834	0.68	1	0.834	0.68	1	CLONAL	1	FALSE	0	0.254731036806109	1		171	263	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034382	42034963	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCAAGACCAGCCTGACCAACATGGAGAAACCTTGTCTCTACTAAAAATACAAAAATTAGCTGGGTTTGGTGGTATGTGCCTGTAATCCCAGCTACTCGGGAAGGCTGAGGCAGGAGAATTGCTTGAACCTGGGAGACAGAGGTTGCAGTGAGCCGAGATCGCGCCATTGCACTCTAGCCTGGGCAACAAGAAAGAAACTCCATCTTAAAAAAGAAAAAAAAGAAATTGGCACAAATAATACAGGTAGGTAGTACCTGTAAGAAATTGACCCAGTAGTGCACAGTAAATGTCGGTAAGCACAGTCACTAAGAGGATAAAATATGAGAACTGAAGATTTTTGACCTGCAAATTTCTGTTTGCAGCGGCTCGACCCTCTCCTGGTGGTGTGTTCACACAGTTTGTGATGAGTAAAGTTGGAGCCTTGCAGCAGAAGATACCTGGAGTTAGCACACCCCAAACCCTGGCAGGGACACAGAAGTTCAGTATCAGACCTTCTCCAGTAATGGTCGTCACACCTGTGGTTTCTTCTGAGCCAGTTCAGGTGTGCAGCCCTGTGACTGCTGCTGTCACTACTACCACCCC	TCAAGACCAGCCTGACCAACATGGAGAAACCTTGTCTCTACTAAAAATACAAAAATTAGCTGGGTTTGGTGGTATGTGCCTGTAATCCCAGCTACTCGGGAAGGCTGAGGCAGGAGAATTGCTTGAACCTGGGAGACAGAGGTTGCAGTGAGCCGAGATCGCGCCATTGCACTCTAGCCTGGGCAACAAGAAAGAAACTCCATCTTAAAAAAGAAAAAAAAGAAATTGGCACAAATAATACAGGTAGGTAGTACCTGTAAGAAATTGACCCAGTAGTGCACAGTAAATGTCGGTAAGCACAGTCACTAAGAGGATAAAATATGAGAACTGAAGATTTTTGACCTGCAAATTTCTGTTTGCAGCGGCTCGACCCTCTCCTGGTGGTGTGTTCACACAGTTTGTGATGAGTAAAGTTGGAGCCTTGCAGCAGAAGATACCTGGAGTTAGCACACCCCAAACCCTGGCAGGGACACAGAAGTTCAGTATCAGACCTTCTCCAGTAATGGTCGTCACACCTGTGGTTTCTTCTGAGCCAGTTCAGGTGTGCAGCCCTGTGACTGCTGCTGTCACTACTACCACCCC	-	novel	NA	P-0058643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	26	2	0	ENST00000219905.7:c.4586-357_4810del		p.X1529_splice	ENST00000219905	NM_001164273.1	1529		15/24	1	2	FACETS	1	0.907	1	1	0.972	1	CLONAL	6	FALSE	1	0.254731036806109	2		2	33	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473627	67473627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	58	419	0	ENST00000327367.4:c.707C>T	p.Ser236Phe	p.S236F	ENST00000327367	NM_005902.3	236	tCc/tTc	6/9	1	2	FACETS	0.648	0.556	0.749	0.648	0.556	0.749	SUBCLONAL	1	FALSE	1	0.254731036806109	2		419	703	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90645594	90645594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1234438811	NA	P-0058643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	42	379	0	ENST00000330062.3:c.29C>T	p.Ser10Leu	p.S10L	ENST00000330062	NM_002168.2	10	tCg/tTg	1/11	1	2	FACETS	0.87	0.728	1	0.87	0.728	1	CLONAL	1	FALSE	1	0.254731036806109	2		379	379	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866444	37866444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	72	535	0	ENST00000269571.5:c.749C>T	p.Ser250Phe	p.S250F	ENST00000269571		250	tCt/tTt	6/27	0.0461576630229499	3	FACETS	1	0.937	1	0.559	0.489	0.635	INDETERMINATE	1	FALSE	1	0.254731036806109	3		535	570	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119974	70120026	+	frameshift_variant	Frame_Shift_Del	DEL	GCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAGGCGCCGCC	GCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAGGCGCCGCC	-	novel	NA	P-0058643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	50	606	0	ENST00000245479.2:c.984_1036del	p.Ser330AlafsTer230	p.S330Afs*230	ENST00000245479	NM_000346.3	326	GCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAGGCGCCGCCg/g	3/3	1	2	FACETS	0.823	0.699	0.959	0.823	0.699	0.959	CLONAL	1	FALSE	1	0.254731036806109	2		606	477	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52693425	52693425	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	81	629	0	ENST00000322088.6:c.76C>G	p.Gln26Glu	p.Q26E	ENST00000322088	NM_014225.5	26	Cag/Gag	1/15	0.254731036806109	1	FACETS	0.779	0.686	0.879	0.779	0.686	0.879	SUBCLONAL	1	FALSE	0	0.254731036806109	1		629	712	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741498	39741498	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	36	273	0	ENST00000361337.2:c.1385G>T	p.Arg462Leu	p.R462L	ENST00000361337	NM_003286.2	462	cGa/cTa	14/21	1	2	FACETS	0.482	0.396	0.58	0.482	0.396	0.58	SUBCLONAL	1	FALSE	1	0.254731036806109	2		273	586	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204917	128204917	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	91	533	1	ENST00000341105.2:c.524C>T	p.Pro175Leu	p.P175L	ENST00000341105	NM_032638.4	175	cCc/cTc	3/6	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.254731036806109	2		534	534	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259759	142259759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	27	156	0	ENST00000350721.4:c.3568G>A	p.Glu1190Lys	p.E1190K	ENST00000350721	NM_001184.3	1190	Gaa/Aaa	18/47	1	2	FACETS	0.552	0.439	0.681	0.552	0.439	0.681	SUBCLONAL	1	FALSE	1	0.254731036806109	2		156	384	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151602	55151602	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	22	154	0	ENST00000257290.5:c.2388G>C	p.Leu796Phe	p.L796F	ENST00000257290	NM_006206.4	796	ttG/ttC	17/23	1	2	FACETS	0.596	0.462	0.75	0.596	0.462	0.75	SUBCLONAL	1	FALSE	1	0.254731036806109	2		154	290	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592045	67592045	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	62	247	0	ENST00000274335.5:c.1861G>T	p.Glu621Ter	p.E621*	ENST00000274335		621	Gag/Tag	14/15	1	2	FACETS	0.906	0.784	1	0.906	0.784	1	CLONAL	1	FALSE	1	0.254731036806109	2		247	537	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860435	151860435	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058643-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	110	311	0	ENST00000262189.6:c.10227G>C	p.Glu3409Asp	p.E3409D	ENST00000262189	NM_170606.2	3409	gaG/gaC	43/59	0.254731036806109	3	FACETS	0.81	0.73	0.895	0.81	0.73	0.895	CLONAL	2	FALSE	1	0.254731036806109	3		311	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0058644-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	118	804	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.478893862188639	1	FACETS	0.908	0.825	0.993	0.908	0.825	0.993	CLONAL	1	TRUE	0	0.478893862188639	1		804	413	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258611	16258611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370428398	NA	P-0058644-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	174	571	0	ENST00000375759.3:c.5876G>A	p.Arg1959Gln	p.R1959Q	ENST00000375759	NM_015001.2	1959	cGa/cAa	11/15	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.478893862188639	2		571	707	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812200	43812200	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058644-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	165	468	0	ENST00000372470.3:c.1065G>C	p.Lys355Asn	p.K355N	ENST00000372470	NM_005373.2	355	aaG/aaC	7/12	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.478893862188639	2		468	651	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512400	38512412	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCCCCCCGCCA	GGCCCCCCCGCCA	-	novel	NA	P-0058644-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	132	384	0	ENST00000254066.5:c.1314_1326del	p.Pro439AlafsTer200	p.P439Afs*200	ENST00000254066	NM_000964.3	437	ctGGCCCCCCCGCCA/ct	9/9	0.462877776273281	3	FACETS	0.916	0.841	0.993	0.611	0.56	0.662	CLONAL	2	TRUE	0	0.478893862188639	3		384	373	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55334128	55334128	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058644-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	229	287	0	ENST00000284073.2:c.25A>C	p.Thr9Pro	p.T9P	ENST00000284073	NM_138962.2	9	Acc/Ccc	1/14	0.462877776273281	3	FACETS	0.95	0.9	1	0.95	0.9	1	CLONAL	3	TRUE	0	0.478893862188639	3		287	416	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535465	187535465	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058644-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	140	390	0	ENST00000441802.2:c.9109C>G	p.Leu3037Val	p.L3037V	ENST00000441802	NM_005245.3	3037	Ctt/Gtt	12/27	0.477909675132792	1	FACETS	0.965	0.885	1	0.965	0.885	1	CLONAL	1	TRUE	0	0.478893862188639	1		390	461	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200240	123200266	+	inframe_deletion	In_Frame_Del	DEL	TAATCCTTTGGCAACTTGCTAAGATAA	TAATCCTTTGGCAACTTGCTAAGATAA	-	novel	NA	P-0058644-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	98	368	0	ENST00000218089.9:c.2219_2245del	p.Val740_Thr749delinsAla	p.V740_T749delinsA	ENST00000218089	NM_001042749.1	740	gTAATCCTTTGGCAACTTGCTAAGATAAct/gct	23/35	0.478893862188639	1	FACETS	0.811	0.729	0.896	0.811	0.729	0.896	CLONAL	1	TRUE	0	0.478893862188639	1		368	384	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912656	32912664	+	inframe_deletion	In_Frame_Del	DEL	TTTTTTGGA	TTTTTTGGA	-	novel	NA	P-0058644-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	157	166	0	ENST00000380152.3:c.4164_4172del	p.Phe1389_Glu1391del	p.F1389_E1391del	ENST00000380152		1388	acTTTTTTGGAa/aca	11/27	0.478893862188639	2	FACETS	1	0.982	1	0.613	0.565	0.662	CLONAL	1	TRUE	0	0.478893862188639	2		166	535	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0058645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	238	396	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.290320273754587	5	FACETS	0.965	0.904	1	0.965	0.904	1	CLONAL	3	TRUE	2	0.330024328409094	5		396	745	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs864622237	NA	P-0058645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	303	363	0	ENST00000269305.4:c.700T>C	p.Tyr234His	p.Y234H	ENST00000269305	NM_001126112.2	234	Tac/Cac	7/11	0.330024328409094	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.330024328409094	3		363	629	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117192	7117192	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	69	434	0	ENST00000302850.5:c.4024G>A	p.Gly1342Ser	p.G1342S	ENST00000302850	NM_000208.2	1342	Ggc/Agc	22/22	0.330024328409094	3	FACETS	0.647	0.563	0.738	0.323	0.281	0.369	SUBCLONAL	1	TRUE	1	0.330024328409094	3		434	753	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259369	36259370	+	missense_variant	Missense_Mutation	DNP	GT	GT	AA	novel	NA	P-0058645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	176	427	0	ENST00000300305.3:c.121_122delinsTT	p.Thr41Leu	p.T41L	ENST00000300305		41	ACg/TTg	3/8	0.166111774611164	4	FACETS	1	0.954	1	1	0.954	1	INDETERMINATE	2	TRUE	2	0.330024328409094	4		427	679	SUCCESS
ALB	213	MSKCC	GRCh37	4	74283985	74283985	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058645-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	93	372	0	ENST00000295897.4:c.1609A>G	p.Ile537Val	p.I537V	ENST00000295897	NM_000477.5	537	Ata/Gta	12/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.330024328409094	2		372	466	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0058646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	87	738	0				ENST00000310581	NM_198253.2	-/1132			0.306523667979391	0	FACETS	0.355	0.317	0.395			1	INDETERMINATE	1	TRUE	0	0.604273857617648	0		738	321	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	484	520	0	ENST00000324856.7:c.4555del	p.Gln1519ArgfsTer8	p.Q1519Rfs*8	ENST00000324856	NM_006015.4	1517	gCc/gc	18/20	0.55818141967259	2	FACETS	0.947	0.913	0.98	0.947	0.913	0.98	CLONAL	2	TRUE	0	0.604273857617648	2		520	846	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0058646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	181	308	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.153807229005766	5	FACETS	0.761	0.704	0.821	0.508	0.469	0.547	INDETERMINATE	2	TRUE	2	0.604273857617648	5		308	750	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0058646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	324	567	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.153807229005766	5	FACETS	1	0.99	1	0.785	0.744	0.827	INDETERMINATE	2	TRUE	2	0.604273857617648	5		567	868	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877391	40877391	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372713520	NA	P-0058646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3275	185	447	0	ENST00000373198.4:c.2305G>A	p.Val769Met	p.V769M	ENST00000373198	NM_133170.3	769	Gtg/Atg	15/32	0.604273857617648	17	FACETS	0.979	0.898	1	0.058	0.052	0.063	CLONAL	1	TRUE	0	0.604273857617648	17		447	3460	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295254	1295254	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0058646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	74	443	0				ENST00000310581	NM_198253.2	-/1132			0.306523667979391	0	FACETS	0.298	0.263	0.336			1	INDETERMINATE	1	TRUE	0	0.604273857617648	0		443	325	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851097	151851097	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	122	367	0	ENST00000262189.6:c.12274G>A	p.Glu4092Lys	p.E4092K	ENST00000262189	NM_170606.2	4092	Gag/Aag	48/59	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.604273857617648	2		367	370	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295239	1295239	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0058646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	60	381	0				ENST00000310581	NM_198253.2	-/1132			0.306523667979391	0	FACETS	0.288	0.25	0.328			1	INDETERMINATE	1	TRUE	0	0.604273857617648	0		381	273	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984369	201984370	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0058646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	624	492	0	ENST00000359651.3:c.1036dup	p.Asp346GlyfsTer125	p.D346Gfs*125	ENST00000359651		345	gtg/gtGg	8/8	0.580420960753722	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.604273857617648	2		492	863	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453547	138453547	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	166	352	0	ENST00000289153.2:c.901G>A	p.Glu301Lys	p.E301K	ENST00000289153	NM_006219.2	301	Gag/Aag	5/22	0.604273857617648	3	FACETS	0.969	0.904	1	0.969	0.904	1	CLONAL	2	TRUE	1	0.604273857617648	3		352	369	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737677	145737677	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058646-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	125	670	0	ENST00000428558.2:c.3086A>C	p.Glu1029Ala	p.E1029A	ENST00000428558	NM_004260.3	1029	gAg/gCg	19/22	0.263158535670428	2	FACETS	0.467	0.423	0.515	0.234	0.211	0.258	INDETERMINATE	1	TRUE	0	0.604273857617648	2		670	885	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741707	145741707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543009701	NA	P-0058647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	108	452	0	ENST00000428558.2:c.796G>A	p.Glu266Lys	p.E266K	ENST00000428558	NM_004260.3	266	Gag/Aag	5/22	0.481054719946178	4	FACETS	0.845	0.758	0.937	0.282	0.252	0.313	CLONAL	1	TRUE	1	0.50381435396251	4		452	763	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237731	133237731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	111	318	0	ENST00000320574.5:c.2884G>A	p.Asp962Asn	p.D962N	ENST00000320574	NM_006231.2	962	Gac/Aac	25/49	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.50381435396251	2		318	401	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179029	123179029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	85	124	0	ENST00000218089.9:c.478C>T	p.Pro160Ser	p.P160S	ENST00000218089	NM_001042749.1	160	Cca/Tca	8/35	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.50381435396251	1		124	179	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910587	29910587	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	201	435	0	ENST00000376809.5:c.127G>T	p.Glu43Ter	p.E43*	ENST00000376809	NM_002116.7	43	Gag/Tag	2/8	0.50381435396251	3	FACETS	0.866	0.808	0.925	0.866	0.808	0.925	CLONAL	2	TRUE	1	0.50381435396251	3		435	577	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911075	29911075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	104	355	0	ENST00000376809.5:c.374G>A	p.Cys125Tyr	p.C125Y	ENST00000376809	NM_002116.7	125	tGc/tAc	3/8	0.50381435396251	3	FACETS	1	0.97	1	0.601	0.541	0.663	CLONAL	1	TRUE	1	0.50381435396251	3		355	430	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692932	89692932	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0058647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	214	325	0	ENST00000371953.3:c.416T>A	p.Leu139Ter	p.L139*	ENST00000371953	NM_000314.4	139	tTa/tAa	5/9	0.499614480425472	2	FACETS	0.946	0.891	1	0.946	0.891	1	CLONAL	2	TRUE	0	0.50381435396251	2		325	449	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911553	114911553	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	146	356	0	ENST00000543371.1:c.1071C>G	p.Phe357Leu	p.F357L	ENST00000543371	NM_001198531.1	357	ttC/ttG	10/14	0.499614480425472	2	FACETS	1	0.978	1	0.594	0.546	0.643	CLONAL	1	TRUE	0	0.50381435396251	2		356	488	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939075	48939075	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1411089830	NA	P-0058647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	75	170	0	ENST00000267163.4:c.907C>G	p.Leu303Val	p.L303V	ENST00000267163	NM_000321.2	303	Ctt/Gtt	9/27	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.50381435396251	2		170	264	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89846347	89846347	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs779745863	NA	P-0058647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	124	413	0	ENST00000389301.3:c.1645C>T	p.Gln549Ter	p.Q549*	ENST00000389301	NM_000135.2	549	Cag/Tag	18/43	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.50381435396251	2		413	464	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068438	16068438	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	47	75	0	ENST00000268712.3:c.473C>G	p.Ser158Cys	p.S158C	ENST00000268712	NM_006311.3	158	tCt/tGt	5/46	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.50381435396251	2		75	126	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478100	138478100	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	103	343	0	ENST00000289153.2:c.86C>T	p.Ser29Phe	p.S29F	ENST00000289153	NM_006219.2	29	tCc/tTc	1/22	0.50381435396251	3	FACETS	1	0.931	1	0.522	0.469	0.578	CLONAL	1	TRUE	1	0.50381435396251	3		343	490	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633443	8633443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745977244	NA	P-0058647-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	60	274	0	ENST00000356435.5:c.226G>A	p.Asp76Asn	p.D76N	ENST00000356435		76	Gat/Aat	3/35	1	2	FACETS	0.686	0.595	0.785	0.686	0.595	0.785	SUBCLONAL	1	TRUE	1	0.50381435396251	2		274	347	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	14	697	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.284	0.205	0.381	0.284	0.205	0.381	SUBCLONAL	1	FALSE	1	0.31493181434639	2		699	313	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	21	391	2	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	0.149709330415769	0	FACETS	0.499	0.387	0.629			1	INDETERMINATE	1	FALSE	0	0.31493181434639	0		393	183	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	24	434	4	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.918	0.726	1	0.918	0.726	1	CLONAL	1	FALSE	1	0.31493181434639	2		438	166	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	149	544	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.968	0.899	1	1	0.994	1	CLONAL	3	FALSE	1	0.31493181434639	2		548	326	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	37	374	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.1951871774244	3	FACETS	1	0.849	1	0.513	0.425	0.61	CLONAL	1	FALSE	1	0.31493181434639	3		374	265	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324892	31324892	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs765875917	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	18	422	0	ENST00000412585.2:c.44del	p.Ala15GlyfsTer5	p.A15Gfs*5	ENST00000412585	NM_005514.6	15	gCg/gg	1/8	0.1951871774244	3	FACETS	0.503	0.379	0.65	0.252	0.189	0.325	SUBCLONAL	1	FALSE	1	0.31493181434639	3		422	263	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	44	516	0	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	1	0.31493181434639	2		516	218	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	51	486	4	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	NA	2	FACETS	1	0.96	1			1	INDETERMINATE	1	FALSE	NA	0.31493181434639	2		490	236	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	32	495	4	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	0.31493181434639	1	FACETS	0.732	0.597	0.881	0.732	0.597	0.881	SUBCLONAL	1	FALSE	0	0.31493181434639	1		499	234	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	22	520	0	ENST00000324856.7:c.4555del	p.Gln1519ArgfsTer8	p.Q1519Rfs*8	ENST00000324856	NM_006015.4	1517	gCc/gc	18/20	1	2	FACETS	0.575	0.447	0.723	0.575	0.447	0.723	SUBCLONAL	1	FALSE	1	0.31493181434639	2		520	243	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649922	88649922	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786201038	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	14	212	0	ENST00000372037.3:c.176del	p.Leu59Ter	p.L59*	ENST00000372037	NM_004329.2	57	ccT/cc	4/13	1	2	FACETS	0.729	0.531	0.963	0.729	0.531	0.963	CLONAL	1	FALSE	1	0.31493181434639	2		212	122	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	14	352	0	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	1	2	FACETS	0.539	0.391	0.716	0.539	0.391	0.716	SUBCLONAL	1	FALSE	1	0.31493181434639	2		352	165	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	28	513	1	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.633	0.507	0.775	0.633	0.507	0.775	SUBCLONAL	1	FALSE	1	0.31493181434639	2		514	281	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288710	15288710	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	22	328	0	ENST00000263388.2:c.4029del	p.Cys1344ValfsTer76	p.C1344Vfs*76	ENST00000263388	NM_000435.2	1343	ccC/cc	24/33	0.293866622827925	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	FALSE	0	0.31493181434639	1		328	88	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221340	1221340	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	63	521	0	ENST00000326873.7:c.862+1G>A		p.X288_splice	ENST00000326873	NM_000455.4	288			0.203419178298892	1	FACETS	0.96	0.835	1	0.96	0.835	1	CLONAL	1	FALSE	0	0.31493181434639	1		521	351	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	33	305	0	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	0.1951871774244	3	FACETS	0.793	0.647	0.955	0.396	0.323	0.478	CLONAL	1	FALSE	1	0.31493181434639	3		305	306	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119781	70119781	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1274036689	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	41	363	0	ENST00000245479.2:c.788del	p.Gly263AlafsTer16	p.G263Afs*16	ENST00000245479	NM_000346.3	261	gaG/ga	3/3	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.31493181434639	2		363	188	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	37	414	1	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	FALSE	1	0.31493181434639	2		415	217	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533939	63533940	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs771001164	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	23	461	4	ENST00000307078.5:c.1214_1215del	p.Glu405GlyfsTer56	p.E405Gfs*56	ENST00000307078	NM_004655.3	405	gAG/g	6/11	1	2	FACETS	0.769	0.603	0.958	0.769	0.603	0.958	CLONAL	1	FALSE	1	0.31493181434639	2		465	190	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099332	157099333	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCA	rs754114025	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	30	457	0	ENST00000346085.5:c.285_287dup	p.His96dup	p.H96dup	ENST00000346085	NM_020732.3	96	gcc/gcCCAc	1/20	1	2	FACETS	0.526	0.424	0.642	0.526	0.424	0.642	SUBCLONAL	1	FALSE	1	0.31493181434639	2		457	362	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216091	7216091	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1332522267	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	55	420	0	ENST00000380728.2:c.968G>A	p.Arg323Gln	p.R323Q	ENST00000380728		323	cGa/cAa	11/11	1	2	FACETS	0.84	0.72	0.969	0.84	0.72	0.969	CLONAL	1	FALSE	1	0.31493181434639	2		420	416	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199945	138199945	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	45	485	0	ENST00000237289.4:c.1368del	p.Pro457LeufsTer20	p.P457Lfs*20	ENST00000237289	NM_001270507.1	455	Ggg/gg	7/9	0.31493181434639	6	FACETS	1	0.876	1	0.35	0.294	0.411	CLONAL	1	FALSE	3	0.31493181434639	6		485	444	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486281	8486281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	21	416	0	ENST00000356435.5:c.2536C>T	p.Pro846Ser	p.P846S	ENST00000356435		846	Ccg/Tcg	17/35	1	2	FACETS	0.644	0.498	0.813	0.644	0.498	0.813	SUBCLONAL	1	FALSE	1	0.31493181434639	2		416	207	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589576	67589576	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1289537429	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	17	124	0	ENST00000274335.5:c.1344del	p.Lys448AsnfsTer32	p.K448Nfs*32	ENST00000274335		447	Aaa/aa	10/15	0.1951871774244	3	FACETS	0.619	0.463	0.802	0.309	0.231	0.401	SUBCLONAL	1	FALSE	1	0.31493181434639	3		124	202	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434685	99434685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs543792941	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	45	492	0	ENST00000268035.6:c.772G>A	p.Gly258Ser	p.G258S	ENST00000268035	NM_000875.3	258	Ggt/Agt	3/21	0.1951871774244	3	FACETS	1	0.882	1	0.527	0.445	0.617	CLONAL	1	FALSE	1	0.31493181434639	3		492	314	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26970441	26970441	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	18	95	0	ENST00000381527.3:c.815del	p.Lys272ArgfsTer8	p.K272Rfs*8	ENST00000381527	NM_001260.1	270	atA/at	8/13	0.176851903749343	0	FACETS	0.559	0.425	0.715			1	INDETERMINATE	1	FALSE	0	0.31493181434639	0		95	140	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304140	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	24	402	0	ENST00000355112.3:c.1543_1544del	p.Asn515Ter	p.N515*	ENST00000355112	NM_000057.2	512	ggAAaa/ggaa	7/22	0.1951871774244	3	FACETS	0.615	0.483	0.766	0.307	0.241	0.383	SUBCLONAL	1	FALSE	1	0.31493181434639	3		402	287	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421586	49421586	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	53	441	0	ENST00000301067.7:c.14643G>T	p.Gln4881His	p.Q4881H	ENST00000301067	NM_003482.3	4881	caG/caT	47/54	0.31493181434639	4	FACETS	1	0.961	1	0.696	0.597	0.803	CLONAL	1	FALSE	2	0.31493181434639	4		441	318	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89871774	89871774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144420697	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	38	367	0	ENST00000389301.3:c.623C>T	p.Ser208Leu	p.S208L	ENST00000389301	NM_000135.2	208	tCg/tTg	7/43	0.176851903749343	0	FACETS	0.698	0.581	0.826			1	INDETERMINATE	1	FALSE	0	0.31493181434639	0		367	237	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984019	2984019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41319046	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	21	430	0	ENST00000396946.4:c.511G>A	p.Val171Met	p.V171M	ENST00000396946	NM_032415.4	171	Gtg/Atg	5/25	0.149709330415769	0	FACETS	0.317	0.244	0.402			1	INDETERMINATE	1	FALSE	0	0.31493181434639	0		430	288	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437424	49437424	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	54	446	0	ENST00000301067.7:c.5461C>T	p.Gln1821Ter	p.Q1821*	ENST00000301067	NM_003482.3	1821	Cag/Tag	23/54	0.31493181434639	4	FACETS	0.857	0.739	0.984	0.857	0.739	0.984	CLONAL	2	FALSE	2	0.31493181434639	4		446	263	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224532	36224532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759167832	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	39	507	0	ENST00000222270.7:c.6994C>T	p.Arg2332Cys	p.R2332C	ENST00000222270	NM_014727.1	2332	Cgt/Tgt	29/37	0.203419178298892	1	FACETS	0.919	0.768	1	0.919	0.768	1	CLONAL	1	FALSE	0	0.31493181434639	1		507	227	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827463	72827463	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750717662	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	35	442	0	ENST00000268489.5:c.9118C>T	p.Arg3040Cys	p.R3040C	ENST00000268489	NM_006885.3	3040	Cgt/Tgt	9/10	0.176851903749343	0	FACETS	0.708	0.585	0.844			1	INDETERMINATE	1	FALSE	0	0.31493181434639	0		442	215	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670657	134670657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1441537601	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	23	484	0	ENST00000398015.3:c.568C>T	p.Arg190Cys	p.R190C	ENST00000398015	NM_004441.4	190	Cgt/Tgt	3/16	0.31493181434639	0	FACETS	0.599	0.471	0.745			1	SUBCLONAL	1	FALSE	0	0.31493181434639	0		484	167	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15967427	15967427	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1468999160	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	48	403	2	ENST00000268712.3:c.5176C>T	p.Arg1726Trp	p.R1726W	ENST00000268712	NM_006311.3	1726	Cgg/Tgg	35/46	1	2	FACETS	0.881	0.748	1	0.881	0.748	1	CLONAL	1	FALSE	1	0.31493181434639	2		405	346	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170270	32170270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187627302	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	25	478	0	ENST00000375023.3:c.3338G>A	p.Arg1113His	p.R1113H	ENST00000375023	NM_004557.3	1113	cGc/cAc	21/30	0.304701763900874	0	FACETS	0.494	0.391	0.611			1	SUBCLONAL	1	FALSE	0	0.31493181434639	0		478	220	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120881	115120881	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	33	495	0	ENST00000257566.3:c.125C>A	p.Pro42His	p.P42H	ENST00000257566	NM_016569.3	42	cCc/cAc	1/8	1	2	FACETS	0.936	0.767	1	0.936	0.767	1	CLONAL	1	FALSE	1	0.31493181434639	2		495	224	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155367	185155367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs902931460	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	20	388	0	ENST00000265026.3:c.608C>T	p.Thr203Met	p.T203M	ENST00000265026	NM_004721.4	203	aCg/aTg	3/14	0.1951871774244	3	FACETS	0.674	0.517	0.857	0.337	0.258	0.429	SUBCLONAL	1	FALSE	1	0.31493181434639	3		388	218	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438550	49438550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	64	428	0	ENST00000301067.7:c.4940C>T	p.Thr1647Ile	p.T1647I	ENST00000301067	NM_003482.3	1647	aCc/aTc	19/54	0.31493181434639	4	FACETS	0.965	0.844	1	0.965	0.844	1	CLONAL	2	FALSE	2	0.31493181434639	4		428	277	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967284	25967284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1338721842	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	23	443	0	ENST00000435504.4:c.1922G>A	p.Arg641His	p.R641H	ENST00000435504		641	cGt/cAt	13/13	1	2	FACETS	0.611	0.478	0.764	0.611	0.478	0.764	SUBCLONAL	1	FALSE	1	0.31493181434639	2		443	239	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048638	180048638	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	15	461	0	ENST00000261937.6:c.1924del	p.Arg642AlafsTer43	p.R642Afs*43	ENST00000261937	NM_182925.4	642	Cgc/gc	13/30	0.31493181434639	0	FACETS	0.522	0.385	0.683			1	SUBCLONAL	1	FALSE	0	0.31493181434639	0		461	125	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143059	30143059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	15	576	0	ENST00000389048.3:c.467G>A	p.Gly156Glu	p.G156E	ENST00000389048	NM_004304.4	156	gGg/gAg	1/29	0.304701763900874	0	FACETS	0.48	0.353	0.629			1	SUBCLONAL	1	FALSE	0	0.31493181434639	0		576	136	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468083	50468083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775617502	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	22	494	0	ENST00000331340.3:c.1318G>A	p.Ala440Thr	p.A440T	ENST00000331340	NM_006060.4	440	Gcc/Acc	8/8	1	2	FACETS	0.688	0.536	0.863	0.688	0.536	0.863	SUBCLONAL	1	FALSE	1	0.31493181434639	2		494	203	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509083	66509083	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	11	265	0	ENST00000273854.3:c.244G>T	p.Gly82Trp	p.G82W	ENST00000273854	NM_004439.5	82	Ggg/Tgg	2/18	0.149709330415769	0	FACETS	0.352	0.244	0.485			1	INDETERMINATE	1	FALSE	0	0.31493181434639	0		265	136	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	40	344	4	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	0.31493181434639	4	FACETS	1	0.924	1	0.599	0.5	0.707	CLONAL	1	FALSE	2	0.31493181434639	4		348	279	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1684408	1684408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	30	482	0	ENST00000378625.1:c.1711C>T	p.His571Tyr	p.H571Y	ENST00000378625	NM_001198994.1	571	Cat/Tat	14/14	1	2	FACETS	0.714	0.577	0.867	0.714	0.577	0.867	SUBCLONAL	1	FALSE	1	0.31493181434639	2		482	267	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101470	27101470	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	36	408	0	ENST00000324856.7:c.4752G>T	p.Gln1584His	p.Q1584H	ENST00000324856	NM_006015.4	1584	caG/caT	18/20	1	2	FACETS	0.879	0.727	1	0.879	0.727	1	CLONAL	1	FALSE	1	0.31493181434639	2		408	260	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156848925	156848925	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	24	497	0	ENST00000524377.1:c.1817C>A	p.Pro606His	p.P606H	ENST00000524377	NM_002529.3	606	cCt/cAt	15/17	1	2	FACETS	0.847	0.669	1	0.847	0.669	1	CLONAL	1	FALSE	1	0.31493181434639	2		497	180	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218962	193218962	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	37	333	0	ENST00000367435.3:c.1520A>G	p.Asp507Gly	p.D507G	ENST00000367435	NM_024529.4	507	gAt/gGt	16/17	1	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	FALSE	1	0.31493181434639	2		333	232	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230468634	230468634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	13	497	0	ENST00000391860.1:c.884G>A	p.Gly295Glu	p.G295E	ENST00000391860	NM_001258311.1	295	gGa/gAa	5/7	0.23874895914067	0	FACETS	0.335	0.239	0.45			1	SUBCLONAL	1	FALSE	0	0.31493181434639	0		497	169	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114901001	114901001	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	62	485	0	ENST00000543371.1:c.611T>C	p.Ile204Thr	p.I204T	ENST00000543371	NM_001198531.1	204	aTc/aCc	6/14	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.31493181434639	2		485	271	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572092	64572093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767319284	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	22	514	1	ENST00000312049.6:c.1546dup	p.Arg516ProfsTer15	p.R516Pfs*15	ENST00000312049	NM_130799.2	516	cgg/cCgg	10/10	1	2	FACETS	0.494	0.383	0.622	0.494	0.383	0.622	SUBCLONAL	1	FALSE	1	0.31493181434639	2		515	283	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123597	108123597	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	28	151	0	ENST00000278616.4:c.1856A>T	p.Asn619Ile	p.N619I	ENST00000278616	NM_000051.3	619	aAc/aTc	12/63	1	2	FACETS	0.936	0.754	1	0.936	0.754	1	CLONAL	1	FALSE	1	0.31493181434639	2		151	190	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022717	12022717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	40	575	0	ENST00000396373.4:c.823C>T	p.His275Tyr	p.H275Y	ENST00000396373	NM_001987.4	275	Cac/Tac	5/8	0.31493181434639	7	FACETS	0.998	0.829	1	0.249	0.207	0.297	CLONAL	1	FALSE	3	0.31493181434639	7		575	455	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479312	50479312	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	13	323	0	ENST00000394963.4:c.160C>T	p.Pro54Ser	p.P54S	ENST00000394963	NM_003076.4	54	Ccc/Tcc	1/13	0.31493181434639	4	FACETS	0.505	0.36	0.681	0.252	0.18	0.341	SUBCLONAL	1	FALSE	2	0.31493181434639	4		323	215	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112194	115112194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	42	471	0	ENST00000257566.3:c.1546C>T	p.His516Tyr	p.H516Y	ENST00000257566	NM_016569.3	516	Cac/Tac	7/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.31493181434639	2		471	194	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436375	110436375	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	41	640	0	ENST00000375856.3:c.2026A>G	p.Met676Val	p.M676V	ENST00000375856	NM_003749.2	676	Atg/Gtg	1/2	0.137046951553168	4	FACETS	1	0.862	1	0.517	0.432	0.611	INDETERMINATE	1	FALSE	2	0.31493181434639	4		640	331	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988367	36988367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	12	353	0	ENST00000354822.5:c.286G>A	p.Ala96Thr	p.A96T	ENST00000354822	NM_001079668.2	96	Gcc/Acc	2/3	1	2	FACETS	0.965	0.689	1	0.965	0.689	1	CLONAL	1	FALSE	1	0.31493181434639	2		353	79	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007852	45007852	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	49	431	0	ENST00000558401.1:c.299G>A	p.Cys100Tyr	p.C100Y	ENST00000558401	NM_004048.2	100	tGc/tAc	2/4	1	2	FACETS	0.748	0.635	0.872	0.748	0.635	0.872	SUBCLONAL	1	FALSE	1	0.31493181434639	2		431	416	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778099	3778099	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	32	541	0	ENST00000262367.5:c.6949del	p.Gln2317SerfsTer79	p.Q2317Sfs*79	ENST00000262367	NM_004380.2	2317	Cag/ag	31/31	0.23874895914067	0	FACETS	0.744	0.61	0.893			1	SUBCLONAL	1	FALSE	0	0.31493181434639	0		541	187	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265093	10265093	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	24	514	0	ENST00000340748.4:c.1847C>T	p.Thr616Met	p.T616M	ENST00000340748		616	aCg/aTg	21/40	0.149709330415769	0	FACETS	0.493	0.388	0.612			1	INDETERMINATE	1	FALSE	0	0.31493181434639	0		514	212	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626790	14626790	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	80	410	0	ENST00000254322.2:c.985A>G	p.Thr329Ala	p.T329A	ENST00000254322	NM_006145.1	329	Aca/Gca	3/3	0.31493181434639	6	FACETS	1	0.964	1			1	CLONAL	1	FALSE	NA	0.31493181434639	6		410	659	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17386633	17386633	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	32	335	0	ENST00000359435.4:c.568A>G	p.Ile190Val	p.I190V	ENST00000359435	NM_001033549.1	190	Atc/Gtc	6/9	0.293866622827925	1	FACETS	0.931	0.763	1	0.931	0.763	1	CLONAL	1	FALSE	0	0.31493181434639	1		335	184	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741989	40741989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	32	592	0	ENST00000392038.2:c.983G>A	p.Gly328Asp	p.G328D	ENST00000392038	NM_001626.4	328	gGc/gAc	11/14	0.203419178298892	1	FACETS	0.916	0.75	1	0.916	0.75	1	CLONAL	1	FALSE	0	0.31493181434639	1		592	187	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798789	42798789	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	10	363	0	ENST00000575354.2:c.4361A>C	p.Glu1454Ala	p.E1454A	ENST00000575354	NM_015125.3	1454	gAg/gCg	19/20	0.274988753872835	4	FACETS	0.5	0.339	0.702			1	SUBCLONAL	1	FALSE	NA	0.31493181434639	4		363	167	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101034	26101034	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1266141035	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	50	371	0	ENST00000435504.4:c.57+1G>A		p.X19_splice	ENST00000435504		19			1	2	FACETS	0.959	0.818	1	0.959	0.818	1	CLONAL	1	FALSE	1	0.31493181434639	2		371	331	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046920	128046920	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	38	315	0	ENST00000285398.2:c.815T>C	p.Val272Ala	p.V272A	ENST00000285398	NM_000122.1	272	gTc/gCc	6/15	0.21923190485377	1	FACETS	0.865	0.721	1	0.865	0.721	1	CLONAL	1	FALSE	0	0.31493181434639	1		315	235	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488661	212488661	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	17	400	1	ENST00000342788.4:c.2188G>A	p.Gly730Arg	p.G730R	ENST00000342788	NM_005235.2	730	Gga/Aga	18/28	1	2	FACETS	0.474	0.354	0.615	0.474	0.354	0.615	SUBCLONAL	1	FALSE	1	0.31493181434639	2		401	228	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663101	227663101	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	37	452	0	ENST00000305123.5:c.354G>T	p.Lys118Asn	p.K118N	ENST00000305123	NM_005544.2	118	aaG/aaT	1/2	1	2	FACETS	0.932	0.774	1	0.932	0.774	1	CLONAL	1	FALSE	1	0.31493181434639	2		452	252	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663307	227663307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1469971676	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	37	417	0	ENST00000305123.5:c.148G>A	p.Glu50Lys	p.E50K	ENST00000305123	NM_005544.2	50	Gag/Aag	1/2	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	FALSE	1	0.31493181434639	2		417	217	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31025055	31025055	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	14	448	0	ENST00000375687.4:c.4540A>T	p.Ile1514Phe	p.I1514F	ENST00000375687	NM_015338.5	1514	Atc/Ttc	13/13	0.203419178298892	1	FACETS	0.345	0.249	0.461	0.345	0.249	0.461	SUBCLONAL	1	FALSE	0	0.31493181434639	1		448	217	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395573	31395573	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	26	420	0	ENST00000328111.2:c.2426T>A	p.Phe809Tyr	p.F809Y	ENST00000328111	NM_006892.3	809	tTt/tAt	23/23	0.203419178298892	1	FACETS	0.589	0.469	0.726	0.589	0.469	0.726	SUBCLONAL	1	FALSE	0	0.31493181434639	1		420	236	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545988	41545988	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	32	474	0	ENST00000263253.7:c.2603C>T	p.Ala868Val	p.A868V	ENST00000263253	NM_001429.3	868	gCc/gTc	14/31	0.149709330415769	0	FACETS	0.679	0.556	0.816			1	INDETERMINATE	1	FALSE	0	0.31493181434639	0		474	205	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41554447	41554447	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	39	312	0	ENST00000263253.7:c.3533A>G	p.Tyr1178Cys	p.Y1178C	ENST00000263253	NM_001429.3	1178	tAc/tGc	19/31	0.149709330415769	0	FACETS	0.875	0.733	1			1	INDETERMINATE	1	FALSE	0	0.31493181434639	0		312	194	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63976433	63976433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201198489	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	23	388	0	ENST00000398590.3:c.1580G>A	p.Arg527Gln	p.R527Q	ENST00000398590	NM_001177387.1	527	cGg/cAg	11/14	1	2	FACETS	0.493	0.385	0.619	0.493	0.385	0.619	SUBCLONAL	1	FALSE	1	0.31493181434639	2		388	296	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987024	69987024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200583343	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	20	430	0	ENST00000394351.3:c.85C>T	p.Arg29Trp	p.R29W	ENST00000394351	NM_000248.3	29	Cgg/Tgg	2/9	1	2	FACETS	0.545	0.418	0.693	0.545	0.418	0.693	SUBCLONAL	1	FALSE	1	0.31493181434639	2		430	233	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259484	89259484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	14	446	0	ENST00000336596.2:c.628G>A	p.Ala210Thr	p.A210T	ENST00000336596	NM_005233.5	210	Gct/Act	3/17	1	2	FACETS	0.319	0.23	0.426	0.319	0.23	0.426	SUBCLONAL	1	FALSE	1	0.31493181434639	2		446	279	SUCCESS
REST	5978	MSKCC	GRCh37	4	57797518	57797518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367963860	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	21	516	1	ENST00000309042.7:c.2494C>T	p.Arg832Trp	p.R832W	ENST00000309042	NM_005612.4	832	Cgg/Tgg	4/4	0.149709330415769	0	FACETS	0.446	0.345	0.562			1	INDETERMINATE	1	FALSE	0	0.31493181434639	0		517	205	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157939	106157939	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	29	511	0	ENST00000380013.4:c.2843del	p.Lys948SerfsTer5	p.K948Sfs*5	ENST00000380013	NM_001127208.2	947	cAa/ca	3/11	0.1951871774244	3	FACETS	0.82	0.661	0.999	0.41	0.33	0.5	CLONAL	1	FALSE	1	0.31493181434639	3		511	260	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056197	26056197	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs548795634	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	78	539	0	ENST00000343677.2:c.460A>G	p.Thr154Ala	p.T154A	ENST00000343677	NM_005319.3	154	Aca/Gca	1/1	0.31493181434639	7	FACETS	0.757	0.666	0.854			1	SUBCLONAL	2	FALSE	NA	0.31493181434639	7		539	585	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508248	106508248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1335642291	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	29	486	0	ENST00000359195.3:c.242C>T	p.Thr81Ile	p.T81I	ENST00000359195	NM_002649.2	81	aCc/aTc	2/11	0.31493181434639	4	FACETS	0.631	0.506	0.772	0.315	0.253	0.386	SUBCLONAL	1	FALSE	2	0.31493181434639	4		486	384	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124532340	124532340	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	29	208	0	ENST00000357628.3:c.104del	p.Pro35HisfsTer3	p.P35Hfs*3	ENST00000357628	NM_015450.2	35	cCa/ca	6/19	1	2	FACETS	0.944	0.764	1	0.944	0.764	1	CLONAL	1	FALSE	1	0.31493181434639	2		208	195	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476770	140476770	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	34	329	0	ENST00000288602.6:c.1636A>G	p.Thr546Ala	p.T546A	ENST00000288602	NM_004333.4	546	Acc/Gcc	13/18	1	2	FACETS	1	0.842	1	1	0.842	1	CLONAL	1	FALSE	1	0.31493181434639	2		329	211	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842350	151842350	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs768809958	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	44	442	0	ENST00000262189.6:c.14062A>G	p.Thr4688Ala	p.T4688A	ENST00000262189	NM_170606.2	4688	Acc/Gcc	54/59	1	2	FACETS	0.991	0.836	1	0.991	0.836	1	CLONAL	1	FALSE	1	0.31493181434639	2		442	282	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873405	151873405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	34	465	0	ENST00000262189.6:c.9133C>T	p.Pro3045Ser	p.P3045S	ENST00000262189	NM_170606.2	3045	Ccc/Tcc	38/59	1	2	FACETS	0.843	0.693	1	0.843	0.693	1	CLONAL	1	FALSE	1	0.31493181434639	2		465	256	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879307	151879307	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	46	488	0	ENST00000262189.6:c.5638C>T	p.Gln1880Ter	p.Q1880*	ENST00000262189	NM_170606.2	1880	Caa/Taa	36/59	1	2	FACETS	0.902	0.763	1	0.902	0.763	1	CLONAL	1	FALSE	1	0.31493181434639	2		488	324	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561505	141561505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	39	473	0	ENST00000220592.5:c.1300G>A	p.Val434Ile	p.V434I	ENST00000220592	NM_012154.3	434	Gtc/Atc	11/19	1	2	FACETS	0.935	0.779	1	0.935	0.779	1	CLONAL	1	FALSE	1	0.31493181434639	2		473	265	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250314	110250314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	18	498	0	ENST00000374672.4:c.361G>A	p.Ala121Thr	p.A121T	ENST00000374672	NM_004235.4	121	Gcc/Acc	3/5	1	2	FACETS	0.382	0.288	0.494	0.382	0.288	0.494	SUBCLONAL	1	FALSE	1	0.31493181434639	2		498	299	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339293	70339293	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058648-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	19	308	0	ENST00000374080.3:c.170G>A	p.Gly57Asp	p.G57D	ENST00000374080		57	gGc/gAc	2/45	0.287311691720168	0	FACETS	0.374	0.284	0.479			1	SUBCLONAL	1	FALSE	0	0.31493181434639	0		308	221	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0058650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	61	190	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.286940268802311	3	FACETS	1	0.968	1	0.703	0.613	0.799	CLONAL	1	TRUE	1	0.407812465252755	3		190	256	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0058650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	15	187	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.286940268802311	3	FACETS	0.509	0.374	0.67	0.254	0.187	0.335	SUBCLONAL	1	TRUE	1	0.407812465252755	3		188	174	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0058650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	237	327	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.407812465252755	3	FACETS	0.843	0.794	0.893	0.843	0.794	0.893	CLONAL	3	TRUE	0	0.407812465252755	3		327	553	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795103	242795104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768249210	NA	P-0058650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	63	460	0	ENST00000334409.5:c.105dup	p.Thr36HisfsTer70	p.T36Hfs*70	ENST00000334409	NM_005018.2	35	-/C	2/5	0.286940268802311	3	FACETS	0.56	0.484	0.643	0.28	0.242	0.322	SUBCLONAL	1	TRUE	1	0.407812465252755	3		460	664	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050372	176050372	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs766634588	NA	P-0058650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	12	343	0	ENST00000367669.3:c.1193A>C	p.Lys398Thr	p.K398T	ENST00000367669	NM_022457.5	398	aAg/aCg	11/20	0.286940268802311	3	FACETS	0.341	0.239	0.465	0.17	0.119	0.233	SUBCLONAL	1	TRUE	1	0.407812465252755	3		343	208	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46251014	46251015	+	missense_variant	Missense_Mutation	DNP	TG	TG	AT	novel	NA	P-0058650-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	23	233	0	ENST00000371998.3:c.23_24delinsAT	p.Leu8Tyr	p.L8Y	ENST00000371998		8	tTG/tAT	3/23	0.256786611249287	5	FACETS	0.405	0.315	0.51	0.135	0.105	0.17	SUBCLONAL	1	TRUE	2	0.407812465252755	5		233	449	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048631	180048631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1391338478	NA	P-0058652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	82	435	0	ENST00000261937.6:c.1931C>T	p.Ala644Val	p.A644V	ENST00000261937	NM_182925.4	644	gCg/gTg	13/30	0.389145738982378	3	FACETS	1	0.9	1	0.509	0.45	0.572	CLONAL	1	TRUE	1	0.407203989533235	3		435	476	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022592	31022592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs373221034	NA	P-0058652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	183	454	0	ENST00000375687.4:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000375687	NM_015338.5	693	Cga/Tga	13/13	0.389145738982378	3	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	1	0.407203989533235	3		454	536	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807454	36807454	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	60	407	0	ENST00000373129.3:c.1210T>C	p.Phe404Leu	p.F404L	ENST00000373129	NM_032017.1	404	Ttc/Ctc	12/12	1	2	FACETS	0.761	0.659	0.872	0.761	0.659	0.872	SUBCLONAL	1	TRUE	1	0.407203989533235	2		407	387	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805648	43805648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	77	329	0	ENST00000372470.3:c.704C>T	p.Thr235Ile	p.T235I	ENST00000372470	NM_005373.2	235	aCa/aTa	5/12	1	2	FACETS	0.953	0.841	1	0.953	0.841	1	CLONAL	1	TRUE	1	0.407203989533235	2		329	397	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349224	11349225	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0058652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	67	380	0	ENST00000332029.2:c.111_112delinsTT	p.Arg38Cys	p.R38C	ENST00000332029	NM_003745.1	37	gcGCgc/gcTTgc	2/2	0.389145738982378	3	FACETS	1	0.945	1	0.574	0.502	0.651	CLONAL	1	TRUE	1	0.407203989533235	3		380	345	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217426	7217426	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747205747	NA	P-0058652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	91	403	0	ENST00000380728.2:c.370A>G	p.Thr124Ala	p.T124A	ENST00000380728		124	Aca/Gca	5/11	0.389145738982378	3	FACETS	0.975	0.867	1	0.487	0.433	0.544	CLONAL	1	TRUE	1	0.407203989533235	3		403	552	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610451	215610451	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs761883180	NA	P-0058652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	142	254	0	ENST00000260947.4:c.1805G>C	p.Ser602Thr	p.S602T	ENST00000260947	NM_000465.2	602	aGt/aCt	8/11	0.407203989533235	3	FACETS	0.845	0.782	0.909	0.845	0.782	0.909	CLONAL	3	TRUE	0	0.407203989533235	3		254	331	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125610	47125610	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	82	401	0	ENST00000409792.3:c.5660A>G	p.Asn1887Ser	p.N1887S	ENST00000409792	NM_014159.6	1887	aAt/aGt	12/21	0.389145738982378	3	FACETS	1	0.927	1	0.532	0.47	0.596	CLONAL	1	TRUE	1	0.407203989533235	3		401	456	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495508	149495508	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058652-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	81	448	0	ENST00000261799.4:c.3139T>G	p.Ser1047Ala	p.S1047A	ENST00000261799	NM_002609.3	1047	Tcc/Gcc	23/23	0.389145738982378	3	FACETS	0.836	0.737	0.941	0.418	0.368	0.471	CLONAL	1	TRUE	1	0.407203989533235	3		448	573	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	73	544	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.358	0.312	0.407	0.358	0.312	0.407	SUBCLONAL	1	TRUE	1	0.49	2		548	833	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47594882	47594883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs756343868	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	181	470	1	ENST00000430070.2:c.1204dup	p.Glu402GlyfsTer4	p.E402Gfs*4	ENST00000430070	NM_018095.4	402	gag/gGag	4/4	1	2	FACETS	0.885	0.817	0.955	0.885	0.817	0.955	CLONAL	1	TRUE	1	0.49	2		471	835	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	181	404	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.923	0.853	0.996	0.923	0.853	0.996	CLONAL	1	TRUE	1	0.49	2		404	800	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	152	156	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.952	0.885	1	1	0.992	1	CLONAL	2	TRUE	1	0.49	2		157	326	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	115	478	4	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.59	0.531	0.652	0.59	0.531	0.652	SUBCLONAL	1	TRUE	1	0.49	2		482	796	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	165	549	5	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.49	2		554	651	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	123	344	2	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	1	2	FACETS	0.803	0.728	0.882	0.803	0.728	0.882	CLONAL	1	TRUE	1	0.49	2		346	625	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	88	347	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	0.505	0.447	0.567	0.505	0.447	0.567	SUBCLONAL	1	TRUE	1	0.49	2		347	711	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263973	104263974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776579	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	28	303	3	ENST00000369902.3:c.71dup	p.Ala25GlyfsTer23	p.A25Gfs*23	ENST00000369902	NM_016169.3	22	gcc/gCcc	1/12	1	2	FACETS	0.255	0.203	0.314	0.255	0.203	0.314	SUBCLONAL	1	TRUE	1	0.49	2		306	448	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	42	155	3	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	0.647	0.544	0.76	0.647	0.544	0.76	SUBCLONAL	1	TRUE	1	0.49	2		158	265	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	150	381	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.969	0.889	1	0.969	0.889	1	CLONAL	1	TRUE	1	0.49	2		381	632	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	175	471	0	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.893	0.823	0.965	0.893	0.823	0.965	CLONAL	1	TRUE	1	0.49	2		471	800	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs1057519842	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	131	292	0	ENST00000274335.5:c.1727_1729del	p.Thr576del	p.T576del	ENST00000274335		575	aaGACg/aag	12/15	1	2	FACETS	0.928	0.846	1	0.928	0.846	1	CLONAL	1	TRUE	1	0.49	2		292	576	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	163	425	1	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.97	0.893	1	0.97	0.893	1	CLONAL	1	TRUE	1	0.49	2		426	686	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084146	47084146	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	97	410	0	ENST00000409792.3:c.7143del	p.Ser2382LeufsTer29	p.S2382Lfs*29	ENST00000409792	NM_014159.6	2381	ccC/cc	17/21	0.488152078491184	2	FACETS	0.499	0.444	0.557	0.249	0.222	0.279	SUBCLONAL	1	TRUE	0	0.49	2		410	794	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354038	15354038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201742792	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	76	241	0	ENST00000263377.2:c.2842G>A	p.Val948Met	p.V948M	ENST00000263377	NM_058243.2	948	Gtg/Atg	14/20	1	2	FACETS	0.843	0.744	0.948	0.843	0.744	0.948	CLONAL	1	TRUE	1	0.49	2		241	368	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099579	157099579	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1562376341	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	57	344	3	ENST00000346085.5:c.521del	p.Pro174ArgfsTer6	p.P174Rfs*6	ENST00000346085	NM_020732.3	172	gaC/ga	1/20	1	2	FACETS	0.48	0.412	0.553	0.48	0.412	0.553	SUBCLONAL	1	TRUE	1	0.49	2		347	485	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830751	72830751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761415382	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	88	427	0	ENST00000268489.5:c.5830G>A	p.Ala1944Thr	p.A1944T	ENST00000268489	NM_006885.3	1944	Gcc/Acc	9/10	1	2	FACETS	0.487	0.431	0.546	0.487	0.431	0.546	SUBCLONAL	1	TRUE	1	0.49	2		427	738	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790122	40790122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372056802	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	141	379	0	ENST00000373198.4:c.2609G>A	p.Arg870His	p.R870H	ENST00000373198	NM_133170.3	870	cGc/cAc	18/32	1	2	FACETS	0.905	0.827	0.986	0.905	0.827	0.986	CLONAL	1	TRUE	1	0.49	2		379	636	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144864	58144864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778185	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	187	384	0	ENST00000257904.6:c.364C>T	p.Arg122Cys	p.R122C	ENST00000257904	NM_000075.3	122	Cgc/Tgc	4/8	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.49	2		384	711	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647657	3647657	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs774532876	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	151	413	2	ENST00000294008.3:c.1406del	p.Pro469HisfsTer4	p.P469Hfs*4	ENST00000294008	NM_032444.2	469	cCa/ca	7/15	1	2	FACETS	0.906	0.831	0.985	0.906	0.831	0.985	CLONAL	1	TRUE	1	0.49	2		415	680	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948208	71948209	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs749079348	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	143	484	0	ENST00000298229.2:c.2927dup	p.Pro977ThrfsTer7	p.P977Tfs*7	ENST00000298229	NM_001567.3	974	gcc/gCcc	26/28	1	2	FACETS	0.765	0.698	0.835	0.765	0.698	0.835	SUBCLONAL	1	TRUE	1	0.49	2		484	763	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527398	157527398	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	74	366	1	ENST00000346085.5:c.5127del	p.Ala1710HisfsTer56	p.A1710Hfs*56	ENST00000346085	NM_020732.3	1708	cAa/ca	20/20	1	2	FACETS	0.51	0.447	0.578	0.51	0.447	0.578	SUBCLONAL	1	TRUE	1	0.49	2		367	592	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856434	111856434	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs776317487	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	110	419	3	ENST00000341259.2:c.489del	p.Thr165ProfsTer32	p.T165Pfs*32	ENST00000341259	NM_005475.2	162	gCc/gc	2/8	1	2	FACETS	0.854	0.77	0.941	0.854	0.77	0.941	CLONAL	1	TRUE	1	0.49	2		422	526	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719875	52719875	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751218909	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	110	378	0	ENST00000322088.6:c.1087G>A	p.Glu363Lys	p.E363K	ENST00000322088	NM_014225.5	363	Gag/Aag	9/15	1	2	FACETS	0.642	0.577	0.711	0.642	0.577	0.711	SUBCLONAL	1	TRUE	1	0.49	2		378	699	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139799	55139799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764214258	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	157	362	0	ENST00000257290.5:c.1460G>A	p.Arg487His	p.R487H	ENST00000257290	NM_006206.4	487	cGt/cAt	10/23	1	2	FACETS	0.989	0.909	1	0.989	0.909	1	CLONAL	1	TRUE	1	0.49	2		362	648	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41251812	41251812	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782747	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	134	286	0	ENST00000357654.3:c.527C>T	p.Thr176Met	p.T176M	ENST00000357654	NM_007294.3	176	aCg/aTg	7/23	1	2	FACETS	0.956	0.872	1	0.956	0.872	1	CLONAL	1	TRUE	1	0.49	2		286	572	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912733	32912733	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs70953664	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	134	276	0	ENST00000380152.3:c.4241C>T	p.Thr1414Met	p.T1414M	ENST00000380152		1414	aCg/aTg	11/27	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.49	2		276	492	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229369	36229369	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	186	427	0	ENST00000222270.7:c.8059A>G	p.Thr2687Ala	p.T2687A	ENST00000222270	NM_014727.1	2687	Acc/Gcc	37/37	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.49	2		427	750	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40880888	40880888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	58	255	0	ENST00000428826.2:c.72G>A	p.Met24Ile	p.M24I	ENST00000428826		24	atG/atA	3/21	1	2	FACETS	0.433	0.372	0.499	0.433	0.372	0.499	SUBCLONAL	1	TRUE	1	0.49	2		255	547	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112764373	112764373	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	41	224	0	ENST00000369452.4:c.982T>G	p.Ser328Ala	p.S328A	ENST00000369452	NM_007373.3	328	Tca/Gca	5/9	1	2	FACETS	0.374	0.311	0.443	0.374	0.311	0.443	SUBCLONAL	1	TRUE	1	0.49	2		224	448	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445929	49445929	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	194	508	0	ENST00000301067.7:c.1537del	p.Ser513LeufsTer417	p.S513Lfs*417	ENST00000301067	NM_003482.3	513	Tct/ct	10/54	1	2	FACETS	0.959	0.888	1	0.959	0.888	1	CLONAL	1	TRUE	1	0.49	2		508	826	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779011	3779011	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	175	494	0	ENST00000262367.5:c.6037A>G	p.Met2013Val	p.M2013V	ENST00000262367	NM_004380.2	2013	Atg/Gtg	31/31	1	2	FACETS	0.985	0.91	1	0.985	0.91	1	CLONAL	1	TRUE	1	0.49	2		494	725	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821503	72821506	+	frameshift_variant	Frame_Shift_Del	DEL	TTGT	TTGT	-	novel	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	111	497	0	ENST00000268489.5:c.10669_10672del	p.Thr3557SerfsTer136	p.T3557Sfs*136	ENST00000268489	NM_006885.3	3557	ACAAtc/tc	10/10	1	2	FACETS	0.769	0.693	0.849	0.769	0.693	0.849	SUBCLONAL	1	TRUE	1	0.49	2		497	589	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347447	89347447	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	100	443	0	ENST00000301030.4:c.5503del	p.Leu1835CysfsTer128	p.L1835Cfs*128	ENST00000301030	NM_001256183.1	1835	Ctg/tg	9/13	1	2	FACETS	0.536	0.478	0.597	0.536	0.478	0.597	SUBCLONAL	1	TRUE	1	0.49	2		443	762	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627455	37627455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	88	334	0	ENST00000447079.4:c.1370C>T	p.Ala457Val	p.A457V	ENST00000447079	NM_015083.1	457	gCc/gTc	2/14	1	2	FACETS	0.547	0.484	0.613	0.547	0.484	0.613	SUBCLONAL	1	TRUE	1	0.49	2		334	657	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007183	62007183	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	139	435	0	ENST00000392795.3:c.499A>G	p.Thr167Ala	p.T167A	ENST00000392795	NM_001039933.1	167	Acg/Gcg	4/6	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.49	2		435	562	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425090	47425091	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	147	389	0	ENST00000404338.3:c.3163dup	p.Asp1055GlyfsTer10	p.D1055Gfs*10	ENST00000404338	NM_004491.4	1053	aag/aaGg	1/6	1	2	FACETS	0.938	0.859	1	0.938	0.859	1	CLONAL	1	TRUE	1	0.49	2		389	640	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281788	46281788	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	74	286	0	ENST00000371998.3:c.4235T>C	p.Met1412Thr	p.M1412T	ENST00000371998		1412	aTg/aCg	22/23	1	2	FACETS	0.524	0.459	0.594	0.524	0.459	0.594	SUBCLONAL	1	TRUE	1	0.49	2		286	576	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968248	134968248	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	151	361	0	ENST00000398015.3:c.2761A>G	p.Ser921Gly	p.S921G	ENST00000398015	NM_004441.4	921	Agc/Ggc	15/16	1	2	FACETS	0.98	0.899	1	0.98	0.899	1	CLONAL	1	TRUE	1	0.49	2		361	629	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215318	142215318	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	106	226	0	ENST00000350721.4:c.5783C>T	p.Ala1928Val	p.A1928V	ENST00000350721	NM_001184.3	1928	gCc/gTc	34/47	1	2	FACETS	0.949	0.856	1	0.949	0.856	1	CLONAL	1	TRUE	1	0.49	2		226	456	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808286	1808286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	121	589	0	ENST00000260795.2:c.2044G>A	p.Val682Ile	p.V682I	ENST00000260795		682	Gtc/Atc	15/17	1	2	FACETS	0.602	0.543	0.663	0.602	0.543	0.663	SUBCLONAL	1	TRUE	1	0.49	2		589	821	SUCCESS
REST	5978	MSKCC	GRCh37	4	57796874	57796874	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	97	465	0	ENST00000309042.7:c.1850C>A	p.Pro617His	p.P617H	ENST00000309042	NM_005612.4	617	cCc/cAc	4/4	1	2	FACETS	0.503	0.448	0.562	0.503	0.448	0.562	SUBCLONAL	1	TRUE	1	0.49	2		465	787	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144359354	144359354	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	147	308	0	ENST00000262995.4:c.796T>A	p.Ser266Thr	p.S266T	ENST00000262995	NM_207123.2	266	Tcc/Acc	4/11	1	2	FACETS	0.987	0.905	1	0.987	0.905	1	CLONAL	1	TRUE	1	0.49	2		308	608	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950249	38950249	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	163	333	0	ENST00000357387.3:c.3701C>A	p.Ser1234Ter	p.S1234*	ENST00000357387	NM_152756.3	1234	tCa/tAa	31/38	1	2	FACETS	0.983	0.905	1	0.983	0.905	1	CLONAL	1	TRUE	1	0.49	2		333	677	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707590	176707590	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	150	312	0	ENST00000439151.2:c.5647C>T	p.Gln1883Ter	p.Q1883*	ENST00000439151	NM_022455.4	1883	Cag/Tag	18/23	1	2	FACETS	0.957	0.877	1	0.957	0.877	1	CLONAL	1	TRUE	1	0.49	2		312	640	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032090	26032090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1329616402	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	196	598	0	ENST00000244661.2:c.199C>T	p.Pro67Ser	p.P67S	ENST00000244661	NM_003537.3	67	Ccg/Tcg	1/1	1	2	FACETS	0.926	0.858	0.996	0.926	0.858	0.996	CLONAL	1	TRUE	1	0.49	2		598	864	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324124	31324124	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	15	209	0	ENST00000412585.2:c.439T>C	p.Tyr147His	p.Y147H	ENST00000412585	NM_005514.6	147	Tac/Cac	3/8	1	2	FACETS	0.233	0.17	0.308	0.233	0.17	0.308	SUBCLONAL	1	TRUE	1	0.49	2		209	263	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371959	55371959	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	163	427	0	ENST00000297316.4:c.649T>G	p.Tyr217Asp	p.Y217D	ENST00000297316	NM_022454.3	217	Tac/Gac	2/2	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.49	2		427	588	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993639	90993640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	78	206	0	ENST00000265433.3:c.283dup	p.Asp95GlyfsTer11	p.D95Gfs*11	ENST00000265433	NM_002485.4	95	gat/gGat	3/16	1	2	FACETS	0.777	0.686	0.873	0.777	0.686	0.873	SUBCLONAL	1	TRUE	1	0.49	2		206	410	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44935998	44935998	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	41	220	0	ENST00000377967.4:c.2759C>A	p.Pro920His	p.P920H	ENST00000377967	NM_021140.2	920	cCt/cAt	18/29	1	2	FACETS	0.378	0.315	0.448	0.378	0.315	0.448	SUBCLONAL	1	TRUE	1	0.49	2		220	443	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040781	47040781	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	147	401	0	ENST00000377604.3:c.1416A>T	p.Lys472Asn	p.K472N	ENST00000377604	NM_001204468.1	472	aaA/aaT	13/24	1	2	FACETS	0.935	0.856	1	0.935	0.856	1	CLONAL	1	TRUE	1	0.49	2		401	642	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858026	152858026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058653-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	123	370	0	ENST00000406277.2:c.589G>A	p.Ala197Thr	p.A197T	ENST00000406277	NM_152274.4	197	Gcc/Acc	6/7	1	2	FACETS	0.837	0.759	0.918	0.837	0.759	0.918	CLONAL	1	TRUE	1	0.49	2		370	600	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105551	27105551	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	371	376	0	ENST00000324856.7:c.5162G>C	p.Arg1721Pro	p.R1721P	ENST00000324856	NM_006015.4	1721	cGa/cCa	20/20	0.472267989084848	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.472267989084848	3		376	589	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652140	36652140	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	119	427	0	ENST00000244741.5:c.262G>T	p.Glu88Ter	p.E88*	ENST00000244741	NM_000389.4	88	Gag/Tag	2/3	0.446781965317367	4	FACETS	0.959	0.866	1	0.32	0.288	0.353	CLONAL	1	TRUE	1	0.472267989084848	4		427	774	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486842	56486842	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	228	361	0	ENST00000267101.3:c.1256G>C	p.Gly419Ala	p.G419A	ENST00000267101	NM_001982.3	419	gGa/gCa	11/28	0.472267989084848	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.472267989084848	3		361	526	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882319	89882319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	93	391	0	ENST00000389301.3:c.155G>A	p.Arg52Gln	p.R52Q	ENST00000389301	NM_000135.2	52	cGa/cAa	2/43	0.472267989084848	3	FACETS	0.866	0.772	0.966	0.433	0.386	0.483	CLONAL	1	TRUE	1	0.472267989084848	3		391	562	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265192	5265192	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	141	418	0	ENST00000357368.4:c.395C>G	p.Ser132Cys	p.S132C	ENST00000357368	NM_002850.3	132	tCt/tGt	5/38	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.472267989084848	2		418	466	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022422	31022422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370230857	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	267	513	0	ENST00000375687.4:c.1907C>T	p.Ala636Val	p.A636V	ENST00000375687	NM_015338.5	636	gCg/gTg	13/13	0.175761297500244	6	FACETS	0.988	0.931	1	0.988	0.931	1	INDETERMINATE	3	TRUE	3	0.472267989084848	6		513	742	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828827	26828827	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	101	427	0	ENST00000381527.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000381527	NM_001260.1	17	Gag/Aag	1/13	0.472267989084848	3	FACETS	1	0.929	1	0.522	0.469	0.579	CLONAL	1	TRUE	1	0.472267989084848	3		427	506	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021828	71021828	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	153	328	0	ENST00000318789.4:c.1531-1G>C		p.X511_splice	ENST00000318789	NM_032682.5	511			0.472267989084848	3	FACETS	0.88	0.812	0.95	0.88	0.812	0.95	CLONAL	2	TRUE	1	0.472267989084848	3		328	455	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538326	187538326	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	74	307	0	ENST00000441802.2:c.8908G>A	p.Glu2970Lys	p.E2970K	ENST00000441802	NM_005245.3	2970	Gaa/Aaa	11/27	0.472267989084848	3	FACETS	1	0.936	1	0.547	0.482	0.616	CLONAL	1	TRUE	1	0.472267989084848	3		307	354	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652031	36652031	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	409	496	0	ENST00000244741.5:c.153C>G	p.Phe51Leu	p.F51L	ENST00000244741	NM_000389.4	51	ttC/ttG	2/3	0.446781965317367	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	1	0.472267989084848	4		496	802	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827919	40827919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	93	389	0	ENST00000373198.4:c.2509G>A	p.Glu837Lys	p.E837K	ENST00000373198	NM_133170.3	837	Gaa/Aaa	17/32	0.175761297500244	6	FACETS	1	0.962	1	0.395	0.351	0.442	INDETERMINATE	1	TRUE	3	0.472267989084848	6		389	646	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662301	227662301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1289819083	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	150	537	0	ENST00000305123.5:c.1154C>T	p.Ser385Leu	p.S385L	ENST00000305123	NM_005544.2	385	tCg/tTg	1/2	1	2	FACETS	0.993	0.91	1	0.993	0.91	1	CLONAL	1	TRUE	1	0.472267989084848	2		537	640	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874893	151874893	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1473097808	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	125	410	0	ENST00000262189.6:c.7645C>T	p.Gln2549Ter	p.Q2549*	ENST00000262189	NM_170606.2	2549	Cag/Tag	38/59	0.472267989084848	3	FACETS	1	0.958	1	0.547	0.497	0.6	CLONAL	1	TRUE	1	0.472267989084848	3		410	598	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551990	150551990	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	106	355	0	ENST00000369026.2:c.17G>C	p.Arg6Thr	p.R6T	ENST00000369026	NM_021960.4	6	aGa/aCa	1/3	0.197925162353947	5	FACETS	1	0.959	1	0.379	0.34	0.42	INDETERMINATE	1	TRUE	2	0.472267989084848	5		355	675	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845334	151845334	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	144	445	0	ENST00000262189.6:c.13678C>T	p.Gln4560Ter	p.Q4560*	ENST00000262189	NM_170606.2	4560	Cag/Tag	52/59	0.472267989084848	3	FACETS	1	0.981	1	0.627	0.574	0.682	CLONAL	1	TRUE	1	0.472267989084848	3		445	601	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997819	149997819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	120	364	0	ENST00000253339.5:c.2648C>T	p.Ser883Leu	p.S883L	ENST00000253339		883	tCa/tTa	5/7	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.472267989084848	2		364	467	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50827573	50827573	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	81	270	0	ENST00000398568.2:c.2458C>G	p.Gln820Glu	p.Q820E	ENST00000398568	NM_001042412.1	820	Caa/Gaa	16/18	0.472267989084848	3	FACETS	1	0.945	1	0.555	0.492	0.622	CLONAL	1	TRUE	1	0.472267989084848	3		270	382	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1720648	1720648	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	126	366	0	ENST00000378609.4:c.760G>C	p.Asp254His	p.D254H	ENST00000378609	NM_002074.3	254	Gac/Cac	10/12	0.472267989084848	3	FACETS	1	0.957	1	0.364	0.33	0.399	CLONAL	1	TRUE	0	0.472267989084848	3		366	604	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202735	16202735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	239	371	0	ENST00000375759.3:c.443C>T	p.Ala148Val	p.A148V	ENST00000375759	NM_015001.2	148	gCc/gTc	3/15	0.472267989084848	3	FACETS	1	0.965	1	0.69	0.649	0.732	CLONAL	2	TRUE	0	0.472267989084848	3		371	604	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599944	28599944	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	104	386	0	ENST00000253063.3:c.826G>T	p.Glu276Ter	p.E276*	ENST00000253063	NM_031459.4	276	Gag/Tag	6/10	0.472267989084848	3	FACETS	1	0.907	1	0.337	0.302	0.373	CLONAL	1	TRUE	0	0.472267989084848	3		386	539	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938201	36938201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	288	393	0	ENST00000361632.4:c.760G>A	p.Glu254Lys	p.E254K	ENST00000361632		254	Gag/Aag	6/16	0.472267989084848	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	3	TRUE	0	0.472267989084848	3		393	495	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150933602	150933602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	217	381	0	ENST00000271640.5:c.3064G>A	p.Glu1022Lys	p.E1022K	ENST00000271640	NM_001145415.1	1022	Gag/Aag	16/22	0.197925162353947	5	FACETS	0.847	0.792	0.902	0.847	0.792	0.902	INDETERMINATE	3	TRUE	2	0.472267989084848	5		381	618	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981202	201981202	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	141	405	0	ENST00000359651.3:c.281G>T	p.Arg94Leu	p.R94L	ENST00000359651		94	cGa/cTa	2/8	0.472267989084848	2	FACETS	1	0.977	1	0.591	0.542	0.642	CLONAL	1	TRUE	0	0.472267989084848	2		405	505	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230493024	230493024	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	114	461	0	ENST00000391860.1:c.30C>G	p.Phe10Leu	p.F10L	ENST00000391860	NM_001258311.1	10	ttC/ttG	2/7	0.472267989084848	2	FACETS	1	0.947	1	0.533	0.483	0.585	CLONAL	1	TRUE	0	0.472267989084848	2		461	453	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977167	85977167	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	26	193	0	ENST00000263360.6:c.769G>C	p.Asp257His	p.D257H	ENST00000263360	NM_003797.3	257	Gat/Cat	8/12	0.472267989084848	3	FACETS	0.84	0.672	1	0.42	0.336	0.514	CLONAL	1	TRUE	1	0.472267989084848	3		193	162	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920777	100920777	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	60	257	0	ENST00000325455.5:c.2371G>C	p.Glu791Gln	p.E791Q	ENST00000325455	NM_001202474.3	791	Gaa/Caa	6/8	0.296744025300244	6	FACETS	1	0.938	1			1	CLONAL	1	TRUE	NA	0.472267989084848	6		257	428	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141845	108141845	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	94	249	0	ENST00000278616.4:c.2893G>A	p.Asp965Asn	p.D965N	ENST00000278616	NM_000051.3	965	Gat/Aat	19/63	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.472267989084848	2		249	328	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49430593	49431582	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTTTGCACCACTTCTCTTCAAGTCTTAAGCTTTCAACTTCACTACAGCTACAAAGGCTCTGCTAATTAGGCTTCATTCATACATTCATTCCATTTATTCAAACATCTGCTACATGCCTACTATATGCCAGGAACTGTTCTCTCTCTTCTTAAAAGCTACAGTGTTTCTGCCTCTACCACTAGTATGATATTTAGCCAAAGTTCTTTGTGTCCCATCTTAAGTAGGGATTATCTGAGGTCTCTAGCCTCAGTGCCCATTTAGGGATAACAATAATCACCCTGAGTAACTTGGCTATGTTACCAGCTGAGGTTACCTGTATCTGGGAAGAAGCTGTTTGCCAGCTGCTGCTGCATTGCCAATTGCTGCGGCTTCATGCACATGGAAGGTGGCATGGTGCCCATGGGCTTCTGTGATAGCACTGGCTGTGAGCTCTGCTGGGGTACCAAGCCTGCCTGCCCTCCATGCTGCCCACTTAGCATATGCCCTTGATTGGACACCATAGCCATGGATGGAGCCAGGCGTTGCTGGAGGGCATGAGCTGGTGGCTGGGTGGGCATCAGTGGCTGGGGCAAACCTGGCTGTCGGGCACCTGCAAGACCCAGGGAAAGCTGCTGTTGGGACCCAGCCAAACTGGGAGAAGAGCCCTCATGTGGCAAAGACATGGCCTGGGCAGGGCCTGGTGCAGACAGTAGGGAATGCTGCTGCTGCTGTTGCTGCTGCTGCTGGGCAGGCTGCAACTGTGCTGAAAGCTGCTGCTTCTTCTGCAGCTCCTTCTTCTCATGCTCCAACAGGTCCTCAATGAGCAGGGGTAACTCGCTGGCTACCAGTGAGCTCTCCATCTTGTCTAGCTCATCCCCAGATGCTGCAGGTCCACCAGGCAAGGTCAAAGCCCCACTCTCGAGCTCAAACTTTTCCAGCAGGGAGGATCCTCCTGGGCCACTCAGTGGGCTGGGGGTCAGCAGGTGAGCTGGTGGTCCTCCCGTGGCCC	TTTTTTGCACCACTTCTCTTCAAGTCTTAAGCTTTCAACTTCACTACAGCTACAAAGGCTCTGCTAATTAGGCTTCATTCATACATTCATTCCATTTATTCAAACATCTGCTACATGCCTACTATATGCCAGGAACTGTTCTCTCTCTTCTTAAAAGCTACAGTGTTTCTGCCTCTACCACTAGTATGATATTTAGCCAAAGTTCTTTGTGTCCCATCTTAAGTAGGGATTATCTGAGGTCTCTAGCCTCAGTGCCCATTTAGGGATAACAATAATCACCCTGAGTAACTTGGCTATGTTACCAGCTGAGGTTACCTGTATCTGGGAAGAAGCTGTTTGCCAGCTGCTGCTGCATTGCCAATTGCTGCGGCTTCATGCACATGGAAGGTGGCATGGTGCCCATGGGCTTCTGTGATAGCACTGGCTGTGAGCTCTGCTGGGGTACCAAGCCTGCCTGCCCTCCATGCTGCCCACTTAGCATATGCCCTTGATTGGACACCATAGCCATGGATGGAGCCAGGCGTTGCTGGAGGGCATGAGCTGGTGGCTGGGTGGGCATCAGTGGCTGGGGCAAACCTGGCTGTCGGGCACCTGCAAGACCCAGGGAAAGCTGCTGTTGGGACCCAGCCAAACTGGGAGAAGAGCCCTCATGTGGCAAAGACATGGCCTGGGCAGGGCCTGGTGCAGACAGTAGGGAATGCTGCTGCTGCTGTTGCTGCTGCTGCTGGGCAGGCTGCAACTGTGCTGAAAGCTGCTGCTTCTTCTGCAGCTCCTTCTTCTCATGCTCCAACAGGTCCTCAATGAGCAGGGGTAACTCGCTGGCTACCAGTGAGCTCTCCATCTTGTCTAGCTCATCCCCAGATGCTGCAGGTCCACCAGGCAAGGTCAAAGCCCCACTCTCGAGCTCAAACTTTTCCAGCAGGGAGGATCCTCCTGGGCCACTCAGTGGGCTGGGGGTCAGCAGGTGAGCTGGTGGTCCTCCCGTGGCCC	-	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	159	18	0	ENST00000301067.7:c.9557_10231+315del		p.X3186_splice	ENST00000301067	NM_003482.3	3186		34/54	0.472267989084848	3	FACETS	1	0.984	1	0.636	0.585	0.689	CLONAL	1	TRUE	1	0.472267989084848	3		18	654	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885334	111885334	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	167	333	0	ENST00000341259.2:c.1222C>T	p.Gln408Ter	p.Q408*	ENST00000341259	NM_005475.2	408	Cag/Tag	6/8	0.472267989084848	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.472267989084848	3		333	414	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245249	133245249	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	116	457	0	ENST00000320574.5:c.1998G>T	p.Lys666Asn	p.K666N	ENST00000320574	NM_006231.2	666	aaG/aaT	18/49	0.472267989084848	3	FACETS	0.947	0.856	1	0.474	0.428	0.522	CLONAL	1	TRUE	1	0.472267989084848	3		457	641	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248909	133248909	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	216	315	0	ENST00000320574.5:c.1687-1G>C		p.X563_splice	ENST00000320574	NM_006231.2	563			0.472267989084848	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.472267989084848	3		315	514	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035314	42035314	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	124	372	0	ENST00000219905.7:c.5156C>A	p.Ser1719Tyr	p.S1719Y	ENST00000219905	NM_001164273.1	1719	tCt/tAt	15/24	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.472267989084848	2		372	444	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465510	99465510	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	234	406	0	ENST00000268035.6:c.2335G>C	p.Glu779Gln	p.E779Q	ENST00000268035	NM_000875.3	779	Gag/Cag	11/21	0.472267989084848	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.472267989084848	3		406	584	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647249	2647249	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	103	325	0	ENST00000342085.4:c.1527G>T	p.Lys509Asn	p.K509N	ENST00000342085	NM_002613.4	509	aaG/aaT	13/14	0.472267989084848	3	FACETS	1	0.962	1	0.571	0.514	0.632	CLONAL	1	TRUE	1	0.472267989084848	3		325	472	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786740	3786740	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	130	353	0	ENST00000262367.5:c.4471C>T	p.Gln1491Ter	p.Q1491*	ENST00000262367	NM_004380.2	1491	Caa/Taa	27/31	0.472267989084848	3	FACETS	1	0.974	1	0.591	0.538	0.646	CLONAL	1	TRUE	1	0.472267989084848	3		353	576	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845920	72845920	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1167212887	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	110	377	0	ENST00000268489.5:c.3547G>C	p.Glu1183Gln	p.E1183Q	ENST00000268489	NM_006885.3	1183	Gag/Cag	6/10	0.472267989084848	3	FACETS	1	0.94	1	0.529	0.477	0.584	CLONAL	1	TRUE	1	0.472267989084848	3		377	544	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81960765	81960765	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	96	353	0	ENST00000359376.3:c.2496C>A	p.Phe832Leu	p.F832L	ENST00000359376	NM_002661.3	832	ttC/ttA	23/33	0.472267989084848	3	FACETS	0.963	0.861	1	0.481	0.43	0.536	CLONAL	1	TRUE	1	0.472267989084848	3		353	522	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347245	89347245	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	164	565	0	ENST00000301030.4:c.5705C>A	p.Ser1902Tyr	p.S1902Y	ENST00000301030	NM_001256183.1	1902	tCc/tAc	9/13	0.472267989084848	3	FACETS	1	0.984	1	0.642	0.591	0.694	CLONAL	1	TRUE	1	0.472267989084848	3		565	669	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243563	41243563	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	120	432	0	ENST00000357654.3:c.3985G>T	p.Glu1329Ter	p.E1329*	ENST00000357654	NM_007294.3	1329	Gaa/Taa	10/23	0.472267989084848	3	FACETS	1	0.921	1	0.51	0.461	0.561	CLONAL	1	TRUE	1	0.472267989084848	3		432	616	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923296	78923296	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	115	356	0	ENST00000306801.3:c.3319G>C	p.Glu1107Gln	p.E1107Q	ENST00000306801	NM_020761.2	1107	Gag/Cag	28/34	0.472267989084848	3	FACETS	1	0.948	1	0.537	0.485	0.591	CLONAL	1	TRUE	1	0.472267989084848	3		356	561	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395628	45395628	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	221	273	0	ENST00000262160.6:c.506G>C	p.Arg169Thr	p.R169T	ENST00000262160	NM_005901.5	169	aGa/aCa	4/11	0.433683164910661	4	FACETS	1	0.947	1	1	0.947	1	CLONAL	3	TRUE	1	0.472267989084848	4		273	457	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985691	60985691	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	120	446	0	ENST00000333681.4:c.209C>A	p.Ser70Ter	p.S70*	ENST00000333681		70	tCg/tAg	2/3	0.433683164910661	4	FACETS	1	0.977	1	0.418	0.379	0.46	CLONAL	1	TRUE	1	0.472267989084848	4		446	596	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220976	36220976	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	183	444	0	ENST00000222270.7:c.5026G>A	p.Asp1676Asn	p.D1676N	ENST00000222270	NM_014727.1	1676	Gat/Aat	23/37	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.472267989084848	2		444	544	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96931053	96931053	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	119	480	0	ENST00000258439.3:c.67C>G	p.Leu23Val	p.L23V	ENST00000258439	NM_001193304.2	23	Ctg/Gtg	2/4	0.472267989084848	3	FACETS	1	0.977	1	0.622	0.564	0.682	CLONAL	1	TRUE	1	0.472267989084848	3		480	501	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248410	212248410	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1213182678	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	111	402	0	ENST00000342788.4:c.3857C>G	p.Ser1286Cys	p.S1286C	ENST00000342788	NM_005235.2	1286	tCt/tGt	28/28	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.472267989084848	2		402	441	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408920	41408920	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	103	361	0	ENST00000373198.4:c.506C>G	p.Ser169Ter	p.S169*	ENST00000373198	NM_133170.3	169	tCa/tGa	4/32	0.175761297500244	6	FACETS	1	0.981	1	0.478	0.428	0.53	INDETERMINATE	1	TRUE	3	0.472267989084848	6		361	592	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262832	46262832	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	94	343	0	ENST00000371998.3:c.1005C>A	p.Phe335Leu	p.F335L	ENST00000371998		335	ttC/ttA	10/23	0.175761297500244	6	FACETS	1	0.972	1	0.429	0.382	0.479	INDETERMINATE	1	TRUE	3	0.472267989084848	6		343	601	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281282	46281282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	100	323	0	ENST00000371998.3:c.4079C>T	p.Ser1360Leu	p.S1360L	ENST00000371998		1360	tCa/tTa	21/23	0.175761297500244	6	FACETS	1	0.973	1	0.424	0.379	0.471	INDETERMINATE	1	TRUE	3	0.472267989084848	6		323	648	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498490	89498490	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	100	314	0	ENST00000336596.2:c.2462G>C	p.Gly821Ala	p.G821A	ENST00000336596	NM_005233.5	821	gGa/gCa	14/17	0.472267989084848	3	FACETS	1	0.967	1	0.592	0.532	0.655	CLONAL	1	TRUE	1	0.472267989084848	3		314	442	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332691	153332691	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	263	406	0	ENST00000281708.4:c.265G>T	p.Glu89Ter	p.E89*	ENST00000281708	NM_033632.3	89	Gag/Tag	2/12	0.472267989084848	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.472267989084848	3		406	635	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519279	187519279	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	202	253	0	ENST00000441802.2:c.12104G>T	p.Gly4035Val	p.G4035V	ENST00000441802	NM_005245.3	4035	gGt/gTt	23/27	0.472267989084848	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.472267989084848	3		253	458	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032111	26032111	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	202	587	0	ENST00000244661.2:c.178G>C	p.Glu60Gln	p.E60Q	ENST00000244661	NM_003537.3	60	Gag/Cag	1/1	0.472267989084848	4	FACETS	1	0.986	1	0.419	0.388	0.451	CLONAL	1	TRUE	1	0.472267989084848	4		587	1003	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158464	26158464	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs916752202	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	137	414	0	ENST00000289316.2:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000289316	NM_138720.2	23	Cag/Tag	1/2	0.472267989084848	4	FACETS	1	0.958	1	0.363	0.33	0.397	CLONAL	1	TRUE	1	0.472267989084848	4		414	785	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197454	26197454	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	148	477	0	ENST00000356476.2:c.25C>G	p.Arg9Gly	p.R9G	ENST00000356476		9	Cgc/Ggc	1/1	0.472267989084848	4	FACETS	1	0.965	1	0.369	0.337	0.402	CLONAL	1	TRUE	1	0.472267989084848	4		477	834	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745314	43745314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	127	368	0	ENST00000523873.1:c.227C>T	p.Ser76Phe	p.S76F	ENST00000523873		76	tCc/tTc	3/8	0.446781965317367	4	FACETS	1	0.913	1	0.336	0.304	0.369	CLONAL	1	TRUE	1	0.472267989084848	4		368	786	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681555	117681555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	62	239	0	ENST00000368508.3:c.3395C>T	p.Thr1132Ile	p.T1132I	ENST00000368508	NM_002944.2	1132	aCa/aTa	22/43	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.472267989084848	2		239	249	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505448	157505448	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	110	353	1	ENST00000346085.5:c.3429G>C	p.Lys1143Asn	p.K1143N	ENST00000346085	NM_020732.3	1143	aaG/aaC	13/20	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.472267989084848	2		354	450	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505494	157505494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	95	333	0	ENST00000346085.5:c.3475G>A	p.Gly1159Arg	p.G1159R	ENST00000346085	NM_020732.3	1159	Ggg/Agg	13/20	1	2	FACETS	0.886	0.793	0.984	0.886	0.793	0.984	CLONAL	1	TRUE	1	0.472267989084848	2		333	454	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505511	157505512	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	89	310	0	ENST00000346085.5:c.3492_3493delinsAA	p.Glu1165Lys	p.E1165K	ENST00000346085	NM_020732.3	1164	ccGGaa/ccAAaa	13/20	1	2	FACETS	0.857	0.763	0.955	0.857	0.763	0.955	CLONAL	1	TRUE	1	0.472267989084848	2		310	440	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133182	38133182	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	125	338	0	ENST00000317025.8:c.4291C>A	p.His1431Asn	p.H1431N	ENST00000317025	NM_023034.1	1431	Cat/Aat	24/24	0.197925162353947	5	FACETS	1	0.984	1	0.478	0.433	0.524	INDETERMINATE	1	TRUE	2	0.472267989084848	5		338	631	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133819	38133819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	117	404	0	ENST00000317025.8:c.4067C>T	p.Pro1356Leu	p.P1356L	ENST00000317025	NM_023034.1	1356	cCa/cTa	23/24	0.197925162353947	5	FACETS	1	0.982	1	0.47	0.425	0.518	INDETERMINATE	1	TRUE	2	0.472267989084848	5		404	600	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146228	38146228	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	112	328	0	ENST00000317025.8:c.3278C>T	p.Ser1093Leu	p.S1093L	ENST00000317025	NM_023034.1	1093	tCa/tTa	19/24	0.197925162353947	5	FACETS	1	0.974	1	0.413	0.372	0.456	INDETERMINATE	1	TRUE	2	0.472267989084848	5		328	654	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549178	87549178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	80	321	0	ENST00000277120.3:c.1735G>A	p.Glu579Lys	p.E579K	ENST00000277120		579	Gag/Aag	15/19	0.472267989084848	2	FACETS	1	0.907	1	0.512	0.454	0.572	CLONAL	1	TRUE	0	0.472267989084848	2		321	331	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195673	123195674	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0058654-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	86	114	0	ENST00000218089.9:c.1589_1590dup	p.Gln531AspfsTer46	p.Q531Dfs*46	ENST00000218089	NM_001042749.1	529	-/AG	17/35	0.402843667956089	2	FACETS	1	0.961	1			1	CLONAL	2	TRUE	NA	0.472267989084848	2		114	165	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0058655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	77	265	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.0921598769459189	4	FACETS	0.965	0.874	1	1	0.981	1	INDETERMINATE	3	TRUE	2	0.53288705685075	4		265	153	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0058655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	443	335	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	0.53288705685075	2	FACETS	1	0.997	1	1	0.998	1	CLONAL	3	TRUE	0	0.53288705685075	2		335	488	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39214712	39214712	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs56248239	NA	P-0058655-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	44	252	0	ENST00000402219.2:c.3412A>G	p.Ile1138Val	p.I1138V	ENST00000402219	NM_005633.3	1138	Ata/Gta	22/23	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.53288705685075	2		252	131	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847399	68847399	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0058656-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	35	430	0	ENST00000261769.5:c.1320+1G>T		p.X440_splice	ENST00000261769	NM_004360.3	440			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		430	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0058657-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	165	632	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.455188219272964	1	FACETS	0.997	0.924	1	0.997	0.924	1	CLONAL	1	TRUE	0	0.520878961997981	1		632	470	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0058657-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	52	378	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	1	2	FACETS	0.504	0.43	0.585	0.504	0.43	0.585	SUBCLONAL	1	TRUE	1	0.520878961997981	2		378	396	SUCCESS
ALK	238	MSKCC	GRCh37	2	29473981	29473981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768366852	NA	P-0058657-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	80	300	0	ENST00000389048.3:c.2194G>A	p.Asp732Asn	p.D732N	ENST00000389048	NM_004304.4	732	Gac/Aac	12/29	0.503160104471915	1	FACETS	0.864	0.77	0.961	0.864	0.77	0.961	CLONAL	1	TRUE	0	0.520878961997981	1		300	263	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069076	5069076	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058657-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	25	286	0	ENST00000381652.3:c.1381G>T	p.Glu461Ter	p.E461*	ENST00000381652	NM_004972.3	461	Gag/Tag	11/25	0.288550373700438	1	FACETS	0.321	0.254	0.398	0.321	0.254	0.398	INDETERMINATE	1	TRUE	0	0.520878961997981	1		286	221	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408924	41408924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778928297	NA	P-0058657-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	216	301	0	ENST00000373198.4:c.502G>A	p.Val168Ile	p.V168I	ENST00000373198	NM_133170.3	168	Gtc/Atc	4/32	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.520878961997981	2		301	567	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245831	5245831	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058657-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	105	387	0	ENST00000357368.4:c.944C>A	p.Ser315Tyr	p.S315Y	ENST00000357368	NM_002850.3	315	tCc/tAc	10/38	0.380597353220677	1	FACETS	0.761	0.687	0.837	0.761	0.687	0.837	SUBCLONAL	1	TRUE	0	0.520878961997981	1		387	392	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151579	55151579	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058657-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	39	230	0	ENST00000257290.5:c.2365G>T	p.Gly789Cys	p.G789C	ENST00000257290	NM_006206.4	789	Ggc/Tgc	17/23	0.436605922891737	1	FACETS	0.394	0.328	0.467	0.394	0.328	0.467	SUBCLONAL	1	TRUE	0	0.520878961997981	1		230	281	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	223625	223625	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058657-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	52	201	0	ENST00000264932.6:c.92G>T	p.Arg31Leu	p.R31L	ENST00000264932	NM_004168.2	31	cGa/cTa	2/15	0.431846884106704	1	FACETS	0.642	0.553	0.738	0.642	0.553	0.738	SUBCLONAL	1	TRUE	0	0.520878961997981	1		201	230	SUCCESS
APC	324	MSKCC	GRCh37	5	112174946	112174947	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCACA	novel	NA	P-0058657-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	116	339	0	ENST00000257430.4:c.3658_3662dup	p.Ser1222HisfsTer45	p.S1222Hfs*45	ENST00000257430	NM_000038.5	1219	tcc/tCCACAcc	16/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.520878961997981	2		339	408	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250597	26250597	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058657-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	44	483	0	ENST00000446824.2:c.237C>A	p.Phe79Leu	p.F79L	ENST00000446824	NM_021018.2	79	ttC/ttA	1/1	1	2	FACETS	0.22	0.184	0.26	0.22	0.184	0.26	SUBCLONAL	1	TRUE	1	0.520878961997981	2		483	768	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0058658-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	154	462	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.573424345774635	1	FACETS	0.925	0.856	0.996	0.925	0.856	0.996	CLONAL	1	TRUE	0	0.580489294154913	1		462	407	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099415	157099426	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAA	CAGCAGCAGCAA	-	rs797045275	NA	P-0058658-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	109	635	0	ENST00000346085.5:c.363_374del	p.Gln128_Gln131del	p.Q128_Q131del	ENST00000346085	NM_020732.3	118	CAGCAGCAGCAA/-	1/20	1	2	FACETS	0.484	0.434	0.537	0.484	0.434	0.537	SUBCLONAL	1	TRUE	1	0.580489294154913	2		635	776	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0058659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	47	187	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.934	0.802	1	0.934	0.802	1	CLONAL	1	TRUE	1	0.61	2		188	165	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578266	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs942158624	NA	P-0058659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	250	576	0	ENST00000269305.4:c.583A>T	p.Ile195Phe	p.I195F	ENST00000269305	NM_001126112.2	195	Atc/Ttc	6/11	0.298544190796199	0	FACETS	0.598	0.565	0.631			1	INDETERMINATE	1	TRUE	0	0.61	0		576	535	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961562	54961562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188825988	NA	P-0058659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	66	348	0	ENST00000312783.6:c.70C>T	p.Arg24Cys	p.R24C	ENST00000312783	NM_198436.1	24	Cgt/Tgt	4/10	1	2	FACETS	0.425	0.369	0.485	0.425	0.369	0.485	SUBCLONAL	1	TRUE	1	0.61	2		348	509	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738774	43738774	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	100	427	0	ENST00000382044.4:c.2851C>T	p.Pro951Ser	p.P951S	ENST00000382044	NM_001141980.1	951	Cca/Tca	14/28	0.298544190796199	5	FACETS	0.667	0.595	0.744	0.167	0.148	0.186	INDETERMINATE	1	TRUE	1	0.61	5		427	941	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540071	187540071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	109	462	0	ENST00000441802.2:c.7669G>A	p.Glu2557Lys	p.E2557K	ENST00000441802	NM_005245.3	2557	Gaa/Aaa	10/27	1	2	FACETS	0.535	0.481	0.592	0.535	0.481	0.592	SUBCLONAL	1	TRUE	1	0.61	2		462	668	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752929	128752929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1197838517	NA	P-0058659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1669	3507	455	0	ENST00000377970.2:c.1090G>A	p.Asp364Asn	p.D364N	ENST00000377970	NM_002467.4	364	Gac/Aac	3/3	0.298544190796199	35	FACETS	0.983	0.972	0.995			1	INDETERMINATE	25	TRUE	NA	0.61	35		455	5176	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176456	123176456	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058659-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	39	271	0	ENST00000218089.9:c.423C>A	p.Asn141Lys	p.N141K	ENST00000218089	NM_001042749.1	141	aaC/aaA	7/35	0.298544190796199	1	FACETS	0.349	0.29	0.412	0.349	0.29	0.412	INDETERMINATE	1	TRUE	0	0.61	1		271	255	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539105	23539105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	539	456	0	ENST00000380871.4:c.334G>A	p.Ala112Thr	p.A112T	ENST00000380871	NM_006167.3	112	Gcc/Acc	2/2	0.759247726639548	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.794729424144563	2		456	656	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258640	19258640	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs533071900	NA	P-0058661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	522	426	0	ENST00000162023.5:c.260C>T	p.Thr87Met	p.T87M	ENST00000162023		87	aCg/aTg	8/13	0.349878755072623	5	FACETS	1	0.965	1	1	0.965	1	INDETERMINATE	3	TRUE	2	0.794729424144563	5		426	960	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226361	2226361	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	511	889	0	ENST00000398665.3:c.3841G>T	p.Glu1281Ter	p.E1281*	ENST00000398665	NM_032482.2	1281	Gag/Tag	27/28	0.349878755072623	5	FACETS	0.934	0.899	0.969	0.934	0.899	0.969	INDETERMINATE	3	TRUE	2	0.794729424144563	5		889	1006	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150913847	150913847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	196	262	0	ENST00000271640.5:c.490G>A	p.Val164Ile	p.V164I	ENST00000271640	NM_001145415.1	164	Gtt/Att	5/22	0.408284000957646	4	FACETS	1	0.948	1	1	0.948	1	INDETERMINATE	2	TRUE	2	0.794729424144563	4		262	437	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943769	71943769	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	486	479	0	ENST00000298229.2:c.1812G>A	p.Trp604Ter	p.W604*	ENST00000298229	NM_001567.3	604	tgG/tgA	15/28	0.765825020785225	2	FACETS	0.999	0.974	1	0.999	0.974	1	CLONAL	2	TRUE	0	0.794729424144563	2		479	612	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447033	49447033	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	266	447	0	ENST00000301067.7:c.911A>T	p.Lys304Ile	p.K304I	ENST00000301067	NM_003482.3	304	aAa/aTa	7/54	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.794729424144563	2		447	648	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347200	347200	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	254	354	0	ENST00000262320.3:c.1811del	p.Arg604LysfsTer101	p.R604Kfs*101	ENST00000262320	NM_003502.3	604	aGa/aa	7/11	0.794729424144563	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.794729424144563	1		354	351	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508451	29508451	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0058661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	126	203	0	ENST00000356175.3:c.598A>T	p.Lys200Ter	p.K200*	ENST00000356175	NM_000267.3	200	Aaa/Taa	6/57	0.765825020785225	2	FACETS	0.985	0.934	1	0.985	0.934	1	CLONAL	2	TRUE	0	0.794729424144563	2		203	161	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33689768	33689768	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	348	356	0	ENST00000308377.4:c.1059C>A	p.Asp353Glu	p.D353E	ENST00000308377	NM_152270.3	353	gaC/gaA	2/5	0.765825020785225	2	FACETS	0.973	0.943	1	0.973	0.943	1	CLONAL	2	TRUE	0	0.794729424144563	2		356	450	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526480	66526480	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0058661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	554	429	0	ENST00000358598.2:c.1036A>T	p.Lys346Ter	p.K346*	ENST00000358598	NM_212471.2	346	Aag/Tag	11/11	0.765825020785225	2	FACETS	0.993	0.969	1	0.993	0.969	1	CLONAL	2	TRUE	0	0.794729424144563	2		429	702	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575223	48575224	+	stop_gained	Nonsense_Mutation	DNP	TG	TG	CT	novel	NA	P-0058661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	68	224	0	ENST00000342988.3:c.417_418delinsCT	p.Gly140Ter	p.G140*	ENST00000342988	NM_005359.5	139	ccTGga/ccCTga	3/12	0.794729424144563	1	FACETS	0.964	0.879	1	0.964	0.879	1	CLONAL	1	TRUE	0	0.794729424144563	1		224	107	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610083	10610083	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	435	399	0	ENST00000171111.5:c.627G>T	p.Met209Ile	p.M209I	ENST00000171111	NM_203500.1	209	atG/atT	2/6	0.349878755072623	5	FACETS	1	0.993	1	0.781	0.747	0.815	INDETERMINATE	2	TRUE	2	0.794729424144563	5		399	1024	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61710178	61710178	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	173	240	0	ENST00000401558.2:c.2726C>G	p.Ala909Gly	p.A909G	ENST00000401558	NM_003400.3	909	gCt/gGt	22/25	0.36723203710742	3	FACETS	0.852	0.797	0.907	0.852	0.797	0.907	INDETERMINATE	2	TRUE	1	0.794729424144563	3		240	357	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39726901	39726901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	144	305	0	ENST00000361337.2:c.899G>A	p.Cys300Tyr	p.C300Y	ENST00000361337	NM_003286.2	300	tGt/tAt	11/21	0.36723203710742	3	FACETS	0.898	0.836	0.96	0.898	0.836	0.96	INDETERMINATE	2	TRUE	1	0.794729424144563	3		305	282	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46280006	46280006	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	215	397	0	ENST00000371998.3:c.3932A>T	p.Tyr1311Phe	p.Y1311F	ENST00000371998		1311	tAt/tTt	20/23	0.36723203710742	3	FACETS	1	0.986	1	0.597	0.558	0.637	INDETERMINATE	1	TRUE	1	0.794729424144563	3		397	633	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112025257	112025257	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	297	324	0	ENST00000368678.4:c.492G>T	p.Leu164Phe	p.L164F	ENST00000368678		164	ttG/ttT	6/13	0.794729424144563	2	FACETS	0.968	0.935	1	0.968	0.935	1	CLONAL	2	TRUE	0	0.794729424144563	2		324	386	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508291	106508291	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	261	463	0	ENST00000359195.3:c.285C>A	p.His95Gln	p.H95Q	ENST00000359195	NM_002649.2	95	caC/caA	2/11	0.433738816510502	1	FACETS	0.736	0.697	0.775	0.736	0.697	0.775	INDETERMINATE	1	TRUE	0	0.794729424144563	1		463	538	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141557656	141557656	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	474	446	0	ENST00000220592.5:c.1659G>T	p.Gln553His	p.Q553H	ENST00000220592	NM_012154.3	553	caG/caT	13/19	0.759247726639548	2	FACETS	0.971	0.945	0.996	0.971	0.945	0.996	CLONAL	2	TRUE	0	0.794729424144563	2		446	614	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778780	76778780	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	65	153	0	ENST00000373344.5:c.6799A>C	p.Thr2267Pro	p.T2267P	ENST00000373344	NM_000489.3	2267	Act/Cct	31/35	0.76203766669162	0	FACETS		NA	1			1	NA	1	TRUE	NA	0.794729424144563	0		153	88	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615678	100615678	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058661-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	174	224	0	ENST00000308731.7:c.654G>T	p.Lys218Asn	p.K218N	ENST00000308731	NM_000061.2	218	aaG/aaT	8/19	0.76203766669162	0	FACETS		NA	1			1	NA	1	TRUE	NA	0.794729424144563	0		224	253	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274304	5274304	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	97	409	1	ENST00000357368.4:c.143del	p.Gly48ValfsTer17	p.G48Vfs*17	ENST00000357368	NM_002850.3	48	gGt/gt	3/38	1	2	FACETS	0.844	0.756	0.937	0.844	0.756	0.937	CLONAL	1	TRUE	1	0.48	2		410	479	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	68	245	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.877	0.769	0.992	0.877	0.769	0.992	CLONAL	1	TRUE	1	0.48	2		245	323	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	23	98	0	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	1	FACETS	0.714	0.568	0.876	0.714	0.568	0.876	SUBCLONAL	1	TRUE	0	0.48	1		98	102	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161907	47161907	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	144	374	1	ENST00000409792.3:c.4219del	p.Arg1407GlyfsTer5	p.R1407Gfs*5	ENST00000409792	NM_014159.6	1407	Agg/gg	3/21	1	2	FACETS	0.938	0.858	1	0.938	0.858	1	CLONAL	1	TRUE	1	0.48	2		375	640	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	83	344	2	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	1	2	FACETS	0.709	0.627	0.795	0.709	0.627	0.795	SUBCLONAL	1	TRUE	1	0.48	2		346	488	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	117	333	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.979	0.887	1	0.979	0.887	1	CLONAL	1	TRUE	1	0.48	2		333	498	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214398	36214398	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs868041281	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	95	308	1	ENST00000222270.7:c.3057del	p.Gly1020AlafsTer4	p.G1020Afs*4	ENST00000222270	NM_014727.1	1018	Aaa/aa	7/37	1	2	FACETS	0.844	0.755	0.938	0.844	0.755	0.938	CLONAL	1	TRUE	1	0.48	2		309	469	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	123	378	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	1	2	FACETS	0.825	0.748	0.906	0.825	0.748	0.906	CLONAL	1	TRUE	1	0.48	2		378	621	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	104	294	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.48	2		294	407	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	102	338	0	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	0.86	0.773	0.952	0.86	0.773	0.952	CLONAL	1	TRUE	1	0.48	2		338	494	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	82	317	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.48	2		317	306	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	77	286	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.914	0.808	1	0.914	0.808	1	CLONAL	1	TRUE	1	0.48	2		286	351	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	61	387	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	1	2	FACETS	0.481	0.415	0.553	0.481	0.415	0.553	SUBCLONAL	1	TRUE	1	0.48	2		387	528	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	82	268	0	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.8	0.709	0.897	0.8	0.709	0.897	SUBCLONAL	1	TRUE	1	0.48	2		268	427	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	119	415	1	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	1	2	FACETS	0.95	0.861	1	0.95	0.861	1	CLONAL	1	TRUE	1	0.48	2		416	522	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	123	310	0	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	0.984	0.894	1	0.984	0.894	1	CLONAL	1	TRUE	1	0.48	2		310	521	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	75	381	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.586	0.515	0.663	0.586	0.515	0.663	SUBCLONAL	1	TRUE	1	0.48	2		381	533	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255658	16255658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	136	403	0	ENST00000375759.3:c.2923G>A	p.Ala975Thr	p.A975T	ENST00000375759	NM_015001.2	975	Gct/Act	11/15	1	2	FACETS	0.842	0.767	0.92	0.842	0.767	0.92	CLONAL	1	TRUE	1	0.48	2		403	673	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150915528	150915528	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	33	285	0	ENST00000271640.5:c.874A>G	p.Arg292Gly	p.R292G	ENST00000271640	NM_001145415.1	292	Agg/Ggg	7/22	1	2	FACETS	0.315	0.256	0.381	0.315	0.256	0.381	SUBCLONAL	1	TRUE	1	0.48	2		285	437	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	75	208	0	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	0.933	0.824	1	0.933	0.824	1	CLONAL	1	TRUE	1	0.48	2		208	335	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076743	102076743	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	119	389	0	ENST00000282441.5:c.922C>G	p.Leu308Val	p.L308V	ENST00000282441	NM_001130145.2	308	Ctg/Gtg	5/9	1	2	FACETS	0.836	0.757	0.919	0.836	0.757	0.919	CLONAL	1	TRUE	1	0.48	2		389	593	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106510	108106510	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	24	267	0	ENST00000278616.4:c.445A>C	p.Ile149Leu	p.I149L	ENST00000278616	NM_000051.3	149	Att/Ctt	5/63	1	2	FACETS	0.23	0.18	0.289	0.23	0.18	0.289	SUBCLONAL	1	TRUE	1	0.48	2		267	434	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944914	31944914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	60	179	0	ENST00000340398.3:c.187C>T	p.Arg63Trp	p.R63W	ENST00000340398	NM_001013699.2	63	Cgg/Tgg	1/1	1	2	FACETS	0.847	0.736	0.967	0.847	0.736	0.967	CLONAL	1	TRUE	1	0.48	2		179	295	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445230	49445230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201896284	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	158	555	0	ENST00000301067.7:c.2236C>T	p.Arg746Trp	p.R746W	ENST00000301067	NM_003482.3	746	Cgg/Tgg	10/54	1	2	FACETS	0.955	0.878	1	0.955	0.878	1	CLONAL	1	TRUE	1	0.48	2		555	689	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563294	21563294	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1249786123	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	39	537	0	ENST00000382592.4:c.625C>T	p.Arg209Trp	p.R209W	ENST00000382592	NM_014572.2	209	Cgg/Tgg	4/8	1	2	FACETS	0.305	0.253	0.364	0.305	0.253	0.364	SUBCLONAL	1	TRUE	1	0.48	2		537	532	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240072	41240072	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs989533582	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	61	210	0	ENST00000379561.5:c.278C>T	p.Ala93Val	p.A93V	ENST00000379561	NM_002015.3	93	gCg/gTg	1/3	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.48	2		210	223	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030396	49030396	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	49	268	0	ENST00000267163.4:c.1871C>G	p.Ser624Cys	p.S624C	ENST00000267163	NM_000321.2	624	tCt/tGt	19/27	1	2	FACETS	0.451	0.382	0.526	0.451	0.382	0.526	SUBCLONAL	1	TRUE	1	0.48	2		268	453	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515036	103515036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775996769	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	144	391	0	ENST00000355739.4:c.1537G>A	p.Ala513Thr	p.A513T	ENST00000355739	NM_000123.3	513	Gca/Aca	8/15	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.48	2		391	572	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436554	110436554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781776925	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	60	471	0	ENST00000375856.3:c.1847G>A	p.Cys616Tyr	p.C616Y	ENST00000375856	NM_003749.2	616	tGc/tAc	1/2	1	2	FACETS	0.469	0.404	0.539	0.469	0.404	0.539	SUBCLONAL	1	TRUE	1	0.48	2		471	533	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437427	110437427	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	69	319	0	ENST00000375856.3:c.974A>G	p.His325Arg	p.H325R	ENST00000375856	NM_003749.2	325	cAc/cGc	1/2	1	2	FACETS	0.73	0.638	0.827	0.73	0.638	0.827	SUBCLONAL	1	TRUE	1	0.48	2		319	394	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30047522	30047522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	61	217	0	ENST00000331968.5:c.2479C>T	p.Arg827Cys	p.R827C	ENST00000331968	NM_002742.2	827	Cgc/Tgc	17/18	1	2	FACETS	0.792	0.688	0.903	0.792	0.688	0.903	CLONAL	1	TRUE	1	0.48	2		217	321	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003813	45003813	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	57	395	0	ENST00000558401.1:c.67+2T>C		p.X23_splice	ENST00000558401	NM_004048.2	23			1	2	FACETS	0.451	0.387	0.52	0.451	0.387	0.52	SUBCLONAL	1	TRUE	1	0.48	2		395	527	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292892	91292892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765089689	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	54	357	1	ENST00000355112.3:c.394C>T	p.Arg132Trp	p.R132W	ENST00000355112	NM_000057.2	132	Cgg/Tgg	3/22	1	2	FACETS	0.41	0.35	0.475	0.41	0.35	0.475	SUBCLONAL	1	TRUE	1	0.48	2		358	549	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2089996	2089996	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	50	459	0	ENST00000219066.1:c.868T>C	p.Cys290Arg	p.C290R	ENST00000219066	NM_002528.5	290	Tgt/Cgt	6/6	1	2	FACETS	0.373	0.316	0.435	0.373	0.316	0.435	SUBCLONAL	1	TRUE	1	0.48	2		459	559	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129091	2129091	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	124	382	0	ENST00000219476.3:c.3025G>A	p.Ala1009Thr	p.A1009T	ENST00000219476	NM_000548.3	1009	Gcc/Acc	27/42	1	2	FACETS	0.895	0.813	0.982	0.895	0.813	0.982	CLONAL	1	TRUE	1	0.48	2		382	577	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223541	2223541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs942789564	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	55	461	0	ENST00000326181.6:c.1072G>A	p.Ala358Thr	p.A358T	ENST00000326181	NM_032271.2	358	Gca/Aca	11/21	1	2	FACETS	0.387	0.331	0.449	0.387	0.331	0.449	SUBCLONAL	1	TRUE	1	0.48	2		461	592	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656528	3656528	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200803578	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	122	401	0	ENST00000294008.3:c.707C>T	p.Ala236Val	p.A236V	ENST00000294008	NM_032444.2	236	gCg/gTg	3/15	1	2	FACETS	0.843	0.764	0.926	0.843	0.764	0.926	CLONAL	1	TRUE	1	0.48	2		401	603	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783988	50783988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1402238737	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	100	313	0	ENST00000398568.2:c.379G>A	p.Val127Met	p.V127M	ENST00000398568	NM_001042412.1	127	Gtg/Atg	3/18	1	2	FACETS	0.774	0.694	0.859	0.774	0.694	0.859	SUBCLONAL	1	TRUE	1	0.48	2		313	538	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991344	72991344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148024459	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	117	318	1	ENST00000268489.5:c.2701G>A	p.Ala901Thr	p.A901T	ENST00000268489	NM_006885.3	901	Gcc/Acc	2/10	1	2	FACETS	0.962	0.871	1	0.962	0.871	1	CLONAL	1	TRUE	1	0.48	2		319	507	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86544951	86544951	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	28	352	1	ENST00000262426.4:c.776C>A	p.Pro259Gln	p.P259Q	ENST00000262426	NM_001451.2	259	cCg/cAg	1/2	1	2	FACETS	0.334	0.267	0.411	0.334	0.267	0.411	SUBCLONAL	1	TRUE	1	0.48	2		353	349	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973548	15973548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1000518180	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	149	365	0	ENST00000268712.3:c.4444C>T	p.Arg1482Trp	p.R1482W	ENST00000268712	NM_006311.3	1482	Cgg/Tgg	31/46	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.48	2		365	600	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029445	16029446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	101	310	2	ENST00000268712.3:c.1584dup	p.Glu529ArgfsTer7	p.E529Rfs*7	ENST00000268712	NM_006311.3	528	-/A	15/46	1	2	FACETS	0.776	0.696	0.861	0.776	0.696	0.861	SUBCLONAL	1	TRUE	1	0.48	2		312	542	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676298	37676298	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	57	261	0	ENST00000447079.4:c.3053A>G	p.Asp1018Gly	p.D1018G	ENST00000447079	NM_015083.1	1018	gAc/gGc	11/14	1	2	FACETS	0.44	0.377	0.508	0.44	0.377	0.508	SUBCLONAL	1	TRUE	1	0.48	2		261	540	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485689	40485689	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	44	283	0	ENST00000264657.5:c.1049+2T>C		p.X350_splice	ENST00000264657	NM_139276.2	350			1	2	FACETS	0.381	0.319	0.449	0.381	0.319	0.449	SUBCLONAL	1	TRUE	1	0.48	2		283	481	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40864339	40864339	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	59	329	0	ENST00000428826.2:c.1369G>A	p.Ala457Thr	p.A457T	ENST00000428826		457	Gcc/Acc	12/21	1	2	FACETS	0.454	0.39	0.522	0.454	0.39	0.522	SUBCLONAL	1	TRUE	1	0.48	2		329	542	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876570	59876570	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	118	361	0	ENST00000259008.2:c.1231A>T	p.Thr411Ser	p.T411S	ENST00000259008	NM_032043.2	411	Aca/Tca	9/20	1	2	FACETS	0.989	0.897	1	0.989	0.897	1	CLONAL	1	TRUE	1	0.48	2		361	497	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584467	39584467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554581051	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	40	267	0	ENST00000262039.4:c.1132C>T	p.Arg378Cys	p.R378C	ENST00000262039	NM_002647.2	378	Cgt/Tgt	10/25	1	2	FACETS	0.301	0.249	0.358	0.301	0.249	0.358	SUBCLONAL	1	TRUE	1	0.48	2		267	554	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213545	2213545	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	46	373	0	ENST00000398665.3:c.1565A>G	p.Asn522Ser	p.N522S	ENST00000398665	NM_032482.2	522	aAc/aGc	17/28	1	2	FACETS	0.397	0.334	0.466	0.397	0.334	0.466	SUBCLONAL	1	TRUE	1	0.48	2		373	483	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216451	2216451	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	139	410	1	ENST00000398665.3:c.2095T>C	p.Phe699Leu	p.F699L	ENST00000398665	NM_032482.2	699	Ttc/Ctc	20/28	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.48	2		411	568	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246525	10246525	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	96	299	0	ENST00000340748.4:c.4612C>T	p.Arg1538Cys	p.R1538C	ENST00000340748		1538	Cgc/Tgc	38/40	1	2	FACETS	0.855	0.765	0.949	0.855	0.765	0.949	CLONAL	1	TRUE	1	0.48	2		299	468	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031170	11031170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	141	408	0	ENST00000327064.4:c.1255C>T	p.Arg419Trp	p.R419W	ENST00000327064	NM_199141.1	419	Cgg/Tgg	11/16	1	2	FACETS	0.999	0.914	1	0.999	0.914	1	CLONAL	1	TRUE	1	0.48	2		408	588	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271919	15271919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376494303	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	129	550	0	ENST00000263388.2:c.6520C>T	p.Arg2174Trp	p.R2174W	ENST00000263388	NM_000435.2	2174	Cgg/Tgg	33/33	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.48	2		550	485	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961556	18961556	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	32	302	0	ENST00000262803.5:c.689A>G	p.Gln230Arg	p.Q230R	ENST00000262803	NM_002911.3	230	cAg/cGg	5/24	1	2	FACETS	0.323	0.262	0.392	0.323	0.262	0.392	SUBCLONAL	1	TRUE	1	0.48	2		302	413	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976917	18976917	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	45	364	0	ENST00000262803.5:c.3302A>G	p.Tyr1101Cys	p.Y1101C	ENST00000262803	NM_002911.3	1101	tAc/tGc	23/24	1	2	FACETS	0.376	0.316	0.442	0.376	0.316	0.442	SUBCLONAL	1	TRUE	1	0.48	2		364	499	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229453	36229453	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	68	352	0	ENST00000222270.7:c.8143A>G	p.Asn2715Asp	p.N2715D	ENST00000222270	NM_014727.1	2715	Aac/Gac	37/37	1	2	FACETS	0.558	0.486	0.635	0.558	0.486	0.635	SUBCLONAL	1	TRUE	1	0.48	2		352	508	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912858	50912858	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1306540639	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	107	383	0	ENST00000440232.2:c.2089G>A	p.Ala697Thr	p.A697T	ENST00000440232	NM_002691.3	697	Gcc/Acc	17/27	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.48	2		383	430	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607487	46607487	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	137	440	4	ENST00000263734.3:c.1681del	p.Gln561SerfsTer7	p.Q561Sfs*7	ENST00000263734	NM_001430.4	559	aCc/ac	12/16	1	2	FACETS	0.933	0.851	1	0.933	0.851	1	CLONAL	1	TRUE	1	0.48	2		444	612	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182139	99182139	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	94	310	0	ENST00000074304.5:c.2204G>T	p.Gly735Val	p.G735V	ENST00000074304	NM_001134224.1	735	gGg/gTg	21/26	1	2	FACETS	0.911	0.815	1	0.911	0.815	1	CLONAL	1	TRUE	1	0.48	2		310	430	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736166	204736166	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	58	329	0	ENST00000302823.3:c.529del	p.Tyr177IlefsTer10	p.Y177Ifs*10	ENST00000302823	NM_005214.4	175	Ttt/tt	3/4	1	2	FACETS	0.448	0.385	0.517	0.448	0.385	0.517	SUBCLONAL	1	TRUE	1	0.48	2		329	539	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	245	477	9	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	0.921	0.869	0.974	1	0.995	1	CLONAL	2	TRUE	1	0.48	2		486	554	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790171	40790171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760735173	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	126	308	0	ENST00000373198.4:c.2560C>T	p.Arg854Cys	p.R854C	ENST00000373198	NM_133170.3	854	Cgc/Tgc	18/32	0.3	1	FACETS	0.793	0.722	0.867	0.793	0.722	0.867	SUBCLONAL	1	TRUE	0	0.48	1		308	503	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755704	39755704	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1404777513	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	112	362	0	ENST00000288319.7:c.1061G>A	p.Arg354Gln	p.R354Q	ENST00000288319	NM_182918.3	354	cGg/cAg	10/10	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.48	2		362	464	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446733	29446733	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	109	379	0	ENST00000544604.2:c.2567del	p.Gly856ValfsTer100	p.G856Vfs*100	ENST00000544604	NM_001206998.1	855	tGg/tg	8/9	1	2	FACETS	0.994	0.898	1	0.994	0.898	1	CLONAL	1	TRUE	1	0.48	2		379	457	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37061799	37061799	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs267607805	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	117	331	0	ENST00000231790.2:c.885-2A>G		p.X295_splice	ENST00000231790	NM_000249.3	295			1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.48	2		331	465	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437161	52437161	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	123	333	0	ENST00000460680.1:c.1883C>A	p.Ser628Ter	p.S628*	ENST00000460680	NM_004656.3	628	tCa/tAa	14/17	1	2	FACETS	0.982	0.892	1	0.982	0.892	1	CLONAL	1	TRUE	1	0.48	2		333	522	SUCCESS
ATR	545	MSKCC	GRCh37	3	142255005	142255005	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	86	233	0	ENST00000350721.4:c.3764del	p.Leu1255TyrfsTer7	p.L1255Yfs*7	ENST00000350721	NM_001184.3	1255	tTa/ta	20/47	1	2	FACETS	0.916	0.816	1	0.916	0.816	1	CLONAL	1	TRUE	1	0.48	2		233	391	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197848	66197848	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	33	207	0	ENST00000273854.3:c.2853-2A>G		p.X951_splice	ENST00000273854	NM_004439.5	951			1	2	FACETS	0.385	0.314	0.465	0.385	0.314	0.465	SUBCLONAL	1	TRUE	1	0.48	2		207	357	SUCCESS
ALB	213	MSKCC	GRCh37	4	74283928	74283928	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs75920790	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	99	275	0	ENST00000295897.4:c.1552G>A	p.Asp518Asn	p.D518N	ENST00000295897	NM_000477.5	518	Gat/Aat	12/15	1	2	FACETS	0.863	0.774	0.957	0.863	0.774	0.957	CLONAL	1	TRUE	1	0.48	2		275	478	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967280	38967280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770728330	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	93	313	0	ENST00000357387.3:c.1201C>T	p.Arg401Cys	p.R401C	ENST00000357387	NM_152756.3	401	Cgt/Tgt	14/38	1	2	FACETS	0.83	0.741	0.923	0.83	0.741	0.923	CLONAL	1	TRUE	1	0.48	2		313	467	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178023	56178023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	122	390	0	ENST00000399503.3:c.2996C>T	p.Thr999Ile	p.T999I	ENST00000399503	NM_005921.1	999	aCa/aTa	14/20	1	2	FACETS	0.892	0.809	0.978	0.892	0.809	0.978	CLONAL	1	TRUE	1	0.48	2		390	570	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950580	79950580	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	109	296	0	ENST00000265081.6:c.34G>A	p.Ala12Thr	p.A12T	ENST00000265081	NM_002439.4	12	Gct/Act	1/24	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.48	2		296	436	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79974893	79974894	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	41	302	0	ENST00000265081.6:c.1323_1324del	p.His441GlnfsTer6	p.H441Qfs*6	ENST00000265081	NM_002439.4	441	CAc/c	8/24	1	2	FACETS	0.345	0.287	0.41	0.345	0.287	0.41	SUBCLONAL	1	TRUE	1	0.48	2		302	495	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460474	149460474	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	57	458	0	ENST00000286301.3:c.163T>C	p.Ser55Pro	p.S55P	ENST00000286301	NM_005211.3	55	Tca/Cca	3/22	1	2	FACETS	0.454	0.39	0.524	0.454	0.39	0.524	SUBCLONAL	1	TRUE	1	0.48	2		458	523	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460500	149460500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	116	447	2	ENST00000286301.3:c.137G>A	p.Gly46Asp	p.G46D	ENST00000286301	NM_005211.3	46	gGc/gAc	3/22	1	2	FACETS	0.876	0.792	0.963	0.876	0.792	0.963	CLONAL	1	TRUE	1	0.48	2		449	552	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520696	176520696	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	39	318	0	ENST00000292408.4:c.1439A>G	p.Gln480Arg	p.Q480R	ENST00000292408	NM_213647.1	480	cAg/cGg	11/18	1	2	FACETS	0.366	0.303	0.436	0.366	0.303	0.436	SUBCLONAL	1	TRUE	1	0.48	2		318	444	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187939	32187939	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	58	397	0	ENST00000375023.3:c.1282A>G	p.Thr428Ala	p.T428A	ENST00000375023	NM_004557.3	428	Acc/Gcc	7/30	1	2	FACETS	0.441	0.379	0.509	0.441	0.379	0.509	SUBCLONAL	1	TRUE	1	0.48	2		397	548	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001540	150001540	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	88	282	0	ENST00000253339.5:c.2064del	p.Glu689AsnfsTer18	p.E689Nfs*18	ENST00000253339		688	aaA/aa	4/7	1	2	FACETS	0.869	0.774	0.969	0.869	0.774	0.969	CLONAL	1	TRUE	1	0.48	2		282	422	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099411	157099412	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCAA	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	77	505	0	ENST00000346085.5:c.353_354insACAGCA	p.Gln130_Gln131dup	p.Q130_Q131dup	ENST00000346085	NM_020732.3	130	-/CAGCAA	1/20	1	2	FACETS	0.434	0.381	0.492	0.434	0.381	0.492	SUBCLONAL	1	TRUE	1	0.48	2		505	739	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522022	157522022	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs745566888	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	46	449	0	ENST00000346085.5:c.4294A>G	p.Met1432Val	p.M1432V	ENST00000346085	NM_020732.3	1432	Atg/Gtg	18/20	1	2	FACETS	0.316	0.265	0.372	0.316	0.265	0.372	SUBCLONAL	1	TRUE	1	0.48	2		449	607	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527805	157527805	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	40	445	0	ENST00000346085.5:c.5530A>G	p.Arg1844Gly	p.R1844G	ENST00000346085	NM_020732.3	1844	Agg/Ggg	20/20	1	2	FACETS	0.275	0.228	0.328	0.275	0.228	0.328	SUBCLONAL	1	TRUE	1	0.48	2		445	605	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381571	81381571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	31	229	0	ENST00000222390.5:c.490C>T	p.Pro164Ser	p.P164S	ENST00000222390	NM_000601.4	164	Cct/Tct	5/18	1	2	FACETS	0.313	0.253	0.381	0.313	0.253	0.381	SUBCLONAL	1	TRUE	1	0.48	2		229	413	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508646	106508646	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	48	411	0	ENST00000359195.3:c.640A>G	p.Lys214Glu	p.K214E	ENST00000359195	NM_002649.2	214	Aag/Gag	2/11	1	2	FACETS	0.398	0.337	0.466	0.398	0.337	0.466	SUBCLONAL	1	TRUE	1	0.48	2		411	502	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371830	55371830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1457048078	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	73	417	0	ENST00000297316.4:c.520G>A	p.Val174Met	p.V174M	ENST00000297316	NM_022454.3	174	Gtg/Atg	2/2	1	2	FACETS	0.827	0.727	0.932	0.827	0.727	0.932	CLONAL	1	TRUE	1	0.48	2		417	368	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534987	5534987	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs773744325	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	48	347	0	ENST00000397747.3:c.298T>C	p.Tyr100His	p.Y100H	ENST00000397747	NM_025239.3	100	Tac/Cac	3/7	1	2	FACETS	0.386	0.326	0.452	0.386	0.326	0.452	SUBCLONAL	1	TRUE	1	0.48	2		347	518	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549526	5549526	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	117	392	0	ENST00000397747.3:c.557del	p.Pro186LeufsTer14	p.P186Lfs*14	ENST00000397747	NM_025239.3	185	Ccc/cc	4/7	1	2	FACETS	0.845	0.764	0.929	0.845	0.764	0.929	CLONAL	1	TRUE	1	0.48	2		392	577	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815506	139815506	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	55	308	0	ENST00000247668.2:c.977G>T	p.Arg326Met	p.R326M	ENST00000247668	NM_021138.3	326	aGg/aTg	9/11	1	2	FACETS	0.417	0.357	0.484	0.417	0.357	0.484	SUBCLONAL	1	TRUE	1	0.48	2		308	549	SUCCESS
AR	367	MSKCC	GRCh37	X	66765182	66765182	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058662-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	18	97	1	ENST00000374690.3:c.194A>T	p.Gln65Leu	p.Q65L	ENST00000374690	NM_000044.3	65	cAg/cTg	1/8	1	1	FACETS	0.6	0.46	0.76	0.6	0.46	0.76	SUBCLONAL	1	TRUE	0	0.48	1		98	95	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0058666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	9	259	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.361705511477708	2	FACETS	0.179	0.118	0.257	0.089	0.059	0.129	SUBCLONAL	1	TRUE	0	0.382676238723544	2		259	263	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0058666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	85	452	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.48	0.423	0.541	0.48	0.423	0.541	SUBCLONAL	1	TRUE	1	0.382676238723544	2		452	926	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268766	41268766	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	28	353	0	ENST00000349496.5:c.1004A>T	p.Lys335Ile	p.K335I	ENST00000349496	NM_001904.3	335	aAa/aTa	7/15	0.327325232623686	3	FACETS	0.182	0.145	0.225	0.061	0.048	0.075	SUBCLONAL	1	TRUE	0	0.382676238723544	3		353	957	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0058666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	294	947	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.367091660403151	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.382676238723544	2		947	740	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259092	89259092	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	45	403	0	ENST00000336596.2:c.236A>C	p.Asn79Thr	p.N79T	ENST00000336596	NM_005233.5	79	aAc/aCc	3/17	0.361705511477708	2	FACETS	0.378	0.317	0.446	0.189	0.158	0.223	SUBCLONAL	1	TRUE	0	0.382676238723544	2		403	622	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730910	40730910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370873414	NA	P-0058666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	129	448	0	ENST00000373198.4:c.3625C>T	p.Arg1209Trp	p.R1209W	ENST00000373198	NM_133170.3	1209	Cgg/Tgg	27/32	0.319753672953771	1	FACETS	0.79	0.718	0.866	0.79	0.718	0.866	SUBCLONAL	1	TRUE	0	0.382676238723544	1		448	690	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570064	212570064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55671017	NA	P-0058666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	278	309	0	ENST00000342788.4:c.1177C>T	p.Arg393Trp	p.R393W	ENST00000342788	NM_005235.2	393	Cgg/Tgg	10/28	0.327974916855819	5	FACETS	1	0.979	1	0.642	0.607	0.679	CLONAL	3	TRUE	0	0.382676238723544	5		309	712	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675071	40675071	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	142	376	1	ENST00000249776.8:c.35T>G	p.Val12Gly	p.V12G	ENST00000249776	NM_033286.3	12	gTt/gGt	1/9	1	2	FACETS	0.974	0.889	1	0.974	0.889	1	CLONAL	1	TRUE	1	0.382676238723544	2		377	762	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999633	100999633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3740754	NA	P-0058666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	73	490	0	ENST00000325455.5:c.169G>A	p.Gly57Arg	p.G57R	ENST00000325455	NM_001202474.3	57	Ggg/Agg	1/8	0.325163879215902	3	FACETS	0.766	0.671	0.87	0.383	0.335	0.435	SUBCLONAL	1	TRUE	1	0.382676238723544	3		490	593	SUCCESS
ATM	472	MSKCC	GRCh37	11	108213982	108213982	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	42	346	0	ENST00000278616.4:c.8302G>C	p.Glu2768Gln	p.E2768Q	ENST00000278616	NM_000051.3	2768	Gaa/Caa	57/63	0.325163879215902	3	FACETS	0.393	0.327	0.467	0.197	0.163	0.234	SUBCLONAL	1	TRUE	1	0.382676238723544	3		346	665	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288466	15288466	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	167	444	0	ENST00000263388.2:c.4273T>C	p.Trp1425Arg	p.W1425R	ENST00000263388	NM_000435.2	1425	Tgg/Cgg	24/33	0.382676238723544	2	FACETS	0.994	0.923	1	0.994	0.923	1	CLONAL	2	TRUE	0	0.382676238723544	2		444	439	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566749	212566749	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	126	407	0	ENST00000342788.4:c.1432T>A	p.Phe478Ile	p.F478I	ENST00000342788	NM_005235.2	478	Ttc/Atc	12/28	0.327974916855819	5	FACETS	1	0.971	1	0.237	0.215	0.262	CLONAL	1	TRUE	0	0.382676238723544	5		407	873	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168771	56168771	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	45	361	0	ENST00000399503.3:c.1625C>G	p.Thr542Ser	p.T542S	ENST00000399503	NM_005921.1	542	aCt/aGt	9/20	0.186099438388911	3	FACETS	0.465	0.39	0.548	0.232	0.195	0.274	INDETERMINATE	1	TRUE	1	0.382676238723544	3		361	603	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394370	162394370	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	48	377	0	ENST00000366898.1:c.698G>C	p.Ser233Thr	p.S233T	ENST00000366898	NM_004562.2	233	aGt/aCt	6/12	0.214816973942724	2	FACETS	0.594	0.503	0.694	0.297	0.251	0.347	INDETERMINATE	1	TRUE	0	0.382676238723544	2		377	422	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133957	38133957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758159008	NA	P-0058666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	73	437	0	ENST00000317025.8:c.3929G>A	p.Arg1310Gln	p.R1310Q	ENST00000317025	NM_023034.1	1310	cGa/cAa	23/24	0.382676238723544	1	FACETS	0.479	0.419	0.544	0.479	0.419	0.544	SUBCLONAL	1	TRUE	0	0.382676238723544	1		437	644	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965532	90965532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1586052885	NA	P-0058666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	73	344	0	ENST00000265433.3:c.1785G>A	p.Met595Ile	p.M595I	ENST00000265433	NM_002485.4	595	atG/atA	11/16	0.382676238723544	5	FACETS	0.962	0.842	1	0.241	0.21	0.273	CLONAL	1	TRUE	1	0.382676238723544	5		344	624	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373820	118373822	+	missense_variant	Missense_Mutation	TNP	TTG	TTG	ATA	novel	NA	P-0058666-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	81	453	0	ENST00000534358.1:c.7213_7215delinsATA	p.Leu2405Ile	p.L2405I	ENST00000534358	NM_005933.3	2405	TTG/ATA	27/36	0.382676238723544	4	FACETS	0.698	0.614	0.788			1	SUBCLONAL	1	TRUE	NA	0.382676238723544	4		453	839	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577569	7577569	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519981	NA	P-0058667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	231	490	0	ENST00000269305.4:c.712T>G	p.Cys238Gly	p.C238G	ENST00000269305	NM_001126112.2	238	Tgt/Ggt	7/11	0.439778793124183	3	FACETS	0.962	0.911	1	0.962	0.911	1	CLONAL	3	TRUE	0	0.454658094452999	3		490	432	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97934348	97934348	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs759387035	NA	P-0058667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	79	293	0	ENST00000289081.3:c.427A>G	p.Ile143Val	p.I143V	ENST00000289081	NM_000136.2	143	Ata/Gta	5/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.454658094452999	2		293	284	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088778	27088778	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs772620836	NA	P-0058667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	336	433	0	ENST00000324856.7:c.2387A>G	p.Tyr796Cys	p.Y796C	ENST00000324856	NM_006015.4	796	tAt/tGt	7/20	0.415600530331191	4	FACETS	0.913	0.874	0.951	0.913	0.874	0.951	CLONAL	4	TRUE	0	0.454658094452999	4		433	589	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276645	115276645	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	44	432	0	ENST00000438362.2:c.814G>C	p.Gly272Arg	p.G272R	ENST00000438362	NM_001242891.1	272	Ggc/Cgc	8/20	0.309967810649793	3	FACETS	0.533	0.447	0.627	0.266	0.223	0.314	SUBCLONAL	1	TRUE	1	0.454658094452999	3		432	446	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59934479	59934479	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	81	364	0	ENST00000259008.2:c.319C>T	p.His107Tyr	p.H107Y	ENST00000259008	NM_032043.2	107	Cat/Tat	4/20	0.45474703284453	4	FACETS	0.778	0.686	0.878			1	SUBCLONAL	1	TRUE	NA	0.454658094452999	4		364	666	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793435	42793435	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	74	572	0	ENST00000575354.2:c.1237A>G	p.Thr413Ala	p.T413A	ENST00000575354	NM_015125.3	413	Act/Gct	8/20	0.454658094452999	6	FACETS	0.73	0.638	0.83	0.183	0.159	0.208	SUBCLONAL	1	TRUE	2	0.454658094452999	6		572	851	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231215	142231215	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	93	364	0	ENST00000350721.4:c.4739C>G	p.Thr1580Ser	p.T1580S	ENST00000350721	NM_001184.3	1580	aCt/aGt	27/47	0.454658094452999	6	FACETS	1	0.968	1	0.311	0.277	0.348	CLONAL	1	TRUE	2	0.454658094452999	6		364	628	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2047220	2047255	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTCCCGCAGGCCCGGGGCCGGAGCTGAGCGGCCCGA	GTCCCGCAGGCCCGGGGCCGGAGCTGAGCGGCCCGA	-	novel	NA	P-0058667-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	56	248	0	ENST00000349721.2:c.791-8_818del		p.X264_splice	ENST00000349721	NM_003070.3	264		5/34	0.45474703284453	4	FACETS	0.845	0.734	0.963	0.845	0.734	0.963	CLONAL	2	TRUE	2	0.454658094452999	4		248	212	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0058668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	83	256	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.163693952803175	3	FACETS	0.942	0.843	1	0.942	0.843	1	INDETERMINATE	2	TRUE	1	0.417735870103275	3		256	255	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519975	NA	P-0058668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	72	472	0	ENST00000269305.4:c.403T>C	p.Cys135Arg	p.C135R	ENST00000269305	NM_001126112.2	135	Tgc/Cgc	5/11	0.39198613519896	1	FACETS	0.999	0.883	1	0.999	0.883	1	CLONAL	1	TRUE	0	0.417735870103275	1		472	273	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971124	21971125	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0058668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	64	480	0	ENST00000304494.5:c.233_234del	p.Leu78HisfsTer41	p.L78Hfs*41	ENST00000304494	NM_000077.4	78	cTC/c	2/3	0.417735870103275	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.417735870103275	1		480	216	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591891	48591891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912581	NA	P-0058668-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	42	417	0	ENST00000342988.3:c.1054G>A	p.Gly352Arg	p.G352R	ENST00000342988	NM_005359.5	352	Gga/Aga	9/12	0.417735870103275	1	FACETS	0.647	0.544	0.759	0.647	0.544	0.759	SUBCLONAL	1	TRUE	0	0.417735870103275	1		417	246	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	96	302	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.927	0.84	1	0.927	0.84	1	CLONAL	1	TRUE	1	0.825356094044913	2		302	251	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439918	56439918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367688879	NA	P-0058669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	461	428	0	ENST00000407977.2:c.674G>A	p.Arg225His	p.R225H	ENST00000407977		225	cGc/cAc	6/10	0.811320584289572	2	FACETS	0.99	0.966	1	0.99	0.966	1	CLONAL	2	TRUE	0	0.825356094044913	2		428	564	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0058669-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	10438	578	0	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.825356094044913	27	FACETS	1	0.999	1	1	0.999	1	CLONAL	27	TRUE	0	0.825356094044913	27		578	10527	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0058670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	125	545	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.574758433248484	1	FACETS	0.547	0.499	0.597	0.547	0.499	0.597	SUBCLONAL	1	TRUE	0	0.710036574168184	1		545	415	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0058670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	96	885	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.445	0.397	0.496	0.445	0.397	0.496	SUBCLONAL	1	TRUE	1	0.710036574168184	2		885	608	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696653	47696653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866898949	NA	P-0058670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	34	362	0	ENST00000347630.2:c.295C>T	p.Arg99Trp	p.R99W	ENST00000347630	NM_001007230.1	99	Cgg/Tgg	5/11	1	2	FACETS	0.159	0.129	0.192	0.159	0.129	0.192	SUBCLONAL	1	TRUE	1	0.710036574168184	2		362	603	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112201	115112201	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	142	491	0	ENST00000257566.3:c.1539C>A	p.Phe513Leu	p.F513L	ENST00000257566	NM_016569.3	513	ttC/ttA	7/8	0.143010999388898	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.710036574168184	0		491	479	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485137	57485137	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0058670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	66	381	0	ENST00000371085.3:c.970+1G>T		p.X324_splice	ENST00000371085	NM_000516.4	324			1	2	FACETS	0.264	0.229	0.303	0.264	0.229	0.303	SUBCLONAL	1	TRUE	1	0.710036574168184	2		381	703	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089638	27089639	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0058670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	448	582	0	ENST00000324856.7:c.2596dup	p.Arg866ProfsTer6	p.R866Pfs*6	ENST00000324856	NM_006015.4	865	aac/aaCc	8/20	0.609877323775254	2	FACETS	0.862	0.831	0.892	0.862	0.831	0.892	CLONAL	2	TRUE	0	0.710036574168184	2		582	732	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137318	64137318	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	32	408	0	ENST00000334205.4:c.1750C>T	p.Gln584Ter	p.Q584*	ENST00000334205	NM_003942.2	584	Cag/Tag	14/17	1	2	FACETS	0.146	0.118	0.178	0.146	0.118	0.178	SUBCLONAL	1	TRUE	1	0.710036574168184	2		408	618	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740606	58740606	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	110	439	0	ENST00000305921.3:c.1511C>A	p.Thr504Lys	p.T504K	ENST00000305921	NM_003620.3	504	aCa/aAa	6/6	0.335615803659981	3	FACETS	0.493	0.443	0.547	0.247	0.221	0.274	INDETERMINATE	1	TRUE	1	0.710036574168184	3		439	851	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125545	47125545	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	86	452	0	ENST00000409792.3:c.5725C>A	p.Leu1909Ile	p.L1909I	ENST00000409792	NM_014159.6	1909	Ctt/Att	12/21	1	2	FACETS	0.404	0.357	0.453	0.404	0.357	0.453	SUBCLONAL	1	TRUE	1	0.710036574168184	2		452	600	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100058	157100058	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	197	548	0	ENST00000346085.5:c.995G>A	p.Gly332Glu	p.G332E	ENST00000346085	NM_020732.3	332	gGa/gAa	1/20	0.37543913475804	1	FACETS	0.773	0.724	0.823	0.773	0.724	0.823	INDETERMINATE	1	TRUE	0	0.710036574168184	1		548	463	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527968	157527968	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	250	487	0	ENST00000346085.5:c.5693C>G	p.Thr1898Ser	p.T1898S	ENST00000346085	NM_020732.3	1898	aCc/aGc	20/20	0.37543913475804	1	FACETS	0.763	0.72	0.807	0.763	0.72	0.807	INDETERMINATE	1	TRUE	0	0.710036574168184	1		487	595	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923036	44923037	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0058670-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	184	232	0	ENST00000377967.4:c.1900_1901del	p.Asn634ProfsTer4	p.N634Pfs*4	ENST00000377967	NM_021140.2	633	AAa/a	16/29	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.710036574168184	1		232	268	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0058671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	353	522	1	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.361328961094357	3	FACETS	0.835	0.797	0.874	0.835	0.797	0.874	CLONAL	3	TRUE	0	0.468757777240328	3		523	742	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813023	89813023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142833057	NA	P-0058671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	290	472	0	ENST00000389301.3:c.3482C>T	p.Thr1161Met	p.T1161M	ENST00000389301	NM_000135.2	1161	aCg/aTg	35/43	0.473442032255939	4	FACETS	0.994	0.937	1	0.994	0.937	1	CLONAL	2	TRUE	2	0.468757777240328	4		472	914	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43699634	43699634	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0058671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	295	483	0	ENST00000382044.4:c.5881A>T	p.Arg1961Ter	p.R1961*	ENST00000382044	NM_001141980.1	1961	Aga/Tga	28/28	0.473442032255939	2	FACETS	0.949	0.9	0.998	0.949	0.9	0.998	CLONAL	2	TRUE	0	0.468757777240328	2		483	663	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121077	3121103	+	inframe_deletion	In_Frame_Del	DEL	ACTTCACGTGTGCCACCGACACGGAGA	ACTTCACGTGTGCCACCGACACGGAGA	-	novel	NA	P-0058671-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	261	557	0	ENST00000078429.4:c.982_1008del	p.Phe328_Asn336del	p.F328_N336del	ENST00000078429	NM_002067.2	327	cACTTCACGTGTGCCACCGACACGGAGAac/cac	7/7	0.473442032255939	2	FACETS	0.842	0.794	0.891	0.842	0.794	0.891	CLONAL	2	TRUE	0	0.468757777240328	2		557	661	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	390	302	0				ENST00000310581	NM_198253.2	-/1132			0.565196577149016	4	FACETS	0.907	0.868	0.945	0.907	0.868	0.945	CLONAL	3	TRUE	1	0.600879369483309	4		302	764	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0058672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	246	368	0	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.600879369483309	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.600879369483309	1		368	540	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545821	106545821	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	105	291	0	ENST00000359195.3:c.3298C>A	p.His1100Asn	p.H1100N	ENST00000359195	NM_002649.2	1100	Cat/Aat	11/11	1	2	FACETS	0.979	0.886	1	0.979	0.886	1	CLONAL	1	TRUE	1	0.600879369483309	2		291	357	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937703	44937703	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058672-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	65	125	0	ENST00000377967.4:c.2891A>G	p.Asn964Ser	p.N964S	ENST00000377967	NM_021140.2	964	aAc/aGc	19/29	1	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.600879369483309	1		125	108	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463196	25463197	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	rs750475955	NA	P-0058673-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	285	472	0	ENST00000264709.3:c.2296_2297del	p.Lys766GlufsTer15	p.K766Efs*15	ENST00000264709	NM_175629.2	766	AAg/g	19/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.807606688369767	2		472	687	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	110	302	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.914	0.832	0.999	0.914	0.832	0.999	CLONAL	1	TRUE	1	0.747175069660054	2		302	322	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467675	50467675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759124417	NA	P-0058675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	14	510	0	ENST00000331340.3:c.910G>A	p.Glu304Lys	p.E304K	ENST00000331340	NM_006060.4	304	Gaa/Aaa	8/8	0.741111305921233	3	FACETS	0.074	0.053	0.1	0.037	0.026	0.05	SUBCLONAL	1	TRUE	1	0.747175069660054	3		510	694	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175780	176175780	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	210	534	0	ENST00000367669.3:c.335A>T	p.Lys112Met	p.K112M	ENST00000367669	NM_022457.5	112	aAg/aTg	1/20	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.747175069660054	2		534	421	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231418	46231418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	157	422	0	ENST00000334344.6:c.1258G>A	p.Glu420Lys	p.E420K	ENST00000334344	NM_152641.2	420	Gag/Aag	10/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.747175069660054	2		422	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578429	7578429	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1567553148	NA	P-0058675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	57	645	0	ENST00000269305.4:c.501del	p.Gln167HisfsTer3	p.Q167Hfs*3	ENST00000269305	NM_001126112.2	167	caG/ca	5/11	1	2	FACETS	0.204	0.175	0.237	0.204	0.175	0.237	SUBCLONAL	1	TRUE	1	0.747175069660054	2		645	747	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0058675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	59	641	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	1	2	FACETS	0.208	0.178	0.24	0.208	0.178	0.24	SUBCLONAL	1	TRUE	1	0.747175069660054	2		641	760	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106898	11106898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	226	559	0	ENST00000358026.2:c.1603G>A	p.Glu535Lys	p.E535K	ENST00000358026	NM_001128849.1	535	Gag/Aag	10/36	0.741111305921233	3	FACETS	1	0.974	1	0.54	0.504	0.576	CLONAL	1	TRUE	1	0.747175069660054	3		559	770	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0058675-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1873	9310	435	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.747175069660054	32	FACETS	1	0.998	1	0.878	0.873	0.882	CLONAL	27	TRUE	1	0.747175069660054	32		435	11183	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0058683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	64	286	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.26712844585777	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.26712844585777	1		286	362	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372744	81372744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168082930	NA	P-0058683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	57	354	0	ENST00000222390.5:c.790G>A	p.Asp264Asn	p.D264N	ENST00000222390	NM_000601.4	264	Gat/Aat	7/18	1	2	FACETS	0.822	0.706	0.949	0.822	0.706	0.949	CLONAL	1	TRUE	1	0.26712844585777	2		354	519	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0058683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	96	426	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.26712844585777	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.26712844585777	1		426	607	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444791	49444791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	100	638	0	ENST00000301067.7:c.2675C>T	p.Ser892Phe	p.S892F	ENST00000301067	NM_003482.3	892	tCt/tTt	10/54	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.26712844585777	2		638	661	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813375	102813375	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	66	504	0	ENST00000307046.8:c.314T>C	p.Leu105Pro	p.L105P	ENST00000307046	NM_001111285.1	105	cTg/cCg	3/4	1	2	FACETS	0.814	0.707	0.93	0.814	0.707	0.93	CLONAL	1	TRUE	1	0.26712844585777	2		504	607	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107995	30107995	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	53	389	0	ENST00000331968.5:c.812A>T	p.His271Leu	p.H271L	ENST00000331968	NM_002742.2	271	cAc/cTc	5/18	0.220846988759948	1	FACETS	0.65	0.554	0.755	0.65	0.554	0.755	SUBCLONAL	1	TRUE	0	0.26712844585777	1		389	529	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653010	29653014	+	frameshift_variant	Frame_Shift_Del	DEL	GCTTA	GCTTA	-	novel	NA	P-0058683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	100	403	0	ENST00000356175.3:c.4945_4949del	p.Ala1649ArgfsTer10	p.A1649Rfs*10	ENST00000356175	NM_000267.3	1649	GCTTAc/c	36/57	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.26712844585777	2		403	684	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221954	1221955	+	missense_variant	Missense_Mutation	DNP	TT	TT	CA	novel	NA	P-0058683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	60	376	0	ENST00000326873.7:c.869_870delinsCA	p.Leu290Pro	p.L290P	ENST00000326873	NM_000455.4	290	cTT/cCA	7/10	0.26712844585777	1	FACETS	0.841	0.726	0.965	0.841	0.726	0.965	CLONAL	1	TRUE	0	0.26712844585777	1		376	463	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872250	45872250	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	83	569	0	ENST00000391945.4:c.184del	p.Ala62HisfsTer6	p.A62Hfs*6	ENST00000391945	NM_000400.3	62	Gca/ca	4/23	1	2	FACETS	0.857	0.756	0.966	0.857	0.756	0.966	CLONAL	1	TRUE	1	0.26712844585777	2		569	725	SUCCESS
APC	324	MSKCC	GRCh37	5	112177115	112177115	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1370108946	NA	P-0058683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	111	512	0	ENST00000257430.4:c.5824G>T	p.Asp1942Tyr	p.D1942Y	ENST00000257430	NM_000038.5	1942	Gac/Tac	16/16	0.26712844585777	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.26712844585777	1		512	671	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041115	180041115	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	71	489	0	ENST00000261937.6:c.3284G>T	p.Ser1095Ile	p.S1095I	ENST00000261937	NM_182925.4	1095	aGt/aTt	24/30	1	2	FACETS	0.757	0.66	0.862	0.757	0.66	0.862	SUBCLONAL	1	TRUE	1	0.26712844585777	2		489	702	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401686	401686	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	79	618	0	ENST00000380956.4:c.1008G>T	p.Trp336Cys	p.W336C	ENST00000380956	NM_001195286.1	336	tgG/tgT	7/9	0.101145858832275	5	FACETS	0.952	0.836	1	0.238	0.209	0.27	INDETERMINATE	1	TRUE	1	0.26712844585777	5		618	870	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671439	30671439	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	123	581	0	ENST00000376406.3:c.5521del	p.Glu1841LysfsTer17	p.E1841Kfs*17	ENST00000376406	NM_014641.2	1841	Gaa/aa	10/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.26712844585777	2		581	760	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500796	8500796	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058683-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	91	435	0	ENST00000356435.5:c.2086G>T	p.Gly696Cys	p.G696C	ENST00000356435		696	Ggc/Tgc	13/35	0.26712844585777	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.26712844585777	1		435	565	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0058684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	31	461	0	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	1	2	FACETS	0.44	0.355	0.537	0.44	0.355	0.537	SUBCLONAL	1	TRUE	1	0.28	2		461	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574030	7574030	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	46	332	0	ENST00000269305.4:c.997del	p.Arg333ValfsTer12	p.R333Vfs*12	ENST00000269305	NM_001126112.2	333	Cgt/gt	10/11	1	2	FACETS	0.888	0.75	1	0.888	0.75	1	CLONAL	1	TRUE	1	0.28	2		332	370	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847282	68847282	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	82	369	0	ENST00000261769.5:c.1204G>T	p.Asp402Tyr	p.D402Y	ENST00000261769	NM_004360.3	402	Gat/Tat	9/16	0.258792901904188	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.28	1		369	448	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274217	5274217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	63	370	0	ENST00000357368.4:c.230G>A	p.Arg77His	p.R77H	ENST00000357368	NM_002850.3	77	cGc/cAc	3/38	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.28	2		370	445	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456872	32456872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	35	312	0	ENST00000332351.3:c.20C>T	p.Thr7Met	p.T7M	ENST00000332351	NM_024426.4	7	aCg/aTg	1/10	0.148971668264809	5	FACETS	0.777	0.636	0.935			1	INDETERMINATE	1	TRUE	NA	0.28	5		312	457	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246674	46246674	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1367200406	NA	P-0058684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	55	322	1	ENST00000334344.6:c.4768C>A	p.Pro1590Thr	p.P1590T	ENST00000334344	NM_152641.2	1590	Ccg/Acg	15/21	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.28	2		323	374	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509579	29509579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754343223	NA	P-0058684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	50	307	0	ENST00000356175.3:c.784C>T	p.Arg262Cys	p.R262C	ENST00000356175	NM_000267.3	262	Cgt/Tgt	8/57	0.137194135725217	3	FACETS	0.776	0.658	0.905	0.388	0.329	0.453	INDETERMINATE	1	TRUE	1	0.28	3		307	525	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058729	47058729	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	28	356	0	ENST00000409792.3:c.7549A>T	p.Met2517Leu	p.M2517L	ENST00000409792	NM_014159.6	2517	Atg/Ttg	21/21	1	2	FACETS	0.435	0.347	0.535	0.435	0.347	0.535	SUBCLONAL	1	TRUE	1	0.28	2		356	460	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974681	21974681	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs199907548	NA	P-0058684-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	67	455	0	ENST00000304494.5:c.146T>G	p.Ile49Ser	p.I49S	ENST00000304494	NM_000077.4	49	aTc/aGc	1/3	0.3	1	FACETS	0.959	0.837	1	0.959	0.837	1	CLONAL	1	TRUE	0	0.28	1		455	429	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067836	30067836	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315499	NA	P-0058685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	271	355	0	ENST00000338641.4:c.1021C>T	p.Arg341Ter	p.R341*	ENST00000338641	NM_000268.3	341	Cga/Tga	11/16	0.754397587163265	1	FACETS	0.948	0.903	0.992	0.948	0.903	0.992	CLONAL	1	TRUE	0	0.754397587163265	1		355	472	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282556	1282556	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058685-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	51	372	0	ENST00000310581.5:c.1757G>T	p.Ser586Ile	p.S586I	ENST00000310581	NM_198253.2	586	aGc/aTc	3/16	1	2	FACETS	0.241	0.205	0.282	0.241	0.205	0.282	SUBCLONAL	1	TRUE	1	0.754397587163265	2		372	560	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0058686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	298	394	0	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	1	2	FACETS	0.97	0.918	1	0.97	0.918	1	CLONAL	1	TRUE	1	0.812949755815414	2		394	756	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398088	4398088	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	241	386	0	ENST00000261254.3:c.652G>A	p.Glu218Lys	p.E218K	ENST00000261254	NM_001759.3	218	Gag/Aag	4/5	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.812949755815414	2		386	574	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713449	40713449	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058686-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	276	439	0	ENST00000373198.4:c.4066T>C	p.Tyr1356His	p.Y1356H	ENST00000373198	NM_133170.3	1356	Tac/Cac	30/32	0.142962603162042	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.812949755815414	0		439	742	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056181	27056181	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058687-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	213	462	0	ENST00000324856.7:c.1177C>T	p.Gln393Ter	p.Q393*	ENST00000324856	NM_006015.4	393	Cag/Tag	2/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.780526886871222	2		462	508	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0058687-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	116	431	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.898	0.82	0.979	0.898	0.82	0.979	CLONAL	1	TRUE	1	0.780526886871222	2		431	331	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058687-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	13	536	0	ENST00000269571.5:c.829G>C	p.Asp277His	p.D277H	ENST00000269571		277	Gac/Cac	7/27	1	2	FACETS	0.052	0.037	0.071	0.052	0.037	0.071	SUBCLONAL	1	TRUE	1	0.780526886871222	2		536	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578505	7578510	+	inframe_deletion	In_Frame_Del	DEL	GGGCAG	GGGCAG	-	novel	NA	P-0058687-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	284	518	0	ENST00000269305.4:c.420_425del	p.Cys141_Pro142del	p.C141_P142del	ENST00000269305	NM_001126112.2	140	acCTGCCCt/act	5/11	0.779540794802544	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.780526886871222	1		518	390	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056214	27056214	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058687-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	219	517	0	ENST00000324856.7:c.1210C>T	p.Gln404Ter	p.Q404*	ENST00000324856	NM_006015.4	404	Caa/Taa	2/20	1	2	FACETS	0.979	0.918	1	0.979	0.918	1	CLONAL	1	TRUE	1	0.780526886871222	2		517	573	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258276	16258281	+	inframe_deletion	In_Frame_Del	DEL	AGACCG	AGACCG	-	novel	NA	P-0058687-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	254	542	0	ENST00000375759.3:c.5541_5546del	p.Ile1847_Arg1849delinsMet	p.I1847_R1849delinsM	ENST00000375759	NM_015001.2	1847	atAGACCGg/atg	11/15	1	2	FACETS	0.969	0.912	1	0.969	0.912	1	CLONAL	1	TRUE	1	0.780526886871222	2		542	672	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263919	104263919	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058687-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	37	420	0	ENST00000369902.3:c.10C>G	p.Leu4Val	p.L4V	ENST00000369902	NM_016169.3	4	Ctg/Gtg	1/12	0.780526886871222	1	FACETS	0.251	0.208	0.298	0.251	0.208	0.298	SUBCLONAL	1	TRUE	0	0.780526886871222	1		420	230	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447872	49447872	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058687-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	214	477	0	ENST00000301067.7:c.562G>T	p.Gly188Ter	p.G188*	ENST00000301067	NM_003482.3	188	Gga/Tga	5/54	0.740887301081423	3	FACETS	1	0.944	1	0.507	0.472	0.542	CLONAL	1	TRUE	1	0.780526886871222	3		477	752	SUCCESS
ATR	545	MSKCC	GRCh37	3	142211994	142211994	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058687-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	125	272	0	ENST00000350721.4:c.6058G>A	p.Ala2020Thr	p.A2020T	ENST00000350721	NM_001184.3	2020	Gca/Aca	35/47	1	2	FACETS	0.986	0.905	1	0.986	0.905	1	CLONAL	1	TRUE	1	0.780526886871222	2		272	325	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259800	142259800	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058687-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	44	385	0	ENST00000350721.4:c.3527C>G	p.Thr1176Ser	p.T1176S	ENST00000350721	NM_001184.3	1176	aCc/aGc	18/47	1	2	FACETS	0.257	0.216	0.303	0.257	0.216	0.303	SUBCLONAL	1	TRUE	1	0.780526886871222	2		385	438	SUCCESS
ALB	213	MSKCC	GRCh37	4	74270072	74270072	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058687-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	106	319	0	ENST00000295897.4:c.28C>G	p.Leu10Val	p.L10V	ENST00000295897	NM_000477.5	10	Ctt/Gtt	1/15	1	2	FACETS	0.927	0.843	1	0.927	0.843	1	CLONAL	1	TRUE	1	0.780526886871222	2		319	293	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247155	153247156	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	novel	NA	P-0058687-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	224	282	0	ENST00000281708.4:c.1644+2dup		p.X548_splice	ENST00000281708	NM_033632.3	548			0.780526886871222	2	FACETS	0.932	0.892	0.97	0.932	0.892	0.97	CLONAL	2	TRUE	0	0.780526886871222	2		282	308	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235361	235361	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058687-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	135	410	0	ENST00000264932.6:c.1167C>G	p.Ile389Met	p.I389M	ENST00000264932	NM_004168.2	389	atC/atG	9/15	1	2	FACETS	0.846	0.776	0.917	0.846	0.776	0.917	CLONAL	1	TRUE	1	0.780526886871222	2		410	409	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152357824	152357824	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058687-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	59	241	0	ENST00000359321.1:c.83A>T	p.Glu28Val	p.E28V	ENST00000359321	NM_005431.1	28	gAa/gTa	2/3	1	2	FACETS	0.429	0.371	0.492	0.429	0.371	0.492	SUBCLONAL	1	TRUE	1	0.780526886871222	2		241	352	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0058688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	159	374	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.974	1	1	0.993	1	CLONAL	2	TRUE	1	0.31	2		374	459	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0058688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	133	244	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.916	1	1	0.991	1	CLONAL	2	TRUE	1	0.31	2		244	429	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850704	63850705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0058688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	184	423	0	ENST00000279873.7:c.1489dup	p.Ile497AsnfsTer31	p.I497Nfs*31	ENST00000279873	NM_032199.2	494	-/A	10/10	1	2	FACETS	0.945	0.877	1	1	0.993	1	CLONAL	2	TRUE	1	0.31	2		423	628	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515664	31515664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560794749	NA	P-0058688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	44	246	0	ENST00000344624.3:c.955G>A	p.Gly319Ser	p.G319S	ENST00000344624		319	Ggt/Agt	4/33	0.3	2	FACETS	1	0.843	1			1	CLONAL	1	TRUE	NA	0.31	2		246	284	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624296	89624300	+	frameshift_variant	Frame_Shift_Del	DEL	GACTT	GACTT	-	novel	NA	P-0058688-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	124	267	0	ENST00000371953.3:c.73_77del	p.Thr26TyrfsTer16	p.T26Yfs*16	ENST00000371953	NM_000314.4	24	GACTTg/g	1/9	1	2	FACETS	1	0.913	1	1	0.99	1	CLONAL	2	TRUE	1	0.31	2		267	400	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0058690-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	101	285	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.699743748898618	2		285	245	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015104	27015104	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058690-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	163	289	0	ENST00000335756.4:c.206G>T	p.Arg69Leu	p.R69L	ENST00000335756	NM_001809.3	69	cGc/cTc	2/5	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.699743748898618	2		289	451	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058691-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	143	302	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.905	0.835	0.976	0.905	0.835	0.976	CLONAL	1	TRUE	1	0.845231122079276	2		302	374	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0058691-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	503	413	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	0.845231122079276	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.845231122079276	2		413	565	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982392	201982393	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058691-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	233	487	0	ENST00000359651.3:c.772dup	p.Trp258LeufsTer43	p.W258Lfs*43	ENST00000359651		257	-/T	6/8	1	2	FACETS	0.829	0.778	0.882	0.829	0.778	0.882	CLONAL	1	TRUE	1	0.845231122079276	2		487	665	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857056	9857056	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058691-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	207	409	0	ENST00000330684.3:c.4345A>G	p.Ser1449Gly	p.S1449G	ENST00000330684	NM_001134407.1	1449	Agc/Ggc	13/13	NA	2	FACETS	0.942	0.882	1			1	INDETERMINATE	1	TRUE	NA	0.845231122079276	2		409	520	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63898387	63898388	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCAGCC	rs1553686130	NA	P-0058691-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	74	247	0	ENST00000398590.3:c.116_121dup	p.Gln39_Pro40dup	p.Q39_P40dup	ENST00000398590	NM_001177387.1	39	cag/caGCAGCCg	3/14	1	2	FACETS	0.505	0.445	0.568	0.505	0.445	0.568	SUBCLONAL	1	TRUE	1	0.845231122079276	2		247	347	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2110325	2110325	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058691-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	222	357	0	ENST00000349721.2:c.3364T>G	p.Phe1122Val	p.F1122V	ENST00000349721	NM_003070.3	1122	Ttc/Gtc	24/34	1	2	FACETS	0.964	0.905	1	0.964	0.905	1	CLONAL	1	TRUE	1	0.845231122079276	2		357	545	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63898387	63898387	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1477342245	NA	P-0058691-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	65	245	0	ENST00000398590.3:c.113A>C	p.Gln38Pro	p.Q38P	ENST00000398590	NM_001177387.1	38	cAg/cCg	3/14	1	2	FACETS	0.445	0.388	0.505	0.445	0.388	0.505	SUBCLONAL	1	TRUE	1	0.845231122079276	2		245	346	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023174	48023174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	61	479	0	ENST00000234420.5:c.599C>T	p.Ser200Leu	p.S200L	ENST00000234420	NM_000179.2	200	tCa/tTa	3/10	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.201804203766942	2		479	552	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846036	68846036	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0058695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	51	443	0	ENST00000261769.5:c.1009-2A>G		p.X337_splice	ENST00000261769	NM_004360.3	337			0.201804203766942	1	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	0	0.201804203766942	1		443	448	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023383	27023384	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0058695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	46	416	0	ENST00000324856.7:c.490_491del	p.Ala164ArgfsTer235	p.A164Rfs*235	ENST00000324856	NM_006015.4	163	gcCGcc/gccc	1/20	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.201804203766942	2		416	400	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856093	68856170	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGAGTGCCAACTGGACCATTCAGTACAACGACCCAAGTGGGTACCTGAGTTTTATTTTGGCAACTTTGCTCCAACTGC	CGAGTGCCAACTGGACCATTCAGTACAACGACCCAAGTGGGTACCTGAGTTTTATTTTGGCAACTTTGCTCCAACTGC	-	novel	NA	P-0058695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	35	450	0	ENST00000261769.5:c.1902_1936+43del		p.X634_splice	ENST00000261769	NM_004360.3	634		12/16	0.201804203766942	1	FACETS	0.699	0.573	0.841	0.699	0.573	0.841	SUBCLONAL	1	TRUE	0	0.201804203766942	1		450	446	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827162	72827162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	28	449	0	ENST00000268489.5:c.9419C>T	p.Ser3140Phe	p.S3140F	ENST00000268489	NM_006885.3	3140	tCc/tTc	9/10	0.201804203766942	1	FACETS	0.595	0.475	0.732	0.595	0.475	0.732	SUBCLONAL	1	TRUE	0	0.201804203766942	1		449	419	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405956	49405956	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	65	446	0	ENST00000418115.1:c.182C>A	p.Ala61Asp	p.A61D	ENST00000418115	NM_001664.2	61	gCt/gAt	3/5	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.201804203766942	2		446	488	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322639	109322639	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779364145	NA	P-0058695-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	43	407	0	ENST00000436639.2:c.398C>A	p.Ser133Tyr	p.S133Y	ENST00000436639	NM_014454.2	133	tCt/tAt	3/10	1	2	FACETS	0.895	0.749	1	0.895	0.749	1	CLONAL	1	TRUE	1	0.201804203766942	2		407	476	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0058696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	89	431	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.485134327878775	2		431	311	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0058696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	57	307	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.485134327878775	2		307	227	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0058696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	159	428	0	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	0.300523760525308	3	FACETS	0.866	0.801	0.934	0.866	0.801	0.934	CLONAL	2	TRUE	1	0.485134327878775	3		428	470	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256799	133256799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500863	NA	P-0058696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	41	398	0	ENST00000320574.5:c.295C>T	p.Pro99Ser	p.P99S	ENST00000320574	NM_006231.2	99	Ccc/Tcc	4/49	0.300523760525308	3	FACETS	0.635	0.53	0.75	0.317	0.265	0.375	SUBCLONAL	1	TRUE	1	0.485134327878775	3		398	331	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120469155	120469156	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTACTGGC	novel	NA	P-0058696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	45	537	0	ENST00000256646.2:c.3964_3971dup	p.Asn1324LysfsTer29	p.N1324Kfs*29	ENST00000256646	NM_024408.3	1324	aac/aaGCCAGTAAc	24/34	1	2	FACETS	0.442	0.372	0.519	0.442	0.372	0.519	SUBCLONAL	1	TRUE	1	0.485134327878775	2		537	420	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111886026	111886027	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0058696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	43	549	0	ENST00000341259.2:c.1648_1649delinsTT	p.Ala550Phe	p.A550F	ENST00000341259	NM_005475.2	550	GCc/TTc	8/8	0.300523760525308	3	FACETS	0.428	0.358	0.506	0.214	0.179	0.253	SUBCLONAL	1	TRUE	1	0.485134327878775	3		549	515	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143396	30143396	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	97	478	0	ENST00000389048.3:c.130C>T	p.Leu44Phe	p.L44F	ENST00000389048	NM_004304.4	44	Ctc/Ttc	1/29	0.485134327878775	3	FACETS	1	0.967	1	0.596	0.534	0.66	CLONAL	1	TRUE	1	0.485134327878775	3		478	417	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235312	235316	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAG	CAGAG	-	novel	NA	P-0058696-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	21	410	0	ENST00000264932.6:c.1121_1125del	p.Glu374AlafsTer34	p.E374Afs*34	ENST00000264932	NM_004168.2	373	cCAGAG/c	9/15	0.437153783232425	3	FACETS	0.316	0.243	0.402	0.158	0.121	0.201	SUBCLONAL	1	TRUE	1	0.485134327878775	3		410	340	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0058697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	54	425	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.49455291041033	2		425	194	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981315	68981315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866864487	NA	P-0058697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	32	166	0	ENST00000288368.4:c.1387C>T	p.Arg463Cys	p.R463C	ENST00000288368	NM_024870.2	463	Cgc/Tgc	12/40	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.49455291041033	2		166	118	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418715	49418715	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	76	383	0	ENST00000301067.7:c.15799A>G	p.Ile5267Val	p.I5267V	ENST00000301067	NM_003482.3	5267	Atc/Gtc	49/54	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.49455291041033	2		383	263	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299096	15299096	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	64	412	0	ENST00000263388.2:c.1442del	p.Gly481ValfsTer118	p.G481Vfs*118	ENST00000263388	NM_000435.2	481	gGt/gt	9/33	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.49455291041033	2		412	224	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909578	50909579	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0058697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	72	520	0	ENST00000440232.2:c.1383+1dup		p.Q461fs	ENST00000440232	NM_002691.3	461	cag/caGg	11/27	1	2	FACETS	0.919	0.809	1	0.919	0.809	1	CLONAL	1	TRUE	1	0.49455291041033	2		520	317	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144862	47144862	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	74	258	0	ENST00000409792.3:c.4891T>G	p.Cys1631Gly	p.C1631G	ENST00000409792	NM_014159.6	1631	Tgt/Ggt	7/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.49455291041033	2		258	208	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164520	47164520	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	62	360	0	ENST00000409792.3:c.1606G>T	p.Glu536Ter	p.E536*	ENST00000409792	NM_014159.6	536	Gaa/Taa	3/21	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.49455291041033	2		360	233	SUCCESS
AR	367	MSKCC	GRCh37	X	66765360	66765360	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058697-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	47	496	0	ENST00000374690.3:c.372del	p.Glu124AspfsTer51	p.E124Dfs*51	ENST00000374690	NM_000044.3	124	gaG/ga	1/8	0.49455291041033	3	FACETS	0.723	0.613	0.843	0.361	0.306	0.422	SUBCLONAL	1	TRUE	1	0.49455291041033	3		496	328	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273218	115273218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	22	692	0	ENST00000438362.2:c.1240C>T	p.Arg414Cys	p.R414C	ENST00000438362	NM_001242891.1	414	Cgt/Tgt	11/20	0.12908242572598	3	FACETS	0.792	0.616	0.995	0.792	0.616	0.995	CLONAL	2	FALSE	1	0.12908242572598	3		692	229	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039374	49039374	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853293	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	11	724	0	ENST00000267163.4:c.2359C>T	p.Arg787Ter	p.R787*	ENST00000267163	NM_000321.2	787	Cga/Tga	23/27	0.12908242572598	4	FACETS	0.912	0.63	1	0.456	0.315	0.631	CLONAL	1	FALSE	2	0.12908242572598	4		724	211	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288979	212288979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	12	612	0	ENST00000342788.4:c.2767G>A	p.Gly923Arg	p.G923R	ENST00000342788	NM_005235.2	923	Gga/Aga	23/28	1	2	FACETS	0.768	0.544	1	1	0.87	1	CLONAL	2	FALSE	1	0.12908242572598	2		612	121	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287262	33287262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	35	815	0	ENST00000374542.5:c.1835C>T	p.Ser612Phe	p.S612F	ENST00000374542	NM_001141970.1	612	tCc/tTc	6/8	0.12908242572598	13	FACETS	1	0.941	1	0.237	0.193	0.286	CLONAL	1	FALSE	7	0.12908242572598	13		815	653	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171607	36171607	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1569008655	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	42	660	0	ENST00000300305.3:c.958C>T	p.Arg320Ter	p.R320*	ENST00000300305		320	Cga/Tga	7/8	0.12908242572598	1	FACETS	0.954	0.8	1	1	0.968	1	CLONAL	2	FALSE	0	0.12908242572598	1		660	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	13	725	0	ENST00000269305.4:c.166G>T	p.Glu56Ter	p.E56*	ENST00000269305	NM_001126112.2	56	Gaa/Taa	4/11	0.12908242572598	3	FACETS	0.828	0.59	1	0.414	0.295	0.56	CLONAL	1	FALSE	1	0.12908242572598	3		725	259	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397695	116397695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	12	635	0	ENST00000397752.3:c.1969C>T	p.Pro657Ser	p.P657S	ENST00000397752	NM_000245.2	657	Cct/Tct	8/21	1	2	FACETS	1	0.796	1	1	0.796	1	CLONAL	1	FALSE	1	0.12908242572598	2		635	158	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279534	1279534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1368095577	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	16	747	0	ENST00000310581.5:c.2002G>A	p.Glu668Lys	p.E668K	ENST00000310581	NM_198253.2	668	Gag/Aag	5/16	1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	FALSE	1	0.12908242572598	2		747	202	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976476	25976476	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	13	488	0	ENST00000435504.4:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000435504		357	Cga/Tga	11/13	1	2	FACETS	0.846	0.609	1	1	0.892	1	CLONAL	2	FALSE	1	0.12908242572598	2		488	119	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796574	42796574	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	15	795	0	ENST00000575354.2:c.3131C>T	p.Ser1044Leu	p.S1044L	ENST00000575354	NM_015125.3	1044	tCg/tTg	13/20	0.12908242572598	4	FACETS	0.994	0.727	1	0.497	0.363	0.658	CLONAL	1	FALSE	2	0.12908242572598	4		795	264	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056291	180056291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199942873	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	11	851	0	ENST00000261937.6:c.953G>A	p.Arg318Gln	p.R318Q	ENST00000261937	NM_182925.4	318	cGa/cAa	7/30	1	2	FACETS	0.789	0.545	1	0.789	0.545	1	CLONAL	1	FALSE	1	0.12908242572598	2		851	216	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937446	178937446	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	17	301	0	ENST00000263967.3:c.1834C>T	p.Arg612Ter	p.R612*	ENST00000263967	NM_006218.2	612	Cga/Tga	12/21	1	2	FACETS	1	0.808	1	1	0.946	1	CLONAL	3	FALSE	1	0.12908242572598	2		301	82	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437478	110437478	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	29	695	0	ENST00000375856.3:c.923C>T	p.Ser308Leu	p.S308L	ENST00000375856	NM_003749.2	308	tCg/tTg	1/2	0.12908242572598	4	FACETS	0.837	0.673	1	0.837	0.673	1	CLONAL	2	FALSE	2	0.12908242572598	4		695	303	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630029	117630029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs976517290	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	14	587	0	ENST00000368508.3:c.6497C>T	p.Ser2166Phe	p.S2166F	ENST00000368508	NM_002944.2	2166	tCc/tTc	41/43	1	2	FACETS	0.927	0.676	1	1	0.908	1	CLONAL	2	FALSE	1	0.12908242572598	2		587	117	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73351598	73351598	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144464538	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	15	575	0	ENST00000377767.4:c.614C>T	p.Pro205Leu	p.P205L	ENST00000377767	NM_014953.3	205	cCc/cTc	4/21	0.12908242572598	4	FACETS	1	0.869	1	0.68	0.498	0.896	CLONAL	1	FALSE	2	0.12908242572598	4		575	193	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423551	88423551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	19	632	0	ENST00000360948.2:c.2284G>A	p.Glu762Lys	p.E762K	ENST00000360948	NM_001012338.2	762	Gag/Aag	18/19	1	2	FACETS	0.861	0.657	1	1	0.925	1	CLONAL	2	FALSE	1	0.12908242572598	2		632	171	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938967	76938967	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782774889	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	10	419	0	ENST00000373344.5:c.1781C>T	p.Ser594Phe	p.S594F	ENST00000373344	NM_000489.3	594	tCc/tTc	9/35	1	1	FACETS	1	0.778	1	1	0.896	1	CLONAL	2	FALSE	0	0.12908242572598	1		419	62	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255076	16255076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1283954838	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	18	754	0	ENST00000375759.3:c.2341C>T	p.Arg781Cys	p.R781C	ENST00000375759	NM_015001.2	781	Cgt/Tgt	11/15	0.12908242572598	3	FACETS	1	0.758	1	0.503	0.379	0.65	CLONAL	1	FALSE	1	0.12908242572598	3		754	295	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332577	153332577	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	13	706	0	ENST00000281708.4:c.379C>T	p.Gln127Ter	p.Q127*	ENST00000281708	NM_033632.3	127	Cag/Tag	2/12	1	2	FACETS	0.92	0.656	1	0.92	0.656	1	CLONAL	1	FALSE	1	0.12908242572598	2		706	219	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40872305	40872305	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs773742282	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	20	611	0	ENST00000428826.2:c.650G>T	p.Arg217Leu	p.R217L	ENST00000428826		217	cGa/cTa	7/21	0.12908242572598	3	FACETS	0.801	0.615	1	0.801	0.615	1	CLONAL	2	FALSE	1	0.12908242572598	3		611	206	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276929	123276929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200204947	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	12	674	0	ENST00000358487.5:c.988C>T	p.Arg330Trp	p.R330W	ENST00000358487	NM_000141.4	330	Cgg/Tgg	8/18	1	2	FACETS	0.808	0.573	1	1	0.878	1	CLONAL	2	FALSE	1	0.12908242572598	2		674	115	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192078	108192078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200431631	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	17	560	0	ENST00000278616.4:c.6503C>T	p.Ser2168Leu	p.S2168L	ENST00000278616	NM_000051.3	2168	tCg/tTg	45/63	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	FALSE	1	0.12908242572598	2		560	180	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796963	78796963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	20	667	0	ENST00000306801.3:c.1076C>T	p.Ser359Leu	p.S359L	ENST00000306801	NM_020761.2	359	tCg/tTg	9/34	0.12908242572598	3	FACETS	0.948	0.724	1	0.474	0.362	0.605	CLONAL	1	FALSE	1	0.12908242572598	3		667	348	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223166	41223166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357002	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	18	729	0	ENST00000357654.3:c.4765C>T	p.Arg1589Cys	p.R1589C	ENST00000357654	NM_007294.3	1589	Cgt/Tgt	15/23	0.12908242572598	3	FACETS	0.9	0.682	1	0.9	0.682	1	CLONAL	2	FALSE	1	0.12908242572598	3		729	165	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43769857	43769857	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	14	598	0	ENST00000382044.4:c.889C>T	p.Gln297Ter	p.Q297*	ENST00000382044	NM_001141980.1	297	Cag/Tag	8/28	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	FALSE	1	0.12908242572598	2		598	154	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816545	32816545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778774698	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	37	786	0	ENST00000354258.4:c.1630C>T	p.Arg544Cys	p.R544C	ENST00000354258	NM_000593.5	544	Cgc/Tgc	7/11	0.12908242572598	13	FACETS	1	0.948	1	0.247	0.203	0.297	CLONAL	1	FALSE	7	0.12908242572598	13		786	661	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894949	101894949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519144	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	13	652	0	ENST00000374994.4:c.502C>T	p.Arg168Cys	p.R168C	ENST00000374994	NM_004612.2	168	Cgc/Tgc	3/9	1	2	FACETS	0.832	0.593	1	0.832	0.593	1	CLONAL	1	FALSE	1	0.12908242572598	2		652	242	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413568	32413568	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1421664466	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	11	578	0	ENST00000332351.3:c.1382C>T	p.Ser461Phe	p.S461F	ENST00000332351	NM_024426.4	461	tCc/tTc	9/10	1	2	FACETS	1	0.698	1	1	0.698	1	CLONAL	1	FALSE	1	0.12908242572598	2		578	169	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158117	27158117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760573137	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	18	767	0	ENST00000380036.4:c.341G>A	p.Arg114Gln	p.R114Q	ENST00000380036	NM_000459.3	114	cGa/cAa	2/23	1	2	FACETS	0.775	0.586	0.995	1	0.91	1	CLONAL	2	FALSE	1	0.12908242572598	2		767	180	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685209	86685209	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	18	504	0	ENST00000274376.6:c.2926-1G>A		p.X976_splice	ENST00000274376	NM_002890.2	976			1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	FALSE	1	0.12908242572598	2		504	222	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458414	120458414	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	20	962	0	ENST00000256646.2:c.6931C>T	p.Pro2311Ser	p.P2311S	ENST00000256646	NM_024408.3	2311	Cct/Tct	34/34	0.12908242572598	3	FACETS	1	0.879	1	0.63	0.482	0.802	CLONAL	1	FALSE	1	0.12908242572598	3		962	262	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928225	178928225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	14	621	0	ENST00000263967.3:c.1411C>T	p.Pro471Ser	p.P471S	ENST00000263967	NM_006218.2	471	Cca/Tca	9/21	1	2	FACETS	0.792	0.576	1	1	0.891	1	CLONAL	2	FALSE	1	0.12908242572598	2		621	137	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562372	21562372	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775535885	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	17	735	1	ENST00000382592.4:c.1547C>T	p.Pro516Leu	p.P516L	ENST00000382592	NM_014572.2	516	cCg/cTg	4/8	0.12908242572598	1	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	FALSE	0	0.12908242572598	1		736	186	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396796	396796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	15	862	0	ENST00000262320.3:c.230C>T	p.Ser77Phe	p.S77F	ENST00000262320	NM_003502.3	77	tCc/tTc	2/11	1	2	FACETS	0.833	0.609	1	0.833	0.609	1	CLONAL	1	FALSE	1	0.12908242572598	2		862	279	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910779	32910779	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	17	670	0	ENST00000380152.3:c.2287C>T	p.His763Tyr	p.H763Y	ENST00000380152		763	Cat/Tat	11/27	0.12908242572598	1	FACETS	0.913	0.687	1	1	0.922	1	CLONAL	2	FALSE	0	0.12908242572598	1		670	135	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250268	133250268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	26	774	0	ENST00000320574.5:c.1252C>T	p.Pro418Ser	p.P418S	ENST00000320574	NM_006231.2	418	Cct/Tct	13/49	1	2	FACETS	0.846	0.673	1	1	0.943	1	CLONAL	2	FALSE	1	0.12908242572598	2		774	238	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102033237	102033237	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	31	716	0	ENST00000282441.5:c.623C>T	p.Ser208Phe	p.S208F	ENST00000282441	NM_001130145.2	208	tCc/tTc	3/9	1	2	FACETS	0.79	0.641	0.958	1	0.946	1	CLONAL	2	FALSE	1	0.12908242572598	2		716	304	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021756	71021756	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	18	712	0	ENST00000318789.4:c.1602G>A	p.Trp534Ter	p.W534*	ENST00000318789	NM_032682.5	534	tgG/tgA	18/21	1	2	FACETS	1	0.798	1	1	0.798	1	CLONAL	1	FALSE	1	0.12908242572598	2		712	261	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199480	16199480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	64	662	0	ENST00000375759.3:c.253C>T	p.Pro85Ser	p.P85S	ENST00000375759	NM_015001.2	85	Ccg/Tcg	2/15	0.12908242572598	3	FACETS	1	0.914	1	1	0.975	1	CLONAL	3	FALSE	1	0.12908242572598	3		662	331	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097779	27097779	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	35	688	0	ENST00000324856.7:c.3368C>T	p.Ser1123Phe	p.S1123F	ENST00000324856	NM_006015.4	1123	tCc/tTc	12/20	0.12908242572598	3	FACETS	0.959	0.789	1	0.959	0.789	1	CLONAL	2	FALSE	1	0.12908242572598	3		688	301	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106700	27106700	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1322532917	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	32	880	0	ENST00000324856.7:c.6311C>T	p.Ser2104Phe	p.S2104F	ENST00000324856	NM_006015.4	2104	tCc/tTc	20/20	0.12908242572598	3	FACETS	1	0.923	1	0.645	0.524	0.783	CLONAL	1	FALSE	1	0.12908242572598	3		880	409	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363547	40363547	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1317819335	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	38	762	0	ENST00000397332.2:c.682C>T	p.Pro228Ser	p.P228S	ENST00000397332	NM_001033082.2	228	Ccc/Tcc	3/3	0.12908242572598	3	FACETS	1	0.889	1	1	0.889	1	CLONAL	2	FALSE	1	0.12908242572598	3		762	286	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623571	43623571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775583354	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	20	603	0	ENST00000355710.3:c.3199C>T	p.Pro1067Ser	p.P1067S	ENST00000355710	NM_020975.4	1067	Ccg/Tcg	20/20	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	FALSE	1	0.12908242572598	2		603	229	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003696	57003696	+	stop_gained,NMD_transcript_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	15	810	0	ENST00000257254.3:c.783G>A	p.Trp261Ter	p.W261*	ENST00000257254		261	tgG/tgA	1/2	1	2	FACETS	1	0.794	1	1	0.794	1	CLONAL	1	FALSE	1	0.12908242572598	2		810	211	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94224088	94224088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753346527	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	14	464	0	ENST00000323929.3:c.64C>T	p.His22Tyr	p.H22Y	ENST00000323929	NM_005591.3	22	Cat/Tat	3/20	1	2	FACETS	0.828	0.603	1	1	0.897	1	CLONAL	2	FALSE	1	0.12908242572598	2		464	131	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201786	102201786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	15	660	0	ENST00000263464.3:c.1138C>T	p.Pro380Ser	p.P380S	ENST00000263464	NM_001165.4	380	Cct/Tct	6/9	1	2	FACETS	0.88	0.644	1	0.88	0.644	1	CLONAL	1	FALSE	1	0.12908242572598	2		660	264	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199878	108199878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	11	569	0	ENST00000278616.4:c.7220C>T	p.Ser2407Leu	p.S2407L	ENST00000278616	NM_000051.3	2407	tCa/tTa	49/63	1	2	FACETS	1	0.751	1	1	0.751	1	CLONAL	1	FALSE	1	0.12908242572598	2		569	155	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245031	46245031	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	19	866	0	ENST00000334344.6:c.3125C>T	p.Pro1042Leu	p.P1042L	ENST00000334344	NM_152641.2	1042	cCt/cTt	15/21	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	FALSE	1	0.12908242572598	2		866	231	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416804	121416804	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	32	810	0	ENST00000257555.6:c.233G>A	p.Gly78Glu	p.G78E	ENST00000257555		78	gGg/gAg	1/10	1	2	FACETS	0.901	0.735	1	1	0.956	1	CLONAL	2	FALSE	1	0.12908242572598	2		810	275	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891717	28891717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	14	663	0	ENST00000282397.4:c.3304G>A	p.Gly1102Arg	p.G1102R	ENST00000282397	NM_002019.4	1102	Gga/Aga	25/30	0.12908242572598	1	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	FALSE	0	0.12908242572598	1		663	148	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971337	15971338	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	22	717	0	ENST00000268712.3:c.4611_4612delinsAA	p.Val1538Met	p.V1538M	ENST00000268712	NM_006311.3	1537	ggGGtg/ggAAtg	32/46	0.12908242572598	3	FACETS	1	0.845	1	0.56	0.434	0.706	CLONAL	1	FALSE	1	0.12908242572598	3		717	324	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15978961	15978961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	19	670	0	ENST00000268712.3:c.3557C>T	p.Ser1186Phe	p.S1186F	ENST00000268712	NM_006311.3	1186	tCc/tTc	27/46	0.12908242572598	3	FACETS	1	0.813	1	0.542	0.411	0.696	CLONAL	1	FALSE	1	0.12908242572598	3		670	289	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546050	29546050	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	13	642	0	ENST00000356175.3:c.1555C>T	p.Gln519Ter	p.Q519*	ENST00000356175	NM_000267.3	519	Caa/Taa	14/57	0.12908242572598	3	FACETS	1	0.751	1	0.528	0.377	0.712	CLONAL	1	FALSE	1	0.12908242572598	3		642	203	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663722	29663722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1026776734	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	19	606	0	ENST00000356175.3:c.6154C>T	p.Leu2052Phe	p.L2052F	ENST00000356175	NM_000267.3	2052	Ctt/Ttt	41/57	0.12908242572598	3	FACETS	0.944	0.721	1	0.944	0.721	1	CLONAL	2	FALSE	1	0.12908242572598	3		606	166	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663923	29663923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	23	519	0	ENST00000356175.3:c.6355C>T	p.His2119Tyr	p.H2119Y	ENST00000356175	NM_000267.3	2119	Cat/Tat	41/57	0.12908242572598	3	FACETS	0.884	0.697	1	1	0.909	1	CLONAL	3	FALSE	1	0.12908242572598	3		519	143	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6230582	6230582	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	17	664	0	ENST00000252674.7:c.419G>A	p.Gly140Glu	p.G140E	ENST00000252674	NM_005934.3	140	gGg/gAg	4/12	0.12908242572598	4	FACETS	1	0.88	1	0.673	0.503	0.873	CLONAL	1	FALSE	2	0.12908242572598	4		664	221	SUCCESS
ALK	238	MSKCC	GRCh37	2	29420463	29420463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	17	656	0	ENST00000389048.3:c.4018G>A	p.Glu1340Lys	p.E1340K	ENST00000389048	NM_004304.4	1340	Gag/Aag	27/29	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	FALSE	1	0.12908242572598	2		656	212	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095857	178095857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	23	737	0	ENST00000397062.3:c.1474G>A	p.Glu492Lys	p.E492K	ENST00000397062	NM_006164.4	492	Gaa/Aaa	5/5	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	FALSE	1	0.12908242572598	2		737	259	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958200	54958201	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	15	614	0	ENST00000312783.6:c.406_407delinsAA	p.Gly136Asn	p.G136N	ENST00000312783	NM_198436.1	136	GGt/AAt	6/10	1	2	FACETS	0.785	0.578	1	1	0.896	1	CLONAL	2	FALSE	1	0.12908242572598	2		614	148	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764344	39764345	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	22	622	0	ENST00000288319.7:c.767_768delinsAA	p.Arg256Lys	p.R256K	ENST00000288319	NM_182918.3	256	aGG/aAA	7/10	0.12908242572598	1	FACETS	1	0.82	1	1	0.82	1	CLONAL	1	FALSE	0	0.12908242572598	1		622	299	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21304080	21304080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	11	608	0	ENST00000354336.3:c.859C>T	p.Pro287Ser	p.P287S	ENST00000354336	NM_005207.3	287	Ccc/Tcc	3/3	1	2	FACETS	1	0.718	1	1	0.718	1	CLONAL	1	FALSE	1	0.12908242572598	2		608	164	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22153383	22153383	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	27	643	0	ENST00000215832.6:c.527C>T	p.Pro176Leu	p.P176L	ENST00000215832	NM_002745.4	176	cCa/cTa	4/9	1	2	FACETS	0.833	0.666	1	1	0.943	1	CLONAL	2	FALSE	1	0.12908242572598	2		643	251	SUCCESS
ALB	213	MSKCC	GRCh37	4	74270067	74270067	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1445148767	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	10	529	0	ENST00000295897.4:c.23C>T	p.Ser8Phe	p.S8F	ENST00000295897	NM_000477.5	8	tCc/tTc	1/15	1	2	FACETS	1	0.785	1	1	0.785	1	CLONAL	1	FALSE	1	0.12908242572598	2		529	127	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564296	86564296	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769821061	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	17	833	0	ENST00000274376.6:c.28G>A	p.Glu10Lys	p.E10K	ENST00000274376	NM_002890.2	10	Gag/Aag	1/25	1	2	FACETS	0.987	0.737	1	0.987	0.737	1	CLONAL	1	FALSE	1	0.12908242572598	2		833	267	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31939880	31939880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	32	843	0	ENST00000375333.2:c.107C>T	p.Thr36Ile	p.T36I	ENST00000375333	NM_032454.1	36	aCc/aTc	1/8	0.12908242572598	13	FACETS	0.892	0.724	1	0.297	0.241	0.361	CLONAL	2	FALSE	7	0.12908242572598	13		843	475	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120325	94120326	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	14	706	0	ENST00000369303.4:c.725_726insA	p.Glu243GlyfsTer35	p.E243Gfs*35	ENST00000369303	NM_004440.3	242	gcg/gcAg	3/17	1	2	FACETS	0.847	0.612	1	0.847	0.612	1	CLONAL	1	FALSE	1	0.12908242572598	2		706	256	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536250	106536250	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	30	677	0	ENST00000369096.4:c.217G>A	p.Gly73Ser	p.G73S	ENST00000369096	NM_001198.3	73	Ggc/Agc	2/7	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	FALSE	1	0.12908242572598	2		677	410	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38137168	38137168	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	17	633	0	ENST00000317025.8:c.3650A>T	p.Asn1217Ile	p.N1217I	ENST00000317025	NM_023034.1	1217	aAt/aTt	21/24	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	FALSE	1	0.12908242572598	2		633	212	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146031	38146032	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	17	664	1	ENST00000317025.8:c.3474_3475delinsTT	p.Leu1159Phe	p.L1159F	ENST00000317025	NM_023034.1	1158	ggCCtc/ggTTtc	19/24	1	2	FACETS	0.979	0.731	1	0.979	0.731	1	CLONAL	1	FALSE	1	0.12908242572598	2		665	269	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040983	47040983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556779506	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	21	401	0	ENST00000377604.3:c.1513C>T	p.Pro505Ser	p.P505S	ENST00000377604	NM_001204468.1	505	Cct/Tct	14/24	1	1	FACETS	0.906	0.703	1	1	0.936	1	CLONAL	2	FALSE	0	0.12908242572598	1		401	168	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019553	123019553	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058698-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	11	261	0	ENST00000355640.3:c.41C>G	p.Pro14Arg	p.P14R	ENST00000355640		14	cCt/cGt	2/7	1	1	FACETS	0.844	0.595	1	1	0.909	1	CLONAL	3	FALSE	0	0.12908242572598	1		261	63	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0058699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	15	192	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.543	0.396	0.721	0.543	0.396	0.721	SUBCLONAL	1	TRUE	1	0.16	2		192	345	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0058699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	8	206	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.311	0.199	0.456	0.311	0.199	0.456	SUBCLONAL	1	TRUE	1	0.16	2		206	322	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0058699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	29	603	0	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	1	2	FACETS	0.747	0.599	0.917	0.747	0.599	0.917	CLONAL	1	TRUE	1	0.16	2		603	485	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0058699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	16	393	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	1	2	FACETS	0.563	0.415	0.741	0.563	0.415	0.741	SUBCLONAL	1	TRUE	1	0.16	2		393	355	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591145	67591145	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	21	208	0	ENST00000274335.5:c.1738T>G	p.Tyr580Asp	p.Y580D	ENST00000274335		580	Tac/Gac	12/15	1	2	FACETS	0.875	0.674	1	0.875	0.674	1	CLONAL	1	TRUE	1	0.16	2		208	300	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624265	89624267	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs1114167625	NA	P-0058699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	18	144	0	ENST00000371953.3:c.39_41del	p.Arg15del	p.R15del	ENST00000371953	NM_000314.4	13	aaAAGg/aag	1/9	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.16	2		144	171	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690810	89690810	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058699-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	23	105	0	ENST00000371953.3:c.217del	p.Glu73LysfsTer26	p.E73Kfs*26	ENST00000371953	NM_000314.4	73	Gaa/aa	4/9	1	2	FACETS	0.761	0.597	0.947	1	0.926	1	CLONAL	2	TRUE	1	0.16	2		105	189	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0058700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	127	409	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.887	0.811	0.966	0.887	0.811	0.966	CLONAL	1	TRUE	1	0.69	2		409	415	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0058700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	115	366	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.69	2		366	319	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913396	NA	P-0058700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	212	760	0	ENST00000349496.5:c.95A>C	p.Asp32Ala	p.D32A	ENST00000349496	NM_001904.3	32	gAc/gCc	3/15	1	2	FACETS	0.924	0.863	0.987	0.924	0.863	0.987	CLONAL	1	TRUE	1	0.69	2		760	665	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466022	69466022	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	248	1003	0	ENST00000227507.2:c.860C>G	p.Pro287Arg	p.P287R	ENST00000227507	NM_053056.2	287	cCc/cGc	5/5	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.69	2		1003	703	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849456	68849456	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	174	772	0	ENST00000261769.5:c.1359C>A	p.His453Gln	p.H453Q	ENST00000261769	NM_004360.3	453	caC/caA	10/16	1	2	FACETS	0.864	0.799	0.93	0.864	0.799	0.93	CLONAL	1	TRUE	1	0.69	2		772	584	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057788	27057788	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	251	984	0	ENST00000324856.7:c.1496C>A	p.Ser499Ter	p.S499*	ENST00000324856	NM_006015.4	499	tCg/tAg	3/20	1	2	FACETS	0.951	0.893	1	0.951	0.893	1	CLONAL	1	TRUE	1	0.69	2		984	765	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099478	27099478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	181	711	2	ENST00000324856.7:c.3715G>T	p.Ala1239Ser	p.A1239S	ENST00000324856	NM_006015.4	1239	Gct/Tct	14/20	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.69	2		713	522	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505488	157505488	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554231865	NA	P-0058700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	153	745	0	ENST00000346085.5:c.3469G>T	p.Glu1157Ter	p.E1157*	ENST00000346085	NM_020732.3	1157	Gaa/Taa	13/20	1	2	FACETS	0.792	0.728	0.858	0.792	0.728	0.858	SUBCLONAL	1	TRUE	1	0.69	2		745	560	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932602	39932602	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058700-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	212	1015	0	ENST00000378444.4:c.1997T>C	p.Ile666Thr	p.I666T	ENST00000378444	NM_001123385.1	666	aTt/aCt	4/15	1	2	FACETS	0.893	0.833	0.954	0.893	0.833	0.954	CLONAL	1	TRUE	1	0.69	2		1015	688	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601893	43601893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057521089	NA	P-0058701-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	17	811	0	ENST00000355710.3:c.937C>T	p.Arg313Trp	p.R313W	ENST00000355710	NM_020975.4	313	Cgg/Tgg	5/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		811	318	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134514501	134514502	+	protein_altering_variant	In_Frame_Ins	INS	-	-	AGG	novel	NA	P-0058701-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	92	562	0	ENST00000398015.3:c.28_29insAGG	p.Leu10delinsGlnVal	p.L10delinsQV	ENST00000398015	NM_004441.4	10	ctc/cAGGtc	1/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		562	220	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891489	76891489	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058701-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	66	264	0	ENST00000373344.5:c.4616T>C	p.Leu1539Ser	p.L1539S	ENST00000373344	NM_000489.3	1539	tTa/tCa	16/35	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		264	92	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913343	NA	P-0058702-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	57	567	0	ENST00000269305.4:c.817C>G	p.Arg273Gly	p.R273G	ENST00000269305	NM_001126112.2	273	Cgt/Ggt	8/11	0.341440530767846	1	FACETS	0.678	0.584	0.779	0.678	0.584	0.779	SUBCLONAL	1	TRUE	0	0.378548010194965	1		567	360	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422005	47422005	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058702-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	31	695	0	ENST00000404338.3:c.73G>A	p.Glu25Lys	p.E25K	ENST00000404338	NM_004491.4	25	Gag/Aag	1/6	0.371853185034876	1	FACETS	0.353	0.286	0.43	0.353	0.286	0.43	SUBCLONAL	1	TRUE	0	0.378548010194965	1		695	376	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858119	152858119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370810560	NA	P-0058702-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	29	718	0	ENST00000406277.2:c.496G>A	p.Val166Ile	p.V166I	ENST00000406277	NM_152274.4	166	Gtc/Atc	6/7	0.364220308418701	1	FACETS	0.376	0.302	0.46	0.376	0.302	0.46	SUBCLONAL	1	TRUE	0	0.378548010194965	1		718	330	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0058703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	39	403	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.958	0.816	1	0.958	0.816	1	CLONAL	1	TRUE	1	0.726585670519768	2		403	112	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0058703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	217	535	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.489710281373678	1	FACETS	0.912	0.861	0.963	0.912	0.861	0.963	CLONAL	1	TRUE	0	0.726585670519768	1		535	417	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0058703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	85	261	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.725880711761198	2	FACETS	0.991	0.922	1	0.991	0.922	1	CLONAL	2	TRUE	0	0.726585670519768	2		261	118	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578247	7578247	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0058703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	230	717	0	ENST00000269305.4:c.602T>A	p.Leu201Ter	p.L201*	ENST00000269305	NM_001126112.2	201	tTg/tAg	6/11	0.715954821929985	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.726585670519768	1		717	395	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371722	55371722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	231	737	0	ENST00000297316.4:c.412C>T	p.Arg138Trp	p.R138W	ENST00000297316	NM_022454.3	138	Cgg/Tgg	2/2	0.726585670519768	3	FACETS	1	0.971	1	0.534	0.499	0.57	CLONAL	1	TRUE	1	0.726585670519768	3		737	812	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099098	27099098	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	516	720	0	ENST00000324856.7:c.3514C>T	p.Gln1172Ter	p.Q1172*	ENST00000324856	NM_006015.4	1172	Cag/Tag	13/20	0.726585670519768	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.726585670519768	2		720	696	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528585	89528587	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs748710353	NA	P-0058703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	148	512	0	ENST00000336596.2:c.2891_2893del	p.Lys964del	p.K964del	ENST00000336596	NM_005233.5	962	cAGAag/cag	17/17	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.726585670519768	2		512	404	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434325	49434325	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	324	742	1	ENST00000301067.7:c.7228C>T	p.Arg2410Ter	p.R2410*	ENST00000301067	NM_003482.3	2410	Cga/Tga	31/54	0.207398510827495	3	FACETS	0.785	0.746	0.825	0.785	0.746	0.825	INDETERMINATE	2	TRUE	1	0.726585670519768	3		743	774	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117875371	117875377	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GGCCGAA	GGCCGAA	-	novel	NA	P-0058703-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	165	406	0	ENST00000297338.2:c.266_272del	p.Phe89Ter	p.F89*	ENST00000297338	NM_006265.2	89	tTTCGGCCa/ta	3/14	0.726585670519768	5	FACETS	1	0.984	1	0.854	0.803	0.903	CLONAL	3	TRUE	1	0.726585670519768	5		406	278	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	253	302	0				ENST00000310581	NM_198253.2	-/1132			0.304824983363803	6	FACETS	0.916	0.864	0.968	0.916	0.864	0.968	CLONAL	5	TRUE	1	0.29	6		302	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	175	725	0	ENST00000269305.4:c.166G>T	p.Glu56Ter	p.E56*	ENST00000269305	NM_001126112.2	56	Gaa/Taa	4/11	0.304824983363803	2	FACETS	0.937	0.867	1	0.937	0.867	1	CLONAL	2	TRUE	0	0.29	2		725	644	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465997	69465997	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	509	777	0	ENST00000227507.2:c.835G>T	p.Glu279Ter	p.E279*	ENST00000227507	NM_053056.2	279	Gag/Tag	5/5	0.304824983363803	5	FACETS	0.94	0.904	0.976			1	CLONAL	5	TRUE	NA	0.29	5		777	1072	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144711	119144711	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	54	512	0	ENST00000264033.4:c.724G>C	p.Asp242His	p.D242H	ENST00000264033	NM_005188.3	242	Gac/Cac	4/16	0.226894850742766	3	FACETS	0.808	0.69	0.936	0.404	0.345	0.468	CLONAL	1	TRUE	1	0.29	3		512	528	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906476	32906476	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	64	414	0	ENST00000380152.3:c.861G>C	p.Met287Ile	p.M287I	ENST00000380152		287	atG/atC	10/27	0.206042652607077	4	FACETS	1	0.891	1			1	CLONAL	1	TRUE	NA	0.29	4		414	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	201	718	0	ENST00000269305.4:c.511G>C	p.Glu171Gln	p.E171Q	ENST00000269305	NM_001126112.2	171	Gag/Cag	5/11	0.304824983363803	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	0	0.29	2		718	686	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	224	536	0	ENST00000269571.5:c.829G>C	p.Asp277His	p.D277H	ENST00000269571		277	Gac/Cac	7/27	0.304824983363803	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.29	3		536	804	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866689	37866689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149210045	NA	P-0058704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	221	737	0	ENST00000269571.5:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269571		286	Gag/Aag	7/27	0.304824983363803	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.29	3		737	772	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100110	11100110	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	189	644	0	ENST00000358026.2:c.1237del	p.Gln413ArgfsTer88	p.Q413Rfs*88	ENST00000358026	NM_001128849.1	412	ttC/tt	7/36	0.304824983363803	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.29	2		644	563	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442579	52442579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1312611941	NA	P-0058704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	113	638	2	ENST00000460680.1:c.166C>T	p.Arg56Cys	p.R56C	ENST00000460680	NM_004656.3	56	Cgc/Tgc	4/17	0.226894850742766	3	FACETS	1	0.976	1	0.638	0.575	0.705	CLONAL	1	TRUE	1	0.29	3		640	699	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748048	41748048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	48	373	0	ENST00000226382.2:c.721G>A	p.Ala241Thr	p.A241T	ENST00000226382	NM_003924.3	241	Gca/Aca	3/3	1	2	FACETS	0.971	0.824	1	0.971	0.824	1	CLONAL	1	TRUE	1	0.29	2		373	341	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120222	94120222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	54	662	0	ENST00000369303.4:c.829G>A	p.Glu277Lys	p.E277K	ENST00000369303	NM_004440.3	277	Gaa/Aaa	3/17	1	2	FACETS	0.522	0.445	0.607	0.522	0.445	0.607	SUBCLONAL	1	TRUE	1	0.29	2		662	713	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528270	157528270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058704-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	90	727	0	ENST00000346085.5:c.5995G>A	p.Glu1999Lys	p.E1999K	ENST00000346085	NM_020732.3	1999	Gag/Aag	20/20	1	2	FACETS	0.862	0.765	0.966	0.862	0.765	0.966	CLONAL	1	TRUE	1	0.29	2		727	720	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0058705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	106	947	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.598879516304895	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.598879516304895	1		947	226	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426574	49426574	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	128	1126	0	ENST00000301067.7:c.11914C>T	p.Gln3972Ter	p.Q3972*	ENST00000301067	NM_003482.3	3972	Cag/Tag	39/54	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.598879516304895	2		1126	368	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39647463	39647463	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	110	505	0	ENST00000262039.4:c.2635C>A	p.His879Asn	p.H879N	ENST00000262039	NM_002647.2	879	Cac/Aac	24/25	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.598879516304895	2		505	351	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549350	187549350	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	92	749	0	ENST00000441802.2:c.4768G>T	p.Asp1590Tyr	p.D1590Y	ENST00000441802	NM_005245.3	1590	Gac/Tac	9/27	0.598879516304895	1	FACETS	0.965	0.875	1	0.965	0.875	1	CLONAL	1	TRUE	0	0.598879516304895	1		749	223	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286804	33286804	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	129	890	0	ENST00000374542.5:c.2133T>G	p.His711Gln	p.H711Q	ENST00000374542	NM_001141970.1	711	caT/caG	7/8	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.598879516304895	2		890	380	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381517	81381517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058705-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	42	371	0	ENST00000222390.5:c.544G>A	p.Gly182Arg	p.G182R	ENST00000222390	NM_000601.4	182	Ggg/Agg	5/18	1	2	FACETS	0.417	0.349	0.492	0.417	0.349	0.492	SUBCLONAL	1	TRUE	1	0.598879516304895	2		371	336	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806092	1806092	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913484	NA	P-0058706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	169	632	0	ENST00000260795.2:c.1111A>T	p.Ser371Cys	p.S371C	ENST00000260795		371	Agt/Tgt	8/17	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.599187611075985	2		632	387	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961104	55961104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371148535	NA	P-0058706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	153	484	0	ENST00000263923.4:c.2836C>T	p.Arg946Cys	p.R946C	ENST00000263923	NM_002253.2	946	Cgt/Tgt	21/30	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.599187611075985	2		484	360	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982990	201982990	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	217	767	0	ENST00000359651.3:c.839G>C	p.Arg280Pro	p.R280P	ENST00000359651		280	cGg/cCg	7/8	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.599187611075985	2		767	505	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427002	49427035	+	frameshift_variant	Frame_Shift_Del	DEL	ATAAGCACCTGTCTGTGAGGGCCCTGGGGGCCCA	ATAAGCACCTGTCTGTGAGGGCCCTGGGGGCCCA	-	novel	NA	P-0058706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	168	756	0	ENST00000301067.7:c.11453_11486del	p.Leu3818Ter	p.L3818*	ENST00000301067	NM_003482.3	3818	tTGGGCCCCCAGGGCCCTCACAGACAGGTGCTTATg/tg	39/54	0.256828432320674	3	FACETS	0.893	0.831	0.956	0.893	0.831	0.956	INDETERMINATE	2	TRUE	1	0.599187611075985	3		756	408	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978898	25978899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	20	412	0	ENST00000435504.4:c.1024dup	p.Arg342LysfsTer6	p.R342Kfs*6	ENST00000435504		342	aga/aAga	10/13	1	2	FACETS	0.171	0.13	0.219	0.171	0.13	0.219	SUBCLONAL	1	TRUE	1	0.599187611075985	2		412	391	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44527576	44527576	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	134	595	0	ENST00000291552.4:c.29G>C	p.Gly10Ala	p.G10A	ENST00000291552	NM_006758.2	10	gGc/gCc	1/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.599187611075985	2		595	362	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820638	44820639	+	splice_donor_variant	Splice_Site	DEL	GT	GT	-	novel	NA	P-0058706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	131	200	0	ENST00000377967.4:c.334+1_334+2del		p.X112_splice	ENST00000377967	NM_021140.2	112			1	1	FACETS	1	0.959	1	1	0.993	1	CLONAL	2	TRUE	0	0.599187611075985	1		200	153	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200205	123200208	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GATT	GATT	-	novel	NA	P-0058706-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	165	222	0	ENST00000218089.9:c.2185_2188del		p.X729_splice	ENST00000218089	NM_001042749.1	729		23/35	1	1	FACETS	0.999	0.962	1	1	0.995	1	CLONAL	2	TRUE	0	0.599187611075985	1		222	193	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0058707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	69	366	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.336750893182301	4	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	2	0.352605639762333	4		366	231	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0058707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	133	695	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.345280276661977	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	2	TRUE	0	0.352605639762333	2		695	377	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	66	488	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	0.352605639762333	3	FACETS	0.77	0.674	0.871	0.77	0.674	0.871	SUBCLONAL	2	TRUE	1	0.352605639762333	3		488	286	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028656	12028656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	66	449	0	ENST00000353533.5:c.859C>T	p.Arg287Cys	p.R287C	ENST00000353533	NM_003010.3	287	Cgc/Tgc	8/11	0.345280276661977	2	FACETS	0.793	0.698	0.894	0.793	0.698	0.894	SUBCLONAL	2	TRUE	0	0.352605639762333	2		449	236	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670128	86670128	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058707-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	44	384	0	ENST00000274376.6:c.1925T>C	p.Phe642Ser	p.F642S	ENST00000274376	NM_002890.2	642	tTt/tCt	14/25	0.344502254452365	3	FACETS	0.935	0.798	1	0.935	0.798	1	CLONAL	2	TRUE	1	0.352605639762333	3		384	157	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879853	44879853	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0058708-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	154	403	0	ENST00000377967.4:c.444-2A>C		p.X148_splice	ENST00000377967	NM_021140.2	148			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		403	413	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519985	NA	P-0058709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	40	755	0	ENST00000269305.4:c.857A>G	p.Glu286Gly	p.E286G	ENST00000269305	NM_001126112.2	286	gAa/gGa	8/11	1	2	FACETS	0.431	0.357	0.514	0.431	0.357	0.514	SUBCLONAL	1	TRUE	1	0.29	2		755	640	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469122	25469122	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058709-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	42	717	0	ENST00000264709.3:c.1336G>C	p.Ala446Pro	p.A446P	ENST00000264709	NM_175629.2	446	Gct/Cct	11/23	0.117734287065645	3	FACETS	0.479	0.398	0.568	0.239	0.199	0.284	INDETERMINATE	1	TRUE	1	0.29	3		717	693	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0058710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	410	632	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.651238678207437	2	FACETS	0.988	0.953	1	0.988	0.953	1	CLONAL	2	TRUE	0	0.651238678207437	2		632	637	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254791	16254791	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	323	530	1	ENST00000375759.3:c.2056G>T	p.Asp686Tyr	p.D686Y	ENST00000375759	NM_015001.2	686	Gat/Tat	11/15	0.597357793238315	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.651238678207437	4		531	775	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614789	23614789	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	65	341	0	ENST00000261584.4:c.3552C>G	p.His1184Gln	p.H1184Q	ENST00000261584	NM_024675.3	1184	caC/caG	13/13	0.651238678207437	3	FACETS	0.723	0.63	0.823	0.362	0.315	0.412	SUBCLONAL	1	TRUE	1	0.651238678207437	3		341	366	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906786	50906786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778843530	NA	P-0058710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	361	595	0	ENST00000440232.2:c.1174G>A	p.Val392Met	p.V392M	ENST00000440232	NM_002691.3	392	Gtg/Atg	10/27	0.651238678207437	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.651238678207437	3		595	712	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266142	+	inframe_deletion	In_Frame_Del	DEL	CTCTGA	CTCTGA	-	novel	NA	P-0058710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	411	537	0	ENST00000349496.5:c.134_139del	p.Ser45_Ser47delinsCys	p.S45_S47delinsC	ENST00000349496	NM_001904.3	45	tCTCTGAgt/tgt	3/15	0.651238678207437	3	FACETS	0.957	0.926	0.987	0.957	0.926	0.987	CLONAL	3	TRUE	0	0.651238678207437	3		537	583	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2949752	2949752	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058710-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	271	528	0	ENST00000396946.4:c.3192G>T	p.Leu1064Phe	p.L1064F	ENST00000396946	NM_032415.4	1064	ttG/ttT	24/25	0.597357793238315	4	FACETS	0.986	0.931	1	0.986	0.931	1	CLONAL	2	TRUE	2	0.651238678207437	4		528	697	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063630	67063631	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058717-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	55	442	0	ENST00000412916.2:c.81dup	p.Lys28Ter	p.K28*	ENST00000412916		27	att/aTtt	2/6	0.303854289852781	1	FACETS	0.971	0.846	1	1	0.978	1	CLONAL	2	TRUE	0	0.28	1		442	174	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844173	68844178	+	frameshift_variant	Frame_Shift_Del	DEL	ATCAGA	ATCAGA	C	novel	NA	P-0058717-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	66	445	0	ENST00000261769.5:c.761_766delinsC	p.Asp254AlafsTer2	p.D254Afs*2	ENST00000261769	NM_004360.3	254	gATCAGAat/gCat	6/16	0.303854289852781	1	FACETS	1	0.886	1	1	0.982	1	CLONAL	2	TRUE	0	0.28	1		445	202	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0058719-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	465	695	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.751484293923305	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.751484293923305	2		695	544	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508080	106508080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058719-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	142	384	0	ENST00000359195.3:c.74C>T	p.Pro25Leu	p.P25L	ENST00000359195	NM_002649.2	25	cCg/cTg	2/11	0.751484293923305	3	FACETS	1	0.934	1	0.511	0.468	0.555	CLONAL	1	TRUE	1	0.751484293923305	3		384	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0058722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	88	303	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.191383107578172	2	FACETS	0.84	0.748	0.938	0.84	0.748	0.938	CLONAL	2	TRUE	0	0.241306332542231	2		303	434	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0058722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	119	362	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.238681117310679	2	FACETS	0.986	0.895	1	0.986	0.895	1	CLONAL	2	TRUE	0	0.241306332542231	2		362	500	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393576	139393576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774262180	NA	P-0058722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	113	431	0	ENST00000277541.6:c.6070G>A	p.Val2024Ile	p.V2024I	ENST00000277541	NM_017617.3	2024	Gta/Ata	32/34	0.241306332542231	2	FACETS	0.935	0.845	1	0.935	0.845	1	CLONAL	2	TRUE	0	0.241306332542231	2		431	501	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467661	66467661	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058722-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	51	421	0	ENST00000273854.3:c.608G>T	p.Gly203Val	p.G203V	ENST00000273854	NM_004439.5	203	gGa/gTa	3/18	1	2	FACETS	0.913	0.777	1	0.913	0.777	1	CLONAL	1	TRUE	1	0.241306332542231	2		421	463	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0058732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	205	341	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.584059626115093	4	FACETS	0.979	0.935	1	0.979	0.935	1	CLONAL	4	TRUE	0	0.584059626115093	4		341	284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0058732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	315	308	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.579970690831046	4	FACETS	0.964	0.929	0.999	0.964	0.929	0.999	CLONAL	4	TRUE	0	0.584059626115093	4		308	443	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424520	47424520	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058732-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	241	657	0	ENST00000404338.3:c.2588G>C	p.Arg863Pro	p.R863P	ENST00000404338	NM_004491.4	863	cGt/cCt	1/6	0.506753161956528	5	FACETS	0.954	0.9	1	0.954	0.9	1	CLONAL	3	TRUE	2	0.584059626115093	5		657	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058735-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	43	661	0	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	1	2	FACETS	0.551	0.46	0.652	0.551	0.46	0.652	SUBCLONAL	1	TRUE	1	0.26	2		661	600	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	72	575	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	1	2	FACETS	0.983	0.861	1	0.983	0.861	1	CLONAL	1	TRUE	1	0.307796303717876	2		575	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0058736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	72	523	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.307796303717876	1	FACETS	0.884	0.775	1	0.884	0.775	1	CLONAL	1	TRUE	0	0.307796303717876	1		523	448	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604569	43604569	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs906695652	NA	P-0058736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	71	593	0	ENST00000355710.3:c.1154G>A	p.Gly385Glu	p.G385E	ENST00000355710	NM_020975.4	385	gGa/gAa	6/20	1	2	FACETS	0.961	0.841	1	0.961	0.841	1	CLONAL	1	TRUE	1	0.307796303717876	2		593	480	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440084	49440084	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	73	608	0	ENST00000301067.7:c.4542C>A	p.Tyr1514Ter	p.Y1514*	ENST00000301067	NM_003482.3	1514	taC/taA	16/54	0.223585037587803	3	FACETS	1	0.929	1	0.544	0.477	0.616	CLONAL	1	TRUE	1	0.307796303717876	3		608	503	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050827	5050827	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs375180351	NA	P-0058736-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	35	390	2	ENST00000381652.3:c.610A>G	p.Ile204Val	p.I204V	ENST00000381652	NM_004972.3	204	Atc/Gtc	6/25	1	2	FACETS	0.849	0.699	1	0.849	0.699	1	CLONAL	1	TRUE	1	0.307796303717876	2		392	268	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0058737-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	40	411	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.193515249756609	5	FACETS	1	0.912	1	1	0.912	1	CLONAL	2	FALSE	3	0.193515249756609	5		411	234	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0058737-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	36	397	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.193515249756609	4	FACETS	0.835	0.69	0.995	0.835	0.69	0.995	CLONAL	2	FALSE	2	0.193515249756609	4		397	266	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0058737-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	36	547	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.193515249756609	5	FACETS	1	0.851	1	0.515	0.426	0.613	CLONAL	2	FALSE	1	0.193515249756609	5		547	233	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575191	48575191	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058737-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	33	277	0	ENST00000342988.3:c.385A>C	p.Asn129His	p.N129H	ENST00000342988	NM_005359.5	129	Aat/Cat	3/12	0.193515249756609	2	FACETS	0.974	0.803	1	0.974	0.803	1	CLONAL	2	FALSE	0	0.193515249756609	2		277	175	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428276	47428276	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058737-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	20	338	0	ENST00000377045.4:c.1236G>C	p.Gln412His	p.Q412H	ENST00000377045	NM_001654.4	412	caG/caC	11/16	0.193515249756609	2	FACETS	0.915	0.71	1			1	CLONAL	2	FALSE	NA	0.193515249756609	2		338	113	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522515	157522519	+	missense_variant	Missense_Mutation	ONP	CACCC	CACCC	GTGCA	novel	NA	P-0058737-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	33	689	1	ENST00000346085.5:c.4787_4791delinsGTGCA	p.Pro1596_Pro1597delinsArgAla	p.P1596_P1597delinsRA	ENST00000346085	NM_020732.3	1596	cCACCC/cGTGCA	18/20	0.193515249756609	3	FACETS	1	0.888	1	0.563	0.46	0.68	CLONAL	1	FALSE	1	0.193515249756609	3		690	332	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0058738-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	453	393	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	0.226430153193811	9	FACETS	1	0.981	1			1	CLONAL	9	TRUE	NA	0.226430153193811	9		393	776	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0058739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	77	508	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.44	2		508	344	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258042	123258042	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519798	NA	P-0058739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	87	403	0	ENST00000358487.5:c.1639A>G	p.Ile547Val	p.I547V	ENST00000358487	NM_000141.4	547	Atc/Gtc	12/18	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.44	2		403	367	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685305	89685306	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0058739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	20	171	0	ENST00000371953.3:c.201dup	p.Tyr68IlefsTer6	p.Y68Ifs*6	ENST00000371953	NM_000314.4	67	ata/atAa	3/9	1	2	FACETS	0.812	0.63	1	0.812	0.63	1	CLONAL	1	TRUE	1	0.44	2		171	112	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560464	95560464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	128	572	0	ENST00000393063.1:c.5125G>A	p.Asp1709Asn	p.D1709N	ENST00000393063	NM_030621.3	1709	Gat/Aat	25/28	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.44	2		572	582	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572453	95572453	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	86	494	0	ENST00000393063.1:c.2912A>G	p.Tyr971Cys	p.Y971C	ENST00000393063	NM_030621.3	971	tAt/tGt	19/28	1	2	FACETS	0.88	0.783	0.984	0.88	0.783	0.984	CLONAL	1	TRUE	1	0.44	2		494	444	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144146	11144146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058739-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	17	628	0	ENST00000358026.2:c.3727C>T	p.Arg1243Trp	p.R1243W	ENST00000358026	NM_001128849.1	1243	Cgg/Tgg	26/36	1	2	FACETS	0.122	0.09	0.16	0.122	0.09	0.16	SUBCLONAL	1	TRUE	1	0.44	2		628	634	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0058740-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	569	265	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.604416227664805	7	FACETS	1	0.983	1	1	0.983	1	CLONAL	6	TRUE	1	0.604416227664805	7		265	778	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0058740-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	120	265	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.932	0.848	1	0.932	0.848	1	CLONAL	1	TRUE	1	0.604416227664805	2		265	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs886039483	NA	P-0058740-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	205	564	0	ENST00000269305.4:c.376T>G	p.Tyr126Asp	p.Y126D	ENST00000269305	NM_001126112.2	126	Tac/Gac	5/11	0.604416227664805	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.604416227664805	1		564	398	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248519	212248519	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754829537	NA	P-0058740-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	219	735	0	ENST00000342788.4:c.3748C>T	p.Arg1250Trp	p.R1250W	ENST00000342788	NM_005235.2	1250	Cgg/Tgg	28/28	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.604416227664805	2		735	702	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206933	162206933	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777074432	NA	P-0058740-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	160	565	0	ENST00000366898.1:c.742G>A	p.Val248Ile	p.V248I	ENST00000366898	NM_004562.2	248	Gtc/Atc	7/12	1	2	FACETS	0.975	0.899	1	0.975	0.899	1	CLONAL	1	TRUE	1	0.604416227664805	2		565	543	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0058741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	194	695	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.644882849007973	4	FACETS	0.982	0.917	1	0.982	0.917	1	CLONAL	2	TRUE	2	0.64923551309395	4		695	502	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240058	41240069	+	inframe_deletion	In_Frame_Del	DEL	CCGCCGCCGCCA	CCGCCGCCGCCA	-	rs1368861222	NA	P-0058741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	22	350	0	ENST00000379561.5:c.281_292del	p.Val94_Ala97del	p.V94_A97del	ENST00000379561	NM_002015.3	94	gTGGCGGCGGCGGcc/gcc	1/3	0.644284600086242	3	FACETS	0.602	0.471	0.751	0.301	0.235	0.376	SUBCLONAL	1	TRUE	1	0.64923551309395	3		350	149	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917489	178917489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754044428	NA	P-0058741-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	69	347	0	ENST00000263967.3:c.364G>A	p.Gly122Ser	p.G122S	ENST00000263967	NM_006218.2	122	Ggc/Agc	3/21	0.64923551309395	5	FACETS	1	0.938	1	0.725	0.643	0.809	CLONAL	2	TRUE	2	0.64923551309395	5		347	193	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0058742-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	107	420	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.242582383089233	1	FACETS	0.927	0.842	1	1	0.988	1	CLONAL	2	TRUE	0	0.313931615001673	1		420	310	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0058742-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	85	598	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	0.313931615001673	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.313931615001673	1		598	407	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245976	5245976	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058742-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	57	675	2	ENST00000357368.4:c.799G>A	p.Val267Met	p.V267M	ENST00000357368	NM_002850.3	267	Gtg/Atg	10/38	1	2	FACETS	0.65	0.557	0.75	0.65	0.557	0.75	SUBCLONAL	1	TRUE	1	0.313931615001673	2		677	559	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249510	153249510	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1157879635	NA	P-0058742-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	56	442	0	ENST00000281708.4:c.1268G>T	p.Gly423Val	p.G423V	ENST00000281708	NM_033632.3	423	gGa/gTa	9/12	1	2	FACETS	0.919	0.791	1	0.919	0.791	1	CLONAL	1	TRUE	1	0.313931615001673	2		442	388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863224683	NA	P-0058742-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	243	600	0	ENST00000269305.4:c.388C>T	p.Leu130Phe	p.L130F	ENST00000269305	NM_001126112.2	130	Ctc/Ttc	5/11	0.313931615001673	3	FACETS	0.901	0.852	0.95	1	0.99	1	CLONAL	4	TRUE	0	0.313931615001673	3		600	497	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200616	67200616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201207505	NA	P-0058742-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	45	680	0	ENST00000312629.5:c.727C>T	p.Arg243Cys	p.R243C	ENST00000312629	NM_003952.2	243	Cgc/Tgc	9/15	1	2	FACETS	0.575	0.483	0.676	0.575	0.483	0.676	SUBCLONAL	1	TRUE	1	0.313931615001673	2		680	499	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0058766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	54	259	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.365136782986174	3	FACETS	1	0.893	1	0.686	0.597	0.779	CLONAL	2	TRUE	0	0.365136782986174	3		259	170	SUCCESS
APC	324	MSKCC	GRCh37	5	112175328	112175328	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0058766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	129	338	0	ENST00000257430.4:c.4037C>G	p.Ser1346Ter	p.S1346*	ENST00000257430	NM_000038.5	1346	tCa/tGa	16/16	0.279615425112566	3	FACETS	0.893	0.815	0.973	0.893	0.815	0.973	CLONAL	2	TRUE	1	0.365136782986174	3		338	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0058766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	162	350	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.280047236027073	3	FACETS	1	0.984	1	0.823	0.763	0.884	CLONAL	2	TRUE	0	0.365136782986174	3		350	425	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0058766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	36	261	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	0.167063912287994	3	FACETS	0.956	0.791	1	0.478	0.395	0.569	INDETERMINATE	1	TRUE	1	0.365136782986174	3		261	244	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274043	10274043	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1236030143	NA	P-0058766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	154	443	0	ENST00000330684.3:c.226C>T	p.Arg76Cys	p.R76C	ENST00000330684	NM_001134407.1	76	Cgc/Tgc	2/13	0.36165322105878	4	FACETS	0.949	0.872	1	0.632	0.581	0.686	CLONAL	2	TRUE	1	0.365136782986174	4		443	607	SUCCESS
APC	324	MSKCC	GRCh37	5	112174677	112174678	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0058766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	61	379	0	ENST00000257430.4:c.3389_3390del	p.Cys1130SerfsTer4	p.C1130Sfs*4	ENST00000257430	NM_000038.5	1129	tTG/t	16/16	0.279615425112566	3	FACETS	1	0.898	1	0.521	0.452	0.596	CLONAL	1	TRUE	1	0.365136782986174	3		379	379	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661369	227661369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	31	486	0	ENST00000305123.5:c.2086G>A	p.Gly696Arg	p.G696R	ENST00000305123	NM_005544.2	696	Gga/Aga	1/2	0.365136782986174	3	FACETS	0.398	0.321	0.485	0.133	0.107	0.162	SUBCLONAL	1	TRUE	0	0.365136782986174	3		486	505	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374739	149374739	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058766-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	72	356	0	ENST00000360632.3:c.355G>A	p.Asp119Asn	p.D119N	ENST00000360632	NM_015472.4	119	Gac/Aac	2/7	0.365136782986174	3	FACETS	1	0.89	1	0.339	0.297	0.384	CLONAL	1	TRUE	0	0.365136782986174	3		356	459	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0058767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	63	408	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.686	0.594	0.785	0.686	0.594	0.785	SUBCLONAL	1	TRUE	1	0.350745158244307	2		408	524	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0058767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	197	528	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.127357423395067	3	FACETS	0.907	0.842	0.973	0.907	0.842	0.973	INDETERMINATE	2	TRUE	1	0.350745158244307	3		528	728	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127484	55127484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs538480165	NA	P-0058767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	107	384	0	ENST00000257290.5:c.272C>T	p.Ser91Leu	p.S91L	ENST00000257290	NM_006206.4	91	tCg/tTg	3/23	1	2	FACETS	0.987	0.887	1	0.987	0.887	1	CLONAL	1	TRUE	1	0.350745158244307	2		384	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	231	447	0	ENST00000269305.4:c.991del	p.Gln331ArgfsTer14	p.Q331Rfs*14	ENST00000269305	NM_001126112.2	331	Cag/ag	9/11	0.270281382789908	3	FACETS	1	0.988	1	0.811	0.761	0.863	CLONAL	2	TRUE	0	0.350745158244307	3		447	636	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525140	9525140	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	66	318	0	ENST00000353224.5:c.1745T>A	p.Ile582Lys	p.I582K	ENST00000353224	NM_177990.2	582	aTa/aAa	8/10	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.350745158244307	2		318	344	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178943821	178943821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	63	218	0	ENST00000263967.3:c.2488G>A	p.Asp830Asn	p.D830N	ENST00000263967	NM_006218.2	830	Gat/Aat	17/21	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.350745158244307	2		218	320	SUCCESS
APC	324	MSKCC	GRCh37	5	112164619	112164625	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGTTG	GAAGTTG	-	novel	NA	P-0058767-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	48	315	0	ENST00000257430.4:c.1698_1704del	p.Gly567Ter	p.G567*	ENST00000257430	NM_000038.5	565	GAAGTTGga/ga	14/16	1	2	FACETS	0.653	0.553	0.763	0.653	0.553	0.763	SUBCLONAL	1	TRUE	1	0.350745158244307	2		315	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579426	7579426	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058768-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	57	598	0	ENST00000269305.4:c.261del	p.Ala88ProfsTer35	p.A88Pfs*35	ENST00000269305	NM_001126112.2	87	ccA/cc	4/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		598	919	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0058769-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	239	535	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.922213608813273	2		535	515	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692991	89692991	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786202688	NA	P-0058769-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	320	355	0	ENST00000371953.3:c.475A>G	p.Arg159Gly	p.R159G	ENST00000371953	NM_000314.4	159	Agg/Ggg	5/9	0.922213608813273	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.922213608813273	2		355	334	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913400	NA	P-0058769-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	274	471	0	ENST00000349496.5:c.98C>A	p.Ser33Tyr	p.S33Y	ENST00000349496	NM_001904.3	33	tCt/tAt	3/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.922213608813273	2		471	565	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557879	187557879	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767041778	NA	P-0058769-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	316	544	1	ENST00000441802.2:c.3832G>A	p.Asp1278Asn	p.D1278N	ENST00000441802	NM_005245.3	1278	Gac/Aac	5/27	1	2	FACETS	0.983	0.935	1	0.983	0.935	1	CLONAL	1	TRUE	1	0.922213608813273	2		545	697	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589620	67589640	+	inframe_deletion	In_Frame_Del	DEL	AGAATATGATAGATTATATGA	AGAATATGATAGATTATATGA	-	novel	NA	P-0058769-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	112	277	0	ENST00000274335.5:c.1390_1410del	p.Asp464_Tyr470del	p.D464_Y470del	ENST00000274335		461	cgAGAATATGATAGATTATATGAa/cga	10/15	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.922213608813273	2		277	239	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593290	67593290	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058769-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	225	481	0	ENST00000274335.5:c.2036A>C	p.Tyr679Ser	p.Y679S	ENST00000274335		679	tAt/tCt	15/15	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.922213608813273	2		481	484	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828921	72828921	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058769-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	315	569	0	ENST00000268489.5:c.7660del	p.Leu2554Ter	p.L2554*	ENST00000268489	NM_006885.3	2554	Ctg/tg	9/10	1	2	FACETS	0.932	0.885	0.979	0.932	0.885	0.979	CLONAL	1	TRUE	1	0.922213608813273	2		569	733	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841808	151841809	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	ACCGTGCCAGATACACATTGGATTTCCATTCAGT	novel	NA	P-0058769-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	145	444	0	ENST00000262189.6:c.14299_14332dup	p.Ser4778TyrfsTer2	p.S4778Yfs*2	ENST00000262189	NM_170606.2	4778	tct/tACTGAATGGAAATCCAATGTGTATCTGGCACGGTct	55/59	1	2	FACETS	0.588	0.539	0.638	0.588	0.539	0.638	SUBCLONAL	1	TRUE	1	0.922213608813273	2		444	535	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	34	302	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.727	0.593	0.879	0.727	0.593	0.879	SUBCLONAL	1	TRUE	1	0.17	2		302	550	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0058770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	52	538	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	0.93	0.79	1	0.93	0.79	1	CLONAL	1	TRUE	1	0.17	2		538	658	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	58	130	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	1	1	FACETS	0.964	0.833	1	1	0.977	1	CLONAL	2	TRUE	0	0.17	1		130	324	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105820	27105844	+	frameshift_variant	Frame_Shift_Del	DEL	AAGCTTCCAGTAAAGATCGTACAGA	AAGCTTCCAGTAAAGATCGTACAGA	-	novel	NA	P-0058770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	57	565	0	ENST00000324856.7:c.5432_5456del	p.Lys1811ArgfsTer64	p.K1811Rfs*64	ENST00000324856	NM_006015.4	1811	AAGCTTCCAGTAAAGATCGTACAGAag/ag	20/20	1	2	FACETS	0.978	0.838	1	0.978	0.838	1	CLONAL	1	TRUE	1	0.17	2		565	686	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846327	156846327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	45	570	0	ENST00000524377.1:c.1768G>A	p.Glu590Lys	p.E590K	ENST00000524377	NM_002529.3	590	Gag/Aag	14/17	1	2	FACETS	0.757	0.635	0.893	0.757	0.635	0.893	SUBCLONAL	1	TRUE	1	0.17	2		570	699	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577418	64577418	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	51	587	0	ENST00000312049.6:c.164C>G	p.Pro55Arg	p.P55R	ENST00000312049	NM_130799.2	55	cCt/cGt	2/10	1	2	FACETS	0.849	0.72	0.991	0.849	0.72	0.991	CLONAL	1	TRUE	1	0.17	2		587	707	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047235	77047235	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	46	501	0	ENST00000356341.3:c.1309A>G	p.Thr437Ala	p.T437A	ENST00000356341	NM_002576.4	437	Aca/Gca	13/15	1	2	FACETS	0.77	0.647	0.906	0.77	0.647	0.906	CLONAL	1	TRUE	1	0.17	2		501	703	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230590	46230590	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	44	449	0	ENST00000334344.6:c.839A>C	p.Asp280Ala	p.D280A	ENST00000334344	NM_152641.2	280	gAt/gCt	8/21	1	2	FACETS	0.979	0.82	1	0.979	0.82	1	CLONAL	1	TRUE	1	0.17	2		449	529	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254641	46254641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	42	367	0	ENST00000334344.6:c.4831C>T	p.Gln1611Ter	p.Q1611*	ENST00000334344	NM_152641.2	1611	Cag/Tag	16/21	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.17	2		367	474	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447070	49447070	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	45	527	0	ENST00000301067.7:c.874G>A	p.Glu292Lys	p.E292K	ENST00000301067	NM_003482.3	292	Gag/Aag	7/54	1	2	FACETS	0.76	0.637	0.896	0.76	0.637	0.896	SUBCLONAL	1	TRUE	1	0.17	2		527	697	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	45	506	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	1	2	FACETS	0.888	0.746	1	0.888	0.746	1	CLONAL	1	TRUE	1	0.17	2		506	596	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915096	32915096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	33	393	0	ENST00000380152.3:c.6604G>A	p.Asp2202Asn	p.D2202N	ENST00000380152		2202	Gat/Aat	11/27	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.17	2		393	346	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041388	42041388	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	39	505	0	ENST00000219905.7:c.5583C>G	p.Phe1861Leu	p.F1861L	ENST00000219905	NM_001164273.1	1861	ttC/ttG	17/24	1	2	FACETS	0.685	0.566	0.818	0.685	0.566	0.818	SUBCLONAL	1	TRUE	1	0.17	2		505	670	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50776529	50776529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	15	315	0	ENST00000307179.4:c.1861G>A	p.Glu621Lys	p.E621K	ENST00000307179		621	Gag/Aag	12/20	1	2	FACETS	0.639	0.467	0.847	0.639	0.467	0.847	SUBCLONAL	1	TRUE	1	0.17	2		315	276	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	47	401	0	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.17	2		401	546	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957141	81957141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778927156	NA	P-0058770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	50	431	0	ENST00000359376.3:c.2359G>A	p.Glu787Lys	p.E787K	ENST00000359376	NM_002661.3	787	Gag/Aag	22/33	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.17	2		431	563	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298685	15298713	+	splice_donor_variant,splice_donor_5th_base_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCCTCACCCTCGGCACAGCGGCACTCGTA	GCCTCACCCTCGGCACAGCGGCACTCGTA	CCGCTGT	novel	NA	P-0058770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	37	542	2	ENST00000263388.2:c.1585_1606+7delinsACAGCGG		p.X529_splice	ENST00000263388	NM_000435.2	529		10/33	1	2	FACETS	0.656	0.539	0.787	0.656	0.539	0.787	SUBCLONAL	1	TRUE	1	0.17	2		544	664	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860629	45860629	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	55	652	0	ENST00000391945.4:c.1378A>G	p.Thr460Ala	p.T460A	ENST00000391945	NM_000400.3	460	Aca/Gca	15/23	1	2	FACETS	0.741	0.632	0.861	0.741	0.632	0.861	SUBCLONAL	1	TRUE	1	0.17	2		652	873	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423805	47423805	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	35	487	0	ENST00000404338.3:c.1874del	p.Lys625SerfsTer3	p.K625Sfs*3	ENST00000404338	NM_004491.4	625	Aag/ag	1/6	1	2	FACETS	0.685	0.56	0.826	0.685	0.56	0.826	SUBCLONAL	1	TRUE	1	0.17	2		487	601	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519886	NA	P-0058770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	36	403	0	ENST00000349496.5:c.97T>G	p.Ser33Ala	p.S33A	ENST00000349496	NM_001904.3	33	Tct/Gct	3/15	1	2	FACETS	0.681	0.558	0.819	0.681	0.558	0.819	SUBCLONAL	1	TRUE	1	0.17	2		403	622	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400006	49400006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	27	430	1	ENST00000418115.1:c.331C>T	p.Pro111Ser	p.P111S	ENST00000418115	NM_001664.2	111	Ccc/Tcc	4/5	1	2	FACETS	0.609	0.483	0.753	0.609	0.483	0.753	SUBCLONAL	1	TRUE	1	0.17	2		431	522	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890306	72890306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	32	371	0	ENST00000325599.8:c.376G>A	p.Asp126Asn	p.D126N	ENST00000325599	NM_018130.2	126	Gat/Aat	4/11	1	2	FACETS	0.856	0.694	1	0.856	0.694	1	CLONAL	1	TRUE	1	0.17	2		371	440	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045902	143045902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	32	392	0	ENST00000262992.4:c.1732G>A	p.Glu578Lys	p.E578K	ENST00000262992	NM_001101669.1	578	Gaa/Aaa	17/24	1	2	FACETS	0.745	0.604	0.906	0.745	0.604	0.906	CLONAL	1	TRUE	1	0.17	2		392	505	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247280	153247280	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	37	451	0	ENST00000281708.4:c.1522C>T	p.Gln508Ter	p.Q508*	ENST00000281708	NM_033632.3	508	Caa/Taa	10/12	1	2	FACETS	0.721	0.593	0.864	0.721	0.593	0.864	SUBCLONAL	1	TRUE	1	0.17	2		451	604	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131972841	131972841	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	33	188	0	ENST00000265335.6:c.3424G>C	p.Glu1142Gln	p.E1142Q	ENST00000265335		1142	Gaa/Caa	22/25	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.17	2		188	275	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382236	152382236	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	21	314	0	ENST00000206249.3:c.1346A>G	p.Lys449Arg	p.K449R	ENST00000206249	NM_000125.3	449	aAa/aGa	6/8	1	2	FACETS	0.63	0.484	0.801	0.63	0.484	0.801	SUBCLONAL	1	TRUE	1	0.17	2		314	392	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739611	41739611	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	30	281	0	ENST00000242208.4:c.362C>T	p.Ser121Leu	p.S121L	ENST00000242208	NM_002192.2	121	tCg/tTg	2/3	1	2	FACETS	0.914	0.737	1	0.914	0.737	1	CLONAL	1	TRUE	1	0.17	2		281	386	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128305425	128305425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058770-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	34	353	0	ENST00000265960.3:c.871C>T	p.Leu291Phe	p.L291F	ENST00000265960	NM_001006617.1	291	Ctt/Ttt	7/12	1	2	FACETS	0.903	0.738	1	0.903	0.738	1	CLONAL	1	TRUE	1	0.17	2		353	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0058775-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	130	495	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.439966069045806	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.439966069045806	1		495	439	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259442	55259442	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397517127	NA	P-0058775-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	279	438	0	ENST00000275493.2:c.2500G>C	p.Val834Leu	p.V834L	ENST00000275493	NM_005228.3	834	Gtg/Ctg	21/28	0.439966069045806	4	FACETS	0.938	0.888	0.989	0.938	0.888	0.989	CLONAL	3	TRUE	1	0.439966069045806	4		438	649	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259514	55259515	+	missense_variant	Missense_Mutation	DNP	CT	CT	AG	rs1057519847	NA	P-0058775-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	288	408	0	ENST00000275493.2:c.2572_2573inv	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	CTg/AGg	21/28	0.439966069045806	4	FACETS	1	0.951	1	1	0.951	1	CLONAL	3	TRUE	1	0.439966069045806	4		408	627	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047173	77047173	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058775-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	120	531	0	ENST00000356341.3:c.1371G>C	p.Met457Ile	p.M457I	ENST00000356341	NM_002576.4	457	atG/atC	13/15	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.439966069045806	2		531	537	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821646	72821646	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058775-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	75	568	0	ENST00000268489.5:c.10529G>T	p.Gly3510Val	p.G3510V	ENST00000268489	NM_006885.3	3510	gGc/gTc	10/10	0.184002381426947	1	FACETS	0.477	0.419	0.54	0.477	0.419	0.54	INDETERMINATE	1	TRUE	0	0.439966069045806	1		568	557	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132309	7132309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058775-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	113	452	0	ENST00000302850.5:c.2702C>T	p.Ser901Phe	p.S901F	ENST00000302850	NM_000208.2	901	tCc/tTc	14/22	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.439966069045806	2		452	511	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311687	30311687	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058775-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	73	330	1	ENST00000262643.3:c.541G>T	p.Glu181Ter	p.E181*	ENST00000262643	NM_001238.2	181	Gaa/Taa	7/12	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.439966069045806	2		331	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0058777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	316	358	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.903785955204431	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.903785955204431	1		358	345	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030368	49030368	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	329	241	1	ENST00000267163.4:c.1848del	p.Gly617ValfsTer6	p.G617Vfs*6	ENST00000267163	NM_000321.2	615	Aaa/aa	19/27	0.903785955204431	2	FACETS	0.966	0.942	0.987	0.966	0.942	0.987	CLONAL	2	TRUE	0	0.903785955204431	2		242	377	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751901	57751901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148954251	NA	P-0058777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	72	352	0	ENST00000274289.3:c.1336C>T	p.Arg446Trp	p.R446W	ENST00000274289	NM_006622.3	446	Cgg/Tgg	10/14	0.873232680980838	2	FACETS	0.293	0.256	0.333	0.146	0.128	0.167	SUBCLONAL	1	TRUE	0	0.903785955204431	2		352	544	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280131	66280131	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	42	323	0	ENST00000273854.3:c.1558T>C	p.Ser520Pro	p.S520P	ENST00000273854	NM_004439.5	520	Tct/Cct	7/18	0.903785955204431	2	FACETS	0.226	0.188	0.267	0.113	0.094	0.134	SUBCLONAL	1	TRUE	0	0.903785955204431	2		323	412	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779413	3779413	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	705	510	0	ENST00000262367.5:c.5635C>T	p.Gln1879Ter	p.Q1879*	ENST00000262367	NM_004380.2	1879	Cag/Tag	31/31	0.278952924698373	5	FACETS	0.858	0.83	0.885	0.858	0.83	0.885	INDETERMINATE	3	TRUE	2	0.903785955204431	5		510	1428	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743865	40743865	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	60	290	0	ENST00000373198.4:c.3130G>C	p.Val1044Leu	p.V1044L	ENST00000373198	NM_133170.3	1044	Gtc/Ctc	23/32	0.525607191784405	3	FACETS	0.258	0.222	0.298	0.129	0.111	0.149	INDETERMINATE	1	TRUE	1	0.903785955204431	3		290	747	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825309	134825309	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	151	390	0	ENST00000398015.3:c.825C>G	p.Phe275Leu	p.F275L	ENST00000398015	NM_004441.4	275	ttC/ttG	4/16	0.885771171467359	3	FACETS	0.475	0.433	0.518	0.237	0.216	0.259	SUBCLONAL	1	TRUE	1	0.903785955204431	3		390	1022	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922616	56922616	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs527508795	NA	P-0058777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	201	416	0	ENST00000519728.1:c.1486G>A	p.Val496Ile	p.V496I	ENST00000519728	NM_002350.3	496	Gtc/Atc	13/13	0.885771171467359	3	FACETS	0.606	0.561	0.652	0.303	0.28	0.326	SUBCLONAL	1	TRUE	1	0.903785955204431	3		416	1066	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344108	70344108	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	464	380	0	ENST00000374080.3:c.1844C>G	p.Thr615Ser	p.T615S	ENST00000374080		615	aCt/aGt	13/45	0.629007616078088	3	FACETS	0.929	0.896	0.963	0.929	0.896	0.963	CLONAL	2	TRUE	1	0.903785955204431	3		380	802	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242482	+	protein_altering_variant	In_Frame_Del	DEL	GAATTAAGAGAAGCAAC	GAATTAAGAGAAGCAAC	TT	novel	NA	P-0058777-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	567	297	1	ENST00000275493.2:c.2236_2252delinsTT	p.Glu746_Thr751delinsLeu	p.E746_T751delinsL	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCAACa/TTa	19/28	0.903785955204431	3	FACETS	0.965	0.949	0.98	0.965	0.949	0.98	CLONAL	3	TRUE	0	0.903785955204431	3		298	629	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0058787-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	162	376	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.20652402205122	2	FACETS	0.808	0.743	0.877	0.808	0.743	0.877	CLONAL	2	TRUE	0	0.263684985402324	2		376	760	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417803	32417829	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CAGTGTGCTTCCTGCTGTGCATCTGTA	CAGTGTGCTTCCTGCTGTGCATCTGTA	-	novel	NA	P-0058787-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	44	267	0	ENST00000332351.3:c.1223_1249del	p.Leu408_Gly417delinsCys	p.L408_G417delinsC	ENST00000332351	NM_024426.4	408	tTACAGATGCACAGCAGGAAGCACACTGgt/tgt	7/10	0.212346231788893	3	FACETS	0.784	0.657	0.923	0.392	0.328	0.462	CLONAL	1	TRUE	1	0.263684985402324	3		267	482	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235807	108235807	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0058787-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	33	237	0	ENST00000278616.4:c.8851-2A>C		p.X2951_splice	ENST00000278616	NM_000051.3	2951			0.241719846667579	3	FACETS	0.515	0.419	0.624	0.172	0.139	0.208	SUBCLONAL	1	TRUE	0	0.263684985402324	3		237	550	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646495	23646495	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058787-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	42	274	0	ENST00000261584.4:c.1372del	p.Thr458LeufsTer27	p.T458Lfs*27	ENST00000261584	NM_024675.3	458	Act/ct	4/13	0.212346231788893	3	FACETS	0.664	0.554	0.787	0.332	0.277	0.394	SUBCLONAL	1	TRUE	1	0.263684985402324	3		274	543	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877855	151877867	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCTGAAGTTGG	CTCCTGAAGTTGG	-	novel	NA	P-0058787-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	129	301	0	ENST00000262189.6:c.7078_7090del	p.Pro2360Ter	p.P2360*	ENST00000262189	NM_170606.2	2360	CCAACTTCAGGAGta/ta	36/59	0.218600606768391	2	FACETS	0.802	0.729	0.878	0.802	0.729	0.878	CLONAL	2	TRUE	0	0.263684985402324	2		301	610	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395071	139395114	+	frameshift_variant	Frame_Shift_Del	DEL	ATGTTGGCATCTGCGCTGGCCTCCAGCAGGCGCTTGGCGGCATC	ATGTTGGCATCTGCGCTGGCCTCCAGCAGGCGCTTGGCGGCATC	-	novel	NA	P-0058787-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	82	332	0	ENST00000277541.6:c.5824_5867del	p.Asp1942ProfsTer38	p.D1942Pfs*38	ENST00000277541	NM_017617.3	1942	GATGCCGCCAAGCGCCTGCTGGAGGCCAGCGCAGATGCCAACATc/c	31/34	0.212346231788893	3	FACETS	1	0.915	1	0.523	0.461	0.589	CLONAL	1	TRUE	1	0.263684985402324	3		332	673	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0058800-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	294	411	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.526018380283841	4	FACETS	0.99	0.942	1	0.99	0.942	1	CLONAL	3	TRUE	1	0.525461050494179	4		411	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0058800-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	203	495	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.471270176468702	2	FACETS	0.886	0.832	0.94	0.886	0.832	0.94	CLONAL	2	TRUE	0	0.525461050494179	2		495	436	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175951	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1392778905	NA	P-0058800-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	164	289	0	ENST00000257430.4:c.4660G>T	p.Glu1554Ter	p.E1554*	ENST00000257430	NM_000038.5	1554	Gaa/Taa	16/16	0.480693601017814	3	FACETS	0.927	0.861	0.995	0.927	0.861	0.995	CLONAL	2	TRUE	1	0.525461050494179	3		289	425	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274899	41274899	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058800-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	92	235	0	ENST00000349496.5:c.1149G>T	p.Trp383Cys	p.W383C	ENST00000349496	NM_001904.3	383	tgG/tgT	8/15	0.480693601017814	3	FACETS	0.943	0.841	1	0.471	0.42	0.525	CLONAL	1	TRUE	1	0.525461050494179	3		235	469	SUCCESS
APC	324	MSKCC	GRCh37	5	112174425	112174426	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAAT	novel	NA	P-0058800-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	57	256	0	ENST00000257430.4:c.3138_3141dup	p.Arg1048Ter	p.R1048*	ENST00000257430	NM_000038.5	1045	cag/caGAATg	16/16	0.480693601017814	3	FACETS	0.685	0.589	0.788	0.342	0.294	0.394	SUBCLONAL	1	TRUE	1	0.525461050494179	3		256	400	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0058802-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	55	187	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.904	1	1	0.98	1	CLONAL	2	FALSE	1	0.382504453189549	2		188	139	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0058802-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	155	327	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.382504453189549	1	FACETS	1	0.961	1	1	0.993	1	CLONAL	2	FALSE	0	0.382504453189549	1		327	314	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217651	7217651	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058802-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	131	428	0	ENST00000380728.2:c.276del	p.Val93PhefsTer16	p.V93Ffs*16	ENST00000380728		92	aaA/aa	4/11	0.382504453189549	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	0	0.382504453189549	1		428	378	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100152	27100155	+	frameshift_variant	Frame_Shift_Del	DEL	GGGG	GGGG	-	novel	NA	P-0058802-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	159	508	0	ENST00000324856.7:c.3948_3951del	p.Gly1317CysfsTer163	p.G1317Cfs*163	ENST00000324856	NM_006015.4	1316	tcGGGG/tc	16/20	1	2	FACETS	0.813	0.751	0.878	1	0.99	1	CLONAL	2	FALSE	1	0.382504453189549	2		508	511	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161806	56161806	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0058802-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	144	198	0	ENST00000399503.3:c.1301+2T>G		p.X434_splice	ENST00000399503	NM_005921.1	434			0.331117405281762	1	FACETS	0.948	0.879	1	1	0.992	1	CLONAL	2	FALSE	0	0.382504453189549	1		198	321	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680734	88680734	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	89	263	0	ENST00000360948.2:c.523C>T	p.Gln175Ter	p.Q175*	ENST00000360948	NM_001012338.2	175	Cag/Tag	6/19	0.373314067906721	0	FACETS	1	0.956	1			1	CLONAL	1	FALSE	0	0.373314067906721	0		263	268	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16052794	16052795	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0058803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	24	119	0	ENST00000268712.3:c.879dup	p.Lys294Ter	p.K294*	ENST00000268712	NM_006311.3	293	-/T	9/46	0.373314067906721	0	FACETS	0.848	0.68	1			1	CLONAL	1	FALSE	0	0.373314067906721	0		119	95	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539134	23539135	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0058803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	75	285	0	ENST00000380871.4:c.304_305insC	p.Tyr102SerfsTer6	p.Y102Sfs*6	ENST00000380871	NM_006167.3	102	tat/tCat	2/2	0.373314067906721	1	FACETS	0.529	0.463	0.599	0.529	0.463	0.599	SUBCLONAL	1	FALSE	0	0.373314067906721	1		285	618	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820535	44820535	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058803-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	113	113	0	ENST00000377967.4:c.232del	p.Arg78AlafsTer6	p.R78Afs*6	ENST00000377967	NM_021140.2	78	Cgc/gc	3/29	0.316628476524811	2	FACETS	1	0.973	1			1	CLONAL	4	FALSE	NA	0.373314067906721	2		113	144	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0058805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	46	261	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.281931960637052	2		261	254	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711927	89711928	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554900593	NA	P-0058805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	39	250	0	ENST00000371953.3:c.548dup	p.Asn184GlufsTer6	p.N184Efs*6	ENST00000371953	NM_000314.4	182	tta/ttAa	6/9	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.281931960637052	2		250	227	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591135	67591136	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0058805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	68	279	0	ENST00000274335.5:c.1732_1733del	p.Asp578ProfsTer23	p.D578Pfs*23	ENST00000274335		576	acGAga/acga	12/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.281931960637052	2		279	358	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936127	71936137	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGCTGGCCC	GCTGCTGGCCC	-	novel	NA	P-0058805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	80	319	0	ENST00000298229.2:c.100_110del	p.Leu34GlyfsTer37	p.L34Gfs*37	ENST00000298229	NM_001567.3	33	gaGCTGCTGGCCCgg/gagg	1/28	1	2	FACETS	0.83	0.736	0.928	1	0.981	1	CLONAL	2	TRUE	1	0.281931960637052	2		319	342	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939811	71939811	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	87	408	0	ENST00000298229.2:c.438del	p.Ser147ProfsTer32	p.S147Pfs*32	ENST00000298229	NM_001567.3	146	ggC/gg	4/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.281931960637052	2		408	471	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933330	100933330	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	101	343	0	ENST00000325455.5:c.2060T>A	p.Leu687Gln	p.L687Q	ENST00000325455	NM_001202474.3	687	cTg/cAg	4/8	1	2	FACETS	0.772	0.694	0.855	1	0.983	1	SUBCLONAL	2	TRUE	1	0.281931960637052	2		343	464	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176700707	176700708	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0058805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	83	329	0	ENST00000439151.2:c.5544_5545insG	p.Lys1849GlufsTer16	p.K1849Efs*16	ENST00000439151	NM_022455.4	1848	-/G	17/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.281931960637052	2		329	434	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196843	138196843	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058805-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	30	352	0	ENST00000237289.4:c.505G>T	p.Asp169Tyr	p.D169Y	ENST00000237289	NM_001270507.1	169	Gac/Tac	4/9	1	2	FACETS	0.471	0.379	0.575	0.471	0.379	0.575	SUBCLONAL	1	TRUE	1	0.281931960637052	2		352	452	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	45	190	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.802	0.682	0.931	0.802	0.682	0.931	CLONAL	1	TRUE	1	0.547580990017577	2		190	205	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	157	468	1	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.946	0.871	1	0.946	0.871	1	CLONAL	1	TRUE	1	0.547580990017577	2		469	606	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567646	226567647	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1159330096	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	160	475	0	ENST00000366794.5:c.1519dup	p.Ser507LysfsTer14	p.S507Kfs*14	ENST00000366794	NM_001618.3	507	agc/aAgc	10/23	1	2	FACETS	0.92	0.847	0.996	0.92	0.847	0.996	CLONAL	1	TRUE	1	0.547580990017577	2		475	635	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241895	133241895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483635586	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	140	440	0	ENST00000320574.5:c.2461C>T	p.Arg821Cys	p.R821C	ENST00000320574	NM_006231.2	821	Cgc/Tgc	21/49	1	2	FACETS	0.983	0.901	1	0.983	0.901	1	CLONAL	1	TRUE	1	0.547580990017577	2		440	520	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	68	323	4	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	0.875	0.768	0.987	0.875	0.768	0.987	CLONAL	1	TRUE	1	0.547580990017577	2		327	284	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860928	45860928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143710107	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	165	464	0	ENST00000391945.4:c.1267G>A	p.Asp423Asn	p.D423N	ENST00000391945	NM_000400.3	423	Gac/Aac	13/23	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.547580990017577	2		464	597	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276316	15276316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372834264	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	141	441	0	ENST00000263388.2:c.5678G>A	p.Arg1893Gln	p.R1893Q	ENST00000263388	NM_000435.2	1893	cGa/cAa	31/33	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.547580990017577	2		441	459	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207066	1207066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	162	452	0	ENST00000326873.7:c.154G>A	p.Gly52Arg	p.G52R	ENST00000326873	NM_000455.4	52	Ggg/Agg	1/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.547580990017577	2		452	540	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17371320	17371320	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs74315370	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	139	312	0	ENST00000375499.3:c.136C>T	p.Arg46Ter	p.R46*	ENST00000375499	NM_003000.2	46	Cga/Tga	2/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.547580990017577	2		312	436	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259374	89259374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141287594	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	121	423	0	ENST00000336596.2:c.518C>T	p.Pro173Leu	p.P173L	ENST00000336596	NM_005233.5	173	cCt/cTt	3/17	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.547580990017577	2		423	399	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589168	67589168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	48	340	0	ENST00000274335.5:c.1156C>T	p.Arg386Ter	p.R386*	ENST00000274335		386	Cga/Tga	9/15	1	2	FACETS	0.724	0.618	0.839	0.724	0.618	0.839	SUBCLONAL	1	TRUE	1	0.547580990017577	2		340	242	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	141	579	1	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	0.857	0.784	0.933	0.857	0.784	0.933	CLONAL	1	TRUE	1	0.547580990017577	2		580	601	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911534	101911534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111426349	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	87	304	0	ENST00000374994.4:c.1459C>T	p.Arg487Trp	p.R487W	ENST00000374994	NM_004612.2	487	Cgg/Tgg	9/9	1	2	FACETS	0.893	0.797	0.993	0.893	0.797	0.993	CLONAL	1	TRUE	1	0.547580990017577	2		304	356	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534451	63534451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs8081536	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	170	474	0	ENST00000307078.5:c.1070G>A	p.Arg357His	p.R357H	ENST00000307078	NM_004655.3	357	cGc/cAc	5/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.547580990017577	2		474	577	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443345	187443345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	162	464	0	ENST00000232014.4:c.1781G>A	p.Arg594Gln	p.R594Q	ENST00000232014	NM_001130845.1	594	cGa/cAa	8/10	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.547580990017577	2		464	569	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038902	12038902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159945	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	137	352	0	ENST00000396373.4:c.1195C>T	p.Arg399Cys	p.R399C	ENST00000396373	NM_001987.4	399	Cgc/Tgc	7/8	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.547580990017577	2		352	499	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244091	153244091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	166	436	0	ENST00000281708.4:c.2066G>A	p.Arg689Gln	p.R689Q	ENST00000281708	NM_033632.3	689	cGg/cAg	12/12	1	2	FACETS	0.956	0.882	1	0.956	0.882	1	CLONAL	1	TRUE	1	0.547580990017577	2		436	634	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274159	10274159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	111	359	0	ENST00000330684.3:c.110C>T	p.Ala37Val	p.A37V	ENST00000330684	NM_001134407.1	37	gCg/gTg	2/13	1	2	FACETS	0.956	0.866	1	0.956	0.866	1	CLONAL	1	TRUE	1	0.547580990017577	2		359	424	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243045	105243045	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	143	458	0	ENST00000349310.3:c.238T>C	p.Trp80Arg	p.W80R	ENST00000349310	NM_001014432.1	80	Tgg/Cgg	5/15	1	2	FACETS	0.962	0.882	1	0.962	0.882	1	CLONAL	1	TRUE	1	0.547580990017577	2		458	543	SUCCESS
EED	8726	MSKCC	GRCh37	11	85979574	85979574	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1301151502	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	63	247	0	ENST00000263360.6:c.937C>T	p.Arg313Ter	p.R313*	ENST00000263360	NM_003797.3	313	Cga/Tga	9/12	1	2	FACETS	0.759	0.662	0.863	0.759	0.662	0.863	SUBCLONAL	1	TRUE	1	0.547580990017577	2		247	303	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371524413	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	164	546	0	ENST00000269305.4:c.467G>A	p.Arg156His	p.R156H	ENST00000269305	NM_001126112.2	156	cGc/cAc	5/11	1	2	FACETS	0.942	0.868	1	0.942	0.868	1	CLONAL	1	TRUE	1	0.547580990017577	2		546	636	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149450022	149450022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	118	389	0	ENST00000286301.3:c.1195C>T	p.Arg399Ter	p.R399*	ENST00000286301	NM_005211.3	399	Cga/Tga	8/22	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.547580990017577	2		389	404	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737702	145737702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137853232	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	44	580	1	ENST00000428558.2:c.3061C>T	p.Arg1021Trp	p.R1021W	ENST00000428558	NM_004260.3	1021	Cgg/Tgg	19/22	1	2	FACETS	0.242	0.202	0.286	0.242	0.202	0.286	SUBCLONAL	1	TRUE	1	0.547580990017577	2		581	665	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085972	16085972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs998174759	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	156	412	1	ENST00000281043.3:c.1148G>A	p.Arg383His	p.R383H	ENST00000281043	NM_005378.4	383	cGc/cAc	3/3	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.547580990017577	2		413	520	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52725412	52725412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770194852	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	128	478	0	ENST00000322088.6:c.1579C>T	p.Arg527Cys	p.R527C	ENST00000322088	NM_014225.5	527	Cgc/Tgc	13/15	1	2	FACETS	0.904	0.824	0.988	0.904	0.824	0.988	CLONAL	1	TRUE	1	0.547580990017577	2		478	517	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827886	40827886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201911869	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	150	375	0	ENST00000373198.4:c.2542G>A	p.Gly848Arg	p.G848R	ENST00000373198	NM_133170.3	848	Gga/Aga	17/32	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.547580990017577	2		375	489	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133761036	133761036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1456042173	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	110	400	0	ENST00000318560.5:c.3359C>T	p.Ser1120Leu	p.S1120L	ENST00000318560	NM_005157.4	1120	tCg/tTg	11/11	1	2	FACETS	0.827	0.746	0.911	0.827	0.746	0.911	CLONAL	1	TRUE	1	0.547580990017577	2		400	486	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552909	106552909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	186	482	0	ENST00000369096.4:c.874C>T	p.Pro292Ser	p.P292S	ENST00000369096	NM_001198.3	292	Ccc/Tcc	5/7	1	2	FACETS	0.998	0.925	1	0.998	0.925	1	CLONAL	1	TRUE	1	0.547580990017577	2		482	681	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020582	14020582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	69	299	0	ENST00000311895.7:c.553C>T	p.Leu185Phe	p.L185F	ENST00000311895	NM_005236.2	185	Ctt/Ttt	3/11	1	2	FACETS	0.951	0.838	1	0.951	0.838	1	CLONAL	1	TRUE	1	0.547580990017577	2		299	265	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804267	46804267	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767502912	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	144	412	0	ENST00000290295.7:c.740G>A	p.Arg247His	p.R247H	ENST00000290295	NM_006361.5	247	cGc/cAc	2/2	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.547580990017577	2		412	513	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593424	67593424	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764019194	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	133	331	0	ENST00000274335.5:c.2170C>T	p.Arg724Ter	p.R724*	ENST00000274335		724	Cga/Tga	15/15	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.547580990017577	2		331	476	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911520	134911520	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756316035	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	146	446	0	ENST00000398015.3:c.1985G>A	p.Arg662His	p.R662H	ENST00000398015	NM_004441.4	662	cGt/cAt	11/16	1	2	FACETS	0.984	0.903	1	0.984	0.903	1	CLONAL	1	TRUE	1	0.547580990017577	2		446	542	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184657	185184657	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs56408536	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	129	380	0	ENST00000265026.3:c.1549C>T	p.Arg517Ter	p.R517*	ENST00000265026	NM_004721.4	517	Cga/Tga	10/14	1	2	FACETS	0.948	0.865	1	0.948	0.865	1	CLONAL	1	TRUE	1	0.547580990017577	2		380	497	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099430	27099430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1227227387	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	134	439	0	ENST00000324856.7:c.3667C>T	p.Arg1223Cys	p.R1223C	ENST00000324856	NM_006015.4	1223	Cgc/Tgc	14/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.547580990017577	2		439	457	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105240286	105240286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369698909	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	109	348	0	ENST00000349310.3:c.665G>A	p.Arg222His	p.R222H	ENST00000349310	NM_001014432.1	222	cGc/cAc	9/15	1	2	FACETS	0.976	0.883	1	0.976	0.883	1	CLONAL	1	TRUE	1	0.547580990017577	2		348	408	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473648	67473648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223736	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	149	375	0	ENST00000327367.4:c.728G>A	p.Arg243His	p.R243H	ENST00000327367	NM_005902.3	243	cGc/cAc	6/9	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.547580990017577	2		375	536	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412946	49412946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	141	409	1	ENST00000418115.1:c.77G>A	p.Ser26Asn	p.S26N	ENST00000418115	NM_001664.2	26	aGc/aAc	2/5	0.547580990017577	2	FACETS	1	0.965	1	0.547	0.502	0.593	CLONAL	1	TRUE	0	0.547580990017577	2		410	471	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982073	38982073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	65	377	0	ENST00000357387.3:c.649G>A	p.Asp217Asn	p.D217N	ENST00000357387	NM_152756.3	217	Gat/Aat	8/38	1	2	FACETS	0.87	0.762	0.984	0.87	0.762	0.984	CLONAL	1	TRUE	1	0.547580990017577	2		377	273	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166773	32166773	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1231739465	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	146	387	0	ENST00000375023.3:c.4465C>T	p.Arg1489Ter	p.R1489*	ENST00000375023	NM_004557.3	1489	Cga/Tga	24/30	0.547580990017577	2	FACETS	0.964	0.885	1	0.482	0.442	0.524	CLONAL	1	TRUE	0	0.547580990017577	2		387	553	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511611	38511611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs899025600	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	163	411	0	ENST00000254066.5:c.1109G>A	p.Arg370His	p.R370H	ENST00000254066	NM_000964.3	370	cGc/cAc	8/9	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.547580990017577	2		411	497	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162123	47162123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1216047088	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	96	371	0	ENST00000409792.3:c.4003C>T	p.Arg1335Cys	p.R1335C	ENST00000409792	NM_014159.6	1335	Cgt/Tgt	3/21	0.547580990017577	2	FACETS	0.92	0.826	1	0.46	0.413	0.51	CLONAL	1	TRUE	0	0.547580990017577	2		371	381	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713407	40713407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768298187	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	142	523	0	ENST00000373198.4:c.4108C>T	p.Arg1370Cys	p.R1370C	ENST00000373198	NM_133170.3	1370	Cgc/Tgc	30/32	1	2	FACETS	0.955	0.875	1	0.955	0.875	1	CLONAL	1	TRUE	1	0.547580990017577	2		523	543	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033396	48033396	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	52	298	0	ENST00000234420.5:c.3700G>T	p.Glu1234Ter	p.E1234*	ENST00000234420	NM_000179.2	1234	Gaa/Taa	8/10	1	2	FACETS	0.574	0.491	0.664	0.574	0.491	0.664	SUBCLONAL	1	TRUE	1	0.547580990017577	2		298	331	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913692	32913692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786202543	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	58	323	0	ENST00000380152.3:c.5200G>A	p.Glu1734Lys	p.E1734K	ENST00000380152		1734	Gaa/Aaa	11/27	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.547580990017577	2		323	208	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740416	58740416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777279856	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	106	406	0	ENST00000305921.3:c.1321C>T	p.Arg441Cys	p.R441C	ENST00000305921	NM_003620.3	441	Cgt/Tgt	6/6	1	2	FACETS	0.838	0.755	0.925	0.838	0.755	0.925	CLONAL	1	TRUE	1	0.547580990017577	2		406	462	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340097	116340097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35776110	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	20	367	0	ENST00000397752.3:c.959C>T	p.Ala320Val	p.A320V	ENST00000397752	NM_000245.2	320	gCg/gTg	2/21	1	2	FACETS	0.206	0.157	0.264	0.206	0.157	0.264	SUBCLONAL	1	TRUE	1	0.547580990017577	2		367	354	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2116002	2116002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs281875238	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	129	389	0	ENST00000349721.2:c.3637C>T	p.Arg1213Trp	p.R1213W	ENST00000349721	NM_003070.3	1213	Cgg/Tgg	25/34	1	2	FACETS	0.922	0.841	1	0.922	0.841	1	CLONAL	1	TRUE	1	0.547580990017577	2		389	511	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779578	3779578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	171	474	0	ENST00000262367.5:c.5470G>A	p.Ala1824Thr	p.A1824T	ENST00000262367	NM_004380.2	1824	Gcc/Acc	31/31	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.547580990017577	2		474	613	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006005	22006005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	151	509	0	ENST00000276925.6:c.398G>A	p.Arg133His	p.R133H	ENST00000276925	NM_004936.3	133	cGc/cAc	2/2	1	2	FACETS	0.99	0.91	1	0.99	0.91	1	CLONAL	1	TRUE	1	0.547580990017577	2		509	557	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983877	2983877	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	134	387	0	ENST00000396946.4:c.653C>T	p.Ala218Val	p.A218V	ENST00000396946	NM_032415.4	218	gCg/gTg	5/25	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.547580990017577	2		387	451	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308419	30308419	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	96	361	0	ENST00000262643.3:c.433C>T	p.Arg145Ter	p.R145*	ENST00000262643	NM_001238.2	145	Cga/Tga	6/12	1	2	FACETS	0.781	0.699	0.867	0.781	0.699	0.867	SUBCLONAL	1	TRUE	1	0.547580990017577	2		361	449	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285669	46285669	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1368075571	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	113	372	0	ENST00000334344.6:c.5029C>T	p.Arg1677Ter	p.R1677*	ENST00000334344	NM_152641.2	1677	Cga/Tga	17/21	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.547580990017577	2		372	407	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28979946	28979946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764045713	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	45	302	0	ENST00000282397.4:c.1522C>T	p.Arg508Cys	p.R508C	ENST00000282397	NM_002019.4	508	Cgc/Tgc	11/30	1	2	FACETS	0.63	0.533	0.735	0.63	0.533	0.735	SUBCLONAL	1	TRUE	1	0.547580990017577	2		302	261	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022656	36022656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143889833	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	170	388	0	ENST00000358208.4:c.529G>A	p.Val177Met	p.V177M	ENST00000358208		177	Gtg/Atg	5/12	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.547580990017577	2		388	497	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41276095	41276095	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80356994	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	59	272	0	ENST00000357654.3:c.19C>T	p.Arg7Cys	p.R7C	ENST00000357654	NM_007294.3	7	Cgc/Tgc	2/23	1	2	FACETS	0.798	0.693	0.91	0.798	0.693	0.91	CLONAL	1	TRUE	1	0.547580990017577	2		272	270	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429758	78429758	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	66	342	0	ENST00000370768.2:c.1030C>T	p.Arg344Ter	p.R344*	ENST00000370768	NM_003902.3	344	Cga/Tga	12/20	1	2	FACETS	0.817	0.716	0.925	0.817	0.716	0.925	CLONAL	1	TRUE	1	0.547580990017577	2		342	295	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793386	242793386	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs756100729	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	147	511	0	ENST00000334409.5:c.691C>T	p.Arg231Ter	p.R231*	ENST00000334409	NM_005018.2	231	Cga/Tga	5/5	1	2	FACETS	0.898	0.823	0.975	0.898	0.823	0.975	CLONAL	1	TRUE	1	0.547580990017577	2		511	598	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750454	57750454	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	95	383	0	ENST00000274289.3:c.2014C>T	p.Arg672Ter	p.R672*	ENST00000274289	NM_006622.3	672	Cga/Tga	14/14	1	2	FACETS	0.878	0.788	0.974	0.878	0.788	0.974	CLONAL	1	TRUE	1	0.547580990017577	2		383	395	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81939065	81939065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867345397	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	126	397	0	ENST00000359376.3:c.1420G>A	p.Glu474Lys	p.E474K	ENST00000359376	NM_002661.3	474	Gaa/Aaa	15/33	1	2	FACETS	0.979	0.893	1	0.979	0.893	1	CLONAL	1	TRUE	1	0.547580990017577	2		397	470	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348223	348223	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755028316	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	185	472	1	ENST00000262320.3:c.1283C>T	p.Ser428Leu	p.S428L	ENST00000262320	NM_003502.3	428	tCg/tTg	6/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.547580990017577	2		473	585	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181425	185181425	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1435276633	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	91	289	1	ENST00000265026.3:c.1366C>T	p.Arg456Ter	p.R456*	ENST00000265026	NM_004721.4	456	Cga/Tga	8/14	1	2	FACETS	0.879	0.787	0.977	0.879	0.787	0.977	CLONAL	1	TRUE	1	0.547580990017577	2		290	378	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595622	55595622	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	61	255	0	ENST00000288135.5:c.2112G>T	p.Lys704Asn	p.K704N	ENST00000288135	NM_000222.2	704	aaG/aaT	14/21	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.547580990017577	2		255	183	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552838	106552838	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367766895	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	194	463	0	ENST00000369096.4:c.803G>A	p.Arg268His	p.R268H	ENST00000369096	NM_001198.3	268	cGt/cAt	5/7	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.547580990017577	2		463	643	SUCCESS
APC	324	MSKCC	GRCh37	5	112179788	112179788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201459013	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	122	427	0	ENST00000257430.4:c.8497C>T	p.Arg2833Cys	p.R2833C	ENST00000257430	NM_000038.5	2833	Cgc/Tgc	16/16	1	2	FACETS	0.999	0.91	1	0.999	0.91	1	CLONAL	1	TRUE	1	0.547580990017577	2		427	446	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681051	37681051	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	137	393	0	ENST00000447079.4:c.3220A>G	p.Thr1074Ala	p.T1074A	ENST00000447079	NM_015083.1	1074	Aca/Gca	12/14	1	2	FACETS	0.876	0.801	0.955	0.876	0.801	0.955	CLONAL	1	TRUE	1	0.547580990017577	2		393	571	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759832	133759832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145494071	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	111	390	0	ENST00000318560.5:c.2155G>A	p.Ala719Thr	p.A719T	ENST00000318560	NM_005157.4	719	Gcc/Acc	11/11	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.547580990017577	2		390	392	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268413	142268413	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	65	293	0	ENST00000350721.4:c.3079G>T	p.Glu1027Ter	p.E1027*	ENST00000350721	NM_001184.3	1027	Gag/Tag	15/47	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.547580990017577	2		293	205	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631701	90631701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1472765685	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	136	529	1	ENST00000330062.3:c.568G>A	p.Gly190Ser	p.G190S	ENST00000330062	NM_002168.2	190	Ggc/Agc	5/11	1	2	FACETS	0.878	0.801	0.957	0.878	0.801	0.957	CLONAL	1	TRUE	1	0.547580990017577	2		530	566	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223235	2223235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773787910	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	183	484	0	ENST00000326181.6:c.847C>T	p.Arg283Cys	p.R283C	ENST00000326181	NM_032271.2	283	Cgc/Tgc	10/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.547580990017577	2		484	585	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245501	153245501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1024060344	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	87	345	0	ENST00000281708.4:c.1690C>T	p.Arg564Cys	p.R564C	ENST00000281708	NM_033632.3	564	Cgt/Tgt	11/12	1	2	FACETS	0.85	0.758	0.946	0.85	0.758	0.946	CLONAL	1	TRUE	1	0.547580990017577	2		345	374	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146656	185146656	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145694468	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	131	373	2	ENST00000265026.3:c.287C>T	p.Ala96Val	p.A96V	ENST00000265026	NM_004721.4	96	gCg/gTg	2/14	1	2	FACETS	0.873	0.796	0.954	0.873	0.796	0.954	CLONAL	1	TRUE	1	0.547580990017577	2		375	548	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354308	354308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757610038	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	165	327	0	ENST00000262320.3:c.1250G>A	p.Arg417His	p.R417H	ENST00000262320	NM_003502.3	417	cGc/cAc	5/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.547580990017577	2		327	500	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928978	49928978	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs200454353	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	170	500	0	ENST00000296474.3:c.3388C>T	p.Arg1130Ter	p.R1130*	ENST00000296474	NM_002447.2	1130	Cga/Tga	16/20	0.547580990017577	2	FACETS	1	0.969	1	0.546	0.504	0.588	CLONAL	1	TRUE	0	0.547580990017577	2		500	569	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18958620	18958620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	112	276	0	ENST00000262803.5:c.439G>A	p.Gly147Arg	p.G147R	ENST00000262803	NM_002911.3	147	Gga/Aga	3/24	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.547580990017577	2		276	403	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100109	27100109	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	152	504	0	ENST00000324856.7:c.3905C>T	p.Thr1302Ile	p.T1302I	ENST00000324856	NM_006015.4	1302	aCt/aTt	16/20	1	2	FACETS	0.903	0.829	0.979	0.903	0.829	0.979	CLONAL	1	TRUE	1	0.547580990017577	2		504	615	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557912	21557912	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757472527	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	136	334	0	ENST00000382592.4:c.1933C>T	p.Arg645Trp	p.R645W	ENST00000382592	NM_014572.2	645	Cgg/Tgg	5/8	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.547580990017577	2		334	456	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458536	12458536	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs780238349	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	153	423	0	ENST00000287820.6:c.1153C>T	p.Arg385Ter	p.R385*	ENST00000287820	NM_015869.4	385	Cga/Tga	6/7	0.547580990017577	2	FACETS	1	0.927	1	0.504	0.464	0.546	CLONAL	1	TRUE	0	0.547580990017577	2		423	554	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182052	38182052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1190702008	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	165	495	0	ENST00000396334.3:c.676G>A	p.Glu226Lys	p.E226K	ENST00000396334	NM_002468.4	226	Gaa/Aaa	3/5	0.547580990017577	2	FACETS	1	0.972	1	0.553	0.511	0.596	CLONAL	1	TRUE	0	0.547580990017577	2		495	545	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303035	15303035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777257132	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	159	508	0	ENST00000263388.2:c.415G>A	p.Asp139Asn	p.D139N	ENST00000263388	NM_000435.2	139	Gat/Aat	4/33	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.547580990017577	2		508	560	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563419	87563419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	142	391	0	ENST00000277120.3:c.1807C>T	p.Arg603Cys	p.R603C	ENST00000277120		603	Cgt/Tgt	16/19	1	2	FACETS	0.95	0.87	1	0.95	0.87	1	CLONAL	1	TRUE	1	0.547580990017577	2		391	546	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356361	66356361	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772108237	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	25	451	1	ENST00000273854.3:c.1136C>T	p.Pro379Leu	p.P379L	ENST00000273854	NM_004439.5	379	cCg/cTg	5/18	1	2	FACETS	0.205	0.161	0.256	0.205	0.161	0.256	SUBCLONAL	1	TRUE	1	0.547580990017577	2		452	445	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223345	53223345	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	96	191	0	ENST00000375401.3:c.4014G>T	p.Glu1338Asp	p.E1338D	ENST00000375401	NM_004187.3	1338	gaG/gaT	23/26	1	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.547580990017577	1		191	191	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041084	29041084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	96	347	0	ENST00000282397.4:c.344C>T	p.Ser115Leu	p.S115L	ENST00000282397	NM_002019.4	115	tCa/tTa	3/30	1	2	FACETS	0.979	0.881	1	0.979	0.881	1	CLONAL	1	TRUE	1	0.547580990017577	2		347	358	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438018	49438018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs111266743	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	152	425	1	ENST00000301067.7:c.5153C>T	p.Ala1718Val	p.A1718V	ENST00000301067	NM_003482.3	1718	gCg/gTg	21/54	1	2	FACETS	0.944	0.867	1	0.944	0.867	1	CLONAL	1	TRUE	1	0.547580990017577	2		426	588	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396277	139396277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878855028	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	134	531	2	ENST00000277541.6:c.5561G>A	p.Arg1854His	p.R1854H	ENST00000277541	NM_017617.3	1854	cGc/cAc	30/34	1	2	FACETS	0.854	0.779	0.932	0.854	0.779	0.932	CLONAL	1	TRUE	1	0.547580990017577	2		533	573	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410472	63410472	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	123	266	0	ENST00000330258.3:c.2695G>A	p.Ala899Thr	p.A899T	ENST00000330258	NM_152424.3	899	Gca/Aca	2/2	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.547580990017577	1		266	249	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188148	108188148	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	62	266	0	ENST00000278616.4:c.6247G>T	p.Gly2083Ter	p.G2083*	ENST00000278616	NM_000051.3	2083	Gga/Tga	43/63	1	2	FACETS	0.899	0.785	1	0.899	0.785	1	CLONAL	1	TRUE	1	0.547580990017577	2		266	252	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90634844	90634844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201999104	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	142	470	0	ENST00000330062.3:c.148G>A	p.Val50Met	p.V50M	ENST00000330062	NM_002168.2	50	Gtg/Atg	2/11	1	2	FACETS	0.957	0.877	1	0.957	0.877	1	CLONAL	1	TRUE	1	0.547580990017577	2		470	542	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600336	10600336	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs751088754	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	180	467	1	ENST00000171111.5:c.1519C>T	p.Arg507Ter	p.R507*	ENST00000171111	NM_203500.1	507	Cga/Tga	4/6	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.547580990017577	2		468	580	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710693	117710693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	132	439	0	ENST00000368508.3:c.1579G>A	p.Glu527Lys	p.E527K	ENST00000368508	NM_002944.2	527	Gaa/Aaa	12/43	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.547580990017577	2		439	423	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660507	67660507	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	107	284	0	ENST00000264010.4:c.1407C>A	p.Cys469Ter	p.C469*	ENST00000264010	NM_006565.3	469	tgC/tgA	8/12	1	2	FACETS	0.92	0.831	1	0.92	0.831	1	CLONAL	1	TRUE	1	0.547580990017577	2		284	425	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964903	25964903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561088610	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	144	410	0	ENST00000435504.4:c.4303C>T	p.Arg1435Trp	p.R1435W	ENST00000435504		1435	Cgg/Tgg	13/13	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.547580990017577	2		410	524	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183551	185183551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	128	273	0	ENST00000265026.3:c.1405C>T	p.Arg469Cys	p.R469C	ENST00000265026	NM_004721.4	469	Cgt/Tgt	9/14	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.547580990017577	2		273	455	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383903	15383903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324868843	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	135	369	0	ENST00000263377.2:c.8C>T	p.Ala3Val	p.A3V	ENST00000263377	NM_058243.2	3	gCg/gTg	2/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.547580990017577	2		369	445	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808246	99808246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776434815	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	53	248	0	ENST00000280892.6:c.443G>A	p.Arg148His	p.R148H	ENST00000280892	NM_001130678.1	148	cGc/cAc	5/7	1	2	FACETS	0.756	0.651	0.869	0.756	0.651	0.869	SUBCLONAL	1	TRUE	1	0.547580990017577	2		248	256	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620051	21620051	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750829854	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	183	407	0	ENST00000382592.4:c.115G>A	p.Ala39Thr	p.A39T	ENST00000382592	NM_014572.2	39	Gca/Aca	2/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.547580990017577	2		407	537	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214367	55214367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778252	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	137	431	0	ENST00000275493.2:c.493C>T	p.Arg165Trp	p.R165W	ENST00000275493	NM_005228.3	165	Cgg/Tgg	4/28	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.547580990017577	2		431	482	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152357789	152357789	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	61	217	0	ENST00000359321.1:c.118C>T	p.His40Tyr	p.H40Y	ENST00000359321	NM_005431.1	40	Cat/Tat	2/3	1	2	FACETS	0.932	0.814	1	0.932	0.814	1	CLONAL	1	TRUE	1	0.547580990017577	2		217	239	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249728	39249728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	87	277	0	ENST00000402219.2:c.1841C>T	p.Thr614Met	p.T614M	ENST00000402219	NM_005633.3	614	aCg/aTg	10/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.547580990017577	2		277	259	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905505	11905505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774396176	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	146	353	0	ENST00000396373.4:c.155C>T	p.Ala52Val	p.A52V	ENST00000396373	NM_001987.4	52	gCg/gTg	2/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.547580990017577	2		353	475	SUCCESS
CBL	867	MSKCC	GRCh37	11	119168162	119168162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763213265	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	82	342	0	ENST00000264033.4:c.2222C>T	p.Ala741Val	p.A741V	ENST00000264033	NM_005188.3	741	gCg/gTg	14/16	1	2	FACETS	0.799	0.709	0.893	0.799	0.709	0.893	SUBCLONAL	1	TRUE	1	0.547580990017577	2		342	375	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117861199	117861199	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	67	273	0	ENST00000297338.2:c.1690C>A	p.Leu564Ile	p.L564I	ENST00000297338	NM_006265.2	564	Ctt/Att	13/14	1	2	FACETS	0.827	0.725	0.935	0.827	0.725	0.935	CLONAL	1	TRUE	1	0.547580990017577	2		273	296	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779728	3779728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	178	436	0	ENST00000262367.5:c.5320C>T	p.Arg1774Cys	p.R1774C	ENST00000262367	NM_004380.2	1774	Cgc/Tgc	31/31	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.547580990017577	2		436	558	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187560908	187560908	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	109	328	0	ENST00000441802.2:c.3610G>A	p.Asp1204Asn	p.D1204N	ENST00000441802	NM_005245.3	1204	Gac/Aac	4/27	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.547580990017577	2		328	387	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042482	16042482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	67	248	0	ENST00000268712.3:c.1192C>T	p.Arg398Trp	p.R398W	ENST00000268712	NM_006311.3	398	Cgg/Tgg	12/46	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.547580990017577	2		248	235	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739584	145739584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772515188	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	130	523	0	ENST00000428558.2:c.1867C>T	p.Arg623Cys	p.R623C	ENST00000428558	NM_004260.3	623	Cgc/Tgc	11/22	1	2	FACETS	0.893	0.814	0.975	0.893	0.814	0.975	CLONAL	1	TRUE	1	0.547580990017577	2		523	532	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770575	40770575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1294592345	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	99	394	0	ENST00000373198.4:c.2807G>A	p.Arg936Gln	p.R936Q	ENST00000373198	NM_133170.3	936	cGa/cAa	19/32	1	2	FACETS	0.888	0.799	0.982	0.888	0.799	0.982	CLONAL	1	TRUE	1	0.547580990017577	2		394	407	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500576	99500576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141802822	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	140	519	0	ENST00000268035.6:c.4009C>T	p.Arg1337Cys	p.R1337C	ENST00000268035	NM_000875.3	1337	Cgc/Tgc	21/21	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.547580990017577	2		519	506	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732626	190732626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139826569	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	60	290	0	ENST00000441310.2:c.2444C>T	p.Ala815Val	p.A815V	ENST00000441310	NM_000534.4	815	gCg/gTg	11/13	1	2	FACETS	0.887	0.773	1	0.887	0.773	1	CLONAL	1	TRUE	1	0.547580990017577	2		290	247	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433950	49433950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780306423	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	151	507	1	ENST00000301067.7:c.7603C>T	p.Arg2535Cys	p.R2535C	ENST00000301067	NM_003482.3	2535	Cgt/Tgt	31/54	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.547580990017577	2		508	541	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614469	38614469	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	52	251	0	ENST00000299084.4:c.235G>T	p.Asp79Tyr	p.D79Y	ENST00000299084	NM_152594.2	79	Gac/Tac	3/7	1	2	FACETS	0.936	0.808	1	0.936	0.808	1	CLONAL	1	TRUE	1	0.547580990017577	2		251	203	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026041	14026041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750883282	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	75	302	0	ENST00000311895.7:c.1001C>T	p.Ser334Leu	p.S334L	ENST00000311895	NM_005236.2	334	tCg/tTg	6/11	1	2	FACETS	0.801	0.707	0.9	0.801	0.707	0.9	CLONAL	1	TRUE	1	0.547580990017577	2		302	342	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074433	39074433	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	103	355	0	ENST00000357387.3:c.47G>A	p.Arg16Gln	p.R16Q	ENST00000357387	NM_152756.3	16	cGa/cAa	1/38	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.547580990017577	2		355	326	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367969	15367969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759001252	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	130	361	1	ENST00000263377.2:c.1357C>T	p.Arg453Cys	p.R453C	ENST00000263377	NM_058243.2	453	Cgc/Tgc	8/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.547580990017577	2		362	458	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467760	99467760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs150221450	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	126	388	0	ENST00000268035.6:c.2629C>T	p.Arg877Ter	p.R877*	ENST00000268035	NM_000875.3	877	Cga/Tga	13/21	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.547580990017577	2		388	444	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807167	1807167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751635116	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	157	514	0	ENST00000260795.2:c.1498G>A	p.Ala500Thr	p.A500T	ENST00000260795		500	Gcc/Acc	10/17	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.547580990017577	2		514	551	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100645	8100645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1218595084	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	131	581	0	ENST00000346208.3:c.619G>A	p.Ala207Thr	p.A207T	ENST00000346208		207	Gcc/Acc	3/6	1	2	FACETS	0.901	0.822	0.984	0.901	0.822	0.984	CLONAL	1	TRUE	1	0.547580990017577	2		581	531	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480624	50480624	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	148	452	1	ENST00000394963.4:c.494G>A	p.Arg165Gln	p.R165Q	ENST00000394963	NM_003076.4	165	cGg/cAg	4/13	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.547580990017577	2		453	514	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31381401	31381401	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs201681031	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	67	205	0	ENST00000328111.2:c.1126G>A	p.Glu376Lys	p.E376K	ENST00000328111	NM_006892.3	376	Gag/Aag	10/23	1	2	FACETS	0.927	0.815	1	0.927	0.815	1	CLONAL	1	TRUE	1	0.547580990017577	2		205	264	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50816324	50816324	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	67	321	0	ENST00000398568.2:c.1764G>T	p.Lys588Asn	p.K588N	ENST00000398568	NM_001042412.1	588	aaG/aaT	10/18	1	2	FACETS	0.827	0.725	0.935	0.827	0.725	0.935	CLONAL	1	TRUE	1	0.547580990017577	2		321	296	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699295	117699295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773228516	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	133	347	1	ENST00000369458.3:c.346C>T	p.Arg116Trp	p.R116W	ENST00000369458	NM_024626.3	116	Cgg/Tgg	3/6	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.547580990017577	2		348	465	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121040	29121040	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876659804	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	78	317	0	ENST00000328354.6:c.517G>A	p.Glu173Lys	p.E173K	ENST00000328354	NM_007194.3	173	Gag/Aag	4/15	1	2	FACETS	0.928	0.823	1	0.928	0.823	1	CLONAL	1	TRUE	1	0.547580990017577	2		317	307	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977555	2977555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349696922	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	70	316	0	ENST00000396946.4:c.1129C>T	p.Arg377Trp	p.R377W	ENST00000396946	NM_032415.4	377	Cgg/Tgg	8/25	1	2	FACETS	0.94	0.829	1	0.94	0.829	1	CLONAL	1	TRUE	1	0.547580990017577	2		316	272	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239981	98239981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142791675	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	121	282	1	ENST00000331920.6:c.1351G>A	p.Ala451Thr	p.A451T	ENST00000331920	NM_000264.3	451	Gcc/Acc	10/24	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.547580990017577	2		283	386	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138055	64138055	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	139	410	0	ENST00000334205.4:c.1978G>A	p.Ala660Thr	p.A660T	ENST00000334205	NM_003942.2	660	Gcc/Acc	16/17	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.547580990017577	2		410	486	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259270	16259270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774668447	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	160	474	2	ENST00000375759.3:c.6535G>A	p.Ala2179Thr	p.A2179T	ENST00000375759	NM_015001.2	2179	Gca/Aca	11/15	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.547580990017577	2		476	562	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209358	98209358	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1297685477	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	150	458	1	ENST00000331920.6:c.4180C>T	p.Arg1394Ter	p.R1394*	ENST00000331920	NM_000264.3	1394	Cga/Tga	23/24	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.547580990017577	2		459	514	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268831	115268831	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	63	226	0	ENST00000438362.2:c.1778+1G>A		p.X593_splice	ENST00000438362	NM_001242891.1	593			1	2	FACETS	0.971	0.85	1	0.971	0.85	1	CLONAL	1	TRUE	1	0.547580990017577	2		226	237	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609958	81609958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780018604	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	140	486	0	ENST00000298171.2:c.1556G>A	p.Arg519His	p.R519H	ENST00000298171	NM_000369.2	519	cGc/cAc	10/10	1	2	FACETS	0.891	0.815	0.97	0.891	0.815	0.97	CLONAL	1	TRUE	1	0.547580990017577	2		486	574	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176719015	176719015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1321310131	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	146	379	0	ENST00000439151.2:c.6319C>T	p.Arg2107Cys	p.R2107C	ENST00000439151	NM_022455.4	2107	Cgc/Tgc	22/23	1	2	FACETS	0.988	0.906	1	0.988	0.906	1	CLONAL	1	TRUE	1	0.547580990017577	2		379	540	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562133	176562133	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	173	420	0	ENST00000439151.2:c.29G>T	p.Arg10Ile	p.R10I	ENST00000439151	NM_022455.4	10	aGa/aTa	2/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.547580990017577	2		420	578	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877404	28877404	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	137	312	0	ENST00000282397.4:c.3917G>T	p.Arg1306Met	p.R1306M	ENST00000282397	NM_002019.4	1306	aGg/aTg	30/30	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.547580990017577	2		312	481	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1918616	1918616	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	112	305	0	ENST00000382891.5:c.779G>A	p.Arg260His	p.R260H	ENST00000382891	NM_133335.3	260	cGc/cAc	4/22	1	2	FACETS	0.905	0.819	0.995	0.905	0.819	0.995	CLONAL	1	TRUE	1	0.547580990017577	2		305	452	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033228	69033228	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	94	306	0	ENST00000288368.4:c.3668G>A	p.Trp1223Ter	p.W1223*	ENST00000288368	NM_024870.2	1223	tGg/tAg	30/40	1	2	FACETS	0.901	0.808	0.999	0.901	0.808	0.999	CLONAL	1	TRUE	1	0.547580990017577	2		306	381	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149894	99149894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368448330	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	114	402	0	ENST00000074304.5:c.206C>T	p.Ala69Val	p.A69V	ENST00000074304	NM_001134224.1	69	gCg/gTg	5/26	1	2	FACETS	0.871	0.789	0.957	0.871	0.789	0.957	CLONAL	1	TRUE	1	0.547580990017577	2		402	478	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961790	15961790	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762874617	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	111	319	0	ENST00000268712.3:c.6005C>T	p.Ala2002Val	p.A2002V	ENST00000268712	NM_006311.3	2002	gCg/gTg	38/46	1	2	FACETS	0.924	0.836	1	0.924	0.836	1	CLONAL	1	TRUE	1	0.547580990017577	2		319	439	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489573	40489573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	146	455	0	ENST00000264657.5:c.677C>T	p.Ser226Leu	p.S226L	ENST00000264657	NM_139276.2	226	tCa/tTa	8/24	1	2	FACETS	0.944	0.866	1	0.944	0.866	1	CLONAL	1	TRUE	1	0.547580990017577	2		455	565	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360862	118360862	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781990391	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	122	285	0	ENST00000534358.1:c.4594C>T	p.Arg1532Cys	p.R1532C	ENST00000534358	NM_005933.3	1532	Cgc/Tgc	13/36	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.547580990017577	2		285	411	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677762	47677762	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1380705599	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	149	349	0	ENST00000347630.2:c.1103G>A	p.Arg368His	p.R368H	ENST00000347630	NM_001007230.1	368	cGc/cAc	11/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.547580990017577	2		349	516	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99154412	99154412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750703654	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	132	424	0	ENST00000074304.5:c.554G>A	p.Arg185Gln	p.R185Q	ENST00000074304	NM_001134224.1	185	cGg/cAg	8/26	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.547580990017577	2		424	473	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927989	49927989	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374259168	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	158	403	0	ENST00000296474.3:c.3739G>A	p.Ala1247Thr	p.A1247T	ENST00000296474	NM_002447.2	1247	Gct/Act	18/20	0.547580990017577	2	FACETS	1	0.974	1	0.564	0.52	0.609	CLONAL	1	TRUE	0	0.547580990017577	2		403	512	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436597	110436597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1267707947	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	114	519	0	ENST00000375856.3:c.1804C>T	p.Arg602Trp	p.R602W	ENST00000375856	NM_003749.2	602	Cgg/Tgg	1/2	1	2	FACETS	0.919	0.833	1	0.919	0.833	1	CLONAL	1	TRUE	1	0.547580990017577	2		519	453	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519179	137519179	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1562281992	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	61	297	0	ENST00000367739.4:c.1459G>T	p.Glu487Ter	p.E487*	ENST00000367739	NM_000416.2	487	Gaa/Taa	7/7	1	2	FACETS	0.763	0.664	0.869	0.763	0.664	0.869	SUBCLONAL	1	TRUE	1	0.547580990017577	2		297	292	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961631	18961631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339234477	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	118	386	0	ENST00000262803.5:c.764G>A	p.Arg255His	p.R255H	ENST00000262803	NM_002911.3	255	cGc/cAc	5/24	1	2	FACETS	0.88	0.798	0.965	0.88	0.798	0.965	CLONAL	1	TRUE	1	0.547580990017577	2		386	490	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143326445	143326445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	108	337	0	ENST00000262992.4:c.169C>T	p.Arg57Cys	p.R57C	ENST00000262992	NM_001101669.1	57	Cgt/Tgt	4/24	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.547580990017577	2		337	394	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216398	2216398	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749779365	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	157	458	0	ENST00000398665.3:c.2042G>A	p.Arg681His	p.R681H	ENST00000398665	NM_032482.2	681	cGc/cAc	20/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.547580990017577	2		458	508	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345989	152345989	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775565256	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	119	413	0	ENST00000359321.1:c.581C>T	p.Thr194Met	p.T194M	ENST00000359321	NM_005431.1	194	aCg/aTg	3/3	1	2	FACETS	0.873	0.792	0.957	0.873	0.792	0.957	CLONAL	1	TRUE	1	0.547580990017577	2		413	498	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197830	66197830	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373548243	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	48	303	0	ENST00000273854.3:c.2869G>A	p.Ala957Thr	p.A957T	ENST00000273854	NM_004439.5	957	Gca/Aca	17/18	1	2	FACETS	0.749	0.64	0.867	0.749	0.64	0.867	SUBCLONAL	1	TRUE	1	0.547580990017577	2		303	234	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856059	111856059	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242525317	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	122	416	0	ENST00000341259.2:c.110C>T	p.Ala37Val	p.A37V	ENST00000341259	NM_005475.2	37	gCg/gTg	2/8	1	2	FACETS	0.948	0.862	1	0.948	0.862	1	CLONAL	1	TRUE	1	0.547580990017577	2		416	470	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150931775	150931775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	159	375	0	ENST00000271640.5:c.2452C>T	p.Arg818Cys	p.R818C	ENST00000271640	NM_001145415.1	818	Cgc/Tgc	15/22	1	2	FACETS	0.937	0.862	1	0.937	0.862	1	CLONAL	1	TRUE	1	0.547580990017577	2		375	620	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409980	139409980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	139	494	0	ENST00000277541.6:c.1858G>A	p.Asp620Asn	p.D620N	ENST00000277541	NM_017617.3	620	Gac/Aac	11/34	1	2	FACETS	0.856	0.782	0.933	0.856	0.782	0.933	CLONAL	1	TRUE	1	0.547580990017577	2		494	593	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589518	69589518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755540122	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	224	740	0	ENST00000168712.1:c.335G>A	p.Arg112His	p.R112H	ENST00000168712	NM_002007.2	112	cGc/cAc	1/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.547580990017577	2		740	697	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258094	16258094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	152	390	0	ENST00000375759.3:c.5359G>A	p.Ala1787Thr	p.A1787T	ENST00000375759	NM_015001.2	1787	Gca/Aca	11/15	1	2	FACETS	0.957	0.88	1	0.957	0.88	1	CLONAL	1	TRUE	1	0.547580990017577	2		390	580	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442757	187442757	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	147	404	0	ENST00000232014.4:c.1949G>A	p.Arg650Gln	p.R650Q	ENST00000232014	NM_001130845.1	650	cGa/cAa	9/10	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.547580990017577	2		404	514	SUCCESS
APC	324	MSKCC	GRCh37	5	112176882	112176882	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	103	393	0	ENST00000257430.4:c.5591C>A	p.Ser1864Tyr	p.S1864Y	ENST00000257430	NM_000038.5	1864	tCt/tAt	16/16	1	2	FACETS	0.911	0.821	1	0.911	0.821	1	CLONAL	1	TRUE	1	0.547580990017577	2		393	413	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253157	133253157	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	123	316	0	ENST00000320574.5:c.884T>G	p.Met295Arg	p.M295R	ENST00000320574	NM_006231.2	295	aTg/aGg	9/49	1	2	FACETS	0.994	0.905	1	0.994	0.905	1	CLONAL	1	TRUE	1	0.547580990017577	2		316	452	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647068	23647068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	98	420	0	ENST00000261584.4:c.799C>T	p.Pro267Ser	p.P267S	ENST00000261584	NM_024675.3	267	Cct/Tct	4/13	1	2	FACETS	0.957	0.861	1	0.957	0.861	1	CLONAL	1	TRUE	1	0.547580990017577	2		420	374	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257875	19257875	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	160	532	0	ENST00000162023.5:c.511C>T	p.Arg171Ter	p.R171*	ENST00000162023		171	Cga/Tga	9/13	1	2	FACETS	0.896	0.825	0.971	0.896	0.825	0.971	CLONAL	1	TRUE	1	0.547580990017577	2		532	652	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194671	29194671	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370779406	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	120	412	0	ENST00000240100.2:c.1057C>T	p.Arg353Trp	p.R353W	ENST00000240100	NM_001394.6	353	Cgg/Tgg	4/4	1	2	FACETS	0.945	0.858	1	0.945	0.858	1	CLONAL	1	TRUE	1	0.547580990017577	2		412	464	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041555	14041555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762543560	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	103	379	0	ENST00000311895.7:c.2102G>A	p.Arg701His	p.R701H	ENST00000311895	NM_005236.2	701	cGt/cAt	11/11	1	2	FACETS	0.883	0.795	0.975	0.883	0.795	0.975	CLONAL	1	TRUE	1	0.547580990017577	2		379	426	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574268	41574268	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	159	417	0	ENST00000263253.7:c.6553C>T	p.Arg2185Ter	p.R2185*	ENST00000263253	NM_001429.3	2185	Cga/Tga	31/31	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.547580990017577	2		417	537	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564440	139564440	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139118330	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	123	381	0	ENST00000308874.7:c.388C>T	p.Arg130Trp	p.R130W	ENST00000308874		130	Cgg/Tgg	6/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.547580990017577	2		381	417	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201756	66201756	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	127	364	0	ENST00000273854.3:c.2746C>T	p.Gln916Ter	p.Q916*	ENST00000273854	NM_004439.5	916	Cag/Tag	16/18	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.547580990017577	2		364	458	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540254	187540254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1221380402	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	128	428	1	ENST00000441802.2:c.7486G>A	p.Glu2496Lys	p.E2496K	ENST00000441802	NM_005245.3	2496	Gaa/Aaa	10/27	1	2	FACETS	0.913	0.832	0.998	0.913	0.832	0.998	CLONAL	1	TRUE	1	0.547580990017577	2		429	512	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246794	41246794	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs273902786	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	137	334	0	ENST00000357654.3:c.754C>T	p.Arg252Cys	p.R252C	ENST00000357654	NM_007294.3	252	Cgt/Tgt	10/23	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.547580990017577	2		334	459	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005482	42005482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775446234	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	167	519	0	ENST00000219905.7:c.3218G>A	p.Arg1073Gln	p.R1073Q	ENST00000219905	NM_001164273.1	1073	cGa/cAa	9/24	1	2	FACETS	0.992	0.915	1	0.992	0.915	1	CLONAL	1	TRUE	1	0.547580990017577	2		519	615	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971052	21971052	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	131	464	0	ENST00000579755.1:c.349G>A	p.Ala117Thr	p.A117T	ENST00000579755		117	Gcg/Acg	2/3	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.547580990017577	2		464	436	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526179	63526179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755508971	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	136	401	0	ENST00000307078.5:c.2447C>T	p.Ala816Val	p.A816V	ENST00000307078	NM_004655.3	816	gCg/gTg	11/11	1	2	FACETS	0.906	0.828	0.988	0.906	0.828	0.988	CLONAL	1	TRUE	1	0.547580990017577	2		401	548	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050412	128050412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1246605943	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	132	340	0	ENST00000285398.2:c.245G>A	p.Gly82Asp	p.G82D	ENST00000285398	NM_000122.1	82	gGc/gAc	3/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.547580990017577	2		340	444	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970957	21970957	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757497674	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	172	502	1	ENST00000304494.5:c.401C>T	p.Ala134Val	p.A134V	ENST00000304494	NM_000077.4	134	gCg/gTg	2/3	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.547580990017577	2		503	594	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339238	116339238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764246939	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	125	406	1	ENST00000397752.3:c.100G>A	p.Glu34Lys	p.E34K	ENST00000397752	NM_000245.2	34	Gag/Aag	2/21	1	2	FACETS	0.941	0.857	1	0.941	0.857	1	CLONAL	1	TRUE	1	0.547580990017577	2		407	485	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1684399	1684399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760542689	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	148	482	0	ENST00000378625.1:c.1720G>A	p.Val574Ile	p.V574I	ENST00000378625	NM_001198994.1	574	Gtc/Atc	14/14	1	2	FACETS	0.94	0.863	1	0.94	0.863	1	CLONAL	1	TRUE	1	0.547580990017577	2		482	575	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782585	9782585	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	113	295	0	ENST00000377346.4:c.2348-1G>A		p.X783_splice	ENST00000377346	NM_005026.3	783			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.547580990017577	2		295	391	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303317	11303317	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	127	366	0	ENST00000361445.4:c.1266C>A	p.Ser422Arg	p.S422R	ENST00000361445	NM_004958.3	422	agC/agA	9/58	1	2	FACETS	0.939	0.856	1	0.939	0.856	1	CLONAL	1	TRUE	1	0.547580990017577	2		366	494	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254678	16254678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377688121	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	124	423	1	ENST00000375759.3:c.1943G>A	p.Arg648Gln	p.R648Q	ENST00000375759	NM_015001.2	648	cGg/cAg	11/15	1	2	FACETS	0.922	0.839	1	0.922	0.839	1	CLONAL	1	TRUE	1	0.547580990017577	2		424	491	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22413300	22413300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	51	114	0	ENST00000344548.3:c.427G>A	p.Glu143Lys	p.E143K	ENST00000344548	NM_001039802.1	143	Gaa/Aaa	6/7	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.547580990017577	2		114	165	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057938	27057938	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	203	434	0	ENST00000324856.7:c.1646C>T	p.Pro549Leu	p.P549L	ENST00000324856	NM_006015.4	549	cCc/cTc	3/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.547580990017577	2		434	711	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100839	27100839	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1487753987	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	114	400	0	ENST00000324856.7:c.4121A>G	p.Asp1374Gly	p.D1374G	ENST00000324856	NM_006015.4	1374	gAt/gGt	18/20	1	2	FACETS	0.925	0.839	1	0.925	0.839	1	CLONAL	1	TRUE	1	0.547580990017577	2		400	450	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797166	45797166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773370513	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	145	502	0	ENST00000450313.1:c.1249C>T	p.Arg417Cys	p.R417C	ENST00000450313	NM_012222.2	417	Cgc/Tgc	13/16	1	2	FACETS	0.99	0.908	1	0.99	0.908	1	CLONAL	1	TRUE	1	0.547580990017577	2		502	535	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726483	46726483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767399408	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	148	432	0	ENST00000371975.4:c.562G>A	p.Gly188Arg	p.G188R	ENST00000371975	NM_003579.3	188	Gga/Aga	7/18	1	2	FACETS	0.979	0.899	1	0.979	0.899	1	CLONAL	1	TRUE	1	0.547580990017577	2		432	552	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65300267	65300267	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs944229309	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	83	294	0	ENST00000342505.4:c.3443G>T	p.Gly1148Val	p.G1148V	ENST00000342505	NM_002227.2	1148	gGa/gTa	25/25	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.547580990017577	2		294	294	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150936017	150936017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	140	432	0	ENST00000271640.5:c.3469C>T	p.Arg1157Cys	p.R1157C	ENST00000271640	NM_001145415.1	1157	Cgt/Tgt	20/22	1	2	FACETS	0.903	0.826	0.983	0.903	0.826	0.983	CLONAL	1	TRUE	1	0.547580990017577	2		432	566	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107285	193107285	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	91	310	0	ENST00000367435.3:c.494T>C	p.Val165Ala	p.V165A	ENST00000367435	NM_024529.4	165	gTa/gCa	6/17	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.547580990017577	2		310	316	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981780	201981780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	149	471	0	ENST00000359651.3:c.491C>T	p.Pro164Leu	p.P164L	ENST00000359651		164	cCc/cTc	4/8	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.547580990017577	2		471	525	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612761	228612761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	235	634	0	ENST00000366696.1:c.266C>T	p.Ala89Val	p.A89V	ENST00000366696	NM_003493.2	89	gCc/gTc	1/1	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.547580990017577	2		634	839	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612819	228612819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761689329	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	239	694	0	ENST00000366696.1:c.208C>T	p.Arg70Trp	p.R70W	ENST00000366696	NM_003493.2	70	Cgg/Tgg	1/1	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.547580990017577	2		694	861	SUCCESS
SPRTN	83932	MSKCC	GRCh37	1	231474322	231474322	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	105	405	0	ENST00000295050.7:c.193G>A	p.Glu65Lys	p.E65K	ENST00000295050	NM_032018.5	65	Gag/Aag	1/5	1	2	FACETS	0.759	0.683	0.839	0.759	0.683	0.839	SUBCLONAL	1	TRUE	1	0.547580990017577	2		405	505	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675439	241675439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	58	256	0	ENST00000366560.3:c.383C>T	p.Ala128Val	p.A128V	ENST00000366560	NM_000143.3	128	gCt/gTt	4/10	1	2	FACETS	0.929	0.808	1	0.929	0.808	1	CLONAL	1	TRUE	1	0.547580990017577	2		256	228	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851233	63851233	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	140	483	1	ENST00000279873.7:c.2011G>T	p.Gly671Ter	p.G671*	ENST00000279873	NM_032199.2	671	Gga/Tga	10/10	1	2	FACETS	0.938	0.859	1	0.938	0.859	1	CLONAL	1	TRUE	1	0.547580990017577	2		484	545	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47595284	47595284	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746451387	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	124	339	0	ENST00000430070.2:c.803C>T	p.Ser268Leu	p.S268L	ENST00000430070	NM_018095.4	268	tCg/tTg	4/4	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.547580990017577	2		339	430	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47598986	47598986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779866095	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	156	435	1	ENST00000430070.2:c.614G>A	p.Arg205His	p.R205H	ENST00000430070	NM_018095.4	205	cGc/cAc	2/4	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.547580990017577	2		436	533	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47599185	47599185	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	115	431	0	ENST00000430070.2:c.415G>T	p.Asp139Tyr	p.D139Y	ENST00000430070	NM_018095.4	139	Gac/Tac	2/4	1	2	FACETS	0.877	0.794	0.963	0.877	0.794	0.963	CLONAL	1	TRUE	1	0.547580990017577	2		431	479	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137768	64137768	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1176040217	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	182	435	0	ENST00000334205.4:c.1869G>T	p.Glu623Asp	p.E623D	ENST00000334205	NM_003942.2	623	gaG/gaT	15/17	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.547580990017577	2		435	621	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69458599	69458599	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	101	315	0	ENST00000227507.2:c.415-1G>A		p.X139_splice	ENST00000227507	NM_053056.2	139			1	2	FACETS	0.939	0.846	1	0.939	0.846	1	CLONAL	1	TRUE	1	0.547580990017577	2		315	393	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941484	71941484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762820798	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	167	532	0	ENST00000298229.2:c.1169G>A	p.Arg390His	p.R390H	ENST00000298229	NM_001567.3	390	cGc/cAc	10/28	1	2	FACETS	0.952	0.878	1	0.952	0.878	1	CLONAL	1	TRUE	1	0.547580990017577	2		532	641	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948509	71948509	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	135	524	0	ENST00000298229.2:c.3221G>A	p.Gly1074Glu	p.G1074E	ENST00000298229	NM_001567.3	1074	gGg/gAg	26/28	1	2	FACETS	0.917	0.837	0.999	0.917	0.837	0.999	CLONAL	1	TRUE	1	0.547580990017577	2		524	538	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77034329	77034329	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	170	450	0	ENST00000356341.3:c.1628A>G	p.Asn543Ser	p.N543S	ENST00000356341	NM_002576.4	543	aAc/aGc	15/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.547580990017577	2		450	586	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77054972	77054972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	105	324	2	ENST00000356341.3:c.890C>T	p.Ala297Val	p.A297V	ENST00000356341	NM_002576.4	297	gCc/gTc	10/15	1	2	FACETS	0.961	0.868	1	0.961	0.868	1	CLONAL	1	TRUE	1	0.547580990017577	2		326	399	SUCCESS
EED	8726	MSKCC	GRCh37	11	85963281	85963281	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	50	257	0	ENST00000263360.6:c.359G>A	p.Arg120Lys	p.R120K	ENST00000263360	NM_003797.3	120	aGa/aAa	3/12	1	2	FACETS	0.797	0.684	0.919	0.797	0.684	0.919	CLONAL	1	TRUE	1	0.547580990017577	2		257	229	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999389	100999389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755905259	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	135	525	0	ENST00000325455.5:c.413G>A	p.Ser138Asn	p.S138N	ENST00000325455	NM_001202474.3	138	aGc/aAc	1/8	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.547580990017577	2		525	483	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172509	108172509	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	55	299	0	ENST00000278616.4:c.5312G>T	p.Arg1771Ile	p.R1771I	ENST00000278616	NM_000051.3	1771	aGa/aTa	35/63	1	2	FACETS	0.851	0.736	0.974	0.851	0.736	0.974	CLONAL	1	TRUE	1	0.547580990017577	2		299	236	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186596	108186596	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs755694394	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	86	362	0	ENST00000278616.4:c.6053T>G	p.Leu2018Trp	p.L2018W	ENST00000278616	NM_000051.3	2018	tTg/tGg	41/63	1	2	FACETS	0.997	0.891	1	0.997	0.891	1	CLONAL	1	TRUE	1	0.547580990017577	2		362	315	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	495106	495107	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	74	264	0	ENST00000399788.2:c.199dup	p.Ser67LysfsTer13	p.S67Kfs*13	ENST00000399788	NM_001042603.1	67	agc/aAgc	2/28	1	2	FACETS	0.8	0.705	0.9	0.8	0.705	0.9	SUBCLONAL	1	TRUE	1	0.547580990017577	2		264	338	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	495113	495113	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	81	272	0	ENST00000399788.2:c.193G>A	p.Val65Ile	p.V65I	ENST00000399788	NM_001042603.1	65	Gta/Ata	2/28	1	2	FACETS	0.875	0.778	0.978	0.875	0.778	0.978	CLONAL	1	TRUE	1	0.547580990017577	2		272	338	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18762562	18762562	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	40	232	0	ENST00000266497.5:c.4058T>G	p.Ile1353Ser	p.I1353S	ENST00000266497		1353	aTt/aGt	29/31	1	2	FACETS	0.864	0.729	1	0.864	0.729	1	CLONAL	1	TRUE	1	0.547580990017577	2		232	169	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21630862	21630862	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202110155	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	117	309	0	ENST00000421138.2:c.742G>A	p.Ala248Thr	p.A248T	ENST00000421138		248	Gca/Aca	8/16	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.547580990017577	2		309	385	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432540	49432540	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	149	442	1	ENST00000301067.7:c.8599C>T	p.Pro2867Ser	p.P2867S	ENST00000301067	NM_003482.3	2867	Cca/Tca	34/54	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.547580990017577	2		443	534	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432762	49432762	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	140	404	0	ENST00000301067.7:c.8377G>T	p.Gly2793Ter	p.G2793*	ENST00000301067	NM_003482.3	2793	Gga/Tga	34/54	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.547580990017577	2		404	503	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446849	49446849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1204392134	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	176	473	0	ENST00000301067.7:c.961C>T	p.Arg321Trp	p.R321W	ENST00000301067	NM_003482.3	321	Cgg/Tgg	8/54	1	2	FACETS	0.987	0.913	1	0.987	0.913	1	CLONAL	1	TRUE	1	0.547580990017577	2		473	651	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481390	56481390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	198	471	0	ENST00000267101.3:c.577C>T	p.Arg193Ter	p.R193*	ENST00000267101	NM_001982.3	193	Cga/Tga	5/28	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.547580990017577	2		471	641	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69210645	69210645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	69	253	0	ENST00000462284.1:c.228G>T	p.Lys76Asn	p.K76N	ENST00000462284	NM_002392.5	76	aaG/aaT	4/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.547580990017577	2		253	231	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112893855	112893855	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	76	222	0	ENST00000351677.2:c.744G>T	p.Trp248Cys	p.W248C	ENST00000351677	NM_002834.3	248	tgG/tgT	6/16	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.547580990017577	2		222	275	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112940045	112940045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150730493	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	145	363	0	ENST00000351677.2:c.1697C>T	p.Thr566Met	p.T566M	ENST00000351677	NM_002834.3	566	aCg/aTg	14/16	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.547580990017577	2		363	509	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120805870	120805870	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1038401875	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	145	455	0	ENST00000257552.2:c.208G>A	p.Asp70Asn	p.D70N	ENST00000257552	NM_002442.3	70	Gac/Aac	4/15	1	2	FACETS	0.927	0.85	1	0.927	0.85	1	CLONAL	1	TRUE	1	0.547580990017577	2		455	571	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241958	133241958	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	152	418	0	ENST00000320574.5:c.2398C>A	p.Leu800Met	p.L800M	ENST00000320574	NM_006231.2	800	Ctg/Atg	21/49	1	2	FACETS	0.946	0.869	1	0.946	0.869	1	CLONAL	1	TRUE	1	0.547580990017577	2		418	587	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245017	133245017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145793634	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	148	497	0	ENST00000320574.5:c.2098C>T	p.Pro700Ser	p.P700S	ENST00000320574	NM_006231.2	700	Cca/Tca	19/49	1	2	FACETS	0.972	0.893	1	0.972	0.893	1	CLONAL	1	TRUE	1	0.547580990017577	2		497	556	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28644702	28644702	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	66	305	0	ENST00000241453.7:c.91C>T	p.Pro31Ser	p.P31S	ENST00000241453	NM_004119.2	31	Cct/Tct	2/24	1	2	FACETS	0.873	0.766	0.987	0.873	0.766	0.987	CLONAL	1	TRUE	1	0.547580990017577	2		305	276	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28674644	28674644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	196	715	0	ENST00000241453.7:c.4C>T	p.Pro2Ser	p.P2S	ENST00000241453	NM_004119.2	2	Ccg/Tcg	1/24	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.547580990017577	2		715	634	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880875	28880875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1415091072	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	145	387	0	ENST00000282397.4:c.3755C>A	p.Ser1252Tyr	p.S1252Y	ENST00000282397	NM_002019.4	1252	tCt/tAt	29/30	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.547580990017577	2		387	524	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29068938	29068938	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	93	300	0	ENST00000282397.4:c.43C>T	p.Leu15Phe	p.L15F	ENST00000282397	NM_002019.4	15	Ctc/Ttc	1/30	1	2	FACETS	0.999	0.897	1	0.999	0.897	1	CLONAL	1	TRUE	1	0.547580990017577	2		300	340	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911208	32911208	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs80358528	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	73	381	0	ENST00000380152.3:c.2716A>G	p.Thr906Ala	p.T906A	ENST00000380152		906	Act/Gct	11/27	1	2	FACETS	0.988	0.874	1	0.988	0.874	1	CLONAL	1	TRUE	1	0.547580990017577	2		381	270	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32932021	32932021	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	103	339	1	ENST00000380152.3:c.7760T>G	p.Leu2587Arg	p.L2587R	ENST00000380152		2587	cTc/cGc	16/27	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.547580990017577	2		340	367	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937575	32937575	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	117	367	1	ENST00000380152.3:c.8236A>G	p.Thr2746Ala	p.T2746A	ENST00000380152		2746	Aca/Gca	18/27	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.547580990017577	2		368	406	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033824	49033824	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs769113950	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	21	314	0	ENST00000267163.4:c.1961T>C	p.Val654Ala	p.V654A	ENST00000267163	NM_000321.2	654	gTg/gCg	20/27	1	2	FACETS	0.216	0.166	0.275	0.216	0.166	0.275	SUBCLONAL	1	TRUE	1	0.547580990017577	2		314	355	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103508430	103508430	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	53	225	1	ENST00000355739.4:c.496C>T	p.Gln166Ter	p.Q166*	ENST00000355739	NM_000123.3	166	Caa/Taa	5/15	1	2	FACETS	0.756	0.651	0.869	0.756	0.651	0.869	SUBCLONAL	1	TRUE	1	0.547580990017577	2		226	256	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515217	103515217	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	97	400	0	ENST00000355739.4:c.1718C>A	p.Ser573Tyr	p.S573Y	ENST00000355739	NM_000123.3	573	tCt/tAt	8/15	1	2	FACETS	0.888	0.797	0.983	0.888	0.797	0.983	CLONAL	1	TRUE	1	0.547580990017577	2		400	399	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988288	36988288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756395940	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	88	364	0	ENST00000354822.5:c.365G>A	p.Gly122Asp	p.G122D	ENST00000354822	NM_001079668.2	122	gGc/gAc	2/3	1	2	FACETS	0.857	0.765	0.954	0.857	0.765	0.954	CLONAL	1	TRUE	1	0.547580990017577	2		364	375	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81574798	81574798	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	92	380	0	ENST00000298171.2:c.692+2T>C		p.X231_splice	ENST00000298171	NM_000369.2	231			1	2	FACETS	0.911	0.816	1	0.911	0.816	1	CLONAL	1	TRUE	1	0.547580990017577	2		380	369	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610127	81610127	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	122	489	0	ENST00000298171.2:c.1725G>T	p.Glu575Asp	p.E575D	ENST00000298171	NM_000369.2	575	gaG/gaT	10/10	1	2	FACETS	0.852	0.774	0.934	0.852	0.774	0.934	CLONAL	1	TRUE	1	0.547580990017577	2		489	523	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557626	95557626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060503625	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	127	429	0	ENST00000393063.1:c.5441C>T	p.Ser1814Leu	p.S1814L	ENST00000393063	NM_030621.3	1814	tCg/tTg	26/28	1	2	FACETS	0.919	0.837	1	0.919	0.837	1	CLONAL	1	TRUE	1	0.547580990017577	2		429	505	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701235	43701235	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	162	435	0	ENST00000382044.4:c.5460C>A	p.Tyr1820Ter	p.Y1820*	ENST00000382044	NM_001141980.1	1820	taC/taA	26/28	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.547580990017577	2		435	570	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701845	43701845	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	103	248	0	ENST00000382044.4:c.5400G>T	p.Gln1800His	p.Q1800H	ENST00000382044	NM_001141980.1	1800	caG/caT	25/28	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.547580990017577	2		248	354	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43773212	43773212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	98	357	0	ENST00000382044.4:c.380G>A	p.Gly127Glu	p.G127E	ENST00000382044	NM_001141980.1	127	gGa/gAa	5/28	1	2	FACETS	0.96	0.863	1	0.96	0.863	1	CLONAL	1	TRUE	1	0.547580990017577	2		357	373	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50774230	50774230	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	76	384	0	ENST00000307179.4:c.1771A>G	p.Thr591Ala	p.T591A	ENST00000307179		591	Aca/Gca	11/20	1	2	FACETS	0.786	0.695	0.884	0.786	0.695	0.884	SUBCLONAL	1	TRUE	1	0.547580990017577	2		384	353	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292641	91292641	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	78	306	0	ENST00000355112.3:c.143C>A	p.Ser48Tyr	p.S48Y	ENST00000355112	NM_000057.2	48	tCt/tAt	3/22	1	2	FACETS	0.94	0.835	1	0.94	0.835	1	CLONAL	1	TRUE	1	0.547580990017577	2		306	303	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110710	2110710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559727962	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	127	444	0	ENST00000219476.3:c.1015G>A	p.Val339Ile	p.V339I	ENST00000219476	NM_000548.3	339	Gtc/Atc	11/42	1	2	FACETS	0.904	0.823	0.988	0.904	0.823	0.988	CLONAL	1	TRUE	1	0.547580990017577	2		444	513	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122928	2122928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	135	399	0	ENST00000219476.3:c.2299G>A	p.Val767Ile	p.V767I	ENST00000219476	NM_000548.3	767	Gtt/Att	21/42	1	2	FACETS	0.973	0.889	1	0.973	0.889	1	CLONAL	1	TRUE	1	0.547580990017577	2		399	507	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134341	2134341	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	167	505	0	ENST00000219476.3:c.4118A>G	p.Asp1373Gly	p.D1373G	ENST00000219476	NM_000548.3	1373	gAc/gGc	34/42	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.547580990017577	2		505	543	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14016020	14016020	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	70	256	0	ENST00000311895.7:c.340C>A	p.Leu114Ile	p.L114I	ENST00000311895	NM_005236.2	114	Ctt/Att	2/11	1	2	FACETS	0.873	0.768	0.983	0.873	0.768	0.983	CLONAL	1	TRUE	1	0.547580990017577	2		256	293	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634289	23634289	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	89	263	0	ENST00000261584.4:c.2996+1G>A		p.X999_splice	ENST00000261584	NM_024675.3	999			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.547580990017577	2		263	300	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645270	67645270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	138	455	0	ENST00000264010.4:c.535G>A	p.Glu179Lys	p.E179K	ENST00000264010	NM_006565.3	179	Gaa/Aaa	3/12	1	2	FACETS	0.962	0.88	1	0.962	0.88	1	CLONAL	1	TRUE	1	0.547580990017577	2		455	524	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842408	68842408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	147	430	1	ENST00000261769.5:c.469G>A	p.Val157Ile	p.V157I	ENST00000261769	NM_004360.3	157	Gtt/Att	4/16	1	2	FACETS	0.934	0.856	1	0.934	0.856	1	CLONAL	1	TRUE	1	0.547580990017577	2		431	575	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828457	72828457	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	139	476	0	ENST00000268489.5:c.8124G>T	p.Gln2708His	p.Q2708H	ENST00000268489	NM_006885.3	2708	caG/caT	9/10	1	2	FACETS	0.926	0.848	1	0.926	0.848	1	CLONAL	1	TRUE	1	0.547580990017577	2		476	548	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86545061	86545061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767146795	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	106	419	0	ENST00000262426.4:c.886G>A	p.Ala296Thr	p.A296T	ENST00000262426	NM_001451.2	296	Gcg/Acg	1/2	1	2	FACETS	0.825	0.744	0.911	0.825	0.744	0.911	CLONAL	1	TRUE	1	0.547580990017577	2		419	469	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350783	89350783	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	125	305	0	ENST00000301030.4:c.2167G>T	p.Asp723Tyr	p.D723Y	ENST00000301030	NM_001256183.1	723	Gac/Tac	9/13	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.547580990017577	2		305	427	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924292	11924292	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	153	629	0	ENST00000353533.5:c.89G>A	p.Gly30Asp	p.G30D	ENST00000353533	NM_003010.3	30	gGc/gAc	1/11	1	2	FACETS	0.916	0.842	0.993	0.916	0.842	0.993	CLONAL	1	TRUE	1	0.547580990017577	2		629	610	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958259	11958259	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	43	180	0	ENST00000353533.5:c.169G>T	p.Ala57Ser	p.A57S	ENST00000353533	NM_003010.3	57	Gca/Tca	2/11	1	2	FACETS	0.975	0.83	1	0.975	0.83	1	CLONAL	1	TRUE	1	0.547580990017577	2		180	161	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509661	29509661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs749251299	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	79	407	0	ENST00000356175.3:c.866T>C	p.Val289Ala	p.V289A	ENST00000356175	NM_000267.3	289	gTt/gCt	8/57	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.547580990017577	2		407	286	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553516	29553516	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	129	302	0	ENST00000356175.3:c.2065G>T	p.Val689Leu	p.V689L	ENST00000356175	NM_000267.3	689	Gtg/Ttg	18/57	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.547580990017577	2		302	412	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30310112	30310112	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	27	74	0	ENST00000322652.5:c.1012C>A	p.Leu338Ile	p.L338I	ENST00000322652	NM_015355.2	338	Ctt/Att	9/16	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.547580990017577	2		74	76	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33434093	33434093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201141245	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	127	458	0	ENST00000345365.6:c.394G>A	p.Val132Ile	p.V132I	ENST00000345365	NM_002878.3	132	Gtc/Atc	5/10	1	2	FACETS	0.983	0.896	1	0.983	0.896	1	CLONAL	1	TRUE	1	0.547580990017577	2		458	472	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679455	33679455	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	79	165	0	ENST00000308377.4:c.2626G>T	p.Ala876Ser	p.A876S	ENST00000308377	NM_152270.3	876	Gct/Tct	5/5	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.547580990017577	2		165	216	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883650	37883650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1193632490	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	130	511	0	ENST00000269571.5:c.3262G>A	p.Gly1088Ser	p.G1088S	ENST00000269571		1088	Ggt/Agt	26/27	1	2	FACETS	0.891	0.812	0.973	0.891	0.812	0.973	CLONAL	1	TRUE	1	0.547580990017577	2		511	533	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883740	37883740	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs928539621	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	179	491	0	ENST00000269571.5:c.3352G>A	p.Val1118Ile	p.V1118I	ENST00000269571		1118	Gta/Ata	26/27	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.547580990017577	2		491	645	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40864368	40864368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	131	392	0	ENST00000428826.2:c.1340G>A	p.Gly447Asp	p.G447D	ENST00000428826		447	gGc/gAc	12/21	1	2	FACETS	0.861	0.784	0.94	0.861	0.784	0.94	CLONAL	1	TRUE	1	0.547580990017577	2		392	556	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244846	41244846	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397507202	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	102	384	0	ENST00000357654.3:c.2702T>C	p.Phe901Ser	p.F901S	ENST00000357654	NM_007294.3	901	tTt/tCt	10/23	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.547580990017577	2		384	360	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436110	56436110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369745984	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	177	490	0	ENST00000407977.2:c.1027C>T	p.Arg343Cys	p.R343C	ENST00000407977		343	Cgc/Tgc	9/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.547580990017577	2		490	622	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554575	63554575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	179	514	0	ENST00000307078.5:c.164C>T	p.Thr55Ile	p.T55I	ENST00000307078	NM_004655.3	55	aCc/aTc	2/11	1	2	FACETS	0.949	0.878	1	0.949	0.878	1	CLONAL	1	TRUE	1	0.547580990017577	2		514	689	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117737	70117737	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	151	446	0	ENST00000245479.2:c.205T>C	p.Phe69Leu	p.F69L	ENST00000245479	NM_000346.3	69	Ttc/Ctc	1/3	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.547580990017577	2		446	534	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581157	48581157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	84	241	0	ENST00000342988.3:c.461C>T	p.Ser154Leu	p.S154L	ENST00000342988	NM_005359.5	154	tCa/tTa	5/12	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.547580990017577	2		241	268	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219345	1219345	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567769257	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	139	414	0	ENST00000326873.7:c.397G>A	p.Val133Met	p.V133M	ENST00000326873	NM_000455.4	133	Gtg/Atg	3/10	1	2	FACETS	0.984	0.901	1	0.984	0.901	1	CLONAL	1	TRUE	1	0.547580990017577	2		414	516	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4095400	4095400	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	130	443	0	ENST00000262948.5:c.1032G>T	p.Glu344Asp	p.E344D	ENST00000262948	NM_030662.3	344	gaG/gaT	9/11	1	2	FACETS	0.857	0.781	0.937	0.857	0.781	0.937	CLONAL	1	TRUE	1	0.547580990017577	2		443	554	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211642	5211642	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	119	361	0	ENST00000357368.4:c.5193G>T	p.Glu1731Asp	p.E1731D	ENST00000357368	NM_002850.3	1731	gaG/gaT	33/38	1	2	FACETS	0.972	0.884	1	0.972	0.884	1	CLONAL	1	TRUE	1	0.547580990017577	2		361	447	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132173	7132173	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	108	373	0	ENST00000302850.5:c.2838C>A	p.Asp946Glu	p.D946E	ENST00000302850	NM_000208.2	946	gaC/gaA	14/22	1	2	FACETS	0.88	0.795	0.97	0.88	0.795	0.97	CLONAL	1	TRUE	1	0.547580990017577	2		373	448	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254536	10254536	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	170	476	0	ENST00000340748.4:c.2974C>T	p.Arg992Ter	p.R992*	ENST00000340748		992	Cga/Tga	28/40	1	2	FACETS	0.979	0.904	1	0.979	0.904	1	CLONAL	1	TRUE	1	0.547580990017577	2		476	634	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144152	11144152	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	202	464	0	ENST00000358026.2:c.3733G>A	p.Ala1245Thr	p.A1245T	ENST00000358026	NM_001128849.1	1245	Gcc/Acc	26/36	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.547580990017577	2		464	584	SUCCESS
CALR	811	MSKCC	GRCh37	19	13049533	13049533	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	108	401	0	ENST00000316448.5:c.40C>A	p.Leu14Met	p.L14M	ENST00000316448	NM_004343.3	14	Ctg/Atg	1/9	1	2	FACETS	0.832	0.751	0.917	0.832	0.751	0.917	CLONAL	1	TRUE	1	0.547580990017577	2		401	474	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366231	15366231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	142	395	0	ENST00000263377.2:c.1924C>T	p.Pro642Ser	p.P642S	ENST00000263377	NM_058243.2	642	Ccc/Tcc	10/20	1	2	FACETS	0.941	0.862	1	0.941	0.862	1	CLONAL	1	TRUE	1	0.547580990017577	2		395	551	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383802	15383802	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35177876	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	191	504	0	ENST00000263377.2:c.109C>T	p.Pro37Ser	p.P37S	ENST00000263377	NM_058243.2	37	Cca/Tca	2/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.547580990017577	2		504	620	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18960988	18960988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1189194959	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	151	430	2	ENST00000262803.5:c.566G>A	p.Arg189His	p.R189H	ENST00000262803	NM_002911.3	189	cGc/cAc	4/24	1	2	FACETS	0.968	0.889	1	0.968	0.889	1	CLONAL	1	TRUE	1	0.547580990017577	2		432	570	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19261498	19261498	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	108	287	0	ENST00000162023.5:c.47A>G	p.Asn16Ser	p.N16S	ENST00000162023		16	aAt/aGt	6/13	1	2	FACETS	0.996	0.901	1	0.996	0.901	1	CLONAL	1	TRUE	1	0.547580990017577	2		287	396	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748844	41748844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	131	402	0	ENST00000301178.4:c.1369G>A	p.Ala457Thr	p.A457T	ENST00000301178	NM_021913.4	457	Gca/Aca	11/20	1	2	FACETS	0.878	0.8	0.959	0.878	0.8	0.959	CLONAL	1	TRUE	1	0.547580990017577	2		402	545	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797149	42797149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs916100307	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	158	567	0	ENST00000575354.2:c.3511C>T	p.Arg1171Trp	p.R1171W	ENST00000575354	NM_015125.3	1171	Cgg/Tgg	15/20	1	2	FACETS	0.995	0.916	1	0.995	0.916	1	CLONAL	1	TRUE	1	0.547580990017577	2		567	580	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797874	42797874	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1162455794	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	149	561	0	ENST00000575354.2:c.3926G>A	p.Ser1309Asn	p.S1309N	ENST00000575354	NM_015125.3	1309	aGc/aAc	16/20	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.547580990017577	2		561	543	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422621	47422621	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	128	363	0	ENST00000404338.3:c.689C>T	p.Ala230Val	p.A230V	ENST00000404338	NM_004491.4	230	gCg/gTg	1/6	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.547580990017577	2		363	449	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423101	47423101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	140	446	0	ENST00000404338.3:c.1169C>T	p.Ala390Val	p.A390V	ENST00000404338	NM_004491.4	390	gCc/gTc	1/6	1	2	FACETS	0.991	0.908	1	0.991	0.908	1	CLONAL	1	TRUE	1	0.547580990017577	2		446	516	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912476	50912476	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	119	406	2	ENST00000440232.2:c.1990C>A	p.Leu664Ile	p.L664I	ENST00000440232	NM_002691.3	664	Ctc/Atc	16/27	1	2	FACETS	0.979	0.89	1	0.979	0.89	1	CLONAL	1	TRUE	1	0.547580990017577	2		408	444	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714717	52714717	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	139	441	0	ENST00000322088.6:c.475T>C	p.Ser159Pro	p.S159P	ENST00000322088	NM_014225.5	159	Tcc/Ccc	4/15	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.547580990017577	2		441	491	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723458	52723458	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	109	315	0	ENST00000322088.6:c.1319A>G	p.Asp440Gly	p.D440G	ENST00000322088	NM_014225.5	440	gAt/gGt	11/15	1	2	FACETS	0.901	0.814	0.991	0.901	0.814	0.991	CLONAL	1	TRUE	1	0.547580990017577	2		315	442	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25459867	25459867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	113	305	0	ENST00000264709.3:c.2416G>A	p.Ala806Thr	p.A806T	ENST00000264709	NM_175629.2	806	Gca/Aca	21/23	1	2	FACETS	0.932	0.844	1	0.932	0.844	1	CLONAL	1	TRUE	1	0.547580990017577	2		305	443	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965233	25965233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757158204	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	125	444	0	ENST00000435504.4:c.3973C>T	p.Pro1325Ser	p.P1325S	ENST00000435504		1325	Cca/Tca	13/13	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.547580990017577	2		444	414	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966109	25966109	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	133	446	0	ENST00000435504.4:c.3097C>T	p.Pro1033Ser	p.P1033S	ENST00000435504		1033	Cca/Tca	13/13	1	2	FACETS	0.97	0.886	1	0.97	0.886	1	CLONAL	1	TRUE	1	0.547580990017577	2		446	501	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917802	29917802	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	116	394	0	ENST00000389048.3:c.866C>A	p.Ser289Tyr	p.S289Y	ENST00000389048	NM_004304.4	289	tCc/tAc	3/29	1	2	FACETS	0.95	0.862	1	0.95	0.862	1	CLONAL	1	TRUE	1	0.547580990017577	2		394	446	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605824	46605824	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	103	363	0	ENST00000263734.3:c.1472C>A	p.Ser491Tyr	p.S491Y	ENST00000263734	NM_001430.4	491	tCt/tAt	11/16	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.547580990017577	2		363	365	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637430	47637430	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	135	381	0	ENST00000233146.2:c.564G>T	p.Glu188Asp	p.E188D	ENST00000233146	NM_000251.2	188	gaG/gaT	3/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.547580990017577	2		381	469	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715809	61715809	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	88	393	0	ENST00000401558.2:c.2120T>C	p.Val707Ala	p.V707A	ENST00000401558	NM_003400.3	707	gTa/gCa	18/25	1	2	FACETS	0.853	0.761	0.949	0.853	0.761	0.949	CLONAL	1	TRUE	1	0.547580990017577	2		393	377	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630749	67630749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	85	397	0	ENST00000272342.5:c.935C>T	p.Thr312Ile	p.T312I	ENST00000272342	NM_019002.3	312	aCc/aTc	5/6	1	2	FACETS	0.97	0.866	1	0.97	0.866	1	CLONAL	1	TRUE	1	0.547580990017577	2		397	320	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67632065	67632065	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	63	371	0	ENST00000272342.5:c.2251C>T	p.His751Tyr	p.H751Y	ENST00000272342	NM_019002.3	751	Cat/Tat	5/6	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.547580990017577	2		371	215	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99136581	99136581	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528195084	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	144	377	0	ENST00000074304.5:c.70G>A	p.Asp24Asn	p.D24N	ENST00000074304	NM_001134224.1	24	Gac/Aac	3/26	1	2	FACETS	0.99	0.909	1	0.99	0.909	1	CLONAL	1	TRUE	1	0.547580990017577	2		377	531	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098983	178098983	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	105	347	0	ENST00000397062.3:c.62A>G	p.Asp21Gly	p.D21G	ENST00000397062	NM_006164.4	21	gAc/gGc	2/5	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.547580990017577	2		347	356	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265593	198265593	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	83	322	0	ENST00000335508.6:c.2564A>G	p.Asp855Gly	p.D855G	ENST00000335508	NM_012433.2	855	gAt/gGt	18/25	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.547580990017577	2		322	300	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198269866	198269866	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	72	292	0	ENST00000335508.6:c.1473G>T	p.Glu491Asp	p.E491D	ENST00000335508	NM_012433.2	491	gaG/gaT	11/25	1	2	FACETS	0.916	0.809	1	0.916	0.809	1	CLONAL	1	TRUE	1	0.547580990017577	2		292	287	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285263	198285263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	61	308	0	ENST00000335508.6:c.304G>A	p.Asp102Asn	p.D102N	ENST00000335508	NM_012433.2	102	Gat/Aat	4/25	1	2	FACETS	0.75	0.652	0.855	0.75	0.652	0.855	SUBCLONAL	1	TRUE	1	0.547580990017577	2		308	297	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131474	202131474	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	120	415	0	ENST00000358485.4:c.442G>T	p.Glu148Ter	p.E148*	ENST00000358485	NM_001080125.1	148	Gaa/Taa	2/9	1	2	FACETS	0.965	0.878	1	0.965	0.878	1	CLONAL	1	TRUE	1	0.547580990017577	2		415	454	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566711	212566711	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	94	377	0	ENST00000342788.4:c.1470C>A	p.Asn490Lys	p.N490K	ENST00000342788	NM_005235.2	490	aaC/aaA	12/28	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.547580990017577	2		377	308	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645673	215645673	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	80	380	0	ENST00000260947.4:c.925A>G	p.Thr309Ala	p.T309A	ENST00000260947	NM_000465.2	309	Aca/Gca	4/11	1	2	FACETS	0.928	0.824	1	0.928	0.824	1	CLONAL	1	TRUE	1	0.547580990017577	2		380	315	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225360560	225360560	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	47	241	0	ENST00000264414.4:c.1831T>C	p.Tyr611His	p.Y611H	ENST00000264414	NM_003590.4	611	Tac/Cac	13/16	1	2	FACETS	0.76	0.647	0.88	0.76	0.647	0.88	SUBCLONAL	1	TRUE	1	0.547580990017577	2		241	226	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538269	9538269	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	140	399	0	ENST00000353224.5:c.1729A>G	p.Thr577Ala	p.T577A	ENST00000353224	NM_177990.2	577	Aca/Gca	7/10	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.547580990017577	2		399	498	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272338	21272338	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs966859460	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	160	503	0	ENST00000354336.3:c.116G>A	p.Arg39His	p.R39H	ENST00000354336	NM_005207.3	39	cGc/cAc	1/3	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.547580990017577	2		503	547	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288087	21288087	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	132	361	0	ENST00000354336.3:c.332G>T	p.Gly111Val	p.G111V	ENST00000354336	NM_005207.3	111	gGa/gTa	2/3	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.547580990017577	2		361	467	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21304011	21304011	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	98	308	0	ENST00000354336.3:c.790G>A	p.Val264Met	p.V264M	ENST00000354336	NM_005207.3	264	Gtg/Atg	3/3	1	2	FACETS	0.983	0.885	1	0.983	0.885	1	CLONAL	1	TRUE	1	0.547580990017577	2		308	364	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21347181	21347181	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	134	414	0	ENST00000215739.8:c.1248G>A	p.Met416Ile	p.M416I	ENST00000215739	NM_006767.3	416	atG/atA	11/21	1	2	FACETS	0.971	0.888	1	0.971	0.888	1	CLONAL	1	TRUE	1	0.547580990017577	2		414	504	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21351225	21351225	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	158	455	0	ENST00000215739.8:c.2376C>A	p.Cys792Ter	p.C792*	ENST00000215739	NM_006767.3	792	tgC/tgA	20/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.547580990017577	2		455	523	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22153324	22153324	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	107	299	0	ENST00000215832.6:c.586C>A	p.Pro196Thr	p.P196T	ENST00000215832	NM_002745.4	196	Cca/Aca	4/9	1	2	FACETS	0.861	0.777	0.949	0.861	0.777	0.949	CLONAL	1	TRUE	1	0.547580990017577	2		299	454	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37628942	37628942	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	140	311	1	ENST00000249071.6:c.124G>T	p.Ala42Ser	p.A42S	ENST00000249071	NM_002872.4	42	Gcc/Tcc	3/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.547580990017577	2		312	434	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533658	41533658	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	119	336	0	ENST00000263253.7:c.1624C>T	p.Pro542Ser	p.P542S	ENST00000263253	NM_001429.3	542	Cca/Tca	8/31	1	2	FACETS	0.957	0.87	1	0.957	0.87	1	CLONAL	1	TRUE	1	0.547580990017577	2		336	454	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568536	41568536	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	84	306	0	ENST00000263253.7:c.4486A>G	p.Thr1496Ala	p.T1496A	ENST00000263253	NM_001429.3	1496	Aca/Gca	28/31	1	2	FACETS	0.953	0.85	1	0.953	0.85	1	CLONAL	1	TRUE	1	0.547580990017577	2		306	322	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12393124	12393124	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	96	399	0	ENST00000287820.6:c.33C>G	p.Asp11Glu	p.D11E	ENST00000287820	NM_015869.4	11	gaC/gaG	1/7	0.547580990017577	2	FACETS	1	0.922	1	0.514	0.462	0.568	CLONAL	1	TRUE	0	0.547580990017577	2		399	341	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265592	41266289	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAGTTACTGAATTGGGGCTCTGCTTCGTTGCCATTAAGCCAGTCTGGCTGAGATCCCCCTGCTTTCCTCTCTCCCTGCTTACTTGTCAGGCTACCTTTTGCTCCATTTTCTGCTCACTCCTCCTAATGGCTTGGTGAAATAGCAAACAAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAG	TAGTTACTGAATTGGGGCTCTGCTTCGTTGCCATTAAGCCAGTCTGGCTGAGATCCCCCTGCTTTCCTCTCTCCCTGCTTACTTGTCAGGCTACCTTTTGCTCCATTTTCTGCTCACTCCTCCTAATGGCTTGGTGAAATAGCAAACAAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAG	-	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	92	243	0	ENST00000349496.5:c.13+21_241+46del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.547580990017577	2	FACETS	0.757	0.686	0.829	0.757	0.686	0.829	SUBCLONAL	2	TRUE	0	0.547580990017577	2		243	222	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723747	49723747	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1160337817	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	22	84	0	ENST00000449682.2:c.1015A>G	p.Lys339Glu	p.K339E	ENST00000449682	NM_020998.3	339	Aaa/Gaa	8/18	0.547580990017577	2	FACETS	1	0.903	1	0.618	0.496	0.748	CLONAL	1	TRUE	0	0.547580990017577	2		84	65	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582107	52582107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371624499	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	140	351	2	ENST00000394830.3:c.4721G>A	p.Arg1574His	p.R1574H	ENST00000394830	NM_018313.4	1574	cGc/cAc	30/30	0.547580990017577	2	FACETS	1	0.93	1	0.508	0.466	0.552	CLONAL	1	TRUE	0	0.547580990017577	2		353	503	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584635	52584635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	171	502	0	ENST00000394830.3:c.4378C>T	p.Pro1460Ser	p.P1460S	ENST00000394830	NM_018313.4	1460	Cca/Tca	29/30	0.547580990017577	2	FACETS	1	0.962	1	0.532	0.492	0.573	CLONAL	1	TRUE	0	0.547580990017577	2		502	587	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72881622	72881622	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	93	244	0	ENST00000325599.8:c.497G>T	p.Ser166Ile	p.S166I	ENST00000325599	NM_018130.2	166	aGt/aTt	5/11	1	2	FACETS	0.946	0.849	1	0.946	0.849	1	CLONAL	1	TRUE	1	0.547580990017577	2		244	359	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851862	134851862	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	142	443	0	ENST00000398015.3:c.1268T>C	p.Val423Ala	p.V423A	ENST00000398015	NM_004441.4	423	gTc/gCc	5/16	1	2	FACETS	0.975	0.893	1	0.975	0.893	1	CLONAL	1	TRUE	1	0.547580990017577	2		443	532	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188217	142188217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	58	303	0	ENST00000350721.4:c.6514C>T	p.Pro2172Ser	p.P2172S	ENST00000350721	NM_001184.3	2172	Cct/Tct	38/47	1	2	FACETS	0.834	0.724	0.951	0.834	0.724	0.951	CLONAL	1	TRUE	1	0.547580990017577	2		303	254	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952039	178952039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	90	349	0	ENST00000263967.3:c.3094G>A	p.Glu1032Lys	p.E1032K	ENST00000263967	NM_006218.2	1032	Gag/Aag	21/21	1	2	FACETS	0.993	0.89	1	0.993	0.89	1	CLONAL	1	TRUE	1	0.547580990017577	2		349	331	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503745	186503745	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	34	348	0	ENST00000323963.5:c.422T>C	p.Val141Ala	p.V141A	ENST00000323963		141	gTt/gCt	5/11	1	2	FACETS	0.311	0.254	0.375	0.311	0.254	0.375	SUBCLONAL	1	TRUE	1	0.547580990017577	2		348	399	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447289	187447289	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	152	493	0	ENST00000232014.4:c.904G>T	p.Glu302Ter	p.E302*	ENST00000232014	NM_001130845.1	302	Gaa/Taa	5/10	1	2	FACETS	0.938	0.861	1	0.938	0.861	1	CLONAL	1	TRUE	1	0.547580990017577	2		493	592	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612239	189612239	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1037603668	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	153	415	0	ENST00000264731.3:c.1991A>G	p.Asp664Gly	p.D664G	ENST00000264731	NM_003722.4	664	gAc/gGc	14/14	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.547580990017577	2		415	476	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1918711	1918711	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	94	310	0	ENST00000382891.5:c.874A>C	p.Lys292Gln	p.K292Q	ENST00000382891	NM_133335.3	292	Aaa/Caa	4/22	1	2	FACETS	0.97	0.871	1	0.97	0.871	1	CLONAL	1	TRUE	1	0.547580990017577	2		310	354	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561771	55561771	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	120	367	1	ENST00000288135.5:c.161T>A	p.Ile54Asn	p.I54N	ENST00000288135	NM_000222.2	54	aTt/aAt	2/21	1	2	FACETS	0.913	0.829	1	0.913	0.829	1	CLONAL	1	TRUE	1	0.547580990017577	2		368	480	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361141	66361141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761254180	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	99	351	3	ENST00000273854.3:c.1031G>A	p.Arg344Lys	p.R344K	ENST00000273854	NM_004439.5	344	aGg/aAg	4/18	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.547580990017577	2		354	354	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391500	84391500	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553936765	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	37	145	0	ENST00000321945.7:c.332C>T	p.Thr111Met	p.T111M	ENST00000321945	NM_139076.2	111	aCg/aTg	5/9	1	2	FACETS	0.986	0.829	1	0.986	0.829	1	CLONAL	1	TRUE	1	0.547580990017577	2		145	137	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196445	106196445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	103	433	0	ENST00000380013.4:c.4778G>A	p.Ser1593Asn	p.S1593N	ENST00000380013	NM_001127208.2	1593	aGc/aAc	11/11	1	2	FACETS	0.855	0.77	0.944	0.855	0.77	0.944	CLONAL	1	TRUE	1	0.547580990017577	2		433	440	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007298	143007298	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs199647396	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	90	236	0	ENST00000262992.4:c.2486C>T	p.Thr829Met	p.T829M	ENST00000262992	NM_001101669.1	829	aCg/aTg	22/24	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.547580990017577	2		236	301	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144258393	144258393	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	104	332	0	ENST00000262995.4:c.52G>A	p.Glu18Lys	p.E18K	ENST00000262995	NM_207123.2	18	Gag/Aag	1/11	1	2	FACETS	0.967	0.872	1	0.967	0.872	1	CLONAL	1	TRUE	1	0.547580990017577	2		332	393	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630714	187630714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	138	440	0	ENST00000441802.2:c.268C>T	p.Leu90Phe	p.L90F	ENST00000441802	NM_005245.3	90	Ctc/Ttc	2/27	1	2	FACETS	0.992	0.908	1	0.992	0.908	1	CLONAL	1	TRUE	1	0.547580990017577	2		440	508	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251108	251108	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	31	211	0	ENST00000264932.6:c.1553C>T	p.Ser518Leu	p.S518L	ENST00000264932	NM_004168.2	518	tCa/tTa	12/15	1	2	FACETS	0.453	0.368	0.548	0.453	0.368	0.548	SUBCLONAL	1	TRUE	1	0.547580990017577	2		211	250	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31451671	31451671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	60	312	0	ENST00000344624.3:c.2651G>A	p.Gly884Glu	p.G884E	ENST00000344624		884	gGa/gAa	18/33	1	2	FACETS	0.803	0.698	0.914	0.803	0.698	0.914	CLONAL	1	TRUE	1	0.547580990017577	2		312	273	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38975660	38975660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	94	354	0	ENST00000357387.3:c.868G>A	p.Ala290Thr	p.A290T	ENST00000357387	NM_152756.3	290	Gca/Aca	10/38	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.547580990017577	2		354	341	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176627	56176627	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	68	296	0	ENST00000399503.3:c.2177C>T	p.Ala726Val	p.A726V	ENST00000399503	NM_005921.1	726	gCt/gTt	12/20	1	2	FACETS	0.801	0.703	0.906	0.801	0.703	0.906	CLONAL	1	TRUE	1	0.547580990017577	2		296	310	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522571	67522571	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	108	361	0	ENST00000274335.5:c.68A>G	p.Asp23Gly	p.D23G	ENST00000274335		23	gAc/gGc	1/15	1	2	FACETS	0.955	0.864	1	0.955	0.864	1	CLONAL	1	TRUE	1	0.547580990017577	2		361	413	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628356	86628356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	63	279	0	ENST00000274376.6:c.725G>A	p.Gly242Asp	p.G242D	ENST00000274376	NM_002890.2	242	gGt/gAt	3/25	1	2	FACETS	0.939	0.822	1	0.939	0.822	1	CLONAL	1	TRUE	1	0.547580990017577	2		279	245	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675930	30675930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	321	419	0	ENST00000376406.3:c.2426C>T	p.Thr809Ile	p.T809I	ENST00000376406	NM_014641.2	809	aCt/aTt	8/15	0.547580990017577	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.547580990017577	2		419	553	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32182004	32182004	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	160	431	0	ENST00000375023.3:c.2050A>G	p.Thr684Ala	p.T684A	ENST00000375023	NM_004557.3	684	Acg/Gcg	13/30	0.547580990017577	2	FACETS	1	0.979	1	0.583	0.539	0.629	CLONAL	1	TRUE	0	0.547580990017577	2		431	501	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64286816	64286816	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	84	301	0	ENST00000370651.3:c.31G>A	p.Glu11Lys	p.E11K	ENST00000370651	NM_003463.4	11	Gaa/Aaa	2/6	1	2	FACETS	0.894	0.797	0.997	0.894	0.797	0.997	CLONAL	1	TRUE	1	0.547580990017577	2		301	343	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89791085	89791085	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	89	277	0	ENST00000336032.3:c.472G>T	p.Glu158Ter	p.E158*	ENST00000336032	NM_006813.2	158	Gag/Tag	1/2	1	2	FACETS	0.918	0.821	1	0.918	0.821	1	CLONAL	1	TRUE	1	0.547580990017577	2		277	354	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955151	93955151	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	68	280	0	ENST00000369303.4:c.2747A>G	p.Asp916Gly	p.D916G	ENST00000369303	NM_004440.3	916	gAt/gGt	16/17	1	2	FACETS	0.89	0.782	1	0.89	0.782	1	CLONAL	1	TRUE	1	0.547580990017577	2		280	279	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106543511	106543511	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	103	316	0	ENST00000369096.4:c.313G>T	p.Glu105Ter	p.E105*	ENST00000369096	NM_001198.3	105	Gaa/Taa	3/7	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.547580990017577	2		316	333	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553288	106553288	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	172	441	0	ENST00000369096.4:c.1253A>G	p.Tyr418Cys	p.Y418C	ENST00000369096	NM_001198.3	418	tAc/tGc	5/7	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.547580990017577	2		441	564	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015835	112015835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	118	358	0	ENST00000368678.4:c.1106C>T	p.Ala369Val	p.A369V	ENST00000368678		369	gCa/gTa	10/13	1	2	FACETS	0.9	0.816	0.987	0.9	0.816	0.987	CLONAL	1	TRUE	1	0.547580990017577	2		358	479	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415654	152415654	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	128	428	0	ENST00000206249.3:c.1504C>A	p.Gln502Lys	p.Q502K	ENST00000206249	NM_000125.3	502	Cag/Aag	7/8	1	2	FACETS	0.915	0.834	0.999	0.915	0.834	0.999	CLONAL	1	TRUE	1	0.547580990017577	2		428	511	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100494	157100494	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	64	224	0	ENST00000346085.5:c.1431G>T	p.Lys477Asn	p.K477N	ENST00000346085	NM_020732.3	477	aaG/aaT	1/20	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.547580990017577	2		224	224	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157519946	157519946	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	102	339	0	ENST00000346085.5:c.4015C>T	p.His1339Tyr	p.H1339Y	ENST00000346085	NM_020732.3	1339	Cat/Tat	17/20	1	2	FACETS	0.953	0.859	1	0.953	0.859	1	CLONAL	1	TRUE	1	0.547580990017577	2		339	391	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781146	161781146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531247345	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	133	372	0	ENST00000366898.1:c.1259G>A	p.Arg420His	p.R420H	ENST00000366898	NM_004562.2	420	cGc/cAc	11/12	1	2	FACETS	0.96	0.877	1	0.96	0.877	1	CLONAL	1	TRUE	1	0.547580990017577	2		372	506	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683577	162683577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	99	355	0	ENST00000366898.1:c.392C>T	p.Ser131Leu	p.S131L	ENST00000366898	NM_004562.2	131	tCa/tTa	3/12	1	2	FACETS	0.985	0.887	1	0.985	0.887	1	CLONAL	1	TRUE	1	0.547580990017577	2		355	367	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683718	162683718	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	139	387	0	ENST00000366898.1:c.251G>A	p.Gly84Glu	p.G84E	ENST00000366898	NM_004562.2	84	gGa/gAa	3/12	1	2	FACETS	0.94	0.86	1	0.94	0.86	1	CLONAL	1	TRUE	1	0.547580990017577	2		387	540	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963888	2963888	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	142	440	0	ENST00000396946.4:c.1919T>G	p.Phe640Cys	p.F640C	ENST00000396946	NM_032415.4	640	tTc/tGc	15/25	1	2	FACETS	0.999	0.916	1	0.999	0.916	1	CLONAL	1	TRUE	1	0.547580990017577	2		440	519	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55260523	55260523	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1334821010	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	91	293	0	ENST00000275493.2:c.2690T>C	p.Val897Ala	p.V897A	ENST00000275493	NM_005228.3	897	gTc/gCc	22/28	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.547580990017577	2		293	291	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508162	106508162	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	125	417	0	ENST00000359195.3:c.156G>T	p.Lys52Asn	p.K52N	ENST00000359195	NM_002649.2	52	aaG/aaT	2/11	1	2	FACETS	0.928	0.845	1	0.928	0.845	1	CLONAL	1	TRUE	1	0.547580990017577	2		417	492	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508568	106508568	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs946794098	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	135	378	0	ENST00000359195.3:c.562G>A	p.Val188Met	p.V188M	ENST00000359195	NM_002649.2	188	Gtg/Atg	2/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.547580990017577	2		378	426	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513035	106513035	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1444356091	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	114	333	0	ENST00000359195.3:c.2049G>T	p.Lys683Asn	p.K683N	ENST00000359195	NM_002649.2	683	aaG/aaT	3/11	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.547580990017577	2		333	391	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494148	140494148	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	137	452	1	ENST00000288602.6:c.1100C>A	p.Pro367His	p.P367H	ENST00000288602	NM_004333.4	367	cCc/cAc	8/18	1	2	FACETS	0.946	0.865	1	0.946	0.865	1	CLONAL	1	TRUE	1	0.547580990017577	2		453	529	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534477	140534477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769648920	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	102	350	0	ENST00000288602.6:c.436C>T	p.Arg146Trp	p.R146W	ENST00000288602	NM_004333.4	146	Cgg/Tgg	3/18	1	2	FACETS	0.847	0.762	0.936	0.847	0.762	0.936	CLONAL	1	TRUE	1	0.547580990017577	2		350	440	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534557	140534557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	113	382	1	ENST00000288602.6:c.356C>T	p.Thr119Ile	p.T119I	ENST00000288602	NM_004333.4	119	aCc/aTc	3/18	1	2	FACETS	0.901	0.816	0.99	0.901	0.816	0.99	CLONAL	1	TRUE	1	0.547580990017577	2		383	458	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873746	151873746	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	151	441	0	ENST00000262189.6:c.8792A>G	p.Asp2931Gly	p.D2931G	ENST00000262189	NM_170606.2	2931	gAc/gGc	38/59	1	2	FACETS	0.98	0.9	1	0.98	0.9	1	CLONAL	1	TRUE	1	0.547580990017577	2		441	563	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346215	152346215	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	113	411	0	ENST00000359321.1:c.355T>C	p.Tyr119His	p.Y119H	ENST00000359321	NM_005431.1	119	Tac/Cac	3/3	1	2	FACETS	0.983	0.891	1	0.983	0.891	1	CLONAL	1	TRUE	1	0.547580990017577	2		411	420	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69012038	69012038	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	52	302	0	ENST00000288368.4:c.2675G>A	p.Arg892Lys	p.R892K	ENST00000288368	NM_024870.2	892	aGa/aAa	23/40	1	2	FACETS	0.717	0.615	0.826	0.717	0.615	0.826	SUBCLONAL	1	TRUE	1	0.547580990017577	2		302	265	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958399	90958399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1425101720	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	57	293	0	ENST00000265433.3:c.2039G>A	p.Gly680Asp	p.G680D	ENST00000265433	NM_002485.4	680	gGt/gAt	13/16	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.547580990017577	2		293	203	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90990546	90990546	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1554566760	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	20	218	0	ENST00000265433.3:c.486A>G	p.Ile162Met	p.I162M	ENST00000265433	NM_002485.4	162	atA/atG	5/16	1	2	FACETS	0.468	0.361	0.592	0.468	0.361	0.592	SUBCLONAL	1	TRUE	1	0.547580990017577	2		218	156	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145736897	145736897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376981214	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	136	400	0	ENST00000428558.2:c.3544C>T	p.Arg1182Cys	p.R1182C	ENST00000428558	NM_004260.3	1182	Cgc/Tgc	22/22	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.547580990017577	2		400	496	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738673	145738673	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	180	451	0	ENST00000428558.2:c.2391C>A	p.Ser797Arg	p.S797R	ENST00000428558	NM_004260.3	797	agC/agA	15/22	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.547580990017577	2		451	584	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2161770	2161770	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	100	373	0	ENST00000349721.2:c.4066C>T	p.Pro1356Ser	p.P1356S	ENST00000349721	NM_003070.3	1356	Cct/Tct	28/34	1	2	FACETS	0.808	0.726	0.895	0.808	0.726	0.895	CLONAL	1	TRUE	1	0.547580990017577	2		373	452	SUCCESS
MTAP	4507	MSKCC	GRCh37	9	21859365	21859365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868490964	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	121	344	0	ENST00000380172.4:c.754C>T	p.Leu252Phe	p.L252F	ENST00000380172	NM_002451.3	252	Ctc/Ttc	7/8	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.547580990017577	2		344	439	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994210	21994210	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793582	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	141	417	0	ENST00000579755.1:c.121G>A	p.Ala41Thr	p.A41T	ENST00000579755		41	Gcc/Acc	1/3	1				0.96	1				CLONAL	1	TRUE	1	0.547580990017577	2		417	479	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27204908	27204908	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	116	318	0	ENST00000380036.4:c.2210-1G>T		p.X737_splice	ENST00000380036	NM_000459.3	737			1	2	FACETS	0.95	0.862	1	0.95	0.862	1	CLONAL	1	TRUE	1	0.547580990017577	2		318	446	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212803	27212803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	147	431	0	ENST00000380036.4:c.2785G>A	p.Ala929Thr	p.A929T	ENST00000380036	NM_000459.3	929	Gcc/Acc	17/23	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.547580990017577	2		431	518	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80343495	80343495	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	76	323	0	ENST00000286548.4:c.824A>G	p.Lys275Arg	p.K275R	ENST00000286548	NM_002072.3	275	aAg/aGg	6/7	1	2	FACETS	0.881	0.78	0.988	0.881	0.78	0.988	CLONAL	1	TRUE	1	0.547580990017577	2		323	315	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238367	98238367	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	154	414	0	ENST00000331920.6:c.1677C>A	p.Phe559Leu	p.F559L	ENST00000331920	NM_000264.3	559	ttC/ttA	12/24	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.547580990017577	2		414	524	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911513	101911513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs925777307	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	115	313	1	ENST00000374994.4:c.1438G>A	p.Ala480Thr	p.A480T	ENST00000374994	NM_004612.2	480	Gca/Aca	9/9	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.547580990017577	2		314	360	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127916010	127916010	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	101	361	0	ENST00000373547.4:c.471G>T	p.Glu157Asp	p.E157D	ENST00000373547	NM_002721.4	157	gaG/gaT	6/7	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.547580990017577	2		361	362	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772646	135772646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	118	447	0	ENST00000298552.3:c.2900G>A	p.Gly967Asp	p.G967D	ENST00000298552	NM_001162426.1	967	gGc/gAc	22/23	1	2	FACETS	0.931	0.845	1	0.931	0.845	1	CLONAL	1	TRUE	1	0.547580990017577	2		447	463	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321010	137321010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	142	449	0	ENST00000481739.1:c.967G>A	p.Gly323Arg	p.G323R	ENST00000481739	NM_002957.4	323	Ggg/Agg	7/10	1	2	FACETS	0.931	0.853	1	0.931	0.853	1	CLONAL	1	TRUE	1	0.547580990017577	2		449	557	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391193	139391193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	182	607	0	ENST00000277541.6:c.6998G>A	p.Gly2333Asp	p.G2333D	ENST00000277541	NM_017617.3	2333	gGc/gAc	34/34	1	2	FACETS	0.985	0.912	1	0.985	0.912	1	CLONAL	1	TRUE	1	0.547580990017577	2		607	675	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391488	139391488	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	142	527	0	ENST00000277541.6:c.6703C>A	p.Pro2235Thr	p.P2235T	ENST00000277541	NM_017617.3	2235	Cct/Act	34/34	1	2	FACETS	0.962	0.882	1	0.962	0.882	1	CLONAL	1	TRUE	1	0.547580990017577	2		527	539	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395183	139395183	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	141	484	0	ENST00000277541.6:c.5755A>C	p.Ser1919Arg	p.S1919R	ENST00000277541	NM_017617.3	1919	Agc/Cgc	31/34	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.547580990017577	2		484	501	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317548	1317548	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	83	215	0	ENST00000400841.2:c.517G>T	p.Glu173Ter	p.E173*	ENST00000400841		173	Gaa/Taa	5/6	1	1	FACETS	0.717	0.639	0.799	0.717	0.639	0.799	SUBCLONAL	1	TRUE	0	0.547580990017577	1		215	307	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422673	47422673	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	169	214	0	ENST00000377045.4:c.145C>A	p.Leu49Met	p.L49M	ENST00000377045	NM_001654.4	49	Ctg/Atg	3/16	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.547580990017577	1		214	320	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224213	53224213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	149	242	0	ENST00000375401.3:c.3338C>T	p.Thr1113Ile	p.T1113I	ENST00000375401	NM_004187.3	1113	aCc/aTc	22/26	1	1	FACETS	0.754	0.706	0.802	1	0.991	1	SUBCLONAL	2	TRUE	0	0.547580990017577	1		242	262	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227014	53227014	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782479257	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	106	172	1	ENST00000375401.3:c.2561G>A	p.Arg854Gln	p.R854Q	ENST00000375401	NM_004187.3	854	cGg/cAg	18/26	1	1	FACETS	0.768	0.71	0.825	1	0.988	1	SUBCLONAL	2	TRUE	0	0.547580990017577	1		173	183	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410976	63410976	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	129	271	0	ENST00000330258.3:c.2191G>T	p.Asp731Tyr	p.D731Y	ENST00000330258	NM_152424.3	731	Gac/Tac	2/2	1	1	FACETS	0.75	0.698	0.802	1	0.99	1	SUBCLONAL	2	TRUE	0	0.547580990017577	1		271	228	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356464	70356464	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	201	210	0	ENST00000374080.3:c.5359A>G	p.Thr1787Ala	p.T1787A	ENST00000374080		1787	Acc/Gcc	37/45	1	1	FACETS	0.755	0.713	0.797	1	0.993	1	SUBCLONAL	2	TRUE	0	0.547580990017577	1		210	353	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763836	76763836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	90	162	0	ENST00000373344.5:c.7472C>T	p.Ser2491Leu	p.S2491L	ENST00000373344	NM_000489.3	2491	tCa/tTa	35/35	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.547580990017577	1		162	177	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613342	100613342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555978139	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	118	178	0	ENST00000308731.7:c.1058G>A	p.Ser353Asn	p.S353N	ENST00000308731	NM_000061.2	353	aGc/aAc	12/19	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.547580990017577	1		178	218	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277535	142277535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	77	261	0	ENST00000350721.4:c.1816G>A	p.Gly606Ser	p.G606S	ENST00000350721	NM_001184.3	606	Ggc/Agc	8/47	1	2	FACETS	0.904	0.801	1	0.904	0.801	1	CLONAL	1	TRUE	1	0.547580990017577	2		261	311	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411206	63411208	+	missense_variant	Missense_Mutation	TNP	TAC	TAC	CAA	novel	NA	P-0058806-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	118	248	0	ENST00000330258.3:c.1959_1961delinsTTG	p.Glu653_Tyr654delinsAspCys	p.E653_Y654delinsDC	ENST00000330258	NM_152424.3	653	gaGTAt/gaTTGt	2/2	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.547580990017577	1		248	226	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0058807-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	270	359	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.584091738302983	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.57993482530307	2		359	456	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791719	42791719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058807-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	147	498	1	ENST00000575354.2:c.605G>A	p.Arg202Gln	p.R202Q	ENST00000575354	NM_015125.3	202	cGg/cAg	5/20	0.119272477964135	6	FACETS	0.836	0.765	0.909			1	INDETERMINATE	2	TRUE	NA	0.57993482530307	6		499	655	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058807-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	464	395	0	ENST00000256196.4:c.68G>T	p.Gly23Val	p.G23V	ENST00000256196		23	gGc/gTc	1/6	0.57993482530307	7	FACETS	0.951	0.912	0.99			1	CLONAL	4	TRUE	NA	0.57993482530307	7		395	1031	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244477	41244477	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757579891	NA	P-0058807-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	88	298	0	ENST00000357654.3:c.3071G>A	p.Ser1024Asn	p.S1024N	ENST00000357654	NM_007294.3	1024	aGc/aAc	10/23	0.584091738302983	3	FACETS	0.91	0.811	1	0.303	0.27	0.339	CLONAL	1	TRUE	0	0.57993482530307	3		298	430	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213912	36213912	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058807-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1844	119	436	0	ENST00000222270.7:c.2738C>G	p.Ser913Cys	p.S913C	ENST00000222270	NM_014727.1	913	tCc/tGc	6/37	0.57993482530307	12	FACETS	0.815	0.732	0.904			1	CLONAL	1	TRUE	NA	0.57993482530307	12		436	1963	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143324151	143324155	+	frameshift_variant	Frame_Shift_Del	DEL	GATGG	GATGG	-	novel	NA	P-0058807-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	81	255	0	ENST00000262992.4:c.308_312del	p.Pro103LeufsTer2	p.P103Lfs*2	ENST00000262992	NM_001101669.1	103	cCCATC/c	5/24	0.584091738302983	2	FACETS	0.934	0.832	1	0.467	0.416	0.521	CLONAL	1	TRUE	0	0.57993482530307	2		255	299	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032271	26032271	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1278314228	NA	P-0058807-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	136	438	0	ENST00000244661.2:c.18G>C	p.Gln6His	p.Q6H	ENST00000244661	NM_003537.3	6	caG/caC	1/1	0.51131011054722	4	FACETS	1	0.948	1	0.529	0.481	0.578	CLONAL	1	TRUE	2	0.57993482530307	4		438	701	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0058808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	119	374	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.64732798114361	2		374	352	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	211	547	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.64732798114361	2		547	573	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0058808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	234	643	0	ENST00000346208.3:c.1220_1221insA	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcAg	6/6	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.64732798114361	2		643	680	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260068	16260068	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	209	622	0	ENST00000375759.3:c.7333C>T	p.Gln2445Ter	p.Q2445*	ENST00000375759	NM_015001.2	2445	Caa/Taa	11/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.64732798114361	2		622	615	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574788	95574788	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	125	433	0	ENST00000393063.1:c.2309T>C	p.Leu770Pro	p.L770P	ENST00000393063	NM_030621.3	770	cTg/cCg	16/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.64732798114361	2		433	338	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790176	40790176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393395259	NA	P-0058808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	306	457	0	ENST00000373198.4:c.2555G>A	p.Gly852Asp	p.G852D	ENST00000373198	NM_133170.3	852	gGc/gAc	18/32	0.602991583876264	4	FACETS	0.912	0.863	0.962	0.912	0.863	0.962	CLONAL	2	TRUE	2	0.64732798114361	4		457	854	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399968	139399968	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058808-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	148	589	0	ENST00000277541.6:c.4380C>A	p.Asn1460Lys	p.N1460K	ENST00000277541	NM_017617.3	1460	aaC/aaA	25/34	1	2	FACETS	0.848	0.779	0.92	0.848	0.779	0.92	CLONAL	1	TRUE	1	0.64732798114361	2		589	539	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058810-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	82	302	0				ENST00000310581	NM_198253.2	-/1132			0.246237474999256	4	FACETS	0.961	0.857	1	0.961	0.857	1	CLONAL	3	TRUE	1	0.246237474999256	4		302	288	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0058810-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	52	537	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	1	2	FACETS	0.72	0.612	0.837	0.72	0.612	0.837	SUBCLONAL	1	TRUE	1	0.246237474999256	2		537	587	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0058810-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	83	374	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.246237474999256	2		374	513	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0058810-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	48	488	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	0.837	0.708	0.978	0.837	0.708	0.978	CLONAL	1	TRUE	1	0.246237474999256	2		488	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0058810-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	51	438	0	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	1	2	FACETS	0.782	0.664	0.91	0.782	0.664	0.91	CLONAL	1	TRUE	1	0.246237474999256	2		438	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0058812-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	246	804	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.348780998666898	2	FACETS	0.92	0.865	0.976	0.92	0.865	0.976	CLONAL	2	TRUE	0	0.398365564718519	2		804	671	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437675	49437675	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058812-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	114	1029	1	ENST00000301067.7:c.5295G>T	p.Glu1765Asp	p.E1765D	ENST00000301067	NM_003482.3	1765	gaG/gaT	22/54	0.230691239060587	1	FACETS	0.585	0.526	0.646	0.585	0.526	0.646	INDETERMINATE	1	TRUE	0	0.398365564718519	1		1030	784	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018167	48018168	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0058812-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	139	673	0	ENST00000234420.5:c.363dup	p.Glu122ArgfsTer14	p.E122Rfs*14	ENST00000234420	NM_000179.2	121	cgc/cgCc	2/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.398365564718519	2		673	645	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0058813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	150	341	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.549832265554398	3	FACETS	0.99	0.919	1	0.99	0.919	1	CLONAL	2	TRUE	1	0.579703688198901	3		341	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0058813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	403	1110	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.579703688198901	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.579703688198901	2		1111	648	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0058813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	54	259	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.579703688198901	3	FACETS	1	0.875	1	0.507	0.438	0.581	CLONAL	1	TRUE	1	0.579703688198901	3		259	237	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974715	21974732	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCCCCCGCCTCCA	GCAGCGCCCCCGCCTCCA	-	novel	NA	P-0058813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	210	565	0	ENST00000304494.5:c.95_112del	p.Leu32_Leu37del	p.L32_L37del	ENST00000304494	NM_000077.4	32	cTGGAGGCGGGGGCGCTGCcc/ccc	1/3	0.577937220159547	2	FACETS	0.875	0.825	0.925	0.875	0.825	0.925	CLONAL	2	TRUE	0	0.579703688198901	2		565	414	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967921	93967921	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	71	451	0	ENST00000369303.4:c.2006T>G	p.Val669Gly	p.V669G	ENST00000369303	NM_004440.3	669	gTt/gGt	11/17	0.579703688198901	2	FACETS	0.745	0.655	0.84	0.372	0.327	0.42	SUBCLONAL	1	TRUE	0	0.579703688198901	2		451	329	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865447	57865447	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	284	651	0	ENST00000228682.2:c.2924T>C	p.Val975Ala	p.V975A	ENST00000228682	NM_005269.2	975	gTa/gCa	12/12	0.579703688198901	4	FACETS	0.922	0.87	0.976	0.922	0.87	0.976	CLONAL	2	TRUE	2	0.579703688198901	4		651	839	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942965	15942965	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0058813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	86	444	0	ENST00000268712.3:c.6737C>G	p.Ser2246Ter	p.S2246*	ENST00000268712	NM_006311.3	2246	tCa/tGa	44/46	0.579703688198901	2	FACETS	0.641	0.569	0.717	0.32	0.284	0.359	SUBCLONAL	1	TRUE	0	0.579703688198901	2		444	463	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132428	11132430	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0058813-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	157	614	0	ENST00000358026.2:c.2645_2647del	p.Glu882del	p.E882del	ENST00000358026	NM_001128849.1	882	GAA/-	19/36	0.290438514916007	3	FACETS	1	0.986	1	0.658	0.606	0.711	INDETERMINATE	1	TRUE	1	0.579703688198901	3		614	531	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0058814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	28	366	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.3	6	FACETS	0.566	0.451	0.698	0.189	0.15	0.233	SUBCLONAL	1	TRUE	3	0.24	6		366	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0058814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	34	675	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	1	2	FACETS	0.553	0.451	0.668	0.553	0.451	0.668	SUBCLONAL	1	TRUE	1	0.24	2		675	512	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860098	151860098	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs571653303	NA	P-0058814-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	23	554	0	ENST00000262189.6:c.10564A>G	p.Ile3522Val	p.I3522V	ENST00000262189	NM_170606.2	3522	Atc/Gtc	43/59	1	2	FACETS	0.418	0.325	0.526	0.418	0.325	0.526	SUBCLONAL	1	TRUE	1	0.24	2		554	459	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0058815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	140	362	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.973	0.889	1	0.973	0.889	1	CLONAL	1	TRUE	1	0.44	2		362	654	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0058815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	129	265	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.44	2		265	506	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932476	39932476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1353823807	NA	P-0058815-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	102	753	0	ENST00000378444.4:c.2123C>T	p.Thr708Ile	p.T708I	ENST00000378444	NM_001123385.1	708	aCc/aTc	4/15	1	2	FACETS	0.793	0.71	0.879	0.793	0.71	0.879	SUBCLONAL	1	TRUE	1	0.44	2		753	585	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0058816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	48	374	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.588560209742617	3	FACETS	0.981	0.88	1	1	0.975	1	CLONAL	3	FALSE	1	0.575641528977109	3		374	73	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0058816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	17	397	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.184955374041522	1	FACETS	1	0.855	1	1	0.855	1	INDETERMINATE	1	FALSE	0	0.575641528977109	1		397	38	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225060	NA	P-0058816-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	18	294	0	ENST00000263967.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000263967	NM_006218.2	104	cCa/cTa	2/21	0.588560209742617	3	FACETS	0.982	0.756	1	0.491	0.378	0.619	CLONAL	1	FALSE	1	0.575641528977109	3		294	82	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	85	302	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.857	0.764	0.956	0.857	0.764	0.956	CLONAL	1	TRUE	1	0.558618906343023	2		302	355	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418232	139418232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	145	581	0	ENST00000277541.6:c.340G>A	p.Gly114Arg	p.G114R	ENST00000277541	NM_017617.3	114	Ggg/Agg	3/34	1	2	FACETS	0.927	0.85	1	0.927	0.85	1	CLONAL	1	TRUE	1	0.558618906343023	2		581	560	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459239	120459239	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	192	518	0	ENST00000256646.2:c.6106C>T	p.Arg2036Ter	p.R2036*	ENST00000256646	NM_024408.3	2036	Cga/Tga	34/34	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.558618906343023	2		518	603	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517201	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	81	255	0	ENST00000263967.3:c.1637A>C	p.Gln546Pro	p.Q546P	ENST00000263967	NM_006218.2	546	cAg/cCg	10/21	1	2	FACETS	0.98	0.873	1	0.98	0.873	1	CLONAL	1	TRUE	1	0.558618906343023	2		255	296	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924381	131924381	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1341798216	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	126	314	0	ENST00000265335.6:c.1054C>T	p.Arg352Cys	p.R352C	ENST00000265335		352	Cgt/Tgt	8/25	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.558618906343023	2		314	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574004	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	117	424	1	ENST00000269305.4:c.1023_1024delinsTT	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	341	ttCCga/ttTTga	10/11	1	2	FACETS	0.829	0.752	0.911	0.829	0.752	0.911	CLONAL	1	TRUE	1	0.558618906343023	2		425	505	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247417	71247417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	186	485	0	ENST00000318789.4:c.116G>A	p.Gly39Glu	p.G39E	ENST00000318789	NM_032682.5	39	gGa/gAa	6/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.558618906343023	2		485	638	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578253	28578253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144397269	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	129	501	0	ENST00000241453.7:c.2918G>A	p.Arg973Gln	p.R973Q	ENST00000241453	NM_004119.2	973	cGa/cAa	24/24	0.558618906343023	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.558618906343023	1		501	333	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654610	67654610	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	139	399	0	ENST00000264010.4:c.1097T>A	p.Leu366Ter	p.L366*	ENST00000264010	NM_006565.3	366	tTa/tAa	6/12	1	2	FACETS	0.968	0.887	1	0.968	0.887	1	CLONAL	1	TRUE	1	0.558618906343023	2		399	514	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521619	89521619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	132	470	0	ENST00000336596.2:c.2696C>T	p.Ser899Leu	p.S899L	ENST00000336596	NM_005233.5	899	tCa/tTa	16/17	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.558618906343023	2		470	463	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628266	187628266	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	180	599	0	ENST00000441802.2:c.2716C>T	p.Gln906Ter	p.Q906*	ENST00000441802	NM_005245.3	906	Cag/Tag	2/27	0.18960904257987	1	FACETS	0.791	0.734	0.85	0.791	0.734	0.85	INDETERMINATE	1	TRUE	0	0.558618906343023	1		599	587	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741513	39741513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	141	462	0	ENST00000361337.2:c.1400C>T	p.Ser467Phe	p.S467F	ENST00000361337	NM_003286.2	467	tCc/tTc	14/21	NA	2	FACETS	0.916	0.839	0.996			1	INDETERMINATE	1	TRUE	NA	0.558618906343023	2		462	551	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873760	35873760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	145	498	0	ENST00000216797.5:c.91G>A	p.Asp31Asn	p.D31N	ENST00000216797	NM_020529.2	31	Gac/Aac	1/6	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.558618906343023	2		498	452	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607666	46607666	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745687417	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	140	563	0	ENST00000263734.3:c.1855C>T	p.Pro619Ser	p.P619S	ENST00000263734	NM_001430.4	619	Ccg/Tcg	12/16	1	2	FACETS	0.991	0.908	1	0.991	0.908	1	CLONAL	1	TRUE	1	0.558618906343023	2		563	506	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208398	5208398	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	133	475	0	ENST00000357368.4:c.5492G>A	p.Gly1831Asp	p.G1831D	ENST00000357368	NM_002850.3	1831	gGc/gAc	36/38	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.558618906343023	2		475	463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578396	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	171	644	0	ENST00000269305.4:c.534_535delinsTT	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	178	caCCat/caTTat	5/11	1	2	FACETS	0.997	0.922	1	0.997	0.922	1	CLONAL	1	TRUE	1	0.558618906343023	2		644	614	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165596	118165596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	168	587	0	ENST00000369448.3:c.106C>T	p.His36Tyr	p.H36Y	ENST00000369448	NM_017709.3	36	Cac/Tac	2/2	1	2	FACETS	0.975	0.9	1	0.975	0.9	1	CLONAL	1	TRUE	1	0.558618906343023	2		587	617	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844186	156844187	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	220	836	0	ENST00000524377.1:c.1189_1190delinsTT	p.Pro397Leu	p.P397L	ENST00000524377	NM_002529.3	397	CCg/TTg	9/17	0.18960904257987	1	FACETS	0.751	0.701	0.802	0.751	0.701	0.802	INDETERMINATE	1	TRUE	0	0.558618906343023	1		836	756	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450699	70450699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	110	549	0	ENST00000373644.4:c.5539G>A	p.Gly1847Ser	p.G1847S	ENST00000373644	NM_030625.2	1847	Ggc/Agc	12/12	0.263879997300174	1	FACETS	0.535	0.482	0.59	0.535	0.482	0.59	INDETERMINATE	1	TRUE	0	0.558618906343023	1		549	531	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343657	343657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	94	580	0	ENST00000262320.3:c.2017C>T	p.Pro673Ser	p.P673S	ENST00000262320	NM_003502.3	673	Ccc/Tcc	8/11	1	2	FACETS	0.715	0.639	0.795	0.715	0.639	0.795	SUBCLONAL	1	TRUE	1	0.558618906343023	2		580	471	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942765	15942765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	124	462	0	ENST00000268712.3:c.6937G>A	p.Asp2313Asn	p.D2313N	ENST00000268712	NM_006311.3	2313	Gac/Aac	44/46	1	2	FACETS	0.995	0.907	1	0.995	0.907	1	CLONAL	1	TRUE	1	0.558618906343023	2		462	446	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576057	29576057	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	112	461	0	ENST00000356175.3:c.4030G>A	p.Glu1344Lys	p.E1344K	ENST00000356175	NM_000267.3	1344	Gaa/Aaa	30/57	0.151456114858869	0	FACETS	0.325	0.293	0.359			1	INDETERMINATE	1	TRUE	0	0.558618906343023	0		461	544	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811486	56811486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1489906607	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	120	283	0	ENST00000337432.4:c.1034G>A	p.Gly345Glu	p.G345E	ENST00000337432	NM_058216.2	345	gGa/gAa	9/9	1	2	FACETS	0.922	0.838	1	0.922	0.838	1	CLONAL	1	TRUE	1	0.558618906343023	2		283	466	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78931480	78931480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	147	493	0	ENST00000306801.3:c.3427G>A	p.Asp1143Asn	p.D1143N	ENST00000306801	NM_020761.2	1143	Gac/Aac	29/34	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.558618906343023	2		493	488	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752960	42752960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773915281	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	159	660	1	ENST00000222329.4:c.1304C>T	p.Ser435Leu	p.S435L	ENST00000222329	NM_006494.2	435	tCg/tTg	4/4	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.558618906343023	2		661	563	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422280	47422280	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	183	463	0	ENST00000404338.3:c.348T>A	p.Tyr116Ter	p.Y116*	ENST00000404338	NM_004491.4	116	taT/taA	1/6	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.558618906343023	2		463	601	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047078	128047078	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	138	447	0	ENST00000285398.2:c.658-1G>A		p.X220_splice	ENST00000285398	NM_000122.1	220			1	2	FACETS	0.975	0.892	1	0.975	0.892	1	CLONAL	1	TRUE	1	0.558618906343023	2		447	507	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682823	190682823	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	141	321	0	ENST00000441310.2:c.499G>A	p.Asp167Asn	p.D167N	ENST00000441310	NM_000534.4	167	Gat/Aat	5/13	0.171191616049867	3	FACETS	1	0.982	1	0.633	0.58	0.688	INDETERMINATE	1	TRUE	1	0.558618906343023	3		321	510	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678751	52678751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	93	236	0	ENST00000394830.3:c.868C>T	p.His290Tyr	p.H290Y	ENST00000394830	NM_018313.4	290	Cat/Tat	9/30	1	2	FACETS	0.985	0.884	1	0.985	0.884	1	CLONAL	1	TRUE	1	0.558618906343023	2		236	338	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538272	187538272	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	137	401	0	ENST00000441802.2:c.8962A>T	p.Lys2988Ter	p.K2988*	ENST00000441802	NM_005245.3	2988	Aaa/Taa	11/27	0.18960904257987	1	FACETS	0.706	0.646	0.768	0.706	0.646	0.768	INDETERMINATE	1	TRUE	0	0.558618906343023	1		401	501	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675402	30675402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1422379570	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	181	647	0	ENST00000376406.3:c.2954C>T	p.Pro985Leu	p.P985L	ENST00000376406	NM_014641.2	985	cCt/cTt	8/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.558618906343023	2		647	559	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997434	149997434	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	187	410	0	ENST00000253339.5:c.2845C>G	p.Pro949Ala	p.P949A	ENST00000253339		949	Cct/Gct	6/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.558618906343023	2		410	599	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842326	151842326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs931161566	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	193	534	0	ENST00000262189.6:c.14086C>T	p.Leu4696Phe	p.L4696F	ENST00000262189	NM_170606.2	4696	Ctc/Ttc	54/59	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.558618906343023	2		534	589	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401425	139401426	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	114	509	0	ENST00000277541.6:c.3644-1_3644delinsAA		p.X1215_splice	ENST00000277541	NM_017617.3	1215		23/34	1	2	FACETS	0.789	0.714	0.869	0.789	0.714	0.869	SUBCLONAL	1	TRUE	1	0.558618906343023	2		509	517	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402771	139402772	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	177	661	0	ENST00000277541.6:c.3237_3238delinsTT	p.Gln1080Ter	p.Q1080*	ENST00000277541	NM_017617.3	1079	acCCag/acTTag	20/34	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.558618906343023	2		661	605	SUCCESS
APC	324	MSKCC	GRCh37	5	112174428	112174435	+	frameshift_variant	Frame_Shift_Del	DEL	ATGAAAGA	ATGAAAGA	T	novel	NA	P-0058817-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	136	472	0	ENST00000257430.4:c.3137_3144delinsT	p.Asn1046IlefsTer8	p.N1046Ifs*8	ENST00000257430	NM_000038.5	1046	aATGAAAGA/aT	16/16	1	2	FACETS	0.865	0.79	0.943	0.865	0.79	0.943	CLONAL	1	TRUE	1	0.558618906343023	2		472	563	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	89	302	0				ENST00000310581	NM_198253.2	-/1132			0.233065703030499	5	FACETS	0.904	0.807	1	0.602	0.538	0.67	INDETERMINATE	2	TRUE	2	0.424011965324286	5		302	380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574000	7574000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	260	455	0	ENST00000269305.4:c.1027G>T	p.Glu343Ter	p.E343*	ENST00000269305	NM_001126112.2	343	Gag/Tag	10/11	0.413570123655212	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.424011965324286	2		455	557	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66781598	66781598	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs754765552	NA	P-0058818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	109	433	0	ENST00000307102.5:c.1006G>C	p.Asp336His	p.D336H	ENST00000307102	NM_002755.3	336	Gat/Cat	9/11	0.421158100074279	3	FACETS	1	0.915	1	0.509	0.458	0.563	CLONAL	1	TRUE	1	0.424011965324286	3		433	612	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797282	135797282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	257	506	0	ENST00000298552.3:c.587C>T	p.Pro196Leu	p.P196L	ENST00000298552	NM_001162426.1	196	cCt/cTt	7/23	0.423760370491285	2	FACETS	0.974	0.919	1	0.974	0.919	1	CLONAL	2	TRUE	0	0.424011965324286	2		506	622	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357753	70357753	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	157	621	0	ENST00000374080.3:c.6004C>T	p.Gln2002Ter	p.Q2002*	ENST00000374080		2002	Cag/Tag	41/45	0.423760370491285	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.424011965324286	1		621	514	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004664	16004664	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	275	595	0	ENST00000268712.3:c.2590C>T	p.Gln864Ter	p.Q864*	ENST00000268712	NM_006311.3	864	Cag/Tag	20/46	0.413570123655212	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.424011965324286	2		595	620	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874524	155874524	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	140	401	0	ENST00000368323.3:c.235C>T	p.Gln79Ter	p.Q79*	ENST00000368323	NM_006912.5	79	Cag/Tag	4/6	0.423760370491285	3	FACETS	1	0.978	1	0.606	0.553	0.662	CLONAL	1	TRUE	1	0.424011965324286	3		401	660	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51519993	51519993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377298859	NA	P-0058818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	118	398	0	ENST00000260433.2:c.434G>A	p.Arg145Gln	p.R145Q	ENST00000260433		145	cGa/cAa	4/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.424011965324286	2		398	498	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23652436	23652436	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs730881884	NA	P-0058818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	175	432	0	ENST00000261584.4:c.43G>T	p.Glu15Ter	p.E15*	ENST00000261584	NM_024675.3	15	Gaa/Taa	1/13	0.423760370491285	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.424011965324286	2		432	405	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15943788	15943788	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	197	307	0	ENST00000268712.3:c.6700G>C	p.Glu2234Gln	p.E2234Q	ENST00000268712	NM_006311.3	2234	Gag/Cag	43/46	0.413570123655212	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.424011965324286	2		307	418	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799110	42799110	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	191	524	0	ENST00000575354.2:c.4594G>C	p.Glu1532Gln	p.E1532Q	ENST00000575354	NM_015125.3	1532	Gag/Cag	20/20	0.423760370491285	4	FACETS	0.872	0.808	0.937	0.872	0.808	0.937	CLONAL	2	TRUE	2	0.424011965324286	4		524	736	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026194	48026194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	128	522	0	ENST00000234420.5:c.1072G>A	p.Asp358Asn	p.D358N	ENST00000234420	NM_000179.2	358	Gac/Aac	4/10	1	2	FACETS	0.919	0.835	1	0.919	0.835	1	CLONAL	1	TRUE	1	0.424011965324286	2		522	657	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566451	41566451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	129	445	0	ENST00000263253.7:c.4328G>A	p.Gly1443Glu	p.G1443E	ENST00000263253	NM_001429.3	1443	gGa/gAa	27/31	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.424011965324286	2		445	590	SUCCESS
ALB	213	MSKCC	GRCh37	4	74274467	74274467	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs75522063	NA	P-0058818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	144	474	0	ENST00000295897.4:c.427G>A	p.Glu143Lys	p.E143K	ENST00000295897	NM_000477.5	143	Gag/Aag	4/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.424011965324286	2		474	613	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176718993	176718993	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1294287656	NA	P-0058818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	257	504	0	ENST00000439151.2:c.6297C>G	p.Phe2099Leu	p.F2099L	ENST00000439151	NM_022455.4	2099	ttC/ttG	22/23	0.423760370491285	2	FACETS	0.924	0.871	0.978	0.924	0.871	0.978	CLONAL	2	TRUE	0	0.424011965324286	2		504	656	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922787	44922787	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	516	515	0	ENST00000377967.4:c.1648del	p.Val550CysfsTer43	p.V550Cfs*43	ENST00000377967	NM_021140.2	550	Gtg/tg	16/29	0.371585373726589	5	FACETS	1	0.994	1			1	CLONAL	4	TRUE	NA	0.424011965324286	5		515	886	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171455	123171455	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	192	372	0	ENST00000218089.9:c.367C>A	p.Gln123Lys	p.Q123K	ENST00000218089	NM_001042749.1	123	Cag/Aag	6/35	0.423760370491285	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	0	0.424011965324286	2		372	453	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196762	123196762	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	179	335	0	ENST00000218089.9:c.1649del	p.Ala550GlufsTer26	p.A550Efs*26	ENST00000218089	NM_001042749.1	550	gCa/ga	18/35	0.423760370491285	2	FACETS	0.991	0.925	1	0.991	0.925	1	CLONAL	2	TRUE	0	0.424011965324286	2		335	426	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386450	31386450	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0058818-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	115	523	0	ENST00000328111.2:c.1674+1G>A		p.X558_splice	ENST00000328111	NM_006892.3	558			0.423760370491285	5	FACETS	0.974	0.877	1	0.325	0.292	0.36	CLONAL	1	TRUE	2	0.424011965324286	5		523	911	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0058820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	488	362	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.751542445707699	3	FACETS	0.968	0.933	1	0.968	0.933	1	CLONAL	2	TRUE	1	0.805504293687549	3		362	878	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0058820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	802	771	6	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.797582855765708	2	FACETS	0.997	0.977	1	0.997	0.977	1	CLONAL	2	TRUE	0	0.805504293687549	2		777	999	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279807	46279809	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	rs553605982	NA	P-0058820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	188	753	4	ENST00000371998.3:c.3739_3741del	p.Met1247del	p.M1247del	ENST00000371998		1245	ATG/-	20/23	0.805504293687549	3	FACETS	0.523	0.482	0.566			1	SUBCLONAL	1	TRUE	NA	0.805504293687549	3		757	1251	SUCCESS
APC	324	MSKCC	GRCh37	5	112116585	112116585	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	232	485	2	ENST00000257430.4:c.631del	p.Glu211LysfsTer8	p.E211Kfs*8	ENST00000257430	NM_000038.5	210	atG/at	6/16	0.800387308659383	1	FACETS	0.977	0.932	1	0.977	0.932	1	CLONAL	1	TRUE	0	0.805504293687549	1		487	352	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858774	9858774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs199784503	NA	P-0058820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	304	668	2	ENST00000330684.3:c.2627T>C	p.Ile876Thr	p.I876T	ENST00000330684	NM_001134407.1	876	aTt/aCt	13/13	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.805504293687549	2		670	754	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350054	89350054	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1156384694	NA	P-0058820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	462	973	9	ENST00000301030.4:c.2896G>A	p.Ala966Thr	p.A966T	ENST00000301030	NM_001256183.1	966	Gcc/Acc	9/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.805504293687549	2		982	1134	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390125	89390125	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	260	655	0	ENST00000336596.2:c.874C>A	p.Pro292Thr	p.P292T	ENST00000336596	NM_005233.5	292	Cct/Act	4/17	0.805504293687549	1	FACETS	0.943	0.9	0.984	0.943	0.9	0.984	CLONAL	1	TRUE	0	0.805504293687549	1		655	409	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974794	21974795	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0058820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	411	731	2	ENST00000304494.5:c.32dup	p.Ser12PhefsTer3	p.S12Ffs*3	ENST00000304494	NM_000077.4	11	cct/ccCt	1/3	0.800387308659383	1	FACETS	0.933	0.9	0.967	0.933	0.9	0.967	CLONAL	1	TRUE	0	0.805504293687549	1		733	653	SUCCESS
APC	324	MSKCC	GRCh37	5	112116586	112116586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058820-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	19	482	0	ENST00000257430.4:c.631G>A	p.Glu211Lys	p.E211K	ENST00000257430	NM_000038.5	211	Gaa/Aaa	6/16	0.800387308659383	1	FACETS	0.08	0.06	0.103	0.08	0.06	0.103	SUBCLONAL	1	TRUE	0	0.805504293687549	1		482	354	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	123	302	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.843	0.777	0.91	1	0.989	1	CLONAL	2	TRUE	1	0.534208699622926	2		302	273	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0058821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	193	697	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.29418004309768	3	FACETS	0.896	0.836	0.957	0.896	0.836	0.957	INDETERMINATE	2	TRUE	1	0.534208699622926	3		699	511	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0058821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	148	396	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.534208699622926	2		396	403	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0058821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	118	471	1	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.108571180423129	4	FACETS	1	0.981	1	1	0.981	1	INDETERMINATE	2	TRUE	2	0.534208699622926	4		472	272	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720711	89720712	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0058821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	53	90	0	ENST00000371953.3:c.867dup	p.Val290SerfsTer8	p.V290Sfs*8	ENST00000371953	NM_000314.4	288	gaa/gAaa	8/9	0.534208699622926	2	FACETS	0.973	0.894	1	1	0.981	1	CLONAL	3	TRUE	0	0.534208699622926	2		90	68	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968149	68968149	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	80	461	0	ENST00000288368.4:c.1178G>A	p.Gly393Glu	p.G393E	ENST00000288368	NM_024870.2	393	gGa/gAa	10/40	0.3590023300164	0	FACETS	0.701	0.63	0.774			1	SUBCLONAL	1	TRUE	0	0.534208699622926	0		461	199	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421239	12421239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	109	510	0	ENST00000287820.6:c.119C>T	p.Pro40Leu	p.P40L	ENST00000287820	NM_015869.4	40	cCc/cTc	2/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.534208699622926	2		510	327	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050852	49050852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1231557654	NA	P-0058821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	346	326	0	ENST00000267163.4:c.2536C>T	p.Gln846Ter	p.Q846*	ENST00000267163	NM_000321.2	846	Cag/Tag	25/27	0.534208699622926	3	FACETS	1	0.992	1	1	0.997	1	CLONAL	4	TRUE	0	0.534208699622926	3		326	395	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657031	45657031	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	196	485	0	ENST00000407780.3:c.125G>A	p.Gly42Glu	p.G42E	ENST00000407780	NM_001283052.1	42	gGa/gAa	3/7	1	2	FACETS	0.814	0.762	0.866	1	0.993	1	CLONAL	2	TRUE	1	0.534208699622926	2		485	451	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076726	72076726	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	177	535	0	ENST00000357731.5:c.771G>A	p.Trp257Ter	p.W257*	ENST00000357731	NM_173808.2	257	tgG/tgA	5/7	1	2	FACETS	0.791	0.737	0.845	1	0.992	1	SUBCLONAL	2	TRUE	1	0.534208699622926	2		535	419	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488315	56488315	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	242	469	0	ENST00000267101.3:c.1834C>T	p.Pro612Ser	p.P612S	ENST00000267101	NM_001982.3	612	Ccc/Tcc	15/28	1	2	FACETS	0.86	0.811	0.908	1	0.995	1	CLONAL	2	TRUE	1	0.534208699622926	2		469	527	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462130	120462130	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	191	577	0	ENST00000256646.2:c.5586G>T	p.Leu1862Phe	p.L1862F	ENST00000256646	NM_024408.3	1862	ttG/ttT	31/34	1	2	FACETS	0.874	0.819	0.929	1	0.993	1	CLONAL	2	TRUE	1	0.534208699622926	2		577	409	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18649062	18649062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	52	363	0	ENST00000266497.5:c.2737G>A	p.Gly913Ser	p.G913S	ENST00000266497		913	Ggc/Agc	19/31	0.403368338156749	0	FACETS	0.708	0.62	0.799			1	SUBCLONAL	1	TRUE	0	0.534208699622926	0		363	128	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040847	42040847	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1330248572	NA	P-0058821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	167	580	0	ENST00000219905.7:c.5225A>G	p.Gln1742Arg	p.Q1742R	ENST00000219905	NM_001164273.1	1742	cAa/cGa	16/24	1	2	FACETS	0.766	0.712	0.821	1	0.991	1	SUBCLONAL	2	TRUE	1	0.534208699622926	2		580	408	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729148	66729148	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	251	619	0	ENST00000307102.5:c.356A>G	p.His119Arg	p.H119R	ENST00000307102	NM_002755.3	119	cAt/cGt	3/11	1	2	FACETS	0.888	0.84	0.937	1	0.995	1	CLONAL	2	TRUE	1	0.534208699622926	2		619	529	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896567	78896567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	187	546	0	ENST00000306801.3:c.2564C>T	p.Ser855Phe	p.S855F	ENST00000306801	NM_020761.2	855	tCc/tTc	22/34	0.166894679581201	0	FACETS	0.73	0.681	0.778			1	INDETERMINATE	1	TRUE	0	0.534208699622926	0		546	447	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054431	13054431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	261	659	0	ENST00000316448.5:c.1041G>A	p.Trp347Ter	p.W347*	ENST00000316448	NM_004343.3	347	tgG/tgA	8/9	1	2	FACETS	0.823	0.777	0.868	1	0.995	1	CLONAL	2	TRUE	1	0.534208699622926	2		659	594	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920431	134920431	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	209	568	0	ENST00000398015.3:c.2246A>G	p.Asn749Ser	p.N749S	ENST00000398015	NM_004441.4	749	aAc/aGc	12/16	0.50704419849316	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.534208699622926	1		568	434	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332691	153332691	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	191	606	0	ENST00000281708.4:c.265G>C	p.Glu89Gln	p.E89Q	ENST00000281708	NM_033632.3	89	Gag/Cag	2/12	1	2	FACETS	0.774	0.723	0.825	1	0.992	1	SUBCLONAL	2	TRUE	1	0.534208699622926	2		606	462	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524652	176524652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	203	654	0	ENST00000292408.4:c.2384C>T	p.Pro795Leu	p.P795L	ENST00000292408	NM_213647.1	795	cCc/cTc	18/18	0.17283014319862	3	FACETS	1	0.973	1	1	0.973	1	INDETERMINATE	2	TRUE	1	0.534208699622926	3		654	451	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289296	33289296	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	218	529	0	ENST00000374542.5:c.256C>T	p.Pro86Ser	p.P86S	ENST00000374542	NM_001141970.1	86	Cca/Tca	3/8	0.534208699622926	5	FACETS	0.838	0.781	0.897	0.419	0.39	0.449	CLONAL	2	TRUE	1	0.534208699622926	5		529	877	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127933426	127933426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	130	359	0	ENST00000373547.4:c.109G>A	p.Glu37Lys	p.E37K	ENST00000373547	NM_002721.4	37	Gaa/Aaa	2/7	1	2	FACETS	0.851	0.786	0.916	1	0.99	1	CLONAL	2	TRUE	1	0.534208699622926	2		359	286	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755499	133755499	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1336603476	NA	P-0058821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	170	460	0	ENST00000318560.5:c.1468C>T	p.His490Tyr	p.H490Y	ENST00000318560	NM_005157.4	490	Cac/Tac	9/11	1	2	FACETS	0.82	0.764	0.876	1	0.992	1	CLONAL	2	TRUE	1	0.534208699622926	2		460	388	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779091	135779091	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058821-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	195	554	0	ENST00000298552.3:c.2155C>T	p.Leu719Phe	p.L719F	ENST00000298552	NM_001162426.1	719	Ctc/Ttc	17/23	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.534208699622926	2		554	516	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240285	41240285	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	173	529	0	ENST00000379561.5:c.65C>G	p.Ser22Trp	p.S22W	ENST00000379561	NM_002015.3	22	tCg/tGg	1/3	0.488370104220052	2	FACETS	0.947	0.885	1	0.947	0.885	1	CLONAL	2	TRUE	0	0.488370104220052	2		529	374	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	160	302	0				ENST00000310581	NM_198253.2	-/1132			0.437761789527008	4	FACETS	0.874	0.806	0.944	0.874	0.806	0.944	CLONAL	2	TRUE	2	0.488370104220052	4		302	558	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180999	108180999	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	86	388	0	ENST00000278616.4:c.5875G>C	p.Glu1959Gln	p.E1959Q	ENST00000278616	NM_000051.3	1959	Gaa/Caa	39/63	0.304158743232743	4	FACETS	1	0.958	1	0.584	0.519	0.653	CLONAL	1	TRUE	2	0.488370104220052	4		388	449	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994730	73994730	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	296	898	0	ENST00000318443.5:c.214A>T	p.Thr72Ser	p.T72S	ENST00000318443	NM_001024736.1	72	Acc/Tcc	3/10	0.488370104220052	4	FACETS	0.958	0.903	1	0.479	0.451	0.507	CLONAL	2	TRUE	0	0.488370104220052	4		898	942	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149238714	149238714	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	173	631	0	ENST00000360632.3:c.1081C>G	p.Leu361Val	p.L361V	ENST00000360632	NM_015472.4	361	Ctt/Gtt	7/7	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.488370104220052	2		631	642	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984936	55984936	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058822-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	69	440	1	ENST00000263923.4:c.193A>T	p.Asn65Tyr	p.N65Y	ENST00000263923	NM_002253.2	65	Aat/Tat	3/30	0.488370104220052	1	FACETS	0.763	0.671	0.86	0.763	0.671	0.86	SUBCLONAL	1	TRUE	0	0.488370104220052	1		441	280	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0058823-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	27	409	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.365930746990169	4	FACETS	0.229	0.181	0.284	0.115	0.09	0.142	SUBCLONAL	1	TRUE	2	0.457795289871512	4		409	750	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0058823-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	21	265	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.458518014563323	4	FACETS	0.263	0.201	0.335	0.131	0.1	0.168	SUBCLONAL	1	TRUE	2	0.457795289871512	4		265	509	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692791	89692791	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058823-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	17	235	0	ENST00000371953.3:c.275A>T	p.Asp92Val	p.D92V	ENST00000371953	NM_000314.4	92	gAc/gTc	5/9	0.10496315912563	6	FACETS	0.307	0.228	0.402	0.102	0.076	0.134	INDETERMINATE	1	TRUE	3	0.457795289871512	6		235	463	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519896	NA	P-0058823-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	46	469	0	ENST00000281708.4:c.1514G>T	p.Arg505Leu	p.R505L	ENST00000281708	NM_033632.3	505	cGc/cTc	10/12	0.457795289871512	4	FACETS	0.29	0.243	0.342	0.145	0.121	0.171	SUBCLONAL	1	TRUE	2	0.457795289871512	4		469	1010	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988709	41988709	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs199666635	NA	P-0058823-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	28	476	0	ENST00000219905.7:c.1501A>G	p.Met501Val	p.M501V	ENST00000219905	NM_001164273.1	501	Atg/Gtg	3/24	0.131696747825458	5	FACETS	0.413	0.33	0.509	0.138	0.11	0.17	INDETERMINATE	1	TRUE	2	0.457795289871512	5		476	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0058841-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	409	695	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.802590445491817	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.802590445491817	2		695	488	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111855975	111855975	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058841-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	150	528	0	ENST00000341259.2:c.26C>T	p.Ser9Phe	p.S9F	ENST00000341259	NM_005475.2	9	tCc/tTc	2/8	0.802590445491817	3	FACETS	0.956	0.878	1	0.478	0.439	0.518	CLONAL	1	TRUE	1	0.802590445491817	3		528	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0058845-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	202	632	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.651310833128174	1	FACETS	0.945	0.888	1	0.945	0.888	1	CLONAL	1	TRUE	0	0.659945535340993	1		632	434	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586261	48586261	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058845-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	120	299	0	ENST00000342988.3:c.931del	p.Gln311SerfsTer25	p.Q311Sfs*25	ENST00000342988	NM_005359.5	310	ttC/tt	8/12	0.659945535340993	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.659945535340993	1		299	219	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218456	1218463	+	frameshift_variant	Frame_Shift_Del	DEL	ATCCAGCT	ATCCAGCT	-	novel	NA	P-0058845-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	190	408	0	ENST00000326873.7:c.331_338del	p.Ile111GlyfsTer49	p.I111Gfs*49	ENST00000326873	NM_000455.4	111	ATCCAGCTg/g	2/10	0.659945535340993	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.659945535340993	1		408	362	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627235	86627241	+	frameshift_variant	Frame_Shift_Del	DEL	TATCTTA	TATCTTA	-	novel	NA	P-0058845-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	178	453	0	ENST00000274376.6:c.612_618del	p.Tyr204Ter	p.Y204*	ENST00000274376	NM_002890.2	204	TATCTTAta/ta	2/25	0.659945535340993	1	FACETS	0.939	0.878	1	0.939	0.878	1	CLONAL	1	TRUE	0	0.659945535340993	1		453	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0058846-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	21	1110	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.508800224780168	2	FACETS	0.11	0.084	0.141	0.055	0.042	0.071	SUBCLONAL	1	TRUE	0	0.523777537078676	2		1111	727	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0058846-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	354	773	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.508800224780168	2	FACETS	0.99	0.946	1	0.99	0.946	1	CLONAL	2	TRUE	0	0.523777537078676	2		773	683	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058846-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	113	501	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	0.514860176583856	3	FACETS	0.842	0.759	0.929	0.421	0.379	0.465	CLONAL	1	TRUE	1	0.523777537078676	3		501	647	SUCCESS
APC	324	MSKCC	GRCh37	5	112173578	112173578	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058846-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	112	327	0	ENST00000257430.4:c.2287G>T	p.Glu763Ter	p.E763*	ENST00000257430	NM_000038.5	763	Gaa/Taa	16/16	0.523777537078676	2	FACETS	0.981	0.904	1	0.981	0.904	1	CLONAL	2	TRUE	0	0.523777537078676	2		327	218	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127487	55127487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759729258	NA	P-0058846-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	299	436	0	ENST00000257290.5:c.275C>T	p.Ala92Val	p.A92V	ENST00000257290	NM_006206.4	92	gCg/gTg	3/23	0.521147442084254	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.523777537078676	2		436	551	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044550	47044550	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	97	227	0	ENST00000377604.3:c.2047G>T	p.Glu683Ter	p.E683*	ENST00000377604	NM_001204468.1	683	Gag/Tag	18/24	1	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.365535398241689	1		227	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	172	377	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.322073974349612	2	FACETS	0.937	0.869	1	0.937	0.869	1	CLONAL	2	TRUE	0	0.365535398241689	2		377	502	SUCCESS
APC	324	MSKCC	GRCh37	5	112174388	112174388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	68	388	0	ENST00000257430.4:c.3097G>A	p.Asp1033Asn	p.D1033N	ENST00000257430	NM_000038.5	1033	Gat/Aat	16/16	1	2	FACETS	0.935	0.817	1	0.935	0.817	1	CLONAL	1	TRUE	1	0.365535398241689	2		388	398	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841431	156841431	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	67	502	0	ENST00000524377.1:c.734C>A	p.Pro245Gln	p.P245Q	ENST00000524377	NM_002529.3	245	cCa/cAa	7/17	1	2	FACETS	0.67	0.583	0.764	0.67	0.583	0.764	SUBCLONAL	1	TRUE	1	0.365535398241689	2		502	547	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044340	128044340	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	107	427	0	ENST00000285398.2:c.1281G>T	p.Met427Ile	p.M427I	ENST00000285398	NM_000122.1	427	atG/atT	8/15	0.182129452845776	2	FACETS	0.773	0.694	0.858	0.387	0.347	0.429	INDETERMINATE	1	TRUE	0	0.365535398241689	2		427	757	SUCCESS
APC	324	MSKCC	GRCh37	5	112176467	112176467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	91	389	0	ENST00000257430.4:c.5176G>A	p.Glu1726Lys	p.E1726K	ENST00000257430	NM_000038.5	1726	Gaa/Aaa	16/16	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.365535398241689	2		389	458	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953016	2953016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764229454	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	91	416	0	ENST00000396946.4:c.2924G>A	p.Arg975Gln	p.R975Q	ENST00000396946	NM_032415.4	975	cGg/cAg	22/25	0.365535398241689	4	FACETS	0.794	0.704	0.891	0.397	0.352	0.446	SUBCLONAL	1	TRUE	2	0.365535398241689	4		416	856	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781116	135781116	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1564481122	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	95	477	0	ENST00000298552.3:c.1849del	p.His617IlefsTer12	p.H617Ifs*12	ENST00000298552	NM_001162426.1	617	Cat/at	15/23	0.322073974349612	2	FACETS	0.869	0.775	0.969	0.435	0.387	0.485	CLONAL	1	TRUE	0	0.365535398241689	2		477	598	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440961	56440961	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	153	487	0	ENST00000407977.2:c.376G>C	p.Ala126Pro	p.A126P	ENST00000407977		126	Gct/Cct	4/10	0.326210285417435	4	FACETS	0.802	0.735	0.871	0.802	0.735	0.871	CLONAL	2	TRUE	2	0.365535398241689	4		487	713	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726689	46726689	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1170180432	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	73	396	0	ENST00000371975.4:c.766+2T>C		p.X256_splice	ENST00000371975	NM_003579.3	256			1	2	FACETS	0.747	0.654	0.846	0.747	0.654	0.846	SUBCLONAL	1	TRUE	1	0.365535398241689	2		396	535	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266594	115266594	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	75	320	0	ENST00000438362.2:c.1921A>C	p.Thr641Pro	p.T641P	ENST00000438362	NM_001242891.1	641	Acc/Ccc	16/20	1	2	FACETS	0.952	0.838	1	0.952	0.838	1	CLONAL	1	TRUE	1	0.365535398241689	2		320	431	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491062	120491062	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	88	447	0	ENST00000256646.2:c.2727G>T	p.Glu909Asp	p.E909D	ENST00000256646	NM_024408.3	909	gaG/gaT	17/34	1	2	FACETS	0.813	0.722	0.911	0.813	0.722	0.911	CLONAL	1	TRUE	1	0.365535398241689	2		447	592	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226568812	226568812	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	414	433	1	ENST00000366794.5:c.1257G>T	p.Leu419Phe	p.L419F	ENST00000366794	NM_001618.3	419	ttG/ttT	9/23	0.365535398241689	5	FACETS	1	0.982	1	1	0.982	1	CLONAL	4	TRUE	1	0.365535398241689	5		434	840	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851523	63851523	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	95	446	0	ENST00000279873.7:c.2301G>T	p.Lys767Asn	p.K767N	ENST00000279873	NM_032199.2	767	aaG/aaT	10/10	0.309875013954515	4	FACETS	1	0.906	1			1	CLONAL	1	TRUE	NA	0.365535398241689	4		446	697	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154428	2154428	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	96	483	0	ENST00000434045.2:c.500G>A	p.Gly167Asp	p.G167D	ENST00000434045	NM_001127598.1	167	gGc/gAc	5/5	0.120113822652911	5	FACETS	1	0.964	1	0.297	0.265	0.332	INDETERMINATE	1	TRUE	1	0.365535398241689	5		483	684	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456791	32456791	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	150	413	0	ENST00000332351.3:c.101G>T	p.Arg34Leu	p.R34L	ENST00000332351	NM_024426.4	34	cGg/cTg	1/10	0.120113822652911	5	FACETS	1	0.978	1	0.594	0.546	0.643	INDETERMINATE	2	TRUE	1	0.365535398241689	5		413	535	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691094	18691095	+	missense_variant	Missense_Mutation	DNP	CG	CG	GA	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	241	371	0	ENST00000266497.5:c.3205_3206delinsGA	p.Arg1069Glu	p.R1069E	ENST00000266497		1069	CGa/GAa	23/31	0.365535398241689	5	FACETS	0.989	0.94	1	0.989	0.94	1	CLONAL	5	TRUE	0	0.365535398241689	5		371	413	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25362814	25362814	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	36	321	0	ENST00000311936.3:c.482G>A	p.Arg161Gln	p.R161Q	ENST00000311936	NM_004985.3	161	cGa/cAa	5/5	0.365535398241689	6	FACETS	0.736	0.605	0.884	0.123	0.1	0.148	SUBCLONAL	1	TRUE	0	0.365535398241689	6		321	463	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231319	46231319	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	124	371	0	ENST00000334344.6:c.1159A>T	p.Asn387Tyr	p.N387Y	ENST00000334344	NM_152641.2	387	Aat/Tat	10/21	NA	2	FACETS	0.966	0.885	1			1	INDETERMINATE	2	TRUE	NA	0.365535398241689	2		371	351	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042391	42042391	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	104	545	0	ENST00000219905.7:c.6586G>T	p.Glu2196Ter	p.E2196*	ENST00000219905	NM_001164273.1	2196	Gag/Tag	17/24	1	2	FACETS	0.827	0.741	0.918	0.827	0.741	0.918	CLONAL	1	TRUE	1	0.365535398241689	2		545	688	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774125	66774125	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	83	492	0	ENST00000307102.5:c.601C>A	p.Arg201Ser	p.R201S	ENST00000307102	NM_002755.3	201	Cgt/Agt	6/11	1	2	FACETS	0.748	0.661	0.841	0.748	0.661	0.841	SUBCLONAL	1	TRUE	1	0.365535398241689	2		492	607	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679171	88679171	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs890457420	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	63	419	0	ENST00000360948.2:c.866T>C	p.Val289Ala	p.V289A	ENST00000360948	NM_001012338.2	289	gTg/gCg	8/19	1	2	FACETS	0.759	0.658	0.868	0.759	0.658	0.868	SUBCLONAL	1	TRUE	1	0.365535398241689	2		419	454	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222473	2222473	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1275009442	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	118	514	0	ENST00000326181.6:c.667G>T	p.Glu223Ter	p.E223*	ENST00000326181	NM_032271.2	223	Gag/Tag	9/21	0.315601939790997	3	FACETS	1	0.941	1	0.53	0.478	0.584	CLONAL	1	TRUE	1	0.365535398241689	3		514	721	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645871	67645871	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	132	327	0	ENST00000264010.4:c.799C>T	p.Gln267Ter	p.Q267*	ENST00000264010	NM_006565.3	267	Cag/Tag	4/12	0.326210285417435	4	FACETS	0.839	0.764	0.916	0.839	0.764	0.916	CLONAL	2	TRUE	2	0.365535398241689	4		327	588	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33679977	33679977	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	78	392	0	ENST00000308377.4:c.2104C>G	p.Leu702Val	p.L702V	ENST00000308377	NM_152270.3	702	Ctg/Gtg	5/5	0.326210285417435	4	FACETS	0.834	0.732	0.943	0.417	0.366	0.472	CLONAL	1	TRUE	2	0.365535398241689	4		392	699	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096901	11096901	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555752952	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	80	493	0	ENST00000358026.2:c.392C>G	p.Ser131Cys	p.S131C	ENST00000358026	NM_001128849.1	131	tCt/tGt	4/36	0.322073974349612	2	FACETS	0.68	0.598	0.767	0.34	0.299	0.384	SUBCLONAL	1	TRUE	0	0.365535398241689	2		493	644	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272198	15272198	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	160	507	0	ENST00000263388.2:c.6241G>C	p.Gly2081Arg	p.G2081R	ENST00000263388	NM_000435.2	2081	Ggc/Cgc	33/33	0.322073974349612	2	FACETS	0.933	0.863	1	0.933	0.863	1	CLONAL	2	TRUE	0	0.365535398241689	2		507	469	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227668	36227668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	221	512	0	ENST00000222270.7:c.7237C>T	p.His2413Tyr	p.H2413Y	ENST00000222270	NM_014727.1	2413	Cat/Tat	31/37	0.326210285417435	4	FACETS	0.89	0.829	0.953	0.89	0.829	0.953	CLONAL	2	TRUE	2	0.365535398241689	4		512	928	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967173	25967173	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	213	461	0	ENST00000435504.4:c.2033C>T	p.Ala678Val	p.A678V	ENST00000435504		678	gCc/gTc	13/13	0.120113822652911	5	FACETS	0.907	0.847	0.969	0.68	0.635	0.727	INDETERMINATE	3	TRUE	1	0.365535398241689	5		461	663	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979302	40979302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	165	429	0	ENST00000373198.4:c.1831C>A	p.Leu611Met	p.L611M	ENST00000373198	NM_133170.3	611	Ctg/Atg	11/32	0.059777900702255	3	FACETS	0.846	0.78	0.914			1	INDETERMINATE	2	TRUE	NA	0.365535398241689	3		429	631	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21340185	21340185	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	72	351	0	ENST00000215739.8:c.319A>T	p.Arg107Trp	p.R107W	ENST00000215739	NM_006767.3	107	Agg/Tgg	3/21	0.326506220288985	4	FACETS	0.814	0.711	0.925	0.271	0.237	0.309	CLONAL	1	TRUE	1	0.365535398241689	4		351	661	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478140	138478140	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	82	382	0	ENST00000289153.2:c.46G>C	p.Asp16His	p.D16H	ENST00000289153	NM_006219.2	16	Gac/Cac	1/22	0.326210285417435	4	FACETS	0.927	0.818	1	0.463	0.409	0.522	CLONAL	1	TRUE	2	0.365535398241689	4		382	661	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748093	41748093	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	40	275	0	ENST00000226382.2:c.676del	p.Ala226ArgfsTer83	p.A226Rfs*83	ENST00000226382	NM_003924.3	226	Gcg/cg	3/3	0.365535398241689	3	FACETS	0.809	0.675	0.957	0.404	0.337	0.479	CLONAL	1	TRUE	1	0.365535398241689	3		275	320	SUCCESS
REST	5978	MSKCC	GRCh37	4	57797416	57797416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763356980	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	211	613	0	ENST00000309042.7:c.2392C>T	p.Pro798Ser	p.P798S	ENST00000309042	NM_005612.4	798	Cct/Tct	4/4	0.365535398241689	3	FACETS	0.853	0.794	0.914	0.853	0.794	0.914	CLONAL	2	TRUE	1	0.365535398241689	3		613	800	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874568	35874568	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	74	396	0	ENST00000303115.3:c.724T>A	p.Leu242Ile	p.L242I	ENST00000303115	NM_002185.3	242	Tta/Ata	6/8	1	2	FACETS	0.865	0.76	0.978	0.865	0.76	0.978	CLONAL	1	TRUE	1	0.365535398241689	2		396	468	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497350	149497350	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	95	411	0	ENST00000261799.4:c.2968G>T	p.Ala990Ser	p.A990S	ENST00000261799	NM_002609.3	990	Gcc/Tcc	22/23	0.365535398241689	1	FACETS	0.917	0.821	1	0.917	0.821	1	CLONAL	1	TRUE	0	0.365535398241689	1		411	463	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048893	180048893	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	89	421	0	ENST00000261937.6:c.1669G>T	p.Gly557Cys	p.G557C	ENST00000261937	NM_182925.4	557	Ggc/Tgc	13/30	1	2	FACETS	0.876	0.778	0.98	0.876	0.778	0.98	CLONAL	1	TRUE	1	0.365535398241689	2		421	556	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058756	180058756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	81	504	0	ENST00000261937.6:c.81G>A	p.Met27Ile	p.M27I	ENST00000261937	NM_182925.4	27	atG/atA	2/30	1	2	FACETS	0.819	0.723	0.922	0.819	0.723	0.922	CLONAL	1	TRUE	1	0.365535398241689	2		504	541	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161807906	161807906	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	78	376	0	ENST00000366898.1:c.1087G>T	p.Ala363Ser	p.A363S	ENST00000366898	NM_004562.2	363	Gcc/Tcc	10/12	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.365535398241689	2		376	420	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072493	5072493	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	70	300	0	ENST00000381652.3:c.1643A>G	p.Asn548Ser	p.N548S	ENST00000381652	NM_004972.3	548	aAt/aGt	13/25	0.365535398241689	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	0	0.365535398241689	1		300	301	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486160	8486160	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	81	414	0	ENST00000356435.5:c.2657A>C	p.His886Pro	p.H886P	ENST00000356435		886	cAc/cCc	17/35	0.365535398241689	1	FACETS	0.833	0.737	0.934	0.833	0.737	0.934	CLONAL	1	TRUE	0	0.365535398241689	1		414	435	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882100	36882100	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	141	400	0	ENST00000358127.4:c.913C>A	p.Arg305Ser	p.R305S	ENST00000358127	NM_001280556.1	305	Cgt/Agt	8/10	0.322073974349612	2	FACETS	0.873	0.802	0.946	0.873	0.802	0.946	CLONAL	2	TRUE	0	0.365535398241689	2		400	442	SUCCESS
BTK	695	MSKCC	GRCh37	X	100609646	100609646	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058847-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	77	207	0	ENST00000308731.7:c.1603G>C	p.Val535Leu	p.V535L	ENST00000308731	NM_000061.2	535	Gtt/Ctt	16/19	1	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.365535398241689	1		207	246	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0058848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	92	738	0				ENST00000310581	NM_198253.2	-/1132			0.252554680606762	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.893040403549689	0		738	187	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690405	33690405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777285142	NA	P-0058848-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	248	498	0	ENST00000308377.4:c.422G>A	p.Arg141His	p.R141H	ENST00000308377	NM_152270.3	141	cGt/cAt	2/5	1	2	FACETS	0.987	0.931	1	0.987	0.931	1	CLONAL	1	FALSE	1	0.893040403549689	2		498	563	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27228229	27228229	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757379347	NA	P-0058849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	26	329	0	ENST00000380036.4:c.3226C>T	p.Arg1076Trp	p.R1076W	ENST00000380036	NM_000459.3	1076	Cgg/Tgg	22/23	1	2	FACETS	0.67	0.53	0.829	0.67	0.53	0.829	SUBCLONAL	1	TRUE	1	0.22	2		329	353	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230723	46230728	+	inframe_deletion	In_Frame_Del	DEL	TATTTC	TATTTC	-	novel	NA	P-0058849-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	29	397	0	ENST00000334344.6:c.973_978del	p.Ile325_Ser326del	p.I325_S326del	ENST00000334344	NM_152641.2	324	ttTATTTCt/ttt	8/21	1	2	FACETS	0.619	0.496	0.759	0.619	0.496	0.759	SUBCLONAL	1	TRUE	1	0.22	2		397	426	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	15	302	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.438	0.32	0.58	0.438	0.32	0.58	SUBCLONAL	1	TRUE	1	0.25	2		302	274	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0058850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	9	77	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	1	2	FACETS	0.818	0.547	1	0.818	0.547	1	CLONAL	1	TRUE	1	0.25	2		77	88	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250247	39250247	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs727504295	NA	P-0058850-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	19	259	0	ENST00000402219.2:c.1322G>A	p.Cys441Tyr	p.C441Y	ENST00000402219	NM_005633.3	441	tGt/tAt	10/23	1	2	FACETS	0.589	0.448	0.755	0.589	0.448	0.755	SUBCLONAL	1	TRUE	1	0.25	2		259	258	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650552	18650552	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0058851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	77	344	0	ENST00000266497.5:c.2764-1G>A		p.X922_splice	ENST00000266497		922			0.339213794564592	2	FACETS	0.932	0.822	1	0.466	0.411	0.525	CLONAL	1	TRUE	0	0.398153366036719	2		344	415	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715789	18715789	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	122	403	0	ENST00000266497.5:c.3620G>C	p.Arg1207Thr	p.R1207T	ENST00000266497		1207	aGa/aCa	25/31	0.339213794564592	2	FACETS	1	0.957	1	0.547	0.496	0.6	CLONAL	1	TRUE	0	0.398153366036719	2		403	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579473	7579473	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587782769	NA	P-0058851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	233	608	0	ENST00000269305.4:c.214C>A	p.Pro72Thr	p.P72T	ENST00000269305	NM_001126112.2	72	Ccc/Acc	4/11	0.339213794564592	2	FACETS	1	0.987	1	0.61	0.569	0.652	CLONAL	1	TRUE	0	0.398153366036719	2		608	960	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157495234	157495234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368880015	NA	P-0058851-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	204	436	0	ENST00000346085.5:c.3118C>T	p.Pro1040Ser	p.P1040S	ENST00000346085	NM_020732.3	1040	Ccc/Tcc	11/20	0.339213794564592	2	FACETS	1	0.988	1	0.651	0.605	0.698	CLONAL	1	TRUE	0	0.398153366036719	2		436	787	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0058853-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	168	879	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.178402614738855	3	FACETS	0.763	0.703	0.826	0.509	0.468	0.551	INDETERMINATE	2	TRUE	0	0.351216804791889	3		879	737	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911693	32911693	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs864622672	NA	P-0058853-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	39	422	0	ENST00000380152.3:c.3201del	p.Val1068TyrfsTer9	p.V1068Yfs*9	ENST00000380152		1067	acT/ac	11/27	0.351216804791889	1	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	0	0.351216804791889	1		422	178	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	277	738	0				ENST00000310581	NM_198253.2	-/1132			0.577907484192751	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.699895544596286	4		738	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	204	493	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.119664574757721	6	FACETS	0.936	0.871	1			1	INDETERMINATE	2	TRUE	NA	0.699895544596286	6		493	747	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	220	632	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.119664574757721	6	FACETS	0.983	0.918	1			1	INDETERMINATE	2	TRUE	NA	0.699895544596286	6		632	767	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005419	29005419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55687105	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	33	356	0	ENST00000282397.4:c.842G>A	p.Arg281Gln	p.R281Q	ENST00000282397	NM_002019.4	281	cGa/cAa	7/30	1	2	FACETS	0.26	0.211	0.314	0.26	0.211	0.314	SUBCLONAL	1	TRUE	1	0.699895544596286	2		356	363	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259451	55259451	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761920220	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	162	382	0	ENST00000275493.2:c.2509G>A	p.Asp837Asn	p.D837N	ENST00000275493	NM_005228.3	837	Gac/Aac	21/28	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.699895544596286	2		382	431	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521763	89521763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	140	333	0	ENST00000336596.2:c.2840C>T	p.Ser947Phe	p.S947F	ENST00000336596	NM_005233.5	947	tCc/tTc	16/17	0.699895544596286	2	FACETS	0.976	0.898	1	0.488	0.449	0.528	CLONAL	1	TRUE	0	0.699895544596286	2		333	410	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436600	8436600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs888423638	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	99	270	0	ENST00000356435.5:c.4078G>A	p.Glu1360Lys	p.E1360K	ENST00000356435		1360	Gaa/Aaa	24/35	0.699895544596286	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.699895544596286	1		270	165	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143551	108143551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201780199	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	120	335	0	ENST00000278616.4:c.3256C>T	p.Arg1086Cys	p.R1086C	ENST00000278616	NM_000051.3	1086	Cgc/Tgc	22/63	0.699895544596286	2	FACETS	0.932	0.85	1	0.466	0.425	0.508	CLONAL	1	TRUE	0	0.699895544596286	2		335	368	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857784	9857784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145861983	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	213	556	0	ENST00000330684.3:c.3617G>A	p.Arg1206Gln	p.R1206Q	ENST00000330684	NM_001134407.1	1206	cGa/cAa	13/13	0.699895544596286	2	FACETS	0.995	0.93	1	0.497	0.465	0.53	CLONAL	1	TRUE	0	0.699895544596286	2		556	612	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476370	88476370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	194	432	0	ENST00000360948.2:c.1762G>A	p.Glu588Lys	p.E588K	ENST00000360948	NM_001012338.2	588	Gag/Aag	15/19	0.699895544596286	3	FACETS	1	0.976	1	0.372	0.345	0.399	CLONAL	1	TRUE	0	0.699895544596286	3		432	671	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573894	18573894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759658584	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	102	269	0	ENST00000266497.5:c.2212C>T	p.Arg738Cys	p.R738C	ENST00000266497		738	Cgt/Tgt	15/31	0.699895544596286	3	FACETS	1	0.956	1	0.553	0.499	0.609	CLONAL	1	TRUE	1	0.699895544596286	3		269	356	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386589	81386589	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	97	297	0	ENST00000222390.5:c.398G>A	p.Gly133Glu	p.G133E	ENST00000222390	NM_000601.4	133	gGa/gAa	4/18	0.699895544596286	4	FACETS	0.831	0.743	0.925	0.277	0.247	0.309	CLONAL	1	TRUE	1	0.699895544596286	4		297	567	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980318	7980318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774333332	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	177	513	0	ENST00000319144.4:c.1265C>T	p.Pro422Leu	p.P422L	ENST00000319144	NM_001139.2	422	cCc/cTc	9/15	0.119664574757721	6	FACETS	0.889	0.822	0.958			1	INDETERMINATE	2	TRUE	NA	0.699895544596286	6		513	683	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922973	44922973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	213	215	0	ENST00000377967.4:c.1834C>T	p.Arg612Ter	p.R612*	ENST00000377967	NM_021140.2	612	Cga/Tga	16/29	0.699895544596286	2	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.699895544596286	2		215	468	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467675	50467675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759124417	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	145	510	0	ENST00000331340.3:c.910G>A	p.Glu304Lys	p.E304K	ENST00000331340	NM_006060.4	304	Gaa/Aaa	8/8	1	2	FACETS	0.946	0.871	1	0.946	0.871	1	CLONAL	1	TRUE	1	0.699895544596286	2		510	438	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849110	156849110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	184	508	0	ENST00000524377.1:c.2002G>A	p.Asp668Asn	p.D668N	ENST00000524377	NM_002529.3	668	Gat/Aat	15/17	0.699895544596286	3	FACETS	0.948	0.877	1	0.474	0.438	0.511	CLONAL	1	TRUE	1	0.699895544596286	3		508	749	SUCCESS
ALK	238	MSKCC	GRCh37	2	29450509	29450509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774004991	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	186	535	0	ENST00000389048.3:c.2845G>A	p.Glu949Lys	p.E949K	ENST00000389048	NM_004304.4	949	Gaa/Aaa	17/29	0.682474216679635	5	FACETS	0.919	0.848	0.994	0.23	0.212	0.249	CLONAL	1	TRUE	1	0.699895544596286	5		535	1185	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333555	70333555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150689919	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	142	452	0	ENST00000373644.4:c.1460C>T	p.Ser487Leu	p.S487L	ENST00000373644	NM_030625.2	487	tCa/tTa	2/12	0.699895544596286	3	FACETS	0.961	0.88	1	0.481	0.44	0.523	CLONAL	1	TRUE	1	0.699895544596286	3		452	570	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650629	18650629	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	110	404	0	ENST00000266497.5:c.2840G>A	p.Gly947Asp	p.G947D	ENST00000266497		947	gGc/gAc	20/31	0.699895544596286	3	FACETS	0.899	0.812	0.99	0.45	0.406	0.495	CLONAL	1	TRUE	1	0.699895544596286	3		404	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577537	7577538	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	309	412	0	ENST00000269305.4:c.743_744delinsAA	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGG/cAA	7/11	0.119664574757721	6	FACETS	0.899	0.857	0.941			1	INDETERMINATE	4	TRUE	NA	0.699895544596286	6		412	589	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916767	48916767	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs794727481	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	149	262	0	ENST00000267163.4:c.297G>A	p.Trp99Ter	p.W99*	ENST00000267163	NM_000321.2	99	tgG/tgA	3/27	0.119664574757721	6	FACETS	1	0.976	1			1	INDETERMINATE	3	TRUE	NA	0.699895544596286	6		262	307	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955086	93955086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	106	307	0	ENST00000369303.4:c.2812G>A	p.Glu938Lys	p.E938K	ENST00000369303	NM_004440.3	938	Gaa/Aaa	16/17	0.699895544596286	3	FACETS	1	0.921	1			1	CLONAL	1	TRUE	NA	0.699895544596286	3		307	400	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332591	70332591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115711488	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	149	332	0	ENST00000373644.4:c.496C>T	p.Leu166Phe	p.L166F	ENST00000373644	NM_030625.2	166	Ctt/Ttt	2/12	0.699895544596286	3	FACETS	1	0.943	1	0.517	0.474	0.561	CLONAL	1	TRUE	1	0.699895544596286	3		332	556	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076812	72076812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	140	374	0	ENST00000357731.5:c.685G>A	p.Glu229Lys	p.E229K	ENST00000357731	NM_173808.2	229	Gaa/Aaa	5/7	0.699895544596286	4	FACETS	0.758	0.69	0.83			1	SUBCLONAL	1	TRUE	NA	0.699895544596286	4		374	897	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	135	367	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	0.166470176131058	3	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.699895544596286	3		367	389	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965601	25965601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	179	517	0	ENST00000435504.4:c.3605C>T	p.Ser1202Phe	p.S1202F	ENST00000435504		1202	tCc/tTc	13/13	0.682474216679635	5	FACETS	0.973	0.896	1	0.243	0.224	0.264	CLONAL	1	TRUE	1	0.699895544596286	5		517	1078	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672740	47672740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	90	313	1	ENST00000233146.2:c.1330C>T	p.Arg444Cys	p.R444C	ENST00000233146	NM_000251.2	444	Cgt/Tgt	8/16	0.699895544596286	4	FACETS	0.856	0.762	0.955	0.285	0.254	0.319	CLONAL	1	TRUE	1	0.699895544596286	4		314	511	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804298	43804298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760631916	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	182	554	0	ENST00000372470.3:c.298G>A	p.Glu100Lys	p.E100K	ENST00000372470	NM_005373.2	100	Gaa/Aaa	3/12	0.699895544596286	3	FACETS	0.924	0.854	0.996	0.462	0.427	0.498	CLONAL	1	TRUE	1	0.699895544596286	3		554	760	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001422	29001422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752383804	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	161	411	1	ENST00000282397.4:c.1310C>T	p.Ser437Leu	p.S437L	ENST00000282397	NM_002019.4	437	tCg/tTg	10/30	1	2	FACETS	0.926	0.856	0.998	0.926	0.856	0.998	CLONAL	1	TRUE	1	0.699895544596286	2		412	497	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254614	1254614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201330213	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	150	400	2	ENST00000310581.5:c.3164C>T	p.Ser1055Leu	p.S1055L	ENST00000310581	NM_198253.2	1055	tCg/tTg	15/16	0.577907484192751	4	FACETS	0.998	0.914	1	0.499	0.457	0.543	CLONAL	1	TRUE	2	0.699895544596286	4		402	730	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844404	156844404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199826686	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	177	714	1	ENST00000524377.1:c.1237G>A	p.Glu413Lys	p.E413K	ENST00000524377	NM_002529.3	413	Gaa/Aaa	10/17	0.699895544596286	3	FACETS	0.667	0.614	0.722	0.333	0.307	0.361	SUBCLONAL	1	TRUE	1	0.699895544596286	3		715	1024	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	159	553	0	ENST00000304494.5:c.143C>T	p.Pro48Leu	p.P48L	ENST00000304494	NM_000077.4	48	cCg/cTg	1/3	0.699895544596286	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.699895544596286	1		553	291	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671711	30671711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	170	521	0	ENST00000376406.3:c.5249C>T	p.Ser1750Phe	p.S1750F	ENST00000376406	NM_014641.2	1750	tCc/tTc	10/15	0.452443576366385	3	FACETS	1	0.948	1	0.517	0.477	0.558	CLONAL	1	TRUE	1	0.699895544596286	3		521	634	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933480	100933480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766277966	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	98	216	0	ENST00000325455.5:c.1910G>A	p.Arg637Gln	p.R637Q	ENST00000325455	NM_001202474.3	637	cGa/cAa	4/8	0.699895544596286	2	FACETS	0.959	0.867	1	0.48	0.433	0.527	CLONAL	1	TRUE	0	0.699895544596286	2		216	292	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084111	47084111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	64	502	0	ENST00000409792.3:c.7178C>T	p.Pro2393Leu	p.P2393L	ENST00000409792	NM_014159.6	2393	cCc/cTc	17/21	0.699895544596286	2	FACETS	0.289	0.25	0.331	0.144	0.125	0.166	SUBCLONAL	1	TRUE	0	0.699895544596286	2		502	633	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850891	63850891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	214	535	0	ENST00000279873.7:c.1669C>T	p.Pro557Ser	p.P557S	ENST00000279873	NM_032199.2	557	Cct/Tct	10/10	0.699895544596286	3	FACETS	1	0.932	1	0.5	0.466	0.536	CLONAL	1	TRUE	1	0.699895544596286	3		535	825	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454591	99454591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768988732	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	35	431	0	ENST00000268035.6:c.1510C>T	p.Arg504Cys	p.R504C	ENST00000268035	NM_000875.3	504	Cgc/Tgc	7/21	0.699895544596286	3	FACETS	0.204	0.167	0.247	0.068	0.055	0.083	SUBCLONAL	1	TRUE	0	0.699895544596286	3		431	661	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273901	10273901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	183	470	0	ENST00000330684.3:c.368C>T	p.Pro123Leu	p.P123L	ENST00000330684	NM_001134407.1	123	cCc/cTc	2/13	0.699895544596286	2	FACETS	1	0.932	1	0.501	0.466	0.537	CLONAL	1	TRUE	0	0.699895544596286	2		470	522	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2132497	2132497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs796053497	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	140	396	0	ENST00000219476.3:c.3875C>T	p.Ser1292Phe	p.S1292F	ENST00000219476	NM_000548.3	1292	tCc/tTc	32/42	0.699895544596286	2	FACETS	1	0.944	1	0.516	0.475	0.557	CLONAL	1	TRUE	0	0.699895544596286	2		396	388	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638349	117638349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	153	393	0	ENST00000368508.3:c.6092G>A	p.Gly2031Glu	p.G2031E	ENST00000368508	NM_002944.2	2031	gGa/gAa	38/43	1	2	FACETS	0.959	0.885	1	0.959	0.885	1	CLONAL	1	TRUE	1	0.699895544596286	2		393	456	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312713	91312713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1279814185	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	285	339	0	ENST00000355112.3:c.2452C>T	p.Arg818Cys	p.R818C	ENST00000355112	NM_000057.2	818	Cgc/Tgc	12/22	0.699895544596286	3	FACETS	0.973	0.925	1	0.649	0.616	0.681	CLONAL	2	TRUE	0	0.699895544596286	3		339	565	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608113	28608113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	164	435	0	ENST00000241453.7:c.1853C>T	p.Ser618Leu	p.S618L	ENST00000241453	NM_004119.2	618	tCa/tTa	15/24	1	2	FACETS	0.976	0.904	1	0.976	0.904	1	CLONAL	1	TRUE	1	0.699895544596286	2		435	480	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068025	94068025	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	162	363	0	ENST00000369303.4:c.937G>A	p.Glu313Lys	p.E313K	ENST00000369303	NM_004440.3	313	Gaa/Aaa	4/17	0.699895544596286	3	FACETS	1	0.921	1			1	CLONAL	1	TRUE	NA	0.699895544596286	3		363	625	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140487360	140487360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507472	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	142	417	0	ENST00000288602.6:c.1165C>T	p.Arg389Cys	p.R389C	ENST00000288602	NM_004333.4	389	Cgt/Tgt	9/18	0.699895544596286	3	FACETS	1	0.924	1	0.504	0.462	0.548	CLONAL	1	TRUE	1	0.699895544596286	3		417	543	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922300	178922300	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	70	211	0	ENST00000263967.3:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000263967	NM_006218.2	357	Cga/Tga	6/21	0.699895544596286	2	FACETS	0.957	0.849	1	0.479	0.424	0.535	CLONAL	1	TRUE	0	0.699895544596286	2		211	209	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561097	9561097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	158	447	0	ENST00000353224.5:c.685G>A	p.Asp229Asn	p.D229N	ENST00000353224	NM_177990.2	229	Gat/Aat	4/10	1	2	FACETS	0.967	0.894	1	0.967	0.894	1	CLONAL	1	TRUE	1	0.699895544596286	2		447	467	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997434	149997434	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	156	353	0	ENST00000253339.5:c.2845C>T	p.Pro949Ser	p.P949S	ENST00000253339		949	Cct/Tct	6/7	1	2	FACETS	0.937	0.865	1	0.937	0.865	1	CLONAL	1	TRUE	1	0.699895544596286	2		353	476	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286179	66286179	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	128	303	0	ENST00000273854.3:c.1507G>A	p.Glu503Lys	p.E503K	ENST00000273854	NM_004439.5	503	Gaa/Aaa	6/18	0.699895544596286	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.699895544596286	1		303	223	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647734	206647734	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782440026	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	147	474	0	ENST00000367120.3:c.148G>A	p.Glu50Lys	p.E50K	ENST00000367120	NM_014002.3	50	Gag/Aag	4/22	0.699895544596286	3	FACETS	0.759	0.694	0.827	0.38	0.347	0.414	SUBCLONAL	1	TRUE	1	0.699895544596286	3		474	747	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710759	117710759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	196	499	0	ENST00000368508.3:c.1513G>A	p.Glu505Lys	p.E505K	ENST00000368508	NM_002944.2	505	Gaa/Aaa	12/43	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.699895544596286	2		499	548	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744416	41744416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	161	474	0	ENST00000301178.4:c.1036G>A	p.Gly346Arg	p.G346R	ENST00000301178	NM_021913.4	346	Ggg/Agg	8/20	0.699895544596286	3	FACETS	0.938	0.863	1	0.469	0.431	0.508	CLONAL	1	TRUE	1	0.699895544596286	3		474	662	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444070	49444070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	197	552	0	ENST00000301067.7:c.3301C>T	p.Leu1101Phe	p.L1101F	ENST00000301067	NM_003482.3	1101	Ctt/Ttt	11/54	1	2	FACETS	0.934	0.87	0.999	0.934	0.87	0.999	CLONAL	1	TRUE	1	0.699895544596286	2		552	603	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919688	28919688	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	153	347	0	ENST00000282397.4:c.2249G>A	p.Gly750Glu	p.G750E	ENST00000282397	NM_002019.4	750	gGa/gAa	16/30	1	2	FACETS	0.998	0.922	1	0.998	0.922	1	CLONAL	1	TRUE	1	0.699895544596286	2		347	438	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80074606	80074606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372431614	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	185	332	0	ENST00000265081.6:c.2386C>T	p.Arg796Trp	p.R796W	ENST00000265081	NM_002439.4	796	Cgg/Tgg	17/24	0.699895544596286	2	FACETS	1	0.946	1	0.509	0.474	0.546	CLONAL	1	TRUE	0	0.699895544596286	2		332	519	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98222022	98222022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	147	381	0	ENST00000331920.6:c.2747C>T	p.Pro916Leu	p.P916L	ENST00000331920	NM_000264.3	916	cCc/cTc	17/24	1	2	FACETS	0.888	0.817	0.961	0.888	0.817	0.961	CLONAL	1	TRUE	1	0.699895544596286	2		381	473	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400977	72400977	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	58	364	0	ENST00000357731.5:c.194G>A	p.Gly65Glu	p.G65E	ENST00000357731	NM_173808.2	65	gGa/gAa	2/7	0.699895544596286	4	FACETS	0.349	0.299	0.404			1	SUBCLONAL	1	TRUE	NA	0.699895544596286	4		364	808	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876467	35876467	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	202	522	0	ENST00000303115.3:c.1259C>T	p.Ser420Phe	p.S420F	ENST00000303115	NM_002185.3	420	tCt/tTt	8/8	0.699895544596286	2	FACETS	0.995	0.929	1	0.498	0.464	0.532	CLONAL	1	TRUE	0	0.699895544596286	2		522	580	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953820	55953820	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	196	433	0	ENST00000263923.4:c.3616G>A	p.Glu1206Lys	p.E1206K	ENST00000263923	NM_002253.2	1206	Gaa/Aaa	27/30	0.699895544596286	3	FACETS	1	0.976	1	0.557	0.517	0.597	CLONAL	1	TRUE	1	0.699895544596286	3		433	679	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665371	117665371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765083865	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	152	401	0	ENST00000368508.3:c.4376C>T	p.Ala1459Val	p.A1459V	ENST00000368508	NM_002944.2	1459	gCc/gTc	27/43	1	2	FACETS	0.955	0.881	1	0.955	0.881	1	CLONAL	1	TRUE	1	0.699895544596286	2		401	455	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747912	41747912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1844	116	378	0	ENST00000226382.2:c.857C>T	p.Ser286Leu	p.S286L	ENST00000226382	NM_003924.3	286	tCg/tTg	3/3	0.699895544596286	11	FACETS	0.702	0.629	0.779			1	SUBCLONAL	1	TRUE	NA	0.699895544596286	11		378	1960	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465632	8465632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	306	345	0	ENST00000356435.5:c.3548G>A	p.Gly1183Glu	p.G1183E	ENST00000356435		1183	gGg/gAg	21/35	0.699895544596286	1	FACETS	0.994	0.948	1	0.994	0.948	1	CLONAL	1	TRUE	0	0.699895544596286	1		345	572	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807646	1807646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	207	596	0	ENST00000260795.2:c.1815G>A	p.Met605Ile	p.M605I	ENST00000260795		605	atG/atA	12/17	0.699895544596286	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.699895544596286	1		596	359	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262578	39262578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867539471	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	141	327	0	ENST00000402219.2:c.928C>T	p.Arg310Cys	p.R310C	ENST00000402219	NM_005633.3	310	Cgt/Tgt	7/23	0.682474216679635	5	FACETS	1	0.927	1	0.255	0.232	0.279	CLONAL	1	TRUE	1	0.699895544596286	5		327	810	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857232	9857232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377337296	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	213	527	0	ENST00000330684.3:c.4169C>T	p.Ser1390Leu	p.S1390L	ENST00000330684	NM_001134407.1	1390	tCg/tTg	13/13	0.699895544596286	2	FACETS	0.969	0.906	1	0.485	0.453	0.517	CLONAL	1	TRUE	0	0.699895544596286	2		527	628	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109720	115109720	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	64	516	0	ENST00000257566.3:c.2158G>A	p.Glu720Lys	p.E720K	ENST00000257566	NM_016569.3	720	Gaa/Aaa	8/8	1	2	FACETS	0.323	0.279	0.37	0.323	0.279	0.37	SUBCLONAL	1	TRUE	1	0.699895544596286	2		516	567	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976184	18976184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770076869	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	55	634	0	ENST00000262803.5:c.2944C>T	p.Pro982Ser	p.P982S	ENST00000262803	NM_002911.3	982	Ccc/Tcc	21/24	0.699895544596286	3	FACETS	0.239	0.203	0.278	0.119	0.101	0.139	SUBCLONAL	1	TRUE	1	0.699895544596286	3		634	889	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564581	55564581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276125047	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	173	428	0	ENST00000288135.5:c.469C>T	p.Pro157Ser	p.P157S	ENST00000288135	NM_000222.2	157	Ccc/Tcc	3/21	0.699895544596286	3	FACETS	0.917	0.846	0.99	0.458	0.423	0.495	CLONAL	1	TRUE	1	0.699895544596286	3		428	728	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572607	141572607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	183	505	0	ENST00000220592.5:c.463C>T	p.Pro155Ser	p.P155S	ENST00000220592	NM_012154.3	155	Cct/Tct	4/19	0.699895544596286	3	FACETS	1	0.938	1	0.507	0.469	0.546	CLONAL	1	TRUE	1	0.699895544596286	3		505	696	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169975	32169975	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	161	529	0	ENST00000375023.3:c.3633G>A	p.Trp1211Ter	p.W1211*	ENST00000375023	NM_004557.3	1211	tgG/tgA	21/30	0.452443576366385	3	FACETS	1	0.964	1	0.539	0.497	0.583	CLONAL	1	TRUE	1	0.699895544596286	3		529	576	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213370	36213370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	416	506	0	ENST00000222270.7:c.2567C>T	p.Pro856Leu	p.P856L	ENST00000222270	NM_014727.1	856	cCc/cTc	4/37	0.699895544596286	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.699895544596286	3		506	766	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235887	133235887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1030360914	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	209	626	0	ENST00000320574.5:c.3269C>T	p.Thr1090Met	p.T1090M	ENST00000320574	NM_006231.2	1090	aCg/aTg	26/49	1	2	FACETS	0.968	0.904	1	0.968	0.904	1	CLONAL	1	TRUE	1	0.699895544596286	2		626	617	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509562	106509562	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	211	539	0	ENST00000359195.3:c.1556T>C	p.Leu519Pro	p.L519P	ENST00000359195	NM_002649.2	519	cTt/cCt	2/11	0.699895544596286	3	FACETS	1	0.974	1	0.545	0.507	0.583	CLONAL	1	TRUE	1	0.699895544596286	3		539	747	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844112	68844112	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	46	393	0	ENST00000261769.5:c.700G>T	p.Ala234Ser	p.A234S	ENST00000261769	NM_004360.3	234	Gct/Tct	6/16	0.699895544596286	2	FACETS	0.275	0.231	0.323	0.137	0.115	0.162	SUBCLONAL	1	TRUE	0	0.699895544596286	2		393	478	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223703	36223703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	253	631	0	ENST00000222270.7:c.6253C>T	p.Pro2085Ser	p.P2085S	ENST00000222270	NM_014727.1	2085	Cct/Tct	28/37	0.699895544596286	3	FACETS	1	0.966	1	0.523	0.49	0.557	CLONAL	1	TRUE	1	0.699895544596286	3		631	933	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45864881	45864881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756071720	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	202	615	0	ENST00000391945.4:c.1138C>T	p.Arg380Trp	p.R380W	ENST00000391945	NM_000400.3	380	Cgg/Tgg	12/23	0.699895544596286	3	FACETS	0.994	0.924	1	0.497	0.462	0.533	CLONAL	1	TRUE	1	0.699895544596286	3		615	784	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058052	27058052	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	194	518	0	ENST00000324856.7:c.1760C>T	p.Ser587Phe	p.S587F	ENST00000324856	NM_006015.4	587	tCc/tTc	3/20	0.594387563566133	4	FACETS	0.938	0.867	1			1	CLONAL	1	TRUE	NA	0.699895544596286	4		518	1005	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893667	28893667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753623232	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	105	386	0	ENST00000282397.4:c.3179G>A	p.Arg1060Gln	p.R1060Q	ENST00000282397	NM_002019.4	1060	cGa/cAa	24/30	1	2	FACETS	0.75	0.677	0.826	0.75	0.677	0.826	SUBCLONAL	1	TRUE	1	0.699895544596286	2		386	400	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675096	40675097	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1566921463	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	184	483	0	ENST00000249776.8:c.62_63del	p.Glu21ValfsTer9	p.E21Vfs*9	ENST00000249776	NM_033286.3	20	acAGag/acag	1/9	0.699895544596286	3	FACETS	1	0.93	1	0.335	0.31	0.361	CLONAL	1	TRUE	0	0.699895544596286	3		483	707	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374422	31374422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	155	526	0	ENST00000328111.2:c.421C>T	p.Pro141Ser	p.P141S	ENST00000328111	NM_006892.3	141	Ccg/Tcg	5/23	0.699895544596286	3	FACETS	0.702	0.643	0.764	0.351	0.321	0.382	SUBCLONAL	1	TRUE	1	0.699895544596286	3		526	852	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858448	9858448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	158	474	0	ENST00000330684.3:c.2953C>T	p.Pro985Ser	p.P985S	ENST00000330684	NM_001134407.1	985	Cct/Tct	13/13	0.699895544596286	2	FACETS	0.971	0.898	1	0.485	0.449	0.523	CLONAL	1	TRUE	0	0.699895544596286	2		474	465	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944545	40944545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200852571	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	156	408	0	ENST00000373198.4:c.1957C>T	p.Arg653Trp	p.R653W	ENST00000373198	NM_133170.3	653	Cgg/Tgg	12/32	0.699895544596286	3	FACETS	0.936	0.86	1	0.468	0.43	0.508	CLONAL	1	TRUE	1	0.699895544596286	3		408	643	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724637	43724637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	165	501	0	ENST00000382044.4:c.3430C>T	p.Pro1144Ser	p.P1144S	ENST00000382044	NM_001141980.1	1144	Cct/Tct	17/28	0.699895544596286	3	FACETS	0.996	0.918	1	0.332	0.306	0.359	CLONAL	1	TRUE	0	0.699895544596286	3		501	639	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805552	46805552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769634543	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	182	550	0	ENST00000290295.7:c.404G>A	p.Gly135Glu	p.G135E	ENST00000290295	NM_006361.5	135	gGa/gAa	1/2	1	2	FACETS	0.967	0.898	1	0.967	0.898	1	CLONAL	1	TRUE	1	0.699895544596286	2		550	538	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803005	32803005	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	177	474	0	ENST00000374899.4:c.871C>T	p.Arg291Ter	p.R291*	ENST00000374899	NM_018833.2	291	Cga/Tga	5/12	0.452443576366385	3	FACETS	1	0.986	1	0.631	0.585	0.678	CLONAL	1	TRUE	1	0.699895544596286	3		474	541	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366227	15366227	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868727577	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	179	449	1	ENST00000263377.2:c.1928C>T	p.Ser643Phe	p.S643F	ENST00000263377	NM_058243.2	643	tCc/tTc	10/20	0.699895544596286	3	FACETS	0.936	0.865	1	0.468	0.432	0.505	CLONAL	1	TRUE	1	0.699895544596286	3		450	738	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279562	123279562	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	202	527	0	ENST00000358487.5:c.870G>A	p.Trp290Ter	p.W290*	ENST00000358487	NM_000141.4	290	tgG/tgA	7/18	0.699895544596286	2	FACETS	1	0.942	1	0.505	0.471	0.539	CLONAL	1	TRUE	0	0.699895544596286	2		527	572	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787794	135787794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	136	297	0	ENST00000298552.3:c.788C>T	p.Ser263Phe	p.S263F	ENST00000298552	NM_001162426.1	263	tCt/tTt	9/23	1	2	FACETS	0.991	0.911	1	0.991	0.911	1	CLONAL	1	TRUE	1	0.699895544596286	2		297	392	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729933	41729933	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111379520	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	155	490	0	ENST00000242208.4:c.596G>A	p.Gly199Glu	p.G199E	ENST00000242208	NM_002192.2	199	gGg/gAg	3/3	1	2	FACETS	0.908	0.837	0.98	0.908	0.837	0.98	CLONAL	1	TRUE	1	0.699895544596286	2		490	488	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945136	151945136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1443491328	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	11	76	0	ENST00000262189.6:c.2383G>A	p.Asp795Asn	p.D795N	ENST00000262189	NM_170606.2	795	Gac/Aac	14/59	0.699895544596286	3	FACETS	0.442	0.308	0.604	0.221	0.154	0.302	SUBCLONAL	1	TRUE	1	0.699895544596286	3		76	96	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743919	41743919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201003955	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	211	564	0	ENST00000301178.4:c.854C>T	p.Ser285Leu	p.S285L	ENST00000301178	NM_021913.4	285	tCg/tTg	7/20	0.699895544596286	3	FACETS	1	0.968	1	0.533	0.496	0.57	CLONAL	1	TRUE	1	0.699895544596286	3		564	764	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65323386	65323386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1387066409	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	182	487	0	ENST00000342505.4:c.1411G>A	p.Asp471Asn	p.D471N	ENST00000342505	NM_002227.2	471	Gac/Aac	10/25	0.699895544596286	3	FACETS	0.94	0.869	1	0.47	0.434	0.507	CLONAL	1	TRUE	1	0.699895544596286	3		487	747	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402692	20402692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343489714	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	177	541	0	ENST00000346618.3:c.229G>A	p.Gly77Ser	p.G77S	ENST00000346618	NM_001949.4	77	Ggc/Agc	1/7	0.128595787204697	5	FACETS	0.916	0.849	0.984	0.458	0.424	0.492	INDETERMINATE	2	TRUE	1	0.699895544596286	5		541	566	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199963	138199963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	218	525	0	ENST00000237289.4:c.1381C>T	p.Pro461Ser	p.P461S	ENST00000237289	NM_001270507.1	461	Cca/Tca	7/9	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.699895544596286	2		525	610	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475168	475168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	156	399	0	ENST00000399788.2:c.469C>T	p.Leu157Phe	p.L157F	ENST00000399788	NM_001042603.1	157	Ctt/Ttt	4/28	0.699895544596286	3	FACETS	0.963	0.885	1	0.481	0.442	0.522	CLONAL	1	TRUE	1	0.699895544596286	3		399	625	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172197	99172197	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	252	651	0	ENST00000074304.5:c.1763C>T	p.Pro588Leu	p.P588L	ENST00000074304	NM_001134224.1	588	cCc/cTc	17/26	0.699895544596286	4	FACETS	1	0.978	1	0.368	0.343	0.392	CLONAL	1	TRUE	1	0.699895544596286	4		651	1110	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912095	127912095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	146	387	0	ENST00000373547.4:c.775C>T	p.Pro259Ser	p.P259S	ENST00000373547	NM_002721.4	259	Cct/Tct	7/7	1	2	FACETS	0.97	0.894	1	0.97	0.894	1	CLONAL	1	TRUE	1	0.699895544596286	2		387	430	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626883	14626883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	446	534	0	ENST00000254322.2:c.892C>T	p.Pro298Ser	p.P298S	ENST00000254322	NM_006145.1	298	Cct/Tct	3/3	0.699895544596286	3	FACETS	0.997	0.958	1	0.997	0.958	1	CLONAL	2	TRUE	1	0.699895544596286	3		534	863	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427681	72427681	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772981068	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	195	465	1	ENST00000477973.2:c.809C>T	p.Ser270Leu	p.S270L	ENST00000477973	NM_012234.5	270	tCg/tTg	4/4	0.699895544596286	2	FACETS	1	0.954	1	0.514	0.479	0.55	CLONAL	1	TRUE	0	0.699895544596286	2		466	542	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363883	118363883	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	301	353	0	ENST00000534358.1:c.5116C>T	p.Gln1706Ter	p.Q1706*	ENST00000534358	NM_005933.3	1706	Cag/Tag	16/36	0.699895544596286	2	FACETS	0.989	0.95	1	0.989	0.95	1	CLONAL	2	TRUE	0	0.699895544596286	2		353	435	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987377	2987377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	156	433	0	ENST00000396946.4:c.52G>A	p.Glu18Lys	p.E18K	ENST00000396946	NM_032415.4	18	Gaa/Aaa	3/25	0.192330181529837	4	FACETS	1	0.981	1	0.306	0.281	0.331	INDETERMINATE	1	TRUE	0	0.699895544596286	4		433	620	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279528	123279528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1159063118	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	200	483	0	ENST00000358487.5:c.904G>A	p.Gly302Arg	p.G302R	ENST00000358487	NM_000141.4	302	Ggg/Agg	7/18	0.699895544596286	2	FACETS	1	0.961	1	0.521	0.486	0.556	CLONAL	1	TRUE	0	0.699895544596286	2		483	549	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902232	151902232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559949839	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	156	172	0	ENST00000262189.6:c.3920C>T	p.Ser1307Phe	p.S1307F	ENST00000262189	NM_170606.2	1307	tCc/tTc	25/59	0.699895544596286	3	FACETS	0.961	0.897	1	0.961	0.897	1	CLONAL	2	TRUE	1	0.699895544596286	3		172	313	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552985	106552985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	187	547	0	ENST00000369096.4:c.950G>A	p.Gly317Glu	p.G317E	ENST00000369096	NM_001198.3	317	gGg/gAg	5/7	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.699895544596286	2		547	532	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884888	134884888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1320801657	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	148	453	0	ENST00000398015.3:c.1664C>T	p.Ser555Phe	p.S555F	ENST00000398015	NM_004441.4	555	tCc/tTc	8/16	0.699895544596286	2	FACETS	0.993	0.916	1	0.496	0.458	0.536	CLONAL	1	TRUE	0	0.699895544596286	2		453	426	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866300	42866300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	192	553	0	ENST00000398585.3:c.332G>A	p.Gly111Glu	p.G111E	ENST00000398585	NM_001135099.1	111	gGg/gAg	3/14	1	2	FACETS	0.924	0.859	0.989	0.924	0.859	0.989	CLONAL	1	TRUE	1	0.699895544596286	2		553	594	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156607	55156607	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	162	615	0	ENST00000257290.5:c.3008G>A	p.Trp1003Ter	p.W1003*	ENST00000257290	NM_006206.4	1003	tGg/tAg	22/23	0.699895544596286	3	FACETS	0.782	0.718	0.849	0.391	0.359	0.425	SUBCLONAL	1	TRUE	1	0.699895544596286	3		615	799	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1737949	1737949	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	161	386	0	ENST00000378609.4:c.232A>G	p.Lys78Glu	p.K78E	ENST00000378609	NM_002074.3	78	Aaa/Gaa	6/12	0.699895544596286	3	FACETS	0.9	0.828	0.975	0.45	0.414	0.488	CLONAL	1	TRUE	1	0.699895544596286	3		386	690	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074072	8074073	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	159	433	0	ENST00000377482.5:c.586_587delinsTT	p.Pro196Phe	p.P196F	ENST00000377482	NM_018948.3	196	CCt/TTt	4/4	0.699895544596286	3	FACETS	0.917	0.843	0.993	0.458	0.421	0.497	CLONAL	1	TRUE	1	0.699895544596286	3		433	669	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266597	115266597	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	41	373	0	ENST00000438362.2:c.1918C>T	p.Pro640Ser	p.P640S	ENST00000438362	NM_001242891.1	640	Ccc/Tcc	16/20	0.699895544596286	3	FACETS	0.246	0.204	0.293	0.123	0.102	0.147	SUBCLONAL	1	TRUE	1	0.699895544596286	3		373	643	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150933140	150933140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	194	513	0	ENST00000271640.5:c.2602G>A	p.Glu868Lys	p.E868K	ENST00000271640	NM_001145415.1	868	Gaa/Aaa	16/22	0.699895544596286	3	FACETS	1	0.949	1	0.514	0.477	0.552	CLONAL	1	TRUE	1	0.699895544596286	3		513	728	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163315529	163315537	+	inframe_deletion	In_Frame_Del	DEL	AGTTGGAAG	AGTTGGAAG	-	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	113	365	0	ENST00000271452.3:c.869_877del	p.Gln290_Val293delinsLeu	p.Q290_V293delinsL	ENST00000271452	NM_145697.2	290	cAGTTGGAAGtg/ctg	11/14	0.699895544596286	3	FACETS	0.821	0.742	0.904	0.41	0.371	0.452	CLONAL	1	TRUE	1	0.699895544596286	3		365	531	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206943205	206943205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	142	444	0	ENST00000423557.1:c.413C>T	p.Ala138Val	p.A138V	ENST00000423557	NM_000572.2	138	gCc/gTc	4/5	0.699895544596286	3	FACETS	0.83	0.758	0.905	0.415	0.379	0.453	CLONAL	1	TRUE	1	0.699895544596286	3		444	660	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226553737	226553737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	177	342	0	ENST00000366794.5:c.2423C>T	p.Ser808Phe	p.S808F	ENST00000366794	NM_001618.3	808	tCt/tTt	18/23	0.699895544596286	3	FACETS	1	0.975	1	0.561	0.519	0.603	CLONAL	1	TRUE	1	0.699895544596286	3		342	609	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230486829	230486829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	175	443	0	ENST00000391860.1:c.424G>A	p.Glu142Lys	p.E142K	ENST00000391860	NM_001258311.1	142	Gaa/Aaa	3/7	0.699895544596286	3	FACETS	1	0.936	1	0.507	0.468	0.547	CLONAL	1	TRUE	1	0.699895544596286	3		443	666	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230492877	230492877	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	174	473	0	ENST00000391860.1:c.177G>A	p.Met59Ile	p.M59I	ENST00000391860	NM_001258311.1	59	atG/atA	2/7	0.699895544596286	3	FACETS	1	0.939	1	0.509	0.47	0.549	CLONAL	1	TRUE	1	0.699895544596286	3		473	659	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606673	43606673	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1327111345	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	215	543	0	ENST00000355710.3:c.1282G>A	p.Glu428Lys	p.E428K	ENST00000355710	NM_020975.4	428	Gaa/Aaa	7/20	0.699895544596286	3	FACETS	0.956	0.89	1	0.478	0.445	0.512	CLONAL	1	TRUE	1	0.699895544596286	3		543	868	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405415	70405415	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	183	427	0	ENST00000373644.4:c.2929C>T	p.Leu977Phe	p.L977F	ENST00000373644	NM_030625.2	977	Ctt/Ttt	4/12	0.699895544596286	3	FACETS	0.924	0.855	0.996	0.462	0.427	0.498	CLONAL	1	TRUE	1	0.699895544596286	3		427	764	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912690	100912690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	131	245	0	ENST00000325455.5:c.2632G>A	p.Asp878Asn	p.D878N	ENST00000325455	NM_001202474.3	878	Gat/Aat	7/8	0.699895544596286	2	FACETS	1	0.964	1	0.544	0.5	0.589	CLONAL	1	TRUE	0	0.699895544596286	2		245	344	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115543	108115543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	85	285	0	ENST00000278616.4:c.691C>T	p.His231Tyr	p.H231Y	ENST00000278616	NM_000051.3	231	Cat/Tat	7/63	0.699895544596286	2	FACETS	0.796	0.711	0.885	0.398	0.355	0.443	SUBCLONAL	1	TRUE	0	0.699895544596286	2		285	305	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155051	108155051	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	119	294	0	ENST00000278616.4:c.3844C>T	p.Leu1282Phe	p.L1282F	ENST00000278616	NM_000051.3	1282	Ctt/Ttt	26/63	0.699895544596286	2	FACETS	1	0.931	1	0.511	0.467	0.556	CLONAL	1	TRUE	0	0.699895544596286	2		294	333	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373212	118373212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	183	462	0	ENST00000534358.1:c.6605C>T	p.Ser2202Phe	p.S2202F	ENST00000534358	NM_005933.3	2202	tCc/tTc	27/36	0.699895544596286	2	FACETS	0.947	0.88	1	0.474	0.44	0.508	CLONAL	1	TRUE	0	0.699895544596286	2		462	552	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377012	118377012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1434227722	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	192	520	0	ENST00000534358.1:c.10405C>T	p.His3469Tyr	p.H3469Y	ENST00000534358	NM_005933.3	3469	Cat/Tat	27/36	0.699895544596286	2	FACETS	0.908	0.845	0.973	0.454	0.422	0.487	CLONAL	1	TRUE	0	0.699895544596286	2		520	604	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025887	1025887	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	192	515	0	ENST00000358495.3:c.643G>A	p.Gly215Arg	p.G215R	ENST00000358495	NM_134424.2	215	Gga/Aga	8/12	0.699895544596286	3	FACETS	0.993	0.921	1	0.496	0.46	0.534	CLONAL	1	TRUE	1	0.699895544596286	3		515	746	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800840	18800840	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	90	273	0	ENST00000266497.5:c.4216G>A	p.Gly1406Arg	p.G1406R	ENST00000266497		1406	Gga/Aga	31/31	0.699895544596286	3	FACETS	0.967	0.865	1	0.484	0.432	0.537	CLONAL	1	TRUE	1	0.699895544596286	3		273	359	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46215218	46215218	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	32	149	0	ENST00000334344.6:c.653C>T	p.Ser218Phe	p.S218F	ENST00000334344	NM_152641.2	218	tCc/tTc	6/21	1	2	FACETS	0.775	0.642	0.918	0.775	0.642	0.918	CLONAL	1	TRUE	1	0.699895544596286	2		149	118	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431754	49431754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200089754	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	199	554	0	ENST00000301067.7:c.9385C>T	p.Pro3129Ser	p.P3129S	ENST00000301067	NM_003482.3	3129	Cct/Tct	34/54	1	2	FACETS	0.945	0.88	1	0.945	0.88	1	CLONAL	1	TRUE	1	0.699895544596286	2		554	602	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443506	49443506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	169	518	0	ENST00000301067.7:c.3865G>A	p.Gly1289Arg	p.G1289R	ENST00000301067	NM_003482.3	1289	Ggg/Agg	11/54	1	2	FACETS	0.903	0.835	0.972	0.903	0.835	0.972	CLONAL	1	TRUE	1	0.699895544596286	2		518	535	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446373	49446373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	208	571	0	ENST00000301067.7:c.1232C>T	p.Pro411Leu	p.P411L	ENST00000301067	NM_003482.3	411	cCc/cTc	9/54	1	2	FACETS	0.981	0.916	1	0.981	0.916	1	CLONAL	1	TRUE	1	0.699895544596286	2		571	606	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112009	115112010	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	174	547	0	ENST00000257566.3:c.1730_1731delinsTT	p.Thr577Ile	p.T577I	ENST00000257566	NM_016569.3	577	aCC/aTT	7/8	1	2	FACETS	0.964	0.894	1	0.964	0.894	1	CLONAL	1	TRUE	1	0.699895544596286	2		547	516	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416827	121416827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	196	555	0	ENST00000257555.6:c.256C>T	p.Leu86Phe	p.L86F	ENST00000257555		86	Ctc/Ttc	1/10	1	2	FACETS	0.977	0.911	1	0.977	0.911	1	CLONAL	1	TRUE	1	0.699895544596286	2		555	573	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959156	28959156	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	135	382	0	ENST00000282397.4:c.1982C>T	p.Pro661Leu	p.P661L	ENST00000282397	NM_002019.4	661	cCa/cTa	14/30	1	2	FACETS	0.853	0.782	0.928	0.853	0.782	0.928	CLONAL	1	TRUE	1	0.699895544596286	2		382	452	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937450	32937450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80359054	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	154	419	0	ENST00000380152.3:c.8111C>T	p.Ser2704Phe	p.S2704F	ENST00000380152		2704	tCt/tTt	18/27	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.699895544596286	2		419	426	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134065	41134066	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	191	534	0	ENST00000379561.5:c.1562_1563delinsTT	p.Ser521Phe	p.S521F	ENST00000379561	NM_002015.3	521	tCC/tTT	2/3	0.699895544596286	3	FACETS	0.931	0.863	1			1	CLONAL	1	TRUE	NA	0.699895544596286	3		534	791	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609520	81609520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	223	475	0	ENST00000298171.2:c.1118C>T	p.Pro373Leu	p.P373L	ENST00000298171	NM_000369.2	373	cCc/cTc	10/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.699895544596286	2		475	568	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574717	95574717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060503620	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	136	382	0	ENST00000393063.1:c.2380C>T	p.Pro794Ser	p.P794S	ENST00000393063	NM_030621.3	794	Cct/Tct	16/28	1	2	FACETS	0.822	0.752	0.893	0.822	0.752	0.893	CLONAL	1	TRUE	1	0.699895544596286	2		382	473	SUCCESS
SCG5	6447	MSKCC	GRCh37	15	32935962	32935962	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs750372565	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	357	465	0	ENST00000300175.4:c.169C>T	p.Arg57Ter	p.R57*	ENST00000300175	NM_001144757.1	57	Cga/Tga	2/6	0.676936776514307	2	FACETS	1	0.995	1	0.722	0.69	0.755	CLONAL	1	TRUE	0	0.699895544596286	2		465	706	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058966	42058967	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTATCAGTC	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	170	432	0	ENST00000219905.7:c.8688_8696dup	p.Ile2897_Pro2899dup	p.I2897_P2899dup	ENST00000219905	NM_001164273.1	2897	tct/tCTATCAGTCct	24/24	0.699895544596286	3	FACETS	0.855	0.788	0.925	0.285	0.262	0.309	CLONAL	1	TRUE	0	0.699895544596286	3		432	767	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777989	3777990	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	421	609	0	ENST00000262367.5:c.7058_7059delinsAA	p.Arg2353Gln	p.R2353Q	ENST00000262367	NM_004380.2	2353	cGG/cAA	31/31	0.699895544596286	2	FACETS	0.999	0.967	1	0.999	0.967	1	CLONAL	2	TRUE	0	0.699895544596286	2		609	602	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9927968	9927968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1397649822	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	170	352	0	ENST00000330684.3:c.1771G>A	p.Gly591Arg	p.G591R	ENST00000330684	NM_001134407.1	591	Ggg/Agg	8/13	0.699895544596286	2	FACETS	1	0.973	1	0.547	0.508	0.587	CLONAL	1	TRUE	0	0.699895544596286	2		352	444	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783802	50783803	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	130	423	1	ENST00000398568.2:c.193_194delinsAA	p.Gly65Asn	p.G65N	ENST00000398568	NM_001042412.1	65	GGc/AAc	3/18	0.699895544596286	2	FACETS	0.87	0.796	0.947	0.435	0.398	0.474	CLONAL	1	TRUE	0	0.699895544596286	2		424	427	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828174	50828174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	320	405	0	ENST00000398568.2:c.2512C>T	p.Pro838Ser	p.P838S	ENST00000398568	NM_001042412.1	838	Ccc/Tcc	17/18	0.699895544596286	2	FACETS	0.979	0.942	1	0.979	0.942	1	CLONAL	2	TRUE	0	0.699895544596286	2		405	467	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827994	72827994	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	408	448	0	ENST00000268489.5:c.8587A>G	p.Thr2863Ala	p.T2863A	ENST00000268489	NM_006885.3	2863	Act/Gct	9/10	0.699895544596286	2	FACETS	0.995	0.962	1	0.995	0.962	1	CLONAL	2	TRUE	0	0.699895544596286	2		448	586	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72994014	72994014	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	196	534	0	ENST00000268489.5:c.31G>T	p.Gly11Trp	p.G11W	ENST00000268489	NM_006885.3	11	Ggg/Tgg	2/10	0.699895544596286	2	FACETS	1	0.962	1	0.522	0.487	0.558	CLONAL	1	TRUE	0	0.699895544596286	2		534	536	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347345	89347345	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138587995	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	202	595	0	ENST00000301030.4:c.5605C>T	p.Pro1869Ser	p.P1869S	ENST00000301030	NM_001256183.1	1869	Ccg/Tcg	9/13	0.699895544596286	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.699895544596286	1		595	372	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7978915	7978915	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	160	379	0	ENST00000319144.4:c.1652C>T	p.Ser551Leu	p.S551L	ENST00000319144	NM_001139.2	551	tCa/tTa	12/15	0.119664574757721	6	FACETS	0.895	0.824	0.968			1	INDETERMINATE	2	TRUE	NA	0.699895544596286	6		379	613	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989648	15989648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760980680	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	180	452	0	ENST00000268712.3:c.3125C>T	p.Thr1042Ile	p.T1042I	ENST00000268712	NM_006311.3	1042	aCc/aTc	23/46	1	2	FACETS	0.902	0.837	0.969	0.902	0.837	0.969	CLONAL	1	TRUE	1	0.699895544596286	2		452	570	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663800	29663800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500382	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	183	393	0	ENST00000356175.3:c.6232C>T	p.His2078Tyr	p.H2078Y	ENST00000356175	NM_000267.3	2078	Cat/Tat	41/57	0.699895544596286	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.699895544596286	1		393	335	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315393	30315393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146306622	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	172	392	0	ENST00000322652.5:c.1078C>T	p.Arg360Cys	p.R360C	ENST00000322652	NM_015355.2	360	Cgt/Tgt	10/16	0.699895544596286	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.699895544596286	1		392	294	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40467771	40467771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	164	374	0	ENST00000264657.5:c.2305C>T	p.Pro769Ser	p.P769S	ENST00000264657	NM_139276.2	769	Ccc/Tcc	24/24	1	2	FACETS	0.914	0.845	0.984	0.914	0.845	0.984	CLONAL	1	TRUE	1	0.699895544596286	2		374	513	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59934418	59934419	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	88	279	0	ENST00000259008.2:c.379_379+1delinsAA		p.X127_splice	ENST00000259008	NM_032043.2	127		4/20	1	2	FACETS	0.879	0.789	0.973	0.879	0.789	0.973	CLONAL	1	TRUE	1	0.699895544596286	2		279	286	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120046	70120046	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	308	440	0	ENST00000245479.2:c.1048C>T	p.Pro350Ser	p.P350S	ENST00000245479	NM_000346.3	350	Cca/Tca	3/3	0.699895544596286	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.699895544596286	3		440	562	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61322934	61322934	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	105	246	0	ENST00000283752.5:c.1130A>G	p.Lys377Arg	p.K377R	ENST00000283752	NM_006919.2	377	aAg/aGg	8/8	0.699895544596286	2	FACETS	1	0.966	1	0.564	0.514	0.615	CLONAL	1	TRUE	0	0.699895544596286	2		246	266	SUCCESS
SERPINB3	6317	MSKCC	GRCh37	18	61328042	61328042	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	69	109	0	ENST00000283752.5:c.214A>G	p.Thr72Ala	p.T72A	ENST00000283752	NM_006919.2	72	Aca/Gca	3/8	0.699895544596286	2	FACETS	1	0.966	1	0.609	0.543	0.675	CLONAL	1	TRUE	0	0.699895544596286	2		109	162	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2194522	2194523	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	256	426	1	ENST00000398665.3:c.597_598delinsTT	p.Arg200Cys	p.R200C	ENST00000398665	NM_032482.2	199	gaCCgc/gaTTgc	7/28	0.699895544596286	3	FACETS	0.939	0.889	0.989	0.939	0.889	0.989	CLONAL	2	TRUE	1	0.699895544596286	3		427	526	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216753	2216753	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	482	577	0	ENST00000398665.3:c.2397G>T	p.Glu799Asp	p.E799D	ENST00000398665	NM_032482.2	799	gaG/gaT	20/28	0.699895544596286	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.699895544596286	3		577	909	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7168016	7168016	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1599937180	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	194	420	0	ENST00000302850.5:c.1573C>T	p.Arg525Ter	p.R525*	ENST00000302850	NM_000208.2	525	Cga/Tga	7/22	0.699895544596286	3	FACETS	1	0.948	1	0.513	0.476	0.552	CLONAL	1	TRUE	1	0.699895544596286	3		420	729	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132434	11132434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	55	623	0	ENST00000358026.2:c.2650C>T	p.His884Tyr	p.H884Y	ENST00000358026	NM_001128849.1	884	Cac/Tac	19/36	0.699895544596286	3	FACETS	0.239	0.203	0.278	0.119	0.101	0.139	SUBCLONAL	1	TRUE	1	0.699895544596286	3		623	888	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051368	13051368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	235	582	0	ENST00000316448.5:c.716C>T	p.Pro239Leu	p.P239L	ENST00000316448	NM_004343.3	239	cCc/cTc	6/9	0.699895544596286	3	FACETS	1	0.966	1	0.525	0.491	0.561	CLONAL	1	TRUE	1	0.699895544596286	3		582	863	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955127	17955127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	186	490	0	ENST00000458235.1:c.100G>A	p.Gly34Ser	p.G34S	ENST00000458235	NM_000215.3	34	Ggc/Agc	2/24	0.699895544596286	3	FACETS	1	0.966	1	0.535	0.496	0.575	CLONAL	1	TRUE	1	0.699895544596286	3		490	671	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971789	18971789	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	174	432	0	ENST00000262803.5:c.2455C>T	p.Gln819Ter	p.Q819*	ENST00000262803	NM_002911.3	819	Cag/Tag	17/24	0.699895544596286	3	FACETS	1	0.941	1	0.511	0.472	0.551	CLONAL	1	TRUE	1	0.699895544596286	3		432	657	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976369	18976370	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	178	550	0	ENST00000262803.5:c.3020-1_3020delinsAA		p.X1007_splice	ENST00000262803	NM_002911.3	1007		22/24	0.699895544596286	3	FACETS	1	0.963	1	0.532	0.492	0.573	CLONAL	1	TRUE	1	0.699895544596286	3		550	645	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218842	36218842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1407836135	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	170	636	0	ENST00000222270.7:c.4453C>T	p.Pro1485Ser	p.P1485S	ENST00000222270	NM_014727.1	1485	Ccg/Tcg	18/37	0.699895544596286	3	FACETS	0.83	0.765	0.898	0.415	0.382	0.449	CLONAL	1	TRUE	1	0.699895544596286	3		636	790	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905554	50905554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1184569102	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	202	694	0	ENST00000440232.2:c.682G>A	p.Glu228Lys	p.E228K	ENST00000440232	NM_002691.3	228	Gaa/Aaa	6/27	0.699895544596286	3	FACETS	0.924	0.858	0.993	0.462	0.429	0.497	CLONAL	1	TRUE	1	0.699895544596286	3		694	843	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966465	25966465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771358447	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	194	524	0	ENST00000435504.4:c.2741C>T	p.Ala914Val	p.A914V	ENST00000435504		914	gCt/gTt	13/13	0.682474216679635	5	FACETS	0.957	0.884	1	0.239	0.221	0.259	CLONAL	1	TRUE	1	0.699895544596286	5		524	1187	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456451	29456451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	207	524	1	ENST00000389048.3:c.2467G>A	p.Gly823Arg	p.G823R	ENST00000389048	NM_004304.4	823	Gga/Aga	14/29	0.682474216679635	5	FACETS	1	0.932	1	0.252	0.233	0.271	CLONAL	1	TRUE	1	0.699895544596286	5		525	1205	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474019	29474019	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	157	466	0	ENST00000389048.3:c.2156C>A	p.Pro719His	p.P719H	ENST00000389048	NM_004304.4	719	cCc/cAc	12/29	0.682474216679635	5	FACETS	0.98	0.898	1	0.245	0.224	0.267	CLONAL	1	TRUE	1	0.699895544596286	5		466	938	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61725864	61725864	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	465	349	0	ENST00000401558.2:c.703T>C	p.Trp235Arg	p.W235R	ENST00000401558	NM_003400.3	235	Tgg/Cgg	9/25	0.699895544596286	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	1	0.699895544596286	4		349	731	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872911	136872911	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	636	540	0	ENST00000241393.3:c.587T>G	p.Val196Gly	p.V196G	ENST00000241393	NM_003467.2	196	gTg/gGg	2/2	0.699895544596286	4	FACETS	0.996	0.966	1	0.996	0.966	1	CLONAL	3	TRUE	1	0.699895544596286	4		540	1034	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622696	158622696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	122	323	0	ENST00000263640.3:c.803C>T	p.Ser268Leu	p.S268L	ENST00000263640	NM_001105.4	268	tCa/tTa	8/11	0.699895544596286	4	FACETS	0.953	0.863	1	0.318	0.287	0.349	CLONAL	1	TRUE	1	0.699895544596286	4		323	622	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727068	40727068	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1350144317	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	215	500	0	ENST00000373198.4:c.3896C>T	p.Thr1299Ile	p.T1299I	ENST00000373198	NM_133170.3	1299	aCt/aTt	28/32	0.699895544596286	3	FACETS	1	0.975	1	0.548	0.511	0.586	CLONAL	1	TRUE	1	0.699895544596286	3		500	757	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656865	45656866	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	206	520	0	ENST00000407780.3:c.290_291delinsTT	p.Ser97Phe	p.S97F	ENST00000407780	NM_001283052.1	97	tCC/tTT	3/7	1	2	FACETS	0.892	0.832	0.954	0.892	0.832	0.954	CLONAL	1	TRUE	1	0.699895544596286	2		520	660	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645741	12645741	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	158	425	0	ENST00000251849.4:c.728C>T	p.Ser243Phe	p.S243F	ENST00000251849	NM_002880.3	243	tCc/tTc	7/17	0.699895544596286	2	FACETS	0.959	0.886	1	0.479	0.443	0.517	CLONAL	1	TRUE	0	0.699895544596286	2		425	471	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721478	49721478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	242	309	0	ENST00000449682.2:c.2161G>A	p.Val721Ile	p.V721I	ENST00000449682	NM_020998.3	721	Gtc/Atc	18/18	0.699895544596286	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.699895544596286	2		309	337	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928894	49928894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866072447	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	233	597	0	ENST00000296474.3:c.3472C>T	p.His1158Tyr	p.H1158Y	ENST00000296474	NM_002447.2	1158	Cat/Tat	16/20	0.699895544596286	2	FACETS	1	0.958	1	0.513	0.481	0.545	CLONAL	1	TRUE	0	0.699895544596286	2		597	649	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664826	138664827	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	195	332	0	ENST00000330315.3:c.738_739delinsAA	p.Gly247Arg	p.G247R	ENST00000330315	NM_023067.3	246	aaGGgg/aaAAgg	1/1	0.699895544596286	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.699895544596286	2		332	265	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280134	142280134	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	150	324	0	ENST00000350721.4:c.1300C>T	p.Leu434Phe	p.L434F	ENST00000350721	NM_001184.3	434	Ctc/Ttc	5/47	0.699895544596286	2	FACETS	1	0.943	1	0.513	0.473	0.553	CLONAL	1	TRUE	0	0.699895544596286	2		324	418	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191439	185191439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	172	443	0	ENST00000265026.3:c.2320G>A	p.Glu774Lys	p.E774K	ENST00000265026	NM_004721.4	774	Gag/Aag	11/14	0.699895544596286	2	FACETS	0.991	0.919	1	0.495	0.459	0.532	CLONAL	1	TRUE	0	0.699895544596286	2		443	496	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185200158	185200158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	160	420	0	ENST00000265026.3:c.2815G>A	p.Glu939Lys	p.E939K	ENST00000265026	NM_004721.4	939	Gaa/Aaa	14/14	0.699895544596286	2	FACETS	1	0.932	1	0.504	0.466	0.542	CLONAL	1	TRUE	0	0.699895544596286	2		420	454	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971087	55971087	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	145	361	0	ENST00000263923.4:c.1710G>A	p.Trp570Ter	p.W570*	ENST00000263923	NM_002253.2	570	tgG/tgA	13/30	0.699895544596286	3	FACETS	0.901	0.825	0.98	0.45	0.412	0.49	CLONAL	1	TRUE	1	0.699895544596286	3		361	621	SUCCESS
ALB	213	MSKCC	GRCh37	4	74280793	74280793	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	178	336	0	ENST00000295897.4:c.1100T>A	p.Val367Asp	p.V367D	ENST00000295897	NM_000477.5	367	gTc/gAc	9/15	NA	2	FACETS	0.984	0.914	1			1	INDETERMINATE	1	TRUE	NA	0.699895544596286	2		336	517	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155401	106155401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1156737666	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	161	430	0	ENST00000380013.4:c.302C>T	p.Pro101Leu	p.P101L	ENST00000380013	NM_001127208.2	101	cCt/cTt	3/11	1	2	FACETS	0.994	0.92	1	0.994	0.92	1	CLONAL	1	TRUE	1	0.699895544596286	2		430	463	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143181689	143181689	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	128	304	0	ENST00000262992.4:c.644C>A	p.Pro215Gln	p.P215Q	ENST00000262992	NM_001101669.1	215	cCg/cAg	9/24	0.699895544596286	2	FACETS	0.91	0.832	0.99	0.455	0.416	0.495	CLONAL	1	TRUE	0	0.699895544596286	2		304	402	SUCCESS
GAB1	2549	MSKCC	GRCh37	4	144359343	144359343	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	161	421	0	ENST00000262995.4:c.785C>T	p.Pro262Leu	p.P262L	ENST00000262995	NM_207123.2	262	cCc/cTc	4/11	0.699895544596286	2	FACETS	0.977	0.904	1	0.488	0.452	0.526	CLONAL	1	TRUE	0	0.699895544596286	2		421	471	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535477	187535477	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	147	356	0	ENST00000441802.2:c.9097C>T	p.Pro3033Ser	p.P3033S	ENST00000441802	NM_005245.3	3033	Cct/Tct	12/27	0.699895544596286	2	FACETS	0.972	0.896	1	0.486	0.448	0.525	CLONAL	1	TRUE	0	0.699895544596286	2		356	432	SUCCESS
TRIP13	9319	MSKCC	GRCh37	5	908486	908486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	164	390	0	ENST00000166345.3:c.776C>T	p.Ala259Val	p.A259V	ENST00000166345	NM_004237.3	259	gCc/gTc	9/13	0.577907484192751	4	FACETS	1	0.962	1	0.538	0.495	0.583	CLONAL	1	TRUE	2	0.699895544596286	4		390	740	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295665	1295665	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	211	601	0				ENST00000310581	NM_198253.2	-/1132			0.577907484192751	4	FACETS	1	0.946	1	0.511	0.474	0.549	CLONAL	1	TRUE	2	0.699895544596286	4		601	1003	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295832	1295832	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	210	700	0				ENST00000310581	NM_198253.2	-/1132			0.577907484192751	4	FACETS	0.945	0.876	1	0.472	0.438	0.508	CLONAL	1	TRUE	2	0.699895544596286	4		700	1080	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526643	31526643	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	294	426	0	ENST00000344624.3:c.397C>T	p.Pro133Ser	p.P133S	ENST00000344624		133	Cct/Tct	2/33	0.699895544596286	2	FACETS	0.95	0.912	0.988	0.95	0.912	0.988	CLONAL	2	TRUE	0	0.699895544596286	2		426	442	SUCCESS
APC	324	MSKCC	GRCh37	5	112102948	112102948	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	165	371	0	ENST00000257430.4:c.283T>C	p.Ser95Pro	p.S95P	ENST00000257430	NM_000038.5	95	Tct/Cct	4/16	0.699895544596286	2	FACETS	1	0.946	1	0.512	0.475	0.551	CLONAL	1	TRUE	0	0.699895544596286	2		371	460	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497357	149497358	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	163	432	0	ENST00000261799.4:c.2960_2961delinsAA	p.Arg987Gln	p.R987Q	ENST00000261799	NM_002609.3	987	cGG/cAA	22/23	0.699895544596286	3	FACETS	0.973	0.897	1	0.487	0.448	0.527	CLONAL	1	TRUE	1	0.699895544596286	3		432	646	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503867	149503867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	166	452	0	ENST00000261799.4:c.1969C>T	p.His657Tyr	p.H657Y	ENST00000261799	NM_002609.3	657	Cac/Tac	14/23	0.699895544596286	3	FACETS	1	0.938	1	0.51	0.47	0.551	CLONAL	1	TRUE	1	0.699895544596286	3		452	628	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512409	149512409	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	238	571	0	ENST00000261799.4:c.1031C>T	p.Pro344Leu	p.P344L	ENST00000261799	NM_002609.3	344	cCa/cTa	7/23	0.699895544596286	3	FACETS	1	0.975	1	0.541	0.506	0.577	CLONAL	1	TRUE	1	0.699895544596286	3		571	849	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043393	180043393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	194	497	0	ENST00000261937.6:c.3193G>A	p.Asp1065Asn	p.D1065N	ENST00000261937	NM_182925.4	1065	Gac/Aac	23/30	0.620538590268837	3	FACETS	0.951	0.882	1	0.475	0.441	0.511	CLONAL	1	TRUE	1	0.699895544596286	3		497	787	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052901	180052901	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	205	554	0	ENST00000261937.6:c.1389G>A	p.Trp463Ter	p.W463*	ENST00000261937	NM_182925.4	463	tgG/tgA	10/30	0.620538590268837	3	FACETS	0.998	0.928	1	0.499	0.464	0.536	CLONAL	1	TRUE	1	0.699895544596286	3		554	792	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057699	180057699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	191	606	0	ENST00000261937.6:c.256G>A	p.Gly86Ser	p.G86S	ENST00000261937	NM_182925.4	86	Ggc/Agc	3/30	0.620538590268837	3	FACETS	0.986	0.915	1	0.493	0.457	0.53	CLONAL	1	TRUE	1	0.699895544596286	3		606	747	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057797	180057797	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	225	444	0	ENST00000261937.6:c.158G>A	p.Gly53Glu	p.G53E	ENST00000261937	NM_182925.4	53	gGa/gAa	3/30	0.620538590268837	3	FACETS	1	0.99	1	0.659	0.617	0.701	CLONAL	1	TRUE	1	0.699895544596286	3		444	659	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680281	30680281	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779398158	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	95	504	2	ENST00000376406.3:c.1438C>T	p.Leu480Phe	p.L480F	ENST00000376406	NM_014641.2	480	Ctt/Ttt	5/15	0.452443576366385	3	FACETS	0.57	0.508	0.636	0.285	0.254	0.318	SUBCLONAL	1	TRUE	1	0.699895544596286	3		506	643	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31238182	31238182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	81	156	0	ENST00000376228.5:c.700C>T	p.Pro234Ser	p.P234S	ENST00000376228	NM_002117.5	234	Cct/Tct	4/8	0.452443576366385	3	FACETS	0.989	0.898	1	0.989	0.898	1	CLONAL	2	TRUE	1	0.699895544596286	3		156	158	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43752277	43752277	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	267	451	0	ENST00000523873.1:c.678-1G>A		p.X226_splice	ENST00000523873		226			1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.699895544596286	2		451	610	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93953187	93953187	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	110	270	0	ENST00000369303.4:c.2954G>C	p.Arg985Thr	p.R985T	ENST00000369303	NM_004440.3	985	aGa/aCa	17/17	0.699895544596286	3	FACETS	0.88	0.795	0.97			1	CLONAL	1	TRUE	NA	0.699895544596286	3		270	482	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552744	106552744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	195	488	0	ENST00000369096.4:c.709G>A	p.Glu237Lys	p.E237K	ENST00000369096	NM_001198.3	237	Gaa/Aaa	5/7	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.699895544596286	2		488	554	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647566	117647566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	120	407	0	ENST00000368508.3:c.5378C>T	p.Ser1793Leu	p.S1793L	ENST00000368508	NM_002944.2	1793	tCa/tTa	33/43	1	2	FACETS	0.945	0.862	1	0.945	0.862	1	CLONAL	1	TRUE	1	0.699895544596286	2		407	363	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505370	157505370	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	149	383	0	ENST00000346085.5:c.3351T>A	p.Asn1117Lys	p.N1117K	ENST00000346085	NM_020732.3	1117	aaT/aaA	13/20	1	2	FACETS	0.889	0.818	0.962	0.889	0.818	0.962	CLONAL	1	TRUE	1	0.699895544596286	2		383	479	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683610	162683610	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	190	374	0	ENST00000366898.1:c.359C>T	p.Ala120Val	p.A120V	ENST00000366898	NM_004562.2	120	gCt/gTt	3/12	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.699895544596286	2		374	533	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6038812	6038812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781934	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	201	376	0	ENST00000265849.7:c.632G>A	p.Arg211Gln	p.R211Q	ENST00000265849	NM_000535.5	211	cGa/cAa	6/15	0.699895544596286	6	FACETS	1	0.967	1	0.216	0.199	0.233	CLONAL	1	TRUE	1	0.699895544596286	6		376	1278	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55231471	55231471	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	177	439	0	ENST00000275493.2:c.1677C>A	p.His559Gln	p.H559Q	ENST00000275493	NM_005228.3	559	caC/caA	14/28	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.699895544596286	2		439	500	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335685	81335685	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778704152	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	147	361	0	ENST00000222390.5:c.1675G>A	p.Glu559Lys	p.E559K	ENST00000222390	NM_000601.4	559	Gag/Aag	15/18	0.699895544596286	4	FACETS	0.933	0.853	1	0.311	0.284	0.339	CLONAL	1	TRUE	1	0.699895544596286	4		361	765	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124469328	124469328	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	114	215	0	ENST00000357628.3:c.1574T>A	p.Ile525Asn	p.I525N	ENST00000357628	NM_015450.2	525	aTt/aAt	16/19	NA	2	FACETS	1	0.922	1			1	INDETERMINATE	1	TRUE	NA	0.699895544596286	2		215	322	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878820	151878820	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	47	498	0	ENST00000262189.6:c.6125C>A	p.Pro2042His	p.P2042H	ENST00000262189	NM_170606.2	2042	cCt/cAt	36/59	0.699895544596286	3	FACETS	0.254	0.213	0.298	0.127	0.106	0.149	SUBCLONAL	1	TRUE	1	0.699895544596286	3		498	715	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008888	152008888	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	49	319	0	ENST00000262189.6:c.734C>T	p.Ser245Phe	p.S245F	ENST00000262189	NM_170606.2	245	tCt/tTt	5/59	0.699895544596286	3	FACETS	0.346	0.292	0.404	0.173	0.146	0.202	SUBCLONAL	1	TRUE	1	0.699895544596286	3		319	547	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194829	29194829	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144675383	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	381	515	0	ENST00000240100.2:c.899G>A	p.Arg300Gln	p.R300Q	ENST00000240100	NM_001394.6	300	cGg/cAg	4/4	0.699895544596286	4	FACETS	1	0.984	1	0.71	0.677	0.743	CLONAL	2	TRUE	1	0.699895544596286	4		515	869	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187044	38187044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	184	416	0	ENST00000317025.8:c.1433C>T	p.Ser478Phe	p.S478F	ENST00000317025	NM_023034.1	478	tCc/tTc	6/24	0.699895544596286	4	FACETS	0.951	0.878	1	0.317	0.292	0.343	CLONAL	1	TRUE	1	0.699895544596286	4		416	940	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740582	145740582	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1254532871	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	220	653	0	ENST00000428558.2:c.1435C>T	p.Gln479Ter	p.Q479*	ENST00000428558	NM_004260.3	479	Caa/Taa	8/22	0.699895544596286	3	FACETS	0.995	0.927	1	0.497	0.463	0.532	CLONAL	1	TRUE	1	0.699895544596286	3		653	853	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549344	5549344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	149	373	1	ENST00000397747.3:c.371G>A	p.Arg124Lys	p.R124K	ENST00000397747	NM_025239.3	124	aGg/aAg	4/7	0.699895544596286	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.699895544596286	1		374	235	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517970	8517970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	164	411	0	ENST00000356435.5:c.1421G>A	p.Ser474Asn	p.S474N	ENST00000356435		474	aGc/aAc	10/35	0.699895544596286	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.699895544596286	1		411	275	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27183594	27183594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	153	386	0	ENST00000380036.4:c.1168G>A	p.Gly390Arg	p.G390R	ENST00000380036	NM_000459.3	390	Ggg/Agg	8/23	0.699895544596286	1	FACETS	0.99	0.925	1	0.99	0.925	1	CLONAL	1	TRUE	0	0.699895544596286	1		386	287	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336366	80336366	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	159	482	0	ENST00000286548.4:c.953C>T	p.Pro318Leu	p.P318L	ENST00000286548	NM_002072.3	318	cCa/cTa	7/7	1	2	FACETS	0.848	0.782	0.916	0.848	0.782	0.916	CLONAL	1	TRUE	1	0.699895544596286	2		482	536	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563409	87563410	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	183	449	0	ENST00000277120.3:c.1797_1798delinsAA	p.Asp600Asn	p.D600N	ENST00000277120		599	aaGGac/aaAAac	16/19	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.699895544596286	2		449	513	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249355	110249356	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	199	503	0	ENST00000374672.4:c.1217_1218delinsTT	p.Thr406Ile	p.T406I	ENST00000374672	NM_004235.4	406	aCC/aTT	4/5	1	2	FACETS	0.984	0.918	1	0.984	0.918	1	CLONAL	1	TRUE	1	0.699895544596286	2		503	578	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391981	139391982	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	162	497	1	ENST00000277541.6:c.6209_6210delinsAA	p.Arg2070Gln	p.R2070Q	ENST00000277541	NM_017617.3	2070	cGG/cAA	34/34	1	2	FACETS	0.953	0.881	1	0.953	0.881	1	CLONAL	1	TRUE	1	0.699895544596286	2		498	486	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413075	139413075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	191	435	0	ENST00000277541.6:c.1067C>T	p.Ser356Phe	p.S356F	ENST00000277541	NM_017617.3	356	tCc/tTc	6/34	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.699895544596286	2		435	482	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226050	53226050	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	247	259	0	ENST00000375401.3:c.2799G>C	p.Glu933Asp	p.E933D	ENST00000375401	NM_004187.3	933	gaG/gaC	19/26	0.699895544596286	2	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.699895544596286	2		259	495	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179036	123179036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	105	156	1	ENST00000218089.9:c.485C>T	p.Thr162Ile	p.T162I	ENST00000218089	NM_001042749.1	162	aCc/aTc	8/35	0.699895544596286	2	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.699895544596286	2		157	241	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917689	151917691	+	stop_gained	Nonsense_Mutation	TNP	GAT	GAT	AAA	novel	NA	P-0058855-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	13	107	0	ENST00000262189.6:c.3629_3631delinsTTT	p.Asn1210_Gln1211delinsIleTer	p.N1210_Q1211delinsI*	ENST00000262189	NM_170606.2	1210	aATCag/aTTTag	23/59	0.699895544596286	3	FACETS	0.279	0.199	0.375	0.139	0.099	0.188	SUBCLONAL	1	TRUE	1	0.699895544596286	3		107	180	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0058856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	46	209	0	ENST00000374690.3:c.2105T>A	p.Leu702His	p.L702H	ENST00000374690	NM_000044.3	702	cTc/cAc	4/8	0.738717184063127	2	FACETS	0.279	0.235	0.328			1	SUBCLONAL	1	TRUE	NA	0.738717184063127	2		209	446	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371708	225371708	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	284	324	0	ENST00000264414.4:c.896T>G	p.Met299Arg	p.M299R	ENST00000264414	NM_003590.4	299	aTg/aGg	7/16	0.738717184063127	2	FACETS	0.966	0.929	1	0.966	0.929	1	CLONAL	2	TRUE	0	0.738717184063127	2		324	398	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739325	46739337	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGTGACCCGAA	GCGGTGACCCGAA	-	novel	NA	P-0058856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	107	353	0	ENST00000371975.4:c.1518_1530del	p.Thr508AlafsTer5	p.T508Afs*5	ENST00000371975	NM_003579.3	506	GCGGTGACCCGAAgc/gc	14/18	0.386501720035863	1	FACETS	0.348	0.313	0.385	0.348	0.313	0.385	INDETERMINATE	1	TRUE	0	0.738717184063127	1		353	525	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745960	162745960	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	20	421	0	ENST00000367921.3:c.2083G>A	p.Ala695Thr	p.A695T	ENST00000367921	NM_006182.2	695	Gcc/Acc	16/18	0.738717184063127	1	FACETS	0.101	0.077	0.13	0.101	0.077	0.13	SUBCLONAL	1	TRUE	0	0.738717184063127	1		421	337	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024567	16024567	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0058856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	37	348	0	ENST00000268712.3:c.1651A>T	p.Lys551Ter	p.K551*	ENST00000268712	NM_006311.3	551	Aag/Tag	16/46	1	2	FACETS	0.181	0.149	0.218	0.181	0.149	0.218	SUBCLONAL	1	TRUE	1	0.738717184063127	2		348	552	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424805	47424805	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	124	447	0	ENST00000404338.3:c.2873C>G	p.Ala958Gly	p.A958G	ENST00000404338	NM_004491.4	958	gCc/gGc	1/6	0.26347294842503	3	FACETS	0.565	0.511	0.622	0.283	0.255	0.311	INDETERMINATE	1	TRUE	1	0.738717184063127	3		447	813	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116225	209116225	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	95	308	0	ENST00000345146.2:c.51A>C	p.Glu17Asp	p.E17D	ENST00000345146	NM_005896.2	17	gaA/gaC	3/10	0.738717184063127	2	FACETS	0.483	0.432	0.538	0.242	0.216	0.269	SUBCLONAL	1	TRUE	0	0.738717184063127	2		308	532	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421364	12421364	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	96	397	0	ENST00000287820.6:c.244C>G	p.Pro82Ala	p.P82A	ENST00000287820	NM_015869.4	82	Cca/Gca	2/7	0.386501720035863	1	FACETS	0.341	0.305	0.379	0.341	0.305	0.379	INDETERMINATE	1	TRUE	0	0.738717184063127	1		397	481	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164354	47164354	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	32	260	0	ENST00000409792.3:c.1772A>G	p.Gln591Arg	p.Q591R	ENST00000409792	NM_014159.6	591	cAg/cGg	3/21	0.386501720035863	1	FACETS	0.183	0.148	0.221	0.183	0.148	0.221	INDETERMINATE	1	TRUE	0	0.738717184063127	1		260	299	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979618	55979618	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	146	269	0	ENST00000263923.4:c.829C>A	p.Leu277Ile	p.L277I	ENST00000263923	NM_002253.2	277	Cta/Ata	7/30	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.738717184063127	2		269	394	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504341	149504341	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	179	393	0	ENST00000261799.4:c.1861G>A	p.Gly621Ser	p.G621S	ENST00000261799	NM_002609.3	621	Ggc/Agc	13/23	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.738717184063127	2		393	478	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394428	162394428	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058856-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	81	369	0	ENST00000366898.1:c.640del	p.Ala214HisfsTer11	p.A214Hfs*11	ENST00000366898	NM_004562.2	214	Gca/ca	6/12	0.716601751473937	1	FACETS	0.442	0.393	0.493	0.442	0.393	0.493	SUBCLONAL	1	TRUE	0	0.738717184063127	1		369	313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs786202525	NA	P-0058857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	35	836	10	ENST00000269305.4:c.532del	p.His178ThrfsTer69	p.H178Tfs*69	ENST00000269305	NM_001126112.2	178	Cac/ac	5/11	0.265098813752452	6	FACETS	0.981	0.811	1	0.49	0.405	0.584	CLONAL	2	FALSE	2	0.265098813752452	6		846	206	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0058857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	66	623	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.265098813752452	6	FACETS	0.943	0.833	1	0.943	0.833	1	CLONAL	4	FALSE	2	0.265098813752452	6		623	202	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412898	49412898	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519954	NA	P-0058857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	74	409	0	ENST00000418115.1:c.125A>G	p.Tyr42Cys	p.Y42C	ENST00000418115	NM_001664.2	42	tAt/tGt	2/5	0.245136381271828	3	FACETS	0.945	0.841	1	0.945	0.841	1	CLONAL	3	FALSE	0	0.265098813752452	3		409	223	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712598	52712598	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	86	363	0	ENST00000394830.3:c.154G>T	p.Glu52Ter	p.E52*	ENST00000394830	NM_018313.4	52	Gaa/Taa	3/30	0.245136381271828	3	FACETS	0.896	0.81	0.984	1	0.97	1	CLONAL	4	FALSE	0	0.265098813752452	3		363	205	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351548	89351548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555075240	NA	P-0058857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	53	493	0	ENST00000301030.4:c.1402C>T	p.Arg468Cys	p.R468C	ENST00000301030	NM_001256183.1	468	Cgc/Tgc	9/13	0.16922005344675	4	FACETS	0.869	0.752	0.993	1	0.959	1	CLONAL	3	FALSE	2	0.265098813752452	4		493	194	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437669	52437669	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	53	523	0	ENST00000460680.1:c.1492G>T	p.Glu498Ter	p.E498*	ENST00000460680	NM_004656.3	498	Gag/Tag	13/17	0.245136381271828	3	FACETS	0.987	0.86	1	0.987	0.86	1	CLONAL	3	FALSE	0	0.265098813752452	3		523	153	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38173513	38173513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058857-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	182	346	0	ENST00000317025.8:c.1903C>T	p.Arg635Cys	p.R635C	ENST00000317025	NM_023034.1	635	Cgc/Tgc	10/24	0.265098813752452	17	FACETS	1	0.942	1			1	CLONAL	9	FALSE	NA	0.265098813752452	17		346	451	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0058858-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	84	192	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.731547555121565	2		192	214	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0058858-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	175	740	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.857	0.795	0.922	0.857	0.795	0.922	CLONAL	1	TRUE	1	0.731547555121565	2		740	558	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723067	52723067	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770861676	NA	P-0058858-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	172	678	0	ENST00000322088.6:c.1252C>T	p.Arg418Trp	p.R418W	ENST00000322088	NM_014225.5	418	Cgg/Tgg	10/15	1	2	FACETS	0.897	0.832	0.965	0.897	0.832	0.965	CLONAL	1	TRUE	1	0.731547555121565	2		678	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579718	7579718	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058858-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	125	628	2	ENST00000269305.4:c.78del	p.Pro27LeufsTer17	p.P27Lfs*17	ENST00000269305	NM_001126112.2	26	ctT/ct	3/11	0.731547555121565	1	FACETS	0.972	0.903	1	0.972	0.903	1	CLONAL	1	TRUE	0	0.731547555121565	1		630	223	SUCCESS
APC	324	MSKCC	GRCh37	5	112154967	112154968	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs879254088	NA	P-0058858-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	132	557	0	ENST00000257430.4:c.1239dup	p.Arg414ThrfsTer5	p.R414Tfs*5	ENST00000257430	NM_000038.5	413	ata/atAa	10/16	1	2	FACETS	0.735	0.671	0.801	0.735	0.671	0.801	SUBCLONAL	1	TRUE	1	0.731547555121565	2		557	491	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838111	89838111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148203537	NA	P-0058858-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	73	749	0	ENST00000389301.3:c.2126C>T	p.Pro709Leu	p.P709L	ENST00000389301	NM_000135.2	709	cCg/cTg	23/43	0.427967406429799	2	FACETS	0.322	0.281	0.366	0.161	0.14	0.183	INDETERMINATE	1	TRUE	0	0.731547555121565	2		749	620	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411798	63411798	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058858-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	388	419	2	ENST00000330258.3:c.1369C>T	p.Gln457Ter	p.Q457*	ENST00000330258	NM_152424.3	457	Cag/Tag	2/2	0.669257123860854	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.731547555121565	2		421	449	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194123	94194123	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555009855	NA	P-0058858-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	95	311	0	ENST00000323929.3:c.1305G>C	p.Gln435His	p.Q435H	ENST00000323929	NM_005591.3	435	caG/caC	12/20	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.731547555121565	2		311	256	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049772	16049774	+	frameshift_variant	Frame_Shift_Del	DEL	TAG	TAG	AA	novel	NA	P-0058858-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	51	467	1	ENST00000268712.3:c.998_1000delinsTT	p.Ala333ValfsTer70	p.A333Vfs*70	ENST00000268712	NM_006311.3	333	gCTAaa/gTTaa	10/46	0.731547555121565	1	FACETS	0.378	0.324	0.435	0.378	0.324	0.435	SUBCLONAL	1	TRUE	0	0.731547555121565	1		468	234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0058859-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	101	598	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	0.957	0.857	1	1	0.987	1	CLONAL	2	TRUE	1	0.172424815805254	2		598	612	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828108	243828108	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058859-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	39	271	0	ENST00000263826.5:c.250G>A	p.Glu84Lys	p.E84K	ENST00000263826	NM_005465.4	84	Gag/Aag	3/13	0.172424815805254	5	FACETS	0.813	0.676	0.966	0.542	0.45	0.644	CLONAL	2	TRUE	2	0.172424815805254	5		271	350	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599904	10599904	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058859-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	85	620	0	ENST00000171111.5:c.1672G>C	p.Gly558Arg	p.G558R	ENST00000171111	NM_203500.1	558	Ggg/Cgg	5/6	0.161804281764218	2	FACETS	0.959	0.85	1	0.959	0.85	1	CLONAL	2	TRUE	0	0.172424815805254	2		620	514	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220651	1220651	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058859-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	90	736	0	ENST00000326873.7:c.669G>T	p.Glu223Asp	p.E223D	ENST00000326873	NM_000455.4	223	gaG/gaT	5/10	0.161804281764218	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	0	0.172424815805254	2		736	485	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260177	19260177	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058859-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	138	661	1	ENST00000162023.5:c.116G>T	p.Cys39Phe	p.C39F	ENST00000162023		39	tGt/tTt	7/13	0.147978898413853	3	FACETS	0.878	0.801	0.959	0.878	0.801	0.959	CLONAL	3	TRUE	0	0.172424815805254	3		662	660	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950583	38950583	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058859-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	65	479	0	ENST00000357387.3:c.3367G>T	p.Glu1123Ter	p.E1123*	ENST00000357387	NM_152756.3	1123	Gaa/Taa	31/38	0.172424815805254	6	FACETS	0.844	0.731	0.965	0.422	0.365	0.483	CLONAL	2	TRUE	2	0.172424815805254	6		479	601	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0058862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	149	463	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	0.747	0.688	0.808	0.747	0.688	0.808	SUBCLONAL	1	TRUE	1	0.824055603463649	2		463	484	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436841	52436842	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0058862-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	129	472	0	ENST00000460680.1:c.1936dup	p.Tyr646LeufsTer2	p.Y646Lfs*2	ENST00000460680	NM_004656.3	646	tat/tTat	15/17	0.678483961419145	1	FACETS	0.56	0.514	0.606	0.56	0.514	0.606	SUBCLONAL	1	TRUE	0	0.824055603463649	1		472	329	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654597	29654597	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0058863-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	411	330	0	ENST00000356175.3:c.5286T>A	p.Tyr1762Ter	p.Y1762*	ENST00000356175	NM_000267.3	1762	taT/taA	37/57	0.848665929777403	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.848665929777403	2		330	463	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30302542	30302542	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058863-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	21	7	0	ENST00000322652.5:c.633del	p.Lys211AsnfsTer5	p.K211Nfs*5	ENST00000322652	NM_015355.2	211	aaG/aa	7/16	0.848665929777403	2	FACETS	0.952	0.832	1	0.952	0.832	1	CLONAL	2	TRUE	0	0.848665929777403	2		7	26	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0058864-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	58	265	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		265	433	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0058864-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	45	697	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		699	508	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0058864-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	20	427	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		427	679	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0058864-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	43	250	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		250	435	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23635370	23635370	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45624036	NA	P-0058864-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	64	300	0	ENST00000261584.4:c.2794G>A	p.Val932Met	p.V932M	ENST00000261584	NM_024675.3	932	Gtg/Atg	8/13	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		300	598	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375032	104375032	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058864-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	65	363	0	ENST00000369902.3:c.1030A>G	p.Lys344Glu	p.K344E	ENST00000369902	NM_016169.3	344	Aaa/Gaa	9/12	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		363	503	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943367	71943367	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058864-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	57	505	0	ENST00000298229.2:c.1699G>T	p.Glu567Ter	p.E567*	ENST00000298229	NM_001567.3	567	Gag/Tag	14/28	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		505	617	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857695	78857695	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058864-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	40	476	0	ENST00000306801.3:c.1765G>T	p.Asp589Tyr	p.D589Y	ENST00000306801	NM_020761.2	589	Gac/Tac	16/34	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		476	590	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599320	55599320	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913506	NA	P-0058865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	147	355	0	ENST00000288135.5:c.2446G>C	p.Asp816His	p.D816H	ENST00000288135	NM_000222.2	816	Gac/Cac	17/21	0.553387756345004	4	FACETS	0.858	0.789	0.928	0.858	0.789	0.928	CLONAL	2	TRUE	2	0.579738143955521	4		355	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0058865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	294	399	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	0.551218823997795	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.579738143955521	2		399	506	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678335	88678335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	108	403	0	ENST00000360948.2:c.1201C>T	p.Pro401Ser	p.P401S	ENST00000360948	NM_001012338.2	401	Cca/Tca	9/19	0.496035593466336	4	FACETS	0.904	0.813	1	0.452	0.406	0.501	CLONAL	1	TRUE	2	0.579738143955521	4		403	651	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726433	46726433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145441107	NA	P-0058865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	339	551	0	ENST00000371975.4:c.512G>A	p.Arg171Gln	p.R171Q	ENST00000371975	NM_003579.3	171	cGg/cAg	7/18	0.450802431771462	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	2	0.579738143955521	4		551	912	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514017	125514017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	222	395	0	ENST00000428830.2:c.955C>T	p.Pro319Ser	p.P319S	ENST00000428830	NM_001114121.2	319	Cca/Tca	10/14	0.579738143955521	3	FACETS	1	0.992	1	0.724	0.677	0.772	CLONAL	1	TRUE	1	0.579738143955521	3		395	682	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422693	49422693	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	320	507	0	ENST00000301067.7:c.14300G>C	p.Gly4767Ala	p.G4767A	ENST00000301067	NM_003482.3	4767	gGa/gCa	45/54	0.496035593466336	4	FACETS	0.969	0.918	1	0.969	0.918	1	CLONAL	2	TRUE	2	0.579738143955521	4		507	900	SUCCESS
CYP19A1	1588	MSKCC	GRCh37	15	51507343	51507343	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	95	353	0	ENST00000260433.2:c.945G>C	p.Leu315Phe	p.L315F	ENST00000260433		315	ttG/ttC	8/10	0.496035593466336	4	FACETS	0.872	0.778	0.971	0.436	0.389	0.486	CLONAL	1	TRUE	2	0.579738143955521	4		353	594	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649180	23649180	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	200	293	0	ENST00000261584.4:c.202A>G	p.Lys68Glu	p.K68E	ENST00000261584	NM_024675.3	68	Aaa/Gaa	3/13	0.579738143955521	3	FACETS	0.943	0.883	1	0.943	0.883	1	CLONAL	2	TRUE	1	0.579738143955521	3		293	472	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845593	68845593	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	139	392	0	ENST00000261769.5:c.839C>G	p.Ser280Cys	p.S280C	ENST00000261769	NM_004360.3	280	tCt/tGt	7/16	0.579738143955521	3	FACETS	1	0.947	1	0.525	0.48	0.572	CLONAL	1	TRUE	1	0.579738143955521	3		392	589	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727874	78727874	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	135	414	0	ENST00000306801.3:c.719G>C	p.Cys240Ser	p.C240S	ENST00000306801	NM_020761.2	240	tGc/tCc	6/34	0.450802431771462	4	FACETS	0.992	0.902	1	0.496	0.451	0.543	CLONAL	1	TRUE	2	0.579738143955521	4		414	742	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570060	212570060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	296	349	0	ENST00000342788.4:c.1181C>T	p.Thr394Ile	p.T394I	ENST00000342788	NM_005235.2	394	aCa/aTa	10/28	0.565667797362835	5	FACETS	0.966	0.916	1	0.966	0.916	1	CLONAL	3	TRUE	2	0.579738143955521	5		349	659	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66468021	66468021	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	179	307	0	ENST00000273854.3:c.248G>T	p.Trp83Leu	p.W83L	ENST00000273854	NM_004439.5	83	tGg/tTg	3/18	0.553387756345004	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.579738143955521	4		307	442	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163765	32163765	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	101	463	0	ENST00000375023.3:c.5461G>C	p.Gly1821Arg	p.G1821R	ENST00000375023	NM_004557.3	1821	Ggg/Cgg	30/30	0.579738143955521	3	FACETS	0.842	0.755	0.933	0.421	0.377	0.467	CLONAL	1	TRUE	1	0.579738143955521	3		463	534	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027780	152027780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	128	410	0	ENST00000262189.6:c.295G>A	p.Asp99Asn	p.D99N	ENST00000262189	NM_170606.2	99	Gat/Aat	3/59	0.419649836855186	6	FACETS	1	0.974	1	0.301	0.273	0.331	CLONAL	1	TRUE	2	0.579738143955521	6		410	791	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418400	139418400	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058865-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	272	499	0	ENST00000277541.6:c.172C>T	p.Gln58Ter	p.Q58*	ENST00000277541	NM_017617.3	58	Cag/Tag	3/34	0.579738143955521	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.579738143955521	2		499	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0058867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	32	537	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	1	2	FACETS	0.386	0.313	0.47	0.386	0.313	0.47	SUBCLONAL	1	TRUE	1	0.294685115893602	2		537	562	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115284285	115284285	+	start_lost	Translation_Start_Site	SNP	T	T	A	rs1265169937	NA	P-0058867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	80	280	0	ENST00000438362.2:c.1A>T	p.Met1?	p.M1?	ENST00000438362	NM_001242891.1	1	Atg/Ttg	2/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.294685115893602	2		280	429	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971173	21971173	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058867-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	253	611	0	ENST00000304494.5:c.185T>C	p.Leu62Pro	p.L62P	ENST00000304494	NM_000077.4	62	cTg/cCg	2/3	0.283027032631564	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.294685115893602	3		611	579	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0058868-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	13	250	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.479314043343085	3	FACETS	0.325	0.232	0.438	0.162	0.116	0.219	SUBCLONAL	1	TRUE	1	0.479314043343085	3		250	207	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0058868-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	90	441	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.336886429379652	3	FACETS	1	0.98	1	0.73	0.654	0.808	CLONAL	1	TRUE	1	0.479314043343085	3		441	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0058868-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	244	572	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.479314043343085	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.479314043343085	2		572	444	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0058868-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	181	589	2	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.479314043343085	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.479314043343085	3		591	439	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099124	27099125	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0058868-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	188	596	0	ENST00000324856.7:c.3539+2dup		p.X1180_splice	ENST00000324856	NM_006015.4	1180			0.193307047113139	5	FACETS	0.888	0.828	0.95	0.888	0.828	0.95	INDETERMINATE	3	TRUE	2	0.479314043343085	5		596	506	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271166	38271166	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058868-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	74	360	0	ENST00000425967.3:c.2542G>A	p.Gly848Ser	p.G848S	ENST00000425967	NM_001174067.1	848	Ggc/Agc	19/19	0.479314043343085	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.479314043343085	1		360	193	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0058869-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	145	738	0				ENST00000310581	NM_198253.2	-/1132			0.32632182420321	5	FACETS	1	0.964	1	0.724	0.666	0.783	CLONAL	2	TRUE	2	0.516510434478987	5		738	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579472	7579473	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	C	novel	NA	P-0058869-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	357	576	0	ENST00000269305.4:c.214_215delinsG	p.Pro72AlafsTer51	p.P72Afs*51	ENST00000269305	NM_001126112.2	72	CCc/Gc	4/11	0.511424834489813	3	FACETS	0.884	0.846	0.921	0.884	0.846	0.921	CLONAL	3	TRUE	0	0.516510434478987	3		576	656	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120795636	120795636	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058869-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	120	300	0	ENST00000257552.2:c.517G>A	p.Glu173Lys	p.E173K	ENST00000257552	NM_002442.3	173	Gaa/Aaa	8/15	0.516510434478987	3	FACETS	0.891	0.815	0.969	0.891	0.815	0.969	CLONAL	2	TRUE	1	0.516510434478987	3		300	328	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982395	201982395	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058869-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	538	559	0	ENST00000359651.3:c.774G>A	p.Trp258Ter	p.W258*	ENST00000359651		258	tgG/tgA	6/8	0.516510434478987	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	4	TRUE	0	0.516510434478987	4		559	766	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040949	47040949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781934331	NA	P-0058869-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	79	271	0	ENST00000377604.3:c.1479G>A	p.Met493Ile	p.M493I	ENST00000377604	NM_001204468.1	493	atG/atA	14/24	0.466526935858949	2	FACETS	0.908	0.805	1			1	CLONAL	1	TRUE	NA	0.516510434478987	2		271	337	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237740	16237740	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0058869-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	205	363	0	ENST00000375759.3:c.1187C>G	p.Ser396Ter	p.S396*	ENST00000375759	NM_015001.2	396	tCa/tGa	5/15	0.429045053384469	4	FACETS	0.942	0.878	1	0.942	0.878	1	CLONAL	2	TRUE	2	0.516510434478987	4		363	639	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845481	63845481	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058869-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	181	353	0	ENST00000279873.7:c.1220G>C	p.Arg407Thr	p.R407T	ENST00000279873	NM_032199.2	407	aGa/aCa	9/10	0.32632182420321	5	FACETS	1	0.931	1	0.67	0.621	0.72	CLONAL	2	TRUE	2	0.516510434478987	5		353	619	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633481	69633481	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0058869-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4040	1369	415	1	ENST00000334134.2:c.220+1G>A		p.X74_splice	ENST00000334134	NM_005247.2	74			0.516510434478987	47	FACETS	1	0.989	1			1	CLONAL	12	TRUE	NA	0.516510434478987	47		416	5409	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633497	69633497	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058869-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4252	1246	421	0	ENST00000334134.2:c.205G>A	p.Glu69Lys	p.E69K	ENST00000334134	NM_005247.2	69	Gag/Aag	1/3	0.516510434478987	47	FACETS	1	0.976	1			1	CLONAL	11	TRUE	NA	0.516510434478987	47		421	5498	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111957675	111957675	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058869-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	77	452	0	ENST00000375549.3:c.44G>A	p.Gly15Glu	p.G15E	ENST00000375549	NM_003002.3	15	gGa/gAa	1/4	0.372976442473392	4	FACETS	0.883	0.777	0.996	0.294	0.259	0.333	CLONAL	1	TRUE	1	0.516510434478987	4		452	512	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307243	118307243	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058869-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	119	265	0	ENST00000534358.1:c.16C>G	p.Arg6Gly	p.R6G	ENST00000534358	NM_005933.3	6	Cgg/Ggg	1/36	0.372976442473392	4	FACETS	0.917	0.845	0.99	0.917	0.845	0.99	CLONAL	3	TRUE	1	0.516510434478987	4		265	254	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220062	133220062	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058869-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	100	505	0	ENST00000320574.5:c.4375G>T	p.Glu1459Ter	p.E1459*	ENST00000320574	NM_006231.2	1459	Gaa/Taa	34/49	0.516510434478987	3	FACETS	0.803	0.718	0.892	0.401	0.359	0.446	CLONAL	1	TRUE	1	0.516510434478987	3		505	607	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40684159	40684159	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058869-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	174	279	0	ENST00000249776.8:c.757G>C	p.Glu253Gln	p.E253Q	ENST00000249776	NM_033286.3	253	Gaa/Caa	8/9	0.226013003147606	4	FACETS	1	0.983	1	1	0.983	1	INDETERMINATE	2	TRUE	2	0.516510434478987	4		279	435	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29279771	29279771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058869-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	92	192	0	ENST00000544604.2:c.17G>A	p.Gly6Asp	p.G6D	ENST00000544604	NM_001206998.1	6	gGc/gAc	1/9	0.304358346502937	4	FACETS	1	0.958	1	1	0.958	1	INDETERMINATE	2	TRUE	2	0.516510434478987	4		192	243	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455651	189455651	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058869-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	295	351	0	ENST00000264731.3:c.185T>G	p.Leu62Arg	p.L62R	ENST00000264731	NM_003722.4	62	cTg/cGg	2/14	0.516510434478987	8	FACETS	1	0.978	1			1	CLONAL	2	TRUE	NA	0.516510434478987	8		351	1342	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729909	41729909	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058869-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	227	469	0	ENST00000242208.4:c.620C>G	p.Ser207Cys	p.S207C	ENST00000242208	NM_002192.2	207	tCt/tGt	3/3	0.475478644348514	4	FACETS	0.913	0.854	0.973	0.913	0.854	0.973	CLONAL	2	TRUE	2	0.516510434478987	4		469	730	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0058878-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	44	428	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.788	0.665	0.923	0.788	0.665	0.923	CLONAL	1	TRUE	1	0.389054977440638	2		428	287	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0058878-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	56	450	2	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.389054977440638	1	FACETS	0.664	0.572	0.764	0.664	0.572	0.764	SUBCLONAL	1	TRUE	0	0.389054977440638	1		452	349	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0058878-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	75	498	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	0.389054977440638	1	FACETS	0.848	0.748	0.955	0.848	0.748	0.955	CLONAL	1	TRUE	0	0.389054977440638	1		498	366	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519980	NA	P-0058878-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	105	640	2	ENST00000269305.4:c.528C>G	p.Cys176Trp	p.C176W	ENST00000269305	NM_001126112.2	176	tgC/tgG	5/11	0.389054977440638	1	FACETS	0.854	0.768	0.944	0.854	0.768	0.944	CLONAL	1	TRUE	0	0.389054977440638	1		642	509	SUCCESS
AR	367	MSKCC	GRCh37	X	66766207	66766207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058878-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	92	277	0	ENST00000374690.3:c.1219C>T	p.Arg407Cys	p.R407C	ENST00000374690	NM_000044.3	407	Cgc/Tgc	1/8	1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.389054977440638	1		277	273	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405247	70405247	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058878-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	81	487	0	ENST00000373644.4:c.2761C>T	p.Gln921Ter	p.Q921*	ENST00000373644	NM_030625.2	921	Cag/Tag	4/12	1	2	FACETS	0.921	0.815	1	0.921	0.815	1	CLONAL	1	TRUE	1	0.389054977440638	2		487	452	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492620	56492620	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058878-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	96	497	0	ENST00000267101.3:c.2770C>A	p.Leu924Ile	p.L924I	ENST00000267101	NM_001982.3	924	Cta/Ata	23/28	1	2	FACETS	0.979	0.876	1	0.979	0.876	1	CLONAL	1	TRUE	1	0.389054977440638	2		497	504	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457597	67457597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058878-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	108	595	0	ENST00000327367.4:c.407C>T	p.Pro136Leu	p.P136L	ENST00000327367	NM_005902.3	136	cCt/cTt	3/9	1	2	FACETS	0.947	0.853	1	0.947	0.853	1	CLONAL	1	TRUE	1	0.389054977440638	2		595	586	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562981	29562981	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs376576925	NA	P-0058878-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	61	386	1	ENST00000356175.3:c.3916C>T	p.Arg1306Ter	p.R1306*	ENST00000356175	NM_000267.3	1306	Cga/Tga	29/57	1	2	FACETS	0.925	0.803	1	0.925	0.803	1	CLONAL	1	TRUE	1	0.389054977440638	2		387	339	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143044492	143044492	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058878-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	80	366	0	ENST00000262992.4:c.1970del	p.His657ProfsTer5	p.H657Pfs*5	ENST00000262992	NM_001101669.1	657	cAc/cc	18/24	0.353263326160305	2	FACETS	0.86	0.769	0.955	0.86	0.769	0.955	CLONAL	2	TRUE	0	0.389054977440638	2		366	239	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	62	302	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.833	0.72	0.957	0.833	0.72	0.957	CLONAL	1	TRUE	1	0.24429511114272	2		302	609	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578537	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs879254214	NA	P-0058879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	53	417	0	ENST00000269305.4:c.393_395del	p.Asn131del	p.N131del	ENST00000269305	NM_001126112.2	131	aaCAAg/aag	5/11	1	2	FACETS	0.538	0.458	0.627	0.538	0.458	0.627	SUBCLONAL	1	TRUE	1	0.24429511114272	2		417	806	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206798	102206798	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	39	324	0	ENST00000263464.3:c.1426G>A	p.Glu476Lys	p.E476K	ENST00000263464	NM_001165.4	476	Gaa/Aaa	7/9	1	2	FACETS	0.576	0.477	0.687	0.576	0.477	0.687	SUBCLONAL	1	TRUE	1	0.24429511114272	2		324	554	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129265	152129265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs769634976	NA	P-0058879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	47	432	0	ENST00000206249.3:c.218A>G	p.Tyr73Cys	p.Y73C	ENST00000206249	NM_000125.3	73	tAc/tGc	1/8	1	2	FACETS	0.578	0.486	0.679	0.578	0.486	0.679	SUBCLONAL	1	TRUE	1	0.24429511114272	2		432	666	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64289191	64289191	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	78	286	0	ENST00000370651.3:c.359T>C	p.Ile120Thr	p.I120T	ENST00000370651	NM_003463.4	120	aTt/aCt	5/6	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.24429511114272	2		286	427	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856347	45856347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	42	369	0	ENST00000391945.4:c.1825G>A	p.Asp609Asn	p.D609N	ENST00000391945	NM_000400.3	609	Gac/Aac	19/23	1	2	FACETS	0.483	0.402	0.573	0.483	0.402	0.573	SUBCLONAL	1	TRUE	1	0.24429511114272	2		369	712	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432623	49432623	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555191147	NA	P-0058879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	46	437	0	ENST00000301067.7:c.8516C>G	p.Ser2839Ter	p.S2839*	ENST00000301067	NM_003482.3	2839	tCa/tGa	34/54	1	2	FACETS	0.433	0.364	0.511	0.433	0.364	0.511	SUBCLONAL	1	TRUE	1	0.24429511114272	2		437	869	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944710	71944710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	112	386	0	ENST00000298229.2:c.2134G>A	p.Asp712Asn	p.D712N	ENST00000298229	NM_001567.3	712	Gac/Aac	19/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.24429511114272	2		386	723	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223006	41223006	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0058879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	113	337	0	ENST00000357654.3:c.4925C>G	p.Ser1642Ter	p.S1642*	ENST00000357654	NM_007294.3	1642	tCa/tGa	15/23	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.24429511114272	2		337	779	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422730	47422730	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	55	347	0	ENST00000404338.3:c.798G>C	p.Gln266His	p.Q266H	ENST00000404338	NM_004491.4	266	caG/caC	1/6	1	2	FACETS	0.733	0.627	0.85	0.733	0.627	0.85	SUBCLONAL	1	TRUE	1	0.24429511114272	2		347	614	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628447	187628454	+	frameshift_variant	Frame_Shift_Del	DEL	TTCAACCT	TTCAACCT	-	novel	NA	P-0058879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	45	437	0	ENST00000441802.2:c.2528_2535del	p.Gln843ArgfsTer4	p.Q843Rfs*4	ENST00000441802	NM_005245.3	843	cAGGTTGAA/c	2/27	0.200778074902104	1	FACETS	0.483	0.405	0.569	0.483	0.405	0.569	SUBCLONAL	1	TRUE	0	0.24429511114272	1		437	670	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877941	151877941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	58	397	0	ENST00000262189.6:c.7004G>A	p.Cys2335Tyr	p.C2335Y	ENST00000262189	NM_170606.2	2335	tGt/tAt	36/59	1	2	FACETS	0.617	0.529	0.714	0.617	0.529	0.714	SUBCLONAL	1	TRUE	1	0.24429511114272	2		397	769	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44733214	44733245	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGAAGGCCCTACTGGGCAAGGTAAGGCAGCTG	CGAAGGCCCTACTGGGCAAGGTAAGGCAGCTG	-	novel	NA	P-0058879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	89	308	0	ENST00000377967.4:c.209_225+15del		p.X70_splice	ENST00000377967	NM_021140.2	70		2/29	0.24429511114272	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.24429511114272	1		308	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577111	+	protein_altering_variant	In_Frame_Del	DEL	GGACAGG	GGACAGG	C	novel	NA	P-0058879-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	99	387	0	ENST00000269305.4:c.827_833delinsG	p.Ala276_Pro278delinsGly	p.A276_P278delinsG	ENST00000269305	NM_001126112.2	276	gCCTGTCCt/gGt	8/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.24429511114272	2		387	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0058880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	645	804	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.867585866611769	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.87739181453561	2		804	705	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0058880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	218	224	3	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.87739181453561	2		227	478	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415845	49415845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	220	325	3	ENST00000301067.7:c.16502G>A	p.Arg5501Gln	p.R5501Q	ENST00000301067	NM_003482.3	5501	cGa/cAa	53/54	1	2	FACETS	0.805	0.754	0.857	0.805	0.754	0.857	CLONAL	1	TRUE	1	0.87739181453561	2		328	623	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854961	76854961	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058880-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	120	303	2	ENST00000373344.5:c.5875A>G	p.Asn1959Asp	p.N1959D	ENST00000373344	NM_000489.3	1959	Aat/Gat	25/35	0.197386027614056	1	FACETS	0.503	0.461	0.546	0.503	0.461	0.546	INDETERMINATE	1	TRUE	0	0.87739181453561	1		305	305	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	180	302	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		302	697	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	125	130	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		130	344	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0058881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	151	255	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		255	807	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027160	49027160	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0058881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	148	113	0	ENST00000267163.4:c.1727C>G	p.Ser576Ter	p.S576*	ENST00000267163	NM_000321.2	576	tCa/tGa	18/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		113	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0058881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	147	240	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		240	717	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215302	123215302	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	31	53	0	ENST00000218089.9:c.2848G>T	p.Glu950Ter	p.E950*	ENST00000218089	NM_001042749.1	950	Gaa/Taa	28/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		53	110	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790158	40790158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781621750	NA	P-0058881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	124	163	0	ENST00000373198.4:c.2573C>T	p.Ser858Phe	p.S858F	ENST00000373198	NM_133170.3	858	tCc/tTc	18/32	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		163	722	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259138	36259138	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0058881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	149	201	0	ENST00000300305.3:c.351+2T>C		p.X117_splice	ENST00000300305		117			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		201	829	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155120	108155120	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	63	116	0	ENST00000278616.4:c.3913G>C	p.Asp1305His	p.D1305H	ENST00000278616	NM_000051.3	1305	Gac/Cac	26/63	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		116	313	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422861	49422909	+	frameshift_variant	Frame_Shift_Del	DEL	GGAATGAGGGGGATGACAGGGGAGAGGGCCCGGTCCTCTTGCTCCCACC	GGAATGAGGGGGATGACAGGGGAGAGGGCCCGGTCCTCTTGCTCCCACC	-	novel	NA	P-0058881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	133	214	0	ENST00000301067.7:c.14186_14234del	p.Arg4729LeufsTer52	p.R4729Lfs*52	ENST00000301067	NM_003482.3	4729	cGGTGGGAGCAAGAGGACCGGGCCCTCTCCCCTGTCATCCCCCTCATTCCt/ct	44/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		214	824	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67459117	67459117	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	64	185	0	ENST00000327367.4:c.533A>G	p.Glu178Gly	p.E178G	ENST00000327367	NM_005902.3	178	gAg/gGg	4/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		185	529	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628535	90628539	+	frameshift_variant	Frame_Shift_Del	DEL	ACGGT	ACGGT	CCA	novel	NA	P-0058881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	88	199	1	ENST00000330062.3:c.1048_1052delinsTGG	p.Thr350TrpfsTer129	p.T350Wfs*129	ENST00000330062	NM_002168.2	350	ACCGTc/TGGc	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		200	667	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641136	3641136	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0058881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	98	172	0	ENST00000294008.3:c.2503A>T	p.Lys835Ter	p.K835*	ENST00000294008	NM_032444.2	835	Aaa/Taa	12/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		172	560	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33689760	33689760	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1442895068	NA	P-0058881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	106	195	0	ENST00000308377.4:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000308377	NM_152270.3	356	cCa/cTa	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		195	512	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288519	15288519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	132	63	0	ENST00000263388.2:c.4220G>A	p.Ser1407Asn	p.S1407N	ENST00000263388	NM_000435.2	1407	aGc/aAc	24/33	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		63	517	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536142	41536142	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0058881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	52	132	0	ENST00000263253.7:c.1761-2A>T		p.X587_splice	ENST00000263253	NM_001429.3	587			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		132	380	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133461	55133461	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	21	151	0	ENST00000257290.5:c.765del	p.Gly257AlafsTer19	p.G257Afs*19	ENST00000257290	NM_006206.4	255	ggC/gg	6/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		151	401	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247173	153247198	+	frameshift_variant	Frame_Shift_Del	DEL	TCTATTAGTATGCCCCTGCAACGTGT	TCTATTAGTATGCCCCTGCAACGTGT	-	novel	NA	P-0058881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	51	132	0	ENST00000281708.4:c.1604_1629del	p.His535ArgfsTer7	p.H535Rfs*7	ENST00000281708	NM_033632.3	535	cACACGTTGCAGGGGCATACTAATAGA/c	10/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		132	376	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629999	187629999	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	114	229	0	ENST00000441802.2:c.983A>G	p.His328Arg	p.H328R	ENST00000441802	NM_005245.3	328	cAt/cGt	2/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		229	625	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1266639	1266639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918666	NA	P-0058881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	91	194	0	ENST00000310581.5:c.2594G>A	p.Arg865His	p.R865H	ENST00000310581	NM_198253.2	865	cGt/cAt	10/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		194	653	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964406	70964406	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058881-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	58	174	0	ENST00000276594.2:c.1622A>T	p.Lys541Met	p.K541M	ENST00000276594	NM_024504.3	541	aAg/aTg	8/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		174	496	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0058882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	768	387	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.683665952173654	4	FACETS	0.949	0.93	0.966	0.949	0.93	0.966	CLONAL	4	TRUE	0	0.752010122837927	4		387	943	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0058882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	132	319	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	0.113672312723096	4	FACETS	0.838	0.77	0.908	0.838	0.77	0.908	INDETERMINATE	2	TRUE	2	0.752010122837927	4		319	367	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106648	27106648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553153748	NA	P-0058882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	282	570	0	ENST00000324856.7:c.6259G>A	p.Gly2087Arg	p.G2087R	ENST00000324856	NM_006015.4	2087	Gga/Aga	20/20	0.161222375501219	4	FACETS	0.804	0.758	0.851	0.804	0.758	0.851	INDETERMINATE	2	TRUE	2	0.752010122837927	4		570	817	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915717	131915717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773887771	NA	P-0058882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	107	254	0	ENST00000265335.6:c.715G>A	p.Glu239Lys	p.E239K	ENST00000265335		239	Gaa/Aaa	5/25	NA	2	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.752010122837927	2		254	262	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981851	201981852	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0058882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	400	547	0	ENST00000359651.3:c.567dup	p.Ser190LeufsTer6	p.S190Lfs*6	ENST00000359651		188	gcc/gCcc	4/8	0.752010122837927	3	FACETS	0.801	0.765	0.837	0.801	0.765	0.837	CLONAL	2	TRUE	1	0.752010122837927	3		547	914	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651956	36651957	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0058882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	267	436	0	ENST00000244741.5:c.79dup	p.Ser27LysfsTer9	p.S27Kfs*9	ENST00000244741	NM_000389.4	26	-/A	2/3	0.161222375501219	4	FACETS	0.851	0.802	0.901	0.851	0.802	0.901	INDETERMINATE	2	TRUE	2	0.752010122837927	4		436	731	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78934001	78934001	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	231	495	0	ENST00000306801.3:c.3601G>A	p.Glu1201Lys	p.E1201K	ENST00000306801	NM_020761.2	1201	Gaa/Aaa	30/34	0.113672312723096	4	FACETS	0.874	0.82	0.928	0.874	0.82	0.928	INDETERMINATE	2	TRUE	2	0.752010122837927	4		495	616	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220150	36220150	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	251	487	0	ENST00000222270.7:c.4870G>A	p.Gly1624Ser	p.G1624S	ENST00000222270	NM_014727.1	1624	Ggc/Agc	22/37	0.161222375501219	4	FACETS	0.824	0.774	0.874	0.824	0.774	0.874	INDETERMINATE	2	TRUE	2	0.752010122837927	4		487	710	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024014	27024018	+	frameshift_variant	Frame_Shift_Del	DEL	CTCGC	CTCGC	-	novel	NA	P-0058882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	164	326	0	ENST00000324856.7:c.1121_1125del	p.Leu374ProfsTer24	p.L374Pfs*24	ENST00000324856	NM_006015.4	374	CTCGCc/c	1/20	0.161222375501219	4	FACETS	0.798	0.738	0.858	0.798	0.738	0.858	INDETERMINATE	2	TRUE	2	0.752010122837927	4		326	479	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807382	36807382	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	188	397	0	ENST00000373129.3:c.1282C>G	p.Leu428Val	p.L428V	ENST00000373129	NM_032017.1	428	Ctg/Gtg	12/12	0.161222375501219	4	FACETS	0.791	0.736	0.847	0.791	0.736	0.847	INDETERMINATE	2	TRUE	2	0.752010122837927	4		397	554	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195424	102195424	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	228	394	0	ENST00000263464.3:c.184G>C	p.Asp62His	p.D62H	ENST00000263464	NM_001165.4	62	Gac/Cac	2/9	0.113672312723096	4	FACETS	0.884	0.83	0.939	0.884	0.83	0.939	INDETERMINATE	2	TRUE	2	0.752010122837927	4		394	601	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149337	119149337	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	215	464	0	ENST00000264033.4:c.1345G>A	p.Gly449Arg	p.G449R	ENST00000264033	NM_005188.3	449	Gga/Aga	9/16	0.50349782439757	3	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.752010122837927	3		464	683	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042423	42042423	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	263	482	0	ENST00000219905.7:c.6618G>C	p.Lys2206Asn	p.K2206N	ENST00000219905	NM_001164273.1	2206	aaG/aaC	17/24	0.161222375501219	4	FACETS	0.919	0.867	0.971	0.919	0.867	0.971	INDETERMINATE	2	TRUE	2	0.752010122837927	4		482	667	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533378	29533378	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs878853865	NA	P-0058882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	73	417	0	ENST00000356175.3:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000356175	NM_000267.3	461	Cga/Tga	12/57	0.50349782439757	3	FACETS	0.457	0.399	0.518			1	SUBCLONAL	1	TRUE	NA	0.752010122837927	3		417	585	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556173	29556173	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199474747	NA	P-0058882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	77	182	0	ENST00000356175.3:c.2540T>C	p.Leu847Pro	p.L847P	ENST00000356175	NM_000267.3	847	cTt/cCt	21/57	0.50349782439757	3	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.752010122837927	3		182	217	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33690145	33690145	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0058882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	178	427	0	ENST00000308377.4:c.682A>T	p.Lys228Ter	p.K228*	ENST00000308377	NM_152270.3	228	Aaa/Taa	2/5	NA	2	FACETS	0.921	0.856	0.988			1	INDETERMINATE	1	TRUE	NA	0.752010122837927	2		427	514	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873328	136873328	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	167	491	0	ENST00000241393.3:c.170G>C	p.Gly57Ala	p.G57A	ENST00000241393	NM_003467.2	57	gGa/gCa	2/2	0.752010122837927	1	FACETS	0.761	0.71	0.813	0.761	0.71	0.813	SUBCLONAL	1	TRUE	0	0.752010122837927	1		491	364	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225564	225564	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058882-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	122	243	0	ENST00000264932.6:c.343G>C	p.Glu115Gln	p.E115Q	ENST00000264932	NM_004168.2	115	Gag/Cag	4/15	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.752010122837927	2		243	318	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926885	112926885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507544	NA	P-0058893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	8	334	0	ENST00000351677.2:c.1505C>T	p.Ser502Leu	p.S502L	ENST00000351677	NM_002834.3	502	tCa/tTa	13/16	0.162024853997872	1	FACETS	0.325	0.21	0.472	0.325	0.21	0.472	INDETERMINATE	1	TRUE	0	0.345555947784247	1		334	118	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41276053	41276053	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs80357406	NA	P-0058893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	49	262	0	ENST00000357654.3:c.61A>G	p.Ile21Val	p.I21V	ENST00000357654	NM_007294.3	21	Atc/Gtc	2/23	0.138035001856399	4	FACETS	1	0.888	1	1	0.888	1	INDETERMINATE	2	TRUE	2	0.345555947784247	4		262	184	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183725	10183725	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs5030826	NA	P-0058893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	21	298	0	ENST00000256474.2:c.194C>G	p.Ser65Trp	p.S65W	ENST00000256474	NM_000551.3	65	tCg/tGg	1/3	0.345555947784247	1	FACETS	1	0.811	1	1	0.811	1	CLONAL	1	TRUE	0	0.345555947784247	1		298	97	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210481	5210481	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs747402108	NA	P-0058893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	27	380	0	ENST00000357368.4:c.5486G>A	p.Arg1829Gln	p.R1829Q	ENST00000357368	NM_002850.3	1829	cGg/cAg	35/38	0.162024853997872	1	FACETS	1	0.907	1	1	0.907	1	INDETERMINATE	1	TRUE	0	0.345555947784247	1		380	107	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183710	10183710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	18	289	0	ENST00000256474.2:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000256474	NM_000551.3	60	cGg/cAg	1/3	0.345555947784247	1	FACETS	0.991	0.761	1	0.991	0.761	1	CLONAL	1	TRUE	0	0.345555947784247	1		289	87	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165578	47165600	+	frameshift_variant	Frame_Shift_Del	DEL	ACAGTTGTTGATTCTGCTATCAC	ACAGTTGTTGATTCTGCTATCAC	-	novel	NA	P-0058893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	34	509	0	ENST00000409792.3:c.526_548del	p.Val176ArgfsTer53	p.V176Rfs*53	ENST00000409792	NM_014159.6	176	GTGATAGCAGAATCAACAACTGTa/a	3/21	0.345555947784247	1	FACETS	0.975	0.807	1	0.975	0.807	1	CLONAL	1	TRUE	0	0.345555947784247	1		509	167	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441222	52441222	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058893-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	28	364	1	ENST00000460680.1:c.548T>G	p.Leu183Arg	p.L183R	ENST00000460680	NM_004656.3	183	cTg/cGg	7/17	0.345555947784247	1	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	0	0.345555947784247	1		365	124	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0058894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	118	409	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.48920139833741	3	FACETS	1	0.911	1	0.504	0.456	0.554	CLONAL	1	TRUE	1	0.48920139833741	3		409	596	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913286	NA	P-0058894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	54	206	0	ENST00000263967.3:c.1636C>G	p.Gln546Glu	p.Q546E	ENST00000263967	NM_006218.2	546	Cag/Gag	10/21	0.48920139833741	3	FACETS	1	0.901	1	0.528	0.455	0.607	CLONAL	1	TRUE	1	0.48920139833741	3		206	260	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624301	89624301	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	83	341	0	ENST00000371953.3:c.75G>C	p.Leu25Phe	p.L25F	ENST00000371953	NM_000314.4	25	ttG/ttC	1/9	1	2	FACETS	0.764	0.677	0.856	0.764	0.677	0.856	SUBCLONAL	1	TRUE	1	0.48920139833741	2		341	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0058894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	141	494	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.486598905253196	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.48920139833741	1		494	433	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094324	193094324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	90	358	0	ENST00000367435.3:c.214C>T	p.Pro72Ser	p.P72S	ENST00000367435	NM_024529.4	72	Cct/Tct	2/17	0.48920139833741	3	FACETS	0.799	0.71	0.894	0.266	0.236	0.298	SUBCLONAL	1	TRUE	0	0.48920139833741	3		358	573	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230572	46230572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1170640220	NA	P-0058894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	87	414	0	ENST00000334344.6:c.821G>A	p.Arg274Gln	p.R274Q	ENST00000334344	NM_152641.2	274	cGa/cAa	8/21	1	2	FACETS	0.644	0.572	0.722	0.644	0.572	0.722	SUBCLONAL	1	TRUE	1	0.48920139833741	2		414	552	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226561941	226561941	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	115	368	0	ENST00000366794.5:c.2056A>T	p.Met686Leu	p.M686L	ENST00000366794	NM_001618.3	686	Atg/Ttg	14/23	0.469507258560902	4	FACETS	1	0.908	1	0.252	0.227	0.278	CLONAL	1	TRUE	0	0.48920139833741	4		368	695	SUCCESS
GAB2	9846	MSKCC	GRCh37	11	77937931	77937931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138004774	NA	P-0058894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	123	401	0	ENST00000361507.4:c.787G>A	p.Asp263Asn	p.D263N	ENST00000361507	NM_080491.2	263	Gac/Aac	4/10	0.48920139833741	7	FACETS	0.851	0.767	0.941			1	CLONAL	1	TRUE	NA	0.48920139833741	7		401	1313	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100107	30100107	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1341145583	NA	P-0058894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	135	398	0	ENST00000331968.5:c.1513G>C	p.Glu505Gln	p.E505Q	ENST00000331968	NM_002742.2	505	Gaa/Caa	10/18	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.48920139833741	2		398	471	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482757	67482757	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	77	338	0	ENST00000327367.4:c.1161G>T	p.Gln387His	p.Q387H	ENST00000327367	NM_005902.3	387	caG/caT	9/9	1	2	FACETS	0.811	0.716	0.912	0.811	0.716	0.912	CLONAL	1	TRUE	1	0.48920139833741	2		338	388	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304444	91304444	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	111	329	0	ENST00000355112.3:c.1841C>G	p.Ala614Gly	p.A614G	ENST00000355112	NM_000057.2	614	gCt/gGt	7/22	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.48920139833741	2		329	440	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475610	40475610	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	100	304	0	ENST00000264657.5:c.1634C>T	p.Thr545Ile	p.T545I	ENST00000264657	NM_139276.2	545	aCa/aTa	18/24	0.48920139833741	3	FACETS	0.966	0.866	1	0.483	0.433	0.536	CLONAL	1	TRUE	1	0.48920139833741	3		304	527	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78519547	78519547	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	79	420	0	ENST00000306801.3:c.118G>T	p.Glu40Ter	p.E40*	ENST00000306801	NM_020761.2	40	Gaa/Taa	1/34	0.48920139833741	3	FACETS	0.578	0.508	0.654	0.289	0.254	0.327	SUBCLONAL	1	TRUE	1	0.48920139833741	3		420	695	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46270965	46270965	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	109	320	0	ENST00000371998.3:c.3089T>C	p.Leu1030Pro	p.L1030P	ENST00000371998		1030	cTt/cCt	17/23	0.457342583858141	4	FACETS	1	0.925	1	0.345	0.31	0.381	CLONAL	1	TRUE	1	0.48920139833741	4		320	642	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279987	46279987	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	75	461	0	ENST00000371998.3:c.3913C>G	p.Pro1305Ala	p.P1305A	ENST00000371998		1305	Cct/Gct	20/23	0.457342583858141	4	FACETS	0.564	0.493	0.64	0.188	0.164	0.214	SUBCLONAL	1	TRUE	1	0.48920139833741	4		461	810	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157461	106157461	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	35	412	0	ENST00000380013.4:c.2362G>A	p.Glu788Lys	p.E788K	ENST00000380013	NM_001127208.2	788	Gaa/Aaa	3/11	1	2	FACETS	0.268	0.219	0.323	0.268	0.219	0.323	SUBCLONAL	1	TRUE	1	0.48920139833741	2		412	534	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31239439	31239439	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058894-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	82	503	0	ENST00000376228.5:c.280C>G	p.Gln94Glu	p.Q94E	ENST00000376228	NM_002117.5	94	Cag/Gag	2/8	1	2	FACETS	0.545	0.481	0.614	0.545	0.481	0.614	SUBCLONAL	1	TRUE	1	0.48920139833741	2		503	615	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	21	738	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.855	0.661	1	0.855	0.661	1	CLONAL	1	TRUE	1	0.224226246157144	2		738	219	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984767	11984767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773665341	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	22	183	0	ENST00000353533.5:c.313C>T	p.Leu105Phe	p.L105F	ENST00000353533	NM_003010.3	105	Ctt/Ttt	3/11	1	2	FACETS	0.764	0.593	0.961	0.764	0.593	0.961	CLONAL	1	TRUE	1	0.224226246157144	2		183	257	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220045	5220045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145842090	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	29	405	0	ENST00000357368.4:c.3670G>A	p.Asp1224Asn	p.D1224N	ENST00000357368	NM_002850.3	1224	Gac/Aac	22/38	1	2	FACETS	0.622	0.499	0.762	0.622	0.499	0.762	SUBCLONAL	1	TRUE	1	0.224226246157144	2		405	416	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412266	139412266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776258761	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	51	319	0	ENST00000277541.6:c.1379C>T	p.Pro460Leu	p.P460L	ENST00000277541	NM_017617.3	460	cCg/cTg	8/34	0.224226246157144	3	FACETS	0.953	0.81	1	0.476	0.405	0.555	CLONAL	1	TRUE	1	0.224226246157144	3		319	531	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169081	119169081	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	50	370	0	ENST00000264033.4:c.2265G>T	p.Leu755Phe	p.L755F	ENST00000264033	NM_005188.3	755	ttG/ttT	15/16	1	2	FACETS	0.861	0.731	1	0.861	0.731	1	CLONAL	1	TRUE	1	0.224226246157144	2		370	518	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022637	31022637	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs755789372	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	41	403	0	ENST00000375687.4:c.2122C>T	p.Gln708Ter	p.Q708*	ENST00000375687	NM_015338.5	708	Cag/Tag	13/13	1	2	FACETS	0.663	0.551	0.787	0.663	0.551	0.787	SUBCLONAL	1	TRUE	1	0.224226246157144	2		403	552	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8111101	8111101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1362101464	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	33	332	0	ENST00000585124.1:c.106C>T	p.Pro36Ser	p.P36S	ENST00000585124	NM_004217.3	36	Cca/Tca	3/9	1	2	FACETS	0.718	0.585	0.868	0.718	0.585	0.868	SUBCLONAL	1	TRUE	1	0.224226246157144	2		332	410	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881389	111881389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	31	307	0	ENST00000393256.3:c.67G>A	p.Glu23Lys	p.E23K	ENST00000393256	NM_006538.4	23	Gag/Aag	2/4	1	2	FACETS	0.654	0.528	0.796	0.654	0.528	0.796	SUBCLONAL	1	TRUE	1	0.224226246157144	2		307	423	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416698	29416698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56181542	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	29	391	0	ENST00000389048.3:c.4255G>A	p.Glu1419Lys	p.E1419K	ENST00000389048	NM_004304.4	1419	Gag/Aag	29/29	1	2	FACETS	0.553	0.443	0.678	0.553	0.443	0.678	SUBCLONAL	1	TRUE	1	0.224226246157144	2		391	468	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718148	117718148	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs747794595	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	47	330	0	ENST00000368508.3:c.709C>T	p.Gln237Ter	p.Q237*	ENST00000368508	NM_002944.2	237	Caa/Taa	7/43	0.143016912512539	3	FACETS	1	0.915	1	0.563	0.476	0.659	CLONAL	1	TRUE	1	0.224226246157144	3		330	414	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448200	49448200	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	41	351	0	ENST00000301067.7:c.401-1G>A		p.X134_splice	ENST00000301067	NM_003482.3	134			1	2	FACETS	0.763	0.636	0.905	0.763	0.636	0.905	CLONAL	1	TRUE	1	0.224226246157144	2		351	479	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141567331	141567331	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	36	325	0	ENST00000220592.5:c.883C>T	p.Pro295Ser	p.P295S	ENST00000220592	NM_012154.3	295	Ccg/Tcg	8/19	1	2	FACETS	0.787	0.647	0.943	0.787	0.647	0.943	CLONAL	1	TRUE	1	0.224226246157144	2		325	408	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265824	16265824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	26	350	0	ENST00000375759.3:c.10897G>A	p.Glu3633Lys	p.E3633K	ENST00000375759	NM_015001.2	3633	Gag/Aag	15/15	1	2	FACETS	0.456	0.36	0.566	0.456	0.36	0.566	SUBCLONAL	1	TRUE	1	0.224226246157144	2		350	509	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636191	87636191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	29	319	0	ENST00000277120.3:c.2356C>T	p.Arg786Ter	p.R786*	ENST00000277120		786	Cga/Tga	19/19	0.143016912512539	3	FACETS	0.675	0.541	0.828	0.338	0.27	0.414	SUBCLONAL	1	TRUE	1	0.224226246157144	3		319	426	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574020	46574020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376889179	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	39	299	0	ENST00000263734.3:c.35C>T	p.Ser12Leu	p.S12L	ENST00000263734	NM_001430.4	12	tCg/tTg	2/16	1	2	FACETS	0.8	0.663	0.952	0.8	0.663	0.952	CLONAL	1	TRUE	1	0.224226246157144	2		299	435	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637739	176637739	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201327209	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	39	413	0	ENST00000439151.2:c.2339C>T	p.Ser780Leu	p.S780L	ENST00000439151	NM_022455.4	780	tCg/tTg	5/23	1	2	FACETS	0.601	0.497	0.717	0.601	0.497	0.717	SUBCLONAL	1	TRUE	1	0.224226246157144	2		413	579	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876527	35876527	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	41	347	0	ENST00000303115.3:c.1319C>T	p.Ser440Phe	p.S440F	ENST00000303115	NM_002185.3	440	tCc/tTc	8/8	1	2	FACETS	0.726	0.604	0.861	0.726	0.604	0.861	SUBCLONAL	1	TRUE	1	0.224226246157144	2		347	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	37	493	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	1	2	FACETS	0.598	0.492	0.717	0.598	0.492	0.717	SUBCLONAL	1	TRUE	1	0.224226246157144	2		493	552	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038190	30038190	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	35	296	0	ENST00000338641.4:c.364-1G>A		p.X122_splice	ENST00000338641	NM_000268.3	122			1	2	FACETS	0.731	0.599	0.879	0.731	0.599	0.879	SUBCLONAL	1	TRUE	1	0.224226246157144	2		296	427	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974679	21974680	+	stop_gained,splice_region_variant	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	89	360	0	ENST00000304494.5:c.147_148delinsTT	p.Gln50Ter	p.Q50*	ENST00000304494	NM_000077.4	49	atCCag/atTTag	1/3	0.196146214276764	2	FACETS	0.869	0.774	0.969	0.869	0.774	0.969	CLONAL	2	TRUE	0	0.224226246157144	2		360	457	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867276	45867276	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343419778	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	33	331	1	ENST00000391945.4:c.917C>T	p.Ala306Val	p.A306V	ENST00000391945	NM_000400.3	306	gCc/gTc	10/23	1	2	FACETS	0.699	0.569	0.845	0.699	0.569	0.845	SUBCLONAL	1	TRUE	1	0.224226246157144	2		332	421	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781308	3781308	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	62	393	1	ENST00000262367.5:c.5057G>A	p.Trp1686Ter	p.W1686*	ENST00000262367	NM_004380.2	1686	tGg/tAg	30/31	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.224226246157144	2		394	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578493	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	46	393	0	ENST00000269305.4:c.437_438delinsAA	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tGG/tAA	5/11	1	2	FACETS	0.706	0.594	0.83	0.706	0.594	0.83	SUBCLONAL	1	TRUE	1	0.224226246157144	2		393	581	SUCCESS
APC	324	MSKCC	GRCh37	5	112175372	112175373	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	35	322	1	ENST00000257430.4:c.4081_4082delinsTT	p.Pro1361Phe	p.P1361F	ENST00000257430	NM_000038.5	1361	CCc/TTc	16/16	1	2	FACETS	0.695	0.57	0.836	0.695	0.57	0.836	SUBCLONAL	1	TRUE	1	0.224226246157144	2		323	449	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613073	52613073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	29	335	0	ENST00000394830.3:c.3455G>A	p.Gly1152Asp	p.G1152D	ENST00000394830	NM_018313.4	1152	gGc/gAc	22/30	1	2	FACETS	0.533	0.427	0.654	0.533	0.427	0.654	SUBCLONAL	1	TRUE	1	0.224226246157144	2		335	485	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777109	9777110	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	36	393	0	ENST00000377346.4:c.873_874delinsTT	p.Pro292Ser	p.P292S	ENST00000377346	NM_005026.3	291	aaCCct/aaTTct	7/24	1	2	FACETS	0.742	0.61	0.889	0.742	0.61	0.889	SUBCLONAL	1	TRUE	1	0.224226246157144	2		393	433	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300483	11300484	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	39	364	0	ENST00000361445.4:c.1662_1663delinsTT	p.Pro555Ser	p.P555S	ENST00000361445	NM_004958.3	554	caCCca/caTTca	11/58	1	2	FACETS	0.703	0.582	0.837	0.703	0.582	0.837	SUBCLONAL	1	TRUE	1	0.224226246157144	2		364	495	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797712	45797712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	34	404	0	ENST00000450313.1:c.980C>T	p.Pro327Leu	p.P327L	ENST00000450313	NM_012222.2	327	cCt/cTt	11/16	1	2	FACETS	0.532	0.434	0.643	0.532	0.434	0.643	SUBCLONAL	1	TRUE	1	0.224226246157144	2		404	570	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506296	120506296	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	36	356	0	ENST00000256646.2:c.1816G>A	p.Asp606Asn	p.D606N	ENST00000256646	NM_024408.3	606	Gac/Aac	11/34	1	2	FACETS	0.682	0.56	0.818	0.682	0.56	0.818	SUBCLONAL	1	TRUE	1	0.224226246157144	2		356	471	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828078	243828078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749228367	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	14	207	0	ENST00000263826.5:c.280G>A	p.Glu94Lys	p.E94K	ENST00000263826	NM_005465.4	94	Gaa/Aaa	3/13	1	2	FACETS	0.603	0.437	0.804	0.603	0.437	0.804	SUBCLONAL	1	TRUE	1	0.224226246157144	2		207	207	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333659	70333660	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	34	366	0	ENST00000373644.4:c.1564_1565delinsAA	p.Gly522Lys	p.G522K	ENST00000373644	NM_030625.2	522	GGa/AAa	2/12	1	2	FACETS	0.641	0.523	0.774	0.641	0.523	0.774	SUBCLONAL	1	TRUE	1	0.224226246157144	2		366	473	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324049	123324049	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759550441	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	28	242	0	ENST00000358487.5:c.421G>A	p.Glu141Lys	p.E141K	ENST00000358487	NM_000141.4	141	Gaa/Aaa	4/18	1	2	FACETS	0.611	0.488	0.751	0.611	0.488	0.751	SUBCLONAL	1	TRUE	1	0.224226246157144	2		242	409	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352628	118352629	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	35	391	2	ENST00000534358.1:c.3833_3834delinsTT	p.Ala1278Val	p.A1278V	ENST00000534358	NM_005933.3	1278	gCC/gTT	7/36	1	2	FACETS	0.66	0.541	0.794	0.66	0.541	0.794	SUBCLONAL	1	TRUE	1	0.224226246157144	2		393	473	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21643302	21643302	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	13	218	0	ENST00000421138.2:c.225G>A	p.Trp75Ter	p.W75*	ENST00000421138		75	tgG/tgA	5/16	1	2	FACETS	0.487	0.347	0.658	0.487	0.347	0.658	SUBCLONAL	1	TRUE	1	0.224226246157144	2		218	238	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944926	31944926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768639345	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	26	185	0	ENST00000340398.3:c.175G>A	p.Glu59Lys	p.E59K	ENST00000340398	NM_001013699.2	59	Gag/Aag	1/1	1	2	FACETS	0.797	0.632	0.985	0.797	0.632	0.985	CLONAL	1	TRUE	1	0.224226246157144	2		185	291	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945069	31945069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371692293	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	61	396	0	ENST00000340398.3:c.32C>T	p.Ser11Phe	p.S11F	ENST00000340398	NM_001013699.2	11	tCc/tTc	1/1	1	2	FACETS	0.879	0.758	1	0.879	0.758	1	CLONAL	1	TRUE	1	0.224226246157144	2		396	619	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243373	46243373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	20	316	0	ENST00000334344.6:c.1726C>T	p.Pro576Ser	p.P576S	ENST00000334344	NM_152641.2	576	Cca/Tca	14/21	1	2	FACETS	0.522	0.398	0.666	0.522	0.398	0.666	SUBCLONAL	1	TRUE	1	0.224226246157144	2		316	342	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426363	49426363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	49	390	0	ENST00000301067.7:c.12125C>T	p.Ser4042Phe	p.S4042F	ENST00000301067	NM_003482.3	4042	tCt/tTt	39/54	1	2	FACETS	0.92	0.78	1	0.92	0.78	1	CLONAL	1	TRUE	1	0.224226246157144	2		390	475	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416794	121416794	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs923368594	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	33	328	0	ENST00000257555.6:c.223G>A	p.Asp75Asn	p.D75N	ENST00000257555		75	Gac/Aac	1/10	1	2	FACETS	0.644	0.524	0.779	0.644	0.524	0.779	SUBCLONAL	1	TRUE	1	0.224226246157144	2		328	457	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919596	28919597	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	28	259	0	ENST00000282397.4:c.2340_2341delinsTT	p.Arg781Ter	p.R781*	ENST00000282397	NM_002019.4	780	atCCga/atTTga	16/30	1	2	FACETS	0.635	0.508	0.781	0.635	0.508	0.781	SUBCLONAL	1	TRUE	1	0.224226246157144	2		259	393	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43767799	43767799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	28	361	0	ENST00000382044.4:c.1049C>T	p.Ser350Phe	p.S350F	ENST00000382044	NM_001141980.1	350	tCt/tTt	9/28	1	2	FACETS	0.465	0.371	0.573	0.465	0.371	0.573	SUBCLONAL	1	TRUE	1	0.224226246157144	2		361	537	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73992036	73992036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	26	337	0	ENST00000318443.5:c.56G>A	p.Gly19Glu	p.G19E	ENST00000318443	NM_001024736.1	19	gGa/gAa	2/10	1	2	FACETS	0.575	0.455	0.713	0.575	0.455	0.713	SUBCLONAL	1	TRUE	1	0.224226246157144	2		337	403	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645898	67645898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	56	290	0	ENST00000264010.4:c.826C>T	p.Pro276Ser	p.P276S	ENST00000264010	NM_006565.3	276	Cca/Tca	4/12	1	2	FACETS	0.913	0.783	1	0.913	0.783	1	CLONAL	1	TRUE	1	0.224226246157144	2		290	547	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660554	67660554	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	42	303	0	ENST00000264010.4:c.1454A>T	p.His485Leu	p.H485L	ENST00000264010	NM_006565.3	485	cAt/cTt	8/12	1	2	FACETS	0.729	0.608	0.863	0.729	0.608	0.863	SUBCLONAL	1	TRUE	1	0.224226246157144	2		303	514	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660556	67660556	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555535739	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	45	304	0	ENST00000264010.4:c.1456C>T	p.Gln486Ter	p.Q486*	ENST00000264010	NM_006565.3	486	Cag/Tag	8/12	1	2	FACETS	0.796	0.669	0.937	0.796	0.669	0.937	CLONAL	1	TRUE	1	0.224226246157144	2		304	504	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350753	89350754	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	33	330	0	ENST00000301030.4:c.2196_2197delinsTT	p.Arg733Ter	p.R733*	ENST00000301030	NM_001256183.1	732	ttCCga/ttTTga	9/13	1	2	FACETS	0.706	0.575	0.854	0.706	0.575	0.854	SUBCLONAL	1	TRUE	1	0.224226246157144	2		330	417	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857846	89857846	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1242781028	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	59	364	0	ENST00000389301.3:c.1324C>T	p.Pro442Ser	p.P442S	ENST00000389301	NM_000135.2	442	Ccc/Tcc	14/43	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.224226246157144	2		364	460	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984000	7984000	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	32	368	0	ENST00000319144.4:c.626C>T	p.Ser209Phe	p.S209F	ENST00000319144	NM_001139.2	209	tCc/tTc	5/15	1	2	FACETS	0.653	0.53	0.793	0.653	0.53	0.793	SUBCLONAL	1	TRUE	1	0.224226246157144	2		368	437	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33681069	33681069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1234810749	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	24	258	0	ENST00000308377.4:c.1208G>A	p.Gly403Glu	p.G403E	ENST00000308377	NM_152270.3	403	gGa/gAa	4/5	1	2	FACETS	0.723	0.568	0.902	0.723	0.568	0.902	CLONAL	1	TRUE	1	0.224226246157144	2		258	296	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234504	41234504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	24	316	0	ENST00000357654.3:c.4274C>T	p.Pro1425Leu	p.P1425L	ENST00000357654	NM_007294.3	1425	cCt/cTt	12/23	1	2	FACETS	0.458	0.358	0.574	0.458	0.358	0.574	SUBCLONAL	1	TRUE	1	0.224226246157144	2		316	467	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885956	59885957	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	38	369	0	ENST00000259008.2:c.789_790delinsTT	p.Arg264Trp	p.R264W	ENST00000259008	NM_032043.2	263	ctCCgg/ctTTgg	7/20	1	2	FACETS	0.663	0.548	0.793	0.663	0.548	0.793	SUBCLONAL	1	TRUE	1	0.224226246157144	2		369	511	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220442	1220443	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	35	305	2	ENST00000326873.7:c.535_536delinsTT	p.Pro179Leu	p.P179L	ENST00000326873	NM_000455.4	179	CCg/TTg	4/10	1	2	FACETS	0.673	0.551	0.81	0.673	0.551	0.81	SUBCLONAL	1	TRUE	1	0.224226246157144	2		307	464	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265137	5265138	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	31	406	0	ENST00000357368.4:c.449_450delinsAA	p.Arg150Gln	p.R150Q	ENST00000357368	NM_002850.3	150	cGG/cAA	5/38	1	2	FACETS	0.555	0.448	0.677	0.555	0.448	0.677	SUBCLONAL	1	TRUE	1	0.224226246157144	2		406	498	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425291	47425291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	45	394	0	ENST00000404338.3:c.3359G>A	p.Arg1120Gln	p.R1120Q	ENST00000404338	NM_004491.4	1120	cGg/cAg	1/6	1	2	FACETS	0.775	0.651	0.912	0.775	0.651	0.912	CLONAL	1	TRUE	1	0.224226246157144	2		394	518	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61713089	61713089	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	27	303	1	ENST00000401558.2:c.2322A>T	p.Glu774Asp	p.E774D	ENST00000401558	NM_003400.3	774	gaA/gaT	20/25	1	2	FACETS	0.619	0.492	0.764	0.619	0.492	0.764	SUBCLONAL	1	TRUE	1	0.224226246157144	2		304	389	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67637084	67637084	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	15	252	0	ENST00000272342.5:c.2695C>T	p.Gln899Ter	p.Q899*	ENST00000272342	NM_019002.3	899	Cag/Tag	6/6	1	2	FACETS	0.481	0.352	0.637	0.481	0.352	0.637	SUBCLONAL	1	TRUE	1	0.224226246157144	2		252	278	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919823	96919824	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	40	360	0	ENST00000258439.3:c.439_440delinsAT	p.Ser147Ile	p.S147I	ENST00000258439	NM_001193304.2	147	TCt/ATt	4/4	1	2	FACETS	0.715	0.594	0.85	0.715	0.594	0.85	SUBCLONAL	1	TRUE	1	0.224226246157144	2		360	499	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270159	198270159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	41	282	0	ENST00000335508.6:c.1277C>T	p.Thr426Ile	p.T426I	ENST00000335508	NM_012433.2	426	aCt/aTt	10/25	1	2	FACETS	0.894	0.746	1	0.894	0.746	1	CLONAL	1	TRUE	1	0.224226246157144	2		282	409	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660267	227660268	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	27	353	0	ENST00000305123.5:c.3187_3188delinsTT	p.Pro1063Leu	p.P1063L	ENST00000305123	NM_005544.2	1063	CCa/TTa	1/2	1	2	FACETS	0.578	0.459	0.713	0.578	0.459	0.713	SUBCLONAL	1	TRUE	1	0.224226246157144	2		353	417	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37637643	37637643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	39	387	0	ENST00000249071.6:c.91G>A	p.Glu31Lys	p.E31K	ENST00000249071	NM_002872.4	31	Gag/Aag	2/7	1	2	FACETS	0.735	0.609	0.876	0.735	0.609	0.876	SUBCLONAL	1	TRUE	1	0.224226246157144	2		387	473	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63968671	63968672	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	30	302	0	ENST00000398590.3:c.1069_1070delinsTT	p.Pro357Phe	p.P357F	ENST00000398590	NM_001177387.1	357	CCc/TTc	8/14	1	2	FACETS	0.546	0.439	0.668	0.546	0.439	0.668	SUBCLONAL	1	TRUE	1	0.224226246157144	2		302	490	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259571	89259572	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	27	338	0	ENST00000336596.2:c.715_716delinsTT	p.Pro239Phe	p.P239F	ENST00000336596	NM_005233.5	239	CCt/TTt	3/17	1	2	FACETS	0.565	0.449	0.698	0.565	0.449	0.698	SUBCLONAL	1	TRUE	1	0.224226246157144	2		338	426	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967249	134967249	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	43	377	0	ENST00000398015.3:c.2588A>T	p.Lys863Met	p.K863M	ENST00000398015	NM_004441.4	863	aAg/aTg	14/16	1	2	FACETS	0.687	0.575	0.813	0.687	0.575	0.813	SUBCLONAL	1	TRUE	1	0.224226246157144	2		377	558	SUCCESS
REST	5978	MSKCC	GRCh37	4	57797599	57797599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	33	407	0	ENST00000309042.7:c.2575G>A	p.Asp859Asn	p.D859N	ENST00000309042	NM_005612.4	859	Gat/Aat	4/4	1	2	FACETS	0.53	0.431	0.643	0.53	0.431	0.643	SUBCLONAL	1	TRUE	1	0.224226246157144	2		407	555	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99850107	99850107	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	43	334	0	ENST00000280892.6:c.17C>T	p.Ser6Phe	p.S6F	ENST00000280892	NM_001130678.1	6	tCc/tTc	1/7	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.224226246157144	2		334	345	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520728	176520728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370317404	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	31	259	0	ENST00000292408.4:c.1471C>T	p.Pro491Ser	p.P491S	ENST00000292408	NM_213647.1	491	Cct/Tct	11/18	1	2	FACETS	0.804	0.651	0.976	0.804	0.651	0.976	CLONAL	1	TRUE	1	0.224226246157144	2		259	344	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158756	26158757	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	36	267	0	ENST00000289316.2:c.359_360delinsTT	p.Thr120Ile	p.T120I	ENST00000289316	NM_138720.2	120	aCC/aTT	1/2	0.143016912512539	3	FACETS	1	0.844	1	0.513	0.422	0.614	CLONAL	1	TRUE	1	0.224226246157144	3		267	348	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32191695	32191696	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	33	392	0	ENST00000375023.3:c.10_11delinsTT	p.Pro4Phe	p.P4F	ENST00000375023	NM_004557.3	4	CCt/TTt	1/30	0.143016912512539	3	FACETS	0.596	0.485	0.723	0.298	0.242	0.362	SUBCLONAL	1	TRUE	1	0.224226246157144	3		392	549	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859347	151859347	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	39	377	0	ENST00000262189.6:c.11315C>A	p.Ser3772Ter	p.S3772*	ENST00000262189	NM_170606.2	3772	tCa/tAa	43/59	1	2	FACETS	0.661	0.548	0.788	0.661	0.548	0.788	SUBCLONAL	1	TRUE	1	0.224226246157144	2		377	526	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27172715	27172715	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	85	337	0	ENST00000380036.4:c.730C>T	p.Pro244Ser	p.P244S	ENST00000380036	NM_000459.3	244	Cct/Tct	5/23	0.196146214276764	2	FACETS	0.907	0.806	1	0.907	0.806	1	CLONAL	2	TRUE	0	0.224226246157144	2		337	418	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221884	98221884	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	52	314	0	ENST00000331920.6:c.2885G>A	p.Arg962Lys	p.R962K	ENST00000331920	NM_000264.3	962	aGa/aAa	17/24	0.143016912512539	3	FACETS	1	0.856	1	0.503	0.428	0.585	CLONAL	1	TRUE	1	0.224226246157144	3		314	513	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249690	110249690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	46	356	0	ENST00000374672.4:c.985G>A	p.Asp329Asn	p.D329N	ENST00000374672	NM_004235.4	329	Gac/Aac	3/5	0.143016912512539	3	FACETS	1	0.894	1	0.539	0.455	0.632	CLONAL	1	TRUE	1	0.224226246157144	3		356	423	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412344	139412344	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	85	346	0	ENST00000277541.6:c.1301G>T	p.Gly434Val	p.G434V	ENST00000277541	NM_017617.3	434	gGc/gTc	8/34	0.224226246157144	3	FACETS	0.862	0.765	0.966	0.862	0.765	0.966	CLONAL	2	TRUE	1	0.224226246157144	3		346	489	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653790	206653790	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058896-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	20	294	0	ENST00000367120.3:c.1341G>A	p.Met447Ile	p.M447I	ENST00000367120	NM_014002.3	447	atG/atA	13/22	1	2	FACETS	0.448	0.342	0.573	0.448	0.342	0.573	SUBCLONAL	1	TRUE	1	0.224226246157144	2		294	398	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0058897-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	90	190	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.353710010468259	2	FACETS	0.977	0.881	1	0.977	0.881	1	CLONAL	2	TRUE	0	0.359721379998958	2		190	256	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0058897-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	164	371	0	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	0.353710010468259	2	FACETS	0.98	0.908	1	0.98	0.908	1	CLONAL	2	TRUE	0	0.359721379998958	2		371	465	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542048	187542048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058897-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	84	530	0	ENST00000441802.2:c.5692G>A	p.Val1898Ile	p.V1898I	ENST00000441802	NM_005245.3	1898	Gtc/Atc	10/27	0.170777387951367	5	FACETS	0.933	0.823	1	0.311	0.274	0.35	INDETERMINATE	1	TRUE	2	0.359721379998958	5		530	771	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0058898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	216	444	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	0.39674720493478	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.474038990697675	3		444	499	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0058898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	17	362	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.474038990697675	4	FACETS	0.251	0.187	0.328	0.084	0.062	0.11	SUBCLONAL	1	TRUE	1	0.474038990697675	4		362	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0058898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	162	430	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.474038990697675	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.474038990697675	2		430	315	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097721	27097721	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	185	359	0	ENST00000324856.7:c.3310G>T	p.Glu1104Ter	p.E1104*	ENST00000324856	NM_006015.4	1104	Gaa/Taa	12/20	NA	2	FACETS	0.887	0.828	0.946			1	INDETERMINATE	2	TRUE	NA	0.474038990697675	2		359	440	SUCCESS
APC	324	MSKCC	GRCh37	5	112174286	112174286	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs75239284	NA	P-0058898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	65	380	0	ENST00000257430.4:c.2995C>T	p.Gln999Ter	p.Q999*	ENST00000257430	NM_000038.5	999	Caa/Taa	16/16	0.39674720493478	3	FACETS	1	0.935	1	0.556	0.486	0.631	CLONAL	1	TRUE	1	0.474038990697675	3		380	305	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466933	18466933	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	54	250	0	ENST00000266497.5:c.1072G>C	p.Asp358His	p.D358H	ENST00000266497		358	Gat/Cat	5/31	0.474038990697675	4	FACETS	1	0.912	1	0.361	0.31	0.416	CLONAL	1	TRUE	1	0.474038990697675	4		250	310	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916948	178916948	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs863225460	NA	P-0058898-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	110	264	0	ENST00000263967.3:c.335T>A	p.Ile112Asn	p.I112N	ENST00000263967	NM_006218.2	112	aTc/aAc	2/21	0.474038990697675	3	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	1	0.474038990697675	3		264	276	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0058902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	9	273	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		273	149	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120467956	120467956	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	48	444	0	ENST00000256646.2:c.4483G>C	p.Glu1495Gln	p.E1495Q	ENST00000256646	NM_024408.3	1495	Gaa/Caa	25/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		444	805	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220581	1220647	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CACTGCACCCGTTCGCGGCGGACGACACCTGCCGGACCAGCCAGGGCTCCCCGGCTTTCCAGCCGCC	CACTGCACCCGTTCGCGGCGGACGACACCTGCCGGACCAGCCAGGGCTCCCCGGCTTTCCAGCCGCC	-	novel	NA	P-0058902-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	32	406	0	ENST00000326873.7:c.600_666del	p.Leu201ArgfsTer64	p.L201Rfs*64	ENST00000326873	NM_000455.4	200	gCACTGCACCCGTTCGCGGCGGACGACACCTGCCGGACCAGCCAGGGCTCCCCGGCTTTCCAGCCGCCc/gc	5/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		406	327	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0058903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	121	409	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		409	402	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0058903-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	255	425	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		425	633	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916929	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519931	NA	P-0058904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	248	298	0	ENST00000263967.3:c.316G>C	p.Gly106Arg	p.G106R	ENST00000263967	NM_006218.2	106	Ggc/Cgc	2/21	0.64507299636377	3	FACETS	0.903	0.852	0.954	0.903	0.852	0.954	CLONAL	2	TRUE	1	0.656026703334338	3		298	556	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	131	302	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.656026703334338	2		302	388	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0058904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	104	165	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	0.64507299636377	3	FACETS	0.911	0.833	0.99	0.911	0.833	0.99	CLONAL	2	TRUE	1	0.656026703334338	3		165	231	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0058904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	80	109	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.656026703334338	2	FACETS	0.808	0.734	0.881	0.808	0.734	0.881	CLONAL	2	TRUE	0	0.656026703334338	2		109	151	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866393	37866393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	327	330	0	ENST00000269571.5:c.698C>T	p.Thr233Ile	p.T233I	ENST00000269571		233	aCt/aTt	6/27	0.656026703334338	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.656026703334338	3		330	657	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247367	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747241612	NA	P-0058904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	166	390	0	ENST00000281708.4:c.1435C>G	p.Arg479Gly	p.R479G	ENST00000281708	NM_033632.3	479	Cga/Gga	10/12	1	2	FACETS	0.794	0.733	0.858	0.794	0.733	0.858	SUBCLONAL	1	TRUE	1	0.656026703334338	2		390	637	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967270	134967270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374549505	NA	P-0058904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	256	562	0	ENST00000398015.3:c.2609G>A	p.Arg870Gln	p.R870Q	ENST00000398015	NM_004441.4	870	cGg/cAg	14/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.656026703334338	2		562	710	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456597	32456597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	74	239	0	ENST00000332351.3:c.295G>A	p.Ala99Thr	p.A99T	ENST00000332351	NM_024426.4	99	Gcg/Acg	1/10	1	2	FACETS	0.82	0.726	0.919	0.82	0.726	0.919	CLONAL	1	TRUE	1	0.656026703334338	2		239	275	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402602	20402613	+	inframe_deletion	In_Frame_Del	DEL	GCCGCCGCCGCT	GCCGCCGCCGCT	-	rs759216279	NA	P-0058904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	151	420	0	ENST00000346618.3:c.148_159del	p.Ala50_Ala53del	p.A50_A53del	ENST00000346618	NM_001949.4	47	GCCGCCGCCGCT/-	1/7	1	2	FACETS	0.649	0.595	0.706	0.649	0.595	0.706	SUBCLONAL	1	TRUE	1	0.656026703334338	2		420	709	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397550	116397550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058904-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	124	322	0	ENST00000397752.3:c.1922C>T	p.Ser641Leu	p.S641L	ENST00000397752	NM_000245.2	641	tCa/tTa	7/21	1	2	FACETS	0.992	0.907	1	0.992	0.907	1	CLONAL	1	TRUE	1	0.656026703334338	2		322	381	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0058905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	28	206	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.349845214436499	1	FACETS	0.667	0.539	0.81	0.667	0.539	0.81	SUBCLONAL	1	TRUE	0	0.401722661516285	1		206	167	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535395	66535395	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	91	336	0	ENST00000273854.3:c.66del	p.Ile23SerfsTer39	p.I23Sfs*39	ENST00000273854	NM_004439.5	22	ccC/cc	1/18	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.401722661516285	2		336	447	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152267	99152267	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	42	294	0	ENST00000074304.5:c.346A>C	p.Lys116Gln	p.K116Q	ENST00000074304	NM_001134224.1	116	Aaa/Caa	6/26	1	2	FACETS	0.786	0.661	0.923	0.786	0.661	0.923	CLONAL	1	TRUE	1	0.401722661516285	2		294	266	SUCCESS
APC	324	MSKCC	GRCh37	5	112174777	112174777	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0058905-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	52	417	0	ENST00000257430.4:c.3486T>G	p.Tyr1162Ter	p.Y1162*	ENST00000257430	NM_000038.5	1162	taT/taG	16/16	1	2	FACETS	0.832	0.713	0.962	0.832	0.713	0.962	CLONAL	1	TRUE	1	0.401722661516285	2		417	311	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0058906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	107	425	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.477701940637439	2		425	427	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484315	120484315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	178	437	0	ENST00000256646.2:c.2815C>T	p.Pro939Ser	p.P939S	ENST00000256646	NM_024408.3	939	Ccg/Tcg	18/34	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.477701940637439	2		437	740	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615568	100615568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	156	380	0	ENST00000308731.7:c.764G>A	p.Arg255Gln	p.R255Q	ENST00000308731	NM_000061.2	255	cGa/cAa	8/19	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.477701940637439	2		380	568	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582099	189582099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754080925	NA	P-0058906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	199	465	0	ENST00000264731.3:c.658C>T	p.Pro220Ser	p.P220S	ENST00000264731	NM_003722.4	220	Cct/Tct	5/14	0.169005806130704	3	FACETS	1	0.99	1	0.702	0.652	0.753	INDETERMINATE	1	TRUE	1	0.477701940637439	3		465	735	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230472852	230472852	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1163686095	NA	P-0058906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	129	365	0	ENST00000391860.1:c.730+2T>C		p.X244_splice	ENST00000391860	NM_001258311.1	244			1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.477701940637439	2		365	530	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77070037	77070037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	172	408	0	ENST00000356341.3:c.503C>T	p.Pro168Leu	p.P168L	ENST00000356341	NM_002576.4	168	cCt/cTt	6/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.477701940637439	2		408	663	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437534	56437534	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	125	378	0	ENST00000407977.2:c.928C>T	p.Pro310Ser	p.P310S	ENST00000407977		310	Ccc/Tcc	8/10	1	2	FACETS	0.845	0.767	0.927	0.845	0.767	0.927	CLONAL	1	TRUE	1	0.477701940637439	2		378	619	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339057	225339057	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058906-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	95	329	0	ENST00000264414.4:c.2212C>T	p.Pro738Ser	p.P738S	ENST00000264414	NM_003590.4	738	Cca/Tca	16/16	1	2	FACETS	0.925	0.828	1	0.925	0.828	1	CLONAL	1	TRUE	1	0.477701940637439	2		329	430	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0058907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	44	424	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	1	2	FACETS	0.943	0.79	1	0.943	0.79	1	CLONAL	1	TRUE	1	0.167472430162782	2		424	557	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129128	64129128	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058907-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	57	356	0	ENST00000334205.4:c.666G>A	p.Trp222Ter	p.W222*	ENST00000334205	NM_003942.2	222	tgG/tgA	7/17	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.167472430162782	2		356	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs730881999	NA	P-0058908-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	43	425	0	ENST00000269305.4:c.380C>G	p.Ser127Cys	p.S127C	ENST00000269305	NM_001126112.2	127	tCc/tGc	5/11	1	2	FACETS	0.793	0.665	0.935	0.793	0.665	0.935	CLONAL	1	TRUE	1	0.258786298682776	2		425	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0058909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	120	804	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.194574690160771	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.194574690160771	3		804	585	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	72	302	0				ENST00000310581	NM_198253.2	-/1132			0.184906722349842	3	FACETS	0.955	0.838	1	0.955	0.838	1	CLONAL	2	TRUE	1	0.194574690160771	3		302	425	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0058909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	81	425	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.184906722349842	3	FACETS	0.932	0.824	1	0.932	0.824	1	CLONAL	2	TRUE	1	0.194574690160771	3		425	490	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527869	157527869	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058909-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	54	464	0	ENST00000346085.5:c.5594C>G	p.Ser1865Cys	p.S1865C	ENST00000346085	NM_020732.3	1865	tCt/tGt	20/20	1	2	FACETS	0.738	0.629	0.858	0.738	0.629	0.858	SUBCLONAL	1	TRUE	1	0.194574690160771	2		464	752	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541468	29541468	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs1131691131	NA	P-0058942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	34	83	0	ENST00000356175.3:c.1393-1G>C		p.X465_splice	ENST00000356175	NM_000267.3	465			0.737331826901145	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.737331826901145	2		83	39	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519029	66519029	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	292	349	0	ENST00000358598.2:c.310G>T	p.Val104Phe	p.V104F	ENST00000358598	NM_212471.2	104	Gtc/Ttc	3/11	0.737331826901145	2	FACETS	0.978	0.941	1	0.978	0.941	1	CLONAL	2	TRUE	0	0.737331826901145	2		349	405	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143129637	143129637	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058942-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	22	188	0	ENST00000262992.4:c.1013A>T	p.Glu338Val	p.E338V	ENST00000262992	NM_001101669.1	338	gAa/gTa	12/24	0.681187917124516	4	FACETS	0.381	0.296	0.48	0.191	0.148	0.24	SUBCLONAL	1	TRUE	2	0.737331826901145	4		188	272	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618611	37618626	+	frameshift_variant	Frame_Shift_Del	DEL	ACGACGAACGTCGTGG	ACGACGAACGTCGTGG	-	novel	NA	P-0058943-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	190	477	0	ENST00000447079.4:c.288_303del	p.Asp97GlnfsTer22	p.D97Qfs*22	ENST00000447079	NM_015083.1	96	aACGACGAACGTCGTGGa/aa	1/14	1	2	FACETS	0.969	0.9	1	0.969	0.9	1	CLONAL	1	TRUE	1	0.631615979920538	2		477	621	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649040	37649041	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0058943-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	77	238	0	ENST00000447079.4:c.2146_2147del	p.Glu716LysfsTer12	p.E716Kfs*12	ENST00000447079	NM_015083.1	715	acAGaa/acaa	4/14	1	2	FACETS	0.787	0.697	0.881	0.787	0.697	0.881	SUBCLONAL	1	TRUE	1	0.631615979920538	2		238	310	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359899	87359899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780831721	NA	P-0058943-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	241	302	0	ENST00000277120.3:c.1207G>A	p.Ala403Thr	p.A403T	ENST00000277120		403	Gca/Aca	11/19	0.529962397209274	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.631615979920538	3		302	496	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0058944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	123	261	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	0.662649562112949	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.662649562112949	1		261	241	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651369	52651369	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	121	344	0	ENST00000394830.3:c.1727G>C	p.Arg576Pro	p.R576P	ENST00000394830	NM_018313.4	576	cGc/cCc	15/30	0.662649562112949	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.662649562112949	1		344	243	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553378	41553378	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058944-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	142	331	0	ENST00000263253.7:c.3467T>C	p.Val1156Ala	p.V1156A	ENST00000263253	NM_001429.3	1156	gTg/gCg	18/31	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.662649562112949	2		331	415	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0058945-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	150	696	3	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.711687681742645	1	FACETS	0.966	0.902	1	0.966	0.902	1	CLONAL	1	FALSE	0	0.711687681742645	1		699	281	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0058945-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	40	199	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	1	2	FACETS	0.809	0.685	0.94	0.809	0.685	0.94	CLONAL	1	FALSE	1	0.711687681742645	2		199	139	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720726	89720726	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs878853944	NA	P-0058945-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	14	65	0	ENST00000371953.3:c.877G>T	p.Gly293Ter	p.G293*	ENST00000371953	NM_000314.4	293	Gga/Tga	8/9	0.711687681742645	1	FACETS	0.792	0.61	0.981	0.792	0.61	0.981	CLONAL	1	FALSE	0	0.711687681742645	1		65	32	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101118	41101118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751886972	NA	P-0058945-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	171	471	2	ENST00000373198.4:c.1238C>T	p.Ala413Val	p.A413V	ENST00000373198	NM_133170.3	413	gCg/gTg	8/32	0.711687681742645	3	FACETS	0.987	0.912	1	0.494	0.455	0.533	CLONAL	1	FALSE	1	0.711687681742645	3		473	660	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058999	42058999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755132381	NA	P-0058945-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	164	412	0	ENST00000219905.7:c.8719G>A	p.Asp2907Asn	p.D2907N	ENST00000219905	NM_001164273.1	2907	Gat/Aat	24/24	0.711687681742645	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	FALSE	0	0.711687681742645	1		412	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912654	NA	P-0058945-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	205	451	0	ENST00000269305.4:c.469G>A	p.Val157Ile	p.V157I	ENST00000269305	NM_001126112.2	157	Gtc/Atc	5/11	0.711687681742645	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	0	0.711687681742645	1		451	349	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293686	1293686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058945-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	40	576	0	ENST00000310581.5:c.1315G>A	p.Glu439Lys	p.E439K	ENST00000310581	NM_198253.2	439	Gag/Aag	2/16	1	2	FACETS	0.223	0.185	0.266	0.223	0.185	0.266	SUBCLONAL	1	FALSE	1	0.711687681742645	2		576	504	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0058945-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	77	275	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	1	2	FACETS	0.909	0.81	1	0.909	0.81	1	CLONAL	1	FALSE	1	0.711687681742645	2		275	238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578227	7578227	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058945-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	49	476	0	ENST00000269305.4:c.622G>T	p.Asp208Tyr	p.D208Y	ENST00000269305	NM_001126112.2	208	Gac/Tac	6/11	0.711687681742645	1	FACETS	0.278	0.236	0.323	0.278	0.236	0.323	SUBCLONAL	1	FALSE	0	0.711687681742645	1		476	319	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921536	178921537	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTGCAACCTACGTGAATGTAAATATTC	novel	NA	P-0058945-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	42	283	0	ENST00000263967.3:c.1020_1046dup	p.Ala341_Arg349dup	p.A341_R349dup	ENST00000263967	NM_006218.2	341	tgt/tGTGCAACCTACGTGAATGTAAATATTCgt	5/21	1	2	FACETS	0.544	0.458	0.637	0.544	0.458	0.637	SUBCLONAL	1	FALSE	1	0.711687681742645	2		283	217	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058946-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	200	302	0				ENST00000310581	NM_198253.2	-/1132			0.364381411945668	8	FACETS	1	0.971	1	0.882	0.828	0.937	CLONAL	5	TRUE	2	0.364381411945668	8		302	434	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058946-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	145	341	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	0.364381411945668	4	FACETS	0.954	0.875	1	0.636	0.583	0.691	CLONAL	2	TRUE	1	0.364381411945668	4		341	569	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440378	52440378	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058946-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	81	418	0	ENST00000460680.1:c.674A>T	p.Asp225Val	p.D225V	ENST00000460680	NM_004656.3	225	gAc/gTc	9/17	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.364381411945668	2		418	441	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562727	176562727	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058946-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	177	410	0	ENST00000439151.2:c.623G>T	p.Gly208Val	p.G208V	ENST00000439151	NM_022455.4	208	gGa/gTa	2/23	0.133375301593191	3	FACETS	0.954	0.884	1	0.636	0.589	0.684	INDETERMINATE	2	TRUE	0	0.364381411945668	3		410	602	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94129014	94129014	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058946-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	71	288	0	ENST00000369303.4:c.46A>G	p.Ile16Val	p.I16V	ENST00000369303	NM_004440.3	16	Atc/Gtc	1/17	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.364381411945668	2		288	348	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997874	149997874	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0058946-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	74	307	0	ENST00000253339.5:c.2594-1G>A		p.X865_splice	ENST00000253339		865			1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.364381411945668	2		307	354	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860601	151860601	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058946-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	129	460	0	ENST00000262189.6:c.10061del	p.Pro3354GlnfsTer7	p.P3354Qfs*7	ENST00000262189	NM_170606.2	3354	cCa/ca	43/59	0.334520678979213	3	FACETS	1	0.984	1	0.705	0.641	0.771	CLONAL	1	TRUE	1	0.364381411945668	3		460	594	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786879	135786880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs118203478	NA	P-0058946-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	150	285	0	ENST00000298552.3:c.989dup	p.Ser331GlufsTer10	p.S331Efs*10	ENST00000298552	NM_001162426.1	330	ctg/ctTg	10/23	0.34540938682266	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	0	0.364381411945668	2		285	404	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	139	302	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.967	0.894	1	0.967	0.894	1	CLONAL	1	TRUE	1	0.868341594105678	2		302	331	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0058947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	212	374	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.868341594105678	2		374	471	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0058947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	273	255	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.936	0.884	0.988	0.936	0.884	0.988	CLONAL	1	TRUE	1	0.868341594105678	2		255	672	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740665	58740665	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	256	419	0	ENST00000305921.3:c.1570C>T	p.Gln524Ter	p.Q524*	ENST00000305921	NM_003620.3	524	Caa/Taa	6/6	1	2	FACETS	0.942	0.888	0.996	0.942	0.888	0.996	CLONAL	1	TRUE	1	0.868341594105678	2		419	626	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97897676	97897676	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	179	279	0	ENST00000289081.3:c.795G>C	p.Glu265Asp	p.E265D	ENST00000289081	NM_000136.2	265	gaG/gaC	8/15	0.868341594105678	1	FACETS	0.929	0.884	0.973	0.929	0.884	0.973	CLONAL	1	TRUE	0	0.868341594105678	1		279	251	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348452	89348475	+	inframe_deletion	In_Frame_Del	DEL	GCTCGTCCCTGTGATGCCGCAGGA	GCTCGTCCCTGTGATGCCGCAGGA	-	rs534329317	NA	P-0058947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	200	441	0	ENST00000301030.4:c.4475_4498del	p.Leu1492_Glu1499del	p.L1492_E1499del	ENST00000301030	NM_001256183.1	1492	cTCCTGCGGCATCACAGGGACGAGCag/cag	9/13	1	2	FACETS	0.655	0.609	0.703	0.655	0.609	0.703	SUBCLONAL	1	TRUE	1	0.868341594105678	2		441	703	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855787	45855787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	275	444	0	ENST00000391945.4:c.2023G>T	p.Gly675Cys	p.G675C	ENST00000391945	NM_000400.3	675	Ggc/Tgc	21/23	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.868341594105678	2		444	562	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808029	1808029	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1490564667	NA	P-0058947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	693	592	0	ENST00000260795.2:c.2005C>G	p.Arg669Gly	p.R669G	ENST00000260795		669	Cga/Gga	14/17	0.410801906202859	4	FACETS	0.867	0.842	0.892			1	INDETERMINATE	3	TRUE	NA	0.868341594105678	4		592	1146	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871619	35871619	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201191831	NA	P-0058947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	196	290	0	ENST00000216797.5:c.887C>T	p.Thr296Met	p.T296M	ENST00000216797	NM_020529.2	296	aCg/aTg	5/6	1	2	FACETS	0.877	0.819	0.936	0.877	0.819	0.936	CLONAL	1	TRUE	1	0.868341594105678	2		290	515	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945723	17945723	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199774111	NA	P-0058947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	244	412	0	ENST00000458235.1:c.2137G>A	p.Ala713Thr	p.A713T	ENST00000458235	NM_000215.3	713	Gcc/Acc	16/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.868341594105678	2		412	538	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781606	9781606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	196	418	0	ENST00000377346.4:c.1916C>T	p.Ala639Val	p.A639V	ENST00000377346	NM_005026.3	639	gCc/gTc	15/24	1	2	FACETS	0.954	0.893	1	0.954	0.893	1	CLONAL	1	TRUE	1	0.868341594105678	2		418	473	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057692	27057714	+	frameshift_variant	Frame_Shift_Del	DEL	AGACTCCATATTACAACCAGCAA	AGACTCCATATTACAACCAGCAA	-	novel	NA	P-0058947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	321	432	0	ENST00000324856.7:c.1402_1424del	p.Thr468SerfsTer147	p.T468Sfs*147	ENST00000324856	NM_006015.4	467	cAGACTCCATATTACAACCAGCAA/c	3/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.868341594105678	2		432	736	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150923439	150923439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	203	342	1	ENST00000271640.5:c.2086G>A	p.Glu696Lys	p.E696K	ENST00000271640	NM_001145415.1	696	Gag/Aag	13/22	1	2	FACETS	0.986	0.925	1	0.986	0.925	1	CLONAL	1	TRUE	1	0.868341594105678	2		343	474	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724451	162724451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	235	372	0	ENST00000367921.3:c.223G>A	p.Glu75Lys	p.E75K	ENST00000367921	NM_006182.2	75	Gag/Aag	5/18	1	2	FACETS	0.958	0.902	1	0.958	0.902	1	CLONAL	1	TRUE	1	0.868341594105678	2		372	565	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924722	94924724	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0058947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	265	299	0	ENST00000536441.1:c.186_188del	p.Val63del	p.V63del	ENST00000536441	NM_144665.3	62	ctTGTg/ctg	3/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.868341594105678	2		299	559	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206618	108206618	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	228	281	0	ENST00000278616.4:c.8198A>C	p.Gln2733Pro	p.Q2733P	ENST00000278616	NM_000051.3	2733	cAg/cCg	56/63	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.868341594105678	2		281	496	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491695	56491695	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	245	327	0	ENST00000267101.3:c.2587G>C	p.Asp863His	p.D863H	ENST00000267101	NM_001982.3	863	Gat/Cat	21/28	0.868341594105678	3	FACETS	1	0.972	1	0.532	0.499	0.566	CLONAL	1	TRUE	1	0.868341594105678	3		327	761	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914749	32914767	+	frameshift_variant	Frame_Shift_Del	DEL	TCAGAACTGAGCATAGTCT	TCAGAACTGAGCATAGTCT	-	novel	NA	P-0058947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	136	232	0	ENST00000380152.3:c.6260_6278del	p.Arg2087ThrfsTer26	p.R2087Tfs*26	ENST00000380152		2086	aTCAGAACTGAGCATAGTCTt/at	11/27	1	2	FACETS	0.887	0.817	0.959	0.887	0.817	0.959	CLONAL	1	TRUE	1	0.868341594105678	2		232	353	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310152	91310152	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	116	135	0	ENST00000355112.3:c.2206T>C	p.Tyr736His	p.Y736H	ENST00000355112	NM_000057.2	736	Tat/Cat	10/22	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.868341594105678	2		135	243	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982457	10982457	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1379727163	NA	P-0058947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	181	264	0	ENST00000327064.4:c.79G>A	p.Ala27Thr	p.A27T	ENST00000327064	NM_199141.1	27	Gct/Act	1/16	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.868341594105678	2		264	417	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439812	220439812	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	238	488	0	ENST00000243786.2:c.665G>C	p.Arg222Thr	p.R222T	ENST00000243786	NM_002191.3	222	aGa/aCa	2/2	1	2	FACETS	0.934	0.879	0.99	0.934	0.879	0.99	CLONAL	1	TRUE	1	0.868341594105678	2		488	587	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182638	38182638	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1330095887	NA	P-0058947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	258	354	0	ENST00000396334.3:c.791G>A	p.Arg264Gln	p.R264Q	ENST00000396334	NM_002468.4	264	cGa/cAa	5/5	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.868341594105678	2		354	517	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436646	52436660	+	inframe_deletion	In_Frame_Del	DEL	GCAGATGAACTCATC	GCAGATGAACTCATC	-	novel	NA	P-0058947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	230	403	0	ENST00000460680.1:c.2014_2028del	p.Asp672_Cys676del	p.D672_C676del	ENST00000460680	NM_004656.3	672	GATGAGTTCATCTGC/-	16/17	0.868341594105678	1	FACETS	0.922	0.882	0.961	0.922	0.882	0.961	CLONAL	1	TRUE	0	0.868341594105678	1		403	325	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056823	180056823	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	202	422	0	ENST00000261937.6:c.689A>G	p.Tyr230Cys	p.Y230C	ENST00000261937	NM_182925.4	230	tAt/tGt	6/30	NA	2	FACETS	0.971	0.91	1			1	INDETERMINATE	1	TRUE	NA	0.868341594105678	2		422	479	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835922	151835934	+	frameshift_variant	Frame_Shift_Del	DEL	TTTTGTGTCCTCT	TTTTGTGTCCTCT	-	novel	NA	P-0058947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	192	317	0	ENST00000262189.6:c.14590_14602del	p.Arg4864LeufsTer37	p.R4864Lfs*37	ENST00000262189	NM_170606.2	4864	AGAGGACACAAAAtt/tt	58/59	1	2	FACETS	0.966	0.903	1	0.966	0.903	1	CLONAL	1	TRUE	1	0.868341594105678	2		317	458	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008922	152008922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058947-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	159	292	0	ENST00000262189.6:c.700C>T	p.Pro234Ser	p.P234S	ENST00000262189	NM_170606.2	234	Cca/Tca	5/59	1	2	FACETS	0.812	0.751	0.874	0.812	0.751	0.874	CLONAL	1	TRUE	1	0.868341594105678	2		292	451	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0058948-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	28	366	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.3	4	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	4		366	399	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0058948-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	12	410	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.078587257370625	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		410	463	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964041	28964041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058948-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	39	403	0	ENST00000282397.4:c.1861C>T	p.Leu621Phe	p.L621F	ENST00000282397	NM_002019.4	621	Ctt/Ttt	13/30	0.078587257370625	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		403	376	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0058949-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	20	374	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.672	0.513	0.859	0.672	0.513	0.859	SUBCLONAL	1	TRUE	1	0.16	2		374	372	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188078	11188078	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058950-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	174	410	0	ENST00000361445.4:c.6016G>T	p.Val2006Phe	p.V2006F	ENST00000361445	NM_004958.3	2006	Gtc/Ttc	43/58	0.412543012927695	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.412543012927695	3		410	469	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183788	10183788	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882034	NA	P-0058950-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	139	432	0	ENST00000256474.2:c.257C>G	p.Pro86Arg	p.P86R	ENST00000256474	NM_000551.3	86	cCc/cGc	1/3	0.412543012927695	3	FACETS	0.909	0.843	0.976	0.909	0.843	0.976	CLONAL	3	TRUE	0	0.412543012927695	3		432	298	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782191	56782199	+	inframe_deletion	In_Frame_Del	DEL	AGCAAGCTG	AGCAAGCTG	-	novel	NA	P-0058950-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	69	292	0	ENST00000308159.5:c.33_41del	p.Ala13_Gln15del	p.A13_Q15del	ENST00000308159	NM_014669.4	11	cAGCAAGCTGaa/caa	2/22	0.412543012927695	3	FACETS	1	0.94	1	0.562	0.492	0.636	CLONAL	1	TRUE	1	0.412543012927695	3		292	359	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357140	89357140	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058950-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	89	520	0	ENST00000301030.4:c.494A>G	p.Asn165Ser	p.N165S	ENST00000301030	NM_001256183.1	165	aAc/aGc	6/13	0.412543012927695	3	FACETS	1	0.9	1	0.506	0.45	0.566	CLONAL	1	TRUE	1	0.412543012927695	3		520	514	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47685246	47685246	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058950-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	83	219	0	ENST00000347630.2:c.704A>T	p.Glu235Val	p.E235V	ENST00000347630	NM_001007230.1	235	gAg/gTg	8/11	0.412543012927695	3	FACETS	1	0.919	1	1	0.919	1	CLONAL	2	TRUE	1	0.412543012927695	3		219	236	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441177	52441197	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCATGGTGCCTACCATGGTCA	TCATGGTGCCTACCATGGTCA	-	novel	NA	P-0058950-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	174	422	0	ENST00000460680.1:c.573_580+13del		p.X191_splice	ENST00000460680	NM_004656.3	191		7/17	0.412543012927695	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	3	TRUE	0	0.412543012927695	3		422	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587781702	NA	P-0058951-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	138	498	0	ENST00000269305.4:c.920-1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.358932112323107	2		498	740	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375450	15375450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781618267	NA	P-0058951-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	136	480	0	ENST00000263377.2:c.977G>A	p.Arg326Gln	p.R326Q	ENST00000263377	NM_058243.2	326	cGg/cAg	6/20	1	2	FACETS	0.983	0.895	1	0.983	0.895	1	CLONAL	1	TRUE	1	0.358932112323107	2		480	771	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124503612	124503612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554426986	NA	P-0058951-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	89	339	0	ENST00000357628.3:c.338C>T	p.Pro113Leu	p.P113L	ENST00000357628	NM_015450.2	113	cCt/cTt	8/19	0.358932112323107	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.358932112323107	1		339	368	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	151	302	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.866	0.8	0.934	0.866	0.8	0.934	CLONAL	1	TRUE	1	0.816633885787562	2		302	427	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0058952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	138	420	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.348866466746492	1	FACETS	0.415	0.38	0.451	0.415	0.38	0.451	INDETERMINATE	1	TRUE	0	0.816633885787562	1		420	482	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052632	42052632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779811318	NA	P-0058952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	201	462	0	ENST00000219905.7:c.7303C>T	p.Arg2435Trp	p.R2435W	ENST00000219905	NM_001164273.1	2435	Cgg/Tgg	20/24	1	2	FACETS	0.868	0.81	0.927	0.868	0.81	0.927	CLONAL	1	TRUE	1	0.816633885787562	2		462	567	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418406	139418406	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1348892740	NA	P-0058952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	278	451	0	ENST00000277541.6:c.166C>T	p.Arg56Ter	p.R56*	ENST00000277541	NM_017617.3	56	Cga/Tga	3/34	0.607978537830097	3	FACETS	1	0.965	1			1	CLONAL	1	TRUE	NA	0.816633885787562	3		451	926	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212365	36212365	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	314	643	1	ENST00000222270.7:c.2116C>T	p.Arg706Ter	p.R706*	ENST00000222270	NM_014727.1	706	Cga/Tga	3/37	1	2	FACETS	0.923	0.875	0.972	0.923	0.875	0.972	CLONAL	1	TRUE	1	0.816633885787562	2		644	833	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843231	128843231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs578002520	NA	P-0058952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	238	487	0	ENST00000249373.3:c.338G>A	p.Arg113Gln	p.R113Q	ENST00000249373	NM_005631.4	113	cGg/cAg	2/12	1	2	FACETS	0.919	0.864	0.976	0.919	0.864	0.976	CLONAL	1	TRUE	1	0.816633885787562	2		487	634	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727033	243727033	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	118	260	0	ENST00000263826.5:c.937C>G	p.Leu313Val	p.L313V	ENST00000263826	NM_005465.4	313	Ctg/Gtg	9/13	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.816633885787562	2		260	247	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433712	49433712	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	300	582	1	ENST00000301067.7:c.7841C>A	p.Ser2614Ter	p.S2614*	ENST00000301067	NM_003482.3	2614	tCg/tAg	31/54	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.816633885787562	2		583	725	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227833	36227833	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	231	565	0	ENST00000222270.7:c.7318G>T	p.Glu2440Ter	p.E2440*	ENST00000222270	NM_014727.1	2440	Gag/Tag	32/37	1	2	FACETS	0.92	0.864	0.977	0.92	0.864	0.977	CLONAL	1	TRUE	1	0.816633885787562	2		565	615	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121052	29121052	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876659653	NA	P-0058952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	64	179	1	ENST00000328354.6:c.505T>A	p.Phe169Ile	p.F169I	ENST00000328354	NM_007194.3	169	Ttt/Att	4/15	0.348866466746492	1	FACETS	0.828	0.747	0.907	0.828	0.747	0.907	INDETERMINATE	1	TRUE	0	0.816633885787562	1		180	112	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574665	41574665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149456776	NA	P-0058952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	196	653	0	ENST00000263253.7:c.6950G>A	p.Arg2317Gln	p.R2317Q	ENST00000263253	NM_001429.3	2317	cGg/cAg	31/31	0.348866466746492	1	FACETS	0.353	0.327	0.38	0.353	0.327	0.38	INDETERMINATE	1	TRUE	0	0.816633885787562	1		653	804	SUCCESS
ATR	545	MSKCC	GRCh37	3	142257390	142257390	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	82	283	0	ENST00000350721.4:c.3659T>C	p.Leu1220Ser	p.L1220S	ENST00000350721	NM_001184.3	1220	tTa/tCa	19/47	1	2	FACETS	0.961	0.864	1	0.961	0.864	1	CLONAL	1	TRUE	1	0.816633885787562	2		283	209	SUCCESS
ATR	545	MSKCC	GRCh37	3	142257397	142257397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	84	292	0	ENST00000350721.4:c.3652G>A	p.Ala1218Thr	p.A1218T	ENST00000350721	NM_001184.3	1218	Gct/Act	19/47	1	2	FACETS	0.994	0.896	1	0.994	0.896	1	CLONAL	1	TRUE	1	0.816633885787562	2		292	207	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295620	1295620	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0058952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	355	573	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.816633885787562	2		573	830	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118367034	118367050	+	frameshift_variant	Frame_Shift_Del	DEL	CAATAGACAGTGTGCGT	CAATAGACAGTGTGCGT	GTGCGA	novel	NA	P-0058952-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	120	293	0	ENST00000534358.1:c.5616_5632delinsGTGCGA	p.Asp1872GlufsTer9	p.D1872Efs*9	ENST00000534358	NM_005933.3	1872	gaCAATAGACAGTGTGCGTta/gaGTGCGAta	20/36	1	2	FACETS	0.957	0.877	1	0.957	0.877	1	CLONAL	1	TRUE	1	0.816633885787562	2		293	307	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105238746	105238746	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058954-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	88	416	0	ENST00000349310.3:c.1216C>G	p.Arg406Gly	p.R406G	ENST00000349310	NM_001014432.1	406	Cgc/Ggc	13/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.366138183647441	2		416	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577093	7577093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882008	NA	P-0058954-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	107	651	0	ENST00000269305.4:c.845G>A	p.Arg282Gln	p.R282Q	ENST00000269305	NM_001126112.2	282	cGg/cAg	8/11	0.366138183647441	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.366138183647441	1		651	376	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947088	178947088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1560148927	NA	P-0058954-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	76	248	0	ENST00000263967.3:c.2524G>A	p.Gly842Ser	p.G842S	ENST00000263967	NM_006218.2	842	Ggt/Agt	18/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.366138183647441	2		248	322	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	22	190	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.367860794705018	2	FACETS	0.522	0.406	0.655	0.261	0.203	0.328	SUBCLONAL	1	TRUE	0	0.407131088778871	2		190	207	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	10	157	1	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.334	0.227	0.468	0.334	0.227	0.468	SUBCLONAL	1	TRUE	1	0.407131088778871	2		158	147	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	65	374	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.407131088778871	2		374	291	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128419995	128419995	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1238730432	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	18	229	0	ENST00000265960.3:c.433C>T	p.Arg145Cys	p.R145C	ENST00000265960	NM_001006617.1	145	Cgc/Tgc	4/12	1	2	FACETS	0.318	0.239	0.411	0.318	0.239	0.411	SUBCLONAL	1	TRUE	1	0.407131088778871	2		229	278	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	56	341	1	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.89	0.768	1	0.89	0.768	1	CLONAL	1	TRUE	1	0.407131088778871	2		342	309	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	112	469	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.407131088778871	2		469	464	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	57	196	2	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.407131088778871	2		198	257	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	26	386	4	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	1	2	FACETS	0.292	0.231	0.363	0.292	0.231	0.363	SUBCLONAL	1	TRUE	1	0.407131088778871	2		390	437	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	84	277	3	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.407131088778871	2		280	377	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120031	70120031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	57	460	0	ENST00000245479.2:c.1037del	p.Pro346ArgfsTer37	p.P346Rfs*37	ENST00000245479	NM_000346.3	345	Ccc/cc	3/3	1	2	FACETS	0.979	0.847	1	0.979	0.847	1	CLONAL	1	TRUE	1	0.407131088778871	2		460	286	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007825	45007825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	61	347	0	ENST00000558401.1:c.276del	p.Thr93LeufsTer10	p.T93Lfs*10	ENST00000558401	NM_004048.2	91	aCc/ac	2/4	1	2	FACETS	0.77	0.667	0.881	0.77	0.667	0.881	SUBCLONAL	1	TRUE	1	0.407131088778871	2		347	389	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	26	310	0	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	0.346	0.274	0.429	0.346	0.274	0.429	SUBCLONAL	1	TRUE	1	0.407131088778871	2		310	369	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	33	510	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.367860794705018	2	FACETS	0.387	0.315	0.468	0.193	0.157	0.234	SUBCLONAL	1	TRUE	0	0.407131088778871	2		510	419	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	30	513	1	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.417	0.336	0.509	0.417	0.336	0.509	SUBCLONAL	1	TRUE	1	0.407131088778871	2		514	353	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	64	381	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.941	0.821	1	0.941	0.821	1	CLONAL	1	TRUE	1	0.407131088778871	2		381	334	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	16	412	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	1	2	FACETS	0.23	0.169	0.302	0.23	0.169	0.302	SUBCLONAL	1	TRUE	1	0.407131088778871	2		412	342	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024001	27024002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	36	339	0	ENST00000324856.7:c.1113dup	p.Gln372AlafsTer28	p.Q372Afs*28	ENST00000324856	NM_006015.4	369	-/G	1/20	1	2	FACETS	0.907	0.753	1	0.907	0.753	1	CLONAL	1	TRUE	1	0.407131088778871	2		339	195	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11177103	11177103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	22	267	0	ENST00000361445.4:c.6974C>T	p.Ala2325Val	p.A2325V	ENST00000361445	NM_004958.3	2325	gCg/gTg	50/58	1	2	FACETS	0.406	0.315	0.512	0.406	0.315	0.512	SUBCLONAL	1	TRUE	1	0.407131088778871	2		267	266	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656951	47656951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63749849	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	66	205	0	ENST00000233146.2:c.1147C>T	p.Arg383Ter	p.R383*	ENST00000233146	NM_000251.2	383	Cga/Tga	7/16	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.407131088778871	2		205	290	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440912	52440912	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1205668341	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	26	457	3	ENST00000460680.1:c.592del	p.Glu198ArgfsTer33	p.E198Rfs*33	ENST00000460680	NM_004656.3	198	Gag/ag	8/17	1	2	FACETS	0.295	0.233	0.366	0.295	0.233	0.366	SUBCLONAL	1	TRUE	1	0.407131088778871	2		460	433	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276755	15276755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138265894	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	27	472	0	ENST00000263388.2:c.5510G>A	p.Arg1837His	p.R1837H	ENST00000263388	NM_000435.2	1837	cGt/cAt	30/33	1	2	FACETS	0.351	0.279	0.433	0.351	0.279	0.433	SUBCLONAL	1	TRUE	1	0.407131088778871	2		472	378	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526151	189526151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	33	469	0	ENST00000264731.3:c.415G>A	p.Ala139Thr	p.A139T	ENST00000264731	NM_003722.4	139	Gcg/Acg	4/14	1	2	FACETS	0.297	0.241	0.361	0.297	0.241	0.361	SUBCLONAL	1	TRUE	1	0.407131088778871	2		469	545	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222993	5222993	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762510209	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	61	506	0	ENST00000357368.4:c.2810C>T	p.Ala937Val	p.A937V	ENST00000357368	NM_002850.3	937	gCg/gTg	18/38	1	2	FACETS	0.992	0.863	1	0.992	0.863	1	CLONAL	1	TRUE	1	0.407131088778871	2		506	302	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715979	52715979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205227	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	20	449	0	ENST00000322088.6:c.544C>T	p.Arg182Trp	p.R182W	ENST00000322088	NM_014225.5	182	Cgg/Tgg	5/15	1	2	FACETS	0.278	0.212	0.355	0.278	0.212	0.355	SUBCLONAL	1	TRUE	1	0.407131088778871	2		449	354	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261555	142261555	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	15	104	0	ENST00000350721.4:c.3402del	p.Phe1134LeufsTer6	p.F1134Lfs*6	ENST00000350721	NM_001184.3	1134	ttT/tt	17/47	1	2	FACETS	0.291	0.213	0.386	0.291	0.213	0.386	SUBCLONAL	1	TRUE	1	0.407131088778871	2		104	253	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2949715	2949715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	73	365	0	ENST00000396946.4:c.3229C>T	p.Arg1077Trp	p.R1077W	ENST00000396946	NM_032415.4	1077	Cgg/Tgg	24/25	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.407131088778871	2		365	289	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341141	8341141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1347452833	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	17	252	0	ENST00000356435.5:c.5075G>A	p.Arg1692His	p.R1692H	ENST00000356435		1692	cGt/cAt	30/35	1	2	FACETS	0.334	0.249	0.435	0.334	0.249	0.435	SUBCLONAL	1	TRUE	1	0.407131088778871	2		252	250	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101750	71101751	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	61	244	0	ENST00000318789.4:c.447dup	p.Gln150ThrfsTer20	p.Q150Tfs*20	ENST00000318789	NM_032682.5	149	-/A	9/21	1	2	FACETS	0.916	0.796	1	0.916	0.796	1	CLONAL	1	TRUE	1	0.407131088778871	2		244	327	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991757	72991758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760959844	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	83	510	0	ENST00000268489.5:c.2287dup	p.Glu763GlyfsTer26	p.E763Gfs*26	ENST00000268489	NM_006885.3	763	gag/gGag	2/10	1	2	FACETS	0.86	0.762	0.965	0.86	0.762	0.965	CLONAL	1	TRUE	1	0.407131088778871	2		510	474	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437288	220437288	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1190141661	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	28	439	0	ENST00000243786.2:c.197del	p.Gly66AlafsTer61	p.G66Afs*61	ENST00000243786	NM_002191.3	64	ctG/ct	1/2	1	2	FACETS	0.423	0.338	0.52	0.423	0.338	0.52	SUBCLONAL	1	TRUE	1	0.407131088778871	2		439	325	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781321	3781321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200112956	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	37	528	3	ENST00000262367.5:c.5044C>T	p.Arg1682Cys	p.R1682C	ENST00000262367	NM_004380.2	1682	Cgc/Tgc	30/31	1	2	FACETS	0.493	0.407	0.588	0.493	0.407	0.588	SUBCLONAL	1	TRUE	1	0.407131088778871	2		531	369	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046263	128046263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1308398082	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	34	390	0	ENST00000285398.2:c.1000C>T	p.Arg334Cys	p.R334C	ENST00000285398	NM_000122.1	334	Cgt/Tgt	7/15	1	2	FACETS	0.423	0.345	0.51	0.423	0.345	0.51	SUBCLONAL	1	TRUE	1	0.407131088778871	2		390	395	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354375	354375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910854855	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	109	359	0	ENST00000262320.3:c.1183C>T	p.Arg395Cys	p.R395C	ENST00000262320	NM_003502.3	395	Cgc/Tgc	5/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.407131088778871	2		359	361	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096132	2096133	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs763525759	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	82	338	0	ENST00000219066.1:c.374dup	p.Val127GlyfsTer43	p.V127Gfs*43	ENST00000219066	NM_002528.5	125	cca/ccCa	2/6	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.407131088778871	2		338	316	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375142	31375142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537913125	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	115	555	0	ENST00000328111.2:c.539C>T	p.Thr180Met	p.T180M	ENST00000328111	NM_006892.3	180	aCg/aTg	6/23	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.407131088778871	2		555	447	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726267	46726267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371935755	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	28	429	0	ENST00000371975.4:c.461G>A	p.Arg154Gln	p.R154Q	ENST00000371975	NM_003579.3	154	cGg/cAg	6/18	1	2	FACETS	0.37	0.295	0.455	0.37	0.295	0.455	SUBCLONAL	1	TRUE	1	0.407131088778871	2		429	372	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941121	36941121	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	105	489	2	ENST00000361632.4:c.218del	p.Gly73AlafsTer31	p.G73Afs*31	ENST00000361632		73	gGc/gc	3/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.407131088778871	2		491	349	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40498610	40498610	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	16	264	1	ENST00000264657.5:c.250C>T	p.Arg84Ter	p.R84*	ENST00000264657	NM_139276.2	84	Cga/Tga	3/24	1	2	FACETS	0.266	0.196	0.349	0.266	0.196	0.349	SUBCLONAL	1	TRUE	1	0.407131088778871	2		265	296	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222828	36222828	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	111	457	0	ENST00000222270.7:c.5462del	p.Pro1821HisfsTer74	p.P1821Hfs*74	ENST00000222270	NM_014727.1	1819	gaC/ga	27/37	1	2	FACETS	0.783	0.712	0.857	1	0.986	1	SUBCLONAL	2	TRUE	1	0.407131088778871	2		457	348	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212375	36212375	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	20	496	0	ENST00000222270.7:c.2126C>A	p.Pro709His	p.P709H	ENST00000222270	NM_014727.1	709	cCt/cAt	3/37	1	2	FACETS	0.255	0.194	0.326	0.255	0.194	0.326	SUBCLONAL	1	TRUE	1	0.407131088778871	2		496	386	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930087	68930087	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	12	179	0	ENST00000288368.4:c.148T>G	p.Leu50Val	p.L50V	ENST00000288368	NM_024870.2	50	Tta/Gta	2/40	1	2	FACETS	0.27	0.19	0.37	0.27	0.19	0.37	SUBCLONAL	1	TRUE	1	0.407131088778871	2		179	218	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937422	178937422	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	8	43	0	ENST00000263967.3:c.1810T>C	p.Cys604Arg	p.C604R	ENST00000263967	NM_006218.2	604	Tgt/Cgt	12/21	1	2	FACETS	0.473	0.308	0.683	0.473	0.308	0.683	SUBCLONAL	1	TRUE	1	0.407131088778871	2		43	83	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504995	186504995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	81	355	0	ENST00000323963.5:c.851G>A	p.Arg284His	p.R284H	ENST00000323963		284	cGc/cAc	8/11	1	2	FACETS	0.978	0.866	1	0.978	0.866	1	CLONAL	1	TRUE	1	0.407131088778871	2		355	407	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55963828	55963828	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	15	223	0	ENST00000263923.4:c.2614+1G>A		p.X872_splice	ENST00000263923	NM_002253.2	872			1	2	FACETS	0.378	0.277	0.499	0.378	0.277	0.499	SUBCLONAL	1	TRUE	1	0.407131088778871	2		223	195	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522188	157522188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370838091	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	44	503	0	ENST00000346085.5:c.4460C>T	p.Ala1487Val	p.A1487V	ENST00000346085	NM_020732.3	1487	gCg/gTg	18/20	1	2	FACETS	0.616	0.518	0.723	0.616	0.518	0.723	SUBCLONAL	1	TRUE	1	0.407131088778871	2		503	351	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845958	151845959	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	23	404	0	ENST00000262189.6:c.13053dup	p.Trp4352MetfsTer17	p.W4352Mfs*17	ENST00000262189	NM_170606.2	4351	-/A	52/59	1	2	FACETS	0.31	0.242	0.39	0.31	0.242	0.39	SUBCLONAL	1	TRUE	1	0.407131088778871	2		404	364	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80109527	80109527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766261257	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	83	309	0	ENST00000265081.6:c.2780C>T	p.Ala927Val	p.A927V	ENST00000265081	NM_002439.4	927	gCg/gTg	20/24	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.407131088778871	2		309	305	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683507	182683507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	31	97	0	ENST00000292782.4:c.38G>A	p.Arg13His	p.R13H	ENST00000292782	NM_020640.2	13	cGt/cAt	2/7	1	2	FACETS	0.837	0.683	1	0.837	0.683	1	CLONAL	1	TRUE	1	0.407131088778871	2		97	182	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656915	45656915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs558943057	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	83	476	0	ENST00000407780.3:c.241C>T	p.Arg81Trp	p.R81W	ENST00000407780	NM_001283052.1	81	Cgg/Tgg	3/7	1	2	FACETS	0.89	0.789	0.998	0.89	0.789	0.998	CLONAL	1	TRUE	1	0.407131088778871	2		476	458	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573032	41573032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238889159	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	77	490	0	ENST00000263253.7:c.5317C>T	p.Arg1773Trp	p.R1773W	ENST00000263253	NM_001429.3	1773	Cgg/Tgg	31/31	1	2	FACETS	0.841	0.741	0.947	0.841	0.741	0.947	CLONAL	1	TRUE	1	0.407131088778871	2		490	450	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754617	42754619	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	23	420	0	ENST00000222329.4:c.121_123del	p.Glu41del	p.E41del	ENST00000222329	NM_006494.2	41	GAG/-	2/4	1	2	FACETS	0.336	0.262	0.422	0.336	0.262	0.422	SUBCLONAL	1	TRUE	1	0.407131088778871	2		420	336	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131926963	131926963	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	23	164	0	ENST00000265335.6:c.1504del	p.Met502TrpfsTer3	p.M502Wfs*3	ENST00000265335		500	ttA/tt	10/25	1	2	FACETS	0.533	0.417	0.665	0.533	0.417	0.665	SUBCLONAL	1	TRUE	1	0.407131088778871	2		164	212	SUCCESS
APC	324	MSKCC	GRCh37	5	112178384	112178384	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	45	257	0	ENST00000257430.4:c.7093T>C	p.Ser2365Pro	p.S2365P	ENST00000257430	NM_000038.5	2365	Tca/Cca	16/16	1	2	FACETS	0.996	0.845	1	0.996	0.845	1	CLONAL	1	TRUE	1	0.407131088778871	2		257	222	SUCCESS
APC	324	MSKCC	GRCh37	5	112173686	112173687	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	81	264	0	ENST00000257430.4:c.2396_2397del	p.Tyr799CysfsTer3	p.Y799Cfs*3	ENST00000257430	NM_000038.5	799	TAt/t	16/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.407131088778871	2		264	274	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161298257	161298257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769177037	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	46	281	0	ENST00000367975.2:c.149G>A	p.Arg50His	p.R50H	ENST00000367975	NM_003001.3	50	cGt/cAt	3/6	1	2	FACETS	0.727	0.615	0.849	0.727	0.615	0.849	SUBCLONAL	1	TRUE	1	0.407131088778871	2		281	311	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs749415085	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	9	206	0	ENST00000263967.3:c.112C>A	p.Arg38Ser	p.R38S	ENST00000263967	NM_006218.2	38	Cgt/Agt	2/21	1	2	FACETS	0.242	0.16	0.346	0.242	0.16	0.346	SUBCLONAL	1	TRUE	1	0.407131088778871	2		206	183	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665819	241665819	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	21	304	0	ENST00000366560.3:c.1160T>C	p.Val387Ala	p.V387A	ENST00000366560	NM_000143.3	387	gTc/gCc	8/10	1	2	FACETS	0.277	0.212	0.352	0.277	0.212	0.352	SUBCLONAL	1	TRUE	1	0.407131088778871	2		304	373	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508080	106508080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	15	384	0	ENST00000359195.3:c.74C>T	p.Pro25Leu	p.P25L	ENST00000359195	NM_002649.2	25	cCg/cTg	2/11	1	2	FACETS	0.258	0.188	0.342	0.258	0.188	0.342	SUBCLONAL	1	TRUE	1	0.407131088778871	2		384	286	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991400	72991400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201144589	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	37	433	0	ENST00000268489.5:c.2645C>T	p.Ser882Leu	p.S882L	ENST00000268489	NM_006885.3	882	tCg/tTg	2/10	1	2	FACETS	0.518	0.428	0.618	0.518	0.428	0.618	SUBCLONAL	1	TRUE	1	0.407131088778871	2		433	351	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379845	17379845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1175226015	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	51	358	0	ENST00000359435.4:c.230C>T	p.Pro77Leu	p.P77L	ENST00000359435	NM_001033549.1	77	cCg/cTg	2/9	1	2	FACETS	0.785	0.671	0.909	0.785	0.671	0.909	CLONAL	1	TRUE	1	0.407131088778871	2		358	319	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101066	27101066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1330309030	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	66	407	0	ENST00000324856.7:c.4348G>A	p.Gly1450Ser	p.G1450S	ENST00000324856	NM_006015.4	1450	Ggc/Agc	18/20	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.407131088778871	2		407	311	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820879	36820881	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs1557511475	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	103	422	0	ENST00000373129.3:c.496_498del	p.Glu166del	p.E166del	ENST00000373129	NM_032017.1	166	GAG/-	6/12	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.407131088778871	2		422	417	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150923867	150923870	+	frameshift_variant	Frame_Shift_Del	DEL	CTAT	CTAT	-	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	24	339	0	ENST00000271640.5:c.2241_2244del	p.Ile748ArgfsTer22	p.I748Rfs*22	ENST00000271640	NM_001145415.1	747	aCTATc/ac	14/22	1	2	FACETS	0.274	0.214	0.343	0.274	0.214	0.343	SUBCLONAL	1	TRUE	1	0.407131088778871	2		339	430	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769567	112769570	+	frameshift_variant	Frame_Shift_Del	DEL	ACTC	ACTC	-	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	56	207	0	ENST00000369452.4:c.1521_1524del	p.His508PhefsTer11	p.H508Ffs*11	ENST00000369452	NM_007373.3	507	ACTCac/ac	8/9	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.407131088778871	2		207	237	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8246180	8246180	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1277982924	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	24	320	0	ENST00000335790.3:c.454G>T	p.Glu152Ter	p.E152*	ENST00000335790	NM_002315.2	152	Gaa/Taa	4/4	1	2	FACETS	0.435	0.342	0.542	0.435	0.342	0.542	SUBCLONAL	1	TRUE	1	0.407131088778871	2		320	271	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918590	94918590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	18	281	0	ENST00000536441.1:c.592G>A	p.Ala198Thr	p.A198T	ENST00000536441	NM_144665.3	198	Gca/Aca	5/10	1	2	FACETS	0.283	0.213	0.367	0.283	0.213	0.367	SUBCLONAL	1	TRUE	1	0.407131088778871	2		281	312	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374597	118374597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1451782829	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	82	472	0	ENST00000534358.1:c.7990G>A	p.Ala2664Thr	p.A2664T	ENST00000534358	NM_005933.3	2664	Gct/Act	27/36	1	2	FACETS	0.968	0.858	1	0.968	0.858	1	CLONAL	1	TRUE	1	0.407131088778871	2		472	416	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	106	280	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.367860794705018	2	FACETS	0.829	0.753	0.908	0.829	0.753	0.908	CLONAL	2	TRUE	0	0.407131088778871	2		280	314	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945049	31945049	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs754427138	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	57	490	2	ENST00000340398.3:c.52del	p.Arg18AlafsTer19	p.R18Afs*19	ENST00000340398	NM_001013699.2	18	Cgc/gc	1/1	0.367860794705018	2	FACETS	0.515	0.442	0.594	0.257	0.221	0.297	SUBCLONAL	1	TRUE	0	0.407131088778871	2		492	544	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437166	121437166	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	23	485	0	ENST00000257555.6:c.1597C>A	p.Leu533Met	p.L533M	ENST00000257555		533	Ctg/Atg	8/10	0.367860794705018	2	FACETS	0.281	0.219	0.354	0.141	0.109	0.177	SUBCLONAL	1	TRUE	0	0.407131088778871	2		485	402	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210819	133210819	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	21	393	0	ENST00000320574.5:c.5957del	p.Leu1986CysfsTer13	p.L1986Cfs*13	ENST00000320574	NM_006231.2	1986	tTg/tg	43/49	0.367860794705018	2	FACETS	0.269	0.206	0.342	0.134	0.103	0.171	SUBCLONAL	1	TRUE	0	0.407131088778871	2		393	384	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225533	133225533	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	115	390	1	ENST00000320574.5:c.4131G>T	p.Glu1377Asp	p.E1377D	ENST00000320574	NM_006231.2	1377	gaG/gaT	32/49	0.367860794705018	2	FACETS	0.851	0.776	0.928	0.851	0.776	0.928	CLONAL	2	TRUE	0	0.407131088778871	2		391	332	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562505	21562506	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGGGG	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	17	269	0	ENST00000382592.4:c.1413_1414insCCCCCC	p.Pro471_Ala472insProPro	p.P471_A472insPP	ENST00000382592	NM_014572.2	471	-/CCCCCC	4/8	1	2	FACETS	0.584	0.439	0.753	0.584	0.439	0.753	SUBCLONAL	1	TRUE	1	0.407131088778871	2		269	143	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435979	110435979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1197403582	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	36	533	0	ENST00000375856.3:c.2422C>T	p.Arg808Cys	p.R808C	ENST00000375856	NM_003749.2	808	Cgc/Tgc	1/2	1	2	FACETS	0.385	0.316	0.463	0.385	0.316	0.463	SUBCLONAL	1	TRUE	1	0.407131088778871	2		533	459	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058357	42058357	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	18	345	0	ENST00000219905.7:c.8077A>G	p.Asn2693Asp	p.N2693D	ENST00000219905	NM_001164273.1	2693	Aat/Gat	24/24	1	2	FACETS	0.261	0.196	0.338	0.261	0.196	0.338	SUBCLONAL	1	TRUE	1	0.407131088778871	2		345	339	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714111	43714111	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377516466	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	39	400	0	ENST00000382044.4:c.4042G>A	p.Gly1348Arg	p.G1348R	ENST00000382044	NM_001141980.1	1348	Ggg/Agg	19/28	1	2	FACETS	0.413	0.342	0.492	0.413	0.342	0.492	SUBCLONAL	1	TRUE	1	0.407131088778871	2		400	464	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50773879	50773880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	94	205	0	ENST00000307179.4:c.1427dup	p.Asn476LysfsTer35	p.N476Kfs*35	ENST00000307179		474	gaa/gAaa	11/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.407131088778871	2		205	352	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124261	2124261	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs796053473	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	143	415	1	ENST00000219476.3:c.2416G>A	p.Val806Met	p.V806M	ENST00000219476	NM_000548.3	806	Gtg/Atg	22/42	1	2	FACETS	0.83	0.764	0.898	1	0.99	1	CLONAL	2	TRUE	1	0.407131088778871	2		416	423	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821872	72821872	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	78	442	0	ENST00000268489.5:c.10303C>A	p.Leu3435Met	p.L3435M	ENST00000268489	NM_006885.3	3435	Ctg/Atg	10/10	1	2	FACETS	0.944	0.834	1	0.944	0.834	1	CLONAL	1	TRUE	1	0.407131088778871	2		442	406	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346484	89346484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145822257	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	95	491	1	ENST00000301030.4:c.6466G>A	p.Val2156Met	p.V2156M	ENST00000301030	NM_001256183.1	2156	Gtg/Atg	9/13	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.407131088778871	2		492	349	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770811	59770811	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	15	121	0	ENST00000259008.2:c.2555A>G	p.Asn852Ser	p.N852S	ENST00000259008	NM_032043.2	852	aAc/aGc	18/20	1	2	FACETS	0.351	0.257	0.463	0.351	0.257	0.463	SUBCLONAL	1	TRUE	1	0.407131088778871	2		121	210	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554118	63554119	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	120	514	0	ENST00000307078.5:c.620_621del	p.Thr207SerfsTer5	p.T207Sfs*5	ENST00000307078	NM_004655.3	207	aCA/a	2/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.407131088778871	2		514	422	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78931531	78931531	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	71	352	0	ENST00000306801.3:c.3477+1G>T		p.X1159_splice	ENST00000306801	NM_020761.2	1159			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.407131088778871	2		352	293	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6222401	6222406	+	inframe_deletion	In_Frame_Del	DEL	GGGGTG	GGGGTG	-	rs753690040	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	10	272	2	ENST00000252674.7:c.836_841del	p.Pro279_Pro280del	p.P279_P280del	ENST00000252674	NM_005934.3	279	cCACCCCgg/cgg	6/12	1	2	FACETS	0.251	0.169	0.353	0.251	0.169	0.353	SUBCLONAL	1	TRUE	1	0.407131088778871	2		274	196	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145743	11145743	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199962502	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	93	478	1	ENST00000358026.2:c.4105C>T	p.Arg1369Cys	p.R1369C	ENST00000358026	NM_001128849.1	1369	Cgt/Tgt	29/36	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.407131088778871	2		479	428	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425432	47425432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759708637	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	100	466	0	ENST00000404338.3:c.3500G>A	p.Arg1167Gln	p.R1167Q	ENST00000404338	NM_004491.4	1167	cGg/cAg	1/6	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.407131088778871	2		466	438	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140171	50140171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1437320392	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	99	447	0	ENST00000246792.3:c.254C>T	p.Ala85Val	p.A85V	ENST00000246792	NM_006270.3	85	gCg/gTg	3/6	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.407131088778871	2		447	387	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39216444	39216444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368767111	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	39	128	0	ENST00000402219.2:c.3358G>A	p.Val1120Ile	p.V1120I	ENST00000402219	NM_005633.3	1120	Gtc/Atc	21/23	1	2	FACETS	0.921	0.771	1	0.921	0.771	1	CLONAL	1	TRUE	1	0.407131088778871	2		128	208	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	92	374	0	ENST00000260795.2:c.1118A>T	p.Tyr373Phe	p.Y373F	ENST00000260795		373	tAt/tTt	8/17	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.407131088778871	2		374	332	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356350	66356350	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	47	400	0	ENST00000273854.3:c.1147A>G	p.Thr383Ala	p.T383A	ENST00000273854	NM_004439.5	383	Act/Gct	5/18	1	2	FACETS	0.626	0.529	0.731	0.626	0.529	0.731	SUBCLONAL	1	TRUE	1	0.407131088778871	2		400	369	SUCCESS
ALB	213	MSKCC	GRCh37	4	74276041	74276041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267600248	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	58	266	0	ENST00000295897.4:c.628C>T	p.Arg210Trp	p.R210W	ENST00000295897	NM_000477.5	210	Cgg/Tgg	6/15	1	2	FACETS	0.947	0.819	1	0.947	0.819	1	CLONAL	1	TRUE	1	0.407131088778871	2		266	301	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250898	153250898	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	15	116	0	ENST00000281708.4:c.1162C>T	p.Gln388Ter	p.Q388*	ENST00000281708	NM_033632.3	388	Cag/Tag	8/12	1	2	FACETS	0.358	0.262	0.472	0.358	0.262	0.472	SUBCLONAL	1	TRUE	1	0.407131088778871	2		116	206	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549887	187549887	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	58	175	0	ENST00000441802.2:c.4354C>A	p.His1452Asn	p.H1452N	ENST00000441802	NM_005245.3	1452	Cat/Aat	8/27	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.407131088778871	2		175	229	SUCCESS
APC	324	MSKCC	GRCh37	5	112128153	112128153	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	59	143	0	ENST00000257430.4:c.656C>T	p.Ala219Val	p.A219V	ENST00000257430	NM_000038.5	219	gCc/gTc	7/16	1	2	FACETS	0.838	0.735	0.944	1	0.977	1	CLONAL	2	TRUE	1	0.407131088778871	2		143	173	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673771	176673771	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	23	261	0	ENST00000439151.2:c.4471T>C	p.Ser1491Pro	p.S1491P	ENST00000439151	NM_022455.4	1491	Tcg/Ccg	10/23	1	2	FACETS	0.331	0.258	0.416	0.331	0.258	0.416	SUBCLONAL	1	TRUE	1	0.407131088778871	2		261	341	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250608	26250608	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	36	613	0	ENST00000446824.2:c.226G>A	p.Ala76Thr	p.A76T	ENST00000446824	NM_021018.2	76	Gcg/Acg	1/1	1	2	FACETS	0.335	0.275	0.403	0.335	0.275	0.403	SUBCLONAL	1	TRUE	1	0.407131088778871	2		613	528	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797286	32797286	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	49	380	0	ENST00000374899.4:c.1823C>A	p.Ala608Asp	p.A608D	ENST00000374899	NM_018833.2	608	gCt/gAt	11/12	0.370946893580543	3	FACETS	0.668	0.566	0.779	0.334	0.283	0.39	SUBCLONAL	1	TRUE	1	0.407131088778871	3		380	434	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805917	32805918	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	171	457	0	ENST00000374899.4:c.93dup	p.Pro32SerfsTer135	p.P32Sfs*135	ENST00000374899	NM_018833.2	31	-/T	2/12	0.370946893580543	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.407131088778871	3		457	456	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710621	117710621	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	31	419	0	ENST00000368508.3:c.1651T>C	p.Ser551Pro	p.S551P	ENST00000368508	NM_002944.2	551	Tcc/Ccc	12/43	1	2	FACETS	0.359	0.29	0.437	0.359	0.29	0.437	SUBCLONAL	1	TRUE	1	0.407131088778871	2		419	424	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878187	151878187	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	118	439	0	ENST00000262189.6:c.6758C>T	p.Ala2253Val	p.A2253V	ENST00000262189	NM_170606.2	2253	gCa/gTa	36/59	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.407131088778871	2		439	437	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983496	90983496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	36	123	0	ENST00000265433.3:c.607C>T	p.Pro203Ser	p.P203S	ENST00000265433	NM_002485.4	203	Cca/Tca	6/16	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.407131088778871	2		123	155	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739097	145739097	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs386833849	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	28	455	0	ENST00000428558.2:c.2059-1G>T		p.X687_splice	ENST00000428558	NM_004260.3	687			1	2	FACETS	0.33	0.263	0.406	0.33	0.263	0.406	SUBCLONAL	1	TRUE	1	0.407131088778871	2		455	417	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932831	39932831	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058955-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	95	266	0	ENST00000378444.4:c.1768A>C	p.Thr590Pro	p.T590P	ENST00000378444	NM_001123385.1	590	Acc/Ccc	4/15	1	1	FACETS	0.765	0.693	0.838	1	0.984	1	SUBCLONAL	2	TRUE	0	0.407131088778871	1		266	243	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0058956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	67	390	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.406815389588411	1	FACETS	0.951	0.835	1	0.951	0.835	1	CLONAL	1	TRUE	0	0.407809916505124	1		390	275	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183734	10183734	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs869025617	NA	P-0058956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	54	341	0	ENST00000256474.2:c.203C>A	p.Ser68Ter	p.S68*	ENST00000256474	NM_000551.3	68	tCg/tAg	1/3	0.406815389588411	1	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	0	0.407809916505124	1		341	202	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441235	52441235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910211860	NA	P-0058956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	69	365	0	ENST00000460680.1:c.535C>T	p.Arg179Trp	p.R179W	ENST00000460680	NM_004656.3	179	Cgg/Tgg	7/17	0.407809916505124	1	FACETS	0.942	0.829	1	0.942	0.829	1	CLONAL	1	TRUE	0	0.407809916505124	1		365	286	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851826	134851826	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058956-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	32	446	0	ENST00000398015.3:c.1232G>T	p.Gly411Val	p.G411V	ENST00000398015	NM_004441.4	411	gGa/gTa	5/16	1	2	FACETS	0.467	0.38	0.565	0.467	0.38	0.565	SUBCLONAL	1	TRUE	1	0.407809916505124	2		446	336	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514385	149514385	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058957-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	33	382	0	ENST00000261799.4:c.559A>G	p.Ser187Gly	p.S187G	ENST00000261799	NM_002609.3	187	Agc/Ggc	4/23	1	2	FACETS	0.21	0.171	0.255	0.21	0.171	0.255	SUBCLONAL	1	TRUE	1	0.668557567836999	2		382	469	SUCCESS
POT1	25913	MSKCC	GRCh37	7	124487032	124487032	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058957-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	75	179	0	ENST00000357628.3:c.970T>C	p.Tyr324His	p.Y324H	ENST00000357628	NM_015450.2	324	Tac/Cac	12/19	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.668557567836999	2		179	192	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	56	302	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.78	0.678	0.887	0.78	0.678	0.887	SUBCLONAL	1	TRUE	1	0.725510112324503	2		302	198	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	73	488	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	0.43	0.377	0.487	0.43	0.377	0.487	SUBCLONAL	1	TRUE	1	0.725510112324503	2		488	468	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0058968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	154	356	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.98	0.906	1	0.98	0.906	1	CLONAL	1	TRUE	1	0.725510112324503	2		356	433	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0058968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	93	416	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.571	0.51	0.635	0.571	0.51	0.635	SUBCLONAL	1	TRUE	1	0.725510112324503	2		416	449	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791757	42791757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568504941	NA	P-0058968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	68	554	1	ENST00000575354.2:c.643C>T	p.Arg215Trp	p.R215W	ENST00000575354	NM_015125.3	215	Cgg/Tgg	5/20	0.725510112324503	1	FACETS	0.378	0.331	0.428	0.378	0.331	0.428	SUBCLONAL	1	TRUE	0	0.725510112324503	1		555	316	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799059	42799059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058968-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	19	476	0	ENST00000575354.2:c.4543C>T	p.Arg1515Cys	p.R1515C	ENST00000575354	NM_015125.3	1515	Cgc/Tgc	20/20	0.725510112324503	1	FACETS	0.155	0.117	0.198	0.155	0.117	0.198	SUBCLONAL	1	TRUE	0	0.725510112324503	1		476	216	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0058969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	36	374	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.14	2		374	486	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653796	89653798	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs1554893765	NA	P-0058969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	26	234	0	ENST00000371953.3:c.97_99del	p.Ile33del	p.I33del	ENST00000371953	NM_000314.4	32	ATT/-	2/9	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.14	2		234	291	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70442645	70442645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	35	393	2	ENST00000373644.4:c.4967G>A	p.Arg1656His	p.R1656H	ENST00000373644	NM_030625.2	1656	cGt/cAt	10/12	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.14	2		395	456	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750639	128750639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775522201	NA	P-0058969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	40	474	0	ENST00000377970.2:c.176C>T	p.Ala59Val	p.A59V	ENST00000377970	NM_002467.4	59	gCg/gTg	2/3	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.14	2		474	509	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0058969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	25	437	0	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	0.978	0.771	1	0.978	0.771	1	CLONAL	1	TRUE	1	0.14	2		437	365	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027087	71027087	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	29	509	0	ENST00000318789.4:c.1240del	p.Leu414Ter	p.L414*	ENST00000318789	NM_032682.5	414	Ctg/tg	15/21	1	2	FACETS	0.728	0.583	0.894	0.728	0.583	0.894	SUBCLONAL	1	TRUE	1	0.14	2		509	569	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866606	78866606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	27	368	0	ENST00000306801.3:c.2179C>T	p.Arg727Cys	p.R727C	ENST00000306801	NM_020761.2	727	Cgt/Tgt	19/34	1	2	FACETS	0.749	0.595	0.926	0.749	0.595	0.926	CLONAL	1	TRUE	1	0.14	2		368	515	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273218	115273218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	46	692	0	ENST00000438362.2:c.1240C>T	p.Arg414Cys	p.R414C	ENST00000438362	NM_001242891.1	414	Cgt/Tgt	11/20	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.14	2		692	529	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289896	15289896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs115872852	NA	P-0058969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	34	577	0	ENST00000263388.2:c.3658C>T	p.Arg1220Trp	p.R1220W	ENST00000263388	NM_000435.2	1220	Cgg/Tgg	22/33	1	2	FACETS	0.812	0.662	0.982	0.812	0.662	0.982	CLONAL	1	TRUE	1	0.14	2		577	598	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836296	151836296	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771641625	NA	P-0058969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	26	307	0	ENST00000262189.6:c.14509G>A	p.Ala4837Thr	p.A4837T	ENST00000262189	NM_170606.2	4837	Gcg/Acg	57/59	1	2	FACETS	0.904	0.715	1	0.904	0.715	1	CLONAL	1	TRUE	1	0.14	2		307	411	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17382455	17382455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1365789470	NA	P-0058969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	21	302	0	ENST00000359435.4:c.335C>T	p.Ser112Leu	p.S112L	ENST00000359435	NM_001033549.1	112	tCg/tTg	3/9	1	2	FACETS	0.748	0.575	0.951	0.748	0.575	0.951	CLONAL	1	TRUE	1	0.14	2		302	401	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712704	43712704	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	34	440	0	ENST00000382044.4:c.4480C>T	p.Leu1494Phe	p.L1494F	ENST00000382044	NM_001141980.1	1494	Ctc/Ttc	21/28	1	2	FACETS	0.975	0.796	1	0.975	0.796	1	CLONAL	1	TRUE	1	0.14	2		440	498	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104295	2104295	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs397515316	NA	P-0058969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	27	291	0	ENST00000219476.3:c.337-2A>T		p.X113_splice	ENST00000219476	NM_000548.3	113			1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.14	2		291	335	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23625378	23625378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	29	264	0	ENST00000261584.4:c.3148C>T	p.His1050Tyr	p.H1050Y	ENST00000261584	NM_024675.3	1050	Cac/Tac	11/13	1	2	FACETS	0.913	0.732	1	0.913	0.732	1	CLONAL	1	TRUE	1	0.14	2		264	454	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758764	41758764	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	33	397	0	ENST00000301178.4:c.1818G>T	p.Gln606His	p.Q606H	ENST00000301178	NM_021913.4	606	caG/caT	16/20	1	2	FACETS	0.941	0.765	1	0.941	0.765	1	CLONAL	1	TRUE	1	0.14	2		397	501	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457188	25457188	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058969-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	35	385	0	ENST00000264709.3:c.2699A>T	p.His900Leu	p.H900L	ENST00000264709	NM_175629.2	900	cAc/cTc	23/23	1	2	FACETS	0.949	0.777	1	0.949	0.777	1	CLONAL	1	TRUE	1	0.14	2		385	527	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	60	608	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.39	0.334	0.45	0.39	0.334	0.45	SUBCLONAL	1	TRUE	1	0.344517857700693	2		609	894	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	50	544	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.316	0.267	0.37	0.316	0.267	0.37	SUBCLONAL	1	TRUE	1	0.344517857700693	2		548	918	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	150	549	5	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.344517857700693	2		554	800	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934243	49934243	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1407832113	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	38	458	1	ENST00000296474.3:c.2264del	p.Gly755ValfsTer19	p.G755Vfs*19	ENST00000296474	NM_002447.2	755	gGt/gt	8/20	1	2	FACETS	0.33	0.272	0.396	0.33	0.272	0.396	SUBCLONAL	1	TRUE	1	0.344517857700693	2		459	668	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	126	570	0	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	2	FACETS	0.827	0.748	0.909	0.827	0.748	0.909	CLONAL	1	TRUE	1	0.344517857700693	2		570	885	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733513	85733513	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs387906350	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	75	373	3	ENST00000370580.1:c.499del	p.Ser167LeufsTer6	p.S167Lfs*6	ENST00000370580	NM_003921.4	167	Tct/ct	3/3	1	2	FACETS	0.772	0.677	0.874	0.772	0.677	0.874	SUBCLONAL	1	TRUE	1	0.344517857700693	2		376	564	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931452	131931453	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	75	293	0	ENST00000265335.6:c.2164_2165del	p.Lys722GlyfsTer5	p.K722Gfs*5	ENST00000265335		719	ctAAaa/ctaa	13/25	1	2	FACETS	0.878	0.771	0.992	0.878	0.771	0.992	CLONAL	1	TRUE	1	0.344517857700693	2		293	496	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	11	109	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	0.717	0.501	0.979	0.717	0.501	0.979	CLONAL	1	TRUE	1	0.344517857700693	2		109	89	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	109	535	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.344517857700693	2		535	604	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121791	2121792	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs137854144	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	72	453	0	ENST00000219476.3:c.1959_1960del	p.Gly654LeufsTer2	p.G654Lfs*2	ENST00000219476	NM_000548.3	651	ccAGag/ccag	19/42	1	2	FACETS	0.786	0.688	0.891	0.786	0.688	0.891	SUBCLONAL	1	TRUE	1	0.344517857700693	2		453	532	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299832	15299832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465285176	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	120	503	1	ENST00000263388.2:c.1346G>A	p.Arg449His	p.R449H	ENST00000263388	NM_000435.2	449	cGc/cAc	8/33	1	2	FACETS	0.929	0.839	1	0.929	0.839	1	CLONAL	1	TRUE	1	0.344517857700693	2		504	750	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653782	89653782	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs886041877	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	29	215	0	ENST00000371953.3:c.80A>G	p.Tyr27Cys	p.Y27C	ENST00000371953	NM_000314.4	27	tAt/tGt	2/9	1	2	FACETS	0.941	0.762	1	0.941	0.762	1	CLONAL	1	TRUE	1	0.344517857700693	2		215	179	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916836	178916836	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	48	319	0	ENST00000263967.3:c.223C>G	p.Gln75Glu	p.Q75E	ENST00000263967	NM_006218.2	75	Caa/Gaa	2/21	1	2	FACETS	0.834	0.708	0.972	0.834	0.708	0.972	CLONAL	1	TRUE	1	0.344517857700693	2		319	334	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873634	35873634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778404	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	97	366	1	ENST00000303115.3:c.590C>T	p.Pro197Leu	p.P197L	ENST00000303115	NM_002185.3	197	cCg/cTg	5/8	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.344517857700693	2		367	516	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522601	176522601	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	144	633	1	ENST00000292408.4:c.1703del	p.Pro568GlnfsTer53	p.P568Qfs*53	ENST00000292408	NM_213647.1	566	cgC/cg	13/18	1	2	FACETS	0.965	0.88	1	0.965	0.88	1	CLONAL	1	TRUE	1	0.344517857700693	2		634	866	SUCCESS
AR	367	MSKCC	GRCh37	X	66937326	66937326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137852593	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	123	336	1	ENST00000374690.3:c.2180G>A	p.Arg727His	p.R727H	ENST00000374690	NM_000044.3	727	cGc/cAc	5/8	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.344517857700693	2		337	646	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692991	89692991	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786202688	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	33	355	0	ENST00000371953.3:c.475A>G	p.Arg159Gly	p.R159G	ENST00000371953	NM_000314.4	159	Agg/Ggg	5/9	1	2	FACETS	0.726	0.594	0.873	0.726	0.594	0.873	SUBCLONAL	1	TRUE	1	0.344517857700693	2		355	264	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654721	67654721	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	54	317	0	ENST00000264010.4:c.1207+1G>A		p.X403_splice	ENST00000264010	NM_006565.3	403			1	2	FACETS	0.633	0.541	0.734	0.633	0.541	0.734	SUBCLONAL	1	TRUE	1	0.344517857700693	2		317	495	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481648	56481648	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs774589520	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	138	528	0	ENST00000267101.3:c.683A>G	p.His228Arg	p.H228R	ENST00000267101	NM_001982.3	228	cAt/cGt	6/28	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.344517857700693	2		528	740	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526976	31526976	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1485879154	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	199	381	0	ENST00000344624.3:c.64C>T	p.Arg22Ter	p.R22*	ENST00000344624		22	Cga/Tga	2/33	1	2	FACETS	1	0.937	1	1	0.994	1	CLONAL	2	TRUE	1	0.344517857700693	2		381	575	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515324	31515324	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs187981384	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	91	312	1	ENST00000344624.3:c.1061G>A	p.Arg354His	p.R354H	ENST00000344624		354	cGc/cAc	5/33	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.344517857700693	2		313	487	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031532	11031532	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	150	607	0	ENST00000327064.4:c.1451del	p.Pro484HisfsTer37	p.P484Hfs*37	ENST00000327064	NM_199141.1	483	Ccc/cc	13/16	1	2	FACETS	0.991	0.905	1	0.991	0.905	1	CLONAL	1	TRUE	1	0.344517857700693	2		607	879	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251482	10251482	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	144	481	2	ENST00000340748.4:c.3450del	p.Leu1151CysfsTer29	p.L1151Cfs*29	ENST00000340748		1150	ggG/gg	31/40	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.344517857700693	2		483	777	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457360	67457360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770798158	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	124	509	0	ENST00000327367.4:c.334G>A	p.Ala112Thr	p.A112T	ENST00000327367	NM_005902.3	112	Gcc/Acc	2/9	1	2	FACETS	0.94	0.851	1	0.94	0.851	1	CLONAL	1	TRUE	1	0.344517857700693	2		509	766	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444809	49444809	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	104	595	0	ENST00000301067.7:c.2657del	p.Pro886LeufsTer44	p.P886Lfs*44	ENST00000301067	NM_003482.3	886	cCt/ct	10/54	1	2	FACETS	0.742	0.664	0.825	0.742	0.664	0.825	SUBCLONAL	1	TRUE	1	0.344517857700693	2		595	814	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129309	2129309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1443030830	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	99	500	1	ENST00000219476.3:c.3164G>A	p.Gly1055Asp	p.G1055D	ENST00000219476	NM_000548.3	1055	gGc/gAc	28/42	1	2	FACETS	0.825	0.736	0.918	0.825	0.736	0.918	CLONAL	1	TRUE	1	0.344517857700693	2		501	697	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111855963	111855963	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752520582	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	96	444	0	ENST00000341259.2:c.14C>T	p.Ala5Val	p.A5V	ENST00000341259	NM_005475.2	5	gCc/gTc	2/8	1	2	FACETS	0.798	0.712	0.891	0.798	0.712	0.891	SUBCLONAL	1	TRUE	1	0.344517857700693	2		444	698	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741488	145741488	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1060501384	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	50	520	0	ENST00000428558.2:c.1015del	p.Leu339CysfsTer20	p.L339Cfs*20	ENST00000428558	NM_004260.3	339	Ctg/tg	5/22	1	2	FACETS	0.362	0.306	0.424	0.362	0.306	0.424	SUBCLONAL	1	TRUE	1	0.344517857700693	2		520	801	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776069	9776069	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	136	460	0	ENST00000377346.4:c.537del	p.Pro180LeufsTer37	p.P180Lfs*37	ENST00000377346	NM_005026.3	178	tGg/tg	5/24	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.344517857700693	2		460	735	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742462	17742462	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	76	419	0	ENST00000250003.3:c.644G>C	p.Gly215Ala	p.G215A	ENST00000250003	NM_002478.4	215	gGc/gCc	2/3	1	2	FACETS	0.714	0.626	0.808	0.714	0.626	0.808	SUBCLONAL	1	TRUE	1	0.344517857700693	2		419	618	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246012	46246012	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	23	377	0	ENST00000334344.6:c.4106G>A	p.Gly1369Asp	p.G1369D	ENST00000334344	NM_152641.2	1369	gGt/gAt	15/21	1	2	FACETS	0.348	0.271	0.437	0.348	0.271	0.437	SUBCLONAL	1	TRUE	1	0.344517857700693	2		377	384	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131735	2131735	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs45517308	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	111	556	0	ENST00000219476.3:c.3750C>A	p.Tyr1250Ter	p.Y1250*	ENST00000219476	NM_000548.3	1250	taC/taA	31/42	1	2	FACETS	0.751	0.675	0.832	0.751	0.675	0.832	SUBCLONAL	1	TRUE	1	0.344517857700693	2		556	858	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778798	3778798	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	126	529	0	ENST00000262367.5:c.6250C>T	p.Gln2084Ter	p.Q2084*	ENST00000262367	NM_004380.2	2084	Cag/Tag	31/31	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.344517857700693	2		529	728	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842096	3842096	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	63	262	0	ENST00000262367.5:c.1217-1G>T		p.X406_splice	ENST00000262367	NM_004380.2	406			1	2	FACETS	0.957	0.832	1	0.957	0.832	1	CLONAL	1	TRUE	1	0.344517857700693	2		262	382	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828597	72828609	+	frameshift_variant	Frame_Shift_Del	DEL	GTAGATACTTCTG	GTAGATACTTCTG	-	novel	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	100	466	0	ENST00000268489.5:c.7972_7984del	p.Gln2658TrpfsTer19	p.Q2658Wfs*19	ENST00000268489	NM_006885.3	2658	CAGAAGTATCTACtg/tg	9/10	1	2	FACETS	0.884	0.79	0.983	0.884	0.79	0.983	CLONAL	1	TRUE	1	0.344517857700693	2		466	657	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964819	15964819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	100	418	2	ENST00000268712.3:c.5777C>T	p.Thr1926Ile	p.T1926I	ENST00000268712	NM_006311.3	1926	aCc/aTc	37/46	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.344517857700693	2		420	558	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866345	37866345	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779346332	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	44	370	0	ENST00000269571.5:c.650G>A	p.Arg217His	p.R217H	ENST00000269571		217	cGc/cAc	6/27	1	2	FACETS	0.532	0.446	0.627	0.532	0.446	0.627	SUBCLONAL	1	TRUE	1	0.344517857700693	2		370	480	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40860046	40860046	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	96	397	0	ENST00000428826.2:c.1590del	p.Cys531ValfsTer9	p.C531Vfs*9	ENST00000428826		530	ccC/cc	15/21	1	2	FACETS	0.76	0.677	0.849	0.76	0.677	0.849	SUBCLONAL	1	TRUE	1	0.344517857700693	2		397	733	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804370	46804370	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	108	381	0	ENST00000290295.7:c.637T>C	p.Phe213Leu	p.F213L	ENST00000290295	NM_006361.5	213	Ttt/Ctt	2/2	1	2	FACETS	0.937	0.842	1	0.937	0.842	1	CLONAL	1	TRUE	1	0.344517857700693	2		381	669	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948519	54948519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	24	322	0	ENST00000312783.6:c.799G>A	p.Ala267Thr	p.A267T	ENST00000312783	NM_198436.1	267	Gct/Act	8/10	1	2	FACETS	0.388	0.304	0.485	0.388	0.304	0.485	SUBCLONAL	1	TRUE	1	0.344517857700693	2		322	359	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21350152	21350152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	149	499	0	ENST00000215739.8:c.2060C>T	p.Ala687Val	p.A687V	ENST00000215739	NM_006767.3	687	gCc/gTc	17/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.344517857700693	2		499	814	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160303	22160303	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	85	391	0	ENST00000215832.6:c.328A>G	p.Thr110Ala	p.T110A	ENST00000215832	NM_002745.4	110	Aca/Gca	3/9	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.344517857700693	2		391	466	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574329	41574329	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	134	501	0	ENST00000263253.7:c.6614T>G	p.Met2205Arg	p.M2205R	ENST00000263253	NM_001429.3	2205	aTg/aGg	31/31	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.344517857700693	2		501	673	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254605	1254606	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	62	361	0	ENST00000310581.5:c.3172dup	p.Ala1058GlyfsTer119	p.A1058Gfs*119	ENST00000310581	NM_198253.2	1058	gcc/gGcc	15/16	1	2	FACETS	0.603	0.521	0.692	0.603	0.521	0.692	SUBCLONAL	1	TRUE	1	0.344517857700693	2		361	597	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141570562	141570562	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1224870621	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	139	502	0	ENST00000220592.5:c.566C>G	p.Ser189Cys	p.S189C	ENST00000220592	NM_012154.3	189	tCt/tGt	5/19	1	2	FACETS	0.977	0.89	1	0.977	0.89	1	CLONAL	1	TRUE	1	0.344517857700693	2		502	826	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133761000	133761001	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0058970-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	127	421	0	ENST00000318560.5:c.3323_3324delinsAG	p.Pro1108Gln	p.P1108Q	ENST00000318560	NM_005157.4	1108	cCA/cAG	11/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.344517857700693	2		421	657	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0058971-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	98	738	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.733638761012416	2		738	261	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610402	81610402	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058971-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	211	480	0	ENST00000298171.2:c.2000A>G	p.Tyr667Cys	p.Y667C	ENST00000298171	NM_000369.2	667	tAt/tGt	10/10	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.733638761012416	2		480	574	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0058971-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	193	768	16	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.733638761012416	2		784	480	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0058972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	118	378	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	1	2	FACETS	0.866	0.786	0.95	0.866	0.786	0.95	CLONAL	1	TRUE	1	0.561913262559452	2		378	485	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958177	2958177	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs939117796	NA	P-0058972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	270	399	0	ENST00000396946.4:c.2555G>A	p.Arg852Gln	p.R852Q	ENST00000396946	NM_032415.4	852	cGa/cAa	19/25	0.561913262559452	3	FACETS	0.986	0.933	1	0.986	0.933	1	CLONAL	2	TRUE	1	0.561913262559452	3		399	624	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119752	70119753	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	118	322	0	ENST00000245479.2:c.755dup	p.Lys253GlufsTer43	p.K253Efs*43	ENST00000245479	NM_000346.3	252	ctg/cTtg	3/3	0.310036891884191	1	FACETS	0.886	0.809	0.965	0.886	0.809	0.965	INDETERMINATE	1	TRUE	0	0.561913262559452	1		322	341	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579303	7579314	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCAACTGACCGT	GCAACTGACCGT	-	novel	NA	P-0058972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	114	340	0	ENST00000269305.4:c.373_375+9del		p.X125_splice	ENST00000269305	NM_001126112.2	125		4/11	0.554844262098573	1	FACETS	0.876	0.798	0.956	0.876	0.798	0.956	CLONAL	1	TRUE	0	0.561913262559452	1		340	333	SUCCESS
APC	324	MSKCC	GRCh37	5	112173898	112173898	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	150	466	0	ENST00000257430.4:c.2607del	p.Pro870GlnfsTer46	p.P870Qfs*46	ENST00000257430	NM_000038.5	869	aaT/aa	16/16	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.561913262559452	2		466	519	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963874	2963874	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058972-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	101	415	0	ENST00000396946.4:c.1933C>A	p.Leu645Met	p.L645M	ENST00000396946	NM_032415.4	645	Ctg/Atg	15/25	0.561913262559452	3	FACETS	0.828	0.742	0.919	0.414	0.371	0.46	CLONAL	1	TRUE	1	0.561913262559452	3		415	556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0058973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	100	495	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.257868634942887	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.257868634942887	1		495	581	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575195	48575195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	33	264	0	ENST00000342988.3:c.389C>T	p.Pro130Leu	p.P130L	ENST00000342988	NM_005359.5	130	cCa/cTa	3/12	1	2	FACETS	0.731	0.596	0.883	0.731	0.596	0.883	SUBCLONAL	1	TRUE	1	0.257868634942887	2		264	350	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184998	32184998	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	46	461	0	ENST00000375023.3:c.1670G>A	p.Ser557Asn	p.S557N	ENST00000375023	NM_004557.3	557	aGc/aAc	10/30	1	2	FACETS	0.559	0.47	0.658	0.559	0.47	0.658	SUBCLONAL	1	TRUE	1	0.257868634942887	2		461	638	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712526	43712526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767934572	NA	P-0058973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	42	476	0	ENST00000382044.4:c.4658C>T	p.Ser1553Leu	p.S1553L	ENST00000382044	NM_001141980.1	1553	tCg/tTg	21/28	0.156911483263326	2	FACETS	0.449	0.374	0.533	0.225	0.187	0.267	SUBCLONAL	1	TRUE	0	0.257868634942887	2		476	725	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102094423	102094423	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	81	389	0	ENST00000282441.5:c.1103C>T	p.Pro368Leu	p.P368L	ENST00000282441	NM_001130145.2	368	cCc/cTc	7/9	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.257868634942887	2		389	566	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136354	2136365	+	inframe_deletion	In_Frame_Del	DEL	ACTGCTGGCACG	ACTGCTGGCACG	-	novel	NA	P-0058973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	89	533	0	ENST00000219476.3:c.4824_4835del	p.Cys1609_Asp1612del	p.C1609_D1612del	ENST00000219476	NM_000548.3	1608	tACTGCTGGCACGat/tat	37/42	0.257868634942887	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.257868634942887	1		533	577	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110153	3110153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	31	394	0	ENST00000078429.4:c.143G>A	p.Gly48Asp	p.G48D	ENST00000078429	NM_002067.2	48	gGc/gAc	2/7	0.257868634942887	1	FACETS	0.563	0.455	0.684	0.563	0.455	0.684	SUBCLONAL	1	TRUE	0	0.257868634942887	1		394	372	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133531	55133531	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776121704	NA	P-0058973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	42	428	0	ENST00000257290.5:c.835G>A	p.Glu279Lys	p.E279K	ENST00000257290	NM_006206.4	279	Gag/Aag	6/23	1	2	FACETS	0.533	0.444	0.632	0.533	0.444	0.632	SUBCLONAL	1	TRUE	1	0.257868634942887	2		428	611	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157454233	157454233	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs767477226	NA	P-0058973-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	46	462	0	ENST00000346085.5:c.2443T>C	p.Ser815Pro	p.S815P	ENST00000346085	NM_020732.3	815	Tcg/Ccg	8/20	1	2	FACETS	0.589	0.495	0.692	0.589	0.495	0.692	SUBCLONAL	1	TRUE	1	0.257868634942887	2		462	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750600586	NA	P-0058974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	373	402	1	ENST00000269305.4:c.413C>T	p.Ala138Val	p.A138V	ENST00000269305	NM_001126112.2	138	gCc/gTc	5/11	0.612611943109276	1	FACETS	0.887	0.861	0.912	1	0.997	1	CLONAL	2	TRUE	0	0.612611943109276	1		403	476	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138473	11138473	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	989	312	0	ENST00000358026.2:c.3229C>T	p.Arg1077Ter	p.R1077*	ENST00000358026	NM_001128849.1	1077	Cga/Tga	24/36	0.612611943109276	6	FACETS	0.942	0.925	0.959	1	0.998	1	CLONAL	6	TRUE	1	0.612611943109276	6		312	1271	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927989	178927989	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	43	235	0	ENST00000263967.3:c.1267G>C	p.Ala423Pro	p.A423P	ENST00000263967	NM_006218.2	423	Gca/Cca	8/21	1	2	FACETS	0.253	0.211	0.299	0.253	0.211	0.299	SUBCLONAL	1	TRUE	1	0.612611943109276	2		235	555	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155219	55155219	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058974-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	118	395	0	ENST00000257290.5:c.2818A>G	p.Arg940Gly	p.R940G	ENST00000257290	NM_006206.4	940	Aga/Gga	21/23	0.497472797307976	1	FACETS	0.703	0.641	0.768	0.703	0.641	0.768	SUBCLONAL	1	TRUE	0	0.612611943109276	1		395	380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0058975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	333	447	0	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	0.829063426062385	2	FACETS	0.994	0.968	1	0.994	0.968	1	CLONAL	2	FALSE	0	0.852109951477284	2		447	393	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56870523	56870523	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	141	293	0	ENST00000308159.5:c.1793T>C	p.Ile598Thr	p.I598T	ENST00000308159	NM_014669.4	598	aTa/aCa	17/22	1	2	FACETS	0.935	0.863	1	0.935	0.863	1	CLONAL	1	FALSE	1	0.852109951477284	2		293	354	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703676	47703676	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1114167847	NA	P-0058975-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	97	336	0	ENST00000233146.2:c.2176A>G	p.Met726Val	p.M726V	ENST00000233146	NM_000251.2	726	Atg/Gtg	13/16	0.454910845643298	4	FACETS	1	0.932	1	0.524	0.471	0.581	INDETERMINATE	1	FALSE	2	0.852109951477284	4		336	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0058976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	222	773	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.566315744158449	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.566315744158449	1		773	495	SUCCESS
APC	324	MSKCC	GRCh37	5	112174835	112174835	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0058976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	116	360	0	ENST00000257430.4:c.3544A>T	p.Lys1182Ter	p.K1182*	ENST00000257430	NM_000038.5	1182	Aaa/Taa	16/16	1	2	FACETS	0.883	0.801	0.969	0.883	0.801	0.969	CLONAL	1	TRUE	1	0.566315744158449	2		360	464	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38946638	38946638	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	56	223	0	ENST00000357387.3:c.4331A>T	p.Tyr1444Phe	p.Y1444F	ENST00000357387	NM_152756.3	1444	tAt/tTt	33/38	1	2	FACETS	0.916	0.795	1	0.916	0.795	1	CLONAL	1	TRUE	1	0.566315744158449	2		223	216	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177822	56177822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1443173223	NA	P-0058976-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	148	466	0	ENST00000399503.3:c.2795C>T	p.Ala932Val	p.A932V	ENST00000399503	NM_005921.1	932	gCc/gTc	14/20	1	2	FACETS	0.922	0.846	1	0.922	0.846	1	CLONAL	1	TRUE	1	0.566315744158449	2		466	567	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024001	27024002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0058977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	31	339	0	ENST00000324856.7:c.1113dup	p.Gln372AlafsTer28	p.Q372Afs*28	ENST00000324856	NM_006015.4	369	-/G	1/20	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.2	2		339	264	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348566	89348568	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs753054998	NA	P-0058977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	24	534	1	ENST00000301030.4:c.4382_4384del	p.Lys1461del	p.K1461del	ENST00000301030	NM_001256183.1	1461	aAGAga/aga	9/13	1	2	FACETS	0.491	0.384	0.615	0.491	0.384	0.615	SUBCLONAL	1	TRUE	1	0.2	2		535	489	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942751	44942751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763592177	NA	P-0058977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	30	349	0	ENST00000377967.4:c.3331C>T	p.Arg1111Cys	p.R1111C	ENST00000377967	NM_021140.2	1111	Cgt/Tgt	23/29	1	2	FACETS	0.785	0.633	0.958	0.785	0.633	0.958	CLONAL	1	TRUE	1	0.2	2		349	382	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835613	68835613	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	52	501	0	ENST00000261769.5:c.208del	p.Ser70ProfsTer13	p.S70Pfs*13	ENST00000261769	NM_004360.3	68	taT/ta	3/16	1	2	FACETS	0.974	0.829	1	0.974	0.829	1	CLONAL	1	TRUE	1	0.2	2		501	534	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437711	49437713	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs886049482	NA	P-0058977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	38	559	0	ENST00000301067.7:c.5257_5259del	p.Lys1753del	p.K1753del	ENST00000301067	NM_003482.3	1753	AAG/-	22/54	1	2	FACETS	0.754	0.623	0.901	0.754	0.623	0.901	CLONAL	1	TRUE	1	0.2	2		559	504	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417431	139417431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs979299004	NA	P-0058977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	52	643	0	ENST00000277541.6:c.613G>A	p.Val205Ile	p.V205I	ENST00000277541	NM_017617.3	205	Gtc/Atc	4/34	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.2	2		643	419	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37081742	37081742	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750192	NA	P-0058977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	50	387	0	ENST00000231790.2:c.1624C>T	p.Gln542Ter	p.Q542*	ENST00000231790	NM_000249.3	542	Cag/Tag	14/19	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.2	2		387	494	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0058977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	14	515	0	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	1	2	FACETS	0.34	0.244	0.456	0.34	0.244	0.456	SUBCLONAL	1	TRUE	1	0.2	2		515	412	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245608	46245609	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0058977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	42	511	0	ENST00000334344.6:c.3707dup	p.Phe1237IlefsTer4	p.F1237Ifs*4	ENST00000334344	NM_152641.2	1234	-/C	15/21	1	2	FACETS	0.852	0.711	1	0.852	0.711	1	CLONAL	1	TRUE	1	0.2	2		511	493	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001365	29001365	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755508412	NA	P-0058977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	27	446	0	ENST00000282397.4:c.1367C>T	p.Ala456Val	p.A456V	ENST00000282397	NM_002019.4	456	gCa/gTa	10/30	1	2	FACETS	0.56	0.445	0.693	0.56	0.445	0.693	SUBCLONAL	1	TRUE	1	0.2	2		446	482	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842751	68842752	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TG	TG	-	rs1555515296	NA	P-0058977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	33	369	0	ENST00000261769.5:c.687+1_687+2del		p.X229_splice	ENST00000261769	NM_004360.3	229		5/16	1	2	FACETS	0.859	0.7	1	0.859	0.7	1	CLONAL	1	TRUE	1	0.2	2		369	384	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845552	72845552	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	34	546	0	ENST00000268489.5:c.3788A>G	p.Asn1263Ser	p.N1263S	ENST00000268489	NM_006885.3	1263	aAc/aGc	7/10	1	2	FACETS	0.675	0.55	0.815	0.675	0.55	0.815	SUBCLONAL	1	TRUE	1	0.2	2		546	504	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375070	31375070	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759777486	NA	P-0058977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	47	521	0	ENST00000328111.2:c.467C>T	p.Thr156Met	p.T156M	ENST00000328111	NM_006892.3	156	aCg/aTg	6/23	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.2	2		521	464	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967893	93967893	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	24	320	0	ENST00000369303.4:c.2034del	p.Leu680CysfsTer29	p.L680Cfs*29	ENST00000369303	NM_004440.3	678	gaC/ga	11/17	1	2	FACETS	0.573	0.448	0.717	0.573	0.448	0.717	SUBCLONAL	1	TRUE	1	0.2	2		320	419	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942030	44942031	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0058977-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	24	294	0	ENST00000377967.4:c.3283_3284del	p.Lys1095ValfsTer7	p.K1095Vfs*7	ENST00000377967	NM_021140.2	1094	AAa/a	22/29	1	2	FACETS	0.622	0.487	0.778	0.622	0.487	0.778	SUBCLONAL	1	TRUE	1	0.2	2		294	386	SUCCESS
GNB1	2782	MSKCC	GRCh37	1	1737949	1737949	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058979-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	921	386	0	ENST00000378609.4:c.232A>G	p.Lys78Glu	p.K78E	ENST00000378609	NM_002074.3	78	Aaa/Gaa	6/12	0.83902561928691	6	FACETS	1	0.996	1			1	CLONAL	5	TRUE	NA	0.83902561928691	6		386	1116	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967270	134967270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374549505	NA	P-0058979-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	187	562	0	ENST00000398015.3:c.2609G>A	p.Arg870Gln	p.R870Q	ENST00000398015	NM_004441.4	870	cGg/cAg	14/16	0.195095432869584	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.83902561928691	0		562	432	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743537	46743537	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058979-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	355	521	0	ENST00000371975.4:c.1918G>T	p.Ala640Ser	p.A640S	ENST00000371975	NM_003579.3	640	Gca/Tca	17/18	0.83707145390442	3	FACETS	0.996	0.955	1	0.996	0.955	1	CLONAL	2	TRUE	1	0.83902561928691	3		521	603	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0058989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	20	366	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.804	0.618	1	0.804	0.618	1	CLONAL	1	TRUE	1	0.276552287126868	2		366	180	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0058989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	61	662	1	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.276552287126868	1	FACETS	0.799	0.69	0.916	0.799	0.69	0.916	CLONAL	1	TRUE	0	0.276552287126868	1		663	476	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974678	21974678	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs587778189	NA	P-0058989-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	72	761	0	ENST00000304494.5:c.149A>G	p.Gln50Arg	p.Q50R	ENST00000304494	NM_000077.4	50	cAg/cGg	1/3	0.276552287126868	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.276552287126868	1		761	405	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390867	139390868	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCCT	novel	NA	P-0058990-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	235	760	0	ENST00000277541.6:c.7319_7323dup	p.Asp2442ArgfsTer37	p.D2442Rfs*37	ENST00000277541	NM_017617.3	2441	-/AGGCA	34/34	1	2	FACETS	0.945	0.89	1	0.945	0.89	1	CLONAL	1	TRUE	1	0.888037527428993	2		760	560	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29686029	29686029	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0058992-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	44	337	0	ENST00000356175.3:c.8093C>G	p.Ser2698Ter	p.S2698*	ENST00000356175	NM_000267.3	2698	tCa/tGa	55/57	1	2	FACETS	0.825	0.695	0.967	0.825	0.695	0.967	CLONAL	1	TRUE	1	0.346364615578079	2		337	308	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378241	15378241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058992-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	80	517	0	ENST00000263377.2:c.545G>A	p.Gly182Glu	p.G182E	ENST00000263377	NM_058243.2	182	gGg/gAg	4/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.346364615578079	2		517	399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0058993-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	176	968	0	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	1	2	FACETS	0.836	0.772	0.902	0.836	0.772	0.902	CLONAL	1	TRUE	1	0.568496690654519	2		968	741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0058993-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	216	946	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.568496690654519	2		946	754	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101195	27101195	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058993-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	347	976	0	ENST00000324856.7:c.4477C>T	p.Gln1493Ter	p.Q1493*	ENST00000324856	NM_006015.4	1493	Cag/Tag	18/20	0.529433868735558	2	FACETS	0.915	0.875	0.956	0.915	0.875	0.956	CLONAL	2	TRUE	0	0.568496690654519	2		976	667	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150430	157150430	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057518951	NA	P-0058993-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	194	822	0	ENST00000346085.5:c.1612C>T	p.Gln538Ter	p.Q538*	ENST00000346085	NM_020732.3	538	Cag/Tag	2/20	0.116253221745734	3	FACETS	1	0.991	1	0.721	0.671	0.772	INDETERMINATE	1	TRUE	1	0.568496690654519	3		822	608	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872473	35872474	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058993-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	239	894	0	ENST00000216797.5:c.429dup	p.Gly144ArgfsTer10	p.G144Rfs*10	ENST00000216797	NM_020529.2	143	-/A	3/6	0.568496690654519	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.568496690654519	1		894	581	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562628	29562628	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0058993-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	76	553	0	ENST00000356175.3:c.3709-1G>T		p.X1237_splice	ENST00000356175	NM_000267.3	1237			1	2	FACETS	0.747	0.66	0.839	0.747	0.66	0.839	SUBCLONAL	1	TRUE	1	0.568496690654519	2		553	358	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439906	56439906	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058993-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	159	807	0	ENST00000407977.2:c.686C>G	p.Pro229Arg	p.P229R	ENST00000407977		229	cCg/cGg	6/10	1	2	FACETS	0.885	0.814	0.958	0.885	0.814	0.958	CLONAL	1	TRUE	1	0.568496690654519	2		807	632	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248160	110248160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058993-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	126	634	0	ENST00000374672.4:c.1312G>A	p.Ala438Thr	p.A438T	ENST00000374672	NM_004235.4	438	Gcc/Acc	5/5	0.534143815161847	2	FACETS	0.992	0.905	1	0.496	0.452	0.541	CLONAL	1	TRUE	0	0.568496690654519	2		634	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912664	NA	P-0058994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	411	512	0	ENST00000269305.4:c.1010G>C	p.Arg337Pro	p.R337P	ENST00000269305	NM_001126112.2	337	cGc/cCc	10/11	0.830873685014658	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.830873685014658	2		512	479	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263306	115263306	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	424	447	0	ENST00000438362.2:c.2044A>T	p.Ile682Phe	p.I682F	ENST00000438362	NM_001242891.1	682	Atc/Ttc	17/20	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.830873685014658	2		447	491	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133319	30133319	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs147961867	NA	P-0058994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	211	622	0	ENST00000263025.4:c.179A>G	p.Tyr60Cys	p.Y60C	ENST00000263025	NM_002746.2	60	tAt/tGt	2/9	1	2	FACETS	0.996	0.934	1	0.996	0.934	1	CLONAL	1	TRUE	1	0.830873685014658	2		622	510	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508475	29508475	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	438	417	0	ENST00000356175.3:c.622G>T	p.Ala208Ser	p.A208S	ENST00000356175	NM_000267.3	208	Gcg/Tcg	6/57	0.830873685014658	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.830873685014658	3		417	705	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59886042	59886042	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	291	589	0	ENST00000259008.2:c.704A>G	p.Lys235Arg	p.K235R	ENST00000259008	NM_032043.2	235	aAg/aGg	7/20	0.830873685014658	3	FACETS	1	0.948	1	0.503	0.474	0.533	CLONAL	1	TRUE	1	0.830873685014658	3		589	985	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281236	15281236	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	201	788	0	ENST00000263388.2:c.5020C>G	p.Leu1674Val	p.L1674V	ENST00000263388	NM_000435.2	1674	Ctc/Gtc	27/33	0.148348223929655	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.830873685014658	0		788	495	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630683	67630683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1676115862	NA	P-0058994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	303	529	0	ENST00000272342.5:c.869C>T	p.Thr290Ile	p.T290I	ENST00000272342	NM_019002.3	290	aCt/aTt	5/6	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.830873685014658	2		529	729	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449653	187449653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	462	561	0	ENST00000232014.4:c.227C>T	p.Pro76Leu	p.P76L	ENST00000232014	NM_001130845.1	76	cCt/cTt	4/10	1	2	FACETS	1	0.991	1	1	0.998	1	CLONAL	2	TRUE	1	0.830873685014658	2		561	542	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878165	48878166	+	frameshift_variant	Frame_Shift_Ins	INS	GG	GG	CTT	novel	NA	P-0058994-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	403	676	2	ENST00000267163.4:c.117_118delinsCTT	p.Glu40LeufsTer9	p.E40Lfs*9	ENST00000267163	NM_000321.2	39	ccGGag/ccCTTag	1/27	0.830873685014658	2	FACETS	0.957	0.93	0.982	0.957	0.93	0.982	CLONAL	2	TRUE	0	0.830873685014658	2		678	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0058995-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	180	1110	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.310955561578274	3	FACETS	0.97	0.904	1	0.97	0.904	1	CLONAL	3	TRUE	0	0.324607747840236	3		1111	443	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685315	89685315	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1554897280	NA	P-0058995-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	16	300	0	ENST00000371953.3:c.209+1G>T		p.X70_splice	ENST00000371953	NM_000314.4	70			0.324607747840236	4	FACETS	0.695	0.515	0.907	0.232	0.171	0.303	SUBCLONAL	1	TRUE	1	0.324607747840236	4		300	188	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717630	89717630	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554825168	NA	P-0058995-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	114	507	0	ENST00000371953.3:c.655C>T	p.Gln219Ter	p.Q219*	ENST00000371953	NM_000314.4	219	Cag/Tag	7/9	0.324607747840236	4	FACETS	0.991	0.904	1	0.991	0.904	1	CLONAL	3	TRUE	1	0.324607747840236	4		507	313	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058995-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	147	561	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	0.310955561578274	3	FACETS	0.938	0.867	1	0.938	0.867	1	CLONAL	3	TRUE	0	0.324607747840236	3		561	374	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0058995-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	44	388	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.324607747840236	3	FACETS	0.861	0.732	0.999	0.861	0.732	0.999	CLONAL	2	TRUE	1	0.324607747840236	3		388	183	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229295	36229295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058995-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	141	842	0	ENST00000222270.7:c.7985G>A	p.Arg2662Gln	p.R2662Q	ENST00000222270	NM_014727.1	2662	cGg/cAg	37/37	0.0965864921885242	4	FACETS	0.852	0.783	0.924	1	0.983	1	INDETERMINATE	3	TRUE	2	0.324607747840236	4		842	450	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409978	63409978	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058995-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	28	809	0	ENST00000330258.3:c.3189T>G	p.Ser1063Arg	p.S1063R	ENST00000330258	NM_152424.3	1063	agT/agG	2/2	0.172465074653154	2	FACETS	0.553	0.443	0.678	0.276	0.221	0.339	INDETERMINATE	1	TRUE	0	0.324607747840236	2		809	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0058996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	186	804	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.193416018062732	3	FACETS	1	0.965	1	1	0.993	1	CLONAL	5	TRUE	0	0.193416018062732	3		804	403	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0058996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	90	444	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	0.193416018062732	4	FACETS	1	0.951	1	0.748	0.666	0.835	CLONAL	2	TRUE	1	0.193416018062732	4		444	495	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0058996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	156	519	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.193416018062732	4	FACETS	0.928	0.859	0.998	1	0.99	1	CLONAL	5	TRUE	1	0.193416018062732	4		519	415	SUCCESS
APC	324	MSKCC	GRCh37	5	112174086	112174086	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs878853432	NA	P-0058996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	162	633	0	ENST00000257430.4:c.2795C>A	p.Ser932Ter	p.S932*	ENST00000257430	NM_000038.5	932	tCa/tAa	16/16	0.193416018062732	4	FACETS	0.963	0.894	1	1	0.991	1	CLONAL	5	TRUE	1	0.193416018062732	4		633	415	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235336	235336	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058996-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	25	730	0	ENST00000264932.6:c.1142C>T	p.Pro381Leu	p.P381L	ENST00000264932	NM_004168.2	381	cCt/cTt	9/15	0.193416018062732	4	FACETS	0.714	0.562	0.89	0.238	0.187	0.297	SUBCLONAL	1	TRUE	1	0.193416018062732	4		730	432	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	138	302	0				ENST00000310581	NM_198253.2	-/1132			0.131185385851809	5	FACETS	0.917	0.842	0.994	0.611	0.561	0.663	INDETERMINATE	2	TRUE	2	0.77035157987278	5		302	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0058997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	431	537	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	1	2	FACETS	1	0.995	1	1	0.998	1	CLONAL	2	TRUE	1	0.77035157987278	2		537	509	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058033	27058033	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	355	530	0	ENST00000324856.7:c.1741C>T	p.Gln581Ter	p.Q581*	ENST00000324856	NM_006015.4	581	Cag/Tag	3/20	0.25052985259422	4	FACETS	1	0.99	1	1	0.99	1	INDETERMINATE	2	TRUE	2	0.77035157987278	4		530	728	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919281	48919281	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs587778870	NA	P-0058997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	316	427	0	ENST00000267163.4:c.446C>G	p.Ser149Ter	p.S149*	ENST00000267163	NM_000321.2	149	tCa/tGa	4/27	0.77035157987278	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.77035157987278	2		427	375	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156201	106156201	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1397648058	NA	P-0058997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	107	754	0	ENST00000380013.4:c.1102G>T	p.Glu368Ter	p.E368*	ENST00000380013	NM_001127208.2	368	Gaa/Taa	3/11	1	2	FACETS	0.464	0.417	0.513	0.464	0.417	0.513	SUBCLONAL	1	TRUE	1	0.77035157987278	2		754	599	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162677	47162677	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	63	567	0	ENST00000409792.3:c.3449G>A	p.Arg1150Lys	p.R1150K	ENST00000409792	NM_014159.6	1150	aGa/aAa	3/21	0.500650552147853	3	FACETS	0.385	0.332	0.441	0.192	0.166	0.221	SUBCLONAL	1	TRUE	1	0.77035157987278	3		567	589	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47597242	47597242	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373425472	NA	P-0058997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	126	489	1	ENST00000430070.2:c.647C>T	p.Pro216Leu	p.P216L	ENST00000430070	NM_018095.4	216	cCg/cTg	3/4	1	2	FACETS	0.884	0.809	0.961	0.884	0.809	0.961	CLONAL	1	TRUE	1	0.77035157987278	2		490	370	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432024	49432024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	82	889	0	ENST00000301067.7:c.9115G>A	p.Asp3039Asn	p.D3039N	ENST00000301067	NM_003482.3	3039	Gat/Aat	34/54	0.131185385851809	5	FACETS	0.782	0.69	0.88	0.261	0.23	0.294	INDETERMINATE	1	TRUE	2	0.77035157987278	5		889	587	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306634	41306634	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	242	593	0	ENST00000373198.4:c.1025C>G	p.Ser342Cys	p.S342C	ENST00000373198	NM_133170.3	342	tCt/tGt	7/32	0.18705998590328	4	FACETS	1	0.985	1	1	0.985	1	INDETERMINATE	2	TRUE	2	0.77035157987278	4		593	498	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428236	72428236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	184	494	0	ENST00000477973.2:c.656C>T	p.Ser219Phe	p.S219F	ENST00000477973	NM_012234.5	219	tCt/tTt	3/4	0.500650552147853	3	FACETS	1	0.987	1	0.631	0.587	0.676	CLONAL	1	TRUE	1	0.77035157987278	3		494	524	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72864531	72864531	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	59	390	0	ENST00000325599.8:c.906G>C	p.Arg302Ser	p.R302S	ENST00000325599	NM_018130.2	302	agG/agC	8/11	0.500650552147853	3	FACETS	0.503	0.434	0.578	0.251	0.217	0.289	SUBCLONAL	1	TRUE	1	0.77035157987278	3		390	422	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955539	55955539	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0058997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	154	429	0	ENST00000263923.4:c.3404+2T>C		p.X1135_splice	ENST00000263923	NM_002253.2	1135			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.77035157987278	2		429	355	SUCCESS
HLA-C	3107	MSKCC	GRCh37	6	31237139	31237139	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	78	760	0	ENST00000376228.5:c.1072G>C	p.Asp358His	p.D358H	ENST00000376228	NM_002117.5	358	Gat/Cat	7/8	1	2	FACETS	0.368	0.323	0.415	0.368	0.323	0.415	SUBCLONAL	1	TRUE	1	0.77035157987278	2		760	551	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366456	118366456	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	25	572	0	ENST00000534358.1:c.5405A>G	p.Asp1802Gly	p.D1802G	ENST00000534358	NM_005933.3	1802	gAc/gGc	19/36	1	2	FACETS	0.147	0.115	0.183	0.147	0.115	0.183	SUBCLONAL	1	TRUE	1	0.77035157987278	2		572	442	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264326	30264326	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	40	405	0	ENST00000322652.5:c.61G>A	p.Gly21Arg	p.G21R	ENST00000322652	NM_015355.2	21	Ggg/Agg	1/16	0.131185385851809	5	FACETS	0.885	0.74	1	0.295	0.246	0.348	INDETERMINATE	1	TRUE	2	0.77035157987278	5		405	253	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152233	11152233	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058997-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	19	618	0	ENST00000358026.2:c.4517A>G	p.Asp1506Gly	p.D1506G	ENST00000358026	NM_001128849.1	1506	gAc/gGc	31/36	0.77035157987278	1	FACETS	0.11	0.083	0.142	0.11	0.083	0.142	SUBCLONAL	1	TRUE	0	0.77035157987278	1		618	275	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0058999-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	118	256	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.178049950729407	4	FACETS	1	0.956	1	1	0.956	1	INDETERMINATE	2	TRUE	2	0.345581851762523	4		256	423	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0058999-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	101	408	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.345581851762523	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.345581851762523	1		408	394	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188078	11188078	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058999-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	162	410	0	ENST00000361445.4:c.6016G>T	p.Val2006Phe	p.V2006F	ENST00000361445	NM_004958.3	2006	Gtc/Ttc	43/58	0.345581851762523	2	FACETS	0.971	0.898	1	0.971	0.898	1	CLONAL	2	TRUE	0	0.345581851762523	2		410	483	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858201	9858201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058999-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	98	783	0	ENST00000330684.3:c.3200G>A	p.Arg1067Gln	p.R1067Q	ENST00000330684	NM_001134407.1	1067	cGg/cAg	13/13	0.345581851762523	3	FACETS	1	0.956	1	0.566	0.506	0.629	CLONAL	1	TRUE	1	0.345581851762523	3		783	588	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100309	27100309	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058999-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	206	808	3	ENST00000324856.7:c.4022del	p.Asn1341IlefsTer140	p.N1341Ifs*140	ENST00000324856	NM_006015.4	1341	Aat/at	17/20	0.345581851762523	2	FACETS	0.969	0.905	1	0.969	0.905	1	CLONAL	2	TRUE	0	0.345581851762523	2		811	615	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593274	67593274	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0058999-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	152	607	6	ENST00000274335.5:c.2020A>T	p.Lys674Ter	p.K674*	ENST00000274335		674	Aaa/Taa	15/15	0.304884821919126	3	FACETS	0.946	0.871	1	0.946	0.871	1	CLONAL	2	TRUE	1	0.345581851762523	3		613	545	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129256	152129256	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058999-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	140	773	4	ENST00000206249.3:c.209C>T	p.Ala70Val	p.A70V	ENST00000206249	NM_000125.3	70	gCg/gTg	1/8	0.178049950729407	4	FACETS	1	0.977	1	1	0.977	1	INDETERMINATE	2	TRUE	2	0.345581851762523	4		777	460	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771163	161771163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755627153	NA	P-0058999-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	116	562	6	ENST00000366898.1:c.1366G>A	p.Val456Ile	p.V456I	ENST00000366898	NM_004562.2	456	Gtc/Atc	12/12	0.178049950729407	4	FACETS	0.907	0.822	0.996	0.907	0.822	0.996	INDETERMINATE	2	TRUE	2	0.345581851762523	4		568	498	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0059000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	236	404	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.809	0.756	0.864	0.809	0.756	0.864	CLONAL	1	TRUE	1	0.623257529546385	2		404	936	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0059000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	144	294	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	0.896	0.822	0.972	0.896	0.822	0.972	CLONAL	1	TRUE	1	0.623257529546385	2		294	516	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0059000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	176	609	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	0.766	0.708	0.827	0.766	0.708	0.827	SUBCLONAL	1	TRUE	1	0.623257529546385	2		609	737	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899079	40899079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs951719751	NA	P-0059000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	146	402	0	ENST00000373198.4:c.2191G>A	p.Ala731Thr	p.A731T	ENST00000373198	NM_133170.3	731	Gcc/Acc	14/32	1	2	FACETS	0.911	0.837	0.988	0.911	0.837	0.988	CLONAL	1	TRUE	1	0.623257529546385	2		402	514	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216477	108216477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587782558	NA	P-0059000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	78	306	1	ENST00000278616.4:c.8432del	p.Lys2811SerfsTer46	p.K2811Sfs*46	ENST00000278616	NM_000051.3	2809	cAa/ca	58/63	1	2	FACETS	0.77	0.683	0.862	0.77	0.683	0.862	SUBCLONAL	1	TRUE	1	0.623257529546385	2		307	325	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952086	178952086	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	83	517	0	ENST00000263967.3:c.3141T>A	p.His1047Gln	p.H1047Q	ENST00000263967	NM_006218.2	1047	caT/caA	21/21	1	2	FACETS	0.373	0.328	0.42	0.373	0.328	0.42	SUBCLONAL	1	TRUE	1	0.623257529546385	2		517	715	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0059000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	138	338	0	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	0.648	0.591	0.708	0.648	0.591	0.708	SUBCLONAL	1	TRUE	1	0.623257529546385	2		338	683	SUCCESS
APC	324	MSKCC	GRCh37	5	112177864	112177864	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs775076289	NA	P-0059000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	165	513	0	ENST00000257430.4:c.6579del	p.Val2194PhefsTer5	p.V2194Ffs*5	ENST00000257430	NM_000038.5	2191	ggA/gg	16/16	1	2	FACETS	0.795	0.732	0.86	0.795	0.732	0.86	SUBCLONAL	1	TRUE	1	0.623257529546385	2		513	666	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692886	89692886	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	87	286	0	ENST00000371953.3:c.370T>A	p.Cys124Ser	p.C124S	ENST00000371953	NM_000314.4	124	Tgt/Agt	5/9	1	2	FACETS	0.886	0.793	0.984	0.886	0.793	0.984	CLONAL	1	TRUE	1	0.623257529546385	2		286	315	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	247	791	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	0.797	0.746	0.85	0.797	0.746	0.85	SUBCLONAL	1	TRUE	1	0.623257529546385	2		791	994	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652330	206652330	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1385	101	773	2	ENST00000367120.3:c.1042del	p.Arg348AspfsTer32	p.R348Dfs*32	ENST00000367120	NM_014002.3	346	gCc/gc	10/22	0.546516852422784	4	FACETS	0.354	0.315	0.396	0.118	0.105	0.132	SUBCLONAL	1	TRUE	1	0.623257529546385	4		775	1486	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831063	72831063	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	223	653	0	ENST00000268489.5:c.5518C>T	p.Gln1840Ter	p.Q1840*	ENST00000268489	NM_006885.3	1840	Cag/Tag	9/10	1	2	FACETS	0.858	0.8	0.917	0.858	0.8	0.917	CLONAL	1	TRUE	1	0.623257529546385	2		653	834	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942035	71942035	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0059000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	75	822	0	ENST00000298229.2:c.1301-2A>G		p.X434_splice	ENST00000298229	NM_001567.3	434			1	2	FACETS	0.258	0.225	0.294	0.258	0.225	0.294	SUBCLONAL	1	TRUE	1	0.623257529546385	2		822	932	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68878207	68878207	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34829418	NA	P-0059000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	205	599	0	ENST00000487270.1:c.920G>A	p.Arg307Gln	p.R307Q	ENST00000487270	NM_133509.3	307	cGg/cAg	9/11	1	2	FACETS	0.794	0.738	0.853	0.794	0.738	0.853	SUBCLONAL	1	TRUE	1	0.623257529546385	2		599	828	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774954	73774954	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	118	377	0	ENST00000254810.4:c.219G>T	p.Arg73Ser	p.R73S	ENST00000254810	NM_005324.3	73	agG/agT	3/4	1	2	FACETS	0.759	0.688	0.833	0.759	0.688	0.833	SUBCLONAL	1	TRUE	1	0.623257529546385	2		377	499	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46587790	46587791	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0059000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	144	495	1	ENST00000263734.3:c.475dup	p.Ser159LysfsTer52	p.S159Kfs*52	ENST00000263734	NM_001430.4	156	-/A	5/16	1	2	FACETS	0.715	0.654	0.779	0.715	0.654	0.779	SUBCLONAL	1	TRUE	1	0.623257529546385	2		496	646	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31421453	31421453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	168	492	0	ENST00000344624.3:c.3451G>A	p.Asp1151Asn	p.D1151N	ENST00000344624		1151	Gac/Aac	27/33	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.623257529546385	2		492	517	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569275	67569275	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	181	560	0	ENST00000274335.5:c.392T>C	p.Leu131Pro	p.L131P	ENST00000274335		131	cTt/cCt	2/15	1	2	FACETS	0.845	0.782	0.91	0.845	0.782	0.91	CLONAL	1	TRUE	1	0.623257529546385	2		560	687	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921121	50921121	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	34	460	0	ENST00000440232.2:c.3241A>T	p.Met1081Leu	p.M1081L	ENST00000440232	NM_002691.3	1081	Atg/Ttg	27/27	1	2	FACETS	0.186	0.151	0.225	0.186	0.151	0.225	SUBCLONAL	1	TRUE	1	0.623257529546385	2		460	586	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372284	55372284	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs746754190	NA	P-0059000-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	100	921	0	ENST00000297316.4:c.974A>G	p.His325Arg	p.H325R	ENST00000297316	NM_022454.3	325	cAc/cGc	2/2	1	2	FACETS	0.292	0.26	0.327	0.292	0.26	0.327	SUBCLONAL	1	TRUE	1	0.623257529546385	2		921	1098	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76931731	76931731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059001-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	154	570	0	ENST00000373344.5:c.3799C>T	p.Pro1267Ser	p.P1267S	ENST00000373344	NM_000489.3	1267	Cct/Tct	10/35	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	FALSE	NA	0.685916477092917	2		570	332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747342068	NA	P-0059002-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	218	347	0	ENST00000269305.4:c.394A>G	p.Lys132Glu	p.K132E	ENST00000269305	NM_001126112.2	132	Aag/Gag	5/11	0.776384106999404	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.776384106999404	2		347	273	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874706	151874706	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059002-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	382	860	0	ENST00000262189.6:c.7832del	p.Pro2611LeufsTer36	p.P2611Lfs*36	ENST00000262189	NM_170606.2	2611	cCt/ct	38/59	0.776384106999404	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.776384106999404	2		860	471	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016603	12016603	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	125	471	0	ENST00000353533.5:c.739G>T	p.Asp247Tyr	p.D247Y	ENST00000353533	NM_003010.3	247	Gac/Tac	7/11	0.367382962829969	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.390332864356793	1		471	405	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797944	45797944	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557471507	NA	P-0059032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	51	724	0	ENST00000450313.1:c.827G>A	p.Gly276Glu	p.G276E	ENST00000450313	NM_012222.2	276	gGa/gAa	10/16	1	2	FACETS	0.295	0.249	0.345	0.295	0.249	0.345	SUBCLONAL	1	TRUE	1	0.390332864356793	2		724	887	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837979	156837979	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	145	697	1	ENST00000524377.1:c.512C>A	p.Pro171His	p.P171H	ENST00000524377	NM_002529.3	171	cCt/cAt	5/17	1	2	FACETS	0.876	0.799	0.956	0.876	0.799	0.956	CLONAL	1	TRUE	1	0.390332864356793	2		698	848	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578221	7578225	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTG	TTCTG	-	novel	NA	P-0059032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	53	631	0	ENST00000269305.4:c.624_628del	p.Asp208GlufsTer6	p.D208Efs*6	ENST00000269305	NM_001126112.2	208	gaCAGAAac/gaac	6/11	0.367382962829969	1	FACETS	0.336	0.286	0.391	0.336	0.286	0.391	SUBCLONAL	1	TRUE	0	0.390332864356793	1		631	651	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374983	45374983	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	109	538	0	ENST00000262160.6:c.860G>T	p.Gly287Val	p.G287V	ENST00000262160	NM_005901.5	287	gGa/gTa	8/11	0.367382962829969	1	FACETS	0.858	0.773	0.946	0.858	0.773	0.946	CLONAL	1	TRUE	0	0.390332864356793	1		538	524	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271862	15271862	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	93	791	0	ENST00000263388.2:c.6577C>A	p.Pro2193Thr	p.P2193T	ENST00000263388	NM_000435.2	2193	Ccc/Acc	33/33	1	2	FACETS	0.499	0.443	0.56	0.499	0.443	0.56	SUBCLONAL	1	TRUE	1	0.390332864356793	2		791	954	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968241	18968241	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1277776216	NA	P-0059032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	113	500	0	ENST00000262803.5:c.2081G>A	p.Arg694Gln	p.R694Q	ENST00000262803	NM_002911.3	694	cGg/cAg	15/24	1	2	FACETS	0.903	0.814	0.997	0.903	0.814	0.997	CLONAL	1	TRUE	1	0.390332864356793	2		500	641	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47492905	47492905	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	129	529	0	ENST00000404338.3:c.4009A>C	p.Met1337Leu	p.M1337L	ENST00000404338	NM_004491.4	1337	Atg/Ctg	4/6	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.390332864356793	2		529	659	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394390	162394390	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059032-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	105	494	0	ENST00000366898.1:c.678G>T	p.Leu226Phe	p.L226F	ENST00000366898	NM_004562.2	226	ttG/ttT	6/12	1	2	FACETS	0.853	0.765	0.945	0.853	0.765	0.945	CLONAL	1	TRUE	1	0.390332864356793	2		494	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782620	NA	P-0059033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	381	574	0	ENST00000269305.4:c.427G>A	p.Val143Met	p.V143M	ENST00000269305	NM_001126112.2	143	Gtg/Atg	5/11	0.770803977985719	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.770803977985719	1		574	572	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934265	48934265	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0059033-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	131	276	0	ENST00000267163.4:c.718+2T>G		p.X240_splice	ENST00000267163	NM_000321.2	240			0.770803977985719	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.770803977985719	1		276	188	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877972	151877972	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059034-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	212	605	0	ENST00000262189.6:c.6973C>T	p.Gln2325Ter	p.Q2325*	ENST00000262189	NM_170606.2	2325	Cag/Tag	36/59	1	2	FACETS	0.888	0.829	0.949	0.888	0.829	0.949	CLONAL	1	TRUE	1	0.68	2		605	702	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428071	49428071	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059034-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	206	637	0	ENST00000301067.7:c.10519C>T	p.Gln3507Ter	p.Q3507*	ENST00000301067	NM_003482.3	3507	Cag/Tag	38/54	1	2	FACETS	0.919	0.857	0.983	0.919	0.857	0.983	CLONAL	1	TRUE	1	0.68	2		637	659	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939259	71939259	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059034-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	203	692	0	ENST00000298229.2:c.208C>G	p.Arg70Gly	p.R70G	ENST00000298229	NM_001567.3	70	Cgc/Ggc	2/28	1	2	FACETS	0.816	0.759	0.874	0.816	0.759	0.874	CLONAL	1	TRUE	1	0.68	2		692	732	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431680	49431680	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059034-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	190	793	0	ENST00000301067.7:c.9459del	p.Leu3154Ter	p.L3154*	ENST00000301067	NM_003482.3	3153	ggG/gg	34/54	1	2	FACETS	0.839	0.779	0.901	0.839	0.779	0.901	CLONAL	1	TRUE	1	0.68	2		793	666	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860155	151860155	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059034-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	232	691	1	ENST00000262189.6:c.10507C>T	p.Gln3503Ter	p.Q3503*	ENST00000262189	NM_170606.2	3503	Cag/Tag	43/59	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.68	2		692	681	SUCCESS
SMARCA2	6595	MSKCC	GRCh37	9	2086950	2086950	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs281875188	NA	P-0059034-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	263	634	0	ENST00000349721.2:c.2648C>T	p.Pro883Leu	p.P883L	ENST00000349721	NM_003070.3	883	cCg/cTg	18/34	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.68	2		634	732	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390711	139390714	+	frameshift_variant	Frame_Shift_Del	DEL	CAGG	CAGG	-	novel	NA	P-0059034-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	270	783	0	ENST00000277541.6:c.7477_7480del	p.Pro2493TrpfsTer95	p.P2493Wfs*95	ENST00000277541	NM_017617.3	2493	CCTGtg/tg	34/34	1	2	FACETS	0.994	0.936	1	0.994	0.936	1	CLONAL	1	TRUE	1	0.68	2		783	799	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061220	38061225	+	inframe_deletion	In_Frame_Del	DEL	CGTTCT	CGTTCT	-	novel	NA	P-0059036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	106	356	0	ENST00000250448.2:c.764_769del	p.Glu255_Asn256del	p.E255_N256del	ENST00000250448	NM_004496.3	255	gAGAACGgc/ggc	2/2	1	2	FACETS	0.922	0.839	1	1	0.988	1	CLONAL	2	TRUE	1	0.388262539109271	2		356	296	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47425584	47425584	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	20	243	0	ENST00000404338.3:c.3652A>G	p.Ile1218Val	p.I1218V	ENST00000404338	NM_004491.4	1218	Att/Gtt	1/6	1	2	FACETS	0.305	0.233	0.389	0.305	0.233	0.389	SUBCLONAL	1	TRUE	1	0.388262539109271	2		243	338	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426120	49426120	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	G	G	TT	novel	NA	P-0059036-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	23	413	0	ENST00000301067.7:c.12368delinsAA	p.Ser4123Ter	p.S4123*	ENST00000301067	NM_003482.3	4123	tCa/tAAa	39/54	1	2	FACETS	0.338	0.263	0.424	0.338	0.263	0.424	SUBCLONAL	1	TRUE	1	0.388262539109271	2		413	351	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870815	12870833	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGATGGACGCCAGGCAG	GCGGATGGACGCCAGGCAG	-	novel	NA	P-0059037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	108	579	0	ENST00000228872.4:c.47_65del	p.Met16SerfsTer20	p.M16Sfs*20	ENST00000228872	NM_004064.3	14	gaGCGGATGGACGCCAGGCAG/ga	1/3	0.29469334453622	4	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.321154186328814	4		579	676	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205592	38205592	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059037-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	31	505	0	ENST00000317025.8:c.98C>A	p.Ala33Asp	p.A33D	ENST00000317025	NM_023034.1	33	gCc/gAc	2/24	1	2	FACETS	0.39	0.315	0.475	0.39	0.315	0.475	SUBCLONAL	1	TRUE	1	0.321154186328814	2		505	495	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	150	302	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.91	0.841	0.98	0.91	0.841	0.98	CLONAL	1	TRUE	1	0.837065133210505	2		302	394	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685300	89685300	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs878853936	NA	P-0059038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	49	154	0	ENST00000371953.3:c.195C>G	p.Tyr65Ter	p.Y65*	ENST00000371953	NM_000314.4	65	taC/taG	3/9	0.837065133210505	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.837065133210505	1		154	62	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390071	89390071	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760135022	NA	P-0059038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	171	489	0	ENST00000336596.2:c.820C>T	p.Arg274Ter	p.R274*	ENST00000336596	NM_005233.5	274	Cga/Tga	4/17	1	2	FACETS	0.961	0.894	1	0.961	0.894	1	CLONAL	1	TRUE	1	0.837065133210505	2		489	425	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519920	NA	P-0059038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	134	495	0	ENST00000397062.3:c.85G>A	p.Asp29Asn	p.D29N	ENST00000397062	NM_006164.4	29	Gat/Aat	2/5	1	2	FACETS	0.804	0.738	0.872	0.804	0.738	0.872	CLONAL	1	TRUE	1	0.837065133210505	2		495	398	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056165	27056165	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	225	610	0	ENST00000324856.7:c.1163del	p.Gly388AlafsTer3	p.G388Afs*3	ENST00000324856	NM_006015.4	387	atG/at	2/20	0.113133491688683	3	FACETS	1	0.99	1	0.638	0.598	0.678	INDETERMINATE	1	TRUE	1	0.837065133210505	3		610	598	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087524	27087524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	317	871	0	ENST00000324856.7:c.2098G>A	p.Val700Ile	p.V700I	ENST00000324856	NM_006015.4	700	Gtt/Att	5/20	0.113133491688683	3	FACETS	1	0.994	1	0.712	0.675	0.748	INDETERMINATE	1	TRUE	1	0.837065133210505	3		871	755	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089777	27089777	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0059038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	280	674	0	ENST00000324856.7:c.2732+1G>C		p.X911_splice	ENST00000324856	NM_006015.4	911			0.113133491688683	3	FACETS	0.793	0.752	0.835	0.793	0.752	0.835	INDETERMINATE	2	TRUE	1	0.837065133210505	3		674	598	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243904	41243904	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786203310	NA	P-0059038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	232	655	0	ENST00000357654.3:c.3644A>G	p.Asn1215Ser	p.N1215S	ENST00000357654	NM_007294.3	1215	aAc/aGc	10/23	1	2	FACETS	0.855	0.802	0.909	0.855	0.802	0.909	CLONAL	1	TRUE	1	0.837065133210505	2		655	648	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007565	62007565	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	316	849	0	ENST00000392795.3:c.302A>G	p.Gln101Arg	p.Q101R	ENST00000392795	NM_001039933.1	101	cAg/cGg	3/6	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.837065133210505	2		849	711	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157519944	157519944	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs886044620	NA	P-0059038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	206	544	0	ENST00000346085.5:c.4014-1G>A		p.X1338_splice	ENST00000346085	NM_020732.3	1338			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.837065133210505	2		544	442	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197047	123197047	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059038-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	87	321	0	ENST00000218089.9:c.1814del	p.Leu605Ter	p.L605*	ENST00000218089	NM_001042749.1	605	Tta/ta	19/35	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.837065133210505	2		321	201	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0059039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	36	425	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.42	2		425	148	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914723	39914723	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	18	236	0	ENST00000378444.4:c.4639C>T	p.Arg1547Ter	p.R1547*	ENST00000378444	NM_001123385.1	1547	Cga/Tga	12/15	0.3	2	FACETS	0.449	0.339	0.577	0.224	0.169	0.289	SUBCLONAL	1	TRUE	0	0.42	2		236	191	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467838	99467839	+	missense_variant	Missense_Mutation	DNP	GC	GC	CA	novel	NA	P-0059039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	64	592	0	ENST00000268035.6:c.2707_2708delinsCA	p.Ala903His	p.A903H	ENST00000268035	NM_000875.3	903	GCc/CAc	13/21	1	2	FACETS	0.499	0.432	0.572	0.499	0.432	0.572	SUBCLONAL	1	TRUE	1	0.42	2		592	611	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39021147	39021147	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059039-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	25	321	0	ENST00000357387.3:c.189T>A	p.Phe63Leu	p.F63L	ENST00000357387	NM_152756.3	63	ttT/ttA	3/38	1	2	FACETS	0.992	0.817	1	1	0.957	1	CLONAL	2	TRUE	1	0.42	2		321	60	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0059040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	10	259	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.249672771252033	4	FACETS	1	0.694	1	0.337	0.231	0.466	CLONAL	1	TRUE	1	0.34	4		259	78	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0059040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	236	885	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.303625778568122	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.34	3		885	489	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057988	27057988	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	136	801	0	ENST00000324856.7:c.1696C>T	p.Gln566Ter	p.Q566*	ENST00000324856	NM_006015.4	566	Cag/Tag	3/20	0.303625778568122	3	FACETS	0.828	0.756	0.903	0.828	0.756	0.903	CLONAL	2	TRUE	1	0.34	3		801	565	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099283	157099283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	135	783	0	ENST00000346085.5:c.220G>A	p.Glu74Lys	p.E74K	ENST00000346085	NM_020732.3	74	Gaa/Aaa	1/20	0.274537241722689	2	FACETS	0.88	0.806	0.957	0.88	0.806	0.957	CLONAL	2	TRUE	0	0.34	2		783	451	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911475	131911475	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786201699	NA	P-0059040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	30	364	0	ENST00000265335.6:c.220C>G	p.Gln74Glu	p.Q74E	ENST00000265335		74	Caa/Gaa	3/25	0.220659594138416	3	FACETS	1	0.913	1	1	0.913	1	CLONAL	2	TRUE	1	0.34	3		364	88	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0059040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	44	431	0				ENST00000310581	NM_198253.2	-/1132			0.220659594138416	3	FACETS	1	0.93	1	0.594	0.502	0.694	CLONAL	1	TRUE	1	0.34	3		431	255	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522089	157522089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	100	818	0	ENST00000346085.5:c.4361C>T	p.Ser1454Leu	p.S1454L	ENST00000346085	NM_020732.3	1454	tCg/tTg	18/20	0.274537241722689	2	FACETS	1	0.982	1	0.735	0.662	0.812	CLONAL	1	TRUE	0	0.34	2		818	400	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178941944	178941944	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	35	377	0	ENST00000263967.3:c.2263C>G	p.Leu755Val	p.L755V	ENST00000263967	NM_006218.2	755	Cta/Gta	15/21	0.249672771252033	4	FACETS	0.797	0.662	0.946	0.532	0.441	0.631	CLONAL	2	TRUE	1	0.34	4		377	173	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115757	8115757	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	41	665	0	ENST00000346208.3:c.1103T>C	p.Met368Thr	p.M368T	ENST00000346208		368	aTg/aCg	6/6	1	2	FACETS	0.791	0.662	0.933	0.791	0.662	0.933	CLONAL	1	TRUE	1	0.34	2		665	305	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982089	201982089	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	216	768	0	ENST00000359651.3:c.613C>G	p.Arg205Gly	p.R205G	ENST00000359651		205	Cgg/Ggg	5/8	0.303625778568122	5	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	2	0.34	5		768	592	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982413	201982413	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	111	729	0	ENST00000359651.3:c.792G>C	p.Lys264Asn	p.K264N	ENST00000359651		264	aaG/aaC	6/8	0.303625778568122	5	FACETS	0.761	0.685	0.841	0.507	0.456	0.561	SUBCLONAL	2	TRUE	2	0.34	5		729	648	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418658	49418658	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	94	655	0	ENST00000301067.7:c.15856G>T	p.Glu5286Ter	p.E5286*	ENST00000301067	NM_003482.3	5286	Gag/Tag	49/54	0.217831153037894	4	FACETS	0.765	0.684	0.852	0.765	0.684	0.852	SUBCLONAL	2	TRUE	2	0.34	4		655	484	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447101	49447137	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTCCTGCAGGTGCACATGGAACATTACAGTGTCCTC	TTTCCTGCAGGTGCACATGGAACATTACAGTGTCCTC	-	novel	NA	P-0059040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	49	702	0	ENST00000301067.7:c.840-33_843del		p.X280_splice	ENST00000301067	NM_003482.3	280		7/54	0.217831153037894	4	FACETS	1	0.945	1	0.623	0.53	0.724	CLONAL	1	TRUE	2	0.34	4		702	310	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41023260	41023260	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	38	468	0	ENST00000267868.3:c.904C>G	p.Leu302Val	p.L302V	ENST00000267868	NM_002875.4	302	Ctg/Gtg	10/10	1	2	FACETS	0.993	0.828	1	0.993	0.828	1	CLONAL	1	TRUE	1	0.34	2		468	225	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	397002	397002	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	37	630	0	ENST00000262320.3:c.24C>A	p.Phe8Leu	p.F8L	ENST00000262320	NM_003502.3	8	ttC/ttA	2/11	1	2	FACETS	0.608	0.502	0.726	0.608	0.502	0.726	SUBCLONAL	1	TRUE	1	0.34	2		630	358	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075202	16075202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1311392972	NA	P-0059040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	100	618	0	ENST00000268712.3:c.350C>T	p.Ser117Phe	p.S117F	ENST00000268712	NM_006311.3	117	tCt/tTt	4/46	0.293620614087807	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	2	TRUE	0	0.34	2		618	287	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803641	1803641	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	249	831	0	ENST00000260795.2:c.819C>G	p.Phe273Leu	p.F273L	ENST00000260795		273	ttC/ttG	6/17	0.303625778568122	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.34	3		831	509	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176710887	176710887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	73	523	0	ENST00000439151.2:c.6109G>A	p.Asp2037Asn	p.D2037N	ENST00000439151	NM_022455.4	2037	Gat/Aat	20/23	0.220659594138416	3	FACETS	1	0.918	1	1	0.918	1	CLONAL	2	TRUE	1	0.34	3		523	241	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522269	157522276	+	frameshift_variant	Frame_Shift_Del	DEL	CTCACGTC	CTCACGTC	TTACGTT	novel	NA	P-0059040-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	103	773	1	ENST00000346085.5:c.4541_4548delinsTTACGTT	p.Ser1514PhefsTer65	p.S1514Ffs*65	ENST00000346085	NM_020732.3	1514	tCTCACGTC/tTTACGTT	18/20	0.274537241722689	2	FACETS	1	0.98	1	0.689	0.62	0.761	CLONAL	1	TRUE	0	0.34	2		774	440	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165701	185165701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059042-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	82	531	0	ENST00000265026.3:c.976C>T	p.Arg326Trp	p.R326W	ENST00000265026	NM_004721.4	326	Cgg/Tgg	5/14	0.232766988963842	1	FACETS	0.81	0.717	0.909	0.81	0.717	0.909	CLONAL	1	TRUE	0	0.356356087092997	1		531	467	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360895	118360895	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs782813188	NA	P-0059042-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	91	473	0	ENST00000534358.1:c.4627A>G	p.Lys1543Glu	p.K1543E	ENST00000534358	NM_005933.3	1543	Aaa/Gaa	13/36	1	2	FACETS	0.87	0.774	0.972	0.87	0.774	0.972	CLONAL	1	TRUE	1	0.356356087092997	2		473	587	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845623	68845623	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059042-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	163	550	0	ENST00000261769.5:c.869A>G	p.Asp290Gly	p.D290G	ENST00000261769	NM_004360.3	290	gAc/gGc	7/16	0.287601881805934	2	FACETS	0.805	0.743	0.869	0.805	0.743	0.869	CLONAL	2	TRUE	0	0.356356087092997	2		550	568	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117761	70117761	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059042-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	124	855	0	ENST00000245479.2:c.229G>T	p.Val77Phe	p.V77F	ENST00000245479	NM_000346.3	77	Gtc/Ttc	1/3	1	2	FACETS	0.913	0.827	1	0.913	0.827	1	CLONAL	1	TRUE	1	0.356356087092997	2		855	762	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030320	11030320	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059042-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	94	704	0	ENST00000327064.4:c.1070T>C	p.Val357Ala	p.V357A	ENST00000327064	NM_199141.1	357	gTg/gCg	9/16	1	2	FACETS	0.862	0.768	0.962	0.862	0.768	0.962	CLONAL	1	TRUE	1	0.356356087092997	2		704	612	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729867	41729867	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059042-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	33	698	0	ENST00000242208.4:c.662T>C	p.Phe221Ser	p.F221S	ENST00000242208	NM_002192.2	221	tTc/tCc	3/3	1	2	FACETS	0.353	0.287	0.428	0.353	0.287	0.428	SUBCLONAL	1	TRUE	1	0.356356087092997	2		698	525	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0059044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	317	495	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.558160985512619	3	FACETS	0.948	0.908	0.986	0.948	0.908	0.986	CLONAL	3	TRUE	0	0.558160985512619	3		495	511	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696598	47696598	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059044-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	440	551	0	ENST00000347630.2:c.350T>C	p.Met117Thr	p.M117T	ENST00000347630	NM_001007230.1	117	aTg/aCg	5/11	0.526992374694598	4	FACETS	0.999	0.968	1	0.999	0.968	1	CLONAL	4	TRUE	0	0.558160985512619	4		551	615	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692848	89692848	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	46	129	0	ENST00000371953.3:c.332G>A	p.Trp111Ter	p.W111*	ENST00000371953	NM_000314.4	111	tGg/tAg	5/9	0.386980467605687	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.386980467605687	1		129	148	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926888	112926888	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507546	NA	P-0059045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	12	499	0	ENST00000351677.2:c.1508G>T	p.Gly503Val	p.G503V	ENST00000351677	NM_002834.3	503	gGg/gTg	13/16	1	2	FACETS	0.114	0.079	0.157	0.114	0.079	0.157	SUBCLONAL	1	TRUE	1	0.386980467605687	2		499	545	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0059045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	52	570	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	1	2	FACETS	0.485	0.413	0.564	0.485	0.413	0.564	SUBCLONAL	1	TRUE	1	0.386980467605687	2		570	554	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845116	128845116	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059045-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	116	647	0	ENST00000249373.3:c.611del	p.Lys204ArgfsTer98	p.K204Rfs*98	ENST00000249373	NM_005631.4	204	Aag/ag	3/12	1	2	FACETS	0.998	0.902	1	0.998	0.902	1	CLONAL	1	TRUE	1	0.386980467605687	2		647	601	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0059046-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	73	374	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.602	0.529	0.68	0.602	0.529	0.68	SUBCLONAL	1	TRUE	1	0.612644015478567	2		374	396	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692940	89692940	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs869312779	NA	P-0059046-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	159	475	0	ENST00000371953.3:c.424del	p.Arg142GlyfsTer5	p.R142Gfs*5	ENST00000371953	NM_000314.4	142	Cgg/gg	5/9	0.40124154972434	2	FACETS	1	0.989	1	0.69	0.641	0.74	CLONAL	1	TRUE	0	0.612644015478567	2		475	376	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996756	100996757	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0059046-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	77	485	0	ENST00000325455.5:c.1770_1771del	p.Phe591Ter	p.F591*	ENST00000325455	NM_001202474.3	590	ttCTtt/tttt	2/8	1	2	FACETS	0.613	0.541	0.69	0.613	0.541	0.69	SUBCLONAL	1	TRUE	1	0.612644015478567	2		485	410	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359341	118359341	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059046-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	92	437	0	ENST00000534358.1:c.4345C>T	p.Gln1449Ter	p.Q1449*	ENST00000534358	NM_005933.3	1449	Caa/Taa	11/36	1	2	FACETS	0.719	0.642	0.799	0.719	0.642	0.799	SUBCLONAL	1	TRUE	1	0.612644015478567	2		437	418	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0059047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	120	425	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.278041615073972	3	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	1	0.31078662055928	3		425	431	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0059047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	129	508	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.288674262082738	3	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	1	0.31078662055928	3		508	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0059047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	155	400	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.0740812367850059	3	FACETS	1	0.969	1			1	INDETERMINATE	2	TRUE	NA	0.31078662055928	3		400	522	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201746	66201746	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	58	454	1	ENST00000273854.3:c.2756G>A	p.Arg919Gln	p.R919Q	ENST00000273854	NM_004439.5	919	cGa/cAa	16/18	0.288674262082738	3	FACETS	0.9	0.775	1	0.45	0.387	0.519	CLONAL	1	TRUE	1	0.31078662055928	3		455	479	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420001	152420001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763337967	NA	P-0059047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	137	592	0	ENST00000206249.3:c.1688C>T	p.Thr563Met	p.T563M	ENST00000206249	NM_000125.3	563	aCg/aTg	8/8	0.195649029746516	4	FACETS	0.925	0.844	1	0.925	0.844	1	CLONAL	2	TRUE	2	0.31078662055928	4		592	625	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295211	1295211	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0059047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	163	545	0				ENST00000310581	NM_198253.2	-/1132			0.295193316957267	2	FACETS	0.853	0.792	0.915	1	0.986	1	CLONAL	3	TRUE	0	0.31078662055928	2		545	410	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294226	11294226	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755081819	NA	P-0059047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	80	542	0	ENST00000361445.4:c.2305C>T	p.Arg769Cys	p.R769C	ENST00000361445	NM_004958.3	769	Cgc/Tgc	14/58	0.222272217694614	3	FACETS	1	0.924	1	0.532	0.469	0.6	CLONAL	1	TRUE	1	0.31078662055928	3		542	559	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245594	41245595	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs80357753	NA	P-0059047-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	72	487	0	ENST00000357654.3:c.1953dup	p.Lys652GlufsTer21	p.K652Efs*21	ENST00000357654	NM_007294.3	651	-/G	10/23	0.31078662055928	3	FACETS	1	0.908	1	0.523	0.457	0.593	CLONAL	1	TRUE	1	0.31078662055928	3		487	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0059048-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	360	359	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.368197608003889	5	FACETS	1	0.99	1	0.886	0.848	0.925	CLONAL	4	TRUE	0	0.368197608003889	5		359	685	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	48	302	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.988	0.848	1	0.988	0.848	1	CLONAL	1	TRUE	1	0.539763746094948	2		302	180	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258046	16258046	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	26	613	0	ENST00000375759.3:c.5311G>A	p.Glu1771Lys	p.E1771K	ENST00000375759	NM_015001.2	1771	Gag/Aag	11/15	1	2	FACETS	0.251	0.198	0.311	0.251	0.198	0.311	SUBCLONAL	1	TRUE	1	0.539763746094948	2		613	384	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726606	46726606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	22	623	0	ENST00000371975.4:c.685G>A	p.Glu229Lys	p.E229K	ENST00000371975	NM_003579.3	229	Gag/Aag	7/18	1	2	FACETS	0.218	0.168	0.276	0.218	0.168	0.276	SUBCLONAL	1	TRUE	1	0.539763746094948	2		623	374	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981825	201981826	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0059050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	111	610	0	ENST00000359651.3:c.538dup	p.His180ProfsTer16	p.H180Pfs*16	ENST00000359651		179	tac/taCc	4/8	1	2	FACETS	0.959	0.868	1	0.959	0.868	1	CLONAL	1	TRUE	1	0.539763746094948	2		610	429	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437417	49437417	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0059050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	52	522	0	ENST00000301067.7:c.5467+1G>C		p.X1823_splice	ENST00000301067	NM_003482.3	1823			0.306567151899737	4	FACETS	0.639	0.545	0.743	0.32	0.272	0.372	INDETERMINATE	1	TRUE	2	0.539763746094948	4		522	464	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437439	49437439	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	58	620	0	ENST00000301067.7:c.5446G>C	p.Glu1816Gln	p.E1816Q	ENST00000301067	NM_003482.3	1816	Gaa/Caa	23/54	0.306567151899737	4	FACETS	0.682	0.587	0.786	0.341	0.293	0.393	INDETERMINATE	1	TRUE	2	0.539763746094948	4		620	485	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480426	50480426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	152	466	0	ENST00000394963.4:c.388G>A	p.Asp130Asn	p.D130N	ENST00000394963	NM_003076.4	130	Gac/Aac	3/13	0.306567151899737	4	FACETS	1	0.958	1	1	0.958	1	INDETERMINATE	2	TRUE	2	0.539763746094948	4		466	412	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	207	341	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	0.306567151899737	4	FACETS	1	0.98	1	1	0.98	1	INDETERMINATE	2	TRUE	2	0.539763746094948	4		341	531	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495772	56495772	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	32	495	0	ENST00000267101.3:c.3962C>G	p.Ser1321Cys	p.S1321C	ENST00000267101	NM_001982.3	1321	tCt/tGt	28/28	0.306567151899737	4	FACETS	0.387	0.313	0.47	0.193	0.156	0.235	INDETERMINATE	1	TRUE	2	0.539763746094948	4		495	472	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061334	38061334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	112	610	3	ENST00000250448.2:c.655C>A	p.Arg219Ser	p.R219S	ENST00000250448	NM_004496.3	219	Cgc/Agc	2/2	0.101524150500417	4	FACETS	0.85	0.771	0.931	0.85	0.771	0.931	INDETERMINATE	2	TRUE	2	0.539763746094948	4		613	376	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43773125	43773125	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0059050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	37	470	0	ENST00000382044.4:c.467C>G	p.Ser156Ter	p.S156*	ENST00000382044	NM_001141980.1	156	tCa/tGa	5/28	1	2	FACETS	0.397	0.328	0.474	0.397	0.328	0.474	SUBCLONAL	1	TRUE	1	0.539763746094948	2		470	345	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	359979	359979	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	83	539	0	ENST00000262320.3:c.1110C>G	p.His370Gln	p.H370Q	ENST00000262320	NM_003502.3	370	caC/caG	4/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.539763746094948	2		539	272	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50788319	50788319	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	35	417	0	ENST00000398568.2:c.897C>G	p.Ile299Met	p.I299M	ENST00000398568	NM_001042412.1	299	atC/atG	5/18	1	2	FACETS	0.305	0.25	0.367	0.305	0.25	0.367	SUBCLONAL	1	TRUE	1	0.539763746094948	2		417	425	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47423457	47423457	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1358966033	NA	P-0059050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	46	454	0	ENST00000404338.3:c.1525G>A	p.Asp509Asn	p.D509N	ENST00000404338	NM_004491.4	509	Gat/Aat	1/6	0.539763746094948	5	FACETS	0.475	0.399	0.559	0.158	0.133	0.187	SUBCLONAL	1	TRUE	2	0.539763746094948	5		454	649	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424273	47424273	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1054531443	NA	P-0059050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	41	538	0	ENST00000404338.3:c.2341G>A	p.Asp781Asn	p.D781N	ENST00000404338	NM_004491.4	781	Gat/Aat	1/6	0.539763746094948	5	FACETS	0.397	0.33	0.473	0.132	0.11	0.158	SUBCLONAL	1	TRUE	2	0.539763746094948	5		538	692	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424476	47424476	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	36	552	0	ENST00000404338.3:c.2544G>C	p.Lys848Asn	p.K848N	ENST00000404338	NM_004491.4	848	aaG/aaC	1/6	0.539763746094948	5	FACETS	0.345	0.282	0.415	0.115	0.094	0.139	SUBCLONAL	1	TRUE	2	0.539763746094948	5		552	700	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39239373	39239373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	85	421	1	ENST00000402219.2:c.2284G>A	p.Glu762Lys	p.E762K	ENST00000402219	NM_005633.3	762	Gag/Aag	14/23	0.276015109999709	3	FACETS	1	0.959	1	0.58	0.517	0.646	INDETERMINATE	1	TRUE	1	0.539763746094948	3		422	345	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091855	29091855	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	51	99	0	ENST00000328354.6:c.1102G>C	p.Asp368His	p.D368H	ENST00000328354	NM_007194.3	368	Gat/Cat	11/15	0.193958989896816	2	FACETS	0.926	0.818	1	0.926	0.818	1	INDETERMINATE	2	TRUE	0	0.539763746094948	2		99	102	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722941	49722941	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0059050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	20	410	0	ENST00000449682.2:c.1388-2A>G		p.X463_splice	ENST00000449682	NM_020998.3	463			1	2	FACETS	0.334	0.256	0.424	0.334	0.256	0.424	SUBCLONAL	1	TRUE	1	0.539763746094948	2		410	222	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63898486	63898486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	85	687	0	ENST00000398590.3:c.212C>T	p.Ser71Leu	p.S71L	ENST00000398590	NM_001177387.1	71	tCg/tTg	3/14	1	2	FACETS	0.902	0.804	1	0.902	0.804	1	CLONAL	1	TRUE	1	0.539763746094948	2		687	349	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055756	152055756	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1283285486	NA	P-0059050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	22	265	0	ENST00000262189.6:c.166C>T	p.Arg56Ter	p.R56*	ENST00000262189	NM_170606.2	56	Cga/Tga	2/59	1	2	FACETS	0.263	0.204	0.332	0.263	0.204	0.332	SUBCLONAL	1	TRUE	1	0.539763746094948	2		265	310	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285609	38285609	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs762665767	NA	P-0059050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	97	572	0	ENST00000425967.3:c.544G>A	p.Val182Ile	p.V182I	ENST00000425967	NM_001174067.1	182	Gta/Ata	6/19	0.539763746094948	1	FACETS	0.983	0.89	1	0.983	0.89	1	CLONAL	1	TRUE	0	0.539763746094948	1		572	267	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90995015	90995015	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	33	373	0	ENST00000265433.3:c.106G>C	p.Glu36Gln	p.E36Q	ENST00000265433	NM_002485.4	36	Gaa/Caa	2/16	0.539763746094948	3	FACETS	0.365	0.297	0.442	0.183	0.148	0.221	SUBCLONAL	1	TRUE	1	0.539763746094948	3		373	425	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913381	NA	P-0059050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	151	609	2	ENST00000304494.5:c.322G>A	p.Asp108Asn	p.D108N	ENST00000304494	NM_000077.4	108	Gat/Aat	2/3	0.539763746094948	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.539763746094948	1		611	292	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786842	135786842	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	146	501	0	ENST00000298552.3:c.1027C>T	p.Gln343Ter	p.Q343*	ENST00000298552	NM_001162426.1	343	Caa/Taa	10/23	0.539763746094948	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.539763746094948	1		501	295	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519958	NA	P-0059050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	122	548	0	ENST00000481739.1:c.1280C>A	p.Ser427Tyr	p.S427Y	ENST00000481739	NM_002957.4	427	tCc/tAc	10/10	0.539763746094948	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.539763746094948	1		548	237	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152864466	152864466	+	synonymous_variant	Silent	SNP	G	G	A	rs1557027736	NA	P-0059050-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	31	359	0	ENST00000406277.2:c.60C>T	p.Pro20=	p.P20=	ENST00000406277	NM_152274.4	20	ccC/ccT	3/7	NA		FACETS		0.48	0.71				INDETERMINATE	1	TRUE	NA	0.539763746094948	2		359	195	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023909	27023923	+	inframe_deletion	In_Frame_Del	DEL	GCTGCGGCGGCGGCA	GCTGCGGCGGCGGCA	-	rs751352361	NA	P-0059051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	37	455	0	ENST00000324856.7:c.1029_1043del	p.Ala345_Ala349del	p.A345_A349del	ENST00000324856	NM_006015.4	339	GCTGCGGCGGCGGCA/-	1/20	0.189307827529234	2	FACETS	0.385	0.316	0.462	0.192	0.158	0.231	SUBCLONAL	1	TRUE	0	0.29	2		455	663	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150916403	150916403	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1304916332	NA	P-0059051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	64	345	0	ENST00000271640.5:c.883A>G	p.Ile295Val	p.I295V	ENST00000271640	NM_001145415.1	295	Att/Gtt	8/22	0.295302833339863	4	FACETS	0.949	0.822	1			1	CLONAL	1	TRUE	NA	0.29	4		345	600	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230492698	230492698	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367998194	NA	P-0059051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	47	401	0	ENST00000391860.1:c.356C>T	p.Pro119Leu	p.P119L	ENST00000391860	NM_001258311.1	119	cCc/cTc	2/7	0.173508892828447	4	FACETS	0.639	0.538	0.751	0.32	0.269	0.376	INDETERMINATE	1	TRUE	2	0.29	4		401	654	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964125	28964125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377395740	NA	P-0059051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	75	384	0	ENST00000282397.4:c.1777C>T	p.Arg593Trp	p.R593W	ENST00000282397	NM_002019.4	593	Cgg/Tgg	13/30	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.29	2		384	496	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822232	72822232	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	91	578	0	ENST00000268489.5:c.9943T>C	p.Phe3315Leu	p.F3315L	ENST00000268489	NM_006885.3	3315	Ttt/Ctt	10/10	0.279521546078266	2	FACETS	0.89	0.791	0.997	0.445	0.395	0.499	CLONAL	1	TRUE	0	0.29	2		578	705	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203436	NA	P-0059051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	298	463	0	ENST00000269305.4:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269305	NM_001126112.2	163	Tac/Cac	5/11	0.295302833339863	4	FACETS	1	0.944	1	1	0.944	1	CLONAL	3	TRUE	1	0.29	4		463	884	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181602	32181602	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs757338957	NA	P-0059051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	80	369	0	ENST00000375023.3:c.2183A>G	p.Glu728Gly	p.E728G	ENST00000375023	NM_004557.3	728	gAg/gGg	14/30	1	2	FACETS	0.94	0.828	1	0.94	0.828	1	CLONAL	1	TRUE	1	0.29	2		369	587	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974189	2974200	+	inframe_deletion	In_Frame_Del	DEL	TTGACCATTGGT	TTGACCATTGGT	-	novel	NA	P-0059051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	49	406	0	ENST00000396946.4:c.1405_1416del	p.Thr469_Gln472del	p.T469_Q472del	ENST00000396946	NM_032415.4	469	ACCAATGGTCAA/-	10/25	0.242358268392679	3	FACETS	0.583	0.493	0.682	0.194	0.164	0.228	SUBCLONAL	1	TRUE	0	0.29	3		406	664	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55267285	55268307	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCAGTCTGGCCTAAAATAGCTTGATATGCTGTGGATGGAAAATAAATGTGATCCCTCAAGAGGCATGAGGATTTCCAGGCAGTAGCCATACCTCCAAATTGTTTAATCTGGATTTAGATTGTTGGGTAGTCACATGCAGCAGCACAGTTAACAGTGTGTCCTCCTGTGGAAGTTGCCAGCACAGCCAGCCCTCTCACTTGCATGCATGCCCACCAGCCTTCTCACTTGCATGCATGCCCACTGGGTATGTGCTGTACTGGAGACGCCGGGGGTAGGGGCCCAGTCCCAACCCCAAATTCTTTAAAGCCTATTTTTCTAAGTTGCATCTGGTTTCCTACCTGAAGGAATGCTAAGGGTGGATGTTGAGTGAGGACCTTGGTGCAGGGCACCCTGCAGTCAGGATAGTTCATGGAGAGCAATTGTACAGACCCACACTGCTCCATCCCCTCAGGCGTAACACAGGATGCTGACCCCAGGAAGAGTGGGCGTAGAAAAACTAGAGGGCATTATTGTTATTCTGATTCAAATGTACAGTGCTGGCATGGTCTTTAAACAGTAACCAGTACTAGCTGGCCAAGACAGAAAAGTCTACCACAAAGACTTGGTTCTTTCATCACTTATTTGACTGGAAGTGTCGCATCACCAATGCCTTCTTTAAGCAATGCCATCTTTATCATTTCTTCCAGTGTTCTAATTGCACTGTTTTTTCTCATTCCTTCCCCAGGCTGGATGATAGACGCAGATAGTCGCCCAAAGTTCCGTGAGTTGATCATCGAATTCTCCAAAATGGCCCGAGACCCCCAGCGCTACCTTGTCATTCAGGTACAAATTGCAGTCTGTGCTTCCATTGGGAAGAGTCCCTCTAATGAGCATCTCATGTCACTGTGTTCTGTCACATGCCAGCCTGGCCTCCCTGTGTCCCAGATCGCATTATTAAACCCTCCAGCGCATTAGAGCAAGCCTCAGTAAGGCGCAGGCCACATCGTGAACTAAGCAGCATCCGTGAGTGGGGCCCACCCAACT	GCAGTCTGGCCTAAAATAGCTTGATATGCTGTGGATGGAAAATAAATGTGATCCCTCAAGAGGCATGAGGATTTCCAGGCAGTAGCCATACCTCCAAATTGTTTAATCTGGATTTAGATTGTTGGGTAGTCACATGCAGCAGCACAGTTAACAGTGTGTCCTCCTGTGGAAGTTGCCAGCACAGCCAGCCCTCTCACTTGCATGCATGCCCACCAGCCTTCTCACTTGCATGCATGCCCACTGGGTATGTGCTGTACTGGAGACGCCGGGGGTAGGGGCCCAGTCCCAACCCCAAATTCTTTAAAGCCTATTTTTCTAAGTTGCATCTGGTTTCCTACCTGAAGGAATGCTAAGGGTGGATGTTGAGTGAGGACCTTGGTGCAGGGCACCCTGCAGTCAGGATAGTTCATGGAGAGCAATTGTACAGACCCACACTGCTCCATCCCCTCAGGCGTAACACAGGATGCTGACCCCAGGAAGAGTGGGCGTAGAAAAACTAGAGGGCATTATTGTTATTCTGATTCAAATGTACAGTGCTGGCATGGTCTTTAAACAGTAACCAGTACTAGCTGGCCAAGACAGAAAAGTCTACCACAAAGACTTGGTTCTTTCATCACTTATTTGACTGGAAGTGTCGCATCACCAATGCCTTCTTTAAGCAATGCCATCTTTATCATTTCTTCCAGTGTTCTAATTGCACTGTTTTTTCTCATTCCTTCCCCAGGCTGGATGATAGACGCAGATAGTCGCCCAAAGTTCCGTGAGTTGATCATCGAATTCTCCAAAATGGCCCGAGACCCCCAGCGCTACCTTGTCATTCAGGTACAAATTGCAGTCTGTGCTTCCATTGGGAAGAGTCCCTCTAATGAGCATCTCATGTCACTGTGTTCTGTCACATGCCAGCCTGGCCTCCCTGTGTCCCAGATCGCATTATTAAACCCTCCAGCGCATTAGAGCAAGCCTCAGTAAGGCGCAGGCCACATCGTGAACTAAGCAGCATCCGTGAGTGGGGCCCACCCAACT	-	novel	NA	P-0059051-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	92	0	0	ENST00000275493.2:c.2849-724_2946+201del		p.X950_splice	ENST00000275493	NM_005228.3	950		24/28	0.295302833339863	107	FACETS	1	0.962	1	0.981	0.944	1	CLONAL	104	TRUE	1	0.29	107		0	99	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0059052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	194	556	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.48359670123757	3	FACETS	1	0.989	1	0.807	0.761	0.854	CLONAL	2	TRUE	0	0.582638063265166	3		556	355	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350599	89350599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	246	408	0	ENST00000301030.4:c.2351A>G	p.Glu784Gly	p.E784G	ENST00000301030	NM_001256183.1	784	gAg/gGg	9/13	0.582638063265166	3	FACETS	0.996	0.952	1	0.996	0.952	1	CLONAL	3	TRUE	0	0.582638063265166	3		408	365	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374925	149374925	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	179	679	0	ENST00000360632.3:c.169G>C	p.Asp57His	p.D57H	ENST00000360632	NM_015472.4	57	Gat/Cat	2/7	0.582638063265166	2	FACETS	0.988	0.93	1	0.988	0.93	1	CLONAL	2	TRUE	0	0.582638063265166	2		679	311	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181830	56181830	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059052-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	74	408	0	ENST00000399503.3:c.4054C>G	p.Gln1352Glu	p.Q1352E	ENST00000399503	NM_005921.1	1352	Cag/Gag	17/20	0.582638063265166	2	FACETS	0.914	0.809	1	0.457	0.404	0.512	CLONAL	1	TRUE	0	0.582638063265166	2		408	278	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0059053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	191	374	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		374	307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578376	7578379	+	frameshift_variant	Frame_Shift_Del	DEL	CTAT	CTAT	-	novel	NA	P-0059053-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	133	751	0	ENST00000269305.4:c.551_554del	p.Asp184AlafsTer62	p.D184Afs*62	ENST00000269305	NM_001126112.2	184	gATAGc/gc	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		751	291	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942685	48942685	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913301	NA	P-0059054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	17	359	0	ENST00000267163.4:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000267163	NM_000321.2	358	Cga/Tga	11/27	0.309499966367582	1	FACETS	0.876	0.663	1	0.876	0.663	1	CLONAL	1	TRUE	0	0.309499966367582	1		359	106	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17350532	17350532	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	25	502	0	ENST00000375499.3:c.578G>C	p.Ser193Thr	p.S193T	ENST00000375499	NM_003000.2	193	aGc/aCc	6/8	0.309499966367582	1	FACETS	0.44	0.347	0.547	0.44	0.347	0.547	SUBCLONAL	1	TRUE	0	0.309499966367582	1		502	310	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668640	52668640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	34	422	0	ENST00000394830.3:c.1279C>T	p.Pro427Ser	p.P427S	ENST00000394830	NM_018313.4	427	Ccc/Tcc	12/30	0.309499966367582	1	FACETS	0.8	0.669	0.941	1	0.957	1	CLONAL	2	TRUE	0	0.309499966367582	1		422	116	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0059054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	44	362	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.309499966367582	2		362	240	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205699	108205699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	22	413	0	ENST00000278616.4:c.8014G>A	p.Asp2672Asn	p.D2672N	ENST00000278616	NM_000051.3	2672	Gac/Aac	55/63	0.309499966367582	1	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	0	0.309499966367582	1		413	106	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205747	108205747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565540761	NA	P-0059054-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	28	468	0	ENST00000278616.4:c.8062G>A	p.Ala2688Thr	p.A2688T	ENST00000278616	NM_000051.3	2688	Gca/Aca	55/63	0.309499966367582	1	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	0	0.309499966367582	1		468	136	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041261	29041262	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0059055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	46	674	0	ENST00000282397.4:c.166dup	p.Glu56GlyfsTer5	p.E56Gfs*5	ENST00000282397	NM_002019.4	56	gaa/gGaa	3/30	0.545528733966283	5	FACETS	0.737	0.622	0.864	0.184	0.155	0.216	SUBCLONAL	1	TRUE	1	0.545528733966283	5		674	416	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190818	11190818	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	118	761	0	ENST00000361445.4:c.5381C>T	p.Ala1794Val	p.A1794V	ENST00000361445	NM_004958.3	1794	gCa/gTa	39/58	0.494788602532739	3	FACETS	0.918	0.841	0.996	0.918	0.841	0.996	CLONAL	2	TRUE	1	0.545528733966283	3		761	300	SUCCESS
ATM	472	MSKCC	GRCh37	11	108128239	108128240	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs587781658	NA	P-0059055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	35	403	0	ENST00000278616.4:c.2284_2285del	p.Leu762ValfsTer2	p.L762Vfs*2	ENST00000278616	NM_000051.3	761	aCT/a	15/63	0.545528733966283	1	FACETS	0.784	0.657	0.92	0.784	0.657	0.92	CLONAL	1	TRUE	0	0.545528733966283	1		403	119	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686964	37686964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1314353285	NA	P-0059055-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	159	701	0	ENST00000447079.4:c.3868C>T	p.Pro1290Ser	p.P1290S	ENST00000447079	NM_015083.1	1290	Ccc/Tcc	14/14	0.544355369217548	3	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	1	0.545528733966283	3		701	370	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0059080-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	130	409	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.524589182340701	2		409	448	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842428	68842428	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059080-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	147	428	0	ENST00000261769.5:c.491del	p.Pro164GlnfsTer51	p.P164Qfs*51	ENST00000261769	NM_004360.3	163	tgC/tg	4/16	0.505834179591698	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.524589182340701	1		428	386	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628239	187628239	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059080-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	115	413	0	ENST00000441802.2:c.2743G>T	p.Val915Leu	p.V915L	ENST00000441802	NM_005245.3	915	Gta/Tta	2/27	1	2	FACETS	0.902	0.817	0.991	0.902	0.817	0.991	CLONAL	1	TRUE	1	0.524589182340701	2		413	486	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059097-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	104	366	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.280861173813467	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.280861173813467	3		366	346	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974695	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691187	NA	P-0059097-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	57	501	0	ENST00000304494.5:c.132del	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	taC/ta	1/3	1	2	FACETS	0.946	0.814	1	0.946	0.814	1	CLONAL	1	TRUE	1	0.280861173813467	2		501	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0059097-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	70	556	0	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	0.259783703819649	1	FACETS	0.864	0.755	0.981	0.864	0.755	0.981	CLONAL	1	TRUE	0	0.280861173813467	1		556	496	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971023	21971045	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCCCCAGGCATCGCGCACGTC	CGGCCCCAGGCATCGCGCACGTC	-	novel	NA	P-0059097-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	48	485	0	ENST00000304494.5:c.313_335del	p.Asp105SerfsTer7	p.D105Sfs*7	ENST00000304494	NM_000077.4	105	GACGTGCGCGATGCCTGGGGCCGt/t	2/3	1	2	FACETS	0.753	0.637	0.88	0.753	0.637	0.88	SUBCLONAL	1	TRUE	1	0.280861173813467	2		485	454	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	67	425	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.827	0.722	0.939	0.827	0.722	0.939	CLONAL	1	TRUE	1	0.43	2		425	377	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781297	9781297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138090835	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	115	437	0	ENST00000377346.4:c.1802G>A	p.Arg601Gln	p.R601Q	ENST00000377346	NM_005026.3	601	cGg/cAg	14/24	1	2	FACETS	0.938	0.848	1	0.938	0.848	1	CLONAL	1	TRUE	1	0.43	2		437	570	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188512	11188512	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	43	407	2	ENST00000361445.4:c.5909A>G	p.Gln1970Arg	p.Q1970R	ENST00000361445	NM_004958.3	1970	cAg/cGg	42/58	1	2	FACETS	0.418	0.349	0.493	0.418	0.349	0.493	SUBCLONAL	1	TRUE	1	0.43	2		409	479	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366956	40366956	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	175	634	0	ENST00000397332.2:c.241G>A	p.Ala81Thr	p.A81T	ENST00000397332	NM_001033082.2	81	Gca/Aca	2/3	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.43	2		634	767	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511629	46511629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	66	301	0	ENST00000262741.5:c.1148G>A	p.Arg383His	p.R383H	ENST00000262741	NM_003629.3	383	cGt/cAt	9/10	1	2	FACETS	0.882	0.77	1	0.882	0.77	1	CLONAL	1	TRUE	1	0.43	2		301	348	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	150	578	5	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.949	0.869	1	0.949	0.869	1	CLONAL	1	TRUE	1	0.43	2		583	735	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533860	533860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	63	660	0	ENST00000451590.1:c.196G>A	p.Ala66Thr	p.A66T	ENST00000451590	NM_001130442.1	66	Gcc/Acc	3/5	1	2	FACETS	0.355	0.306	0.408	0.355	0.306	0.408	SUBCLONAL	1	TRUE	1	0.43	2		660	826	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633613	69633613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs901877047	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	119	371	0	ENST00000334134.2:c.89G>A	p.Gly30Asp	p.G30D	ENST00000334134	NM_005247.2	30	gGc/gAc	1/3	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.43	2		371	542	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201783	102201783	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs776315214	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	22	344	0	ENST00000263464.3:c.1135A>G	p.Thr379Ala	p.T379A	ENST00000263464	NM_001165.4	379	Act/Gct	6/9	1	2	FACETS	0.297	0.229	0.375	0.297	0.229	0.375	SUBCLONAL	1	TRUE	1	0.43	2		344	345	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343306	118343306	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	122	428	0	ENST00000534358.1:c.1432C>T	p.Arg478Ter	p.R478*	ENST00000534358	NM_005933.3	478	Cga/Tga	3/36	1	2	FACETS	0.887	0.803	0.974	0.887	0.803	0.974	CLONAL	1	TRUE	1	0.43	2		428	640	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505404	125505404	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	30	333	0	ENST00000428830.2:c.700del	p.Ile234SerfsTer6	p.I234Sfs*6	ENST00000428830	NM_001114121.2	232	Aaa/aa	7/14	1	2	FACETS	0.372	0.3	0.454	0.372	0.3	0.454	SUBCLONAL	1	TRUE	1	0.43	2		333	375	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641389	18641389	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1229278001	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	88	292	0	ENST00000266497.5:c.2393del	p.Asn798MetfsTer16	p.N798Mfs*16	ENST00000266497		796	ctA/ct	17/31	0.187027898016414	3	FACETS	1	0.967	1	0.614	0.547	0.684	INDETERMINATE	1	TRUE	1	0.43	3		292	405	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428256	49428256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201127814	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	138	572	0	ENST00000301067.7:c.10444C>T	p.Arg3482Trp	p.R3482W	ENST00000301067	NM_003482.3	3482	Cgg/Tgg	37/54	0.187027898016414	3	FACETS	0.976	0.889	1	0.488	0.444	0.534	INDETERMINATE	1	TRUE	1	0.43	3		572	799	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111886011	111886011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764533642	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	152	594	0	ENST00000341259.2:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000341259	NM_005475.2	545	Gag/Aag	8/8	0.187027898016414	3	FACETS	1	0.959	1	0.538	0.492	0.586	INDETERMINATE	1	TRUE	1	0.43	3		594	798	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	234	1032	7	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	0.187027898016414	3	FACETS	1	0.992	1	0.745	0.696	0.795	INDETERMINATE	1	TRUE	1	0.43	3		1039	888	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253240	133253240	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	92	361	0	ENST00000320574.5:c.802-1G>T		p.X268_splice	ENST00000320574	NM_006231.2	268			0.187027898016414	3	FACETS	1	0.91	1	0.512	0.456	0.571	INDETERMINATE	1	TRUE	1	0.43	3		361	508	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434477	110434477	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747968639	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	145	484	0	ENST00000375856.3:c.3924del	p.Pro1309ArgfsTer22	p.P1309Rfs*22	ENST00000375856	NM_003749.2	1308	ggG/gg	1/2	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.43	2		484	659	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007824	45007825	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	103	400	0	ENST00000558401.1:c.276dup	p.Thr93HisfsTer2	p.T93Hfs*2	ENST00000558401	NM_004048.2	91	acc/aCcc	2/4	1	2	FACETS	0.884	0.794	0.979	0.884	0.794	0.979	CLONAL	1	TRUE	1	0.43	2		400	542	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007833	45007834	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	101	407	0	ENST00000558401.1:c.285dup	p.Asp96ArgfsTer2	p.D96Rfs*2	ENST00000558401	NM_004048.2	94	gaa/gAaa	2/4	1	2	FACETS	0.878	0.787	0.974	0.878	0.787	0.974	CLONAL	1	TRUE	1	0.43	2		407	535	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576174	88576174	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs960610021	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	117	454	0	ENST00000360948.2:c.1499C>T	p.Thr500Ile	p.T500I	ENST00000360948	NM_001012338.2	500	aCt/aTt	13/19	1	2	FACETS	0.905	0.819	0.997	0.905	0.819	0.997	CLONAL	1	TRUE	1	0.43	2		454	601	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347734	347734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	67	464	0	ENST00000262320.3:c.1772G>A	p.Gly591Asp	p.G591D	ENST00000262320	NM_003502.3	591	gGc/gAc	6/11	1	2	FACETS	0.462	0.401	0.528	0.462	0.401	0.528	SUBCLONAL	1	TRUE	1	0.43	2		464	675	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124310	2124310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs936484229	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	50	508	0	ENST00000219476.3:c.2465C>T	p.Ala822Val	p.A822V	ENST00000219476	NM_000548.3	822	gCg/gTg	22/42	1	2	FACETS	0.319	0.27	0.373	0.319	0.27	0.373	SUBCLONAL	1	TRUE	1	0.43	2		508	729	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786682	3786682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780939128	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	143	432	0	ENST00000262367.5:c.4529C>T	p.Ala1510Val	p.A1510V	ENST00000262367	NM_004380.2	1510	gCg/gTg	27/31	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.43	2		432	610	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808012	3808013	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	88	395	0	ENST00000262367.5:c.3406_3407del	p.Ser1136HisfsTer32	p.S1136Hfs*32	ENST00000262367	NM_004380.2	1136	TCc/c	18/31	1	2	FACETS	0.812	0.722	0.908	0.812	0.722	0.908	CLONAL	1	TRUE	1	0.43	2		395	504	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813797	50813797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200451975	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	119	424	0	ENST00000398568.2:c.1351G>A	p.Val451Ile	p.V451I	ENST00000398568	NM_001042412.1	451	Gtc/Atc	8/18	1	2	FACETS	0.873	0.79	0.961	0.873	0.79	0.961	CLONAL	1	TRUE	1	0.43	2		424	634	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676211	37676211	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	77	348	0	ENST00000447079.4:c.2966T>C	p.Ile989Thr	p.I989T	ENST00000447079	NM_015083.1	989	aTt/aCt	11/14	1	2	FACETS	0.829	0.731	0.934	0.829	0.731	0.934	CLONAL	1	TRUE	1	0.43	2		348	432	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245587	41245587	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357522	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	29	394	1	ENST00000357654.3:c.1961del	p.Lys654SerfsTer47	p.K654Sfs*47	ENST00000357654	NM_007294.3	654	aAg/ag	10/23	1	2	FACETS	0.244	0.195	0.3	0.244	0.195	0.3	SUBCLONAL	1	TRUE	1	0.43	2		395	552	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	35	157	1	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.638	0.526	0.763	0.638	0.526	0.763	SUBCLONAL	1	TRUE	1	0.43	2		158	255	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245891	5245891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1045893958	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	179	598	1	ENST00000357368.4:c.884G>A	p.Arg295Gln	p.R295Q	ENST00000357368	NM_002850.3	295	cGg/cAg	10/38	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.43	2		599	814	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274304	5274304	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	54	409	1	ENST00000357368.4:c.143del	p.Gly48ValfsTer17	p.G48Vfs*17	ENST00000357368	NM_002850.3	48	gGt/gt	3/38	1	2	FACETS	0.394	0.336	0.458	0.394	0.336	0.458	SUBCLONAL	1	TRUE	1	0.43	2		410	637	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965807	18965807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1261829390	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	146	527	0	ENST00000262803.5:c.1385G>A	p.Arg462His	p.R462H	ENST00000262803	NM_002911.3	462	cGc/cAc	10/24	1	2	FACETS	0.955	0.873	1	0.955	0.873	1	CLONAL	1	TRUE	1	0.43	2		527	711	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	172	608	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.863	0.794	0.935	0.863	0.794	0.935	CLONAL	1	TRUE	1	0.43	2		609	927	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229435	36229435	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	147	545	0	ENST00000222270.7:c.8125C>T	p.Arg2709Cys	p.R2709C	ENST00000222270	NM_014727.1	2709	Cgc/Tgc	37/37	1	2	FACETS	0.914	0.836	0.996	0.914	0.836	0.996	CLONAL	1	TRUE	1	0.43	2		545	748	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42381419	42381420	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	123	490	0	ENST00000221972.3:c.47dup	p.Leu17ProfsTer42	p.L17Pfs*42	ENST00000221972	NM_021601.3	15	-/T	1/5	1	2	FACETS	0.88	0.798	0.967	0.88	0.798	0.967	CLONAL	1	TRUE	1	0.43	2		490	650	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424922	47424922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371941437	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	148	407	0	ENST00000404338.3:c.2990G>A	p.Arg997Gln	p.R997Q	ENST00000404338	NM_004491.4	997	cGa/cAa	1/6	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.43	2		407	641	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905055	50905055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	56	437	1	ENST00000440232.2:c.342del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	113	Ggg/gg	4/27	1	2	FACETS	0.486	0.416	0.562	0.486	0.416	0.562	SUBCLONAL	1	TRUE	1	0.43	2		438	536	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523040	25523040	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	135	482	0	ENST00000264709.3:c.145G>A	p.Gly49Arg	p.G49R	ENST00000264709	NM_175629.2	49	Ggg/Agg	3/23	1	2	FACETS	0.936	0.852	1	0.936	0.852	1	CLONAL	1	TRUE	1	0.43	2		482	671	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672778	47672778	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	34	253	0	ENST00000233146.2:c.1369del	p.Thr457LeufsTer2	p.T457Lfs*2	ENST00000233146	NM_000251.2	456	acA/ac	8/16	1	2	FACETS	0.64	0.526	0.767	0.64	0.526	0.767	SUBCLONAL	1	TRUE	1	0.43	2		253	247	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439664	220439664	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	149	634	0	ENST00000243786.2:c.521del	p.Pro174LeufsTer16	p.P174Lfs*16	ENST00000243786	NM_002191.3	173	Ccc/cc	2/2	1	2	FACETS	0.809	0.739	0.882	0.809	0.739	0.882	CLONAL	1	TRUE	1	0.43	2		634	857	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31025133	31025133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	107	357	0	ENST00000375687.4:c.4618G>A	p.Val1540Met	p.V1540M	ENST00000375687	NM_015338.5	1540	Gtg/Atg	13/13	1	2	FACETS	0.976	0.879	1	0.976	0.879	1	CLONAL	1	TRUE	1	0.43	2		357	510	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279753	46279753	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200806631	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	110	373	0	ENST00000371998.3:c.3679G>A	p.Ala1227Thr	p.A1227T	ENST00000371998		1227	Gcc/Acc	20/23	1	2	FACETS	0.894	0.806	0.987	0.894	0.806	0.987	CLONAL	1	TRUE	1	0.43	2		373	572	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	128	697	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.43	2		699	566	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656840	45656840	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	137	497	0	ENST00000407780.3:c.316del	p.Gln106ArgfsTer11	p.Q106Rfs*11	ENST00000407780	NM_001283052.1	106	Cag/ag	3/7	1	2	FACETS	0.89	0.811	0.973	0.89	0.811	0.973	CLONAL	1	TRUE	1	0.43	2		497	716	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644720	134644720	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1240367222	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	49	394	0	ENST00000398015.3:c.121G>A	p.Gly41Arg	p.G41R	ENST00000398015	NM_004441.4	41	Ggg/Agg	2/16	1	2	FACETS	0.374	0.316	0.437	0.374	0.316	0.437	SUBCLONAL	1	TRUE	1	0.43	2		394	610	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670238	134670238	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	53	424	2	ENST00000398015.3:c.152del	p.Asn51ThrfsTer2	p.N51Tfs*2	ENST00000398015	NM_004441.4	50	gAa/ga	3/16	1	2	FACETS	0.419	0.357	0.487	0.419	0.357	0.487	SUBCLONAL	1	TRUE	1	0.43	2		426	588	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138376557	138376557	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	79	261	0	ENST00000289153.2:c.2917A>G	p.Thr973Ala	p.T973A	ENST00000289153	NM_006219.2	973	Aca/Gca	20/22	1	2	FACETS	0.916	0.81	1	0.916	0.81	1	CLONAL	1	TRUE	1	0.43	2		261	401	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182679077	182679077	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1484029696	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	31	215	0	ENST00000292782.4:c.457C>T	p.Arg153Ter	p.R153*	ENST00000292782	NM_020640.2	153	Cga/Tga	4/7	1	2	FACETS	0.869	0.711	1	0.869	0.711	1	CLONAL	1	TRUE	1	0.43	2		215	166	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672224	86672224	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	114	329	0	ENST00000274376.6:c.2026C>T	p.Gln676Ter	p.Q676*	ENST00000274376	NM_002890.2	676	Cag/Tag	16/25	1	2	FACETS	0.999	0.903	1	0.999	0.903	1	CLONAL	1	TRUE	1	0.43	2		329	531	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86686679	86686679	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	91	381	0	ENST00000274376.6:c.3127del	p.Thr1043ProfsTer?	p.T1043Pfs*?	ENST00000274376	NM_002890.2	1041	acA/ac	25/25	1	2	FACETS	0.906	0.808	1	0.906	0.808	1	CLONAL	1	TRUE	1	0.43	2		381	467	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523291	176523291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776973649	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	185	707	0	ENST00000292408.4:c.1948C>T	p.Arg650Cys	p.R650C	ENST00000292408	NM_213647.1	650	Cgc/Tgc	15/18	1	2	FACETS	0.888	0.82	0.959	0.888	0.82	0.959	CLONAL	1	TRUE	1	0.43	2		707	969	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046700	180046700	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	172	630	0	ENST00000261937.6:c.2612G>T	p.Ser871Ile	p.S871I	ENST00000261937	NM_182925.4	871	aGc/aTc	18/30	1	2	FACETS	0.95	0.875	1	0.95	0.875	1	CLONAL	1	TRUE	1	0.43	2		630	842	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954909	2954909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775400791	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	140	505	0	ENST00000396946.4:c.2801C>T	p.Ser934Leu	p.S934L	ENST00000396946	NM_032415.4	934	tCg/tTg	21/25	1	2	FACETS	0.937	0.855	1	0.937	0.855	1	CLONAL	1	TRUE	1	0.43	2		505	695	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	121	391	2	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.903	0.818	0.993	0.903	0.818	0.993	CLONAL	1	TRUE	1	0.43	2		393	623	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90995015	90995015	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	67	303	0	ENST00000265433.3:c.106G>A	p.Glu36Lys	p.E36K	ENST00000265433	NM_002485.4	36	Gaa/Aaa	2/16	1	2	FACETS	0.906	0.792	1	0.906	0.792	1	CLONAL	1	TRUE	1	0.43	2		303	344	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785964	135785964	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs118203506	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	54	450	0	ENST00000298552.3:c.1257del	p.Arg420GlyfsTer20	p.R420Gfs*20	ENST00000298552	NM_001162426.1	419	ccC/cc	12/23	1	2	FACETS	0.384	0.327	0.446	0.384	0.327	0.446	SUBCLONAL	1	TRUE	1	0.43	2		450	654	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390697	139390697	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	174	701	1	ENST00000277541.6:c.7494del	p.Ser2499AlafsTer90	p.S2499Afs*90	ENST00000277541	NM_017617.3	2498	ccC/cc	34/34	1	2	FACETS	0.94	0.866	1	0.94	0.866	1	CLONAL	1	TRUE	1	0.43	2		702	861	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	84	329	4	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	1	2	FACETS	0.807	0.715	0.905	0.807	0.715	0.905	CLONAL	1	TRUE	1	0.43	2		333	484	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243974	53243974	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	89	489	0	ENST00000375401.3:c.1019T>C	p.Leu340Pro	p.L340P	ENST00000375401	NM_004187.3	340	cTg/cCg	8/26	1	2	FACETS	0.725	0.644	0.811	0.725	0.644	0.811	SUBCLONAL	1	TRUE	1	0.43	2		489	571	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350031	70350031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059098-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	78	465	0	ENST00000374080.3:c.4018del	p.Gln1340SerfsTer5	p.Q1340Sfs*5	ENST00000374080		1338	aaC/aa	28/45	1	2	FACETS	0.544	0.478	0.615	0.544	0.478	0.615	SUBCLONAL	1	TRUE	1	0.43	2		465	667	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	148	302	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.752	0.692	0.813	0.752	0.692	0.813	SUBCLONAL	1	TRUE	1	0.85	2		302	463	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0059099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	186	538	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	0.865	0.806	0.925	0.865	0.806	0.925	CLONAL	1	TRUE	1	0.85	2		538	506	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0059099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	76	187	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.85	2		188	167	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0059099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	242	413	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.85	2		413	566	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198453	108198453	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	190	307	0	ENST00000278616.4:c.7057C>A	p.Pro2353Thr	p.P2353T	ENST00000278616	NM_000051.3	2353	Cct/Act	48/63	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.85	2		307	405	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867571	45867571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	291	811	0	ENST00000391945.4:c.737C>T	p.Ser246Phe	p.S246F	ENST00000391945	NM_000400.3	246	tCc/tTc	9/23	1	2	FACETS	0.859	0.812	0.907	0.859	0.812	0.907	CLONAL	1	TRUE	1	0.85	2		811	797	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929235	44929235	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	214	207	0	ENST00000377967.4:c.2335C>T	p.Gln779Ter	p.Q779*	ENST00000377967	NM_021140.2	779	Cag/Tag	17/29	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.85	1		207	255	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056181	27056181	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	253	462	0	ENST00000324856.7:c.1177C>T	p.Gln393Ter	p.Q393*	ENST00000324856	NM_006015.4	393	Cag/Tag	2/20	1	2	FACETS	0.881	0.829	0.933	0.881	0.829	0.933	CLONAL	1	TRUE	1	0.85	2		462	676	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973778	131973778	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	156	275	0	ENST00000265335.6:c.3481G>C	p.Glu1161Gln	p.E1161Q	ENST00000265335		1161	Gaa/Caa	23/25	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.85	2		275	339	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186681	11186681	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1024737469	NA	P-0059099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	359	468	0	ENST00000361445.4:c.6524T>C	p.Met2175Thr	p.M2175T	ENST00000361445	NM_004958.3	2175	aTg/aCg	46/58	0.3	4	FACETS	0.836	0.802	0.87			1	INDETERMINATE	3	TRUE	NA	0.85	4		468	623	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265477	198265477	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	142	278	0	ENST00000335508.6:c.2680G>A	p.Asp894Asn	p.D894N	ENST00000335508	NM_012433.2	894	Gat/Aat	18/25	1	2	FACETS	0.968	0.895	1	0.968	0.895	1	CLONAL	1	TRUE	1	0.85	2		278	345	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936176	71936176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	213	483	0	ENST00000298229.2:c.148G>A	p.Glu50Lys	p.E50K	ENST00000298229	NM_001567.3	50	Gag/Aag	1/28	1	2	FACETS	0.979	0.918	1	0.979	0.918	1	CLONAL	1	TRUE	1	0.85	2		483	512	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100088	157100088	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768271181	NA	P-0059099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	209	578	0	ENST00000346085.5:c.1025C>T	p.Ala342Val	p.A342V	ENST00000346085	NM_020732.3	342	gCg/gTg	1/20	1	2	FACETS	0.896	0.838	0.954	0.896	0.838	0.954	CLONAL	1	TRUE	1	0.85	2		578	549	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464935	120464935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	252	485	0	ENST00000256646.2:c.5137G>A	p.Glu1713Lys	p.E1713K	ENST00000256646	NM_024408.3	1713	Gaa/Aaa	28/34	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.85	2		485	589	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981146	201981146	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	325	488	0	ENST00000359651.3:c.225G>A	p.Trp75Ter	p.W75*	ENST00000359651		75	tgG/tgA	2/8	0.3	3	FACETS	0.828	0.789	0.867	0.828	0.789	0.867	INDETERMINATE	2	TRUE	1	0.85	3		488	658	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981162	201981162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	332	507	0	ENST00000359651.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000359651		81	Gag/Aag	2/8	0.3	3	FACETS	0.811	0.773	0.85	0.811	0.773	0.85	INDETERMINATE	2	TRUE	1	0.85	3		507	686	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852755	63852755	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	247	402	0	ENST00000279873.7:c.3533A>C	p.Gln1178Pro	p.Q1178P	ENST00000279873	NM_032199.2	1178	cAg/cCg	10/10	1	2	FACETS	0.975	0.919	1	0.975	0.919	1	CLONAL	1	TRUE	1	0.85	2		402	596	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589677	69589677	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	285	1044	0	ENST00000168712.1:c.176C>G	p.Pro59Arg	p.P59R	ENST00000168712	NM_002007.2	59	cCg/cGg	1/3	1	2	FACETS	0.662	0.623	0.702	0.662	0.623	0.702	SUBCLONAL	1	TRUE	1	0.85	2		1044	1013	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192582	94192582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564511708	NA	P-0059099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	149	269	0	ENST00000323929.3:c.1492G>A	p.Asp498Asn	p.D498N	ENST00000323929	NM_005591.3	498	Gat/Aat	13/20	1	2	FACETS	0.996	0.923	1	0.996	0.923	1	CLONAL	1	TRUE	1	0.85	2		269	352	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425263	49425263	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	289	676	0	ENST00000301067.7:c.13225G>C	p.Glu4409Gln	p.E4409Q	ENST00000301067	NM_003482.3	4409	Gag/Cag	39/54	1	2	FACETS	0.948	0.897	1	0.948	0.897	1	CLONAL	1	TRUE	1	0.85	2		676	717	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425449	49425449	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	389	751	0	ENST00000301067.7:c.13039C>T	p.Gln4347Ter	p.Q4347*	ENST00000301067	NM_003482.3	4347	Cag/Tag	39/54	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.85	2		751	903	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748270	43748270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	240	530	0	ENST00000382044.4:c.2536G>A	p.Asp846Asn	p.D846N	ENST00000382044	NM_001141980.1	846	Gat/Aat	12/28	1	2	FACETS	0.951	0.895	1	0.951	0.895	1	CLONAL	1	TRUE	1	0.85	2		530	594	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964741	15964741	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	36	414	0	ENST00000268712.3:c.5855C>T	p.Ser1952Phe	p.S1952F	ENST00000268712	NM_006311.3	1952	tCt/tTt	37/46	1	2	FACETS	0.175	0.144	0.211	0.175	0.144	0.211	SUBCLONAL	1	TRUE	1	0.85	2		414	483	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661026	227661026	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	240	603	0	ENST00000305123.5:c.2429C>T	p.Ser810Phe	p.S810F	ENST00000305123	NM_005544.2	810	tCc/tTc	1/2	1	2	FACETS	0.799	0.749	0.849	0.799	0.749	0.849	SUBCLONAL	1	TRUE	1	0.85	2		603	707	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121075	29121089	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	TCTATGTATGCAATG	TCTATGTATGCAATG	-	novel	NA	P-0059099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	130	303	0	ENST00000328354.6:c.468_482del	p.Tyr156_Glu161delinsTer	p.Y156_E161delins*	ENST00000328354	NM_007194.3	156	taCATTGCATACATAGAa/taa	4/15	1	2	FACETS	0.833	0.765	0.904	0.833	0.765	0.904	CLONAL	1	TRUE	1	0.85	2		303	367	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542789	187542790	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TATTTCACTCATTGGTGGACTGCCCTTA	novel	NA	P-0059099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	173	381	0	ENST00000441802.2:c.4923_4950dup	p.Thr1651Ter	p.T1651*	ENST00000441802	NM_005245.3	1650	-/TAAGGGCAGTCCACCAATGAGTGAAATA	10/27	1	2	FACETS	0.642	0.593	0.692	0.642	0.593	0.692	SUBCLONAL	1	TRUE	1	0.85	2		381	634	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945643	151945643	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0059099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	124	234	0	ENST00000262189.6:c.1876G>T	p.Glu626Ter	p.E626*	ENST00000262189	NM_170606.2	626	Gaa/Taa	14/59	1	2	FACETS	0.935	0.859	1	0.935	0.859	1	CLONAL	1	TRUE	1	0.85	2		234	312	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760222	133760222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	245	545	0	ENST00000318560.5:c.2545G>A	p.Glu849Lys	p.E849K	ENST00000318560	NM_005157.4	849	Gag/Aag	11/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.85	2		545	576	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390685	139390689	+	frameshift_variant	Frame_Shift_Del	DEL	TAGCT	TAGCT	-	novel	NA	P-0059099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	52	713	0	ENST00000277541.6:c.7502_7506del	p.Gln2501ProfsTer4	p.Q2501Pfs*4	ENST00000277541	NM_017617.3	2501	cAGCTA/c	34/34	1	2	FACETS	0.163	0.138	0.19	0.163	0.138	0.19	SUBCLONAL	1	TRUE	1	0.85	2		713	751	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936102	49936103	+	stop_gained	Nonsense_Mutation	DNP	TG	TG	CA	novel	NA	P-0059099-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	49	659	0	ENST00000296474.3:c.1567_1568inv	p.Gln523Ter	p.Q523*	ENST00000296474	NM_002447.2	523	CAa/TGa	4/20	1	2	FACETS	0.155	0.131	0.182	0.155	0.131	0.182	SUBCLONAL	1	TRUE	1	0.85	2		659	743	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0059100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	18	1110	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.125181181626758	3	FACETS	0.38	0.285	0.494			1	SUBCLONAL	1	FALSE	NA	0.163265011291345	3		1111	627	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0059100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	18	256	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.149052168915741	3	FACETS	0.777	0.585	1	0.388	0.292	0.502	CLONAL	1	FALSE	1	0.163265011291345	3		256	307	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70355017	70355018	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0059100-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	25	254	0	ENST00000374080.3:c.4939_4940delinsTT	p.Asp1647Phe	p.D1647F	ENST00000374080		1647	GAt/TTt	36/45	1	1	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	FALSE	0	0.163265011291345	1		254	248	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0059102-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	261	891	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.453603605520474	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.453603605520474	2		891	489	SUCCESS
APC	324	MSKCC	GRCh37	5	112175513	112175513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059102-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	272	400	0	ENST00000257430.4:c.4222G>T	p.Glu1408Ter	p.E1408*	ENST00000257430	NM_000038.5	1408	Gaa/Taa	16/16	0.453603605520474	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	3	TRUE	1	0.453603605520474	4		400	567	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443676	29443676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56315533	NA	P-0059102-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	221	403	0	ENST00000389048.3:c.3541C>T	p.Arg1181Cys	p.R1181C	ENST00000389048	NM_004304.4	1181	Cgc/Tgc	23/29	0.387367309121343	4	FACETS	0.95	0.894	1	0.95	0.894	1	CLONAL	3	TRUE	1	0.453603605520474	4		403	497	SUCCESS
APC	324	MSKCC	GRCh37	5	112174117	112174117	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059102-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	59	372	0	ENST00000257430.4:c.2827del	p.Ser943GlnfsTer12	p.S943Qfs*12	ENST00000257430	NM_000038.5	942	aaT/aa	16/16	0.453603605520474	4	FACETS	0.987	0.853	1	0.329	0.284	0.378	CLONAL	1	TRUE	1	0.453603605520474	4		372	383	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0059102-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	146	403	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.453603605520474	4	FACETS	0.917	0.858	0.976	0.917	0.858	0.976	CLONAL	4	TRUE	0	0.453603605520474	4		403	255	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789646	3789646	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140133512	NA	P-0059102-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	223	401	0	ENST00000262367.5:c.4213G>A	p.Val1405Met	p.V1405M	ENST00000262367	NM_004380.2	1405	Gtg/Atg	25/31	0.453603605520474	5	FACETS	1	0.988	1	0.823	0.77	0.877	CLONAL	2	TRUE	2	0.453603605520474	5		401	669	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165603	118165603	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148397151	NA	P-0059102-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	187	487	0	ENST00000369448.3:c.113G>A	p.Arg38Gln	p.R38Q	ENST00000369448	NM_017709.3	38	cGa/cAa	2/2	0.453603605520474	3	FACETS	0.996	0.928	1	0.996	0.928	1	CLONAL	2	TRUE	1	0.453603605520474	3		487	508	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910880	114910880	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059102-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	194	384	1	ENST00000543371.1:c.1000del	p.Ser334GlnfsTer17	p.S334Qfs*17	ENST00000543371	NM_001198531.1	333	agT/ag	9/14	0.302255045606292	5	FACETS	1	0.983	1			1	CLONAL	2	TRUE	NA	0.453603605520474	5		385	611	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888733	76888733	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059102-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	74	270	0	ENST00000373344.5:c.5096A>T	p.Lys1699Ile	p.K1699I	ENST00000373344	NM_000489.3	1699	aAa/aTa	19/35	0.453603605520474	6	FACETS	1	0.97	1	0.339	0.297	0.383	CLONAL	1	TRUE	2	0.453603605520474	6		270	459	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0059106-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	25	391	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.801	0.644	0.972	0.801	0.644	0.972	CLONAL	1	TRUE	1	0.612102182402669	2		391	102	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0059106-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	65	449	0	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	0.56220371230014	1	FACETS	0.768	0.678	0.861	0.768	0.678	0.861	SUBCLONAL	1	TRUE	0	0.612102182402669	1		449	192	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0059106-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	330	693	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	0.911	0.871	0.95	1	0.996	1	CLONAL	2	TRUE	1	0.612102182402669	2		693	592	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272100	18272100	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059106-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	112	715	1	ENST00000222254.8:c.610C>T	p.Pro204Ser	p.P204S	ENST00000222254	NM_005027.3	204	Ccc/Tcc	6/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.612102182402669	2		716	306	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441260	52441261	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0059106-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	73	605	0	ENST00000460680.1:c.509_510del	p.Phe170CysfsTer12	p.F170Cfs*12	ENST00000460680	NM_004656.3	170	tTT/t	7/17	0.612102182402669	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.612102182402669	1		605	155	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0059107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	33	190	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.752	0.618	0.9	0.752	0.618	0.9	SUBCLONAL	1	TRUE	1	0.45	2		190	195	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0059107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	143	578	5	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.812	0.741	0.886	0.812	0.741	0.886	CLONAL	1	TRUE	1	0.45	2		583	783	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	143	434	4	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.875	0.799	0.955	0.875	0.799	0.955	CLONAL	1	TRUE	1	0.45	2		438	726	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	114	609	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.91	0.822	1	0.91	0.822	1	CLONAL	1	TRUE	1	0.45	2		609	557	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0059107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	15	73	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.813	0.606	1	0.813	0.606	1	CLONAL	1	TRUE	1	0.45	2		73	82	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0059107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	174	544	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.851	0.783	0.921	0.851	0.783	0.921	CLONAL	1	TRUE	1	0.45	2		548	909	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0059107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	158	1063	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.45	2		1063	678	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0059107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	43	319	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	1	2	FACETS	0.853	0.721	0.997	0.853	0.721	0.997	CLONAL	1	TRUE	1	0.45	2		319	224	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022443	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	rs750318549	NA	P-0059107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	147	701	0	ENST00000375687.4:c.1933_1934del	p.Gly645TrpfsTer12	p.G645Wfs*12	ENST00000375687	NM_015338.5	643	GGg/g	13/13	1	2	FACETS	0.842	0.769	0.918	0.842	0.769	0.918	CLONAL	1	TRUE	1	0.45	2		701	776	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797278	42797278	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs968289754	NA	P-0059107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	120	736	0	ENST00000575354.2:c.3640C>T	p.Arg1214Ter	p.R1214*	ENST00000575354	NM_015125.3	1214	Cga/Tga	15/20	1	2	FACETS	0.806	0.729	0.886	0.806	0.729	0.886	CLONAL	1	TRUE	1	0.45	2		736	662	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039609	180039609	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs954889734	NA	P-0059107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	64	513	0	ENST00000261937.6:c.3434G>A	p.Arg1145His	p.R1145H	ENST00000261937	NM_182925.4	1145	cGc/cAc	26/30	1	2	FACETS	0.513	0.444	0.587	0.513	0.444	0.587	SUBCLONAL	1	TRUE	1	0.45	2		513	555	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225603	2225603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	139	671	0	ENST00000326181.6:c.1606G>A	p.Gly536Ser	p.G536S	ENST00000326181	NM_032271.2	536	Ggc/Agc	17/21	1	2	FACETS	0.971	0.887	1	0.971	0.887	1	CLONAL	1	TRUE	1	0.45	2		671	636	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882050	36882050	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs780753361	NA	P-0059107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	147	882	1	ENST00000358127.4:c.963del	p.Ala322LeufsTer11	p.A322Lfs*11	ENST00000358127	NM_001280556.1	321	ccC/cc	8/10	1	2	FACETS	0.889	0.813	0.968	0.889	0.813	0.968	CLONAL	1	TRUE	1	0.45	2		883	735	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693003	89693003	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs786204900	NA	P-0059107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	38	395	0	ENST00000371953.3:c.491del	p.Lys164ArgfsTer3	p.K164Rfs*3	ENST00000371953	NM_000314.4	163	Aaa/aa	5/9	1	2	FACETS	0.747	0.623	0.884	0.747	0.623	0.884	SUBCLONAL	1	TRUE	1	0.45	2		395	226	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0059107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	119	658	8	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.81	0.732	0.891	0.81	0.732	0.891	CLONAL	1	TRUE	1	0.45	2		666	653	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350146	89350146	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs575811373	NA	P-0059107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	126	581	0	ENST00000301030.4:c.2804C>T	p.Ser935Leu	p.S935L	ENST00000301030	NM_001256183.1	935	tCg/tTg	9/13	1	2	FACETS	0.727	0.659	0.799	0.727	0.659	0.799	SUBCLONAL	1	TRUE	1	0.45	2		581	770	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276860	15276861	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs753725730	NA	P-0059107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	68	909	8	ENST00000263388.2:c.5404dup	p.Ala1802GlyfsTer8	p.A1802Gfs*8	ENST00000263388	NM_000435.2	1802	gct/gGct	30/33	1	2	FACETS	0.408	0.355	0.467	0.408	0.355	0.467	SUBCLONAL	1	TRUE	1	0.45	2		917	740	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063320	67063320	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	57	438	0	ENST00000412916.2:c.10G>T	p.Val4Phe	p.V4F	ENST00000412916		4	Gtc/Ttc	1/6	1	2	FACETS	0.603	0.519	0.695	0.603	0.519	0.695	SUBCLONAL	1	TRUE	1	0.45	2		438	420	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439919	56439919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	183	570	0	ENST00000407977.2:c.673del	p.Arg225AlafsTer194	p.R225Afs*194	ENST00000407977		225	Cgc/gc	6/10	1	2	FACETS	0.971	0.897	1	0.971	0.897	1	CLONAL	1	TRUE	1	0.45	2		570	838	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338671	70338671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	115	436	0	ENST00000374080.3:c.67G>T	p.Asp23Tyr	p.D23Y	ENST00000374080		23	Gat/Tat	1/45	1	2	FACETS	0.961	0.869	1	0.961	0.869	1	CLONAL	1	TRUE	1	0.45	2		436	532	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0059107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	131	726	4	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.719	0.652	0.789	0.719	0.652	0.789	SUBCLONAL	1	TRUE	1	0.45	2		730	810	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214821	36214821	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	120	506	0	ENST00000222270.7:c.3247C>T	p.Arg1083Ter	p.R1083*	ENST00000222270	NM_014727.1	1083	Cga/Tga	8/37	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.45	2		506	526	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224316	36224316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749880112	NA	P-0059107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	179	741	0	ENST00000222270.7:c.6866C>T	p.Pro2289Leu	p.P2289L	ENST00000222270	NM_014727.1	2289	cCg/cTg	28/37	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.45	2		741	790	SUCCESS
KBTBD4	55709	MSKCC	GRCh37	11	47594882	47594883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs756343868	NA	P-0059107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	165	470	1	ENST00000430070.2:c.1204dup	p.Glu402GlyfsTer4	p.E402Gfs*4	ENST00000430070	NM_018095.4	402	gag/gGag	4/4	1	2	FACETS	0.959	0.882	1	0.959	0.882	1	CLONAL	1	TRUE	1	0.45	2		471	765	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101437	27101438	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0059107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	73	500	0	ENST00000324856.7:c.4724dup	p.Pro1576ThrfsTer27	p.P1576Tfs*27	ENST00000324856	NM_006015.4	1573	-/C	18/20	1	2	FACETS	0.741	0.65	0.838	0.741	0.65	0.838	SUBCLONAL	1	TRUE	1	0.45	2		500	438	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305411	65305411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	164	612	0	ENST00000342505.4:c.2717C>T	p.Ala906Val	p.A906V	ENST00000342505	NM_002227.2	906	gCt/gTt	20/25	1	2	FACETS	0.964	0.887	1	0.964	0.887	1	CLONAL	1	TRUE	1	0.45	2		612	756	SUCCESS
PGBD5	79605	MSKCC	GRCh37	1	230492828	230492828	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148064583	NA	P-0059107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	149	539	0	ENST00000391860.1:c.226G>A	p.Gly76Arg	p.G76R	ENST00000391860	NM_001258311.1	76	Gga/Aga	2/7	1	2	FACETS	0.971	0.889	1	0.971	0.889	1	CLONAL	1	TRUE	1	0.45	2		539	682	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655480	67655480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	8	388	0	ENST00000264010.4:c.1343G>A	p.Arg448Gln	p.R448Q	ENST00000264010	NM_006565.3	448	cGa/cAa	7/12	1	2	FACETS	0.103	0.065	0.151	0.103	0.065	0.151	SUBCLONAL	1	TRUE	1	0.45	2		388	346	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828915	72828915	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	202	679	1	ENST00000268489.5:c.7666del	p.Ala2556ArgfsTer56	p.A2556Rfs*56	ENST00000268489	NM_006885.3	2556	Gcg/cg	9/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.45	2		680	814	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247390	71247390	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	171	640	0	ENST00000318789.4:c.143C>A	p.Ala48Glu	p.A48E	ENST00000318789	NM_032682.5	48	gCa/gAa	6/21	1	2	FACETS	0.878	0.808	0.95	0.878	0.808	0.95	CLONAL	1	TRUE	1	0.45	2		640	866	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679935	30679935	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	40	646	0	ENST00000376406.3:c.1784T>C	p.Val595Ala	p.V595A	ENST00000376406	NM_014641.2	595	gTa/gCa	5/15	1	2	FACETS	0.23	0.19	0.275	0.23	0.19	0.275	SUBCLONAL	1	TRUE	1	0.45	2		646	772	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930271	39930271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555917318	NA	P-0059107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	152	555	0	ENST00000378444.4:c.3193G>A	p.Val1065Ile	p.V1065I	ENST00000378444	NM_001123385.1	1065	Gtc/Atc	6/15	1	2	FACETS	0.858	0.786	0.934	0.858	0.786	0.934	CLONAL	1	TRUE	1	0.45	2		555	787	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916929	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519931	NA	P-0059108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	52	298	0	ENST00000263967.3:c.316G>C	p.Gly106Arg	p.G106R	ENST00000263967	NM_006218.2	106	Ggc/Cgc	2/21	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.24688883685003	2		298	374	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856124	111856124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168055611	NA	P-0059108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	132	500	0	ENST00000341259.2:c.175C>T	p.Arg59Cys	p.R59C	ENST00000341259	NM_005475.2	59	Cgc/Tgc	2/8	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.24688883685003	2		500	863	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485013	57485013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	105	497	1	ENST00000371085.3:c.847C>T	p.Arg283Cys	p.R283C	ENST00000371085	NM_000516.4	283	Cgc/Tgc	11/13	1	2	FACETS	0.998	0.894	1	0.998	0.894	1	CLONAL	1	TRUE	1	0.24688883685003	2		498	852	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894229	NA	P-0059108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	155	463	0	ENST00000451590.1:c.34G>T	p.Gly12Cys	p.G12C	ENST00000451590	NM_001130442.1	12	Ggc/Tgc	2/5	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.24688883685003	2		463	859	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0059108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	99	363	0	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	0.24688883685003	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.24688883685003	1		363	588	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916913	178916924	+	inframe_deletion	In_Frame_Del	DEL	AGTAATTGAACC	AGTAATTGAACC	-	novel	NA	P-0059108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	51	302	0	ENST00000263967.3:c.304_315del	p.Ile102_Val105del	p.I102_V105del	ENST00000263967	NM_006218.2	100	aaAGTAATTGAACCa/aaa	2/21	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.24688883685003	2		302	405	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157829	27158123	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GAACTGTGGAAGGTGCCATGGACTTGATCTTGATCAATTCCCTACCTCTTGTATCTGATGCTGAAACATCTCTCACCTGCATTGCCTCTGGGTGGCGCCCCCATGAGCCCATCACCATAGGAAGGGACTTTGAAGCCTTAATGAACCAGCACCAGGATCCGCTGGAAGTTACTCAAGATGTGACCAGAGAATGGGCTAAAAAAGTTGTTTGGAAGAGAGAAAAGGCTAGTAAGATCAATGGTGCTTATTTCTGTGAAGGGCGAGTTCGAGGAGAGGCAATCAGGATACGAACCAT	GAACTGTGGAAGGTGCCATGGACTTGATCTTGATCAATTCCCTACCTCTTGTATCTGATGCTGAAACATCTCTCACCTGCATTGCCTCTGGGTGGCGCCCCCATGAGCCCATCACCATAGGAAGGGACTTTGAAGCCTTAATGAACCAGCACCAGGATCCGCTGGAAGTTACTCAAGATGTGACCAGAGAATGGGCTAAAAAAGTTGTTTGGAAGAGAGAAAAGGCTAGTAAGATCAATGGTGCTTATTTCTGTGAAGGGCGAGTTCGAGGAGAGGCAATCAGGATACGAACCAT	-	novel	NA	P-0059108-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	52	335	0	ENST00000380036.4:c.56_350del	p.Thr19ArgfsTer13	p.T19Rfs*13	ENST00000380036	NM_000459.3	18	gGAACTGTGGAAGGTGCCATGGACTTGATCTTGATCAATTCCCTACCTCTTGTATCTGATGCTGAAACATCTCTCACCTGCATTGCCTCTGGGTGGCGCCCCCATGAGCCCATCACCATAGGAAGGGACTTTGAAGCCTTAATGAACCAGCACCAGGATCCGCTGGAAGTTACTCAAGATGTGACCAGAGAATGGGCTAAAAAAGTTGTTTGGAAGAGAGAAAAGGCTAGTAAGATCAATGGTGCTTATTTCTGTGAAGGGCGAGTTCGAGGAGAGGCAATCAGGATACGAACCATg/gg	2/23	0.24688883685003	1	FACETS	0.717	0.611	0.834	0.717	0.611	0.834	SUBCLONAL	1	TRUE	0	0.24688883685003	1		335	515	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43769928	43769928	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	23	414	1	ENST00000382044.4:c.818C>A	p.Ala273Glu	p.A273E	ENST00000382044	NM_001141980.1	273	gCa/gAa	8/28	0.619842436792783	4	FACETS	0.261	0.203	0.329	0.065	0.05	0.083	SUBCLONAL	1	TRUE	0	0.696872558523297	4		415	429	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274710	198274710	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	166	438	0	ENST00000335508.6:c.688T>A	p.Leu230Ile	p.L230I	ENST00000335508	NM_012433.2	230	Tta/Ata	7/25	0.611997189543398	4	FACETS	0.912	0.847	0.979	0.912	0.847	0.979	CLONAL	2	TRUE	2	0.696872558523297	4		438	443	SUCCESS
APC	324	MSKCC	GRCh37	5	112176718	112176718	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	66	369	0	ENST00000257430.4:c.5427A>T	p.Lys1809Asn	p.K1809N	ENST00000257430	NM_000038.5	1809	aaA/aaT	16/16	0.611997189543398	4	FACETS	0.888	0.787	0.992	0.888	0.787	0.992	CLONAL	2	TRUE	2	0.696872558523297	4		369	181	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412628	63412628	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755983037	NA	P-0059111-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	28	582	0	ENST00000330258.3:c.539G>A	p.Arg180Gln	p.R180Q	ENST00000330258	NM_152424.3	180	cGg/cAg	2/2	0.652064503024386	2	FACETS	0.316	0.254	0.387	0.158	0.127	0.194	SUBCLONAL	1	TRUE	0	0.696872558523297	2		582	254	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0059112-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	171	804	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.239871011077233	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	0	0.251385842760463	2		804	678	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0059112-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	86	256	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.166315292924028	4	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	2	0.251385842760463	4		256	406	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059112-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	44	320	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.251385842760463	1	FACETS	0.872	0.734	1	0.872	0.734	1	CLONAL	1	TRUE	0	0.251385842760463	1		320	351	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059112-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	99	657	0	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	0.934	0.833	1	0.934	0.833	1	CLONAL	1	TRUE	1	0.251385842760463	2		657	843	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313153	30313153	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059112-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	76	562	0	ENST00000262643.3:c.847G>T	p.Asp283Tyr	p.D283Y	ENST00000262643	NM_001238.2	283	Gat/Tat	10/12	0.226457911801363	3	FACETS	0.974	0.854	1	0.487	0.427	0.552	CLONAL	1	TRUE	1	0.251385842760463	3		562	699	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593518	215593518	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs777013688	NA	P-0059112-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	111	571	0	ENST00000260947.4:c.2216A>G	p.Tyr739Cys	p.Y739C	ENST00000260947	NM_000465.2	739	tAt/tGt	11/11	0.226457911801363	3	FACETS	1	0.982	1	0.73	0.657	0.807	CLONAL	1	TRUE	1	0.251385842760463	3		571	681	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056404	26056404	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059112-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	150	580	0	ENST00000343677.2:c.253A>G	p.Lys85Glu	p.K85E	ENST00000343677	NM_005319.3	85	Aag/Gag	1/1	0.239871011077233	2	FACETS	0.961	0.881	1	0.961	0.881	1	CLONAL	2	TRUE	0	0.251385842760463	2		580	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0059113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	86	804	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.210892149175947	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.210892149175947	1		804	660	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094454	27094455	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0059113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	55	545	0	ENST00000324856.7:c.3163dup	p.Tyr1055LeufsTer50	p.Y1055Lfs*50	ENST00000324856	NM_006015.4	1054	-/T	11/20	1	2	FACETS	0.722	0.617	0.838	0.722	0.617	0.838	SUBCLONAL	1	TRUE	1	0.210892149175947	2		545	722	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591140	67591145	+	inframe_deletion	In_Frame_Del	DEL	ACCAAT	ACCAAT	-	rs751582616	NA	P-0059113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	33	277	0	ENST00000274335.5:c.1735_1740del	p.Gln579_Tyr580del	p.Q579_Y580del	ENST00000274335		578	gACCAATac/gac	12/15	1	2	FACETS	0.565	0.459	0.685	0.565	0.459	0.685	SUBCLONAL	1	TRUE	1	0.210892149175947	2		277	554	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087555	27087555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1171422700	NA	P-0059113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	90	603	0	ENST00000324856.7:c.2129G>A	p.Arg710His	p.R710H	ENST00000324856	NM_006015.4	710	cGc/cAc	5/20	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.210892149175947	2		603	847	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424493	47424493	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	78	520	0	ENST00000404338.3:c.2561G>A	p.Gly854Glu	p.G854E	ENST00000404338	NM_004491.4	854	gGg/gAg	1/6	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.210892149175947	2		520	719	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590989	67590990	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0059113-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	40	214	0	ENST00000274335.5:c.1583dup	p.Tyr528Ter	p.Y528*	ENST00000274335		528	tat/tAat	12/15	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.210892149175947	2		214	358	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0059114-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	314	412	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.438529837341592	3	FACETS	0.97	0.925	1	0.97	0.925	1	CLONAL	3	TRUE	0	0.438529837341592	3		412	600	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880449	155880449	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs869025189	NA	P-0059114-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	157	447	0	ENST00000368323.3:c.104G>C	p.Ser35Thr	p.S35T	ENST00000368323	NM_006912.5	35	aGt/aCt	2/6	0.333944388393001	4	FACETS	0.879	0.809	0.951	0.879	0.809	0.951	CLONAL	2	TRUE	2	0.438529837341592	4		447	586	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829795	72829798	+	frameshift_variant	Frame_Shift_Del	DEL	ATCG	ATCG	-	novel	NA	P-0059114-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	78	480	0	ENST00000268489.5:c.6783_6786del	p.Phe2261LeufsTer18	p.F2261Lfs*18	ENST00000268489	NM_006885.3	2261	ttCGAT/tt	9/10	1	2	FACETS	0.796	0.702	0.896	0.796	0.702	0.896	SUBCLONAL	1	TRUE	1	0.438529837341592	2		480	447	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181891	56181891	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0059114-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	74	220	0	ENST00000399503.3:c.4114+1G>T		p.X1372_splice	ENST00000399503	NM_005921.1	1372			0.333944388393001	4	FACETS	0.84	0.743	0.942	0.84	0.743	0.942	CLONAL	2	TRUE	2	0.438529837341592	4		220	289	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589290	67589291	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0059114-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	50	162	0	ENST00000274335.5:c.1280dup	p.Val428SerfsTer14	p.V428Sfs*14	ENST00000274335		426	-/C	9/15	0.333944388393001	4	FACETS	0.796	0.684	0.916	0.796	0.684	0.916	CLONAL	2	TRUE	2	0.438529837341592	4		162	206	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589590	67589593	+	protein_altering_variant	In_Frame_Del	DEL	ATAT	ATAT	G	novel	NA	P-0059114-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	33	81	0	ENST00000274335.5:c.1353_1356delinsG	p.Tyr452del	p.Y452del	ENST00000274335		451	gaATAT/gaG	10/15	0.333944388393001	4	FACETS	0.768	0.636	0.911	0.768	0.636	0.911	CLONAL	2	TRUE	2	0.438529837341592	4		81	141	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0059115-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	127	564	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.146447357189262	3	FACETS	0.871	0.791	0.955	0.871	0.791	0.955	INDETERMINATE	2	TRUE	1	0.25	3		564	656	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0059115-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	87	425	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.181094102580594	2	FACETS	1	0.976	1	0.702	0.623	0.785	CLONAL	1	TRUE	0	0.25	2		425	496	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476311	88476311	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059115-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	39	408	1	ENST00000360948.2:c.1821C>A	p.Cys607Ter	p.C607*	ENST00000360948	NM_001012338.2	607	tgC/tgA	15/19	1	2	FACETS	0.606	0.502	0.722	0.606	0.502	0.722	SUBCLONAL	1	TRUE	1	0.25	2		409	515	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420191	88420191	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059115-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	85	517	0	ENST00000360948.2:c.2495C>T	p.Pro832Leu	p.P832L	ENST00000360948	NM_001012338.2	832	cCa/cTa	19/19	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.25	2		517	553	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	461440	461440	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059115-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	21	334	0	ENST00000399788.2:c.1080G>T	p.Glu360Asp	p.E360D	ENST00000399788	NM_001042603.1	360	gaG/gaT	9/28	1	2	FACETS	0.571	0.44	0.724	0.571	0.44	0.724	SUBCLONAL	1	TRUE	1	0.25	2		334	294	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114195	115114195	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059115-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	61	519	0	ENST00000257566.3:c.1022G>T	p.Ser341Ile	p.S341I	ENST00000257566	NM_016569.3	341	aGt/aTt	6/8	1	2	FACETS	0.904	0.78	1	0.904	0.78	1	CLONAL	1	TRUE	1	0.25	2		519	540	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664548	29664548	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059115-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	45	417	0	ENST00000356175.3:c.6527T>A	p.Phe2176Tyr	p.F2176Y	ENST00000356175	NM_000267.3	2176	tTt/tAt	42/57	1	2	FACETS	0.779	0.655	0.916	0.779	0.655	0.916	CLONAL	1	TRUE	1	0.25	2		417	462	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0059116-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	82	738	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.895	0.791	1	0.895	0.791	1	CLONAL	1	TRUE	1	0.33	2		738	555	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0059116-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	40	425	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.866	0.723	1	0.866	0.723	1	CLONAL	1	TRUE	1	0.33	2		425	280	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059116-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	63	382	0	ENST00000394830.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000394830	NM_018313.4	710	Cga/Tga	17/30	0.302090686777507	1	FACETS	0.857	0.745	0.977	0.857	0.745	0.977	CLONAL	1	TRUE	0	0.33	1		382	372	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950309	17950309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059116-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	117	630	0	ENST00000458235.1:c.1418C>T	p.Ser473Phe	p.S473F	ENST00000458235	NM_000215.3	473	tCc/tTc	10/24	0.302090686777507	1	FACETS	0.914	0.826	1	0.914	0.826	1	CLONAL	1	TRUE	0	0.33	1		630	648	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115838	8115838	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059116-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	110	812	0	ENST00000346208.3:c.1184C>T	p.Ala395Val	p.A395V	ENST00000346208		395	gCc/gTc	6/6	1	2	FACETS	0.765	0.686	0.848	0.765	0.686	0.848	SUBCLONAL	1	TRUE	1	0.33	2		812	872	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755621	39755621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059116-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	115	678	1	ENST00000288319.7:c.1144C>T	p.His382Tyr	p.H382Y	ENST00000288319	NM_182918.3	382	Cat/Tat	10/10	1	2	FACETS	0.863	0.777	0.953	0.863	0.777	0.953	CLONAL	1	TRUE	1	0.33	2		679	808	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495394	149495395	+	missense_variant	Missense_Mutation	DNP	CT	CT	TC	novel	NA	P-0059116-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	118	729	0	ENST00000261799.4:c.3252_3253delinsGA	p.Glu1085Lys	p.E1085K	ENST00000261799	NM_002609.3	1084	ccAGag/ccGAag	23/23	1	2	FACETS	0.867	0.782	0.957	0.867	0.782	0.957	CLONAL	1	TRUE	1	0.33	2		729	825	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188402	142188402	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059133-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	20	327	0	ENST00000350721.4:c.6329C>G	p.Ser2110Cys	p.S2110C	ENST00000350721	NM_001184.3	2110	tCc/tGc	38/47	1	2	FACETS	0.744	0.582	0.926	0.744	0.582	0.926	CLONAL	1	TRUE	1	0.617559651374527	2		327	87	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341923	8341923	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059133-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	68	430	0	ENST00000356435.5:c.4717A>G	p.Ile1573Val	p.I1573V	ENST00000356435		1573	Ata/Gta	29/35	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.617559651374527	2		430	190	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059134-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	90	302	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.949	0.857	1	0.949	0.857	1	CLONAL	1	TRUE	1	0.79	2		302	240	SUCCESS
EED	8726	MSKCC	GRCh37	11	85963276	85963276	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059134-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	166	225	0	ENST00000263360.6:c.354C>A	p.Ser118Arg	p.S118R	ENST00000263360	NM_003797.3	118	agC/agA	3/12	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.79	2		225	401	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965346	25965346	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059134-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	262	539	0	ENST00000435504.4:c.3860A>G	p.Glu1287Gly	p.E1287G	ENST00000435504		1287	gAg/gGg	13/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.79	2		539	603	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	139	544	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.255949832225242	2		548	898	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1232964733	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	66	586	1	ENST00000324856.7:c.1015del	p.Ala339LeufsTer24	p.A339Lfs*24	ENST00000324856	NM_006015.4	337	tGg/tg	1/20	1	2	FACETS	0.687	0.595	0.786	0.687	0.595	0.786	SUBCLONAL	1	TRUE	1	0.255949832225242	2		587	751	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682399	52682400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	46	362	0	ENST00000394830.3:c.773dup	p.Asn258LysfsTer6	p.N258Kfs*6	ENST00000394830	NM_018313.4	258	aat/aaAt	8/30	1	2	FACETS	0.905	0.764	1	0.905	0.764	1	CLONAL	1	TRUE	1	0.255949832225242	2		362	397	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	52	425	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	1	2	FACETS	0.638	0.542	0.743	0.638	0.542	0.743	SUBCLONAL	1	TRUE	1	0.255949832225242	2		425	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	71	870	2	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	1	2	FACETS	0.642	0.559	0.732	0.642	0.559	0.732	SUBCLONAL	1	TRUE	1	0.255949832225242	2		872	864	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	104	539	1	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	0.116463587190152	3	FACETS	1	0.946	1	0.546	0.488	0.607	INDETERMINATE	1	TRUE	1	0.255949832225242	3		540	840	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	62	636	1	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.522	0.45	0.601	0.522	0.45	0.601	SUBCLONAL	1	TRUE	1	0.255949832225242	2		637	928	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413009	49413009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519953	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	60	729	1	ENST00000418115.1:c.14G>A	p.Arg5Gln	p.R5Q	ENST00000418115	NM_001664.2	5	cGg/cAg	2/5	1	2	FACETS	0.677	0.582	0.78	0.677	0.582	0.78	SUBCLONAL	1	TRUE	1	0.255949832225242	2		730	693	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106562	27106562	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	100	657	0	ENST00000324856.7:c.6176del	p.Asn2059ThrfsTer76	p.N2059Tfs*76	ENST00000324856	NM_006015.4	2058	gAa/ga	20/20	1	2	FACETS	0.804	0.717	0.897	0.804	0.717	0.897	CLONAL	1	TRUE	1	0.255949832225242	2		657	972	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240214	5240214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770776322	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	56	408	0	ENST00000357368.4:c.1700G>A	p.Arg567Gln	p.R567Q	ENST00000357368	NM_002850.3	567	cGg/cAg	12/38	1	2	FACETS	0.669	0.572	0.775	0.669	0.572	0.775	SUBCLONAL	1	TRUE	1	0.255949832225242	2		408	654	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643942	52643943	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	26	375	0	ENST00000394830.3:c.1953dup	p.Ser652IlefsTer13	p.S652Ifs*13	ENST00000394830	NM_018313.4	651	-/A	17/30	1	2	FACETS	0.542	0.429	0.671	0.542	0.429	0.671	SUBCLONAL	1	TRUE	1	0.255949832225242	2		375	375	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371779	55371779	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	73	596	0	ENST00000297316.4:c.469C>T	p.His157Tyr	p.H157Y	ENST00000297316	NM_022454.3	157	Cac/Tac	2/2	0.116463587190152	3	FACETS	0.926	0.809	1	0.463	0.404	0.526	INDETERMINATE	1	TRUE	1	0.255949832225242	3		596	695	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349964	15349964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1411701353	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	54	475	0	ENST00000263377.2:c.3688G>A	p.Ala1230Thr	p.A1230T	ENST00000263377	NM_058243.2	1230	Gcc/Acc	18/20	1	2	FACETS	0.693	0.591	0.804	0.693	0.591	0.804	SUBCLONAL	1	TRUE	1	0.255949832225242	2		475	609	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1962801	1962801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772470710	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	71	439	0	ENST00000382891.5:c.3295G>A	p.Glu1099Lys	p.E1099K	ENST00000382891	NM_133335.3	1099	Gag/Aag	18/22	1	2	FACETS	0.822	0.717	0.935	0.822	0.717	0.935	CLONAL	1	TRUE	1	0.255949832225242	2		439	675	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954642	17954643	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	59	563	2	ENST00000458235.1:c.251dup	p.Ser85GlufsTer46	p.S85Efs*46	ENST00000458235	NM_000215.3	84	ccg/ccCg	3/24	1	2	FACETS	0.557	0.478	0.643	0.557	0.478	0.643	SUBCLONAL	1	TRUE	1	0.255949832225242	2		565	828	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344955	118344955	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	58	461	2	ENST00000534358.1:c.3086del	p.Lys1029ArgfsTer65	p.K1029Rfs*65	ENST00000534358	NM_005933.3	1027	ctA/ct	3/36	1	2	FACETS	0.697	0.598	0.805	0.697	0.598	0.805	SUBCLONAL	1	TRUE	1	0.255949832225242	2		463	650	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	55	633	0	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	1	2	FACETS	0.499	0.425	0.579	0.499	0.425	0.579	SUBCLONAL	1	TRUE	1	0.255949832225242	2		633	862	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004813	16004813	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	65	538	0	ENST00000268712.3:c.2441del	p.Pro814HisfsTer13	p.P814Hfs*13	ENST00000268712	NM_006311.3	814	cCa/ca	20/46	1	2	FACETS	0.712	0.617	0.816	0.712	0.617	0.816	SUBCLONAL	1	TRUE	1	0.255949832225242	2		538	713	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31521250	31521250	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	45	354	0	ENST00000344624.3:c.927del	p.Glu310SerfsTer42	p.E310Sfs*42	ENST00000344624		309	aaA/aa	3/33	1	2	FACETS	0.742	0.624	0.872	0.742	0.624	0.872	SUBCLONAL	1	TRUE	1	0.255949832225242	2		354	474	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348864	11348864	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	65	478	0	ENST00000332029.2:c.472C>G	p.Pro158Ala	p.P158A	ENST00000332029	NM_003745.1	158	Ccg/Gcg	2/2	1	2	FACETS	0.934	0.81	1	0.934	0.81	1	CLONAL	1	TRUE	1	0.255949832225242	2		478	544	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821082	72821082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458157669	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	55	418	0	ENST00000268489.5:c.11093C>T	p.Thr3698Met	p.T3698M	ENST00000268489	NM_006885.3	3698	aCg/aTg	10/10	1	2	FACETS	0.745	0.637	0.863	0.745	0.637	0.863	SUBCLONAL	1	TRUE	1	0.255949832225242	2		418	577	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324221	31324221	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	64	362	0	ENST00000412585.2:c.344-2A>G		p.X115_splice	ENST00000412585	NM_005514.6	115			1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.255949832225242	2		362	383	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903688	41903688	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	65	521	0	ENST00000372991.4:c.869T>C	p.Ile290Thr	p.I290T	ENST00000372991	NM_001760.3	290	aTa/aCa	5/5	1	2	FACETS	0.644	0.557	0.738	0.644	0.557	0.738	SUBCLONAL	1	TRUE	1	0.255949832225242	2		521	789	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778977	3778977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745551441	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	77	668	0	ENST00000262367.5:c.6071C>T	p.Ala2024Val	p.A2024V	ENST00000262367	NM_004380.2	2024	gCg/gTg	31/31	1	2	FACETS	0.821	0.72	0.929	0.821	0.72	0.929	CLONAL	1	TRUE	1	0.255949832225242	2		668	733	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273455	5273455	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs758669308	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	72	439	0	ENST00000357368.4:c.377G>A	p.Arg126Gln	p.R126Q	ENST00000357368	NM_002850.3	126	cGa/cAa	4/38	1	2	FACETS	0.938	0.82	1	0.938	0.82	1	CLONAL	1	TRUE	1	0.255949832225242	2		439	600	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446165	49446166	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs398123715	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	46	591	0	ENST00000301067.7:c.1300dup	p.Leu434ProfsTer12	p.L434Pfs*12	ENST00000301067	NM_003482.3	434	cta/cCta	10/54	0.116463587190152	3	FACETS	0.535	0.449	0.63	0.267	0.224	0.315	INDETERMINATE	1	TRUE	1	0.255949832225242	3		591	758	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873125	136873125	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	62	597	0	ENST00000241393.3:c.373C>T	p.Leu125Phe	p.L125F	ENST00000241393	NM_003467.2	125	Ctc/Ttc	2/2	1	2	FACETS	0.586	0.505	0.674	0.586	0.505	0.674	SUBCLONAL	1	TRUE	1	0.255949832225242	2		597	827	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359903	87359903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs556985581	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	60	408	0	ENST00000277120.3:c.1211C>T	p.Ala404Val	p.A404V	ENST00000277120		404	gCg/gTg	11/19	1	2	FACETS	0.779	0.671	0.896	0.779	0.671	0.896	SUBCLONAL	1	TRUE	1	0.255949832225242	2		408	602	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024639	11024641	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	novel	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	69	536	0	ENST00000327064.4:c.763_765del	p.Ile255del	p.I255del	ENST00000327064	NM_199141.1	252	gaCATc/gac	6/16	1	2	FACETS	0.848	0.738	0.966	0.848	0.738	0.966	CLONAL	1	TRUE	1	0.255949832225242	2		536	636	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256718	16256718	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs774004188	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	44	504	0	ENST00000375759.3:c.3983T>C	p.Leu1328Pro	p.L1328P	ENST00000375759	NM_015001.2	1328	cTa/cCa	11/15	1	2	FACETS	0.657	0.551	0.775	0.657	0.551	0.775	SUBCLONAL	1	TRUE	1	0.255949832225242	2		504	523	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391968	139391968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs549258808	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	62	555	1	ENST00000277541.6:c.6223G>A	p.Glu2075Lys	p.E2075K	ENST00000277541	NM_017617.3	2075	Gag/Aag	34/34	1	2	FACETS	0.686	0.592	0.789	0.686	0.592	0.789	SUBCLONAL	1	TRUE	1	0.255949832225242	2		556	706	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129216	64129216	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1373979853	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	77	583	0	ENST00000334205.4:c.754C>T	p.Arg252Ter	p.R252*	ENST00000334205	NM_003942.2	252	Cga/Tga	7/17	1	2	FACETS	0.846	0.743	0.958	0.846	0.743	0.958	CLONAL	1	TRUE	1	0.255949832225242	2		583	711	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912744	100912744	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	30	415	0	ENST00000325455.5:c.2578C>T	p.Gln860Ter	p.Q860*	ENST00000325455	NM_001202474.3	860	Caa/Taa	7/8	1	2	FACETS	0.5	0.402	0.611	0.5	0.402	0.611	SUBCLONAL	1	TRUE	1	0.255949832225242	2		415	469	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975723	26975723	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	85	411	0	ENST00000381527.3:c.1231A>G	p.Thr411Ala	p.T411A	ENST00000381527	NM_001260.1	411	Act/Gct	12/13	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.255949832225242	2		411	625	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435604	110435604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	62	532	0	ENST00000375856.3:c.2797C>T	p.Pro933Ser	p.P933S	ENST00000375856	NM_003749.2	933	Ccg/Tcg	1/2	1	2	FACETS	0.854	0.738	0.98	0.854	0.738	0.98	CLONAL	1	TRUE	1	0.255949832225242	2		532	567	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95579443	95579443	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs878855246	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	29	337	0	ENST00000393063.1:c.2026C>T	p.Arg676Ter	p.R676*	ENST00000393063	NM_030621.3	676	Cga/Tga	13/28	1	2	FACETS	0.738	0.594	0.902	0.738	0.594	0.902	CLONAL	1	TRUE	1	0.255949832225242	2		337	307	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857116	9857116	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	49	481	0	ENST00000330684.3:c.4285A>G	p.Met1429Val	p.M1429V	ENST00000330684	NM_001134407.1	1429	Atg/Gtg	13/13	1	2	FACETS	0.689	0.583	0.805	0.689	0.583	0.805	SUBCLONAL	1	TRUE	1	0.255949832225242	2		481	556	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772304	68772331	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTGGGCAGAGGTGAGGGCGCGCTGCCG	CCTGGGCAGAGGTGAGGGCGCGCTGCCG	-	novel	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	70	472	0	ENST00000261769.5:c.153_163+17del		p.X51_splice	ENST00000261769	NM_004360.3	51		2/16	1	2	FACETS	0.826	0.72	0.941	0.826	0.72	0.941	CLONAL	1	TRUE	1	0.255949832225242	2		472	662	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847220	68847221	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	60	414	0	ENST00000261769.5:c.1145dup	p.Gln383SerfsTer4	p.Q383Sfs*4	ENST00000261769	NM_004360.3	381	aag/aaGg	9/16	1	2	FACETS	0.808	0.696	0.93	0.808	0.696	0.93	CLONAL	1	TRUE	1	0.255949832225242	2		414	580	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007641	62007641	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	65	535	0	ENST00000392795.3:c.226A>G	p.Ser76Gly	p.S76G	ENST00000392795	NM_001039933.1	76	Agc/Ggc	3/6	1	2	FACETS	0.746	0.646	0.854	0.746	0.646	0.854	SUBCLONAL	1	TRUE	1	0.255949832225242	2		535	681	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353728	15353728	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202165230	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	48	435	0	ENST00000263377.2:c.3152C>T	p.Ser1051Leu	p.S1051L	ENST00000263377	NM_058243.2	1051	tCg/tTg	14/20	1	2	FACETS	0.589	0.497	0.69	0.589	0.497	0.69	SUBCLONAL	1	TRUE	1	0.255949832225242	2		435	637	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661756	227661756	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	73	596	0	ENST00000305123.5:c.1699C>T	p.Arg567Ter	p.R567*	ENST00000305123	NM_005544.2	567	Cga/Tga	1/2	1	2	FACETS	0.813	0.71	0.923	0.813	0.71	0.923	CLONAL	1	TRUE	1	0.255949832225242	2		596	702	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729899	39729899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	59	460	0	ENST00000361337.2:c.1214G>A	p.Arg405Gln	p.R405Q	ENST00000361337	NM_003286.2	405	cGg/cAg	13/21	1	2	FACETS	0.771	0.663	0.888	0.771	0.663	0.888	SUBCLONAL	1	TRUE	1	0.255949832225242	2		460	598	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29446618	29446618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775159221	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	65	590	0	ENST00000544604.2:c.2449G>A	p.Gly817Ser	p.G817S	ENST00000544604	NM_001206998.1	817	Ggc/Agc	8/9	1	2	FACETS	0.799	0.692	0.914	0.799	0.692	0.914	CLONAL	1	TRUE	1	0.255949832225242	2		590	636	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63965618	63965618	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780369075	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	63	441	0	ENST00000398590.3:c.527C>T	p.Pro176Leu	p.P176L	ENST00000398590	NM_001177387.1	176	cCg/cTg	6/14	1	2	FACETS	0.842	0.728	0.965	0.842	0.728	0.965	CLONAL	1	TRUE	1	0.255949832225242	2		441	585	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981831	63981831	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs760584775	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	83	586	0	ENST00000398590.3:c.2333G>C	p.Gly778Ala	p.G778A	ENST00000398590	NM_001177387.1	778	gGc/gCc	12/14	1	2	FACETS	0.723	0.637	0.816	0.723	0.637	0.816	SUBCLONAL	1	TRUE	1	0.255949832225242	2		586	897	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182681679	182681679	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	42	287	0	ENST00000292782.4:c.379A>G	p.Thr127Ala	p.T127A	ENST00000292782	NM_020640.2	127	Aca/Gca	3/7	1	2	FACETS	0.837	0.7	0.989	0.837	0.7	0.989	CLONAL	1	TRUE	1	0.255949832225242	2		287	392	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750792	57750792	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	37	463	0	ENST00000274289.3:c.1812G>T	p.Gln604His	p.Q604H	ENST00000274289	NM_006622.3	604	caG/caT	13/14	1	2	FACETS	0.55	0.452	0.659	0.55	0.452	0.659	SUBCLONAL	1	TRUE	1	0.255949832225242	2		463	526	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055741	152055741	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1401414033	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	61	391	0	ENST00000262189.6:c.181del	p.Thr61LeufsTer44	p.T61Lfs*44	ENST00000262189	NM_170606.2	61	Act/ct	2/59	0.116463587190152	3	FACETS	1	0.944	1	0.591	0.511	0.677	INDETERMINATE	1	TRUE	1	0.255949832225242	3		391	455	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636791	8636791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059135-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	70	467	0	ENST00000356435.5:c.118G>A	p.Val40Ile	p.V40I	ENST00000356435		40	Gtt/Att	2/35	1	2	FACETS	0.691	0.601	0.788	0.691	0.601	0.788	SUBCLONAL	1	TRUE	1	0.255949832225242	2		467	792	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0059136-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	153	425	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.971	1	1	0.992	1	CLONAL	2	TRUE	1	0.29	2		425	475	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0059136-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	164	396	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.983	1	1	0.993	1	CLONAL	2	TRUE	1	0.29	2		396	464	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0059136-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	183	461	0	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	1	2	FACETS	1	0.979	1	1	0.994	1	CLONAL	2	TRUE	1	0.29	2		461	553	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242732	66242732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059136-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	168	538	0	ENST00000273854.3:c.1840C>T	p.His614Tyr	p.H614Y	ENST00000273854	NM_004439.5	614	Cat/Tat	9/18	1	2	FACETS	1	0.978	1	1	0.993	1	CLONAL	2	TRUE	1	0.29	2		538	508	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247809	10247809	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1368186167	NA	P-0059136-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	175	630	0	ENST00000340748.4:c.4393G>A	p.Gly1465Ser	p.G1465S	ENST00000340748		1465	Ggc/Agc	36/40	1	2	FACETS	1	0.977	1	1	0.993	1	CLONAL	2	TRUE	1	0.29	2		630	536	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67630386	67630390	+	frameshift_variant	Frame_Shift_Del	DEL	TTATG	TTATG	A	novel	NA	P-0059136-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	147	362	0	ENST00000272342.5:c.572_576delinsA	p.Leu191GlnfsTer14	p.L191Qfs*14	ENST00000272342	NM_019002.3	191	cTTATG/cA	5/6	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	2	TRUE	NA	0.29	2		362	464	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0059137-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	100	398	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.764835709274162	2		398	190	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236087	108236087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781894	NA	P-0059139-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	63	470	0	ENST00000278616.4:c.9023G>A	p.Arg3008His	p.R3008H	ENST00000278616	NM_000051.3	3008	cGt/cAt	63/63	0.295972533804616	0	FACETS	0.578	0.501	0.661			1	SUBCLONAL	1	TRUE	0	0.334842075236404	0		470	433	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119791	70119791	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059139-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	100	460	0	ENST00000245479.2:c.793C>T	p.Gln265Ter	p.Q265*	ENST00000245479	NM_000346.3	265	Cag/Tag	3/3	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.334842075236404	2		460	543	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023961	27023962	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGCC	novel	NA	P-0059139-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	21	432	0	ENST00000324856.7:c.1068_1072dup	p.His358ArgfsTer7	p.H358Rfs*7	ENST00000324856	NM_006015.4	356	agg/agGAGCCg	1/20	0.334842075236404	1	FACETS	0.263	0.202	0.335	0.263	0.202	0.335	SUBCLONAL	1	TRUE	0	0.334842075236404	1		432	397	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907170	101907170	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059139-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	34	317	0	ENST00000374994.4:c.1130G>T	p.Arg377Met	p.R377M	ENST00000374994	NM_004612.2	377	aGg/aTg	6/9	0.334842075236404	1	FACETS	0.881	0.727	1	0.881	0.727	1	CLONAL	1	TRUE	0	0.334842075236404	1		317	192	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0059141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	166	447	0	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.559982649826946	1	FACETS	0.997	0.926	1	0.997	0.926	1	CLONAL	1	TRUE	0	0.559982649826946	1		447	428	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390222	89390222	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs754818412	NA	P-0059141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	84	455	0	ENST00000336596.2:c.970+1G>A		p.X324_splice	ENST00000336596	NM_005233.5	324			1	2	FACETS	0.523	0.462	0.587	0.523	0.462	0.587	SUBCLONAL	1	TRUE	1	0.559982649826946	2		455	574	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423610	88423610	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	192	492	0	ENST00000360948.2:c.2225T>C	p.Ile742Thr	p.I742T	ENST00000360948	NM_001012338.2	742	aTc/aCc	18/19	0.270835407563777	1	FACETS	0.785	0.73	0.842	0.785	0.73	0.842	INDETERMINATE	1	TRUE	0	0.559982649826946	1		492	629	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313174	30313174	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	36	501	0	ENST00000262643.3:c.868G>T	p.Asp290Tyr	p.D290Y	ENST00000262643	NM_001238.2	290	Gac/Tac	10/12	0.532637324031563	2	FACETS	0.203	0.166	0.245	0.102	0.083	0.123	SUBCLONAL	1	TRUE	0	0.559982649826946	2		501	633	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281803	142281803	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059141-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	54	401	0	ENST00000350721.4:c.441A>T	p.Lys147Asn	p.K147N	ENST00000350721	NM_001184.3	147	aaA/aaT	4/47	1	2	FACETS	0.357	0.305	0.414	0.357	0.305	0.414	SUBCLONAL	1	TRUE	1	0.559982649826946	2		401	540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0059142-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	115	1110	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.426056321753014	1	FACETS	0.977	0.886	1	0.977	0.886	1	CLONAL	1	TRUE	0	0.426056321753014	1		1111	435	SUCCESS
APC	324	MSKCC	GRCh37	5	112175945	112175945	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059142-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	32	522	0	ENST00000257430.4:c.4654G>T	p.Glu1552Ter	p.E1552*	ENST00000257430	NM_000038.5	1552	Gag/Tag	16/16	0.426056321753014	1	FACETS	0.324	0.263	0.393	0.324	0.263	0.393	SUBCLONAL	1	TRUE	0	0.426056321753014	1		522	365	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105765	27105766	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0059142-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	54	578	0	ENST00000324856.7:c.5378dup	p.Asp1794GlyfsTer8	p.D1794Gfs*8	ENST00000324856	NM_006015.4	1792	-/A	20/20	1	2	FACETS	0.463	0.395	0.537	0.463	0.395	0.537	SUBCLONAL	1	TRUE	1	0.426056321753014	2		578	548	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640571	3640571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	16	658	0	ENST00000294008.3:c.3068C>T	p.Ala1023Val	p.A1023V	ENST00000294008	NM_032444.2	1023	gCt/gTt	12/15	0.220514871240435	1	FACETS	0.402	0.297	0.527	0.402	0.297	0.527	SUBCLONAL	1	FALSE	0	0.287640258208692	1		658	237	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164946	123164946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059143-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	10	213	0	ENST00000218089.9:c.259G>T	p.Val87Phe	p.V87F	ENST00000218089	NM_001042749.1	87	Gtt/Ttt	5/35	0.272207729501739	2	FACETS	0.473	0.321	0.662			1	SUBCLONAL	1	FALSE	NA	0.287640258208692	2		213	147	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	74	366	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.48	2		366	289	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0059144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	113	404	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.795	0.718	0.877	0.795	0.718	0.877	SUBCLONAL	1	TRUE	1	0.48	2		404	592	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692775	89692775	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554898053	NA	P-0059144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	55	283	0	ENST00000371953.3:c.259C>T	p.Gln87Ter	p.Q87*	ENST00000371953	NM_000314.4	87	Caa/Taa	5/9	1	2	FACETS	0.746	0.643	0.858	0.746	0.643	0.858	SUBCLONAL	1	TRUE	1	0.48	2		283	307	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518216	187518216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	93	557	0	ENST00000441802.2:c.12478C>T	p.Arg4160Cys	p.R4160C	ENST00000441802	NM_005245.3	4160	Cgt/Tgt	25/27	1	2	FACETS	0.821	0.733	0.914	0.821	0.733	0.914	CLONAL	1	TRUE	1	0.48	2		557	472	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617533	158617533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751000395	NA	P-0059144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	40	541	0	ENST00000263640.3:c.1123C>T	p.Arg375Cys	p.R375C	ENST00000263640	NM_001105.4	375	Cgt/Tgt	9/11	1	2	FACETS	0.294	0.244	0.351	0.294	0.244	0.351	SUBCLONAL	1	TRUE	1	0.48	2		541	566	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102136	27102137	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0059144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	186	522	0	ENST00000324856.7:c.5063_5064dup	p.Asp1689Ter	p.D1689*	ENST00000324856	NM_006015.4	1688	tta/tTAta	19/20	0.434626083164813	2	FACETS	0.873	0.815	0.931	0.873	0.815	0.931	CLONAL	2	TRUE	0	0.48	2		522	444	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692875	89692875	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1114167647	NA	P-0059144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	53	200	0	ENST00000371953.3:c.359C>A	p.Ala120Glu	p.A120E	ENST00000371953	NM_000314.4	120	gCa/gAa	5/9	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.48	2		200	212	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120327	70120328	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0059144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	28	668	0	ENST00000245479.2:c.1329_1330del	p.Asp444ProfsTer133	p.D444Pfs*133	ENST00000245479	NM_000346.3	443	acCGac/acac	3/3	1	2	FACETS	0.241	0.192	0.297	0.241	0.192	0.297	SUBCLONAL	1	TRUE	1	0.48	2		668	484	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229256	36229256	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	48	723	0	ENST00000222270.7:c.7946del	p.Arg2649ProfsTer89	p.R2649Pfs*89	ENST00000222270	NM_014727.1	2649	cGc/cc	37/37	1	2	FACETS	0.357	0.301	0.419	0.357	0.301	0.419	SUBCLONAL	1	TRUE	1	0.48	2		723	560	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39347488	39347488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	22	337	0	ENST00000402219.2:c.76G>A	p.Ala26Thr	p.A26T	ENST00000402219	NM_005633.3	26	Gcg/Acg	1/23	1	2	FACETS	0.374	0.29	0.471	0.374	0.29	0.471	SUBCLONAL	1	TRUE	1	0.48	2		337	245	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589563	67589598	+	inframe_deletion	In_Frame_Del	DEL	TGAAGCTGTAGGGAAAAAATTACATGAATATAACAC	TGAAGCTGTAGGGAAAAAATTACATGAATATAACAC	-	novel	NA	P-0059144-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	62	208	0	ENST00000274335.5:c.1327_1362del	p.Glu443_Thr454del	p.E443_T454del	ENST00000274335		442	atTGAAGCTGTAGGGAAAAAATTACATGAATATAACACt/att	10/15	1	2	FACETS	0.783	0.681	0.892	0.783	0.681	0.892	SUBCLONAL	1	TRUE	1	0.48	2		208	330	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	162	302	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.959	0.895	1	1	0.994	1	CLONAL	4	TRUE	1	0.248420949524692	2		302	340	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0059145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	286	885	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA	2	FACETS	0.892	0.846	0.939			1	INDETERMINATE	4	TRUE	NA	0.248420949524692	2		885	645	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940366	49940366	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770141981	NA	P-0059145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	464	376	0	ENST00000296474.3:c.677C>T	p.Ser226Leu	p.S226L	ENST00000296474	NM_002447.2	226	tCg/tTg	1/20	0.248420949524692	4	FACETS	1	0.99	1	1	0.998	1	CLONAL	5	TRUE	2	0.248420949524692	4		376	863	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977891	134977891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	183	328	0	ENST00000398015.3:c.2884C>T	p.Gln962Ter	p.Q962*	ENST00000398015	NM_004441.4	962	Cag/Tag	16/16	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	3	TRUE	NA	0.248420949524692	2		328	444	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349317	89349318	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	rs1555528400	NA	P-0059145-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	44	390	1	ENST00000301030.4:c.3632_3633del	p.Lys1211ArgfsTer21	p.K1211Rfs*21	ENST00000301030	NM_001256183.1	1211	aAA/a	9/13	1	2	FACETS	0.585	0.489	0.69	0.585	0.489	0.69	SUBCLONAL	1	TRUE	1	0.248420949524692	2		391	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578195	7578197	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0059163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	244	432	0	ENST00000269305.4:c.652_654del	p.Val218del	p.V218del	ENST00000269305	NM_001126112.2	218	GTG/-	6/11	0.769590532253196	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.764812453858603	2		432	295	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891498	76891498	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	30	264	0	ENST00000373344.5:c.4607A>C	p.Lys1536Thr	p.K1536T	ENST00000373344	NM_000489.3	1536	aAg/aCg	16/35	0.235015785075346	3	FACETS	0.262	0.211	0.32	0.087	0.07	0.107	INDETERMINATE	1	TRUE	0	0.764812453858603	3		264	414	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414227	32414227	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	74	359	0	ENST00000332351.3:c.1324C>A	p.Gln442Lys	p.Q442K	ENST00000332351	NM_024426.4	442	Caa/Aaa	8/10	0.523336781144953	1	FACETS	0.381	0.336	0.428	0.381	0.336	0.428	SUBCLONAL	1	TRUE	0	0.764812453858603	1		359	314	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857044	9857044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201707833	NA	P-0059163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	53	317	1	ENST00000330684.3:c.4357G>A	p.Val1453Met	p.V1453M	ENST00000330684	NM_001134407.1	1453	Gtg/Atg	13/13	0.75792656303671	3	FACETS	0.448	0.382	0.519	0.224	0.191	0.26	SUBCLONAL	1	TRUE	1	0.764812453858603	3		318	428	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406597	70406597	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	55	366	0	ENST00000373644.4:c.4111A>G	p.Ser1371Gly	p.S1371G	ENST00000373644	NM_030625.2	1371	Agt/Ggt	4/12	0.512096272982522	5	FACETS	0.575	0.492	0.666	0.192	0.164	0.222	SUBCLONAL	1	TRUE	2	0.764812453858603	5		366	537	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380577	31380577	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0059163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	53	396	0	ENST00000328111.2:c.1066+1G>A		p.X356_splice	ENST00000328111	NM_006892.3	356			0.585787625927362	3	FACETS	0.41	0.35	0.476	0.205	0.175	0.238	SUBCLONAL	1	TRUE	1	0.764812453858603	3		396	467	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604181	189604181	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0059163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	298	343	0	ENST00000264731.3:c.1350-2A>T		p.X450_splice	ENST00000264731	NM_003722.4	450			0.769590532253196	3	FACETS	1	0.971	1	0.683	0.651	0.714	CLONAL	2	TRUE	0	0.764812453858603	3		343	526	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517945	8517946	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0059163-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	68	363	0	ENST00000356435.5:c.1445dup	p.Leu482PhefsTer25	p.L482Ffs*25	ENST00000356435		482	tta/ttTa	10/35	0.764812453858603	6	FACETS	0.468	0.405	0.535	0.117	0.101	0.134	SUBCLONAL	1	TRUE	2	0.764812453858603	6		363	962	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	73	302	0				ENST00000310581	NM_198253.2	-/1132			0.704112068997625	3	FACETS	0.899	0.794	1	0.45	0.397	0.506	CLONAL	1	TRUE	1	0.718915557977255	3		302	307	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0059164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	263	885	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.718915557977255	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.718915557977255	2		885	365	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879322	151879322	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	165	470	0	ENST00000262189.6:c.5623C>T	p.Gln1875Ter	p.Q1875*	ENST00000262189	NM_170606.2	1875	Cag/Tag	36/59	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.718915557977255	2		470	401	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098502	108098502	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0059164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	66	220	0	ENST00000278616.4:c.73-1G>T		p.X25_splice	ENST00000278616	NM_000051.3	25			0.718915557977255	1	FACETS	0.948	0.854	1	0.948	0.854	1	CLONAL	1	TRUE	0	0.718915557977255	1		220	124	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564853	41564853	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	108	423	0	ENST00000263253.7:c.4154G>T	p.Cys1385Phe	p.C1385F	ENST00000263253	NM_001429.3	1385	tGc/tTc	25/31	1	2	FACETS	0.969	0.881	1	0.969	0.881	1	CLONAL	1	TRUE	1	0.718915557977255	2		423	310	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877154	151877154	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs767365126	NA	P-0059164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	152	438	0	ENST00000262189.6:c.7207C>T	p.Arg2403Ter	p.R2403*	ENST00000262189	NM_170606.2	2403	Cga/Tga	37/59	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.718915557977255	2		438	374	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425201	49425201	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	163	544	0	ENST00000301067.7:c.13287del	p.Gln4429HisfsTer3	p.Q4429Hfs*3	ENST00000301067	NM_003482.3	4429	caG/ca	39/54	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.718915557977255	2		544	426	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426203	49426204	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0059164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	158	539	0	ENST00000301067.7:c.12284dup	p.Arg4096GlufsTer11	p.R4096Efs*11	ENST00000301067	NM_003482.3	4095	ctg/ctTg	39/54	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.718915557977255	2		539	406	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636730	176636730	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0059164-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	107	400	0	ENST00000439151.2:c.1331del	p.Pro444LeufsTer33	p.P444Lfs*33	ENST00000439151	NM_022455.4	444	Cct/ct	5/23	0.718915557977255	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.718915557977255	1		400	153	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223331	36223331	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	35	641	0	ENST00000222270.7:c.5881C>T	p.Pro1961Ser	p.P1961S	ENST00000222270	NM_014727.1	1961	Cct/Tct	28/37	0.722044568156748	1	FACETS	0.198	0.162	0.238	0.198	0.162	0.238	SUBCLONAL	1	TRUE	0	0.722044568156748	1		641	313	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745938	162745938	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	53	381	0	ENST00000367921.3:c.2061del	p.Lys688SerfsTer11	p.K688Sfs*11	ENST00000367921	NM_006182.2	687	ctG/ct	16/18	1	2	FACETS	0.415	0.355	0.48	0.415	0.355	0.48	SUBCLONAL	1	TRUE	1	0.722044568156748	2		381	354	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572408	95572408	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059165-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	117	333	0	ENST00000393063.1:c.2957C>A	p.Pro986Gln	p.P986Q	ENST00000393063	NM_030621.3	986	cCa/cAa	19/28	1	2	FACETS	0.939	0.857	1	0.939	0.857	1	CLONAL	1	TRUE	1	0.722044568156748	2		333	345	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0059166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	258	738	0				ENST00000310581	NM_198253.2	-/1132			0.536254876162241	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.596653725397436	3		738	543	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0059166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	68	259	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.95	0.837	1	0.95	0.837	1	CLONAL	1	TRUE	1	0.596653725397436	2		259	240	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66518960	66518960	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	173	421	0	ENST00000358598.2:c.241G>A	p.Glu81Lys	p.E81K	ENST00000358598	NM_212471.2	81	Gag/Aag	3/11	1	2	FACETS	0.971	0.899	1	0.971	0.899	1	CLONAL	1	TRUE	1	0.596653725397436	2		421	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0059166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	232	582	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.596653725397436	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.596653725397436	1		582	481	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872380	45872380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	222	447	0	ENST00000391945.4:c.131C>T	p.Ser44Leu	p.S44L	ENST00000391945	NM_000400.3	44	tCa/tTa	3/23	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.596653725397436	2		447	650	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045016	47045016	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0059166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	207	298	0	ENST00000377604.3:c.2342C>G	p.Ser781Ter	p.S781*	ENST00000377604	NM_001204468.1	781	tCa/tGa	20/24	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.596653725397436	1		298	367	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843447	3843447	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783461	NA	P-0059166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	86	477	0	ENST00000262367.5:c.1156C>T	p.Arg386Ter	p.R386*	ENST00000262367	NM_004380.2	386	Cga/Tga	4/31	0.38045961152102	1	FACETS	0.385	0.341	0.432	0.385	0.341	0.432	SUBCLONAL	1	TRUE	0	0.596653725397436	1		477	525	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793152	33793152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	164	403	1	ENST00000498907.2:c.169G>A	p.Glu57Lys	p.E57K	ENST00000498907	NM_004364.3	57	Gag/Aag	1/1	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.596653725397436	2		404	488	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974152	2974152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	186	464	0	ENST00000396946.4:c.1453G>A	p.Glu485Lys	p.E485K	ENST00000396946	NM_032415.4	485	Gaa/Aaa	10/25	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.596653725397436	2		464	556	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11015753	11015753	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0059166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	187	495	0	ENST00000327064.4:c.346+1G>A		p.X116_splice	ENST00000327064	NM_199141.1	116			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.596653725397436	2		495	601	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924914	49924914	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	179	513	0	ENST00000296474.3:c.4029G>C	p.Gln1343His	p.Q1343H	ENST00000296474	NM_002447.2	1343	caG/caC	20/20	1	2	FACETS	0.962	0.891	1	0.962	0.891	1	CLONAL	1	TRUE	1	0.596653725397436	2		513	624	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112445	115112445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	171	531	0	ENST00000257566.3:c.1295C>T	p.Ser432Leu	p.S432L	ENST00000257566	NM_016569.3	432	tCg/tTg	7/8	1	2	FACETS	0.951	0.879	1	0.951	0.879	1	CLONAL	1	TRUE	1	0.596653725397436	2		531	603	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128848686	128848686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763192441	NA	P-0059166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	163	447	1	ENST00000249373.3:c.1351C>T	p.Arg451Cys	p.R451C	ENST00000249373	NM_005631.4	451	Cgc/Tgc	7/12	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.596653725397436	2		448	528	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023262	33023262	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	192	516	0	ENST00000300177.4:c.371C>G	p.Ser124Cys	p.S124C	ENST00000300177	NM_001191322.1	124	tCt/tGt	2/2	0.289980619468349	1	FACETS	0.71	0.66	0.762	0.71	0.66	0.762	INDETERMINATE	1	TRUE	0	0.596653725397436	1		516	636	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982298	201982364	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCGTCCCCACAGATGGTTTTCGTGACTGCAAGAAGGGGGATCCCAAGCACGGGAAGCGGAAACGAGG	CCGTCCCCACAGATGGTTTTCGTGACTGCAAGAAGGGGGATCCCAAGCACGGGAAGCGGAAACGAGG	-	novel	NA	P-0059166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	85	506	0	ENST00000359651.3:c.689-9_746del		p.X230_splice	ENST00000359651		230		6/8	0.29027463758627	2	FACETS	0.388	0.343	0.437	0.194	0.171	0.219	INDETERMINATE	1	TRUE	0	0.596653725397436	2		506	734	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870827	12870834	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGCAGG	CAGGCAGG	-	novel	NA	P-0059166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	207	450	0	ENST00000228872.4:c.55_62del	p.Arg19GlyfsTer103	p.R19Gfs*103	ENST00000228872	NM_004064.3	18	gcCAGGCAGGcg/gccg	1/3	0.289980619468349	1	FACETS	0.924	0.865	0.984	0.924	0.865	0.984	INDETERMINATE	1	TRUE	0	0.596653725397436	1		450	527	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50789385	50789385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	150	326	0	ENST00000307179.4:c.2995G>A	p.Glu999Lys	p.E999K	ENST00000307179		999	Gaa/Aaa	18/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.596653725397436	2		326	437	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127418	17127418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	228	456	0	ENST00000285071.4:c.436G>A	p.Glu146Lys	p.E146K	ENST00000285071	NM_144997.5	146	Gag/Aag	6/14	0.38045961152102	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.596653725397436	1		456	432	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11015665	11015665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1481268617	NA	P-0059166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	178	516	0	ENST00000327064.4:c.259G>A	p.Glu87Lys	p.E87K	ENST00000327064	NM_199141.1	87	Gag/Aag	2/16	1	2	FACETS	0.921	0.852	0.992	0.921	0.852	0.992	CLONAL	1	TRUE	1	0.596653725397436	2		516	648	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11015671	11015671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	184	508	0	ENST00000327064.4:c.265G>A	p.Glu89Lys	p.E89K	ENST00000327064	NM_199141.1	89	Gag/Aag	2/16	1	2	FACETS	0.955	0.885	1	0.955	0.885	1	CLONAL	1	TRUE	1	0.596653725397436	2		508	646	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976481	25976503	+	frameshift_variant	Frame_Shift_Del	DEL	CTCACCTGCATCTCAGGTGTAAA	CTCACCTGCATCTCAGGTGTAAA	-	novel	NA	P-0059166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	102	293	0	ENST00000435504.4:c.1042_1064del	p.Phe348AsnfsTer6	p.F348Nfs*6	ENST00000435504		348	TTTACACCTGAGATGCAGGTGAGa/a	11/13	1	2	FACETS	0.83	0.747	0.916	0.83	0.747	0.916	CLONAL	1	TRUE	1	0.596653725397436	2		293	412	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994388	25994388	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0059166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	185	462	0	ENST00000435504.4:c.425C>G	p.Ser142Ter	p.S142*	ENST00000435504		142	tCa/tGa	6/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.596653725397436	2		462	543	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028268	48028268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395294066	NA	P-0059166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	67	331	0	ENST00000234420.5:c.3146C>T	p.Ser1049Phe	p.S1049F	ENST00000234420	NM_000179.2	1049	tCt/tTt	4/10	1	2	FACETS	0.428	0.372	0.488	0.428	0.372	0.488	SUBCLONAL	1	TRUE	1	0.596653725397436	2		331	525	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400332	225400332	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	67	246	0	ENST00000264414.4:c.291G>C	p.Leu97Phe	p.L97F	ENST00000264414	NM_003590.4	97	ttG/ttC	3/16	1	2	FACETS	0.593	0.517	0.673	0.593	0.517	0.673	SUBCLONAL	1	TRUE	1	0.596653725397436	2		246	379	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130639	29130639	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	99	479	0	ENST00000328354.6:c.71G>C	p.Ser24Thr	p.S24T	ENST00000328354	NM_007194.3	24	aGc/aCc	2/15	NA	2	FACETS	0.612	0.548	0.68			1	INDETERMINATE	1	TRUE	NA	0.596653725397436	2		479	542	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525125	187525125	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	123	304	0	ENST00000441802.2:c.10555G>C	p.Asp3519His	p.D3519H	ENST00000441802	NM_005245.3	3519	Gat/Cat	19/27	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.596653725397436	2		304	393	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410961	31410961	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	301	424	0	ENST00000344624.3:c.3559C>G	p.Gln1187Glu	p.Q1187E	ENST00000344624		1187	Cag/Gag	28/33	0.536254876162241	3	FACETS	0.89	0.843	0.937	0.89	0.843	0.937	CLONAL	2	TRUE	1	0.596653725397436	3		424	736	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750750	128750750	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	93	513	0	ENST00000377970.2:c.287C>G	p.Ser96Cys	p.S96C	ENST00000377970	NM_002467.4	96	tCc/tGc	2/3	0.289980619468349	1	FACETS	0.396	0.353	0.442	0.396	0.353	0.442	INDETERMINATE	1	TRUE	0	0.596653725397436	1		513	552	SUCCESS
MTAP	4507	MSKCC	GRCh37	9	21854850	21854850	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs374944293	NA	P-0059166-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	191	391	0	ENST00000380172.4:c.671G>A	p.Trp224Ter	p.W224*	ENST00000380172	NM_002451.3	224	tGg/tAg	6/8	0.596653725397436	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.596653725397436	1		391	379	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131161	55131161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	2679	412	0	ENST00000257290.5:c.704G>A	p.Cys235Tyr	p.C235Y	ENST00000257290	NM_006206.4	235	tGt/tAt	5/23	0.897090889675613	23	FACETS	0.992	0.985	1	0.947	0.94	0.955	CLONAL	21	TRUE	1	0.897090889675613	23		412	2986	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416781	29416781	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059167-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	113	427	0	ENST00000389048.3:c.4172A>G	p.Asp1391Gly	p.D1391G	ENST00000389048	NM_004304.4	1391	gAt/gGt	29/29	0.352924020354376	1	FACETS	0.671	0.62	0.721	0.671	0.62	0.721	INDETERMINATE	1	TRUE	0	0.897090889675613	1		427	207	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0059168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	63	327	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.331284397669436	1	FACETS	0.795	0.691	0.908	0.795	0.691	0.908	CLONAL	1	TRUE	0	0.331284397669436	1		327	399	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652981	29652982	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0059168-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	119	375	0	ENST00000356175.3:c.4917dup	p.Lys1640Ter	p.K1640*	ENST00000356175	NM_000267.3	1639	tct/tcTt	36/57	0.331284397669436	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.331284397669436	1		375	515	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467763	50467763	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059169-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	91	611	0	ENST00000331340.3:c.998C>G	p.Thr333Arg	p.T333R	ENST00000331340	NM_006060.4	333	aCg/aGg	8/8	1	2	FACETS	0.86	0.769	0.954	0.86	0.769	0.954	CLONAL	1	TRUE	1	0.584913655962631	2		611	362	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0059170-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	13	566	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		566	557	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0059170-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	24	518	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		518	761	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486295	8486295	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs755670388	NA	P-0059171-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	152	443	0	ENST00000356435.5:c.2522T>C	p.Ile841Thr	p.I841T	ENST00000356435		841	aTt/aCt	17/35	0.262162980445417	2	FACETS	0.989	0.91	1	0.989	0.91	1	CLONAL	2	TRUE	0	0.29271466429129	2		443	525	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249977	110249977	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059171-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	83	515	0	ENST00000374672.4:c.698C>T	p.Ala233Val	p.A233V	ENST00000374672	NM_004235.4	233	gCg/gTg	3/5	0.262162980445417	2	FACETS	1	0.904	1	0.513	0.453	0.576	CLONAL	1	TRUE	0	0.29271466429129	2		515	553	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242494	+	protein_altering_variant	In_Frame_Del	DEL	TAAGAGAAGCAACATCTCCGAAAGC	TAAGAGAAGCAACATCTCCGAAAGC	CGAAAGG	novel	NA	P-0059171-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	94	365	0	ENST00000275493.2:c.2240_2264delinsCGAAAGG	p.Leu747_Ala755delinsSerLysGly	p.L747_A755delinsSKG	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCCGAAAGCc/tCGAAAGGc	19/28	0.198150603306273	4	FACETS	0.785	0.7	0.874	0.785	0.7	0.874	SUBCLONAL	2	TRUE	2	0.29271466429129	4		365	529	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101037	27101037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	62	486	0	ENST00000324856.7:c.4319C>T	p.Thr1440Ile	p.T1440I	ENST00000324856	NM_006015.4	1440	aCa/aTa	18/20	0.187390093863745	1	FACETS	0.572	0.495	0.656	0.572	0.495	0.656	INDETERMINATE	1	TRUE	0	0.353342448129021	1		486	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578400	7578400	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	114	645	1	ENST00000269305.4:c.530C>A	p.Pro177His	p.P177H	ENST00000269305	NM_001126112.2	177	cCc/cAc	5/11	0.353342448129021	1	FACETS	0.966	0.873	1	0.966	0.873	1	CLONAL	1	TRUE	0	0.353342448129021	1		646	550	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121912580	NA	P-0059172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	150	381	0	ENST00000342988.3:c.1157G>T	p.Gly386Val	p.G386V	ENST00000342988	NM_005359.5	386	gGt/gTt	10/12	0.353342448129021	2	FACETS	0.879	0.809	0.951	0.879	0.809	0.951	CLONAL	2	TRUE	0	0.353342448129021	2		381	483	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18943047	18943047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	126	583	0	ENST00000262803.5:c.29C>T	p.Ser10Leu	p.S10L	ENST00000262803	NM_002911.3	10	tCg/tTg	1/24	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.353342448129021	2		583	682	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721166	176721166	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	47	535	0	ENST00000439151.2:c.6797A>G	p.Lys2266Arg	p.K2266R	ENST00000439151	NM_022455.4	2266	aAa/aGa	23/23	0.192685636993482	3	FACETS	0.476	0.401	0.56	0.159	0.133	0.187	INDETERMINATE	1	TRUE	0	0.353342448129021	3		535	657	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342174	70342174	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059172-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	44	511	0	ENST00000374080.3:c.1226G>T	p.Gly409Val	p.G409V	ENST00000374080		409	gGt/gTt	8/45	0.230538604009393	2	FACETS	0.42	0.352	0.496	0.21	0.176	0.248	SUBCLONAL	1	TRUE	0	0.353342448129021	2		511	593	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592139	55592139	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059191-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	60	380	0	ENST00000288135.5:c.1463C>A	p.Thr488Lys	p.T488K	ENST00000288135	NM_000222.2	488	aCg/aAg	9/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.380433291775712	2		380	226	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	111	575	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.119578440287354	5	FACETS	1	0.972	1	0.805	0.726	0.887	INDETERMINATE	2	TRUE	2	0.236997354941819	5		575	526	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874263	155874263	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1557960039	NA	P-0059192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	138	443	0	ENST00000368323.3:c.268A>G	p.Met90Val	p.M90V	ENST00000368323	NM_006912.5	90	Atg/Gtg	5/6	0.236997354941819	3	FACETS	0.918	0.841	0.997	1	0.985	1	CLONAL	3	TRUE	1	0.236997354941819	3		443	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577534	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	novel	NA	P-0059192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	110	431	0	ENST00000269305.4:c.747_749del	p.Arg249_Pro250delinsSer	p.R249_P250delinsS	ENST00000269305	NM_001126112.2	249	agGCCc/agc	7/11	0.236997354941819	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.236997354941819	2		431	417	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47422636	47422638	+	inframe_deletion	In_Frame_Del	DEL	ACG	ACG	-	novel	NA	P-0059192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	102	415	0	ENST00000404338.3:c.704_706del	p.Asn235_Val236delinsMet	p.N235_V236delinsM	ENST00000404338	NM_004491.4	235	aACGtg/atg	1/6	0.119578440287354	5	FACETS	1	0.961	1	0.764	0.686	0.846	INDETERMINATE	2	TRUE	2	0.236997354941819	5		415	509	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111406	56111407	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCGGCGGCGGGGAATCGCGCC	novel	NA	P-0059192-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	20	539	0	ENST00000399503.3:c.7_27dup	p.Ala3_Ala9dup	p.A3_A9dup	ENST00000399503	NM_005921.1	3	-/GCGGCGGCGGGGAATCGCGCC	1/20	1	2	FACETS	0.623	0.477	0.793	0.623	0.477	0.793	SUBCLONAL	1	TRUE	1	0.236997354941819	2		539	271	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183794	10183794	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	51	474	0	ENST00000256474.2:c.264del	p.Trp88CysfsTer71	p.W88Cfs*71	ENST00000256474	NM_000551.3	88	tGg/tg	1/3	0.452422811503412	2	FACETS	0.762	0.662	0.866	0.762	0.662	0.866	SUBCLONAL	2	FALSE	0	0.452422811503412	2		474	148	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651447	52651447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	33	442	1	ENST00000394830.3:c.1649C>T	p.Pro550Leu	p.P550L	ENST00000394830	NM_018313.4	550	cCa/cTa	15/30	0.452422811503412	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	2	FALSE	0	0.452422811503412	2		443	66	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174418	11174418	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0059193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	42	342	0	ENST00000361445.4:c.7257A>C	p.Glu2419Asp	p.E2419D	ENST00000361445	NM_004958.3	2419	gaA/gaC	53/58	0.452422811503412	3	FACETS	0.791	0.673	0.915	0.791	0.673	0.915	CLONAL	2	FALSE	1	0.452422811503412	3		342	144	SUCCESS
ATXN7	6314	MSKCC	GRCh37	3	63981678	63981678	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2075753068	NA	P-0059193-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	59	629	0	ENST00000398590.3:c.2180C>T	p.Ser727Phe	p.S727F	ENST00000398590	NM_001177387.1	727	tCt/tTt	12/14	0.452422811503412	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	FALSE	0	0.452422811503412	2		629	105	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912664	NA	P-0059194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	183	377	0	ENST00000269305.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000269305	NM_001126112.2	337	cGc/cAc	10/11	0.869601426865683	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.869601426865683	1		377	224	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923159	48923159	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059194-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	56	179	0	ENST00000267163.4:c.607+1del		p.G203fs	ENST00000267163	NM_000321.2	203	Ggg/gg	6/27	0.869601426865683	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.869601426865683	1		179	71	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129198	2129198	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0059196-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	61	687	0	ENST00000219476.3:c.3131+1G>T		p.X1044_splice	ENST00000219476	NM_000548.3	1044			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		687	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0059206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	425	303	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.598163802181536	3	FACETS	0.944	0.914	0.974	0.944	0.914	0.974	CLONAL	3	TRUE	0	0.662490245709353	3		303	603	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197020	123197020	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	23	250	0	ENST00000218089.9:c.1786G>C	p.Asp596His	p.D596H	ENST00000218089	NM_001042749.1	596	Gat/Cat	19/35	0.609345194000688	3	FACETS	0.4	0.313	0.5	0.2	0.156	0.25	SUBCLONAL	1	TRUE	1	0.662490245709353	3		250	231	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462326	89462326	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	170	383	0	ENST00000336596.2:c.1798C>T	p.His600Tyr	p.H600Y	ENST00000336596	NM_005233.5	600	Cat/Tat	10/17	0.652879357986909	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.662490245709353	2		383	255	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256461	115256461	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs376177995	NA	P-0059206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	62	367	0	ENST00000369535.4:c.250A>G	p.Ile84Val	p.I84V	ENST00000369535	NM_002524.4	84	Atc/Gtc	3/7	0.541042880774512	3	FACETS	0.579	0.502	0.663	0.29	0.251	0.332	SUBCLONAL	1	TRUE	1	0.662490245709353	3		367	430	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878073	48878074	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0059206-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	253	611	0	ENST00000267163.4:c.25_26insG	p.Thr9SerfsTer22	p.T9Sfs*22	ENST00000267163	NM_000321.2	9	acg/aGcg	1/27	0.662490245709353	2	FACETS	0.957	0.913	1	0.957	0.913	1	CLONAL	2	TRUE	0	0.662490245709353	2		611	399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0059207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	213	891	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.657432924265453	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.657432924265453	1		891	408	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608919	100608919	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	194	337	0	ENST00000308731.7:c.1689G>A	p.Trp563Ter	p.W563*	ENST00000308731	NM_000061.2	563	tgG/tgA	17/19	0.657432924265453	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.657432924265453	1		337	317	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0059207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	207	190	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.657432924265453	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.657432924265453	3		190	412	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0059207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	95	341	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.657432924265453	3	FACETS	0.932	0.835	1	0.466	0.417	0.517	CLONAL	1	TRUE	1	0.657432924265453	3		341	412	SUCCESS
RET	5979	MSKCC	GRCh37	10	43602015	43602015	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	183	461	0	ENST00000355710.3:c.1059C>A	p.Asp353Glu	p.D353E	ENST00000355710	NM_020975.4	353	gaC/gaA	5/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.657432924265453	2		461	515	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243801	41243801	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	517	431	0	ENST00000357654.3:c.3747del	p.Glu1250SerfsTer14	p.E1250Sfs*14	ENST00000357654	NM_007294.3	1249	acC/ac	10/23	0.657432924265453	3	FACETS	0.988	0.961	1	0.988	0.961	1	CLONAL	3	TRUE	0	0.657432924265453	3		431	705	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251813	212251814	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0059207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	187	418	0	ENST00000342788.4:c.3245_3246delinsTT	p.Arg1082Ile	p.R1082I	ENST00000342788	NM_005235.2	1082	aGA/aTT	27/28	1	2	FACETS	0.996	0.926	1	0.996	0.926	1	CLONAL	1	TRUE	1	0.657432924265453	2		418	571	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845241	151845241	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059207-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	173	518	0	ENST00000262189.6:c.13771T>A	p.Tyr4591Asn	p.Y4591N	ENST00000262189	NM_170606.2	4591	Tat/Aat	52/59	0.453743832722366	4	FACETS	0.95	0.875	1	0.475	0.437	0.515	CLONAL	1	TRUE	2	0.657432924265453	4		518	918	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0059208-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	133	804	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.215618584280901	2	FACETS	1	0.971	1	0.58	0.527	0.635	CLONAL	1	FALSE	0	0.315855134254519	2		804	726	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0059209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	114	328	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.351493012961751	5	FACETS	0.828	0.748	0.913	0.828	0.748	0.913	CLONAL	2	TRUE	3	0.351493012961751	5		328	598	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240285	41240285	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	9	529	0	ENST00000379561.5:c.65C>G	p.Ser22Trp	p.S22W	ENST00000379561	NM_002015.3	22	tCg/tGg	1/3	1	2	FACETS	0.123	0.081	0.178	0.123	0.081	0.178	SUBCLONAL	1	TRUE	1	0.351493012961751	2		529	415	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55231508	55231508	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	90	536	0	ENST00000275493.2:c.1714A>G	p.Thr572Ala	p.T572A	ENST00000275493	NM_005228.3	572	Aca/Gca	14/28	0.327578904541229	3	FACETS	1	0.973	1	0.656	0.584	0.731	CLONAL	1	TRUE	1	0.351493012961751	3		536	459	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221230	1221255	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGTACCCCTTCGAAGGGGACAACA	TCTGTACCCCTTCGAAGGGGACAACA	-	novel	NA	P-0059209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	117	557	0	ENST00000326873.7:c.756_781del	p.Tyr253GlnfsTer4	p.Y253Qfs*4	ENST00000326873	NM_000455.4	251	ggTCTGTACCCCTTCGAAGGGGACAACAtc/ggtc	6/10	0.351493012961751	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.351493012961751	1		557	421	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291545	15291545	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	105	628	0	ENST00000263388.2:c.3089G>C	p.Gly1030Ala	p.G1030A	ENST00000263388	NM_000435.2	1030	gGa/gCa	19/33	0.263917877951855	4	FACETS	1	0.981	1	0.722	0.649	0.799	CLONAL	1	TRUE	2	0.351493012961751	4		628	559	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056557	26056557	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0059209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	130	546	0	ENST00000343677.2:c.100A>T	p.Lys34Ter	p.K34*	ENST00000343677	NM_005319.3	34	Aag/Tag	1/1	0.350522212441654	4	FACETS	1	0.984	1	0.711	0.646	0.779	CLONAL	1	TRUE	2	0.351493012961751	4		546	703	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139677	202139703	+	splice_donor_variant,intron_variant	Splice_Site	DEL	GTAGACGGAAACCTCCAAATCCTTTTT	GTAGACGGAAACCTCCAAATCCTTTTT	ATTCTAGTTA	novel	NA	P-0059209-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	36	440	5	ENST00000358485.4:c.837+1_837+27delinsATTCTAGTTA		p.X279_splice	ENST00000358485	NM_001080125.1	279			0.351493012961751	1	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	0	0.351493012961751	1		445	160	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0059210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	422	1110	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	0.951	0.916	0.985			1	INDETERMINATE	2	TRUE	NA	0.635059238298047	2		1111	699	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617518	158617518	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs984482376	NA	P-0059210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	333	496	0	ENST00000263640.3:c.1138C>T	p.Arg380Cys	p.R380C	ENST00000263640	NM_001105.4	380	Cgc/Tgc	9/11	0.635059238298047	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.635059238298047	1		496	538	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827927	40827927	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536150112	NA	P-0059210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	347	507	2	ENST00000373198.4:c.2501G>A	p.Arg834His	p.R834H	ENST00000373198	NM_133170.3	834	cGc/cAc	17/32	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	1	TRUE	NA	0.635059238298047	2		509	745	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0059210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	464	366	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.635059238298047	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	1	0.635059238298047	4		366	764	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117396	115117415	+	frameshift_variant	Frame_Shift_Del	DEL	TGTCATTGGCTCTTACAATG	TGTCATTGGCTCTTACAATG	-	novel	NA	P-0059210-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	284	502	0	ENST00000257566.3:c.759_778del	p.Ile254LeufsTer6	p.I254Lfs*6	ENST00000257566	NM_016569.3	253	caCATTGTAAGAGCCAATGACAtc/catc	4/8	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.635059238298047	2		502	805	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0059212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	144	545	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.494313019096205	1	FACETS	0.775	0.71	0.842	0.775	0.71	0.842	SUBCLONAL	1	TRUE	0	0.494313019096205	1		545	566	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0059212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	41	258	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	0.507	0.424	0.599	0.507	0.424	0.599	SUBCLONAL	1	TRUE	1	0.494313019096205	2		258	327	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851983	63851983	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	137	632	0	ENST00000279873.7:c.2761G>A	p.Val921Ile	p.V921I	ENST00000279873	NM_032199.2	921	Gtc/Atc	10/10	1	2	FACETS	0.736	0.67	0.805	0.736	0.67	0.805	SUBCLONAL	1	TRUE	1	0.494313019096205	2		632	753	SUCCESS
APC	324	MSKCC	GRCh37	5	112175749	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	novel	NA	P-0059212-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	160	637	0	ENST00000257430.4:c.4459_4462del	p.Thr1487TyrfsTer19	p.T1487Yfs*19	ENST00000257430	NM_000038.5	1486	gaTACT/ga	16/16	1	2	FACETS	0.847	0.778	0.919	0.847	0.778	0.919	CLONAL	1	TRUE	1	0.494313019096205	2		637	764	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	116	302	0				ENST00000310581	NM_198253.2	-/1132			0.185711668136277	3	FACETS	0.894	0.81	0.982	1	0.981	1	CLONAL	3	TRUE	1	0.185711668136277	3		302	509	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652134	36652135	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0059214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	184	578	0	ENST00000244741.5:c.259dup	p.Asp87GlyfsTer2	p.D87Gfs*2	ENST00000244741	NM_000389.4	86	cgg/cGgg	2/3	0.162490979845488	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.185711668136277	3		578	879	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0059214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	105	712	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.185711668136277	2		712	882	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0059214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	95	538	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	0.761	0.678	0.85	1	0.981	1	SUBCLONAL	2	TRUE	1	0.185711668136277	2		538	672	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792429	33792430	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0059214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	92	546	0	ENST00000498907.2:c.891dup	p.Lys298GlnfsTer23	p.K298Qfs*23	ENST00000498907	NM_004364.3	297	-/C	1/1	1	2	FACETS	0.815	0.725	0.91	1	0.982	1	CLONAL	2	TRUE	1	0.185711668136277	2		546	608	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0059214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	1251	192	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.185711668136277	26	FACETS	0.994	0.977	1			1	CLONAL	27	TRUE	NA	0.185711668136277	26		192	1621	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259317	89259317	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	54	483	0	ENST00000336596.2:c.461A>G	p.Gln154Arg	p.Q154R	ENST00000336596	NM_005233.5	154	cAa/cGa	3/17	1	2	FACETS	0.718	0.612	0.835	0.718	0.612	0.835	SUBCLONAL	1	TRUE	1	0.185711668136277	2		483	810	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630365	187630365	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	A	A	TT	novel	NA	P-0059214-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	129	542	0	ENST00000441802.2:c.617delinsAA	p.Leu206Ter	p.L206*	ENST00000441802	NM_005245.3	206	tTa/tAAa	2/27	0.185711668136277	1	FACETS	0.911	0.827	0.998	1	0.989	1	CLONAL	2	TRUE	0	0.185711668136277	1		542	692	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0059216-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	109	190	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.932	0.846	1	0.932	0.846	1	CLONAL	1	TRUE	1	0.658903689933574	2		190	355	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780232	9780921	+	splice_donor_variant,splice_acceptor_variant,frameshift_variant,stop_lost,intron_variant	Splice_Site	DEL	GCCGCTGCCCTGCTCATCTGCCTGCCCGAGGTGGCCCCGCACCCCGTGTACTACCCCGCCCTGGAGAAGGTCAGTGGGGGCCCCGCCGCGTGAGGCTGAGGGGCTGGCGCGGAGCTCTCCTGGCCCTGCTCCTGGAGCTCTTCAGAGGGTGCTCCCTGGCCACGTCGGGGCTGGGCTACCAGGCATATCTGGGGCCTTCCCAGGGGCCATTTTGCCTGCAGGGATGCTGCGCAGTCTGATGACATTTTCGGTTGTCACAGCTGCCAGGAGGGATGCTCTTGGCATCTCGTGAGTGGAGGCCAGAGCTGCTGTGGATGCGCCTCCATGCAGAGGACAGCGCCCCCTCAAGGATGATTGGGGTGGCAATGCCCGGCCTGGGGGTCCTGCCCGGGCTGGTCCAGGCCCCTGGGGACGCTGAGTGCAGCCGTTTGTTGCAGATCTTGGAGCTGGGGCGACACAGCGAGTGTGTGCATGTCACCGAGGAGGAGGTGAGTGGGGTGGGGGTGTGGGGTGGGGGGCATGGAGCCGGCGTGGAACCAGAGCCCTCACTCCTGCCCACACCCCTCAGCAGCTGCAGCTGCGGGAAATCCTGGAGCGGCGGGGGTCTGGGGAGCTGTATGAGCACGAGAAGGACCTGGTGTGGAAGCTGCGGCATGAAGTCCAGGAGCACTTCCCGGAGGCGCTAGCCCG	GCCGCTGCCCTGCTCATCTGCCTGCCCGAGGTGGCCCCGCACCCCGTGTACTACCCCGCCCTGGAGAAGGTCAGTGGGGGCCCCGCCGCGTGAGGCTGAGGGGCTGGCGCGGAGCTCTCCTGGCCCTGCTCCTGGAGCTCTTCAGAGGGTGCTCCCTGGCCACGTCGGGGCTGGGCTACCAGGCATATCTGGGGCCTTCCCAGGGGCCATTTTGCCTGCAGGGATGCTGCGCAGTCTGATGACATTTTCGGTTGTCACAGCTGCCAGGAGGGATGCTCTTGGCATCTCGTGAGTGGAGGCCAGAGCTGCTGTGGATGCGCCTCCATGCAGAGGACAGCGCCCCCTCAAGGATGATTGGGGTGGCAATGCCCGGCCTGGGGGTCCTGCCCGGGCTGGTCCAGGCCCCTGGGGACGCTGAGTGCAGCCGTTTGTTGCAGATCTTGGAGCTGGGGCGACACAGCGAGTGTGTGCATGTCACCGAGGAGGAGGTGAGTGGGGTGGGGGTGTGGGGTGGGGGGCATGGAGCCGGCGTGGAACCAGAGCCCTCACTCCTGCCCACACCCCTCAGCAGCTGCAGCTGCGGGAAATCCTGGAGCGGCGGGGGTCTGGGGAGCTGTATGAGCACGAGAAGGACCTGGTGTGGAAGCTGCGGCATGAAGTCCAGGAGCACTTCCCGGAGGCGCTAGCCCG	-	novel	NA	P-0059216-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	253	583	0	ENST00000377346.4:c.1404_1645del		p.X468_splice	ENST00000377346	NM_005026.3	468	GCCGCTGCCCTGCTCATCTGCCTGCCCGAGGTGGCCCCGCACCCCGTGTACTACCCCGCCCTGGAGAAGGTCAGTGGGGGCCCCGCCGCGTGAGGCTGAGGGGCTGGCGCGGAGCTCTCCTGGCCCTGCTCCTGGAGCTCTTCAGAGGGTGCTCCCTGGCCACGTCGGGGCTGGGCTACCAGGCATATCTGGGGCCTTCCCAGGGGCCATTTTGCCTGCAGGGATGCTGCGCAGTCTGATGACATTTTCGGTTGTCACAGCTGCCAGGAGGGATGCTCTTGGCATCTCGTGAGTGGAGGCCAGAGCTGCTGTGGATGCGCCTCCATGCAGAGGACAGCGCCCCCTCAAGGATGATTGGGGTGGCAATGCCCGGCCTGGGGGTCCTGCCCGGGCTGGTCCAGGCCCCTGGGGACGCTGAGTGCAGCCGTTTGTTGCAGATCTTGGAGCTGGGGCGACACAGCGAGTGTGTGCATGTCACCGAGGAGGAGGTGAGTGGGGTGGGGGTGTGGGGTGGGGGGCATGGAGCCGGCGTGGAACCAGAGCCCTCACTCCTGCCCACACCCCTCAGCAGCTGCAGCTGCGGGAAATCCTGGAGCGGCGGGGGTCTGGGGAGCTGTATGAGCACGAGAAGGACCTGGTGTGGAAGCTGCGGCATGAAGTCCAGGAGCACTTCCCGGAGGCGCTAGCCCGg/g	11-13/24	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.658903689933574	2		583	758	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115267889	115267889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059216-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	194	450	0	ENST00000438362.2:c.1844G>A	p.Gly615Asp	p.G615D	ENST00000438362	NM_001242891.1	615	gGc/gAc	15/20	1	2	FACETS	0.986	0.918	1	0.986	0.918	1	CLONAL	1	TRUE	1	0.658903689933574	2		450	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578418	7578418	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059216-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	296	550	0	ENST00000269305.4:c.512A>G	p.Glu171Gly	p.E171G	ENST00000269305	NM_001126112.2	171	gAg/gGg	5/11	0.658903689933574	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.658903689933574	1		550	553	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017740	31017740	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1164268660	NA	P-0059216-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	588	393	0	ENST00000375687.4:c.602G>A	p.Ser201Asn	p.S201N	ENST00000375687	NM_015338.5	201	aGc/aAc	8/13	0.658903689933574	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.658903689933574	3		393	765	SUCCESS
APC	324	MSKCC	GRCh37	5	112175224	112175225	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0059216-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	198	484	1	ENST00000257430.4:c.3933_3934del	p.Ile1311MetfsTer3	p.I1311Mfs*3	ENST00000257430	NM_000038.5	1311	atTGga/atga	16/16	0.658903689933574	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.658903689933574	1		485	390	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793211	139793212	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748531430	NA	P-0059216-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	497	396	1	ENST00000247668.2:c.26dup	p.Gly10TrpfsTer70	p.G10Wfs*70	ENST00000247668	NM_021138.3	7	acc/aCcc	2/11	0.658903689933574	4	FACETS	0.948	0.914	0.981	0.948	0.914	0.981	CLONAL	3	TRUE	1	0.658903689933574	4		397	880	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACAACCCCC	rs397517115	NA	P-0059221-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	31	430	0	ENST00000275493.2:c.2311_2319dup	p.Asn771_His773dup	p.N771_H773dup	ENST00000275493	NM_005228.3	771	gac/gACAACCCCCac	20/28	1	2	FACETS	0.401	0.323	0.491	0.401	0.323	0.491	SUBCLONAL	1	TRUE	1	0.16	2		430	966	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0059222-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	170	303	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.924343590828843	2		303	367	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0059222-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	193	773	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	0.964	0.903	1	0.964	0.903	1	CLONAL	1	TRUE	1	0.924343590828843	2		773	433	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274192	10274192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765986049	NA	P-0059222-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	113	560	0	ENST00000330684.3:c.77C>T	p.Ala26Val	p.A26V	ENST00000330684	NM_001134407.1	26	gCg/gTg	2/13	1	2	FACETS	0.876	0.802	0.952	0.876	0.802	0.952	CLONAL	1	TRUE	1	0.924343590828843	2		560	279	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0059222-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	87	738	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.924343590828843	2		738	186	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624263	89624267	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	novel	NA	P-0059222-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	141	247	0	ENST00000371953.3:c.37_41del	p.Lys13GlufsTer29	p.K13Efs*29	ENST00000371953	NM_000314.4	13	AAAAGg/g	1/9	0.924343590828843	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.924343590828843	1		247	148	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218807	36218807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059222-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	155	769	1	ENST00000222270.7:c.4418G>A	p.Gly1473Asp	p.G1473D	ENST00000222270	NM_014727.1	1473	gGc/gAc	18/37	1	2	FACETS	0.853	0.791	0.917	0.853	0.791	0.917	CLONAL	1	TRUE	1	0.924343590828843	2		770	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	DEL	C	C	-	rs1567550969	NA	P-0059223-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	221	630	0	ENST00000269305.4:c.672+1del		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.306332577463695	3	FACETS	1	0.989	1	0.816	0.767	0.865	CLONAL	2	FALSE	0	0.432362061815212	3		630	508	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0059223-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	42	265	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.378992631375556	3	FACETS	1	0.92	1	0.736	0.633	0.842	CLONAL	2	FALSE	0	0.432362061815212	3		265	107	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249311	133249311	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059223-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	421	674	0	ENST00000320574.5:c.1588G>C	p.Asp530His	p.D530H	ENST00000320574	NM_006231.2	530	Gac/Cac	15/49	0.378992631375556	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	FALSE	0	0.432362061815212	3		674	757	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434754	99434754	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1347122792	NA	P-0059223-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	143	572	0	ENST00000268035.6:c.841T>A	p.Phe281Ile	p.F281I	ENST00000268035	NM_000875.3	281	Ttc/Atc	3/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.432362061815212	2		572	566	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349079	11349079	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059223-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	274	681	0	ENST00000332029.2:c.257T>G	p.Val86Gly	p.V86G	ENST00000332029	NM_003745.1	86	gTg/gGg	2/2	0.432923421209483	3	FACETS	0.9	0.853	0.947	0.9	0.853	0.947	CLONAL	3	FALSE	0	0.432362061815212	3		681	571	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984566	72984566	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059223-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	143	673	0	ENST00000268489.5:c.3018C>G	p.Asp1006Glu	p.D1006E	ENST00000268489	NM_006885.3	1006	gaC/gaG	3/10	0.430796244271575	2	FACETS	0.974	0.89	1	0.487	0.445	0.531	CLONAL	1	FALSE	0	0.432362061815212	2		673	679	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81954821	81954821	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059223-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	52	356	0	ENST00000359376.3:c.2254C>A	p.Leu752Ile	p.L752I	ENST00000359376	NM_002661.3	752	Ctc/Atc	21/33	0.430796244271575	2	FACETS	1	0.965	1	0.699	0.606	0.797	CLONAL	1	FALSE	0	0.432362061815212	2		356	172	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40864396	40864396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059223-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	117	483	1	ENST00000428826.2:c.1312G>A	p.Glu438Lys	p.E438K	ENST00000428826		438	Gaa/Aaa	12/21	0.324405996293776	3	FACETS	1	0.974	1	0.612	0.554	0.672	CLONAL	1	FALSE	1	0.432362061815212	3		484	538	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243464	41243464	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059223-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	39	247	0	ENST00000357654.3:c.4084G>T	p.Asp1362Tyr	p.D1362Y	ENST00000357654	NM_007294.3	1362	Gat/Tat	10/23	0.324405996293776	3	FACETS	0.864	0.732	1	0.864	0.732	1	CLONAL	2	FALSE	1	0.432362061815212	3		247	127	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424552	47424552	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059223-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	63	338	0	ENST00000404338.3:c.2620C>G	p.Leu874Val	p.L874V	ENST00000404338	NM_004491.4	874	Ctt/Gtt	1/6	0.373741555847171	3	FACETS	0.757	0.663	0.856	0.505	0.442	0.571	SUBCLONAL	2	FALSE	0	0.432362061815212	3		338	234	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661253	227661253	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059223-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	204	680	0	ENST00000305123.5:c.2202C>G	p.Asn734Lys	p.N734K	ENST00000305123	NM_005544.2	734	aaC/aaG	1/2	0.324405996293776	3	FACETS	0.776	0.722	0.832	0.776	0.722	0.832	SUBCLONAL	2	FALSE	1	0.432362061815212	3		680	739	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966576	36966576	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059223-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	292	608	0	ENST00000358127.4:c.750C>G	p.Phe250Leu	p.F250L	ENST00000358127	NM_001280556.1	250	ttC/ttG	6/10	0.430796244271575	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	FALSE	0	0.432362061815212	2		608	639	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98011513	98011513	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059223-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	104	309	0	ENST00000289081.3:c.61G>T	p.Val21Leu	p.V21L	ENST00000289081	NM_000136.2	21	Gta/Tta	2/15	0.432362061815212	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	FALSE	0	0.432362061815212	2		309	209	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509702	106509704	+	missense_variant	Missense_Mutation	TNP	CCT	CCT	ACA	novel	NA	P-0059223-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	113	514	0	ENST00000359195.3:c.1696_1698delinsACA	p.Pro566Thr	p.P566T	ENST00000359195	NM_002649.2	566	CCT/ACA	2/11	0.295008898183651	4	FACETS	1	0.984	1	0.735	0.665	0.809	CLONAL	1	FALSE	2	0.432362061815212	4		514	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882019	NA	P-0059227-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	348	675	3	ENST00000269305.4:c.455del	p.Pro152ArgfsTer18	p.P152Rfs*18	ENST00000269305	NM_001126112.2	152	cCg/cg	5/11	0.832047208214253	1	FACETS	0.981	0.946	1	0.981	0.946	1	CLONAL	1	TRUE	0	0.832047208214253	1		678	498	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243048	105243048	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519804	NA	P-0059227-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	263	546	0	ENST00000349310.3:c.235C>A	p.Gln79Lys	p.Q79K	ENST00000349310	NM_001014432.1	79	Cag/Aag	5/15	NA	2	FACETS	0.961	0.907	1			1	INDETERMINATE	1	TRUE	NA	0.832047208214253	2		546	658	SUCCESS
APC	324	MSKCC	GRCh37	5	112176008	112176008	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0059227-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	183	471	0	ENST00000257430.4:c.4717G>T	p.Glu1573Ter	p.E1573*	ENST00000257430	NM_000038.5	1573	Gaa/Taa	16/16	0.832047208214253	1	FACETS	0.921	0.873	0.967	0.921	0.873	0.967	CLONAL	1	TRUE	0	0.832047208214253	1		471	279	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030338	49030356	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGGTATCTTTCTCCTGTAA	AGGTATCTTTCTCCTGTAA	-	novel	NA	P-0059227-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	106	319	0	ENST00000267163.4:c.1815-2_1831del		p.X605_splice	ENST00000267163	NM_000321.2	605		19/27	0.832047208214253	1	FACETS	0.966	0.903	1	0.966	0.903	1	CLONAL	1	TRUE	0	0.832047208214253	1		319	154	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20153890	20153890	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059227-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	83	295	0	ENST00000379607.5:c.170G>C	p.Arg57Thr	p.R57T	ENST00000379607	NM_001412.3	57	aGg/aCg	3/7	1	2	FACETS	0.983	0.886	1	0.983	0.886	1	CLONAL	1	TRUE	1	0.832047208214253	2		295	203	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0059228-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	359	358	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.499339789316531	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.499339789316531	3		358	568	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863017	56863017	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0059228-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	68	243	0	ENST00000519728.1:c.285-1G>T		p.X95_splice	ENST00000519728	NM_002350.3	95			0.499339789316531	6	FACETS	1	0.923	1	0.217	0.189	0.247	CLONAL	1	TRUE	1	0.499339789316531	6		243	502	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0059229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	64	418	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.299004707242757	3	FACETS	0.88	0.764	1	0.44	0.382	0.502	CLONAL	1	TRUE	1	0.386775874777054	3		418	449	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852248	63852248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145564601	NA	P-0059229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	40	607	0	ENST00000279873.7:c.3026C>T	p.Ala1009Val	p.A1009V	ENST00000279873	NM_032199.2	1009	gCg/gTg	10/10	1	2	FACETS	0.311	0.257	0.37	0.311	0.257	0.37	SUBCLONAL	1	TRUE	1	0.386775874777054	2		607	666	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653806	89653806	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0059229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	52	200	0	ENST00000371953.3:c.104T>A	p.Met35Lys	p.M35K	ENST00000371953	NM_000314.4	35	aTg/aAg	2/9	0.295006525836398	2	FACETS	0.967	0.844	1	0.967	0.844	1	CLONAL	2	TRUE	0	0.386775874777054	2		200	139	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987209	36987231	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCCCATGAAGCGGGAGACTGTAA	GCCCATGAAGCGGGAGACTGTAA	-	novel	NA	P-0059229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	81	533	0	ENST00000354822.5:c.464-6_480del		p.X155_splice	ENST00000354822	NM_001079668.2	155		3/3	1	2	FACETS	0.818	0.723	0.92	0.818	0.723	0.92	CLONAL	1	TRUE	1	0.386775874777054	2		533	512	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23625324	23625324	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0059229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	117	337	0	ENST00000261584.4:c.3201+1G>A		p.X1067_splice	ENST00000261584	NM_024675.3	1067			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.386775874777054	2		337	406	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424511	47424511	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0059229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	99	494	0	ENST00000404338.3:c.2579C>G	p.Ser860Ter	p.S860*	ENST00000404338	NM_004491.4	860	tCa/tGa	1/6	1	2	FACETS	0.917	0.821	1	0.917	0.821	1	CLONAL	1	TRUE	1	0.386775874777054	2		494	558	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295862	1295880	+	upstream_gene_variant	5'Flank	DEL	CCCCACCATGAGCAAACCA	CCCCACCATGAGCAAACCA	-	novel	NA	P-0059229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	162	732	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.386775874777054	2		732	696	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225440	26225440	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0059229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	45	724	0	ENST00000360408.1:c.58C>T	p.Gln20Ter	p.Q20*	ENST00000360408	NM_003532.2	20	Cag/Tag	1/1	1	2	FACETS	0.265	0.221	0.313	0.265	0.221	0.313	SUBCLONAL	1	TRUE	1	0.386775874777054	2		724	879	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642524	117642524	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0059229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	44	491	0	ENST00000368508.3:c.5675C>A	p.Ala1892Asp	p.A1892D	ENST00000368508	NM_002944.2	1892	gCc/gAc	35/43	1	2	FACETS	0.406	0.34	0.479	0.406	0.34	0.479	SUBCLONAL	1	TRUE	1	0.386775874777054	2		491	561	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439986	56439990	+	frameshift_variant	Frame_Shift_Ins	INS	TAGGA	TAGGA	AATGATG	novel	NA	P-0059229-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	44	463	0	ENST00000407977.2:c.602_606delinsCATCATT	p.Ile201ThrfsTer4	p.I201Tfs*4	ENST00000407977		201	aTCCTA/aCATCATT	6/10	0.266372813832884	3	FACETS	0.422	0.353	0.499	0.211	0.176	0.25	SUBCLONAL	1	TRUE	1	0.386775874777054	3		463	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0059230-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	459	891	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.952445796137323	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.952445796137323	1		891	479	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717615	89717615	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909227	NA	P-0059230-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	334	335	0	ENST00000371953.3:c.640C>T	p.Gln214Ter	p.Q214*	ENST00000371953	NM_000314.4	214	Cag/Tag	7/9	0.952445796137323	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.952445796137323	1		335	356	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218052	108218052	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1064794840	NA	P-0059230-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	269	187	0	ENST00000278616.4:c.8631G>C	p.Leu2877Phe	p.L2877F	ENST00000278616	NM_000051.3	2877	ttG/ttC	59/63	0.952445796137323	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.952445796137323	1		187	284	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942151	71942204	+	inframe_deletion	In_Frame_Del	DEL	AGGAGAACTCAGTGGGCGACCGCGAGTGGCTGGACCTACTGCGCGGGGGCCTCA	AGGAGAACTCAGTGGGCGACCGCGAGTGGCTGGACCTACTGCGCGGGGGCCTCA	-	novel	NA	P-0059230-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	355	865	0	ENST00000298229.2:c.1420_1473del	p.Asn474_Glu491del	p.N474_E491del	ENST00000298229	NM_001567.3	472	cAGGAGAACTCAGTGGGCGACCGCGAGTGGCTGGACCTACTGCGCGGGGGCCTCAag/cag	12/28	0.952445796137323	1	FACETS	0.948	0.924	0.969	0.948	0.924	0.969	CLONAL	1	TRUE	0	0.952445796137323	1		865	412	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189497	94189497	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059230-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	259	189	0	ENST00000323929.3:c.1508G>C	p.Arg503Pro	p.R503P	ENST00000323929	NM_005591.3	503	cGt/cCt	14/20	0.952445796137323	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.952445796137323	1		189	272	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872825	35873003	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCTGGGGTGACTCTGCTACATCAGCTACGTCCCAGGGTCAGAGAGAACCCGGGCCAGGCAAGCGGCGCACCTGCTGCAGGTTGTTCTGGAAGTTGAGGAAGGCCAGGTCTCCCTTCACCTGGCGGATCACTTCCATGGTCAGTGCCTTTTCTTCATGGATGATGGCCAAGTGCAGGAA	ATCTGGGGTGACTCTGCTACATCAGCTACGTCCCAGGGTCAGAGAGAACCCGGGCCAGGCAAGCGGCGCACCTGCTGCAGGTTGTTCTGGAAGTTGAGGAAGGCCAGGTCTCCCTTCACCTGGCGGATCACTTCCATGGTCAGTGCCTTTTCTTCATGGATGATGGCCAAGTGCAGGAA	-	novel	NA	P-0059230-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	247	403	0	ENST00000216797.5:c.229_336+71del		p.X77_splice	ENST00000216797	NM_020529.2	77		2/6	1	2	FACETS	0.98	0.926	1	0.98	0.926	1	CLONAL	1	TRUE	1	0.952445796137323	2		403	529	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292829	91292841	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTTGCAGACTC	TTCTTGCAGACTC	-	novel	NA	P-0059230-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	524	444	1	ENST00000355112.3:c.331_343del	p.Phe111ArgfsTer14	p.F111Rfs*14	ENST00000355112	NM_000057.2	111	TTCTTGCAGACTCcg/cg	3/22	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.952445796137323	2		445	1046	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223271	5223271	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0059230-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	473	811	0	ENST00000357368.4:c.2532del	p.Glu845ArgfsTer77	p.E845Rfs*77	ENST00000357368	NM_002850.3	844	ccC/cc	18/38	0.952445796137323	1	FACETS	0.955	0.935	0.973	0.955	0.935	0.973	CLONAL	1	TRUE	0	0.952445796137323	1		811	545	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964421	70964421	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059230-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	59	684	0	ENST00000276594.2:c.1607T>A	p.Val536Asp	p.V536D	ENST00000276594	NM_024504.3	536	gTc/gAc	8/8	0.952445796137323	1	FACETS	0.132	0.114	0.153	0.132	0.114	0.153	SUBCLONAL	1	TRUE	0	0.952445796137323	1		684	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579409	7579409	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1567556114	NA	P-0059231-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	472	731	0	ENST00000269305.4:c.278del	p.Leu93ArgfsTer30	p.L93Rfs*30	ENST00000269305	NM_001126112.2	93	cTg/cg	4/11	0.626795807828314	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.623021981556503	2		731	680	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0059232-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	78	190	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.415269255507877	2		190	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750600586	NA	P-0059232-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	185	402	1	ENST00000269305.4:c.413C>T	p.Ala138Val	p.A138V	ENST00000269305	NM_001126112.2	138	gCc/gTc	5/11	0.415269255507877	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.415269255507877	1		403	663	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0059232-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	62	280	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	0.805	0.699	0.919	0.805	0.699	0.919	CLONAL	1	TRUE	1	0.415269255507877	2		280	371	SUCCESS
APC	324	MSKCC	GRCh37	5	112175761	112175761	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0059232-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	109	491	0	ENST00000257430.4:c.4473del	p.Phe1491LeufsTer16	p.F1491Lfs*16	ENST00000257430	NM_000038.5	1490	caT/ca	16/16	1	2	FACETS	0.852	0.767	0.942	0.852	0.767	0.942	CLONAL	1	TRUE	1	0.415269255507877	2		491	616	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016264	150016264	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059232-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	82	265	0	ENST00000253339.5:c.442C>T	p.Arg148Ter	p.R148*	ENST00000253339		148	Cga/Tga	2/7	1	2	FACETS	0.975	0.865	1	0.975	0.865	1	CLONAL	1	TRUE	1	0.415269255507877	2		265	405	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457804	69457804	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0059232-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	34	397	0	ENST00000227507.2:c.204C>G	p.Cys68Trp	p.C68W	ENST00000227507	NM_053056.2	68	tgC/tgG	2/5	0.415269255507877	1	FACETS	0.369	0.301	0.444	0.369	0.301	0.444	SUBCLONAL	1	TRUE	0	0.415269255507877	1		397	352	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142950069	142950069	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0059232-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	27	324	0	ENST00000262992.4:c.2643-2A>G		p.X881_splice	ENST00000262992	NM_001101669.1	881			1	2	FACETS	0.403	0.32	0.496	0.403	0.32	0.496	SUBCLONAL	1	TRUE	1	0.415269255507877	2		324	323	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172093	32172093	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0059232-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	41	478	0	ENST00000375023.3:c.2939A>G	p.His980Arg	p.H980R	ENST00000375023	NM_004557.3	980	cAt/cGt	19/30	1	2	FACETS	0.269	0.223	0.321	0.269	0.223	0.321	SUBCLONAL	1	TRUE	1	0.415269255507877	2		478	733	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324615	31324615	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1050529	NA	P-0059335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	11	194	1	ENST00000412585.2:c.193G>A	p.Ala65Thr	p.A65T	ENST00000412585	NM_005514.6	65	Gcg/Acg	2/8	0.642495034201523	4	FACETS	0.417	0.289	0.573	0.139	0.096	0.191	SUBCLONAL	1	TRUE	1	0.642495034201523	4		195	135	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461576	138461576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	98	282	0	ENST00000289153.2:c.445C>T	p.Arg149Ter	p.R149*	ENST00000289153	NM_006219.2	149	Cga/Tga	3/22	0.642495034201523	5	FACETS	1	0.953	1	0.373	0.333	0.414	CLONAL	1	TRUE	2	0.642495034201523	5		282	536	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72881571	72881571	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	198	307	0	ENST00000325599.8:c.548G>T	p.Arg183Ile	p.R183I	ENST00000325599	NM_018130.2	183	aGa/aTa	5/11	0.642495034201523	5	FACETS	1	0.972	1	0.718	0.67	0.767	CLONAL	2	TRUE	2	0.642495034201523	5		307	562	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724495	112724495	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	116	397	0	ENST00000369452.4:c.379G>C	p.Glu127Gln	p.E127Q	ENST00000369452	NM_007373.3	127	Gaa/Caa	2/9	0.642495034201523	3	FACETS	0.95	0.861	1	0.475	0.43	0.522	CLONAL	1	TRUE	1	0.642495034201523	3		397	502	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673350	30673350	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0059335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	200	805	0	ENST00000376406.3:c.3610C>G	p.Pro1204Ala	p.P1204A	ENST00000376406	NM_014641.2	1204	Ccc/Gcc	10/15	0.642495034201523	4	FACETS	0.935	0.865	1	0.312	0.288	0.336	CLONAL	1	TRUE	1	0.642495034201523	4		805	1094	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020540	69020540	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0059335-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	723	409	0	ENST00000288368.4:c.2912A>T	p.Asp971Val	p.D971V	ENST00000288368	NM_024870.2	971	gAt/gTt	24/40	0.642495034201523	9	FACETS	1	0.987	1	1	0.987	1	CLONAL	7	TRUE	2	0.642495034201523	9		409	1026	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0059336-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	85	302	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.846	0.756	0.94	0.846	0.756	0.94	CLONAL	1	TRUE	1	0.652479778074679	2		302	308	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374298	138374298	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0059336-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	123	375	0	ENST00000289153.2:c.3146T>G	p.Leu1049Arg	p.L1049R	ENST00000289153	NM_006219.2	1049	cTc/cGc	22/22	0.652479778074679	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.652479778074679	1		375	248	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952993	2952993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369115970	NA	P-0059336-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	153	507	0	ENST00000396946.4:c.2947G>A	p.Val983Met	p.V983M	ENST00000396946	NM_032415.4	983	Gtg/Atg	22/25	0.610059088463768	4	FACETS	1	0.96	1	0.54	0.495	0.587	CLONAL	1	TRUE	2	0.652479778074679	4		507	718	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976727	2976727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1298741148	NA	P-0059336-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	130	496	0	ENST00000396946.4:c.1285G>A	p.Val429Ile	p.V429I	ENST00000396946	NM_032415.4	429	Gtc/Atc	9/25	0.610059088463768	4	FACETS	0.918	0.834	1	0.459	0.417	0.504	CLONAL	1	TRUE	2	0.652479778074679	4		496	717	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220274	55220274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0059336-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	2761	359	1	ENST00000275493.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000275493	NM_005228.3	222	Cgc/Tgc	6/28	0.652479778074679	26	FACETS	0.988	0.978	0.998	0.906	0.896	0.915	CLONAL	22	TRUE	2	0.652479778074679	26		360	3438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0059337-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	135	405	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.44319553546825	2	FACETS	1	0.987	1	0.707	0.651	0.764	CLONAL	1	FALSE	0	0.547326730847255	2		405	349	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0059337-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	111	495	0	ENST00000347630.2:c.397T>C	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	Ttc/Ctc	6/11	1	2	FACETS	0.808	0.73	0.89	0.808	0.73	0.89	CLONAL	1	FALSE	1	0.547326730847255	2		495	502	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061313	38061313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1204900727	NA	P-0059337-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	117	625	0	ENST00000250448.2:c.676G>A	p.Asp226Asn	p.D226N	ENST00000250448	NM_004496.3	226	Gac/Aac	2/2	1	2	FACETS	0.769	0.696	0.846	0.769	0.696	0.846	SUBCLONAL	1	FALSE	1	0.547326730847255	2		625	556	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287955	33287955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0059337-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	78	570	0	ENST00000374542.5:c.1298C>T	p.Ala433Val	p.A433V	ENST00000374542	NM_001141970.1	433	gCt/gTt	5/8	1	2	FACETS	0.735	0.649	0.825	0.735	0.649	0.825	SUBCLONAL	1	FALSE	1	0.547326730847255	2		570	388	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152009027	152009027	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0059337-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	45	351	3	ENST00000262189.6:c.595C>T	p.Arg199Ter	p.R199*	ENST00000262189	NM_170606.2	199	Cga/Tga	5/59	1	2	FACETS	0.424	0.357	0.498	0.424	0.357	0.498	SUBCLONAL	1	FALSE	1	0.547326730847255	2		354	388	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060682	38060682	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059337-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	162	801	0	ENST00000250448.2:c.1307G>T	p.Ser436Ile	p.S436I	ENST00000250448	NM_004496.3	436	aGc/aTc	2/2	1	2	FACETS	0.885	0.814	0.958	0.885	0.814	0.958	CLONAL	1	FALSE	1	0.547326730847255	2		801	669	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878966	117878966	+	start_lost	Translation_Start_Site	SNP	C	C	A	novel	NA	P-0059337-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	183	374	0	ENST00000297338.2:c.3G>T	p.Met1?	p.M1?	ENST00000297338	NM_006265.2	1	atG/atT	2/14	0.481887773746096	4	FACETS	1	0.989	1	0.712	0.658	0.767	CLONAL	1	FALSE	2	0.547326730847255	4		374	727	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611416	28611416	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0059339-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	29	311	0	ENST00000241453.7:c.1215G>T	p.Lys405Asn	p.K405N	ENST00000241453	NM_004119.2	405	aaG/aaT	10/24	1	2	FACETS	0.174	0.14	0.214	0.174	0.14	0.214	SUBCLONAL	1	TRUE	1	0.886871091212819	2		311	375	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0001766-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	286	546	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.494866899203758	6	FACETS	1	0.95	1	1	0.95	1	CLONAL	4	TRUE	2	0.494866899203758	6		546	575	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178129298	178129298	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001766-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	151	336	0	ENST00000397062.3:c.7G>A	p.Asp3Asn	p.D3N	ENST00000397062	NM_006164.4	3	Gac/Aac	1/5	0.494866899203758	3	FACETS	0.947	0.866	1	0.473	0.433	0.516	CLONAL	1	TRUE	1	0.494866899203758	3		336	804	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004316-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	377	534	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	0.59824289448421	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	2	0.59824289448421	4		534	1001	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692791	89692791	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004316-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	198	169	0	ENST00000371953.3:c.275A>T	p.Asp92Val	p.D92V	ENST00000371953	NM_000314.4	92	gAc/gTc	5/9	0.59824289448421	3	FACETS	0.955	0.895	1	0.955	0.895	1	CLONAL	2	TRUE	1	0.59824289448421	3		169	450	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164867	36164868	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004316-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	484	761	1	ENST00000300305.3:c.1007dup	p.Ala338ArgfsTer262	p.A338Rfs*262	ENST00000300305		336	ttc/ttTc	8/8	0.59824289448421	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.59824289448421	4		762	1243	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170864	56170865	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004316-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	153	192	2	ENST00000399503.3:c.1694dup	p.Met566AsnfsTer10	p.M566Nfs*10	ENST00000399503	NM_005921.1	564	-/G	10/20	0.557519585601349	5	FACETS	0.862	0.793	0.934	0.575	0.528	0.623	CLONAL	2	TRUE	2	0.59824289448421	5		194	563	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913274	NA	P-0004316-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	11	214	0	ENST00000263967.3:c.1634A>C	p.Glu545Ala	p.E545A	ENST00000263967	NM_006218.2	545	gAg/gCg	10/21	0.59824289448421	3	FACETS	0.139	0.095	0.193	0.069	0.047	0.097	SUBCLONAL	1	TRUE	1	0.59824289448421	3		214	344	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717709	89717709	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057518538	NA	P-0004316-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	110	306	0	ENST00000371953.3:c.734A>C	p.Gln245Pro	p.Q245P	ENST00000371953	NM_000314.4	245	cAg/cCg	7/9	0.59824289448421	3	FACETS	0.859	0.775	0.948	0.43	0.387	0.474	CLONAL	1	TRUE	1	0.59824289448421	3		306	556	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118705	115118706	+	missense_variant	Missense_Mutation	DNP	GT	GT	AA	novel	NA	P-0004316-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	244	435	1	ENST00000257566.3:c.635_636delinsTT	p.Asn212Ile	p.N212I	ENST00000257566	NM_016569.3	212	aAC/aTT	2/8	0.59824289448421	4	FACETS	0.845	0.793	0.899	0.845	0.793	0.899	CLONAL	2	TRUE	2	0.59824289448421	4		436	771	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527996	103527996	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs769146699	NA	P-0004316-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	19	258	0	ENST00000355739.4:c.3304A>G	p.Ser1102Gly	p.S1102G	ENST00000355739	NM_000123.3	1102	Agt/Ggt	15/15	0.55998414269776	1	FACETS	0.2	0.152	0.256	0.2	0.152	0.256	SUBCLONAL	1	TRUE	0	0.59824289448421	1		258	223	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160762	56160763	+	splice_donor_variant	Splice_Site	DNP	GT	GT	TG	novel	NA	P-0004316-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	226	257	0	ENST00000399503.3:c.1035+1_1035+2delinsTG		p.X345_splice	ENST00000399503	NM_005921.1	345			0.557519585601349	5	FACETS	0.948	0.893	1	0.948	0.893	1	CLONAL	3	TRUE	2	0.59824289448421	5		257	504	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131463	202131463	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004747-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	161	554	0	ENST00000358485.4:c.431A>T	p.Glu144Val	p.E144V	ENST00000358485	NM_001080125.1	144	gAg/gTg	2/9	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.376272910720027	2		554	781	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638347	117638347	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519788	NA	P-0004747-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	133	448	0	ENST00000368508.3:c.6094G>A	p.Gly2032Arg	p.G2032R	ENST00000368508	NM_002944.2	2032	Gga/Aga	38/43	0.376272910720027	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.376272910720027	1		448	508	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218917	193218917	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004747-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	97	430	0	ENST00000367435.3:c.1477del	p.Asp493MetfsTer2	p.D493Mfs*2	ENST00000367435	NM_024529.4	492	tGg/tg	16/17	1	2	FACETS	0.765	0.689	0.844	1	0.983	1	SUBCLONAL	2	TRUE	1	0.376272910720027	2		430	337	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47503744	47503746	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1387779417	NA	P-0004747-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	146	630	0	ENST00000404338.3:c.4307_4309del	p.Phe1436del	p.F1436del	ENST00000404338	NM_004491.4	1433	ccCTTc/ccc	6/6	0.0949898346971931	3	FACETS	1	0.93	1	0.511	0.466	0.558	INDETERMINATE	1	TRUE	1	0.376272910720027	3		630	902	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47061226	47061278	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTGCTTATATCCACCAAACCTTACCTCTTTTCTGAATACTTCTTTGCTTTTCT	GTGCTTATATCCACCAAACCTTACCTCTTTTCTGAATACTTCTTTGCTTTTCT	-	novel	NA	P-0004747-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	134	451	0	ENST00000409792.3:c.7403_7431+24del		p.X2468_splice	ENST00000409792	NM_014159.6	2468		19/21	0.376272910720027	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.376272910720027	1		451	541	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125281	47125281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004747-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	34	512	0	ENST00000409792.3:c.5989G>A	p.Glu1997Lys	p.E1997K	ENST00000409792	NM_014159.6	1997	Gaa/Aaa	12/21	0.376272910720027	1	FACETS	0.284	0.231	0.343	0.284	0.231	0.343	SUBCLONAL	1	TRUE	0	0.376272910720027	1		512	517	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177629	56177629	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004747-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	73	574	0	ENST00000399503.3:c.2602G>A	p.Ala868Thr	p.A868T	ENST00000399503	NM_005921.1	868	Gcc/Acc	14/20	0.376272910720027	1	FACETS	0.494	0.432	0.561	0.494	0.432	0.561	SUBCLONAL	1	TRUE	0	0.376272910720027	1		574	638	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508092	106508092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004747-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	106	544	0	ENST00000359195.3:c.86C>T	p.Ala29Val	p.A29V	ENST00000359195	NM_002649.2	29	gCg/gTg	2/11	1	2	FACETS	0.734	0.658	0.814	0.734	0.658	0.814	SUBCLONAL	1	TRUE	1	0.376272910720027	2		544	768	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949719	151949719	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004747-T04-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	92	467	0	ENST00000262189.6:c.1381C>T	p.Gln461Ter	p.Q461*	ENST00000262189	NM_170606.2	461	Caa/Taa	10/59	1	2	FACETS	0.965	0.86	1	0.965	0.86	1	CLONAL	1	TRUE	1	0.376272910720027	2		467	507	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0006660-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	113	284	2	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.47243595140718	2		286	478	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879885	37879885	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006660-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	173	582	0	ENST00000269571.5:c.2180G>C	p.Gly727Ala	p.G727A	ENST00000269571		727	gGa/gCa	18/27	1	2	FACETS	0.933	0.86	1	0.933	0.86	1	CLONAL	1	TRUE	1	0.47243595140718	2		582	785	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840603	36840603	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs966082163	NA	P-0006660-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	147	476	0	ENST00000358127.4:c.1130G>A	p.Arg377Gln	p.R377Q	ENST00000358127	NM_001280556.1	377	cGa/cAa	10/10	0.47243595140718	1	FACETS	0.947	0.87	1	0.947	0.87	1	CLONAL	1	TRUE	0	0.47243595140718	1		476	502	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185619	27185619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217204389	NA	P-0006660-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	178	549	0	ENST00000380036.4:c.1319C>T	p.Ser440Phe	p.S440F	ENST00000380036	NM_000459.3	440	tCt/tTt	9/23	0.47243595140718	1	FACETS	0.934	0.865	1	0.934	0.865	1	CLONAL	1	TRUE	0	0.47243595140718	1		549	616	SUCCESS
APC	324	MSKCC	GRCh37	5	112137069	112137069	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006660-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	82	340	0	ENST00000257430.4:c.823G>A	p.Gly275Ser	p.G275S	ENST00000257430	NM_000038.5	275	Ggt/Agt	8/16	0.427986825908936	3	FACETS	0.85	0.751	0.955	0.425	0.375	0.478	CLONAL	1	TRUE	1	0.47243595140718	3		340	505	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958565	175958565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006660-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	227	457	0	ENST00000367669.3:c.1780G>A	p.Val594Ile	p.V594I	ENST00000367669	NM_022457.5	594	Gta/Ata	16/20	0.47243595140718	5	FACETS	0.812	0.757	0.869	0.541	0.504	0.58	CLONAL	2	TRUE	2	0.47243595140718	5		457	1011	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821844	59821844	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006660-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	191	493	0	ENST00000259008.2:c.2206G>C	p.Asp736His	p.D736H	ENST00000259008	NM_032043.2	736	Gat/Cat	15/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.47243595140718	2		493	738	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66518939	66518939	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853303	NA	P-0006660-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	107	380	0	ENST00000358598.2:c.220C>T	p.Arg74Cys	p.R74C	ENST00000358598	NM_212471.2	74	Cgt/Tgt	3/11	1	2	FACETS	0.97	0.875	1	0.97	0.875	1	CLONAL	1	TRUE	1	0.47243595140718	2		380	467	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091205	29091205	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006660-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	35	140	0	ENST00000328354.6:c.1285G>C	p.Glu429Gln	p.E429Q	ENST00000328354	NM_007194.3	429	Gag/Cag	12/15	0.448118373486496	1	FACETS	0.976	0.818	1	0.976	0.818	1	CLONAL	1	TRUE	0	0.47243595140718	1		140	116	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835935	151835935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006660-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	139	414	0	ENST00000262189.6:c.14589G>T	p.Glu4863Asp	p.E4863D	ENST00000262189	NM_170606.2	4863	gaG/gaT	58/59	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.47243595140718	2		414	522	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930372	39930372	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006660-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	155	508	0	ENST00000378444.4:c.3092G>C	p.Arg1031Thr	p.R1031T	ENST00000378444	NM_001123385.1	1031	aGa/aCa	6/15	1	2	FACETS	0.951	0.873	1	0.951	0.873	1	CLONAL	1	TRUE	1	0.47243595140718	2		508	690	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0006660-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	302	421	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.650808806435689	3	FACETS	0.914	0.869	0.959	0.609	0.579	0.64	CLONAL	2	TRUE	0	0.697494792034375	3		421	639	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0006660-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	337	284	2	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.650808806435689	3	FACETS	0.942	0.91	0.974	0.942	0.91	0.974	CLONAL	3	TRUE	0	0.697494792034375	3		286	461	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100438	8100440	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0006660-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	403	1089	0	ENST00000346208.3:c.419_421del	p.Ser140del	p.S140del	ENST00000346208		138	TCC/-	3/6	1	2	FACETS	0.978	0.932	1	0.978	0.932	1	CLONAL	1	TRUE	1	0.697494792034375	2		1089	1181	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437343	121437343	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006660-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	301	963	1	ENST00000257555.6:c.1681C>G	p.Gln561Glu	p.Q561E	ENST00000257555		561	Cag/Gag	9/10	1	2	FACETS	0.82	0.773	0.868	0.82	0.773	0.868	CLONAL	1	TRUE	1	0.697494792034375	2		964	1053	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038623	14038623	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006660-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	236	252	0	ENST00000311895.7:c.1948G>C	p.Asp650His	p.D650H	ENST00000311895	NM_005236.2	650	Gat/Cat	10/11	0.415285759302033	3	FACETS	0.905	0.855	0.957			1	INDETERMINATE	2	TRUE	NA	0.697494792034375	3		252	504	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525048	9525048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006660-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	187	423	1	ENST00000353224.5:c.1837G>A	p.Glu613Lys	p.E613K	ENST00000353224	NM_177990.2	613	Gag/Aag	8/10	0.643116570925961	3	FACETS	1	0.962	1	0.529	0.491	0.569	CLONAL	1	TRUE	1	0.697494792034375	3		424	683	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528837	157528837	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006660-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	213	536	0	ENST00000346085.5:c.6562G>C	p.Glu2188Gln	p.E2188Q	ENST00000346085	NM_020732.3	2188	Gaa/Caa	20/20	0.697494792034375	1	FACETS	0.902	0.849	0.955	0.902	0.849	0.955	CLONAL	1	TRUE	0	0.697494792034375	1		536	441	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856106	151856106	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs772980746	NA	P-0006660-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	150	347	0	ENST00000262189.6:c.11512C>G	p.Pro3838Ala	p.P3838A	ENST00000262189	NM_170606.2	3838	Cca/Gca	44/59	1	2	FACETS	0.883	0.813	0.955	0.883	0.813	0.955	CLONAL	1	TRUE	1	0.697494792034375	2		347	487	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229582	5229582	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	10	185	0	ENST00000357368.4:c.2269C>A	p.Gln757Lys	p.Q757K	ENST00000357368	NM_002850.3	757	Cag/Aag	15/38	0.429767802609774	1	FACETS	0.193	0.131	0.272	0.193	0.131	0.272	SUBCLONAL	1	TRUE	0	0.429767802609774	1		185	189	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474716	138474716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	18	506	1	ENST00000289153.2:c.277G>A	p.Glu93Lys	p.E93K	ENST00000289153	NM_006219.2	93	Gaa/Aaa	2/22	0.429767802609774	2	FACETS	1	0.883	1	0.625	0.484	0.781	CLONAL	1	TRUE	0	0.429767802609774	2		507	67	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467675	50467675	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	8	643	1	ENST00000331340.3:c.910G>T	p.Glu304Ter	p.E304*	ENST00000331340	NM_006060.4	304	Gaa/Taa	8/8	0.406531730443436	5	FACETS	0.16	0.102	0.236	0.053	0.034	0.079	SUBCLONAL	1	TRUE	2	0.429767802609774	5		644	382	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231437	46231437	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008524-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	51	396	0	ENST00000334344.6:c.1277C>T	p.Thr426Met	p.T426M	ENST00000334344	NM_152641.2	426	aCg/aTg	10/21	0.697358647744249	4	FACETS	0.715	0.611	0.829	0.238	0.203	0.277	SUBCLONAL	1	TRUE	1	0.697358647744249	4		396	347	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0008524-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1233	472	555	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	0.697358647744249	14	FACETS	1	0.973	1	0.343	0.327	0.359	CLONAL	4	TRUE	2	0.697358647744249	14		555	1705	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008524-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	70	394	0	ENST00000335508.6:c.1874G>T	p.Arg625Leu	p.R625L	ENST00000335508	NM_012433.2	625	cGt/cTt	14/25	0.697358647744249	4	FACETS	0.936	0.821	1	0.312	0.273	0.353	CLONAL	1	TRUE	1	0.697358647744249	4		394	364	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239843	98239843	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1398130707	NA	P-0008524-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	337	823	0	ENST00000331920.6:c.1489G>A	p.Ala497Thr	p.A497T	ENST00000331920	NM_000264.3	497	Gct/Act	10/24	0.697358647744249	3	FACETS	0.97	0.925	1	0.97	0.925	1	CLONAL	2	TRUE	1	0.697358647744249	3		823	672	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524714	137524716	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs587776858	NA	P-0008524-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	173	482	0	ENST00000367739.4:c.653_655del	p.Glu218del	p.E218del	ENST00000367739	NM_000416.2	218	gAAGga/gga	5/7	0.697358647744249	2	FACETS	0.981	0.93	1	0.981	0.93	1	CLONAL	2	TRUE	0	0.697358647744249	2		482	253	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170381	119170381	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008524-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	117	492	0	ENST00000264033.4:c.2611T>C	p.Tyr871His	p.Y871H	ENST00000264033	NM_005188.3	871	Tac/Cac	16/16	0.697358647744249	2	FACETS	1	0.967	1	0.557	0.51	0.606	CLONAL	1	TRUE	0	0.697358647744249	2		492	301	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820806	3820806	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008524-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	335	1338	0	ENST00000262367.5:c.2645C>G	p.Pro882Arg	p.P882R	ENST00000262367	NM_004380.2	882	cCa/cGa	14/31	0.670433384713494	4	FACETS	1	0.975	1	0.529	0.499	0.56	CLONAL	1	TRUE	2	0.697358647744249	4		1338	1542	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046297	69046297	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008524-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	105	508	0	ENST00000288368.4:c.3770G>C	p.Ser1257Thr	p.S1257T	ENST00000288368	NM_024870.2	1257	aGt/aCt	32/40	0.697358647744249	6	FACETS	1	0.956	1	0.28	0.251	0.311	CLONAL	1	TRUE	2	0.697358647744249	6		508	643	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0008662-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	51	414	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.0923088737933737	4	FACETS	1	0.956	1	0.685	0.582	0.798	CLONAL	1	FALSE	2	0.150824852848033	4		414	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579463	7579463	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008662-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	75	1046	0	ENST00000269305.4:c.224del	p.Pro75LeufsTer48	p.P75Lfs*48	ENST00000269305	NM_001126112.2	75	cCt/ct	4/11	0.150824852848033	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	0	0.150824852848033	1		1046	844	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069291	30069291	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008662-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	56	777	0	ENST00000338641.4:c.1156G>T	p.Glu386Ter	p.E386*	ENST00000338641	NM_000268.3	386	Gaa/Taa	12/16	0.147498784930618	2	FACETS	1	0.885	1	0.52	0.445	0.603	CLONAL	1	FALSE	0	0.150824852848033	2		777	714	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748080	72748080	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008662-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	57	635	0	ENST00000357731.5:c.98C>A	p.Pro33Gln	p.P33Q	ENST00000357731	NM_173808.2	33	cCg/cAg	1/7	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.150824852848033	2		635	600	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843671	156843671	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008662-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	162	1120	0	ENST00000524377.1:c.1097C>A	p.Pro366His	p.P366H	ENST00000524377	NM_002529.3	366	cCc/cAc	8/17	0.127071968928704	2	FACETS	0.907	0.831	0.988	0.907	0.831	0.988	CLONAL	2	FALSE	0	0.150824852848033	2		1120	1184	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729603	162729603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008662-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	74	517	0	ENST00000367921.3:c.689G>A	p.Gly230Asp	p.G230D	ENST00000367921	NM_006182.2	230	gGc/gAc	8/18	0.127071968928704	2	FACETS	0.776	0.68	0.88	0.776	0.68	0.88	SUBCLONAL	2	FALSE	0	0.150824852848033	2		517	632	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615193	43615193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008662-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	50	867	1	ENST00000355710.3:c.2607G>T	p.Lys869Asn	p.K869N	ENST00000355710	NM_020975.4	869	aaG/aaT	14/20	1	2	FACETS	0.845	0.715	0.988	0.845	0.715	0.988	CLONAL	1	FALSE	1	0.150824852848033	2		868	785	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644445	18644445	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008662-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	48	324	0	ENST00000266497.5:c.2623C>A	p.His875Asn	p.H875N	ENST00000266497		875	Cat/Aat	18/31	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.150824852848033	2		324	481	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120806867	120806867	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008662-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	20	103	0	ENST00000257552.2:c.28C>A	p.Leu10Ile	p.L10I	ENST00000257552	NM_002442.3	10	Ctc/Atc	1/15	0.148750079018585	2	FACETS	0.975	0.754	1	0.975	0.754	1	CLONAL	2	FALSE	0	0.150824852848033	2		103	136	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114282	73114282	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008662-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	42	195	0	ENST00000356692.5:c.919del	p.Glu307LysfsTer7	p.E307Kfs*7	ENST00000356692		306	gaG/ga	8/9	0.150824852848033	2	FACETS	0.888	0.75	1	1	0.948	1	CLONAL	3	FALSE	0	0.150824852848033	2		195	209	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521688	89521688	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008662-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	49	498	0	ENST00000336596.2:c.2765G>T	p.Gly922Val	p.G922V	ENST00000336596	NM_005233.5	922	gGt/gTt	16/17	0.150824852848033	2	FACETS	1	0.864	1	0.512	0.433	0.599	CLONAL	1	FALSE	0	0.150824852848033	2		498	635	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980432	55980432	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008662-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	22	248	0	ENST00000263923.4:c.659G>T	p.Gly220Val	p.G220V	ENST00000263923	NM_002253.2	220	gGg/gTg	6/30	0.150824852848033	1	FACETS	0.96	0.745	1	0.96	0.745	1	CLONAL	1	FALSE	0	0.150824852848033	1		248	281	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875621	35875621	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008662-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	39	264	0	ENST00000303115.3:c.808C>A	p.Pro270Thr	p.P270T	ENST00000303115	NM_002185.3	270	Cct/Act	7/8	0.143879571741121	3	FACETS	1	0.929	1	0.623	0.517	0.742	CLONAL	1	FALSE	1	0.150824852848033	3		264	446	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250781	26250781	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008662-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	68	529	0	ENST00000446824.2:c.53del	p.Arg18ProfsTer19	p.R18Pfs*19	ENST00000446824	NM_021018.2	18	cGc/cc	1/1	0.148750079018585	2	FACETS	0.943	0.823	1	0.943	0.823	1	CLONAL	2	FALSE	0	0.150824852848033	2		529	478	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184844	32184844	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008662-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	91	624	0	ENST00000375023.3:c.1739G>T	p.Gly580Val	p.G580V	ENST00000375023	NM_004557.3	580	gGc/gTc	11/30	0.148750079018585	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	FALSE	0	0.150824852848033	2		624	560	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248104	110248104	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008662-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	111	514	0	ENST00000374672.4:c.1368C>A	p.Phe456Leu	p.F456L	ENST00000374672	NM_004235.4	456	ttC/ttA	5/5	0.147498784930618	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	FALSE	0	0.150824852848033	2		514	617	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	356	718	5	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	0.92869126487266	3	FACETS	0.985	0.934	1	0.492	0.467	0.519	CLONAL	1	TRUE	1	0.92869126487266	3		723	1140	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261555	142261555	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	162	287	2	ENST00000350721.4:c.3402del	p.Phe1134LeufsTer6	p.F1134Lfs*6	ENST00000350721	NM_001184.3	1134	ttT/tt	17/47	1	2	FACETS	0.916	0.851	0.981	0.916	0.851	0.981	CLONAL	1	TRUE	1	0.92869126487266	2		289	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	322	609	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.92869126487266	3	FACETS	0.903	0.853	0.955	0.452	0.426	0.478	CLONAL	1	TRUE	1	0.92869126487266	3		609	1124	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	320	669	6	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.877	0.832	0.922	0.877	0.832	0.922	CLONAL	1	TRUE	1	0.92869126487266	2		675	786	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	192	391	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	0.92869126487266	2	FACETS	0.944	0.884	1	0.472	0.442	0.503	CLONAL	1	TRUE	0	0.92869126487266	2		391	438	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782094	9782094	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	431	868	0	ENST00000377346.4:c.2121del	p.Lys708SerfsTer7	p.K708Sfs*7	ENST00000377346	NM_005026.3	706	aCc/ac	17/24	0.92869126487266	2	FACETS	0.929	0.889	0.969	0.465	0.444	0.485	CLONAL	1	TRUE	0	0.92869126487266	2		868	999	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217234	11217234	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1031980569	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	317	606	0	ENST00000361445.4:c.4444C>T	p.Arg1482Cys	p.R1482C	ENST00000361445	NM_004958.3	1482	Cgc/Tgc	30/58	0.92869126487266	2	FACETS	1	0.962	1	0.506	0.482	0.531	CLONAL	1	TRUE	0	0.92869126487266	2		606	674	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259480	16259480	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	246	488	0	ENST00000375759.3:c.6750del	p.Ala2251GlnfsTer102	p.A2251Qfs*102	ENST00000375759	NM_015001.2	2249	Ccc/cc	11/15	0.92869126487266	2	FACETS	0.941	0.888	0.995	0.47	0.444	0.498	CLONAL	1	TRUE	0	0.92869126487266	2		488	563	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458147	120458147	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1325403451	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	706	686	0	ENST00000256646.2:c.7198C>T	p.Arg2400Ter	p.R2400*	ENST00000256646	NM_024408.3	2400	Cga/Tga	34/34	0.92869126487266	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.92869126487266	2		686	740	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458869	120458869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755184344	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	721	753	1	ENST00000256646.2:c.6476C>T	p.Thr2159Met	p.T2159M	ENST00000256646	NM_024408.3	2159	aCg/aTg	34/34	0.92869126487266	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.92869126487266	2		754	766	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653377	206653377	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376382831	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1500	508	828	2	ENST00000367120.3:c.1261G>A	p.Ala421Thr	p.A421T	ENST00000367120	NM_014002.3	421	Gcc/Acc	12/22	0.92869126487266	4	FACETS	1	0.981	1	0.525	0.501	0.55	CLONAL	1	TRUE	2	0.92869126487266	4		830	2008	SUCCESS
RET	5979	MSKCC	GRCh37	10	43613833	43613833	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1017108031	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	706	732	1	ENST00000355710.3:c.2297C>T	p.Pro766Leu	p.P766L	ENST00000355710	NM_020975.4	766	cCg/cTg	13/20	0.92869126487266	3	FACETS	0.948	0.921	0.975	0.948	0.921	0.975	CLONAL	2	TRUE	1	0.92869126487266	3		733	1174	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	104	176	3	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	0.92869126487266	3	FACETS	0.889	0.803	0.978	0.444	0.401	0.489	CLONAL	1	TRUE	1	0.92869126487266	3		179	369	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406037	70406037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	284	528	0	ENST00000373644.4:c.3551G>A	p.Gly1184Asp	p.G1184D	ENST00000373644	NM_030625.2	1184	gGc/gAc	4/12	0.92869126487266	3	FACETS	0.994	0.937	1	0.497	0.468	0.527	CLONAL	1	TRUE	1	0.92869126487266	3		528	901	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446140	70446140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	444	428	0	ENST00000373644.4:c.5080C>T	p.Arg1694Cys	p.R1694C	ENST00000373644	NM_030625.2	1694	Cgc/Tgc	11/12	0.92869126487266	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.92869126487266	3		428	681	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692791	89692791	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1114167623	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	182	293	0	ENST00000371953.3:c.275A>G	p.Asp92Gly	p.D92G	ENST00000371953	NM_000314.4	92	gAc/gGc	5/9	0.92869126487266	3	FACETS	1	0.935	1	0.503	0.467	0.541	CLONAL	1	TRUE	1	0.92869126487266	3		293	570	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771514	112771514	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1564732148	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	525	453	1	ENST00000369452.4:c.1692del	p.Pro565LeufsTer8	p.P565Lfs*8	ENST00000369452	NM_007373.3	563	Ggg/gg	9/9	0.92869126487266	3	FACETS	0.935	0.904	0.966	0.935	0.904	0.966	CLONAL	2	TRUE	1	0.92869126487266	3		454	885	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912188	114912188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	553	555	2	ENST00000543371.1:c.1258C>T	p.Arg420Trp	p.R420W	ENST00000543371	NM_001198531.1	420	Cgg/Tgg	11/14	0.92869126487266	3	FACETS	0.932	0.901	0.962	0.932	0.901	0.962	CLONAL	2	TRUE	1	0.92869126487266	3		557	936	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	585	511	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	0.92869126487266	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.92869126487266	3		511	918	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533873	533873	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913496	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	856	805	1	ENST00000451590.1:c.183G>T	p.Gln61His	p.Q61H	ENST00000451590	NM_001130442.1	61	caG/caT	3/5	0.92869126487266	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.92869126487266	3		806	1327	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129325	64129325	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs376604355	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	407	910	1	ENST00000334205.4:c.757C>T	p.Arg253Trp	p.R253W	ENST00000334205	NM_003942.2	253	Cgg/Tgg	8/17	0.92869126487266	3	FACETS	0.921	0.875	0.967	0.46	0.437	0.484	CLONAL	1	TRUE	1	0.92869126487266	3		911	1394	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948483	71948484	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1292	520	1054	5	ENST00000298229.2:c.3201dup	p.Ser1068GlnfsTer17	p.S1068Qfs*17	ENST00000298229	NM_001567.3	1065	-/C	26/28	0.92869126487266	3	FACETS	0.905	0.865	0.945	0.452	0.432	0.473	CLONAL	1	TRUE	1	0.92869126487266	3		1059	1812	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037475	12037475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs724159946	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	440	363	0	ENST00000396373.4:c.1106G>A	p.Arg369Gln	p.R369Q	ENST00000396373	NM_001987.4	369	cGg/cAg	6/8	0.92869126487266	3	FACETS	0.994	0.959	1	0.994	0.959	1	CLONAL	2	TRUE	1	0.92869126487266	3		363	698	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944961	31944961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1441610501	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	346	565	0	ENST00000340398.3:c.140C>T	p.Ala47Val	p.A47V	ENST00000340398	NM_001013699.2	47	gCg/gTg	1/1	0.92869126487266	3	FACETS	1	0.979	1	0.531	0.503	0.559	CLONAL	1	TRUE	1	0.92869126487266	3		565	1028	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425047	49425047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778628310	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	464	860	0	ENST00000301067.7:c.13441G>A	p.Glu4481Lys	p.E4481K	ENST00000301067	NM_003482.3	4481	Gag/Aag	39/54	0.92869126487266	3	FACETS	0.984	0.939	1	0.492	0.469	0.515	CLONAL	1	TRUE	1	0.92869126487266	3		860	1487	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440431	49440431	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1240601136	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	374	761	1	ENST00000301067.7:c.4379del	p.Pro1460HisfsTer46	p.P1460Hfs*46	ENST00000301067	NM_003482.3	1460	cCa/ca	15/54	0.92869126487266	3	FACETS	0.876	0.831	0.923	0.438	0.415	0.462	CLONAL	1	TRUE	1	0.92869126487266	3		762	1346	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445095	49445095	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	739	784	3	ENST00000301067.7:c.2371del	p.Gln791ArgfsTer139	p.Q791Rfs*139	ENST00000301067	NM_003482.3	791	Cag/ag	10/54	0.92869126487266	3	FACETS	0.91	0.884	0.936	0.91	0.884	0.936	CLONAL	2	TRUE	1	0.92869126487266	3		787	1280	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959073	28959073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761475937	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	169	348	0	ENST00000282397.4:c.2065G>A	p.Glu689Lys	p.E689K	ENST00000282397	NM_002019.4	689	Gag/Aag	14/30	1	2	FACETS	0.896	0.834	0.959	0.896	0.834	0.959	CLONAL	1	TRUE	1	0.92869126487266	2		348	406	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987204	36987204	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	430	716	0	ENST00000354822.5:c.485C>T	p.Ala162Val	p.A162V	ENST00000354822	NM_001079668.2	162	gCg/gTg	3/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.92869126487266	2		716	892	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987211	36987211	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	383	677	1	ENST00000354822.5:c.478G>T	p.Gly160Cys	p.G160C	ENST00000354822	NM_001079668.2	160	Ggc/Tgc	3/3	1	2	FACETS	0.983	0.939	1	0.983	0.939	1	CLONAL	1	TRUE	1	0.92869126487266	2		678	839	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028735	42028735	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	267	536	0	ENST00000219905.7:c.4276del	p.Met1426TrpfsTer15	p.M1426Wfs*15	ENST00000219905	NM_001164273.1	1425	Aaa/aa	13/24	1	2	FACETS	0.952	0.9	1	0.952	0.9	1	CLONAL	1	TRUE	1	0.92869126487266	2		536	604	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434817	99434817	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774794966	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	334	618	0	ENST00000268035.6:c.904G>A	p.Glu302Lys	p.E302K	ENST00000268035	NM_000875.3	302	Gag/Aag	3/21	1	2	FACETS	0.921	0.876	0.967	0.921	0.876	0.967	CLONAL	1	TRUE	1	0.92869126487266	2		618	781	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647423	3647423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755156257	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	408	801	2	ENST00000294008.3:c.1640C>T	p.Thr547Met	p.T547M	ENST00000294008	NM_032444.2	547	aCg/aTg	7/15	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.92869126487266	2		803	878	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346158	89346158	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs878855327	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	151	339	0	ENST00000301030.4:c.6792del	p.Ala2265ProfsTer72	p.A2265Pfs*72	ENST00000301030	NM_001256183.1	2264	ccC/cc	9/13	1	2	FACETS	0.926	0.859	0.994	0.926	0.859	0.994	CLONAL	1	TRUE	1	0.92869126487266	2		339	351	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849432	89849432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778309	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	382	747	0	ENST00000389301.3:c.1549C>T	p.Arg517Trp	p.R517W	ENST00000389301	NM_000135.2	517	Cgg/Tgg	16/43	1	2	FACETS	0.962	0.919	1	0.962	0.919	1	CLONAL	1	TRUE	1	0.92869126487266	2		747	855	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217705	7217707	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs757139280	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	251	461	0	ENST00000380728.2:c.220_222del	p.Glu74del	p.E74del	ENST00000380728		74	GAG/-	4/11	0.92869126487266	3	FACETS	0.969	0.909	1	0.484	0.454	0.515	CLONAL	1	TRUE	1	0.92869126487266	3		461	817	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882019	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	1056	1070	0	ENST00000269305.4:c.455dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	ccg/ccCg	5/11	0.92869126487266	3	FACETS	0.938	0.915	0.96	0.938	0.915	0.96	CLONAL	2	TRUE	1	0.92869126487266	3		1070	1776	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	602	637	8	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	0.92869126487266	3	FACETS	0.858	0.83	0.886	0.858	0.83	0.886	CLONAL	2	TRUE	1	0.92869126487266	3		645	1106	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664455	29664455	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	514	473	0	ENST00000356175.3:c.6434G>A	p.Gly2145Asp	p.G2145D	ENST00000356175	NM_000267.3	2145	gGc/gAc	42/57	0.92869126487266	3	FACETS	0.964	0.932	0.995	0.964	0.932	0.995	CLONAL	2	TRUE	1	0.92869126487266	3		473	841	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29686010	29686010	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757391670	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	288	336	0	ENST00000356175.3:c.8074C>T	p.Arg2692Trp	p.R2692W	ENST00000356175	NM_000267.3	2692	Cgg/Tgg	55/57	0.92869126487266	3	FACETS	0.952	0.91	0.994	0.952	0.91	0.994	CLONAL	2	TRUE	1	0.92869126487266	3		336	477	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55693419	55693419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759162213	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	411	729	1	ENST00000284073.2:c.626C>T	p.Ala209Val	p.A209V	ENST00000284073	NM_138962.2	209	gCg/gTg	9/14	0.92869126487266	3	FACETS	1	0.964	1	0.507	0.483	0.532	CLONAL	1	TRUE	1	0.92869126487266	3		730	1278	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985819	60985820	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	267	405	0	ENST00000333681.4:c.80dup	p.Tyr28LeufsTer125	p.Y28Lfs*125	ENST00000333681		27	ggc/ggGc	2/3	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.92869126487266	2		405	561	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619821	1619821	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	420	884	2	ENST00000344749.5:c.1125del	p.Gly376ValfsTer18	p.G376Vfs*18	ENST00000344749	NM_001136139.2	375	ccC/cc	14/19	1	2	FACETS	0.855	0.816	0.894	0.855	0.816	0.894	CLONAL	1	TRUE	1	0.92869126487266	2		886	1058	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5207998	5207998	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757213585	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	461	872	0	ENST00000357368.4:c.5713G>A	p.Val1905Met	p.V1905M	ENST00000357368	NM_002850.3	1905	Gtg/Atg	37/38	1	2	FACETS	0.983	0.943	1	0.983	0.943	1	CLONAL	1	TRUE	1	0.92869126487266	2		872	1010	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262102	10262102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	314	639	2	ENST00000340748.4:c.2189G>A	p.Arg730His	p.R730H	ENST00000340748		730	cGc/cAc	23/40	1	2	FACETS	0.9	0.855	0.947	0.9	0.855	0.947	CLONAL	1	TRUE	1	0.92869126487266	2		641	751	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031732	11031732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752644931	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	525	992	1	ENST00000327064.4:c.1544C>T	p.Pro515Leu	p.P515L	ENST00000327064	NM_199141.1	515	cCg/cTg	14/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.92869126487266	2		993	1119	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350248	15350248	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	504	994	1	ENST00000263377.2:c.3531G>T	p.Lys1177Asn	p.K1177N	ENST00000263377	NM_058243.2	1177	aaG/aaT	17/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.92869126487266	2		995	1023	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937673	17937673	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	392	737	0	ENST00000458235.1:c.3254G>A	p.Arg1085Gln	p.R1085Q	ENST00000458235	NM_000215.3	1085	cGg/cAg	24/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.92869126487266	2		737	800	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266705	18266705	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	418	726	1	ENST00000222254.8:c.16G>T	p.Gly6Cys	p.G6C	ENST00000222254	NM_005027.3	6	Ggc/Tgc	2/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.92869126487266	2		727	891	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905055	50905055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	372	687	0	ENST00000440232.2:c.342del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	113	Ggg/gg	4/27	1	2	FACETS	0.964	0.92	1	0.964	0.92	1	CLONAL	1	TRUE	1	0.92869126487266	2		687	831	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905566	50905566	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	578	1122	1	ENST00000440232.2:c.694C>A	p.Arg232Ser	p.R232S	ENST00000440232	NM_002691.3	232	Cgt/Agt	6/27	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.92869126487266	2		1123	1240	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085941	16085941	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs754137452	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	280	471	0	ENST00000281043.3:c.1117C>T	p.Arg373Ter	p.R373*	ENST00000281043	NM_005378.4	373	Cga/Tga	3/3	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.92869126487266	2		471	592	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632248	215632248	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553619225	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	247	428	0	ENST00000260947.4:c.1526T>C	p.Ile509Thr	p.I509T	ENST00000260947	NM_000465.2	509	aTa/aCa	6/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.92869126487266	2		428	502	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383338	31383338	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs753480369	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	285	540	0	ENST00000328111.2:c.1250G>A	p.Arg417Gln	p.R417Q	ENST00000328111	NM_006892.3	417	cGa/cAa	11/23	1	2	FACETS	0.984	0.933	1	0.984	0.933	1	CLONAL	1	TRUE	1	0.92869126487266	2		540	624	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36014556	36014556	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747298865	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	332	669	0	ENST00000358208.4:c.329G>A	p.Arg110Gln	p.R110Q	ENST00000358208		110	cGg/cAg	3/12	1	2	FACETS	0.941	0.895	0.987	0.941	0.895	0.987	CLONAL	1	TRUE	1	0.92869126487266	2		669	760	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181923	38181923	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1177134850	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	259	486	0	ENST00000396334.3:c.547A>G	p.Ser183Gly	p.S183G	ENST00000396334	NM_002468.4	183	Agc/Ggc	3/5	1	2	FACETS	0.953	0.901	1	0.953	0.901	1	CLONAL	1	TRUE	1	0.92869126487266	2		486	585	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144879	47144879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	243	450	0	ENST00000409792.3:c.4874G>A	p.Arg1625His	p.R1625H	ENST00000409792	NM_014159.6	1625	cGt/cAt	7/21	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.92869126487266	2		450	514	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413010	49413010	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519952	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	270	531	0	ENST00000418115.1:c.13C>T	p.Arg5Trp	p.R5W	ENST00000418115	NM_001664.2	5	Cgg/Tgg	2/5	1	2	FACETS	0.923	0.873	0.974	0.923	0.873	0.974	CLONAL	1	TRUE	1	0.92869126487266	2		531	630	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584583	52584583	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	337	652	1	ENST00000394830.3:c.4430del	p.Pro1477LeufsTer12	p.P1477Lfs*12	ENST00000394830	NM_018313.4	1477	cCt/ct	29/30	1	2	FACETS	0.977	0.93	1	0.977	0.93	1	CLONAL	1	TRUE	1	0.92869126487266	2		653	743	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269075	142269075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28910271	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	210	408	0	ENST00000350721.4:c.2875G>A	p.Val959Met	p.V959M	ENST00000350721	NM_001184.3	959	Gtg/Atg	14/47	1	2	FACETS	0.917	0.861	0.975	0.917	0.861	0.975	CLONAL	1	TRUE	1	0.92869126487266	2		408	493	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278281	142278281	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs746970647	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	221	434	2	ENST00000350721.4:c.1544G>A	p.Arg515His	p.R515H	ENST00000350721	NM_001184.3	515	cGt/cAt	7/47	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.92869126487266	2		436	454	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916935	178916935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	188	361	0	ENST00000263967.3:c.322C>T	p.Arg108Cys	p.R108C	ENST00000263967	NM_006218.2	108	Cgt/Tgt	2/21	1	2	FACETS	0.953	0.891	1	0.953	0.891	1	CLONAL	1	TRUE	1	0.92869126487266	2		361	425	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683389	182683389	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	196	348	0	ENST00000292782.4:c.156A>G	p.Ile52Met	p.I52M	ENST00000292782	NM_020640.2	52	atA/atG	2/7	1	2	FACETS	0.896	0.838	0.955	0.896	0.838	0.955	CLONAL	1	TRUE	1	0.92869126487266	2		348	471	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807119	1807119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	513	1036	3	ENST00000260795.2:c.1450G>A	p.Gly484Ser	p.G484S	ENST00000260795		484	Ggc/Agc	10/17	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.92869126487266	2		1039	1092	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007332	143007332	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	159	291	0	ENST00000262992.4:c.2452del	p.Arg818GlufsTer4	p.R818Efs*4	ENST00000262992	NM_001101669.1	818	Aga/ga	22/24	1	2	FACETS	0.913	0.848	0.979	0.913	0.848	0.979	CLONAL	1	TRUE	1	0.92869126487266	2		291	375	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31422969	31422969	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	312	536	0	ENST00000344624.3:c.3344G>A	p.Gly1115Glu	p.G1115E	ENST00000344624		1115	gGa/gAa	26/33	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.92869126487266	2		536	657	SUCCESS
APC	324	MSKCC	GRCh37	5	112116587	112116587	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	163	269	0	ENST00000257430.4:c.636del	p.Lys212AsnfsTer7	p.K212Nfs*7	ENST00000257430	NM_000038.5	211	gAa/ga	6/16	1	2	FACETS	0.981	0.914	1	0.981	0.914	1	CLONAL	1	TRUE	1	0.92869126487266	2		269	358	SUCCESS
APC	324	MSKCC	GRCh37	5	112179566	112179566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755366812	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	166	302	0	ENST00000257430.4:c.8275C>T	p.Arg2759Cys	p.R2759C	ENST00000257430	NM_000038.5	2759	Cgt/Tgt	16/16	1	2	FACETS	0.993	0.926	1	0.993	0.926	1	CLONAL	1	TRUE	1	0.92869126487266	2		302	360	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931452	131931452	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507178	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	178	308	8	ENST00000265335.6:c.2165del	p.Lys722ArgfsTer14	p.K722Rfs*14	ENST00000265335		719	ctA/ct	13/25	1	2	FACETS	0.93	0.868	0.993	0.93	0.868	0.993	CLONAL	1	TRUE	1	0.92869126487266	2		316	412	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481637	20481637	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	91	215	0	ENST00000346618.3:c.710del	p.Asn237ThrfsTer27	p.N237Tfs*27	ENST00000346618	NM_001949.4	236	Aaa/aa	3/7	NA	2	FACETS	0.903	0.819	0.989			1	INDETERMINATE	1	TRUE	NA	0.92869126487266	2		215	217	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	244	571	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	0.171545721720758	4	FACETS	0.76	0.714	0.806	0.76	0.714	0.806	INDETERMINATE	2	TRUE	2	0.92869126487266	4		571	667	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553788	106553788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1281186824	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	196	253	0	ENST00000369096.4:c.1753G>A	p.Gly585Ser	p.G585S	ENST00000369096	NM_001198.3	585	Ggc/Agc	5/7	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.92869126487266	2		253	407	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137522041	137522041	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	106	202	0	ENST00000367739.4:c.838del	p.Ser280AlafsTer2	p.S280Afs*2	ENST00000367739	NM_000416.2	280	Agc/gc	6/7	1	2	FACETS	0.852	0.776	0.929	0.852	0.776	0.929	CLONAL	1	TRUE	1	0.92869126487266	2		202	268	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099332	157099333	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCA	rs754114025	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	119	402	0	ENST00000346085.5:c.285_287dup	p.His96dup	p.H96dup	ENST00000346085	NM_020732.3	96	gcc/gcCCAc	1/20	1	2	FACETS	0.544	0.494	0.596	0.544	0.494	0.596	SUBCLONAL	1	TRUE	1	0.92869126487266	2		402	471	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367244	50367244	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	171	303	0	ENST00000331340.3:c.56del	p.Pro19LeufsTer2	p.P19Lfs*2	ENST00000331340	NM_006060.4	17	agC/ag	3/8	0.92869126487266	3	FACETS	0.906	0.838	0.977	0.453	0.419	0.489	CLONAL	1	TRUE	1	0.92869126487266	3		303	595	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468287	50468287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	318	617	0	ENST00000331340.3:c.1522C>T	p.His508Tyr	p.H508Y	ENST00000331340	NM_006060.4	508	Cac/Tac	8/8	0.92869126487266	3	FACETS	0.945	0.893	0.998	0.473	0.446	0.499	CLONAL	1	TRUE	1	0.92869126487266	3		617	1061	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508257	106508257	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766854286	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	219	419	0	ENST00000359195.3:c.251C>T	p.Ala84Val	p.A84V	ENST00000359195	NM_002649.2	84	gCg/gTg	2/11	0.92869126487266	3	FACETS	1	0.944	1	0.506	0.472	0.54	CLONAL	1	TRUE	1	0.92869126487266	3		419	683	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509420	106509420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622026	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	304	557	0	ENST00000359195.3:c.1414C>T	p.Arg472Cys	p.R472C	ENST00000359195	NM_002649.2	472	Cgt/Tgt	2/11	0.92869126487266	3	FACETS	0.976	0.922	1	0.488	0.461	0.516	CLONAL	1	TRUE	1	0.92869126487266	3		557	982	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140487360	140487360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507472	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	529	498	0	ENST00000288602.6:c.1165C>T	p.Arg389Cys	p.R389C	ENST00000288602	NM_004333.4	389	Cgt/Tgt	9/18	0.92869126487266	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.92869126487266	3		498	820	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372029	55372029	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1332803887	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	505	385	1	ENST00000297316.4:c.719C>T	p.Pro240Leu	p.P240L	ENST00000297316	NM_022454.3	240	cCg/cTg	2/2	0.92869126487266	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	1	0.92869126487266	3		386	726	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372232	55372232	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	409	304	0	ENST00000297316.4:c.922G>A	p.Gly308Arg	p.G308R	ENST00000297316	NM_022454.3	308	Ggg/Agg	2/2	0.92869126487266	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	1	0.92869126487266	3		304	576	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404576	8404576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146844299	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	129	258	0	ENST00000356435.5:c.4171G>A	p.Ala1391Thr	p.A1391T	ENST00000356435		1391	Gca/Aca	25/35	1	2	FACETS	0.852	0.784	0.922	0.852	0.784	0.922	CLONAL	1	TRUE	1	0.92869126487266	2		258	326	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570332	87570332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	405	775	1	ENST00000277120.3:c.2072G>A	p.Arg691His	p.R691H	ENST00000277120		691	cGc/cAc	17/19	1	2	FACETS	0.966	0.924	1	0.966	0.924	1	CLONAL	1	TRUE	1	0.92869126487266	2		776	903	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229496	98229496	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	260	383	0	ENST00000331920.6:c.2462A>G	p.Asp821Gly	p.D821G	ENST00000331920	NM_000264.3	821	gAc/gGc	15/24	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.92869126487266	2		383	503	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759406	133759406	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1371645607	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	378	691	0	ENST00000318560.5:c.1729C>T	p.Arg577Ter	p.R577*	ENST00000318560	NM_005157.4	577	Cga/Tga	11/11	1	2	FACETS	0.988	0.944	1	0.988	0.944	1	CLONAL	1	TRUE	1	0.92869126487266	2		691	824	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933722	39933722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs899486642	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	368	738	0	ENST00000378444.4:c.877G>A	p.Val293Ile	p.V293I	ENST00000378444	NM_001123385.1	293	Gtc/Atc	4/15	0.92869126487266	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.92869126487266	1		738	423	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820536	44820536	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772197961	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	155	351	0	ENST00000377967.4:c.233G>A	p.Arg78His	p.R78H	ENST00000377967	NM_021140.2	78	cGc/cAc	3/29	0.92869126487266	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.92869126487266	1		351	166	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224137	53224137	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	457	854	0	ENST00000375401.3:c.3414G>T	p.Gln1138His	p.Q1138H	ENST00000375401	NM_004187.3	1138	caG/caT	22/26	0.92869126487266	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.92869126487266	1		854	513	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231067	53231067	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	213	598	0	ENST00000375401.3:c.1835C>T	p.Ala612Val	p.A612V	ENST00000375401	NM_004187.3	612	gCc/gTc	13/26	0.92869126487266	1	FACETS	0.627	0.592	0.661	0.627	0.592	0.661	SUBCLONAL	1	TRUE	0	0.92869126487266	1		598	392	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821594	72821596	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs374416547	NA	P-0010783-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	18	102	0	ENST00000268489.5:c.10579_10581del	p.Gly3527del	p.G3527del	ENST00000268489	NM_006885.3	3527	GGC/-	10/10	1	2	FACETS	0.218	0.164	0.28	0.218	0.164	0.28	SUBCLONAL	1	TRUE	1	0.92869126487266	2		102	178	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913286	NA	P-0012425-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	15	225	0	ENST00000263967.3:c.1636C>G	p.Gln546Glu	p.Q546E	ENST00000263967	NM_006218.2	546	Cag/Gag	10/21	1	2	FACETS	0.08	0.058	0.107	0.08	0.058	0.107	SUBCLONAL	1	TRUE	1	0.916454402832471	2		225	408	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745954	162745954	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012425-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	37	410	0	ENST00000367921.3:c.2077C>G	p.Gln693Glu	p.Q693E	ENST00000367921	NM_006182.2	693	Caa/Gaa	16/18	0.916454402832471	1	FACETS	0.078	0.064	0.094	0.078	0.064	0.094	SUBCLONAL	1	TRUE	0	0.916454402832471	1		410	562	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091740	29091740	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200649225	NA	P-0012425-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	142	134	2	ENST00000328354.6:c.1217G>A	p.Arg406His	p.R406H	ENST00000328354	NM_007194.3	406	cGt/cAt	11/15	1	2	FACETS	0.948	0.877	1	0.948	0.877	1	CLONAL	1	TRUE	1	0.916454402832471	2		136	327	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650566	48650566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012425-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	54	353	0	ENST00000376670.3:c.536C>T	p.Pro179Leu	p.P179L	ENST00000376670	NM_002049.3	179	cCc/cTc	3/6	1	1	FACETS	0.098	0.083	0.114	0.098	0.083	0.114	SUBCLONAL	1	TRUE	0	0.916454402832471	1		353	654	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	374	557	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.955	0.907	1	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		558	1156	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	356	737	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	1	2	FACETS	0.922	0.875	0.971	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		737	1139	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556079	29556079	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886041347	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	102	284	0	ENST00000356175.3:c.2446C>T	p.Arg816Ter	p.R816*	ENST00000356175	NM_000267.3	816	Cga/Tga	21/57	1	2	FACETS	0.877	0.793	0.965	1	0.991	1	CLONAL	4	TRUE	1	0.16945068635343	2		284	343	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584478	52584478	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142726131	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	289	610	1	ENST00000394830.3:c.4535C>T	p.Ala1512Val	p.A1512V	ENST00000394830	NM_018313.4	1512	gCg/gTg	29/30	1	2	FACETS	1	0.972	1	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		611	815	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144146	11144146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	419	893	4	ENST00000358026.2:c.3727C>T	p.Arg1243Trp	p.R1243W	ENST00000358026	NM_001128849.1	1243	Cgg/Tgg	26/36	1	2	FACETS	1	0.979	1	1	0.998	1	CLONAL	4	TRUE	1	0.16945068635343	2		897	1181	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	424	785	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	1	0.983	1	1	0.998	1	CLONAL	4	TRUE	1	0.16945068635343	2		786	1180	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922298	178922298	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	150	394	0	ENST00000263967.3:c.1067T>C	p.Val356Ala	p.V356A	ENST00000263967	NM_006218.2	356	gTt/gCt	6/21	1	2	FACETS	0.969	0.893	1	1	0.994	1	CLONAL	4	TRUE	1	0.16945068635343	2		394	457	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118598	17118598	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41419545	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	339	758	3	ENST00000285071.4:c.1333G>A	p.Ala445Thr	p.A445T	ENST00000285071	NM_144997.5	445	Gca/Aca	12/14	1	2	FACETS	1	0.988	1	1	0.997	1	CLONAL	3	TRUE	1	0.16945068635343	2		761	1167	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177584	56177584	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368201444	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	135	468	2	ENST00000399503.3:c.2557C>T	p.Arg853Cys	p.R853C	ENST00000399503	NM_005921.1	853	Cgt/Tgt	14/20	1	2	FACETS	0.913	0.833	0.996	1	0.992	1	CLONAL	3	TRUE	1	0.16945068635343	2		470	582	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	173	453	0	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	1	2	FACETS	0.897	0.831	0.966	1	0.994	1	CLONAL	4	TRUE	1	0.16945068635343	2		453	569	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517592	176517592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767045353	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	574	1196	1	ENST00000292408.4:c.293G>A	p.Arg98His	p.R98H	ENST00000292408	NM_213647.1	98	cGc/cAc	3/18	1	2	FACETS	1	0.991	1	1	0.998	1	CLONAL	4	TRUE	1	0.16945068635343	2		1197	1542	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	159	440	1	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.942	0.87	1	1	0.994	1	CLONAL	4	TRUE	1	0.16945068635343	2		441	498	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783301	9783301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763402967	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	368	889	2	ENST00000377346.4:c.2545G>A	p.Ala849Thr	p.A849T	ENST00000377346	NM_005026.3	849	Gcc/Acc	20/24	1	2	FACETS	0.946	0.898	0.995	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		891	1148	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101370	27101370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748819428	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	334	1053	0	ENST00000324856.7:c.4652G>A	p.Arg1551His	p.R1551H	ENST00000324856	NM_006015.4	1551	cGc/cAc	18/20	1	2	FACETS	0.992	0.937	1	1	0.997	1	CLONAL	3	TRUE	1	0.16945068635343	2		1053	1325	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645169	86645169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs191759701	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	124	276	0	ENST00000274376.6:c.1241G>A	p.Arg414Gln	p.R414Q	ENST00000274376	NM_002890.2	414	cGg/cAg	8/25	1	2	FACETS	0.96	0.882	1	1	0.993	1	CLONAL	5	TRUE	1	0.16945068635343	2		276	305	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685330	86685330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	53	171	0	ENST00000274376.6:c.3046C>T	p.Arg1016Cys	p.R1016C	ENST00000274376	NM_002890.2	1016	Cgt/Tgt	24/25	1	2	FACETS	0.907	0.782	1	1	0.981	1	CLONAL	3	TRUE	1	0.16945068635343	2		171	230	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198389	138198389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751123351	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	104	314	0	ENST00000237289.4:c.982G>A	p.Ala328Thr	p.A328T	ENST00000237289	NM_001270507.1	328	Gca/Aca	6/9	1	2	FACETS	0.958	0.864	1	1	0.99	1	CLONAL	3	TRUE	1	0.16945068635343	2		314	427	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3827631	3827631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141098117	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	150	477	0	ENST00000262367.5:c.2141G>A	p.Arg714His	p.R714H	ENST00000262367	NM_004380.2	714	cGc/cAc	11/31	1	2	FACETS	0.941	0.863	1	1	0.993	1	CLONAL	3	TRUE	1	0.16945068635343	2		477	627	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654642	67654642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	251	398	2	ENST00000264010.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000264010	NM_006565.3	377	Cgt/Tgt	6/12	1	2	FACETS	0.904	0.849	0.961	1	0.996	1	CLONAL	4	TRUE	1	0.16945068635343	2		400	819	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131402	17131402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398124537	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1443	101	1028	1	ENST00000285071.4:c.50G>A	p.Arg17His	p.R17H	ENST00000285071	NM_144997.5	17	cGc/cAc	4/14	1	2	FACETS	0.772	0.687	0.863	0.772	0.687	0.863	SUBCLONAL	1	TRUE	1	0.16945068635343	2		1029	1544	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509508	149509508	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs74943037	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	302	889	1	ENST00000261799.4:c.1391C>T	p.Thr464Met	p.T464M	ENST00000261799	NM_002609.3	464	aCg/aTg	10/23	1	2	FACETS	0.993	0.936	1	1	0.996	1	CLONAL	3	TRUE	1	0.16945068635343	2		890	1196	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276250	15276250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747223569	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	320	939	1	ENST00000263388.2:c.5744G>A	p.Arg1915His	p.R1915H	ENST00000263388	NM_000435.2	1915	cGc/cAc	31/33	1	2	FACETS	1	0.984	1	1	0.997	1	CLONAL	3	TRUE	1	0.16945068635343	2		940	1136	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726436	46726436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139448277	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	261	667	0	ENST00000371975.4:c.515G>A	p.Arg172His	p.R172H	ENST00000371975	NM_003579.3	172	cGc/cAc	7/18	1	2	FACETS	0.901	0.846	0.957	1	0.996	1	CLONAL	4	TRUE	1	0.16945068635343	2		667	855	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2972186	2972186	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748468563	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	309	712	0	ENST00000396946.4:c.1553G>A	p.Arg518Gln	p.R518Q	ENST00000396946	NM_032415.4	518	cGa/cAa	11/25	1	2	FACETS	0.884	0.835	0.935	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		712	1031	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928347	69928347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	43	530	3	ENST00000352241.4:c.167G>A	p.Arg56His	p.R56H	ENST00000352241	NM_198159.2	56	cGc/cAc	2/10	1	2	FACETS	0.67	0.559	0.793	0.67	0.559	0.793	SUBCLONAL	1	TRUE	1	0.16945068635343	2		533	758	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50483736	50483736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768972786	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	340	721	0	ENST00000394963.4:c.841C>T	p.Arg281Trp	p.R281W	ENST00000394963	NM_003076.4	281	Cgg/Tgg	7/13	1	2	FACETS	0.942	0.892	0.993	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		721	1065	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778785	9778785	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759798937	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	474	887	0	ENST00000377346.4:c.1054G>A	p.Glu352Lys	p.E352K	ENST00000377346	NM_005026.3	352	Gag/Aag	9/24	1	2	FACETS	0.974	0.931	1	1	0.998	1	CLONAL	4	TRUE	1	0.16945068635343	2		887	1436	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216546	108216546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529296539	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	110	312	0	ENST00000278616.4:c.8495G>A	p.Arg2832His	p.R2832H	ENST00000278616	NM_000051.3	2832	cGt/cAt	58/63	1	2	FACETS	1	0.965	1	1	0.991	1	CLONAL	3	TRUE	1	0.16945068635343	2		312	381	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721511	49721511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1255375162	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	367	788	0	ENST00000449682.2:c.2128C>T	p.Arg710Cys	p.R710C	ENST00000449682	NM_020998.3	710	Cgt/Tgt	18/18	1	2	FACETS	0.934	0.887	0.983	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		788	1159	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967305	25967305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766049052	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	168	396	0	ENST00000435504.4:c.1901C>T	p.Ser634Leu	p.S634L	ENST00000435504		634	tCg/tTg	13/13	1	2	FACETS	1	0.977	1	1	0.994	1	CLONAL	3	TRUE	1	0.16945068635343	2		396	576	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968673	55968673	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs755067067	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	146	515	1	ENST00000263923.4:c.1990C>T	p.Arg664Cys	p.R664C	ENST00000263923	NM_002253.2	664	Cgt/Tgt	14/30	1	2	FACETS	0.959	0.879	1	1	0.993	1	CLONAL	3	TRUE	1	0.16945068635343	2		516	599	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346205	89346205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202081612	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	245	637	1	ENST00000301030.4:c.6745C>T	p.Arg2249Cys	p.R2249C	ENST00000301030	NM_001256183.1	2249	Cgc/Tgc	9/13	1	2	FACETS	0.886	0.83	0.943	1	0.996	1	CLONAL	4	TRUE	1	0.16945068635343	2		638	816	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195701	123195701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777363856	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	239	664	0	ENST00000218089.9:c.1615G>A	p.Val539Met	p.V539M	ENST00000218089	NM_001042749.1	539	Gtg/Atg	17/35	1	2	FACETS	0.979	0.919	1	1	0.996	1	CLONAL	4	TRUE	1	0.16945068635343	2		664	720	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940012	76940012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs122445105	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	239	666	0	ENST00000373344.5:c.736C>T	p.Arg246Cys	p.R246C	ENST00000373344	NM_000489.3	246	Cgc/Tgc	9/35	1	2	FACETS	1	0.984	1	1	0.996	1	CLONAL	3	TRUE	1	0.16945068635343	2		666	816	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233039	55233039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	280	610	0	ENST00000275493.2:c.1789G>A	p.Ala597Thr	p.A597T	ENST00000275493	NM_005228.3	597	Gca/Aca	15/28	1	2	FACETS	0.92	0.866	0.975	1	0.996	1	CLONAL	4	TRUE	1	0.16945068635343	2		610	898	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428511	78428511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408536007	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	178	505	0	ENST00000370768.2:c.1288C>T	p.Arg430Cys	p.R430C	ENST00000370768	NM_003902.3	430	Cgt/Tgt	14/20	1	2	FACETS	0.901	0.835	0.969	1	0.995	1	CLONAL	4	TRUE	1	0.16945068635343	2		505	583	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612028	189612028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs900140738	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	241	544	0	ENST00000264731.3:c.1780C>T	p.Arg594Ter	p.R594*	ENST00000264731	NM_003722.4	594	Cga/Tga	14/14	1	2	FACETS	0.897	0.84	0.955	1	0.996	1	CLONAL	4	TRUE	1	0.16945068635343	2		544	793	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434592	110434592	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	305	939	5	ENST00000375856.3:c.3809C>A	p.Pro1270Gln	p.P1270Q	ENST00000375856	NM_003749.2	1270	cCg/cAg	1/2	0.16945068635343	4	FACETS	1	0.958	1	0.767	0.721	0.813	CLONAL	3	TRUE	0	0.16945068635343	4		944	1373	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533838	533838	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	603	1123	1	ENST00000451590.1:c.218G>A	p.Arg73His	p.R73H	ENST00000451590	NM_001130442.1	73	cGc/cAc	3/5	1	2	FACETS	1	0.96	1	1	0.998	1	CLONAL	4	TRUE	1	0.16945068635343	2		1124	1780	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31025035	31025035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375101983	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	252	512	0	ENST00000375687.4:c.4520C>T	p.Ala1507Val	p.A1507V	ENST00000375687	NM_015338.5	1507	gCg/gTg	13/13	1	2	FACETS	1	0.943	1	1	0.996	1	CLONAL	4	TRUE	1	0.16945068635343	2		512	741	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145645	11145645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	426	1155	1	ENST00000358026.2:c.4007G>A	p.Arg1336His	p.R1336H	ENST00000358026	NM_001128849.1	1336	cGc/cAc	29/36	1	2	FACETS	0.897	0.854	0.941	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		1156	1401	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	125	415	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.994	0.91	1	1	0.993	1	CLONAL	4	TRUE	1	0.16945068635343	2		415	371	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557367	187557367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746932852	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	180	456	0	ENST00000441802.2:c.3995G>A	p.Arg1332His	p.R1332H	ENST00000441802	NM_005245.3	1332	cGc/cAc	6/27	1	2	FACETS	0.943	0.876	1	1	0.995	1	CLONAL	4	TRUE	1	0.16945068635343	2		456	563	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434413	140434413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775889922	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	186	477	0	ENST00000288602.6:c.2285C>T	p.Ala762Val	p.A762V	ENST00000288602	NM_004333.4	762	gCg/gTg	18/18	1	2	FACETS	1	0.98	1	1	0.995	1	CLONAL	3	TRUE	1	0.16945068635343	2		477	637	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622039	43622039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1371891301	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	220	492	0	ENST00000355710.3:c.3056C>T	p.Ala1019Val	p.A1019V	ENST00000355710	NM_020975.4	1019	gCg/gTg	19/20	0.169374935467926	1	FACETS	0.9	0.842	0.96	1	0.996	1	CLONAL	4	TRUE	0	0.16945068635343	1		492	660	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172064	99172064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	325	676	1	ENST00000074304.5:c.1630C>T	p.Arg544Cys	p.R544C	ENST00000074304	NM_001134224.1	544	Cgt/Tgt	17/26	1	2	FACETS	0.938	0.888	0.99	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		677	1022	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041025	112041025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779126684	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	238	564	0	ENST00000368678.4:c.230G>A	p.Arg77His	p.R77H	ENST00000368678		77	cGt/cAt	3/13	1	2	FACETS	0.916	0.858	0.975	1	0.996	1	CLONAL	4	TRUE	1	0.16945068635343	2		564	767	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142913	7142913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1283504748	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	364	966	1	ENST00000302850.5:c.2456G>A	p.Arg819His	p.R819H	ENST00000302850	NM_000208.2	819	cGc/cAc	12/22	1	2	FACETS	0.905	0.858	0.952	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		967	1187	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513012	106513012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758968659	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	104	250	0	ENST00000359195.3:c.2026G>A	p.Ala676Thr	p.A676T	ENST00000359195	NM_002649.2	676	Gcc/Acc	3/11	1	2	FACETS	0.922	0.834	1	1	0.991	1	CLONAL	4	TRUE	1	0.16945068635343	2		250	333	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508824	106508824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226994105	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	312	742	1	ENST00000359195.3:c.818G>A	p.Arg273His	p.R273H	ENST00000359195	NM_002649.2	273	cGc/cAc	2/11	1	2	FACETS	0.935	0.883	0.987	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		743	985	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169083	32169083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1056526093	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	514	1151	0	ENST00000375023.3:c.3950G>A	p.Arg1317Gln	p.R1317Q	ENST00000375023	NM_004557.3	1317	cGg/cAg	22/30	0.16945068635343	4	FACETS	1	0.989	1	1	0.997	1	CLONAL	4	TRUE	2	0.16945068635343	4		1151	1615	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808917	3808917	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	316	712	0	ENST00000262367.5:c.3307C>T	p.Arg1103Ter	p.R1103*	ENST00000262367	NM_004380.2	1103	Cga/Tga	17/31	1	2	FACETS	1	0.969	1	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		712	903	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034435	47034435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	350	840	0	ENST00000377604.3:c.520G>A	p.Ala174Thr	p.A174T	ENST00000377604	NM_001204468.1	174	Gcc/Acc	6/24	1	2	FACETS	1	0.986	1	1	0.997	1	CLONAL	3	TRUE	1	0.16945068635343	2		840	1235	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137020	64137020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1174133485	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	460	1001	0	ENST00000334205.4:c.1531C>T	p.Arg511Cys	p.R511C	ENST00000334205	NM_003942.2	511	Cgc/Tgc	13/17	1	2	FACETS	0.979	0.935	1	1	0.998	1	CLONAL	4	TRUE	1	0.16945068635343	2		1001	1387	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557552	95557552	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1447120867	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	116	397	1	ENST00000393063.1:c.5515C>T	p.Arg1839Trp	p.R1839W	ENST00000393063	NM_030621.3	1839	Cgg/Tgg	26/28	1	2	FACETS	1	0.947	1	1	0.992	1	CLONAL	3	TRUE	1	0.16945068635343	2		398	430	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137232	64137232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	505	1223	1	ENST00000334205.4:c.1664C>T	p.Ala555Val	p.A555V	ENST00000334205	NM_003942.2	555	gCg/gTg	14/17	1	2	FACETS	0.956	0.915	0.998	1	0.998	1	CLONAL	4	TRUE	1	0.16945068635343	2		1224	1558	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226445	133226445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	312	700	0	ENST00000320574.5:c.3613C>T	p.Pro1205Ser	p.P1205S	ENST00000320574	NM_006231.2	1205	Ccg/Tcg	30/49	1	2	FACETS	0.971	0.918	1	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		700	948	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669547	88669547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56394626	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	112	482	0	ENST00000360948.2:c.1351G>A	p.Val451Ile	p.V451I	ENST00000360948	NM_001012338.2	451	Gtc/Atc	12/19	0.122980603616098	0	FACETS	1	0.955	1			1	CLONAL	2	TRUE	0	0.16945068635343	0		482	501	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661663	227661664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761880048	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	341	946	13	ENST00000305123.5:c.1791dup	p.His598AlafsTer13	p.H598Afs*13	ENST00000305123	NM_005544.2	597	-/G	1/2	1	2	FACETS	1	0.973	1	1	0.997	1	CLONAL	3	TRUE	1	0.16945068635343	2		959	1283	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739881	145739881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764297840	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1786	441	1086	0	ENST00000428558.2:c.1649C>T	p.Ala550Val	p.A550V	ENST00000428558	NM_004260.3	550	gCg/gTg	10/22	0.16945068635343	9	FACETS	0.931	0.884	0.979	0.465	0.442	0.49	CLONAL	4	TRUE	1	0.16945068635343	9		1086	2227	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552821	226552821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182639036	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	250	701	0	ENST00000366794.5:c.2540G>A	p.Arg847His	p.R847H	ENST00000366794	NM_001618.3	847	cGt/cAt	19/23	1	2	FACETS	1	0.985	1	1	0.996	1	CLONAL	3	TRUE	1	0.16945068635343	2		701	854	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40993338	40993338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145617142	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	130	430	0	ENST00000267868.3:c.164C>T	p.Ala55Val	p.A55V	ENST00000267868	NM_002875.4	55	gCg/gTg	3/10	0.122980603616098	0	FACETS	1	0.919	1			1	CLONAL	3	TRUE	0	0.16945068635343	0		430	423	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710983	117710983	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	127	287	0	ENST00000368508.3:c.1289G>A	p.Gly430Asp	p.G430D	ENST00000368508	NM_002944.2	430	gGc/gAc	12/43	1	2	FACETS	1	0.948	1	1	0.993	1	CLONAL	4	TRUE	1	0.16945068635343	2		287	358	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136143	11136143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770014321	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	353	892	1	ENST00000358026.2:c.3127C>T	p.Arg1043Trp	p.R1043W	ENST00000358026	NM_001128849.1	1043	Cgg/Tgg	22/36	1	2	FACETS	0.881	0.835	0.928	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		893	1182	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729399	41729399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	47	769	0	ENST00000242208.4:c.1130G>A	p.Arg377His	p.R377H	ENST00000242208	NM_002192.2	377	cGc/cAc	3/3	1	2	FACETS	0.591	0.497	0.696	0.591	0.497	0.696	SUBCLONAL	1	TRUE	1	0.16945068635343	2		769	938	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446294	70446294	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144991411	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	43	651	1	ENST00000373644.4:c.5234C>T	p.Thr1745Met	p.T1745M	ENST00000373644	NM_030625.2	1745	aCg/aTg	11/12	0.169374935467926	1	FACETS	0.543	0.453	0.644	0.543	0.453	0.644	SUBCLONAL	1	TRUE	0	0.16945068635343	1		652	855	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672759	86672759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	114	373	0	ENST00000274376.6:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000274376	NM_002890.2	749	cGa/cAa	17/25	1	2	FACETS	1	0.963	1	1	0.992	1	CLONAL	3	TRUE	1	0.16945068635343	2		373	400	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892293	9892293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs796052550	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	234	472	1	ENST00000330684.3:c.2197G>A	p.Ala733Thr	p.A733T	ENST00000330684	NM_001134407.1	733	Gca/Aca	11/13	1	2	FACETS	0.906	0.851	0.961	1	0.996	1	CLONAL	5	TRUE	1	0.16945068635343	2		473	610	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993737	72993737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776936617	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	73	904	1	ENST00000268489.5:c.308G>A	p.Arg103His	p.R103H	ENST00000268489	NM_006885.3	103	cGc/cAc	2/10	1	2	FACETS	0.749	0.653	0.854	0.749	0.653	0.854	SUBCLONAL	1	TRUE	1	0.16945068635343	2		905	1150	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11172938	11172938	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555337942	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	286	667	1	ENST00000361445.4:c.7337C>T	p.Thr2446Met	p.T2446M	ENST00000361445	NM_004958.3	2446	aCg/aTg	54/58	1	2	FACETS	0.988	0.932	1	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		668	854	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593563	215593563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782662	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	141	405	2	ENST00000260947.4:c.2171C>T	p.Ala724Val	p.A724V	ENST00000260947	NM_000465.2	724	gCg/gTg	11/11	1	2	FACETS	1	0.971	1	1	0.993	1	CLONAL	3	TRUE	1	0.16945068635343	2		407	491	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73991994	73991994	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139808700	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	342	1249	2	ENST00000318443.5:c.14G>A	p.Arg5Gln	p.R5Q	ENST00000318443	NM_001024736.1	5	cGg/cAg	2/10	0.122980603616098	0	FACETS	0.898	0.85	0.948			1	CLONAL	3	TRUE	0	0.16945068635343	0		1251	1244	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436057	110436057	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1204032443	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1729	429	1290	1	ENST00000375856.3:c.2344G>A	p.Asp782Asn	p.D782N	ENST00000375856	NM_003749.2	782	Gac/Aac	1/2	0.16945068635343	4	FACETS	0.915	0.868	0.962	0.686	0.651	0.722	CLONAL	3	TRUE	0	0.16945068635343	4		1291	2158	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606697	29606697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779282861	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	216	692	0	ENST00000389048.3:c.1183C>T	p.Arg395Cys	p.R395C	ENST00000389048	NM_004304.4	395	Cgt/Tgt	5/29	1	2	FACETS	1	0.976	1	1	0.995	1	CLONAL	3	TRUE	1	0.16945068635343	2		692	775	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268138	153268138	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1406877044	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	167	493	1	ENST00000281708.4:c.670C>T	p.Arg224Ter	p.R224*	ENST00000281708	NM_033632.3	224	Cga/Tga	4/12	1	2	FACETS	0.919	0.85	0.99	1	0.994	1	CLONAL	4	TRUE	1	0.16945068635343	2		494	536	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832175	72832175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371424734	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	266	636	0	ENST00000268489.5:c.4406C>T	p.Ala1469Val	p.A1469V	ENST00000268489	NM_006885.3	1469	gCc/gTc	9/10	1	2	FACETS	0.907	0.853	0.963	1	0.996	1	CLONAL	4	TRUE	1	0.16945068635343	2		636	865	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119007	3119007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769503200	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	343	1150	2	ENST00000078429.4:c.691G>A	p.Ala231Thr	p.A231T	ENST00000078429	NM_002067.2	231	Gcc/Acc	5/7	1	2	FACETS	1	0.978	1	1	0.997	1	CLONAL	3	TRUE	1	0.16945068635343	2		1152	1268	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	359996	359996	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324067997	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	398	1156	1	ENST00000262320.3:c.1093C>T	p.Arg365Trp	p.R365W	ENST00000262320	NM_003502.3	365	Cgg/Tgg	4/11	1	2	FACETS	1	0.983	1	1	0.997	1	CLONAL	3	TRUE	1	0.16945068635343	2		1157	1455	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33446562	33446562	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	457	861	0	ENST00000345365.6:c.71G>T	p.Arg24Met	p.R24M	ENST00000345365	NM_002878.3	24	aGg/aTg	1/10	1	2	FACETS	1	0.975	1	1	0.998	1	CLONAL	4	TRUE	1	0.16945068635343	2		861	1311	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238944	5238944	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs946180785	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	316	701	0	ENST00000357368.4:c.1835G>A	p.Arg612His	p.R612H	ENST00000357368	NM_002850.3	612	cGc/cAc	13/38	1	2	FACETS	1	0.968	1	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		701	904	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775583	39775583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369318352	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	215	550	3	ENST00000288319.7:c.437C>T	p.Ala146Val	p.A146V	ENST00000288319	NM_182918.3	146	gCg/gTg	4/10	0.169374935467926	1	FACETS	1	0.968	1	1	0.995	1	CLONAL	3	TRUE	0	0.16945068635343	1		553	730	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974830	15974830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	210	545	0	ENST00000268712.3:c.4045C>T	p.Arg1349Cys	p.R1349C	ENST00000268712	NM_006311.3	1349	Cgt/Tgt	30/46	1	2	FACETS	0.925	0.863	0.988	1	0.995	1	CLONAL	4	TRUE	1	0.16945068635343	2		545	670	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226860	2226860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	334	550	2	ENST00000398665.3:c.4340C>T	p.Ala1447Val	p.A1447V	ENST00000398665	NM_032482.2	1447	gCg/gTg	27/28	1	2	FACETS	0.925	0.882	0.969	1	0.997	1	CLONAL	6	TRUE	1	0.16945068635343	2		552	710	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046611	30046611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556530827	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	187	646	3	ENST00000331968.5:c.2572C>T	p.Arg858Cys	p.R858C	ENST00000331968	NM_002742.2	858	Cgc/Tgc	18/18	1	2	FACETS	1	0.968	1	1	0.995	1	CLONAL	3	TRUE	1	0.16945068635343	2		649	682	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321073	137321073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768721235	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	415	924	0	ENST00000481739.1:c.1030G>A	p.Ala344Thr	p.A344T	ENST00000481739	NM_002957.4	344	Gcc/Acc	7/10	1	2	FACETS	0.954	0.909	1	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		924	1283	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288765	15288765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1317504991	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	65	160	0	ENST00000263388.2:c.3974G>A	p.Arg1325His	p.R1325H	ENST00000263388	NM_000435.2	1325	cGc/cAc	24/33	1	2	FACETS	1	0.934	1	1	0.986	1	CLONAL	3	TRUE	1	0.16945068635343	2		160	233	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967089	18967089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334288478	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	409	1013	0	ENST00000262803.5:c.1804G>A	p.Ala602Thr	p.A602T	ENST00000262803	NM_002911.3	602	Gca/Aca	13/24	1	2	FACETS	0.973	0.927	1	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		1013	1240	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798379	42798379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749470261	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	534	1021	0	ENST00000575354.2:c.4250G>A	p.Arg1417His	p.R1417H	ENST00000575354	NM_015125.3	1417	cGc/cAc	18/20	1	2	FACETS	1	0.969	1	1	0.998	1	CLONAL	4	TRUE	1	0.16945068635343	2		1021	1555	SUCCESS
BLM	641	MSKCC	GRCh37	15	91328208	91328208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367953471	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	155	506	0	ENST00000355112.3:c.2720C>T	p.Thr907Met	p.T907M	ENST00000355112	NM_000057.2	907	aCg/aTg	14/22	0.122980603616098	0	FACETS	0.834	0.767	0.904			1	CLONAL	3	TRUE	0	0.16945068635343	0		506	607	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754050	42754050	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	341	791	2	ENST00000222329.4:c.302G>A	p.Arg101Gln	p.R101Q	ENST00000222329	NM_006494.2	101	cGg/cAg	3/4	1	2	FACETS	0.933	0.883	0.983	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		793	1079	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670340	134670340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415689583	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	224	457	0	ENST00000398015.3:c.251G>A	p.Arg84His	p.R84H	ENST00000398015	NM_004441.4	84	cGc/cAc	3/16	1	2	FACETS	0.928	0.868	0.99	1	0.996	1	CLONAL	4	TRUE	1	0.16945068635343	2		457	712	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416516	49416516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	336	713	0	ENST00000301067.7:c.16195G>A	p.Val5399Met	p.V5399M	ENST00000301067	NM_003482.3	5399	Gtg/Atg	51/54	1	2	FACETS	0.896	0.848	0.945	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		713	1106	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032123	48032124	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs63751327	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	132	332	0	ENST00000234420.5:c.3514dup	p.Arg1172LysfsTer5	p.R1172Kfs*5	ENST00000234420	NM_000179.2	1171	-/A	6/10	1	2	FACETS	1	0.972	1	1	0.993	1	CLONAL	3	TRUE	1	0.16945068635343	2		332	451	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991508	72991508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755878058	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	327	892	2	ENST00000268489.5:c.2537G>A	p.Arg846His	p.R846H	ENST00000268489	NM_006885.3	846	cGc/cAc	2/10	1	2	FACETS	1	0.976	1	1	0.997	1	CLONAL	3	TRUE	1	0.16945068635343	2		894	1216	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218488	5218488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1361339357	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	351	901	1	ENST00000357368.4:c.3991G>A	p.Ala1331Thr	p.A1331T	ENST00000357368	NM_002850.3	1331	Gcc/Acc	25/38	1	2	FACETS	0.942	0.894	0.992	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		902	1099	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650720	67650720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	368	703	2	ENST00000264010.4:c.1025G>A	p.Arg342His	p.R342H	ENST00000264010	NM_006565.3	342	cGt/cAt	5/12	1	2	FACETS	1	0.985	1	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		705	1003	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132501	11132501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	413	1130	2	ENST00000358026.2:c.2717G>A	p.Arg906His	p.R906H	ENST00000358026	NM_001128849.1	906	cGc/cAc	19/36	1	2	FACETS	1	0.991	1	1	0.997	1	CLONAL	3	TRUE	1	0.16945068635343	2		1132	1404	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754574	42754574	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768322408	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1222	574	1133	3	ENST00000222329.4:c.166G>A	p.Val56Ile	p.V56I	ENST00000222329	NM_006494.2	56	Gtc/Atc	2/4	1	2	FACETS	0.943	0.905	0.982	1	0.998	1	CLONAL	4	TRUE	1	0.16945068635343	2		1136	1796	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344671	118344671	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782407414	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	160	405	0	ENST00000534358.1:c.2797C>T	p.Arg933Trp	p.R933W	ENST00000534358	NM_005933.3	933	Cgg/Tgg	3/36	1	2	FACETS	0.898	0.828	0.969	1	0.994	1	CLONAL	4	TRUE	1	0.16945068635343	2		405	526	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553770	106553770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	37	466	0	ENST00000369096.4:c.1735G>A	p.Val579Ile	p.V579I	ENST00000369096	NM_001198.3	579	Gtt/Att	5/7	1	2	FACETS	0.717	0.59	0.86	0.717	0.59	0.86	SUBCLONAL	1	TRUE	1	0.16945068635343	2		466	609	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376683	118376683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149340870	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	215	561	0	ENST00000534358.1:c.10076C>T	p.Ala3359Val	p.A3359V	ENST00000534358	NM_005933.3	3359	gCg/gTg	27/36	1	2	FACETS	1	0.974	1	1	0.995	1	CLONAL	3	TRUE	1	0.16945068635343	2		561	777	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845415	151845415	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	306	753	1	ENST00000262189.6:c.13597C>T	p.Arg4533Ter	p.R4533*	ENST00000262189	NM_170606.2	4533	Cga/Tga	52/59	1	2	FACETS	1	0.988	1	1	0.997	1	CLONAL	3	TRUE	1	0.16945068635343	2		754	1036	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100906	41100906	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs560503250	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	225	712	1	ENST00000373198.4:c.1450G>A	p.Val484Ile	p.V484I	ENST00000373198	NM_133170.3	484	Gtt/Att	8/32	1	2	FACETS	1	0.969	1	1	0.995	1	CLONAL	3	TRUE	1	0.16945068635343	2		713	832	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572925	41572925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1389352663	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	346	971	1	ENST00000263253.7:c.5210G>A	p.Arg1737His	p.R1737H	ENST00000263253	NM_001429.3	1737	cGc/cAc	31/31	1	2	FACETS	1	0.974	1	1	0.997	1	CLONAL	3	TRUE	1	0.16945068635343	2		972	1297	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38139044	38139044	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	189	485	0	ENST00000317025.8:c.3559C>T	p.Arg1187Ter	p.R1187*	ENST00000317025	NM_023034.1	1187	Cga/Tga	20/24	1	2	FACETS	0.952	0.885	1	1	0.995	1	CLONAL	4	TRUE	1	0.16945068635343	2		485	586	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993075	72993075	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	411	1062	2	ENST00000268489.5:c.970G>A	p.Ala324Thr	p.A324T	ENST00000268489	NM_006885.3	324	Gct/Act	2/10	1	2	FACETS	0.98	0.933	1	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		1064	1238	SUCCESS
AR	367	MSKCC	GRCh37	X	66766603	66766603	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	332	952	0	ENST00000374690.3:c.1615C>T	p.Arg539Cys	p.R539C	ENST00000374690	NM_000044.3	539	Cgt/Tgt	1/8	1	2	FACETS	1	0.987	1	1	0.997	1	CLONAL	3	TRUE	1	0.16945068635343	2		952	1148	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1646375	1646375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528980993	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	303	1151	0	ENST00000344749.5:c.124G>A	p.Gly42Arg	p.G42R	ENST00000344749	NM_001136139.2	42	Ggg/Agg	3/19	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.16945068635343	2		1151	1443	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2180751	2180751	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	64	735	2	ENST00000398665.3:c.121A>T	p.Ile41Phe	p.I41F	ENST00000398665	NM_032482.2	41	Atc/Ttc	2/28	1	2	FACETS	0.722	0.623	0.83	0.722	0.623	0.83	SUBCLONAL	1	TRUE	1	0.16945068635343	2		737	1046	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511562	66511562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1224297486	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	151	296	0	ENST00000358598.2:c.22G>A	p.Ala8Thr	p.A8T	ENST00000358598	NM_212471.2	8	Gcc/Acc	2/11	1	2	FACETS	0.924	0.852	0.999	1	0.994	1	CLONAL	4	TRUE	1	0.16945068635343	2		296	482	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191069	2191069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746714270	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	348	690	0	ENST00000398665.3:c.323G>A	p.Arg108His	p.R108H	ENST00000398665	NM_032482.2	108	cGc/cAc	5/28	1	2	FACETS	1	0.956	1	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		690	1018	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46736426	46736426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150138364	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	64	571	2	ENST00000371975.4:c.1138C>T	p.Arg380Trp	p.R380W	ENST00000371975	NM_003579.3	380	Cgg/Tgg	10/18	1	2	FACETS	0.948	0.819	1	0.948	0.819	1	CLONAL	1	TRUE	1	0.16945068635343	2		573	797	SUCCESS
ATM	472	MSKCC	GRCh37	11	108213987	108213987	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs778269655	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	154	342	0	ENST00000278616.4:c.8307G>A	p.Trp2769Ter	p.W2769*	ENST00000278616	NM_000051.3	2769	tgG/tgA	57/63	1	2	FACETS	1	0.941	1	1	0.994	1	CLONAL	4	TRUE	1	0.16945068635343	2		342	445	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612740	228612740	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747322437	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	406	1093	1	ENST00000366696.1:c.287C>T	p.Ala96Val	p.A96V	ENST00000366696	NM_003493.2	96	gCg/gTg	1/1	1	2	FACETS	1	0.99	1	1	0.997	1	CLONAL	3	TRUE	1	0.16945068635343	2		1094	1381	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969845	81969845	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369090249	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	279	645	1	ENST00000359376.3:c.2914G>A	p.Val972Ile	p.V972I	ENST00000359376	NM_002661.3	972	Gtc/Atc	27/33	1	2	FACETS	0.937	0.882	0.992	1	0.996	1	CLONAL	4	TRUE	1	0.16945068635343	2		646	879	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420607	49420607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123724	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	426	967	1	ENST00000301067.7:c.15142C>T	p.Arg5048Cys	p.R5048C	ENST00000301067	NM_003482.3	5048	Cgt/Tgt	48/54	1	2	FACETS	0.942	0.898	0.987	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		968	1334	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041623	14041623	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1204895453	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	193	549	0	ENST00000311895.7:c.2170G>A	p.Val724Met	p.V724M	ENST00000311895	NM_005236.2	724	Gtg/Atg	11/11	1	2	FACETS	0.97	0.899	1	1	0.995	1	CLONAL	3	TRUE	1	0.16945068635343	2		549	783	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526083	66526083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768253469	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	32	374	0	ENST00000358598.2:c.914G>A	p.Arg305His	p.R305H	ENST00000358598	NM_212471.2	305	cGt/cAt	10/11	1	2	FACETS	0.694	0.562	0.844	0.694	0.562	0.844	SUBCLONAL	1	TRUE	1	0.16945068635343	2		374	544	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729187	66729187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	223	707	0	ENST00000307102.5:c.395C>T	p.Ala132Val	p.A132V	ENST00000307102	NM_002755.3	132	gCg/gTg	3/11	0.122980603616098	0	FACETS	0.919	0.858	0.982			1	CLONAL	3	TRUE	0	0.16945068635343	0		707	793	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911893	32911893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	172	582	0	ENST00000380152.3:c.3401G>A	p.Ser1134Asn	p.S1134N	ENST00000380152		1134	aGc/aAc	11/27	0.169374935467926	1	FACETS	1	0.956	1	1	0.994	1	CLONAL	3	TRUE	0	0.16945068635343	1		582	591	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158764	26158764	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	470	881	0	ENST00000289316.2:c.367A>G	p.Thr123Ala	p.T123A	ENST00000289316	NM_138720.2	123	Acc/Gcc	1/2	0.16945068635343	8	FACETS	0.922	0.88	0.964	1	0.989	1	CLONAL	6	TRUE	3	0.16945068635343	8		881	1513	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246446	53246446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201805773	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	341	723	0	ENST00000375401.3:c.536G>A	p.Arg179His	p.R179H	ENST00000375401	NM_004187.3	179	cGt/cAt	5/26	1	2	FACETS	0.955	0.905	1	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		723	1054	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202926	27202926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772637203	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	211	510	1	ENST00000380036.4:c.2018G>A	p.Arg673His	p.R673H	ENST00000380036	NM_000459.3	673	cGt/cAt	13/23	0.16945068635343	1	FACETS	1	0.978	1	1	0.996	1	CLONAL	5	TRUE	0	0.16945068635343	1		511	423	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210709	36210709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780868475	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	527	999	0	ENST00000222270.7:c.460C>T	p.Arg154Cys	p.R154C	ENST00000222270	NM_014727.1	154	Cgc/Tgc	3/37	1	2	FACETS	1	0.981	1	1	0.998	1	CLONAL	4	TRUE	1	0.16945068635343	2		999	1497	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436109	49436109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755573725	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	277	596	0	ENST00000301067.7:c.5872C>T	p.Arg1958Cys	p.R1958C	ENST00000301067	NM_003482.3	1958	Cgc/Tgc	28/54	1	2	FACETS	0.985	0.928	1	1	0.996	1	CLONAL	4	TRUE	1	0.16945068635343	2		596	830	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946376	71946376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1433	101	1088	1	ENST00000298229.2:c.2540G>A	p.Ser847Asn	p.S847N	ENST00000298229	NM_001567.3	847	aGc/aAc	23/28	1	2	FACETS	0.777	0.692	0.869	0.777	0.692	0.869	SUBCLONAL	1	TRUE	1	0.16945068635343	2		1089	1534	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339039	225339039	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752958265	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	157	454	0	ENST00000264414.4:c.2230C>T	p.Arg744Cys	p.R744C	ENST00000264414	NM_003590.4	744	Cgt/Tgt	16/16	1	2	FACETS	0.944	0.871	1	1	0.994	1	CLONAL	4	TRUE	1	0.16945068635343	2		454	491	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463271	25463271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770568549	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	273	654	0	ENST00000264709.3:c.2222C>T	p.Ala741Val	p.A741V	ENST00000264709	NM_175629.2	741	gCg/gTg	19/23	1	2	FACETS	0.941	0.886	0.997	1	0.996	1	CLONAL	4	TRUE	1	0.16945068635343	2		654	856	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572622	141572622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772067763	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1364	350	845	1	ENST00000220592.5:c.448C>T	p.Arg150Trp	p.R150W	ENST00000220592	NM_012154.3	150	Cgg/Tgg	4/19	0.16945068635343	9	FACETS	0.96	0.906	1	0.48	0.453	0.508	CLONAL	4	TRUE	1	0.16945068635343	9		846	1714	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10259612	10259612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	318	807	0	ENST00000340748.4:c.2620G>A	p.Ala874Thr	p.A874T	ENST00000340748		874	Gcg/Acg	26/40	1	2	FACETS	1	0.986	1	1	0.997	1	CLONAL	3	TRUE	1	0.16945068635343	2		807	1109	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223533	36223533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1347423104	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1322	648	1500	0	ENST00000222270.7:c.6083C>T	p.Ser2028Phe	p.S2028F	ENST00000222270	NM_014727.1	2028	tCc/tTc	28/37	1	2	FACETS	0.971	0.934	1	1	0.998	1	CLONAL	4	TRUE	1	0.16945068635343	2		1500	1970	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796750	135796750	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs118203436	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	47	296	0	ENST00000298552.3:c.737G>A	p.Arg246Lys	p.R246K	ENST00000298552	NM_001162426.1	246	aGg/aAg	8/23	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.16945068635343	2		296	395	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968235	2968235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1188731718	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	442	1080	0	ENST00000396946.4:c.1751G>A	p.Arg584His	p.R584H	ENST00000396946	NM_032415.4	584	cGc/cAc	13/25	1	2	FACETS	0.913	0.87	0.956	1	0.998	1	CLONAL	4	TRUE	1	0.16945068635343	2		1080	1429	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894950	101894950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777965779	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	131	394	0	ENST00000374994.4:c.503G>A	p.Arg168His	p.R168H	ENST00000374994	NM_004612.2	168	cGc/cAc	3/9	1	2	FACETS	1	0.959	1	1	0.993	1	CLONAL	3	TRUE	1	0.16945068635343	2		394	475	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302857	15302857	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140914494	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	477	1288	3	ENST00000263388.2:c.593C>T	p.Ala198Val	p.A198V	ENST00000263388	NM_000435.2	198	gCg/gTg	4/33	1	2	FACETS	1	0.992	1	1	0.998	1	CLONAL	3	TRUE	1	0.16945068635343	2		1291	1611	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21630862	21630862	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202110155	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	227	563	0	ENST00000421138.2:c.742G>A	p.Ala248Thr	p.A248T	ENST00000421138		248	Gca/Aca	8/16	1	2	FACETS	0.929	0.869	0.99	1	0.996	1	CLONAL	4	TRUE	1	0.16945068635343	2		563	721	SUCCESS
BLM	641	MSKCC	GRCh37	15	91352442	91352442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760554566	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	101	346	0	ENST00000355112.3:c.3827C>T	p.Ala1276Val	p.A1276V	ENST00000355112	NM_000057.2	1276	gCg/gTg	20/22	0.122980603616098	0	FACETS	1	0.958	1			1	CLONAL	2	TRUE	0	0.16945068635343	0		346	440	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134255	41134255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs994659376	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	146	486	0	ENST00000379561.5:c.1373C>T	p.Ala458Val	p.A458V	ENST00000379561	NM_002015.3	458	gCg/gTg	2/3	0.169374935467926	1	FACETS	0.929	0.852	1	1	0.993	1	CLONAL	3	TRUE	0	0.16945068635343	1		486	566	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244184	133244184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768004570	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	61	797	1	ENST00000320574.5:c.2224C>T	p.Arg742Cys	p.R742C	ENST00000320574	NM_006231.2	742	Cgt/Tgt	20/49	1	2	FACETS	0.649	0.558	0.749	0.649	0.558	0.749	SUBCLONAL	1	TRUE	1	0.16945068635343	2		798	1109	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918709	50918709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501818	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	398	808	0	ENST00000440232.2:c.2579C>T	p.Ala860Val	p.A860V	ENST00000440232	NM_002691.3	860	gCg/gTg	21/27	1	2	FACETS	1	0.97	1	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		808	1145	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994796	73994796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	219	880	0	ENST00000318443.5:c.280G>A	p.Ala94Thr	p.A94T	ENST00000318443	NM_001024736.1	94	Gcc/Acc	3/10	0.122980603616098	0	FACETS	0.855	0.797	0.915			1	CLONAL	3	TRUE	0	0.16945068635343	0		880	837	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815530	139815530	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528114067	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	391	1007	1	ENST00000247668.2:c.1001C>T	p.Ala334Val	p.A334V	ENST00000247668	NM_021138.3	334	gCg/gTg	9/11	1	2	FACETS	1	0.987	1	1	0.997	1	CLONAL	3	TRUE	1	0.16945068635343	2		1008	1381	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371691	225371691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	179	524	0	ENST00000264414.4:c.913C>T	p.Arg305Cys	p.R305C	ENST00000264414	NM_003590.4	305	Cgt/Tgt	7/16	1	2	FACETS	1	0.976	1	1	0.994	1	CLONAL	3	TRUE	1	0.16945068635343	2		524	627	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559777	29559777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs902739109	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	152	312	0	ENST00000356175.3:c.3374C>T	p.Ala1125Val	p.A1125V	ENST00000356175	NM_000267.3	1125	gCg/gTg	26/57	1	2	FACETS	0.988	0.912	1	1	0.994	1	CLONAL	4	TRUE	1	0.16945068635343	2		312	454	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200616	67200616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201207505	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	519	1106	0	ENST00000312629.5:c.727C>T	p.Arg243Cys	p.R243C	ENST00000312629	NM_003952.2	243	Cgc/Tgc	9/15	1	2	FACETS	0.97	0.929	1	1	0.998	1	CLONAL	4	TRUE	1	0.16945068635343	2		1106	1579	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945764	17945764	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201784993	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	361	1051	0	ENST00000458235.1:c.2096C>T	p.Ala699Val	p.A699V	ENST00000458235	NM_000215.3	699	gCg/gTg	16/24	1	2	FACETS	1	0.974	1	1	0.997	1	CLONAL	3	TRUE	1	0.16945068635343	2		1051	1358	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213515	36213515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746928288	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1404	651	1557	2	ENST00000222270.7:c.2617C>T	p.Arg873Cys	p.R873C	ENST00000222270	NM_014727.1	873	Cgt/Tgt	5/37	1	2	FACETS	0.935	0.899	0.971	1	0.998	1	CLONAL	4	TRUE	1	0.16945068635343	2		1559	2055	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118687	11118687	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1248744047	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	282	806	3	ENST00000358026.2:c.2111G>A	p.Arg704Gln	p.R704Q	ENST00000358026	NM_001128849.1	704	cGg/cAg	14/36	1	2	FACETS	1	0.97	1	1	0.996	1	CLONAL	3	TRUE	1	0.16945068635343	2		809	1057	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628365	187628365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143802989	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	265	803	1	ENST00000441802.2:c.2617G>A	p.Val873Met	p.V873M	ENST00000441802	NM_005245.3	873	Gtg/Atg	2/27	1	2	FACETS	0.942	0.883	1	1	0.996	1	CLONAL	3	TRUE	1	0.16945068635343	2		804	1107	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11168277	11168277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	52	646	0	ENST00000361445.4:c.7595C>T	p.Ala2532Val	p.A2532V	ENST00000361445	NM_004958.3	2532	gCg/gTg	57/58	1	2	FACETS	0.638	0.541	0.745	0.638	0.541	0.745	SUBCLONAL	1	TRUE	1	0.16945068635343	2		646	962	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31015992	31015992	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749495615	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	248	564	3	ENST00000375687.4:c.314C>T	p.Thr105Met	p.T105M	ENST00000375687	NM_015338.5	105	aCg/aTg	5/13	1	2	FACETS	0.954	0.896	1	1	0.996	1	CLONAL	4	TRUE	1	0.16945068635343	2		567	767	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194706	29194706	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs974286158	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	381	1339	4	ENST00000240100.2:c.1022C>T	p.Ala341Val	p.A341V	ENST00000240100	NM_001394.6	341	gCg/gTg	4/4	1	2	FACETS	1	0.979	1	1	0.997	1	CLONAL	3	TRUE	1	0.16945068635343	2		1343	1414	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634732	158634732	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771363719	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	186	425	0	ENST00000263640.3:c.454C>T	p.Arg152Cys	p.R152C	ENST00000263640	NM_001105.4	152	Cgc/Tgc	5/11	1	2	FACETS	0.992	0.923	1	1	0.995	1	CLONAL	4	TRUE	1	0.16945068635343	2		425	553	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249829	133249829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555228490	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	237	556	0	ENST00000320574.5:c.1394C>T	p.Ala465Val	p.A465V	ENST00000320574	NM_006231.2	465	gCc/gTc	14/49	1	2	FACETS	0.932	0.874	0.993	1	0.996	1	CLONAL	4	TRUE	1	0.16945068635343	2		556	750	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100432	2100432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397514949	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	322	547	2	ENST00000219476.3:c.170G>A	p.Arg57His	p.R57H	ENST00000219476	NM_000548.3	57	cGc/cAc	3/42	1	2	FACETS	0.909	0.862	0.957	1	0.997	1	CLONAL	5	TRUE	1	0.16945068635343	2		549	836	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368313	45368313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747308534	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	138	361	0	ENST00000262160.6:c.1289C>T	p.Thr430Met	p.T430M	ENST00000262160	NM_005901.5	430	aCg/aTg	11/11	1	2	FACETS	0.943	0.865	1	1	0.993	1	CLONAL	4	TRUE	1	0.16945068635343	2		361	432	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165800	118165800	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	203	525	1	ENST00000369448.3:c.310G>T	p.Glu104Ter	p.E104*	ENST00000369448	NM_017709.3	104	Gaa/Taa	2/2	1	2	FACETS	0.943	0.879	1	1	0.995	1	CLONAL	4	TRUE	1	0.16945068635343	2		526	635	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217916	2217916	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs759690350	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1354	110	1127	1	ENST00000398665.3:c.2690C>T	p.Ala897Val	p.A897V	ENST00000398665	NM_032482.2	897	gCg/gTg	22/28	1	2	FACETS	0.887	0.794	0.986	0.887	0.794	0.986	CLONAL	1	TRUE	1	0.16945068635343	2		1128	1464	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856094	111856094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs895574020	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	359	796	0	ENST00000341259.2:c.145G>A	p.Ala49Thr	p.A49T	ENST00000341259	NM_005475.2	49	Gcc/Acc	2/8	1	2	FACETS	0.998	0.948	1	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		796	1061	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121089	3121089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	450	962	0	ENST00000078429.4:c.992C>T	p.Ala331Val	p.A331V	ENST00000078429	NM_002067.2	331	gCc/gTc	7/7	1	2	FACETS	1	0.967	1	1	0.998	1	CLONAL	4	TRUE	1	0.16945068635343	2		962	1307	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416647	29416647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201129468	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	289	665	0	ENST00000389048.3:c.4306C>T	p.Arg1436Cys	p.R1436C	ENST00000389048	NM_004304.4	1436	Cgc/Tgc	29/29	1	2	FACETS	0.985	0.929	1	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		665	866	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149894	99149894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368448330	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	234	612	1	ENST00000074304.5:c.206C>T	p.Ala69Val	p.A69V	ENST00000074304	NM_001134224.1	69	gCg/gTg	5/26	1	2	FACETS	0.889	0.832	0.947	1	0.996	1	CLONAL	4	TRUE	1	0.16945068635343	2		613	777	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524611	103524612	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs752661599	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	213	327	12	ENST00000355739.4:c.2751dup	p.Leu918IlefsTer12	p.L918Ifs*12	ENST00000355739	NM_000123.3	914	-/A	13/15	0.16945068635343	4	FACETS	1	0.971	1	1	0.99	1	CLONAL	5	TRUE	0	0.16945068635343	4		339	553	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467047	25467047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	325	792	0	ENST00000264709.3:c.1828G>A	p.Ala610Thr	p.A610T	ENST00000264709	NM_175629.2	610	Gct/Act	15/23	1	2	FACETS	1	0.985	1	1	0.997	1	CLONAL	3	TRUE	1	0.16945068635343	2		792	1147	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266725	198266725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	188	569	2	ENST00000335508.6:c.2207G>A	p.Arg736His	p.R736H	ENST00000335508	NM_012433.2	736	cGc/cAc	15/25	1	2	FACETS	1	0.979	1	1	0.995	1	CLONAL	3	TRUE	1	0.16945068635343	2		571	648	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971194	21971194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561034503	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	288	648	0	ENST00000304494.5:c.164G>A	p.Gly55Asp	p.G55D	ENST00000304494	NM_000077.4	55	gGc/gAc	2/3	0.16945068635343	1	FACETS	1	0.985	1	1	0.997	1	CLONAL	5	TRUE	0	0.16945068635343	1		648	569	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440290	187440290	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200887028	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	274	599	0	ENST00000232014.4:c.2077G>A	p.Val693Met	p.V693M	ENST00000232014	NM_001130845.1	693	Gtg/Atg	10/10	1	2	FACETS	1	0.943	1	1	0.996	1	CLONAL	4	TRUE	1	0.16945068635343	2		599	808	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464541	25464541	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	380	898	0	ENST00000264709.3:c.1972G>T	p.Asp658Tyr	p.D658Y	ENST00000264709	NM_175629.2	658	Gac/Tac	17/23	1	2	FACETS	0.937	0.89	0.984	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		898	1197	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779475	3779475	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770325046	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1246	451	1380	1	ENST00000262367.5:c.5573G>A	p.Arg1858His	p.R1858H	ENST00000262367	NM_004380.2	1858	cGc/cAc	31/31	1	2	FACETS	1	0.978	1	1	0.997	1	CLONAL	3	TRUE	1	0.16945068635343	2		1381	1697	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426830	121426830	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201934320	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	261	653	0	ENST00000257555.6:c.521C>T	p.Ala174Val	p.A174V	ENST00000257555		174	gCg/gTg	2/10	1	2	FACETS	1	0.983	1	1	0.996	1	CLONAL	3	TRUE	1	0.16945068635343	2		653	908	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432154	121432154	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555681479	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	413	1147	4	ENST00000257555.6:c.901G>A	p.Ala301Thr	p.A301T	ENST00000257555		301	Gct/Act	4/10	1	2	FACETS	1	0.991	1	1	0.997	1	CLONAL	3	TRUE	1	0.16945068635343	2		1151	1398	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100411	157100411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752684703	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	74	91	0	ENST00000346085.5:c.1348C>T	p.Pro450Ser	p.P450S	ENST00000346085	NM_020732.3	450	Ccg/Tcg	1/20	1	2	FACETS	0.976	0.874	1	1	0.989	1	CLONAL	5	TRUE	1	0.16945068635343	2		91	179	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43806138	43806138	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1219805775	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	259	661	0	ENST00000372470.3:c.934C>A	p.Gln312Lys	p.Q312K	ENST00000372470	NM_005373.2	312	Caa/Aaa	6/12	1	2	FACETS	1	0.983	1	1	0.996	1	CLONAL	3	TRUE	1	0.16945068635343	2		661	906	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265039	5265039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748364975	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	349	968	1	ENST00000357368.4:c.548G>A	p.Arg183His	p.R183H	ENST00000357368	NM_002850.3	183	cGc/cAc	5/38	1	2	FACETS	1	0.984	1	1	0.997	1	CLONAL	3	TRUE	1	0.16945068635343	2		969	1256	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094713	2094713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748576083	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1596	129	1247	0	ENST00000219066.1:c.467C>T	p.Ala156Val	p.A156V	ENST00000219066	NM_002528.5	156	gCg/gTg	3/6	1	2	FACETS	0.883	0.797	0.974	0.883	0.797	0.974	CLONAL	1	TRUE	1	0.16945068635343	2		1247	1725	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771908	135771908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060503200	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	359	795	0	ENST00000298552.3:c.3209C>T	p.Ala1070Val	p.A1070V	ENST00000298552	NM_001162426.1	1070	gCg/gTg	23/23	1	2	FACETS	0.928	0.88	0.976	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		795	1142	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11019846	11019846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	282	785	1	ENST00000327064.4:c.521G>A	p.Arg174His	p.R174H	ENST00000327064	NM_199141.1	174	cGc/cAc	4/16	1	2	FACETS	1	0.982	1	1	0.996	1	CLONAL	3	TRUE	1	0.16945068635343	2		786	1006	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228789	36228789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	451	1016	0	ENST00000222270.7:c.7688C>T	p.Ala2563Val	p.A2563V	ENST00000222270	NM_014727.1	2563	gCc/gTc	35/37	1	2	FACETS	1	0.988	1	1	0.997	1	CLONAL	3	TRUE	1	0.16945068635343	2		1016	1611	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027015	71027015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	253	627	0	ENST00000318789.4:c.1312C>T	p.Arg438Trp	p.R438W	ENST00000318789	NM_032682.5	438	Cgg/Tgg	15/21	1	2	FACETS	1	0.981	1	1	0.996	1	CLONAL	3	TRUE	1	0.16945068635343	2		627	893	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22417991	22417991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756680625	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	21	39	0	ENST00000344548.3:c.557G>A	p.Arg186His	p.R186H	ENST00000344548	NM_001039802.1	186	cGc/cAc	7/7	1	2	FACETS	1	0.872	1	1	0.958	1	CLONAL	3	TRUE	1	0.16945068635343	2		39	72	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863334	57863334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	423	919	0	ENST00000228682.2:c.1429G>A	p.Asp477Asn	p.D477N	ENST00000228682	NM_005269.2	477	Gac/Aac	11/12	1	2	FACETS	0.944	0.899	0.99	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		919	1322	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257729	16257729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199930614	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	295	590	0	ENST00000375759.3:c.4994C>T	p.Ala1665Val	p.A1665V	ENST00000375759	NM_015001.2	1665	gCg/gTg	11/15	1	2	FACETS	0.978	0.923	1	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		590	890	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993348	72993348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759852645	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	403	1140	0	ENST00000268489.5:c.697G>A	p.Val233Met	p.V233M	ENST00000268489	NM_006885.3	233	Gtg/Atg	2/10	1	2	FACETS	1	0.988	1	1	0.997	1	CLONAL	3	TRUE	1	0.16945068635343	2		1140	1411	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533808	533808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	565	1097	1	ENST00000451590.1:c.248C>T	p.Ala83Val	p.A83V	ENST00000451590	NM_001130442.1	83	gCc/gTc	3/5	1	2	FACETS	0.959	0.92	0.999	1	0.998	1	CLONAL	4	TRUE	1	0.16945068635343	2		1098	1738	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405170	139405170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199506721	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	608	1399	2	ENST00000277541.6:c.2675G>A	p.Arg892His	p.R892H	ENST00000277541	NM_017617.3	892	cGc/cAc	17/34	1	2	FACETS	0.976	0.938	1	1	0.998	1	CLONAL	4	TRUE	1	0.16945068635343	2		1401	1838	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863271	56863271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752739111	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	599	611	1	ENST00000519728.1:c.415G>A	p.Ala139Thr	p.A139T	ENST00000519728	NM_002350.3	139	Gca/Aca	6/13	0.16945068635343	9	FACETS	1	0.984	1	1	0.997	1	CLONAL	10	TRUE	1	0.16945068635343	9		612	1096	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127694	64127694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1387218415	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	607	1282	2	ENST00000334205.4:c.187G>A	p.Ala63Thr	p.A63T	ENST00000334205	NM_003942.2	63	Gcc/Acc	3/17	1	2	FACETS	0.984	0.945	1	1	0.998	1	CLONAL	4	TRUE	1	0.16945068635343	2		1284	1821	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679780	30679780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	380	826	0	ENST00000376406.3:c.1939G>A	p.Asp647Asn	p.D647N	ENST00000376406	NM_014641.2	647	Gat/Aat	5/15	0.16945068635343	4	FACETS	1	0.98	1	1	0.997	1	CLONAL	4	TRUE	2	0.16945068635343	4		826	1237	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931873	39931873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	412	813	0	ENST00000378444.4:c.2726G>A	p.Gly909Asp	p.G909D	ENST00000378444	NM_001123385.1	909	gGc/gAc	4/15	1	2	FACETS	0.994	0.947	1	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		813	1223	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256717	46256717	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	169	436	0	ENST00000371998.3:c.773G>T	p.Arg258Ile	p.R258I	ENST00000371998		258	aGa/aTa	8/23	1	2	FACETS	0.913	0.845	0.983	1	0.994	1	CLONAL	4	TRUE	1	0.16945068635343	2		436	546	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121110	3121110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	414	953	0	ENST00000078429.4:c.1013G>A	p.Arg338His	p.R338H	ENST00000078429	NM_002067.2	338	cGc/cAc	7/7	1	2	FACETS	0.994	0.947	1	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		953	1229	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989642	68989642	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767992923	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	532	519	1	ENST00000288368.4:c.1580G>A	p.Arg527His	p.R527H	ENST00000288368	NM_024870.2	527	cGc/cAc	15/40	0.16945068635343	9	FACETS	1	0.986	1	1	0.996	1	CLONAL	10	TRUE	1	0.16945068635343	9		520	963	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221649	22221649	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	166	328	0	ENST00000215832.6:c.82C>A	p.Leu28Ile	p.L28I	ENST00000215832	NM_002745.4	28	Ctc/Atc	1/9	1	2	FACETS	0.881	0.814	0.95	1	0.994	1	CLONAL	4	TRUE	1	0.16945068635343	2		328	556	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228415	228415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745309710	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	125	576	0	ENST00000264932.6:c.737G>A	p.Arg246His	p.R246H	ENST00000264932	NM_004168.2	246	cGc/cAc	6/15	0.16945068635343	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.16945068635343	4		576	715	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220135	5220135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269111261	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	358	885	0	ENST00000357368.4:c.3580C>T	p.Arg1194Cys	p.R1194C	ENST00000357368	NM_002850.3	1194	Cgc/Tgc	22/38	1	2	FACETS	0.999	0.949	1	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		885	1057	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518693	103518693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142438319	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	115	376	0	ENST00000355739.4:c.2281G>A	p.Ala761Thr	p.A761T	ENST00000355739	NM_000123.3	761	Gct/Act	10/15	0.16945068635343	4	FACETS	0.933	0.843	1	0.7	0.632	0.771	CLONAL	3	TRUE	0	0.16945068635343	4		376	567	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935762	15935762	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	198	458	1	ENST00000268712.3:c.7171C>T	p.Arg2391Trp	p.R2391W	ENST00000268712	NM_006311.3	2391	Cgg/Tgg	46/46	1	2	FACETS	0.916	0.852	0.981	1	0.995	1	CLONAL	4	TRUE	1	0.16945068635343	2		459	638	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012253	152012253	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1563831738	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	184	484	0	ENST00000262189.6:c.560C>G	p.Ser187Ter	p.S187*	ENST00000262189	NM_170606.2	187	tCa/tGa	4/59	1	2	FACETS	1	0.975	1	1	0.995	1	CLONAL	3	TRUE	1	0.16945068635343	2		484	651	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348938	89348938	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753576509	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	415	1075	1	ENST00000301030.4:c.4012G>A	p.Ala1338Thr	p.A1338T	ENST00000301030	NM_001256183.1	1338	Gcc/Acc	9/13	1	2	FACETS	0.915	0.871	0.959	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		1076	1339	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40685763	40685763	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777913445	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	145	491	0	ENST00000249776.8:c.916G>A	p.Ala306Thr	p.A306T	ENST00000249776	NM_033286.3	306	Gcc/Acc	9/9	0.122980603616098	0	FACETS	0.909	0.835	0.987			1	CLONAL	3	TRUE	0	0.16945068635343	0		491	521	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862869	9862869	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	107	833	0	ENST00000330684.3:c.2434C>A	p.Leu812Met	p.L812M	ENST00000330684	NM_001134407.1	812	Ctg/Atg	12/13	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.16945068635343	2		833	1011	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194789	30194789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761853569	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	218	670	1	ENST00000331968.5:c.356C>T	p.Ala119Val	p.A119V	ENST00000331968	NM_002742.2	119	gCg/gTg	2/18	1	2	FACETS	1	0.976	1	1	0.995	1	CLONAL	3	TRUE	1	0.16945068635343	2		671	780	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940153	71940153	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs780137670	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1327	107	1027	0	ENST00000298229.2:c.538A>G	p.Thr180Ala	p.T180A	ENST00000298229	NM_001567.3	180	Acc/Gcc	5/28	1	2	FACETS	0.881	0.787	0.981	0.881	0.787	0.981	CLONAL	1	TRUE	1	0.16945068635343	2		1027	1434	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933535	39933535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747038834	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	423	972	1	ENST00000378444.4:c.1064C>T	p.Ser355Leu	p.S355L	ENST00000378444	NM_001123385.1	355	tCg/tTg	4/15	1	2	FACETS	0.928	0.884	0.973	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		973	1345	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262373	16262373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372303430	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	244	444	0	ENST00000375759.3:c.9638C>T	p.Ala3213Val	p.A3213V	ENST00000375759	NM_015001.2	3213	gCg/gTg	11/15	1	2	FACETS	1	0.95	1	1	0.996	1	CLONAL	4	TRUE	1	0.16945068635343	2		444	711	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276215	15276215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748889237	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	339	821	1	ENST00000263388.2:c.5779G>A	p.Ala1927Thr	p.A1927T	ENST00000263388	NM_000435.2	1927	Gcc/Acc	31/33	1	2	FACETS	0.958	0.908	1	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		822	1044	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905275	50905275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1253	591	1411	0	ENST00000440232.2:c.483G>A	p.Met161Ile	p.M161I	ENST00000440232	NM_002691.3	161	atG/atA	5/27	1	2	FACETS	0.946	0.908	0.984	1	0.998	1	CLONAL	4	TRUE	1	0.16945068635343	2		1411	1844	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3634860	3634860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369852048	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	364	765	0	ENST00000294008.3:c.4649G>A	p.Arg1550Gln	p.R1550Q	ENST00000294008	NM_032444.2	1550	cGg/cAg	13/15	1	2	FACETS	1	0.982	1	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		765	1007	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925507	114925507	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	331	981	1	ENST00000543371.1:c.1585C>A	p.Leu529Met	p.L529M	ENST00000543371	NM_001198531.1	529	Ctg/Atg	14/14	0.169374935467926	1	FACETS	1	0.945	1	1	0.997	1	CLONAL	3	TRUE	0	0.16945068635343	1		982	1192	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199696	11199696	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	57	595	0	ENST00000361445.4:c.4892A>C	p.Glu1631Ala	p.E1631A	ENST00000361445	NM_004958.3	1631	gAg/gCg	35/58	1	2	FACETS	0.796	0.681	0.922	0.796	0.681	0.922	CLONAL	1	TRUE	1	0.16945068635343	2		595	845	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291078	11291078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	260	613	0	ENST00000361445.4:c.2683G>A	p.Asp895Asn	p.D895N	ENST00000361445	NM_004958.3	895	Gat/Aat	18/58	1	2	FACETS	0.9	0.846	0.956	1	0.996	1	CLONAL	4	TRUE	1	0.16945068635343	2		613	852	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316113	11316113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs968103570	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	345	795	0	ENST00000361445.4:c.641G>A	p.Arg214His	p.R214H	ENST00000361445	NM_004958.3	214	cGt/cAt	5/58	1	2	FACETS	1	0.987	1	1	0.997	1	CLONAL	3	TRUE	1	0.16945068635343	2		795	1198	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319454	11319454	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774041749	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	340	769	0	ENST00000361445.4:c.13G>A	p.Gly5Arg	p.G5R	ENST00000361445	NM_004958.3	5	Gga/Aga	2/58	1	2	FACETS	1	0.952	1	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		769	999	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245459	16245459	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	70	470	0	ENST00000375759.3:c.1434T>A	p.Tyr478Ter	p.Y478*	ENST00000375759	NM_015001.2	478	taT/taA	7/15	1	2	FACETS	0.766	0.669	0.871	1	0.974	1	SUBCLONAL	2	TRUE	1	0.16945068635343	2		470	539	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254951	16254951	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759877253	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	240	476	0	ENST00000375759.3:c.2216C>T	p.Ala739Val	p.A739V	ENST00000375759	NM_015001.2	739	gCg/gTg	11/15	1	2	FACETS	0.889	0.832	0.946	1	0.996	1	CLONAL	4	TRUE	1	0.16945068635343	2		476	797	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695956	117695956	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	263	629	1	ENST00000369458.3:c.481G>A	p.Ala161Thr	p.A161T	ENST00000369458	NM_024626.3	161	Gcc/Acc	4/6	1	2	FACETS	1	0.983	1	1	0.996	1	CLONAL	3	TRUE	1	0.16945068635343	2		630	916	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120469168	120469168	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	278	647	0	ENST00000256646.2:c.3959C>A	p.Ala1320Asp	p.A1320D	ENST00000256646	NM_024408.3	1320	gCt/gAt	24/34	1	2	FACETS	0.963	0.907	1	1	0.996	1	CLONAL	4	TRUE	1	0.16945068635343	2		647	852	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846250	156846250	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1294	192	1092	0	ENST00000524377.1:c.1691T>A	p.Leu564His	p.L564H	ENST00000524377	NM_002529.3	564	cTc/cAc	14/17	1	2	FACETS	0.762	0.703	0.825	1	0.99	1	SUBCLONAL	2	TRUE	1	0.16945068635343	2		1092	1486	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741970	162741970	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	209	477	0	ENST00000367921.3:c.1661C>A	p.Ala554Asp	p.A554D	ENST00000367921	NM_006182.2	554	gCt/gAt	13/18	1	2	FACETS	0.877	0.818	0.938	1	0.995	1	CLONAL	4	TRUE	1	0.16945068635343	2		477	703	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649613	206649613	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	358	883	1	ENST00000367120.3:c.448C>T	p.Gln150Ter	p.Q150*	ENST00000367120	NM_014002.3	150	Cag/Tag	6/22	1	2	FACETS	0.944	0.896	0.993	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		884	1119	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759939	63759939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	119	395	0	ENST00000279873.7:c.592C>T	p.Pro198Ser	p.P198S	ENST00000279873	NM_032199.2	198	Cca/Tca	4/10	0.169374935467926	1	FACETS	0.889	0.807	0.974	1	0.991	1	CLONAL	3	TRUE	0	0.16945068635343	1		395	482	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112760215	112760215	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	122	415	0	ENST00000369452.4:c.884G>A	p.Arg295Lys	p.R295K	ENST00000369452	NM_007373.3	295	aGa/aAa	4/9	0.169374935467926	1	FACETS	0.941	0.856	1	1	0.992	1	CLONAL	3	TRUE	0	0.16945068635343	1		415	467	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456372	32456372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	550	1149	0	ENST00000332351.3:c.520G>A	p.Ala174Thr	p.A174T	ENST00000332351	NM_024426.4	174	Gcc/Acc	1/10	1	2	FACETS	1	0.975	1	1	0.998	1	CLONAL	4	TRUE	1	0.16945068635343	2		1149	1589	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136948	64136948	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767081339	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	377	847	0	ENST00000334205.4:c.1459C>T	p.Arg487Trp	p.R487W	ENST00000334205	NM_003942.2	487	Cgg/Tgg	13/17	1	2	FACETS	1	0.969	1	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		847	1085	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944716	71944716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750542712	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	439	1074	3	ENST00000298229.2:c.2140G>A	p.Val714Ile	p.V714I	ENST00000298229	NM_001567.3	714	Gtc/Atc	19/28	1	2	FACETS	1	0.991	1	1	0.997	1	CLONAL	3	TRUE	1	0.16945068635343	2		1077	1505	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196936	108196936	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060501640	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	129	331	0	ENST00000278616.4:c.6959A>G	p.Asp2320Gly	p.D2320G	ENST00000278616	NM_000051.3	2320	gAt/gGt	47/63	1	2	FACETS	0.911	0.833	0.991	1	0.993	1	CLONAL	4	TRUE	1	0.16945068635343	2		331	418	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348795	118348795	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	158	351	0	ENST00000534358.1:c.3448C>T	p.Arg1150Cys	p.R1150C	ENST00000534358	NM_005933.3	1150	Cgt/Tgt	5/36	1	2	FACETS	0.909	0.839	0.981	1	0.994	1	CLONAL	4	TRUE	1	0.16945068635343	2		351	513	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245612	46245612	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1020744272	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	148	397	0	ENST00000334344.6:c.3706C>T	p.Pro1236Ser	p.P1236S	ENST00000334344	NM_152641.2	1236	Cca/Tca	15/21	1	2	FACETS	1	0.976	1	1	0.994	1	CLONAL	3	TRUE	1	0.16945068635343	2		397	502	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432179	49432179	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1422	81	1014	0	ENST00000301067.7:c.8960C>A	p.Pro2987His	p.P2987H	ENST00000301067	NM_003482.3	2987	cCc/cAc	34/54	1	2	FACETS	0.636	0.558	0.721	0.636	0.558	0.721	SUBCLONAL	1	TRUE	1	0.16945068635343	2		1014	1503	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437710	49437710	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	402	995	0	ENST00000301067.7:c.5260C>T	p.Gln1754Ter	p.Q1754*	ENST00000301067	NM_003482.3	1754	Caa/Taa	22/54	1	2	FACETS	1	0.99	1	1	0.997	1	CLONAL	3	TRUE	1	0.16945068635343	2		995	1385	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112910782	112910782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	159	402	1	ENST00000351677.2:c.791G>A	p.Ser264Asn	p.S264N	ENST00000351677	NM_002834.3	264	aGc/aAc	7/16	1	2	FACETS	1	0.963	1	1	0.994	1	CLONAL	3	TRUE	1	0.16945068635343	2		403	581	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112527	115112527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370551433	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1349	78	1175	1	ENST00000257566.3:c.1213C>T	p.Arg405Cys	p.R405C	ENST00000257566	NM_016569.3	405	Cgt/Tgt	7/8	1	2	FACETS	0.645	0.564	0.733	0.645	0.564	0.733	SUBCLONAL	1	TRUE	1	0.16945068635343	2		1176	1427	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120789188	120789188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	276	629	0	ENST00000257552.2:c.749G>A	p.Arg250Gln	p.R250Q	ENST00000257552	NM_002442.3	250	cGg/cAg	11/15	1	2	FACETS	1	0.948	1	1	0.996	1	CLONAL	4	TRUE	1	0.16945068635343	2		629	809	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879779	123879779	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	81	407	0	ENST00000330479.4:c.475A>C	p.Lys159Gln	p.K159Q	ENST00000330479	NM_020382.3	159	Aag/Cag	4/9	1	2	FACETS	0.864	0.763	0.973	1	0.981	1	CLONAL	2	TRUE	1	0.16945068635343	2		407	553	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514928	103514928	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	257	399	0	ENST00000355739.4:c.1429T>C	p.Ser477Pro	p.S477P	ENST00000355739	NM_000123.3	477	Tca/Cca	8/15	0.16945068635343	4	FACETS	1	0.971	1	1	0.994	1	CLONAL	6	TRUE	0	0.16945068635343	4		399	568	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528179	103528179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs183317723	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	300	415	0	ENST00000355739.4:c.3487G>A	p.Val1163Met	p.V1163M	ENST00000355739	NM_000123.3	1163	Gtg/Atg	15/15	0.16945068635343	4	FACETS	1	0.973	1	1	0.995	1	CLONAL	6	TRUE	0	0.16945068635343	4		415	665	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434823	110434823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1383650129	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1427	369	1175	0	ENST00000375856.3:c.3578G>A	p.Gly1193Asp	p.G1193D	ENST00000375856	NM_003749.2	1193	gGc/gAc	1/2	0.16945068635343	4	FACETS	0.945	0.894	0.998	0.709	0.67	0.749	CLONAL	3	TRUE	0	0.16945068635343	4		1175	1796	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435355	110435355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1437839141	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	516	666	1	ENST00000375856.3:c.3046C>T	p.Pro1016Ser	p.P1016S	ENST00000375856	NM_003749.2	1016	Ccg/Tcg	1/2	0.16945068635343	4	FACETS	1	0.988	1	1	0.997	1	CLONAL	6	TRUE	0	0.16945068635343	4		667	1112	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436287	110436287	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	174	366	0	ENST00000375856.3:c.2114C>T	p.Ala705Val	p.A705V	ENST00000375856	NM_003749.2	705	gCg/gTg	1/2	0.16945068635343	4	FACETS	1	0.979	1	0.874	0.807	0.943	CLONAL	3	TRUE	0	0.16945068635343	4		366	687	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436348	110436348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1373634609	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	620	777	4	ENST00000375856.3:c.2053G>A	p.Ala685Thr	p.A685T	ENST00000375856	NM_003749.2	685	Gcc/Acc	1/2	0.16945068635343	4	FACETS	0.969	0.936	1	1	0.998	1	CLONAL	7	TRUE	0	0.16945068635343	4		781	1261	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436647	110436647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1891	554	1492	2	ENST00000375856.3:c.1754G>A	p.Arg585Gln	p.R585Q	ENST00000375856	NM_003749.2	585	cGg/cAg	1/2	0.16945068635343	4	FACETS	1	0.98	1	0.782	0.747	0.817	CLONAL	3	TRUE	0	0.16945068635343	4		1494	2445	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331751	68331751	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	20	330	0	ENST00000487270.1:c.347A>G	p.Gln116Arg	p.Q116R	ENST00000487270	NM_133509.3	116	cAg/cGg	5/11	1	2	FACETS	0.596	0.455	0.762	0.596	0.455	0.762	SUBCLONAL	1	TRUE	1	0.16945068635343	2		330	396	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582851	95582851	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201298288	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	104	335	0	ENST00000393063.1:c.1691C>T	p.Ala564Val	p.A564V	ENST00000393063	NM_030621.3	564	gCg/gTg	11/28	1	2	FACETS	1	0.966	1	1	0.991	1	CLONAL	3	TRUE	1	0.16945068635343	2		335	355	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023148	33023148	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	59	743	2	ENST00000300177.4:c.257G>A	p.Arg86His	p.R86H	ENST00000300177	NM_001191322.1	86	cGc/cAc	2/2	0.122980603616098	0	FACETS	0.764	0.656	0.882			1	SUBCLONAL	1	TRUE	0	0.16945068635343	0		745	757	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41999990	41999990	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	61	782	0	ENST00000219905.7:c.2253G>T	p.Gln751His	p.Q751H	ENST00000219905	NM_001164273.1	751	caG/caT	6/24	0.122980603616098	0	FACETS	0.793	0.683	0.913			1	CLONAL	1	TRUE	0	0.16945068635343	0		782	754	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712535	43712535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756376679	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	226	866	0	ENST00000382044.4:c.4649C>T	p.Thr1550Met	p.T1550M	ENST00000382044	NM_001141980.1	1550	aCg/aTg	21/28	0.122980603616098	0	FACETS	0.85	0.793	0.908			1	CLONAL	3	TRUE	0	0.16945068635343	0		866	869	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720329	43720329	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770349820	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	184	696	0	ENST00000382044.4:c.3713G>A	p.Gly1238Asp	p.G1238D	ENST00000382044	NM_001141980.1	1238	gGc/gAc	18/28	0.122980603616098	0	FACETS	0.835	0.773	0.899			1	CLONAL	3	TRUE	0	0.16945068635343	0		696	720	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295050	91295050	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	74	247	0	ENST00000355112.3:c.833C>T	p.Ala278Val	p.A278V	ENST00000355112	NM_000057.2	278	gCt/gTt	4/22	0.122980603616098	0	FACETS	1	0.919	1			1	CLONAL	3	TRUE	0	0.16945068635343	0		247	232	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251015	99251015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375153085	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	283	770	0	ENST00000268035.6:c.319C>T	p.Arg107Cys	p.R107C	ENST00000268035	NM_000875.3	107	Cgc/Tgc	2/21	0.122980603616098	0	FACETS	0.819	0.772	0.867			1	CLONAL	4	TRUE	0	0.16945068635343	0		770	847	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251042	99251042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	246	723	0	ENST00000268035.6:c.346G>A	p.Ala116Thr	p.A116T	ENST00000268035	NM_000875.3	116	Gcc/Acc	2/21	0.122980603616098	0	FACETS	0.807	0.757	0.858			1	CLONAL	4	TRUE	0	0.16945068635343	0		723	747	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130378	2130378	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	350	1181	0	ENST00000219476.3:c.3610G>T	p.Gly1204Trp	p.G1204W	ENST00000219476	NM_000548.3	1204	Ggg/Tgg	30/42	1	2	FACETS	0.964	0.912	1	1	0.997	1	CLONAL	3	TRUE	1	0.16945068635343	2		1181	1428	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778362	3778362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1194793942	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	569	1266	2	ENST00000262367.5:c.6686G>A	p.Gly2229Asp	p.G2229D	ENST00000262367	NM_004380.2	2229	gGc/gAc	31/31	1	2	FACETS	1	0.99	1	1	0.998	1	CLONAL	4	TRUE	1	0.16945068635343	2		1268	1541	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779037	3779037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1279369054	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	585	1026	1	ENST00000262367.5:c.6011G>A	p.Arg2004Gln	p.R2004Q	ENST00000262367	NM_004380.2	2004	cGa/cAa	31/31	1	2	FACETS	0.936	0.9	0.972	1	0.998	1	CLONAL	5	TRUE	1	0.16945068635343	2		1027	1476	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781408	3781408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329802754	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	452	1084	0	ENST00000262367.5:c.4957G>A	p.Asp1653Asn	p.D1653N	ENST00000262367	NM_004380.2	1653	Gac/Aac	30/31	1	2	FACETS	1	0.977	1	1	0.998	1	CLONAL	4	TRUE	1	0.16945068635343	2		1084	1289	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808034	3808034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774047746	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	35	421	0	ENST00000262367.5:c.3385G>A	p.Val1129Ile	p.V1129I	ENST00000262367	NM_004380.2	1129	Gta/Ata	18/31	1	2	FACETS	0.667	0.546	0.805	0.667	0.546	0.805	SUBCLONAL	1	TRUE	1	0.16945068635343	2		421	619	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900879	3900879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	363	777	1	ENST00000262367.5:c.217C>T	p.Leu73Phe	p.L73F	ENST00000262367	NM_004380.2	73	Ctt/Ttt	2/31	1	2	FACETS	1	0.956	1	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		778	1064	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23635412	23635412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs515726094	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	207	456	0	ENST00000261584.4:c.2752C>T	p.Pro918Ser	p.P918S	ENST00000261584	NM_024675.3	918	Cca/Tca	8/13	1	2	FACETS	0.954	0.894	1	1	0.996	1	CLONAL	5	TRUE	1	0.16945068635343	2		456	512	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646329	23646329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778890869	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	223	702	2	ENST00000261584.4:c.1538C>T	p.Thr513Ile	p.T513I	ENST00000261584	NM_024675.3	513	aCa/aTa	4/13	1	2	FACETS	0.936	0.872	1	1	0.995	1	CLONAL	3	TRUE	1	0.16945068635343	2		704	937	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875737	56875737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773614710	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	239	469	0	ENST00000308159.5:c.2341C>T	p.Arg781Cys	p.R781C	ENST00000308159	NM_014669.4	781	Cgc/Tgc	21/22	1	2	FACETS	1	0.972	1	1	0.996	1	CLONAL	4	TRUE	1	0.16945068635343	2		469	666	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12043161	12043161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755523599	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	108	250	1	ENST00000353533.5:c.1046C>T	p.Thr349Met	p.T349M	ENST00000353533	NM_003010.3	349	aCg/aTg	10/11	1	2	FACETS	0.905	0.821	0.993	1	0.991	1	CLONAL	4	TRUE	1	0.16945068635343	2		251	352	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968868	15968868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754505756	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	243	592	1	ENST00000268712.3:c.4882C>T	p.Arg1628Cys	p.R1628C	ENST00000268712	NM_006311.3	1628	Cgt/Tgt	33/46	1	2	FACETS	0.886	0.831	0.943	1	0.996	1	CLONAL	4	TRUE	1	0.16945068635343	2		593	809	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657337	29657337	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	253	604	1	ENST00000356175.3:c.5570G>A	p.Cys1857Tyr	p.C1857Y	ENST00000356175	NM_000267.3	1857	tGt/tAt	38/57	1	2	FACETS	0.985	0.925	1	1	0.996	1	CLONAL	4	TRUE	1	0.16945068635343	2		605	758	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872073	37872073	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1572	110	1155	0	ENST00000269571.5:c.1394T>C	p.Leu465Pro	p.L465P	ENST00000269571		465	cTg/cCg	12/27	1	2	FACETS	0.772	0.69	0.859	0.772	0.69	0.859	SUBCLONAL	1	TRUE	1	0.16945068635343	2		1155	1682	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40468908	40468908	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	190	450	0	ENST00000264657.5:c.2156G>A	p.Ser719Asn	p.S719N	ENST00000264657	NM_139276.2	719	aGc/aAc	23/24	1	2	FACETS	1	0.981	1	1	0.995	1	CLONAL	3	TRUE	1	0.16945068635343	2		450	646	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41203078	41203078	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs80358182	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	63	779	0	ENST00000357654.3:c.5332+2T>C		p.X1778_splice	ENST00000357654	NM_007294.3	1778			1	2	FACETS	0.742	0.64	0.854	0.742	0.64	0.854	SUBCLONAL	1	TRUE	1	0.16945068635343	2		779	1002	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696709	47696709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	173	499	0	ENST00000347630.2:c.239G>A	p.Ser80Asn	p.S80N	ENST00000347630	NM_001007230.1	80	aGc/aAc	5/11	1	2	FACETS	1	0.974	1	1	0.994	1	CLONAL	3	TRUE	1	0.16945068635343	2		499	608	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78519506	78519506	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	133	668	0	ENST00000306801.3:c.77T>A	p.Leu26Gln	p.L26Q	ENST00000306801	NM_020761.2	26	cTa/cAa	1/34	1	2	FACETS	0.756	0.686	0.831	1	0.986	1	SUBCLONAL	2	TRUE	1	0.16945068635343	2		668	1038	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39618815	39618815	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	57	189	0	ENST00000262039.4:c.2038+1G>A		p.X680_splice	ENST00000262039	NM_002647.2	680			1	2	FACETS	1	0.904	1	1	0.983	1	CLONAL	3	TRUE	1	0.16945068635343	2		189	214	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625625	1625625	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1434	190	1342	0	ENST00000344749.5:c.449A>G	p.Tyr150Cys	p.Y150C	ENST00000344749	NM_001136139.2	150	tAc/tGc	7/19	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.16945068635343	2		1342	1624	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191237	2191237	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	67	767	0	ENST00000398665.3:c.491G>T	p.Ser164Ile	p.S164I	ENST00000398665	NM_032482.2	164	aGc/aTc	5/28	1	2	FACETS	0.784	0.679	0.898	0.784	0.679	0.898	SUBCLONAL	1	TRUE	1	0.16945068635343	2		767	1009	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229651	5229651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	22	61	0	ENST00000357368.4:c.2200G>A	p.Ala734Thr	p.A734T	ENST00000357368	NM_002850.3	734	Gcc/Acc	15/38	1	2	FACETS	0.921	0.729	1	1	0.956	1	CLONAL	3	TRUE	1	0.16945068635343	2		61	94	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5239062	5239062	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1292	88	1093	0	ENST00000357368.4:c.1717T>C	p.Phe573Leu	p.F573L	ENST00000357368	NM_002850.3	573	Ttc/Ctc	13/38	1	2	FACETS	0.753	0.664	0.848	0.753	0.664	0.848	SUBCLONAL	1	TRUE	1	0.16945068635343	2		1093	1380	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273512	5273512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	419	1053	0	ENST00000357368.4:c.320G>A	p.Cys107Tyr	p.C107Y	ENST00000357368	NM_002850.3	107	tGt/tAt	4/38	1	2	FACETS	0.933	0.889	0.978	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		1053	1325	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184541	7184541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	336	767	0	ENST00000302850.5:c.760G>A	p.Ala254Thr	p.A254T	ENST00000302850	NM_000208.2	254	Gcc/Acc	3/22	1	2	FACETS	0.984	0.932	1	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		767	1008	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031413	11031413	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	439	1104	1	ENST00000327064.4:c.1413C>A	p.Asn471Lys	p.N471K	ENST00000327064	NM_199141.1	471	aaC/aaA	12/16	1	2	FACETS	0.942	0.898	0.987	1	0.998	1	CLONAL	4	TRUE	1	0.16945068635343	2		1105	1375	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101865	11101865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	406	1232	1	ENST00000358026.2:c.1285G>A	p.Ala429Thr	p.A429T	ENST00000358026	NM_001128849.1	429	Gcg/Acg	8/36	1	2	FACETS	1	0.984	1	1	0.997	1	CLONAL	3	TRUE	1	0.16945068635343	2		1233	1477	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629101	14629101	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	111	663	0	ENST00000254322.2:c.61A>G	p.Lys21Glu	p.K21E	ENST00000254322	NM_006145.1	21	Aag/Gag	1/3	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.16945068635343	2		663	1287	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376376	15376376	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1055405627	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	508	1249	1	ENST00000263377.2:c.638C>T	p.Pro213Leu	p.P213L	ENST00000263377	NM_058243.2	213	cCg/cTg	5/20	1	2	FACETS	0.997	0.955	1	1	0.998	1	CLONAL	4	TRUE	1	0.16945068635343	2		1250	1503	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965822	18965822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	79	988	0	ENST00000262803.5:c.1400G>A	p.Gly467Asp	p.G467D	ENST00000262803	NM_002911.3	467	gGc/gAc	10/24	1	2	FACETS	0.748	0.656	0.849	0.748	0.656	0.849	SUBCLONAL	1	TRUE	1	0.16945068635343	2		988	1246	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971210	18971210	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	92	882	0	ENST00000262803.5:c.2263G>A	p.Glu755Lys	p.E755K	ENST00000262803	NM_002911.3	755	Gag/Aag	16/24	1	2	FACETS	0.85	0.752	0.954	0.85	0.752	0.954	CLONAL	1	TRUE	1	0.16945068635343	2		882	1278	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976941	18976941	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs765661177	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	53	710	0	ENST00000262803.5:c.3326A>G	p.His1109Arg	p.H1109R	ENST00000262803	NM_002911.3	1109	cAt/cGt	23/24	1	2	FACETS	0.656	0.558	0.765	0.656	0.558	0.765	SUBCLONAL	1	TRUE	1	0.16945068635343	2		710	953	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313422	30313422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200042616	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	249	703	0	ENST00000262643.3:c.1022C>T	p.Thr341Met	p.T341M	ENST00000262643	NM_001238.2	341	aCg/aTg	11/12	1	2	FACETS	1	0.978	1	1	0.996	1	CLONAL	3	TRUE	1	0.16945068635343	2		703	894	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212526	36212526	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	503	1298	0	ENST00000222270.7:c.2277G>T	p.Gln759His	p.Q759H	ENST00000222270	NM_014727.1	759	caG/caT	3/37	1	2	FACETS	0.884	0.845	0.924	1	0.998	1	CLONAL	4	TRUE	1	0.16945068635343	2		1298	1679	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919665	50919665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs565328583	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	596	1346	0	ENST00000440232.2:c.2833G>A	p.Val945Met	p.V945M	ENST00000440232	NM_002691.3	945	Gtg/Atg	23/27	1	2	FACETS	0.981	0.942	1	1	0.998	1	CLONAL	4	TRUE	1	0.16945068635343	2		1346	1792	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919785	50919785	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs780926432	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1521	104	1198	0	ENST00000440232.2:c.2953C>T	p.Arg985Trp	p.R985W	ENST00000440232	NM_002691.3	985	Cgg/Tgg	23/27	1	2	FACETS	0.755	0.673	0.843	0.755	0.673	0.843	SUBCLONAL	1	TRUE	1	0.16945068635343	2		1198	1625	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432739	29432739	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	22	576	0	ENST00000389048.3:c.3749T>G	p.Ile1250Ser	p.I1250S	ENST00000389048	NM_004304.4	1250	aTt/aGt	25/29	1	2	FACETS	0.405	0.312	0.514	0.405	0.312	0.514	SUBCLONAL	1	TRUE	1	0.16945068635343	2		576	641	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702339	47702339	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587780684	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	166	398	0	ENST00000233146.2:c.1935A>C	p.Gln645His	p.Q645H	ENST00000233146	NM_000251.2	645	caA/caC	12/16	1	2	FACETS	1	0.926	1	1	0.994	1	CLONAL	4	TRUE	1	0.16945068635343	2		398	490	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026683	48026684	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	205	449	0	ENST00000234420.5:c.1564_1565del	p.Gln522AspfsTer8	p.Q522Dfs*8	ENST00000234420	NM_000179.2	521	ACa/a	4/10	1	2	FACETS	1	0.952	1	1	0.995	1	CLONAL	4	TRUE	1	0.16945068635343	2		449	591	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050412	128050412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1246605943	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	184	446	0	ENST00000285398.2:c.245G>A	p.Gly82Asp	p.G82D	ENST00000285398	NM_000122.1	82	gGc/gAc	3/15	1	2	FACETS	0.964	0.896	1	1	0.995	1	CLONAL	4	TRUE	1	0.16945068635343	2		446	563	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149606	202149606	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	230	483	0	ENST00000358485.4:c.1047G>T	p.Glu349Asp	p.E349D	ENST00000358485	NM_001080125.1	349	gaG/gaT	8/9	1	2	FACETS	0.997	0.934	1	1	0.996	1	CLONAL	4	TRUE	1	0.16945068635343	2		483	681	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209101880	209101880	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	32	374	0	ENST00000345146.2:c.1168G>C	p.Asp390His	p.D390H	ENST00000345146	NM_005896.2	390	Gac/Cac	10/10	1	2	FACETS	0.757	0.613	0.919	0.757	0.613	0.919	CLONAL	1	TRUE	1	0.16945068635343	2		374	499	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103831	209103831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754957038	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	199	459	0	ENST00000345146.2:c.1118C>T	p.Thr373Ile	p.T373I	ENST00000345146	NM_005896.2	373	aCc/aTc	9/10	1	2	FACETS	0.94	0.875	1	1	0.995	1	CLONAL	4	TRUE	1	0.16945068635343	2		459	625	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646007	215646007	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	191	569	0	ENST00000260947.4:c.591G>T	p.Lys197Asn	p.K197N	ENST00000260947	NM_000465.2	197	aaG/aaT	4/11	1	2	FACETS	1	0.981	1	1	0.995	1	CLONAL	3	TRUE	1	0.16945068635343	2		569	651	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400249	225400249	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	72	188	0	ENST00000264414.4:c.374A>G	p.Tyr125Cys	p.Y125C	ENST00000264414	NM_003590.4	125	tAc/tGc	3/16	1	2	FACETS	0.97	0.862	1	1	0.988	1	CLONAL	4	TRUE	1	0.16945068635343	2		188	219	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661509	227661509	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs865937681	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1251	97	1037	0	ENST00000305123.5:c.1946C>T	p.Pro649Leu	p.P649L	ENST00000305123	NM_005544.2	649	cCc/cTc	1/2	1	2	FACETS	0.849	0.754	0.951	0.849	0.754	0.951	CLONAL	1	TRUE	1	0.16945068635343	2		1037	1348	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624929	9624929	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	158	477	1	ENST00000353224.5:c.48C>A	p.Asn16Lys	p.N16K	ENST00000353224	NM_177990.2	16	aaC/aaA	3/10	1	2	FACETS	1	0.956	1	1	0.994	1	CLONAL	3	TRUE	1	0.16945068635343	2		478	588	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022830	31022830	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1463010740	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	278	655	0	ENST00000375687.4:c.2315C>T	p.Ala772Val	p.A772V	ENST00000375687	NM_015338.5	772	gCt/gTt	13/13	1	2	FACETS	0.943	0.888	0.999	1	0.996	1	CLONAL	4	TRUE	1	0.16945068635343	2		655	870	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077487	30077487	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	35	374	0	ENST00000338641.4:c.1636del	p.Ile546SerfsTer4	p.I546Sfs*4	ENST00000338641	NM_000268.3	545	gAa/ga	15/16	1	2	FACETS	0.843	0.69	1	0.843	0.69	1	CLONAL	1	TRUE	1	0.16945068635343	2		374	490	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573362	41573362	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1320303195	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1417	96	1073	1	ENST00000263253.7:c.5647A>G	p.Met1883Val	p.M1883V	ENST00000263253	NM_001429.3	1883	Atg/Gtg	31/31	1	2	FACETS	0.749	0.664	0.84	0.749	0.664	0.84	SUBCLONAL	1	TRUE	1	0.16945068635343	2		1074	1513	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645777	12645777	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	34	405	1	ENST00000251849.4:c.692G>T	p.Arg231Ile	p.R231I	ENST00000251849	NM_002880.3	231	aGa/aTa	7/17	1	2	FACETS	0.714	0.582	0.863	0.714	0.582	0.863	SUBCLONAL	1	TRUE	1	0.16945068635343	2		406	562	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52685758	52685758	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	32	447	0	ENST00000394830.3:c.714G>T	p.Gln238His	p.Q238H	ENST00000394830	NM_018313.4	238	caG/caT	7/30	1	2	FACETS	0.823	0.667	0.999	0.823	0.667	0.999	CLONAL	1	TRUE	1	0.16945068635343	2		447	459	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987093	69987093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1221504326	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	270	585	0	ENST00000394351.3:c.154C>T	p.Pro52Ser	p.P52S	ENST00000394351	NM_000248.3	52	Cca/Tca	2/9	1	2	FACETS	0.973	0.916	1	1	0.996	1	CLONAL	4	TRUE	1	0.16945068635343	2		585	819	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114166	73114166	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	90	395	0	ENST00000356692.5:c.802A>T	p.Ile268Phe	p.I268F	ENST00000356692		268	Att/Ttt	8/9	1	2	FACETS	0.92	0.818	1	1	0.984	1	CLONAL	2	TRUE	1	0.16945068635343	2		395	577	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149243827	149243827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	332	799	0	ENST00000360632.3:c.991C>A	p.Leu331Ile	p.L331I	ENST00000360632	NM_015472.4	331	Ctc/Atc	6/7	1	2	FACETS	0.932	0.882	0.983	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		799	1051	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149290669	149290669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	276	633	0	ENST00000360632.3:c.550G>A	p.Val184Ile	p.V184I	ENST00000360632	NM_015472.4	184	Gta/Ata	3/7	1	2	FACETS	0.88	0.828	0.934	1	0.996	1	CLONAL	4	TRUE	1	0.16945068635343	2		633	925	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136880	55136880	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs397514549	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	157	413	0	ENST00000257290.5:c.1202C>A	p.Ala401Asp	p.A401D	ENST00000257290	NM_006206.4	401	gCt/gAt	8/23	1	2	FACETS	1	0.936	1	1	0.994	1	CLONAL	4	TRUE	1	0.16945068635343	2		413	457	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152027	55152027	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	160	526	0	ENST00000257290.5:c.2459C>T	p.Ala820Val	p.A820V	ENST00000257290	NM_006206.4	820	gCt/gTt	18/23	1	2	FACETS	0.879	0.808	0.953	1	0.993	1	CLONAL	3	TRUE	1	0.16945068635343	2		526	716	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196589	106196589	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	33	536	0	ENST00000380013.4:c.4922A>G	p.Asn1641Ser	p.N1641S	ENST00000380013	NM_001127208.2	1641	aAc/aGc	11/11	1	2	FACETS	0.711	0.578	0.861	0.711	0.578	0.861	SUBCLONAL	1	TRUE	1	0.16945068635343	2		536	548	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045791	143045791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	137	549	0	ENST00000262992.4:c.1843C>T	p.Pro615Ser	p.P615S	ENST00000262992	NM_001101669.1	615	Ccc/Tcc	17/24	1	2	FACETS	0.91	0.831	0.993	1	0.992	1	CLONAL	3	TRUE	1	0.16945068635343	2		549	592	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250921	153250921	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	20	291	0	ENST00000281708.4:c.1139A>G	p.Asp380Gly	p.D380G	ENST00000281708	NM_033632.3	380	gAt/gGt	8/12	1	2	FACETS	0.774	0.592	0.987	0.774	0.592	0.987	CLONAL	1	TRUE	1	0.16945068635343	2		291	305	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540032	187540032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	140	485	0	ENST00000441802.2:c.7708G>A	p.Ala2570Thr	p.A2570T	ENST00000441802	NM_005245.3	2570	Gct/Act	10/27	1	2	FACETS	0.946	0.865	1	1	0.993	1	CLONAL	3	TRUE	1	0.16945068635343	2		485	582	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1253902	1253902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	416	1065	1	ENST00000310581.5:c.3340G>A	p.Ala1114Thr	p.A1114T	ENST00000310581	NM_198253.2	1114	Gcc/Acc	16/16	0.16945068635343	4	FACETS	0.914	0.869	0.96	1	0.996	1	CLONAL	4	TRUE	2	0.16945068635343	4		1066	1571	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293634	1293634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1407	731	1542	1	ENST00000310581.5:c.1367G>A	p.Ser456Asn	p.S456N	ENST00000310581	NM_198253.2	456	aGc/aAc	2/16	0.16945068635343	4	FACETS	0.944	0.91	0.978	1	0.998	1	CLONAL	5	TRUE	2	0.16945068635343	4		1543	2138	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38954957	38954957	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	15	219	0	ENST00000357387.3:c.2616G>T	p.Gln872His	p.Q872H	ENST00000357387	NM_152756.3	872	caG/caT	27/38	0.16945068635343	4	FACETS	0.812	0.594	1	0.406	0.297	0.537	CLONAL	1	TRUE	2	0.16945068635343	4		219	255	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39002653	39002653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	183	347	0	ENST00000357387.3:c.376G>A	p.Asp126Asn	p.D126N	ENST00000357387	NM_152756.3	126	Gac/Aac	5/38	0.16945068635343	4	FACETS	0.915	0.85	0.982	1	0.994	1	CLONAL	5	TRUE	2	0.16945068635343	4		347	552	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522781	67522781	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765266397	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	156	287	0	ENST00000274335.5:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000274335		93	cGg/cAg	1/15	1	2	FACETS	1	0.975	1	1	0.994	1	CLONAL	4	TRUE	1	0.16945068635343	2		287	410	SUCCESS
APC	324	MSKCC	GRCh37	5	112173534	112173534	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1561575700	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	101	324	0	ENST00000257430.4:c.2243G>A	p.Ser748Asn	p.S748N	ENST00000257430	NM_000038.5	748	aGc/aAc	16/16	1	2	FACETS	0.993	0.895	1	1	0.99	1	CLONAL	3	TRUE	1	0.16945068635343	2		324	400	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923317	131923317	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	65	218	0	ENST00000265335.6:c.820G>A	p.Ala274Thr	p.A274T	ENST00000265335		274	Gcc/Acc	6/25	1	2	FACETS	1	0.923	1	1	0.985	1	CLONAL	3	TRUE	1	0.16945068635343	2		218	239	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722000	176722000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758398402	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	222	653	0	ENST00000439151.2:c.7631C>T	p.Ala2544Val	p.A2544V	ENST00000439151	NM_022455.4	2544	gCc/gTc	23/23	1	2	FACETS	1	0.959	1	1	0.995	1	CLONAL	3	TRUE	1	0.16945068635343	2		653	841	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046111	180046111	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	45	236	1	ENST00000261937.6:c.2762-2A>T		p.X921_splice	ENST00000261937	NM_182925.4	921			1	2	FACETS	0.846	0.714	0.99	1	0.966	1	CLONAL	2	TRUE	1	0.16945068635343	2		237	314	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046686	180046686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1696	99	1450	4	ENST00000261937.6:c.2626G>A	p.Val876Met	p.V876M	ENST00000261937	NM_182925.4	876	Gtg/Atg	18/30	1	2	FACETS	0.651	0.578	0.729	0.651	0.578	0.729	SUBCLONAL	1	TRUE	1	0.16945068635343	2		1454	1795	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818254	32818254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	359	782	0	ENST00000354258.4:c.1271G>A	p.Ser424Asn	p.S424N	ENST00000354258	NM_000593.5	424	aGc/aAc	5/11	0.16945068635343	4	FACETS	1	0.983	1	1	0.996	1	CLONAL	4	TRUE	2	0.16945068635343	4		782	1146	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287912	33287912	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	70	601	0	ENST00000374542.5:c.1341G>T	p.Glu447Asp	p.E447D	ENST00000374542	NM_001141970.1	447	gaG/gaT	5/8	0.16945068635343	4	FACETS	0.908	0.789	1	0.454	0.394	0.519	CLONAL	1	TRUE	2	0.16945068635343	4		601	1064	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202196	138202196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	202	649	0	ENST00000237289.4:c.2113C>T	p.Pro705Ser	p.P705S	ENST00000237289	NM_001270507.1	705	Cct/Tct	9/9	1	2	FACETS	0.923	0.857	0.992	1	0.995	1	CLONAL	3	TRUE	1	0.16945068635343	2		649	861	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001551	150001551	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	173	432	0	ENST00000253339.5:c.2053C>T	p.Leu685Phe	p.L685F	ENST00000253339		685	Ctt/Ttt	4/7	1	2	FACETS	0.987	0.916	1	1	0.995	1	CLONAL	4	TRUE	1	0.16945068635343	2		432	517	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100048	157100048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	55	91	0	ENST00000346085.5:c.985G>A	p.Ala329Thr	p.A329T	ENST00000346085	NM_020732.3	329	Gca/Aca	1/20	1	2	FACETS	1	0.88	1	1	0.984	1	CLONAL	4	TRUE	1	0.16945068635343	2		91	161	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55270270	55270270	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1234	87	1072	0	ENST00000275493.2:c.3223G>T	p.Gly1075Cys	p.G1075C	ENST00000275493	NM_005228.3	1075	Ggc/Tgc	27/28	1	2	FACETS	0.777	0.686	0.876	0.777	0.686	0.876	SUBCLONAL	1	TRUE	1	0.16945068635343	2		1072	1321	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350145	81350145	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745854997	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	30	329	0	ENST00000222390.5:c.1187G>A	p.Gly396Asp	p.G396D	ENST00000222390	NM_000601.4	396	gGc/gAc	10/18	1	2	FACETS	0.724	0.583	0.885	0.724	0.583	0.885	SUBCLONAL	1	TRUE	1	0.16945068635343	2		329	489	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359054	81359054	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	49	563	0	ENST00000222390.5:c.907A>C	p.Thr303Pro	p.T303P	ENST00000222390	NM_000601.4	303	Act/Cct	8/18	1	2	FACETS	0.829	0.7	0.97	0.829	0.7	0.97	CLONAL	1	TRUE	1	0.16945068635343	2		563	698	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877990	151877990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178963726	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	174	400	0	ENST00000262189.6:c.6955G>A	p.Ala2319Thr	p.A2319T	ENST00000262189	NM_170606.2	2319	Gcc/Acc	36/59	1	2	FACETS	0.93	0.862	1	1	0.995	1	CLONAL	4	TRUE	1	0.16945068635343	2		400	552	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194787	29194787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769407772	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	392	1257	0	ENST00000240100.2:c.941G>A	p.Arg314His	p.R314H	ENST00000240100	NM_001394.6	314	cGc/cAc	4/4	1	2	FACETS	1	0.977	1	1	0.997	1	CLONAL	3	TRUE	1	0.16945068635343	2		1257	1468	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38173048	38173048	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	29	393	0	ENST00000317025.8:c.2001G>C	p.Lys667Asn	p.K667N	ENST00000317025	NM_023034.1	667	aaG/aaC	11/24	1	2	FACETS	0.665	0.532	0.816	0.665	0.532	0.816	SUBCLONAL	1	TRUE	1	0.16945068635343	2		393	515	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205614	38205614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	374	743	0	ENST00000317025.8:c.76G>A	p.Ala26Thr	p.A26T	ENST00000317025	NM_023034.1	26	Gcc/Acc	2/24	1	2	FACETS	1	0.979	1	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		743	1047	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542602	141542602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	1034	1002	1	ENST00000220592.5:c.2384G>A	p.Arg795His	p.R795H	ENST00000220592	NM_012154.3	795	cGc/cAc	18/19	0.16945068635343	9	FACETS	0.995	0.969	1	1	0.998	1	CLONAL	10	TRUE	1	0.16945068635343	9		1003	1954	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141570511	141570511	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1810	173	965	2	ENST00000220592.5:c.617T>C	p.Val206Ala	p.V206A	ENST00000220592	NM_012154.3	206	gTc/gCc	5/19	0.16945068635343	9	FACETS	0.82	0.751	0.893	0.205	0.187	0.224	CLONAL	2	TRUE	1	0.16945068635343	9		967	1983	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570226	87570226	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	50	581	0	ENST00000277120.3:c.1966G>A	p.Ala656Thr	p.A656T	ENST00000277120		656	Gct/Act	17/19	1	2	FACETS	0.72	0.609	0.842	0.72	0.609	0.842	SUBCLONAL	1	TRUE	1	0.16945068635343	2		581	820	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900147	101900147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	25	232	0	ENST00000374994.4:c.581C>T	p.Pro194Leu	p.P194L	ENST00000374994	NM_004612.2	194	cCa/cTa	4/9	1	2	FACETS	0.831	0.655	1	0.831	0.655	1	CLONAL	1	TRUE	1	0.16945068635343	2		232	355	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325383	1325383	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	285	658	0	ENST00000400841.2:c.292T>C	p.Ser98Pro	p.S98P	ENST00000400841		98	Tcc/Ccc	3/6	1	2	FACETS	0.918	0.865	0.972	1	0.996	1	CLONAL	4	TRUE	1	0.16945068635343	2		658	916	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429048	47429048	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	322	822	0	ENST00000377045.4:c.1411C>A	p.Leu471Met	p.L471M	ENST00000377045	NM_001654.4	471	Ctg/Atg	13/16	1	2	FACETS	0.904	0.855	0.954	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		822	1051	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650294	48650295	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1317	72	1074	0	ENST00000376670.3:c.264_265insT	p.Gly89TrpfsTer73	p.G89Wfs*73	ENST00000376670	NM_002049.3	88	-/T	3/6	1	2	FACETS	0.612	0.532	0.699	0.612	0.532	0.699	SUBCLONAL	1	TRUE	1	0.16945068635343	2		1074	1389	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240019	53240019	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	338	880	0	ENST00000375401.3:c.1422G>A	p.Trp474Ter	p.W474*	ENST00000375401	NM_004187.3	474	tgG/tgA	11/26	1	2	FACETS	0.899	0.851	0.948	1	0.997	1	CLONAL	4	TRUE	1	0.16945068635343	2		880	1109	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354685	70354685	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753061449	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	266	643	0	ENST00000374080.3:c.4850C>T	p.Ala1617Val	p.A1617V	ENST00000374080		1617	gCg/gTg	35/45	1	2	FACETS	1	0.978	1	1	0.996	1	CLONAL	3	TRUE	1	0.16945068635343	2		643	961	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76777778	76777778	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	47	679	0	ENST00000373344.5:c.6938T>C	p.Leu2313Ser	p.L2313S	ENST00000373344	NM_000489.3	2313	tTg/tCg	32/35	1	2	FACETS	0.706	0.594	0.83	0.706	0.594	0.83	SUBCLONAL	1	TRUE	1	0.16945068635343	2		679	786	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890104	76890104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	194	464	1	ENST00000373344.5:c.4790G>A	p.Gly1597Asp	p.G1597D	ENST00000373344	NM_000489.3	1597	gGc/gAc	17/35	1	2	FACETS	0.959	0.893	1	1	0.995	1	CLONAL	4	TRUE	1	0.16945068635343	2		465	597	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912062	76912062	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557119995	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	127	413	0	ENST00000373344.5:c.4202G>A	p.Arg1401Gln	p.R1401Q	ENST00000373344	NM_000489.3	1401	cGg/cAg	13/35	1	2	FACETS	1	0.971	1	1	0.993	1	CLONAL	3	TRUE	1	0.16945068635343	2		413	434	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630191	100630191	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	191	536	1	ENST00000308731.7:c.82C>T	p.Arg28Cys	p.R28C	ENST00000308731	NM_000061.2	28	Cgc/Tgc	2/19	1	2	FACETS	1	0.966	1	1	0.995	1	CLONAL	3	TRUE	1	0.16945068635343	2		537	703	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732506	74732506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1419789271	NA	P-0015081-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	194	282	0	ENST00000359995.5:c.403C>T	p.Arg135Cys	p.R135C	ENST00000359995	NM_001195427.1	135	Cgt/Tgt	2/3	1	2	FACETS	0.942	0.876	1	1	0.995	1	CLONAL	4	TRUE	1	0.16945068635343	2		282	608	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032794	30032794	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434259	NA	P-0015370-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	192	328	1	ENST00000338641.4:c.169C>T	p.Arg57Ter	p.R57*	ENST00000338641	NM_000268.3	57	Cga/Tga	2/16	0.372064988564618	3	FACETS	0.989	0.93	1	0.989	0.93	1	CLONAL	3	TRUE	0	0.413101328377305	3		329	378	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400853	72400853	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015370-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	20	304	0	ENST00000357731.5:c.318G>T	p.Gln106His	p.Q106H	ENST00000357731	NM_173808.2	106	caG/caT	2/7	0.266828548118891	2	FACETS	0.556	0.428	0.705	0.278	0.214	0.353	SUBCLONAL	1	TRUE	0	0.413101328377305	2		304	174	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630453	187630453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015370-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	20	585	0	ENST00000441802.2:c.529G>A	p.Asp177Asn	p.D177N	ENST00000441802	NM_005245.3	177	Gac/Aac	2/27	0.287023207173842	2	FACETS	0.245	0.186	0.313	0.122	0.093	0.157	SUBCLONAL	1	TRUE	0	0.413101328377305	2		585	396	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5029876	5029876	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0015370-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	199	353	0	ENST00000381652.3:c.320C>G	p.Ser107Ter	p.S107*	ENST00000381652	NM_004972.3	107	tCa/tGa	4/25	0.413101328377305	5	FACETS	1	0.982	1	0.877	0.827	0.925	CLONAL	4	TRUE	0	0.413101328377305	5		353	356	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0015961-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	79	656	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.162893561867722	3	FACETS	1	0.903	1	1	0.903	1	INDETERMINATE	2	TRUE	1	0.470749537888698	3		657	206	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775719	9775719	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015961-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	70	622	0	ENST00000377346.4:c.262C>A	p.Arg88Ser	p.R88S	ENST00000377346	NM_005026.3	88	Cgt/Agt	4/24	0.132700447205102	3	FACETS	0.811	0.709	0.92			1	INDETERMINATE	1	TRUE	NA	0.470749537888698	3		622	453	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730074	41730074	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377167564	NA	P-0016499-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	137	458	0	ENST00000242208.4:c.455G>A	p.Arg152His	p.R152H	ENST00000242208	NM_002192.2	152	cGt/cAt	3/3	0.41069972960459	4	FACETS	0.795	0.723	0.871	0.398	0.361	0.436	SUBCLONAL	1	TRUE	2	0.649519249079433	4		458	875	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692780	89692780	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1554898056	NA	P-0016499-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	175	283	1	ENST00000371953.3:c.264T>A	p.Tyr88Ter	p.Y88*	ENST00000371953	NM_000314.4	88	taT/taA	5/9	0.649519249079433	2	FACETS	0.994	0.94	1	0.994	0.94	1	CLONAL	2	TRUE	0	0.649519249079433	2		284	271	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200428	138200428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016499-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	155	475	0	ENST00000237289.4:c.1846G>A	p.Gly616Arg	p.G616R	ENST00000237289	NM_001270507.1	616	Ggg/Agg	7/9	1	2	FACETS	0.889	0.819	0.961	0.889	0.819	0.961	CLONAL	1	TRUE	1	0.649519249079433	2		475	537	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0016503-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	1333	157	2	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.681786305305112	4	FACETS	0.983	0.962	1	0.983	0.962	1	CLONAL	3	TRUE	1	0.681786305305112	4		159	2230	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0016733-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	46	559	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	0.181	0.151	0.214	0.181	0.151	0.214	SUBCLONAL	1	TRUE	1	0.555965246599604	2		559	915	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63810652	63810652	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs753041204	NA	P-0016733-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	71	187	0	ENST00000279873.7:c.739A>G	p.Asn247Asp	p.N247D	ENST00000279873	NM_032199.2	247	Aat/Gat	5/10	1	2	FACETS	0.837	0.737	0.943	0.837	0.737	0.943	CLONAL	1	TRUE	1	0.555965246599604	2		187	305	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427700	72427700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016733-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	149	324	0	ENST00000477973.2:c.790G>A	p.Glu264Lys	p.E264K	ENST00000477973	NM_012234.5	264	Gaa/Aaa	4/4	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.555965246599604	2		324	533	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84406180	84406180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016733-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	168	376	2	ENST00000321945.7:c.46G>A	p.Gly16Ser	p.G16S	ENST00000321945	NM_139076.2	16	Ggc/Agc	1/9	1	2	FACETS	0.95	0.877	1	0.95	0.877	1	CLONAL	1	TRUE	1	0.555965246599604	2		378	636	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960216	151960216	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0016733-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	62	111	0	ENST00000262189.6:c.1185-1G>C		p.X395_splice	ENST00000262189	NM_170606.2	395			0.551761473582071	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.555965246599604	1		111	147	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631850	90631850	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016733-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	273	710	0	ENST00000330062.3:c.503T>C	p.Ile168Thr	p.I168T	ENST00000330062	NM_002168.2	168	aTc/aCc	4/11	1	2	FACETS	0.987	0.927	1	0.987	0.927	1	CLONAL	1	TRUE	1	0.555965246599604	2		710	995	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0017166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	30	157	2	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		159	76	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410903	31410903	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	17	799	0	ENST00000344624.3:c.3617C>G	p.Thr1206Ser	p.T1206S	ENST00000344624		1206	aCc/aGc	28/33	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		799	67	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468065	50468065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749084924	NA	P-0017166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	31	384	0	ENST00000331340.3:c.1300G>A	p.Ala434Thr	p.A434T	ENST00000331340	NM_006060.4	434	Gcc/Acc	8/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		384	48	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556079	29556079	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886041347	NA	P-0017259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	120	284	0	ENST00000356175.3:c.2446C>T	p.Arg816Ter	p.R816*	ENST00000356175	NM_000267.3	816	Cga/Tga	21/57	1	2	FACETS	0.955	0.911	0.995	1	0.993	1	CLONAL	2	TRUE	1	0.872314587697262	2		284	144	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157470066	157470066	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs770377920	NA	P-0017259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	106	291	0	ENST00000346085.5:c.2860G>T	p.Ala954Ser	p.A954S	ENST00000346085	NM_020732.3	954	Gcg/Tcg	9/20	1	2	FACETS	0.976	0.892	1	0.976	0.892	1	CLONAL	1	TRUE	1	0.872314587697262	2		291	249	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556079	29556079	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886041347	NA	P-0017259-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	26	284	0	ENST00000356175.3:c.2446C>T	p.Arg816Ter	p.R816*	ENST00000356175	NM_000267.3	816	Cga/Tga	21/57	1	2	FACETS	0.961	0.772	1	1	0.952	1	CLONAL	2	TRUE	1	0.200430682713899	2		284	135	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157470066	157470066	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs770377920	NA	P-0017259-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	21	291	0	ENST00000346085.5:c.2860G>T	p.Ala954Ser	p.A954S	ENST00000346085	NM_020732.3	954	Gcg/Tcg	9/20	1	2	FACETS	0.812	0.627	1	0.812	0.627	1	CLONAL	1	TRUE	1	0.200430682713899	2		291	258	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532472	63532472	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017259-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	42	564	0	ENST00000307078.5:c.2107A>G	p.Arg703Gly	p.R703G	ENST00000307078	NM_004655.3	703	Agg/Ggg	8/11	0.200430682713899	3	FACETS	0.835	0.697	0.989	0.418	0.348	0.495	CLONAL	1	TRUE	1	0.200430682713899	3		564	552	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0017783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	152	172	0				ENST00000310581	NM_198253.2	-/1132			0.513483060693148	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.513483060693148	2		172	255	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0017783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	325	770	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.478125294451342	2	FACETS	0.897	0.853	0.94	0.897	0.853	0.94	CLONAL	2	TRUE	0	0.513483060693148	2		770	706	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94910940	94910940	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	111	437	0	ENST00000536441.1:c.1190A>T	p.Asp397Val	p.D397V	ENST00000536441	NM_144665.3	397	gAc/gTc	8/10	0.513483060693148	1	FACETS	0.737	0.667	0.81	0.737	0.667	0.81	SUBCLONAL	1	TRUE	0	0.513483060693148	1		437	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0018300-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	86	618	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.379200714563722	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.379200714563722	1		618	327	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143350346	143350346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483862322	NA	P-0018300-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	17	155	0	ENST00000262992.4:c.116C>T	p.Pro39Leu	p.P39L	ENST00000262992	NM_001101669.1	39	cCg/cTg	3/24	0.379200714563722	3	FACETS	1	0.898	1	0.702	0.536	0.889	CLONAL	1	TRUE	1	0.379200714563722	3		155	76	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287568	33287568	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018300-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	98	543	0	ENST00000374542.5:c.1529C>G	p.Pro510Arg	p.P510R	ENST00000374542	NM_001141970.1	510	cCt/cGt	6/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.379200714563722	2		543	425	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841842	151841842	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018300-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	45	237	0	ENST00000262189.6:c.14299del	p.Thr4767LeufsTer43	p.T4767Lfs*43	ENST00000262189	NM_170606.2	4767	Act/ct	55/59	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.379200714563722	2		237	207	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107225	27107225	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019531-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	130	460	0	ENST00000324856.7:c.6836T>C	p.Leu2279Pro	p.L2279P	ENST00000324856	NM_006015.4	2279	cTg/cCg	20/20	1	2	FACETS	0.899	0.819	0.983	0.899	0.819	0.983	CLONAL	1	TRUE	1	0.52	2		460	556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576863	7576863	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	38	784	0	ENST00000269305.4:c.983del	p.Phe328SerfsTer17	p.F328Sfs*17	ENST00000269305	NM_001126112.2	328	tTc/tc	9/11	0.202698049853354	3	FACETS	0.807	0.666	0.964	0.403	0.333	0.482	CLONAL	1	FALSE	1	0.202698049853354	3		784	512	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146687	185146688	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGA	novel	NA	P-0019689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	57	794	0	ENST00000265026.3:c.320_322dup	p.Gly107dup	p.G107dup	ENST00000265026	NM_004721.4	107	-/GGA	2/14	0.202698049853354	3	FACETS	0.943	0.808	1	0.471	0.404	0.545	CLONAL	1	FALSE	1	0.202698049853354	3		794	657	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0019689-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	255	764	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	0.716654616004926	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.724715262049741	1		764	443	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031875	10031875	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019689-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	219	813	0	ENST00000330684.3:c.948del	p.Lys317ArgfsTer47	p.K317Rfs*47	ENST00000330684	NM_001134407.1	316	gcC/gc	3/13	1	2	FACETS	0.959	0.898	1	0.959	0.898	1	CLONAL	1	TRUE	1	0.724715262049741	2		813	630	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649249	23649249	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1555462067	NA	P-0019689-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	190	502	0	ENST00000261584.4:c.133A>C	p.Lys45Gln	p.K45Q	ENST00000261584	NM_024675.3	45	Aag/Cag	3/13	1	2	FACETS	0.946	0.881	1	0.946	0.881	1	CLONAL	1	TRUE	1	0.724715262049741	2		502	554	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213582	36213582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019689-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	74	1213	1	ENST00000222270.7:c.2684C>T	p.Ala895Val	p.A895V	ENST00000222270	NM_014727.1	895	gCc/gTc	5/37	0.256050454689807	1	FACETS	0.125	0.109	0.143	0.125	0.109	0.143	INDETERMINATE	1	TRUE	0	0.724715262049741	1		1214	1042	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0021007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	534	380	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.794556715931272	2		380	656	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0021007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	206	270	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.777864799873562	2	FACETS	0.957	0.917	0.994	0.957	0.917	0.994	CLONAL	2	TRUE	0	0.794556715931272	2		270	271	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245553	46245553	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369610372	NA	P-0021007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	127	219	0	ENST00000334344.6:c.3647C>T	p.Thr1216Met	p.T1216M	ENST00000334344	NM_152641.2	1216	aCg/aTg	15/21	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.794556715931272	2		219	309	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143226687	143226687	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	134	212	0	ENST00000262992.4:c.427A>C	p.Ser143Arg	p.S143R	ENST00000262992	NM_001101669.1	143	Agt/Cgt	7/24	0.794556715931272	2	FACETS	1	0.958	1	0.529	0.488	0.57	CLONAL	1	TRUE	0	0.794556715931272	2		212	319	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937017	48937017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752342013	NA	P-0021007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	98	253	1	ENST00000267163.4:c.785G>A	p.Arg262Gln	p.R262Q	ENST00000267163	NM_000321.2	262	cGg/cAg	8/27	0.794556715931272	6	FACETS	0.87	0.776	0.97	0.218	0.194	0.243	CLONAL	1	TRUE	2	0.794556715931272	6		254	734	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226551643	226551643	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0021007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	181	368	0	ENST00000366794.5:c.2786+1G>T		p.X929_splice	ENST00000366794	NM_001618.3	929			0.794556715931272	5	FACETS	1	0.946	1			1	CLONAL	1	TRUE	NA	0.794556715931272	5		368	967	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412066	116412066	+	intron_variant	Intron	SNP	G	G	C	novel	NA	P-0021007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	191	498	0	ENST00000397752.3:c.3028+23G>C		p.*1010*	ENST00000397752	NM_000245.2	-/1390			0.794556715931272	3	FACETS	0.816	0.756	0.879	0.408	0.378	0.44	CLONAL	1	TRUE	1	0.794556715931272	3		498	823	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291801	15291801	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021124-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	766	1211	1	ENST00000263388.2:c.2965C>A	p.Leu989Ile	p.L989I	ENST00000263388	NM_000435.2	989	Ctc/Atc	18/33	0.584407370658339	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.681275183837583	4		1212	1863	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563527	87563528	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0021124-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	133	641	0	ENST00000277120.3:c.1915_1916delinsTT	p.Gly639Leu	p.G639L	ENST00000277120		639	GGg/TTg	16/19	0.681275183837583	3	FACETS	0.693	0.63	0.76	0.347	0.315	0.38	SUBCLONAL	1	TRUE	1	0.681275183837583	3		641	755	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	48	276	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.2	2		276	377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0022085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	44	380	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.882	0.739	1	0.882	0.739	1	CLONAL	1	TRUE	1	0.2	2		380	499	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477089	67477103	+	inframe_deletion	In_Frame_Del	DEL	TCGGAGGGGAGGTCT	TCGGAGGGGAGGTCT	-	novel	NA	P-0022085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	72	518	0	ENST00000327367.4:c.899_913del	p.Gly300_Phe304del	p.G300_F304del	ENST00000327367	NM_005902.3	299	aTCGGAGGGGAGGTCTtc/atc	7/9	1	2	FACETS	0.824	0.722	0.932	1	0.978	1	CLONAL	2	TRUE	1	0.2	2		518	437	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753597	42753597	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	48	832	0	ENST00000222329.4:c.667G>T	p.Ala223Ser	p.A223S	ENST00000222329	NM_006494.2	223	Gcc/Tcc	4/4	1	2	FACETS	0.807	0.681	0.945	0.807	0.681	0.945	CLONAL	1	TRUE	1	0.2	2		832	595	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200670	128200670	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	39	635	0	ENST00000341105.2:c.1135C>G	p.Leu379Val	p.L379V	ENST00000341105	NM_032638.4	379	Ctg/Gtg	5/6	1	2	FACETS	0.901	0.747	1	0.901	0.747	1	CLONAL	1	TRUE	1	0.2	2		635	433	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268984	142268984	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558627427	NA	P-0022085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	27	277	0	ENST00000350721.4:c.2966G>A	p.Arg989His	p.R989H	ENST00000350721	NM_001184.3	989	cGt/cAt	14/47	1	2	FACETS	0.687	0.546	0.848	0.687	0.546	0.848	SUBCLONAL	1	TRUE	1	0.2	2		277	393	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098912	47098912	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022195-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	137	709	0	ENST00000409792.3:c.6362G>T	p.Arg2121Leu	p.R2121L	ENST00000409792	NM_014159.6	2121	cGc/cTc	15/21	1	2	FACETS	0.866	0.788	0.947	0.866	0.788	0.947	CLONAL	1	TRUE	1	0.402156565550827	2		709	787	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255832	16255832	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023959-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	257	505	1	ENST00000375759.3:c.3097G>A	p.Gly1033Arg	p.G1033R	ENST00000375759	NM_015001.2	1033	Gga/Aga	11/15	0.94762041016552	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.94762041016552	1		506	276	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720876	89720876	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs786201041	NA	P-0023959-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	204	447	0	ENST00000371953.3:c.1026+1G>C		p.X342_splice	ENST00000371953	NM_000314.4	342			0.94762041016552	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.94762041016552	1		447	223	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526594	31526594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023959-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	258	593	0	ENST00000344624.3:c.446C>T	p.Pro149Leu	p.P149L	ENST00000344624		149	cCc/cTc	2/33	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.94762041016552	2		593	501	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005491	42005491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023959-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	437	767	1	ENST00000219905.7:c.3227G>A	p.Cys1076Tyr	p.C1076Y	ENST00000219905	NM_001164273.1	1076	tGc/tAc	9/24	0.836427996012362	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.94762041016552	1		768	475	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101887	11101887	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023959-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1343	78	1406	0	ENST00000358026.2:c.1307C>G	p.Ala436Gly	p.A436G	ENST00000358026	NM_001128849.1	436	gCt/gGt	8/36	1	2	FACETS	0.116	0.101	0.132	0.116	0.101	0.132	SUBCLONAL	1	TRUE	1	0.94762041016552	2		1406	1421	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595633	55595633	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023959-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	14	301	0	ENST00000288135.5:c.2123A>T	p.His708Leu	p.H708L	ENST00000288135	NM_000222.2	708	cAt/cTt	14/21	1	2	FACETS	0.11	0.079	0.147	0.11	0.079	0.147	SUBCLONAL	1	TRUE	1	0.94762041016552	2		301	269	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023992-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	326	199	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	NA	2	FACETS	0.976	0.923	1			1	INDETERMINATE	1	TRUE	NA	0.651186085229578	2		199	1026	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189845	11189845	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023992-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	291	185	0	ENST00000361445.4:c.5664C>A	p.Phe1888Leu	p.F1888L	ENST00000361445	NM_004958.3	1888	ttC/ttA	40/58	0.633753645804073	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.651186085229578	1		185	558	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106016	8106016	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023992-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	150	156	0	ENST00000346208.3:c.836C>G	p.Thr279Arg	p.T279R	ENST00000346208		279	aCg/aGg	4/6	1	2	FACETS	0.493	0.45	0.538	0.493	0.45	0.538	SUBCLONAL	1	TRUE	1	0.651186085229578	2		156	935	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367275	50367275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778910457	NA	P-0025251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	261	360	0	ENST00000331340.3:c.82G>A	p.Asp28Asn	p.D28N	ENST00000331340	NM_006060.4	28	Gat/Aat	3/8	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.924743176258712	2		360	558	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993630	72993630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780015879	NA	P-0026014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	189	1088	1	ENST00000268489.5:c.415G>A	p.Gly139Ser	p.G139S	ENST00000268489	NM_006885.3	139	Ggc/Agc	2/10	0.542184290977249	3	FACETS	1	0.937	1	0.507	0.469	0.547	CLONAL	1	TRUE	1	0.542184290977249	3		1089	874	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577611	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TA	TA	-	novel	NA	P-0026014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	334	526	0	ENST00000269305.4:c.673-3_673-2del		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.0891837738307733	5	FACETS	1	0.986	1			1	INDETERMINATE	4	TRUE	NA	0.542184290977249	5		526	527	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339502	116339502	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	53	276	0	ENST00000397752.3:c.364G>C	p.Val122Leu	p.V122L	ENST00000397752	NM_000245.2	122	Gtc/Ctc	2/21	0.542184290977249	3	FACETS	0.71	0.608	0.821	0.355	0.304	0.411	SUBCLONAL	1	TRUE	1	0.542184290977249	3		276	350	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026308-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	594	692	0	ENST00000397752.3:c.3028G>C	p.Asp1010His	p.D1010H	ENST00000397752	NM_000245.2	1010	Gat/Cat	14/21	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.520020418415092	2		692	1054	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977967	131977967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026308-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	108	403	0	ENST00000265335.6:c.3850G>A	p.Glu1284Lys	p.E1284K	ENST00000265335		1284	Gag/Aag	25/25	0.453667631119973	4	FACETS	0.719	0.645	0.798	0.24	0.215	0.266	SUBCLONAL	1	TRUE	1	0.520020418415092	4		403	878	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977980	131977980	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026308-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	106	382	0	ENST00000265335.6:c.3863G>A	p.Arg1288Lys	p.R1288K	ENST00000265335		1288	aGg/aAg	25/25	0.453667631119973	4	FACETS	0.698	0.625	0.776	0.233	0.208	0.259	SUBCLONAL	1	TRUE	1	0.520020418415092	4		382	888	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131978040	131978040	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026308-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	103	329	0	ENST00000265335.6:c.3923G>A	p.Gly1308Glu	p.G1308E	ENST00000265335		1308	gGa/gAa	25/25	0.453667631119973	4	FACETS	0.757	0.677	0.842	0.252	0.225	0.281	SUBCLONAL	1	TRUE	1	0.520020418415092	4		329	795	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730199	133730199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375582718	NA	P-0026308-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	189	452	0	ENST00000318560.5:c.265C>T	p.Arg89Trp	p.R89W	ENST00000318560	NM_005157.4	89	Cgg/Tgg	3/11	0.288592085316058	1	FACETS	0.848	0.788	0.911	0.848	0.788	0.911	INDETERMINATE	1	TRUE	0	0.520020418415092	1		452	634	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0026521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	326	399	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.296123532629269	5	FACETS	0.982	0.938	1			1	INDETERMINATE	3	TRUE	NA	0.810930703318136	5		399	605	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462123	120462123	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	460	796	0	ENST00000256646.2:c.5593C>T	p.Gln1865Ter	p.Q1865*	ENST00000256646	NM_024408.3	1865	Cag/Tag	31/34	0.631216807971891	4	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.810930703318136	4		796	878	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	508	781	0	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	0.533342347709206	4	FACETS	1	0.994	1	0.766	0.738	0.795	CLONAL	2	TRUE	1	0.810930703318136	4		781	987	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038529	47038529	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	525	505	0	ENST00000377604.3:c.691G>T	p.Glu231Ter	p.E231*	ENST00000377604	NM_001204468.1	231	Gag/Tag	8/24	0.686389308279845	2	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.810930703318136	2		505	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	919	971	0	ENST00000269305.4:c.880del	p.Glu294SerfsTer51	p.E294Sfs*51	ENST00000269305	NM_001126112.2	294	Gag/ag	8/11	0.713109458437657	4	FACETS	0.919	0.904	0.935	0.919	0.904	0.935	CLONAL	4	TRUE	0	0.810930703318136	4		971	1116	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610085	28610085	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	287	474	0	ENST00000241453.7:c.1405G>T	p.Asp469Tyr	p.D469Y	ENST00000241453	NM_004119.2	469	Gac/Tac	11/24	0.792778520496065	4	FACETS	0.952	0.902	1	0.952	0.902	1	CLONAL	2	TRUE	2	0.810930703318136	4		474	673	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774216	66774216	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1473690179	NA	P-0026521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	547	931	0	ENST00000307102.5:c.692C>T	p.Ser231Leu	p.S231L	ENST00000307102	NM_002755.3	231	tCg/tTg	6/11	0.792778520496065	4	FACETS	0.932	0.896	0.968	0.932	0.896	0.968	CLONAL	2	TRUE	2	0.810930703318136	4		931	1311	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81399260	81399260	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1390087672	NA	P-0026521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	686	795	0	ENST00000222390.5:c.28C>A	p.Leu10Met	p.L10M	ENST00000222390	NM_000601.4	10	Ctg/Atg	1/18	0.810930703318136	6	FACETS	1	0.994	1			1	CLONAL	3	TRUE	NA	0.810930703318136	6		795	1340	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940083	76940083	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	239	205	0	ENST00000373344.5:c.665G>T	p.Trp222Leu	p.W222L	ENST00000373344	NM_000489.3	222	tGg/tTg	9/35	0.686389308279845	2	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.810930703318136	2		205	280	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631170	69631170	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	630	716	0	ENST00000334134.2:c.242T>A	p.Val81Glu	p.V81E	ENST00000334134	NM_005247.2	81	gTg/gAg	2/3	0.713109458437657	4	FACETS	0.928	0.909	0.946	0.928	0.909	0.946	CLONAL	4	TRUE	0	0.810930703318136	4		716	758	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999179	100999179	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	891	1279	1	ENST00000325455.5:c.623C>A	p.Ala208Asp	p.A208D	ENST00000325455	NM_001202474.3	208	gCc/gAc	1/8	0.772975916825237	4	FACETS	0.997	0.973	1	0.997	0.973	1	CLONAL	3	TRUE	1	0.810930703318136	4		1280	1331	SUCCESS
ATM	472	MSKCC	GRCh37	11	108137947	108137947	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	73	396	0	ENST00000278616.4:c.2516A>T	p.Glu839Val	p.E839V	ENST00000278616	NM_000051.3	839	gAa/gTa	17/63	0.772975916825237	4	FACETS	0.778	0.683	0.879	0.259	0.227	0.293	SUBCLONAL	1	TRUE	1	0.810930703318136	4		396	419	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509684	29509684	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1135402799	NA	P-0026521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	158	321	0	ENST00000356175.3:c.888+1G>A		p.X296_splice	ENST00000356175	NM_000267.3	296			0.810930703318136	3	FACETS	0.901	0.842	0.96	0.901	0.842	0.96	CLONAL	2	TRUE	1	0.810930703318136	3		321	304	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257165	198257166	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0026521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	150	381	0	ENST00000335508.6:c.3776_3777delinsTT	p.Arg1259Leu	p.R1259L	ENST00000335508	NM_012433.2	1259	cGG/cTT	25/25	0.547585916300604	4	FACETS	1	0.969	1	0.716	0.666	0.766	CLONAL	2	TRUE	1	0.810930703318136	4		381	312	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757450	40757450	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	458	741	0	ENST00000373198.4:c.2848C>G	p.Leu950Val	p.L950V	ENST00000373198	NM_133170.3	950	Ctg/Gtg	20/32	0.810930703318136	3	FACETS	0.95	0.914	0.985	0.95	0.914	0.985	CLONAL	2	TRUE	1	0.810930703318136	3		741	836	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866424	42866424	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	562	1029	1	ENST00000398585.3:c.208G>T	p.Val70Phe	p.V70F	ENST00000398585	NM_001135099.1	70	Gtc/Ttc	3/14	0.759698184120451	2	FACETS	0.931	0.908	0.954	0.931	0.908	0.954	CLONAL	2	TRUE	0	0.810930703318136	2		1030	744	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523507	41523507	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	131	486	0	ENST00000263253.7:c.923C>A	p.Pro308Gln	p.P308Q	ENST00000263253	NM_001429.3	308	cCg/cAg	4/31	NA	2	FACETS	0.844	0.774	0.915			1	INDETERMINATE	1	TRUE	NA	0.810930703318136	2		486	383	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750464	41750464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	491	767	0	ENST00000226382.2:c.164C>T	p.Ser55Phe	p.S55F	ENST00000226382	NM_003924.3	55	tCc/tTc	1/3	0.810930703318136	4	FACETS	0.982	0.942	1			1	CLONAL	2	TRUE	NA	0.810930703318136	4		767	1117	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271240	1271240	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	122	374	0	ENST00000310581.5:c.2462G>T	p.Arg821Met	p.R821M	ENST00000310581	NM_198253.2	821	aGg/aTg	8/16	0.809711322545288	5	FACETS	1	0.916	1			1	CLONAL	1	TRUE	NA	0.810930703318136	5		374	659	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588928	67588928	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0026521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	57	190	0	ENST00000274335.5:c.1020-1G>T		p.X340_splice	ENST00000274335		340			1	2	FACETS	0.925	0.812	1	0.925	0.812	1	CLONAL	1	TRUE	1	0.810930703318136	2		190	152	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520524	176520524	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763461529	NA	P-0026521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	349	1237	0	ENST00000292408.4:c.1369G>A	p.Asp457Asn	p.D457N	ENST00000292408	NM_213647.1	457	Gac/Aac	10/18	1	2	FACETS	0.954	0.907	1	0.954	0.907	1	CLONAL	1	TRUE	1	0.810930703318136	2		1237	902	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188563	32188563	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	780	1033	0	ENST00000375023.3:c.892T>A	p.Tyr298Asn	p.Y298N	ENST00000375023	NM_004557.3	298	Tac/Aac	5/30	0.79932464428689	5	FACETS	0.934	0.906	0.962	0.934	0.906	0.962	CLONAL	3	TRUE	2	0.810930703318136	5		1033	1521	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748574	43748574	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	322	532	1	ENST00000523873.1:c.528G>T	p.Trp176Cys	p.W176C	ENST00000523873		176	tgG/tgT	6/8	0.810930703318136	4	FACETS	0.906	0.86	0.952			1	CLONAL	2	TRUE	NA	0.810930703318136	4		533	794	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965349	68965350	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0026521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	346	470	0	ENST00000288368.4:c.961_962delinsTT	p.Gly321Leu	p.G321L	ENST00000288368	NM_024870.2	321	GGa/TTa	9/40	0.810930703318136	5	FACETS	1	0.993	1	0.86	0.826	0.893	CLONAL	3	TRUE	1	0.810930703318136	5		470	550	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528761	8528761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	200	375	1	ENST00000356435.5:c.371G>T	p.Gly124Val	p.G124V	ENST00000356435		124	gGc/gTc	4/35	0.72461598546791	2	FACETS	0.924	0.884	0.962	0.924	0.884	0.962	CLONAL	2	TRUE	0	0.810930703318136	2		376	267	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638334	117638334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026521-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	94	356	0	ENST00000368508.3:c.6107C>T	p.Thr2036Ile	p.T2036I	ENST00000368508	NM_002944.2	2036	aCt/aTt	38/43	0.810930703318136	3	FACETS	0.915	0.822	1	0.458	0.411	0.507	CLONAL	1	TRUE	1	0.810930703318136	3		356	356	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0027531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9005	306	321	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.897419350116896	13	FACETS	0.435	0.406	0.465			1	SUBCLONAL	1	TRUE	NA	0.897419350116896	13		321	9311	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0027531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	272	302	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.838206219889873	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.897419350116896	1		302	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0027531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	1133	1030	3	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	NA	2	FACETS	1	0.999	1			1	INDETERMINATE	2	TRUE	NA	0.897419350116896	2		1033	1172	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829368	72829368	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201280219	NA	P-0027531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1287	90	639	1	ENST00000268489.5:c.7213G>A	p.Ala2405Thr	p.A2405T	ENST00000268489	NM_006885.3	2405	Gct/Act	9/10	0.291334401245382	5	FACETS	0.342	0.302	0.385	0.114	0.1	0.129	INDETERMINATE	1	TRUE	2	0.897419350116896	5		640	1377	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0027577-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	115	172	0				ENST00000310581	NM_198253.2	-/1132			0.125560552106211	3	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	1	0.17	3		172	692	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0027577-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	53	414	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.125560552106211	3	FACETS	1	0.941	1	0.607	0.518	0.706	CLONAL	1	TRUE	1	0.17	3		414	557	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023895	27023895	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027577-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	14	145	1	ENST00000324856.7:c.1001C>A	p.Ser334Ter	p.S334*	ENST00000324856	NM_006015.4	334	tCg/tAg	1/20	1	2	FACETS	0.619	0.447	0.828	0.619	0.447	0.828	SUBCLONAL	1	TRUE	1	0.17	2		146	266	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263992	104263992	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027577-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	37	425	0	ENST00000369902.3:c.83C>A	p.Ser28Ter	p.S28*	ENST00000369902	NM_016169.3	28	tCg/tAg	1/12	1	2	FACETS	0.71	0.584	0.852	0.71	0.584	0.852	SUBCLONAL	1	TRUE	1	0.17	2		425	613	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061656	38061692	+	frameshift_variant	Frame_Shift_Del	DEL	GCTCGGGCTCAGCGCCGTACCCATGGCCGTCACGCCG	GCTCGGGCTCAGCGCCGTACCCATGGCCGTCACGCCG	-	novel	NA	P-0027577-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	44	374	0	ENST00000250448.2:c.297_333del	p.Gly100AlafsTer13	p.G100Afs*13	ENST00000250448	NM_004496.3	99	gcCGGCGTGACGGCCATGGGTACGGCGCTGAGCCCGAGC/gc	2/2	1	2	FACETS	0.905	0.758	1	0.905	0.758	1	CLONAL	1	TRUE	1	0.17	2		374	572	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566459	41566459	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027577-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	42	409	0	ENST00000263253.7:c.4336T>C	p.Tyr1446His	p.Y1446H	ENST00000263253	NM_001429.3	1446	Tat/Cat	27/31	1	2	FACETS	0.826	0.689	0.979	0.826	0.689	0.979	CLONAL	1	TRUE	1	0.17	2		409	598	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836299	151836299	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027577-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	92	569	0	ENST00000262189.6:c.14506G>C	p.Asp4836His	p.D4836H	ENST00000262189	NM_170606.2	4836	Gac/Cac	57/59	0.125560552106211	3	FACETS	1	0.972	1	0.655	0.581	0.735	CLONAL	1	TRUE	1	0.17	3		569	896	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164467	36164467	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	57	258	0	ENST00000300305.3:c.1408G>A	p.Ala470Thr	p.A470T	ENST00000300305		470	Gcg/Acg	8/8	1	2	FACETS	0.793	0.684	0.911	0.793	0.684	0.911	CLONAL	1	TRUE	1	0.431537012736583	2		258	333	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027127	49027128	+	splice_acceptor_variant	Splice_Site	INS	-	-	GGATTCACCTTTATTT	novel	NA	P-0028137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	116	176	0	ENST00000267163.4:c.1696_1711dup		p.X566_splice	ENST00000267163	NM_000321.2	566			1	2	FACETS	1	0.955	1	1	0.993	1	CLONAL	4	TRUE	1	0.305559986588479	2		176	184	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030485	49030485	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028137-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	53	215	0	ENST00000267163.4:c.1960+1del		p.V654fs	ENST00000267163	NM_000321.2	654	Gtg/tg	19/27	0.3	3	FACETS	0.952	0.82	1			1	CLONAL	4	TRUE	NA	0.12	3		215	246	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0028284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	128	818	0	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.474464713119411	2		818	379	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061435	38061447	+	frameshift_variant	Frame_Shift_Del	DEL	TGCTGGATGGCCA	TGCTGGATGGCCA	-	novel	NA	P-0028284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	69	685	0	ENST00000250448.2:c.542_554del	p.Met181ArgfsTer9	p.M181Rfs*9	ENST00000250448	NM_004496.3	181	aTGGCCATCCAGCAg/ag	2/2	1	2	FACETS	0.866	0.759	0.979	0.866	0.759	0.979	CLONAL	1	TRUE	1	0.474464713119411	2		685	336	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449504	32449504	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028484-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	65	692	1	ENST00000332351.3:c.870C>A	p.Ser290Arg	p.S290R	ENST00000332351	NM_024426.4	290	agC/agA	3/10	1	2	FACETS	0.922	0.801	1	0.922	0.801	1	CLONAL	1	TRUE	1	0.278625446490289	2		693	506	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511686	46511686	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs775490161	NA	P-0028484-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	114	468	0	ENST00000262741.5:c.1091A>G	p.Asn364Ser	p.N364S	ENST00000262741	NM_003629.3	364	aAt/aGt	9/10	0.278625446490289	3	FACETS	1	0.97	1	0.599	0.539	0.662	CLONAL	1	TRUE	1	0.278625446490289	3		468	778	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847326	68847326	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs772622537	NA	P-0028484-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	73	628	0	ENST00000261769.5:c.1248G>C	p.Leu416Phe	p.L416F	ENST00000261769	NM_004360.3	416	ttG/ttC	9/16	0.274474627816246	2	FACETS	0.801	0.701	0.91	0.401	0.35	0.455	CLONAL	1	TRUE	0	0.278625446490289	2		628	654	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211198	36211198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028484-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	148	950	0	ENST00000222270.7:c.949G>A	p.Gly317Arg	p.G317R	ENST00000222270	NM_014727.1	317	Gga/Aga	3/37	0.273847167405844	4	FACETS	1	0.968	1			1	CLONAL	1	TRUE	NA	0.278625446490289	4		950	1197	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881413	111881413	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028484-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	79	564	1	ENST00000393256.3:c.91G>T	p.Gly31Trp	p.G31W	ENST00000393256	NM_006538.4	31	Ggg/Tgg	2/4	0.274474627816246	2	FACETS	1	0.884	1	0.502	0.442	0.566	CLONAL	1	TRUE	0	0.278625446490289	2		565	565	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569678	41569678	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028484-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	41	265	0	ENST00000263253.7:c.4669A>G	p.Ser1557Gly	p.S1557G	ENST00000263253	NM_001429.3	1557	Agc/Ggc	29/31	0.278625446490289	4	FACETS	0.789	0.657	0.935	0.394	0.328	0.468	CLONAL	1	TRUE	2	0.278625446490289	4		265	477	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242845	98242845	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028484-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	50	425	0	ENST00000331920.6:c.772A>T	p.Asn258Tyr	p.N258Y	ENST00000331920	NM_000264.3	258	Aac/Tac	6/24	0.267428681161663	4	FACETS	0.778	0.659	0.908	0.194	0.164	0.227	CLONAL	1	TRUE	0	0.278625446490289	4		425	590	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401014	139401014	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028484-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	68	729	0	ENST00000277541.6:c.3979A>C	p.Asn1327His	p.N1327H	ENST00000277541	NM_017617.3	1327	Aac/Cac	24/34	0.241723667508757	3	FACETS	0.814	0.708	0.929	0.271	0.236	0.31	CLONAL	1	TRUE	0	0.278625446490289	3		729	683	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0028707-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	205	512	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	0.987	0.92	1	0.987	0.92	1	CLONAL	1	TRUE	1	0.648075085025476	2		512	641	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442069	52442081	+	frameshift_variant	Frame_Shift_Del	DEL	GAGTTGCACAAGA	GAGTTGCACAAGA	-	novel	NA	P-0028707-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	160	584	0	ENST00000460680.1:c.268_280del	p.Ser90MetfsTer4	p.S90Mfs*4	ENST00000460680	NM_004656.3	90	TCTTGTGCAACTCat/at	5/17	0.648075085025476	1	FACETS	0.909	0.846	0.974	0.909	0.846	0.974	CLONAL	1	TRUE	0	0.648075085025476	1		584	367	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0028920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	245	432	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.237896248203715	6	FACETS	1	0.97	1	1	0.97	1	CLONAL	4	FALSE	2	0.237896248203715	6		432	722	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0028920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	93	340	0				ENST00000310581	NM_198253.2	-/1132			0.237896248203715	1	FACETS	1	0.913	1	1	0.987	1	CLONAL	2	FALSE	0	0.237896248203715	1		340	338	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0028920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	112	421	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.0911874792411254	4	FACETS	1	0.973	1	1	0.973	1	INDETERMINATE	2	FALSE	2	0.237896248203715	4		421	481	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866378	42866378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	87	736	0	ENST00000398585.3:c.254C>T	p.Pro85Leu	p.P85L	ENST00000398585	NM_001135099.1	85	cCc/cTc	3/14	0.237896248203715	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	0	0.237896248203715	1		736	589	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716344	18716344	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778895247	NA	P-0028920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	49	382	0	ENST00000266497.5:c.3691G>A	p.Glu1231Lys	p.E1231K	ENST00000266497		1231	Gaa/Aaa	26/31	NA	2	FACETS	0.867	0.735	1			1	INDETERMINATE	1	FALSE	NA	0.237896248203715	2		382	475	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492784	56492784	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	233	576	0	ENST00000407977.2:c.155C>T	p.Pro52Leu	p.P52L	ENST00000407977		52	cCc/cTc	2/10	0.235086143701223	4	FACETS	0.927	0.866	0.989	0.927	0.866	0.989	CLONAL	3	FALSE	1	0.237896248203715	4		576	872	SUCCESS
APC	324	MSKCC	GRCh37	5	112116491	112116491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	38	315	0	ENST00000257430.4:c.536C>T	p.Ser179Phe	p.S179F	ENST00000257430	NM_000038.5	179	tCc/tTc	6/16	0.237896248203715	5	FACETS	1	0.933	1	0.425	0.352	0.506	CLONAL	1	FALSE	2	0.237896248203715	5		315	340	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441265	52441265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	42	511	0	ENST00000460680.1:c.505C>T	p.His169Tyr	p.H169Y	ENST00000460680	NM_004656.3	169	Cac/Tac	7/17	0.237896248203715	5	FACETS	0.684	0.57	0.812	0.228	0.19	0.271	SUBCLONAL	1	FALSE	2	0.237896248203715	5		511	700	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796963	78796963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	69	544	0	ENST00000306801.3:c.1076C>T	p.Ser359Leu	p.S359L	ENST00000306801	NM_020761.2	359	tCg/tTg	9/34	0.235086143701223	4	FACETS	1	0.875	1	0.335	0.291	0.383	CLONAL	1	FALSE	1	0.237896248203715	4		544	714	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097752	27097752	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	57	567	0	ENST00000324856.7:c.3341C>T	p.Pro1114Leu	p.P1114L	ENST00000324856	NM_006015.4	1114	cCc/cTc	12/20	0.237896248203715	5	FACETS	0.887	0.76	1	0.296	0.253	0.342	CLONAL	1	FALSE	2	0.237896248203715	5		567	733	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187776	11187776	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	74	623	0	ENST00000361445.4:c.6121G>A	p.Glu2041Lys	p.E2041K	ENST00000361445	NM_004958.3	2041	Gaa/Aaa	44/58	0.237896248203715	5	FACETS	1	0.939	1	0.375	0.327	0.426	CLONAL	1	FALSE	2	0.237896248203715	5		623	751	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059183	27059183	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1010301017	NA	P-0028920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	119	436	0	ENST00000324856.7:c.1820C>T	p.Ser607Leu	p.S607L	ENST00000324856	NM_006015.4	607	tCa/tTa	4/20	0.237896248203715	5	FACETS	1	0.939	1	0.7	0.633	0.771	CLONAL	2	FALSE	2	0.237896248203715	5		436	646	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444711	49444711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	265	898	1	ENST00000301067.7:c.2755C>T	p.Pro919Ser	p.P919S	ENST00000301067	NM_003482.3	919	Cca/Tca	10/54	0.237896248203715	8	FACETS	1	0.974	1	0.643	0.602	0.685	CLONAL	3	FALSE	3	0.237896248203715	8		899	1187	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445118	49445118	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	113	719	0	ENST00000301067.7:c.2348C>T	p.Pro783Leu	p.P783L	ENST00000301067	NM_003482.3	783	cCt/cTt	10/54	0.237896248203715	8	FACETS	0.81	0.728	0.898	0.324	0.291	0.359	CLONAL	2	FALSE	3	0.237896248203715	8		719	1005	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479211	50479211	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	145	322	0	ENST00000394963.4:c.59G>A	p.Gly20Glu	p.G20E	ENST00000394963	NM_003076.4	20	gGa/gAa	1/13	0.237896248203715	8	FACETS	1	0.934	1	0.614	0.562	0.669	CLONAL	3	FALSE	3	0.237896248203715	8		322	680	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924348	112924348	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	126	607	0	ENST00000351677.2:c.1294C>T	p.Pro432Ser	p.P432S	ENST00000351677	NM_002834.3	432	Cct/Tct	11/16	1	2	FACETS	0.798	0.724	0.875	1	0.987	1	SUBCLONAL	2	FALSE	1	0.237896248203715	2		607	664	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880909	28880910	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0028920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	52	415	2	ENST00000282397.4:c.3721-1_3721delinsAA		p.X1241_splice	ENST00000282397	NM_002019.4	1241		29/30	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	1	0.237896248203715	2		417	357	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184489	7184489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200199169	NA	P-0028920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	63	621	1	ENST00000302850.5:c.812C>T	p.Pro271Leu	p.P271L	ENST00000302850	NM_000208.2	271	cCg/cTg	3/22	0.16532606273038	5	FACETS	1	0.93	1	0.374	0.323	0.429	CLONAL	1	FALSE	2	0.237896248203715	5		622	641	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731433	47731433	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0028920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	74	97	0	ENST00000449228.1:c.359del	p.Pro120ArgfsTer109	p.P120Rfs*109	ENST00000449228	NM_001127240.2	120	cCg/cg	2/4	0.237896248203715	3	FACETS	0.879	0.785	0.976	1	0.983	1	CLONAL	4	FALSE	1	0.237896248203715	3		97	198	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574701	41574701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	160	810	0	ENST00000263253.7:c.6986C>T	p.Pro2329Leu	p.P2329L	ENST00000263253	NM_001429.3	2329	cCa/cTa	31/31	0.237896248203715	5	FACETS	0.926	0.849	1	0.926	0.849	1	CLONAL	2	FALSE	3	0.237896248203715	5		810	985	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480451	89480451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	68	348	0	ENST00000336596.2:c.2288C>T	p.Ser763Phe	p.S763F	ENST00000336596	NM_005233.5	763	tCt/tTt	13/17	0.237896248203715	5	FACETS	0.841	0.734	0.957	0.561	0.489	0.638	CLONAL	2	FALSE	2	0.237896248203715	5		348	461	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631608	119631608	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1289744832	NA	P-0028920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	63	415	1	ENST00000316626.5:c.658C>T	p.Arg220Trp	p.R220W	ENST00000316626		220	Cgg/Tgg	6/12	0.237896248203715	5	FACETS	1	0.929	1	0.373	0.322	0.428	CLONAL	1	FALSE	2	0.237896248203715	5		416	643	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751427	57751427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	69	421	0	ENST00000274289.3:c.1564G>A	p.Asp522Asn	p.D522N	ENST00000274289	NM_006622.3	522	Gac/Aac	11/14	0.237896248203715	5	FACETS	0.823	0.719	0.936	0.549	0.479	0.624	CLONAL	2	FALSE	2	0.237896248203715	5		421	478	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157868	27157868	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	46	490	0	ENST00000380036.4:c.92C>T	p.Ser31Phe	p.S31F	ENST00000380036	NM_000459.3	31	tCc/tTc	2/23	0.0911874792411254	4	FACETS	0.885	0.745	1	0.442	0.372	0.52	INDETERMINATE	1	FALSE	2	0.237896248203715	4		490	541	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031885	26031885	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	113	176	0	ENST00000244661.2:c.404G>C	p.Arg135Thr	p.R135T	ENST00000244661	NM_003537.3	135	aGa/aCa	1/1	0.680092633431354	4	FACETS	1	0.968	1	0.387	0.35	0.426	CLONAL	1	TRUE	1	0.675619504460809	4		176	483	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575049	64575049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs386134259	NA	P-0029177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	173	414	0	ENST00000312049.6:c.758C>T	p.Ser253Leu	p.S253L	ENST00000312049	NM_130799.2	253	tCg/tTg	4/10	0.675619504460809	6	FACETS	1	0.946	1			1	CLONAL	1	TRUE	NA	0.675619504460809	6		414	1159	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472168	472168	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	189	404	0	ENST00000399788.2:c.633G>A	p.Met211Ile	p.M211I	ENST00000399788	NM_001042603.1	211	atG/atA	5/28	0.675619504460809	5	FACETS	0.907	0.837	0.981	0.227	0.209	0.246	CLONAL	1	TRUE	1	0.675619504460809	5		404	1242	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636329	21636329	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	271	332	1	ENST00000421138.2:c.681G>A	p.Trp227Ter	p.W227*	ENST00000421138		227	tgG/tgA	7/16	0.536881309706193	3	FACETS	0.985	0.934	1	0.985	0.934	1	CLONAL	2	TRUE	1	0.675619504460809	3		333	545	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021503	31021503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	172	397	0	ENST00000375687.4:c.1502C>T	p.Ser501Phe	p.S501F	ENST00000375687	NM_015338.5	501	tCt/tTt	12/13	0.657786852990548	4	FACETS	0.937	0.862	1	0.468	0.431	0.507	CLONAL	1	TRUE	2	0.675619504460809	4		397	911	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62320457	62320457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1257	222	462	0	ENST00000360203.5:c.1850C>T	p.Ala617Val	p.A617V	ENST00000360203	NM_001283009.1	617	gCc/gTc	22/35	0.675619504460809	6	FACETS	1	0.958	1			1	CLONAL	1	TRUE	NA	0.675619504460809	6		462	1479	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204689	128204689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	311	618	1	ENST00000341105.2:c.752C>T	p.Ser251Phe	p.S251F	ENST00000341105	NM_032638.4	251	tCc/tTc	3/6	0.350339709263123	5	FACETS	0.783	0.739	0.829			1	INDETERMINATE	2	TRUE	NA	0.675619504460809	5		619	1183	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286179	66286179	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	64	252	0	ENST00000273854.3:c.1507G>C	p.Glu503Gln	p.E503Q	ENST00000273854	NM_004439.5	503	Gaa/Caa	6/18	0.150045342075812	5	FACETS	1	0.969	1	0.348	0.304	0.395	INDETERMINATE	1	TRUE	1	0.675619504460809	5		252	274	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62294239	62294239	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1191	220	477	0	ENST00000360203.5:c.535G>A	p.Glu179Lys	p.E179K	ENST00000360203	NM_001283009.1	179	Gaa/Aaa	6/35	0.675619504460809	6	FACETS	1	0.971	1			1	CLONAL	1	TRUE	NA	0.675619504460809	6		477	1411	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0121431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	249	414	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.458140538399756	4	FACETS	1	0.987	1	0.777	0.73	0.824	CLONAL	2	NA	1	0.457494370234707	4		414	681	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244134	5244134	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0121431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	214	646	0	ENST00000357368.4:c.1348C>G	p.Pro450Ala	p.P450A	ENST00000357368	NM_002850.3	450	Ccg/Gcg	11/38	0.458140538399756	3	FACETS	1	0.972	1	0.546	0.507	0.586	CLONAL	1	NA	1	0.457494370234707	3		646	1053	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875919	76875919	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0121431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	126	300	0	ENST00000373344.5:c.5216del	p.Arg1739HisfsTer8	p.R1739Hfs*8	ENST00000373344	NM_000489.3	1739	cGa/ca	20/35	1	1	FACETS	0.84	0.777	0.902	1	0.99	1	CLONAL	2	NA	0	0.457494370234707	1		300	253	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0121431-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	46	414	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.191718837340597	3	FACETS		NA	1			1	NA	NA	NA	1	NA	3		414	547	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875865	76875878	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TCAATTAGGTTATT	TCAATTAGGTTATT	-	novel	NA	P-0121431-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	23	272	0	ENST00000373344.5:c.5257_5270del	p.Asn1753ValfsTer6	p.N1753Vfs*6	ENST00000373344	NM_000489.3	1753	AATAACCTAATTGAg/g	20/35	1	1	FACETS		NA	1			1	NA	NA	NA	0	NA	1		272	252	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249002	55249003	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGTGGA	rs397517109	NA	P-0121431-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	104	552	0	ENST00000275493.2:c.2303_2311dup	p.Ser768_Asp770dup	p.S768_D770dup	ENST00000275493	NM_005228.3	768	gcc/gcCAGCGTGGAc	20/28	1	2	FACETS		NA	1			1	NA	NA	NA	1	NA	2		552	617	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0121431-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	90	414	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.51598969114579	4	FACETS	0.955	0.849	1	0.477	0.424	0.534	CLONAL	1	NA	2	0.51598969114579	4		414	554	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244134	5244134	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0121431-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	179	646	0	ENST00000357368.4:c.1348C>G	p.Pro450Ala	p.P450A	ENST00000357368	NM_002850.3	450	Ccg/Gcg	11/38	0.506646337208979	3	FACETS	1	0.978	1	0.576	0.532	0.621	CLONAL	1	NA	1	0.51598969114579	3		646	758	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875919	76875919	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0121431-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	97	300	0	ENST00000373344.5:c.5216del	p.Arg1739HisfsTer8	p.R1739Hfs*8	ENST00000373344	NM_000489.3	1739	cGa/ca	20/35	1	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	NA	0	0.51598969114579	1		300	249	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0121431-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	101	414	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.420299628050166	4	FACETS	0.989	0.885	1	0.495	0.442	0.55	CLONAL	1	NA	2	0.420299628050166	4		414	690	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875865	76875878	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TCAATTAGGTTATT	TCAATTAGGTTATT	-	novel	NA	P-0121431-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	101	272	0	ENST00000373344.5:c.5257_5270del	p.Asn1753ValfsTer6	p.N1753Vfs*6	ENST00000373344	NM_000489.3	1753	AATAACCTAATTGAg/g	20/35	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	NA	0	0.420299628050166	1		272	281	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0121431-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	94	414	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.686958529329447	4	FACETS	0.806	0.718	0.898	0.403	0.359	0.449	CLONAL	1	NA	2	0.686958529329447	4		414	573	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911841	32911841	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397507307	NA	P-0121431-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	158	493	0	ENST00000380152.3:c.3349A>G	p.Ile1117Val	p.I1117V	ENST00000380152		1117	Ata/Gta	11/27	0.623240828495804	4	FACETS	0.907	0.831	0.985	0.453	0.415	0.493	CLONAL	1	NA	2	0.686958529329447	4		493	856	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76856034	76856037	+	splice_acceptor_variant,intron_variant	Splice_Site	ONP	CTGA	CTGA	AGGT	novel	NA	P-0121431-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	88	168	0	ENST00000373344.5:c.5567-4_5567-1delinsACCT		p.X1856_splice	ENST00000373344	NM_000489.3	1856			1	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	NA	0	0.686958529329447	1		168	128	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0031318-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	20	286	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.535	0.408	0.686	0.535	0.408	0.686	SUBCLONAL	1	TRUE	1	0.15	2		286	498	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0031318-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	44	639	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.594	0.496	0.704	0.594	0.496	0.704	SUBCLONAL	1	TRUE	1	0.15	2		639	987	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193748	106193748	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs974106601	NA	P-0031318-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	16	178	1	ENST00000380013.4:c.4210C>T	p.Arg1404Ter	p.R1404*	ENST00000380013	NM_001127208.2	1404	Cga/Tga	10/11	1	2	FACETS	0.693	0.511	0.91	0.693	0.511	0.91	SUBCLONAL	1	TRUE	1	0.15	2		179	308	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347909	347909	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031318-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1344	124	1014	1	ENST00000262320.3:c.1597C>T	p.Arg533Ter	p.R533*	ENST00000262320	NM_003502.3	533	Cga/Tga	6/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.15	2		1015	1468	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482861	67482861	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031318-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	50	454	0	ENST00000327367.4:c.1265C>G	p.Ser422Cys	p.S422C	ENST00000327367	NM_005902.3	422	tCc/tGc	9/9	1	2	FACETS	0.972	0.823	1	0.972	0.823	1	CLONAL	1	TRUE	1	0.15	2		454	686	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0031686-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	178	643	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	0.866707160871608	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.867390188812971	1		643	205	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527854	157527854	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031686-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	199	686	0	ENST00000346085.5:c.5579A>T	p.Glu1860Val	p.E1860V	ENST00000346085	NM_020732.3	1860	gAa/gTa	20/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.867390188812971	2		686	420	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433352	78433352	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0031686-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	37	357	0	ENST00000370768.2:c.251-2A>G		p.X84_splice	ENST00000370768	NM_003902.3	84			1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.867390188812971	2		357	85	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15379839	15379839	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031686-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	90	505	0	ENST00000263377.2:c.300C>G	p.Ile100Met	p.I100M	ENST00000263377	NM_058243.2	100	atC/atG	3/20	1	2	FACETS	0.979	0.887	1	0.979	0.887	1	CLONAL	1	TRUE	1	0.867390188812971	2		505	212	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117639392	117639392	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031686-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	31	476	0	ENST00000368508.3:c.5964C>A	p.Asp1988Glu	p.D1988E	ENST00000368508	NM_002944.2	1988	gaC/gaA	37/43	1	2	FACETS	0.777	0.647	0.915	0.777	0.647	0.915	CLONAL	1	TRUE	1	0.867390188812971	2		476	92	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658377	117658377	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031686-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	34	699	0	ENST00000368508.3:c.5206G>C	p.Gly1736Arg	p.G1736R	ENST00000368508	NM_002944.2	1736	Gga/Cga	31/43	1	2	FACETS	0.861	0.727	1	0.861	0.727	1	CLONAL	1	TRUE	1	0.867390188812971	2		699	91	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983049	149983049	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031686-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	34	597	0	ENST00000253339.5:c.3209A>C	p.His1070Pro	p.H1070P	ENST00000253339		1070	cAt/cCt	7/7	1	2	FACETS	0.871	0.735	1	0.871	0.735	1	CLONAL	1	TRUE	1	0.867390188812971	2		597	90	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455153	50455153	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031686-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	162	523	0	ENST00000331340.3:c.700G>T	p.Gly234Cys	p.G234C	ENST00000331340	NM_006060.4	234	Ggc/Tgc	6/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.867390188812971	2		523	315	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818727	32818727	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	30	544	0	ENST00000354258.4:c.1224G>T	p.Trp408Cys	p.W408C	ENST00000354258	NM_000593.5	408	tgG/tgT	4/11	0.322968697638678	1	FACETS	0.365	0.294	0.446	0.365	0.294	0.446	SUBCLONAL	1	NA	0	0.322968697638678	1		544	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0033091-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	317	641	1	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.50508123315109	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.508281366408051	2		642	596	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214821	36214821	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033091-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	252	604	1	ENST00000222270.7:c.3247C>T	p.Arg1083Ter	p.R1083*	ENST00000222270	NM_014727.1	1083	Cga/Tga	8/37	0.508281366408051	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.508281366408051	3		605	562	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726433	46726433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145441107	NA	P-0033091-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	77	447	1	ENST00000371975.4:c.512G>A	p.Arg171Gln	p.R171Q	ENST00000371975	NM_003579.3	171	cGg/cAg	7/18	0.508281366408051	3	FACETS	0.898	0.792	1	0.449	0.396	0.506	CLONAL	1	TRUE	1	0.508281366408051	3		448	423	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087893	27087905	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCACCCAGTGG	GGCCACCCAGTGG	-	novel	NA	P-0033091-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	137	500	0	ENST00000324856.7:c.2180_2192del	p.Arg727ProfsTer11	p.R727Pfs*11	ENST00000324856	NM_006015.4	727	cGGCCACCCAGTGGc/cc	6/20	0.106677029196615	3	FACETS	1	0.982	1	0.64	0.585	0.697	INDETERMINATE	1	TRUE	1	0.508281366408051	3		500	528	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717691	89717697	+	frameshift_variant	Frame_Shift_Del	DEL	TGTACTT	TGTACTT	-	novel	NA	P-0033091-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	193	402	0	ENST00000371953.3:c.718_724del	p.Tyr240SerfsTer14	p.Y240Sfs*14	ENST00000371953	NM_000314.4	239	aTGTACTTt/at	7/9	0.50508123315109	2	FACETS	0.896	0.839	0.952	0.896	0.839	0.952	CLONAL	2	TRUE	0	0.508281366408051	2		402	424	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033279-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	102	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.925	0.84	1	0.925	0.84	1	CLONAL	1	TRUE	1	0.807974677344087	2		306	273	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0033279-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	249	432	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.94	0.884	0.996	0.94	0.884	0.996	CLONAL	1	TRUE	1	0.807974677344087	2		432	656	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0034513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	107	172	0				ENST00000310581	NM_198253.2	-/1132			0.345387687951044	1	FACETS	0.695	0.635	0.755	0.695	0.635	0.755	INDETERMINATE	1	TRUE	0	0.76993522781862	1		172	246	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0034513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	334	476	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.714918091726319	2	FACETS	0.929	0.896	0.961	0.929	0.896	0.961	CLONAL	2	TRUE	0	0.76993522781862	2		476	467	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0034513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	75	254	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.76993522781862	2		254	185	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225532	133225532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	111	439	1	ENST00000320574.5:c.4132G>A	p.Gly1378Ser	p.G1378S	ENST00000320574	NM_006231.2	1378	Ggt/Agt	32/49	0.203214682974745	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.76993522781862	0		440	352	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971202	21971203	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0034513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	128	213	0	ENST00000304494.5:c.155_156insTT	p.Met52IlefsTer2	p.M52Ifs*2	ENST00000304494	NM_000077.4	52	atg/atTTg	2/3	1	2	FACETS	0.819	0.766	0.87	1	0.991	1	CLONAL	2	TRUE	1	0.76993522781862	2		213	203	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	323	306	0				ENST00000310581	NM_198253.2	-/1132			0.308963961573597	6	FACETS	0.886	0.839	0.935	0.886	0.839	0.935	CLONAL	4	TRUE	2	0.308963961573597	6		306	954	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0034675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	313	641	1	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.308963961573597	3	FACETS	0.871	0.824	0.919	0.871	0.824	0.919	CLONAL	3	TRUE	0	0.308963961573597	3		642	895	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196653	67196653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	185	1193	2	ENST00000312629.5:c.182G>A	p.Arg61His	p.R61H	ENST00000312629	NM_003952.2	61	cGc/cAc	3/15	0.215658930150746	5	FACETS	0.845	0.78	0.913	0.563	0.52	0.609	CLONAL	2	TRUE	2	0.308963961573597	5		1195	1037	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540823	187540823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	242	1013	0	ENST00000441802.2:c.6917G>A	p.Arg2306Lys	p.R2306K	ENST00000441802	NM_005245.3	2306	aGa/aAa	10/27	0.187664142727191	3	FACETS	1	0.977	1	0.726	0.68	0.774	CLONAL	2	TRUE	0	0.308963961573597	3		1013	830	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266662	142266662	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	56	429	0	ENST00000350721.4:c.3262C>G	p.Gln1088Glu	p.Q1088E	ENST00000350721	NM_001184.3	1088	Caa/Gaa	16/47	0.217908043672456	3	FACETS	0.865	0.742	0.999	0.432	0.371	0.5	CLONAL	1	TRUE	1	0.308963961573597	3		429	484	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102096	27102097	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCCC	novel	NA	P-0034675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	69	972	0	ENST00000324856.7:c.5025_5028dup	p.Lys1677ProfsTer22	p.K1677Pfs*22	ENST00000324856	NM_006015.4	1674	-/TCCC	19/20	0.277785165487836	3	FACETS	0.657	0.571	0.75	0.328	0.285	0.375	SUBCLONAL	1	TRUE	1	0.308963961573597	3		972	785	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344714	65344714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	132	925	0	ENST00000342505.4:c.323G>A	p.Arg108Gln	p.R108Q	ENST00000342505	NM_002227.2	108	cGg/cAg	4/25	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.308963961573597	2		925	715	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40444041	40444041	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	206	1164	0	ENST00000345506.4:c.337C>G	p.Leu113Val	p.L113V	ENST00000345506	NM_003152.3	113	Ctg/Gtg	5/20	0.277785165487836	3	FACETS	0.881	0.818	0.945	0.881	0.818	0.945	CLONAL	2	TRUE	1	0.308963961573597	3		1164	874	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827980	40827980	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	65	1022	0	ENST00000373198.4:c.2448G>C	p.Glu816Asp	p.E816D	ENST00000373198	NM_133170.3	816	gaG/gaC	17/32	0.271415904273711	3	FACETS	0.556	0.481	0.638			1	SUBCLONAL	1	TRUE	NA	0.308963961573597	3		1022	873	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903701	41903701	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	103	1173	0	ENST00000372991.4:c.856G>C	p.Asp286His	p.D286H	ENST00000372991	NM_001760.3	286	Gat/Cat	5/5	1	2	FACETS	0.797	0.712	0.886	0.797	0.712	0.886	SUBCLONAL	1	TRUE	1	0.308963961573597	2		1173	837	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080645	5080645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	50	375	0	ENST00000381652.3:c.2396G>A	p.Arg799Lys	p.R799K	ENST00000381652	NM_004972.3	799	aGa/aAa	18/25	0.217908043672456	3	FACETS	0.769	0.653	0.896	0.384	0.326	0.448	SUBCLONAL	1	TRUE	1	0.308963961573597	3		375	486	SUCCESS
MTAP	4507	MSKCC	GRCh37	9	21854705	21854705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs569692278	NA	P-0034675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	170	949	0	ENST00000380172.4:c.526C>T	p.Arg176Cys	p.R176C	ENST00000380172	NM_002451.3	176	Cgt/Tgt	6/8	0.308963961573597	3	FACETS	0.876	0.808	0.947			1	CLONAL	2	TRUE	NA	0.308963961573597	3		949	725	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110175	3110178	+	missense_variant	Missense_Mutation	ONP	CATC	CATC	AATA	novel	NA	P-0034675-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	84	924	0	ENST00000078429.4:c.165_168delinsAATA	p.Phe55Leu	p.F55L	ENST00000078429	NM_002067.2	55	ttCATC/ttAATA	2/7	0.277785165487836	3	FACETS	0.873	0.771	0.983	0.437	0.385	0.492	CLONAL	1	TRUE	1	0.308963961573597	3		924	719	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880257	37880257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	281	322	0	ENST00000269571.5:c.2301C>G	p.Ile767Met	p.I767M	ENST00000269571		767	atC/atG	19/27	1	2	FACETS	0.973	0.92	1	0.973	0.92	1	CLONAL	1	TRUE	1	0.814628802500775	2		322	709	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480320	56480320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	238	387	0	ENST00000267101.3:c.427C>A	p.Leu143Met	p.L143M	ENST00000267101	NM_001982.3	143	Ctg/Atg	4/28	1	2	FACETS	0.994	0.935	1	0.994	0.935	1	CLONAL	1	TRUE	1	0.814628802500775	2		387	588	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008403	71008403	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	189	273	0	ENST00000318789.4:c.2029G>C	p.Glu677Gln	p.E677Q	ENST00000318789	NM_032682.5	677	Gag/Cag	21/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.814628802500775	2		273	447	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486587	56486587	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	330	608	0	ENST00000267101.3:c.1166C>A	p.Thr389Lys	p.T389K	ENST00000267101	NM_001982.3	389	aCa/aAa	10/28	1	2	FACETS	0.953	0.905	1	0.953	0.905	1	CLONAL	1	TRUE	1	0.814628802500775	2		608	850	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441235	52441235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910211860	NA	P-0034694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	282	519	0	ENST00000460680.1:c.535C>T	p.Arg179Trp	p.R179W	ENST00000460680	NM_004656.3	179	Cgg/Tgg	7/17	1	2	FACETS	0.945	0.892	0.997	0.945	0.892	0.997	CLONAL	1	TRUE	1	0.814628802500775	2		519	733	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023211	27023220	+	frameshift_variant	Frame_Shift_Del	DEL	ACGCGGGCCC	ACGCGGGCCC	-	novel	NA	P-0034694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	149	260	0	ENST00000324856.7:c.317_326del	p.Asn106IlefsTer5	p.N106Ifs*5	ENST00000324856	NM_006015.4	106	aACGCGGGCCCt/at	1/20	1	2	FACETS	0.845	0.779	0.912	0.845	0.779	0.912	CLONAL	1	TRUE	1	0.814628802500775	2		260	433	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442562	52442573	+	inframe_deletion	In_Frame_Del	DEL	CTTTCGCCGGGA	CTTTCGCCGGGA	-	novel	NA	P-0034694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	214	446	0	ENST00000460680.1:c.172_183del	p.Ser58_Lys61del	p.S58_K61del	ENST00000460680	NM_004656.3	58	TCCCGGCGAAAG/-	4/17	1	2	FACETS	0.833	0.778	0.888	0.833	0.778	0.888	CLONAL	1	TRUE	1	0.814628802500775	2		446	631	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843604	156843604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1044149705	NA	P-0034694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1285	530	966	2	ENST00000524377.1:c.1030G>A	p.Gly344Arg	p.G344R	ENST00000524377	NM_002529.3	344	Ggg/Agg	8/17	0.814628802500775	3	FACETS	1	0.964	1	0.504	0.482	0.527	CLONAL	1	TRUE	1	0.814628802500775	3		968	1815	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495714	56495715	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	250	457	0	ENST00000267101.3:c.3910dup	p.His1304ProfsTer12	p.H1304Pfs*12	ENST00000267101	NM_001982.3	1302	gcc/gCcc	28/28	1	2	FACETS	0.93	0.875	0.985	0.93	0.875	0.985	CLONAL	1	TRUE	1	0.814628802500775	2		457	660	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866377	42866384	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGGACG	GGGGGACG	-	novel	NA	P-0034694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	576	896	0	ENST00000398585.3:c.248_255del	p.Pro83ArgfsTer34	p.P83Rfs*34	ENST00000398585	NM_001135099.1	83	cCGTCCCCC/c	3/14	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.814628802500775	2		896	1361	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0035364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	118	284	2	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.941	0.854	1	0.941	0.854	1	CLONAL	1	TRUE	1	0.544151145805199	2		286	461	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070575	67070575	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	100	266	0	ENST00000412916.2:c.199C>T	p.Gln67Ter	p.Q67*	ENST00000412916		67	Cag/Tag	3/6	0.544151145805199	1	FACETS	0.801	0.723	0.882	0.801	0.723	0.882	CLONAL	1	TRUE	0	0.544151145805199	1		266	334	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945343	151945343	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	139	145	0	ENST00000262189.6:c.2176C>T	p.Gln726Ter	p.Q726*	ENST00000262189	NM_170606.2	726	Cag/Tag	14/59	0.544151145805199	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.544151145805199	3		145	306	SUCCESS
AR	367	MSKCC	GRCh37	X	66766109	66766109	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	309	776	0	ENST00000374690.3:c.1121C>T	p.Pro374Leu	p.P374L	ENST00000374690	NM_000044.3	374	cCg/cTg	1/8	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.544151145805199	2		776	1074	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041554-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	500	857	1	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	0.599576751276347	2	FACETS	0.934	0.904	0.965	0.934	0.904	0.965	CLONAL	2	TRUE	0	0.668915363793314	2		858	800	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587167	189587167	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1209841422	NA	P-0041554-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	123	369	0	ENST00000264731.3:c.1184C>T	p.Ser395Phe	p.S395F	ENST00000264731	NM_003722.4	395	tCc/tTc	9/14	0.502858688967616	5	FACETS	0.926	0.837	1	0.309	0.279	0.34	CLONAL	1	TRUE	2	0.668915363793314	5		369	796	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62316910	62316926	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGTTCCCCAGCAGGG	CTGGTTCCCCAGCAGGG	-	novel	NA	P-0041554-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	204	1045	0	ENST00000360203.5:c.1230_1246del	p.Ser411GlyfsTer6	p.S411Gfs*6	ENST00000360203	NM_001283009.1	409	cCTGGTTCCCCAGCAGGG/c	15/35	0.586616295603928	4	FACETS	0.859	0.795	0.925	0.286	0.265	0.309	CLONAL	1	TRUE	1	0.668915363793314	4		1045	1185	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188337	32188337	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs772628389	NA	P-0041554-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	234	1151	0	ENST00000375023.3:c.1004C>G	p.Ser335Cys	p.S335C	ENST00000375023	NM_004557.3	335	tCt/tGt	6/30	0.502858688967616	5	FACETS	1	0.967	1	0.354	0.33	0.38	CLONAL	1	TRUE	2	0.668915363793314	5		1151	1318	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849610	68849610	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041554-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	214	846	0	ENST00000261769.5:c.1513A>T	p.Ile505Phe	p.I505F	ENST00000261769	NM_004360.3	505	Atc/Ttc	10/16	0.615653203580074	2	FACETS	0.84	0.783	0.898	0.42	0.391	0.449	CLONAL	1	TRUE	0	0.668915363793314	2		846	762	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934254	48934254	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1131690904	NA	P-0042678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	227	367	0	ENST00000267163.4:c.709G>T	p.Glu237Ter	p.E237*	ENST00000267163	NM_000321.2	237	Gaa/Taa	7/27	0.971832054136245	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.971832054136245	2		367	233	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525062	187525062	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	97	503	0	ENST00000441802.2:c.10618A>T	p.Ile3540Phe	p.I3540F	ENST00000441802	NM_005245.3	3540	Atc/Ttc	19/27	1	2	FACETS	0.28	0.25	0.313	0.28	0.25	0.313	SUBCLONAL	1	TRUE	1	0.971832054136245	2		503	712	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937001	48937005	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAA	CAGAA	-	rs1566192530	NA	P-0043327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	140	554	0	ENST00000267163.4:c.772_776del	p.Asn258GlufsTer11	p.N258Efs*11	ENST00000267163	NM_000321.2	257	CAGAAc/c	8/27	0.16139369674426	3	FACETS	1	0.969	1	1	0.99	1	CLONAL	3	FALSE	1	0.208425227194088	3		554	445	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932634	39932635	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTGG	novel	NA	P-0043327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	100	614	0	ENST00000378444.4:c.1961_1964dup	p.Arg655SerfsTer11	p.R655Sfs*11	ENST00000378444	NM_001123385.1	655	agg/agCCAGg	4/15	0.208425227194088	2	FACETS	1	0.95	1			1	CLONAL	2	FALSE	NA	0.208425227194088	2		614	438	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592099	67592099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043585-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	152	255	0	ENST00000274335.5:c.1915C>T	p.Arg639Ter	p.R639*	ENST00000274335		639	Cga/Tga	14/15	1	2	FACETS	0.96	0.891	1	0.96	0.891	1	CLONAL	1	TRUE	1	0.90709779726313	2		255	349	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255680	16255689	+	frameshift_variant	Frame_Shift_Del	DEL	AAGCCAGGAA	AAGCCAGGAA	-	novel	NA	P-0043585-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	157	401	0	ENST00000375759.3:c.2948_2957del	p.Ala983GlyfsTer8	p.A983Gfs*8	ENST00000375759	NM_015001.2	982	gAAGCCAGGAAa/ga	11/15	1	2	FACETS	0.805	0.745	0.866	0.805	0.745	0.866	CLONAL	1	TRUE	1	0.90709779726313	2		401	430	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845613	128845613	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043585-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	104	492	0	ENST00000249373.3:c.910G>C	p.Gly304Arg	p.G304R	ENST00000249373	NM_005631.4	304	Ggg/Cgg	4/12	0.154092312278703	4	FACETS	0.957	0.862	1	0.478	0.431	0.529	INDETERMINATE	1	TRUE	2	0.90709779726313	4		492	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0044025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	505	1139	1	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.660342540517335	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.660342540517335	2		1140	710	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727451	66727451	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519729	NA	P-0044025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	607	593	0	ENST00000307102.5:c.167A>C	p.Gln56Pro	p.Q56P	ENST00000307102	NM_002755.3	56	cAg/cCg	2/11	0.660342540517335	4	FACETS	1	0.996	1	1	0.996	1	CLONAL	4	TRUE	0	0.660342540517335	4		593	710	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023019	150023019	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	169	683	0	ENST00000253339.5:c.244C>T	p.Arg82Ter	p.R82*	ENST00000253339		82	Cga/Tga	1/7	0.504283663141726	4	FACETS	0.869	0.798	0.943	0.434	0.399	0.472	CLONAL	1	TRUE	2	0.660342540517335	4		683	978	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938264	36938264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150616658	NA	P-0044025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	208	1296	1	ENST00000361632.4:c.697C>T	p.Arg233Trp	p.R233W	ENST00000361632		233	Cgg/Tgg	6/16	0.660342540517335	2	FACETS	0.855	0.796	0.915	0.427	0.398	0.458	CLONAL	1	TRUE	0	0.660342540517335	2		1297	737	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903747	114903747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	338	666	1	ENST00000543371.1:c.751G>A	p.Gly251Arg	p.G251R	ENST00000543371	NM_001198531.1	251	Gga/Aga	7/14	0.660342540517335	4	FACETS	0.955	0.907	1	0.477	0.453	0.502	CLONAL	2	TRUE	0	0.660342540517335	4		667	890	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127760	64127760	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	602	1242	0	ENST00000334205.4:c.253G>A	p.Glu85Lys	p.E85K	ENST00000334205	NM_003942.2	85	Gag/Aag	3/17	0.504283663141726	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	2	0.660342540517335	4		1242	1324	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451872	29451872	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	12	0	0	ENST00000389048.3:c.2693A>T	p.Glu898Val	p.E898V	ENST00000389048	NM_004304.4	898	gAg/gTg	16/29	0.660342540517335	2	FACETS	0.045	0.031	0.062	0.022	0.015	0.031	SUBCLONAL	1	TRUE	0	0.660342540517335	2		0	808	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171642	32171643	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CACCTCA	novel	NA	P-0044025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	384	943	0	ENST00000375023.3:c.3129_3135dup	p.Glu1046Ter	p.E1046*	ENST00000375023	NM_004557.3	1045	-/TGAGGTG	20/30	0.576952623464399	5	FACETS	0.93	0.884	0.978	0.62	0.589	0.652	CLONAL	2	TRUE	2	0.660342540517335	5		943	1244	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324161	62324161	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2063	240	935	0	ENST00000360203.5:c.2656G>C	p.Glu886Gln	p.E886Q	ENST00000360203	NM_001283009.1	886	Gag/Cag	29/35	0.660342540517335	10	FACETS	1	0.981	1	0.144	0.133	0.155	CLONAL	1	TRUE	2	0.660342540517335	10		935	2303	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923378	131923378	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1296577319	NA	P-0044025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	48	172	0	ENST00000265335.6:c.881A>T	p.Glu294Val	p.E294V	ENST00000265335		294	gAa/gTa	6/25	0.660342540517335	2	FACETS	0.996	0.86	1	0.498	0.43	0.569	CLONAL	1	TRUE	0	0.660342540517335	2		172	146	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884821	134884821	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0121538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	153	438	0	ENST00000398015.3:c.1597T>G	p.Ser533Ala	p.S533A	ENST00000398015	NM_004441.4	533	Tca/Gca	8/16	1	2	FACETS	0.93	0.858	1	0.93	0.858	1	CLONAL	1	NA	1	0.672603012631984	2		438	489	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32802963	32802963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0121538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	230	432	0	ENST00000374899.4:c.913G>A	p.Ala305Thr	p.A305T	ENST00000374899	NM_018833.2	305	Gca/Aca	5/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	NA	1	0.672603012631984	2		432	643	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884821	134884821	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0121538-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	305	438	0	ENST00000398015.3:c.1597T>G	p.Ser533Ala	p.S533A	ENST00000398015	NM_004441.4	533	Tca/Gca	8/16	NA	2	FACETS	1	0.952	1			1	INDETERMINATE	1	NA	NA	0.907341990136409	2		438	671	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32802963	32802963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0121538-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	333	432	0	ENST00000374899.4:c.913G>A	p.Ala305Thr	p.A305T	ENST00000374899	NM_018833.2	305	Gca/Aca	5/12	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	NA	1	0.907341990136409	2		432	733	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884821	134884821	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0121538-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	210	438	0	ENST00000398015.3:c.1597T>G	p.Ser533Ala	p.S533A	ENST00000398015	NM_004441.4	533	Tca/Gca	8/16	0.70018281531044	1	FACETS	0.563	0.528	0.598	0.563	0.528	0.598	SUBCLONAL	1	NA	0	0.867857126951853	1		438	487	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32802963	32802963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0121538-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	271	432	0	ENST00000374899.4:c.913G>A	p.Ala305Thr	p.A305T	ENST00000374899	NM_018833.2	305	Gca/Aca	5/12	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	NA	1	0.867857126951853	2		432	623	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142872	30142873	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0121538-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	356	810	0	ENST00000389048.3:c.653dup	p.Ile219AspfsTer7	p.I219Dfs*7	ENST00000389048	NM_004304.4	218	cag/caAg	1/29	0.495599944371269	4	FACETS	1	0.991	1	0.602	0.57	0.635	INDETERMINATE	1	NA	2	0.867857126951853	4		810	1273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0045809-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	651	747	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.565879603448264	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	0	0.565879603448264	3		747	975	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0045809-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	628	157	2	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.565879603448264	3	FACETS	0.954	0.926	0.981	0.954	0.926	0.981	CLONAL	3	TRUE	0	0.565879603448264	3		159	995	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31448661	31448661	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045809-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	74	438	0	ENST00000344624.3:c.2875C>T	p.Pro959Ser	p.P959S	ENST00000344624		959	Ccc/Tcc	20/33	0.565879603448264	7	FACETS	0.51	0.444	0.581			1	SUBCLONAL	1	TRUE	NA	0.565879603448264	7		438	1239	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346014	152346014	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045809-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	83	469	0	ENST00000359321.1:c.556G>C	p.Asp186His	p.D186H	ENST00000359321	NM_005431.1	186	Gac/Cac	3/3	0.285678778526407	3	FACETS	0.468	0.412	0.528	0.156	0.137	0.176	INDETERMINATE	1	TRUE	0	0.565879603448264	3		469	804	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953994	32953994	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045809-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	57	334	0	ENST00000380152.3:c.9061G>T	p.Glu3021Ter	p.E3021*	ENST00000380152		3021	Gaa/Taa	23/27	0.300220173271011	2	FACETS	0.54	0.465	0.621	0.27	0.232	0.311	INDETERMINATE	1	TRUE	0	0.565879603448264	2		334	373	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783730	50783730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045809-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	74	498	0	ENST00000398568.2:c.121G>A	p.Val41Ile	p.V41I	ENST00000398568	NM_001042412.1	41	Gta/Ata	3/18	NA	2	FACETS	0.332	0.29	0.378			1	INDETERMINATE	1	TRUE	NA	0.565879603448264	2		498	787	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79974795	79974795	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045809-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	234	541	0	ENST00000265081.6:c.1223C>G	p.Ser408Cys	p.S408C	ENST00000265081	NM_002439.4	408	tCt/tGt	8/24	0.565879603448264	3	FACETS	0.955	0.89	1			1	CLONAL	1	TRUE	NA	0.565879603448264	3		541	1111	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584556	189584556	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045809-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	76	313	0	ENST00000264731.3:c.852G>C	p.Gln284His	p.Q284H	ENST00000264731	NM_003722.4	284	caG/caC	6/14	0.565879603448264	3	FACETS	0.602	0.529	0.681	0.201	0.176	0.227	SUBCLONAL	1	TRUE	0	0.565879603448264	3		313	572	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587436	29587436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045809-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	71	333	0	ENST00000356175.3:c.4417C>T	p.His1473Tyr	p.H1473Y	ENST00000356175	NM_000267.3	1473	Cat/Tat	33/57	0.513274436539084	3	FACETS	0.493	0.43	0.561			1	SUBCLONAL	1	TRUE	NA	0.565879603448264	3		333	653	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100671	102100671	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0045809-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	40	219	0	ENST00000282441.5:c.1515G>C	p.Ter505TyrextTer6	p.*505Yext*6	ENST00000282441	NM_001130145.2	505	taG/taC	9/9	0.565879603448264	3	FACETS	0.481	0.4	0.571			1	SUBCLONAL	1	TRUE	NA	0.565879603448264	3		219	377	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493439	56493439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045809-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	84	375	0	ENST00000267101.3:c.2847G>A	p.Met949Ile	p.M949I	ENST00000267101	NM_001982.3	949	atG/atA	24/28	0.38795438591711	3	FACETS	0.605	0.534	0.68	0.202	0.178	0.227	SUBCLONAL	1	TRUE	0	0.565879603448264	3		375	630	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552237	29552237	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045809-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	66	382	0	ENST00000356175.3:c.1970C>G	p.Ser657Cys	p.S657C	ENST00000356175	NM_000267.3	657	tCt/tGt	17/57	0.513274436539084	3	FACETS	0.451	0.391	0.516			1	SUBCLONAL	1	TRUE	NA	0.565879603448264	3		382	663	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117822	70117822	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045809-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	140	500	0	ENST00000245479.2:c.290G>T	p.Gly97Val	p.G97V	ENST00000245479	NM_000346.3	97	gGc/gTc	1/3	0.317616418008637	2	FACETS	0.606	0.552	0.662	0.303	0.276	0.331	INDETERMINATE	1	TRUE	0	0.565879603448264	2		500	817	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7120684	7120684	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045809-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	129	612	0	ENST00000302850.5:c.3606G>C	p.Trp1202Cys	p.W1202C	ENST00000302850	NM_000208.2	1202	tgG/tgC	20/22	0.565879603448264	1	FACETS	0.397	0.359	0.436	0.397	0.359	0.436	SUBCLONAL	1	TRUE	0	0.565879603448264	1		612	824	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196849	138196849	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045809-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	52	250	0	ENST00000237289.4:c.511C>T	p.Leu171Phe	p.L171F	ENST00000237289	NM_001270507.1	171	Ctt/Ttt	4/9	NA	2	FACETS	0.472	0.403	0.548			1	INDETERMINATE	1	TRUE	NA	0.565879603448264	2		250	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0046022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	243	876	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.871309536279809	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.871309536279809	1		876	275	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	226	643	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	0.191939424825834	4	FACETS	1	0.949	1	1	0.949	1	INDETERMINATE	2	TRUE	2	0.871309536279809	4		643	482	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239982	98239982	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	465	648	0	ENST00000331920.6:c.1350del	p.Ala451ProfsTer5	p.A451Pfs*5	ENST00000331920	NM_000264.3	450	ctC/ct	10/24	0.871309536279809	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.871309536279809	3		648	484	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11273532	11273532	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	164	730	0	ENST00000361445.4:c.3209A>G	p.Tyr1070Cys	p.Y1070C	ENST00000361445	NM_004958.3	1070	tAc/tGc	21/58	0.191939424825834	4	FACETS	1	0.937	1	0.51	0.47	0.553	INDETERMINATE	1	TRUE	2	0.871309536279809	4		730	690	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239826	105239826	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	156	1446	2	ENST00000349310.3:c.794A>T	p.His265Leu	p.H265L	ENST00000349310	NM_001014432.1	265	cAc/cTc	10/15	0.191939424825834	4	FACETS	1	0.973	1	0.565	0.52	0.612	INDETERMINATE	1	TRUE	2	0.871309536279809	4		1448	593	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046090-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	138	276	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.400619976900964	5	FACETS	1	0.98	1	0.611	0.561	0.664	CLONAL	2	TRUE	1	0.400619976900964	5		276	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0046090-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	534	380	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.343553321270863	2	FACETS	0.906	0.868	0.943	0.906	0.868	0.943	CLONAL	2	TRUE	0	0.400619976900964	2		380	1472	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157488271	157488271	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1358728441	NA	P-0046090-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	242	506	0	ENST00000346085.5:c.2977C>T	p.Gln993Ter	p.Q993*	ENST00000346085	NM_020732.3	993	Cag/Tag	10/20	0.196875444810461	3	FACETS	0.785	0.734	0.837	0.785	0.734	0.837	INDETERMINATE	2	TRUE	1	0.400619976900964	3		506	924	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971206	21971207	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	CCTG	novel	NA	P-0046090-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	268	487	0	ENST00000304494.5:c.151-3_151dup	p.Val51AlafsTer70	p.V51Afs*70	ENST00000304494	NM_000077.4	51	gtc/gCAGGtc	2/3	0.400619976900964	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.400619976900964	1		487	804	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762263	43762263	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046090-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	40	558	0	ENST00000382044.4:c.1182T>G	p.Asp394Glu	p.D394E	ENST00000382044	NM_001141980.1	394	gaT/gaG	11/28	0.16912911983423	2	FACETS	0.405	0.336	0.482	0.203	0.168	0.241	INDETERMINATE	1	TRUE	0	0.400619976900964	2		558	493	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46596988	46596988	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150945320	NA	P-0121505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	76	398	0	ENST00000263734.3:c.802C>T	p.His268Tyr	p.H268Y	ENST00000263734	NM_001430.4	268	Cac/Tac	7/16	0.347949156820088	3	FACETS	0.882	0.775	0.996	0.441	0.387	0.498	CLONAL	1	NA	1	0.380700444807864	3		398	539	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0046499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	94	382	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.319591198540639	1	FACETS	0.843	0.766	0.921	0.843	0.766	0.921	INDETERMINATE	1	TRUE	0	0.678682770258839	1		382	217	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0046499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	76	202	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	0.319591198540639	1	FACETS	0.638	0.568	0.71	0.638	0.568	0.71	INDETERMINATE	1	TRUE	0	0.678682770258839	1		202	232	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	112	306	0				ENST00000310581	NM_198253.2	-/1132			0.3	4	FACETS	0.966	0.881	1	1	0.987	1	CLONAL	5	TRUE	1	0.18	4		306	304	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893318	32893318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507603	NA	P-0046605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	33	305	0	ENST00000380152.3:c.172G>A	p.Glu58Lys	p.E58K	ENST00000380152		58	Gaa/Aaa	3/27	0.3	3	FACETS	0.856	0.696	1	0.428	0.348	0.518	CLONAL	1	TRUE	1	0.18	3		305	467	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111012	193111012	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	63	188	0	ENST00000367435.3:c.545T>A	p.Ile182Asn	p.I182N	ENST00000367435	NM_024529.4	182	aTt/aAt	7/17	0.3	1	FACETS	0.965	0.847	1	1	0.985	1	CLONAL	3	TRUE	0	0.18	1		188	220	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26970472	26970472	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	78	167	0	ENST00000381527.3:c.841A>G	p.Lys281Glu	p.K281E	ENST00000381527	NM_001260.1	281	Aaa/Gaa	8/13	0.3	3	FACETS	1	0.942	1	1	0.981	1	CLONAL	3	TRUE	1	0.18	3		167	287	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951110	48951110	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0046605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	113	269	0	ENST00000267163.4:c.1272C>G	p.Tyr424Ter	p.Y424*	ENST00000267163	NM_000321.2	424	taC/taG	13/27	0.3	3	FACETS	0.908	0.824	0.994	1	0.988	1	CLONAL	4	TRUE	1	0.18	3		269	377	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105238728	105238728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1444891733	NA	P-0046605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	152	943	2	ENST00000349310.3:c.1234G>A	p.Val412Met	p.V412M	ENST00000349310	NM_001014432.1	412	Gtg/Atg	13/15	0.125976876973739	3	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	1	0.18	3		945	894	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710596	117710596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	35	332	0	ENST00000368508.3:c.1676G>A	p.Gly559Asp	p.G559D	ENST00000368508	NM_002944.2	559	gGc/gAc	12/43	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.18	2		332	307	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338689	70338914	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCAAACAGAAGGAGGTGCGTTCGAAAATCGGGGCTCTGGAGGGGCCGGGGGCACGCGGTCAGCCTAGGAGGAGGCACTGACGGCTGGGAATGGGGGGCGGGGCGGTTCGGTGAGAGCAAAAGTCCCGAAAGGGGGAAGAGTAAAGTGGGCTGGCGTGGGAGGGCAGGACGGGGGGCGGTGGGGGGTTCCAAGGTATGAATAGGGGGTGGTGTAGGGGCCGCACCA	CCCAAACAGAAGGAGGTGCGTTCGAAAATCGGGGCTCTGGAGGGGCCGGGGGCACGCGGTCAGCCTAGGAGGAGGCACTGACGGCTGGGAATGGGGGGCGGGGCGGTTCGGTGAGAGCAAAAGTCCCGAAAGGGGGAAGAGTAAAGTGGGCTGGCGTGGGAGGGCAGGACGGGGGGCGGTGGGGGGTTCCAAGGTATGAATAGGGGGTGGTGTAGGGGCCGCACCA	-	novel	NA	P-0046605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	89	384	0	ENST00000374080.3:c.85_99+211del		p.X29_splice	ENST00000374080		29		1/45	0.104068692741518	2	FACETS	0.987	0.883	1			1	INDETERMINATE	3	TRUE	NA	0.18	2		384	334	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870853	12870853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500190	NA	P-0046605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	23	278	1	ENST00000228872.4:c.80C>T	p.Ser27Leu	p.S27L	ENST00000228872	NM_004064.3	27	tCg/tTg	1/3	1	2	FACETS	0.671	0.522	0.843	0.671	0.522	0.843	SUBCLONAL	1	TRUE	1	0.18	2		279	381	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458033	120458033	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	48	687	2	ENST00000256646.2:c.7312G>A	p.Asp2438Asn	p.D2438N	ENST00000256646	NM_024408.3	2438	Gat/Aat	34/34	0.125976876973739	3	FACETS	0.935	0.789	1	0.467	0.394	0.548	CLONAL	1	TRUE	1	0.18	3		689	622	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518560	204518560	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0046605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	19	318	0	ENST00000367182.3:c.1223C>G	p.Ser408Ter	p.S408*	ENST00000367182	NM_001278516.1	408	tCa/tGa	11/11	0.3	1	FACETS	0.667	0.506	0.856	0.667	0.506	0.856	SUBCLONAL	1	TRUE	0	0.18	1		318	288	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222277	2222277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	62	997	1	ENST00000398665.3:c.3109C>T	p.Pro1037Ser	p.P1037S	ENST00000398665	NM_032482.2	1037	Cct/Tct	24/28	1	2	FACETS	0.768	0.662	0.884	0.768	0.662	0.884	SUBCLONAL	1	TRUE	1	0.18	2		998	897	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168991	32168991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	56	1051	5	ENST00000375023.3:c.4042G>A	p.Glu1348Lys	p.E1348K	ENST00000375023	NM_004557.3	1348	Gaa/Aaa	22/30	0.3	5	FACETS	0.734	0.627	0.853	0.245	0.209	0.285	SUBCLONAL	1	TRUE	2	0.18	5		1056	1076	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249758	39249758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	29	413	0	ENST00000402219.2:c.1811G>A	p.Gly604Glu	p.G604E	ENST00000402219	NM_005633.3	604	gGa/gAa	10/23	1	2	FACETS	0.736	0.59	0.902	0.736	0.59	0.902	CLONAL	1	TRUE	1	0.18	2		413	438	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265192	5265192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760753054	NA	P-0046605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	58	923	0	ENST00000357368.4:c.395C>T	p.Ser132Phe	p.S132F	ENST00000357368	NM_002850.3	132	tCt/tTt	5/38	1	2	FACETS	0.905	0.777	1	0.905	0.777	1	CLONAL	1	TRUE	1	0.18	2		923	712	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446227	187446227	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	50	938	0	ENST00000232014.4:c.1461G>C	p.Glu487Asp	p.E487D	ENST00000232014	NM_001130845.1	487	gaG/gaC	6/10	0.0750015773141495	4	FACETS	0.71	0.601	0.832	0.355	0.3	0.416	INDETERMINATE	1	TRUE	2	0.18	4		938	923	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248520	59248520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	48	813	2	ENST00000371222.2:c.223G>A	p.Glu75Lys	p.E75K	ENST00000371222	NM_002228.3	75	Gag/Aag	1/1	0.125976876973739	3	FACETS	0.644	0.542	0.756	0.322	0.271	0.378	SUBCLONAL	1	TRUE	1	0.18	3		815	903	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464986	120464986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	38	483	0	ENST00000256646.2:c.5086G>A	p.Gly1696Arg	p.G1696R	ENST00000256646	NM_024408.3	1696	Ggg/Agg	28/34	0.125976876973739	3	FACETS	0.817	0.675	0.977	0.409	0.337	0.489	CLONAL	1	TRUE	1	0.18	3		483	563	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444726	49444726	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	73	1208	1	ENST00000301067.7:c.2740G>C	p.Glu914Gln	p.E914Q	ENST00000301067	NM_003482.3	914	Gag/Cag	10/54	0.0750015773141495	4	FACETS	0.837	0.73	0.954	0.419	0.365	0.477	INDETERMINATE	1	TRUE	2	0.18	4		1209	1143	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347482	89347482	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs372569223	NA	P-0046605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	49	829	0	ENST00000301030.4:c.5468C>G	p.Ser1823Cys	p.S1823C	ENST00000301030	NM_001256183.1	1823	tCt/tGt	9/13	0.3	3	FACETS	0.835	0.705	0.977	0.417	0.352	0.489	CLONAL	1	TRUE	1	0.18	3		829	711	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657620	37657620	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	46	547	0	ENST00000447079.4:c.2537G>C	p.Gly846Ala	p.G846A	ENST00000447079	NM_015083.1	846	gGa/gCa	6/14	0.3	3	FACETS	0.889	0.747	1	0.444	0.373	0.523	CLONAL	1	TRUE	1	0.18	3		547	627	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865266	40865266	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	59	725	0	ENST00000428826.2:c.1165G>C	p.Asp389His	p.D389H	ENST00000428826		389	Gac/Cac	11/21	0.3	3	FACETS	0.846	0.726	0.977	0.423	0.363	0.489	CLONAL	1	TRUE	1	0.18	3		725	845	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278168	15278168	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	53	988	0	ENST00000263388.2:c.5254C>A	p.Gln1752Lys	p.Q1752K	ENST00000263388	NM_000435.2	1752	Caa/Aaa	29/33	1	2	FACETS	0.714	0.607	0.831	0.714	0.607	0.831	SUBCLONAL	1	TRUE	1	0.18	2		988	825	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62293239	62293239	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	52	762	0	ENST00000360203.5:c.338C>G	p.Ser113Cys	p.S113C	ENST00000360203	NM_001283009.1	113	tCc/tGc	4/35	0.125976876973739	3	FACETS	0.707	0.6	0.825	0.353	0.3	0.413	SUBCLONAL	1	TRUE	1	0.18	3		762	891	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140549992	140549992	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	30	275	0	ENST00000288602.6:c.159G>A	p.Met53Ile	p.M53I	ENST00000288602	NM_004333.4	53	atG/atA	2/18	0.0750015773141495	4	FACETS	0.978	0.788	1	0.489	0.394	0.597	INDETERMINATE	1	TRUE	2	0.18	4		275	402	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148526844	148526844	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	27	289	0	ENST00000320356.2:c.460G>C	p.Asp154His	p.D154H	ENST00000320356	NM_004456.4	154	Gat/Cat	5/20	0.0750015773141495	4	FACETS	0.885	0.704	1	0.443	0.352	0.546	INDETERMINATE	1	TRUE	2	0.18	4		289	400	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782121	135782121	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	37	397	0	ENST00000298552.3:c.1435del	p.Glu479LysfsTer53	p.E479Kfs*53	ENST00000298552	NM_001162426.1	479	Gaa/aa	14/23	0.169414383696331	2	FACETS	0.991	0.817	1	0.495	0.408	0.592	CLONAL	1	TRUE	0	0.18	2		397	415	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046605-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	48	306	0				ENST00000310581	NM_198253.2	-/1132			0.216340488889371	3	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	1	0.216340488889371	3		306	216	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893318	32893318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507603	NA	P-0046605-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	45	305	0	ENST00000380152.3:c.172G>A	p.Glu58Lys	p.E58K	ENST00000380152		58	Gaa/Aaa	3/27	0.216340488889371	6	FACETS	1	0.854	1	0.204	0.171	0.24	CLONAL	1	TRUE	1	0.216340488889371	6		305	585	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24133968	24133968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046605-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	43	369	0	ENST00000263121.7:c.119G>A	p.Arg40Gln	p.R40Q	ENST00000263121	NM_003073.3	40	cGa/cAa	2/9	1	2	FACETS	0.942	0.789	1	0.942	0.789	1	CLONAL	1	TRUE	1	0.216340488889371	2		369	422	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111012	193111012	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046605-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	73	188	0	ENST00000367435.3:c.545T>A	p.Ile182Asn	p.I182N	ENST00000367435	NM_024529.4	182	aTt/aAt	7/17	0.216340488889371	3	FACETS	0.92	0.814	1	0.92	0.814	1	CLONAL	3	TRUE	0	0.216340488889371	3		188	271	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36821013	36821013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046605-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	95	780	1	ENST00000373129.3:c.364G>A	p.Glu122Lys	p.E122K	ENST00000373129	NM_032017.1	122	Gag/Aag	6/12	0.216340488889371	6	FACETS	1	0.972	1			1	CLONAL	1	TRUE	NA	0.216340488889371	6		781	965	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26970472	26970472	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046605-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	98	167	0	ENST00000381527.3:c.841A>G	p.Lys281Glu	p.K281E	ENST00000381527	NM_001260.1	281	Aaa/Gaa	8/13	0.119918273628026	3	FACETS	0.979	0.882	1			1	INDETERMINATE	3	TRUE	NA	0.216340488889371	3		167	342	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951110	48951110	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0046605-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	188	269	0	ENST00000267163.4:c.1272C>G	p.Tyr424Ter	p.Y424*	ENST00000267163	NM_000321.2	424	taC/taG	13/27	0.216340488889371	6	FACETS	0.958	0.892	1	0.958	0.892	1	CLONAL	5	TRUE	1	0.216340488889371	6		269	520	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105238728	105238728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1444891733	NA	P-0046605-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	92	943	2	ENST00000349310.3:c.1234G>A	p.Val412Met	p.V412M	ENST00000349310	NM_001014432.1	412	Gtg/Atg	13/15	0.216340488889371	3	FACETS	1	0.956	1	0.578	0.513	0.648	CLONAL	1	TRUE	1	0.216340488889371	3		945	815	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130419	29130419	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046605-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	64	695	0	ENST00000328354.6:c.291G>A	p.Trp97Ter	p.W97*	ENST00000328354	NM_007194.3	97	tgG/tgA	2/15	1	2	FACETS	0.996	0.863	1	0.996	0.863	1	CLONAL	1	TRUE	1	0.216340488889371	2		695	594	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710596	117710596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046605-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	81	332	0	ENST00000368508.3:c.1676G>A	p.Gly559Asp	p.G559D	ENST00000368508	NM_002944.2	559	gGc/gAc	12/43	0.100422389221441	4	FACETS	0.906	0.805	1	1	0.974	1	INDETERMINATE	3	TRUE	2	0.216340488889371	4		332	335	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6045547	6045547	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs766203500	NA	P-0046605-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	41	331	0	ENST00000265849.7:c.139C>G	p.Leu47Val	p.L47V	ENST00000265849	NM_000535.5	47	Ctg/Gtg	2/15	0.216340488889371	5	FACETS	1	0.901	1	0.373	0.31	0.442	CLONAL	1	TRUE	2	0.216340488889371	5		331	449	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338689	70338914	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCAAACAGAAGGAGGTGCGTTCGAAAATCGGGGCTCTGGAGGGGCCGGGGGCACGCGGTCAGCCTAGGAGGAGGCACTGACGGCTGGGAATGGGGGGCGGGGCGGTTCGGTGAGAGCAAAAGTCCCGAAAGGGGGAAGAGTAAAGTGGGCTGGCGTGGGAGGGCAGGACGGGGGGCGGTGGGGGGTTCCAAGGTATGAATAGGGGGTGGTGTAGGGGCCGCACCA	CCCAAACAGAAGGAGGTGCGTTCGAAAATCGGGGCTCTGGAGGGGCCGGGGGCACGCGGTCAGCCTAGGAGGAGGCACTGACGGCTGGGAATGGGGGGCGGGGCGGTTCGGTGAGAGCAAAAGTCCCGAAAGGGGGAAGAGTAAAGTGGGCTGGCGTGGGAGGGCAGGACGGGGGGCGGTGGGGGGTTCCAAGGTATGAATAGGGGGTGGTGTAGGGGCCGCACCA	-	novel	NA	P-0046605-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	83	384	0	ENST00000374080.3:c.85_99+211del		p.X29_splice	ENST00000374080		29		1/45	0.216340488889371	2	FACETS	1	0.951	1			1	CLONAL	2	TRUE	NA	0.216340488889371	2		384	341	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649942	88649942	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760515128	NA	P-0046605-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	48	577	0	ENST00000372037.3:c.191C>T	p.Ser64Leu	p.S64L	ENST00000372037	NM_004329.2	64	tCa/tTa	4/13	0.172585068401382	4	FACETS	0.672	0.567	0.789	0.336	0.283	0.395	SUBCLONAL	1	TRUE	2	0.216340488889371	4		577	803	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549035	21549035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046605-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	34	310	0	ENST00000382592.4:c.3241G>A	p.Glu1081Lys	p.E1081K	ENST00000382592	NM_014572.2	1081	Gaa/Aaa	8/8	0.216340488889371	5	FACETS	1	0.909	1			1	CLONAL	1	TRUE	NA	0.216340488889371	5		310	350	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107195	27107195	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046605-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	49	603	0	ENST00000324856.7:c.6806C>A	p.Ser2269Ter	p.S2269*	ENST00000324856	NM_006015.4	2269	tCa/tAa	20/20	0.216340488889371	6	FACETS	0.748	0.631	0.877			1	SUBCLONAL	1	TRUE	NA	0.216340488889371	6		603	868	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628452	187628452	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs745890477	NA	P-0046605-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	87	755	0	ENST00000441802.2:c.2530G>T	p.Val844Phe	p.V844F	ENST00000441802	NM_005245.3	844	Gtt/Ttt	2/27	0.16574298307261	3	FACETS	1	0.931	1	0.537	0.475	0.604	CLONAL	1	TRUE	1	0.216340488889371	3		755	830	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106316	27106316	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046605-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	60	724	0	ENST00000324856.7:c.5927C>G	p.Ser1976Cys	p.S1976C	ENST00000324856	NM_006015.4	1976	tCt/tGt	20/20	0.216340488889371	6	FACETS	0.868	0.745	1			1	CLONAL	1	TRUE	NA	0.216340488889371	6		724	916	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106812	27106812	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046605-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	89	759	0	ENST00000324856.7:c.6423C>A	p.Phe2141Leu	p.F2141L	ENST00000324856	NM_006015.4	2141	ttC/ttA	20/20	0.216340488889371	6	FACETS	1	0.963	1			1	CLONAL	1	TRUE	NA	0.216340488889371	6		759	965	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831306	89831306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046605-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	74	731	0	ENST00000389301.3:c.2770G>A	p.Asp924Asn	p.D924N	ENST00000389301	NM_000135.2	924	Gat/Aat	28/43	0.167579929688591	4	FACETS	1	0.932	1	0.367	0.321	0.417	CLONAL	1	TRUE	1	0.216340488889371	4		731	756	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375550	15375550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046605-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	90	1085	0	ENST00000263377.2:c.877G>A	p.Asp293Asn	p.D293N	ENST00000263377	NM_058243.2	293	Gac/Aac	6/20	0.216340488889371	2	FACETS	0.983	0.872	1	0.492	0.436	0.552	CLONAL	1	TRUE	0	0.216340488889371	2		1085	846	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793154	42793154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046605-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	56	1176	1	ENST00000575354.2:c.1046C>T	p.Ser349Leu	p.S349L	ENST00000575354	NM_015125.3	349	tCa/tTa	7/20	0.216340488889371	6	FACETS	0.668	0.57	0.775			1	SUBCLONAL	1	TRUE	NA	0.216340488889371	6		1177	1111	SUCCESS
APC	324	MSKCC	GRCh37	5	112176446	112176446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046605-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	27	272	0	ENST00000257430.4:c.5155G>A	p.Glu1719Lys	p.E1719K	ENST00000257430	NM_000038.5	1719	Gag/Aag	16/16	0.216340488889371	3	FACETS	0.816	0.65	1	0.408	0.325	0.503	CLONAL	1	TRUE	1	0.216340488889371	3		272	339	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932369	39932369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046605-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	81	511	0	ENST00000378444.4:c.2230G>A	p.Glu744Lys	p.E744K	ENST00000378444	NM_001123385.1	744	Gag/Aag	4/15	0.216340488889371	2	FACETS	0.787	0.695	0.884			1	SUBCLONAL	2	TRUE	NA	0.216340488889371	2		511	476	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046605-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	161	306	0				ENST00000310581	NM_198253.2	-/1132			0.427630666665282	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.431551608618686	2		306	326	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893318	32893318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507603	NA	P-0046605-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	46	305	0	ENST00000380152.3:c.172G>A	p.Glu58Lys	p.E58K	ENST00000380152		58	Gaa/Aaa	3/27	0.431551608618686	5	FACETS	0.944	0.797	1	0.236	0.199	0.277	CLONAL	1	TRUE	1	0.431551608618686	5		305	372	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721812	49721812	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs142690032	NA	P-0046605-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	13	20	0	ENST00000449682.2:c.1951C>T	p.Arg651Ter	p.R651*	ENST00000449682	NM_020998.3	651	Cga/Tga	17/18	0.431551608618686	3	FACETS	1	0.834	1	1	0.834	1	CLONAL	2	TRUE	1	0.431551608618686	3		20	32	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24133968	24133968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046605-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	71	369	0	ENST00000263121.7:c.119G>A	p.Arg40Gln	p.R40Q	ENST00000263121	NM_003073.3	40	cGa/cAa	2/9	1	2	FACETS	0.906	0.796	1	0.906	0.796	1	CLONAL	1	TRUE	1	0.431551608618686	2		369	363	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111012	193111012	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046605-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	96	188	0	ENST00000367435.3:c.545T>A	p.Ile182Asn	p.I182N	ENST00000367435	NM_024529.4	182	aTt/aAt	7/17	0.431551608618686	3	FACETS	0.944	0.864	1	0.944	0.864	1	CLONAL	3	TRUE	0	0.431551608618686	3		188	191	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36821013	36821013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046605-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	113	780	1	ENST00000373129.3:c.364G>A	p.Glu122Lys	p.E122K	ENST00000373129	NM_032017.1	122	Gag/Aag	6/12	0.409306089784632	4	FACETS	0.84	0.756	0.931	0.28	0.252	0.311	CLONAL	1	TRUE	1	0.431551608618686	4		781	892	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26970472	26970472	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046605-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	88	167	0	ENST00000381527.3:c.841A>G	p.Lys281Glu	p.K281E	ENST00000381527	NM_001260.1	281	Aaa/Gaa	8/13	0.431551608618686	5	FACETS	1	0.967	1	0.866	0.786	0.947	CLONAL	3	TRUE	1	0.431551608618686	5		167	194	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951110	48951110	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0046605-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	193	269	0	ENST00000267163.4:c.1272C>G	p.Tyr424Ter	p.Y424*	ENST00000267163	NM_000321.2	424	taC/taG	13/27	0.431551608618686	5	FACETS	0.976	0.925	1	1	0.99	1	CLONAL	5	TRUE	1	0.431551608618686	5		269	302	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105238728	105238728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1444891733	NA	P-0046605-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	131	943	2	ENST00000349310.3:c.1234G>A	p.Val412Met	p.V412M	ENST00000349310	NM_001014432.1	412	Gtg/Atg	13/15	0.431551608618686	3	FACETS	0.976	0.887	1	0.488	0.443	0.535	CLONAL	1	TRUE	1	0.431551608618686	3		945	756	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130419	29130419	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046605-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	113	695	0	ENST00000328354.6:c.291G>A	p.Trp97Ter	p.W97*	ENST00000328354	NM_007194.3	97	tgG/tgA	2/15	1	2	FACETS	0.983	0.888	1	0.983	0.888	1	CLONAL	1	TRUE	1	0.431551608618686	2		695	533	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710596	117710596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046605-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	60	332	0	ENST00000368508.3:c.1676G>A	p.Gly559Asp	p.G559D	ENST00000368508	NM_002944.2	559	gGc/gAc	12/43	0.403156788763688	3	FACETS	0.926	0.802	1	0.463	0.401	0.53	CLONAL	1	TRUE	1	0.431551608618686	3		332	365	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6045547	6045547	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs766203500	NA	P-0046605-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	61	331	0	ENST00000265849.7:c.139C>G	p.Leu47Val	p.L47V	ENST00000265849	NM_000535.5	47	Ctg/Gtg	2/15	0.140157693020841	6	FACETS	1	0.967	1	0.475	0.411	0.543	INDETERMINATE	1	TRUE	3	0.431551608618686	6		331	370	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338689	70338914	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCAAACAGAAGGAGGTGCGTTCGAAAATCGGGGCTCTGGAGGGGCCGGGGGCACGCGGTCAGCCTAGGAGGAGGCACTGACGGCTGGGAATGGGGGGCGGGGCGGTTCGGTGAGAGCAAAAGTCCCGAAAGGGGGAAGAGTAAAGTGGGCTGGCGTGGGAGGGCAGGACGGGGGGCGGTGGGGGGTTCCAAGGTATGAATAGGGGGTGGTGTAGGGGCCGCACCA	CCCAAACAGAAGGAGGTGCGTTCGAAAATCGGGGCTCTGGAGGGGCCGGGGGCACGCGGTCAGCCTAGGAGGAGGCACTGACGGCTGGGAATGGGGGGCGGGGCGGTTCGGTGAGAGCAAAAGTCCCGAAAGGGGGAAGAGTAAAGTGGGCTGGCGTGGGAGGGCAGGACGGGGGGCGGTGGGGGGTTCCAAGGTATGAATAGGGGGTGGTGTAGGGGCCGCACCA	-	novel	NA	P-0046605-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	184	384	0	ENST00000374080.3:c.85_99+211del		p.X29_splice	ENST00000374080		29		1/45	0.431551608618686	2	FACETS	0.851	0.801	0.901			1	CLONAL	3	TRUE	NA	0.431551608618686	2		384	334	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649942	88649942	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760515128	NA	P-0046605-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	56	577	0	ENST00000372037.3:c.191C>T	p.Ser64Leu	p.S64L	ENST00000372037	NM_004329.2	64	tCa/tTa	4/13	0.431551608618686	3	FACETS	0.661	0.567	0.764	0.331	0.283	0.382	SUBCLONAL	1	TRUE	1	0.431551608618686	3		577	477	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549035	21549035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046605-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	50	310	0	ENST00000382592.4:c.3241G>A	p.Glu1081Lys	p.E1081K	ENST00000382592	NM_014572.2	1081	Gaa/Aaa	8/8	0.431551608618686	5	FACETS	0.974	0.829	1	0.243	0.207	0.283	CLONAL	1	TRUE	1	0.431551608618686	5		310	392	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500369	99500369	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046605-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	108	582	0	ENST00000268035.6:c.3802G>C	p.Glu1268Gln	p.E1268Q	ENST00000268035	NM_000875.3	1268	Gag/Cag	21/21	0.403156788763688	3	FACETS	0.843	0.757	0.934	0.421	0.378	0.467	CLONAL	1	TRUE	1	0.431551608618686	3		582	722	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047321-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	15	306	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		306	115	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0047321-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	51	432	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		432	300	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0047321-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	10	402	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		402	328	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762959	40762959	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs387906659	NA	P-0047321-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	64	726	0	ENST00000392038.2:c.49G>A	p.Glu17Lys	p.E17K	ENST00000392038	NM_001626.4	17	Gaa/Aaa	3/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		726	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0048215-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	14	867	9	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		876	462	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0048215-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	14	464	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.214381994407056	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		464	535	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649101	37649101	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	39	378	0	ENST00000447079.4:c.2206G>C	p.Gly736Arg	p.G736R	ENST00000447079	NM_015083.1	736	Gga/Cga	4/14	0.449171641167953	1	FACETS	0.46	0.382	0.545	0.46	0.382	0.545	SUBCLONAL	1	TRUE	0	0.449171641167953	1		378	293	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435793	110435793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761634910	NA	P-0048454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	48	320	0	ENST00000375856.3:c.2608G>A	p.Val870Met	p.V870M	ENST00000375856	NM_003749.2	870	Gtg/Atg	1/2	0.449171641167953	2	FACETS	0.786	0.669	0.912	0.393	0.334	0.456	CLONAL	1	TRUE	0	0.449171641167953	2		320	272	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38064133	38064133	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1157025978	NA	P-0048454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	42	441	0	ENST00000250448.2:c.45G>C	p.Trp15Cys	p.W15C	ENST00000250448	NM_004496.3	15	tgG/tgC	1/2	0.169463809483042	4	FACETS	0.626	0.523	0.74	0.313	0.261	0.37	INDETERMINATE	1	TRUE	2	0.449171641167953	4		441	433	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106912	27106912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	71	773	0	ENST00000324856.7:c.6523G>A	p.Ala2175Thr	p.A2175T	ENST00000324856	NM_006015.4	2175	Gct/Act	20/20	1	2	FACETS	0.437	0.381	0.498	0.437	0.381	0.498	SUBCLONAL	1	TRUE	1	0.449171641167953	2		773	723	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531747	46531748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCATA	novel	NA	P-0048454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	54	324	0	ENST00000262741.5:c.595_599dup	p.Glu200AspfsTer14	p.E200Dfs*14	ENST00000262741	NM_003629.3	200	gaa/gaTATGAa	5/10	1	2	FACETS	0.771	0.662	0.888	0.771	0.662	0.888	SUBCLONAL	1	TRUE	1	0.449171641167953	2		324	312	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467904	99467904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	83	366	0	ENST00000268035.6:c.2773C>T	p.Gln925Ter	p.Q925*	ENST00000268035	NM_000875.3	925	Cag/Tag	13/21	0.449171641167953	1	FACETS	0.94	0.838	1	0.94	0.838	1	CLONAL	1	TRUE	0	0.449171641167953	1		366	305	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18963797	18963797	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	73	357	0	ENST00000262803.5:c.974C>T	p.Thr325Ile	p.T325I	ENST00000262803	NM_002911.3	325	aCt/aTt	7/24	0.232999894938909	1	FACETS	0.714	0.629	0.805	0.714	0.629	0.805	INDETERMINATE	1	TRUE	0	0.449171641167953	1		357	353	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872377	45872377	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	200	823	0	ENST00000391945.4:c.134G>C	p.Gly45Ala	p.G45A	ENST00000391945	NM_000400.3	45	gGc/gCc	3/23	0.449171641167953	3	FACETS	1	0.984	1	0.605	0.56	0.65	CLONAL	1	TRUE	1	0.449171641167953	3		823	902	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468385	89468385	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0048454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	27	236	0	ENST00000336596.2:c.1919T>G	p.Leu640Ter	p.L640*	ENST00000336596	NM_005233.5	640	tTa/tGa	11/17	0.232999894938909	1	FACETS	0.405	0.324	0.497	0.405	0.324	0.497	INDETERMINATE	1	TRUE	0	0.449171641167953	1		236	230	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002728	37002728	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	161	800	0	ENST00000358127.4:c.521del	p.Ser174TrpfsTer104	p.S174Wfs*104	ENST00000358127	NM_001280556.1	174	tCg/tg	5/10	0.181895017165134	1	FACETS	0.85	0.782	0.92	0.85	0.782	0.92	INDETERMINATE	1	TRUE	0	0.449171641167953	1		800	654	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904878	101904890	+	frameshift_variant	Frame_Shift_Del	DEL	TTGATTACTTAAA	TTGATTACTTAAA	-	novel	NA	P-0048454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	69	358	0	ENST00000374994.4:c.866_878del	p.Phe289SerfsTer10	p.F289Sfs*10	ENST00000374994	NM_004612.2	289	tTTGATTACTTAAAc/tc	5/9	0.449171641167953	1	FACETS	0.879	0.774	0.99	0.879	0.774	0.99	CLONAL	1	TRUE	0	0.449171641167953	1		358	271	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821229	72821229	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1326500716	NA	P-0048454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	72	772	0	ENST00000268489.5:c.10946C>T	p.Ser3649Leu	p.S3649L	ENST00000268489	NM_006885.3	3649	tCa/tTa	10/10	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.449171641167953	NA		772	698	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843541	156843541	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	86	981	0	ENST00000524377.1:c.967A>G	p.Asn323Asp	p.N323D	ENST00000524377	NM_002529.3	323	Aat/Gat	8/17	0.181895017165134	1	FACETS	0.385	0.34	0.433	0.385	0.34	0.433	INDETERMINATE	1	TRUE	0	0.449171641167953	1		981	771	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241007	133241007	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	80	858	1	ENST00000320574.5:c.2510T>A	p.Phe837Tyr	p.F837Y	ENST00000320574	NM_006231.2	837	tTc/tAc	22/49	1	2	FACETS	0.453	0.398	0.512	0.453	0.398	0.512	SUBCLONAL	1	TRUE	1	0.449171641167953	2		859	787	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651549	52651549	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1412410494	NA	P-0048454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	43	370	0	ENST00000394830.3:c.1547A>G	p.Lys516Arg	p.K516R	ENST00000394830	NM_018313.4	516	aAg/aGg	15/30	0.181895017165134	1	FACETS	0.536	0.451	0.629	0.536	0.451	0.629	INDETERMINATE	1	TRUE	0	0.449171641167953	1		370	277	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1064795203	NA	P-0048835-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2	25	438	0	ENST00000269305.4:c.532C>G	p.His178Asp	p.H178D	ENST00000269305	NM_001126112.2	178	Cac/Gac	5/11	0.917724873959076	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.917724873959076	1		438	27	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440019	220440019	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048835-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	56	813	0	ENST00000243786.2:c.872G>C	p.Cys291Ser	p.C291S	ENST00000243786	NM_002191.3	291	tGt/tCt	2/2	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.917724873959076	2		813	120	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645693	12645693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397516827	NA	P-0049179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	161	549	0	ENST00000251849.4:c.776C>T	p.Ser259Phe	p.S259F	ENST00000251849	NM_002880.3	259	tCc/tTc	7/17	1	2	FACETS	0.972	0.892	1	0.972	0.892	1	CLONAL	1	TRUE	1	0.41580978806402	2		549	797	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220505	1220505	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs886039554	NA	P-0049179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	178	816	0	ENST00000326873.7:c.597+1G>T		p.X199_splice	ENST00000326873	NM_000455.4	199			0.41580978806402	1	FACETS	0.904	0.835	0.976	0.904	0.835	0.976	CLONAL	1	TRUE	0	0.41580978806402	1		816	750	SUCCESS
BLM	641	MSKCC	GRCh37	15	91333968	91333968	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	145	534	0	ENST00000355112.3:c.2913G>C	p.Glu971Asp	p.E971D	ENST00000355112	NM_000057.2	971	gaG/gaC	15/22	1	2	FACETS	0.957	0.874	1	0.957	0.874	1	CLONAL	1	TRUE	1	0.41580978806402	2		534	729	SUCCESS
SLFN11	91607	MSKCC	GRCh37	17	33689963	33689963	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	173	598	0	ENST00000308377.4:c.864A>C	p.Gln288His	p.Q288H	ENST00000308377	NM_152270.3	288	caA/caC	2/5	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.41580978806402	2		598	829	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391215	89391215	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	123	523	0	ENST00000336596.2:c.1282del	p.Val428SerfsTer14	p.V428Sfs*14	ENST00000336596	NM_005233.5	427	gcG/gc	5/17	1	2	FACETS	0.819	0.742	0.901	0.819	0.742	0.901	CLONAL	1	TRUE	1	0.41580978806402	2		523	722	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665327	117665327	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1308794945	NA	P-0049179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	107	507	0	ENST00000368508.3:c.4420A>G	p.Asn1474Asp	p.N1474D	ENST00000368508	NM_002944.2	1474	Aac/Gac	27/43	1	2	FACETS	0.799	0.718	0.885	0.799	0.718	0.885	SUBCLONAL	1	TRUE	1	0.41580978806402	2		507	644	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426532	47426532	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0049179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	154	860	1	ENST00000377045.4:c.873+2T>A		p.X291_splice	ENST00000377045	NM_001654.4	291			1	2	FACETS	0.756	0.691	0.824	0.756	0.691	0.824	SUBCLONAL	1	TRUE	1	0.41580978806402	2		861	980	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410219	63410219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049179-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	121	757	0	ENST00000330258.3:c.2948C>T	p.Pro983Leu	p.P983L	ENST00000330258	NM_152424.3	983	cCt/cTt	2/2	1	2	FACETS	0.773	0.699	0.851	0.773	0.699	0.851	SUBCLONAL	1	TRUE	1	0.41580978806402	2		757	753	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0049711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	67	421	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.2953863830404	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.387746568033748	1		421	244	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285675	46285675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1201192337	NA	P-0049711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	90	305	0	ENST00000334344.6:c.5035C>T	p.Arg1679Trp	p.R1679W	ENST00000334344	NM_152641.2	1679	Cgg/Tgg	17/21	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.387746568033748	2		305	448	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740867	58740867	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049833-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	24	0	0	ENST00000305921.3:c.1772G>C	p.Gly591Ala	p.G591A	ENST00000305921	NM_003620.3	591	gGa/gCa	6/6	1	2	FACETS	0.151	0.118	0.19	0.151	0.118	0.19	SUBCLONAL	1	TRUE	1	0.59	2		0	538	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339373	116339373	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049833-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	18	0	0	ENST00000397752.3:c.235C>T	p.Gln79Ter	p.Q79*	ENST00000397752	NM_000245.2	79	Cag/Tag	2/21	1	2	FACETS	0.149	0.112	0.194	0.149	0.112	0.194	SUBCLONAL	1	TRUE	1	0.59	2		0	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0050107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	359	968	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.580383015594402	2	FACETS	0.919	0.88	0.959	0.919	0.88	0.959	CLONAL	2	TRUE	0	0.580383015594402	2		968	673	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650710	67650710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243010179	NA	P-0050107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	125	552	0	ENST00000264010.4:c.1015C>T	p.Arg339Trp	p.R339W	ENST00000264010	NM_006565.3	339	Cgg/Tgg	5/12	0.563457959060857	2	FACETS	0.617	0.559	0.678	0.309	0.279	0.339	SUBCLONAL	1	TRUE	0	0.580383015594402	2		552	698	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578421	7578421	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	357	700	2	ENST00000269305.4:c.509C>A	p.Thr170Lys	p.T170K	ENST00000269305	NM_001126112.2	170	aCg/aAg	5/11	0.580383015594402	2	FACETS	0.951	0.91	0.991	0.951	0.91	0.991	CLONAL	2	TRUE	0	0.580383015594402	2		702	647	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120842	115120842	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	141	661	0	ENST00000257566.3:c.164C>A	p.Ser55Ter	p.S55*	ENST00000257566	NM_016569.3	55	tCg/tAg	1/8	0.301342670824948	3	FACETS	1	0.982	1	0.631	0.578	0.685	INDETERMINATE	1	TRUE	1	0.580383015594402	3		661	497	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633349	3633349	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs749720194	NA	P-0050107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	169	791	1	ENST00000294008.3:c.4902C>G	p.Tyr1634Ter	p.Y1634*	ENST00000294008	NM_032444.2	1634	taC/taG	14/15	0.536612280854611	4	FACETS	0.959	0.881	1	0.32	0.293	0.347	CLONAL	1	TRUE	1	0.580383015594402	4		792	960	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390295	56390295	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	47	368	0	ENST00000348428.3:c.1034C>A	p.Ala345Asp	p.A345D	ENST00000348428	NM_006785.3	345	gCc/gAc	10/17	0.133155134801189	0	FACETS	0.4	0.343	0.46			1	INDETERMINATE	1	TRUE	0	0.580383015594402	0		368	170	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538169	187538169	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050107-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	61	486	0	ENST00000441802.2:c.9065T>G	p.Val3022Gly	p.V3022G	ENST00000441802	NM_005245.3	3022	gTt/gGt	11/27	0.461814000554094	4	FACETS	1	0.958	1			1	CLONAL	1	TRUE	NA	0.580383015594402	4		486	264	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	310	306	0				ENST00000310581	NM_198253.2	-/1132			0.65271167866579	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	4	TRUE	0	0.65271167866579	4		306	384	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	401	706	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.507007007607916	3	FACETS	0.87	0.831	0.909	0.87	0.831	0.909	CLONAL	2	TRUE	1	0.65271167866579	3		706	937	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059260	27059260	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	134	486	0	ENST00000324856.7:c.1897C>T	p.Gln633Ter	p.Q633*	ENST00000324856	NM_006015.4	633	Cag/Tag	4/20	1	2	FACETS	0.782	0.714	0.853	0.782	0.714	0.853	SUBCLONAL	1	TRUE	1	0.65271167866579	2		486	525	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	627	770	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.507007007607916	3	FACETS	0.875	0.85	0.9	1	0.997	1	CLONAL	3	TRUE	1	0.65271167866579	3		770	971	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913315	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	38	772	1	ENST00000326873.7:c.580G>A	p.Asp194Asn	p.D194N	ENST00000326873	NM_000455.4	194	Gac/Aac	4/10	1	2	FACETS	0.15	0.123	0.18	0.15	0.123	0.18	SUBCLONAL	1	TRUE	1	0.65271167866579	2		773	776	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920463	50920463	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	204	885	0	ENST00000440232.2:c.3155C>G	p.Ser1052Trp	p.S1052W	ENST00000440232	NM_002691.3	1052	tCg/tGg	26/27	0.65271167866579	4	FACETS	0.755	0.698	0.814	0.252	0.232	0.272	SUBCLONAL	1	TRUE	1	0.65271167866579	4		885	1369	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872105	76872105	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	96	410	1	ENST00000373344.5:c.5542C>T	p.Gln1848Ter	p.Q1848*	ENST00000373344	NM_000489.3	1848	Cag/Tag	22/35	0.395232485355929	4	FACETS	0.951	0.851	1	0.476	0.425	0.529	CLONAL	1	TRUE	2	0.65271167866579	4		411	511	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877455	89877455	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	180	610	0	ENST00000389301.3:c.308C>G	p.Ser103Ter	p.S103*	ENST00000389301	NM_000135.2	103	tCa/tGa	4/43	1	2	FACETS	0.796	0.736	0.857	0.796	0.736	0.857	SUBCLONAL	1	TRUE	1	0.65271167866579	2		610	693	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397107	397107	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	22	327	0	ENST00000380956.4:c.493-1G>C		p.X165_splice	ENST00000380956	NM_001195286.1	165			NA	2	FACETS	0.202	0.156	0.256			1	INDETERMINATE	1	TRUE	NA	0.65271167866579	2		327	333	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263992	104263992	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758001170	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	86	356	0	ENST00000369902.3:c.83C>T	p.Ser28Leu	p.S28L	ENST00000369902	NM_016169.3	28	tCg/tTg	1/12	1	2	FACETS	0.662	0.589	0.739	0.662	0.589	0.739	SUBCLONAL	1	TRUE	1	0.65271167866579	2		356	398	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640791	3640791	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	200	886	0	ENST00000294008.3:c.2848G>C	p.Glu950Gln	p.E950Q	ENST00000294008	NM_032444.2	950	Gag/Cag	12/15	0.548702323032814	2	FACETS	0.789	0.733	0.847	0.394	0.366	0.424	SUBCLONAL	1	TRUE	0	0.65271167866579	2		886	777	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31423030	31423030	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	98	468	0	ENST00000344624.3:c.3283C>T	p.Arg1095Ter	p.R1095*	ENST00000344624		1095	Cga/Tga	26/33	0.65271167866579	4	FACETS	0.592	0.528	0.661	0.148	0.132	0.166	SUBCLONAL	1	TRUE	0	0.65271167866579	4		468	838	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109308772	109308772	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	61	202	0	ENST00000436639.2:c.1631G>C	p.Arg544Thr	p.R544T	ENST00000436639	NM_014454.2	544	aGa/aCa	10/10	0.644371166681566	3	FACETS	0.76	0.66	0.868	0.38	0.33	0.434	SUBCLONAL	1	TRUE	1	0.65271167866579	3		202	326	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221930	98221930	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs768039033	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	125	594	0	ENST00000331920.6:c.2839G>C	p.Glu947Gln	p.E947Q	ENST00000331920	NM_000264.3	947	Gaa/Caa	17/24	0.52177411797959	3	FACETS	0.648	0.587	0.713	0.216	0.195	0.238	SUBCLONAL	1	TRUE	0	0.65271167866579	3		594	784	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147508	47147508	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	33	427	1	ENST00000409792.3:c.4818C>A	p.Phe1606Leu	p.F1606L	ENST00000409792	NM_014159.6	1606	ttC/ttA	6/21	0.52825281645004	3	FACETS	0.246	0.2	0.299	0.123	0.1	0.15	SUBCLONAL	1	TRUE	1	0.65271167866579	3		428	545	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072553	5072553	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	63	327	0	ENST00000381652.3:c.1703G>C	p.Gly568Ala	p.G568A	ENST00000381652	NM_004972.3	568	gGa/gCa	13/25	0.52177411797959	3	FACETS	0.595	0.516	0.681	0.198	0.172	0.227	SUBCLONAL	1	TRUE	0	0.65271167866579	3		327	430	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106045	27106045	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	147	522	0	ENST00000324856.7:c.5656G>C	p.Glu1886Gln	p.E1886Q	ENST00000324856	NM_006015.4	1886	Gag/Cag	20/20	1	2	FACETS	0.863	0.793	0.936	0.863	0.793	0.936	CLONAL	1	TRUE	1	0.65271167866579	2		522	522	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106770	27106770	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	74	683	0	ENST00000324856.7:c.6381C>G	p.Ile2127Met	p.I2127M	ENST00000324856	NM_006015.4	2127	atC/atG	20/20	1	2	FACETS	0.332	0.29	0.377	0.332	0.29	0.377	SUBCLONAL	1	TRUE	1	0.65271167866579	2		683	683	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818442	43818442	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1244	131	483	0	ENST00000372470.3:c.1907G>C	p.Ter636SerextTer?	p.*636Sext*?	ENST00000372470	NM_005373.2	636	tGa/tCa	12/12	0.65271167866579	6	FACETS	0.673	0.609	0.741			1	SUBCLONAL	1	TRUE	NA	0.65271167866579	6		483	1375	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46714183	46714183	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	120	564	0	ENST00000371975.4:c.4-1G>C		p.X2_splice	ENST00000371975	NM_003579.3	2			0.546142313019898	4	FACETS	0.712	0.642	0.785			1	SUBCLONAL	1	TRUE	NA	0.65271167866579	4		564	854	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248427	59248427	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1302903080	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	337	641	1	ENST00000371222.2:c.316G>A	p.Glu106Lys	p.E106K	ENST00000371222	NM_002228.3	106	Gag/Aag	1/1	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.65271167866579	NA		642	1041	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65349143	65349143	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	125	438	0	ENST00000342505.4:c.22G>C	p.Glu8Gln	p.E8Q	ENST00000342505	NM_002227.2	8	Gag/Cag	3/25	0.500776350102683	6	FACETS	0.864	0.781	0.952			1	CLONAL	1	TRUE	NA	0.65271167866579	6		438	1022	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262249	115262249	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	125	363	0	ENST00000438362.2:c.2305C>T	p.Leu769Phe	p.L769F	ENST00000438362	NM_001242891.1	769	Ctt/Ttt	18/20	0.65271167866579	4	FACETS	0.911	0.826	1			1	CLONAL	1	TRUE	NA	0.65271167866579	4		363	695	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514014	125514014	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	160	435	0	ENST00000428830.2:c.952C>T	p.Gln318Ter	p.Q318*	ENST00000428830	NM_001114121.2	318	Cag/Tag	10/14	1	2	FACETS	0.988	0.913	1	0.988	0.913	1	CLONAL	1	TRUE	1	0.65271167866579	2		435	496	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49423206	49423206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	181	744	0	ENST00000301067.7:c.14053C>T	p.His4685Tyr	p.H4685Y	ENST00000301067	NM_003482.3	4685	Cac/Tac	43/54	0.507007007607916	3	FACETS	0.73	0.673	0.789	0.365	0.336	0.395	SUBCLONAL	1	TRUE	1	0.65271167866579	3		744	1008	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218405	69218405	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	83	392	0	ENST00000462284.1:c.497C>G	p.Ser166Cys	p.S166C	ENST00000462284	NM_002392.5	166	tCt/tGt	7/11	0.507007007607916	3	FACETS	0.613	0.542	0.689	0.307	0.271	0.345	SUBCLONAL	1	TRUE	1	0.65271167866579	3		392	550	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42026730	42026730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376993513	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	96	333	0	ENST00000219905.7:c.3854C>T	p.Ser1285Phe	p.S1285F	ENST00000219905	NM_001164273.1	1285	tCt/tTt	12/24	0.548702323032814	2	FACETS	0.795	0.714	0.88	0.398	0.357	0.44	SUBCLONAL	1	TRUE	0	0.65271167866579	2		333	370	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003799	45003799	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	141	565	0	ENST00000558401.1:c.55G>C	p.Glu19Gln	p.E19Q	ENST00000558401	NM_004048.2	19	Gag/Cag	1/4	0.548702323032814	2	FACETS	0.787	0.72	0.856	0.393	0.36	0.428	SUBCLONAL	1	TRUE	0	0.65271167866579	2		565	549	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122890	2122890	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	113	787	0	ENST00000219476.3:c.2261C>G	p.Pro754Arg	p.P754R	ENST00000219476	NM_000548.3	754	cCa/cGa	21/42	0.548702323032814	2	FACETS	0.446	0.401	0.493	0.223	0.2	0.247	SUBCLONAL	1	TRUE	0	0.65271167866579	2		787	777	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647741	2647741	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	157	594	0	ENST00000342085.4:c.1644G>C	p.Gln548His	p.Q548H	ENST00000342085	NM_002613.4	548	caG/caC	14/14	0.548702323032814	2	FACETS	0.832	0.766	0.901	0.416	0.383	0.451	CLONAL	1	TRUE	0	0.65271167866579	2		594	578	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819774	81819774	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	67	548	0	ENST00000359376.3:c.180G>C	p.Lys60Asn	p.K60N	ENST00000359376	NM_002661.3	60	aaG/aaC	2/33	1	2	FACETS	0.332	0.288	0.379	0.332	0.288	0.379	SUBCLONAL	1	TRUE	1	0.65271167866579	2		548	619	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944221	81944221	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	81	820	0	ENST00000359376.3:c.1830C>G	p.Ile610Met	p.I610M	ENST00000359376	NM_002661.3	610	atC/atG	18/33	1	2	FACETS	0.301	0.265	0.341	0.301	0.265	0.341	SUBCLONAL	1	TRUE	1	0.65271167866579	2		820	824	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349833	89349833	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	105	970	0	ENST00000301030.4:c.3117G>C	p.Glu1039Asp	p.E1039D	ENST00000301030	NM_001256183.1	1039	gaG/gaC	9/13	1	2	FACETS	0.284	0.253	0.316	0.284	0.253	0.316	SUBCLONAL	1	TRUE	1	0.65271167866579	2		970	1134	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351329	89351329	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	69	898	0	ENST00000301030.4:c.1621C>T	p.Gln541Ter	p.Q541*	ENST00000301030	NM_001256183.1	541	Cag/Tag	9/13	1	2	FACETS	0.225	0.195	0.257	0.225	0.195	0.257	SUBCLONAL	1	TRUE	1	0.65271167866579	2		898	940	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573949	7573949	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	373	731	0	ENST00000269305.4:c.1078G>C	p.Gly360Arg	p.G360R	ENST00000269305	NM_001126112.2	360	Ggg/Cgg	10/11	0.507007007607916	3	FACETS	0.817	0.778	0.856	0.817	0.778	0.856	CLONAL	2	TRUE	1	0.65271167866579	3		731	928	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456650	40456650	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	213	776	0	ENST00000345506.4:c.1360G>C	p.Glu454Gln	p.E454Q	ENST00000345506	NM_003152.3	454	Gag/Cag	12/20	0.507007007607916	3	FACETS	0.86	0.799	0.924	0.43	0.399	0.462	CLONAL	1	TRUE	1	0.65271167866579	3		776	1006	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41209073	41209073	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	57	574	0	ENST00000357654.3:c.5273G>C	p.Arg1758Thr	p.R1758T	ENST00000357654	NM_007294.3	1758	aGa/aCa	19/23	0.507007007607916	3	FACETS	0.29	0.248	0.336	0.145	0.124	0.168	SUBCLONAL	1	TRUE	1	0.65271167866579	3		574	800	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758753	41758753	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	179	723	0	ENST00000301178.4:c.1807G>A	p.Val603Ile	p.V603I	ENST00000301178	NM_021913.4	603	Gtc/Atc	16/20	0.65271167866579	4	FACETS	0.669	0.615	0.726	0.223	0.205	0.242	SUBCLONAL	1	TRUE	1	0.65271167866579	4		723	1354	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165386	47165386	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	228	395	0	ENST00000409792.3:c.740C>G	p.Pro247Arg	p.P247R	ENST00000409792	NM_014159.6	247	cCa/cGa	3/21	0.52825281645004	3	FACETS	0.917	0.864	0.971	0.917	0.864	0.971	CLONAL	2	TRUE	1	0.65271167866579	3		395	505	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165630	47165630	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	246	500	0	ENST00000409792.3:c.496C>G	p.Pro166Ala	p.P166A	ENST00000409792	NM_014159.6	166	Cca/Gca	3/21	0.52825281645004	3	FACETS	0.833	0.785	0.882	0.833	0.785	0.882	CLONAL	2	TRUE	1	0.65271167866579	3		500	600	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911440	134911440	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	35	443	0	ENST00000398015.3:c.1908del	p.Arg637ValfsTer2	p.R637Vfs*2	ENST00000398015	NM_004441.4	635	aaG/aa	11/16	0.52825281645004	3	FACETS	0.225	0.183	0.271	0.112	0.091	0.136	SUBCLONAL	1	TRUE	1	0.65271167866579	3		443	633	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274778	142274778	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	26	353	0	ENST00000350721.4:c.2282C>G	p.Ser761Cys	p.S761C	ENST00000350721	NM_001184.3	761	tCt/tGt	10/47	0.507007007607916	3	FACETS	0.21	0.165	0.261	0.105	0.082	0.131	SUBCLONAL	1	TRUE	1	0.65271167866579	3		353	504	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637218	176637218	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	67	636	0	ENST00000439151.2:c.1818G>C	p.Lys606Asn	p.K606N	ENST00000439151	NM_022455.4	606	aaG/aaC	5/23	1	2	FACETS	0.314	0.272	0.359	0.314	0.272	0.359	SUBCLONAL	1	TRUE	1	0.65271167866579	2		636	654	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176700758	176700758	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	39	294	0	ENST00000439151.2:c.5595G>C	p.Lys1865Asn	p.K1865N	ENST00000439151	NM_022455.4	1865	aaG/aaC	17/23	1	2	FACETS	0.332	0.275	0.395	0.332	0.275	0.395	SUBCLONAL	1	TRUE	1	0.65271167866579	2		294	360	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056283	180056283	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	240	939	0	ENST00000261937.6:c.961G>A	p.Glu321Lys	p.E321K	ENST00000261937	NM_182925.4	321	Gag/Aag	7/30	1	2	FACETS	0.817	0.764	0.872	0.817	0.764	0.872	CLONAL	1	TRUE	1	0.65271167866579	2		939	900	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778143	27778143	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	85	807	0	ENST00000369163.2:c.292G>C	p.Glu98Gln	p.E98Q	ENST00000369163	NM_003536.2	98	Gag/Cag	1/1	0.65271167866579	4	FACETS	0.357	0.314	0.403	0.179	0.157	0.202	SUBCLONAL	1	TRUE	2	0.65271167866579	4		807	1205	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955149	93955149	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	113	411	0	ENST00000369303.4:c.2749C>G	p.Gln917Glu	p.Q917E	ENST00000369303	NM_004440.3	917	Caa/Gaa	16/17	0.644371166681566	3	FACETS	0.917	0.829	1	0.458	0.414	0.505	CLONAL	1	TRUE	1	0.65271167866579	3		411	501	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001581	150001581	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	88	347	0	ENST00000253339.5:c.2023C>G	p.Gln675Glu	p.Q675E	ENST00000253339		675	Caa/Gaa	4/7	0.644371166681566	3	FACETS	0.864	0.77	0.963	0.432	0.385	0.482	CLONAL	1	TRUE	1	0.65271167866579	3		347	414	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977558	2977558	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	72	651	0	ENST00000396946.4:c.1126G>C	p.Glu376Gln	p.E376Q	ENST00000396946	NM_032415.4	376	Gag/Cag	8/25	0.65271167866579	3	FACETS	0.353	0.308	0.402	0.176	0.154	0.201	SUBCLONAL	1	TRUE	1	0.65271167866579	3		651	829	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418982	116418982	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	72	217	0	ENST00000397752.3:c.3493C>G	p.Leu1165Val	p.L1165V	ENST00000397752	NM_000245.2	1165	Ctt/Gtt	17/21	1	2	FACETS	0.955	0.847	1	0.955	0.847	1	CLONAL	1	TRUE	1	0.65271167866579	2		217	231	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285689	87285689	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	145	639	0	ENST00000277120.3:c.26G>C	p.Gly9Ala	p.G9A	ENST00000277120		9	gGa/gCa	2/19	0.52177411797959	3	FACETS	0.797	0.729	0.869	0.266	0.243	0.29	SUBCLONAL	1	TRUE	0	0.65271167866579	3		639	739	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932661	39932661	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	194	1099	0	ENST00000378444.4:c.1938C>G	p.Phe646Leu	p.F646L	ENST00000378444	NM_001123385.1	646	ttC/ttG	4/15	0.395232485355929	4	FACETS	0.738	0.681	0.798	0.369	0.34	0.399	SUBCLONAL	1	TRUE	2	0.65271167866579	4		1099	1331	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949104	44949104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	148	486	0	ENST00000377967.4:c.3665C>T	p.Ala1222Val	p.A1222V	ENST00000377967	NM_021140.2	1222	gCa/gTa	25/29	0.395232485355929	4	FACETS	0.942	0.861	1	0.471	0.43	0.513	CLONAL	1	TRUE	2	0.65271167866579	4		486	796	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224193	53224193	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	242	923	0	ENST00000375401.3:c.3358G>C	p.Glu1120Gln	p.E1120Q	ENST00000375401	NM_004187.3	1120	Gag/Cag	22/26	0.395232485355929	4	FACETS	0.913	0.851	0.977	0.456	0.425	0.489	CLONAL	1	TRUE	2	0.65271167866579	4		923	1343	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0050287-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	462	590	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.319363701777407	3	FACETS	1	0.961	1			1	CLONAL	3	TRUE	NA	0.319363701777407	3		590	1115	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242651	46242651	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050287-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	52	191	0	ENST00000334344.6:c.1613G>C	p.Cys538Ser	p.C538S	ENST00000334344	NM_152641.2	538	tGt/tCt	13/21	NA	2	FACETS	1	0.903	1			1	INDETERMINATE	1	TRUE	NA	0.319363701777407	2		191	304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0050287-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	175	681	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.319363701777407	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.319363701777407	1		681	916	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244766	41244912	+	inframe_deletion	In_Frame_Del	DEL	CTGCAGTGATATTAACTGTCTGTACAGGCTTGATATTAGACTCATTCTTTCCTTGATTTTCTTCCTTTTGTTCACATTCAAAAGTGACTTTTGGACTTTGTTTCTTTAAGGACCCAGAGTGGGCAGAGAATGTTGCACATTCCTCTT	CTGCAGTGATATTAACTGTCTGTACAGGCTTGATATTAGACTCATTCTTTCCTTGATTTTCTTCCTTTTGTTCACATTCAAAAGTGACTTTTGGACTTTGTTTCTTTAAGGACCCAGAGTGGGCAGAGAATGTTGCACATTCCTCTT	-	novel	NA	P-0050287-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	48	445	0	ENST00000357654.3:c.2636_2782del	p.Glu879_Ala927del	p.E879_A927del	ENST00000357654	NM_007294.3	879	gAAGAGGAATGTGCAACATTCTCTGCCCACTCTGGGTCCTTAAAGAAACAAAGTCCAAAAGTCACTTTTGAATGTGAACAAAAGGAAGAAAATCAAGGAAAGAATGAGTCTAATATCAAGCCTGTACAGACAGTTAATATCACTGCAGgc/ggc	10/23	0.319363701777407	2	FACETS	0.324	0.272	0.38	0.162	0.136	0.19	SUBCLONAL	1	TRUE	0	0.319363701777407	2		445	929	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535430	66535430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050287-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	149	495	0	ENST00000273854.3:c.31C>T	p.Arg11Cys	p.R11C	ENST00000273854	NM_004439.5	11	Cgc/Tgc	1/18	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.319363701777407	2		495	724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579349	7579349	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050487-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	323	877	1	ENST00000269305.4:c.338T>C	p.Phe113Ser	p.F113S	ENST00000269305	NM_001126112.2	113	tTc/tCc	4/11	0.472263197589367	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.472263197589367	1		878	1040	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151834002	151834002	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs748426014	NA	P-0050487-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	167	467	0	ENST00000262189.6:c.14651A>G	p.Tyr4884Cys	p.Y4884C	ENST00000262189	NM_170606.2	4884	tAt/tGt	59/59	0.161634980781715	3	FACETS	1	0.987	1	0.671	0.619	0.726	INDETERMINATE	1	TRUE	1	0.472263197589367	3		467	651	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050685-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	193	306	0				ENST00000310581	NM_198253.2	-/1132			0.581388873511836	1	FACETS	0.398	0.371	0.426	0.398	0.371	0.426	SUBCLONAL	1	TRUE	0	0.938696838315899	1		306	548	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833924	44833924	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0050685-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	355	406	0	ENST00000377967.4:c.348C>G	p.Tyr116Ter	p.Y116*	ENST00000377967	NM_021140.2	116	taC/taG	4/29	0.4971874323204	1	FACETS	0.644	0.617	0.671	0.644	0.617	0.671	INDETERMINATE	1	TRUE	0	0.938696838315899	1		406	623	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870966	12870966	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050685-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	371	430	0	ENST00000228872.4:c.193C>T	p.Gln65Ter	p.Q65*	ENST00000228872	NM_004064.3	65	Cag/Tag	1/3	0.4971874323204	1	FACETS	0.678	0.651	0.704	0.678	0.651	0.704	INDETERMINATE	1	TRUE	0	0.938696838315899	1		430	619	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0050685-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	362	402	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	1	2	FACETS	0.978	0.933	1	0.978	0.933	1	CLONAL	1	TRUE	1	0.938696838315899	2		402	789	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211778	5211778	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs370553812	NA	P-0050685-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	532	614	0	ENST00000357368.4:c.5057G>A	p.Arg1686Gln	p.R1686Q	ENST00000357368	NM_002850.3	1686	cGg/cAg	33/38	0.575091113037601	1	FACETS	0.71	0.687	0.733	0.71	0.687	0.733	SUBCLONAL	1	TRUE	0	0.938696838315899	1		614	847	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217872	7217875	+	frameshift_variant	Frame_Shift_Del	DEL	CTTC	CTTC	-	novel	NA	P-0050685-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	700	521	0	ENST00000380728.2:c.136_139del	p.Glu46AsnfsTer16	p.E46Nfs*16	ENST00000380728		46	GAAGaa/aa	3/11	0.917821207573966	2	FACETS	0.968	0.954	0.981	0.968	0.954	0.981	CLONAL	2	TRUE	0	0.938696838315899	2		521	770	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183592	10183592	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050685-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	805	841	0	ENST00000256474.2:c.61G>A	p.Glu21Lys	p.E21K	ENST00000256474	NM_000551.3	21	Gaa/Aaa	1/3	1	2	FACETS	0.944	0.914	0.974	0.944	0.914	0.974	CLONAL	1	TRUE	1	0.938696838315899	2		841	1817	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505435	25505435	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050685-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1593	300	712	0	ENST00000264709.3:c.323G>A	p.Gly108Glu	p.G108E	ENST00000264709	NM_175629.2	108	gGg/gAg	4/23	0.938696838315899	3	FACETS	0.496	0.465	0.528	0.248	0.232	0.264	SUBCLONAL	1	TRUE	1	0.938696838315899	3		712	1893	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94963999	94963999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318902387	NA	P-0050685-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	318	297	0	ENST00000536441.1:c.26C>T	p.Ser9Leu	p.S9L	ENST00000536441	NM_144665.3	9	tCg/tTg	1/10	0.4971874323204	1	FACETS	0.754	0.724	0.783	0.754	0.724	0.783	INDETERMINATE	1	TRUE	0	0.938696838315899	1		297	477	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727420	66727420	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050685-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	182	400	0	ENST00000307102.5:c.136C>A	p.Gln46Lys	p.Q46K	ENST00000307102	NM_002755.3	46	Cag/Aag	2/11	0.938696838315899	2	FACETS	0.403	0.372	0.436	0.202	0.186	0.218	SUBCLONAL	1	TRUE	0	0.938696838315899	2		400	962	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137833	64137833	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050685-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	412	1006	0	ENST00000334205.4:c.1934A>T	p.Glu645Val	p.E645V	ENST00000334205	NM_003942.2	645	gAg/gTg	15/17	0.4971874323204	1	FACETS	0.341	0.324	0.358	0.341	0.324	0.358	INDETERMINATE	1	TRUE	0	0.938696838315899	1		1006	1367	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418391	49418391	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1337235778	NA	P-0050685-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	496	597	0	ENST00000301067.7:c.16022C>G	p.Ser5341Ter	p.S5341*	ENST00000301067	NM_003482.3	5341	tCa/tGa	50/54	1	2	FACETS	0.951	0.913	0.989	0.951	0.913	0.989	CLONAL	1	TRUE	1	0.938696838315899	2		597	1111	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542057	187542057	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050685-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	199	380	0	ENST00000441802.2:c.5683G>A	p.Gly1895Arg	p.G1895R	ENST00000441802	NM_005245.3	1895	Gga/Aga	10/27	0.4971874323204	1	FACETS	0.378	0.352	0.405	0.378	0.352	0.405	INDETERMINATE	1	TRUE	0	0.938696838315899	1		380	595	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051210-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	87	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.979	0.876	1	0.979	0.876	1	CLONAL	1	TRUE	1	0.582887758663153	2		306	305	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624537	93624537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237227040	NA	P-0051210-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	316	886	0	ENST00000375746.1:c.628G>A	p.Glu210Lys	p.E210K	ENST00000375746	NM_001174167.1	210	Gaa/Aaa	4/14	0.582887758663153	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.582887758663153	2		886	515	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069437	30069437	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051210-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	180	904	0	ENST00000338641.4:c.1303del	p.Val435CysfsTer4	p.V435Cfs*4	ENST00000338641	NM_000268.3	434	gaG/ga	12/16	0.582887758663153	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.582887758663153	1		904	396	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182277	38182277	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051210-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	163	915	0	ENST00000396334.3:c.713A>T	p.Asp238Val	p.D238V	ENST00000396334	NM_002468.4	238	gAt/gTt	4/5	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.582887758663153	2		915	515	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562738	29562739	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555615472	NA	P-0051210-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	177	635	0	ENST00000356175.3:c.3822_3823del	p.Phe1275ProfsTer8	p.F1275Pfs*8	ENST00000356175	NM_000267.3	1273	aCT/a	28/57	0.582887758663153	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.582887758663153	1		635	367	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0051294-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	31	584	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.233913383302886	3	FACETS	1	0.95	1	0.737	0.616	0.865	INDETERMINATE	1	TRUE	1	0.646936565389274	3		584	86	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0051294-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	13	526	1	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	0.233913383302886	3	FACETS	0.419	0.301	0.561	0.209	0.15	0.281	INDETERMINATE	1	TRUE	1	0.646936565389274	3		527	127	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251839	212251839	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051294-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	49	354	1	ENST00000342788.4:c.3220G>A	p.Glu1074Lys	p.E1074K	ENST00000342788	NM_005235.2	1074	Gaa/Aaa	27/28	0.233913383302886	3	FACETS	0.903	0.79	1	0.903	0.79	1	INDETERMINATE	2	TRUE	1	0.646936565389274	3		355	111	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458878	120458878	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051294-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	33	803	0	ENST00000256646.2:c.6467C>G	p.Ser2156Cys	p.S2156C	ENST00000256646	NM_024408.3	2156	tCt/tGt	34/34	0.521229647614842	4	FACETS	1	0.927	1			1	CLONAL	1	TRUE	NA	0.646936565389274	4		803	135	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256735	16256735	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051294-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	65	497	0	ENST00000375759.3:c.4000G>T	p.Glu1334Ter	p.E1334*	ENST00000375759	NM_015001.2	1334	Gaa/Taa	11/15	0.233913383302886	3	FACETS	0.773	0.685	0.864	0.773	0.685	0.864	INDETERMINATE	2	TRUE	1	0.646936565389274	3		497	172	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799201	45799201	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051294-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	58	686	2	ENST00000450313.1:c.232C>T	p.Gln78Ter	p.Q78*	ENST00000450313	NM_012222.2	78	Cag/Tag	3/16	0.233913383302886	3	FACETS	1	0.902	1	1	0.902	1	INDETERMINATE	2	TRUE	1	0.646936565389274	3		688	117	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425263	49425263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051294-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	89	1061	5	ENST00000301067.7:c.13225G>A	p.Glu4409Lys	p.E4409K	ENST00000301067	NM_003482.3	4409	Gag/Aag	39/54	0.232497522329838	4	FACETS	0.938	0.859	1			1	INDETERMINATE	3	TRUE	NA	0.646936565389274	4		1066	161	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249332	133249332	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1275423655	NA	P-0051294-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	56	933	3	ENST00000320574.5:c.1567G>C	p.Glu523Gln	p.E523Q	ENST00000320574	NM_006231.2	523	Gag/Cag	15/49	0.646936565389274	3	FACETS	0.983	0.852	1	0.492	0.426	0.562	CLONAL	1	TRUE	1	0.646936565389274	3		936	233	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954040	32954040	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051294-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	55	347	2	ENST00000380152.3:c.9107A>C	p.Gln3036Pro	p.Q3036P	ENST00000380152		3036	cAa/cCa	23/27	0.646936565389274	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.646936565389274	1		349	98	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350954	89350954	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs747922528	NA	P-0051294-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	55	842	1	ENST00000301030.4:c.1996C>T	p.Gln666Ter	p.Q666*	ENST00000301030	NM_001256183.1	666	Cag/Tag	9/13	0.646936565389274	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.646936565389274	1		843	88	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528752	157528752	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051294-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	54	550	1	ENST00000346085.5:c.6477G>C	p.Leu2159Phe	p.L2159F	ENST00000346085	NM_020732.3	2159	ttG/ttC	20/20	0.646936565389274	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.646936565389274	1		551	99	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946451	2946451	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051294-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	37	970	2	ENST00000396946.4:c.3286G>C	p.Glu1096Gln	p.E1096Q	ENST00000396946	NM_032415.4	1096	Gag/Cag	25/25	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.646936565389274	2		972	106	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813107	76813107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051294-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	32	376	0	ENST00000373344.5:c.6514G>A	p.Glu2172Lys	p.E2172K	ENST00000373344	NM_000489.3	2172	Gaa/Aaa	30/35	0.233913383302886	3	FACETS	0.949	0.783	1	0.474	0.391	0.565	INDETERMINATE	1	TRUE	1	0.646936565389274	3		376	138	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332828	70332828	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051294-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	47	618	0	ENST00000373644.4:c.733C>G	p.Gln245Glu	p.Q245E	ENST00000373644	NM_030625.2	245	Cag/Gag	2/12	0.233913383302886	3	FACETS	1	0.924	1	0.562	0.482	0.647	INDETERMINATE	1	TRUE	1	0.646936565389274	3		618	171	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664577	29664577	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051294-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	13	366	0	ENST00000356175.3:c.6556G>C	p.Glu2186Gln	p.E2186Q	ENST00000356175	NM_000267.3	2186	Gaa/Caa	42/57	1	2	FACETS	0.324	0.233	0.434	0.324	0.233	0.434	SUBCLONAL	1	TRUE	1	0.646936565389274	2		366	124	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128018827	128018827	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051294-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	31	505	0	ENST00000285398.2:c.2041G>C	p.Val681Leu	p.V681L	ENST00000285398	NM_000122.1	681	Gta/Cta	13/15	0.564469042342844	2	FACETS	1	0.847	1	0.51	0.424	0.601	CLONAL	1	TRUE	0	0.646936565389274	2		505	94	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051681-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	270	276	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.587594163371306	2	FACETS	0.945	0.9	0.99	0.945	0.9	0.99	CLONAL	2	TRUE	0	0.596190386102728	2		276	479	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0051681-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	404	410	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.592843021156183	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.596190386102728	2		410	647	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0051681-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	611	608	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.592843021156183	2	FACETS	0.97	0.94	1	0.97	0.94	1	CLONAL	2	TRUE	0	0.596190386102728	2		608	1056	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472598	88472598	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1186552712	NA	P-0051681-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	228	343	0	ENST00000360948.2:c.1957C>T	p.Leu653Phe	p.L653F	ENST00000360948	NM_001012338.2	653	Ctc/Ttc	16/19	0.223797905588311	4	FACETS	0.894	0.837	0.952	0.894	0.837	0.952	INDETERMINATE	2	TRUE	2	0.596190386102728	4		343	683	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114216	115114216	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051681-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	427	472	0	ENST00000257566.3:c.1001G>T	p.Gly334Val	p.G334V	ENST00000257566	NM_016569.3	334	gGg/gTg	6/8	0.592843021156183	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.596190386102728	2		472	697	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858384	9858384	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200526162	NA	P-0051681-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	164	358	0	ENST00000330684.3:c.3017C>T	p.Ala1006Val	p.A1006V	ENST00000330684	NM_001134407.1	1006	gCg/gTg	13/13	0.535627441089591	4	FACETS	1	0.936	1	0.511	0.469	0.555	CLONAL	1	TRUE	2	0.596190386102728	4		358	859	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544726	65544728	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	novel	NA	P-0051681-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	363	467	0	ENST00000358664.4:c.198_200del	p.Lys66_Ala67delinsAsn	p.K66_A67delinsN	ENST00000358664	NM_002382.4	66	aaAGCc/aac	4/5	0.587594163371306	2	FACETS	0.924	0.885	0.963	0.924	0.885	0.963	CLONAL	2	TRUE	0	0.596190386102728	2		467	659	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980913	40980913	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051681-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	246	324	0	ENST00000373198.4:c.1573G>T	p.Ala525Ser	p.A525S	ENST00000373198	NM_133170.3	525	Gct/Tct	10/32	0.535627441089591	4	FACETS	0.934	0.878	0.992	0.934	0.878	0.992	CLONAL	2	TRUE	2	0.596190386102728	4		324	705	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186501404	186501404	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764605841	NA	P-0051716-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	116	243	0	ENST00000323963.5:c.5C>G	p.Ser2Cys	p.S2C	ENST00000323963		2	tCt/tGt	1/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.29	2		243	708	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557424	21557430	+	frameshift_variant	Frame_Shift_Del	DEL	GAGTTTA	GAGTTTA	-	novel	NA	P-0051716-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	132	298	0	ENST00000382592.4:c.2415_2421del	p.Lys806GlnfsTer47	p.K806Qfs*47	ENST00000382592	NM_014572.2	805	atTAAACTC/at	5/8	0.299909283656	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.29	1		298	710	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0051983-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	113	172	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.63235124130126	2		172	301	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138729528	NA	P-0051983-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	323	870	0	ENST00000269305.4:c.523C>G	p.Arg175Gly	p.R175G	ENST00000269305	NM_001126112.2	175	Cgc/Ggc	5/11	0.613972887881552	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.63235124130126	2		870	483	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027153	49027156	+	frameshift_variant	Frame_Shift_Del	DEL	AAAC	AAAC	-	novel	NA	P-0051983-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	94	254	1	ENST00000267163.4:c.1722_1725del	p.Lys574AsnfsTer36	p.K574Nfs*36	ENST00000267163	NM_000321.2	574	AAACaa/aa	18/27	0.63235124130126	1	FACETS	0.696	0.627	0.768	0.696	0.627	0.768	SUBCLONAL	1	TRUE	0	0.63235124130126	1		255	292	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653782	89653783	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	TC	rs786203477	NA	P-0051983-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	88	246	0	ENST00000371953.3:c.81_82insCT	p.Ile28LeufsTer27	p.I28Lfs*27	ENST00000371953	NM_000314.4	27	tat/taTCt	2/9	0.63235124130126	1	FACETS	0.749	0.674	0.827	0.749	0.674	0.827	SUBCLONAL	1	TRUE	0	0.63235124130126	1		246	254	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228085	36228085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051983-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	76	980	0	ENST00000222270.7:c.7471C>T	p.Arg2491Cys	p.R2491C	ENST00000222270	NM_014727.1	2491	Cgt/Tgt	33/37	0.322643974000217	1	FACETS	0.259	0.227	0.294	0.259	0.227	0.294	INDETERMINATE	1	TRUE	0	0.63235124130126	1		980	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0052273-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	33	1015	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	1	2	FACETS	0.496	0.403	0.602	0.496	0.403	0.602	SUBCLONAL	1	TRUE	1	0.18	2		1015	739	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0052273-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	29	380	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.558	0.447	0.686	0.558	0.447	0.686	SUBCLONAL	1	TRUE	1	0.18	2		380	577	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845583	128845583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764495218	NA	P-0052273-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	23	0	0	ENST00000249373.3:c.880G>A	p.Val294Ile	p.V294I	ENST00000249373	NM_005631.4	294	Gtc/Atc	4/12	1	2	FACETS	0.526	0.409	0.662	0.526	0.409	0.662	SUBCLONAL	1	TRUE	1	0.18	2		0	486	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570763	226570763	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052273-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	56	293	0	ENST00000366794.5:c.1133C>G	p.Ala378Gly	p.A378G	ENST00000366794	NM_001618.3	378	gCt/gGt	8/23	0.217504336256228	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.18	1		293	495	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114811	108114811	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052273-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	26	280	0	ENST00000278616.4:c.628T>G	p.Leu210Val	p.L210V	ENST00000278616	NM_000051.3	210	Ttg/Gtg	6/63	1	2	FACETS	0.574	0.454	0.713	0.574	0.454	0.713	SUBCLONAL	1	TRUE	1	0.18	2		280	503	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0052286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	29	292	3	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	0.433993910446534	1	FACETS	0.434	0.35	0.529	0.434	0.35	0.529	SUBCLONAL	1	TRUE	0	0.433993910446534	1		295	241	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005552	150005552	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	117	412	0	ENST00000253339.5:c.673C>G	p.Gln225Glu	p.Q225E	ENST00000253339		225	Caa/Gaa	3/7	1	2	FACETS	0.939	0.85	1	0.939	0.85	1	CLONAL	1	TRUE	1	0.433993910446534	2		412	574	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0052453-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	125	706	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	1	2	FACETS	0.349	0.316	0.384	0.349	0.316	0.384	SUBCLONAL	1	TRUE	1	0.902615118519415	2		706	794	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788651	3788651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052453-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	182	602	0	ENST00000262367.5:c.4303G>A	p.Asp1435Asn	p.D1435N	ENST00000262367	NM_004380.2	1435	Gat/Aat	26/31	0.448135190273411	1	FACETS	0.711	0.671	0.752	0.711	0.671	0.752	INDETERMINATE	1	TRUE	0	0.902615118519415	1		602	311	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0052453-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	107	333	0	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	0.902615118519415	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.902615118519415	1		333	123	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872214	45872214	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052453-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	354	1062	0	ENST00000391945.4:c.220T>C	p.Ser74Pro	p.S74P	ENST00000391945	NM_000400.3	74	Tca/Cca	4/23	1	2	FACETS	0.979	0.933	1	0.979	0.933	1	CLONAL	1	TRUE	1	0.902615118519415	2		1062	801	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052453-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	406	1212	0	ENST00000269571.5:c.829G>T	p.Asp277Tyr	p.D277Y	ENST00000269571		277	Gac/Tac	7/27	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.902615118519415	2		1212	875	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056160	27056160	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052453-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	415	703	0	ENST00000324856.7:c.1156C>T	p.Gln386Ter	p.Q386*	ENST00000324856	NM_006015.4	386	Cag/Tag	2/20	0.489127768985836	3	FACETS	0.893	0.858	0.928	0.893	0.858	0.928	INDETERMINATE	2	TRUE	1	0.902615118519415	3		703	747	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939848	49939848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750979879	NA	P-0052453-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	189	1072	0	ENST00000296474.3:c.1195G>A	p.Asp399Asn	p.D399N	ENST00000296474	NM_002447.2	399	Gac/Aac	1/20	0.902615118519415	3	FACETS	0.539	0.497	0.582	0.269	0.248	0.291	SUBCLONAL	1	TRUE	1	0.902615118519415	3		1072	1128	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725046	49725046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371656831	NA	P-0052453-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	815	1194	0	ENST00000449682.2:c.298C>T	p.His100Tyr	p.H100Y	ENST00000449682	NM_020998.3	100	Cac/Tac	3/18	0.902615118519415	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	1	0.902615118519415	3		1194	1236	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094308	27094308	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052453-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	284	654	2	ENST00000324856.7:c.3016G>T	p.Glu1006Ter	p.E1006*	ENST00000324856	NM_006015.4	1006	Gag/Tag	11/20	0.489127768985836	3	FACETS	1	0.992	1	0.632	0.598	0.668	INDETERMINATE	1	TRUE	1	0.902615118519415	3		656	722	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63760050	63760050	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052453-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	176	773	0	ENST00000279873.7:c.703A>G	p.Ile235Val	p.I235V	ENST00000279873	NM_032199.2	235	Ata/Gta	4/10	0.406699201857384	1	FACETS	0.448	0.416	0.48	0.448	0.416	0.48	INDETERMINATE	1	TRUE	0	0.902615118519415	1		773	478	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662352	67662352	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052453-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	384	1057	1	ENST00000264010.4:c.1598G>A	p.Arg533His	p.R533H	ENST00000264010	NM_006565.3	533	cGc/cAc	9/12	0.448135190273411	1	FACETS	0.725	0.697	0.753	0.725	0.697	0.753	INDETERMINATE	1	TRUE	0	0.902615118519415	1		1058	644	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122985	7122985	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052453-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	123	1106	0	ENST00000302850.5:c.3274G>T	p.Val1092Leu	p.V1092L	ENST00000302850	NM_000208.2	1092	Gtg/Ttg	18/22	1	2	FACETS	0.447	0.405	0.491	0.447	0.405	0.491	SUBCLONAL	1	TRUE	1	0.902615118519415	2		1106	610	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295889	1295889	+	upstream_gene_variant	5'Flank	SNP	C	C	G	novel	NA	P-0052453-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	470	1822	0				ENST00000310581	NM_198253.2	-/1132			0.367627589442091	4	FACETS	0.763	0.729	0.796			1	INDETERMINATE	2	TRUE	NA	0.902615118519415	4		1822	1299	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721899	176721919	+	frameshift_variant	Frame_Shift_Del	DEL	AGATCCTCTTCAGACATCTGG	AGATCCTCTTCAGACATCTGG	T	novel	NA	P-0052453-T05-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	401	1018	0	ENST00000439151.2:c.7530_7550delinsT	p.Asp2511GlufsTer14	p.D2511Efs*14	ENST00000439151	NM_022455.4	2510	tcAGATCCTCTTCAGACATCTGGg/tcTg	23/23	0.406699201857384	1	FACETS	0.654	0.627	0.68	0.654	0.627	0.68	INDETERMINATE	1	TRUE	0	0.902615118519415	1		1018	746	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0053464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	165	442	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.214929928983237	4	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	2	0.214929928983237	4		442	913	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577526	7577526	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121912653	NA	P-0053464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	282	674	0	ENST00000269305.4:c.755T>C	p.Leu252Pro	p.L252P	ENST00000269305	NM_001126112.2	252	cTc/cCc	7/11	0.214929928983237	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.214929928983237	2		674	1207	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604749	48604749	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	137	365	0	ENST00000342988.3:c.1571G>A	p.Trp524Ter	p.W524*	ENST00000342988	NM_005359.5	524	tGg/tAg	12/12	0.214929928983237	2	FACETS	0.915	0.833	0.999	0.915	0.833	0.999	CLONAL	2	TRUE	0	0.214929928983237	2		365	697	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195454	102195454	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	58	261	1	ENST00000263464.3:c.214A>G	p.Met72Val	p.M72V	ENST00000263464	NM_001165.4	72	Atg/Gtg	2/9	0.214929928983237	3	FACETS	0.943	0.809	1	0.471	0.404	0.544	CLONAL	1	TRUE	1	0.214929928983237	3		262	634	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427183	49427183	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs758131988	NA	P-0053464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1677	176	919	0	ENST00000301067.7:c.11305C>G	p.Leu3769Val	p.L3769V	ENST00000301067	NM_003482.3	3769	Ctg/Gtg	39/54	0.214929928983237	3	FACETS	0.979	0.898	1	0.489	0.449	0.532	CLONAL	1	TRUE	1	0.214929928983237	3		919	1853	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097191	178097191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	145	373	0	ENST00000397062.3:c.523G>A	p.Val175Ile	p.V175I	ENST00000397062	NM_006164.4	175	Gtt/Att	4/5	0.214929928983237	3	FACETS	0.925	0.844	1	0.925	0.844	1	CLONAL	2	TRUE	1	0.214929928983237	3		373	808	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971049	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGCACGTCCAGC	CGCGCACGTCCAGC	-	novel	NA	P-0053464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	303	517	0	ENST00000304494.5:c.309_322del	p.Leu104CysfsTer11	p.L104Cfs*11	ENST00000304494	NM_000077.4	103	cgGCTGGACGTGCGCGat/cgat	2/3	0.214929928983237	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.214929928983237	2		517	1142	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577529	7577529	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs730882027	NA	P-0053553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	497	515	1	ENST00000269305.4:c.752T>A	p.Ile251Asn	p.I251N	ENST00000269305	NM_001126112.2	251	aTc/aAc	7/11	0.69666517471978	2	FACETS	0.976	0.946	1	0.976	0.946	1	CLONAL	2	TRUE	0	0.69666517471978	2		516	731	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578178	7578178	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	19	571	0	ENST00000269305.4:c.671A>G	p.Glu224Gly	p.E224G	ENST00000269305	NM_001126112.2	224	gAg/gGg	6/11	0.69666517471978	2	FACETS	0.069	0.051	0.089	0.034	0.025	0.045	SUBCLONAL	1	TRUE	0	0.69666517471978	2		571	794	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775482	39775482	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs568944041	NA	P-0053553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	125	622	0	ENST00000288319.7:c.538A>G	p.Thr180Ala	p.T180A	ENST00000288319	NM_182918.3	180	Acc/Gcc	4/10	0.436979196669995	4	FACETS	0.626	0.565	0.689	0.313	0.282	0.345	SUBCLONAL	1	TRUE	2	0.69666517471978	4		622	973	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265852	16265852	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	142	564	0	ENST00000375759.3:c.10925T>G	p.Leu3642Arg	p.L3642R	ENST00000375759	NM_015001.2	3642	cTg/cGg	15/15	0.692204138921373	2	FACETS	0.519	0.473	0.567	0.259	0.236	0.284	SUBCLONAL	1	TRUE	0	0.69666517471978	2		564	786	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163325204	163325204	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	59	288	0	ENST00000271452.3:c.1340A>C	p.Lys447Thr	p.K447T	ENST00000271452	NM_145697.2	447	aAg/aCg	14/14	0.668814027340968	5	FACETS	0.604	0.52	0.697	0.202	0.173	0.233	SUBCLONAL	1	TRUE	2	0.69666517471978	5		288	573	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852338	63852338	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1620	142	542	0	ENST00000279873.7:c.3116A>G	p.Glu1039Gly	p.E1039G	ENST00000279873	NM_032199.2	1039	gAg/gGg	10/10	0.69666517471978	6	FACETS	0.554	0.502	0.608			1	SUBCLONAL	1	TRUE	NA	0.69666517471978	6		542	1762	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427360	427372	+	frameshift_variant	Frame_Shift_Del	DEL	CATGGTGGGGTGC	CATGGTGGGGTGC	-	novel	NA	P-0053553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	134	569	0	ENST00000399788.2:c.2797_2809del	p.Ala933LeufsTer38	p.A933Lfs*38	ENST00000399788	NM_001042603.1	933	GCACCCCACCATGct/ct	19/28	0.408211773670665	5	FACETS	0.737	0.669	0.81	0.246	0.223	0.27	INDETERMINATE	1	TRUE	2	0.69666517471978	5		569	1067	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444372	49444372	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs375587213	NA	P-0053553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	73	603	0	ENST00000301067.7:c.2999T>G	p.Ile1000Ser	p.I1000S	ENST00000301067	NM_003482.3	1000	aTc/aGc	11/54	0.692204138921373	2	FACETS	0.288	0.252	0.328	0.144	0.126	0.164	SUBCLONAL	1	TRUE	0	0.69666517471978	2		603	727	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675071	40675071	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	27	633	0	ENST00000249776.8:c.35T>A	p.Val12Asp	p.V12D	ENST00000249776	NM_033286.3	12	gTt/gAt	1/9	0.69666517471978	1	FACETS	0.098	0.077	0.121	0.098	0.077	0.121	SUBCLONAL	1	TRUE	0	0.69666517471978	1		633	516	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354627	91354627	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	86	353	0	ENST00000355112.3:c.4067A>C	p.Lys1356Thr	p.K1356T	ENST00000355112	NM_000057.2	1356	aAg/aCg	21/22	0.692204138921373	2	FACETS	0.554	0.492	0.619	0.277	0.246	0.31	SUBCLONAL	1	TRUE	0	0.69666517471978	2		353	446	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990430	81990430	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1332140540	NA	P-0053553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	115	440	0	ENST00000359376.3:c.3701A>C	p.Glu1234Ala	p.E1234A	ENST00000359376	NM_002661.3	1234	gAg/gCg	32/33	0.66750416021752	4	FACETS	0.62	0.557	0.686	0.31	0.278	0.343	SUBCLONAL	1	TRUE	2	0.69666517471978	4		440	904	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226723	2226723	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	144	453	0	ENST00000398665.3:c.4203C>A	p.Asp1401Glu	p.D1401E	ENST00000398665	NM_032482.2	1401	gaC/gaA	27/28	0.69666517471978	3	FACETS	0.787	0.719	0.858	0.394	0.359	0.429	SUBCLONAL	1	TRUE	1	0.69666517471978	3		453	708	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119002	3119002	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	58	625	0	ENST00000078429.4:c.686T>C	p.Leu229Pro	p.L229P	ENST00000078429	NM_002067.2	229	cTc/cCc	5/7	0.69666517471978	3	FACETS	0.254	0.217	0.294	0.127	0.108	0.147	SUBCLONAL	1	TRUE	1	0.69666517471978	3		625	885	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123773	11123786	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TCATCGTGCCTCTC	TCATCGTGCCTCTC	-	novel	NA	P-0053553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	61	445	0	ENST00000358026.2:c.2425_2438del	p.Ile809AsnfsTer10	p.I809Nfs*10	ENST00000358026	NM_001128849.1	808	aTCATCGTGCCTCTC/a	16/36	0.656074868840317	5	FACETS	0.302	0.259	0.349			1	SUBCLONAL	1	TRUE	NA	0.69666517471978	5		445	1186	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291966	15291966	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	160	618	0	ENST00000263388.2:c.2800T>G	p.Phe934Val	p.F934V	ENST00000263388	NM_000435.2	934	Ttc/Gtc	18/33	0.247877884861172	6	FACETS	0.987	0.903	1	0.247	0.225	0.269	INDETERMINATE	1	TRUE	2	0.69666517471978	6		618	1114	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965338	25965338	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	153	568	0	ENST00000435504.4:c.3868A>G	p.Ser1290Gly	p.S1290G	ENST00000435504		1290	Agt/Ggt	13/13	0.69666517471978	3	FACETS	0.581	0.53	0.633	0.29	0.265	0.317	SUBCLONAL	1	TRUE	1	0.69666517471978	3		568	1020	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462577	29462577	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	136	543	0	ENST00000389048.3:c.2324T>G	p.Val775Gly	p.V775G	ENST00000389048	NM_004304.4	775	gTt/gGt	13/29	0.69666517471978	3	FACETS	0.533	0.484	0.585	0.267	0.242	0.293	SUBCLONAL	1	TRUE	1	0.69666517471978	3		543	987	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159005	24159005	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	907	569	0	ENST00000263121.7:c.677T>A	p.Leu226Gln	p.L226Q	ENST00000263121	NM_003073.3	226	cTg/cAg	6/9	0.69666517471978	4	FACETS	0.98	0.962	0.997	0.98	0.962	0.997	CLONAL	4	TRUE	0	0.69666517471978	4		569	1127	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159010	24159010	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	908	567	0	ENST00000263121.7:c.682T>G	p.Leu228Val	p.L228V	ENST00000263121	NM_003073.3	228	Ttg/Gtg	6/9	0.69666517471978	4	FACETS	0.974	0.956	0.991	0.974	0.956	0.991	CLONAL	4	TRUE	0	0.69666517471978	4		567	1135	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279201	142279201	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	35	367	0	ENST00000350721.4:c.1445T>G	p.Leu482Arg	p.L482R	ENST00000350721	NM_001184.3	482	cTa/cGa	6/47	0.436979196669995	4	FACETS	0.255	0.208	0.308	0.127	0.104	0.154	SUBCLONAL	1	TRUE	2	0.69666517471978	4		367	669	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671057	30671057	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	152	582	0	ENST00000376406.3:c.5689T>G	p.Phe1897Val	p.F1897V	ENST00000376406	NM_014641.2	1897	Ttc/Gtc	12/15	0.18506678351228	5	FACETS	0.932	0.852	1	0.311	0.284	0.339	INDETERMINATE	1	TRUE	2	0.69666517471978	5		582	957	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168907	32168907	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	179	634	0	ENST00000375023.3:c.4126T>C	p.Ser1376Pro	p.S1376P	ENST00000375023	NM_004557.3	1376	Tcc/Ccc	22/30	0.18506678351228	5	FACETS	1	0.947	1	0.345	0.318	0.374	INDETERMINATE	1	TRUE	2	0.69666517471978	5		634	1014	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967184	93967184	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	74	340	0	ENST00000369303.4:c.2168T>C	p.Leu723Pro	p.L723P	ENST00000369303	NM_004440.3	723	cTc/cCc	12/17	0.18506678351228	5	FACETS	0.961	0.844	1	0.32	0.281	0.362	INDETERMINATE	1	TRUE	2	0.69666517471978	5		340	452	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874320	76874320	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	151	438	0	ENST00000373344.5:c.5402A>C	p.Lys1801Thr	p.K1801T	ENST00000373344	NM_000489.3	1801	aAa/aCa	21/35	0.69666517471978	3	FACETS	0.866	0.794	0.941	0.433	0.397	0.471	CLONAL	1	TRUE	1	0.69666517471978	3		438	675	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054120-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	83	276	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.179086370883541	3	FACETS	0.988	0.875	1	0.988	0.875	1	CLONAL	2	TRUE	1	0.179086370883541	3		276	511	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629025	14629025	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1306302394	NA	P-0054120-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	57	1073	0	ENST00000254322.2:c.137A>G	p.Lys46Arg	p.K46R	ENST00000254322	NM_006145.1	46	aAg/aGg	1/3	1	2	FACETS	0.665	0.569	0.771	0.665	0.569	0.771	SUBCLONAL	1	TRUE	1	0.179086370883541	2		1073	957	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793175	33793186	+	inframe_deletion	In_Frame_Del	DEL	GGGGCGGCAGGT	GGGGCGGCAGGT	-	novel	NA	P-0054120-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	17	407	0	ENST00000498907.2:c.135_146del	p.Pro46_Pro49del	p.P46_P49del	ENST00000498907	NM_004364.3	45	ccACCTGCCGCCCCg/ccg	1/1	1	2	FACETS	0.515	0.383	0.671	0.515	0.383	0.671	SUBCLONAL	1	TRUE	1	0.179086370883541	2		407	369	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951162	48951162	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054563-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	116	302	0	ENST00000267163.4:c.1324G>T	p.Gly442Ter	p.G442*	ENST00000267163	NM_000321.2	442	Gga/Tga	13/27	0.704456769507735	1	FACETS	0.936	0.864	1	0.936	0.864	1	CLONAL	1	TRUE	0	0.704456769507735	1		302	228	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531859	41531859	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054563-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	168	425	0	ENST00000263253.7:c.1571C>G	p.Thr524Arg	p.T524R	ENST00000263253	NM_001429.3	524	aCg/aGg	7/31	0.479513568783102	1	FACETS	0.461	0.425	0.499	0.461	0.425	0.499	SUBCLONAL	1	TRUE	0	0.704456769507735	1		425	670	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0054719-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	33	234	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.509	0.414	0.617	0.509	0.414	0.617	SUBCLONAL	1	FALSE	1	0.260859772771718	2		234	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0054719-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	111	1040	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	1	2	FACETS	0.654	0.586	0.727	0.654	0.586	0.727	SUBCLONAL	1	FALSE	1	0.260859772771718	2		1040	1301	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220371	1220371	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0054719-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	104	541	0	ENST00000326873.7:c.465-1G>C		p.X155_splice	ENST00000326873	NM_000455.4	155			1	2	FACETS	0.931	0.833	1	0.931	0.833	1	CLONAL	1	FALSE	1	0.260859772771718	2		541	856	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608225	28608225	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054719-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	59	403	0	ENST00000241453.7:c.1831G>T	p.Glu611Ter	p.E611*	ENST00000241453	NM_004119.2	611	Gag/Tag	14/24	1	2	FACETS	0.746	0.642	0.86	0.746	0.642	0.86	SUBCLONAL	1	FALSE	1	0.260859772771718	2		403	606	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426832	70426832	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054719-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	38	263	0	ENST00000373644.4:c.4492G>C	p.Val1498Leu	p.V1498L	ENST00000373644	NM_030625.2	1498	Gtt/Ctt	7/12	1	2	FACETS	0.551	0.455	0.658	0.551	0.455	0.658	SUBCLONAL	1	FALSE	1	0.260859772771718	2		263	529	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123260430	123260430	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054719-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	53	399	0	ENST00000358487.5:c.1471del	p.Cys491AlafsTer26	p.C491Afs*26	ENST00000358487	NM_000141.4	491	Tgc/gc	11/18	1	2	FACETS	0.488	0.415	0.569	0.488	0.415	0.569	SUBCLONAL	1	FALSE	1	0.260859772771718	2		399	832	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416618	121416618	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054719-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	78	556	0	ENST00000257555.6:c.47T>A	p.Leu16Gln	p.L16Q	ENST00000257555		16	cTg/cAg	1/10	1	2	FACETS	0.667	0.585	0.755	0.667	0.585	0.755	SUBCLONAL	1	FALSE	1	0.260859772771718	2		556	897	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222265	2222265	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054719-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	144	619	0	ENST00000398665.3:c.3097G>T	p.Gly1033Cys	p.G1033C	ENST00000398665	NM_032482.2	1033	Ggc/Tgc	24/28	1	2	FACETS	0.895	0.814	0.98	0.895	0.814	0.98	CLONAL	1	FALSE	1	0.260859772771718	2		619	1234	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597459	10597459	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054719-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	152	622	0	ENST00000171111.5:c.1744G>T	p.Glu582Ter	p.E582*	ENST00000171111	NM_203500.1	582	Gag/Tag	6/6	1	2	FACETS	0.981	0.895	1	0.981	0.895	1	CLONAL	1	FALSE	1	0.260859772771718	2		622	1188	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457189	25457189	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054719-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	51	461	1	ENST00000264709.3:c.2698C>T	p.His900Tyr	p.H900Y	ENST00000264709	NM_175629.2	900	Cac/Tac	23/23	1	2	FACETS	0.404	0.342	0.472	0.404	0.342	0.472	SUBCLONAL	1	FALSE	1	0.260859772771718	2		462	969	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022782	31022782	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054719-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	64	442	0	ENST00000375687.4:c.2267A>T	p.Asp756Val	p.D756V	ENST00000375687	NM_015338.5	756	gAc/gTc	13/13	1	2	FACETS	0.663	0.573	0.761	0.663	0.573	0.761	SUBCLONAL	1	FALSE	1	0.260859772771718	2		442	740	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980861	40980861	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054719-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	40	455	0	ENST00000373198.4:c.1625T>A	p.Val542Glu	p.V542E	ENST00000373198	NM_133170.3	542	gTg/gAg	10/32	0.260859772771718	0	FACETS	0.322	0.266	0.383			1	SUBCLONAL	1	FALSE	0	0.260859772771718	0		455	705	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411882	116411883	+	intron_variant	Intron	DNP	TT	TT	GC	novel	NA	P-0054719-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	72	730	0	ENST00000397752.3:c.2888-21_2888-20delinsGC		p.*963*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.478	0.416	0.546	0.478	0.416	0.546	SUBCLONAL	1	FALSE	1	0.260859772771718	2		730	1154	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020519	69020519	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054719-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	37	406	0	ENST00000288368.4:c.2891G>C	p.Ser964Thr	p.S964T	ENST00000288368	NM_024870.2	964	aGc/aCc	24/40	1	2	FACETS	0.449	0.369	0.539	0.449	0.369	0.539	SUBCLONAL	1	FALSE	1	0.260859772771718	2		406	632	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871798	12871798	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055121-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	56	494	3	ENST00000228872.4:c.518del	p.Asn173MetfsTer52	p.N173Mfs*52	ENST00000228872	NM_004064.3	172	gAa/ga	2/3	0.0972186937582207	3	FACETS	1	0.948	1	0.621	0.531	0.718	INDETERMINATE	1	TRUE	1	0.17	3		497	576	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962309	2962309	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	61	767	0	ENST00000396946.4:c.2228G>T	p.Cys743Phe	p.C743F	ENST00000396946	NM_032415.4	743	tGc/tTc	17/25	0.237241730268506	5	FACETS	0.77	0.664	0.885	0.257	0.221	0.295	INDETERMINATE	1	TRUE	2	0.445885308618522	5		767	593	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0055303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	854	559	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.442074735240246	5	FACETS	1	0.994	1			1	CLONAL	4	TRUE	NA	0.442074735240246	5		559	1495	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508867	106508867	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1247	231	537	0	ENST00000359195.3:c.861C>G	p.Ile287Met	p.I287M	ENST00000359195	NM_002649.2	287	atC/atG	2/11	0.27193678727011	5	FACETS	1	0.983	1	0.392	0.364	0.421	CLONAL	1	TRUE	2	0.442074735240246	5		537	1478	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950054	38950054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	110	456	0	ENST00000357387.3:c.3896G>A	p.Arg1299Lys	p.R1299K	ENST00000357387	NM_152756.3	1299	aGa/aAa	31/38	0.442414515297804	3	FACETS	0.787	0.707	0.872			1	SUBCLONAL	1	TRUE	NA	0.442074735240246	3		456	772	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40478213	40478213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	134	298	0	ENST00000264657.5:c.1286C>T	p.Ser429Phe	p.S429F	ENST00000264657	NM_139276.2	429	tCc/tTc	15/24	0.400211350405985	5	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.442074735240246	5		298	812	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55569969	55569969	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	74	302	0	ENST00000288135.5:c.836C>T	p.Ser279Leu	p.S279L	ENST00000288135	NM_000222.2	279	tCa/tTa	5/21	0.355077438772079	3	FACETS	0.833	0.731	0.942	0.416	0.365	0.471	CLONAL	1	TRUE	1	0.442074735240246	3		302	491	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231410	46231410	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0055303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	106	389	0	ENST00000334344.6:c.1250C>G	p.Ser417Ter	p.S417*	ENST00000334344	NM_152641.2	417	tCa/tGa	10/21	0.307941665866342	3	FACETS	0.996	0.895	1	0.498	0.447	0.551	CLONAL	1	TRUE	1	0.442074735240246	3		389	588	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73343046	73343046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144957541	NA	P-0055303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	41	205	0	ENST00000377767.4:c.1760C>T	p.Ser587Phe	p.S587F	ENST00000377767	NM_014953.3	587	tCt/tTt	14/21	0.442414515297804	1	FACETS	0.66	0.555	0.774	0.66	0.555	0.774	SUBCLONAL	1	TRUE	0	0.442074735240246	1		205	219	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984936	101984936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1192221094	NA	P-0055303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	81	263	0	ENST00000282441.5:c.383C>T	p.Ser128Phe	p.S128F	ENST00000282441	NM_001130145.2	128	tCt/tTt	2/9	0.337067851476666	5	FACETS	0.892	0.786	1	0.297	0.262	0.336	CLONAL	1	TRUE	2	0.442074735240246	5		263	683	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229272	55229272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768627073	NA	P-0055303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	130	454	0	ENST00000275493.2:c.1579C>T	p.Arg527Trp	p.R527W	ENST00000275493	NM_005228.3	527	Cgg/Tgg	13/28	0.364609879230506	3	FACETS	0.662	0.6	0.729	0.331	0.3	0.365	SUBCLONAL	1	TRUE	1	0.442074735240246	3		454	1084	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221457	36221457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2160	256	376	0	ENST00000222270.7:c.5216C>T	p.Ser1739Phe	p.S1739F	ENST00000222270	NM_014727.1	1739	tCc/tTc	25/37	0.442074735240246	9	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.442074735240246	9		376	2416	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449749	149449749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774962435	NA	P-0055303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	154	416	0	ENST00000286301.3:c.1315G>A	p.Asp439Asn	p.D439N	ENST00000286301	NM_005211.3	439	Gat/Aat	9/22	0.392209593123112	2	FACETS	0.826	0.757	0.899	0.413	0.378	0.45	CLONAL	1	TRUE	0	0.442074735240246	2		416	843	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419937	152419937	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	559	530	0	ENST00000206249.3:c.1624G>C	p.Glu542Gln	p.E542Q	ENST00000206249	NM_000125.3	542	Gag/Cag	8/8	0.27193678727011	5	FACETS	1	0.994	1	0.797	0.764	0.831	CLONAL	2	TRUE	2	0.442074735240246	5		530	1758	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144119	55144119	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	113	402	0	ENST00000257290.5:c.1948C>T	p.His650Tyr	p.H650Y	ENST00000257290	NM_006206.4	650	Cac/Tac	14/23	0.355077438772079	3	FACETS	0.801	0.721	0.886	0.401	0.36	0.443	CLONAL	1	TRUE	1	0.442074735240246	3		402	779	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602897	10602897	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	466	466	0	ENST00000171111.5:c.681del	p.Gln227HisfsTer3	p.Q227Hfs*3	ENST00000171111	NM_203500.1	227	caA/ca	3/6	0.275695427946527	4	FACETS	0.858	0.821	0.895			1	CLONAL	3	TRUE	NA	0.442074735240246	4		466	1181	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022540	12022540	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	219	668	0	ENST00000396373.4:c.646G>T	p.Glu216Ter	p.E216*	ENST00000396373	NM_001987.4	216	Gag/Tag	5/8	0.442414515297804	3	FACETS	1	0.932	1	0.502	0.466	0.539	CLONAL	1	TRUE	1	0.442074735240246	3		668	1206	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001386	29001386	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	100	371	0	ENST00000282397.4:c.1346G>T	p.Arg449Ile	p.R449I	ENST00000282397	NM_002019.4	449	aGa/aTa	10/30	0.442074735240246	5	FACETS	0.85	0.758	0.948	0.213	0.189	0.237	CLONAL	1	TRUE	1	0.442074735240246	5		371	885	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570386	95570386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	51	256	0	ENST00000393063.1:c.3347C>T	p.Ala1116Val	p.A1116V	ENST00000393063	NM_030621.3	1116	gCt/gTt	22/28	0.28341899738624	6	FACETS	0.813	0.691	0.946	0.203	0.172	0.237	CLONAL	1	TRUE	2	0.442074735240246	6		256	535	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40682109	40682109	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	282	354	0	ENST00000249776.8:c.664G>C	p.Glu222Gln	p.E222Q	ENST00000249776	NM_033286.3	222	Gag/Cag	6/9	0.442414515297804	3	FACETS	0.804	0.756	0.852	0.804	0.756	0.852	CLONAL	2	TRUE	1	0.442074735240246	3		354	969	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845523	72845523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	138	518	0	ENST00000268489.5:c.3817C>T	p.His1273Tyr	p.H1273Y	ENST00000268489	NM_006885.3	1273	Cac/Tac	7/10	0.390160677132941	2	FACETS	0.649	0.59	0.711	0.324	0.295	0.356	SUBCLONAL	1	TRUE	0	0.442074735240246	2		518	962	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475604	40475604	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	84	262	0	ENST00000264657.5:c.1640C>G	p.Ala547Gly	p.A547G	ENST00000264657	NM_139276.2	547	gCt/gGt	18/24	0.400211350405985	5	FACETS	0.909	0.803	1			1	CLONAL	1	TRUE	NA	0.442074735240246	5		262	695	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40477040	40477040	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	160	344	1	ENST00000264657.5:c.1405C>T	p.Gln469Ter	p.Q469*	ENST00000264657	NM_139276.2	469	Cag/Tag	16/24	0.400211350405985	5	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.442074735240246	5		345	948	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223188	36223188	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2461	282	488	0	ENST00000222270.7:c.5738C>G	p.Ser1913Cys	p.S1913C	ENST00000222270	NM_014727.1	1913	tCc/tGc	28/37	0.442074735240246	9	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.442074735240246	9		488	2743	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851758	134851758	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	369	566	0	ENST00000398015.3:c.1164G>T	p.Glu388Asp	p.E388D	ENST00000398015	NM_004441.4	388	gaG/gaT	5/16	0.337067851476666	5	FACETS	0.922	0.873	0.972	0.615	0.582	0.648	CLONAL	2	TRUE	2	0.442074735240246	5		566	1506	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960105	134960105	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	474	481	0	ENST00000398015.3:c.2462G>T	p.Gly821Val	p.G821V	ENST00000398015	NM_004441.4	821	gGa/gTa	13/16	0.337067851476666	5	FACETS	0.877	0.839	0.916	0.877	0.839	0.916	CLONAL	3	TRUE	2	0.442074735240246	5		481	1355	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977852	134977852	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0055303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	268	245	0	ENST00000398015.3:c.2847-2A>T		p.X949_splice	ENST00000398015	NM_004441.4	949			0.337067851476666	5	FACETS	0.964	0.91	1	0.964	0.91	1	CLONAL	3	TRUE	2	0.442074735240246	5		245	697	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274837	142274837	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	268	547	0	ENST00000350721.4:c.2223C>G	p.Phe741Leu	p.F741L	ENST00000350721	NM_001184.3	741	ttC/ttG	10/47	0.337067851476666	5	FACETS	0.996	0.935	1	0.664	0.623	0.706	CLONAL	2	TRUE	2	0.442074735240246	5		547	1012	SUCCESS
APC	324	MSKCC	GRCh37	5	112102885	112102885	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs863225327	NA	P-0055303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	57	263	0	ENST00000257430.4:c.221-1G>C		p.X74_splice	ENST00000257430	NM_000038.5	74			0.392209593123112	2	FACETS	0.854	0.738	0.979	0.427	0.369	0.49	CLONAL	1	TRUE	0	0.442074735240246	2		263	302	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965512	90965512	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	103	342	0	ENST00000265433.3:c.1805C>A	p.Thr602Asn	p.T602N	ENST00000265433	NM_002485.4	602	aCt/aAt	11/16	0.442074735240246	5	FACETS	1	0.973	1	0.252	0.225	0.28	CLONAL	1	TRUE	0	0.442074735240246	5		342	616	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141549433	141549433	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	111	203	0	ENST00000220592.5:c.2155G>C	p.Asp719His	p.D719H	ENST00000220592	NM_012154.3	719	Gac/Cac	16/19	0.442074735240246	5	FACETS	0.945	0.848	1	0.189	0.169	0.21	CLONAL	1	TRUE	0	0.442074735240246	5		203	884	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0055393-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	84	351	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.336037667226932	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.336037667226932	1		351	398	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0055393-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	51	254	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.958	0.818	1	0.958	0.818	1	CLONAL	1	TRUE	1	0.336037667226932	2		254	317	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363842	118363842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055393-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	116	493	0	ENST00000534358.1:c.5075C>A	p.Pro1692His	p.P1692H	ENST00000534358	NM_005933.3	1692	cCt/cAt	16/36	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.336037667226932	2		493	659	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969117	93969117	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055393-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	77	363	1	ENST00000369303.4:c.1879G>T	p.Glu627Ter	p.E627*	ENST00000369303	NM_004440.3	627	Gag/Tag	10/17	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.336037667226932	2		364	439	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344119	70344119	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055393-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	150	865	0	ENST00000374080.3:c.1855A>G	p.Ile619Val	p.I619V	ENST00000374080		619	Atc/Gtc	13/45	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.336037667226932	2		865	830	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578192	7578200	+	inframe_deletion	In_Frame_Del	DEL	GGGCACCAC	GGGCACCAC	-	novel	NA	P-0055536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	378	844	0	ENST00000269305.4:c.649_657del	p.Val217_Pro219del	p.V217_P219del	ENST00000269305	NM_001126112.2	217	GTGGTGCCC/-	6/11	0.473989475245096	3	FACETS	0.941	0.903	0.98	0.941	0.903	0.98	CLONAL	3	TRUE	0	0.486543520461358	3		844	684	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218843	36218843	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs569194163	NA	P-0055536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1256	109	1097	1	ENST00000222270.7:c.4454C>T	p.Pro1485Leu	p.P1485L	ENST00000222270	NM_014727.1	1485	cCg/cTg	18/37	0.486543520461358	6	FACETS	0.648	0.579	0.721			1	SUBCLONAL	1	TRUE	NA	0.486543520461358	6		1098	1365	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794952	242794952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1044516789	NA	P-0055536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1314	84	1222	2	ENST00000334409.5:c.257G>A	p.Arg86His	p.R86H	ENST00000334409	NM_005018.2	86	cGc/cAc	2/5	0.486543520461358	6	FACETS	0.487	0.428	0.551	0.122	0.107	0.138	SUBCLONAL	1	TRUE	2	0.486543520461358	6		1224	1398	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374867	149374867	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	85	505	0	ENST00000360632.3:c.227C>G	p.Pro76Arg	p.P76R	ENST00000360632	NM_015472.4	76	cCt/cGt	2/7	0.486543520461358	4	FACETS	0.989	0.877	1	0.495	0.438	0.555	CLONAL	1	TRUE	2	0.486543520461358	4		505	525	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880257	37880257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055621-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	207	322	0	ENST00000269571.5:c.2301C>G	p.Ile767Met	p.I767M	ENST00000269571		767	atC/atG	19/27	0.112992647468177	5	FACETS	1	0.982	1	0.777	0.722	0.834	INDETERMINATE	2	FALSE	2	0.297076917623645	5		322	864	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052636	42052636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1054243525	NA	P-0055621-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	190	420	0	ENST00000219905.7:c.7307G>A	p.Arg2436His	p.R2436H	ENST00000219905	NM_001164273.1	2436	cGt/cAt	20/24	0.264368009371513	3	FACETS	1	0.966	1	0.713	0.661	0.766	CLONAL	2	FALSE	0	0.297076917623645	3		420	687	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426526	49426526	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055621-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1315	189	962	0	ENST00000301067.7:c.11962C>T	p.Gln3988Ter	p.Q3988*	ENST00000301067	NM_003482.3	3988	Cag/Tag	39/54	0.115529411970446	4	FACETS	1	0.968	1			1	INDETERMINATE	1	FALSE	NA	0.297076917623645	4		962	1504	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883753	37883753	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055621-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1351	418	1126	0	ENST00000269571.5:c.3365C>T	p.Ser1122Phe	p.S1122F	ENST00000269571		1122	tCt/tTt	26/27	0.112992647468177	5	FACETS	1	0.99	1	0.767	0.728	0.806	INDETERMINATE	2	FALSE	2	0.297076917623645	5		1126	1769	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025558	1025558	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1467957407	NA	P-0055621-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1261	321	939	1	ENST00000358495.3:c.817G>A	p.Glu273Lys	p.E273K	ENST00000358495	NM_134424.2	273	Gag/Aag	9/12	0.297076917623645	5	FACETS	0.987	0.93	1	0.658	0.62	0.698	CLONAL	2	FALSE	2	0.297076917623645	5		940	1582	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880991	37880992	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCTG	novel	NA	P-0055621-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1152	297	922	0	ENST00000269571.5:c.2321_2326dup	p.Ala775_Gly776insValAla	p.A775_G776insVA	ENST00000269571		774	atg/aTGGCTGtg	20/27	0.112992647468177	5	FACETS	0.997	0.937	1	0.665	0.625	0.707	INDETERMINATE	2	FALSE	2	0.297076917623645	5		922	1449	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883636	37883636	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055621-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1251	396	1070	0	ENST00000269571.5:c.3248C>G	p.Ser1083Cys	p.S1083C	ENST00000269571		1083	tCc/tGc	26/27	0.112992647468177	5	FACETS	1	0.99	1	0.78	0.74	0.821	INDETERMINATE	2	FALSE	2	0.297076917623645	5		1070	1647	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896460	151896460	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780537762	NA	P-0055621-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	106	269	0	ENST00000262189.6:c.4177C>T	p.Leu1393Phe	p.L1393F	ENST00000262189	NM_170606.2	1393	Ctt/Ttt	27/59	0.297076917623645	9	FACETS	0.864	0.774	0.96	0.247	0.221	0.275	CLONAL	2	FALSE	2	0.297076917623645	9		269	842	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156836724	156836724	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055621-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1522	142	871	0	ENST00000524377.1:c.382G>C	p.Glu128Gln	p.E128Q	ENST00000524377	NM_002529.3	128	Gag/Cag	4/17	0.297076917623645	5	FACETS	0.831	0.754	0.912			1	CLONAL	1	FALSE	NA	0.297076917623645	5		871	1664	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404741	70404741	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055621-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	71	394	0	ENST00000373644.4:c.2255T>C	p.Phe752Ser	p.F752S	ENST00000373644	NM_030625.2	752	tTt/tCt	4/12	0.112992647468177	5	FACETS	0.977	0.852	1	0.326	0.284	0.371	INDETERMINATE	1	FALSE	2	0.297076917623645	5		394	707	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805851	46805851	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055621-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	100	754	0	ENST00000290295.7:c.105C>G	p.Ser35Arg	p.S35R	ENST00000290295	NM_006361.5	35	agC/agG	1/2	0.112992647468177	5	FACETS	0.966	0.862	1	0.322	0.287	0.36	INDETERMINATE	1	FALSE	2	0.297076917623645	5		754	1007	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0055809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	51	639	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.386	0.329	0.45	0.386	0.329	0.45	SUBCLONAL	1	TRUE	1	0.559139195577953	2		639	472	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913355	NA	P-0055809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	43	381	0	ENST00000288602.6:c.1406G>T	p.Gly469Val	p.G469V	ENST00000288602	NM_004333.4	469	gGa/gTa	11/18	0.273084497251785	4	FACETS	0.836	0.703	0.981			1	INDETERMINATE	1	TRUE	NA	0.559139195577953	4		381	287	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859782	151859782	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0055809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	15	426	0	ENST00000262189.6:c.10880C>G	p.Ser3627Ter	p.S3627*	ENST00000262189	NM_170606.2	3627	tCa/tGa	43/59	1	2	FACETS	0.199	0.145	0.263	0.199	0.145	0.263	SUBCLONAL	1	TRUE	1	0.559139195577953	2		426	270	SUCCESS
APC	324	MSKCC	GRCh37	5	112179012	112179013	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0056247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	48	249	0	ENST00000257430.4:c.7722_7723del	p.Ser2575CysfsTer7	p.S2575Cfs*7	ENST00000257430	NM_000038.5	2574	cTT/c	16/16	0.215287572775853	4	FACETS	0.941	0.801	1	0.47	0.4	0.547	CLONAL	2	TRUE	0	0.215287572775853	4		249	288	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098533	108098533	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs55861249	NA	P-0056391-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	20	247	0	ENST00000278616.4:c.103C>T	p.Arg35Ter	p.R35*	ENST00000278616	NM_000051.3	35	Cga/Tga	3/63	1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	FALSE	1	0.481062028323461	2		247	76	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797776	32797776	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056391-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	45	747	0	ENST00000374899.4:c.1726G>A	p.Val576Met	p.V576M	ENST00000374899	NM_018833.2	576	Gtg/Atg	10/12	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.481062028323461	2		747	142	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891575	151891576	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0056391-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	16	384	0	ENST00000262189.6:c.4456_4457del	p.Glu1486ThrfsTer9	p.E1486Tfs*9	ENST00000262189	NM_170606.2	1486	GAa/a	29/59	0.481062028323461	1	FACETS	0.765	0.581	0.973	0.765	0.581	0.973	CLONAL	1	FALSE	0	0.481062028323461	1		384	66	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212242	36212242	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056391-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	10	1020	0	ENST00000222270.7:c.1993G>A	p.Val665Met	p.V665M	ENST00000222270	NM_014727.1	665	Gtg/Atg	3/37	0.443456773198938	1	FACETS	0.227	0.154	0.318	0.227	0.154	0.318	SUBCLONAL	1	FALSE	0	0.481062028323461	1		1020	139	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0056418-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	188	819	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	1	2	FACETS	0.88	0.813	0.951	1	0.992	1	CLONAL	2	TRUE	1	0.208719996666718	2		819	1023	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653808	89653808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056418-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	32	335	0	ENST00000371953.3:c.106G>A	p.Gly36Arg	p.G36R	ENST00000371953	NM_000314.4	36	Gga/Aga	2/9	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.208719996666718	2		335	248	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594221	55594221	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913512	NA	P-0056418-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	92	348	0	ENST00000288135.5:c.1924A>G	p.Lys642Glu	p.K642E	ENST00000288135	NM_000222.2	642	Aaa/Gaa	13/21	0.159606616729334	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	TRUE	0	0.208719996666718	2		348	424	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215817	133215817	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056418-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	149	684	0	ENST00000320574.5:c.5446A>C	p.Asn1816His	p.N1816H	ENST00000320574	NM_006231.2	1816	Aac/Cac	40/49	1	2	FACETS	0.909	0.832	0.991	1	0.99	1	CLONAL	2	TRUE	1	0.208719996666718	2		684	785	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912055	56912055	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056464-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	62	401	0	ENST00000519728.1:c.1283C>G	p.Ser428Cys	p.S428C	ENST00000519728	NM_002350.3	428	tCc/tGc	12/13	0.167930157942687	1	FACETS	0.424	0.365	0.487	0.424	0.365	0.487	INDETERMINATE	1	TRUE	0	0.347737077966533	1		401	695	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617631	100617631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056464-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	46	376	0	ENST00000308731.7:c.438C>A	p.Phe146Leu	p.F146L	ENST00000308731	NM_000061.2	146	ttC/ttA	6/19	1	2	FACETS	0.399	0.335	0.47	0.399	0.335	0.47	SUBCLONAL	1	TRUE	1	0.347737077966533	2		376	663	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	42	539	2	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	0.48	0.4	0.568	0.48	0.4	0.568	SUBCLONAL	1	FALSE	1	0.356449124969392	2		541	491	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0056486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	38	347	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	FALSE	1	0.356449124969392	2		347	192	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100728	8100728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs771019738	NA	P-0056486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	82	1003	10	ENST00000346208.3:c.708del	p.Ser237AlafsTer28	p.S237Afs*28	ENST00000346208		234	ttC/tt	3/6	0.356449124969392	4	FACETS	0.997	0.88	1	0.498	0.44	0.561	CLONAL	1	FALSE	2	0.356449124969392	4		1013	626	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225060	NA	P-0056486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	58	372	0	ENST00000263967.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000263967	NM_006218.2	104	cCa/cTa	2/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.356449124969392	2		372	242	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220394	1220394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	41	933	1	ENST00000326873.7:c.487G>A	p.Gly163Ser	p.G163S	ENST00000326873	NM_000455.4	163	Ggc/Agc	4/10	1	2	FACETS	0.372	0.309	0.443	0.372	0.309	0.443	SUBCLONAL	1	FALSE	1	0.356449124969392	2		934	618	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497863	25497863	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	37	974	0	ENST00000264709.3:c.586T>C	p.Tyr196His	p.Y196H	ENST00000264709	NM_175629.2	196	Tac/Cac	6/23	0.303624350226238	3	FACETS	0.398	0.327	0.477	0.199	0.163	0.239	SUBCLONAL	1	FALSE	1	0.356449124969392	3		974	615	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338672	70338683	+	inframe_deletion	In_Frame_Del	DEL	ATGTTTACCCTC	ATGTTTACCCTC	-	novel	NA	P-0056486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	121	816	0	ENST00000374080.3:c.69_80del	p.Asp23_Gln27delinsGlu	p.D23_Q27delinsE	ENST00000374080		23	gATGTTTACCCTCag/gag	1/45	0.356458349940229	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	0	0.356449124969392	1		816	509	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324990	123324990	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	32	562	0	ENST00000358487.5:c.338T>C	p.Val113Ala	p.V113A	ENST00000358487	NM_000141.4	113	gTa/gCa	3/18	0.356449124969392	4	FACETS	0.512	0.415	0.621	0.256	0.207	0.311	SUBCLONAL	1	FALSE	2	0.356449124969392	4		562	476	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345555	70345555	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	43	652	0	ENST00000374080.3:c.2414C>A	p.Thr805Lys	p.T805K	ENST00000374080		805	aCa/aAa	17/45	0.356458349940229	1	FACETS	0.638	0.536	0.749	0.638	0.536	0.749	SUBCLONAL	1	FALSE	0	0.356449124969392	1		652	311	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0056503-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	230	785	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.618675505863184	2	FACETS	0.901	0.855	0.946	0.901	0.855	0.946	CLONAL	2	TRUE	0	0.648204281081888	2		785	394	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743988	41743988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776310618	NA	P-0056503-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	145	1304	1	ENST00000301178.4:c.923G>A	p.Arg308His	p.R308H	ENST00000301178	NM_021913.4	308	cGc/cAc	7/20	0.314537987098388	5	FACETS	1	0.947	1			1	INDETERMINATE	1	TRUE	NA	0.648204281081888	5		1305	839	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0056503-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	11	1131	0	ENST00000269305.4:c.376-1G>T		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.618675505863184	2	FACETS	0.064	0.044	0.09	0.032	0.022	0.045	SUBCLONAL	1	TRUE	0	0.648204281081888	2		1131	527	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942771	44942773	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs398122829	NA	P-0056503-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	152	454	0	ENST00000377967.4:c.3354_3356del	p.Leu1119del	p.L1119del	ENST00000377967	NM_021140.2	1117	aaTCTt/aat	23/29	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.648204281081888	1		454	266	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427258	49427258	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056503-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	122	1191	1	ENST00000301067.7:c.11230C>T	p.Gln3744Ter	p.Q3744*	ENST00000301067	NM_003482.3	3744	Cag/Tag	39/54	1	2	FACETS	0.963	0.879	1	0.963	0.879	1	CLONAL	1	TRUE	1	0.648204281081888	2		1192	391	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545981	41545981	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056503-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	375	1202	0	ENST00000263253.7:c.2597del	p.Pro866LeufsTer80	p.P866Lfs*80	ENST00000263253	NM_001429.3	866	Cct/ct	14/31	0.648204281081888	3	FACETS	0.908	0.866	0.949	0.908	0.866	0.949	CLONAL	2	TRUE	1	0.648204281081888	3		1202	844	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9779983	9779983	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056503-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	9	1050	0	ENST00000377346.4:c.1247G>T	p.Cys416Phe	p.C416F	ENST00000377346	NM_005026.3	416	tGc/tTc	10/24	0.645079987862649	2	FACETS	0.065	0.043	0.095	0.033	0.021	0.048	SUBCLONAL	1	TRUE	0	0.648204281081888	2		1050	424	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0056580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	10	785	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	0.658235504492473	4	FACETS	0.097	0.065	0.138			1	SUBCLONAL	1	TRUE	NA	0.767871222641604	4		786	475	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858336	9858336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1349281989	NA	P-0056580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	76	510	2	ENST00000330684.3:c.3065G>A	p.Arg1022His	p.R1022H	ENST00000330684	NM_001134407.1	1022	cGc/cAc	13/13	0.753120811942047	2	FACETS	1	0.938	1	0.532	0.477	0.588	CLONAL	1	TRUE	0	0.767871222641604	2		512	186	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250921	153250922	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0056580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	112	289	0	ENST00000281708.4:c.1138dup	p.Asp380GlyfsTer2	p.D380Gfs*2	ENST00000281708	NM_033632.3	380	gat/gGat	8/12	0.754253284024614	2	FACETS	0.895	0.837	0.95	0.895	0.837	0.95	CLONAL	2	TRUE	0	0.767871222641604	2		289	163	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104389875	104389875	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	230	755	0	ENST00000369902.3:c.1418T>C	p.Ile473Thr	p.I473T	ENST00000369902	NM_016169.3	473	aTc/aCc	12/12	0.749003025900717	2	FACETS	0.894	0.854	0.933	0.894	0.854	0.933	CLONAL	2	TRUE	0	0.767871222641604	2		755	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578459	7578467	+	inframe_deletion	In_Frame_Del	DEL	GACGCGGGT	GACGCGGGT	-	novel	NA	P-0056580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	503	986	0	ENST00000269305.4:c.463_471del	p.Thr155_Val157del	p.T155_V157del	ENST00000269305	NM_001126112.2	155	ACCCGCGTC/-	5/11	0.737899125272681	3	FACETS	0.98	0.956	1	0.98	0.956	1	CLONAL	3	TRUE	0	0.767871222641604	3		986	617	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865400	40865400	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	441	735	0	ENST00000428826.2:c.1031C>G	p.Ala344Gly	p.A344G	ENST00000428826		344	gCa/gGa	11/21	0.744783501843255	3	FACETS	0.99	0.966	1	0.99	0.966	1	CLONAL	3	TRUE	0	0.767871222641604	3		735	535	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985635	60985636	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0056580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	38	146	0	ENST00000333681.4:c.264_265delinsTT	p.Val89Leu	p.V89L	ENST00000333681		88	ccGGtg/ccTTtg	2/3	0.220251408310721	2	FACETS	1	0.945	1	0.611	0.526	0.697	INDETERMINATE	1	TRUE	0	0.767871222641604	2		146	81	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610535	10610535	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	258	984	0	ENST00000171111.5:c.175C>A	p.His59Asn	p.H59N	ENST00000171111	NM_203500.1	59	Cat/Aat	2/6	0.749003025900717	2	FACETS	0.901	0.863	0.937	0.901	0.863	0.937	CLONAL	2	TRUE	0	0.767871222641604	2		984	373	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902109	50902109	+	start_lost,splice_region_variant	Translation_Start_Site	SNP	A	A	T	novel	NA	P-0056580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	194	732	0	ENST00000440232.2:c.1A>T	p.Met1?	p.M1?	ENST00000440232	NM_002691.3	1	Atg/Ttg	2/27	0.562564036356811	4	FACETS	0.95	0.889	1	0.95	0.889	1	CLONAL	2	TRUE	2	0.767871222641604	4		732	470	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523528	106523528	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	170	300	0	ENST00000359195.3:c.2680A>T	p.Ser894Cys	p.S894C	ENST00000359195	NM_002649.2	894	Agc/Tgc	8/11	0.668599428933045	4	FACETS	0.983	0.916	1	0.983	0.916	1	CLONAL	2	TRUE	2	0.767871222641604	4		300	398	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245086	53245086	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0056580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	265	428	0	ENST00000375401.3:c.854C>G	p.Ser285Ter	p.S285*	ENST00000375401	NM_004187.3	285	tCa/tGa	7/26	0.573656089572332	2	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.767871222641604	2		428	304	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199769	108199769	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	62	210	0	ENST00000278616.4:c.7111T>A	p.Tyr2371Asn	p.Y2371N	ENST00000278616	NM_000051.3	2371	Tat/Aat	49/63	0.767871222641604	3	FACETS	1	0.929	1	0.542	0.476	0.612	CLONAL	1	TRUE	1	0.767871222641604	3		210	206	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588930	67588930	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	59	286	0	ENST00000274335.5:c.1021G>A	p.Glu341Lys	p.E341K	ENST00000274335		341	Gaa/Aaa	8/15	0.755249755722975	5	FACETS	1	0.965	1	0.452	0.393	0.514	CLONAL	1	TRUE	2	0.767871222641604	5		286	244	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591894	48591894	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056657-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	42	481	0	ENST00000342988.3:c.1057T>G	p.Tyr353Asp	p.Y353D	ENST00000342988	NM_005359.5	353	Tac/Gac	9/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		481	573	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436686	110436686	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056657-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	64	558	0	ENST00000375856.3:c.1715G>T	p.Arg572Leu	p.R572L	ENST00000375856	NM_003749.2	572	cGc/cTc	1/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		558	833	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508804	29508804	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs1060500274	NA	P-0056657-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	44	279	0	ENST00000356175.3:c.730+1G>C		p.X244_splice	ENST00000356175	NM_000267.3	244			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		279	343	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685324	86685325	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0056657-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	17	182	0	ENST00000274376.6:c.3041_3042dup	p.Glu1015MetfsTer10	p.E1015Mfs*10	ENST00000274376	NM_002890.2	1014	aat/aATat	24/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		182	225	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0056664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	16	501	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		501	617	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	13	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.655	0.467	0.883	0.655	0.467	0.883	SUBCLONAL	1	TRUE	1	0.19	2		306	209	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778096	135778096	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203671	NA	P-0056687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	44	602	0	ENST00000298552.3:c.2287C>T	p.Gln763Ter	p.Q763*	ENST00000298552	NM_001162426.1	763	Cag/Tag	18/23	0.22456152127217	1	FACETS	0.886	0.743	1	0.886	0.743	1	CLONAL	1	TRUE	0	0.19	1		602	473	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397742	49397742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552757	NA	P-0056687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	92	555	3	ENST00000418115.1:c.482C>T	p.Ala161Val	p.A161V	ENST00000418115	NM_001664.2	161	gCa/gTa	5/5	0.176128991256749	3	FACETS	0.842	0.749	0.941	0.842	0.749	0.941	CLONAL	2	TRUE	1	0.19	3		558	630	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630137	100630137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	44	209	0	ENST00000308731.7:c.136C>T	p.Arg46Cys	p.R46C	ENST00000308731	NM_000061.2	46	Cgt/Tgt	2/19	1	1	FACETS	1	0.88	1	1	0.973	1	CLONAL	2	TRUE	0	0.19	1		209	201	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128532	30128532	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs748363746	NA	P-0056687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	54	897	0	ENST00000263025.4:c.850C>G	p.Leu284Val	p.L284V	ENST00000263025	NM_002746.2	284	Ctg/Gtg	6/9	1	2	FACETS	0.943	0.805	1	0.943	0.805	1	CLONAL	1	TRUE	1	0.19	2		897	603	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505389	157505389	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056687-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	35	484	0	ENST00000346085.5:c.3370G>C	p.Glu1124Gln	p.E1124Q	ENST00000346085	NM_020732.3	1124	Gag/Cag	13/20	1	2	FACETS	0.937	0.769	1	0.937	0.769	1	CLONAL	1	TRUE	1	0.19	2		484	393	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246317	41246317	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056887-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	58	532	0	ENST00000357654.3:c.1231G>C	p.Asp411His	p.D411H	ENST00000357654	NM_007294.3	411	Gat/Cat	10/23	0.400617991529009	3	FACETS	1	0.884	1	0.513	0.443	0.588	CLONAL	1	TRUE	1	0.400617991529009	3		532	339	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	252	276	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.317064157998056	6	FACETS	0.928	0.873	0.984	0.928	0.873	0.984	CLONAL	4	TRUE	2	0.317064157998056	6		276	700	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028638	12028638	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	57	386	3	ENST00000353533.5:c.841C>T	p.Arg281Ter	p.R281*	ENST00000353533	NM_003010.3	281	Cga/Tga	8/11	0.312291483331213	2	FACETS	0.86	0.74	0.99	0.43	0.37	0.495	CLONAL	1	TRUE	0	0.317064157998056	2		389	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577579	7577579	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0057014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	177	581	2	ENST00000269305.4:c.702C>G	p.Tyr234Ter	p.Y234*	ENST00000269305	NM_001126112.2	234	taC/taG	7/11	0.312291483331213	2	FACETS	0.885	0.819	0.953	0.885	0.819	0.953	CLONAL	2	TRUE	0	0.317064157998056	2		583	631	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056181	27056181	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	167	584	0	ENST00000324856.7:c.1177C>T	p.Gln393Ter	p.Q393*	ENST00000324856	NM_006015.4	393	Cag/Tag	2/20	0.317064157998056	3	FACETS	0.821	0.756	0.889	0.548	0.504	0.593	CLONAL	2	TRUE	0	0.317064157998056	3		584	743	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641146	117641146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1562267726	NA	P-0057014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	108	765	2	ENST00000368508.3:c.5825G>A	p.Arg1942Gln	p.R1942Q	ENST00000368508	NM_002944.2	1942	cGg/cAg	36/43	0.312291483331213	2	FACETS	0.933	0.838	1	0.467	0.419	0.517	CLONAL	1	TRUE	0	0.317064157998056	2		767	730	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446922	18446922	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	96	285	0	ENST00000266497.5:c.1007T>C	p.Val336Ala	p.V336A	ENST00000266497		336	gTa/gCa	4/31	0.317064157998056	6	FACETS	0.834	0.745	0.929	0.417	0.372	0.465	CLONAL	2	TRUE	2	0.317064157998056	6		285	593	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	38	306	0				ENST00000310581	NM_198253.2	-/1132			0.228732017747086	1	FACETS	0.653	0.539	0.78	0.653	0.539	0.78	SUBCLONAL	1	TRUE	0	0.21	1		306	496	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584593	48584593	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	43	314	0	ENST00000342988.3:c.766C>T	p.Gln256Ter	p.Q256*	ENST00000342988	NM_005359.5	256	Cag/Tag	6/12	1	2	FACETS	0.767	0.641	0.906	0.767	0.641	0.906	CLONAL	1	TRUE	1	0.21	2		314	534	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692961	89692961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060500122	NA	P-0057061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	48	486	0	ENST00000371953.3:c.445C>T	p.Gln149Ter	p.Q149*	ENST00000371953	NM_000314.4	149	Caa/Taa	5/9	0.3	1	FACETS	0.772	0.652	0.904	0.772	0.652	0.904	CLONAL	1	TRUE	0	0.21	1		486	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578537	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs879254214	NA	P-0057061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	111	914	1	ENST00000269305.4:c.393_395del	p.Asn131del	p.N131del	ENST00000269305	NM_001126112.2	131	aaCAAg/aag	5/11	1	2	FACETS	0.864	0.775	0.96	0.864	0.775	0.96	CLONAL	1	TRUE	1	0.21	2		915	1223	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552837	106552837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1399614609	NA	P-0057061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	94	558	1	ENST00000369096.4:c.802C>T	p.Arg268Cys	p.R268C	ENST00000369096	NM_001198.3	268	Cgt/Tgt	5/7	1	2	FACETS	0.854	0.758	0.957	0.854	0.758	0.957	CLONAL	1	TRUE	1	0.21	2		559	1048	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771344	68771344	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	48	349	0	ENST00000261769.5:c.26C>A	p.Ser9Ter	p.S9*	ENST00000261769	NM_004360.3	9	tCg/tAg	1/16	1	2	FACETS	0.748	0.632	0.877	0.748	0.632	0.877	SUBCLONAL	1	TRUE	1	0.21	2		349	611	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134599	2134599	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555514409	NA	P-0057061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1185	98	1052	0	ENST00000219476.3:c.4376G>A	p.Arg1459Gln	p.R1459Q	ENST00000219476	NM_000548.3	1459	cGa/cAa	34/42	0.3	1	FACETS	0.651	0.579	0.729	0.651	0.579	0.729	SUBCLONAL	1	TRUE	0	0.21	1		1052	1283	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325216	39325216	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	73	595	0	ENST00000373001.3:c.103G>A	p.Glu35Lys	p.E35K	ENST00000373001	NM_022157.3	35	Gag/Aag	1/7	1	2	FACETS	0.705	0.615	0.803	0.705	0.615	0.803	SUBCLONAL	1	TRUE	1	0.21	2		595	986	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444333	49444333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	83	905	2	ENST00000301067.7:c.3038C>T	p.Ser1013Phe	p.S1013F	ENST00000301067	NM_003482.3	1013	tCt/tTt	11/54	1	2	FACETS	0.615	0.54	0.695	0.615	0.54	0.695	SUBCLONAL	1	TRUE	1	0.21	2		907	1286	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47700115	47700115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	40	349	0	ENST00000347630.2:c.58G>A	p.Glu20Lys	p.E20K	ENST00000347630	NM_001007230.1	20	Gag/Aag	3/11	1	2	FACETS	0.583	0.484	0.695	0.583	0.484	0.695	SUBCLONAL	1	TRUE	1	0.21	2		349	653	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39237771	39237771	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	29	283	0	ENST00000402219.2:c.2464C>G	p.Leu822Val	p.L822V	ENST00000402219	NM_005633.3	822	Ctg/Gtg	15/23	1	2	FACETS	0.619	0.496	0.759	0.619	0.496	0.759	SUBCLONAL	1	TRUE	1	0.21	2		283	446	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151189	202151189	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	16	148	0	ENST00000358485.4:c.1489G>C	p.Asp497His	p.D497H	ENST00000358485	NM_001080125.1	497	Gat/Cat	9/9	1	2	FACETS	0.571	0.422	0.749	0.571	0.422	0.749	SUBCLONAL	1	TRUE	1	0.21	2		148	267	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250522	110250522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	72	599	0	ENST00000374672.4:c.153G>A	p.Met51Ile	p.M51I	ENST00000374672	NM_004235.4	51	atG/atA	3/5	0.3	1	FACETS	0.848	0.74	0.964	0.848	0.74	0.964	CLONAL	1	TRUE	0	0.21	1		599	724	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841222	15841230	+	inframe_deletion	In_Frame_Del	DEL	GGCCGGGGC	GGCCGGGGC	-	novel	NA	P-0057061-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	34	253	0	ENST00000307771.7:c.1306_1314del	p.Gly436_Gly438del	p.G436_G438del	ENST00000307771	NM_005089.3	436	GGCCGGGGC/-	11/11	1	2	FACETS	0.777	0.635	0.936	0.777	0.635	0.936	CLONAL	1	TRUE	1	0.21	2		253	417	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950719	79950731	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCGGCCGCAGC	CAGCGGCCGCAGC	-	novel	NA	P-0057061-T02-IM6	NA	-	-	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	59	119	0	ENST00000265081.6:c.173_185del	p.Ala58GlyfsTer18	p.A58Gfs*18	ENST00000265081	NM_002439.4	58	gCAGCGGCCGCAGCg/gg	1/24	1				0.756	0.998				CLONAL	2	TRUE	1	0.21	2		119	322	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0057062-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	317	608	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	0.512522276040542	4	FACETS	0.935	0.893	0.978	0.935	0.893	0.978	CLONAL	3	TRUE	1	0.631039767277736	4		608	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579408	7579430	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGGGCCAGGAGGGGGCTGGTG	CAGGGGCCAGGAGGGGGCTGGTG	-	rs886041861	NA	P-0057062-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	614	1026	0	ENST00000269305.4:c.257_279del	p.Ala86ValfsTer55	p.A86Vfs*55	ENST00000269305	NM_001126112.2	86	gCACCAGCCCCCTCCTGGCCCCTG/g	4/11	0.631039767277736	2	FACETS	0.985	0.955	1	0.985	0.955	1	CLONAL	2	TRUE	0	0.631039767277736	2		1026	988	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182050	11182050	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057062-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	201	645	0	ENST00000361445.4:c.6796C>T	p.Arg2266Cys	p.R2266C	ENST00000361445	NM_004958.3	2266	Cgc/Tgc	48/58	0.370433762401715	3	FACETS	1	0.957	1			1	INDETERMINATE	1	TRUE	NA	0.631039767277736	3		645	805	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870853	12870853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500190	NA	P-0057062-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	28	278	1	ENST00000228872.4:c.80C>T	p.Ser27Leu	p.S27L	ENST00000228872	NM_004064.3	27	tCg/tTg	1/3	0.631039767277736	3	FACETS	0.228	0.182	0.281	0.114	0.091	0.141	SUBCLONAL	1	TRUE	1	0.631039767277736	3		279	512	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023202	27023262	+	frameshift_variant	Frame_Shift_Del	DEL	CGAACGGGAACGCGGGCCCTAGGCCCGCCCTGAACAATAACCTCACGGAGCCGCCCGGCGG	CGAACGGGAACGCGGGCCCTAGGCCCGCCCTGAACAATAACCTCACGGAGCCGCCCGGCGG	-	novel	NA	P-0057062-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	35	179	1	ENST00000324856.7:c.310_370del	p.Asn104AlafsTer108	p.N104Afs*108	ENST00000324856	NM_006015.4	103	tCGAACGGGAACGCGGGCCCTAGGCCCGCCCTGAACAATAACCTCACGGAGCCGCCCGGCGGc/tc	1/20	1	2	FACETS	0.634	0.526	0.752	0.634	0.526	0.752	SUBCLONAL	1	TRUE	1	0.631039767277736	2		180	175	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100143	30100143	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057062-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	163	664	0	ENST00000331968.5:c.1477G>C	p.Glu493Gln	p.E493Q	ENST00000331968	NM_002742.2	493	Gaa/Caa	10/18	0.631039767277736	3	FACETS	1	0.95	1	0.521	0.48	0.564	CLONAL	1	TRUE	1	0.631039767277736	3		664	652	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379721	17379721	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057062-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1420	97	1158	0	ENST00000359435.4:c.106G>T	p.Asp36Tyr	p.D36Y	ENST00000359435	NM_001033549.1	36	Gac/Tac	2/9	0.631039767277736	3	FACETS	0.267	0.236	0.299	0.133	0.118	0.15	SUBCLONAL	1	TRUE	1	0.631039767277736	3		1158	1517	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379769	17379769	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057062-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1497	105	1230	0	ENST00000359435.4:c.154G>C	p.Glu52Gln	p.E52Q	ENST00000359435	NM_001033549.1	52	Gag/Cag	2/9	0.631039767277736	3	FACETS	0.273	0.243	0.305	0.137	0.121	0.153	SUBCLONAL	1	TRUE	1	0.631039767277736	3		1230	1602	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957798	1957798	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057062-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	171	751	0	ENST00000382891.5:c.2764T>C	p.Phe922Leu	p.F922L	ENST00000382891	NM_133335.3	922	Ttc/Ctc	15/22	0.631039767277736	3	FACETS	0.936	0.862	1	0.468	0.431	0.506	CLONAL	1	TRUE	1	0.631039767277736	3		751	762	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56911023	56911023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057062-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	121	471	0	ENST00000519728.1:c.1169G>A	p.Arg390Lys	p.R390K	ENST00000519728	NM_002350.3	390	aGa/aAa	11/13	0.631039767277736	10	FACETS	1	0.937	1			1	CLONAL	1	TRUE	NA	0.631039767277736	10		471	1282	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756730	756730	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057071-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	21	474	0	ENST00000314574.4:c.98G>C	p.Gly33Ala	p.G33A	ENST00000314574	NM_005433.3	33	gGa/gCa	2/12	0.147178678843405	3	FACETS	0.582	0.449	0.737	0.194	0.149	0.246	INDETERMINATE	1	TRUE	0	0.318011657795198	3		474	263	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478638	57478638	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057071-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	83	498	0	ENST00000371085.3:c.310G>A	p.Glu104Lys	p.E104K	ENST00000371085	NM_000516.4	104	Gaa/Aaa	4/13	0.318011657795198	5	FACETS	1	0.961	1	0.404	0.357	0.455	CLONAL	1	TRUE	2	0.318011657795198	5		498	636	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057071-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	8	816	1	ENST00000374080.3:c.3670C>A	p.Leu1224Ile	p.L1224I	ENST00000374080		1224	Ctc/Atc	26/45	0.318011657795198	1	FACETS	0.121	0.077	0.177	0.121	0.077	0.177	SUBCLONAL	1	TRUE	0	0.318011657795198	1		817	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0057086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	292	968	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.318391293523163	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.318391293523163	1		968	1085	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0057086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	63	172	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.813	0.704	0.93	0.813	0.704	0.93	CLONAL	1	TRUE	1	0.318391293523163	2		172	487	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541660	120541660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	112	791	0	ENST00000229340.5:c.197G>A	p.Gly66Glu	p.G66E	ENST00000229340	NM_006861.6	66	gGg/gAg	3/6	1	2	FACETS	0.823	0.74	0.911	0.823	0.74	0.911	CLONAL	1	TRUE	1	0.318391293523163	2		791	855	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11027451	11027451	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	152	975	0	ENST00000327064.4:c.1018G>A	p.Val340Met	p.V340M	ENST00000327064	NM_199141.1	340	Gtg/Atg	8/16	1	2	FACETS	0.902	0.824	0.985	0.902	0.824	0.985	CLONAL	1	TRUE	1	0.318391293523163	2		975	1058	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0057140-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	331	399	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.299384624219364	7	FACETS	0.94	0.892	0.987	0.94	0.892	0.987	CLONAL	5	FALSE	2	0.299384624219364	7		399	823	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491662	120491663	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs312262800	NA	P-0057140-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	37	280	1	ENST00000256646.2:c.2566_2567del	p.Ser856LeufsTer17	p.S856Lfs*17	ENST00000256646	NM_024408.3	856	AGt/t	16/34	0.299384624219364	3	FACETS	0.598	0.493	0.716	0.299	0.246	0.358	SUBCLONAL	1	FALSE	1	0.299384624219364	3		281	475	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0057140-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	215	790	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.24105764299672	2	FACETS	0.789	0.734	0.846	0.789	0.734	0.846	SUBCLONAL	2	FALSE	0	0.299384624219364	2		790	910	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211534	98211534	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057140-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	86	822	0	ENST00000331920.6:c.3621C>A	p.Phe1207Leu	p.F1207L	ENST00000331920	NM_000264.3	1207	ttC/ttA	22/24	0.22997039213029	2	FACETS	0.718	0.635	0.808	0.359	0.317	0.404	SUBCLONAL	1	FALSE	0	0.299384624219364	2		822	800	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141018	55141019	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGAAATTCGCTGGAGGGTCAT	novel	NA	P-0057152-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	26	300	0	ENST00000257290.5:c.1669_1689dup	p.Ile557_Glu563dup	p.I557_E563dup	ENST00000257290	NM_006206.4	557	tat/taTGAAATTCGCTGGAGGGTCATt	12/23	0.136850086078847	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.803147009979861	0		300	408	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242715	98242716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGGC	novel	NA	P-0057152-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	711	505	0	ENST00000331920.6:c.898_901dup	p.Asp301GlyfsTer19	p.D301Gfs*19	ENST00000331920	NM_000264.3	301	gat/gGCCGat	6/24	0.803147009979861	3	FACETS	0.913	0.893	0.932	0.913	0.893	0.932	CLONAL	3	TRUE	0	0.803147009979861	3		505	906	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65311325	65311325	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0057201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	52	323	0	ENST00000342505.4:c.1988-2A>G		p.X663_splice	ENST00000342505	NM_002227.2	663			0.317208657861442	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.317208657861442	1		323	236	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981851	201981852	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0057201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	141	1026	0	ENST00000359651.3:c.566_567dup	p.Ser190ProfsTer65	p.S190Pfs*65	ENST00000359651		188	gcc/gCCcc	4/8	0.165778611265737	3	FACETS	0.753	0.687	0.821	0.753	0.687	0.821	INDETERMINATE	2	TRUE	1	0.317208657861442	3		1026	684	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243536	46243537	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	115	301	0	ENST00000334344.6:c.1890dup	p.Ser631IlefsTer76	p.S631Ifs*76	ENST00000334344	NM_152641.2	630	gta/gtAa	14/21	0.277897511046561	3	FACETS	1	0.973	1	0.789	0.718	0.862	CLONAL	2	TRUE	0	0.317208657861442	3		301	355	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254010	133254010	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	26	486	0	ENST00000320574.5:c.740G>A	p.Arg247Lys	p.R247K	ENST00000320574	NM_006231.2	247	aGa/aAa	8/49	0.317208657861442	2	FACETS	0.403	0.318	0.5	0.201	0.159	0.25	SUBCLONAL	1	TRUE	0	0.317208657861442	2		486	407	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910851	32910851	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0057201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	124	317	0	ENST00000380152.3:c.2359A>T	p.Arg787Ter	p.R787*	ENST00000380152		787	Aga/Tga	11/27	0.317208657861442	3	FACETS	0.865	0.792	0.94	0.865	0.792	0.94	CLONAL	3	TRUE	0	0.317208657861442	3		317	349	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640959	3640959	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	107	1048	0	ENST00000294008.3:c.2680G>T	p.Val894Phe	p.V894F	ENST00000294008	NM_032444.2	894	Gtc/Ttc	12/15	0.317208657861442	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.317208657861442	1		1048	477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0057201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	87	747	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.317208657861442	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.317208657861442	1		747	344	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515198	106515198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146675267	NA	P-0057201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	71	374	0	ENST00000359195.3:c.2341G>A	p.Glu781Lys	p.E781K	ENST00000359195	NM_002649.2	781	Gaa/Aaa	5/11	0.174247359926372	1	FACETS	1	0.916	1	1	0.916	1	INDETERMINATE	1	TRUE	0	0.317208657861442	1		374	357	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949060	44949060	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	101	216	0	ENST00000377967.4:c.3621del	p.Tyr1208IlefsTer13	p.Y1208Ifs*13	ENST00000377967	NM_021140.2	1207	gtG/gt	25/29	1	1	FACETS	0.947	0.859	1	1	0.988	1	CLONAL	2	TRUE	0	0.317208657861442	1		216	283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0057249-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	22	557	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.581091929101814	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.575364183241096	1		558	43	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057249-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	45	276	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.581091929101814	3	FACETS	0.846	0.731	0.966	0.846	0.731	0.966	CLONAL	2	TRUE	1	0.575364183241096	3		276	119	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0057249-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	222	410	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.575364183241096	14	FACETS	0.992	0.937	1			1	CLONAL	8	TRUE	NA	0.575364183241096	14		410	433	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2493118	2493118	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs386352373	NA	P-0057249-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	29	436	0	ENST00000355716.4:c.558C>G	p.Ser186Arg	p.S186R	ENST00000355716	NM_003820.2	186	agC/agG	6/8	0.392016313420171	1	FACETS	0.352	0.284	0.428	0.352	0.284	0.428	SUBCLONAL	1	TRUE	0	0.575364183241096	1		436	204	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687644	29687644	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057249-T03-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	28	461	0	ENST00000356175.3:c.8237A>T	p.Gln2746Leu	p.Q2746L	ENST00000356175	NM_000267.3	2746	cAg/cTg	56/57	0.575364183241096	12	FACETS	0.968	0.808	1			1	CLONAL	6	TRUE	NA	0.575364183241096	12		461	65	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523605	148523605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778304	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	62	385	0	ENST00000320356.2:c.848C>T	p.Thr283Met	p.T283M	ENST00000320356	NM_004456.4	283	aCg/aTg	8/20	1	2	FACETS	0.876	0.765	0.995	0.876	0.765	0.995	CLONAL	1	TRUE	1	0.54	2		385	262	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	61	332	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.893	0.779	1	0.893	0.779	1	CLONAL	1	TRUE	1	0.54	2		332	253	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	121	822	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	0.968	0.88	1	0.968	0.88	1	CLONAL	1	TRUE	1	0.54	2		822	463	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427721	72427721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1382885623	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	86	536	0	ENST00000477973.2:c.769G>A	p.Val257Ile	p.V257I	ENST00000477973	NM_012234.5	257	Gtc/Atc	4/4	1	2	FACETS	0.929	0.829	1	0.929	0.829	1	CLONAL	1	TRUE	1	0.54	2		536	343	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	24	292	3	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	2	FACETS	0.413	0.325	0.514	0.413	0.325	0.514	SUBCLONAL	1	TRUE	1	0.54	2		295	215	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	129	729	8	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.84	0.764	0.918	0.84	0.764	0.918	CLONAL	1	TRUE	1	0.54	2		737	569	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027494	48027494	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755587950	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	79	513	0	ENST00000234420.5:c.2372G>A	p.Arg791His	p.R791H	ENST00000234420	NM_000179.2	791	cGt/cAt	4/10	1	2	FACETS	0.938	0.833	1	0.938	0.833	1	CLONAL	1	TRUE	1	0.54	2		513	312	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	62	225	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.54	2		225	225	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	150	881	2	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.54	2		883	548	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206579	108206579	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs745901025	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	14	342	1	ENST00000278616.4:c.8159A>G	p.Asp2720Gly	p.D2720G	ENST00000278616	NM_000051.3	2720	gAt/gGt	56/63	1	2	FACETS	0.194	0.14	0.26	0.194	0.14	0.26	SUBCLONAL	1	TRUE	1	0.54	2		343	267	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	270	1035	1	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.87	0.824	0.916	1	0.995	1	CLONAL	2	TRUE	1	0.54	2		1036	575	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101300	27101300	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	108	1141	3	ENST00000324856.7:c.4582C>T	p.Arg1528Ter	p.R1528*	ENST00000324856	NM_006015.4	1528	Cga/Tga	18/20	1	2	FACETS	0.739	0.666	0.817	0.739	0.666	0.817	SUBCLONAL	1	TRUE	1	0.54	2		1144	541	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752960	128752960	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	83	512	0	ENST00000377970.2:c.1121A>G	p.His374Arg	p.H374R	ENST00000377970	NM_002467.4	374	cAc/cGc	3/3	1	2	FACETS	0.807	0.717	0.902	0.807	0.717	0.902	CLONAL	1	TRUE	1	0.54	2		512	381	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	68	352	5	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.785	0.688	0.888	0.785	0.688	0.888	SUBCLONAL	1	TRUE	1	0.54	2		357	321	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422384	47422384	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	90	628	3	ENST00000377045.4:c.23del	p.Pro8LeufsTer26	p.P8Lfs*26	ENST00000377045	NM_001654.4	6	ggC/gg	2/16	1	2	FACETS	0.906	0.81	1	0.906	0.81	1	CLONAL	1	TRUE	1	0.54	2		631	368	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741936	17741936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	26	289	0	ENST00000250003.3:c.607C>T	p.Arg203Cys	p.R203C	ENST00000250003	NM_002478.4	203	Cgc/Tgc	1/3	1	2	FACETS	0.669	0.536	0.816	0.669	0.536	0.816	SUBCLONAL	1	TRUE	1	0.54	2		289	144	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	120	681	0	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.54	2		681	444	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487510	38487510	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567751372	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	126	689	0	ENST00000254066.5:c.40G>A	p.Gly14Arg	p.G14R	ENST00000254066	NM_000964.3	14	Ggg/Agg	2/9	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.54	2		689	438	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592099	67592099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	65	255	0	ENST00000274335.5:c.1915C>T	p.Arg639Ter	p.R639*	ENST00000274335		639	Cga/Tga	14/15	1	2	FACETS	0.959	0.841	1	0.959	0.841	1	CLONAL	1	TRUE	1	0.54	2		255	251	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761459	59761460	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs774684620	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	83	539	0	ENST00000259008.2:c.2947dup	p.Ile983AsnfsTer19	p.I983Nfs*19	ENST00000259008	NM_032043.2	983	att/aAtt	20/20	1	2	FACETS	0.92	0.819	1	0.92	0.819	1	CLONAL	1	TRUE	1	0.54	2		539	334	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692896	89692896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123322	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	96	557	0	ENST00000371953.3:c.380G>A	p.Gly127Glu	p.G127E	ENST00000371953	NM_000314.4	127	gGa/gAa	5/9	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.54	2		557	327	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243999	53243999	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	145	893	1	ENST00000375401.3:c.994C>T	p.Arg332Ter	p.R332*	ENST00000375401	NM_004187.3	332	Cga/Tga	8/26	1	2	FACETS	0.87	0.797	0.947	0.87	0.797	0.947	CLONAL	1	TRUE	1	0.54	2		894	617	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs371769427	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	68	345	0	ENST00000291552.4:c.101C>A	p.Ser34Tyr	p.S34Y	ENST00000291552	NM_006758.2	34	tCt/tAt	2/8	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.54	2		345	239	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526314	189526314	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	97	573	1	ENST00000264731.3:c.578C>T	p.Thr193Met	p.T193M	ENST00000264731	NM_003722.4	193	aCg/aTg	4/14	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.54	2		574	349	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582118	189582118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs193921145	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	117	641	1	ENST00000264731.3:c.677G>A	p.Arg226His	p.R226H	ENST00000264731	NM_003722.4	226	cGc/cAc	5/14	1	2	FACETS	0.946	0.859	1	0.946	0.859	1	CLONAL	1	TRUE	1	0.54	2		642	458	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562266	95562266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs988095775	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	75	339	0	ENST00000393063.1:c.4991C>T	p.Ser1664Leu	p.S1664L	ENST00000393063	NM_030621.3	1664	tCg/tTg	24/28	1	2	FACETS	0.905	0.8	1	0.905	0.8	1	CLONAL	1	TRUE	1	0.54	2		339	307	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528252	157528252	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554237801	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	122	811	1	ENST00000346085.5:c.5977C>T	p.Gln1993Ter	p.Q1993*	ENST00000346085	NM_020732.3	1993	Cag/Tag	20/20	1	2	FACETS	0.835	0.758	0.916	0.835	0.758	0.916	CLONAL	1	TRUE	1	0.54	2		812	541	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265313	10265313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762421501	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	104	861	0	ENST00000340748.4:c.1733C>T	p.Thr578Ile	p.T578I	ENST00000340748		578	aCa/aTa	20/40	1	2	FACETS	0.742	0.667	0.821	0.742	0.667	0.821	SUBCLONAL	1	TRUE	1	0.54	2		861	519	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40486033	40486033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555566945	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	116	808	0	ENST00000264657.5:c.832C>T	p.Arg278Cys	p.R278C	ENST00000264657	NM_139276.2	278	Cgt/Tgt	9/24	1	2	FACETS	0.817	0.739	0.898	0.817	0.739	0.898	CLONAL	1	TRUE	1	0.54	2		808	526	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202184	138202184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772293188	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	95	590	0	ENST00000237289.4:c.2101C>T	p.Arg701Cys	p.R701C	ENST00000237289	NM_001270507.1	701	Cgc/Tgc	9/9	1	2	FACETS	0.914	0.82	1	0.914	0.82	1	CLONAL	1	TRUE	1	0.54	2		590	385	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638222	176638222	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs189716582	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	164	965	0	ENST00000439151.2:c.2822G>A	p.Arg941His	p.R941H	ENST00000439151	NM_022455.4	941	cGt/cAt	5/23	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.54	2		965	575	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56878465	56878465	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	31	606	0	ENST00000308159.5:c.2404C>T	p.Arg802Ter	p.R802*	ENST00000308159	NM_014669.4	802	Cga/Tga	22/22	1	2	FACETS	0.282	0.228	0.344	0.282	0.228	0.344	SUBCLONAL	1	TRUE	1	0.54	2		606	407	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568636	41568636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	78	495	0	ENST00000263253.7:c.4586G>A	p.Arg1529Gln	p.R1529Q	ENST00000263253	NM_001429.3	1529	cGa/cAa	28/31	1	2	FACETS	0.908	0.806	1	0.908	0.806	1	CLONAL	1	TRUE	1	0.54	2		495	318	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822584	72822584	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555515881	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	41	735	1	ENST00000268489.5:c.9591G>C	p.Gln3197His	p.Q3197H	ENST00000268489	NM_006885.3	3197	caG/caC	10/10	1	2	FACETS	0.389	0.325	0.461	0.389	0.325	0.461	SUBCLONAL	1	TRUE	1	0.54	2		736	390	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822585	72822585	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs141461385	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	53	739	0	ENST00000268489.5:c.9590A>C	p.Gln3197Pro	p.Q3197P	ENST00000268489	NM_006885.3	3197	cAg/cCg	10/10	1	2	FACETS	0.497	0.425	0.575	0.497	0.425	0.575	SUBCLONAL	1	TRUE	1	0.54	2		739	395	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584478	52584478	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142726131	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	106	610	1	ENST00000394830.3:c.4535C>T	p.Ala1512Val	p.A1512V	ENST00000394830	NM_018313.4	1512	gCg/gTg	29/30	1	2	FACETS	0.93	0.84	1	0.93	0.84	1	CLONAL	1	TRUE	1	0.54	2		611	422	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422085	81422085	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1006500286	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	61	706	1	ENST00000298171.2:c.61G>A	p.Gly21Arg	p.G21R	ENST00000298171	NM_000369.2	21	Gga/Aga	1/10	1	2	FACETS	0.611	0.529	0.698	0.611	0.529	0.698	SUBCLONAL	1	TRUE	1	0.54	2		707	370	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	256476	256476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376986935	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	123	769	0	ENST00000264932.6:c.1936G>A	p.Asp646Asn	p.D646N	ENST00000264932	NM_004168.2	646	Gac/Aac	15/15	1	2	FACETS	0.986	0.898	1	0.986	0.898	1	CLONAL	1	TRUE	1	0.54	2		769	462	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126103	2126103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376801256	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	146	1053	2	ENST00000219476.3:c.2674G>A	p.Val892Ile	p.V892I	ENST00000219476	NM_000548.3	892	Gtc/Atc	24/42	1	2	FACETS	0.932	0.855	1	0.932	0.855	1	CLONAL	1	TRUE	1	0.54	2		1055	580	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993822	72993822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374552910	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	73	916	3	ENST00000268489.5:c.223G>A	p.Ala75Thr	p.A75T	ENST00000268489	NM_006885.3	75	Gcc/Acc	2/10	1	2	FACETS	0.753	0.663	0.849	0.753	0.663	0.849	SUBCLONAL	1	TRUE	1	0.54	2		919	359	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948545	71948545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138596491	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	193	1211	2	ENST00000298229.2:c.3257G>A	p.Arg1086His	p.R1086H	ENST00000298229	NM_001567.3	1086	cGt/cAt	26/28	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.54	2		1213	691	SUCCESS
APC	324	MSKCC	GRCh37	5	112175265	112175265	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	51	276	0	ENST00000257430.4:c.3974C>T	p.Ala1325Val	p.A1325V	ENST00000257430	NM_000038.5	1325	gCa/gTa	16/16	1	2	FACETS	0.994	0.858	1	0.994	0.858	1	CLONAL	1	TRUE	1	0.54	2		276	190	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864062	97864062	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779902	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	117	744	3	ENST00000289081.3:c.1604G>A	p.Arg535His	p.R535H	ENST00000289081	NM_000136.2	535	cGt/cAt	15/15	1	2	FACETS	0.998	0.907	1	0.998	0.907	1	CLONAL	1	TRUE	1	0.54	2		747	434	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859420	151859420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148366561	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	113	629	0	ENST00000262189.6:c.11242G>A	p.Ala3748Thr	p.A3748T	ENST00000262189	NM_170606.2	3748	Gct/Act	43/59	1	2	FACETS	0.999	0.906	1	0.999	0.906	1	CLONAL	1	TRUE	1	0.54	2		629	419	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196150	138196150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750716064	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	59	446	0	ENST00000237289.4:c.464C>T	p.Thr155Met	p.T155M	ENST00000237289	NM_001270507.1	155	aCg/aTg	3/9	1	2	FACETS	0.751	0.651	0.858	0.751	0.651	0.858	SUBCLONAL	1	TRUE	1	0.54	2		446	291	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997810	149997810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765740626	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	99	736	0	ENST00000253339.5:c.2657G>A	p.Arg886Gln	p.R886Q	ENST00000253339		886	cGa/cAa	5/7	1	2	FACETS	0.824	0.74	0.913	0.824	0.74	0.913	CLONAL	1	TRUE	1	0.54	2		736	445	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864451	151864451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs535118581	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	59	409	1	ENST00000262189.6:c.9530G>A	p.Arg3177His	p.R3177H	ENST00000262189	NM_170606.2	3177	cGt/cAt	42/59	1	2	FACETS	0.778	0.675	0.888	0.778	0.675	0.888	SUBCLONAL	1	TRUE	1	0.54	2		410	281	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533878	533878	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	163	1055	1	ENST00000451590.1:c.178G>T	p.Gly60Cys	p.G60C	ENST00000451590	NM_001130442.1	60	Ggc/Tgc	3/5	1	2	FACETS	0.94	0.866	1	0.94	0.866	1	CLONAL	1	TRUE	1	0.54	2		1056	642	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94963997	94963997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	37	173	0	ENST00000536441.1:c.28G>A	p.Ala10Thr	p.A10T	ENST00000536441	NM_144665.3	10	Gcc/Acc	1/10	1	2	FACETS	0.926	0.776	1	0.926	0.776	1	CLONAL	1	TRUE	1	0.54	2		173	148	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118367047	118367047	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	95	679	0	ENST00000534358.1:c.5629G>A	p.Ala1877Thr	p.A1877T	ENST00000534358	NM_005933.3	1877	Gcg/Acg	20/36	1	2	FACETS	0.919	0.824	1	0.919	0.824	1	CLONAL	1	TRUE	1	0.54	2		679	383	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50490655	50490655	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	93	653	0	ENST00000394963.4:c.1292T>C	p.Ile431Thr	p.I431T	ENST00000394963	NM_003076.4	431	aTc/aCc	11/13	1	2	FACETS	0.788	0.705	0.876	0.788	0.705	0.876	SUBCLONAL	1	TRUE	1	0.54	2		653	437	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911442	32911442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	61	517	0	ENST00000380152.3:c.2950G>A	p.Glu984Lys	p.E984K	ENST00000380152		984	Gaa/Aaa	11/27	1	2	FACETS	0.796	0.692	0.906	0.796	0.692	0.906	CLONAL	1	TRUE	1	0.54	2		517	284	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335872	73335872	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	91	563	0	ENST00000377767.4:c.2423A>T	p.His808Leu	p.H808L	ENST00000377767	NM_014953.3	808	cAc/cTc	18/21	1	2	FACETS	0.971	0.87	1	0.971	0.87	1	CLONAL	1	TRUE	1	0.54	2		563	347	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95598932	95598932	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	105	580	0	ENST00000393063.1:c.227T>C	p.Leu76Pro	p.L76P	ENST00000393063	NM_030621.3	76	cTa/cCa	4/28	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.54	2		580	387	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096331	2096331	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773364076	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	164	1166	1	ENST00000219066.1:c.176G>A	p.Arg59Gln	p.R59Q	ENST00000219066	NM_002528.5	59	cGg/cAg	2/6	1	2	FACETS	0.79	0.726	0.856	0.79	0.726	0.856	SUBCLONAL	1	TRUE	1	0.54	2		1167	769	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868165	56868165	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	107	821	0	ENST00000308159.5:c.1663A>G	p.Arg555Gly	p.R555G	ENST00000308159	NM_014669.4	555	Agg/Ggg	14/22	1	2	FACETS	0.974	0.88	1	0.974	0.88	1	CLONAL	1	TRUE	1	0.54	2		821	407	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822584	72822585	+	missense_variant	Missense_Mutation	DNP	CT	CT	GG	novel	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	53	734	5	ENST00000268489.5:c.9590_9591delinsCC	p.Gln3197Pro	p.Q3197P	ENST00000268489	NM_006885.3	3197	cAG/cCC	10/10	1	2	FACETS	0.497	0.425	0.575	0.497	0.425	0.575	SUBCLONAL	1	TRUE	1	0.54	2		739	395	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828550	72828550	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	139	961	1	ENST00000268489.5:c.8031G>T	p.Glu2677Asp	p.E2677D	ENST00000268489	NM_006885.3	2677	gaG/gaT	9/10	1	2	FACETS	0.812	0.741	0.886	0.812	0.741	0.886	CLONAL	1	TRUE	1	0.54	2		962	634	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934300	81934300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	148	966	0	ENST00000359376.3:c.1277G>A	p.Gly426Asp	p.G426D	ENST00000359376	NM_002661.3	426	gGc/gAc	14/33	1	2	FACETS	0.917	0.841	0.996	0.917	0.841	0.996	CLONAL	1	TRUE	1	0.54	2		966	598	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532579	63532579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878854724	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	181	1082	0	ENST00000307078.5:c.2000G>A	p.Ser667Asn	p.S667N	ENST00000307078	NM_004655.3	667	aGc/aAc	8/11	1	2	FACETS	0.984	0.911	1	0.984	0.911	1	CLONAL	1	TRUE	1	0.54	2		1082	681	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56339030	56339030	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	18	84	0	ENST00000348428.3:c.155G>C	p.Arg52Pro	p.R52P	ENST00000348428	NM_006785.3	52	cGg/cCg	1/17	1	2	FACETS	0.766	0.588	0.967	0.766	0.588	0.967	CLONAL	1	TRUE	1	0.54	2		84	87	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222469	2222469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370099172	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	105	541	0	ENST00000398665.3:c.3301G>A	p.Ala1101Thr	p.A1101T	ENST00000398665	NM_032482.2	1101	Gca/Aca	24/28	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.54	2		541	343	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602691	10602691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146609162	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	149	1017	4	ENST00000171111.5:c.887G>A	p.Arg296His	p.R296H	ENST00000171111	NM_203500.1	296	cGc/cAc	3/6	1	2	FACETS	0.825	0.756	0.897	0.825	0.756	0.897	CLONAL	1	TRUE	1	0.54	2		1021	669	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027350	48027351	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs786201050	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	79	460	0	ENST00000234420.5:c.2230dup	p.Glu744GlyfsTer12	p.E744Gfs*12	ENST00000234420	NM_000179.2	743	ttg/ttGg	4/10	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.54	2		460	288	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719547	61719547	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	122	693	0	ENST00000401558.2:c.1636T>C	p.Tyr546His	p.Y546H	ENST00000401558	NM_003400.3	546	Tac/Cac	15/25	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.54	2		693	432	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594123	158594123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1256476437	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	77	498	0	ENST00000263640.3:c.1450G>A	p.Ala484Thr	p.A484T	ENST00000263640	NM_001105.4	484	Gca/Aca	11/11	1	2	FACETS	0.914	0.81	1	0.914	0.81	1	CLONAL	1	TRUE	1	0.54	2		498	312	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149982	202149982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	29	844	2	ENST00000358485.4:c.1423G>A	p.Ala475Thr	p.A475T	ENST00000358485	NM_001080125.1	475	Gca/Aca	8/9	1	2	FACETS	0.196	0.157	0.241	0.196	0.157	0.241	SUBCLONAL	1	TRUE	1	0.54	2		846	547	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665195	138665195	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	162	910	0	ENST00000330315.3:c.370A>T	p.Lys124Ter	p.K124*	ENST00000330315	NM_023067.3	124	Aag/Tag	1/1	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.54	2		910	589	SUCCESS
ATR	545	MSKCC	GRCh37	3	142241601	142241601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371292374	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	72	515	2	ENST00000350721.4:c.4235G>A	p.Arg1412Gln	p.R1412Q	ENST00000350721	NM_001184.3	1412	cGa/cAa	23/47	1	2	FACETS	0.874	0.771	0.984	0.874	0.771	0.984	CLONAL	1	TRUE	1	0.54	2		517	305	SUCCESS
APC	324	MSKCC	GRCh37	5	112177854	112177854	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	83	418	0	ENST00000257430.4:c.6563T>G	p.Ile2188Ser	p.I2188S	ENST00000257430	NM_000038.5	2188	aTc/aGc	16/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.54	2		418	247	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818423	170818423	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	46	286	0	ENST00000296930.5:c.253C>A	p.Pro85Thr	p.P85T	ENST00000296930	NM_002520.6	85	Cca/Aca	3/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.54	2		286	146	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004339	150004339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	110	600	0	ENST00000253339.5:c.1886C>T	p.Ser629Phe	p.S629F	ENST00000253339		629	tCt/tTt	3/7	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.54	2		600	368	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739478	145739478	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771179943	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	116	949	0	ENST00000428558.2:c.1892G>A	p.Arg631His	p.R631H	ENST00000428558	NM_004260.3	631	cGc/cAc	12/22	1	2	FACETS	0.863	0.781	0.948	0.863	0.781	0.948	CLONAL	1	TRUE	1	0.54	2		949	498	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401399	139401399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757508359	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	155	1016	1	ENST00000277541.6:c.3670G>A	p.Asp1224Asn	p.D1224N	ENST00000277541	NM_017617.3	1224	Gac/Aac	23/34	1	2	FACETS	0.867	0.796	0.941	0.867	0.796	0.941	CLONAL	1	TRUE	1	0.54	2		1017	662	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352265	70352265	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	140	976	0	ENST00000374080.3:c.4292T>C	p.Leu1431Pro	p.L1431P	ENST00000374080		1431	cTc/cCc	31/45	1	2	FACETS	0.9	0.823	0.98	0.9	0.823	0.98	CLONAL	1	TRUE	1	0.54	2		976	576	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945129	32945129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80359104	NA	P-0057376-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	49	270	0	ENST00000380152.3:c.8524C>T	p.Arg2842Cys	p.R2842C	ENST00000380152		2842	Cgc/Tgc	20/27	1	2	FACETS	0.734	0.625	0.852	0.734	0.625	0.852	SUBCLONAL	1	TRUE	1	0.435011839378428	2		270	307	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0057378-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	188	293	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.718564885705161	2		293	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0057378-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	367	559	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.718564885705161	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.718564885705161	1		559	598	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971170	21971170	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057378-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	187	564	0	ENST00000304494.5:c.188T>G	p.Leu63Arg	p.L63R	ENST00000304494	NM_000077.4	63	cTg/cGg	2/3	0.718564885705161	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.718564885705161	1		564	333	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420016	49420017	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057378-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	281	852	0	ENST00000301067.7:c.15732dup	p.Val5245SerfsTer13	p.V5245Sfs*13	ENST00000301067	NM_003482.3	5244	-/A	48/54	1	2	FACETS	0.994	0.938	1	0.994	0.938	1	CLONAL	1	TRUE	1	0.718564885705161	2		852	787	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438217	56438217	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057378-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	683	1158	0	ENST00000407977.2:c.776G>A	p.Trp259Ter	p.W259*	ENST00000407977		259	tGg/tAg	7/10	0.718564885705161	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.718564885705161	3		1158	1275	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0057388-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	123	546	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.282913162805806	3	FACETS	1	0.982	1	0.671	0.609	0.735	CLONAL	1	TRUE	1	0.4292704798552	3		546	519	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0057388-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	295	953	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.354430231983359	2	FACETS	0.898	0.85	0.947	0.898	0.85	0.947	CLONAL	2	TRUE	0	0.4292704798552	2		953	765	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797425	42797425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057388-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	50	1356	0	ENST00000575354.2:c.3787G>A	p.Glu1263Lys	p.E1263K	ENST00000575354	NM_015125.3	1263	Gag/Aag	15/20	0.392020087708853	2	FACETS	0.269	0.227	0.315	0.135	0.113	0.158	SUBCLONAL	1	TRUE	0	0.4292704798552	2		1356	866	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850721	63850723	+	missense_variant	Missense_Mutation	TNP	ATC	ATC	GTG	novel	NA	P-0057388-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	78	378	0	ENST00000279873.7:c.1499_1501delinsGTG	p.Tyr500_Gln501delinsCysGlu	p.Y500_Q501delinsCE	ENST00000279873	NM_032199.2	500	tATCag/tGTGag	10/10	0.288869927181003	1	FACETS	0.78	0.69	0.875	0.78	0.69	0.875	SUBCLONAL	1	TRUE	0	0.4292704798552	1		378	366	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0057391-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	124	380	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.283187810587324	1	FACETS	0.891	0.806	0.981	0.891	0.806	0.981	CLONAL	1	TRUE	0	0.293148632271809	1		380	810	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443613	29443613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519783	NA	P-0057391-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	141	743	0	ENST00000389048.3:c.3604G>A	p.Gly1202Arg	p.G1202R	ENST00000389048	NM_004304.4	1202	Gga/Aga	23/29	0.190015062185598	1	FACETS	0.861	0.783	0.942	0.861	0.783	0.942	CLONAL	1	TRUE	0	0.293148632271809	1		743	954	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433416	138433416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1194347036	NA	P-0057391-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	71	447	0	ENST00000289153.2:c.1196G>A	p.Arg399Gln	p.R399Q	ENST00000289153	NM_006219.2	399	cGa/cAa	7/22	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.293148632271809	2		447	460	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805826	46805826	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1176443254	NA	P-0057391-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	125	751	2	ENST00000290295.7:c.130C>T	p.Pro44Ser	p.P44S	ENST00000290295	NM_006361.5	44	Cct/Tct	1/2	1	2	FACETS	0.952	0.861	1	0.952	0.861	1	CLONAL	1	TRUE	1	0.293148632271809	2		753	896	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0057422-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	619	546	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.549891462149113	5	FACETS	1	0.97	1	1	0.97	1	CLONAL	4	TRUE	1	0.563430053446624	5		546	1013	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161391	2161391	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057422-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	207	539	1	ENST00000434045.2:c.136C>T	p.Arg46Cys	p.R46C	ENST00000434045	NM_001127598.1	46	Cgc/Tgc	2/5	NA	2	FACETS	0.957	0.89	1			1	INDETERMINATE	1	TRUE	NA	0.563430053446624	2		540	768	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577514	7577516	+	inframe_deletion	In_Frame_Del	DEL	GTG	GTG	-	novel	NA	P-0057422-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	188	401	0	ENST00000269305.4:c.765_767del	p.Thr256del	p.T256del	ENST00000269305	NM_001126112.2	255	atCACa/ata	7/11	0.563430053446624	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.563430053446624	1		401	452	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679376	29679376	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057422-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	188	408	0	ENST00000356175.3:c.7496A>C	p.Lys2499Thr	p.K2499T	ENST00000356175	NM_000267.3	2499	aAa/aCa	50/57	0.563430053446624	3	FACETS	0.992	0.918	1	0.496	0.459	0.535	CLONAL	1	TRUE	1	0.563430053446624	3		408	862	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630930	187630937	+	frameshift_variant	Frame_Shift_Del	DEL	AATGTTGG	AATGTTGG	-	novel	NA	P-0057422-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	577	524	0	ENST00000441802.2:c.45_52del	p.Gln16TrpfsTer4	p.Q16Wfs*4	ENST00000441802	NM_005245.3	15	ttCCAACATTtt/tttt	2/27	0.538491139121595	3	FACETS	0.954	0.925	0.983	0.954	0.925	0.983	CLONAL	3	TRUE	0	0.563430053446624	3		524	917	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748111	72748111	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	32	631	0	ENST00000357731.5:c.67A>C	p.Ser23Arg	p.S23R	ENST00000357731	NM_173808.2	23	Agc/Cgc	1/7	0.337617319127759	5	FACETS	0.47	0.38	0.571	0.157	0.126	0.191	SUBCLONAL	1	FALSE	2	0.337617319127759	5		631	608	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243675634	243675634	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	51	250	0	ENST00000263826.5:c.1346C>A	p.Pro449His	p.P449H	ENST00000263826	NM_005465.4	449	cCt/cAt	12/13	0.215633731071263	5	FACETS	0.798	0.683	0.923	0.532	0.455	0.615	CLONAL	2	FALSE	2	0.337617319127759	5		250	285	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456268	32456268	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	333	1133	0	ENST00000332351.3:c.624C>G	p.Ser208Arg	p.S208R	ENST00000332351	NM_024426.4	208	agC/agG	1/10	0.262612346478253	5	FACETS	0.946	0.896	0.997	0.946	0.896	0.997	CLONAL	3	FALSE	2	0.337617319127759	5		1133	1047	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246424	105246424	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0057426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	180	703	2	ENST00000349310.3:c.175+1G>T		p.X59_splice	ENST00000349310	NM_001014432.1	59			0.337617319127759	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	FALSE	1	0.337617319127759	3		705	606	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680662	88680662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	157	682	0	ENST00000360948.2:c.595C>A	p.Leu199Ile	p.L199I	ENST00000360948	NM_001012338.2	199	Ctc/Atc	6/19	0.215633731071263	5	FACETS	1	0.98	1	0.802	0.739	0.868	CLONAL	2	FALSE	2	0.337617319127759	5		682	582	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799180	88799180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	140	628	0	ENST00000360948.2:c.205G>A	p.Ala69Thr	p.A69T	ENST00000360948	NM_001012338.2	69	Gcc/Acc	2/19	0.215633731071263	5	FACETS	1	0.978	1	0.799	0.732	0.869	CLONAL	2	FALSE	2	0.337617319127759	5		628	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs878854073	NA	P-0057426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	120	570	0	ENST00000269305.4:c.673-1G>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.240854627177842	3	FACETS	0.955	0.869	1	0.637	0.579	0.696	CLONAL	2	FALSE	0	0.337617319127759	3		570	435	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546041	29546044	+	stop_gained	Nonsense_Mutation	ONP	CCCG	CCCG	TCCT	novel	NA	P-0057426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	110	433	0	ENST00000356175.3:c.1546_1549delinsTCCT	p.Pro516_Glu517delinsSerTer	p.P516_E517delinsS*	ENST00000356175	NM_000267.3	516	CCCGaa/TCCTaa	14/57	0.240854627177842	3	FACETS	0.947	0.858	1	0.632	0.572	0.694	CLONAL	2	FALSE	0	0.337617319127759	3		433	402	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557869	29557869	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555614624	NA	P-0057426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	17	270	1	ENST00000356175.3:c.3124del	p.Val1042Ter	p.V1042*	ENST00000356175	NM_000267.3	1041	atG/at	24/57	0.240854627177842	3	FACETS	0.519	0.388	0.673	0.173	0.129	0.225	SUBCLONAL	1	FALSE	0	0.337617319127759	3		271	227	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805552	46805552	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	224	1131	0	ENST00000290295.7:c.404G>T	p.Gly135Val	p.G135V	ENST00000290295	NM_006361.5	135	gGa/gTa	1/2	0.240854627177842	3	FACETS	0.959	0.895	1	0.639	0.596	0.683	CLONAL	2	FALSE	0	0.337617319127759	3		1131	809	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637944	39637944	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs771812389	NA	P-0057426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	89	594	0	ENST00000262039.4:c.2361G>T	p.Met787Ile	p.M787I	ENST00000262039	NM_002647.2	787	atG/atT	22/25	0.165041265883663	2	FACETS	1	0.962	1	0.592	0.528	0.661	INDETERMINATE	1	FALSE	0	0.337617319127759	2		594	445	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584723	48584724	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	78	427	0	ENST00000342988.3:c.802dup	p.Trp268LeufsTer5	p.W268Lfs*5	ENST00000342988	NM_005359.5	267	-/T	7/12	0.165041265883663	2	FACETS	1	0.974	1	0.688	0.609	0.771	INDETERMINATE	1	FALSE	0	0.337617319127759	2		427	336	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0057426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	300	940	1	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.264944901060264	3	FACETS	0.974	0.923	1	0.974	0.923	1	CLONAL	3	FALSE	0	0.337617319127759	3		941	711	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546758	9546758	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	25	435	0	ENST00000353224.5:c.1264C>G	p.Gln422Glu	p.Q422E	ENST00000353224	NM_177990.2	422	Cag/Gag	5/10	0.337617319127759	5	FACETS	0.52	0.409	0.648	0.173	0.136	0.216	SUBCLONAL	1	FALSE	2	0.337617319127759	5		435	429	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714397	40714397	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753905388	NA	P-0057426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	55	589	0	ENST00000373198.4:c.4000A>G	p.Arg1334Gly	p.R1334G	ENST00000373198	NM_133170.3	1334	Aga/Gga	29/32	0.337617319127759	3	FACETS	0.704	0.602	0.815			1	SUBCLONAL	1	FALSE	NA	0.337617319127759	3		589	541	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730897	40730897	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	238	734	1	ENST00000373198.4:c.3638G>T	p.Cys1213Phe	p.C1213F	ENST00000373198	NM_133170.3	1213	tGc/tTc	27/32	0.337617319127759	3	FACETS	1	0.982	1			1	CLONAL	2	FALSE	NA	0.337617319127759	3		735	732	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973918	55973918	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	198	568	0	ENST00000263923.4:c.1398C>G	p.Cys466Trp	p.C466W	ENST00000263923	NM_002253.2	466	tgC/tgG	10/30	0.264944901060264	3	FACETS	0.944	0.883	1	0.944	0.883	1	CLONAL	3	FALSE	0	0.337617319127759	3		568	484	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519643	137519643	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	78	378	0	ENST00000367739.4:c.995C>T	p.Pro332Leu	p.P332L	ENST00000367739	NM_000416.2	332	cCa/cTa	7/7	0.337617319127759	3	FACETS	1	0.976	1	0.732	0.647	0.821	CLONAL	1	FALSE	1	0.337617319127759	3		378	369	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38194913	38194913	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	63	605	0	ENST00000317025.8:c.820del	p.Val274CysfsTer106	p.V274Cfs*106	ENST00000317025	NM_023034.1	274	Gtg/tg	4/24	0.337617319127759	3	FACETS	0.58	0.501	0.666			1	SUBCLONAL	1	FALSE	NA	0.337617319127759	3		605	752	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923388	36923389	+	missense_variant	Missense_Mutation	DNP	TG	TG	CT	novel	NA	P-0057426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	74	941	0	ENST00000358127.4:c.873_874delinsAG	p.Ser291_Ser292delinsArgGly	p.S291_S292delinsRG	ENST00000358127	NM_001280556.1	291	agCAgt/agAGgt	7/10	0.337617319127759	3	FACETS	0.761	0.666	0.864			1	SUBCLONAL	1	FALSE	NA	0.337617319127759	3		941	673	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781501	135781501	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	116	466	0	ENST00000298552.3:c.1464G>T	p.Glu488Asp	p.E488D	ENST00000298552	NM_001162426.1	488	gaG/gaT	15/23	0.23536387725594	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	FALSE	2	0.337617319127759	4		466	420	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835670	68835670	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057427-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	324	614	0	ENST00000261769.5:c.261G>T	p.Arg87Ser	p.R87S	ENST00000261769	NM_004360.3	87	agG/agT	3/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.646777790967665	2		614	1000	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65300294	65300294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057427-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	96	168	0	ENST00000342505.4:c.3416G>A	p.Arg1139Gln	p.R1139Q	ENST00000342505	NM_002227.2	1139	cGg/cAg	25/25	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.646777790967665	NA		168	265	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604671	48604671	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0057427-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	21	367	0	ENST00000342988.3:c.1493T>A	p.Leu498Ter	p.L498*	ENST00000342988	NM_005359.5	498	tTa/tAa	12/12	0.646777790967665	1	FACETS	0.114	0.087	0.145	0.114	0.087	0.145	SUBCLONAL	1	TRUE	0	0.646777790967665	1		367	386	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419921	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0057427-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	267	627	0	ENST00000206249.3:c.1607_1608delinsAA	p.Leu536Gln	p.L536Q	ENST00000206249	NM_000125.3	536	cTC/cAA	8/8	0.646777790967665	1	FACETS	0.957	0.905	1	0.957	0.905	1	CLONAL	1	TRUE	0	0.646777790967665	1		627	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0057431-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	334	641	1	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.662657888789789	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.904107447474053	1		642	366	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829040	128829042	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	rs570242755	NA	P-0057431-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	14	74	0	ENST00000249373.3:c.67_69del	p.Leu23del	p.L23del	ENST00000249373	NM_005631.4	16	ggGCTg/ggg	1/12	0.702037944542717	3	FACETS	0.18	0.13	0.241			1	SUBCLONAL	1	TRUE	NA	0.904107447474053	3		74	250	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563272	21563272	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057431-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	9	1778	4	ENST00000382592.4:c.647del	p.Phe216SerfsTer24	p.F216Sfs*24	ENST00000382592	NM_014572.2	216	tTc/tc	4/8	0.904107447474053	1	FACETS	0.032	0.021	0.046	0.032	0.021	0.046	SUBCLONAL	1	TRUE	0	0.904107447474053	1		1782	341	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65316506	65316506	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057435-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	102	353	0	ENST00000342505.4:c.1736T>G	p.Leu579Arg	p.L579R	ENST00000342505	NM_002227.2	579	cTc/cGc	12/25	0.649336119896771	3	FACETS	1	0.926	1	0.517	0.465	0.571	CLONAL	1	TRUE	1	0.6441598597807	3		353	405	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176176062	176176062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057435-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	172	706	0	ENST00000367669.3:c.53C>T	p.Ser18Phe	p.S18F	ENST00000367669	NM_022457.5	18	tCc/tTc	1/20	0.268157775141354	6	FACETS	0.869	0.802	0.939			1	INDETERMINATE	2	TRUE	NA	0.6441598597807	6		706	703	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61197642	61197663	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACTTCGTCGCTGGTGAGGAGA	GACTTCGTCGCTGGTGAGGAGA	-	novel	NA	P-0057435-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	203	516	0	ENST00000301761.2:c.26_36+11del		p.X9_splice	ENST00000301761	NM_017841.2	9		1/4	0.649336119896771	3	FACETS	0.856	0.801	0.91	0.856	0.801	0.91	CLONAL	2	TRUE	1	0.6441598597807	3		516	487	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566193	95566193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057435-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	150	502	1	ENST00000393063.1:c.4130C>T	p.Pro1377Leu	p.P1377L	ENST00000393063	NM_030621.3	1377	cCt/cTt	23/28	0.649336119896771	3	FACETS	1	0.97	1	0.372	0.342	0.404	CLONAL	1	TRUE	0	0.6441598597807	3		503	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0057435-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	390	490	1	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.643864091145915	3	FACETS	0.981	0.949	1	0.981	0.949	1	CLONAL	3	TRUE	0	0.6441598597807	3		491	544	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470474	25470474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024296111	NA	P-0057435-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	167	624	1	ENST00000264709.3:c.1000G>A	p.Gly334Ser	p.G334S	ENST00000264709	NM_175629.2	334	Ggc/Agc	8/23	0.649336119896771	2	FACETS	1	0.961	1	0.528	0.489	0.568	CLONAL	1	TRUE	0	0.6441598597807	2		625	491	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590445	67590518	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGGTACAGCAAAGAATACATAGAAAAGTTTAAACGTGAAGGCAATGAGAAAGAAATACAAAGGTTGGTGTTTCC	CGGTACAGCAAAGAATACATAGAAAAGTTTAAACGTGAAGGCAATGAGAAAGAAATACAAAGGTTGGTGTTTCC	-	novel	NA	P-0057435-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	19	127	0	ENST00000274335.5:c.1508_1568+13del		p.X503_splice	ENST00000274335		503		11/15	0.298102421404967	4	FACETS	0.77	0.591	0.975			1	INDETERMINATE	1	TRUE	NA	0.6441598597807	4		127	126	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987423	2987423	+	splice_acceptor_variant	Splice_Site	DEL	T	T	-	rs747113439	NA	P-0057435-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	90	331	1	ENST00000396946.4:c.8-2del		p.X3_splice	ENST00000396946	NM_032415.4	3			NA	2	FACETS	0.776	0.694	0.862			1	INDETERMINATE	1	TRUE	NA	0.6441598597807	2		332	360	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	106	276	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.16	NA		276	418	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0057466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	156	823	1	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	0.16198918677189	4	FACETS	0.886	0.815	0.961	1	0.991	1	CLONAL	4	TRUE	2	0.16	4		824	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578412	7578412	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519747	NA	P-0057466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	113	912	0	ENST00000269305.4:c.518T>C	p.Val173Ala	p.V173A	ENST00000269305	NM_001126112.2	173	gTg/gCg	5/11	0.16198918677189	1	FACETS	1	0.924	1	1	0.992	1	CLONAL	4	TRUE	0	0.16	1		912	320	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735503	40735503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763584414	NA	P-0057466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	88	646	1	ENST00000373198.4:c.3370G>A	p.Glu1124Lys	p.E1124K	ENST00000373198	NM_133170.3	1124	Gag/Aag	25/32	1	2	FACETS	1	0.908	1	1	0.989	1	CLONAL	3	TRUE	1	0.16	2		647	360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0057468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	474	795	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			NA	2	FACETS	1	0.977	1			1	INDETERMINATE	2	TRUE	NA	0.576431166627096	2		795	809	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399409	139399411	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	rs761020817	NA	P-0057468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	776	1121	3	ENST00000277541.6:c.4732_4734del	p.Val1578del	p.V1578del	ENST00000277541	NM_017617.3	1578	GTG/-	26/34	0.576431166627096	3	FACETS	0.851	0.827	0.875	0.851	0.827	0.875	CLONAL	3	TRUE	0	0.576431166627096	3		1124	1358	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80160683	80160684	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	282	631	0	ENST00000265081.6:c.3059dup	p.Asn1020LysfsTer17	p.N1020Kfs*17	ENST00000265081	NM_002439.4	1018	gaa/gAaa	22/24	0.576431166627096	1	FACETS	0.973	0.919	1	0.973	0.919	1	CLONAL	1	TRUE	0	0.576431166627096	1		631	716	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391370	139391371	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0057468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1406	112	1229	0	ENST00000277541.6:c.6820_6821del	p.Ser2274ProfsTer79	p.S2274Pfs*79	ENST00000277541	NM_017617.3	2274	TCc/c	34/34	0.576431166627096	3	FACETS	0.33	0.295	0.367	0.11	0.098	0.123	SUBCLONAL	1	TRUE	0	0.576431166627096	3		1229	1518	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593609	55593611	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	rs121913685	NA	P-0057514-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	235	494	0	ENST00000288135.5:c.1679_1681del	p.Val560del	p.V560del	ENST00000288135	NM_000222.2	559	GTT/-	11/21	1	2	FACETS	1	0.983	1	1	0.996	1	CLONAL	3	TRUE	1	0.229708355511312	2		494	609	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380269	25380269	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057514-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	70	642	1	ENST00000311936.3:c.189G>T	p.Glu63Asp	p.E63D	ENST00000311936	NM_004985.3	63	gaG/gaT	3/5	1	2	FACETS	0.77	0.67	0.878	0.77	0.67	0.878	SUBCLONAL	1	TRUE	1	0.229708355511312	2		643	792	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0057575-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	66	464	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.157799224680572	3	FACETS	1	0.962	1	0.64	0.56	0.726	INDETERMINATE	1	TRUE	1	0.371543296213614	3		464	329	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219336	1219336	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057575-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	101	709	0	ENST00000326873.7:c.388G>T	p.Glu130Ter	p.E130*	ENST00000326873	NM_000455.4	130	Gag/Tag	3/10	0.371543296213614	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.371543296213614	1		709	418	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520180	9520180	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057575-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	27	427	0	ENST00000353224.5:c.2089C>A	p.His697Asn	p.H697N	ENST00000353224	NM_177990.2	697	Cat/Aat	10/10	1	2	FACETS	0.427	0.34	0.527	0.427	0.34	0.527	SUBCLONAL	1	TRUE	1	0.371543296213614	2		427	340	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602485	10602488	+	frameshift_variant	Frame_Shift_Del	DEL	GGCC	GGCC	-	novel	NA	P-0057575-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	88	800	0	ENST00000171111.5:c.1090_1093del	p.Gly364TrpfsTer35	p.G364Wfs*35	ENST00000171111	NM_203500.1	364	GGCCtg/tg	3/6	0.371543296213614	1	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	0	0.371543296213614	1		800	382	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998685	100998685	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057575-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	98	770	0	ENST00000325455.5:c.1117G>T	p.Ala373Ser	p.A373S	ENST00000325455	NM_001202474.3	373	Gcg/Tcg	1/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.371543296213614	2		770	428	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266918	18266918	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057575-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	42	270	0	ENST00000222254.8:c.229T>G	p.Phe77Val	p.F77V	ENST00000222254	NM_005027.3	77	Ttc/Gtc	2/16	0.298915367590986	1	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	0	0.371543296213614	1		270	183	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142907	30142908	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0057575-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	73	886	2	ENST00000389048.3:c.618_619delinsTA	p.Ala207Thr	p.A207T	ENST00000389048	NM_004304.4	206	gcGGca/gcTAca	1/29	1	2	FACETS	0.787	0.69	0.892	0.787	0.69	0.892	SUBCLONAL	1	TRUE	1	0.371543296213614	2		888	499	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570063	212570063	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057575-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	33	360	0	ENST00000342788.4:c.1178G>C	p.Arg393Pro	p.R393P	ENST00000342788	NM_005235.2	393	cGg/cCg	10/28	1	2	FACETS	0.854	0.701	1	0.854	0.701	1	CLONAL	1	TRUE	1	0.371543296213614	2		360	208	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1253893	1253893	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs749874887	NA	P-0057575-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	143	787	0	ENST00000310581.5:c.3349G>T	p.Ala1117Ser	p.A1117S	ENST00000310581	NM_198253.2	1117	Gcc/Tcc	16/16	0.371543296213614	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.371543296213614	1		787	446	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0057576-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	153	293	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.818	0.758	0.878	1	0.991	1	CLONAL	2	TRUE	1	0.507164452795846	2		293	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578541	7578541	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1131691013	NA	P-0057576-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	148	934	1	ENST00000269305.4:c.389T>C	p.Leu130Pro	p.L130P	ENST00000269305	NM_001126112.2	130	cTc/cCc	5/11	0.507164452795846	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.507164452795846	1		935	405	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971047	21971047	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057576-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	46	634	0	ENST00000304494.5:c.311T>G	p.Leu104Arg	p.L104R	ENST00000304494	NM_000077.4	104	cTg/cGg	2/3	0.507164452795846	1	FACETS	0.369	0.311	0.432	0.369	0.311	0.432	SUBCLONAL	1	TRUE	0	0.507164452795846	1		634	367	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732918	30732919	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0057576-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	75	435	0	ENST00000295754.5:c.1533_1534dup	p.Met512ArgfsTer7	p.M512Rfs*7	ENST00000295754	NM_003242.5	511	cag/cAGag	7/7	0.507164452795846	1	FACETS	0.897	0.797	1	0.897	0.797	1	CLONAL	1	TRUE	0	0.507164452795846	1		435	246	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0057577-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	100	284	2	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.148168172185964	3	FACETS	0.955	0.855	1	1	0.98	1	CLONAL	3	TRUE	1	0.13	3		286	572	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497907	25497907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057577-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	71	806	1	ENST00000264709.3:c.542G>A	p.Arg181His	p.R181H	ENST00000264709	NM_175629.2	181	cGt/cAt	6/23	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.13	2		807	996	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535363	66535363	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057577-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	42	615	0	ENST00000273854.3:c.98C>A	p.Ser33Tyr	p.S33Y	ENST00000273854	NM_004439.5	33	tCt/tAt	1/18	1	2	FACETS	0.947	0.789	1	0.947	0.789	1	CLONAL	1	TRUE	1	0.13	2		615	682	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743383	162743383	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057577-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	33	280	0	ENST00000367921.3:c.1853C>G	p.Ala618Gly	p.A618G	ENST00000367921	NM_006182.2	618	gCc/gGc	14/18	0.171183272955795	4	FACETS	0.961	0.781	1	0.48	0.39	0.583	CLONAL	1	TRUE	2	0.13	4		280	597	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873741	35873741	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1566591073	NA	P-0057577-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	53	536	0	ENST00000216797.5:c.110T>G	p.Met37Arg	p.M37R	ENST00000216797	NM_020529.2	37	aTg/aGg	1/6	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.13	2		536	775	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473631	67473631	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057577-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	60	704	0	ENST00000327367.4:c.711C>A	p.Tyr237Ter	p.Y237*	ENST00000327367	NM_005902.3	237	taC/taA	6/9	1	2	FACETS	0.953	0.818	1	0.953	0.818	1	CLONAL	1	TRUE	1	0.13	2		704	969	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857427	68857428	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs587781276	NA	P-0057577-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	103	583	0	ENST00000261769.5:c.2064_2065del	p.Cys688Ter	p.C688*	ENST00000261769	NM_004360.3	688	TGt/t	13/16	1	2	FACETS	1	0.919	1	1	0.987	1	CLONAL	2	TRUE	1	0.13	2		583	768	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0057581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	122	553	0	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.285841307509737	2		553	780	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0057581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	366	229	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.285841307509737	8	FACETS	1	0.979	1			1	CLONAL	7	TRUE	NA	0.285841307509737	8		229	657	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857311	68857312	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	77	360	0	ENST00000261769.5:c.1947dup	p.Ile650TyrfsTer13	p.I650Yfs*13	ENST00000261769	NM_004360.3	649	tct/tcTt	13/16	0.285841307509737	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.285841307509737	1		360	395	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073739	8073739	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1361059014	NA	P-0057581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	72	333	1	ENST00000377482.5:c.920C>T	p.Ser307Leu	p.S307L	ENST00000377482	NM_018948.3	307	tCg/tTg	4/4	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.285841307509737	2		334	477	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47730006	47730006	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	63	366	0	ENST00000449228.1:c.383C>A	p.Ser128Ter	p.S128*	ENST00000449228	NM_001127240.2	128	tCa/tAa	3/4	1	2	FACETS	0.812	0.703	0.93	0.812	0.703	0.93	CLONAL	1	TRUE	1	0.285841307509737	2		366	543	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982328	25982373	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTTAAGGAGTTCAATGACGCACCTGTCGATCTACCTCTGGGAGTA	TCTTAAGGAGTTCAATGACGCACCTGTCGATCTACCTCTGGGAGTA	CCT	novel	NA	P-0057581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	56	247	1	ENST00000435504.4:c.917_939+23delinsAGG		p.X306_splice	ENST00000435504		306		9/13	0.280578958742371	2	FACETS	1	0.968	1	0.739	0.639	0.847	CLONAL	1	TRUE	0	0.285841307509737	2		248	265	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0057585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	62	590	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.763	0.658	0.877	0.763	0.658	0.877	SUBCLONAL	1	TRUE	1	0.22	2		590	739	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0057585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	120	561	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.22	2		561	1011	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586089	29586089	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	54	283	0	ENST00000356175.3:c.4309G>C	p.Glu1437Gln	p.E1437Q	ENST00000356175	NM_000267.3	1437	Gaa/Caa	32/57	1	2	FACETS	0.88	0.751	1	0.88	0.751	1	CLONAL	1	TRUE	1	0.22	2		283	558	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850636	63850636	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	43	196	0	ENST00000279873.7:c.1414G>C	p.Glu472Gln	p.E472Q	ENST00000279873	NM_032199.2	472	Gaa/Caa	10/10	1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	1	0.22	2		196	387	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371679	89371679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	106	553	1	ENST00000301030.4:c.161G>A	p.Arg54Gln	p.R54Q	ENST00000301030	NM_001256183.1	54	cGa/cAa	4/13	1	2	FACETS	0.924	0.826	1	0.924	0.826	1	CLONAL	1	TRUE	1	0.22	2		554	1043	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138400832	138400832	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	43	341	0	ENST00000289153.2:c.2481G>C	p.Trp827Cys	p.W827C	ENST00000289153	NM_006219.2	827	tgG/tgC	17/22	1	2	FACETS	0.562	0.469	0.666	0.562	0.469	0.666	SUBCLONAL	1	TRUE	1	0.22	2		341	695	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	rs1567554542	NA	P-0057586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	32	691	0	ENST00000269305.4:c.376del	p.Tyr126ThrfsTer44	p.Y126Tfs*44	ENST00000269305	NM_001126112.2	126	Tac/ac	5/11	1	2	FACETS	0.059	0.047	0.072	0.059	0.047	0.072	SUBCLONAL	1	TRUE	1	0.988523053132006	2		691	1102	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663716	29663717	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	11	0	0	ENST00000356175.3:c.6150dup	p.His2051ThrfsTer6	p.H2051Tfs*6	ENST00000356175	NM_000267.3	2050	caa/cAaa	41/57	1	2	FACETS	0.035	0.024	0.05	0.035	0.024	0.05	SUBCLONAL	1	TRUE	1	0.988523053132006	2		0	632	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0057588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	13	293	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.645	0.46	0.871	0.645	0.46	0.871	SUBCLONAL	1	TRUE	1	0.16	2		293	252	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0057588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	24	867	9	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	1	2	FACETS	0.815	0.639	1	0.815	0.639	1	CLONAL	1	TRUE	1	0.16	2		876	368	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0057588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	8	581	1	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	1	2	FACETS	0.442	0.284	0.648	0.442	0.284	0.648	SUBCLONAL	1	TRUE	1	0.16	2		582	226	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150457	157150457	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554256715	NA	P-0057588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	20	746	0	ENST00000346085.5:c.1639G>T	p.Gly547Ter	p.G547*	ENST00000346085	NM_020732.3	547	Gga/Tga	2/20	1	2	FACETS	0.712	0.544	0.91	0.712	0.544	0.91	CLONAL	1	TRUE	1	0.16	2		746	351	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080613	5080613	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	19	364	0	ENST00000381652.3:c.2364G>T	p.Met788Ile	p.M788I	ENST00000381652	NM_004972.3	788	atG/atT	18/25	1	2	FACETS	0.981	0.746	1	0.981	0.746	1	CLONAL	1	TRUE	1	0.16	2		364	242	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611246	100611246	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	15	565	0	ENST00000308731.7:c.1360C>A	p.His454Asn	p.H454N	ENST00000308731	NM_000061.2	454	Cat/Aat	15/19	1	2	FACETS	0.653	0.477	0.865	0.653	0.477	0.865	SUBCLONAL	1	TRUE	1	0.16	2		565	287	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451206	70451206	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	22	870	0	ENST00000373644.4:c.6046G>T	p.Gly2016Cys	p.G2016C	ENST00000373644	NM_030625.2	2016	Ggc/Tgc	12/12	1	2	FACETS	0.741	0.574	0.936	0.741	0.574	0.936	CLONAL	1	TRUE	1	0.16	2		870	371	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514736	103514736	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	21	467	0	ENST00000355739.4:c.1237G>C	p.Gly413Arg	p.G413R	ENST00000355739	NM_000123.3	413	Ggg/Cgg	8/15	0.3	3	FACETS	0.978	0.753	1			1	CLONAL	1	TRUE	NA	0.16	3		467	290	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562968	95562968	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	17	425	0	ENST00000393063.1:c.4289G>T	p.Arg1430Met	p.R1430M	ENST00000393063	NM_030621.3	1430	aGg/aTg	24/28	1	2	FACETS	0.746	0.556	0.971	0.746	0.556	0.971	CLONAL	1	TRUE	1	0.16	2		425	285	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99439984	99439984	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0057588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	10	330	0	ENST00000268035.6:c.954-2A>T		p.X318_splice	ENST00000268035	NM_000875.3	318			1	2	FACETS	0.702	0.476	0.986	0.702	0.476	0.986	CLONAL	1	TRUE	1	0.16	2		330	178	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984937	9984937	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1231057100	NA	P-0057588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	15	549	0	ENST00000330684.3:c.1028G>T	p.Trp343Leu	p.W343L	ENST00000330684	NM_001134407.1	343	tGg/tTg	4/13	1	2	FACETS	0.647	0.472	0.856	0.647	0.472	0.856	SUBCLONAL	1	TRUE	1	0.16	2		549	290	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098488	11098488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111491424	NA	P-0057588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	15	826	3	ENST00000358026.2:c.1006C>T	p.Pro336Ser	p.P336S	ENST00000358026	NM_001128849.1	336	Ccg/Tcg	6/36	1	2	FACETS	0.627	0.458	0.831	0.627	0.458	0.831	SUBCLONAL	1	TRUE	1	0.16	2		829	299	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31015983	31015983	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	21	602	0	ENST00000375687.4:c.305C>G	p.Pro102Arg	p.P102R	ENST00000375687	NM_015338.5	102	cCa/cGa	5/13	1	2	FACETS	0.82	0.632	1	0.82	0.632	1	CLONAL	1	TRUE	1	0.16	2		602	320	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628829	187628829	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	15	670	2	ENST00000441802.2:c.2153G>T	p.Ser718Ile	p.S718I	ENST00000441802	NM_005245.3	718	aGc/aTc	2/27	1	2	FACETS	0.66	0.482	0.874	0.66	0.482	0.874	SUBCLONAL	1	TRUE	1	0.16	2		672	284	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509506	149509506	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	19	989	1	ENST00000261799.4:c.1393C>A	p.Leu465Met	p.L465M	ENST00000261799	NM_002609.3	465	Ctg/Atg	10/23	1	2	FACETS	0.677	0.513	0.87	0.677	0.513	0.87	SUBCLONAL	1	TRUE	1	0.16	2		990	351	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402482	20402482	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	22	925	0	ENST00000346618.3:c.19C>G	p.Pro7Ala	p.P7A	ENST00000346618	NM_001949.4	7	Ccc/Gcc	1/7	0.247221714880587	3	FACETS	0.777	0.602	0.982	0.389	0.301	0.491	CLONAL	1	TRUE	1	0.16	3		925	382	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161990437	161990437	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	36	548	0	ENST00000366898.1:c.883A>T	p.Asn295Tyr	p.N295Y	ENST00000366898	NM_004562.2	295	Aac/Tac	8/12	1	2	FACETS	0.833	0.689	0.994	1	0.957	1	CLONAL	2	TRUE	1	0.16	2		548	270	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374426	81374426	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	13	408	0	ENST00000222390.5:c.636G>C	p.Met212Ile	p.M212I	ENST00000222390	NM_000601.4	212	atG/atC	6/18	1	2	FACETS	0.691	0.493	0.933	0.691	0.493	0.933	SUBCLONAL	1	TRUE	1	0.16	2		408	235	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960183	151960183	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	10	352	0	ENST00000262189.6:c.1217G>T	p.Cys406Phe	p.C406F	ENST00000262189	NM_170606.2	406	tGt/tTt	9/59	1	2	FACETS	0.648	0.439	0.91	0.648	0.439	0.91	SUBCLONAL	1	TRUE	1	0.16	2		352	193	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38314921	38314921	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	26	838	0	ENST00000425967.3:c.143del	p.Thr48LysfsTer88	p.T48Kfs*88	ENST00000425967	NM_001174067.1	48	aCa/aa	3/19	0.113295473548053	0	FACETS	0.848	0.672	1			1	CLONAL	1	TRUE	0	0.16	0		838	322	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220524	98220524	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	14	620	0	ENST00000331920.6:c.2939G>T	p.Gly980Val	p.G980V	ENST00000331920	NM_000264.3	980	gGc/gTc	18/24	1	2	FACETS	0.634	0.458	0.848	0.634	0.458	0.848	SUBCLONAL	1	TRUE	1	0.16	2		620	276	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411855	63411855	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057588-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	31	1297	0	ENST00000330258.3:c.1312C>A	p.Leu438Ile	p.L438I	ENST00000330258	NM_152424.3	438	Ctc/Atc	2/2	1	2	FACETS	0.844	0.682	1	0.844	0.682	1	CLONAL	1	TRUE	1	0.16	2		1297	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0057592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	403	842	1	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.609732275425711	1	FACETS	0.861	0.821	0.902	0.861	0.821	0.902	CLONAL	1	TRUE	0	0.609732275425711	1		843	1067	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919613	28919619	+	frameshift_variant	Frame_Shift_Del	DEL	AGGAGCC	AGGAGCC	-	novel	NA	P-0057592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	169	396	2	ENST00000282397.4:c.2318_2324del	p.Trp773TyrfsTer2	p.W773Yfs*2	ENST00000282397	NM_002019.4	773	tGGCTCCTa/ta	16/30	0.609732275425711	1	FACETS	0.783	0.726	0.842	0.783	0.726	0.842	SUBCLONAL	1	TRUE	0	0.609732275425711	1		398	492	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645480	67645480	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	99	218	0	ENST00000264010.4:c.745A>C	p.Met249Leu	p.M249L	ENST00000264010	NM_006565.3	249	Atg/Ctg	3/12	1	2	FACETS	0.868	0.782	0.959	0.868	0.782	0.959	CLONAL	1	TRUE	1	0.609732275425711	2		218	374	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591059	67591073	+	inframe_deletion	In_Frame_Del	DEL	AGCAGGCAGCTGAGT	AGCAGGCAGCTGAGT	-	novel	NA	P-0057592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	20	171	0	ENST00000274335.5:c.1653_1667del	p.Lys551_Tyr556delinsAsn	p.K551_Y556delinsN	ENST00000274335		551	aAGCAGGCAGCTGAGTat/aat	12/15	1	2	FACETS	0.325	0.249	0.412	0.325	0.249	0.412	SUBCLONAL	1	TRUE	1	0.609732275425711	2		171	202	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400302	139400302	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	310	731	0	ENST00000277541.6:c.4046C>G	p.Ala1349Gly	p.A1349G	ENST00000277541	NM_017617.3	1349	gCt/gGt	25/34	0.609732275425711	1	FACETS	0.819	0.775	0.864	0.819	0.775	0.864	CLONAL	1	TRUE	0	0.609732275425711	1		731	863	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0057593-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	63	324	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	0.221292763468991	2	FACETS	0.989	0.855	1	0.494	0.427	0.567	CLONAL	1	TRUE	0	0.221292763468991	2		324	576	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988856	41988856	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057593-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	64	471	0	ENST00000219905.7:c.1648C>T	p.Gln550Ter	p.Q550*	ENST00000219905	NM_001164273.1	550	Cag/Tag	3/24	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.221292763468991	2		471	567	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249002	55249003	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGTGGA	rs397517109	NA	P-0057593-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	221	552	0	ENST00000275493.2:c.2303_2311dup	p.Ser768_Asp770dup	p.S768_D770dup	ENST00000275493	NM_005228.3	768	gcc/gcCAGCGTGGAc	20/28	0.221292763468991	5	FACETS	0.925	0.864	0.987	0.925	0.864	0.987	CLONAL	4	TRUE	1	0.221292763468991	5		552	719	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0057627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	133	1090	1	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	0.198821196232672	0	FACETS	1	0.96	1			1	CLONAL	2	FALSE	0	0.23938594686457	0		1091	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0057627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	250	1082	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.167943464545522	1	FACETS	1	0.993	1	1	0.997	1	CLONAL	6	FALSE	0	0.23938594686457	1		1082	283	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0057627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	11	0	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.919	0.653	1	1	0.891	1	CLONAL	2	FALSE	1	0.23938594686457	2		0	50	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685315	89685316	+	splice_donor_variant	Splice_Site	INS	-	-	T	rs1064794925	NA	P-0057671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	23	197	0	ENST00000371953.3:c.209+2dup		p.X70_splice	ENST00000371953	NM_000314.4	70			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		197	220	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0057691-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	139	432	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.827	0.76	0.895	0.827	0.76	0.895	CLONAL	1	TRUE	1	0.82	2		432	410	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0057711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	14	318	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	0.115428614997664	5	FACETS	0.509	0.367	0.682	0.17	0.122	0.228	INDETERMINATE	1	TRUE	2	0.208893525097412	5		318	346	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	178	306	0				ENST00000310581	NM_198253.2	-/1132			0.525765349933869	4	FACETS	0.938	0.873	1	0.938	0.873	1	CLONAL	2	TRUE	2	0.65149399052444	4		306	481	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166010	118166010	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767827215	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	174	305	0	ENST00000369448.3:c.520C>T	p.Arg174Trp	p.R174W	ENST00000369448	NM_017709.3	174	Cgg/Tgg	2/2	0.560457133019345	4	FACETS	0.824	0.764	0.886	0.824	0.764	0.886	CLONAL	2	TRUE	2	0.65149399052444	4		305	535	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36846865	36846865	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	291	495	0	ENST00000358127.4:c.1074G>A	p.Trp358Ter	p.W358*	ENST00000358127	NM_001280556.1	358	tgG/tgA	9/10	0.14656264222341	6	FACETS	0.99	0.937	1	0.99	0.937	1	INDETERMINATE	3	TRUE	3	0.65149399052444	6		495	693	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	385	773	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.65149399052444	2	FACETS	0.998	0.962	1	0.998	0.962	1	CLONAL	2	TRUE	0	0.65149399052444	2		773	592	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	167	827	0	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	0.588991787983473	4	FACETS	0.819	0.752	0.889	0.273	0.25	0.297	CLONAL	1	TRUE	1	0.65149399052444	4		827	1034	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437548	110437548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	487	831	0	ENST00000375856.3:c.853G>A	p.Glu285Lys	p.E285K	ENST00000375856	NM_003749.2	285	Gag/Aag	1/2	0.177294184215942	5	FACETS	1	0.969	1			1	INDETERMINATE	3	TRUE	NA	0.65149399052444	5		831	977	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592318	29592318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	172	345	0	ENST00000356175.3:c.4733C>T	p.Ser1578Phe	p.S1578F	ENST00000356175	NM_000267.3	1578	tCc/tTc	35/57	0.65149399052444	2	FACETS	0.92	0.867	0.972	0.92	0.867	0.972	CLONAL	2	TRUE	0	0.65149399052444	2		345	287	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101044	41101044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143164081	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	355	651	1	ENST00000373198.4:c.1312G>A	p.Glu438Lys	p.E438K	ENST00000373198	NM_133170.3	438	Gag/Aag	8/32	0.208843253358113	6	FACETS	0.916	0.871	0.962	0.916	0.871	0.962	INDETERMINATE	3	TRUE	3	0.65149399052444	6		652	913	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332699	153332699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780061054	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	114	384	0	ENST00000281708.4:c.257C>T	p.Ser86Leu	p.S86L	ENST00000281708	NM_033632.3	86	tCg/tTg	2/12	1	2	FACETS	0.946	0.86	1	0.946	0.86	1	CLONAL	1	TRUE	1	0.65149399052444	2		384	370	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149511632	149511632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167658274	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	321	471	0	ENST00000261799.4:c.1153C>T	p.Arg385Cys	p.R385C	ENST00000261799	NM_002609.3	385	Cgc/Tgc	8/23	0.525765349933869	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.65149399052444	4		471	761	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448393	56448393	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	414	680	0	ENST00000407977.2:c.254C>T	p.Ser85Phe	p.S85F	ENST00000407977		85	tCc/tTc	3/10	0.538090684506363	5	FACETS	0.962	0.916	1	0.641	0.61	0.673	CLONAL	2	TRUE	2	0.65149399052444	5		680	1306	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341785	8341785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776356704	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	227	473	0	ENST00000356435.5:c.4855G>A	p.Glu1619Lys	p.E1619K	ENST00000356435		1619	Gaa/Aaa	29/35	0.14656264222341	6	FACETS	1	0.987	1	0.801	0.75	0.853	INDETERMINATE	2	TRUE	3	0.65149399052444	6		473	668	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231457	46231457	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	160	271	0	ENST00000334344.6:c.1297T>G	p.Cys433Gly	p.C433G	ENST00000334344	NM_152641.2	433	Tgc/Ggc	10/21	0.560457133019345	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.65149399052444	4		271	378	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339863	116339863	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	206	353	1	ENST00000397752.3:c.725G>A	p.Arg242Lys	p.R242K	ENST00000397752	NM_000245.2	242	aGa/aAa	2/21	0.645495534236813	4	FACETS	0.983	0.92	1	0.983	0.92	1	CLONAL	2	TRUE	2	0.65149399052444	4		354	531	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31504673	31504673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	271	471	0	ENST00000344624.3:c.1657C>T	p.Pro553Ser	p.P553S	ENST00000344624		553	Cct/Tct	8/33	0.525765349933869	4	FACETS	0.942	0.889	0.997	0.942	0.889	0.997	CLONAL	2	TRUE	2	0.65149399052444	4		471	729	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420990	49420990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	288	423	0	ENST00000301067.7:c.14759C>T	p.Pro4920Leu	p.P4920L	ENST00000301067	NM_003482.3	4920	cCc/cTc	48/54	0.560457133019345	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.65149399052444	4		423	630	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420106	41420106	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	80	283	0	ENST00000373198.4:c.215G>A	p.Gly72Glu	p.G72E	ENST00000373198	NM_133170.3	72	gGa/gAa	3/32	0.208843253358113	6	FACETS	0.75	0.665	0.841	0.5	0.443	0.561	INDETERMINATE	2	TRUE	3	0.65149399052444	6		283	377	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831566	72831566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	173	554	0	ENST00000268489.5:c.5015G>A	p.Gly1672Asp	p.G1672D	ENST00000268489	NM_006885.3	1672	gGc/gAc	9/10	0.169411813391313	3	FACETS	1	0.979	1	0.388	0.359	0.418	INDETERMINATE	1	TRUE	0	0.65149399052444	3		554	605	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593395	55593395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1560416964	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	70	242	0	ENST00000288135.5:c.1552C>T	p.Pro518Ser	p.P518S	ENST00000288135	NM_000222.2	518	Ccc/Tcc	10/21	1	2	FACETS	0.918	0.812	1	0.918	0.812	1	CLONAL	1	TRUE	1	0.65149399052444	2		242	234	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261949	16261949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772442954	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	306	427	0	ENST00000375759.3:c.9214C>T	p.His3072Tyr	p.H3072Y	ENST00000375759	NM_015001.2	3072	Cac/Tac	11/15	0.645495534236813	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	2	0.65149399052444	4		427	757	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874562	35874562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	225	355	0	ENST00000303115.3:c.718C>T	p.Pro240Ser	p.P240S	ENST00000303115	NM_002185.3	240	Cct/Tct	6/8	0.525765349933869	4	FACETS	0.962	0.902	1	0.962	0.902	1	CLONAL	2	TRUE	2	0.65149399052444	4		355	593	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455542	189455542	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	66	332	0	ENST00000264731.3:c.76C>T	p.Pro26Ser	p.P26S	ENST00000264731	NM_003722.4	26	Cca/Tca	2/14	0.588991787983473	4	FACETS	0.697	0.606	0.795	0.232	0.202	0.265	SUBCLONAL	1	TRUE	1	0.65149399052444	4		332	480	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432191	121432191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	443	721	0	ENST00000257555.6:c.938C>T	p.Ser313Phe	p.S313F	ENST00000257555		313	tCc/tTc	4/10	0.65149399052444	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.65149399052444	2		721	674	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480014	120480014	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173598104	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	389	561	0	ENST00000256646.2:c.3413C>T	p.Pro1138Leu	p.P1138L	ENST00000256646	NM_024408.3	1138	cCc/cTc	21/34	0.560457133019345	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	2	0.65149399052444	4		561	878	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131945040	131945040	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	91	129	0	ENST00000265335.6:c.2988G>C	p.Lys996Asn	p.K996N	ENST00000265335		996	aaG/aaC	19/25	0.525765349933869	4	FACETS	0.851	0.767	0.939	0.851	0.767	0.939	CLONAL	2	TRUE	2	0.65149399052444	4		129	271	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597802	43597802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	399	751	0	ENST00000355710.3:c.350C>T	p.Pro117Leu	p.P117L	ENST00000355710	NM_020975.4	117	cCc/cTc	3/20	0.208843253358113	6	FACETS	0.887	0.846	0.929	0.887	0.846	0.929	INDETERMINATE	3	TRUE	3	0.65149399052444	6		751	1060	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319054	62319054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	539	929	1	ENST00000360203.5:c.1412G>A	p.Gly471Asp	p.G471D	ENST00000360203	NM_001283009.1	471	gGc/gAc	17/35	0.208843253358113	6	FACETS	0.914	0.877	0.951	0.914	0.877	0.951	INDETERMINATE	3	TRUE	3	0.65149399052444	6		930	1390	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127364	55127364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	155	470	2	ENST00000257290.5:c.152G>A	p.Gly51Glu	p.G51E	ENST00000257290	NM_006206.4	51	gGg/gAg	3/23	1	2	FACETS	0.993	0.917	1	0.993	0.917	1	CLONAL	1	TRUE	1	0.65149399052444	2		472	479	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695829	117695829	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	375	499	0	ENST00000369458.3:c.608C>T	p.Ser203Phe	p.S203F	ENST00000369458	NM_024626.3	203	tCt/tTt	4/6	0.560457133019345	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	2	0.65149399052444	4		499	823	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054920	176054920	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	151	277	0	ENST00000367669.3:c.1133G>T	p.Arg378Leu	p.R378L	ENST00000367669	NM_022457.5	378	cGt/cTt	10/20	0.560457133019345	4	FACETS	0.905	0.836	0.976	0.905	0.836	0.976	CLONAL	2	TRUE	2	0.65149399052444	4		277	423	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622140	43622140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	293	478	0	ENST00000355710.3:c.3157C>T	p.Pro1053Ser	p.P1053S	ENST00000355710	NM_020975.4	1053	Cct/Tct	19/20	0.208843253358113	6	FACETS	0.927	0.877	0.977	0.927	0.877	0.977	INDETERMINATE	3	TRUE	3	0.65149399052444	6		478	745	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148958	119148959	+	missense_variant	Missense_Mutation	DNP	TT	TT	GA	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	198	342	0	ENST00000264033.4:c.1178_1179delinsGA	p.Ile393Arg	p.I393R	ENST00000264033	NM_005188.3	393	aTT/aGA	8/16	0.65149399052444	2	FACETS	0.927	0.877	0.975	0.927	0.877	0.975	CLONAL	2	TRUE	0	0.65149399052444	2		342	328	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442815	442816	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	139	274	0	ENST00000399788.2:c.1491-1_1491delinsAA		p.X497_splice	ENST00000399788	NM_001042603.1	497		12/28	0.594277485535709	4	FACETS	0.795	0.73	0.863			1	SUBCLONAL	2	TRUE	NA	0.65149399052444	4		274	443	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466930	18466930	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	172	256	2	ENST00000266497.5:c.1069A>C	p.Lys357Gln	p.K357Q	ENST00000266497		357	Aaa/Caa	5/31	0.560457133019345	4	FACETS	0.892	0.827	0.957	0.892	0.827	0.957	CLONAL	2	TRUE	2	0.65149399052444	4		258	489	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21626485	21626485	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	152	333	0	ENST00000421138.2:c.1447G>A	p.Ala483Thr	p.A483T	ENST00000421138		483	Gca/Aca	13/16	0.560457133019345	4	FACETS	0.771	0.71	0.833	0.771	0.71	0.833	SUBCLONAL	2	TRUE	2	0.65149399052444	4		333	500	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630696	90630696	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	386	575	0	ENST00000330062.3:c.790G>A	p.Asp264Asn	p.D264N	ENST00000330062	NM_002168.2	264	Gac/Aac	6/11	0.208843253358113	6	FACETS	0.968	0.923	1	0.968	0.923	1	INDETERMINATE	3	TRUE	3	0.65149399052444	6		575	940	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122952	2122952	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	364	597	0	ENST00000219476.3:c.2323T>C	p.Ser775Pro	p.S775P	ENST00000219476	NM_000548.3	775	Tct/Cct	21/42	0.207914406265889	3	FACETS	0.985	0.941	1	0.657	0.627	0.686	INDETERMINATE	2	TRUE	0	0.65149399052444	3		597	752	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639330	3639330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	450	969	2	ENST00000294008.3:c.4309C>T	p.Pro1437Ser	p.P1437S	ENST00000294008	NM_032444.2	1437	Ccc/Tcc	12/15	0.207914406265889	3	FACETS	0.954	0.915	0.993	0.636	0.61	0.662	INDETERMINATE	2	TRUE	0	0.65149399052444	3		971	960	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828017	3828017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	257	456	0	ENST00000262367.5:c.2108C>T	p.Pro703Leu	p.P703L	ENST00000262367	NM_004380.2	703	cCt/cTt	10/31	0.14656264222341	6	FACETS	1	0.961	1	1	0.961	1	INDETERMINATE	3	TRUE	3	0.65149399052444	6		456	593	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56792464	56792464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	200	408	0	ENST00000308159.5:c.194G>A	p.Gly65Glu	p.G65E	ENST00000308159	NM_014669.4	65	gGg/gAg	3/22	0.169411813391313	3	FACETS	0.817	0.765	0.871	0.545	0.51	0.581	INDETERMINATE	2	TRUE	0	0.65149399052444	3		408	498	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872540	136872540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	152	213	0	ENST00000241393.3:c.958G>A	p.Val320Met	p.V320M	ENST00000241393	NM_003467.2	320	Gtg/Atg	2/2	0.521085001880203	3	FACETS	0.871	0.808	0.935	0.871	0.808	0.935	CLONAL	2	TRUE	1	0.65149399052444	3		213	355	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543811	212543811	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	141	340	0	ENST00000342788.4:c.1588A>T	p.Arg530Trp	p.R530W	ENST00000342788	NM_005235.2	530	Agg/Tgg	13/28	0.169411813391313	3	FACETS	1	0.976	1	0.39	0.358	0.424	INDETERMINATE	1	TRUE	0	0.65149399052444	3		340	490	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525129	9525129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	97	294	0	ENST00000353224.5:c.1756G>A	p.Asp586Asn	p.D586N	ENST00000353224	NM_177990.2	586	Gat/Aat	8/10	0.207914406265889	3	FACETS	0.975	0.875	1	0.325	0.291	0.36	INDETERMINATE	1	TRUE	0	0.65149399052444	3		294	405	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391081	89391081	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	557	516	1	ENST00000336596.2:c.1147C>T	p.Leu383Phe	p.L383F	ENST00000336596	NM_005233.5	383	Ctc/Ttc	5/17	0.65149399052444	6	FACETS	0.955	0.918	0.992	0.955	0.918	0.992	CLONAL	3	TRUE	3	0.65149399052444	6		517	1375	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55991405	55991405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	220	815	1	ENST00000263923.4:c.56C>T	p.Ala19Val	p.A19V	ENST00000263923	NM_002253.2	19	gCc/gTc	1/30	1	2	FACETS	0.904	0.844	0.966	0.904	0.844	0.966	CLONAL	1	TRUE	1	0.65149399052444	2		816	747	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542668	187542668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	93	367	0	ENST00000441802.2:c.5072C>T	p.Ala1691Val	p.A1691V	ENST00000441802	NM_005245.3	1691	gCc/gTc	10/27	0.624955310595002	1	FACETS	0.921	0.837	1	0.921	0.837	1	CLONAL	1	TRUE	0	0.65149399052444	1		367	209	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915730	131915730	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	126	263	0	ENST00000265335.6:c.728C>T	p.Ser243Phe	p.S243F	ENST00000265335		243	tCc/tTc	5/25	0.525765349933869	4	FACETS	0.956	0.878	1	0.956	0.878	1	CLONAL	2	TRUE	2	0.65149399052444	4		263	334	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997726	149997726	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	202	332	0	ENST00000253339.5:c.2741C>T	p.Pro914Leu	p.P914L	ENST00000253339		914	cCc/cTc	5/7	0.560457133019345	4	FACETS	0.987	0.923	1	0.987	0.923	1	CLONAL	2	TRUE	2	0.65149399052444	4		332	519	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683560	162683560	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	233	411	0	ENST00000366898.1:c.409C>G	p.Pro137Ala	p.P137A	ENST00000366898	NM_004562.2	137	Cca/Gca	3/12	0.560457133019345	4	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	2	0.65149399052444	4		411	588	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983968	2983968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	420	736	0	ENST00000396946.4:c.562G>A	p.Asp188Asn	p.D188N	ENST00000396946	NM_032415.4	188	Gac/Aac	5/25	0.399342877764227	4	FACETS	0.958	0.915	1	0.958	0.915	1	CLONAL	2	TRUE	2	0.65149399052444	4		736	1111	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467736	50467736	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	241	593	0	ENST00000331340.3:c.972del	p.Glu325SerfsTer90	p.E325Sfs*90	ENST00000331340	NM_006060.4	324	gCc/gc	8/8	0.399342877764227	4	FACETS	0.792	0.743	0.843	0.792	0.743	0.843	SUBCLONAL	2	TRUE	2	0.65149399052444	4		593	771	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214397	55214397	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	308	544	0	ENST00000275493.2:c.523A>G	p.Asn175Asp	p.N175D	ENST00000275493	NM_005228.3	175	Aac/Gac	4/28	0.399342877764227	4	FACETS	0.907	0.858	0.956	0.907	0.858	0.956	CLONAL	2	TRUE	2	0.65149399052444	4		544	861	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439667	140439667	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	161	275	0	ENST00000288602.6:c.2072G>A	p.Arg691Lys	p.R691K	ENST00000288602	NM_004333.4	691	aGa/aAa	17/18	0.645495534236813	4	FACETS	0.96	0.89	1	0.96	0.89	1	CLONAL	2	TRUE	2	0.65149399052444	4		275	425	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836834	151836834	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	287	398	0	ENST00000262189.6:c.14386A>G	p.Met4796Val	p.M4796V	ENST00000262189	NM_170606.2	4796	Atg/Gtg	56/59	0.645495534236813	4	FACETS	0.984	0.931	1	0.984	0.931	1	CLONAL	2	TRUE	2	0.65149399052444	4		398	739	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136827	69136827	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	129	311	0	ENST00000288368.4:c.4741G>A	p.Gly1581Arg	p.G1581R	ENST00000288368	NM_024870.2	1581	Gga/Aga	39/40	0.65149399052444	4	FACETS	1	0.945	1	0.351	0.319	0.385	CLONAL	1	TRUE	1	0.65149399052444	4		311	621	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117875395	117875395	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	165	307	1	ENST00000297338.2:c.248T>G	p.Ile83Ser	p.I83S	ENST00000297338	NM_006265.2	83	aTt/aGt	3/14	0.65149399052444	5	FACETS	0.888	0.82	0.958	0.592	0.546	0.639	CLONAL	2	TRUE	2	0.65149399052444	5		308	564	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215835	98215835	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1429444084	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	354	511	0	ENST00000331920.6:c.3374C>T	p.Pro1125Leu	p.P1125L	ENST00000331920	NM_000264.3	1125	cCc/cTc	20/24	0.14656264222341	6	FACETS	1	0.974	1	1	0.974	1	INDETERMINATE	3	TRUE	3	0.65149399052444	6		511	808	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128230358	128230358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	249	446	0	ENST00000265960.3:c.1238C>T	p.Pro413Leu	p.P413L	ENST00000265960	NM_001006617.1	413	cCt/cTt	10/12	0.14656264222341	6	FACETS	1	0.982	1	0.746	0.7	0.793	INDETERMINATE	2	TRUE	3	0.65149399052444	6		446	787	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786026	135786027	+	missense_variant	Missense_Mutation	DNP	GG	GG	TA	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	344	713	0	ENST00000298552.3:c.1194_1195delinsTA	p.Pro399Thr	p.P399T	ENST00000298552	NM_001162426.1	398	gcCCca/gcTAca	12/23	0.14656264222341	6	FACETS	1	0.991	1	0.803	0.762	0.846	INDETERMINATE	2	TRUE	3	0.65149399052444	6		713	1009	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597493	52597495	+	stop_gained	Nonsense_Mutation	TNP	GAG	GAG	AAA	novel	NA	P-0057721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	234	0	0	ENST00000394830.3:c.3815_3817delinsTTT	p.Pro1272_Gln1273delinsLeuTer	p.P1272_Q1273delinsL*	ENST00000394830	NM_018313.4	1272	cCTCag/cTTTag	25/30	0.644158430407683	4	FACETS	0.907	0.869	0.944	0.907	0.869	0.944	CLONAL	4	TRUE	0	0.65149399052444	4		0	327	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	24	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.818	0.644	1	0.818	0.644	1	CLONAL	1	TRUE	1	0.24337961213055	2		306	241	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872380	45872380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	184	841	0	ENST00000391945.4:c.131C>T	p.Ser44Leu	p.S44L	ENST00000391945	NM_000400.3	44	tCa/tTa	3/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.24337961213055	2		841	1162	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0057741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	185	486	0	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	0.244712242963704	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.24337961213055	3		486	769	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412884	49412884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	23	606	0	ENST00000418115.1:c.139G>A	p.Glu47Lys	p.E47K	ENST00000418115	NM_001664.2	47	Gag/Aag	2/5	1	2	FACETS	0.221	0.171	0.279	0.221	0.171	0.279	SUBCLONAL	1	TRUE	1	0.24337961213055	2		606	856	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618602	37618602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	159	639	0	ENST00000447079.4:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000447079	NM_015083.1	93	cGa/cAa	1/14	0.244712242963704	3	FACETS	0.907	0.832	0.985	0.907	0.832	0.985	CLONAL	2	TRUE	1	0.24337961213055	3		639	808	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0057741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	11	341	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.184	0.126	0.257	0.184	0.126	0.257	SUBCLONAL	1	TRUE	1	0.24337961213055	2		341	490	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158626	26158626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772836222	NA	P-0057741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	31	319	1	ENST00000289316.2:c.229G>A	p.Glu77Lys	p.E77K	ENST00000289316	NM_138720.2	77	Gag/Aag	1/2	1	2	FACETS	0.634	0.512	0.771	0.634	0.512	0.771	SUBCLONAL	1	TRUE	1	0.24337961213055	2		320	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1472	74	1092	0	ENST00000269305.4:c.434T>G	p.Leu145Arg	p.L145R	ENST00000269305	NM_001126112.2	145	cTg/cGg	5/11	0.223053128512891	2	FACETS	0.393	0.343	0.449	0.197	0.171	0.225	SUBCLONAL	1	TRUE	0	0.24337961213055	2		1092	1546	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481620	56481620	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	145	862	0	ENST00000267101.3:c.655T>C	p.Phe219Leu	p.F219L	ENST00000267101	NM_001982.3	219	Ttt/Ctt	6/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.24337961213055	2		862	1041	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44896902	44896902	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	56	242	0	ENST00000377967.4:c.622C>T	p.Gln208Ter	p.Q208*	ENST00000377967	NM_021140.2	208	Caa/Taa	8/29	1	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.24337961213055	1		242	357	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132465	11132465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	199	990	0	ENST00000358026.2:c.2681C>T	p.Thr894Met	p.T894M	ENST00000358026	NM_001128849.1	894	aCg/aTg	19/36	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.24337961213055	2		990	1221	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271393	26271393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	171	774	0	ENST00000305910.3:c.220G>A	p.Glu74Lys	p.E74K	ENST00000305910	NM_003534.2	74	Gaa/Aaa	1/1	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.24337961213055	2		774	990	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805601	46805601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1441	185	1151	0	ENST00000290295.7:c.355G>A	p.Glu119Lys	p.E119K	ENST00000290295	NM_006361.5	119	Gag/Aag	1/2	0.244712242963704	3	FACETS	1	0.952	1	0.524	0.482	0.569	CLONAL	1	TRUE	1	0.24337961213055	3		1151	1626	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870331	155870331	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	141	551	0	ENST00000368323.3:c.508T>G	p.Tyr170Asp	p.Y170D	ENST00000368323	NM_006912.5	170	Tat/Gat	6/6	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.24337961213055	2		551	875	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426628	49426628	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	131	726	0	ENST00000301067.7:c.11860del	p.Gln3954SerfsTer25	p.Q3954Sfs*25	ENST00000301067	NM_003482.3	3954	Cag/ag	39/54	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.24337961213055	2		726	1000	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32932026	32932026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753047043	NA	P-0057741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	57	295	0	ENST00000380152.3:c.7765C>T	p.Pro2589Ser	p.P2589S	ENST00000380152		2589	Ccc/Tcc	16/27	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.24337961213055	2		295	399	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570431	95570431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	46	267	0	ENST00000393063.1:c.3302C>T	p.Ser1101Phe	p.S1101F	ENST00000393063	NM_030621.3	1101	tCt/tTt	22/28	0.24337961213055	1	FACETS	0.991	0.838	1	0.991	0.838	1	CLONAL	1	TRUE	0	0.24337961213055	1		267	335	SUCCESS
BLM	641	MSKCC	GRCh37	15	91328268	91328268	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	63	488	0	ENST00000355112.3:c.2780G>C	p.Arg927Thr	p.R927T	ENST00000355112	NM_000057.2	927	aGa/aCa	14/22	1	2	FACETS	0.69	0.596	0.793	0.69	0.596	0.793	SUBCLONAL	1	TRUE	1	0.24337961213055	2		488	750	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215595143	215595143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876658544	NA	P-0057741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	50	330	0	ENST00000260947.4:c.1993G>A	p.Glu665Lys	p.E665K	ENST00000260947	NM_000465.2	665	Gaa/Aaa	10/11	0.123041263117595	0	FACETS	0.713	0.606	0.83			1	INDETERMINATE	1	TRUE	0	0.24337961213055	0		330	436	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321690	62321690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	168	707	0	ENST00000360203.5:c.2309G>A	p.Gly770Glu	p.G770E	ENST00000360203	NM_001283009.1	770	gGa/gAa	26/35	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.24337961213055	2		707	1090	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629046	187629046	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	78	625	0	ENST00000441802.2:c.1936A>G	p.Thr646Ala	p.T646A	ENST00000441802	NM_005245.3	646	Aca/Gca	2/27	1	2	FACETS	0.857	0.752	0.97	0.857	0.752	0.97	CLONAL	1	TRUE	1	0.24337961213055	2		625	748	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686291	117686291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	47	324	0	ENST00000368508.3:c.3050C>T	p.Ser1017Phe	p.S1017F	ENST00000368508	NM_002944.2	1017	tCt/tTt	20/43	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.24337961213055	2		324	350	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6036957	6036957	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	82	347	0	ENST00000265849.7:c.803A>C	p.Tyr268Ser	p.Y268S	ENST00000265849	NM_000535.5	268	tAc/tCc	7/15	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.24337961213055	2		347	655	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0057744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	185	311	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.530840455180799	2	FACETS	0.937	0.879	0.995	0.937	0.879	0.995	CLONAL	2	TRUE	0	0.530840455180799	2		311	372	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922321	178922321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	111	297	0	ENST00000263967.3:c.1090G>A	p.Gly364Arg	p.G364R	ENST00000263967	NM_006218.2	364	Gga/Aga	6/21	0.488888554477022	2	FACETS	0.795	0.728	0.864	0.795	0.728	0.864	SUBCLONAL	2	TRUE	0	0.530840455180799	2		297	263	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310860	123310860	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147987917	NA	P-0057744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	467	567	1	ENST00000358487.5:c.568C>T	p.Arg190Trp	p.R190W	ENST00000358487	NM_000141.4	190	Cgg/Tgg	5/18	0.522062711722641	3	FACETS	0.964	0.923	1	0.643	0.615	0.67	CLONAL	2	TRUE	0	0.530840455180799	3		568	1155	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457216	25457216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	243	620	2	ENST00000264709.3:c.2671C>T	p.Arg891Trp	p.R891W	ENST00000264709	NM_175629.2	891	Cgg/Tgg	23/23	1	2	FACETS	0.893	0.835	0.954	0.893	0.835	0.954	CLONAL	1	TRUE	1	0.530840455180799	2		622	1025	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910698	32910698	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881513	NA	P-0057744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	50	368	0	ENST00000380152.3:c.2206G>A	p.Ala736Thr	p.A736T	ENST00000380152		736	Gca/Aca	11/27	0.452899651941129	4	FACETS	0.824	0.702	0.957	0.275	0.234	0.319	CLONAL	1	TRUE	1	0.530840455180799	4		368	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577590	7577591	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0057744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	400	516	0	ENST00000269305.4:c.690dup	p.Thr231HisfsTer9	p.T231Hfs*9	ENST00000269305	NM_001126112.2	230	-/C	7/11	0.504045630486685	2	FACETS	0.984	0.943	1	0.984	0.943	1	CLONAL	2	TRUE	0	0.530840455180799	2		516	766	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0057784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	45	656	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.222305075849309	3	FACETS	0.916	0.77	1	0.305	0.256	0.359	CLONAL	1	TRUE	0	0.237523559977186	3		657	463	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158626	26158626	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	24	282	0	ENST00000289316.2:c.229G>C	p.Glu77Gln	p.E77Q	ENST00000289316	NM_138720.2	77	Gag/Cag	1/2	0.237523559977186	6	FACETS	1	0.891	1	0.411	0.323	0.511	CLONAL	1	TRUE	3	0.237523559977186	6		282	242	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251907	8251907	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773156387	NA	P-0057784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	80	784	1	ENST00000335790.3:c.170G>A	p.Arg57His	p.R57H	ENST00000335790	NM_002315.2	57	cGc/cAc	2/4	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.237523559977186	2		785	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0057784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	165	719	0	ENST00000269305.4:c.376-2del		p.X126_splice	ENST00000269305	NM_001126112.2	126			NA	2	FACETS	1	0.97	1			1	INDETERMINATE	2	TRUE	NA	0.237523559977186	2		719	630	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112482	115112482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	151	831	1	ENST00000257566.3:c.1258G>A	p.Glu420Lys	p.E420K	ENST00000257566	NM_016569.3	420	Gag/Aag	7/8	1	2	FACETS	1	0.976	1	1	0.992	1	CLONAL	2	TRUE	1	0.237523559977186	2		832	549	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383136	42383136	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	43	637	0	ENST00000221972.3:c.156C>G	p.Phe52Leu	p.F52L	ENST00000221972	NM_021601.3	52	ttC/ttG	2/5	0.15742610139556	3	FACETS	0.818	0.685	0.966	0.409	0.342	0.483	CLONAL	1	TRUE	1	0.237523559977186	3		637	495	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386288	31386288	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	39	819	0	ENST00000328111.2:c.1513G>C	p.Glu505Gln	p.E505Q	ENST00000328111	NM_006892.3	505	Gag/Cag	15/23	0.15742610139556	3	FACETS	0.623	0.515	0.743	0.311	0.257	0.372	SUBCLONAL	1	TRUE	1	0.237523559977186	3		819	590	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31390217	31390217	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	38	475	0	ENST00000328111.2:c.2172C>G	p.Ile724Met	p.I724M	ENST00000328111	NM_006892.3	724	atC/atG	20/23	0.15742610139556	3	FACETS	0.773	0.639	0.923	0.387	0.319	0.462	CLONAL	1	TRUE	1	0.237523559977186	3		475	463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0057785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	346	783	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.272594649009154	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	3	TRUE	0	0.272594649009154	3		783	962	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	87	306	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		306	194	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0057787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	40	351	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.871	0.725	1	0.871	0.725	1	CLONAL	1	TRUE	1	0.23805251745886	2		351	386	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579312	7579312	+	splice_region_variant,synonymous_variant	Splice_Region	SNP	C	C	T	rs55863639	NA	P-0057787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	52	385	2	ENST00000269305.4:c.375G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125	acG/acA	4/11	1	2	FACETS	0.815	0.694	0.948	0.815	0.694	0.948	CLONAL	1	TRUE	1	0.23805251745886	2		387	536	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591931	48591931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	40	338	0	ENST00000342988.3:c.1094G>A	p.Gly365Asp	p.G365D	ENST00000342988	NM_005359.5	365	gGt/gAt	9/12	1	2	FACETS	0.83	0.69	0.985	0.83	0.69	0.985	CLONAL	1	TRUE	1	0.23805251745886	2		338	405	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14303157	14303157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782079709	NA	P-0057787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	48	401	0	ENST00000256196.4:c.518G>A	p.Arg173Gln	p.R173Q	ENST00000256196		173	cGg/cAg	5/6	1	2	FACETS	0.815	0.689	0.953	0.815	0.689	0.953	CLONAL	1	TRUE	1	0.23805251745886	2		401	495	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190670387	190670389	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0057787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	28	324	0	ENST00000441310.2:c.329_331del	p.Thr110del	p.T110del	ENST00000441310	NM_000534.4	109	ACA/-	4/13	1	2	FACETS	0.565	0.451	0.696	0.565	0.451	0.696	SUBCLONAL	1	TRUE	1	0.23805251745886	2		324	416	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620705	52620705	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0057787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	30	201	0	ENST00000394830.3:c.3049-1G>C		p.X1017_splice	ENST00000394830	NM_018313.4	1017			1	2	FACETS	0.962	0.778	1	0.962	0.778	1	CLONAL	1	TRUE	1	0.23805251745886	2		201	262	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0057788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	26	361	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.37073800294926	3	FACETS	0.552	0.438	0.683	0.276	0.219	0.342	SUBCLONAL	1	TRUE	1	0.37073800294926	3		361	301	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0057788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	15	257	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.47	0.345	0.62	0.47	0.345	0.62	SUBCLONAL	1	TRUE	1	0.37073800294926	2		257	172	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176715849	176715849	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	39	321	0	ENST00000439151.2:c.6181G>A	p.Glu2061Lys	p.E2061K	ENST00000439151	NM_022455.4	2061	Gaa/Aaa	21/23	1	2	FACETS	0.567	0.471	0.674	0.567	0.471	0.674	SUBCLONAL	1	TRUE	1	0.37073800294926	2		321	371	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647749	2647749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1007127163	NA	P-0057788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	45	375	0	ENST00000342085.4:c.1652C>T	p.Pro551Leu	p.P551L	ENST00000342085	NM_002613.4	551	cCg/cTg	14/14	1	2	FACETS	0.539	0.454	0.634	0.539	0.454	0.634	SUBCLONAL	1	TRUE	1	0.37073800294926	2		375	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0057789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	29	557	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.25	0.199	0.307	0.25	0.199	0.307	SUBCLONAL	1	TRUE	1	0.361198050981819	2		558	643	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	24	542	2	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.297	0.232	0.372	0.297	0.232	0.372	SUBCLONAL	1	TRUE	1	0.361198050981819	2		544	447	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0057789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	40	399	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	0.52	0.432	0.617	0.52	0.432	0.617	SUBCLONAL	1	TRUE	1	0.361198050981819	2		399	426	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692922	89692922	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201044	NA	P-0057789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	35	373	0	ENST00000371953.3:c.406T>C	p.Cys136Arg	p.C136R	ENST00000371953	NM_000314.4	136	Tgt/Cgt	5/9	1	2	FACETS	0.441	0.362	0.531	0.441	0.362	0.531	SUBCLONAL	1	TRUE	1	0.361198050981819	2		373	439	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417861	138417861	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	43	311	0	ENST00000289153.2:c.1658A>G	p.Asn553Ser	p.N553S	ENST00000289153	NM_006219.2	553	aAt/aGt	11/22	1	2	FACETS	0.661	0.555	0.779	0.661	0.555	0.779	SUBCLONAL	1	TRUE	1	0.361198050981819	2		311	360	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692814	89692815	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0057789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	20	171	0	ENST00000371953.3:c.299_300dup	p.Ile101LeufsTer13	p.I101Lfs*13	ENST00000371953	NM_000314.4	100	ctt/cTTtt	5/9	1	2	FACETS	0.595	0.458	0.755	0.595	0.458	0.755	SUBCLONAL	1	TRUE	1	0.361198050981819	2		171	186	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692944	89692944	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	36	383	0	ENST00000371953.3:c.428G>C	p.Gly143Ala	p.G143A	ENST00000371953	NM_000314.4	143	gGc/gCc	5/9	1	2	FACETS	0.447	0.367	0.536	0.447	0.367	0.536	SUBCLONAL	1	TRUE	1	0.361198050981819	2		383	446	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349923	89349925	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0057789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	36	666	0	ENST00000301030.4:c.3025_3027del	p.Lys1009del	p.K1009del	ENST00000301030	NM_001256183.1	1009	AAG/-	9/13	1	2	FACETS	0.233	0.19	0.281	0.233	0.19	0.281	SUBCLONAL	1	TRUE	1	0.361198050981819	2		666	856	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730343	133730343	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs775748939	NA	P-0057789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	46	395	0	ENST00000318560.5:c.409G>T	p.Ala137Ser	p.A137S	ENST00000318560	NM_005157.4	137	Gct/Tct	3/11	1	2	FACETS	0.559	0.471	0.655	0.559	0.471	0.655	SUBCLONAL	1	TRUE	1	0.361198050981819	2		395	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0057790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	139	490	1	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.78690848607966	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	0	0.78565159172734	3		491	160	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44896923	44896923	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1402339766	NA	P-0057790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	26	322	0	ENST00000377967.4:c.643T>C	p.Tyr215His	p.Y215H	ENST00000377967	NM_021140.2	215	Tat/Cat	8/29	NA	2	FACETS	0.827	0.676	0.989			1	INDETERMINATE	1	TRUE	NA	0.78565159172734	2		322	80	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76812977	76812978	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0057790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	30	384	0	ENST00000373344.5:c.6642_6643dup	p.Leu2215TyrfsTer2	p.L2215Yfs*2	ENST00000373344	NM_000489.3	2215	tta/tATta	30/35	0.796623913665384	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.78565159172734	1		384	35	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0057791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	104	225	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.147026042633963	2	FACETS	1	0.972	1	0.587	0.534	0.64	INDETERMINATE	1	TRUE	0	0.676356656244506	2		225	262	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0057791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	390	605	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.676356656244506	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.676356656244506	2		605	565	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0057791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	177	246	1	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	0.274147432992477	5	FACETS	0.87	0.812	0.928	0.87	0.812	0.928	INDETERMINATE	3	TRUE	2	0.676356656244506	5		247	404	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	601	707	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.251496242847344	5	FACETS	0.95	0.922	0.978	0.76	0.738	0.782	INDETERMINATE	4	TRUE	0	0.676356656244506	5		707	942	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117746771	117746771	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	100	265	0	ENST00000368508.3:c.49C>G	p.Leu17Val	p.L17V	ENST00000368508	NM_002944.2	17	Ctt/Gtt	1/43	1	2	FACETS	0.96	0.868	1	0.96	0.868	1	CLONAL	1	TRUE	1	0.676356656244506	2		265	308	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56787286	56787286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782474	NA	P-0057791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	67	428	1	ENST00000337432.4:c.772C>T	p.Arg258Cys	p.R258C	ENST00000337432	NM_058216.2	258	Cgt/Tgt	5/9	0.591633639431111	4	FACETS	0.321	0.278	0.368			1	SUBCLONAL	1	TRUE	NA	0.676356656244506	4		429	1035	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248156	110248156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	57	372	0	ENST00000374672.4:c.1316G>A	p.Arg439His	p.R439H	ENST00000374672	NM_004235.4	439	cGc/cAc	5/5	0.533869254580198	3	FACETS	0.378	0.324	0.437	0.189	0.162	0.219	SUBCLONAL	1	TRUE	1	0.676356656244506	3		372	597	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431614	431614	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	141	352	0	ENST00000399788.2:c.2395C>T	p.Gln799Ter	p.Q799*	ENST00000399788	NM_001042603.1	799	Cag/Tag	17/28	0.676356656244506	3	FACETS	1	0.943	1	0.519	0.475	0.564	CLONAL	1	TRUE	1	0.676356656244506	3		352	538	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478920	56478920	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	452	657	0	ENST00000267101.3:c.376A>G	p.Asn126Asp	p.N126D	ENST00000267101	NM_001982.3	126	Aac/Gac	3/28	0.676356656244506	3	FACETS	0.956	0.918	0.995	0.956	0.918	0.995	CLONAL	2	TRUE	1	0.676356656244506	3		657	935	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683544	29683544	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	45	256	0	ENST00000356175.3:c.7619C>A	p.Ser2540Ter	p.S2540*	ENST00000356175	NM_000267.3	2540	tCa/tAa	51/57	0.577401362842849	3	FACETS	0.466	0.392	0.547	0.233	0.196	0.274	SUBCLONAL	1	TRUE	1	0.676356656244506	3		256	382	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971292	13971292	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	55	391	0	ENST00000405192.2:c.637C>G	p.Arg213Gly	p.R213G	ENST00000405192	NM_001163147.1	213	Cgc/Ggc	8/12	0.676356656244506	3	FACETS	0.379	0.324	0.439	0.19	0.162	0.22	SUBCLONAL	1	TRUE	1	0.676356656244506	3		391	574	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	102	306	0				ENST00000310581	NM_198253.2	-/1132			0.259147221371125	4	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	2	0.36998550478461	4		306	365	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0057792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	41	584	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.363396410843961	3	FACETS	0.504	0.419	0.598	0.252	0.209	0.299	SUBCLONAL	1	TRUE	1	0.36998550478461	3		584	521	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	132	276	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.36998550478461	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.36998550478461	3		276	381	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879277	151879277	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs956673837	NA	P-0057792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	39	348	1	ENST00000262189.6:c.5668C>T	p.Arg1890Ter	p.R1890*	ENST00000262189	NM_170606.2	1890	Cga/Tga	36/59	0.247017082450364	5	FACETS	0.811	0.673	0.965	0.27	0.224	0.322	CLONAL	1	TRUE	2	0.36998550478461	5		349	404	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0057792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	12	229	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.363396410843961	3	FACETS	0.277	0.194	0.379	0.138	0.097	0.19	SUBCLONAL	1	TRUE	1	0.36998550478461	3		229	278	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0057792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	255	632	0	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	0.36759094681558	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.36998550478461	2		632	625	SUCCESS
APC	324	MSKCC	GRCh37	5	112175322	112175322	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1114167578	NA	P-0057792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	57	176	0	ENST00000257430.4:c.4031C>G	p.Ser1344Ter	p.S1344*	ENST00000257430	NM_000038.5	1344	tCa/tGa	16/16	0.252094438559087	5	FACETS	1	0.919	1	0.719	0.625	0.819	CLONAL	2	TRUE	2	0.36998550478461	5		176	222	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526268	189526268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	64	494	1	ENST00000264731.3:c.532G>A	p.Asp178Asn	p.D178N	ENST00000264731	NM_003722.4	178	Gac/Aac	4/14	0.363396410843961	3	FACETS	0.785	0.681	0.898	0.393	0.34	0.449	SUBCLONAL	1	TRUE	1	0.36998550478461	3		495	522	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856056	111856056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs574829930	NA	P-0057792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	126	493	3	ENST00000341259.2:c.107C>T	p.Ala36Val	p.A36V	ENST00000341259	NM_005475.2	36	gCg/gTg	2/8	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.36998550478461	NA		496	730	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266033	41266838	+	splice_donor_variant,splice_acceptor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	GGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCAAGATGATGCAGAACTTGCCACACGTGCAATCCCTGAACTGACAAAACTGCTAAATGACGAGGACCAGGTAAGCAATGACATAGCTAGCTTTTTAGTCTGCTTTGAAGTAAATGCTCAAGGGGAGTAGTTTCAGAATGTCTACCCAATACCAGTACTTGAAAACTAACGATGTTTCTGAATTCCTGTATTACAGGTGGTGGTTAATAA	GGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCAAGATGATGCAGAACTTGCCACACGTGCAATCCCTGAACTGACAAAACTGCTAAATGACGAGGACCAGGTAAGCAATGACATAGCTAGCTTTTTAGTCTGCTTTGAAGTAAATGCTCAAGGGGAGTAGTTTCAGAATGTCTACCCAATACCAGTACTTGAAAACTAACGATGTTTCTGAATTCCTGTATTACAGGTGGTGGTTAATAA	-	novel	NA	P-0057792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	25	210	0	ENST00000349496.5:c.32_511del		p.X11_splice	ENST00000349496	NM_001904.3	11	ttGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCAAGATGATGCAGAACTTGCCACACGTGCAATCCCTGAACTGACAAAACTGCTAAATGACGAGGACCAGGTAAGCAATGACATAGCTAGCTTTTTAGTCTGCTTTGAAGTAAATGCTCAAGGGGAGTAGTTTCAGAATGTCTACCCAATACCAGTACTTGAAAACTAACGATGTTTCTGAATTCCTGTATTACAGGTGGTGGTTAATAAg/ttg	3-5/15	1	2	FACETS	0.659	0.523	0.814	0.659	0.523	0.814	SUBCLONAL	1	TRUE	1	0.36998550478461	2		210	205	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745597	162745597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748984839	NA	P-0057793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	119	300	0	ENST00000367921.3:c.2012C>T	p.Pro671Leu	p.P671L	ENST00000367921	NM_006182.2	671	cCc/cTc	15/18	0.315387481982166	2	FACETS	0.875	0.797	0.957	0.438	0.398	0.479	INDETERMINATE	1	TRUE	0	0.674569553640309	2		300	403	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711874	89711874	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0057793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	106	254	0	ENST00000371953.3:c.493-1G>T		p.X165_splice	ENST00000371953	NM_000314.4	165			0.674569553640309	1	FACETS	0.894	0.818	0.97	0.894	0.818	0.97	CLONAL	1	TRUE	0	0.674569553640309	1		254	233	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577803	7578469	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTAGCTGGGACTACAGGTGCCCAGCACCACGCCCGGCTAATTTTTTTTTGTATTTTTCAGTAGAGACGGGGTTTCACCGTTAGCCAGGATGGTCTCGATCTCCCAACCTCGTGATCCGCCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTGCGCCCAGCCAAGCAGGGGAGGCCCTTAGCCTCTGTAAGCTTCAGTTTTTTCAACTGTGCAATAGTTAAACCCATTTACTTTGCACATCTCATGGGGTTATAGGGAGGTCAAATAAGCAGCAGGAGAAAGCCCCCCTACTGCTCACCTGGAGGGCCACTGACAACCACCCTTAACCCCTCCTCCCAGAGACCCCAGTTGCAAACCAGACCTCAGGCGGCTCATAGGGCACCACCACACTATGTCGAAAAGTGTTTCTGTCATCCAAATACTCCACACGCAAATTTCCTTCCACTCGGATAAGATGCTGAGGAGGGGCCAGACCTAAGAGCAATCAGTGAGGAATCAGAGGCCTGGGGACCCTGGGCAACCAGCCCTGTCGTCTCTCCAGCCCCAGCTGCTCACCATCGCTATCTGAGCAGCGCTCATGGTGGGGGCAGCGCCTCACAACCTCCGTCATGTGCTGTGACTGCTTGTAGATGGCCATGGCGCGGACGCGGGTGC	AGTAGCTGGGACTACAGGTGCCCAGCACCACGCCCGGCTAATTTTTTTTTGTATTTTTCAGTAGAGACGGGGTTTCACCGTTAGCCAGGATGGTCTCGATCTCCCAACCTCGTGATCCGCCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTGCGCCCAGCCAAGCAGGGGAGGCCCTTAGCCTCTGTAAGCTTCAGTTTTTTCAACTGTGCAATAGTTAAACCCATTTACTTTGCACATCTCATGGGGTTATAGGGAGGTCAAATAAGCAGCAGGAGAAAGCCCCCCTACTGCTCACCTGGAGGGCCACTGACAACCACCCTTAACCCCTCCTCCCAGAGACCCCAGTTGCAAACCAGACCTCAGGCGGCTCATAGGGCACCACCACACTATGTCGAAAAGTGTTTCTGTCATCCAAATACTCCACACGCAAATTTCCTTCCACTCGGATAAGATGCTGAGGAGGGGCCAGACCTAAGAGCAATCAGTGAGGAATCAGAGGCCTGGGGACCCTGGGCAACCAGCCCTGTCGTCTCTCCAGCCCCAGCTGCTCACCATCGCTATCTGAGCAGCGCTCATGGTGGGGGCAGCGCCTCACAACCTCCGTCATGTGCTGTGACTGCTTGTAGATGGCCATGGCGCGGACGCGGGTGC	-	novel	NA	P-0057793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	158	31	0	ENST00000269305.4:c.461_673-195del		p.X154_splice	ENST00000269305	NM_001126112.2	154		5-6/11	0.664719880074182	1	FACETS		NA	1	1	0.995	1	NA	2	TRUE	0	0.674569553640309	1		31	163	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0057794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	33	584	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.125	0.101	0.152	0.125	0.101	0.152	SUBCLONAL	1	FALSE	1	0.846058093903184	2		584	625	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	294	276	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	FALSE	1	0.846058093903184	2		276	528	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0057794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	167	172	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.846058093903184	2		172	287	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0057794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	142	254	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.846058093903184	2		254	294	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753175	57753175	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	113	206	0	ENST00000274289.3:c.841G>C	p.Glu281Gln	p.E281Q	ENST00000274289	NM_006622.3	281	Gaa/Caa	7/14	1	2	FACETS	0.918	0.839	0.999	0.918	0.839	0.999	CLONAL	1	FALSE	1	0.846058093903184	2		206	291	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205217	46205217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	138	242	0	ENST00000334344.6:c.301G>A	p.Glu101Lys	p.E101K	ENST00000334344	NM_152641.2	101	Gag/Aag	4/21	1	2	FACETS	0.865	0.797	0.936	0.865	0.797	0.936	CLONAL	1	FALSE	1	0.846058093903184	2		242	377	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426469	49426469	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs188017299	NA	P-0057794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	375	684	0	ENST00000301067.7:c.12019C>T	p.Gln4007Ter	p.Q4007*	ENST00000301067	NM_003482.3	4007	Caa/Taa	39/54	1	2	FACETS	0.954	0.909	1	0.954	0.909	1	CLONAL	1	FALSE	1	0.846058093903184	2		684	929	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156122	99156122	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	216	424	0	ENST00000074304.5:c.802G>T	p.Glu268Ter	p.E268*	ENST00000074304	NM_001134224.1	268	Gag/Tag	10/26	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	1	FALSE	NA	0.846058093903184	2		424	482	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916636	178916665	+	inframe_deletion	In_Frame_Del	DEL	GTGAACTGTGGGGCATCCACTTGATGCCCC	GTGAACTGTGGGGCATCCACTTGATGCCCC	-	novel	NA	P-0057794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	86	197	0	ENST00000263967.3:c.23_52del	p.Gly8_Pro18delinsAla	p.G8_P18delinsA	ENST00000263967	NM_006218.2	8	gGTGAACTGTGGGGCATCCACTTGATGCCCCca/gca	2/21	1	2	FACETS	0.804	0.722	0.888	0.804	0.722	0.888	CLONAL	1	FALSE	1	0.846058093903184	2		197	253	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504385	186504395	+	frameshift_variant	Frame_Shift_Del	DEL	AATTGACCCTT	AATTGACCCTT	-	novel	NA	P-0057794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	157	249	0	ENST00000323963.5:c.722_732del	p.Glu241GlyfsTer9	p.E241Gfs*9	ENST00000323963		241	gAATTGACCCTT/g	7/11	1	2	FACETS	0.907	0.841	0.975	0.907	0.841	0.975	CLONAL	1	FALSE	1	0.846058093903184	2		249	409	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557781	187557782	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAAA	novel	NA	P-0057794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	127	264	0	ENST00000441802.2:c.3926_3929dup	p.Ser1311PhefsTer12	p.S1311Ffs*12	ENST00000441802	NM_005245.3	1310	tcg/tcTTTCg	5/27	0.165894099423309	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.846058093903184	0		264	339	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38196080	38196080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	297	407	0	ENST00000317025.8:c.721G>A	p.Glu241Lys	p.E241K	ENST00000317025	NM_023034.1	241	Gaa/Aaa	3/24	0.846058093903184	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	0	0.846058093903184	1		407	377	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969357	44969357	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	228	146	0	ENST00000377967.4:c.4039G>T	p.Glu1347Ter	p.E1347*	ENST00000377967	NM_021140.2	1347	Gag/Tag	28/29	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	FALSE	0	0.846058093903184	1		146	256	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591940	48591940	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	10	234	0	ENST00000342988.3:c.1103C>T	p.Ser368Phe	p.S368F	ENST00000342988	NM_005359.5	368	tCc/tTc	9/12	0.846058093903184	1	FACETS	0.073	0.049	0.103	0.073	0.049	0.103	SUBCLONAL	1	FALSE	0	0.846058093903184	1		234	186	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560219	29560219	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	117	216	0	ENST00000356175.3:c.3697del	p.Cys1233ValfsTer7	p.C1233Vfs*7	ENST00000356175	NM_000267.3	1232	ccT/cc	27/57	0.164315072326118	3	FACETS	1	0.977	1	0.792	0.726	0.858	INDETERMINATE	2	TRUE	0	0.434557633632967	3		216	276	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0057798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	80	293	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.358066117308394	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.358066117308394	1		293	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0057798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	269	608	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.245961037466806	3	FACETS	1	0.99	1	0.818	0.771	0.865	CLONAL	2	TRUE	0	0.358066117308394	3		608	722	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	47	645	0	ENST00000269305.4:c.166G>T	p.Glu56Ter	p.E56*	ENST00000269305	NM_001126112.2	56	Gaa/Taa	4/11	0.245961037466806	3	FACETS	0.419	0.352	0.493	0.14	0.117	0.165	SUBCLONAL	1	TRUE	0	0.358066117308394	3		645	739	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031973	26031973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	12	398	0	ENST00000244661.2:c.316G>A	p.Glu106Lys	p.E106K	ENST00000244661	NM_003537.3	106	Gag/Aag	1/1	0.245961037466806	3	FACETS	0.151	0.105	0.208	0.05	0.035	0.07	SUBCLONAL	1	TRUE	0	0.358066117308394	3		398	524	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943749	9943749	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	145	628	1	ENST00000330684.3:c.1192G>T	p.Asp398Tyr	p.D398Y	ENST00000330684	NM_001134407.1	398	Gac/Tac	5/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.358066117308394	2		629	651	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129463	30129463	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780719391	NA	P-0057798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	58	601	0	ENST00000263025.4:c.565C>T	p.Arg189Trp	p.R189W	ENST00000263025	NM_002746.2	189	Cgg/Tgg	4/9	0.245961037466806	3	FACETS	0.427	0.365	0.494	0.142	0.121	0.165	SUBCLONAL	1	TRUE	0	0.358066117308394	3		601	895	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023724	27023734	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCCCCTCC	GCGGCCCCTCC	-	novel	NA	P-0057798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	24	201	0	ENST00000324856.7:c.836_846del	p.Pro279ArgfsTer117	p.P279Rfs*117	ENST00000324856	NM_006015.4	277	gGCGGCCCCTCC/g	1/20	0.358066117308394	1	FACETS	0.435	0.342	0.542	0.435	0.342	0.542	SUBCLONAL	1	TRUE	0	0.358066117308394	1		201	253	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69032484	69032484	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	31	538	0	ENST00000288368.4:c.3558C>A	p.Asp1186Glu	p.D1186E	ENST00000288368	NM_024870.2	1186	gaC/gaA	29/40	1	2	FACETS	0.306	0.247	0.373	0.306	0.247	0.373	SUBCLONAL	1	TRUE	1	0.358066117308394	2		538	566	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209366	98209366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773676486	NA	P-0057798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	89	474	0	ENST00000331920.6:c.4172G>A	p.Arg1391Gln	p.R1391Q	ENST00000331920	NM_000264.3	1391	cGg/cAg	23/24	0.358066117308394	1	FACETS	0.843	0.75	0.942	0.843	0.75	0.942	CLONAL	1	TRUE	0	0.358066117308394	1		474	484	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717678	89717678	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	148	456	1	ENST00000371953.3:c.703G>A	p.Glu235Lys	p.E235K	ENST00000371953	NM_000314.4	235	Gaa/Aaa	7/9	0.358066117308394	3	FACETS	0.914	0.84	0.991	0.914	0.84	0.991	CLONAL	2	TRUE	1	0.358066117308394	3		457	533	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73995338	73995338	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	66	235	0	ENST00000318443.5:c.644A>T	p.Asn215Ile	p.N215I	ENST00000318443	NM_001024736.1	215	aAt/aTt	4/10	0.351670578171299	2	FACETS	0.794	0.699	0.895	0.794	0.699	0.895	SUBCLONAL	2	TRUE	0	0.358066117308394	2		235	232	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263864	16263864	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	185	608	0	ENST00000375759.3:c.10233G>C	p.Arg3411Ser	p.R3411S	ENST00000375759	NM_015001.2	3411	agG/agC	12/15	0.358066117308394	5	FACETS	0.804	0.742	0.868	0.402	0.371	0.434	CLONAL	2	TRUE	1	0.358066117308394	5		608	988	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445110	49445110	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	76	692	1	ENST00000301067.7:c.2356C>A	p.Pro786Thr	p.P786T	ENST00000301067	NM_003482.3	786	Cca/Aca	10/54	0.358066117308394	1	FACETS	0.534	0.468	0.604	0.534	0.468	0.604	SUBCLONAL	1	TRUE	0	0.358066117308394	1		693	653	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446202	49446202	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	183	666	0	ENST00000301067.7:c.1264G>C	p.Ala422Pro	p.A422P	ENST00000301067	NM_003482.3	422	Gca/Cca	10/54	0.358066117308394	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.358066117308394	1		666	656	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281528	49281528	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	239	550	0	ENST00000282018.3:c.575T>G	p.Leu192Arg	p.L192R	ENST00000282018	NM_020377.2	192	cTc/cGc	1/1	0.303805131576943	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.358066117308394	2		550	656	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609601	81609601	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	75	530	0	ENST00000298171.2:c.1199C>A	p.Pro400His	p.P400H	ENST00000298171	NM_000369.2	400	cCc/cAc	10/10	1	2	FACETS	0.882	0.775	0.996	0.882	0.775	0.996	CLONAL	1	TRUE	1	0.358066117308394	2		530	475	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569751	95569751	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	35	203	0	ENST00000393063.1:c.3982A>C	p.Thr1328Pro	p.T1328P	ENST00000393063	NM_030621.3	1328	Acc/Ccc	22/28	1	2	FACETS	0.973	0.805	1	0.973	0.805	1	CLONAL	1	TRUE	1	0.358066117308394	2		203	201	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630490	90630490	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs774183637	NA	P-0057798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	206	543	0	ENST00000330062.3:c.821A>G	p.Tyr274Cys	p.Y274C	ENST00000330062	NM_002168.2	274	tAt/tGt	7/11	0.351670578171299	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	0	0.358066117308394	2		543	567	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15952210	15952210	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	59	682	0	ENST00000268712.3:c.6485A>G	p.Gln2162Arg	p.Q2162R	ENST00000268712	NM_006311.3	2162	cAg/cGg	41/46	0.245961037466806	3	FACETS	0.524	0.45	0.605	0.175	0.15	0.202	SUBCLONAL	1	TRUE	0	0.358066117308394	3		682	741	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732460	74732460	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	22	274	0	ENST00000359995.5:c.449G>C	p.Arg150Pro	p.R150P	ENST00000359995	NM_001195427.1	150	cGg/cCg	2/3	0.245961037466806	3	FACETS	0.375	0.29	0.474	0.125	0.096	0.158	SUBCLONAL	1	TRUE	0	0.358066117308394	3		274	386	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954608	17954608	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	161	992	0	ENST00000458235.1:c.286C>A	p.Gln96Lys	p.Q96K	ENST00000458235	NM_000215.3	96	Caa/Aaa	3/24	0.358066117308394	3	FACETS	0.958	0.877	1	0.479	0.438	0.521	CLONAL	1	TRUE	1	0.358066117308394	3		992	1107	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795766	42795766	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568519274	NA	P-0057798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	122	601	1	ENST00000575354.2:c.2755C>T	p.Pro919Ser	p.P919S	ENST00000575354	NM_015125.3	919	Cct/Tct	11/20	0.351670578171299	2	FACETS	0.945	0.855	1	0.473	0.427	0.52	CLONAL	1	TRUE	0	0.358066117308394	2		602	721	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973903	55973903	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0057798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	88	453	0	ENST00000263923.4:c.1412+1G>T		p.X471_splice	ENST00000263923	NM_002253.2	471			0.358066117308394	11	FACETS	0.991	0.875	1	0.099	0.087	0.112	CLONAL	1	TRUE	1	0.358066117308394	11		453	1295	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86658437	86658437	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	20	145	0	ENST00000274376.6:c.1402A>G	p.Lys468Glu	p.K468E	ENST00000274376	NM_002890.2	468	Aag/Gag	10/25	0.358066117308394	1	FACETS	0.771	0.597	0.968	0.771	0.597	0.968	CLONAL	1	TRUE	0	0.358066117308394	1		145	119	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852222	128852222	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs776156624	NA	P-0057798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	40	637	0	ENST00000249373.3:c.2294G>T	p.Gly765Val	p.G765V	ENST00000249373	NM_005631.4	765	gGc/gTc	12/12	0.248890991977001	3	FACETS	0.348	0.288	0.416	0.116	0.096	0.139	SUBCLONAL	1	TRUE	0	0.358066117308394	3		637	756	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231103	98231103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	38	505	0	ENST00000331920.6:c.2180G>A	p.Cys727Tyr	p.C727Y	ENST00000331920	NM_000264.3	727	tGt/tAt	14/24	0.358066117308394	1	FACETS	0.354	0.292	0.423	0.354	0.292	0.423	SUBCLONAL	1	TRUE	0	0.358066117308394	1		505	492	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356783	70356783	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	208	385	0	ENST00000374080.3:c.5455G>T	p.Asp1819Tyr	p.D1819Y	ENST00000374080		1819	Gac/Tac	38/45	0.241615369531921	2	FACETS	0.942	0.888	0.997			1	CLONAL	3	TRUE	NA	0.358066117308394	2		385	411	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357430	70357430	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	200	357	0	ENST00000374080.3:c.5771A>T	p.Gln1924Leu	p.Q1924L	ENST00000374080		1924	cAg/cTg	40/45	0.241615369531921	2	FACETS	0.872	0.819	0.926			1	CLONAL	3	TRUE	NA	0.358066117308394	2		357	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0057800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	948	559	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	NA	2	FACETS	1	0.998	1			1	INDETERMINATE	2	TRUE	NA	0.861352200366383	2		559	1039	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690584	88690584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368222977	NA	P-0057800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	182	319	0	ENST00000360948.2:c.446C>T	p.Thr149Met	p.T149M	ENST00000360948	NM_001012338.2	149	aCg/aTg	5/19	0.847214661342293	4	FACETS	0.768	0.708	0.831	0.384	0.354	0.416	SUBCLONAL	1	TRUE	2	0.861352200366383	4		319	1024	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288657	33288657	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1213838920	NA	P-0057800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	708	356	0	ENST00000374542.5:c.895C>T	p.Arg299Ter	p.R299*	ENST00000374542	NM_001141970.1	299	Cga/Tga	3/8	0.8610486753296	4	FACETS	0.991	0.977	1	0.991	0.977	1	CLONAL	4	TRUE	0	0.861352200366383	4		356	772	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468318	120468318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	37	386	0	ENST00000256646.2:c.4121G>A	p.Cys1374Tyr	p.C1374Y	ENST00000256646	NM_024408.3	1374	tGc/tAc	25/34	0.822302083704927	3	FACETS	0.171	0.14	0.205	0.085	0.07	0.103	SUBCLONAL	1	TRUE	1	0.861352200366383	3		386	720	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449466	149449466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772168972	NA	P-0057800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	220	405	1	ENST00000286301.3:c.1480G>A	p.Gly494Ser	p.G494S	ENST00000286301	NM_005211.3	494	Ggc/Agc	10/22	0.637614524694857	3	FACETS	1	0.981	1	0.563	0.527	0.6	CLONAL	1	TRUE	1	0.861352200366383	3		406	649	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056650	26056650	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	24	113	0	ENST00000343677.2:c.7G>C	p.Glu3Gln	p.E3Q	ENST00000343677	NM_005319.3	3	Gag/Cag	1/1	0.8610486753296	4	FACETS	0.372	0.292	0.464	0.093	0.073	0.116	SUBCLONAL	1	TRUE	0	0.861352200366383	4		113	279	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0057801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	160	639	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.211311704821181	3	FACETS	0.904	0.829	0.983	0.904	0.829	0.983	CLONAL	2	TRUE	1	0.211311704821181	3		639	926	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0057801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	54	370	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	0.211311704821181	3	FACETS	0.939	0.807	1	0.939	0.807	1	CLONAL	2	TRUE	1	0.211311704821181	3		370	301	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231290	98231290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767947110	NA	P-0057801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	73	634	0	ENST00000331920.6:c.1993C>T	p.Arg665Cys	p.R665C	ENST00000331920	NM_000264.3	665	Cgc/Tgc	14/24	0.211311704821181	3	FACETS	0.9	0.785	1	0.45	0.392	0.512	CLONAL	1	TRUE	1	0.211311704821181	3		634	849	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912580	NA	P-0057801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	74	266	0	ENST00000342988.3:c.1157G>A	p.Gly386Asp	p.G386D	ENST00000342988	NM_005359.5	386	gGt/gAt	10/12	0.211311704821181	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	2	TRUE	0	0.211311704821181	2		266	333	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243708852	243708852	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	57	334	0	ENST00000263826.5:c.1211T>C	p.Phe404Ser	p.F404S	ENST00000263826	NM_005465.4	404	tTc/tCc	11/13	0.211311704821181	4	FACETS	0.864	0.745	0.994			1	CLONAL	2	TRUE	NA	0.211311704821181	4		334	378	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554008	63554009	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1056103847	NA	P-0057801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	232	453	0	ENST00000307078.5:c.730dup	p.Ser244PhefsTer25	p.S244Ffs*25	ENST00000307078	NM_004655.3	244	tcg/tTcg	2/11	0.211311704821181	3	FACETS	0.889	0.833	0.946	1	0.986	1	CLONAL	4	TRUE	0	0.211311704821181	3		453	683	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864256	151864256	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	69	326	2	ENST00000262189.6:c.9725G>T	p.Ser3242Ile	p.S3242I	ENST00000262189	NM_170606.2	3242	aGc/aTc	42/59	0.211311704821181	4	FACETS	0.981	0.859	1	0.981	0.859	1	CLONAL	2	TRUE	2	0.211311704821181	4		328	403	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0057802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	77	297	0	ENST00000374690.3:c.2105T>A	p.Leu702His	p.L702H	ENST00000374690	NM_000044.3	702	cTc/cAc	4/8	0.77704325001772	2	FACETS	0.254	0.222	0.288			1	SUBCLONAL	1	TRUE	NA	0.77704325001772	2		297	781	SUCCESS
AR	367	MSKCC	GRCh37	X	66943552	66943552	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	204	187	0	ENST00000374690.3:c.2632A>T	p.Thr878Ser	p.T878S	ENST00000374690	NM_000044.3	878	Act/Tct	8/8	0.77704325001772	2	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.77704325001772	2		187	480	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058563	72058563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1489300985	NA	P-0057802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	197	397	0	ENST00000357731.5:c.877G>A	p.Gly293Ser	p.G293S	ENST00000357731	NM_173808.2	293	Ggc/Agc	6/7	0.77704325001772	4	FACETS	0.99	0.917	1			1	CLONAL	1	TRUE	NA	0.77704325001772	4		397	910	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24158996	24158996	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	295	619	0	ENST00000263121.7:c.668G>C	p.Cys223Ser	p.C223S	ENST00000263121	NM_003073.3	223	tGt/tCt	6/9	1	2	FACETS	0.872	0.823	0.921	0.872	0.823	0.921	CLONAL	1	TRUE	1	0.77704325001772	2		619	871	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	70	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.956	0.856	1	0.956	0.856	1	CLONAL	1	TRUE	1	0.945272965702591	2		306	155	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880257	37880257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	348	322	0	ENST00000269571.5:c.2301C>G	p.Ile767Met	p.I767M	ENST00000269571		767	atC/atG	19/27	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.945272965702591	2		322	722	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	276	292	0	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	0.436356626420645	1	FACETS	0.65	0.619	0.68	0.65	0.619	0.68	INDETERMINATE	1	TRUE	0	0.945272965702591	1		292	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0057803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	289	292	0	ENST00000269305.4:c.673-1G>C		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.937622062695128	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.945272965702591	1		292	308	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161456	2161456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs970922682	NA	P-0057803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	421	456	0	ENST00000434045.2:c.71G>A	p.Arg24His	p.R24H	ENST00000434045	NM_001127598.1	24	cGc/cAc	2/5	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.945272965702591	2		456	875	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61197641	61197641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	303	346	0	ENST00000301761.2:c.23C>T	p.Ser8Leu	p.S8L	ENST00000301761	NM_017841.2	8	tCg/tTg	1/4	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.945272965702591	2		346	605	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259453	16259453	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	326	353	0	ENST00000375759.3:c.6718C>G	p.Pro2240Ala	p.P2240A	ENST00000375759	NM_015001.2	2240	Cct/Gct	11/15	0.434397515797881	3	FACETS	1	0.992	1	0.615	0.583	0.647	INDETERMINATE	1	TRUE	1	0.945272965702591	3		353	826	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197299	94197299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	217	247	0	ENST00000323929.3:c.1205G>A	p.Arg402Lys	p.R402K	ENST00000323929	NM_005591.3	402	aGa/aAa	11/20	1	2	FACETS	0.947	0.89	1	0.947	0.89	1	CLONAL	1	TRUE	1	0.945272965702591	2		247	485	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121877	2121877	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs756536921	NA	P-0057803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	237	413	0	ENST00000219476.3:c.2039G>T	p.Arg680Leu	p.R680L	ENST00000219476	NM_000548.3	680	cGg/cTg	19/42	0.436356626420645	1	FACETS	0.423	0.397	0.449	0.423	0.397	0.449	INDETERMINATE	1	TRUE	0	0.945272965702591	1		413	625	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39002745	39002745	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	97	189	0	ENST00000357387.3:c.284A>C	p.Glu95Ala	p.E95A	ENST00000357387	NM_152756.3	95	gAa/gCa	5/38	1	2	FACETS	0.419	0.375	0.465	0.419	0.375	0.465	SUBCLONAL	1	TRUE	1	0.945272965702591	2		189	490	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969406	44969408	+	stop_gained	Nonsense_Mutation	TNP	GAA	GAA	TAT	novel	NA	P-0057803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	295	167	0	ENST00000377967.4:c.4088_4090delinsTAT	p.Arg1363_Lys1364delinsLeuTer	p.R1363_K1364delinsL*	ENST00000377967	NM_021140.2	1363	cGAAaa/cTATaa	28/29	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.945272965702591	1		167	312	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713733	30713733	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553630235	NA	P-0057804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	162	492	0	ENST00000295754.5:c.1058C>T	p.Ser353Phe	p.S353F	ENST00000295754	NM_003242.5	353	tCc/tTc	4/7	0.821136490168849	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.821136490168849	1		492	220	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593664	55593665	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTATGATCACAAATGGGAGTTTCCCAGAAACAGGCTGAGTTTTGG	novel	NA	P-0057804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	178	260	0	ENST00000288135.5:c.1732_1774+2dup		p.P578_G593dup	ENST00000288135	NM_000222.2	578	cct/ccTTATGATCACAAATGGGAGTTTCCCAGAAACAGGCTGAGTTTTGGt	11/21	0.821136490168849	3	FACETS	0.853	0.788	0.92	0.426	0.394	0.46	CLONAL	1	TRUE	1	0.821136490168849	3		260	717	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0057810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	233	172	0				ENST00000310581	NM_198253.2	-/1132			0.565150686806904	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.753409969122729	4		172	479	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0057810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	1474	422	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	0.753409969122729	7	FACETS	0.992	0.982	1			1	CLONAL	7	TRUE	NA	0.753409969122729	7		422	1625	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0057810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	321	827	0	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.753409969122729	2		827	851	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435596	18435596	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	129	335	0	ENST00000266497.5:c.581G>A	p.Arg194Lys	p.R194K	ENST00000266497		194	aGg/aAg	1/31	1	2	FACETS	0.916	0.839	0.994	0.916	0.839	0.994	CLONAL	1	TRUE	1	0.753409969122729	2		335	374	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492743	50492743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	290	644	0	ENST00000394963.4:c.1508G>A	p.Arg503Gln	p.R503Q	ENST00000394963	NM_003076.4	503	cGa/cAa	13/13	1	2	FACETS	0.983	0.929	1	0.983	0.929	1	CLONAL	1	TRUE	1	0.753409969122729	2		644	783	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857436	9857436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	230	619	0	ENST00000330684.3:c.3965G>A	p.Gly1322Glu	p.G1322E	ENST00000330684	NM_001134407.1	1322	gGa/gAa	13/13	1	2	FACETS	0.89	0.834	0.947	0.89	0.834	0.947	CLONAL	1	TRUE	1	0.753409969122729	2		619	686	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098365	11098365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs970190031	NA	P-0057810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	285	562	0	ENST00000358026.2:c.883C>T	p.Pro295Ser	p.P295S	ENST00000358026	NM_001128849.1	295	Ccc/Tcc	6/36	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.753409969122729	2		562	719	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212180	36212180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	197	503	0	ENST00000222270.7:c.1931C>T	p.Pro644Leu	p.P644L	ENST00000222270	NM_014727.1	644	cCc/cTc	3/37	1	2	FACETS	0.873	0.813	0.934	0.873	0.813	0.934	CLONAL	1	TRUE	1	0.753409969122729	2		503	599	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419837	41419837	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs267605939	NA	P-0057810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	241	576	0	ENST00000373198.4:c.484C>T	p.Gln162Ter	p.Q162*	ENST00000373198	NM_133170.3	162	Cag/Tag	3/32	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.753409969122729	2		576	597	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374998	138374998	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	199	461	0	ENST00000289153.2:c.3061A>G	p.Ile1021Val	p.I1021V	ENST00000289153	NM_006219.2	1021	Ata/Gta	21/22	1	2	FACETS	0.942	0.879	1	0.942	0.879	1	CLONAL	1	TRUE	1	0.753409969122729	2		461	561	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950523	38950523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	252	545	1	ENST00000357387.3:c.3427C>T	p.His1143Tyr	p.H1143Y	ENST00000357387	NM_152756.3	1143	Cat/Tat	31/38	0.725134199095375	3	FACETS	1	0.966	1	0.522	0.489	0.556	CLONAL	1	TRUE	1	0.753409969122729	3		546	882	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	164	276	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.239433817595556	4	FACETS	0.898	0.831	0.966	0.673	0.623	0.725	CLONAL	3	TRUE	0	0.334475665219986	4		276	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0057811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	127	649	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.216772467564075	2	FACETS	0.778	0.709	0.85	0.778	0.709	0.85	SUBCLONAL	2	TRUE	0	0.334475665219986	2		649	488	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604828	48604842	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	TTTAGACTGAGGTCT	TTTAGACTGAGGTCT	-	novel	NA	P-0057811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	51	375	0	ENST00000342988.3:c.1654_*9del		p.*552*	ENST00000342988	NM_005359.5	550		12/12	0.143372050232162	3	FACETS	1	0.937	1	0.394	0.337	0.456	INDETERMINATE	1	TRUE	0	0.334475665219986	3		375	301	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138399	11138506	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGCCTGCAGGGTTCCAGGTTTAACATCCTGCGCCTTCTCTCCTGCCTCCTCCACACTCCAGGCTGGACCTGTACCGAGCCTCGGGTAAATTTGAGCTTCTTGATAGAA	TGCCTGCAGGGTTCCAGGTTTAACATCCTGCGCCTTCTCTCCTGCCTCCTCCACACTCCAGGCTGGACCTGTACCGAGCCTCGGGTAAATTTGAGCTTCTTGATAGAA	-	novel	NA	P-0057811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	69	213	0	ENST00000358026.2:c.3216-60_3263del		p.X1072_splice	ENST00000358026	NM_001128849.1	1072		24/36	0.248915116414317	2	FACETS	0.844	0.753	0.936	1	0.97	1	CLONAL	3	TRUE	0	0.334475665219986	2		213	163	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266092	41266092	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	18	417	0	ENST00000349496.5:c.89A>C	p.Tyr30Ser	p.Y30S	ENST00000349496	NM_001904.3	30	tAc/tCc	3/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		417	591	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266111	+	inframe_deletion	In_Frame_Del	DEL	TCTGGAATCCAT	TCTGGAATCCAT	-	novel	NA	P-0057813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	18	431	0	ENST00000349496.5:c.102_113del	p.Ile35_Gly38del	p.I35_G38del	ENST00000349496	NM_001904.3	33	TCTGGAATCCAT/-	3/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		431	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0057816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	246	605	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.143221873336623	6	FACETS	1	0.984	1	0.76	0.712	0.808	INDETERMINATE	2	TRUE	3	0.605960833451717	6		605	788	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949994	44949994	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1450363794	NA	P-0057816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	62	369	0	ENST00000377967.4:c.3763C>T	p.Arg1255Trp	p.R1255W	ENST00000377967	NM_021140.2	1255	Cgg/Tgg	26/29	0.605960833451717	3	FACETS	0.857	0.746	0.976	0.286	0.248	0.326	CLONAL	1	TRUE	0	0.605960833451717	3		369	311	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0057816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	54	203	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.512925226638991	3	FACETS	1	0.968	1	0.712	0.621	0.808	CLONAL	1	TRUE	1	0.605960833451717	3		203	163	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578525	7578525	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	317	742	1	ENST00000269305.4:c.405C>A	p.Cys135Ter	p.C135*	ENST00000269305	NM_001126112.2	135	tgC/tgA	5/11	0.143221873336623	6	FACETS	1	0.99	1	0.79	0.747	0.834	INDETERMINATE	2	TRUE	3	0.605960833451717	6		743	976	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068078	94068078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765322526	NA	P-0057816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	89	264	0	ENST00000369303.4:c.884G>A	p.Arg295His	p.R295H	ENST00000369303	NM_004440.3	295	cGt/cAt	4/17	0.486126279872897	4	FACETS	1	0.98	1	0.737	0.66	0.817	CLONAL	1	TRUE	2	0.605960833451717	4		264	320	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31437383	31437383	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	160	581	0	ENST00000344624.3:c.2905G>A	p.Glu969Lys	p.E969K	ENST00000344624		969	Gaa/Aaa	21/33	0.605960833451717	5	FACETS	1	0.988	1	0.475	0.437	0.515	CLONAL	1	TRUE	2	0.605960833451717	5		581	707	SUCCESS
APC	324	MSKCC	GRCh37	5	112173892	112173898	+	frameshift_variant	Frame_Shift_Del	DEL	AGAAAAT	AGAAAAT	-	novel	NA	P-0057816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	60	324	0	ENST00000257430.4:c.2601_2607del	p.Glu868GlnfsTer46	p.E868Qfs*46	ENST00000257430	NM_000038.5	867	acAGAAAAT/ac	16/16	0.512925226638991	3	FACETS	0.872	0.757	0.994	0.436	0.378	0.497	CLONAL	1	TRUE	1	0.605960833451717	3		324	296	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820941	32820941	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	109	721	0	ENST00000354258.4:c.653G>C	p.Gly218Ala	p.G218A	ENST00000354258	NM_000593.5	218	gGg/gCg	1/11	0.486126279872897	4	FACETS	0.893	0.803	0.988	0.446	0.401	0.494	CLONAL	1	TRUE	2	0.605960833451717	4		721	647	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394938	394938	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	106	610	0	ENST00000380956.4:c.334G>C	p.Glu112Gln	p.E112Q	ENST00000380956	NM_001195286.1	112	Gag/Cag	3/9	0.250762396015707	5	FACETS	0.821	0.735	0.913			1	INDETERMINATE	1	FALSE	NA	0.490872101600632	5		610	913	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115267844	115267844	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0057817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	61	573	0	ENST00000438362.2:c.1889C>G	p.Ser630Ter	p.S630*	ENST00000438362	NM_001242891.1	630	tCa/tGa	15/20	0.287185527128278	4	FACETS	0.679	0.586	0.78	0.339	0.293	0.39	INDETERMINATE	1	FALSE	2	0.490872101600632	4		573	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578258	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AT	novel	NA	P-0057817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	298	783	0	ENST00000269305.4:c.591_592delinsAT	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	197	gtGGaa/gtATaa	6/11	0.490872101600632	3	FACETS	0.841	0.794	0.889	0.841	0.794	0.889	CLONAL	2	FALSE	1	0.490872101600632	3		783	899	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262438	39262439	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0057817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	69	594	2	ENST00000402219.2:c.988_989delinsTT	p.Gly330Phe	p.G330F	ENST00000402219	NM_005633.3	330	GGt/TTt	8/23	0.405344255390515	3	FACETS	0.873	0.764	0.99	0.437	0.382	0.495	CLONAL	1	FALSE	1	0.490872101600632	3		596	401	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430477	181430477	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	339	636	0	ENST00000325404.1:c.329A>G	p.Tyr110Cys	p.Y110C	ENST00000325404	NM_003106.3	110	tAc/tGc	1/1	0.380565506194376	5	FACETS	0.862	0.818	0.907	0.862	0.818	0.907	CLONAL	3	FALSE	2	0.490872101600632	5		636	927	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287313	38287313	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	45	761	0	ENST00000425967.3:c.344C>A	p.Thr115Lys	p.T115K	ENST00000425967	NM_001174067.1	115	aCa/aAa	4/19	NA	2	FACETS	0.207	0.173	0.245			1	INDETERMINATE	1	FALSE	NA	0.490872101600632	2		761	884	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0057818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	39	464	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.276380775650242	4	FACETS	1	0.952	1	0.711	0.596	0.836	CLONAL	1	TRUE	2	0.405512863668282	4		464	190	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579361	7579361	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1064796722	NA	P-0057818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	33	737	0	ENST00000269305.4:c.326T>C	p.Phe109Ser	p.F109S	ENST00000269305	NM_001126112.2	109	tTc/tCc	4/11	0.405512863668282	1	FACETS	0.895	0.74	1	0.895	0.74	1	CLONAL	1	TRUE	0	0.405512863668282	1		737	145	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276307	15276307	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	18	783	0	ENST00000263388.2:c.5687C>G	p.Ser1896Cys	p.S1896C	ENST00000263388	NM_000435.2	1896	tCt/tGt	31/33	1	2	FACETS	0.48	0.363	0.617	0.48	0.363	0.617	SUBCLONAL	1	TRUE	1	0.405512863668282	2		783	185	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121092	3121092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	41	632	0	ENST00000078429.4:c.995C>T	p.Thr332Ile	p.T332I	ENST00000078429	NM_002067.2	332	aCc/aTc	7/7	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.405512863668282	2		632	179	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662909	52662909	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0057820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	65	384	0	ENST00000394830.3:c.1443+1G>T		p.X481_splice	ENST00000394830	NM_018313.4	481			0.278289943182326	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	0	0.278289943182326	1		384	285	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188322	10188322	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs5030814	NA	P-0057820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	61	518	0	ENST00000256474.2:c.463+2T>C		p.X155_splice	ENST00000256474	NM_000551.3	155			0.278289943182326	1	FACETS	0.848	0.734	0.972	0.848	0.734	0.972	CLONAL	1	FALSE	0	0.278289943182326	1		518	445	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045823	180045823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1446557372	NA	P-0057820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	32	746	1	ENST00000261937.6:c.2948C>T	p.Ala983Val	p.A983V	ENST00000261937	NM_182925.4	983	gCg/gTg	21/30	NA	2	FACETS	0.446	0.361	0.542			1	INDETERMINATE	1	FALSE	NA	0.278289943182326	2		747	516	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098416	47098416	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	83	731	0	ENST00000409792.3:c.6858del	p.Ser2287LeufsTer22	p.S2287Lfs*22	ENST00000409792	NM_014159.6	2286	taC/ta	15/21	0.278289943182326	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	0	0.278289943182326	1		731	468	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594236	55594236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	41	467	0	ENST00000288135.5:c.1939C>T	p.Leu647Phe	p.L647F	ENST00000288135	NM_000222.2	647	Ctt/Ttt	13/21	1	2	FACETS	0.688	0.574	0.816	0.688	0.574	0.816	SUBCLONAL	1	FALSE	1	0.278289943182326	2		467	428	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494197	140494197	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	151	849	0	ENST00000288602.6:c.1051G>T	p.Glu351Ter	p.E351*	ENST00000288602	NM_004333.4	351	Gaa/Taa	8/18	0.24952615660304	4	FACETS	1	0.982	1	0.649	0.592	0.708	CLONAL	1	FALSE	2	0.278289943182326	4		849	1069	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0057821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	1104	463	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.756283627092061	7	FACETS	0.951	0.933	0.968			1	CLONAL	6	TRUE	NA	0.756283627092061	7		463	1479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	735	524	0	ENST00000269305.4:c.528C>A	p.Cys176Ter	p.C176*	ENST00000269305	NM_001126112.2	176	tgC/tgA	5/11	0.756283627092061	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.756283627092061	3		524	878	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524486	44524486	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	180	238	0	ENST00000291552.4:c.71T>C	p.Ile24Thr	p.I24T	ENST00000291552	NM_006758.2	24	aTt/aCt	2/8	0.62322847842789	3	FACETS	0.894	0.837	0.95	0.894	0.837	0.95	CLONAL	2	TRUE	1	0.756283627092061	3		238	367	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141568653	141568653	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	267	636	0	ENST00000220592.5:c.809C>G	p.Thr270Arg	p.T270R	ENST00000220592	NM_012154.3	270	aCg/aGg	7/19	0.723859838879577	4	FACETS	0.958	0.897	1	0.479	0.448	0.511	CLONAL	1	TRUE	2	0.756283627092061	4		636	1295	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	31	306	0				ENST00000310581	NM_198253.2	-/1132			0.455794725023438	3	FACETS	1	0.948	1	0.747	0.618	0.886	CLONAL	1	TRUE	1	0.465047898587578	3		306	110	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0057828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	376	432	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.465047898587578	10	FACETS	0.967	0.927	1	0.967	0.927	1	CLONAL	7	TRUE	3	0.465047898587578	10		432	683	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0057828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	132	590	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.401500589422591	5	FACETS	0.92	0.839	1	0.613	0.559	0.669	CLONAL	2	TRUE	2	0.465047898587578	5		590	524	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186791	11186791	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	85	666	0	ENST00000361445.4:c.6414G>T	p.Leu2138Phe	p.L2138F	ENST00000361445	NM_004958.3	2138	ttG/ttT	46/58	0.465047898587578	2	FACETS	1	0.949	1	0.556	0.495	0.619	CLONAL	1	TRUE	0	0.465047898587578	2		666	329	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69103983	69103983	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	135	649	1	ENST00000288368.4:c.4373C>T	p.Ser1458Leu	p.S1458L	ENST00000288368	NM_024870.2	1458	tCa/tTa	36/40	0.455794725023438	3	FACETS	0.906	0.832	0.982	0.906	0.832	0.982	CLONAL	2	TRUE	1	0.465047898587578	3		650	395	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680603	241680603	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1200934499	NA	P-0057828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	111	451	1	ENST00000366560.3:c.146C>T	p.Ser49Phe	p.S49F	ENST00000366560	NM_000143.3	49	tCc/tTc	2/10	0.339917590094879	4	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	2	0.465047898587578	4		452	327	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861263	57861263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1447419974	NA	P-0057828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	153	771	0	ENST00000228682.2:c.1060C>T	p.Arg354Trp	p.R354W	ENST00000228682	NM_005269.2	354	Cgg/Tgg	9/12	0.457853581900804	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.465047898587578	3		771	383	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642833	3642833	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202189103	NA	P-0057828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	87	830	1	ENST00000294008.3:c.2194G>A	p.Gly732Arg	p.G732R	ENST00000294008	NM_032444.2	732	Ggg/Agg	11/15	0.455794725023438	3	FACETS	0.973	0.865	1	0.486	0.432	0.544	CLONAL	1	TRUE	1	0.465047898587578	3		831	474	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138861	64138862	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	118	388	0	ENST00000334205.4:c.2228_2229delinsAA	p.Arg743Gln	p.R743Q	ENST00000334205	NM_003942.2	743	cGG/cAA	17/17	0.455794725023438	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.465047898587578	3		388	259	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181600	32181600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1041838804	NA	P-0057828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	242	1161	1	ENST00000375023.3:c.2185G>A	p.Glu729Lys	p.E729K	ENST00000375023	NM_004557.3	729	Gag/Aag	14/30	0.46116380023228	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.465047898587578	4		1162	635	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397505	116397505	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	174	500	0	ENST00000397752.3:c.1877T>C	p.Val626Ala	p.V626A	ENST00000397752	NM_000245.2	626	gTt/gCt	7/21	0.465047898587578	10	FACETS	1	0.972	1	0.475	0.439	0.512	CLONAL	3	TRUE	3	0.465047898587578	10		500	644	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412156	63412156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	91	1069	0	ENST00000330258.3:c.1011G>A	p.Met337Ile	p.M337I	ENST00000330258	NM_152424.3	337	atG/atA	2/2	0.465047898587578	3	FACETS	0.912	0.812	1	0.456	0.406	0.509	CLONAL	1	TRUE	1	0.465047898587578	3		1069	529	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0057831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	427	656	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.793626101996223	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.793626101996223	2		657	524	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	220	707	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.375505046937428	5	FACETS	1	0.978	1	0.224	0.208	0.241	INDETERMINATE	1	TRUE	0	0.793626101996223	5		707	1084	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056237	26056245	+	inframe_deletion	In_Frame_Del	DEL	CTTCTTGGG	CTTCTTGGG	-	rs749190253	NA	P-0057831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	82	768	0	ENST00000343677.2:c.412_420del	p.Pro138_Lys140del	p.P138_K140del	ENST00000343677	NM_005319.3	138	CCCAAGAAG/-	1/1	0.299140783013026	1	FACETS	0.207	0.182	0.233	0.207	0.182	0.233	INDETERMINATE	1	TRUE	0	0.793626101996223	1		768	603	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099975	27099976	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0057831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	167	881	0	ENST00000324856.7:c.3855_3856dup	p.Asp1286ValfsTer4	p.D1286Vfs*4	ENST00000324856	NM_006015.4	1285	tat/taTGt	15/20	0.261556199327991	1	FACETS	0.388	0.357	0.419	0.388	0.357	0.419	INDETERMINATE	1	TRUE	0	0.793626101996223	1		881	655	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805579	89805579	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	64	856	0	ENST00000389301.3:c.4129T>A	p.Ser1377Thr	p.S1377T	ENST00000389301	NM_000135.2	1377	Tca/Aca	41/43	0.649722790994455	3	FACETS	0.197	0.17	0.227	0.099	0.085	0.114	SUBCLONAL	1	TRUE	1	0.793626101996223	3		856	1142	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878151	151878151	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	343	757	0	ENST00000262189.6:c.6794del	p.Leu2265TrpfsTer2	p.L2265Wfs*2	ENST00000262189	NM_170606.2	2265	tTg/tg	36/59	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.793626101996223	2		757	685	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0057832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	26	172	0				ENST00000310581	NM_198253.2	-/1132			0.306965248810368	3	FACETS	1	0.918	1	0.655	0.526	0.798	CLONAL	1	TRUE	1	0.35388304308372	3		172	132	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0057832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	71	622	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.306965248810368	3	FACETS	0.906	0.793	1	0.453	0.396	0.515	CLONAL	1	TRUE	1	0.35388304308372	3		622	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0057832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	86	618	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.35388304308372	1	FACETS	0.875	0.778	0.979	0.875	0.778	0.979	CLONAL	1	TRUE	0	0.35388304308372	1		618	457	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944527	40944527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371433526	NA	P-0057832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	46	553	2	ENST00000373198.4:c.1975G>A	p.Asp659Asn	p.D659N	ENST00000373198	NM_133170.3	659	Gat/Aat	12/32	1	2	FACETS	0.778	0.658	0.91	0.778	0.658	0.91	CLONAL	1	TRUE	1	0.35388304308372	2		555	334	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0057832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	87	895	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	1	2	FACETS	0.937	0.831	1	0.937	0.831	1	CLONAL	1	TRUE	1	0.35388304308372	2		895	525	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710585	117710585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	32	347	0	ENST00000368508.3:c.1687G>A	p.Glu563Lys	p.E563K	ENST00000368508	NM_002944.2	563	Gag/Aag	12/43	1	2	FACETS	0.807	0.66	0.972	0.807	0.66	0.972	CLONAL	1	TRUE	1	0.35388304308372	2		347	224	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181958	32181958	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	104	835	0	ENST00000375023.3:c.2096C>T	p.Pro699Leu	p.P699L	ENST00000375023	NM_004557.3	699	cCc/cTc	13/30	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.35388304308372	2		835	531	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005353	42005353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	65	445	0	ENST00000219905.7:c.3089C>T	p.Ser1030Phe	p.S1030F	ENST00000219905	NM_001164273.1	1030	tCc/tTc	9/24	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.35388304308372	2		445	337	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970976	70970976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1208665663	NA	P-0057832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	93	872	0	ENST00000276594.2:c.1285G>A	p.Asp429Asn	p.D429N	ENST00000276594	NM_024504.3	429	Gat/Aat	6/8	0.294073377151575	4	FACETS	0.958	0.851	1	0.319	0.283	0.357	CLONAL	1	TRUE	1	0.35388304308372	4		872	743	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813400	32813401	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0057832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	103	1105	0	ENST00000354258.4:c.2382dup	p.Cys795ValfsTer41	p.C795Vfs*41	ENST00000354258	NM_000593.5	794	-/G	11/11	1	2	FACETS	0.92	0.824	1	0.92	0.824	1	CLONAL	1	TRUE	1	0.35388304308372	2		1105	633	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	64	276	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.24888632312081	3	FACETS	1	0.953	1	0.793	0.695	0.897	CLONAL	2	FALSE	0	0.24888632312081	3		276	243	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434415	49434415	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	160	621	0	ENST00000301067.7:c.7138C>T	p.Gln2380Ter	p.Q2380*	ENST00000301067	NM_003482.3	2380	Cag/Tag	31/54	0.24888632312081	4	FACETS	1	0.93	1	1	0.93	1	CLONAL	3	FALSE	1	0.24888632312081	4		621	531	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834542	156834542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746825886	NA	P-0057839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	75	756	0	ENST00000524377.1:c.310C>T	p.Arg104Cys	p.R104C	ENST00000524377	NM_002529.3	104	Cgt/Tgt	3/17	0.122609659841829	4	FACETS	1	0.974	1	0.731	0.642	0.826	INDETERMINATE	1	FALSE	2	0.24888632312081	4		756	515	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241969	72241969	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	48	222	1	ENST00000357731.5:c.421A>T	p.Ile141Leu	p.I141L	ENST00000357731	NM_173808.2	141	Ata/Tta	3/7	0.122609659841829	4	FACETS	1	0.934	1	1	0.934	1	INDETERMINATE	2	FALSE	2	0.24888632312081	4		223	206	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663349	29663349	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0057839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	52	307	0	ENST00000356175.3:c.5944-2A>C		p.X1982_splice	ENST00000356175	NM_000267.3	1982			0.219555447577999	2	FACETS	0.832	0.715	0.958	0.832	0.715	0.958	CLONAL	2	FALSE	0	0.24888632312081	2		307	251	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532622	46532637	+	frameshift_variant	Frame_Shift_Del	DEL	AAGTTTGGGATTGTAC	AAGTTTGGGATTGTAC	CAGTT	novel	NA	P-0057839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	31	313	1	ENST00000262741.5:c.441_456delinsAACTG	p.Tyr148ThrfsTer22	p.Y148Tfs*22	ENST00000262741	NM_003629.3	147	caGTACAATCCCAAACTT/caAACTG	4/10	0.122609659841829	4	FACETS	1	0.873	1	0.55	0.446	0.666	INDETERMINATE	1	FALSE	2	0.24888632312081	4		314	283	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0057841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	96	293	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.51163731262117	2		293	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0057841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	157	380	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.51163731262117	2		380	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579312	7579312	+	splice_region_variant,synonymous_variant	Splice_Region	SNP	C	C	T	rs55863639	NA	P-0057841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	124	385	2	ENST00000269305.4:c.375G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125	acG/acA	4/11	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.51163731262117	2		387	468	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266035	41266624	+	splice_donor_variant,splice_acceptor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	ACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTA	ACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTA	-	novel	NA	P-0057841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	50	231	0	ENST00000349496.5:c.34_423del		p.X12_splice	ENST00000349496	NM_001904.3	12	gACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAac/gac	3-4/15	1	2	FACETS	0.769	0.659	0.889	0.769	0.659	0.889	SUBCLONAL	1	TRUE	1	0.51163731262117	2		231	254	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	85	276	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.223087042803005	1	FACETS	0.844	0.75	0.943	0.844	0.75	0.943	INDETERMINATE	1	TRUE	0	0.399901974035408	1		276	403	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0057842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	59	257	0	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	0.223087042803005	1	FACETS	0.862	0.748	0.983	0.862	0.748	0.983	INDETERMINATE	1	TRUE	0	0.399901974035408	1		257	274	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0057842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	34	286	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	0.223087042803005	1	FACETS	0.463	0.379	0.556	0.463	0.379	0.556	INDETERMINATE	1	TRUE	0	0.399901974035408	1		286	294	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29579995	29579996	+	intron_variant	Intron	INS	-	-	A	novel	NA	P-0057842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	30	266	0	ENST00000356175.3:c.4110+3865dup		p.*1370*	ENST00000356175	NM_000267.3	1384/2839			0.243388993357343	3	FACETS	0.368	0.296	0.45	0.184	0.148	0.225	SUBCLONAL	1	TRUE	1	0.399901974035408	3		266	489	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089908	16089908	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	90	280	1	ENST00000268712.3:c.202C>T	p.Arg68Ter	p.R68*	ENST00000268712	NM_006311.3	68	Cga/Tga	3/46	0.399901974035408	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.399901974035408	1		281	328	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827739	72827739	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	69	491	0	ENST00000268489.5:c.8842C>T	p.Arg2948Cys	p.R2948C	ENST00000268489	NM_006885.3	2948	Cgt/Tgt	9/10	1	2	FACETS	0.557	0.485	0.634	0.557	0.485	0.634	SUBCLONAL	1	TRUE	1	0.399901974035408	2		491	620	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	45	276	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.23	2		276	367	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422655	47422655	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1569319031	NA	P-0057843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	55	494	1	ENST00000377045.4:c.127G>A	p.Asp43Asn	p.D43N	ENST00000377045	NM_001654.4	43	Gac/Aac	3/16	1	2	FACETS	0.589	0.502	0.684	0.589	0.502	0.684	SUBCLONAL	1	TRUE	1	0.23	2		495	812	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117550	4117550	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121434497	NA	P-0057843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	89	342	0	ENST00000262948.5:c.170T>G	p.Phe57Cys	p.F57C	ENST00000262948	NM_030662.3	57	tTt/tGt	2/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.23	2		342	535	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752966	128752966	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	45	336	0	ENST00000377970.2:c.1127T>C	p.Val376Ala	p.V376A	ENST00000377970	NM_002467.4	376	gTc/gCc	3/3	0.109329348841628	3	FACETS	0.731	0.613	0.861	0.365	0.306	0.431	INDETERMINATE	1	TRUE	1	0.23	3		336	597	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801500	1801500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	414	827	0	ENST00000260795.2:c.406G>A	p.Asp136Asn	p.D136N	ENST00000260795		136	Gac/Aac	3/17	0.106059949541218	5	FACETS	0.92	0.881	0.96	0.92	0.881	0.96	INDETERMINATE	4	TRUE	1	0.410025574159046	5		827	886	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231233	142231233	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	49	503	0	ENST00000350721.4:c.4721G>T	p.Cys1574Phe	p.C1574F	ENST00000350721	NM_001184.3	1574	tGt/tTt	27/47	1	2	FACETS	0.682	0.578	0.796	0.682	0.578	0.796	SUBCLONAL	1	TRUE	1	0.305714437390468	2		503	470	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843683	151843684	+	stop_gained,frameshift_variant,splice_region_variant	Nonsense_Mutation	INS	-	-	TGATTCCGCTA	novel	NA	P-0057845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	38	257	0	ENST00000262189.6:c.14021_14031dup	p.Leu4678Ter	p.L4678*	ENST00000262189	NM_170606.2	4677	-/TAGCGGAATCA		1	2	FACETS	0.687	0.569	0.818	0.687	0.569	0.818	SUBCLONAL	1	TRUE	1	0.305714437390468	2		257	362	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0057846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	215	544	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.601419310694543	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.633833379477543	2		544	317	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70353052	70353052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	20	415	0	ENST00000374080.3:c.4607G>A	p.Arg1536Gln	p.R1536Q	ENST00000374080		1536	cGg/cAg	33/45	0.633833379477543	3	FACETS	0.212	0.161	0.271	0.106	0.08	0.136	SUBCLONAL	1	TRUE	1	0.633833379477543	3		415	392	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087423	27087423	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	249	691	0	ENST00000324856.7:c.1999del	p.Ser667ProfsTer75	p.S667Pfs*75	ENST00000324856	NM_006015.4	666	aTt/at	5/20	0.633833379477543	3	FACETS	0.881	0.831	0.932	0.881	0.831	0.932	CLONAL	2	TRUE	1	0.633833379477543	3		691	587	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248659	212248660	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CATACTCATC	novel	NA	P-0057846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	16	442	0	ENST00000342788.4:c.3598_3607dup	p.Val1203GlyfsTer2	p.V1203Gfs*2	ENST00000342788	NM_005235.2	1203	gtg/gGATGAGTATGtg	28/28	1	2	FACETS	0.185	0.136	0.243	0.185	0.136	0.243	SUBCLONAL	1	TRUE	1	0.633833379477543	2		442	273	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057849-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	194	199	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.328595340899462	4	FACETS	1	0.97	1	0.542	0.503	0.583	INDETERMINATE	1	TRUE	2	0.838955098951891	4		199	784	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928073	178928073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057849-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	49	514	0	ENST00000263967.3:c.1351G>A	p.Gly451Arg	p.G451R	ENST00000263967	NM_006218.2	451	Gga/Aga	8/21	0.471227745538695	4	FACETS	1	0.959	1	0.667	0.576	0.763	INDETERMINATE	1	TRUE	2	0.838955098951891	4		514	161	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720732	89720733	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs587780006	NA	P-0057849-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	20	266	0	ENST00000371953.3:c.884dup	p.Cys296MetfsTer2	p.C296Mfs*2	ENST00000371953	NM_000314.4	295	cta/cTta	8/9	0.838955098951891	2	FACETS	0.851	0.724	0.962	0.851	0.724	0.962	CLONAL	2	TRUE	0	0.838955098951891	2		266	28	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160496	108160501	+	inframe_deletion	In_Frame_Del	DEL	TATTTA	TATTTA	-	novel	NA	P-0057849-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	35	475	0	ENST00000278616.4:c.4406_4411del	p.Ile1469_Tyr1470del	p.I1469_Y1470del	ENST00000278616	NM_000051.3	1468	gtTATTTAt/gtt	29/63	0.838955098951891	1	FACETS	0.544	0.461	0.63	0.544	0.461	0.63	SUBCLONAL	1	TRUE	0	0.838955098951891	1		475	89	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942661	71942661	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0057849-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	309	753	0	ENST00000298229.2:c.1615+2T>A		p.X539_splice	ENST00000298229	NM_001567.3	539			0.526002152820128	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.838955098951891	1		753	392	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0057851-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	248	157	2	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.228773345253925	4	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	2	0.228773345253925	4		159	1327	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0057851-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	247	732	1	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.228773345253925	4	FACETS	0.936	0.873	1	0.936	0.873	1	CLONAL	2	TRUE	2	0.228773345253925	4		733	1417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577137	7577137	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057851-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	258	727	0	ENST00000269305.4:c.801del	p.Asn268ThrfsTer77	p.N268Tfs*77	ENST00000269305	NM_001126112.2	267	cgG/cg	8/11	0.202714843852529	2	FACETS	0.997	0.933	1	0.997	0.933	1	CLONAL	2	TRUE	0	0.228773345253925	2		727	1131	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347099	347099	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057851-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1442	187	1051	0	ENST00000262320.3:c.1912G>C	p.Glu638Gln	p.E638Q	ENST00000262320	NM_003502.3	638	Gag/Cag	7/11	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.228773345253925	2		1051	1629	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650681	67650681	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057851-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	97	607	0	ENST00000264010.4:c.986T>C	p.Met329Thr	p.M329T	ENST00000264010	NM_006565.3	329	aTg/aCg	5/12	1	2	FACETS	0.97	0.864	1	0.97	0.864	1	CLONAL	1	TRUE	1	0.228773345253925	2		607	874	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998132	169998132	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057851-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	100	533	0	ENST00000295797.4:c.823A>G	p.Lys275Glu	p.K275E	ENST00000295797	NM_002740.5	275	Aaa/Gaa	9/18	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.228773345253925	2		533	794	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0057855-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	62	546	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.260866637838382	3	FACETS	0.928	0.802	1	0.464	0.401	0.533	CLONAL	1	TRUE	1	0.260866637838382	3		546	579	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0057855-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	26	656	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.353	0.279	0.439	0.353	0.279	0.439	SUBCLONAL	1	TRUE	1	0.260866637838382	2		657	564	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0057855-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	24	558	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	0.453	0.355	0.567	0.453	0.355	0.567	SUBCLONAL	1	TRUE	1	0.260866637838382	2		558	406	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591825	48591825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767342	NA	P-0057855-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	16	375	0	ENST00000342988.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000342988	NM_005359.5	330	Gaa/Aaa	9/12	0.260866637838382	1	FACETS	0.252	0.185	0.332	0.252	0.185	0.332	SUBCLONAL	1	TRUE	0	0.260866637838382	1		375	423	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936103	178936103	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057855-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	37	563	0	ENST00000263967.3:c.1645G>T	p.Asp549Tyr	p.D549Y	ENST00000263967	NM_006218.2	549	Gat/Tat	10/21	1	2	FACETS	0.396	0.325	0.475	0.396	0.325	0.475	SUBCLONAL	1	TRUE	1	0.260866637838382	2		563	717	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611379	28611379	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057855-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	103	326	0	ENST00000241453.7:c.1252T>G	p.Phe418Val	p.F418V	ENST00000241453	NM_004119.2	418	Ttc/Gtc	10/24	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.260866637838382	2		326	562	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0057856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	72	401	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.163982941482939	3	FACETS	1	0.95	1	0.586	0.512	0.664	CLONAL	1	TRUE	1	0.263528561218782	3		401	528	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0057856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	34	319	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.629	0.514	0.759	0.629	0.514	0.759	SUBCLONAL	1	TRUE	1	0.263528561218782	2		319	410	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020733	37020733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	47	545	0	ENST00000358127.4:c.112C>T	p.Arg38Cys	p.R38C	ENST00000358127	NM_001280556.1	38	Cgc/Tgc	2/10	0.263528561218782	1	FACETS	0.48	0.404	0.564	0.48	0.404	0.564	SUBCLONAL	1	TRUE	0	0.263528561218782	1		545	645	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740498	58740498	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs375975790	NA	P-0057856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	35	484	0	ENST00000305921.3:c.1403C>G	p.Ser468Ter	p.S468*	ENST00000305921	NM_003620.3	468	tCa/tGa	6/6	1	2	FACETS	0.423	0.346	0.51	0.423	0.346	0.51	SUBCLONAL	1	TRUE	1	0.263528561218782	2		484	628	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965247	25965247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339768293	NA	P-0057856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	36	486	0	ENST00000435504.4:c.3959C>T	p.Pro1320Leu	p.P1320L	ENST00000435504		1320	cCc/cTc	13/13	1	2	FACETS	0.54	0.443	0.649	0.54	0.443	0.649	SUBCLONAL	1	TRUE	1	0.263528561218782	2		486	506	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168765	56168765	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	66	368	0	ENST00000399503.3:c.1619A>T	p.Asn540Ile	p.N540I	ENST00000399503	NM_005921.1	540	aAc/aTc	9/20	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.263528561218782	2		368	496	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	128	276	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.511099143001402	2		276	487	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0057871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1617	335	1297	1	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	0.511099143001402	4	FACETS	1	0.954	1	0.338	0.318	0.359	CLONAL	1	TRUE	1	0.511099143001402	4		1298	1952	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0057871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	136	495	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.954	0.871	1	0.954	0.871	1	CLONAL	1	TRUE	1	0.511099143001402	2		497	558	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0057871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	141	668	2	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.89	0.813	0.97	0.89	0.813	0.97	CLONAL	1	TRUE	1	0.511099143001402	2		670	620	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446222	29446223	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	175	664	0	ENST00000389048.3:c.3344dup	p.Asn1115LysfsTer18	p.N1115Kfs*18	ENST00000389048	NM_004304.4	1115	aac/aaAc	20/29	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.511099143001402	2		664	634	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971095	21971096	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0057871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	184	759	0	ENST00000304494.5:c.262dup	p.Glu88GlyfsTer32	p.E88Gfs*32	ENST00000304494	NM_000077.4	88	gag/gGag	2/3	1	2	FACETS	0.997	0.923	1	0.997	0.923	1	CLONAL	1	TRUE	1	0.511099143001402	2		759	722	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106803	27106804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0057871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	221	839	0	ENST00000324856.7:c.6420dup	p.Phe2141LeufsTer9	p.F2141Lfs*9	ENST00000324856	NM_006015.4	2138	-/C	20/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.511099143001402	2		839	786	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405953	157405954	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1554294674	NA	P-0057871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	158	698	0	ENST00000346085.5:c.2201dup	p.Ser736IlefsTer27	p.S736Ifs*27	ENST00000346085	NM_020732.3	732	ccg/ccGg	6/20	1	2	FACETS	0.83	0.762	0.901	0.83	0.762	0.901	CLONAL	1	TRUE	1	0.511099143001402	2		698	745	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266112	41266112	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913228	NA	P-0057871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	109	397	0	ENST00000349496.5:c.109T>C	p.Ser37Pro	p.S37P	ENST00000349496	NM_001904.3	37	Tct/Cct	3/15	1	2	FACETS	0.972	0.878	1	0.972	0.878	1	CLONAL	1	TRUE	1	0.511099143001402	2		397	439	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347172	89347173	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0057871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	42	941	1	ENST00000301030.4:c.5777dup	p.Glu1927GlyfsTer23	p.E1927Gfs*23	ENST00000301030	NM_001256183.1	1926	ccg/ccCg	9/13	1	2	FACETS	0.217	0.18	0.258	0.217	0.18	0.258	SUBCLONAL	1	TRUE	1	0.511099143001402	2		942	757	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405777	70405778	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	145	376	0	ENST00000373644.4:c.3297dup	p.Val1100SerfsTer2	p.V1100Sfs*2	ENST00000373644	NM_030625.2	1097	-/A	4/12	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.511099143001402	2		376	490	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99136537	99136537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746072331	NA	P-0057871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	197	904	2	ENST00000074304.5:c.26G>A	p.Arg9His	p.R9H	ENST00000074304	NM_001134224.1	9	cGc/cAc	3/26	1	2	FACETS	0.988	0.917	1	0.988	0.917	1	CLONAL	1	TRUE	1	0.511099143001402	2		906	780	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922363	178922363	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	116	368	0	ENST00000263967.3:c.1132T>C	p.Cys378Arg	p.C378R	ENST00000263967	NM_006218.2	378	Tgt/Cgt	6/21	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.511099143001402	2		368	450	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231610	5231611	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0057871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	33	269	0	ENST00000357368.4:c.1865dup	p.Gln623SerfsTer4	p.Q623Sfs*4	ENST00000357368	NM_002850.3	622	cct/ccCt	14/38	1	2	FACETS	0.504	0.413	0.607	0.504	0.413	0.607	SUBCLONAL	1	TRUE	1	0.511099143001402	2		269	256	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511205	148511205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	188	571	2	ENST00000320356.2:c.1697G>A	p.Arg566His	p.R566H	ENST00000320356	NM_004456.4	566	cGc/cAc	15/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.511099143001402	2		573	660	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273905	10273905	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	208	1103	4	ENST00000330684.3:c.364G>A	p.Val122Ile	p.V122I	ENST00000330684	NM_001134407.1	122	Gtc/Atc	2/13	1	2	FACETS	0.89	0.826	0.955	0.89	0.826	0.955	CLONAL	1	TRUE	1	0.511099143001402	2		1107	915	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749137	43749137	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	185	693	0	ENST00000382044.4:c.1669T>C	p.Ser557Pro	p.S557P	ENST00000382044	NM_001141980.1	557	Tct/Cct	12/28	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.511099143001402	2		693	723	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38949853	38949853	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	101	328	0	ENST00000357387.3:c.4097T>C	p.Met1366Thr	p.M1366T	ENST00000357387	NM_152756.3	1366	aTg/aCg	31/38	1	2	FACETS	0.986	0.888	1	0.986	0.888	1	CLONAL	1	TRUE	1	0.511099143001402	2		328	401	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224219	36224219	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	184	927	0	ENST00000222270.7:c.6773del	p.Pro2258LeufsTer3	p.P2258Lfs*3	ENST00000222270	NM_014727.1	2257	Ccc/cc	28/37	1	2	FACETS	0.994	0.921	1	0.994	0.921	1	CLONAL	1	TRUE	1	0.511099143001402	2		927	724	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023099	33023099	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	118	649	1	ENST00000300177.4:c.211del	p.Glu71ArgfsTer13	p.E71Rfs*13	ENST00000300177	NM_001191322.1	70	Ggg/gg	2/2	1	2	FACETS	0.94	0.853	1	0.94	0.853	1	CLONAL	1	TRUE	1	0.511099143001402	2		650	491	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40458407	40458407	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	95	250	0	ENST00000345506.4:c.1622G>A	p.Ser541Asn	p.S541N	ENST00000345506	NM_003152.3	541	aGc/aAc	14/20	0.511099143001402	3	FACETS	0.813	0.734	0.895	0.813	0.734	0.895	CLONAL	2	TRUE	1	0.511099143001402	3		250	287	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4123821	4123821	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs774968670	NA	P-0057871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	152	753	0	ENST00000262948.5:c.52A>G	p.Ile18Val	p.I18V	ENST00000262948	NM_030662.3	18	Atc/Gtc	1/11	1	2	FACETS	0.897	0.823	0.974	0.897	0.823	0.974	CLONAL	1	TRUE	1	0.511099143001402	2		753	663	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257772	198257772	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	100	363	0	ENST00000335508.6:c.3680T>A	p.Ile1227Asn	p.I1227N	ENST00000335508	NM_012433.2	1227	aTt/aAt	24/25	1	2	FACETS	0.799	0.716	0.885	0.799	0.716	0.885	SUBCLONAL	1	TRUE	1	0.511099143001402	2		363	490	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1940178	1940178	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	63	165	0	ENST00000382891.5:c.1675A>G	p.Arg559Gly	p.R559G	ENST00000382891	NM_133335.3	559	Aga/Gga	8/22	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.511099143001402	2		165	192	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750539	41750539	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	128	662	0	ENST00000226382.2:c.89A>G	p.Tyr30Cys	p.Y30C	ENST00000226382	NM_003924.3	30	tAt/tGt	1/3	1	2	FACETS	0.805	0.732	0.882	0.805	0.732	0.882	CLONAL	1	TRUE	1	0.511099143001402	2		662	622	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5029897	5029897	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	87	332	0	ENST00000381652.3:c.341A>G	p.Tyr114Cys	p.Y114C	ENST00000381652	NM_004972.3	114	tAc/tGc	4/25	1	2	FACETS	0.92	0.821	1	0.92	0.821	1	CLONAL	1	TRUE	1	0.511099143001402	2		332	370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579415	7579415	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	250	1053	1	ENST00000269305.4:c.272G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tGg/tAg	4/11	0.582671081228331	1	FACETS	0.859	0.807	0.911	0.859	0.807	0.911	CLONAL	1	TRUE	0	0.582671081228331	1		1054	708	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285059	15285059	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs367543285	NA	P-0057873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	344	1229	0	ENST00000263388.2:c.4556T>C	p.Leu1519Pro	p.L1519P	ENST00000263388	NM_000435.2	1519	cTg/cCg	25/33	0.555270118591807	3	FACETS	1	0.988	1	0.575	0.543	0.607	CLONAL	1	TRUE	1	0.582671081228331	3		1229	1326	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63661953	63661953	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0057873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	119	459	0	ENST00000279873.7:c.57C>G	p.Tyr19Ter	p.Y19*	ENST00000279873	NM_032199.2	19	taC/taG	2/10	1	2	FACETS	0.809	0.734	0.887	0.809	0.734	0.887	CLONAL	1	TRUE	1	0.582671081228331	2		459	505	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120802545	120802545	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	195	615	0	ENST00000257552.2:c.281T>C	p.Val94Ala	p.V94A	ENST00000257552	NM_002442.3	94	gTg/gCg	5/15	1	2	FACETS	0.932	0.866	1	0.932	0.866	1	CLONAL	1	TRUE	1	0.582671081228331	2		615	718	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855939	68855948	+	frameshift_variant	Frame_Shift_Del	DEL	CTGATCCTGT	CTGATCCTGT	-	novel	NA	P-0057873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	160	512	0	ENST00000261769.5:c.1752_1761del	p.Ile584MetfsTer2	p.I584Mfs*2	ENST00000261769	NM_004360.3	583	CTGATCCTGTct/ct	12/16	0.582671081228331	1	FACETS	0.988	0.917	1	0.988	0.917	1	CLONAL	1	TRUE	0	0.582671081228331	1		512	394	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917627	178917627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	89	295	0	ENST00000263967.3:c.502C>T	p.Pro168Ser	p.P168S	ENST00000263967	NM_006218.2	168	Cct/Tct	3/21	0.555270118591807	3	FACETS	1	0.914	1	0.514	0.458	0.572	CLONAL	1	TRUE	1	0.582671081228331	3		295	384	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980635	1980636	+	frameshift_variant,stop_lost	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0057873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	131	675	0	ENST00000382891.5:c.4097_4098del	p.Ter1366SerfsTer68	p.*1366Sfs*68	ENST00000382891	NM_133335.3	1366	tAG/t	22/22	0.582671081228331	1	FACETS	0.98	0.903	1	0.98	0.903	1	CLONAL	1	TRUE	0	0.582671081228331	1		675	325	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969921	161969921	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	220	707	0	ENST00000366898.1:c.1048del	p.Val350SerfsTer85	p.V350Sfs*85	ENST00000366898	NM_004562.2	350	Gtc/tc	9/12	1	2	FACETS	0.995	0.929	1	0.995	0.929	1	CLONAL	1	TRUE	1	0.582671081228331	2		707	759	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157921	27157921	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	175	603	0	ENST00000380036.4:c.145T>C	p.Trp49Arg	p.W49R	ENST00000380036	NM_000459.3	49	Tgg/Cgg	2/23	0.582671081228331	1	FACETS	0.957	0.89	1	0.957	0.89	1	CLONAL	1	TRUE	0	0.582671081228331	1		603	445	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894884	101894884	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	98	321	0	ENST00000374994.4:c.437A>G	p.Tyr146Cys	p.Y146C	ENST00000374994	NM_004612.2	146	tAt/tGt	3/9	0.229800590169458	2	FACETS	0.932	0.839	1	0.466	0.419	0.515	INDETERMINATE	1	TRUE	0	0.582671081228331	2		321	361	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402436	139402436	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	352	1217	0	ENST00000277541.6:c.3481A>G	p.Thr1161Ala	p.T1161A	ENST00000277541	NM_017617.3	1161	Acg/Gcg	21/34	0.229800590169458	2	FACETS	0.856	0.809	0.903	0.428	0.404	0.452	INDETERMINATE	1	TRUE	0	0.582671081228331	2		1217	1412	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183725	10183725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs5030826	NA	P-0057874-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	124	1093	0	ENST00000256474.2:c.194C>T	p.Ser65Leu	p.S65L	ENST00000256474	NM_000551.3	65	tCg/tTg	1/3	0.488680291195087	2	FACETS	0.812	0.746	0.878	0.812	0.746	0.878	CLONAL	2	TRUE	0	0.51785988972464	2		1093	295	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56871635	56871635	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057874-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	117	486	0	ENST00000308159.5:c.2015A>G	p.Glu672Gly	p.E672G	ENST00000308159	NM_014669.4	672	gAa/gGa	18/22	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.51785988972464	2		486	385	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165031	47165031	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057874-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	40	314	0	ENST00000409792.3:c.1095del	p.Lys365AsnfsTer119	p.K365Nfs*119	ENST00000409792	NM_014159.6	365	aaA/aa	3/21	0.488680291195087	2	FACETS	1	0.955	1	0.684	0.583	0.788	CLONAL	1	TRUE	0	0.51785988972464	2		314	113	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751147	57751165	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	ATTTCAGCACCGTCACTTG	ATTTCAGCACCGTCACTTG	CAAAT	novel	NA	P-0057874-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	100	316	1	ENST00000274289.3:c.1702_1720delinsATTTG	p.Gln568IlefsTer2	p.Q568Ifs*2	ENST00000274289	NM_006622.3	568	CAAGTGACGGTGCTGAAATac/ATTTGac	12/14	0.386541365345938	6	FACETS	1	0.97	1	0.792	0.715	0.871	CLONAL	2	TRUE	3	0.51785988972464	6		317	331	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437799	52437817	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTTTGAGCTTCTCAGCC	CTCTTTGAGCTTCTCAGCC	GCA	novel	NA	P-0057874-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	78	912	2	ENST00000460680.1:c.1344_1362delinsTGC	p.Leu448PhefsTer118	p.L448Ffs*118	ENST00000460680	NM_004656.3	448	ttGGCTGAGAAGCTCAAAGAG/ttTGC	13/17	0.488680291195087	2	FACETS	1	0.98	1	0.749	0.672	0.829	CLONAL	1	TRUE	0	0.51785988972464	2		914	201	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074200	30074207	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGCACC	CCAGCACC	T	novel	NA	P-0057874-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	101	543	0	ENST00000338641.4:c.1462_1469delinsT	p.Pro488CysfsTer25	p.P488Cfs*25	ENST00000338641	NM_000268.3	488	CCAGCACCg/Tg	14/16	0.51785988972464	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.51785988972464	1		543	195	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	34	306	0				ENST00000310581	NM_198253.2	-/1132			0.106606291474702	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.730313625324103	0		306	98	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943632	9943632	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	164	635	0	ENST00000330684.3:c.1309C>G	p.Arg437Gly	p.R437G	ENST00000330684	NM_001134407.1	437	Cgg/Ggg	5/13	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.730313625324103	2		635	426	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66521989	66521989	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	91	234	0	ENST00000358598.2:c.644T>G	p.Val215Gly	p.V215G	ENST00000358598	NM_212471.2	215	gTc/gGc	7/11	1	2	FACETS	0.916	0.825	1	0.916	0.825	1	CLONAL	1	TRUE	1	0.730313625324103	2		234	272	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410958	63410958	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	80	753	0	ENST00000330258.3:c.2209T>A	p.Phe737Ile	p.F737I	ENST00000330258	NM_152424.3	737	Ttt/Att	2/2	0.410969661113247	3	FACETS	0.806	0.714	0.903	0.403	0.357	0.452	INDETERMINATE	1	TRUE	1	0.730313625324103	3		753	371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0057933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	368	380	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.230733165631482	3	FACETS	0.895	0.851	0.94	0.895	0.851	0.94	CLONAL	3	TRUE	0	0.31	3		380	1021	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514495	NA	P-0057933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	44	773	1	ENST00000269305.4:c.542G>A	p.Arg181His	p.R181H	ENST00000269305	NM_001126112.2	181	cGc/cAc	5/11	0.230733165631482	3	FACETS	0.345	0.288	0.409	0.115	0.096	0.137	SUBCLONAL	1	TRUE	0	0.31	3		774	949	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0057933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	31	203	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.939	0.765	1	0.939	0.765	1	CLONAL	1	TRUE	1	0.31	2		203	213	SUCCESS
APC	324	MSKCC	GRCh37	5	112173730	112173730	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	43	294	0	ENST00000257430.4:c.2442del	p.Phe814LeufsTer6	p.F814Lfs*6	ENST00000257430	NM_000038.5	813	aaT/aa	16/16	1	2	FACETS	0.799	0.671	0.941	0.799	0.671	0.941	CLONAL	1	TRUE	1	0.31	2		294	347	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520141	9520141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560752200	NA	P-0057933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	47	451	1	ENST00000353224.5:c.2128G>A	p.Val710Ile	p.V710I	ENST00000353224	NM_177990.2	710	Gtc/Atc	10/10	0.3	3	FACETS	0.611	0.515	0.717	0.306	0.257	0.359	SUBCLONAL	1	TRUE	1	0.31	3		452	573	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863046	56863046	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	137	442	0	ENST00000519728.1:c.313C>T	p.Leu105Phe	p.L105F	ENST00000519728	NM_002350.3	105	Ctt/Ttt	5/13	0.199362240540767	5	FACETS	0.932	0.849	1	0.621	0.566	0.679	CLONAL	2	TRUE	2	0.31	5		442	695	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945493	17945493	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	96	671	0	ENST00000458235.1:c.2237C>T	p.Ala746Val	p.A746V	ENST00000458235	NM_000215.3	746	gCc/gTc	17/24	0.193833781187002	3	FACETS	0.904	0.805	1	0.452	0.402	0.505	CLONAL	1	TRUE	1	0.31	3		671	791	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324535	62324535	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	514	986	1	ENST00000360203.5:c.2891T>A	p.Phe964Tyr	p.F964Y	ENST00000360203	NM_001283009.1	964	tTt/tAt	30/35	0.199362240540767	5	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	2	0.31	5		987	1435	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127792	47127792	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	42	358	0	ENST00000409792.3:c.5290C>T	p.Gln1764Ter	p.Q1764*	ENST00000409792	NM_014159.6	1764	Cag/Tag	11/21	0.3	3	FACETS	0.555	0.463	0.658	0.277	0.231	0.329	SUBCLONAL	1	TRUE	1	0.31	3		358	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0057935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	140	725	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.232734678857395	2		725	1100	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367315	50367315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751092583	NA	P-0057935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	90	421	0	ENST00000331340.3:c.122C>T	p.Ser41Leu	p.S41L	ENST00000331340	NM_006060.4	41	tCg/tTg	3/8	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.232734678857395	2		421	767	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636808	8636808	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	130	421	0	ENST00000356435.5:c.101C>A	p.Thr34Lys	p.T34K	ENST00000356435		34	aCa/aAa	2/35	0.232734678857395	3	FACETS	0.79	0.717	0.867	0.527	0.478	0.578	SUBCLONAL	2	TRUE	0	0.232734678857395	3		421	789	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349417	73349417	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	43	387	0	ENST00000377767.4:c.919T>C	p.Ser307Pro	p.S307P	ENST00000377767	NM_014953.3	307	Tct/Cct	6/21	1	2	FACETS	0.635	0.531	0.751	0.635	0.531	0.751	SUBCLONAL	1	TRUE	1	0.232734678857395	2		387	582	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215202	142215202	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0057935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	37	175	0	ENST00000350721.4:c.5898+1G>A		p.X1966_splice	ENST00000350721	NM_001184.3	1966			1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.232734678857395	2		175	304	SUCCESS
ATR	545	MSKCC	GRCh37	3	142224075	142224075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	41	428	0	ENST00000350721.4:c.5102C>T	p.Ser1701Phe	p.S1701F	ENST00000350721	NM_001184.3	1701	tCt/tTt	29/47	1	2	FACETS	0.498	0.414	0.593	0.498	0.414	0.593	SUBCLONAL	1	TRUE	1	0.232734678857395	2		428	707	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947379	38947379	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	21	164	0	ENST00000357387.3:c.4301A>G	p.Asn1434Ser	p.N1434S	ENST00000357387	NM_152756.3	1434	aAt/aGt	32/38	1	2	FACETS	0.719	0.555	0.909	0.719	0.555	0.909	CLONAL	1	TRUE	1	0.232734678857395	2		164	251	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371928	55371928	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	34	257	1	ENST00000297316.4:c.618C>A	p.Cys206Ter	p.C206*	ENST00000297316	NM_022454.3	206	tgC/tgA	2/2	0.212731787748321	3	FACETS	0.635	0.518	0.766	0.317	0.259	0.383	SUBCLONAL	1	TRUE	1	0.232734678857395	3		258	514	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	41	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.20597081574622	2		306	324	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287214	38287214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	89	709	0	ENST00000425967.3:c.443C>T	p.Ser148Phe	p.S148F	ENST00000425967	NM_001174067.1	148	tCc/tTc	4/19	1	2	FACETS	0.843	0.746	0.948	0.843	0.746	0.948	CLONAL	1	TRUE	1	0.20597081574622	2		709	1025	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500505	99500505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	101	779	0	ENST00000268035.6:c.3938C>T	p.Ser1313Phe	p.S1313F	ENST00000268035	NM_000875.3	1313	tCc/tTc	21/21	1	2	FACETS	0.974	0.869	1	0.974	0.869	1	CLONAL	1	TRUE	1	0.20597081574622	2		779	1007	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641447	18641447	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	29	204	1	ENST00000266497.5:c.2446C>T	p.Leu816Phe	p.L816F	ENST00000266497		816	Ctc/Ttc	17/31	1	2	FACETS	0.861	0.692	1	0.861	0.692	1	CLONAL	1	TRUE	1	0.20597081574622	2		205	327	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233016	55233016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751570775	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	60	390	1	ENST00000275493.2:c.1766C>T	p.Pro589Leu	p.P589L	ENST00000275493	NM_005228.3	589	cCc/cTc	15/28	1	2	FACETS	0.932	0.803	1	0.932	0.803	1	CLONAL	1	TRUE	1	0.20597081574622	2		391	625	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252143	226252143	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	18	99	0	ENST00000366813.1:c.91C>T	p.Pro31Ser	p.P31S	ENST00000366813		31	Ccc/Tcc	1/3	1	2	FACETS	0.935	0.707	1	0.935	0.707	1	CLONAL	1	TRUE	1	0.20597081574622	2		99	187	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566827	212566827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202247795	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	39	215	0	ENST00000342788.4:c.1354G>A	p.Glu452Lys	p.E452K	ENST00000342788	NM_005235.2	452	Gaa/Aaa	12/28	1	2	FACETS	0.994	0.825	1	0.994	0.825	1	CLONAL	1	TRUE	1	0.20597081574622	2		215	381	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971121	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	84	355	1	ENST00000304494.5:c.237_238delinsTT	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	79	acCCga/acTTga	2/3	0.20597081574622	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.20597081574622	1		356	557	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144697	119144697	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	43	371	0	ENST00000264033.4:c.710C>T	p.Ser237Leu	p.S237L	ENST00000264033	NM_005188.3	237	tCg/tTg	4/16	0.20597081574622	1	FACETS	0.729	0.609	0.861	0.729	0.609	0.861	SUBCLONAL	1	TRUE	0	0.20597081574622	1		371	514	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244911	46244911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	70	391	0	ENST00000334344.6:c.3005C>T	p.Thr1002Ile	p.T1002I	ENST00000334344	NM_152641.2	1002	aCt/aTt	15/21	1	2	FACETS	0.971	0.846	1	0.971	0.846	1	CLONAL	1	TRUE	1	0.20597081574622	2		391	700	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923394	36923394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759191217	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	97	751	1	ENST00000358127.4:c.868G>A	p.Gly290Arg	p.G290R	ENST00000358127	NM_001280556.1	290	Ggg/Agg	7/10	0.20597081574622	1	FACETS	0.882	0.785	0.986	0.882	0.785	0.986	CLONAL	1	TRUE	0	0.20597081574622	1		752	958	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955873	55955873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	37	266	0	ENST00000263923.4:c.3289G>A	p.Glu1097Lys	p.E1097K	ENST00000263923	NM_002253.2	1097	Gaa/Aaa	24/30	1	2	FACETS	0.851	0.702	1	0.851	0.702	1	CLONAL	1	TRUE	1	0.20597081574622	2		266	422	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024491	31024491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	78	588	0	ENST00000375687.4:c.3976C>T	p.Pro1326Ser	p.P1326S	ENST00000375687	NM_015338.5	1326	Cct/Tct	13/13	1	2	FACETS	0.915	0.803	1	0.915	0.803	1	CLONAL	1	TRUE	1	0.20597081574622	2		588	828	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044847	47044847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	110	501	0	ENST00000377604.3:c.2173C>T	p.Pro725Ser	p.P725S	ENST00000377604	NM_001204468.1	725	Ccg/Tcg	20/24	1	1	FACETS	0.775	0.698	0.857	1	0.984	1	SUBCLONAL	2	TRUE	0	0.20597081574622	1		501	618	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602589	10602589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1378587016	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	104	782	0	ENST00000171111.5:c.989C>T	p.Thr330Ile	p.T330I	ENST00000171111	NM_203500.1	330	aCc/aTc	3/6	1	2	FACETS	0.898	0.802	1	0.898	0.802	1	CLONAL	1	TRUE	1	0.20597081574622	2		782	1124	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576905	7576905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751440465	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	75	611	0	ENST00000269305.4:c.941C>T	p.Ser314Phe	p.S314F	ENST00000269305	NM_001126112.2	314	tCc/tTc	9/11	1	2	FACETS	0.835	0.73	0.948	0.835	0.73	0.948	CLONAL	1	TRUE	1	0.20597081574622	2		611	872	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519874	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	53	359	0	ENST00000356142.4:c.85C>A	p.Pro29Thr	p.P29T	ENST00000356142	NM_018890.3	29	Cct/Act	2/7	1	2	FACETS	0.851	0.725	0.989	0.851	0.725	0.989	CLONAL	1	TRUE	1	0.20597081574622	2		359	605	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332970	70332970	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	88	575	0	ENST00000373644.4:c.875G>A	p.Ser292Asn	p.S292N	ENST00000373644	NM_030625.2	292	aGt/aAt	2/12	0.20597081574622	4	FACETS	1	0.911	1			1	CLONAL	1	TRUE	NA	0.20597081574622	4		575	995	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984919	9984919	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	67	410	1	ENST00000330684.3:c.1046C>T	p.Ser349Phe	p.S349F	ENST00000330684	NM_001134407.1	349	tCc/tTc	4/13	1	2	FACETS	0.986	0.856	1	0.986	0.856	1	CLONAL	1	TRUE	1	0.20597081574622	2		411	660	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104658	209104658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	66	405	1	ENST00000345146.2:c.920C>T	p.Ala307Val	p.A307V	ENST00000345146	NM_005896.2	307	gCt/gTt	8/10	1	2	FACETS	0.889	0.771	1	0.889	0.771	1	CLONAL	1	TRUE	1	0.20597081574622	2		406	721	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451797	29451797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs79530637	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	64	433	1	ENST00000389048.3:c.2768G>A	p.Gly923Glu	p.G923E	ENST00000389048	NM_004304.4	923	gGg/gAg	16/29	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.20597081574622	2		434	544	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756806	756806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760359350	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	64	342	0	ENST00000314574.4:c.22G>A	p.Glu8Lys	p.E8K	ENST00000314574	NM_005433.3	8	Gaa/Aaa	2/12	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.20597081574622	2		342	581	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099977	157099977	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	70	157	0	ENST00000346085.5:c.914G>A	p.Gly305Asp	p.G305D	ENST00000346085	NM_020732.3	305	gGc/gAc	1/20	1	2	FACETS	1	0.893	1	1	0.982	1	CLONAL	2	TRUE	1	0.20597081574622	2		157	334	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923423	9923423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	80	486	0	ENST00000330684.3:c.1864C>T	p.Pro622Ser	p.P622S	ENST00000330684	NM_001134407.1	622	Cct/Tct	9/13	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.20597081574622	2		486	692	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821353	72821353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	37	300	1	ENST00000268489.5:c.10822G>A	p.Ala3608Thr	p.A3608T	ENST00000268489	NM_006885.3	3608	Gct/Act	10/10	0.20597081574622	1	FACETS	0.782	0.645	0.935	0.782	0.645	0.935	CLONAL	1	TRUE	0	0.20597081574622	1		301	412	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169504	27169504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866968099	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	52	460	0	ENST00000380036.4:c.505G>A	p.Glu169Lys	p.E169K	ENST00000380036	NM_000459.3	169	Gaa/Aaa	4/23	0.20597081574622	1	FACETS	0.691	0.588	0.805	0.691	0.588	0.805	SUBCLONAL	1	TRUE	0	0.20597081574622	1		460	655	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556190	29556190	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	26	114	0	ENST00000356175.3:c.2557C>T	p.Gln853Ter	p.Q853*	ENST00000356175	NM_000267.3	853	Cag/Tag	21/57	1	2	FACETS	0.774	0.62	0.948	1	0.937	1	CLONAL	2	TRUE	1	0.20597081574622	2		114	163	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561247	9561247	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1485168039	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	60	410	0	ENST00000353224.5:c.535G>A	p.Glu179Lys	p.E179K	ENST00000353224	NM_177990.2	179	Gag/Aag	4/10	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.20597081574622	2		410	567	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564701	86564701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290733136	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	73	720	0	ENST00000274376.6:c.433C>T	p.Pro145Ser	p.P145S	ENST00000274376	NM_002890.2	145	Cct/Tct	1/25	1	2	FACETS	0.706	0.616	0.804	0.706	0.616	0.804	SUBCLONAL	1	TRUE	1	0.20597081574622	2		720	1004	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456797	32456797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	105	569	0	ENST00000332351.3:c.95G>A	p.Gly32Glu	p.G32E	ENST00000332351	NM_024426.4	32	gGa/gAa	1/10	0.143961339594482	3	FACETS	1	0.975	1	0.652	0.583	0.724	CLONAL	1	TRUE	1	0.20597081574622	3		569	863	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436084	49436084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	58	527	0	ENST00000301067.7:c.5897C>T	p.Pro1966Leu	p.P1966L	ENST00000301067	NM_003482.3	1966	cCc/cTc	28/54	1	2	FACETS	0.857	0.736	0.99	0.857	0.736	0.99	CLONAL	1	TRUE	1	0.20597081574622	2		527	657	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546653	9546653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	66	368	0	ENST00000353224.5:c.1369G>A	p.Glu457Lys	p.E457K	ENST00000353224	NM_177990.2	457	Gaa/Aaa	5/10	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.20597081574622	2		368	596	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197104	106197104	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1315434367	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	28	297	0	ENST00000380013.4:c.5437C>T	p.Gln1813Ter	p.Q1813*	ENST00000380013	NM_001127208.2	1813	Caa/Taa	11/11	1	2	FACETS	0.695	0.556	0.855	0.695	0.556	0.855	SUBCLONAL	1	TRUE	1	0.20597081574622	2		297	391	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641159	117641159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	67	637	0	ENST00000368508.3:c.5812C>T	p.Pro1938Ser	p.P1938S	ENST00000368508	NM_002944.2	1938	Cct/Tct	36/43	1	2	FACETS	0.747	0.648	0.855	0.747	0.648	0.855	SUBCLONAL	1	TRUE	1	0.20597081574622	2		637	871	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880253	155880253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	41	299	0	ENST00000368323.3:c.151G>A	p.Asp51Asn	p.D51N	ENST00000368323	NM_006912.5	51	Gat/Aat	3/6	1	2	FACETS	0.726	0.604	0.862	0.726	0.604	0.862	SUBCLONAL	1	TRUE	1	0.20597081574622	2		299	548	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857163	9857163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	40	407	0	ENST00000330684.3:c.4238C>T	p.Ser1413Phe	p.S1413F	ENST00000330684	NM_001134407.1	1413	tCc/tTc	13/13	1	2	FACETS	0.699	0.58	0.831	0.699	0.58	0.831	SUBCLONAL	1	TRUE	1	0.20597081574622	2		407	556	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752909	57752909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151304321	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	46	293	0	ENST00000274289.3:c.1019C>T	p.Pro340Leu	p.P340L	ENST00000274289	NM_006622.3	340	cCg/cTg	8/14	1	2	FACETS	0.892	0.751	1	0.892	0.751	1	CLONAL	1	TRUE	1	0.20597081574622	2		293	501	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776050	9776050	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	87	776	0	ENST00000377346.4:c.514G>A	p.Glu172Lys	p.E172K	ENST00000377346	NM_005026.3	172	Gag/Aag	5/24	1	2	FACETS	0.816	0.721	0.919	0.816	0.721	0.919	CLONAL	1	TRUE	1	0.20597081574622	2		776	1035	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927443	245927443	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	57	410	0	ENST00000388985.4:c.1085T>C	p.Phe362Ser	p.F362S	ENST00000388985		362	tTc/tCc	11/12	1	2	FACETS	0.883	0.757	1	0.883	0.757	1	CLONAL	1	TRUE	1	0.20597081574622	2		410	627	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121793	108121793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782212	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	35	247	0	ENST00000278616.4:c.1601C>T	p.Pro534Leu	p.P534L	ENST00000278616	NM_000051.3	534	cCt/cTt	10/63	0.20597081574622	1	FACETS	0.802	0.658	0.963	0.802	0.658	0.963	CLONAL	1	TRUE	0	0.20597081574622	1		247	380	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432361	432361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	17	213	1	ENST00000399788.2:c.2162C>T	p.Pro721Leu	p.P721L	ENST00000399788	NM_001042603.1	721	cCa/cTa	16/28	1	2	FACETS	0.694	0.518	0.901	0.694	0.518	0.901	SUBCLONAL	1	TRUE	1	0.20597081574622	2		214	238	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434127	121434127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746055869	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	105	707	0	ENST00000257555.6:c.1018C>T	p.Pro340Ser	p.P340S	ENST00000257555		340	Ccc/Tcc	5/10	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.20597081574622	2		707	951	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713311	43713311	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	102	836	0	ENST00000382044.4:c.4162C>T	p.Leu1388Phe	p.L1388F	ENST00000382044	NM_001141980.1	1388	Ctt/Ttt	20/28	1	2	FACETS	0.755	0.673	0.843	0.755	0.673	0.843	SUBCLONAL	1	TRUE	1	0.20597081574622	2		836	1311	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678506	88678506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	60	497	0	ENST00000360948.2:c.1030G>A	p.Glu344Lys	p.E344K	ENST00000360948	NM_001012338.2	344	Gag/Aag	9/19	1	2	FACETS	0.973	0.838	1	0.973	0.838	1	CLONAL	1	TRUE	1	0.20597081574622	2		497	599	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031825	10031825	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	63	536	0	ENST00000330684.3:c.998C>T	p.Thr333Ile	p.T333I	ENST00000330684	NM_001134407.1	333	aCc/aTc	3/13	1	2	FACETS	0.749	0.646	0.861	0.749	0.646	0.861	SUBCLONAL	1	TRUE	1	0.20597081574622	2		536	817	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618341	37618341	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1191853065	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	103	281	0	ENST00000447079.4:c.17G>C	p.Arg6Thr	p.R6T	ENST00000447079	NM_015083.1	6	aGa/aCa	1/14	0.181959181831379	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.20597081574622	2		281	438	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66520200	66520200	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	102	305	0	ENST00000358598.2:c.484G>T	p.Glu162Ter	p.E162*	ENST00000358598	NM_212471.2	162	Gag/Tag	5/11	0.181959181831379	2	FACETS	0.9	0.808	0.998	0.9	0.808	0.998	CLONAL	2	TRUE	0	0.20597081574622	2		305	550	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226314	2226314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	140	1029	0	ENST00000398665.3:c.3794C>T	p.Ser1265Phe	p.S1265F	ENST00000398665	NM_032482.2	1265	tCc/tTc	27/28	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.20597081574622	2		1029	1359	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229260	36229260	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	70	721	0	ENST00000222270.7:c.7950C>A	p.Phe2650Leu	p.F2650L	ENST00000222270	NM_014727.1	2650	ttC/ttA	37/37	1	2	FACETS	0.655	0.57	0.749	0.655	0.57	0.749	SUBCLONAL	1	TRUE	1	0.20597081574622	2		721	1037	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462659	29462659	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	79	690	0	ENST00000389048.3:c.2242A>T	p.Lys748Ter	p.K748*	ENST00000389048	NM_004304.4	748	Aag/Tag	13/29	1	2	FACETS	0.714	0.626	0.809	0.714	0.626	0.809	SUBCLONAL	1	TRUE	1	0.20597081574622	2		690	1075	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265034	46265035	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	38	416	0	ENST00000371998.3:c.1904_1905delinsTT	p.Ser635Phe	p.S635F	ENST00000371998		635	tCC/tTT	12/23	1	2	FACETS	0.654	0.54	0.782	0.654	0.54	0.782	SUBCLONAL	1	TRUE	1	0.20597081574622	2		416	564	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24133957	24133958	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	36	261	1	ENST00000263121.7:c.108_109delinsTT	p.Arg37Cys	p.R37C	ENST00000263121	NM_003073.3	36	ctCCgt/ctTTgt	2/9	1	2	FACETS	0.809	0.665	0.97	0.809	0.665	0.97	CLONAL	1	TRUE	1	0.20597081574622	2		262	432	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147517	47147517	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	44	354	0	ENST00000409792.3:c.4809T>A	p.His1603Gln	p.H1603Q	ENST00000409792	NM_014159.6	1603	caT/caA	6/21	1	2	FACETS	0.797	0.668	0.94	0.797	0.668	0.94	CLONAL	1	TRUE	1	0.20597081574622	2		354	536	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933771	49933771	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	102	728	0	ENST00000296474.3:c.2506G>A	p.Gly836Arg	p.G836R	ENST00000296474	NM_002447.2	836	Gga/Aga	10/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.20597081574622	2		728	879	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455559	189455559	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	32	329	0	ENST00000264731.3:c.93G>T	p.Trp31Cys	p.W31C	ENST00000264731	NM_003722.4	31	tgG/tgT	2/14	1	2	FACETS	0.742	0.602	0.9	0.742	0.602	0.9	SUBCLONAL	1	TRUE	1	0.20597081574622	2		329	419	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747901	41747901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	59	365	0	ENST00000226382.2:c.868C>T	p.Pro290Ser	p.P290S	ENST00000226382	NM_003924.3	290	Ccc/Tcc	3/3	1	2	FACETS	0.921	0.792	1	0.921	0.792	1	CLONAL	1	TRUE	1	0.20597081574622	2		365	622	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968181	55968182	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	43	359	1	ENST00000263923.4:c.2148_2149delinsAA	p.Asp717Asn	p.D717N	ENST00000263923	NM_002253.2	716	aaGGat/aaAAat	15/30	1	2	FACETS	0.709	0.592	0.838	0.709	0.592	0.838	SUBCLONAL	1	TRUE	1	0.20597081574622	2		360	589	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155802	106155802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	24	321	0	ENST00000380013.4:c.703C>T	p.Pro235Ser	p.P235S	ENST00000380013	NM_001127208.2	235	Cca/Tca	3/11	1	2	FACETS	0.511	0.4	0.64	0.511	0.4	0.64	SUBCLONAL	1	TRUE	1	0.20597081574622	2		321	456	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190812	106190812	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	51	385	0	ENST00000380013.4:c.4090G>A	p.Glu1364Lys	p.E1364K	ENST00000380013	NM_001127208.2	1364	Gaa/Aaa	9/11	1	2	FACETS	0.714	0.605	0.833	0.714	0.605	0.833	SUBCLONAL	1	TRUE	1	0.20597081574622	2		385	694	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517849	187517849	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	45	357	0	ENST00000441802.2:c.12845C>T	p.Pro4282Leu	p.P4282L	ENST00000441802	NM_005245.3	4282	cCc/cTc	25/27	1	2	FACETS	0.814	0.683	0.958	0.814	0.683	0.958	CLONAL	1	TRUE	1	0.20597081574622	2		357	537	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518927	187518927	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	52	354	0	ENST00000441802.2:c.12277T>C	p.Cys4093Arg	p.C4093R	ENST00000441802	NM_005245.3	4093	Tgc/Cgc	24/27	1	2	FACETS	0.795	0.676	0.926	0.795	0.676	0.926	CLONAL	1	TRUE	1	0.20597081574622	2		354	635	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38949820	38949821	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	23	226	0	ENST00000357387.3:c.4129_4130delinsTT	p.Pro1377Leu	p.P1377L	ENST00000357387	NM_152756.3	1377	CCa/TTa	31/38	1	2	FACETS	0.757	0.591	0.949	0.757	0.591	0.949	CLONAL	1	TRUE	1	0.20597081574622	2		226	295	SUCCESS
APC	324	MSKCC	GRCh37	5	112173899	112173900	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	40	303	1	ENST00000257430.4:c.2608_2609delinsTT	p.Pro870Leu	p.P870L	ENST00000257430	NM_000038.5	870	CCa/TTa	16/16	1	2	FACETS	0.859	0.714	1	0.859	0.714	1	CLONAL	1	TRUE	1	0.20597081574622	2		304	452	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721039	176721039	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	69	465	0	ENST00000439151.2:c.6670C>T	p.Pro2224Ser	p.P2224S	ENST00000439151	NM_022455.4	2224	Ccc/Tcc	23/23	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.20597081574622	2		465	656	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681107	117681107	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	41	390	0	ENST00000368508.3:c.3513A>C	p.Gln1171His	p.Q1171H	ENST00000368508	NM_002944.2	1171	caA/caC	23/43	1	2	FACETS	0.716	0.596	0.85	0.716	0.596	0.85	SUBCLONAL	1	TRUE	1	0.20597081574622	2		390	556	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706855	117706856	+	missense_variant	Missense_Mutation	DNP	CT	CT	TC	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	38	282	0	ENST00000368508.3:c.2294_2295delinsGA	p.Lys765Arg	p.K765R	ENST00000368508	NM_002944.2	765	aAG/aGA	15/43	1	2	FACETS	0.86	0.711	1	0.86	0.711	1	CLONAL	1	TRUE	1	0.20597081574622	2		282	429	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161990394	161990394	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	47	324	0	ENST00000366898.1:c.926A>C	p.Glu309Ala	p.E309A	ENST00000366898	NM_004562.2	309	gAa/gCa	8/12	1	2	FACETS	0.92	0.777	1	0.92	0.777	1	CLONAL	1	TRUE	1	0.20597081574622	2		324	496	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29197688	29197688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	135	739	0	ENST00000240100.2:c.506C>T	p.Pro169Leu	p.P169L	ENST00000240100	NM_001394.6	169	cCc/cTc	2/4	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.20597081574622	2		739	1140	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965482	68965482	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	27	401	0	ENST00000288368.4:c.1093+1G>A		p.X365_splice	ENST00000288368	NM_024870.2	365			1	2	FACETS	0.493	0.391	0.61	0.493	0.391	0.61	SUBCLONAL	1	TRUE	1	0.20597081574622	2		401	532	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090811	5090811	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs550229414	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	18	184	1	ENST00000381652.3:c.2959G>A	p.Glu987Lys	p.E987K	ENST00000381652	NM_004972.3	987	Gag/Aag	22/25	0.20597081574622	1	FACETS	0.847	0.641	1	0.847	0.641	1	CLONAL	1	TRUE	0	0.20597081574622	1		185	185	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966650	36966650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	58	511	0	ENST00000358127.4:c.676G>A	p.Gly226Arg	p.G226R	ENST00000358127	NM_001280556.1	226	Gga/Aga	6/10	1	2	FACETS	0.732	0.628	0.847	0.732	0.628	0.847	SUBCLONAL	1	TRUE	1	0.20597081574622	2		511	769	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099982	157099999	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGCGGCGGCGGC	GGCGGCGGCGGCGGCGGC	-	rs587779747	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	47	140	0	ENST00000346085.5:c.927_944del	p.Gly314_Gly319del	p.G314_G319del	ENST00000346085	NM_020732.3	307	GGCGGCGGCGGCGGCGGC/-	1/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.20597081574622	2		140	308	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224394	36224396	+	frameshift_variant	Frame_Shift_Del	DEL	GGC	GGC	A	novel	NA	P-0057937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1210	128	897	1	ENST00000222270.7:c.6944_6946delinsA	p.Gly2315AspfsTer7	p.G2315Dfs*7	ENST00000222270	NM_014727.1	2315	gGGCtt/gAtt	28/37	1	2	FACETS	0.929	0.839	1	0.929	0.839	1	CLONAL	1	TRUE	1	0.20597081574622	2		898	1338	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	518	1040	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	0.507966371325029	2	FACETS	0.922	0.89	0.955	0.922	0.89	0.955	CLONAL	2	TRUE	0	0.601335304530767	2		1040	934	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610637	10610637	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	230	731	0	ENST00000171111.5:c.73G>C	p.Glu25Gln	p.E25Q	ENST00000171111	NM_203500.1	25	Gag/Cag	2/6	0.601335304530767	2	FACETS	0.746	0.696	0.799	0.373	0.348	0.4	SUBCLONAL	1	TRUE	0	0.601335304530767	2		731	1025	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104356924	104356924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	50	570	0	ENST00000369902.3:c.784G>A	p.Asp262Asn	p.D262N	ENST00000369902	NM_016169.3	262	Gat/Aat	7/12	0.519422812187276	1	FACETS	0.208	0.176	0.244	0.208	0.176	0.244	SUBCLONAL	1	TRUE	0	0.601335304530767	1		570	558	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683508	29683508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	75	278	0	ENST00000356175.3:c.7583C>T	p.Ser2528Leu	p.S2528L	ENST00000356175	NM_000267.3	2528	tCa/tTa	51/57	1	2	FACETS	0.723	0.638	0.813	0.723	0.638	0.813	SUBCLONAL	1	TRUE	1	0.601335304530767	2		278	345	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141997	108141997	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780619	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	277	456	0	ENST00000278616.4:c.2941C>T	p.Arg981Cys	p.R981C	ENST00000278616	NM_000051.3	981	Cgt/Tgt	20/63	0.493739050121846	3	FACETS	0.982	0.931	1			1	CLONAL	2	TRUE	NA	0.601335304530767	3		456	610	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193205417	193205417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1386267118	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	160	422	0	ENST00000367435.3:c.1348C>T	p.Pro450Ser	p.P450S	ENST00000367435	NM_024529.4	450	Cct/Tct	15/17	0.493739050121846	3	FACETS	0.934	0.858	1			1	CLONAL	1	TRUE	NA	0.601335304530767	3		422	741	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280094	66280094	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	71	275	0	ENST00000273854.3:c.1595C>A	p.Pro532Gln	p.P532Q	ENST00000273854	NM_004439.5	532	cCa/cAa	7/18	NA	2	FACETS	0.552	0.483	0.625			1	INDETERMINATE	1	TRUE	NA	0.601335304530767	2		275	428	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692819	89692819	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	15	235	0	ENST00000371953.3:c.303C>G	p.Ile101Met	p.I101M	ENST00000371953	NM_000314.4	101	atC/atG	5/9	0.519422812187276	1	FACETS	0.149	0.109	0.197	0.149	0.109	0.197	SUBCLONAL	1	TRUE	0	0.601335304530767	1		235	234	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418328	139418328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs571831870	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	332	1116	1	ENST00000277541.6:c.244G>A	p.Val82Met	p.V82M	ENST00000277541	NM_017617.3	82	Gtg/Atg	3/34	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.601335304530767	2		1117	1088	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632618	3632618	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	226	866	0	ENST00000294008.3:c.5230C>T	p.Gln1744Ter	p.Q1744*	ENST00000294008	NM_032444.2	1744	Cag/Tag	15/15	1	2	FACETS	0.923	0.862	0.986	0.923	0.862	0.986	CLONAL	1	TRUE	1	0.601335304530767	2		866	814	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661578	227661578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770397566	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	265	760	1	ENST00000305123.5:c.1877G>A	p.Arg626Gln	p.R626Q	ENST00000305123	NM_005544.2	626	cGa/cAa	1/2	NA	2	FACETS	1	0.954	1			1	INDETERMINATE	1	TRUE	NA	0.601335304530767	2		761	866	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919021	50919021	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501811	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	214	919	0	ENST00000440232.2:c.2758G>A	p.Asp920Asn	p.D920N	ENST00000440232	NM_002691.3	920	Gac/Aac	22/27	1	2	FACETS	0.878	0.817	0.94	0.878	0.817	0.94	CLONAL	1	TRUE	1	0.601335304530767	2		919	811	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405437	70405437	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	73	537	0	ENST00000373644.4:c.2951C>G	p.Ser984Ter	p.S984*	ENST00000373644	NM_030625.2	984	tCa/tGa	4/12	0.519422812187276	1	FACETS	0.352	0.309	0.399	0.352	0.309	0.399	SUBCLONAL	1	TRUE	0	0.601335304530767	1		537	482	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536716	120536716	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	194	751	0	ENST00000229340.5:c.376G>C	p.Glu126Gln	p.E126Q	ENST00000229340	NM_006861.6	126	Gag/Cag	5/6	1	2	FACETS	0.872	0.809	0.937	0.872	0.809	0.937	CLONAL	1	TRUE	1	0.601335304530767	2		751	740	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10244895	10244895	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	216	842	0	ENST00000340748.4:c.4814C>T	p.Ser1605Leu	p.S1605L	ENST00000340748		1605	tCa/tTa	39/40	0.601335304530767	2	FACETS	0.679	0.631	0.729	0.34	0.315	0.365	SUBCLONAL	1	TRUE	0	0.601335304530767	2		842	1058	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786887	135786887	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	131	386	0	ENST00000298552.3:c.982C>G	p.Gln328Glu	p.Q328E	ENST00000298552	NM_001162426.1	328	Cag/Gag	10/23	1	2	FACETS	0.984	0.9	1	0.984	0.9	1	CLONAL	1	TRUE	1	0.601335304530767	2		386	443	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994865	73994865	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200105637	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	12	36	0	ENST00000318443.5:c.349G>A	p.Glu117Lys	p.E117K	ENST00000318443	NM_001024736.1	117	Gag/Aag	3/10	1	2	FACETS	1	0.828	1	1	0.828	1	CLONAL	1	TRUE	1	0.601335304530767	2		36	34	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568501	41568501	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	115	302	0	ENST00000263253.7:c.4453-2A>T		p.X1485_splice	ENST00000263253	NM_001429.3	1485			0.171939901405513	6	FACETS	0.815	0.737	0.896			1	INDETERMINATE	2	TRUE	NA	0.601335304530767	6		302	517	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383804	84383804	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs751068863	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	197	510	0	ENST00000321945.7:c.1048G>C	p.Asp350His	p.D350H	ENST00000321945	NM_139076.2	350	Gac/Cac	9/9	0.572944605211568	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.601335304530767	1		510	455	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945021	151945021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756918375	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	27	19	0	ENST00000262189.6:c.2498G>A	p.Arg833Lys	p.R833K	ENST00000262189	NM_170606.2	833	aGa/aAa	14/59	1	2	FACETS	0.802	0.672	0.933	1	0.954	1	CLONAL	2	TRUE	1	0.601335304530767	2		19	56	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37622754	37622754	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	173	869	0	ENST00000249071.6:c.538C>T	p.Gln180Ter	p.Q180*	ENST00000249071	NM_002872.4	180	Cag/Tag	6/7	NA	2	FACETS	0.634	0.584	0.687			1	INDETERMINATE	1	TRUE	NA	0.601335304530767	2		869	907	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911061	29911061	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs199474481	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	622	1097	0	ENST00000376809.5:c.360G>C	p.Gln120His	p.Q120H	ENST00000376809	NM_002116.7	120	caG/caC	3/8	0.513165908776589	2	FACETS	0.885	0.856	0.914	0.885	0.856	0.914	CLONAL	2	TRUE	0	0.601335304530767	2		1097	1169	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094310	27094310	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	78	438	0	ENST00000324856.7:c.3018del	p.Lys1007ArgfsTer32	p.K1007Rfs*32	ENST00000324856	NM_006015.4	1006	gaG/ga	11/20	1	2	FACETS	0.527	0.464	0.594	0.527	0.464	0.594	SUBCLONAL	1	TRUE	1	0.601335304530767	2		438	492	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366737	40366737	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	107	355	0	ENST00000397332.2:c.460A>G	p.Lys154Glu	p.K154E	ENST00000397332	NM_001033082.2	154	Aag/Gag	2/3	1	2	FACETS	0.939	0.85	1	0.939	0.85	1	CLONAL	1	TRUE	1	0.601335304530767	2		355	379	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268862	115268862	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs768709264	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	159	480	0	ENST00000438362.2:c.1748A>G	p.Asn583Ser	p.N583S	ENST00000438362	NM_001242891.1	583	aAt/aGt	14/20	1	2	FACETS	0.834	0.767	0.903	0.834	0.767	0.903	CLONAL	1	TRUE	1	0.601335304530767	2		480	634	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550727	150550727	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	125	332	0	ENST00000369026.2:c.929G>C	p.Arg310Thr	p.R310T	ENST00000369026	NM_021960.4	310	aGa/aCa	2/3	0.533972083773276	5	FACETS	1	0.936	1			1	CLONAL	1	TRUE	NA	0.601335304530767	5		332	759	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830872	156830872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	140	509	0	ENST00000524377.1:c.146G>A	p.Arg49Gln	p.R49Q	ENST00000524377	NM_002529.3	49	cGa/cAa	1/17	0.166734797479612	3	FACETS	0.887	0.809	0.968	0.296	0.269	0.323	INDETERMINATE	1	TRUE	0	0.601335304530767	3		509	683	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32439155	32439155	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	115	494	0	ENST00000332351.3:c.918G>C	p.Trp306Cys	p.W306C	ENST00000332351	NM_024426.4	306	tgG/tgC	4/10	0.601335304530767	1	FACETS	0.904	0.826	0.982	0.904	0.826	0.982	CLONAL	1	TRUE	0	0.601335304530767	1		494	296	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343227	118343227	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	92	294	0	ENST00000534358.1:c.1353C>A	p.Phe451Leu	p.F451L	ENST00000534358	NM_005933.3	451	ttC/ttA	3/36	0.601335304530767	1	FACETS	0.836	0.755	0.92	0.836	0.755	0.92	CLONAL	1	TRUE	0	0.601335304530767	1		294	256	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424443	49424443	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	172	797	0	ENST00000301067.7:c.13780del	p.Ala4594ProfsTer23	p.A4594Pfs*23	ENST00000301067	NM_003482.3	4594	Gcc/cc	41/54	0.121929997846683	4	FACETS	1	0.972	1	0.558	0.514	0.604	INDETERMINATE	1	TRUE	2	0.601335304530767	4		797	821	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028445	42028445	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	116	345	0	ENST00000219905.7:c.3983C>G	p.Ser1328Ter	p.S1328*	ENST00000219905	NM_001164273.1	1328	tCa/tGa	13/24	1	2	FACETS	0.895	0.813	0.981	0.895	0.813	0.981	CLONAL	1	TRUE	1	0.601335304530767	2		345	431	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961354	15961354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	143	435	0	ENST00000268712.3:c.6035G>A	p.Gly2012Glu	p.G2012E	ENST00000268712	NM_006311.3	2012	gGa/gAa	39/46	0.507966371325029	2	FACETS	0.855	0.784	0.93	0.428	0.392	0.465	CLONAL	1	TRUE	0	0.601335304530767	2		435	556	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481591	40481591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	178	639	0	ENST00000264657.5:c.1214C>T	p.Ser405Phe	p.S405F	ENST00000264657	NM_139276.2	405	tCt/tTt	13/24	1	2	FACETS	0.867	0.802	0.934	0.867	0.802	0.934	CLONAL	1	TRUE	1	0.601335304530767	2		639	683	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291971	15291971	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs1285561290	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	225	1009	0	ENST00000263388.2:c.2795C>G	p.Ser932Cys	p.S932C	ENST00000263388	NM_000435.2	932	tCc/tGc	18/33	0.601335304530767	1	FACETS	0.912	0.856	0.968	0.912	0.856	0.968	CLONAL	1	TRUE	0	0.601335304530767	1		1009	574	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139958	50139958	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	344	890	1	ENST00000246792.3:c.371C>A	p.Thr124Lys	p.T124K	ENST00000246792	NM_006270.3	124	aCg/aAg	4/6	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.601335304530767	2		891	1114	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483946	212483946	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	128	444	0	ENST00000342788.4:c.2257C>G	p.Leu753Val	p.L753V	ENST00000342788	NM_005235.2	753	Ctt/Gtt	19/28	1	2	FACETS	0.914	0.834	0.996	0.914	0.834	0.996	CLONAL	1	TRUE	1	0.601335304530767	2		444	466	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627994	37627994	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444340015	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	157	777	0	ENST00000249071.6:c.266C>T	p.Ser89Phe	p.S89F	ENST00000249071	NM_002872.4	89	tCt/tTt	4/7	NA	2	FACETS	0.611	0.56	0.664			1	INDETERMINATE	1	TRUE	NA	0.601335304530767	2		777	855	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71161689	71161689	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	74	248	0	ENST00000318789.4:c.280C>T	p.Gln94Ter	p.Q94*	ENST00000318789	NM_032682.5	94	Cag/Tag	7/21	0.572944605211568	1	FACETS	0.729	0.648	0.814	0.729	0.648	0.814	SUBCLONAL	1	TRUE	0	0.601335304530767	1		248	236	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453562	138453562	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	101	328	0	ENST00000289153.2:c.886G>C	p.Glu296Gln	p.E296Q	ENST00000289153	NM_006219.2	296	Gaa/Caa	5/22	NA	2	FACETS	0.663	0.594	0.734			1	INDETERMINATE	1	TRUE	NA	0.601335304530767	2		328	507	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258998	153258998	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	67	239	0	ENST00000281708.4:c.817G>C	p.Glu273Gln	p.E273Q	ENST00000281708	NM_033632.3	273	Gaa/Caa	5/12	0.413298441644779	1	FACETS	0.791	0.7	0.886	0.791	0.7	0.886	SUBCLONAL	1	TRUE	0	0.601335304530767	1		239	197	SUCCESS
APC	324	MSKCC	GRCh37	5	112170705	112170705	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	137	435	1	ENST00000257430.4:c.1801G>A	p.Glu601Lys	p.E601K	ENST00000257430	NM_000038.5	601	Gag/Aag	15/16	0.572944605211568	1	FACETS	0.89	0.82	0.962	0.89	0.82	0.962	CLONAL	1	TRUE	0	0.601335304530767	1		436	358	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324712	31324712	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	458	1169	0	ENST00000412585.2:c.96del	p.Tyr33ThrfsTer26	p.Y33Tfs*26	ENST00000412585	NM_005514.6	32	ttC/tt	2/8	0.513165908776589	2	FACETS	0.823	0.791	0.856	0.823	0.791	0.856	CLONAL	2	TRUE	0	0.601335304530767	2		1169	925	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741205	145741205	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	289	924	0	ENST00000428558.2:c.1201G>C	p.Glu401Gln	p.E401Q	ENST00000428558	NM_004260.3	401	Gag/Cag	6/22	NA	2	FACETS	0.917	0.863	0.972			1	INDETERMINATE	1	TRUE	NA	0.601335304530767	2		924	1048	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742998	145742998	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	38	56	0	ENST00000428558.2:c.106G>C	p.Glu36Gln	p.E36Q	ENST00000428558	NM_004260.3	36	Gag/Cag	2/22	NA	2	FACETS	0.752	0.631	0.884			1	INDETERMINATE	1	TRUE	NA	0.601335304530767	2		56	168	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779192	135779192	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs118203629	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	100	371	0	ENST00000298552.3:c.2054C>A	p.Ser685Ter	p.S685*	ENST00000298552	NM_001162426.1	685	tCa/tAa	17/23	1	2	FACETS	0.866	0.78	0.956	0.866	0.78	0.956	CLONAL	1	TRUE	1	0.601335304530767	2		371	384	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391508	139391508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	259	1056	1	ENST00000277541.6:c.6683C>T	p.Ser2228Phe	p.S2228F	ENST00000277541	NM_017617.3	2228	tCc/tTc	34/34	1	2	FACETS	0.959	0.9	1	0.959	0.9	1	CLONAL	1	TRUE	1	0.601335304530767	2		1057	898	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0057945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	49	219	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.523684195702523	3	FACETS	0.667	0.568	0.775	0.334	0.284	0.388	SUBCLONAL	1	TRUE	1	0.623292529592352	3		219	309	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534285	534286	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0057945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	500	520	0	ENST00000451590.1:c.37_38delinsAA	p.Gly13Asn	p.G13N	ENST00000451590	NM_001130442.1	13	GGt/AAt	2/5	0.623292529592352	4	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.623292529592352	4		520	1065	SUCCESS
APC	324	MSKCC	GRCh37	5	112175657	112175657	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0057945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	253	259	0	ENST00000257430.4:c.4366A>T	p.Lys1456Ter	p.K1456*	ENST00000257430	NM_000038.5	1456	Aaa/Taa	16/16	0.486206183980273	4	FACETS	0.886	0.848	0.923	0.886	0.848	0.923	CLONAL	4	TRUE	0	0.623292529592352	4		259	372	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411267	63411267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866313799	NA	P-0057945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	357	425	0	ENST00000330258.3:c.1900C>T	p.Arg634Cys	p.R634C	ENST00000330258	NM_152424.3	634	Cgt/Tgt	2/2	0.482201241435214	2	FACETS	0.976	0.937	1			1	CLONAL	2	TRUE	NA	0.623292529592352	2		425	587	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812205	43812205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866559375	NA	P-0057945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	213	546	1	ENST00000372470.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000372470	NM_005373.2	357	cGa/cAa	7/12	0.417459538454541	4	FACETS	1	0.991	1	0.727	0.677	0.778	CLONAL	1	TRUE	2	0.623292529592352	4		547	763	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528636	89528636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	58	148	2	ENST00000336596.2:c.2936G>A	p.Gly979Asp	p.G979D	ENST00000336596	NM_005233.5	979	gGc/gAc	17/17	0.468640938218633	4	FACETS	1	0.964	1	0.674	0.587	0.767	CLONAL	1	TRUE	2	0.623292529592352	4		150	224	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970899	55970899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	217	448	1	ENST00000263923.4:c.1898C>T	p.Ser633Phe	p.S633F	ENST00000263923	NM_002253.2	633	tCc/tTc	13/30	0.483563671576346	2	FACETS	0.793	0.748	0.839	0.793	0.748	0.839	SUBCLONAL	2	TRUE	0	0.623292529592352	2		449	439	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560043	29560043	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs868450405	NA	P-0057945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	103	218	0	ENST00000356175.3:c.3520C>T	p.Gln1174Ter	p.Q1174*	ENST00000356175	NM_000267.3	1174	Cag/Tag	27/57	0.490055754991624	2	FACETS	1	0.984	1	0.712	0.651	0.775	CLONAL	1	TRUE	0	0.623292529592352	2		218	232	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845580	151845580	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1287135873	NA	P-0057945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	135	528	2	ENST00000262189.6:c.13432C>T	p.Arg4478Ter	p.R4478*	ENST00000262189	NM_170606.2	4478	Cga/Tga	52/59	1	2	FACETS	0.84	0.767	0.914	0.84	0.767	0.914	CLONAL	1	TRUE	1	0.623292529592352	2		530	516	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458329	12458329	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1364613522	NA	P-0057945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	273	476	0	ENST00000287820.6:c.946C>T	p.Arg316Cys	p.R316C	ENST00000287820	NM_015869.4	316	Cgc/Tgc	6/7	0.468640938218633	4	FACETS	0.856	0.806	0.907	0.856	0.806	0.907	CLONAL	2	TRUE	2	0.623292529592352	4		476	831	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253808	153253808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1217890531	NA	P-0057945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	129	328	0	ENST00000281708.4:c.925C>T	p.Arg309Cys	p.R309C	ENST00000281708	NM_033632.3	309	Cgc/Tgc	6/12	0.468640938218633	4	FACETS	0.769	0.703	0.837	0.769	0.703	0.837	SUBCLONAL	2	TRUE	2	0.623292529592352	4		328	437	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543901	212543901	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	71	300	0	ENST00000342788.4:c.1498G>T	p.Gly500Ter	p.G500*	ENST00000342788	NM_005235.2	500	Gga/Tga	13/28	0.508658909666134	3	FACETS	0.749	0.657	0.847	0.374	0.328	0.424	SUBCLONAL	1	TRUE	1	0.623292529592352	3		300	399	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864720	57864720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	310	774	0	ENST00000228682.2:c.2197G>A	p.Gly733Arg	p.G733R	ENST00000228682	NM_005269.2	733	Ggg/Agg	12/12	0.452037434535068	3	FACETS	0.807	0.765	0.851	0.807	0.765	0.851	CLONAL	2	TRUE	1	0.623292529592352	3		774	808	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344819	118344820	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0057945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	106	262	0	ENST00000534358.1:c.2945_2946delinsTT	p.Ser982Phe	p.S982F	ENST00000534358	NM_005933.3	982	tCC/tTT	3/36	0.468640938218633	4	FACETS	1	0.981	1	0.692	0.625	0.762	CLONAL	1	TRUE	2	0.623292529592352	4		262	399	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212615382	212615382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	97	430	0	ENST00000342788.4:c.604G>A	p.Glu202Lys	p.E202K	ENST00000342788	NM_005235.2	202	Gaa/Aaa	5/28	0.508658909666134	3	FACETS	0.775	0.693	0.861	0.387	0.346	0.431	SUBCLONAL	1	TRUE	1	0.623292529592352	3		430	527	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104377156	104377156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	392	815	0	ENST00000369902.3:c.1267C>T	p.Pro423Ser	p.P423S	ENST00000369902	NM_016169.3	423	Cct/Tct	10/12	0.241085155494181	5	FACETS	1	0.975	1	0.693	0.659	0.727	INDETERMINATE	2	TRUE	2	0.623292529592352	5		815	1171	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858971	57858971	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	432	779	0	ENST00000228682.2:c.467C>T	p.Pro156Leu	p.P156L	ENST00000228682	NM_005269.2	156	cCc/cTc	5/12	0.452037434535068	3	FACETS	0.88	0.842	0.919	0.88	0.842	0.919	CLONAL	2	TRUE	1	0.623292529592352	3		779	1033	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579836	7579837	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	novel	NA	P-0057945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	457	625	0	ENST00000269305.4:c.74+2_74+3del		p.X25_splice	ENST00000269305	NM_001126112.2	25			0.490055754991624	2	FACETS	0.921	0.887	0.955	0.921	0.887	0.955	CLONAL	2	TRUE	0	0.623292529592352	2		625	796	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55693414	55693414	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	330	655	0	ENST00000284073.2:c.621G>A	p.Met207Ile	p.M207I	ENST00000284073	NM_138962.2	207	atG/atA	9/14	0.417459538454541	4	FACETS	0.769	0.728	0.812	0.769	0.728	0.812	SUBCLONAL	2	TRUE	2	0.623292529592352	4		655	1117	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792891	33792891	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	65	99	0	ENST00000498907.2:c.430G>T	p.Glu144Ter	p.E144*	ENST00000498907	NM_004364.3	144	Gag/Tag	1/1	0.330665969736484	4	FACETS	0.756	0.665	0.851	0.756	0.665	0.851	INDETERMINATE	2	TRUE	2	0.623292529592352	4		99	224	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152497	56152497	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	95	220	0	ENST00000399503.3:c.553A>T	p.Ile185Phe	p.I185F	ENST00000399503	NM_005921.1	185	Atc/Ttc	2/20	0.417459538454541	4	FACETS	1	0.98	1	0.703	0.631	0.777	CLONAL	1	TRUE	2	0.623292529592352	4		220	352	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43742084	43742084	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	350	692	0	ENST00000523873.1:c.73C>G	p.Gln25Glu	p.Q25E	ENST00000523873		25	Cag/Gag	2/8	0.623292529592352	3	FACETS	1	0.993	1	0.44	0.416	0.463	CLONAL	1	TRUE	0	0.623292529592352	3		692	1117	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194884	29194885	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0057945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	254	772	0	ENST00000240100.2:c.843_844delinsAA	p.Ala282Thr	p.A282T	ENST00000240100	NM_001394.6	281	caGGcg/caAAcg	4/4	0.352429934398599	3	FACETS	1	0.983	1	0.569	0.533	0.605	INDETERMINATE	1	TRUE	1	0.623292529592352	3		772	940	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866505	117866505	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	117	250	0	ENST00000297338.2:c.1140G>T	p.Leu380Phe	p.L380F	ENST00000297338	NM_006265.2	380	ttG/ttT	9/14	0.623292529592352	6	FACETS	1	0.979	1	0.329	0.297	0.363	CLONAL	1	TRUE	2	0.623292529592352	6		250	641	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212786	27212786	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	315	645	0	ENST00000380036.4:c.2768A>T	p.Asp923Val	p.D923V	ENST00000380036	NM_000459.3	923	gAc/gTc	17/23	0.330665969736484	4	FACETS	0.825	0.78	0.872	0.825	0.78	0.872	INDETERMINATE	2	TRUE	2	0.623292529592352	4		645	994	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295252	+	upstream_gene_variant	5'Flank	TNP	GAG	GAG	AAA	novel	NA	P-0057945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	158	210	0				ENST00000310581	NM_198253.2	-/1132			0.417459538454541	4	FACETS	0.999	0.926	1	0.999	0.926	1	CLONAL	2	TRUE	2	0.623292529592352	4		210	412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0057946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	115	785	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.272102646211263	2		785	830	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216382	7216382	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs765011305	NA	P-0057946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	133	761	0	ENST00000380728.2:c.866C>A	p.Pro289His	p.P289H	ENST00000380728		289	cCc/cAc	10/11	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.272102646211263	2		761	946	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544087	18544087	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs757230788	NA	P-0057946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	122	267	0	ENST00000266497.5:c.1904T>A	p.Met635Lys	p.M635K	ENST00000266497		635	aTg/aAg	13/31	0.235558909249074	5	FACETS	1	0.958	1	0.812	0.741	0.885	CLONAL	3	TRUE	1	0.272102646211263	5		267	389	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570030	95570030	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	124	435	0	ENST00000393063.1:c.3703T>C	p.Cys1235Arg	p.C1235R	ENST00000393063	NM_030621.3	1235	Tgt/Cgt	22/28	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.272102646211263	2		435	650	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748297	41748297	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	51	768	0	ENST00000226382.2:c.472C>T	p.Arg158Cys	p.R158C	ENST00000226382	NM_003924.3	158	Cgc/Tgc	3/3	0.272102646211263	1	FACETS	0.349	0.295	0.408	0.349	0.295	0.408	SUBCLONAL	1	TRUE	0	0.272102646211263	1		768	929	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197138	106197138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	42	346	0	ENST00000380013.4:c.5471G>A	p.Gly1824Asp	p.G1824D	ENST00000380013	NM_001127208.2	1824	gGt/gAt	11/11	0.272102646211263	1	FACETS	0.704	0.589	0.831	0.704	0.589	0.831	SUBCLONAL	1	TRUE	0	0.272102646211263	1		346	379	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007323	143007323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	21	342	0	ENST00000262992.4:c.2461G>T	p.Val821Leu	p.V821L	ENST00000262992	NM_001101669.1	821	Gta/Tta	22/24	0.272102646211263	1	FACETS	0.34	0.261	0.432	0.34	0.261	0.432	SUBCLONAL	1	TRUE	0	0.272102646211263	1		342	392	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278791	1278791	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	103	707	0	ENST00000310581.5:c.2251G>C	p.Ala751Pro	p.A751P	ENST00000310581	NM_198253.2	751	Gcc/Ccc	6/16	0.272102646211263	3	FACETS	0.732	0.653	0.816	0.366	0.326	0.408	SUBCLONAL	1	TRUE	1	0.272102646211263	3		707	1175	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729898	41729898	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	136	585	0	ENST00000242208.4:c.631G>T	p.Val211Leu	p.V211L	ENST00000242208	NM_002192.2	211	Gta/Tta	3/3	0.240666490163666	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.272102646211263	1		585	775	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128849154	128849154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	145	681	1	ENST00000249373.3:c.1382G>A	p.Gly461Asp	p.G461D	ENST00000249373	NM_005631.4	461	gGc/gAc	8/12	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.272102646211263	2		682	1001	SUCCESS
AR	367	MSKCC	GRCh37	X	66766432	66766432	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	42	112	0	ENST00000374690.3:c.1444G>T	p.Gly482Cys	p.G482C	ENST00000374690	NM_000044.3	482	Ggc/Tgc	1/8	0.0526524626231439	2	FACETS	0.897	0.76	1			1	INDETERMINATE	2	TRUE	NA	0.272102646211263	2		112	172	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107040	27107040	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	88	558	1	ENST00000324856.7:c.6651C>A	p.His2217Gln	p.H2217Q	ENST00000324856	NM_006015.4	2217	caC/caA	20/20	1	2	FACETS	0.754	0.674	0.839	0.754	0.674	0.839	SUBCLONAL	1	TRUE	1	0.66102540734817	2		559	353	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359636	40359637	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATC	novel	NA	P-0057948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	150	537	1	ENST00000293328.3:c.2014_2016dup	p.Asp672dup	p.D672dup	ENST00000293328	NM_012448.3	672	-/GAT	16/19	0.66102540734817	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	1	0.66102540734817	3		538	295	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035078	30035078	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0057949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	38	278	1	ENST00000338641.4:c.241-1G>A		p.X81_splice	ENST00000338641	NM_000268.3	81			0.300208587314623	1	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	0	0.25	1		279	246	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148892	119148892	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs387906666	NA	P-0057949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	27	247	0	ENST00000264033.4:c.1112A>G	p.Tyr371Cys	p.Y371C	ENST00000264033	NM_005188.3	371	tAc/tGc	8/16	1	2	FACETS	0.622	0.495	0.767	0.622	0.495	0.767	SUBCLONAL	1	TRUE	1	0.25	2		247	347	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061207	38061207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	256	577	1	ENST00000250448.2:c.782G>A	p.Arg261His	p.R261H	ENST00000250448	NM_004496.3	261	cGc/cAc	2/2	0.382811748344152	4	FACETS	0.906	0.848	0.965			1	CLONAL	2	TRUE	NA	0.382811748344152	4		578	1021	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685271	89685271	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	115	186	0	ENST00000371953.3:c.170del	p.Leu57TrpfsTer42	p.L57Wfs*42	ENST00000371953	NM_000314.4	56	Ttt/tt	3/9	1	2	FACETS	1	0.924	1	1	0.99	1	CLONAL	2	TRUE	1	0.382811748344152	2		186	297	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650795	37650795	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	607	593	0	ENST00000447079.4:c.2267A>G	p.Lys756Arg	p.K756R	ENST00000447079	NM_015083.1	756	aAg/aGg	5/14	0.382811748344152	2	FACETS	1	0.99	1	1	0.998	1	CLONAL	4	TRUE	0	0.382811748344152	2		593	774	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416413	49416413	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	317	561	0	ENST00000301067.7:c.16298A>C	p.Asn5433Thr	p.N5433T	ENST00000301067	NM_003482.3	5433	aAc/aCc	51/54	1	2	FACETS	1	0.971	1	1	0.996	1	CLONAL	2	TRUE	1	0.382811748344152	2		561	800	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993720	72993720	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0057963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	146	758	0	ENST00000268489.5:c.325A>T	p.Arg109Ter	p.R109*	ENST00000268489	NM_006885.3	109	Aga/Tga	2/10	0.340765571819641	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.382811748344152	1		758	616	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	155	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.98	0.905	1	0.98	0.905	1	CLONAL	1	TRUE	1	0.687650412202707	2		306	460	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0057964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	806	632	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.685826672052677	3	FACETS	0.982	0.961	1			1	CLONAL	3	TRUE	NA	0.687650412202707	3		632	1069	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798734	135798734	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs118203390	NA	P-0057964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	19	189	0	ENST00000298552.3:c.508+1G>A		p.X170_splice	ENST00000298552	NM_001162426.1	170			0.687650412202707	1	FACETS	0.273	0.209	0.346	0.273	0.209	0.346	SUBCLONAL	1	TRUE	0	0.687650412202707	1		189	133	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911979	32911979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	49	469	1	ENST00000380152.3:c.3487G>A	p.Asp1163Asn	p.D1163N	ENST00000380152		1163	Gat/Aat	11/27	1	2	FACETS	0.333	0.282	0.389	0.333	0.282	0.389	SUBCLONAL	1	TRUE	1	0.687650412202707	2		470	428	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919653	96919653	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767190490	NA	P-0057964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	219	545	0	ENST00000258439.3:c.610G>A	p.Glu204Lys	p.E204K	ENST00000258439	NM_001193304.2	204	Gag/Aag	4/4	0.559295115538229	1	FACETS	0.746	0.7	0.793	0.746	0.7	0.793	SUBCLONAL	1	TRUE	0	0.687650412202707	1		545	560	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920608	96920608	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	182	374	0	ENST00000258439.3:c.372G>C	p.Lys124Asn	p.K124N	ENST00000258439	NM_001193304.2	124	aaG/aaC	3/4	0.559295115538229	1	FACETS	0.882	0.825	0.939	0.882	0.825	0.939	CLONAL	1	TRUE	0	0.687650412202707	1		374	394	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196474	106196474	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	73	381	0	ENST00000380013.4:c.4807C>G	p.Gln1603Glu	p.Q1603E	ENST00000380013	NM_001127208.2	1603	Caa/Gaa	11/11	1	2	FACETS	0.708	0.625	0.795	0.708	0.625	0.795	SUBCLONAL	1	TRUE	1	0.687650412202707	2		381	300	SUCCESS
APC	324	MSKCC	GRCh37	5	112178573	112178573	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	46	264	0	ENST00000257430.4:c.7282G>C	p.Glu2428Gln	p.E2428Q	ENST00000257430	NM_000038.5	2428	Gaa/Caa	16/16	1	2	FACETS	0.752	0.643	0.868	0.752	0.643	0.868	SUBCLONAL	1	TRUE	1	0.687650412202707	2		264	178	SUCCESS
APC	324	MSKCC	GRCh37	5	112178627	112178627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	69	269	0	ENST00000257430.4:c.7336G>A	p.Glu2446Lys	p.E2446K	ENST00000257430	NM_000038.5	2446	Gaa/Aaa	16/16	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.687650412202707	2		269	188	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652049	36652050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0057964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	438	985	0	ENST00000244741.5:c.172_173dup	p.Leu59HisfsTer90	p.L59Hfs*90	ENST00000244741	NM_000389.4	57	-/CC	2/3	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.687650412202707	2		985	1260	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157454239	157454239	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1288082874	NA	P-0057964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	173	504	0	ENST00000346085.5:c.2449C>T	p.His817Tyr	p.H817Y	ENST00000346085	NM_020732.3	817	Cat/Tat	8/20	1	2	FACETS	0.891	0.825	0.958	0.891	0.825	0.958	CLONAL	1	TRUE	1	0.687650412202707	2		504	565	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797312	135797313	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0057964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	78	245	0	ENST00000298552.3:c.556dup	p.Ala186GlyfsTer32	p.A186Gfs*32	ENST00000298552	NM_001162426.1	186	gca/gGca	7/23	0.687650412202707	1	FACETS	0.677	0.605	0.751	0.677	0.605	0.751	SUBCLONAL	1	TRUE	0	0.687650412202707	1		245	220	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	100	729	8	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.878	0.789	0.97	1	0.986	1	CLONAL	2	TRUE	1	0.27	2		737	422	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	58	542	2	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.27	2		544	424	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	57	486	9	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.3	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.27	1		495	304	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	35	988	5	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.599	0.491	0.72	0.599	0.491	0.72	SUBCLONAL	1	TRUE	1	0.27	2		993	433	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114817	108114817	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786204543	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	20	412	0	ENST00000278616.4:c.640del	p.Ser214ProfsTer16	p.S214Pfs*16	ENST00000278616	NM_000051.3	212	Ttt/tt	6/63	1	2	FACETS	0.709	0.544	0.9	0.709	0.544	0.9	SUBCLONAL	1	TRUE	1	0.27	2		412	209	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923087	39923087	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	65	298	0	ENST00000378444.4:c.3621del	p.Lys1207AsnfsTer31	p.K1207Nfs*31	ENST00000378444	NM_001123385.1	1207	aaA/aa	8/15	1	1	FACETS	0.843	0.74	0.952	1	0.978	1	CLONAL	2	TRUE	0	0.27	1		298	247	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576098	29576098	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1135402852	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	17	400	0	ENST00000356175.3:c.4076del	p.Pro1359LeufsTer26	p.P1359Lfs*26	ENST00000356175	NM_000267.3	1357	ttC/tt	30/57	1	2	FACETS	0.391	0.291	0.51	0.391	0.291	0.51	SUBCLONAL	1	TRUE	1	0.27	2		400	322	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715678	30715678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039551	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	9	235	0	ENST00000295754.5:c.1336G>A	p.Asp446Asn	p.D446N	ENST00000295754	NM_003242.5	446	Gat/Aat	5/7	1	2	FACETS	0.274	0.181	0.394	0.274	0.181	0.394	SUBCLONAL	1	TRUE	1	0.27	2		235	243	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863319	57863319	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	42	751	0	ENST00000228682.2:c.1418del	p.Gly473AlafsTer40	p.G473Afs*40	ENST00000228682	NM_005269.2	472	Ggg/gg	11/12	0.102837753612007	3	FACETS	0.674	0.562	0.798	0.337	0.281	0.399	INDETERMINATE	1	TRUE	1	0.27	3		751	524	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481454	20481455	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	16	244	0	ENST00000346618.3:c.529dup	p.Thr177AsnfsTer4	p.T177Nfs*4	ENST00000346618	NM_001949.4	175	gaa/gAaa	3/7	0.17209630278824	5	FACETS	0.747	0.553	0.977	0.249	0.184	0.326	CLONAL	1	TRUE	2	0.27	5		244	223	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112153	115112154	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	20	813	0	ENST00000257566.3:c.1586dup	p.Ala530ArgfsTer162	p.A530Rfs*162	ENST00000257566	NM_016569.3	529	ggc/ggGc	7/8	1	2	FACETS	0.376	0.287	0.481	0.376	0.287	0.481	SUBCLONAL	1	TRUE	1	0.27	2		813	394	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510166	149510166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747109578	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	64	731	0	ENST00000261799.4:c.1303C>T	p.Arg435Cys	p.R435C	ENST00000261799	NM_002609.3	435	Cgc/Tgc	9/23	0.3	1	FACETS	0.801	0.695	0.916	0.801	0.695	0.916	CLONAL	1	TRUE	0	0.27	1		731	512	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023894	31023894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201009558	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	37	613	0	ENST00000375687.4:c.3379G>A	p.Asp1127Asn	p.D1127N	ENST00000375687	NM_015338.5	1127	Gat/Aat	13/13	1	2	FACETS	0.737	0.608	0.88	0.737	0.608	0.88	SUBCLONAL	1	TRUE	1	0.27	2		613	372	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81939094	81939094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201746780	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	31	470	0	ENST00000359376.3:c.1449G>A	p.Met483Ile	p.M483I	ENST00000359376	NM_002661.3	483	atG/atA	15/33	1	2	FACETS	0.626	0.506	0.761	0.626	0.506	0.761	SUBCLONAL	1	TRUE	1	0.27	2		470	367	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348371	89348371	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777979146	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	73	888	1	ENST00000301030.4:c.4579G>A	p.Asp1527Asn	p.D1527N	ENST00000301030	NM_001256183.1	1527	Gat/Aat	9/13	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.27	2		889	532	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	54	1163	3	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.763	0.652	0.885	0.763	0.652	0.885	SUBCLONAL	1	TRUE	1	0.27	2		1166	524	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324205	31324205	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs281864615	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	23	483	0	ENST00000412585.2:c.358C>T	p.Gln120Ter	p.Q120*	ENST00000412585	NM_005514.6	120	Cag/Tag	3/8	0.17209630278824	5	FACETS	0.946	0.74	1	0.315	0.246	0.395	CLONAL	1	TRUE	2	0.27	5		483	253	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662662	227662662	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1412312472	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	31	720	0	ENST00000305123.5:c.793C>T	p.Arg265Cys	p.R265C	ENST00000305123	NM_005544.2	265	Cgc/Tgc	1/2	1	2	FACETS	0.525	0.425	0.64	0.525	0.425	0.64	SUBCLONAL	1	TRUE	1	0.27	2		720	437	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920185	76920185	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	16	190	0	ENST00000373344.5:c.3892G>A	p.Glu1298Lys	p.E1298K	ENST00000373344	NM_000489.3	1298	Gaa/Aaa	11/35	1	1	FACETS	0.688	0.512	0.895	0.688	0.512	0.895	SUBCLONAL	1	TRUE	0	0.27	1		190	149	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023715	27023716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	67	497	0	ENST00000324856.7:c.827dup	p.Gly277ArgfsTer123	p.G277Rfs*123	ENST00000324856	NM_006015.4	274	atg/atGg	1/20	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.27	2		497	439	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683658	162683658	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748892763	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	75	556	0	ENST00000366898.1:c.311G>A	p.Arg104Gln	p.R104Q	ENST00000366898	NM_004562.2	104	cGg/cAg	3/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.27	2		556	422	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098443	11098443	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1344296942	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	18	483	1	ENST00000358026.2:c.961G>A	p.Ala321Thr	p.A321T	ENST00000358026	NM_001128849.1	321	Gcc/Acc	6/36	1	2	FACETS	0.503	0.379	0.65	0.503	0.379	0.65	SUBCLONAL	1	TRUE	1	0.27	2		484	265	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434246	49434247	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	35	997	1	ENST00000301067.7:c.7306dup	p.Cys2436LeufsTer13	p.C2436Lfs*13	ENST00000301067	NM_003482.3	2436	tgc/tTgc	31/54	0.102837753612007	3	FACETS	0.459	0.375	0.554	0.23	0.187	0.277	INDETERMINATE	1	TRUE	1	0.27	3		998	641	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602650	10602650	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	27	950	0	ENST00000171111.5:c.928del	p.Leu310CysfsTer7	p.L310Cfs*7	ENST00000171111	NM_203500.1	310	Ctg/tg	3/6	1	2	FACETS	0.403	0.32	0.499	0.403	0.32	0.499	SUBCLONAL	1	TRUE	1	0.27	2		950	496	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136216	64136216	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	27	870	0	ENST00000334205.4:c.1375C>A	p.Leu459Met	p.L459M	ENST00000334205	NM_003942.2	459	Ctg/Atg	12/17	1	2	FACETS	0.451	0.359	0.558	0.451	0.359	0.558	SUBCLONAL	1	TRUE	1	0.27	2		870	443	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986583	36986583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs537209983	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	30	571	0	ENST00000354822.5:c.1106C>T	p.Ala369Val	p.A369V	ENST00000354822	NM_001079668.2	369	gCg/gTg	3/3	1	2	FACETS	0.832	0.673	1	0.832	0.673	1	CLONAL	1	TRUE	1	0.27	2		571	267	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572387	95572387	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	14	346	0	ENST00000393063.1:c.2978C>T	p.Thr993Ile	p.T993I	ENST00000393063	NM_030621.3	993	aCa/aTa	19/28	1	2	FACETS	0.374	0.27	0.501	0.374	0.27	0.501	SUBCLONAL	1	TRUE	1	0.27	2		346	277	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126495	2126495	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	30	728	0	ENST00000219476.3:c.2746C>A	p.Leu916Met	p.L916M	ENST00000219476	NM_000548.3	916	Ctg/Atg	25/42	1	2	FACETS	0.504	0.406	0.616	0.504	0.406	0.616	SUBCLONAL	1	TRUE	1	0.27	2		728	441	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346384	89346384	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	22	728	1	ENST00000301030.4:c.6566C>T	p.Ala2189Val	p.A2189V	ENST00000301030	NM_001256183.1	2189	gCa/gTa	9/13	1	2	FACETS	0.429	0.332	0.542	0.429	0.332	0.542	SUBCLONAL	1	TRUE	1	0.27	2		729	380	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032606	12032606	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	19	433	0	ENST00000353533.5:c.1040+2T>C		p.X347_splice	ENST00000353533	NM_003010.3	347			1	2	FACETS	0.474	0.36	0.608	0.474	0.36	0.608	SUBCLONAL	1	TRUE	1	0.27	2		433	297	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745971	745971	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	12	400	0	ENST00000314574.4:c.551T>C	p.Val184Ala	p.V184A	ENST00000314574	NM_005433.3	184	gTa/gCa	5/12	1	2	FACETS	0.502	0.353	0.684	0.502	0.353	0.684	SUBCLONAL	1	TRUE	1	0.27	2		400	177	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227729	36227729	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	68	624	0	ENST00000222270.7:c.7297+1G>A		p.X2433_splice	ENST00000222270	NM_014727.1	2433			1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.27	2		624	442	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47735813	47735813	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	49	715	0	ENST00000449228.1:c.47C>A	p.Pro16His	p.P16H	ENST00000449228	NM_001127240.2	16	cCc/cAc	1/4	1	2	FACETS	0.578	0.489	0.676	0.578	0.489	0.676	SUBCLONAL	1	TRUE	1	0.27	2		715	628	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705650	47705650	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	17	243	0	ENST00000233146.2:c.2450T>C	p.Val817Ala	p.V817A	ENST00000233146	NM_000251.2	817	gTg/gCg	14/16	1	2	FACETS	0.636	0.476	0.824	0.636	0.476	0.824	SUBCLONAL	1	TRUE	1	0.27	2		243	198	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023093	48023093	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	32	338	0	ENST00000234420.5:c.518T>C	p.Leu173Pro	p.L173P	ENST00000234420	NM_000179.2	173	cTg/cCg	3/10	1	2	FACETS	0.782	0.637	0.946	0.782	0.637	0.946	CLONAL	1	TRUE	1	0.27	2		338	303	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812323	212812323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	11	234	0	ENST00000342788.4:c.253G>T	p.Gly85Cys	p.G85C	ENST00000342788	NM_005235.2	85	Ggc/Tgc	3/28	1	2	FACETS	0.436	0.301	0.603	0.436	0.301	0.603	SUBCLONAL	1	TRUE	1	0.27	2		234	187	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546830	9546830	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	26	421	0	ENST00000353224.5:c.1192G>T	p.Ala398Ser	p.A398S	ENST00000353224	NM_177990.2	398	Gct/Tct	5/10	1	2	FACETS	0.566	0.449	0.701	0.566	0.449	0.701	SUBCLONAL	1	TRUE	1	0.27	2		421	340	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573011	41573011	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	58	765	2	ENST00000263253.7:c.5296C>T	p.Gln1766Ter	p.Q1766*	ENST00000263253	NM_001429.3	1766	Cag/Tag	31/31	1	2	FACETS	0.934	0.804	1	0.934	0.804	1	CLONAL	1	TRUE	1	0.27	2		767	460	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056342	180056342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	37	945	0	ENST00000261937.6:c.902G>A	p.Ser301Asn	p.S301N	ENST00000261937	NM_182925.4	301	aGc/aAc	7/30	0.3	1	FACETS	0.555	0.458	0.664	0.555	0.458	0.664	SUBCLONAL	1	TRUE	0	0.27	1		945	427	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250427	110250427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	39	765	0	ENST00000374672.4:c.248G>A	p.Cys83Tyr	p.C83Y	ENST00000374672	NM_004235.4	83	tGc/tAc	3/5	1	2	FACETS	0.636	0.527	0.758	0.636	0.527	0.758	SUBCLONAL	1	TRUE	1	0.27	2		765	454	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426057	47426057	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	38	445	0	ENST00000377045.4:c.577G>T	p.Asp193Tyr	p.D193Y	ENST00000377045	NM_001654.4	193	Gac/Tac	7/16	1	1	FACETS	0.848	0.705	1	0.848	0.705	1	CLONAL	1	TRUE	0	0.27	1		445	287	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670340	134670340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415689583	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	121	457	0	ENST00000398015.3:c.251G>A	p.Arg84His	p.R84H	ENST00000398015	NM_004441.4	84	cGc/cAc	3/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.363517011554297	2		457	572	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	123	876	1	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	2	FACETS	0.67	0.605	0.739	0.67	0.605	0.739	SUBCLONAL	1	TRUE	1	0.363517011554297	2		877	1010	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	234	397	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.363517011554297	4	FACETS	1	0.988	1	0.824	0.772	0.877	CLONAL	2	TRUE	1	0.363517011554297	4		397	710	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596008	43596008	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376565365	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	192	980	2	ENST00000355710.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000355710	NM_020975.4	59	Gcc/Acc	2/20	0.0427980657560054	3	FACETS	1	0.982	1	0.597	0.551	0.644	INDETERMINATE	1	TRUE	1	0.363517011554297	3		982	1046	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	198	872	1	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.363517011554297	2		873	1052	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231221	98231221	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554695039	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	193	810	0	ENST00000331920.6:c.2062C>T	p.Gln688Ter	p.Q688*	ENST00000331920	NM_000264.3	688	Cag/Tag	14/24	1	2	FACETS	0.92	0.85	0.993	0.92	0.85	0.993	CLONAL	1	TRUE	1	0.363517011554297	2		810	1154	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023769	27023769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	87	568	0	ENST00000324856.7:c.879del	p.Thr294ProfsTer69	p.T294Pfs*69	ENST00000324856	NM_006015.4	292	aCc/ac	1/20	1	2	FACETS	0.818	0.726	0.917	0.818	0.726	0.917	CLONAL	1	TRUE	1	0.363517011554297	2		568	585	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624275	89624275	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204910	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	205	453	0	ENST00000371953.3:c.49C>T	p.Gln17Ter	p.Q17*	ENST00000371953	NM_000314.4	17	Caa/Taa	1/9	0.363517011554297	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.363517011554297	2		453	534	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120031	70120031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	16	120	0	ENST00000245479.2:c.1037del	p.Pro346ArgfsTer37	p.P346Rfs*37	ENST00000245479	NM_000346.3	345	Ccc/cc	3/3	0.363517011554297	2	FACETS	0.88	0.66	1	0.44	0.33	0.568	CLONAL	1	TRUE	0	0.363517011554297	2		120	100	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649592	206649592	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	161	775	1	ENST00000367120.3:c.427C>T	p.Arg143Cys	p.R143C	ENST00000367120	NM_014002.3	143	Cgc/Tgc	6/22	1	2	FACETS	0.96	0.88	1	0.96	0.88	1	CLONAL	1	TRUE	1	0.363517011554297	2		776	923	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032401	10032401	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs78631453	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	68	346	2	ENST00000330684.3:c.422C>T	p.Thr141Met	p.T141M	ENST00000330684	NM_001134407.1	141	aCg/aTg	3/13	1	2	FACETS	0.931	0.813	1	0.931	0.813	1	CLONAL	1	TRUE	1	0.363517011554297	2		348	402	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085996	16085996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	111	606	0	ENST00000281043.3:c.1172G>A	p.Arg391His	p.R391H	ENST00000281043	NM_005378.4	391	cGc/cAc	3/3	NA	2	FACETS	0.67	0.602	0.743			1	INDETERMINATE	1	TRUE	NA	0.363517011554297	2		606	911	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938088	76938089	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	75	574	0	ENST00000373344.5:c.2658_2659dup	p.Thr887ArgfsTer19	p.T887Rfs*19	ENST00000373344	NM_000489.3	887	act/aGAct	9/35	1	2	FACETS	0.577	0.505	0.655	0.577	0.505	0.655	SUBCLONAL	1	TRUE	1	0.363517011554297	2		574	715	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	238	1132	1	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.363517011554297	2		1133	1254	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	135	1231	6	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.699	0.634	0.768	0.699	0.634	0.768	SUBCLONAL	1	TRUE	1	0.363517011554297	2		1237	1062	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944308	81944308	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	144	746	0	ENST00000359376.3:c.1921del	p.His641ThrfsTer11	p.H641Tfs*11	ENST00000359376	NM_002661.3	639	aaC/aa	18/33	1	2	FACETS	0.872	0.795	0.952	0.872	0.795	0.952	CLONAL	1	TRUE	1	0.363517011554297	2		746	909	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867058	45867058	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	204	929	0	ENST00000391945.4:c.1061C>T	p.Pro354Leu	p.P354L	ENST00000391945	NM_000400.3	354	cCg/cTg	11/23	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.363517011554297	2		929	1045	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066472	94066472	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	102	325	0	ENST00000369303.4:c.1287G>T	p.Arg429Ser	p.R429S	ENST00000369303	NM_004440.3	429	agG/agT	5/17	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.363517011554297	2		325	441	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466000	69466000	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	211	1093	1	ENST00000227507.2:c.838G>T	p.Glu280Ter	p.E280*	ENST00000227507	NM_053056.2	280	Gag/Tag	5/5	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.363517011554297	2		1094	1047	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026895	6026895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540287433	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	84	370	0	ENST00000265849.7:c.1501G>A	p.Val501Met	p.V501M	ENST00000265849	NM_000535.5	501	Gtg/Atg	11/15	1	2	FACETS	0.988	0.876	1	0.988	0.876	1	CLONAL	1	TRUE	1	0.363517011554297	2		370	468	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99136593	99136593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770686205	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	258	848	1	ENST00000074304.5:c.82G>A	p.Asp28Asn	p.D28N	ENST00000074304	NM_001134224.1	28	Gac/Aac	3/26	1	2	FACETS	0.751	0.704	0.799	1	0.993	1	SUBCLONAL	2	TRUE	1	0.363517011554297	2		849	945	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599890	28599890	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	156	641	0	ENST00000253063.3:c.772G>A	p.Val258Met	p.V258M	ENST00000253063	NM_031459.4	258	Gtg/Atg	6/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.363517011554297	2		641	772	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100045	157100045	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	31	129	0	ENST00000346085.5:c.982G>T	p.Gly328Ter	p.G328*	ENST00000346085	NM_020732.3	328	Gga/Tga	1/20	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.363517011554297	2		129	159	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099033	27099033	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	130	548	1	ENST00000324856.7:c.3450del	p.Ser1151AlafsTer10	p.S1151Afs*10	ENST00000324856	NM_006015.4	1150	aCc/ac	13/20	1	2	FACETS	0.899	0.815	0.986	0.899	0.815	0.986	CLONAL	1	TRUE	1	0.363517011554297	2		549	796	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549146	21549146	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	166	734	0	ENST00000382592.4:c.3130A>G	p.Arg1044Gly	p.R1044G	ENST00000382592	NM_014572.2	1044	Agg/Ggg	8/8	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.363517011554297	2		734	879	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639839	3639839	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	196	951	0	ENST00000294008.3:c.3800del	p.Arg1267LeufsTer21	p.R1267Lfs*21	ENST00000294008	NM_032444.2	1267	cGt/ct	12/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.363517011554297	2		951	990	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821554	72821554	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	56	323	0	ENST00000268489.5:c.10621del	p.Glu3541ArgfsTer4	p.E3541Rfs*4	ENST00000268489	NM_006885.3	3541	Gag/ag	10/10	1	2	FACETS	0.811	0.697	0.934	0.811	0.697	0.934	CLONAL	1	TRUE	1	0.363517011554297	2		323	380	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346940	89346940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1247123083	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	94	593	0	ENST00000301030.4:c.6010G>A	p.Ala2004Thr	p.A2004T	ENST00000301030	NM_001256183.1	2004	Gcc/Acc	9/13	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.363517011554297	2		593	496	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7119461	7119462	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	175	596	0	ENST00000302850.5:c.3792_3793del	p.Arg1264SerfsTer3	p.R1264Sfs*3	ENST00000302850	NM_000208.2	1264	agAGtc/agtc	21/22	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.363517011554297	2		596	926	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982555	10982555	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	62	202	0	ENST00000327064.4:c.177G>T	p.Glu59Asp	p.E59D	ENST00000327064	NM_199141.1	59	gaG/gaT	1/16	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.363517011554297	2		202	328	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212537	36212537	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370359238	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	283	1183	0	ENST00000222270.7:c.2288C>T	p.Pro763Leu	p.P763L	ENST00000222270	NM_014727.1	763	cCg/cTg	3/37	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.363517011554297	2		1183	1458	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909440	50909440	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	185	885	0	ENST00000440232.2:c.1244T>C	p.Val415Ala	p.V415A	ENST00000440232	NM_002691.3	415	gTa/gCa	11/27	1	2	FACETS	0.944	0.871	1	0.944	0.871	1	CLONAL	1	TRUE	1	0.363517011554297	2		885	1078	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170347	32170347	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	247	1004	0	ENST00000375023.3:c.3261G>T	p.Arg1087Ser	p.R1087S	ENST00000375023	NM_004557.3	1087	agG/agT	21/30	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.363517011554297	2		1004	1174	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151868395	151868395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	134	523	0	ENST00000262189.6:c.9407C>T	p.Thr3136Ile	p.T3136I	ENST00000262189	NM_170606.2	3136	aCa/aTa	40/59	1	2	FACETS	0.959	0.872	1	0.959	0.872	1	CLONAL	1	TRUE	1	0.363517011554297	2		523	769	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549371	5549371	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	106	505	0	ENST00000397747.3:c.398T>C	p.Val133Ala	p.V133A	ENST00000397747	NM_025239.3	133	gTt/gCt	4/7	0.353844743084681	2	FACETS	0.888	0.797	0.984	0.444	0.398	0.492	CLONAL	1	TRUE	0	0.363517011554297	2		505	657	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030467	47030472	+	inframe_deletion	In_Frame_Del	DEL	GGCGGC	GGCGGC	-	novel	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	190	993	1	ENST00000377604.3:c.251_256del	p.Arg84_Arg85del	p.R84_R85del	ENST00000377604	NM_001204468.1	81	aGGCGGCgg/agg	4/24	1	2	FACETS	0.99	0.914	1	0.99	0.914	1	CLONAL	1	TRUE	1	0.363517011554297	2		994	1056	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184103	123184103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	55	379	0	ENST00000218089.9:c.961G>A	p.Asp321Asn	p.D321N	ENST00000218089	NM_001042749.1	321	Gat/Aat	11/35	1	2	FACETS	0.911	0.784	1	0.911	0.784	1	CLONAL	1	TRUE	1	0.363517011554297	2		379	332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0057971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	456	618	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.428345076713276	2	FACETS	0.937	0.897	0.977	0.937	0.897	0.977	CLONAL	2	TRUE	0	0.449450246863443	2		618	1083	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907164	101907164	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	35	322	2	ENST00000374994.4:c.1124C>A	p.Thr375Lys	p.T375K	ENST00000374994	NM_004612.2	375	aCa/aAa	6/9	0.15971954503448	2	FACETS	0.372	0.304	0.447	0.186	0.152	0.224	INDETERMINATE	1	TRUE	0	0.449450246863443	2		324	419	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092912	29092912	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	175	513	0	ENST00000328354.6:c.1072C>G	p.Gln358Glu	p.Q358E	ENST00000328354	NM_007194.3	358	Caa/Gaa	10/15	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.449450246863443	NA		513	720	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0057972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	220	432	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.59949888186192	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.605141328135054	3		432	438	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873475	45873476	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCGTCCACGTTGAGCCTGGCGG	novel	NA	P-0057972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	62	800	0	ENST00000391945.4:c.6-7_20dup	p.Leu8ArgfsTer81	p.L8Rfs*81	ENST00000391945	NM_000400.3	7	ggg/ggCCGCCAGGCTCAACGTGGACGGg	2/23	0.405891671948795	1	FACETS	0.326	0.282	0.373	0.326	0.282	0.373	SUBCLONAL	1	TRUE	0	0.605141328135054	1		800	439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0057976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	289	681	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.497927350864659	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.497927350864659	1		681	869	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0057976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	174	328	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.264035850735074	1	FACETS	0.942	0.873	1	0.942	0.873	1	INDETERMINATE	1	TRUE	0	0.497927350864659	1		328	557	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0057976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	163	415	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	0.961	0.885	1	0.961	0.885	1	CLONAL	1	TRUE	1	0.497927350864659	2		415	681	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175481	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0057976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	61	299	0	ENST00000257430.4:c.4192_4193del	p.Arg1399PhefsTer9	p.R1399Ffs*9	ENST00000257430	NM_000038.5	1397	GAg/g	16/16	0.264035850735074	1	FACETS	0.412	0.356	0.472	0.412	0.356	0.472	INDETERMINATE	1	TRUE	0	0.497927350864659	1		299	447	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992720	68992720	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs182978151	NA	P-0057976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	204	552	0	ENST00000288368.4:c.1685G>A	p.Arg562His	p.R562H	ENST00000288368	NM_024870.2	562	cGt/cAt	16/40	1	2	FACETS	0.885	0.821	0.951	0.885	0.821	0.951	CLONAL	1	TRUE	1	0.497927350864659	2		552	926	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554397	141554397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	307	947	1	ENST00000220592.5:c.1754C>T	p.Pro585Leu	p.P585L	ENST00000220592	NM_012154.3	585	cCg/cTg	14/19	1	2	FACETS	0.876	0.825	0.93	0.876	0.825	0.93	CLONAL	1	TRUE	1	0.497927350864659	2		948	1407	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371820	45371820	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	151	296	0	ENST00000262160.6:c.1171G>A	p.Ala391Thr	p.A391T	ENST00000262160	NM_005901.5	391	Gct/Act	10/11	0.497927350864659	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.497927350864659	1		296	429	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518381	8518381	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	30	254	0	ENST00000356435.5:c.1010C>A	p.Thr337Lys	p.T337K	ENST00000356435		337	aCa/aAa	10/35	1	2	FACETS	0.268	0.216	0.328	0.268	0.216	0.328	SUBCLONAL	1	TRUE	1	0.497927350864659	2		254	449	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63829525	63829525	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	182	358	0	ENST00000279873.7:c.1168G>A	p.Ala390Thr	p.A390T	ENST00000279873	NM_032199.2	390	Gct/Act	8/10	0.641450883188903	3	FACETS	0.82	0.764	0.876	0.82	0.764	0.876	CLONAL	2	TRUE	1	0.641450883188903	3		358	457	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969821	81969821	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	209	515	0	ENST00000359376.3:c.2890G>T	p.Asp964Tyr	p.D964Y	ENST00000359376	NM_002661.3	964	Gac/Tac	27/33	0.597344377289371	3	FACETS	0.797	0.746	0.849	0.797	0.746	0.849	SUBCLONAL	2	TRUE	1	0.641450883188903	3		515	540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577526	7577527	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0057977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	478	741	0	ENST00000269305.4:c.754dup	p.Leu252ProfsTer12	p.L252Pfs*12	ENST00000269305	NM_001126112.2	252	ctc/cCtc	7/11	0.641450883188903	3	FACETS	0.887	0.858	0.915	0.887	0.858	0.915	CLONAL	3	TRUE	0	0.641450883188903	3		741	740	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753122	42753122	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1063897	NA	P-0057977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	125	996	2	ENST00000222329.4:c.1142C>T	p.Pro381Leu	p.P381L	ENST00000222329	NM_006494.2	381	cCg/cTg	4/4	0.137518599082459	3	FACETS	0.83	0.753	0.911	0.277	0.251	0.304	INDETERMINATE	1	TRUE	0	0.641450883188903	3		998	620	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436358	52436358	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	267	943	0	ENST00000460680.1:c.2136G>T	p.Gln712His	p.Q712H	ENST00000460680	NM_004656.3	712	caG/caT	17/17	0.530473238935727	2	FACETS	0.818	0.777	0.859	0.818	0.777	0.859	CLONAL	2	TRUE	0	0.641450883188903	2		943	509	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974799	21974799	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057977-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	204	275	1	ENST00000304494.5:c.28G>T	p.Glu10Ter	p.E10*	ENST00000304494	NM_000077.4	10	Gag/Tag	1/3	0.753804166304036	3	FACETS	0.99	0.953	1	0.99	0.953	1	CLONAL	3	TRUE	0	0.753804166304036	3		276	251	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0057977-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	834	770	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.730466542428324	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.753804166304036	3		770	1007	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422997	49422997	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369583907	NA	P-0057977-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	270	827	0	ENST00000301067.7:c.14098G>A	p.Asp4700Asn	p.D4700N	ENST00000301067	NM_003482.3	4700	Gat/Aat	44/54	0.753804166304036	3	FACETS	0.993	0.933	1	0.497	0.466	0.528	CLONAL	1	TRUE	1	0.753804166304036	3		827	993	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41228578	41228578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567779701	NA	P-0057977-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	529	645	0	ENST00000357654.3:c.4411G>A	p.Gly1471Ser	p.G1471S	ENST00000357654	NM_007294.3	1471	Ggc/Agc	13/23	0.744219864349253	3	FACETS	0.983	0.96	1	0.983	0.96	1	CLONAL	3	TRUE	0	0.753804166304036	3		645	655	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602412	10602412	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057977-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	874	897	0	ENST00000171111.5:c.1166A>C	p.Asp389Ala	p.D389A	ENST00000171111	NM_203500.1	389	gAc/gCc	3/6	0.744219864349253	3	FACETS	0.977	0.959	0.995	0.977	0.959	0.995	CLONAL	3	TRUE	0	0.753804166304036	3		897	1089	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278065	18278065	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057977-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	927	754	0	ENST00000222254.8:c.1685G>T	p.Ser562Ile	p.S562I	ENST00000222254	NM_005027.3	562	aGc/aTc	13/16	0.753804166304036	4	FACETS	0.928	0.905	0.951			1	CLONAL	3	TRUE	NA	0.753804166304036	4		754	1549	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803467	32803467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057977-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	568	727	3	ENST00000374899.4:c.692C>T	p.Ser231Phe	p.S231F	ENST00000374899	NM_018833.2	231	tCc/tTc	4/12	0.743407047052294	2	FACETS	0.994	0.969	1	0.994	0.969	1	CLONAL	2	TRUE	0	0.753804166304036	2		730	758	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	185	276	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.152653997513708	2	FACETS	1	0.976	1	1	0.976	1	INDETERMINATE	2	TRUE	0	0.297665800030998	2		276	558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0057978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	142	380	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.297665800030998	1	FACETS	0.796	0.725	0.872	0.796	0.725	0.872	SUBCLONAL	1	TRUE	0	0.297665800030998	1		380	1020	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030460	49030461	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0057978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	118	287	0	ENST00000267163.4:c.1939_1940del	p.Leu647PhefsTer5	p.L647Ffs*5	ENST00000267163	NM_000321.2	645	acCTct/acct	19/27	0.260969844007482	3	FACETS	1	0.961	1	0.737	0.67	0.806	CLONAL	2	TRUE	0	0.297665800030998	3		287	412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0057979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	409	681	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.717160989417412	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.716251681256933	1		681	568	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0057979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	93	257	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.281803243628607	4	FACETS	1	0.926	1	1	0.926	1	INDETERMINATE	2	TRUE	2	0.716251681256933	4		257	218	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166010	118166010	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767827215	NA	P-0057979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	27	305	0	ENST00000369448.3:c.520C>T	p.Arg174Trp	p.R174W	ENST00000369448	NM_017709.3	174	Cgg/Tgg	2/2	0.354205403366719	3	FACETS	0.21	0.166	0.26	0.105	0.083	0.13	INDETERMINATE	1	TRUE	1	0.716251681256933	3		305	488	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057773	27057774	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0057979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	526	898	0	ENST00000324856.7:c.1482_1483del	p.His495CysfsTer127	p.H495Cfs*127	ENST00000324856	NM_006015.4	494	cCT/c	3/20	0.354205403366719	3	FACETS	0.825	0.793	0.857	0.825	0.793	0.857	INDETERMINATE	2	TRUE	1	0.716251681256933	3		898	1209	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495446	56495472	+	inframe_deletion	In_Frame_Del	DEL	TAGGCCAAGTTCCCTTGAGGAGCTGGG	TAGGCCAAGTTCCCTTGAGGAGCTGGG	-	novel	NA	P-0057979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	137	776	0	ENST00000267101.3:c.3637_3663del	p.Arg1213_Gly1221del	p.R1213_G1221del	ENST00000267101	NM_001982.3	1212	ccTAGGCCAAGTTCCCTTGAGGAGCTGGGt/cct	28/28	1	2	FACETS	0.628	0.573	0.685	0.628	0.573	0.685	SUBCLONAL	1	TRUE	1	0.716251681256933	2		776	609	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0057983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	65	213	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	0.211270076472119	3	FACETS	0.997	0.878	1	0.665	0.585	0.748	INDETERMINATE	2	TRUE	0	0.365359169896238	3		213	211	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782061	66782062	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	18	234	0	ENST00000307102.5:c.1034dup	p.Asn345LysfsTer21	p.N345Kfs*21	ENST00000307102	NM_002755.3	343	ata/atAa	10/11	0.244274073162724	1	FACETS	0.326	0.246	0.421	0.326	0.246	0.421	SUBCLONAL	1	TRUE	0	0.365359169896238	1		234	247	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944279	206944279	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	32	456	0	ENST00000423557.1:c.351G>C	p.Lys117Asn	p.K117N	ENST00000423557	NM_000572.2	117	aaG/aaC	3/5	0.27498930692882	4	FACETS	0.505	0.409	0.613	0.252	0.204	0.307	SUBCLONAL	1	TRUE	2	0.365359169896238	4		456	474	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849417	68849417	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0057983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	43	464	0	ENST00000261769.5:c.1321-1G>T		p.X441_splice	ENST00000261769	NM_004360.3	441			1	2	FACETS	0.542	0.454	0.64	0.542	0.454	0.64	SUBCLONAL	1	TRUE	1	0.365359169896238	2		464	434	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455309	29455309	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	20	451	0	ENST00000389048.3:c.2493G>T	p.Lys831Asn	p.K831N	ENST00000389048	NM_004304.4	831	aaG/aaT	15/29	0.211270076472119	3	FACETS	0.349	0.266	0.446	0.116	0.088	0.149	INDETERMINATE	1	TRUE	0	0.365359169896238	3		451	371	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184065	56184065	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	19	248	1	ENST00000399503.3:c.4270C>A	p.Gln1424Lys	p.Q1424K	ENST00000399503	NM_005921.1	1424	Caa/Aaa	19/20	0.261949558695692	3	FACETS	0.406	0.308	0.521	0.135	0.102	0.174	SUBCLONAL	1	TRUE	0	0.365359169896238	3		249	303	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820544	44820544	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	14	395	0	ENST00000377967.4:c.241G>C	p.Glu81Gln	p.E81Q	ENST00000377967	NM_021140.2	81	Gaa/Caa	3/29	0.365359169896238	1	FACETS	0.238	0.172	0.319	0.238	0.172	0.319	SUBCLONAL	1	TRUE	0	0.365359169896238	1		395	263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	76	747	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	1	2	FACETS	0.76	0.667	0.861	0.76	0.667	0.861	SUBCLONAL	1	TRUE	1	0.307635346701987	2		747	650	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	144	718	5	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.307635346701987	2		723	817	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	73	366	3	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.929	0.814	1	0.929	0.814	1	CLONAL	1	TRUE	1	0.307635346701987	2		369	511	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501449	149501449	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	126	534	0	ENST00000261799.4:c.2338C>T	p.Pro780Ser	p.P780S	ENST00000261799	NM_002609.3	780	Ccc/Tcc	16/23	0.307635346701987	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.307635346701987	1		534	565	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	72	392	1	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.771	0.674	0.876	0.771	0.674	0.876	SUBCLONAL	1	TRUE	1	0.307635346701987	2		393	607	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251173	115251173	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374061873	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	21	322	0	ENST00000369535.4:c.553C>T	p.Pro185Ser	p.P185S	ENST00000369535	NM_002524.4	185	Cca/Tca	5/7	0.307635346701987	1	FACETS	0.344	0.264	0.437	0.344	0.264	0.437	SUBCLONAL	1	TRUE	0	0.307635346701987	1		322	336	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777792	3777792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200566758	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	108	939	0	ENST00000262367.5:c.7256C>T	p.Ala2419Val	p.A2419V	ENST00000262367	NM_004380.2	2419	gCg/gTg	31/31	0.307635346701987	1	FACETS	0.565	0.506	0.628	0.565	0.506	0.628	SUBCLONAL	1	TRUE	0	0.307635346701987	1		939	1051	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985380	60985380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178840163	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	60	583	1	ENST00000333681.4:c.520G>A	p.Ala174Thr	p.A174T	ENST00000333681		174	Gcc/Acc	2/3	1	2	FACETS	0.537	0.461	0.619	0.537	0.461	0.619	SUBCLONAL	1	TRUE	1	0.307635346701987	2		584	727	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468088	120468088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	176	579	0	ENST00000256646.2:c.4351G>A	p.Asp1451Asn	p.D1451N	ENST00000256646	NM_024408.3	1451	Gat/Aat	25/34	0.307635346701987	1	FACETS	0.753	0.696	0.811	1	0.99	1	SUBCLONAL	2	TRUE	0	0.307635346701987	1		579	643	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582133	52582133	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	61	269	0	ENST00000394830.3:c.4695G>C	p.Leu1565Phe	p.L1565F	ENST00000394830	NM_018313.4	1565	ttG/ttC	30/30	0.307635346701987	1	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	0	0.307635346701987	1		269	329	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553478	29553478	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781807	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	134	593	3	ENST00000356175.3:c.2033del	p.Pro678ArgfsTer10	p.P678Rfs*10	ENST00000356175	NM_000267.3	676	aCc/ac	18/57	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.307635346701987	2		596	701	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	30	356	3	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	0.307635346701987	1	FACETS	0.387	0.312	0.473	0.387	0.312	0.473	SUBCLONAL	1	TRUE	0	0.307635346701987	1		359	426	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	34	204	0	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	0.307635346701987	1	FACETS	0.447	0.365	0.54	0.447	0.365	0.54	SUBCLONAL	1	TRUE	0	0.307635346701987	1		204	418	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971138	21971138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760640852	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	138	370	0	ENST00000304494.5:c.220G>A	p.Asp74Asn	p.D74N	ENST00000304494	NM_000077.4	74	Gac/Aac	2/3	0.307635346701987	1	FACETS	0.756	0.692	0.822	1	0.988	1	SUBCLONAL	2	TRUE	0	0.307635346701987	1		370	502	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881680	111881680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1405228237	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	101	489	0	ENST00000393256.3:c.358C>T	p.Pro120Ser	p.P120S	ENST00000393256	NM_006538.4	120	Cct/Tct	2/4	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.307635346701987	2		489	586	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308348	15308348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555730189	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	100	777	0	ENST00000263388.2:c.160C>T	p.Arg54Cys	p.R54C	ENST00000263388	NM_000435.2	54	Cgt/Tgt	2/33	0.307635346701987	1	FACETS	0.609	0.543	0.68	0.609	0.543	0.68	SUBCLONAL	1	TRUE	0	0.307635346701987	1		777	903	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508176	106508176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752039271	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	78	265	0	ENST00000359195.3:c.170C>T	p.Ala57Val	p.A57V	ENST00000359195	NM_002649.2	57	gCg/gTg	2/11	0.16712536941324	2	FACETS	1	0.966	1	0.634	0.56	0.712	INDETERMINATE	1	TRUE	0	0.307635346701987	2		265	400	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164563	36164563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1340631548	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	125	543	0	ENST00000300305.3:c.1312G>A	p.Gly438Ser	p.G438S	ENST00000300305		438	Ggc/Agc	8/8	0.307635346701987	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.307635346701987	1		543	583	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537918	212537918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146197533	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	94	389	0	ENST00000342788.4:c.1687G>A	p.Glu563Lys	p.E563K	ENST00000342788	NM_005235.2	563	Gaa/Aaa	14/28	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.307635346701987	2		389	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579547	7579547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567557016	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	113	659	0	ENST00000269305.4:c.140del	p.Pro47ArgfsTer76	p.P47Rfs*76	ENST00000269305	NM_001126112.2	47	cCg/cg	4/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.307635346701987	2		659	667	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288468	15288468	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	136	308	0	ENST00000263388.2:c.4271C>T	p.Pro1424Leu	p.P1424L	ENST00000263388	NM_000435.2	1424	cCc/cTc	24/33	0.307635346701987	1	FACETS	0.895	0.821	0.971	1	0.99	1	CLONAL	2	TRUE	0	0.307635346701987	1		308	418	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293439	1293439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060503002	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	75	674	0	ENST00000310581.5:c.1562G>A	p.Arg521His	p.R521H	ENST00000310581	NM_198253.2	521	cGc/cAc	2/16	1	2	FACETS	0.592	0.518	0.673	0.592	0.518	0.673	SUBCLONAL	1	TRUE	1	0.307635346701987	2		674	823	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	64	606	3	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	0.16712536941324	2	FACETS	0.66	0.572	0.757	0.33	0.286	0.379	INDETERMINATE	1	TRUE	0	0.307635346701987	2		609	630	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156493	55156493	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	60	353	0	ENST00000257290.5:c.2894T>A	p.Ile965Asn	p.I965N	ENST00000257290	NM_006206.4	965	aTt/aAt	22/23	0.152640070885813	0	FACETS	0.64	0.553	0.734			1	INDETERMINATE	1	TRUE	0	0.307635346701987	0		353	422	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857869	9857869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	88	452	0	ENST00000330684.3:c.3532C>T	p.Leu1178Phe	p.L1178F	ENST00000330684	NM_001134407.1	1178	Ctt/Ttt	13/13	0.307635346701987	1	FACETS	0.875	0.777	0.98	0.875	0.777	0.98	CLONAL	1	TRUE	0	0.307635346701987	1		452	553	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856608	111856608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	48	171	0	ENST00000341259.2:c.659G>A	p.Gly220Glu	p.G220E	ENST00000341259	NM_005475.2	220	gGg/gAg	2/8	0.16712536941324	2	FACETS	0.984	0.836	1	0.492	0.418	0.573	INDETERMINATE	1	TRUE	0	0.307635346701987	2		171	317	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050272	128050272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145762413	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	95	446	0	ENST00000285398.2:c.385G>A	p.Val129Ile	p.V129I	ENST00000285398	NM_000122.1	129	Gtt/Att	3/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.307635346701987	2		446	523	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258764	16258764	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530603850	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	109	407	0	ENST00000375759.3:c.6029G>A	p.Arg2010His	p.R2010H	ENST00000375759	NM_015001.2	2010	cGt/cAt	11/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.307635346701987	2		407	558	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779755	3779755	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	56	630	2	ENST00000262367.5:c.5293del	p.Gln1765ArgfsTer6	p.Q1765Rfs*6	ENST00000262367	NM_004380.2	1765	Cag/ag	31/31	0.307635346701987	1	FACETS	0.465	0.397	0.538	0.465	0.397	0.538	SUBCLONAL	1	TRUE	0	0.307635346701987	1		632	663	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375316	15375316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200264318	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	166	590	3	ENST00000263377.2:c.1111G>A	p.Ala371Thr	p.A371T	ENST00000263377	NM_058243.2	371	Gcc/Acc	6/20	0.307635346701987	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.307635346701987	1		593	702	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630190	100630190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs128620185	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	32	406	0	ENST00000308731.7:c.83G>A	p.Arg28His	p.R28H	ENST00000308731	NM_000061.2	28	cGc/cAc	2/19	NA	2	FACETS	0.402	0.326	0.489			1	INDETERMINATE	1	TRUE	NA	0.307635346701987	2		406	517	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264849	46264849	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	62	299	0	ENST00000371998.3:c.1719T>G	p.Phe573Leu	p.F573L	ENST00000371998		573	ttT/ttG	12/23	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.307635346701987	2		299	357	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38954955	38954955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111974076	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	24	152	0	ENST00000357387.3:c.2618G>A	p.Arg873His	p.R873H	ENST00000357387	NM_152756.3	873	cGt/cAt	27/38	1	2	FACETS	0.912	0.721	1	0.912	0.721	1	CLONAL	1	TRUE	1	0.307635346701987	2		152	171	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813903	50813903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1363261645	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	83	509	0	ENST00000398568.2:c.1457G>A	p.Arg486His	p.R486H	ENST00000398568	NM_001042412.1	486	cGt/cAt	8/18	0.307635346701987	1	FACETS	0.85	0.752	0.955	0.85	0.752	0.955	CLONAL	1	TRUE	0	0.307635346701987	1		509	537	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65312411	65312413	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	44	381	0	ENST00000342505.4:c.1906_1908del	p.Phe636del	p.F636del	ENST00000342505	NM_002227.2	636	TTC/-	14/25	1	2	FACETS	0.489	0.409	0.577	0.489	0.409	0.577	SUBCLONAL	1	TRUE	1	0.307635346701987	2		381	585	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59924571	59924571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761432927	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	18	203	0	ENST00000259008.2:c.518G>A	p.Arg173His	p.R173H	ENST00000259008	NM_032043.2	173	cGt/cAt	6/20	0.307635346701987	1	FACETS	0.631	0.478	0.808	0.631	0.478	0.808	SUBCLONAL	1	TRUE	0	0.307635346701987	1		203	157	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225768	26225768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	51	434	0	ENST00000360408.1:c.386G>A	p.Arg129His	p.R129H	ENST00000360408	NM_003532.2	129	cGc/cAc	1/1	1	2	FACETS	0.472	0.4	0.551	0.472	0.4	0.551	SUBCLONAL	1	TRUE	1	0.307635346701987	2		434	702	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807847	3807847	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	65	326	0	ENST00000262367.5:c.3572C>A	p.Pro1191His	p.P1191H	ENST00000262367	NM_004380.2	1191	cCt/cAt	18/31	0.307635346701987	1	FACETS	0.843	0.734	0.961	0.843	0.734	0.961	CLONAL	1	TRUE	0	0.307635346701987	1		326	424	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300369	11300369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	75	333	0	ENST00000361445.4:c.1777G>A	p.Glu593Lys	p.E593K	ENST00000361445	NM_004958.3	593	Gaa/Aaa	11/58	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.307635346701987	2		333	478	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254767	16254767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777619234	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	42	408	0	ENST00000375759.3:c.2032C>T	p.Arg678Trp	p.R678W	ENST00000375759	NM_015001.2	678	Cgg/Tgg	11/15	1	2	FACETS	0.66	0.551	0.779	0.66	0.551	0.779	SUBCLONAL	1	TRUE	1	0.307635346701987	2		408	414	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262711	16262711	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1207710170	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	90	363	0	ENST00000375759.3:c.9976C>T	p.Pro3326Ser	p.P3326S	ENST00000375759	NM_015001.2	3326	Ccc/Tcc	11/15	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.307635346701987	2		363	538	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057850	27057850	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	171	661	0	ENST00000324856.7:c.1558C>A	p.Gln520Lys	p.Q520K	ENST00000324856	NM_006015.4	520	Cag/Aag	3/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.307635346701987	2		661	914	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795073	45795073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754364718	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	53	432	0	ENST00000450313.1:c.1555C>T	p.Arg519Trp	p.R519W	ENST00000450313	NM_012222.2	519	Cgg/Tgg	16/16	1	2	FACETS	0.503	0.428	0.585	0.503	0.428	0.585	SUBCLONAL	1	TRUE	1	0.307635346701987	2		432	685	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433888	78433888	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	23	221	0	ENST00000370768.2:c.212-1G>A		p.X71_splice	ENST00000370768	NM_003902.3	71			1	2	FACETS	0.665	0.52	0.83	0.665	0.52	0.83	SUBCLONAL	1	TRUE	1	0.307635346701987	2		221	225	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056760	102056760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1326770138	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	17	206	0	ENST00000282441.5:c.700G>A	p.Asp234Asn	p.D234N	ENST00000282441	NM_001130145.2	234	Gat/Aat	4/9	0.307635346701987	1	FACETS	0.678	0.51	0.873	0.678	0.51	0.873	SUBCLONAL	1	TRUE	0	0.307635346701987	1		206	138	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447881	49447882	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	119	474	0	ENST00000301067.7:c.552_553delinsTT	p.Arg185Cys	p.R185C	ENST00000301067	NM_003482.3	184	tgCCgc/tgTTgc	5/54	0.16712536941324	2	FACETS	1	0.98	1	0.658	0.595	0.723	INDETERMINATE	1	TRUE	0	0.307635346701987	2		474	588	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215715	133215715	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	35	298	0	ENST00000320574.5:c.5548C>A	p.Leu1850Met	p.L1850M	ENST00000320574	NM_006231.2	1850	Ctg/Atg	40/49	0.16712536941324	2	FACETS	0.523	0.429	0.629	0.262	0.214	0.315	INDETERMINATE	1	TRUE	0	0.307635346701987	2		298	435	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591725	38591726	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	24	335	0	ENST00000299084.4:c.184_185delinsAA	p.Gly62Lys	p.G62K	ENST00000299084	NM_152594.2	62	GGa/AAa	2/7	0.152640070885813	0	FACETS	0.258	0.202	0.323			1	INDETERMINATE	1	TRUE	0	0.307635346701987	0		335	419	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347056	89347056	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	58	578	0	ENST00000301030.4:c.5894del	p.Gly1965AlafsTer7	p.G1965Afs*7	ENST00000301030	NM_001256183.1	1965	gGc/gc	9/13	0.307635346701987	1	FACETS	0.541	0.464	0.624	0.541	0.464	0.624	SUBCLONAL	1	TRUE	0	0.307635346701987	1		578	590	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351826	89351826	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	43	716	0	ENST00000301030.4:c.1124C>G	p.Thr375Arg	p.T375R	ENST00000301030	NM_001256183.1	375	aCg/aGg	9/13	0.307635346701987	1	FACETS	0.407	0.34	0.482	0.407	0.34	0.482	SUBCLONAL	1	TRUE	0	0.307635346701987	1		716	581	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216313	2216313	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	63	722	0	ENST00000398665.3:c.1957C>T	p.Gln653Ter	p.Q653*	ENST00000398665	NM_032482.2	653	Cag/Tag	20/28	0.307635346701987	1	FACETS	0.457	0.394	0.525	0.457	0.394	0.525	SUBCLONAL	1	TRUE	0	0.307635346701987	1		722	759	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271598	15271598	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759021628	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	93	1016	0	ENST00000263388.2:c.6841G>A	p.Ala2281Thr	p.A2281T	ENST00000263388	NM_000435.2	2281	Gcc/Acc	33/33	0.307635346701987	1	FACETS	0.613	0.545	0.687	0.613	0.545	0.687	SUBCLONAL	1	TRUE	0	0.307635346701987	1		1016	834	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965987	18965988	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	138	669	1	ENST00000262803.5:c.1480_1481delinsTT	p.Pro494Leu	p.P494L	ENST00000262803	NM_002911.3	494	CCa/TTa	11/24	0.307635346701987	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.307635346701987	1		670	680	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872238	45872239	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	66	574	0	ENST00000391945.4:c.195_196delinsAA	p.Glu66Lys	p.E66K	ENST00000391945	NM_000400.3	65	ctGGag/ctAAag	4/23	0.307635346701987	1	FACETS	0.522	0.453	0.598	0.522	0.453	0.598	SUBCLONAL	1	TRUE	0	0.307635346701987	1		574	695	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139946	50139946	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	79	731	0	ENST00000246792.3:c.383G>T	p.Arg128Leu	p.R128L	ENST00000246792	NM_006270.3	128	cGg/cTg	4/6	0.307635346701987	1	FACETS	0.511	0.448	0.578	0.511	0.448	0.578	SUBCLONAL	1	TRUE	0	0.307635346701987	1		731	851	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455258	29455259	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	112	562	0	ENST00000389048.3:c.2543_2544delinsTT	p.Ala848Val	p.A848V	ENST00000389048	NM_004304.4	848	gCC/gTT	15/29	0.307635346701987	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	0	0.307635346701987	1		562	611	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659839	227659839	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	58	287	0	ENST00000305123.5:c.3616C>T	p.Pro1206Ser	p.P1206S	ENST00000305123	NM_005544.2	1206	Ccc/Tcc	1/2	0.307635346701987	1	FACETS	0.947	0.818	1	0.947	0.818	1	CLONAL	1	TRUE	0	0.307635346701987	1		287	337	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651272	45651272	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	139	531	0	ENST00000407780.3:c.753G>T	p.Glu251Asp	p.E251D	ENST00000407780	NM_001283052.1	251	gaG/gaT	5/7	0.307635346701987	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.307635346701987	1		531	657	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035113	37035114	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	175	374	0	ENST00000231790.2:c.75_76delinsTT	p.Gln26Ter	p.Q26*	ENST00000231790	NM_000249.3	25	atCCag/atTTag	1/19	0.307635346701987	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.307635346701987	1		374	852	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582123	52582123	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	62	265	0	ENST00000394830.3:c.4705G>A	p.Asp1569Asn	p.D1569N	ENST00000394830	NM_018313.4	1569	Gac/Aac	30/30	0.307635346701987	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.307635346701987	1		265	306	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149238691	149238691	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	71	453	0	ENST00000360632.3:c.1104C>A	p.Asn368Lys	p.N368K	ENST00000360632	NM_015472.4	368	aaC/aaA	7/7	1	2	FACETS	0.836	0.731	0.95	0.836	0.731	0.95	CLONAL	1	TRUE	1	0.307635346701987	2		453	552	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228372	228372	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878854635	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	160	385	0	ENST00000264932.6:c.694C>T	p.Arg232Cys	p.R232C	ENST00000264932	NM_004168.2	232	Cgt/Tgt	6/15	1	2	FACETS	0.934	0.861	1	1	0.992	1	CLONAL	2	TRUE	1	0.307635346701987	2		385	557	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449387	31449403	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CCTTTCTTCCGCATGTG	CCTTTCTTCCGCATGTG	-	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	21	289	0	ENST00000344624.3:c.2806_2821+1del		p.X936_splice	ENST00000344624		936		19/33	1	2	FACETS	0.506	0.39	0.64	0.506	0.39	0.64	SUBCLONAL	1	TRUE	1	0.307635346701987	2		289	270	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39003682	39003682	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	18	250	0	ENST00000357387.3:c.238C>T	p.His80Tyr	p.H80Y	ENST00000357387	NM_152756.3	80	Cac/Tac	4/38	1	2	FACETS	0.525	0.396	0.676	0.525	0.396	0.676	SUBCLONAL	1	TRUE	1	0.307635346701987	2		250	223	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755621	57755621	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	81	639	1	ENST00000274289.3:c.166C>A	p.Pro56Thr	p.P56T	ENST00000274289	NM_006622.3	56	Cct/Act	1/14	1	2	FACETS	0.8	0.705	0.902	0.8	0.705	0.902	CLONAL	1	TRUE	1	0.307635346701987	2		640	658	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858315	27858315	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	123	577	0	ENST00000359303.2:c.256C>T	p.Gln86Ter	p.Q86*	ENST00000359303	NM_003535.2	86	Cag/Tag	1/1	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.307635346701987	2		577	736	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672146	30672146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	147	609	0	ENST00000376406.3:c.4814C>T	p.Ser1605Phe	p.S1605F	ENST00000376406	NM_014641.2	1605	tCt/tTt	10/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.307635346701987	2		609	759	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508058	106508058	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	24	161	0	ENST00000359195.3:c.52C>T	p.Arg18Ter	p.R18*	ENST00000359195	NM_002649.2	18	Cga/Tga	2/11	0.16712536941324	2	FACETS	0.507	0.397	0.632	0.253	0.198	0.316	INDETERMINATE	1	TRUE	0	0.307635346701987	2		161	308	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151174465	151174465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	11	188	0	ENST00000262187.5:c.229G>A	p.Asp77Asn	p.D77N	ENST00000262187	NM_005614.3	77	Gat/Aat	4/8	0.16712536941324	2	FACETS	0.354	0.244	0.49	0.177	0.122	0.245	INDETERMINATE	1	TRUE	0	0.307635346701987	2		188	202	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272113	38272113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	55	593	0	ENST00000425967.3:c.2105C>T	p.Ala702Val	p.A702V	ENST00000425967	NM_001174067.1	702	gCa/gTa	16/19	1	2	FACETS	0.495	0.423	0.575	0.495	0.423	0.575	SUBCLONAL	1	TRUE	1	0.307635346701987	2		593	722	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864673	56864673	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	24	367	0	ENST00000519728.1:c.636A>T	p.Gln212His	p.Q212H	ENST00000519728	NM_002350.3	212	caA/caT	7/13	1	2	FACETS	0.474	0.372	0.592	0.474	0.372	0.592	SUBCLONAL	1	TRUE	1	0.307635346701987	2		367	329	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982053	70982053	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	142	724	0	ENST00000276594.2:c.43G>A	p.Val15Met	p.V15M	ENST00000276594	NM_024504.3	15	Gtg/Atg	2/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.307635346701987	2		724	703	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611851	100611851	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	97	515	0	ENST00000308731.7:c.1270C>T	p.Gln424Ter	p.Q424*	ENST00000308731	NM_000061.2	424	Cag/Tag	14/19	NA	2	FACETS	0.936	0.835	1			1	INDETERMINATE	1	TRUE	NA	0.307635346701987	2		515	674	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391933	139391937	+	frameshift_variant	Frame_Shift_Del	DEL	GTTGG	GTTGG	ATA	novel	NA	P-0057986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	330	969	0	ENST00000277541.6:c.6254_6258delinsTAT	p.Ala2085ValfsTer182	p.A2085Vfs*182	ENST00000277541	NM_017617.3	2085	gCCAAC/gTAT	34/34	0.307635346701987	1	FACETS	1	0.955	1	1	0.996	1	CLONAL	2	TRUE	0	0.307635346701987	1		969	901	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589618	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519838	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	91	202	0	ENST00000274335.5:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000274335		461	Cga/Tga	10/15	0.2528221364215	3	FACETS	1	0.92	1	0.688	0.617	0.763	CLONAL	2	TRUE	0	0.29	3		202	348	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557367	187557367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746932852	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	37	456	0	ENST00000441802.2:c.3995G>A	p.Arg1332His	p.R1332H	ENST00000441802	NM_005245.3	1332	cGc/cAc	6/27	1	2	FACETS	0.471	0.387	0.564	0.471	0.387	0.564	SUBCLONAL	1	TRUE	1	0.29	2		456	542	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	268	618	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.297405684049862	1	FACETS	0.84	0.789	0.892	1	0.994	1	CLONAL	2	TRUE	0	0.29	1		618	941	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	138	398	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.2528221364215	3	FACETS	1	0.963	1	0.729	0.668	0.793	CLONAL	2	TRUE	0	0.29	3		398	498	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900288	101900288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111854391	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	47	374	1	ENST00000374994.4:c.722C>T	p.Ser241Leu	p.S241L	ENST00000374994	NM_004612.2	241	tCg/tTg	4/9	0.297405684049862	2	FACETS	0.61	0.515	0.716	0.305	0.257	0.358	SUBCLONAL	1	TRUE	0	0.29	2		375	531	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068357	26068357	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	181	347	0	ENST00000435504.4:c.133G>T	p.Glu45Ter	p.E45*	ENST00000435504		45	Gaa/Taa	2/13	1	2	FACETS	1	0.978	1	1	0.994	1	CLONAL	2	TRUE	1	0.29	2		347	551	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118502	17118502	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs879255678	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	63	849	0	ENST00000285071.4:c.1429C>T	p.Arg477Ter	p.R477*	ENST00000285071	NM_144997.5	477	Cga/Tga	12/14	0.297405684049862	1	FACETS	0.504	0.435	0.579	0.504	0.435	0.579	SUBCLONAL	1	TRUE	0	0.29	1		849	737	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374245	138374245	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	62	449	0	ENST00000289153.2:c.3199G>T	p.Asp1067Tyr	p.D1067Y	ENST00000289153	NM_006219.2	1067	Gac/Tac	22/22	0.252600629635874	2	FACETS	0.669	0.578	0.769	0.335	0.289	0.385	SUBCLONAL	1	TRUE	0	0.29	2		449	639	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029218	14029218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41557814	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	25	247	0	ENST00000311895.7:c.1429C>T	p.Arg477Trp	p.R477W	ENST00000311895	NM_005236.2	477	Cgg/Tgg	8/11	1	2	FACETS	0.454	0.357	0.565	0.454	0.357	0.565	SUBCLONAL	1	TRUE	1	0.29	2		247	380	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624245	89624245	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554890335	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	64	216	1	ENST00000371953.3:c.19G>T	p.Glu7Ter	p.E7*	ENST00000371953	NM_000314.4	7	Gag/Tag	1/9	0.265588387423359	2	FACETS	1	0.971	1	0.721	0.629	0.819	CLONAL	1	TRUE	0	0.29	2		217	306	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984773	11984773	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	58	319	0	ENST00000353533.5:c.319G>T	p.Glu107Ter	p.E107*	ENST00000353533	NM_003010.3	107	Gaa/Taa	3/11	0.297405684049862	1	FACETS	0.893	0.77	1	0.893	0.77	1	CLONAL	1	TRUE	0	0.29	1		319	383	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251236	115251236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	36	408	0	ENST00000369535.4:c.490C>T	p.Arg164Cys	p.R164C	ENST00000369535	NM_002524.4	164	Cgc/Tgc	5/7	1	2	FACETS	0.386	0.316	0.465	0.386	0.316	0.465	SUBCLONAL	1	TRUE	1	0.29	2		408	643	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432651	49432651	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs727503983	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	101	1068	0	ENST00000301067.7:c.8488C>T	p.Arg2830Ter	p.R2830*	ENST00000301067	NM_003482.3	2830	Cga/Tga	34/54	1	2	FACETS	0.604	0.538	0.674	0.604	0.538	0.674	SUBCLONAL	1	TRUE	1	0.29	2		1068	1154	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045136	47045136	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	245	832	1	ENST00000377604.3:c.2377C>T	p.Arg793Ter	p.R793*	ENST00000377604	NM_001204468.1	793	Cga/Tga	21/24	0.145484417056633	3	FACETS	1	0.966	1	1	0.966	1	INDETERMINATE	2	TRUE	1	0.29	3		833	922	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135384	30135384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373748041	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	42	369	0	ENST00000331968.5:c.434G>A	p.Arg145His	p.R145H	ENST00000331968	NM_002742.2	145	cGt/cAt	3/18	1	2	FACETS	0.631	0.527	0.746	0.631	0.527	0.746	SUBCLONAL	1	TRUE	1	0.29	2		369	459	SUCCESS
BLM	641	MSKCC	GRCh37	15	91333930	91333930	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs762354041	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	44	502	0	ENST00000355112.3:c.2875C>T	p.Arg959Ter	p.R959*	ENST00000355112	NM_000057.2	959	Cga/Tga	15/22	0.265588387423359	2	FACETS	0.452	0.378	0.534	0.226	0.189	0.267	SUBCLONAL	1	TRUE	0	0.29	2		502	672	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100975	41100975	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	87	714	2	ENST00000373198.4:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000373198	NM_133170.3	461	Cga/Tga	8/32	0.197784850120111	3	FACETS	0.74	0.653	0.832	0.37	0.326	0.416	SUBCLONAL	1	TRUE	1	0.29	3		716	929	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028086	69028086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774652439	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	69	554	0	ENST00000288368.4:c.3245G>A	p.Ser1082Asn	p.S1082N	ENST00000288368	NM_024870.2	1082	aGc/aAc	26/40	0.252600629635874	2	FACETS	0.901	0.786	1	0.451	0.393	0.513	CLONAL	1	TRUE	0	0.29	2		554	528	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155429	106155429	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	54	408	0	ENST00000380013.4:c.330G>T	p.Lys110Asn	p.K110N	ENST00000380013	NM_001127208.2	110	aaG/aaT	3/11	1	2	FACETS	0.774	0.662	0.897	0.774	0.662	0.897	SUBCLONAL	1	TRUE	1	0.29	2		408	481	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953023	2953023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754645078	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1215	68	1035	3	ENST00000396946.4:c.2917C>T	p.Arg973Cys	p.R973C	ENST00000396946	NM_032415.4	973	Cgc/Tgc	22/25	0.197784850120111	3	FACETS	0.419	0.362	0.48	0.209	0.181	0.24	SUBCLONAL	1	TRUE	1	0.29	3		1038	1283	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32438039	32438039	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	47	684	0	ENST00000332351.3:c.998G>T	p.Ser333Ile	p.S333I	ENST00000332351	NM_024426.4	333	aGc/aTc	5/10	0.270968970331366	3	FACETS	0.395	0.332	0.465	0.197	0.166	0.233	SUBCLONAL	1	TRUE	1	0.29	3		684	940	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427558	427558	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	68	443	0	ENST00000399788.2:c.2611T>G	p.Ser871Ala	p.S871A	ENST00000399788	NM_001042603.1	871	Tct/Gct	19/28	1	2	FACETS	0.807	0.703	0.92	0.807	0.703	0.92	CLONAL	1	TRUE	1	0.29	2		443	581	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779616	3779616	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	67	1153	0	ENST00000262367.5:c.5432A>G	p.Lys1811Arg	p.K1811R	ENST00000262367	NM_004380.2	1811	aAg/aGg	31/31	1	2	FACETS	0.398	0.344	0.457	0.398	0.344	0.457	SUBCLONAL	1	TRUE	1	0.29	2		1153	1161	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303250	15303250	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	110	1306	0	ENST00000263388.2:c.278G>T	p.Cys93Phe	p.C93F	ENST00000263388	NM_000435.2	93	tGc/tTc	3/33	1	2	FACETS	0.653	0.585	0.726	0.653	0.585	0.726	SUBCLONAL	1	TRUE	1	0.29	2		1306	1161	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271883	18271901	+	frameshift_variant	Frame_Shift_Del	DEL	GGATCAGTGGGACACGGCA	GGATCAGTGGGACACGGCA	-	novel	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	60	861	0	ENST00000222254.8:c.487_505del	p.Asp163ProfsTer18	p.D163Pfs*18	ENST00000222254	NM_005027.3	162	gtGGATCAGTGGGACACGGCA/gt	5/16	1	2	FACETS	0.415	0.356	0.479	0.415	0.356	0.479	SUBCLONAL	1	TRUE	1	0.29	2		861	998	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223203	36223203	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1269	97	1445	0	ENST00000222270.7:c.5753C>G	p.Pro1918Arg	p.P1918R	ENST00000222270	NM_014727.1	1918	cCt/cGt	28/37	1	2	FACETS	0.49	0.435	0.549	0.49	0.435	0.549	SUBCLONAL	1	TRUE	1	0.29	2		1445	1366	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660774	227660774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770995196	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	52	919	0	ENST00000305123.5:c.2681G>A	p.Gly894Glu	p.G894E	ENST00000305123	NM_005544.2	894	gGg/gAg	1/2	1	2	FACETS	0.394	0.334	0.46	0.394	0.334	0.46	SUBCLONAL	1	TRUE	1	0.29	2		919	911	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62322296	62322296	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	219	1152	0	ENST00000360203.5:c.2552A>C	p.Glu851Ala	p.E851A	ENST00000360203	NM_001283009.1	851	gAg/gCg	27/35	0.197784850120111	3	FACETS	1	0.986	1	0.624	0.579	0.671	CLONAL	1	TRUE	1	0.29	3		1152	1386	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151543	55151543	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	28	348	0	ENST00000257290.5:c.2329G>T	p.Glu777Ter	p.E777*	ENST00000257290	NM_006206.4	777	Gaa/Taa	17/23	1	2	FACETS	0.376	0.299	0.463	0.376	0.299	0.463	SUBCLONAL	1	TRUE	1	0.29	2		348	514	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753163	57753163	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	26	320	0	ENST00000274289.3:c.853C>A	p.Leu285Ile	p.L285I	ENST00000274289	NM_006622.3	285	Ctc/Atc	7/14	0.2528221364215	3	FACETS	0.475	0.376	0.59	0.158	0.125	0.197	SUBCLONAL	1	TRUE	0	0.29	3		320	432	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157192772	157192772	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs201653711	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	31	431	0	ENST00000346085.5:c.1762G>T	p.Glu588Ter	p.E588*	ENST00000346085	NM_020732.3	588	Gaa/Taa	3/20	1	2	FACETS	0.383	0.309	0.467	0.383	0.309	0.467	SUBCLONAL	1	TRUE	1	0.29	2		431	558	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157495141	157495141	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	67	355	0	ENST00000346085.5:c.3026-1G>T		p.X1009_splice	ENST00000346085	NM_020732.3	1009			1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.29	2		355	426	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934007	39934007	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	60	777	0	ENST00000378444.4:c.592G>C	p.Gly198Arg	p.G198R	ENST00000378444	NM_001123385.1	198	Ggt/Cgt	4/15	0.145484417056633	3	FACETS	0.44	0.377	0.508	0.22	0.188	0.254	INDETERMINATE	1	TRUE	1	0.29	3		777	1077	SUCCESS
AR	367	MSKCC	GRCh37	X	66942696	66942696	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	40	375	0	ENST00000374690.3:c.2477A>C	p.Lys826Thr	p.K826T	ENST00000374690	NM_000044.3	826	aAa/aCa	7/8	0.145484417056633	3	FACETS	0.529	0.439	0.63	0.265	0.219	0.315	INDETERMINATE	1	TRUE	1	0.29	3		375	597	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0058006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	85	553	0	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	1	2	FACETS	0.945	0.836	1	0.945	0.836	1	CLONAL	1	TRUE	1	0.283392731007846	2		553	635	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	154	882	1	ENST00000269305.4:c.476C>A	p.Ala159Asp	p.A159D	ENST00000269305	NM_001126112.2	159	gCc/gAc	5/11	0.283392731007846	1	FACETS	0.717	0.654	0.783	0.717	0.654	0.783	SUBCLONAL	1	TRUE	0	0.283392731007846	1		883	1301	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111494	8111495	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTGGAGG	novel	NA	P-0058006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	96	674	0	ENST00000346208.3:c.981_987dup	p.Arg330LeufsTer24	p.R330Lfs*24	ENST00000346208		327	ctc/ctCTGGAGGc	5/6	1	2	FACETS	0.686	0.61	0.768	0.686	0.61	0.768	SUBCLONAL	1	TRUE	1	0.283392731007846	2		674	987	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818420	43818420	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	80	575	1	ENST00000372470.3:c.1885C>A	p.Leu629Ile	p.L629I	ENST00000372470	NM_005373.2	629	Cta/Ata	12/12	1	2	FACETS	0.655	0.575	0.741	0.655	0.575	0.741	SUBCLONAL	1	TRUE	1	0.283392731007846	2		576	862	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999099	100999099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	117	841	0	ENST00000325455.5:c.703C>T	p.Pro235Ser	p.P235S	ENST00000325455	NM_001202474.3	235	Ccg/Tcg	1/8	1	2	FACETS	0.91	0.82	1	0.91	0.82	1	CLONAL	1	TRUE	1	0.283392731007846	2		841	907	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104619	69104619	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	167	676	0	ENST00000288368.4:c.4463C>G	p.Ser1488Trp	p.S1488W	ENST00000288368	NM_024870.2	1488	tCg/tGg	37/40	1	2	FACETS	0.985	0.904	1	0.985	0.904	1	CLONAL	1	TRUE	1	0.283392731007846	2		676	1196	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0058006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	80	553	0	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.351687801687344	2		553	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	168	882	1	ENST00000269305.4:c.476C>A	p.Ala159Asp	p.A159D	ENST00000269305	NM_001126112.2	159	gCc/gAc	5/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.351687801687344	2		883	844	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111494	8111495	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTGGAGG	novel	NA	P-0058006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	106	674	0	ENST00000346208.3:c.981_987dup	p.Arg330LeufsTer24	p.R330Lfs*24	ENST00000346208		327	ctc/ctCTGGAGGc	5/6	1	2	FACETS	0.923	0.829	1	0.923	0.829	1	CLONAL	1	TRUE	1	0.351687801687344	2		674	653	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818420	43818420	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	98	575	1	ENST00000372470.3:c.1885C>A	p.Leu629Ile	p.L629I	ENST00000372470	NM_005373.2	629	Cta/Ata	12/12	1	2	FACETS	0.905	0.808	1	0.905	0.808	1	CLONAL	1	TRUE	1	0.351687801687344	2		576	616	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999099	100999099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	77	841	0	ENST00000325455.5:c.703C>T	p.Pro235Ser	p.P235S	ENST00000325455	NM_001202474.3	235	Ccg/Tcg	1/8	1	2	FACETS	0.839	0.738	0.947	0.839	0.738	0.947	CLONAL	1	TRUE	1	0.351687801687344	2		841	522	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104619	69104619	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	143	676	0	ENST00000288368.4:c.4463C>G	p.Ser1488Trp	p.S1488W	ENST00000288368	NM_024870.2	1488	tCg/tGg	37/40	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.351687801687344	2		676	675	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0058034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	270	634	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.602670496813138	3	FACETS	1	0.991	1	0.646	0.608	0.684	CLONAL	1	TRUE	1	0.703084229997043	3		634	804	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223338	36223338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146177906	NA	P-0058034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	415	1418	2	ENST00000222270.7:c.5888C>T	p.Pro1963Leu	p.P1963L	ENST00000222270	NM_014727.1	1963	cCg/cTg	28/37	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.703084229997043	2		1420	1177	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348181	70348181	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	257	753	0	ENST00000374080.3:c.3245C>A	p.Thr1082Asn	p.T1082N	ENST00000374080		1082	aCc/aAc	23/45	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.703084229997043	2		753	726	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0058043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	181	276	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.297369235715977	3	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.3	3		276	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577513	7577517	+	frameshift_variant	Frame_Shift_Del	DEL	TGTGA	TGTGA	-	novel	NA	P-0058043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	109	648	0	ENST00000269305.4:c.764_768del	p.Ile255ThrfsTer7	p.I255Tfs*7	ENST00000269305	NM_001126112.2	255	aTCACA/a	7/11	1	2	FACETS	0.857	0.769	0.95	0.857	0.769	0.95	CLONAL	1	TRUE	1	0.3	2		648	848	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575101	48575101	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	62	282	0	ENST00000342988.3:c.295T>G	p.Trp99Gly	p.W99G	ENST00000342988	NM_005359.5	99	Tgg/Ggg	3/12	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.3	2		282	376	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	70	306	0				ENST00000310581	NM_198253.2	-/1132			0.311849870616522	3	FACETS	1	0.927	1	0.543	0.475	0.616	CLONAL	1	TRUE	1	0.34347492717152	3		306	440	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112250	115112250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1345506334	NA	P-0058045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	59	372	0	ENST00000257566.3:c.1490C>T	p.Pro497Leu	p.P497L	ENST00000257566	NM_016569.3	497	cCc/cTc	7/8	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.34347492717152	2		372	332	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056277	27056277	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	77	588	0	ENST00000324856.7:c.1273C>T	p.Gln425Ter	p.Q425*	ENST00000324856	NM_006015.4	425	Cag/Tag	2/20	0.192754252462482	4	FACETS	1	0.93	1	0.361	0.317	0.408	INDETERMINATE	1	TRUE	1	0.34347492717152	4		588	556	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916948	178916950	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0058045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	52	328	0	ENST00000263967.3:c.337_339del	p.Leu113del	p.L113del	ENST00000263967	NM_006218.2	112	aTCCtc/atc	2/21	0.137423779441121	4	FACETS	1	0.945	1	0.788	0.683	0.899	INDETERMINATE	2	TRUE	1	0.34347492717152	4		328	172	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939033	48939033	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1131690901	NA	P-0058045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	33	201	0	ENST00000267163.4:c.869del	p.Asn290MetfsTer11	p.N290Mfs*11	ENST00000267163	NM_000321.2	289	Aaa/aa	9/27	0.28386771076878	4	FACETS	1	0.83	1	1	0.83	1	CLONAL	2	TRUE	2	0.34347492717152	4		201	129	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050845	49050846	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0058045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	46	218	0	ENST00000267163.4:c.2531dup	p.Phe845ValfsTer10	p.F845Vfs*10	ENST00000267163	NM_000321.2	843	-/A	25/27	0.28386771076878	4	FACETS	1	0.877	1	1	0.877	1	CLONAL	2	TRUE	2	0.34347492717152	4		218	175	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023513	27023519	+	frameshift_variant	Frame_Shift_Del	DEL	TTCCCCA	TTCCCCA	-	novel	NA	P-0058045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	254	657	1	ENST00000324856.7:c.619_625del	p.Phe207ThrfsTer23	p.F207Tfs*23	ENST00000324856	NM_006015.4	207	TTCCCCAac/ac	1/20	0.192754252462482	4	FACETS	1	0.988	1	0.803	0.754	0.853	INDETERMINATE	2	TRUE	1	0.34347492717152	4		658	825	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202617	108202617	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	67	247	0	ENST00000278616.4:c.7642del	p.Ile2548PhefsTer16	p.I2548Ffs*16	ENST00000278616	NM_000051.3	2547	agA/ag	52/63	0.34347492717152	3	FACETS	0.937	0.845	1	1	0.972	1	CLONAL	4	TRUE	0	0.34347492717152	3		247	122	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857669	9857669	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	222	420	0	ENST00000330684.3:c.3732C>G	p.Asn1244Lys	p.N1244K	ENST00000330684	NM_001134407.1	1244	aaC/aaG	13/13	0.34347492717152	8	FACETS	1	0.967	1	0.744	0.7	0.789	CLONAL	5	TRUE	1	0.34347492717152	8		420	504	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40855796	40855796	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	154	494	0	ENST00000428826.2:c.2060T>G	p.Phe687Cys	p.F687C	ENST00000428826		687	tTt/tGt	19/21	0.311849870616522	3	FACETS	0.907	0.841	0.975	1	0.988	1	CLONAL	3	TRUE	1	0.34347492717152	3		494	386	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735538	204735538	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	48	475	0	ENST00000302823.3:c.339C>A	p.Asn113Lys	p.N113K	ENST00000302823	NM_005214.4	113	aaC/aaA	2/4	0.311849870616522	3	FACETS	0.885	0.751	1	0.443	0.375	0.516	CLONAL	1	TRUE	1	0.34347492717152	3		475	370	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091822	29091822	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	52	460	0	ENST00000328354.6:c.1135T>G	p.Ser379Ala	p.S379A	ENST00000328354	NM_007194.3	379	Tct/Gct	11/15	0.34347492717152	4	FACETS	1	0.965	1	0.488	0.418	0.563	CLONAL	1	TRUE	1	0.34347492717152	4		460	278	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513247	41513263	+	frameshift_variant	Frame_Shift_Del	DEL	ACAGAATTGGGACTAAC	ACAGAATTGGGACTAAC	-	novel	NA	P-0058045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	51	463	1	ENST00000263253.7:c.151_167del	p.Thr51GlnfsTer4	p.T51Qfs*4	ENST00000263253	NM_001429.3	51	ACAGAATTGGGACTAACc/c	2/31	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.34347492717152	2		464	229	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0058046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	245	584	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.810575936500655	3	FACETS	0.968	0.906	1	0.484	0.453	0.516	CLONAL	1	TRUE	1	0.810575936500655	3		584	878	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466022	69466022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	1469	1236	0	ENST00000227507.2:c.860C>T	p.Pro287Leu	p.P287L	ENST00000227507	NM_053056.2	287	cCc/cTc	5/5	0.8101647485756	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.810575936500655	3		1236	1691	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0058046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	460	893	1	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.810575936500655	2		894	1135	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098966	178098966	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	158	324	1	ENST00000397062.3:c.79G>T	p.Asp27Tyr	p.D27Y	ENST00000397062	NM_006164.4	27	Gat/Tat	2/5	1	2	FACETS	0.98	0.908	1	0.98	0.908	1	CLONAL	1	TRUE	1	0.810575936500655	2		325	398	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106031	27106032	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	288	612	0	ENST00000324856.7:c.5643dup	p.Val1882CysfsTer19	p.V1882Cfs*19	ENST00000324856	NM_006015.4	1881	cat/caTt	20/20	1	2	FACETS	0.955	0.903	1	0.955	0.903	1	CLONAL	1	TRUE	1	0.810575936500655	2		612	744	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425796	49425814	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTGCCGCTGCATGAGGA	AGCTGCCGCTGCATGAGGA	-	novel	NA	P-0058046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	371	1037	0	ENST00000301067.7:c.12674_12692del	p.Leu4225ArgfsTer47	p.L4225Rfs*47	ENST00000301067	NM_003482.3	4225	cTCCTCATGCAGCGGCAGCTg/cg	39/54	1	2	FACETS	0.983	0.936	1	0.983	0.936	1	CLONAL	1	TRUE	1	0.810575936500655	2		1037	931	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576848	7576877	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTACCTGAAGGGTGAAATATTCTCCATCC	AGTACCTGAAGGGTGAAATATTCTCCATCC	-	novel	NA	P-0058046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	237	734	0	ENST00000269305.4:c.969_993+5del		p.X323_splice	ENST00000269305	NM_001126112.2	323		9/11	1	2	FACETS	0.752	0.704	0.801	0.752	0.704	0.801	SUBCLONAL	1	TRUE	1	0.810575936500655	2		734	778	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0058047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	22	90	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.866246130330662	5	FACETS	0.277	0.214	0.351	0.092	0.071	0.117	SUBCLONAL	1	TRUE	2	0.866246130330662	5		90	421	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595519	55595519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913516	NA	P-0058047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	89	100	0	ENST00000288135.5:c.2009C>T	p.Thr670Ile	p.T670I	ENST00000288135	NM_000222.2	670	aCa/aTa	14/21	0.296778674967952	3	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.866246130330662	3		100	207	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447085	49447086	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0058047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	115	131	0	ENST00000301067.7:c.858dup	p.Lys287Ter	p.K287*	ENST00000301067	NM_003482.3	286	-/T	7/54	0.866246130330662	3	FACETS	1	0.915	1	0.503	0.458	0.551	CLONAL	1	TRUE	1	0.866246130330662	3		131	378	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593608	55593610	+	inframe_deletion	In_Frame_Del	DEL	GGT	GGT	-	novel	NA	P-0058047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	174	113	0	ENST00000288135.5:c.1674_1676del	p.Lys558_Val559delinsAsn	p.K558_V559delinsN	ENST00000288135	NM_000222.2	558	aaGGTt/aat	11/21	0.296778674967952	3	FACETS	0.853	0.815	0.888			1	INDETERMINATE	3	TRUE	NA	0.866246130330662	3		113	225	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0058048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	115	284	2	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.132442822675944	4	FACETS	1	0.934	1	0.69	0.627	0.756	INDETERMINATE	2	TRUE	1	0.381932274929826	4		286	402	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0058048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	167	839	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.381932274929826	2		839	817	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0058048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	168	544	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.381932274929826	1	FACETS	0.954	0.879	1	0.954	0.879	1	CLONAL	1	TRUE	0	0.381932274929826	1		544	746	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430613	78430613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs953338703	NA	P-0058048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	96	420	0	ENST00000370768.2:c.677C>T	p.Pro226Leu	p.P226L	ENST00000370768	NM_003902.3	226	cCg/cTg	9/20	1	2	FACETS	0.827	0.738	0.921	0.827	0.738	0.921	CLONAL	1	TRUE	1	0.381932274929826	2		420	608	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36163486	36164467	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	GGATAACCAAGCGATCACATTACTCATTCTTTTTTTCTAGCCTTCTTCAATGTGATACATTTAACTTTGGCTACTATCAAGAACAAAAGAAAATGTAGTACTTGATATTTTTCTTAATATAAGTACATTTAAATAATTAAAAAATTATCAACACATAAATGTCTGAACATCAAGATACATAAATATCTGGGGATTCCTTGTGGGAATACAGTAGTTAAAAATGACCCAAAGCTGTAGCTGTTTCTCAAAAAAACAAAACAAAACAAAAAAAAACAACTACCCAAAAGTCCAAAAGAAAAGTTAAATAAAACTTAAAGAAAAGGGAATCATATTTCTTTCCATGGTCAAAGCAAGAAAGAAGCAAGCTCAATTTATATATATTTATATAAACGTATATAAAAATAAAAACCACCCAAATGCAAATACGCATTTTGCAATTGATAAGGTGCGGAAAAATTAAAAATAAGAATTAGATGCCAAACAGGGCGAGTTGCATCCCTCCTCTCCCCCCACCCCAACCAAAATTCCACACTCTTTGGAATAAACAACTTGGTTAAAAAGTTAAGTCAAGGGTATAAAATCTTTCTTTTTATTCACAGCATTGCTAAATCAGAAGCATTCACAGTTTCCCTCCGGGAATCTTCCTGTTTGCTTTCCAGCGCGTCCCCTGGGTGCTGGGGCCGGCGGACACCCTCGAGGTGCGTCGCCTCGGACACCTCCGCGAGGGCCGGGGCGCCAGCAGACGGCGGCGGCGTGGGCTTCTGGGCGCAGGAGGCTGCGCGGGCCTGACCTACAGCGAGATCCTGGCCGTCGGGCGCCCTCGGCCCCAGGACGGTGGCCGGGCCCAGGGCCCGGGATCCCGGCGGGCTTGTCGCGAACAGGAGGCCCGCGCGCCCGGAGGCGAAGGCGGCGGCCCGCGGGGCCCAGCCGGGCCAGGCCTGGCGCCTCAGTAGGGCCTCCACACGGCCTCCTCCAGGCGCGC	GGATAACCAAGCGATCACATTACTCATTCTTTTTTTCTAGCCTTCTTCAATGTGATACATTTAACTTTGGCTACTATCAAGAACAAAAGAAAATGTAGTACTTGATATTTTTCTTAATATAAGTACATTTAAATAATTAAAAAATTATCAACACATAAATGTCTGAACATCAAGATACATAAATATCTGGGGATTCCTTGTGGGAATACAGTAGTTAAAAATGACCCAAAGCTGTAGCTGTTTCTCAAAAAAACAAAACAAAACAAAAAAAAACAACTACCCAAAAGTCCAAAAGAAAAGTTAAATAAAACTTAAAGAAAAGGGAATCATATTTCTTTCCATGGTCAAAGCAAGAAAGAAGCAAGCTCAATTTATATATATTTATATAAACGTATATAAAAATAAAAACCACCCAAATGCAAATACGCATTTTGCAATTGATAAGGTGCGGAAAAATTAAAAATAAGAATTAGATGCCAAACAGGGCGAGTTGCATCCCTCCTCTCCCCCCACCCCAACCAAAATTCCACACTCTTTGGAATAAACAACTTGGTTAAAAAGTTAAGTCAAGGGTATAAAATCTTTCTTTTTATTCACAGCATTGCTAAATCAGAAGCATTCACAGTTTCCCTCCGGGAATCTTCCTGTTTGCTTTCCAGCGCGTCCCCTGGGTGCTGGGGCCGGCGGACACCCTCGAGGTGCGTCGCCTCGGACACCTCCGCGAGGGCCGGGGCGCCAGCAGACGGCGGCGGCGTGGGCTTCTGGGCGCAGGAGGCTGCGCGGGCCTGACCTACAGCGAGATCCTGGCCGTCGGGCGCCCTCGGCCCCAGGACGGTGGCCGGGCCCAGGGCCCGGGATCCCGGCGGGCTTGTCGCGAACAGGAGGCCCGCGCGCCCGGAGGCGAAGGCGGCGGCCCGCGGGGCCCAGCCGGGCCAGGCCTGGCGCCTCAGTAGGGCCTCCACACGGCCTCCTCCAGGCGCGC	-	novel	NA	P-0058048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1	154	0	0	ENST00000300305.3:c.1408_*946del		p.*470*	ENST00000300305		470		8/8	0.381932274929826	1	FACETS	1	0.994	1	1	0.995	1	CLONAL	4	TRUE	0	0.381932274929826	1		0	155	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0058049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	43	432	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.813	0.68	0.959	0.813	0.68	0.959	CLONAL	1	TRUE	1	0.219128690123825	2		432	483	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0058049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	132	590	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.219128690123825	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	0	0.219128690123825	2		590	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577115	7577115	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	120	729	0	ENST00000269305.4:c.823T>G	p.Cys275Gly	p.C275G	ENST00000269305	NM_001126112.2	275	Tgt/Ggt	8/11	0.219128690123825	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.219128690123825	1		729	804	SUCCESS
APC	324	MSKCC	GRCh37	5	112175944	112175945	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0058049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	24	164	0	ENST00000257430.4:c.4655_4656del	p.Glu1552GlyfsTer6	p.E1552Gfs*6	ENST00000257430	NM_000038.5	1551	aaAGag/aaag	16/16	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.219128690123825	2		164	194	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374480	118374480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	30	419	0	ENST00000534358.1:c.7873C>T	p.Arg2625Cys	p.R2625C	ENST00000534358	NM_005933.3	2625	Cgt/Tgt	27/36	0.219128690123825	2	FACETS	0.466	0.375	0.571	0.233	0.187	0.286	SUBCLONAL	1	TRUE	0	0.219128690123825	2		419	587	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753078	42753078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs567417863	NA	P-0058049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	98	1018	0	ENST00000222329.4:c.1186G>A	p.Val396Ile	p.V396I	ENST00000222329	NM_006494.2	396	Gta/Ata	4/4	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.219128690123825	2		1018	812	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249504	153249504	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	62	382	0	ENST00000281708.4:c.1274G>T	p.Trp425Leu	p.W425L	ENST00000281708	NM_033632.3	425	tGg/tTg	9/12	1	2	FACETS	0.951	0.822	1	0.951	0.822	1	CLONAL	1	TRUE	1	0.219128690123825	2		382	595	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988334	36988334	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	21	593	0	ENST00000354822.5:c.319C>T	p.Gln107Ter	p.Q107*	ENST00000354822	NM_001079668.2	107	Cag/Tag	2/3	1	2	FACETS	0.696	0.535	0.884	0.696	0.535	0.884	SUBCLONAL	1	TRUE	1	0.16	2		593	377	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246301	46246323	+	frameshift_variant	Frame_Shift_Del	DEL	AAGTGTAGTTGTCTCACCACATT	AAGTGTAGTTGTCTCACCACATT	-	novel	NA	P-0058066-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	43	576	0	ENST00000334344.6:c.4395_4417del	p.Ser1466TyrfsTer29	p.S1466Yfs*29	ENST00000334344	NM_152641.2	1465	ccAAGTGTAGTTGTCTCACCACATTct/ccct	15/21	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.16	2		576	515	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552152	29552152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199474738	NA	P-0058068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	94	319	0	ENST00000356175.3:c.1885G>A	p.Gly629Arg	p.G629R	ENST00000356175	NM_000267.3	629	Ggg/Agg	17/57	0.463170849920207	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.463170849920207	1		319	263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577576	7577578	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	novel	NA	P-0058068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	283	670	0	ENST00000269305.4:c.703_705del	p.Asn235del	p.N235del	ENST00000269305	NM_001126112.2	235	AAC/-	7/11	0.463170849920207	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.463170849920207	1		670	844	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0058068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	73	328	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.340457325892461	1	FACETS	0.537	0.471	0.608	0.537	0.471	0.608	SUBCLONAL	1	TRUE	0	0.463170849920207	1		328	451	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959064	2959064	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	342	1023	0	ENST00000396946.4:c.2452C>T	p.Arg818Trp	p.R818W	ENST00000396946	NM_032415.4	818	Cgg/Tgg	18/25	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.463170849920207	2		1023	1344	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227999	36227999	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751795961	NA	P-0058068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1314	82	1057	1	ENST00000222270.7:c.7385C>T	p.Ala2462Val	p.A2462V	ENST00000222270	NM_014727.1	2462	gCg/gTg	33/37	1	2	FACETS	0.254	0.222	0.287	0.254	0.222	0.287	SUBCLONAL	1	TRUE	1	0.463170849920207	2		1058	1396	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076662	102076662	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	47	438	0	ENST00000282441.5:c.841C>A	p.Gln281Lys	p.Q281K	ENST00000282441	NM_001130145.2	281	Cag/Aag	5/9	0.258503571654597	1	FACETS	0.226	0.19	0.266	0.226	0.19	0.266	INDETERMINATE	1	TRUE	0	0.463170849920207	1		438	690	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129171	152129171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	545	1072	0	ENST00000206249.3:c.124G>A	p.Val42Met	p.V42M	ENST00000206249	NM_000125.3	42	Gtg/Atg	1/8	0.428169130075204	2	FACETS	0.902	0.867	0.937	0.902	0.867	0.937	CLONAL	2	TRUE	0	0.463170849920207	2		1072	1305	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038790	47038811	+	protein_altering_variant	In_Frame_Del	DEL	GCCAGGGCCTGCTTCCCCTGCC	GCCAGGGCCTGCTTCCCCTGCC	A	novel	NA	P-0058068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	577	1242	0	ENST00000377604.3:c.797_818delinsA	p.Ser266_Pro273delinsLys	p.S266_P273delinsK	ENST00000377604	NM_001204468.1	266	aGCCAGGGCCTGCTTCCCCTGCCg/aAg	9/24	0.27136405370597	2	FACETS	0.751	0.721	0.781	0.751	0.721	0.781	INDETERMINATE	2	TRUE	0	0.463170849920207	2		1242	1659	SUCCESS
APC	324	MSKCC	GRCh37	5	112175472	112175476	+	frameshift_variant	Frame_Shift_Del	DEL	ATAGT	ATAGT	TTGG	novel	NA	P-0058068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	89	329	1	ENST00000257430.4:c.4181_4185delinsTTGG	p.Asp1394ValfsTer21	p.D1394Vfs*21	ENST00000257430	NM_000038.5	1394	gATAGT/gTTGG	16/16	0.340457325892461	1	FACETS	0.726	0.647	0.808	0.726	0.647	0.808	SUBCLONAL	1	TRUE	0	0.463170849920207	1		330	407	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0058069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	131	276	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.352325017014891	2	FACETS	0.782	0.717	0.85	0.782	0.717	0.85	SUBCLONAL	2	TRUE	0	0.416597788558032	2		276	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0058069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	500	380	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.345247312158765	2	FACETS	0.853	0.817	0.89	0.853	0.817	0.89	CLONAL	2	TRUE	0	0.416597788558032	2		380	1407	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971150	21971173	+	inframe_deletion	In_Frame_Del	DEL	GCTCCGCGCCGTGGAGCAGCAGCA	GCTCCGCGCCGTGGAGCAGCAGCA	-	novel	NA	P-0058069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	239	597	0	ENST00000304494.5:c.185_208del	p.Leu62_Glu69del	p.L62_E69del	ENST00000304494	NM_000077.4	62	cTGCTGCTGCTCCACGGCGCGGAGCcc/ccc	2/3	0.416597788558032	1	FACETS	0.994	0.929	1	0.994	0.929	1	CLONAL	1	TRUE	0	0.416597788558032	1		597	914	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0058070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	74	293	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.253969551995684	1	FACETS	0.992	0.872	1	0.992	0.872	1	CLONAL	1	TRUE	0	0.306008378289772	1		293	413	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944157	81944157	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761094228	NA	P-0058070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	92	875	0	ENST00000359376.3:c.1766G>A	p.Arg589His	p.R589H	ENST00000359376	NM_002661.3	589	cGc/cAc	18/33	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.306008378289772	2		875	570	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440372	52440372	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	162	806	0	ENST00000460680.1:c.680G>C	p.Arg227Pro	p.R227P	ENST00000460680	NM_004656.3	227	cGc/cCc	9/17	1	2	FACETS	0.865	0.795	0.938	1	0.991	1	CLONAL	2	TRUE	1	0.242539367136937	2		806	772	SUCCESS
AR	367	MSKCC	GRCh37	X	66766426	66766426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	20	334	0	ENST00000374690.3:c.1438C>T	p.Pro480Ser	p.P480S	ENST00000374690	NM_000044.3	480	Ccc/Tcc	1/8	0.169335907118372	2	FACETS	0.563	0.43	0.718	0.281	0.215	0.359	SUBCLONAL	1	TRUE	0	0.242539367136937	2		334	293	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109903	115109903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1182290035	NA	P-0058072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	59	794	0	ENST00000257566.3:c.1975G>A	p.Ala659Thr	p.A659T	ENST00000257566	NM_016569.3	659	Gcc/Acc	8/8	1	2	FACETS	0.559	0.479	0.646	0.559	0.479	0.646	SUBCLONAL	1	TRUE	1	0.242539367136937	2		794	871	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057799	27057799	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	65	830	1	ENST00000324856.7:c.1507C>T	p.Gln503Ter	p.Q503*	ENST00000324856	NM_006015.4	503	Cag/Tag	3/20	1	2	FACETS	0.538	0.465	0.617	0.538	0.465	0.617	SUBCLONAL	1	TRUE	1	0.242539367136937	2		831	997	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129864	69129864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs984252518	NA	P-0058072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	36	388	0	ENST00000288368.4:c.4618G>A	p.Val1540Met	p.V1540M	ENST00000288368	NM_024870.2	1540	Gtg/Atg	38/40	0.169335907118372	2	FACETS	0.777	0.64	0.931	0.389	0.32	0.466	CLONAL	1	TRUE	0	0.242539367136937	2		388	382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0058073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	405	781	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.460421989879761	2	FACETS	0.885	0.846	0.925	0.885	0.846	0.925	CLONAL	2	TRUE	0	0.488253684409493	2		781	937	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372025	55372025	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	166	747	1	ENST00000297316.4:c.715G>A	p.Ala239Thr	p.A239T	ENST00000297316	NM_022454.3	239	Gcc/Acc	2/2	0.47253815015239	5	FACETS	0.854	0.782	0.929	0.285	0.26	0.31	CLONAL	1	TRUE	2	0.488253684409493	5		748	1380	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802689	135802689	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1309560054	NA	P-0058073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	69	232	1	ENST00000298552.3:c.109C>T	p.Arg37Cys	p.R37C	ENST00000298552	NM_001162426.1	37	Cgt/Tgt	4/23	0.488253684409493	3	FACETS	1	0.909	1	0.522	0.457	0.59	CLONAL	1	TRUE	1	0.488253684409493	3		233	337	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650833	48650833	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	508	427	0	ENST00000376670.3:c.702G>A	p.Met234Ile	p.M234I	ENST00000376670	NM_002049.3	234	atG/atA	4/6	0.463202569027815	2	FACETS	0.882	0.854	0.91			1	CLONAL	3	TRUE	NA	0.488253684409493	2		427	786	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285182	212285182	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	75	369	0	ENST00000342788.4:c.3119G>T	p.Arg1040Ile	p.R1040I	ENST00000342788	NM_005235.2	1040	aGa/aTa	25/28	0.468330175543506	4	FACETS	1	0.901	1	0.514	0.452	0.58	CLONAL	1	TRUE	2	0.488253684409493	4		369	445	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076731	72076731	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1320611514	NA	P-0058073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	128	493	0	ENST00000357731.5:c.766G>C	p.Glu256Gln	p.E256Q	ENST00000357731	NM_173808.2	256	Gaa/Caa	5/7	0.488253684409493	4	FACETS	0.915	0.829	1	0.305	0.276	0.335	CLONAL	1	TRUE	1	0.488253684409493	4		493	853	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998282	100998282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	149	214	0	ENST00000325455.5:c.1520C>T	p.Ala507Val	p.A507V	ENST00000325455	NM_001202474.3	507	gCg/gTg	1/8	0.488253684409493	3	FACETS	0.956	0.884	1	0.956	0.884	1	CLONAL	2	TRUE	1	0.488253684409493	3		214	397	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241117	39241117	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1408868952	NA	P-0058073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	67	391	0	ENST00000402219.2:c.1954G>C	p.Glu652Gln	p.E652Q	ENST00000402219	NM_005633.3	652	Gag/Cag	12/23	1	2	FACETS	0.837	0.732	0.948	0.837	0.732	0.948	CLONAL	1	TRUE	1	0.488253684409493	2		391	328	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1978310	1978310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376629334	NA	P-0058073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	457	936	1	ENST00000382891.5:c.3730C>T	p.Arg1244Cys	p.R1244C	ENST00000382891	NM_133335.3	1244	Cgc/Tgc	21/22	0.443320739999205	4	FACETS	0.914	0.872	0.957	0.609	0.581	0.638	CLONAL	2	TRUE	1	0.488253684409493	4		937	1524	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602493	10602493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	395	1406	2	ENST00000171111.5:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000171111	NM_203500.1	362	cGg/cAg	3/6	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.437006814228396	2		1408	809	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882025	NA	P-0058074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	228	998	0	ENST00000269305.4:c.646G>T	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ttg	6/11	NA	2	FACETS	0.836	0.784	0.889			1	INDETERMINATE	2	TRUE	NA	0.437006814228396	2		998	624	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993996	72993996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376729347	NA	P-0058074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	60	1090	1	ENST00000268489.5:c.49G>A	p.Gly17Ser	p.G17S	ENST00000268489	NM_006885.3	17	Ggt/Agt	2/10	0.387765162540405	3	FACETS	0.451	0.388	0.52	0.225	0.194	0.26	SUBCLONAL	1	TRUE	1	0.437006814228396	3		1091	742	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629030	14629032	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs759159082	NA	P-0058074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	53	918	0	ENST00000254322.2:c.130_132del	p.Lys44del	p.K44del	ENST00000254322	NM_006145.1	44	AAG/-	1/3	0.111204726967294	5	FACETS	0.646	0.55	0.751			1	INDETERMINATE	1	TRUE	NA	0.437006814228396	5		918	622	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101702	27101702	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	270	1073	0	ENST00000324856.7:c.4986del	p.Asp1663ThrfsTer10	p.D1663Tfs*10	ENST00000324856	NM_006015.4	1662	Aaa/aa	18/20	0.371690653588293	3	FACETS	1	0.984	1	0.738	0.697	0.78	CLONAL	2	TRUE	0	0.437006814228396	3		1073	680	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625368	69625368	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs782459734	NA	P-0058074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	266	1382	0	ENST00000334134.2:c.425G>T	p.Gly142Val	p.G142V	ENST00000334134	NM_005247.2	142	gGg/gTg	3/3	0.335304328809782	4	FACETS	0.889	0.834	0.945	0.889	0.834	0.945	CLONAL	2	TRUE	2	0.437006814228396	4		1382	984	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144624	119144624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	172	536	1	ENST00000264033.4:c.637C>T	p.His213Tyr	p.H213Y	ENST00000264033	NM_005188.3	213	Cat/Tat	4/16	0.335304328809782	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	2	0.437006814228396	4		537	541	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112453	115112453	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	167	1254	0	ENST00000257566.3:c.1287C>A	p.Asp429Glu	p.D429E	ENST00000257566	NM_016569.3	429	gaC/gaA	7/8	0.244729546010411	4	FACETS	1	0.988	1	0.719	0.662	0.778	INDETERMINATE	1	TRUE	2	0.437006814228396	4		1254	764	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679825	88679825	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	67	568	0	ENST00000360948.2:c.638G>T	p.Ser213Ile	p.S213I	ENST00000360948	NM_001012338.2	213	aGc/aTc	7/19	1	2	FACETS	0.755	0.659	0.858	0.755	0.659	0.858	SUBCLONAL	1	TRUE	1	0.437006814228396	2		568	406	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224400	36224400	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	637	1505	0	ENST00000222270.7:c.6950G>T	p.Gly2317Val	p.G2317V	ENST00000222270	NM_014727.1	2317	gGc/gTc	28/37	0.437006814228396	4	FACETS	0.917	0.888	0.946	0.917	0.888	0.946	CLONAL	4	TRUE	0	0.437006814228396	4		1505	1142	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498292	29498292	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	199	720	0	ENST00000389048.3:c.1888A>T	p.Ile630Phe	p.I630F	ENST00000389048	NM_004304.4	630	Atc/Ttc	10/29	0.268425598914945	4	FACETS	0.914	0.85	0.98	0.914	0.85	0.98	CLONAL	2	TRUE	2	0.437006814228396	4		720	716	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426108	138426108	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	143	395	0	ENST00000289153.2:c.1423C>G	p.Pro475Ala	p.P475A	ENST00000289153	NM_006219.2	475	Cca/Gca	9/22	0.347275385391262	5	FACETS	1	0.979	1	0.794	0.73	0.86	CLONAL	2	TRUE	2	0.437006814228396	5		395	455	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161313	55161313	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	61	500	0	ENST00000257290.5:c.3144T>A	p.Ser1048Arg	p.S1048R	ENST00000257290	NM_006206.4	1048	agT/agA	23/23	NA	2	FACETS	0.665	0.575	0.761			1	INDETERMINATE	1	TRUE	NA	0.437006814228396	2		500	420	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534437	187534437	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	104	555	0	ENST00000441802.2:c.9289G>T	p.Val3097Phe	p.V3097F	ENST00000441802	NM_005245.3	3097	Gtc/Ttc	13/27	0.214897102311414	2	FACETS	1	0.962	1	0.568	0.512	0.627	INDETERMINATE	1	TRUE	0	0.437006814228396	2		555	419	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867538	35867538	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	111	342	0	ENST00000303115.3:c.352T>A	p.Cys118Ser	p.C118S	ENST00000303115	NM_002185.3	118	Tgc/Agc	3/8	0.347275385391262	5	FACETS	1	0.966	1	0.76	0.69	0.832	CLONAL	2	TRUE	2	0.437006814228396	5		342	369	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910542	29910542	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	125	1390	0	ENST00000376809.5:c.82T>A	p.Ser28Thr	p.S28T	ENST00000376809	NM_002116.7	28	Tcc/Acc	2/8	0.202546021906628	3	FACETS	1	0.98	1	0.429	0.39	0.47	INDETERMINATE	1	TRUE	0	0.437006814228396	3		1390	541	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169152	32169152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	315	1298	0	ENST00000375023.3:c.3881G>A	p.Gly1294Glu	p.G1294E	ENST00000375023	NM_004557.3	1294	gGg/gAg	22/30	0.202546021906628	3	FACETS	1	0.974	1	0.696	0.659	0.734	INDETERMINATE	2	TRUE	0	0.437006814228396	3		1298	841	SUCCESS
AR	367	MSKCC	GRCh37	X	66766139	66766139	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	143	459	0	ENST00000374690.3:c.1151A>G	p.His384Arg	p.H384R	ENST00000374690	NM_000044.3	384	cAc/cGc	1/8	0.230499024255448	2	FACETS	1	0.955	1			1	INDETERMINATE	2	TRUE	NA	0.437006814228396	2		459	314	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0058075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	286	357	0	ENST00000288602.6:c.1397G>T	p.Gly466Val	p.G466V	ENST00000288602	NM_004333.4	466	gGa/gTa	11/18	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.909060735488608	2		357	595	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037866	49037866	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs587778860	NA	P-0058075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	135	229	0	ENST00000267163.4:c.2107-1G>C		p.X703_splice	ENST00000267163	NM_000321.2	703			0.909060735488608	1	FACETS	0.959	0.913	1	0.959	0.913	1	CLONAL	1	TRUE	0	0.909060735488608	1		229	169	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031749	69031749	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	326	476	0	ENST00000288368.4:c.3504G>T	p.Gln1168His	p.Q1168H	ENST00000288368	NM_024870.2	1168	caG/caT	28/40	1	2	FACETS	0.893	0.848	0.939	0.893	0.848	0.939	CLONAL	1	TRUE	1	0.909060735488608	2		476	803	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341264	8341264	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	207	253	0	ENST00000356435.5:c.4952T>C	p.Leu1651Pro	p.L1651P	ENST00000356435		1651	cTa/cCa	30/35	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.909060735488608	2		253	441	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0058076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	133	297	0	ENST00000374690.3:c.2105T>A	p.Leu702His	p.L702H	ENST00000374690	NM_000044.3	702	cTc/cAc	4/8	1	1	FACETS	0.613	0.564	0.663	0.613	0.564	0.663	SUBCLONAL	1	TRUE	0	0.772136219207162	1		297	345	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006098	22006098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	97	1081	1	ENST00000276925.6:c.305C>T	p.Ala102Val	p.A102V	ENST00000276925	NM_004936.3	102	gCc/gTc	2/2	0.481121383314449	1	FACETS	0.37	0.332	0.41	0.37	0.332	0.41	SUBCLONAL	1	TRUE	0	0.772136219207162	1		1082	417	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249788	110249788	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	137	1235	4	ENST00000374672.4:c.887A>G	p.Asn296Ser	p.N296S	ENST00000374672	NM_004235.4	296	aAt/aGt	3/5	0.481121383314449	1	FACETS	0.387	0.353	0.422	0.387	0.353	0.422	SUBCLONAL	1	TRUE	0	0.772136219207162	1		1239	563	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0058078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	147	286	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.98	1	1	0.993	1	CLONAL	2	FALSE	1	0.291956529761442	2		286	423	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0058078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	290	588	0	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	1	2	FACETS	1	0.948	1	1	0.995	1	CLONAL	2	FALSE	1	0.291956529761442	2		588	987	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579312	7579312	+	splice_region_variant,synonymous_variant	Splice_Region	SNP	C	C	T	rs55863639	NA	P-0058078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	323	385	2	ENST00000269305.4:c.375G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125	acG/acA	4/11	0.245097765463903	0	FACETS	1	0.973	1			1	CLONAL	2	FALSE	0	0.291956529761442	0		387	757	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052632	42052632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779811318	NA	P-0058078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	268	387	1	ENST00000219905.7:c.7303C>T	p.Arg2435Trp	p.R2435W	ENST00000219905	NM_001164273.1	2435	Cgg/Tgg	20/24	1	2	FACETS	1	0.979	1	1	0.995	1	CLONAL	2	FALSE	1	0.291956529761442	2		388	845	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114799886	114799886	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs377242639	NA	P-0058078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	249	473	0	ENST00000543371.1:c.552+1G>A		p.X184_splice	ENST00000543371	NM_001198531.1	184			1	2	FACETS	0.97	0.909	1	1	0.995	1	CLONAL	2	FALSE	1	0.291956529761442	2		473	879	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254542	10254542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	325	597	0	ENST00000340748.4:c.2968C>T	p.Pro990Ser	p.P990S	ENST00000340748		990	Ccc/Tcc	28/40	1	2	FACETS	0.975	0.921	1	1	0.996	1	CLONAL	2	FALSE	1	0.291956529761442	2		597	1142	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106630	27106633	+	frameshift_variant	Frame_Shift_Del	DEL	TGCC	TGCC	-	novel	NA	P-0058078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	343	679	0	ENST00000324856.7:c.6247_6250del	p.Pro2083SerfsTer51	p.P2083Sfs*51	ENST00000324856	NM_006015.4	2081	TGCCtg/tg	20/20	1	2	FACETS	0.911	0.861	0.961	1	0.996	1	CLONAL	2	FALSE	1	0.291956529761442	2		679	1290	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16041516	16041516	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	110	218	0	ENST00000268712.3:c.1363C>T	p.His455Tyr	p.H455Y	ENST00000268712	NM_006311.3	455	Cat/Tat	13/46	0.245097765463903	0	FACETS	0.892	0.813	0.973			1	CLONAL	2	FALSE	0	0.291956529761442	0		218	299	SUCCESS
APC	324	MSKCC	GRCh37	5	112173619	112173623	+	frameshift_variant	Frame_Shift_Del	DEL	AGACA	AGACA	-	novel	NA	P-0058078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	117	261	0	ENST00000257430.4:c.2329_2333del	p.Asp777PhefsTer9	p.D777Ffs*9	ENST00000257430	NM_000038.5	776	atAGACAat/atat	16/16	0.273653757298147	0	FACETS	0.982	0.9	1			1	CLONAL	2	FALSE	0	0.291956529761442	0		261	289	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0058079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	122	286	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.885	0.801	0.972	0.885	0.801	0.972	CLONAL	1	TRUE	1	0.419794450053961	2		286	657	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0058079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	105	656	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.872	0.783	0.965	0.872	0.783	0.965	CLONAL	1	TRUE	1	0.419794450053961	2		657	574	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0058079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	74	257	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.993	0.875	1	0.993	0.875	1	CLONAL	1	TRUE	1	0.419794450053961	2		257	355	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0058079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	200	839	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.419794450053961	1	FACETS	0.739	0.684	0.795	0.739	0.684	0.795	SUBCLONAL	1	TRUE	0	0.419794450053961	1		839	1019	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121912580	NA	P-0058079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	118	409	0	ENST00000342988.3:c.1157G>C	p.Gly386Ala	p.G386A	ENST00000342988	NM_005359.5	386	gGt/gCt	10/12	0.419794450053961	1	FACETS	0.976	0.887	1	0.976	0.887	1	CLONAL	1	TRUE	0	0.419794450053961	1		409	455	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117872	70117872	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	268	947	0	ENST00000245479.2:c.340G>C	p.Val114Leu	p.V114L	ENST00000245479	NM_000346.3	114	Gtg/Ctg	1/3	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.419794450053961	2		947	1181	SUCCESS
APC	324	MSKCC	GRCh37	5	112164663	112164664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0058079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	31	228	0	ENST00000257430.4:c.1742dup	p.Glu582GlyfsTer20	p.E582Gfs*20	ENST00000257430	NM_000038.5	579	-/A	14/16	1	2	FACETS	0.492	0.399	0.597	0.492	0.399	0.597	SUBCLONAL	1	TRUE	1	0.419794450053961	2		228	300	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983107	7983107	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	243	952	0	ENST00000319144.4:c.907T>C	p.Cys303Arg	p.C303R	ENST00000319144	NM_001139.2	303	Tgc/Cgc	7/15	1	2	FACETS	0.985	0.92	1	0.985	0.92	1	CLONAL	1	TRUE	1	0.419794450053961	2		952	1175	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274631	198274631	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	182	792	0	ENST00000335508.6:c.767C>G	p.Pro256Arg	p.P256R	ENST00000335508	NM_012433.2	256	cCt/cGt	7/25	1	2	FACETS	0.753	0.693	0.815	0.753	0.693	0.815	SUBCLONAL	1	TRUE	1	0.419794450053961	2		792	1152	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931898	39931898	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	303	514	0	ENST00000378444.4:c.2701C>G	p.Leu901Val	p.L901V	ENST00000378444	NM_001123385.1	901	Ctg/Gtg	4/15	1	1	FACETS	0.842	0.8	0.885	1	0.995	1	CLONAL	2	TRUE	0	0.419794450053961	1		514	677	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412174	63412175	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0058079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	297	581	0	ENST00000330258.3:c.992_993del	p.Ile331AsnfsTer46	p.I331Nfs*46	ENST00000330258	NM_152424.3	331	aTA/a	2/2	1	1	FACETS	0.812	0.77	0.855	1	0.995	1	CLONAL	2	TRUE	0	0.419794450053961	1		581	688	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119704	70119705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	rs1567911132	NA	P-0058079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	160	1003	1	ENST00000245479.2:c.709_710dup	p.Pro238HisfsTer16	p.P238Hfs*16	ENST00000245479	NM_000346.3	236	acc/aCCcc	3/3	1	2	FACETS	0.638	0.583	0.695	0.638	0.583	0.695	SUBCLONAL	1	TRUE	1	0.419794450053961	2		1004	1195	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0058080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	215	380	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.179657785738264	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.233718083949781	2		380	890	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0058080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	108	622	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.225134791008153	3	FACETS	0.94	0.847	1	0.94	0.847	1	CLONAL	2	TRUE	1	0.233718083949781	3		622	549	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591888	48591888	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519739	NA	P-0058080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	77	438	0	ENST00000342988.3:c.1051G>C	p.Asp351His	p.D351H	ENST00000342988	NM_005359.5	351	Gat/Cat	9/12	0.233718083949781	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.233718083949781	1		438	423	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330632	+	inframe_deletion	In_Frame_Del	DEL	TTT	TTT	-	novel	NA	P-0058080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	53	304	0	ENST00000342505.4:c.1014_1016del	p.Lys338del	p.K338del	ENST00000342505	NM_002227.2	338	aaAAAt/aat	8/25	0.225134791008153	3	FACETS	1	0.953	1	0.649	0.555	0.752	CLONAL	1	TRUE	1	0.233718083949781	3		304	390	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779128	3779128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395505964	NA	P-0058080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	47	807	2	ENST00000262367.5:c.5920C>T	p.Arg1974Trp	p.R1974W	ENST00000262367	NM_004380.2	1974	Cgg/Tgg	31/31	0.132036740632832	1	FACETS	0.5	0.42	0.587	0.5	0.42	0.587	INDETERMINATE	1	TRUE	0	0.233718083949781	1		809	711	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679392	29679392	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	33	375	0	ENST00000356175.3:c.7512C>A	p.Asp2504Glu	p.D2504E	ENST00000356175	NM_000267.3	2504	gaC/gaA	50/57	0.233718083949781	1	FACETS	0.613	0.499	0.741	0.613	0.499	0.741	SUBCLONAL	1	TRUE	0	0.233718083949781	1		375	407	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612245	1612245	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	63	760	0	ENST00000344749.5:c.1774G>C	p.Ala592Pro	p.A592P	ENST00000344749	NM_001136139.2	592	Gcc/Ccc	18/19	0.225134791008153	3	FACETS	0.808	0.698	0.928	0.404	0.349	0.464	CLONAL	1	TRUE	1	0.233718083949781	3		760	745	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257667	19257667	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	124	974	0	ENST00000162023.5:c.559T>C	p.Phe187Leu	p.F187L	ENST00000162023		187	Ttc/Ctc	10/13	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.233718083949781	2		974	897	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851696	134851696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576710309	NA	P-0058080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	53	663	0	ENST00000398015.3:c.1102C>T	p.Arg368Trp	p.R368W	ENST00000398015	NM_004441.4	368	Cgg/Tgg	5/16	0.233718083949781	1	FACETS	0.763	0.651	0.886	0.763	0.651	0.886	SUBCLONAL	1	TRUE	0	0.233718083949781	1		663	525	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430368	181430368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	64	625	1	ENST00000325404.1:c.220C>T	p.Arg74Cys	p.R74C	ENST00000325404	NM_003106.3	74	Cgc/Tgc	1/1	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.233718083949781	2		626	510	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779163	135779163	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	34	384	0	ENST00000298552.3:c.2083T>G	p.Leu695Val	p.L695V	ENST00000298552	NM_001162426.1	695	Ttg/Gtg	17/23	0.225134791008153	3	FACETS	0.646	0.527	0.78	0.323	0.263	0.39	SUBCLONAL	1	TRUE	1	0.233718083949781	3		384	503	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786859	135786859	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	44	409	0	ENST00000298552.3:c.1010T>C	p.Leu337Pro	p.L337P	ENST00000298552	NM_001162426.1	337	cTg/cCg	10/23	0.225134791008153	3	FACETS	0.744	0.624	0.878	0.372	0.312	0.439	SUBCLONAL	1	TRUE	1	0.233718083949781	3		409	565	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0058081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	32	622	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.77	0.625	0.935	0.77	0.625	0.935	CLONAL	1	TRUE	1	0.186688878433437	2		622	445	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829040	128829042	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	rs570242755	NA	P-0058081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	12	74	0	ENST00000249373.3:c.67_69del	p.Leu23del	p.L23del	ENST00000249373	NM_005631.4	16	ggGCTg/ggg	1/12	1	2	FACETS	0.73	0.514	0.995	0.73	0.514	0.995	CLONAL	1	TRUE	1	0.186688878433437	2		74	176	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs79184941	NA	P-0058081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	71	398	0	ENST00000358487.5:c.755C>T	p.Ser252Leu	p.S252L	ENST00000358487	NM_000141.4	252	tCg/tTg	7/18	0.118382997828968	4	FACETS	0.966	0.846	1	0.966	0.846	1	CLONAL	2	TRUE	2	0.186688878433437	4		398	467	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404693	70404693	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756914683	NA	P-0058081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	33	443	1	ENST00000373644.4:c.2207C>T	p.Ser736Leu	p.S736L	ENST00000373644	NM_030625.2	736	tCg/tTg	4/12	0.118382997828968	4	FACETS	0.916	0.746	1	0.458	0.373	0.554	CLONAL	1	TRUE	2	0.186688878433437	4		444	458	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675184	40675184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762955185	NA	P-0058081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	56	866	0	ENST00000249776.8:c.148G>A	p.Ala50Thr	p.A50T	ENST00000249776	NM_033286.3	50	Gct/Act	1/9	0.186688878433437	1	FACETS	0.764	0.653	0.885	0.764	0.653	0.885	SUBCLONAL	1	TRUE	0	0.186688878433437	1		866	712	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202459	123202459	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	71	359	0	ENST00000218089.9:c.2311A>G	p.Ile771Val	p.I771V	ENST00000218089	NM_001042749.1	771	Ata/Gta	24/35	1	2	FACETS	0.851	0.745	0.964	1	0.979	1	CLONAL	2	TRUE	1	0.186688878433437	2		359	447	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0058085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	117	276	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.269476084135417	6	FACETS	1	0.97	1	0.863	0.786	0.944	CLONAL	3	FALSE	2	0.269476084135417	6		276	387	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184159	56184159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	23	459	0	ENST00000399503.3:c.4364C>T	p.Ser1455Phe	p.S1455F	ENST00000399503	NM_005921.1	1455	tCc/tTc	19/20	0.192634759891484	3	FACETS	0.769	0.601	0.962	0.256	0.2	0.321	CLONAL	1	FALSE	0	0.269476084135417	3		459	252	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577111	7577112	+	inframe_insertion	In_Frame_Ins	INS	-	-	CACAAA	novel	NA	P-0058085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	200	887	1	ENST00000269305.4:c.821_826dup	p.Val274_Cys275dup	p.V274_C275dup	ENST00000269305	NM_001126112.2	274	gcc/gTTTGTGcc	8/11	0.269476084135417	6	FACETS	0.879	0.818	0.941	0.879	0.818	0.941	CLONAL	4	FALSE	2	0.269476084135417	6		888	650	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16097870	16097870	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs76145228	NA	P-0058085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	46	230	0	ENST00000268712.3:c.14G>T	p.Gly5Val	p.G5V	ENST00000268712	NM_006311.3	5	gGt/gTt	2/46	0.269476084135417	6	FACETS	1	0.895	1	0.791	0.678	0.912	CLONAL	3	FALSE	2	0.269476084135417	6		230	166	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955085	17955085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	158	1190	0	ENST00000458235.1:c.142C>T	p.His48Tyr	p.H48Y	ENST00000458235	NM_000215.3	48	Cac/Tac	2/24	0.269476084135417	2	FACETS	0.922	0.848	0.999	0.922	0.848	0.999	CLONAL	2	FALSE	0	0.269476084135417	2		1190	636	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917813	29917813	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	66	1024	0	ENST00000389048.3:c.855C>A	p.Asn285Lys	p.N285K	ENST00000389048	NM_004304.4	285	aaC/aaA	3/29	0.180472388354415	4	FACETS	1	0.951	1	0.401	0.348	0.458	CLONAL	1	FALSE	1	0.269476084135417	4		1024	517	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5055739	5055739	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0058085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	24	486	0	ENST00000381652.3:c.1007C>G	p.Ser336Ter	p.S336*	ENST00000381652	NM_004972.3	336	tCa/tGa	8/25	NA	2	FACETS	0.768	0.604	0.955			1	INDETERMINATE	1	FALSE	NA	0.269476084135417	2		486	232	SUCCESS
APC	324	MSKCC	GRCh37	5	112173928	112173928	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs763546422	NA	P-0058085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	31	494	0	ENST00000257430.4:c.2637G>T	p.Gln879His	p.Q879H	ENST00000257430	NM_000038.5	879	caG/caT	16/16	0.192634759891484	3	FACETS	0.974	0.791	1	0.325	0.263	0.393	CLONAL	1	FALSE	0	0.269476084135417	3		494	268	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247868	59247868	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	71	1064	0	ENST00000371222.2:c.875C>A	p.Ser292Ter	p.S292*	ENST00000371222	NM_002228.3	292	tCg/tAg	1/1	0.16939629386953	3	FACETS	0.834	0.727	0.949	0.417	0.363	0.475	CLONAL	1	FALSE	1	0.269476084135417	3		1064	717	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120508171	120508171	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	53	550	0	ENST00000256646.2:c.1586G>T	p.Cys529Phe	p.C529F	ENST00000256646	NM_024408.3	529	tGc/tTc	10/34	0.16939629386953	3	FACETS	1	0.91	1	0.544	0.465	0.63	CLONAL	1	FALSE	1	0.269476084135417	3		550	410	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843468	156843468	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	45	918	0	ENST00000524377.1:c.894C>A	p.His298Gln	p.H298Q	ENST00000524377	NM_002529.3	298	caC/caA	8/17	0.269476084135417	7	FACETS	0.828	0.695	0.976			1	CLONAL	1	FALSE	NA	0.269476084135417	7		918	675	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625305	69625305	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	33	1147	1	ENST00000334134.2:c.488C>A	p.Pro163His	p.P163H	ENST00000334134	NM_005247.2	163	cCc/cAc	3/3	0.16939629386953	3	FACETS	0.729	0.594	0.881	0.365	0.297	0.441	SUBCLONAL	1	FALSE	1	0.269476084135417	3		1148	381	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281356	49281356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	58	1087	2	ENST00000282018.3:c.403G>A	p.Val135Met	p.V135M	ENST00000282018	NM_020377.2	135	Gtg/Atg	1/1	0.209963685922509	3	FACETS	1	0.868	1	0.336	0.289	0.388	CLONAL	1	FALSE	0	0.269476084135417	3		1089	484	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031828	10031828	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	78	875	0	ENST00000330684.3:c.995A>T	p.His332Leu	p.H332L	ENST00000330684	NM_001134407.1	332	cAc/cTc	3/13	0.269476084135417	2	FACETS	0.774	0.684	0.869	0.774	0.684	0.869	SUBCLONAL	2	FALSE	0	0.269476084135417	2		875	374	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40368058	40368058	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161384430	NA	P-0058085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	58	750	0	ENST00000293328.3:c.1447C>T	p.Leu483Phe	p.L483F	ENST00000293328	NM_012448.3	483	Ctc/Ttc	12/19	0.269476084135417	6	FACETS	0.909	0.78	1	0.227	0.195	0.263	CLONAL	1	FALSE	2	0.269476084135417	6		750	729	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462550	29462550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	43	751	0	ENST00000389048.3:c.2351C>A	p.Pro784His	p.P784H	ENST00000389048	NM_004304.4	784	cCc/cAc	13/29	0.180472388354415	4	FACETS	1	0.93	1	0.402	0.337	0.473	CLONAL	1	FALSE	1	0.269476084135417	4		751	336	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662161	227662161	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	76	1125	0	ENST00000305123.5:c.1294G>T	p.Gly432Cys	p.G432C	ENST00000305123	NM_005544.2	432	Ggc/Tgc	1/2	0.269476084135417	5	FACETS	1	0.96	1	0.411	0.361	0.466	CLONAL	1	FALSE	2	0.269476084135417	5		1125	642	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546761	9546761	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs768724288	NA	P-0058085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	18	681	0	ENST00000353224.5:c.1261G>T	p.Asp421Tyr	p.D421Y	ENST00000353224	NM_177990.2	421	Gac/Tac	5/10	0.114099313364205	5	FACETS	0.977	0.739	1	0.326	0.246	0.419	INDETERMINATE	1	FALSE	2	0.269476084135417	5		681	192	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733301	40733301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	44	632	0	ENST00000373198.4:c.3505G>A	p.Ala1169Thr	p.A1169T	ENST00000373198	NM_133170.3	1169	Gcc/Acc	26/32	0.269476084135417	0	FACETS	0.666	0.56	0.783			1	SUBCLONAL	1	FALSE	0	0.269476084135417	0		632	358	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851763	134851763	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	33	980	0	ENST00000398015.3:c.1169G>C	p.Arg390Pro	p.R390P	ENST00000398015	NM_004441.4	390	cGc/cCc	5/16	1	2	FACETS	0.636	0.518	0.769	0.636	0.518	0.769	SUBCLONAL	1	FALSE	1	0.269476084135417	2		980	385	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286188	66286188	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	32	527	0	ENST00000273854.3:c.1498C>A	p.Leu500Ile	p.L500I	ENST00000273854	NM_004439.5	500	Cta/Ata	6/18	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	FALSE	1	0.269476084135417	2		527	178	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356134	66356134	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	48	720	0	ENST00000273854.3:c.1363C>G	p.Arg455Gly	p.R455G	ENST00000273854	NM_004439.5	455	Cgg/Ggg	5/18	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	FALSE	1	0.269476084135417	2		720	301	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956586	93956586	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	83	530	0	ENST00000369303.4:c.2650G>T	p.Glu884Ter	p.E884*	ENST00000369303	NM_004440.3	884	Gaa/Taa	15/17	0.269476084135417	0	FACETS	0.843	0.754	0.935			1	CLONAL	2	FALSE	0	0.269476084135417	0		530	267	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112025283	112025283	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	98	722	0	ENST00000368678.4:c.466C>G	p.Arg156Gly	p.R156G	ENST00000368678		156	Cga/Gga	6/13	0.252293667764722	4	FACETS	0.834	0.75	0.921			1	CLONAL	3	FALSE	NA	0.269476084135417	4		722	369	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265504	152265504	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	140	864	0	ENST00000206249.3:c.957G>T	p.Leu319Phe	p.L319F	ENST00000206249	NM_000125.3	319	ttG/ttT	4/8	0.192634759891484	3	FACETS	0.956	0.88	1	0.956	0.88	1	CLONAL	3	FALSE	0	0.269476084135417	3		864	411	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681087	117681089	+	missense_variant	Missense_Mutation	TNP	AAC	AAC	GAA	novel	NA	P-0058085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	91	702	0	ENST00000368508.3:c.3531_3533delinsTTC	p.Phe1178Ser	p.F1178S	ENST00000368508	NM_002944.2	1177	acGTTt/acTTCt	23/43	0.269476084135417	1	FACETS	1	0.924	1	1	0.987	1	CLONAL	2	FALSE	0	0.269476084135417	1		702	283	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970912	70970914	+	missense_variant	Missense_Mutation	TNP	TGG	TGG	AGA	novel	NA	P-0058085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	46	757	0	ENST00000276594.2:c.1347_1349delinsTCT	p.His450Leu	p.H450L	ENST00000276594	NM_024504.3	449	atCCAc/atTCTc	6/8	0.217611045678002	0	FACETS	0.617	0.521	0.723			1	SUBCLONAL	1	FALSE	0	0.269476084135417	0		757	404	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	169	526	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.41322600205796	2		526	777	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402491	20402491	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1304084051	NA	P-0058086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	196	628	0	ENST00000346618.3:c.28G>A	p.Glu10Lys	p.E10K	ENST00000346618	NM_001949.4	10	Gag/Aag	1/7	0.412133913322752	2	FACETS	0.947	0.876	1	0.473	0.438	0.51	CLONAL	1	TRUE	0	0.41322600205796	2		628	1002	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851177	151851177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141966811	NA	P-0058086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	49	239	2	ENST00000262189.6:c.12194C>T	p.Ala4065Val	p.A4065V	ENST00000262189	NM_170606.2	4065	gCg/gTg	48/59	0.152622198996967	0	FACETS	0.462	0.394	0.537			1	INDETERMINATE	1	TRUE	0	0.41322600205796	0		241	301	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983981	2983981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866164446	NA	P-0058086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	214	832	0	ENST00000396946.4:c.549G>A	p.Met183Ile	p.M183I	ENST00000396946	NM_032415.4	183	atG/atA	5/25	1	2	FACETS	0.872	0.809	0.937	0.872	0.809	0.937	CLONAL	1	TRUE	1	0.41322600205796	2		832	1188	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127318	17127318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369906553	NA	P-0058086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	248	735	0	ENST00000285071.4:c.536G>A	p.Arg179Gln	p.R179Q	ENST00000285071	NM_144997.5	179	cGg/cAg	6/14	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.41322600205796	2		735	1065	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595542	55595542	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	28	320	0	ENST00000288135.5:c.2032C>G	p.Leu678Val	p.L678V	ENST00000288135	NM_000222.2	678	Ctt/Gtt	14/21	1	2	FACETS	0.338	0.27	0.416	0.338	0.27	0.416	SUBCLONAL	1	TRUE	1	0.41322600205796	2		320	401	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0058089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	64	660	1	ENST00000269305.4:c.96+1G>A		p.X32_splice	ENST00000269305	NM_001126112.2	32			0.425821098980809	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.425821098980809	1		661	194	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0058089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	8	275	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.414573854121206	5	FACETS	1	0.661	1	0.336	0.22	0.481	CLONAL	1	TRUE	2	0.425821098980809	5		275	61	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	19	270	0	ENST00000397062.3:c.92G>C	p.Gly31Ala	p.G31A	ENST00000397062	NM_006164.4	31	gGa/gCa	2/5	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.425821098980809	2		270	71	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741681	17741681	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	41	458	0	ENST00000250003.3:c.352G>C	p.Glu118Gln	p.E118Q	ENST00000250003	NM_002478.4	118	Gag/Cag	1/3	1	2	FACETS	0.764	0.641	0.899	0.764	0.641	0.899	SUBCLONAL	1	TRUE	1	0.425821098980809	2		458	252	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057904	27057904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	310	772	0	ENST00000324856.7:c.1612C>T	p.Gln538Ter	p.Q538*	ENST00000324856	NM_006015.4	538	Cag/Tag	3/20	0.386809279654579	3	FACETS	1	0.99	1	0.601	0.567	0.635	INDETERMINATE	1	TRUE	1	0.693163880376309	3		772	1002	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400827	72400827	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	106	424	0	ENST00000357731.5:c.344C>T	p.Pro115Leu	p.P115L	ENST00000357731	NM_173808.2	115	cCa/cTa	2/7	0.386809279654579	3	FACETS	0.636	0.57	0.704	0.318	0.285	0.352	INDETERMINATE	1	TRUE	1	0.693163880376309	3		424	648	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112401	115112401	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs888338239	NA	P-0058090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	104	720	0	ENST00000257566.3:c.1339C>T	p.Arg447Cys	p.R447C	ENST00000257566	NM_016569.3	447	Cgc/Tgc	7/8	0.693735484610064	3	FACETS	0.471	0.421	0.524	0.235	0.21	0.262	SUBCLONAL	1	TRUE	1	0.693163880376309	3		720	858	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0058090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	590	564	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	0.693735484610064	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.693163880376309	2		564	768	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306661	41306661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755794681	NA	P-0058090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	185	528	0	ENST00000373198.4:c.998C>T	p.Thr333Met	p.T333M	ENST00000373198	NM_133170.3	333	aCg/aTg	7/32	0.693004192295583	4	FACETS	0.898	0.829	0.971	0.449	0.414	0.486	CLONAL	1	TRUE	2	0.693163880376309	4		528	1006	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0058090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4862	653	157	2	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.693163880376309	24	FACETS	0.982	0.94	1	0.14	0.134	0.147	CLONAL	3	TRUE	3	0.693163880376309	24		159	5515	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846107	151846107	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	283	653	0	ENST00000262189.6:c.12905C>T	p.Pro4302Leu	p.P4302L	ENST00000262189	NM_170606.2	4302	cCt/cTt	52/59	0.386809279654579	3	FACETS	1	0.992	1	0.648	0.611	0.686	INDETERMINATE	1	TRUE	1	0.693163880376309	3		653	848	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044898	47044898	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058090-T02-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	750	390	0	ENST00000377604.3:c.2224C>T	p.Gln742Ter	p.Q742*	ENST00000377604	NM_001204468.1	742	Cag/Tag	20/24	0.693735484610064	2	FACETS		NA	1			1	NA	3	TRUE	NA	0.693163880376309	2		390	846	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0058091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	5882	157	2	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.524679177795428	11	FACETS	1	0.995	1	1	0.999	1	CLONAL	11	TRUE	1	0.524679177795428	11		159	6844	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0058091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	712	922	2	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.380257956024976	2	FACETS	1	0.997	1	0.707	0.682	0.732	CLONAL	1	TRUE	0	0.524679177795428	2		924	1920	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034491	47034491	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	581	275	0	ENST00000377604.3:c.576G>T	p.Gln192His	p.Q192H	ENST00000377604	NM_001204468.1	192	caG/caT	6/24	0.524679177795428	2	FACETS	0.999	0.964	1			1	CLONAL	2	TRUE	NA	0.524679177795428	2		275	1109	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518453	204518453	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	48	306	0	ENST00000367182.3:c.1116A>T	p.Arg372Ser	p.R372S	ENST00000367182	NM_001278516.1	372	agA/agT	11/11	0.156142408883396	2	FACETS	0.457	0.387	0.534	0.229	0.193	0.267	INDETERMINATE	1	TRUE	0	0.524679177795428	2		306	400	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0058102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	435	763	1	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.838615196319775	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.838615196319775	1		764	587	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981817	201981818	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0058102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	32	1057	0	ENST00000359651.3:c.529dup	p.Ser177LysfsTer19	p.S177Kfs*19	ENST00000359651		176	-/A	4/8	0.838615196319775	1	FACETS	0.101	0.081	0.123	0.101	0.081	0.123	SUBCLONAL	1	TRUE	0	0.838615196319775	1		1057	440	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77043890	77043890	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs748742535	NA	P-0058102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	453	727	2	ENST00000356341.3:c.1436A>G	p.Asn479Ser	p.N479S	ENST00000356341	NM_002576.4	479	aAt/aGt	14/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.838615196319775	2		729	1078	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489820	2489820	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	48	953	0	ENST00000355716.4:c.217A>G	p.Thr73Ala	p.T73A	ENST00000355716	NM_003820.2	73	Aca/Gca	3/8	1	2	FACETS	0.132	0.111	0.156	0.132	0.111	0.156	SUBCLONAL	1	TRUE	1	0.84	2		953	865	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693001	89693001	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	21	384	0	ENST00000371953.3:c.485A>G	p.Asp162Gly	p.D162G	ENST00000371953	NM_000314.4	162	gAc/gGc	5/9	1	2	FACETS	0.121	0.092	0.154	0.121	0.092	0.154	SUBCLONAL	1	TRUE	1	0.84	2		384	414	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0058104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	230	416	1	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.327530530516779	3	FACETS	0.986	0.928	1	0.986	0.928	1	CLONAL	3	TRUE	0	0.350252912389445	3		417	522	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380345	14380346	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0058104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	79	337	0	ENST00000256196.4:c.71_72delinsAA	p.Gly24Glu	p.G24E	ENST00000256196		24	gGC/gAA	1/6	1	2	FACETS	0.962	0.849	1	0.962	0.849	1	CLONAL	1	TRUE	1	0.350252912389445	2		337	469	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591104	67591105	+	inframe_insertion	In_Frame_Ins	INS	-	-	TAAACC	novel	NA	P-0058104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	32	296	0	ENST00000274335.5:c.1698_1703dup	p.Lys567_Pro568dup	p.K567_P568dup	ENST00000274335		567	att/atTAAACCt	12/15	1	2	FACETS	0.582	0.473	0.704	0.582	0.473	0.704	SUBCLONAL	1	TRUE	1	0.350252912389445	2		296	314	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974799	21974799	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	95	275	1	ENST00000304494.5:c.28G>T	p.Glu10Ter	p.E10*	ENST00000304494	NM_000077.4	10	Gag/Tag	1/3	1	2	FACETS	0.79	0.712	0.871	1	0.984	1	SUBCLONAL	2	TRUE	1	0.391728848731016	2		276	307	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0058106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	3035	486	0	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	0.391728848731016	19	FACETS	1	0.997	1			1	CLONAL	18	TRUE	NA	0.391728848731016	19		486	3666	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436026	56436026	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771831816	NA	P-0058106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	401	641	0	ENST00000407977.2:c.1111C>T	p.Arg371Ter	p.R371*	ENST00000407977		371	Cga/Tga	9/10	0.391728848731016	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.391728848731016	2		641	934	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921347	178921347	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	115	506	1	ENST00000263967.3:c.829A>T	p.Ile277Leu	p.I277L	ENST00000263967	NM_006218.2	277	Ata/Tta	5/21	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.391728848731016	2		507	586	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921365	178921365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	138	574	0	ENST00000263967.3:c.847C>T	p.Pro283Ser	p.P283S	ENST00000263967	NM_006218.2	283	Ccc/Tcc	5/21	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.391728848731016	2		574	672	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044497	12044498	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0058106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	119	351	0	ENST00000353533.5:c.1122dup	p.Val375ArgfsTer2	p.V375Rfs*2	ENST00000353533	NM_003010.3	374	gcc/gCcc	11/11	0.370541097401835	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.391728848731016	1		351	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574030	7574031	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GG	GG	C	novel	NA	P-0058106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	182	714	0	ENST00000269305.4:c.996_997delinsG	p.Ile332MetfsTer13	p.I332Mfs*13	ENST00000269305	NM_001126112.2	332	atCCgt/atGgt	10/11	0.370541097401835	1	FACETS	0.96	0.888	1	0.96	0.888	1	CLONAL	1	TRUE	0	0.391728848731016	1		714	778	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0058108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	29	351	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.599	0.48	0.735	0.599	0.48	0.735	SUBCLONAL	1	TRUE	1	0.22	2		351	440	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0058108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	37	254	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.837	0.69	1	0.837	0.69	1	CLONAL	1	TRUE	1	0.22	2		254	402	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451473	70451473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	73	631	0	ENST00000373644.4:c.6313C>T	p.Pro2105Ser	p.P2105S	ENST00000373644	NM_030625.2	2105	Cct/Tct	12/12	1	2	FACETS	0.89	0.777	1	0.89	0.777	1	CLONAL	1	TRUE	1	0.22	2		631	746	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792467	33792467	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	70	710	0	ENST00000498907.2:c.854A>T	p.Tyr285Phe	p.Y285F	ENST00000498907	NM_004364.3	285	tAc/tTc	1/1	1	2	FACETS	0.831	0.723	0.947	0.831	0.723	0.947	CLONAL	1	TRUE	1	0.22	2		710	766	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262305	46262305	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	63	372	0	ENST00000371998.3:c.889A>T	p.Ile297Phe	p.I297F	ENST00000371998		297	Atc/Ttc	9/23	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.22	2		372	560	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976698	55976698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	48	543	0	ENST00000263923.4:c.1127C>T	p.Thr376Ile	p.T376I	ENST00000263923	NM_002253.2	376	aCa/aTa	9/30	1	2	FACETS	0.689	0.582	0.808	0.689	0.582	0.808	SUBCLONAL	1	TRUE	1	0.22	2		543	633	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983481	90983491	+	frameshift_variant	Frame_Shift_Del	DEL	TACTTCCAATA	TACTTCCAATA	-	novel	NA	P-0058108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	50	273	0	ENST00000265433.3:c.612_622del	p.Ile205LysfsTer3	p.I205Kfs*3	ENST00000265433	NM_002485.4	204	tcTATTGGAAGTAaa/tcaa	6/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.22	2		273	358	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	96	306	0				ENST00000310581	NM_198253.2	-/1132			0.616265523386376	3	FACETS	1	0.961	1	0.565	0.509	0.622	CLONAL	1	FALSE	1	0.786763795101884	3		306	301	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0058109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	376	706	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.658117250376072	6	FACETS	0.819	0.776	0.863	0.546	0.517	0.576	CLONAL	2	FALSE	3	0.786763795101884	6		706	1501	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682991	241682991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226883651	NA	P-0058109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	125	745	0	ENST00000366560.3:c.32C>T	p.Ser11Leu	p.S11L	ENST00000366560	NM_000143.3	11	tCg/tTg	1/10	0.292509991750653	5	FACETS	0.962	0.872	1	0.192	0.174	0.212	INDETERMINATE	1	FALSE	0	0.786763795101884	5		745	720	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0058109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	582	722	2	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	0.774600823855019	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	FALSE	0	0.786763795101884	3		724	638	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075194	16075194	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	385	453	0	ENST00000268712.3:c.358C>T	p.Gln120Ter	p.Q120*	ENST00000268712	NM_006311.3	120	Cag/Tag	4/46	0.774600823855019	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	FALSE	0	0.786763795101884	3		453	420	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551932	150551932	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	58	721	0	ENST00000369026.2:c.75C>A	p.Ser25Arg	p.S25R	ENST00000369026	NM_021960.4	25	agC/agA	1/3	0.786763795101884	7	FACETS	0.387	0.331	0.449			1	SUBCLONAL	1	FALSE	NA	0.786763795101884	7		721	1130	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868682	37868682	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	327	837	0	ENST00000269571.5:c.1129C>G	p.Leu377Val	p.L377V	ENST00000269571		377	Ctg/Gtg	9/27	0.658117250376072	6	FACETS	0.887	0.838	0.937	0.591	0.558	0.625	CLONAL	2	FALSE	3	0.786763795101884	6		837	1206	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260290	10260290	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	54	841	0	ENST00000340748.4:c.2377C>T	p.His793Tyr	p.H793Y	ENST00000340748		793	Cac/Tac	25/40	0.494200806059345	5	FACETS	0.317	0.27	0.37	0.106	0.09	0.124	SUBCLONAL	1	FALSE	2	0.786763795101884	5		841	943	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61753598	61753598	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	44	483	0	ENST00000401558.2:c.185G>C	p.Arg62Thr	p.R62T	ENST00000401558	NM_003400.3	62	aGa/aCa	3/25	0.323144120240658	5	FACETS	0.516	0.432	0.608	0.172	0.144	0.203	INDETERMINATE	1	FALSE	2	0.786763795101884	5		483	473	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600468	43600468	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	200	1038	1	ENST00000355710.3:c.694G>A	p.Glu232Lys	p.E232K	ENST00000355710	NM_020975.4	232	Gag/Aag	4/20	0.258289280348473	5	FACETS	1	0.987	1	0.431	0.4	0.464	INDETERMINATE	1	FALSE	2	0.786763795101884	5		1039	857	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981084	201981084	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0058109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	47	699	0	ENST00000359651.3:c.164-1G>C		p.X55_splice	ENST00000359651		55			0.786763795101884	1	FACETS	0.336	0.286	0.389	0.336	0.286	0.389	SUBCLONAL	1	FALSE	0	0.786763795101884	1		699	216	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864774	57864774	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	136	1003	0	ENST00000228682.2:c.2251C>G	p.Leu751Val	p.L751V	ENST00000228682	NM_005269.2	751	Ctg/Gtg	12/12	0.727790789855735	5	FACETS	0.669	0.607	0.735	0.223	0.202	0.245	SUBCLONAL	1	FALSE	2	0.786763795101884	5		1003	1126	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022374	31022374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750708574	NA	P-0058109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	121	565	0	ENST00000375687.4:c.1859G>A	p.Arg620His	p.R620H	ENST00000375687	NM_015338.5	620	cGt/cAt	13/13	0.786763795101884	6	FACETS	1	0.929	1	0.207	0.186	0.228	CLONAL	1	FALSE	1	0.786763795101884	6		565	766	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023050	27023051	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0058109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	107	127	0	ENST00000324856.7:c.157dup	p.Ala53GlyfsTer58	p.A53Gfs*58	ENST00000324856	NM_006015.4	52	-/G	1/20	0.612218448656191	6	FACETS	0.98	0.898	1	0.98	0.898	1	CLONAL	3	FALSE	3	0.786763795101884	6		127	238	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105744	27105744	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1557619847	NA	P-0058109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	154	490	0	ENST00000324856.7:c.5355T>A	p.Asp1785Glu	p.D1785E	ENST00000324856	NM_006015.4	1785	gaT/gaA	20/20	0.612218448656191	6	FACETS	0.875	0.804	0.947	0.583	0.536	0.632	CLONAL	2	FALSE	3	0.786763795101884	6		490	576	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90634794	90634794	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	101	733	0	ENST00000330062.3:c.198C>G	p.Ile66Met	p.I66M	ENST00000330062	NM_002168.2	66	atC/atG	2/11	0.786763795101884	4	FACETS	0.544	0.486	0.606	0.181	0.162	0.202	SUBCLONAL	1	FALSE	1	0.786763795101884	4		733	843	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304237	91304237	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	48	455	0	ENST00000355112.3:c.1634G>C	p.Arg545Thr	p.R545T	ENST00000355112	NM_000057.2	545	aGa/aCa	7/22	0.786763795101884	4	FACETS	0.637	0.541	0.743	0.212	0.18	0.248	SUBCLONAL	1	FALSE	1	0.786763795101884	4		455	342	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56878455	56878455	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	132	615	1	ENST00000308159.5:c.2394G>A	p.Met798Ile	p.M798I	ENST00000308159	NM_014669.4	798	atG/atA	22/22	0.786763795101884	4	FACETS	0.76	0.69	0.833	0.38	0.345	0.417	SUBCLONAL	1	FALSE	2	0.786763795101884	4		616	789	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315366	30315366	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	125	519	0	ENST00000322652.5:c.1051C>G	p.Gln351Glu	p.Q351E	ENST00000322652	NM_015355.2	351	Cag/Gag	10/16	0.786763795101884	8	FACETS	1	0.949	1			1	CLONAL	1	FALSE	NA	0.786763795101884	8		519	991	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315421	30315421	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1298450451	NA	P-0058109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	141	578	0	ENST00000322652.5:c.1106C>A	p.Ser369Tyr	p.S369Y	ENST00000322652	NM_015355.2	369	tCt/tAt	10/16	0.786763795101884	8	FACETS	1	0.946	1			1	CLONAL	1	FALSE	NA	0.786763795101884	8		578	1139	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72864551	72864551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	38	388	0	ENST00000325599.8:c.886G>A	p.Glu296Lys	p.E296K	ENST00000325599	NM_018130.2	296	Gaa/Aaa	8/11	0.727790789855735	5	FACETS	0.556	0.46	0.662	0.185	0.153	0.221	SUBCLONAL	1	FALSE	2	0.786763795101884	5		388	379	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109315743	109315743	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	128	632	0	ENST00000436639.2:c.1042G>T	p.Glu348Ter	p.E348*	ENST00000436639	NM_014454.2	348	Gaa/Taa	6/10	0.786763795101884	6	FACETS	0.851	0.77	0.936			1	CLONAL	1	FALSE	NA	0.786763795101884	6		632	984	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411583	116411583	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	185	484	0	ENST00000397752.3:c.2762G>C	p.Gly921Ala	p.G921A	ENST00000397752	NM_000245.2	921	gGa/gCa	13/21	0.3178282483379	6	FACETS	0.949	0.887	1	0.949	0.887	1	INDETERMINATE	3	FALSE	3	0.786763795101884	6		484	425	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843359	128843359	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs749414966	NA	P-0058109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	419	1088	0	ENST00000249373.3:c.466A>G	p.Ile156Val	p.I156V	ENST00000249373	NM_005631.4	156	Atc/Gtc	2/12	0.3178282483379	6	FACETS	1	0.962	1	1	0.962	1	INDETERMINATE	3	FALSE	3	0.786763795101884	6		1088	909	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001317	150001317	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	48	504	0	ENST00000253339.5:c.2287G>T	p.Glu763Ter	p.E763*	ENST00000253339		763	Gaa/Taa	4/7	0.233530992949498	3	FACETS	0.808	0.683	0.946	0.404	0.341	0.473	CLONAL	1	TRUE	1	0.249780888530117	3		504	535	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054422	42054422	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	85	338	1	ENST00000219905.7:c.7606G>T	p.Asp2536Tyr	p.D2536Y	ENST00000219905	NM_001164273.1	2536	Gat/Tat	22/24	0.18999085357319	4	FACETS	0.973	0.864	1	0.973	0.864	1	CLONAL	2	TRUE	2	0.249780888530117	4		339	437	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111470	8111483	+	frameshift_variant	Frame_Shift_Del	DEL	ACTGTCAGACCACC	ACTGTCAGACCACC	-	novel	NA	P-0058110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	167	603	0	ENST00000346208.3:c.958_971del	p.Cys320AsnfsTer27	p.C320Nfs*27	ENST00000346208		319	aACTGTCAGACCACC/a	5/6	0.233530992949498	3	FACETS	0.954	0.878	1	0.954	0.878	1	CLONAL	2	TRUE	1	0.249780888530117	3		603	788	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0058111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	281	922	2	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.27673075392444	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.27673075392444	2		924	981	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039356	47039358	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0058111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	120	494	0	ENST00000377604.3:c.985_987del	p.Ser329del	p.S329del	ENST00000377604	NM_001204468.1	327	TCC/-	10/24	1	1	FACETS	0.855	0.778	0.935	1	0.988	1	CLONAL	2	TRUE	0	0.27673075392444	1		494	437	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254709	46254709	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768922410	NA	P-0058111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	56	376	0	ENST00000334344.6:c.4899G>A	p.Met1633Ile	p.M1633I	ENST00000334344	NM_152641.2	1633	atG/atA	16/21	0.24688405044075	3	FACETS	0.861	0.738	0.995	0.431	0.369	0.498	CLONAL	1	TRUE	1	0.27673075392444	3		376	535	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0058112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	115	361	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.357373246187501	3	FACETS	0.948	0.862	1	0.948	0.862	1	CLONAL	2	TRUE	1	0.357328271903442	3		361	400	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0058112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	188	698	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.351275539279269	2	FACETS	0.976	0.909	1	0.976	0.909	1	CLONAL	2	TRUE	0	0.357328271903442	2		698	539	SUCCESS
APC	324	MSKCC	GRCh37	5	112175171	112175171	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085373	NA	P-0058112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	32	181	0	ENST00000257430.4:c.3880C>T	p.Gln1294Ter	p.Q1294*	ENST00000257430	NM_000038.5	1294	Cag/Tag	16/16	1	2	FACETS	0.909	0.745	1	0.909	0.745	1	CLONAL	1	TRUE	1	0.357328271903442	2		181	197	SUCCESS
APC	324	MSKCC	GRCh37	5	112174597	112174597	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs879254092	NA	P-0058112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	54	376	0	ENST00000257430.4:c.3306C>G	p.Tyr1102Ter	p.Y1102*	ENST00000257430	NM_000038.5	1102	taC/taG	16/16	1	2	FACETS	0.939	0.806	1	0.939	0.806	1	CLONAL	1	TRUE	1	0.357328271903442	2		376	322	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440268	187440268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760088914	NA	P-0058112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	102	642	1	ENST00000232014.4:c.2099C>T	p.Pro700Leu	p.P700L	ENST00000232014	NM_001130845.1	700	cCg/cTg	10/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.357328271903442	2		643	503	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193181197	193181197	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	29	241	0	ENST00000367435.3:c.1033T>C	p.Ser345Pro	p.S345P	ENST00000367435	NM_024529.4	345	Tct/Cct	12/17	1	2	FACETS	0.984	0.798	1	0.984	0.798	1	CLONAL	1	TRUE	1	0.357328271903442	2		241	165	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575150	48575150	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	57	321	0	ENST00000342988.3:c.344G>T	p.Cys115Phe	p.C115F	ENST00000342988	NM_005359.5	115	tGt/tTt	3/12	0.357328271903442	1	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	0	0.357328271903442	1		321	261	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957470	1957470	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	116	854	0	ENST00000382891.5:c.2569T>C	p.Cys857Arg	p.C857R	ENST00000382891	NM_133335.3	857	Tgc/Cgc	14/22	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.357328271903442	2		854	611	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946203	55946203	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs778737297	NA	P-0058112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	79	586	0	ENST00000263923.4:c.3976C>A	p.Leu1326Ile	p.L1326I	ENST00000263923	NM_002253.2	1326	Ctt/Att	30/30	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.357328271903442	2		586	436	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0058113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	197	305	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.888	0.829	0.948	1	0.995	1	CLONAL	3	FALSE	1	0.277390923584863	2		305	533	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553492	29553492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768638173	NA	P-0058135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	62	529	0	ENST00000356175.3:c.2041C>T	p.Arg681Ter	p.R681*	ENST00000356175	NM_000267.3	681	Cga/Tga	18/57	1	2	FACETS	0.98	0.848	1	0.98	0.848	1	CLONAL	1	TRUE	1	0.24	2		529	527	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347236	89347236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	63	564	0	ENST00000301030.4:c.5714G>A	p.Gly1905Glu	p.G1905E	ENST00000301030	NM_001256183.1	1905	gGg/gAg	9/13	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.24	2		564	402	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483141	29483142	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0058135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	22	310	0	ENST00000356175.3:c.202_203insAA	p.Met68LysfsTer2	p.M68Kfs*2	ENST00000356175	NM_000267.3	67	-/AA	2/57	1	2	FACETS	0.494	0.382	0.624	0.494	0.382	0.624	SUBCLONAL	1	TRUE	1	0.24	2		310	371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0058136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	414	609	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.728891758627612	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.728891758627612	1		609	644	SUCCESS
APC	324	MSKCC	GRCh37	5	112175417	112175418	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	rs1554085533	NA	P-0058136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	232	228	0	ENST00000257430.4:c.4127_4128del	p.Tyr1376CysfsTer9	p.Y1376Cfs*9	ENST00000257430	NM_000038.5	1376	TAt/t	16/16	0.706386886131349	2	FACETS	0.897	0.855	0.937	0.897	0.855	0.937	CLONAL	2	TRUE	0	0.728891758627612	2		228	355	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951955	178951955	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	151	368	0	ENST00000263967.3:c.3010A>G	p.Met1004Val	p.M1004V	ENST00000263967	NM_006218.2	1004	Atg/Gtg	21/21	0.352486612640654	1	FACETS	0.44	0.403	0.477	0.44	0.403	0.477	INDETERMINATE	1	TRUE	0	0.728891758627612	1		368	599	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966665	36966665	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	337	427	0	ENST00000358127.4:c.661C>T	p.Arg221Trp	p.R221W	ENST00000358127	NM_001280556.1	221	Cgg/Tgg	6/10	0.441972139169056	1	FACETS	0.823	0.784	0.862	0.823	0.784	0.862	CLONAL	1	TRUE	0	0.728891758627612	1		427	714	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120381	70120382	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0058136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	594	700	0	ENST00000245479.2:c.1386_1387dup	p.Tyr463SerfsTer8	p.Y463Sfs*8	ENST00000245479	NM_000346.3	461	-/CT	3/3	0.387865579700241	1	FACETS	0.778	0.749	0.806	0.778	0.749	0.806	INDETERMINATE	1	TRUE	0	0.728891758627612	1		700	1332	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911499	114911500	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0058136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	155	195	0	ENST00000543371.1:c.1022dup	p.Glu342GlyfsTer14	p.E342Gfs*14	ENST00000543371	NM_001198531.1	339	-/A	10/14	0.414291369479856	1	FACETS	0.757	0.703	0.812	0.757	0.703	0.812	INDETERMINATE	1	TRUE	0	0.728891758627612	1		195	357	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456421	99456421	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	144	416	0	ENST00000268035.6:c.1738T>A	p.Tyr580Asn	p.Y580N	ENST00000268035	NM_000875.3	580	Tac/Aac	8/21	NA	2	FACETS	0.448	0.408	0.49			1	INDETERMINATE	1	TRUE	NA	0.728891758627612	2		416	882	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182228	99182228	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	223	416	0	ENST00000074304.5:c.2293C>A	p.Arg765Ser	p.R765S	ENST00000074304	NM_001134224.1	765	Cgc/Agc	21/26	0.414291369479856	1	FACETS	0.484	0.451	0.517	0.484	0.451	0.517	INDETERMINATE	1	TRUE	0	0.728891758627612	1		416	804	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620610	52620610	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	340	350	0	ENST00000394830.3:c.3143T>C	p.Ile1048Thr	p.I1048T	ENST00000394830	NM_018313.4	1048	aTt/aCt	21/30	0.387865579700241	1	FACETS	0.782	0.745	0.82	0.782	0.745	0.82	INDETERMINATE	1	TRUE	0	0.728891758627612	1		350	758	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797749	32797749	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	159	469	0	ENST00000374899.4:c.1753G>T	p.Ala585Ser	p.A585S	ENST00000374899	NM_018833.2	585	Gca/Tca	10/12	1	2	FACETS	0.437	0.4	0.476	0.437	0.4	0.476	SUBCLONAL	1	TRUE	1	0.728891758627612	2		469	998	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421574	32421574	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	29	475	0	ENST00000332351.3:c.1018G>C	p.Glu340Gln	p.E340Q	ENST00000332351	NM_024426.4	340	Gag/Cag	6/10	1	2	FACETS	0.622	0.498	0.764	0.622	0.498	0.764	SUBCLONAL	1	TRUE	1	0.18	2		475	518	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0058137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	86	440	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	1	2	FACETS	0.788	0.698	0.885	1	0.98	1	SUBCLONAL	2	TRUE	1	0.18	2		440	606	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805493	46805493	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	46	702	0	ENST00000290295.7:c.463C>A	p.Pro155Thr	p.P155T	ENST00000290295	NM_006361.5	155	Cct/Act	1/2	1	2	FACETS	0.687	0.577	0.809	0.687	0.577	0.809	SUBCLONAL	1	TRUE	1	0.18	2		702	744	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56860202	56860202	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	37	473	0	ENST00000519728.1:c.205del	p.Val69Ter	p.V69*	ENST00000519728	NM_002350.3	68	gtG/gt	4/13	1	2	FACETS	0.715	0.588	0.857	0.715	0.588	0.857	SUBCLONAL	1	TRUE	1	0.18	2		473	575	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0058138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	54	254	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.700748677224088	2		254	132	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100175	27100176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0058138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	87	451	0	ENST00000324856.7:c.3977dup	p.Gln1327AlafsTer11	p.Q1327Afs*11	ENST00000324856	NM_006015.4	1324	tac/taCc	16/20	1	2	FACETS	0.85	0.762	0.943	0.85	0.762	0.943	CLONAL	1	TRUE	1	0.700748677224088	2		451	292	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0058138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	315	793	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.700748677224088	2		793	412	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	92	262	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	0.700748677224088	3	FACETS	0.933	0.851	1	0.933	0.851	1	CLONAL	2	TRUE	1	0.700748677224088	3		262	190	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95556956	95556956	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1299000813	NA	P-0058138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	53	431	0	ENST00000393063.1:c.5648A>G	p.Glu1883Gly	p.E1883G	ENST00000393063	NM_030621.3	1883	gAa/gGa	28/28	1	2	FACETS	0.615	0.529	0.706	0.615	0.529	0.706	SUBCLONAL	1	TRUE	1	0.700748677224088	2		431	246	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221552	36221819	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCCATAGCTGGATCCCATTTCCCAAGCATCCTAACCGTCTTATCCCACATGCCAGGTGCTCCCGTCTGTACTGGAGCACAGTGGATGCTCGGAGGCGCTGCTGGTATCGGTGCCGAATTCTGGAGTATCGGCCATGGGGGCCGAGGGAAGAGCCAGCTCACCTGGAGGCTGCAGAGGAGAACCAGACCATTGTGCACAGCCCCGCCCCTTCCTCAGGTGTGGCTTTGGCTCTGTCTTCTTCCTGAATACCGCTCTCCCTAAACAAAC	CTCCATAGCTGGATCCCATTTCCCAAGCATCCTAACCGTCTTATCCCACATGCCAGGTGCTCCCGTCTGTACTGGAGCACAGTGGATGCTCGGAGGCGCTGCTGGTATCGGTGCCGAATTCTGGAGTATCGGCCATGGGGGCCGAGGGAAGAGCCAGCTCACCTGGAGGCTGCAGAGGAGAACCAGACCATTGTGCACAGCCCCGCCCCTTCCTCAGGTGTGGCTTTGGCTCTGTCTTCTTCCTGAATACCGCTCTCCCTAAACAAAC	-	novel	NA	P-0058138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	18	586	0	ENST00000222270.7:c.5276+37_5437+53del		p.X1759_splice	ENST00000222270	NM_014727.1	1759		26/37	1	2	FACETS	0.154	0.115	0.199	0.154	0.115	0.199	SUBCLONAL	1	TRUE	1	0.700748677224088	2		586	334	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285841	198285841	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1261996759	NA	P-0058138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	81	330	0	ENST00000335508.6:c.212C>T	p.Ser71Leu	p.S71L	ENST00000335508	NM_012433.2	71	tCa/tTa	3/25	0.130499049175278	3	FACETS	0.784	0.706	0.865	0.784	0.706	0.865	INDETERMINATE	2	TRUE	1	0.700748677224088	3		330	199	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942724	44942724	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	72	206	0	ENST00000377967.4:c.3304G>T	p.Glu1102Ter	p.E1102*	ENST00000377967	NM_021140.2	1102	Gag/Tag	23/29	1	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.700748677224088	1		206	95	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045183	47045184	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0058138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	127	250	0	ENST00000377604.3:c.2425dup	p.Met809AsnfsTer12	p.M809Nfs*12	ENST00000377604	NM_001204468.1	808	-/A	21/24	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.700748677224088	1		250	201	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0058139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	117	172	0				ENST00000310581	NM_198253.2	-/1132			0.13885741579821	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.720489326232161	0		172	314	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894230	NA	P-0058139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	129	495	0	ENST00000451590.1:c.35G>A	p.Gly12Asp	p.G12D	ENST00000451590	NM_001130442.1	12	gGc/gAc	2/5	1	2	FACETS	0.682	0.621	0.745	0.682	0.621	0.745	SUBCLONAL	1	TRUE	1	0.720489326232161	2		495	525	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702630	52702630	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	95	314	0	ENST00000394830.3:c.268C>T	p.Gln90Ter	p.Q90*	ENST00000394830	NM_018313.4	90	Cag/Tag	4/30	0.663339746701197	1	FACETS	0.893	0.816	0.969	0.893	0.816	0.969	CLONAL	1	TRUE	0	0.720489326232161	1		314	189	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs1202793339	NA	P-0058139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	110	551	0	ENST00000269305.4:c.560-1G>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.370656787312314	1	FACETS	0.428	0.387	0.472	0.428	0.387	0.472	INDETERMINATE	1	TRUE	0	0.720489326232161	1		551	456	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641447	18641447	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	72	204	1	ENST00000266497.5:c.2446C>T	p.Leu816Phe	p.L816F	ENST00000266497		816	Ctc/Ttc	17/31	NA	2	FACETS	1	0.924	1			1	INDETERMINATE	1	TRUE	NA	0.720489326232161	2		205	191	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377154	118377154	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149137886	NA	P-0058139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	71	402	0	ENST00000534358.1:c.10547G>A	p.Gly3516Glu	p.G3516E	ENST00000534358	NM_005933.3	3516	gGg/gAg	27/36	1	2	FACETS	0.431	0.377	0.489	0.431	0.377	0.489	SUBCLONAL	1	TRUE	1	0.720489326232161	2		402	457	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652006	36652007	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0058139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	239	624	0	ENST00000244741.5:c.130dup	p.Glu44GlyfsTer4	p.E44Gfs*4	ENST00000244741	NM_000389.4	43	cag/caGg	2/3	0.120904944372031	4	FACETS	0.79	0.741	0.841	0.79	0.741	0.841	INDETERMINATE	2	TRUE	2	0.720489326232161	4		624	722	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934193	39934193	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	112	643	0	ENST00000378444.4:c.406G>T	p.Ala136Ser	p.A136S	ENST00000378444	NM_001123385.1	136	Gcc/Tcc	4/15	NA	2	FACETS	0.488	0.44	0.539			1	INDETERMINATE	1	TRUE	NA	0.720489326232161	2		643	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0058150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	233	749	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.234754419331609	2	FACETS	0.818	0.764	0.874	0.818	0.764	0.874	CLONAL	2	TRUE	0	0.306525194762658	2		749	929	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0058150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	202	544	0	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	0.306525194762658	2	FACETS	0.941	0.876	1	0.941	0.876	1	CLONAL	2	TRUE	0	0.306525194762658	2		544	700	SUCCESS
APC	324	MSKCC	GRCh37	5	112175378	112175378	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0058150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	76	273	0	ENST00000257430.4:c.4087A>T	p.Lys1363Ter	p.K1363*	ENST00000257430	NM_000038.5	1363	Aaa/Taa	16/16	0.236789413151253	2	FACETS	1	0.968	1	0.651	0.574	0.732	CLONAL	1	TRUE	0	0.306525194762658	2		273	381	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891471	76891471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	60	238	0	ENST00000373344.5:c.4634C>T	p.Thr1545Ile	p.T1545I	ENST00000373344	NM_000489.3	1545	aCc/aTc	16/35	0.306525194762658	2	FACETS	0.833	0.719	0.956			1	CLONAL	1	TRUE	NA	0.306525194762658	2		238	470	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112025277	112025277	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	38	379	0	ENST00000368678.4:c.472G>C	p.Asp158His	p.D158H	ENST00000368678		158	Gat/Cat	6/13	1	2	FACETS	0.527	0.434	0.631	0.527	0.434	0.631	SUBCLONAL	1	TRUE	1	0.201137007576763	2		379	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0058151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	63	525	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			1	2	FACETS	0.758	0.654	0.872	0.758	0.654	0.872	SUBCLONAL	1	TRUE	1	0.201137007576763	2		525	826	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524651	187524651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754963553	NA	P-0058151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	48	564	0	ENST00000441802.2:c.11029G>A	p.Asp3677Asn	p.D3677N	ENST00000441802	NM_005245.3	3677	Gac/Aac	19/27	1	2	FACETS	0.555	0.468	0.652	0.555	0.468	0.652	SUBCLONAL	1	TRUE	1	0.201137007576763	2		564	860	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438728	49438728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290729871	NA	P-0058151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	61	607	0	ENST00000301067.7:c.4762G>A	p.Glu1588Lys	p.E1588K	ENST00000301067	NM_003482.3	1588	Gaa/Aaa	19/54	1	2	FACETS	0.658	0.566	0.759	0.658	0.566	0.759	SUBCLONAL	1	TRUE	1	0.201137007576763	2		607	922	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788618	3788618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398124146	NA	P-0058152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	49	449	0	ENST00000262367.5:c.4336C>T	p.Arg1446Cys	p.R1446C	ENST00000262367	NM_004380.2	1446	Cgc/Tgc	26/31	1	2	FACETS	0.287	0.242	0.336	0.287	0.242	0.336	SUBCLONAL	1	TRUE	1	0.572117274987411	2		449	597	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0058152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	163	632	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.494	0.452	0.538	0.494	0.452	0.538	SUBCLONAL	1	TRUE	1	0.572117274987411	2		632	1153	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0058152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	318	785	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	0.977	0.922	1	0.977	0.922	1	CLONAL	1	TRUE	1	0.572117274987411	2		786	1138	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918502	44918502	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	52	201	0	ENST00000377967.4:c.985C>T	p.Gln329Ter	p.Q329*	ENST00000377967	NM_021140.2	329	Cag/Tag	12/29	1	1	FACETS	0.421	0.361	0.487	0.421	0.361	0.487	SUBCLONAL	1	TRUE	0	0.572117274987411	1		201	308	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143985	11143985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	551	738	1	ENST00000358026.2:c.3566G>A	p.Arg1189Gln	p.R1189Q	ENST00000358026	NM_001128849.1	1189	cGa/cAa	26/36	0.560298277531001	2	FACETS	0.962	0.929	0.995	0.962	0.929	0.995	CLONAL	2	TRUE	0	0.572117274987411	2		739	1001	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132500	11132500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs898406635	NA	P-0058152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1292	112	945	1	ENST00000358026.2:c.2716C>T	p.Arg906Cys	p.R906C	ENST00000358026	NM_001128849.1	906	Cgc/Tgc	19/36	0.560298277531001	2	FACETS	0.279	0.25	0.31	0.139	0.125	0.155	SUBCLONAL	1	TRUE	0	0.572117274987411	2		946	1404	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418670	49418670	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783698	NA	P-0058152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	80	700	0	ENST00000301067.7:c.15844C>T	p.Arg5282Ter	p.R5282*	ENST00000301067	NM_003482.3	5282	Cga/Tga	49/54	1	2	FACETS	0.325	0.285	0.368	0.325	0.285	0.368	SUBCLONAL	1	TRUE	1	0.572117274987411	2		700	861	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022761	31022761	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	82	736	0	ENST00000375687.4:c.2246del	p.Leu749ProfsTer23	p.L749Pfs*23	ENST00000375687	NM_015338.5	749	cTc/cc	13/13	1	2	FACETS	0.276	0.243	0.312	0.276	0.243	0.312	SUBCLONAL	1	TRUE	1	0.572117274987411	2		736	1038	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432708	49432708	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	303	816	1	ENST00000301067.7:c.8431C>T	p.Gln2811Ter	p.Q2811*	ENST00000301067	NM_003482.3	2811	Cag/Tag	34/54	1	2	FACETS	0.908	0.855	0.962	0.908	0.855	0.962	CLONAL	1	TRUE	1	0.572117274987411	2		817	1167	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094480	27094480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	56	576	0	ENST00000324856.7:c.3188G>A	p.Gly1063Glu	p.G1063E	ENST00000324856	NM_006015.4	1063	gGa/gAa	11/20	1	2	FACETS	0.245	0.209	0.285	0.245	0.209	0.285	SUBCLONAL	1	TRUE	1	0.572117274987411	2		576	798	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436366	49436366	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	268	743	0	ENST00000301067.7:c.5845C>T	p.Gln1949Ter	p.Q1949*	ENST00000301067	NM_003482.3	1949	Cag/Tag	27/54	1	2	FACETS	0.966	0.907	1	0.966	0.907	1	CLONAL	1	TRUE	1	0.572117274987411	2		743	970	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243047	105243048	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCAGGCAGCGGATGATGAAGGTGTTGGGCCGGGGCCGCTCCGTCTTCATCAGCTGGCACTCTGCGG	novel	NA	P-0058152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1555	107	1056	0	ENST00000349310.3:c.176-6_235dup	p.Leu78_Gln79insProAlaGluCysGlnLeuMetLysThrGluArgProArgProAsnThrPheIleIleArgCysLeu	p.L78_Q79insPAECQLMKTERPRPNTFIIRCL	ENST00000349310	NM_001014432.1	79	cag/cCCGCAGAGTGCCAGCTGATGAAGACGGAGCGGCCCCGGCCCAACACCTTCATCATCCGCTGCCTGCag	5/15	1	2	FACETS	0.225	0.201	0.251	0.225	0.201	0.251	SUBCLONAL	1	TRUE	1	0.572117274987411	2		1056	1662	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134297	11134297	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	136	689	0	ENST00000358026.2:c.2963T>G	p.Leu988Trp	p.L988W	ENST00000358026	NM_001128849.1	988	tTg/tGg	20/36	0.560298277531001	2	FACETS	0.486	0.441	0.533	0.243	0.22	0.267	SUBCLONAL	1	TRUE	0	0.572117274987411	2		689	979	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211611	36211612	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0058152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	182	649	1	ENST00000222270.7:c.1362_1363delinsTT	p.Glu454_Glu455delinsAspTer	p.E454_E455delinsD*	ENST00000222270	NM_014727.1	454	gaGGaa/gaTTaa	3/37	1	2	FACETS	0.724	0.668	0.782	0.724	0.668	0.782	SUBCLONAL	1	TRUE	1	0.572117274987411	2		650	879	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213194	39213194	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs140991871	NA	P-0058152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	324	884	0	ENST00000402219.2:c.3773C>G	p.Pro1258Arg	p.P1258R	ENST00000402219	NM_005633.3	1258	cCa/cGa	23/23	1	2	FACETS	0.838	0.791	0.887	0.838	0.791	0.887	CLONAL	1	TRUE	1	0.572117274987411	2		884	1351	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918641	44918645	+	frameshift_variant	Frame_Shift_Del	DEL	ACTTA	ACTTA	-	novel	NA	P-0058152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	177	299	0	ENST00000377967.4:c.1125_1129del	p.Tyr375Ter	p.Y375*	ENST00000377967	NM_021140.2	375	tACTTA/t	12/29	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.572117274987411	1		299	365	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213581	27213581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	136	467	0	ENST00000380036.4:c.2977G>A	p.Val993Met	p.V993M	ENST00000380036	NM_000459.3	993	Gtg/Atg	18/23	1	2	FACETS	0.746	0.681	0.815	0.746	0.681	0.815	SUBCLONAL	1	TRUE	1	0.572117274987411	2		467	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0058154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	206	681	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.336273305016377	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.336273305016377	1		681	967	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0058155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	244	382	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.997	0.938	1	0.997	0.938	1	CLONAL	1	TRUE	1	0.793352404166069	2		382	617	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212737	27212737	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	342	703	0	ENST00000380036.4:c.2719C>G	p.His907Asp	p.H907D	ENST00000380036	NM_000459.3	907	Cat/Gat	17/23	0.793352404166069	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.793352404166069	1		703	506	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0058156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	159	416	1	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.54	2		417	553	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0058156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	240	729	8	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.977	0.914	1	0.977	0.914	1	CLONAL	1	TRUE	1	0.54	2		737	910	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0058156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	159	722	5	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.672	0.616	0.731	0.672	0.616	0.731	SUBCLONAL	1	TRUE	1	0.54	2		727	876	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0058156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	199	622	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.974	0.904	1	0.974	0.904	1	CLONAL	1	TRUE	1	0.54	2		622	757	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0058156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	155	465	5	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.813	0.746	0.883	0.813	0.746	0.883	CLONAL	1	TRUE	1	0.54	2		470	706	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0058156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	168	496	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.996	0.919	1	0.996	0.919	1	CLONAL	1	TRUE	1	0.54	2		496	625	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	106	391	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.796	0.717	0.879	0.796	0.717	0.879	SUBCLONAL	1	TRUE	1	0.54	2		391	493	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087503	27087503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	326	768	0	ENST00000324856.7:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000324856	NM_006015.4	693	Cga/Tga	5/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.54	2		768	1058	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0058156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	118	500	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.713	0.645	0.785	0.713	0.645	0.785	SUBCLONAL	1	TRUE	1	0.54	2		500	613	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781324	3781326	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs587783502	NA	P-0058156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	34	901	1	ENST00000262367.5:c.5039_5041del	p.Ser1680del	p.S1680del	ENST00000262367	NM_004380.2	1680	tCCTtg/ttg	30/31	1	2	FACETS	0.108	0.087	0.131	0.108	0.087	0.131	SUBCLONAL	1	TRUE	1	0.54	2		902	1167	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	274	917	2	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.965	0.906	1	0.965	0.906	1	CLONAL	1	TRUE	1	0.54	2		919	1052	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101612	27101612	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	295	807	0	ENST00000324856.7:c.4899del	p.Met1634Ter	p.M1634*	ENST00000324856	NM_006015.4	1632	Ccc/cc	18/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.54	2		807	1064	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615698	1615698	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	236	915	6	ENST00000344749.5:c.1573del	p.Arg525GlyfsTer18	p.R525Gfs*18	ENST00000344749	NM_001136139.2	525	Cgg/gg	17/19	1	2	FACETS	0.823	0.768	0.88	0.823	0.768	0.88	CLONAL	1	TRUE	1	0.54	2		921	1062	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0058156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	165	652	2	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	1	2	FACETS	0.708	0.65	0.768	0.708	0.65	0.768	SUBCLONAL	1	TRUE	1	0.54	2		654	863	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238356	98238356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	165	454	3	ENST00000331920.6:c.1688C>T	p.Ala563Val	p.A563V	ENST00000331920	NM_000264.3	563	gCg/gTg	12/24	1	2	FACETS	0.958	0.883	1	0.958	0.883	1	CLONAL	1	TRUE	1	0.54	2		457	638	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270529	98270530	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs751977093	NA	P-0058156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	73	229	1	ENST00000331920.6:c.114dup	p.Leu39AlafsTer51	p.L39Afs*51	ENST00000331920	NM_000264.3	38	-/G	1/24	1	2	FACETS	0.832	0.733	0.936	0.832	0.733	0.936	CLONAL	1	TRUE	1	0.54	2		230	325	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589625	67589627	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	novel	NA	P-0058156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	50	204	0	ENST00000274335.5:c.1390_1392del	p.Asp464del	p.D464del	ENST00000274335		463	tATGat/tat	10/15	1	2	FACETS	0.775	0.664	0.894	0.775	0.664	0.894	SUBCLONAL	1	TRUE	1	0.54	2		204	239	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655479	67655479	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs769948988	NA	P-0058156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	153	408	0	ENST00000264010.4:c.1342C>T	p.Arg448Ter	p.R448*	ENST00000264010	NM_006565.3	448	Cga/Tga	7/12	1	2	FACETS	0.989	0.909	1	0.989	0.909	1	CLONAL	1	TRUE	1	0.54	2		408	573	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523645	176523645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	242	822	0	ENST00000292408.4:c.2056G>T	p.Gly686Trp	p.G686W	ENST00000292408	NM_213647.1	686	Ggg/Tgg	16/18	1	2	FACETS	0.916	0.856	0.977	0.916	0.856	0.977	CLONAL	1	TRUE	1	0.54	2		822	979	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831462	89831462	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	103	500	0	ENST00000389301.3:c.2614A>G	p.Met872Val	p.M872V	ENST00000389301	NM_000135.2	872	Atg/Gtg	28/43	1	2	FACETS	0.617	0.553	0.685	0.617	0.553	0.685	SUBCLONAL	1	TRUE	1	0.54	2		500	618	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948484	71948484	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	299	909	2	ENST00000298229.2:c.3201del	p.Ser1068AlafsTer63	p.S1068Afs*63	ENST00000298229	NM_001567.3	1066	Ccc/cc	26/28	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.54	2		911	1071	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422383	47422384	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1453474773	NA	P-0058156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	145	467	0	ENST00000377045.4:c.23dup	p.Ala9CysfsTer84	p.A9Cfs*84	ENST00000377045	NM_001654.4	6	ggc/ggCc	2/16	1	2	FACETS	0.928	0.85	1	0.928	0.85	1	CLONAL	1	TRUE	1	0.54	2		467	579	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256479	115256480	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCCTTC	novel	NA	P-0058156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	171	551	0	ENST00000369535.4:c.226_231dup	p.Glu76_Gly77dup	p.E76_G77dup	ENST00000369535	NM_002524.4	76	-/GAAGGC	3/7	1	2	FACETS	0.922	0.851	0.996	0.922	0.851	0.996	CLONAL	1	TRUE	1	0.54	2		551	687	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716078	243716078	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	145	472	0	ENST00000263826.5:c.1116T>G	p.Asp372Glu	p.D372E	ENST00000263826	NM_005465.4	372	gaT/gaG	10/13	1	2	FACETS	0.886	0.812	0.964	0.886	0.812	0.964	CLONAL	1	TRUE	1	0.54	2		472	606	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63760042	63760042	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	111	300	1	ENST00000279873.7:c.695C>A	p.Pro232Gln	p.P232Q	ENST00000279873	NM_032199.2	232	cCg/cAg	4/10	1	2	FACETS	0.979	0.886	1	0.979	0.886	1	CLONAL	1	TRUE	1	0.54	2		301	420	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139229	108139229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	222	600	0	ENST00000278616.4:c.2731G>A	p.Ala911Thr	p.A911T	ENST00000278616	NM_000051.3	911	Gct/Act	18/63	1	2	FACETS	0.993	0.926	1	0.993	0.926	1	CLONAL	1	TRUE	1	0.54	2		600	828	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253166	133253166	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	113	460	0	ENST00000320574.5:c.875A>G	p.Gln292Arg	p.Q292R	ENST00000320574	NM_006231.2	292	cAg/cGg	9/49	1	2	FACETS	0.632	0.57	0.698	0.632	0.57	0.698	SUBCLONAL	1	TRUE	1	0.54	2		460	662	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554342	63554342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	59	683	0	ENST00000307078.5:c.397G>A	p.Ala133Thr	p.A133T	ENST00000307078	NM_004655.3	133	Gcg/Acg	2/11	1	2	FACETS	0.255	0.218	0.295	0.255	0.218	0.295	SUBCLONAL	1	TRUE	1	0.54	2		683	857	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218821	36218831	+	frameshift_variant	Frame_Shift_Del	DEL	CACTCGGAGGA	CACTCGGAGGA	-	novel	NA	P-0058156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	275	883	0	ENST00000222270.7:c.4432_4442del	p.His1478GlyfsTer196	p.H1478Gfs*196	ENST00000222270	NM_014727.1	1478	CACTCGGAGGAg/g	18/37	1	2	FACETS	0.981	0.922	1	0.981	0.922	1	CLONAL	1	TRUE	1	0.54	2		883	1038	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462326	89462326	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	95	450	0	ENST00000336596.2:c.1798C>T	p.His600Tyr	p.H600Y	ENST00000336596	NM_005233.5	600	Cat/Tat	10/17	1	2	FACETS	0.622	0.555	0.693	0.622	0.555	0.693	SUBCLONAL	1	TRUE	1	0.54	2		450	566	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409091	139409091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	233	880	0	ENST00000277541.6:c.2078G>A	p.Cys693Tyr	p.C693Y	ENST00000277541	NM_017617.3	693	tGc/tAc	13/34	1	2	FACETS	0.76	0.708	0.814	0.76	0.708	0.814	SUBCLONAL	1	TRUE	1	0.54	2		880	1135	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613302	100613303	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0058156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	151	530	0	ENST00000308731.7:c.1097_1098del	p.Ser366CysfsTer32	p.S366Cfs*32	ENST00000308731	NM_000061.2	366	tCT/t	12/19	1	2	FACETS	0.932	0.856	1	0.932	0.856	1	CLONAL	1	TRUE	1	0.54	2		530	600	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0058157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	652	293	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.285048396453676	9	FACETS	0.992	0.963	1			1	CLONAL	9	FALSE	NA	0.285048396453676	9		293	1024	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577527	7577527	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555525470	NA	P-0058157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	179	691	0	ENST00000269305.4:c.754del	p.Leu252SerfsTer93	p.L252Sfs*93	ENST00000269305	NM_001126112.2	252	Ctc/tc	7/11	0.271676116024393	2	FACETS	0.933	0.863	1	0.933	0.863	1	CLONAL	2	FALSE	0	0.285048396453676	2		691	673	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228794	36228794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	86	936	3	ENST00000222270.7:c.7693C>T	p.Arg2565Cys	p.R2565C	ENST00000222270	NM_014727.1	2565	Cgt/Tgt	35/37	0.258633566696426	4	FACETS	0.799	0.706	0.9	0.4	0.353	0.45	SUBCLONAL	1	FALSE	2	0.285048396453676	4		939	970	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0058158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	468	747	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.49320180436634	3	FACETS	1	0.993	1	0.74	0.714	0.767	CLONAL	2	FALSE	0	0.71877890981026	3		747	797	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0058158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	3446	636	1	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.71877890981026	19	FACETS	1	0.994	1	0.947	0.939	0.955	CLONAL	17	FALSE	1	0.71877890981026	19		637	3999	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56852610	56852610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764790250	NA	P-0058158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	49	542	0	ENST00000308159.5:c.524G>A	p.Arg175Gln	p.R175Q	ENST00000308159	NM_014669.4	175	cGa/cAa	6/22	0.392320961423688	4	FACETS	0.522	0.442	0.609			1	INDETERMINATE	1	FALSE	NA	0.71877890981026	4		542	449	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948601	71948601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1441314714	NA	P-0058158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1863	612	923	1	ENST00000298229.2:c.3313C>T	p.Pro1105Ser	p.P1105S	ENST00000298229	NM_001567.3	1105	Cca/Tca	26/28	0.71877890981026	6	FACETS	0.839	0.804	0.874	0.419	0.402	0.437	CLONAL	2	FALSE	2	0.71877890981026	6		924	2475	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321013	30321013	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	71	400	0	ENST00000322652.5:c.1423A>T	p.Ile475Phe	p.I475F	ENST00000322652	NM_015355.2	475	Atc/Ttc	12/16	0.71877890981026	10	FACETS	1	0.962	1			1	CLONAL	1	FALSE	NA	0.71877890981026	10		400	600	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222032	2222032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs530743556	NA	P-0058158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1470	213	864	1	ENST00000398665.3:c.2864C>T	p.Ser955Phe	p.S955F	ENST00000398665	NM_032482.2	955	tCt/tTt	24/28	0.723328596712345	5	FACETS	0.732	0.677	0.789	0.244	0.225	0.263	SUBCLONAL	1	FALSE	2	0.71877890981026	5		865	1683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0058160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	745	611	3	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.682488088076794	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.683992432038106	2		614	1049	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354226	70354226	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1423751717	NA	P-0058160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	698	610	0	ENST00000374080.3:c.4637C>T	p.Thr1546Met	p.T1546M	ENST00000374080		1546	aCg/aTg	34/45	0.589208150792547	4	FACETS	0.976	0.942	1	0.976	0.942	1	CLONAL	2	TRUE	2	0.683992432038106	4		610	1761	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881489	48881490	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs587778862	NA	P-0058160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	230	220	0	ENST00000267163.4:c.219_220del	p.Arg73SerfsTer36	p.R73Sfs*36	ENST00000267163	NM_000321.2	71	AGa/a	2/27	0.682488088076794	2	FACETS	0.924	0.879	0.967	0.924	0.879	0.967	CLONAL	2	TRUE	0	0.683992432038106	2		220	364	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635539	47635539	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs267607914	NA	P-0058160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	212	223	0	ENST00000233146.2:c.212-1G>A		p.X71_splice	ENST00000233146	NM_000251.2	71			0.682866090003781	2	FACETS	0.928	0.882	0.973	0.928	0.882	0.973	CLONAL	2	TRUE	0	0.683992432038106	2		223	334	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793008	33793010	+	inframe_deletion	In_Frame_Del	DEL	CGC	CGC	-	rs780345232	NA	P-0058160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	9	68	0	ENST00000498907.2:c.311_313del	p.Gly104del	p.G104del	ENST00000498907	NM_004364.3	104	gGCGac/gac	1/1	0.682866090003781	2	FACETS	0.194	0.128	0.276	0.097	0.064	0.138	SUBCLONAL	1	TRUE	0	0.683992432038106	2		68	136	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73995319	73995319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148316620	NA	P-0058160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	54	157	0	ENST00000318443.5:c.625C>T	p.Arg209Trp	p.R209W	ENST00000318443	NM_001024736.1	209	Cgg/Tgg	4/10	0.683992432038106	3	FACETS	0.765	0.659	0.879	0.382	0.329	0.44	SUBCLONAL	1	TRUE	1	0.683992432038106	3		157	277	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874011	123874013	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs780061449	NA	P-0058160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	10	23	0	ENST00000330479.4:c.62_64del	p.Ala21del	p.A21del	ENST00000330479	NM_020382.3	14	gaGGCg/gag	2/9	0.669268053268075	3	FACETS	0.265	0.18	0.372	0.088	0.06	0.124	SUBCLONAL	1	TRUE	0	0.683992432038106	3		23	148	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120209	70120209	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	754	537	0	ENST00000245479.2:c.1211C>A	p.Pro404His	p.P404H	ENST00000245479	NM_000346.3	404	cCc/cAc	3/3	0.682866090003781	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.683992432038106	2		537	1015	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	404	787	3	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.682488088076794	2	FACETS	1	0.962	1	0.506	0.481	0.53	CLONAL	1	TRUE	0	0.683992432038106	2		790	1168	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863054	56863054	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1266824391	NA	P-0058160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	202	447	1	ENST00000519728.1:c.327del	p.Glu110LysfsTer15	p.E110Kfs*15	ENST00000519728	NM_002350.3	107	acA/ac	5/13	0.682488088076794	2	FACETS	0.967	0.901	1	0.483	0.45	0.517	CLONAL	1	TRUE	0	0.683992432038106	2		448	611	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972589	32972590	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs431825381	NA	P-0058160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	188	379	0	ENST00000380152.3:c.9945dup	p.Glu3316ArgfsTer11	p.E3316Rfs*11	ENST00000380152		3313	-/A	27/27	0.682488088076794	2	FACETS	1	0.97	1	0.537	0.5	0.574	CLONAL	1	TRUE	0	0.683992432038106	2		379	512	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426649	121426649	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774996577	NA	P-0058160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	232	530	0	ENST00000257555.6:c.340C>T	p.Arg114Cys	p.R114C	ENST00000257555		114	Cgt/Tgt	2/10	0.669268053268075	3	FACETS	0.77	0.717	0.825	0.257	0.239	0.275	SUBCLONAL	1	TRUE	0	0.683992432038106	3		530	1182	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514020	103514020	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	143	378	0	ENST00000355739.4:c.836G>T	p.Arg279Met	p.R279M	ENST00000355739	NM_000123.3	279	aGg/aTg	7/15	0.682488088076794	2	FACETS	0.86	0.79	0.933	0.43	0.395	0.467	CLONAL	1	TRUE	0	0.683992432038106	2		378	486	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673712	176673712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751194525	NA	P-0058160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	292	266	0	ENST00000439151.2:c.4412G>A	p.Arg1471Gln	p.R1471Q	ENST00000439151	NM_022455.4	1471	cGa/cAa	10/23	0.683992432038106	4	FACETS	0.947	0.896	0.999	0.947	0.896	0.999	CLONAL	2	TRUE	2	0.683992432038106	4		266	759	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721510	49721510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368191700	NA	P-0058160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	300	527	1	ENST00000449682.2:c.2129G>A	p.Arg710His	p.R710H	ENST00000449682	NM_020998.3	710	cGt/cAt	18/18	0.682488088076794	2	FACETS	0.999	0.944	1	0.5	0.472	0.528	CLONAL	1	TRUE	0	0.683992432038106	2		528	878	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104359302	104359302	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776578	NA	P-0058160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	522	388	1	ENST00000369902.3:c.1022+1G>A		p.X341_splice	ENST00000369902	NM_016169.3	341			0.682488088076794	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.683992432038106	2		389	761	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128420046	128420047	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	469	566	0	ENST00000265960.3:c.381dup	p.Ser128IlefsTer28	p.S128Ifs*28	ENST00000265960	NM_001006617.1	127	-/A	4/12	0.683992432038106	2	FACETS	0.852	0.821	0.882	0.852	0.821	0.882	CLONAL	2	TRUE	0	0.683992432038106	2		566	805	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042170	6042170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758561884	NA	P-0058160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	266	509	0	ENST00000265849.7:c.451C>T	p.Arg151Cys	p.R151C	ENST00000265849	NM_000535.5	151	Cgc/Tgc	5/15	0.651110425852641	4	FACETS	0.898	0.84	0.958	0.449	0.42	0.479	CLONAL	1	TRUE	2	0.683992432038106	4		509	1459	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456290	99456290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	144	259	0	ENST00000268035.6:c.1607C>T	p.Thr536Ile	p.T536I	ENST00000268035	NM_000875.3	536	aCa/aTa	8/21	0.683992432038106	3	FACETS	0.984	0.902	1	0.492	0.451	0.535	CLONAL	1	TRUE	1	0.683992432038106	3		259	574	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639305	3639305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756660911	NA	P-0058160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	850	815	1	ENST00000294008.3:c.4334G>A	p.Arg1445Gln	p.R1445Q	ENST00000294008	NM_032444.2	1445	cGg/cAg	12/15	0.682866090003781	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.683992432038106	2		816	1173	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348233	89348233	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	394	746	0	ENST00000301030.4:c.4717C>A	p.Leu1573Met	p.L1573M	ENST00000301030	NM_001256183.1	1573	Ctg/Atg	9/13	0.682488088076794	2	FACETS	0.947	0.901	0.995	0.474	0.45	0.498	CLONAL	1	TRUE	0	0.683992432038106	2		746	1216	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158008	106158008	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	324	273	0	ENST00000380013.4:c.2909C>G	p.Thr970Ser	p.T970S	ENST00000380013	NM_001127208.2	970	aCt/aGt	3/11	0.682488088076794	2	FACETS	0.997	0.959	1	0.997	0.959	1	CLONAL	2	TRUE	0	0.683992432038106	2		273	475	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0058161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	33	361	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.224742497106907	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		361	267	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591894	48591894	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	8	436	0	ENST00000342988.3:c.1057T>A	p.Tyr353Asn	p.Y353N	ENST00000342988	NM_005359.5	353	Tac/Aac	9/12	0.168662902980222	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		436	317	SUCCESS
APC	324	MSKCC	GRCh37	5	112173597	112173622	+	frameshift_variant	Frame_Shift_Del	DEL	TATCAGAAACTTTTGACAATATAGAC	TATCAGAAACTTTTGACAATATAGAC	-	novel	NA	P-0058161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	23	255	0	ENST00000257430.4:c.2306_2331del	p.Leu769Ter	p.L769*	ENST00000257430	NM_000038.5	769	tTATCAGAAACTTTTGACAATATAGAC/t	16/16	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		255	159	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740361	58740363	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0058162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	64	462	0	ENST00000305921.3:c.1272_1274del	p.Glu424del	p.E424del	ENST00000305921	NM_003620.3	422	ctGGAg/ctg	6/6	0.305065511379917	1	FACETS	0.426	0.371	0.485	0.426	0.371	0.485	INDETERMINATE	1	TRUE	0	0.587608254903099	1		462	361	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613158	52613159	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0058162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	283	582	0	ENST00000394830.3:c.3369dup	p.Glu1124Ter	p.E1124*	ENST00000394830	NM_018313.4	1123	-/T	22/30	0.538623051781924	2	FACETS	0.895	0.852	0.939	0.895	0.852	0.939	CLONAL	2	TRUE	0	0.587608254903099	2		582	538	SUCCESS
APC	324	MSKCC	GRCh37	5	112177496	112177496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	39	315	0	ENST00000257430.4:c.6205G>A	p.Gly2069Ser	p.G2069S	ENST00000257430	NM_000038.5	2069	Ggt/Agt	16/16	0.305065511379917	1	FACETS	0.378	0.315	0.447	0.378	0.315	0.447	INDETERMINATE	1	TRUE	0	0.587608254903099	1		315	248	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0058164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	140	276	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.287246839154667	4	FACETS	1	0.942	1	1	0.942	1	INDETERMINATE	2	TRUE	2	0.584298740584235	4		276	370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs864622237	NA	P-0058164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	160	567	0	ENST00000269305.4:c.700T>C	p.Tyr234His	p.Y234H	ENST00000269305	NM_001126112.2	234	Tac/Cac	7/11	0.389089799796263	2	FACETS	1	0.987	1	0.666	0.618	0.716	CLONAL	1	TRUE	0	0.584298740584235	2		567	411	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70441156	70441157	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0058164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	74	312	0	ENST00000373644.4:c.4832dup	p.Asn1611LysfsTer3	p.N1611Kfs*3	ENST00000373644	NM_030625.2	1609	gaa/gAaa	9/12	0.425562407185812	3	FACETS	1	0.968	1	0.634	0.562	0.71	CLONAL	1	TRUE	1	0.584298740584235	3		312	258	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0058165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	180	421	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	0.835	0.777	0.894	1	0.992	1	CLONAL	2	TRUE	1	0.448305302810493	2		421	481	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593609	55593611	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	rs121913685	NA	P-0058165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	96	494	0	ENST00000288135.5:c.1679_1681del	p.Val560del	p.V560del	ENST00000288135	NM_000222.2	559	GTT/-	11/21	0.22044844120835	1	FACETS	0.835	0.749	0.925	0.835	0.749	0.925	INDETERMINATE	1	TRUE	0	0.448305302810493	1		494	398	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202351	138202351	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	166	553	2	ENST00000237289.4:c.2274del	p.Lys759SerfsTer57	p.K759Sfs*57	ENST00000237289	NM_001270507.1	756	gaC/ga	9/9	0.430821611638557	2	FACETS	0.84	0.771	0.911	0.42	0.385	0.456	CLONAL	1	TRUE	0	0.448305302810493	2		555	882	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495714	72495714	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	135	428	0	ENST00000477973.2:c.358A>G	p.Thr120Ala	p.T120A	ENST00000477973	NM_012234.5	120	Acc/Gcc	1/4	1	2	FACETS	0.882	0.803	0.964	0.882	0.803	0.964	CLONAL	1	TRUE	1	0.448305302810493	2		428	683	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0058166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	90	172	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.409215305175883	2		172	416	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0058166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	66	276	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.409215305175883	1	FACETS	0.882	0.772	0.998	0.882	0.772	0.998	CLONAL	1	TRUE	0	0.409215305175883	1		276	291	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435399	110435399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1264962918	NA	P-0058166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	123	683	0	ENST00000375856.3:c.3002C>T	p.Ser1001Phe	p.S1001F	ENST00000375856	NM_003749.2	1001	tCc/tTc	1/2	1	2	FACETS	0.959	0.869	1	0.959	0.869	1	CLONAL	1	TRUE	1	0.409215305175883	2		683	627	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170325	32170325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	175	878	2	ENST00000375023.3:c.3283C>T	p.His1095Tyr	p.H1095Y	ENST00000375023	NM_004557.3	1095	Cac/Tac	21/30	0.409215305175883	3	FACETS	0.896	0.824	0.971	0.448	0.412	0.486	CLONAL	1	TRUE	1	0.409215305175883	3		880	1150	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828074	72828074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766287350	NA	P-0058166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	188	810	0	ENST00000268489.5:c.8507C>T	p.Ser2836Phe	p.S2836F	ENST00000268489	NM_006885.3	2836	tCc/tTc	9/10	1	2	FACETS	0.999	0.923	1	0.999	0.923	1	CLONAL	1	TRUE	1	0.409215305175883	2		810	920	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233249	46233249	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs865903558	NA	P-0058166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	142	291	0	ENST00000334344.6:c.1468C>T	p.Gln490Ter	p.Q490*	ENST00000334344	NM_152641.2	490	Caa/Taa	11/21	0.371003589581205	2	FACETS	0.883	0.814	0.954	0.883	0.814	0.954	CLONAL	2	TRUE	0	0.409215305175883	2		291	393	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175955	176175955	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	18	120	0	ENST00000367669.3:c.160C>T	p.Gln54Ter	p.Q54*	ENST00000367669	NM_022457.5	54	Cag/Tag	1/20	1	2	FACETS	0.739	0.563	0.942	0.739	0.563	0.942	CLONAL	1	TRUE	1	0.409215305175883	2		120	119	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274718	123274718	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	135	593	1	ENST00000358487.5:c.1200G>A	p.Met400Ile	p.M400I	ENST00000358487	NM_000141.4	400	atG/atA	9/18	1	2	FACETS	0.939	0.855	1	0.939	0.855	1	CLONAL	1	TRUE	1	0.409215305175883	2		594	703	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212880	94212880	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	61	363	0	ENST00000323929.3:c.362C>T	p.Pro121Leu	p.P121L	ENST00000323929	NM_005591.3	121	cCa/cTa	5/20	1	2	FACETS	0.801	0.695	0.916	0.801	0.695	0.916	CLONAL	1	TRUE	1	0.409215305175883	2		363	372	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346479	89346479	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	158	807	0	ENST00000301030.4:c.6471del	p.Glu2158LysfsTer17	p.E2158Kfs*17	ENST00000301030	NM_001256183.1	2157	gaA/ga	9/13	1	2	FACETS	0.855	0.784	0.93	0.855	0.784	0.93	CLONAL	1	TRUE	1	0.409215305175883	2		807	903	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117534	4117557	+	inframe_deletion	In_Frame_Del	DEL	GGCTTTCTGGGTGAGAAAGGCTTC	GGCTTTCTGGGTGAGAAAGGCTTC	-	novel	NA	P-0058166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	189	304	2	ENST00000262948.5:c.163_186del	p.Glu55_Ala62del	p.E55_A62del	ENST00000262948	NM_030662.3	55	GAAGCCTTTCTCACCCAGAAAGCC/-	2/11	1	2	FACETS	1	0.968	1	1	0.994	1	CLONAL	2	TRUE	1	0.409215305175883	2		306	437	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167513	24167514	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	160	739	1	ENST00000263121.7:c.897_898delinsAA	p.Glu300Lys	p.E300K	ENST00000263121	NM_003073.3	299	tcGGag/tcAAag	7/9	1	2	FACETS	0.928	0.851	1	0.928	0.851	1	CLONAL	1	TRUE	1	0.409215305175883	2		740	843	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751880	57751880	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	125	439	0	ENST00000274289.3:c.1357C>A	p.Leu453Ile	p.L453I	ENST00000274289	NM_006622.3	453	Ctt/Att	10/14	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.409215305175883	2		439	554	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932393	39932393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	156	858	1	ENST00000378444.4:c.2206G>A	p.Glu736Lys	p.E736K	ENST00000378444	NM_001123385.1	736	Gag/Aag	4/15	1	2	FACETS	0.861	0.788	0.936	0.861	0.788	0.936	CLONAL	1	TRUE	1	0.409215305175883	2		859	886	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608326	100608326	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	112	568	0	ENST00000308731.7:c.1764G>A	p.Trp588Ter	p.W588*	ENST00000308731	NM_000061.2	588	tgG/tgA	18/19	1	2	FACETS	0.912	0.823	1	0.912	0.823	1	CLONAL	1	TRUE	1	0.409215305175883	2		568	600	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0058174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	41	324	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.21	2		324	337	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0058174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	39	656	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.777	0.644	0.926	0.777	0.644	0.926	CLONAL	1	TRUE	1	0.21	2		657	478	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0058174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	61	681	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.888	0.766	1	0.888	0.766	1	CLONAL	1	TRUE	1	0.21	2		681	654	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0058174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	56	557	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.21	2		557	404	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100940	27100941	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0058174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	45	660	0	ENST00000324856.7:c.4225dup	p.Gln1409ProfsTer36	p.Q1409Pfs*36	ENST00000324856	NM_006015.4	1408	gcc/gCcc	18/20	1	2	FACETS	0.712	0.597	0.839	0.712	0.597	0.839	SUBCLONAL	1	TRUE	1	0.21	2		660	602	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105610	27105610	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	44	497	0	ENST00000324856.7:c.5221C>T	p.Gln1741Ter	p.Q1741*	ENST00000324856	NM_006015.4	1741	Cag/Tag	20/20	1	2	FACETS	0.811	0.679	0.956	0.811	0.679	0.956	CLONAL	1	TRUE	1	0.21	2		497	517	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670605	67670609	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAT	CAGAT	-	novel	NA	P-0058174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	33	366	0	ENST00000264010.4:c.1851_1855del	p.Asp618GlyfsTer4	p.D618Gfs*4	ENST00000264010	NM_006565.3	617	cCAGAT/c	11/12	1	2	FACETS	0.863	0.704	1	0.863	0.704	1	CLONAL	1	TRUE	1	0.21	2		366	364	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247208	153247208	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	38	328	0	ENST00000281708.4:c.1594A>G	p.Thr532Ala	p.T532A	ENST00000281708	NM_033632.3	532	Acc/Gcc	10/12	1	2	FACETS	0.975	0.808	1	0.975	0.808	1	CLONAL	1	TRUE	1	0.21	2		328	371	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589565	67589594	+	inframe_deletion	In_Frame_Del	DEL	AAGCTGTAGGGAAAAAATTACATGAATATA	AAGCTGTAGGGAAAAAATTACATGAATATA	-	novel	NA	P-0058174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	10	145	0	ENST00000274335.5:c.1329_1358del	p.Glu443_Asn453delinsAsp	p.E443_N453delinsD	ENST00000274335		443	gAAGCTGTAGGGAAAAAATTACATGAATATAac/gac	10/15	1	2	FACETS	0.671	0.456	0.939	0.671	0.456	0.939	SUBCLONAL	1	TRUE	1	0.21	2		145	142	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0058175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	1024	720	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.729077424418802	5	FACETS	1	0.994	1			1	CLONAL	3	TRUE	NA	0.763540470613466	5		721	1818	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579355	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519997	NA	P-0058175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	559	822	1	ENST00000269305.4:c.332T>C	p.Leu111Pro	p.L111P	ENST00000269305	NM_001126112.2	111	cTg/cCg	4/11	0.733965249574919	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.763540470613466	1		823	714	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814826	139814826	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	532	954	0	ENST00000247668.2:c.819G>C	p.Glu273Asp	p.E273D	ENST00000247668	NM_021138.3	273	gaG/gaC	8/11	0.733965249574919	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.763540470613466	1		954	832	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981791	201981791	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	43	953	0	ENST00000359651.3:c.502G>C	p.Glu168Gln	p.E168Q	ENST00000359651		168	Gag/Cag	4/8	0.422148877341983	1	FACETS	0.091	0.075	0.108	0.091	0.075	0.108	INDETERMINATE	1	TRUE	0	0.763540470613466	1		953	769	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425287	49425287	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	653	926	0	ENST00000301067.7:c.13201del	p.Gln4401ArgfsTer2	p.Q4401Rfs*2	ENST00000301067	NM_003482.3	4401	Cag/ag	39/54	0.750886632152822	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.763540470613466	2		926	841	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272429	15272429	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	234	1151	0	ENST00000263388.2:c.6010C>G	p.Leu2004Val	p.L2004V	ENST00000263388	NM_000435.2	2004	Ctg/Gtg	33/33	0.421958978170186	3	FACETS	0.789	0.735	0.844	0.394	0.367	0.422	INDETERMINATE	1	TRUE	1	0.763540470613466	3		1151	1074	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391202	89391202	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	67	375	0	ENST00000336596.2:c.1268G>C	p.Arg423Thr	p.R423T	ENST00000336596	NM_005233.5	423	aGa/aCa	5/17	1	2	FACETS	0.49	0.428	0.556	0.49	0.428	0.556	SUBCLONAL	1	TRUE	1	0.763540470613466	2		375	358	SUCCESS
AR	367	MSKCC	GRCh37	X	66941736	66941736	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	61	560	0	ENST00000374690.3:c.2380G>A	p.Glu794Lys	p.E794K	ENST00000374690	NM_000044.3	794	Gag/Aag	6/8	0.763540470613466	1	FACETS	0.236	0.204	0.271	0.236	0.204	0.271	SUBCLONAL	1	TRUE	0	0.763540470613466	1		560	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0058176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	56	559	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	0.84	0.718	0.974	0.84	0.718	0.974	CLONAL	1	TRUE	1	0.15	2		559	889	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610129	28610129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	43	392	0	ENST00000241453.7:c.1361C>T	p.Ser454Leu	p.S454L	ENST00000241453	NM_004119.2	454	tCg/tTg	11/24	1	2	FACETS	0.922	0.77	1	0.922	0.77	1	CLONAL	1	TRUE	1	0.15	2		392	622	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678518	88678518	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	59	490	1	ENST00000360948.2:c.1018C>T	p.Gln340Ter	p.Q340*	ENST00000360948	NM_001012338.2	340	Cag/Tag	9/19	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.15	2		491	625	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0058178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	49	219	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.225293193967952	3	FACETS	0.972	0.831	1	0.972	0.831	1	CLONAL	2	TRUE	1	0.225293193967952	3		219	249	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390347	118390348	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0058178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	48	509	0	ENST00000534358.1:c.11163dup	p.Met3722AspfsTer7	p.M3722Dfs*7	ENST00000534358	NM_005933.3	3721	agg/aGgg	32/36	0.225293193967952	1	FACETS	0.929	0.787	1	0.929	0.787	1	CLONAL	1	TRUE	0	0.225293193967952	1		509	407	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396524	396524	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	107	869	0	ENST00000262320.3:c.502A>G	p.Ile168Val	p.I168V	ENST00000262320	NM_003502.3	168	Ata/Gta	2/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.225293193967952	2		869	785	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0058179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	173	172	0				ENST00000310581	NM_198253.2	-/1132			0.445065768106603	3	FACETS	0.863	0.807	0.92	1	0.988	1	CLONAL	3	FALSE	1	0.439132535035569	3		172	371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0058179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	426	1219	2	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.445065768106603	3	FACETS	0.954	0.915	0.992	0.954	0.915	0.992	CLONAL	3	FALSE	0	0.439132535035569	3		1221	827	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528895	157528895	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs763772159	NA	P-0058179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	88	629	0	ENST00000346085.5:c.6620G>C	p.Arg2207Thr	p.R2207T	ENST00000346085	NM_020732.3	2207	aGa/aCa	20/20	0.286486251986278	3	FACETS	1	0.957	1	0.575	0.512	0.642	CLONAL	1	FALSE	1	0.439132535035569	3		629	425	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651995	36651995	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	574	1052	0	ENST00000244741.5:c.119del	p.Gly40AlafsTer108	p.G40Afs*108	ENST00000244741	NM_000389.4	39	gcG/gc	2/3	0.439132535035569	7	FACETS	0.949	0.915	0.982	0.949	0.915	0.982	CLONAL	5	FALSE	2	0.439132535035569	7		1052	1156	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100093	157100117	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCGGCGGCGGCAGCAGCAGGAG	GCGGCGGCGGCGGCAGCAGCAGGAG	-	novel	NA	P-0058179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	14	38	0	ENST00000346085.5:c.1044_1068del	p.Ala350MetfsTer11	p.A350Mfs*11	ENST00000346085	NM_020732.3	344	GCGGCGGCGGCGGCAGCAGCAGGAGgc/gc	1/20	0.286486251986278	3	FACETS	1	0.887	1	0.72	0.537	0.926	CLONAL	1	FALSE	1	0.439132535035569	3		38	54	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420107	41420107	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0058179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	36	406	0	ENST00000373198.4:c.215-1G>A		p.X72_splice	ENST00000373198	NM_133170.3	72			NA	2	FACETS	0.773	0.641	0.919			1	INDETERMINATE	1	FALSE	NA	0.439132535035569	2		406	212	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194134	94194134	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	49	432	0	ENST00000323929.3:c.1294C>T	p.Leu432Phe	p.L432F	ENST00000323929	NM_005591.3	432	Ctt/Ttt	12/20	0.445065768106603	4	FACETS	0.942	0.801	1	0.471	0.4	0.548	CLONAL	1	FALSE	2	0.439132535035569	4		432	341	SUCCESS
ATM	472	MSKCC	GRCh37	11	108128236	108128236	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	38	290	0	ENST00000278616.4:c.2279T>C	p.Ile760Thr	p.I760T	ENST00000278616	NM_000051.3	760	aTc/aCc	15/63	0.445065768106603	4	FACETS	0.969	0.806	1	0.485	0.403	0.575	CLONAL	1	FALSE	2	0.439132535035569	4		290	257	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385192	4385192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	126	455	0	ENST00000261254.3:c.217G>A	p.Glu73Lys	p.E73K	ENST00000261254	NM_001759.3	73	Gaa/Aaa	2/5	0.439132535035569	5	FACETS	0.922	0.84	1	0.615	0.56	0.673	CLONAL	2	FALSE	2	0.439132535035569	5		455	516	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129422	2129422	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	93	991	0	ENST00000219476.3:c.3277G>C	p.Glu1093Gln	p.E1093Q	ENST00000219476	NM_000548.3	1093	Gag/Cag	28/42	0.445065768106603	3	FACETS	0.828	0.737	0.924	0.414	0.368	0.462	CLONAL	1	FALSE	1	0.439132535035569	3		991	624	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879854	37879854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	552	928	0	ENST00000269571.5:c.2149G>C	p.Glu717Gln	p.E717Q	ENST00000269571		717	Gag/Cag	18/27	0.439132535035569	6	FACETS	0.974	0.941	1			1	CLONAL	5	FALSE	NA	0.439132535035569	6		928	970	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191232	2191232	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	93	747	0	ENST00000398665.3:c.486G>C	p.Leu162Phe	p.L162F	ENST00000398665	NM_032482.2	162	ttG/ttC	5/28	0.445065768106603	4	FACETS	0.915	0.814	1			1	CLONAL	1	FALSE	NA	0.439132535035569	4		747	666	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426813	212426813	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	97	297	0	ENST00000342788.4:c.2302G>A	p.Glu768Lys	p.E768K	ENST00000342788	NM_005235.2	768	Gaa/Aaa	20/28	0.12152380919478	5	FACETS	0.977	0.886	1			1	INDETERMINATE	3	FALSE	NA	0.439132535035569	5		297	250	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436403	52436403	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	327	950	0	ENST00000460680.1:c.2091del	p.Val698CysfsTer38	p.V698Cfs*38	ENST00000460680	NM_004656.3	697	tcC/tc	17/17	0.439132535035569	8	FACETS	0.995	0.94	1			1	CLONAL	3	FALSE	NA	0.439132535035569	8		950	1156	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629376	187629376	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs888101917	NA	P-0058179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	159	742	0	ENST00000441802.2:c.1606C>G	p.Leu536Val	p.L536V	ENST00000441802	NM_005245.3	536	Ctg/Gtg	2/27	0.251074660894721	4	FACETS	1	0.939	1	1	0.939	1	INDETERMINATE	2	FALSE	2	0.439132535035569	4		742	511	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527786	157527786	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	83	509	0	ENST00000346085.5:c.5511G>C	p.Lys1837Asn	p.K1837N	ENST00000346085	NM_020732.3	1837	aaG/aaC	20/20	0.286486251986278	3	FACETS	1	0.975	1	0.688	0.612	0.768	CLONAL	1	FALSE	1	0.439132535035569	3		509	335	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56910937	56910937	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	83	510	0	ENST00000519728.1:c.1083G>C	p.Lys361Asn	p.K361N	ENST00000519728	NM_002350.3	361	aaG/aaC	11/13	0.286486251986278	3	FACETS	1	0.928	1	0.531	0.471	0.595	CLONAL	1	FALSE	1	0.439132535035569	3		510	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0058180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	179	605	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.751391644686164	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.771940734788675	1		605	245	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107151	27107151	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0058180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	69	578	0	ENST00000324856.7:c.6762C>G	p.Tyr2254Ter	p.Y2254*	ENST00000324856	NM_006015.4	2254	taC/taG	20/20	0.702995940186167	1	FACETS	0.578	0.513	0.645	0.578	0.513	0.645	SUBCLONAL	1	TRUE	0	0.771940734788675	1		578	190	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197472	26197472	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	53	312	0	ENST00000356476.2:c.7C>G	p.Arg3Gly	p.R3G	ENST00000356476		3	Cgt/Ggt	1/1	0.563636257404499	4	FACETS	1	0.912	1	0.359	0.309	0.412	CLONAL	1	TRUE	1	0.771940734788675	4		312	226	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0058181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	63	351	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.753	0.653	0.862	1	0.971	1	SUBCLONAL	2	TRUE	1	0.17	2		351	492	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141976	108141976	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0058181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	25	136	0	ENST00000278616.4:c.2922-2A>C		p.X974_splice	ENST00000278616	NM_000051.3	974			1	2	FACETS	0.611	0.481	0.762	0.611	0.481	0.762	SUBCLONAL	1	TRUE	1	0.17	2		136	481	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042436	16042436	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	35	166	0	ENST00000268712.3:c.1238G>T	p.Arg413Ile	p.R413I	ENST00000268712	NM_006311.3	413	aGa/aTa	12/46	1	2	FACETS	0.758	0.621	0.914	0.758	0.621	0.914	CLONAL	1	TRUE	1	0.17	2		166	543	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533908	63533908	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	87	336	0	ENST00000307078.5:c.1246G>T	p.Gly416Trp	p.G416W	ENST00000307078	NM_004655.3	416	Ggg/Tgg	6/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.17	2		336	913	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952349	17952349	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	94	533	0	ENST00000458235.1:c.991G>T	p.Glu331Ter	p.E331*	ENST00000458235	NM_000215.3	331	Gag/Tag	8/24	1	2	FACETS	0.864	0.766	0.969	0.864	0.766	0.969	CLONAL	1	TRUE	1	0.17	2		533	1280	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274701	198274701	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	40	189	0	ENST00000335508.6:c.697G>T	p.Asp233Tyr	p.D233Y	ENST00000335508	NM_012433.2	233	Gat/Tat	7/25	1	2	FACETS	0.792	0.657	0.943	0.792	0.657	0.943	CLONAL	1	TRUE	1	0.17	2		189	594	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046445	69046445	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	87	272	0	ENST00000288368.4:c.3918G>T	p.Arg1306Ser	p.R1306S	ENST00000288368	NM_024870.2	1306	agG/agT	32/40	1	2	FACETS	0.783	0.693	0.878	1	0.98	1	SUBCLONAL	2	TRUE	1	0.17	2		272	654	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034455	47034456	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	68	428	0	ENST00000377604.3:c.542dup	p.Leu181PhefsTer28	p.L181Ffs*28	ENST00000377604	NM_001204468.1	180	-/T	6/24	1	2	FACETS	0.697	0.604	0.798	0.697	0.604	0.798	SUBCLONAL	1	TRUE	1	0.17	2		428	1148	SUCCESS
AR	367	MSKCC	GRCh37	X	66765608	66765608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1284	91	569	0	ENST00000374690.3:c.620G>A	p.Ser207Asn	p.S207N	ENST00000374690	NM_000044.3	207	aGc/aAc	1/8	1	2	FACETS	0.779	0.689	0.875	0.779	0.689	0.875	SUBCLONAL	1	TRUE	1	0.17	2		569	1375	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24135841	24135841	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	133	454	0	ENST00000263121.7:c.328G>C	p.Val110Leu	p.V110L	ENST00000263121	NM_003073.3	110	Gtg/Ctg	3/9	1	2	FACETS	0.78	0.71	0.852	0.78	0.71	0.852	SUBCLONAL	1	TRUE	1	0.565853926554766	2		454	603	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468089	50468089	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	132	696	0	ENST00000331340.3:c.1324T>C	p.Ser442Pro	p.S442P	ENST00000331340	NM_006060.4	442	Tcc/Ccc	8/8	0.404462985469464	3	FACETS	0.864	0.785	0.946	0.432	0.392	0.473	CLONAL	1	TRUE	1	0.565853926554766	3		696	693	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0058183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	107	500	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.309760575200439	2		500	662	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032138	26032138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	90	542	0	ENST00000244661.2:c.151G>A	p.Glu51Lys	p.E51K	ENST00000244661	NM_003537.3	51	Gag/Aag	1/1	1	2	FACETS	0.942	0.837	1	0.942	0.837	1	CLONAL	1	TRUE	1	0.309760575200439	2		542	617	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061482	38061483	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0058183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	77	681	0	ENST00000250448.2:c.506_507delinsAT	p.Ala169Asp	p.A169D	ENST00000250448	NM_004496.3	169	gCC/gAT	2/2	1	2	FACETS	0.754	0.662	0.853	0.754	0.662	0.853	SUBCLONAL	1	TRUE	1	0.309760575200439	2		681	659	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866330	42866330	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	175	893	0	ENST00000398585.3:c.302T>C	p.Val101Ala	p.V101A	ENST00000398585	NM_001135099.1	101	gTc/gCc	3/14	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.309760575200439	2		893	1036	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517877	187517884	+	frameshift_variant	Frame_Shift_Del	DEL	AGGAATTT	AGGAATTT	-	novel	NA	P-0058183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	83	466	0	ENST00000441802.2:c.12810_12817del	p.Asn4271ArgfsTer15	p.N4271Rfs*15	ENST00000441802	NM_005245.3	4270	cgAAATTCCTtc/cgtc	25/27	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.309760575200439	2		466	525	SUCCESS
APC	324	MSKCC	GRCh37	5	112154974	112154974	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	40	606	0	ENST00000257430.4:c.1246del	p.Tyr416ThrfsTer38	p.Y416Tfs*38	ENST00000257430	NM_000038.5	415	gcT/gc	10/16	0.309760575200439	1	FACETS	0.355	0.295	0.424	0.355	0.295	0.424	SUBCLONAL	1	TRUE	0	0.309760575200439	1		606	614	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0058184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	44	157	2	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.485	0.405	0.573	0.485	0.405	0.573	SUBCLONAL	1	FALSE	1	0.253561496358231	2		159	716	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294703	1294703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	58	655	0	ENST00000310581.5:c.298G>A	p.Gly100Ser	p.G100S	ENST00000310581	NM_198253.2	100	Ggc/Agc	2/16	0.253561496358231	5	FACETS	0.684	0.586	0.792	0.171	0.146	0.198	SUBCLONAL	1	FALSE	1	0.253561496358231	5		655	923	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981503	201981503	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	74	889	0	ENST00000359651.3:c.417C>G	p.Ile139Met	p.I139M	ENST00000359651		139	atC/atG	3/8	1	2	FACETS	0.728	0.636	0.827	0.728	0.636	0.827	SUBCLONAL	1	FALSE	1	0.253561496358231	2		889	802	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032564	47032567	+	frameshift_variant	Frame_Shift_Del	DEL	GGGA	GGGA	-	novel	NA	P-0058184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	97	908	0	ENST00000377604.3:c.472_475del	p.Glu158PhefsTer3	p.E158Ffs*3	ENST00000377604	NM_001204468.1	157	cGGGAg/cg	5/24	0.253561496358231	1	FACETS	0.606	0.539	0.678	0.606	0.539	0.678	SUBCLONAL	1	FALSE	0	0.253561496358231	1		908	1102	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593594	55593608	+	inframe_deletion	In_Frame_Del	DEL	GAAGTACAGTGGAAG	GAAGTACAGTGGAAG	-	novel	NA	P-0058185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	81	390	0	ENST00000288135.5:c.1661_1675del	p.Glu554_Lys558del	p.E554_K558del	ENST00000288135	NM_000222.2	554	GAAGTACAGTGGAAG/-	11/21	1	2	FACETS	0.722	0.642	0.805	0.722	0.642	0.805	SUBCLONAL	1	TRUE	1	0.724007984613021	2		390	310	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0058186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	199	584	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.501237821559691	4	FACETS	0.815	0.758	0.875	0.544	0.505	0.583	CLONAL	2	TRUE	1	0.501124037031164	4		584	731	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922256	100922256	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	33	301	0	ENST00000325455.5:c.2256G>T	p.Gln752His	p.Q752H	ENST00000325455	NM_001202474.3	752	caG/caT	5/8	0.501237821559691	3	FACETS	0.403	0.328	0.487	0.201	0.164	0.244	SUBCLONAL	1	TRUE	1	0.501124037031164	3		301	409	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039133	49039133	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs587776786	NA	P-0058186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	129	122	0	ENST00000267163.4:c.2212-1G>A		p.X738_splice	ENST00000267163	NM_000321.2	738			0.332503279814123	3	FACETS	0.933	0.868	0.997			1	CLONAL	3	TRUE	NA	0.501124037031164	3		122	230	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0058186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	527	949	1	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	2	TRUE	NA	0.501124037031164	2		950	1040	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56411570	56411570	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	29	143	0	ENST00000348428.3:c.1754A>T	p.Glu585Val	p.E585V	ENST00000348428	NM_006785.3	585	gAa/gTa	15/17	0.501124037031164	2	FACETS	0.467	0.376	0.569	0.233	0.188	0.285	SUBCLONAL	1	TRUE	0	0.501124037031164	2		143	248	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933289	49933289	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	300	1187	0	ENST00000296474.3:c.2821A>T	p.Ile941Phe	p.I941F	ENST00000296474	NM_002447.2	941	Atc/Ttc	12/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.501124037031164	2		1187	1069	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911071	29911071	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1238	118	1210	0	ENST00000376809.5:c.370G>C	p.Gly124Arg	p.G124R	ENST00000376809	NM_002116.7	124	Ggc/Cgc	3/8	0.501237821559691	3	FACETS	0.434	0.39	0.481	0.217	0.195	0.241	SUBCLONAL	1	TRUE	1	0.501124037031164	3		1210	1356	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911157	29911157	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs41558424	NA	P-0058186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	316	1043	0	ENST00000376809.5:c.456G>C	p.Glu152Asp	p.E152D	ENST00000376809	NM_002116.7	152	gaG/gaC	3/8	0.501237821559691	3	FACETS	1	0.994	1	0.727	0.686	0.768	CLONAL	1	TRUE	1	0.501124037031164	3		1043	1085	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510884	157510884	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	161	748	0	ENST00000346085.5:c.3659A>C	p.His1220Pro	p.H1220P	ENST00000346085	NM_020732.3	1220	cAc/cCc	14/20	0.501237821559691	3	FACETS	0.91	0.835	0.989	0.455	0.417	0.495	CLONAL	1	TRUE	1	0.501124037031164	3		748	883	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241659	55241659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1273890779	NA	P-0058186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	607	925	0	ENST00000275493.2:c.2107C>T	p.Leu703Phe	p.L703F	ENST00000275493	NM_005228.3	703	Ctc/Ttc	18/28	0.501124037031164	5	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.501124037031164	5		925	1702	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0058186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	339	401	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.501124037031164	5	FACETS	1	0.988	1			1	CLONAL	3	TRUE	NA	0.501124037031164	5		401	715	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212922	94212922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	70	310	0	ENST00000323929.3:c.320C>T	p.Pro107Leu	p.P107L	ENST00000323929	NM_005591.3	107	cCa/cTa	5/20	0.634516372854815	1	FACETS	0.846	0.754	0.941	0.846	0.754	0.941	CLONAL	1	TRUE	0	0.634516372854815	1		310	178	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877467	28877467	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	93	572	0	ENST00000282397.4:c.3854C>A	p.Ser1285Tyr	p.S1285Y	ENST00000282397	NM_002019.4	1285	tCt/tAt	30/30	1	2	FACETS	0.735	0.658	0.816	0.735	0.658	0.816	SUBCLONAL	1	TRUE	1	0.634516372854815	2		572	399	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557327	29557327	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1135402839	NA	P-0058187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	91	289	0	ENST00000356175.3:c.3040A>T	p.Lys1014Ter	p.K1014*	ENST00000356175	NM_000267.3	1014	Aaa/Taa	23/57	0.439514389903196	1	FACETS	0.739	0.666	0.814	0.739	0.666	0.814	SUBCLONAL	1	TRUE	0	0.634516372854815	1		289	265	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679432	29679433	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0058187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	40	381	1	ENST00000356175.3:c.7552_7552+1delinsTT		p.X2518_splice	ENST00000356175	NM_000267.3	2518		50/57	0.439514389903196	1	FACETS	0.298	0.248	0.352	0.298	0.248	0.352	SUBCLONAL	1	TRUE	0	0.634516372854815	1		382	289	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475586	12475586	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	203	583	0	ENST00000287820.6:c.1460C>A	p.Thr487Lys	p.T487K	ENST00000287820	NM_015869.4	487	aCg/aAg	7/7	0.621985498792949	2	FACETS	0.86	0.811	0.908	0.86	0.811	0.908	CLONAL	2	TRUE	0	0.634516372854815	2		583	372	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0058188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	195	172	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.817031034355899	2		172	430	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0058188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	87	632	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.277	0.245	0.312	0.277	0.245	0.312	SUBCLONAL	1	TRUE	1	0.817031034355899	2		632	768	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0058188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	114	793	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	0.259	0.232	0.287	0.259	0.232	0.287	SUBCLONAL	1	TRUE	1	0.817031034355899	2		793	1077	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609902	117609902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781588795	NA	P-0058188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	120	471	1	ENST00000368508.3:c.6797C>T	p.Thr2266Met	p.T2266M	ENST00000368508	NM_002944.2	2266	aCg/aTg	43/43	1	2	FACETS	0.532	0.482	0.584	0.532	0.482	0.584	SUBCLONAL	1	TRUE	1	0.817031034355899	2		472	552	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430779	78430779	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	46	469	1	ENST00000370768.2:c.610G>A	p.Gly204Arg	p.G204R	ENST00000370768	NM_003902.3	204	Ggg/Agg	8/20	1	2	FACETS	0.178	0.15	0.21	0.178	0.15	0.21	SUBCLONAL	1	TRUE	1	0.817031034355899	2		470	631	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933421	49933421	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	345	976	2	ENST00000296474.3:c.2769G>T	p.Gln923His	p.Q923H	ENST00000296474	NM_002447.2	923	caG/caT	11/20	1	2	FACETS	0.962	0.914	1	0.962	0.914	1	CLONAL	1	TRUE	1	0.817031034355899	2		978	878	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204981	128204982	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0058188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	92	1153	0	ENST00000341105.2:c.459dup	p.Ser154GlufsTer31	p.S154Efs*31	ENST00000341105	NM_032638.4	153	-/G	3/6	1	2	FACETS	0.253	0.224	0.284	0.253	0.224	0.284	SUBCLONAL	1	TRUE	1	0.817031034355899	2		1153	889	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6029523	6029523	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	60	490	0	ENST00000265849.7:c.1052T>C	p.Leu351Ser	p.L351S	ENST00000265849	NM_000535.5	351	tTg/tCg	10/15	0.419747800947708	3	FACETS	0.287	0.247	0.331	0.144	0.123	0.166	INDETERMINATE	1	TRUE	1	0.817031034355899	3		490	720	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	148	306	0				ENST00000310581	NM_198253.2	-/1132			0.122327067986641	6	FACETS	1	0.959	1	0.708	0.653	0.765	INDETERMINATE	2	TRUE	3	0.852747387004066	6		306	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0058189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	458	1005	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.81271619474558	2	FACETS	0.937	0.913	0.96	0.937	0.913	0.96	CLONAL	2	TRUE	0	0.852747387004066	2		1005	573	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105761	27105761	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	120	484	0	ENST00000324856.7:c.5372C>A	p.Ser1791Ter	p.S1791*	ENST00000324856	NM_006015.4	1791	tCa/tAa	20/20	1	2	FACETS	0.695	0.633	0.759	0.695	0.633	0.759	SUBCLONAL	1	TRUE	1	0.852747387004066	2		484	405	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097721	27097721	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	170	688	0	ENST00000324856.7:c.3310G>C	p.Glu1104Gln	p.E1104Q	ENST00000324856	NM_006015.4	1104	Gaa/Caa	12/20	1	2	FACETS	0.713	0.66	0.768	0.713	0.66	0.768	SUBCLONAL	1	TRUE	1	0.852747387004066	2		688	559	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3795281	3795281	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	199	514	0	ENST00000262367.5:c.3911C>A	p.Ser1304Ter	p.S1304*	ENST00000262367	NM_004380.2	1304	tCa/tAa	22/31	0.468388265001406	1	FACETS	0.783	0.74	0.825	0.783	0.74	0.825	INDETERMINATE	1	TRUE	0	0.852747387004066	1		514	342	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55569972	55569972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs386833402	NA	P-0058190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	111	332	0	ENST00000288135.5:c.839C>T	p.Ala280Val	p.A280V	ENST00000288135	NM_000222.2	280	gCg/gTg	5/21	0.426041320912811	2	FACETS	1	0.972	1	0.597	0.541	0.656	CLONAL	1	TRUE	0	0.455425937332431	2		332	408	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793483	18793483	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs267603405	NA	P-0058190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	87	260	0	ENST00000266497.5:c.4180G>T	p.Glu1394Ter	p.E1394*	ENST00000266497		1394	Gaa/Taa	30/31	0.455425937332431	3	FACETS	1	0.9	1	0.507	0.45	0.566	CLONAL	1	TRUE	1	0.455425937332431	3		260	463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579575	7579576	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0058190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	317	703	0	ENST00000269305.4:c.111_112del	p.Gln38SerfsTer4	p.Q38Sfs*4	ENST00000269305	NM_001126112.2	37	tcCCaa/tcaa	4/11	0.426041320912811	2	FACETS	0.955	0.907	1	0.955	0.907	1	CLONAL	2	TRUE	0	0.455425937332431	2		703	729	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022722	31022792	+	frameshift_variant	Frame_Shift_Del	DEL	CAGTTGGACTCACAGATGGGCTAGGAGATGCCTCCCAACTCCCCGTTGCTCCCACTGGGGACCAGCCATGC	CAGTTGGACTCACAGATGGGCTAGGAGATGCCTCCCAACTCCCCGTTGCTCCCACTGGGGACCAGCCATGC	-	novel	NA	P-0058190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	123	668	0	ENST00000375687.4:c.2210_2280del	p.Val737GlyfsTer13	p.V737Gfs*13	ENST00000375687	NM_015338.5	736	aCAGTTGGACTCACAGATGGGCTAGGAGATGCCTCCCAACTCCCCGTTGCTCCCACTGGGGACCAGCCATGC/a	13/13	0.247686606203493	4	FACETS	0.757	0.683	0.835	0.378	0.341	0.418	INDETERMINATE	1	TRUE	2	0.455425937332431	4		668	1039	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514337	148514337	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	166	336	0	ENST00000320356.2:c.1387A>G	p.Ile463Val	p.I463V	ENST00000320356	NM_004456.4	463	Att/Gtt	11/20	0.44189909353529	2	FACETS	0.878	0.816	0.941	0.878	0.816	0.941	CLONAL	2	TRUE	0	0.455425937332431	2		336	415	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0058191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	58	351	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.21	2		351	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578224	7578224	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1429743956	NA	P-0058191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	73	924	0	ENST00000269305.4:c.625A>T	p.Arg209Ter	p.R209*	ENST00000269305	NM_001126112.2	209	Aga/Tga	6/11	0.158796791724646	1	FACETS	0.822	0.718	0.934	0.822	0.718	0.934	CLONAL	1	TRUE	0	0.21	1		924	757	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102199	27102199	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0058191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	43	422	0	ENST00000324856.7:c.5124+1G>T		p.X1708_splice	ENST00000324856	NM_006015.4	1708			1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.21	2		422	393	SUCCESS
EED	8726	MSKCC	GRCh37	11	85975246	85975246	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	33	267	0	ENST00000263360.6:c.667G>A	p.Asp223Asn	p.D223N	ENST00000263360	NM_003797.3	223	Gac/Aac	7/12	1	2	FACETS	0.916	0.748	1	0.916	0.748	1	CLONAL	1	TRUE	1	0.21	2		267	343	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865134	57865134	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	84	1248	1	ENST00000228682.2:c.2611G>T	p.Asp871Tyr	p.D871Y	ENST00000228682	NM_005269.2	871	Gat/Tat	12/12	1	2	FACETS	0.884	0.779	0.997	0.884	0.779	0.997	CLONAL	1	TRUE	1	0.21	2		1249	905	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041725	29041725	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779103709	NA	P-0058191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	52	361	0	ENST00000282397.4:c.94C>A	p.Pro32Thr	p.P32T	ENST00000282397	NM_002019.4	32	Cct/Act	2/30	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.21	2		361	480	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107698	30107698	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	65	511	0	ENST00000331968.5:c.982G>T	p.Gly328Ter	p.G328*	ENST00000331968	NM_002742.2	328	Gga/Tga	6/18	1	2	FACETS	0.925	0.802	1	0.925	0.802	1	CLONAL	1	TRUE	1	0.21	2		511	669	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376398	15376398	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	108	1215	0	ENST00000263377.2:c.616C>T	p.Pro206Ser	p.P206S	ENST00000263377	NM_058243.2	206	Ccg/Tcg	5/20	0.208547549346434	1	FACETS	0.845	0.757	0.94	0.845	0.757	0.94	CLONAL	1	TRUE	0	0.21	1		1215	1089	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027406	48027406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	47	493	0	ENST00000234420.5:c.2284G>A	p.Val762Ile	p.V762I	ENST00000234420	NM_000179.2	762	Gtt/Att	4/10	1	2	FACETS	0.881	0.744	1	0.881	0.744	1	CLONAL	1	TRUE	1	0.21	2		493	508	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114125	73114125	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	30	341	0	ENST00000356692.5:c.761G>T	p.Gly254Val	p.G254V	ENST00000356692		254	gGt/gTt	8/9	1	2	FACETS	0.69	0.556	0.843	0.69	0.556	0.843	SUBCLONAL	1	TRUE	1	0.21	2		341	414	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372100	55372100	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	90	801	2	ENST00000297316.4:c.790G>T	p.Glu264Ter	p.E264*	ENST00000297316	NM_022454.3	264	Gag/Tag	2/2	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.21	2		803	781	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221935	98221935	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs201118857	NA	P-0058191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	67	813	0	ENST00000331920.6:c.2834G>T	p.Arg945Leu	p.R945L	ENST00000331920	NM_000264.3	945	cGa/cTa	17/24	0.158796791724646	1	FACETS	0.805	0.699	0.921	0.805	0.699	0.921	CLONAL	1	TRUE	0	0.21	1		813	709	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030486	49030486	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0058192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	137	263	4	ENST00000267163.4:c.1960+1G>T		p.X654_splice	ENST00000267163	NM_000321.2	654			0.934462987822634	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.934462987822634	1		267	150	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1427441061	NA	P-0058192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	426	764	7	ENST00000269305.4:c.560-2A>G		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.934462987822634	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.934462987822634	1		771	455	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960109	134960109	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	443	653	0	ENST00000398015.3:c.2466G>T	p.Glu822Asp	p.E822D	ENST00000398015	NM_004441.4	822	gaG/gaT	13/16	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.934462987822634	2		653	878	SUCCESS
CBL	867	MSKCC	GRCh37	11	119145593	119145595	+	missense_variant	Missense_Mutation	TNP	GGC	GGC	TTT	novel	NA	P-0058192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1842	196	399	1	ENST00000264033.4:c.799_801delinsTTT	p.Gly267Phe	p.G267F	ENST00000264033	NM_005188.3	267	GGC/TTT	5/16	0.934462987822634	7	FACETS	0.687	0.633	0.743			1	SUBCLONAL	1	TRUE	NA	0.934462987822634	7		400	2038	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220047	133220047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	243	955	1	ENST00000320574.5:c.4390G>A	p.Ala1464Thr	p.A1464T	ENST00000320574	NM_006231.2	1464	Gct/Act	34/49	0.490101755035753	1	FACETS	0.382	0.358	0.406	0.382	0.358	0.406	INDETERMINATE	1	TRUE	0	0.934462987822634	1		956	726	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030462	49030462	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1173892082	NA	P-0058192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	176	328	4	ENST00000267163.4:c.1937C>G	p.Ser646Cys	p.S646C	ENST00000267163	NM_000321.2	646	tCt/tGt	19/27	0.934462987822634	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.934462987822634	1		332	195	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678565	88678565	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	432	521	2	ENST00000360948.2:c.971T>A	p.Val324Glu	p.V324E	ENST00000360948	NM_001012338.2	324	gTg/gAg	9/19	0.525734612308978	3	FACETS	0.927	0.892	0.961			1	INDETERMINATE	2	TRUE	NA	0.934462987822634	3		523	732	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665353	138665353	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1306598987	NA	P-0058192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	560	1180	2	ENST00000330315.3:c.212C>A	p.Ala71Glu	p.A71E	ENST00000330315	NM_023067.3	71	gCg/gAg	1/1	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.934462987822634	2		1182	1181	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6045541	6045541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	195	282	3	ENST00000265849.7:c.145G>A	p.Ala49Thr	p.A49T	ENST00000265849	NM_000535.5	49	Gct/Act	2/15	0.486939490813759	3	FACETS	1	0.989	1	0.638	0.596	0.68	INDETERMINATE	1	TRUE	1	0.934462987822634	3		285	480	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0058193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	679	491	6	ENST00000311936.3:c.180_181delinsAA	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggAAaa	3/5	0.759387571651474	8	FACETS	0.917	0.888	0.946			1	CLONAL	5	TRUE	NA	0.759387571651474	8		497	1279	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs80338963	NA	P-0058193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	384	480	0	ENST00000342988.3:c.1081C>G	p.Arg361Gly	p.R361G	ENST00000342988	NM_005359.5	361	Cgc/Ggc	9/12	0.759387571651474	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.759387571651474	3		480	455	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380261	25380261	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	765	509	6	ENST00000311936.3:c.197C>A	p.Ala66Glu	p.A66E	ENST00000311936	NM_004985.3	66	gCa/gAa	3/5	0.759387571651474	8	FACETS	0.962	0.934	0.99			1	CLONAL	5	TRUE	NA	0.759387571651474	8		515	1373	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193461	99193461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	271	968	0	ENST00000074304.5:c.2656C>T	p.Arg886Cys	p.R886C	ENST00000074304	NM_001134224.1	886	Cgc/Tgc	25/26	0.748691955710243	3	FACETS	0.853	0.8	0.908	0.427	0.4	0.454	CLONAL	1	TRUE	1	0.759387571651474	3		968	1154	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273268	115273268	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	112	376	2	ENST00000438362.2:c.1190G>A	p.Gly397Asp	p.G397D	ENST00000438362	NM_001242891.1	397	gGt/gAt	11/20	0.537812799339438	3	FACETS	0.993	0.9	1			1	CLONAL	1	TRUE	NA	0.759387571651474	3		378	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578277	+	frameshift_variant	Frame_Shift_Del	DEL	AGATGCTGAG	AGATGCTGAG	-	novel	NA	P-0058193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	718	799	0	ENST00000269305.4:c.572_581del	p.Pro191LeufsTer53	p.P191Lfs*53	ENST00000269305	NM_001126112.2	191	cCTCAGCATCTt/ct	6/11	0.224742779728032	6	FACETS	1	0.996	1			1	INDETERMINATE	5	TRUE	NA	0.759387571651474	6		799	893	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765694	41765694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61737385	NA	P-0058194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	118	803	1	ENST00000301178.4:c.2570C>T	p.Ala857Val	p.A857V	ENST00000301178	NM_021913.4	857	gCg/gTg	20/20	1	2	FACETS	0.303	0.272	0.335	0.303	0.272	0.335	SUBCLONAL	1	TRUE	1	0.643052061626307	2		804	1213	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs967461896	NA	P-0058194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	393	942	0	ENST00000269305.4:c.526T>A	p.Cys176Ser	p.C176S	ENST00000269305	NM_001126112.2	176	Tgc/Agc	5/11	1	2	FACETS	0.854	0.811	0.898	0.854	0.811	0.898	CLONAL	1	TRUE	1	0.643052061626307	2		942	1431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578509	7578509	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1202	642	1181	0	ENST00000269305.4:c.421del	p.Cys141AlafsTer29	p.C141Afs*29	ENST00000269305	NM_001126112.2	141	Tgc/gc	5/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.643052061626307	2		1181	1844	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259153	16259153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	109	581	1	ENST00000375759.3:c.6418G>A	p.Asp2140Asn	p.D2140N	ENST00000375759	NM_015001.2	2140	Gat/Aat	11/15	1	2	FACETS	0.367	0.329	0.407	0.367	0.329	0.407	SUBCLONAL	1	TRUE	1	0.643052061626307	2		582	924	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612187	189612187	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	1322	667	0	ENST00000264731.3:c.1939C>G	p.Arg647Gly	p.R647G	ENST00000264731	NM_003722.4	647	Cgc/Ggc	14/14	0.640494132773387	5	FACETS	1	0.984	1	1	0.984	1	CLONAL	4	TRUE	1	0.643052061626307	5		667	2012	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323293	31323293	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	96	332	0	ENST00000412585.2:c.696C>G	p.Phe232Leu	p.F232L	ENST00000412585	NM_005514.6	232	ttC/ttG	4/8	1	2	FACETS	0.536	0.479	0.597	0.536	0.479	0.597	SUBCLONAL	1	TRUE	1	0.643052061626307	2		332	557	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190381	32190381	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	188	1054	0	ENST00000375023.3:c.358G>C	p.Asp120His	p.D120H	ENST00000375023	NM_004557.3	120	Gac/Cac	3/30	1	2	FACETS	0.419	0.385	0.453	0.419	0.385	0.453	SUBCLONAL	1	TRUE	1	0.643052061626307	2		1054	1397	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993822	72993822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374552910	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	43	916	3	ENST00000268489.5:c.223G>A	p.Ala75Thr	p.A75T	ENST00000268489	NM_006885.3	75	Gcc/Acc	2/10	1	2	FACETS	0.301	0.251	0.357	0.301	0.251	0.357	SUBCLONAL	1	TRUE	1	0.41	2		919	697	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	35	415	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.41	2		415	151	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606697	29606697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779282861	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	100	692	0	ENST00000389048.3:c.1183C>T	p.Arg395Cys	p.R395C	ENST00000389048	NM_004304.4	395	Cgt/Tgt	5/29	1	2	FACETS	0.745	0.666	0.828	0.745	0.666	0.828	SUBCLONAL	1	TRUE	1	0.41	2		692	655	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339039	225339039	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752958265	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	26	454	0	ENST00000264414.4:c.2230C>T	p.Arg744Cys	p.R744C	ENST00000264414	NM_003590.4	744	Cgt/Tgt	16/16	1	2	FACETS	0.613	0.488	0.754	0.613	0.488	0.754	SUBCLONAL	1	TRUE	1	0.41	2		454	207	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894950	101894950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777965779	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	15	394	0	ENST00000374994.4:c.503G>A	p.Arg168His	p.R168H	ENST00000374994	NM_004612.2	168	cGc/cAc	3/9	1	2	FACETS	0.249	0.181	0.33	0.249	0.181	0.33	SUBCLONAL	1	TRUE	1	0.41	2		394	294	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023019	150023019	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	73	683	0	ENST00000253339.5:c.244C>T	p.Arg82Ter	p.R82*	ENST00000253339		82	Cga/Tga	1/7	1	2	FACETS	0.774	0.679	0.876	0.774	0.679	0.876	SUBCLONAL	1	TRUE	1	0.41	2		683	460	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959064	2959064	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	197	1023	0	ENST00000396946.4:c.2452C>T	p.Arg818Trp	p.R818W	ENST00000396946	NM_032415.4	818	Cgg/Tgg	18/25	1	2	FACETS	0.963	0.891	1	0.963	0.891	1	CLONAL	1	TRUE	1	0.41	2		1023	998	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	46	557	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	0.828	0.702	0.965	0.828	0.702	0.965	CLONAL	1	TRUE	1	0.41	2		557	271	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	195	1084	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.41	2		1085	951	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126343	5126343	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41316003	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	20	284	0	ENST00000381652.3:c.3188G>A	p.Arg1063His	p.R1063H	ENST00000381652	NM_004972.3	1063	cGt/cAt	24/25	1	2	FACETS	0.976	0.759	1	0.976	0.759	1	CLONAL	1	TRUE	1	0.41	2		284	100	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533469	63533469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149764887	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	212	1189	3	ENST00000307078.5:c.1685C>T	p.Pro562Leu	p.P562L	ENST00000307078	NM_004655.3	562	cCg/cTg	6/11	1	2	FACETS	0.979	0.909	1	0.979	0.909	1	CLONAL	1	TRUE	1	0.41	2		1192	1056	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589168	67589168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	27	372	0	ENST00000274335.5:c.1156C>T	p.Arg386Ter	p.R386*	ENST00000274335		386	Cga/Tga	9/15	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.41	2		372	111	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209283	98209283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139942632	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	68	1226	1	ENST00000331920.6:c.4255C>T	p.Arg1419Trp	p.R1419W	ENST00000331920	NM_000264.3	1419	Cgg/Tgg	23/24	1	2	FACETS	0.307	0.266	0.352	0.307	0.266	0.352	SUBCLONAL	1	TRUE	1	0.41	2		1227	1080	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030323	180030323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745546499	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	256	1345	3	ENST00000261937.6:c.3961C>T	p.Arg1321Trp	p.R1321W	ENST00000261937	NM_182925.4	1321	Cgg/Tgg	30/30	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.41	2		1348	1228	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057702	180057702	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202063909	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	213	1341	1	ENST00000261937.6:c.253G>A	p.Glu85Lys	p.E85K	ENST00000261937	NM_182925.4	85	Gag/Aag	3/30	1	2	FACETS	0.849	0.787	0.913	0.849	0.787	0.913	CLONAL	1	TRUE	1	0.41	2		1342	1224	SUCCESS
APC	324	MSKCC	GRCh37	5	112177049	112177049	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	48	412	0	ENST00000257430.4:c.5758C>T	p.Arg1920Ter	p.R1920*	ENST00000257430	NM_000038.5	1920	Cga/Tga	16/16	1	2	FACETS	0.851	0.725	0.989	0.851	0.725	0.989	CLONAL	1	TRUE	1	0.41	2		412	275	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333863	70333863	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs750883311	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	24	470	2	ENST00000373644.4:c.1768C>T	p.Arg590Ter	p.R590*	ENST00000373644	NM_030625.2	590	Cga/Tga	2/12	1	2	FACETS	0.348	0.273	0.435	0.348	0.273	0.435	SUBCLONAL	1	TRUE	1	0.41	2		472	336	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575121	64575121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878855197	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	113	863	0	ENST00000312049.6:c.686G>A	p.Arg229His	p.R229H	ENST00000312049	NM_130799.2	229	cGc/cAc	4/10	1	2	FACETS	0.737	0.663	0.815	0.737	0.663	0.815	SUBCLONAL	1	TRUE	1	0.41	2		863	748	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143020	58143020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144657355	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	129	1195	3	ENST00000257904.6:c.764G>A	p.Arg255His	p.R255H	ENST00000257904	NM_000075.3	255	cGc/cAc	7/8	1	2	FACETS	0.495	0.448	0.546	0.495	0.448	0.546	SUBCLONAL	1	TRUE	1	0.41	2		1198	1270	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	60	564	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.41	2		564	271	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221161	5221161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs575201235	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	110	1104	1	ENST00000357368.4:c.3305G>A	p.Arg1102His	p.R1102H	ENST00000357368	NM_002850.3	1102	cGc/cAc	20/38	1	2	FACETS	0.554	0.497	0.615	0.554	0.497	0.615	SUBCLONAL	1	TRUE	1	0.41	2		1105	968	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415537	152415537	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519714	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	126	642	0	ENST00000206249.3:c.1387T>C	p.Ser463Pro	p.S463P	ENST00000206249	NM_000125.3	463	Tcc/Ccc	7/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.41	2		642	527	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	69	496	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.948	0.831	1	0.948	0.831	1	CLONAL	1	TRUE	1	0.41	2		496	355	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043377	180043377	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771345898	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	63	894	3	ENST00000261937.6:c.3209G>A	p.Arg1070His	p.R1070H	ENST00000261937	NM_182925.4	1070	cGc/cAc	23/30	1	2	FACETS	0.382	0.329	0.439	0.382	0.329	0.439	SUBCLONAL	1	TRUE	1	0.41	2		897	805	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390539	139390539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774680812	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	248	1244	1	ENST00000277541.6:c.7652C>T	p.Pro2551Leu	p.P2551L	ENST00000277541	NM_017617.3	2551	cCg/cTg	34/34	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.41	2		1245	1136	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	84	373	1	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.41	2		374	398	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359924	87359924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs78629699	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	24	402	0	ENST00000277120.3:c.1232C>T	p.Thr411Met	p.T411M	ENST00000277120		411	aCg/aTg	11/19	1	2	FACETS	0.261	0.204	0.327	0.261	0.204	0.327	SUBCLONAL	1	TRUE	1	0.41	2		402	449	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55143617	55143617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878854825	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	73	422	0	ENST00000257290.5:c.1849C>T	p.Arg617Trp	p.R617W	ENST00000257290	NM_006206.4	617	Cgg/Tgg	13/23	1	2	FACETS	0.869	0.763	0.981	0.869	0.763	0.981	CLONAL	1	TRUE	1	0.41	2		422	410	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753987	57753988	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	35	340	0	ENST00000274289.3:c.636dup	p.Ile213TyrfsTer2	p.I213Yfs*2	ENST00000274289	NM_006622.3	212	-/T	5/14	1	2	FACETS	0.61	0.502	0.73	0.61	0.502	0.73	SUBCLONAL	1	TRUE	1	0.41	2		340	280	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335079	65335079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	136	599	0	ENST00000342505.4:c.562G>A	p.Glu188Lys	p.E188K	ENST00000342505	NM_002227.2	188	Gag/Aag	6/25	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.41	2		599	600	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876305	35876305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778728560	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	79	651	0	ENST00000303115.3:c.1097C>T	p.Ser366Phe	p.S366F	ENST00000303115	NM_002185.3	366	tCc/tTc	8/8	1	2	FACETS	0.667	0.587	0.752	0.667	0.587	0.752	SUBCLONAL	1	TRUE	1	0.41	2		651	578	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740216	162740216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775098890	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	49	642	0	ENST00000367921.3:c.1418G>A	p.Arg473His	p.R473H	ENST00000367921	NM_006182.2	473	cGc/cAc	12/18	1	2	FACETS	0.378	0.32	0.443	0.378	0.32	0.443	SUBCLONAL	1	TRUE	1	0.41	2		642	632	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721622	49721622	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs200268600	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	12	47	0	ENST00000449682.2:c.2017G>A	p.Gly673Ser	p.G673S	ENST00000449682	NM_020998.3	673	Ggt/Agt	18/18	1	2	FACETS	0.929	0.668	1	0.929	0.668	1	CLONAL	1	TRUE	1	0.41	2		47	63	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539951	187539951	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs777631605	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	71	466	0	ENST00000441802.2:c.7789C>T	p.Arg2597Ter	p.R2597*	ENST00000441802	NM_005245.3	2597	Cga/Tga	10/27	1	2	FACETS	0.837	0.733	0.947	0.837	0.733	0.947	CLONAL	1	TRUE	1	0.41	2		466	414	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	42	296	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.41	2		296	189	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222993	5222993	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762510209	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	62	1336	0	ENST00000357368.4:c.2810C>T	p.Ala937Val	p.A937V	ENST00000357368	NM_002850.3	937	gCg/gTg	18/38	1	2	FACETS	0.271	0.233	0.312	0.271	0.233	0.312	SUBCLONAL	1	TRUE	1	0.41	2		1336	1117	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021428	42021428	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	68	551	0	ENST00000219905.7:c.3724C>T	p.Arg1242Ter	p.R1242*	ENST00000219905	NM_001164273.1	1242	Cga/Tga	11/24	1	2	FACETS	0.993	0.87	1	0.993	0.87	1	CLONAL	1	TRUE	1	0.41	2		551	334	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131277	17131277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778275358	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	82	1320	2	ENST00000285071.4:c.175C>T	p.Arg59Cys	p.R59C	ENST00000285071	NM_144997.5	59	Cgt/Tgt	4/14	1	2	FACETS	0.328	0.288	0.371	0.328	0.288	0.371	SUBCLONAL	1	TRUE	1	0.41	2		1322	1220	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178095	56178095	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374455781	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	71	347	1	ENST00000399503.3:c.3068G>A	p.Arg1023His	p.R1023H	ENST00000399503	NM_005921.1	1023	cGc/cAc	14/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.41	2		348	289	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205534	61205534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140191819	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	45	578	1	ENST00000301761.2:c.319C>T	p.Arg107Cys	p.R107C	ENST00000301761	NM_017841.2	107	Cgc/Tgc	3/4	1	2	FACETS	0.48	0.404	0.565	0.48	0.404	0.565	SUBCLONAL	1	TRUE	1	0.41	2		579	457	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	128	734	0	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.41	2		734	593	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577569	7577569	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519981	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	56	754	0	ENST00000269305.4:c.712T>C	p.Cys238Arg	p.C238R	ENST00000269305	NM_001126112.2	238	Tgt/Cgt	7/11	1	2	FACETS	0.33	0.282	0.383	0.33	0.282	0.383	SUBCLONAL	1	TRUE	1	0.41	2		754	828	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944326	81944326	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	143	808	0	ENST00000359376.3:c.1934+1G>A		p.X645_splice	ENST00000359376	NM_002661.3	645			1	2	FACETS	0.97	0.886	1	0.97	0.886	1	CLONAL	1	TRUE	1	0.41	2		808	719	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803121	1803121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745863884	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	74	1394	0	ENST00000260795.2:c.473G>A	p.Arg158Gln	p.R158Q	ENST00000260795		158	cGg/cAg	4/17	1	2	FACETS	0.296	0.258	0.338	0.296	0.258	0.338	SUBCLONAL	1	TRUE	1	0.41	2		1394	1219	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431010	181431010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	245	1111	4	ENST00000325404.1:c.862G>A	p.Ala288Thr	p.A288T	ENST00000325404	NM_003106.3	288	Gcc/Acc	1/1	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.41	2		1115	1092	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46527650	46527650	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1287980956	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	19	507	1	ENST00000262741.5:c.715G>T	p.Glu239Ter	p.E239*	ENST00000262741	NM_003629.3	239	Gaa/Taa	6/10	1	2	FACETS	0.257	0.195	0.331	0.257	0.195	0.331	SUBCLONAL	1	TRUE	1	0.41	2		508	360	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967276	134967276	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs534330476	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	199	816	2	ENST00000398015.3:c.2615C>T	p.Ala872Val	p.A872V	ENST00000398015	NM_004441.4	872	gCg/gTg	14/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.41	2		818	850	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898755	134898755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs546798910	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	59	467	0	ENST00000398015.3:c.1813G>A	p.Glu605Lys	p.E605K	ENST00000398015	NM_004441.4	605	Gaa/Aaa	10/16	1	2	FACETS	0.825	0.713	0.945	0.825	0.713	0.945	CLONAL	1	TRUE	1	0.41	2		467	349	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164889	36164889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1358657401	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	75	1250	0	ENST00000300305.3:c.986C>T	p.Ala329Val	p.A329V	ENST00000300305		329	gCg/gTg	8/8	1	2	FACETS	0.303	0.264	0.345	0.303	0.264	0.345	SUBCLONAL	1	TRUE	1	0.41	2		1250	1209	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438159	438159	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs192267587	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	25	452	0	ENST00000399788.2:c.1810C>T	p.Arg604Cys	p.R604C	ENST00000399788	NM_001042603.1	604	Cgc/Tgc	14/28	1	2	FACETS	0.296	0.233	0.369	0.296	0.233	0.369	SUBCLONAL	1	TRUE	1	0.41	2		452	412	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940458	13940458	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	15	350	0	ENST00000405192.2:c.1048C>T	p.Arg350Ter	p.R350*	ENST00000405192	NM_001163147.1	350	Cga/Tga	11/12	1	2	FACETS	0.255	0.186	0.338	0.255	0.186	0.338	SUBCLONAL	1	TRUE	1	0.41	2		350	287	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434503	110434503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	56	1122	0	ENST00000375856.3:c.3898G>A	p.Gly1300Ser	p.G1300S	ENST00000375856	NM_003749.2	1300	Ggc/Agc	1/2	1	2	FACETS	0.29	0.248	0.337	0.29	0.248	0.337	SUBCLONAL	1	TRUE	1	0.41	2		1122	941	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526442	66526442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	95	507	0	ENST00000358598.2:c.998G>A	p.Arg333His	p.R333H	ENST00000358598	NM_212471.2	333	cGt/cAt	11/11	1	2	FACETS	0.972	0.869	1	0.972	0.869	1	CLONAL	1	TRUE	1	0.41	2		507	477	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109935	115109935	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	59	1154	2	ENST00000257566.3:c.1943C>T	p.Pro648Leu	p.P648L	ENST00000257566	NM_016569.3	648	cCg/cTg	8/8	1	2	FACETS	0.281	0.24	0.325	0.281	0.24	0.325	SUBCLONAL	1	TRUE	1	0.41	2		1156	1026	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976831	2976831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753594488	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	284	997	0	ENST00000396946.4:c.1181C>T	p.Ser394Leu	p.S394L	ENST00000396946	NM_032415.4	394	tCg/tTg	9/25	1	2	FACETS	0.792	0.746	0.838	1	0.994	1	SUBCLONAL	2	TRUE	1	0.41	2		997	875	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799059	42799059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	209	1508	1	ENST00000575354.2:c.4543C>T	p.Arg1515Cys	p.R1515C	ENST00000575354	NM_015125.3	1515	Cgc/Tgc	20/20	1	2	FACETS	0.827	0.766	0.89	0.827	0.766	0.89	CLONAL	1	TRUE	1	0.41	2		1509	1233	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715847	117715847	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	28	418	0	ENST00000368508.3:c.911G>T	p.Arg304Ile	p.R304I	ENST00000368508	NM_002944.2	304	aGa/aTa	9/43	1	2	FACETS	0.843	0.681	1	0.843	0.681	1	CLONAL	1	TRUE	1	0.41	2		418	162	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738094	145738094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561220929	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	301	1351	0	ENST00000428558.2:c.2816C>T	p.Ala939Val	p.A939V	ENST00000428558	NM_004260.3	939	gCg/gTg	17/22	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.41	2		1351	1260	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412494	80412494	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	31	447	0	ENST00000286548.4:c.547C>T	p.Arg183Ter	p.R183*	ENST00000286548	NM_002072.3	183	Cga/Tga	4/7	1	2	FACETS	0.371	0.299	0.451	0.371	0.299	0.451	SUBCLONAL	1	TRUE	1	0.41	2		447	408	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342807	87342807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	89	508	0	ENST00000277120.3:c.1092G>T	p.Lys364Asn	p.K364N	ENST00000277120		364	aaG/aaT	9/19	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.41	2		508	371	SUCCESS
AR	367	MSKCC	GRCh37	X	66765875	66765875	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	74	1371	0	ENST00000374690.3:c.887A>G	p.Asp296Gly	p.D296G	ENST00000374690	NM_000044.3	296	gAc/gGc	1/8	1	2	FACETS	0.303	0.264	0.345	0.303	0.264	0.345	SUBCLONAL	1	TRUE	1	0.41	2		1371	1192	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527578	157527578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142466273	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	108	615	0	ENST00000346085.5:c.5303C>T	p.Pro1768Leu	p.P1768L	ENST00000346085	NM_020732.3	1768	cCg/cTg	20/20	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.41	2		615	527	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962529	100962529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767360879	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	152	586	0	ENST00000325455.5:c.1868G>A	p.Arg623His	p.R623H	ENST00000325455	NM_001202474.3	623	cGc/cAc	3/8	1	2	FACETS	0.824	0.76	0.889	1	0.99	1	CLONAL	2	TRUE	1	0.41	2		586	450	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158212	47158212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553699111	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	33	418	0	ENST00000409792.3:c.4487G>A	p.Arg1496Gln	p.R1496Q	ENST00000409792	NM_014159.6	1496	cGa/cAa	4/21	1	2	FACETS	0.641	0.525	0.771	0.641	0.525	0.771	SUBCLONAL	1	TRUE	1	0.41	2		418	251	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198218	138198218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs864321626	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	37	220	0	ENST00000237289.4:c.811C>T	p.Arg271Ter	p.R271*	ENST00000237289	NM_001270507.1	271	Cga/Tga	6/9	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.41	2		220	171	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276764	15276764	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202027632	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	239	1243	0	ENST00000263388.2:c.5501G>A	p.Arg1834Gln	p.R1834Q	ENST00000263388	NM_000435.2	1834	cGg/cAg	30/33	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.41	2		1243	1103	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136804	55136804	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	45	351	0	ENST00000257290.5:c.1126C>T	p.Arg376Ter	p.R376*	ENST00000257290	NM_006206.4	376	Cga/Tga	8/23	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.41	2		351	211	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846031	128846031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1307431013	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	158	1027	0	ENST00000249373.3:c.961G>A	p.Val321Met	p.V321M	ENST00000249373	NM_005631.4	321	Gtg/Atg	5/12	1	2	FACETS	0.94	0.862	1	0.94	0.862	1	CLONAL	1	TRUE	1	0.41	2		1027	820	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518086	187518086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200185840	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	39	759	0	ENST00000441802.2:c.12608G>A	p.Arg4203His	p.R4203H	ENST00000441802	NM_005245.3	4203	cGt/cAt	25/27	1	2	FACETS	0.371	0.307	0.442	0.371	0.307	0.442	SUBCLONAL	1	TRUE	1	0.41	2		759	513	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294448	1294448	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770436206	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	154	1210	2	ENST00000310581.5:c.553C>T	p.Arg185Trp	p.R185W	ENST00000310581	NM_198253.2	185	Cgg/Tgg	2/16	1	2	FACETS	0.68	0.621	0.742	0.68	0.621	0.742	SUBCLONAL	1	TRUE	1	0.41	2		1212	1105	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421514	32421514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	98	733	0	ENST00000332351.3:c.1078G>A	p.Gly360Ser	p.G360S	ENST00000332351	NM_024426.4	360	Ggt/Agt	6/10	1	2	FACETS	0.718	0.641	0.799	0.718	0.641	0.799	SUBCLONAL	1	TRUE	1	0.41	2		733	666	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472565	88472565	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371959662	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	122	759	2	ENST00000360948.2:c.1990G>A	p.Ala664Thr	p.A664T	ENST00000360948	NM_001012338.2	664	Gcc/Acc	16/19	1	2	FACETS	0.854	0.773	0.939	0.854	0.773	0.939	CLONAL	1	TRUE	1	0.41	2		761	697	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21304066	21304066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444326760	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	70	695	0	ENST00000354336.3:c.845G>A	p.Arg282His	p.R282H	ENST00000354336	NM_005207.3	282	cGc/cAc	3/3	1	2	FACETS	0.48	0.418	0.547	0.48	0.418	0.547	SUBCLONAL	1	TRUE	1	0.41	2		695	711	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306960	65306960	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	11	546	0	ENST00000342505.4:c.2617C>T	p.Arg873Cys	p.R873C	ENST00000342505	NM_002227.2	873	Cgc/Tgc	19/25	1	2	FACETS	0.105	0.071	0.146	0.105	0.071	0.146	SUBCLONAL	1	TRUE	1	0.41	2		546	513	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797910	42797910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367735541	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	296	1427	2	ENST00000575354.2:c.3962G>A	p.Arg1321His	p.R1321H	ENST00000575354	NM_015125.3	1321	cGc/cAc	16/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.41	2		1429	1328	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224449	123224449	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747270306	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	60	518	0	ENST00000218089.9:c.3302G>A	p.Ser1101Asn	p.S1101N	ENST00000218089	NM_001042749.1	1101	aGt/aAt	31/35	1	2	FACETS	0.903	0.783	1	0.903	0.783	1	CLONAL	1	TRUE	1	0.41	2		518	324	SUCCESS
APC	324	MSKCC	GRCh37	5	112179788	112179788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201459013	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	14	282	0	ENST00000257430.4:c.8497C>T	p.Arg2833Cys	p.R2833C	ENST00000257430	NM_000038.5	2833	Cgc/Tgc	16/16	1	2	FACETS	0.283	0.205	0.379	0.283	0.205	0.379	SUBCLONAL	1	TRUE	1	0.41	2		282	241	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821425	72821425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769841511	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	52	851	1	ENST00000268489.5:c.10750G>A	p.Ala3584Thr	p.A3584T	ENST00000268489	NM_006885.3	3584	Gca/Aca	10/10	1	2	FACETS	0.291	0.246	0.339	0.291	0.246	0.339	SUBCLONAL	1	TRUE	1	0.41	2		852	873	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430633	80430633	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	22	343	0	ENST00000286548.4:c.375G>T	p.Glu125Asp	p.E125D	ENST00000286548	NM_002072.3	125	gaG/gaT	3/7	1	2	FACETS	0.767	0.601	0.954	0.767	0.601	0.954	CLONAL	1	TRUE	1	0.41	2		343	140	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040978	42040978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755286142	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	105	831	3	ENST00000219905.7:c.5356C>T	p.Arg1786Trp	p.R1786W	ENST00000219905	NM_001164273.1	1786	Cgg/Tgg	16/24	1	2	FACETS	0.687	0.615	0.762	0.687	0.615	0.762	SUBCLONAL	1	TRUE	1	0.41	2		834	746	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281517	15281517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	153	1195	0	ENST00000263388.2:c.4856G>A	p.Arg1619His	p.R1619H	ENST00000263388	NM_000435.2	1619	cGc/cAc	26/33	1	2	FACETS	0.774	0.708	0.844	0.774	0.708	0.844	SUBCLONAL	1	TRUE	1	0.41	2		1195	964	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299983	15299983	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1390414547	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	244	1327	2	ENST00000263388.2:c.1195G>A	p.Ala399Thr	p.A399T	ENST00000263388	NM_000435.2	399	Gcc/Acc	8/33	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.41	2		1329	1099	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569823	67569823	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1230037871	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	69	303	0	ENST00000274335.5:c.484C>T	p.Arg162Ter	p.R162*	ENST00000274335		162	Cga/Tga	3/15	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.41	2		303	293	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277519	142277519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	27	358	0	ENST00000350721.4:c.1832C>T	p.Thr611Ile	p.T611I	ENST00000350721	NM_001184.3	611	aCc/aTc	8/47	1	2	FACETS	0.475	0.379	0.585	0.475	0.379	0.585	SUBCLONAL	1	TRUE	1	0.41	2		358	277	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381520	81381520	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	56	420	1	ENST00000222390.5:c.541C>T	p.Arg181Ter	p.R181*	ENST00000222390	NM_000601.4	181	Cga/Tga	5/18	1	2	FACETS	0.893	0.77	1	0.893	0.77	1	CLONAL	1	TRUE	1	0.41	2		421	306	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251561	251561	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367621815	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	172	938	1	ENST00000264932.6:c.1772C>T	p.Ala591Val	p.A591V	ENST00000264932	NM_004168.2	591	gCg/gTg	13/15	1	2	FACETS	0.885	0.814	0.959	0.885	0.814	0.959	CLONAL	1	TRUE	1	0.41	2		939	948	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508473	106508473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370328855	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	53	511	1	ENST00000359195.3:c.467C>T	p.Ala156Val	p.A156V	ENST00000359195	NM_002649.2	156	gCg/gTg	2/11	1	2	FACETS	0.774	0.663	0.894	0.774	0.663	0.894	SUBCLONAL	1	TRUE	1	0.41	2		512	334	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755756	39755756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	141	792	1	ENST00000288319.7:c.1009G>A	p.Gly337Arg	p.G337R	ENST00000288319	NM_182918.3	337	Ggg/Agg	10/10	1	2	FACETS	0.994	0.907	1	0.994	0.907	1	CLONAL	1	TRUE	1	0.41	2		793	692	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184830	32184830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150609093	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	140	832	2	ENST00000375023.3:c.1753C>T	p.Arg585Cys	p.R585C	ENST00000375023	NM_004557.3	585	Cgc/Tgc	11/30	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.41	2		834	670	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137323819	137323819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	196	1304	1	ENST00000481739.1:c.1112G>A	p.Arg371His	p.R371H	ENST00000481739	NM_002957.4	371	cGc/cAc	8/10	1	2	FACETS	0.799	0.739	0.863	0.799	0.739	0.863	SUBCLONAL	1	TRUE	1	0.41	2		1305	1196	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39600670	39600670	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	15	225	0	ENST00000262039.4:c.1484+1G>A		p.X495_splice	ENST00000262039	NM_002647.2	495			1	2	FACETS	0.787	0.584	1	0.787	0.584	1	CLONAL	1	TRUE	1	0.41	2		225	93	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961438	41961438	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	74	603	0	ENST00000219905.7:c.346G>A	p.Asp116Asn	p.D116N	ENST00000219905	NM_001164273.1	116	Gat/Aat	2/24	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.41	2		603	361	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842075	3842075	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1302427305	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	58	397	1	ENST00000262367.5:c.1237C>T	p.Arg413Ter	p.R413*	ENST00000262367	NM_004380.2	413	Cga/Tga	5/31	1	2	FACETS	0.827	0.715	0.949	0.827	0.715	0.949	CLONAL	1	TRUE	1	0.41	2		398	342	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344958	70344958	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	135	1024	2	ENST00000374080.3:c.2188C>T	p.Arg730Ter	p.R730*	ENST00000374080		730	Cga/Tga	15/45	1	2	FACETS	0.819	0.745	0.897	0.819	0.745	0.897	CLONAL	1	TRUE	1	0.41	2		1026	804	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945647	206945647	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550164520	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	38	657	0	ENST00000423557.1:c.134G>A	p.Arg45Gln	p.R45Q	ENST00000423557	NM_000572.2	45	cGa/cAa	1/5	1	2	FACETS	0.298	0.246	0.357	0.298	0.246	0.357	SUBCLONAL	1	TRUE	1	0.41	2		657	622	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609394	39609394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1360571803	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	37	392	0	ENST00000262039.4:c.1696C>T	p.Arg566Cys	p.R566C	ENST00000262039	NM_002647.2	566	Cgt/Tgt	15/25	1	2	FACETS	0.531	0.439	0.633	0.531	0.439	0.633	SUBCLONAL	1	TRUE	1	0.41	2		392	340	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5246051	5246051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	109	674	0	ENST00000357368.4:c.724C>T	p.Arg242Cys	p.R242C	ENST00000357368	NM_002850.3	242	Cgc/Tgc	10/38	1	2	FACETS	0.877	0.79	0.97	0.877	0.79	0.97	CLONAL	1	TRUE	1	0.41	2		674	606	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143181675	143181675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377427325	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	28	503	2	ENST00000262992.4:c.658G>A	p.Gly220Arg	p.G220R	ENST00000262992	NM_001101669.1	220	Gga/Aga	9/24	1	2	FACETS	0.523	0.42	0.641	0.523	0.42	0.641	SUBCLONAL	1	TRUE	1	0.41	2		505	261	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009413	69009413	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	92	548	0	ENST00000288368.4:c.2530G>T	p.Gly844Cys	p.G844C	ENST00000288368	NM_024870.2	844	Ggt/Tgt	22/40	1	2	FACETS	0.927	0.827	1	0.927	0.827	1	CLONAL	1	TRUE	1	0.41	2		548	484	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63829504	63829504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529464997	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	40	447	0	ENST00000279873.7:c.1147G>A	p.Gly383Ser	p.G383S	ENST00000279873	NM_032199.2	383	Ggt/Agt	8/10	1	2	FACETS	0.49	0.408	0.582	0.49	0.408	0.582	SUBCLONAL	1	TRUE	1	0.41	2		447	398	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263191	115263191	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1306278892	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	137	764	1	ENST00000438362.2:c.2159G>A	p.Arg720His	p.R720H	ENST00000438362	NM_001242891.1	720	cGc/cAc	17/20	1	2	FACETS	0.874	0.795	0.956	0.874	0.795	0.956	CLONAL	1	TRUE	1	0.41	2		765	765	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705201	52705201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1372727039	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	112	520	0	ENST00000322088.6:c.83G>A	p.Arg28His	p.R28H	ENST00000322088	NM_014225.5	28	cGc/cAc	2/15	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.41	2		520	511	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106519993	106519994	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs770069386	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	25	257	0	ENST00000359195.3:c.2427dup	p.Pro810ThrfsTer5	p.P810Tfs*5	ENST00000359195	NM_002649.2	807	-/A	6/11	1	2	FACETS	0.871	0.695	1	0.871	0.695	1	CLONAL	1	TRUE	1	0.41	2		257	140	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357196	70357196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200663107	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	54	894	0	ENST00000374080.3:c.5711C>T	p.Ala1904Val	p.A1904V	ENST00000374080		1904	gCg/gTg	39/45	1	2	FACETS	0.319	0.271	0.371	0.319	0.271	0.371	SUBCLONAL	1	TRUE	1	0.41	2		894	827	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226590008	226590008	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377491451	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	118	967	0	ENST00000366794.5:c.193C>T	p.Arg65Trp	p.R65W	ENST00000366794	NM_001618.3	65	Cgg/Tgg	2/23	1	2	FACETS	0.634	0.571	0.7	0.634	0.571	0.7	SUBCLONAL	1	TRUE	1	0.41	2		967	908	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446282	70446282	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371499355	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	126	728	0	ENST00000373644.4:c.5222G>A	p.Arg1741His	p.R1741H	ENST00000373644	NM_030625.2	1741	cGc/cAc	11/12	1	2	FACETS	0.928	0.842	1	0.928	0.842	1	CLONAL	1	TRUE	1	0.41	2		728	662	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222168	53222168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556831986	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	178	891	0	ENST00000375401.3:c.4664C>T	p.Pro1555Leu	p.P1555L	ENST00000375401	NM_004187.3	1555	cCg/cTg	26/26	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.41	2		891	754	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007833	45007834	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	43	469	1	ENST00000558401.1:c.285dup	p.Asp96ArgfsTer2	p.D96Rfs*2	ENST00000558401	NM_004048.2	94	gaa/gAaa	2/4	1	2	FACETS	0.706	0.594	0.829	0.706	0.594	0.829	SUBCLONAL	1	TRUE	1	0.41	2		470	297	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435967	49435967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	228	1094	0	ENST00000301067.7:c.6014G>A	p.Arg2005His	p.R2005H	ENST00000301067	NM_003482.3	2005	cGc/cAc	28/54	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.41	2		1094	999	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225669	225669	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542980860	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	252	1221	2	ENST00000264932.6:c.448G>A	p.Val150Met	p.V150M	ENST00000264932	NM_004168.2	150	Gtg/Atg	4/15	1	2	FACETS	0.922	0.861	0.985	0.922	0.861	0.985	CLONAL	1	TRUE	1	0.41	2		1223	1333	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468210	120468210	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202022988	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	214	1093	0	ENST00000256646.2:c.4229G>A	p.Arg1410His	p.R1410H	ENST00000256646	NM_024408.3	1410	cGc/cAc	25/34	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.41	2		1093	987	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459167	120459167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746551843	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	171	798	0	ENST00000256646.2:c.6178C>T	p.Arg2060Cys	p.R2060C	ENST00000256646	NM_024408.3	2060	Cgc/Tgc	34/34	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.41	2		798	754	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526322	31526322	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs970742651	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	270	1201	0	ENST00000344624.3:c.718C>T	p.Arg240Ter	p.R240*	ENST00000344624		240	Cga/Tga	2/33	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.41	2		1201	1223	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795032	45795032	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768671057	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	153	815	2	ENST00000450313.1:c.1596C>A	p.Phe532Leu	p.F532L	ENST00000450313	NM_012222.2	532	ttC/ttA	16/16	1	2	FACETS	0.957	0.876	1	0.957	0.876	1	CLONAL	1	TRUE	1	0.41	2		817	780	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401429	401429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	70	305	0	ENST00000380956.4:c.751C>T	p.Arg251Trp	p.R251W	ENST00000380956	NM_001195286.1	251	Cgg/Tgg	7/9	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.41	2		305	264	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46275928	46275928	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs756248799	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	109	589	0	ENST00000371998.3:c.3364A>G	p.Met1122Val	p.M1122V	ENST00000371998		1122	Atg/Gtg	18/23	1	2	FACETS	0.963	0.868	1	0.963	0.868	1	CLONAL	1	TRUE	1	0.41	2		589	552	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637062	93637062	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369986984	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	126	580	0	ENST00000375746.1:c.1112C>T	p.Thr371Met	p.T371M	ENST00000375746	NM_001174167.1	371	aCg/aTg	9/14	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.41	2		580	591	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300039	137300040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755912201	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	153	1317	10	ENST00000481739.1:c.331dup	p.Leu111ProfsTer70	p.L111Pfs*70	ENST00000481739	NM_002957.4	108	-/C	3/10	1	2	FACETS	0.576	0.526	0.63	0.576	0.526	0.63	SUBCLONAL	1	TRUE	1	0.41	2		1327	1295	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137320990	137320990	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1220410660	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	287	1395	2	ENST00000481739.1:c.947G>A	p.Arg316His	p.R316H	ENST00000481739	NM_002957.4	316	cGc/cAc	7/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.41	2		1397	1321	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80057379	80057379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764832633	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	38	345	0	ENST00000265081.6:c.1778G>A	p.Arg593Gln	p.R593Q	ENST00000265081	NM_002439.4	593	cGg/cAg	13/24	1	2	FACETS	0.997	0.834	1	0.997	0.834	1	CLONAL	1	TRUE	1	0.41	2		345	186	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912137	50912137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	221	1279	0	ENST00000440232.2:c.1871C>T	p.Pro624Leu	p.P624L	ENST00000440232	NM_002691.3	624	cCc/cTc	15/27	1	2	FACETS	0.894	0.831	0.96	0.894	0.831	0.96	CLONAL	1	TRUE	1	0.41	2		1279	1206	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396206	139396206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	198	1249	1	ENST00000277541.6:c.5632G>A	p.Gly1878Arg	p.G1878R	ENST00000277541	NM_017617.3	1878	Ggg/Agg	30/34	1	2	FACETS	0.855	0.791	0.922	0.855	0.791	0.922	CLONAL	1	TRUE	1	0.41	2		1250	1129	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209372	98209372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	172	1129	0	ENST00000331920.6:c.4166C>T	p.Pro1389Leu	p.P1389L	ENST00000331920	NM_000264.3	1389	cCt/cTt	23/24	1	2	FACETS	0.948	0.873	1	0.948	0.873	1	CLONAL	1	TRUE	1	0.41	2		1129	885	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715988	52715988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1348762266	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	57	983	2	ENST00000322088.6:c.553G>A	p.Ala185Thr	p.A185T	ENST00000322088	NM_014225.5	185	Gca/Aca	5/15	1	2	FACETS	0.303	0.259	0.352	0.303	0.259	0.352	SUBCLONAL	1	TRUE	1	0.41	2		985	917	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430410	181430410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	230	1240	2	ENST00000325404.1:c.262C>T	p.Arg88Trp	p.R88W	ENST00000325404	NM_003106.3	88	Cgg/Tgg	1/1	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.41	2		1242	1088	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409089	139409089	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs79782048	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1278	76	1415	0	ENST00000277541.6:c.2080G>A	p.Glu694Lys	p.E694K	ENST00000277541	NM_017617.3	694	Gag/Aag	13/34	1	2	FACETS	0.274	0.239	0.312	0.274	0.239	0.312	SUBCLONAL	1	TRUE	1	0.41	2		1415	1354	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716301	52716301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	160	958	0	ENST00000322088.6:c.745C>T	p.Arg249Cys	p.R249C	ENST00000322088	NM_014225.5	249	Cgc/Tgc	6/15	1	2	FACETS	0.846	0.775	0.919	0.846	0.775	0.919	CLONAL	1	TRUE	1	0.41	2		958	923	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294138	1294138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774657340	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	126	1583	2	ENST00000310581.5:c.863C>T	p.Ala288Val	p.A288V	ENST00000310581	NM_198253.2	288	gCg/gTg	2/16	1	2	FACETS	0.487	0.44	0.538	0.487	0.44	0.538	SUBCLONAL	1	TRUE	1	0.41	2		1585	1261	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416536	49416536	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	161	827	0	ENST00000301067.7:c.16175G>A	p.Arg5392His	p.R5392H	ENST00000301067	NM_003482.3	5392	cGc/cAc	51/54	1	2	FACETS	0.983	0.903	1	0.983	0.903	1	CLONAL	1	TRUE	1	0.41	2		827	799	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213861	2213861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1204733528	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	246	1285	2	ENST00000398665.3:c.1673C>T	p.Ala558Val	p.A558V	ENST00000398665	NM_032482.2	558	gCg/gTg	18/28	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.41	2		1287	1198	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226125	226125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762956849	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	242	1134	0	ENST00000264932.6:c.584G>A	p.Arg195Gln	p.R195Q	ENST00000264932	NM_004168.2	195	cGg/cAg	5/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.41	2		1134	1128	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72994020	72994020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200637584	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	171	988	0	ENST00000268489.5:c.25G>A	p.Val9Ile	p.V9I	ENST00000268489	NM_006885.3	9	Gtc/Atc	2/10	1	2	FACETS	0.9	0.828	0.975	0.9	0.828	0.975	CLONAL	1	TRUE	1	0.41	2		988	927	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268929	55268929	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866928399	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	138	968	0	ENST00000275493.2:c.2995C>T	p.Arg999Cys	p.R999C	ENST00000275493	NM_005228.3	999	Cgt/Tgt	25/28	1	2	FACETS	0.853	0.777	0.933	0.853	0.777	0.933	CLONAL	1	TRUE	1	0.41	2		968	789	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164464	36164464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	38	626	1	ENST00000300305.3:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000300305		471	Cgc/Tgc	8/8	1	2	FACETS	0.262	0.215	0.314	0.262	0.215	0.314	SUBCLONAL	1	TRUE	1	0.41	2		627	708	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145678	61145678	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773764180	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	49	450	0	ENST00000295025.8:c.790C>T	p.Arg264Trp	p.R264W	ENST00000295025	NM_002908.2	264	Cgg/Tgg	7/11	1	2	FACETS	0.742	0.632	0.863	0.742	0.632	0.863	SUBCLONAL	1	TRUE	1	0.41	2		450	322	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251184	99251184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182472366	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	62	814	2	ENST00000268035.6:c.488C>T	p.Ala163Val	p.A163V	ENST00000268035	NM_000875.3	163	gCg/gTg	2/21	1	2	FACETS	0.418	0.36	0.481	0.418	0.36	0.481	SUBCLONAL	1	TRUE	1	0.41	2		816	724	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433373	49433373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771966959	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	140	1060	0	ENST00000301067.7:c.8074C>T	p.Arg2692Trp	p.R2692W	ENST00000301067	NM_003482.3	2692	Cgg/Tgg	32/54	1	2	FACETS	0.829	0.755	0.906	0.829	0.755	0.906	CLONAL	1	TRUE	1	0.41	2		1060	824	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007713	45007713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148494241	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	46	456	0	ENST00000558401.1:c.160G>A	p.Asp54Asn	p.D54N	ENST00000558401	NM_004048.2	54	Gac/Aac	2/4	1	2	FACETS	0.87	0.738	1	0.87	0.738	1	CLONAL	1	TRUE	1	0.41	2		456	258	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518061	176518061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	221	1043	1	ENST00000292408.4:c.559G>A	p.Asp187Asn	p.D187N	ENST00000292408	NM_213647.1	187	Gat/Aat	5/18	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.41	2		1044	1049	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422455	47422455	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398289359	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	163	1084	5	ENST00000377045.4:c.89G>A	p.Arg30His	p.R30H	ENST00000377045	NM_001654.4	30	cGc/cAc	2/16	1	2	FACETS	0.799	0.733	0.869	0.799	0.733	0.869	SUBCLONAL	1	TRUE	1	0.41	2		1089	995	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642754	3642754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747563780	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	243	1123	1	ENST00000294008.3:c.2273C>T	p.Ala758Val	p.A758V	ENST00000294008	NM_032444.2	758	gCg/gTg	11/15	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.41	2		1124	1185	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69012038	69012038	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	47	613	0	ENST00000288368.4:c.2675G>T	p.Arg892Ile	p.R892I	ENST00000288368	NM_024870.2	892	aGa/aTa	23/40	1	2	FACETS	0.74	0.627	0.862	0.74	0.627	0.862	SUBCLONAL	1	TRUE	1	0.41	2		613	310	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288743	33288743	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs533137350	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	129	725	0	ENST00000374542.5:c.809G>A	p.Arg270His	p.R270H	ENST00000374542	NM_001141970.1	270	cGc/cAc	3/8	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.41	2		725	603	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185169095	185169095	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1245142546	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	66	583	0	ENST00000265026.3:c.1190G>A	p.Arg397Gln	p.R397Q	ENST00000265026	NM_004721.4	397	cGa/cAa	7/14	1	2	FACETS	0.72	0.627	0.821	0.72	0.627	0.821	SUBCLONAL	1	TRUE	1	0.41	2		583	447	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347980	89347980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749114664	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	172	1277	5	ENST00000301030.4:c.4970C>T	p.Ser1657Leu	p.S1657L	ENST00000301030	NM_001256183.1	1657	tCg/tTg	9/13	1	2	FACETS	0.819	0.753	0.888	0.819	0.753	0.888	CLONAL	1	TRUE	1	0.41	2		1282	1024	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514997	103514997	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137877463	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	52	417	0	ENST00000355739.4:c.1498C>T	p.Arg500Trp	p.R500W	ENST00000355739	NM_000123.3	500	Cgg/Tgg	8/15	1	2	FACETS	0.826	0.708	0.954	0.826	0.708	0.954	CLONAL	1	TRUE	1	0.41	2		417	307	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094828	143094828	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	23	409	0	ENST00000262992.4:c.1316C>A	p.Ser439Tyr	p.S439Y	ENST00000262992	NM_001101669.1	439	tCt/tAt	14/24	1	2	FACETS	0.594	0.466	0.74	0.594	0.466	0.74	SUBCLONAL	1	TRUE	1	0.41	2		409	189	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281629	49281629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749662416	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	188	1003	1	ENST00000282018.3:c.676C>T	p.Arg226Trp	p.R226W	ENST00000282018	NM_020377.2	226	Cgg/Tgg	1/1	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.41	2		1004	870	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727075	243727075	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	23	551	0	ENST00000263826.5:c.895G>T	p.Asp299Tyr	p.D299Y	ENST00000263826	NM_005465.4	299	Gat/Tat	9/13	1	2	FACETS	0.294	0.229	0.37	0.294	0.229	0.37	SUBCLONAL	1	TRUE	1	0.41	2		551	381	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760927	133760927	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	180	1131	0	ENST00000318560.5:c.3250C>T	p.Arg1084Ter	p.R1084*	ENST00000318560	NM_005157.4	1084	Cga/Tga	11/11	1	2	FACETS	0.982	0.906	1	0.982	0.906	1	CLONAL	1	TRUE	1	0.41	2		1131	894	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647685	3647685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1160715108	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	182	1082	0	ENST00000294008.3:c.1378C>T	p.Arg460Cys	p.R460C	ENST00000294008	NM_032444.2	460	Cgc/Tgc	7/15	1	2	FACETS	0.999	0.922	1	0.999	0.922	1	CLONAL	1	TRUE	1	0.41	2		1082	889	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210233	123210233	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	16	532	0	ENST00000218089.9:c.2585G>T	p.Arg862Ile	p.R862I	ENST00000218089	NM_001042749.1	862	aGa/aTa	26/35	1	2	FACETS	0.312	0.231	0.409	0.312	0.231	0.409	SUBCLONAL	1	TRUE	1	0.41	2		532	250	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538214	187538214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750202307	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	71	683	1	ENST00000441802.2:c.9020C>T	p.Ala3007Val	p.A3007V	ENST00000441802	NM_005245.3	3007	gCg/gTg	11/27	1	2	FACETS	0.831	0.728	0.94	0.831	0.728	0.94	CLONAL	1	TRUE	1	0.41	2		684	417	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411056	63411056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768098639	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	151	845	0	ENST00000330258.3:c.2111G>A	p.Arg704His	p.R704H	ENST00000330258	NM_152424.3	704	cGt/cAt	2/2	1	2	FACETS	0.994	0.91	1	0.994	0.91	1	CLONAL	1	TRUE	1	0.41	2		845	741	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2199895	2199895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1304185199	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	224	1247	1	ENST00000398665.3:c.664G>A	p.Asp222Asn	p.D222N	ENST00000398665	NM_032482.2	222	Gat/Aat	8/28	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.41	2		1248	1064	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267523	7267523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	140	805	1	ENST00000302850.5:c.485G>A	p.Arg162His	p.R162H	ENST00000302850	NM_000208.2	162	cGt/cAt	2/22	1	2	FACETS	0.969	0.884	1	0.969	0.884	1	CLONAL	1	TRUE	1	0.41	2		806	705	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477161	67477161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758586312	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	172	830	1	ENST00000327367.4:c.968G>A	p.Arg323His	p.R323H	ENST00000327367	NM_005902.3	323	cGc/cAc	7/9	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.41	2		831	818	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992274	72992274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767435394	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	117	1170	3	ENST00000268489.5:c.1771G>A	p.Ala591Thr	p.A591T	ENST00000268489	NM_006885.3	591	Gct/Act	2/10	1	2	FACETS	0.49	0.44	0.543	0.49	0.44	0.543	SUBCLONAL	1	TRUE	1	0.41	2		1173	1165	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341353	89341353	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1417276333	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	115	1000	2	ENST00000301030.4:c.7582G>A	p.Val2528Ile	p.V2528I	ENST00000301030	NM_001256183.1	2528	Gta/Ata	11/13	1	2	FACETS	0.798	0.72	0.881	0.798	0.72	0.881	SUBCLONAL	1	TRUE	1	0.41	2		1002	703	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348079	89348079	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	173	1239	3	ENST00000301030.4:c.4871C>T	p.Ala1624Val	p.A1624V	ENST00000301030	NM_001256183.1	1624	gCg/gTg	9/13	1	2	FACETS	0.748	0.687	0.812	0.748	0.687	0.812	SUBCLONAL	1	TRUE	1	0.41	2		1242	1128	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841812	151841812	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	24	320	0	ENST00000262189.6:c.14329C>T	p.Arg4777Trp	p.R4777W	ENST00000262189	NM_170606.2	4777	Cgg/Tgg	55/59	1	2	FACETS	0.38	0.298	0.475	0.38	0.298	0.475	SUBCLONAL	1	TRUE	1	0.41	2		320	308	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598096	55598096	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs760112920	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	42	620	0	ENST00000288135.5:c.2293G>T	p.Asp765Tyr	p.D765Y	ENST00000288135	NM_000222.2	765	Gac/Tac	16/21	1	2	FACETS	0.313	0.261	0.372	0.313	0.261	0.372	SUBCLONAL	1	TRUE	1	0.41	2		620	654	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519075	103519075	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs899478069	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	122	676	0	ENST00000355739.4:c.2413G>A	p.Gly805Arg	p.G805R	ENST00000355739	NM_000123.3	805	Gga/Aga	11/15	1	2	FACETS	0.966	0.876	1	0.966	0.876	1	CLONAL	1	TRUE	1	0.41	2		676	616	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741786	17741786	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	140	749	0	ENST00000250003.3:c.457G>A	p.Ala153Thr	p.A153T	ENST00000250003	NM_002478.4	153	Gcc/Acc	1/3	1	2	FACETS	0.832	0.758	0.909	0.832	0.758	0.909	CLONAL	1	TRUE	1	0.41	2		749	821	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434086	121434086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369764257	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	161	970	0	ENST00000257555.6:c.977C>T	p.Ala326Val	p.A326V	ENST00000257555		326	gCg/gTg	5/10	1	2	FACETS	0.905	0.83	0.983	0.905	0.83	0.983	CLONAL	1	TRUE	1	0.41	2		970	868	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163784	72163784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	25	546	0	ENST00000357731.5:c.574G>A	p.Gly192Arg	p.G192R	ENST00000357731	NM_173808.2	192	Gga/Aga	4/7	1	2	FACETS	0.735	0.584	0.904	0.735	0.584	0.904	CLONAL	1	TRUE	1	0.41	2		546	166	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411963	63411963	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	67	1009	0	ENST00000330258.3:c.1204G>T	p.Glu402Ter	p.E402*	ENST00000330258	NM_152424.3	402	Gaa/Taa	2/2	1	2	FACETS	0.506	0.439	0.578	0.506	0.439	0.578	SUBCLONAL	1	TRUE	1	0.41	2		1009	646	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355131	15355131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1322882125	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	327	1410	0	ENST00000263377.2:c.2492C>T	p.Pro831Leu	p.P831L	ENST00000263377	NM_058243.2	831	cCg/cTg	13/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.41	2		1410	1399	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533274	29533274	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	33	341	1	ENST00000356175.3:c.1277G>A	p.Trp426Ter	p.W426*	ENST00000356175	NM_000267.3	426	tGg/tAg	12/57	1	2	FACETS	0.644	0.527	0.774	0.644	0.527	0.774	SUBCLONAL	1	TRUE	1	0.41	2		342	250	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741603	17741603	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749172312	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	141	724	1	ENST00000250003.3:c.274C>T	p.Arg92Cys	p.R92C	ENST00000250003	NM_002478.4	92	Cgc/Tgc	1/3	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.41	2		725	629	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280799	41280799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	80	579	0	ENST00000349496.5:c.2312G>A	p.Ser771Asn	p.S771N	ENST00000349496	NM_001904.3	771	aGc/aAc	15/15	1	2	FACETS	0.753	0.665	0.848	0.753	0.665	0.848	SUBCLONAL	1	TRUE	1	0.41	2		579	518	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950056	44950056	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	12	584	0	ENST00000377967.4:c.3825G>A	p.Trp1275Ter	p.W1275*	ENST00000377967	NM_021140.2	1275	tgG/tgA	26/29	1	2	FACETS	0.264	0.185	0.36	0.264	0.185	0.36	SUBCLONAL	1	TRUE	1	0.41	2		584	222	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566300	141566300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	151	616	0	ENST00000220592.5:c.1112C>T	p.Ser371Leu	p.S371L	ENST00000220592	NM_012154.3	371	tCg/tTg	9/19	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.41	2		616	610	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420253	49420253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758730277	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	221	1009	1	ENST00000301067.7:c.15496G>A	p.Ala5166Thr	p.A5166T	ENST00000301067	NM_003482.3	5166	Gct/Act	48/54	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.41	2		1010	850	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546901	9546901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs924744761	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	144	680	0	ENST00000353224.5:c.1121C>T	p.Pro374Leu	p.P374L	ENST00000353224	NM_177990.2	374	cCg/cTg	5/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.41	2		680	640	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449821	8449821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754699635	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	22	600	0	ENST00000356435.5:c.3892G>A	p.Asp1298Asn	p.D1298N	ENST00000356435		1298	Gac/Aac	23/35	1	2	FACETS	0.254	0.196	0.322	0.254	0.196	0.322	SUBCLONAL	1	TRUE	1	0.41	2		600	422	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497842	25497842	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	69	1202	1	ENST00000264709.3:c.607C>T	p.Arg203Trp	p.R203W	ENST00000264709	NM_175629.2	203	Cgg/Tgg	6/23	1	2	FACETS	0.299	0.26	0.343	0.299	0.26	0.343	SUBCLONAL	1	TRUE	1	0.41	2		1203	1124	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665341	138665341	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	293	1344	0	ENST00000330315.3:c.224T>C	p.Leu75Pro	p.L75P	ENST00000330315	NM_023067.3	75	cTc/cCc	1/1	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.41	2		1344	1293	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228794	36228794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	62	936	3	ENST00000222270.7:c.7693C>T	p.Arg2565Cys	p.R2565C	ENST00000222270	NM_014727.1	2565	Cgt/Tgt	35/37	1	2	FACETS	0.289	0.249	0.334	0.289	0.249	0.334	SUBCLONAL	1	TRUE	1	0.41	2		939	1045	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255085	16255085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557758293	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	71	404	1	ENST00000375759.3:c.2350C>T	p.Arg784Cys	p.R784C	ENST00000375759	NM_015001.2	784	Cgc/Tgc	11/15	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.41	2		405	332	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845589	63845589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759435915	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	20	223	0	ENST00000279873.7:c.1328G>A	p.Arg443His	p.R443H	ENST00000279873	NM_032199.2	443	cGc/cAc	9/10	1	2	FACETS	0.564	0.434	0.714	0.564	0.434	0.714	SUBCLONAL	1	TRUE	1	0.41	2		223	173	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662683	227662683	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866580419	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	241	1159	6	ENST00000305123.5:c.772C>T	p.Arg258Trp	p.R258W	ENST00000305123	NM_005544.2	258	Cgg/Tgg	1/2	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.41	2		1165	1039	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436687	110436687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	306	1620	2	ENST00000375856.3:c.1714C>T	p.Arg572Cys	p.R572C	ENST00000375856	NM_003749.2	572	Cgc/Tgc	1/2	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.41	2		1622	1334	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435606	110435606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	50	677	0	ENST00000375856.3:c.2795C>T	p.Ser932Leu	p.S932L	ENST00000375856	NM_003749.2	932	tCg/tTg	1/2	1	2	FACETS	0.36	0.305	0.421	0.36	0.305	0.421	SUBCLONAL	1	TRUE	1	0.41	2		677	677	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877417	28877417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758531658	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	155	662	0	ENST00000282397.4:c.3904G>A	p.Glu1302Lys	p.E1302K	ENST00000282397	NM_002019.4	1302	Gaa/Aaa	30/30	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.41	2		662	706	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798257	45798257	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369854269	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	47	1030	0	ENST00000450313.1:c.679G>A	p.Ala227Thr	p.A227T	ENST00000450313	NM_012222.2	227	Gcc/Acc	8/16	1	2	FACETS	0.264	0.222	0.311	0.264	0.222	0.311	SUBCLONAL	1	TRUE	1	0.41	2		1030	867	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735460	40735460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	48	987	0	ENST00000373198.4:c.3413T>G	p.Leu1138Arg	p.L1138R	ENST00000373198	NM_133170.3	1138	cTc/cGc	25/32	1	2	FACETS	0.271	0.228	0.319	0.271	0.228	0.319	SUBCLONAL	1	TRUE	1	0.41	2		987	863	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109974	115109974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1286841573	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	64	1192	2	ENST00000257566.3:c.1904G>A	p.Arg635His	p.R635H	ENST00000257566	NM_016569.3	635	cGc/cAc	8/8	1	2	FACETS	0.283	0.244	0.325	0.283	0.244	0.325	SUBCLONAL	1	TRUE	1	0.41	2		1194	1104	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225929	133225929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs550525366	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	165	1239	0	ENST00000320574.5:c.3968C>T	p.Ala1323Val	p.A1323V	ENST00000320574	NM_006231.2	1323	gCc/gTc	31/49	1	2	FACETS	0.705	0.647	0.767	0.705	0.647	0.767	SUBCLONAL	1	TRUE	1	0.41	2		1239	1141	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994649	73994649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs541095307	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	261	1450	3	ENST00000318443.5:c.133G>A	p.Asp45Asn	p.D45N	ENST00000318443	NM_001024736.1	45	Gat/Aat	3/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.41	2		1453	1243	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845609	151845609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369745886	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	150	827	0	ENST00000262189.6:c.13403C>T	p.Thr4468Met	p.T4468M	ENST00000262189	NM_170606.2	4468	aCg/aTg	52/59	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.41	2		827	668	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220119	5220119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755452432	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	41	878	1	ENST00000357368.4:c.3596C>T	p.Ser1199Leu	p.S1199L	ENST00000357368	NM_002850.3	1199	tCg/tTg	22/38	1	2	FACETS	0.256	0.212	0.305	0.256	0.212	0.305	SUBCLONAL	1	TRUE	1	0.41	2		879	782	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176105672	176105672	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	27	412	2	ENST00000367669.3:c.843G>T	p.Gln281His	p.Q281H	ENST00000367669	NM_022457.5	281	caG/caT	7/20	1	2	FACETS	0.77	0.619	0.94	0.77	0.619	0.94	CLONAL	1	TRUE	1	0.41	2		414	171	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549265	21549265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	193	1002	1	ENST00000382592.4:c.3011C>T	p.Pro1004Leu	p.P1004L	ENST00000382592	NM_014572.2	1004	cCc/cTc	8/8	1	2	FACETS	0.95	0.879	1	0.95	0.879	1	CLONAL	1	TRUE	1	0.41	2		1003	991	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128030502	128030502	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	73	722	0	ENST00000285398.2:c.1766G>T	p.Arg589Met	p.R589M	ENST00000285398	NM_000122.1	589	aGg/aTg	11/15	1	2	FACETS	0.645	0.565	0.731	0.645	0.565	0.731	SUBCLONAL	1	TRUE	1	0.41	2		722	552	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584488	39584488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs375465653	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	85	375	0	ENST00000262039.4:c.1153C>T	p.Arg385Ter	p.R385*	ENST00000262039	NM_002647.2	385	Cga/Tga	10/25	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.41	2		375	369	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144997	58144997	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501931	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	154	747	0	ENST00000257904.6:c.347C>T	p.Thr116Met	p.T116M	ENST00000257904	NM_000075.3	116	aCg/aTg	3/8	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.41	2		747	720	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382229	152382229	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	22	430	0	ENST00000206249.3:c.1339T>C	p.Cys447Arg	p.C447R	ENST00000206249	NM_000125.3	447	Tgc/Cgc	6/8	1	2	FACETS	0.295	0.228	0.373	0.295	0.228	0.373	SUBCLONAL	1	TRUE	1	0.41	2		430	364	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110129	8110129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746973523	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	114	798	0	ENST00000585124.1:c.476G>A	p.Arg159His	p.R159H	ENST00000585124	NM_004217.3	159	cGc/cAc	6/9	1	2	FACETS	0.73	0.657	0.807	0.73	0.657	0.807	SUBCLONAL	1	TRUE	1	0.41	2		798	762	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517531	176517531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	212	1480	0	ENST00000292408.4:c.232C>T	p.Arg78Cys	p.R78C	ENST00000292408	NM_213647.1	78	Cgt/Tgt	3/18	1	2	FACETS	0.823	0.763	0.885	0.823	0.763	0.885	CLONAL	1	TRUE	1	0.41	2		1480	1257	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393169	393169	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	36	682	0	ENST00000380956.4:c.17G>A	p.Gly6Asp	p.G6D	ENST00000380956	NM_001195286.1	6	gGc/gAc	2/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.41	NA		682	716	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57474013	57474013	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140388147	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	112	388	0	ENST00000371085.3:c.230C>T	p.Pro77Leu	p.P77L	ENST00000371085	NM_000516.4	77	cCg/cTg	3/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.41	2		388	471	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971232	13971232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758005694	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	86	662	2	ENST00000405192.2:c.697G>A	p.Asp233Asn	p.D233N	ENST00000405192	NM_001163147.1	233	Gac/Aac	8/12	1	2	FACETS	0.64	0.566	0.718	0.64	0.566	0.718	SUBCLONAL	1	TRUE	1	0.41	2		664	656	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742519	17742519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	51	1052	1	ENST00000250003.3:c.701C>T	p.Ala234Val	p.A234V	ENST00000250003	NM_002478.4	234	gCg/gTg	2/3	1	2	FACETS	0.279	0.236	0.326	0.279	0.236	0.326	SUBCLONAL	1	TRUE	1	0.41	2		1053	892	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624582	21624582	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	52	455	0	ENST00000421138.2:c.1448-1G>T		p.X483_splice	ENST00000421138		483			1	2	FACETS	0.954	0.819	1	0.954	0.819	1	CLONAL	1	TRUE	1	0.41	2		455	266	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375954	8375954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	54	414	0	ENST00000356435.5:c.4643C>T	p.Pro1548Leu	p.P1548L	ENST00000356435		1548	cCg/cTg	28/35	1	2	FACETS	0.691	0.593	0.799	0.691	0.593	0.799	SUBCLONAL	1	TRUE	1	0.41	2		414	381	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431709	49431709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752428122	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	161	1213	2	ENST00000301067.7:c.9430G>A	p.Ala3144Thr	p.A3144T	ENST00000301067	NM_003482.3	3144	Gca/Aca	34/54	1	2	FACETS	0.795	0.728	0.864	0.795	0.728	0.864	SUBCLONAL	1	TRUE	1	0.41	2		1215	988	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678616	88678616	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	23	547	0	ENST00000360948.2:c.920T>C	p.Val307Ala	p.V307A	ENST00000360948	NM_001012338.2	307	gTg/gCg	9/19	1	2	FACETS	0.266	0.207	0.335	0.266	0.207	0.335	SUBCLONAL	1	TRUE	1	0.41	2		547	422	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656299	18656299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	25	469	0	ENST00000266497.5:c.2978C>T	p.Thr993Ile	p.T993I	ENST00000266497		993	aCa/aTa	21/31	1	2	FACETS	0.53	0.42	0.656	0.53	0.42	0.656	SUBCLONAL	1	TRUE	1	0.41	2		469	230	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087555	27087555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1171422700	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	220	1023	1	ENST00000324856.7:c.2129G>A	p.Arg710His	p.R710H	ENST00000324856	NM_006015.4	710	cGc/cAc	5/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.41	2		1024	996	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984848	11984848	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	53	430	0	ENST00000353533.5:c.393+1G>T		p.X131_splice	ENST00000353533	NM_003010.3	131			1	2	FACETS	0.923	0.794	1	0.923	0.794	1	CLONAL	1	TRUE	1	0.41	2		430	280	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222173	53222173	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	150	914	0	ENST00000375401.3:c.4659G>T	p.Gln1553His	p.Q1553H	ENST00000375401	NM_004187.3	1553	caG/caT	26/26	1	2	FACETS	0.923	0.844	1	0.923	0.844	1	CLONAL	1	TRUE	1	0.41	2		914	793	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929492	81929492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777445397	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	60	765	0	ENST00000359376.3:c.1153G>A	p.Val385Ile	p.V385I	ENST00000359376	NM_002661.3	385	Gtc/Atc	13/33	1	2	FACETS	0.401	0.345	0.463	0.401	0.345	0.463	SUBCLONAL	1	TRUE	1	0.41	2		765	729	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129735	30129735	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769159731	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	156	773	0	ENST00000263025.4:c.478G>A	p.Ala160Thr	p.A160T	ENST00000263025	NM_002746.2	160	Gcc/Acc	3/9	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.41	2		773	706	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686794	117686794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	48	431	0	ENST00000368508.3:c.2923G>A	p.Val975Ile	p.V975I	ENST00000368508	NM_002944.2	975	Gta/Ata	19/43	1	2	FACETS	0.911	0.777	1	0.911	0.777	1	CLONAL	1	TRUE	1	0.41	2		431	257	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120802531	120802531	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	111	827	2	ENST00000257552.2:c.295C>T	p.Arg99Ter	p.R99*	ENST00000257552	NM_002442.3	99	Cga/Tga	5/15	1	2	FACETS	0.714	0.642	0.791	0.714	0.642	0.791	SUBCLONAL	1	TRUE	1	0.41	2		829	758	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434811	128434811	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	109	834	2	ENST00000265960.3:c.43C>T	p.Arg15Ter	p.R15*	ENST00000265960	NM_001006617.1	15	Cga/Tga	2/12	1	2	FACETS	0.944	0.851	1	0.944	0.851	1	CLONAL	1	TRUE	1	0.41	2		836	563	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961465	54961465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749883403	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	51	547	1	ENST00000312783.6:c.167G>A	p.Arg56His	p.R56H	ENST00000312783	NM_198436.1	56	cGc/cAc	4/10	1	2	FACETS	0.445	0.378	0.519	0.445	0.378	0.519	SUBCLONAL	1	TRUE	1	0.41	2		548	559	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285555	38285555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	171	731	0	ENST00000425967.3:c.598C>T	p.Pro200Ser	p.P200S	ENST00000425967	NM_001174067.1	200	Ccg/Tcg	6/19	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.41	2		731	665	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609717	46609717	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765717751	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	68	1157	2	ENST00000263734.3:c.2441C>T	p.Ser814Leu	p.S814L	ENST00000263734	NM_001430.4	814	tCg/tTg	15/16	1	2	FACETS	0.326	0.283	0.374	0.326	0.283	0.374	SUBCLONAL	1	TRUE	1	0.41	2		1159	1017	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953617	32953617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80359143	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	27	474	0	ENST00000380152.3:c.8918G>A	p.Arg2973His	p.R2973H	ENST00000380152		2973	cGt/cAt	22/27	1	2	FACETS	0.649	0.52	0.794	0.649	0.52	0.794	SUBCLONAL	1	TRUE	1	0.41	2		474	203	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634653	158634653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	57	383	2	ENST00000263640.3:c.533G>A	p.Ser178Asn	p.S178N	ENST00000263640	NM_001105.4	178	aGc/aAc	5/11	1	2	FACETS	0.756	0.651	0.869	0.756	0.651	0.869	SUBCLONAL	1	TRUE	1	0.41	2		385	368	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775713	9775713	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	71	1371	0	ENST00000377346.4:c.256C>T	p.Gln86Ter	p.Q86*	ENST00000377346	NM_005026.3	86	Caa/Taa	4/24	1	2	FACETS	0.32	0.278	0.366	0.32	0.278	0.366	SUBCLONAL	1	TRUE	1	0.41	2		1371	1081	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182071	11182071	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	41	773	0	ENST00000361445.4:c.6775A>G	p.Ile2259Val	p.I2259V	ENST00000361445	NM_004958.3	2259	Atc/Gtc	48/58	1	2	FACETS	0.245	0.203	0.292	0.245	0.203	0.292	SUBCLONAL	1	TRUE	1	0.41	2		773	815	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193151	11193151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371091288	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	149	770	0	ENST00000361445.4:c.5350C>T	p.Arg1784Cys	p.R1784C	ENST00000361445	NM_004958.3	1784	Cgc/Tgc	38/58	1	2	FACETS	0.893	0.816	0.973	0.893	0.816	0.973	CLONAL	1	TRUE	1	0.41	2		770	814	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11204731	11204731	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17848545	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	119	549	0	ENST00000361445.4:c.4846C>T	p.Arg1616Cys	p.R1616C	ENST00000361445	NM_004958.3	1616	Cgc/Tgc	34/58	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.41	2		549	567	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264670	11264670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	213	950	0	ENST00000361445.4:c.3892C>T	p.Pro1298Ser	p.P1298S	ENST00000361445	NM_004958.3	1298	Ccc/Tcc	26/58	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.41	2		950	983	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288729	11288729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778855567	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	88	661	0	ENST00000361445.4:c.3026G>A	p.Arg1009Gln	p.R1009Q	ENST00000361445	NM_004958.3	1009	cGg/cAg	19/58	1	2	FACETS	0.748	0.664	0.837	0.748	0.664	0.837	SUBCLONAL	1	TRUE	1	0.41	2		661	574	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288736	11288736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778161719	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	104	690	0	ENST00000361445.4:c.3019G>A	p.Ala1007Thr	p.A1007T	ENST00000361445	NM_004958.3	1007	Gcc/Acc	19/58	1	2	FACETS	0.824	0.739	0.913	0.824	0.739	0.913	CLONAL	1	TRUE	1	0.41	2		690	616	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254645	16254645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149954308	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	94	545	0	ENST00000375759.3:c.1910G>A	p.Arg637Gln	p.R637Q	ENST00000375759	NM_015001.2	637	cGa/cAa	11/15	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.41	2		545	427	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265255	16265255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749521610	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	140	788	0	ENST00000375759.3:c.10747C>T	p.Arg3583Cys	p.R3583C	ENST00000375759	NM_015001.2	3583	Cgt/Tgt	14/15	1	2	FACETS	0.983	0.897	1	0.983	0.897	1	CLONAL	1	TRUE	1	0.41	2		788	695	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057688	27057688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	199	797	0	ENST00000324856.7:c.1396G>A	p.Gly466Ser	p.G466S	ENST00000324856	NM_006015.4	466	Ggc/Agc	3/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.41	2		797	790	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46733138	46733138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	37	474	0	ENST00000371975.4:c.899G>A	p.Arg300Lys	p.R300K	ENST00000371975	NM_003579.3	300	aGg/aAg	9/18	1	2	FACETS	0.347	0.286	0.416	0.347	0.286	0.416	SUBCLONAL	1	TRUE	1	0.41	2		474	520	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436159	51436159	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	18	374	0	ENST00000262662.1:c.119C>A	p.Thr40Asn	p.T40N	ENST00000262662		40	aCt/aAt	3/4	1	2	FACETS	0.281	0.211	0.363	0.281	0.211	0.363	SUBCLONAL	1	TRUE	1	0.41	2		374	313	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309844	65309844	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	40	740	0	ENST00000342505.4:c.2306A>G	p.Asn769Ser	p.N769S	ENST00000342505	NM_002227.2	769	aAc/aGc	17/25	1	2	FACETS	0.295	0.244	0.351	0.295	0.244	0.351	SUBCLONAL	1	TRUE	1	0.41	2		740	662	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330525	65330525	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	76	594	0	ENST00000342505.4:c.1121A>C	p.His374Pro	p.H374P	ENST00000342505	NM_002227.2	374	cAc/cCc	8/25	1	2	FACETS	0.835	0.735	0.941	0.835	0.735	0.941	CLONAL	1	TRUE	1	0.41	2		594	444	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748017	72748017	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	119	968	0	ENST00000357731.5:c.161A>G	p.Asp54Gly	p.D54G	ENST00000357731	NM_173808.2	54	gAc/gGc	1/7	1	2	FACETS	0.715	0.645	0.789	0.715	0.645	0.789	SUBCLONAL	1	TRUE	1	0.41	2		968	812	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276687	115276687	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	31	502	0	ENST00000438362.2:c.772C>A	p.His258Asn	p.H258N	ENST00000438362	NM_001242891.1	258	Cac/Aac	8/20	1	2	FACETS	0.72	0.587	0.869	0.72	0.587	0.869	SUBCLONAL	1	TRUE	1	0.41	2		502	210	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120509109	120509109	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs890700085	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	33	378	0	ENST00000256646.2:c.1457T>C	p.Phe486Ser	p.F486S	ENST00000256646	NM_024408.3	486	tTc/tCc	9/34	1	2	FACETS	0.524	0.428	0.632	0.524	0.428	0.632	SUBCLONAL	1	TRUE	1	0.41	2		378	307	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724638	162724638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	80	453	0	ENST00000367921.3:c.410G>A	p.Gly137Glu	p.G137E	ENST00000367921	NM_006182.2	137	gGg/gAg	5/18	1	2	FACETS	0.871	0.77	0.979	0.871	0.77	0.979	CLONAL	1	TRUE	1	0.41	2		453	448	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012401	176012401	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	18	421	1	ENST00000367669.3:c.1533G>T	p.Glu511Asp	p.E511D	ENST00000367669	NM_022457.5	511	gaG/gaT	14/20	1	2	FACETS	0.369	0.278	0.476	0.369	0.278	0.476	SUBCLONAL	1	TRUE	1	0.41	2		422	238	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012847	176012847	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	17	398	0	ENST00000367669.3:c.1529A>G	p.Gln510Arg	p.Q510R	ENST00000367669	NM_022457.5	510	cAg/cGg	13/20	1	2	FACETS	0.553	0.415	0.713	0.553	0.415	0.713	SUBCLONAL	1	TRUE	1	0.41	2		398	150	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111026	193111026	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	28	229	0	ENST00000367435.3:c.559G>A	p.Ala187Thr	p.A187T	ENST00000367435	NM_024529.4	187	Gcc/Acc	7/17	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.41	2		229	103	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828117	243828117	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs773758145	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	39	475	0	ENST00000263826.5:c.241A>G	p.Thr81Ala	p.T81A	ENST00000263826	NM_005465.4	81	Act/Gct	3/13	1	2	FACETS	0.715	0.596	0.846	0.715	0.596	0.846	SUBCLONAL	1	TRUE	1	0.41	2		475	266	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097701	8097701	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	139	766	0	ENST00000346208.3:c.83A>C	p.His28Pro	p.H28P	ENST00000346208		28	cAc/cCc	2/6	1	2	FACETS	0.911	0.831	0.996	0.911	0.831	0.996	CLONAL	1	TRUE	1	0.41	2		766	744	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106042	8106042	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	143	690	1	ENST00000346208.3:c.862G>T	p.Gly288Trp	p.G288W	ENST00000346208		288	Ggg/Tgg	4/6	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.41	2		691	683	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70412351	70412351	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	11	308	0	ENST00000373644.4:c.4461G>A	p.Trp1487Ter	p.W1487*	ENST00000373644	NM_030625.2	1487	tgG/tgA	6/12	1	2	FACETS	0.292	0.201	0.403	0.292	0.201	0.403	SUBCLONAL	1	TRUE	1	0.41	2		308	184	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88672063	88672063	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	25	292	0	ENST00000372037.3:c.597T>G	p.Phe199Leu	p.F199L	ENST00000372037	NM_004329.2	199	ttT/ttG	8/13	1	2	FACETS	1	0.801	1	1	0.801	1	CLONAL	1	TRUE	1	0.41	2		292	122	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653827	89653827	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	23	446	0	ENST00000371953.3:c.125T>G	p.Leu42Arg	p.L42R	ENST00000371953	NM_000314.4	42	cTt/cGt	2/9	1	2	FACETS	0.71	0.559	0.882	0.71	0.559	0.882	SUBCLONAL	1	TRUE	1	0.41	2		446	158	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717675	89717675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201730	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	21	561	0	ENST00000371953.3:c.700C>T	p.Arg234Trp	p.R234W	ENST00000371953	NM_000314.4	234	Cgg/Tgg	7/9	1	2	FACETS	0.299	0.23	0.379	0.299	0.23	0.379	SUBCLONAL	1	TRUE	1	0.41	2		561	343	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325110	123325110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	153	896	0	ENST00000358487.5:c.218C>T	p.Thr73Ile	p.T73I	ENST00000358487	NM_000141.4	73	aCt/aTt	3/18	1	2	FACETS	0.91	0.833	0.991	0.91	0.833	0.991	CLONAL	1	TRUE	1	0.41	2		896	820	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202072	67202072	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs372739497	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	80	1313	0	ENST00000312629.5:c.1175C>A	p.Pro392Gln	p.P392Q	ENST00000312629	NM_003952.2	392	cCg/cAg	14/15	1	2	FACETS	0.316	0.277	0.358	0.316	0.277	0.358	SUBCLONAL	1	TRUE	1	0.41	2		1313	1235	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462879	69462879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	74	1056	3	ENST00000227507.2:c.692G>A	p.Arg231His	p.R231H	ENST00000227507	NM_053056.2	231	cGc/cAc	4/5	1	2	FACETS	0.366	0.319	0.417	0.366	0.319	0.417	SUBCLONAL	1	TRUE	1	0.41	2		1059	986	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948467	71948467	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1263	146	1511	0	ENST00000298229.2:c.3179A>G	p.Asp1060Gly	p.D1060G	ENST00000298229	NM_001567.3	1060	gAc/gGc	26/28	1	2	FACETS	0.505	0.46	0.554	0.505	0.46	0.554	SUBCLONAL	1	TRUE	1	0.41	2		1511	1409	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918550	94918550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	68	537	0	ENST00000536441.1:c.632G>A	p.Gly211Asp	p.G211D	ENST00000536441	NM_144665.3	211	gGt/gAt	5/10	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.41	2		537	322	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164151	108164151	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1408892416	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	17	266	0	ENST00000278616.4:c.4723C>T	p.Arg1575Cys	p.R1575C	ENST00000278616	NM_000051.3	1575	Cgt/Tgt	31/63	1	2	FACETS	0.564	0.424	0.728	0.564	0.424	0.728	SUBCLONAL	1	TRUE	1	0.41	2		266	147	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196267	108196267	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	31	394	0	ENST00000278616.4:c.6803C>T	p.Thr2268Ile	p.T2268I	ENST00000278616	NM_000051.3	2268	aCt/aTt	46/63	1	2	FACETS	0.911	0.745	1	0.911	0.745	1	CLONAL	1	TRUE	1	0.41	2		394	166	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214001	108214001	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	58	391	0	ENST00000278616.4:c.8321T>A	p.Val2774Asp	p.V2774D	ENST00000278616	NM_000051.3	2774	gTc/gAc	57/63	1	2	FACETS	0.966	0.836	1	0.966	0.836	1	CLONAL	1	TRUE	1	0.41	2		391	293	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344156	118344156	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	108	752	0	ENST00000534358.1:c.2282G>A	p.Arg761Lys	p.R761K	ENST00000534358	NM_005933.3	761	aGg/aAg	3/36	1	2	FACETS	0.874	0.786	0.966	0.874	0.786	0.966	CLONAL	1	TRUE	1	0.41	2		752	603	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352558	118352558	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs782739484	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	128	607	0	ENST00000534358.1:c.3763A>G	p.Lys1255Glu	p.K1255E	ENST00000534358	NM_005933.3	1255	Aag/Gag	7/36	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.41	2		607	575	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374169	118374169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555046685	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	68	456	2	ENST00000534358.1:c.7562G>A	p.Arg2521His	p.R2521H	ENST00000534358	NM_005933.3	2521	cGc/cAc	27/36	1	2	FACETS	0.95	0.832	1	0.95	0.832	1	CLONAL	1	TRUE	1	0.41	2		458	349	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376758	118376758	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	30	576	0	ENST00000534358.1:c.10151T>A	p.Leu3384His	p.L3384H	ENST00000534358	NM_005933.3	3384	cTt/cAt	27/36	1	2	FACETS	0.317	0.255	0.388	0.317	0.255	0.388	SUBCLONAL	1	TRUE	1	0.41	2		576	461	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392863	118392863	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	84	603	0	ENST00000534358.1:c.11895G>T	p.Lys3965Asn	p.K3965N	ENST00000534358	NM_005933.3	3965	aaG/aaT	36/36	1	2	FACETS	0.921	0.817	1	0.921	0.817	1	CLONAL	1	TRUE	1	0.41	2		603	445	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169088	119169088	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	25	631	0	ENST00000264033.4:c.2272G>A	p.Ala758Thr	p.A758T	ENST00000264033	NM_005188.3	758	Gcc/Acc	15/16	1	2	FACETS	0.248	0.195	0.309	0.248	0.195	0.309	SUBCLONAL	1	TRUE	1	0.41	2		631	492	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125499136	125499136	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	59	514	0	ENST00000428830.2:c.299T>C	p.Ile100Thr	p.I100T	ENST00000428830	NM_001114121.2	100	aTa/aCa	4/14	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.41	2		514	254	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21643181	21643181	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	26	756	0	ENST00000421138.2:c.346G>T	p.Gly116Ter	p.G116*	ENST00000421138		116	Gga/Tga	5/16	1	2	FACETS	0.36	0.285	0.446	0.36	0.285	0.446	SUBCLONAL	1	TRUE	1	0.41	2		756	352	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244320	46244320	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	65	504	0	ENST00000334344.6:c.2414T>C	p.Val805Ala	p.V805A	ENST00000334344	NM_152641.2	805	gTa/gCa	15/21	1	2	FACETS	0.857	0.747	0.975	0.857	0.747	0.975	CLONAL	1	TRUE	1	0.41	2		504	370	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420064	49420064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs914453109	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	165	839	0	ENST00000301067.7:c.15685C>T	p.Arg5229Cys	p.R5229C	ENST00000301067	NM_003482.3	5229	Cgc/Tgc	48/54	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.41	2		839	738	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433346	49433346	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	191	1089	2	ENST00000301067.7:c.8101C>T	p.Arg2701Trp	p.R2701W	ENST00000301067	NM_003482.3	2701	Cgg/Tgg	32/54	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.41	2		1091	836	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50488357	50488357	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	37	530	0	ENST00000394963.4:c.1269+2T>C		p.X423_splice	ENST00000394963	NM_003076.4	423			1	2	FACETS	0.375	0.309	0.449	0.375	0.309	0.449	SUBCLONAL	1	TRUE	1	0.41	2		530	481	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864667	57864667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	184	1252	0	ENST00000228682.2:c.2144G>A	p.Gly715Asp	p.G715D	ENST00000228682	NM_005269.2	715	gGc/gAc	12/12	1	2	FACETS	0.859	0.792	0.928	0.859	0.792	0.928	CLONAL	1	TRUE	1	0.41	2		1252	1045	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233066	69233066	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	48	357	0	ENST00000462284.1:c.931T>C	p.Cys311Arg	p.C311R	ENST00000462284	NM_002392.5	311	Tgc/Cgc	11/11	1	2	FACETS	0.956	0.815	1	0.956	0.815	1	CLONAL	1	TRUE	1	0.41	2		357	245	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869423	102869423	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	97	530	0	ENST00000307046.8:c.218T>C	p.Phe73Ser	p.F73S	ENST00000307046	NM_001111285.1	73	tTc/tCc	2/4	1	2	FACETS	0.919	0.822	1	0.919	0.822	1	CLONAL	1	TRUE	1	0.41	2		530	515	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888251	112888251	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	24	566	0	ENST00000351677.2:c.267A>C	p.Lys89Asn	p.K89N	ENST00000351677	NM_002834.3	89	aaA/aaC	3/16	1	2	FACETS	0.311	0.243	0.388	0.311	0.243	0.388	SUBCLONAL	1	TRUE	1	0.41	2		566	377	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926312	112926312	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	54	548	0	ENST00000351677.2:c.1445A>G	p.Lys482Arg	p.K482R	ENST00000351677	NM_002834.3	482	aAa/aGa	12/16	1	2	FACETS	0.516	0.441	0.599	0.516	0.441	0.599	SUBCLONAL	1	TRUE	1	0.41	2		548	510	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549182	21549182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	198	1106	0	ENST00000382592.4:c.3094C>T	p.His1032Tyr	p.H1032Y	ENST00000382592	NM_014572.2	1032	Cat/Tat	8/8	1	2	FACETS	0.952	0.881	1	0.952	0.881	1	CLONAL	1	TRUE	1	0.41	2		1106	1015	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563007	21563007	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	207	1492	1	ENST00000382592.4:c.912C>A	p.Phe304Leu	p.F304L	ENST00000382592	NM_014572.2	304	ttC/ttA	4/8	1	2	FACETS	0.775	0.717	0.835	0.775	0.717	0.835	SUBCLONAL	1	TRUE	1	0.41	2		1493	1303	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28903757	28903757	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	36	784	0	ENST00000282397.4:c.2702A>G	p.Gln901Arg	p.Q901R	ENST00000282397	NM_002019.4	901	cAa/cGa	19/30	1	2	FACETS	0.256	0.21	0.308	0.256	0.21	0.308	SUBCLONAL	1	TRUE	1	0.41	2		784	686	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28971189	28971189	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	59	326	0	ENST00000282397.4:c.1568T>C	p.Val523Ala	p.V523A	ENST00000282397	NM_002019.4	523	gTt/gCt	12/30	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.41	2		326	210	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939037	48939037	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	37	290	0	ENST00000267163.4:c.869A>C	p.Asn290Thr	p.N290T	ENST00000267163	NM_000321.2	290	aAt/aCt	9/27	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.41	2		290	129	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103498684	103498684	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	140	726	0	ENST00000355739.4:c.68A>C	p.Glu23Ala	p.E23A	ENST00000355739	NM_000123.3	23	gAa/gCa	1/15	1	2	FACETS	0.742	0.675	0.812	0.742	0.675	0.812	SUBCLONAL	1	TRUE	1	0.41	2		726	921	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527945	103527945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760907430	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	52	386	1	ENST00000355739.4:c.3253G>A	p.Gly1085Ser	p.G1085S	ENST00000355739	NM_000123.3	1085	Ggt/Agt	15/15	1	2	FACETS	0.834	0.715	0.964	0.834	0.715	0.964	CLONAL	1	TRUE	1	0.41	2		387	304	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437482	110437482	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	181	1042	0	ENST00000375856.3:c.919C>T	p.Gln307Ter	p.Q307*	ENST00000375856	NM_003749.2	307	Caa/Taa	1/2	1	2	FACETS	0.841	0.775	0.91	0.841	0.775	0.91	CLONAL	1	TRUE	1	0.41	2		1042	1050	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061838	38061838	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	173	1182	0	ENST00000250448.2:c.151A>C	p.Asn51His	p.N51H	ENST00000250448	NM_004496.3	51	Aac/Cac	2/2	1	2	FACETS	0.718	0.659	0.779	0.718	0.659	0.779	SUBCLONAL	1	TRUE	1	0.41	2		1182	1176	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331755	68331755	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	12	415	0	ENST00000487270.1:c.351T>G	p.Phe117Leu	p.F117L	ENST00000487270	NM_133509.3	117	ttT/ttG	5/11	1	2	FACETS	0.27	0.189	0.369	0.27	0.189	0.369	SUBCLONAL	1	TRUE	1	0.41	2		415	217	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331757	68331757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772627187	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	35	418	0	ENST00000487270.1:c.353G>A	p.Cys118Tyr	p.C118Y	ENST00000487270	NM_133509.3	118	tGt/tAt	5/11	1	2	FACETS	0.783	0.647	0.933	0.783	0.647	0.933	CLONAL	1	TRUE	1	0.41	2		418	218	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105236685	105236685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201291259	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	181	1092	1	ENST00000349310.3:c.1436C>T	p.Thr479Met	p.T479M	ENST00000349310	NM_001014432.1	479	aCg/aTg	15/15	1	2	FACETS	0.759	0.698	0.821	0.759	0.698	0.821	SUBCLONAL	1	TRUE	1	0.41	2		1093	1164	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059045	42059045	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	47	493	0	ENST00000219905.7:c.8765A>G	p.Glu2922Gly	p.E2922G	ENST00000219905	NM_001164273.1	2922	gAg/gGg	24/24	1	2	FACETS	0.843	0.716	0.98	0.843	0.716	0.98	CLONAL	1	TRUE	1	0.41	2		493	272	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457406	67457406	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	177	984	1	ENST00000327367.4:c.380A>G	p.Tyr127Cys	p.Y127C	ENST00000327367	NM_005902.3	127	tAc/tGc	2/9	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.41	2		985	799	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679783	88679783	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	128	756	0	ENST00000360948.2:c.680C>A	p.Ala227Asp	p.A227D	ENST00000360948	NM_001012338.2	227	gCt/gAt	7/19	1	2	FACETS	0.988	0.898	1	0.988	0.898	1	CLONAL	1	TRUE	1	0.41	2		756	632	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799176	88799176	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	124	797	3	ENST00000360948.2:c.209G>T	p.Ser70Ile	p.S70I	ENST00000360948	NM_001012338.2	70	aGt/aTt	2/19	1	2	FACETS	0.778	0.705	0.856	0.778	0.705	0.856	SUBCLONAL	1	TRUE	1	0.41	2		800	777	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628100	90628100	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	218	1222	1	ENST00000330062.3:c.1219G>A	p.Glu407Lys	p.E407K	ENST00000330062	NM_002168.2	407	Gag/Aag	10/11	1	2	FACETS	0.907	0.843	0.974	0.907	0.843	0.974	CLONAL	1	TRUE	1	0.41	2		1223	1172	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440054	99440054	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	110	576	0	ENST00000268035.6:c.1022T>G	p.Ile341Ser	p.I341S	ENST00000268035	NM_000875.3	341	aTt/aGt	4/21	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.41	2		576	481	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442774	99442774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771834417	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	178	761	0	ENST00000268035.6:c.1171C>T	p.Arg391Cys	p.R391C	ENST00000268035	NM_000875.3	391	Cgc/Tgc	5/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.41	2		761	730	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99472819	99472819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755569322	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	73	583	0	ENST00000268035.6:c.2815G>A	p.Ala939Thr	p.A939T	ENST00000268035	NM_000875.3	939	Gct/Act	14/21	1	2	FACETS	0.646	0.566	0.733	0.646	0.566	0.733	SUBCLONAL	1	TRUE	1	0.41	2		583	551	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500600	99500600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1309250208	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	39	865	1	ENST00000268035.6:c.4033C>T	p.Pro1345Ser	p.P1345S	ENST00000268035	NM_000875.3	1345	Cct/Tct	21/21	1	2	FACETS	0.253	0.209	0.303	0.253	0.209	0.303	SUBCLONAL	1	TRUE	1	0.41	2		866	752	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354309	354309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746262710	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	58	1149	1	ENST00000262320.3:c.1249C>T	p.Arg417Cys	p.R417C	ENST00000262320	NM_003502.3	417	Cgc/Tgc	5/11	1	2	FACETS	0.277	0.237	0.321	0.277	0.237	0.321	SUBCLONAL	1	TRUE	1	0.41	2		1150	1021	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647236	2647236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	92	781	0	ENST00000342085.4:c.1514G>A	p.Arg505Gln	p.R505Q	ENST00000342085	NM_002613.4	505	cGa/cAa	13/14	1	2	FACETS	0.78	0.695	0.871	0.78	0.695	0.871	SUBCLONAL	1	TRUE	1	0.41	2		781	575	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647397	3647397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	149	1103	1	ENST00000294008.3:c.1666C>T	p.Pro556Ser	p.P556S	ENST00000294008	NM_032444.2	556	Ccc/Tcc	7/15	1	2	FACETS	0.796	0.727	0.868	0.796	0.727	0.868	SUBCLONAL	1	TRUE	1	0.41	2		1104	913	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3651073	3651073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	161	944	0	ENST00000294008.3:c.1070C>T	p.Ala357Val	p.A357V	ENST00000294008	NM_032444.2	357	gCt/gTt	5/15	1	2	FACETS	0.878	0.805	0.953	0.878	0.805	0.953	CLONAL	1	TRUE	1	0.41	2		944	895	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656528	3656528	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200803578	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	69	1098	3	ENST00000294008.3:c.707C>T	p.Ala236Val	p.A236V	ENST00000294008	NM_032444.2	236	gCg/gTg	3/15	1	2	FACETS	0.313	0.271	0.358	0.313	0.271	0.358	SUBCLONAL	1	TRUE	1	0.41	2		1101	1077	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790467	3790467	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	48	836	1	ENST00000262367.5:c.4066G>A	p.Glu1356Lys	p.E1356K	ENST00000262367	NM_004380.2	1356	Gag/Aag	24/31	1	2	FACETS	0.274	0.23	0.322	0.274	0.23	0.322	SUBCLONAL	1	TRUE	1	0.41	2		837	855	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857641	9857641	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	28	564	0	ENST00000330684.3:c.3760C>T	p.Leu1254Phe	p.L1254F	ENST00000330684	NM_001134407.1	1254	Ctt/Ttt	13/13	1	2	FACETS	0.292	0.233	0.36	0.292	0.233	0.36	SUBCLONAL	1	TRUE	1	0.41	2		564	468	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853283	68853283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660399	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	40	693	0	ENST00000261769.5:c.1666G>A	p.Val556Met	p.V556M	ENST00000261769	NM_004360.3	556	Gtg/Atg	11/16	1	2	FACETS	0.26	0.215	0.31	0.26	0.215	0.31	SUBCLONAL	1	TRUE	1	0.41	2		693	750	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821181	72821181	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	186	924	0	ENST00000268489.5:c.10994A>G	p.Asp3665Gly	p.D3665G	ENST00000268489	NM_006885.3	3665	gAc/gGc	10/10	1	2	FACETS	0.915	0.844	0.988	0.915	0.844	0.988	CLONAL	1	TRUE	1	0.41	2		924	992	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827774	72827774	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057249065	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	109	732	0	ENST00000268489.5:c.8807A>G	p.Lys2936Arg	p.K2936R	ENST00000268489	NM_006885.3	2936	aAa/aGa	9/10	1	2	FACETS	0.827	0.744	0.915	0.827	0.744	0.915	CLONAL	1	TRUE	1	0.41	2		732	643	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828293	72828293	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	115	812	0	ENST00000268489.5:c.8288A>G	p.Asp2763Gly	p.D2763G	ENST00000268489	NM_006885.3	2763	gAt/gGt	9/10	1	2	FACETS	0.875	0.79	0.965	0.875	0.79	0.965	CLONAL	1	TRUE	1	0.41	2		812	641	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832370	72832370	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	79	645	0	ENST00000268489.5:c.4211A>T	p.Asn1404Ile	p.N1404I	ENST00000268489	NM_006885.3	1404	aAt/aTt	9/10	1	2	FACETS	0.795	0.701	0.894	0.795	0.701	0.894	SUBCLONAL	1	TRUE	1	0.41	2		645	485	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923737	72923737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187631913	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	201	936	0	ENST00000268489.5:c.3341G>A	p.Arg1114Gln	p.R1114Q	ENST00000268489	NM_006885.3	1114	cGa/cAa	4/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.41	2		936	872	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953244	81953244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	33	433	0	ENST00000359376.3:c.2210C>T	p.Pro737Leu	p.P737L	ENST00000359376	NM_002661.3	737	cCc/cTc	20/33	1	2	FACETS	0.362	0.294	0.438	0.362	0.294	0.438	SUBCLONAL	1	TRUE	1	0.41	2		433	445	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81973512	81973512	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771833349	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	27	599	0	ENST00000359376.3:c.3329G>A	p.Ser1110Asn	p.S1110N	ENST00000359376	NM_002661.3	1110	aGc/aAc	30/33	1	2	FACETS	0.286	0.227	0.353	0.286	0.227	0.353	SUBCLONAL	1	TRUE	1	0.41	2		599	461	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89345551	89345551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	16	368	0	ENST00000301030.4:c.7399G>A	p.Ala2467Thr	p.A2467T	ENST00000301030	NM_001256183.1	2467	Gcc/Acc	9/13	1	2	FACETS	0.327	0.241	0.428	0.327	0.241	0.428	SUBCLONAL	1	TRUE	1	0.41	2		368	239	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971426	15971426	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	100	622	0	ENST00000268712.3:c.4523C>A	p.Ser1508Tyr	p.S1508Y	ENST00000268712	NM_006311.3	1508	tCt/tAt	32/46	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.41	2		622	457	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042329	16042329	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	28	380	0	ENST00000268712.3:c.1345A>G	p.Lys449Glu	p.K449E	ENST00000268712	NM_006311.3	449	Aag/Gag	12/46	1	2	FACETS	0.838	0.677	1	0.838	0.677	1	CLONAL	1	TRUE	1	0.41	2		380	163	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483109	29483109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779727341	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	38	505	0	ENST00000356175.3:c.169G>A	p.Gly57Ser	p.G57S	ENST00000356175	NM_000267.3	57	Ggc/Agc	2/57	1	2	FACETS	1	0.838	1	1	0.838	1	CLONAL	1	TRUE	1	0.41	2		505	185	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486040	29486040	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	12	317	0	ENST00000356175.3:c.217G>A	p.Glu73Lys	p.E73K	ENST00000356175	NM_000267.3	73	Gaa/Aaa	3/57	1	2	FACETS	0.5	0.354	0.677	0.5	0.354	0.677	SUBCLONAL	1	TRUE	1	0.41	2		317	117	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653037	29653037	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	88	495	0	ENST00000356175.3:c.4972A>T	p.Ile1658Phe	p.I1658F	ENST00000356175	NM_000267.3	1658	Atc/Ttc	36/57	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.41	2		495	394	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33446563	33446563	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs781611267	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	48	1021	1	ENST00000345365.6:c.70A>G	p.Arg24Gly	p.R24G	ENST00000345365	NM_002878.3	24	Agg/Ggg	1/10	1	2	FACETS	0.265	0.223	0.312	0.265	0.223	0.312	SUBCLONAL	1	TRUE	1	0.41	2		1022	882	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55693353	55693353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	48	951	2	ENST00000284073.2:c.560C>T	p.Pro187Leu	p.P187L	ENST00000284073	NM_138962.2	187	cCg/cTg	9/14	1	2	FACETS	0.247	0.208	0.291	0.247	0.208	0.291	SUBCLONAL	1	TRUE	1	0.41	2		953	947	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59886003	59886003	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	109	675	0	ENST00000259008.2:c.743T>G	p.Phe248Cys	p.F248C	ENST00000259008	NM_032043.2	248	tTt/tGt	7/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.41	2		675	479	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007482	62007482	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	135	906	0	ENST00000392795.3:c.385A>G	p.Asn129Asp	p.N129D	ENST00000392795	NM_001039933.1	129	Aac/Gac	3/6	1	2	FACETS	0.782	0.711	0.857	0.782	0.711	0.857	SUBCLONAL	1	TRUE	1	0.41	2		906	842	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120023	70120023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1182134893	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	12	150	0	ENST00000245479.2:c.1025C>T	p.Pro342Leu	p.P342L	ENST00000245479	NM_000346.3	342	cCg/cTg	3/3	1	2	FACETS	0.409	0.289	0.556	0.409	0.289	0.556	SUBCLONAL	1	TRUE	1	0.41	2		150	143	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371822	45371822	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	15	417	0	ENST00000262160.6:c.1169T>C	p.Phe390Ser	p.F390S	ENST00000262160	NM_005901.5	390	tTt/tCt	10/11	1	2	FACETS	0.322	0.236	0.426	0.322	0.236	0.426	SUBCLONAL	1	TRUE	1	0.41	2		417	227	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3114962	3114962	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	166	1105	1	ENST00000078429.4:c.497G>A	p.Arg166His	p.R166H	ENST00000078429	NM_002067.2	166	cGc/cAc	4/7	1	2	FACETS	0.797	0.731	0.866	0.797	0.731	0.866	SUBCLONAL	1	TRUE	1	0.41	2		1106	1016	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210580	5210580	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	46	955	2	ENST00000357368.4:c.5387C>T	p.Ala1796Val	p.A1796V	ENST00000357368	NM_002850.3	1796	gCc/gTc	35/38	1	2	FACETS	0.258	0.216	0.304	0.258	0.216	0.304	SUBCLONAL	1	TRUE	1	0.41	2		957	870	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7168022	7168023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750974293	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	105	684	0	ENST00000302850.5:c.1566dup	p.Asp523ArgfsTer40	p.D523Rfs*40	ENST00000302850	NM_000208.2	522	-/C	7/22	1	2	FACETS	0.743	0.667	0.825	0.743	0.667	0.825	SUBCLONAL	1	TRUE	1	0.41	2		684	689	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7174629	7174629	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	137	937	0	ENST00000302850.5:c.1088T>C	p.Ile363Thr	p.I363T	ENST00000302850	NM_000208.2	363	aTc/aCc	4/22	1	2	FACETS	0.703	0.639	0.771	0.703	0.639	0.771	SUBCLONAL	1	TRUE	1	0.41	2		937	950	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250960	10250960	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	185	1016	0	ENST00000340748.4:c.3520G>A	p.Ala1174Thr	p.A1174T	ENST00000340748		1174	Gcc/Acc	32/40	1	2	FACETS	0.942	0.87	1	0.942	0.87	1	CLONAL	1	TRUE	1	0.41	2		1016	958	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10264985	10264985	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	107	543	1	ENST00000340748.4:c.1955G>A	p.Arg652Gln	p.R652Q	ENST00000340748		652	cGa/cAa	21/40	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.41	2		544	482	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284963	15284963	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1470429510	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	260	1425	1	ENST00000263388.2:c.4652G>T	p.Gly1551Val	p.G1551V	ENST00000263388	NM_000435.2	1551	gGc/gTc	25/33	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.41	2		1426	1155	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290082	15290082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769083544	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	228	1229	1	ENST00000263388.2:c.3472G>A	p.Glu1158Lys	p.E1158K	ENST00000263388	NM_000435.2	1158	Gag/Aag	22/33	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.41	2		1230	1064	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298775	15298775	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1403582449	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1191	68	1339	0	ENST00000263388.2:c.1523T>C	p.Val508Ala	p.V508A	ENST00000263388	NM_000435.2	508	gTg/gCg	10/33	1	2	FACETS	0.263	0.228	0.302	0.263	0.228	0.302	SUBCLONAL	1	TRUE	1	0.41	2		1339	1259	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17389660	17389660	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	132	835	0	ENST00000359435.4:c.793T>C	p.Phe265Leu	p.F265L	ENST00000359435	NM_001033549.1	265	Ttt/Ctt	9/9	1	2	FACETS	0.831	0.755	0.911	0.831	0.755	0.911	CLONAL	1	TRUE	1	0.41	2		835	775	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950363	17950363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	245	1154	0	ENST00000458235.1:c.1364C>T	p.Ala455Val	p.A455V	ENST00000458235	NM_000215.3	455	gCa/gTa	10/24	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.41	2		1154	1171	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976392	18976392	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	240	1391	1	ENST00000262803.5:c.3042G>T	p.Lys1014Asn	p.K1014N	ENST00000262803	NM_002911.3	1014	aaG/aaT	22/24	1	2	FACETS	0.901	0.84	0.965	0.901	0.84	0.965	CLONAL	1	TRUE	1	0.41	2		1392	1299	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214651	36214651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752780080	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	148	1095	2	ENST00000222270.7:c.3077C>T	p.Thr1026Met	p.T1026M	ENST00000222270	NM_014727.1	1026	aCg/aTg	8/37	1	2	FACETS	0.701	0.639	0.766	0.701	0.639	0.766	SUBCLONAL	1	TRUE	1	0.41	2		1097	1030	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221447	36221447	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763021860	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	187	1244	1	ENST00000222270.7:c.5206C>T	p.Arg1736Cys	p.R1736C	ENST00000222270	NM_014727.1	1736	Cgc/Tgc	25/37	1	2	FACETS	0.767	0.707	0.83	0.767	0.707	0.83	SUBCLONAL	1	TRUE	1	0.41	2		1245	1189	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223620	36223620	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs374062006	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	276	1587	1	ENST00000222270.7:c.6170G>T	p.Arg2057Leu	p.R2057L	ENST00000222270	NM_014727.1	2057	cGc/cTc	28/37	1	2	FACETS	0.977	0.916	1	0.977	0.916	1	CLONAL	1	TRUE	1	0.41	2		1588	1378	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741845	40741845	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	165	1011	0	ENST00000392038.2:c.1127A>G	p.Glu376Gly	p.E376G	ENST00000392038	NM_001626.4	376	gAg/gGg	11/14	1	2	FACETS	0.92	0.845	0.998	0.92	0.845	0.998	CLONAL	1	TRUE	1	0.41	2		1011	875	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40744840	40744840	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	67	1015	0	ENST00000392038.2:c.680T>G	p.Phe227Cys	p.F227C	ENST00000392038	NM_001626.4	227	tTt/tGt	8/14	1	2	FACETS	0.339	0.293	0.388	0.339	0.293	0.388	SUBCLONAL	1	TRUE	1	0.41	2		1015	965	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748823	41748823	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	187	1145	0	ENST00000301178.4:c.1348T>C	p.Trp450Arg	p.W450R	ENST00000301178	NM_021913.4	450	Tgg/Cgg	11/20	1	2	FACETS	0.863	0.796	0.932	0.863	0.796	0.932	CLONAL	1	TRUE	1	0.41	2		1145	1057	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383222	42383222	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	135	997	0	ENST00000221972.3:c.242T>C	p.Leu81Ser	p.L81S	ENST00000221972	NM_021601.3	81	tTg/tCg	2/5	1	2	FACETS	0.699	0.635	0.767	0.699	0.635	0.767	SUBCLONAL	1	TRUE	1	0.41	2		997	942	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753740	42753740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	228	1418	2	ENST00000222329.4:c.524C>T	p.Ala175Val	p.A175V	ENST00000222329	NM_006494.2	175	gCt/gTt	4/4	1	2	FACETS	0.888	0.826	0.953	0.888	0.826	0.953	CLONAL	1	TRUE	1	0.41	2		1420	1252	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42790966	42790966	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	185	1178	0	ENST00000575354.2:c.111G>T	p.Trp37Cys	p.W37C	ENST00000575354	NM_015125.3	37	tgG/tgT	2/20	1	2	FACETS	0.767	0.707	0.829	0.767	0.707	0.829	SUBCLONAL	1	TRUE	1	0.41	2		1178	1177	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471010	25471010	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	81	1172	0	ENST00000264709.3:c.751A>G	p.Thr251Ala	p.T251A	ENST00000264709	NM_175629.2	251	Act/Gct	7/23	1	2	FACETS	0.374	0.328	0.424	0.374	0.328	0.424	SUBCLONAL	1	TRUE	1	0.41	2		1172	1056	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025993	48025993	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	53	482	0	ENST00000234420.5:c.871A>C	p.Asn291His	p.N291H	ENST00000234420	NM_000179.2	291	Aac/Cac	4/10	1	2	FACETS	0.673	0.576	0.779	0.673	0.576	0.779	SUBCLONAL	1	TRUE	1	0.41	2		482	384	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028159	48028159	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	48	374	0	ENST00000234420.5:c.3037A>C	p.Lys1013Gln	p.K1013Q	ENST00000234420	NM_000179.2	1013	Aag/Cag	4/10	1	2	FACETS	0.858	0.73	0.996	0.858	0.73	0.996	CLONAL	1	TRUE	1	0.41	2		374	273	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145420	61145420	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	12	314	0	ENST00000295025.8:c.630A>C	p.Lys210Asn	p.K210N	ENST00000295025	NM_002908.2	210	aaA/aaC	6/11	1	2	FACETS	0.43	0.304	0.584	0.43	0.304	0.584	SUBCLONAL	1	TRUE	1	0.41	2		314	136	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873007	136873007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	101	541	0	ENST00000241393.3:c.491C>T	p.Ala164Val	p.A164V	ENST00000241393	NM_003467.2	164	gCc/gTc	2/2	1	2	FACETS	0.924	0.829	1	0.924	0.829	1	CLONAL	1	TRUE	1	0.41	2		541	533	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738354	190738354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	38	324	0	ENST00000441310.2:c.2606G>A	p.Arg869Lys	p.R869K	ENST00000441310	NM_000534.4	869	aGa/aAa	12/13	1	2	FACETS	0.913	0.763	1	0.913	0.763	1	CLONAL	1	TRUE	1	0.41	2		324	203	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735369	204735369	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	27	490	0	ENST00000302823.3:c.170T>C	p.Val57Ala	p.V57A	ENST00000302823	NM_005214.4	57	gTg/gCg	2/4	1	2	FACETS	0.283	0.224	0.35	0.283	0.224	0.35	SUBCLONAL	1	TRUE	1	0.41	2		490	466	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212252716	212252716	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs755459959	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	20	194	0	ENST00000342788.4:c.3137G>A	p.Ser1046Asn	p.S1046N	ENST00000342788	NM_005235.2	1046	aGt/aAt	26/28	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.41	2		194	81	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568910	212568910	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	50	426	0	ENST00000342788.4:c.1208A>G	p.Asn403Ser	p.N403S	ENST00000342788	NM_005235.2	403	aAc/aGc	11/28	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.41	2		426	173	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645931	215645931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	32	625	0	ENST00000260947.4:c.667G>A	p.Glu223Lys	p.E223K	ENST00000260947	NM_000465.2	223	Gaa/Aaa	4/11	1	2	FACETS	0.47	0.382	0.569	0.47	0.382	0.569	SUBCLONAL	1	TRUE	1	0.41	2		625	332	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439475	220439475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	141	1045	0	ENST00000243786.2:c.328C>T	p.Leu110Phe	p.L110F	ENST00000243786	NM_002191.3	110	Ctc/Ttc	2/2	1	2	FACETS	0.885	0.807	0.967	0.885	0.807	0.967	CLONAL	1	TRUE	1	0.41	2		1045	777	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523356	9523356	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	79	535	0	ENST00000353224.5:c.1881G>T	p.Trp627Cys	p.W627C	ENST00000353224	NM_177990.2	627	tgG/tgT	9/10	1	2	FACETS	0.763	0.673	0.859	0.763	0.673	0.859	SUBCLONAL	1	TRUE	1	0.41	2		535	505	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023029	31023029	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs763660723	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	34	720	0	ENST00000375687.4:c.2514G>T	p.Lys838Asn	p.K838N	ENST00000375687	NM_015338.5	838	aaG/aaT	13/13	1	2	FACETS	0.285	0.232	0.345	0.285	0.232	0.345	SUBCLONAL	1	TRUE	1	0.41	2		720	582	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31369193	31369193	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	43	772	1	ENST00000328111.2:c.177G>T	p.Glu59Asp	p.E59D	ENST00000328111	NM_006892.3	59	gaG/gaT	3/23	1	2	FACETS	0.265	0.22	0.314	0.265	0.22	0.314	SUBCLONAL	1	TRUE	1	0.41	2		773	793	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386438	31386438	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	48	982	2	ENST00000328111.2:c.1663G>A	p.Gly555Arg	p.G555R	ENST00000328111	NM_006892.3	555	Ggg/Agg	15/23	1	2	FACETS	0.259	0.218	0.305	0.259	0.218	0.305	SUBCLONAL	1	TRUE	1	0.41	2		984	903	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030037	36030037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	211	866	1	ENST00000358208.4:c.1072G>A	p.Gly358Ser	p.G358S	ENST00000358208		358	Ggc/Agc	9/12	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.41	2		867	925	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728714	39728714	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	24	291	0	ENST00000361337.2:c.994G>T	p.Glu332Ter	p.E332*	ENST00000361337	NM_003286.2	332	Gaa/Taa	12/21	1	2	FACETS	0.591	0.466	0.734	0.591	0.466	0.734	SUBCLONAL	1	TRUE	1	0.41	2		291	198	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979355	40979355	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	45	632	0	ENST00000373198.4:c.1778A>C	p.Glu593Ala	p.E593A	ENST00000373198	NM_133170.3	593	gAg/gCg	11/32	1	2	FACETS	0.383	0.321	0.451	0.383	0.321	0.451	SUBCLONAL	1	TRUE	1	0.41	2		632	573	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281776	46281776	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	140	816	0	ENST00000371998.3:c.4223A>G	p.Asn1408Ser	p.N1408S	ENST00000371998		1408	aAc/aGc	22/23	1	2	FACETS	0.952	0.869	1	0.952	0.869	1	CLONAL	1	TRUE	1	0.41	2		816	717	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627980	37627980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749761322	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	63	1059	0	ENST00000249071.6:c.280C>T	p.Arg94Cys	p.R94C	ENST00000249071	NM_002872.4	94	Cgc/Tgc	4/7	1	2	FACETS	0.273	0.235	0.315	0.273	0.235	0.315	SUBCLONAL	1	TRUE	1	0.41	2		1059	1124	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627259	12627259	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs397516815	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	78	549	0	ENST00000251849.4:c.1457A>G	p.Asp486Gly	p.D486G	ENST00000251849	NM_002880.3	486	gAt/gGt	14/17	1	2	FACETS	0.815	0.718	0.918	0.815	0.718	0.918	CLONAL	1	TRUE	1	0.41	2		549	467	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30733055	30733055	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	96	610	0	ENST00000295754.5:c.1668G>T	p.Lys556Asn	p.K556N	ENST00000295754	NM_003242.5	556	aaG/aaT	7/7	1	2	FACETS	0.771	0.688	0.86	0.771	0.688	0.86	SUBCLONAL	1	TRUE	1	0.41	2		610	607	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37055964	37055964	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	48	387	0	ENST00000231790.2:c.719T>C	p.Phe240Ser	p.F240S	ENST00000231790	NM_000249.3	240	tTc/tCc	9/19	1	2	FACETS	0.87	0.741	1	0.87	0.741	1	CLONAL	1	TRUE	1	0.41	2		387	269	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268825	41268825	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	36	495	0	ENST00000349496.5:c.1063C>T	p.Pro355Ser	p.P355S	ENST00000349496	NM_001904.3	355	Ccg/Tcg	7/15	1	2	FACETS	0.658	0.543	0.784	0.658	0.543	0.784	SUBCLONAL	1	TRUE	1	0.41	2		495	267	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280721	41280721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	142	761	0	ENST00000349496.5:c.2234G>A	p.Gly745Asp	p.G745D	ENST00000349496	NM_001904.3	745	gGt/gAt	15/15	1	2	FACETS	0.954	0.871	1	0.954	0.871	1	CLONAL	1	TRUE	1	0.41	2		761	726	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125341	47125341	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	63	532	0	ENST00000409792.3:c.5929G>T	p.Glu1977Ter	p.E1977*	ENST00000409792	NM_014159.6	1977	Gaa/Taa	12/21	1	2	FACETS	0.842	0.732	0.96	0.842	0.732	0.96	CLONAL	1	TRUE	1	0.41	2		532	365	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162465	47162465	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs760833718	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	52	476	0	ENST00000409792.3:c.3661A>G	p.Thr1221Ala	p.T1221A	ENST00000409792	NM_014159.6	1221	Act/Gct	3/21	1	2	FACETS	0.86	0.737	0.993	0.86	0.737	0.993	CLONAL	1	TRUE	1	0.41	2		476	295	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165078	47165078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	38	353	0	ENST00000409792.3:c.1048G>A	p.Asp350Asn	p.D350N	ENST00000409792	NM_014159.6	350	Gat/Aat	3/21	1	2	FACETS	0.991	0.829	1	0.991	0.829	1	CLONAL	1	TRUE	1	0.41	2		353	187	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723084	49723084	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	28	312	1	ENST00000449682.2:c.1332G>A	p.Trp444Ter	p.W444*	ENST00000449682	NM_020998.3	444	tgG/tgA	11/18	1	2	FACETS	0.396	0.316	0.486	0.396	0.316	0.486	SUBCLONAL	1	TRUE	1	0.41	2		313	345	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134885798	134885798	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	49	705	2	ENST00000398015.3:c.1709G>T	p.Ser570Ile	p.S570I	ENST00000398015	NM_004441.4	570	aGc/aTc	9/16	1	2	FACETS	0.352	0.297	0.412	0.352	0.297	0.412	SUBCLONAL	1	TRUE	1	0.41	2		707	679	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426084	138426084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	29	463	0	ENST00000289153.2:c.1447C>T	p.Pro483Ser	p.P483S	ENST00000289153	NM_006219.2	483	Cca/Tca	9/22	1	2	FACETS	0.733	0.593	0.889	0.733	0.593	0.889	SUBCLONAL	1	TRUE	1	0.41	2		463	193	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280098	142280098	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	84	557	0	ENST00000350721.4:c.1336A>C	p.Lys446Gln	p.K446Q	ENST00000350721	NM_001184.3	446	Aaa/Caa	5/47	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.41	2		557	367	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281858	142281858	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	26	514	0	ENST00000350721.4:c.386C>A	p.Ser129Ter	p.S129*	ENST00000350721	NM_001184.3	129	tCa/tAa	4/47	1	2	FACETS	0.604	0.481	0.743	0.604	0.481	0.743	SUBCLONAL	1	TRUE	1	0.41	2		514	210	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181443	185181443	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	55	497	0	ENST00000265026.3:c.1384C>T	p.Leu462Phe	p.L462F	ENST00000265026	NM_004721.4	462	Ctc/Ttc	8/14	1	2	FACETS	0.582	0.499	0.673	0.582	0.499	0.673	SUBCLONAL	1	TRUE	1	0.41	2		497	461	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131154	55131154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	104	612	0	ENST00000257290.5:c.697G>A	p.Val233Ile	p.V233I	ENST00000257290	NM_006206.4	233	Gtc/Atc	5/23	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.41	2		612	475	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976584	55976584	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	18	514	2	ENST00000263923.4:c.1241C>A	p.Ser414Tyr	p.S414Y	ENST00000263923	NM_002253.2	414	tCt/tAt	9/30	1	2	FACETS	0.251	0.188	0.325	0.251	0.188	0.325	SUBCLONAL	1	TRUE	1	0.41	2		516	350	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155193	106155193	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	83	455	0	ENST00000380013.4:c.94A>G	p.Thr32Ala	p.T32A	ENST00000380013	NM_001127208.2	32	Aca/Gca	3/11	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.41	2		455	394	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157113	106157113	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	39	558	0	ENST00000380013.4:c.2014C>A	p.His672Asn	p.H672N	ENST00000380013	NM_001127208.2	672	Cat/Aat	3/11	1	2	FACETS	0.441	0.366	0.526	0.441	0.366	0.526	SUBCLONAL	1	TRUE	1	0.41	2		558	431	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510122	187510122	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	123	605	0	ENST00000441802.2:c.13391C>A	p.Pro4464His	p.P4464H	ENST00000441802	NM_005245.3	4464	cCt/cAt	27/27	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.41	2		605	544	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521306	187521306	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	40	753	0	ENST00000441802.2:c.11849T>C	p.Val3950Ala	p.V3950A	ENST00000441802	NM_005245.3	3950	gTg/gCg	22/27	1	2	FACETS	0.268	0.222	0.32	0.268	0.222	0.32	SUBCLONAL	1	TRUE	1	0.41	2		753	728	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532608	187532608	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	57	414	0	ENST00000441802.2:c.9785A>G	p.Asn3262Ser	p.N3262S	ENST00000441802	NM_005245.3	3262	aAt/aGt	14/27	1	2	FACETS	0.962	0.832	1	0.962	0.832	1	CLONAL	1	TRUE	1	0.41	2		414	289	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532675	187532675	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	37	560	0	ENST00000441802.2:c.9718T>C	p.Ser3240Pro	p.S3240P	ENST00000441802	NM_005245.3	3240	Tct/Cct	14/27	1	2	FACETS	0.395	0.325	0.473	0.395	0.325	0.473	SUBCLONAL	1	TRUE	1	0.41	2		560	457	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532791	187532791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	110	637	0	ENST00000441802.2:c.9602C>T	p.Ala3201Val	p.A3201V	ENST00000441802	NM_005245.3	3201	gCt/gTt	14/27	1	2	FACETS	0.976	0.88	1	0.976	0.88	1	CLONAL	1	TRUE	1	0.41	2		637	550	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540065	187540065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	49	510	0	ENST00000441802.2:c.7675C>T	p.Pro2559Ser	p.P2559S	ENST00000441802	NM_005245.3	2559	Ccg/Tcg	10/27	1	2	FACETS	0.65	0.552	0.756	0.65	0.552	0.756	SUBCLONAL	1	TRUE	1	0.41	2		510	368	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629495	187629495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	40	772	0	ENST00000441802.2:c.1487G>A	p.Gly496Glu	p.G496E	ENST00000441802	NM_005245.3	496	gGg/gAg	2/27	1	2	FACETS	0.316	0.262	0.377	0.316	0.262	0.377	SUBCLONAL	1	TRUE	1	0.41	2		772	617	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279489	1279489	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	59	1568	0	ENST00000310581.5:c.2047C>A	p.Leu683Met	p.L683M	ENST00000310581	NM_198253.2	683	Ctg/Atg	5/16	1	2	FACETS	0.249	0.213	0.288	0.249	0.213	0.288	SUBCLONAL	1	TRUE	1	0.41	2		1568	1158	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280310	1280310	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1554041073	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	65	1341	0	ENST00000310581.5:c.1913A>G	p.Tyr638Cys	p.Y638C	ENST00000310581	NM_198253.2	638	tAc/tGc	4/16	1	2	FACETS	0.286	0.247	0.329	0.286	0.247	0.329	SUBCLONAL	1	TRUE	1	0.41	2		1341	1108	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38949833	38949833	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	32	366	0	ENST00000357387.3:c.4117T>A	p.Ser1373Thr	p.S1373T	ENST00000357387	NM_152756.3	1373	Tcc/Acc	31/38	1	2	FACETS	0.736	0.602	0.885	0.736	0.602	0.885	SUBCLONAL	1	TRUE	1	0.41	2		366	212	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963055	38963055	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	31	387	0	ENST00000357387.3:c.1489A>C	p.Ile497Leu	p.I497L	ENST00000357387	NM_152756.3	497	Att/Ctt	17/38	1	2	FACETS	0.922	0.755	1	0.922	0.755	1	CLONAL	1	TRUE	1	0.41	2		387	164	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56171007	56171007	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	32	441	0	ENST00000399503.3:c.1835G>T	p.Ser612Ile	p.S612I	ENST00000399503	NM_005921.1	612	aGc/aTc	10/20	1	2	FACETS	0.323	0.262	0.393	0.323	0.262	0.393	SUBCLONAL	1	TRUE	1	0.41	2		441	483	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752863	57752863	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	32	453	1	ENST00000274289.3:c.1065C>A	p.His355Gln	p.H355Q	ENST00000274289	NM_006622.3	355	caC/caA	8/14	1	2	FACETS	0.632	0.516	0.762	0.632	0.516	0.762	SUBCLONAL	1	TRUE	1	0.41	2		454	247	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753054	57753054	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs907676004	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	34	471	0	ENST00000274289.3:c.962A>T	p.Asp321Val	p.D321V	ENST00000274289	NM_006622.3	321	gAt/gTt	7/14	1	2	FACETS	0.465	0.38	0.559	0.465	0.38	0.559	SUBCLONAL	1	TRUE	1	0.41	2		471	357	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86637132	86637133	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	23	304	0	ENST00000274376.6:c.1048dup	p.Ile350AsnfsTer14	p.I350Nfs*14	ENST00000274376	NM_002890.2	348	gga/ggAa	6/25	1	2	FACETS	0.943	0.746	1	0.943	0.746	1	CLONAL	1	TRUE	1	0.41	2		304	119	SUCCESS
APC	324	MSKCC	GRCh37	5	112174440	112174440	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753145833	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	22	307	0	ENST00000257430.4:c.3149C>T	p.Ala1050Val	p.A1050V	ENST00000257430	NM_000038.5	1050	gCa/gTa	16/16	1	2	FACETS	0.917	0.722	1	0.917	0.722	1	CLONAL	1	TRUE	1	0.41	2		307	117	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915638	131915638	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	18	326	0	ENST00000265335.6:c.636T>G	p.Tyr212Ter	p.Y212*	ENST00000265335		212	taT/taG	5/25	1	2	FACETS	0.777	0.593	0.988	0.777	0.593	0.988	CLONAL	1	TRUE	1	0.41	2		326	113	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923709	131923709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501938	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	10	353	0	ENST00000265335.6:c.979C>T	p.Arg327Cys	p.R327C	ENST00000265335		327	Cgt/Tgt	7/25	1	2	FACETS	0.378	0.257	0.529	0.378	0.257	0.529	SUBCLONAL	1	TRUE	1	0.41	2		353	129	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519358	176519358	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	54	1073	0	ENST00000292408.4:c.764T>C	p.Leu255Pro	p.L255P	ENST00000292408	NM_213647.1	255	cTc/cCc	7/18	1	2	FACETS	0.293	0.249	0.341	0.293	0.249	0.341	SUBCLONAL	1	TRUE	1	0.41	2		1073	900	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036922	180036922	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	159	995	0	ENST00000261937.6:c.3790A>G	p.Thr1264Ala	p.T1264A	ENST00000261937	NM_182925.4	1264	Acc/Gcc	28/30	1	2	FACETS	0.89	0.816	0.968	0.89	0.816	0.968	CLONAL	1	TRUE	1	0.41	2		995	871	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045738	26045738	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	119	542	1	ENST00000540144.1:c.100G>A	p.Gly34Ser	p.G34S	ENST00000540144	NM_003531.2	34	Ggt/Agt	1/1	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.41	2		543	484	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271507	26271507	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs567908596	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	125	782	0	ENST00000305910.3:c.106G>A	p.Val36Met	p.V36M	ENST00000305910	NM_003534.2	36	Gtg/Atg	1/1	1	2	FACETS	0.979	0.888	1	0.979	0.888	1	CLONAL	1	TRUE	1	0.41	2		782	623	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858483	27858483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	35	769	0	ENST00000359303.2:c.88G>A	p.Ala30Thr	p.A30T	ENST00000359303	NM_003535.2	30	Gct/Act	1/1	1	2	FACETS	0.282	0.23	0.34	0.282	0.23	0.34	SUBCLONAL	1	TRUE	1	0.41	2		769	606	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672008	30672008	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	49	1012	0	ENST00000376406.3:c.4952A>C	p.Lys1651Thr	p.K1651T	ENST00000376406	NM_014641.2	1651	aAa/aCa	10/15	1	2	FACETS	0.25	0.21	0.293	0.25	0.21	0.293	SUBCLONAL	1	TRUE	1	0.41	2		1012	958	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165314	32165314	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1356245765	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	330	1442	3	ENST00000375023.3:c.4814T>C	p.Phe1605Ser	p.F1605S	ENST00000375023	NM_004557.3	1605	tTc/tCc	27/30	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.41	2		1445	1393	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797280	32797280	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	169	1217	1	ENST00000374899.4:c.1829G>T	p.Gly610Val	p.G610V	ENST00000374899	NM_018833.2	610	gGa/gTa	11/12	1	2	FACETS	0.749	0.687	0.813	0.749	0.687	0.813	SUBCLONAL	1	TRUE	1	0.41	2		1218	1101	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800449	32800449	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	262	1365	0	ENST00000374899.4:c.1098T>G	p.Tyr366Ter	p.Y366*	ENST00000374899	NM_018833.2	366	taT/taG	6/12	1	2	FACETS	0.998	0.934	1	0.998	0.934	1	CLONAL	1	TRUE	1	0.41	2		1365	1280	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662715	117662715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	61	481	0	ENST00000368508.3:c.4750C>T	p.Pro1584Ser	p.P1584S	ENST00000368508	NM_002944.2	1584	Cca/Tca	29/43	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.41	2		481	296	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674257	117674257	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	89	647	0	ENST00000368508.3:c.4217A>G	p.Gln1406Arg	p.Q1406R	ENST00000368508	NM_002944.2	1406	cAg/cGg	26/43	1	2	FACETS	0.94	0.837	1	0.94	0.837	1	CLONAL	1	TRUE	1	0.41	2		647	462	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528250	157528250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368420323	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	140	813	0	ENST00000346085.5:c.5975C>T	p.Pro1992Leu	p.P1992L	ENST00000346085	NM_020732.3	1992	cCg/cTg	20/20	1	2	FACETS	0.961	0.876	1	0.961	0.876	1	CLONAL	1	TRUE	1	0.41	2		813	711	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6029487	6029487	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	79	539	0	ENST00000265849.7:c.1088T>C	p.Phe363Ser	p.F363S	ENST00000265849	NM_000535.5	363	tTt/tCt	10/15	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.41	2		539	384	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92355067	92355067	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	52	267	0	ENST00000265734.4:c.410A>G	p.His137Arg	p.H137R	ENST00000265734	NM_001259.6	137	cAt/cGt	4/8	1	2	FACETS	0.762	0.652	0.881	0.762	0.652	0.881	SUBCLONAL	1	TRUE	1	0.41	2		267	333	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509085	106509085	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	42	877	0	ENST00000359195.3:c.1079A>G	p.Lys360Arg	p.K360R	ENST00000359195	NM_002649.2	360	aAg/aGg	2/11	1	2	FACETS	0.277	0.23	0.329	0.277	0.23	0.329	SUBCLONAL	1	TRUE	1	0.41	2		877	740	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829000	128829000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	46	86	0	ENST00000249373.3:c.8C>T	p.Ala3Val	p.A3V	ENST00000249373	NM_005631.4	3	gCt/gTt	1/12	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.41	2		86	187	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506163	148506163	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	53	458	0	ENST00000320356.2:c.2195G>T	p.Arg732Ile	p.R732I	ENST00000320356	NM_004456.4	732	aGa/aTa	19/20	1	2	FACETS	0.783	0.672	0.905	0.783	0.672	0.905	CLONAL	1	TRUE	1	0.41	2		458	330	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148516702	148516702	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	32	424	0	ENST00000320356.2:c.985T>C	p.Cys329Arg	p.C329R	ENST00000320356	NM_004456.4	329	Tgt/Cgt	9/20	1	2	FACETS	0.465	0.378	0.562	0.465	0.378	0.562	SUBCLONAL	1	TRUE	1	0.41	2		424	336	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151216548	151216548	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	81	326	0	ENST00000262187.5:c.50T>C	p.Val17Ala	p.V17A	ENST00000262187	NM_005614.3	17	gTg/gCg	1/8	1	2	FACETS	0.91	0.806	1	0.91	0.806	1	CLONAL	1	TRUE	1	0.41	2		326	434	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835985	151835985	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1374055649	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	66	520	0	ENST00000262189.6:c.14539A>G	p.Ile4847Val	p.I4847V	ENST00000262189	NM_170606.2	4847	Atc/Gtc	58/59	1	2	FACETS	0.897	0.783	1	0.897	0.783	1	CLONAL	1	TRUE	1	0.41	2		520	359	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877943	151877943	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	82	451	0	ENST00000262189.6:c.7002C>A	p.Phe2334Leu	p.F2334L	ENST00000262189	NM_170606.2	2334	ttC/ttA	36/59	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.41	2		451	383	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879348	56879348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	50	839	0	ENST00000519728.1:c.865G>A	p.Glu289Lys	p.E289K	ENST00000519728	NM_002350.3	289	Gaa/Aaa	9/13	1	2	FACETS	0.287	0.242	0.336	0.287	0.242	0.336	SUBCLONAL	1	TRUE	1	0.41	2		839	851	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879402	56879402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	198	750	0	ENST00000519728.1:c.919G>A	p.Ala307Thr	p.A307T	ENST00000519728	NM_002350.3	307	Gct/Act	9/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.41	2		750	866	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922570	56922570	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	151	705	0	ENST00000519728.1:c.1440G>A	p.Trp480Ter	p.W480*	ENST00000519728	NM_002350.3	480	tgG/tgA	13/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.41	2		705	631	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005875	69005875	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	61	549	1	ENST00000288368.4:c.2286G>T	p.Glu762Asp	p.E762D	ENST00000288368	NM_024870.2	762	gaG/gaT	21/40	1	2	FACETS	0.896	0.778	1	0.896	0.778	1	CLONAL	1	TRUE	1	0.41	2		550	332	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009426	69009426	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	81	516	0	ENST00000288368.4:c.2543T>C	p.Leu848Ser	p.L848S	ENST00000288368	NM_024870.2	848	tTa/tCa	22/40	1	2	FACETS	0.936	0.829	1	0.936	0.829	1	CLONAL	1	TRUE	1	0.41	2		516	422	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031734	69031734	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1357669036	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	23	667	0	ENST00000288368.4:c.3489G>T	p.Glu1163Asp	p.E1163D	ENST00000288368	NM_024870.2	1163	gaG/gaT	28/40	1	2	FACETS	0.27	0.21	0.339	0.27	0.21	0.339	SUBCLONAL	1	TRUE	1	0.41	2		667	416	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980564	70980564	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	35	871	0	ENST00000276594.2:c.813T>G	p.Ser271Arg	p.S271R	ENST00000276594	NM_024504.3	271	agT/agG	4/8	1	2	FACETS	0.253	0.207	0.306	0.253	0.207	0.306	SUBCLONAL	1	TRUE	1	0.41	2		871	674	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561500	141561500	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	60	889	0	ENST00000220592.5:c.1305G>A	p.Trp435Ter	p.W435*	ENST00000220592	NM_012154.3	435	tgG/tgA	11/19	1	2	FACETS	0.345	0.296	0.399	0.345	0.296	0.399	SUBCLONAL	1	TRUE	1	0.41	2		889	848	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737108	145737108	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	256	1308	0	ENST00000428558.2:c.3458A>G	p.Glu1153Gly	p.E1153G	ENST00000428558	NM_004260.3	1153	gAg/gGg	21/22	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.41	2		1308	1090	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737773	145737773	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	71	1348	0	ENST00000428558.2:c.3055+2T>C		p.X1019_splice	ENST00000428558	NM_004260.3	1019			1	2	FACETS	0.333	0.29	0.381	0.333	0.29	0.381	SUBCLONAL	1	TRUE	1	0.41	2		1348	1039	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331617	8331617	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	68	564	0	ENST00000356435.5:c.5499G>T	p.Gln1833His	p.Q1833H	ENST00000356435		1833	caG/caT	33/35	1	2	FACETS	0.737	0.643	0.838	0.737	0.643	0.838	SUBCLONAL	1	TRUE	1	0.41	2		564	450	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970957	21970957	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757497674	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	227	1090	3	ENST00000304494.5:c.401C>T	p.Ala134Val	p.A134V	ENST00000304494	NM_000077.4	134	gCg/gTg	2/3	1	2	FACETS	0.897	0.834	0.962	0.897	0.834	0.962	CLONAL	1	TRUE	1	0.41	2		1093	1235	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27228284	27228284	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1386891182	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	73	551	0	ENST00000380036.4:c.3281G>T	p.Arg1094Ile	p.R1094I	ENST00000380036	NM_000459.3	1094	aGa/aTa	22/23	1	2	FACETS	0.869	0.763	0.981	0.869	0.763	0.981	CLONAL	1	TRUE	1	0.41	2		551	410	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87338550	87338550	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	102	714	1	ENST00000277120.3:c.646T>G	p.Leu216Val	p.L216V	ENST00000277120		216	Tta/Gta	7/19	1	2	FACETS	0.997	0.896	1	0.997	0.896	1	CLONAL	1	TRUE	1	0.41	2		715	499	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636173	87636173	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	94	455	0	ENST00000277120.3:c.2338G>T	p.Glu780Ter	p.E780*	ENST00000277120		780	Gag/Tag	19/19	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.41	2		455	433	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606530	93606530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	164	1204	3	ENST00000375746.1:c.350C>T	p.Thr117Ile	p.T117I	ENST00000375746	NM_001174167.1	117	aCt/aTt	2/14	1	2	FACETS	0.819	0.751	0.89	0.819	0.751	0.89	CLONAL	1	TRUE	1	0.41	2		1207	977	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404401	139404401	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs367586502	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	88	1320	0	ENST00000277541.6:c.2753A>G	p.Asn918Ser	p.N918S	ENST00000277541	NM_017617.3	918	aAc/aGc	18/34	1	2	FACETS	0.344	0.303	0.388	0.344	0.303	0.388	SUBCLONAL	1	TRUE	1	0.41	2		1320	1248	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417446	139417446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	228	1582	2	ENST00000277541.6:c.598G>A	p.Gly200Ser	p.G200S	ENST00000277541	NM_017617.3	200	Ggc/Agc	4/34	1	2	FACETS	0.83	0.772	0.891	0.83	0.772	0.891	CLONAL	1	TRUE	1	0.41	2		1584	1340	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15833997	15833997	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	48	853	0	ENST00000307771.7:c.755A>C	p.Lys252Thr	p.K252T	ENST00000307771	NM_005089.3	252	aAa/aCa	8/11	1	2	FACETS	0.259	0.218	0.305	0.259	0.218	0.305	SUBCLONAL	1	TRUE	1	0.41	2		853	904	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034468	47034468	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	209	959	0	ENST00000377604.3:c.553A>G	p.Thr185Ala	p.T185A	ENST00000377604	NM_001204468.1	185	Aca/Gca	6/24	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.41	2		959	921	SUCCESS
AR	367	MSKCC	GRCh37	X	66931447	66931447	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	42	857	1	ENST00000374690.3:c.2089T>C	p.Ser697Pro	p.S697P	ENST00000374690	NM_000044.3	697	Tcc/Ccc	4/8	1	2	FACETS	0.249	0.207	0.296	0.249	0.207	0.296	SUBCLONAL	1	TRUE	1	0.41	2		858	823	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347931	70347931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	174	832	1	ENST00000374080.3:c.3170C>T	p.Ala1057Val	p.A1057V	ENST00000374080		1057	gCc/gTc	22/45	1	2	FACETS	0.972	0.896	1	0.972	0.896	1	CLONAL	1	TRUE	1	0.41	2		833	873	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70355104	70355104	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	191	1117	0	ENST00000374080.3:c.5025+1G>T		p.X1675_splice	ENST00000374080		1675			1	2	FACETS	0.984	0.91	1	0.984	0.91	1	CLONAL	1	TRUE	1	0.41	2		1117	947	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849185	76849185	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	17	354	0	ENST00000373344.5:c.6091G>A	p.Glu2031Lys	p.E2031K	ENST00000373344	NM_000489.3	2031	Gag/Aag	26/35	1	2	FACETS	0.461	0.345	0.596	0.461	0.345	0.596	SUBCLONAL	1	TRUE	1	0.41	2		354	180	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872122	76872122	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	38	500	0	ENST00000373344.5:c.5525T>C	p.Ile1842Thr	p.I1842T	ENST00000373344	NM_000489.3	1842	aTt/aCt	22/35	1	2	FACETS	0.981	0.82	1	0.981	0.82	1	CLONAL	1	TRUE	1	0.41	2		500	189	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034382	123034382	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	34	457	0	ENST00000355640.3:c.1139T>C	p.Ile380Thr	p.I380T	ENST00000355640		380	aTa/aCa	6/7	1	2	FACETS	0.782	0.644	0.935	0.782	0.644	0.935	CLONAL	1	TRUE	1	0.41	2		457	212	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937962	76937962	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	25	690	0	ENST00000373344.5:c.2786A>C	p.Gln929Pro	p.Q929P	ENST00000373344	NM_000489.3	929	cAg/cCg	9/35	1	2	FACETS	0.376	0.297	0.468	0.376	0.297	0.468	SUBCLONAL	1	TRUE	1	0.41	2		690	324	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0058196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	40	276	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		276	474	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986565	36986566	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATACCTGGCCCTGCAGCGCCGCGGGGCTGGCGGCGTGGTGCGC	novel	NA	P-0058196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	32	895	0	ENST00000354822.5:c.1081_1123dup	p.Ser375CysfsTer78	p.S375Cfs*78	ENST00000354822	NM_001079668.2	375	tcc/tGCGCACCACGCCGCCAGCCCCGCGGCGCTGCAGGGCCAGGTATcc	3/3	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		895	631	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	120	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.47591729631043	2		306	467	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0058197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	398	818	0	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	1	2	FACETS	1	0.987	1	1	0.997	1	CLONAL	2	TRUE	1	0.47591729631043	2		818	781	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481417	140481417	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913348	NA	P-0058197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	127	425	0	ENST00000288602.6:c.1391G>T	p.Gly464Val	p.G464V	ENST00000288602	NM_004333.4	464	gGa/gTa	11/18	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.47591729631043	2		425	423	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936072	44936072	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1135401809	NA	P-0058197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	39	228	0	ENST00000377967.4:c.2832+1G>A		p.X944_splice	ENST00000377967	NM_021140.2	944			1	1	FACETS	0.603	0.505	0.711	0.603	0.505	0.711	SUBCLONAL	1	TRUE	0	0.47591729631043	1		228	207	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953742	48953742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1131690851	NA	P-0058197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	44	202	0	ENST00000267163.4:c.1345G>A	p.Gly449Arg	p.G449R	ENST00000267163	NM_000321.2	449	Gga/Aga	14/27	NA	3	FACETS	1	0.955	1			1	INDETERMINATE	1	TRUE	NA	0.47591729631043	3		202	168	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830776	3830776	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	97	517	1	ENST00000262367.5:c.1780G>T	p.Glu594Ter	p.E594*	ENST00000262367	NM_004380.2	594	Gaa/Taa	8/31	1	2	FACETS	0.577	0.515	0.644	0.577	0.515	0.644	SUBCLONAL	1	TRUE	1	0.47591729631043	2		518	706	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578403	+	inframe_deletion	In_Frame_Del	DEL	GGGGGC	GGGGGC	-	novel	NA	P-0058198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	121	1062	2	ENST00000269305.4:c.527_532del	p.Cys176_His178delinsTyr	p.C176_H178delinsY	ENST00000269305	NM_001126112.2	176	tGCCCCCac/tac	5/11	0.513980597875563	4	FACETS	1	0.98	1	1	0.991	1	CLONAL	3	TRUE	2	0.638351288196744	4		1064	183	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940517	29940519	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs1311300230	NA	P-0058198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	32	541	0	ENST00000389048.3:c.712_714del	p.Pro238del	p.P238del	ENST00000389048	NM_004304.4	238	CCT/-	2/29	0.604771080031306	2	FACETS	0.809	0.691	0.925	0.809	0.691	0.925	CLONAL	2	TRUE	0	0.638351288196744	2		541	62	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721132	39721132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	21	475	0	ENST00000361337.2:c.635C>T	p.Pro212Leu	p.P212L	ENST00000361337	NM_003286.2	212	cCt/cTt	9/21	0.451095849986375	4	FACETS	0.743	0.578	0.932	0.372	0.289	0.466	CLONAL	1	TRUE	2	0.638351288196744	4		475	145	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0058199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	168	245	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.553726405094667	4	FACETS	1	0.985	1			1	CLONAL	2	TRUE	NA	0.553726405094667	4		245	386	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519988	NA	P-0058199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	403	749	0	ENST00000269305.4:c.808T>C	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	Ttt/Ctt	8/11	0.515571384679131	3	FACETS	0.874	0.84	0.908	0.874	0.84	0.908	CLONAL	3	TRUE	0	0.553726405094667	3		749	709	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202748	108202748	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	28	276	0	ENST00000278616.4:c.7772G>T	p.Ser2591Ile	p.S2591I	ENST00000278616	NM_000051.3	2591	aGc/aTc	52/63	0.474128793580896	3	FACETS	0.463	0.371	0.567	0.231	0.185	0.284	SUBCLONAL	1	TRUE	1	0.553726405094667	3		276	279	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056814	180056814	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	115	980	0	ENST00000261937.6:c.698A>G	p.Gln233Arg	p.Q233R	ENST00000261937	NM_182925.4	233	cAg/cGg	6/30	NA	2	FACETS	0.635	0.573	0.701			1	INDETERMINATE	1	TRUE	NA	0.553726405094667	2		980	654	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030485	49030485	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs483352690	NA	P-0058200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	76	248	0	ENST00000267163.4:c.1960G>A	p.Val654Met	p.V654M	ENST00000267163	NM_000321.2	654	Gtg/Atg	19/27	0.659371360924301	1	FACETS	0.911	0.822	1	0.911	0.822	1	CLONAL	1	TRUE	0	0.691009720951119	1		248	158	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579372	7579372	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	605	977	1	ENST00000269305.4:c.315del	p.Ser106AlafsTer17	p.S106Afs*17	ENST00000269305	NM_001126112.2	105	ggC/gg	4/11	0.649190407986189	2	FACETS	0.962	0.935	0.989	0.962	0.935	0.989	CLONAL	2	TRUE	0	0.691009720951119	2		978	910	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0058201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	175	373	1	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	0.410638332951393	4	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	2	0.449452131976614	4		374	544	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061228	38061228	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	74	985	0	ENST00000250448.2:c.761T>C	p.Phe254Ser	p.F254S	ENST00000250448	NM_004496.3	254	tTc/tCc	2/2	1	2	FACETS	0.889	0.779	1	0.889	0.779	1	CLONAL	1	TRUE	1	0.3	2		985	555	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056209	26056211	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs779842031	NA	P-0058204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	105	631	0	ENST00000343677.2:c.446_448del	p.Lys149del	p.K149del	ENST00000343677	NM_005319.3	149	aAGAgc/agc	1/1	0.546395027343639	6	FACETS	0.676	0.604	0.754	0.113	0.1	0.126	SUBCLONAL	1	TRUE	0	0.546395027343639	6		631	1189	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649872	88649872	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	157	362	0	ENST00000372037.3:c.121C>T	p.Gln41Ter	p.Q41*	ENST00000372037	NM_004329.2	41	Cag/Tag	4/13	NA	2	FACETS	0.772	0.717	0.828			1	INDETERMINATE	2	TRUE	NA	0.546395027343639	2		362	372	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196118	108196118	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs876658603	NA	P-0058204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	179	470	0	ENST00000278616.4:c.6657del	p.Gln2220ArgfsTer15	p.Q2220Rfs*15	ENST00000278616	NM_000051.3	2218	agT/ag	46/63	0.438752812490272	2	FACETS	1	0.991	1	0.75	0.699	0.801	CLONAL	1	TRUE	0	0.546395027343639	2		470	437	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99165434	99165434	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0058204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	71	376	0	ENST00000074304.5:c.1178+2T>C		p.X393_splice	ENST00000074304	NM_001134224.1	393			0.435667436228351	4	FACETS	0.763	0.667	0.866	0.191	0.166	0.217	SUBCLONAL	1	TRUE	0	0.546395027343639	4		376	527	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130063	143130063	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	66	456	0	ENST00000262992.4:c.953T>G	p.Leu318Arg	p.L318R	ENST00000262992	NM_001101669.1	318	cTt/cGt	11/24	0.518243321430476	3	FACETS	0.648	0.563	0.738	0.216	0.187	0.246	SUBCLONAL	1	TRUE	0	0.546395027343639	3		456	475	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441952	6441953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0058204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1602	189	1067	0	ENST00000356142.4:c.512_513insTT	p.Lys172Ter	p.K172*	ENST00000356142	NM_018890.3	171	gta/gTTta	7/7	0.546395027343639	6	FACETS	0.808	0.744	0.876	0.269	0.248	0.292	CLONAL	1	TRUE	3	0.546395027343639	6		1067	1791	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0058210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	53	327	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	0.556744041052089	3	FACETS	1	0.958	1	0.429	0.372	0.49	CLONAL	1	FALSE	0	0.556744041052089	3		327	189	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs770248150	NA	P-0058210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	259	314	0	ENST00000311936.3:c.351A>T	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaT	4/5	0.556744041052089	9	FACETS	1	0.978	1			1	CLONAL	7	FALSE	NA	0.556744041052089	9		314	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0058210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	276	725	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.426285934731085	4	FACETS	1	0.977	1	0.783	0.745	0.82	CLONAL	3	FALSE	0	0.556744041052089	4		725	493	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929116	44929116	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	51	516	0	ENST00000377967.4:c.2216A>C	p.Asn739Thr	p.N739T	ENST00000377967	NM_021140.2	739	aAc/aCc	17/29	0.556744041052089	1	FACETS	0.59	0.507	0.679	0.59	0.507	0.679	SUBCLONAL	1	FALSE	0	0.556744041052089	1		516	224	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870913	12870914	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCACT	novel	NA	P-0058212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	146	358	0	ENST00000228872.4:c.144_148dup	p.Arg50ThrfsTer23	p.R50Tfs*23	ENST00000228872	NM_004064.3	47	aag/aaGCACTg	1/3	0.837935388985507	1	FACETS	0.794	0.743	0.845	0.794	0.743	0.845	SUBCLONAL	1	FALSE	0	0.837935388985507	1		358	255	SUCCESS
AR	367	MSKCC	GRCh37	X	66765521	66765521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	52	945	1	ENST00000374690.3:c.533C>T	p.Ser178Phe	p.S178F	ENST00000374690	NM_000044.3	178	tCc/tTc	1/8	0.670986674622094	3	FACETS	0.237	0.2	0.276	0.118	0.1	0.138	SUBCLONAL	1	TRUE	1	0.670986674622094	3		946	875	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425121	49425121	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555187461	NA	P-0058213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	263	1075	0	ENST00000301067.7:c.13367C>G	p.Ser4456Ter	p.S4456*	ENST00000301067	NM_003482.3	4456	tCa/tGa	39/54	1	2	FACETS	0.909	0.855	0.966	0.909	0.855	0.966	CLONAL	1	TRUE	1	0.670986674622094	2		1075	862	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621190	1621190	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	284	931	0	ENST00000344749.5:c.956G>T	p.Gly319Val	p.G319V	ENST00000344749	NM_001136139.2	319	gGc/gTc	12/19	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.670986674622094	2		931	754	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0058214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	50	584	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.692	0.587	0.807	0.692	0.587	0.807	SUBCLONAL	1	TRUE	1	0.26	2		584	556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747342068	NA	P-0058214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	89	1002	0	ENST00000269305.4:c.394A>G	p.Lys132Glu	p.K132E	ENST00000269305	NM_001126112.2	132	Aag/Gag	5/11	1	2	FACETS	0.689	0.61	0.775	0.689	0.61	0.775	SUBCLONAL	1	TRUE	1	0.26	2		1002	993	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658296	18658296	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371412006	NA	P-0058214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	46	406	0	ENST00000266497.5:c.3101G>A	p.Arg1034His	p.R1034H	ENST00000266497		1034	cGt/cAt	22/31	0.3	1	FACETS	0.984	0.832	1	0.984	0.832	1	CLONAL	1	TRUE	0	0.26	1		406	313	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450105	32450105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1190263054	NA	P-0058214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	66	984	2	ENST00000332351.3:c.707C>T	p.Ala236Val	p.A236V	ENST00000332351	NM_024426.4	236	gCg/gTg	2/10	0.3	1	FACETS	0.84	0.73	0.958	0.84	0.73	0.958	CLONAL	1	TRUE	0	0.26	1		986	526	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610023	43610023	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	51	983	0	ENST00000355710.3:c.1975del	p.Cys659AlafsTer16	p.C659Afs*16	ENST00000355710	NM_020975.4	659	Tgc/gc	11/20	1	2	FACETS	0.605	0.514	0.706	0.605	0.514	0.706	SUBCLONAL	1	TRUE	1	0.26	2		983	648	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444779	49444779	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	10	873	0	ENST00000301067.7:c.2687G>T	p.Gly896Val	p.G896V	ENST00000301067	NM_003482.3	896	gGa/gTa	10/54	0.146175581943449	3	FACETS	0.219	0.148	0.308	0.073	0.049	0.103	INDETERMINATE	1	TRUE	0	0.716657627808495	3		873	173	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539079	23539080	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGGGTTTGGG	novel	NA	P-0058224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	43	487	0	ENST00000380871.4:c.350_359dup	p.Lys121ProfsTer4	p.K121Pfs*4	ENST00000380871	NM_006167.3	120	cct/ccCCCAAACCCCt	2/2	0.716657627808495	1	FACETS	0.428	0.363	0.498	0.428	0.363	0.498	SUBCLONAL	1	TRUE	0	0.716657627808495	1		487	180	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061220	38061229	+	protein_altering_variant	In_Frame_Del	DEL	CGTTCTCGAA	CGTTCTCGAA	G	novel	NA	P-0058224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	107	509	0	ENST00000250448.2:c.760_769delinsC	p.Phe254_Gly257delinsArg	p.F254_G257delinsR	ENST00000250448	NM_004496.3	254	TTCGAGAACGgc/Cgc	2/2	0.716657627808495	4	FACETS	1	0.974	1			1	CLONAL	2	TRUE	NA	0.716657627808495	4		509	221	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0058226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	501	570	0	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	0.714107351328559	2	FACETS	0.993	0.964	1	0.993	0.964	1	CLONAL	2	TRUE	0	0.725156251149931	2		570	696	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001366	29001366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779189056	NA	P-0058226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	209	315	0	ENST00000282397.4:c.1366G>A	p.Ala456Thr	p.A456T	ENST00000282397	NM_002019.4	456	Gca/Aca	10/30	0.725156251149931	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.725156251149931	1		315	324	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62309645	62309645	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	144	534	0	ENST00000360203.5:c.983C>A	p.Ala328Asp	p.A328D	ENST00000360203	NM_001283009.1	328	gCc/gAc	12/35	0.721307705549487	4	FACETS	0.598	0.544	0.655	0.15	0.136	0.164	SUBCLONAL	1	TRUE	0	0.725156251149931	4		534	1145	SUCCESS
APC	324	MSKCC	GRCh37	5	112176395	112176395	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	19	234	0	ENST00000257430.4:c.5104G>C	p.Gly1702Arg	p.G1702R	ENST00000257430	NM_000038.5	1702	Gga/Cga	16/16	0.698664442831915	2	FACETS	0.265	0.201	0.338	0.132	0.1	0.169	SUBCLONAL	1	TRUE	0	0.725156251149931	2		234	198	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0058227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	39	639	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		639	967	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534285	534285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894226	NA	P-0058227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	42	615	0	ENST00000451590.1:c.38G>T	p.Gly13Val	p.G13V	ENST00000451590	NM_001130442.1	13	gGt/gTt	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		615	804	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	116	306	0				ENST00000310581	NM_198253.2	-/1132			0.161564013552087	1	FACETS	0.969	0.875	1	1	0.988	1	CLONAL	2	TRUE	0	0.161564013552087	1		306	681	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0058244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	63	90	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.161564013552087	2	FACETS	0.797	0.691	0.913	0.797	0.691	0.913	CLONAL	2	TRUE	0	0.161564013552087	2		90	489	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39623751	39623751	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	39	377	1	ENST00000262039.4:c.2158G>T	p.Glu720Ter	p.E720*	ENST00000262039	NM_002647.2	720	Gag/Tag	20/25	1	2	FACETS	0.82	0.678	0.978	0.82	0.678	0.978	CLONAL	1	TRUE	1	0.161564013552087	2		378	589	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188275	10188275	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768637170	NA	P-0058244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1204	74	615	0	ENST00000256474.2:c.418C>T	p.Leu140Phe	p.L140F	ENST00000256474	NM_000551.3	140	Ctc/Ttc	2/3	0.161564013552087	3	FACETS	0.775	0.676	0.882			1	SUBCLONAL	1	TRUE	NA	0.161564013552087	3		615	1278	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426571	49426571	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1562	133	995	1	ENST00000301067.7:c.11917C>T	p.Gln3973Ter	p.Q3973*	ENST00000301067	NM_003482.3	3973	Cag/Tag	39/54	0.161564013552087	3	FACETS	1	0.938	1	0.525	0.474	0.578	CLONAL	1	TRUE	1	0.161564013552087	3		996	1695	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994394	25994394	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs565110158	NA	P-0058244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	56	289	0	ENST00000435504.4:c.419C>T	p.Pro140Leu	p.P140L	ENST00000435504		140	cCg/cTg	6/13	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.161564013552087	2		289	531	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433515	49433515	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1440	229	1072	2	ENST00000301067.7:c.8038C>T	p.Gln2680Ter	p.Q2680*	ENST00000301067	NM_003482.3	2680	Caa/Taa	31/54	0.161564013552087	3	FACETS	0.918	0.852	0.986	0.918	0.852	0.986	CLONAL	2	TRUE	1	0.161564013552087	3		1074	1669	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695761	117695761	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	48	421	0	ENST00000369458.3:c.676A>G	p.Met226Val	p.M226V	ENST00000369458	NM_024626.3	226	Atg/Gtg	4/6	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.161564013552087	2		421	556	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624254	89624254	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	63	254	0	ENST00000371953.3:c.28A>T	p.Ser10Cys	p.S10C	ENST00000371953	NM_000314.4	10	Agc/Tgc	1/9	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.161564013552087	2		254	567	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170439	108170439	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0058244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	72	253	0	ENST00000278616.4:c.5006-2A>T		p.X1669_splice	ENST00000278616	NM_000051.3	1669			0.124380392450197	3	FACETS	0.836	0.735	0.945	0.836	0.735	0.945	CLONAL	3	TRUE	0	0.161564013552087	3		253	384	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506723	103506723	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	16	143	0	ENST00000355739.4:c.466A>T	p.Ser156Cys	p.S156C	ENST00000355739	NM_000123.3	156	Agt/Tgt	4/15	1	2	FACETS	0.728	0.538	0.955	0.728	0.538	0.955	CLONAL	1	TRUE	1	0.161564013552087	2		143	272	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641276	3641276	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1259	84	887	0	ENST00000294008.3:c.2363A>T	p.Gln788Leu	p.Q788L	ENST00000294008	NM_032444.2	788	cAg/cTg	12/15	1	2	FACETS	0.774	0.681	0.875	0.774	0.681	0.875	SUBCLONAL	1	TRUE	1	0.161564013552087	2		887	1343	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799653	3799653	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0058244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	46	346	0	ENST00000262367.5:c.3811A>T	p.Lys1271Ter	p.K1271*	ENST00000262367	NM_004380.2	1271	Aaa/Taa	21/31	1	2	FACETS	0.847	0.712	0.997	0.847	0.712	0.997	CLONAL	1	TRUE	1	0.161564013552087	2		346	672	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831309	3831309	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0058244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	62	300	0	ENST00000262367.5:c.1574-2A>T		p.X525_splice	ENST00000262367	NM_004380.2	525			1	2	FACETS	0.771	0.667	0.883	1	0.971	1	SUBCLONAL	2	TRUE	1	0.161564013552087	2		300	498	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422455	225422455	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	129	458	0	ENST00000264414.4:c.185A>T	p.Tyr62Phe	p.Y62F	ENST00000264414	NM_003590.4	62	tAt/tTt	2/16	0.161564013552087	2	FACETS	0.993	0.901	1	0.993	0.901	1	CLONAL	2	TRUE	0	0.161564013552087	2		458	804	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095927	29095927	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0058244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	98	560	0	ENST00000328354.6:c.909-2A>T		p.X303_splice	ENST00000328354	NM_007194.3	303			0.161564013552087	3	FACETS	0.781	0.696	0.872	0.781	0.696	0.872	SUBCLONAL	2	TRUE	1	0.161564013552087	3		560	839	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274977	142274977	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0058244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	33	294	0	ENST00000350721.4:c.2083A>T	p.Lys695Ter	p.K695*	ENST00000350721	NM_001184.3	695	Aaa/Taa	10/47	0.161564013552087	2	FACETS	0.822	0.669	0.995	0.411	0.334	0.498	CLONAL	1	TRUE	0	0.161564013552087	2		294	497	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279148	142279148	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	102	365	0	ENST00000350721.4:c.1498A>T	p.Thr500Ser	p.T500S	ENST00000350721	NM_001184.3	500	Act/Tct	6/47	0.161564013552087	2	FACETS	0.99	0.886	1	0.99	0.886	1	CLONAL	2	TRUE	0	0.161564013552087	2		365	638	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859560	151859560	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	212	505	0	ENST00000262189.6:c.11102del	p.Asn3701IlefsTer4	p.N3701Ifs*4	ENST00000262189	NM_170606.2	3701	aAt/at	43/59	0.161564013552087	6	FACETS	0.882	0.82	0.947	0.882	0.82	0.947	CLONAL	4	TRUE	2	0.161564013552087	6		505	984	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0058245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	207	373	1	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	0.5354890679005	3	FACETS	0.973	0.927	1	0.973	0.927	1	CLONAL	3	TRUE	0	0.611014246013267	3		374	303	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62298845	62298845	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770742969	NA	P-0058245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	365	891	0	ENST00000360203.5:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000360203	NM_001283009.1	213	cGg/cAg	8/35	0.367684513668454	5	FACETS	1	0.991	1	0.777	0.739	0.816	CLONAL	2	TRUE	2	0.611014246013267	5		891	982	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226491	2226491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748004837	NA	P-0058245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	594	1445	5	ENST00000398665.3:c.3971C>T	p.Ala1324Val	p.A1324V	ENST00000398665	NM_032482.2	1324	gCg/gTg	27/28	0.60835069369482	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.611014246013267	2		1450	946	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333758	70333758	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1056215784	NA	P-0058245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	144	565	0	ENST00000373644.4:c.1663C>A	p.His555Asn	p.H555N	ENST00000373644	NM_030625.2	555	Cat/Aat	2/12	0.583961806826656	3	FACETS	1	0.97	1	0.562	0.515	0.611	CLONAL	1	TRUE	1	0.611014246013267	3		565	547	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143570	108143570	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	141	307	0	ENST00000278616.4:c.3275C>A	p.Ser1092Ter	p.S1092*	ENST00000278616	NM_000051.3	1092	tCa/tAa	22/63	0.60835069369482	2	FACETS	0.958	0.895	1	0.958	0.895	1	CLONAL	2	TRUE	0	0.611014246013267	2		307	241	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608439	28608439	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	129	441	0	ENST00000241453.7:c.1703A>T	p.Lys568Met	p.K568M	ENST00000241453	NM_004119.2	568	aAg/aTg	13/24	0.479077323540561	5	FACETS	0.777	0.708	0.848	0.518	0.472	0.566	SUBCLONAL	2	TRUE	2	0.611014246013267	5		441	521	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913233	NA	P-0058246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	773	955	2	ENST00000451590.1:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000451590	NM_001130442.1	61	cAg/cTg	3/5	1	2	FACETS	0.785	0.764	0.804	1	0.998	1	SUBCLONAL	2	TRUE	1	0.84	2		957	1173	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220458	123220459	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	39	277	0	ENST00000218089.9:c.3117dup	p.Pro1040SerfsTer14	p.P1040Sfs*14	ENST00000218089	NM_001042749.1	1039	ctt/cTtt	30/35	1	1	FACETS	0.106	0.087	0.127	0.106	0.087	0.127	SUBCLONAL	1	TRUE	0	0.84	1		277	508	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544642	65544642	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	51	647	0	ENST00000358664.4:c.284T>A	p.Leu95Gln	p.L95Q	ENST00000358664	NM_002382.4	95	cTg/cAg	4/5	0.289386114856642	1	FACETS	0.38	0.322	0.444	0.38	0.322	0.444	SUBCLONAL	1	FALSE	0	0.289386114856642	1		647	793	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39595501	39595501	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	45	298	0	ENST00000262039.4:c.1387A>G	p.Lys463Glu	p.K463E	ENST00000262039	NM_002647.2	463	Aaa/Gaa	12/25	1	2	FACETS	0.585	0.491	0.688	0.585	0.491	0.688	SUBCLONAL	1	FALSE	1	0.289386114856642	2		298	532	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0058250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	533	839	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.316534325055511	3	FACETS	0.935	0.9	0.971	0.624	0.6	0.648	INDETERMINATE	2	TRUE	0	0.643798793304933	3		839	1170	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0058250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	797	999	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.643798793304933	2	FACETS	0.98	0.955	1	0.98	0.955	1	CLONAL	2	TRUE	0	0.643798793304933	2		999	1263	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589149	67589151	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	novel	NA	P-0058250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	173	232	0	ENST00000274335.5:c.1138_1140del	p.Leu380del	p.L380del	ENST00000274335		379	aaATTa/aaa	9/15	0.622205597385704	2	FACETS	0.974	0.919	1	0.974	0.919	1	CLONAL	2	TRUE	0	0.643798793304933	2		232	276	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447565	187447565	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151194132	NA	P-0058250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	400	749	1	ENST00000232014.4:c.628G>A	p.Asp210Asn	p.D210N	ENST00000232014	NM_001130845.1	210	Gat/Aat	5/10	0.157346894764498	2	FACETS	1	0.995	1	0.667	0.637	0.698	INDETERMINATE	1	TRUE	0	0.643798793304933	2		750	931	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004246	150004246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	72	298	0	ENST00000253339.5:c.1979G>A	p.Arg660His	p.R660H	ENST00000253339		660	cGt/cAt	3/7	1	2	FACETS	0.616	0.542	0.696	0.616	0.542	0.696	SUBCLONAL	1	TRUE	1	0.643798793304933	2		298	363	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205025	128205025	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	174	1016	0	ENST00000341105.2:c.416C>T	p.Ser139Phe	p.S139F	ENST00000341105	NM_032638.4	139	tCt/tTt	3/6	0.157346894764498	2	FACETS	0.418	0.384	0.454	0.209	0.192	0.227	INDETERMINATE	1	TRUE	0	0.643798793304933	2		1016	1292	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003419	42003419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	70	516	1	ENST00000219905.7:c.2956C>T	p.Pro986Ser	p.P986S	ENST00000219905	NM_001164273.1	986	Cca/Tca	8/24	0.204419952377975	3	FACETS	0.354	0.308	0.404	0.118	0.102	0.135	INDETERMINATE	1	TRUE	0	0.643798793304933	3		517	812	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858386	89858386	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	130	662	0	ENST00000389301.3:c.1174T>G	p.Phe392Val	p.F392V	ENST00000389301	NM_000135.2	392	Ttt/Gtt	13/43	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.643798793304933	NA		662	800	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812281	212812281	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	63	270	0	ENST00000342788.4:c.295C>G	p.Leu99Val	p.L99V	ENST00000342788	NM_005235.2	99	Ctg/Gtg	3/28	0.157346894764498	2	FACETS	0.461	0.399	0.526	0.23	0.199	0.263	INDETERMINATE	1	TRUE	0	0.643798793304933	2		270	425	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6038613	6038774	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCCTCTCAAAAAAAAAAAAAAAATCAATTCTAAGATTTTATTCTCCATTCTACTGGAAGGGACAATGGAAACCCGCTATAATCACTAGAGCAATAAGAGGCGTTGAAGTAACCGGCCATCACTACCTGCTTCTGCCCAAACACAGAGCCGATATTTTCCTT	TCCCTCTCAAAAAAAAAAAAAAAATCAATTCTAAGATTTTATTCTCCATTCTACTGGAAGGGACAATGGAAACCCGCTATAATCACTAGAGCAATAAGAGGCGTTGAAGTAACCGGCCATCACTACCTGCTTCTGCCCAAACACAGAGCCGATATTTTCCTT	-	novel	NA	P-0058250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	73	155	0	ENST00000265849.7:c.670_705+126del		p.X224_splice	ENST00000265849	NM_000535.5	224		6/15	0.377206643288049	3	FACETS	1	0.975	1	0.697	0.62	0.777	INDETERMINATE	1	TRUE	1	0.643798793304933	3		155	215	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564114	139564114	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1224	88	1140	0	ENST00000308874.7:c.254G>C	p.Arg85Pro	p.R85P	ENST00000308874		85	cGc/cCc	5/10	0.63147175135256	2	FACETS	0.208	0.184	0.235	0.104	0.092	0.118	SUBCLONAL	1	TRUE	0	0.643798793304933	2		1140	1312	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803445	1803586	+	splice_acceptor_variant,splice_donor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	GCAGACGTACACGCTGGACGTGCTGGGTGAGGGCCCTGGGGCGGCGCGGGGGTGGGGGCGGCAGTGGCGGTGGTGGTGAGGGAGGGGGTGGCCCCTGAGCGTCATCTGCCCCCACAGAGCGCTCCCCGCACCGGCCCATCCT	GCAGACGTACACGCTGGACGTGCTGGGTGAGGGCCCTGGGGCGGCGCGGGGGTGGGGGCGGCAGTGGCGGTGGTGGTGAGGGAGGGGGTGGCCCCTGAGCGTCATCTGCCCCCACAGAGCGCTCCCCGCACCGGCCCATCCT	-	novel	NA	P-0058250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	131	940	0	ENST00000260795.2:c.718_768del		p.X240_splice	ENST00000260795		240	cgGCAGACGTACACGCTGGACGTGCTGGGTGAGGGCCCTGGGGCGGCGCGGGGGTGGGGGCGGCAGTGGCGGTGGTGGTGAGGGAGGGGGTGGCCCCTGAGCGTCATCTGCCCCCACAGAGCGCTCCCCGCACCGGCCCATCCTg/cgg	5-6/17	0.516894602591359	1	FACETS	0.312	0.282	0.343	0.312	0.282	0.343	SUBCLONAL	1	TRUE	0	0.643798793304933	1		940	885	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0058251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	38	351	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.256240858058016	1	FACETS	0.691	0.572	0.824	0.691	0.572	0.824	SUBCLONAL	1	TRUE	0	0.24	1		351	403	SUCCESS
APC	324	MSKCC	GRCh37	5	112176383	112176383	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	26	278	1	ENST00000257430.4:c.5092G>T	p.Asp1698Tyr	p.D1698Y	ENST00000257430	NM_000038.5	1698	Gat/Tat	16/16	1	2	FACETS	0.614	0.486	0.76	0.614	0.486	0.76	SUBCLONAL	1	TRUE	1	0.24	2		279	353	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775475	39775475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	78	678	0	ENST00000288319.7:c.545G>A	p.Ser182Asn	p.S182N	ENST00000288319	NM_182918.3	182	aGc/aAc	4/10	1	2	FACETS	0.933	0.819	1	0.933	0.819	1	CLONAL	1	TRUE	1	0.24	2		678	697	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333092	70333092	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	100	625	0	ENST00000373644.4:c.997G>T	p.Gly333Cys	p.G333C	ENST00000373644	NM_030625.2	333	Ggc/Tgc	2/12	1	2	FACETS	0.977	0.872	1	0.977	0.872	1	CLONAL	1	TRUE	1	0.24	2		625	853	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717647	89717647	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786204946	NA	P-0058251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	41	406	0	ENST00000371953.3:c.672A>G	p.Ile224Met	p.I224M	ENST00000371953	NM_000314.4	224	atA/atG	7/9	1	2	FACETS	0.59	0.491	0.701	0.59	0.491	0.701	SUBCLONAL	1	TRUE	1	0.24	2		406	579	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446027	49446027	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	133	1186	0	ENST00000301067.7:c.1439del	p.Pro480LeufsTer450	p.P480Lfs*450	ENST00000301067	NM_003482.3	480	cCt/ct	10/54	1	2	FACETS	0.912	0.826	1	0.912	0.826	1	CLONAL	1	TRUE	1	0.24	2		1186	1215	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987088	36987088	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	193	887	0	ENST00000354822.5:c.601del	p.Ala201ArgfsTer27	p.A201Rfs*27	ENST00000354822	NM_001079668.2	201	Gcg/cg	3/3	0.236104332470933	2	FACETS	0.931	0.862	1	0.931	0.862	1	CLONAL	2	TRUE	0	0.24	2		887	864	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945577	151945577	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	45	176	0	ENST00000262189.6:c.1942G>T	p.Glu648Ter	p.E648*	ENST00000262189	NM_170606.2	648	Gaa/Taa	14/59	0.211590480263424	3	FACETS	0.827	0.7	0.964	0.827	0.7	0.964	CLONAL	2	TRUE	1	0.24	3		176	254	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5055702	5055702	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	52	214	0	ENST00000381652.3:c.970A>T	p.Ile324Phe	p.I324F	ENST00000381652	NM_004972.3	324	Att/Ttt	8/25	0.236104332470933	2	FACETS	0.83	0.713	0.956	0.83	0.713	0.956	CLONAL	2	TRUE	0	0.24	2		214	261	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98003000	98003000	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	25	293	0	ENST00000289081.3:c.276G>T	p.Trp92Cys	p.W92C	ENST00000289081	NM_000136.2	92	tgG/tgT	4/15	1	2	FACETS	0.645	0.509	0.801	0.645	0.509	0.801	SUBCLONAL	1	TRUE	1	0.24	2		293	323	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0058263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	102	293	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.314179288057089	3	FACETS	1	0.981	1	0.721	0.647	0.799	CLONAL	1	TRUE	1	0.314179288057089	3		293	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0058263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	157	557	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.303631061287399	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.314179288057089	1		558	705	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923059	39923059	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	158	350	0	ENST00000378444.4:c.3649C>T	p.Arg1217Ter	p.R1217*	ENST00000378444	NM_001123385.1	1217	Cga/Tga	8/15	0.214048098757249	2	FACETS	1	0.977	1			1	CLONAL	2	TRUE	NA	0.314179288057089	2		350	440	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598832	28598832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs986992433	NA	P-0058263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	92	909	0	ENST00000253063.3:c.392C>T	p.Ser131Phe	p.S131F	ENST00000253063	NM_031459.4	131	tCc/tTc	4/10	1	2	FACETS	0.675	0.599	0.756	0.675	0.599	0.756	SUBCLONAL	1	TRUE	1	0.314179288057089	2		909	868	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573498	48573499	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0058263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	35	235	0	ENST00000342988.3:c.84dup	p.Gly29ArgfsTer5	p.G29Rfs*5	ENST00000342988	NM_005359.5	28	caa/cAaa	2/12	1	2	FACETS	0.956	0.789	1	0.956	0.789	1	CLONAL	1	TRUE	1	0.314179288057089	2		235	233	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324587	31324587	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	213	559	0	ENST00000412585.2:c.221del	p.Pro74ArgfsTer3	p.P74Rfs*3	ENST00000412585	NM_005514.6	74	cCg/cg	2/8	0.314179288057089	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.314179288057089	3		559	707	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979406	2979406	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	78	654	0	ENST00000396946.4:c.841C>A	p.Gln281Lys	p.Q281K	ENST00000396946	NM_032415.4	281	Cag/Aag	6/25	1	2	FACETS	0.852	0.749	0.962	0.852	0.749	0.962	CLONAL	1	TRUE	1	0.314179288057089	2		654	583	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74858954	74858954	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	67	500	0	ENST00000284811.8:c.250A>G	p.Thr84Ala	p.T84A	ENST00000284811		84	Act/Gct	4/4	0.282592773039837	3	FACETS	0.738	0.641	0.843	0.369	0.32	0.422	SUBCLONAL	1	TRUE	1	0.314179288057089	3		500	669	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0058264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	76	351	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.806	0.712	0.906	1	0.979	1	CLONAL	2	TRUE	1	0.265526281882231	2		351	355	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0058264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	98	571	0	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	1	2	FACETS	0.854	0.767	0.946	1	0.985	1	CLONAL	2	TRUE	1	0.265526281882231	2		571	432	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143132	30143132	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1262491330	NA	P-0058264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	58	626	2	ENST00000389048.3:c.394G>T	p.Val132Leu	p.V132L	ENST00000389048	NM_004304.4	132	Gtg/Ttg	1/29	1	2	FACETS	0.753	0.652	0.861	1	0.97	1	SUBCLONAL	2	TRUE	1	0.265526281882231	2		628	290	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659551	88659551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	65	323	0	ENST00000372037.3:c.334G>T	p.Asp112Tyr	p.D112Y	ENST00000372037	NM_004329.2	112	Gat/Tat	6/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.265526281882231	2		323	372	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223917	36223917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	106	1059	1	ENST00000222270.7:c.6467C>T	p.Pro2156Leu	p.P2156L	ENST00000222270	NM_014727.1	2156	cCa/cTa	28/37	0.265526281882231	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.265526281882231	1		1060	478	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209101894	209101894	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0058264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	61	270	0	ENST00000345146.2:c.1155-1G>T		p.X385_splice	ENST00000345146	NM_005896.2	385			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.265526281882231	2		270	309	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248546	212248546	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	105	572	0	ENST00000342788.4:c.3721G>T	p.Asp1241Tyr	p.D1241Y	ENST00000342788	NM_005235.2	1241	Gac/Tac	28/28	1	2	FACETS	0.82	0.739	0.906	1	0.985	1	CLONAL	2	TRUE	1	0.265526281882231	2		572	482	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659919	227659919	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	81	734	1	ENST00000305123.5:c.3536A>T	p.Tyr1179Phe	p.Y1179F	ENST00000305123	NM_005544.2	1179	tAc/tTc	1/2	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.265526281882231	2		735	479	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260211	149260211	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	105	750	1	ENST00000360632.3:c.682C>T	p.Gln228Ter	p.Q228*	ENST00000360632	NM_015472.4	228	Cag/Tag	4/7	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.265526281882231	2		751	543	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170106	32170106	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	110	1026	0	ENST00000375023.3:c.3502C>A	p.Pro1168Thr	p.P1168T	ENST00000375023	NM_004557.3	1168	Ccc/Acc	21/30	1	2	FACETS	0.883	0.798	0.972	1	0.987	1	CLONAL	2	TRUE	1	0.265526281882231	2		1026	469	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032531	47032531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	73	720	0	ENST00000377604.3:c.437G>A	p.Arg146His	p.R146H	ENST00000377604	NM_001204468.1	146	cGt/cAt	5/24	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.265526281882231	2		720	389	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0058265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	76	157	2	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.94	0.826	1	0.94	0.826	1	CLONAL	1	FALSE	1	0.3	2		159	539	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041662	47041663	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0058265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	98	169	0	ENST00000377604.3:c.1887_1888del	p.Ala631ThrfsTer41	p.A631Tfs*41	ENST00000377604	NM_001204468.1	629	acAGgg/acgg	17/24	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	1	0.3	2		169	600	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0058266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	36	432	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.67	0.551	0.803	0.67	0.551	0.803	SUBCLONAL	1	TRUE	1	0.265383547781398	2		432	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579346	7579348	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs764486868	NA	P-0058266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	102	770	0	ENST00000269305.4:c.339_341del	p.Phe113del	p.F113del	ENST00000269305	NM_001126112.2	113	ttCTTg/ttg	4/11	0.265383547781398	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.265383547781398	1		770	652	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602393	28602393	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753200838	NA	P-0058266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	61	456	0	ENST00000241453.7:c.1975A>G	p.Met659Val	p.M659V	ENST00000241453	NM_004119.2	659	Atg/Gtg	16/24	0.265383547781398	1	FACETS	0.845	0.73	0.969	0.845	0.73	0.969	CLONAL	1	TRUE	0	0.265383547781398	1		456	472	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45391445	45391445	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	24	326	0	ENST00000262160.6:c.715C>T	p.Gln239Ter	p.Q239*	ENST00000262160	NM_005901.5	239	Caa/Taa	6/11	0.265383547781398	1	FACETS	0.475	0.373	0.594	0.475	0.373	0.594	SUBCLONAL	1	TRUE	0	0.265383547781398	1		326	330	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087929	27087929	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	60	662	0	ENST00000324856.7:c.2216C>G	p.Pro739Arg	p.P739R	ENST00000324856	NM_006015.4	739	cCt/cGt	6/20	1	2	FACETS	0.664	0.571	0.765	0.664	0.571	0.765	SUBCLONAL	1	TRUE	1	0.265383547781398	2		662	681	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78865626	78865626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	64	526	0	ENST00000306801.3:c.2090C>T	p.Pro697Leu	p.P697L	ENST00000306801	NM_020761.2	697	cCa/cTa	18/34	1	2	FACETS	0.988	0.858	1	0.988	0.858	1	CLONAL	1	TRUE	1	0.265383547781398	2		526	488	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0058267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	171	172	0				ENST00000310581	NM_198253.2	-/1132			0.3	4	FACETS	0.963	0.896	1	1	0.992	1	CLONAL	5	TRUE	1	0.2	4		172	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578448	7578448	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1064795691	NA	P-0058267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	54	702	0	ENST00000269305.4:c.482C>A	p.Ala161Asp	p.A161D	ENST00000269305	NM_001126112.2	161	gCc/gAc	5/11	1	2	FACETS	0.499	0.424	0.581	0.499	0.424	0.581	SUBCLONAL	1	TRUE	1	0.2	2		702	1082	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652126	36652136	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGAGGCCGG	GGCGAGGCCGG	-	novel	NA	P-0058267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	77	644	0	ENST00000244741.5:c.249_259del	p.Arg84Ter	p.R84*	ENST00000244741	NM_000389.4	83	cGGCGAGGCCGG/c	2/3	0.0823780808081878	4	FACETS	0.924	0.809	1	0.462	0.404	0.524	INDETERMINATE	1	TRUE	2	0.2	4		644	1000	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092769	27092769	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0058267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	93	464	0	ENST00000324856.7:c.2790T>G	p.Tyr930Ter	p.Y930*	ENST00000324856	NM_006015.4	930	taT/taG	9/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.2	2		464	692	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033819	49033825	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CACAGTG	CACAGTG	-	novel	NA	P-0058267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	35	246	0	ENST00000267163.4:c.1961-5_1962del		p.X654_splice	ENST00000267163	NM_000321.2	654		20/27	1	2	FACETS	0.972	0.798	1	0.972	0.798	1	CLONAL	1	TRUE	1	0.2	2		246	360	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39214627	39214627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	68	375	0	ENST00000402219.2:c.3497C>T	p.Ser1166Phe	p.S1166F	ENST00000402219	NM_005633.3	1166	tCt/tTt	22/23	1	2	FACETS	0.978	0.851	1	0.978	0.851	1	CLONAL	1	TRUE	1	0.2	2		375	695	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0058268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	100	1090	1	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	1	2	FACETS	0.925	0.829	1	0.925	0.829	1	CLONAL	1	TRUE	1	0.373269955811156	2		1091	579	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545855	41545855	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867077693	NA	P-0058268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	62	766	0	ENST00000263253.7:c.2470C>T	p.Gln824Ter	p.Q824*	ENST00000263253	NM_001429.3	824	Caa/Taa	14/31	0.373269955811156	1	FACETS	0.394	0.34	0.453	0.394	0.34	0.453	SUBCLONAL	1	TRUE	0	0.373269955811156	1		766	686	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481856	56481856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	153	665	0	ENST00000267101.3:c.784C>T	p.Pro262Ser	p.P262S	ENST00000267101	NM_001982.3	262	Cct/Tct	7/28	0.159971290917962	3	FACETS	0.772	0.709	0.838	0.772	0.709	0.838	INDETERMINATE	2	TRUE	1	0.373269955811156	3		665	630	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7168103	7168103	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	20	372	0	ENST00000302850.5:c.1486G>A	p.Glu496Lys	p.E496K	ENST00000302850	NM_000208.2	496	Gaa/Aaa	7/22	1	2	FACETS	0.395	0.302	0.504	0.395	0.302	0.504	SUBCLONAL	1	TRUE	1	0.373269955811156	2		372	271	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120479976	120479976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782503548	NA	P-0058268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	81	610	2	ENST00000256646.2:c.3451G>A	p.Asp1151Asn	p.D1151N	ENST00000256646	NM_024408.3	1151	Gat/Aat	21/34	0.105475022299637	3	FACETS	0.765	0.674	0.863	0.383	0.337	0.432	INDETERMINATE	1	TRUE	1	0.373269955811156	3		612	673	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346626	225346626	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	15	342	0	ENST00000264414.4:c.2012G>C	p.Arg671Thr	p.R671T	ENST00000264414	NM_003590.4	671	aGa/aCa	14/16	0.373269955811156	1	FACETS	0.332	0.243	0.438	0.332	0.243	0.438	SUBCLONAL	1	TRUE	0	0.373269955811156	1		342	197	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545802	41545802	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	46	660	0	ENST00000263253.7:c.2417C>A	p.Pro806His	p.P806H	ENST00000263253	NM_001429.3	806	cCt/cAt	14/31	0.373269955811156	1	FACETS	0.345	0.29	0.406	0.345	0.29	0.406	SUBCLONAL	1	TRUE	0	0.373269955811156	1		660	581	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548211	41548211	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs1434557433	NA	P-0058268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	22	255	0	ENST00000263253.7:c.2999C>G	p.Ser1000Cys	p.S1000C	ENST00000263253	NM_001429.3	1000	tCt/tGt	16/31	0.373269955811156	1	FACETS	0.502	0.391	0.629	0.502	0.391	0.629	SUBCLONAL	1	TRUE	0	0.373269955811156	1		255	191	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796766	135796766	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	33	257	0	ENST00000298552.3:c.721G>A	p.Glu241Lys	p.E241K	ENST00000298552	NM_001162426.1	241	Gaa/Aaa	8/23	0.373269955811156	1	FACETS	0.56	0.458	0.673	0.56	0.458	0.673	SUBCLONAL	1	TRUE	0	0.373269955811156	1		257	257	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	20	744	0	ENST00000269305.4:c.853G>C	p.Glu285Gln	p.E285Q	ENST00000269305	NM_001126112.2	285	Gag/Cag	8/11	0.373269955811156	1	FACETS	0.141	0.107	0.182	0.141	0.107	0.182	SUBCLONAL	1	TRUE	0	0.373269955811156	1		744	616	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982129	201982139	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTGGATCCC	ACCTGGATCCC	-	novel	NA	P-0058268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	35	870	0	ENST00000359651.3:c.655_665del	p.Leu219Ter	p.L219*	ENST00000359651		218	gACCTGGATCCC/g	5/8	1	2	FACETS	0.272	0.222	0.329	0.272	0.222	0.329	SUBCLONAL	1	TRUE	1	0.373269955811156	2		870	689	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56474097	56474097	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	76	750	1	ENST00000267101.3:c.13G>A	p.Asp5Asn	p.D5N	ENST00000267101	NM_001982.3	5	Gac/Aac	1/28	0.159971290917962	3	FACETS	0.637	0.558	0.722	0.318	0.279	0.361	INDETERMINATE	1	TRUE	1	0.373269955811156	3		751	759	SUCCESS
BLM	641	MSKCC	GRCh37	15	91290635	91290635	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	21	336	0	ENST00000355112.3:c.13C>A	p.Pro5Thr	p.P5T	ENST00000355112	NM_000057.2	5	Cct/Act	2/22	1	2	FACETS	0.467	0.36	0.59	0.467	0.36	0.59	SUBCLONAL	1	TRUE	1	0.373269955811156	2		336	241	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098790	47098790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	41	721	0	ENST00000409792.3:c.6484C>T	p.His2162Tyr	p.H2162Y	ENST00000409792	NM_014159.6	2162	Cat/Tat	15/21	1	2	FACETS	0.296	0.246	0.352	0.296	0.246	0.352	SUBCLONAL	1	TRUE	1	0.373269955811156	2		721	742	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965694	93965694	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	21	329	0	ENST00000369303.4:c.2234G>C	p.Gly745Ala	p.G745A	ENST00000369303	NM_004440.3	745	gGa/gCa	13/17	0.159971290917962	3	FACETS	0.479	0.369	0.606	0.239	0.184	0.303	INDETERMINATE	1	TRUE	1	0.373269955811156	3		329	279	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0058268-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	243	1090	1	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	1	2	FACETS	0.978	0.918	1	0.978	0.918	1	CLONAL	1	FALSE	1	0.69229040091731	2		1091	718	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545855	41545855	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867077693	NA	P-0058268-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	298	766	0	ENST00000263253.7:c.2470C>T	p.Gln824Ter	p.Q824*	ENST00000263253	NM_001429.3	824	Caa/Taa	14/31	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.69229040091731	2		766	797	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481856	56481856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058268-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	243	665	0	ENST00000267101.3:c.784C>T	p.Pro262Ser	p.P262S	ENST00000267101	NM_001982.3	262	Cct/Tct	7/28	0.359945118643888	4	FACETS	1	0.992	1	0.712	0.667	0.759	INDETERMINATE	1	FALSE	2	0.69229040091731	4		665	834	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7168103	7168103	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058268-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	83	372	0	ENST00000302850.5:c.1486G>A	p.Glu496Lys	p.E496K	ENST00000302850	NM_000208.2	496	Gaa/Aaa	7/22	1	2	FACETS	0.882	0.788	0.979	0.882	0.788	0.979	CLONAL	1	FALSE	1	0.69229040091731	2		372	272	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428366	33428366	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137886232	NA	P-0058268-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	168	796	0	ENST00000345365.6:c.757C>T	p.Arg253Ter	p.R253*	ENST00000345365	NM_002878.3	253	Cga/Tga	9/10	0.69229040091731	3	FACETS	0.909	0.837	0.983	0.454	0.418	0.492	CLONAL	1	FALSE	1	0.69229040091731	3		796	719	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120479976	120479976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782503548	NA	P-0058268-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	213	610	2	ENST00000256646.2:c.3451G>A	p.Asp1151Asn	p.D1151N	ENST00000256646	NM_024408.3	1151	Gat/Aat	21/34	1	2	FACETS	0.93	0.868	0.992	0.93	0.868	0.992	CLONAL	1	FALSE	1	0.69229040091731	2		612	662	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346626	225346626	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058268-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	113	342	0	ENST00000264414.4:c.2012G>C	p.Arg671Thr	p.R671T	ENST00000264414	NM_003590.4	671	aGa/aCa	14/16	0.675568521981388	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	0	0.69229040091731	1		342	192	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545802	41545802	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058268-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	254	660	0	ENST00000263253.7:c.2417C>A	p.Pro806His	p.P806H	ENST00000263253	NM_001429.3	806	cCt/cAt	14/31	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.69229040091731	2		660	667	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548211	41548211	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs1434557433	NA	P-0058268-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	77	255	0	ENST00000263253.7:c.2999C>G	p.Ser1000Cys	p.S1000C	ENST00000263253	NM_001429.3	1000	tCt/tGt	16/31	1	2	FACETS	0.943	0.84	1	0.943	0.84	1	CLONAL	1	FALSE	1	0.69229040091731	2		255	236	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796766	135796766	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058268-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	108	257	0	ENST00000298552.3:c.721G>A	p.Glu241Lys	p.E241K	ENST00000298552	NM_001162426.1	241	Gaa/Aaa	8/23	0.69229040091731	1	FACETS	0.868	0.796	0.941	0.868	0.796	0.941	CLONAL	1	FALSE	0	0.69229040091731	1		257	235	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044962	47044962	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	239	895	0	ENST00000377604.3:c.2288T>C	p.Leu763Pro	p.L763P	ENST00000377604	NM_001204468.1	763	cTc/cCc	20/24	0.392330416696815	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	0	0.563140637254237	1		895	502	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999354	100999354	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	147	944	0	ENST00000325455.5:c.448G>T	p.Asp150Tyr	p.D150Y	ENST00000325455	NM_001202474.3	150	Gat/Tat	1/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.563140637254237	2		944	418	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0058275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	244	172	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.851578261492489	2		172	559	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387092	31387092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764722946	NA	P-0058275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	368	606	0	ENST00000328111.2:c.1717C>T	p.Arg573Trp	p.R573W	ENST00000328111	NM_006892.3	573	Cgg/Tgg	16/23	1	2	FACETS	0.983	0.937	1	0.983	0.937	1	CLONAL	1	TRUE	1	0.851578261492489	2		606	879	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0058276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	415	793	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.878879546732895	2		793	920	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249780	110249780	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142583665	NA	P-0058276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	364	760	0	ENST00000374672.4:c.895C>T	p.Arg299Trp	p.R299W	ENST00000374672	NM_004235.4	299	Cgg/Tgg	3/5	0.878879546732895	2	FACETS	1	0.963	1	0.506	0.482	0.53	CLONAL	1	TRUE	0	0.878879546732895	2		760	819	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434514	49434514	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	372	749	0	ENST00000301067.7:c.7039del	p.Leu2347Ter	p.L2347*	ENST00000301067	NM_003482.3	2347	Cta/ta	31/54	0.878879546732895	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.878879546732895	1		749	456	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835751	68835752	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0058278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	45	566	0	ENST00000261769.5:c.343dup	p.Thr115AsnfsTer53	p.T115Nfs*53	ENST00000261769	NM_004360.3	114	-/A	3/16	0.130137601941925	0	FACETS	0.318	0.267	0.375			1	INDETERMINATE	1	TRUE	0	0.32	0		566	601	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2199905	2199905	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	41	633	0	ENST00000398665.3:c.674C>T	p.Ser225Leu	p.S225L	ENST00000398665	NM_032482.2	225	tCa/tTa	8/28	1	2	FACETS	0.476	0.396	0.566	0.476	0.396	0.566	SUBCLONAL	1	TRUE	1	0.32	2		633	538	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117458	115117458	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0058278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	26	239	0	ENST00000257566.3:c.718-2A>G		p.X240_splice	ENST00000257566	NM_016569.3	240			0.192814830099751	0	FACETS	0.377	0.299	0.466			1	SUBCLONAL	1	TRUE	0	0.32	0		239	293	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939961	76939961	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	76	230	0	ENST00000373344.5:c.787T>C	p.Trp263Arg	p.W263R	ENST00000373344	NM_000489.3	263	Tgg/Cgg	9/35	1	1	FACETS	1	0.933	1	1	0.986	1	CLONAL	2	TRUE	0	0.315920994815151	1		230	192	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0058281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	266	717	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.548840026632192	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.551104644800033	1		717	692	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0058281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	105	399	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	1	2	FACETS	0.882	0.795	0.973	0.882	0.795	0.973	CLONAL	1	TRUE	1	0.551104644800033	2		399	432	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900158	101900158	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	40	198	0	ENST00000374994.4:c.592C>T	p.Gln198Ter	p.Q198*	ENST00000374994	NM_004612.2	198	Cag/Tag	4/9	0.551104644800033	1	FACETS	0.401	0.335	0.474	0.401	0.335	0.474	SUBCLONAL	1	TRUE	0	0.551104644800033	1		198	262	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514602	44514602	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	124	417	0	ENST00000291552.4:c.554T>C	p.Leu185Pro	p.L185P	ENST00000291552	NM_006758.2	185	cTg/cCg	7/8	1	2	FACETS	0.788	0.716	0.864	0.788	0.716	0.864	SUBCLONAL	1	TRUE	1	0.551104644800033	2		417	571	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593558	48593558	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587781618	NA	P-0058281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	13	165	0	ENST00000342988.3:c.1308+1G>T		p.X436_splice	ENST00000342988	NM_005359.5	436			0.515344360026566	1	FACETS	0.162	0.115	0.219	0.162	0.115	0.219	SUBCLONAL	1	TRUE	0	0.551104644800033	1		165	211	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599939	10599939	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1463180402	NA	P-0058281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	38	684	0	ENST00000171111.5:c.1637T>G	p.Phe546Cys	p.F546C	ENST00000171111	NM_203500.1	546	tTc/tGc	5/6	0.551104644800033	1	FACETS	0.177	0.146	0.213	0.177	0.146	0.213	SUBCLONAL	1	TRUE	0	0.551104644800033	1		684	563	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953637	38953637	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	87	157	0	ENST00000357387.3:c.2716T>C	p.Cys906Arg	p.C906R	ENST00000357387	NM_152756.3	906	Tgt/Cgt	28/38	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.551104644800033	2		157	310	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202263	138202263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	139	446	0	ENST00000237289.4:c.2180G>A	p.Cys727Tyr	p.C727Y	ENST00000237289	NM_001270507.1	727	tGc/tAc	9/9	0.278953978434513	1	FACETS	0.7	0.641	0.762	0.7	0.641	0.762	INDETERMINATE	1	TRUE	0	0.551104644800033	1		446	522	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0058283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	96	276	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.348645599491775	3	FACETS	0.898	0.801	1	0.449	0.4	0.501	CLONAL	1	TRUE	1	0.376381263719372	3		276	675	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0058283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	113	402	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	1	2	FACETS	0.967	0.872	1	0.967	0.872	1	CLONAL	1	TRUE	1	0.376381263719372	2		402	621	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591105	67591107	+	inframe_deletion	In_Frame_Del	DEL	TAA	TAA	-	novel	NA	P-0058283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	53	212	0	ENST00000274335.5:c.1698_1700del	p.Lys567del	p.K567del	ENST00000274335		566	atTAAa/ata	12/15	1	2	FACETS	0.65	0.556	0.754	0.65	0.556	0.754	SUBCLONAL	1	TRUE	1	0.376381263719372	2		212	433	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372446	55372447	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0058283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1258	221	920	0	ENST00000297316.4:c.1138dup	p.Gln380ProfsTer4	p.Q380Pfs*4	ENST00000297316	NM_022454.3	379	tac/taCc	2/2	0.101470010648252	3	FACETS	0.943	0.875	1			1	INDETERMINATE	1	TRUE	NA	0.376381263719372	3		920	1479	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254966	16254967	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0058283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	105	287	1	ENST00000375759.3:c.2232dup	p.Glu745ArgfsTer6	p.E745Rfs*6	ENST00000375759	NM_015001.2	744	gca/gcAa	11/15	0.36791536594531	1	FACETS	0.89	0.801	0.984	0.89	0.801	0.984	CLONAL	1	TRUE	0	0.376381263719372	1		288	509	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0058314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	90	425	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		425	408	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0058315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	39	270	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.723	0.6	0.86	0.723	0.6	0.86	SUBCLONAL	1	TRUE	1	0.284612058321641	2		270	379	SUCCESS
APC	324	MSKCC	GRCh37	5	112175036	112175037	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0058315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	23	205	0	ENST00000257430.4:c.3746dup	p.Cys1249TrpfsTer7	p.C1249Wfs*7	ENST00000257430	NM_000038.5	1249	tgc/tGgc	16/16	1	2	FACETS	0.77	0.603	0.96	0.77	0.603	0.96	CLONAL	1	TRUE	1	0.284612058321641	2		205	210	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713421	40713421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199947379	NA	P-0058315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	82	1045	4	ENST00000373198.4:c.4094C>T	p.Thr1365Met	p.T1365M	ENST00000373198	NM_133170.3	1365	aCg/aTg	30/32	1	2	FACETS	0.606	0.533	0.685	0.606	0.533	0.685	SUBCLONAL	1	TRUE	1	0.284612058321641	2		1049	951	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962580	100962580	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	46	519	0	ENST00000325455.5:c.1817G>T	p.Arg606Ile	p.R606I	ENST00000325455	NM_001202474.3	606	aGa/aTa	3/8	1	2	FACETS	0.679	0.572	0.797	0.679	0.572	0.797	SUBCLONAL	1	TRUE	1	0.284612058321641	2		519	476	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101300	27101300	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	56	1141	3	ENST00000324856.7:c.4582C>T	p.Arg1528Ter	p.R1528*	ENST00000324856	NM_006015.4	1528	Cga/Tga	18/20	1	2	FACETS	0.512	0.437	0.595	0.512	0.437	0.595	SUBCLONAL	1	TRUE	1	0.24	2		1144	911	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720877	89720877	+	splice_donor_variant	Splice_Site	SNP	T	T	G	rs1114167624	NA	P-0058316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	28	344	0	ENST00000371953.3:c.1026+2T>G		p.X342_splice	ENST00000371953	NM_000314.4	342			1	2	FACETS	0.707	0.566	0.868	0.707	0.566	0.868	SUBCLONAL	1	TRUE	1	0.24	2		344	330	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692902	89692902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909218	NA	P-0058316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	24	481	0	ENST00000371953.3:c.386G>A	p.Gly129Glu	p.G129E	ENST00000371953	NM_000314.4	129	gGa/gAa	5/9	1	2	FACETS	0.595	0.467	0.743	0.595	0.467	0.743	SUBCLONAL	1	TRUE	1	0.24	2		481	336	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026184	71026184	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	37	405	1	ENST00000318789.4:c.1438G>T	p.Glu480Ter	p.E480*	ENST00000318789	NM_032682.5	480	Gaa/Taa	17/21	1	2	FACETS	0.694	0.572	0.831	0.694	0.572	0.831	SUBCLONAL	1	TRUE	1	0.24	2		406	444	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589602	67589604	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	novel	NA	P-0058316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	31	190	0	ENST00000274335.5:c.1365_1367del	p.Gln455_Phe456delinsHis	p.Q455_F456delinsH	ENST00000274335		455	caGTTt/cat	10/15	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.24	2		190	181	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023427	27023436	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCTGGCCT	GCCCTGGCCT	-	novel	NA	P-0058316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	91	744	0	ENST00000324856.7:c.534_543del	p.Ser178ArgfsTer51	p.S178Rfs*51	ENST00000324856	NM_006015.4	178	aGCCCTGGCCTg/ag	1/20	1	2	FACETS	0.965	0.856	1	0.965	0.856	1	CLONAL	1	TRUE	1	0.24	2		744	786	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274746	123274757	+	inframe_deletion	In_Frame_Del	DEL	ATACAGGCGATT	ATACAGGCGATT	-	novel	NA	P-0058316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	56	712	1	ENST00000358487.5:c.1161_1172del	p.Ile388_Met391del	p.I388_M391del	ENST00000358487	NM_000141.4	387	ttAATCGCCTGTATg/ttg	9/18	1	2	FACETS	0.631	0.54	0.732	0.631	0.54	0.732	SUBCLONAL	1	TRUE	1	0.24	2		713	739	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961068	55961068	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	121	843	0	ENST00000263923.4:c.2872G>T	p.Asp958Tyr	p.D958Y	ENST00000263923	NM_002253.2	958	Gat/Tat	21/30	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.24	2		843	929	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0058318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	54	495	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.694	0.592	0.805	0.694	0.592	0.805	SUBCLONAL	1	TRUE	1	0.258938403935651	2		497	601	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0058318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	138	397	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.15970738669688	3	FACETS	0.969	0.885	1	0.646	0.59	0.705	CLONAL	2	TRUE	0	0.258938403935651	3		397	621	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0058318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	21	295	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	1	2	FACETS	0.424	0.325	0.538	0.424	0.325	0.538	SUBCLONAL	1	TRUE	1	0.258938403935651	2		295	383	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651115	206651115	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781821296	NA	P-0058318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1252	85	1262	0	ENST00000367120.3:c.725C>T	p.Pro242Leu	p.P242L	ENST00000367120	NM_014002.3	242	cCg/cTg	8/22	1	2	FACETS	0.491	0.432	0.555	0.491	0.432	0.555	SUBCLONAL	1	TRUE	1	0.258938403935651	2		1262	1337	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	82	610	0	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	1	2	FACETS	0.826	0.727	0.931	0.826	0.727	0.931	CLONAL	1	TRUE	1	0.258938403935651	2		610	767	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781440	135781440	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203542	NA	P-0058318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	111	627	1	ENST00000298552.3:c.1525C>T	p.Arg509Ter	p.R509*	ENST00000298552	NM_001162426.1	509	Cga/Tga	15/23	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.258938403935651	2		628	742	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191804	123191804	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	26	429	0	ENST00000218089.9:c.1393G>T	p.Val465Phe	p.V465F	ENST00000218089	NM_001042749.1	465	Gtt/Ttt	15/35	1	2	FACETS	0.412	0.326	0.512	0.412	0.326	0.512	SUBCLONAL	1	TRUE	1	0.258938403935651	2		429	487	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976421	25976421	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	90	491	0	ENST00000435504.4:c.1124A>G	p.Glu375Gly	p.E375G	ENST00000435504		375	gAa/gGa	11/13	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.258938403935651	2		491	675	SUCCESS
APC	324	MSKCC	GRCh37	5	112111417	112111420	+	frameshift_variant	Frame_Shift_Del	DEL	CTTC	CTTC	-	novel	NA	P-0058318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	17	246	0	ENST00000257430.4:c.517_520del	p.Pro173Ter	p.P173*	ENST00000257430	NM_000038.5	172	CTTCct/ct	5/16	1	2	FACETS	0.687	0.515	0.891	0.687	0.515	0.891	SUBCLONAL	1	TRUE	1	0.258938403935651	2		246	191	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	323	306	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.773334900527924	2		306	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0058319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	578	1015	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.755944147063333	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.773334900527924	2		1015	747	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923060	44923060	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	366	649	0	ENST00000377967.4:c.1921C>T	p.Gln641Ter	p.Q641*	ENST00000377967	NM_021140.2	641	Cag/Tag	16/29	0.773334900527924	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.773334900527924	1		649	505	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs121913468	NA	P-0058319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	359	576	0	ENST00000269571.5:c.2305G>A	p.Asp769Asn	p.D769N	ENST00000269571		769	Gac/Aac	19/27	0.375961827962218	5	FACETS	0.885	0.845	0.926	0.885	0.845	0.926	INDETERMINATE	3	TRUE	2	0.773334900527924	5		576	755	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427647	49427647	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0058319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	517	826	0	ENST00000301067.7:c.10841C>G	p.Ser3614Ter	p.S3614*	ENST00000301067	NM_003482.3	3614	tCa/tGa	39/54	0.755755742728938	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.773334900527924	4		826	1132	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257272	16257272	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	358	606	0	ENST00000375759.3:c.4537G>C	p.Glu1513Gln	p.E1513Q	ENST00000375759	NM_015001.2	1513	Gag/Cag	11/15	0.755944147063333	2	FACETS	0.996	0.965	1	0.996	0.965	1	CLONAL	2	TRUE	0	0.773334900527924	2		606	465	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199839	108199839	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	185	258	0	ENST00000278616.4:c.7181C>A	p.Ser2394Ter	p.S2394*	ENST00000278616	NM_000051.3	2394	tCa/tAa	49/63	0.773334900527924	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.773334900527924	2		258	225	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256687	16256687	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	365	555	0	ENST00000375759.3:c.3952G>C	p.Glu1318Gln	p.E1318Q	ENST00000375759	NM_015001.2	1318	Gaa/Caa	11/15	0.755944147063333	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.773334900527924	2		555	463	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257131	16257131	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	354	581	0	ENST00000375759.3:c.4396G>C	p.Asp1466His	p.D1466H	ENST00000375759	NM_015001.2	1466	Gat/Cat	11/15	0.755944147063333	2	FACETS	0.97	0.938	1	0.97	0.938	1	CLONAL	2	TRUE	0	0.773334900527924	2		581	472	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257389	16257389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	337	462	0	ENST00000375759.3:c.4654G>A	p.Asp1552Asn	p.D1552N	ENST00000375759	NM_015001.2	1552	Gat/Aat	11/15	0.755944147063333	2	FACETS	0.979	0.947	1	0.979	0.947	1	CLONAL	2	TRUE	0	0.773334900527924	2		462	445	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257434	16257434	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	324	512	0	ENST00000375759.3:c.4699G>C	p.Glu1567Gln	p.E1567Q	ENST00000375759	NM_015001.2	1567	Gag/Cag	11/15	0.755944147063333	2	FACETS	0.948	0.915	0.98	0.948	0.915	0.98	CLONAL	2	TRUE	0	0.773334900527924	2		512	442	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711350	114711350	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	123	486	0	ENST00000543371.1:c.365C>A	p.Ser122Ter	p.S122*	ENST00000543371	NM_001198531.1	122	tCg/tAg	3/14	NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.773334900527924	2		486	303	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281556	49281556	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	553	880	0	ENST00000282018.3:c.603G>T	p.Met201Ile	p.M201I	ENST00000282018	NM_020377.2	201	atG/atT	1/1	0.773334900527924	3	FACETS	0.985	0.951	1	0.985	0.951	1	CLONAL	2	TRUE	1	0.773334900527924	3		880	1007	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218482	5218482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367722276	NA	P-0058319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	397	943	0	ENST00000357368.4:c.3997C>T	p.His1333Tyr	p.H1333Y	ENST00000357368	NM_002850.3	1333	Cac/Tac	25/38	0.461326940287154	4	FACETS	0.849	0.809	0.89	0.849	0.809	0.89	INDETERMINATE	2	TRUE	2	0.773334900527924	4		943	1072	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715733	61715733	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	189	325	0	ENST00000401558.2:c.2196C>G	p.Ile732Met	p.I732M	ENST00000401558	NM_003400.3	732	atC/atG	18/25	0.715431567234487	4	FACETS	0.916	0.855	0.978	0.611	0.57	0.652	CLONAL	2	TRUE	1	0.773334900527924	4		325	473	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44527585	44527585	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	259	834	0	ENST00000291552.4:c.20C>G	p.Ser7Cys	p.S7C	ENST00000291552	NM_006758.2	7	tCc/tGc	1/8	0.319585537545889	6	FACETS	1	0.944	1	0.503	0.472	0.534	INDETERMINATE	2	TRUE	2	0.773334900527924	6		834	848	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259163	89259163	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	151	419	0	ENST00000336596.2:c.307C>G	p.Leu103Val	p.L103V	ENST00000336596	NM_005233.5	103	Cta/Gta	3/17	0.773334900527924	3	FACETS	1	0.958	1			1	CLONAL	1	TRUE	NA	0.773334900527924	3		419	509	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976612	55976613	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0058319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	77	598	0	ENST00000263923.4:c.1212_1213del	p.Ser405LysfsTer20	p.S405Kfs*20	ENST00000263923	NM_002253.2	404	atTTca/atca	9/30	0.718360281967422	3	FACETS	0.396	0.347	0.448	0.132	0.115	0.15	SUBCLONAL	1	TRUE	0	0.773334900527924	3		598	698	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622174	162622174	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	117	480	0	ENST00000366898.1:c.523A>T	p.Thr175Ser	p.T175S	ENST00000366898	NM_004562.2	175	Acc/Tcc	4/12	0.375961827962218	5	FACETS	1	0.96	1	0.371	0.335	0.409	INDETERMINATE	1	TRUE	2	0.773334900527924	5		480	587	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191749	123191779	+	frameshift_variant	Frame_Shift_Del	DEL	AATGATGAAAAGAAGAGGAAGACAAGGTCCA	AATGATGAAAAGAAGAGGAAGACAAGGTCCA	-	novel	NA	P-0058319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	69	401	0	ENST00000218089.9:c.1342_1372del	p.Met448ProfsTer12	p.M448Pfs*12	ENST00000218089	NM_001042749.1	446	ggAATGATGAAAAGAAGAGGAAGACAAGGTCCA/gg	15/35	0.773334900527924	1	FACETS	0.706	0.632	0.782	0.706	0.632	0.782	SUBCLONAL	1	TRUE	0	0.773334900527924	1		401	155	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0058320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	186	605	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.641400021178931	2	FACETS	0.891	0.842	0.938	0.891	0.842	0.938	CLONAL	2	FALSE	0	0.693660329248468	2		605	301	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588117	69588117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763955342	NA	P-0058320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	35	936	0	ENST00000168712.1:c.581C>T	p.Ser194Leu	p.S194L	ENST00000168712	NM_002007.2	194	tCg/tTg	3/3	0.653671937417008	2	FACETS	0.303	0.249	0.364	0.152	0.124	0.182	SUBCLONAL	1	FALSE	0	0.693660329248468	2		936	333	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784455	9784455	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	13	610	0	ENST00000377346.4:c.2840C>G	p.Thr947Ser	p.T947S	ENST00000377346	NM_005026.3	947	aCt/aGt	22/24	0.641400021178931	2	FACETS	0.197	0.141	0.266	0.099	0.07	0.133	SUBCLONAL	1	FALSE	0	0.693660329248468	2		610	190	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439906	51439906	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	199	426	0	ENST00000262662.1:c.471G>T	p.Gln157His	p.Q157H	ENST00000262662		157	caG/caT	4/4	0.50677670076164	3	FACETS	1	0.947	1	1	0.947	1	CLONAL	3	TRUE	0	0.50677670076164	3		426	328	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100361	8100361	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	499	1298	1	ENST00000346208.3:c.335G>T	p.Trp112Leu	p.W112L	ENST00000346208		112	tGg/tTg	3/6	0.50677670076164	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	1	0.50677670076164	4		1299	982	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332222	70332222	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	51	310	0	ENST00000373644.4:c.127A>T	p.Thr43Ser	p.T43S	ENST00000373644	NM_030625.2	43	Act/Tct	2/12	0.50677670076164	4	FACETS	0.857	0.731	0.993	0.286	0.243	0.331	CLONAL	1	TRUE	1	0.50677670076164	4		310	354	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156232	119156232	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	79	514	0	ENST00000264033.4:c.1897G>C	p.Asp633His	p.D633H	ENST00000264033	NM_005188.3	633	Gat/Cat	11/16	0.50677670076164	3	FACETS	0.888	0.784	0.998	0.444	0.392	0.499	CLONAL	1	TRUE	1	0.50677670076164	3		514	440	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125523664	125523664	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	53	250	0	ENST00000428830.2:c.1257G>T	p.Arg419Ser	p.R419S	ENST00000428830	NM_001114121.2	419	agG/agT	12/14	0.50677670076164	3	FACETS	0.933	0.802	1	0.466	0.401	0.537	CLONAL	1	TRUE	1	0.50677670076164	3		250	281	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441755	49441755	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	209	525	0	ENST00000301067.7:c.4229A>G	p.Asn1410Ser	p.N1410S	ENST00000301067	NM_003482.3	1410	aAc/aGc	14/54	0.50677670076164	3	FACETS	0.99	0.928	1	0.99	0.928	1	CLONAL	2	TRUE	1	0.50677670076164	3		525	522	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69214112	69214112	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	48	253	0	ENST00000462284.1:c.316T>C	p.Tyr106His	p.Y106H	ENST00000462284	NM_002392.5	106	Tat/Cat	5/11	0.50677670076164	3	FACETS	1	0.859	1	0.503	0.429	0.583	CLONAL	1	TRUE	1	0.50677670076164	3		253	236	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515036	103515036	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	67	311	0	ENST00000355739.4:c.1537G>T	p.Ala513Ser	p.A513S	ENST00000355739	NM_000123.3	513	Gca/Tca	8/15	0.50677670076164	3	FACETS	0.975	0.853	1	0.487	0.426	0.553	CLONAL	1	TRUE	1	0.50677670076164	3		311	340	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435418	110435418	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	214	837	1	ENST00000375856.3:c.2983A>T	p.Ser995Cys	p.S995C	ENST00000375856	NM_003749.2	995	Agc/Tgc	1/2	0.50677670076164	3	FACETS	0.975	0.914	1	0.975	0.914	1	CLONAL	2	TRUE	1	0.50677670076164	3		838	543	SUCCESS
BLM	641	MSKCC	GRCh37	15	91333910	91333910	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs367543034	NA	P-0058321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	171	431	0	ENST00000355112.3:c.2855G>T	p.Gly952Val	p.G952V	ENST00000355112	NM_000057.2	952	gGg/gTg	15/22	0.50677670076164	3	FACETS	0.94	0.873	1	0.94	0.873	1	CLONAL	2	TRUE	1	0.50677670076164	3		431	450	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020460	14020460	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	78	336	0	ENST00000311895.7:c.431A>T	p.Gln144Leu	p.Q144L	ENST00000311895	NM_005236.2	144	cAa/cTa	3/11	0.50677670076164	3	FACETS	1	0.938	1	0.546	0.484	0.613	CLONAL	1	TRUE	1	0.50677670076164	3		336	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577032	7577032	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs786202055	NA	P-0058321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	303	922	0	ENST00000269305.4:c.906del	p.Ser303AlafsTer42	p.S303Afs*42	ENST00000269305	NM_001126112.2	302	ggG/gg	8/11	NA	2	FACETS	0.93	0.884	0.976			1	INDETERMINATE	2	TRUE	NA	0.50677670076164	2		922	643	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222982	1222982	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs727504172	NA	P-0058321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	219	682	1	ENST00000326873.7:c.921-2A>T		p.X307_splice	ENST00000326873	NM_000455.4	307			0.50677670076164	2	FACETS	0.969	0.914	1	0.969	0.914	1	CLONAL	2	TRUE	0	0.50677670076164	2		683	446	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610265	10610265	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	165	1031	0	ENST00000171111.5:c.445G>A	p.Glu149Lys	p.E149K	ENST00000171111	NM_203500.1	149	Gag/Aag	2/6	0.50677670076164	2	FACETS	1	0.965	1	0.539	0.497	0.582	CLONAL	1	TRUE	0	0.50677670076164	2		1031	604	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223444	36223445	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0058321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	323	1285	0	ENST00000222270.7:c.5994_5995delinsTT	p.Gly1999Trp	p.G1999W	ENST00000222270	NM_014727.1	1998	ctGGgg/ctTTgg	28/37	0.451431972929578	4	FACETS	0.956	0.904	1			1	CLONAL	2	TRUE	NA	0.50677670076164	4		1285	1005	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514493	41514493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	122	518	1	ENST00000373198.4:c.168G>T	p.Gln56His	p.Q56H	ENST00000373198	NM_133170.3	56	caG/caT	2/32	0.50677670076164	4	FACETS	1	0.943	1	0.264	0.239	0.291	CLONAL	1	TRUE	0	0.50677670076164	4		519	686	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356209	66356209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs745740802	NA	P-0058321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	237	595	0	ENST00000273854.3:c.1288del	p.Asp430IlefsTer15	p.D430Ifs*15	ENST00000273854	NM_004439.5	430	Gat/at	5/18	0.50677670076164	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.50677670076164	3		595	539	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356263	66356263	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	234	560	0	ENST00000273854.3:c.1234G>T	p.Val412Phe	p.V412F	ENST00000273854	NM_004439.5	412	Gtc/Ttc	5/18	0.50677670076164	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.50677670076164	3		560	545	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155649	106155649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	180	286	0	ENST00000380013.4:c.550G>T	p.Glu184Ter	p.E184*	ENST00000380013	NM_001127208.2	184	Gag/Tag	3/11	0.50677670076164	3	FACETS	0.96	0.905	1	0.96	0.905	1	CLONAL	3	TRUE	0	0.50677670076164	3		286	309	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295348	1295348	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0058321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	92	590	1				ENST00000310581	NM_198253.2	-/1132			0.413673912116268	6	FACETS	1	0.975	1	0.336	0.299	0.375	CLONAL	1	TRUE	2	0.50677670076164	6		591	544	SUCCESS
APC	324	MSKCC	GRCh37	5	112174736	112174736	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	140	218	0	ENST00000257430.4:c.3445G>T	p.Glu1149Ter	p.E1149*	ENST00000257430	NM_000038.5	1149	Gaa/Taa	16/16	0.50677670076164	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	3	TRUE	0	0.50677670076164	3		218	223	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923780	131923786	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGTAGG	GGGTAGG	AATAA	novel	NA	P-0058321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	25	207	0	ENST00000265335.6:c.1050_1051+5delinsAATAA		p.X350_splice	ENST00000265335		350		7/25	0.50677670076164	3	FACETS	0.668	0.531	0.824	0.223	0.177	0.275	SUBCLONAL	1	TRUE	0	0.50677670076164	3		207	185	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671952	30671952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200530869	NA	P-0058321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	142	891	0	ENST00000376406.3:c.5008G>A	p.Val1670Ile	p.V1670I	ENST00000376406	NM_014641.2	1670	Gtc/Atc	10/15	0.50677670076164	6	FACETS	0.982	0.893	1	0.196	0.178	0.216	CLONAL	1	TRUE	1	0.50677670076164	6		891	1149	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168659	32168659	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	724	884	0	ENST00000375023.3:c.4264G>C	p.Glu1422Gln	p.E1422Q	ENST00000375023	NM_004557.3	1422	Gag/Cag	23/30	0.50677670076164	5	FACETS	1	0.995	1	1	0.995	1	CLONAL	4	TRUE	1	0.50677670076164	5		884	1133	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157519989	157519989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	130	759	0	ENST00000346085.5:c.4058C>T	p.Ser1353Leu	p.S1353L	ENST00000346085	NM_020732.3	1353	tCg/tTg	17/20	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.50677670076164	2		759	509	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946167	13946167	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	112	418	0	ENST00000405192.2:c.929G>T	p.Gly310Val	p.G310V	ENST00000405192	NM_001163147.1	310	gGa/gTa	10/12	0.50677670076164	3	FACETS	1	0.95	1	0.541	0.489	0.596	CLONAL	1	TRUE	1	0.50677670076164	3		418	512	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526604	106526604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	145	346	0	ENST00000359195.3:c.2897G>A	p.Gly966Glu	p.G966E	ENST00000359195	NM_002649.2	966	gGg/gAg	10/11	0.50677670076164	3	FACETS	0.908	0.838	0.98	0.908	0.838	0.98	CLONAL	2	TRUE	1	0.50677670076164	3		346	395	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246342	53246342	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0058321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	255	339	1	ENST00000375401.3:c.640A>T	p.Lys214Ter	p.K214*	ENST00000375401	NM_004187.3	214	Aag/Tag	5/26	0.451431972929578	2	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.50677670076164	2		340	410	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928690	49928691	+	missense_variant	Missense_Mutation	DNP	CT	CT	AC	novel	NA	P-0058321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	161	1082	2	ENST00000296474.3:c.3583_3584delinsGT	p.Ser1195Val	p.S1195V	ENST00000296474	NM_002447.2	1195	AGc/GTc	17/20	1	2	FACETS	0.975	0.897	1	0.975	0.897	1	CLONAL	1	TRUE	1	0.50677670076164	2		1084	652	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847283	68847283	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	182	1030	1	ENST00000261769.5:c.1205A>T	p.Asp402Val	p.D402V	ENST00000261769	NM_004360.3	402	gAt/gTt	9/16	0.313693285766372	1	FACETS	0.968	0.892	1	0.968	0.892	1	CLONAL	1	TRUE	0	0.313693285766372	1		1031	1011	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400040	49400040	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	200	831	0	ENST00000418115.1:c.297G>A	p.Trp99Ter	p.W99*	ENST00000418115	NM_001664.2	99	tgG/tgA	4/5	1	2	FACETS	0.98	0.906	1	0.98	0.906	1	CLONAL	1	TRUE	1	0.313693285766372	2		831	1301	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518722	176518722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775100440	NA	P-0058323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1352	293	1337	0	ENST00000292408.4:c.640G>A	p.Val214Met	p.V214M	ENST00000292408	NM_213647.1	214	Gtg/Atg	6/18	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.313693285766372	2		1337	1645	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112035599	112035599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	159	705	0	ENST00000368678.4:c.295G>A	p.Asp99Asn	p.D99N	ENST00000368678		99	Gat/Aat	4/13	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.313693285766372	2		705	1004	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005924	69005924	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	135	845	0	ENST00000288368.4:c.2335G>T	p.Glu779Ter	p.E779*	ENST00000288368	NM_024870.2	779	Gaa/Taa	21/40	1	2	FACETS	0.754	0.684	0.829	0.754	0.684	0.829	SUBCLONAL	1	TRUE	1	0.313693285766372	2		845	1141	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046501	69046501	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	68	789	0	ENST00000288368.4:c.3974C>A	p.Ser1325Ter	p.S1325*	ENST00000288368	NM_024870.2	1325	tCa/tAa	32/40	1	2	FACETS	0.4	0.347	0.459	0.4	0.347	0.459	SUBCLONAL	1	TRUE	1	0.313693285766372	2		789	1083	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45864835	45864835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	247	1179	1	ENST00000391945.4:c.1184C>T	p.Ser395Phe	p.S395F	ENST00000391945	NM_000400.3	395	tCc/tTc	12/23	0.149438412011264	3	FACETS	0.896	0.836	0.959	1	0.99	1	CLONAL	3	FALSE	1	0.149438412011264	3		1180	1321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0058326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	273	748	1	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	0.321975007807979	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.331577629014944	2		749	797	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243542	41243542	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	348	779	0	ENST00000357654.3:c.4006A>G	p.Ser1336Gly	p.S1336G	ENST00000357654	NM_007294.3	1336	Agt/Ggt	10/23	0.162303509966954	5	FACETS	1	0.99	1	0.79	0.747	0.834	INDETERMINATE	2	TRUE	2	0.331577629014944	5		779	1326	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0058327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	167	432	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.160996891102368	5	FACETS	0.913	0.841	0.987	0.609	0.56	0.658	INDETERMINATE	2	FALSE	2	0.412476410520934	5		432	718	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0058327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	141	657	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.412476410520934	0	FACETS	0.742	0.68	0.807			1	SUBCLONAL	1	FALSE	0	0.412476410520934	0		657	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0058327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	503	1161	1	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.412476410520934	0	FACETS	0.613	0.588	0.638			1	SUBCLONAL	2	FALSE	0	0.412476410520934	0		1162	1169	SUCCESS
AR	367	MSKCC	GRCh37	X	66765779	66765779	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1244	576	1452	1	ENST00000374690.3:c.791G>A	p.Arg264Gln	p.R264Q	ENST00000374690	NM_000044.3	264	cGg/cAg	1/8	0.160996891102368	5	FACETS	1	0.995	1	0.828	0.794	0.862	INDETERMINATE	2	FALSE	2	0.412476410520934	5		1453	1820	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	48	365	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	0.673	0.571	0.784	0.673	0.571	0.784	SUBCLONAL	1	FALSE	1	0.412476410520934	2		365	346	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198027	185198027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184685567	NA	P-0058327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	44	521	0	ENST00000265026.3:c.2509C>T	p.Arg837Cys	p.R837C	ENST00000265026	NM_004721.4	837	Cgc/Tgc	13/14	0.231706931910191	3	FACETS	0.456	0.382	0.539	0.152	0.127	0.18	INDETERMINATE	1	FALSE	0	0.412476410520934	3		521	564	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212615384	212615384	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	65	737	0	ENST00000342788.4:c.602C>T	p.Thr201Ile	p.T201I	ENST00000342788	NM_005235.2	201	aCa/aTa	5/28	0.412476410520934	3	FACETS	0.347	0.3	0.399	0.174	0.15	0.2	SUBCLONAL	1	FALSE	1	0.412476410520934	3		737	1095	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438164	56438164	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	519	1242	0	ENST00000407977.2:c.829G>T	p.Glu277Ter	p.E277*	ENST00000407977		277	Gag/Tag	7/10	0.412476410520934	0	FACETS	0.606	0.582	0.63			1	SUBCLONAL	2	FALSE	0	0.412476410520934	0		1242	1220	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659591	88659592	+	missense_variant	Missense_Mutation	DNP	GT	GT	TG	novel	NA	P-0058327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	437	702	0	ENST00000372037.3:c.374_375delinsTG	p.Cys125Leu	p.C125L	ENST00000372037	NM_004329.2	125	tGT/tTG	6/13	0.412476410520934	3	FACETS	0.955	0.916	0.994	0.955	0.916	0.994	CLONAL	3	FALSE	0	0.412476410520934	3		702	892	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858466	9858466	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	150	810	1	ENST00000330684.3:c.2935G>T	p.Val979Leu	p.V979L	ENST00000330684	NM_001134407.1	979	Gta/Tta	13/13	0.39774659850995	3	FACETS	0.959	0.876	1	0.479	0.438	0.523	CLONAL	1	FALSE	1	0.412476410520934	3		811	915	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267026	41267026	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	50	701	0	ENST00000349496.5:c.697A>C	p.Lys233Gln	p.K233Q	ENST00000349496	NM_001904.3	233	Aag/Cag	5/15	0.231706931910191	3	FACETS	0.36	0.304	0.422	0.12	0.101	0.141	INDETERMINATE	1	FALSE	0	0.412476410520934	3		701	812	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5462945	5462945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	241	511	0	ENST00000381577.3:c.506G>A	p.Ser169Asn	p.S169N	ENST00000381577	NM_014143.3	169	aGc/aAc	4/7	0.321273502526016	3	FACETS	0.975	0.915	1	0.975	0.915	1	CLONAL	2	FALSE	1	0.412476410520934	3		511	723	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0058328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	314	361	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.265464645157688	0	FACETS	0.881	0.845	0.917			1	CLONAL	4	TRUE	0	0.265464645157688	0		361	493	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0058328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	459	421	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.265464645157688	0	FACETS	0.825	0.801	0.848			1	CLONAL	5	TRUE	0	0.265464645157688	0		421	616	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0058328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	478	681	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.265464645157688	0	FACETS	0.908	0.879	0.937			1	CLONAL	4	TRUE	0	0.265464645157688	0		681	728	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013691	12013691	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0058328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	99	459	0	ENST00000353533.5:c.634-1G>C		p.X212_splice	ENST00000353533	NM_003010.3	212			0.265464645157688	0	FACETS	0.734	0.661	0.811			1	SUBCLONAL	2	TRUE	0	0.265464645157688	0		459	373	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584602	48584602	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	19	650	0	ENST00000342988.3:c.775del	p.Thr259LeufsTer77	p.T259Lfs*77	ENST00000342988	NM_005359.5	259	Act/ct	6/12	0.265464645157688	0	FACETS	0.539	0.411	0.689			1	SUBCLONAL	1	TRUE	0	0.265464645157688	0		650	195	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230792	66230792	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	196	502	0	ENST00000273854.3:c.2179A>G	p.Ile727Val	p.I727V	ENST00000273854	NM_004439.5	727	Atc/Gtc	12/18	1	2	FACETS	1	0.981	1	1	0.994	1	CLONAL	2	TRUE	1	0.265464645157688	2		502	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0058329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	667	1011	1	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.261672031365174	3	FACETS	0.978	0.945	1	1	0.997	1	CLONAL	4	TRUE	0	0.261672031365174	3		1012	1473	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	195	437	1	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	0.193761467872425	3	FACETS	0.951	0.885	1	1	0.99	1	CLONAL	3	TRUE	1	0.261672031365174	3		438	591	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332868	152332868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745723014	NA	P-0058329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	291	575	3	ENST00000206249.3:c.1174G>A	p.Val392Ile	p.V392I	ENST00000206249	NM_000125.3	392	Gtc/Atc	5/8	0.0966617743026101	4	FACETS	1	0.984	1	1	0.995	1	INDETERMINATE	3	TRUE	2	0.261672031365174	4		578	844	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678783	52678784	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	250	340	0	ENST00000394830.3:c.835dup	p.Ile279AsnfsTer8	p.I279Nfs*8	ENST00000394830	NM_018313.4	279	ata/aAta	9/30	0.261672031365174	4	FACETS	0.988	0.931	1	0.988	0.931	1	CLONAL	4	TRUE	0	0.261672031365174	4		340	610	SUCCESS
APC	324	MSKCC	GRCh37	5	112170682	112170682	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1064794226	NA	P-0058329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	152	489	0	ENST00000257430.4:c.1778G>A	p.Trp593Ter	p.W593*	ENST00000257430	NM_000038.5	593	tGg/tAg	15/16	0.193761467872425	3	FACETS	0.821	0.752	0.894	0.821	0.752	0.894	CLONAL	2	TRUE	1	0.261672031365174	3		489	800	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856619	111856631	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCGCCGGGCCC	CTGCGCCGGGCCC	-	novel	NA	P-0058329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	324	205	0	ENST00000341259.2:c.671_683del	p.Leu224ArgfsTer50	p.L224Rfs*50	ENST00000341259	NM_005475.2	224	CTGCGCCGGGCCCcg/cg	2/8	0.177997435773284	5	FACETS	1	0.979	1	1	0.996	1	CLONAL	5	TRUE	2	0.261672031365174	5		205	659	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477081	67477083	+	inframe_deletion	In_Frame_Del	DEL	CTA	CTA	-	novel	NA	P-0058329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	476	689	1	ENST00000327367.4:c.892_894del	p.Tyr298del	p.Y298del	ENST00000327367	NM_005902.3	296	ctCTAc/ctc	7/9	NA	2	FACETS	0.989	0.951	1			1	INDETERMINATE	4	TRUE	NA	0.261672031365174	2		690	920	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410209	63410209	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	172	1102	0	ENST00000330258.3:c.2958G>C	p.Gln986His	p.Q986H	ENST00000330258	NM_152424.3	986	caG/caC	2/2	0.178494071150455	3	FACETS	1	0.984	1	0.426	0.391	0.463	CLONAL	1	TRUE	0	0.261672031365174	3		1102	1163	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0058330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	516	557	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.843777159726474	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.843777159726474	1		558	692	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795885	42795886	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0058330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	466	2265	0	ENST00000575354.2:c.2880dup	p.Ser961GlnfsTer190	p.S961Qfs*190	ENST00000575354	NM_015125.3	958	-/C	11/20	1	2	FACETS	0.91	0.871	0.95	0.91	0.871	0.95	CLONAL	1	TRUE	1	0.843777159726474	2		2265	1214	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475188	475188	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	330	1244	0	ENST00000399788.2:c.449C>G	p.Pro150Arg	p.P150R	ENST00000399788	NM_001042603.1	150	cCa/cGa	4/28	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.843777159726474	2		1244	699	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655240	45655240	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	528	1864	1	ENST00000407780.3:c.612G>T	p.Arg204Ser	p.R204S	ENST00000407780	NM_001283052.1	204	agG/agT	4/7	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.843777159726474	2		1865	1145	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878322	151878322	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	515	1280	0	ENST00000262189.6:c.6623G>C	p.Gly2208Ala	p.G2208A	ENST00000262189	NM_170606.2	2208	gGa/gCa	36/59	0.843777159726474	3	FACETS	1	0.994	1	0.613	0.587	0.639	CLONAL	1	TRUE	1	0.843777159726474	3		1280	1416	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561489	141561489	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	430	1896	0	ENST00000220592.5:c.1316A>G	p.Asn439Ser	p.N439S	ENST00000220592	NM_012154.3	439	aAc/aGc	11/19	0.236277531427	4	FACETS	1	0.992	1	0.298	0.283	0.313	INDETERMINATE	1	TRUE	0	0.843777159726474	4		1896	1576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0058331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	311	611	3	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.762800751910413	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.762800751910413	1		614	456	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023616	27023616	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	69	211	0	ENST00000324856.7:c.722C>G	p.Ser241Cys	p.S241C	ENST00000324856	NM_006015.4	241	tCc/tGc	1/20	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.762800751910413	2		211	175	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921510	39921510	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0058331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	305	890	0	ENST00000378444.4:c.4310C>G	p.Ser1437Ter	p.S1437*	ENST00000378444	NM_001123385.1	1437	tCa/tGa	10/15	0.762800751910413	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.762800751910413	1		890	494	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109319829	109319829	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	48	522	0	ENST00000436639.2:c.859G>C	p.Asp287His	p.D287H	ENST00000436639	NM_014454.2	287	Gat/Cat	5/10	1	2	FACETS	0.213	0.179	0.25	0.213	0.179	0.25	SUBCLONAL	1	TRUE	1	0.762800751910413	2		522	591	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166279	118166279	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	37	466	0	ENST00000369448.3:c.789C>G	p.Ile263Met	p.I263M	ENST00000369448	NM_017709.3	263	atC/atG	2/2	1	2	FACETS	0.209	0.172	0.251	0.209	0.172	0.251	SUBCLONAL	1	TRUE	1	0.762800751910413	2		466	464	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62009557	62009557	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0058331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	61	783	0	ENST00000392795.3:c.65C>G	p.Ser22Ter	p.S22*	ENST00000392795	NM_001039933.1	22	tCa/tGa	1/6	0.762800751910413	2	FACETS	0.212	0.182	0.244	0.106	0.091	0.122	SUBCLONAL	1	TRUE	0	0.762800751910413	2		783	756	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549385	5549385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	34	690	0	ENST00000397747.3:c.412G>A	p.Glu138Lys	p.E138K	ENST00000397747	NM_025239.3	138	Gag/Aag	4/7	1	2	FACETS	0.16	0.13	0.193	0.16	0.13	0.193	SUBCLONAL	1	TRUE	1	0.762800751910413	2		690	558	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880869	134880869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	188	637	0	ENST00000398015.3:c.1432G>A	p.Glu478Lys	p.E478K	ENST00000398015	NM_004441.4	478	Gag/Aag	7/16	0.750047213095516	4	FACETS	1	0.96	1	0.352	0.325	0.379	CLONAL	1	TRUE	1	0.762800751910413	4		637	823	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661293	227661293	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	276	933	0	ENST00000305123.5:c.2162G>T	p.Ser721Ile	p.S721I	ENST00000305123	NM_005544.2	721	aGc/aTc	1/2	1	2	FACETS	0.955	0.901	1	0.955	0.901	1	CLONAL	1	TRUE	1	0.762800751910413	2		933	758	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259248	36259316	+	inframe_deletion	In_Frame_Del	DEL	CACCTCCACCATGCTGCGGTCGCCGCTCCTCAGCTTGCCGGCCAGGGCAGCGCCGGCGTCCGGGGCGCC	CACCTCCACCATGCTGCGGTCGCCGCTCCTCAGCTTGCCGGCCAGGGCAGCGCCGGCGTCCGGGGCGCC	-	novel	NA	P-0058331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	218	399	0	ENST00000300305.3:c.175_243del	p.Gly59_Val81del	p.G59_V81del	ENST00000300305		59	GGCGCCCCGGACGCCGGCGCTGCCCTGGCCGGCAAGCTGAGGAGCGGCGACCGCAGCATGGTGGAGGTG/-	3/8	0.755692834602197	3	FACETS	0.987	0.933	1	0.658	0.622	0.694	CLONAL	2	TRUE	0	0.762800751910413	3		399	400	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520252	176520252	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs373745683	NA	P-0058331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	394	1002	0	ENST00000292408.4:c.1171C>G	p.Arg391Gly	p.R391G	ENST00000292408	NM_213647.1	391	Cga/Gga	9/18	0.224543313801526	3	FACETS	0.798	0.762	0.834	0.798	0.762	0.834	INDETERMINATE	2	TRUE	1	0.762800751910413	3		1002	894	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874446	76874446	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	114	279	0	ENST00000373344.5:c.5276A>T	p.His1759Leu	p.H1759L	ENST00000373344	NM_000489.3	1759	cAt/cTt	21/35	0.699551767314221	3	FACETS	1	0.98	1	0.643	0.587	0.701	CLONAL	1	TRUE	1	0.762800751910413	3		279	321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0058332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	98	609	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.248829257773451	4	FACETS	0.949	0.846	1	0.475	0.423	0.53	CLONAL	1	FALSE	2	0.313171737390206	4		609	866	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593504	48593504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	138	292	0	ENST00000342988.3:c.1255G>A	p.Gly419Arg	p.G419R	ENST00000342988	NM_005359.5	419	Ggg/Agg	10/12	0.238357269200564	3	FACETS	1	0.979	1	0.805	0.739	0.873	CLONAL	2	FALSE	0	0.313171737390206	3		292	422	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930598	32930598	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11571707	NA	P-0058332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	154	424	0	ENST00000380152.3:c.7469T>C	p.Ile2490Thr	p.I2490T	ENST00000380152		2490	aTa/aCa	15/27	0.313171737390206	5	FACETS	1	0.976	1	0.772	0.709	0.837	CLONAL	2	FALSE	2	0.313171737390206	5		424	624	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998478	100998478	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772295478	NA	P-0058332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	273	436	0	ENST00000325455.5:c.1324G>A	p.Ala442Thr	p.A442T	ENST00000325455	NM_001202474.3	442	Gca/Aca	1/8	0.313171737390206	4	FACETS	1	0.983	1	1	0.995	1	CLONAL	3	FALSE	2	0.313171737390206	4		436	695	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0058332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	192	660	1	ENST00000269305.4:c.96+1G>A		p.X32_splice	ENST00000269305	NM_001126112.2	32			0.248829257773451	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	FALSE	2	0.313171737390206	4		661	726	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348452	89348475	+	inframe_deletion	In_Frame_Del	DEL	GCTCGTCCCTGTGATGCCGCAGGA	GCTCGTCCCTGTGATGCCGCAGGA	-	rs534329317	NA	P-0058332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	162	1035	0	ENST00000301030.4:c.4475_4498del	p.Leu1492_Glu1499del	p.L1492_E1499del	ENST00000301030	NM_001256183.1	1492	cTCCTGCGGCATCACAGGGACGAGCag/cag	9/13	0.284098912457476	5	FACETS	1	0.987	1	0.469	0.429	0.51	CLONAL	1	FALSE	2	0.313171737390206	5		1035	1081	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202123063	202123063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	154	544	0	ENST00000358485.4:c.109G>A	p.Gly37Arg	p.G37R	ENST00000358485	NM_001080125.1	37	Ggg/Agg	1/9	0.313171737390206	5	FACETS	1	0.946	1	0.694	0.637	0.754	CLONAL	2	FALSE	2	0.313171737390206	5		544	694	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405615	139405615	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199505287	NA	P-0058332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	275	1041	2	ENST00000277541.6:c.2576C>T	p.Thr859Met	p.T859M	ENST00000277541	NM_017617.3	859	aCg/aTg	16/34	0.258318786833322	4	FACETS	0.987	0.926	1	0.987	0.926	1	CLONAL	2	FALSE	2	0.313171737390206	4		1043	1168	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243470	46243470	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	153	423	0	ENST00000334344.6:c.1823T>G	p.Ile608Ser	p.I608S	ENST00000334344	NM_152641.2	608	aTt/aGt	14/21	0.313171737390206	5	FACETS	1	0.971	1	0.749	0.688	0.813	CLONAL	2	FALSE	2	0.313171737390206	5		423	639	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391447	84391447	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	123	336	0	ENST00000321945.7:c.385G>T	p.Asp129Tyr	p.D129Y	ENST00000321945	NM_139076.2	129	Gac/Tac	5/9	0.238357269200564	3	FACETS	1	0.974	1	0.785	0.716	0.855	CLONAL	2	FALSE	0	0.313171737390206	3		336	386	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0058334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	311	293	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.49948468976021	3	FACETS	1	0.993	1	0.832	0.794	0.87	CLONAL	2	FALSE	0	0.566971092078408	3		293	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0058334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	599	898	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.566971092078408	2	FACETS	0.967	0.935	0.998	0.967	0.935	0.998	CLONAL	2	FALSE	0	0.566971092078408	2		898	1093	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857449	9857449	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774419037	NA	P-0058334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	487	736	1	ENST00000330684.3:c.3952C>T	p.Arg1318Trp	p.R1318W	ENST00000330684	NM_001134407.1	1318	Cgg/Tgg	13/13	0.543036654674745	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	FALSE	0	0.566971092078408	2		737	826	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322767	30322767	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	63	347	0	ENST00000322652.5:c.1780G>T	p.Glu594Ter	p.E594*	ENST00000322652	NM_015355.2	594	Gaa/Taa	14/16	0.535464637748951	4	FACETS	0.494	0.427	0.567	0.247	0.213	0.284	SUBCLONAL	1	FALSE	2	0.566971092078408	4		347	705	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575092	48575093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0058334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	292	464	0	ENST00000342988.3:c.289dup	p.Arg97ProfsTer7	p.R97Pfs*7	ENST00000342988	NM_005359.5	96	gcc/gCcc	3/12	0.543036654674745	2	FACETS	0.821	0.78	0.863	0.821	0.78	0.863	CLONAL	2	FALSE	0	0.566971092078408	2		464	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0058336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	639	380	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	1	0.997	1			1	INDETERMINATE	2	TRUE	NA	0.538891270248781	2		380	987	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0058336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	365	720	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.474943170876255	5	FACETS	0.979	0.928	1	0.653	0.619	0.687	CLONAL	2	TRUE	2	0.538891270248781	5		721	1251	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591888	48591888	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519739	NA	P-0058336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	241	438	0	ENST00000342988.3:c.1051G>C	p.Asp351His	p.D351H	ENST00000342988	NM_005359.5	351	Gat/Cat	9/12	0.538891270248781	2	FACETS	0.863	0.815	0.912	0.863	0.815	0.912	CLONAL	2	TRUE	0	0.538891270248781	2		438	518	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644501	3644501	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749913190	NA	P-0058336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	199	942	0	ENST00000294008.3:c.2113G>A	p.Ala705Thr	p.A705T	ENST00000294008	NM_032444.2	705	Gcc/Acc	10/15	0.143564608409366	4	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.538891270248781	4		942	1045	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406571	70406597	+	inframe_deletion	In_Frame_Del	DEL	GTGGAATTACAGTGGTTTCTACCAAAA	GTGGAATTACAGTGGTTTCTACCAAAA	-	novel	NA	P-0058336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	342	788	1	ENST00000373644.4:c.4088_4114del	p.Gly1363_Ser1371del	p.G1363_S1371del	ENST00000373644	NM_030625.2	1362	gGTGGAATTACAGTGGTTTCTACCAAAAgt/ggt	4/12	0.538891270248781	3	FACETS	0.901	0.856	0.947	0.901	0.856	0.947	CLONAL	2	TRUE	1	0.538891270248781	3		789	894	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151871268	151871268	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	122	501	0	ENST00000262189.6:c.9322A>C	p.Asn3108His	p.N3108H	ENST00000262189	NM_170606.2	3108	Aat/Cat	39/59	0.500071868474753	4	FACETS	0.935	0.846	1	0.468	0.423	0.515	CLONAL	1	TRUE	2	0.538891270248781	4		501	745	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs587781702	NA	P-0058337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	418	906	0	ENST00000269305.4:c.920-1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.212853450547399	3	FACETS	1	0.986	1	0.725	0.69	0.76	CLONAL	2	TRUE	0	0.341638384770527	3		906	1317	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970900	21970900	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0058337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	351	873	0	ENST00000304494.5:c.457+1G>A		p.X153_splice	ENST00000304494	NM_000077.4	153			1	2	FACETS	0.957	0.907	1	1	0.996	1	CLONAL	2	TRUE	1	0.341638384770527	2		873	1074	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039620	47039620	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	340	914	1	ENST00000377604.3:c.1072C>T	p.Gln358Ter	p.Q358*	ENST00000377604	NM_001204468.1	358	Cag/Tag	11/24	NA	2	FACETS	0.906	0.858	0.955			1	INDETERMINATE	2	TRUE	NA	0.341638384770527	2		915	1098	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677894	58677894	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1251	147	685	0	ENST00000305921.3:c.119C>T	p.Ser40Leu	p.S40L	ENST00000305921	NM_003620.3	40	tCg/tTg	1/6	0.341638384770527	7	FACETS	1	0.969	1	0.228	0.207	0.25	CLONAL	1	TRUE	2	0.341638384770527	7		685	1398	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639779	3639779	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1529	415	1216	0	ENST00000294008.3:c.3860T>A	p.Val1287Glu	p.V1287E	ENST00000294008	NM_032444.2	1287	gTg/gAg	12/15	0.247531127907458	4	FACETS	0.838	0.795	0.882	0.838	0.795	0.882	CLONAL	2	TRUE	2	0.341638384770527	4		1216	1944	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618766	37618766	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2241	378	823	0	ENST00000447079.4:c.442T>C	p.Ser148Pro	p.S148P	ENST00000447079	NM_015083.1	148	Tcg/Ccg	1/14	0.341638384770527	9	FACETS	0.928	0.876	0.981			1	CLONAL	2	TRUE	NA	0.341638384770527	9		823	2619	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212704	27212704	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0058337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	54	879	0	ENST00000380036.4:c.2687-1G>C		p.X896_splice	ENST00000380036	NM_000459.3	896			1	2	FACETS	0.303	0.257	0.353	0.303	0.257	0.353	SUBCLONAL	1	TRUE	1	0.341638384770527	2		879	1045	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0058338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	23	605	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.254736093234405	1	FACETS	0.072	0.055	0.091	0.072	0.055	0.091	INDETERMINATE	1	TRUE	0	0.479754473076811	1		605	1011	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0058338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	54	290	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.255218304007258	0	FACETS	0.332	0.284	0.383			1	INDETERMINATE	1	TRUE	0	0.479754473076811	0		290	353	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682991	241682991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226883651	NA	P-0058338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	181	745	0	ENST00000366560.3:c.32C>T	p.Ser11Leu	p.S11L	ENST00000366560	NM_000143.3	11	tCg/tTg	1/10	NA	2	FACETS	0.943	0.871	1			1	INDETERMINATE	1	TRUE	NA	0.479754473076811	2		745	800	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685270	89685271	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0058338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	40	283	0	ENST00000371953.3:c.165_166del	p.Arg55SerfsTer7	p.R55Sfs*7	ENST00000371953	NM_000314.4	55	agGTtt/agtt	3/9	0.255218304007258	0	FACETS	0.258	0.215	0.306			1	INDETERMINATE	1	TRUE	0	0.479754473076811	0		283	336	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103270	119103270	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	216	575	0	ENST00000264033.4:c.308A>T	p.Glu103Val	p.E103V	ENST00000264033	NM_005188.3	103	gAg/gTg	2/16	0.479754473076811	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.479754473076811	1		575	646	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804362	43804362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	156	781	0	ENST00000372470.3:c.362C>T	p.Thr121Ile	p.T121I	ENST00000372470	NM_005373.2	121	aCt/aTt	3/12	0.672429039165464	4	FACETS	0.945	0.875	1	0.945	0.875	1	CLONAL	2	TRUE	2	0.67973489939659	4		781	408	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630535	47630535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1376434666	NA	P-0058339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	163	1044	1	ENST00000233146.2:c.205C>T	p.Pro69Ser	p.P69S	ENST00000233146	NM_000251.2	69	Ccg/Tcg	1/16	0.67973489939659	6	FACETS	0.962	0.888	1	0.481	0.444	0.52	CLONAL	2	TRUE	2	0.67973489939659	6		1045	588	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912361	32912361	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41293485	NA	P-0058341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	113	419	0	ENST00000380152.3:c.3869G>A	p.Cys1290Tyr	p.C1290Y	ENST00000380152		1290	tGc/tAc	11/27	0.30758926412649	2	FACETS	1	0.976	1	0.626	0.565	0.689	CLONAL	1	TRUE	0	0.355590639842322	2		419	508	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0058342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	279	293	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.466598280927293	2	FACETS	1	0.972	1	0.519	0.492	0.547	INDETERMINATE	1	TRUE	0	0.882410943228177	2		293	609	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0058342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	265	584	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.466598280927293	2	FACETS	1	0.984	1	0.546	0.517	0.575	INDETERMINATE	1	TRUE	0	0.882410943228177	2		584	550	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779782	3779782	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	250	968	0	ENST00000262367.5:c.5266C>T	p.Gln1756Ter	p.Q1756*	ENST00000262367	NM_004380.2	1756	Cag/Tag	31/31	1	2	FACETS	0.57	0.533	0.608	0.57	0.533	0.608	SUBCLONAL	1	TRUE	1	0.882410943228177	2		968	994	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738660	145738660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs897118164	NA	P-0058342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	230	1150	1	ENST00000428558.2:c.2404G>A	p.Val802Met	p.V802M	ENST00000428558	NM_004260.3	802	Gtg/Atg	15/22	1	2	FACETS	0.519	0.484	0.556	0.519	0.484	0.556	SUBCLONAL	1	TRUE	1	0.882410943228177	2		1151	1004	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107128	27107129	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACCACTCAGAGTTTACTCTGTACGT	novel	NA	P-0058342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	226	698	0	ENST00000324856.7:c.6763_6764insTACCACTCAGAGTTTACTCTGTACG	p.Glu2255ValfsTer31	p.E2255Vfs*31	ENST00000324856	NM_006015.4	2247	aac/aACCACTCAGAGTTTACTCTGTACGTac	20/20	NA	2	FACETS	0.532	0.496	0.569			1	INDETERMINATE	1	TRUE	NA	0.882410943228177	2		698	963	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024036	31024036	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	203	829	0	ENST00000375687.4:c.3521A>G	p.Lys1174Arg	p.K1174R	ENST00000375687	NM_015338.5	1174	aAg/aGg	13/13	1	2	FACETS	0.483	0.448	0.519	0.483	0.448	0.519	SUBCLONAL	1	TRUE	1	0.882410943228177	2		829	953	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389399	8389400	+	stop_gained	Nonsense_Mutation	DNP	CT	CT	AC	novel	NA	P-0058342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	60	440	0	ENST00000356435.5:c.4218_4219delinsGT	p.Gly1407Ter	p.G1407*	ENST00000356435		1406	ccAGga/ccGTga	26/35	1	2	FACETS	0.241	0.207	0.278	0.241	0.207	0.278	SUBCLONAL	1	TRUE	1	0.882410943228177	2		440	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578476	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTGCCGGGCGG	GGGTGCCGGGCGG	-	rs876659215	NA	P-0058345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	788	1089	0	ENST00000269305.4:c.454_466del	p.Pro152AlafsTer14	p.P152Afs*14	ENST00000269305	NM_001126112.2	152	CCGCCCGGCACCCgc/gc	5/11	0.712715264466728	2	FACETS	0.91	0.887	0.932	0.91	0.887	0.932	CLONAL	2	TRUE	0	0.742156576614011	2		1089	1167	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918943	76918943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782726588	NA	P-0058345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1181	131	672	1	ENST00000373344.5:c.4048G>A	p.Gly1350Arg	p.G1350R	ENST00000373344	NM_000489.3	1350	Gga/Aga	12/35	0.742156576614011	3	FACETS	0.369	0.333	0.406	0.184	0.166	0.203	SUBCLONAL	1	TRUE	1	0.742156576614011	3		673	1312	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173713	108173713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	192	410	2	ENST00000278616.4:c.5453G>A	p.Gly1818Asp	p.G1818D	ENST00000278616	NM_000051.3	1818	gGc/gAc	36/63	0.742156576614011	2	FACETS	1	0.987	1	0.603	0.565	0.642	CLONAL	1	TRUE	0	0.742156576614011	2		412	429	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5246012	5246012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558548676	NA	P-0058345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	473	947	0	ENST00000357368.4:c.763G>A	p.Glu255Lys	p.E255K	ENST00000357368	NM_002850.3	255	Gag/Aag	10/38	0.194864191240756	4	FACETS	0.863	0.826	0.901	0.863	0.826	0.901	INDETERMINATE	2	TRUE	2	0.742156576614011	4		947	1286	SUCCESS
APC	324	MSKCC	GRCh37	5	112172545	112173567	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCACTACCATGCCCGGCTAATTTTTGTATTTTTAGTAGAGACAGGGTTTCACCATGTTGGCCAGGCTGGTCTTGATCTCCTAATCTCAGGTGATCCGCCTGCCTCAGCCTCCTAAAGTGCTGGGATTACAGGCATGAGCCACTGTGTCTGGCCAAGAGCACTCGTAAGAAGGATGGCAGTATCACAAAATCAAGCCAGAGATACAGAGATTACTCTAAAAAGTAAGTGTTCTAATCTAAGAGCTTATAATGTGCACTGACTGCAGAAAAATCTTCAATCAATTCTATCTACCTCTTCCAAGATAACTCAATATCAATATCAGAGTGGCACCCAACCATAGATTAAATTACCACAAAGTTCCTATTCAACATAGGATTTCATGATATAGTTTTTAAATTGGGAAACTGTTATATGAATAGAGTAAATGTATGTGCCCCACCCCCTGCAAATGTTTTAAGCTATTGGGTCAGAATAGGAAATGTAGAATTGACAAAAAATAACACCTTTACTTTTTTTAGTGTGACAGATTAGTACTTTAAAACATTAAACATTACATGAAATTAGAACAAAAGGAGATGTGGAATACTTGGAATTTATAGGATAATTGGTACAATCATATTATGCCTTTTGTCTTCTATCCTTTTATTTGTTGTTACTGCATACACATTGTGACCTTAATTTTGTGATCTCTTGATTTTATTTCAGGCAAATCCTAAGAGAGAACAACTGTCTACAAACTTTATTACAACACTTAAAATCTCATAGTTTGACAATAGTCAGTAATGCATGTGGAACTTTGTGGAATCTCTCAGCAAGAAATCCTAAAGACCAGGAAGCATTATGGGACATGGGGGCAGTTAGCATGCTCAAGAACCTCATTCATTCAAAGCACAAAATGATTGCTATGGGAAGTGCTGCAGCTTTAAGGAATCTCATGGCAAATAGGCCTGCGAAGTACAAGGATGCCAATATTATGTCTCCTGGCTCAAGCTTGCCATCTCTTCATGTTAGGAAACAAAAAGC	GCACTACCATGCCCGGCTAATTTTTGTATTTTTAGTAGAGACAGGGTTTCACCATGTTGGCCAGGCTGGTCTTGATCTCCTAATCTCAGGTGATCCGCCTGCCTCAGCCTCCTAAAGTGCTGGGATTACAGGCATGAGCCACTGTGTCTGGCCAAGAGCACTCGTAAGAAGGATGGCAGTATCACAAAATCAAGCCAGAGATACAGAGATTACTCTAAAAAGTAAGTGTTCTAATCTAAGAGCTTATAATGTGCACTGACTGCAGAAAAATCTTCAATCAATTCTATCTACCTCTTCCAAGATAACTCAATATCAATATCAGAGTGGCACCCAACCATAGATTAAATTACCACAAAGTTCCTATTCAACATAGGATTTCATGATATAGTTTTTAAATTGGGAAACTGTTATATGAATAGAGTAAATGTATGTGCCCCACCCCCTGCAAATGTTTTAAGCTATTGGGTCAGAATAGGAAATGTAGAATTGACAAAAAATAACACCTTTACTTTTTTTAGTGTGACAGATTAGTACTTTAAAACATTAAACATTACATGAAATTAGAACAAAAGGAGATGTGGAATACTTGGAATTTATAGGATAATTGGTACAATCATATTATGCCTTTTGTCTTCTATCCTTTTATTTGTTGTTACTGCATACACATTGTGACCTTAATTTTGTGATCTCTTGATTTTATTTCAGGCAAATCCTAAGAGAGAACAACTGTCTACAAACTTTATTACAACACTTAAAATCTCATAGTTTGACAATAGTCAGTAATGCATGTGGAACTTTGTGGAATCTCTCAGCAAGAAATCCTAAAGACCAGGAAGCATTATGGGACATGGGGGCAGTTAGCATGCTCAAGAACCTCATTCATTCAAAGCACAAAATGATTGCTATGGGAAGTGCTGCAGCTTTAAGGAATCTCATGGCAAATAGGCCTGCGAAGTACAAGGATGCCAATATTATGTCTCCTGGCTCAAGCTTGCCATCTCTTCATGTTAGGAAACAAAAAGC	-	novel	NA	P-0058345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	49	1	0	ENST00000257430.4:c.1959-705_2276del		p.X653_splice	ENST00000257430	NM_000038.5	653		16/16	0.225942381705919	2	FACETS	0.333	0.283	0.389	0.167	0.141	0.195	INDETERMINATE	1	TRUE	0	0.742156576614011	2		1	396	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843455	3843455	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	222	536	0	ENST00000262367.5:c.1148C>T	p.Pro383Leu	p.P383L	ENST00000262367	NM_004380.2	383	cCg/cTg	4/31	0.792644255168969	2	FACETS	0.577	0.537	0.618	0.288	0.268	0.309	SUBCLONAL	1	TRUE	0	0.792644255168969	2		536	971	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0058347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	300	558	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	0.973	0.922	1	0.973	0.922	1	CLONAL	1	TRUE	1	0.84861950681224	2		558	727	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	369	727	1	ENST00000347630.2:c.399C>A	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttA	6/11	1	2	FACETS	0.949	0.904	0.995	0.949	0.904	0.995	CLONAL	1	TRUE	1	0.84861950681224	2		728	916	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528244	157528244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762342896	NA	P-0058347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	395	871	0	ENST00000346085.5:c.5969G>A	p.Arg1990Gln	p.R1990Q	ENST00000346085	NM_020732.3	1990	cGa/cAa	20/20	1	2	FACETS	0.952	0.908	0.996	0.952	0.908	0.996	CLONAL	1	TRUE	1	0.84861950681224	2		871	978	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	125	557	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.86	0.779	0.946	0.86	0.779	0.946	CLONAL	1	TRUE	1	0.391567802715765	2		558	742	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	48	729	8	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.342	0.288	0.401	0.342	0.288	0.401	SUBCLONAL	1	TRUE	1	0.391567802715765	2		737	717	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	70	1286	7	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	1	2	FACETS	0.415	0.361	0.474	0.415	0.361	0.474	SUBCLONAL	1	TRUE	1	0.391567802715765	2		1293	861	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	119	608	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.352078679437761	2	FACETS	0.81	0.739	0.884	0.81	0.739	0.884	CLONAL	2	TRUE	0	0.391567802715765	2		609	375	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101050	41101050	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs192944843	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	152	1154	1	ENST00000373198.4:c.1306G>A	p.Glu436Lys	p.E436K	ENST00000373198	NM_133170.3	436	Gag/Aag	8/32	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.391567802715765	2		1155	712	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660469	67660469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	96	627	0	ENST00000264010.4:c.1369C>T	p.Arg457Ter	p.R457*	ENST00000264010	NM_006565.3	457	Cga/Tga	8/12	1	2	FACETS	0.947	0.846	1	0.947	0.846	1	CLONAL	1	TRUE	1	0.391567802715765	2		627	518	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934037	39934037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	132	1074	0	ENST00000378444.4:c.562C>T	p.Arg188Trp	p.R188W	ENST00000378444	NM_001123385.1	188	Cgg/Tgg	4/15	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.391567802715765	2		1074	644	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972626	32972626	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs11571833	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	87	608	0	ENST00000380152.3:c.9976A>T	p.Lys3326Ter	p.K3326*	ENST00000380152		3326	Aaa/Taa	27/27	1	2	FACETS	0.941	0.837	1	0.941	0.837	1	CLONAL	1	TRUE	1	0.391567802715765	2		608	472	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272337	15272337	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs771517374	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	107	1139	11	ENST00000263388.2:c.6102del	p.Gly2035ValfsTer50	p.G2035Vfs*50	ENST00000263388	NM_000435.2	2034	ccC/cc	33/33	1	2	FACETS	0.863	0.776	0.956	0.863	0.776	0.956	CLONAL	1	TRUE	1	0.391567802715765	2		1150	633	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651264	45651264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772294235	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	54	1137	3	ENST00000407780.3:c.761C>T	p.Ala254Val	p.A254V	ENST00000407780	NM_001283052.1	254	gCg/gTg	5/7	1	2	FACETS	0.355	0.302	0.412	0.355	0.302	0.412	SUBCLONAL	1	TRUE	1	0.391567802715765	2		1140	778	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135777085	135777085	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1331635112	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	85	745	0	ENST00000298552.3:c.2393C>T	p.Thr798Met	p.T798M	ENST00000298552	NM_001162426.1	798	aCg/aTg	19/23	1	2	FACETS	0.727	0.644	0.817	0.727	0.644	0.817	SUBCLONAL	1	TRUE	1	0.391567802715765	2		745	597	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	107	588	0	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	1	2	FACETS	0.88	0.791	0.974	0.88	0.791	0.974	CLONAL	1	TRUE	1	0.391567802715765	2		588	621	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156719	20156719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	84	617	1	ENST00000379607.5:c.38G>A	p.Arg13His	p.R13H	ENST00000379607	NM_001412.3	13	cGc/cAc	2/7	1	2	FACETS	0.858	0.76	0.962	0.858	0.76	0.962	CLONAL	1	TRUE	1	0.391567802715765	2		618	500	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949994	44949994	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1450363794	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	78	369	0	ENST00000377967.4:c.3763C>T	p.Arg1255Trp	p.R1255W	ENST00000377967	NM_021140.2	1255	Cgg/Tgg	26/29	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.391567802715765	2		369	311	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564644	55564644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs115585711	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	28	888	0	ENST00000288135.5:c.532G>A	p.Ala178Thr	p.A178T	ENST00000288135	NM_000222.2	178	Gcc/Acc	3/21	1	2	FACETS	0.285	0.227	0.351	0.285	0.227	0.351	SUBCLONAL	1	TRUE	1	0.391567802715765	2		888	502	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589618	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519838	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	33	202	0	ENST00000274335.5:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000274335		461	Cga/Tga	10/15	1	2	FACETS	0.83	0.682	0.994	0.83	0.682	0.994	CLONAL	1	TRUE	1	0.391567802715765	2		202	203	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481621	56481621	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	172	1150	0	ENST00000267101.3:c.656T>G	p.Phe219Cys	p.F219C	ENST00000267101	NM_001982.3	219	tTt/tGt	6/28	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.391567802715765	2		1150	878	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101100	27101100	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1257406381	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	131	1163	0	ENST00000324856.7:c.4382G>A	p.Arg1461Gln	p.R1461Q	ENST00000324856	NM_006015.4	1461	cGa/cAa	18/20	1	2	FACETS	0.933	0.848	1	0.933	0.848	1	CLONAL	1	TRUE	1	0.391567802715765	2		1163	717	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129454	30129454	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1284498604	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	133	1082	0	ENST00000263025.4:c.574G>A	p.Asp192Asn	p.D192N	ENST00000263025	NM_002746.2	192	Gat/Aat	4/9	1	2	FACETS	0.902	0.82	0.988	0.902	0.82	0.988	CLONAL	1	TRUE	1	0.391567802715765	2		1082	753	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794062	42794062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	93	965	1	ENST00000575354.2:c.1423G>A	p.Glu475Lys	p.E475K	ENST00000575354	NM_015125.3	475	Gag/Aag	9/20	1	2	FACETS	0.781	0.696	0.872	0.781	0.696	0.872	SUBCLONAL	1	TRUE	1	0.391567802715765	2		966	608	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220895	36220895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	56	501	0	ENST00000222270.7:c.4945G>A	p.Ala1649Thr	p.A1649T	ENST00000222270	NM_014727.1	1649	Gcc/Acc	23/37	1	2	FACETS	0.856	0.738	0.984	0.856	0.738	0.984	CLONAL	1	TRUE	1	0.391567802715765	2		501	334	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383903	15383903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324868843	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	101	752	2	ENST00000263377.2:c.8C>T	p.Ala3Val	p.A3V	ENST00000263377	NM_058243.2	3	gCg/gTg	2/20	1	2	FACETS	0.955	0.857	1	0.955	0.857	1	CLONAL	1	TRUE	1	0.391567802715765	2		754	540	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871940	45871940	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142462393	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	157	1005	0	ENST00000391945.4:c.308C>T	p.Pro103Leu	p.P103L	ENST00000391945	NM_000400.3	103	cCg/cTg	5/23	1	2	FACETS	0.99	0.908	1	0.99	0.908	1	CLONAL	1	TRUE	1	0.391567802715765	2		1005	810	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931472	131931472	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28903092	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	71	699	0	ENST00000265335.6:c.2177G>A	p.Arg726His	p.R726H	ENST00000265335		726	cGt/cAt	13/25	1	2	FACETS	0.819	0.717	0.927	0.819	0.717	0.927	CLONAL	1	TRUE	1	0.391567802715765	2		699	443	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815644	139815644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763841128	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	84	932	0	ENST00000247668.2:c.1115G>A	p.Arg372His	p.R372H	ENST00000247668	NM_021138.3	372	cGc/cAc	9/11	1	2	FACETS	0.75	0.664	0.842	0.75	0.664	0.842	SUBCLONAL	1	TRUE	1	0.391567802715765	2		932	572	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778500	3778500	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779996604	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	45	1382	0	ENST00000262367.5:c.6548C>T	p.Ala2183Val	p.A2183V	ENST00000262367	NM_004380.2	2183	gCg/gTg	31/31	1	2	FACETS	0.286	0.24	0.338	0.286	0.24	0.338	SUBCLONAL	1	TRUE	1	0.391567802715765	2		1382	803	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102121	27102121	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	99	780	0	ENST00000324856.7:c.5047G>T	p.Glu1683Ter	p.E1683*	ENST00000324856	NM_006015.4	1683	Gag/Tag	19/20	1	2	FACETS	0.853	0.763	0.948	0.853	0.763	0.948	CLONAL	1	TRUE	1	0.391567802715765	2		780	593	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197299	106197299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	69	573	1	ENST00000380013.4:c.5632C>T	p.Arg1878Cys	p.R1878C	ENST00000380013	NM_001127208.2	1878	Cgt/Tgt	11/11	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.391567802715765	2		574	346	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420628	49420628	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	123	1178	2	ENST00000301067.7:c.15121G>A	p.Gly5041Arg	p.G5041R	ENST00000301067	NM_003482.3	5041	Ggg/Agg	48/54	1	2	FACETS	0.831	0.752	0.914	0.831	0.752	0.914	CLONAL	1	TRUE	1	0.391567802715765	2		1180	756	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244151	153244151	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	38	870	0	ENST00000281708.4:c.2006G>T	p.Gly669Val	p.G669V	ENST00000281708	NM_033632.3	669	gGg/gTg	12/12	1	2	FACETS	0.262	0.216	0.314	0.262	0.216	0.314	SUBCLONAL	1	TRUE	1	0.391567802715765	2		870	740	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396824	139396824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356199208	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	140	959	4	ENST00000277541.6:c.5284C>T	p.Arg1762Trp	p.R1762W	ENST00000277541	NM_017617.3	1762	Cgg/Tgg	28/34	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.391567802715765	2		963	636	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246943	10246943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749413587	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	135	1196	0	ENST00000340748.4:c.4462G>A	p.Ala1488Thr	p.A1488T	ENST00000340748		1488	Gca/Aca	37/40	1	2	FACETS	0.928	0.845	1	0.928	0.845	1	CLONAL	1	TRUE	1	0.391567802715765	2		1196	743	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405122	139405122	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	40	1395	0	ENST00000277541.6:c.2723T>C	p.Ile908Thr	p.I908T	ENST00000277541	NM_017617.3	908	aTc/aCc	17/34	1	2	FACETS	0.259	0.214	0.31	0.259	0.214	0.31	SUBCLONAL	1	TRUE	1	0.391567802715765	2		1395	788	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255775	16255775	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199847404	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	93	636	0	ENST00000375759.3:c.3040G>A	p.Val1014Met	p.V1014M	ENST00000375759	NM_015001.2	1014	Gtg/Atg	11/15	1	2	FACETS	0.851	0.759	0.949	0.851	0.759	0.949	CLONAL	1	TRUE	1	0.391567802715765	2		636	558	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589151	67589152	+	inframe_insertion	In_Frame_Ins	INS	-	-	AATCAA	novel	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	33	427	0	ENST00000274335.5:c.1143_1148dup	p.Lys382_Ile383dup	p.K382_I383dup	ENST00000274335		382	tta/ttAATCAAa	9/15	1	2	FACETS	0.664	0.543	0.798	0.664	0.543	0.798	SUBCLONAL	1	TRUE	1	0.391567802715765	2		427	254	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40740954	40740954	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs778976738	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	129	1293	4	ENST00000392038.2:c.1364G>A	p.Arg455His	p.R455H	ENST00000392038	NM_001626.4	455	cGc/cAc	13/14	1	2	FACETS	0.876	0.795	0.961	0.876	0.795	0.961	CLONAL	1	TRUE	1	0.391567802715765	2		1297	752	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459187	120459187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	119	889	4	ENST00000256646.2:c.6158G>A	p.Arg2053His	p.R2053H	ENST00000256646	NM_024408.3	2053	cGc/cAc	34/34	1	2	FACETS	0.969	0.877	1	0.969	0.877	1	CLONAL	1	TRUE	1	0.391567802715765	2		893	627	SUCCESS
ATM	472	MSKCC	GRCh37	11	108225596	108225596	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782497	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	24	488	1	ENST00000278616.4:c.8845G>A	p.Val2949Ile	p.V2949I	ENST00000278616	NM_000051.3	2949	Gta/Ata	61/63	1	2	FACETS	0.355	0.278	0.444	0.355	0.278	0.444	SUBCLONAL	1	TRUE	1	0.391567802715765	2		489	345	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042178	14042178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140726146	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	39	405	4	ENST00000311895.7:c.2725G>A	p.Val909Ile	p.V909I	ENST00000311895	NM_005236.2	909	Gta/Ata	11/11	1	2	FACETS	0.636	0.529	0.755	0.636	0.529	0.755	SUBCLONAL	1	TRUE	1	0.391567802715765	2		409	313	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805324	89805324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370507983	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	113	1052	1	ENST00000389301.3:c.4226G>A	p.Arg1409Gln	p.R1409Q	ENST00000389301	NM_000135.2	1409	cGg/cAg	42/43	1	2	FACETS	0.865	0.78	0.955	0.865	0.78	0.955	CLONAL	1	TRUE	1	0.391567802715765	2		1053	667	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212342	36212342	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1172835308	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	145	1211	2	ENST00000222270.7:c.2093G>A	p.Arg698His	p.R698H	ENST00000222270	NM_014727.1	698	cGc/cAc	3/37	1	2	FACETS	0.934	0.853	1	0.934	0.853	1	CLONAL	1	TRUE	1	0.391567802715765	2		1213	793	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856397	45856397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147224585	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	112	1224	1	ENST00000391945.4:c.1775G>A	p.Arg592His	p.R592H	ENST00000391945	NM_000400.3	592	cGc/cAc	19/23	1	2	FACETS	0.817	0.736	0.903	0.817	0.736	0.903	CLONAL	1	TRUE	1	0.391567802715765	2		1225	700	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437203	220437203	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	51	1514	0	ENST00000243786.2:c.107T>G	p.Leu36Arg	p.L36R	ENST00000243786	NM_002191.3	36	cTg/cGg	1/2	1	2	FACETS	0.326	0.276	0.381	0.326	0.276	0.381	SUBCLONAL	1	TRUE	1	0.391567802715765	2		1514	799	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47088008	47088008	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	100	730	0	ENST00000409792.3:c.7067T>C	p.Val2356Ala	p.V2356A	ENST00000409792	NM_014159.6	2356	gTt/gCt	16/21	1	2	FACETS	0.781	0.698	0.869	0.781	0.698	0.869	SUBCLONAL	1	TRUE	1	0.391567802715765	2		730	654	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225521	26225521	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	105	976	0	ENST00000360408.1:c.139G>A	p.Val47Met	p.V47M	ENST00000360408	NM_003532.2	47	Gtg/Atg	1/1	1	2	FACETS	0.833	0.747	0.923	0.833	0.747	0.923	CLONAL	1	TRUE	1	0.391567802715765	2		976	644	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553171	106553171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368185616	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	107	953	1	ENST00000369096.4:c.1136C>T	p.Ala379Val	p.A379V	ENST00000369096	NM_001198.3	379	gCg/gTg	5/7	1	2	FACETS	0.939	0.845	1	0.939	0.845	1	CLONAL	1	TRUE	1	0.391567802715765	2		954	582	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956760	68956760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745582647	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	115	979	1	ENST00000288368.4:c.878G>A	p.Arg293Gln	p.R293Q	ENST00000288368	NM_024870.2	293	cGg/cAg	8/40	1	2	FACETS	0.775	0.698	0.856	0.775	0.698	0.856	SUBCLONAL	1	TRUE	1	0.391567802715765	2		980	758	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141570578	141570578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	109	1030	2	ENST00000220592.5:c.550G>A	p.Ala184Thr	p.A184T	ENST00000220592	NM_012154.3	184	Gcg/Acg	5/19	1	2	FACETS	0.789	0.709	0.873	0.789	0.709	0.873	SUBCLONAL	1	TRUE	1	0.391567802715765	2		1032	706	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742874	145742874	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	27	321	0	ENST00000428558.2:c.137G>C	p.Arg46Pro	p.R46P	ENST00000428558	NM_004260.3	46	cGc/cCc	3/22	1	2	FACETS	0.938	0.756	1	0.938	0.756	1	CLONAL	1	TRUE	1	0.391567802715765	2		321	147	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225141	53225141	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	175	1114	0	ENST00000375401.3:c.3077T>C	p.Leu1026Pro	p.L1026P	ENST00000375401	NM_004187.3	1026	cTt/cCt	20/26	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.391567802715765	2		1114	859	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426324	49426324	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	670	1313	0	ENST00000301067.7:c.12164del	p.Pro4055LeufsTer11	p.P4055Lfs*11	ENST00000301067	NM_003482.3	4055	cCt/ct	39/54	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.786391469345141	2		1313	1593	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555774	21555774	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	468	874	0	ENST00000382592.4:c.2496A>T	p.Arg832Ser	p.R832S	ENST00000382592	NM_014572.2	832	agA/agT	6/8	0.786391469345141	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.786391469345141	1		874	704	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3651186	3651186	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	584	951	0	ENST00000294008.3:c.957G>T	p.Leu319Phe	p.L319F	ENST00000294008	NM_032444.2	319	ttG/ttT	5/15	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.786391469345141	2		951	1375	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984790	72984790	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	547	1038	0	ENST00000268489.5:c.2794G>C	p.Glu932Gln	p.E932Q	ENST00000268489	NM_006885.3	932	Gag/Cag	3/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.786391469345141	2		1038	1369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs864622237	NA	P-0058349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	552	567	0	ENST00000269305.4:c.700T>C	p.Tyr234His	p.Y234H	ENST00000269305	NM_001126112.2	234	Tac/Cac	7/11	0.786391469345141	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.786391469345141	1		567	782	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745983	745983	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	137	646	0	ENST00000314574.4:c.539G>T	p.Gly180Val	p.G180V	ENST00000314574	NM_005433.3	180	gGt/gTt	5/12	0.277044184082684	3	FACETS	0.75	0.684	0.819	0.375	0.342	0.41	INDETERMINATE	1	TRUE	1	0.786391469345141	3		646	647	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210766	2210766	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	532	921	0	ENST00000398665.3:c.1266del	p.Glu423SerfsTer66	p.E423Sfs*66	ENST00000398665	NM_032482.2	421	aaC/aa	14/28	NA	2	FACETS	0.957	0.918	0.996			1	INDETERMINATE	1	TRUE	NA	0.786391469345141	2		921	1414	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920325	50920325	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	612	1416	0	ENST00000440232.2:c.3094del	p.Arg1032GlyfsTer13	p.R1032Gfs*13	ENST00000440232	NM_002691.3	1031	Ccc/cc	25/27	1	2	FACETS	0.966	0.93	1	0.966	0.93	1	CLONAL	1	TRUE	1	0.786391469345141	2		1416	1611	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672697	86672698	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GC	GC	T	novel	NA	P-0058349-T01-IM6	NA	A	A	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	109	315	1	ENST00000274376.6:c.2185-1_2185delinsT		p.X729_splice	ENST00000274376	NM_002890.2	729		17/25	0.786391469345141	1	FACETS	0.935	0.867	1	0.935	0.867	1	CLONAL	1	TRUE	0	0.786391469345141	1		316	180	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937121	39937121	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	581	1117	0	ENST00000378444.4:c.62G>T	p.Arg21Leu	p.R21L	ENST00000378444	NM_001123385.1	21	cGc/cTc	2/15	1	2	FACETS	0.949	0.912	0.986	0.949	0.912	0.986	CLONAL	1	TRUE	1	0.786391469345141	2		1117	1557	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412120	63412120	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	634	1259	0	ENST00000330258.3:c.1047G>C	p.Gln349His	p.Q349H	ENST00000330258	NM_152424.3	349	caG/caC	2/2	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.786391469345141	2		1259	1527	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123189998	123189998	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	232	662	0	ENST00000218089.9:c.1217C>A	p.Thr406Asn	p.T406N	ENST00000218089	NM_001042749.1	406	aCt/aAt	14/35	1	2	FACETS	0.897	0.841	0.953	0.897	0.841	0.953	CLONAL	1	TRUE	1	0.786391469345141	2		662	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0058350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	301	639	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.653098285817839	1	FACETS	0.948	0.9	0.996	0.948	0.9	0.996	CLONAL	1	TRUE	0	0.653098285817839	1		639	655	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884917	151884917	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	143	346	0	ENST00000262189.6:c.4676T>A	p.Met1559Lys	p.M1559K	ENST00000262189	NM_170606.2	1559	aTg/aAg	32/59	1	2	FACETS	0.903	0.829	0.979	0.903	0.829	0.979	CLONAL	1	TRUE	1	0.653098285817839	2		346	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0058352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	556	681	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.424229875823826	3	FACETS	0.893	0.861	0.924	0.893	0.861	0.924	CLONAL	3	TRUE	0	0.476377916784763	3		681	1079	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552152	29552152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199474738	NA	P-0058352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	50	319	0	ENST00000356175.3:c.1885G>A	p.Gly629Arg	p.G629R	ENST00000356175	NM_000267.3	629	Ggg/Agg	17/57	1	2	FACETS	0.729	0.623	0.844	0.729	0.623	0.844	SUBCLONAL	1	TRUE	1	0.476377916784763	2		319	288	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098807	178098807	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	173	732	0	ENST00000397062.3:c.238A>G	p.Thr80Ala	p.T80A	ENST00000397062	NM_006164.4	80	Aca/Gca	2/5	1	2	FACETS	0.789	0.726	0.854	0.789	0.726	0.854	SUBCLONAL	1	TRUE	1	0.476377916784763	2		732	921	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129912	55129912	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	129	734	1	ENST00000257290.5:c.446C>A	p.Pro149His	p.P149H	ENST00000257290	NM_006206.4	149	cCt/cAt	4/23	0.476377916784763	2	FACETS	0.623	0.564	0.684	0.311	0.282	0.342	SUBCLONAL	1	TRUE	0	0.476377916784763	2		735	870	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131627	2131627	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	225	1207	0	ENST00000219476.3:c.3644del	p.Pro1215ArgfsTer110	p.P1215Rfs*110	ENST00000219476	NM_000548.3	1214	aaC/aa	31/42	0.476377916784763	1	FACETS	0.894	0.835	0.955	0.894	0.835	0.955	CLONAL	1	TRUE	0	0.476377916784763	1		1207	805	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86669995	86669998	+	frameshift_variant	Frame_Shift_Del	DEL	TTAC	TTAC	-	novel	NA	P-0058352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	16	286	0	ENST00000274376.6:c.1792_1795del	p.Leu598IlefsTer10	p.L598Ifs*10	ENST00000274376	NM_002890.2	598	TTACat/at	14/25	0.469550823382231	1	FACETS	0.211	0.156	0.277	0.211	0.156	0.277	SUBCLONAL	1	TRUE	0	0.476377916784763	1		286	242	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0058353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	536	276	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.856275818567075	3	FACETS	0.932	0.9	0.963	0.932	0.9	0.963	CLONAL	2	TRUE	1	0.867454710454345	3		276	951	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348206	348207	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0058353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	979	1476	0	ENST00000262320.3:c.1299dup	p.Pro434AlafsTer35	p.P434Afs*35	ENST00000262320	NM_003502.3	433	-/G	6/11	1	2	FACETS	0.944	0.928	0.959	1	0.999	1	CLONAL	2	TRUE	1	0.867454710454345	2		1476	1196	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517201	NA	P-0058353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	719	687	0	ENST00000263967.3:c.1637A>C	p.Gln546Pro	p.Q546P	ENST00000263967	NM_006218.2	546	cAg/cCg	10/21	0.856275818567075	3	FACETS	0.994	0.965	1	0.994	0.965	1	CLONAL	2	TRUE	1	0.867454710454345	3		687	1196	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075389	8075389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	106	487	0	ENST00000377482.5:c.181C>T	p.Gln61Ter	p.Q61*	ENST00000377482	NM_018948.3	61	Cag/Tag	3/4	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.365435701875162	2		487	543	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778892	9778892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	231	1245	0	ENST00000377346.4:c.1161G>A	p.Met387Ile	p.M387I	ENST00000377346	NM_005026.3	387	atG/atA	9/24	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.365435701875162	2		1245	1100	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254884	16254884	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1226968107	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	194	852	0	ENST00000375759.3:c.2149C>T	p.His717Tyr	p.H717Y	ENST00000375759	NM_015001.2	717	Cat/Tat	11/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.365435701875162	2		852	893	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885644	23885645	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	201	1082	0	ENST00000374561.5:c.273_274delinsTT	p.Pro92Ser	p.P92S	ENST00000374561	NM_002167.4	91	ccCCct/ccTTct	1/3	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.365435701875162	2		1082	873	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057649	27057649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	116	778	0	ENST00000324856.7:c.1357C>T	p.Pro453Ser	p.P453S	ENST00000324856	NM_006015.4	453	Cct/Tct	3/20	1	2	FACETS	0.871	0.785	0.961	0.871	0.785	0.961	CLONAL	1	TRUE	1	0.365435701875162	2		778	729	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105656	27105656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	132	750	0	ENST00000324856.7:c.5267C>T	p.Pro1756Leu	p.P1756L	ENST00000324856	NM_006015.4	1756	cCa/cTa	20/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.365435701875162	2		750	631	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598966	28598966	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	200	1312	0	ENST00000253063.3:c.526G>A	p.Glu176Lys	p.E176K	ENST00000253063	NM_031459.4	176	Gaa/Aaa	4/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.365435701875162	2		1312	968	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599254	28599254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	220	1263	0	ENST00000253063.3:c.700C>T	p.Pro234Ser	p.P234S	ENST00000253063	NM_031459.4	234	Cct/Tct	5/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.365435701875162	2		1263	1063	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322669	39322669	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776038485	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	159	757	0	ENST00000373001.3:c.323C>T	p.Ser108Phe	p.S108F	ENST00000373001	NM_022157.3	108	tCc/tTc	2/7	1	2	FACETS	0.94	0.861	1	0.94	0.861	1	CLONAL	1	TRUE	1	0.365435701875162	2		757	926	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604478	43604478	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	318	972	0	ENST00000355710.3:c.1064-1G>A		p.X355_splice	ENST00000355710	NM_020975.4	355			0.365435701875162	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.365435701875162	3		972	937	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720864	89720864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	104	439	0	ENST00000371953.3:c.1015C>T	p.Pro339Ser	p.P339S	ENST00000371953	NM_000314.4	339	Cca/Tca	8/9	0.365435701875162	3	FACETS	0.902	0.808	1	0.451	0.404	0.501	CLONAL	1	TRUE	1	0.365435701875162	3		439	746	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720871	89720871	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	106	452	0	ENST00000371953.3:c.1022T>C	p.Phe341Ser	p.F341S	ENST00000371953	NM_000314.4	341	tTt/tCt	8/9	0.365435701875162	3	FACETS	0.898	0.805	0.997	0.449	0.402	0.499	CLONAL	1	TRUE	1	0.365435701875162	3		452	764	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104386956	104386956	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	147	544	0	ENST00000369902.3:c.1321G>A	p.Glu441Lys	p.E441K	ENST00000369902	NM_016169.3	441	Gag/Aag	11/12	0.365435701875162	3	FACETS	1	0.982	1	0.646	0.59	0.703	CLONAL	1	TRUE	1	0.365435701875162	3		544	737	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946982	71946982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	171	1351	1	ENST00000298229.2:c.2831C>T	p.Pro944Leu	p.P944L	ENST00000298229	NM_001567.3	944	cCc/cTc	25/28	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.365435701875162	2		1352	909	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94926650	94926650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	170	681	0	ENST00000536441.1:c.115G>A	p.Gly39Arg	p.G39R	ENST00000536441	NM_144665.3	39	Gga/Aga	2/10	1	2	FACETS	0.909	0.835	0.986	0.909	0.835	0.986	CLONAL	1	TRUE	1	0.365435701875162	2		681	1024	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922235	100922235	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	142	566	1	ENST00000325455.5:c.2277G>A	p.Met759Ile	p.M759I	ENST00000325455	NM_001202474.3	759	atG/atA	5/8	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.365435701875162	2		567	743	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962527	100962527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	136	693	0	ENST00000325455.5:c.1870C>T	p.Leu624Phe	p.L624F	ENST00000325455	NM_001202474.3	624	Ctt/Ttt	3/8	1	2	FACETS	0.891	0.811	0.976	0.891	0.811	0.976	CLONAL	1	TRUE	1	0.365435701875162	2		693	835	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376289	118376289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778675942	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	154	765	0	ENST00000534358.1:c.9682C>T	p.Arg3228Cys	p.R3228C	ENST00000534358	NM_005933.3	3228	Cgt/Tgt	27/36	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.365435701875162	2		765	757	SUCCESS
CBL	867	MSKCC	GRCh37	11	119145630	119145630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	165	587	0	ENST00000264033.4:c.836C>T	p.Ala279Val	p.A279V	ENST00000264033	NM_005188.3	279	gCt/gTt	5/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.365435701875162	2		587	810	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022763	12022763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	118	913	0	ENST00000396373.4:c.869C>T	p.Ser290Phe	p.S290F	ENST00000396373	NM_001987.4	290	tCc/tTc	5/8	0.1637249703741	4	FACETS	1	0.973	1	0.608	0.549	0.671	INDETERMINATE	1	TRUE	2	0.365435701875162	4		913	725	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432351	49432351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	214	1240	0	ENST00000301067.7:c.8788C>T	p.Pro2930Ser	p.P2930S	ENST00000301067	NM_003482.3	2930	Ccc/Tcc	34/54	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.365435701875162	2		1240	997	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433776	49433776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	214	1638	1	ENST00000301067.7:c.7777C>T	p.Pro2593Ser	p.P2593S	ENST00000301067	NM_003482.3	2593	Ccc/Tcc	31/54	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.365435701875162	2		1639	1007	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434820	49434820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201931833	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	222	1449	1	ENST00000301067.7:c.6733C>T	p.Leu2245Phe	p.L2245F	ENST00000301067	NM_003482.3	2245	Ctc/Ttc	31/54	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.365435701875162	2		1450	1072	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444514	49444514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	208	1219	0	ENST00000301067.7:c.2857C>T	p.Pro953Ser	p.P953S	ENST00000301067	NM_003482.3	953	Cct/Tct	11/54	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.365435701875162	2		1219	979	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444920	49444920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370492566	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	182	1128	2	ENST00000301067.7:c.2546C>T	p.Ser849Leu	p.S849L	ENST00000301067	NM_003482.3	849	tCg/tTg	10/54	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.365435701875162	2		1130	906	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869555	102869555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867154929	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	142	857	0	ENST00000307046.8:c.86C>T	p.Ser29Phe	p.S29F	ENST00000307046	NM_001111285.1	29	tCc/tTc	2/4	1	2	FACETS	0.996	0.909	1	0.996	0.909	1	CLONAL	1	TRUE	1	0.365435701875162	2		857	780	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109845	115109845	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1490395317	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	81	370	0	ENST00000257566.3:c.2033C>T	p.Ala678Val	p.A678V	ENST00000257566	NM_016569.3	678	gCc/gTc	8/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.365435701875162	2		370	346	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241002	133241002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	154	1022	0	ENST00000320574.5:c.2515G>A	p.Gly839Arg	p.G839R	ENST00000320574	NM_006231.2	839	Ggg/Agg	22/49	1	2	FACETS	0.967	0.885	1	0.967	0.885	1	CLONAL	1	TRUE	1	0.365435701875162	2		1022	872	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008335	29008335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	23	438	0	ENST00000282397.4:c.536C>T	p.Pro179Leu	p.P179L	ENST00000282397	NM_002019.4	179	cCt/cTt	5/30	0.365435701875162	1	FACETS	0.24	0.187	0.303	0.24	0.187	0.303	SUBCLONAL	1	TRUE	0	0.365435701875162	1		438	428	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878134	48878134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs938094455	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	25	111	0	ENST00000267163.4:c.86C>T	p.Pro29Leu	p.P29L	ENST00000267163	NM_000321.2	29	cCt/cTt	1/27	0.365435701875162	1	FACETS	0.834	0.667	1	0.834	0.667	1	CLONAL	1	TRUE	0	0.365435701875162	1		111	134	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436371	110436371	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	118	681	1	ENST00000375856.3:c.2030C>T	p.Pro677Leu	p.P677L	ENST00000375856	NM_003749.2	677	cCc/cTc	1/2	0.246187414691963	3	FACETS	1	0.968	1	0.582	0.526	0.641	CLONAL	1	TRUE	1	0.365435701875162	3		682	656	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30069014	30069014	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	89	539	0	ENST00000331968.5:c.1915C>T	p.His639Tyr	p.H639Y	ENST00000331968	NM_002742.2	639	Cac/Tac	14/18	1	2	FACETS	0.772	0.685	0.865	0.772	0.685	0.865	SUBCLONAL	1	TRUE	1	0.365435701875162	2		539	631	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562362	95562362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	177	657	0	ENST00000393063.1:c.4895C>T	p.Ser1632Phe	p.S1632F	ENST00000393063	NM_030621.3	1632	tCt/tTt	24/28	0.187951012340772	5	FACETS	0.757	0.697	0.819			1	INDETERMINATE	2	TRUE	NA	0.365435701875162	5		657	991	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035248	42035248	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	196	938	0	ENST00000219905.7:c.5090C>T	p.Ser1697Phe	p.S1697F	ENST00000219905	NM_001164273.1	1697	tCc/tTc	15/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.365435701875162	2		938	991	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640916	3640916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767927663	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	396	1312	2	ENST00000294008.3:c.2723C>T	p.Pro908Leu	p.P908L	ENST00000294008	NM_032444.2	908	cCg/cTg	12/15	0.365435701875162	1	FACETS	0.921	0.879	0.963	1	0.997	1	CLONAL	2	TRUE	0	0.365435701875162	1		1314	962	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788618	3788618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398124146	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	282	449	0	ENST00000262367.5:c.4336C>T	p.Arg1446Cys	p.R1446C	ENST00000262367	NM_004380.2	1446	Cgc/Tgc	26/31	0.365435701875162	1	FACETS	0.809	0.763	0.855	1	0.995	1	CLONAL	2	TRUE	0	0.365435701875162	1		449	780	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857089	9857089	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	195	511	0	ENST00000330684.3:c.4312A>C	p.Met1438Leu	p.M1438L	ENST00000330684	NM_001134407.1	1438	Atg/Ctg	13/13	0.365435701875162	1	FACETS	0.879	0.821	0.938	1	0.993	1	CLONAL	2	TRUE	0	0.365435701875162	1		511	496	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857366	9857367	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	255	747	1	ENST00000330684.3:c.4034_4035delinsTT	p.Pro1345Leu	p.P1345L	ENST00000330684	NM_001134407.1	1345	cCC/cTT	13/13	0.365435701875162	1	FACETS	0.844	0.794	0.894	1	0.994	1	CLONAL	2	TRUE	0	0.365435701875162	1		748	676	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828214	50828214	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	159	694	0	ENST00000398568.2:c.2552T>A	p.Ile851Asn	p.I851N	ENST00000398568	NM_001042412.1	851	aTc/aAc	17/18	1	2	FACETS	0.926	0.848	1	0.926	0.848	1	CLONAL	1	TRUE	1	0.365435701875162	2		694	940	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	324	749	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.363773200382367	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.365435701875162	2		749	831	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557285	29557285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367684252	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	58	355	0	ENST00000356175.3:c.2998C>T	p.Arg1000Cys	p.R1000C	ENST00000356175	NM_000267.3	1000	Cgt/Tgt	23/57	1	2	FACETS	0.769	0.662	0.884	0.769	0.662	0.884	SUBCLONAL	1	TRUE	1	0.365435701875162	2		355	413	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246059	41246059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	129	931	0	ENST00000357654.3:c.1489C>T	p.Pro497Ser	p.P497S	ENST00000357654	NM_007294.3	497	Ccc/Tcc	10/23	1	2	FACETS	0.762	0.69	0.837	0.762	0.69	0.837	SUBCLONAL	1	TRUE	1	0.365435701875162	2		931	927	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246196	41246196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	98	807	0	ENST00000357654.3:c.1352C>T	p.Ser451Leu	p.S451L	ENST00000357654	NM_007294.3	451	tCa/tTa	10/23	1	2	FACETS	0.694	0.619	0.774	0.694	0.619	0.774	SUBCLONAL	1	TRUE	1	0.365435701875162	2		807	773	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805863	46805864	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	118	1090	0	ENST00000290295.7:c.92_93delinsTT	p.Ser31Phe	p.S31F	ENST00000290295	NM_006361.5	31	tCC/tTT	1/2	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.365435701875162	2		1090	611	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763235	59763235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761639530	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	161	846	1	ENST00000259008.2:c.2867C>T	p.Ser956Leu	p.S956L	ENST00000259008	NM_032043.2	956	tCa/tTa	19/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.365435701875162	2		847	808	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62009583	62009583	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	219	1017	1	ENST00000392795.3:c.39G>A	p.Trp13Ter	p.W13*	ENST00000392795	NM_001039933.1	13	tgG/tgA	1/6	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.365435701875162	2		1018	955	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727831	78727831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	215	1024	0	ENST00000306801.3:c.676C>T	p.His226Tyr	p.H226Y	ENST00000306801	NM_020761.2	226	Cac/Tac	6/34	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.365435701875162	2		1024	1037	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390460	56390460	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	97	404	0	ENST00000348428.3:c.1199T>A	p.Leu400His	p.L400H	ENST00000348428	NM_006785.3	400	cTc/cAc	10/17	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.365435701875162	2		404	491	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210417	2210417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	171	837	3	ENST00000398665.3:c.1024C>T	p.Arg342Trp	p.R342W	ENST00000398665	NM_032482.2	342	Cgg/Tgg	13/28	0.365435701875162	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.365435701875162	1		840	726	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272218	15272218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs114447350	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	110	479	0	ENST00000263388.2:c.6221C>T	p.Pro2074Leu	p.P2074L	ENST00000263388	NM_000435.2	2074	cCg/cTg	33/33	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.365435701875162	2		479	460	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300137	15300137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748814154	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	240	1250	1	ENST00000263388.2:c.1139C>T	p.Pro380Leu	p.P380L	ENST00000263388	NM_000435.2	380	cCt/cTt	7/33	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.365435701875162	2		1251	1019	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354043	15354043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	125	812	0	ENST00000263377.2:c.2837C>T	p.Pro946Leu	p.P946L	ENST00000263377	NM_058243.2	946	cCt/cTt	14/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.365435701875162	2		812	635	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367899	15367899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	231	1264	0	ENST00000263377.2:c.1427C>T	p.Pro476Leu	p.P476L	ENST00000263377	NM_058243.2	476	cCc/cTc	8/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.365435701875162	2		1264	1003	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383620	42383620	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201206281	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	148	953	0	ENST00000221972.3:c.395C>T	p.Pro132Leu	p.P132L	ENST00000221972	NM_021601.3	132	cCc/cTc	3/5	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.365435701875162	2		953	710	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50138882	50138882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	247	1438	0	ENST00000246792.3:c.608C>T	p.Pro203Leu	p.P203L	ENST00000246792	NM_006270.3	203	cCc/cTc	6/6	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.365435701875162	2		1438	1179	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	250	1371	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	0.142726603059955	3	FACETS	1	0.981	1	0.379	0.353	0.405	INDETERMINATE	1	TRUE	0	0.365435701875162	3		1371	1425	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967237	25967237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	144	714	0	ENST00000435504.4:c.1969C>T	p.Leu657Phe	p.L657F	ENST00000435504		657	Ctt/Ttt	13/13	0.142726603059955	3	FACETS	1	0.934	1	0.343	0.312	0.375	INDETERMINATE	1	TRUE	0	0.365435701875162	3		714	906	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606679	29606679	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs865931787	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	363	900	1	ENST00000389048.3:c.1201C>T	p.Arg401Ter	p.R401*	ENST00000389048	NM_004304.4	401	Cga/Tga	5/29	0.142726603059955	3	FACETS	1	0.985	1	0.73	0.693	0.767	INDETERMINATE	2	TRUE	0	0.365435701875162	3		901	1073	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917787	29917787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	408	1152	0	ENST00000389048.3:c.881C>T	p.Pro294Leu	p.P294L	ENST00000389048	NM_004304.4	294	cCc/cTc	3/29	0.142726603059955	3	FACETS	1	0.989	1	0.742	0.707	0.778	INDETERMINATE	2	TRUE	0	0.365435701875162	3		1152	1186	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222498	39222498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	191	861	1	ENST00000402219.2:c.3112C>T	p.Pro1038Ser	p.P1038S	ENST00000402219	NM_005633.3	1038	Cct/Tct	20/23	0.142726603059955	3	FACETS	1	0.985	1	0.417	0.385	0.45	INDETERMINATE	1	TRUE	0	0.365435701875162	3		862	989	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241081	39241081	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	156	722	0	ENST00000402219.2:c.1990G>T	p.Glu664Ter	p.E664*	ENST00000402219	NM_005633.3	664	Gag/Tag	12/23	0.142726603059955	3	FACETS	1	0.966	1	0.369	0.337	0.402	INDETERMINATE	1	TRUE	0	0.365435701875162	3		722	913	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609198	46609198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781751711	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	181	1066	0	ENST00000263734.3:c.2257G>A	p.Asp753Asn	p.D753N	ENST00000263734	NM_001430.4	753	Gac/Aac	14/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.365435701875162	2		1066	864	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251709	212251709	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771882543	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	251	728	2	ENST00000342788.4:c.3350C>T	p.Pro1117Leu	p.P1117L	ENST00000342788	NM_005235.2	1117	cCc/cTc	27/28	0.0147523567474614	3	FACETS	0.937	0.879	0.997			1	INDETERMINATE	2	TRUE	NA	0.365435701875162	3		730	867	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578311	212578311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs944175943	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	160	647	1	ENST00000342788.4:c.946G>A	p.Glu316Lys	p.E316K	ENST00000342788	NM_005235.2	316	Gaa/Aaa	8/28	0.0147523567474614	3	FACETS	1	0.95	1			1	INDETERMINATE	1	TRUE	NA	0.365435701875162	3		648	986	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659826	227659826	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1312009930	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	123	611	0	ENST00000305123.5:c.3629C>T	p.Pro1210Leu	p.P1210L	ENST00000305123	NM_005544.2	1210	cCc/cTc	1/2	0.365435701875162	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.365435701875162	1		611	400	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024491	31024492	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	128	972	1	ENST00000375687.4:c.3976_3977delinsTT	p.Pro1326Phe	p.P1326F	ENST00000375687	NM_015338.5	1326	CCt/TTt	13/13	1	2	FACETS	0.879	0.797	0.965	0.879	0.797	0.965	CLONAL	1	TRUE	1	0.365435701875162	2		973	797	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374336	31374336	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	173	1121	0	ENST00000328111.2:c.335C>T	p.Ser112Phe	p.S112F	ENST00000328111	NM_006892.3	112	tCc/tTc	5/23	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.365435701875162	2		1121	932	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374374	31374374	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	197	1173	1	ENST00000328111.2:c.373C>T	p.Arg125Ter	p.R125*	ENST00000328111	NM_006892.3	125	Cga/Tga	5/23	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.365435701875162	2		1174	1006	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730798	40730798	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	183	970	0	ENST00000373198.4:c.3737A>T	p.Glu1246Val	p.E1246V	ENST00000373198	NM_133170.3	1246	gAa/gTa	27/32	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.365435701875162	2		970	823	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748611	40748611	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	156	656	0	ENST00000373198.4:c.2905G>A	p.Gly969Arg	p.G969R	ENST00000373198	NM_133170.3	969	Gga/Aga	21/32	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.365435701875162	2		656	695	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164901	36164901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	260	1035	1	ENST00000300305.3:c.974C>T	p.Pro325Leu	p.P325L	ENST00000300305		325	cCc/cTc	8/8	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.365435701875162	2		1036	1068	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163121	47163121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs184493846	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	107	529	0	ENST00000409792.3:c.3005C>T	p.Ser1002Phe	p.S1002F	ENST00000409792	NM_014159.6	1002	tCt/tTt	3/21	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.365435701875162	2		529	544	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	148	858	0	ENST00000394830.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000394830	NM_018313.4	710	Cga/Tga	17/30	1	2	FACETS	0.924	0.844	1	0.924	0.844	1	CLONAL	1	TRUE	1	0.365435701875162	2		858	877	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71161719	71161719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	111	579	0	ENST00000318789.4:c.250C>T	p.Pro84Ser	p.P84S	ENST00000318789	NM_032682.5	84	Ccc/Tcc	7/21	1	2	FACETS	0.817	0.734	0.904	0.817	0.734	0.904	CLONAL	1	TRUE	1	0.365435701875162	2		579	744	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259561	89259562	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	115	650	0	ENST00000336596.2:c.705_706delinsAA	p.Glu236Lys	p.E236K	ENST00000336596	NM_005233.5	235	aaGGag/aaAAag	3/17	1	2	FACETS	0.922	0.831	1	0.922	0.831	1	CLONAL	1	TRUE	1	0.365435701875162	2		650	683	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448615	89448615	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	161	741	0	ENST00000336596.2:c.1579G>A	p.Glu527Lys	p.E527K	ENST00000336596	NM_005233.5	527	Gaa/Aaa	7/17	1	2	FACETS	0.891	0.817	0.969	0.891	0.817	0.969	CLONAL	1	TRUE	1	0.365435701875162	2		741	989	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670403	134670403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	137	756	0	ENST00000398015.3:c.314C>T	p.Ser105Phe	p.S105F	ENST00000398015	NM_004441.4	105	tCc/tTc	3/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.365435701875162	2		756	663	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461593	138461593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	117	593	0	ENST00000289153.2:c.428C>T	p.Pro143Leu	p.P143L	ENST00000289153	NM_006219.2	143	cCt/cTt	3/22	1	2	FACETS	0.837	0.755	0.924	0.837	0.755	0.924	CLONAL	1	TRUE	1	0.365435701875162	2		593	765	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190830	185190830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs961866050	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	236	1030	0	ENST00000265026.3:c.1711G>A	p.Gly571Arg	p.G571R	ENST00000265026	NM_004721.4	571	Gga/Aga	11/14	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.365435701875162	2		1030	1020	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1976666	1976666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	208	961	0	ENST00000382891.5:c.3449C>T	p.Thr1150Ile	p.T1150I	ENST00000382891	NM_133335.3	1150	aCc/aTc	19/22	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.365435701875162	2		961	965	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564554	55564554	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	193	996	0	ENST00000288135.5:c.442C>A	p.Leu148Ile	p.L148I	ENST00000288135	NM_000222.2	148	Ctc/Atc	3/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.365435701875162	2		996	937	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55962486	55962486	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	96	571	0	ENST00000263923.4:c.2638C>T	p.Arg880Ter	p.R880*	ENST00000263923	NM_002253.2	880	Cga/Tga	19/30	1	2	FACETS	0.785	0.7	0.876	0.785	0.7	0.876	SUBCLONAL	1	TRUE	1	0.365435701875162	2		571	669	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970953	55970953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	127	842	0	ENST00000263923.4:c.1844C>T	p.Thr615Ile	p.T615I	ENST00000263923	NM_002253.2	615	aCc/aTc	13/30	1	2	FACETS	0.867	0.785	0.952	0.867	0.785	0.952	CLONAL	1	TRUE	1	0.365435701875162	2		842	802	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286179	66286179	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	79	466	0	ENST00000273854.3:c.1507G>A	p.Glu503Lys	p.E503K	ENST00000273854	NM_004439.5	503	Gaa/Aaa	6/18	1	2	FACETS	0.773	0.681	0.872	0.773	0.681	0.872	SUBCLONAL	1	TRUE	1	0.365435701875162	2		466	559	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467767	66467767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	136	535	0	ENST00000273854.3:c.502G>A	p.Glu168Lys	p.E168K	ENST00000273854	NM_004439.5	168	Gaa/Aaa	3/18	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.365435701875162	2		535	591	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143191824	143191824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	144	611	0	ENST00000262992.4:c.607G>A	p.Gly203Arg	p.G203R	ENST00000262992	NM_001101669.1	203	Gga/Aga	8/24	0.365435701875162	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.365435701875162	1		611	628	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260636	1260636	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	162	1053	0	ENST00000310581.5:c.2923T>G	p.Phe975Val	p.F975V	ENST00000310581	NM_198253.2	975	Ttt/Gtt	12/16	0.246187414691963	3	FACETS	0.954	0.874	1	0.477	0.437	0.519	CLONAL	1	TRUE	1	0.365435701875162	3		1053	1099	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	129	172	0				ENST00000310581	NM_198253.2	-/1132			0.246187414691963	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.365435701875162	3		172	337	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38968099	38968099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	225	454	0	ENST00000357387.3:c.1006C>T	p.Arg336Cys	p.R336C	ENST00000357387	NM_152756.3	336	Cgt/Tgt	12/38	0.246187414691963	3	FACETS	0.965	0.901	1	0.965	0.901	1	CLONAL	2	TRUE	1	0.365435701875162	3		454	755	SUCCESS
APC	324	MSKCC	GRCh37	5	112154789	112154789	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs556566281	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	148	832	0	ENST00000257430.4:c.1060C>T	p.Pro354Ser	p.P354S	ENST00000257430	NM_000038.5	354	Cct/Tct	10/16	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.365435701875162	2		832	805	SUCCESS
APC	324	MSKCC	GRCh37	5	112173608	112173608	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	98	439	0	ENST00000257430.4:c.2317T>C	p.Phe773Leu	p.F773L	ENST00000257430	NM_000038.5	773	Ttt/Ctt	16/16	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.365435701875162	2		439	503	SUCCESS
APC	324	MSKCC	GRCh37	5	112175136	112175136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	78	323	0	ENST00000257430.4:c.3845C>T	p.Ser1282Leu	p.S1282L	ENST00000257430	NM_000038.5	1282	tCa/tTa	16/16	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.365435701875162	2		323	404	SUCCESS
APC	324	MSKCC	GRCh37	5	112176362	112176362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	103	521	0	ENST00000257430.4:c.5071C>T	p.Pro1691Ser	p.P1691S	ENST00000257430	NM_000038.5	1691	Cct/Tct	16/16	1	2	FACETS	0.97	0.87	1	0.97	0.87	1	CLONAL	1	TRUE	1	0.365435701875162	2		521	581	SUCCESS
APC	324	MSKCC	GRCh37	5	112177101	112177101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561602823	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	129	581	0	ENST00000257430.4:c.5810C>T	p.Ser1937Phe	p.S1937F	ENST00000257430	NM_000038.5	1937	tCc/tTc	16/16	1	2	FACETS	0.989	0.898	1	0.989	0.898	1	CLONAL	1	TRUE	1	0.365435701875162	2		581	714	SUCCESS
APC	324	MSKCC	GRCh37	5	112178943	112178943	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1060503314	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	105	501	0	ENST00000257430.4:c.7652A>T	p.His2551Leu	p.H2551L	ENST00000257430	NM_000038.5	2551	cAc/cTc	16/16	1	2	FACETS	0.987	0.887	1	0.987	0.887	1	CLONAL	1	TRUE	1	0.365435701875162	2		501	582	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940581	131940581	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	119	413	0	ENST00000265335.6:c.2608C>G	p.Leu870Val	p.L870V	ENST00000265335		870	Cta/Gta	16/25	1	2	FACETS	0.996	0.901	1	0.996	0.901	1	CLONAL	1	TRUE	1	0.365435701875162	2		413	654	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495349	149495349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	164	1187	0	ENST00000261799.4:c.3298G>A	p.Glu1100Lys	p.E1100K	ENST00000261799	NM_002609.3	1100	Gaa/Aaa	23/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.365435701875162	2		1187	776	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562508	176562508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	160	922	0	ENST00000439151.2:c.404C>T	p.Ser135Phe	p.S135F	ENST00000439151	NM_022455.4	135	tCc/tTc	2/23	1	2	FACETS	0.925	0.847	1	0.925	0.847	1	CLONAL	1	TRUE	1	0.365435701875162	2		922	947	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721994	176721994	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	320	869	0	ENST00000439151.2:c.7625C>A	p.Pro2542His	p.P2542H	ENST00000439151	NM_022455.4	2542	cCt/cAt	23/23	1	2	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	TRUE	1	0.365435701875162	2		869	740	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170168	32170168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	233	1406	0	ENST00000375023.3:c.3440C>T	p.Ser1147Leu	p.S1147L	ENST00000375023	NM_004557.3	1147	tCa/tTa	21/30	0.0724150627852587	3	FACETS	1	0.991	1	0.71	0.662	0.76	INDETERMINATE	1	TRUE	1	0.365435701875162	3		1406	1062	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821524	32821524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	178	1114	1	ENST00000354258.4:c.70C>T	p.Pro24Ser	p.P24S	ENST00000354258	NM_000593.5	24	Cct/Tct	1/11	0.0724150627852587	3	FACETS	1	0.988	1	0.684	0.631	0.739	INDETERMINATE	1	TRUE	1	0.365435701875162	3		1115	842	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790755	89790755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1368223422	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	271	1321	0	ENST00000336032.3:c.142C>T	p.Pro48Ser	p.P48S	ENST00000336032	NM_006813.2	48	Ccc/Tcc	1/2	0.0724150627852587	3	FACETS	0.761	0.714	0.81	0.761	0.714	0.81	INDETERMINATE	2	TRUE	1	0.365435701875162	3		1321	1152	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964415	93964415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867402067	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	234	494	0	ENST00000369303.4:c.2482G>A	p.Glu828Lys	p.E828K	ENST00000369303	NM_004440.3	828	Gaa/Aaa	14/17	0.0724150627852587	3	FACETS	0.883	0.825	0.942	0.883	0.825	0.942	INDETERMINATE	2	TRUE	1	0.365435701875162	3		494	858	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068031	94068031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747304855	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	117	433	0	ENST00000369303.4:c.931G>A	p.Glu311Lys	p.E311K	ENST00000369303	NM_004440.3	311	Gaa/Aaa	4/17	0.0724150627852587	3	FACETS	1	0.966	1	0.575	0.52	0.634	INDETERMINATE	1	TRUE	1	0.365435701875162	3		433	658	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068057	94068057	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	127	421	0	ENST00000369303.4:c.905C>T	p.Ser302Phe	p.S302F	ENST00000369303	NM_004440.3	302	tCt/tTt	4/17	0.0724150627852587	3	FACETS	1	0.974	1	0.6	0.544	0.658	INDETERMINATE	1	TRUE	1	0.365435701875162	3		421	685	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124437	94124437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	155	598	0	ENST00000369303.4:c.146C>T	p.Ser49Phe	p.S49F	ENST00000369303	NM_004440.3	49	tCc/tTc	2/17	0.0724150627852587	3	FACETS	1	0.961	1	0.542	0.496	0.591	INDETERMINATE	1	TRUE	1	0.365435701875162	3		598	925	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683789	117683789	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	134	576	0	ENST00000368508.3:c.3358C>T	p.Pro1120Ser	p.P1120S	ENST00000368508	NM_002944.2	1120	Ccc/Tcc	21/43	0.365435701875162	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.365435701875162	1		576	534	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522149	157522149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	212	1065	0	ENST00000346085.5:c.4421C>T	p.Pro1474Leu	p.P1474L	ENST00000346085	NM_020732.3	1474	cCc/cTc	18/20	0.365435701875162	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.365435701875162	1		1065	703	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527818	157527818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs962264300	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	148	781	3	ENST00000346085.5:c.5543C>T	p.Pro1848Leu	p.P1848L	ENST00000346085	NM_020732.3	1848	cCc/cTc	20/20	0.365435701875162	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.365435701875162	1		784	507	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984166	2984166	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	98	652	0	ENST00000396946.4:c.364G>A	p.Glu122Lys	p.E122K	ENST00000396946	NM_032415.4	122	Gaa/Aaa	5/25	0.365435701875162	0	FACETS	0.621	0.556	0.69			1	SUBCLONAL	1	TRUE	0	0.365435701875162	0		652	548	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729525	41729525	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	197	997	0	ENST00000242208.4:c.1004G>A	p.Trp335Ter	p.W335*	ENST00000242208	NM_002192.2	335	tGg/tAg	3/3	0.0724150627852587	3	FACETS	1	0.989	1	0.686	0.636	0.739	INDETERMINATE	1	TRUE	1	0.365435701875162	3		997	929	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334803	81334803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	137	582	0	ENST00000222390.5:c.1913G>A	p.Gly638Glu	p.G638E	ENST00000222390	NM_000601.4	638	gGa/gAa	17/18	0.0724150627852587	3	FACETS	1	0.982	1	0.649	0.592	0.709	INDETERMINATE	1	TRUE	1	0.365435701875162	3		582	683	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358998	81358998	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	169	821	0	ENST00000222390.5:c.963G>A	p.Trp321Ter	p.W321*	ENST00000222390	NM_000601.4	321	tgG/tgA	8/18	0.0724150627852587	3	FACETS	1	0.983	1	0.624	0.573	0.676	INDETERMINATE	1	TRUE	1	0.365435701875162	3		821	877	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372774	81372775	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	108	484	0	ENST00000222390.5:c.759_760delinsAA	p.Gly254Ser	p.G254S	ENST00000222390	NM_000601.4	253	aaGGgc/aaAAgc	7/18	0.0724150627852587	3	FACETS	1	0.943	1	0.536	0.482	0.594	INDETERMINATE	1	TRUE	1	0.365435701875162	3		484	652	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508310	106508310	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	131	670	0	ENST00000359195.3:c.304A>C	p.Lys102Gln	p.K102Q	ENST00000359195	NM_002649.2	102	Aag/Cag	2/11	0.0724150627852587	3	FACETS	1	0.976	1	0.61	0.554	0.668	INDETERMINATE	1	TRUE	1	0.365435701875162	3		670	695	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513314	106513314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559655430	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	114	501	2	ENST00000359195.3:c.2218G>A	p.Glu740Lys	p.E740K	ENST00000359195	NM_002649.2	740	Gag/Aag	4/11	0.0724150627852587	3	FACETS	1	0.938	1	0.527	0.475	0.582	INDETERMINATE	1	TRUE	1	0.365435701875162	3		503	700	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852030	128852030	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	176	1170	3	ENST00000249373.3:c.2102T>G	p.Ile701Ser	p.I701S	ENST00000249373	NM_005631.4	701	aTt/aGt	12/12	0.0724150627852587	3	FACETS	1	0.99	1	0.749	0.692	0.809	INDETERMINATE	1	TRUE	1	0.365435701875162	3		1173	760	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917611	151917611	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs938655561	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	120	718	1	ENST00000262189.6:c.3709C>T	p.Arg1237Ter	p.R1237*	ENST00000262189	NM_170606.2	1237	Cga/Tga	23/59	0.0724150627852587	3	FACETS	1	0.947	1	0.535	0.483	0.589	INDETERMINATE	1	TRUE	1	0.365435701875162	3		719	726	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538787	23538787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	92	674	0	ENST00000380871.4:c.652C>T	p.Pro218Ser	p.P218S	ENST00000380871	NM_006167.3	218	Cct/Tct	2/2	0.365435701875162	1	FACETS	0.852	0.76	0.949	0.852	0.76	0.949	CLONAL	1	TRUE	0	0.365435701875162	1		674	483	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069574	69069574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1335517478	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	140	522	0	ENST00000288368.4:c.4249G>A	p.Gly1417Arg	p.G1417R	ENST00000288368	NM_024870.2	1417	Gga/Aga	35/40	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.365435701875162	2		522	708	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970913	70970914	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	137	877	2	ENST00000276594.2:c.1347_1348delinsTT	p.His450Tyr	p.H450Y	ENST00000276594	NM_024504.3	449	atCCac/atTTac	6/8	1	2	FACETS	0.966	0.88	1	0.966	0.88	1	CLONAL	1	TRUE	1	0.365435701875162	2		879	776	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141570514	141570514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	215	1117	1	ENST00000220592.5:c.614C>T	p.Ser205Phe	p.S205F	ENST00000220592	NM_012154.3	205	tCc/tTc	5/19	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.365435701875162	2		1118	986	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022124	5022124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	141	808	0	ENST00000381652.3:c.137C>T	p.Ser46Phe	p.S46F	ENST00000381652	NM_004972.3	46	tCc/tTc	3/25	1	2	FACETS	0.963	0.878	1	0.963	0.878	1	CLONAL	1	TRUE	1	0.365435701875162	2		808	801	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492909	8492909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	198	812	1	ENST00000356435.5:c.2420G>A	p.Gly807Glu	p.G807E	ENST00000356435		807	gGa/gAa	16/35	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.365435701875162	2		813	1043	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499727	8499727	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	173	775	1	ENST00000356435.5:c.2242C>T	p.Gln748Ter	p.Q748*	ENST00000356435		748	Cag/Tag	14/35	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.365435701875162	2		776	938	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197556	27197556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	210	818	0	ENST00000380036.4:c.1868G>A	p.Gly623Glu	p.G623E	ENST00000380036	NM_000459.3	623	gGg/gAg	12/23	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.365435701875162	2		818	941	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209358	98209358	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1297685477	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	466	950	0	ENST00000331920.6:c.4180C>T	p.Arg1394Ter	p.R1394*	ENST00000331920	NM_000264.3	1394	Cga/Tga	23/24	0.363773200382367	2	FACETS	0.855	0.821	0.89	1	0.995	1	CLONAL	3	TRUE	0	0.365435701875162	2		950	994	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98247967	98247967	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	271	592	0	ENST00000331920.6:c.584G>A	p.Arg195Lys	p.R195K	ENST00000331920	NM_000264.3	195	aGg/aAg	3/24	0.363773200382367	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.365435701875162	2		592	633	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	126	276	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.365435701875162	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.365435701875162	1		276	510	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418372	139418372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	214	1391	1	ENST00000277541.6:c.200C>T	p.Pro67Leu	p.P67L	ENST00000277541	NM_017617.3	67	cCc/cTc	3/34	0.365435701875162	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.365435701875162	1		1392	746	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041355	47041355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	175	570	1	ENST00000377604.3:c.1699C>T	p.Pro567Ser	p.P567S	ENST00000377604	NM_001204468.1	567	Ccc/Tcc	16/24	1	1	FACETS	0.878	0.817	0.939	1	0.992	1	CLONAL	2	TRUE	0	0.365435701875162	1		571	446	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223488	53223488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	178	575	0	ENST00000375401.3:c.3871C>T	p.Arg1291Cys	p.R1291C	ENST00000375401	NM_004187.3	1291	Cgc/Tgc	23/26	1	1	FACETS	0.937	0.874	1	1	0.993	1	CLONAL	2	TRUE	0	0.365435701875162	1		575	425	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854906	76854906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	190	431	0	ENST00000373344.5:c.5930C>T	p.Pro1977Leu	p.P1977L	ENST00000373344	NM_000489.3	1977	cCt/cTt	25/35	1	1	FACETS	0.88	0.821	0.939	1	0.993	1	CLONAL	2	TRUE	0	0.365435701875162	1		431	483	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066928	30066928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238310800	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	115	724	0	ENST00000331968.5:c.2203G>A	p.Gly735Arg	p.G735R	ENST00000331968	NM_002742.2	735	Gga/Aga	16/18	1	2	FACETS	0.767	0.69	0.847	0.767	0.69	0.847	SUBCLONAL	1	TRUE	1	0.365435701875162	2		724	821	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799311	42799311	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	71	338	0	ENST00000575354.2:c.4795C>T	p.Pro1599Ser	p.P1599S	ENST00000575354	NM_015125.3	1599	Cca/Tca	20/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.365435701875162	2		338	308	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	27	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.757	0.611	0.918	0.757	0.611	0.918	CLONAL	1	TRUE	1	0.528741214416165	2		306	135	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124226	2124226	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	240	1209	0	ENST00000219476.3:c.2381A>C	p.Gln794Pro	p.Q794P	ENST00000219476	NM_000548.3	794	cAg/cCg	22/42	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.528741214416165	2		1209	861	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124237	2124237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375809212	NA	P-0058355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	248	1256	0	ENST00000219476.3:c.2392C>T	p.His798Tyr	p.H798Y	ENST00000219476	NM_000548.3	798	Cac/Tac	22/42	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.528741214416165	2		1256	910	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135165	2135271	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCCTGGGTGGGGCGGCCTCCTGTGGACGGGCGTCTGGGGCTCAGGCAGGGCTCTGTGTGCCACAGTCACAGTCCTTTGAGCGGTCGGTGCAGCTCCTCGACCAGAT	GGCCTGGGTGGGGCGGCCTCCTGTGGACGGGCGTCTGGGGCTCAGGCAGGGCTCTGTGTGCCACAGTCACAGTCCTTTGAGCGGTCGGTGCAGCTCCTCGACCAGAT	-	novel	NA	P-0058355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	206	813	0	ENST00000219476.3:c.4570-66_4610del		p.X1524_splice	ENST00000219476	NM_000548.3	1524		36/42	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.528741214416165	2		813	614	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589619	67589621	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0058355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	125	325	0	ENST00000274335.5:c.1382_1384del	p.Arg461_Glu462delinsGln	p.R461_E462delinsQ	ENST00000274335		461	cGAGaa/caa	10/15	1	2	FACETS	0.817	0.742	0.895	0.817	0.742	0.895	CLONAL	1	TRUE	1	0.528741214416165	2		325	579	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0058356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	190	559	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.350279938491757	1	FACETS	0.926	0.856	0.999	0.926	0.856	0.999	CLONAL	1	TRUE	0	0.350279938491757	1		559	966	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625435	69625435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376445217	NA	P-0058356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	57	1202	1	ENST00000334134.2:c.358C>T	p.Arg120Trp	p.R120W	ENST00000334134	NM_005247.2	120	Cgg/Tgg	3/3	1	2	FACETS	0.3	0.256	0.348	0.3	0.256	0.348	SUBCLONAL	1	TRUE	1	0.350279938491757	2		1203	1084	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271265	38271265	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377149398	NA	P-0058356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	181	1430	0	ENST00000425967.3:c.2443C>T	p.Arg815Trp	p.R815W	ENST00000425967	NM_001174067.1	815	Cgg/Tgg	19/19	0.350279938491757	1	FACETS	0.843	0.777	0.912	0.843	0.777	0.912	CLONAL	1	TRUE	0	0.350279938491757	1		1430	1011	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657082	47657082	+	splice_donor_variant	Splice_Site	SNP	T	T	A	rs267607953	NA	P-0058356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	76	282	1	ENST00000233146.2:c.1276+2T>A		p.X426_splice	ENST00000233146	NM_000251.2	426			0.309170088223029	3	FACETS	0.95	0.834	1	0.475	0.417	0.537	CLONAL	1	TRUE	1	0.350279938491757	3		283	537	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728578	190728578	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	33	296	0	ENST00000441310.2:c.1966C>A	p.Pro656Thr	p.P656T	ENST00000441310	NM_000534.4	656	Ccc/Acc	10/13	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		296	209	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0058369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	176	490	1	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.20642902265842	5	FACETS	1	0.971	1	0.723	0.672	0.775	INDETERMINATE	2	TRUE	2	0.694254966563036	5		491	477	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100117	157100119	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs797045268	NA	P-0058369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	11	74	0	ENST00000346085.5:c.1069_1071del	p.Gly357del	p.G357del	ENST00000346085	NM_020732.3	352	GGC/-	1/20	0.381356002689765	4	FACETS	0.278	0.192	0.385	0.139	0.096	0.193	INDETERMINATE	1	TRUE	2	0.694254966563036	4		74	193	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829753	76829756	+	frameshift_variant	Frame_Shift_Del	DEL	CTTC	CTTC	-	novel	NA	P-0058369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	65	425	0	ENST00000373344.5:c.6285_6288del	p.Lys2096SerfsTer12	p.K2096Sfs*12	ENST00000373344	NM_000489.3	2095	agGAAG/ag	28/35	0.513054498514849	1	FACETS	0.994	0.894	1	0.994	0.894	1	CLONAL	1	TRUE	0	0.694254966563036	1		425	123	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602736	55602736	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	29	518	0	ENST00000288135.5:c.2557T>C	p.Trp853Arg	p.W853R	ENST00000288135	NM_000222.2	853	Tgg/Cgg	18/21	0.399789484683802	3	FACETS	0.922	0.754	1	0.461	0.377	0.553	INDETERMINATE	1	TRUE	1	0.694254966563036	3		518	122	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827156	72827156	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	98	661	0	ENST00000268489.5:c.9425C>T	p.Thr3142Ile	p.T3142I	ENST00000268489	NM_006885.3	3142	aCa/aTa	9/10	0.694254966563036	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.694254966563036	1		661	148	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324928	31324928	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	239	864	0	ENST00000412585.2:c.8T>G	p.Val3Gly	p.V3G	ENST00000412585	NM_005514.6	3	gTc/gGc	1/8	0.381356002689765	4	FACETS	0.813	0.763	0.865	0.813	0.763	0.865	INDETERMINATE	2	TRUE	2	0.694254966563036	4		864	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579301	7579318	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGCAACTGACCGTGCAA	GGGCAACTGACCGTGCAA	C	novel	NA	P-0058369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	171	702	0	ENST00000269305.4:c.369_375+11delinsG		p.X123_splice	ENST00000269305	NM_001126112.2	123		4/11	0.20642902265842	5	FACETS	0.851	0.793	0.909	0.851	0.793	0.909	INDETERMINATE	3	TRUE	2	0.694254966563036	5		702	394	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0058370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	69	432	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.193888026761749	2		432	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0058370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	263	867	9	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.146463254986887	3	FACETS	0.908	0.85	0.966	0.908	0.85	0.966	CLONAL	3	TRUE	0	0.193888026761749	3		876	1093	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911535	101911535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113605875	NA	P-0058370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	92	422	1	ENST00000374994.4:c.1460G>A	p.Arg487Gln	p.R487Q	ENST00000374994	NM_004612.2	487	cGg/cAg	9/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.193888026761749	NA		423	583	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248633	59248634	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0058370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	160	1127	2	ENST00000371222.2:c.109_110del	p.Ser37HisfsTer69	p.S37Hfs*69	ENST00000371222	NM_002228.3	37	AGc/c	1/1	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.193888026761749	2		1129	1208	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100998	41100998	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772057709	NA	P-0058370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	244	957	8	ENST00000373198.4:c.1358G>A	p.Arg453His	p.R453H	ENST00000373198	NM_133170.3	453	cGc/cAc	8/32	1	2	FACETS	1	0.976	1	1	0.995	1	CLONAL	2	TRUE	1	0.193888026761749	2		965	1149	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987204	36987204	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	65	1072	2	ENST00000354822.5:c.485C>G	p.Ala162Gly	p.A162G	ENST00000354822	NM_001079668.2	162	gCg/gGg	3/3	1	2	FACETS	0.567	0.49	0.652	0.567	0.49	0.652	SUBCLONAL	1	TRUE	1	0.193888026761749	2		1074	1182	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62290852	62290852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	77	550	0	ENST00000360203.5:c.97C>T	p.Gln33Ter	p.Q33*	ENST00000360203	NM_001283009.1	33	Cag/Tag	2/35	0.193888026761749	3	FACETS	1	0.946	1	0.572	0.502	0.649	CLONAL	1	TRUE	1	0.193888026761749	3		550	761	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0058371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	173	245	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.557946484068532	4	FACETS	0.896	0.84	0.951	0.896	0.84	0.951	CLONAL	3	TRUE	1	0.636903207535881	4		245	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0058371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	431	795	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.621650008263582	2	FACETS	0.994	0.959	1	0.994	0.959	1	CLONAL	2	TRUE	0	0.636903207535881	2		795	681	SUCCESS
APC	324	MSKCC	GRCh37	5	112174379	112174379	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs587779786	NA	P-0058371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	57	193	0	ENST00000257430.4:c.3088A>T	p.Lys1030Ter	p.K1030*	ENST00000257430	NM_000038.5	1030	Aaa/Taa	16/16	0.636903207535881	3	FACETS	1	0.872	1	0.502	0.436	0.573	CLONAL	1	TRUE	1	0.636903207535881	3		193	235	SUCCESS
APC	324	MSKCC	GRCh37	5	112175530	112175530	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	214	333	0	ENST00000257430.4:c.4240del	p.Val1414Ter	p.V1414*	ENST00000257430	NM_000038.5	1413	atG/at	16/16	0.636903207535881	3	FACETS	0.941	0.884	0.997	0.941	0.884	0.997	CLONAL	2	TRUE	1	0.636903207535881	3		333	471	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821082	72821082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458157669	NA	P-0058371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	386	592	0	ENST00000268489.5:c.11093C>T	p.Thr3698Met	p.T3698M	ENST00000268489	NM_006885.3	3698	aCg/aTg	10/10	0.636903207535881	3	FACETS	0.955	0.912	0.997	0.955	0.912	0.997	CLONAL	2	TRUE	1	0.636903207535881	3		592	837	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796011	78796011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757676238	NA	P-0058371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	228	755	1	ENST00000306801.3:c.901C>T	p.Arg301Cys	p.R301C	ENST00000306801	NM_020761.2	301	Cgc/Tgc	8/34	0.621650008263582	2	FACETS	0.994	0.931	1	0.497	0.465	0.53	CLONAL	1	TRUE	0	0.636903207535881	2		756	720	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575143	48575162	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	AAATATTGTCAGTATGCGTT	AAATATTGTCAGTATGCGTT	TAAGTC	novel	NA	P-0058371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	72	272	1	ENST00000342988.3:c.337_356delinsTAAGTC	p.Lys113Ter	p.K113*	ENST00000342988	NM_005359.5	113	AAATATTGTCAGTATGCGTTt/TAAGTCt	3/12	0.628330340192109	1	FACETS	0.866	0.774	0.96	0.866	0.774	0.96	CLONAL	1	TRUE	0	0.636903207535881	1		273	178	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	54	306	0				ENST00000310581	NM_198253.2	-/1132			0.510978443642913	3	FACETS	0.587	0.502	0.68	0.294	0.251	0.34	SUBCLONAL	1	TRUE	1	0.510978443642913	3		306	452	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806089	1806089	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913479	NA	P-0058372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	432	870	0	ENST00000260795.2:c.1108G>T	p.Gly370Cys	p.G370C	ENST00000260795		370	Ggc/Tgc	8/17	0.50983936353966	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.510978443642913	3		870	901	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518452	69518452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	76	359	0	ENST00000294312.3:c.193G>A	p.Asp65Asn	p.D65N	ENST00000294312	NM_005117.2	65	Gac/Aac	1/3	0.510978443642913	11	FACETS	0.896	0.783	1			1	CLONAL	1	TRUE	NA	0.510978443642913	11		359	1096	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118353185	118353185	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	54	188	0	ENST00000534358.1:c.4061C>T	p.Pro1354Leu	p.P1354L	ENST00000534358	NM_005933.3	1354	cCt/cTt	8/36	1	2	FACETS	0.877	0.757	1	0.877	0.757	1	CLONAL	1	TRUE	1	0.510978443642913	2		188	241	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467457	66467457	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	185	339	0	ENST00000273854.3:c.812C>A	p.Pro271His	p.P271H	ENST00000273854	NM_004439.5	271	cCt/cAt	3/18	0.50983936353966	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	1	0.510978443642913	3		339	443	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638317	176638317	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1156773906	NA	P-0058372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	170	615	0	ENST00000439151.2:c.2917C>G	p.Gln973Glu	p.Q973E	ENST00000439151	NM_022455.4	973	Cag/Gag	5/23	NA	2	FACETS	1	0.954	1			1	INDETERMINATE	1	TRUE	NA	0.510978443642913	2		615	636	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966728	44966735	+	frameshift_variant	Frame_Shift_Del	DEL	ATATGGCA	ATATGGCA	G	novel	NA	P-0058372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	177	422	0	ENST00000377967.4:c.3952_3959delinsG	p.Ile1318ValfsTer36	p.I1318Vfs*36	ENST00000377967	NM_021140.2	1318	ATATGGCAt/Gt	27/29	NA	2	FACETS	1	0.946	1			1	INDETERMINATE	2	TRUE	NA	0.510978443642913	2		422	343	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0058373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	110	276	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.535479621827957	2		276	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0058373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	179	605	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.535479621827957	1	FACETS	0.913	0.848	0.98	0.913	0.848	0.98	CLONAL	1	TRUE	0	0.535479621827957	1		605	536	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0058373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	103	656	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.535479621827957	2		657	304	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0058373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	115	310	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.535479621827957	2		310	393	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041571	42041571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	163	420	0	ENST00000219905.7:c.5767del	p.Thr1923LeufsTer46	p.T1923Lfs*46	ENST00000219905	NM_001164273.1	1922	atA/at	17/24	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.535479621827957	2		420	604	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747114	40747114	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	46	528	0	ENST00000373198.4:c.2968T>C	p.Phe990Leu	p.F990L	ENST00000373198	NM_133170.3	990	Ttt/Ctt	22/32	0.535479621827957	3	FACETS	0.25	0.21	0.295	0.125	0.105	0.148	SUBCLONAL	1	TRUE	1	0.535479621827957	3		528	870	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972871	55972871	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1336457631	NA	P-0058373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	60	234	0	ENST00000263923.4:c.1519A>G	p.Ile507Val	p.I507V	ENST00000263923	NM_002253.2	507	Att/Gtt	11/30	1	2	FACETS	0.907	0.791	1	0.907	0.791	1	CLONAL	1	TRUE	1	0.535479621827957	2		234	247	SUCCESS
APC	324	MSKCC	GRCh37	5	112175735	112175750	+	frameshift_variant	Frame_Shift_Del	DEL	CTTCCAGATGCTGATA	CTTCCAGATGCTGATA	-	novel	NA	P-0058373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	140	227	0	ENST00000257430.4:c.4447_4462del	p.Pro1483TyrfsTer19	p.P1483Yfs*19	ENST00000257430	NM_000038.5	1482	CTTCCAGATGCTGATAct/ct	16/16	0.535479621827957	2	FACETS	0.883	0.819	0.948	0.883	0.819	0.948	CLONAL	2	TRUE	0	0.535479621827957	2		227	296	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0058375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	159	284	2	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.49951751250599	3	FACETS	0.968	0.897	1	0.968	0.897	1	CLONAL	2	TRUE	1	0.49951751250599	3		286	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201059	NA	P-0058375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	264	688	0	ENST00000269305.4:c.856G>T	p.Glu286Ter	p.E286*	ENST00000269305	NM_001126112.2	286	Gaa/Taa	8/11	0.457893968498346	1	FACETS	0.934	0.878	0.991	0.934	0.878	0.991	CLONAL	1	TRUE	0	0.49951751250599	1		688	849	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400191	139400191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367710569	NA	P-0058375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	207	893	1	ENST00000277541.6:c.4157C>T	p.Pro1386Leu	p.P1386L	ENST00000277541	NM_017617.3	1386	cCg/cTg	25/34	NA	2	FACETS	0.838	0.778	0.901			1	INDETERMINATE	1	TRUE	NA	0.49951751250599	2		894	989	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141691	202141691	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	70	222	1	ENST00000358485.4:c.979G>A	p.Gly327Arg	p.G327R	ENST00000358485	NM_001080125.1	327	Ggg/Agg	7/9	1	2	FACETS	0.97	0.854	1	0.97	0.854	1	CLONAL	1	TRUE	1	0.49951751250599	2		223	289	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662404	67662404	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	145	648	1	ENST00000264010.4:c.1650del	p.Phe550LeufsTer34	p.F550Lfs*34	ENST00000264010	NM_006565.3	550	ttC/tt	9/12	1	2	FACETS	0.564	0.514	0.617	0.564	0.514	0.617	SUBCLONAL	1	TRUE	1	0.49951751250599	2		649	1029	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881543	48881543	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1131690907	NA	P-0058376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	36	102	0	ENST00000267163.4:c.264+1G>A		p.X88_splice	ENST00000267163	NM_000321.2	88			0.340763130624468	1	FACETS	0.785	0.654	0.927	0.785	0.654	0.927	CLONAL	1	TRUE	0	0.435159882533343	1		102	165	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577138	7577138	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587780075	NA	P-0058376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	250	678	0	ENST00000269305.4:c.800G>C	p.Arg267Pro	p.R267P	ENST00000269305	NM_001126112.2	267	cGg/cCg	8/11	0.419670539612026	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.435159882533343	1		678	847	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0058376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	87	293	0	ENST00000311936.3:c.34_35delinsCT	p.Gly12Leu	p.G12L	ENST00000311936	NM_004985.3	12	GGt/CTt	2/5	1	2	FACETS	0.856	0.761	0.957	0.856	0.761	0.957	CLONAL	1	TRUE	1	0.435159882533343	2		293	467	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879277	151879277	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs956673837	NA	P-0058376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	171	348	1	ENST00000262189.6:c.5668C>T	p.Arg1890Ter	p.R1890*	ENST00000262189	NM_170606.2	1890	Cga/Tga	36/59	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.435159882533343	2		349	784	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420631	49420631	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	329	916	1	ENST00000301067.7:c.15118G>T	p.Asp5040Tyr	p.D5040Y	ENST00000301067	NM_003482.3	5040	Gac/Tac	48/54	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.435159882533343	2		917	1231	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717633	89717634	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0058376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	87	305	0	ENST00000371953.3:c.659_660dup	p.Lys221Ter	p.K221*	ENST00000371953	NM_000314.4	220	cta/cTAta	7/9	1	2	FACETS	0.662	0.587	0.742	0.662	0.587	0.742	SUBCLONAL	1	TRUE	1	0.435159882533343	2		305	604	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974704	21974704	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	210	611	0	ENST00000304494.5:c.123del	p.Asn42IlefsTer11	p.N42Ifs*11	ENST00000304494	NM_000077.4	41	ccG/cc	1/3	0.435159882533343	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.435159882533343	1		611	688	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900327	101900328	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0058376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	79	165	0	ENST00000374994.4:c.762dup	p.Arg255ThrfsTer3	p.R255Tfs*3	ENST00000374994	NM_004612.2	254	tta/ttAa	4/9	0.402735887457289	1	FACETS	0.874	0.776	0.978	0.874	0.776	0.978	CLONAL	1	TRUE	0	0.435159882533343	1		165	325	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	181	475	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.966	0.895	1	1	0.993	1	CLONAL	2	TRUE	1	0.29	2		480	646	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	69	656	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.29	2		657	395	SUCCESS
BLM	641	MSKCC	GRCh37	15	91352442	91352442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760554566	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	59	346	0	ENST00000355112.3:c.3827C>T	p.Ala1276Val	p.A1276V	ENST00000355112	NM_000057.2	1276	gCg/gTg	20/22	1	2	FACETS	0.9	0.776	1	0.9	0.776	1	CLONAL	1	TRUE	1	0.29	2		346	452	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829040	128829042	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	rs570242755	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	10	74	0	ENST00000249373.3:c.67_69del	p.Leu23del	p.L23del	ENST00000249373	NM_005631.4	16	ggGCTg/ggg	1/12	1	2	FACETS	0.522	0.355	0.73	0.522	0.355	0.73	SUBCLONAL	1	TRUE	1	0.29	2		74	132	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	138	669	6	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.29	2		675	945	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	87	373	0	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.29	2		373	531	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	121	876	1	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.29	1		877	510	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979987	7979987	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746723399	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	85	807	5	ENST00000319144.4:c.1350del	p.Leu451SerfsTer16	p.L451Sfs*16	ENST00000319144	NM_001139.2	450	ggG/gg	10/15	1	2	FACETS	0.596	0.526	0.672	0.596	0.526	0.672	SUBCLONAL	1	TRUE	1	0.29	2		812	983	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	23	257	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.612	0.479	0.767	0.612	0.479	0.767	SUBCLONAL	1	TRUE	1	0.29	2		257	259	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	134	465	5	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.29	2		470	744	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8733795	8733795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138127948	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	113	552	0	ENST00000356435.5:c.49C>T	p.Arg17Cys	p.R17C	ENST00000356435		17	Cgc/Tgc	1/35	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.29	2		552	687	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	69	495	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.29	2		497	469	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	63	311	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.905	0.784	1	0.905	0.784	1	CLONAL	1	TRUE	1	0.29	2		311	480	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123246935	123246935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113014479	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	57	402	0	ENST00000358487.5:c.1990C>T	p.Arg664Trp	p.R664W	ENST00000358487	NM_000141.4	664	Cgg/Tgg	15/18	1	2	FACETS	0.822	0.707	0.948	0.822	0.707	0.948	CLONAL	1	TRUE	1	0.29	2		402	478	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	22	807	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	1	2	FACETS	0.162	0.125	0.206	0.162	0.125	0.206	SUBCLONAL	1	TRUE	1	0.29	2		807	935	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115727	108115727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747727055	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	21	154	0	ENST00000278616.4:c.875C>T	p.Pro292Leu	p.P292L	ENST00000278616	NM_000051.3	292	cCg/cTg	7/63	1	2	FACETS	1	0.808	1	1	0.808	1	CLONAL	1	TRUE	1	0.29	2		154	139	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736907	736907	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs986350587	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	34	453	0	ENST00000314574.4:c.1192C>T	p.Arg398Trp	p.R398W	ENST00000314574	NM_005433.3	398	Cgg/Tgg	10/12	1	2	FACETS	0.553	0.452	0.667	0.553	0.452	0.667	SUBCLONAL	1	TRUE	1	0.29	2		453	424	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	93	521	0	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.29	2		521	641	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802567	139802567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138185376	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	165	990	0	ENST00000247668.2:c.412G>A	p.Ala138Thr	p.A138T	ENST00000247668	NM_021138.3	138	Gcg/Acg	5/11	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.29	2		990	1128	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482169	87482169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201028496	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	62	586	0	ENST00000277120.3:c.1456G>A	p.Val486Ile	p.V486I	ENST00000277120		486	Gtt/Att	14/19	1	2	FACETS	0.583	0.503	0.671	0.583	0.503	0.671	SUBCLONAL	1	TRUE	1	0.29	2		586	733	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5077503	5077503	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	45	186	0	ENST00000381652.3:c.1919del	p.Lys640ArgfsTer6	p.K640Rfs*6	ENST00000381652	NM_004972.3	639	Aaa/aa	15/25	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.29	2		186	277	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403254	213403254	+	frameshift_variant,start_lost,start_retained_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	99	486	0	ENST00000342788.4:c.1del	p.Met1?	p.M1?	ENST00000342788	NM_005235.2	1	Atg/tg	1/28	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.29	2		486	660	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007580	62007580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778771873	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	154	819	0	ENST00000392795.3:c.287G>A	p.Arg96His	p.R96H	ENST00000392795	NM_001039933.1	96	cGc/cAc	3/6	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.29	2		819	951	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508470	106508470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1463222028	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	54	420	0	ENST00000359195.3:c.464C>T	p.Thr155Met	p.T155M	ENST00000359195	NM_002649.2	155	aCg/aTg	2/11	1	2	FACETS	0.924	0.792	1	0.924	0.792	1	CLONAL	1	TRUE	1	0.29	2		420	403	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636803	2636803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	151	731	0	ENST00000342085.4:c.1252G>A	p.Asp418Asn	p.D418N	ENST00000342085	NM_002613.4	418	Gat/Aat	11/14	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.29	2		731	990	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461100	120461100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs312262797	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	97	493	1	ENST00000256646.2:c.5858G>A	p.Arg1953His	p.R1953H	ENST00000256646	NM_024408.3	1953	cGc/cAc	32/34	1	2	FACETS	0.967	0.862	1	0.967	0.862	1	CLONAL	1	TRUE	1	0.29	2		494	692	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497937	25497937	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	128	826	0	ENST00000264709.3:c.512G>A	p.Arg171Gln	p.R171Q	ENST00000264709	NM_175629.2	171	cGg/cAg	6/23	1	2	FACETS	0.989	0.895	1	0.989	0.895	1	CLONAL	1	TRUE	1	0.29	2		826	893	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911445	134911445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571583026	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	88	495	0	ENST00000398015.3:c.1910G>A	p.Arg637His	p.R637H	ENST00000398015	NM_004441.4	637	cGt/cAt	11/16	1	2	FACETS	0.845	0.749	0.948	0.845	0.749	0.948	CLONAL	1	TRUE	1	0.29	2		495	718	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915852	127915852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	80	465	0	ENST00000373547.4:c.629G>A	p.Arg210Gln	p.R210Q	ENST00000373547	NM_002721.4	210	cGa/cAa	6/7	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.29	2		465	545	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128849225	128849225	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756828715	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	110	631	0	ENST00000249373.3:c.1453C>T	p.Arg485Trp	p.R485W	ENST00000249373	NM_005631.4	485	Cgg/Tgg	8/12	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.29	2		631	729	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46252683	46252683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372533478	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	34	237	0	ENST00000371998.3:c.112C>T	p.Arg38Trp	p.R38W	ENST00000371998		38	Cgg/Tgg	4/23	1	2	FACETS	0.659	0.539	0.793	0.659	0.539	0.793	SUBCLONAL	1	TRUE	1	0.29	2		237	356	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112035608	112035608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	61	443	1	ENST00000368678.4:c.286C>T	p.Arg96Trp	p.R96W	ENST00000368678		96	Cgg/Tgg	4/13	1	2	FACETS	0.738	0.637	0.848	0.738	0.637	0.848	SUBCLONAL	1	TRUE	1	0.29	2		444	570	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120851	94120851	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs889062730	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	62	453	0	ENST00000369303.4:c.200C>T	p.Pro67Leu	p.P67L	ENST00000369303	NM_004440.3	67	cCg/cTg	3/17	1	2	FACETS	0.687	0.594	0.79	0.687	0.594	0.79	SUBCLONAL	1	TRUE	1	0.29	2		453	622	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1620979	1620979	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1329397192	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	106	1066	5	ENST00000344749.5:c.1081del	p.Gln361ArgfsTer33	p.Q361Rfs*33	ENST00000344749	NM_001136139.2	361	Cag/ag	13/19	1	2	FACETS	0.597	0.533	0.665	0.597	0.533	0.665	SUBCLONAL	1	TRUE	1	0.29	2		1071	1225	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873409	136873409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs923351521	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	58	370	0	ENST00000241393.3:c.89G>A	p.Arg30His	p.R30H	ENST00000241393	NM_003467.2	30	cGt/cAt	2/2	1	2	FACETS	0.808	0.695	0.931	0.808	0.695	0.931	CLONAL	1	TRUE	1	0.29	2		370	495	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962853	2962854	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	104	926	1	ENST00000396946.4:c.2054dup	p.Asn686GlnfsTer23	p.N686Qfs*23	ENST00000396946	NM_032415.4	685	ggc/ggGc	16/25	1	2	FACETS	0.711	0.635	0.792	0.711	0.635	0.792	SUBCLONAL	1	TRUE	1	0.29	2		927	1009	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101352	27101352	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	124	872	0	ENST00000324856.7:c.4634G>A	p.Trp1545Ter	p.W1545*	ENST00000324856	NM_006015.4	1545	tGg/tAg	18/20	1	2	FACETS	0.922	0.833	1	0.922	0.833	1	CLONAL	1	TRUE	1	0.29	2		872	928	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137038	64137038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1372636808	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	115	954	1	ENST00000334205.4:c.1549G>A	p.Val517Met	p.V517M	ENST00000334205	NM_003942.2	517	Gtg/Atg	13/17	1	2	FACETS	0.748	0.673	0.829	0.748	0.673	0.829	SUBCLONAL	1	TRUE	1	0.29	2		955	1060	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074276	8074276	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	112	549	0	ENST00000377482.5:c.383del	p.Pro128LeufsTer3	p.P128Lfs*3	ENST00000377482	NM_018948.3	128	cCt/ct	4/4	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.29	2		549	654	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214145	36214145	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	125	935	1	ENST00000222270.7:c.2975del	p.Gly992AlafsTer17	p.G992Afs*17	ENST00000222270	NM_014727.1	991	Ggg/gg	6/37	1	2	FACETS	0.822	0.742	0.906	0.822	0.742	0.906	CLONAL	1	TRUE	1	0.29	2		936	1049	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257932	16257932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	100	632	0	ENST00000375759.3:c.5197G>A	p.Ala1733Thr	p.A1733T	ENST00000375759	NM_015001.2	1733	Gcc/Acc	11/15	1	2	FACETS	0.841	0.751	0.937	0.841	0.751	0.937	CLONAL	1	TRUE	1	0.29	2		632	820	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117750	108117750	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	30	216	0	ENST00000278616.4:c.961A>G	p.Asn321Asp	p.N321D	ENST00000278616	NM_000051.3	321	Aat/Gat	8/63	1	2	FACETS	0.932	0.756	1	0.932	0.756	1	CLONAL	1	TRUE	1	0.29	2		216	222	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125523717	125523717	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	26	144	0	ENST00000428830.2:c.1310T>C	p.Ile437Thr	p.I437T	ENST00000428830	NM_001114121.2	437	aTa/aCa	12/14	1	2	FACETS	0.8	0.637	0.986	0.8	0.637	0.986	CLONAL	1	TRUE	1	0.29	2		144	224	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109874	115109874	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	77	896	0	ENST00000257566.3:c.2004del	p.Leu670TrpfsTer219	p.L670Wfs*219	ENST00000257566	NM_016569.3	668	ggG/gg	8/8	1	2	FACETS	0.662	0.58	0.75	0.662	0.58	0.75	SUBCLONAL	1	TRUE	1	0.29	2		896	802	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865370	40865370	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1287970047	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	150	758	2	ENST00000428826.2:c.1061G>A	p.Arg354His	p.R354H	ENST00000428826		354	cGc/cAc	11/21	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.29	2		760	1030	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031592	11031592	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	99	1062	2	ENST00000327064.4:c.1507T>C	p.Tyr503His	p.Y503H	ENST00000327064	NM_199141.1	503	Tac/Cac	13/16	1	2	FACETS	0.673	0.6	0.752	0.673	0.6	0.752	SUBCLONAL	1	TRUE	1	0.29	2		1064	1014	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349771	15349771	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781555424	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	135	955	0	ENST00000263377.2:c.3803C>T	p.Ala1268Val	p.A1268V	ENST00000263377	NM_058243.2	1268	gCg/gTg	19/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.29	2		955	870	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211576	36211576	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	58	456	0	ENST00000222270.7:c.1327T>C	p.Ser443Pro	p.S443P	ENST00000222270	NM_014727.1	443	Tcc/Ccc	3/37	1	2	FACETS	0.955	0.823	1	0.955	0.823	1	CLONAL	1	TRUE	1	0.29	2		456	419	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905993	50905993	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs980303681	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	167	1017	2	ENST00000440232.2:c.965G>A	p.Arg322His	p.R322H	ENST00000440232	NM_002691.3	322	cGc/cAc	8/27	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.29	2		1019	996	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924778	49924778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368818557	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	146	1006	2	ENST00000296474.3:c.4165C>T	p.Arg1389Trp	p.R1389W	ENST00000296474	NM_002447.2	1389	Cgg/Tgg	20/20	1	2	FACETS	0.92	0.838	1	0.92	0.838	1	CLONAL	1	TRUE	1	0.29	2		1008	1095	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713658	52713658	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	68	611	0	ENST00000394830.3:c.70C>A	p.His24Asn	p.H24N	ENST00000394830	NM_018313.4	24	Cat/Aat	2/30	1	2	FACETS	0.583	0.506	0.666	0.583	0.506	0.666	SUBCLONAL	1	TRUE	1	0.29	2		611	805	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155181	55155181	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	78	599	0	ENST00000257290.5:c.2780A>T	p.Glu927Val	p.E927V	ENST00000257290	NM_006206.4	927	gAg/gTg	21/23	1	2	FACETS	0.879	0.773	0.993	0.879	0.773	0.993	CLONAL	1	TRUE	1	0.29	2		599	612	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200059	138200059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775952412	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	100	605	1	ENST00000237289.4:c.1477G>A	p.Gly493Arg	p.G493R	ENST00000237289	NM_001270507.1	493	Gga/Aga	7/9	1	2	FACETS	0.994	0.888	1	0.994	0.888	1	CLONAL	1	TRUE	1	0.29	2		606	694	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355302	81355302	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	73	302	1	ENST00000222390.5:c.1072G>T	p.Asp358Tyr	p.D358Y	ENST00000222390	NM_000601.4	358	Gat/Tat	9/18	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.29	2		303	405	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852162	128852162	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs377501107	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	92	1077	0	ENST00000249373.3:c.2234A>G	p.Gln745Arg	p.Q745R	ENST00000249373	NM_005631.4	745	cAg/cGg	12/12	1	2	FACETS	0.67	0.594	0.751	0.67	0.594	0.751	SUBCLONAL	1	TRUE	1	0.29	2		1077	947	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561474	141561474	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	91	782	0	ENST00000220592.5:c.1331del	p.Thr444ArgfsTer24	p.T444Rfs*24	ENST00000220592	NM_012154.3	444	aCg/ag	11/19	1	2	FACETS	0.661	0.585	0.741	0.661	0.585	0.741	SUBCLONAL	1	TRUE	1	0.29	2		782	950	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396814	139396814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446572888	NA	P-0058377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	146	894	0	ENST00000277541.6:c.5294G>A	p.Gly1765Asp	p.G1765D	ENST00000277541	NM_017617.3	1765	gGc/gAc	28/34	1	2	FACETS	0.969	0.883	1	0.969	0.883	1	CLONAL	1	TRUE	1	0.29	2		894	1039	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451087	70451087	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	38	627	0	ENST00000373644.4:c.5927C>G	p.Ser1976Cys	p.S1976C	ENST00000373644	NM_030625.2	1976	tCt/tGt	12/12	0.365962818510165	5	FACETS	0.501	0.413	0.6	0.167	0.137	0.2	SUBCLONAL	1	FALSE	2	0.365962818510165	5		627	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578206	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs886039484	NA	P-0058378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	126	800	0	ENST00000269305.4:c.643A>G	p.Ser215Gly	p.S215G	ENST00000269305	NM_001126112.2	215	Agt/Ggt	6/11	0.365962818510165	3	FACETS	0.658	0.594	0.726	0.329	0.297	0.363	SUBCLONAL	1	FALSE	1	0.365962818510165	3		800	1238	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794419	242794419	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	162	1197	0	ENST00000334409.5:c.523G>T	p.Gly175Cys	p.G175C	ENST00000334409	NM_005018.2	175	Ggc/Tgc	3/5	1	2	FACETS	0.962	0.881	1	0.962	0.881	1	CLONAL	1	TRUE	1	0.31	2		1197	1087	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623085	52623085	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0058379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	81	431	0	ENST00000394830.3:c.2965+1G>A		p.X989_splice	ENST00000394830	NM_018313.4	989			0.298668937761111	1	FACETS	0.975	0.862	1	0.975	0.862	1	CLONAL	1	TRUE	0	0.31	1		431	453	SUCCESS
APC	324	MSKCC	GRCh37	5	112157613	112157613	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658802	NA	P-0058380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	36	435	0	ENST00000257430.4:c.1333C>T	p.Gln445Ter	p.Q445*	ENST00000257430	NM_000038.5	445	Cag/Tag	11/16	0.485845905724472	4	FACETS	0.992	0.824	1	0.496	0.412	0.588	CLONAL	1	TRUE	2	0.607650062919776	4		435	192	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696450	47696450	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	17	489	0	ENST00000347630.2:c.373T>C	p.Phe125Leu	p.F125L	ENST00000347630	NM_001007230.1	125	Ttt/Ctt	6/11	0.272628872550132	5	FACETS	0.401	0.299	0.521	0.134	0.099	0.174	INDETERMINATE	1	TRUE	2	0.607650062919776	5		489	267	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246793	41246793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80357138	NA	P-0058380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	16	483	0	ENST00000357654.3:c.755G>A	p.Arg252His	p.R252H	ENST00000357654	NM_007294.3	252	cGt/cAt	10/23	0.272628872550132	5	FACETS	0.645	0.48	0.84	0.215	0.16	0.28	INDETERMINATE	1	TRUE	2	0.607650062919776	5		483	156	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061188	38061209	+	protein_altering_variant	In_Frame_Del	DEL	CTTGAAGCGCTTCTGGCGGCGC	CTTGAAGCGCTTCTGGCGGCGC	A	novel	NA	P-0058380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	91	678	0	ENST00000250448.2:c.780_801delinsT	p.Leu260_Lys267delinsPhe	p.L260_K267delinsF	ENST00000250448	NM_004496.3	260	ttGCGCCGCCAGAAGCGCTTCAAG/ttT	2/2	0.278982470973442	5	FACETS	1	0.894	1	0.335	0.298	0.374	INDETERMINATE	1	TRUE	2	0.607650062919776	5		678	570	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274911	41274911	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	18	352	0	ENST00000349496.5:c.1161T>G	p.Asn387Lys	p.N387K	ENST00000349496	NM_001904.3	387	aaT/aaG	8/15	0.150606911865513	3	FACETS	0.94	0.724	1	0.94	0.724	1	INDETERMINATE	2	TRUE	1	0.28	3		352	78	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs80338963	NA	P-0058381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	14	388	0	ENST00000342988.3:c.1081C>A	p.Arg361Ser	p.R361S	ENST00000342988	NM_005359.5	361	Cgc/Agc	9/12	0.16895118351846	1	FACETS	1	0.811	1	1	0.811	1	CLONAL	1	TRUE	0	0.28	1		388	76	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527822	103527822	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs768440346	NA	P-0058381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	11	303	0	ENST00000355739.4:c.3130G>T	p.Glu1044Ter	p.E1044*	ENST00000355739	NM_000123.3	1044	Gaa/Taa	15/15	0.150606911865513	3	FACETS	0.963	0.673	1	0.482	0.336	0.658	INDETERMINATE	1	TRUE	1	0.28	3		303	93	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186796	108186796	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	18	401	1	ENST00000278616.4:c.6154G>T	p.Glu2052Ter	p.E2052*	ENST00000278616	NM_000051.3	2052	Gaa/Taa	42/63	0.150606911865513	3	FACETS	1	0.871	1	0.621	0.473	0.791	INDETERMINATE	1	TRUE	1	0.28	3		402	118	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959067	2959067	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376539147	NA	P-0058381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	102	708	0	ENST00000396946.4:c.2449G>A	p.Ala817Thr	p.A817T	ENST00000396946	NM_032415.4	817	Gcg/Acg	18/25	1	2	FACETS	0.804	0.718	0.896	0.804	0.718	0.896	CLONAL	1	TRUE	1	0.28	2		708	906	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720676	89720676	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	25	337	0	ENST00000371953.3:c.827A>T	p.Asn276Ile	p.N276I	ENST00000371953	NM_000314.4	276	aAt/aTt	8/9	0.3	3	FACETS	1	0.841	1	1	0.841	1	CLONAL	2	TRUE	1	0.28	3		337	97	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413574	32413574	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	25	400	0	ENST00000332351.3:c.1376A>C	p.Lys459Thr	p.K459T	ENST00000332351	NM_024426.4	459	aAg/aCg	9/10	0.150606911865513	3	FACETS	0.628	0.495	0.781	0.314	0.247	0.391	INDETERMINATE	1	TRUE	1	0.28	3		400	324	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858001	9858001	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs748967552	NA	P-0058381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	26	571	0	ENST00000330684.3:c.3400C>T	p.Gln1134Ter	p.Q1134*	ENST00000330684	NM_001134407.1	1134	Cag/Tag	13/13	1	2	FACETS	0.678	0.538	0.837	0.678	0.538	0.837	SUBCLONAL	1	TRUE	1	0.28	2		571	274	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0058383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	103	293	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.0848167709110121	4	FACETS	0.971	0.873	1	0.971	0.873	1	INDETERMINATE	2	TRUE	2	0.28	4		293	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0058383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1919	434	1011	1	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.296644014460907	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.28	1		1012	2353	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488315	56488315	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	256	514	0	ENST00000267101.3:c.1834C>T	p.Pro612Ser	p.P612S	ENST00000267101	NM_001982.3	612	Ccc/Tcc	15/28	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.28	2		514	1341	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794636	42794637	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1555768427	NA	P-0058383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1785	164	939	1	ENST00000575354.2:c.1721dup	p.Pro575ThrfsTer115	p.P575Tfs*115	ENST00000575354	NM_015125.3	572	-/C	10/20	0.296644014460907	1	FACETS	0.517	0.472	0.564	0.517	0.472	0.564	SUBCLONAL	1	TRUE	0	0.28	1		940	1949	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044579	128044579	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1298	168	480	0	ENST00000285398.2:c.1042del	p.Leu348TrpfsTer4	p.L348Wfs*4	ENST00000285398	NM_000122.1	348	Ctg/tg	8/15	1	2	FACETS	0.819	0.75	0.891	0.819	0.75	0.891	CLONAL	1	TRUE	1	0.28	2		480	1466	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253775	30253775	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	212	624	0	ENST00000307677.4:c.679G>T	p.Gly227Cys	p.G227C	ENST00000307677	NM_138578.1	227	Ggc/Tgc	3/3	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.539074331894401	2		624	752	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40469240	40469240	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs747667389	NA	P-0058384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	189	315	0	ENST00000264657.5:c.2104G>A	p.Ala702Thr	p.A702T	ENST00000264657	NM_139276.2	702	Gct/Act	22/24	0.436571203941299	4	FACETS	0.803	0.745	0.863	0.803	0.745	0.863	CLONAL	2	TRUE	2	0.539074331894401	4		315	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576893	7576893	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	471	779	1	ENST00000269305.4:c.953del	p.Pro318GlnfsTer27	p.P318Qfs*27	ENST00000269305	NM_001126112.2	318	cCa/ca	9/11	0.525432042691561	2	FACETS	0.933	0.897	0.97	0.933	0.897	0.97	CLONAL	2	TRUE	0	0.539074331894401	2		780	936	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0058385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	43	495	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.784	0.655	0.928	0.784	0.655	0.928	CLONAL	1	TRUE	1	0.17	2		497	645	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100907	27100907	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	69	822	0	ENST00000324856.7:c.4189C>T	p.Gln1397Ter	p.Q1397*	ENST00000324856	NM_006015.4	1397	Cag/Tag	18/20	1	2	FACETS	0.879	0.763	1	0.879	0.763	1	CLONAL	1	TRUE	1	0.17	2		822	924	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856604	111856604	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1177556874	NA	P-0058385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	55	436	2	ENST00000341259.2:c.655C>T	p.Arg219Cys	p.R219C	ENST00000341259	NM_005475.2	219	Cgc/Tgc	2/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.17	2		438	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0058385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	75	1219	2	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	NA	2	FACETS	0.726	0.634	0.826			1	INDETERMINATE	1	TRUE	NA	0.17	2		1221	1215	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144113	11144113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	79	1050	3	ENST00000358026.2:c.3694G>A	p.Gly1232Ser	p.G1232S	ENST00000358026	NM_001128849.1	1232	Ggc/Agc	26/36	1	2	FACETS	0.798	0.699	0.904	0.798	0.699	0.904	CLONAL	1	TRUE	1	0.17	2		1053	1165	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902847	1902847	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	41	677	0	ENST00000382891.5:c.466G>T	p.Glu156Ter	p.E156*	ENST00000382891	NM_133335.3	156	Gaa/Taa	2/22	1	2	FACETS	0.614	0.509	0.73	0.614	0.509	0.73	SUBCLONAL	1	TRUE	1	0.17	2		677	786	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0058386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	611	1082	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.738560203159285	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.84361650043711	1		1082	834	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318796	163318796	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1347093988	NA	P-0058386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	64	377	0	ENST00000271452.3:c.1186C>G	p.Gln396Glu	p.Q396E	ENST00000271452	NM_145697.2	396	Caa/Gaa	13/14	0.84361650043711	1	FACETS	0.261	0.227	0.297	0.261	0.227	0.297	SUBCLONAL	1	TRUE	0	0.84361650043711	1		377	336	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230377	46230377	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	226	238	0	ENST00000334344.6:c.711G>T	p.Trp237Cys	p.W237C	ENST00000334344	NM_152641.2	237	tgG/tgT	7/21	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.84361650043711	2		238	535	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063671	67063682	+	inframe_deletion	In_Frame_Del	DEL	CCAGGCACGCTT	CCAGGCACGCTT	-	novel	NA	P-0058386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	122	562	1	ENST00000412916.2:c.124_135del	p.Ala42_Gln45del	p.A42_Q45del	ENST00000412916		40	cgCCAGGCACGCTTc/cgc	2/6	0.84361650043711	1	FACETS	0.463	0.423	0.504	0.463	0.423	0.504	SUBCLONAL	1	TRUE	0	0.84361650043711	1		563	361	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653208	29653212	+	frameshift_variant	Frame_Shift_Del	DEL	GACCT	GACCT	-	novel	NA	P-0058386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	266	348	0	ENST00000356175.3:c.5145_5149del	p.Asp1715GlufsTer19	p.D1715Efs*19	ENST00000356175	NM_000267.3	1715	GACCTg/g	36/57	0.738560203159285	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.84361650043711	1		348	358	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0058388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	50	432	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.945	0.801	1	0.945	0.801	1	CLONAL	1	TRUE	1	0.19	2		432	557	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740213	46740213	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	24	341	0	ENST00000371975.4:c.1693C>G	p.Pro565Ala	p.P565A	ENST00000371975	NM_003579.3	565	Cct/Gct	16/18	1	2	FACETS	0.548	0.429	0.686	0.548	0.429	0.686	SUBCLONAL	1	TRUE	1	0.19	2		341	461	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0058389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	48	422	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	1	2	FACETS	0.848	0.719	0.99	0.848	0.719	0.99	CLONAL	1	TRUE	1	0.278794545580778	2		422	406	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023151	27023179	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	-	novel	NA	P-0058389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	100	87	1	ENST00000324856.7:c.267_295del	p.Ser90ProfsTer11	p.S90Pfs*11	ENST00000324856	NM_006015.4	86	gGCGGAGCCGGCAGCGGCGGCGGGCCCGGC/g	1/20	0.225730557234323	1	FACETS	0.85	0.774	0.928	1	0.99	1	CLONAL	3	TRUE	0	0.278794545580778	1		88	242	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604690	48604690	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	71	438	0	ENST00000342988.3:c.1512T>A	p.Ser504Arg	p.S504R	ENST00000342988	NM_005359.5	504	agT/agA	12/12	0.225730557234323	1	FACETS	0.845	0.738	0.959	0.845	0.738	0.959	CLONAL	1	TRUE	0	0.278794545580778	1		438	519	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412955	63412955	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	84	892	0	ENST00000330258.3:c.212G>A	p.Ser71Asn	p.S71N	ENST00000330258	NM_152424.3	71	aGt/aAt	2/2	1	2	FACETS	0.593	0.522	0.669	0.593	0.522	0.669	SUBCLONAL	1	TRUE	1	0.278794545580778	2		892	1017	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0058394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	217	172	0				ENST00000310581	NM_198253.2	-/1132			0.662770336768804	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.662770336768804	1		172	391	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0058394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	907	622	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.662770336768804	3	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.662770336768804	3		622	1567	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233129	46233129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371956323	NA	P-0058394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	199	272	0	ENST00000334344.6:c.1348G>A	p.Val450Ile	p.V450I	ENST00000334344	NM_152641.2	450	Gtt/Att	11/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.662770336768804	2		272	505	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218335	69218335	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	242	385	0	ENST00000462284.1:c.427G>A	p.Asp143Asn	p.D143N	ENST00000462284	NM_002392.5	143	Gac/Aac	7/11	1	2	FACETS	0.986	0.924	1	0.986	0.924	1	CLONAL	1	TRUE	1	0.662770336768804	2		385	741	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120805818	120805818	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	457	875	0	ENST00000257552.2:c.260C>T	p.Ser87Phe	p.S87F	ENST00000257552	NM_002442.3	87	tCc/tTc	4/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.662770336768804	2		875	1344	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061775	38061776	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	345	703	2	ENST00000250448.2:c.213_214delinsAA	p.Gly72Ser	p.G72S	ENST00000250448	NM_004496.3	71	ccGGgc/ccAAgc	2/2	0.662770336768804	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.662770336768804	1		705	686	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500505	99500505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	525	779	0	ENST00000268035.6:c.3938C>T	p.Ser1313Phe	p.S1313F	ENST00000268035	NM_000875.3	1313	tCc/tTc	21/21	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.662770336768804	2		779	1397	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349094	89349094	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779425691	NA	P-0058394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	533	889	1	ENST00000301030.4:c.3856G>A	p.Glu1286Lys	p.E1286K	ENST00000301030	NM_001256183.1	1286	Gaa/Aaa	9/13	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.662770336768804	2		890	1512	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47700153	47700153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	275	438	0	ENST00000347630.2:c.20C>T	p.Pro7Leu	p.P7L	ENST00000347630	NM_001007230.1	7	cCt/cTt	3/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.662770336768804	2		438	768	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277064	18277064	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	368	552	1	ENST00000222254.8:c.1511A>T	p.Glu504Val	p.E504V	ENST00000222254	NM_005027.3	504	gAa/gTa	12/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.662770336768804	2		553	1067	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793311	242793311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1021665035	NA	P-0058394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	1134	1014	0	ENST00000334409.5:c.766G>A	p.Gly256Arg	p.G256R	ENST00000334409	NM_005018.2	256	Gga/Aga	5/5	0.662770336768804	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	1	0.662770336768804	3		1014	2128	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624942	9624942	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	180	388	0	ENST00000353224.5:c.35C>T	p.Ser12Phe	p.S12F	ENST00000353224	NM_177990.2	12	tCt/tTt	3/10	0.662770336768804	3	FACETS	0.925	0.854	0.998	0.462	0.427	0.499	CLONAL	1	TRUE	1	0.662770336768804	3		388	782	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394046	31394046	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	207	380	0	ENST00000328111.2:c.2333C>T	p.Ser778Leu	p.S778L	ENST00000328111	NM_006892.3	778	tCg/tTg	22/23	0.662770336768804	3	FACETS	0.904	0.839	0.971	0.452	0.419	0.486	CLONAL	1	TRUE	1	0.662770336768804	3		380	920	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274864	41274864	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	226	440	0	ENST00000349496.5:c.1114G>A	p.Asp372Asn	p.D372N	ENST00000349496	NM_001904.3	372	Gat/Aat	8/15	1	2	FACETS	0.928	0.868	0.99	0.928	0.868	0.99	CLONAL	1	TRUE	1	0.662770336768804	2		440	735	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197140	106197140	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	201	394	0	ENST00000380013.4:c.5473C>A	p.Gln1825Lys	p.Q1825K	ENST00000380013	NM_001127208.2	1825	Cag/Aag	11/11	1	2	FACETS	0.964	0.899	1	0.964	0.899	1	CLONAL	1	TRUE	1	0.662770336768804	2		394	629	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120729	94120729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	249	502	0	ENST00000369303.4:c.322G>A	p.Asp108Asn	p.D108N	ENST00000369303	NM_004440.3	108	Gat/Aat	3/17	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.662770336768804	2		502	746	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965469	68965469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	315	540	0	ENST00000288368.4:c.1081G>A	p.Glu361Lys	p.E361K	ENST00000288368	NM_024870.2	361	Gaa/Aaa	9/40	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.662770336768804	2		540	921	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0058397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	12	258	1				ENST00000310581	NM_198253.2	-/1132			0.579380568572252	0	FACETS	0.148	0.104	0.2			1	SUBCLONAL	1	TRUE	0	0.579365054506953	0		259	118	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578390	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0058397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	35	743	2	ENST00000269305.4:c.540_541delinsTT	p.Glu180_Arg181delinsAspCys	p.E180_R181delinsDC	ENST00000269305	NM_001126112.2	180	gaGCgc/gaTTgc	5/11	0.193625305149437	4	FACETS	0.296	0.242	0.357	0.148	0.121	0.179	INDETERMINATE	1	TRUE	2	0.579365054506953	4		745	645	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874031	123874031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1447464550	NA	P-0058398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	10	30	0	ENST00000330479.4:c.62C>T	p.Ala21Val	p.A21V	ENST00000330479	NM_020382.3	21	gCg/gTg	2/9	0.730587393147831	3	FACETS	0.492	0.338	0.679	0.246	0.169	0.34	SUBCLONAL	1	TRUE	1	0.730587393147831	3		30	76	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578448	7578449	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0058398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	486	891	0	ENST00000269305.4:c.481dup	p.Ala161GlyfsTer20	p.A161Gfs*20	ENST00000269305	NM_001126112.2	161	gcc/gGcc	5/11	0.730587393147831	2	FACETS	0.952	0.923	0.98	0.952	0.923	0.98	CLONAL	2	TRUE	0	0.730587393147831	2		891	699	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18962995	18962995	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	219	869	0	ENST00000262803.5:c.862G>T	p.Glu288Ter	p.E288*	ENST00000262803	NM_002911.3	288	Gag/Tag	6/24	0.667961367450846	4	FACETS	1	0.941	1	0.506	0.471	0.543	CLONAL	1	TRUE	2	0.730587393147831	4		869	1025	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	130	306	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.684853312463667	2		306	302	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845511	128845511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs111694017	NA	P-0058400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	343	687	0	ENST00000249373.3:c.808G>A	p.Val270Ile	p.V270I	ENST00000249373	NM_005631.4	270	Gtc/Atc	4/12	0.684853312463667	3	FACETS	1	0.98	1	0.536	0.507	0.566	CLONAL	1	TRUE	1	0.684853312463667	3		687	1255	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221800	55221800	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199796955	NA	P-0058400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18547	978	795	0	ENST00000275493.2:c.844G>A	p.Glu282Lys	p.E282K	ENST00000275493	NM_005228.3	282	Gag/Aag	7/28	0.684853312463667	35	FACETS	0.9	0.866	0.934	0.051	0.049	0.054	CLONAL	2	TRUE	0	0.684853312463667	35		795	19525	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350307	15350307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs562849437	NA	P-0058400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	288	734	0	ENST00000263377.2:c.3472G>A	p.Gly1158Arg	p.G1158R	ENST00000263377	NM_058243.2	1158	Ggg/Agg	17/20	0.204172173183953	3	FACETS	1	0.983	1	0.37	0.348	0.393	INDETERMINATE	1	TRUE	0	0.684853312463667	3		734	1016	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711951	89711951	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554900617	NA	P-0058400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	272	374	0	ENST00000371953.3:c.569C>T	p.Pro190Leu	p.P190L	ENST00000371953	NM_000314.4	190	cCa/cTa	6/9	0.684853312463667	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.684853312463667	1		374	454	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0058401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	1263	361	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.311332750954362	7	FACETS	1	0.997	1			1	CLONAL	9	TRUE	NA	0.311332750954362	7		361	1540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138729528	NA	P-0058401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	114	870	0	ENST00000269305.4:c.523C>G	p.Arg175Gly	p.R175G	ENST00000269305	NM_001126112.2	175	Cgc/Ggc	5/11	0.311332750954362	1	FACETS	0.931	0.84	1	0.931	0.84	1	CLONAL	1	TRUE	0	0.311332750954362	1		870	664	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0058403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	24	421	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.250519382855668	5	FACETS	0.489	0.382	0.613	0.122	0.095	0.154	SUBCLONAL	1	TRUE	1	0.250519382855668	5		421	539	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906916	32906919	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	rs80359277	NA	P-0058403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	18	191	0	ENST00000380152.3:c.1310_1313del	p.Lys437IlefsTer22	p.K437Ifs*22	ENST00000380152		434	aAAAGa/aa	10/27	0.201336349303946	1	FACETS	0.566	0.427	0.73	0.566	0.427	0.73	SUBCLONAL	1	TRUE	0	0.250519382855668	1		191	222	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830895	72830895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770650936	NA	P-0058403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	153	579	0	ENST00000268489.5:c.5686G>A	p.Ala1896Thr	p.A1896T	ENST00000268489	NM_006885.3	1896	Gcc/Acc	9/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.250519382855668	2		579	1153	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248058	110248058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755781036	NA	P-0058403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	59	452	1	ENST00000374672.4:c.1414G>A	p.Ala472Thr	p.A472T	ENST00000374672	NM_004235.4	472	Gcc/Acc	5/5	0.233774009494918	2	FACETS	0.448	0.384	0.519	0.224	0.192	0.26	SUBCLONAL	1	TRUE	0	0.250519382855668	2		453	1051	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076712	72076712	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	50	441	0	ENST00000357731.5:c.785A>T	p.Lys262Met	p.K262M	ENST00000357731	NM_173808.2	262	aAg/aTg	5/7	1	2	FACETS	0.479	0.405	0.56	0.479	0.405	0.56	SUBCLONAL	1	TRUE	1	0.250519382855668	2		441	834	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243777014	243777014	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	16	140	0	ENST00000263826.5:c.655G>C	p.Asp219His	p.D219H	ENST00000263826	NM_005465.4	219	Gac/Cac	7/13	1	2	FACETS	0.71	0.527	0.926	0.71	0.527	0.926	CLONAL	1	TRUE	1	0.250519382855668	2		140	180	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852172	63852172	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	64	577	0	ENST00000279873.7:c.2950G>C	p.Glu984Gln	p.E984Q	ENST00000279873	NM_032199.2	984	Gag/Cag	10/10	1	2	FACETS	0.51	0.44	0.587	0.51	0.44	0.587	SUBCLONAL	1	TRUE	1	0.250519382855668	2		577	1001	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478574	99478598	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGCCAACACTGGTCATCATGGAA	CCAGCCAACACTGGTCATCATGGAA	-	novel	NA	P-0058403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	56	447	0	ENST00000268035.6:c.3217_3241del	p.Gln1073Ter	p.Q1073*	ENST00000268035	NM_000875.3	1072	ggCCAGCCAACACTGGTCATCATGGAA/gg	17/21	1	2	FACETS	0.486	0.415	0.564	0.486	0.415	0.564	SUBCLONAL	1	TRUE	1	0.250519382855668	2		447	920	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351918	89351918	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1475	131	791	0	ENST00000301030.4:c.1032G>C	p.Lys344Asn	p.K344N	ENST00000301030	NM_001256183.1	344	aaG/aaC	9/13	1	2	FACETS	0.651	0.588	0.718	0.651	0.588	0.718	SUBCLONAL	1	TRUE	1	0.250519382855668	2		791	1606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577572	7577573	+	stop_gained	Nonsense_Mutation	DNP	TG	TG	AT	novel	NA	P-0058403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	167	594	1	ENST00000269305.4:c.708_709delinsAT	p.Tyr236_Met237delinsTer	p.Y236_M237delins*	ENST00000269305	NM_001126112.2	236	taCAtg/taATtg	7/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.250519382855668	2		595	1048	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226967	2226967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1233	85	623	0	ENST00000398665.3:c.4447G>A	p.Ala1483Thr	p.A1483T	ENST00000398665	NM_032482.2	1483	Gcc/Acc	27/28	0.250519382855668	1	FACETS	0.45	0.396	0.509	0.45	0.396	0.509	SUBCLONAL	1	TRUE	0	0.250519382855668	1		623	1318	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198233	185198238	+	frameshift_variant	Frame_Shift_Del	DEL	GCTCTC	GCTCTC	AGTG	novel	NA	P-0058403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1494	101	605	0	ENST00000265026.3:c.2715_2720delinsAGTG	p.Leu906ValfsTer2	p.L906Vfs*2	ENST00000265026	NM_004721.4	905	ggGCTCTCt/ggAGTGt	13/14	0.250519382855668	5	FACETS	0.696	0.619	0.778	0.174	0.154	0.195	SUBCLONAL	1	TRUE	1	0.250519382855668	5		605	1595	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0058405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	144	380	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.175166537650076	2		380	1105	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578551	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	31	938	0	ENST00000269305.4:c.379T>A	p.Ser127Thr	p.S127T	ENST00000269305	NM_001126112.2	127	Tcc/Acc	5/11	1	2	FACETS	0.362	0.291	0.443	0.362	0.291	0.443	SUBCLONAL	1	FALSE	1	0.175166537650076	2		938	978	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24133944	24133944	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	47	314	0	ENST00000263121.7:c.95T>A	p.Val32Glu	p.V32E	ENST00000263121	NM_003073.3	32	gTg/gAg	2/9	1	2	FACETS	0.769	0.651	0.898	1	0.963	1	SUBCLONAL	2	FALSE	1	0.175166537650076	2		314	349	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974744	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAGCAGCGCCCGCA	CCTCCAGCAGCGCCCGCA	-	novel	NA	P-0058405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	47	558	0	ENST00000304494.5:c.83_100del	p.Val28_Glu33del	p.V28_E33del	ENST00000304494	NM_000077.4	28	gTGCGGGCGCTGCTGGAGGcg/gcg	1/3	0.175166537650076	1	FACETS	0.617	0.519	0.726	0.617	0.519	0.726	SUBCLONAL	1	FALSE	0	0.175166537650076	1		558	793	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413049	139413049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064795070	NA	P-0058405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	75	814	0	ENST00000277541.6:c.1093C>T	p.Arg365Cys	p.R365C	ENST00000277541	NM_017617.3	365	Cgc/Tgc	6/34	0.152715879557741	2	FACETS	0.838	0.732	0.952	0.419	0.366	0.476	CLONAL	1	FALSE	0	0.175166537650076	2		814	1022	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413070	139413072	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0058405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	48	939	0	ENST00000277541.6:c.1070_1072del	p.Phe357del	p.F357del	ENST00000277541	NM_017617.3	357	tTCTac/tac	6/34	0.152715879557741	2	FACETS	0.486	0.409	0.572	0.243	0.204	0.286	SUBCLONAL	1	FALSE	0	0.175166537650076	2		939	1127	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0058406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	337	380	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.561957609897933	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.561957609897933	1		380	806	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102181	27102187	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTTCA	ACCTTCA	-	novel	NA	P-0058406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	74	470	0	ENST00000324856.7:c.5111_5117del	p.Phe1704SerfsTer8	p.F1704Sfs*8	ENST00000324856	NM_006015.4	1703	ACCTTCAac/ac	19/20	0.319050050901013	1	FACETS	0.443	0.39	0.501	0.443	0.39	0.501	INDETERMINATE	1	TRUE	0	0.561957609897933	1		470	427	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920401	114920401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1422891742	NA	P-0058406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	213	575	0	ENST00000543371.1:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000543371	NM_001198531.1	448	Cgg/Tgg	13/14	0.319050050901013	1	FACETS	0.811	0.757	0.866	0.811	0.757	0.866	INDETERMINATE	1	TRUE	0	0.561957609897933	1		575	672	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2214480	2214480	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1285640382	NA	P-0058406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	604	877	1	ENST00000398665.3:c.1808G>A	p.Arg603His	p.R603H	ENST00000398665	NM_032482.2	603	cGc/cAc	19/28	0.561957609897933	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.561957609897933	2		878	1049	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223485	2223485	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	58	391	0	ENST00000398665.3:c.3596G>A	p.Arg1199Gln	p.R1199Q	ENST00000398665	NM_032482.2	1199	cGa/cAa	25/28	0.561957609897933	2	FACETS	0.491	0.423	0.565	0.246	0.211	0.283	SUBCLONAL	1	TRUE	0	0.561957609897933	2		391	420	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445424	29445424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762571775	NA	P-0058406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	139	812	3	ENST00000389048.3:c.3409G>A	p.Gly1137Arg	p.G1137R	ENST00000389048	NM_004304.4	1137	Gga/Aga	21/29	0.27067548114103	2	FACETS	0.493	0.448	0.541	0.247	0.224	0.271	INDETERMINATE	1	TRUE	0	0.561957609897933	2		815	1003	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570063	212570063	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746784831	NA	P-0058406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	28	477	0	ENST00000342788.4:c.1178G>A	p.Arg393Gln	p.R393Q	ENST00000342788	NM_005235.2	393	cGg/cAg	10/28	0.27067548114103	2	FACETS	0.287	0.229	0.353	0.144	0.114	0.177	INDETERMINATE	1	TRUE	0	0.561957609897933	2		477	347	SUCCESS
APC	324	MSKCC	GRCh37	5	112162918	112162919	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	rs886039509	NA	P-0058406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	45	385	0	ENST00000257430.4:c.1522_1523del	p.Leu508AspfsTer28	p.L508Dfs*28	ENST00000257430	NM_000038.5	508	TTg/g	12/16	0.358574228976735	1	FACETS	0.729	0.624	0.841	0.729	0.624	0.841	SUBCLONAL	1	TRUE	0	0.561957609897933	1		385	158	SUCCESS
APC	324	MSKCC	GRCh37	5	112175353	112175366	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTTCAGGAGCGA	TTCTTCAGGAGCGA	-	novel	NA	P-0058406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	43	313	0	ENST00000257430.4:c.4062_4075del	p.Phe1354LeufsTer16	p.F1354Lfs*16	ENST00000257430	NM_000038.5	1354	ttTTCTTCAGGAGCGAaa/ttaa	16/16	0.358574228976735	1	FACETS	0.376	0.316	0.441	0.376	0.316	0.441	SUBCLONAL	1	TRUE	0	0.561957609897933	1		313	293	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131893080	131893080	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	69	444	0	ENST00000265335.6:c.64A>G	p.Lys22Glu	p.K22E	ENST00000265335		22	Aag/Gag	1/25	0.358574228976735	1	FACETS	0.411	0.359	0.466	0.411	0.359	0.466	SUBCLONAL	1	TRUE	0	0.561957609897933	1		444	430	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0058407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	66	225	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.495	0.431	0.564	0.495	0.431	0.564	SUBCLONAL	1	TRUE	1	0.610599812565776	2		225	437	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0058407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	176	720	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.513	0.472	0.556	0.513	0.472	0.556	SUBCLONAL	1	TRUE	1	0.610599812565776	2		721	1124	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488228	56488228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	149	607	2	ENST00000267101.3:c.1747C>T	p.Pro583Ser	p.P583S	ENST00000267101	NM_001982.3	583	Ccc/Tcc	15/28	1	2	FACETS	0.509	0.465	0.556	0.509	0.465	0.556	SUBCLONAL	1	TRUE	1	0.610599812565776	2		609	958	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76949379	76949379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	36	395	0	ENST00000373344.5:c.418G>A	p.Asp140Asn	p.D140N	ENST00000373344	NM_000489.3	140	Gat/Aat	6/35	1	2	FACETS	0.387	0.319	0.462	0.387	0.319	0.462	SUBCLONAL	1	TRUE	1	0.610599812565776	2		395	305	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999366	100999366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1215	221	1057	2	ENST00000325455.5:c.436G>A	p.Glu146Lys	p.E146K	ENST00000325455	NM_001202474.3	146	Gaa/Aaa	1/8	1	2	FACETS	0.504	0.468	0.542	0.504	0.468	0.542	SUBCLONAL	1	TRUE	1	0.610599812565776	2		1059	1436	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39240655	39240655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730880385	NA	P-0058407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	82	341	0	ENST00000402219.2:c.2113G>A	p.Glu705Lys	p.E705K	ENST00000402219	NM_005633.3	705	Gaa/Aaa	13/23	0.317788979871603	2	FACETS	0.802	0.713	0.895	0.401	0.356	0.448	INDETERMINATE	1	TRUE	0	0.610599812565776	2		341	335	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617453	158617453	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	49	488	0	ENST00000263640.3:c.1203G>T	p.Arg401Ser	p.R401S	ENST00000263640	NM_001105.4	401	agG/agT	9/11	1	2	FACETS	0.206	0.173	0.241	0.206	0.173	0.241	SUBCLONAL	1	TRUE	1	0.610599812565776	2		488	780	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675633	86675633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	29	301	1	ENST00000274376.6:c.2569G>A	p.Glu857Lys	p.E857K	ENST00000274376	NM_002890.2	857	Gag/Aag	19/25	1	2	FACETS	0.444	0.358	0.54	0.444	0.358	0.54	SUBCLONAL	1	TRUE	1	0.610599812565776	2		302	214	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	118	352	5	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.412014113526028	2		357	567	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	210	486	9	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.905	0.847	0.965	1	0.994	1	CLONAL	2	TRUE	1	0.412014113526028	2		495	563	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	240	718	5	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.412014113526028	2		723	891	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487554	38487554	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	195	688	1	ENST00000254066.5:c.89del	p.Pro30LeufsTer12	p.P30Lfs*12	ENST00000254066	NM_000964.3	28	ttC/tt	2/9	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.412014113526028	2		689	903	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	148	430	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.959	0.877	1	0.959	0.877	1	CLONAL	1	TRUE	1	0.412014113526028	2		430	749	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	135	421	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	0.892	0.811	0.976	0.892	0.811	0.976	CLONAL	1	TRUE	1	0.412014113526028	2		421	735	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523009	25523009	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	200	826	3	ENST00000264709.3:c.176del	p.Pro59ArgfsTer13	p.P59Rfs*13	ENST00000264709	NM_175629.2	59	cCg/cg	3/23	1	2	FACETS	0.962	0.891	1	0.962	0.891	1	CLONAL	1	TRUE	1	0.412014113526028	2		829	1009	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755670	57755670	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	210	764	2	ENST00000274289.3:c.117del	p.Glu40ArgfsTer60	p.E40Rfs*60	ENST00000274289	NM_006622.3	39	ccC/cc	1/14	1	2	FACETS	0.991	0.92	1	0.991	0.92	1	CLONAL	1	TRUE	1	0.412014113526028	2		766	1029	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	245	771	1	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.412014113526028	2		772	1026	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	151	721	4	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.93	0.851	1	0.93	0.851	1	CLONAL	1	TRUE	1	0.412014113526028	2		725	788	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821959	72821960	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762108866	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	109	498	6	ENST00000268489.5:c.10215dup	p.Gly3406ArgfsTer25	p.G3406Rfs*25	ENST00000268489	NM_006885.3	3405	-/C	10/10	1	2	FACETS	0.879	0.791	0.971	0.879	0.791	0.971	CLONAL	1	TRUE	1	0.412014113526028	2		504	602	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439919	56439919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	206	543	1	ENST00000407977.2:c.673del	p.Arg225AlafsTer194	p.R225Afs*194	ENST00000407977		225	Cgc/gc	6/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.412014113526028	2		544	878	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076932	41076932	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	185	544	0	ENST00000373198.4:c.1488del	p.Phe498LeufsTer103	p.F498Lfs*103	ENST00000373198	NM_133170.3	496	ggG/gg	9/32	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.412014113526028	2		544	758	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066648	94066648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371089003	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	46	480	0	ENST00000369303.4:c.1111C>T	p.Arg371Trp	p.R371W	ENST00000369303	NM_004440.3	371	Cgg/Tgg	5/17	1	2	FACETS	0.274	0.23	0.323	0.274	0.23	0.323	SUBCLONAL	1	TRUE	1	0.412014113526028	2		480	815	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480010	50480010	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	226	634	0	ENST00000394963.4:c.249del	p.Asn84ThrfsTer79	p.N84Tfs*79	ENST00000394963	NM_003076.4	82	Ggg/gg	2/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.412014113526028	2		634	1002	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130337	11130337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs281875226	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	222	714	2	ENST00000358026.2:c.2576C>T	p.Thr859Met	p.T859M	ENST00000358026	NM_001128849.1	859	aCg/aTg	18/36	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.412014113526028	2		716	974	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	198	763	8	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.412014113526028	2		771	909	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543825	212543825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770003740	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	97	408	0	ENST00000342788.4:c.1574G>A	p.Arg525His	p.R525H	ENST00000342788	NM_005235.2	525	cGc/cAc	13/28	1	2	FACETS	0.683	0.61	0.762	0.683	0.61	0.762	SUBCLONAL	1	TRUE	1	0.412014113526028	2		408	689	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339110	65339111	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	104	393	2	ENST00000342505.4:c.425dup	p.Ile143AspfsTer9	p.I143Dfs*9	ENST00000342505	NM_002227.2	142	aag/aaAg	5/25	1	2	FACETS	0.717	0.642	0.796	0.717	0.642	0.796	SUBCLONAL	1	TRUE	1	0.412014113526028	2		395	704	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323362	31323363	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748204482	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	76	390	0	ENST00000412585.2:c.626dup	p.Thr211AspfsTer10	p.T211Dfs*10	ENST00000412585	NM_005514.6	209	cca/ccCa	4/8	1	2	FACETS	0.745	0.655	0.841	0.745	0.655	0.841	SUBCLONAL	1	TRUE	1	0.412014113526028	2		390	495	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	224	839	9	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.412014113526028	2		848	967	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448296	56448297	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	198	682	0	ENST00000407977.2:c.350_351insA	p.Cys119LeufsTer6	p.C119Lfs*6	ENST00000407977		117	cgc/cgAc	3/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.412014113526028	2		682	937	SUCCESS
CBL	867	MSKCC	GRCh37	11	119077131	119077131	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	43	490	2	ENST00000264033.4:c.4G>A	p.Ala2Thr	p.A2T	ENST00000264033	NM_005188.3	2	Gcc/Acc	1/16	1	2	FACETS	0.33	0.276	0.391	0.33	0.276	0.391	SUBCLONAL	1	TRUE	1	0.412014113526028	2		492	632	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523271	9523271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775109543	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	169	540	0	ENST00000353224.5:c.1966C>T	p.Arg656Trp	p.R656W	ENST00000353224	NM_177990.2	656	Cgg/Tgg	9/10	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.412014113526028	2		540	813	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589716	69589716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	16	139	2	ENST00000168712.1:c.137G>A	p.Arg46His	p.R46H	ENST00000168712	NM_002007.2	46	cGc/cAc	1/3	1	2	FACETS	0.42	0.311	0.548	0.42	0.311	0.548	SUBCLONAL	1	TRUE	1	0.412014113526028	2		141	185	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879706	37879706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	179	555	0	ENST00000269571.5:c.2081C>T	p.Thr694Met	p.T694M	ENST00000269571		694	aCg/aTg	17/27	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.412014113526028	2		555	750	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437222	220437223	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1286117855	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	212	884	1	ENST00000243786.2:c.132dup	p.Ala45ArgfsTer29	p.A45Rfs*29	ENST00000243786	NM_002191.3	42	-/C	1/2	1	2	FACETS	0.942	0.875	1	0.942	0.875	1	CLONAL	1	TRUE	1	0.412014113526028	2		885	1092	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970951	21970951	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	237	710	2	ENST00000304494.5:c.407del	p.Gly136AlafsTer10	p.G136Afs*10	ENST00000304494	NM_000077.4	136	gGc/gc	2/3	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.412014113526028	2		712	1006	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348536	89348536	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	250	751	0	ENST00000301030.4:c.4414G>A	p.Glu1472Lys	p.E1472K	ENST00000301030	NM_001256183.1	1472	Gag/Aag	9/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.412014113526028	2		751	1105	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298066	15298066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374767079	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	226	929	1	ENST00000263388.2:c.1690G>A	p.Ala564Thr	p.A564T	ENST00000263388	NM_000435.2	564	Gcc/Acc	11/33	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.412014113526028	2		930	1017	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273901	10273901	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	193	762	0	ENST00000330684.3:c.368C>A	p.Pro123His	p.P123H	ENST00000330684	NM_001134407.1	123	cCc/cAc	2/13	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.412014113526028	2		762	929	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114901004	114901004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	196	581	1	ENST00000543371.1:c.614C>T	p.Thr205Met	p.T205M	ENST00000543371	NM_001198531.1	205	aCg/aTg	6/14	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.412014113526028	2		582	869	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49724701	49724701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776673101	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	153	566	0	ENST00000449682.2:c.488G>A	p.Arg163Gln	p.R163Q	ENST00000449682	NM_020998.3	163	cGg/cAg	5/18	1	2	FACETS	0.973	0.892	1	0.973	0.892	1	CLONAL	1	TRUE	1	0.412014113526028	2		566	763	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127274	17127274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138070947	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	45	663	0	ENST00000285071.4:c.580C>T	p.Arg194Trp	p.R194W	ENST00000285071	NM_144997.5	194	Cgg/Tgg	6/14	1	2	FACETS	0.259	0.217	0.306	0.259	0.217	0.306	SUBCLONAL	1	TRUE	1	0.412014113526028	2		663	843	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303838	91303838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775209685	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	68	322	0	ENST00000355112.3:c.1235C>T	p.Thr412Met	p.T412M	ENST00000355112	NM_000057.2	412	aCg/aTg	7/22	1	2	FACETS	0.752	0.656	0.855	0.752	0.656	0.855	SUBCLONAL	1	TRUE	1	0.412014113526028	2		322	439	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348080	348080	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1450742711	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	158	869	1	ENST00000262320.3:c.1426C>T	p.Gln476Ter	p.Q476*	ENST00000262320	NM_003502.3	476	Cag/Tag	6/11	1	2	FACETS	0.711	0.65	0.774	0.711	0.65	0.774	SUBCLONAL	1	TRUE	1	0.412014113526028	2		870	1079	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973646	15973646	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779429826	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	171	437	0	ENST00000268712.3:c.4346C>T	p.Thr1449Met	p.T1449M	ENST00000268712	NM_006311.3	1449	aCg/aTg	31/46	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.412014113526028	2		437	756	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130301	2130303	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs1060500937	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	116	799	0	ENST00000219476.3:c.3535_3537del	p.Glu1179del	p.E1179del	ENST00000219476	NM_000548.3	1178	cAGGag/cag	30/42	1	2	FACETS	0.546	0.491	0.605	0.546	0.491	0.605	SUBCLONAL	1	TRUE	1	0.412014113526028	2		799	1031	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885736	23885736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377385656	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	75	849	2	ENST00000374561.5:c.182G>A	p.Gly61Asp	p.G61D	ENST00000374561	NM_002167.4	61	gGc/gAc	1/3	1	2	FACETS	0.346	0.302	0.394	0.346	0.302	0.394	SUBCLONAL	1	TRUE	1	0.412014113526028	2		851	1051	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104377103	104377103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760076290	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	89	675	0	ENST00000369902.3:c.1214C>T	p.Ala405Val	p.A405V	ENST00000369902	NM_016169.3	405	gCc/gTc	10/12	1	2	FACETS	0.557	0.494	0.626	0.557	0.494	0.626	SUBCLONAL	1	TRUE	1	0.412014113526028	2		675	775	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12043874	12043874	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	65	313	0	ENST00000396373.4:c.1254-1G>T		p.X418_splice	ENST00000396373	NM_001987.4	418			1	2	FACETS	0.625	0.542	0.714	0.625	0.542	0.714	SUBCLONAL	1	TRUE	1	0.412014113526028	2		313	505	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241954	133241954	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060500825	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	213	616	0	ENST00000320574.5:c.2402A>G	p.Tyr801Cys	p.Y801C	ENST00000320574	NM_006231.2	801	tAt/tGt	21/49	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.412014113526028	2		616	966	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249776	133249776	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs777736640	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	130	451	0	ENST00000320574.5:c.1447A>G	p.Thr483Ala	p.T483A	ENST00000320574	NM_006231.2	483	Acc/Gcc	14/49	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.412014113526028	2		451	615	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937489	32937489	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876659220	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	116	547	0	ENST00000380152.3:c.8150C>T	p.Ala2717Val	p.A2717V	ENST00000380152		2717	gCc/gTc	18/27	1	2	FACETS	0.954	0.863	1	0.954	0.863	1	CLONAL	1	TRUE	1	0.412014113526028	2		547	590	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434621	110434621	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	192	576	0	ENST00000375856.3:c.3780G>T	p.Glu1260Asp	p.E1260D	ENST00000375856	NM_003749.2	1260	gaG/gaT	1/2	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.412014113526028	2		576	896	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994916	73994916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs538781194	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	45	185	0	ENST00000318443.5:c.400G>A	p.Val134Ile	p.V134I	ENST00000318443	NM_001024736.1	134	Gtc/Atc	3/10	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.412014113526028	2		185	195	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641245	3641245	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	164	741	0	ENST00000294008.3:c.2394A>C	p.Lys798Asn	p.K798N	ENST00000294008	NM_032444.2	798	aaA/aaC	12/15	1	2	FACETS	0.826	0.758	0.897	0.826	0.758	0.897	CLONAL	1	TRUE	1	0.412014113526028	2		741	964	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641109	23641109	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	176	632	1	ENST00000261584.4:c.2366T>C	p.Leu789Pro	p.L789P	ENST00000261584	NM_024675.3	789	cTg/cCg	5/13	1	2	FACETS	0.907	0.835	0.981	0.907	0.835	0.981	CLONAL	1	TRUE	1	0.412014113526028	2		633	942	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868073	56868073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776964186	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	163	526	0	ENST00000308159.5:c.1571G>A	p.Arg524Gln	p.R524Q	ENST00000308159	NM_014669.4	524	cGg/cAg	14/22	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.412014113526028	2		526	782	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346815	89346815	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	21	565	0	ENST00000301030.4:c.6135del	p.Ala2046ProfsTer41	p.A2046Pfs*41	ENST00000301030	NM_001256183.1	2045	ccC/cc	9/13	1	2	FACETS	0.162	0.124	0.207	0.162	0.124	0.207	SUBCLONAL	1	TRUE	1	0.412014113526028	2		565	628	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940546	29940546	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	97	435	0	ENST00000389048.3:c.685T>C	p.Ser229Pro	p.S229P	ENST00000389048	NM_004304.4	229	Tca/Cca	2/29	1	2	FACETS	0.899	0.804	0.999	0.899	0.804	0.999	CLONAL	1	TRUE	1	0.412014113526028	2		435	524	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033412	48033412	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786203816	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	109	403	0	ENST00000234420.5:c.3716T>C	p.Ile1239Thr	p.I1239T	ENST00000234420	NM_000179.2	1239	aTa/aCa	8/10	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.412014113526028	2		403	512	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389096	31389096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	103	425	0	ENST00000328111.2:c.2009G>A	p.Arg670Gln	p.R670Q	ENST00000328111	NM_006892.3	670	cGg/cAg	19/23	1	2	FACETS	0.779	0.698	0.864	0.779	0.698	0.864	SUBCLONAL	1	TRUE	1	0.412014113526028	2		425	642	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504404	186504407	+	frameshift_variant	Frame_Shift_Del	DEL	CAAA	CAAA	-	novel	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	78	362	0	ENST00000323963.5:c.743_746del	p.Lys248SerfsTer23	p.K248Sfs*23	ENST00000323963		247	atCAAA/at	7/11	1	2	FACETS	0.799	0.704	0.9	0.799	0.704	0.9	SUBCLONAL	1	TRUE	1	0.412014113526028	2		362	474	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197818	66197818	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	84	251	0	ENST00000273854.3:c.2881C>A	p.Pro961Thr	p.P961T	ENST00000273854	NM_004439.5	961	Cca/Aca	17/18	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.412014113526028	2		251	385	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38942975	38942975	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	55	248	0	ENST00000357387.3:c.5012G>T	p.Arg1671Met	p.R1671M	ENST00000357387	NM_152756.3	1671	aGg/aTg	37/38	1	2	FACETS	0.72	0.618	0.83	0.72	0.618	0.83	SUBCLONAL	1	TRUE	1	0.412014113526028	2		248	371	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685214	86685214	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs755271409	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	78	235	0	ENST00000274376.6:c.2930T>C	p.Val977Ala	p.V977A	ENST00000274376	NM_002890.2	977	gTa/gCa	24/25	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.412014113526028	2		235	375	SUCCESS
APC	324	MSKCC	GRCh37	5	112176129	112176129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561595794	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	110	422	0	ENST00000257430.4:c.4838C>T	p.Pro1613Leu	p.P1613L	ENST00000257430	NM_000038.5	1613	cCt/cTt	16/16	1	2	FACETS	0.947	0.853	1	0.947	0.853	1	CLONAL	1	TRUE	1	0.412014113526028	2		422	564	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194872	29194872	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754204824	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1195	241	914	4	ENST00000240100.2:c.856C>T	p.Arg286Trp	p.R286W	ENST00000240100	NM_001394.6	286	Cgg/Tgg	4/4	0.412014113526028	3	FACETS	0.982	0.915	1	0.491	0.457	0.526	CLONAL	1	TRUE	1	0.412014113526028	3		918	1436	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798821	135798821	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	106	243	0	ENST00000298552.3:c.422C>A	p.Pro141Gln	p.P141Q	ENST00000298552	NM_001162426.1	141	cCa/cAa	6/23	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.412014113526028	2		243	438	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357659	70357659	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	196	768	0	ENST00000374080.3:c.5910C>A	p.Ser1970Arg	p.S1970R	ENST00000374080		1970	agC/agA	41/45	1	2	FACETS	0.968	0.896	1	0.968	0.896	1	CLONAL	1	TRUE	1	0.412014113526028	2		768	983	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0058409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	611	380	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.42606437535354	2	FACETS	0.912	0.879	0.945	0.912	0.879	0.945	CLONAL	2	TRUE	0	0.477223389897956	2		380	1404	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588880	69588880	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3674	211	817	1	ENST00000168712.1:c.356C>A	p.Ser119Ter	p.S119*	ENST00000168712	NM_002007.2	119	tCg/tAg	2/3	0.477223389897956	12	FACETS	0.771	0.711	0.833			1	SUBCLONAL	1	TRUE	NA	0.477223389897956	12		818	3885	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060925	38060927	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0058409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	58	659	0	ENST00000250448.2:c.1062_1064del	p.Ser355del	p.S355del	ENST00000250448	NM_004496.3	354	tcCTCa/tca	2/2	0.112151743474206	5	FACETS	0.344	0.294	0.398	0.115	0.098	0.133	INDETERMINATE	1	TRUE	2	0.477223389897956	5		659	1214	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974705	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCTCCGACCGTAACTATTCG	GGCCTCCGACCGTAACTATTCG	-	novel	NA	P-0058409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	268	593	0	ENST00000304494.5:c.122_143del	p.Pro41ArgfsTer5	p.P41Rfs*5	ENST00000304494	NM_000077.4	41	cCGAATAGTTACGGTCGGAGGCCg/cg	1/3	0.477223389897956	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.477223389897956	1		593	775	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0058410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1197	199	982	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.19318747535373	2		982	1396	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843595	156843595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139875058	NA	P-0058410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1327	127	873	0	ENST00000524377.1:c.1021G>A	p.Val341Met	p.V341M	ENST00000524377	NM_002529.3	341	Gtg/Atg	8/17	0.19318747535373	4	FACETS	1	0.949	1	0.36	0.324	0.397	CLONAL	1	TRUE	1	0.19318747535373	4		873	1454	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467746	66467746	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	52	348	0	ENST00000273854.3:c.523G>C	p.Asp175His	p.D175H	ENST00000273854	NM_004439.5	175	Gat/Cat	3/18	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.19318747535373	2		348	483	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210913	36210913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1462444181	NA	P-0058410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1289	124	1040	3	ENST00000222270.7:c.664C>T	p.Arg222Trp	p.R222W	ENST00000222270	NM_014727.1	222	Cgg/Tgg	3/37	1	2	FACETS	0.909	0.819	1	0.909	0.819	1	CLONAL	1	TRUE	1	0.19318747535373	2		1043	1413	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351181	89351188	+	frameshift_variant	Frame_Shift_Del	DEL	TTCAGCGA	TTCAGCGA	-	novel	NA	P-0058410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	62	799	0	ENST00000301030.4:c.1762_1769del	p.Ser588AlafsTer43	p.S588Afs*43	ENST00000301030	NM_001256183.1	588	TCGCTGAAg/g	9/13	0.19318747535373	2	FACETS	0.635	0.547	0.732	0.317	0.273	0.366	SUBCLONAL	1	TRUE	0	0.19318747535373	2		799	1011	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38506098	38506099	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0058411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	335	790	0	ENST00000254066.5:c.390_391del	p.Ile131HisfsTer19	p.I131Hfs*19	ENST00000254066	NM_000964.3	130	tgCAtc/tgtc	4/9	1	2	FACETS	0.976	0.924	1	0.976	0.924	1	CLONAL	1	TRUE	1	0.601392003652722	2		790	1141	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147511	47147511	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0058411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	225	456	0	ENST00000409792.3:c.4815T>G	p.Tyr1605Ter	p.Y1605*	ENST00000409792	NM_014159.6	1605	taT/taG	6/21	0.601392003652722	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.601392003652722	1		456	492	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436867	52436884	+	inframe_deletion	In_Frame_Del	DEL	CTTCAGCAGTGCCAGCAG	CTTCAGCAGTGCCAGCAG	-	novel	NA	P-0058411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	325	760	0	ENST00000460680.1:c.1894_1911del	p.Leu632_Lys637del	p.L632_K637del	ENST00000460680	NM_004656.3	632	CTGCTGGCACTGCTGAAG/-	15/17	0.601392003652722	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.601392003652722	1		760	751	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117621	70117633	+	protein_altering_variant	In_Frame_Del	DEL	CCGCGGGCTCGCC	CCGCGGGCTCGCC	G	novel	NA	P-0058411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	127	985	0	ENST00000245479.2:c.89_101delinsG	p.Ser30_Pro34delinsCys	p.S30_P34delinsC	ENST00000245479	NM_000346.3	30	tCCGCGGGCTCGCCc/tGc	1/3	1	2	FACETS	0.32	0.289	0.353	0.32	0.289	0.353	SUBCLONAL	1	TRUE	1	0.601392003652722	2		985	1320	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0058412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	16	219	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.774	0.592	0.974	0.774	0.592	0.974	CLONAL	1	TRUE	1	0.752014761046914	2		219	55	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541640	187541640	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	42	395	0	ENST00000441802.2:c.6100A>T	p.Thr2034Ser	p.T2034S	ENST00000441802	NM_005245.3	2034	Acc/Tcc	10/27	1	2	FACETS	0.745	0.633	0.863	0.745	0.633	0.863	SUBCLONAL	1	TRUE	1	0.752014761046914	2		395	150	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0058413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	788	877	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.903672736357266	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.903672736357266	1		877	919	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947540	48947540	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0058413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	21	72	0	ENST00000267163.4:c.1128-1G>C		p.X376_splice	ENST00000267163	NM_000321.2	376			0.903672736357266	1	FACETS	0.849	0.723	0.961	0.849	0.723	0.961	CLONAL	1	TRUE	0	0.903672736357266	1		72	30	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692847	89692847	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123321	NA	P-0058413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	11	137	0	ENST00000371953.3:c.331T>C	p.Trp111Arg	p.W111R	ENST00000371953	NM_000314.4	111	Tgg/Cgg	5/9	0.903672736357266	1	FACETS	0.252	0.178	0.338	0.252	0.178	0.338	SUBCLONAL	1	TRUE	0	0.903672736357266	1		137	53	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224484	123224484	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	180	551	0	ENST00000218089.9:c.3337C>A	p.Pro1113Thr	p.P1113T	ENST00000218089	NM_001042749.1	1113	Cct/Act	31/35	0.414128722072488	1	FACETS	0.443	0.412	0.475	0.443	0.412	0.475	INDETERMINATE	1	TRUE	0	0.903672736357266	1		551	493	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588082	69588082	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs776338094	NA	P-0058413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	303	709	0	ENST00000168712.1:c.616C>A	p.Leu206Met	p.L206M	ENST00000168712	NM_002007.2	206	Ctg/Atg	3/3	0.426048163706971	1	FACETS	0.392	0.37	0.414	0.392	0.37	0.414	INDETERMINATE	1	TRUE	0	0.903672736357266	1		709	938	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40681813	40681813	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0058413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	131	265	0	ENST00000249776.8:c.591+1G>A		p.X197_splice	ENST00000249776	NM_033286.3	197			0.333073525568795	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.903672736357266	0		265	335	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297996	15297996	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1250	1087	1182	0	ENST00000263388.2:c.1760G>C	p.Arg587Pro	p.R587P	ENST00000263388	NM_000435.2	587	cGc/cCc	11/33	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.903672736357266	2		1182	2337	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339238	116339238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764246939	NA	P-0058413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	241	387	0	ENST00000397752.3:c.100G>A	p.Glu34Lys	p.E34K	ENST00000397752	NM_000245.2	34	Gag/Aag	2/21	1	2	FACETS	0.961	0.906	1	0.961	0.906	1	CLONAL	1	TRUE	1	0.903672736357266	2		387	555	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981360	68981360	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	60	207	0	ENST00000288368.4:c.1432G>T	p.Val478Leu	p.V478L	ENST00000288368	NM_024870.2	478	Gtg/Ttg	12/40	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.903672736357266	2		207	106	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229250	123229250	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	72	234	0	ENST00000218089.9:c.3734C>A	p.Thr1245Lys	p.T1245K	ENST00000218089	NM_001042749.1	1245	aCa/aAa	34/35	0.414128722072488	1	FACETS	0.388	0.344	0.434	0.388	0.344	0.434	INDETERMINATE	1	TRUE	0	0.903672736357266	1		234	225	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0058414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	112	351	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.821	0.738	0.908	1	0.985	1	CLONAL	2	TRUE	1	0.18	2		351	758	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178712	108178712	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs869312756	NA	P-0058414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	42	224	0	ENST00000278616.4:c.5762+1G>A		p.X1921_splice	ENST00000278616	NM_000051.3	1921			1	2	FACETS	0.985	0.822	1	0.985	0.822	1	CLONAL	1	TRUE	1	0.18	2		224	474	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0058420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	93	351	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.279457825924047	4	FACETS	0.843	0.753	0.938	0.843	0.753	0.938	CLONAL	2	TRUE	2	0.30912915291078	4		351	467	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508133	106508133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1346474355	NA	P-0058420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	80	495	0	ENST00000359195.3:c.127G>A	p.Val43Met	p.V43M	ENST00000359195	NM_002649.2	43	Gtg/Atg	2/11	0.290055025394993	3	FACETS	0.887	0.787	0.992	0.887	0.787	0.992	CLONAL	2	TRUE	1	0.30912915291078	3		495	337	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792557	33792557	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	33	71	0	ENST00000498907.2:c.764G>T	p.Gly255Val	p.G255V	ENST00000498907	NM_004364.3	255	gGg/gTg	1/1	0.279457825924047	4	FACETS	1	0.859	1	1	0.956	1	CLONAL	3	TRUE	2	0.30912915291078	4		71	91	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599944	10599944	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	275	1000	0	ENST00000171111.5:c.1632del	p.Trp544Ter	p.W544*	ENST00000171111	NM_203500.1	544	tgG/tg	5/6	0.30912915291078	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.30912915291078	2		1000	829	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318779	163318779	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	82	430	0	ENST00000271452.3:c.1169G>T	p.Arg390Leu	p.R390L	ENST00000271452	NM_145697.2	390	cGa/cTa	13/14	0.30912915291078	10	FACETS	0.845	0.745	0.952	0.211	0.186	0.239	CLONAL	2	TRUE	2	0.30912915291078	10		430	702	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663821	29663821	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	147	698	0	ENST00000356175.3:c.6253G>T	p.Val2085Phe	p.V2085F	ENST00000356175	NM_000267.3	2085	Gtt/Ttt	41/57	0.279457825924047	4	FACETS	0.846	0.773	0.921	0.846	0.773	0.921	CLONAL	2	TRUE	2	0.30912915291078	4		698	736	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589616	67589616	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	52	242	0	ENST00000274335.5:c.1379G>T	p.Ser460Ile	p.S460I	ENST00000274335		460	aGt/aTt	10/15	0.279457825924047	4	FACETS	0.804	0.69	0.927	0.804	0.69	0.927	CLONAL	2	TRUE	2	0.30912915291078	4		242	274	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509811	106509811	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	178	792	0	ENST00000359195.3:c.1805A>C	p.Glu602Ala	p.E602A	ENST00000359195	NM_002649.2	602	gAa/gCa	2/11	0.290055025394993	3	FACETS	0.961	0.888	1	0.961	0.888	1	CLONAL	2	TRUE	1	0.30912915291078	3		792	692	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410586	63410586	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	200	1016	0	ENST00000330258.3:c.2581G>T	p.Gly861Cys	p.G861C	ENST00000330258	NM_152424.3	861	Ggc/Tgc	2/2	0.21549714665647	4	FACETS	0.948	0.88	1	0.948	0.88	1	CLONAL	2	TRUE	2	0.30912915291078	4		1016	893	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796008	78796009	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	T	novel	NA	P-0058420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	195	894	0	ENST00000306801.3:c.898_899delinsT	p.Gly300SerfsTer3	p.G300Sfs*3	ENST00000306801	NM_020761.2	300	GGc/Tc	8/34	0.279457825924047	4	FACETS	0.948	0.878	1	0.948	0.878	1	CLONAL	2	TRUE	2	0.30912915291078	4		894	871	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70442645	70442645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	285	601	0	ENST00000373644.4:c.4967G>A	p.Arg1656His	p.R1656H	ENST00000373644	NM_030625.2	1656	cGt/cAt	10/12	0.772243000773691	3	FACETS	0.946	0.889	1	0.473	0.444	0.502	CLONAL	1	TRUE	1	0.772243000773691	3		601	1082	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398282	+	missense_variant	Missense_Mutation	DNP	CC	CC	GG	novel	NA	P-0058421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	175	474	1	ENST00000311936.3:c.37_38inv	p.Gly13Pro	p.G13P	ENST00000311936	NM_004985.3	13	GGc/CCc	2/5	0.772243000773691	3	FACETS	0.838	0.783	0.893	0.838	0.783	0.893	CLONAL	2	TRUE	1	0.772243000773691	3		475	375	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871674	35871674	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs373499073	NA	P-0058421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	268	569	0	ENST00000216797.5:c.832C>A	p.Gln278Lys	p.Q278K	ENST00000216797	NM_020529.2	278	Cag/Aag	5/6	1	2	FACETS	0.896	0.843	0.949	0.896	0.843	0.949	CLONAL	1	TRUE	1	0.772243000773691	2		569	775	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7120730	7120730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766867210	NA	P-0058421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	366	763	1	ENST00000302850.5:c.3560C>T	p.Thr1187Met	p.T1187M	ENST00000302850	NM_000208.2	1187	aCg/aTg	20/22	1	2	FACETS	0.951	0.904	0.998	0.951	0.904	0.998	CLONAL	1	TRUE	1	0.772243000773691	2		764	997	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0058422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	133	258	1				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		259	311	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	73	306	0				ENST00000310581	NM_198253.2	-/1132			0.248851905213478	0	FACETS	0.899	0.809	0.99			1	CLONAL	3	FALSE	0	0.257533892486512	0		306	156	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337278	89337278	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	257	745	0	ENST00000301030.4:c.7753C>G	p.Arg2585Gly	p.R2585G	ENST00000301030	NM_001256183.1	2585	Cgc/Ggc	12/13	1	2	FACETS	0.907	0.858	0.956	1	0.996	1	CLONAL	4	FALSE	1	0.257533892486512	2		745	550	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0058426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	14	263	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.0859398855565434	7	FACETS	0.862	0.626	1	0.517	0.376	0.687	CLONAL	3	FALSE	2	0.0859398855565434	7		263	153	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589594	67589596	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	novel	NA	P-0058426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	8	133	0	ENST00000274335.5:c.1358_1360del	p.Asn453del	p.N453del	ENST00000274335		453	AAC/-	10/15	1	2	FACETS	0.922	0.597	1	1	0.846	1	CLONAL	2	FALSE	1	0.0859398855565434	2		133	101	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624305	89624305	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	rs746128825	NA	P-0058426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	150	691	0	ENST00000371953.3:c.79T>A	p.Tyr27Asn	p.Y27N	ENST00000371953	NM_000314.4	27	Tat/Aat	1/9	0.0859398855565434	7	FACETS	1	0.962	1	1	0.962	1	CLONAL	5	FALSE	2	0.0859398855565434	7		691	777	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106562	27106562	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1306	174	1054	0	ENST00000324856.7:c.6176del	p.Asn2059ThrfsTer76	p.N2059Tfs*76	ENST00000324856	NM_006015.4	2058	gAa/ga	20/20	0.0858245237823505	4	FACETS	0.99	0.909	1	1	0.988	1	CLONAL	3	FALSE	2	0.0859398855565434	4		1054	1480	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988785	41988785	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0058426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	34	513	0	ENST00000219905.7:c.1577C>G	p.Ser526Ter	p.S526*	ENST00000219905	NM_001164273.1	526	tCa/tGa	3/24	1	2	FACETS	1	0.86	1	1	0.972	1	CLONAL	3	FALSE	1	0.0859398855565434	2		513	250	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910391	50910391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201038430	NA	P-0058426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1353	88	1164	2	ENST00000440232.2:c.1646G>A	p.Arg549His	p.R549H	ENST00000440232	NM_002691.3	549	cGt/cAt	13/27	0.0858245237823505	4	FACETS	0.772	0.681	0.87	0.772	0.681	0.87	SUBCLONAL	2	FALSE	2	0.0859398855565434	4		1166	1441	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624229	89624229	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0058426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	41	193	0	ENST00000371953.3:c.3G>A	p.Met1?	p.M1?	ENST00000371953	NM_000314.4	1	atG/atA	1/9	0.0859398855565434	7	FACETS	0.966	0.811	1	0.966	0.811	1	CLONAL	5	FALSE	2	0.0859398855565434	7		193	240	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023521	27023530	+	frameshift_variant	Frame_Shift_Del	DEL	CCACCAGTAC	CCACCAGTAC	-	novel	NA	P-0058426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	104	591	0	ENST00000324856.7:c.627_636del	p.Asn209LysfsTer20	p.N209Kfs*20	ENST00000324856	NM_006015.4	209	aaCCACCAGTAC/aa	1/20	0.0858245237823505	4	FACETS	0.894	0.799	0.995	1	0.976	1	CLONAL	3	FALSE	2	0.0859398855565434	4		591	980	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0058427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	348	293	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.257547668233252	9	FACETS	1	0.969	1			1	CLONAL	5	TRUE	NA	0.257547668233252	9		293	999	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777134	9777134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1445282622	NA	P-0058427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	118	992	1	ENST00000377346.4:c.898C>T	p.Arg300Cys	p.R300C	ENST00000377346	NM_005026.3	300	Cgt/Tgt	7/24	1	2	FACETS	0.91	0.82	1	0.91	0.82	1	CLONAL	1	TRUE	1	0.257547668233252	2		993	1007	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591812	48591813	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0058427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	84	473	0	ENST00000342988.3:c.976_977insAA	p.Ile326LysfsTer11	p.I326Kfs*11	ENST00000342988	NM_005359.5	325	-/AA	9/12	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.257547668233252	2		473	487	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426776	121426776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150513055	NA	P-0058455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	47	553	1	ENST00000257555.6:c.467C>T	p.Thr156Met	p.T156M	ENST00000257555		156	aCg/aTg	2/10	0.2315806434494	3	FACETS	0.447	0.376	0.525	0.224	0.188	0.263	SUBCLONAL	1	TRUE	1	0.361958735003472	3		554	686	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170301	119170301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	41	205	0	ENST00000264033.4:c.2531G>A	p.Ser844Asn	p.S844N	ENST00000264033	NM_005188.3	844	aGt/aAt	16/16	1	2	FACETS	0.981	0.824	1	0.981	0.824	1	CLONAL	1	TRUE	1	0.361958735003472	2		205	231	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541651	120541651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752816549	NA	P-0058455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	65	387	1	ENST00000229340.5:c.206G>A	p.Arg69His	p.R69H	ENST00000229340	NM_006861.6	69	cGc/cAc	3/6	0.2315806434494	3	FACETS	0.735	0.638	0.841	0.368	0.319	0.421	SUBCLONAL	1	TRUE	1	0.361958735003472	3		388	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0058456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	278	380	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.283241237706001	8	FACETS	1	0.982	1			1	CLONAL	6	FALSE	NA	0.283241237706001	8		380	564	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0058457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	372	584	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.602829828182322	6	FACETS	1	0.97	1	1	0.97	1	CLONAL	4	TRUE	2	0.602829828182322	6		584	671	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	153	570	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.602829828182322	3	FACETS	1	0.946	1	0.52	0.477	0.565	CLONAL	1	TRUE	1	0.602829828182322	3		570	635	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0058457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	104	421	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.602829828182322	6	FACETS	0.963	0.862	1	0.241	0.215	0.268	CLONAL	1	TRUE	2	0.602829828182322	6		421	790	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226349	133226349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	201	782	0	ENST00000320574.5:c.3709G>A	p.Glu1237Lys	p.E1237K	ENST00000320574	NM_006231.2	1237	Gag/Aag	30/49	0.505787169957356	4	FACETS	0.975	0.903	1	0.488	0.451	0.525	CLONAL	1	TRUE	2	0.602829828182322	4		782	1096	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478833	56478833	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	168	743	0	ENST00000267101.3:c.289C>G	p.Leu97Val	p.L97V	ENST00000267101	NM_001982.3	97	Cta/Gta	3/28	0.505787169957356	4	FACETS	0.889	0.816	0.965	0.444	0.408	0.483	CLONAL	1	TRUE	2	0.602829828182322	4		743	1005	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28644659	28644659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	121	507	0	ENST00000241453.7:c.134C>T	p.Ser45Leu	p.S45L	ENST00000241453	NM_004119.2	45	tCa/tTa	2/24	0.602829828182322	3	FACETS	0.984	0.893	1	0.492	0.446	0.54	CLONAL	1	TRUE	1	0.602829828182322	3		507	531	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435954	56435954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	124	483	0	ENST00000407977.2:c.1183C>T	p.His395Tyr	p.H395Y	ENST00000407977		395	Cat/Tat	9/10	0.552518697958661	5	FACETS	1	0.947	1	0.356	0.322	0.391	CLONAL	1	TRUE	2	0.602829828182322	5		483	734	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910359	29910359	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	199	941	0	ENST00000376809.5:c.29T>C	p.Leu10Pro	p.L10P	ENST00000376809	NM_002116.7	10	cTc/cCc	1/8	0.602829828182322	3	FACETS	0.931	0.863	1	0.465	0.431	0.501	CLONAL	1	TRUE	1	0.602829828182322	3		941	923	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419911	152419911	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	156	561	0	ENST00000206249.3:c.1598T>A	p.Val533Glu	p.V533E	ENST00000206249	NM_000125.3	533	gTg/gAg	8/8	0.602829828182322	3	FACETS	1	0.957	1	0.532	0.489	0.577	CLONAL	1	TRUE	1	0.602829828182322	3		561	633	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	143	306	0				ENST00000310581	NM_198253.2	-/1132			0.552886393489001	4	FACETS	0.864	0.805	0.922	1	0.987	1	CLONAL	3	TRUE	2	0.691482350339838	4		306	270	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0058458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	204	608	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	0.658382797220661	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	2	0.691482350339838	4		608	474	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0058458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	160	254	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.691482350339838	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.691482350339838	3		254	297	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004922	150004922	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	89	262	0	ENST00000253339.5:c.1303C>T	p.Gln435Ter	p.Q435*	ENST00000253339		435	Cag/Tag	3/7	0.678100342029975	3	FACETS	0.853	0.774	0.934	0.853	0.774	0.934	CLONAL	2	TRUE	1	0.691482350339838	3		262	203	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114277	143114277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs76891221	NA	P-0058458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	77	216	0	ENST00000262992.4:c.1144C>T	p.Arg382Trp	p.R382W	ENST00000262992	NM_001101669.1	382	Cgg/Tgg	13/24	0.356633595433643	3	FACETS	1	0.98	1	0.749	0.671	0.83	INDETERMINATE	1	TRUE	1	0.691482350339838	3		216	200	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332663	70332663	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	62	411	0	ENST00000373644.4:c.568C>G	p.Gln190Glu	p.Q190E	ENST00000373644	NM_030625.2	190	Cag/Gag	2/12	0.678100342029975	3	FACETS	0.85	0.741	0.966	0.425	0.37	0.483	CLONAL	1	TRUE	1	0.691482350339838	3		411	284	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254743	16254743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	23	437	0	ENST00000375759.3:c.2008G>A	p.Glu670Lys	p.E670K	ENST00000375759	NM_015001.2	670	Gaa/Aaa	11/15	0.646232605458413	5	FACETS	0.327	0.254	0.411			1	SUBCLONAL	1	TRUE	NA	0.691482350339838	5		437	415	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105850	27105851	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	109	398	0	ENST00000324856.7:c.5461_5462insT	p.Asp1821ValfsTer10	p.D1821Vfs*10	ENST00000324856	NM_006015.4	1821	gat/gTat	20/20	0.323249802476578	4	FACETS	0.777	0.706	0.851	0.777	0.706	0.851	INDETERMINATE	2	TRUE	2	0.691482350339838	4		398	343	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308343	15308343	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	32	615	1	ENST00000263388.2:c.165C>A	p.Cys55Ter	p.C55*	ENST00000263388	NM_000435.2	55	tgC/tgA	2/33	0.691482350339838	3	FACETS	0.264	0.214	0.321	0.132	0.107	0.161	SUBCLONAL	1	TRUE	1	0.691482350339838	3		616	472	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367882	15367882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	232	588	1	ENST00000263377.2:c.1444C>T	p.Pro482Ser	p.P482S	ENST00000263377	NM_058243.2	482	Ccg/Tcg	8/20	0.691482350339838	3	FACETS	0.979	0.926	1	0.979	0.926	1	CLONAL	2	TRUE	1	0.691482350339838	3		589	461	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662936	52662936	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	22	250	0	ENST00000394830.3:c.1417G>C	p.Val473Leu	p.V473L	ENST00000394830	NM_018313.4	473	Gtt/Ctt	13/30	0.658382797220661	4	FACETS	0.27	0.209	0.342	0.135	0.104	0.171	SUBCLONAL	1	TRUE	2	0.691482350339838	4		250	398	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004316	150004316	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	117	252	0	ENST00000253339.5:c.1909C>G	p.Gln637Glu	p.Q637E	ENST00000253339		637	Caa/Gaa	3/7	0.678100342029975	3	FACETS	0.876	0.805	0.947	0.876	0.805	0.947	CLONAL	2	TRUE	1	0.691482350339838	3		252	260	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941836	44941837	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0058458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	97	88	0	ENST00000377967.4:c.3161_3162del	p.Arg1054LysfsTer4	p.R1054Kfs*4	ENST00000377967	NM_021140.2	1054	AGa/a	21/29	0.674994179821086	2	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.691482350339838	2		88	124	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038813	47038813	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	168	280	0	ENST00000377604.3:c.820C>T	p.Gln274Ter	p.Q274*	ENST00000377604	NM_001204468.1	274	Cag/Tag	9/24	0.674994179821086	2	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.691482350339838	2		280	195	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231437	46231437	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	23	396	0	ENST00000334344.6:c.1277C>T	p.Thr426Met	p.T426M	ENST00000334344	NM_152641.2	426	aCg/aTg	10/21	1	2	FACETS	0.977	0.763	1	0.977	0.763	1	CLONAL	1	TRUE	1	0.17	2		396	277	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965426	15965426	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567776756	NA	P-0058459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	22	212	0	ENST00000268712.3:c.5380C>T	p.Arg1794Ter	p.R1794*	ENST00000268712	NM_006311.3	1794	Cga/Tga	36/46	1	2	FACETS	0.822	0.637	1	0.822	0.637	1	CLONAL	1	TRUE	1	0.17	2		212	315	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856028	151856028	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144222590	NA	P-0058459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	26	315	0	ENST00000262189.6:c.11590C>T	p.Arg3864Cys	p.R3864C	ENST00000262189	NM_170606.2	3864	Cgc/Tgc	44/59	1	2	FACETS	0.656	0.519	0.815	0.656	0.519	0.815	SUBCLONAL	1	TRUE	1	0.17	2		315	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121912651	NA	P-0058463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	159	590	0	ENST00000269305.4:c.742C>G	p.Arg248Gly	p.R248G	ENST00000269305	NM_001126112.2	248	Cgg/Ggg	7/11	0.361314406903342	1	FACETS	0.986	0.906	1	0.986	0.906	1	CLONAL	1	TRUE	0	0.361314406903342	1		590	731	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509636	106509636	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867282260	NA	P-0058463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	34	622	0	ENST00000359195.3:c.1630C>T	p.Arg544Ter	p.R544*	ENST00000359195	NM_002649.2	544	Cga/Tga	2/11	0.361314406903342	1	FACETS	0.251	0.204	0.304	0.251	0.204	0.304	SUBCLONAL	1	TRUE	0	0.361314406903342	1		622	614	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554293	29554293	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	161	613	0	ENST00000356175.3:c.2309C>G	p.Thr770Ser	p.T770S	ENST00000356175	NM_000267.3	770	aCt/aGt	19/57	0.361314406903342	1	FACETS	0.947	0.87	1	0.947	0.87	1	CLONAL	1	TRUE	0	0.361314406903342	1		613	771	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46724357	46724357	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0058463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	91	286	0	ENST00000371975.4:c.211-1G>A		p.X71_splice	ENST00000371975	NM_003579.3	71			1	2	FACETS	0.963	0.858	1	0.963	0.858	1	CLONAL	1	TRUE	1	0.361314406903342	2		286	523	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977145	85977145	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	16	221	0	ENST00000263360.6:c.747A>T	p.Glu249Asp	p.E249D	ENST00000263360	NM_003797.3	249	gaA/gaT	8/12	1	2	FACETS	0.394	0.291	0.516	0.394	0.291	0.516	SUBCLONAL	1	TRUE	1	0.361314406903342	2		221	225	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977182	85977182	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	19	271	0	ENST00000263360.6:c.784C>G	p.Leu262Val	p.L262V	ENST00000263360	NM_003797.3	262	Ctt/Gtt	8/12	1	2	FACETS	0.457	0.348	0.585	0.457	0.348	0.585	SUBCLONAL	1	TRUE	1	0.361314406903342	2		271	230	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205309	46205309	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	77	314	0	ENST00000334344.6:c.393C>A	p.Tyr131Ter	p.Y131*	ENST00000334344	NM_152641.2	131	taC/taA	4/21	1	2	FACETS	0.879	0.774	0.991	0.879	0.774	0.991	CLONAL	1	TRUE	1	0.361314406903342	2		314	485	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93953222	93953222	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	71	345	0	ENST00000369303.4:c.2919T>A	p.His973Gln	p.H973Q	ENST00000369303	NM_004440.3	973	caT/caA	17/17	1	2	FACETS	0.853	0.746	0.966	0.853	0.746	0.966	CLONAL	1	TRUE	1	0.361314406903342	2		345	461	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459513	50459513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	55	215	0	ENST00000331340.3:c.802G>A	p.Ala268Thr	p.A268T	ENST00000331340	NM_006060.4	268	Gca/Aca	7/8	1	2	FACETS	0.998	0.86	1	0.998	0.86	1	CLONAL	1	TRUE	1	0.361314406903342	2		215	305	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0058464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	17	172	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.972	0.725	1	0.972	0.725	1	CLONAL	1	TRUE	1	0.11	2		172	318	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0058464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	11	284	2	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.708	1	1	0.708	1	CLONAL	1	TRUE	1	0.11	2		286	195	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720843	89720844	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0058464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	19	370	0	ENST00000371953.3:c.995_996del	p.Lys332SerfsTer10	p.K332Sfs*10	ENST00000371953	NM_000314.4	332	AAa/a	8/9	1	2	FACETS	0.96	0.727	1	0.96	0.727	1	CLONAL	1	TRUE	1	0.11	2		370	360	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879458	151879458	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	25	475	0	ENST00000262189.6:c.5487del	p.Phe1830LeufsTer19	p.F1830Lfs*19	ENST00000262189	NM_170606.2	1829	ctG/ct	36/59	1	2	FACETS	1	0.793	1	1	0.793	1	CLONAL	1	TRUE	1	0.11	2		475	451	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941973	44941973	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	57	160	0	ENST00000377967.4:c.3223del	p.Arg1075GlyfsTer8	p.R1075Gfs*8	ENST00000377967	NM_021140.2	1075	Agg/gg	22/29	1	1	FACETS	1	0.923	1	1	0.985	1	CLONAL	4	TRUE	0	0.183556664071423	1		160	133	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546784	9546784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1252319558	NA	P-0058467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	45	388	0	ENST00000353224.5:c.1238C>T	p.Pro413Leu	p.P413L	ENST00000353224	NM_177990.2	413	cCg/cTg	5/10	0.327658935936106	3	FACETS	0.399	0.336	0.468			1	INDETERMINATE	1	TRUE	NA	0.851148976072285	3		388	378	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022413	31022413	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	144	293	0	ENST00000375687.4:c.1898A>T	p.His633Leu	p.H633L	ENST00000375687	NM_015338.5	633	cAt/cTt	13/13	0.17985559342134	3	FACETS	0.812	0.755	0.87	0.812	0.755	0.87	INDETERMINATE	2	TRUE	1	0.851148976072285	3		293	297	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629315	187629315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	345	565	0	ENST00000441802.2:c.1667C>T	p.Thr556Ile	p.T556I	ENST00000441802	NM_005245.3	556	aCa/aTa	2/27	0.239076167758459	4	FACETS	1	0.97	1	1	0.97	1	INDETERMINATE	2	TRUE	2	0.851148976072285	4		565	734	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875681	35875681	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1036740256	NA	P-0058467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	117	199	0	ENST00000303115.3:c.868C>T	p.Pro290Ser	p.P290S	ENST00000303115	NM_002185.3	290	Cca/Tca	7/8	0.847951732128753	5	FACETS	1	0.962	1	0.281	0.254	0.31	CLONAL	1	TRUE	1	0.851148976072285	5		199	556	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0058469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	236	590	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.611617243376245	2		590	686	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266810	198266810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	214	388	0	ENST00000335508.6:c.2122G>A	p.Ala708Thr	p.A708T	ENST00000335508	NM_012433.2	708	Gcc/Acc	15/25	1	2	FACETS	0.885	0.824	0.947	0.885	0.824	0.947	CLONAL	1	TRUE	1	0.611617243376245	2		388	791	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430626	181430627	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0058469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	235	571	0	ENST00000325404.1:c.479dup	p.Tyr160Ter	p.Y160*	ENST00000325404	NM_003106.3	160	tac/tAac	1/1	0.611617243376245	5	FACETS	1	0.973	1	0.272	0.253	0.292	CLONAL	1	TRUE	1	0.611617243376245	5		571	1353	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501582	149501582	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	194	431	0	ENST00000261799.4:c.2205G>C	p.Glu735Asp	p.E735D	ENST00000261799	NM_002609.3	735	gaG/gaC	16/23	0.388296908483024	1	FACETS	0.705	0.655	0.755	0.705	0.655	0.755	SUBCLONAL	1	TRUE	0	0.611617243376245	1		431	625	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137540413	137540413	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	256	584	0	ENST00000367739.4:c.52G>C	p.Glu18Gln	p.E18Q	ENST00000367739	NM_000416.2	18	Gag/Cag	1/7	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.611617243376245	2		584	815	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057520000	NA	P-0058471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	337	1190	0	ENST00000269305.4:c.452C>G	p.Pro151Arg	p.P151R	ENST00000269305	NM_001126112.2	151	cCc/cGc	5/11	0.623877494054451	3	FACETS	0.846	0.815	0.876	0.846	0.815	0.876	CLONAL	3	TRUE	0	0.748004203119005	3		1190	488	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390122	89390122	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	98	321	1	ENST00000336596.2:c.871C>T	p.Pro291Ser	p.P291S	ENST00000336596	NM_005233.5	291	Ccg/Tcg	4/17	0.734247222514082	5	FACETS	1	0.953	1	0.371	0.332	0.412	CLONAL	1	TRUE	2	0.748004203119005	5		322	500	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313214	65313214	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0058471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	83	501	0	ENST00000342505.4:c.1899+1G>T		p.X633_splice	ENST00000342505	NM_002227.2	633			0.593065994115038	3	FACETS	1	0.943	1	0.362	0.323	0.402	CLONAL	1	TRUE	0	0.748004203119005	3		501	281	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593681	215593681	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	65	322	0	ENST00000260947.4:c.2053del	p.His685ThrfsTer29	p.H685Tfs*29	ENST00000260947	NM_000465.2	685	Cac/ac	11/11	0.748004203119005	5	FACETS	0.695	0.603	0.794	0.174	0.15	0.199	SUBCLONAL	1	TRUE	1	0.748004203119005	5		322	531	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42842574	42842574	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0058471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	364	847	0	ENST00000398585.3:c.1282+1G>T		p.X428_splice	ENST00000398585	NM_001135099.1	428			0.748004203119005	4	FACETS	0.841	0.806	0.877	1	0.994	1	CLONAL	3	TRUE	2	0.748004203119005	4		847	674	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125848	47125848	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	63	251	0	ENST00000409792.3:c.5422C>G	p.Pro1808Ala	p.P1808A	ENST00000409792	NM_014159.6	1808	Ccc/Gcc	12/21	0.600612327934871	4	FACETS	1	0.937	1	0.373	0.326	0.423	CLONAL	1	TRUE	1	0.748004203119005	4		251	263	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573365	55573365	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	96	440	0	ENST00000288135.5:c.1027C>A	p.Pro343Thr	p.P343T	ENST00000288135	NM_000222.2	343	Cct/Act	6/21	NA	2	FACETS	0.858	0.775	0.945			1	INDETERMINATE	1	TRUE	NA	0.748004203119005	2		440	299	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64288779	64288822	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTTTAAATATTCTTCTGACTTAGGATTGGCCTTTTGATGATGG	TGTTTAAATATTCTTCTGACTTAGGATTGGCCTTTTGATGATGG	-	novel	NA	P-0058471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	52	316	0	ENST00000370651.3:c.199-22_220del		p.X67_splice	ENST00000370651	NM_003463.4	67		4/6	0.682797874431295	5	FACETS	0.612	0.521	0.711	0.204	0.173	0.237	SUBCLONAL	1	TRUE	2	0.748004203119005	5		316	482	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846146	68846146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0121485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	280	538	0	ENST00000261769.5:c.1117C>T	p.Pro373Ser	p.P373S	ENST00000261769	NM_004360.3	373	Ccg/Tcg	8/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	NA	1	0.679801321897653	2		538	788	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251512	251512	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301370839	NA	P-0121485-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	33	197	0	ENST00000264932.6:c.1723G>A	p.Ala575Thr	p.A575T	ENST00000264932	NM_004168.2	575	Gcg/Acg	13/15	0.670134663627536	3	FACETS	0.471	0.385	0.567	0.236	0.192	0.284	SUBCLONAL	1	NA	1	0.679801321897653	3		197	276	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0058473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	825	590	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.881572498327045	3	FACETS	0.994	0.968	1	0.994	0.968	1	CLONAL	2	TRUE	1	0.898764727710217	3		590	1339	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0058473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	421	284	2	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.898764727710217	2		286	924	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0058473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	296	414	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.871492488277057	3	FACETS	0.998	0.941	1	0.499	0.47	0.528	CLONAL	1	TRUE	1	0.898764727710217	3		414	957	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615036	43615036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1345166214	NA	P-0058473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	539	800	0	ENST00000355710.3:c.2450G>A	p.Arg817His	p.R817H	ENST00000355710	NM_020975.4	817	cGc/cAc	14/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.898764727710217	2		800	1126	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793483	18793483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603405	NA	P-0058473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	242	369	2	ENST00000266497.5:c.4180G>A	p.Glu1394Lys	p.E1394K	ENST00000266497		1394	Gaa/Aaa	30/31	1	2	FACETS	0.97	0.915	1	0.97	0.915	1	CLONAL	1	TRUE	1	0.898764727710217	2		371	555	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186757	108186757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs864622251	NA	P-0058473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	424	492	0	ENST00000278616.4:c.6115G>A	p.Glu2039Lys	p.E2039K	ENST00000278616	NM_000051.3	2039	Gaa/Aaa	42/63	0.898764727710217	1	FACETS	0.973	0.947	0.998	0.973	0.947	0.998	CLONAL	1	TRUE	0	0.898764727710217	1		492	534	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061313	38061313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1204900727	NA	P-0058473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	501	746	0	ENST00000250448.2:c.676G>A	p.Asp226Asn	p.D226N	ENST00000250448	NM_004496.3	226	Gac/Aac	2/2	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.898764727710217	2		746	1094	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349538	70349538	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	424	645	0	ENST00000374080.3:c.3700G>A	p.Glu1234Lys	p.E1234K	ENST00000374080		1234	Gaa/Aaa	27/45	1	2	FACETS	0.875	0.836	0.915	0.875	0.836	0.915	CLONAL	1	TRUE	1	0.898764727710217	2		645	1078	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257570	19257570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368120349	NA	P-0058473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	549	748	2	ENST00000162023.5:c.656G>A	p.Arg219Gln	p.R219Q	ENST00000162023		219	cGa/cAa	10/13	1	2	FACETS	0.94	0.904	0.977	0.94	0.904	0.977	CLONAL	1	TRUE	1	0.898764727710217	2		750	1299	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164744	47164744	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0058473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	468	634	0	ENST00000409792.3:c.1382C>G	p.Ser461Ter	p.S461*	ENST00000409792	NM_014159.6	461	tCa/tGa	3/21	1	2	FACETS	0.977	0.937	1	0.977	0.937	1	CLONAL	1	TRUE	1	0.898764727710217	2		634	1066	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862084	68862085	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0058473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	428	588	0	ENST00000261769.5:c.2173_2174del	p.Leu725AlafsTer22	p.L725Afs*22	ENST00000261769	NM_004360.3	724	atTCtg/attg	14/16	0.898764727710217	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.898764727710217	1		588	509	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165684	47165684	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	555	634	0	ENST00000409792.3:c.442C>G	p.Leu148Val	p.L148V	ENST00000409792	NM_014159.6	148	Ctg/Gtg	3/21	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.898764727710217	2		634	1150	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902666	50902666	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752124373	NA	P-0058473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	538	681	0	ENST00000440232.2:c.241C>T	p.Arg81Trp	p.R81W	ENST00000440232	NM_002691.3	81	Cgg/Tgg	3/27	1	2	FACETS	0.999	0.961	1	0.999	0.961	1	CLONAL	1	TRUE	1	0.898764727710217	2		681	1198	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711029	114711029	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	178	287	0	ENST00000543371.1:c.253G>T	p.Glu85Ter	p.E85*	ENST00000543371	NM_001198531.1	85	Gaa/Taa	2/14	1	2	FACETS	0.923	0.861	0.986	0.923	0.861	0.986	CLONAL	1	TRUE	1	0.898764727710217	2		287	429	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874251	155874251	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1520	422	569	0	ENST00000368323.3:c.280G>A	p.Glu94Lys	p.E94K	ENST00000368323	NM_006912.5	94	Gaa/Aaa	5/6	0.898764727710217	4	FACETS	0.918	0.872	0.966	0.306	0.29	0.322	CLONAL	1	TRUE	1	0.898764727710217	4		569	1942	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625401	69625401	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	453	753	0	ENST00000334134.2:c.392C>G	p.Ser131Cys	p.S131C	ENST00000334134	NM_005247.2	131	tCc/tGc	3/3	0.898764727710217	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.898764727710217	1		753	531	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383231	4383231	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	426	658	0	ENST00000261254.3:c.25G>C	p.Asp9His	p.D9H	ENST00000261254	NM_001759.3	9	Gac/Cac	1/5	1	2	FACETS	0.925	0.884	0.966	0.925	0.884	0.966	CLONAL	1	TRUE	1	0.898764727710217	2		658	1025	SUCCESS
USP8	9101	MSKCC	GRCh37	15	50773935	50773935	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1312685935	NA	P-0058473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	514	634	0	ENST00000307179.4:c.1476G>C	p.Glu492Asp	p.E492D	ENST00000307179		492	gaG/gaC	11/20	1	2	FACETS	0.969	0.931	1	0.969	0.931	1	CLONAL	1	TRUE	1	0.898764727710217	2		634	1180	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965527	15965527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	420	552	0	ENST00000268712.3:c.5279C>T	p.Ser1760Leu	p.S1760L	ENST00000268712	NM_006311.3	1760	tCa/tTa	36/46	1	2	FACETS	0.957	0.915	0.999	0.957	0.915	0.999	CLONAL	1	TRUE	1	0.898764727710217	2		552	977	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40384042	40384042	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	386	530	0	ENST00000293328.3:c.104C>G	p.Ser35Cys	p.S35C	ENST00000293328	NM_012448.3	35	tCc/tGc	2/19	1	2	FACETS	0.961	0.917	1	0.961	0.917	1	CLONAL	1	TRUE	1	0.898764727710217	2		530	894	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67626375	67626375	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	264	428	0	ENST00000272342.5:c.298G>A	p.Asp100Asn	p.D100N	ENST00000272342	NM_019002.3	100	Gat/Aat	2/6	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.898764727710217	2		428	584	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165905	47165905	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	433	542	0	ENST00000409792.3:c.221C>A	p.Ser74Ter	p.S74*	ENST00000409792	NM_014159.6	74	tCa/tAa	3/21	1	2	FACETS	0.998	0.956	1	0.998	0.956	1	CLONAL	1	TRUE	1	0.898764727710217	2		542	965	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032281	26032281	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	414	563	0	ENST00000244661.2:c.8G>T	p.Arg3Leu	p.R3L	ENST00000244661	NM_003537.3	3	cGt/cTt	1/1	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.898764727710217	2		563	921	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976752	2976752	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	542	649	0	ENST00000396946.4:c.1260G>C	p.Glu420Asp	p.E420D	ENST00000396946	NM_032415.4	420	gaG/gaC	9/25	0.871492488277057	3	FACETS	1	0.985	1	0.528	0.506	0.55	CLONAL	1	TRUE	1	0.898764727710217	3		649	1656	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439656	140439656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	172	177	0	ENST00000288602.6:c.2083G>A	p.Glu695Lys	p.E695K	ENST00000288602	NM_004333.4	695	Gag/Aag	17/18	0.871492488277057	3	FACETS	1	0.984	1	0.608	0.565	0.652	CLONAL	1	TRUE	1	0.898764727710217	3		177	456	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874259	151874259	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	371	490	0	ENST00000262189.6:c.8279C>G	p.Thr2760Arg	p.T2760R	ENST00000262189	NM_170606.2	2760	aCa/aGa	38/59	0.871492488277057	3	FACETS	1	0.967	1	0.512	0.486	0.538	CLONAL	1	TRUE	1	0.898764727710217	3		490	1169	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874550	151874550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	467	641	0	ENST00000262189.6:c.7988C>T	p.Ser2663Leu	p.S2663L	ENST00000262189	NM_170606.2	2663	tCa/tTa	38/59	0.871492488277057	3	FACETS	0.973	0.929	1	0.487	0.464	0.509	CLONAL	1	TRUE	1	0.898764727710217	3		641	1548	SUCCESS
MTAP	4507	MSKCC	GRCh37	9	21815481	21815481	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058473-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	199	304	0	ENST00000380172.4:c.83G>A	p.Gly28Glu	p.G28E	ENST00000380172	NM_002451.3	28	gGa/gAa	2/8	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.898764727710217	2		304	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0058474-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	256	968	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.284829129244825	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.296332373634164	2		968	833	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0058474-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	196	572	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.250495686139654	4	FACETS	0.972	0.901	1	0.972	0.901	1	CLONAL	2	TRUE	2	0.296332373634164	4		572	882	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356748	70356748	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058474-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	127	357	0	ENST00000374080.3:c.5420G>T	p.Gly1807Val	p.G1807V	ENST00000374080		1807	gGt/gTt	38/45	1	1	FACETS	0.833	0.761	0.909	1	0.988	1	CLONAL	2	TRUE	0	0.296332373634164	1		357	438	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484167	120484167	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058474-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	119	570	0	ENST00000256646.2:c.2963T>A	p.Ile988Asn	p.I988N	ENST00000256646	NM_024408.3	988	aTc/aAc	18/34	0.284829129244825	2	FACETS	1	0.966	1	0.577	0.521	0.636	CLONAL	1	TRUE	0	0.296332373634164	2		570	696	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526840	31526840	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058474-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	200	681	0	ENST00000344624.3:c.200C>T	p.Pro67Leu	p.P67L	ENST00000344624		67	cCa/cTa	2/33	0.16250629940222	4	FACETS	1	0.956	1	0.694	0.643	0.745	INDETERMINATE	2	TRUE	1	0.296332373634164	4		681	841	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124470	94124470	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058474-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	47	357	0	ENST00000369303.4:c.113C>A	p.Ser38Tyr	p.S38Y	ENST00000369303	NM_004440.3	38	tCt/tAt	2/17	0.278702016244748	3	FACETS	1	0.923	1	0.574	0.487	0.67	CLONAL	1	TRUE	1	0.296332373634164	3		357	317	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0058475-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	67	781	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.938	0.813	1	0.938	0.813	1	CLONAL	1	TRUE	1	0.18	2		781	794	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051678	13051678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1026947469	NA	P-0058475-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	100	500	0	ENST00000316448.5:c.937G>A	p.Val313Met	p.V313M	ENST00000316448	NM_004343.3	313	Gtg/Atg	7/9	1	2	FACETS	0.953	0.849	1	0.953	0.849	1	CLONAL	1	TRUE	1	0.18	2		500	1166	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0058475-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	70	361	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.917	0.803	1	1	0.98	1	CLONAL	2	TRUE	1	0.18	2		361	424	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970988	21970989	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058475-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	137	616	0	ENST00000304494.5:c.369_370insA	p.Arg124ThrfsTer18	p.R124Tfs*18	ENST00000304494	NM_000077.4	123	-/A	2/3	0.3	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.18	1		616	1011	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151625	55151625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571523023	NA	P-0058476-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	117	390	0	ENST00000257290.5:c.2411G>A	p.Arg804Gln	p.R804Q	ENST00000257290	NM_006206.4	804	cGa/cAa	17/23	0.44583264264118	2	FACETS	1	0.922	1	0.51	0.461	0.56	CLONAL	1	TRUE	0	0.44583264264118	2		390	515	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115944	8115959	+	frameshift_variant	Frame_Shift_Del	DEL	TGGACCACACCACCCC	TGGACCACACCACCCC	-	novel	NA	P-0058476-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	452	644	0	ENST00000346208.3:c.1291_1306del	p.Gly431ProfsTer39	p.G431Pfs*39	ENST00000346208		430	ttTGGACCACACCACCCC/tt	6/6	0.44583264264118	2	FACETS	0.963	0.922	1	0.963	0.922	1	CLONAL	2	TRUE	0	0.44583264264118	2		644	1053	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720663	89720665	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0058476-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	22	67	0	ENST00000371953.3:c.814_816del	p.His272del	p.H272del	ENST00000371953	NM_000314.4	272	CAC/-	8/9	0.44583264264118	2	FACETS	0.851	0.687	1	0.851	0.687	1	CLONAL	2	TRUE	0	0.44583264264118	2		67	58	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578518	7578518	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934875	NA	P-0058477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	105	522	0	ENST00000269305.4:c.412G>C	p.Ala138Pro	p.A138P	ENST00000269305	NM_001126112.2	138	Gcc/Ccc	5/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.226219647789542	2		522	755	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098962	178098962	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	16	427	0	ENST00000397062.3:c.83T>C	p.Ile28Thr	p.I28T	ENST00000397062	NM_006164.4	28	aTa/aCa	2/5	1	2	FACETS	0.294	0.216	0.388	0.294	0.216	0.388	SUBCLONAL	1	TRUE	1	0.226219647789542	2		427	481	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562463	21562463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	42	534	1	ENST00000382592.4:c.1456G>A	p.Ala486Thr	p.A486T	ENST00000382592	NM_014572.2	486	Gcc/Acc	4/8	1	2	FACETS	0.99	0.829	1	0.99	0.829	1	CLONAL	1	TRUE	1	0.226219647789542	2		535	375	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226590062	226590062	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1360722722	NA	P-0058477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	55	543	0	ENST00000366794.5:c.139A>G	p.Lys47Glu	p.K47E	ENST00000366794	NM_001618.3	47	Aaa/Gaa	2/23	1	2	FACETS	0.653	0.557	0.758	0.653	0.557	0.758	SUBCLONAL	1	TRUE	1	0.226219647789542	2		543	745	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999183	100999183	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs567928186	NA	P-0058477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	40	658	0	ENST00000325455.5:c.619G>C	p.Gly207Arg	p.G207R	ENST00000325455	NM_001202474.3	207	Ggg/Cgg	1/8	1	2	FACETS	0.645	0.536	0.768	0.645	0.536	0.768	SUBCLONAL	1	TRUE	1	0.226219647789542	2		658	548	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665722	29665722	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	40	269	0	ENST00000356175.3:c.6757G>A	p.Ala2253Thr	p.A2253T	ENST00000356175	NM_000267.3	2253	Gca/Aca	45/57	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.226219647789542	2		269	340	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158549	26158549	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	39	535	0	ENST00000289316.2:c.152C>T	p.Pro51Leu	p.P51L	ENST00000289316	NM_138720.2	51	cCc/cTc	1/2	1	2	FACETS	0.574	0.474	0.685	0.574	0.474	0.685	SUBCLONAL	1	TRUE	1	0.226219647789542	2		535	601	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510895	157510895	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	50	511	0	ENST00000346085.5:c.3670A>G	p.Thr1224Ala	p.T1224A	ENST00000346085	NM_020732.3	1224	Act/Gct	14/20	1	2	FACETS	0.675	0.572	0.789	0.675	0.572	0.789	SUBCLONAL	1	TRUE	1	0.226219647789542	2		511	655	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907645	76907645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058477-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	43	426	0	ENST00000373344.5:c.4516C>T	p.Arg1506Cys	p.R1506C	ENST00000373344	NM_000489.3	1506	Cgt/Tgt	15/35	1	2	FACETS	0.634	0.529	0.75	0.634	0.529	0.75	SUBCLONAL	1	TRUE	1	0.226219647789542	2		426	600	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0058478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	284	172	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.660721372197835	2		172	701	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220274	55220274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8700	4643	410	0	ENST00000275493.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000275493	NM_005228.3	222	Cgc/Tgc	6/28	0.660721372197835	41	FACETS	0.975	0.961	0.989			1	CLONAL	15	TRUE	NA	0.660721372197835	41		410	13343	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867333	45867333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765839639	NA	P-0058478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	392	628	0	ENST00000391945.4:c.860G>A	p.Arg287His	p.R287H	ENST00000391945	NM_000400.3	287	cGt/cAt	10/23	0.660721372197835	4	FACETS	1	0.994	1	0.446	0.423	0.469	CLONAL	1	TRUE	1	0.660721372197835	4		628	1474	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861149	57861149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774058977	NA	P-0058478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	353	556	0	ENST00000228682.2:c.946G>A	p.Glu316Lys	p.E316K	ENST00000228682	NM_005269.2	316	Gaa/Aaa	9/12	0.143778217689271	4	FACETS	0.866	0.822	0.91	0.866	0.822	0.91	INDETERMINATE	2	TRUE	2	0.660721372197835	4		556	1025	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414970	56414970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146335154	NA	P-0058478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	54	449	0	ENST00000348428.3:c.2371G>A	p.Ala791Thr	p.A791T	ENST00000348428	NM_006785.3	791	Gct/Act	17/17	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.660721372197835	2		449	156	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221716	55221716	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11364	4675	585	0	ENST00000275493.2:c.760T>A	p.Phe254Ile	p.F254I	ENST00000275493	NM_005228.3	254	Ttc/Atc	7/28	0.660721372197835	41	FACETS	1	0.995	1			1	CLONAL	12	TRUE	NA	0.660721372197835	41		585	16039	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150902534	150902534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778212727	NA	P-0058478-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	22	423	0	ENST00000271640.5:c.352C>T	p.Arg118Trp	p.R118W	ENST00000271640	NM_001145415.1	118	Cgg/Tgg	3/22	1	2	FACETS	0.204	0.158	0.258	0.204	0.158	0.258	SUBCLONAL	1	TRUE	1	0.660721372197835	2		423	326	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0058482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	802	293	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.474328201153088	11	FACETS	0.964	0.945	0.982			1	CLONAL	11	TRUE	NA	0.474328201153088	11		293	1000	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0058482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	488	559	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.474328201153088	2	FACETS	0.984	0.945	1	0.984	0.945	1	CLONAL	2	TRUE	0	0.474328201153088	2		559	1046	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971115	21971133	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTCGGGTGAGAGTGGCG	GGGTCGGGTGAGAGTGGCG	-	rs730881674	NA	P-0058482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	318	660	0	ENST00000304494.5:c.225_243del	p.Ala76CysfsTer64	p.A76Cfs*64	ENST00000304494	NM_000077.4	75	ccCGCCACTCTCACCCGACCC/cc	2/3	0.474328201153088	2	FACETS	1	0.993	1	0.66	0.624	0.697	CLONAL	1	TRUE	0	0.474328201153088	2		660	1016	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094426	27094426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	244	578	0	ENST00000324856.7:c.3134G>A	p.Gly1045Asp	p.G1045D	ENST00000324856	NM_006015.4	1045	gGt/gAt	11/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.474328201153088	2		578	1027	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437518	52437518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779877855	NA	P-0058482-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	261	591	0	ENST00000460680.1:c.1643G>A	p.Arg548His	p.R548H	ENST00000460680	NM_004656.3	548	cGt/cAt	13/17	0.474328201153088	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.474328201153088	1		591	734	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	42	432	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.2	2		432	338	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	32	486	9	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.2	2		495	246	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	47	539	2	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.2	2		541	445	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	23	491	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.788	0.615	0.987	0.788	0.615	0.987	CLONAL	1	TRUE	1	0.2	2		491	292	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165213	47165213	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	34	388	0	ENST00000409792.3:c.913del	p.Thr305GlnfsTer35	p.T305Qfs*35	ENST00000409792	NM_014159.6	305	Aca/ca	3/21	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.2	2		388	276	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	49	741	3	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.2	2		744	423	SUCCESS
APC	324	MSKCC	GRCh37	5	112175651	112175651	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	40	733	0	ENST00000257430.4:c.4364del	p.Asn1455IlefsTer18	p.N1455Ifs*18	ENST00000257430	NM_000038.5	1454	Aaa/aa	16/16	1	2	FACETS	0.941	0.783	1	0.941	0.783	1	CLONAL	1	TRUE	1	0.2	2		733	425	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438317	110438322	+	inframe_deletion	In_Frame_Del	DEL	GTTGTT	GTTGTT	-	rs532810290	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	39	637	3	ENST00000375856.3:c.79_84del	p.Asn27_Asn28del	p.N27_N28del	ENST00000375856	NM_003749.2	27	AACAAC/-	1/2	0.264990514502766	3	FACETS	1	0.843	1	0.508	0.421	0.605	CLONAL	1	TRUE	1	0.2	3		640	422	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473722	67473722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs794727798	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	63	803	0	ENST00000327367.4:c.802C>T	p.Arg268Cys	p.R268C	ENST00000327367	NM_005902.3	268	Cgc/Tgc	6/9	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.2	2		803	462	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	28	475	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.798	0.638	0.98	0.798	0.638	0.98	CLONAL	1	TRUE	1	0.2	2		480	351	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261555	142261555	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	27	287	2	ENST00000350721.4:c.3402del	p.Phe1134LeufsTer6	p.F1134Lfs*6	ENST00000350721	NM_001184.3	1134	ttT/tt	17/47	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.2	2		289	241	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132896	64132896	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	49	926	3	ENST00000334205.4:c.1034del	p.Pro345LeufsTer30	p.P345Lfs*30	ENST00000334205	NM_003942.2	344	Ccc/cc	9/17	1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	1	0.2	2		929	489	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139625	202139626	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	61	595	0	ENST00000358485.4:c.790dup	p.Val264GlyfsTer13	p.V264Gfs*13	ENST00000358485	NM_001080125.1	262	-/G	6/9	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.2	2		595	463	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871053	12871053	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	57	881	1	ENST00000228872.4:c.285del	p.Gly97ValfsTer22	p.G97Vfs*22	ENST00000228872	NM_004064.3	94	Ccc/cc	1/3	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.2	2		882	423	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354393	354393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1488869543	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	60	669	0	ENST00000262320.3:c.1165G>A	p.Ala389Thr	p.A389T	ENST00000262320	NM_003502.3	389	Gcg/Acg	5/11	0.0874289595547819	3	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.2	3		669	448	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026290	48026290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147737737	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	44	655	0	ENST00000234420.5:c.1168G>A	p.Asp390Asn	p.D390N	ENST00000234420	NM_000179.2	390	Gat/Aat	4/10	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.2	2		655	387	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110129	8110130	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs745673717	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	70	803	2	ENST00000585124.1:c.475dup	p.Arg159ProfsTer15	p.R159Pfs*15	ENST00000585124	NM_004217.3	159	cgc/cCgc	6/9	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.2	2		805	497	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394992	394992	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	74	743	0	ENST00000380956.4:c.388G>T	p.Glu130Ter	p.E130*	ENST00000380956	NM_001195286.1	130	Gag/Tag	3/9	1	2	FACETS	0.752	0.66	0.851	1	0.975	1	SUBCLONAL	2	TRUE	1	0.2	2		743	492	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425823	49425824	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs754290613	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	43	965	0	ENST00000301067.7:c.12662_12664dup	p.Gln4221dup	p.Q4221dup	ENST00000301067	NM_003482.3	4221	cta/cAGCta	39/54	1	2	FACETS	0.765	0.64	0.905	0.765	0.64	0.905	CLONAL	1	TRUE	1	0.2	2		965	562	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111736	56111737	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	16	681	0	ENST00000399503.3:c.340dup	p.His114ProfsTer50	p.H114Pfs*50	ENST00000399503	NM_005921.1	112	-/C	1/20	1	2	FACETS	0.724	0.536	0.948	0.724	0.536	0.948	CLONAL	1	TRUE	1	0.2	2		681	221	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040062	180040062	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376188634	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	62	900	1	ENST00000261937.6:c.3380G>A	p.Arg1127Gln	p.R1127Q	ENST00000261937	NM_182925.4	1127	cGg/cAg	25/30	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.2	2		901	470	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8252007	8252007	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	72	934	0	ENST00000335790.3:c.70T>C	p.Cys24Arg	p.C24R	ENST00000335790	NM_002315.2	24	Tgt/Cgt	2/4	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.2	2		934	556	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214059	36214059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	87	902	0	ENST00000222270.7:c.2885G>A	p.Arg962His	p.R962H	ENST00000222270	NM_014727.1	962	cGc/cAc	6/37	0.0200853114856367	3	FACETS	1	0.978	1	0.742	0.657	0.832	INDETERMINATE	1	TRUE	1	0.2	3		902	645	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781500	9781500	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	34	651	0	ENST00000377346.4:c.1812-2A>G		p.X604_splice	ENST00000377346	NM_005026.3	604			1	2	FACETS	0.872	0.713	1	0.872	0.713	1	CLONAL	1	TRUE	1	0.2	2		651	390	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11204803	11204803	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	44	661	0	ENST00000361445.4:c.4774del	p.Ser1592LeufsTer39	p.S1592Lfs*39	ENST00000361445	NM_004958.3	1592	Tct/ct	34/58	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.2	2		661	407	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261791	16261791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	74	918	0	ENST00000375759.3:c.9056C>T	p.Ala3019Val	p.A3019V	ENST00000375759	NM_015001.2	3019	gCa/gTa	11/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.2	2		918	524	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598919	28598919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754474817	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	73	981	0	ENST00000253063.3:c.479G>A	p.Ser160Asn	p.S160N	ENST00000253063	NM_031459.4	160	aGc/aAc	4/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.2	2		981	550	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246518349	246518349	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	37	465	0	ENST00000388985.4:c.212G>C	p.Cys71Ser	p.C71S	ENST00000388985		71	tGt/tCt	2/12	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.2	2		465	346	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609972	43609972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759073728	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	85	1028	0	ENST00000355710.3:c.1924G>A	p.Val642Ile	p.V642I	ENST00000355710	NM_020975.4	642	Gtc/Atc	11/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.2	2		1028	576	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241978	133241978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1422986795	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	50	722	0	ENST00000320574.5:c.2378G>A	p.Arg793His	p.R793H	ENST00000320574	NM_006231.2	793	cGc/cAc	21/49	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.2	2		722	482	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828863	26828863	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	65	775	0	ENST00000381527.3:c.85C>T	p.Arg29Ter	p.R29*	ENST00000381527	NM_001260.1	29	Cga/Tga	1/13	0.264990514502766	3	FACETS	0.802	0.697	0.914	0.802	0.697	0.914	CLONAL	2	TRUE	1	0.2	3		775	446	SUCCESS
FOXF1	2294	MSKCC	GRCh37	16	86546539	86546539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761162914	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	68	895	0	ENST00000262426.4:c.988C>T	p.Arg330Trp	p.R330W	ENST00000262426	NM_001451.2	330	Cgg/Tgg	2/2	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.2	2		895	467	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676245	29676245	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	21	431	0	ENST00000356175.3:c.7234A>G	p.Thr2412Ala	p.T2412A	ENST00000356175	NM_000267.3	2412	Aca/Gca	48/57	1	2	FACETS	0.686	0.529	0.87	0.686	0.529	0.87	SUBCLONAL	1	TRUE	1	0.2	2		431	306	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724581	724581	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750831029	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	30	381	0	ENST00000314574.4:c.1475C>T	p.Pro492Leu	p.P492L	ENST00000314574	NM_005433.3	492	cCg/cTg	12/12	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.2	2		381	238	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349642	15349642	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	61	852	0	ENST00000263377.2:c.3932A>G	p.Gln1311Arg	p.Q1311R	ENST00000263377	NM_058243.2	1311	cAg/cGg	19/20	0.0200853114856367	3	FACETS	1	0.964	1	0.689	0.595	0.79	INDETERMINATE	1	TRUE	1	0.2	3		852	487	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566845	212566845	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	43	677	0	ENST00000342788.4:c.1336C>T	p.Gln446Ter	p.Q446*	ENST00000342788	NM_005235.2	446	Cag/Tag	12/28	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.2	2		677	389	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230914	66230914	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	25	432	0	ENST00000273854.3:c.2057T>C	p.Phe686Ser	p.F686S	ENST00000273854	NM_004439.5	686	tTt/tCt	12/18	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.2	2		432	221	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295959	1295959	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1167265119	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	67	1126	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.2	2		1126	569	SUCCESS
APC	324	MSKCC	GRCh37	5	112179249	112179252	+	frameshift_variant	Frame_Shift_Del	DEL	AAAC	AAAC	-	rs1554088793	NA	P-0058487-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	29	541	0	ENST00000257430.4:c.7959_7962del	p.Thr2654ArgfsTer5	p.T2654Rfs*5	ENST00000257430	NM_000038.5	2653	aAAACa/aa	16/16	1	2	FACETS	0.898	0.722	1	0.898	0.722	1	CLONAL	1	TRUE	1	0.2	2		541	323	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	97	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.44248618953665	2		306	362	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0058513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	50	584	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.44248618953665	2		584	185	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0058513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	190	351	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.270716559539964	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	1	0.44248618953665	4		351	382	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023108	27023108	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	46	810	0	ENST00000324856.7:c.214G>T	p.Glu72Ter	p.E72*	ENST00000324856	NM_006015.4	72	Gag/Tag	1/20	1	2	FACETS	0.422	0.355	0.495	0.422	0.355	0.495	SUBCLONAL	1	TRUE	1	0.44248618953665	2		810	493	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482437	56482437	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	195	749	0	ENST00000267101.3:c.985A>G	p.Lys329Glu	p.K329E	ENST00000267101	NM_001982.3	329	Aaa/Gaa	8/28	1	2	FACETS	0.775	0.722	0.828	1	0.992	1	SUBCLONAL	2	TRUE	1	0.44248618953665	2		749	569	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724559	43724559	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748353199	NA	P-0058513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	170	798	0	ENST00000382044.4:c.3508G>A	p.Glu1170Lys	p.E1170K	ENST00000382044	NM_001141980.1	1170	Gaa/Aaa	17/28	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.44248618953665	2		798	549	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324497	31324497	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs66473235	NA	P-0058513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	254	523	0	ENST00000412585.2:c.311del	p.Asn104ThrfsTer47	p.N104Tfs*47	ENST00000412585	NM_005514.6	104	aAc/ac	2/8	1	2	FACETS	0.976	0.932	1	1	0.996	1	CLONAL	3	TRUE	1	0.44248618953665	2		523	392	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138197249	138197249	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	191	757	0	ENST00000237289.4:c.751G>T	p.Gly251Cys	p.G251C	ENST00000237289	NM_001270507.1	251	Ggc/Tgc	5/9	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.44248618953665	2		757	677	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833924	44833924	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0058513-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	65	406	0	ENST00000377967.4:c.348C>G	p.Tyr116Ter	p.Y116*	ENST00000377967	NM_021140.2	116	taC/taG	4/29	0.387158119649513	3	FACETS	1	0.962	1	0.638	0.559	0.723	CLONAL	1	TRUE	1	0.44248618953665	3		406	281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0058514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	384	559	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.929357016327178	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.929357016327178	1		559	419	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939412	76939412	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058514-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	177	661	0	ENST00000373344.5:c.1336G>T	p.Gly446Ter	p.G446*	ENST00000373344	NM_000489.3	446	Gga/Tga	9/35	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.929357016327178	2		661	372	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0058515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	41	631	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	0.475	0.395	0.565	0.475	0.395	0.565	SUBCLONAL	1	TRUE	1	0.28	2		631	616	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0058515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	183	555	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	0.3	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.28	3		555	618	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643777	38643777	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	69	696	0	ENST00000299084.4:c.1247G>A	p.Cys416Tyr	p.C416Y	ENST00000299084	NM_152594.2	416	tGt/tAt	7/7	0.3	1	FACETS	0.788	0.687	0.896	0.788	0.687	0.896	SUBCLONAL	1	TRUE	0	0.28	1		696	538	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877361	40877361	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058515-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	56	648	0	ENST00000373198.4:c.2335A>G	p.Ile779Val	p.I779V	ENST00000373198	NM_133170.3	779	Att/Gtt	15/32	1	2	FACETS	0.753	0.646	0.871	0.753	0.646	0.871	SUBCLONAL	1	TRUE	1	0.28	2		648	531	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0058516-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	12	293	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		293	488	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303684	30303684	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0058517-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	30	703	0	ENST00000262643.3:c.111+1G>T		p.X37_splice	ENST00000262643	NM_001238.2	37			0.3	1	FACETS	0.38	0.306	0.465	0.38	0.306	0.465	SUBCLONAL	1	FALSE	0	0.3	1		703	447	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912375	29912376	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0058517-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	69	555	0	ENST00000376809.5:c.996dup	p.Arg333GlufsTer7	p.R333Efs*7	ENST00000376809	NM_002116.7	332	tgg/tGgg	5/8	0.0846044450213608	3	FACETS	1	0.891	1	0.512	0.446	0.582	INDETERMINATE	1	FALSE	1	0.3	3		555	517	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0058518-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	106	213	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	0.186310680185823	4	FACETS	0.862	0.775	0.954	0.575	0.517	0.636	CLONAL	2	TRUE	1	0.270108594810843	4		213	578	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956221	55956221	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs767542615	NA	P-0058518-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	13	457	0	ENST00000263923.4:c.3094C>T	p.Arg1032Ter	p.R1032*	ENST00000263923	NM_002253.2	1032	Cga/Tga	23/30	1	2	FACETS	0.231	0.164	0.314	0.231	0.164	0.314	SUBCLONAL	1	TRUE	1	0.270108594810843	2		457	416	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845838	72845838	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762268017	NA	P-0058518-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	87	644	0	ENST00000268489.5:c.3629G>T	p.Arg1210Leu	p.R1210L	ENST00000268489	NM_006885.3	1210	cGa/cTa	6/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.270108594810843	2		644	519	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905595	50905595	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058518-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	113	927	0	ENST00000440232.2:c.723C>G	p.Phe241Leu	p.F241L	ENST00000440232	NM_002691.3	241	ttC/ttG	6/27	0.186310680185823	4	FACETS	0.814	0.733	0.898	0.542	0.489	0.599	CLONAL	2	TRUE	1	0.270108594810843	4		927	653	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932039	39932049	+	frameshift_variant	Frame_Shift_Del	DEL	CGATGAAATCA	CGATGAAATCA	-	novel	NA	P-0058518-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	99	649	0	ENST00000378444.4:c.2550_2560del	p.Asp851ProfsTer10	p.D851Pfs*10	ENST00000378444	NM_001123385.1	850	cgTGATTTCATCGcc/cgcc	4/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.270108594810843	2		649	498	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0058519-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	71	432	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.399627497307094	1	FACETS	0.862	0.758	0.972	0.862	0.758	0.972	CLONAL	1	TRUE	0	0.399627497307094	1		432	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0058519-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	191	816	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	1	2	FACETS	0.982	0.908	1	0.982	0.908	1	CLONAL	1	TRUE	1	0.399627497307094	2		816	973	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0058519-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	169	615	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.399627497307094	2		615	751	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829887	72829887	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058519-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	162	669	0	ENST00000268489.5:c.6694del	p.Glu2232AsnfsTer23	p.E2232Nfs*23	ENST00000268489	NM_006885.3	2232	Gaa/aa	9/10	1	2	FACETS	0.918	0.843	0.997	0.918	0.843	0.997	CLONAL	1	TRUE	1	0.399627497307094	2		669	883	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949998	44949998	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058519-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	86	256	0	ENST00000377967.4:c.3767A>G	p.Tyr1256Cys	p.Y1256C	ENST00000377967	NM_021140.2	1256	tAc/tGc	26/29	1	1	FACETS	0.926	0.84	1	1	0.987	1	CLONAL	2	TRUE	0	0.399627497307094	1		256	186	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	14	292	3	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	0.237513588246775	2	FACETS	0.244	0.176	0.327			1	INDETERMINATE	1	TRUE	NA	0.434396076583152	2		295	264	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	261	729	8	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.897	0.839	0.958	0.897	0.839	0.958	CLONAL	1	TRUE	1	0.434396076583152	2		737	1339	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11175453	11175453	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	177	468	0	ENST00000361445.4:c.7089G>T	p.Glu2363Asp	p.E2363D	ENST00000361445	NM_004958.3	2363	gaG/gaT	51/58	1	2	FACETS	0.94	0.867	1	0.94	0.867	1	CLONAL	1	TRUE	1	0.434396076583152	2		468	867	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	193	553	0	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	1	2	FACETS	0.976	0.904	1	0.976	0.904	1	CLONAL	1	TRUE	1	0.434396076583152	2		553	910	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	170	542	2	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.835	0.768	0.905	0.835	0.768	0.905	CLONAL	1	TRUE	1	0.434396076583152	2		544	937	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106922	27106922	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	200	625	0	ENST00000324856.7:c.6533A>G	p.Asp2178Gly	p.D2178G	ENST00000324856	NM_006015.4	2178	gAc/gGc	20/20	1	2	FACETS	0.897	0.83	0.965	0.897	0.83	0.965	CLONAL	1	TRUE	1	0.434396076583152	2		625	1027	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429977	78429978	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1200882279	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	33	233	0	ENST00000370768.2:c.901dup	p.Ile301AsnfsTer4	p.I301Nfs*4	ENST00000370768	NM_003902.3	301	ata/aAta	11/20	1	2	FACETS	0.316	0.257	0.383	0.316	0.257	0.383	SUBCLONAL	1	TRUE	1	0.434396076583152	2		233	481	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161298253	161298253	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	123	340	0	ENST00000367975.2:c.145A>C	p.Asn49His	p.N49H	ENST00000367975	NM_003001.3	49	Aac/Cac	3/6	1	2	FACETS	0.871	0.79	0.957	0.871	0.79	0.957	CLONAL	1	TRUE	1	0.434396076583152	2		340	650	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193205391	193205391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778432682	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	136	289	0	ENST00000367435.3:c.1322G>A	p.Arg441His	p.R441H	ENST00000367435	NM_024529.4	441	cGc/cAc	15/17	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.434396076583152	2		289	616	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927443	245927443	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	37	393	1	ENST00000388985.4:c.1085del	p.Phe362SerfsTer12	p.F362Sfs*12	ENST00000388985		362	tTc/tc	11/12	1	2	FACETS	0.249	0.204	0.299	0.249	0.204	0.299	SUBCLONAL	1	TRUE	1	0.434396076583152	2		394	684	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741910	17741910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	64	239	0	ENST00000250003.3:c.581G>A	p.Ser194Asn	p.S194N	ENST00000250003	NM_002478.4	194	aGc/aAc	1/3	0.434396076583152	3	FACETS	0.729	0.632	0.833	0.364	0.316	0.417	SUBCLONAL	1	TRUE	1	0.434396076583152	3		239	492	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137231	64137231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1410769083	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1716	113	980	1	ENST00000334205.4:c.1663G>A	p.Ala555Thr	p.A555T	ENST00000334205	NM_003942.2	555	Gcg/Acg	14/17	0.434396076583152	3	FACETS	0.346	0.31	0.385	0.173	0.155	0.193	SUBCLONAL	1	TRUE	1	0.434396076583152	3		981	1829	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633577	69633577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	239	212	1	ENST00000334134.2:c.125C>T	p.Ala42Val	p.A42V	ENST00000334134	NM_005247.2	42	gCg/gTg	1/3	0.434396076583152	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.434396076583152	3		213	605	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	54	379	2	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	0.351387455081935	2	FACETS	0.289	0.246	0.337	0.145	0.123	0.169	SUBCLONAL	1	TRUE	0	0.434396076583152	2		381	860	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	118	286	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.351387455081935	2	FACETS	0.898	0.812	0.988	0.449	0.406	0.494	CLONAL	1	TRUE	0	0.434396076583152	2		286	605	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445094	49445095	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	478	806	2	ENST00000301067.7:c.2371dup	p.Gln791ProfsTer3	p.Q791Pfs*3	ENST00000301067	NM_003482.3	791	cag/cCag	10/54	0.340202997447051	3	FACETS	0.973	0.93	1	0.648	0.62	0.677	CLONAL	2	TRUE	0	0.434396076583152	3		808	1377	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445727	49445727	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	849	1106	2	ENST00000301067.7:c.1739C>A	p.Pro580His	p.P580H	ENST00000301067	NM_003482.3	580	cCc/cAc	10/54	0.340202997447051	3	FACETS	1	0.996	1	0.794	0.769	0.819	CLONAL	2	TRUE	0	0.434396076583152	3		1108	1998	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1374	85	722	5	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	0.297507561714325	3	FACETS	0.326	0.287	0.369	0.109	0.095	0.123	SUBCLONAL	1	TRUE	0	0.434396076583152	3		727	1459	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929279	32929279	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	213	357	0	ENST00000380152.3:c.7292del	p.Asn2431ThrfsTer36	p.N2431Tfs*36	ENST00000380152		2430	gAa/ga	14/27	0.333223967980535	3	FACETS	1	0.992	1	0.749	0.697	0.802	CLONAL	1	TRUE	1	0.434396076583152	3		357	797	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930649	32930649	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876658948	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	214	321	1	ENST00000380152.3:c.7520C>T	p.Pro2507Leu	p.P2507L	ENST00000380152		2507	cCa/cTa	15/27	0.333223967980535	3	FACETS	1	0.99	1	0.705	0.656	0.755	CLONAL	1	TRUE	1	0.434396076583152	3		322	851	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103510654	103510654	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	144	246	0	ENST00000355739.4:c.558A>G	p.Ile186Met	p.I186M	ENST00000355739	NM_000123.3	186	atA/atG	6/15	0.333223967980535	3	FACETS	0.776	0.712	0.842	0.776	0.712	0.842	SUBCLONAL	2	TRUE	1	0.434396076583152	3		246	520	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	168	229	5	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	0.333223967980535	3	FACETS	0.772	0.713	0.833	0.772	0.713	0.833	SUBCLONAL	2	TRUE	1	0.434396076583152	3		234	610	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435128	110435129	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs772322568	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1567	250	852	0	ENST00000375856.3:c.3272dup	p.Lys1092GlufsTer233	p.K1092Efs*233	ENST00000375856	NM_003749.2	1091	ccg/ccCg	1/2	0.333223967980535	3	FACETS	0.771	0.718	0.826	0.386	0.359	0.413	SUBCLONAL	1	TRUE	1	0.434396076583152	3		852	1817	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68758661	68758661	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	126	334	0	ENST00000487270.1:c.817C>A	p.Leu273Met	p.L273M	ENST00000487270	NM_133509.3	273	Ctg/Atg	8/11	1	2	FACETS	0.88	0.799	0.966	0.88	0.799	0.966	CLONAL	1	TRUE	1	0.434396076583152	2		334	659	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246475	105246475	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	270	741	0	ENST00000349310.3:c.125C>T	p.Pro42Leu	p.P42L	ENST00000349310	NM_001014432.1	42	cCg/cTg	4/15	1	2	FACETS	0.989	0.927	1	0.989	0.927	1	CLONAL	1	TRUE	1	0.434396076583152	2		741	1257	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643812	38643812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs941091989	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	213	589	2	ENST00000299084.4:c.1282C>T	p.Arg428Cys	p.R428C	ENST00000299084	NM_152594.2	428	Cgc/Tgc	7/7	1	2	FACETS	0.82	0.761	0.882	0.82	0.761	0.882	CLONAL	1	TRUE	1	0.434396076583152	2		591	1196	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007687	45007687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	73	287	1	ENST00000558401.1:c.134G>A	p.Cys45Tyr	p.C45Y	ENST00000558401	NM_004048.2	45	tGc/tAc	2/4	1	2	FACETS	0.662	0.58	0.749	0.662	0.58	0.749	SUBCLONAL	1	TRUE	1	0.434396076583152	2		288	508	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007888	45007891	+	frameshift_variant	Frame_Shift_Del	DEL	TAGT	TAGT	-	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	75	248	0	ENST00000558401.1:c.337_340del	p.Val113SerfsTer31	p.V113Sfs*31	ENST00000558401	NM_004048.2	112	aTAGTt/at	2/4	1	2	FACETS	0.696	0.612	0.787	0.696	0.612	0.787	SUBCLONAL	1	TRUE	1	0.434396076583152	2		248	496	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007896	45007897	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	89	248	0	ENST00000558401.1:c.346+1dup		p.W115fs	ENST00000558401	NM_004048.2	115	tgg/tGgg	2/4	1	2	FACETS	0.82	0.729	0.915	0.82	0.729	0.915	CLONAL	1	TRUE	1	0.434396076583152	2		248	500	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312442	91312442	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	39	338	1	ENST00000355112.3:c.2387A>G	p.Glu796Gly	p.E796G	ENST00000355112	NM_000057.2	796	gAa/gGa	11/22	1	2	FACETS	0.271	0.224	0.324	0.271	0.224	0.324	SUBCLONAL	1	TRUE	1	0.434396076583152	2		339	662	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347446	91347446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757088548	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	165	298	0	ENST00000355112.3:c.3608C>T	p.Ala1203Val	p.A1203V	ENST00000355112	NM_000057.2	1203	gCg/gTg	19/22	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.434396076583152	2		298	665	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	48	336	0	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.35	0.295	0.41	0.35	0.295	0.41	SUBCLONAL	1	TRUE	1	0.434396076583152	2		336	632	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832811	3832811	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555484797	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	136	505	0	ENST00000262367.5:c.1447C>T	p.Arg483Ter	p.R483*	ENST00000262367	NM_004380.2	483	Cga/Tga	6/31	1	2	FACETS	0.654	0.594	0.718	0.654	0.594	0.718	SUBCLONAL	1	TRUE	1	0.434396076583152	2		505	957	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857044	9857044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201707833	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	62	232	0	ENST00000330684.3:c.4357G>A	p.Val1453Met	p.V1453M	ENST00000330684	NM_001134407.1	1453	Gtg/Atg	13/13	1	2	FACETS	0.765	0.664	0.874	0.765	0.664	0.874	SUBCLONAL	1	TRUE	1	0.434396076583152	2		232	373	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647028	23647028	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1555461597	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	202	529	0	ENST00000261584.4:c.839del	p.Asn280ThrfsTer8	p.N280Tfs*8	ENST00000261584	NM_024675.3	280	aAc/ac	4/13	1	2	FACETS	0.897	0.831	0.965	0.897	0.831	0.965	CLONAL	1	TRUE	1	0.434396076583152	2		529	1037	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821565	72821565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1369608013	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	86	198	1	ENST00000268489.5:c.10610C>T	p.Ala3537Val	p.A3537V	ENST00000268489	NM_006885.3	3537	gCg/gTg	10/10	1	2	FACETS	0.91	0.809	1	0.91	0.809	1	CLONAL	1	TRUE	1	0.434396076583152	2		199	435	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347878	89347878	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763039848	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	231	669	1	ENST00000301030.4:c.5072C>T	p.Ala1691Val	p.A1691V	ENST00000301030	NM_001256183.1	1691	gCg/gTg	9/13	1	2	FACETS	0.986	0.919	1	0.986	0.919	1	CLONAL	1	TRUE	1	0.434396076583152	2		670	1079	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459742	40459742	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1288217526	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	63	516	0	ENST00000345506.4:c.1906+1G>A		p.X636_splice	ENST00000345506	NM_003152.3	636			1	2	FACETS	0.299	0.257	0.344	0.299	0.257	0.344	SUBCLONAL	1	TRUE	1	0.434396076583152	2		516	971	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437565	56437566	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	242	598	0	ENST00000407977.2:c.896_897del	p.Val299GlyfsTer143	p.V299Gfs*143	ENST00000407977		299	gTG/g	8/10	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.434396076583152	2		598	1100	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1252	299	1297	1	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.888	0.834	0.943	0.888	0.834	0.943	CLONAL	1	TRUE	1	0.434396076583152	2		1298	1551	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526074	66526074	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	94	256	0	ENST00000358598.2:c.905T>C	p.Val302Ala	p.V302A	ENST00000358598	NM_212471.2	302	gTg/gCg	10/11	1	2	FACETS	0.883	0.789	0.983	0.883	0.789	0.983	CLONAL	1	TRUE	1	0.434396076583152	2		256	490	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985524	60985524	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	231	596	0	ENST00000333681.4:c.376G>A	p.Ala126Thr	p.A126T	ENST00000333681		126	Gcg/Acg	2/3	1	2	FACETS	0.891	0.829	0.954	0.891	0.829	0.954	CLONAL	1	TRUE	1	0.434396076583152	2		596	1194	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612205	1612205	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	174	527	0	ENST00000344749.5:c.1813+1G>A		p.X605_splice	ENST00000344749	NM_001136139.2	605			1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.434396076583152	2		527	798	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101033	4101033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369714097	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	188	581	0	ENST00000262948.5:c.689C>T	p.Thr230Met	p.T230M	ENST00000262948	NM_030662.3	230	aCg/aTg	6/11	1	2	FACETS	0.859	0.793	0.927	0.859	0.793	0.927	CLONAL	1	TRUE	1	0.434396076583152	2		581	1008	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144146	11144146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	184	893	4	ENST00000358026.2:c.3727C>T	p.Arg1243Trp	p.R1243W	ENST00000358026	NM_001128849.1	1243	Cgg/Tgg	26/36	1	2	FACETS	0.645	0.594	0.699	0.645	0.594	0.699	SUBCLONAL	1	TRUE	1	0.434396076583152	2		897	1313	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300158	15300158	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1247	223	839	0	ENST00000263388.2:c.1118G>A	p.Gly373Asp	p.G373D	ENST00000263388	NM_000435.2	373	gGc/gAc	7/33	1	2	FACETS	0.698	0.648	0.751	0.698	0.648	0.751	SUBCLONAL	1	TRUE	1	0.434396076583152	2		839	1470	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349553	15349553	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1398	92	1043	1	ENST00000263377.2:c.4020+1G>A		p.X1340_splice	ENST00000263377	NM_058243.2	1340			1	2	FACETS	0.284	0.251	0.32	0.284	0.251	0.32	SUBCLONAL	1	TRUE	1	0.434396076583152	2		1044	1490	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366330	15366330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	195	598	0	ENST00000263377.2:c.1825C>T	p.Pro609Ser	p.P609S	ENST00000263377	NM_058243.2	609	Cct/Tct	10/20	1	2	FACETS	0.96	0.889	1	0.96	0.889	1	CLONAL	1	TRUE	1	0.434396076583152	2		598	935	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257082	19257082	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1316	100	846	0	ENST00000162023.5:c.881G>T	p.Ser294Ile	p.S294I	ENST00000162023		294	aGt/aTt	12/13	1	2	FACETS	0.325	0.289	0.364	0.325	0.289	0.364	SUBCLONAL	1	TRUE	1	0.434396076583152	2		846	1416	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1280	302	1286	7	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	1	2	FACETS	0.879	0.826	0.934	0.879	0.826	0.934	CLONAL	1	TRUE	1	0.434396076583152	2		1293	1582	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214711	36214711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779455230	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	215	712	1	ENST00000222270.7:c.3137G>A	p.Arg1046His	p.R1046H	ENST00000222270	NM_014727.1	1046	cGc/cAc	8/37	1	2	FACETS	0.893	0.83	0.959	0.893	0.83	0.959	CLONAL	1	TRUE	1	0.434396076583152	2		713	1108	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214893	36214894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	264	865	0	ENST00000222270.7:c.3325dup	p.Arg1109ProfsTer4	p.R1109Pfs*4	ENST00000222270	NM_014727.1	1107	acc/aCcc	8/37	1	2	FACETS	0.858	0.802	0.915	0.858	0.802	0.915	CLONAL	1	TRUE	1	0.434396076583152	2		865	1417	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218803	36218803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	273	922	0	ENST00000222270.7:c.4414G>A	p.Val1472Met	p.V1472M	ENST00000222270	NM_014727.1	1472	Gtg/Atg	18/37	1	2	FACETS	0.901	0.844	0.96	0.901	0.844	0.96	CLONAL	1	TRUE	1	0.434396076583152	2		922	1395	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791865	42791865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1312	99	830	1	ENST00000575354.2:c.751G>A	p.Asp251Asn	p.D251N	ENST00000575354	NM_015125.3	251	Gac/Aac	5/20	1	2	FACETS	0.323	0.287	0.362	0.323	0.287	0.362	SUBCLONAL	1	TRUE	1	0.434396076583152	2		831	1411	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	698	958	2	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	0.929	0.896	0.961	1	0.998	1	CLONAL	2	TRUE	1	0.434396076583152	2		960	1730	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725019	47725019	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs762488821	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1481	246	1088	4	ENST00000449228.1:c.725del	p.Gly242AlafsTer48	p.G242Afs*48	ENST00000449228	NM_001127240.2	242	gGc/gc	4/4	1	2	FACETS	0.656	0.611	0.703	0.656	0.611	0.703	SUBCLONAL	1	TRUE	1	0.434396076583152	2		1092	1727	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451843	29451843	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	133	572	0	ENST00000389048.3:c.2722del	p.Gln908ArgfsTer3	p.Q908Rfs*3	ENST00000389048	NM_004304.4	908	Cag/ag	16/29	1	2	FACETS	0.577	0.523	0.634	0.577	0.523	0.634	SUBCLONAL	1	TRUE	1	0.434396076583152	2		572	1061	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917748	29917748	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1191	166	731	0	ENST00000389048.3:c.920C>A	p.Pro307His	p.P307H	ENST00000389048	NM_004304.4	307	cCt/cAt	3/29	1	2	FACETS	0.563	0.516	0.613	0.563	0.516	0.613	SUBCLONAL	1	TRUE	1	0.434396076583152	2		731	1357	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437288	220437288	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1190141661	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1371	301	1145	2	ENST00000243786.2:c.197del	p.Gly66AlafsTer61	p.G66Afs*61	ENST00000243786	NM_002191.3	64	ctG/ct	1/2	1	2	FACETS	0.829	0.778	0.881	0.829	0.778	0.881	CLONAL	1	TRUE	1	0.434396076583152	2		1147	1672	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384650	31384651	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs756395138	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1228	208	657	3	ENST00000328111.2:c.1359dup	p.Leu454AlafsTer11	p.L454Afs*11	ENST00000328111	NM_006892.3	451	gag/gaGg	13/23	0.434396076583152	3	FACETS	0.812	0.751	0.875	0.406	0.375	0.438	CLONAL	1	TRUE	1	0.434396076583152	3		660	1436	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385068	31385068	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1348	272	727	0	ENST00000328111.2:c.1453C>T	p.Arg485Ter	p.R485*	ENST00000328111	NM_006892.3	485	Cga/Tga	14/23	0.434396076583152	3	FACETS	0.941	0.88	1	0.47	0.44	0.502	CLONAL	1	TRUE	1	0.434396076583152	3		727	1620	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743874	40743874	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	367	457	0	ENST00000373198.4:c.3121G>T	p.Ala1041Ser	p.A1041S	ENST00000373198	NM_133170.3	1041	Gca/Tca	23/32	NA	2	FACETS	0.853	0.811	0.895			1	INDETERMINATE	2	TRUE	NA	0.434396076583152	2		457	991	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30061040	30061040	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755200117	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	126	288	0	ENST00000338641.4:c.872G>A	p.Arg291His	p.R291H	ENST00000338641	NM_000268.3	291	cGt/cAt	9/16	1	2	FACETS	0.956	0.868	1	0.956	0.868	1	CLONAL	1	TRUE	1	0.434396076583152	2		288	607	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513701	41513701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773342339	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	218	563	0	ENST00000263253.7:c.605G>A	p.Arg202Gln	p.R202Q	ENST00000263253	NM_001429.3	202	cGa/cAa	2/31	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.434396076583152	2		563	983	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573261	41573261	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1389	94	896	1	ENST00000263253.7:c.5550del	p.Thr1851LeufsTer55	p.T1851Lfs*55	ENST00000263253	NM_001429.3	1849	tCc/tc	31/31	1	2	FACETS	0.292	0.258	0.328	0.292	0.258	0.328	SUBCLONAL	1	TRUE	1	0.434396076583152	2		897	1483	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434182	12434182	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776687	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	105	333	1	ENST00000287820.6:c.556del	p.Ser186ValfsTer47	p.S186Vfs*47	ENST00000287820	NM_015869.4	184	Aaa/aa	4/7	1	2	FACETS	0.755	0.678	0.837	0.755	0.678	0.837	SUBCLONAL	1	TRUE	1	0.434396076583152	2		334	640	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053348	37053348	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63751653	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	128	354	0	ENST00000231790.2:c.588del	p.Lys196AsnfsTer6	p.K196Nfs*6	ENST00000231790	NM_000249.3	195	Aaa/aa	7/19	1	2	FACETS	0.992	0.902	1	0.992	0.902	1	CLONAL	1	TRUE	1	0.434396076583152	2		354	594	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723126	49723128	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs751306787	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	287	656	0	ENST00000449682.2:c.1288_1290del	p.Glu430del	p.E430del	ENST00000449682	NM_020998.3	430	GAG/-	11/18	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.434396076583152	2		656	1190	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590764	189590764	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	165	388	0	ENST00000264731.3:c.1329C>G	p.His443Gln	p.H443Q	ENST00000264731	NM_003722.4	443	caC/caG	10/14	1	2	FACETS	0.936	0.86	1	0.936	0.86	1	CLONAL	1	TRUE	1	0.434396076583152	2		388	812	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808056	1808056	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1252	312	1094	0	ENST00000260795.2:c.2030+2T>C		p.X677_splice	ENST00000260795		677			1	2	FACETS	0.918	0.864	0.975	0.918	0.864	0.975	CLONAL	1	TRUE	1	0.434396076583152	2		1094	1564	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217223	66217223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	56	342	0	ENST00000273854.3:c.2392C>T	p.His798Tyr	p.H798Y	ENST00000273854	NM_004439.5	798	Cat/Tat	14/18	1	2	FACETS	0.468	0.401	0.541	0.468	0.401	0.541	SUBCLONAL	1	TRUE	1	0.434396076583152	2		342	551	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106162494	106162494	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	26	187	1	ENST00000380013.4:c.3410-2A>C		p.X1137_splice	ENST00000380013	NM_001127208.2	1137			1	2	FACETS	0.471	0.374	0.582	0.471	0.374	0.582	SUBCLONAL	1	TRUE	1	0.434396076583152	2		188	254	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180785	106180785	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs533538484	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	41	226	2	ENST00000380013.4:c.3813C>G	p.Cys1271Trp	p.C1271W	ENST00000380013	NM_001127208.2	1271	tgC/tgG	7/11	1	2	FACETS	0.392	0.326	0.465	0.392	0.326	0.465	SUBCLONAL	1	TRUE	1	0.434396076583152	2		228	482	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142949967	142949967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	73	349	0	ENST00000262992.4:c.2743C>T	p.Pro915Ser	p.P915S	ENST00000262992	NM_001101669.1	915	Cca/Tca	24/24	1	2	FACETS	0.662	0.58	0.749	0.662	0.58	0.749	SUBCLONAL	1	TRUE	1	0.434396076583152	2		349	508	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	281	486	9	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.434396076583152	2		495	885	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053023	180053023	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	272	977	4	ENST00000261937.6:c.1267del	p.Gln423ArgfsTer70	p.Q423Rfs*70	ENST00000261937	NM_182925.4	423	Cag/ag	10/30	NA	2	FACETS	0.925	0.866	0.985			1	INDETERMINATE	1	TRUE	NA	0.434396076583152	2		981	1354	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190367	32190367	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1375	86	811	0	ENST00000375023.3:c.372del	p.Ser125ProfsTer127	p.S125Pfs*127	ENST00000375023	NM_004557.3	124	ccC/cc	3/30	0.216506653962313	3	FACETS	0.33	0.29	0.373	0.165	0.145	0.187	INDETERMINATE	1	TRUE	1	0.434396076583152	3		811	1461	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286992	33286992	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	176	499	0	ENST00000374542.5:c.1945G>A	p.Val649Met	p.V649M	ENST00000374542	NM_001141970.1	649	Gtg/Atg	7/8	0.216506653962313	3	FACETS	0.947	0.871	1	0.473	0.435	0.513	INDETERMINATE	1	TRUE	1	0.434396076583152	3		499	1042	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120713	94120713	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	36	351	0	ENST00000369303.4:c.338C>A	p.Pro113His	p.P113H	ENST00000369303	NM_004440.3	113	cCt/cAt	3/17	1	2	FACETS	0.295	0.242	0.355	0.295	0.242	0.355	SUBCLONAL	1	TRUE	1	0.434396076583152	2		351	561	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099890	157099890	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	139	591	0	ENST00000346085.5:c.831del	p.Gly278AlafsTer91	p.G278Afs*91	ENST00000346085	NM_020732.3	276	gCc/gc	1/20	1	2	FACETS	0.494	0.448	0.543	0.494	0.448	0.543	SUBCLONAL	1	TRUE	1	0.434396076583152	2		591	1295	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502286	157502286	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1282312643	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	114	481	0	ENST00000346085.5:c.3319G>A	p.Val1107Ile	p.V1107I	ENST00000346085	NM_020732.3	1107	Gtc/Atc	12/20	1	2	FACETS	0.53	0.476	0.587	0.53	0.476	0.587	SUBCLONAL	1	TRUE	1	0.434396076583152	2		481	991	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	408	718	5	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	0.333223967980535	3	FACETS	0.775	0.736	0.814	0.775	0.736	0.814	SUBCLONAL	2	TRUE	1	0.434396076583152	3		723	1476	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	166	311	5	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	0.333223967980535	3	FACETS	1	0.985	1	0.651	0.6	0.705	CLONAL	1	TRUE	1	0.434396076583152	3		316	714	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482927	140482927	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	99	462	4	ENST00000288602.6:c.1208del	p.Pro403LeufsTer8	p.P403Lfs*8	ENST00000288602	NM_004333.4	403	cCt/ct	10/18	0.333223967980535	3	FACETS	0.605	0.539	0.675	0.303	0.269	0.338	SUBCLONAL	1	TRUE	1	0.434396076583152	3		466	917	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511172	148511172	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	123	455	0	ENST00000320356.2:c.1730C>A	p.Pro577Gln	p.P577Q	ENST00000320356	NM_004456.4	577	cCg/cAg	15/20	0.333223967980535	3	FACETS	0.611	0.551	0.675	0.306	0.275	0.338	SUBCLONAL	1	TRUE	1	0.434396076583152	3		455	1128	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874149	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	166	319	0	ENST00000262189.6:c.8389_8390del	p.Lys2797GlyfsTer11	p.K2797Gfs*11	ENST00000262189	NM_170606.2	2797	AAg/g	38/59	0.333223967980535	3	FACETS	1	0.983	1	0.625	0.575	0.677	CLONAL	1	TRUE	1	0.434396076583152	3		319	744	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	64	210	5	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	0.286755928032973	5	FACETS	0.96	0.833	1	0.32	0.277	0.366	CLONAL	1	TRUE	2	0.434396076583152	5		215	507	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971023	21971023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782797	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	247	666	1	ENST00000304494.5:c.335G>A	p.Arg112His	p.R112H	ENST00000304494	NM_000077.4	112	cGt/cAt	2/3	0.434396076583152	3	FACETS	1	0.949	1	0.51	0.476	0.546	CLONAL	1	TRUE	1	0.434396076583152	3		667	1357	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93627351	93627351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139520862	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	55	393	0	ENST00000375746.1:c.818G>A	p.Arg273His	p.R273H	ENST00000375746	NM_001174167.1	273	cGt/cAt	6/14	0.434396076583152	3	FACETS	0.346	0.294	0.402	0.173	0.147	0.201	SUBCLONAL	1	TRUE	1	0.434396076583152	3		393	892	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923603	39923603	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1048287551	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	101	405	0	ENST00000378444.4:c.3488G>A	p.Arg1163Gln	p.R1163Q	ENST00000378444	NM_001123385.1	1163	cGa/cAa	7/15	0.237513588246775	2	FACETS	0.481	0.429	0.536			1	INDETERMINATE	1	TRUE	NA	0.434396076583152	2		405	967	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426094	47426094	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	293	440	1	ENST00000377045.4:c.619del	p.Leu207TyrfsTer85	p.L207Yfs*85	ENST00000377045	NM_001654.4	205	gCc/gc	7/16	0.237513588246775	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.434396076583152	2		441	1076	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361097	70361098	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAG	rs766775649	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	151	266	0	ENST00000374080.3:c.6306_6308dup	p.Gln2115dup	p.Q2115dup	ENST00000374080		2115	-/CAG	43/45	0.237513588246775	2	FACETS	1	0.949	1			1	INDETERMINATE	1	TRUE	NA	0.434396076583152	2		266	663	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1225	81	715	2	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	1	2	FACETS	0.286	0.25	0.324	0.286	0.25	0.324	SUBCLONAL	1	TRUE	1	0.434396076583152	2		717	1306	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099415	157099426	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAA	CAGCAGCAGCAA	-	rs797045275	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	49	312	2	ENST00000346085.5:c.363_374del	p.Gln128_Gln131del	p.Q128_Q131del	ENST00000346085	NM_020732.3	118	CAGCAGCAGCAA/-	1/20	1	2	FACETS	0.369	0.312	0.432	0.369	0.312	0.432	SUBCLONAL	1	TRUE	1	0.434396076583152	2		314	612	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100006	157100008	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	rs587779748	NA	P-0058522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	27	166	2	ENST00000346085.5:c.954_956del	p.Gly319del	p.G319del	ENST00000346085	NM_020732.3	315	GGA/-	1/20	1	2	FACETS	0.292	0.232	0.361	0.292	0.232	0.361	SUBCLONAL	1	TRUE	1	0.434396076583152	2		168	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0058524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	850	953	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.931012461407744	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.931012461407744	2		953	870	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149566	202149590	+	frameshift_variant	Frame_Shift_Del	DEL	TTCATTTTGAGATCAAGCCCCACGA	TTCATTTTGAGATCAAGCCCCACGA	-	novel	NA	P-0058524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	254	475	0	ENST00000358485.4:c.1008_1032del	p.His337ThrfsTer4	p.H337Tfs*4	ENST00000358485	NM_001080125.1	336	cTTCATTTTGAGATCAAGCCCCACGAt/ct	8/9	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.931012461407744	2		475	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0058526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	893	898	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.685593335502642	2	FACETS	0.988	0.965	1	0.988	0.965	1	CLONAL	2	TRUE	0	0.685593335502642	2		898	1318	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120871	115120871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	934	778	0	ENST00000257566.3:c.135del	p.Leu46CysfsTer42	p.L46Cfs*42	ENST00000257566	NM_016569.3	45	acG/ac	1/8	0.685593335502642	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.685593335502642	2		778	1297	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050980	49050980	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0058526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	165	231	0	ENST00000267163.4:c.2663+1G>T		p.X888_splice	ENST00000267163	NM_000321.2	888			0.685593335502642	1	FACETS	0.93	0.869	0.992	0.93	0.869	0.992	CLONAL	1	TRUE	0	0.685593335502642	1		231	340	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933256	49933271	+	frameshift_variant	Frame_Shift_Del	DEL	CATCTGGCCCTGGCCG	CATCTGGCCCTGGCCG	-	novel	NA	P-0058526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1303	538	1065	0	ENST00000296474.3:c.2839_2854del	p.Arg947GlyfsTer36	p.R947Gfs*36	ENST00000296474	NM_002447.2	947	CGGCCAGGGCCAGATGgg/gg	12/20	1	2	FACETS	0.852	0.816	0.89	0.852	0.816	0.89	CLONAL	1	TRUE	1	0.685593335502642	2		1065	1841	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0058528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	486	622	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.447583484792317	3	FACETS	0.968	0.932	1	0.968	0.932	1	CLONAL	3	TRUE	0	0.45119884915571	3		622	909	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971116	21971116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552823	NA	P-0058528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	549	596	0	ENST00000304494.5:c.242C>T	p.Pro81Leu	p.P81L	ENST00000304494	NM_000077.4	81	cCc/cTc	2/3	0.398054646080164	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.45119884915571	3		596	932	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587781525	NA	P-0058528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	430	727	0	ENST00000269305.4:c.842A>T	p.Asp281Val	p.D281V	ENST00000269305	NM_001126112.2	281	gAc/gTc	8/11	0.45119884915571	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.45119884915571	2		727	900	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546029	41546029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	217	704	0	ENST00000263253.7:c.2644C>T	p.Pro882Ser	p.P882S	ENST00000263253	NM_001429.3	882	Cca/Tca	14/31	0.353711799442052	3	FACETS	1	0.966	1	0.533	0.495	0.572	CLONAL	1	TRUE	1	0.45119884915571	3		704	1106	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0058528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	148	340	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.45119884915571	NA		340	431	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765640	41765640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	372	691	1	ENST00000301178.4:c.2516G>A	p.Gly839Glu	p.G839E	ENST00000301178	NM_021913.4	839	gGa/gAa	20/20	0.230854976267602	3	FACETS	1	0.983	1	0.712	0.678	0.747	INDETERMINATE	2	TRUE	0	0.45119884915571	3		692	946	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692818	89692818	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	250	163	0	ENST00000371953.3:c.302T>G	p.Ile101Ser	p.I101S	ENST00000371953	NM_000314.4	101	aTc/aGc	5/9	0.45119884915571	3	FACETS	0.924	0.875	0.972	0.924	0.875	0.972	CLONAL	3	TRUE	0	0.45119884915571	3		163	490	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40709539	40709539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159851	NA	P-0058528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	326	364	1	ENST00000373198.4:c.4363G>A	p.Glu1455Lys	p.E1455K	ENST00000373198	NM_133170.3	1455	Gaa/Aaa	32/32	0.405342048514682	5	FACETS	0.958	0.909	1	0.958	0.909	1	CLONAL	3	TRUE	2	0.45119884915571	5		365	843	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259608	89259608	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	42	296	0	ENST00000336596.2:c.752T>C	p.Leu251Pro	p.L251P	ENST00000336596	NM_005233.5	251	cTt/cCt	3/17	0.139723966280572	5	FACETS	0.511	0.426	0.606	0.17	0.142	0.202	INDETERMINATE	1	TRUE	2	0.45119884915571	5		296	611	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350794	15350794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	206	764	0	ENST00000263377.2:c.3209C>T	p.Ser1070Phe	p.S1070F	ENST00000263377	NM_058243.2	1070	tCc/tTc	15/20	0.45119884915571	3	FACETS	1	0.969	1	0.54	0.501	0.581	CLONAL	1	TRUE	1	0.45119884915571	3		764	1036	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274265	10274265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1304533759	NA	P-0058528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	47	426	0	ENST00000330684.3:c.4G>A	p.Gly2Ser	p.G2S	ENST00000330684	NM_001134407.1	2	Ggc/Agc	2/13	0.45119884915571	3	FACETS	0.645	0.545	0.754	0.322	0.272	0.377	SUBCLONAL	1	TRUE	1	0.45119884915571	3		426	396	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69998222	69998222	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	216	414	0	ENST00000394351.3:c.462G>C	p.Leu154Phe	p.L154F	ENST00000394351	NM_000248.3	154	ttG/ttC	5/9	0.405342048514682	5	FACETS	0.823	0.766	0.883	0.549	0.51	0.589	CLONAL	2	TRUE	2	0.45119884915571	5		414	975	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146109	38146109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1159628992	NA	P-0058528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	428	633	0	ENST00000317025.8:c.3397C>T	p.Arg1133Cys	p.R1133C	ENST00000317025	NM_023034.1	1133	Cgt/Tgt	19/24	0.360987845368406	3	FACETS	0.964	0.92	1	0.964	0.92	1	CLONAL	2	TRUE	1	0.45119884915571	3		633	1206	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287214	38287214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	368	709	0	ENST00000425967.3:c.443C>T	p.Ser148Phe	p.S148F	ENST00000425967	NM_001174067.1	148	tCc/tTc	4/19	0.360987845368406	3	FACETS	0.982	0.934	1	0.982	0.934	1	CLONAL	2	TRUE	1	0.45119884915571	3		709	1018	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865090	57865090	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	213	879	0	ENST00000228682.2:c.2567C>G	p.Pro856Arg	p.P856R	ENST00000228682	NM_005269.2	856	cCt/cGt	12/12	0.397169692018226	5	FACETS	1	0.989	1	0.457	0.424	0.492	CLONAL	1	TRUE	2	0.45119884915571	5		879	1154	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986793	36986793	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779736041	NA	P-0058528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	118	179	1	ENST00000354822.5:c.896C>T	p.Pro299Leu	p.P299L	ENST00000354822	NM_001079668.2	299	cCg/cTg	3/3	0.119713544673394	6	FACETS	1	0.978	1	0.831	0.757	0.909	INDETERMINATE	2	TRUE	3	0.45119884915571	6		180	399	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126491	2126491	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs45517263	NA	P-0058528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	140	677	0	ENST00000219476.3:c.2743-1G>C		p.X915_splice	ENST00000219476	NM_000548.3	915			0.45119884915571	3	FACETS	0.993	0.905	1	0.496	0.452	0.543	CLONAL	1	TRUE	1	0.45119884915571	3		677	766	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296107	15296107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	217	1008	0	ENST00000263388.2:c.2257G>A	p.Gly753Arg	p.G753R	ENST00000263388	NM_000435.2	753	Gga/Aga	14/33	0.45119884915571	3	FACETS	1	0.957	1	0.52	0.483	0.559	CLONAL	1	TRUE	1	0.45119884915571	3		1008	1133	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945789	17945790	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	261	809	0	ENST00000458235.1:c.2070_2071delinsAA	p.Trp690_Val691delinsTer	p.W690_V691delins*	ENST00000458235	NM_000215.3	690	tgGGtg/tgAAtg	16/24	0.45119884915571	3	FACETS	0.819	0.769	0.87	0.819	0.769	0.87	CLONAL	2	TRUE	1	0.45119884915571	3		809	866	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188203	32188203	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	91	737	0	ENST00000375023.3:c.1138C>T	p.Leu380Phe	p.L380F	ENST00000375023	NM_004557.3	380	Ctc/Ttc	6/30	0.45119884915571	3	FACETS	0.627	0.557	0.703	0.314	0.278	0.352	SUBCLONAL	1	TRUE	1	0.45119884915571	3		737	788	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398280	25398281	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0058529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	97	410	0	ENST00000311936.3:c.38_39delinsAA	p.Gly13Glu	p.G13E	ENST00000311936	NM_004985.3	13	gGC/gAA	2/5	1	2	FACETS	0.602	0.54	0.668	0.602	0.54	0.668	SUBCLONAL	1	TRUE	1	0.725738806045496	2		410	444	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904959	101904959	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	167	362	0	ENST00000374994.4:c.948del	p.His317ThrfsTer18	p.H317Tfs*18	ENST00000374994	NM_004612.2	316	cTt/ct	5/9	0.725738806045496	1	FACETS	0.77	0.717	0.823	0.77	0.717	0.823	SUBCLONAL	1	TRUE	0	0.725738806045496	1		362	381	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	189	306	0				ENST00000310581	NM_198253.2	-/1132			0.50751209597176	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	1	0.533419660774239	3		306	442	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562266	95562266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs988095775	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	103	339	0	ENST00000393063.1:c.4991C>T	p.Ser1664Leu	p.S1664L	ENST00000393063	NM_030621.3	1664	tCg/tTg	24/28	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.533419660774239	2		339	383	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300415	11300415	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	193	588	0	ENST00000361445.4:c.1731C>G	p.Ser577Arg	p.S577R	ENST00000361445	NM_004958.3	577	agC/agG	11/58	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.533419660774239	2		588	637	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106207	27106207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	235	572	0	ENST00000324856.7:c.5818C>T	p.Pro1940Ser	p.P1940S	ENST00000324856	NM_006015.4	1940	Cca/Tca	20/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.533419660774239	2		572	764	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739373	46739373	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	453	518	2	ENST00000371975.4:c.1564T>A	p.Tyr522Asn	p.Y522N	ENST00000371975	NM_003579.3	522	Tac/Aac	14/18	0.417012094965943	3	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.533419660774239	3		520	969	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432754	78432754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	82	305	0	ENST00000370768.2:c.322C>T	p.Pro108Ser	p.P108S	ENST00000370768	NM_003902.3	108	Cca/Tca	5/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.533419660774239	2		305	272	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120496247	120496247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	127	397	0	ENST00000256646.2:c.2284C>T	p.Leu762Phe	p.L762F	ENST00000256646	NM_024408.3	762	Ctt/Ttt	14/34	1	2	FACETS	0.879	0.799	0.961	0.879	0.799	0.961	CLONAL	1	TRUE	1	0.533419660774239	2		397	542	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100357	8100357	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200765508	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	118	1174	0	ENST00000346208.3:c.331C>T	p.Pro111Ser	p.P111S	ENST00000346208		111	Ccc/Tcc	3/6	0.235566039769816	2	FACETS	0.457	0.411	0.505	0.228	0.205	0.253	INDETERMINATE	1	TRUE	0	0.533419660774239	2		1174	969	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421568	32421568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267602851	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	207	648	0	ENST00000332351.3:c.1024G>A	p.Asp342Asn	p.D342N	ENST00000332351	NM_024426.4	342	Gat/Aat	6/10	0.27530036408621	1	FACETS	0.711	0.662	0.763	0.711	0.662	0.763	INDETERMINATE	1	TRUE	0	0.533419660774239	1		648	800	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369218	118369218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782785673	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	66	311	1	ENST00000534358.1:c.5936G>A	p.Arg1979Gln	p.R1979Q	ENST00000534358	NM_005933.3	1979	cGa/cAa	22/36	0.27530036408621	1	FACETS	0.497	0.434	0.565	0.497	0.434	0.565	INDETERMINATE	1	TRUE	0	0.533419660774239	1		312	365	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118370627	118370627	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	63	232	0	ENST00000534358.1:c.6157C>T	p.Gln2053Ter	p.Q2053*	ENST00000534358	NM_005933.3	2053	Cag/Tag	24/36	0.27530036408621	1	FACETS	0.784	0.688	0.885	0.784	0.688	0.885	INDETERMINATE	1	TRUE	0	0.533419660774239	1		232	221	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374552	118374552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	65	355	0	ENST00000534358.1:c.7945C>T	p.Pro2649Ser	p.P2649S	ENST00000534358	NM_005933.3	2649	Cca/Tca	27/36	0.27530036408621	1	FACETS	0.452	0.394	0.515	0.452	0.394	0.515	INDETERMINATE	1	TRUE	0	0.533419660774239	1		355	395	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416855	416855	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	156	483	0	ENST00000399788.2:c.3695C>T	p.Ser1232Phe	p.S1232F	ENST00000399788	NM_001042603.1	1232	tCc/tTc	23/28	1	2	FACETS	0.998	0.918	1	0.998	0.918	1	CLONAL	1	TRUE	1	0.533419660774239	2		483	586	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650628	18650628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	87	358	0	ENST00000266497.5:c.2839G>A	p.Gly947Ser	p.G947S	ENST00000266497		947	Ggc/Agc	20/31	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.533419660774239	2		358	316	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800952	18800952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	36	271	0	ENST00000266497.5:c.4328G>A	p.Ser1443Asn	p.S1443N	ENST00000266497		1443	aGt/aAt	31/31	1	2	FACETS	0.628	0.52	0.746	0.628	0.52	0.746	SUBCLONAL	1	TRUE	1	0.533419660774239	2		271	215	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425560	49425560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756978181	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	227	1166	0	ENST00000301067.7:c.12928C>T	p.Pro4310Ser	p.P4310S	ENST00000301067	NM_003482.3	4310	Cca/Tca	39/54	1	2	FACETS	0.807	0.751	0.864	0.807	0.751	0.864	CLONAL	1	TRUE	1	0.533419660774239	2		1166	1055	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856287	111856287	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1403072205	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	32	33	0	ENST00000341259.2:c.338C>T	p.Pro113Leu	p.P113L	ENST00000341259	NM_005475.2	113	cCt/cTt	2/8	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.533419660774239	2		33	105	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112004	115112004	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375482722	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	201	1034	0	ENST00000257566.3:c.1736C>T	p.Pro579Leu	p.P579L	ENST00000257566	NM_016569.3	579	cCc/cTc	7/8	1	2	FACETS	0.835	0.774	0.897	0.835	0.774	0.897	CLONAL	1	TRUE	1	0.533419660774239	2		1034	903	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608234	28608234	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	99	517	0	ENST00000241453.7:c.1822G>A	p.Glu608Lys	p.E608K	ENST00000241453	NM_004119.2	608	Gaa/Aaa	14/24	1	2	FACETS	0.917	0.824	1	0.917	0.824	1	CLONAL	1	TRUE	1	0.533419660774239	2		517	405	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039393	49039393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	139	616	0	ENST00000267163.4:c.2378C>T	p.Pro793Leu	p.P793L	ENST00000267163	NM_000321.2	793	cCt/cTt	23/27	1	2	FACETS	0.872	0.796	0.95	0.872	0.796	0.95	CLONAL	1	TRUE	1	0.533419660774239	2		616	598	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028397	42028397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	60	219	0	ENST00000219905.7:c.3935C>T	p.Ser1312Phe	p.S1312F	ENST00000219905	NM_001164273.1	1312	tCc/tTc	13/24	0.33012615664172	1	FACETS	0.771	0.674	0.873	0.771	0.674	0.873	SUBCLONAL	1	TRUE	0	0.533419660774239	1		219	214	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729162	66729163	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	197	696	1	ENST00000307102.5:c.370_371delinsTT	p.Pro124Leu	p.P124L	ENST00000307102	NM_002755.3	124	CCg/TTg	3/11	0.33012615664172	1	FACETS	0.8	0.744	0.858	0.8	0.744	0.858	SUBCLONAL	1	TRUE	0	0.533419660774239	1		697	677	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423632	88423632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1478926904	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	131	450	1	ENST00000360948.2:c.2203C>T	p.Arg735Cys	p.R735C	ENST00000360948	NM_001012338.2	735	Cgc/Tgc	18/19	0.33012615664172	1	FACETS	0.843	0.772	0.917	0.843	0.772	0.917	CLONAL	1	TRUE	0	0.533419660774239	1		451	427	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483945	88483945	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1313486936	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	182	745	0	ENST00000360948.2:c.1625G>A	p.Arg542Gln	p.R542Q	ENST00000360948	NM_001012338.2	542	cGa/cAa	14/19	0.33012615664172	1	FACETS	0.745	0.69	0.801	0.745	0.69	0.801	SUBCLONAL	1	TRUE	0	0.533419660774239	1		745	672	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500633	99500633	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746562843	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	197	717	0	ENST00000268035.6:c.4066G>A	p.Glu1356Lys	p.E1356K	ENST00000268035	NM_000875.3	1356	Gag/Aag	21/21	0.33012615664172	1	FACETS	0.867	0.807	0.928	0.867	0.807	0.928	CLONAL	1	TRUE	0	0.533419660774239	1		717	625	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096136	2096136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	232	947	0	ENST00000219066.1:c.371C>T	p.Pro124Leu	p.P124L	ENST00000219066	NM_002528.5	124	cCc/cTc	2/6	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.533419660774239	2		947	861	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640673	3640673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	258	1075	0	ENST00000294008.3:c.2966C>T	p.Ser989Leu	p.S989L	ENST00000294008	NM_032444.2	989	tCa/tTa	12/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.533419660774239	2		1075	910	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3651118	3651118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564092523	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	227	876	0	ENST00000294008.3:c.1025C>T	p.Pro342Leu	p.P342L	ENST00000294008	NM_032444.2	342	cCg/cTg	5/15	1	2	FACETS	0.975	0.91	1	0.975	0.91	1	CLONAL	1	TRUE	1	0.533419660774239	2		876	873	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892206	9892206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	165	640	0	ENST00000330684.3:c.2284G>A	p.Gly762Arg	p.G762R	ENST00000330684	NM_001134407.1	762	Gga/Aga	11/13	1	2	FACETS	0.839	0.772	0.909	0.839	0.772	0.909	CLONAL	1	TRUE	1	0.533419660774239	2		640	737	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274100	10274100	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	224	1036	0	ENST00000330684.3:c.169C>T	p.Pro57Ser	p.P57S	ENST00000330684	NM_001134407.1	57	Ccc/Tcc	2/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.533419660774239	2		1036	815	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81939065	81939065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867345397	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	177	632	1	ENST00000359376.3:c.1420G>A	p.Glu474Lys	p.E474K	ENST00000359376	NM_002661.3	474	Gaa/Aaa	15/33	1	2	FACETS	0.941	0.87	1	0.941	0.87	1	CLONAL	1	TRUE	1	0.533419660774239	2		633	705	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944280	81944280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771359979	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	243	903	0	ENST00000359376.3:c.1889G>A	p.Arg630Gln	p.R630Q	ENST00000359376	NM_002661.3	630	cGg/cAg	18/33	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.533419660774239	2		903	833	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578140	7578183	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AACCCCTCCTCCCAGAGACCCCAGTTGCAAACCAGACCTCAGGC	AACCCCTCCTCCCAGAGACCCCAGTTGCAAACCAGACCTCAGGC	-	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	298	681	0	ENST00000269305.4:c.666_672+37del		p.X222_splice	ENST00000269305	NM_001126112.2	222		6/11	0.533419660774239	2	FACETS	0.885	0.841	0.93	0.885	0.841	0.93	CLONAL	2	TRUE	0	0.533419660774239	2		681	631	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805377	46805378	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	235	950	0	ENST00000290295.7:c.578_579delinsTT	p.Pro193Leu	p.P193L	ENST00000290295	NM_006361.5	193	cCC/cTT	1/2	0.533419660774239	2	FACETS	0.957	0.894	1	0.478	0.447	0.511	CLONAL	1	TRUE	0	0.533419660774239	2		950	921	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760671	59760671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	166	422	0	ENST00000259008.2:c.3736C>T	p.Pro1246Ser	p.P1246S	ENST00000259008	NM_032043.2	1246	Cct/Tct	20/20	0.533419660774239	2	FACETS	0.921	0.86	0.981	0.921	0.86	0.981	CLONAL	2	TRUE	0	0.533419660774239	2		422	338	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220485	1220485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	335	992	0	ENST00000326873.7:c.578C>T	p.Ser193Phe	p.S193F	ENST00000326873	NM_000455.4	193	tCc/tTc	4/10	0.533419660774239	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.533419660774239	1		992	768	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248527	10248527	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	396	1014	1	ENST00000340748.4:c.4226T>C	p.Leu1409Pro	p.L1409P	ENST00000340748		1409	cTc/cCc	35/40	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	1	TRUE	NA	0.533419660774239	2		1015	1097	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276890	15276890	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1250718112	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	301	799	0	ENST00000263388.2:c.5375C>T	p.Pro1792Leu	p.P1792L	ENST00000263388	NM_000435.2	1792	cCg/cTg	30/33	0.533419660774239	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.533419660774239	1		799	684	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295142	15295142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375223296	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	406	1082	0	ENST00000263388.2:c.2530C>T	p.Pro844Ser	p.P844S	ENST00000263388	NM_000435.2	844	Cct/Tct	16/33	0.533419660774239	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.533419660774239	1		1082	875	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793142	42793142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763646546	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	451	1156	0	ENST00000575354.2:c.1034G>A	p.Gly345Glu	p.G345E	ENST00000575354	NM_015125.3	345	gGg/gAg	7/20	0.273820936611018	3	FACETS	0.858	0.82	0.897	0.858	0.82	0.897	INDETERMINATE	2	TRUE	1	0.533419660774239	3		1156	1248	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082365	16082365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	269	1259	0	ENST00000281043.3:c.179C>T	p.Pro60Leu	p.P60L	ENST00000281043	NM_005378.4	60	cCg/cTg	2/3	1	2	FACETS	0.981	0.921	1	0.981	0.921	1	CLONAL	1	TRUE	1	0.533419660774239	2		1259	1028	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082712	16082713	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	24	70	0	ENST00000281043.3:c.526_527delinsTT	p.Pro176Phe	p.P176F	ENST00000281043	NM_005378.4	176	CCc/TTc	2/3	1	2	FACETS	1	0.821	1	1	0.821	1	CLONAL	1	TRUE	1	0.533419660774239	2		70	88	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085753	16085753	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	142	580	0	ENST00000281043.3:c.929C>T	p.Pro310Leu	p.P310L	ENST00000281043	NM_005378.4	310	cCc/cTc	3/3	1	2	FACETS	0.804	0.735	0.877	0.804	0.735	0.877	CLONAL	1	TRUE	1	0.533419660774239	2		580	662	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085921	16085921	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	160	561	1	ENST00000281043.3:c.1097A>T	p.Lys366Met	p.K366M	ENST00000281043	NM_005378.4	366	aAg/aTg	3/3	1	2	FACETS	0.924	0.851	1	0.924	0.851	1	CLONAL	1	TRUE	1	0.533419660774239	2		562	649	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456502	29456502	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80227749	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	283	700	3	ENST00000389048.3:c.2416C>T	p.Arg806Cys	p.R806C	ENST00000389048	NM_004304.4	806	Cgt/Tgt	14/29	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.533419660774239	2		703	886	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278296	39278296	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	152	520	0	ENST00000402219.2:c.853G>C	p.Asp285His	p.D285H	ENST00000402219	NM_005633.3	285	Gac/Cac	6/23	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.533419660774239	2		520	442	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530090	212530090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756272680	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	90	303	0	ENST00000342788.4:c.1829C>T	p.Pro610Leu	p.P610L	ENST00000342788	NM_005235.2	610	cCa/cTa	15/28	1	2	FACETS	0.748	0.667	0.834	0.748	0.667	0.834	SUBCLONAL	1	TRUE	1	0.533419660774239	2		303	451	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989496	212989496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	109	356	0	ENST00000342788.4:c.215G>A	p.Arg72Gln	p.R72Q	ENST00000342788	NM_005235.2	72	cGg/cAg	2/28	1	2	FACETS	0.831	0.75	0.916	0.831	0.75	0.916	CLONAL	1	TRUE	1	0.533419660774239	2		356	492	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400336	225400336	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	90	192	0	ENST00000264414.4:c.287C>T	p.Ser96Leu	p.S96L	ENST00000264414	NM_003590.4	96	tCa/tTa	3/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.533419660774239	2		192	263	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546683	9546683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	135	415	0	ENST00000353224.5:c.1339G>A	p.Glu447Lys	p.E447K	ENST00000353224	NM_177990.2	447	Gaa/Aaa	5/10	0.33012615664172	1	FACETS	0.855	0.784	0.929	0.855	0.784	0.929	CLONAL	1	TRUE	0	0.533419660774239	1		415	434	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419989	41419989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	197	662	0	ENST00000373198.4:c.332G>A	p.Ser111Asn	p.S111N	ENST00000373198	NM_133170.3	111	aGc/aAc	3/32	0.50751209597176	3	FACETS	0.89	0.824	0.959	0.445	0.412	0.48	CLONAL	1	TRUE	1	0.533419660774239	3		662	1051	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514563	41514563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	244	460	0	ENST00000373198.4:c.98C>T	p.Ser33Phe	p.S33F	ENST00000373198	NM_133170.3	33	tCc/tTc	2/32	0.50751209597176	3	FACETS	0.923	0.868	0.978	0.923	0.868	0.978	CLONAL	2	TRUE	1	0.533419660774239	3		460	628	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281167	46281167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	266	520	0	ENST00000371998.3:c.3964G>A	p.Asp1322Asn	p.D1322N	ENST00000371998		1322	Gat/Aat	21/23	0.260682889588624	5	FACETS	1	0.988	1	0.782	0.737	0.829	INDETERMINATE	2	TRUE	2	0.533419660774239	5		520	765	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057302	30057302	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315496	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	171	484	0	ENST00000338641.4:c.784C>T	p.Arg262Ter	p.R262*	ENST00000338641	NM_000268.3	262	Cga/Tga	8/16	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.533419660774239	2		484	626	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641893	12641893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147453956	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	61	279	0	ENST00000251849.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000251849	NM_002880.3	286	Gaa/Aaa	8/17	0.273820936611018	3	FACETS	0.926	0.804	1	0.463	0.402	0.528	INDETERMINATE	1	TRUE	1	0.533419660774239	3		279	313	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021742	71021743	+	missense_variant	Missense_Mutation	DNP	AC	AC	TG	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	118	406	0	ENST00000318789.4:c.1615_1616delinsCA	p.Val539Gln	p.V539Q	ENST00000318789	NM_032682.5	539	GTa/CAa	18/21	0.273820936611018	3	FACETS	1	0.964	1	0.564	0.511	0.619	INDETERMINATE	1	TRUE	1	0.533419660774239	3		406	497	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72891463	72891463	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	144	445	0	ENST00000325599.8:c.299C>T	p.Ser100Phe	p.S100F	ENST00000325599	NM_018130.2	100	tCc/tTc	3/11	0.273820936611018	3	FACETS	1	0.966	1	0.552	0.505	0.601	INDETERMINATE	1	TRUE	1	0.533419660774239	3		445	619	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448583	89448583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	186	548	0	ENST00000336596.2:c.1547G>A	p.Gly516Glu	p.G516E	ENST00000336596	NM_005233.5	516	gGa/gAa	7/17	0.273820936611018	3	FACETS	1	0.966	1	0.538	0.497	0.58	INDETERMINATE	1	TRUE	1	0.533419660774239	3		548	821	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499372	89499372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	244	465	0	ENST00000336596.2:c.2542G>A	p.Asp848Asn	p.D848N	ENST00000336596	NM_005233.5	848	Gac/Aac	15/17	0.273820936611018	3	FACETS	0.828	0.777	0.879	0.828	0.777	0.879	INDETERMINATE	2	TRUE	1	0.533419660774239	3		465	700	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528629	89528629	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	96	173	0	ENST00000336596.2:c.2929A>G	p.Lys977Glu	p.K977E	ENST00000336596	NM_005233.5	977	Aag/Gag	17/17	0.273820936611018	3	FACETS	0.789	0.712	0.868	0.789	0.712	0.868	INDETERMINATE	2	TRUE	1	0.533419660774239	3		173	289	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189585728	189585728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	172	411	0	ENST00000264731.3:c.989G>A	p.Arg330Lys	p.R330K	ENST00000264731	NM_003722.4	330	aGa/aAa	7/14	0.533419660774239	2	FACETS	0.886	0.828	0.944	0.886	0.828	0.944	CLONAL	2	TRUE	0	0.533419660774239	2		411	364	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604206	189604206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	300	471	2	ENST00000264731.3:c.1373C>T	p.Ser458Leu	p.S458L	ENST00000264731	NM_003722.4	458	tCa/tTa	11/14	0.533419660774239	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.533419660774239	2		473	550	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961252	1961252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	91	562	0	ENST00000382891.5:c.3040C>T	p.Pro1014Ser	p.P1014S	ENST00000382891	NM_133335.3	1014	Cct/Tct	17/22	0.33012615664172	1	FACETS	0.392	0.348	0.439	0.392	0.348	0.439	SUBCLONAL	1	TRUE	0	0.533419660774239	1		562	638	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955063	55955063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	181	491	0	ENST00000263923.4:c.3482G>A	p.Gly1161Glu	p.G1161E	ENST00000263923	NM_002253.2	1161	gGa/gAa	26/30	0.33012615664172	1	FACETS	0.805	0.746	0.866	0.805	0.746	0.866	CLONAL	1	TRUE	0	0.533419660774239	1		491	618	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956220	55956220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190050670	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	76	510	0	ENST00000263923.4:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000263923	NM_002253.2	1032	cGa/cAa	23/30	0.33012615664172	1	FACETS	0.406	0.356	0.459	0.406	0.356	0.459	SUBCLONAL	1	TRUE	0	0.533419660774239	1		510	515	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254609	1254609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	172	756	0	ENST00000310581.5:c.3169G>A	p.Gly1057Arg	p.G1057R	ENST00000310581	NM_198253.2	1057	Ggg/Agg	15/16	0.50751209597176	3	FACETS	0.976	0.899	1	0.488	0.449	0.528	CLONAL	1	TRUE	1	0.533419660774239	3		756	837	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294896	1294896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	51	142	0	ENST00000310581.5:c.209C>T	p.Ser70Phe	p.S70F	ENST00000310581	NM_198253.2	70	tCc/tTc	1/16	0.50751209597176	3	FACETS	1	0.938	1	0.585	0.504	0.672	CLONAL	1	TRUE	1	0.533419660774239	3		142	207	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166839	32166839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs535575989	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	477	1149	3	ENST00000375023.3:c.4399G>A	p.Val1467Ile	p.V1467I	ENST00000375023	NM_004557.3	1467	Gtc/Atc	24/30	0.497560346420472	3	FACETS	0.872	0.834	0.91	0.581	0.556	0.607	CLONAL	2	TRUE	0	0.533419660774239	3		1152	1299	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967209	93967209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	81	330	0	ENST00000369303.4:c.2143G>A	p.Glu715Lys	p.E715K	ENST00000369303	NM_004440.3	715	Gaa/Aaa	12/17	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.533419660774239	2		330	284	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415014	109415014	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	108	415	0	ENST00000436639.2:c.263T>C	p.Ile88Thr	p.I88T	ENST00000436639	NM_014454.2	88	aTt/aCt	1/10	1	2	FACETS	0.845	0.763	0.932	0.845	0.763	0.932	CLONAL	1	TRUE	1	0.533419660774239	2		415	479	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641144	117641144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866970127	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	197	642	0	ENST00000368508.3:c.5827G>A	p.Glu1943Lys	p.E1943K	ENST00000368508	NM_002944.2	1943	Gaa/Aaa	36/43	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.533419660774239	2		642	671	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683807	117683807	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	93	384	0	ENST00000368508.3:c.3340C>T	p.Gln1114Ter	p.Q1114*	ENST00000368508	NM_002944.2	1114	Caa/Taa	21/43	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.533419660774239	2		384	332	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686778	117686778	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	74	294	0	ENST00000368508.3:c.2939T>C	p.Val980Ala	p.V980A	ENST00000368508	NM_002944.2	980	gTt/gCt	19/43	1	2	FACETS	0.881	0.778	0.99	0.881	0.778	0.99	CLONAL	1	TRUE	1	0.533419660774239	2		294	315	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725482	117725482	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867025812	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	98	442	0	ENST00000368508.3:c.399G>A	p.Trp133Ter	p.W133*	ENST00000368508	NM_002944.2	133	tgG/tgA	5/43	1	2	FACETS	0.912	0.819	1	0.912	0.819	1	CLONAL	1	TRUE	1	0.533419660774239	2		442	403	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969900	161969900	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	189	690	0	ENST00000366898.1:c.1069G>A	p.Gly357Ser	p.G357S	ENST00000366898	NM_004562.2	357	Ggc/Agc	9/12	1	2	FACETS	0.872	0.807	0.939	0.872	0.807	0.939	CLONAL	1	TRUE	1	0.533419660774239	2		690	813	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969950	161969950	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1318163167	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	225	727	0	ENST00000366898.1:c.1019G>A	p.Gly340Glu	p.G340E	ENST00000366898	NM_004562.2	340	gGg/gAg	9/12	1	2	FACETS	0.987	0.921	1	0.987	0.921	1	CLONAL	1	TRUE	1	0.533419660774239	2		727	855	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979502	2979502	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	66	546	2	ENST00000396946.4:c.745C>T	p.Gln249Ter	p.Q249*	ENST00000396946	NM_032415.4	249	Cag/Tag	6/25	0.33225276125101	3	FACETS	0.431	0.374	0.494	0.144	0.124	0.165	SUBCLONAL	1	TRUE	0	0.533419660774239	3		548	727	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468185	50468185	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	398	829	0	ENST00000331340.3:c.1420C>T	p.His474Tyr	p.H474Y	ENST00000331340	NM_006060.4	474	Cac/Tac	8/8	0.285784961130483	5	FACETS	0.933	0.89	0.976	0.56	0.534	0.586	INDETERMINATE	3	TRUE	0	0.533419660774239	5		829	960	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	193	321	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.275801151897475	4	FACETS	0.893	0.838	0.949	0.67	0.628	0.712	INDETERMINATE	3	TRUE	0	0.533419660774239	4		321	414	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846108	151846108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	106	521	0	ENST00000262189.6:c.12904C>T	p.Pro4302Ser	p.P4302S	ENST00000262189	NM_170606.2	4302	Cct/Tct	52/59	0.275801151897475	4	FACETS	0.693	0.621	0.77	0.173	0.155	0.193	INDETERMINATE	1	TRUE	0	0.533419660774239	4		521	879	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931794	68931794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1357812958	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	62	376	0	ENST00000288368.4:c.224C>T	p.Ser75Leu	p.S75L	ENST00000288368	NM_024870.2	75	tCa/tTa	3/40	0.317618772648753	2	FACETS	0.672	0.584	0.767	0.336	0.292	0.384	INDETERMINATE	1	TRUE	0	0.533419660774239	2		376	346	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934283	68934283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773476490	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	61	382	1	ENST00000288368.4:c.349C>T	p.Arg117Cys	p.R117C	ENST00000288368	NM_024870.2	117	Cgt/Tgt	4/40	0.317618772648753	2	FACETS	0.669	0.58	0.764	0.334	0.29	0.382	INDETERMINATE	1	TRUE	0	0.533419660774239	2		383	342	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376684	8376684	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs724159862	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	240	473	0	ENST00000356435.5:c.4429C>T	p.His1477Tyr	p.H1477Y	ENST00000356435		1477	Cac/Tac	27/35	0.533419660774239	2	FACETS	1	0.993	1	0.723	0.68	0.767	CLONAL	1	TRUE	0	0.533419660774239	2		473	622	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517925	8517925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	206	326	1	ENST00000356435.5:c.1466C>T	p.Ser489Phe	p.S489F	ENST00000356435		489	tCt/tTt	10/35	0.533419660774239	2	FACETS	0.993	0.936	1	0.993	0.936	1	CLONAL	2	TRUE	0	0.533419660774239	2		327	389	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524996	8524996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	90	308	0	ENST00000356435.5:c.608G>A	p.Gly203Glu	p.G203E	ENST00000356435		203	gGa/gAa	7/35	0.533419660774239	2	FACETS	0.742	0.661	0.827	0.371	0.33	0.414	SUBCLONAL	1	TRUE	0	0.533419660774239	2		308	455	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	486	764	2	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.533419660774239	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.533419660774239	2		766	830	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27183528	27183528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868328598	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	110	451	0	ENST00000380036.4:c.1102C>T	p.Pro368Ser	p.P368S	ENST00000380036	NM_000459.3	368	Ccc/Tcc	8/23	0.533419660774239	2	FACETS	0.906	0.819	0.997	0.453	0.409	0.499	CLONAL	1	TRUE	0	0.533419660774239	2		451	455	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206652	27206652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	277	471	0	ENST00000380036.4:c.2437C>T	p.Pro813Ser	p.P813S	ENST00000380036	NM_000459.3	813	Cct/Tct	15/23	0.533419660774239	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.533419660774239	2		471	513	SUCCESS
AR	367	MSKCC	GRCh37	X	66937319	66937319	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	165	257	0	ENST00000374690.3:c.2174-1G>A		p.X725_splice	ENST00000374690	NM_000044.3	725			1	1	FACETS	0.751	0.704	0.798	1	0.992	1	SUBCLONAL	2	TRUE	0	0.533419660774239	1		257	302	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611185	100611185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	193	273	0	ENST00000308731.7:c.1421C>T	p.Thr474Ile	p.T474I	ENST00000308731	NM_000061.2	474	aCt/aTt	15/19	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.533419660774239	1		273	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0058532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	245	380	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.513413968408892	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.513413968408892	1		380	672	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209358	98209358	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1297685477	NA	P-0058532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	194	950	0	ENST00000331920.6:c.4180C>T	p.Arg1394Ter	p.R1394*	ENST00000331920	NM_000264.3	1394	Cga/Tga	23/24	1	2	FACETS	0.974	0.903	1	0.974	0.903	1	CLONAL	1	TRUE	1	0.513413968408892	2		950	776	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0058532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	310	286	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.513413968408892	4	FACETS	0.946	0.9	0.992	0.946	0.9	0.992	CLONAL	3	TRUE	1	0.513413968408892	4		286	644	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591140	67591145	+	inframe_deletion	In_Frame_Del	DEL	ACCAAT	ACCAAT	-	rs751582616	NA	P-0058532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	65	247	0	ENST00000274335.5:c.1735_1740del	p.Gln579_Tyr580del	p.Q579_Y580del	ENST00000274335		578	gACCAATac/gac	12/15	1	2	FACETS	0.85	0.743	0.963	0.85	0.743	0.963	CLONAL	1	TRUE	1	0.513413968408892	2		247	298	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918342	44918342	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	103	425	1	ENST00000377967.4:c.967T>A	p.Ser323Thr	p.S323T	ENST00000377967	NM_021140.2	323	Tca/Aca	11/29	0.506142447654619	3	FACETS	0.889	0.798	0.986	0.445	0.399	0.493	CLONAL	1	TRUE	1	0.513413968408892	3		426	567	SUCCESS
APC	324	MSKCC	GRCh37	5	112175606	112175609	+	frameshift_variant	Frame_Shift_Ins	INS	CCTC	CCTC	GAAGTAAAA	novel	NA	P-0058532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	151	265	0	ENST00000257430.4:c.4315_4318delinsGAAGTAAAA	p.Pro1439GlufsTer36	p.P1439Efs*36	ENST00000257430	NM_000038.5	1439	CCTCca/GAAGTAAAAca	16/16	1	2	FACETS	0.824	0.764	0.885	1	0.991	1	CLONAL	2	TRUE	1	0.513413968408892	2		265	357	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0058536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	122	432	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.851	0.778	0.927	1	0.989	1	CLONAL	2	TRUE	1	0.386323937368282	2		432	371	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0058536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	382	172	0				ENST00000310581	NM_198253.2	-/1132			0.363640940599016	4	FACETS	0.949	0.91	0.989	1	0.995	1	CLONAL	4	TRUE	1	0.386323937368282	4		172	722	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190759	108190760	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0058536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	22	131	0	ENST00000278616.4:c.6426_6427del	p.Phe2143LeufsTer2	p.F2143Lfs*2	ENST00000278616	NM_000051.3	2142	acATtt/actt	44/63	NA	2	FACETS	0.502	0.39	0.63			1	INDETERMINATE	1	TRUE	NA	0.386323937368282	2		131	227	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564763	41564763	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	191	733	0	ENST00000263253.7:c.4064A>G	p.Tyr1355Cys	p.Y1355C	ENST00000263253	NM_001429.3	1355	tAc/tGc	25/31	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.386323937368282	2		733	838	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0058537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	260	432	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.439115618454117	3	FACETS	0.865	0.821	0.909	0.865	0.821	0.909	CLONAL	3	TRUE	0	0.508676565955736	3		432	494	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0058537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	275	172	0				ENST00000310581	NM_198253.2	-/1132			0.508676565955736	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.508676565955736	1		172	634	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964415	93964415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867402067	NA	P-0058537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	94	494	0	ENST00000369303.4:c.2482G>A	p.Glu828Lys	p.E828K	ENST00000369303	NM_004440.3	828	Gaa/Aaa	14/17	0.278354612552919	1	FACETS	0.504	0.449	0.562	0.504	0.449	0.562	INDETERMINATE	1	TRUE	0	0.508676565955736	1		494	547	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041265	29041265	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	188	316	0	ENST00000282397.4:c.163G>A	p.Gly55Arg	p.G55R	ENST00000282397	NM_002019.4	55	Ggg/Agg	3/30	0.508676565955736	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.508676565955736	1		316	457	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060869	38060869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	472	952	0	ENST00000250448.2:c.1120C>T	p.His374Tyr	p.H374Y	ENST00000250448	NM_004496.3	374	Cac/Tac	2/2	0.205491867757571	4	FACETS	0.94	0.898	0.983	0.94	0.898	0.983	INDETERMINATE	2	TRUE	2	0.508676565955736	4		952	1489	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347034	89347035	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0058537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	448	869	0	ENST00000301030.4:c.5915_5916del	p.Ser1972MetfsTer59	p.S1972Mfs*59	ENST00000301030	NM_001256183.1	1972	aGC/a	9/13	0.508676565955736	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.508676565955736	1		869	980	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578483	7578484	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0058537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1290	640	1333	2	ENST00000269305.4:c.446_447delinsAA	p.Ser149Ter	p.S149*	ENST00000269305	NM_001126112.2	149	tCC/tAA	5/11	0.124770051792617	3	FACETS	0.818	0.786	0.85	0.545	0.524	0.567	INDETERMINATE	2	TRUE	0	0.508676565955736	3		1335	1930	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579487	7579487	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1262	286	1002	0	ENST00000269305.4:c.200del	p.Pro67GlnfsTer56	p.P67Qfs*56	ENST00000269305	NM_001126112.2	67	cCa/ca	4/11	0.124770051792617	3	FACETS	0.911	0.854	0.97	0.304	0.284	0.324	INDETERMINATE	1	TRUE	0	0.508676565955736	3		1002	1548	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385005	31385006	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGCT	novel	NA	P-0058537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	166	667	0	ENST00000328111.2:c.1391_1394dup	p.Phe466AlafsTer6	p.F466Afs*6	ENST00000328111	NM_006892.3	464	gag/gAGCTag	14/23	0.205491867757571	4	FACETS	0.762	0.698	0.829	0.381	0.349	0.415	INDETERMINATE	1	TRUE	2	0.508676565955736	4		667	1293	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566468	41566468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	249	420	0	ENST00000263253.7:c.4345C>T	p.His1449Tyr	p.H1449Y	ENST00000263253	NM_001429.3	1449	Cat/Tat	27/31	0.205491867757571	4	FACETS	0.843	0.79	0.897	0.843	0.79	0.897	INDETERMINATE	2	TRUE	2	0.508676565955736	4		420	876	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182720	38182721	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	338	642	0	ENST00000396334.3:c.873_874delinsTT	p.Pro292Ser	p.P292S	ENST00000396334	NM_002468.4	291	aaCCcc/aaTTcc	5/5	0.124770051792617	3	FACETS	0.773	0.732	0.815	0.515	0.488	0.544	INDETERMINATE	2	TRUE	0	0.508676565955736	3		642	1078	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670334	134670334	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	103	523	0	ENST00000398015.3:c.245C>G	p.Ala82Gly	p.A82G	ENST00000398015	NM_004441.4	82	gCc/gGc	3/16	0.124770051792617	3	FACETS	0.65	0.581	0.722	0.217	0.193	0.241	INDETERMINATE	1	TRUE	0	0.508676565955736	3		523	782	SUCCESS
APC	324	MSKCC	GRCh37	5	112175876	112175876	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085992	NA	P-0058537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	89	191	0	ENST00000257430.4:c.4585C>T	p.Gln1529Ter	p.Q1529*	ENST00000257430	NM_000038.5	1529	Cag/Tag	16/16	0.508676565955736	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.508676565955736	1		191	213	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553761	106553761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	142	490	0	ENST00000369096.4:c.1726G>A	p.Glu576Lys	p.E576K	ENST00000369096	NM_001198.3	576	Gaa/Aaa	5/7	0.278354612552919	1	FACETS	0.62	0.566	0.676	0.62	0.566	0.676	INDETERMINATE	1	TRUE	0	0.508676565955736	1		490	672	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431595	6431596	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	87	204	2	ENST00000356142.4:c.148_149delinsTT	p.Pro50Leu	p.P50L	ENST00000356142	NM_018890.3	50	CCg/TTg	3/7	0.508676565955736	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.508676565955736	1		206	222	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974799	21974799	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	162	275	1	ENST00000304494.5:c.28G>T	p.Glu10Ter	p.E10*	ENST00000304494	NM_000077.4	10	Gag/Tag	1/3	0.508676565955736	1	FACETS	0.771	0.721	0.82	1	0.992	1	SUBCLONAL	2	TRUE	0	0.508676565955736	1		276	308	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197354	27197354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	288	559	1	ENST00000380036.4:c.1666C>T	p.Gln556Ter	p.Q556*	ENST00000380036	NM_000459.3	556	Cag/Tag	12/23	0.508676565955736	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.508676565955736	1		560	683	SUCCESS
AR	367	MSKCC	GRCh37	X	66765418	66765418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	426	471	0	ENST00000374690.3:c.430G>A	p.Gly144Arg	p.G144R	ENST00000374690	NM_000044.3	144	Ggg/Agg	1/8	0.426302158924996	2	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.508676565955736	2		471	716	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0058540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	21	172	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.915	0.705	1	0.915	0.705	1	CLONAL	1	TRUE	1	0.16	2		172	287	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0058540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	86	632	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.3	1	FACETS	0.989	0.878	1	1	0.985	1	CLONAL	2	TRUE	0	0.16	1		632	500	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174892	11174892	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	32	612	0	ENST00000361445.4:c.7142G>C	p.Arg2381Thr	p.R2381T	ENST00000361445	NM_004958.3	2381	aGa/aCa	52/58	1	2	FACETS	0.957	0.777	1	0.957	0.777	1	CLONAL	1	TRUE	1	0.16	2		612	418	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416115	416115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	20	397	0	ENST00000399788.2:c.4071G>A	p.Met1357Ile	p.M1357I	ENST00000399788	NM_001042603.1	1357	atG/atA	24/28	1	2	FACETS	0.899	0.688	1	0.899	0.688	1	CLONAL	1	TRUE	1	0.16	2		397	278	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416171	416171	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	23	442	0	ENST00000399788.2:c.4015G>C	p.Asp1339His	p.D1339H	ENST00000399788	NM_001042603.1	1339	Gat/Cat	24/28	1	2	FACETS	0.975	0.761	1	0.975	0.761	1	CLONAL	1	TRUE	1	0.16	2		442	295	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929007	44929035	+	frameshift_variant	Frame_Shift_Del	DEL	ACTGCTACCTCAGGTGGACAACAAGGCAT	ACTGCTACCTCAGGTGGACAACAAGGCAT	-	novel	NA	P-0058540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	30	332	0	ENST00000377967.4:c.2107_2135del	p.Thr703TyrfsTer17	p.T703Yfs*17	ENST00000377967	NM_021140.2	703	ACTGCTACCTCAGGTGGACAACAAGGCATt/t	17/29	1	1	FACETS	0.863	0.701	1	1	0.952	1	CLONAL	2	TRUE	0	0.16	1		332	200	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006899	47006899	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0058540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	75	512	1	ENST00000377604.3:c.17+2T>A		p.X6_splice	ENST00000377604	NM_001204468.1	6			1	1	FACETS	0.919	0.812	1	1	0.986	1	CLONAL	3	TRUE	0	0.16	1		513	313	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	126	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.864	0.791	0.939	1	0.992	1	CLONAL	3	TRUE	1	0.26	2		306	374	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0058541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	136	754	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.26	2		754	902	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0058541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	19	590	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	1	2	FACETS	0.252	0.191	0.326	0.252	0.191	0.326	SUBCLONAL	1	TRUE	1	0.26	2		590	579	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0058541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	78	656	1	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.26	2		657	495	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650756	67650756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	275	635	0	ENST00000264010.4:c.1061C>T	p.Ser354Phe	p.S354F	ENST00000264010	NM_006565.3	354	tCc/tTc	5/12	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.26	2		635	874	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0058541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	224	785	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	0.908	0.846	0.972	1	0.994	1	CLONAL	2	TRUE	1	0.26	2		786	949	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375964	8375964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144763077	NA	P-0058541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	59	417	0	ENST00000356435.5:c.4633G>A	p.Asp1545Asn	p.D1545N	ENST00000356435		1545	Gat/Aat	28/35	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.26	2		417	454	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440379	52440379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	173	795	1	ENST00000460680.1:c.673G>A	p.Asp225Asn	p.D225N	ENST00000460680	NM_004656.3	225	Gac/Aac	9/17	1	2	FACETS	0.811	0.748	0.878	1	0.991	1	CLONAL	2	TRUE	1	0.26	2		796	820	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872380	45872380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	351	841	0	ENST00000391945.4:c.131C>T	p.Ser44Leu	p.S44L	ENST00000391945	NM_000400.3	44	tCa/tTa	3/23	1	2	FACETS	0.913	0.867	0.96	1	0.997	1	CLONAL	3	TRUE	1	0.26	2		841	986	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591246	67591246	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0058541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	77	327	0	ENST00000274335.5:c.1746-2A>G		p.X582_splice	ENST00000274335		582			1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.26	2		327	514	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870966	12870966	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	97	430	0	ENST00000228872.4:c.193C>T	p.Gln65Ter	p.Q65*	ENST00000228872	NM_004064.3	65	Cag/Tag	1/3	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.26	2		430	577	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247171	153247171	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	75	280	0	ENST00000281708.4:c.1631T>C	p.Val544Ala	p.V544A	ENST00000281708	NM_033632.3	544	gTc/gCc	10/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.26	2		280	403	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106665	27106666	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0058541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	145	885	0	ENST00000324856.7:c.6276_6277del	p.Val2093LeufsTer5	p.V2093Lfs*5	ENST00000324856	NM_006015.4	2092	gcAGtt/gctt	20/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.26	2		885	979	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624278	89624289	+	inframe_deletion	In_Frame_Del	DEL	GAGGATGGATTC	GAGGATGGATTC	-	novel	NA	P-0058541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	169	448	0	ENST00000371953.3:c.54_65del	p.Glu18_Phe21del	p.E18_F21del	ENST00000371953	NM_000314.4	18	GAGGATGGATTC/-	1/9	0.3	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.26	2		448	571	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923317	26923317	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	138	334	0	ENST00000381527.3:c.313T>A	p.Trp105Arg	p.W105R	ENST00000381527	NM_001260.1	105	Tgg/Agg	3/13	1	2	FACETS	0.898	0.826	0.972	1	0.993	1	CLONAL	3	TRUE	1	0.26	2		334	394	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348025	348025	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767214854	NA	P-0058541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	191	1476	2	ENST00000262320.3:c.1481C>T	p.Pro494Leu	p.P494L	ENST00000262320	NM_003502.3	494	cCg/cTg	6/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.26	2		1478	1152	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786785	3786785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	92	481	0	ENST00000262367.5:c.4426C>T	p.Pro1476Ser	p.P1476S	ENST00000262367	NM_004380.2	1476	Cca/Tca	27/31	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.26	2		481	619	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626632	12626632	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	214	453	0	ENST00000251849.4:c.1657A>G	p.Asn553Asp	p.N553D	ENST00000251849	NM_002880.3	553	Aac/Gac	15/17	1	2	FACETS	1	0.962	1	1	0.995	1	CLONAL	3	TRUE	1	0.26	2		453	530	SUCCESS
ATR	545	MSKCC	GRCh37	3	142189026	142189026	+	splice_acceptor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0058541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	34	208	0	ENST00000350721.4:c.6222-1del		p.X2074_splice	ENST00000350721	NM_001184.3	2074			1	2	FACETS	0.965	0.792	1	0.965	0.792	1	CLONAL	1	TRUE	1	0.26	2		208	271	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524980	187524982	+	inframe_deletion	In_Frame_Del	DEL	ATC	ATC	-	novel	NA	P-0058541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	94	662	0	ENST00000441802.2:c.10698_10700del	p.Lys3566_Ile3567delinsAsn	p.K3566_I3567delinsN	ENST00000441802	NM_005245.3	3566	aaGATc/aac	19/27	1	2	FACETS	0.875	0.778	0.979	0.875	0.778	0.979	CLONAL	1	TRUE	1	0.26	2		662	826	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624418	140624426	+	inframe_deletion	In_Frame_Del	DEL	GCGCCGGCC	GCGCCGGCC	-	novel	NA	P-0058541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	202	225	0	ENST00000288602.6:c.78_86del	p.Glu26_Ala29delinsAsp	p.E26_A29delinsD	ENST00000288602	NM_004333.4	26	gaGGCCGGCGCc/gac	1/18	1	2	FACETS	0.91	0.855	0.965	1	0.995	1	CLONAL	4	TRUE	1	0.26	2		225	427	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864886	117864886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	203	475	0	ENST00000297338.2:c.1223G>A	p.Gly408Glu	p.G408E	ENST00000297338	NM_006265.2	408	gGa/gAa	10/14	1	2	FACETS	1	0.981	1	1	0.994	1	CLONAL	2	TRUE	1	0.26	2		475	682	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922708	44922709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0058541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	90	243	0	ENST00000377967.4:c.1571dup	p.Asn525Ter	p.N525*	ENST00000377967	NM_021140.2	523	-/C	16/29	1	1	FACETS	0.962	0.863	1	1	0.986	1	CLONAL	2	TRUE	0	0.26	1		243	313	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44935997	44936023	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAAGACCACCATCTTCACCATAC	CCTCCAAGACCACCATCTTCACCATAC	-	novel	NA	P-0058541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	82	307	0	ENST00000377967.4:c.2763_2789del	p.Arg922_Pro930del	p.R922_P930del	ENST00000377967	NM_021140.2	920	CCTCCAAGACCACCATCTTCACCATAC/-	18/29	1	1	FACETS	0.849	0.756	0.948	1	0.982	1	CLONAL	2	TRUE	0	0.26	1		307	323	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044856	47044866	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGTGGCAGC	CTGGTGGCAGC	-	novel	NA	P-0058541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	183	689	0	ENST00000377604.3:c.2184_2194del	p.Val729GlnfsTer5	p.V729Qfs*5	ENST00000377604	NM_001204468.1	728	CTGGTGGCAGCc/c	20/24	1	1	FACETS	1	0.964	1	1	0.993	1	CLONAL	2	TRUE	0	0.26	1		689	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0058562-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	116	1015	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.224096874218643	2	FACETS	0.825	0.746	0.908	0.825	0.746	0.908	CLONAL	2	TRUE	0	0.252804511857269	2		1015	556	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0058562-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	19	432	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.208580548966909	2	FACETS	1	0.906	1	0.709	0.546	0.894	CLONAL	1	TRUE	0	0.252804511857269	2		432	106	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0058563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	18	351	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.891	0.673	1	0.891	0.673	1	CLONAL	1	TRUE	1	0.2	2		351	202	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220578	1220578	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0058563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	44	627	0	ENST00000326873.7:c.598-2A>T		p.X200_splice	ENST00000326873	NM_000455.4	200			1	2	FACETS	0.83	0.696	0.979	0.83	0.696	0.979	CLONAL	1	TRUE	1	0.2	2		627	530	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696688	47696688	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519971	NA	P-0058563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	30	439	0	ENST00000347630.2:c.260A>C	p.Tyr87Ser	p.Y87S	ENST00000347630	NM_001007230.1	87	tAc/tCc	5/11	1	2	FACETS	0.713	0.574	0.87	0.713	0.574	0.87	SUBCLONAL	1	TRUE	1	0.2	2		439	421	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612160	43612161	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0058563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	43	533	0	ENST00000355710.3:c.2265_2266delinsTT	p.Ala756Ser	p.A756S	ENST00000355710	NM_020975.4	755	gtGGcc/gtTTcc	12/20	1	2	FACETS	0.813	0.68	0.961	0.813	0.68	0.961	CLONAL	1	TRUE	1	0.2	2		533	529	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57004232	57004232	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	37	717	0	ENST00000257254.3:c.247C>T	p.Pro83Ser	p.P83S	ENST00000257254		83	Ccc/Tcc	1/2	1	2	FACETS	0.572	0.47	0.686	0.572	0.47	0.686	SUBCLONAL	1	TRUE	1	0.2	2		717	647	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599943	10599944	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0058563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	60	571	1	ENST00000171111.5:c.1632_1633delinsTT	p.Trp544_Thr545delinsCysSer	p.W544_T545delinsCS	ENST00000171111	NM_203500.1	544	tgGAct/tgTTct	5/6	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.2	2		572	583	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874253	151874253	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	17	368	0	ENST00000262189.6:c.8285C>T	p.Pro2762Leu	p.P2762L	ENST00000262189	NM_170606.2	2762	cCa/cTa	38/59	1	2	FACETS	0.592	0.442	0.771	0.592	0.442	0.771	SUBCLONAL	1	TRUE	1	0.2	2		368	287	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845395	76845395	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058563-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	21	149	0	ENST00000373344.5:c.6126G>T	p.Gln2042His	p.Q2042H	ENST00000373344	NM_000489.3	2042	caG/caT	27/35	1	1	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	0	0.2	1		149	137	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0058565-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	23	621	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		621	623	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0058566-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	403	557	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.701301517881753	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.701301517881753	1		558	695	SUCCESS
APC	324	MSKCC	GRCh37	5	112157627	112157628	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs1554080698	NA	P-0058566-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	59	260	0	ENST00000257430.4:c.1354_1355del	p.Val452SerfsTer7	p.V452Sfs*7	ENST00000257430	NM_000038.5	449	gcTGtg/gctg	11/16	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.701301517881753	2		260	152	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022286	31022287	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs762036456	NA	P-0058566-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	1242	535	0	ENST00000375687.4:c.1772dup	p.Tyr591Ter	p.Y591*	ENST00000375687	NM_015338.5	591	tac/tAac	13/13	0.701301517881753	6	FACETS	0.984	0.962	1	0.984	0.962	1	CLONAL	4	TRUE	2	0.701301517881753	6		535	2163	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427193	49427196	+	frameshift_variant	Frame_Shift_Del	DEL	TGTC	TGTC	-	novel	NA	P-0058566-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	157	561	0	ENST00000301067.7:c.11292_11295del	p.Asn3766LysfsTer63	p.N3766Kfs*63	ENST00000301067	NM_003482.3	3764	caGACA/ca	39/54	0.170023721569128	4	FACETS	0.601	0.549	0.656	0.301	0.274	0.328	INDETERMINATE	1	TRUE	2	0.701301517881753	4		561	1267	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0058567-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	62	306	0	ENST00000311936.3:c.34_35delinsAT	p.Gly12Ile	p.G12I	ENST00000311936	NM_004985.3	12	GGt/ATt	2/5	0.3	4	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	4		306	311	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066702	94066702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1191331342	NA	P-0058567-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	27	534	0	ENST00000369303.4:c.1057C>T	p.Pro353Ser	p.P353S	ENST00000369303	NM_004440.3	353	Cct/Tct	5/17	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		534	398	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	25	754	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	1	2	FACETS	0.105	0.082	0.132	0.105	0.082	0.132	SUBCLONAL	1	TRUE	1	0.643776331549337	2		754	737	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857785	9857785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555482324	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	255	518	2	ENST00000330684.3:c.3616C>T	p.Arg1206Ter	p.R1206*	ENST00000330684	NM_001134407.1	1206	Cga/Tga	13/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.643776331549337	2		520	742	SUCCESS
AR	367	MSKCC	GRCh37	X	66765149	66765151	+	inframe_deletion	In_Frame_Del	DEL	TGC	TGC	-	rs752055010	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	20	337	1	ENST00000374690.3:c.170_172del	p.Leu57del	p.L57del	ENST00000374690	NM_000044.3	54	tTGCtg/ttg	1/8	1	2	FACETS	0.2	0.153	0.256	0.2	0.153	0.256	SUBCLONAL	1	TRUE	1	0.643776331549337	2		338	310	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030479	49030479	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	96	252	0	ENST00000267163.4:c.1959del	p.Val654CysfsTer4	p.V654Cfs*4	ENST00000267163	NM_000321.2	652	Aaa/aa	19/27	0.643776331549337	1	FACETS	0.941	0.857	1	0.941	0.857	1	CLONAL	1	TRUE	0	0.643776331549337	1		252	215	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97879669	97879669	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140348260	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	149	333	0	ENST00000289081.3:c.1000C>T	p.Arg334Trp	p.R334W	ENST00000289081	NM_000136.2	334	Cgg/Tgg	11/15	1	2	FACETS	0.895	0.823	0.97	0.895	0.823	0.97	CLONAL	1	TRUE	1	0.643776331549337	2		333	517	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	276	540	12	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	0.643776331549337	2	FACETS	0.984	0.927	1	0.492	0.463	0.522	CLONAL	1	TRUE	0	0.643776331549337	2		552	871	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874637	35874637	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	142	343	2	ENST00000303115.3:c.799del	p.Arg267GlyfsTer28	p.R267Gfs*28	ENST00000303115	NM_002185.3	265	Aaa/aa	6/8	1	2	FACETS	0.983	0.903	1	0.983	0.903	1	CLONAL	1	TRUE	1	0.643776331549337	2		345	449	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687471	37687472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs760014508	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	237	456	0	ENST00000447079.4:c.4382dup	p.Thr1463AsnfsTer50	p.T1463Nfs*50	ENST00000447079	NM_015083.1	1459	tgg/tGgg	14/14	1	2	FACETS	0.906	0.848	0.965	0.906	0.848	0.965	CLONAL	1	TRUE	1	0.643776331549337	2		456	813	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	198	394	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	0.997	0.929	1	0.997	0.929	1	CLONAL	1	TRUE	1	0.643776331549337	2		394	617	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218483	1218483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775595174	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	224	387	0	ENST00000326873.7:c.358G>A	p.Glu120Lys	p.E120K	ENST00000326873	NM_000455.4	120	Gaa/Aaa	2/10	0.643776331549337	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.643776331549337	1		387	446	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	208	395	1	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	0.620567793296877	1	FACETS	0.878	0.823	0.934	0.878	0.823	0.934	CLONAL	1	TRUE	0	0.643776331549337	1		396	499	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116168	67116168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1467426352	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	165	317	0	ENST00000412916.2:c.452G>A	p.Arg151His	p.R151H	ENST00000412916		151	cGc/cAc	5/6	1	2	FACETS	0.92	0.85	0.993	0.92	0.85	0.993	CLONAL	1	TRUE	1	0.643776331549337	2		317	557	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727920	41727920	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138094666	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	210	447	0	ENST00000301178.4:c.545C>T	p.Thr182Met	p.T182M	ENST00000301178	NM_021913.4	182	aCg/aTg	4/20	1	2	FACETS	0.924	0.862	0.988	0.924	0.862	0.988	CLONAL	1	TRUE	1	0.643776331549337	2		447	706	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727513	88727513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374069724	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	227	473	0	ENST00000360948.2:c.266G>A	p.Arg89His	p.R89H	ENST00000360948	NM_001012338.2	89	cGc/cAc	3/19	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.643776331549337	2		473	665	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556727	41556727	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	177	354	0	ENST00000263253.7:c.3671+1G>A		p.X1224_splice	ENST00000263253	NM_001429.3	1224			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.643776331549337	2		354	518	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	271	536	0	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.643776331549337	2		536	842	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434851	49434851	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1460481305	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	314	575	0	ENST00000301067.7:c.6702del	p.Arg2235AspfsTer29	p.R2235Dfs*29	ENST00000301067	NM_003482.3	2234	ccC/cc	31/54	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.643776331549337	2		575	962	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512344	149512344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368602685	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	205	564	0	ENST00000261799.4:c.1096G>A	p.Ala366Thr	p.A366T	ENST00000261799	NM_002609.3	366	Gcc/Acc	7/23	1	2	FACETS	0.742	0.689	0.797	0.742	0.689	0.797	SUBCLONAL	1	TRUE	1	0.643776331549337	2		564	858	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73047245	73047245	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	116	273	0	ENST00000356692.5:c.56del	p.Lys19ArgfsTer14	p.K19Rfs*14	ENST00000356692		18	Aaa/aa	2/9	0.643776331549337	1	FACETS	0.87	0.797	0.944	0.87	0.797	0.944	CLONAL	1	TRUE	0	0.643776331549337	1		273	281	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627747	187627747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143694311	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	153	441	0	ENST00000441802.2:c.3235G>A	p.Val1079Ile	p.V1079I	ENST00000441802	NM_005245.3	1079	Gtt/Att	2/27	1	2	FACETS	0.813	0.747	0.881	0.813	0.747	0.881	CLONAL	1	TRUE	1	0.643776331549337	2		441	585	SUCCESS
NADK	65220	MSKCC	GRCh37	1	1688550	1688550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199931813	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	82	434	0	ENST00000378625.1:c.775G>A	p.Ala259Thr	p.A259T	ENST00000378625	NM_001198994.1	259	Gcc/Acc	6/14	1	2	FACETS	0.346	0.305	0.391	0.346	0.305	0.391	SUBCLONAL	1	TRUE	1	0.643776331549337	2		434	736	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260132	16260132	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	84	584	1	ENST00000375759.3:c.7397G>A	p.Ser2466Asn	p.S2466N	ENST00000375759	NM_015001.2	2466	aGc/aAc	11/15	1	2	FACETS	0.288	0.253	0.325	0.288	0.253	0.325	SUBCLONAL	1	TRUE	1	0.643776331549337	2		585	907	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983060	201983060	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	583	491	0	ENST00000359651.3:c.909C>G	p.Phe303Leu	p.F303L	ENST00000359651		303	ttC/ttG	7/8	0.643776331549337	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.643776331549337	2		491	856	SUCCESS
APLNR	187	MSKCC	GRCh37	11	57003772	57003772	+	missense_variant,NMD_transcript_variant	Missense_Mutation	SNP	C	C	T	rs199589565	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	259	545	1	ENST00000257254.3:c.707G>A	p.Arg236His	p.R236H	ENST00000257254		236	cGc/cAc	1/2	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.643776331549337	2		546	748	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495493	56495493	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	282	594	0	ENST00000267101.3:c.3683G>A	p.Gly1228Glu	p.G1228E	ENST00000267101	NM_001982.3	1228	gGg/gAg	28/28	1	2	FACETS	0.966	0.91	1	0.966	0.91	1	CLONAL	1	TRUE	1	0.643776331549337	2		594	907	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967618	26967618	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	93	298	0	ENST00000381527.3:c.761G>T	p.Arg254Ile	p.R254I	ENST00000381527	NM_001260.1	254	aGa/aTa	7/13	0.643776331549337	1	FACETS	0.929	0.844	1	0.929	0.844	1	CLONAL	1	TRUE	0	0.643776331549337	1		298	211	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434592	110434592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762228655	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	259	556	1	ENST00000375856.3:c.3809C>T	p.Pro1270Leu	p.P1270L	ENST00000375856	NM_003749.2	1270	cCg/cTg	1/2	0.643776331549337	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.643776331549337	1		557	541	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752427	55752427	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	54	438	0	ENST00000284073.2:c.888del	p.Asn297IlefsTer3	p.N297Ifs*3	ENST00000284073	NM_138962.2	295	gtG/gt	12/14	1	2	FACETS	0.216	0.184	0.251	0.216	0.184	0.251	SUBCLONAL	1	TRUE	1	0.643776331549337	2		438	777	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302918	15302918	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	292	627	0	ENST00000263388.2:c.532C>T	p.Pro178Ser	p.P178S	ENST00000263388	NM_000435.2	178	Cct/Tct	4/33	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.643776331549337	2		627	903	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374305	15374305	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	233	458	0	ENST00000263377.2:c.1267C>T	p.Arg423Ter	p.R423*	ENST00000263377	NM_058243.2	423	Cga/Tga	7/20	1	2	FACETS	0.935	0.875	0.997	0.935	0.875	0.997	CLONAL	1	TRUE	1	0.643776331549337	2		458	774	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855496	45855496	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	68	466	0	ENST00000391945.4:c.2161C>A	p.Leu721Met	p.L721M	ENST00000391945	NM_000400.3	721	Ctg/Atg	22/23	1	2	FACETS	0.273	0.237	0.312	0.273	0.237	0.312	SUBCLONAL	1	TRUE	1	0.643776331549337	2		466	774	SUCCESS
ARHGAP35	2909	MSKCC	GRCh37	19	47424417	47424417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	210	412	0	ENST00000404338.3:c.2485C>T	p.His829Tyr	p.H829Y	ENST00000404338	NM_004491.4	829	Cac/Tac	1/6	1	2	FACETS	0.885	0.825	0.947	0.885	0.825	0.947	CLONAL	1	TRUE	1	0.643776331549337	2		412	737	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36028689	36028689	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	232	379	0	ENST00000358208.4:c.1031T>C	p.Met344Thr	p.M344T	ENST00000358208		344	aTg/aCg	8/12	0.643776331549337	2	FACETS	1	0.988	1	0.605	0.568	0.642	CLONAL	1	TRUE	0	0.643776331549337	2		379	596	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37092129	37092130	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	152	334	0	ENST00000231790.2:c.2259dup	p.Glu754Ter	p.E754*	ENST00000231790	NM_000249.3	752	-/T	19/19	0.620567793296877	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.643776331549337	1		334	315	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637697	52637701	+	frameshift_variant	Frame_Shift_Del	DEL	AATAA	AATAA	-	novel	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	103	271	0	ENST00000394830.3:c.2615_2619del	p.Phe872Ter	p.F872*	ENST00000394830	NM_018313.4	872	tTTATT/t	18/30	0.620567793296877	1	FACETS	0.858	0.781	0.935	0.858	0.781	0.935	CLONAL	1	TRUE	0	0.643776331549337	1		271	253	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1976614	1976618	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGG	AAAGG	-	novel	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	184	453	0	ENST00000382891.5:c.3400_3404del	p.Gly1134LeufsTer14	p.G1134Lfs*14	ENST00000382891	NM_133335.3	1133	AAAGGa/a	19/22	0.643776331549337	1	FACETS	0.943	0.882	1	0.943	0.882	1	CLONAL	1	TRUE	0	0.643776331549337	1		453	411	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662357	117662357	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	133	401	0	ENST00000368508.3:c.5020T>A	p.Phe1674Ile	p.F1674I	ENST00000368508	NM_002944.2	1674	Ttt/Att	30/43	0.260415626262754	1	FACETS	0.614	0.562	0.669	0.614	0.562	0.669	INDETERMINATE	1	TRUE	0	0.643776331549337	1		401	456	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146944	38146945	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	119	291	0	ENST00000317025.8:c.3197dup	p.Asn1066LysfsTer14	p.N1066Kfs*14	ENST00000317025	NM_023034.1	1066	aac/aaAc	18/24	NA	2	FACETS	0.846	0.769	0.926			1	INDETERMINATE	1	TRUE	NA	0.643776331549337	2		291	437	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371761	55371761	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	214	558	0	ENST00000297316.4:c.451G>C	p.Val151Leu	p.V151L	ENST00000297316	NM_022454.3	151	Gtg/Ctg	2/2	1	2	FACETS	0.866	0.807	0.926	0.866	0.807	0.926	CLONAL	1	TRUE	1	0.643776331549337	2		558	768	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249435	110249435	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	282	508	0	ENST00000374672.4:c.1138A>G	p.Lys380Glu	p.K380E	ENST00000374672	NM_004235.4	380	Aag/Gag	4/5	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.643776331549337	2		508	876	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921450	39921450	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	31	399	0	ENST00000378444.4:c.4370T>C	p.Ile1457Thr	p.I1457T	ENST00000378444	NM_001123385.1	1457	aTt/aCt	10/15	0.643776331549337	1	FACETS	0.141	0.114	0.173	0.141	0.114	0.173	SUBCLONAL	1	TRUE	0	0.643776331549337	1		399	462	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152864501	152864501	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1557027814	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	97	239	0	ENST00000406277.2:c.27del	p.Pro10LeufsTer30	p.P10Lfs*30	ENST00000406277	NM_152274.4	9	ggG/gg	2/7	1		FACETS		0.716	0.882				SUBCLONAL	1	TRUE	1	0.643776331549337	2		239	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577582	7577586	+	missense_variant	Missense_Mutation	ONP	GTGGA	GTGGA	TTGAT	novel	NA	P-0058568-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	173	419	1	ENST00000269305.4:c.695_699delinsATCAA	p.Ile232_His233delinsAsnGln	p.I232_H233delinsNQ	ENST00000269305	NM_001126112.2	232	aTCCAC/aATCAA	7/11	0.620567793296877	1	FACETS	0.92	0.858	0.983	0.92	0.858	0.983	CLONAL	1	TRUE	0	0.643776331549337	1		420	396	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020703	26020718	+	coding_sequence_variant,5_prime_UTR_variant	Frame_Shift_Del	DEL	TGCTGTTTTTCCGTCA	TGCTGTTTTTCCGTCA	-	novel	NA	P-0058569-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	121	473	0				ENST00000357647	NM_003529.2	?-1/136		1/1	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		473	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0058570-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	58	611	3	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.157221991431268	2	FACETS	0.783	0.674	0.902	0.783	0.674	0.902	CLONAL	2	TRUE	0	0.157221991431268	2		614	471	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435477	56435477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372129321	NA	P-0058570-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	147	508	0	ENST00000407977.2:c.1660C>T	p.Arg554Trp	p.R554W	ENST00000407977		554	Cgg/Tgg	9/10	0.157221991431268	3	FACETS	0.922	0.843	1	0.922	0.843	1	CLONAL	3	TRUE	0	0.157221991431268	3		508	729	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18975016	18975016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761111860	NA	P-0058570-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	25	392	0	ENST00000262803.5:c.2813G>A	p.Arg938Gln	p.R938Q	ENST00000262803	NM_002911.3	938	cGg/cAg	20/24	1	2	FACETS	0.688	0.541	0.858	0.688	0.541	0.858	SUBCLONAL	1	TRUE	1	0.157221991431268	2		392	462	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379773	17379773	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058570-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	38	515	0	ENST00000359435.4:c.158G>C	p.Gly53Ala	p.G53A	ENST00000359435	NM_001033549.1	53	gGt/gCt	2/9	1	2	FACETS	0.741	0.611	0.887	0.741	0.611	0.887	SUBCLONAL	1	TRUE	1	0.157221991431268	2		515	652	SUCCESS
AXL	558	MSKCC	GRCh37	19	41736872	41736872	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058570-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	30	451	0	ENST00000301178.4:c.587G>T	p.Gly196Val	p.G196V	ENST00000301178	NM_021913.4	196	gGg/gTg	5/20	1	2	FACETS	0.64	0.514	0.784	0.64	0.514	0.784	SUBCLONAL	1	TRUE	1	0.157221991431268	2		451	596	SUCCESS
LZTR1	8216	MSKCC	GRCh37	22	21348256	21348256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777180	NA	P-0058570-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	63	625	0	ENST00000215739.8:c.1397G>A	p.Arg466Gln	p.R466Q	ENST00000215739	NM_006767.3	466	cGg/cAg	13/21	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.157221991431268	2		625	732	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0058574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	36	416	1	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.83	1	1	0.83	1	CLONAL	1	TRUE	1	0.22	2		417	325	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435422	18435422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	45	307	0	ENST00000266497.5:c.407C>T	p.Ala136Val	p.A136V	ENST00000266497		136	gCt/gTt	1/31	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.22	2		307	398	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs1057519842	NA	P-0058574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	30	264	0	ENST00000274335.5:c.1727_1729del	p.Thr576del	p.T576del	ENST00000274335		575	aaGACg/aag	12/15	1	2	FACETS	0.739	0.596	0.901	0.739	0.596	0.901	CLONAL	1	TRUE	1	0.22	2		264	369	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587777893	NA	P-0058574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	75	425	0	ENST00000361445.4:c.5930C>A	p.Thr1977Lys	p.T1977K	ENST00000361445	NM_004958.3	1977	aCa/aAa	43/58	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.22	2		425	644	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717609	89717609	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs876661024	NA	P-0058574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	67	251	0	ENST00000371953.3:c.635-1G>T		p.X212_splice	ENST00000371953	NM_000314.4	212			1	2	FACETS	0.781	0.682	0.887	1	0.975	1	SUBCLONAL	2	TRUE	1	0.22	2		251	390	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0058574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	42	498	2	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.557	0.463	0.66	0.557	0.463	0.66	SUBCLONAL	1	TRUE	1	0.22	2		500	686	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188081	151188081	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	27	201	0	ENST00000262187.5:c.72T>G	p.Ile24Met	p.I24M	ENST00000262187	NM_005614.3	24	atT/atG	2/8	1	2	FACETS	0.774	0.617	0.954	0.774	0.617	0.954	CLONAL	1	TRUE	1	0.22	2		201	317	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0058574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	34	276	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.978	0.802	1	0.978	0.802	1	CLONAL	1	TRUE	1	0.22	2		276	316	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023119	27023152	+	frameshift_variant	Frame_Shift_Del	DEL	CGGGGCCGAGAGCAATGGGGGTGGCGGCGGCGGC	CGGGGCCGAGAGCAATGGGGGTGGCGGCGGCGGC	-	novel	NA	P-0058574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	33	421	0	ENST00000324856.7:c.225_258del	p.Asp75GlufsTer15	p.D75Efs*15	ENST00000324856	NM_006015.4	75	gaCGGGGCCGAGAGCAATGGGGGTGGCGGCGGCGGC/ga	1/20	1	2	FACETS	0.701	0.571	0.848	0.701	0.571	0.848	SUBCLONAL	1	TRUE	1	0.22	2		421	428	SUCCESS
FH	2271	MSKCC	GRCh37	1	241671917	241671917	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	32	235	0	ENST00000366560.3:c.724C>T	p.Leu242Phe	p.L242F	ENST00000366560	NM_000143.3	242	Ctt/Ttt	5/10	1	2	FACETS	0.863	0.702	1	0.863	0.702	1	CLONAL	1	TRUE	1	0.22	2		235	337	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720658	89720658	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	11	86	0	ENST00000371953.3:c.809T>G	p.Met270Arg	p.M270R	ENST00000371953	NM_000314.4	270	aTg/aGg	8/9	1	2	FACETS	0.8	0.556	1	0.8	0.556	1	CLONAL	1	TRUE	1	0.22	2		86	125	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052520	42052520	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0058574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	54	298	0	ENST00000219905.7:c.7192-1G>A		p.X2398_splice	ENST00000219905	NM_001164273.1	2398			1	2	FACETS	0.94	0.804	1	0.94	0.804	1	CLONAL	1	TRUE	1	0.22	2		298	522	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670593	67670593	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	72	325	1	ENST00000264010.4:c.1841del	p.Asn614MetfsTer17	p.N614Mfs*17	ENST00000264010	NM_006565.3	613	gAa/ga	11/12	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.22	2		326	500	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188050	151188050	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	28	202	0	ENST00000262187.5:c.103T>G	p.Tyr35Asp	p.Y35D	ENST00000262187	NM_005614.3	35	Tac/Gac	2/8	1	2	FACETS	0.786	0.629	0.964	0.786	0.629	0.964	CLONAL	1	TRUE	1	0.22	2		202	324	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590475	67590488	+	frameshift_variant	Frame_Shift_Del	DEL	AAACGTGAAGGCAA	AAACGTGAAGGCAA	T	novel	NA	P-0058574-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	44	296	0	ENST00000274335.5:c.1537_1550delinsT	p.Lys513LeufsTer15	p.K513Lfs*15	ENST00000274335		513	AAACGTGAAGGCAAt/Tt	11/15	1	2	FACETS	0.905	0.76	1	0.905	0.76	1	CLONAL	1	TRUE	1	0.22	2		296	442	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419926	41419926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	93	549	0	ENST00000373198.4:c.395G>A	p.Gly132Glu	p.G132E	ENST00000373198	NM_133170.3	132	gGg/gAg	3/32	1	2	FACETS	0.736	0.654	0.824	0.736	0.654	0.824	SUBCLONAL	1	TRUE	1	0.328550158641702	2		549	769	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338701	70338701	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs769202858	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	126	157	0	ENST00000374080.3:c.97G>A	p.Glu33Lys	p.E33K	ENST00000374080		33	Gag/Aag	1/45	0.248557963021009	2	FACETS	0.907	0.836	0.978			1	CLONAL	3	TRUE	NA	0.328550158641702	2		157	282	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661836	227661836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs577407654	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	50	521	1	ENST00000305123.5:c.1619C>T	p.Pro540Leu	p.P540L	ENST00000305123	NM_005544.2	540	cCg/cTg	1/2	0.21114539532915	1	FACETS	0.414	0.351	0.484	0.414	0.351	0.484	SUBCLONAL	1	TRUE	0	0.328550158641702	1		522	614	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372497	55372497	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	68	562	0	ENST00000297316.4:c.1187C>T	p.Ser396Phe	p.S396F	ENST00000297316	NM_022454.3	396	tCc/tTc	2/2	1	2	FACETS	0.623	0.542	0.712	0.623	0.542	0.712	SUBCLONAL	1	TRUE	1	0.328550158641702	2		562	664	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630411	187630411	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	117	514	0	ENST00000441802.2:c.571C>T	p.Arg191Ter	p.R191*	ENST00000441802	NM_005245.3	191	Cga/Tga	2/27	1	2	FACETS	0.9	0.812	0.994	0.9	0.812	0.994	CLONAL	1	TRUE	1	0.328550158641702	2		514	791	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401823	139401823	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	204	670	0	ENST00000277541.6:c.3577C>T	p.Gln1193Ter	p.Q1193*	ENST00000277541	NM_017617.3	1193	Cag/Tag	22/34	0.328550158641702	1	FACETS	0.751	0.699	0.804	1	0.991	1	SUBCLONAL	2	TRUE	0	0.328550158641702	1		670	691	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955074	93955074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	21	259	0	ENST00000369303.4:c.2824G>A	p.Asp942Asn	p.D942N	ENST00000369303	NM_004440.3	942	Gat/Aat	16/17	1	2	FACETS	0.406	0.312	0.515	0.406	0.312	0.515	SUBCLONAL	1	TRUE	1	0.328550158641702	2		259	315	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444318	50444318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1427077431	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	111	581	0	ENST00000331340.3:c.248G>A	p.Arg83Gln	p.R83Q	ENST00000331340	NM_006060.4	83	cGa/cAa	4/8	1	2	FACETS	0.903	0.812	1	0.903	0.812	1	CLONAL	1	TRUE	1	0.328550158641702	2		581	748	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739091	40739091	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	46	464	0	ENST00000373198.4:c.3193C>A	p.His1065Asn	p.H1065N	ENST00000373198	NM_133170.3	1065	Cac/Aac	24/32	1	2	FACETS	0.456	0.383	0.537	0.456	0.383	0.537	SUBCLONAL	1	TRUE	1	0.328550158641702	2		464	614	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs878854073	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	144	434	0	ENST00000269305.4:c.673-1G>A		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.157474902435876	2	FACETS	0.803	0.736	0.872	0.803	0.736	0.872	INDETERMINATE	2	TRUE	0	0.328550158641702	2		434	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577031	7577032	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	64	569	0	ENST00000269305.4:c.906dup	p.Ser303GlufsTer3	p.S303Efs*3	ENST00000269305	NM_001126112.2	302	-/G	8/11	0.157474902435876	2	FACETS	0.479	0.413	0.55	0.239	0.206	0.275	INDETERMINATE	1	TRUE	0	0.328550158641702	2		569	814	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61717908	61717908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778783944	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	92	352	0	ENST00000401558.2:c.1891C>T	p.His631Tyr	p.H631Y	ENST00000401558	NM_003400.3	631	Cat/Tat	17/25	0.314384200027672	3	FACETS	1	0.95	1	0.559	0.498	0.625	CLONAL	1	TRUE	1	0.328550158641702	3		352	583	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231413	98231413	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	220	536	0	ENST00000331920.6:c.1870C>T	p.Gln624Ter	p.Q624*	ENST00000331920	NM_000264.3	624	Cag/Tag	14/24	0.328550158641702	1	FACETS	0.838	0.783	0.893	1	0.993	1	CLONAL	2	TRUE	0	0.328550158641702	1		536	668	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617729	39617729	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	67	353	0	ENST00000262039.4:c.1913G>A	p.Gly638Glu	p.G638E	ENST00000262039	NM_002647.2	638	gGa/gAa	17/25	1	2	FACETS	0.997	0.87	1	0.997	0.87	1	CLONAL	1	TRUE	1	0.328550158641702	2		353	409	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385255	4385255	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	132	477	0	ENST00000261254.3:c.280C>T	p.Pro94Ser	p.P94S	ENST00000261254	NM_001759.3	94	Ccg/Tcg	2/5	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.328550158641702	2		477	701	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272871	11272871	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	56	451	0	ENST00000361445.4:c.3380C>A	p.Ala1127Asp	p.A1127D	ENST00000361445	NM_004958.3	1127	gCt/gAt	22/58	1	2	FACETS	0.549	0.47	0.636	0.549	0.47	0.636	SUBCLONAL	1	TRUE	1	0.328550158641702	2		451	621	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414944	78414944	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	62	457	0	ENST00000370768.2:c.1822C>A	p.Gln608Lys	p.Q608K	ENST00000370768	NM_003902.3	608	Cag/Aag	19/20	1	2	FACETS	0.605	0.522	0.695	0.605	0.522	0.695	SUBCLONAL	1	TRUE	1	0.328550158641702	2		457	624	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115272938	115272938	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	40	409	0	ENST00000438362.2:c.1435G>T	p.Glu479Ter	p.E479*	ENST00000438362	NM_001242891.1	479	Gaa/Taa	12/20	1	2	FACETS	0.443	0.367	0.527	0.443	0.367	0.527	SUBCLONAL	1	TRUE	1	0.328550158641702	2		409	550	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458038	120458038	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	53	605	0	ENST00000256646.2:c.7307G>T	p.Trp2436Leu	p.W2436L	ENST00000256646	NM_024408.3	2436	tGg/tTg	34/34	1	2	FACETS	0.414	0.352	0.482	0.414	0.352	0.482	SUBCLONAL	1	TRUE	1	0.328550158641702	2		605	779	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551899	150551899	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	45	559	0	ENST00000369026.2:c.108G>T	p.Leu36Phe	p.L36F	ENST00000369026	NM_021960.4	36	ttG/ttT	1/3	0.254106810342706	3	FACETS	0.388	0.324	0.458	0.194	0.162	0.229	SUBCLONAL	1	TRUE	1	0.328550158641702	3		559	823	SUCCESS
SETDB1	9869	MSKCC	GRCh37	1	150915396	150915396	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	70	479	0	ENST00000271640.5:c.742G>T	p.Ala248Ser	p.A248S	ENST00000271640	NM_001145415.1	248	Gcc/Tcc	7/22	0.254106810342706	3	FACETS	0.679	0.591	0.774	0.339	0.295	0.387	SUBCLONAL	1	TRUE	1	0.328550158641702	3		479	731	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945717	206945717	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	138	567	0	ENST00000423557.1:c.64C>A	p.Gln22Lys	p.Q22K	ENST00000423557	NM_000572.2	22	Cag/Aag	1/5	0.254106810342706	3	FACETS	1	0.967	1	0.565	0.514	0.618	CLONAL	1	TRUE	1	0.328550158641702	3		567	866	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670374	246670374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	43	441	0	ENST00000388985.4:c.146G>T	p.Cys49Phe	p.C49F	ENST00000388985		49	tGc/tTc	1/12	0.254106810342706	3	FACETS	0.602	0.504	0.712	0.301	0.252	0.356	SUBCLONAL	1	TRUE	1	0.328550158641702	3		441	506	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332745	70332745	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	37	379	0	ENST00000373644.4:c.650C>A	p.Pro217Gln	p.P217Q	ENST00000373644	NM_030625.2	217	cCa/cAa	2/12	0.157474902435876	2	FACETS	0.427	0.351	0.511	0.213	0.175	0.256	INDETERMINATE	1	TRUE	0	0.328550158641702	2		379	528	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518418	69518418	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	19	240	0	ENST00000294312.3:c.227C>A	p.Ala76Glu	p.A76E	ENST00000294312	NM_005117.2	76	gCg/gAg	1/3	0.21114539532915	1	FACETS	0.373	0.283	0.478	0.373	0.283	0.478	SUBCLONAL	1	TRUE	0	0.328550158641702	1		240	259	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936116	71936116	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	54	475	0	ENST00000298229.2:c.88G>T	p.Ala30Ser	p.A30S	ENST00000298229	NM_001567.3	30	Gcc/Tcc	1/28	0.21114539532915	1	FACETS	0.563	0.481	0.652	0.563	0.481	0.652	SUBCLONAL	1	TRUE	0	0.328550158641702	1		475	488	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342760	118342761	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	76	443	1	ENST00000534358.1:c.886_887delinsAA	p.Gly296Lys	p.G296K	ENST00000534358	NM_005933.3	296	GGg/AAg	3/36	0.148496078471779	1	FACETS	0.703	0.617	0.795	0.703	0.617	0.795	INDETERMINATE	1	TRUE	0	0.328550158641702	1		444	550	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118365439	118365439	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	44	350	0	ENST00000534358.1:c.5320G>T	p.Val1774Phe	p.V1774F	ENST00000534358	NM_005933.3	1774	Gtc/Ttc	18/36	0.148496078471779	1	FACETS	0.481	0.404	0.567	0.481	0.404	0.567	INDETERMINATE	1	TRUE	0	0.328550158641702	1		350	465	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366579	118366579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782665690	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	47	439	0	ENST00000534358.1:c.5528C>T	p.Pro1843Leu	p.P1843L	ENST00000534358	NM_005933.3	1843	cCt/cTt	19/36	0.148496078471779	1	FACETS	0.372	0.313	0.438	0.372	0.313	0.438	INDETERMINATE	1	TRUE	0	0.328550158641702	1		439	642	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434948	49434949	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	60	608	0	ENST00000301067.7:c.6604_6605delinsTT	p.Pro2202Phe	p.P2202F	ENST00000301067	NM_003482.3	2202	CCt/TTt	31/54	1	2	FACETS	0.502	0.432	0.579	0.502	0.432	0.579	SUBCLONAL	1	TRUE	1	0.328550158641702	2		608	727	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437145	49437145	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	143	523	0	ENST00000301067.7:c.5533+1G>T		p.X1845_splice	ENST00000301067	NM_003482.3	1845			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.328550158641702	2		523	689	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861990	57861990	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	66	534	0	ENST00000228682.2:c.1291G>T	p.Val431Leu	p.V431L	ENST00000228682	NM_005269.2	431	Gtg/Ttg	10/12	1	2	FACETS	0.626	0.543	0.716	0.626	0.543	0.716	SUBCLONAL	1	TRUE	1	0.328550158641702	2		534	642	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120795645	120795645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	42	256	0	ENST00000257552.2:c.508C>T	p.His170Tyr	p.H170Y	ENST00000257552	NM_002442.3	170	Cat/Tat	8/15	1	2	FACETS	0.58	0.484	0.686	0.58	0.484	0.686	SUBCLONAL	1	TRUE	1	0.328550158641702	2		256	441	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896493	28896493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757344268	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	65	313	0	ENST00000282397.4:c.2957C>T	p.Ser986Phe	p.S986F	ENST00000282397	NM_002019.4	986	tCt/tTt	22/30	0.21114539532915	1	FACETS	0.707	0.614	0.806	0.707	0.614	0.806	SUBCLONAL	1	TRUE	0	0.328550158641702	1		313	468	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953650	32953650	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	rs80359146	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	30	302	0	ENST00000380152.3:c.8951C>A	p.Ser2984Ter	p.S2984*	ENST00000380152		2984	tCa/tAa	22/27	0.21114539532915	1	FACETS	0.424	0.342	0.517	0.424	0.342	0.517	SUBCLONAL	1	TRUE	0	0.328550158641702	1		302	360	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514610	103514610	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	51	535	0	ENST00000355739.4:c.1111G>T	p.Gly371Trp	p.G371W	ENST00000355739	NM_000123.3	371	Ggg/Tgg	8/15	0.21114539532915	1	FACETS	0.386	0.327	0.451	0.386	0.327	0.451	SUBCLONAL	1	TRUE	0	0.328550158641702	1		535	672	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66781616	66781616	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	40	403	0	ENST00000307102.5:c.1022+2T>G		p.X341_splice	ENST00000307102	NM_002755.3	341			0.157474902435876	2	FACETS	0.415	0.344	0.494	0.207	0.172	0.247	INDETERMINATE	1	TRUE	0	0.328550158641702	2		403	587	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304219	91304219	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	60	414	0	ENST00000355112.3:c.1616C>A	p.Ser539Ter	p.S539*	ENST00000355112	NM_000057.2	539	tCa/tAa	7/22	0.157474902435876	2	FACETS	0.575	0.495	0.662	0.288	0.247	0.331	INDETERMINATE	1	TRUE	0	0.328550158641702	2		414	635	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2089947	2089947	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	68	613	0	ENST00000219066.1:c.917G>T	p.Cys306Phe	p.C306F	ENST00000219066	NM_002528.5	306	tGc/tTc	6/6	0.157474902435876	2	FACETS	0.556	0.483	0.635	0.278	0.241	0.318	INDETERMINATE	1	TRUE	0	0.328550158641702	2		613	745	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640350	3640350	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	55	539	0	ENST00000294008.3:c.3289C>A	p.His1097Asn	p.H1097N	ENST00000294008	NM_032444.2	1097	Cac/Aac	12/15	0.157474902435876	2	FACETS	0.478	0.408	0.555	0.239	0.204	0.278	INDETERMINATE	1	TRUE	0	0.328550158641702	2		539	700	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677317	29677317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555536166	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	80	244	0	ENST00000356175.3:c.7375C>T	p.His2459Tyr	p.H2459Y	ENST00000356175	NM_000267.3	2459	Cat/Tat	49/57	0.157474902435876	2	FACETS	0.771	0.685	0.861	0.771	0.685	0.861	INDETERMINATE	2	TRUE	0	0.328550158641702	2		244	316	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097636	11097636	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	57	553	0	ENST00000358026.2:c.816G>T	p.Met272Ile	p.M272I	ENST00000358026	NM_001128849.1	272	atG/atT	5/36	1	2	FACETS	0.51	0.437	0.59	0.51	0.437	0.59	SUBCLONAL	1	TRUE	1	0.328550158641702	2		553	680	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130306	11130306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	116	435	0	ENST00000358026.2:c.2545C>T	p.Arg849Trp	p.R849W	ENST00000358026	NM_001128849.1	849	Cgg/Tgg	18/36	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.328550158641702	2		435	602	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144477	11144477	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	51	386	0	ENST00000358026.2:c.3809G>T	p.Ser1270Ile	p.S1270I	ENST00000358026	NM_001128849.1	1270	aGc/aTc	27/36	1	2	FACETS	0.541	0.459	0.631	0.541	0.459	0.631	SUBCLONAL	1	TRUE	1	0.328550158641702	2		386	574	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313403	30313403	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	70	431	0	ENST00000262643.3:c.1003G>T	p.Ala335Ser	p.A335S	ENST00000262643	NM_001238.2	335	Gcc/Tcc	11/12	1	2	FACETS	0.694	0.605	0.79	0.694	0.605	0.79	SUBCLONAL	1	TRUE	1	0.328550158641702	2		431	614	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131254	202131254	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	70	452	0	ENST00000358485.4:c.222C>A	p.Asp74Glu	p.D74E	ENST00000358485	NM_001080125.1	74	gaC/gaA	2/9	0.21114539532915	1	FACETS	0.638	0.557	0.726	0.638	0.557	0.726	SUBCLONAL	1	TRUE	0	0.328550158641702	1		452	558	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016016	31016017	+	missense_variant	Missense_Mutation	DNP	CT	CT	TC	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	87	513	0	ENST00000375687.4:c.338_339delinsTC	p.Ser113Phe	p.S113F	ENST00000375687	NM_015338.5	113	tCT/tTC	5/13	1	2	FACETS	0.737	0.652	0.827	0.737	0.652	0.827	SUBCLONAL	1	TRUE	1	0.328550158641702	2		513	719	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380540	31380540	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	64	571	0	ENST00000328111.2:c.1030G>T	p.Gly344Trp	p.G344W	ENST00000328111	NM_006892.3	344	Ggg/Tgg	9/23	1	2	FACETS	0.567	0.49	0.65	0.567	0.49	0.65	SUBCLONAL	1	TRUE	1	0.328550158641702	2		571	687	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385084	31385084	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	61	467	0	ENST00000328111.2:c.1469G>T	p.Cys490Phe	p.C490F	ENST00000328111	NM_006892.3	490	tGc/tTc	14/23	1	2	FACETS	0.57	0.492	0.656	0.57	0.492	0.656	SUBCLONAL	1	TRUE	1	0.328550158641702	2		467	651	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022312	36022312	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	68	577	0	ENST00000358208.4:c.365G>T	p.Trp122Leu	p.W122L	ENST00000358208		122	tGg/tTg	4/12	1	2	FACETS	0.592	0.515	0.676	0.592	0.515	0.676	SUBCLONAL	1	TRUE	1	0.328550158641702	2		577	699	SUCCESS
ZNRF3	84133	MSKCC	GRCh37	22	29445545	29445545	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	42	578	0	ENST00000544604.2:c.1376C>A	p.Ala459Glu	p.A459E	ENST00000544604	NM_001206998.1	459	gCa/gAa	8/9	0.148496078471779	1	FACETS	0.335	0.279	0.398	0.335	0.279	0.398	INDETERMINATE	1	TRUE	0	0.328550158641702	1		578	637	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543855	41543855	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	57	381	0	ENST00000263253.7:c.2146G>T	p.Gly716Cys	p.G716C	ENST00000263253	NM_001429.3	716	Ggc/Tgc	12/31	0.148496078471779	1	FACETS	0.529	0.454	0.611	0.529	0.454	0.611	INDETERMINATE	1	TRUE	0	0.328550158641702	1		381	548	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441226	52441226	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1060503726	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	230	588	0	ENST00000460680.1:c.544G>T	p.Glu182Ter	p.E182*	ENST00000460680	NM_004656.3	182	Gag/Tag	7/17	0.328550158641702	1	FACETS	0.823	0.77	0.876	1	0.993	1	CLONAL	2	TRUE	0	0.328550158641702	1		588	711	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430539	181430539	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	61	631	0	ENST00000325404.1:c.391C>A	p.Leu131Met	p.L131M	ENST00000325404	NM_003106.3	131	Ctg/Atg	1/1	0.125948266024522	4	FACETS	0.566	0.487	0.652	0.283	0.243	0.326	INDETERMINATE	1	TRUE	2	0.328550158641702	4		631	872	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805546	1805546	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	87	554	0	ENST00000260795.2:c.1058G>T	p.Trp353Leu	p.W353L	ENST00000260795		353	tGg/tTg	7/17	0.21114539532915	1	FACETS	0.622	0.55	0.698	0.622	0.55	0.698	SUBCLONAL	1	TRUE	0	0.328550158641702	1		554	712	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254510	1254510	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	113	481	0	ENST00000310581.5:c.3268G>T	p.Val1090Leu	p.V1090L	ENST00000310581	NM_198253.2	1090	Gtg/Ttg	15/16	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.328550158641702	2		481	544	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923751	131923751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	28	345	0	ENST00000265335.6:c.1021C>T	p.Gln341Ter	p.Q341*	ENST00000265335		341	Cag/Tag	7/25	1	2	FACETS	0.443	0.354	0.544	0.443	0.354	0.544	SUBCLONAL	1	TRUE	1	0.328550158641702	2		345	385	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973808	131973808	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	28	338	0	ENST00000265335.6:c.3511G>T	p.Glu1171Ter	p.E1171*	ENST00000265335		1171	Gaa/Taa	23/25	1	2	FACETS	0.354	0.282	0.437	0.354	0.282	0.437	SUBCLONAL	1	TRUE	1	0.328550158641702	2		338	481	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519426	176519426	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	50	625	0	ENST00000292408.4:c.832C>A	p.Gln278Lys	p.Q278K	ENST00000292408	NM_213647.1	278	Cag/Aag	7/18	1	2	FACETS	0.439	0.372	0.514	0.439	0.372	0.514	SUBCLONAL	1	TRUE	1	0.328550158641702	2		625	693	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180050960	180050960	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	138	556	0	ENST00000261937.6:c.1523C>T	p.Thr508Ile	p.T508I	ENST00000261937	NM_182925.4	508	aCc/aTc	11/30	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.328550158641702	2		556	776	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671753	30671753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	145	615	0	ENST00000376406.3:c.5207C>T	p.Pro1736Leu	p.P1736L	ENST00000376406	NM_014641.2	1736	cCc/cTc	10/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.328550158641702	2		615	716	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673026	30673026	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1246639057	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	146	746	0	ENST00000376406.3:c.3934A>G	p.Ser1312Gly	p.S1312G	ENST00000376406	NM_014641.2	1312	Agc/Ggc	10/15	1	2	FACETS	0.9	0.821	0.984	0.9	0.821	0.984	CLONAL	1	TRUE	1	0.328550158641702	2		746	987	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188904	32188904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	117	695	0	ENST00000375023.3:c.650C>T	p.Ser217Phe	p.S217F	ENST00000375023	NM_004557.3	217	tCc/tTc	4/30	1	2	FACETS	0.962	0.868	1	0.962	0.868	1	CLONAL	1	TRUE	1	0.328550158641702	2		695	740	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706886	117706886	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs372359152	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	55	353	0	ENST00000368508.3:c.2264G>T	p.Trp755Leu	p.W755L	ENST00000368508	NM_002944.2	755	tGg/tTg	15/43	0.169242172609622	1	FACETS	0.472	0.403	0.547	0.472	0.403	0.547	INDETERMINATE	1	TRUE	0	0.328550158641702	1		353	593	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708094	117708094	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	33	288	0	ENST00000368508.3:c.2083G>T	p.Gly695Cys	p.G695C	ENST00000368508	NM_002944.2	695	Ggc/Tgc	14/43	0.169242172609622	1	FACETS	0.477	0.389	0.576	0.477	0.389	0.576	INDETERMINATE	1	TRUE	0	0.328550158641702	1		288	352	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004546	150004546	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	77	602	0	ENST00000253339.5:c.1679C>A	p.Pro560Gln	p.P560Q	ENST00000253339		560	cCa/cAa	3/7	1	2	FACETS	0.525	0.46	0.596	0.525	0.46	0.596	SUBCLONAL	1	TRUE	1	0.328550158641702	2		602	892	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946185	13946185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1299587625	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	98	380	0	ENST00000405192.2:c.911C>T	p.Pro304Leu	p.P304L	ENST00000405192	NM_001163147.1	304	cCc/cTc	10/12	NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.328550158641702	2		380	539	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227977	55227977	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	55	347	0	ENST00000275493.2:c.1444G>T	p.Gly482Trp	p.G482W	ENST00000275493	NM_005228.3	482	Ggg/Tgg	12/28	1	2	FACETS	0.628	0.537	0.727	0.628	0.537	0.727	SUBCLONAL	1	TRUE	1	0.328550158641702	2		347	533	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878218	151878218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	125	539	0	ENST00000262189.6:c.6727C>T	p.Leu2243Phe	p.L2243F	ENST00000262189	NM_170606.2	2243	Ctc/Ttc	36/59	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.328550158641702	2		539	686	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146201	38146201	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	39	478	0	ENST00000317025.8:c.3305C>A	p.Pro1102Gln	p.P1102Q	ENST00000317025	NM_023034.1	1102	cCa/cAa	19/24	1	2	FACETS	0.387	0.32	0.462	0.387	0.32	0.462	SUBCLONAL	1	TRUE	1	0.328550158641702	2		478	614	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172221	38172221	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	31	470	0	ENST00000317025.8:c.2186G>T	p.Cys729Phe	p.C729F	ENST00000317025	NM_023034.1	729	tGc/tTc	12/24	1	2	FACETS	0.322	0.26	0.393	0.322	0.26	0.393	SUBCLONAL	1	TRUE	1	0.328550158641702	2		470	586	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021848	69021848	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	54	347	0	ENST00000288368.4:c.3136C>T	p.Gln1046Ter	p.Q1046*	ENST00000288368	NM_024870.2	1046	Caa/Taa	25/40	1	2	FACETS	0.624	0.533	0.723	0.624	0.533	0.723	SUBCLONAL	1	TRUE	1	0.328550158641702	2		347	527	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145736918	145736918	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	45	566	0	ENST00000428558.2:c.3523C>A	p.Gln1175Lys	p.Q1175K	ENST00000428558	NM_004260.3	1175	Cag/Aag	22/22	0.150029795702518	4	FACETS	0.427	0.358	0.505	0.214	0.179	0.253	INDETERMINATE	1	TRUE	2	0.328550158641702	4		566	852	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485999	8485999	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	34	504	0	ENST00000356435.5:c.2818C>A	p.Gln940Lys	p.Q940K	ENST00000356435		940	Caa/Aaa	17/35	1	2	FACETS	0.313	0.254	0.378	0.313	0.254	0.378	SUBCLONAL	1	TRUE	1	0.328550158641702	2		504	662	SUCCESS
MTAP	4507	MSKCC	GRCh37	9	21815513	21815513	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs762020837	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	47	207	0	ENST00000380172.4:c.115G>T	p.Gly39Cys	p.G39C	ENST00000380172	NM_002451.3	39	Ggc/Tgc	2/8	0.148496078471779	1	FACETS	0.745	0.631	0.869	0.745	0.631	0.869	INDETERMINATE	1	TRUE	0	0.328550158641702	1		207	321	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180262	27180262	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	58	535	0	ENST00000380036.4:c.926C>A	p.Pro309Gln	p.P309Q	ENST00000380036	NM_000459.3	309	cCa/cAa	7/23	0.148496078471779	1	FACETS	0.423	0.362	0.489	0.423	0.362	0.489	INDETERMINATE	1	TRUE	0	0.328550158641702	1		535	698	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781127	135781127	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	99	575	0	ENST00000298552.3:c.1838C>A	p.Pro613Gln	p.P613Q	ENST00000298552	NM_001162426.1	613	cCa/cAa	15/23	0.328550158641702	1	FACETS	0.797	0.712	0.887	0.797	0.712	0.887	SUBCLONAL	1	TRUE	0	0.328550158641702	1		575	632	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797211	135797211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs397514830	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	101	347	0	ENST00000298552.3:c.658G>T	p.Val220Phe	p.V220F	ENST00000298552	NM_001162426.1	220	Gtc/Ttc	7/23	0.328550158641702	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.328550158641702	1		347	458	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949020	44949020	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	37	143	0	ENST00000377967.4:c.3581G>T	p.Trp1194Leu	p.W1194L	ENST00000377967	NM_021140.2	1194	tGg/tTg	25/29	0.248557963021009	2	FACETS	1	0.843	1			1	CLONAL	1	TRUE	NA	0.328550158641702	2		143	222	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651617	48651617	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058575-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	39	297	0	ENST00000376670.3:c.783C>A	p.Cys261Ter	p.C261*	ENST00000376670	NM_002049.3	261	tgC/tgA	5/6	0.248557963021009	2	FACETS	0.553	0.459	0.659			1	SUBCLONAL	1	TRUE	NA	0.328550158641702	2		297	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574013	7574013	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	215	402	0	ENST00000269305.4:c.1014del	p.Phe338LeufsTer7	p.F338Lfs*7	ENST00000269305	NM_001126112.2	338	ttC/tt	10/11	0.30447129752503	2	FACETS	0.845	0.79	0.901	0.845	0.79	0.901	CLONAL	2	TRUE	0	0.403732705095165	2		402	630	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008552	70008692	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTTGTTGCTCAGAATACAGGTACGCAGCCTGAGTTGTGTAAAGTTTACTGCTTTTTACCGACTTCAAGACAGTAGAAACAGGGATATAATGAGCCATAGGGGAGTTGACTTACGTGATCCTAACACAGTCAATCCTTATT	ATTTGTTGCTCAGAATACAGGTACGCAGCCTGAGTTGTGTAAAGTTTACTGCTTTTTACCGACTTCAAGACAGTAGAAACAGGGATATAATGAGCCATAGGGGAGTTGACTTACGTGATCCTAACACAGTCAATCCTTATT	-	novel	NA	P-0058577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	54	405	0	ENST00000394351.3:c.845_858+127del		p.X282_splice	ENST00000394351	NM_000248.3	282		8/9	0.292365824136126	4	FACETS	0.471	0.401	0.548	0.236	0.2	0.274	SUBCLONAL	1	TRUE	2	0.403732705095165	4		405	797	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590770	189590770	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	225	504	0	ENST00000264731.3:c.1335C>A	p.His445Gln	p.H445Q	ENST00000264731	NM_003722.4	445	caC/caA	10/14	0.292365824136126	4	FACETS	0.795	0.741	0.851	0.795	0.741	0.851	SUBCLONAL	2	TRUE	2	0.403732705095165	4		504	984	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738802	145738802	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269867447	NA	P-0058577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1879	706	835	3	ENST00000428558.2:c.2263C>T	p.Arg755Trp	p.R755W	ENST00000428558	NM_004260.3	755	Cgg/Tgg	14/22	0.403732705095165	7	FACETS	0.906	0.872	0.941	0.453	0.436	0.471	CLONAL	3	TRUE	1	0.403732705095165	7		838	2585	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740327	145740327	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058577-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1588	98	525	1	ENST00000428558.2:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000428558	NM_004260.3	538	gAt/gGt	9/22	0.403732705095165	7	FACETS	0.579	0.514	0.648	0.096	0.085	0.108	SUBCLONAL	1	TRUE	1	0.403732705095165	7		526	1686	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0058578-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	216	717	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.545357090225052	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.545357090225052	1		717	540	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937102	36937102	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058578-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	200	602	0	ENST00000361632.4:c.1217T>A	p.Val406Glu	p.V406E	ENST00000361632		406	gTg/gAg	9/16	0.298451340639182	3	FACETS	1	0.979	1	0.572	0.531	0.615	INDETERMINATE	1	TRUE	1	0.545357090225052	3		602	816	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553624	29553624	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058578-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	192	487	0	ENST00000356175.3:c.2173G>T	p.Glu725Ter	p.E725*	ENST00000356175	NM_000267.3	725	Gaa/Taa	18/57	0.545357090225052	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.545357090225052	1		487	486	SUCCESS
APC	324	MSKCC	GRCh37	5	112175945	112175945	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	23	488	0	ENST00000257430.4:c.4654G>T	p.Glu1552Ter	p.E1552*	ENST00000257430	NM_000038.5	1552	Gag/Tag	16/16	0.573414379864687	1	FACETS	0.129	0.1	0.162	0.129	0.1	0.162	SUBCLONAL	1	TRUE	0	0.593829420101379	1		488	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0058579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	151	795	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.593829420101379	1	FACETS	0.843	0.779	0.909	0.843	0.779	0.909	CLONAL	1	TRUE	0	0.593829420101379	1		795	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0058579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	9	741	0	ENST00000269305.4:c.559+1G>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.593829420101379	1	FACETS	0.052	0.034	0.075	0.052	0.034	0.075	SUBCLONAL	1	TRUE	0	0.593829420101379	1		741	411	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813089	76813089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057517707	NA	P-0058579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	110	368	0	ENST00000373344.5:c.6532C>T	p.Arg2178Trp	p.R2178W	ENST00000373344	NM_000489.3	2178	Cgg/Tgg	30/35	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.593829420101379	2		368	369	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488481	20488481	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0058579-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	148	396	0	ENST00000346618.3:c.1135+2T>G		p.X379_splice	ENST00000346618	NM_001949.4	379			1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.593829420101379	2		396	484	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061191	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs879499034	NA	P-0058580-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	108	661	0	ENST00000250448.2:c.798C>A	p.Phe266Leu	p.F266L	ENST00000250448	NM_004496.3	266	ttC/ttA	2/2	1	2	FACETS	0.972	0.872	1	0.972	0.872	1	CLONAL	1	TRUE	1	0.265058014214918	2		661	838	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578664	7579565	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCACTAGCGAGCTAGAGAGAGTTGGCGTCTACACCTCAGGAGCTTTTCTTTTTTTTTTTTTTTTTTGAGATAGGGTCTTGCTCTGTCACTCAGGCTGGAGCACAGTGGTGTGATCACAGCTCACTGCAGCCTCCATCTCCTGGCCTCAAGTGATCTTCCCACCTCAGCCTCCTAAGTGGCTGGGACTATAGGTGTGCACCACCATGCCTGGCTAATTTTTTGTATTTTTTTGTAGAGACGAGGTTTCATCATGTTACCCAGGCTGGTCTTGAACTCCTGGGCTCAGGTGATCTGCCTGCCTTGGCCTCTTTGAGAGTGCTGGGATTGCAGGTGTGAGCCACCAAGCCTGGTCAGGAGCTTATTTTCAAAAGCCAAGGAATACACGTGGATGAAGAAAAAGAAAAGTTCTGCATCCCCAGGAGAGATGCTGAGGGTGTGATGGGATGGATAAAAGCCCAAATTCAAGGGGGGAATATTCAACTTTGGGACAGGAGTCAGAGATCACACATTAAGTGGGTAAACTATAAAAAAACACTGACAGGAAGCCAAAGGGTGAAGAGGAATCCCAAAGTTCCAAACAAAAGAAATGCAGGGGGATACGGCCAGGCATTGAAGTCTCATGGAAGCCAGCCCCTCAGGGCAACTGACCGTGCAAGTCACAGACTTGGCTGTCCCAGAATGCAAGAAGCCCAGACGGAAACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGGACAGAAGATGACAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTGCAGGGGCCACGGGGGGAGCAGCCTCTGGCATTCTGGGAGCTTCATCTGGACCTGGGTCTTCAGTGAACCATTGTTCAATATCGTCCGGGGACAGCATCAAATCAT	CCACTAGCGAGCTAGAGAGAGTTGGCGTCTACACCTCAGGAGCTTTTCTTTTTTTTTTTTTTTTTTGAGATAGGGTCTTGCTCTGTCACTCAGGCTGGAGCACAGTGGTGTGATCACAGCTCACTGCAGCCTCCATCTCCTGGCCTCAAGTGATCTTCCCACCTCAGCCTCCTAAGTGGCTGGGACTATAGGTGTGCACCACCATGCCTGGCTAATTTTTTGTATTTTTTTGTAGAGACGAGGTTTCATCATGTTACCCAGGCTGGTCTTGAACTCCTGGGCTCAGGTGATCTGCCTGCCTTGGCCTCTTTGAGAGTGCTGGGATTGCAGGTGTGAGCCACCAAGCCTGGTCAGGAGCTTATTTTCAAAAGCCAAGGAATACACGTGGATGAAGAAAAAGAAAAGTTCTGCATCCCCAGGAGAGATGCTGAGGGTGTGATGGGATGGATAAAAGCCCAAATTCAAGGGGGGAATATTCAACTTTGGGACAGGAGTCAGAGATCACACATTAAGTGGGTAAACTATAAAAAAACACTGACAGGAAGCCAAAGGGTGAAGAGGAATCCCAAAGTTCCAAACAAAAGAAATGCAGGGGGATACGGCCAGGCATTGAAGTCTCATGGAAGCCAGCCCCTCAGGGCAACTGACCGTGCAAGTCACAGACTTGGCTGTCCCAGAATGCAAGAAGCCCAGACGGAAACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGGACAGAAGATGACAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTGCAGGGGCCACGGGGGGAGCAGCCTCTGGCATTCTGGGAGCTTCATCTGGACCTGGGTCTTCAGTGAACCATTGTTCAATATCGTCCGGGGACAGCATCAAATCAT	-	novel	NA	P-0058580-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	75	234	0	ENST00000269305.4:c.122_376-110del		p.X41_splice	ENST00000269305	NM_001126112.2	41		4/11	0.265058014214918	1	FACETS	0.877	0.777	0.982	1	0.982	1	CLONAL	2	TRUE	0	0.265058014214918	1		234	280	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309659	30309659	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058580-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	138	690	0	ENST00000307677.4:c.363G>T	p.Gln121His	p.Q121H	ENST00000307677	NM_138578.1	121	caG/caT	2/3	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.265058014214918	2		690	939	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143164	24143167	+	frameshift_variant	Frame_Shift_Del	DEL	ACCC	ACCC	-	novel	NA	P-0058580-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	110	617	0	ENST00000263121.7:c.400_403del	p.Thr134CysfsTer8	p.T134Cfs*8	ENST00000263121	NM_003073.3	132	gtACCC/gt	4/9	1	2	FACETS	0.981	0.881	1	0.981	0.881	1	CLONAL	1	TRUE	1	0.265058014214918	2		617	846	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274261	10274261	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058581-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	86	391	0	ENST00000330684.3:c.8G>C	p.Arg3Thr	p.R3T	ENST00000330684	NM_001134407.1	3	aGa/aCa	2/13	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.226439775736421	2		391	729	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56871608	56871608	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1317460977	NA	P-0058581-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	87	372	0	ENST00000308159.5:c.1988T>C	p.Leu663Pro	p.L663P	ENST00000308159	NM_014669.4	663	cTg/cCg	18/22	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.226439775736421	2		372	714	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795036	42795036	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058581-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	65	530	0	ENST00000575354.2:c.2116G>T	p.Gly706Cys	p.G706C	ENST00000575354	NM_015125.3	706	Ggt/Tgt	10/20	1	2	FACETS	0.621	0.537	0.713	0.621	0.537	0.713	SUBCLONAL	1	TRUE	1	0.226439775736421	2		530	924	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033688	48033688	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058581-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	64	326	0	ENST00000234420.5:c.3899T>G	p.Phe1300Cys	p.F1300C	ENST00000234420	NM_000179.2	1300	tTt/tGt	9/10	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.226439775736421	2		326	553	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423413	116423414	+	missense_variant	Missense_Mutation	DNP	TA	TA	GG	novel	NA	P-0058581-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	161	303	0	ENST00000397752.3:c.3688_3689delinsGG	p.Tyr1230Gly	p.Y1230G	ENST00000397752	NM_000245.2	1230	TAt/GGt	19/21	0.226439775736421	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.226439775736421	3		303	673	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224451	53224451	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058581-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	92	438	0	ENST00000375401.3:c.3262A>G	p.Thr1088Ala	p.T1088A	ENST00000375401	NM_004187.3	1088	Acc/Gcc	21/26	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.226439775736421	2		438	791	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163775	47163779	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAC	GAAAC	A	novel	NA	P-0058581-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	144	346	0	ENST00000409792.3:c.2347_2351delinsT	p.Val783PhefsTer14	p.V783Ffs*14	ENST00000409792	NM_014159.6	783	GTTTCt/Tt	3/21	0.226439775736421	2	FACETS	0.984	0.901	1	0.984	0.901	1	CLONAL	2	TRUE	0	0.226439775736421	2		346	646	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106536	27106536	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058582-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	78	719	0	ENST00000324856.7:c.6147G>A	p.Trp2049Ter	p.W2049*	ENST00000324856	NM_006015.4	2049	tgG/tgA	20/20	1	2	FACETS	0.548	0.48	0.62	0.548	0.48	0.62	SUBCLONAL	1	TRUE	1	0.337136595444477	2		719	845	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664555	29664555	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058584-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	23	422	0	ENST00000356175.3:c.6534del	p.Thr2179HisfsTer18	p.T2179Hfs*18	ENST00000356175	NM_000267.3	2178	ttG/tt	42/57	0.168005852582281	1	FACETS	0.951	0.743	1	0.951	0.743	1	CLONAL	1	TRUE	0	0.16	1		422	278	SUCCESS
MLLT1	4298	MSKCC	GRCh37	19	6213982	6213982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058584-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	61	536	0	ENST00000252674.7:c.1375C>T	p.Pro459Ser	p.P459S	ENST00000252674	NM_005934.3	459	Ccc/Tcc	9/12	1	2	FACETS	1	0.907	1	1	0.98	1	CLONAL	2	TRUE	1	0.16	2		536	360	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662736	117662736	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1278454013	NA	P-0058584-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	49	528	0	ENST00000368508.3:c.4729T>C	p.Ser1577Pro	p.S1577P	ENST00000368508	NM_002944.2	1577	Tct/Cct	29/43	0.254839065791165	0	FACETS	0.912	0.778	1			1	CLONAL	2	TRUE	0	0.16	0		528	282	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74859028	74859028	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058584-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	12	202	0	ENST00000284811.8:c.176A>G	p.Glu59Gly	p.E59G	ENST00000284811		59	gAg/gGg	4/4	1	2	FACETS	1	0.835	1	1	0.835	1	CLONAL	1	TRUE	1	0.16	2		202	115	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0058585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	11	608	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	0.345969956614948	4	FACETS	0.316	0.218	0.438			1	SUBCLONAL	1	TRUE	NA	0.379678976398453	4		608	253	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412898	49412898	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519954	NA	P-0058585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	141	502	0	ENST00000418115.1:c.125A>G	p.Tyr42Cys	p.Y42C	ENST00000418115	NM_001664.2	42	tAt/tGt	2/5	0.379678976398453	6	FACETS	0.902	0.827	0.979	0.902	0.827	0.979	CLONAL	3	TRUE	3	0.379678976398453	6		502	483	SUCCESS
RET	5979	MSKCC	GRCh37	10	43598056	43598056	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751572082	NA	P-0058585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	24	718	0	ENST00000355710.3:c.604G>A	p.Val202Met	p.V202M	ENST00000355710	NM_020975.4	202	Gtg/Atg	3/20	0.175314610254298	0	FACETS	0.368	0.29	0.457			1	INDETERMINATE	1	TRUE	0	0.379678976398453	0		718	213	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847399	68847399	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0058585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	112	590	0	ENST00000261769.5:c.1320+1G>A		p.X440_splice	ENST00000261769	NM_004360.3	440			0.141666478214337	5	FACETS	1	0.949	1	1	0.949	1	INDETERMINATE	3	TRUE	2	0.379678976398453	5		590	292	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275319	115275319	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	43	516	0	ENST00000438362.2:c.1094A>G	p.Asn365Ser	p.N365S	ENST00000438362	NM_001242891.1	365	aAt/aGt	10/20	0.388179898854336	4	FACETS	0.698	0.584	0.823	0.349	0.292	0.412	SUBCLONAL	1	TRUE	2	0.379678976398453	4		516	448	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435933	56435933	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	34	820	0	ENST00000407977.2:c.1204C>T	p.Gln402Ter	p.Q402*	ENST00000407977		402	Cag/Tag	9/10	0.388179898854336	4	FACETS	0.519	0.424	0.627	0.26	0.212	0.314	SUBCLONAL	1	TRUE	2	0.379678976398453	4		820	476	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275629	41275629	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0058585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	22	560	0	ENST00000349496.5:c.1525-1G>T		p.X509_splice	ENST00000349496	NM_001904.3	509			0.376872547792752	4	FACETS	0.401	0.31	0.507	0.2	0.155	0.254	SUBCLONAL	1	TRUE	2	0.379678976398453	4		560	399	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046512	69046512	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0058585-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	14	481	0	ENST00000288368.4:c.3984+1G>T		p.X1328_splice	ENST00000288368	NM_024870.2	1328			0.319580139962552	2	FACETS	0.279	0.201	0.374	0.14	0.1	0.187	SUBCLONAL	1	TRUE	0	0.379678976398453	2		481	264	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0058586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	78	321	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		321	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0058586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	84	737	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		737	534	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434964	56434964	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	53	834	0	ENST00000407977.2:c.2173G>T	p.Val725Leu	p.V725L	ENST00000407977		725	Gtg/Ttg	9/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		834	859	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508416	106508416	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058586-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	36	1104	0	ENST00000359195.3:c.410T>C	p.Leu137Pro	p.L137P	ENST00000359195	NM_002649.2	137	cTg/cCg	2/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1104	709	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577557	7577557	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519982	NA	P-0058588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	43	578	0	ENST00000269305.4:c.724T>C	p.Cys242Arg	p.C242R	ENST00000269305	NM_001126112.2	242	Tgc/Cgc	7/11	1	2	FACETS	0.854	0.716	1	0.854	0.716	1	CLONAL	1	TRUE	1	0.251858431144891	2		578	400	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968118	68968118	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	52	499	0	ENST00000288368.4:c.1147G>A	p.Glu383Lys	p.E383K	ENST00000288368	NM_024870.2	383	Gag/Aag	10/40	0.251858431144891	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.251858431144891	1		499	272	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893598	28893598	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	42	490	0	ENST00000282397.4:c.3248G>A	p.Trp1083Ter	p.W1083*	ENST00000282397	NM_002019.4	1083	tGg/tAg	24/30	0.251858431144891	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.251858431144891	1		490	256	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066729	77066729	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	27	629	0	ENST00000356341.3:c.756G>T	p.Glu252Asp	p.E252D	ENST00000356341	NM_002576.4	252	gaG/gaT	7/15	1	2	FACETS	0.654	0.521	0.805	0.654	0.521	0.805	SUBCLONAL	1	TRUE	1	0.251858431144891	2		629	328	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999495	100999495	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	48	875	0	ENST00000325455.5:c.307C>A	p.Pro103Thr	p.P103T	ENST00000325455	NM_001202474.3	103	Ccc/Acc	1/8	1	2	FACETS	0.853	0.722	0.997	0.853	0.722	0.997	CLONAL	1	TRUE	1	0.251858431144891	2		875	447	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211486	46211486	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	57	465	0	ENST00000334344.6:c.452A>T	p.Asp151Val	p.D151V	ENST00000334344	NM_152641.2	151	gAc/gTc	5/21	0.143968393639562	3	FACETS	1	0.965	1	0.71	0.612	0.816	INDETERMINATE	1	TRUE	1	0.251858431144891	3		465	359	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11018748	11018748	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs148378841	NA	P-0058588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	33	678	0	ENST00000327064.4:c.380G>T	p.Cys127Phe	p.C127F	ENST00000327064	NM_199141.1	127	tGc/tTc	3/16	0.251858431144891	1	FACETS	0.543	0.442	0.656	0.543	0.442	0.656	SUBCLONAL	1	TRUE	0	0.251858431144891	1		678	422	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215237	142215237	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	120	356	0	ENST00000350721.4:c.5864T>A	p.Leu1955Gln	p.L1955Q	ENST00000350721	NM_001184.3	1955	cTg/cAg	34/47	0.251858431144891	4	FACETS	0.979	0.892	1	0.979	0.892	1	CLONAL	3	TRUE	1	0.251858431144891	4		356	406	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526295	189526295	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	209	856	0	ENST00000264731.3:c.559G>C	p.Ala187Pro	p.A187P	ENST00000264731	NM_003722.4	187	Gcc/Ccc	4/14	0.251858431144891	4	FACETS	0.896	0.837	0.955	1	0.986	1	CLONAL	4	TRUE	1	0.251858431144891	4		856	580	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55130032	55130032	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	49	679	0	ENST00000257290.5:c.566G>T	p.Cys189Phe	p.C189F	ENST00000257290	NM_006206.4	189	tGt/tTt	4/23	0.251858431144891	1	FACETS	0.852	0.724	0.993	0.852	0.724	0.993	CLONAL	1	TRUE	0	0.251858431144891	1		679	399	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31464451	31464451	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0058588-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	30	597	0	ENST00000344624.3:c.2467-1G>A		p.X823_splice	ENST00000344624		823			1	2	FACETS	0.764	0.617	0.93	0.764	0.617	0.93	CLONAL	1	TRUE	1	0.251858431144891	2		597	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0058757-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	96	304	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.291744042562082	1	FACETS	0.921	0.822	1	0.921	0.822	1	CLONAL	1	TRUE	0	0.291744042562082	1		304	610	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56477631	56477631	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058757-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	120	315	0	ENST00000267101.3:c.179T>A	p.Met60Lys	p.M60K	ENST00000267101	NM_001982.3	60	aTg/aAg	2/28	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.291744042562082	2		315	755	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	493198	493198	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058757-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	40	265	0	ENST00000399788.2:c.365A>G	p.Lys122Arg	p.K122R	ENST00000399788	NM_001042603.1	122	aAg/aGg	3/28	1	2	FACETS	0.972	0.812	1	0.972	0.812	1	CLONAL	1	TRUE	1	0.291744042562082	2		265	282	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828274	72828274	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058757-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	39	392	0	ENST00000268489.5:c.8307C>A	p.Ser2769Arg	p.S2769R	ENST00000268489	NM_006885.3	2769	agC/agA	9/10	1	2	FACETS	0.467	0.387	0.558	0.467	0.387	0.558	SUBCLONAL	1	TRUE	1	0.291744042562082	2		392	572	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119881	70119881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058757-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	60	351	0	ENST00000245479.2:c.883G>A	p.Asp295Asn	p.D295N	ENST00000245479	NM_000346.3	295	Gac/Aac	3/3	1	2	FACETS	0.569	0.489	0.656	0.569	0.489	0.656	SUBCLONAL	1	TRUE	1	0.291744042562082	2		351	723	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141507	11141507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058757-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	109	389	0	ENST00000358026.2:c.3484G>A	p.Gly1162Ser	p.G1162S	ENST00000358026	NM_001128849.1	1162	Ggc/Agc	25/36	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.291744042562082	2		389	714	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845628	151845628	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058757-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	127	384	0	ENST00000262189.6:c.13384T>G	p.Cys4462Gly	p.C4462G	ENST00000262189	NM_170606.2	4462	Tgt/Ggt	52/59	0.291744042562082	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.291744042562082	1		384	581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578467	7578467	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	357	547	1	ENST00000269305.4:c.463A>C	p.Thr155Pro	p.T155P	ENST00000269305	NM_001126112.2	155	Acc/Ccc	5/11	0.487027714685719	2	FACETS	0.956	0.912	1	0.956	0.912	1	CLONAL	2	TRUE	0	0.491929444326394	2		548	759	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040683	47040683	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	271	245	0	ENST00000377604.3:c.1318C>T	p.Gln440Ter	p.Q440*	ENST00000377604	NM_001204468.1	440	Cag/Tag	13/24	0.369388762198236	2	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.491929444326394	2		245	441	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610198	10610198	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	380	498	0	ENST00000171111.5:c.512G>T	p.Cys171Phe	p.C171F	ENST00000171111	NM_203500.1	171	tGc/tTc	2/6	0.491929444326394	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.491929444326394	2		498	764	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778785	76778787	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1557042392	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	74	218	0	ENST00000373344.5:c.6792_6794del	p.Glu2265del	p.E2265del	ENST00000373344	NM_000489.3	2264	gaAGAg/gag	31/35	0.377796511345669	2	FACETS	1	0.95	1			1	CLONAL	1	TRUE	NA	0.491929444326394	2		218	265	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484335	8484335	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	83	352	0	ENST00000356435.5:c.3197G>T	p.Arg1066Leu	p.R1066L	ENST00000356435		1066	cGa/cTa	19/35	0.491929444326394	1	FACETS	0.902	0.806	1	0.902	0.806	1	CLONAL	1	TRUE	0	0.491929444326394	1		352	282	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629328	187629328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772458580	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	148	519	1	ENST00000441802.2:c.1654G>A	p.Glu552Lys	p.E552K	ENST00000441802	NM_005245.3	552	Gaa/Aaa	2/27	0.491929444326394	3	FACETS	1	0.95	1	0.527	0.482	0.574	CLONAL	1	TRUE	1	0.491929444326394	3		520	711	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244158	153244158	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	195	523	2	ENST00000281708.4:c.1999G>T	p.Gly667Trp	p.G667W	ENST00000281708	NM_033632.3	667	Ggg/Tgg	12/12	0.491929444326394	3	FACETS	1	0.967	1	0.539	0.499	0.58	CLONAL	1	TRUE	1	0.491929444326394	3		525	917	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120863	115120863	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	423	516	0	ENST00000257566.3:c.143C>A	p.Pro48His	p.P48H	ENST00000257566	NM_016569.3	48	cCc/cAc	1/8	0.491929444326394	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	0	0.491929444326394	3		516	679	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575666	48575667	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TC	TC	-	rs377767328	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	54	240	0	ENST00000342988.3:c.430_431del	p.Ser144ArgfsTer7	p.S144Rfs*7	ENST00000342988	NM_005359.5	142	gaTCtc/gatc	4/12	0.491929444326394	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.491929444326394	1		240	158	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030338	11030340	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	310	468	0	ENST00000327064.4:c.1091_1093del	p.Glu364del	p.E364del	ENST00000327064	NM_199141.1	363	aAAGaa/aaa	9/16	0.491929444326394	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.491929444326394	2		468	591	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46608737	46608737	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	305	470	0	ENST00000263734.3:c.2048C>A	p.Ser683Tyr	p.S683Y	ENST00000263734	NM_001430.4	683	tCt/tAt	13/16	0.491929444326394	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.491929444326394	3		470	722	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573654	48573654	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	89	372	0	ENST00000342988.3:c.238G>T	p.Gly80Trp	p.G80W	ENST00000342988	NM_005359.5	80	Ggg/Tgg	2/12	0.491929444326394	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.491929444326394	1		372	253	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166125	118166125	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	371	571	2	ENST00000369448.3:c.635G>T	p.Gly212Val	p.G212V	ENST00000369448	NM_017709.3	212	gGg/gTg	2/2	0.491929444326394	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.491929444326394	2		573	747	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121529	108121529	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	410	429	0	ENST00000278616.4:c.1337A>T	p.Gln446Leu	p.Q446L	ENST00000278616	NM_000051.3	446	cAg/cTg	10/63	0.491929444326394	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	TRUE	1	0.491929444326394	4		429	808	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245891	46245891	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	413	441	0	ENST00000334344.6:c.3985G>T	p.Glu1329Ter	p.E1329*	ENST00000334344	NM_152641.2	1329	Gaa/Taa	15/21	0.491929444326394	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	0	0.491929444326394	3		441	683	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061172	38061172	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	585	525	0	ENST00000250448.2:c.817G>T	p.Gly273Trp	p.G273W	ENST00000250448	NM_004496.3	273	Ggg/Tgg	2/2	0.491929444326394	5	FACETS	1	0.989	1	1	0.989	1	CLONAL	4	TRUE	1	0.491929444326394	5		525	987	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799243	88799243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	291	447	1	ENST00000360948.2:c.142C>T	p.Pro48Ser	p.P48S	ENST00000360948	NM_001012338.2	48	Ccg/Tcg	2/19	0.491929444326394	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.491929444326394	2		448	556	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821427	72821427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	303	461	0	ENST00000268489.5:c.10748C>T	p.Thr3583Ile	p.T3583I	ENST00000268489	NM_006885.3	3583	aCc/aTc	10/10	0.411687396878645	4	FACETS	0.95	0.897	1	0.95	0.897	1	CLONAL	2	TRUE	2	0.491929444326394	4		461	967	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528087	29528088	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	96	149	0	ENST00000356175.3:c.1095_1096del	p.Gly367GlnfsTer11	p.G367Qfs*11	ENST00000356175	NM_000267.3	365	tcAAga/tcga	10/57	0.487027714685719	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.491929444326394	2		149	183	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556953	29556953	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	41	157	0	ENST00000356175.3:c.2951G>T	p.Gly984Val	p.G984V	ENST00000356175	NM_000267.3	984	gGg/gTg	22/57	0.487027714685719	2	FACETS	1	0.953	1	0.667	0.569	0.77	CLONAL	1	TRUE	0	0.491929444326394	2		157	125	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905764	50905764	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	394	625	0	ENST00000440232.2:c.812G>T	p.Gly271Val	p.G271V	ENST00000440232	NM_002691.3	271	gGg/gTg	7/27	0.491929444326394	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.491929444326394	2		625	781	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028233	48028233	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587781673	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	163	365	0	ENST00000234420.5:c.3111C>G	p.Phe1037Leu	p.F1037L	ENST00000234420	NM_000179.2	1037	ttC/ttG	4/10	0.491929444326394	3	FACETS	1	0.975	1	0.572	0.526	0.62	CLONAL	1	TRUE	1	0.491929444326394	3		365	722	SUCCESS
ETAA1	54465	MSKCC	GRCh37	2	67637160	67637160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	90	315	0	ENST00000272342.5:c.2771C>T	p.Ser924Leu	p.S924L	ENST00000272342	NM_019002.3	924	tCa/tTa	6/6	0.491929444326394	3	FACETS	1	0.919	1	1	0.919	1	CLONAL	2	TRUE	1	0.491929444326394	3		315	224	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288897	212288897	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	143	383	0	ENST00000342788.4:c.2849A>T	p.Tyr950Phe	p.Y950F	ENST00000342788	NM_005235.2	950	tAc/tTc	23/28	0.411687396878645	4	FACETS	0.861	0.79	0.934	0.861	0.79	0.934	CLONAL	2	TRUE	2	0.491929444326394	4		383	504	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660919	227660919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	317	578	0	ENST00000305123.5:c.2536G>A	p.Asp846Asn	p.D846N	ENST00000305123	NM_005544.2	846	Gac/Aac	1/2	0.411687396878645	4	FACETS	0.891	0.842	0.942	0.891	0.842	0.942	CLONAL	2	TRUE	2	0.491929444326394	4		578	1079	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138376660	138376661	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	98	279	0	ENST00000289153.2:c.2813_2814del	p.Phe938TrpfsTer10	p.F938Wfs*10	ENST00000289153	NM_006219.2	938	tTT/t	20/22	0.491929444326394	3	FACETS	1	0.926	1	0.52	0.466	0.577	CLONAL	1	TRUE	1	0.491929444326394	3		279	477	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274969	142274969	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	173	300	0	ENST00000350721.4:c.2091A>T	p.Lys697Asn	p.K697N	ENST00000350721	NM_001184.3	697	aaA/aaT	10/47	0.491929444326394	3	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	1	0.491929444326394	3		300	431	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114349	143114349	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	140	293	0	ENST00000262992.4:c.1073-1G>T		p.X358_splice	ENST00000262992	NM_001101669.1	358			0.491929444326394	3	FACETS	0.838	0.771	0.908	0.838	0.771	0.908	CLONAL	2	TRUE	1	0.491929444326394	3		293	423	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180049789	180049789	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	255	380	0	ENST00000261937.6:c.1599G>T	p.Lys533Asn	p.K533N	ENST00000261937	NM_182925.4	533	aaG/aaT	12/30	0.46051593456009	4	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	2	0.491929444326394	4		380	771	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052983	180052983	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	340	576	1	ENST00000261937.6:c.1307C>A	p.Ser436Ter	p.S436*	ENST00000261937	NM_182925.4	436	tCg/tAg	10/30	0.46051593456009	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	2	0.491929444326394	4		577	1015	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271470	26271470	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	200	639	0	ENST00000305910.3:c.143C>A	p.Ala48Asp	p.A48D	ENST00000305910	NM_003534.2	48	gCt/gAt	1/1	0.470116533261868	1	FACETS	0.782	0.726	0.84	0.782	0.726	0.84	SUBCLONAL	1	TRUE	0	0.491929444326394	1		639	784	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335028	81335028	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	136	334	1	ENST00000222390.5:c.1799C>A	p.Pro600His	p.P600H	ENST00000222390	NM_000601.4	600	cCt/cAt	16/18	0.491929444326394	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	1	0.491929444326394	3		335	330	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508395	106508395	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	122	472	0	ENST00000359195.3:c.390del	p.Ser131AlafsTer27	p.S131Afs*27	ENST00000359195	NM_002649.2	130	cGg/cg	2/11	0.491929444326394	3	FACETS	0.834	0.754	0.918	0.417	0.377	0.459	CLONAL	1	TRUE	1	0.491929444326394	3		472	741	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151868349	151868349	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	148	379	0	ENST00000262189.6:c.9453G>T	p.Gln3151His	p.Q3151H	ENST00000262189	NM_170606.2	3151	caG/caT	40/59	0.491929444326394	3	FACETS	1	0.973	1	0.575	0.527	0.625	CLONAL	1	TRUE	1	0.491929444326394	3		379	652	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995598	68995598	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	59	313	0	ENST00000288368.4:c.2002G>T	p.Val668Phe	p.V668F	ENST00000288368	NM_024870.2	668	Gtt/Ttt	18/40	0.168412827972106	3	FACETS	0.934	0.809	1	0.311	0.269	0.356	INDETERMINATE	1	TRUE	0	0.491929444326394	3		313	320	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341740	8341740	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	142	422	0	ENST00000356435.5:c.4900C>A	p.Gln1634Lys	p.Q1634K	ENST00000356435		1634	Caa/Aaa	29/35	0.491929444326394	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.491929444326394	1		422	375	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484260	8484260	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	114	384	0	ENST00000356435.5:c.3272G>T	p.Ser1091Ile	p.S1091I	ENST00000356435		1091	aGt/aTt	19/35	0.491929444326394	1	FACETS	0.979	0.891	1	0.979	0.891	1	CLONAL	1	TRUE	0	0.491929444326394	1		384	357	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231032	98231032	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	347	374	0	ENST00000331920.6:c.2250+1G>T		p.X750_splice	ENST00000331920	NM_000264.3	750			0.491929444326394	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	0	0.491929444326394	3		374	558	SUCCESS
BTK	695	MSKCC	GRCh37	X	100614296	100614296	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058758-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	214	126	0	ENST00000308731.7:c.879A>T	p.Gln293His	p.Q293H	ENST00000308731	NM_000061.2	293	caA/caT	10/19	0.377796511345669	2	FACETS	0.901	0.858	0.942			1	CLONAL	3	TRUE	NA	0.491929444326394	2		126	322	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435201	18435202	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1565550462	NA	P-0058760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	154	404	0	ENST00000266497.5:c.192dup	p.Val65CysfsTer16	p.V65Cfs*16	ENST00000266497		62	-/T	1/31	0.128014532342173	5	FACETS	0.772	0.71	0.836	0.386	0.355	0.418	INDETERMINATE	2	TRUE	1	0.786227680245644	5		404	553	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0058760-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	178	293	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.128014532342173	5	FACETS	0.877	0.821	0.934	0.658	0.615	0.7	INDETERMINATE	3	TRUE	1	0.786227680245644	5		293	375	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	82	306	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		306	393	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888210	112888210	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121918464	NA	P-0058761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	43	601	0	ENST00000351677.2:c.226G>C	p.Glu76Gln	p.E76Q	ENST00000351677	NM_002834.3	76	Gag/Cag	3/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		601	517	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888210	112888210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121918464	NA	P-0058761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	16	601	0	ENST00000351677.2:c.226G>A	p.Glu76Lys	p.E76K	ENST00000351677	NM_002834.3	76	Gag/Aag	3/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		601	517	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624263	89624264	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs587776671	NA	P-0058761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	79	193	0	ENST00000371953.3:c.39_40del	p.Arg14GlufsTer29	p.R14Efs*29	ENST00000371953	NM_000314.4	13	AAa/a	1/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		193	206	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548947	29548947	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1555613206	NA	P-0058761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	19	138	0	ENST00000356175.3:c.1721G>A	p.Ser574Asn	p.S574N	ENST00000356175	NM_000267.3	574	aGc/aAc	15/57	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		138	145	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33434395	33434395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782848	NA	P-0058761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	158	907	0	ENST00000345365.6:c.335G>A	p.Gly112Asp	p.G112D	ENST00000345365	NM_002878.3	112	gGc/gAc	4/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		907	664	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630377	47630377	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058761-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	182	677	1	ENST00000233146.2:c.47A>G	p.Glu16Gly	p.E16G	ENST00000233146	NM_000251.2	16	gAg/gGg	1/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		678	648	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0058774-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	58	432	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		432	363	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	119	306	0				ENST00000310581	NM_198253.2	-/1132			0.190164906536377	3	FACETS	0.844	0.764	0.928	0.844	0.764	0.928	CLONAL	2	TRUE	1	0.277220544702772	3		306	579	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0058778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	118	616	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.197634276678628	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.277220544702772	1		616	654	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030486	49030486	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0058778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	46	263	4	ENST00000267163.4:c.1960+1G>T		p.X654_splice	ENST00000267163	NM_000321.2	654			0.277220544702772	1	FACETS	0.94	0.796	1	0.94	0.796	1	CLONAL	1	TRUE	0	0.277220544702772	1		267	304	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871992	45871992	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	81	463	0	ENST00000391945.4:c.256G>C	p.Glu86Gln	p.E86Q	ENST00000391945	NM_000400.3	86	Gag/Cag	5/23	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.277220544702772	2		463	518	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510305	187510305	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs758757364	NA	P-0058778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	84	575	0	ENST00000441802.2:c.13208A>G	p.Tyr4403Cys	p.Y4403C	ENST00000441802	NM_005245.3	4403	tAt/tGt	27/27	1	2	FACETS	0.921	0.814	1	0.921	0.814	1	CLONAL	1	TRUE	1	0.277220544702772	2		575	658	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375287	118375287	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1290291018	NA	P-0058778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	63	584	0	ENST00000534358.1:c.8680A>G	p.Met2894Val	p.M2894V	ENST00000534358	NM_005933.3	2894	Atg/Gtg	27/36	1	2	FACETS	0.831	0.719	0.952	0.831	0.719	0.952	CLONAL	1	TRUE	1	0.277220544702772	2		584	547	SUCCESS
SMARCE1	6605	MSKCC	GRCh37	17	38792779	38792779	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0058778-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	75	354	0	ENST00000348513.6:c.238-1G>C		p.X80_splice	ENST00000348513	NM_003079.4	80			0.209966374828311	2	FACETS	1	0.975	1	0.735	0.648	0.827	CLONAL	1	TRUE	0	0.277220544702772	2		354	368	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0058811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	54	584	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.419094721194582	2		584	243	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0058811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	283	379	1	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.379749571376157	2	FACETS	0.947	0.895	0.999	0.947	0.895	0.999	CLONAL	2	TRUE	0	0.419094721194582	2		380	713	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006827	47006827	+	5_prime_UTR_variant	5'UTR	SNP	C	C	T	novel	NA	P-0058811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	74	384	0	ENST00000377604.3:c.-54C>T		p.*18*	ENST00000377604	NM_001204468.1	-/852		2/24	0.17666773389112	3	FACETS	0.543	0.475	0.617	0.181	0.158	0.206	INDETERMINATE	1	TRUE	0	0.419094721194582	3		384	786	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0058811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	202	351	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.33290702505742	4	FACETS	0.874	0.817	0.931	0.874	0.817	0.931	CLONAL	3	TRUE	1	0.419094721194582	4		351	522	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748195	41748195	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	37	397	0	ENST00000226382.2:c.574C>A	p.Pro192Thr	p.P192T	ENST00000226382	NM_003924.3	192	Ccg/Acg	3/3	1	2	FACETS	0.307	0.252	0.368	0.307	0.252	0.368	SUBCLONAL	1	TRUE	1	0.419094721194582	2		397	575	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213874	66213874	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	52	312	0	ENST00000273854.3:c.2556C>A	p.Phe852Leu	p.F852L	ENST00000273854	NM_004439.5	852	ttC/ttA	15/18	1	2	FACETS	0.495	0.422	0.576	0.495	0.422	0.576	SUBCLONAL	1	TRUE	1	0.419094721194582	2		312	501	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953605	38953605	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058811-T01-IM7	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	59	237	0	ENST00000357387.3:c.2748G>T	p.Lys916Asn	p.K916N	ENST00000357387	NM_152756.3	916	aaG/aaT	28/38	0.379329788275268	3	FACETS	0.801	0.691	0.92	0.401	0.345	0.46	CLONAL	1	TRUE	1	0.419094721194582	3		237	425	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	169	339	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.477835719224837	2	FACETS	0.878	0.808	0.95	0.439	0.404	0.475	CLONAL	1	FALSE	0	0.477835719224837	2		339	806	SUCCESS
AR	367	MSKCC	GRCh37	X	66766350	66766351	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGT	rs746958859	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	27	29	0	ENST00000374690.3:c.1368_1370dup	p.Gly473dup	p.G473dup	ENST00000374690	NM_000044.3	473	-/GGT	1/8	0.173272683118745	6	FACETS	1	0.911	1			1	INDETERMINATE	2	FALSE	NA	0.477835719224837	6		29	91	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199714	11199714	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	89	155	0	ENST00000361445.4:c.4874G>C	p.Gly1625Ala	p.G1625A	ENST00000361445	NM_004958.3	1625	gGc/gCc	35/58	0.477835719224837	1	FACETS	0.581	0.517	0.649	0.581	0.517	0.649	SUBCLONAL	1	FALSE	0	0.477835719224837	1		155	488	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11205033	11205033	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	134	267	0	ENST00000361445.4:c.4756G>C	p.Ala1586Pro	p.A1586P	ENST00000361445	NM_004958.3	1586	Gca/Cca	33/58	0.477835719224837	1	FACETS	0.549	0.499	0.602	0.549	0.499	0.602	SUBCLONAL	1	FALSE	0	0.477835719224837	1		267	777	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294278	11294278	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	89	206	0	ENST00000361445.4:c.2253G>C	p.Glu751Asp	p.E751D	ENST00000361445	NM_004958.3	751	gaG/gaC	14/58	0.477835719224837	1	FACETS	0.56	0.498	0.626	0.56	0.498	0.626	SUBCLONAL	1	FALSE	0	0.477835719224837	1		206	506	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258048	16258048	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	81	119	0	ENST00000375759.3:c.5313G>C	p.Glu1771Asp	p.E1771D	ENST00000375759	NM_015001.2	1771	gaG/gaC	11/15	0.477835719224837	1	FACETS	0.719	0.638	0.804	0.719	0.638	0.804	SUBCLONAL	1	FALSE	0	0.477835719224837	1		119	359	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259495	16259495	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	50	96	0	ENST00000375759.3:c.6760C>G	p.Gln2254Glu	p.Q2254E	ENST00000375759	NM_015001.2	2254	Cag/Gag	11/15	0.477835719224837	1	FACETS	0.59	0.504	0.682	0.59	0.504	0.682	SUBCLONAL	1	FALSE	0	0.477835719224837	1		96	270	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094349	27094349	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	68	146	0	ENST00000324856.7:c.3057G>C	p.Glu1019Asp	p.E1019D	ENST00000324856	NM_006015.4	1019	gaG/gaC	11/20	0.477835719224837	1	FACETS	0.563	0.492	0.638	0.563	0.492	0.638	SUBCLONAL	1	FALSE	0	0.477835719224837	1		146	385	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814592	43814592	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	163	265	0	ENST00000372470.3:c.1387G>C	p.Ala463Pro	p.A463P	ENST00000372470	NM_005373.2	463	Gcc/Ccc	9/12	0.477835719224837	1	FACETS	0.61	0.56	0.662	0.61	0.56	0.662	SUBCLONAL	1	FALSE	0	0.477835719224837	1		265	851	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818263	43818263	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	211	309	0	ENST00000372470.3:c.1728G>C	p.Glu576Asp	p.E576D	ENST00000372470	NM_005373.2	576	gaG/gaC	12/12	0.477835719224837	1	FACETS	0.792	0.736	0.849	0.792	0.736	0.849	SUBCLONAL	1	FALSE	0	0.477835719224837	1		309	849	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509356	46509356	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	75	125	0	ENST00000262741.5:c.1375C>G	p.Leu459Val	p.L459V	ENST00000262741	NM_003629.3	459	Ctt/Gtt	10/10	0.477835719224837	1	FACETS	0.605	0.533	0.682	0.605	0.533	0.682	SUBCLONAL	1	FALSE	0	0.477835719224837	1		125	395	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436062	51436062	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	105	186	0	ENST00000262662.1:c.22G>C	p.Glu8Gln	p.E8Q	ENST00000262662		8	Gag/Cag	3/4	0.477835719224837	1	FACETS	0.575	0.516	0.637	0.575	0.516	0.637	SUBCLONAL	1	FALSE	0	0.477835719224837	1		186	582	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459046	120459046	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	85	192	0	ENST00000256646.2:c.6299G>C	p.Gly2100Ala	p.G2100A	ENST00000256646	NM_024408.3	2100	gGc/gCc	34/34	0.477835719224837	1	FACETS	0.544	0.482	0.609	0.544	0.482	0.609	SUBCLONAL	1	FALSE	0	0.477835719224837	1		192	498	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874172	155874172	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs753425443	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	109	213	0	ENST00000368323.3:c.359G>C	p.Arg120Pro	p.R120P	ENST00000368323	NM_006912.5	120	cGa/cCa	5/6	0.477835719224837	1	FACETS	0.41	0.368	0.455	0.41	0.368	0.455	SUBCLONAL	1	FALSE	0	0.477835719224837	1		213	847	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851379	156851379	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1268901114	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	27	119	0	ENST00000524377.1:c.2336C>G	p.Ala779Gly	p.A779G	ENST00000524377	NM_002529.3	779	gCc/gGc	17/17	0.477835719224837	1	FACETS	0.295	0.235	0.363	0.295	0.235	0.363	SUBCLONAL	1	FALSE	0	0.477835719224837	1		119	292	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176145047	176145047	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	94	204	0	ENST00000367669.3:c.564G>C	p.Leu188Phe	p.L188F	ENST00000367669	NM_022457.5	188	ttG/ttC	3/20	0.477835719224837	1	FACETS	0.382	0.339	0.427	0.382	0.339	0.427	SUBCLONAL	1	FALSE	0	0.477835719224837	1		204	784	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649641	206649641	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	116	76	0	ENST00000367120.3:c.476G>C	p.Gly159Ala	p.G159A	ENST00000367120	NM_014002.3	159	gGc/gCc	6/22	0.477835719224837	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	0	0.477835719224837	1		76	333	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653821	206653821	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	68	163	0	ENST00000367120.3:c.1372C>G	p.Leu458Val	p.L458V	ENST00000367120	NM_014002.3	458	Ctg/Gtg	13/22	0.477835719224837	1	FACETS	0.384	0.334	0.438	0.384	0.334	0.438	SUBCLONAL	1	FALSE	0	0.477835719224837	1		163	564	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474101	29474101	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	48	183	1	ENST00000389048.3:c.2074G>C	p.Gly692Arg	p.G692R	ENST00000389048	NM_004304.4	692	Ggg/Cgg	12/29	0.477835719224837	1	FACETS	0.379	0.321	0.443	0.379	0.321	0.443	SUBCLONAL	1	FALSE	0	0.477835719224837	1		184	403	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172167	99172167	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	54	154	0	ENST00000074304.5:c.1733G>C	p.Ser578Thr	p.S578T	ENST00000074304	NM_001134224.1	578	aGc/aCc	17/26	0.477835719224837	1	FACETS	0.396	0.339	0.459	0.396	0.339	0.459	SUBCLONAL	1	FALSE	0	0.477835719224837	1		154	434	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131261	202131261	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	92	165	0	ENST00000358485.4:c.229G>C	p.Asp77His	p.D77H	ENST00000358485	NM_001080125.1	77	Gat/Cat	2/9	0.477835719224837	1	FACETS	0.616	0.549	0.686	0.616	0.549	0.686	SUBCLONAL	1	FALSE	0	0.477835719224837	1		165	476	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371704	225371704	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	114	188	0	ENST00000264414.4:c.900C>G	p.Tyr300Ter	p.Y300*	ENST00000264414	NM_003590.4	300	taC/taG	7/16	0.477835719224837	1	FACETS	0.526	0.474	0.58	0.526	0.474	0.58	SUBCLONAL	1	FALSE	0	0.477835719224837	1		188	691	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225449660	225449660	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	137	316	0	ENST00000264414.4:c.66+1G>C		p.X22_splice	ENST00000264414	NM_003590.4	22			0.477835719224837	1	FACETS	0.482	0.438	0.529	0.482	0.438	0.529	SUBCLONAL	1	FALSE	0	0.477835719224837	1		316	905	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794836	242794836	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	53	128	0	ENST00000334409.5:c.373G>C	p.Ala125Pro	p.A125P	ENST00000334409	NM_005018.2	125	Gcc/Ccc	2/5	0.477835719224837	1	FACETS	0.5	0.428	0.577	0.5	0.428	0.577	SUBCLONAL	1	FALSE	0	0.477835719224837	1		128	338	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103679	47103679	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	123	218	0	ENST00000409792.3:c.6267G>C	p.Glu2089Asp	p.E2089D	ENST00000409792	NM_014159.6	2089	gaG/gaC	14/21	0.151153533000461	6	FACETS	1	0.981	1			1	INDETERMINATE	1	FALSE	NA	0.477835719224837	6		218	746	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696244	52696244	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	206	301	0	ENST00000394830.3:c.433C>G	p.Leu145Val	p.L145V	ENST00000394830	NM_018313.4	145	Ctt/Gtt	5/30	0.151153533000461	6	FACETS	0.848	0.787	0.912			1	INDETERMINATE	2	FALSE	NA	0.477835719224837	6		301	994	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259131	89259131	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	84	110	0	ENST00000336596.2:c.275C>G	p.Ala92Gly	p.A92G	ENST00000336596	NM_005233.5	92	gCt/gGt	3/17	0.477835719224837	1	FACETS	0.562	0.498	0.63	0.562	0.498	0.63	SUBCLONAL	1	FALSE	0	0.477835719224837	1		110	476	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920315	134920315	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	87	192	0	ENST00000398015.3:c.2131-1G>C		p.X711_splice	ENST00000398015	NM_004441.4	711			0.477835719224837	1	FACETS	0.602	0.536	0.673	0.602	0.536	0.673	SUBCLONAL	1	FALSE	0	0.477835719224837	1		192	460	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664489	138664489	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	32	52	0	ENST00000330315.3:c.1076C>G	p.Ser359Cys	p.S359C	ENST00000330315	NM_023067.3	359	tCt/tGt	1/1	0.477835719224837	1	FACETS	0.645	0.53	0.771	0.645	0.53	0.771	SUBCLONAL	1	FALSE	0	0.477835719224837	1		52	158	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188981	142188981	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	182	196	0	ENST00000350721.4:c.6266G>C	p.Arg2089Pro	p.R2089P	ENST00000350721	NM_001184.3	2089	cGa/cCa	37/47	0.477835719224837	1	FACETS	0.634	0.585	0.685	0.634	0.585	0.685	SUBCLONAL	1	FALSE	0	0.477835719224837	1		196	914	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805418	1805418	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	111	163	0	ENST00000260795.2:c.931-1G>A		p.X311_splice	ENST00000260795		311			0.477835719224837	1	FACETS	0.66	0.595	0.727	0.66	0.595	0.727	SUBCLONAL	1	FALSE	0	0.477835719224837	1		163	536	SUCCESS
FIP1L1	81608	MSKCC	GRCh37	4	54280879	54280879	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	75	106	0	ENST00000358575.5:c.868C>A	p.Pro290Thr	p.P290T	ENST00000358575	NM_001134937.1	290	Cct/Act	10/18	0.477835719224837	1	FACETS	0.511	0.449	0.577	0.511	0.449	0.577	SUBCLONAL	1	FALSE	0	0.477835719224837	1		106	468	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593383	55593383	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	117	204	0	ENST00000288135.5:c.1541-1G>C		p.X514_splice	ENST00000288135	NM_000222.2	514			0.477835719224837	1	FACETS	0.557	0.503	0.614	0.557	0.503	0.614	SUBCLONAL	1	FALSE	0	0.477835719224837	1		204	669	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594176	55594176	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	78	159	0	ENST00000288135.5:c.1880-1G>C		p.X627_splice	ENST00000288135	NM_000222.2	627			0.477835719224837	1	FACETS	0.519	0.457	0.585	0.519	0.457	0.585	SUBCLONAL	1	FALSE	0	0.477835719224837	1		159	479	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604709	55604709	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	54	141	0	ENST00000288135.5:c.2917C>G	p.His973Asp	p.H973D	ENST00000288135	NM_000222.2	973	Cac/Gac	21/21	0.477835719224837	1	FACETS	0.446	0.382	0.515	0.446	0.382	0.515	SUBCLONAL	1	FALSE	0	0.477835719224837	1		141	386	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972024	55972024	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	99	214	0	ENST00000263923.4:c.1620G>C	p.Glu540Asp	p.E540D	ENST00000263923	NM_002253.2	540	gaG/gaC	12/30	0.477835719224837	1	FACETS	0.491	0.439	0.547	0.491	0.439	0.547	SUBCLONAL	1	FALSE	0	0.477835719224837	1		214	642	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532732	187532732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	90	234	0	ENST00000441802.2:c.9661C>T	p.Leu3221Phe	p.L3221F	ENST00000441802	NM_005245.3	3221	Ctt/Ttt	14/27	0.477835719224837	1	FACETS	0.362	0.321	0.406	0.362	0.321	0.406	SUBCLONAL	1	FALSE	0	0.477835719224837	1		234	792	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541934	187541934	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs780270871	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	112	223	0	ENST00000441802.2:c.5806C>G	p.Leu1936Val	p.L1936V	ENST00000441802	NM_005245.3	1936	Ctc/Gtc	10/27	0.477835719224837	1	FACETS	0.529	0.477	0.585	0.529	0.477	0.585	SUBCLONAL	1	FALSE	0	0.477835719224837	1		223	674	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584540	187584540	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	106	188	0	ENST00000441802.2:c.3493G>C	p.Asp1165His	p.D1165H	ENST00000441802	NM_005245.3	1165	Gat/Cat	3/27	0.477835719224837	1	FACETS	0.548	0.492	0.607	0.548	0.492	0.607	SUBCLONAL	1	FALSE	0	0.477835719224837	1		188	616	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959383	38959383	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1250474891	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	106	160	0	ENST00000357387.3:c.2092C>G	p.Leu698Val	p.L698V	ENST00000357387	NM_152756.3	698	Cta/Gta	22/38	0.477835719224837	1	FACETS	0.494	0.443	0.548	0.494	0.443	0.548	SUBCLONAL	1	FALSE	0	0.477835719224837	1		160	684	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576550	67576550	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	94	169	0	ENST00000274335.5:c.829G>C	p.Ala277Pro	p.A277P	ENST00000274335		277	Gca/Cca	5/15	0.477835719224837	1	FACETS	0.611	0.546	0.68	0.611	0.546	0.68	SUBCLONAL	1	FALSE	0	0.477835719224837	1		169	490	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911491	131911491	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	104	163	0	ENST00000265335.6:c.236G>C	p.Arg79Thr	p.R79T	ENST00000265335		79	aGa/aCa	3/25	0.477835719224837	1	FACETS	0.642	0.577	0.71	0.642	0.577	0.71	SUBCLONAL	1	FALSE	0	0.477835719224837	1		163	516	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940691	131940691	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	80	137	0	ENST00000265335.6:c.2718G>C	p.Lys906Asn	p.K906N	ENST00000265335		906	aaG/aaC	16/25	0.477835719224837	1	FACETS	0.55	0.486	0.619	0.55	0.486	0.619	SUBCLONAL	1	FALSE	0	0.477835719224837	1		137	463	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449754	149449754	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	55	111	0	ENST00000286301.3:c.1310A>T	p.His437Leu	p.H437L	ENST00000286301	NM_005211.3	437	cAc/cTc	9/22	0.477835719224837	1	FACETS	0.474	0.406	0.546	0.474	0.406	0.546	SUBCLONAL	1	FALSE	0	0.477835719224837	1		111	370	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827184	170827184	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	147	164	0	ENST00000296930.5:c.552G>C	p.Glu184Asp	p.E184D	ENST00000296930	NM_002520.6	184	gaG/gaC	7/11	0.477835719224837	1	FACETS	0.75	0.687	0.816	0.75	0.687	0.816	SUBCLONAL	1	FALSE	0	0.477835719224837	1		164	624	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665424	176665424	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	97	190	0	ENST00000439151.2:c.4108C>A	p.Gln1370Lys	p.Q1370K	ENST00000439151	NM_022455.4	1370	Cag/Aag	7/23	0.477835719224837	1	FACETS	0.537	0.48	0.598	0.537	0.48	0.598	SUBCLONAL	1	FALSE	0	0.477835719224837	1		190	575	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043980	180043980	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1205297853	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	86	173	0	ENST00000261937.6:c.3016C>G	p.Leu1006Val	p.L1006V	ENST00000261937	NM_182925.4	1006	Ctg/Gtg	22/30	0.477835719224837	1	FACETS	0.606	0.538	0.678	0.606	0.538	0.678	SUBCLONAL	1	FALSE	0	0.477835719224837	1		173	452	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056417	26056417	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs114826548	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	97	121	0	ENST00000343677.2:c.240C>G	p.Ile80Met	p.I80M	ENST00000343677	NM_005319.3	80	atC/atG	1/1	NA	2	FACETS	0.896	0.803	0.994			1	INDETERMINATE	1	FALSE	NA	0.477835719224837	2		121	453	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139036	37139036	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	85	148	0	ENST00000373509.5:c.376G>T	p.Val126Leu	p.V126L	ENST00000373509	NM_002648.3	126	Gtg/Ttg	4/6	0.477835719224837	1	FACETS	0.472	0.417	0.53	0.472	0.417	0.53	SUBCLONAL	1	FALSE	0	0.477835719224837	1		148	574	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781164	161781164	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	132	269	0	ENST00000366898.1:c.1241C>G	p.Thr414Ser	p.T414S	ENST00000366898	NM_004562.2	414	aCc/aGc	11/12	0.477835719224837	1	FACETS	0.599	0.545	0.656	0.599	0.545	0.656	SUBCLONAL	1	FALSE	0	0.477835719224837	1		269	702	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853111	151853111	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	70	80	0	ENST00000262189.6:c.11844G>C	p.Gln3948His	p.Q3948H	ENST00000262189	NM_170606.2	3948	caG/caC	46/59	0.477835719224837	1	FACETS	0.802	0.707	0.903	0.802	0.707	0.903	CLONAL	1	FALSE	0	0.477835719224837	1		80	278	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971054	21971054	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	71	133	0	ENST00000304494.5:c.304G>C	p.Ala102Pro	p.A102P	ENST00000304494	NM_000077.4	102	Gcg/Ccg	2/3	0.477835719224837	1	FACETS	0.705	0.62	0.794	0.705	0.62	0.794	SUBCLONAL	1	FALSE	0	0.477835719224837	1		133	321	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971060	21971060	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	56	141	0	ENST00000304494.5:c.298G>C	p.Ala100Pro	p.A100P	ENST00000304494	NM_000077.4	100	Gcc/Ccc	2/3	0.477835719224837	1	FACETS	0.551	0.474	0.633	0.551	0.474	0.633	SUBCLONAL	1	FALSE	0	0.477835719224837	1		141	324	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549155	87549155	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	48	203	0	ENST00000277120.3:c.1712C>G	p.Ala571Gly	p.A571G	ENST00000277120		571	gCt/gGt	15/19	0.477835719224837	1	FACETS	0.341	0.289	0.399	0.341	0.289	0.399	SUBCLONAL	1	FALSE	0	0.477835719224837	1		203	448	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606514	93606514	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	48	174	0	ENST00000375746.1:c.334G>C	p.Gly112Arg	p.G112R	ENST00000375746	NM_001174167.1	112	Ggg/Cgg	2/14	0.477835719224837	1	FACETS	0.368	0.312	0.431	0.368	0.312	0.431	SUBCLONAL	1	FALSE	0	0.477835719224837	1		174	415	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231293	98231293	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1564033840	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	56	136	0	ENST00000331920.6:c.1990C>G	p.Leu664Val	p.L664V	ENST00000331920	NM_000264.3	664	Ctc/Gtc	14/24	0.477835719224837	1	FACETS	0.483	0.416	0.557	0.483	0.416	0.557	SUBCLONAL	1	FALSE	0	0.477835719224837	1		136	369	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391824	139391824	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	65	161	0	ENST00000277541.6:c.6367C>T	p.Gln2123Ter	p.Q2123*	ENST00000277541	NM_017617.3	2123	Cag/Tag	34/34	0.477835719224837	1	FACETS	0.57	0.497	0.649	0.57	0.497	0.649	SUBCLONAL	1	FALSE	0	0.477835719224837	1		161	363	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405160	139405160	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	58	174	0	ENST00000277541.6:c.2685C>G	p.Cys895Trp	p.C895W	ENST00000277541	NM_017617.3	895	tgC/tgG	17/34	0.477835719224837	1	FACETS	0.376	0.323	0.433	0.376	0.323	0.433	SUBCLONAL	1	FALSE	0	0.477835719224837	1		174	492	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409078	139409078	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	89	151	0	ENST00000277541.6:c.2091C>G	p.Ile697Met	p.I697M	ENST00000277541	NM_017617.3	697	atC/atG	13/34	0.477835719224837	1	FACETS	0.585	0.52	0.653	0.585	0.52	0.653	SUBCLONAL	1	FALSE	0	0.477835719224837	1		151	485	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404615	70404615	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	83	200	0	ENST00000373644.4:c.2129G>T	p.Trp710Leu	p.W710L	ENST00000373644	NM_030625.2	710	tGg/tTg	4/12	0.477835719224837	1	FACETS	0.455	0.402	0.512	0.455	0.402	0.512	SUBCLONAL	1	FALSE	0	0.477835719224837	1		200	581	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243247	123243247	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	119	240	0	ENST00000358487.5:c.2266G>C	p.Asp756His	p.D756H	ENST00000358487	NM_000141.4	756	Gac/Cac	17/18	0.477835719224837	1	FACETS	0.537	0.485	0.592	0.537	0.485	0.592	SUBCLONAL	1	FALSE	0	0.477835719224837	1		240	706	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279549	123279549	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	148	263	0	ENST00000358487.5:c.883G>C	p.Glu295Gln	p.E295Q	ENST00000358487	NM_000141.4	295	Gaa/Caa	7/18	0.477835719224837	1	FACETS	0.655	0.599	0.713	0.655	0.599	0.713	SUBCLONAL	1	FALSE	0	0.477835719224837	1		263	720	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127734	64127734	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	79	97	0	ENST00000334205.4:c.227C>G	p.Ala76Gly	p.A76G	ENST00000334205	NM_003942.2	76	gCc/gGc	3/17	0.477835719224837	1	FACETS	0.742	0.658	0.831	0.742	0.658	0.831	SUBCLONAL	1	FALSE	0	0.477835719224837	1		97	339	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416735	416735	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1388597811	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	109	172	0	ENST00000399788.2:c.3815C>G	p.Ala1272Gly	p.A1272G	ENST00000399788	NM_001042603.1	1272	gCc/gGc	23/28	NA	2	FACETS	0.889	0.802	0.981			1	INDETERMINATE	1	FALSE	NA	0.477835719224837	2		172	513	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12043921	12043921	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	108	201	0	ENST00000396373.4:c.1300C>G	p.Leu434Val	p.L434V	ENST00000396373	NM_001987.4	434	Ctg/Gtg	8/8	0.477835719224837	2	FACETS	0.836	0.753	0.923	0.418	0.376	0.462	CLONAL	1	FALSE	0	0.477835719224837	2		201	541	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287316	46287316	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	96	163	0	ENST00000334344.6:c.5261G>C	p.Arg1754Pro	p.R1754P	ENST00000334344	NM_152641.2	1754	cGa/cCa	19/21	0.477835719224837	2	FACETS	0.731	0.653	0.813	0.365	0.326	0.407	SUBCLONAL	1	FALSE	0	0.477835719224837	2		163	550	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415831	49415831	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	96	175	0	ENST00000301067.7:c.16516G>C	p.Glu5506Gln	p.E5506Q	ENST00000301067	NM_003482.3	5506	Gag/Cag	53/54	0.477835719224837	2	FACETS	0.721	0.644	0.803	0.361	0.322	0.402	SUBCLONAL	1	FALSE	0	0.477835719224837	2		175	557	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421682	49421682	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	155	250	0	ENST00000301067.7:c.14547C>G	p.Ser4849Arg	p.S4849R	ENST00000301067	NM_003482.3	4849	agC/agG	47/54	0.477835719224837	2	FACETS	0.81	0.742	0.881	0.405	0.371	0.441	CLONAL	1	FALSE	0	0.477835719224837	2		250	801	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435117	49435117	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	63	95	0	ENST00000301067.7:c.6436C>A	p.Pro2146Thr	p.P2146T	ENST00000301067	NM_003482.3	2146	Ccg/Acg	31/54	0.477835719224837	2	FACETS	1	0.903	1	0.519	0.454	0.588	CLONAL	1	FALSE	0	0.477835719224837	2		95	254	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495048	56495048	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	107	234	0	ENST00000267101.3:c.3405G>C	p.Gln1135His	p.Q1135H	ENST00000267101	NM_001982.3	1135	caG/caC	27/28	0.477835719224837	2	FACETS	0.661	0.593	0.732	0.33	0.296	0.366	SUBCLONAL	1	FALSE	0	0.477835719224837	2		234	678	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495656	56495656	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	110	131	0	ENST00000267101.3:c.3846C>G	p.Cys1282Trp	p.C1282W	ENST00000267101	NM_001982.3	1282	tgC/tgG	28/28	0.477835719224837	2	FACETS	1	0.96	1	0.557	0.504	0.613	CLONAL	1	FALSE	0	0.477835719224837	2		131	413	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109672	115109672	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	118	208	0	ENST00000257566.3:c.2206G>C	p.Asp736His	p.D736H	ENST00000257566	NM_016569.3	736	Gac/Cac	8/8	0.477835719224837	2	FACETS	0.803	0.726	0.884	0.402	0.363	0.442	CLONAL	1	FALSE	0	0.477835719224837	2		208	615	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112624	115112624	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	74	150	0	ENST00000257566.3:c.1116G>C	p.Glu372Asp	p.E372D	ENST00000257566	NM_016569.3	372	gaG/gaC	7/8	0.477835719224837	2	FACETS	0.815	0.718	0.919	0.408	0.359	0.46	CLONAL	1	FALSE	0	0.477835719224837	2		150	380	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416777	121416777	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	111	316	0	ENST00000257555.6:c.206G>C	p.Gly69Ala	p.G69A	ENST00000257555		69	gGc/gCc	1/10	0.477835719224837	2	FACETS	0.681	0.613	0.753	0.341	0.306	0.377	SUBCLONAL	1	FALSE	0	0.477835719224837	2		316	682	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560257	95560257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	46	107	0	ENST00000393063.1:c.5332G>C	p.Glu1778Gln	p.E1778Q	ENST00000393063	NM_030621.3	1778	Gag/Cag	25/28	0.477835719224837	2	FACETS	0.561	0.474	0.657	0.281	0.237	0.329	SUBCLONAL	1	FALSE	0	0.477835719224837	2		107	343	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241296	105241296	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	88	178	0	ENST00000349310.3:c.612C>A	p.Asn204Lys	p.N204K	ENST00000349310	NM_001014432.1	204	aaC/aaA	8/15	0.477835719224837	2	FACETS	0.501	0.444	0.563	0.251	0.222	0.282	SUBCLONAL	1	FALSE	0	0.477835719224837	2		178	735	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358538	67358538	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	60	149	0	ENST00000327367.4:c.46C>G	p.Leu16Val	p.L16V	ENST00000327367	NM_005902.3	16	Ctg/Gtg	1/9	0.477835719224837	1	FACETS	0.42	0.362	0.482	0.42	0.362	0.482	SUBCLONAL	1	FALSE	0	0.477835719224837	1		149	455	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420268	88420268	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	80	188	0	ENST00000360948.2:c.2418C>G	p.Cys806Trp	p.C806W	ENST00000360948	NM_001012338.2	806	tgC/tgG	19/19	0.477835719224837	1	FACETS	0.528	0.466	0.594	0.528	0.466	0.594	SUBCLONAL	1	FALSE	0	0.477835719224837	1		188	483	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467866	99467866	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	72	203	0	ENST00000268035.6:c.2735G>T	p.Gly912Val	p.G912V	ENST00000268035	NM_000875.3	912	gGg/gTg	13/21	0.477835719224837	1	FACETS	0.412	0.36	0.468	0.412	0.36	0.468	SUBCLONAL	1	FALSE	0	0.477835719224837	1		203	557	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396196	396196	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	103	178	0	ENST00000262320.3:c.830C>G	p.Ala277Gly	p.A277G	ENST00000262320	NM_003502.3	277	gCc/gGc	2/11	0.477835719224837	2	FACETS	0.859	0.772	0.95	0.429	0.386	0.475	CLONAL	1	FALSE	0	0.477835719224837	2		178	502	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857609	9857609	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	53	148	0	ENST00000330684.3:c.3792G>C	p.Glu1264Asp	p.E1264D	ENST00000330684	NM_001134407.1	1264	gaG/gaC	13/13	0.477835719224837	2	FACETS	0.596	0.51	0.69	0.298	0.255	0.345	SUBCLONAL	1	FALSE	0	0.477835719224837	2		148	372	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641471	23641471	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	133	341	0	ENST00000261584.4:c.2004G>C	p.Met668Ile	p.M668I	ENST00000261584	NM_024675.3	668	atG/atC	5/13	0.477835719224837	2	FACETS	0.712	0.647	0.78	0.356	0.323	0.39	SUBCLONAL	1	FALSE	0	0.477835719224837	2		341	782	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645423	67645423	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	52	97	0	ENST00000264010.4:c.688G>T	p.Glu230Ter	p.E230*	ENST00000264010	NM_006565.3	230	Gaa/Taa	3/12	0.477835719224837	2	FACETS	0.654	0.559	0.756	0.327	0.279	0.378	SUBCLONAL	1	FALSE	0	0.477835719224837	2		97	333	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842692	68842692	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	131	263	0	ENST00000261769.5:c.628G>C	p.Glu210Gln	p.E210Q	ENST00000261769	NM_004360.3	210	Gaa/Caa	5/16	0.477835719224837	2	FACETS	0.863	0.786	0.945	0.432	0.393	0.473	CLONAL	1	FALSE	0	0.477835719224837	2		263	635	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587781702	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	107	190	0	ENST00000269305.4:c.920-1G>C		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.382081680981482	3	FACETS	1	0.966	1	0.388	0.349	0.428	CLONAL	1	FALSE	0	0.477835719224837	3		190	477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578390	7578390	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	64	129	0	ENST00000269305.4:c.540G>C	p.Glu180Asp	p.E180D	ENST00000269305	NM_001126112.2	180	gaG/gaC	5/11	0.382081680981482	3	FACETS	1	0.874	1	0.334	0.291	0.38	CLONAL	1	FALSE	0	0.477835719224837	3		129	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	66	154	1	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	0.382081680981482	3	FACETS	0.807	0.703	0.919	0.269	0.234	0.307	CLONAL	1	FALSE	0	0.477835719224837	3		155	424	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974887	15974887	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	182	344	0	ENST00000268712.3:c.3988G>C	p.Gly1330Arg	p.G1330R	ENST00000268712	NM_006311.3	1330	Ggt/Cgt	30/46	0.382081680981482	3	FACETS	0.911	0.84	0.985	0.304	0.28	0.329	CLONAL	1	FALSE	0	0.477835719224837	3		344	1036	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15979006	15979006	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	83	180	0	ENST00000268712.3:c.3512C>G	p.Ala1171Gly	p.A1171G	ENST00000268712	NM_006311.3	1171	gCt/gGt	27/46	0.382081680981482	3	FACETS	0.996	0.884	1	0.332	0.294	0.372	CLONAL	1	FALSE	0	0.477835719224837	3		180	432	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681084	37681084	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	81	119	0	ENST00000447079.4:c.3253G>C	p.Ala1085Pro	p.A1085P	ENST00000447079	NM_015083.1	1085	Gca/Cca	12/14	0.382081680981482	3	FACETS	0.784	0.699	0.871	0.522	0.466	0.581	SUBCLONAL	2	FALSE	0	0.477835719224837	3		119	268	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526111	63526111	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	179	254	0	ENST00000307078.5:c.2515G>C	p.Val839Leu	p.V839L	ENST00000307078	NM_004655.3	839	Gtg/Ctg	11/11	0.382081680981482	3	FACETS	1	0.977	1	0.383	0.353	0.414	CLONAL	1	FALSE	0	0.477835719224837	3		254	808	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223034	1223034	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs367807476	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	119	157	0	ENST00000326873.7:c.971C>G	p.Pro324Arg	p.P324R	ENST00000326873	NM_000455.4	324	cCg/cGg	8/10	0.477835719224837	1	FACETS	0.63	0.57	0.693	0.63	0.57	0.693	SUBCLONAL	1	FALSE	0	0.477835719224837	1		157	602	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211757	2211757	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	220	330	0	ENST00000398665.3:c.1473C>G	p.Phe491Leu	p.F491L	ENST00000398665	NM_032482.2	491	ttC/ttG	16/28	0.477835719224837	1	FACETS	0.72	0.67	0.772	0.72	0.67	0.772	SUBCLONAL	1	FALSE	0	0.477835719224837	1		330	973	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254627	10254627	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	80	137	0	ENST00000340748.4:c.2883G>C	p.Lys961Asn	p.K961N	ENST00000340748		961	aaG/aaC	28/40	0.477835719224837	1	FACETS	0.574	0.507	0.645	0.574	0.507	0.645	SUBCLONAL	1	FALSE	0	0.477835719224837	1		137	444	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602432	10602432	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	138	269	0	ENST00000171111.5:c.1146C>G	p.Asn382Lys	p.N382K	ENST00000171111	NM_203500.1	382	aaC/aaG	3/6	0.477835719224837	1	FACETS	0.689	0.629	0.752	0.689	0.629	0.752	SUBCLONAL	1	FALSE	0	0.477835719224837	1		269	638	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602641	10602641	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	127	197	0	ENST00000171111.5:c.937C>G	p.Pro313Ala	p.P313A	ENST00000171111	NM_203500.1	313	Ccc/Gcc	3/6	0.477835719224837	1	FACETS	0.861	0.785	0.939	0.861	0.785	0.939	CLONAL	1	FALSE	0	0.477835719224837	1		197	470	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123705	11123705	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	109	181	0	ENST00000358026.2:c.2355G>C	p.Lys785Asn	p.K785N	ENST00000358026	NM_001128849.1	785	aaG/aaC	16/36	0.477835719224837	1	FACETS	0.752	0.679	0.828	0.752	0.679	0.828	SUBCLONAL	1	FALSE	0	0.477835719224837	1		181	462	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366932	15366932	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1270	384	487	0	ENST00000263377.2:c.1694C>G	p.Ala565Gly	p.A565G	ENST00000263377	NM_058243.2	565	gCc/gGc	9/20	0.477835719224837	1	FACETS	0.74	0.701	0.779	0.74	0.701	0.779	SUBCLONAL	1	FALSE	0	0.477835719224837	1		487	1654	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15379774	15379774	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	173	273	0	ENST00000263377.2:c.365C>G	p.Ala122Gly	p.A122G	ENST00000263377	NM_058243.2	122	gCt/gGt	3/20	0.477835719224837	1	FACETS	0.578	0.531	0.626	0.578	0.531	0.626	SUBCLONAL	1	FALSE	0	0.477835719224837	1		273	954	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945387	17945387	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	79	197	0	ENST00000458235.1:c.2343C>G	p.Ile781Met	p.I781M	ENST00000458235	NM_000215.3	781	atC/atG	17/24	0.477835719224837	1	FACETS	0.507	0.447	0.571	0.507	0.447	0.571	SUBCLONAL	1	FALSE	0	0.477835719224837	1		197	496	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953175	17953175	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	89	109	0	ENST00000458235.1:c.811C>G	p.Leu271Val	p.L271V	ENST00000458235	NM_000215.3	271	Ctc/Gtc	6/24	0.477835719224837	1	FACETS	0.841	0.753	0.934	0.841	0.753	0.934	CLONAL	1	FALSE	0	0.477835719224837	1		109	337	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42790996	42790996	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	237	207	0	ENST00000575354.2:c.141C>G	p.Ser47Arg	p.S47R	ENST00000575354	NM_015125.3	47	agC/agG	2/20	0.477835719224837	1	FACETS	0.813	0.759	0.868	0.813	0.759	0.868	CLONAL	1	FALSE	0	0.477835719224837	1		207	929	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022985	31022985	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs532964069	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	597	193	0	ENST00000375687.4:c.2470G>C	p.Glu824Gln	p.E824Q	ENST00000375687	NM_015338.5	824	Gag/Cag	13/13	0.419738763070556	6	FACETS	1	0.994	1			1	CLONAL	4	FALSE	NA	0.477835719224837	6		193	1100	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022992	31022992	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	602	194	0	ENST00000375687.4:c.2477G>T	p.Gly826Val	p.G826V	ENST00000375687	NM_015338.5	826	gGa/gTa	13/13	0.419738763070556	6	FACETS	1	0.993	1			1	CLONAL	4	FALSE	NA	0.477835719224837	6		194	1116	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206859	36206859	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	73	89	0	ENST00000300305.3:c.653G>C	p.Ser218Thr	p.S218T	ENST00000300305		218	aGc/aCc	6/8	0.470205754511887	0	FACETS	0.558	0.493	0.626			1	SUBCLONAL	1	FALSE	0	0.477835719224837	0		89	286	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845307	42845307	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	86	180	0	ENST00000398585.3:c.955G>C	p.Gly319Arg	p.G319R	ENST00000398585	NM_001135099.1	319	Gga/Cga	9/14	0.470205754511887	0	FACETS	0.381	0.338	0.427			1	SUBCLONAL	1	FALSE	0	0.477835719224837	0		180	493	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531911	41531911	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	115	216	0	ENST00000263253.7:c.1622+1G>C		p.X541_splice	ENST00000263253	NM_001429.3	541			0.470205754511887	0	FACETS	0.441	0.398	0.486			1	SUBCLONAL	1	FALSE	0	0.477835719224837	0		216	570	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874303	76874303	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	273	169	0	ENST00000373344.5:c.5419C>G	p.Leu1807Val	p.L1807V	ENST00000373344	NM_000489.3	1807	Ctc/Gtc	21/35	0.173272683118745	6	FACETS	1	0.986	1			1	INDETERMINATE	3	FALSE	NA	0.477835719224837	6		169	660	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179189	123179189	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	201	112	0	ENST00000218089.9:c.638G>C	p.Arg213Thr	p.R213T	ENST00000218089	NM_001042749.1	213	aGa/aCa	8/35	0.173272683118745	6	FACETS	1	0.95	1			1	INDETERMINATE	4	FALSE	NA	0.477835719224837	6		112	407	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190067	123190067	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	229	167	0	ENST00000218089.9:c.1286G>C	p.Gly429Ala	p.G429A	ENST00000218089	NM_001042749.1	429	gGa/gCa	14/35	0.173272683118745	6	FACETS	1	0.963	1			1	INDETERMINATE	3	FALSE	NA	0.477835719224837	6		167	603	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197055	123197055	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	286	163	0	ENST00000218089.9:c.1821G>C	p.Lys607Asn	p.K607N	ENST00000218089	NM_001042749.1	607	aaG/aaC	19/35	0.173272683118745	6	FACETS	1	0.968	1			1	INDETERMINATE	3	FALSE	NA	0.477835719224837	6		163	754	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263980	104263981	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	132	232	0	ENST00000369902.3:c.71_72insT	p.Ala25GlyfsTer23	p.A25Gfs*23	ENST00000369902	NM_016169.3	24	ccg/ccTg	1/12	0.477835719224837	1	FACETS	0.593	0.539	0.65	0.593	0.539	0.65	SUBCLONAL	1	FALSE	0	0.477835719224837	1		232	709	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176104222	176104222	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	35	91	0	ENST00000367669.3:c.892G>A	p.Glu298Lys	p.E298K	ENST00000367669	NM_022457.5	298	Gaa/Aaa	8/20	0.477835719224837	1	FACETS	0.246	0.201	0.296	0.246	0.201	0.296	SUBCLONAL	1	FALSE	0	0.477835719224837	1		91	454	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748112	41748112	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	33	87	0	ENST00000226382.2:c.657C>G	p.Ser219Arg	p.S219R	ENST00000226382	NM_003924.3	219	agC/agG	3/3	0.477835719224837	1	FACETS	0.553	0.455	0.662	0.553	0.455	0.662	SUBCLONAL	1	FALSE	0	0.477835719224837	1		87	190	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692854	89692854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	53	51	0	ENST00000371953.3:c.338G>C	p.Ser113Thr	p.S113T	ENST00000371953	NM_000314.4	113	aGt/aCt	5/9	0.477835719224837	1	FACETS	0.804	0.695	0.92	0.804	0.695	0.92	CLONAL	1	FALSE	0	0.477835719224837	1		51	210	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297921	15297921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1206256945	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	52	932	0	ENST00000263388.2:c.1835C>T	p.Thr612Ile	p.T612I	ENST00000263388	NM_000435.2	612	aCc/aTc	11/33	0.477835719224837	1	FACETS	0.642	0.551	0.74	0.642	0.551	0.74	SUBCLONAL	1	FALSE	0	0.477835719224837	1		932	258	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858091	45858092	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	94	167	0	ENST00000391945.4:c.1561_1562delinsAT	p.Gly521Met	p.G521M	ENST00000391945	NM_000400.3	521	GGg/ATg	17/23	0.477835719224837	1	FACETS	0.701	0.628	0.779	0.701	0.628	0.779	SUBCLONAL	1	FALSE	0	0.477835719224837	1		167	427	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599950	10599952	+	missense_variant	Missense_Mutation	TNP	CTC	CTC	GTT	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	173	290	0	ENST00000171111.5:c.1624_1626delinsAAC	p.Glu542Asn	p.E542N	ENST00000171111	NM_203500.1	542	GAG/AAC	5/6	0.477835719224837	1	FACETS	0.651	0.599	0.704	0.651	0.599	0.704	SUBCLONAL	1	FALSE	0	0.477835719224837	1		290	847	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020683	37020684	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0000083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	84	154	0	ENST00000358127.4:c.161_162delinsAA	p.Ile54Lys	p.I54K	ENST00000358127	NM_001280556.1	54	aTC/aAA	2/10	0.477835719224837	1	FACETS	0.674	0.599	0.753	0.674	0.599	0.753	SUBCLONAL	1	FALSE	0	0.477835719224837	1		154	397	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	168	561	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.29775048335836	2	FACETS	0.754	0.694	0.815	0.754	0.694	0.815	SUBCLONAL	2	TRUE	0	0.31	2		561	719	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297921	15297921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1206256945	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	166	932	0	ENST00000263388.2:c.1835C>T	p.Thr612Ile	p.T612I	ENST00000263388	NM_000435.2	612	aCc/aTc	11/33	0.29775048335836	2	FACETS	1	0.952	1	0.527	0.483	0.572	CLONAL	1	TRUE	0	0.31	2		932	1017	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	145	802	2	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	0.29775048335836	2	FACETS	1	0.982	1	0.644	0.589	0.702	CLONAL	1	TRUE	0	0.31	2		804	726	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098894	178098895	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	122	619	0	ENST00000397062.3:c.150dup	p.Gln51ThrfsTer5	p.Q51Tfs*5	ENST00000397062	NM_006164.4	50	-/A	2/5	0.29775048335836	2	FACETS	1	0.979	1	0.647	0.587	0.711	CLONAL	1	TRUE	0	0.31	2		619	608	SUCCESS
APC	324	MSKCC	GRCh37	5	112175060	112175060	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	56	275	0	ENST00000257430.4:c.3769G>T	p.Glu1257Ter	p.E1257*	ENST00000257430	NM_000038.5	1257	Gaa/Taa	16/16	0.29775048335836	2	FACETS	0.775	0.672	0.885	0.775	0.672	0.885	SUBCLONAL	2	TRUE	0	0.31	2		275	233	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590403	67590403	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	53	242	0	ENST00000274335.5:c.1465G>T	p.Glu489Ter	p.E489*	ENST00000274335		489	Gaa/Taa	11/15	0.29775048335836	2	FACETS	1	0.961	1	0.687	0.591	0.789	CLONAL	1	TRUE	0	0.31	2		242	249	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717699	89717699	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554825210	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	131	607	0	ENST00000371953.3:c.724G>T	p.Glu242Ter	p.E242*	ENST00000371953	NM_000314.4	242	Gag/Tag	7/9	0.29646572873215	2	FACETS	1	0.982	1	0.669	0.608	0.732	CLONAL	1	TRUE	0	0.31	2		607	632	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230813	66230813	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	69	480	2	ENST00000273854.3:c.2158G>T	p.Asp720Tyr	p.D720Y	ENST00000273854	NM_004439.5	720	Gat/Tat	12/18	0.29775048335836	2	FACETS	1	0.943	1	0.569	0.498	0.645	CLONAL	1	TRUE	0	0.31	2		482	391	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944943	31944943	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	175	618	0	ENST00000340398.3:c.158G>T	p.Arg53Leu	p.R53L	ENST00000340398	NM_001013699.2	53	cGt/cTt	1/1	0.29775048335836	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.31	1		618	678	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333960	70333960	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	110	470	0	ENST00000373644.4:c.1865G>T	p.Arg622Ile	p.R622I	ENST00000373644	NM_030625.2	622	aGa/aTa	2/12	0.29646572873215	2	FACETS	1	0.984	1	0.744	0.672	0.819	CLONAL	1	TRUE	0	0.31	2		470	477	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272506	21272506	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	260	946	0	ENST00000354336.3:c.284C>A	p.Thr95Asn	p.T95N	ENST00000354336	NM_005207.3	95	aCc/aAc	1/3	0.29646572873215	2	FACETS	0.83	0.778	0.883	0.83	0.778	0.883	CLONAL	2	TRUE	0	0.31	2		946	1011	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295229	1295229	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	125	224	0				ENST00000310581	NM_198253.2	-/1132			0.29775048335836	2	FACETS	0.908	0.828	0.991	0.908	0.828	0.991	CLONAL	2	TRUE	0	0.31	2		224	444	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101309	27101309	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	208	914	0	ENST00000324856.7:c.4591G>T	p.Glu1531Ter	p.E1531*	ENST00000324856	NM_006015.4	1531	Gaa/Taa	18/20	0.29775048335836	2	FACETS	1	0.991	1	0.748	0.695	0.803	CLONAL	1	TRUE	0	0.31	2		914	897	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032064	10032064	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	193	854	0	ENST00000330684.3:c.759C>A	p.Phe253Leu	p.F253L	ENST00000330684	NM_001134407.1	253	ttC/ttA	3/13	0.29646572873215	2	FACETS	0.75	0.695	0.807	0.75	0.695	0.807	SUBCLONAL	2	TRUE	0	0.31	2		854	830	SUCCESS
APC	324	MSKCC	GRCh37	5	112174262	112174262	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs786202995	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	70	474	0	ENST00000257430.4:c.2971G>T	p.Glu991Ter	p.E991*	ENST00000257430	NM_000038.5	991	Gaa/Taa	16/16	0.29775048335836	2	FACETS	1	0.973	1	0.724	0.636	0.816	CLONAL	1	TRUE	0	0.31	2		474	312	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565580	41565580	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	121	509	0	ENST00000263253.7:c.4246G>T	p.Glu1416Ter	p.E1416*	ENST00000263253	NM_001429.3	1416	Gaa/Taa	26/31	0.29646572873215	2	FACETS	0.901	0.821	0.985	0.901	0.821	0.985	CLONAL	2	TRUE	0	0.31	2		509	433	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40457661	40457661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1307657759	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	98	828	1	ENST00000345506.4:c.1414G>A	p.Gly472Ser	p.G472S	ENST00000345506	NM_003152.3	472	Ggc/Agc	13/20	0.29775048335836	2	FACETS	0.613	0.546	0.685	0.307	0.273	0.343	SUBCLONAL	1	TRUE	0	0.31	2		829	1031	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717715	89717715	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs1057519368	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	170	593	0	ENST00000371953.3:c.740T>G	p.Leu247Ter	p.L247*	ENST00000371953	NM_000314.4	247	tTa/tGa	7/9	0.29646572873215	2	FACETS	0.886	0.818	0.956	0.886	0.818	0.956	CLONAL	2	TRUE	0	0.31	2		593	619	SUCCESS
APC	324	MSKCC	GRCh37	5	112174365	112174365	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	57	339	0	ENST00000257430.4:c.3074T>G	p.Ile1025Arg	p.I1025R	ENST00000257430	NM_000038.5	1025	aTa/aGa	16/16	0.29775048335836	2	FACETS	0.803	0.697	0.915	0.803	0.697	0.915	CLONAL	2	TRUE	0	0.31	2		339	229	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591303	67591303	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	86	419	0	ENST00000274335.5:c.1801G>T	p.Glu601Ter	p.E601*	ENST00000274335		601	Gaa/Taa	13/15	0.29775048335836	2	FACETS	1	0.972	1	0.656	0.583	0.733	CLONAL	1	TRUE	0	0.31	2		419	423	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255939	16255939	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	196	632	0	ENST00000375759.3:c.3204G>C	p.Glu1068Asp	p.E1068D	ENST00000375759	NM_015001.2	1068	gaG/gaC	11/15	0.29775048335836	2	FACETS	1	0.99	1	0.725	0.672	0.78	CLONAL	1	TRUE	0	0.31	2		632	872	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39317428	39317428	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	125	662	0	ENST00000373001.3:c.758A>T	p.Asn253Ile	p.N253I	ENST00000373001	NM_022157.3	253	aAt/aTt	5/7	0.29775048335836	2	FACETS	0.755	0.687	0.827	0.755	0.687	0.827	SUBCLONAL	2	TRUE	0	0.31	2		662	534	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115272932	115272932	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	189	907	0	ENST00000438362.2:c.1441G>T	p.Glu481Ter	p.E481*	ENST00000438362	NM_001242891.1	481	Gaa/Taa	12/20	0.29775048335836	2	FACETS	1	0.989	1	0.717	0.664	0.773	CLONAL	1	TRUE	0	0.31	2		907	850	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166050	118166050	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	168	558	0	ENST00000369448.3:c.560T>G	p.Ile187Ser	p.I187S	ENST00000369448	NM_017709.3	187	aTc/aGc	2/2	0.29775048335836	2	FACETS	0.851	0.785	0.919	0.851	0.785	0.919	CLONAL	2	TRUE	0	0.31	2		558	637	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736346	243736346	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	132	440	0	ENST00000263826.5:c.701T>G	p.Phe234Cys	p.F234C	ENST00000263826	NM_005465.4	234	tTt/tGt	8/13	0.29775048335836	2	FACETS	0.771	0.703	0.842	0.771	0.703	0.842	SUBCLONAL	2	TRUE	0	0.31	2		440	552	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925322	114925322	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	175	666	0	ENST00000543371.1:c.1400A>C	p.Lys467Thr	p.K467T	ENST00000543371	NM_001198531.1	467	aAa/aCa	14/14	0.29646572873215	2	FACETS	0.784	0.724	0.846	0.784	0.724	0.846	SUBCLONAL	2	TRUE	0	0.31	2		666	720	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942179	71942179	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	320	956	0	ENST00000298229.2:c.1443G>T	p.Trp481Cys	p.W481C	ENST00000298229	NM_001567.3	481	tgG/tgT	12/28	0.29646572873215	2	FACETS	0.85	0.802	0.899	0.85	0.802	0.899	CLONAL	2	TRUE	0	0.31	2		956	1215	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911976	94911976	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	118	636	0	ENST00000536441.1:c.954G>T	p.Met318Ile	p.M318I	ENST00000536441	NM_144665.3	318	atG/atT	7/10	0.29646572873215	2	FACETS	0.806	0.732	0.884	0.806	0.732	0.884	CLONAL	2	TRUE	0	0.31	2		636	472	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94964005	94964005	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	55	166	0	ENST00000536441.1:c.20G>T	p.Ser7Ile	p.S7I	ENST00000536441	NM_144665.3	7	aGc/aTc	1/10	0.29646572873215	2	FACETS	0.792	0.686	0.905	0.792	0.686	0.905	CLONAL	2	TRUE	0	0.31	2		166	224	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909968	100909968	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	67	555	0	ENST00000325455.5:c.2681C>A	p.Thr894Lys	p.T894K	ENST00000325455	NM_001202474.3	894	aCa/aAa	8/8	0.29646572873215	2	FACETS	1	0.937	1	0.56	0.489	0.636	CLONAL	1	TRUE	0	0.31	2		555	386	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102098222	102098222	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	175	578	0	ENST00000282441.5:c.1186G>T	p.Glu396Ter	p.E396*	ENST00000282441	NM_001130145.2	396	Gag/Tag	8/9	0.29646572873215	2	FACETS	0.825	0.763	0.89	0.825	0.763	0.89	CLONAL	2	TRUE	0	0.31	2		578	684	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100545	102100545	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	189	691	0	ENST00000282441.5:c.1389G>T	p.Met463Ile	p.M463I	ENST00000282441	NM_001130145.2	463	atG/atT	9/9	0.29646572873215	2	FACETS	0.8	0.741	0.861	0.8	0.741	0.861	SUBCLONAL	2	TRUE	0	0.31	2		691	762	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374869	118374869	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	78	468	0	ENST00000534358.1:c.8262G>T	p.Glu2754Asp	p.E2754D	ENST00000534358	NM_005933.3	2754	gaG/gaT	27/36	0.29646572873215	2	FACETS	1	0.964	1	0.623	0.55	0.7	CLONAL	1	TRUE	0	0.31	2		468	404	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148948	119148948	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs267606707	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	134	631	0	ENST00000264033.4:c.1168G>T	p.Asp390Tyr	p.D390Y	ENST00000264033	NM_005188.3	390	Gat/Tat	8/16	0.29646572873215	2	FACETS	1	0.986	1	0.729	0.665	0.796	CLONAL	1	TRUE	0	0.31	2		631	593	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420357	49420357	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	232	817	0	ENST00000301067.7:c.15392T>C	p.Met5131Thr	p.M5131T	ENST00000301067	NM_003482.3	5131	aTg/aCg	48/54	0.29775048335836	3	FACETS	0.953	0.89	1	0.953	0.89	1	CLONAL	2	TRUE	1	0.31	3		817	907	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439908	49439908	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	234	788	0	ENST00000301067.7:c.4633C>G	p.Gln1545Glu	p.Q1545E	ENST00000301067	NM_003482.3	1545	Cag/Gag	17/54	0.29775048335836	3	FACETS	0.806	0.751	0.862	0.806	0.751	0.862	CLONAL	2	TRUE	1	0.31	3		788	1082	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481626	56481626	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	245	840	0	ENST00000267101.3:c.661C>G	p.Pro221Ala	p.P221A	ENST00000267101	NM_001982.3	221	Ccc/Gcc	6/28	0.29775048335836	3	FACETS	0.841	0.785	0.898	0.841	0.785	0.898	CLONAL	2	TRUE	1	0.31	3		840	1086	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915179	32915179	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	121	720	0	ENST00000380152.3:c.6687A>C	p.Glu2229Asp	p.E2229D	ENST00000380152		2229	gaA/gaC	11/27	0.231168790233854	3	FACETS	1	0.983	1	0.469	0.424	0.516	CLONAL	1	TRUE	0	0.31	3		720	641	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930601	32930601	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs185012573	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	257	484	0	ENST00000380152.3:c.7472A>G	p.Gln2491Arg	p.Q2491R	ENST00000380152		2491	cAg/cGg	15/27	0.231168790233854	3	FACETS	0.887	0.834	0.94	0.887	0.834	0.94	CLONAL	3	TRUE	0	0.31	3		484	720	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972677	32972677	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	219	624	0	ENST00000380152.3:c.10027G>T	p.Glu3343Ter	p.E3343*	ENST00000380152		3343	Gaa/Taa	27/27	0.231168790233854	3	FACETS	0.873	0.817	0.93	0.873	0.817	0.93	CLONAL	3	TRUE	0	0.31	3		624	623	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543274	65543274	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs201312694	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	165	640	0	ENST00000358664.4:c.403G>C	p.Asp135His	p.D135H	ENST00000358664	NM_002382.4	135	Gat/Cat	5/5	0.29646572873215	2	FACETS	1	0.989	1	0.741	0.682	0.803	CLONAL	1	TRUE	0	0.31	2		640	718	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571424	95571424	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	89	316	0	ENST00000393063.1:c.3253C>G	p.Leu1085Val	p.L1085V	ENST00000393063	NM_030621.3	1085	Ctt/Gtt	21/28	0.29646572873215	2	FACETS	1	0.98	1	0.75	0.669	0.834	CLONAL	1	TRUE	0	0.31	2		316	383	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701151	43701151	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	205	659	0	ENST00000382044.4:c.5544C>A	p.Tyr1848Ter	p.Y1848*	ENST00000382044	NM_001141980.1	1848	taC/taA	26/28	0.29775048335836	2	FACETS	0.824	0.766	0.883	0.824	0.766	0.883	CLONAL	2	TRUE	0	0.31	2		659	803	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2645801	2645801	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	151	596	0	ENST00000342085.4:c.1351T>C	p.Phe451Leu	p.F451L	ENST00000342085	NM_002613.4	451	Ttt/Ctt	12/14	0.29646572873215	2	FACETS	1	0.982	1	0.633	0.58	0.689	CLONAL	1	TRUE	0	0.31	2		596	769	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639309	3639309	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	289	1068	2	ENST00000294008.3:c.4330G>C	p.Glu1444Gln	p.E1444Q	ENST00000294008	NM_032444.2	1444	Gag/Cag	12/15	0.29646572873215	2	FACETS	0.807	0.759	0.857	0.807	0.759	0.857	CLONAL	2	TRUE	0	0.31	2		1070	1155	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3794916	3794916	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	158	564	0	ENST00000262367.5:c.3961G>T	p.Glu1321Ter	p.E1321*	ENST00000262367	NM_004380.2	1321	Gaa/Taa	23/31	0.29646572873215	2	FACETS	0.76	0.698	0.823	0.76	0.698	0.823	SUBCLONAL	2	TRUE	0	0.31	2		564	671	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819244	3819244	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs766440192	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	235	819	0	ENST00000262367.5:c.2991G>T	p.Met997Ile	p.M997I	ENST00000262367	NM_004380.2	997	atG/atT	15/31	0.29646572873215	2	FACETS	1	0.992	1	0.741	0.691	0.792	CLONAL	1	TRUE	0	0.31	2		819	1023	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026093	14026093	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	101	329	0	ENST00000311895.7:c.1053G>T	p.Met351Ile	p.M351I	ENST00000311895	NM_005236.2	351	atG/atT	6/11	0.29646572873215	2	FACETS	0.855	0.771	0.943	0.855	0.771	0.943	CLONAL	2	TRUE	0	0.31	2		329	381	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972504	81972504	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	183	654	1	ENST00000359376.3:c.3297C>A	p.Phe1099Leu	p.F1099L	ENST00000359376	NM_002661.3	1099	ttC/ttA	29/33	0.29646572873215	2	FACETS	0.78	0.721	0.84	0.78	0.721	0.84	SUBCLONAL	2	TRUE	0	0.31	2		655	757	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983569	7983569	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	217	629	0	ENST00000319144.4:c.738G>T	p.Lys246Asn	p.K246N	ENST00000319144	NM_001139.2	246	aaG/aaT	6/15	0.238037704430607	2	FACETS	0.807	0.752	0.865	0.807	0.752	0.865	CLONAL	2	TRUE	0	0.31	2		629	867	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029445	16029445	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	113	486	0	ENST00000268712.3:c.1585G>T	p.Glu529Ter	p.E529*	ENST00000268712	NM_006311.3	529	Gaa/Taa	15/46	0.238037704430607	2	FACETS	1	0.983	1	0.73	0.661	0.804	CLONAL	1	TRUE	0	0.31	2		486	499	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884223	37884223	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	246	832	0	ENST00000269571.5:c.3694G>T	p.Ala1232Ser	p.A1232S	ENST00000269571		1232	Gct/Tct	27/27	0.29775048335836	2	FACETS	0.795	0.744	0.848	0.795	0.744	0.848	SUBCLONAL	2	TRUE	0	0.31	2		832	998	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508294	38508294	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	209	724	0	ENST00000254066.5:c.602C>G	p.Ala201Gly	p.A201G	ENST00000254066	NM_000964.3	201	gCc/gGc	5/9	0.29775048335836	2	FACETS	0.757	0.703	0.812	0.757	0.703	0.812	SUBCLONAL	2	TRUE	0	0.31	2		724	891	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40451826	40451826	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	176	549	0	ENST00000345506.4:c.608C>G	p.Ala203Gly	p.A203G	ENST00000345506	NM_003152.3	203	gCc/gGc	7/20	0.29775048335836	2	FACETS	0.925	0.856	0.995	0.925	0.856	0.995	CLONAL	2	TRUE	0	0.31	2		549	614	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475124	40475124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758127158	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	146	782	1	ENST00000264657.5:c.1786G>A	p.Ala596Thr	p.A596T	ENST00000264657	NM_139276.2	596	Gcc/Acc	20/24	0.29775048335836	2	FACETS	1	0.967	1	0.561	0.512	0.612	CLONAL	1	TRUE	0	0.31	2		783	840	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41201202	41201202	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	193	727	0	ENST00000357654.3:c.5342A>G	p.Glu1781Gly	p.E1781G	ENST00000357654	NM_007294.3	1781	gAa/gGa	21/23	0.29775048335836	2	FACETS	0.771	0.714	0.829	0.771	0.714	0.829	SUBCLONAL	2	TRUE	0	0.31	2		727	808	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62009561	62009561	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	268	783	0	ENST00000392795.3:c.61C>G	p.Leu21Val	p.L21V	ENST00000392795	NM_001039933.1	21	Ctc/Gtc	1/6	0.29775048335836	2	FACETS	0.839	0.787	0.892	0.839	0.787	0.892	CLONAL	2	TRUE	0	0.31	2		783	1031	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119106	70119106	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	110	551	0	ENST00000245479.2:c.678G>C	p.Glu226Asp	p.E226D	ENST00000245479	NM_000346.3	226	gaG/gaC	2/3	0.29775048335836	2	FACETS	1	0.983	1	0.72	0.65	0.793	CLONAL	1	TRUE	0	0.31	2		551	493	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39573264	39573264	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1261163931	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	100	541	0	ENST00000262039.4:c.745A>G	p.Ser249Gly	p.S249G	ENST00000262039	NM_002647.2	249	Agt/Ggt	7/25	0.29775048335836	2	FACETS	0.777	0.699	0.859	0.777	0.699	0.859	SUBCLONAL	2	TRUE	0	0.31	2		541	415	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573583	48573583	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	75	342	0	ENST00000342988.3:c.167C>A	p.Ser56Tyr	p.S56Y	ENST00000342988	NM_005359.5	56	tCt/tAt	2/12	0.29775048335836	2	FACETS	1	0.974	1	0.712	0.628	0.8	CLONAL	1	TRUE	0	0.31	2		342	340	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11019809	11019809	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	222	729	0	ENST00000327064.4:c.484A>G	p.Met162Val	p.M162V	ENST00000327064	NM_199141.1	162	Atg/Gtg	4/16	0.29775048335836	2	FACETS	0.819	0.764	0.877	0.819	0.764	0.877	CLONAL	2	TRUE	0	0.31	2		729	874	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754067	42754067	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	217	718	0	ENST00000222329.4:c.285C>G	p.His95Gln	p.H95Q	ENST00000222329	NM_006494.2	95	caC/caG	3/4	0.29775048335836	2	FACETS	1	0.991	1	0.74	0.688	0.793	CLONAL	1	TRUE	0	0.31	2		718	946	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867545	45867545	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	329	1071	0	ENST00000391945.4:c.763A>C	p.Thr255Pro	p.T255P	ENST00000391945	NM_000400.3	255	Acc/Ccc	9/23	0.29775048335836	2	FACETS	0.842	0.795	0.89	0.842	0.795	0.89	CLONAL	2	TRUE	0	0.31	2		1071	1260	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909714	50909714	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	616	984	0	ENST00000440232.2:c.1434C>G	p.Ser478Arg	p.S478R	ENST00000440232	NM_002691.3	478	agC/agG	12/27	0.29775048335836	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	3	TRUE	0	0.31	2		984	1228	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940547	29940547	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	106	574	0	ENST00000389048.3:c.684A>T	p.Glu228Asp	p.E228D	ENST00000389048	NM_004304.4	228	gaA/gaT	2/29	0.29775048335836	2	FACETS	1	0.98	1	0.684	0.616	0.755	CLONAL	1	TRUE	0	0.31	2		574	500	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605158	46605158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1457723486	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	133	734	1	ENST00000263734.3:c.1375G>A	p.Val459Met	p.V459M	ENST00000263734	NM_001430.4	459	Gtg/Atg	10/16	0.29775048335836	2	FACETS	1	0.969	1	0.575	0.523	0.63	CLONAL	1	TRUE	0	0.31	2		735	746	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705613	47705613	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	80	450	0	ENST00000233146.2:c.2413C>G	p.Leu805Val	p.L805V	ENST00000233146	NM_000251.2	805	Ctc/Gtc	14/16	0.29775048335836	2	FACETS	1	0.978	1	0.744	0.66	0.832	CLONAL	1	TRUE	0	0.31	2		450	347	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873257	136873257	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	139	466	0	ENST00000241393.3:c.241T>G	p.Ser81Ala	p.S81A	ENST00000241393	NM_003467.2	81	Tca/Gca	2/2	0.29775048335836	2	FACETS	0.804	0.735	0.875	0.804	0.735	0.875	CLONAL	2	TRUE	0	0.31	2		466	558	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137378	202137378	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	92	428	0	ENST00000358485.4:c.606C>A	p.Phe202Leu	p.F202L	ENST00000358485	NM_001080125.1	202	ttC/ttA	4/9	0.29775048335836	2	FACETS	1	0.976	1	0.674	0.602	0.751	CLONAL	1	TRUE	0	0.31	2		428	440	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645706	215645706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	101	684	0	ENST00000260947.4:c.892G>A	p.Val298Met	p.V298M	ENST00000260947	NM_000465.2	298	Gtg/Atg	4/11	0.29775048335836	2	FACETS	1	0.975	1	0.646	0.58	0.716	CLONAL	1	TRUE	0	0.31	2		684	504	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30954262	30954262	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	96	467	0	ENST00000375687.4:c.133G>T	p.Glu45Ter	p.E45*	ENST00000375687	NM_015338.5	45	Gaa/Taa	2/13	0.151758680601038	2	FACETS	0.759	0.681	0.841	0.759	0.681	0.841	INDETERMINATE	2	TRUE	0	0.31	2		467	408	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159103	24159103	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	178	579	0	ENST00000263121.7:c.775G>C	p.Asp259His	p.D259H	ENST00000263121	NM_003073.3	259	Gac/Cac	6/9	0.29646572873215	2	FACETS	0.776	0.717	0.837	0.776	0.717	0.837	SUBCLONAL	2	TRUE	0	0.31	2		579	740	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130552	29130552	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs753204096	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	242	744	0	ENST00000328354.6:c.158C>G	p.Ser53Cys	p.S53C	ENST00000328354	NM_007194.3	53	tCt/tGt	2/15	0.29646572873215	2	FACETS	0.886	0.829	0.944	0.886	0.829	0.944	CLONAL	2	TRUE	0	0.31	2		744	881	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41562649	41562649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	101	452	0	ENST00000263253.7:c.3853G>T	p.Glu1285Ter	p.E1285*	ENST00000263253	NM_001429.3	1285	Gaa/Taa	23/31	0.29646572873215	2	FACETS	1	0.981	1	0.713	0.641	0.789	CLONAL	1	TRUE	0	0.31	2		452	457	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280784	41280784	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	130	549	0	ENST00000349496.5:c.2297T>A	p.Leu766Gln	p.L766Q	ENST00000349496	NM_001904.3	766	cTg/cAg	15/15	0.29775048335836	2	FACETS	1	0.984	1	0.692	0.63	0.757	CLONAL	1	TRUE	0	0.31	2		549	606	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163110	47163110	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	75	463	0	ENST00000409792.3:c.3016A>C	p.Asn1006His	p.N1006H	ENST00000409792	NM_014159.6	1006	Aat/Cat	3/21	0.29775048335836	2	FACETS	1	0.977	1	0.749	0.662	0.841	CLONAL	1	TRUE	0	0.31	2		463	323	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723755	49723755	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	17	40	0	ENST00000449682.2:c.1007A>T	p.Tyr336Phe	p.Y336F	ENST00000449682	NM_020998.3	336	tAc/tTc	8/18	0.29775048335836	2	FACETS	0.892	0.702	1	1	0.905	1	CLONAL	3	TRUE	0	0.31	2		40	41	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940094	49940094	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	217	935	0	ENST00000296474.3:c.949C>G	p.Pro317Ala	p.P317A	ENST00000296474	NM_002447.2	317	Ccc/Gcc	1/20	0.29775048335836	2	FACETS	1	0.991	1	0.713	0.663	0.764	CLONAL	1	TRUE	0	0.31	2		935	982	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428241	72428241	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	132	592	0	ENST00000477973.2:c.651A>G	p.Ile217Met	p.I217M	ENST00000477973	NM_012234.5	217	atA/atG	3/4	0.29775048335836	2	FACETS	1	0.985	1	0.722	0.657	0.789	CLONAL	1	TRUE	0	0.31	2		592	590	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281328	142281328	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	118	659	0	ENST00000350721.4:c.916G>T	p.Glu306Ter	p.E306*	ENST00000350721	NM_001184.3	306	Gaa/Taa	4/47	0.29775048335836	2	FACETS	1	0.984	1	0.736	0.667	0.808	CLONAL	1	TRUE	0	0.31	2		659	517	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936037	178936037	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	34	130	0	ENST00000263967.3:c.1579G>T	p.Asp527Tyr	p.D527Y	ENST00000263967	NM_006218.2	527	Gac/Tac	10/21	0.29775048335836	2	FACETS	0.979	0.819	1	0.979	0.819	1	CLONAL	2	TRUE	0	0.31	2		130	112	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803563	1803563	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	139	459	0	ENST00000260795.2:c.741G>C	p.Glu247Asp	p.E247D	ENST00000260795		247	gaG/gaC	6/17	0.29775048335836	2	FACETS	1	0.986	1	0.713	0.651	0.777	CLONAL	1	TRUE	0	0.31	2		459	629	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1918635	1918635	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	205	573	0	ENST00000382891.5:c.798C>A	p.Phe266Leu	p.F266L	ENST00000382891	NM_133335.3	266	ttC/ttA	4/22	0.29775048335836	2	FACETS	0.816	0.759	0.876	0.816	0.759	0.876	CLONAL	2	TRUE	0	0.31	2		573	810	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127289	55127289	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	134	617	0	ENST00000257290.5:c.77C>A	p.Ser26Ter	p.S26*	ENST00000257290	NM_006206.4	26	tCa/tAa	3/23	0.29775048335836	2	FACETS	1	0.985	1	0.716	0.652	0.782	CLONAL	1	TRUE	0	0.31	2		617	604	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157624	106157624	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	67	358	0	ENST00000380013.4:c.2525C>A	p.Ser842Ter	p.S842*	ENST00000380013	NM_001127208.2	842	tCa/tAa	3/11	0.29775048335836	2	FACETS	1	0.966	1	0.663	0.58	0.751	CLONAL	1	TRUE	0	0.31	2		358	326	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244077	153244077	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	154	593	0	ENST00000281708.4:c.2080G>T	p.Glu694Ter	p.E694*	ENST00000281708	NM_033632.3	694	Gaa/Taa	12/12	0.29775048335836	2	FACETS	1	0.987	1	0.718	0.659	0.78	CLONAL	1	TRUE	0	0.31	2		593	692	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526829	31526829	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	224	1002	0	ENST00000344624.3:c.211T>G	p.Phe71Val	p.F71V	ENST00000344624		71	Ttt/Gtt	2/33	0.29775048335836	2	FACETS	1	0.991	1	0.713	0.663	0.763	CLONAL	1	TRUE	0	0.31	2		1002	1014	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589307	67589307	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	50	323	0	ENST00000274335.5:c.1295A>C	p.Gln432Pro	p.Q432P	ENST00000274335		432	cAa/cCa	9/15	0.29775048335836	2	FACETS	1	0.958	1	0.678	0.581	0.782	CLONAL	1	TRUE	0	0.31	2		323	238	SUCCESS
APC	324	MSKCC	GRCh37	5	112178988	112178988	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	87	404	0	ENST00000257430.4:c.7697G>T	p.Arg2566Ile	p.R2566I	ENST00000257430	NM_000038.5	2566	aGa/aTa	16/16	0.29775048335836	2	FACETS	0.761	0.678	0.847	0.761	0.678	0.847	SUBCLONAL	2	TRUE	0	0.31	2		404	369	SUCCESS
APC	324	MSKCC	GRCh37	5	112179270	112179270	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs775012353	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	76	476	0	ENST00000257430.4:c.7979G>T	p.Arg2660Ile	p.R2660I	ENST00000257430	NM_000038.5	2660	aGa/aTa	16/16	0.29775048335836	2	FACETS	1	0.968	1	0.647	0.571	0.728	CLONAL	1	TRUE	0	0.31	2		476	379	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687127	176687127	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	164	645	0	ENST00000439151.2:c.5104C>A	p.His1702Asn	p.H1702N	ENST00000439151	NM_022455.4	1702	Cat/Aat	14/23	0.29775048335836	2	FACETS	0.767	0.706	0.83	0.767	0.706	0.83	SUBCLONAL	2	TRUE	0	0.31	2		645	690	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910606	29910607	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	270	922	0	ENST00000376809.5:c.149dup	p.Tyr51LeufsTer48	p.Y51Lfs*48	ENST00000376809	NM_002116.7	49	gtg/gtGg	2/8	0.238037704430607	2	FACETS	0.9	0.845	0.956	0.9	0.845	0.956	CLONAL	2	TRUE	0	0.31	2		922	968	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680576	30680576	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	164	721	0	ENST00000376406.3:c.1143A>T	p.Glu381Asp	p.E381D	ENST00000376406	NM_014641.2	381	gaA/gaT	5/15	0.238037704430607	2	FACETS	1	0.988	1	0.725	0.667	0.785	CLONAL	1	TRUE	0	0.31	2		721	730	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37141769	37141769	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	209	658	0	ENST00000373509.5:c.844G>T	p.Glu282Ter	p.E282*	ENST00000373509	NM_002648.3	282	Gaa/Taa	6/6	0.238037704430607	2	FACETS	0.848	0.789	0.909	0.848	0.789	0.909	CLONAL	2	TRUE	0	0.31	2		658	795	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196114	138196114	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	134	425	0	ENST00000237289.4:c.428A>G	p.Gln143Arg	p.Q143R	ENST00000237289	NM_001270507.1	143	cAa/cGa	3/9	0.29646572873215	2	FACETS	0.768	0.701	0.838	0.768	0.701	0.838	SUBCLONAL	2	TRUE	0	0.31	2		425	563	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001539	150001539	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	108	568	0	ENST00000253339.5:c.2065G>T	p.Glu689Ter	p.E689*	ENST00000253339		689	Gaa/Taa	4/7	0.29646572873215	2	FACETS	1	0.983	1	0.748	0.675	0.824	CLONAL	1	TRUE	0	0.31	2		568	466	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946210	13946210	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	143	579	0	ENST00000405192.2:c.886G>C	p.Glu296Gln	p.E296Q	ENST00000405192	NM_001163147.1	296	Gag/Cag	10/12	0.238037704430607	2	FACETS	1	0.987	1	0.746	0.683	0.813	CLONAL	1	TRUE	0	0.31	2		579	618	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878671	151878671	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	108	634	0	ENST00000262189.6:c.6274G>T	p.Asp2092Tyr	p.D2092Y	ENST00000262189	NM_170606.2	2092	Gat/Tat	36/59	0.238037704430607	2	FACETS	1	0.983	1	0.733	0.662	0.809	CLONAL	1	TRUE	0	0.31	2		634	475	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880129	151880129	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	130	578	1	ENST00000262189.6:c.5195A>T	p.Asp1732Val	p.D1732V	ENST00000262189	NM_170606.2	1732	gAt/gTt	35/59	0.238037704430607	2	FACETS	0.796	0.725	0.869	0.796	0.725	0.869	SUBCLONAL	2	TRUE	0	0.31	2		579	527	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346229	152346229	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	146	676	0	ENST00000359321.1:c.341G>T	p.Arg114Ile	p.R114I	ENST00000359321	NM_005431.1	114	aGa/aTa	3/3	0.238037704430607	2	FACETS	1	0.987	1	0.744	0.681	0.809	CLONAL	1	TRUE	0	0.31	2		676	633	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271192	38271192	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	216	733	0	ENST00000425967.3:c.2516C>A	p.Pro839His	p.P839H	ENST00000425967	NM_001174067.1	839	cCc/cAc	19/19	0.238037704430607	2	FACETS	0.94	0.877	1	0.94	0.877	1	CLONAL	2	TRUE	0	0.31	2		733	741	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279318	38279318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs982371464	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	257	905	0	ENST00000425967.3:c.1171G>A	p.Glu391Lys	p.E391K	ENST00000425967	NM_001174067.1	391	Gaa/Aaa	9/19	0.238037704430607	2	FACETS	0.795	0.744	0.847	0.795	0.744	0.847	SUBCLONAL	2	TRUE	0	0.31	2		905	1043	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033172	69033172	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	116	607	0	ENST00000288368.4:c.3612G>T	p.Met1204Ile	p.M1204I	ENST00000288368	NM_024870.2	1204	atG/atT	30/40	0.238037704430607	2	FACETS	1	0.975	1	0.621	0.561	0.684	CLONAL	1	TRUE	0	0.31	2		607	603	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136846	69136846	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	142	466	0	ENST00000288368.4:c.4760C>G	p.Pro1587Arg	p.P1587R	ENST00000288368	NM_024870.2	1587	cCa/cGa	39/40	0.238037704430607	2	FACETS	0.767	0.702	0.835	0.767	0.702	0.835	SUBCLONAL	2	TRUE	0	0.31	2		466	597	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967767	90967767	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	51	218	0	ENST00000265433.3:c.1141C>A	p.Pro381Thr	p.P381T	ENST00000265433	NM_002485.4	381	Cca/Aca	10/16	0.238037704430607	2	FACETS	0.81	0.698	0.93	0.81	0.698	0.93	CLONAL	2	TRUE	0	0.31	2		218	203	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141570479	141570479	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	204	724	0	ENST00000220592.5:c.649A>G	p.Ile217Val	p.I217V	ENST00000220592	NM_012154.3	217	Att/Gtt	5/19	0.238037704430607	2	FACETS	0.75	0.697	0.806	0.75	0.697	0.806	SUBCLONAL	2	TRUE	0	0.31	2		724	877	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970964	21970964	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	232	729	2	ENST00000304494.5:c.394G>T	p.Ala132Ser	p.A132S	ENST00000304494	NM_000077.4	132	Gcg/Tcg	2/3	0.29775048335836	2	FACETS	0.78	0.728	0.834	0.78	0.728	0.834	SUBCLONAL	2	TRUE	0	0.31	2		731	959	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250378	110250378	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs767551221	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	255	1054	1	ENST00000374672.4:c.297C>A	p.Phe99Leu	p.F99L	ENST00000374672	NM_004235.4	99	ttC/ttA	3/5	0.29775048335836	2	FACETS	0.845	0.792	0.9	0.845	0.792	0.9	CLONAL	2	TRUE	0	0.31	2		1055	973	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128432114	128432114	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	131	500	0	ENST00000265960.3:c.332G>T	p.Arg111Ile	p.R111I	ENST00000265960	NM_001006617.1	111	aGa/aTa	3/12	0.29775048335836	2	FACETS	1	0.986	1	0.735	0.669	0.803	CLONAL	1	TRUE	0	0.31	2		500	575	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779122	135779122	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1328198866	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	177	530	0	ENST00000298552.3:c.2124G>C	p.Lys708Asn	p.K708N	ENST00000298552	NM_001162426.1	708	aaG/aaC	17/23	0.137206132812046	5	FACETS	1	0.974	1	0.561	0.518	0.606	INDETERMINATE	2	TRUE	1	0.31	5		530	745	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417622	139417622	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	333	964	0	ENST00000277541.6:c.422C>G	p.Ala141Gly	p.A141G	ENST00000277541	NM_017617.3	141	gCt/gGt	4/34	NA	2	FACETS	0.779	0.735	0.824			1	INDETERMINATE	2	TRUE	NA	0.31	2		964	1379	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30323856	30323856	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001002-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	408	374	0	ENST00000322652.5:c.1834G>T	p.Glu612Ter	p.E612*	ENST00000322652	NM_015355.2	612	Gaa/Taa	15/16	0.760196099092611	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.798254001697687	3		374	464	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971198	21971228	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCATCATGACCTGCCAGAGAGAACAGAATGG	TCATCATGACCTGCCAGAGAGAACAGAATGG	-	novel	NA	P-0001002-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	17	87	0	ENST00000304494.5:c.151-21_160del		p.X51_splice	ENST00000304494	NM_000077.4	51		2/3	0.798254001697687	2	FACETS	0.56	0.428	0.71	0.28	0.214	0.355	SUBCLONAL	1	TRUE	0	0.798254001697687	2		87	76	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002202-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	74	390	0	ENST00000342988.3:c.1610A>T	p.Asp537Val	p.D537V	ENST00000342988	NM_005359.5	537	gAc/gTc	12/12	0.23548194109259	2	FACETS	1	0.966	1	0.646	0.567	0.731	CLONAL	1	TRUE	0	0.23604445161402	2		390	485	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287502	33287502	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0002202-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	167	514	0	ENST00000374542.5:c.1595T>A	p.Leu532Ter	p.L532*	ENST00000374542	NM_001141970.1	532	tTa/tAa	6/8	0.192074596070893	3	FACETS	1	0.965	1	0.722	0.665	0.782	CLONAL	2	TRUE	0	0.23604445161402	3		514	730	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575526	64575526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565648547	NA	P-0002202-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	160	542	2	ENST00000312049.6:c.491C>T	p.Ala164Val	p.A164V	ENST00000312049	NM_130799.2	164	gCc/gTc	3/10	0.23604445161402	2	FACETS	0.949	0.873	1	0.949	0.873	1	CLONAL	2	TRUE	0	0.23604445161402	2		544	714	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955521	90955521	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002202-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	39	390	0	ENST00000265433.3:c.2144A>G	p.Lys715Arg	p.K715R	ENST00000265433	NM_002485.4	715	aAg/aGg	14/16	0.23604445161402	5	FACETS	0.673	0.556	0.803	0.224	0.185	0.268	SUBCLONAL	1	TRUE	2	0.23604445161402	5		390	665	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023559	27023560	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	36	299	0	ENST00000324856.7:c.671dup	p.Pro225AlafsTer175	p.P225Afs*175	ENST00000324856	NM_006015.4	222	tac/taCc	1/20	0.40984694592841	3	FACETS	0.784	0.648	0.935	0.392	0.324	0.468	CLONAL	1	TRUE	1	0.40984694592841	3		299	270	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460515	149460515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777239066	NA	P-0004458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	171	756	1	ENST00000286301.3:c.122G>A	p.Arg41Gln	p.R41Q	ENST00000286301	NM_005211.3	41	cGa/cAa	3/22	0.40984694592841	4	FACETS	0.922	0.852	0.995	0.922	0.852	0.995	CLONAL	2	TRUE	2	0.40984694592841	4		757	638	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023052	31023052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148575778	NA	P-0004458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	131	586	0	ENST00000375687.4:c.2537G>A	p.Ser846Asn	p.S846N	ENST00000375687	NM_015338.5	846	aGt/aAt	13/13	0.40984694592841	4	FACETS	0.98	0.895	1	0.98	0.895	1	CLONAL	2	TRUE	2	0.40984694592841	4		586	460	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230752	53230752	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	162	339	0	ENST00000375401.3:c.2041C>T	p.Arg681Ter	p.R681*	ENST00000375401	NM_004187.3	681	Cga/Tga	14/26	0.40984694592841	2	FACETS	0.941	0.884	0.998			1	CLONAL	3	TRUE	NA	0.40984694592841	2		339	280	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183865	10183866	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0004458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	111	508	0	ENST00000256474.2:c.335dup	p.Tyr112Ter	p.Y112*	ENST00000256474	NM_000551.3	112	tac/tAac	1/3	0.300523762085509	3	FACETS	1	0.933	1	0.686	0.625	0.749	CLONAL	2	TRUE	0	0.40984694592841	3		508	317	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108259	8108267	+	inframe_deletion	In_Frame_Del	DEL	GAGACCTGG	GAGACCTGG	-	novel	NA	P-0004458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	104	713	0	ENST00000585124.1:c.957_965del	p.Gln320_Ser322del	p.Q320_S322del	ENST00000585124	NM_004217.3	319	gcCCAGGTCTCa/gca	9/9	0.40984694592841	3	FACETS	1	0.973	1	0.621	0.559	0.687	CLONAL	1	TRUE	1	0.40984694592841	3		713	492	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643328	52643329	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	CGATTCATCCTTCTTGCTCGTTCCAATACTT	novel	NA	P-0004458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	56	269	0	ENST00000394830.3:c.2537_2567dup	p.Thr857SerfsTer17	p.T857Sfs*17	ENST00000394830	NM_018313.4	856	cgg/cgAAGTATTGGAACGAGCAAGAAGGATGAATCGg		0.300523762085509	3	FACETS	0.784	0.681	0.893	0.523	0.454	0.595	SUBCLONAL	2	TRUE	0	0.40984694592841	3		269	210	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0007137-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	398	464	1	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.78620579685429	1		465	509	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	208	619	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.508187019446561	2	FACETS	0.874	0.82	0.928	0.874	0.82	0.928	CLONAL	2	TRUE	0	0.509704714957483	2		619	467	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	337	390	0	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.509704714957483	2		390	1317	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	292	662	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.845	0.801	0.89	1	0.995	1	CLONAL	2	TRUE	1	0.509704714957483	2		664	678	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	265	418	2	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	1	2	FACETS	0.901	0.844	0.96	0.901	0.844	0.96	CLONAL	1	TRUE	1	0.509704714957483	2		420	1154	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1232964733	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	50	100	0	ENST00000324856.7:c.1015del	p.Ala339LeufsTer24	p.A339Lfs*24	ENST00000324856	NM_006015.4	337	tGg/tg	1/20	1	2	FACETS	0.708	0.605	0.82	0.708	0.605	0.82	SUBCLONAL	1	TRUE	1	0.509704714957483	2		100	277	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221161	5221161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs575201235	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	284	281	0	ENST00000357368.4:c.3305G>A	p.Arg1102His	p.R1102H	ENST00000357368	NM_002850.3	1102	cGc/cAc	20/38	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.509704714957483	2		281	1026	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662691	117662691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368206665	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	130	197	0	ENST00000368508.3:c.4774C>T	p.Arg1592Cys	p.R1592C	ENST00000368508	NM_002944.2	1592	Cgt/Tgt	29/43	1	2	FACETS	0.812	0.739	0.889	0.812	0.739	0.889	CLONAL	1	TRUE	1	0.509704714957483	2		197	628	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799098	42799098	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	218	244	0	ENST00000575354.2:c.4586del	p.Pro1529LeufsTer91	p.P1529Lfs*91	ENST00000575354	NM_015125.3	1528	Ccc/cc	20/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.509704714957483	2		244	812	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	169	190	1	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	0.795	0.732	0.861	0.795	0.732	0.861	SUBCLONAL	1	TRUE	1	0.509704714957483	2		191	834	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699208	117699208	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	44	270	0	ENST00000369458.3:c.433T>C	p.Tyr145His	p.Y145H	ENST00000369458	NM_024626.3	145	Tat/Cat	3/6	1	2	FACETS	0.204	0.17	0.241	0.204	0.17	0.241	SUBCLONAL	1	TRUE	1	0.509704714957483	2		270	847	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12629134	12629134	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	48	198	0	ENST00000251849.4:c.1373A>T	p.Tyr458Phe	p.Y458F	ENST00000251849	NM_002880.3	458	tAt/tTt	13/17	1	2	FACETS	0.291	0.245	0.341	0.291	0.245	0.341	SUBCLONAL	1	TRUE	1	0.509704714957483	2		198	648	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162957	47162957	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	131	218	0	ENST00000409792.3:c.3169G>A	p.Asp1057Asn	p.D1057N	ENST00000409792	NM_014159.6	1057	Gat/Aat	3/21	NA	2	FACETS	0.998	0.911	1			1	INDETERMINATE	1	TRUE	NA	0.509704714957483	2		218	515	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200152	128200152	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	95	147	0	ENST00000341105.2:c.1153C>T	p.Pro385Ser	p.P385S	ENST00000341105	NM_032638.4	385	Cca/Tca	6/6	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.509704714957483	2		147	369	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522504	67522504	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	50	87	0	ENST00000274335.5:c.1A>G	p.Met1?	p.M1?	ENST00000274335		1	Atg/Gtg	1/15	0.374186839719265	3	FACETS	0.739	0.63	0.858	0.37	0.315	0.429	SUBCLONAL	1	TRUE	1	0.509704714957483	3		87	333	SUCCESS
APC	324	MSKCC	GRCh37	5	112137022	112137022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767457050	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	52	186	0	ENST00000257430.4:c.776G>A	p.Arg259Gln	p.R259Q	ENST00000257430	NM_000038.5	259	cGg/cAg	8/16	0.374186839719265	3	FACETS	0.399	0.339	0.465	0.199	0.169	0.233	SUBCLONAL	1	TRUE	1	0.509704714957483	3		186	642	SUCCESS
APC	324	MSKCC	GRCh37	5	112177085	112177085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs777604445	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	61	306	0	ENST00000257430.4:c.5794A>G	p.Thr1932Ala	p.T1932A	ENST00000257430	NM_000038.5	1932	Act/Gct	16/16	0.374186839719265	3	FACETS	0.324	0.278	0.374	0.162	0.139	0.187	SUBCLONAL	1	TRUE	1	0.509704714957483	3		306	927	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100003	157100003	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	29	117	0	ENST00000346085.5:c.940G>C	p.Gly314Arg	p.G314R	ENST00000346085	NM_020732.3	314	Ggc/Cgc	1/20	0.153843543145041	4	FACETS	0.571	0.459	0.697	0.285	0.229	0.349	INDETERMINATE	1	TRUE	2	0.509704714957483	4		117	301	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157488299	157488299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	128	93	0	ENST00000346085.5:c.3005C>T	p.Ala1002Val	p.A1002V	ENST00000346085	NM_020732.3	1002	gCc/gTc	10/20	0.153843543145041	4	FACETS	1	0.984	1	0.699	0.637	0.765	INDETERMINATE	1	TRUE	2	0.509704714957483	4		93	542	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737070	145737070	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779410033	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	211	339	1	ENST00000428558.2:c.3496G>A	p.Gly1166Ser	p.G1166S	ENST00000428558	NM_004260.3	1166	Ggc/Agc	21/22	0.374186839719265	3	FACETS	1	0.944	1	0.509	0.473	0.547	CLONAL	1	TRUE	1	0.509704714957483	3		340	1020	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145743006	145743006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	178	150	0	ENST00000428558.2:c.98C>T	p.Ala33Val	p.A33V	ENST00000428558	NM_004260.3	33	gCg/gTg	2/22	0.374186839719265	3	FACETS	0.953	0.887	1	0.953	0.887	1	CLONAL	2	TRUE	1	0.509704714957483	3		150	460	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020733	37020733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	291	251	0	ENST00000358127.4:c.112C>T	p.Arg38Cys	p.R38C	ENST00000358127	NM_001280556.1	38	Cgc/Tgc	2/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.509704714957483	2		251	1097	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900252	101900252	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	91	182	0	ENST00000374994.4:c.686T>A	p.Val229Asp	p.V229D	ENST00000374994	NM_004612.2	229	gTt/gAt	4/9	1	2	FACETS	0.92	0.823	1	0.92	0.823	1	CLONAL	1	TRUE	1	0.509704714957483	2		182	388	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375222	118375222	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	146	186	0	ENST00000534358.1:c.8615C>G	p.Ser2872Ter	p.S2872*	ENST00000534358	NM_005933.3	2872	tCa/tGa	27/36	1	2	FACETS	0.821	0.751	0.894	0.821	0.751	0.894	CLONAL	1	TRUE	1	0.509704714957483	2		186	698	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944743	31944743	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	31	41	0	ENST00000340398.3:c.358A>G	p.Met120Val	p.M120V	ENST00000340398	NM_001013699.2	120	Atg/Gtg	1/1	0.508187019446561	2	FACETS	0.489	0.397	0.591	0.244	0.198	0.296	SUBCLONAL	1	TRUE	0	0.509704714957483	2		41	249	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439877	49439877	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210295814	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1226	112	362	0	ENST00000301067.7:c.4664C>T	p.Ser1555Phe	p.S1555F	ENST00000301067	NM_003482.3	1555	tCc/tTc	17/54	0.508187019446561	2	FACETS	0.328	0.294	0.365	0.164	0.147	0.183	SUBCLONAL	1	TRUE	0	0.509704714957483	2		362	1338	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877407	28877407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759739030	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	52	142	0	ENST00000282397.4:c.3914G>A	p.Arg1305His	p.R1305H	ENST00000282397	NM_002019.4	1305	cGc/cAc	30/30	0.252392705072544	0	FACETS	0.178	0.151	0.207			1	INDETERMINATE	1	TRUE	0	0.509704714957483	0		142	562	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912064	32912064	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	193	443	0	ENST00000380152.3:c.3572A>T	p.Lys1191Met	p.K1191M	ENST00000380152		1191	aAg/aTg	11/27	0.252392705072544	0	FACETS	0.451	0.417	0.485			1	INDETERMINATE	1	TRUE	0	0.509704714957483	0		443	824	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930633	32930633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55716624	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	140	172	0	ENST00000380152.3:c.7504C>T	p.Arg2502Cys	p.R2502C	ENST00000380152		2502	Cgc/Tgc	15/27	0.252392705072544	0	FACETS	0.46	0.42	0.501			1	INDETERMINATE	1	TRUE	0	0.509704714957483	0		172	586	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778116	3778116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761751428	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	318	338	0	ENST00000262367.5:c.6932C>T	p.Pro2311Leu	p.P2311L	ENST00000262367	NM_004380.2	2311	cCg/cTg	31/31	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.509704714957483	2		338	1187	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041518	14041518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149364215	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	176	150	0	ENST00000311895.7:c.2065C>T	p.Arg689Cys	p.R689C	ENST00000311895	NM_005236.2	689	Cgt/Tgt	11/11	1	2	FACETS	0.946	0.874	1	0.946	0.874	1	CLONAL	1	TRUE	1	0.509704714957483	2		150	730	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828582	72828582	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1496	262	492	0	ENST00000268489.5:c.7999A>G	p.Thr2667Ala	p.T2667A	ENST00000268489	NM_006885.3	2667	Act/Gct	9/10	1	2	FACETS	0.585	0.546	0.625	0.585	0.546	0.625	SUBCLONAL	1	TRUE	1	0.509704714957483	2		492	1758	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944283	81944283	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1695	99	414	0	ENST00000359376.3:c.1892T>G	p.Leu631Arg	p.L631R	ENST00000359376	NM_002661.3	631	cTc/cGc	18/33	1	2	FACETS	0.217	0.192	0.243	0.217	0.192	0.243	SUBCLONAL	1	TRUE	1	0.509704714957483	2		414	1794	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688712	47688712	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	267	274	0	ENST00000347630.2:c.588T>G	p.Asn196Lys	p.N196K	ENST00000347630	NM_001007230.1	196	aaT/aaG	7/11	1	2	FACETS	0.954	0.895	1	0.954	0.895	1	CLONAL	1	TRUE	1	0.509704714957483	2		274	1098	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221331	1221331	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1555738724	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	171	380	0	ENST00000326873.7:c.854T>G	p.Leu285Arg	p.L285R	ENST00000326873	NM_000455.4	285	cTg/cGg	6/10	1	2	FACETS	0.67	0.615	0.726	0.67	0.615	0.726	SUBCLONAL	1	TRUE	1	0.509704714957483	2		380	1002	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184465	7184465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329693158	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	330	272	0	ENST00000302850.5:c.836G>A	p.Arg279His	p.R279H	ENST00000302850	NM_000208.2	279	cGc/cAc	3/22	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.509704714957483	2		272	1166	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258583	19258583	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1434	104	499	0	ENST00000162023.5:c.317C>A	p.Pro106His	p.P106H	ENST00000162023		106	cCt/cAt	8/13	1	2	FACETS	0.265	0.236	0.296	0.265	0.236	0.296	SUBCLONAL	1	TRUE	1	0.509704714957483	2		499	1538	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741483	39741483	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	122	175	0	ENST00000361337.2:c.1370T>C	p.Ile457Thr	p.I457T	ENST00000361337	NM_003286.2	457	aTc/aCc	14/21	0.509704714957483	3	FACETS	0.562	0.507	0.62	0.281	0.253	0.31	SUBCLONAL	1	TRUE	1	0.509704714957483	3		175	1069	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076915	41076915	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	245	197	0	ENST00000373198.4:c.1505T>C	p.Ile502Thr	p.I502T	ENST00000373198	NM_133170.3	502	aTc/aCc	9/32	0.509704714957483	3	FACETS	1	0.973	1	0.539	0.503	0.575	CLONAL	1	TRUE	1	0.509704714957483	3		197	1120	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070890	30070890	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	116	296	0	ENST00000338641.4:c.1406A>G	p.Lys469Arg	p.K469R	ENST00000338641	NM_000268.3	469	aAg/aGg	13/16	1	2	FACETS	0.382	0.343	0.423	0.382	0.343	0.423	SUBCLONAL	1	TRUE	1	0.509704714957483	2		296	1193	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933022	39933022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778509267	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	608	382	0	ENST00000378444.4:c.1577C>T	p.Ser526Leu	p.S526L	ENST00000378444	NM_001123385.1	526	tCg/tTg	4/15	0.374186839719265	3	FACETS	0.902	0.868	0.937	0.902	0.868	0.937	CLONAL	2	TRUE	1	0.509704714957483	3		382	1659	SUCCESS
AR	367	MSKCC	GRCh37	X	66765403	66765403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1264061748	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1294	82	315	2	ENST00000374690.3:c.415G>A	p.Val139Met	p.V139M	ENST00000374690	NM_000044.3	139	Gtg/Atg	1/8	0.374186839719265	3	FACETS	0.293	0.257	0.332	0.147	0.128	0.166	SUBCLONAL	1	TRUE	1	0.509704714957483	3		317	1376	SUCCESS
AR	367	MSKCC	GRCh37	X	66765826	66765826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1646	111	426	3	ENST00000374690.3:c.838C>T	p.Arg280Cys	p.R280C	ENST00000374690	NM_000044.3	280	Cgt/Tgt	1/8	0.374186839719265	3	FACETS	0.311	0.278	0.346	0.156	0.139	0.173	SUBCLONAL	1	TRUE	1	0.509704714957483	3		429	1757	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954643	17954643	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	295	321	0	ENST00000458235.1:c.251del	p.Pro84ArgfsTer63	p.P84Rfs*63	ENST00000458235	NM_000215.3	84	cCg/cg	3/24	1	2	FACETS	0.988	0.929	1	0.988	0.929	1	CLONAL	1	TRUE	1	0.509704714957483	2		321	1172	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003784	+	frameshift_variant	Frame_Shift_Del	DEL	CTCT	CTCT	-	novel	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	391	237	0	ENST00000558401.1:c.41_44del	p.Ser14PhefsTer29	p.S14Ffs*29	ENST00000558401	NM_004048.2	13	CTCTct/ct	1/4	0.509704714957483	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.509704714957483	1		237	928	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881668	111881669	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	199	265	0	ENST00000393256.3:c.350dup	p.Ser118LysfsTer21	p.S118Kfs*21	ENST00000393256	NM_006538.4	116	acc/aCcc	2/4	1	2	FACETS	0.919	0.852	0.987	0.919	0.852	0.987	CLONAL	1	TRUE	1	0.509704714957483	2		265	850	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37081785	37081786	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	GG	GG	-	novel	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	184	147	0	ENST00000231790.2:c.1667_1667+1del		p.X556_splice	ENST00000231790	NM_000249.3	556		14/19	1	2	FACETS	0.876	0.81	0.945	0.876	0.81	0.945	CLONAL	1	TRUE	1	0.509704714957483	2		147	824	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178258	56178258	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	302	239	0	ENST00000399503.3:c.3236del	p.Asn1079IlefsTer3	p.N1079Ifs*3	ENST00000399503	NM_005921.1	1077	tcA/tc	14/20	0.374186839719265	3	FACETS	1	0.994	1	0.743	0.701	0.786	CLONAL	1	TRUE	1	0.509704714957483	3		239	1001	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805045	89805046	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1030509993	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	309	302	0	ENST00000389301.3:c.4331_4332del	p.Pro1444ArgfsTer3	p.P1444Rfs*3	ENST00000389301	NM_000135.2	1444	cCT/c	43/43	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.509704714957483	2		302	1153	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443612	29443612	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	178	251	0	ENST00000389048.3:c.3605del	p.Gly1202GlufsTer56	p.G1202Efs*56	ENST00000389048	NM_004304.4	1202	gGa/ga	23/29	1	2	FACETS	0.711	0.655	0.77	0.711	0.655	0.77	SUBCLONAL	1	TRUE	1	0.509704714957483	2		251	982	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222233	2222235	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	novel	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	363	635	0	ENST00000326181.6:c.521_523del	p.Asn174del	p.N174del	ENST00000326181	NM_032271.2	173	AAC/-	8/21	NA	2	FACETS	0.911	0.862	0.962			1	INDETERMINATE	1	TRUE	NA	0.509704714957483	2		635	1563	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742041	145742041	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007565-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	312	284	0	ENST00000428558.2:c.462del	p.Val155SerfsTer25	p.V155Sfs*25	ENST00000428558	NM_004260.3	154	aaA/aa	5/22	0.374186839719265	3	FACETS	0.813	0.768	0.858	0.813	0.768	0.858	CLONAL	2	TRUE	1	0.509704714957483	3		284	945	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0007565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	196	619	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.342382694735023	3	FACETS	1	0.985	1	0.628	0.581	0.677	CLONAL	1	TRUE	1	0.365240215722628	3		619	1011	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0007565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	348	740	3	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.364858040464024	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.365240215722628	2		743	795	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0007565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	275	662	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.364858040464024	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.365240215722628	2		664	659	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085678	16085678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747134309	NA	P-0007565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	154	757	2	ENST00000281043.3:c.854G>A	p.Arg285Gln	p.R285Q	ENST00000281043	NM_005378.4	285	cGg/cAg	3/3	0.365240215722628	3	FACETS	1	0.934	1	0.512	0.468	0.559	CLONAL	1	TRUE	1	0.365240215722628	3		759	973	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117225	7117225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374098153	NA	P-0007565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	143	708	2	ENST00000302850.5:c.3991C>T	p.Arg1331Cys	p.R1331C	ENST00000302850	NM_000208.2	1331	Cgt/Tgt	22/22	0.365240215722628	2	FACETS	1	0.948	1	0.527	0.481	0.575	CLONAL	1	TRUE	0	0.365240215722628	2		710	743	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588798	52588798	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1559827261	NA	P-0007565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	189	638	1	ENST00000394830.3:c.4230del	p.Pro1411LeufsTer21	p.P1411Lfs*21	ENST00000394830	NM_018313.4	1410	ggG/gg	27/30	0.365240215722628	2	FACETS	0.903	0.84	0.968	0.903	0.84	0.968	CLONAL	2	TRUE	0	0.365240215722628	2		639	573	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855019	76855019	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	125	571	1	ENST00000373344.5:c.5817del	p.Asp1940IlefsTer15	p.D1940Ifs*15	ENST00000373344	NM_000489.3	1939	aaA/aa	25/35	0.186672637626569	4	FACETS	0.929	0.839	1	0.464	0.419	0.512	INDETERMINATE	1	TRUE	2	0.365240215722628	4		572	1006	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256514	115256514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	285	714	1	ENST00000369535.4:c.197C>T	p.Ala66Val	p.A66V	ENST00000369535	NM_002524.4	66	gCc/gTc	3/7	0.133786855792205	5	FACETS	1	0.99	1	0.622	0.585	0.659	INDETERMINATE	2	TRUE	1	0.365240215722628	5		715	971	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	274	749	2	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	0.138048233670339	4	FACETS	0.991	0.93	1	0.991	0.93	1	INDETERMINATE	2	TRUE	2	0.365240215722628	4		751	1034	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645975	215645975	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs587780033	NA	P-0007565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	110	493	1	ENST00000260947.4:c.623del	p.Lys208ArgfsTer4	p.K208Rfs*4	ENST00000260947	NM_000465.2	208	aAg/ag	4/11	0.342382694735023	3	FACETS	1	0.912	1	0.507	0.456	0.562	CLONAL	1	TRUE	1	0.365240215722628	3		494	702	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202350	138202351	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775280214	NA	P-0007565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	187	577	1	ENST00000237289.4:c.2274dup	p.Lys759GlnfsTer10	p.K759Qfs*10	ENST00000237289	NM_001270507.1	756	gac/gaCc	9/9	0.365240215722628	3	FACETS	0.869	0.805	0.934	0.869	0.805	0.934	CLONAL	2	TRUE	1	0.365240215722628	3		578	697	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425535	49425536	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0007565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	138	887	0	ENST00000301067.7:c.12952_12953del	p.Lys4318GlufsTer15	p.K4318Efs*15	ENST00000301067	NM_003482.3	4318	AAg/g	39/54	0.342382694735023	3	FACETS	0.957	0.87	1	0.478	0.435	0.524	CLONAL	1	TRUE	1	0.365240215722628	3		887	934	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626734	28626734	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	159	589	0	ENST00000241453.7:c.562A>C	p.Ser188Arg	p.S188R	ENST00000241453	NM_004119.2	188	Agc/Cgc	5/24	0.365240215722628	3	FACETS	1	0.97	1	0.563	0.515	0.612	CLONAL	1	TRUE	1	0.365240215722628	3		589	915	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098719	2098719	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854105	NA	P-0007565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	51	755	0	ENST00000219476.3:c.103C>T	p.Gln35Ter	p.Q35*	ENST00000219476	NM_000548.3	35	Cag/Tag	2/42	0.133786855792205	5	FACETS	0.465	0.394	0.544	0.116	0.098	0.136	INDETERMINATE	1	TRUE	1	0.365240215722628	5		755	930	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866068	37866068	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	152	705	1	ENST00000269571.5:c.577C>A	p.His193Asn	p.H193N	ENST00000269571		193	Cac/Aac	5/27	0.364858040464024	2	FACETS	1	0.92	1	0.503	0.46	0.547	CLONAL	1	TRUE	0	0.365240215722628	2		706	828	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221211	1221211	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0007565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	448	669	0	ENST00000326873.7:c.735-1G>T		p.X245_splice	ENST00000326873	NM_000455.4	245			0.102695785000647	3	FACETS	1	0.989	1			1	INDETERMINATE	3	TRUE	NA	0.365240215722628	3		669	892	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2193702	2193702	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	129	689	0	ENST00000398665.3:c.508G>C	p.Val170Leu	p.V170L	ENST00000398665	NM_032482.2	170	Gtg/Ctg	6/28	NA	2	FACETS	0.839	0.761	0.922			1	INDETERMINATE	1	TRUE	NA	0.365240215722628	2		689	842	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793517	42793517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560617801	NA	P-0007565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	253	786	0	ENST00000575354.2:c.1319G>A	p.Arg440His	p.R440H	ENST00000575354	NM_015125.3	440	cGc/cAc	8/20	0.138048233670339	4	FACETS	0.997	0.934	1	0.997	0.934	1	INDETERMINATE	2	TRUE	2	0.365240215722628	4		786	949	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770632	40770632	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	75	433	0	ENST00000373198.4:c.2750A>T	p.Glu917Val	p.E917V	ENST00000373198	NM_133170.3	917	gAg/gTg	19/32	0.365240215722628	0	FACETS	0.76	0.671	0.854			1	SUBCLONAL	1	TRUE	0	0.365240215722628	0		433	343	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446892	187446892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	170	744	0	ENST00000232014.4:c.1301G>A	p.Ser434Asn	p.S434N	ENST00000232014	NM_001130845.1	434	aGc/aAc	5/10	0.299624411222842	4	FACETS	1	0.973	1	0.568	0.522	0.617	CLONAL	1	TRUE	2	0.365240215722628	4		744	1118	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250479	26250479	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	97	659	0	ENST00000446824.2:c.355A>G	p.Thr119Ala	p.T119A	ENST00000446824	NM_021018.2	119	Act/Gct	1/1	0.299624411222842	4	FACETS	0.818	0.728	0.913	0.409	0.364	0.457	CLONAL	1	TRUE	2	0.365240215722628	4		659	887	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739852	41739852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs984438766	NA	P-0007565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	139	473	1	ENST00000242208.4:c.121G>A	p.Ala41Thr	p.A41T	ENST00000242208	NM_002192.2	41	Gcc/Acc	2/3	0.342382694735023	3	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	1	0.365240215722628	3		474	444	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293666	137293666	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	124	786	0	ENST00000481739.1:c.217G>T	p.Gly73Cys	p.G73C	ENST00000481739	NM_002957.4	73	Ggc/Tgc	2/10	0.133786855792205	5	FACETS	0.793	0.718	0.87	0.396	0.359	0.435	INDETERMINATE	2	TRUE	1	0.365240215722628	5		786	663	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430392	47430392	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	184	643	0	ENST00000377045.4:c.1667A>G	p.Glu556Gly	p.E556G	ENST00000377045	NM_001654.4	556	gAg/gGg	15/16	0.186672637626569	4	FACETS	0.907	0.84	0.978	0.907	0.84	0.978	INDETERMINATE	2	TRUE	2	0.365240215722628	4		643	758	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0007607-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	135	323	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.645952730784147	8	FACETS	1	0.973	1			1	CLONAL	3	TRUE	NA	0.645952730784147	8		323	362	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100175	27100176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0007607-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	385	179	0	ENST00000324856.7:c.3977dup	p.Gln1327AlafsTer11	p.Q1327Afs*11	ENST00000324856	NM_006015.4	1324	tac/taCc	16/20	0.651575414946387	4	FACETS	0.898	0.855	0.943	0.898	0.855	0.943	CLONAL	2	TRUE	2	0.645952730784147	4		179	1092	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436026	56436026	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771831816	NA	P-0007607-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1377	734	143	0	ENST00000407977.2:c.1111C>T	p.Arg371Ter	p.R371*	ENST00000407977		371	Cga/Tga	9/10	0.535211789770749	5	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.645952730784147	5		143	2111	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143190	24143190	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007607-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	186	207	0	ENST00000263121.7:c.422A>G	p.His141Arg	p.H141R	ENST00000263121	NM_003073.3	141	cAc/cGc	4/9	0.651575414946387	3	FACETS	0.673	0.621	0.728			1	SUBCLONAL	1	TRUE	NA	0.645952730784147	3		207	1132	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0007687-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	413	1121	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.234687098918508	3	FACETS	0.873	0.83	0.917	0.582	0.553	0.611	INDETERMINATE	2	TRUE	0	0.391818113532776	3		1121	1444	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271774	15271774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1489373939	NA	P-0007687-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1766	146	1492	0	ENST00000263388.2:c.6665C>T	p.Pro2222Leu	p.P2222L	ENST00000263388	NM_000435.2	2222	cCg/cTg	33/33	0.289973323414747	3	FACETS	0.466	0.423	0.512	0.155	0.141	0.171	SUBCLONAL	1	TRUE	0	0.391818113532776	3		1492	1912	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517313	157517313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752398721	NA	P-0007687-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	201	576	0	ENST00000346085.5:c.3877G>A	p.Glu1293Lys	p.E1293K	ENST00000346085	NM_020732.3	1293	Gag/Aag	16/20	0.37238127111338	4	FACETS	0.806	0.748	0.866			1	CLONAL	2	TRUE	NA	0.391818113532776	4		576	886	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400214	139400214	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007687-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1673	92	1046	1	ENST00000277541.6:c.4134C>A	p.Phe1378Leu	p.F1378L	ENST00000277541	NM_017617.3	1378	ttC/ttA	25/34	0.391818113532776	5	FACETS	0.422	0.373	0.475	0.141	0.124	0.159	SUBCLONAL	1	TRUE	2	0.391818113532776	5		1047	1765	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0007705-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	12	554	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.689114661238978	2	FACETS	0.67	0.484	0.883	0.335	0.242	0.442	SUBCLONAL	1	TRUE	0	0.689114661238978	2		554	52	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711968	89711968	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776670	NA	P-0007705-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	31	341	0	ENST00000371953.3:c.586del	p.His196ThrfsTer3	p.H196Tfs*3	ENST00000371953	NM_000314.4	196	Cac/ac	6/9	0.650375327347976	2	FACETS	0.762	0.651	0.873	0.762	0.651	0.873	SUBCLONAL	2	TRUE	0	0.689114661238978	2		341	59	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0007705-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	23	620	1	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	0.689114661238978	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.689114661238978	1		621	34	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965638	93965638	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs773047453	NA	P-0007705-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	23	438	0	ENST00000369303.4:c.2290A>G	p.Ile764Val	p.I764V	ENST00000369303	NM_004440.3	764	Att/Gtt	13/17	0.423678990307755	4	FACETS	0.688	0.541	0.854	0.344	0.27	0.427	SUBCLONAL	1	TRUE	2	0.689114661238978	4		438	164	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813300	102813300	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1436683139	NA	P-0008462-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	89	403	0	ENST00000307046.8:c.389C>A	p.Pro130His	p.P130H	ENST00000307046	NM_001111285.1	130	cCc/cAc	3/4	0.688893137306929	2	FACETS	0.651	0.581	0.725	0.325	0.29	0.363	SUBCLONAL	1	TRUE	0	0.688893137306929	2		403	397	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284997	15284997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008462-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	212	319	0	ENST00000263388.2:c.4618C>T	p.Arg1540Cys	p.R1540C	ENST00000263388	NM_000435.2	1540	Cgc/Tgc	25/33	0.688893137306929	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.688893137306929	3		319	400	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971074	21971081	+	frameshift_variant	Frame_Shift_Del	DEL	ACCAGCGT	ACCAGCGT	-	novel	NA	P-0008462-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	130	215	0	ENST00000304494.5:c.277_284del	p.Thr93GlyfsTer24	p.T93Gfs*24	ENST00000304494	NM_000077.4	93	ACGCTGGTg/g	2/3	0.678746440204267	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.688893137306929	2		215	183	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653796	89653798	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs1554893765	NA	P-0008548-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	117	250	0	ENST00000371953.3:c.97_99del	p.Ile33del	p.I33del	ENST00000371953	NM_000314.4	32	ATT/-	2/9	0.73362445945501	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.73362445945501	1		250	187	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954309	48954309	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008548-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	129	207	0	ENST00000267163.4:c.1430T>G	p.Leu477Arg	p.L477R	ENST00000267163	NM_000321.2	477	cTg/cGg	16/27	0.73362445945501	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.73362445945501	1		207	214	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593640	55593660	+	inframe_deletion	In_Frame_Del	DEL	TTTACATAGACCCAACACAAC	TTTACATAGACCCAACACAAC	-	novel	NA	P-0008548-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	411	329	0	ENST00000288135.5:c.1708_1728del	p.Tyr570_Leu576del	p.Y570_L576del	ENST00000288135	NM_000222.2	569	gTTTACATAGACCCAACACAACtt/gtt	11/21	0.725719072550448	3	FACETS	0.958	0.919	0.998	0.958	0.919	0.998	CLONAL	2	TRUE	1	0.73362445945501	3		329	799	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662344	67662351	+	frameshift_variant	Frame_Shift_Del	DEL	GACCTTCC	GACCTTCC	-	novel	NA	P-0008548-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	251	400	0	ENST00000264010.4:c.1591_1598del	p.Thr531ProfsTer26	p.T531Pfs*26	ENST00000264010	NM_006565.3	530	aaGACCTTCCgc/aagc	9/12	1	2	FACETS	0.972	0.914	1	0.972	0.914	1	CLONAL	1	TRUE	1	0.73362445945501	2		400	704	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599320	55599321	+	protein_altering_variant	In_Frame_Ins	INS	-	-	GAA	novel	NA	P-0008548-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	139	337	0	ENST00000288135.5:c.2446_2447insGAA	p.Asp816delinsGlyAsn	p.D816delinsGN	ENST00000288135	NM_000222.2	816	gac/gGAAac	17/21	0.725719072550448	3	FACETS	0.799	0.73	0.872	0.4	0.365	0.436	SUBCLONAL	1	TRUE	1	0.73362445945501	3		337	648	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255265	16255265	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011155-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	27	344	1	ENST00000375759.3:c.2530C>T	p.Arg844Ter	p.R844*	ENST00000375759	NM_015001.2	844	Cga/Tga	11/15	0.122264868030285	3	FACETS	0.219	0.174	0.271	0.11	0.087	0.136	INDETERMINATE	1	TRUE	1	0.61	3		345	527	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130397	29130421	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCAAATCCATCCTGAAGGGCCCA	TGGCAAATCCATCCTGAAGGGCCCA	-	novel	NA	P-0011155-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	107	461	0	ENST00000328354.6:c.289_313del	p.Trp97IlefsTer5	p.W97Ifs*5	ENST00000328354	NM_007194.3	97	TGGGCCCTTCAGGATGGATTTGCCAat/at	2/15	0.3	0	FACETS	0.421	0.382	0.461			1	INDETERMINATE	1	TRUE	0	0.61	0		461	325	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0012873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	203	1005	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.60180992935201	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.788806179895028	1		1006	303	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636974	176636974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138405802	NA	P-0012873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	102	511	0	ENST00000439151.2:c.1574G>A	p.Arg525Gln	p.R525Q	ENST00000439151	NM_022455.4	525	cGg/cAg	5/23	0.392838013788482	3	FACETS	0.612	0.549	0.679	0.204	0.183	0.227	INDETERMINATE	1	TRUE	0	0.788806179895028	3		511	589	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937845	36937845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748394788	NA	P-0012873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	120	845	1	ENST00000361632.4:c.991G>A	p.Glu331Lys	p.E331K	ENST00000361632		331	Gaa/Aaa	7/16	0.378830661059319	1	FACETS	0.352	0.319	0.387	0.352	0.319	0.387	INDETERMINATE	1	TRUE	0	0.788806179895028	1		846	523	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197847	66197847	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0012873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	41	180	0	ENST00000273854.3:c.2853-1G>C		p.X951_splice	ENST00000273854	NM_004439.5	951			0.347671665072567	3	FACETS	0.751	0.633	0.879	0.25	0.211	0.293	INDETERMINATE	1	TRUE	0	0.788806179895028	3		180	193	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0012922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	58	458	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.210438344351995	2	FACETS	0.998	0.863	1	0.998	0.863	1	CLONAL	2	TRUE	0	0.18	2		458	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0012922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	24	836	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	0.602	0.471	0.754	0.602	0.471	0.754	SUBCLONAL	1	TRUE	1	0.18	2		837	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	49	701	3	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.18	2		704	460	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164123	47164123	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	16	333	0	ENST00000409792.3:c.2003C>T	p.Pro668Leu	p.P668L	ENST00000409792	NM_014159.6	668	cCc/cTc	3/21	1	2	FACETS	0.666	0.492	0.873	0.666	0.492	0.873	SUBCLONAL	1	TRUE	1	0.18	2		333	267	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530423	187530423	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs138364727	NA	P-0012922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	13	0	0	ENST00000441802.2:c.10120A>G	p.Ile3374Val	p.I3374V	ENST00000441802	NM_005245.3	3374	Att/Gtt	16/27	0.146900444774857	0	FACETS	0.364	0.259	0.494			1	SUBCLONAL	1	TRUE	0	0.18	0		0	325	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	65	365	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.569302231398161	2		365	219	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0013048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	85	351	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.933	0.833	1	0.933	0.833	1	CLONAL	1	TRUE	1	0.569302231398161	2		351	320	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0013048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	52	345	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.774	0.666	0.89	0.774	0.666	0.89	SUBCLONAL	1	TRUE	1	0.569302231398161	2		345	236	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358478	91358478	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1022266595	NA	P-0013048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	115	478	1	ENST00000355112.3:c.4223C>T	p.Pro1408Leu	p.P1408L	ENST00000355112	NM_000057.2	1408	cCg/cTg	22/22	1	2	FACETS	0.978	0.888	1	0.978	0.888	1	CLONAL	1	TRUE	1	0.569302231398161	2		479	413	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429778	78429783	+	inframe_deletion	In_Frame_Del	DEL	TCTGCA	TCTGCA	-	novel	NA	P-0013048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	71	338	0	ENST00000370768.2:c.1005_1010del	p.Ala336_Glu337del	p.A336_E337del	ENST00000370768	NM_003902.3	335	gcTGCAGAa/gca	12/20	0.569302231398161	1	FACETS	0.572	0.503	0.645	0.572	0.503	0.645	SUBCLONAL	1	TRUE	0	0.569302231398161	1		338	312	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433318	78433318	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	33	393	1	ENST00000370768.2:c.283C>T	p.Gln95Ter	p.Q95*	ENST00000370768	NM_003902.3	95	Cag/Tag	4/20	0.569302231398161	1	FACETS	0.212	0.172	0.256	0.212	0.172	0.256	SUBCLONAL	1	TRUE	0	0.569302231398161	1		394	392	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0013567-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	353	473	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.837137136586292	4	FACETS	0.984	0.948	1	0.984	0.948	1	CLONAL	3	TRUE	1	0.837137136586292	4		474	525	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803899	43803899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61754776	NA	P-0013567-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	463	630	0	ENST00000372470.3:c.209C>T	p.Pro70Leu	p.P70L	ENST00000372470	NM_005373.2	70	cCg/cTg	2/12	0.837137136586292	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.837137136586292	2		630	529	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602584	10602584	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1208201314	NA	P-0013567-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	713	1134	0	ENST00000171111.5:c.994G>T	p.Gly332Cys	p.G332C	ENST00000171111	NM_203500.1	332	Ggc/Tgc	3/6	0.837137136586292	3	FACETS	0.97	0.953	0.987	0.97	0.953	0.987	CLONAL	3	TRUE	0	0.837137136586292	3		1134	830	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221303	1221307	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGA	GGCGA	-	novel	NA	P-0013567-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	662	932	0	ENST00000326873.7:c.826_830del	p.Gly276LeufsTer7	p.G276Lfs*7	ENST00000326873	NM_000455.4	276	GGCGAc/c	6/10	0.819692322569178	3	FACETS	0.983	0.966	0.999	0.983	0.966	0.999	CLONAL	3	TRUE	0	0.837137136586292	3		932	761	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368482	225368482	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013567-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	294	376	0	ENST00000264414.4:c.1264A>T	p.Met422Leu	p.M422L	ENST00000264414	NM_003590.4	422	Atg/Ttg	9/16	0.743281295244489	3	FACETS	0.953	0.909	0.996	0.953	0.909	0.996	CLONAL	2	TRUE	1	0.837137136586292	3		376	523	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576823	67576823	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013567-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	171	217	0	ENST00000274335.5:c.905A>T	p.Gln302Leu	p.Q302L	ENST00000274335		302	cAg/cTg	6/15	0.837137136586292	3	FACETS	0.959	0.902	1	0.959	0.902	1	CLONAL	2	TRUE	1	0.837137136586292	3		217	302	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032198	26032199	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0013567-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	436	482	0	ENST00000244661.2:c.90_91del	p.Pro31GlyfsTer67	p.P31Gfs*67	ENST00000244661	NM_003537.3	30	gcGCcg/gccg	1/1	0.812704362073655	3	FACETS	0.944	0.921	0.965	0.944	0.921	0.965	CLONAL	3	TRUE	0	0.837137136586292	3		482	522	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350155	81350155	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs758567520	NA	P-0013567-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	283	289	0	ENST00000222390.5:c.1177C>G	p.Arg393Gly	p.R393G	ENST00000222390	NM_000601.4	393	Cgt/Ggt	10/18	0.837137136586292	4	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	2	0.837137136586292	4		289	610	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046560	30046560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs541601115	NA	P-0013567-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	161	696	1	ENST00000331968.5:c.2623G>A	p.Glu875Lys	p.E875K	ENST00000331968	NM_002742.2	875	Gag/Aag	18/18	0.754967263879653	3	FACETS	0.912	0.841	0.987	0.456	0.42	0.494	CLONAL	1	TRUE	1	0.837137136586292	3		697	598	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957538	175957538	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013567-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	74	368	0	ENST00000367669.3:c.1858A>T	p.Ser620Cys	p.S620C	ENST00000367669	NM_022457.5	620	Agt/Tgt	17/20	0.837137136586292	6	FACETS	0.753	0.659	0.854	0.188	0.164	0.214	SUBCLONAL	1	TRUE	2	0.837137136586292	6		368	628	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814308	76814308	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013567-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	68	119	0	ENST00000373344.5:c.6336A>T	p.Leu2112Phe	p.L2112F	ENST00000373344	NM_000489.3	2112	ttA/ttT	29/35	0.837137136586292	2	FACETS	0.991	0.883	1			1	CLONAL	1	TRUE	NA	0.837137136586292	2		119	164	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	36	619	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.165094976724318	2	FACETS	0.705	0.585	0.836	0.352	0.292	0.418	INDETERMINATE	1	FALSE	0	0.498416130637605	2		619	205	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0013792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	163	367	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	0.498416130637605	9	FACETS	0.813	0.745	0.884			1	CLONAL	2	FALSE	NA	0.498416130637605	9		367	1104	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610446	215610446	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1553615089	NA	P-0013792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	40	590	1	ENST00000260947.4:c.1810G>A	p.Val604Ile	p.V604I	ENST00000260947	NM_000465.2	604	Gta/Ata	8/11	0.289771412422238	5	FACETS	1	0.843	1	0.336	0.281	0.398	INDETERMINATE	1	FALSE	2	0.498416130637605	5		591	278	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578188	7578197	+	frameshift_variant	Frame_Shift_Del	DEL	CATAGGGCAC	CATAGGGCAC	-	novel	NA	P-0013792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	134	879	0	ENST00000269305.4:c.652_661del	p.Val218SerfsTer26	p.V218Sfs*26	ENST00000269305	NM_001126112.2	218	GTGCCCTATGag/ag	6/11	0.462125608565475	3	FACETS	0.787	0.714	0.862	0.393	0.357	0.431	SUBCLONAL	1	FALSE	1	0.498416130637605	3		879	854	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287929	33287929	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014331-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	282	530	0	ENST00000374542.5:c.1324G>T	p.Glu442Ter	p.E442*	ENST00000374542	NM_001141970.1	442	Gag/Tag	5/8	0.769727898161888	1	FACETS	0.959	0.916	1	0.959	0.916	1	CLONAL	1	TRUE	0	0.769727898161888	1		530	470	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652067	36652073	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCTGG	CGCCTGG	-	novel	NA	P-0014331-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	393	806	0	ENST00000244741.5:c.189_195del	p.Phe63LeufsTer83	p.F63Lfs*83	ENST00000244741	NM_000389.4	63	ttCGCCTGG/tt	2/3	0.769727898161888	1	FACETS	0.887	0.851	0.923	0.887	0.851	0.923	CLONAL	1	TRUE	0	0.769727898161888	1		806	708	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37038174	37038174	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014331-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	132	201	0	ENST00000231790.2:c.181A>T	p.Ile61Phe	p.I61F	ENST00000231790	NM_000249.3	61	Atc/Ttc	2/19	0.769727898161888	1	FACETS	0.847	0.787	0.907	0.847	0.787	0.907	CLONAL	1	TRUE	0	0.769727898161888	1		201	249	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280076	18280076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014568-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	11	148	0	ENST00000222254.8:c.2159G>A	p.Gly720Asp	p.G720D	ENST00000222254	NM_005027.3	720	gGc/gAc	16/16	1	2	FACETS	0.473	0.327	0.654	0.473	0.327	0.654	SUBCLONAL	1	TRUE	1	0.240963373781348	2		148	193	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0014718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	348	554	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.574666811043935	2		554	1136	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772311	68772311	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0014718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	246	610	0	ENST00000261769.5:c.160A>T	p.Arg54Ter	p.R54*	ENST00000261769	NM_004360.3	54	Aga/Tga	2/16	0.574666811043935	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.574666811043935	1		610	563	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023461	27023462	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	187	516	0	ENST00000324856.7:c.572dup	p.Leu192ProfsTer208	p.L192Pfs*208	ENST00000324856	NM_006015.4	189	-/G	1/20	1	2	FACETS	0.91	0.843	0.979	0.91	0.843	0.979	CLONAL	1	TRUE	1	0.574666811043935	2		516	715	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653851	89653851	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1554893824	NA	P-0014718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	203	378	0	ENST00000371953.3:c.149T>C	p.Ile50Thr	p.I50T	ENST00000371953	NM_000314.4	50	aTt/aCt	2/9	0.561885994278754	1	FACETS	0.904	0.844	0.965	0.904	0.844	0.965	CLONAL	1	TRUE	0	0.574666811043935	1		378	557	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965417	15965417	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0014718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	126	239	0	ENST00000268712.3:c.5387+2T>G		p.X1796_splice	ENST00000268712	NM_006311.3	1796			0.564617534627861	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.574666811043935	1		239	300	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265086	198265086	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	224	402	0	ENST00000335508.6:c.2791C>G	p.Gln931Glu	p.Q931E	ENST00000335508	NM_012433.2	931	Cag/Gag	19/25	1	2	FACETS	0.992	0.926	1	0.992	0.926	1	CLONAL	1	TRUE	1	0.574666811043935	2		402	786	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231787	36231787	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	245	628	0	ENST00000300305.3:c.597del	p.Arg201GlufsTer10	p.R201Efs*10	ENST00000300305		199	ggG/gg	5/8	1	2	FACETS	0.898	0.84	0.957	0.898	0.84	0.957	CLONAL	1	TRUE	1	0.574666811043935	2		628	950	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923781	39923781	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0014718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	306	746	0	ENST00000378444.4:c.3310A>T	p.Lys1104Ter	p.K1104*	ENST00000378444	NM_001123385.1	1104	Aag/Tag	7/15	1	2	FACETS	0.982	0.927	1	0.982	0.927	1	CLONAL	1	TRUE	1	0.574666811043935	2		746	1084	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0015493-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	483	636	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.46867508629036	2	FACETS	0.928	0.893	0.963	0.928	0.893	0.963	CLONAL	2	TRUE	0	0.55984856734487	2		636	930	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190320	32190320	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377458854	NA	P-0015493-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	185	474	1	ENST00000375023.3:c.419G>A	p.Arg140His	p.R140H	ENST00000375023	NM_004557.3	140	cGc/cAc	3/30	0.551276604087313	3	FACETS	0.875	0.808	0.945	0.437	0.404	0.473	CLONAL	1	TRUE	1	0.55984856734487	3		475	967	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551900	150551901	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0015493-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	232	286	0	ENST00000369026.2:c.106_107del	p.Leu36GlyfsTer73	p.L36Gfs*73	ENST00000369026	NM_021960.4	36	TTg/g	1/3	0.377990328493721	6	FACETS	0.866	0.808	0.926	0.433	0.404	0.463	CLONAL	2	TRUE	2	0.55984856734487	6		286	1014	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879367	56879367	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015493-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	136	530	0	ENST00000519728.1:c.884A>T	p.Lys295Met	p.K295M	ENST00000519728	NM_002350.3	295	aAg/aTg	9/13	0.255097144738726	3	FACETS	0.618	0.561	0.678	0.309	0.28	0.339	INDETERMINATE	1	TRUE	1	0.55984856734487	3		530	1006	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0015802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	48	680	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.181908948078807	1	FACETS	0.521	0.439	0.612	0.521	0.439	0.612	SUBCLONAL	1	TRUE	0	0.181908948078807	1		680	921	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0015802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	35	298	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.721	0.59	0.868	0.721	0.59	0.868	SUBCLONAL	1	TRUE	1	0.181908948078807	2		298	534	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0016035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	348	0	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.731432911197129	2		0	939	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692832	89692832	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1085308039	NA	P-0016035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	160	207	0	ENST00000371953.3:c.316G>T	p.Glu106Ter	p.E106*	ENST00000371953	NM_000314.4	106	Gaa/Taa	5/9	0.731432911197129	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.731432911197129	1		207	243	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577428	64577428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555166664	NA	P-0016035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	524	717	0	ENST00000312049.6:c.154C>T	p.Arg52Cys	p.R52C	ENST00000312049	NM_130799.2	52	Cgc/Tgc	2/10	0.731432911197129	1	FACETS	0.988	0.954	1	0.988	0.954	1	CLONAL	1	TRUE	0	0.731432911197129	1		717	920	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944516	71944516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293622519	NA	P-0016035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	490	713	1	ENST00000298229.2:c.2072G>A	p.Arg691Gln	p.R691Q	ENST00000298229	NM_001567.3	691	cGg/cAg	18/28	0.731432911197129	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.731432911197129	1		714	826	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572547	95572547	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	184	278	0	ENST00000393063.1:c.2818G>C	p.Asp940His	p.D940H	ENST00000393063	NM_030621.3	940	Gat/Cat	19/28	1	2	FACETS	0.878	0.816	0.942	0.878	0.816	0.942	CLONAL	1	TRUE	1	0.731432911197129	2		278	573	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287533	33287534	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	AT	novel	NA	P-0016035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	402	645	1	ENST00000374542.5:c.1563_1564delinsAT	p.Gln522Ter	p.Q522*	ENST00000374542	NM_001141970.1	521	caGCaa/caATaa	6/8	0.731432911197129	1	FACETS	0.956	0.918	0.994	0.956	0.918	0.994	CLONAL	1	TRUE	0	0.731432911197129	1		646	729	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300906	137300906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	578	703	0	ENST00000481739.1:c.551G>A	p.Arg184Gln	p.R184Q	ENST00000481739	NM_002957.4	184	cGg/cAg	4/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.731432911197129	2		703	1442	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793195	139793195	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0016035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	378	560	0	ENST00000247668.2:c.3G>A	p.Met1?	p.M1?	ENST00000247668	NM_021138.3	1	atG/atA	2/11	1	2	FACETS	0.924	0.878	0.97	0.924	0.878	0.97	CLONAL	1	TRUE	1	0.731432911197129	2		560	1119	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159041	24159042	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0016457-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	412	962	0	ENST00000263121.7:c.716_717dup	p.Ala240LeufsTer28	p.A240Lfs*28	ENST00000263121	NM_003073.3	238	gcc/gcCTc	6/9	0.810916009892159	1	FACETS	0.947	0.913	0.98	0.947	0.913	0.98	CLONAL	1	TRUE	0	0.810916009892159	1		962	638	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018707-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	43	365	0				ENST00000310581	NM_198253.2	-/1132			0.411309488319584	3	FACETS	0.84	0.728	0.956			1	CLONAL	3	TRUE	NA	0.411309488319584	3		365	100	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0018707-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	162	405	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.411309488319584	3	FACETS	0.926	0.863	0.988	0.926	0.863	0.988	CLONAL	3	TRUE	0	0.411309488319584	3		405	342	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098816	178098816	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018707-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	25	279	0	ENST00000397062.3:c.229G>C	p.Asp77His	p.D77H	ENST00000397062	NM_006164.4	77	Gat/Cat	2/5	0.411309488319584	2	FACETS	0.21	0.165	0.262	0.105	0.082	0.131	SUBCLONAL	1	TRUE	0	0.411309488319584	2		279	579	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161458	2161467	+	frameshift_variant	Frame_Shift_Del	DEL	TTGGACTTGC	TTGGACTTGC	-	novel	NA	P-0018707-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	47	156	0	ENST00000434045.2:c.60_69del	p.Met20IlefsTer7	p.M20Ifs*7	ENST00000434045	NM_001127598.1	20	atGCAAGTCCAA/at	2/5	1	2	FACETS	0.859	0.73	0.999	0.859	0.73	0.999	CLONAL	1	TRUE	1	0.411309488319584	2		156	266	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954199	48954199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018707-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	67	104	0	ENST00000267163.4:c.1400G>A	p.Arg467Gln	p.R467Q	ENST00000267163	NM_000321.2	467	cGa/cAa	15/27	0.411309488319584	3	FACETS	0.847	0.746	0.952	0.847	0.746	0.952	CLONAL	2	TRUE	1	0.411309488319584	3		104	232	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039158	49039158	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018707-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	67	121	2	ENST00000267163.4:c.2236G>T	p.Glu746Ter	p.E746*	ENST00000267163	NM_000321.2	746	Gaa/Taa	22/27	0.411309488319584	3	FACETS	1	0.908	1	1	0.908	1	CLONAL	2	TRUE	1	0.411309488319584	3		123	191	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643348	38643348	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs946203764	NA	P-0018707-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	20	98	0	ENST00000299084.4:c.818G>C	p.Arg273Thr	p.R273T	ENST00000299084	NM_152594.2	273	aGa/aCa	7/7	0.349526772988973	4	FACETS	0.817	0.629	1	0.408	0.314	0.517	CLONAL	1	TRUE	2	0.411309488319584	4		98	168	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639653	3639653	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018707-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	58	283	0	ENST00000294008.3:c.3986C>G	p.Ser1329Cys	p.S1329C	ENST00000294008	NM_032444.2	1329	tCt/tGt	12/15	0.303265642340893	3	FACETS	1	0.97	1	0.733	0.637	0.834	CLONAL	1	TRUE	1	0.411309488319584	3		283	232	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646348	3646348	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0018707-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	40	191	0	ENST00000294008.3:c.1730C>G	p.Ser577Ter	p.S577*	ENST00000294008	NM_032444.2	577	tCa/tGa	8/15	0.303265642340893	3	FACETS	1	0.954	1	0.706	0.596	0.825	CLONAL	1	TRUE	1	0.411309488319584	3		191	166	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508787	31508787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370207689	NA	P-0018707-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	47	193	1	ENST00000344624.3:c.1528C>T	p.Arg510Cys	p.R510C	ENST00000344624		510	Cgc/Tgc	7/33	0.411309488319584	3	FACETS	0.95	0.807	1			1	CLONAL	1	TRUE	NA	0.411309488319584	3		194	290	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815544	139815544	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018707-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	79	252	0	ENST00000247668.2:c.1015G>A	p.Glu339Lys	p.E339K	ENST00000247668	NM_021138.3	339	Gag/Aag	9/11	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.411309488319584	2		252	377	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369130	118369130	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018707-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	14	168	0	ENST00000534358.1:c.5848C>G	p.Leu1950Val	p.L1950V	ENST00000534358	NM_005933.3	1950	Ctc/Gtc	22/36	0.322994873702909	1	FACETS	0.231	0.167	0.309	0.231	0.167	0.309	SUBCLONAL	1	TRUE	0	0.411309488319584	1		168	234	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633462	3633462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018707-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	15	263	0	ENST00000294008.3:c.4789G>A	p.Glu1597Lys	p.E1597K	ENST00000294008	NM_032444.2	1597	Gag/Aag	14/15	0.303265642340893	3	FACETS	0.322	0.235	0.427	0.161	0.117	0.214	SUBCLONAL	1	TRUE	1	0.411309488319584	3		263	273	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456433	29456433	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018707-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	23	161	0	ENST00000389048.3:c.2485A>C	p.Lys829Gln	p.K829Q	ENST00000389048	NM_004304.4	829	Aag/Cag	14/29	0.382623534746469	3	FACETS	0.684	0.537	0.853	0.228	0.179	0.285	SUBCLONAL	1	TRUE	0	0.411309488319584	3		161	197	SUCCESS
ATR	545	MSKCC	GRCh37	3	142243002	142243002	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018707-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	53	115	0	ENST00000350721.4:c.3985G>C	p.Glu1329Gln	p.E1329Q	ENST00000350721	NM_001184.3	1329	Gaa/Caa	22/47	0.408745565738634	4	FACETS	1	0.955	1	0.647	0.556	0.745	CLONAL	1	TRUE	2	0.411309488319584	4		115	281	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281117	49281117	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0121423-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	29	641	0	ENST00000282018.3:c.164G>A	p.Gly55Glu	p.G55E	ENST00000282018	NM_020377.2	55	gGa/gAa	1/1	0.106200887826648	4	FACETS	0.658	0.533	0.799	0.329	0.266	0.4	INDETERMINATE	1	NA	2	0.831721268528343	4		641	194	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858585	9858585	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0121423-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	19	471	0	ENST00000330684.3:c.2816G>C	p.Gly939Ala	p.G939A	ENST00000330684	NM_001134407.1	939	gGg/gCg	13/13	0.119087903045696	0	FACETS		NA	1			1	INDETERMINATE	1	NA	0	0.831721268528343	0		471	137	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211212	2211212	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0121423-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	37	940	1	ENST00000398665.3:c.1465+1G>T		p.X489_splice	ENST00000398665	NM_032482.2	489			0.299744862362044	1	FACETS	0.086	0.07	0.104	0.086	0.07	0.104	INDETERMINATE	1	NA	0	0.831721268528343	1		941	603	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210805	36210805	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0121423-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	35	1023	0	ENST00000222270.7:c.556A>C	p.Thr186Pro	p.T186P	ENST00000222270	NM_014727.1	186	Aca/Cca	3/37	0.299744862362044	1	FACETS	0.107	0.087	0.129	0.107	0.087	0.129	INDETERMINATE	1	NA	0	0.831721268528343	1		1023	461	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743967	41743967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0121423-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	31	1059	0	ENST00000301178.4:c.902C>T	p.Pro301Leu	p.P301L	ENST00000301178	NM_021913.4	301	cCt/cTt	7/20	0.299744862362044	1	FACETS	0.114	0.092	0.139	0.114	0.092	0.139	INDETERMINATE	1	NA	0	0.831721268528343	1		1059	383	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702202	47702202	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587778526	NA	P-0121423-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	53	345	0	ENST00000233146.2:c.1798G>T	p.Ala600Ser	p.A600S	ENST00000233146	NM_000251.2	600	Gct/Tct	12/16	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	NA	1	0.831721268528343	2		345	126	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295688	212295688	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0121423-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	18	401	0	ENST00000342788.4:c.2625C>A	p.Tyr875Ter	p.Y875*	ENST00000342788	NM_005235.2	875	taC/taA	21/28	1	2	FACETS	0.264	0.2	0.339	0.264	0.2	0.339	SUBCLONAL	1	NA	1	0.831721268528343	2		401	164	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713665	30713665	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121423-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	28	563	0	ENST00000295754.5:c.990G>T	p.Lys330Asn	p.K330N	ENST00000295754	NM_003242.5	330	aaG/aaT	4/7	0.831721268528343	1	FACETS	0.275	0.223	0.333	0.275	0.223	0.333	SUBCLONAL	1	NA	0	0.831721268528343	1		563	143	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074231	39074231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs980024517	NA	P-0021104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	388	435	0	ENST00000357387.3:c.79C>T	p.Pro27Ser	p.P27S	ENST00000357387	NM_152756.3	27	Ccg/Tcg	2/38	1	2	FACETS	0.982	0.935	1	0.982	0.935	1	CLONAL	1	TRUE	1	0.701511859405931	2		435	1126	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437578	56437578	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs746762909	NA	P-0021104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	350	622	0	ENST00000407977.2:c.884A>G	p.His295Arg	p.H295R	ENST00000407977		295	cAt/cGt	8/10	0.522375809981987	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.701511859405931	1		622	645	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9787061	9787061	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	202	764	0	ENST00000377346.4:c.3092T>G	p.Val1031Gly	p.V1031G	ENST00000377346	NM_005026.3	1031	gTg/gGg	24/24	1	2	FACETS	0.876	0.815	0.939	0.876	0.815	0.939	CLONAL	1	TRUE	1	0.641488024818034	2		764	719	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322622	39322622	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	169	614	0	ENST00000373001.3:c.370T>C	p.Phe124Leu	p.F124L	ENST00000373001	NM_022157.3	124	Ttt/Ctt	2/7	0.641488024818034	3	FACETS	0.878	0.808	0.95	0.439	0.404	0.475	CLONAL	1	TRUE	1	0.641488024818034	3		614	793	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830876	156830876	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	249	923	0	ENST00000524377.1:c.150C>A	p.Cys50Ter	p.C50*	ENST00000524377	NM_002529.3	50	tgC/tgA	1/17	0.641488024818034	3	FACETS	0.946	0.884	1	0.473	0.442	0.505	CLONAL	1	TRUE	1	0.641488024818034	3		923	1084	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982332	201982332	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	342	1297	0	ENST00000359651.3:c.715del	p.Asp239IlefsTer15	p.D239Ifs*15	ENST00000359651		237	aaG/aa	6/8	0.641488024818034	3	FACETS	0.953	0.9	1	0.476	0.45	0.504	CLONAL	1	TRUE	1	0.641488024818034	3		1297	1478	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154387	2154387	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	367	1541	0	ENST00000434045.2:c.541C>G	p.Arg181Gly	p.R181G	ENST00000434045	NM_001127598.1	181	Cgc/Ggc	5/5	0.62565335670579	3	FACETS	1	0.952	1			1	CLONAL	1	TRUE	NA	0.641488024818034	3		1541	1503	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	115	416	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.641488024818034	3	FACETS	0.843	0.762	0.928	0.421	0.381	0.464	CLONAL	1	TRUE	1	0.641488024818034	3		416	562	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110783	2110783	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1567423658	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	319	1201	0	ENST00000219476.3:c.1088A>G	p.Asn363Ser	p.N363S	ENST00000219476	NM_000548.3	363	aAc/aGc	11/42	0.634009211234148	2	FACETS	0.992	0.938	1	0.496	0.469	0.524	CLONAL	1	TRUE	0	0.641488024818034	2		1201	1003	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642720	3642720	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	283	948	0	ENST00000294008.3:c.2307G>T	p.Glu769Asp	p.E769D	ENST00000294008	NM_032444.2	769	gaG/gaT	11/15	0.634009211234148	2	FACETS	0.958	0.902	1	0.479	0.451	0.508	CLONAL	1	TRUE	0	0.641488024818034	2		948	921	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	596	958	0	ENST00000269305.4:c.672G>C	p.Glu224Asp	p.E224D	ENST00000269305	NM_001126112.2	224	gaG/gaC	6/11	0.634009211234148	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.641488024818034	2		958	912	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512261	38512261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	311	1111	0	ENST00000254066.5:c.1172G>T	p.Gly391Val	p.G391V	ENST00000254066	NM_000964.3	391	gGg/gTg	9/9	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.641488024818034	2		1111	916	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117895	70117895	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	182	724	0	ENST00000245479.2:c.363G>C	p.Arg121Ser	p.R121S	ENST00000245479	NM_000346.3	121	agG/agC	1/3	0.635582099875837	3	FACETS	0.962	0.889	1	0.481	0.444	0.519	CLONAL	1	TRUE	1	0.641488024818034	3		724	779	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743260	743260	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	608	727	0	ENST00000314574.4:c.880G>T	p.Gly294Ter	p.G294*	ENST00000314574	NM_005433.3	294	Gga/Tga	7/12	0.504892993593228	6	FACETS	1	0.99	1			1	CLONAL	3	TRUE	NA	0.641488024818034	6		727	1349	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308434	30308434	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	341	627	0	ENST00000262643.3:c.448G>T	p.Asp150Tyr	p.D150Y	ENST00000262643	NM_001238.2	150	Gat/Tat	6/12	0.635582099875837	3	FACETS	0.929	0.884	0.973	0.929	0.884	0.973	CLONAL	2	TRUE	1	0.641488024818034	3		627	756	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741015	40741015	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	596	1147	0	ENST00000392038.2:c.1303G>T	p.Asp435Tyr	p.D435Y	ENST00000392038	NM_001626.4	435	Gac/Tac	13/14	0.635582099875837	3	FACETS	0.945	0.911	0.979	0.945	0.911	0.979	CLONAL	2	TRUE	1	0.641488024818034	3		1147	1299	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966456	25966456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866685548	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	267	944	0	ENST00000435504.4:c.2750C>T	p.Ser917Leu	p.S917L	ENST00000435504		917	tCg/tTg	13/13	0.641488024818034	3	FACETS	1	0.951	1	0.508	0.476	0.541	CLONAL	1	TRUE	1	0.641488024818034	3		944	1082	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259296	89259296	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	253	494	0	ENST00000336596.2:c.440del	p.Ala147GlufsTer16	p.A147Efs*16	ENST00000336596	NM_005233.5	147	gCa/ga	3/17	0.579365541363768	4	FACETS	1	0.991	1	0.821	0.776	0.865	CLONAL	2	TRUE	1	0.641488024818034	4		494	526	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278129	142278129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	168	471	0	ENST00000350721.4:c.1696G>A	p.Val566Met	p.V566M	ENST00000350721	NM_001184.3	566	Gtg/Atg	7/47	0.579365541363768	4	FACETS	1	0.97	1	0.37	0.341	0.401	CLONAL	1	TRUE	1	0.641488024818034	4		471	774	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982091	38982091	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs201132232	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	541	490	0	ENST00000357387.3:c.631A>G	p.Ile211Val	p.I211V	ENST00000357387	NM_152756.3	211	Atc/Gtc	8/38	0.504892993593228	6	FACETS	0.978	0.945	1			1	CLONAL	4	TRUE	NA	0.641488024818034	6		490	984	SUCCESS
APC	324	MSKCC	GRCh37	5	112179752	112179752	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	98	326	0	ENST00000257430.4:c.8461G>C	p.Asp2821His	p.D2821H	ENST00000257430	NM_000038.5	2821	Gac/Cac	16/16	0.321892242715412	4	FACETS	1	0.924	1			1	INDETERMINATE	1	TRUE	NA	0.641488024818034	4		326	483	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394894	394894	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	207	643	0	ENST00000380956.4:c.290T>A	p.Leu97Gln	p.L97Q	ENST00000380956	NM_001195286.1	97	cTg/cAg	3/9	0.591846045808637	4	FACETS	1	0.933	1	0.503	0.466	0.541	CLONAL	1	TRUE	2	0.641488024818034	4		643	1053	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190522	32190522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770403231	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	285	1189	1	ENST00000375023.3:c.217C>T	p.Leu73Phe	p.L73F	ENST00000375023	NM_004557.3	73	Ctc/Ttc	3/30	0.591846045808637	4	FACETS	0.976	0.916	1	0.488	0.458	0.52	CLONAL	1	TRUE	2	0.641488024818034	4		1190	1494	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652007	36652007	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	561	1296	0	ENST00000244741.5:c.129G>T	p.Gln43His	p.Q43H	ENST00000244741	NM_000389.4	43	caG/caT	2/3	0.591846045808637	4	FACETS	0.907	0.87	0.944	0.907	0.87	0.944	CLONAL	2	TRUE	2	0.641488024818034	4		1296	1583	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984065	2984065	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	325	788	0	ENST00000396946.4:c.465G>T	p.Arg155Ser	p.R155S	ENST00000396946	NM_032415.4	155	agG/agT	5/25	0.332940953138455	3	FACETS	0.86	0.817	0.904	0.86	0.817	0.904	INDETERMINATE	2	TRUE	1	0.641488024818034	3		788	778	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971216	13971216	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754217454	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	152	630	0	ENST00000405192.2:c.713A>G	p.His238Arg	p.H238R	ENST00000405192	NM_001163147.1	238	cAc/cGc	8/12	0.332940953138455	3	FACETS	0.873	0.8	0.949	0.436	0.4	0.475	INDETERMINATE	1	TRUE	1	0.641488024818034	3		630	717	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273024	55273024	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	129	862	0	ENST00000275493.2:c.3347A>T	p.Asn1116Ile	p.N1116I	ENST00000275493	NM_005228.3	1116	aAc/aTc	28/28	0.332940953138455	3	FACETS	0.631	0.572	0.693	0.315	0.286	0.347	INDETERMINATE	1	TRUE	1	0.641488024818034	3		862	842	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358979	81358979	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	239	630	2	ENST00000222390.5:c.982C>A	p.Arg328Ser	p.R328S	ENST00000222390	NM_000601.4	328	Cgt/Agt	8/18	0.332940953138455	3	FACETS	0.755	0.709	0.801	0.755	0.709	0.801	INDETERMINATE	2	TRUE	1	0.641488024818034	3		632	652	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509625	106509625	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	189	754	0	ENST00000359195.3:c.1619G>T	p.Gly540Val	p.G540V	ENST00000359195	NM_002649.2	540	gGg/gTg	2/11	0.332940953138455	3	FACETS	1	0.976	1	0.561	0.52	0.603	INDETERMINATE	1	TRUE	1	0.641488024818034	3		754	694	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863040	56863040	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	144	555	1	ENST00000519728.1:c.307A>T	p.Lys103Ter	p.K103*	ENST00000519728	NM_002350.3	103	Aag/Tag	5/13	0.535034253907811	4	FACETS	0.922	0.842	1	0.307	0.28	0.336	CLONAL	1	TRUE	1	0.641488024818034	4		556	799	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080555	5080555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	50	288	0	ENST00000381652.3:c.2306G>A	p.Arg769Lys	p.R769K	ENST00000381652	NM_004972.3	769	aGg/aAg	18/25	1	2	FACETS	0.586	0.501	0.678	0.586	0.501	0.678	SUBCLONAL	1	TRUE	1	0.641488024818034	2		288	266	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317318	87317318	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	130	552	0	ENST00000277120.3:c.343A>T	p.Ser115Cys	p.S115C	ENST00000277120		115	Agc/Tgc	4/19	1	2	FACETS	0.875	0.8	0.954	0.875	0.8	0.954	CLONAL	1	TRUE	1	0.641488024818034	2		552	463	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566442	139566442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200483435	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	329	1314	1	ENST00000308874.7:c.701C>T	p.Pro234Leu	p.P234L	ENST00000308874		234	cCg/cTg	9/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.641488024818034	2		1315	1004	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916521	39916521	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	536	1069	0	ENST00000378444.4:c.4482C>A	p.Asp1494Glu	p.D1494E	ENST00000378444	NM_001123385.1	1494	gaC/gaA	11/15	0.321892242715412	4	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.641488024818034	4		1069	1213	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934394	39934394	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	428	767	1	ENST00000378444.4:c.205G>T	p.Ala69Ser	p.A69S	ENST00000378444	NM_001123385.1	69	Gca/Tca	4/15	0.321892242715412	4	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.641488024818034	4		768	913	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929072	44929072	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	186	619	0	ENST00000377967.4:c.2172A>G	p.Ile724Met	p.I724M	ENST00000377967	NM_021140.2	724	atA/atG	17/29	0.321892242715412	4	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.641488024818034	4		619	754	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650771	48650771	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	263	1058	0	ENST00000376670.3:c.640C>A	p.Leu214Met	p.L214M	ENST00000376670	NM_002049.3	214	Ctg/Atg	4/6	0.321892242715412	4	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.641488024818034	4		1058	1050	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409860	63409860	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	181	778	0	ENST00000330258.3:c.3307G>T	p.Gly1103Trp	p.G1103W	ENST00000330258	NM_152424.3	1103	Ggg/Tgg	2/2	1	2	FACETS	0.689	0.636	0.744	0.689	0.636	0.744	SUBCLONAL	1	TRUE	1	0.641488024818034	2		778	819	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023023-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	220	669	0	ENST00000397752.3:c.3028G>T	p.Asp1010Tyr	p.D1010Y	ENST00000397752	NM_000245.2	1010	Gat/Tat	14/21	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	2	TRUE	NA	0.341444995372249	2		669	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578483	7578483	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023023-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	219	845	1	ENST00000269305.4:c.447del	p.Thr150HisfsTer20	p.T150Hfs*20	ENST00000269305	NM_001126112.2	149	tcC/tc	5/11	0.324823547201981	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.341444995372249	2		846	574	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39567832	39567832	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023023-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	35	222	0	ENST00000262039.4:c.588G>T	p.Leu196Phe	p.L196F	ENST00000262039	NM_002647.2	196	ttG/ttT	5/25	1	2	FACETS	0.891	0.736	1	0.891	0.736	1	CLONAL	1	TRUE	1	0.341444995372249	2		222	230	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279235	142279235	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023023-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	151	380	1	ENST00000350721.4:c.1411G>A	p.Glu471Lys	p.E471K	ENST00000350721	NM_001184.3	471	Gaa/Aaa	6/47	0.294269505019438	5	FACETS	1	0.95	1	0.7	0.642	0.76	CLONAL	2	TRUE	2	0.341444995372249	5		381	637	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293660	137293660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023023-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	164	935	0	ENST00000481739.1:c.211C>T	p.Pro71Ser	p.P71S	ENST00000481739	NM_002957.4	71	Ccc/Tcc	2/10	0.341444995372249	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.341444995372249	2		935	468	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325345	1325345	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023023-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	122	448	0	ENST00000400841.2:c.330T>A	p.Ser110Arg	p.S110R	ENST00000400841		110	agT/agA	3/6	1	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.341444995372249	1		448	443	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514458	41514459	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0023023-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	28	402	0	ENST00000373198.4:c.202_203delinsTT	p.Ala68Leu	p.A68L	ENST00000373198	NM_133170.3	68	GCa/TTa	2/32	0.184272062521277	2	FACETS	0.592	0.474	0.725	0.296	0.237	0.363	INDETERMINATE	1	TRUE	0	0.341444995372249	2		402	277	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0023306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	62	397	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.400079306200867	3	FACETS	0.974	0.845	1	0.487	0.422	0.556	CLONAL	1	TRUE	1	0.400079306200867	3		397	382	SUCCESS
MET	4233	MSKCC	GRCh37	7	116417463	116417463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913244	NA	P-0023306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	123	335	0	ENST00000397752.3:c.3280C>T	p.His1094Tyr	p.H1094Y	ENST00000397752	NM_000245.2	1094	Cat/Tat	16/21	0.400079306200867	3	FACETS	0.835	0.76	0.912	0.556	0.507	0.608	CLONAL	2	TRUE	0	0.400079306200867	3		335	442	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574055	46574055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	99	969	3	ENST00000263734.3:c.70C>T	p.Arg24Trp	p.R24W	ENST00000263734	NM_001430.4	24	Cgg/Tgg	2/16	0.400079306200867	4	FACETS	0.829	0.739	0.924	0.414	0.369	0.462	CLONAL	1	TRUE	2	0.400079306200867	4		972	836	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778167	27778167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	103	918	0	ENST00000369163.2:c.316G>A	p.Glu106Lys	p.E106K	ENST00000369163	NM_003536.2	106	Gag/Aag	1/1	0.400079306200867	5	FACETS	1	0.965	1	0.295	0.264	0.328	CLONAL	1	TRUE	1	0.400079306200867	5		918	699	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165078	47165078	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	118	311	0	ENST00000409792.3:c.1048G>C	p.Asp350His	p.D350H	ENST00000409792	NM_014159.6	350	Gat/Cat	3/21	0.276111955344755	3	FACETS	0.98	0.894	1			1	CLONAL	2	TRUE	NA	0.400079306200867	3		311	361	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31483667	31483667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	46	275	0	ENST00000344624.3:c.2065C>T	p.Leu689Phe	p.L689F	ENST00000344624		689	Ctt/Ttt	13/33	0.347319049511812	5	FACETS	0.831	0.7	0.974	0.277	0.233	0.325	CLONAL	1	TRUE	2	0.400079306200867	5		275	443	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912304	32912304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	95	426	1	ENST00000380152.3:c.3812C>T	p.Ser1271Leu	p.S1271L	ENST00000380152		1271	tCa/tTa	11/27	0.331268324740272	2	FACETS	0.935	0.835	1	0.467	0.417	0.52	CLONAL	1	TRUE	0	0.400079306200867	2		427	508	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096196	71096196	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	53	317	0	ENST00000318789.4:c.561G>T	p.Gln187His	p.Q187H	ENST00000318789	NM_032682.5	187	caG/caT	10/21	0.400079306200867	3	FACETS	0.862	0.738	0.996	0.431	0.369	0.498	CLONAL	1	TRUE	1	0.400079306200867	3		317	369	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663871	241663871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1131691244	NA	P-0023306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	69	461	0	ENST00000366560.3:c.1256C>T	p.Ser419Leu	p.S419L	ENST00000366560	NM_000143.3	419	tCa/tTa	9/10	0.400079306200867	3	FACETS	0.816	0.712	0.928	0.408	0.356	0.464	CLONAL	1	TRUE	1	0.400079306200867	3		461	507	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979559	2979559	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	49	505	0	ENST00000396946.4:c.688G>C	p.Asp230His	p.D230H	ENST00000396946	NM_032415.4	230	Gat/Cat	6/25	0.400079306200867	5	FACETS	0.863	0.732	1			1	CLONAL	1	TRUE	NA	0.400079306200867	5		505	454	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970898	70970898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	122	552	0	ENST00000276594.2:c.1363C>T	p.His455Tyr	p.H455Y	ENST00000276594	NM_024504.3	455	Cat/Tat	6/8	0.400079306200867	3	FACETS	1	0.985	1	0.482	0.438	0.528	CLONAL	1	TRUE	0	0.400079306200867	3		552	506	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112578	115112578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	123	1005	1	ENST00000257566.3:c.1162G>A	p.Glu388Lys	p.E388K	ENST00000257566	NM_016569.3	388	Gag/Aag	7/8	0.367819855423463	3	FACETS	0.963	0.872	1	0.482	0.436	0.53	CLONAL	1	TRUE	1	0.400079306200867	3		1006	766	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271331	18271331	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753702580	NA	P-0023306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	99	962	0	ENST00000222254.8:c.373C>T	p.Pro125Ser	p.P125S	ENST00000222254	NM_005027.3	125	Ccc/Tcc	3/16	0.372366896402988	3	FACETS	0.953	0.852	1	0.477	0.426	0.53	CLONAL	1	TRUE	1	0.400079306200867	3		962	623	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056314	26056314	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	82	543	1	ENST00000343677.2:c.343G>T	p.Glu115Ter	p.E115*	ENST00000343677	NM_005319.3	115	Gaa/Taa	1/1	0.29152998133254	3	FACETS	1	0.944	1	0.37	0.328	0.415	CLONAL	1	TRUE	0	0.400079306200867	3		544	443	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216491	108216491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	32	213	0	ENST00000278616.4:c.8440G>A	p.Glu2814Lys	p.E2814K	ENST00000278616	NM_000051.3	2814	Gaa/Aaa	58/63	0.221836208507024	5	FACETS	0.748	0.608	0.906	0.249	0.202	0.302	INDETERMINATE	1	TRUE	2	0.400079306200867	5		213	342	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	430272	430272	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	50	240	0	ENST00000399788.2:c.2430G>C	p.Gln810His	p.Q810H	ENST00000399788	NM_001042603.1	810	caG/caC	18/28	0.400079306200867	5	FACETS	0.93	0.791	1			1	CLONAL	1	TRUE	NA	0.400079306200867	5		240	430	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42002963	42002963	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	80	526	0	ENST00000219905.7:c.2500G>T	p.Glu834Ter	p.E834*	ENST00000219905	NM_001164273.1	834	Gaa/Taa	8/24	0.331268324740272	2	FACETS	0.877	0.775	0.986	0.439	0.387	0.493	CLONAL	1	TRUE	0	0.400079306200867	2		526	456	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658927	3658927	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1346974204	NA	P-0023306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	88	572	0	ENST00000294008.3:c.39C>G	p.Tyr13Ter	p.Y13*	ENST00000294008	NM_032444.2	13	taC/taG	2/15	0.347319049511812	5	FACETS	1	0.893	1	0.336	0.298	0.377	CLONAL	1	TRUE	2	0.400079306200867	5		572	698	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805596	89805596	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	74	797	0	ENST00000389301.3:c.4112G>C	p.Gly1371Ala	p.G1371A	ENST00000389301	NM_000135.2	1371	gGg/gCg	41/43	0.400079306200867	3	FACETS	0.786	0.689	0.89			1	SUBCLONAL	1	TRUE	NA	0.400079306200867	3		797	565	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40444068	40444068	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	66	702	0	ENST00000345506.4:c.364G>C	p.Glu122Gln	p.E122Q	ENST00000345506	NM_003152.3	122	Gaa/Caa	5/20	0.347319049511812	5	FACETS	0.858	0.745	0.981	0.286	0.248	0.327	CLONAL	1	TRUE	2	0.400079306200867	5		702	615	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152007	11152007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	31	577	0	ENST00000358026.2:c.4291G>A	p.Glu1431Lys	p.E1431K	ENST00000358026	NM_001128849.1	1431	Gag/Aag	31/36	0.372366896402988	3	FACETS	0.432	0.349	0.527	0.216	0.174	0.264	SUBCLONAL	1	TRUE	1	0.400079306200867	3		577	430	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750683	39750683	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	50	259	0	ENST00000361337.2:c.2083G>C	p.Glu695Gln	p.E695Q	ENST00000361337	NM_003286.2	695	Gag/Cag	20/21	0.29152998133254	3	FACETS	1	0.958	1	0.45	0.386	0.519	CLONAL	1	TRUE	0	0.400079306200867	3		259	222	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430734	181430734	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	117	908	0	ENST00000325404.1:c.586C>A	p.Pro196Thr	p.P196T	ENST00000325404	NM_003106.3	196	Ccc/Acc	1/1	0.400079306200867	3	FACETS	0.99	0.894	1	0.495	0.447	0.546	CLONAL	1	TRUE	1	0.400079306200867	3		908	709	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915621	131915621	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	82	262	0	ENST00000265335.6:c.619C>T	p.Gln207Ter	p.Q207*	ENST00000265335		207	Caa/Taa	5/25	0.221836208507024	5	FACETS	1	0.976	1	0.477	0.422	0.536	INDETERMINATE	1	TRUE	2	0.400079306200867	5		262	458	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827191	170827191	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	57	430	0	ENST00000296930.5:c.559G>A	p.Glu187Lys	p.E187K	ENST00000296930	NM_002520.6	187	Gaa/Aaa	7/11	0.221836208507024	5	FACETS	1	0.862	1	0.334	0.287	0.385	INDETERMINATE	1	TRUE	2	0.400079306200867	5		430	455	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080620	5080620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	67	436	0	ENST00000381652.3:c.2371G>A	p.Glu791Lys	p.E791K	ENST00000381652	NM_004972.3	791	Gaa/Aaa	18/25	0.356520295165801	1	FACETS	0.703	0.614	0.799	0.703	0.614	0.799	SUBCLONAL	1	TRUE	0	0.400079306200867	1		436	381	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937587	76937587	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	77	432	0	ENST00000373344.5:c.3161C>G	p.Ser1054Cys	p.S1054C	ENST00000373344	NM_000489.3	1054	tCt/tGt	9/35	0.400079306200867	4	FACETS	0.917	0.805	1	0.458	0.402	0.518	CLONAL	1	TRUE	2	0.400079306200867	4		432	588	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023746-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	43	365	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.775	0.652	0.911	1	0.96	1	CLONAL	2	FALSE	1	0.181295148111328	2		365	306	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426751	49426751	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023746-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	25	330	0	ENST00000301067.7:c.11737C>T	p.Gln3913Ter	p.Q3913*	ENST00000301067	NM_003482.3	3913	Cag/Tag	39/54	1	2	FACETS	0.584	0.459	0.728	0.584	0.459	0.728	SUBCLONAL	1	FALSE	1	0.181295148111328	2		330	472	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0023746-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	89	642	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.184819266451372	3	FACETS	1	0.972	1	0.665	0.589	0.747	CLONAL	1	FALSE	1	0.181295148111328	3		642	805	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982329	201982330	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0023746-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	85	787	0	ENST00000359651.3:c.709_710dup	p.Gly238ArgfsTer17	p.G238Rfs*17	ENST00000359651		236	-/AA	6/8	1	2	FACETS	0.899	0.793	1	0.899	0.793	1	CLONAL	1	FALSE	1	0.181295148111328	2		787	1043	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426279	49426279	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023746-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	63	785	1	ENST00000301067.7:c.12209C>T	p.Ser4070Phe	p.S4070F	ENST00000301067	NM_003482.3	4070	tCt/tTt	39/54	1	2	FACETS	0.643	0.554	0.74	0.643	0.554	0.74	SUBCLONAL	1	FALSE	1	0.181295148111328	2		786	1081	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426526	49426526	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023746-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	58	824	0	ENST00000301067.7:c.11962C>T	p.Gln3988Ter	p.Q3988*	ENST00000301067	NM_003482.3	3988	Cag/Tag	39/54	1	2	FACETS	0.554	0.474	0.642	0.554	0.474	0.642	SUBCLONAL	1	FALSE	1	0.181295148111328	2		824	1155	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116176	67116176	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023746-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	31	439	0	ENST00000412916.2:c.460G>C	p.Glu154Gln	p.E154Q	ENST00000412916		154	Gaa/Caa	5/6	0.184819266451372	3	FACETS	0.618	0.498	0.754	0.309	0.249	0.377	SUBCLONAL	1	FALSE	1	0.181295148111328	3		439	604	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541890	187541891	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023746-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	54	469	0	ENST00000441802.2:c.5849dup	p.Thr1951AsnfsTer3	p.T1951Nfs*3	ENST00000441802	NM_005245.3	1950	cta/ctTa	10/27	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	FALSE	1	0.181295148111328	2		469	592	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627478	14627478	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023746-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	42	529	0	ENST00000254322.2:c.592C>T	p.Arg198Ter	p.R198*	ENST00000254322	NM_006145.1	198	Cga/Tga	2/3	1	2	FACETS	0.654	0.544	0.776	0.654	0.544	0.776	SUBCLONAL	1	FALSE	1	0.181295148111328	2		529	709	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852289	128852289	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023746-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	41	594	0	ENST00000249373.3:c.2361C>G	p.Phe787Leu	p.F787L	ENST00000249373	NM_005631.4	787	ttC/ttG	12/12	1	2	FACETS	0.637	0.529	0.758	0.637	0.529	0.758	SUBCLONAL	1	FALSE	1	0.181295148111328	2		594	710	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0024319-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	816	756	1	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.299477700154186	12	FACETS	0.969	0.944	0.994			1	CLONAL	11	TRUE	NA	0.28	12		757	1312	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597378	10597378	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024319-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	125	1104	0	ENST00000171111.5:c.1825A>T	p.Thr609Ser	p.T609S	ENST00000171111	NM_203500.1	609	Acc/Tcc	6/6	0.219397539515163	2	FACETS	1	0.985	1	0.738	0.67	0.809	CLONAL	1	TRUE	0	0.28	2		1104	605	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61708412	61708412	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024319-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	23	279	0	ENST00000401558.2:c.2977C>T	p.Gln993Ter	p.Q993*	ENST00000401558	NM_003400.3	993	Caa/Taa	24/25	0.219397539515163	2	FACETS	0.743	0.582	0.928	0.372	0.291	0.464	CLONAL	1	TRUE	0	0.28	2		279	221	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212522506	212522506	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748501593	NA	P-0024319-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	43	429	0	ENST00000342788.4:c.1919G>A	p.Gly640Asp	p.G640D	ENST00000342788	NM_005235.2	640	gGc/gAc	16/28	0.219397539515163	2	FACETS	0.978	0.822	1	0.489	0.411	0.575	CLONAL	1	TRUE	0	0.28	2		429	314	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912679	32912680	+	missense_variant	Missense_Mutation	DNP	AA	AA	TT	novel	NA	P-0024319-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	17	452	1	ENST00000380152.3:c.4187_4188inv	p.Gln1396Leu	p.Q1396L	ENST00000380152		1396	cAA/cTT	11/27	0.264599273113593	1	FACETS	0.352	0.262	0.458	0.352	0.262	0.458	SUBCLONAL	1	TRUE	0	0.28	1		453	297	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0024335-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	187	473	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.450717532840331	3	FACETS	0.883	0.82	0.946	0.883	0.82	0.946	CLONAL	2	TRUE	1	0.450717532840331	3		474	576	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0024335-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	68	210	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.898	0.787	1	0.898	0.787	1	CLONAL	1	TRUE	1	0.450717532840331	2		210	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0024335-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	304	831	0	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	0.444765329124682	1	FACETS	0.937	0.883	0.992	0.937	0.883	0.992	CLONAL	1	TRUE	0	0.450717532840331	1		831	1115	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041576	47041576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024335-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	157	731	1	ENST00000377604.3:c.1801C>T	p.Gln601Ter	p.Q601*	ENST00000377604	NM_001204468.1	601	Cag/Tag	17/24	0.435053072701258	1	FACETS	0.876	0.806	0.949	0.876	0.806	0.949	CLONAL	1	TRUE	0	0.450717532840331	1		732	616	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181987	32181987	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024335-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	190	835	0	ENST00000375023.3:c.2067G>C	p.Glu689Asp	p.E689D	ENST00000375023	NM_004557.3	689	gaG/gaC	13/30	0.450717532840331	3	FACETS	0.833	0.769	0.901	0.417	0.384	0.451	CLONAL	1	TRUE	1	0.450717532840331	3		835	1240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0024692-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	367	1201	2	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.226572976808161	3	FACETS	0.911	0.863	0.959	0.911	0.863	0.959	CLONAL	3	TRUE	0	0.226572976808161	3		1203	1320	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0024692-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	41	286	2	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.226572976808161	2		288	302	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352575	89352575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1301722354	NA	P-0024692-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	79	600	0	ENST00000301030.4:c.764G>A	p.Arg255Gln	p.R255Q	ENST00000301030	NM_001256183.1	255	cGg/cAg	8/13	0.201901543402285	3	FACETS	1	0.922	1	0.532	0.468	0.602	CLONAL	1	TRUE	1	0.226572976808161	3		600	729	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884908	134884908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202034365	NA	P-0024692-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	80	612	0	ENST00000398015.3:c.1684G>A	p.Val562Ile	p.V562I	ENST00000398015	NM_004441.4	562	Gtc/Atc	8/16	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.226572976808161	2		612	609	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120544	2120545	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0024692-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	204	1237	0	ENST00000219476.3:c.1807_1808dup	p.Leu604ProfsTer95	p.L604Pfs*95	ENST00000219476	NM_000548.3	602	tac/tACac	17/42	0.199497846512956	2	FACETS	0.829	0.768	0.892	0.829	0.768	0.892	CLONAL	2	TRUE	0	0.226572976808161	2		1237	1086	SUCCESS
APC	324	MSKCC	GRCh37	5	112176018	112176018	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024692-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	21	299	0	ENST00000257430.4:c.4728del	p.Glu1577AsnfsTer73	p.E1577Nfs*73	ENST00000257430	NM_000038.5	1576	gAa/ga	16/16	1	2	FACETS	0.641	0.494	0.813	0.641	0.494	0.813	SUBCLONAL	1	TRUE	1	0.226572976808161	2		299	289	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0026170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	488	414	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.726566421638932	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.726566421638932	1		414	783	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142524	119142524	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	206	469	0	ENST00000264033.4:c.523C>T	p.Gln175Ter	p.Q175*	ENST00000264033	NM_005188.3	175	Cag/Tag	3/16	0.726566421638932	1	FACETS	0.499	0.464	0.534	0.499	0.464	0.534	SUBCLONAL	1	TRUE	0	0.726566421638932	1		469	724	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602800	10602800	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	958	955	1	ENST00000171111.5:c.778C>T	p.Arg260Ter	p.R260*	ENST00000171111	NM_203500.1	260	Cga/Tga	3/6	0.726566421638932	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.726566421638932	1		956	1632	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865281	57865282	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0026170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	910	788	2	ENST00000228682.2:c.2758_2759delinsTT	p.Ala920Phe	p.A920F	ENST00000228682	NM_005269.2	920	GCc/TTc	12/12	0.726566421638932	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.726566421638932	1		790	1512	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243728	41243729	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0026170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	506	618	1	ENST00000357654.3:c.3819_3820delinsTT	p.Gln1273_Val1274delinsHisLeu	p.Q1273_V1274delinsHL	ENST00000357654	NM_007294.3	1273	caGGta/caTTta	10/23	0.726566421638932	1	FACETS	0.993	0.958	1	0.993	0.958	1	CLONAL	1	TRUE	0	0.726566421638932	1		619	893	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572662	64572662	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	ATG	novel	NA	P-0026170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	671	778	1	ENST00000312049.6:c.1194delinsCAT	p.Gln398HisfsTer48	p.Q398Hfs*48	ENST00000312049	NM_130799.2	398	caG/caCAT	9/10	0.726566421638932	1	FACETS	0.913	0.884	0.942	0.913	0.884	0.942	CLONAL	1	TRUE	0	0.726566421638932	1		779	1288	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910632	50910632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1354117345	NA	P-0026170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	378	809	0	ENST00000440232.2:c.1735G>A	p.Glu579Lys	p.E579K	ENST00000440232	NM_002691.3	579	Gag/Aag	14/27	0.726566421638932	1	FACETS	0.516	0.489	0.543	0.516	0.489	0.543	SUBCLONAL	1	TRUE	0	0.726566421638932	1		809	1285	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100667	8100667	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	433	859	1	ENST00000346208.3:c.641C>T	p.Ser214Leu	p.S214L	ENST00000346208		214	tCg/tTg	3/6	0.726566421638932	1	FACETS	0.507	0.482	0.532	0.507	0.482	0.532	SUBCLONAL	1	TRUE	0	0.726566421638932	1		860	1498	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26971342	26971342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	81	231	0	ENST00000381527.3:c.913G>A	p.Asp305Asn	p.D305N	ENST00000381527	NM_001260.1	305	Gat/Aat	9/13	0.726566421638932	1	FACETS	0.48	0.427	0.535	0.48	0.427	0.535	SUBCLONAL	1	TRUE	0	0.726566421638932	1		231	296	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791367	42791367	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	432	856	0	ENST00000575354.2:c.427G>T	p.Glu143Ter	p.E143*	ENST00000575354	NM_015125.3	143	Gag/Tag	3/20	0.726566421638932	1	FACETS	0.495	0.471	0.52	0.495	0.471	0.52	SUBCLONAL	1	TRUE	0	0.726566421638932	1		856	1529	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161795	56161795	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	135	350	0	ENST00000399503.3:c.1292C>T	p.Ser431Leu	p.S431L	ENST00000399503	NM_005921.1	431	tCa/tTa	6/20	1	2	FACETS	0.433	0.393	0.474	0.433	0.393	0.474	SUBCLONAL	1	TRUE	1	0.726566421638932	2		350	859	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412575	63412575	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	309	420	0	ENST00000330258.3:c.592G>C	p.Glu198Gln	p.E198Q	ENST00000330258	NM_152424.3	198	Gag/Cag	2/2	1	1	FACETS	0.604	0.571	0.637	0.604	0.571	0.637	SUBCLONAL	1	TRUE	0	0.726566421638932	1		420	897	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199839	108199839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779861	NA	P-0026255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	34	236	0	ENST00000278616.4:c.7181C>T	p.Ser2394Leu	p.S2394L	ENST00000278616	NM_000051.3	2394	tCa/tTa	49/63	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.18	2		236	346	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374642	118374642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	29	249	0	ENST00000534358.1:c.8035G>A	p.Glu2679Lys	p.E2679K	ENST00000534358	NM_005933.3	2679	Gaa/Aaa	27/36	1	2	FACETS	0.824	0.661	1	0.824	0.661	1	CLONAL	1	TRUE	1	0.18	2		249	391	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626939	158626939	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	56	382	0	ENST00000263640.3:c.731C>T	p.Ser244Leu	p.S244L	ENST00000263640	NM_001105.4	244	tCa/tTa	7/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.18	2		382	537	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242480	+	frameshift_variant	Frame_Shift_Del	DEL	TTAAGAGAAGCA	TTAAGAGAAGCA	C	novel	NA	P-0026255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	101	390	0	ENST00000275493.2:c.2239_2250delinsC	p.Leu747HisfsTer12	p.L747Hfs*12	ENST00000275493	NM_005228.3	747	TTAAGAGAAGCA/C	19/28	0.3	6	FACETS	0.948	0.847	1	0.474	0.423	0.528	CLONAL	2	TRUE	2	0.18	6		390	805	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0027639-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	324	652	1	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.377180099589511	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.377180099589511	4		653	1085	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578446	7578446	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027639-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	394	1028	0	ENST00000269305.4:c.484A>T	p.Ile162Phe	p.I162F	ENST00000269305	NM_001126112.2	162	Atc/Ttc	5/11	0.373656294533286	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.377180099589511	2		1028	987	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245011	133245011	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027639-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	202	1025	0	ENST00000320574.5:c.2104G>T	p.Gly702Trp	p.G702W	ENST00000320574	NM_006231.2	702	Ggg/Tgg	19/49	0.373656294533286	2	FACETS	1	0.975	1	0.558	0.517	0.6	CLONAL	1	TRUE	0	0.377180099589511	2		1025	960	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061004	38061004	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027639-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	86	443	1	ENST00000250448.2:c.985G>T	p.Ala329Ser	p.A329S	ENST00000250448	NM_004496.3	329	Gcc/Tcc	2/2	0.377180099589511	3	FACETS	1	0.965	1	0.609	0.541	0.681	CLONAL	1	TRUE	1	0.377180099589511	3		444	445	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482863	67482863	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027639-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	139	631	0	ENST00000327367.4:c.1267A>T	p.Ser423Cys	p.S423C	ENST00000327367	NM_005902.3	423	Agt/Tgt	9/9	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.377180099589511	2		631	642	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134284	2134284	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027639-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	205	1094	0	ENST00000219476.3:c.4061G>T	p.Gly1354Val	p.G1354V	ENST00000219476	NM_000548.3	1354	gGc/gTc	34/42	0.326156570537638	2	FACETS	1	0.986	1	0.623	0.579	0.669	CLONAL	1	TRUE	0	0.377180099589511	2		1094	872	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993329	72993329	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027639-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	246	989	0	ENST00000268489.5:c.716A>G	p.Lys239Arg	p.K239R	ENST00000268489	NM_006885.3	239	aAa/aGa	2/10	0.377180099589511	2	FACETS	1	0.988	1	0.616	0.575	0.657	CLONAL	1	TRUE	0	0.377180099589511	2		989	1059	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974981	15974981	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0027639-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	62	372	0	ENST00000268712.3:c.3896-2A>T		p.X1299_splice	ENST00000268712	NM_006311.3	1299			0.373656294533286	2	FACETS	0.884	0.767	1	0.442	0.383	0.505	CLONAL	1	TRUE	0	0.377180099589511	2		372	372	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40761084	40761084	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027639-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	355	811	0	ENST00000392038.2:c.268G>T	p.Val90Leu	p.V90L	ENST00000392038	NM_001626.4	90	Gtg/Ttg	4/14	0.377180099589511	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.377180099589511	2		811	807	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858228	27858228	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027639-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1174	72	851	0	ENST00000359303.2:c.343G>C	p.Ala115Pro	p.A115P	ENST00000359303	NM_003535.2	115	Gcc/Ccc	1/1	0.377180099589511	9	FACETS	0.711	0.619	0.811	0.102	0.088	0.116	SUBCLONAL	1	TRUE	2	0.377180099589511	9		851	1246	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505533	157505533	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027639-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	33	388	0	ENST00000346085.5:c.3514A>T	p.Thr1172Ser	p.T1172S	ENST00000346085	NM_020732.3	1172	Acc/Tcc	13/20	0.189844985281861	1	FACETS	0.412	0.335	0.497	0.412	0.335	0.497	INDETERMINATE	1	TRUE	0	0.377180099589511	1		388	345	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912011	127912012	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0027639-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	168	437	0	ENST00000373547.4:c.858_859delinsTT	p.Ala287Ser	p.A287S	ENST00000373547	NM_002721.4	286	cgGGca/cgTTca	7/7	0.326156570537638	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	0	0.377180099589511	2		437	444	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041029	47041792	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGCTGCCAACAGCCAGGTGAGTGAGCCCTGTGGGTATGTATCCCGGGGAGGCAGGCAGGCGGCAGGGGTGGCATGGGCAGACACTGAGCCCTGTTCTCCTGTCTGGCCCCATGACCAGTCGTATACCATCATGTCACCCGCTGTGCTCAAATCTGAGCTCCAGAGCCCTACCCATCCTAGTTCTGCTCTCCCACCGGCTACCAGCCCCACTGCCCAGGAATCCTACAGCCAGTACCGTGAGTAGCCACAGCCTGTGGGTAGGGGTGGGGAGTTCTTAATAAAGCAGGGAATAGTGTGACCCCGTTCCCCTCACCCCCTAGCTGTTCCCGACGTCTCTACCTACCAGTACGATGAGACCTCCGGCTACTACTATGACCCCCAGACCGGCCTCTACTATGACCCCAACTCCCAGGTAATAGGGCAGCCCAGGGAGGGATGGGATCGGGTCAGGTCGCGTCAGGAACAGCTAGCCCTGCAGGTTCCCTTCACAAGGTCTTCCCTCACATCCCCTCTTCCCTCCTCCTCCCTCAGTATTACTACAATGCTCAGAGCCAGCAGTACCTGTACTGGGATGGGGAGAGGCGGACCTATGTTCCCGCCCTGGAGCAGTCGGCCGACGGACATAAGGAGACAGGGGCACCCTCGAAGGAGGGCAAAGAGAAGAAGGAGAAGCACAAGACCAAGACAGCTCAACAGGTGAACACCAGGGTCCAGCAGTCACTGGCTGGCTGTGTGGTGTCTTCCAGCAACGGCACTCTGTCAG	CTGCTGCCAACAGCCAGGTGAGTGAGCCCTGTGGGTATGTATCCCGGGGAGGCAGGCAGGCGGCAGGGGTGGCATGGGCAGACACTGAGCCCTGTTCTCCTGTCTGGCCCCATGACCAGTCGTATACCATCATGTCACCCGCTGTGCTCAAATCTGAGCTCCAGAGCCCTACCCATCCTAGTTCTGCTCTCCCACCGGCTACCAGCCCCACTGCCCAGGAATCCTACAGCCAGTACCGTGAGTAGCCACAGCCTGTGGGTAGGGGTGGGGAGTTCTTAATAAAGCAGGGAATAGTGTGACCCCGTTCCCCTCACCCCCTAGCTGTTCCCGACGTCTCTACCTACCAGTACGATGAGACCTCCGGCTACTACTATGACCCCCAGACCGGCCTCTACTATGACCCCAACTCCCAGGTAATAGGGCAGCCCAGGGAGGGATGGGATCGGGTCAGGTCGCGTCAGGAACAGCTAGCCCTGCAGGTTCCCTTCACAAGGTCTTCCCTCACATCCCCTCTTCCCTCCTCCTCCCTCAGTATTACTACAATGCTCAGAGCCAGCAGTACCTGTACTGGGATGGGGAGAGGCGGACCTATGTTCCCGCCCTGGAGCAGTCGGCCGACGGACATAAGGAGACAGGGGCACCCTCGAAGGAGGGCAAAGAGAAGAAGGAGAAGCACAAGACCAAGACAGCTCAACAGGTGAACACCAGGGTCCAGCAGTCACTGGCTGGCTGTGTGGTGTCTTCCAGCAACGGCACTCTGTCAG	-	novel	NA	P-0027639-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	98	515	0	ENST00000377604.3:c.1561_1950+69del		p.X521_splice	ENST00000377604	NM_001204468.1	521		14-17/24	1	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.377180099589511	1		515	397	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029093-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	432	323	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.608410296753237	5	FACETS	0.992	0.966	1	0.992	0.966	1	CLONAL	5	TRUE	0	0.609152082002178	5		323	547	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578457	+	frameshift_variant	Frame_Shift_Del	DEL	GCGC	GCGC	-	novel	NA	P-0029093-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	567	744	0	ENST00000269305.4:c.473_476del	p.Arg158ProfsTer11	p.R158Pfs*11	ENST00000269305	NM_001126112.2	158	cGCGCc/cc	5/11	0.609152082002178	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.609152082002178	2		744	916	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131495	202131495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029093-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	103	383	0	ENST00000358485.4:c.463G>A	p.Ala155Thr	p.A155T	ENST00000358485	NM_001080125.1	155	Gct/Act	2/9	0.609152082002178	3	FACETS	0.77	0.691	0.854	0.385	0.345	0.427	SUBCLONAL	1	TRUE	1	0.609152082002178	3		383	573	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918675	44918692	+	inframe_deletion	In_Frame_Del	DEL	TACCTCTGCACTTGCAGC	TACCTCTGCACTTGCAGC	-	novel	NA	P-0029093-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	91	450	0	ENST00000377967.4:c.1158_1175del	p.Asn386_Ala392delinsLys	p.N386_A392delinsK	ENST00000377967	NM_021140.2	386	aaTACCTCTGCACTTGCAGCa/aaa	12/29	NA	2	FACETS	0.684	0.61	0.761			1	INDETERMINATE	1	TRUE	NA	0.609152082002178	2		450	437	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0029432-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	286	652	1	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.622106544968478	2	FACETS	0.888	0.848	0.928	0.888	0.848	0.928	CLONAL	2	TRUE	0	0.673649299156441	2		653	478	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0029432-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	92	474	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.622106544968478	2	FACETS	0.518	0.462	0.578	0.259	0.231	0.289	SUBCLONAL	1	TRUE	0	0.673649299156441	2		474	527	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913396	NA	P-0029432-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	102	247	0	ENST00000349496.5:c.95A>T	p.Asp32Val	p.D32V	ENST00000349496	NM_001904.3	32	gAc/gTc	3/15	0.31310380937337	1	FACETS	0.661	0.598	0.725	0.661	0.598	0.725	INDETERMINATE	1	TRUE	0	0.673649299156441	1		247	304	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249091	55249091	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519861	NA	P-0029432-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	95	471	0	ENST00000275493.2:c.2389T>A	p.Cys797Ser	p.C797S	ENST00000275493	NM_005228.3	797	Tgc/Agc	20/28	0.622106544968478	2	FACETS	0.52	0.464	0.58	0.26	0.232	0.29	SUBCLONAL	1	TRUE	0	0.673649299156441	2		471	542	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285805	46285805	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029432-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	91	255	0	ENST00000334344.6:c.5073T>G	p.Cys1691Trp	p.C1691W	ENST00000334344	NM_152641.2	1691	tgT/tgG	18/21	0.586719326532301	2	FACETS	0.86	0.772	0.952	0.43	0.386	0.476	CLONAL	1	TRUE	0	0.673649299156441	2		255	314	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604786	48604787	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0029432-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	119	259	0	ENST00000342988.3:c.1609_1610del	p.Asp537ArgfsTer39	p.D537Rfs*39	ENST00000342988	NM_005359.5	536	ctAGac/ctac	12/12	0.457436563687864	1	FACETS	0.919	0.846	0.992	0.919	0.846	0.992	CLONAL	1	TRUE	0	0.673649299156441	1		259	255	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0029506-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	765	964	2	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.900019338423518	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.900019338423518	2		966	823	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052632	42052632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779811318	NA	P-0029506-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	323	460	0	ENST00000219905.7:c.7303C>T	p.Arg2435Trp	p.R2435W	ENST00000219905	NM_001164273.1	2435	Cgg/Tgg	20/24	0.900019338423518	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.900019338423518	2		460	337	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860777	45860777	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029506-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	236	651	0	ENST00000391945.4:c.1332C>G	p.Ile444Met	p.I444M	ENST00000391945	NM_000400.3	444	atC/atG	14/23	0.85278026494982	4	FACETS	0.942	0.879	1	0.471	0.439	0.504	CLONAL	1	TRUE	2	0.900019338423518	4		651	1058	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476258	88476258	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029506-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	187	431	0	ENST00000360948.2:c.1874T>G	p.Leu625Arg	p.L625R	ENST00000360948	NM_001012338.2	625	cTg/cGg	15/19	0.792032594561147	4	FACETS	1	0.945	1	0.513	0.474	0.552	CLONAL	1	TRUE	2	0.900019338423518	4		431	770	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587490	29587490	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029506-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	321	375	0	ENST00000356175.3:c.4471T>A	p.Trp1491Arg	p.W1491R	ENST00000356175	NM_000267.3	1491	Tgg/Agg	33/57	0.51040067902688	4	FACETS	0.918	0.882	0.954	0.918	0.882	0.954	INDETERMINATE	3	TRUE	1	0.900019338423518	4		375	492	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0029513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	10	351	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.173	0.117	0.244	0.173	0.117	0.244	SUBCLONAL	1	TRUE	1	0.47	2		351	246	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0029513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	9	345	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.163	0.107	0.234	0.163	0.107	0.234	SUBCLONAL	1	TRUE	1	0.47	2		345	235	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934127	39934127	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	15	374	0	ENST00000378444.4:c.472del	p.Ser158ValfsTer3	p.S158Vfs*3	ENST00000378444	NM_001123385.1	158	Agt/gt	4/15	1	1	FACETS	0.21	0.154	0.279	0.21	0.154	0.279	SUBCLONAL	1	TRUE	0	0.47	1		374	232	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266921	18266921	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	10	526	0	ENST00000222254.8:c.232C>G	p.Leu78Val	p.L78V	ENST00000222254	NM_005027.3	78	Ctg/Gtg	2/16	1	2	FACETS	0.229	0.155	0.322	0.229	0.155	0.322	SUBCLONAL	1	TRUE	1	0.47	2		526	186	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799051	42799051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	21	1489	1	ENST00000575354.2:c.4535G>A	p.Arg1512His	p.R1512H	ENST00000575354	NM_015125.3	1512	cGt/cAt	20/20	1	2	FACETS	0.229	0.175	0.291	0.229	0.175	0.291	SUBCLONAL	1	TRUE	1	0.47	2		1490	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0029586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	591	797	1	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	0.850064707342612	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.855704567184751	2		798	662	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268762	41268762	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1245266458	NA	P-0029586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	131	397	0	ENST00000349496.5:c.1000G>A	p.Glu334Lys	p.E334K	ENST00000349496	NM_001904.3	334	Gaa/Aaa	7/15	0.330800308448954	3	FACETS	1	0.981	1	0.619	0.569	0.671	INDETERMINATE	1	TRUE	1	0.855704567184751	3		397	353	SUCCESS
APC	324	MSKCC	GRCh37	5	112157613	112157613	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658802	NA	P-0029586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	148	420	0	ENST00000257430.4:c.1333C>T	p.Gln445Ter	p.Q445*	ENST00000257430	NM_000038.5	445	Cag/Tag	11/16	0.14934154563071	1	FACETS	0.545	0.504	0.587	0.545	0.504	0.587	INDETERMINATE	1	TRUE	0	0.855704567184751	1		420	363	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727441	66727441	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519728	NA	P-0029586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	702	507	0	ENST00000307102.5:c.157T>C	p.Phe53Leu	p.F53L	ENST00000307102	NM_002755.3	53	Ttt/Ctt	2/11	0.452635623326834	4	FACETS	1	0.997	1	0.844	0.825	0.862	INDETERMINATE	3	TRUE	0	0.855704567184751	4		507	902	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506443	148506443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554481435	NA	P-0029586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	156	386	0	ENST00000320356.2:c.2069G>A	p.Arg690His	p.R690H	ENST00000320356	NM_004456.4	690	cGt/cAt	18/20	0.498654105810326	4	FACETS	1	0.967	1	0.548	0.504	0.594	INDETERMINATE	1	TRUE	2	0.855704567184751	4		386	617	SUCCESS
APC	324	MSKCC	GRCh37	5	112175770	112175771	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0029586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	94	294	0	ENST00000257430.4:c.4479_4480del	p.Glu1494LysfsTer19	p.E1494Kfs*19	ENST00000257430	NM_000038.5	1493	acGGaa/acaa	16/16	0.14934154563071	1	FACETS	0.469	0.423	0.516	0.469	0.423	0.516	INDETERMINATE	1	TRUE	0	0.855704567184751	1		294	268	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249925	39249925	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	220	576	0	ENST00000402219.2:c.1644T>G	p.Ser548Arg	p.S548R	ENST00000402219	NM_005633.3	548	agT/agG	10/23	0.557841593625424	3	FACETS	1	0.97	1	0.532	0.497	0.568	CLONAL	1	TRUE	1	0.855704567184751	3		576	690	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405995	157405995	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	159	627	0	ENST00000346085.5:c.2237G>C	p.Ser746Thr	p.S746T	ENST00000346085	NM_020732.3	746	aGc/aCc	6/20	0.418426067437154	4	FACETS	0.743	0.681	0.808	0.186	0.17	0.202	INDETERMINATE	1	TRUE	0	0.855704567184751	4		627	928	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245720	46245720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030967-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	256	308	5	ENST00000334344.6:c.3814C>T	p.Arg1272Ter	p.R1272*	ENST00000334344	NM_152641.2	1272	Cga/Tga	15/21	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	2	TRUE	NA	0.779729312986873	2		313	328	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533078	63533078	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030967-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	295	586	4	ENST00000307078.5:c.1816C>A	p.Leu606Met	p.L606M	ENST00000307078	NM_004655.3	606	Ctg/Atg	7/11	0.779729312986873	4	FACETS	0.924	0.875	0.973	0.924	0.875	0.973	CLONAL	2	TRUE	2	0.779729312986873	4		590	729	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106385	27106386	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0030967-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	276	530	3	ENST00000324856.7:c.5996_5997insC	p.Glu2000Ter	p.E2000*	ENST00000324856	NM_006015.4	1999	ttt/ttCt	20/20	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	2	TRUE	NA	0.779729312986873	2		533	348	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356193	66356193	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030967-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	326	444	2	ENST00000273854.3:c.1304C>G	p.Thr435Arg	p.T435R	ENST00000273854	NM_004439.5	435	aCa/aGa	5/18	0.777325098774501	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.779729312986873	2		446	406	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524363	176524363	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030967-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	203	862	0	ENST00000292408.4:c.2224G>T	p.Ala742Ser	p.A742S	ENST00000292408	NM_213647.1	742	Gcg/Tcg	17/18	0.779729312986873	3	FACETS	1	0.965	1	0.353	0.328	0.378	CLONAL	1	TRUE	0	0.779729312986873	3		862	684	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578179	7578179	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031560-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	1351	767	0	ENST00000269305.4:c.670G>T	p.Glu224Ter	p.E224*	ENST00000269305	NM_001126112.2	224	Gag/Tag	6/11	0.319686780299707	6	FACETS	1	0.998	1			1	INDETERMINATE	6	TRUE	NA	0.878558873811862	6		767	1390	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115967	8115968	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031560-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	225	452	0	ENST00000346208.3:c.1315dup	p.Val439GlyfsTer68	p.V439Gfs*68	ENST00000346208		438	atg/atGg	6/6	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.878558873811862	2		452	478	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519308	137519308	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031560-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	342	434	1	ENST00000367739.4:c.1330G>T	p.Glu444Ter	p.E444*	ENST00000367739	NM_000416.2	444	Gag/Tag	7/7	0.878558873811862	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.878558873811862	2		435	363	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321067	137321067	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031560-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	371	718	0	ENST00000481739.1:c.1024G>A	p.Val342Met	p.V342M	ENST00000481739	NM_002957.4	342	Gtg/Atg	7/10	0.878558873811862	3	FACETS	1	0.985	1	0.544	0.516	0.572	CLONAL	1	TRUE	1	0.878558873811862	3		718	1118	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14021905	14021905	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0031560-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	137	376	0	ENST00000311895.7:c.605C>G	p.Ser202Ter	p.S202*	ENST00000311895	NM_005236.2	202	tCa/tGa	4/11	0.852458246766988	4	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.878558873811862	4		376	459	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608595	189608595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031560-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	279	565	0	ENST00000264731.3:c.1670G>A	p.Gly557Asp	p.G557D	ENST00000264731	NM_003722.4	557	gGc/gAc	13/14	0.878558873811862	3	FACETS	1	0.963	1	0.515	0.484	0.546	CLONAL	1	TRUE	1	0.878558873811862	3		565	888	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0032358-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	2356	376	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.236804160702252	47	FACETS	0.99	0.979	1			1	CLONAL	44	FALSE	NA	0.236804160702252	47		376	2892	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0032358-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	303	1187	2	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.234026921333066	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	FALSE	0	0.236804160702252	2		1189	1125	SUCCESS
APC	324	MSKCC	GRCh37	5	112090657	112090657	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs145945630	NA	P-0032358-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	23	261	0	ENST00000257430.4:c.70C>T	p.Arg24Ter	p.R24*	ENST00000257430	NM_000038.5	24	Cga/Tga	2/16	0.236804160702252	3	FACETS	0.823	0.643	1	0.274	0.214	0.344	CLONAL	1	FALSE	0	0.236804160702252	3		261	264	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248526	59248526	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032358-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	155	798	0	ENST00000371222.2:c.217T>G	p.Ser73Ala	p.S73A	ENST00000371222	NM_002228.3	73	Tcg/Gcg	1/1	0.162706540805796	5	FACETS	0.944	0.864	1	0.629	0.576	0.685	CLONAL	2	FALSE	2	0.236804160702252	5		798	940	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037924	49037924	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032358-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	63	390	0	ENST00000267163.4:c.2167del	p.Ile723SerfsTer3	p.I723Sfs*3	ENST00000267163	NM_000321.2	722	Aaa/aa	21/27	0.234026921333066	2	FACETS	0.927	0.809	1	0.927	0.809	1	CLONAL	2	FALSE	0	0.236804160702252	2		390	287	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021290	31021290	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0032358-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	64	650	0	ENST00000375687.4:c.1289C>G	p.Ser430Ter	p.S430*	ENST00000375687	NM_015338.5	430	tCa/tGa	12/13	0.162706540805796	5	FACETS	0.911	0.787	1	0.304	0.262	0.349	CLONAL	1	FALSE	2	0.236804160702252	5		650	804	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32790075	32790075	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032358-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	17	163	0	ENST00000374899.4:c.1953G>A	p.Met651Ile	p.M651I	ENST00000374899	NM_018833.2	651	atG/atA	12/12	0.236804160702252	6	FACETS	0.753	0.562	0.98	0.188	0.14	0.245	CLONAL	1	FALSE	2	0.236804160702252	6		163	281	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168726	56168727	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032706-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	130	386	0	ENST00000399503.3:c.1583dup	p.Leu528PhefsTer13	p.L528Ffs*13	ENST00000399503	NM_005921.1	527	cct/ccTt	9/20	1	2	FACETS	0.926	0.843	1	0.926	0.843	1	CLONAL	1	TRUE	1	0.511633706928297	2		386	549	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218357	133218357	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1335665224	NA	P-0032706-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	196	836	0	ENST00000320574.5:c.5254G>T	p.Asp1752Tyr	p.D1752Y	ENST00000320574	NM_006231.2	1752	Gac/Tac	39/49	0.253843680383613	1	FACETS	0.773	0.717	0.83	0.773	0.717	0.83	INDETERMINATE	1	TRUE	0	0.511633706928297	1		836	738	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626967	14626967	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032706-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	104	773	0	ENST00000254322.2:c.808A>G	p.Thr270Ala	p.T270A	ENST00000254322	NM_006145.1	270	Aca/Gca	3/3	0.203488742833069	0	FACETS	0.286	0.256	0.318			1	INDETERMINATE	1	TRUE	0	0.511633706928297	0		773	694	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198283	185198284	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGCAA	novel	NA	P-0032706-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	177	538	0	ENST00000265026.3:c.2767_2772dup	p.Gly923_Lys924dup	p.G923_K924dup	ENST00000265026	NM_004721.4	923	ctg/ctGGGCAAg	13/14	0.253843680383613	1	FACETS	0.79	0.731	0.851	0.79	0.731	0.851	INDETERMINATE	1	TRUE	0	0.511633706928297	1		538	652	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975340	13975340	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032706-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	62	427	0	ENST00000405192.2:c.547G>A	p.Asp183Asn	p.D183N	ENST00000405192	NM_001163147.1	183	Gac/Aac	7/12	1	2	FACETS	0.5	0.432	0.573	0.5	0.432	0.573	SUBCLONAL	1	TRUE	1	0.511633706928297	2		427	485	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0032808-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	152	351	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.198863360065337	3	FACETS	1	0.985	1	0.671	0.616	0.727	INDETERMINATE	1	TRUE	1	0.469501750169997	3		351	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793881	NA	P-0032808-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	265	723	1	ENST00000269305.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGg/gAg	8/11	0.38059032326556	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.469501750169997	1		724	817	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105547	27105553	+	frameshift_variant	Frame_Shift_Del	DEL	TTCCGAC	TTCCGAC	-	novel	NA	P-0032808-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	364	484	1	ENST00000324856.7:c.5158_5164del	p.Phe1720AspfsTer3	p.F1720Dfs*3	ENST00000324856	NM_006015.4	1720	TTCCGACga/ga	20/20	0.469501750169997	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.469501750169997	2		485	756	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141674	202141674	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032808-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	132	281	0	ENST00000358485.4:c.962G>T	p.Gly321Val	p.G321V	ENST00000358485	NM_001080125.1	321	gGa/gTa	7/9	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.469501750169997	2		281	540	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922355	178922355	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032808-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	150	387	0	ENST00000263967.3:c.1124G>C	p.Arg375Thr	p.R375T	ENST00000263967	NM_006218.2	375	aGa/aCa	6/21	0.198863360065337	3	FACETS	1	0.965	1	0.55	0.504	0.599	INDETERMINATE	1	TRUE	1	0.469501750169997	3		387	717	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0033736-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	278	561	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.94	0.887	0.994	0.94	0.887	0.994	CLONAL	1	TRUE	1	0.779228040587288	2		561	759	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0033736-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	171	238	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.108161208610172	3	FACETS	1	0.987	1	0.641	0.594	0.688	INDETERMINATE	1	TRUE	1	0.779228040587288	3		238	476	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808367	1808367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755495007	NA	P-0033736-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	497	961	0	ENST00000260795.2:c.2125G>A	p.Glu709Lys	p.E709K	ENST00000260795		709	Gag/Aag	15/17	1	2	FACETS	0.975	0.934	1	0.975	0.934	1	CLONAL	1	TRUE	1	0.779228040587288	2		961	1308	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420103	41420103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033736-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	114	240	0	ENST00000373198.4:c.218C>T	p.Ser73Phe	p.S73F	ENST00000373198	NM_133170.3	73	tCt/tTt	3/32	1	2	FACETS	0.846	0.77	0.924	0.846	0.77	0.924	CLONAL	1	TRUE	1	0.779228040587288	2		240	346	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475070	40475070	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033736-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	46	536	3	ENST00000264657.5:c.1840A>C	p.Ser614Arg	p.S614R	ENST00000264657	NM_139276.2	614	Agc/Cgc	20/24	1	2	FACETS	0.122	0.102	0.144	0.122	0.102	0.144	SUBCLONAL	1	TRUE	1	0.779228040587288	2		539	969	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319913	8319913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033736-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	175	236	0	ENST00000356435.5:c.5588G>A	p.Arg1863Lys	p.R1863K	ENST00000356435		1863	aGa/aAa	34/35	1	2	FACETS	0.974	0.906	1	0.974	0.906	1	CLONAL	1	TRUE	1	0.779228040587288	2		236	461	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971179	21971179	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs36204594	NA	P-0033736-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	317	540	0	ENST00000304494.5:c.179C>A	p.Ala60Glu	p.A60E	ENST00000304494	NM_000077.4	60	gCg/gAg	2/3	1	2	FACETS	0.98	0.929	1	0.98	0.929	1	CLONAL	1	TRUE	1	0.779228040587288	2		540	830	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738979	145738979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766748490	NA	P-0033736-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	334	645	2	ENST00000428558.2:c.2176G>A	p.Ala726Thr	p.A726T	ENST00000428558	NM_004260.3	726	Gca/Aca	13/22	1	2	FACETS	0.91	0.863	0.958	0.91	0.863	0.958	CLONAL	1	TRUE	1	0.779228040587288	2		647	942	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025542	1025542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1023065435	NA	P-0033736-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	440	703	1	ENST00000358495.3:c.833G>A	p.Arg278Gln	p.R278Q	ENST00000358495	NM_134424.2	278	cGa/cAa	9/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.779228040587288	2		704	1079	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971147	21971160	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGCTCCGCGCCG	TGGGCTCCGCGCCG	-	novel	NA	P-0033736-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	300	633	0	ENST00000304494.5:c.198_211del	p.His66GlnfsTer49	p.H66Qfs*49	ENST00000304494	NM_000077.4	66	caCGGCGCGGAGCCCAac/caac	2/3	1	2	FACETS	0.856	0.808	0.904	0.856	0.808	0.904	CLONAL	1	TRUE	1	0.779228040587288	2		633	900	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4387989	4387989	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033736-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	232	485	0	ENST00000261254.3:c.475T>C	p.Phe159Leu	p.F159L	ENST00000261254	NM_001759.3	159	Ttc/Ctc	3/5	1	2	FACETS	0.845	0.791	0.899	0.845	0.791	0.899	CLONAL	1	TRUE	1	0.779228040587288	2		485	705	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027204	49027204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033736-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	138	222	0	ENST00000267163.4:c.1771C>T	p.Pro591Ser	p.P591S	ENST00000267163	NM_000321.2	591	Cct/Tct	18/27	1	2	FACETS	0.904	0.831	0.978	0.904	0.831	0.978	CLONAL	1	TRUE	1	0.779228040587288	2		222	392	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30323880	30323880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033736-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	103	133	0	ENST00000322652.5:c.1858C>T	p.His620Tyr	p.H620Y	ENST00000322652	NM_015355.2	620	Cat/Tat	15/16	1	2	FACETS	0.948	0.861	1	0.948	0.861	1	CLONAL	1	TRUE	1	0.779228040587288	2		133	279	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855856	45855856	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033736-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	433	786	0	ENST00000391945.4:c.1954C>T	p.Leu652Phe	p.L652F	ENST00000391945	NM_000400.3	652	Ctt/Ttt	21/23	1	2	FACETS	0.982	0.938	1	0.982	0.938	1	CLONAL	1	TRUE	1	0.779228040587288	2		786	1132	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722362	176722362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1203321063	NA	P-0033736-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	277	394	0	ENST00000439151.2:c.7993C>T	p.Leu2665Phe	p.L2665F	ENST00000439151	NM_022455.4	2665	Ctt/Ttt	23/23	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.779228040587288	2		394	641	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508220	106508220	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1183868916	NA	P-0033736-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	181	325	0	ENST00000359195.3:c.214G>A	p.Ala72Thr	p.A72T	ENST00000359195	NM_002649.2	72	Gcc/Acc	2/11	1	2	FACETS	0.942	0.877	1	0.942	0.877	1	CLONAL	1	TRUE	1	0.779228040587288	2		325	493	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618930	37618930	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	326	679	1	ENST00000447079.4:c.610del	p.Arg204GlyfsTer134	p.R204Gfs*134	ENST00000447079	NM_015083.1	202	cgA/cg	1/14	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.490459489033015	2		680	1228	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618736	37618737	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	C	novel	NA	P-0034039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	281	645	0	ENST00000447079.4:c.412_413delinsC	p.Ser138ProfsTer6	p.S138Pfs*6	ENST00000447079	NM_015083.1	138	AGc/Cc	1/14	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.490459489033015	2		645	1131	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579349	7579349	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	233	859	0	ENST00000269305.4:c.338T>C	p.Phe113Ser	p.F113S	ENST00000269305	NM_001126112.2	113	tTc/tCc	4/11	0.693755153788439	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.693755153788439	1		859	370	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412967	49412967	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	195	715	0	ENST00000418115.1:c.56C>A	p.Thr19Lys	p.T19K	ENST00000418115	NM_001664.2	19	aCa/aAa	2/5	0.693755153788439	2	FACETS	1	0.964	1	0.525	0.49	0.562	CLONAL	1	TRUE	0	0.693755153788439	2		715	535	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343652	343653	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0034891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	205	1053	2	ENST00000262320.3:c.2021_2022delinsAA	p.Trp674Ter	p.W674*	ENST00000262320	NM_003502.3	674	tGG/tAA	8/11	0.693755153788439	4	FACETS	1	0.969	1	0.539	0.5	0.58	CLONAL	1	TRUE	2	0.693755153788439	4		1055	928	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517454	176517454	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1429405481	NA	P-0034891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	104	974	0	ENST00000292408.4:c.155C>T	p.Pro52Leu	p.P52L	ENST00000292408	NM_213647.1	52	cCt/cTt	3/18	0.313350615383296	5	FACETS	0.794	0.71	0.882	0.265	0.236	0.294	INDETERMINATE	1	TRUE	2	0.693755153788439	5		974	771	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935589	13935589	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	46	518	0	ENST00000405192.2:c.1267G>A	p.Asp423Asn	p.D423N	ENST00000405192	NM_001163147.1	423	Gac/Aac	12/12	0.313350615383296	5	FACETS	0.422	0.355	0.497	0.141	0.118	0.166	INDETERMINATE	1	TRUE	2	0.693755153788439	5		518	641	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0035843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	144	351	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.452062905238033	2		351	583	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325932	65325932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	153	394	0	ENST00000342505.4:c.1190C>T	p.Ser397Phe	p.S397F	ENST00000342505	NM_002227.2	397	tCt/tTt	9/25	1	2	FACETS	0.98	0.898	1	0.98	0.898	1	CLONAL	1	TRUE	1	0.452062905238033	2		394	691	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843688	151843688	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	141	345	1	ENST00000262189.6:c.14027A>T	p.Glu4676Val	p.E4676V	ENST00000262189	NM_170606.2	4676	gAa/gTa	53/59	0.391006249981405	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.452062905238033	1		346	483	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0036203-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	196	472	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.464454607209194	2	FACETS	1	0.95	1	0.515	0.478	0.553	CLONAL	1	TRUE	0	0.49828450051993	2		472	764	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397742	49397742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552757	NA	P-0036203-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	231	436	0	ENST00000418115.1:c.482C>T	p.Ala161Val	p.A161V	ENST00000418115	NM_001664.2	161	gCa/gTa	5/5	0.363177087069263	3	FACETS	1	0.991	1	0.701	0.655	0.748	CLONAL	1	TRUE	1	0.49828450051993	3		436	826	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250047	53250047	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036203-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	160	275	0	ENST00000375401.3:c.202C>T	p.Arg68Ter	p.R68*	ENST00000375401	NM_004187.3	68	Cga/Tga	2/26	0.498483743791949	2	FACETS	1	0.974	1			1	CLONAL	1	TRUE	NA	0.49828450051993	2		275	568	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37882020	37882020	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201399875	NA	P-0036203-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	214	724	0	ENST00000269571.5:c.2786G>A	p.Arg929Gln	p.R929Q	ENST00000269571		929	cGg/cAg	23/27	1	2	FACETS	0.914	0.85	0.98	0.914	0.85	0.98	CLONAL	1	TRUE	1	0.49828450051993	2		724	940	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650842	93650842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036203-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	187	311	0	ENST00000375746.1:c.1768C>T	p.Arg590Trp	p.R590W	ENST00000375746	NM_001174167.1	590	Cgg/Tgg	13/14	0.484148214436165	2	FACETS	1	0.989	1	0.673	0.625	0.721	CLONAL	1	TRUE	0	0.49828450051993	2		311	558	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549706	187549706	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036203-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	92	282	0	ENST00000441802.2:c.4535G>T	p.Gly1512Val	p.G1512V	ENST00000441802	NM_005245.3	1512	gGc/gTc	8/27	1	2	FACETS	0.919	0.822	1	0.919	0.822	1	CLONAL	1	TRUE	1	0.49828450051993	2		282	402	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932717	39932717	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036203-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	259	510	0	ENST00000378444.4:c.1882G>C	p.Ala628Pro	p.A628P	ENST00000378444	NM_001123385.1	628	Gca/Cca	4/15	0.498483743791949	2	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.49828450051993	2		510	893	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449522	31449522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036203-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	74	162	0	ENST00000344624.3:c.2687C>T	p.Ala896Val	p.A896V	ENST00000344624		896	gCc/gTc	19/33	0.49828450051993	5	FACETS	1	0.938	1	0.278	0.244	0.314	CLONAL	1	TRUE	1	0.49828450051993	5		162	467	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589780	69589780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036203-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	24	48	0	ENST00000168712.1:c.73G>A	p.Gly25Ser	p.G25S	ENST00000168712	NM_002007.2	25	Ggc/Agc	1/3	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.49828450051993	2		48	82	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223394	2223394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036203-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	251	753	1	ENST00000398665.3:c.3505G>A	p.Glu1169Lys	p.E1169K	ENST00000398665	NM_032482.2	1169	Gag/Aag	25/28	1	2	FACETS	0.988	0.924	1	0.988	0.924	1	CLONAL	1	TRUE	1	0.49828450051993	2		754	1020	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125505	47125505	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036203-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	69	309	1	ENST00000409792.3:c.5765A>C	p.Glu1922Ala	p.E1922A	ENST00000409792	NM_014159.6	1922	gAa/gCa	12/21	0.363177087069263	3	FACETS	0.801	0.7	0.909	0.4	0.35	0.455	CLONAL	1	TRUE	1	0.49828450051993	3		310	432	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340417	8340417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036203-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	113	399	0	ENST00000356435.5:c.5179G>A	p.Asp1727Asn	p.D1727N	ENST00000356435		1727	Gac/Aac	31/35	0.486347796228631	2	FACETS	0.808	0.73	0.891	0.404	0.365	0.446	CLONAL	1	TRUE	0	0.49828450051993	2		399	561	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587118	189587118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761885185	NA	P-0036764-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	30	337	0	ENST00000264731.3:c.1135C>T	p.Arg379Cys	p.R379C	ENST00000264731	NM_003722.4	379	Cgt/Tgt	9/14	0.158633946989024	4	FACETS	0.91	0.745	1	0.91	0.745	1	INDETERMINATE	2	TRUE	2	0.320157151466255	4		337	136	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198428	108198428	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1131691162	NA	P-0036764-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	32	494	1	ENST00000278616.4:c.7032G>A	p.Trp2344Ter	p.W2344*	ENST00000278616	NM_000051.3	2344	tgG/tgA	48/63	0.320157151466255	1	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	0	0.320157151466255	1		495	154	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0036810-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	424	323	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.696614034298317	3	FACETS	0.976	0.936	1	0.976	0.936	1	CLONAL	2	TRUE	1	0.696614034298317	3		323	841	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036810-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	313	828	1	ENST00000326873.7:c.667G>T	p.Glu223Ter	p.E223*	ENST00000326873	NM_000455.4	223	Gag/Tag	5/10	0.696614034298317	1	FACETS	0.988	0.942	1	0.988	0.942	1	CLONAL	1	TRUE	0	0.696614034298317	1		829	593	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356205	66356205	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036810-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	99	574	0	ENST00000273854.3:c.1292T>C	p.Leu431Pro	p.L431P	ENST00000273854	NM_004439.5	431	cTa/cCa	5/18	0.458797041234057	1	FACETS	0.333	0.298	0.37	0.333	0.298	0.37	SUBCLONAL	1	TRUE	0	0.696614034298317	1		574	556	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573933	18573933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036810-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	167	322	0	ENST00000266497.5:c.2251G>A	p.Asp751Asn	p.D751N	ENST00000266497		751	Gat/Aat	15/31	0.696614034298317	3	FACETS	0.971	0.895	1	0.485	0.447	0.525	CLONAL	1	TRUE	1	0.696614034298317	3		322	666	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819174	3819174	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0036810-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	184	454	0	ENST00000262367.5:c.3060+1G>A		p.X1020_splice	ENST00000262367	NM_004380.2	1020			0.640765396422948	3	FACETS	0.888	0.821	0.957	0.444	0.41	0.479	CLONAL	1	TRUE	1	0.696614034298317	3		454	802	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644415	18644415	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036810-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	354	333	0	ENST00000266497.5:c.2593G>T	p.Glu865Ter	p.E865*	ENST00000266497		865	Gaa/Taa	18/31	0.696614034298317	3	FACETS	0.983	0.939	1	0.983	0.939	1	CLONAL	2	TRUE	1	0.696614034298317	3		333	697	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47685245	47685245	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036810-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	175	404	0	ENST00000347630.2:c.705G>T	p.Glu235Asp	p.E235D	ENST00000347630	NM_001007230.1	235	gaG/gaT	8/11	1	2	FACETS	0.932	0.864	1	0.932	0.864	1	CLONAL	1	TRUE	1	0.696614034298317	2		404	539	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713696	30713696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036810-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	173	469	0	ENST00000295754.5:c.1021G>A	p.Val341Ile	p.V341I	ENST00000295754	NM_003242.5	341	Gtc/Atc	4/7	0.696614034298317	1	FACETS	0.872	0.815	0.93	0.872	0.815	0.93	CLONAL	1	TRUE	0	0.696614034298317	1		469	371	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214718	133214718	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs557167678	NA	P-0036810-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	187	453	0	ENST00000320574.5:c.5560G>A	p.Ala1854Thr	p.A1854T	ENST00000320574	NM_006231.2	1854	Gct/Act	41/49	0.687237715935964	2	FACETS	0.867	0.805	0.931	0.434	0.402	0.466	CLONAL	1	TRUE	0	0.696614034298317	2		453	619	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739769	41739769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036810-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	247	653	0	ENST00000242208.4:c.204del	p.Lys69ArgfsTer16	p.K69Rfs*16	ENST00000242208	NM_002192.2	68	ttG/tt	2/3	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.696614034298317	2		653	706	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036910-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	49	619	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.413	0.349	0.483	0.413	0.349	0.483	SUBCLONAL	1	TRUE	1	0.415846447832629	2		619	571	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0036910-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	114	410	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.415846447832629	2		410	547	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934945	9934945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036910-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	49	380	0	ENST00000330684.3:c.1345G>A	p.Gly449Arg	p.G449R	ENST00000330684	NM_001134407.1	449	Ggg/Agg	6/13	1	2	FACETS	0.446	0.378	0.522	0.446	0.378	0.522	SUBCLONAL	1	TRUE	1	0.415846447832629	2		380	528	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89809209	89809209	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs373998809	NA	P-0036910-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	84	679	0	ENST00000389301.3:c.3764A>C	p.Glu1255Ala	p.E1255A	ENST00000389301	NM_000135.2	1255	gAg/gCg	37/43	1	2	FACETS	0.43	0.379	0.485	0.43	0.379	0.485	SUBCLONAL	1	TRUE	1	0.415846447832629	2		679	940	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743868	41743868	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036910-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	224	952	0	ENST00000301178.4:c.803G>T	p.Gly268Val	p.G268V	ENST00000301178	NM_021913.4	268	gGg/gTg	7/20	1	2	FACETS	0.841	0.782	0.903	0.841	0.782	0.903	CLONAL	1	TRUE	1	0.415846447832629	2		952	1281	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913534	39913534	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036910-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	153	628	0	ENST00000378444.4:c.4794G>A	p.Trp1598Ter	p.W1598*	ENST00000378444	NM_001123385.1	1598	tgG/tgA	13/15	0.415846447832629	1	FACETS	0.931	0.855	1	0.931	0.855	1	CLONAL	1	TRUE	0	0.415846447832629	1		628	626	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991343	41991344	+	missense_variant	Missense_Mutation	DNP	CT	CT	AC	novel	NA	P-0036910-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	57	530	0	ENST00000219905.7:c.2174_2175delinsAC	p.Pro725His	p.P725H	ENST00000219905	NM_001164273.1	725	cCT/cAC	5/24	0.345651531900227	3	FACETS	0.503	0.431	0.582	0.168	0.143	0.194	SUBCLONAL	1	TRUE	0	0.415846447832629	3		530	658	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577164	64577178	+	inframe_deletion	In_Frame_Del	DEL	TGTGGGCCCGATCCT	TGTGGGCCCGATCCT	-	novel	NA	P-0037474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	420	907	0	ENST00000312049.6:c.404_418del	p.Lys135_His139del	p.K135_H139del	ENST00000312049	NM_130799.2	135	aAGGATCGGGCCCACAtc/atc	2/10	0.657322753922481	2	FACETS	0.922	0.89	0.953	0.922	0.89	0.953	CLONAL	2	TRUE	0	0.709639986759599	2		907	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0037509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	318	0	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.715974931954129	3	FACETS	1	0.974	1	0.524	0.496	0.554	CLONAL	1	TRUE	1	0.885627064216917	3		0	988	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0037509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	194	695	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.885627064216917	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.885627064216917	1		695	233	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413070	139413072	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0037509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	331	525	0	ENST00000277541.6:c.1070_1072del	p.Phe357del	p.F357del	ENST00000277541	NM_017617.3	357	tTCTac/tac	6/34	0.368247165180243	2	FACETS	1	0.996	1	0.715	0.686	0.743	INDETERMINATE	1	TRUE	0	0.885627064216917	2		525	523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578207	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0037509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	618	0	0	ENST00000269305.4:c.642_643del	p.His214GlnfsTer7	p.H214Qfs*7	ENST00000269305	NM_001126112.2	214	caTAgt/cagt	6/11	0.715974931954129	3	FACETS	0.96	0.93	0.989	0.96	0.93	0.989	CLONAL	2	TRUE	1	0.885627064216917	3		0	1049	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133553	55133553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	1388	465	0	ENST00000257290.5:c.857G>A	p.Gly286Glu	p.G286E	ENST00000257290	NM_006206.4	286	gGa/gAa	6/23	0.885627064216917	6	FACETS	1	0.997	1	1	0.997	1	CLONAL	5	TRUE	1	0.885627064216917	6		465	1667	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944358	76944358	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0037509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	238	0	0	ENST00000373344.5:c.547A>T	p.Lys183Ter	p.K183*	ENST00000373344	NM_000489.3	183	Aaa/Taa	7/35	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.885627064216917	1		0	262	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0037509-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1235	20	0	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	1	2	FACETS	0.266	0.202	0.342	0.266	0.202	0.342	SUBCLONAL	1	TRUE	1	0.12	2		0	1255	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0037509-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	15	695	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	0.218	0.158	0.291	0.218	0.158	0.291	SUBCLONAL	1	TRUE	1	0.12	2		695	1145	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578207	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0037509-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1277	23	0	0	ENST00000269305.4:c.642_643del	p.His214GlnfsTer7	p.H214Qfs*7	ENST00000269305	NM_001126112.2	214	caTAgt/cagt	6/11	1	2	FACETS	0.295	0.228	0.373	0.295	0.228	0.373	SUBCLONAL	1	TRUE	1	0.12	2		0	1300	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133553	55133553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037509-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	61	465	0	ENST00000257290.5:c.857G>A	p.Gly286Glu	p.G286E	ENST00000257290	NM_006206.4	286	gGa/gAa	6/23	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.12	2		465	1016	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944358	76944358	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0037509-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	12	0	0	ENST00000373344.5:c.547A>T	p.Lys183Ter	p.K183*	ENST00000373344	NM_000489.3	183	Aaa/Taa	7/35	0.436376224216192	2	FACETS	0.341	0.238	0.469	0.17	0.119	0.235	SUBCLONAL	1	TRUE	0	0.12	2		0	587	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0037710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	128	227	1				ENST00000310581	NM_198253.2	-/1132			0.580908041779688	4	FACETS	0.79	0.721	0.861	0.79	0.721	0.861	SUBCLONAL	2	TRUE	2	0.580908041779688	4		228	441	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262828	46262828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148666287	NA	P-0037710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	161	539	1	ENST00000371998.3:c.1001G>A	p.Arg334Gln	p.R334Q	ENST00000371998		334	cGa/cAa	10/23	0.335157964521038	5	FACETS	0.847	0.786	0.91	0.847	0.786	0.91	INDETERMINATE	3	TRUE	2	0.580908041779688	5		540	408	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717715	89717716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587782341	NA	P-0038250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	182	487	1	ENST00000371953.3:c.741dup	p.Pro248ThrfsTer5	p.P248Tfs*5	ENST00000371953	NM_000314.4	247	tta/ttAa	7/9	0.244365035972756	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.244365035972756	2		488	671	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073671	8073671	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	83	517	0	ENST00000377482.5:c.988T>G	p.Ser330Ala	p.S330A	ENST00000377482	NM_018948.3	330	Tcg/Gcg	4/4	1	2	FACETS	0.94	0.829	1	0.94	0.829	1	CLONAL	1	TRUE	1	0.244365035972756	2		517	723	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820829	36820829	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	105	676	0	ENST00000373129.3:c.548G>T	p.Arg183Leu	p.R183L	ENST00000373129	NM_032017.1	183	cGc/cTc	6/12	1	2	FACETS	0.903	0.807	1	0.903	0.807	1	CLONAL	1	TRUE	1	0.244365035972756	2		676	952	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111065	193111065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	40	268	0	ENST00000367435.3:c.598G>A	p.Asp200Asn	p.D200N	ENST00000367435	NM_024529.4	200	Gat/Aat	7/17	1	2	FACETS	0.866	0.721	1	0.866	0.721	1	CLONAL	1	TRUE	1	0.244365035972756	2		268	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7579437	+	splice_acceptor_variant,splice_donor_variant,frameshift_variant,stop_lost,intron_variant	Splice_Site	DEL	CGCGGACGCGGGTGCCGGGCGGGGGTGTGGAATCAACCCACAGCTGCACAGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAAGCAACTGGAAGACGGCAGCAAAGAAACAAACATGCGTAAGCACCTCCTGCAACCCACTAGCGAGCTAGAGAGAGTTGGCGTCTACACCTCAGGAGCTTTTCTTTTTTTTTTTTTTTTTTGAGATAGGGTCTTGCTCTGTCACTCAGGCTGGAGCACAGTGGTGTGATCACAGCTCACTGCAGCCTCCATCTCCTGGCCTCAAGTGATCTTCCCACCTCAGCCTCCTAAGTGGCTGGGACTATAGGTGTGCACCACCATGCCTGGCTAATTTTTTGTATTTTTTTGTAGAGACGAGGTTTCATCATGTTACCCAGGCTGGTCTTGAACTCCTGGGCTCAGGTGATCTGCCTGCCTTGGCCTCTTTGAGAGTGCTGGGATTGCAGGTGTGAGCCACCAAGCCTGGTCAGGAGCTTATTTTCAAAAGCCAAGGAATACACGTGGATGAAGAAAAAGAAAAGTTCTGCATCCCCAGGAGAGATGCTGAGGGTGTGATGGGATGGATAAAAGCCCAAATTCAAGGGGGGAATATTCAACTTTGGGACAGGAGTCAGAGATCACACATTAAGTGGGTAAACTATAAAAAAACACTGACAGGAAGCCAAAGGGTGAAGAGGAATCCCAAAGTTCCAAACAAAAGAAATGCAGGGGGATACGGCCAGGCATTGAAGTCTCATGGAAGCCAGCCCCTCAGGGCAACTGACCGTGCAAGTCACAGACTTGGCTGTCCCAGAATGCAAGAAGCCCAGACGGAAACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGGACAGAAGATGACAGGGGCCAGGAGGGGGCTGGTGCAGGGGC	CGCGGACGCGGGTGCCGGGCGGGGGTGTGGAATCAACCCACAGCTGCACAGGGCAGGTCTTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAAGCAACTGGAAGACGGCAGCAAAGAAACAAACATGCGTAAGCACCTCCTGCAACCCACTAGCGAGCTAGAGAGAGTTGGCGTCTACACCTCAGGAGCTTTTCTTTTTTTTTTTTTTTTTTGAGATAGGGTCTTGCTCTGTCACTCAGGCTGGAGCACAGTGGTGTGATCACAGCTCACTGCAGCCTCCATCTCCTGGCCTCAAGTGATCTTCCCACCTCAGCCTCCTAAGTGGCTGGGACTATAGGTGTGCACCACCATGCCTGGCTAATTTTTTGTATTTTTTTGTAGAGACGAGGTTTCATCATGTTACCCAGGCTGGTCTTGAACTCCTGGGCTCAGGTGATCTGCCTGCCTTGGCCTCTTTGAGAGTGCTGGGATTGCAGGTGTGAGCCACCAAGCCTGGTCAGGAGCTTATTTTCAAAAGCCAAGGAATACACGTGGATGAAGAAAAAGAAAAGTTCTGCATCCCCAGGAGAGATGCTGAGGGTGTGATGGGATGGATAAAAGCCCAAATTCAAGGGGGGAATATTCAACTTTGGGACAGGAGTCAGAGATCACACATTAAGTGGGTAAACTATAAAAAAACACTGACAGGAAGCCAAAGGGTGAAGAGGAATCCCAAAGTTCCAAACAAAAGAAATGCAGGGGGATACGGCCAGGCATTGAAGTCTCATGGAAGCCAGCCCCTCAGGGCAACTGACCGTGCAAGTCACAGACTTGGCTGTCCCAGAATGCAAGAAGCCCAGACGGAAACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGGACAGAAGATGACAGGGGCCAGGAGGGGGCTGGTGCAGGGGC	-	novel	NA	P-0038250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	188	1249	0	ENST00000269305.4:c.250_475del		p.X84_splice	ENST00000269305	NM_001126112.2	84	GCCCCTGCACCAGCCCCCTCCTGGCCCCTGTCATCTTCTGTCCCTTCCCAGAAAACCTACCAGGGCAGCTACGGTTTCCGTCTGGGCTTCTTGCATTCTGGGACAGCCAAGTCTGTGACTTGCACGGTCAGTTGCCCTGAGGGGCTGGCTTCCATGAGACTTCAATGCCTGGCCGTATCCCCCTGCATTTCTTTTGTTTGGAACTTTGGGATTCCTCTTCACCCTTTGGCTTCCTGTCAGTGTTTTTTTATAGTTTACCCACTTAATGTGTGATCTCTGACTCCTGTCCCAAAGTTGAATATTCCCCCCTTGAATTTGGGCTTTTATCCATCCCATCACACCCTCAGCATCTCTCCTGGGGATGCAGAACTTTTCTTTTTCTTCATCCACGTGTATTCCTTGGCTTTTGAAAATAAGCTCCTGACCAGGCTTGGTGGCTCACACCTGCAATCCCAGCACTCTCAAAGAGGCCAAGGCAGGCAGATCACCTGAGCCCAGGAGTTCAAGACCAGCCTGGGTAACATGATGAAACCTCGTCTCTACAAAAAAATACAAAAAATTAGCCAGGCATGGTGGTGCACACCTATAGTCCCAGCCACTTAGGAGGCTGAGGTGGGAAGATCACTTGAGGCCAGGAGATGGAGGCTGCAGTGAGCTGTGATCACACCACTGTGCTCCAGCCTGAGTGACAGAGCAAGACCCTATCTCAAAAAAAAAAAAAAAAAAGAAAAGCTCCTGAGGTGTAGACGCCAACTCTCTCTAGCTCGCTAGTGGGTTGCAGGAGGTGCTTACGCATGTTTGTTTCTTTGCTGCCGTCTTCCAGTTGCTTTATCTGTTCACTTGTGCCCTGACTTTCAACTCTGTCTCCTTCCTCTTCCTACAGTACTCCCCTGCCCTCAACAAGATGTTTTGCCAACTGGCCAAGACCTGCCCTGTGCAGCTGTGGGTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGcc/cc	4-5/11	0.244365035972756	1	FACETS	0.943	0.868	1	0.943	0.868	1	CLONAL	1	TRUE	0	0.244365035972756	1		1249	1433	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276641	15276641	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1400	182	1157	0	ENST00000263388.2:c.5624C>T	p.Pro1875Leu	p.P1875L	ENST00000263388	NM_000435.2	1875	cCc/cTc	30/33	1	2	FACETS	0.942	0.866	1	0.942	0.866	1	CLONAL	1	TRUE	1	0.244365035972756	2		1157	1582	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946454	2946454	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1247	153	1046	0	ENST00000396946.4:c.3283A>G	p.Thr1095Ala	p.T1095A	ENST00000396946	NM_032415.4	1095	Acg/Gcg	25/25	1	2	FACETS	0.894	0.816	0.977	0.894	0.816	0.977	CLONAL	1	TRUE	1	0.244365035972756	2		1046	1400	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916501	39916501	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	171	1061	0	ENST00000378444.4:c.4502T>C	p.Leu1501Pro	p.L1501P	ENST00000378444	NM_001123385.1	1501	cTg/cCg	11/15	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.244365035972756	2		1061	1367	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424212	47424212	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	131	778	0	ENST00000377045.4:c.217G>T	p.Ala73Ser	p.A73S	ENST00000377045	NM_001654.4	73	Gcc/Tcc	4/16	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.244365035972756	2		778	1054	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345527	70345527	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	111	611	0	ENST00000374080.3:c.2386A>G	p.Ile796Val	p.I796V	ENST00000374080		796	Att/Gtt	17/45	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.244365035972756	2		611	869	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76764102	76764102	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	83	507	0	ENST00000373344.5:c.7206C>G	p.Ile2402Met	p.I2402M	ENST00000373344	NM_000489.3	2402	atC/atG	35/35	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.244365035972756	2		507	650	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058285	42058285	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	48	363	0	ENST00000219905.7:c.8005A>T	p.Ser2669Cys	p.S2669C	ENST00000219905	NM_001164273.1	2669	Agc/Tgc	24/24	1	2	FACETS	0.797	0.674	0.932	0.797	0.674	0.932	CLONAL	1	TRUE	1	0.244365035972756	2		363	493	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405026	405026	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1049908319	NA	P-0038250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	45	510	0	ENST00000380956.4:c.1108G>A	p.Ala370Thr	p.A370T	ENST00000380956	NM_001195286.1	370	Gcg/Acg	8/9	1	2	FACETS	0.508	0.426	0.599	0.508	0.426	0.599	SUBCLONAL	1	TRUE	1	0.244365035972756	2		510	725	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225060	NA	P-0038647-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	81	523	0	ENST00000263967.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000263967	NM_006218.2	104	cCa/cTa	2/21	0.378159549761515	2	FACETS	1	0.9	1	0.509	0.45	0.571	CLONAL	1	TRUE	0	0.378159549761515	2		523	421	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0038647-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	74	473	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.378159549761515	2	FACETS	0.971	0.854	1	0.486	0.427	0.548	CLONAL	1	TRUE	0	0.378159549761515	2		474	403	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0038647-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	79	326	6	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.378159549761515	2	FACETS	1	0.931	1	0.537	0.475	0.603	CLONAL	1	TRUE	0	0.378159549761515	2		332	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0038647-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	339	740	3	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.378159549761515	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.378159549761515	2		743	874	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0038647-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	126	326	3	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.299331353022738	2	FACETS	0.908	0.831	0.987	0.908	0.831	0.987	CLONAL	2	TRUE	0	0.378159549761515	2		329	367	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748596	40748596	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754546663	NA	P-0038647-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	55	503	0	ENST00000373198.4:c.2920C>T	p.Arg974Trp	p.R974W	ENST00000373198	NM_133170.3	974	Cgg/Tgg	21/32	0.323249037899918	3	FACETS	0.553	0.473	0.642			1	SUBCLONAL	1	TRUE	NA	0.378159549761515	3		503	625	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575150	48575150	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038647-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	77	337	0	ENST00000342988.3:c.344G>C	p.Cys115Ser	p.C115S	ENST00000342988	NM_005359.5	115	tGt/tCt	3/12	0.335518253493898	2	FACETS	1	0.969	1	0.642	0.569	0.72	CLONAL	1	TRUE	0	0.378159549761515	2		337	317	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411441	63411441	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038647-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	224	529	1	ENST00000330258.3:c.1726G>T	p.Glu576Ter	p.E576*	ENST00000330258	NM_152424.3	576	Gag/Tag	2/2	0.323249037899918	2	FACETS	1	0.976	1			1	CLONAL	2	TRUE	NA	0.378159549761515	2		530	551	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024255	31024255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760905906	NA	P-0038805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	223	499	2	ENST00000375687.4:c.3740G>A	p.Arg1247His	p.R1247H	ENST00000375687	NM_015338.5	1247	cGt/cAt	13/13	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.7	2		501	579	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692892	89692892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554898129	NA	P-0039402-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	132	349	0	ENST00000371953.3:c.376G>A	p.Ala126Thr	p.A126T	ENST00000371953	NM_000314.4	126	Gct/Act	5/9	0.527691408091574	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.527691408091574	1		349	351	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0039402-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	138	172	0	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	1	1	FACETS	0.792	0.739	0.845	1	0.991	1	SUBCLONAL	2	TRUE	0	0.527691408091574	1		172	243	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627234	86627238	+	frameshift_variant	Frame_Shift_Del	DEL	TTATC	TTATC	-	rs1060503441	NA	P-0039402-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	129	302	0	ENST00000274376.6:c.613_617del	p.Leu205LysfsTer4	p.L205Kfs*4	ENST00000274376	NM_002890.2	203	agTTATCtt/agtt	2/25	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.527691408091574	2		302	464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578552	7578556	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GTACT	GTACT	-	novel	NA	P-0039402-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	255	771	0	ENST00000269305.4:c.376-2_378del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	0.527691408091574	1	FACETS	0.998	0.939	1	0.998	0.939	1	CLONAL	1	TRUE	0	0.527691408091574	1		771	713	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372252	55372252	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039402-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	135	415	0	ENST00000297316.4:c.942G>C	p.Gln314His	p.Q314H	ENST00000297316	NM_022454.3	314	caG/caC	2/2	NA	2	FACETS	0.896	0.818	0.978			1	INDETERMINATE	1	TRUE	NA	0.527691408091574	2		415	571	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215979	142215979	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs766051038	NA	P-0039402-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	92	354	0	ENST00000350721.4:c.5614C>G	p.Pro1872Ala	p.P1872A	ENST00000350721	NM_001184.3	1872	Cca/Gca	33/47	1	2	FACETS	0.642	0.572	0.717	0.642	0.572	0.717	SUBCLONAL	1	TRUE	1	0.527691408091574	2		354	543	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564672	55564672	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039402-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	161	439	0	ENST00000288135.5:c.560C>A	p.Ser187Tyr	p.S187Y	ENST00000288135	NM_000222.2	187	tCt/tAt	3/21	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.527691408091574	2		439	599	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74868290	74868290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0039402-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2707	223	685	0	ENST00000284811.8:c.5-1G>A		p.X2_splice	ENST00000284811		2			0.527691408091574	5	FACETS	0.517	0.478	0.557			1	SUBCLONAL	1	TRUE	NA	0.527691408091574	5		685	2930	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0039410-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	105	410	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.750477300107543	8	FACETS	1	0.954	1	1	0.954	1	CLONAL	7	TRUE	1	0.750477300107543	8		410	129	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0039410-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	19	359	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.370278396428469	3	FACETS	1	0.893	1	0.414	0.327	0.509	INDETERMINATE	1	TRUE	0	0.750477300107543	3		359	56	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222727	5222727	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746980740	NA	P-0039410-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	23	618	0	ENST00000357368.4:c.3076C>T	p.Arg1026Cys	p.R1026C	ENST00000357368	NM_002850.3	1026	Cgc/Tgc	18/38	0.632631121665489	3	FACETS	1	0.874	1	0.562	0.451	0.681	CLONAL	1	TRUE	1	0.750477300107543	3		618	75	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0039410-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	30	227	1				ENST00000310581	NM_198253.2	-/1132			0.558297130351946	4	FACETS	0.915	0.786	1	0.915	0.786	1	CLONAL	3	TRUE	1	0.750477300107543	4		228	51	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504382	149504382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039410-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	16	538	0	ENST00000261799.4:c.1820G>A	p.Gly607Asp	p.G607D	ENST00000261799	NM_002609.3	607	gGc/gAc	13/23	0.558297130351946	4	FACETS	1	0.888	1	0.444	0.339	0.56	CLONAL	1	TRUE	1	0.750477300107543	4		538	56	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677912	117677912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765109582	NA	P-0039410-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	13	396	1	ENST00000368508.3:c.4021G>A	p.Ala1341Thr	p.A1341T	ENST00000368508	NM_002944.2	1341	Gct/Act	25/43	1	2	FACETS	0.642	0.471	0.835	0.642	0.471	0.835	SUBCLONAL	1	TRUE	1	0.750477300107543	2		397	54	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477813	140477813	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs180177037	NA	P-0039410-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	75	433	2	ENST00000288602.6:c.1495A>G	p.Lys499Glu	p.K499E	ENST00000288602	NM_004333.4	499	Aaa/Gaa	12/18	0.750477300107543	8	FACETS	1	0.95	1	0.619	0.559	0.679	CLONAL	4	TRUE	1	0.750477300107543	8		435	150	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956771	68956771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774302685	NA	P-0039410-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	58	666	0	ENST00000288368.4:c.889C>T	p.Arg297Cys	p.R297C	ENST00000288368	NM_024870.2	297	Cgt/Tgt	8/40	0.457967344173629	5	FACETS	1	0.96	1	1	0.96	1	CLONAL	3	TRUE	2	0.750477300107543	5		666	96	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971187	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0039410-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	29	428	0	ENST00000304494.5:c.171_172delinsTT	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	57	gcCCga/gcTTga	2/3	0.706929921044068	2	FACETS	0.899	0.782	1	0.899	0.782	1	CLONAL	2	TRUE	0	0.750477300107543	2		428	43	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870265	44870265	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0039410-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	19	379	0	ENST00000377967.4:c.443+1G>C		p.X148_splice	ENST00000377967	NM_021140.2	148			0.750477300107543	3	FACETS	0.941	0.733	1	0.471	0.366	0.586	CLONAL	1	TRUE	1	0.750477300107543	3		379	74	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0039663-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	232	820	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.260753973307013	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.267186082232485	2		820	811	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5064920	5064920	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039663-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	110	378	0	ENST00000381652.3:c.1094T>A	p.Phe365Tyr	p.F365Y	ENST00000381652	NM_004972.3	365	tTc/tAc	9/25	0.257466753517542	2	FACETS	0.94	0.85	1	0.94	0.85	1	CLONAL	2	TRUE	0	0.267186082232485	2		378	438	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115873	8115874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0039706-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	204	407	0	ENST00000346208.3:c.1220dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tCcg	6/6	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.658625640733287	2		407	585	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729515	41729515	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039706-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	215	472	0	ENST00000242208.4:c.1014G>C	p.Trp338Cys	p.W338C	ENST00000242208	NM_002192.2	338	tgG/tgC	3/3	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.658625640733287	2		472	642	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32969019	32969020	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0039706-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	135	296	0	ENST00000380152.3:c.9452_9453del	p.Lys3151ArgfsTer16	p.K3151Rfs*16	ENST00000380152		3150	ccAAaa/ccaa	25/27	0.658625640733287	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.658625640733287	1		296	251	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828423	72828423	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039706-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	244	492	0	ENST00000268489.5:c.8158T>C	p.Phe2720Leu	p.F2720L	ENST00000268489	NM_006885.3	2720	Ttc/Ctc	9/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.658625640733287	2		492	688	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680291	30680291	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039706-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	313	591	0	ENST00000376406.3:c.1428G>C	p.Lys476Asn	p.K476N	ENST00000376406	NM_014641.2	476	aaG/aaC	5/15	0.22958550561831	4	FACETS	0.875	0.828	0.923	0.875	0.828	0.923	INDETERMINATE	2	TRUE	2	0.658625640733287	4		591	901	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411920	63411920	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1460320166	NA	P-0039706-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	300	743	0	ENST00000330258.3:c.1247A>G	p.Tyr416Cys	p.Y416C	ENST00000330258	NM_152424.3	416	tAt/tGt	2/2	NA	2	FACETS	1	0.957	1			1	INDETERMINATE	1	TRUE	NA	0.658625640733287	2		743	897	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539596	187539596	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039706-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	134	325	0	ENST00000441802.2:c.8144A>G	p.Asp2715Gly	p.D2715G	ENST00000441802	NM_005245.3	2715	gAc/gGc	10/27	0.658625640733287	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.658625640733287	1		325	249	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487283	56487283	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040153-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	174	419	0	ENST00000267101.3:c.1429C>T	p.Pro477Ser	p.P477S	ENST00000267101	NM_001982.3	477	Cct/Tct	12/28	1	2	FACETS	0.992	0.924	1	0.992	0.924	1	CLONAL	1	TRUE	1	0.843534945196884	2		419	416	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476748	140476755	+	frameshift_variant	Frame_Shift_Del	DEL	AGTTTGAT	AGTTTGAT	-	novel	NA	P-0040153-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	19	296	0	ENST00000288602.6:c.1651_1658del	p.Ile551TyrfsTer27	p.I551Yfs*27	ENST00000288602	NM_004333.4	551	ATCAAACTt/t	13/18	1	2	FACETS	0.153	0.116	0.196	0.153	0.116	0.196	SUBCLONAL	1	TRUE	1	0.843534945196884	2		296	295	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578226	7578226	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1464727668	NA	P-0040386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	272	751	0	ENST00000269305.4:c.623A>T	p.Asp208Val	p.D208V	ENST00000269305	NM_001126112.2	208	gAc/gTc	6/11	0.654061063676266	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.654061063676266	1		751	534	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636997	176636997	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	164	717	2	ENST00000439151.2:c.1597C>A	p.Leu533Ile	p.L533I	ENST00000439151	NM_022455.4	533	Ctt/Att	5/23	1	2	FACETS	0.8	0.737	0.865	0.8	0.737	0.865	SUBCLONAL	1	TRUE	1	0.654061063676266	2		719	627	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843683	156843683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	59	938	0	ENST00000524377.1:c.1109C>T	p.Ala370Val	p.A370V	ENST00000524377	NM_002529.3	370	gCc/gTc	8/17	0.654061063676266	3	FACETS	0.256	0.219	0.296	0.128	0.109	0.148	SUBCLONAL	1	TRUE	1	0.654061063676266	3		938	936	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198910	67198910	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	79	615	0	ENST00000312629.5:c.381G>T	p.Lys127Asn	p.K127N	ENST00000312629	NM_003952.2	127	aaG/aaT	5/15	0.654061063676266	4	FACETS	0.344	0.301	0.39	0.115	0.1	0.13	SUBCLONAL	1	TRUE	1	0.654061063676266	4		615	1161	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226417	41226417	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	432	782	0	ENST00000357654.3:c.4606del	p.Glu1536SerfsTer12	p.E1536Sfs*12	ENST00000357654	NM_007294.3	1536	Gag/ag	14/23	0.654061063676266	2	FACETS	0.921	0.888	0.954	0.921	0.888	0.954	CLONAL	2	TRUE	0	0.654061063676266	2		782	717	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149211	61149211	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	98	436	1	ENST00000295025.8:c.1401T>A	p.Asp467Glu	p.D467E	ENST00000295025	NM_002908.2	467	gaT/gaA	11/11	0.330087275056625	6	FACETS	1	0.975	1	0.327	0.292	0.363	INDETERMINATE	1	TRUE	2	0.654061063676266	6		437	529	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721807	176721807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	24	642	1	ENST00000439151.2:c.7438G>T	p.Asp2480Tyr	p.D2480Y	ENST00000439151	NM_022455.4	2480	Gat/Tat	23/23	1	2	FACETS	0.16	0.125	0.201	0.16	0.125	0.201	SUBCLONAL	1	TRUE	1	0.654061063676266	2		643	458	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730075	41730075	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	49	587	0	ENST00000242208.4:c.454C>A	p.Arg152Ser	p.R152S	ENST00000242208	NM_002192.2	152	Cgt/Agt	3/3	0.175990327835723	2	FACETS	0.272	0.23	0.318	0.136	0.115	0.159	INDETERMINATE	1	TRUE	0	0.654061063676266	2		587	551	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356353	70356353	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	116	398	0	ENST00000374080.3:c.5248G>T	p.Glu1750Ter	p.E1750*	ENST00000374080		1750	Gag/Tag	37/45	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		398	459	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242485	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAACATC	ATTAAGAGAAGCAACATC	-	rs121913423	NA	P-0040465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	32	478	0	ENST00000275493.2:c.2238_2255del	p.Glu746_Ser752delinsAsp	p.E746_S752delinsD	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACATCt/gat	19/28	1				NA	1				NA	NA	FALSE	1	NA	2		478	553	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858913	243858913	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs866698621	NA	P-0040740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	247	354	0	ENST00000263826.5:c.152T>G	p.Leu51Arg	p.L51R	ENST00000263826	NM_005465.4	51	cTc/cGc	2/13	0.634492453842053	3	FACETS	0.992	0.938	1	0.992	0.938	1	CLONAL	2	TRUE	1	0.634492453842053	3		354	517	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575073	64575073	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1565646772	NA	P-0040740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	425	610	0	ENST00000312049.6:c.734del	p.Pro245LeufsTer36	p.P245Lfs*36	ENST00000312049	NM_130799.2	245	cCt/ct	4/10	0.634492453842053	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.634492453842053	2		610	630	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769504	112769504	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs767570209	NA	P-0041118-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	34	465	0	ENST00000369452.4:c.1456C>G	p.Leu486Val	p.L486V	ENST00000369452	NM_007373.3	486	Ctt/Gtt	8/9	1	2	FACETS	0.751	0.612	0.907	0.751	0.612	0.907	CLONAL	1	TRUE	1	0.16	2		465	566	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474677	138474677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041118-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	29	418	0	ENST00000289153.2:c.316C>T	p.Leu106Phe	p.L106F	ENST00000289153	NM_006219.2	106	Ctt/Ttt	2/22	1	2	FACETS	0.673	0.538	0.826	0.673	0.538	0.826	SUBCLONAL	1	TRUE	1	0.16	2		418	539	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0041229-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	269	831	0	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	0.365310950144696	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.365310950144696	1		831	1128	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66525088	66525088	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041229-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	101	284	0	ENST00000358598.2:c.847G>A	p.Val283Met	p.V283M	ENST00000358598	NM_212471.2	283	Gtg/Atg	9/11	1	2	FACETS	0.895	0.801	0.994	0.895	0.801	0.994	CLONAL	1	TRUE	1	0.365310950144696	2		284	618	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272493	21272493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041229-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	237	754	0	ENST00000354336.3:c.271C>A	p.His91Asn	p.H91N	ENST00000354336	NM_005207.3	91	Cac/Aac	1/3	0.365310950144696	3	FACETS	1	0.966	1	0.353	0.329	0.379	CLONAL	1	TRUE	0	0.365310950144696	3		754	1448	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1952817	1952817	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041229-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	160	487	0	ENST00000382891.5:c.1900G>C	p.Asp634His	p.D634H	ENST00000382891	NM_133335.3	634	Gac/Cac	10/22	0.365310950144696	1	FACETS	0.964	0.885	1	0.964	0.885	1	CLONAL	1	TRUE	0	0.365310950144696	1		487	743	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707831	176707831	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041229-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	91	264	0	ENST00000439151.2:c.5888A>T	p.Lys1963Ile	p.K1963I	ENST00000439151	NM_022455.4	1963	aAa/aTa	18/23	0.365310950144696	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.365310950144696	1		264	384	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983947	2983947	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs747351557	NA	P-0041229-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1382	215	804	0	ENST00000396946.4:c.583G>C	p.Val195Leu	p.V195L	ENST00000396946	NM_032415.4	195	Gtc/Ctc	5/25	0.365310950144696	3	FACETS	0.872	0.807	0.939	0.436	0.403	0.47	CLONAL	1	TRUE	1	0.365310950144696	3		804	1597	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974740	21974741	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0041229-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	114	397	0	ENST00000304494.5:c.86_87delinsCT	p.Arg29Pro	p.R29P	ENST00000304494	NM_000077.4	29	cGG/cCT	1/3	0.365310950144696	1	FACETS	0.897	0.81	0.988	0.897	0.81	0.988	CLONAL	1	TRUE	0	0.365310950144696	1		397	569	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552152	29552152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199474738	NA	P-0041349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	84	181	0	ENST00000356175.3:c.1885G>A	p.Gly629Arg	p.G629R	ENST00000356175	NM_000267.3	629	Ggg/Agg	17/57	0.760645359350636	1	FACETS	0.925	0.846	1	0.925	0.846	1	CLONAL	1	TRUE	0	0.760645359350636	1		181	148	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411864	63411864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767572122	NA	P-0041349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	120	936	1	ENST00000330258.3:c.1303G>A	p.Gly435Ser	p.G435S	ENST00000330258	NM_152424.3	435	Ggc/Agc	2/2	1	2	FACETS	0.43	0.388	0.474	0.43	0.388	0.474	SUBCLONAL	1	TRUE	1	0.760645359350636	2		937	734	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691178	18691178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	59	272	0	ENST00000266497.5:c.3289G>A	p.Glu1097Lys	p.E1097K	ENST00000266497		1097	Gaa/Aaa	23/31	NA	2	FACETS	0.426	0.368	0.489			1	INDETERMINATE	1	TRUE	NA	0.760645359350636	2		272	364	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673793	37673793	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	223	487	0	ENST00000447079.4:c.2947C>T	p.Arg983Ter	p.R983*	ENST00000447079	NM_015083.1	983	Cga/Tga	10/14	0.760645359350636	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.760645359350636	1		487	342	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272421	11272421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777142056	NA	P-0041349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	44	452	1	ENST00000361445.4:c.3509G>A	p.Arg1170His	p.R1170H	ENST00000361445	NM_004958.3	1170	cGc/cAc	23/58	0.760645359350636	1	FACETS	0.221	0.185	0.259	0.221	0.185	0.259	SUBCLONAL	1	TRUE	0	0.760645359350636	1		453	325	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578274	7578280	+	frameshift_variant	Frame_Shift_Del	DEL	TGAGGAG	TGAGGAG	-	novel	NA	P-0041349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	176	634	0	ENST00000269305.4:c.569_575del	p.Pro190ArgfsTer55	p.P190Rfs*55	ENST00000269305	NM_001126112.2	190	cCTCCTCAg/cg	6/11	0.626804751155028	1	FACETS	0.937	0.882	0.991	0.937	0.882	0.991	CLONAL	1	TRUE	0	0.760645359350636	1		634	306	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0042177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	105	294	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.994	0.905	1	0.994	0.905	1	CLONAL	1	TRUE	1	0.779515485867362	2		294	271	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478795	56478795	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	400	549	0	ENST00000267101.3:c.251C>A	p.Thr84Lys	p.T84K	ENST00000267101	NM_001982.3	84	aCa/aAa	3/28	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.779515485867362	2		549	1020	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060969	38060970	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0042177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	108	430	0	ENST00000250448.2:c.1019dup	p.Thr341AspfsTer74	p.T341Dfs*74	ENST00000250448	NM_004496.3	340	gcg/gcCg	2/2	1	2	FACETS	0.348	0.312	0.386	0.348	0.312	0.386	SUBCLONAL	1	TRUE	1	0.779515485867362	2		430	797	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106660	2106668	+	inframe_deletion	In_Frame_Del	DEL	CTGGACGCC	CTGGACGCC	-	novel	NA	P-0042177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	545	761	0	ENST00000219476.3:c.664_672del	p.Leu222_Ala224del	p.L222_A224del	ENST00000219476	NM_000548.3	222	CTGGACGCC/-	8/42	0.779515485867362	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.779515485867362	1		761	751	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578468	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGGGTG	CGCGGGTG	-	novel	NA	P-0042177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	660	870	0	ENST00000269305.4:c.462_469del	p.Thr155ProfsTer23	p.T155Pfs*23	ENST00000269305	NM_001126112.2	154	ggCACCCGCGtc/ggtc	5/11	0.779515485867362	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.779515485867362	1		870	947	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913355	NA	P-0042701-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	251	381	0	ENST00000288602.6:c.1406G>T	p.Gly469Val	p.G469V	ENST00000288602	NM_004333.4	469	gGa/gTa	11/18	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.784979085551779	2		381	600	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061333	38061333	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042701-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	493	669	0	ENST00000250448.2:c.656G>A	p.Arg219His	p.R219H	ENST00000250448	NM_004496.3	219	cGc/cAc	2/2	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.784979085551779	2		669	1153	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307279	118307281	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs1407741917	NA	P-0042701-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	10	89	0	ENST00000534358.1:c.63_65del	p.Gly23del	p.G23del	ENST00000534358	NM_005933.3	18	GGC/-	1/36	1	2	FACETS	0.131	0.089	0.185	0.131	0.089	0.185	SUBCLONAL	1	TRUE	1	0.784979085551779	2		89	194	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195696	123195696	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042701-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	266	610	0	ENST00000218089.9:c.1610C>T	p.Pro537Leu	p.P537L	ENST00000218089	NM_001042749.1	537	cCt/cTt	17/35	1	2	FACETS	0.801	0.753	0.85	0.801	0.753	0.85	CLONAL	1	TRUE	1	0.784979085551779	2		610	846	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255008	16255008	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753511718	NA	P-0042766-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	14	337	0	ENST00000375759.3:c.2273G>A	p.Arg758Gln	p.R758Q	ENST00000375759	NM_015001.2	758	cGa/cAa	11/15	0.292179179847293	4	FACETS	0.706	0.518	0.927	0.235	0.172	0.309	INDETERMINATE	1	TRUE	1	0.757642471320546	4		337	92	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578264	7578274	+	protein_altering_variant	In_Frame_Del	DEL	GATAAGATGCT	GATAAGATGCT	CA	novel	NA	P-0042766-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	44	735	1	ENST00000269305.4:c.575_585delinsTG	p.Gln192_Ile195delinsLeu	p.Q192_I195delinsL	ENST00000269305	NM_001126112.2	192	cAGCATCTTATC/cTG	6/11	0.649578492756367	2	FACETS	0.88	0.787	0.967	0.88	0.787	0.967	CLONAL	2	TRUE	0	0.757642471320546	2		736	66	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59886067	59886067	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs45459799	NA	P-0042766-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	52	493	1	ENST00000259008.2:c.679C>G	p.Gln227Glu	p.Q227E	ENST00000259008	NM_032043.2	227	Caa/Gaa	7/20	0.63337262861827	2	FACETS	1	0.932	1	0.549	0.481	0.619	CLONAL	1	TRUE	0	0.757642471320546	2		494	125	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0042798-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	40	695	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.903	1	1	0.979	1	CLONAL	4	FALSE	1	0.119258665737776	2		695	153	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242810	98242810	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042798-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	87	540	0	ENST00000331920.6:c.807G>T	p.Lys269Asn	p.K269N	ENST00000331920	NM_000264.3	269	aaG/aaT	6/24	1	2	FACETS	1	0.915	1	1	0.991	1	CLONAL	7	FALSE	1	0.119258665737776	2		540	206	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0042807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	122	227	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.715090004204222	2		228	309	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0042807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5173	154	512	0	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.715090004204222	27	FACETS	0.804	0.73	0.882			1	CLONAL	1	TRUE	NA	0.715090004204222	27		512	5327	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259397	11259397	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	196	699	0	ENST00000361445.4:c.4171C>G	p.Arg1391Gly	p.R1391G	ENST00000361445	NM_004958.3	1391	Cga/Gga	28/58	0.715090004204222	1	FACETS	0.934	0.879	0.989	0.934	0.879	0.989	CLONAL	1	TRUE	0	0.715090004204222	1		699	377	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981164	55981164	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	166	412	0	ENST00000263923.4:c.535T>A	p.Trp179Arg	p.W179R	ENST00000263923	NM_002253.2	179	Tgg/Agg	5/30	1	2	FACETS	0.949	0.879	1	0.949	0.879	1	CLONAL	1	TRUE	1	0.715090004204222	2		412	489	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933028	39933028	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042807-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	150	505	0	ENST00000378444.4:c.1571del	p.Ser524ThrfsTer4	p.S524Tfs*4	ENST00000378444	NM_001123385.1	524	aGc/ac	4/15	1	1	FACETS	0.864	0.804	0.924	0.864	0.804	0.924	CLONAL	1	TRUE	0	0.715090004204222	1		505	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0043656-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	288	646	2	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.354872102321701	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.398128445071574	2		648	655	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528711	8528711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774617096	NA	P-0043656-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	55	495	0	ENST00000356435.5:c.421C>T	p.Arg141Cys	p.R141C	ENST00000356435		141	Cgc/Tgc	4/35	0.310285310358449	3	FACETS	0.638	0.546	0.739	0.319	0.273	0.37	SUBCLONAL	1	TRUE	1	0.398128445071574	3		495	519	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242482	55242506	+	protein_altering_variant	In_Frame_Del	DEL	CATCTCCGAAAGCCAACAAGGAAAT	CATCTCCGAAAGCCAACAAGGAAAT	A	novel	NA	P-0043656-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	134	429	0	ENST00000275493.2:c.2252_2276delinsA	p.Thr751_Ile759delinsAsn	p.T751_I759delinsN	ENST00000275493	NM_005228.3	751	aCATCTCCGAAAGCCAACAAGGAAATc/aAc	19/28	0.398128445071574	8	FACETS	1	0.943	1			1	CLONAL	2	TRUE	NA	0.398128445071574	8		429	705	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040940	47040941	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs1556779417	NA	P-0043656-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	230	912	0	ENST00000377604.3:c.1473_1474del	p.Ser492AspfsTer25	p.S492Dfs*25	ENST00000377604	NM_001204468.1	490	tcTGtg/tctg	14/24	0.398128445071574	2	FACETS	0.976	0.917	1	0.976	0.917	1	CLONAL	2	TRUE	0	0.398128445071574	2		912	592	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951082	48951082	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043656-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	122	238	0	ENST00000267163.4:c.1244T>G	p.Ile415Arg	p.I415R	ENST00000267163	NM_000321.2	415	aTa/aGa	13/27	0.327449799984337	3	FACETS	1	0.981	1	0.825	0.757	0.893	CLONAL	2	TRUE	0	0.398128445071574	3		238	297	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058658	42058658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043656-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	33	258	0	ENST00000219905.7:c.8378G>A	p.Arg2793Lys	p.R2793K	ENST00000219905	NM_001164273.1	2793	aGg/aAg	24/24	1	2	FACETS	0.74	0.607	0.888	0.74	0.607	0.888	SUBCLONAL	1	TRUE	1	0.398128445071574	2		258	224	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374237	138374237	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043656-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	132	453	0	ENST00000289153.2:c.3207A>T	p.Arg1069Ser	p.R1069S	ENST00000289153	NM_006219.2	1069	agA/agT	22/22	0.398128445071574	6	FACETS	0.757	0.687	0.83	0.378	0.343	0.415	SUBCLONAL	2	TRUE	2	0.398128445071574	6		453	787	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285027	15285027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777398556	NA	P-0044229-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1432	1344	1279	0	ENST00000263388.2:c.4588G>A	p.Asp1530Asn	p.D1530N	ENST00000263388	NM_000435.2	1530	Gac/Aac	25/33	0.833030841434138	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.916939347184024	4		1279	2776	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548924	29548925	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0044229-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	171	520	2	ENST00000356175.3:c.1699_1700del	p.Val567ArgfsTer7	p.V567Rfs*7	ENST00000356175	NM_000267.3	566	ccTGta/ccta	15/57	0.916939347184024	2	FACETS	0.892	0.856	0.925	0.892	0.856	0.925	CLONAL	2	TRUE	0	0.916939347184024	2		522	209	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0044921-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	105	339	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.808	0.734	0.884	0.808	0.734	0.884	CLONAL	1	TRUE	1	0.872499542397756	2		339	298	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424409	47424409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779648831	NA	P-0044921-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	253	696	2	ENST00000377045.4:c.329C>T	p.Ala110Val	p.A110V	ENST00000377045	NM_001654.4	110	gCg/gTg	5/16	0.293554297539418	1	FACETS	0.448	0.421	0.476	0.448	0.421	0.476	INDETERMINATE	1	TRUE	0	0.872499542397756	1		698	729	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631129	69631129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs281860303	NA	P-0044921-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	330	739	1	ENST00000334134.2:c.283C>T	p.Arg95Trp	p.R95W	ENST00000334134	NM_005247.2	95	Cgg/Tgg	2/3	1	2	FACETS	0.911	0.865	0.958	0.911	0.865	0.958	CLONAL	1	TRUE	1	0.872499542397756	2		740	830	SUCCESS
APC	324	MSKCC	GRCh37	5	112173388	112173388	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1060503282	NA	P-0044921-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	87	218	1	ENST00000257430.4:c.2097G>A	p.Trp699Ter	p.W699*	ENST00000257430	NM_000038.5	699	tgG/tgA	16/16	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.872499542397756	2		219	185	SUCCESS
ATM	472	MSKCC	GRCh37	11	108100002	108100002	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781545	NA	P-0044921-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	85	221	2	ENST00000278616.4:c.283C>T	p.Gln95Ter	p.Q95*	ENST00000278616	NM_000051.3	95	Cag/Tag	4/63	0.872499542397756	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.872499542397756	1		223	108	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431380	49431381	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044921-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	257	604	4	ENST00000301067.7:c.9758dup	p.Leu3253PhefsTer4	p.L3253Ffs*4	ENST00000301067	NM_003482.3	3253	ttg/ttTg	34/54	1	2	FACETS	0.944	0.891	0.998	0.944	0.891	0.998	CLONAL	1	TRUE	1	0.872499542397756	2		608	624	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554660	63554660	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044921-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	321	545	4	ENST00000307078.5:c.79C>T	p.Pro27Ser	p.P27S	ENST00000307078	NM_004655.3	27	Cca/Tca	2/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.872499542397756	2		549	706	SUCCESS
APC	324	MSKCC	GRCh37	5	112175441	112175442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTAGCAGATGTACTTCTGTCAGTTCACTTGATAG	novel	NA	P-0044921-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	45	238	0	ENST00000257430.4:c.4153_4186dup	p.Phe1396Ter	p.F1396*	ENST00000257430	NM_000038.5	1384	ttt/tTTAGCAGATGTACTTCTGTCAGTTCACTTGATAGtt	16/16	1	2	FACETS	0.379	0.321	0.443	0.379	0.321	0.443	SUBCLONAL	1	TRUE	1	0.872499542397756	2		238	272	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019996	123019996	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044921-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	221	630	2	ENST00000355640.3:c.484A>G	p.Ser162Gly	p.S162G	ENST00000355640		162	Agt/Ggt	2/7	0.293554297539418	1	FACETS	0.491	0.46	0.522	0.491	0.46	0.522	INDETERMINATE	1	TRUE	0	0.872499542397756	1		632	582	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0044960-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	170	554	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.828578634604787	4	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	2	0.914116734505689	4		554	348	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0044960-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	254	376	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.914116734505689	5	FACETS	0.883	0.845	0.92	0.883	0.845	0.92	CLONAL	4	TRUE	1	0.914116734505689	5		376	373	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881426	48881426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044960-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	240	107	0	ENST00000267163.4:c.148G>T	p.Glu50Ter	p.E50*	ENST00000267163	NM_000321.2	50	Gaa/Taa	2/27	0.890130691420034	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	4	TRUE	0	0.914116734505689	4		107	250	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934874	NA	P-0044960-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	186	1065	1	ENST00000269305.4:c.451C>A	p.Pro151Thr	p.P151T	ENST00000269305	NM_001126112.2	151	Ccc/Acc	5/11	0.910030707157965	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.914116734505689	2		1066	193	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456631	40456631	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044960-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	16	674	0	ENST00000345506.4:c.1341G>C	p.Gln447His	p.Q447H	ENST00000345506	NM_003152.3	447	caG/caC	12/20	0.914116734505689	3	FACETS	0.166	0.122	0.218	0.083	0.061	0.109	SUBCLONAL	1	TRUE	1	0.914116734505689	3		674	308	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139736	55139736	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044960-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	232	487	0	ENST00000257290.5:c.1398del	p.Asn467ThrfsTer22	p.N467Tfs*22	ENST00000257290	NM_006206.4	466	gCc/gc	10/23	0.730628568665653	5	FACETS	1	0.987	1			1	CLONAL	3	TRUE	NA	0.914116734505689	5		487	364	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84406150	84406150	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs955473473	NA	P-0044960-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	114	578	0	ENST00000321945.7:c.76G>T	p.Asp26Tyr	p.D26Y	ENST00000321945	NM_139076.2	26	Gac/Tac	1/9	0.914116734505689	3	FACETS	0.886	0.804	0.971	0.443	0.402	0.486	CLONAL	1	TRUE	1	0.914116734505689	3		578	410	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0044970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	140	227	1				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		228	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577528	7577528	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs878854074	NA	P-0044970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	70	668	0	ENST00000269305.4:c.753C>G	p.Ile251Met	p.I251M	ENST00000269305	NM_001126112.2	251	atC/atG	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		668	599	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652976	29652979	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	rs1085307459	NA	P-0044970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	165	487	0	ENST00000356175.3:c.4914_4917del	p.Lys1640GlyfsTer36	p.K1640Gfs*36	ENST00000356175	NM_000267.3	1637	ttTCTC/tt	36/57	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		487	769	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125798	47125799	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0044970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	125	355	0	ENST00000409792.3:c.5471_5472insC	p.Gln1825SerfsTer7	p.Q1825Sfs*7	ENST00000409792	NM_014159.6	1824	att/atCt	12/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		355	356	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101078	27101078	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	79	880	0	ENST00000324856.7:c.4360C>T	p.Gln1454Ter	p.Q1454*	ENST00000324856	NM_006015.4	1454	Caa/Taa	18/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		880	1212	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914638	39914639	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	42	534	0	ENST00000378444.4:c.4723dup	p.Met1575AsnfsTer11	p.M1575Nfs*11	ENST00000378444	NM_001123385.1	1575	atg/aAtg	12/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		534	625	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0045481-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	60	376	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.142089506975749	3	FACETS	0.834	0.719	0.958	0.834	0.719	0.958	CLONAL	2	TRUE	1	0.159591025603065	3		376	487	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581201	48581201	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045481-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	38	353	1	ENST00000342988.3:c.505C>T	p.Gln169Ter	p.Q169*	ENST00000342988	NM_005359.5	169	Cag/Tag	5/12	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.159591025603065	2		354	455	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387324	17387324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374131612	NA	P-0045481-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	73	706	1	ENST00000359435.4:c.590C>T	p.Pro197Leu	p.P197L	ENST00000359435	NM_001033549.1	197	cCg/cTg	7/9	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.159591025603065	2		707	898	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568663	41568663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045481-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	20	229	0	ENST00000263253.7:c.4613C>T	p.Thr1538Ile	p.T1538I	ENST00000263253	NM_001429.3	1538	aCa/aTa	28/31	1	2	FACETS	0.638	0.487	0.815	0.638	0.487	0.815	SUBCLONAL	1	TRUE	1	0.159591025603065	2		229	393	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163182	47163182	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045481-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	31	296	0	ENST00000409792.3:c.2944G>C	p.Asp982His	p.D982H	ENST00000409792	NM_014159.6	982	Gat/Cat	3/21	0.142089506975749	3	FACETS	1	0.812	1	0.502	0.406	0.611	CLONAL	1	TRUE	1	0.159591025603065	3		296	418	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964491	93964491	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045481-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	39	495	0	ENST00000369303.4:c.2406G>C	p.Trp802Cys	p.W802C	ENST00000369303	NM_004440.3	802	tgG/tgC	14/17	1	2	FACETS	0.874	0.724	1	0.874	0.724	1	CLONAL	1	TRUE	1	0.159591025603065	2		495	559	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949031	44949031	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045481-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	56	203	0	ENST00000377967.4:c.3592G>A	p.Glu1198Lys	p.E1198K	ENST00000377967	NM_021140.2	1198	Gaa/Aaa	25/29	0.145767723332839	2	FACETS	1	0.937	1			1	CLONAL	2	TRUE	NA	0.159591025603065	2		203	304	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0046114-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	117	652	1	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.200134921708683	2	FACETS	0.948	0.856	1	0.474	0.428	0.523	INDETERMINATE	1	TRUE	0	0.34269709710808	2		653	720	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578485	7578486	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046114-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	165	794	0	ENST00000269305.4:c.444_445insA	p.Ser149IlefsTer32	p.S149Ifs*32	ENST00000269305	NM_001126112.2	148	-/A	5/11	0.200134921708683	2	FACETS	0.88	0.807	0.957	0.44	0.403	0.479	INDETERMINATE	1	TRUE	0	0.34269709710808	2		794	1094	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249131	55249131	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046114-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	102	724	1	ENST00000275493.2:c.2429G>T	p.Gly810Val	p.G810V	ENST00000275493	NM_005228.3	810	gGc/gTc	20/28	0.200134921708683	2	FACETS	0.739	0.661	0.823	0.37	0.33	0.412	INDETERMINATE	1	TRUE	0	0.34269709710808	2		725	805	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099869	157099869	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774432900	NA	P-0046232-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	73	674	6	ENST00000346085.5:c.806C>T	p.Ala269Val	p.A269V	ENST00000346085	NM_020732.3	269	gCc/gTc	1/20	1	2	FACETS	0.967	0.846	1	0.967	0.846	1	CLONAL	1	TRUE	1	0.245446449399907	2		680	615	SUCCESS
APC	324	MSKCC	GRCh37	5	112151282	112151282	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs786204118	NA	P-0046232-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	35	297	2	ENST00000257430.4:c.925G>T	p.Gly309Ter	p.G309*	ENST00000257430	NM_000038.5	309	Gga/Tga	9/16	1	2	FACETS	0.917	0.754	1	0.917	0.754	1	CLONAL	1	TRUE	1	0.245446449399907	2		299	311	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046449-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	120	365	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.437120571255703	2		365	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0046449-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	272	500	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.437120571255703	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.437120571255703	2		500	590	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0046449-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	125	364	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	0.437120571255703	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.437120571255703	1		364	405	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657025	45657025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542311532	NA	P-0046449-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	48	468	0	ENST00000407780.3:c.131G>A	p.Arg44His	p.R44H	ENST00000407780	NM_001283052.1	44	cGt/cAt	3/7	0.427880084470376	1	FACETS	0.398	0.337	0.465	0.398	0.337	0.465	SUBCLONAL	1	TRUE	0	0.437120571255703	1		468	431	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55272964	55272964	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046449-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	32	383	0	ENST00000275493.2:c.3287C>G	p.Ser1096Cys	p.S1096C	ENST00000275493	NM_005228.3	1096	tCc/tGc	28/28	0.143337097564741	3	FACETS	0.369	0.299	0.448	0.184	0.149	0.224	INDETERMINATE	1	TRUE	1	0.437120571255703	3		383	484	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273020	55273020	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046449-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	45	547	0	ENST00000275493.2:c.3343C>G	p.Leu1115Val	p.L1115V	ENST00000275493	NM_005228.3	1115	Ctg/Gtg	28/28	0.143337097564741	3	FACETS	0.427	0.358	0.503	0.213	0.179	0.252	INDETERMINATE	1	TRUE	1	0.437120571255703	3		547	588	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194830	29194830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046449-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	230	1047	4	ENST00000240100.2:c.898C>T	p.Arg300Trp	p.R300W	ENST00000240100	NM_001394.6	300	Cgg/Tgg	4/4	1	2	FACETS	0.95	0.885	1	0.95	0.885	1	CLONAL	1	TRUE	1	0.437120571255703	2		1051	1108	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259558	55259558	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046449-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	39	447	0	ENST00000275493.2:c.2616A>C	p.Glu872Asp	p.E872D	ENST00000275493	NM_005228.3	872	gaA/gaC	21/28	0.143337097564741	3	FACETS	0.384	0.318	0.458	0.192	0.159	0.229	INDETERMINATE	1	TRUE	1	0.437120571255703	3		447	566	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0046580-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	144	227	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.535102865391152	2		228	386	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061115	38061115	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1016447126	NA	P-0046580-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	31	265	0	ENST00000250448.2:c.874G>A	p.Glu292Lys	p.E292K	ENST00000250448	NM_004496.3	292	Gag/Aag	2/2	0.292446693668411	1	FACETS	0.477	0.389	0.573	0.477	0.389	0.573	INDETERMINATE	1	TRUE	0	0.535102865391152	1		265	178	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908221	28908221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046580-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	47	435	0	ENST00000282397.4:c.2534C>T	p.Ser845Leu	p.S845L	ENST00000282397	NM_002019.4	845	tCa/tTa	18/30	1	2	FACETS	0.364	0.307	0.426	0.364	0.307	0.426	SUBCLONAL	1	TRUE	1	0.535102865391152	2		435	483	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5206850	5206850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046580-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	16	0	0	ENST00000357368.4:c.5782G>A	p.Glu1928Lys	p.E1928K	ENST00000357368	NM_002850.3	1928	Gag/Aag	38/38	0.402247555829632	1	FACETS	0.085	0.062	0.113	0.085	0.062	0.113	SUBCLONAL	1	TRUE	0	0.535102865391152	1		0	515	SUCCESS
ATM	472	MSKCC	GRCh37	11	108183151	108183151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046580-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	8	0	0	ENST00000278616.4:c.5932G>A	p.Glu1978Lys	p.E1978K	ENST00000278616	NM_000051.3	1978	Gaa/Aaa	40/63	0.184131992137316	3	FACETS	0.14	0.09	0.206	0.047	0.03	0.069	INDETERMINATE	1	TRUE	0	0.535102865391152	3		0	270	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369231	118369231	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046580-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	18	242	0	ENST00000534358.1:c.5949G>C	p.Leu1983Phe	p.L1983F	ENST00000534358	NM_005933.3	1983	ttG/ttC	22/36	0.184131992137316	3	FACETS	0.266	0.2	0.345	0.089	0.066	0.115	INDETERMINATE	1	TRUE	0	0.535102865391152	3		242	320	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145488	58145488	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046580-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	22	431	0	ENST00000257904.6:c.13C>G	p.Arg5Gly	p.R5G	ENST00000257904	NM_000075.3	5	Cga/Gga	2/8	NA	2	FACETS	0.209	0.162	0.265			1	INDETERMINATE	1	TRUE	NA	0.535102865391152	2		431	393	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513232	44513232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046580-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	28	487	1	ENST00000291552.4:c.703G>A	p.Glu235Lys	p.E235K	ENST00000291552	NM_006758.2	235	Gaa/Aaa	8/8	0.17010773260124	3	FACETS	0.287	0.229	0.354	0.144	0.114	0.177	INDETERMINATE	1	TRUE	1	0.535102865391152	3		488	462	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778822	76778822	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046580-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	11	0	0	ENST00000373344.5:c.6757G>A	p.Glu2253Lys	p.E2253K	ENST00000373344	NM_000489.3	2253	Gaa/Aaa	31/35	1	1	FACETS	0.13	0.09	0.181	0.13	0.09	0.181	SUBCLONAL	1	TRUE	0	0.535102865391152	1		0	231	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089755	5089755	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046580-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	9	0	0	ENST00000381652.3:c.2653C>T	p.Gln885Ter	p.Q885*	ENST00000381652	NM_004972.3	885	Cag/Tag	20/25	0.535102865391152	1	FACETS	0.111	0.073	0.16	0.111	0.073	0.16	SUBCLONAL	1	TRUE	0	0.535102865391152	1		0	221	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322607	39322607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046580-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	8	0	0	ENST00000373001.3:c.385G>A	p.Asp129Asn	p.D129N	ENST00000373001	NM_022157.3	129	Gac/Aac	2/7	0.292446693668411	1	FACETS	0.035	0.022	0.052	0.035	0.022	0.052	INDETERMINATE	1	TRUE	0	0.535102865391152	1		0	628	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644418	18644418	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs376468347	NA	P-0046580-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	5	0	0	ENST00000266497.5:c.2596G>C	p.Glu866Gln	p.E866Q	ENST00000266497		866	Gag/Cag	18/31	0.535102865391152	1	FACETS	0.054	0.03	0.088	0.054	0.03	0.088	SUBCLONAL	1	TRUE	0	0.535102865391152	1		0	252	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73334716	73334716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754234020	NA	P-0046580-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	11	0	0	ENST00000377767.4:c.2744C>T	p.Ser915Leu	p.S915L	ENST00000377767	NM_014953.3	915	tCa/tTa	20/21	1	2	FACETS	0.122	0.084	0.17	0.122	0.084	0.17	SUBCLONAL	1	TRUE	1	0.535102865391152	2		0	337	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823847	3823847	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046580-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	27	0	0	ENST00000262367.5:c.2368C>T	p.Gln790Ter	p.Q790*	ENST00000262367	NM_004380.2	790	Cag/Tag	13/31	0.439340471607515	1	FACETS	0.134	0.106	0.166	0.134	0.106	0.166	SUBCLONAL	1	TRUE	0	0.535102865391152	1		0	552	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524501	44524501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046580-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	12	0	0	ENST00000291552.4:c.56C>T	p.Ser19Leu	p.S19L	ENST00000291552	NM_006758.2	19	tCa/tTa	2/8	0.17010773260124	3	FACETS	0.193	0.135	0.264	0.096	0.067	0.132	INDETERMINATE	1	TRUE	1	0.535102865391152	3		0	295	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142949964	142949964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046580-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	14	0	0	ENST00000262992.4:c.2746G>A	p.Glu916Lys	p.E916K	ENST00000262992	NM_001101669.1	916	Gag/Aag	24/24	0.37438253394197	1	FACETS	0.095	0.068	0.128	0.095	0.068	0.128	SUBCLONAL	1	TRUE	0	0.535102865391152	1		0	404	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74868196	74868196	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046580-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	6	0	0	ENST00000284811.8:c.98G>C	p.Arg33Thr	p.R33T	ENST00000284811		33	aGa/aCa	3/4	0.174765592321745	5	FACETS	0.334	0.2	0.515	0.111	0.066	0.172	INDETERMINATE	1	TRUE	2	0.535102865391152	5		0	121	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163310173	163310173	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1381252631	NA	P-0046580-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	66	366	0	ENST00000271452.3:c.626A>G	p.Asn209Ser	p.N209S	ENST00000271452	NM_145697.2	209	aAt/aGt	9/14	0.535102865391152	5	FACETS	0.586	0.508	0.671			1	SUBCLONAL	1	TRUE	NA	0.535102865391152	5		366	759	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243714	41243714	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046580-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	66	566	0	ENST00000357654.3:c.3834G>T	p.Lys1278Asn	p.K1278N	ENST00000357654	NM_007294.3	1278	aaG/aaT	10/23	0.174765592321745	5	FACETS	0.713	0.618	0.815	0.238	0.206	0.272	INDETERMINATE	1	TRUE	2	0.535102865391152	5		566	624	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945636	54945636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046580-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	42	302	1	ENST00000312783.6:c.934C>T	p.Leu312Phe	p.L312F	ENST00000312783	NM_198436.1	312	Ctc/Ttc	9/10	1	2	FACETS	0.536	0.449	0.63	0.536	0.449	0.63	SUBCLONAL	1	TRUE	1	0.535102865391152	2		303	293	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978731	70978731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046580-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	55	457	0	ENST00000276594.2:c.922G>A	p.Asp308Asn	p.D308N	ENST00000276594	NM_024504.3	308	Gat/Aat	5/8	0.174765592321745	5	FACETS	0.614	0.524	0.711	0.205	0.174	0.237	INDETERMINATE	1	TRUE	2	0.535102865391152	5		457	604	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0046757-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	265	458	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.555502479841319	4	FACETS	0.984	0.928	1	0.984	0.928	1	CLONAL	2	TRUE	2	0.648346621668748	4		458	685	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0046757-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	229	364	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	2	TRUE	NA	0.648346621668748	2		364	345	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052713	42052716	+	frameshift_variant	Frame_Shift_Del	DEL	CTCA	CTCA	-	novel	NA	P-0046757-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	241	400	0	ENST00000219905.7:c.7384_7387del	p.Leu2462PhefsTer12	p.L2462Ffs*12	ENST00000219905	NM_001164273.1	2462	CTCAtt/tt	20/24	0.616714171028699	4	FACETS	0.95	0.893	1	0.95	0.893	1	CLONAL	2	TRUE	2	0.648346621668748	4		400	645	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046925-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	65	365	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.904	1			1	INDETERMINATE	1	TRUE	NA	0.772100733094396	2		365	165	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0046925-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	145	473	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.257091895940595	3	FACETS	1	0.919	1	0.334	0.306	0.362	INDETERMINATE	1	TRUE	0	0.772100733094396	3		474	520	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857895	9857895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761399460	NA	P-0046925-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	166	497	0	ENST00000330684.3:c.3506G>A	p.Arg1169Gln	p.R1169Q	ENST00000330684	NM_001134407.1	1169	cGg/cAg	13/13	1	2	FACETS	0.758	0.7	0.818	0.758	0.7	0.818	SUBCLONAL	1	TRUE	1	0.772100733094396	2		497	567	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692979	89692979	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123325	NA	P-0046925-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	240	397	0	ENST00000371953.3:c.463T>C	p.Tyr155His	p.Y155H	ENST00000371953	NM_000314.4	155	Tat/Cat	5/9	0.772100733094396	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.772100733094396	1		397	358	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857927	9857927	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046925-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	45	493	0	ENST00000330684.3:c.3474C>G	p.Phe1158Leu	p.F1158L	ENST00000330684	NM_001134407.1	1158	ttC/ttG	13/13	1	2	FACETS	0.203	0.17	0.239	0.203	0.17	0.239	SUBCLONAL	1	TRUE	1	0.772100733094396	2		493	575	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527539	29527539	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555610896	NA	P-0046925-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	112	368	0	ENST00000356175.3:c.988del	p.Ala330GlnfsTer46	p.A330Qfs*46	ENST00000356175	NM_000267.3	330	Gca/ca	9/57	1	2	FACETS	0.523	0.472	0.576	0.523	0.472	0.576	SUBCLONAL	1	TRUE	1	0.772100733094396	2		368	555	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546138	29546138	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0046925-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	107	238	0	ENST00000356175.3:c.1641+2T>G		p.X547_splice	ENST00000356175	NM_000267.3	547			1	2	FACETS	0.674	0.609	0.742	0.674	0.609	0.742	SUBCLONAL	1	TRUE	1	0.772100733094396	2		238	411	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27168571	27168571	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046925-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	25	365	0	ENST00000380036.4:c.443T>A	p.Ile148Asn	p.I148N	ENST00000380036	NM_000459.3	148	aTt/aAt	3/23	0.769395426370091	1	FACETS	0.088	0.069	0.11	0.088	0.069	0.11	SUBCLONAL	1	TRUE	0	0.772100733094396	1		365	453	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0046985-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	125	326	6	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.726971736891745	4	FACETS	0.933	0.847	1	0.467	0.423	0.512	CLONAL	1	TRUE	2	0.723584853648754	4		332	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0046985-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	1143	771	1	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.692904840902796	5	FACETS	0.969	0.955	0.983	0.969	0.955	0.983	CLONAL	5	TRUE	0	0.723584853648754	5		772	1360	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231311	98231311	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1448553293	NA	P-0046985-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	461	969	0	ENST00000331920.6:c.1972A>G	p.Met658Val	p.M658V	ENST00000331920	NM_000264.3	658	Atg/Gtg	14/24	0.663432495286074	4	FACETS	0.901	0.862	0.94	0.901	0.862	0.94	CLONAL	2	TRUE	2	0.723584853648754	4		969	1219	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039505	49039505	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs764754259	NA	P-0046985-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	398	396	0	ENST00000267163.4:c.2489+1G>C		p.X830_splice	ENST00000267163	NM_000321.2	830			0.64364543207442	5	FACETS	0.907	0.881	0.931	0.907	0.881	0.931	CLONAL	5	TRUE	0	0.723584853648754	5		396	506	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518365	204518365	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046985-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	116	361	0	ENST00000367182.3:c.1028C>G	p.Thr343Arg	p.T343R	ENST00000367182	NM_001278516.1	343	aCg/aGg	11/11	0.615522414333046	3	FACETS	0.919	0.833	1			1	CLONAL	1	TRUE	NA	0.723584853648754	3		361	475	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992060	72992060	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046985-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	387	828	0	ENST00000268489.5:c.1985T>C	p.Met662Thr	p.M662T	ENST00000268489	NM_006885.3	662	aTg/aCg	2/10	0.726971736891745	3	FACETS	0.767	0.731	0.803	0.511	0.487	0.535	SUBCLONAL	2	TRUE	0	0.723584853648754	3		828	950	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0047077-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	122	554	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.762688557290937	2	FACETS	1	0.943	1	0.518	0.475	0.561	CLONAL	1	TRUE	0	0.762688557290937	2		554	309	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0047077-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	96	376	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.320092000815676	5	FACETS	0.82	0.739	0.905	0.547	0.492	0.604	INDETERMINATE	2	TRUE	2	0.762688557290937	5		376	329	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0047077-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	330	396	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.762688557290937	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	0	0.762688557290937	3		396	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578509	7578509	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519978	NA	P-0047077-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	198	1265	0	ENST00000269305.4:c.421T>G	p.Cys141Gly	p.C141G	ENST00000269305	NM_001126112.2	141	Tgc/Ggc	5/11	NA	2	FACETS	0.93	0.887	0.972			1	INDETERMINATE	2	TRUE	NA	0.762688557290937	2		1265	279	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502662	149502662	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759436020	NA	P-0047077-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	114	955	1	ENST00000261799.4:c.2126G>A	p.Arg709His	p.R709H	ENST00000261799	NM_002609.3	709	cGc/cAc	15/23	0.762688557290937	3	FACETS	0.96	0.871	1	0.32	0.29	0.351	CLONAL	1	TRUE	0	0.762688557290937	3		956	430	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466769	25466769	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047077-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	305	733	0	ENST00000264709.3:c.1934C>G	p.Thr645Arg	p.T645R	ENST00000264709	NM_175629.2	645	aCa/aGa	16/23	0.762688557290937	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.762688557290937	2		733	376	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0047185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	546	652	1	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.3	5	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	5		653	1469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578509	7578509	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519978	NA	P-0047185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1408	45	938	0	ENST00000269305.4:c.421T>C	p.Cys141Arg	p.C141R	ENST00000269305	NM_001126112.2	141	Tgc/Cgc	5/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		938	1453	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268969	55268969	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	524	724	1	ENST00000275493.2:c.3035A>T	p.Asp1012Val	p.D1012V	ENST00000275493	NM_005228.3	1012	gAt/gTt	25/28	0.3	5	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	5		725	1577	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0047450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	28	473	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.23	2		474	223	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0047450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1333	60	673	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.375	0.321	0.433	0.375	0.321	0.433	SUBCLONAL	1	TRUE	1	0.23	2		673	1393	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0047450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	40	264	0	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	1	2	FACETS	0.665	0.552	0.791	0.665	0.552	0.791	SUBCLONAL	1	TRUE	1	0.23	2		264	523	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0047605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	91	743	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.130393998639251	3	FACETS	1	0.93	1	0.531	0.472	0.594	INDETERMINATE	1	TRUE	1	0.323938529701195	3		743	615	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0047605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	115	721	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.323938529701195	2		721	643	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188234	10188235	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	110	546	0	ENST00000256474.2:c.378dup	p.Gly127TrpfsTer5	p.G127Wfs*5	ENST00000256474	NM_000551.3	126	gat/gaTt	2/3	0.323938529701195	1	FACETS	0.935	0.842	1	0.935	0.842	1	CLONAL	1	TRUE	0	0.323938529701195	1		546	609	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0047724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	18	432	1	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.468	0.352	0.605	0.468	0.352	0.605	SUBCLONAL	1	TRUE	1	0.269940356981658	2		433	285	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0047724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	11	429	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	1	2	FACETS	0.291	0.2	0.404	0.291	0.2	0.404	SUBCLONAL	1	TRUE	1	0.269940356981658	2		429	280	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974679	21974679	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs864622636	NA	P-0047724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	57	1138	0	ENST00000304494.5:c.148C>T	p.Gln50Ter	p.Q50*	ENST00000304494	NM_000077.4	50	Cag/Tag	1/3	0.271576657810576	1	FACETS	0.693	0.595	0.8	0.693	0.595	0.8	SUBCLONAL	1	TRUE	0	0.269940356981658	1		1138	527	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350548	15350548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772431443	NA	P-0047724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	124	1993	6	ENST00000263377.2:c.3367G>A	p.Glu1123Lys	p.E1123K	ENST00000263377	NM_058243.2	1123	Gag/Aag	16/20	1	2	FACETS	0.961	0.868	1	0.961	0.868	1	CLONAL	1	TRUE	1	0.269940356981658	2		1999	956	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438222	56438223	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0047724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	135	1352	0	ENST00000407977.2:c.770dup	p.Glu258Ter	p.E258*	ENST00000407977		257	ggt/ggGt	7/10	0.211793851604886	2	FACETS	1	0.935	1	0.518	0.47	0.569	CLONAL	1	TRUE	0	0.269940356981658	2		1352	965	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0047724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	124	1605	4	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.269940356981658	1	FACETS	0.796	0.719	0.878	0.796	0.719	0.878	SUBCLONAL	1	TRUE	0	0.269940356981658	1		1609	998	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380178	25380178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	28	398	0	ENST00000311936.3:c.280C>T	p.His94Tyr	p.H94Y	ENST00000311936	NM_004985.3	94	Cac/Tac	3/5	1	2	FACETS	0.783	0.628	0.958	0.783	0.628	0.958	CLONAL	1	TRUE	1	0.269940356981658	2		398	265	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627454	14627454	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	60	711	8	ENST00000254322.2:c.616A>G	p.Ile206Val	p.I206V	ENST00000254322	NM_006145.1	206	Atc/Gtc	2/3	0.26647161528418	4	FACETS	0.89	0.767	1			1	CLONAL	1	TRUE	NA	0.269940356981658	4		719	634	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212033	142212033	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374253623	NA	P-0047724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	71	910	2	ENST00000350721.4:c.6019G>A	p.Gly2007Ser	p.G2007S	ENST00000350721	NM_001184.3	2007	Ggc/Agc	35/47	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.269940356981658	2		912	352	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0048030-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	252	750	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.852235300674001	2	FACETS	0.979	0.948	1	0.979	0.948	1	CLONAL	2	TRUE	0	0.858237742776503	2		750	300	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790072	40790072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753667	NA	P-0048030-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	146	748	0	ENST00000373198.4:c.2659G>A	p.Ala887Thr	p.A887T	ENST00000373198	NM_133170.3	887	Gcc/Acc	18/32	0.736074082268819	4	FACETS	0.991	0.907	1	0.33	0.302	0.36	CLONAL	1	TRUE	1	0.858237742776503	4		748	638	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332617	153332617	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769623850	NA	P-0048030-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	104	468	0	ENST00000281708.4:c.339G>T	p.Glu113Asp	p.E113D	ENST00000281708	NM_033632.3	113	gaG/gaT	2/12	0.840921106823821	2	FACETS	1	0.937	1	0.516	0.471	0.561	CLONAL	1	TRUE	0	0.858237742776503	2		468	235	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95598907	95598907	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048030-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	110	495	0	ENST00000393063.1:c.252G>T	p.Gln84His	p.Q84H	ENST00000393063	NM_030621.3	84	caG/caT	4/28	0.858237742776503	3	FACETS	0.891	0.807	0.979	0.297	0.269	0.327	CLONAL	1	TRUE	0	0.858237742776503	3		495	411	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0048051-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	398	381	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		382	455	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544748	65544748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048051-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	431	569	0	ENST00000358664.4:c.178C>T	p.Arg60Trp	p.R60W	ENST00000358664	NM_002382.4	60	Cgg/Tgg	4/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		569	475	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593662	55593664	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0048051-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	1523	462	0	ENST00000288135.5:c.1729_1731del	p.Pro577del	p.P577del	ENST00000288135	NM_000222.2	576	ctTCCt/ctt	11/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		462	2005	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475158	475158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048051-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	433	620	1	ENST00000399788.2:c.479C>T	p.Ser160Leu	p.S160L	ENST00000399788	NM_001042603.1	160	tCa/tTa	4/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		621	956	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991092	41991092	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048051-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	358	485	0	ENST00000219905.7:c.2045C>G	p.Thr682Arg	p.T682R	ENST00000219905	NM_001164273.1	682	aCa/aGa	4/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		485	418	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022324	36022324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760138531	NA	P-0048051-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	637	1096	2	ENST00000358208.4:c.377C>T	p.Ser126Leu	p.S126L	ENST00000358208		126	tCg/tTg	4/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1098	1441	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440833	52440853	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGGGCCCTTACCCTGCAGTG	CAGGGCCCTTACCCTGCAGTG	-	novel	NA	P-0048051-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	497	801	0	ENST00000460680.1:c.651_659+12del		p.X217_splice	ENST00000460680	NM_004656.3	217		8/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		801	568	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342452	118342452	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	GATCT	novel	NA	P-0048051-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	29	0	0	ENST00000534358.1:c.578delinsGATCT	p.Pro193ArgfsTer10	p.P193Rfs*10	ENST00000534358	NM_005933.3	193	cCa/cGATCTa	3/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		0	368	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048166-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	49	576	4	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	0.3	1	FACETS	0.675	0.571	0.79	0.675	0.571	0.79	SUBCLONAL	1	TRUE	0	0.22	1		580	587	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416114	49416114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048166-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	87	623	0	ENST00000301067.7:c.16361G>A	p.Arg5454Gln	p.R5454Q	ENST00000301067	NM_003482.3	5454	cGa/cAa	52/54	1	2	FACETS	0.991	0.877	1	0.991	0.877	1	CLONAL	1	TRUE	1	0.22	2		623	798	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73340149	73340149	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048166-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	21	319	0	ENST00000377767.4:c.1931A>G	p.Glu644Gly	p.E644G	ENST00000377767	NM_014953.3	644	gAa/gGa	15/21	1	2	FACETS	0.458	0.352	0.582	0.458	0.352	0.582	SUBCLONAL	1	TRUE	1	0.22	2		319	417	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346190	89346190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1003478010	NA	P-0048166-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	29	405	0	ENST00000301030.4:c.6760G>A	p.Gly2254Arg	p.G2254R	ENST00000301030	NM_001256183.1	2254	Gga/Aga	9/13	1	2	FACETS	0.666	0.534	0.815	0.666	0.534	0.815	SUBCLONAL	1	TRUE	1	0.22	2		405	396	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991704	25991704	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048166-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	61	460	0	ENST00000435504.4:c.538C>T	p.Gln180Ter	p.Q180*	ENST00000435504		180	Cag/Tag	7/13	1	2	FACETS	0.906	0.782	1	0.906	0.782	1	CLONAL	1	TRUE	1	0.22	2		460	612	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710725	117710725	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048166-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	27	394	0	ENST00000368508.3:c.1547T>C	p.Val516Ala	p.V516A	ENST00000368508	NM_002944.2	516	gTc/gCc	12/43	0.3	1	FACETS	0.567	0.451	0.7	0.567	0.451	0.7	SUBCLONAL	1	TRUE	0	0.22	1		394	385	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945510	151945510	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048166-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	113	842	0	ENST00000262189.6:c.2009del	p.Leu670Ter	p.L670*	ENST00000262189	NM_170606.2	670	tTa/ta	14/59	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.22	2		842	1023	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351422	70351422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048166-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	81	407	0	ENST00000374080.3:c.4070G>A	p.Arg1357His	p.R1357H	ENST00000374080		1357	cGc/cAc	29/45	1	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.22	1		407	506	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	112	554	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.83	0.75	0.914	0.83	0.75	0.914	CLONAL	1	TRUE	1	0.511135755642309	2		554	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0048572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	269	825	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.488880898410984	1	FACETS	0.987	0.929	1	0.987	0.929	1	CLONAL	1	TRUE	0	0.511135755642309	1		825	794	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0048572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	432	622	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.511135755642309	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.511135755642309	3		622	1026	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0048572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	354	597	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.511135755642309	3	FACETS	0.929	0.883	0.976	0.929	0.883	0.976	CLONAL	2	TRUE	1	0.511135755642309	3		597	936	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121508	193121508	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0048572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	204	241	0	ENST00000367435.3:c.908-2A>G		p.X303_splice	ENST00000367435	NM_024529.4	303			0.506547547972057	4	FACETS	0.953	0.896	1	0.953	0.896	1	CLONAL	3	TRUE	1	0.511135755642309	4		241	422	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246091253	246091253	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	140	432	0	ENST00000388985.4:c.682G>C	p.Asp228His	p.D228H	ENST00000388985		228	Gac/Cac	7/12	0.506547547972057	4	FACETS	0.936	0.853	1	0.312	0.284	0.342	CLONAL	1	TRUE	1	0.511135755642309	4		432	884	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315507	30315507	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	107	370	0	ENST00000322652.5:c.1192C>G	p.Gln398Glu	p.Q398E	ENST00000322652	NM_015355.2	398	Caa/Gaa	10/16	1	2	FACETS	0.788	0.71	0.871	0.788	0.71	0.871	SUBCLONAL	1	TRUE	1	0.511135755642309	2		370	531	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226345	2226345	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	226	991	0	ENST00000398665.3:c.3826del	p.Arg1276GlyfsTer51	p.R1276Gfs*51	ENST00000398665	NM_032482.2	1275	ttC/tt	27/28	0.511135755642309	1	FACETS	0.871	0.814	0.929	0.871	0.814	0.929	CLONAL	1	TRUE	0	0.511135755642309	1		991	756	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033433	48033433	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	115	398	0	ENST00000234420.5:c.3737del	p.Ser1246Ter	p.S1246*	ENST00000234420	NM_000179.2	1246	tCa/ta	8/10	1	2	FACETS	0.798	0.721	0.878	0.798	0.721	0.878	SUBCLONAL	1	TRUE	1	0.511135755642309	2		398	564	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440864	52440873	+	frameshift_variant	Frame_Shift_Del	DEL	TACGCTCCAT	TACGCTCCAT	-	novel	NA	P-0048572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	199	708	0	ENST00000460680.1:c.631_640del	p.Met211SerfsTer17	p.M211Sfs*17	ENST00000460680	NM_004656.3	211	ATGGAGCGTAtc/tc	8/17	0.488880898410984	1	FACETS	0.745	0.692	0.8	0.745	0.692	0.8	SUBCLONAL	1	TRUE	0	0.511135755642309	1		708	778	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217310	123217311	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0048572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	146	276	0	ENST00000218089.9:c.2968dup	p.Glu990GlyfsTer12	p.E990Gfs*12	ENST00000218089	NM_001042749.1	988	-/G	29/35	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.511135755642309	1		276	331	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048601-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	35	365	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.634131857905018	2		365	110	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0048601-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	118	719	1	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.634131857905018	2		720	347	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519958	NA	P-0048601-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	220	832	0	ENST00000481739.1:c.1280C>A	p.Ser427Tyr	p.S427Y	ENST00000481739	NM_002957.4	427	tCc/tAc	10/10	0.583854732458924	2	FACETS	0.95	0.902	0.998	0.95	0.902	0.998	CLONAL	2	TRUE	0	0.634131857905018	2		832	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201059	NA	P-0048601-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	207	801	0	ENST00000269305.4:c.856G>T	p.Glu286Ter	p.E286*	ENST00000269305	NM_001126112.2	286	Gaa/Taa	8/11	0.610040091525866	2	FACETS	0.938	0.888	0.987	0.938	0.888	0.987	CLONAL	2	TRUE	0	0.634131857905018	2		801	348	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519710	176519710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150737523	NA	P-0048601-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	132	901	1	ENST00000292408.4:c.982G>A	p.Ala328Thr	p.A328T	ENST00000292408	NM_213647.1	328	Gca/Aca	8/18	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.634131857905018	2		902	392	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944829	31944829	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048601-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	37	891	2	ENST00000340398.3:c.272C>T	p.Ala91Val	p.A91V	ENST00000340398	NM_001013699.2	91	gCg/gTg	1/1	0.146832399347716	3	FACETS	0.347	0.286	0.415	0.116	0.095	0.139	INDETERMINATE	1	TRUE	0	0.634131857905018	3		893	443	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568636	41568636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048601-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	29	330	0	ENST00000263253.7:c.4586G>A	p.Arg1529Gln	p.R1529Q	ENST00000263253	NM_001429.3	1529	cGa/cAa	28/31	1	2	FACETS	0.448	0.362	0.545	0.448	0.362	0.545	SUBCLONAL	1	TRUE	1	0.634131857905018	2		330	204	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118355640	118355640	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048601-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	53	613	0	ENST00000534358.1:c.4282A>G	p.Ile1428Val	p.I1428V	ENST00000534358	NM_005933.3	1428	Ata/Gta	10/36	0.398337325956849	1	FACETS	0.436	0.375	0.501	0.436	0.375	0.501	SUBCLONAL	1	TRUE	0	0.634131857905018	1		613	262	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938390	44938390	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0048601-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	59	169	0	ENST00000377967.4:c.2939-1G>C		p.X980_splice	ENST00000377967	NM_021140.2	980			1	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.634131857905018	1		169	103	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115962	8115963	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0048601-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	139	393	0	ENST00000346208.3:c.1309_1310dup	p.Ser437ArgfsTer39	p.S437Rfs*39	ENST00000346208		436	-/AG	6/6	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.634131857905018	2		393	341	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105238761	105238761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048601-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	125	773	0	ENST00000349310.3:c.1201G>A	p.Glu401Lys	p.E401K	ENST00000349310	NM_001014432.1	401	Gag/Aag	13/15	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.634131857905018	2		773	376	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347409	91347409	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048601-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	41	292	0	ENST00000355112.3:c.3571G>A	p.Glu1191Lys	p.E1191K	ENST00000355112	NM_000057.2	1191	Gaa/Aaa	19/22	0.610040091525866	2	FACETS	0.829	0.702	0.964	0.414	0.351	0.482	CLONAL	1	TRUE	0	0.634131857905018	2		292	156	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143033780	143033780	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048601-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	29	342	0	ENST00000262992.4:c.2191C>G	p.Leu731Val	p.L731V	ENST00000262992	NM_001101669.1	731	Cta/Gta	20/24	0.398337325956849	1	FACETS	0.443	0.36	0.534	0.443	0.36	0.534	SUBCLONAL	1	TRUE	0	0.634131857905018	1		342	141	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524534	176524534	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs192201146	NA	P-0048601-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	117	965	0	ENST00000292408.4:c.2266G>A	p.Asp756Asn	p.D756N	ENST00000292408	NM_213647.1	756	Gac/Aac	18/18	1	2	FACETS	0.946	0.861	1	0.946	0.861	1	CLONAL	1	TRUE	1	0.634131857905018	2		965	390	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250592	26250599	+	frameshift_variant	Frame_Shift_Del	DEL	GTCTTGAA	GTCTTGAA	-	novel	NA	P-0048601-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	163	662	0	ENST00000446824.2:c.235_242del	p.Phe79ArgfsTer25	p.F79Rfs*25	ENST00000446824	NM_021018.2	79	TTCAAGACc/c	1/1	0.634131857905018	3	FACETS	0.915	0.852	0.979	0.915	0.852	0.979	CLONAL	2	TRUE	1	0.634131857905018	3		662	370	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56882326	56882326	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048601-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	294	608	0	ENST00000519728.1:c.1024C>A	p.Pro342Thr	p.P342T	ENST00000519728	NM_002350.3	342	Cca/Aca	10/13	0.417702521594221	4	FACETS	1	0.982	1	0.788	0.753	0.821	CLONAL	3	TRUE	0	0.634131857905018	4		608	481	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900786	3900786	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048601-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	52	710	0	ENST00000262367.5:c.310C>G	p.Gln104Glu	p.Q104E	ENST00000262367	NM_004380.2	104	Caa/Gaa	2/31	1	2	FACETS	0.505	0.432	0.584	0.505	0.432	0.584	SUBCLONAL	1	TRUE	1	0.634131857905018	2		710	325	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048601-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	41	365	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.918	0.768	1	0.918	0.768	1	CLONAL	1	TRUE	1	0.283663235026901	2		365	315	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0048601-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	115	719	1	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.982	0.884	1	0.982	0.884	1	CLONAL	1	TRUE	1	0.283663235026901	2		720	826	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519958	NA	P-0048601-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	256	832	0	ENST00000481739.1:c.1280C>A	p.Ser427Tyr	p.S427Y	ENST00000481739	NM_002957.4	427	tCc/tAc	10/10	0.237272951073486	2	FACETS	0.812	0.759	0.865	0.812	0.759	0.865	CLONAL	2	TRUE	0	0.283663235026901	2		832	1112	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519710	176519710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150737523	NA	P-0048601-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	59	901	1	ENST00000292408.4:c.982G>A	p.Ala328Thr	p.A328T	ENST00000292408	NM_213647.1	328	Gca/Aca	8/18	1	2	FACETS	0.414	0.355	0.479	0.414	0.355	0.479	SUBCLONAL	1	TRUE	1	0.283663235026901	2		902	1005	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938390	44938390	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0048601-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	62	169	0	ENST00000377967.4:c.2939-1G>C		p.X980_splice	ENST00000377967	NM_021140.2	980			1	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.283663235026901	1		169	280	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115962	8115963	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0048601-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	103	393	0	ENST00000346208.3:c.1309_1310dup	p.Ser437ArgfsTer39	p.S437Rfs*39	ENST00000346208		436	-/AG	6/6	0.165523559641364	1	FACETS	0.932	0.835	1	0.932	0.835	1	INDETERMINATE	1	TRUE	0	0.283663235026901	1		393	669	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250592	26250599	+	frameshift_variant	Frame_Shift_Del	DEL	GTCTTGAA	GTCTTGAA	-	novel	NA	P-0048601-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	83	662	0	ENST00000446824.2:c.235_242del	p.Phe79ArgfsTer25	p.F79Rfs*25	ENST00000446824	NM_021018.2	79	TTCAAGACc/c	1/1	0.28176697892582	4	FACETS	0.739	0.65	0.834			1	SUBCLONAL	1	TRUE	NA	0.283663235026901	4		662	1017	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0048601-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	199	760	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.283663235026901	2		760	1013	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998975	100998975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048601-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	123	592	0	ENST00000325455.5:c.827C>T	p.Ser276Leu	p.S276L	ENST00000325455	NM_001202474.3	276	tCa/tTa	1/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.283663235026901	2		592	669	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136811	2136811	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs45517380	NA	P-0048601-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	140	904	1	ENST00000219476.3:c.4928A>T	p.Asn1643Ile	p.N1643I	ENST00000219476	NM_000548.3	1643	aAc/aTc	38/42	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.283663235026901	2		905	978	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39595484	39595484	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048601-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	53	385	0	ENST00000262039.4:c.1370C>G	p.Pro457Arg	p.P457R	ENST00000262039	NM_002647.2	457	cCt/cGt	12/25	1	2	FACETS	0.702	0.599	0.816	0.702	0.599	0.816	SUBCLONAL	1	TRUE	1	0.283663235026901	2		385	532	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576880	212576880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049154-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	31	369	0	ENST00000342788.4:c.1019G>A	p.Gly340Glu	p.G340E	ENST00000342788	NM_005235.2	340	gGa/gAa	9/28	1	2	FACETS	0.165	0.133	0.201	0.165	0.133	0.201	SUBCLONAL	1	TRUE	1	0.866564414782104	2		369	434	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104268978	104268978	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049154-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	380	804	0	ENST00000369902.3:c.235A>C	p.Ser79Arg	p.S79R	ENST00000369902	NM_016169.3	79	Agc/Cgc	2/12	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.866564414782104	2		804	871	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218417	69218417	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049154-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	176	425	0	ENST00000462284.1:c.509C>A	p.Ala170Glu	p.A170E	ENST00000462284	NM_002392.5	170	gCa/gAa	7/11	1	2	FACETS	0.808	0.75	0.866	0.808	0.75	0.866	CLONAL	1	TRUE	1	0.866564414782104	2		425	503	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0049440-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	80	554	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.212794751217229	5	FACETS	1	0.932	1	0.362	0.318	0.41	CLONAL	1	TRUE	2	0.277655181892428	5		554	751	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049440-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	105	365	0				ENST00000310581	NM_198253.2	-/1132			0.277655181892428	4	FACETS	0.833	0.748	0.922	0.833	0.748	0.922	CLONAL	2	TRUE	2	0.277655181892428	4		365	580	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0049440-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	311	1161	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	1	2	FACETS	1	0.958	1	1	0.996	1	CLONAL	2	TRUE	1	0.277655181892428	2		1161	1100	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163749	152163749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1207112399	NA	P-0049440-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	90	448	0	ENST00000206249.3:c.470G>A	p.Arg157Gln	p.R157Q	ENST00000206249	NM_000125.3	157	cGa/cAa	2/8	0.277655181892428	3	FACETS	1	0.977	1	0.7	0.623	0.782	CLONAL	1	TRUE	1	0.277655181892428	3		448	527	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217918	2217918	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0049440-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	139	926	2	ENST00000398665.3:c.2691+1G>A		p.X897_splice	ENST00000398665	NM_032482.2	897			0.277655181892428	3	FACETS	1	0.95	1	0.533	0.484	0.585	CLONAL	1	TRUE	1	0.277655181892428	3		928	1069	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55334132	55334132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049440-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	97	621	0	ENST00000284073.2:c.29C>T	p.Ser10Leu	p.S10L	ENST00000284073	NM_138962.2	10	tCg/tTg	1/14	0.228987063887716	4	FACETS	1	0.968	1	0.616	0.549	0.687	CLONAL	1	TRUE	2	0.277655181892428	4		621	725	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924280	11924280	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1049103069	NA	P-0049440-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	13	205	0	ENST00000353533.5:c.77C>A	p.Ser26Tyr	p.S26Y	ENST00000353533	NM_003010.3	26	tCc/tAc	1/11	1	2	FACETS	0.506	0.362	0.682	0.506	0.362	0.682	SUBCLONAL	1	TRUE	1	0.277655181892428	2		205	185	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426379	49426379	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049440-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1246	160	1195	0	ENST00000301067.7:c.12109del	p.Ala4037ProfsTer13	p.A4037Pfs*13	ENST00000301067	NM_003482.3	4037	Gcc/cc	39/54	0.228987063887716	4	FACETS	1	0.946	1	0.524	0.478	0.571	CLONAL	1	TRUE	2	0.277655181892428	4		1195	1406	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942491	17942491	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049440-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	120	974	0	ENST00000458235.1:c.2797A>C	p.Ile933Leu	p.I933L	ENST00000458235	NM_000215.3	933	Atc/Ctc	20/24	0.277655181892428	3	FACETS	0.889	0.801	0.983	0.445	0.4	0.492	CLONAL	1	TRUE	1	0.277655181892428	3		974	1107	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760253	133760253	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049440-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	101	692	0	ENST00000318560.5:c.2576C>A	p.Ser859Ter	p.S859*	ENST00000318560	NM_005157.4	859	tCa/tAa	11/11	0.243448661946723	3	FACETS	1	0.956	1	0.377	0.337	0.419	CLONAL	1	TRUE	0	0.277655181892428	3		692	733	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0049440-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	157	554	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.14721268210062	5	FACETS	1	0.975	1	0.388	0.355	0.422	INDETERMINATE	1	TRUE	2	0.555566482839577	5		554	890	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049440-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	127	365	0				ENST00000310581	NM_198253.2	-/1132			0.139749748124418	5	FACETS	0.905	0.826	0.988	0.603	0.55	0.659	INDETERMINATE	2	TRUE	2	0.555566482839577	5		365	463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0049440-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	470	1161	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.538173283256139	2	FACETS	0.925	0.889	0.96	0.925	0.889	0.96	CLONAL	2	TRUE	0	0.555566482839577	2		1161	915	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163749	152163749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1207112399	NA	P-0049440-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	158	448	0	ENST00000206249.3:c.470G>A	p.Arg157Gln	p.R157Q	ENST00000206249	NM_000125.3	157	cGa/cAa	2/8	0.386320202071603	1	FACETS	0.87	0.804	0.938	0.87	0.804	0.938	CLONAL	1	TRUE	0	0.555566482839577	1		448	472	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217918	2217918	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0049440-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	145	926	2	ENST00000398665.3:c.2691+1G>A		p.X897_splice	ENST00000398665	NM_032482.2	897			0.207130662417845	2	FACETS	0.549	0.501	0.601	0.275	0.25	0.301	INDETERMINATE	1	TRUE	0	0.555566482839577	2		928	950	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55334132	55334132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049440-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	152	621	0	ENST00000284073.2:c.29C>T	p.Ser10Leu	p.S10L	ENST00000284073	NM_138962.2	10	tCg/tTg	1/14	0.206261812365176	3	FACETS	0.985	0.903	1	0.328	0.301	0.357	INDETERMINATE	1	TRUE	0	0.555566482839577	3		621	710	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426379	49426379	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049440-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	241	1195	0	ENST00000301067.7:c.12109del	p.Ala4037ProfsTer13	p.A4037Pfs*13	ENST00000301067	NM_003482.3	4037	Gcc/cc	39/54	0.258297599857662	3	FACETS	0.833	0.776	0.892	0.278	0.258	0.298	INDETERMINATE	1	TRUE	0	0.555566482839577	3		1195	1331	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942491	17942491	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049440-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	157	974	0	ENST00000458235.1:c.2797A>C	p.Ile933Leu	p.I933L	ENST00000458235	NM_000215.3	933	Atc/Ctc	20/24	0.207130662417845	2	FACETS	0.584	0.535	0.636	0.292	0.267	0.318	INDETERMINATE	1	TRUE	0	0.555566482839577	2		974	967	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760253	133760253	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049440-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	107	692	0	ENST00000318560.5:c.2576C>A	p.Ser859Ter	p.S859*	ENST00000318560	NM_005157.4	859	tCa/tAa	11/11	0.555566482839577	1	FACETS	0.474	0.426	0.524	0.474	0.426	0.524	SUBCLONAL	1	TRUE	0	0.555566482839577	1		692	587	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133887	41133887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755827604	NA	P-0049440-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	37	428	0	ENST00000379561.5:c.1741G>A	p.Val581Met	p.V581M	ENST00000379561	NM_002015.3	581	Gtg/Atg	2/3	0.477869092996067	3	FACETS	0.372	0.306	0.445	0.124	0.102	0.149	SUBCLONAL	1	TRUE	0	0.555566482839577	3		428	458	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69458693	69458693	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049440-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	66	657	0	ENST00000227507.2:c.508G>C	p.Glu170Gln	p.E170Q	ENST00000227507	NM_053056.2	170	Gag/Cag	3/5	0.17964055125387	2	FACETS	0.305	0.264	0.349	0.152	0.132	0.175	INDETERMINATE	1	TRUE	0	0.555566482839577	2		657	780	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868315	56868315	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049440-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	43	328	0	ENST00000308159.5:c.1698T>G	p.Phe566Leu	p.F566L	ENST00000308159	NM_014669.4	566	ttT/ttG	15/22	0.274505377843684	3	FACETS	0.347	0.29	0.411	0.174	0.145	0.206	INDETERMINATE	1	TRUE	1	0.555566482839577	3		328	570	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223153	1223153	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049440-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	76	775	0	ENST00000326873.7:c.1090C>G	p.Gln364Glu	p.Q364E	ENST00000326873	NM_000455.4	364	Cag/Gag	8/10	0.207130662417845	2	FACETS	0.311	0.272	0.353	0.155	0.136	0.177	INDETERMINATE	1	TRUE	0	0.555566482839577	2		775	881	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921786	111921786	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049440-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	56	370	0	ENST00000393256.3:c.575G>T	p.Arg192Leu	p.R192L	ENST00000393256	NM_006538.4	192	cGc/cTc	4/4	0.116924398143983	4	FACETS	0.501	0.429	0.58			1	INDETERMINATE	1	TRUE	NA	0.555566482839577	4		370	626	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0049792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	234	858	1	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.313703342801883	1	FACETS	0.874	0.818	0.93	1	0.994	1	CLONAL	2	TRUE	0	0.313703342801883	1		859	720	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	420	865	2	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.313703342801883	2		867	1149	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928083	178928083	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	110	601	0	ENST00000263967.3:c.1361A>G	p.Asp454Gly	p.D454G	ENST00000263967	NM_006218.2	454	gAt/gGt	8/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.313703342801883	2		601	469	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806564	1806564	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	157	1001	0	ENST00000260795.2:c.1280C>A	p.Ser427Tyr	p.S427Y	ENST00000260795		427	tCc/tAc	9/17	0.313703342801883	3	FACETS	0.906	0.828	0.988			1	CLONAL	1	TRUE	NA	0.313703342801883	3		1001	1278	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896585	78896585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	85	661	1	ENST00000306801.3:c.2582C>T	p.Pro861Leu	p.P861L	ENST00000306801	NM_020761.2	861	cCc/cTc	22/34	1	2	FACETS	0.451	0.398	0.508	0.451	0.398	0.508	SUBCLONAL	1	TRUE	1	0.423807341095174	2		662	889	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248734	212248734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	46	338	0	ENST00000342788.4:c.3533G>A	p.Gly1178Glu	p.G1178E	ENST00000342788	NM_005235.2	1178	gGa/gAa	28/28	0.296756743362526	2	FACETS	0.456	0.384	0.535	0.228	0.192	0.268	SUBCLONAL	1	TRUE	0	0.423807341095174	2		338	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0050357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	64	488	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.423807341095174	2	FACETS	0.425	0.367	0.487	0.212	0.183	0.244	SUBCLONAL	1	TRUE	0	0.423807341095174	2		488	711	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871298	35871298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375672744	NA	P-0050357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	44	286	1	ENST00000303115.3:c.520G>A	p.Asp174Asn	p.D174N	ENST00000303115	NM_002185.3	174	Gat/Aat	4/8	0.293690687435284	3	FACETS	0.529	0.443	0.623	0.176	0.147	0.208	SUBCLONAL	1	TRUE	0	0.423807341095174	3		287	476	SUCCESS
ATR	545	MSKCC	GRCh37	3	142183937	142183937	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0050357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	38	306	0	ENST00000350721.4:c.7041+2T>C		p.X2347_splice	ENST00000350721	NM_001184.3	2347			0.296756743362526	2	FACETS	0.453	0.375	0.54	0.226	0.187	0.27	SUBCLONAL	1	TRUE	0	0.423807341095174	2		306	396	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388710	31388710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	59	526	0	ENST00000328111.2:c.1975C>T	p.Pro659Ser	p.P659S	ENST00000328111	NM_006892.3	659	Cca/Tca	18/23	0.293690687435284	3	FACETS	0.477	0.409	0.55	0.159	0.136	0.184	SUBCLONAL	1	TRUE	0	0.423807341095174	3		526	708	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376293	15376293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753686671	NA	P-0050357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	191	604	0	ENST00000263377.2:c.721G>A	p.Val241Met	p.V241M	ENST00000263377	NM_058243.2	241	Gtg/Atg	5/20	0.423807341095174	2	FACETS	0.992	0.917	1	0.496	0.458	0.535	CLONAL	1	TRUE	0	0.423807341095174	2		604	909	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9770525	9770526	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0050357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	59	594	1	ENST00000377346.4:c.12_13delinsAA	p.Val5Met	p.V5M	ENST00000377346	NM_005026.3	4	ggGGtg/ggAAtg	3/24	1	2	FACETS	0.345	0.296	0.399	0.345	0.296	0.399	SUBCLONAL	1	TRUE	1	0.423807341095174	2		595	807	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125499186	125499186	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1048249612	NA	P-0050357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	60	465	0	ENST00000428830.2:c.349G>A	p.Gly117Arg	p.G117R	ENST00000428830	NM_001114121.2	117	Ggg/Agg	4/14	NA	2	FACETS	0.473	0.408	0.545			1	INDETERMINATE	1	TRUE	NA	0.423807341095174	2		465	598	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434532	49434532	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	76	628	2	ENST00000301067.7:c.7021C>T	p.Gln2341Ter	p.Q2341*	ENST00000301067	NM_003482.3	2341	Cag/Tag	31/54	0.423807341095174	2	FACETS	0.39	0.341	0.443	0.195	0.17	0.222	SUBCLONAL	1	TRUE	0	0.423807341095174	2		630	920	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724750	43724750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	83	458	0	ENST00000382044.4:c.3317C>T	p.Ser1106Phe	p.S1106F	ENST00000382044	NM_001141980.1	1106	tCt/tTt	17/28	0.296756743362526	2	FACETS	0.435	0.383	0.491	0.218	0.191	0.246	SUBCLONAL	1	TRUE	0	0.423807341095174	2		458	900	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831771	72831772	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0050357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	58	568	0	ENST00000268489.5:c.4809_4810delinsAA	p.Ala1604Thr	p.A1604T	ENST00000268489	NM_006885.3	1603	gtGGcc/gtAAcc	9/10	0.423807341095174	2	FACETS	0.311	0.266	0.36	0.156	0.133	0.18	SUBCLONAL	1	TRUE	0	0.423807341095174	2		568	880	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990300	81990300	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs746134531	NA	P-0050357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	84	350	0	ENST00000359376.3:c.3571G>A	p.Glu1191Lys	p.E1191K	ENST00000359376	NM_002661.3	1191	Gag/Aag	32/33	0.423807341095174	2	FACETS	0.731	0.647	0.821	0.366	0.323	0.411	SUBCLONAL	1	TRUE	0	0.423807341095174	2		350	542	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184564	7184564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766992696	NA	P-0050357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	48	433	1	ENST00000302850.5:c.737C>T	p.Pro246Leu	p.P246L	ENST00000302850	NM_000208.2	246	cCc/cTc	3/22	0.423807341095174	2	FACETS	0.358	0.302	0.42	0.179	0.151	0.21	SUBCLONAL	1	TRUE	0	0.423807341095174	2		434	633	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602547	10602547	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1377763147	NA	P-0050357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	63	613	1	ENST00000171111.5:c.1031C>T	p.Ala344Val	p.A344V	ENST00000171111	NM_203500.1	344	gCt/gTt	3/6	0.423807341095174	2	FACETS	0.362	0.312	0.416	0.181	0.156	0.208	SUBCLONAL	1	TRUE	0	0.423807341095174	2		614	821	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278059	15278060	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0050357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	45	538	1	ENST00000263388.2:c.5362_5362+1delinsAA		p.X1788_splice	ENST00000263388	NM_000435.2	1788		29/33	0.423807341095174	2	FACETS	0.287	0.24	0.339	0.143	0.12	0.17	SUBCLONAL	1	TRUE	0	0.423807341095174	2		539	740	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912056	50912056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	77	732	1	ENST00000440232.2:c.1790C>T	p.Pro597Leu	p.P597L	ENST00000440232	NM_002691.3	597	cCc/cTc	15/27	0.423807341095174	2	FACETS	0.372	0.325	0.422	0.186	0.162	0.211	SUBCLONAL	1	TRUE	0	0.423807341095174	2		733	977	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018108	48018109	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0050357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	68	561	1	ENST00000234420.5:c.303_304delinsAA	p.Gly102Ser	p.G102S	ENST00000234420	NM_000179.2	101	gaGGgt/gaAAgt	2/10	1	2	FACETS	0.344	0.298	0.394	0.344	0.298	0.394	SUBCLONAL	1	TRUE	1	0.423807341095174	2		562	932	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390913	89390913	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1315586801	NA	P-0050357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	32	308	0	ENST00000336596.2:c.979T>A	p.Ser327Thr	p.S327T	ENST00000336596	NM_005233.5	327	Tct/Act	5/17	1	2	FACETS	0.346	0.281	0.421	0.346	0.281	0.421	SUBCLONAL	1	TRUE	1	0.423807341095174	2		308	436	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953904	55953904	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754095453	NA	P-0050357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	44	370	0	ENST00000263923.4:c.3532C>T	p.Leu1178Phe	p.L1178F	ENST00000263923	NM_002253.2	1178	Ctt/Ttt	27/30	0.296756743362526	2	FACETS	0.411	0.345	0.485	0.206	0.172	0.243	SUBCLONAL	1	TRUE	0	0.423807341095174	2		370	505	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155902	106155902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	53	331	0	ENST00000380013.4:c.803C>T	p.Ser268Leu	p.S268L	ENST00000380013	NM_001127208.2	268	tCg/tTg	3/11	0.296756743362526	2	FACETS	0.476	0.406	0.553	0.238	0.203	0.277	SUBCLONAL	1	TRUE	0	0.423807341095174	2		331	525	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068065	94068065	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	36	303	0	ENST00000369303.4:c.897C>A	p.His299Gln	p.H299Q	ENST00000369303	NM_004440.3	299	caC/caA	4/17	0.203682524243369	3	FACETS	0.428	0.351	0.514	0.143	0.117	0.172	INDETERMINATE	1	TRUE	0	0.423807341095174	3		303	481	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970900	21970900	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0050357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	62	602	0	ENST00000304494.5:c.457+1G>C		p.X153_splice	ENST00000304494	NM_000077.4	153			1	2	FACETS	0.356	0.307	0.41	0.356	0.307	0.41	SUBCLONAL	1	TRUE	1	0.423807341095174	2		602	821	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93657841	93657841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050357-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	59	440	0	ENST00000375746.1:c.1867G>A	p.Glu623Lys	p.E623K	ENST00000375746	NM_001174167.1	623	Gaa/Aaa	14/14	0.362136192984876	2	FACETS	0.416	0.357	0.48	0.208	0.178	0.24	SUBCLONAL	1	TRUE	0	0.423807341095174	2		440	669	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0050409-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	398	621	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.276576924055967	5	FACETS	1	0.962	1	1	0.962	1	CLONAL	4	TRUE	1	0.276576924055967	5		622	1009	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106592	27106592	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050409-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	114	775	1	ENST00000324856.7:c.6203C>T	p.Ser2068Leu	p.S2068L	ENST00000324856	NM_006015.4	2068	tCg/tTg	20/20	0.222111854971813	2	FACETS	0.924	0.831	1	0.462	0.415	0.512	CLONAL	1	TRUE	0	0.276576924055967	2		776	892	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40860095	40860095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050409-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	204	453	0	ENST00000428826.2:c.1541C>T	p.Ser514Phe	p.S514F	ENST00000428826		514	tCt/tTt	15/21	0.276622764726344	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.276576924055967	3		453	720	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243523	41243523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050409-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	105	662	1	ENST00000357654.3:c.4025C>T	p.Ser1342Leu	p.S1342L	ENST00000357654	NM_007294.3	1342	tCa/tTa	10/23	0.276622764726344	3	FACETS	0.865	0.774	0.963	0.433	0.387	0.482	CLONAL	1	TRUE	1	0.276576924055967	3		663	999	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0050409-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	153	743	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.128167042944728	4	FACETS	1	0.987	1	0.727	0.664	0.792	INDETERMINATE	1	TRUE	2	0.276576924055967	4		743	972	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231788	36231788	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050409-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	208	773	0	ENST00000300305.3:c.596G>A	p.Gly199Glu	p.G199E	ENST00000300305		199	gGg/gAg	5/8	0.213852696326122	3	FACETS	0.764	0.709	0.822	0.764	0.709	0.822	SUBCLONAL	2	TRUE	1	0.276576924055967	3		773	1120	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545855	41545855	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867077693	NA	P-0050409-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	60	746	0	ENST00000263253.7:c.2470C>T	p.Gln824Ter	p.Q824*	ENST00000263253	NM_001429.3	824	Caa/Taa	14/31	1	2	FACETS	0.491	0.422	0.567	0.491	0.422	0.567	SUBCLONAL	1	TRUE	1	0.276576924055967	2		746	884	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547912	41547912	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050409-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	47	621	0	ENST00000263253.7:c.2893C>G	p.Gln965Glu	p.Q965E	ENST00000263253	NM_001429.3	965	Cag/Gag	15/31	1	2	FACETS	0.534	0.449	0.627	0.534	0.449	0.627	SUBCLONAL	1	TRUE	1	0.276576924055967	2		621	637	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244097	153244097	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050409-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	149	579	0	ENST00000281708.4:c.2060G>C	p.Gly687Ala	p.G687A	ENST00000281708	NM_033632.3	687	gGg/gCg	12/12	0.213852696326122	3	FACETS	1	0.983	1	0.652	0.596	0.712	CLONAL	1	TRUE	1	0.276576924055967	3		579	940	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166372	7166372	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050648-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	206	496	0	ENST00000302850.5:c.1654G>C	p.Gly552Arg	p.G552R	ENST00000302850	NM_000208.2	552	Ggt/Cgt	8/22	1	2	FACETS	0.799	0.744	0.855	0.799	0.744	0.855	SUBCLONAL	1	FALSE	1	0.757363041034227	2		496	681	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007622	45007640	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TACTCCAAAGATTCAGGTT	TACTCCAAAGATTCAGGTT	-	novel	NA	P-0051763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	10	193	0	ENST00000558401.1:c.74_92del	p.Pro25HisfsTer13	p.P25Hfs*13	ENST00000558401	NM_004048.2	23	cgTACTCCAAAGATTCAGGTT/cg	2/4	0.624852193548187	2	FACETS	0.223	0.151	0.312	0.112	0.075	0.156	SUBCLONAL	1	TRUE	0	0.645198275348142	2		193	139	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579417	7579417	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	694	900	0	ENST00000269305.4:c.270del	p.Trp91GlyfsTer32	p.W91Gfs*32	ENST00000269305	NM_001126112.2	90	tcC/tc	4/11	0.552036751119024	6	FACETS	0.979	0.96	0.997	0.979	0.96	0.997	CLONAL	6	TRUE	0	0.645198275348142	6		900	839	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178277	56178277	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	108	300	0	ENST00000399503.3:c.3250G>C	p.Asp1084His	p.D1084H	ENST00000399503	NM_005921.1	1084	Gat/Cat	14/20	0.601043059734618	2	FACETS	0.863	0.797	0.928	0.863	0.797	0.928	CLONAL	2	TRUE	0	0.645198275348142	2		300	194	SUCCESS
APC	324	MSKCC	GRCh37	5	112111325	112111325	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs397514031	NA	P-0051763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	56	142	0	ENST00000257430.4:c.423-1G>C		p.X141_splice	ENST00000257430	NM_000038.5	141			0.601043059734618	2	FACETS	0.904	0.811	0.995	0.904	0.811	0.995	CLONAL	2	TRUE	0	0.645198275348142	2		142	96	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929133	44929133	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052021-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	130	354	0	ENST00000377967.4:c.2233G>T	p.Glu745Ter	p.E745*	ENST00000377967	NM_021140.2	745	Gag/Tag	17/29	0.139243214053204	2	FACETS	1	0.984	1			1	INDETERMINATE	1	FALSE	NA	0.281472167317053	2		354	664	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0052021-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	47	227	1				ENST00000310581	NM_198253.2	-/1132			0.281472167317053	0	FACETS	0.525	0.443	0.615			1	SUBCLONAL	1	FALSE	0	0.281472167317053	0		228	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882019	NA	P-0052021-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	201	993	0	ENST00000269305.4:c.455del	p.Pro152ArgfsTer18	p.P152Rfs*18	ENST00000269305	NM_001126112.2	152	cCg/cg	5/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.281472167317053	2		993	1343	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519850	29519850	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052021-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	115	777	1	ENST00000389048.3:c.1721G>T	p.Gly574Val	p.G574V	ENST00000389048	NM_004304.4	574	gGg/gTg	9/29	1	2	FACETS	0.821	0.738	0.909	0.821	0.738	0.909	CLONAL	1	FALSE	1	0.281472167317053	2		778	995	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950806	32950806	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0052021-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	80	294	0	ENST00000380152.3:c.8633-1G>C		p.X2878_splice	ENST00000380152		2878			0.142736286959027	3	FACETS	1	0.935	1	0.547	0.482	0.616	INDETERMINATE	1	FALSE	1	0.281472167317053	3		294	593	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366994	40366994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052021-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1499	100	931	1	ENST00000397332.2:c.203C>T	p.Ser68Leu	p.S68L	ENST00000397332	NM_001033082.2	68	tCg/tTg	2/3	1	2	FACETS	0.444	0.395	0.497	0.444	0.395	0.497	SUBCLONAL	1	FALSE	1	0.281472167317053	2		932	1599	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278106	41278106	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052021-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	43	550	0	ENST00000349496.5:c.1982G>T	p.Arg661Leu	p.R661L	ENST00000349496	NM_001904.3	661	cGa/cTa	13/15	0.0871891233271009	3	FACETS	0.427	0.356	0.506	0.214	0.178	0.253	INDETERMINATE	1	FALSE	1	0.281472167317053	3		550	816	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295239	1295239	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0052021-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	37	279	0				ENST00000310581	NM_198253.2	-/1132			0.281472167317053	0	FACETS	0.484	0.4	0.579			1	SUBCLONAL	1	FALSE	0	0.281472167317053	0		279	390	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115712	8115752	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGA	CCCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGA	-	novel	NA	P-0052057-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	107	355	0	ENST00000346208.3:c.1058_1098del	p.Pro353GlnfsTer4	p.P353Qfs*4	ENST00000346208		353	cCCCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGA/c	6/6	0.339115390828033	3	FACETS	0.898	0.821	0.975	0.898	0.821	0.975	INDETERMINATE	2	TRUE	1	0.639533175367777	3		355	246	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100664	67100664	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052057-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	227	629	2	ENST00000412916.2:c.362G>T	p.Gly121Val	p.G121V	ENST00000412916		121	gGt/gTt	4/6	0.624707546873369	2	FACETS	0.798	0.754	0.842	0.798	0.754	0.842	SUBCLONAL	2	TRUE	0	0.639533175367777	2		631	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0052152-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	158	466	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		466	724	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0052448-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	144	397	7	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.452934576246251	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.452934576246251	1		404	446	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0052448-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	171	564	16	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.431164717839716	1	FACETS	0.836	0.771	0.903	0.836	0.771	0.903	CLONAL	1	TRUE	0	0.452934576246251	1		580	699	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057937	27057937	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052448-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	164	577	19	ENST00000324856.7:c.1650del	p.Tyr551ThrfsTer68	p.Y551Tfs*68	ENST00000324856	NM_006015.4	549	Ccc/cc	3/20	1	2	FACETS	0.835	0.767	0.906	0.835	0.767	0.906	CLONAL	1	TRUE	1	0.452934576246251	2		596	867	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0052448-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	124	615	8	ENST00000346208.3:c.1221_1222del	p.Pro408LeufsTer98	p.P408Lfs*98	ENST00000346208		407	tCG/t	6/6	1	2	FACETS	0.713	0.645	0.784	0.713	0.645	0.784	SUBCLONAL	1	TRUE	1	0.452934576246251	2		623	768	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846108	151846108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052448-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	128	430	7	ENST00000262189.6:c.12904C>T	p.Pro4302Ser	p.P4302S	ENST00000262189	NM_170606.2	4302	Cct/Tct	52/59	0.16524816302547	3	FACETS	1	0.981	1	0.65	0.592	0.711	INDETERMINATE	1	TRUE	1	0.452934576246251	3		437	533	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0052448-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	245	397	7	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.638913345595694	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.638913345595694	1		404	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0052448-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	327	564	16	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.617709803665332	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.638913345595694	1		580	606	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057937	27057937	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052448-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	283	577	19	ENST00000324856.7:c.1650del	p.Tyr551ThrfsTer68	p.Y551Tfs*68	ENST00000324856	NM_006015.4	549	Ccc/cc	3/20	1	2	FACETS	0.919	0.865	0.974	0.919	0.865	0.974	CLONAL	1	TRUE	1	0.638913345595694	2		596	964	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0052448-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	239	615	8	ENST00000346208.3:c.1221_1222del	p.Pro408LeufsTer98	p.P408Lfs*98	ENST00000346208		407	tCG/t	6/6	0.427311833795158	1	FACETS	0.614	0.575	0.655	0.614	0.575	0.655	SUBCLONAL	1	TRUE	0	0.638913345595694	1		623	829	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846108	151846108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052448-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	219	430	7	ENST00000262189.6:c.12904C>T	p.Pro4302Ser	p.P4302S	ENST00000262189	NM_170606.2	4302	Cct/Tct	52/59	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.638913345595694	2		437	658	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133254	38133254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052617-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	361	562	0	ENST00000317025.8:c.4219G>A	p.Glu1407Lys	p.E1407K	ENST00000317025	NM_023034.1	1407	Gaa/Aaa	24/24	0.514909929132574	3	FACETS	0.938	0.892	0.984	0.938	0.892	0.984	CLONAL	2	TRUE	1	0.514909929132574	3		562	940	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578277	7578277	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053229-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	42	731	0	ENST00000269305.4:c.572del	p.Pro191LeufsTer56	p.P191Lfs*56	ENST00000269305	NM_001126112.2	191	cCt/ct	6/11	0.178566057482509	3	FACETS	0.841	0.703	0.995	0.421	0.351	0.498	CLONAL	1	TRUE	1	0.247681642355313	3		731	453	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862856	9862856	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053229-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	26	631	0	ENST00000330684.3:c.2447A>G	p.Asn816Ser	p.N816S	ENST00000330684	NM_001134407.1	816	aAc/aGc	12/13	1	2	FACETS	0.537	0.425	0.666	0.537	0.425	0.666	SUBCLONAL	1	TRUE	1	0.247681642355313	2		631	391	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876099	35876099	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053229-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	11	327	0	ENST00000303115.3:c.891T>A	p.Ser297Arg	p.S297R	ENST00000303115	NM_002185.3	297	agT/agA	8/8	0.178566057482509	3	FACETS	0.464	0.32	0.643	0.232	0.16	0.322	SUBCLONAL	1	TRUE	1	0.247681642355313	3		327	215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0053316-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	139	179	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.240847449886535	1	FACETS	0.902	0.819	0.989	0.902	0.819	0.989	CLONAL	1	TRUE	0	0.240847449886535	1		180	1126	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259247	36259248	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0053316-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	320	705	0	ENST00000300305.3:c.242_243dup	p.Leu82CysfsTer41	p.L82Cfs*41	ENST00000300305		81	-/TG	3/8	0.240847449886535	3	FACETS	0.895	0.845	0.946	1	0.993	1	CLONAL	3	TRUE	1	0.240847449886535	3		705	1109	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797309	135797310	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTGC	novel	NA	P-0053316-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	47	270	0	ENST00000298552.3:c.556_559dup	p.Leu187ArgfsTer32	p.L187Rfs*32	ENST00000298552	NM_001162426.1	187	ctc/cGCACtc	7/23	0.240847449886535	1	FACETS	0.892	0.754	1	0.892	0.754	1	CLONAL	1	TRUE	0	0.240847449886535	1		270	385	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055674	152055675	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053316-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	156	537	0	ENST00000262189.6:c.247dup	p.Thr83AsnfsTer13	p.T83Nfs*13	ENST00000262189	NM_170606.2	83	aca/aAca	2/59	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.240847449886535	2		537	881	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371903	116371903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs544274181	NA	P-0053993-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	68	539	0	ENST00000397752.3:c.1382G>A	p.Arg461His	p.R461H	ENST00000397752	NM_000245.2	461	cGc/cAc	3/21	0.605158974978026	3	FACETS	0.893	0.783	1	0.298	0.261	0.337	CLONAL	1	TRUE	0	0.668679356345154	3		539	304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0053993-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	156	799	0	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	0.660948660632254	3	FACETS	0.833	0.784	0.881	0.833	0.784	0.881	CLONAL	3	TRUE	0	0.668679356345154	3		799	249	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101560	27101560	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053993-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	78	995	0	ENST00000324856.7:c.4842G>T	p.Gln1614His	p.Q1614H	ENST00000324856	NM_006015.4	1614	caG/caT	18/20	0.646204948806639	3	FACETS	0.858	0.759	0.962	0.429	0.379	0.481	CLONAL	1	TRUE	1	0.668679356345154	3		995	363	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741827	17741827	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053993-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	15	365	0	ENST00000250003.3:c.498C>A	p.Asp166Glu	p.D166E	ENST00000250003	NM_002478.4	166	gaC/gaA	1/3	0.498542900201418	4	FACETS	0.563	0.415	0.738	0.281	0.207	0.369	SUBCLONAL	1	TRUE	2	0.668679356345154	4		365	133	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025895	48025895	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053993-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	188	448	0	ENST00000234420.5:c.773T>A	p.Ile258Asn	p.I258N	ENST00000234420	NM_000179.2	258	aTt/aAt	4/10	0.614237389761186	4	FACETS	0.85	0.798	0.901	0.637	0.599	0.676	CLONAL	3	TRUE	0	0.668679356345154	4		448	368	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025916	48025916	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs63749890	NA	P-0053993-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	189	474	0	ENST00000234420.5:c.794T>G	p.Phe265Cys	p.F265C	ENST00000234420	NM_000179.2	265	tTt/tGt	4/10	0.614237389761186	4	FACETS	1	0.988	1	0.617	0.579	0.655	CLONAL	2	TRUE	0	0.668679356345154	4		474	382	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACA	novel	NA	P-0053993-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	2485	922	0	ENST00000275493.2:c.2311_2313dup	p.Asn771dup	p.N771dup	ENST00000275493	NM_005228.3	771	gac/gACAac	20/28	0.668679356345154	27	FACETS	1	0.988	1			1	CLONAL	20	TRUE	NA	0.668679356345154	27		922	3473	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111794	56111794	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs557606535	NA	P-0054221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	14	3	0	ENST00000399503.3:c.394G>C	p.Asp132His	p.D132H	ENST00000399503	NM_005921.1	132	Gac/Cac	1/20	0.473642178739515	5	FACETS	1	0.785	1	0.702	0.527	0.897	CLONAL	2	TRUE	2	0.473642178739515	5		3	48	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579449	7579455	+	frameshift_variant	Frame_Shift_Del	DEL	GAGCTGC	GAGCTGC	-	novel	NA	P-0054221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	264	1098	0	ENST00000269305.4:c.232_238del	p.Ala78LeufsTer43	p.A78Lfs*43	ENST00000269305	NM_001126112.2	78	GCAGCTCct/ct	4/11	0.282111465630198	3	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.473642178739515	3		1098	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578224	7578224	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1429743956	NA	P-0054241-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	9	843	1	ENST00000269305.4:c.625A>T	p.Arg209Ter	p.R209*	ENST00000269305	NM_001126112.2	209	Aga/Tga	6/11	0.361272948551647	3	FACETS	0.146	0.096	0.21	0.073	0.048	0.105	INDETERMINATE	1	FALSE	1	0.655432971342771	3		844	249	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594221	55594221	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913512	NA	P-0054241-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	129	474	0	ENST00000288135.5:c.1924A>G	p.Lys642Glu	p.K642E	ENST00000288135	NM_000222.2	642	Aaa/Gaa	13/21	0.40132987673241	5	FACETS	0.969	0.887	1	0.646	0.591	0.702	CLONAL	2	FALSE	2	0.655432971342771	5		474	403	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661098	227661101	+	missense_variant	Missense_Mutation	ONP	TGCC	TGCC	CGCG	novel	NA	P-0054241-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	39	1016	0	ENST00000305123.5:c.2354_2357delinsCGCG	p.Arg785_His786delinsProArg	p.R785_H786delinsPR	ENST00000305123	NM_005544.2	785	cGGCAt/cCGCGt	1/2	0.370905810948813	4	FACETS	0.504	0.418	0.599	0.252	0.209	0.3	INDETERMINATE	1	FALSE	2	0.655432971342771	4		1016	391	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0054569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	903	351	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.698536505698182	7	FACETS	1	0.994	1			1	CLONAL	6	TRUE	NA	0.698536505698182	7		351	1150	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579359	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587780066	NA	P-0054569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	872	1157	1	ENST00000269305.4:c.328del	p.Arg110ValfsTer13	p.R110Vfs*13	ENST00000269305	NM_001126112.2	110	Cgt/gt	4/11	NA	2	FACETS	0.987	0.964	1			1	INDETERMINATE	2	TRUE	NA	0.698536505698182	2		1158	1265	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0054569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	482	328	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	0.698536505698182	7	FACETS	1	0.968	1			1	CLONAL	5	TRUE	NA	0.698536505698182	7		328	757	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422431	225422431	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	231	612	0	ENST00000264414.4:c.209G>C	p.Gly70Ala	p.G70A	ENST00000264414	NM_003590.4	70	gGa/gCa	2/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.698536505698182	2		612	609	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560524	65560524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	236	554	1	ENST00000358664.4:c.73C>T	p.Arg25Trp	p.R25W	ENST00000358664	NM_002382.4	25	Cgg/Tgg	3/5	0.698536505698182	1	FACETS	0.986	0.933	1	0.986	0.933	1	CLONAL	1	TRUE	0	0.698536505698182	1		555	446	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	65	619	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.489950185706541	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.489950185706541	3		619	148	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0054582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	93	1070	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.309661185053929	3	FACETS	1	0.971	1	0.78	0.71	0.851	CLONAL	2	TRUE	0	0.489950185706541	3		1070	202	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045838	26045838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755131918	NA	P-0054582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	149	948	1	ENST00000540144.1:c.200C>T	p.Pro67Leu	p.P67L	ENST00000540144	NM_003531.2	67	cCg/cTg	1/1	0.489950185706541	5	FACETS	0.994	0.921	1	0.994	0.921	1	CLONAL	3	TRUE	2	0.489950185706541	5		949	354	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953214	81953214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369516453	NA	P-0054582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	99	562	1	ENST00000359376.3:c.2180G>A	p.Arg727Gln	p.R727Q	ENST00000359376	NM_002661.3	727	cGa/cAa	20/33	0.326215988479729	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.489950185706541	4		563	253	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101702	27101702	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	131	1120	2	ENST00000324856.7:c.4986del	p.Asp1663ThrfsTer10	p.D1663Tfs*10	ENST00000324856	NM_006015.4	1662	Aaa/aa	18/20	0.489950185706541	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.489950185706541	3		1122	296	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0055031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	204	2463	2	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.275264375766636	3	FACETS	0.922	0.856	0.99	0.922	0.856	0.99	CLONAL	2	TRUE	1	0.288510612188369	3		2465	878	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121912666	NA	P-0055031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	143	1597	0	ENST00000269305.4:c.659A>C	p.Tyr220Ser	p.Y220S	ENST00000269305	NM_001126112.2	220	tAt/tCt	6/11	0.275264375766636	3	FACETS	1	0.986	1	0.73	0.666	0.797	CLONAL	1	TRUE	1	0.288510612188369	3		1597	777	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591888	48591888	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519739	NA	P-0055031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	104	866	0	ENST00000342988.3:c.1051G>C	p.Asp351His	p.D351H	ENST00000342988	NM_005359.5	351	Gat/Cat	9/12	0.288510612188369	2	FACETS	0.782	0.704	0.864	0.782	0.704	0.864	SUBCLONAL	2	TRUE	0	0.288510612188369	2		866	461	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393211	393211	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	118	1474	5	ENST00000380956.4:c.59G>A	p.Gly20Asp	p.G20D	ENST00000380956	NM_001195286.1	20	gGc/gAc	2/9	0.288510612188369	4	FACETS	1	0.918	1	1	0.918	1	CLONAL	2	TRUE	2	0.288510612188369	4		1479	520	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77085410	77085410	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs963508717	NA	P-0055031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	89	473	0	ENST00000356341.3:c.440A>G	p.Asp147Gly	p.D147G	ENST00000356341	NM_002576.4	147	gAt/gGt	5/15	0.252317898831192	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	2	0.288510612188369	4		473	354	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481895	56481895	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	180	1321	2	ENST00000267101.3:c.823A>T	p.Asn275Tyr	p.N275Y	ENST00000267101	NM_001982.3	275	Aat/Tat	7/28	0.288510612188369	4	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	2	0.288510612188369	4		1323	787	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984735	11984735	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	28	465	0	ENST00000353533.5:c.281A>G	p.His94Arg	p.H94R	ENST00000353533	NM_003010.3	94	cAc/cGc	3/11	0.275264375766636	3	FACETS	0.858	0.688	1	0.429	0.344	0.525	CLONAL	1	TRUE	1	0.288510612188369	3		465	259	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166330	7166330	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	91	1837	0	ENST00000302850.5:c.1696A>G	p.Arg566Gly	p.R566G	ENST00000302850	NM_000208.2	566	Agg/Ggg	8/22	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.288510612188369	2		1837	572	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383604	42383604	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0055031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	129	1155	1	ENST00000221972.3:c.380-1G>A		p.X127_splice	ENST00000221972	NM_021601.3	127			0.237852149742383	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.288510612188369	2		1156	382	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502799	186502799	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	136	761	0	ENST00000323963.5:c.257C>G	p.Thr86Arg	p.T86R	ENST00000323963		86	aCa/aGa	4/11	0.288510612188369	7	FACETS	1	0.965	1	0.446	0.406	0.489	CLONAL	2	TRUE	2	0.288510612188369	7		761	727	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557215	187557215	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	120	931	0	ENST00000441802.2:c.4147G>T	p.Glu1383Ter	p.E1383*	ENST00000441802	NM_005245.3	1383	Gag/Tag	6/27	0.288510612188369	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	0	0.288510612188369	2		931	407	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440180	220440180	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055174-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	76	866	0	ENST00000243786.2:c.1033G>A	p.Asp345Asn	p.D345N	ENST00000243786	NM_002191.3	345	Gat/Aat	2/2	1	2	FACETS	0.777	0.68	0.882	0.777	0.68	0.882	SUBCLONAL	1	TRUE	1	0.192734791447171	2		866	1015	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11018795	11018795	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055174-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	89	840	0	ENST00000327064.4:c.427G>A	p.Glu143Lys	p.E143K	ENST00000327064	NM_199141.1	143	Gag/Aag	3/16	1	2	FACETS	0.858	0.759	0.965	0.858	0.759	0.965	CLONAL	1	TRUE	1	0.192734791447171	2		840	1076	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411877	116411897	+	splice_region_variant,intron_variant	Splice_Region	DEL	AGCTCTTTCTTTCTCTCTGTT	AGCTCTTTCTTTCTCTCTGTT	-	novel	NA	P-0055174-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	135	718	0	ENST00000397752.3:c.2888-26_2888-6del		p.X963_splice	ENST00000397752	NM_000245.2	963			0.17098534863167	2	FACETS	0.769	0.698	0.843	0.769	0.698	0.843	SUBCLONAL	2	TRUE	0	0.192734791447171	2		718	911	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342068	70342068	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055174-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	60	575	1	ENST00000374080.3:c.1120C>T	p.Pro374Ser	p.P374S	ENST00000374080		374	Cct/Tct	8/45	1	2	FACETS	0.939	0.808	1	0.939	0.808	1	CLONAL	1	TRUE	1	0.192734791447171	2		576	663	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0055255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	175	302	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.720904693049152	2		302	437	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523509	41523509	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	60	366	0	ENST00000263253.7:c.925C>T	p.Gln309Ter	p.Q309*	ENST00000263253	NM_001429.3	309	Cag/Tag	4/31	1	2	FACETS	0.425	0.367	0.487	0.425	0.367	0.487	SUBCLONAL	1	TRUE	1	0.720904693049152	2		366	392	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259012	153259012	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	45	190	0	ENST00000281708.4:c.803T>C	p.Met268Thr	p.M268T	ENST00000281708	NM_033632.3	268	aTg/aCg	5/12	1	2	FACETS	0.562	0.477	0.654	0.562	0.477	0.654	SUBCLONAL	1	TRUE	1	0.720904693049152	2		190	222	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587781525	NA	P-0055297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	67	730	0	ENST00000269305.4:c.842A>T	p.Asp281Val	p.D281V	ENST00000269305	NM_001126112.2	281	gAc/gTc	8/11	0.3	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.91	0		730	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578471	7578471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	54	849	0	ENST00000269305.4:c.459del	p.Gly154AlafsTer16	p.G154Afs*16	ENST00000269305	NM_001126112.2	153	ccC/cc	5/11	0.3	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.91	0		849	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578288	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CGGATAAGATGCTGAGGAGGGGCCAGA	CGGATAAGATGCTGAGGAGGGGCCAGA	-	novel	NA	P-0055297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	88	723	0	ENST00000269305.4:c.561_587del	p.Leu188_Arg196del	p.L188_R196del	ENST00000269305	NM_001126112.2	187	ggTCTGGCCCCTCCTCAGCATCTTATCCGa/gga	6/11	0.3	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.91	0		723	326	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506661	103506661	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055378-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	62	164	0	ENST00000355739.4:c.404C>T	p.Thr135Ile	p.T135I	ENST00000355739	NM_000123.3	135	aCc/aTc	4/15	1	2	FACETS	0.535	0.466	0.607	0.535	0.466	0.607	SUBCLONAL	1	TRUE	1	0.875218416629992	2		164	265	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677974	58677974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1406686076	NA	P-0055378-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	63	217	0	ENST00000305921.3:c.199G>A	p.Gly67Ser	p.G67S	ENST00000305921	NM_003620.3	67	Ggc/Agc	1/6	0.875218416629992	3	FACETS	0.635	0.553	0.723	0.317	0.276	0.362	SUBCLONAL	1	TRUE	1	0.875218416629992	3		217	326	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198261011	198261011	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055378-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	58	372	0	ENST00000335508.6:c.3308T>C	p.Val1103Ala	p.V1103A	ENST00000335508	NM_012433.2	1103	gTt/gCt	23/25	1	2	FACETS	0.224	0.192	0.258	0.224	0.192	0.258	SUBCLONAL	1	TRUE	1	0.875218416629992	2		372	593	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708115	117708115	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055378-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	33	364	0	ENST00000368508.3:c.2062A>G	p.Ser688Gly	p.S688G	ENST00000368508	NM_002944.2	688	Agt/Ggt	14/43	1	2	FACETS	0.151	0.122	0.183	0.151	0.122	0.183	SUBCLONAL	1	TRUE	1	0.875218416629992	2		364	501	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339594	70339594	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055378-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	35	506	0	ENST00000374080.3:c.263A>G	p.Asp88Gly	p.D88G	ENST00000374080		88	gAc/gGc	3/45	1	2	FACETS	0.144	0.117	0.173	0.144	0.117	0.173	SUBCLONAL	1	TRUE	1	0.875218416629992	2		506	557	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027171	49027171	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs587778858	NA	P-0055419-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	100	196	0	ENST00000267163.4:c.1738G>T	p.Glu580Ter	p.E580*	ENST00000267163	NM_000321.2	580	Gaa/Taa	18/27	1	2	FACETS	0.919	0.871	0.96	1	0.992	1	CLONAL	5	TRUE	1	0.362897489071033	2		196	120	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0055460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	273	554	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.351009994932316	3	FACETS	0.951	0.896	1	0.951	0.896	1	CLONAL	2	TRUE	1	0.413108480096019	3		554	838	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	55	365	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.59	0.506	0.682	0.59	0.506	0.682	SUBCLONAL	1	TRUE	1	0.413108480096019	2		365	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0055460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	132	931	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.413108480096019	1	FACETS	0.485	0.439	0.533	0.485	0.439	0.533	SUBCLONAL	1	TRUE	0	0.413108480096019	1		931	1046	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0055460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	118	1161	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.413108480096019	1	FACETS	0.353	0.317	0.391	0.353	0.317	0.391	SUBCLONAL	1	TRUE	0	0.413108480096019	1		1161	1285	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806092	1806092	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913484	NA	P-0055460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	498	1472	0	ENST00000260795.2:c.1111A>T	p.Ser371Cys	p.S371C	ENST00000260795		371	Agt/Tgt	8/17	NA	2	FACETS	0.833	0.797	0.869			1	INDETERMINATE	2	TRUE	NA	0.413108480096019	2		1472	1448	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173675	108173675	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	79	479	0	ENST00000278616.4:c.5415G>A	p.Trp1805Ter	p.W1805*	ENST00000278616	NM_000051.3	1805	tgG/tgA	36/63	1	2	FACETS	0.787	0.694	0.886	0.787	0.694	0.886	SUBCLONAL	1	TRUE	1	0.413108480096019	2		479	486	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787737	135787737	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0055460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	227	728	0	ENST00000298552.3:c.845C>G	p.Ser282Ter	p.S282*	ENST00000298552	NM_001162426.1	282	tCa/tGa	9/23	0.413108480096019	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.413108480096019	1		728	760	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666615	206666615	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	201	1088	0	ENST00000367120.3:c.1949C>G	p.Ser650Cys	p.S650C	ENST00000367120	NM_014002.3	650	tCt/tGt	20/22	1	2	FACETS	0.842	0.779	0.907	0.842	0.779	0.907	CLONAL	1	TRUE	1	0.413108480096019	2		1088	1156	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025517	1025517	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	239	1258	0	ENST00000358495.3:c.858G>C	p.Lys286Asn	p.K286N	ENST00000358495	NM_134424.2	286	aaG/aaC	9/12	NA	2	FACETS	0.811	0.756	0.869			1	INDETERMINATE	1	TRUE	NA	0.413108480096019	2		1258	1426	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26927979	26927979	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	82	582	0	ENST00000381527.3:c.418C>G	p.His140Asp	p.H140D	ENST00000381527	NM_001260.1	140	Cac/Gac	4/13	0.222013446137935	1	FACETS	0.568	0.501	0.638	0.568	0.501	0.638	INDETERMINATE	1	TRUE	0	0.413108480096019	1		582	555	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772382	56772382	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555593569	NA	P-0055460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	66	567	0	ENST00000337432.4:c.236C>T	p.Ser79Phe	p.S79F	ENST00000337432	NM_058216.2	79	tCt/tTt	2/9	1	2	FACETS	0.41	0.355	0.47	0.41	0.355	0.47	SUBCLONAL	1	TRUE	1	0.413108480096019	2		567	779	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262921	46262921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	105	535	0	ENST00000371998.3:c.1094C>T	p.Ser365Leu	p.S365L	ENST00000371998		365	tCa/tTa	10/23	1	2	FACETS	0.763	0.685	0.847	0.763	0.685	0.847	SUBCLONAL	1	TRUE	1	0.413108480096019	2		535	666	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032785	30032790	+	inframe_deletion	In_Frame_Del	DEL	CTGGGG	CTGGGG	-	novel	NA	P-0055460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	237	545	0	ENST00000338641.4:c.162_167del	p.Gly55_Leu56del	p.G55_L56del	ENST00000338641	NM_000268.3	54	CTGGGG/-	2/16	0.269599624255795	2	FACETS	0.804	0.753	0.855	0.804	0.753	0.855	CLONAL	2	TRUE	0	0.413108480096019	2		545	714	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233117	55233117	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	177	796	0	ENST00000275493.2:c.1867A>G	p.Asn623Asp	p.N623D	ENST00000275493	NM_005228.3	623	Aac/Gac	15/28	0.341604974889627	1	FACETS	0.675	0.622	0.731	0.675	0.622	0.731	SUBCLONAL	1	TRUE	0	0.413108480096019	1		796	1007	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650893	93650893	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	179	579	0	ENST00000375746.1:c.1819C>A	p.Leu607Met	p.L607M	ENST00000375746	NM_001174167.1	607	Ctg/Atg	13/14	0.413108480096019	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.413108480096019	1		579	666	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945174	44945175	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0055460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	134	758	0	ENST00000377967.4:c.3500_3501dup	p.Val1168LeufsTer11	p.V1168Lfs*11	ENST00000377967	NM_021140.2	1166	-/TT	24/29	1	2	FACETS	0.81	0.736	0.887	0.81	0.736	0.887	CLONAL	1	TRUE	1	0.413108480096019	2		758	801	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210310	123210310	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	76	356	0	ENST00000218089.9:c.2662C>T	p.Gln888Ter	p.Q888*	ENST00000218089	NM_001042749.1	888	Cag/Tag	26/35	1	2	FACETS	0.887	0.781	0.999	0.887	0.781	0.999	CLONAL	1	TRUE	1	0.413108480096019	2		356	415	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546139	41546139	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs774092833	NA	P-0055460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	103	623	0	ENST00000263253.7:c.2754G>C	p.Gln918His	p.Q918H	ENST00000263253	NM_001429.3	918	caG/caC	14/31	0.269599624255795	2	FACETS	0.625	0.559	0.695	0.312	0.279	0.348	SUBCLONAL	1	TRUE	0	0.413108480096019	2		623	798	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259183	36259183	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	127	568	0	ENST00000300305.3:c.308C>A	p.Pro103His	p.P103H	ENST00000300305		103	cCt/cAt	3/8	0.338861932996908	1	FACETS	0.428	0.387	0.471	0.428	0.387	0.471	SUBCLONAL	1	TRUE	0	0.513252073546045	1		568	860	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982053	70982053	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	61	799	0	ENST00000276594.2:c.43G>T	p.Val15Leu	p.V15L	ENST00000276594	NM_024504.3	15	Gtg/Ttg	2/8	1	2	FACETS	0.243	0.209	0.281	0.243	0.209	0.281	SUBCLONAL	1	TRUE	1	0.513252073546045	2		799	977	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982657	90982657	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	46	276	0	ENST00000265433.3:c.831C>G	p.Asn277Lys	p.N277K	ENST00000265433	NM_002485.4	277	aaC/aaG	7/16	1	2	FACETS	0.408	0.344	0.479	0.408	0.344	0.479	SUBCLONAL	1	TRUE	1	0.513252073546045	2		276	439	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218069	36218069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1363001300	NA	P-0055607-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	158	361	0	ENST00000222270.7:c.4016C>T	p.Pro1339Leu	p.P1339L	ENST00000222270	NM_014727.1	1339	cCg/cTg	15/37	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.613048295452887	2		361	507	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80169018	80169018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055607-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	248	601	0	ENST00000265081.6:c.3214G>A	p.Val1072Met	p.V1072M	ENST00000265081	NM_002439.4	1072	Gtg/Atg	23/24	0.602603594352506	4	FACETS	1	0.936	1	0.334	0.312	0.357	CLONAL	1	TRUE	1	0.613048295452887	4		601	1302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579330	7579330	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055667-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	165	415	0	ENST00000269305.4:c.357del	p.Lys120SerfsTer3	p.K120Sfs*3	ENST00000269305	NM_001126112.2	119	gcC/gc	4/11	0.63435811603758	1	FACETS	0.973	0.907	1	0.973	0.907	1	CLONAL	1	TRUE	0	0.63435811603758	1		415	365	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444650	187444650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1246753673	NA	P-0055667-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	157	376	0	ENST00000232014.4:c.1577G>A	p.Arg526His	p.R526H	ENST00000232014	NM_001130845.1	526	cGc/cAc	7/10	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.63435811603758	2		376	485	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628542	187628542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157383372	NA	P-0055667-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	261	624	0	ENST00000441802.2:c.2440G>A	p.Asp814Asn	p.D814N	ENST00000441802	NM_005245.3	814	Gat/Aat	2/27	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.63435811603758	2		624	780	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0055696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	527	1005	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.715736910367717	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.727933534703511	2		1006	700	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101117	27101117	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	527	1163	3	ENST00000324856.7:c.4403del	p.Pro1468LeufsTer13	p.P1468Lfs*13	ENST00000324856	NM_006015.4	1467	Ccc/cc	18/20	0.727933534703511	3	FACETS	0.971	0.936	1	0.971	0.936	1	CLONAL	2	TRUE	1	0.727933534703511	3		1166	1017	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407501	407501	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	131	443	0	ENST00000380956.4:c.1259A>G	p.Asn420Ser	p.N420S	ENST00000380956	NM_001195286.1	420	aAc/aGc	9/9	0.715258431232085	3	FACETS	1	0.952	1	0.531	0.485	0.579	CLONAL	1	TRUE	1	0.727933534703511	3		443	462	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0055769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	17	743	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		743	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	130	1734	0	ENST00000269305.4:c.383del	p.Pro128LeufsTer42	p.P128Lfs*42	ENST00000269305	NM_001126112.2	128	cCt/ct	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1734	784	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509082	66509082	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	27	439	0	ENST00000273854.3:c.245G>T	p.Gly82Val	p.G82V	ENST00000273854	NM_004439.5	82	gGg/gTg	2/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		439	218	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971035	21971035	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	83	912	0	ENST00000304494.5:c.323A>G	p.Asp108Gly	p.D108G	ENST00000304494	NM_000077.4	108	gAt/gGt	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		912	424	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812165	212812165	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	40	376	0	ENST00000342788.4:c.411G>T	p.Lys137Asn	p.K137N	ENST00000342788	NM_005235.2	137	aaG/aaT	3/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		376	236	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528428	29528428	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs876660782	NA	P-0055769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	43	391	0	ENST00000356175.3:c.1186-1G>C		p.X396_splice	ENST00000356175	NM_000267.3	396			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		391	271	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483343	120483343	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	54	666	0	ENST00000256646.2:c.3018T>G	p.Ile1006Met	p.I1006M	ENST00000256646	NM_024408.3	1006	atT/atG	19/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		666	322	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333013	70333013	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	199	1270	0	ENST00000373644.4:c.918A>G	p.Ile306Met	p.I306M	ENST00000373644	NM_030625.2	306	atA/atG	2/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1270	800	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562990	21562990	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs370973977	NA	P-0055769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	114	1617	1	ENST00000382592.4:c.929G>T	p.Gly310Val	p.G310V	ENST00000382592	NM_014572.2	310	gGg/gTg	4/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1618	588	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563439	21563439	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	135	1768	0	ENST00000382592.4:c.480G>C	p.Lys160Asn	p.K160N	ENST00000382592	NM_014572.2	160	aaG/aaC	4/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1768	785	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223340	2223340	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	107	1523	0	ENST00000326181.6:c.952A>C	p.Met318Leu	p.M318L	ENST00000326181	NM_032271.2	318	Atg/Ctg	10/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1523	711	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992641	72992641	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	84	1267	1	ENST00000268489.5:c.1404G>T	p.Glu468Asp	p.E468D	ENST00000268489	NM_006885.3	468	gaG/gaT	2/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1268	598	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302944	15302944	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	157	2115	2	ENST00000263388.2:c.506G>T	p.Arg169Leu	p.R169L	ENST00000263388	NM_000435.2	169	cGc/cTc	4/33	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		2117	810	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719023	190719023	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	40	355	0	ENST00000441310.2:c.1025G>C	p.Ser342Thr	p.S342T	ENST00000441310	NM_000534.4	342	aGt/aCt	9/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		355	282	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573434	55573434	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	50	543	0	ENST00000288135.5:c.1096G>T	p.Glu366Ter	p.E366*	ENST00000288135	NM_000222.2	366	Gag/Tag	6/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		543	313	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980381	55980381	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	43	610	0	ENST00000263923.4:c.710C>G	p.Ser237Cys	p.S237C	ENST00000263923	NM_002253.2	237	tCt/tGt	6/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		610	366	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230791	66230791	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	40	571	0	ENST00000273854.3:c.2180T>A	p.Ile727Asn	p.I727N	ENST00000273854	NM_004439.5	727	aTc/aAc	12/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		571	321	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230893	66230893	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	40	517	0	ENST00000273854.3:c.2078G>T	p.Arg693Leu	p.R693L	ENST00000273854	NM_004439.5	693	cGt/cTt	12/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		517	293	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509082	66509083	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0055769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	27	445	0	ENST00000273854.3:c.244_245delinsTT	p.Gly82Leu	p.G82L	ENST00000273854	NM_004439.5	82	GGg/TTg	2/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		445	225	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196618	106196618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	76	756	0	ENST00000380013.4:c.4951C>T	p.Pro1651Ser	p.P1651S	ENST00000380013	NM_001127208.2	1651	Ccc/Tcc	11/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		756	485	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1268653	1268653	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs775014633	NA	P-0055769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	133	1702	1	ENST00000310581.5:c.2564C>A	p.Ala855Glu	p.A855E	ENST00000310581	NM_198253.2	855	gCg/gAg	9/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1703	1004	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724332	117724332	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs751553775	NA	P-0055769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	101	1078	0	ENST00000368508.3:c.547A>G	p.Ser183Gly	p.S183G	ENST00000368508	NM_002944.2	183	Agt/Ggt	6/43	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1078	598	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382232	152382232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	68	655	0	ENST00000206249.3:c.1342C>T	p.Leu448Phe	p.L448F	ENST00000206249	NM_000125.3	448	Ctc/Ttc	6/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		655	371	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042113	6042113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	28	386	0	ENST00000265849.7:c.508C>T	p.His170Tyr	p.H170Y	ENST00000265849	NM_000535.5	170	Cat/Tat	5/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		386	208	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346199	152346199	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	79	937	0	ENST00000359321.1:c.371C>A	p.Thr124Asn	p.T124N	ENST00000359321	NM_005431.1	124	aCc/aAc	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		937	591	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389344	8389344	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs769310148	NA	P-0055769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	44	826	0	ENST00000356435.5:c.4274A>G	p.Tyr1425Cys	p.Y1425C	ENST00000356435		1425	tAt/tGt	26/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		826	389	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321385	1321385	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	48	865	3	ENST00000400841.2:c.370C>A	p.His124Asn	p.H124N	ENST00000400841		124	Cac/Aac	4/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		868	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0055769-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	90	646	2	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		648	442	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0055769-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	27	331	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		331	260	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948619	71948619	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055769-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	29	1961	0	ENST00000298229.2:c.3331G>A	p.Gly1111Arg	p.G1111R	ENST00000298229	NM_001567.3	1111	Ggg/Agg	26/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1961	325	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385016	31385016	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0055769-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	83	1232	0	ENST00000328111.2:c.1401C>G	p.Tyr467Ter	p.Y467*	ENST00000328111	NM_006892.3	467	taC/taG	14/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1232	341	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206898	36206898	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055769-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	33	549	0	ENST00000300305.3:c.614G>T	p.Arg205Ile	p.R205I	ENST00000300305		205	aGa/aTa	6/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		549	234	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004479	150004479	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055769-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	59	1035	0	ENST00000253339.5:c.1746G>T	p.Glu582Asp	p.E582D	ENST00000253339		582	gaG/gaT	3/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1035	394	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021822	69021822	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055769-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	12	956	2	ENST00000288368.4:c.3110T>A	p.Leu1037Gln	p.L1037Q	ENST00000288368	NM_024870.2	1037	cTg/cAg	25/40	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		958	235	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949005	44949005	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055769-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	39	487	0	ENST00000377967.4:c.3566del	p.Leu1189GlnfsTer32	p.L1189Qfs*32	ENST00000377967	NM_021140.2	1189	cTa/ca	25/29	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		487	147	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044916	47044916	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055769-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	37	1500	0	ENST00000377604.3:c.2242G>C	p.Glu748Gln	p.E748Q	ENST00000377604	NM_001204468.1	748	Gag/Cag	20/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1500	250	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215321	123215322	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055769-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	67	568	0	ENST00000218089.9:c.2870dup	p.Leu957PhefsTer6	p.L957Ffs*6	ENST00000218089	NM_001042749.1	956	gct/gcTt	28/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		568	206	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0055820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	19	454	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.187657496038102	4	FACETS	0.865	0.663	1	0.865	0.663	1	CLONAL	2	TRUE	2	0.187657496038102	4		454	139	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627215	37627215	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	45	550	0	ENST00000447079.4:c.1130C>A	p.Ser377Ter	p.S377*	ENST00000447079	NM_015083.1	377	tCa/tAa	2/14	0.187657496038102	4	FACETS	1	0.893	1	1	0.893	1	CLONAL	2	TRUE	2	0.187657496038102	4		550	266	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183804	10183804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1559426047	NA	P-0055945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	87	1253	0	ENST00000256474.2:c.273del	p.Phe91LeufsTer68	p.F91Lfs*68	ENST00000256474	NM_000551.3	91	ttC/tt	1/3	0.448933161087478	1	FACETS	0.504	0.451	0.558	0.504	0.451	0.558	SUBCLONAL	1	TRUE	0	0.7449237741123	1		1253	291	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440372	52440372	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	23	331	0	ENST00000460680.1:c.680G>C	p.Arg227Pro	p.R227P	ENST00000460680	NM_004656.3	227	cGc/cCc	9/17	0.129087304999497	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		331	403	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0056022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	15	312	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.129087304999497	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		312	295	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0056022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	22	361	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.129087304999497	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		361	485	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781324	3781326	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs587783502	NA	P-0056022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	20	470	0	ENST00000262367.5:c.5039_5041del	p.Ser1680del	p.S1680del	ENST00000262367	NM_004380.2	1680	tCCTtg/ttg	30/31	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		470	448	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855934	68855934	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	36	210	0	ENST00000261769.5:c.1742T>C	p.Leu581Pro	p.L581P	ENST00000261769	NM_004360.3	581	cTt/cCt	12/16	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		210	289	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0056078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	350	750	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.511272146335965	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.714319860883815	1		750	459	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041166	29041166	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	145	597	1	ENST00000282397.4:c.262T>C	p.Phe88Leu	p.F88L	ENST00000282397	NM_002019.4	88	Ttc/Ctc	3/30	0.714319860883815	2	FACETS	1	0.983	1	0.61	0.565	0.655	CLONAL	1	TRUE	0	0.714319860883815	2		598	333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0056146-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	364	616	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.62197700737922	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.626140722426928	2		616	566	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0056146-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	238	362	0	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	0.625998384001723	5	FACETS	1	0.989	1	0.487	0.457	0.516	CLONAL	2	TRUE	0	0.626140722426928	5		362	606	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820938	36820938	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056146-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	325	680	0	ENST00000373129.3:c.439C>G	p.His147Asp	p.H147D	ENST00000373129	NM_032017.1	147	Cat/Gat	6/12	0.62197700737922	2	FACETS	0.987	0.946	1	0.987	0.946	1	CLONAL	2	TRUE	0	0.626140722426928	2		680	526	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555614	21555614	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056146-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	203	518	1	ENST00000382592.4:c.2656C>A	p.Leu886Ile	p.L886I	ENST00000382592	NM_014572.2	886	Ctc/Atc	6/8	0.413964601401644	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.626140722426928	1		519	346	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108778	2108778	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056146-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1507	87	684	1	ENST00000219476.3:c.879A>T	p.Arg293Ser	p.R293S	ENST00000219476	NM_000548.3	293	agA/agT	10/42	0.626140722426928	8	FACETS	0.502	0.442	0.566			1	SUBCLONAL	1	TRUE	NA	0.626140722426928	8		685	1594	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379344	225379344	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056146-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	93	433	0	ENST00000264414.4:c.524G>A	p.Gly175Glu	p.G175E	ENST00000264414	NM_003590.4	175	gGa/gAa	4/16	0.553157355941668	4	FACETS	0.792	0.705	0.884	0.396	0.352	0.442	SUBCLONAL	1	TRUE	2	0.626140722426928	4		433	610	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31025014	31025014	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056146-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	198	449	0	ENST00000375687.4:c.4499A>G	p.Glu1500Gly	p.E1500G	ENST00000375687	NM_015338.5	1500	gAa/gGa	13/13	0.407614008122107	4	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	2	0.626140722426928	4		449	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0056185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	451	673	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.737901531464977	1	FACETS	0.98	0.944	1	0.98	0.944	1	CLONAL	1	TRUE	0	0.737901531464977	1		673	787	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782006	NA	P-0056185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	466	672	0	ENST00000269305.4:c.859G>A	p.Glu287Lys	p.E287K	ENST00000269305	NM_001126112.2	287	Gag/Aag	8/11	0.737901531464977	1	FACETS	0.995	0.959	1	0.995	0.959	1	CLONAL	1	TRUE	0	0.737901531464977	1		672	801	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0056185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	440	738	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.737901531464977	2		738	1160	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061450	38061450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	476	471	0	ENST00000250448.2:c.539C>T	p.Thr180Ile	p.T180I	ENST00000250448	NM_004496.3	180	aCc/aTc	2/2	0.382641278257037	3	FACETS	0.848	0.814	0.883	0.848	0.814	0.883	INDETERMINATE	2	TRUE	1	0.737901531464977	3		471	1041	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575069	64575069	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	391	531	2	ENST00000312049.6:c.738del	p.Ile247LeufsTer34	p.I247Lfs*34	ENST00000312049	NM_130799.2	246	tcC/tc	4/10	0.737901531464977	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.737901531464977	1		533	660	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576870	7576873	+	frameshift_variant	Frame_Shift_Del	DEL	CTCC	CTCC	TCT	novel	NA	P-0056185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	292	616	1	ENST00000269305.4:c.973_976delinsAGA	p.Gly325ArgfsTer20	p.G325Rfs*20	ENST00000269305	NM_001126112.2	325	GGAGaa/AGAaa	9/11	0.737901531464977	1	FACETS	0.916	0.873	0.96	0.916	0.873	0.96	CLONAL	1	TRUE	0	0.737901531464977	1		617	545	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216652	36216652	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1205441044	NA	P-0056213-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	133	734	0	ENST00000222270.7:c.3818A>G	p.His1273Arg	p.H1273R	ENST00000222270	NM_014727.1	1273	cAt/cGt	13/37	1	2	FACETS	0.98	0.891	1	0.98	0.891	1	CLONAL	1	FALSE	1	0.339609422556179	2		734	799	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509128	66509128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1439062174	NA	P-0056213-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	24	284	0	ENST00000273854.3:c.199C>T	p.Arg67Cys	p.R67C	ENST00000273854	NM_004439.5	67	Cgc/Tgc	2/18	1	2	FACETS	0.563	0.443	0.701	0.563	0.443	0.701	SUBCLONAL	1	FALSE	1	0.339609422556179	2		284	251	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998841	100998844	+	frameshift_variant	Frame_Shift_Del	DEL	GAGT	GAGT	-	novel	NA	P-0056213-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	120	806	0	ENST00000325455.5:c.958_961del	p.Thr320GlyfsTer35	p.T320Gfs*35	ENST00000325455	NM_001202474.3	320	ACTCgg/gg	1/8	0.269936032483448	1	FACETS	0.946	0.857	1	0.946	0.857	1	CLONAL	1	FALSE	0	0.339609422556179	1		806	620	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637686	52637696	+	frameshift_variant	Frame_Shift_Del	DEL	TCACGAATTTT	TCACGAATTTT	-	novel	NA	P-0056213-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	64	388	0	ENST00000394830.3:c.2620_2630del	p.Lys874Ter	p.K874*	ENST00000394830	NM_018313.4	874	AAAATTCGTGAt/t	18/30	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	FALSE	1	0.339609422556179	2		388	329	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111495	8111496	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGGA	novel	NA	P-0056249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	402	808	0	ENST00000346208.3:c.982_985dup	p.Arg329MetfsTer24	p.R329Mfs*24	ENST00000346208		327	-/TGGA	5/6	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.711396855488452	2		808	1086	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021637	31021637	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1264792645	NA	P-0056249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	300	694	0	ENST00000375687.4:c.1636C>T	p.Gln546Ter	p.Q546*	ENST00000375687	NM_015338.5	546	Cag/Tag	12/13	1	2	FACETS	0.999	0.945	1	0.999	0.945	1	CLONAL	1	TRUE	1	0.711396855488452	2		694	844	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120385	70120385	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2169	573	1391	0	ENST00000245479.2:c.1387T>C	p.Tyr463His	p.Y463H	ENST00000245479	NM_000346.3	463	Tac/Cac	3/3	0.515687552825336	5	FACETS	1	0.994	1			1	CLONAL	1	TRUE	NA	0.711396855488452	5		1391	2742	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842074	3842074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	171	395	0	ENST00000262367.5:c.1238G>A	p.Arg413Gln	p.R413Q	ENST00000262367	NM_004380.2	413	cGa/cAa	5/31	0.207860910834249	1	FACETS	0.648	0.601	0.696	0.648	0.601	0.696	INDETERMINATE	1	TRUE	0	0.711396855488452	1		395	478	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56911050	56911050	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	236	534	0	ENST00000519728.1:c.1196C>A	p.Ala399Glu	p.A399E	ENST00000519728	NM_002350.3	399	gCa/gAa	11/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.711396855488452	2		534	633	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0056250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	54	619	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.363912055805282	2		619	272	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0056250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	47	771	1	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.303548814131663	1	FACETS	0.788	0.67	0.917	0.788	0.67	0.917	CLONAL	1	TRUE	0	0.363912055805282	1		772	268	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372184	55372184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs915105324	NA	P-0056250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	23	553	0	ENST00000297316.4:c.874G>A	p.Ala292Thr	p.A292T	ENST00000297316	NM_022454.3	292	Gcc/Acc	2/2	1	2	FACETS	0.416	0.324	0.522	0.416	0.324	0.522	SUBCLONAL	1	TRUE	1	0.363912055805282	2		553	304	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100324	27100325	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	69	756	0	ENST00000324856.7:c.4038dup	p.Gly1347ArgfsTer98	p.G1347Rfs*98	ENST00000324856	NM_006015.4	1346	caa/cAaa	17/20	1	2	FACETS	0.965	0.844	1	0.965	0.844	1	CLONAL	1	TRUE	1	0.363912055805282	2		756	393	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0056280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	87	695	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.203569395038356	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.203569395038356	1		695	654	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	53	365	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.873	0.755	0.998	0.873	0.755	0.998	CLONAL	1	TRUE	1	0.610052629937396	2		365	199	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234302	39234302	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	91	361	0	ENST00000402219.2:c.2543G>C	p.Arg848Thr	p.R848T	ENST00000402219	NM_005633.3	848	aGa/aCa	16/23	1	2	FACETS	0.751	0.672	0.835	0.751	0.672	0.835	SUBCLONAL	1	TRUE	1	0.610052629937396	2		361	397	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188322	10188322	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0056281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	163	436	0	ENST00000256474.2:c.463+2T>A		p.X155_splice	ENST00000256474	NM_000551.3	155			0.568976827596836	1	FACETS	0.935	0.869	1	0.935	0.869	1	CLONAL	1	TRUE	0	0.610052629937396	1		436	397	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258571	19258571	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	302	920	0	ENST00000162023.5:c.329G>T	p.Gly110Val	p.G110V	ENST00000162023		110	gGa/gTa	8/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.610052629937396	2		920	938	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0056296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	153	227	0				ENST00000310581	NM_198253.2	-/1132			0.522309708370907	4	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	2	0.560401488215167	4		227	412	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926885	112926885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507544	NA	P-0056296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	142	400	0	ENST00000351677.2:c.1505C>T	p.Ser502Leu	p.S502L	ENST00000351677	NM_002834.3	502	tCa/tTa	13/16	0.560401488215167	3	FACETS	0.967	0.883	1	0.483	0.441	0.527	CLONAL	1	TRUE	1	0.560401488215167	3		400	671	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	292	370	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	0.560401488215167	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.560401488215167	3		370	630	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16001710	16001710	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	288	272	0	ENST00000268712.3:c.2791C>T	p.Gln931Ter	p.Q931*	ENST00000268712	NM_006311.3	931	Cag/Tag	21/46	0.560401488215167	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.560401488215167	2		272	440	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295353	1295353	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0056296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	64	161	0				ENST00000310581	NM_198253.2	-/1132			0.522309708370907	4	FACETS	1	0.913	1	0.53	0.462	0.603	CLONAL	1	TRUE	2	0.560401488215167	4		161	336	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482426	56482426	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	300	411	0	ENST00000267101.3:c.974G>C	p.Gly325Ala	p.G325A	ENST00000267101	NM_001982.3	325	gGa/gCa	8/28	0.560401488215167	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.560401488215167	3		411	638	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512233	120512233	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	242	344	0	ENST00000256646.2:c.1009G>T	p.Glu337Ter	p.E337*	ENST00000256646	NM_024408.3	337	Gag/Tag	6/34	0.560401488215167	3	FACETS	0.965	0.909	1	0.965	0.909	1	CLONAL	2	TRUE	1	0.560401488215167	3		344	573	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199925	108199925	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	144	130	0	ENST00000278616.4:c.7267G>T	p.Glu2423Ter	p.E2423*	ENST00000278616	NM_000051.3	2423	Gaa/Taa	49/63	0.560401488215167	6	FACETS	0.913	0.842	0.986	0.913	0.842	0.986	CLONAL	3	TRUE	3	0.560401488215167	6		130	398	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135777994	135777994	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs397514862	NA	P-0056296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	255	356	0	ENST00000298552.3:c.2389C>T	p.Gln797Ter	p.Q797*	ENST00000298552	NM_001162426.1	797	Cag/Tag	18/23	0.560401488215167	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.560401488215167	2		356	428	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226180	53226180	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	302	226	0	ENST00000375401.3:c.2669C>G	p.Ala890Gly	p.A890G	ENST00000375401	NM_004187.3	890	gCc/gGc	19/26	0.520867015072626	2	FACETS	0.874	0.843	0.904			1	CLONAL	3	TRUE	NA	0.560401488215167	2		226	411	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205836	108205836	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	199	220	0	ENST00000278616.4:c.8151G>C	p.Lys2717Asn	p.K2717N	ENST00000278616	NM_000051.3	2717	aaG/aaC	55/63	0.560401488215167	6	FACETS	1	0.986	1	0.823	0.767	0.881	CLONAL	2	TRUE	3	0.560401488215167	6		220	610	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702512	52702513	+	splice_donor_variant	Splice_Site	INS	-	-	C	novel	NA	P-0056296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	88	217	0	ENST00000394830.3:c.384+1dup		p.X128_splice	ENST00000394830	NM_018313.4	128			1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.560401488215167	2		217	292	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214427	55214427	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	49	294	0	ENST00000275493.2:c.553G>T	p.Gly185Cys	p.G185C	ENST00000275493	NM_005228.3	185	Ggc/Tgc	4/28	1	2	FACETS	0.393	0.333	0.459	0.393	0.333	0.459	SUBCLONAL	1	TRUE	1	0.560401488215167	2		294	445	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	42	365	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.29	2		365	247	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934573	NA	P-0056332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	93	758	0	ENST00000269305.4:c.722C>A	p.Ser241Tyr	p.S241Y	ENST00000269305	NM_001126112.2	241	tCc/tAc	7/11	1	2	FACETS	0.802	0.712	0.897	0.802	0.712	0.897	CLONAL	1	TRUE	1	0.29	2		758	800	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244091	153244091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	85	572	2	ENST00000281708.4:c.2066G>A	p.Arg689Gln	p.R689Q	ENST00000281708	NM_033632.3	689	cGg/cAg	12/12	1	2	FACETS	0.827	0.731	0.93	0.827	0.731	0.93	CLONAL	1	TRUE	1	0.29	2		574	709	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2218149	2218149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757105676	NA	P-0056332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	81	1100	0	ENST00000326181.6:c.211C>T	p.Arg71Trp	p.R71W	ENST00000326181	NM_032271.2	71	Cgg/Tgg	4/21	1	2	FACETS	0.605	0.531	0.683	0.605	0.531	0.683	SUBCLONAL	1	TRUE	1	0.29	2		1100	924	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385240	41385240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	105	738	0	ENST00000373198.4:c.721C>T	p.Arg241Cys	p.R241C	ENST00000373198	NM_133170.3	241	Cgt/Tgt	6/32	1	2	FACETS	0.826	0.739	0.918	0.826	0.739	0.918	CLONAL	1	TRUE	1	0.29	2		738	877	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110085	115110086	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0056332-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	58	977	1	ENST00000257566.3:c.1792_1793delinsTT	p.Gly598Leu	p.G598L	ENST00000257566	NM_016569.3	598	GGa/TTa	8/8	1	2	FACETS	0.383	0.327	0.444	0.383	0.327	0.444	SUBCLONAL	1	TRUE	1	0.29	2		978	1045	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0056335-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	90	447	1	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.396372225719682	2		448	421	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0056335-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	165	1198	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	0.937	0.86	1	0.937	0.86	1	CLONAL	1	TRUE	1	0.396372225719682	2		1198	889	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182195	99182205	+	frameshift_variant	Frame_Shift_Del	DEL	TCCGCAGACAT	TCCGCAGACAT	-	novel	NA	P-0056335-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	54	743	0	ENST00000074304.5:c.2260_2270del	p.Ser754AlafsTer12	p.S754Afs*12	ENST00000074304	NM_001134224.1	754	TCCGCAGACATg/g	21/26	1	2	FACETS	0.402	0.343	0.468	0.402	0.343	0.468	SUBCLONAL	1	TRUE	1	0.396372225719682	2		743	677	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251236	115251236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056366-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	210	543	0	ENST00000369535.4:c.490C>T	p.Arg164Cys	p.R164C	ENST00000369535	NM_002524.4	164	Cgc/Tgc	5/7	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.716053294533284	2		543	563	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0056412-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	66	259	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	0.389997823638035	3	FACETS	1	0.941	1	0.569	0.497	0.646	CLONAL	1	TRUE	1	0.40271233050461	3		259	346	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0056412-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	116	585	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.40271233050461	2		586	512	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1232964733	NA	P-0056412-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	28	100	0	ENST00000324856.7:c.1015del	p.Ala339LeufsTer24	p.A339Lfs*24	ENST00000324856	NM_006015.4	337	tGg/tg	1/20	0.40271233050461	2	FACETS	1	0.94	1	0.717	0.587	0.856	CLONAL	1	TRUE	0	0.40271233050461	2		100	97	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0056412-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	78	314	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.40271233050461	2		314	359	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287210	46287210	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056412-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	65	317	0	ENST00000334344.6:c.5155A>T	p.Thr1719Ser	p.T1719S	ENST00000334344	NM_152641.2	1719	Act/Tct	19/21	1	2	FACETS	0.922	0.804	1	0.922	0.804	1	CLONAL	1	TRUE	1	0.40271233050461	2		317	350	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604764	48604765	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0056412-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	181	331	0	ENST00000342988.3:c.1587_1588insAA	p.His530AsnfsTer8	p.H530Nfs*8	ENST00000342988	NM_005359.5	529	tta/ttAAa	12/12	0.390313363469776	2	FACETS	0.958	0.893	1	0.958	0.893	1	CLONAL	2	TRUE	0	0.40271233050461	2		331	469	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165710	185165710	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056412-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	98	326	0	ENST00000265026.3:c.985C>A	p.Pro329Thr	p.P329T	ENST00000265026	NM_004721.4	329	Cct/Act	5/14	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.40271233050461	2		326	463	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877154	151877154	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs767365126	NA	P-0056412-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	163	407	0	ENST00000262189.6:c.7207C>T	p.Arg2403Ter	p.R2403*	ENST00000262189	NM_170606.2	2403	Cga/Tga	37/59	0.389997823638035	3	FACETS	0.914	0.844	0.986	0.914	0.844	0.986	CLONAL	2	TRUE	1	0.40271233050461	3		407	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579709	7579710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0056414-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	206	686	1	ENST00000269305.4:c.86dup	p.Asn29LysfsTer14	p.N29Kfs*14	ENST00000269305	NM_001126112.2	29	aac/aaAc	3/11	0.602642882219799	3	FACETS	0.892	0.848	0.934	0.892	0.848	0.934	CLONAL	3	TRUE	0	0.658386905881126	3		687	311	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998978	11998978	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056414-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	116	354	0	ENST00000353533.5:c.480C>A	p.Tyr160Ter	p.Y160*	ENST00000353533	NM_003010.3	160	taC/taA	4/11	0.602642882219799	3	FACETS	0.964	0.906	1	0.964	0.906	1	CLONAL	3	TRUE	0	0.658386905881126	3		354	162	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670270	134670270	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056414-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	77	609	0	ENST00000398015.3:c.181T>G	p.Cys61Gly	p.C61G	ENST00000398015	NM_004441.4	61	Tgc/Ggc	3/16	0.658386905881126	3	FACETS	0.948	0.839	1	0.474	0.419	0.532	CLONAL	1	TRUE	1	0.658386905881126	3		609	328	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0056415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	125	410	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.50334571318875	5	FACETS	0.907	0.834	0.981	0.907	0.834	0.981	CLONAL	3	TRUE	2	0.543178736302887	5		410	307	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143272	108143272	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	92	340	0	ENST00000278616.4:c.3091G>T	p.Glu1031Ter	p.E1031*	ENST00000278616	NM_000051.3	1031	Gag/Tag	21/63	0.543178736302887	2	FACETS	0.996	0.913	1	0.996	0.913	1	CLONAL	2	TRUE	0	0.543178736302887	2		340	170	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420204	49420205	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	82	650	0	ENST00000301067.7:c.15544_15545insT	p.Gly5182ValfsTer17	p.G5182Vfs*17	ENST00000301067	NM_003482.3	5182	ggc/gTgc	48/54	0.543178736302887	3	FACETS	1	0.938	1	0.542	0.482	0.606	CLONAL	1	TRUE	1	0.543178736302887	3		650	354	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440403	49440403	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	90	814	0	ENST00000301067.7:c.4407G>A	p.Trp1469Ter	p.W1469*	ENST00000301067	NM_003482.3	1469	tgG/tgA	15/54	0.543178736302887	3	FACETS	0.982	0.876	1	0.491	0.438	0.547	CLONAL	1	TRUE	1	0.543178736302887	3		814	429	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557636	21557636	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	65	729	0	ENST00000382592.4:c.2209G>A	p.Asp737Asn	p.D737N	ENST00000382592	NM_014572.2	737	Gac/Aac	5/8	0.525923024363755	3	FACETS	0.96	0.839	1	0.48	0.419	0.545	CLONAL	1	TRUE	1	0.543178736302887	3		729	317	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32890605	32890605	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	38	328	0	ENST00000380152.3:c.8T>A	p.Ile3Asn	p.I3N	ENST00000380152		3	aTt/aAt	2/27	0.525923024363755	3	FACETS	0.978	0.818	1	0.489	0.409	0.576	CLONAL	1	TRUE	1	0.543178736302887	3		328	182	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458647	12458647	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	58	403	0	ENST00000287820.6:c.1264A>T	p.Ser422Cys	p.S422C	ENST00000287820	NM_015869.4	422	Agt/Tgt	6/7	0.519147048032176	4	FACETS	1	0.962	1	0.662	0.575	0.755	CLONAL	1	TRUE	2	0.543178736302887	4		403	249	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880891	134880891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	65	612	0	ENST00000398015.3:c.1454G>T	p.Arg485Met	p.R485M	ENST00000398015	NM_004441.4	485	aGg/aTg	7/16	0.519147048032176	4	FACETS	1	0.872	1	0.5	0.436	0.57	CLONAL	1	TRUE	2	0.543178736302887	4		612	369	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188869	32188869	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs141236527	NA	P-0056415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	158	784	1	ENST00000375023.3:c.685C>A	p.Pro229Thr	p.P229T	ENST00000375023	NM_004557.3	229	Cca/Aca	4/30	0.543178736302887	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	1	0.543178736302887	3		785	364	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518423	8518423	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	65	274	0	ENST00000356435.5:c.968C>G	p.Pro323Arg	p.P323R	ENST00000356435		323	cCc/cGc	10/35	0.411819326506744	4	FACETS	0.988	0.873	1	0.988	0.873	1	CLONAL	2	TRUE	2	0.543178736302887	4		274	187	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0056418-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	44	561	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.851	0.713	1	0.851	0.713	1	CLONAL	1	TRUE	1	0.15	2		561	689	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0056463-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	85	331	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.862	0.775	0.951	0.862	0.775	0.951	CLONAL	1	FALSE	1	0.83598842947477	2		331	236	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056463-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	224	603	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.825830005641561	1	FACETS	0.925	0.882	0.967	0.925	0.882	0.967	CLONAL	1	FALSE	0	0.83598842947477	1		603	337	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457242	25457242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147001633	NA	P-0056463-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	242	665	4	ENST00000264709.3:c.2645G>A	p.Arg882His	p.R882H	ENST00000264709	NM_175629.2	882	cGc/cAc	23/23	1	2	FACETS	0.965	0.908	1	0.965	0.908	1	CLONAL	1	FALSE	1	0.83598842947477	2		669	600	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702340	47702340	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056463-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	105	393	0	ENST00000233146.2:c.1936G>T	p.Asp646Tyr	p.D646Y	ENST00000233146	NM_000251.2	646	Gat/Tat	12/16	1	2	FACETS	0.92	0.838	1	0.92	0.838	1	CLONAL	1	FALSE	1	0.83598842947477	2		393	273	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350570	89350572	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0056463-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	169	676	0	ENST00000301030.4:c.2378_2380del	p.Lys793del	p.K793del	ENST00000301030	NM_001256183.1	793	aAGAtt/att	9/13	0.12590757117578	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.83598842947477	0		676	502	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411929	63411929	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056463-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	220	943	0	ENST00000330258.3:c.1238C>G	p.Ala413Gly	p.A413G	ENST00000330258	NM_152424.3	413	gCc/gGc	2/2	0.142333860832222	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.83598842947477	0		943	492	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937270	76937270	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs868928195	NA	P-0056463-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	91	459	0	ENST00000373344.5:c.3478G>C	p.Glu1160Gln	p.E1160Q	ENST00000373344	NM_000489.3	1160	Gaa/Caa	9/35	0.142333860832222	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.83598842947477	0		459	242	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0056468-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	221	298	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.601282866772551	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.601282866772551	1		298	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0056468-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	283	542	0	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	0.601282866772551	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.601282866772551	1		542	627	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247169	153247169	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056468-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	166	278	0	ENST00000281708.4:c.1633T>C	p.Tyr545His	p.Y545H	ENST00000281708	NM_033632.3	545	Tat/Cat	10/12	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.601282866772551	2		278	536	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0056471-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	209	574	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.506001368541287	2		574	820	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056471-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	196	549	2	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.506001368541287	2		551	767	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116126	67116127	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056471-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	151	333	1	ENST00000412916.2:c.411dup	p.Leu138IlefsTer7	p.L138Ifs*7	ENST00000412916		137	gca/gcAa	5/6	0.506001368541287	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.506001368541287	1		334	410	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835596	68835605	+	frameshift_variant	Frame_Shift_Del	DEL	CGACAAAGGA	CGACAAAGGA	-	novel	NA	P-0056471-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	144	476	0	ENST00000261769.5:c.188_197del	p.Arg63GlnfsTer17	p.R63Qfs*17	ENST00000261769	NM_004360.3	63	CGACAAAGGAca/ca	3/16	0.506001368541287	1	FACETS	0.866	0.795	0.939	0.866	0.795	0.939	CLONAL	1	TRUE	0	0.506001368541287	1		476	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0056503-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	389	820	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.755626169268615	2	FACETS	0.981	0.95	1	0.981	0.95	1	CLONAL	2	TRUE	0	0.755626169268615	2		820	525	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743988	41743988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776310618	NA	P-0056503-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	245	913	1	ENST00000301178.4:c.923G>A	p.Arg308His	p.R308H	ENST00000301178	NM_021913.4	308	cGc/cAc	7/20	0.6777485656322	4	FACETS	0.887	0.827	0.948			1	CLONAL	1	TRUE	NA	0.755626169268615	4		914	1284	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942771	44942773	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs398122829	NA	P-0056503-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	156	317	0	ENST00000377967.4:c.3354_3356del	p.Leu1119del	p.L1119del	ENST00000377967	NM_021140.2	1117	aaTCTt/aat	23/29	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.755626169268615	1		317	195	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427258	49427258	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056503-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	225	806	0	ENST00000301067.7:c.11230C>T	p.Gln3744Ter	p.Q3744*	ENST00000301067	NM_003482.3	3744	Cag/Tag	39/54	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.755626169268615	2		806	523	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545981	41545981	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056503-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	493	772	0	ENST00000263253.7:c.2597del	p.Pro866LeufsTer80	p.P866Lfs*80	ENST00000263253	NM_001429.3	866	Cct/ct	14/31	0.311825819973481	3	FACETS	0.976	0.94	1	0.651	0.627	0.675	INDETERMINATE	2	TRUE	0	0.755626169268615	3		772	921	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753384	42753385	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0056509-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	435	971	0	ENST00000222329.4:c.879dup	p.Pro294AlafsTer15	p.P294Afs*15	ENST00000222329	NM_006494.2	293	-/G	4/4	0.12966564611963	3	FACETS	0.962	0.919	1			1	INDETERMINATE	3	FALSE	NA	0.3	3		971	1155	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056511-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1320	490	664	0	ENST00000267101.3:c.310G>C	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ctg	3/28	0.299307183213087	3	FACETS	1	0.985	1			1	CLONAL	2	TRUE	NA	0.29	3		664	1810	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0056511-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	228	679	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	0.269943110068406	1	FACETS	0.985	0.916	1	0.985	0.916	1	CLONAL	1	TRUE	0	0.29	1		679	1365	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143985	11143985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056511-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	78	448	0	ENST00000358026.2:c.3566G>A	p.Arg1189Gln	p.R1189Q	ENST00000358026	NM_001128849.1	1189	cGa/cAa	26/36	1	2	FACETS	0.523	0.458	0.593	0.523	0.458	0.593	SUBCLONAL	1	TRUE	1	0.29	2		448	1029	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844229	68844229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056511-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	161	438	0	ENST00000261769.5:c.817G>A	p.Glu273Lys	p.E273K	ENST00000261769	NM_004360.3	273	Gaa/Aaa	6/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.29	2		438	966	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576048	29576048	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854559	NA	P-0056511-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	70	321	0	ENST00000356175.3:c.4021C>T	p.Gln1341Ter	p.Q1341*	ENST00000356175	NM_000267.3	1341	Cag/Tag	30/57	0.269943110068406	1	FACETS	0.702	0.612	0.799	0.702	0.612	0.799	SUBCLONAL	1	TRUE	0	0.29	1		321	588	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591104	67591115	+	inframe_deletion	In_Frame_Del	DEL	TTAAACCAGACC	TTAAACCAGACC	-	novel	NA	P-0056511-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	29	199	0	ENST00000274335.5:c.1700_1711del	p.Lys567_Leu570del	p.K567_L570del	ENST00000274335		566	aTTAAACCAGACCtt/att	12/15	1	2	FACETS	0.588	0.472	0.719	0.588	0.472	0.719	SUBCLONAL	1	TRUE	1	0.29	2		199	340	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0056556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	15	227	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.677	0.495	0.896	0.677	0.495	0.896	SUBCLONAL	1	TRUE	1	0.16	2		228	277	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477136	67477136	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	103	879	0	ENST00000327367.4:c.943G>T	p.Val315Phe	p.V315F	ENST00000327367	NM_005902.3	315	Gtc/Ttc	7/9	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.16	2		879	1268	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256333	16256334	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0056556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	59	590	0	ENST00000375759.3:c.3598_3599delinsTT	p.Asp1200Phe	p.D1200F	ENST00000375759	NM_015001.2	1200	GAt/TTt	11/15	1	2	FACETS	0.783	0.672	0.905	0.783	0.672	0.905	CLONAL	1	TRUE	1	0.16	2		590	942	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223156	1223156	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1242	80	909	0	ENST00000326873.7:c.1093G>A	p.Asp365Asn	p.D365N	ENST00000326873	NM_000455.4	365	Gac/Aac	8/10	1	2	FACETS	0.756	0.663	0.857	0.756	0.663	0.857	SUBCLONAL	1	TRUE	1	0.16	2		909	1322	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183799	10183805	+	frameshift_variant	Frame_Shift_Del	DEL	AACTTCG	AACTTCG	-	novel	NA	P-0056556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	49	738	0	ENST00000256474.2:c.269_275del	p.Asn90ThrfsTer67	p.N90Tfs*67	ENST00000256474	NM_000551.3	90	AACTTCGac/ac	1/3	1	2	FACETS	0.675	0.57	0.792	0.675	0.57	0.792	SUBCLONAL	1	TRUE	1	0.16	2		738	907	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0056576-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	74	335	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.595	0.523	0.671	0.595	0.523	0.671	SUBCLONAL	1	TRUE	1	0.631705991944452	2		335	394	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189448	56189448	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056576-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	153	639	0	ENST00000399503.3:c.4480C>T	p.Gln1494Ter	p.Q1494*	ENST00000399503	NM_005921.1	1494	Cag/Tag	20/20	1	2	FACETS	0.513	0.469	0.559	0.513	0.469	0.559	SUBCLONAL	1	TRUE	1	0.631705991944452	2		639	944	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041037	112041037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761032788	NA	P-0056576-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	152	630	0	ENST00000368678.4:c.218C>T	p.Thr73Met	p.T73M	ENST00000368678		73	aCg/aTg	3/13	1	2	FACETS	0.484	0.442	0.528	0.484	0.442	0.528	SUBCLONAL	1	TRUE	1	0.631705991944452	2		630	995	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870966	12870966	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056576-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	136	555	0	ENST00000228872.4:c.193C>T	p.Gln65Ter	p.Q65*	ENST00000228872	NM_004064.3	65	Cag/Tag	1/3	1	2	FACETS	0.476	0.432	0.522	0.476	0.432	0.522	SUBCLONAL	1	TRUE	1	0.631705991944452	2		555	905	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553356	106553356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056576-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	167	669	0	ENST00000369096.4:c.1321C>T	p.Pro441Ser	p.P441S	ENST00000369096	NM_001198.3	441	Ccg/Tcg	5/7	1	2	FACETS	0.569	0.522	0.617	0.569	0.522	0.617	SUBCLONAL	1	TRUE	1	0.631705991944452	2		669	930	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577151	7577156	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	TACCAC	TACCAC	-	novel	NA	P-0056584-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	145	649	0	ENST00000269305.4:c.783-1_787del		p.X261_splice	ENST00000269305	NM_001126112.2	261		8/11	0.30894193379324	2	FACETS	0.888	0.815	0.962	0.888	0.815	0.962	CLONAL	2	TRUE	0	0.329986246451532	2		649	495	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170481	108170481	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056584-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	43	320	0	ENST00000278616.4:c.5046T>G	p.Asp1682Glu	p.D1682E	ENST00000278616	NM_000051.3	1682	gaT/gaG	34/63	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.329986246451532	2		320	248	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970942	79970942	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1288602933	NA	P-0056584-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	65	587	0	ENST00000265081.6:c.1168A>G	p.Ile390Val	p.I390V	ENST00000265081	NM_002439.4	390	Att/Gtt	7/24	0.18902392708319	2	FACETS	0.791	0.687	0.903	0.396	0.343	0.452	INDETERMINATE	1	TRUE	0	0.329986246451532	2		587	498	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577151	7577156	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	TACCAC	TACCAC	-	novel	NA	P-0056584-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	91	649	0	ENST00000269305.4:c.783-1_787del		p.X261_splice	ENST00000269305	NM_001126112.2	261		8/11	0.390509562204465	3	FACETS	1	0.961	1	0.751	0.678	0.825	CLONAL	2	TRUE	0	0.400921349669283	3		649	242	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170481	108170481	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056584-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	36	320	0	ENST00000278616.4:c.5046T>G	p.Asp1682Glu	p.D1682E	ENST00000278616	NM_000051.3	1682	gaT/gaG	34/63	0.400921349669283	3	FACETS	0.921	0.775	1	0.921	0.775	1	CLONAL	2	TRUE	1	0.400921349669283	3		320	117	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970942	79970942	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1288602933	NA	P-0056584-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	29	587	0	ENST00000265081.6:c.1168A>G	p.Ile390Val	p.I390V	ENST00000265081	NM_002439.4	390	Att/Gtt	7/24	0.400921349669283	3	FACETS	1	0.91	1	0.607	0.494	0.732	CLONAL	1	TRUE	1	0.400921349669283	3		587	143	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577151	7577156	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	TACCAC	TACCAC	-	novel	NA	P-0056584-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	214	649	0	ENST00000269305.4:c.783-1_787del		p.X261_splice	ENST00000269305	NM_001126112.2	261		8/11	0.514620138239708	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.514620138239708	1		649	613	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170481	108170481	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056584-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	104	320	0	ENST00000278616.4:c.5046T>G	p.Asp1682Glu	p.D1682E	ENST00000278616	NM_000051.3	1682	gaT/gaG	34/63	0.38730841497726	1	FACETS	0.984	0.893	1	0.984	0.893	1	CLONAL	1	TRUE	0	0.514620138239708	1		320	305	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970942	79970942	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1288602933	NA	P-0056584-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	145	587	0	ENST00000265081.6:c.1168A>G	p.Ile390Val	p.I390V	ENST00000265081	NM_002439.4	390	Att/Gtt	7/24	0.241930606701737	2	FACETS	0.912	0.835	0.992	0.456	0.417	0.496	INDETERMINATE	1	TRUE	0	0.514620138239708	2		587	618	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720650	89720650	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0056647-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	27	161	0	ENST00000371953.3:c.802-1G>C		p.X268_splice	ENST00000371953	NM_000314.4	268			0.681601224216616	2	FACETS	0.579	0.467	0.702	0.289	0.233	0.351	SUBCLONAL	1	TRUE	0	0.712202822764023	2		161	131	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551457	150551457	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056647-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	72	630	0	ENST00000369026.2:c.550C>G	p.Arg184Gly	p.R184G	ENST00000369026	NM_021960.4	184	Cgg/Ggg	1/3	0.173401344530139	3	FACETS	0.312	0.272	0.356	0.104	0.09	0.119	INDETERMINATE	1	TRUE	0	0.712202822764023	3		630	879	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266822	18266822	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753372060	NA	P-0056647-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	127	272	0	ENST00000222254.8:c.133G>A	p.Glu45Lys	p.E45K	ENST00000222254	NM_005027.3	45	Gag/Aag	2/16	0.712202822764023	2	FACETS	0.914	0.837	0.995	0.457	0.418	0.498	CLONAL	1	TRUE	0	0.712202822764023	2		272	390	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670099	29670099	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056647-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	215	353	1	ENST00000356175.3:c.7072G>T	p.Gly2358Ter	p.G2358*	ENST00000356175	NM_000267.3	2358	Gga/Tga	47/57	0.702345265632318	2	FACETS	0.964	0.92	1	0.964	0.92	1	CLONAL	2	TRUE	0	0.712202822764023	2		354	313	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361232	66361232	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056647-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	90	270	0	ENST00000273854.3:c.940C>A	p.Pro314Thr	p.P314T	ENST00000273854	NM_004439.5	314	Cct/Act	4/18	1	2	FACETS	0.795	0.713	0.88	0.795	0.713	0.88	SUBCLONAL	1	TRUE	1	0.712202822764023	2		270	318	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560460	65560461	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0056647-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	295	389	0	ENST00000358664.4:c.136_137del	p.Leu46AlafsTer40	p.L46Afs*40	ENST00000358664	NM_002382.4	46	TTg/g	3/5	0.684473474585592	2	FACETS	0.874	0.836	0.911	0.874	0.836	0.911	CLONAL	2	TRUE	0	0.712202822764023	2		389	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578480	7578498	+	frameshift_variant	Frame_Shift_Del	DEL	TGTGGAATCAACCCACAGC	TGTGGAATCAACCCACAGC	-	novel	NA	P-0056647-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	683	633	0	ENST00000269305.4:c.432_450del	p.Gln144HisfsTer20	p.Q144Hfs*20	ENST00000269305	NM_001126112.2	144	caGCTGTGGGTTGATTCCACA/ca	5/11	0.702345265632318	2	FACETS	0.993	0.968	1	0.993	0.968	1	CLONAL	2	TRUE	0	0.712202822764023	2		633	966	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971261	15971261	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056647-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	385	434	0	ENST00000268712.3:c.4688A>T	p.His1563Leu	p.H1563L	ENST00000268712	NM_006311.3	1563	cAc/cTc	32/46	0.702345265632318	2	FACETS	0.996	0.962	1	0.996	0.962	1	CLONAL	2	TRUE	0	0.712202822764023	2		434	543	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692895	89692896	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056647-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	54	277	0	ENST00000371953.3:c.379_380insA	p.Gly127GlufsTer53	p.G127Efs*53	ENST00000371953	NM_000314.4	127	gga/gAga	5/9	0.681601224216616				0.678	0.891				SUBCLONAL	1	TRUE	0	0.712202822764023	2		277	194	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858800	9858800	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs768337205	NA	P-0056647-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	35	160	0	ENST00000330684.3:c.2601C>G	p.Ile867Met	p.I867M	ENST00000330684	NM_001134407.1	867	atC/atG	13/13	1	2	FACETS	0.388	0.32	0.464	0.388	0.32	0.464	SUBCLONAL	1	TRUE	1	0.712202822764023	2		160	253	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577123	7577123	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876660333	NA	P-0056655-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	457	488	0	ENST00000269305.4:c.815T>G	p.Val272Gly	p.V272G	ENST00000269305	NM_001126112.2	272	gTg/gGg	8/11	0.666479065470486	2	FACETS	0.916	0.885	0.947	0.916	0.885	0.947	CLONAL	2	TRUE	0	0.698552722831317	2		488	714	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242470	+	missense_variant	Missense_Mutation	DNP	TT	TT	CC	rs397517096	NA	P-0056655-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	485	258	0	ENST00000275493.2:c.2239_2240delinsCC	p.Leu747Pro	p.L747P	ENST00000275493	NM_005228.3	747	TTa/CCa	19/28	0.698552722831317	5	FACETS	0.983	0.952	1	0.983	0.952	1	CLONAL	4	TRUE	1	0.698552722831317	5		258	723	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449815	149449815	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs750922001	NA	P-0056655-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	283	594	0	ENST00000286301.3:c.1249C>A	p.Leu417Ile	p.L417I	ENST00000286301	NM_005211.3	417	Ctt/Att	9/22	1	2	FACETS	0.953	0.899	1	0.953	0.899	1	CLONAL	1	TRUE	1	0.698552722831317	2		594	850	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198282	138198282	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056655-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	77	156	0	ENST00000237289.4:c.875del	p.Thr292LysfsTer7	p.T292Kfs*7	ENST00000237289	NM_001270507.1	292	aCa/aa	6/9	0.698552722831317	3	FACETS	0.877	0.776	0.984	0.439	0.388	0.492	CLONAL	1	TRUE	1	0.698552722831317	3		156	339	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115972	8115973	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0056667-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	199	452	0	ENST00000346208.3:c.1320dup	p.Ala441ArgfsTer66	p.A441Rfs*66	ENST00000346208		440	acc/aCcc	6/6	1	2	FACETS	0.9	0.837	0.965	1	0.993	1	CLONAL	2	FALSE	1	0.317156831281571	2		452	697	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433370	49433370	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056667-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	407	896	1	ENST00000301067.7:c.8077C>T	p.Gln2693Ter	p.Q2693*	ENST00000301067	NM_003482.3	2693	Cag/Tag	32/54	1	2	FACETS	1	0.981	1	1	0.997	1	CLONAL	2	FALSE	1	0.317156831281571	2		897	1213	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0056668-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	213	619	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.81	0.761	0.859	1	0.993	1	CLONAL	2	TRUE	1	0.546877356132104	2		619	481	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0056668-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	126	179	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.546877356132104	1	FACETS	0.999	0.917	1	0.999	0.917	1	CLONAL	1	TRUE	0	0.546877356132104	1		180	335	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849869	156849869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056668-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	110	825	0	ENST00000524377.1:c.2125G>A	p.Asp709Asn	p.D709N	ENST00000524377	NM_002529.3	709	Gac/Aac	16/17	1	2	FACETS	0.929	0.84	1	0.929	0.84	1	CLONAL	1	TRUE	1	0.546877356132104	2		825	433	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570754	226570754	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056668-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	125	612	0	ENST00000366794.5:c.1142A>T	p.Asn381Ile	p.N381I	ENST00000366794	NM_001618.3	381	aAc/aTc	8/23	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.546877356132104	2		612	420	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549110	21549110	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056668-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	97	671	0	ENST00000382592.4:c.3166C>G	p.Pro1056Ala	p.P1056A	ENST00000382592	NM_014572.2	1056	Cca/Gca	8/8	0.546877356132104	1	FACETS	0.927	0.839	1	0.927	0.839	1	CLONAL	1	TRUE	0	0.546877356132104	1		671	278	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925182	81925182	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056668-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	125	561	0	ENST00000359376.3:c.973del	p.Ser325ArgfsTer77	p.S325Rfs*77	ENST00000359376	NM_002661.3	325	Tcg/cg	11/33	0.389427309830328	1	FACETS	0.743	0.677	0.811	0.743	0.677	0.811	SUBCLONAL	1	TRUE	0	0.546877356132104	1		561	447	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119926	70119942	+	frameshift_variant	Frame_Shift_Del	DEL	CACGGCCAGGTCACCTA	CACGGCCAGGTCACCTA	-	novel	NA	P-0056668-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	86	643	0	ENST00000245479.2:c.933_949del	p.Val313LeufsTer259	p.V313Lfs*259	ENST00000245479	NM_000346.3	310	CACGGCCAGGTCACCTAc/c	3/3	1	2	FACETS	0.848	0.755	0.945	0.848	0.755	0.945	CLONAL	1	TRUE	1	0.546877356132104	2		643	371	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48574825	48575095	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTCACTTTTTACATTTTTAAAACCTGAGCACAGGCCTTGAAATTATACCAAGGTTTAAATTCTAGGTCTGATGTATGACATGGCCAAGTTAGTTATTGTGAATTTTAGTTTTCTTATTTATGAAATGGGGATTGTAATACTGAGTTGGTAGGATTGTGAGGATTAAATCAGAATATATAAAAGTGTCTTGCATAATGTGACACATGAATAAATGGTCGTTTATTTTTCTAGGTGGCTGGTCGGAAAGGATTTCCTCATGTGATCTATGCCC	GTCACTTTTTACATTTTTAAAACCTGAGCACAGGCCTTGAAATTATACCAAGGTTTAAATTCTAGGTCTGATGTATGACATGGCCAAGTTAGTTATTGTGAATTTTAGTTTTCTTATTTATGAAATGGGGATTGTAATACTGAGTTGGTAGGATTGTGAGGATTAAATCAGAATATATAAAAGTGTCTTGCATAATGTGACACATGAATAAATGGTCGTTTATTTTTCTAGGTGGCTGGTCGGAAAGGATTTCCTCATGTGATCTATGCCC	-	novel	NA	P-0056668-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	33	20	0	ENST00000342988.3:c.250-228_292del		p.X84_splice	ENST00000342988	NM_005359.5	84		3/12	0.546877356132104	1	FACETS	0.622	0.515	0.738	0.622	0.515	0.738	SUBCLONAL	1	TRUE	0	0.546877356132104	1		20	141	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393308	393308	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056668-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	109	619	0	ENST00000380956.4:c.156C>G	p.Ile52Met	p.I52M	ENST00000380956	NM_001195286.1	52	atC/atG	2/9	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.546877356132104	2		619	364	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0056671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	97	326	6	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.243803000902811	3	FACETS	1	0.952	1	0.56	0.499	0.624	CLONAL	1	TRUE	1	0.308225071109278	3		332	649	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0056671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	125	651	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	0.922	0.834	1	0.922	0.834	1	CLONAL	1	TRUE	1	0.308225071109278	2		651	880	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023637	27023638	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTCCAAGCCGC	novel	NA	P-0056671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	21	207	0	ENST00000324856.7:c.748_758dup	p.Ser255ArgfsTer112	p.S255Rfs*112	ENST00000324856	NM_006015.4	248	ggc/ggCTCCAAGCCGCc	1/20	1	2	FACETS	0.699	0.541	0.881	0.699	0.541	0.881	SUBCLONAL	1	TRUE	1	0.308225071109278	2		207	195	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	91	410	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.349786589379144	2		410	378	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	208	292	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.976	1	1	0.994	1	CLONAL	2	TRUE	1	0.349786589379144	2		292	547	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882049	36882050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs780753361	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1242	66	834	1	ENST00000358127.4:c.963dup	p.Ala322ArgfsTer19	p.A322Rfs*19	ENST00000358127	NM_001280556.1	321	-/C	8/10	1	2	FACETS	0.289	0.249	0.332	0.289	0.249	0.332	SUBCLONAL	1	TRUE	1	0.349786589379144	2		835	1308	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	221	454	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.983	1	1	0.995	1	CLONAL	2	TRUE	1	0.349786589379144	2		460	561	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	526	662	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.873	0.839	0.906	1	0.998	1	CLONAL	3	TRUE	1	0.349786589379144	2		664	1149	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	150	456	5	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.349786589379144	2		461	709	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803738	1803738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774047997	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	308	802	0	ENST00000260795.2:c.916G>A	p.Val306Ile	p.V306I	ENST00000260795		306	Gtt/Att	6/17	1	2	FACETS	0.756	0.712	0.8	1	0.994	1	SUBCLONAL	2	TRUE	1	0.349786589379144	2		802	1165	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	158	521	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.349786589379144	2		527	649	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	162	623	2	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.349786589379144	2		625	765	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108185	209108185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751364381	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	30	385	0	ENST00000345146.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000345146	NM_005896.2	222	Cgt/Tgt	6/10	1	2	FACETS	0.451	0.364	0.551	0.451	0.364	0.551	SUBCLONAL	1	TRUE	1	0.349786589379144	2		385	380	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	227	711	1	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.349786589379144	2		712	940	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349090	11349090	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	34	419	0	ENST00000332029.2:c.246del	p.Leu84Ter	p.L84*	ENST00000332029	NM_003745.1	82	ggG/gg	2/2	1	2	FACETS	0.29	0.236	0.351	0.29	0.236	0.351	SUBCLONAL	1	TRUE	1	0.349786589379144	2		419	670	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	298	991	5	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.349786589379144	2		996	1427	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221711	55221711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760101437	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	44	521	0	ENST00000275493.2:c.755G>A	p.Arg252His	p.R252H	ENST00000275493	NM_005228.3	252	cGc/cAc	7/28	1	2	FACETS	0.346	0.289	0.409	0.346	0.289	0.409	SUBCLONAL	1	TRUE	1	0.349786589379144	2		521	728	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	64	840	4	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.303	0.261	0.349	0.303	0.261	0.349	SUBCLONAL	1	TRUE	1	0.349786589379144	2		844	1208	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	318	804	7	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.349786589379144	2		811	1414	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874637	35874637	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	123	389	4	ENST00000303115.3:c.799del	p.Arg267GlyfsTer28	p.R267Gfs*28	ENST00000303115	NM_002185.3	265	Aaa/aa	6/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.349786589379144	2		393	554	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422384	47422384	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	170	634	0	ENST00000377045.4:c.23del	p.Pro8LeufsTer26	p.P8Lfs*26	ENST00000377045	NM_001654.4	6	ggC/gg	2/16	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.349786589379144	2		634	757	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922301	178922301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	65	343	0	ENST00000263967.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000263967	NM_006218.2	357	cGa/cAa	6/21	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.349786589379144	2		343	339	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	90	452	8	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.349786589379144	2		460	488	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100998	41100998	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772057709	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	217	703	0	ENST00000373198.4:c.1358G>A	p.Arg453His	p.R453H	ENST00000373198	NM_133170.3	453	cGc/cAc	8/32	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.349786589379144	2		703	1067	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851685	134851685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377348490	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	184	587	1	ENST00000398015.3:c.1091G>A	p.Arg364Gln	p.R364Q	ENST00000398015	NM_004441.4	364	cGg/cAg	5/16	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.349786589379144	2		588	772	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460504	8460504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148300682	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	188	493	0	ENST00000356435.5:c.3782C>T	p.Thr1261Met	p.T1261M	ENST00000356435		1261	aCg/aTg	22/35	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.349786589379144	2		493	856	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915588	131915588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769853458	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	33	227	1	ENST00000265335.6:c.586C>T	p.Arg196Cys	p.R196C	ENST00000265335		196	Cgt/Tgt	5/25	1	2	FACETS	0.983	0.808	1	0.983	0.808	1	CLONAL	1	TRUE	1	0.349786589379144	2		228	192	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954189	48954191	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	40	261	0	ENST00000267163.4:c.1396_1398del	p.Glu466del	p.E466del	ENST00000267163	NM_000321.2	464	GAA/-	15/27	1	2	FACETS	0.87	0.727	1	0.87	0.727	1	CLONAL	1	TRUE	1	0.349786589379144	2		261	263	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207168	1207168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520039	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	88	798	1	ENST00000326873.7:c.256C>T	p.Arg86Ter	p.R86*	ENST00000326873	NM_000455.4	86	Cga/Tga	1/10	1	2	FACETS	0.387	0.342	0.437	0.387	0.342	0.437	SUBCLONAL	1	TRUE	1	0.349786589379144	2		799	1299	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735609	204735609	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553657429	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	125	439	0	ENST00000302823.3:c.410C>T	p.Pro137Leu	p.P137L	ENST00000302823	NM_005214.4	137	cCg/cTg	2/4	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.349786589379144	2		439	638	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804304	43804304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763568293	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	61	682	1	ENST00000372470.3:c.304C>T	p.Arg102Cys	p.R102C	ENST00000372470	NM_005373.2	102	Cgt/Tgt	3/12	1	2	FACETS	0.314	0.27	0.363	0.314	0.27	0.363	SUBCLONAL	1	TRUE	1	0.349786589379144	2		683	1111	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384726	17384726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368554117	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	231	674	0	ENST00000359435.4:c.358G>A	p.Ala120Thr	p.A120T	ENST00000359435	NM_001033549.1	120	Gcc/Acc	4/9	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.349786589379144	2		674	1062	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945028	151945028	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	25	67	0	ENST00000262189.6:c.2491A>G	p.Thr831Ala	p.T831A	ENST00000262189	NM_170606.2	831	Act/Gct	14/59	1	2	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	TRUE	1	0.349786589379144	2		67	135	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245461	16245461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465789087	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	68	344	0	ENST00000375759.3:c.1436C>T	p.Ala479Val	p.A479V	ENST00000375759	NM_015001.2	479	gCg/gTg	7/15	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.349786589379144	2		344	352	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161938	47161939	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	93	451	0	ENST00000409792.3:c.4187dup	p.Asn1396LysfsTer2	p.N1396Kfs*2	ENST00000409792	NM_014159.6	1396	aat/aaAt	3/21	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.349786589379144	2		451	487	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410085	139410085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775217381	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1346	79	1023	2	ENST00000277541.6:c.1753G>A	p.Ala585Thr	p.A585T	ENST00000277541	NM_017617.3	585	Gcc/Acc	11/34	1	2	FACETS	0.317	0.277	0.36	0.317	0.277	0.36	SUBCLONAL	1	TRUE	1	0.349786589379144	2		1025	1425	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563051	21563051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	74	820	1	ENST00000382592.4:c.868C>T	p.Pro290Ser	p.P290S	ENST00000382592	NM_014572.2	290	Ccc/Tcc	4/8	1	2	FACETS	0.353	0.308	0.402	0.353	0.308	0.402	SUBCLONAL	1	TRUE	1	0.349786589379144	2		821	1199	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343647	343647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1212	76	887	1	ENST00000262320.3:c.2027G>A	p.Gly676Asp	p.G676D	ENST00000262320	NM_003502.3	676	gGc/gAc	8/11	1	2	FACETS	0.337	0.294	0.384	0.337	0.294	0.384	SUBCLONAL	1	TRUE	1	0.349786589379144	2		888	1288	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994829	73994829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751833994	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	82	315	1	ENST00000318443.5:c.313G>A	p.Ala105Thr	p.A105T	ENST00000318443	NM_001024736.1	105	Gca/Aca	3/10	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.349786589379144	2		316	433	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583310	46583310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770783327	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	155	375	0	ENST00000263734.3:c.238G>A	p.Glu80Lys	p.E80K	ENST00000263734	NM_001430.4	80	Gaa/Aaa	3/16	1	2	FACETS	0.751	0.691	0.814	1	0.989	1	SUBCLONAL	2	TRUE	1	0.349786589379144	2		375	590	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400033	139400033	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200232299	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	291	927	1	ENST00000277541.6:c.4315G>A	p.Asp1439Asn	p.D1439N	ENST00000277541	NM_017617.3	1439	Gac/Aac	25/34	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.349786589379144	2		928	1270	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911125	29911125	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199474508	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	153	487	0	ENST00000376809.5:c.424T>C	p.Tyr142His	p.Y142H	ENST00000376809	NM_002116.7	142	Tac/Cac	3/8	1	2	FACETS	0.77	0.708	0.834	1	0.989	1	SUBCLONAL	2	TRUE	1	0.349786589379144	2		487	568	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224532	36224532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759167832	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	295	954	1	ENST00000222270.7:c.6994C>T	p.Arg2332Cys	p.R2332C	ENST00000222270	NM_014727.1	2332	Cgt/Tgt	29/37	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.349786589379144	2		955	1309	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224183	36224183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771130237	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	199	774	1	ENST00000222270.7:c.6733G>A	p.Val2245Met	p.V2245M	ENST00000222270	NM_014727.1	2245	Gtg/Atg	28/37	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.349786589379144	2		775	918	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972794	25972794	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761581753	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	44	446	0	ENST00000435504.4:c.1631C>T	p.Ala544Val	p.A544V	ENST00000435504		544	gCg/gTg	12/13	1	2	FACETS	0.315	0.263	0.373	0.315	0.263	0.373	SUBCLONAL	1	TRUE	1	0.349786589379144	2		446	799	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100424	8100425	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs772396478	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	274	977	1	ENST00000346208.3:c.404dup	p.Ala136GlyfsTer167	p.A136Gfs*167	ENST00000346208		133	tac/taCc	3/6	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.349786589379144	2		978	1297	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919836	96919836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772153618	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	121	429	2	ENST00000258439.3:c.427G>A	p.Val143Ile	p.V143I	ENST00000258439	NM_001193304.2	143	Gtc/Atc	4/4	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.349786589379144	2		431	581	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660270	227660270	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	217	804	2	ENST00000305123.5:c.3185del	p.Gly1062AlafsTer8	p.G1062Afs*8	ENST00000305123	NM_005544.2	1062	gGc/gc	1/2	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.349786589379144	2		806	1009	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691874	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	124	378	0	ENST00000295754.5:c.381_383del	p.Lys128del	p.K128del	ENST00000295754	NM_003242.5	125	gAAAaa/gaa	3/7	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.349786589379144	2		378	539	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563413	21563413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150428840	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	278	957	1	ENST00000382592.4:c.506G>A	p.Arg169Gln	p.R169Q	ENST00000382592	NM_014572.2	169	cGg/cAg	4/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.349786589379144	2		958	1414	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652330	206652330	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1427	88	782	3	ENST00000367120.3:c.1042del	p.Arg348AspfsTer32	p.R348Dfs*32	ENST00000367120	NM_014002.3	346	gCc/gc	10/22	0.349786589379144	3	FACETS	0.39	0.344	0.44	0.195	0.172	0.22	SUBCLONAL	1	TRUE	1	0.349786589379144	3		785	1515	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804268	46804268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750244360	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	241	761	0	ENST00000290295.7:c.739C>T	p.Arg247Cys	p.R247C	ENST00000290295	NM_006361.5	247	Cgc/Tgc	2/2	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.349786589379144	2		761	1067	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952076	178952076	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	73	298	0	ENST00000263967.3:c.3131A>T	p.Asn1044Ile	p.N1044I	ENST00000263967	NM_006218.2	1044	aAt/aTt	21/21	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.349786589379144	2		298	398	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658880	3658880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149117119	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	83	581	1	ENST00000294008.3:c.86G>A	p.Arg29His	p.R29H	ENST00000294008	NM_032444.2	29	cGc/cAc	2/15	1	2	FACETS	0.541	0.476	0.61	0.541	0.476	0.61	SUBCLONAL	1	TRUE	1	0.349786589379144	2		582	878	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982968	201982968	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1233	65	718	0	ENST00000359651.3:c.817A>G	p.Thr273Ala	p.T273A	ENST00000359651		273	Acc/Gcc	7/8	0.349786589379144	3	FACETS	0.336	0.29	0.387	0.168	0.145	0.194	SUBCLONAL	1	TRUE	1	0.349786589379144	3		718	1298	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949319	71949319	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	199	801	0	ENST00000298229.2:c.3699G>T	p.Glu1233Asp	p.E1233D	ENST00000298229	NM_001567.3	1233	gaG/gaT	28/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.349786589379144	2		801	997	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77051739	77051741	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	233	586	0	ENST00000356341.3:c.1066_1068del	p.Val356del	p.V356del	ENST00000356341	NM_002576.4	356	GTG/-	11/15	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.349786589379144	2		586	1001	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158391	108158391	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs917721053	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	34	453	0	ENST00000278616.4:c.4058A>G	p.Glu1353Gly	p.E1353G	ENST00000278616	NM_000051.3	1353	gAg/gGg	27/63	1	2	FACETS	0.452	0.369	0.545	0.452	0.369	0.545	SUBCLONAL	1	TRUE	1	0.349786589379144	2		453	430	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420427	49420427	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1174064870	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	93	758	0	ENST00000301067.7:c.15322C>T	p.Arg5108Cys	p.R5108C	ENST00000301067	NM_003482.3	5108	Cgt/Tgt	48/54	1	2	FACETS	0.506	0.449	0.568	0.506	0.449	0.568	SUBCLONAL	1	TRUE	1	0.349786589379144	2		758	1050	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424764	49424764	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	304	809	0	ENST00000301067.7:c.13583del	p.Ala4528GlufsTer6	p.A4528Efs*6	ENST00000301067	NM_003482.3	4528	gCa/ga	40/54	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.349786589379144	2		809	1252	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865703	57865705	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	rs777386845	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	253	812	0	ENST00000228682.2:c.3187_3189del	p.Pro1063del	p.P1063del	ENST00000228682	NM_005269.2	1060	agTCCt/agt	12/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.349786589379144	2		812	1161	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254022	133254023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	167	490	0	ENST00000320574.5:c.727dup	p.Trp243LeufsTer20	p.W243Lfs*20	ENST00000320574	NM_006231.2	243	tgg/tTgg	8/49	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.349786589379144	2		490	706	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112553	2112554	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGACG	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	251	775	0	ENST00000219476.3:c.1315_1319dup	p.Trp441ThrfsTer10	p.W441Tfs*10	ENST00000219476	NM_000548.3	438	aag/aaGGACGg	13/42	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.349786589379144	2		775	1158	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2114429	2114429	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs45517182	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	264	828	0	ENST00000219476.3:c.1599+1G>A		p.X533_splice	ENST00000219476	NM_000548.3	533			1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.349786589379144	2		828	1277	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041672	14041672	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	189	550	0	ENST00000311895.7:c.2219G>T	p.Arg740Leu	p.R740L	ENST00000311895	NM_005236.2	740	cGc/cTc	11/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.349786589379144	2		550	832	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813252	89813252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	247	643	0	ENST00000389301.3:c.3395C>T	p.Ala1132Val	p.A1132V	ENST00000389301	NM_000135.2	1132	gCc/gTc	34/43	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.349786589379144	2		643	1038	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667652	29667652	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	112	339	0	ENST00000356175.3:c.6988T>G	p.Phe2330Val	p.F2330V	ENST00000356175	NM_000267.3	2330	Ttc/Gtc	46/57	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.349786589379144	2		339	539	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4123862	4123862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	129	348	0	ENST00000262948.5:c.11G>A	p.Arg4Gln	p.R4Q	ENST00000262948	NM_030662.3	4	cGg/cAg	1/11	1	2	FACETS	0.757	0.691	0.826	1	0.987	1	SUBCLONAL	2	TRUE	1	0.349786589379144	2		348	487	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626907	14626907	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	260	674	0	ENST00000254322.2:c.868A>G	p.Arg290Gly	p.R290G	ENST00000254322	NM_006145.1	290	Agg/Ggg	3/3	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.349786589379144	2		674	1087	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296164	15296164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	324	918	0	ENST00000263388.2:c.2200G>A	p.Ala734Thr	p.A734T	ENST00000263388	NM_000435.2	734	Gcc/Acc	14/33	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.349786589379144	2		918	1334	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946789	17946789	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	132	833	2	ENST00000458235.1:c.1858C>T	p.Pro620Ser	p.P620S	ENST00000458235	NM_000215.3	620	Cca/Tca	14/24	1	2	FACETS	0.6	0.543	0.661	0.6	0.543	0.661	SUBCLONAL	1	TRUE	1	0.349786589379144	2		835	1257	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211727	36211729	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	222	792	1	ENST00000222270.7:c.1482_1484del	p.Pro495del	p.P495del	ENST00000222270	NM_014727.1	493	tCTCct/tct	3/37	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.349786589379144	2		793	1167	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216480	36216480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1188	235	975	3	ENST00000222270.7:c.3743G>A	p.Arg1248His	p.R1248H	ENST00000222270	NM_014727.1	1248	cGc/cAc	12/37	1	2	FACETS	0.944	0.879	1	0.944	0.879	1	CLONAL	1	TRUE	1	0.349786589379144	2		978	1423	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067059	143067059	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	150	392	0	ENST00000262992.4:c.1654A>G	p.Ser552Gly	p.S552G	ENST00000262992	NM_001101669.1	552	Agt/Ggt	16/24	0.349786589379144	3	FACETS	0.773	0.708	0.84	0.515	0.472	0.56	SUBCLONAL	2	TRUE	0	0.349786589379144	3		392	652	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1268635	1268635	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	98	774	0	ENST00000310581.5:c.2582G>T	p.Gly861Val	p.G861V	ENST00000310581	NM_198253.2	861	gGg/gTg	9/16	1	2	FACETS	0.478	0.425	0.534	0.478	0.425	0.534	SUBCLONAL	1	TRUE	1	0.349786589379144	2		774	1173	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790818	89790819	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1350762602	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	217	874	1	ENST00000336032.3:c.211dup	p.Gln71ProfsTer137	p.Q71Pfs*137	ENST00000336032	NM_006813.2	69	acc/aCcc	1/2	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.349786589379144	2		875	1145	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793683	89793683	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs555301723	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	36	338	0	ENST00000336032.3:c.752A>G	p.Lys251Arg	p.K251R	ENST00000336032	NM_006813.2	251	aAg/aGg	2/2	1	2	FACETS	0.492	0.405	0.591	0.492	0.405	0.591	SUBCLONAL	1	TRUE	1	0.349786589379144	2		338	418	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686292	117686292	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1434611083	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	24	299	0	ENST00000368508.3:c.3049T>C	p.Ser1017Pro	p.S1017P	ENST00000368508	NM_002944.2	1017	Tct/Cct	20/43	1	2	FACETS	0.395	0.31	0.494	0.395	0.31	0.494	SUBCLONAL	1	TRUE	1	0.349786589379144	2		299	347	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334794	81334794	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	23	379	0	ENST00000222390.5:c.1922A>G	p.Lys641Arg	p.K641R	ENST00000222390	NM_000601.4	641	aAa/aGa	17/18	1	2	FACETS	0.309	0.24	0.388	0.309	0.24	0.388	SUBCLONAL	1	TRUE	1	0.349786589379144	2		379	426	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418969	116418969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	124	357	0	ENST00000397752.3:c.3480G>A	p.Met1160Ile	p.M1160I	ENST00000397752	NM_000245.2	1160	atG/atA	17/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.349786589379144	2		357	544	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151167707	151167707	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	40	286	0	ENST00000262187.5:c.412G>A	p.Ala138Thr	p.A138T	ENST00000262187	NM_005614.3	138	Gca/Aca	7/8	1	2	FACETS	0.618	0.515	0.733	0.618	0.515	0.733	SUBCLONAL	1	TRUE	1	0.349786589379144	2		286	370	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964316	70964316	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	39	332	0	ENST00000276594.2:c.1712A>C	p.Tyr571Ser	p.Y571S	ENST00000276594	NM_024504.3	571	tAc/tCc	8/8	1	2	FACETS	0.493	0.409	0.588	0.493	0.409	0.588	SUBCLONAL	1	TRUE	1	0.349786589379144	2		332	452	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426118	47426118	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	297	838	0	ENST00000377045.4:c.638C>T	p.Thr213Met	p.T213M	ENST00000377045	NM_001654.4	213	aCg/aTg	7/16	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.349786589379144	2		838	1160	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0056678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	255	326	6	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.941512677168222	2		332	516	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0056678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	255	250	2	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.952	0.9	1	0.952	0.9	1	CLONAL	1	TRUE	1	0.941512677168222	2		252	569	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934194	48934194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	236	312	2	ENST00000267163.4:c.649C>T	p.Gln217Ter	p.Q217*	ENST00000267163	NM_000321.2	217	Cag/Tag	7/27	0.941512677168222	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.941512677168222	1		314	256	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683713	162683713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747891099	NA	P-0056678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	379	401	3	ENST00000366898.1:c.256G>A	p.Asp86Asn	p.D86N	ENST00000366898	NM_004562.2	86	Gac/Aac	3/12	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.941512677168222	2		404	791	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257121	19257121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1368664931	NA	P-0056678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	418	463	4	ENST00000162023.5:c.842C>T	p.Ser281Leu	p.S281L	ENST00000162023		281	tCg/tTg	12/13	0.941512677168222	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.941512677168222	1		467	449	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125350	7125350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762687424	NA	P-0056678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	559	567	5	ENST00000302850.5:c.3202C>T	p.Arg1068Trp	p.R1068W	ENST00000302850	NM_000208.2	1068	Cgg/Tgg	17/22	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.941512677168222	2		572	1100	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791738	42791738	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	514	432	3	ENST00000575354.2:c.624G>A	p.Met208Ile	p.M208I	ENST00000575354	NM_015125.3	208	atG/atA	5/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.941512677168222	2		435	1040	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21565517	21565517	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	403	431	8	ENST00000382592.4:c.369G>C	p.Gln123His	p.Q123H	ENST00000382592	NM_014572.2	123	caG/caC	3/8	0.273480273843968	5	FACETS	0.793	0.754	0.833			1	INDETERMINATE	2	TRUE	NA	0.941512677168222	5		439	1302	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743997	41743997	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	528	617	7	ENST00000301178.4:c.932G>C	p.Cys311Ser	p.C311S	ENST00000301178	NM_021913.4	311	tGc/tCc	7/20	1	2	FACETS	0.987	0.95	1	0.987	0.95	1	CLONAL	1	TRUE	1	0.941512677168222	2		624	1136	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0056684-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	162	432	1	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.96	0.887	1	0.96	0.887	1	CLONAL	1	TRUE	1	0.653010664542852	2		433	517	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0056684-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	37	351	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.287	0.236	0.343	0.287	0.236	0.343	SUBCLONAL	1	TRUE	1	0.653010664542852	2		351	395	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473711	67473711	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056684-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	289	662	1	ENST00000327367.4:c.791C>A	p.Ser264Tyr	p.S264Y	ENST00000327367	NM_005902.3	264	tCc/tAc	6/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.653010664542852	2		663	851	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056696-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	210	365	0				ENST00000310581	NM_198253.2	-/1132			0.3	7	FACETS	1	0.98	1	0.887	0.842	0.93	INDETERMINATE	5	TRUE	1	0.6	7		365	329	SUCCESS
APC	324	MSKCC	GRCh37	5	112174173	112174173	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1554084564	NA	P-0056696-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	70	297	0	ENST00000257430.4:c.2882A>G	p.Asn961Ser	p.N961S	ENST00000257430	NM_000038.5	961	aAt/aGt	16/16	0.160807487711966	3	FACETS	0.978	0.877	1	0.978	0.877	1	INDETERMINATE	2	TRUE	1	0.6	3		297	155	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577157	7577157	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0056748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	201	453	0	ENST00000269305.4:c.783-2A>C		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.758954324289322	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.758954324289322	1		453	314	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842705	68842705	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	428	421	0	ENST00000261769.5:c.641T>G	p.Leu214Arg	p.L214R	ENST00000261769	NM_004360.3	214	cTg/cGg	5/16	0.758954324289322	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.758954324289322	2		421	508	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128579	30128579	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	143	440	0	ENST00000263025.4:c.803A>T	p.Asp268Val	p.D268V	ENST00000263025	NM_002746.2	268	gAc/gTc	6/9	0.758954324289322	2	FACETS	0.769	0.706	0.834	0.385	0.353	0.417	SUBCLONAL	1	TRUE	0	0.758954324289322	2		440	490	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713594	30713594	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	380	493	0	ENST00000295754.5:c.919T>G	p.Phe307Val	p.F307V	ENST00000295754	NM_003242.5	307	Ttc/Gtc	4/7	NA	2	FACETS	0.919	0.887	0.949			1	INDETERMINATE	2	TRUE	NA	0.758954324289322	2		493	545	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713788	30713814	+	inframe_deletion	In_Frame_Del	DEL	CAAGATGCCCATCGTGCACAGGGACCT	CAAGATGCCCATCGTGCACAGGGACCT	-	novel	NA	P-0056748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	359	507	0	ENST00000295754.5:c.1118_1144del	p.Met373_Lys381del	p.M373_K381del	ENST00000295754	NM_003242.5	371	ccCAAGATGCCCATCGTGCACAGGGACCTc/ccc	4/7	NA	2	FACETS	0.891	0.858	0.922			1	INDETERMINATE	2	TRUE	NA	0.758954324289322	2		507	531	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441333	52441333	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0056748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	196	436	0	ENST00000460680.1:c.438-1G>A		p.X146_splice	ENST00000460680	NM_004656.3	146			0.758954324289322	1	FACETS	0.977	0.924	1	0.977	0.924	1	CLONAL	1	TRUE	0	0.758954324289322	1		436	328	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449713	187449713	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	136	274	0	ENST00000232014.4:c.167T>G	p.Leu56Arg	p.L56R	ENST00000232014	NM_001130845.1	56	cTg/cGg	4/10	1	2	FACETS	0.946	0.87	1	0.946	0.87	1	CLONAL	1	TRUE	1	0.758954324289322	2		274	379	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86676324	86676324	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0056748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	151	122	0	ENST00000274376.6:c.2604-2A>G		p.X868_splice	ENST00000274376	NM_002890.2	868			NA	2	FACETS	0.966	0.916	1			1	INDETERMINATE	2	TRUE	NA	0.758954324289322	2		122	206	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180660	32180660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	186	672	1	ENST00000375023.3:c.2467G>A	p.Asp823Asn	p.D823N	ENST00000375023	NM_004557.3	823	Gac/Aac	16/30	1	2	FACETS	0.802	0.745	0.861	0.802	0.745	0.861	CLONAL	1	TRUE	1	0.758954324289322	2		673	611	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527547	29527552	+	frameshift_variant	Frame_Shift_Del	DEL	TTACAT	TTACAT	A	novel	NA	P-0056748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	149	415	0	ENST00000356175.3:c.996_1001delinsA	p.Tyr333GlnfsTer5	p.Y333Qfs*5	ENST00000356175	NM_000267.3	332	acTTACATc/acAc	9/57	0.758954324289322	2	FACETS	0.714	0.656	0.774	0.357	0.328	0.387	SUBCLONAL	1	TRUE	0	0.758954324289322	2		415	550	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888210	112888210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121918464	NA	P-0056756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	303	471	0	ENST00000351677.2:c.226G>A	p.Glu76Lys	p.E76K	ENST00000351677	NM_002834.3	76	Gag/Aag	3/16	0.108425580979811	3	FACETS	1	0.995	1	0.737	0.7	0.774	INDETERMINATE	1	TRUE	1	0.895334302171785	3		471	665	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361160	70361160	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs79912241	NA	P-0056756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	26	328	0	ENST00000374080.3:c.6348C>A	p.His2116Gln	p.H2116Q	ENST00000374080		2116	caC/caA	43/45	1	1	FACETS	0.062	0.049	0.078	0.062	0.049	0.078	SUBCLONAL	1	TRUE	0	0.895334302171785	1		328	516	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436876	110436876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	384	668	0	ENST00000375856.3:c.1525G>A	p.Asp509Asn	p.D509N	ENST00000375856	NM_003749.2	509	Gac/Aac	1/2	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.895334302171785	2		668	801	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496968	29496969	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	411	270	1	ENST00000356175.3:c.540dup	p.Gln181ThrfsTer20	p.Q181Tfs*20	ENST00000356175	NM_000267.3	180	tta/ttAa	5/57	1	2	FACETS	0.966	0.945	0.987	1	0.998	1	CLONAL	2	TRUE	1	0.895334302171785	2		271	475	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155417	185155417	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0056756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	139	258	0	ENST00000265026.3:c.658A>T	p.Lys220Ter	p.K220*	ENST00000265026	NM_004721.4	220	Aag/Tag	3/14	1	2	FACETS	0.867	0.8	0.936	0.867	0.8	0.936	CLONAL	1	TRUE	1	0.895334302171785	2		258	358	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404656	70404656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	76	535	0	ENST00000373644.4:c.2170G>A	p.Gly724Arg	p.G724R	ENST00000373644	NM_030625.2	724	Gga/Aga	4/12	0.329962775418799	3	FACETS	0.79	0.693	0.895	0.395	0.346	0.448	SUBCLONAL	1	TRUE	1	0.329962775418799	3		535	679	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066524	94066524	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	62	380	0	ENST00000369303.4:c.1235C>G	p.Thr412Ser	p.T412S	ENST00000369303	NM_004440.3	412	aCt/aGt	5/17	0.325688532840679	1	FACETS	0.785	0.68	0.897	0.785	0.68	0.897	SUBCLONAL	1	TRUE	0	0.329962775418799	1		380	400	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992692	68992692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529924687	NA	P-0056783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	47	567	0	ENST00000288368.4:c.1657G>A	p.Glu553Lys	p.E553K	ENST00000288368	NM_024870.2	553	Gaa/Aaa	16/40	0.329962775418799	3	FACETS	0.557	0.469	0.654	0.278	0.234	0.327	SUBCLONAL	1	TRUE	1	0.329962775418799	3		567	596	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150327	108150327	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0056783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	73	311	0	ENST00000278616.4:c.3394A>T	p.Arg1132Ter	p.R1132*	ENST00000278616	NM_000051.3	1132	Aga/Tga	23/63	0.329962775418799	2	FACETS	0.889	0.788	0.994	0.889	0.788	0.994	CLONAL	2	TRUE	0	0.329962775418799	2		311	249	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119751	70119770	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGAAGCGAGAGGGGCGCC	CCTGAAGCGAGAGGGGCGCC	-	novel	NA	P-0056783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	206	877	0	ENST00000245479.2:c.756_775del	p.Lys253AlafsTer36	p.K253Afs*36	ENST00000245479	NM_000346.3	251	gaCCTGAAGCGAGAGGGGCGCCcc/gacc	3/3	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.329962775418799	2		877	929	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0056784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	104	339	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.287795081844251	3	FACETS	0.827	0.745	0.914	0.827	0.745	0.914	CLONAL	2	FALSE	1	0.30645974388111	3		339	473	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040905	47040905	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0056784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	157	394	0	ENST00000377604.3:c.1436-1G>A		p.X479_splice	ENST00000377604	NM_001204468.1	479			0.107914615217473	2	FACETS	1	0.981	1			1	INDETERMINATE	2	FALSE	NA	0.30645974388111	2		394	433	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864733	57864733	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	76	735	1	ENST00000228682.2:c.2210G>T	p.Gly737Val	p.G737V	ENST00000228682	NM_005269.2	737	gGg/gTg	12/12	0.287795081844251	3	FACETS	0.869	0.762	0.984	0.435	0.381	0.492	CLONAL	1	FALSE	1	0.30645974388111	3		736	658	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610075	81610075	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	78	413	0	ENST00000298171.2:c.1673T>A	p.Val558Glu	p.V558E	ENST00000298171	NM_000369.2	558	gTg/gAg	10/10	0.0914782284124656	4	FACETS	1	0.974	1	0.706	0.622	0.795	INDETERMINATE	1	FALSE	2	0.30645974388111	4		413	471	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349802	89349802	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	104	874	0	ENST00000301030.4:c.3148A>G	p.Lys1050Glu	p.K1050E	ENST00000301030	NM_001256183.1	1050	Aaa/Gaa	9/13	0.103015556721128	4	FACETS	0.766	0.684	0.854	0.383	0.342	0.427	INDETERMINATE	1	FALSE	2	0.30645974388111	4		874	1157	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621169	1621169	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	186	785	1	ENST00000344749.5:c.977G>A	p.Gly326Asp	p.G326D	ENST00000344749	NM_001136139.2	326	gGc/gAc	12/19	0.0914782284124656	4	FACETS	0.99	0.916	1	0.99	0.916	1	INDETERMINATE	2	FALSE	2	0.30645974388111	4		786	801	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928878	49928878	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	88	874	0	ENST00000296474.3:c.3488A>G	p.Tyr1163Cys	p.Y1163C	ENST00000296474	NM_002447.2	1163	tAt/tGt	16/20	1	2	FACETS	0.838	0.743	0.94	0.838	0.743	0.94	CLONAL	1	FALSE	1	0.30645974388111	2		874	685	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156540	55156540	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	124	474	0	ENST00000257290.5:c.2941C>A	p.Arg981Ser	p.R981S	ENST00000257290	NM_006206.4	981	Cgt/Agt	22/23	0.267247724250674	3	FACETS	0.839	0.762	0.92	0.839	0.762	0.92	CLONAL	2	FALSE	1	0.30645974388111	3		474	556	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273056	55273056	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	90	533	0	ENST00000275493.2:c.3379G>C	p.Asp1127His	p.D1127H	ENST00000275493	NM_005228.3	1127	Gac/Cac	28/28	0.0914782284124656	4	FACETS	1	0.966	1	0.613	0.544	0.686	INDETERMINATE	1	FALSE	2	0.30645974388111	4		533	626	SUCCESS
AR	367	MSKCC	GRCh37	X	66766195	66766195	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	90	239	0	ENST00000374690.3:c.1207G>T	p.Ala403Ser	p.A403S	ENST00000374690	NM_000044.3	403	Gcg/Tcg	1/8	0.107914615217473	2	FACETS	0.964	0.875	1			1	INDETERMINATE	3	FALSE	NA	0.30645974388111	2		239	203	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0056785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	18	448	0	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	1	2	FACETS	0.977	0.736	1	0.977	0.736	1	CLONAL	1	TRUE	1	0.12	2		448	307	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11172467	11172467	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0056785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	33	791	0	ENST00000358026.2:c.5015C>G	p.Ser1672Ter	p.S1672*	ENST00000358026	NM_001128849.1	1672	tCa/tGa	36/36	1	2	FACETS	0.927	0.754	1	0.927	0.754	1	CLONAL	1	TRUE	1	0.12	2		791	593	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23640589	23640590	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0056786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	158	450	0	ENST00000261584.4:c.2521dup	p.Thr841AsnfsTer8	p.T841Nfs*8	ENST00000261584	NM_024675.3	841	aca/aAca	6/13	1	2	FACETS	0.955	0.881	1	0.955	0.881	1	CLONAL	1	TRUE	1	0.661875450285853	2		450	500	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375400	40375400	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	315	533	0	ENST00000293328.3:c.550G>T	p.Ala184Ser	p.A184S	ENST00000293328	NM_012448.3	184	Gct/Tct	5/19	0.587590247968208	3	FACETS	0.93	0.885	0.976	0.93	0.885	0.976	CLONAL	2	TRUE	1	0.661875450285853	3		533	681	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249002	55249003	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCATGGA	novel	NA	P-0056786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	306	613	0	ENST00000275493.2:c.2304_2305insATGGACAGC	p.Ser768_Val769insMetAspSer	p.S768_V769insMDS	ENST00000275493	NM_005228.3	767	gcc/gcCAGCATGGAc	20/28	0.661292745265804	3	FACETS	0.817	0.775	0.86	0.817	0.775	0.86	CLONAL	2	TRUE	1	0.661875450285853	3		613	753	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339531	81339531	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	159	455	0	ENST00000222390.5:c.1473A>T	p.Lys491Asn	p.K491N	ENST00000222390	NM_000601.4	491	aaA/aaT	13/18	NA	2	FACETS	0.691	0.635	0.75			1	INDETERMINATE	1	TRUE	NA	0.661875450285853	2		455	695	SUCCESS
ATR	545	MSKCC	GRCh37	3	142232376	142232376	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	AACAT	novel	NA	P-0056786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	114	347	0	ENST00000350721.4:c.4608delinsATGTT	p.Leu1537CysfsTer6	p.L1537Cfs*6	ENST00000350721	NM_001184.3	1536	gtC/gtATGTT	26/47	1	2	FACETS	0.702	0.635	0.771	0.702	0.635	0.771	SUBCLONAL	1	TRUE	1	0.661875450285853	2		347	491	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0056788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	31	554	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.25379553767368	2		554	218	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579310	7579310	+	splice_donor_variant	Splice_Site	SNP	A	A	C	rs1555526469	NA	P-0056788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	28	470	0	ENST00000269305.4:c.375+2T>G		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.25379553767368	1	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	0	0.25379553767368	1		470	188	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262201	10262201	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	240	589	1	ENST00000340748.4:c.2090A>G	p.Lys697Arg	p.K697R	ENST00000340748		697	aAg/aGg	23/40	1	2	FACETS	0.932	0.872	0.995	0.932	0.872	0.995	CLONAL	1	TRUE	1	0.553678202181545	2		590	930	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0056792-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	304	473	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.625050917827759	3	FACETS	0.962	0.925	0.996	0.962	0.925	0.996	CLONAL	3	TRUE	0	0.651283831535787	3		474	429	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610136	10610136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056792-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	568	948	1	ENST00000171111.5:c.574G>A	p.Glu192Lys	p.E192K	ENST00000171111	NM_203500.1	192	Gag/Aag	2/6	0.621535617456778	2	FACETS	0.9	0.871	0.929	0.9	0.871	0.929	CLONAL	2	TRUE	0	0.651283831535787	2		949	969	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220370	1220370	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0056792-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	514	797	0	ENST00000326873.7:c.465-2A>T		p.X155_splice	ENST00000326873	NM_000455.4	155			0.621535617456778	2	FACETS	0.993	0.961	1	0.993	0.961	1	CLONAL	2	TRUE	0	0.651283831535787	2		797	795	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349314	11349314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056792-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	140	501	0	ENST00000332029.2:c.22G>A	p.Ala8Thr	p.A8T	ENST00000332029	NM_003745.1	8	Gca/Aca	2/2	1	2	FACETS	0.799	0.732	0.869	0.799	0.732	0.869	SUBCLONAL	1	TRUE	1	0.651283831535787	2		501	538	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90960096	90960096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs962092255	NA	P-0056792-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	66	252	0	ENST00000265433.3:c.1870C>T	p.Arg624Cys	p.R624C	ENST00000265433	NM_002485.4	624	Cgt/Tgt	12/16	0.651283831535787	3	FACETS	0.917	0.803	1	0.458	0.401	0.519	CLONAL	1	TRUE	1	0.651283831535787	3		252	293	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210491	2210491	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056792-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	624	1182	0	ENST00000398665.3:c.1101del	p.Ala368ProfsTer19	p.A368Pfs*19	ENST00000398665	NM_032482.2	366	ggC/gg	13/28	0.621535617456778	2	FACETS	0.934	0.906	0.962	0.934	0.906	0.962	CLONAL	2	TRUE	0	0.651283831535787	2		1182	1026	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374971	45374972	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0056792-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	148	542	0	ENST00000262160.6:c.871dup	p.His291ProfsTer30	p.H291Pfs*30	ENST00000262160	NM_005901.5	291	cat/cCat	8/11	0.651283831535787	3	FACETS	0.962	0.882	1	0.481	0.441	0.523	CLONAL	1	TRUE	1	0.651283831535787	3		542	626	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645621	215645621	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs779960429	NA	P-0056792-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	221	644	0	ENST00000260947.4:c.977A>G	p.Asn326Ser	p.N326S	ENST00000260947	NM_000465.2	326	aAt/aGt	4/11	0.183568828593107	3	FACETS	1	0.992	1	0.714	0.668	0.761	INDETERMINATE	1	TRUE	1	0.651283831535787	3		644	630	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485445	57485445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056792-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	122	342	0	ENST00000371085.3:c.1027G>A	p.Asp343Asn	p.D343N	ENST00000371085	NM_000516.4	343	Gat/Aat	12/13	0.651283831535787	8	FACETS	0.908	0.818	1	0.13	0.116	0.144	CLONAL	1	TRUE	1	0.651283831535787	8		342	1219	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069257	30069257	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0056792-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	392	640	1	ENST00000338641.4:c.1123-1G>T		p.X375_splice	ENST00000338641	NM_000268.3	375			0.630253370945677	2	FACETS	0.965	0.929	1	0.965	0.929	1	CLONAL	2	TRUE	0	0.651283831535787	2		641	624	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517865	187517865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056792-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	55	532	0	ENST00000441802.2:c.12829G>A	p.Ala4277Thr	p.A4277T	ENST00000441802	NM_005245.3	4277	Gct/Act	25/27	0.606321962121193	2	FACETS	0.332	0.284	0.384	0.166	0.142	0.192	SUBCLONAL	1	TRUE	0	0.651283831535787	2		532	509	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022114	5022114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056792-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	141	535	0	ENST00000381652.3:c.127C>T	p.Leu43Phe	p.L43F	ENST00000381652	NM_004972.3	43	Ctt/Ttt	3/25	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.651283831535787	2		535	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0056793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1174	124	907	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	1	2	FACETS	0.553	0.499	0.611	0.553	0.499	0.611	SUBCLONAL	1	TRUE	1	0.345470005579485	2		907	1298	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792731	33792732	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCGGGT	rs762459325	NA	P-0056793-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	13	42	1	ENST00000498907.2:c.584_589dup	p.His195_Pro196dup	p.H195_P196dup	ENST00000498907	NM_004364.3	195	ccg/cACCCGCcg	1/1	1	2	FACETS	1	0.738	1	1	0.738	1	CLONAL	1	TRUE	1	0.311282542129265	2		43	82	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578173	7578213	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGACCTCAGGCGGCTCATAGGGCACCACCACACTATGTCGA	AGACCTCAGGCGGCTCATAGGGCACCACCACACTATGTCGA	-	novel	NA	P-0056793-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	116	449	0	ENST00000269305.4:c.636_672+4del		p.X212_splice	ENST00000269305	NM_001126112.2	212		6/11	0.211764458627886	1	FACETS	0.885	0.798	0.976	0.885	0.798	0.976	CLONAL	1	TRUE	0	0.311282542129265	1		449	711	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0056795-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	290	473	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.710364236619581	3	FACETS	0.951	0.904	0.998	0.951	0.904	0.998	CLONAL	2	TRUE	1	0.706798145632667	3		474	584	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207190	1207190	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056795-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	589	939	0	ENST00000326873.7:c.279del	p.Asn94ThrfsTer2	p.N94Tfs*2	ENST00000326873	NM_000455.4	93	gCc/gc	1/10	0.710364236619581	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.706798145632667	2		939	797	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186594	108186594	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056795-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	331	362	0	ENST00000278616.4:c.6051T>A	p.Ser2017Arg	p.S2017R	ENST00000278616	NM_000051.3	2017	agT/agA	41/63	0.710364236619581	3	FACETS	0.921	0.888	0.952	0.921	0.888	0.952	CLONAL	3	TRUE	0	0.706798145632667	3		362	459	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446025	49446025	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056795-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	657	1405	0	ENST00000301067.7:c.1441G>C	p.Glu481Gln	p.E481Q	ENST00000301067	NM_003482.3	481	Gag/Cag	10/54	0.710364236619581	4	FACETS	0.935	0.901	0.97			1	CLONAL	2	TRUE	NA	0.706798145632667	4		1405	1696	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0056796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1993	217	554	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.635668489708932	12	FACETS	1	0.987	1			1	CLONAL	1	FALSE	NA	0.635668489708932	12		554	2210	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0056796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	1418	331	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.635668489708932	12	FACETS	1	0.997	1			1	CLONAL	11	FALSE	NA	0.635668489708932	12		331	1647	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0056796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	446	998	1	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.635668489708932	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	0	0.635668489708932	1		999	873	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115386	115115386	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	187	413	2	ENST00000257566.3:c.940del	p.Arg314GlufsTer9	p.R314Efs*9	ENST00000257566	NM_016569.3	314	Aga/ga	5/8	1	2	FACETS	0.85	0.788	0.914	0.85	0.788	0.914	CLONAL	1	FALSE	1	0.635668489708932	2		415	692	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859782	151859782	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0056796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	150	372	0	ENST00000262189.6:c.10880C>G	p.Ser3627Ter	p.S3627*	ENST00000262189	NM_170606.2	3627	tCa/tGa	43/59	1	2	FACETS	0.989	0.911	1	0.989	0.911	1	CLONAL	1	FALSE	1	0.635668489708932	2		372	477	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955569	48955570	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	46	264	0	ENST00000267163.4:c.1686dup	p.Trp563MetfsTer9	p.W563Mfs*9	ENST00000267163	NM_000321.2	562	gca/gcAa	17/27	0.635668489708932	1	FACETS	0.69	0.594	0.792	0.69	0.594	0.792	SUBCLONAL	1	FALSE	0	0.635668489708932	1		264	143	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907209	32907209	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138734772	NA	P-0056796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	83	372	0	ENST00000380152.3:c.1594G>C	p.Glu532Gln	p.E532Q	ENST00000380152		532	Gaa/Caa	10/27	0.635668489708932	2	FACETS	0.5	0.442	0.562	0.25	0.221	0.281	SUBCLONAL	1	FALSE	0	0.635668489708932	2		372	522	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0056797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	36	646	2	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.677799713645295	3	FACETS	0.924	0.792	1	0.924	0.792	1	CLONAL	2	TRUE	1	0.677799713645295	3		648	77	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423636	88423636	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	15	368	2	ENST00000360948.2:c.2199del	p.Ile734PhefsTer25	p.I734Ffs*25	ENST00000360948	NM_001012338.2	733	ccC/cc	18/19	1	2	FACETS	0.962	0.733	1	0.962	0.733	1	CLONAL	1	TRUE	1	0.677799713645295	2		370	46	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219336	1219336	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	31	513	1	ENST00000326873.7:c.388G>T	p.Glu130Ter	p.E130*	ENST00000326873	NM_000455.4	130	Gag/Tag	3/10	0.677799713645295	3	FACETS	1	0.908	1	1	0.908	1	CLONAL	3	TRUE	0	0.677799713645295	3		514	40	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602329	10602329	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	60	681	3	ENST00000171111.5:c.1249G>T	p.Gly417Trp	p.G417W	ENST00000171111	NM_203500.1	417	Ggg/Tgg	3/6	0.677799713645295	3	FACETS	0.908	0.828	0.983	0.908	0.828	0.983	CLONAL	3	TRUE	0	0.677799713645295	3		684	87	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781514	135781514	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	23	306	2	ENST00000298552.3:c.1451G>C	p.Arg484Thr	p.R484T	ENST00000298552	NM_001162426.1	484	aGa/aCa	15/23	0.642318257639887	3	FACETS	0.909	0.747	1	0.606	0.498	0.716	CLONAL	2	TRUE	0	0.677799713645295	3		308	50	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0056798-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	303	351	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.305692194485984	5	FACETS	0.99	0.945	1	1	0.993	1	CLONAL	5	TRUE	1	0.327677993031264	5		351	557	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0056798-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	87	857	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	1	2	FACETS	0.827	0.733	0.928	0.827	0.733	0.928	CLONAL	1	TRUE	1	0.327677993031264	2		857	642	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845588	63845588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774238244	NA	P-0056798-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	51	257	0	ENST00000279873.7:c.1327C>T	p.Arg443Cys	p.R443C	ENST00000279873	NM_032199.2	443	Cgc/Tgc	9/10	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.327677993031264	2		257	297	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0056805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	12	554	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.491243656028413	3	FACETS	0.113	0.078	0.155	0.056	0.039	0.078	SUBCLONAL	1	TRUE	1	0.529380123769317	3		554	509	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	93	365	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.937	0.84	1	0.937	0.84	1	CLONAL	1	TRUE	1	0.529380123769317	2		365	375	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	59	664	0	ENST00000267101.3:c.310G>C	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ctg	3/28	0.226800893092761	4	FACETS	0.329	0.282	0.38	0.164	0.141	0.19	INDETERMINATE	1	TRUE	2	0.529380123769317	4		664	1037	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874261	155874261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352822	NA	P-0056805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	171	517	0	ENST00000368323.3:c.270G>A	p.Met90Ile	p.M90I	ENST00000368323	NM_006912.5	90	atG/atA	5/6	0.488682738553087	4	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.529380123769317	4		517	711	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482552	56482552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	167	545	0	ENST00000267101.3:c.1009G>A	p.Gly337Arg	p.G337R	ENST00000267101	NM_001982.3	337	Ggg/Agg	9/28	0.226800893092761	4	FACETS	1	0.987	1	0.691	0.637	0.748	INDETERMINATE	1	TRUE	2	0.529380123769317	4		545	698	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860619	45860619	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	73	867	0	ENST00000391945.4:c.1388C>T	p.Pro463Leu	p.P463L	ENST00000391945	NM_000400.3	463	cCg/cTg	15/23	1	2	FACETS	0.394	0.344	0.448	0.394	0.344	0.448	SUBCLONAL	1	TRUE	1	0.529380123769317	2		867	700	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141514	11141514	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	205	752	0	ENST00000358026.2:c.3491A>G	p.Asn1164Ser	p.N1164S	ENST00000358026	NM_001128849.1	1164	aAc/aGc	25/36	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.529380123769317	2		752	719	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099403	157099426	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAGCAA	CAGCAGCAGCAGCAGCAGCAGCAA	-	rs770869529	NA	P-0056805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	107	334	0	ENST00000346085.5:c.369_392del	p.Gln124_Gln131del	p.Q124_Q131del	ENST00000346085	NM_020732.3	114	CAGCAGCAGCAGCAGCAGCAGCAA/-	1/20	0.392065468525036	3	FACETS	0.835	0.759	0.914	0.557	0.506	0.609	CLONAL	2	TRUE	0	0.529380123769317	3		334	306	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847375	68847375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199886166	NA	P-0056805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	112	504	1	ENST00000261769.5:c.1297G>A	p.Asp433Asn	p.D433N	ENST00000261769	NM_004360.3	433	Gat/Aat	9/16	0.529380123769317	1	FACETS	0.806	0.731	0.883	0.806	0.731	0.883	CLONAL	1	TRUE	0	0.529380123769317	1		505	386	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491641	120491641	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	83	337	2	ENST00000256646.2:c.2588C>T	p.Pro863Leu	p.P863L	ENST00000256646	NM_024408.3	863	cCt/cTt	16/34	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.529380123769317	2		339	301	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983134	201983134	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	179	598	0	ENST00000359651.3:c.983A>T	p.Lys328Met	p.K328M	ENST00000359651		328	aAg/aTg	7/8	1	2	FACETS	0.95	0.878	1	0.95	0.878	1	CLONAL	1	TRUE	1	0.529380123769317	2		598	712	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451126	70451126	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	233	666	1	ENST00000373644.4:c.5966A>T	p.His1989Leu	p.H1989L	ENST00000373644	NM_030625.2	1989	cAc/cTc	12/12	0.165273267122785	3	FACETS	0.802	0.752	0.853	0.802	0.752	0.853	INDETERMINATE	2	TRUE	1	0.529380123769317	3		667	694	SUCCESS
ATM	472	MSKCC	GRCh37	11	108183138	108183138	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	50	234	0	ENST00000278616.4:c.5919A>C	p.Arg1973Ser	p.R1973S	ENST00000278616	NM_000051.3	1973	agA/agC	40/63	1	2	FACETS	0.964	0.829	1	0.964	0.829	1	CLONAL	1	TRUE	1	0.529380123769317	2		234	196	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120806020	120806020	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1350244081	NA	P-0056805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	230	746	1	ENST00000257552.2:c.157C>T	p.Arg53Trp	p.R53W	ENST00000257552	NM_002442.3	53	Cgg/Tgg	3/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.529380123769317	2		747	830	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436469	110436469	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	463	911	0	ENST00000375856.3:c.1932C>G	p.Ser644Arg	p.S644R	ENST00000375856	NM_003749.2	644	agC/agG	1/2	0.529380123769317	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.529380123769317	2		911	859	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348789	11348789	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749027399	NA	P-0056805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	116	341	0	ENST00000332029.2:c.547G>A	p.Val183Met	p.V183M	ENST00000332029	NM_003745.1	183	Gtg/Atg	2/2	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.529380123769317	2		341	391	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770143	56770143	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	152	581	0	ENST00000337432.4:c.139A>C	p.Ser47Arg	p.S47R	ENST00000337432	NM_058216.2	47	Agc/Cgc	1/9	0.185321099933155	3	FACETS	1	0.943	1	0.345	0.316	0.376	INDETERMINATE	1	TRUE	0	0.529380123769317	3		581	701	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733077	74733077	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	382	725	0	ENST00000359995.5:c.166G>C	p.Gly56Arg	p.G56R	ENST00000359995	NM_001195427.1	56	Ggc/Cgc	1/3	0.185321099933155	3	FACETS	0.953	0.908	0.998	0.635	0.605	0.665	INDETERMINATE	2	TRUE	0	0.529380123769317	3		725	958	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78854220	78854220	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	403	676	0	ENST00000306801.3:c.1515C>G	p.Cys505Trp	p.C505W	ENST00000306801	NM_020761.2	505	tgC/tgG	14/34	0.185321099933155	3	FACETS	1	0.975	1	0.686	0.655	0.717	INDETERMINATE	2	TRUE	0	0.529380123769317	3		676	936	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098487	11098510	+	inframe_deletion	In_Frame_Del	DEL	GCCGGCCCAGCCCGCGCCCATGGT	GCCGGCCCAGCCCGCGCCCATGGT	-	novel	NA	P-0056805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	168	495	0	ENST00000358026.2:c.1008_1031del	p.Ala337_Pro344del	p.A337_P344del	ENST00000358026	NM_001128849.1	335	caGCCGGCCCAGCCCGCGCCCATGGTg/cag	6/36	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.529380123769317	2		495	523	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346707	225346707	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	147	483	0	ENST00000264414.4:c.1931T>C	p.Leu644Pro	p.L644P	ENST00000264414	NM_003590.4	644	cTt/cCt	14/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.529380123769317	2		483	444	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663445	227663445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1222939491	NA	P-0056805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	115	445	0	ENST00000305123.5:c.10C>T	p.Pro4Ser	p.P4S	ENST00000305123	NM_005544.2	4	Cct/Tct	1/2	1	2	FACETS	0.994	0.902	1	0.994	0.902	1	CLONAL	1	TRUE	1	0.529380123769317	2		445	437	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412992	49412992	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	221	622	0	ENST00000418115.1:c.31G>T	p.Val11Phe	p.V11F	ENST00000418115	NM_001664.2	11	Gtt/Ttt	2/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.529380123769317	2		622	750	SUCCESS
APC	324	MSKCC	GRCh37	5	112176929	112176929	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	59	359	0	ENST00000257430.4:c.5638G>A	p.Glu1880Lys	p.E1880K	ENST00000257430	NM_000038.5	1880	Gaa/Aaa	16/16	1	2	FACETS	0.751	0.651	0.857	0.751	0.651	0.857	SUBCLONAL	1	TRUE	1	0.529380123769317	2		359	297	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652089	36652105	+	frameshift_variant	Frame_Shift_Del	DEL	CTTGGCCTGCCCAAGCT	CTTGGCCTGCCCAAGCT	-	novel	NA	P-0056805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	277	960	0	ENST00000244741.5:c.213_229del	p.Gly72ProfsTer11	p.G72Pfs*11	ENST00000244741	NM_000389.4	71	CTTGGCCTGCCCAAGCTc/c	2/3	0.516921764482591	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.529380123769317	1		960	653	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249915	110249915	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	163	838	1	ENST00000374672.4:c.760A>T	p.Ser254Cys	p.S254C	ENST00000374672	NM_004235.4	254	Agc/Tgc	3/5	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.529380123769317	2		839	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0056812-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	401	179	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.587704847684399	2	FACETS	0.905	0.869	0.941	0.905	0.869	0.941	CLONAL	2	TRUE	0	0.614471217555504	2		180	721	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0056812-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	280	295	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.495080025129716	5	FACETS	0.919	0.871	0.968	0.919	0.871	0.968	CLONAL	3	TRUE	2	0.614471217555504	5		295	635	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916136	9916136	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056812-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	117	341	0	ENST00000330684.3:c.2153T>C	p.Val718Ala	p.V718A	ENST00000330684	NM_001134407.1	718	gTc/gCc	10/13	0.57472300681237	2	FACETS	0.785	0.712	0.862	0.393	0.356	0.431	SUBCLONAL	1	TRUE	0	0.614471217555504	2		341	485	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224354	36224354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056812-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	621	655	0	ENST00000222270.7:c.6904G>A	p.Glu2302Lys	p.E2302K	ENST00000222270	NM_014727.1	2302	Gaa/Aaa	28/37	0.614471217555504	3	FACETS	0.967	0.94	0.993	0.967	0.94	0.993	CLONAL	3	TRUE	0	0.614471217555504	3		655	911	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577524	7577524	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056859-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	273	890	1	ENST00000269305.4:c.757A>G	p.Thr253Ala	p.T253A	ENST00000269305	NM_001126112.2	253	Acc/Gcc	7/11	0.344106332454556	2	FACETS	1	0.993	1	0.739	0.695	0.784	CLONAL	1	TRUE	0	0.413804418968204	2		891	893	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107183	27107183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056859-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	133	745	0	ENST00000324856.7:c.6794C>T	p.Pro2265Leu	p.P2265L	ENST00000324856	NM_006015.4	2265	cCg/cTg	20/20	1	2	FACETS	0.832	0.756	0.911	0.832	0.756	0.911	CLONAL	1	TRUE	1	0.413804418968204	2		745	773	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643583	38643583	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056859-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	212	688	0	ENST00000299084.4:c.1053A>T	p.Lys351Asn	p.K351N	ENST00000299084	NM_152594.2	351	aaA/aaT	7/7	0.287951658599073	3	FACETS	0.821	0.765	0.879	0.821	0.765	0.879	CLONAL	2	TRUE	1	0.413804418968204	3		688	753	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934274	68934274	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056859-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	75	455	1	ENST00000288368.4:c.340G>T	p.Asp114Tyr	p.D114Y	ENST00000288368	NM_024870.2	114	Gac/Tac	4/40	NA	2	FACETS	0.76	0.668	0.858			1	INDETERMINATE	1	TRUE	NA	0.413804418968204	2		456	477	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140165	50140165	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056866-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	144	734	0	ENST00000246792.3:c.260A>T	p.Gln87Leu	p.Q87L	ENST00000246792	NM_006270.3	87	cAg/cTg	3/6	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.34	2		734	832	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8252029	8252029	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056866-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	148	782	1	ENST00000335790.3:c.48G>T	p.Gln16His	p.Q16H	ENST00000335790	NM_002315.2	16	caG/caT	2/4	1	2	FACETS	0.768	0.7	0.839	0.768	0.7	0.839	SUBCLONAL	1	TRUE	1	0.34	2		783	1134	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050415	128050415	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056866-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	81	317	1	ENST00000285398.2:c.242A>T	p.Asp81Val	p.D81V	ENST00000285398	NM_000122.1	81	gAt/gTt	3/15	1	2	FACETS	0.995	0.879	1	0.995	0.879	1	CLONAL	1	TRUE	1	0.34	2		318	479	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604747	48604782	+	inframe_deletion	In_Frame_Del	DEL	CTGGATTGAAATTCACTTACACCGGGCCCTCCAGCT	CTGGATTGAAATTCACTTACACCGGGCCCTCCAGCT	-	novel	NA	P-0056866-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	10	362	0	ENST00000342988.3:c.1570_1605del	p.Trp524_Leu535del	p.W524_L535del	ENST00000342988	NM_005359.5	523	tgCTGGATTGAAATTCACTTACACCGGGCCCTCCAGCTc/tgc	12/12	0.249828640063823	1	FACETS	0.102	0.068	0.144	0.102	0.068	0.144	SUBCLONAL	1	TRUE	0	0.34	1		362	480	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	20	365	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.815	1	1	0.815	1	CLONAL	1	TRUE	1	0.2	2		365	187	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0056871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	96	680	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.2	2		680	726	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730802	40730802	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	11	0	0	ENST00000373198.4:c.3733G>T	p.Gly1245Ter	p.G1245*	ENST00000373198	NM_133170.3	1245	Gga/Tga	27/32	0.3	0	FACETS	0.178	0.122	0.248			1	SUBCLONAL	1	TRUE	0	0.2	0		0	495	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99473487	99473487	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	8	0	0	ENST00000268035.6:c.2909G>A	p.Gly970Glu	p.G970E	ENST00000268035	NM_000875.3	970	gGa/gAa	15/21	1	2	FACETS	0.204	0.13	0.3	0.204	0.13	0.3	SUBCLONAL	1	TRUE	1	0.2	2		0	392	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227889	123227889	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	17	139	0	ENST00000218089.9:c.3600G>A	p.Met1200Ile	p.M1200I	ENST00000218089	NM_001042749.1	1200	atG/atA	33/35	1	1	FACETS	0.722	0.54	0.936	0.722	0.54	0.936	CLONAL	1	TRUE	0	0.2	1		139	212	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030378	49030378	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0056871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	49	264	0	ENST00000267163.4:c.1853C>G	p.Ser618Ter	p.S618*	ENST00000267163	NM_000321.2	618	tCa/tGa	19/27	0.0626449323983373	4	FACETS	1	0.943	1	0.626	0.53	0.73	INDETERMINATE	1	TRUE	2	0.2	4		264	470	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652057	36652058	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0056871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	114	868	0	ENST00000244741.5:c.182dup	p.Asp62Ter	p.D62*	ENST00000244741	NM_000389.4	60	gag/gaGg	2/3	0.290614602753946	3	FACETS	1	0.97	1	0.606	0.545	0.672	CLONAL	1	TRUE	1	0.2	3		868	1034	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940181	31940181	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1307450480	NA	P-0056871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	32	0	0	ENST00000375333.2:c.323C>T	p.Ser108Phe	p.S108F	ENST00000375333	NM_032454.1	108	tCc/tTc	2/8	0.290614602753946	3	FACETS	0.319	0.257	0.389	0.159	0.128	0.195	SUBCLONAL	1	TRUE	1	0.2	3		0	1105	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319512	62319512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs909417142	NA	P-0056871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	21	0	0	ENST00000360203.5:c.1616C>T	p.Ser539Phe	p.S539F	ENST00000360203	NM_001283009.1	539	tCc/tTc	19/35	1	2	FACETS	0.227	0.174	0.29	0.227	0.174	0.29	SUBCLONAL	1	TRUE	1	0.2	2		0	924	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425545	49425545	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	76	991	0	ENST00000301067.7:c.12943C>T	p.Gln4315Ter	p.Q4315*	ENST00000301067	NM_003482.3	4315	Caa/Taa	39/54	0.112259347309247	5	FACETS	1	0.887	1	0.338	0.296	0.384	INDETERMINATE	1	TRUE	2	0.2	5		991	974	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43772095	43772095	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	49	602	0	ENST00000382044.4:c.620C>G	p.Ser207Cys	p.S207C	ENST00000382044	NM_001141980.1	207	tCt/tGt	6/28	1	2	FACETS	0.646	0.545	0.756	0.646	0.545	0.756	SUBCLONAL	1	TRUE	1	0.2	2		602	759	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272366	15272366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	13	0	0	ENST00000263388.2:c.6073G>T	p.Asp2025Tyr	p.D2025Y	ENST00000263388	NM_000435.2	2025	Gat/Tat	33/33	1	2	FACETS	0.193	0.136	0.262	0.193	0.136	0.262	SUBCLONAL	1	TRUE	1	0.2	2		0	675	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010443	48010443	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	19	0	0	ENST00000234420.5:c.71C>A	p.Ser24Ter	p.S24*	ENST00000234420	NM_000179.2	24	tCg/tAg	1/10	1	2	FACETS	0.416	0.314	0.536	0.416	0.314	0.536	SUBCLONAL	1	TRUE	1	0.2	2		0	457	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52675985	52675985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	16	0	0	ENST00000394830.3:c.1072G>C	p.Asp358His	p.D358H	ENST00000394830	NM_018313.4	358	Gat/Cat	11/30	0.0626449323983373	4	FACETS	0.266	0.195	0.352	0.133	0.097	0.176	INDETERMINATE	1	TRUE	2	0.2	4		0	721	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064727	80064727	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	17	0	0	ENST00000265081.6:c.2158C>G	p.Gln720Glu	p.Q720E	ENST00000265081	NM_002439.4	720	Caa/Gaa	15/24	0.0626449323983373	4	FACETS	0.383	0.284	0.501	0.191	0.142	0.251	INDETERMINATE	1	TRUE	2	0.2	4		0	533	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672255	30672255	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	140	805	0	ENST00000376406.3:c.4705G>C	p.Glu1569Gln	p.E1569Q	ENST00000376406	NM_014641.2	1569	Gaa/Caa	10/15	0.3	5	FACETS	0.983	0.894	1			1	CLONAL	2	TRUE	NA	0.2	5		805	926	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90949294	90949294	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554554265	NA	P-0056871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	23	174	0	ENST00000265433.3:c.2194C>T	p.Gln732Ter	p.Q732*	ENST00000265433	NM_002485.4	732	Caa/Taa	15/16	1	2	FACETS	0.623	0.486	0.783	0.623	0.486	0.783	SUBCLONAL	1	TRUE	1	0.2	2		174	369	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045190	47045190	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0056871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	127	324	0	ENST00000377604.3:c.2430+1G>A		p.X810_splice	ENST00000377604	NM_001204468.1	810			0.098562436143474	2	FACETS	1	0.972	1			1	INDETERMINATE	3	TRUE	NA	0.2	2		324	370	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0056884-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	90	743	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.882	0.786	0.985	0.882	0.786	0.985	CLONAL	1	TRUE	1	0.410449196422877	2		743	497	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061469	38061469	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056884-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	93	362	0	ENST00000250448.2:c.520T>C	p.Ser174Pro	p.S174P	ENST00000250448	NM_004496.3	174	Tcg/Ccg	2/2	1	2	FACETS	0.964	0.861	1	0.964	0.861	1	CLONAL	1	TRUE	1	0.410449196422877	2		362	470	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846103	68846104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0056884-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	106	646	0	ENST00000261769.5:c.1075_1076dup	p.Thr360GlnfsTer4	p.T360Qfs*4	ENST00000261769	NM_004360.3	358	-/GC	8/16	0.410449196422877	1	FACETS	0.908	0.819	1	0.908	0.819	1	CLONAL	1	TRUE	0	0.410449196422877	1		646	452	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270478	98270478	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056884-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	78	414	0	ENST00000331920.6:c.166T>C	p.Cys56Arg	p.C56R	ENST00000331920	NM_000264.3	56	Tgc/Cgc	1/24	1	2	FACETS	0.839	0.74	0.944	0.839	0.74	0.944	CLONAL	1	TRUE	1	0.410449196422877	2		414	453	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785665	50785665	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056884-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	45	480	0	ENST00000398568.2:c.655C>A	p.Pro219Thr	p.P219T	ENST00000398568	NM_001042412.1	219	Cct/Act	4/18	1	2	FACETS	0.403	0.338	0.475	0.403	0.338	0.475	SUBCLONAL	1	TRUE	1	0.410449196422877	2		480	544	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741686	145741704	+	frameshift_variant	Frame_Shift_Del	DEL	CGGGGCTCTCCCAGGGCTC	CGGGGCTCTCCCAGGGCTC	-	novel	NA	P-0056884-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	96	631	0	ENST00000428558.2:c.799_817del	p.Glu267HisfsTer20	p.E267Hfs*20	ENST00000428558	NM_004260.3	267	GAGCCCTGGGAGAGCCCCGca/ca	5/22	1	2	FACETS	0.84	0.75	0.935	0.84	0.75	0.935	CLONAL	1	TRUE	1	0.410449196422877	2		631	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579350	7579350	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587781642	NA	P-0056885-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	205	842	0	ENST00000269305.4:c.337T>G	p.Phe113Val	p.F113V	ENST00000269305	NM_001126112.2	113	Ttc/Gtc	4/11	0.595475799512325	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.775379497261133	1		842	321	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275368	115275368	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056885-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	167	567	0	ENST00000438362.2:c.1045G>C	p.Asp349His	p.D349H	ENST00000438362	NM_001242891.1	349	Gat/Cat	10/20	NA	2	FACETS	0.772	0.727	0.817			1	INDETERMINATE	2	TRUE	NA	0.775379497261133	2		567	279	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060529	38060879	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	ACCAGCATGGCTATGCCAGACAAACCCCCCAGTCCCGGGAGCTAGGAAGTGTTTAGGACGGGTCTGGAATACACACCTTGGTAGTACGCCGGCTCCAGGGCTGAGGGCTCGATGGGGCTCCTGGTGGTCACCGAGGCGCTGCCTAGAGGCAGGCTGGCGGGCAACGTAGAGCCGTAAGGCGAGTATTGCAGTGCCTGTTCGTATGCCTTGAAGTCCAGCTTATGCTGCTGCTCCGAGGAGGACATGAGGTTGTTGATGGAGAACGGGTGGTTGAAGGAGTAGTGGGGGTCCCCTTTCAGGTGCAGCTGGGACTCGTGGGGTGCCAAGCCGTGTGCCGGGTGAGAGGCGGGC	ACCAGCATGGCTATGCCAGACAAACCCCCCAGTCCCGGGAGCTAGGAAGTGTTTAGGACGGGTCTGGAATACACACCTTGGTAGTACGCCGGCTCCAGGGCTGAGGGCTCGATGGGGCTCCTGGTGGTCACCGAGGCGCTGCCTAGAGGCAGGCTGGCGGGCAACGTAGAGCCGTAAGGCGAGTATTGCAGTGCCTGTTCGTATGCCTTGAAGTCCAGCTTATGCTGCTGCTCCGAGGAGGACATGAGGTTGTTGATGGAGAACGGGTGGTTGAAGGAGTAGTGGGGGTCCCCTTTCAGGTGCAGCTGGGACTCGTGGGGTGCCAAGCCGTGTGCCGGGTGAGAGGCGGGC	-	novel	NA	P-0056885-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	68	639	0	ENST00000250448.2:c.1110_*41del		p.*370*	ENST00000250448	NM_004496.3	370		2/2	0.130274804894076	5	FACETS	0.776	0.676	0.883	0.259	0.225	0.295	INDETERMINATE	1	TRUE	2	0.775379497261133	5		639	489	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371818	116371818	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056956-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	165	429	0	ENST00000397752.3:c.1297C>T	p.Gln433Ter	p.Q433*	ENST00000397752	NM_000245.2	433	Caa/Taa	3/21	1	2	FACETS	0.808	0.744	0.875	1	0.99	1	CLONAL	2	TRUE	1	0.288300243376652	2		429	708	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1389	158	1122	17	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	1	2	FACETS	0.617	0.563	0.673	0.617	0.563	0.673	SUBCLONAL	1	TRUE	1	0.331210061529699	2		1139	1547	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	202	454	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.774	0.719	0.831	1	0.991	1	SUBCLONAL	2	TRUE	1	0.331210061529699	2		460	788	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	213	662	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.296633963234426	3	FACETS	1	0.973	1	0.55	0.51	0.592	CLONAL	1	TRUE	1	0.331210061529699	3		664	1363	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	60	367	3	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.48	0.412	0.553	0.48	0.412	0.553	SUBCLONAL	1	TRUE	1	0.331210061529699	2		370	755	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	167	875	7	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.855	0.784	0.929	0.855	0.784	0.929	CLONAL	1	TRUE	1	0.331210061529699	2		882	1180	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910372	29910372	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs41548119	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1319	176	1053	1	ENST00000376809.5:c.46del	p.Ala16ProfsTer4	p.A16Pfs*4	ENST00000376809	NM_002116.7	14	tcG/tc	1/8	1	2	FACETS	0.711	0.653	0.772	0.711	0.653	0.772	SUBCLONAL	1	TRUE	1	0.331210061529699	2		1054	1495	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	195	361	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.973	0.899	1	0.973	0.899	1	CLONAL	1	TRUE	1	0.331210061529699	2		361	1210	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263973	104263974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776579	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	70	295	1	ENST00000369902.3:c.71dup	p.Ala25GlyfsTer23	p.A25Gfs*23	ENST00000369902	NM_016169.3	22	gcc/gCcc	1/12	1	2	FACETS	0.937	0.82	1	0.937	0.82	1	CLONAL	1	TRUE	1	0.331210061529699	2		296	451	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	126	784	2	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.753	0.681	0.83	0.753	0.681	0.83	SUBCLONAL	1	TRUE	1	0.331210061529699	2		786	1010	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	65	295	0	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	0.727	0.631	0.831	0.727	0.631	0.831	SUBCLONAL	1	TRUE	1	0.331210061529699	2		295	540	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106078	27106078	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	93	500	0	ENST00000324856.7:c.5693del	p.Pro1898HisfsTer25	p.P1898Hfs*25	ENST00000324856	NM_006015.4	1897	Ccc/cc	20/20	1	2	FACETS	0.732	0.651	0.819	0.732	0.651	0.819	SUBCLONAL	1	TRUE	1	0.331210061529699	2		500	767	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434367	121434367	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	184	847	2	ENST00000257555.6:c.1136del	p.Pro379LeufsTer5	p.P379Lfs*5	ENST00000257555		377	ctC/ct	6/10	1	2	FACETS	0.895	0.824	0.968	0.895	0.824	0.968	CLONAL	1	TRUE	1	0.331210061529699	2		849	1242	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682399	52682400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	73	310	0	ENST00000394830.3:c.773dup	p.Asn258LysfsTer6	p.N258Kfs*6	ENST00000394830	NM_018313.4	258	aat/aaAt	8/30	1	2	FACETS	0.8	0.701	0.907	0.8	0.701	0.907	CLONAL	1	TRUE	1	0.331210061529699	2		310	551	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238958	5238958	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	134	692	1	ENST00000357368.4:c.1821del	p.Val608TrpfsTer30	p.V608Wfs*30	ENST00000357368	NM_002850.3	607	ccC/cc	13/38	1	2	FACETS	0.9	0.817	0.987	0.9	0.817	0.987	CLONAL	1	TRUE	1	0.331210061529699	2		693	899	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440943	56440943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786205215	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	287	712	1	ENST00000407977.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000407977		132	Cga/Tga	4/10	0.296633963234426	3	FACETS	0.885	0.832	0.94	0.885	0.832	0.94	CLONAL	2	TRUE	1	0.331210061529699	3		713	1141	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522601	176522601	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	248	1098	2	ENST00000292408.4:c.1703del	p.Pro568GlnfsTer53	p.P568Qfs*53	ENST00000292408	NM_213647.1	566	cgC/cg	13/18	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.331210061529699	2		1100	1434	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353819	15353819	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	86	520	2	ENST00000263377.2:c.3061del	p.His1021IlefsTer47	p.H1021Ifs*47	ENST00000263377	NM_058243.2	1021	Cat/at	14/20	1	2	FACETS	0.672	0.594	0.756	0.672	0.594	0.756	SUBCLONAL	1	TRUE	1	0.331210061529699	2		522	773	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	77	423	0	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.78	0.685	0.882	0.78	0.685	0.882	SUBCLONAL	1	TRUE	1	0.331210061529699	2		423	596	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911116	29911116	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs199474504	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	220	871	0	ENST00000376809.5:c.415C>T	p.Gln139Ter	p.Q139*	ENST00000376809	NM_002116.7	139	Cag/Tag	3/8	1	2	FACETS	0.954	0.886	1	0.954	0.886	1	CLONAL	1	TRUE	1	0.331210061529699	2		871	1392	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637689	52637689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	60	293	0	ENST00000394830.3:c.2627G>A	p.Arg876His	p.R876H	ENST00000394830	NM_018313.4	876	cGt/cAt	18/30	1	2	FACETS	0.592	0.51	0.682	0.592	0.51	0.682	SUBCLONAL	1	TRUE	1	0.331210061529699	2		293	612	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675170	30675172	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1472156046	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	113	504	0	ENST00000376406.3:c.3073_3075del	p.Lys1025del	p.K1025del	ENST00000376406	NM_014641.2	1025	AAG/-	9/15	1	2	FACETS	0.809	0.728	0.896	0.809	0.728	0.896	CLONAL	1	TRUE	1	0.331210061529699	2		504	843	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748011	72748011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151324323	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	114	651	0	ENST00000357731.5:c.167C>T	p.Ala56Val	p.A56V	ENST00000357731	NM_173808.2	56	gCg/gTg	1/7	1	2	FACETS	0.668	0.6	0.74	0.668	0.6	0.74	SUBCLONAL	1	TRUE	1	0.331210061529699	2		651	1031	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743896	41743896	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1257	203	1050	1	ENST00000301178.4:c.836del	p.Pro279GlnfsTer18	p.P279Qfs*18	ENST00000301178	NM_021913.4	277	gaC/ga	7/20	0.331210061529699	2	FACETS	0.84	0.776	0.906	0.42	0.388	0.453	CLONAL	1	TRUE	0	0.331210061529699	2		1051	1460	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733513	85733513	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs387906350	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	67	381	2	ENST00000370580.1:c.499del	p.Ser167LeufsTer6	p.S167Lfs*6	ENST00000370580	NM_003921.4	167	Tct/ct	3/3	1	2	FACETS	0.65	0.565	0.743	0.65	0.565	0.743	SUBCLONAL	1	TRUE	1	0.331210061529699	2		383	622	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114816	108114817	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	78	419	1	ENST00000278616.4:c.640dup	p.Ser214PhefsTer40	p.S214Ffs*40	ENST00000278616	NM_000051.3	211	-/T	6/63	1	2	FACETS	0.776	0.682	0.876	0.776	0.682	0.876	SUBCLONAL	1	TRUE	1	0.331210061529699	2		420	607	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349689	70349689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs979229015	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	134	311	0	ENST00000374080.3:c.3851G>A	p.Arg1284His	p.R1284H	ENST00000374080		1284	cGc/cAc	27/45	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.331210061529699	1		311	472	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027676	48027678	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs587782858	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	32	212	0	ENST00000234420.5:c.2561_2563del	p.Lys854del	p.K854del	ENST00000234420	NM_000179.2	852	AAG/-	4/10	1	2	FACETS	0.497	0.403	0.602	0.497	0.403	0.602	SUBCLONAL	1	TRUE	1	0.331210061529699	2		212	389	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149982885	149982885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139248642	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	50	291	0	ENST00000253339.5:c.3373C>T	p.Arg1125Cys	p.R1125C	ENST00000253339		1125	Cgc/Tgc	7/7	1	2	FACETS	0.682	0.579	0.794	0.682	0.579	0.794	SUBCLONAL	1	TRUE	1	0.331210061529699	2		291	443	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946224	81946224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755569519	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	125	737	0	ENST00000359376.3:c.1957C>T	p.Arg653Cys	p.R653C	ENST00000359376	NM_002661.3	653	Cgc/Tgc	19/33	1	2	FACETS	0.708	0.64	0.781	0.708	0.64	0.781	SUBCLONAL	1	TRUE	1	0.331210061529699	2		737	1066	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991949	72991949	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs753977275	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	116	610	0	ENST00000268489.5:c.2096del	p.Gly699AlafsTer125	p.G699Afs*125	ENST00000268489	NM_006885.3	699	gGc/gc	2/10	1	2	FACETS	0.755	0.679	0.835	0.755	0.679	0.835	SUBCLONAL	1	TRUE	1	0.331210061529699	2		610	928	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222726	5222726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779918003	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	154	843	2	ENST00000357368.4:c.3077G>A	p.Arg1026His	p.R1026H	ENST00000357368	NM_002850.3	1026	cGc/cAc	18/38	1	2	FACETS	0.798	0.728	0.87	0.798	0.728	0.87	SUBCLONAL	1	TRUE	1	0.331210061529699	2		845	1166	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020769	37020769	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	28	523	1	ENST00000358127.4:c.76G>T	p.Val26Phe	p.V26F	ENST00000358127	NM_001280556.1	26	Gtt/Ttt	2/10	1	2	FACETS	0.186	0.148	0.23	0.186	0.148	0.23	SUBCLONAL	1	TRUE	1	0.331210061529699	2		524	909	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679577	86679577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	55	352	2	ENST00000274376.6:c.2738G>A	p.Arg913Gln	p.R913Q	ENST00000274376	NM_002890.2	913	cGg/cAg	21/25	1	2	FACETS	0.569	0.486	0.659	0.569	0.486	0.659	SUBCLONAL	1	TRUE	1	0.331210061529699	2		354	584	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1396	201	1020	5	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	0.331210061529699	2	FACETS	0.76	0.702	0.821	0.38	0.351	0.411	SUBCLONAL	1	TRUE	0	0.331210061529699	2		1025	1597	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617594	100617594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	27	302	0	ENST00000308731.7:c.475G>A	p.Ala159Thr	p.A159T	ENST00000308731	NM_000061.2	159	Gcc/Acc	6/19	1	1	FACETS	0.257	0.203	0.318	0.257	0.203	0.318	SUBCLONAL	1	TRUE	0	0.331210061529699	1		302	530	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170159	32170159	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559963136	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1309	176	1072	2	ENST00000375023.3:c.3449C>T	p.Thr1150Met	p.T1150M	ENST00000375023	NM_004557.3	1150	aCg/aTg	21/30	1	2	FACETS	0.716	0.657	0.777	0.716	0.657	0.777	SUBCLONAL	1	TRUE	1	0.331210061529699	2		1074	1485	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97888841	97888841	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777732881	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	97	384	0	ENST00000289081.3:c.866C>T	p.Ala289Val	p.A289V	ENST00000289081	NM_000136.2	289	gCc/gTc	9/15	1	2	FACETS	0.879	0.785	0.98	0.879	0.785	0.98	CLONAL	1	TRUE	1	0.331210061529699	2		384	666	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260371	16260371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1185958671	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	88	481	0	ENST00000375759.3:c.7636G>A	p.Ala2546Thr	p.A2546T	ENST00000375759	NM_015001.2	2546	Gcc/Acc	11/15	1	2	FACETS	0.69	0.611	0.775	0.69	0.611	0.775	SUBCLONAL	1	TRUE	1	0.331210061529699	2		481	770	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982474	10982474	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1324350170	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	26	119	0	ENST00000327064.4:c.99del	p.Gly34AlafsTer91	p.G34Afs*91	ENST00000327064	NM_199141.1	32	ttC/tt	1/16	1	2	FACETS	0.822	0.656	1	0.822	0.656	1	CLONAL	1	TRUE	1	0.331210061529699	2		119	191	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231449	5231449	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1233	190	976	2	ENST00000357368.4:c.2027del	p.Pro676ArgfsTer134	p.P676Rfs*134	ENST00000357368	NM_002850.3	676	cCg/cg	14/38	1	2	FACETS	0.806	0.743	0.872	0.806	0.743	0.872	CLONAL	1	TRUE	1	0.331210061529699	2		978	1423	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618494	37618494	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	101	535	0	ENST00000447079.4:c.174del	p.Glu59LysfsTer33	p.E59Kfs*33	ENST00000447079	NM_015083.1	57	aCc/ac	1/14	1	2	FACETS	0.804	0.718	0.894	0.804	0.718	0.894	CLONAL	1	TRUE	1	0.331210061529699	2		535	759	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948484	71948484	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1423	190	1199	2	ENST00000298229.2:c.3201del	p.Ser1068AlafsTer63	p.S1068Afs*63	ENST00000298229	NM_001567.3	1066	Ccc/cc	26/28	1	2	FACETS	0.711	0.655	0.77	0.711	0.655	0.77	SUBCLONAL	1	TRUE	1	0.331210061529699	2		1201	1613	SUCCESS
REL	5966	MSKCC	GRCh37	2	61144018	61144018	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	62	299	0	ENST00000295025.8:c.405del	p.Lys135AsnfsTer3	p.K135Nfs*3	ENST00000295025	NM_002908.2	134	gAa/ga	5/11	1	2	FACETS	0.825	0.714	0.944	0.825	0.714	0.944	CLONAL	1	TRUE	1	0.331210061529699	2		299	454	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798510	32798510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746574637	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	180	793	1	ENST00000374899.4:c.1346G>A	p.Arg449Gln	p.R449Q	ENST00000374899	NM_018833.2	449	cGa/cAa	8/12	1	2	FACETS	0.888	0.817	0.962	0.888	0.817	0.962	CLONAL	1	TRUE	1	0.331210061529699	2		794	1224	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467373	66467373	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	43	198	1	ENST00000273854.3:c.896del	p.Asn299MetfsTer123	p.N299Mfs*123	ENST00000273854	NM_004439.5	299	aAt/at	3/18	1	2	FACETS	0.98	0.826	1	0.98	0.826	1	CLONAL	1	TRUE	1	0.331210061529699	2		199	265	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846165	68846165	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs587782856	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	75	491	0	ENST00000261769.5:c.1136C>T	p.Thr379Met	p.T379M	ENST00000261769	NM_004360.3	379	aCg/aTg	8/16	1	2	FACETS	0.616	0.539	0.699	0.616	0.539	0.699	SUBCLONAL	1	TRUE	1	0.331210061529699	2		491	735	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31511180	31511180	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755611158	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	114	709	0	ENST00000344624.3:c.1394C>T	p.Pro465Leu	p.P465L	ENST00000344624		465	cCg/cTg	6/33	1	2	FACETS	0.688	0.618	0.762	0.688	0.618	0.762	SUBCLONAL	1	TRUE	1	0.331210061529699	2		709	1001	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690387	117690387	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1289431844	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	61	440	0	ENST00000369458.3:c.742C>T	p.Arg248Trp	p.R248W	ENST00000369458	NM_024626.3	248	Cgg/Tgg	5/6	1	2	FACETS	0.55	0.474	0.633	0.55	0.474	0.633	SUBCLONAL	1	TRUE	1	0.331210061529699	2		440	670	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821565	72821565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1369608013	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	58	263	0	ENST00000268489.5:c.10610C>T	p.Ala3537Val	p.A3537V	ENST00000268489	NM_006885.3	3537	gCg/gTg	10/10	1	2	FACETS	0.791	0.681	0.91	0.791	0.681	0.91	CLONAL	1	TRUE	1	0.331210061529699	2		263	443	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729789	41729789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	83	476	0	ENST00000242208.4:c.740G>A	p.Cys247Tyr	p.C247Y	ENST00000242208	NM_002192.2	247	tGc/tAc	3/3	1	2	FACETS	0.82	0.725	0.923	0.82	0.725	0.923	CLONAL	1	TRUE	1	0.331210061529699	2		476	611	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213894	2213896	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1333	189	1021	0	ENST00000398665.3:c.1708_1710del	p.Glu570del	p.E570del	ENST00000398665	NM_032482.2	569	aAGGag/aag	18/28	1	2	FACETS	0.75	0.691	0.812	0.75	0.691	0.812	SUBCLONAL	1	TRUE	1	0.331210061529699	2		1021	1522	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259285	16259290	+	inframe_deletion	In_Frame_Del	DEL	GCCTCT	GCCTCT	-	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	56	374	0	ENST00000375759.3:c.6558_6563del	p.Ser2187_Ala2188del	p.S2187_A2188del	ENST00000375759	NM_015001.2	2184	GCCTCT/-	11/15	1	2	FACETS	0.647	0.554	0.747	0.647	0.554	0.747	SUBCLONAL	1	TRUE	1	0.331210061529699	2		374	523	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406124	70406124	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	94	489	0	ENST00000373644.4:c.3640del	p.Ser1214LeufsTer29	p.S1214Lfs*29	ENST00000373644	NM_030625.2	1213	aTt/at	4/12	1	2	FACETS	0.73	0.649	0.816	0.73	0.649	0.816	SUBCLONAL	1	TRUE	1	0.331210061529699	2		489	778	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936117	71936117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1164589861	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	46	199	0	ENST00000298229.2:c.89C>T	p.Ala30Val	p.A30V	ENST00000298229	NM_001567.3	30	gCc/gTc	1/28	1	2	FACETS	0.765	0.646	0.896	0.765	0.646	0.896	SUBCLONAL	1	TRUE	1	0.331210061529699	2		199	363	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918469	94918469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	66	373	0	ENST00000536441.1:c.713C>T	p.Ala238Val	p.A238V	ENST00000536441	NM_144665.3	238	gCt/gTt	5/10	1	2	FACETS	0.645	0.56	0.737	0.645	0.56	0.737	SUBCLONAL	1	TRUE	1	0.331210061529699	2		373	618	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125513691	125513691	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	49	268	0	ENST00000428830.2:c.823del	p.Arg275GlyfsTer29	p.R275Gfs*29	ENST00000428830	NM_001114121.2	273	gcA/gc	9/14	1	2	FACETS	0.665	0.564	0.776	0.665	0.564	0.776	SUBCLONAL	1	TRUE	1	0.331210061529699	2		268	445	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023674	1023674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368534549	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	87	483	1	ENST00000358495.3:c.890C>T	p.Thr297Met	p.T297M	ENST00000358495	NM_134424.2	297	aCg/aTg	10/12	NA	2	FACETS	0.704	0.623	0.791			1	INDETERMINATE	1	TRUE	NA	0.331210061529699	2		484	746	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442980	49442980	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	107	547	0	ENST00000301067.7:c.3928G>T	p.Gly1310Ter	p.G1310*	ENST00000301067	NM_003482.3	1310	Gga/Tga	12/54	1	2	FACETS	0.728	0.653	0.809	0.728	0.653	0.809	SUBCLONAL	1	TRUE	1	0.331210061529699	2		547	887	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885901	111885901	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	154	793	1	ENST00000341259.2:c.1527del	p.Leu510SerfsTer38	p.L510Sfs*38	ENST00000341259	NM_005475.2	508	cGg/cg	8/8	1	2	FACETS	0.842	0.77	0.919	0.842	0.77	0.919	CLONAL	1	TRUE	1	0.331210061529699	2		794	1104	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112010	115112010	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1229095604	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	135	954	0	ENST00000257566.3:c.1730C>T	p.Thr577Ile	p.T577I	ENST00000257566	NM_016569.3	577	aCc/aTc	7/8	1	2	FACETS	0.644	0.584	0.708	0.644	0.584	0.708	SUBCLONAL	1	TRUE	1	0.331210061529699	2		954	1265	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281282	49281282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	128	664	0	ENST00000282018.3:c.329C>T	p.Ala110Val	p.A110V	ENST00000282018	NM_020377.2	110	gCc/gTc	1/1	1	2	FACETS	0.757	0.685	0.833	0.757	0.685	0.833	SUBCLONAL	1	TRUE	1	0.331210061529699	2		664	1021	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336127	73336127	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	45	193	0	ENST00000377767.4:c.2276A>T	p.Asp759Val	p.D759V	ENST00000377767	NM_014953.3	759	gAt/gTt	17/21	1	2	FACETS	0.86	0.726	1	0.86	0.726	1	CLONAL	1	TRUE	1	0.331210061529699	2		193	316	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988351	36988351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	95	444	1	ENST00000354822.5:c.302C>T	p.Thr101Met	p.T101M	ENST00000354822	NM_001079668.2	101	aCg/aTg	2/3	1	2	FACETS	0.895	0.798	0.998	0.895	0.798	0.998	CLONAL	1	TRUE	1	0.331210061529699	2		445	641	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73992059	73992059	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	168	949	0	ENST00000318443.5:c.79G>T	p.Gly27Ter	p.G27*	ENST00000318443	NM_001024736.1	27	Gga/Tga	2/10	1	2	FACETS	0.796	0.729	0.865	0.796	0.729	0.865	SUBCLONAL	1	TRUE	1	0.331210061529699	2		949	1275	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996198	73996198	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764220550	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	130	800	0	ENST00000318443.5:c.932C>T	p.Thr311Met	p.T311M	ENST00000318443	NM_001024736.1	311	aCg/aTg	5/10	1	2	FACETS	0.714	0.646	0.786	0.714	0.646	0.786	SUBCLONAL	1	TRUE	1	0.331210061529699	2		800	1099	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478609	99478609	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	74	481	1	ENST00000268035.6:c.3254del	p.Gly1085AlafsTer10	p.G1085Afs*10	ENST00000268035	NM_000875.3	1084	cGg/cg	17/21	1	2	FACETS	0.648	0.567	0.735	0.648	0.567	0.735	SUBCLONAL	1	TRUE	1	0.331210061529699	2		482	690	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832765	3832765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777960062	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	117	570	0	ENST00000262367.5:c.1493C>T	p.Thr498Met	p.T498M	ENST00000262367	NM_004380.2	498	aCg/aTg	6/31	1	2	FACETS	0.807	0.727	0.892	0.807	0.727	0.892	CLONAL	1	TRUE	1	0.331210061529699	2		570	875	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857575	9857575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	72	442	0	ENST00000330684.3:c.3826G>A	p.Ala1276Thr	p.A1276T	ENST00000330684	NM_001134407.1	1276	Gcc/Acc	13/13	1	2	FACETS	0.704	0.615	0.799	0.704	0.615	0.799	SUBCLONAL	1	TRUE	1	0.331210061529699	2		442	618	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830355	72830355	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	68	402	0	ENST00000268489.5:c.6226A>T	p.Ile2076Phe	p.I2076F	ENST00000268489	NM_006885.3	2076	Att/Ttt	9/10	1	2	FACETS	0.735	0.64	0.837	0.735	0.64	0.837	SUBCLONAL	1	TRUE	1	0.331210061529699	2		402	559	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371650	89371650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758197438	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	138	822	0	ENST00000301030.4:c.190G>A	p.Ala64Thr	p.A64T	ENST00000301030	NM_001256183.1	64	Gcg/Acg	4/13	1	2	FACETS	0.722	0.656	0.792	0.722	0.656	0.792	SUBCLONAL	1	TRUE	1	0.331210061529699	2		822	1154	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653107	29653107	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	53	369	0	ENST00000356175.3:c.5042G>C	p.Gly1681Ala	p.G1681A	ENST00000356175	NM_000267.3	1681	gGt/gCt	36/57	1	2	FACETS	0.641	0.547	0.744	0.641	0.547	0.744	SUBCLONAL	1	TRUE	1	0.331210061529699	2		369	499	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110581	4110581	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519806	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	143	857	1	ENST00000262948.5:c.376A>G	p.Asn126Asp	p.N126D	ENST00000262948	NM_030662.3	126	Aac/Gac	3/11	1	2	FACETS	0.697	0.634	0.764	0.697	0.634	0.764	SUBCLONAL	1	TRUE	1	0.331210061529699	2		858	1239	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258622	19258622	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	152	825	0	ENST00000162023.5:c.278T>A	p.Ile93Asn	p.I93N	ENST00000162023		93	aTt/aAt	8/13	1	2	FACETS	0.776	0.708	0.847	0.776	0.708	0.847	SUBCLONAL	1	TRUE	1	0.331210061529699	2		825	1183	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792600	33792605	+	inframe_deletion	In_Frame_Del	DEL	GCGCGG	GCGCGG	-	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	11	5	0	ENST00000498907.2:c.716_721del	p.Pro239_Ala240del	p.P239_A240del	ENST00000498907	NM_004364.3	239	cCCGCGCtc/ctc	1/1	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.331210061529699	NA		5	26	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228084	36228084	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	407	980	0	ENST00000222270.7:c.7471del	p.Arg2491ValfsTer14	p.R2491Vfs*14	ENST00000222270	NM_014727.1	2490	ttC/tt	33/37	0.331210061529699	2	FACETS	0.929	0.884	0.975	0.929	0.884	0.975	CLONAL	2	TRUE	0	0.331210061529699	2		980	1323	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917862	29917862	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	129	747	0	ENST00000389048.3:c.806A>T	p.Asp269Val	p.D269V	ENST00000389048	NM_004304.4	269	gAc/gTc	3/29	1	2	FACETS	0.751	0.68	0.827	0.751	0.68	0.827	SUBCLONAL	1	TRUE	1	0.331210061529699	2		747	1037	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609672	46609673	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs769622234	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	155	849	2	ENST00000263734.3:c.2402dup	p.Gln802ThrfsTer31	p.Q802Tfs*31	ENST00000263734	NM_001430.4	799	ttc/ttCc	15/16	1	2	FACETS	0.707	0.645	0.772	0.707	0.645	0.772	SUBCLONAL	1	TRUE	1	0.331210061529699	2		851	1324	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257166	198257166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771847036	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	62	286	0	ENST00000335508.6:c.3776G>A	p.Arg1259Gln	p.R1259Q	ENST00000335508	NM_012433.2	1259	cGg/cAg	25/25	1	2	FACETS	0.755	0.653	0.865	0.755	0.653	0.865	SUBCLONAL	1	TRUE	1	0.331210061529699	2		286	496	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134514511	134514511	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	105	682	1	ENST00000398015.3:c.38C>A	p.Ser13Tyr	p.S13Y	ENST00000398015	NM_004441.4	13	tCc/tAc	1/16	1	2	FACETS	0.641	0.573	0.713	0.641	0.573	0.713	SUBCLONAL	1	TRUE	1	0.331210061529699	2		683	989	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595550	55595550	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	51	262	0	ENST00000288135.5:c.2045del	p.Leu682Ter	p.L682*	ENST00000288135	NM_000222.2	680	aaT/aa	14/21	1	2	FACETS	0.6	0.51	0.699	0.6	0.51	0.699	SUBCLONAL	1	TRUE	1	0.331210061529699	2		262	513	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955881	55955881	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	80	332	0	ENST00000263923.4:c.3281del	p.Leu1094CysfsTer8	p.L1094Cfs*8	ENST00000263923	NM_002253.2	1094	tTg/tg	24/30	1	2	FACETS	0.797	0.702	0.899	0.797	0.702	0.899	SUBCLONAL	1	TRUE	1	0.331210061529699	2		332	606	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197425	106197425	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	57	271	0	ENST00000380013.4:c.5761del	p.Met1921TrpfsTer29	p.M1921Wfs*29	ENST00000380013	NM_001127208.2	1920	Aaa/aa	11/11	1	2	FACETS	0.78	0.671	0.899	0.78	0.671	0.899	SUBCLONAL	1	TRUE	1	0.331210061529699	2		271	441	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143326415	143326415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773384747	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	95	421	0	ENST00000262992.4:c.199G>A	p.Val67Ile	p.V67I	ENST00000262992	NM_001101669.1	67	Gta/Ata	4/24	1	2	FACETS	0.807	0.719	0.901	0.807	0.719	0.901	CLONAL	1	TRUE	1	0.331210061529699	2		421	711	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630207	187630207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	111	506	1	ENST00000441802.2:c.775G>A	p.Ala259Thr	p.A259T	ENST00000441802	NM_005245.3	259	Gca/Aca	2/27	1	2	FACETS	0.85	0.764	0.941	0.85	0.764	0.941	CLONAL	1	TRUE	1	0.331210061529699	2		507	789	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967267	38967267	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	42	181	0	ENST00000357387.3:c.1214del	p.Leu405Ter	p.L405*	ENST00000357387	NM_152756.3	405	tTa/ta	14/38	1	2	FACETS	0.729	0.61	0.859	0.729	0.61	0.859	SUBCLONAL	1	TRUE	1	0.331210061529699	2		181	348	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180076517	180076517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758148540	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	49	139	0	ENST00000261937.6:c.29G>A	p.Arg10Gln	p.R10Q	ENST00000261937	NM_182925.4	10	cGa/cAa	1/30	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.331210061529699	2		139	263	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911285	29911285	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	65	701	0	ENST00000376809.5:c.584A>G	p.Tyr195Cys	p.Y195C	ENST00000376809	NM_002116.7	195	tAc/tGc	3/8	1	2	FACETS	0.445	0.384	0.51	0.445	0.384	0.51	SUBCLONAL	1	TRUE	1	0.331210061529699	2		701	883	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681588	30681588	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	98	495	0	ENST00000376406.3:c.509A>G	p.Glu170Gly	p.E170G	ENST00000376406	NM_014641.2	170	gAg/gGg	3/15	1	2	FACETS	0.817	0.729	0.911	0.817	0.729	0.911	CLONAL	1	TRUE	1	0.331210061529699	2		495	724	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132785	152132785	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	111	698	0	ENST00000262189.6:c.87del	p.Ala30GlnfsTer75	p.A30Qfs*75	ENST00000262189	NM_170606.2	29	ccC/cc	1/59	1	2	FACETS	0.664	0.595	0.736	0.664	0.595	0.736	SUBCLONAL	1	TRUE	1	0.331210061529699	2		698	1010	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240466	98240467	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	79	336	0	ENST00000331920.6:c.1217dup	p.Val407GlyfsTer30	p.V407Gfs*30	ENST00000331920	NM_000264.3	406	gtg/gtTg	9/24	1	2	FACETS	0.822	0.724	0.928	0.822	0.724	0.928	CLONAL	1	TRUE	1	0.331210061529699	2		336	580	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738400	133738400	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	125	545	0	ENST00000318560.5:c.800C>A	p.Thr267Lys	p.T267K	ENST00000318560	NM_005157.4	267	aCg/aAg	4/11	1	2	FACETS	0.906	0.82	0.997	0.906	0.82	0.997	CLONAL	1	TRUE	1	0.331210061529699	2		545	833	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328333	137328333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258357952	NA	P-0057068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	153	764	0	ENST00000481739.1:c.1262G>A	p.Arg421His	p.R421H	ENST00000481739	NM_002957.4	421	cGc/cAc	10/10	1	2	FACETS	0.805	0.735	0.878	0.805	0.735	0.878	CLONAL	1	TRUE	1	0.331210061529699	2		764	1148	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115729	8115729	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057070-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	54	367	0	ENST00000346208.3:c.1075G>T	p.Glu359Ter	p.E359*	ENST00000346208		359	Gaa/Taa	6/6	0.539175687572063	1	FACETS	0.508	0.437	0.585	0.508	0.437	0.585	SUBCLONAL	1	TRUE	0	0.539175687572063	1		367	288	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432497	49432497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775911186	NA	P-0057070-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	66	865	1	ENST00000301067.7:c.8642G>A	p.Arg2881Gln	p.R2881Q	ENST00000301067	NM_003482.3	2881	cGg/cAg	34/54	0.257199579465432	2	FACETS	0.443	0.384	0.506	0.221	0.192	0.253	INDETERMINATE	1	TRUE	0	0.539175687572063	2		866	553	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070623	67070633	+	frameshift_variant	Frame_Shift_Del	DEL	CGAGAGTATGT	CGAGAGTATGT	-	novel	NA	P-0057070-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	56	201	0	ENST00000412916.2:c.250_260del	p.Glu84LeufsTer28	p.E84Lfs*28	ENST00000412916		83	CGAGAGTATGTc/c	3/6	0.539175687572063	1	FACETS	0.762	0.663	0.867	0.762	0.663	0.867	SUBCLONAL	1	TRUE	0	0.539175687572063	1		201	199	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161764	56161765	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTCA	novel	NA	P-0057070-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	78	348	0	ENST00000399503.3:c.1263_1267dup	p.Ser423CysfsTer15	p.S423Cfs*15	ENST00000399503	NM_005921.1	421	ttg/tTGTCAtg	6/20	1	2	FACETS	0.958	0.85	1	0.958	0.85	1	CLONAL	1	TRUE	1	0.539175687572063	2		348	302	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161165	56161177	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGAACTGCAGCTG	AGAACTGCAGCTG	-	novel	NA	P-0057070-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	67	274	0	ENST00000399503.3:c.1036-2_1046del		p.X346_splice	ENST00000399503	NM_005921.1	346		5/20	1	2	FACETS	0.952	0.837	1	0.952	0.837	1	CLONAL	1	TRUE	1	0.539175687572063	2		274	261	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652117	36652117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs114149607	NA	P-0057072-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	108	1071	1	ENST00000244741.5:c.239C>T	p.Thr80Met	p.T80M	ENST00000244741	NM_000389.4	80	aCg/aTg	2/3	1	2	FACETS	0.939	0.844	1	0.939	0.844	1	CLONAL	1	TRUE	1	0.324759585920103	2		1072	708	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596170	43596170	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057072-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	30	575	0	ENST00000355710.3:c.337A>T	p.Asn113Tyr	p.N113Y	ENST00000355710	NM_020975.4	113	Aac/Tac	2/20	1	2	FACETS	0.41	0.33	0.501	0.41	0.33	0.501	SUBCLONAL	1	TRUE	1	0.324759585920103	2		575	451	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670715	67670715	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	285	765	3	ENST00000264010.4:c.1960C>T	p.Arg654Ter	p.R654*	ENST00000264010	NM_006565.3	654	Cga/Tga	11/12	0.716998062026477	4	FACETS	1	0.954	1			1	CLONAL	1	TRUE	NA	0.775128449834566	4		768	1281	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0057168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	163	404	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.206858439139774	3	FACETS	1	0.988	1	0.685	0.635	0.735	INDETERMINATE	1	TRUE	1	0.775128449834566	3		404	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0057168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	992	1042	1	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.762420077616618	3	FACETS	0.987	0.97	1	0.987	0.97	1	CLONAL	3	TRUE	0	0.775128449834566	3		1043	1200	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575080	48575080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	159	505	0	ENST00000342988.3:c.274C>T	p.His92Tyr	p.H92Y	ENST00000342988	NM_005359.5	92	Cat/Tat	3/12	0.705039349322141	1	FACETS	0.948	0.891	1	0.948	0.891	1	CLONAL	1	TRUE	0	0.775128449834566	1		505	265	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944761	31944761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	117	309	0	ENST00000340398.3:c.340G>A	p.Ala114Thr	p.A114T	ENST00000340398	NM_001013699.2	114	Gct/Act	1/1	0.774671184340152	2	FACETS	1	0.924	1	0.505	0.462	0.549	CLONAL	1	TRUE	0	0.775128449834566	2		309	299	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128849141	128849141	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	629	972	0	ENST00000249373.3:c.1369T>C	p.Phe457Leu	p.F457L	ENST00000249373	NM_005631.4	457	Ttc/Ctc	8/12	0.75809428982246	5	FACETS	1	0.968	1	0.671	0.645	0.697	CLONAL	2	TRUE	2	0.775128449834566	5		972	1744	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794987	242794987	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	722	1329	2	ENST00000334409.5:c.222C>A	p.Asn74Lys	p.N74K	ENST00000334409	NM_005018.2	74	aaC/aaA	2/5	0.775128449834566	3	FACETS	1	0.99	1	0.694	0.674	0.714	CLONAL	2	TRUE	0	0.775128449834566	3		1331	1242	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0057200-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	196	282	0	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	1	2	FACETS	0.933	0.874	0.993	0.933	0.874	0.993	CLONAL	1	TRUE	1	0.935341024850137	2		282	449	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243859016	243859016	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs397514606	NA	P-0057200-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	74	261	0	ENST00000263826.5:c.49G>A	p.Glu17Lys	p.E17K	ENST00000263826	NM_005465.4	17	Gaa/Aaa	2/13	1	2	FACETS	0.435	0.383	0.49	0.435	0.383	0.49	SUBCLONAL	1	TRUE	1	0.935341024850137	2		261	364	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132428	11132428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057200-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	519	844	0	ENST00000358026.2:c.2644G>A	p.Glu882Lys	p.E882K	ENST00000358026	NM_001128849.1	882	Gaa/Aaa	19/36	1	2	FACETS	0.966	0.928	1	0.966	0.928	1	CLONAL	1	TRUE	1	0.935341024850137	2		844	1149	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046617	30046617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149150061	NA	P-0057200-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	312	450	1	ENST00000331968.5:c.2566G>A	p.Gly856Arg	p.G856R	ENST00000331968	NM_002742.2	856	Ggg/Agg	18/18	1	2	FACETS	0.952	0.904	1	0.952	0.904	1	CLONAL	1	TRUE	1	0.935341024850137	2		451	701	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357146	89357146	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057200-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	464	712	0	ENST00000301030.4:c.488del	p.Lys163ArgfsTer65	p.K163Rfs*65	ENST00000301030	NM_001256183.1	163	aAg/ag	6/13	1	2	FACETS	0.996	0.956	1	0.996	0.956	1	CLONAL	1	TRUE	1	0.935341024850137	2		712	996	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0057200-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	26	554	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.162	0.128	0.201	0.162	0.128	0.201	SUBCLONAL	1	TRUE	1	0.821223424491869	2		554	391	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0057200-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	185	282	0	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	0.107354325883085	4	FACETS	0.914	0.853	0.975	0.914	0.853	0.975	INDETERMINATE	2	TRUE	2	0.821223424491869	4		282	449	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0057200-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	83	653	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.295	0.26	0.332	0.295	0.26	0.332	SUBCLONAL	1	TRUE	1	0.821223424491869	2		654	686	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243859016	243859016	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs397514606	NA	P-0057200-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	19	261	0	ENST00000263826.5:c.49G>A	p.Glu17Lys	p.E17K	ENST00000263826	NM_005465.4	17	Gaa/Aaa	2/13	1	2	FACETS	0.187	0.141	0.239	0.187	0.141	0.239	SUBCLONAL	1	TRUE	1	0.821223424491869	2		261	248	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132428	11132428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057200-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	350	844	0	ENST00000358026.2:c.2644G>A	p.Glu882Lys	p.E882K	ENST00000358026	NM_001128849.1	882	Gaa/Aaa	19/36	1	2	FACETS	0.991	0.943	1	0.991	0.943	1	CLONAL	1	TRUE	1	0.821223424491869	2		844	860	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174420	11174420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587777900	NA	P-0057200-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	67	720	0	ENST00000361445.4:c.7255G>A	p.Glu2419Lys	p.E2419K	ENST00000361445	NM_004958.3	2419	Gaa/Aaa	53/58	1	2	FACETS	0.23	0.199	0.263	0.23	0.199	0.263	SUBCLONAL	1	TRUE	1	0.821223424491869	2		720	710	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046617	30046617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149150061	NA	P-0057200-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	203	450	1	ENST00000331968.5:c.2566G>A	p.Gly856Arg	p.G856R	ENST00000331968	NM_002742.2	856	Ggg/Agg	18/18	NA	2	FACETS	0.947	0.886	1			1	INDETERMINATE	1	TRUE	NA	0.821223424491869	2		451	522	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357146	89357146	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057200-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	315	712	0	ENST00000301030.4:c.488del	p.Lys163ArgfsTer65	p.K163Rfs*65	ENST00000301030	NM_001256183.1	163	aAg/ag	6/13	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.821223424491869	2		712	727	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220391	1220404	+	frameshift_variant	Frame_Shift_Del	DEL	GACGGCCTGGAGTA	GACGGCCTGGAGTA	-	novel	NA	P-0057234-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	905	763	4	ENST00000326873.7:c.484_497del	p.Asp162ProfsTer3	p.D162Pfs*3	ENST00000326873	NM_000455.4	162	GACGGCCTGGAGTAc/c	4/10	0.551026466945265	3	FACETS	0.927	0.905	0.949	0.927	0.905	0.949	CLONAL	3	TRUE	0	0.597399201653679	3		767	1415	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950068	44950068	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057234-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	309	403	1	ENST00000377967.4:c.3839del	p.Asn1280IlefsTer12	p.N1280Ifs*12	ENST00000377967	NM_021140.2	1279	cgA/cg	26/29	0.582927807586255	2	FACETS	0.883	0.841	0.924	0.883	0.841	0.924	CLONAL	2	TRUE	0	0.597399201653679	2		404	586	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264437	46264437	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057234-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	182	399	0	ENST00000371998.3:c.1484A>T	p.His495Leu	p.H495L	ENST00000371998		495	cAt/cTt	11/23	0.597399201653679	3	FACETS	0.976	0.902	1	0.488	0.451	0.527	CLONAL	1	TRUE	1	0.597399201653679	3		399	811	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553333	41553333	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057234-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	251	485	0	ENST00000263253.7:c.3422A>C	p.Tyr1141Ser	p.Y1141S	ENST00000263253	NM_001429.3	1141	tAc/tCc	18/31	1	2	FACETS	0.983	0.922	1	0.983	0.922	1	CLONAL	1	TRUE	1	0.597399201653679	2		485	855	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	69061316	69061316	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057235-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	19	115	0	ENST00000487270.1:c.1151T>G	p.Phe384Cys	p.F384C	ENST00000487270	NM_133509.3	384	tTt/tGt	11/11	0.122529350484077	4	FACETS	0.771	0.589	0.983	0.193	0.147	0.246	INDETERMINATE	1	TRUE	0	0.395081659225147	4		115	174	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057238-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	325	603	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.486190335914589	3	FACETS	1	0.957	1			1	CLONAL	1	TRUE	NA	0.539187303256359	3		603	1502	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268751	115269472	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCAATACTAAATGTTTTTTATTCCAACACCAAAGAATGGATGGTAAGTTAGCTGTAAAGTTCCTGAAAGTCACGCCTTACCTGTAATGGAAAAAGATTTCCTTATCATGATTGGCTGTTTCAATAAATCCAAAATTATCCTTCAGAGTTGCCACATAACCCAAGAGCCTCTTGGAGTTAGAATTACGACCTAAAAGTCGCACACAAGTTGCAACCTGCTGTCCAGGCCTCTGTTTGTCACTAATACTAAATTCAACCTGTGAAAATTAAGGATGCTCATTAACACCATATCACTTCCACACCAATCTCCTTAACTCAGAAAACAAGACCTATAACTCCCCCAGCGCATGCTTTTCATTCCAAATATCCTTTGTTATTACTTCAATGAAATTGATTTTCACCAAAACATTTATGTCTCATCCCACTTTTCACAAAGGATCAAACTTTTATCTTTCAGTCTGTATTCCTTATAGATTCTGAATTTCTCTAGAGGGCTATCCAAAAACCAAACATATTAAGTATGAGAAAAAATGAACAACAACGTAAAATCTTTGGTGTGCTTTTACTTTGATAATGTTTCAGTAGTAACTGTTTTAACTTTCTTACCAATAACGATTTTATTAAGCATGTTTTATCTAACGTTTAAACAGCTAGATTAACAAGGCTTTGATTAACAAAGAGCTTGACAGACACTTTTAATAAGCTGCTTTCAAATACAAGAT	ATCAATACTAAATGTTTTTTATTCCAACACCAAAGAATGGATGGTAAGTTAGCTGTAAAGTTCCTGAAAGTCACGCCTTACCTGTAATGGAAAAAGATTTCCTTATCATGATTGGCTGTTTCAATAAATCCAAAATTATCCTTCAGAGTTGCCACATAACCCAAGAGCCTCTTGGAGTTAGAATTACGACCTAAAAGTCGCACACAAGTTGCAACCTGCTGTCCAGGCCTCTGTTTGTCACTAATACTAAATTCAACCTGTGAAAATTAAGGATGCTCATTAACACCATATCACTTCCACACCAATCTCCTTAACTCAGAAAACAAGACCTATAACTCCCCCAGCGCATGCTTTTCATTCCAAATATCCTTTGTTATTACTTCAATGAAATTGATTTTCACCAAAACATTTATGTCTCATCCCACTTTTCACAAAGGATCAAACTTTTATCTTTCAGTCTGTATTCCTTATAGATTCTGAATTTCTCTAGAGGGCTATCCAAAAACCAAACATATTAAGTATGAGAAAAAATGAACAACAACGTAAAATCTTTGGTGTGCTTTTACTTTGATAATGTTTCAGTAGTAACTGTTTTAACTTTCTTACCAATAACGATTTTATTAAGCATGTTTTATCTAACGTTTAAACAGCTAGATTAACAAGGCTTTGATTAACAAAGAGCTTGACAGACACTTTTAATAAGCTGCTTTCAAATACAAGAT	-	novel	NA	P-0057238-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	39	208	0	ENST00000438362.2:c.1602+132_1778+81del		p.X534_splice	ENST00000438362	NM_001242891.1	534		14/20	0.539187303256359	1	FACETS	0.457	0.382	0.54	0.457	0.382	0.54	SUBCLONAL	1	TRUE	0	0.539187303256359	1		208	231	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276479	115276479	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0057238-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	125	516	0	ENST00000438362.2:c.850-1G>T		p.X284_splice	ENST00000438362	NM_001242891.1	284			0.539187303256359	1	FACETS	0.485	0.44	0.533	0.485	0.44	0.533	SUBCLONAL	1	TRUE	0	0.539187303256359	1		516	698	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042238	6042238	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057238-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	233	548	0	ENST00000265849.7:c.383del	p.Ser128TrpfsTer8	p.S128Wfs*8	ENST00000265849	NM_000535.5	128	tCg/tg	5/15	0.388564680275601	1	FACETS	0.764	0.714	0.815	0.764	0.714	0.815	SUBCLONAL	1	TRUE	0	0.539187303256359	1		548	826	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0057240-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	45	334	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.481468039333803	3	FACETS	1	0.897	1	0.536	0.455	0.623	CLONAL	1	TRUE	1	0.482627781365069	3		334	216	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0057240-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	462	298	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.482627781365069	6	FACETS	1	0.988	1			1	CLONAL	5	TRUE	NA	0.482627781365069	6		298	719	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691039	NA	P-0057240-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	285	976	0	ENST00000269305.4:c.919+1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.482627781365069	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.482627781365069	2		976	580	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	141	410	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.929	1	1	0.991	1	CLONAL	2	TRUE	1	0.328098993711999	2		410	425	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	231	326	6	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.899	0.847	0.952	1	0.996	1	CLONAL	3	TRUE	1	0.328098993711999	2		332	522	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	193	367	3	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	1	0.947	1	1	0.994	1	CLONAL	2	TRUE	1	0.328098993711999	2		370	577	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	242	585	3	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	1	0.971	1	1	0.995	1	CLONAL	2	TRUE	1	0.328098993711999	2		588	698	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239927	98239927	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1438523462	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	179	504	2	ENST00000331920.6:c.1405G>A	p.Val469Met	p.V469M	ENST00000331920	NM_000264.3	469	Gtg/Atg	10/24	1	2	FACETS	1	0.977	1	1	0.994	1	CLONAL	2	TRUE	1	0.328098993711999	2		506	489	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	96	283	0	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	1	2	FACETS	0.822	0.739	0.909	1	0.984	1	CLONAL	2	TRUE	1	0.328098993711999	2		283	356	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346884	73346884	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	86	211	2	ENST00000377767.4:c.1333del	p.Ser445HisfsTer20	p.S445Hfs*20	ENST00000377767	NM_014953.3	445	Tca/ca	9/21	1	2	FACETS	0.92	0.824	1	1	0.985	1	CLONAL	2	TRUE	1	0.328098993711999	2		213	285	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099008	27099008	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	226	556	0	ENST00000324856.7:c.3424C>T	p.Gln1142Ter	p.Q1142*	ENST00000324856	NM_006015.4	1142	Cag/Tag	13/20	1	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	2	TRUE	1	0.328098993711999	2		556	596	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	237	812	4	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.947	0.887	1	1	0.994	1	CLONAL	2	TRUE	1	0.328098993711999	2		816	763	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509006	106509006	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201525740	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	39	575	0	ENST00000359195.3:c.1000G>A	p.Gly334Ser	p.G334S	ENST00000359195	NM_002649.2	334	Ggc/Agc	2/11	1	2	FACETS	0.475	0.393	0.566	0.475	0.393	0.566	SUBCLONAL	1	TRUE	1	0.328098993711999	2		575	501	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243045	105243045	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	349	1104	0	ENST00000349310.3:c.238T>C	p.Trp80Arg	p.W80R	ENST00000349310	NM_001014432.1	80	Tgg/Cgg	5/15	1	2	FACETS	1	0.987	1	1	0.996	1	CLONAL	2	TRUE	1	0.328098993711999	2		1104	955	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	99	1186	5	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	NA	2	FACETS	0.66	0.588	0.737			1	INDETERMINATE	1	TRUE	NA	0.328098993711999	2		1191	914	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455090	50455090	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	111	330	0	ENST00000331340.3:c.637C>T	p.Arg213Ter	p.R213*	ENST00000331340	NM_006060.4	213	Cga/Tga	6/8	1	2	FACETS	0.953	0.866	1	1	0.989	1	CLONAL	2	TRUE	1	0.328098993711999	2		330	355	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	347	849	1	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	1	2	FACETS	0.859	0.817	0.901	1	0.997	1	CLONAL	3	TRUE	1	0.328098993711999	2		850	821	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	261	875	7	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.328098993711999	2		882	663	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	57	576	4	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	0.821	0.707	0.946	0.821	0.707	0.946	CLONAL	1	TRUE	1	0.328098993711999	2		580	423	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	89	420	10	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	1	0.967	1	1	0.988	1	CLONAL	2	TRUE	1	0.328098993711999	2		430	231	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	144	366	2	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	1	0.94	1	1	0.992	1	CLONAL	2	TRUE	1	0.328098993711999	2		368	428	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255883	16255883	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	192	429	0	ENST00000375759.3:c.3154del	p.Ile1052SerfsTer40	p.I1052Sfs*40	ENST00000375759	NM_015001.2	1050	Aaa/aa	11/15	1	2	FACETS	1	0.986	1	1	0.994	1	CLONAL	2	TRUE	1	0.328098993711999	2		429	481	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910372	29910372	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs41548119	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	376	1053	1	ENST00000376809.5:c.46del	p.Ala16ProfsTer4	p.A16Pfs*4	ENST00000376809	NM_002116.7	14	tcG/tc	1/8	1	2	FACETS	0.823	0.78	0.866	1	0.996	1	CLONAL	2	TRUE	1	0.328098993711999	2		1054	1393	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993730	72993731	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769936196	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	178	818	1	ENST00000268489.5:c.314dup	p.Pro106AlafsTer13	p.P106Afs*13	ENST00000268489	NM_006885.3	105	ccg/ccCg	2/10	1	2	FACETS	0.912	0.845	0.981	1	0.992	1	CLONAL	2	TRUE	1	0.328098993711999	2		819	595	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	282	985	2	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	1	0.982	1	1	0.996	1	CLONAL	2	TRUE	1	0.328098993711999	2		987	788	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872836	37872836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	273	913	1	ENST00000269571.5:c.1715G>A	p.Gly572Asp	p.G572D	ENST00000269571		572	gGc/gAc	14/27	1	2	FACETS	1	0.979	1	1	0.996	1	CLONAL	2	TRUE	1	0.328098993711999	2		914	772	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424734	47424734	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	34	736	0	ENST00000377045.4:c.547del	p.Gln183ArgfsTer109	p.Q183Rfs*109	ENST00000377045	NM_001654.4	181	aCc/ac	6/16	1	2	FACETS	0.338	0.275	0.408	0.338	0.275	0.408	SUBCLONAL	1	TRUE	1	0.328098993711999	2		736	614	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	209	521	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.865	0.811	0.919	1	0.995	1	CLONAL	3	TRUE	1	0.328098993711999	2		527	491	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270530	98270530	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs751977093	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	18	307	0	ENST00000331920.6:c.114del	p.Leu39CysfsTer41	p.L39Cfs*41	ENST00000331920	NM_000264.3	38	ggG/gg	1/24	1	2	FACETS	0.331	0.249	0.429	0.331	0.249	0.429	SUBCLONAL	1	TRUE	1	0.328098993711999	2		307	331	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440757	56440757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774211426	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	211	651	0	ENST00000407977.2:c.461C>T	p.Pro154Leu	p.P154L	ENST00000407977		154	cCg/cTg	5/10	1	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	2	TRUE	1	0.328098993711999	2		651	550	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691872	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs79375991	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	276	347	6	ENST00000295754.5:c.383del	p.Lys128SerfsTer35	p.K128Sfs*35	ENST00000295754	NM_003242.5	125	gAa/ga	3/7	1	2	FACETS	0.976	0.933	1	1	0.997	1	CLONAL	4	TRUE	1	0.328098993711999	2		353	431	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952088	178952088	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553826184	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	118	333	0	ENST00000263967.3:c.3143A>G	p.His1048Arg	p.H1048R	ENST00000263967	NM_006218.2	1048	cAt/cGt	21/21	1	2	FACETS	0.996	0.909	1	1	0.99	1	CLONAL	2	TRUE	1	0.328098993711999	2		333	361	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254166	133254166	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs371882716	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	261	506	0	ENST00000320574.5:c.718G>A	p.Val240Met	p.V240M	ENST00000320574	NM_006231.2	240	Gtg/Atg	7/49	0.0636194786281168	3	FACETS	1	0.975	1	1	0.994	1	INDETERMINATE	3	TRUE	1	0.328098993711999	3		506	586	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262139	10262139	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	53	783	5	ENST00000340748.4:c.2152del	p.Met718CysfsTer59	p.M718Cfs*59	ENST00000340748		718	Atg/tg	23/40	1	2	FACETS	0.393	0.334	0.458	0.393	0.334	0.458	SUBCLONAL	1	TRUE	1	0.328098993711999	2		788	822	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655425	45655425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767656796	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	335	819	1	ENST00000407780.3:c.427G>A	p.Val143Ile	p.V143I	ENST00000407780	NM_001283052.1	143	Gtc/Atc	4/7	1	2	FACETS	1	0.987	1	1	0.996	1	CLONAL	2	TRUE	1	0.328098993711999	2		820	910	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665446	138665446	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	227	730	0	ENST00000330315.3:c.119del	p.Gly40ValfsTer110	p.G40Vfs*110	ENST00000330315	NM_023067.3	40	gGt/gt	1/1	1	2	FACETS	1	0.977	1	1	0.995	1	CLONAL	2	TRUE	1	0.328098993711999	2		730	637	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357715	70357715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1569482448	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	271	905	2	ENST00000374080.3:c.5966G>A	p.Arg1989His	p.R1989H	ENST00000374080		1989	cGc/cAc	41/45	1	2	FACETS	1	0.971	1	1	0.995	1	CLONAL	2	TRUE	1	0.328098993711999	2		907	788	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150039	202150039	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1368296717	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	56	583	0	ENST00000358485.4:c.1480C>T	p.Arg494Ter	p.R494*	ENST00000358485	NM_001080125.1	494	Cga/Tga	8/9	1	2	FACETS	0.536	0.459	0.621	0.536	0.459	0.621	SUBCLONAL	1	TRUE	1	0.328098993711999	2		583	637	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530048	63530048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	35	535	1	ENST00000307078.5:c.2387G>A	p.Ser796Asn	p.S796N	ENST00000307078	NM_004655.3	796	aGc/aAc	10/11	1	2	FACETS	0.347	0.283	0.419	0.347	0.283	0.419	SUBCLONAL	1	TRUE	1	0.328098993711999	2		536	615	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	178	907	0	ENST00000407977.2:c.1975_1976dup	p.Pro660ValfsTer41	p.P660Vfs*41	ENST00000407977		659	ggt/ggGGt	9/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.328098993711999	2		907	746	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15821896	15821896	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	81	290	0	ENST00000307771.7:c.294del	p.Lys98AsnfsTer10	p.K98Nfs*10	ENST00000307771	NM_005089.3	97	Aaa/aa	4/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.328098993711999	2		290	370	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821632	72821632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758349575	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	11	65	1	ENST00000268489.5:c.10543G>A	p.Gly3515Ser	p.G3515S	ENST00000268489	NM_006885.3	3515	Ggc/Agc	10/10	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.328098993711999	2		66	53	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354308	354308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757610038	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	284	839	1	ENST00000262320.3:c.1250G>A	p.Arg417His	p.R417H	ENST00000262320	NM_003502.3	417	cGc/cAc	5/11	1	2	FACETS	1	0.983	1	1	0.996	1	CLONAL	2	TRUE	1	0.328098993711999	2		840	788	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127724	2127724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397515306	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	219	573	0	ENST00000219476.3:c.2963G>A	p.Arg988His	p.R988H	ENST00000219476	NM_000548.3	988	cGc/cAc	26/42	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.328098993711999	2		573	568	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255141	16255142	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	157	415	5	ENST00000375759.3:c.2417_2418dup	p.Arg807AspfsTer3	p.R807Dfs*3	ENST00000375759	NM_015001.2	802	-/GA	11/15	1	2	FACETS	0.936	0.864	1	1	0.992	1	CLONAL	2	TRUE	1	0.328098993711999	2		420	511	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239279	105239279	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs549370342	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	303	901	0	ENST00000349310.3:c.1108C>T	p.Arg370Cys	p.R370C	ENST00000349310	NM_001014432.1	370	Cgc/Tgc	12/15	1	2	FACETS	1	0.984	1	1	0.996	1	CLONAL	2	TRUE	1	0.328098993711999	2		901	838	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396475	30396475	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1474657301	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	121	432	0	ENST00000331968.5:c.244T>C	p.Cys82Arg	p.C82R	ENST00000331968	NM_002742.2	82	Tgc/Cgc	1/18	1	2	FACETS	0.88	0.802	0.961	1	0.989	1	CLONAL	2	TRUE	1	0.328098993711999	2		432	419	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109903	115109903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1182290035	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	177	506	0	ENST00000257566.3:c.1975G>A	p.Ala659Thr	p.A659T	ENST00000257566	NM_016569.3	659	Gcc/Acc	8/8	0.0636194786281168	3	FACETS	0.985	0.918	1	1	0.991	1	INDETERMINATE	3	TRUE	1	0.328098993711999	3		506	425	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188085	151188085	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867628277	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	162	404	0	ENST00000262187.5:c.68C>T	p.Thr23Met	p.T23M	ENST00000262187	NM_005614.3	23	aCg/aTg	2/8	1	2	FACETS	1	0.926	1	1	0.992	1	CLONAL	2	TRUE	1	0.328098993711999	2		404	493	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919865	50919866	+	splice_acceptor_variant	Splice_Site	INS	-	-	G	rs756872503	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	264	975	3	ENST00000440232.2:c.2959dup		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	1	0.948	1	1	0.995	1	CLONAL	2	TRUE	1	0.328098993711999	2		978	798	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109795	115109795	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	258	722	0	ENST00000257566.3:c.2083C>A	p.Arg695Ser	p.R695S	ENST00000257566	NM_016569.3	695	Cgc/Agc	8/8	0.0636194786281168	3	FACETS	0.838	0.789	0.889	1	0.99	1	INDETERMINATE	3	TRUE	1	0.328098993711999	3		722	728	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900081	151900081	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	162	430	0	ENST00000262189.6:c.4030del	p.Ile1344Ter	p.I1344*	ENST00000262189	NM_170606.2	1344	Ata/ta	26/59	1	2	FACETS	1	0.949	1	1	0.993	1	CLONAL	2	TRUE	1	0.328098993711999	2		430	478	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16203172	16203172	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	25	344	0	ENST00000375759.3:c.880A>G	p.Ser294Gly	p.S294G	ENST00000375759	NM_015001.2	294	Agc/Ggc	3/15	1	2	FACETS	0.327	0.257	0.408	0.327	0.257	0.408	SUBCLONAL	1	TRUE	1	0.328098993711999	2		344	466	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970916	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	212	585	0	ENST00000265081.6:c.1147_1148del	p.Lys383GlyfsTer20	p.K383Gfs*20	ENST00000265081	NM_002439.4	381	AAa/a	7/24	1	2	FACETS	0.935	0.872	0.999	1	0.994	1	CLONAL	2	TRUE	1	0.328098993711999	2		585	691	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187719	11187719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767904339	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	36	705	2	ENST00000361445.4:c.6178C>T	p.Arg2060Trp	p.R2060W	ENST00000361445	NM_004958.3	2060	Cgg/Tgg	44/58	1	2	FACETS	0.305	0.249	0.367	0.305	0.249	0.367	SUBCLONAL	1	TRUE	1	0.328098993711999	2		707	720	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502612	149502612	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	137	512	0	ENST00000261799.4:c.2176del	p.Leu726CysfsTer7	p.L726Cfs*7	ENST00000261799	NM_002609.3	726	Ctg/tg	15/23	1	2	FACETS	0.978	0.898	1	1	0.991	1	CLONAL	2	TRUE	1	0.328098993711999	2		512	427	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206715	102206715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759842920	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	137	319	0	ENST00000263464.3:c.1343G>A	p.Arg448Gln	p.R448Q	ENST00000263464	NM_001165.4	448	cGg/cAg	7/9	1	2	FACETS	1	0.937	1	1	0.991	1	CLONAL	2	TRUE	1	0.328098993711999	2		319	408	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199903	128199903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777726701	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	32	785	0	ENST00000341105.2:c.1402G>A	p.Gly468Ser	p.G468S	ENST00000341105	NM_032638.4	468	Ggc/Agc	6/6	1	2	FACETS	0.313	0.253	0.381	0.313	0.253	0.381	SUBCLONAL	1	TRUE	1	0.328098993711999	2		785	623	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100086	27100086	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	130	845	0	ENST00000324856.7:c.3882A>G	p.Ile1294Met	p.I1294M	ENST00000324856	NM_006015.4	1294	atA/atG	16/20	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.328098993711999	2		845	774	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073712	8073712	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs374638182	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	23	388	0	ENST00000377482.5:c.947C>A	p.Pro316His	p.P316H	ENST00000377482	NM_018948.3	316	cCt/cAt	4/4	1	2	FACETS	0.308	0.239	0.388	0.308	0.239	0.388	SUBCLONAL	1	TRUE	1	0.328098993711999	2		388	455	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132815	152132815	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	236	573	4	ENST00000262189.6:c.57del	p.Glu20ArgfsTer85	p.E20Rfs*85	ENST00000262189	NM_170606.2	19	ccC/cc	1/59	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.328098993711999	2		577	635	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40872306	40872306	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs781642151	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	272	628	0	ENST00000428826.2:c.649C>T	p.Arg217Ter	p.R217*	ENST00000428826		217	Cga/Tga	7/21	1	2	FACETS	1	0.987	1	1	0.996	1	CLONAL	2	TRUE	1	0.328098993711999	2		628	723	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626119	12626119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1358060804	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	164	424	1	ENST00000251849.4:c.1841C>T	p.Pro614Leu	p.P614L	ENST00000251849	NM_002880.3	614	cCg/cTg	17/17	1	2	FACETS	1	0.964	1	1	0.993	1	CLONAL	2	TRUE	1	0.328098993711999	2		425	468	SUCCESS
APC	324	MSKCC	GRCh37	5	112176984	112176984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	123	357	0	ENST00000257430.4:c.5693C>T	p.Thr1898Ile	p.T1898I	ENST00000257430	NM_000038.5	1898	aCa/aTa	16/16	1	2	FACETS	0.971	0.887	1	1	0.99	1	CLONAL	2	TRUE	1	0.328098993711999	2		357	386	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025564	1025564	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	290	855	1	ENST00000358495.3:c.811C>T	p.Arg271Trp	p.R271W	ENST00000358495	NM_134424.2	271	Cgg/Tgg	9/12	0.0636194786281168	3	FACETS	0.862	0.814	0.91	1	0.992	1	INDETERMINATE	3	TRUE	1	0.328098993711999	3		856	796	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344949	70344949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs192331892	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	233	783	0	ENST00000374080.3:c.2179G>A	p.Asp727Asn	p.D727N	ENST00000374080		727	Gac/Aac	15/45	1	2	FACETS	1	0.976	1	1	0.995	1	CLONAL	2	TRUE	1	0.328098993711999	2		783	658	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609103	43609103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs77503355	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	319	1023	0	ENST00000355710.3:c.1859G>A	p.Cys620Tyr	p.C620Y	ENST00000355710	NM_020975.4	620	tGc/tAc	10/20	1	2	FACETS	0.845	0.802	0.888	1	0.997	1	CLONAL	3	TRUE	1	0.328098993711999	2		1023	767	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222294	2222294	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751408271	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	294	995	1	ENST00000326181.6:c.578G>A	p.Arg193Gln	p.R193Q	ENST00000326181	NM_032271.2	193	cGg/cAg	8/21	1	2	FACETS	1	0.984	1	1	0.996	1	CLONAL	2	TRUE	1	0.328098993711999	2		996	814	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294297	11294297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	230	550	0	ENST00000361445.4:c.2234G>A	p.Gly745Glu	p.G745E	ENST00000361445	NM_004958.3	745	gGg/gAg	14/58	1	2	FACETS	1	0.982	1	1	0.995	1	CLONAL	2	TRUE	1	0.328098993711999	2		550	627	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465063	120465063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	75	347	0	ENST00000256646.2:c.5009C>T	p.Ser1670Phe	p.S1670F	ENST00000256646	NM_024408.3	1670	tCc/tTc	28/34	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.328098993711999	2		347	374	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466350	120466350	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	45	592	0	ENST00000256646.2:c.4769A>G	p.Tyr1590Cys	p.Y1590C	ENST00000256646	NM_024408.3	1590	tAc/tGc	26/34	1	2	FACETS	0.456	0.383	0.538	0.456	0.383	0.538	SUBCLONAL	1	TRUE	1	0.328098993711999	2		592	601	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276971	123276971	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	21	294	0	ENST00000358487.5:c.946G>A	p.Gly316Ser	p.G316S	ENST00000358487	NM_000141.4	316	Ggt/Agt	8/18	1	2	FACETS	0.375	0.289	0.477	0.375	0.289	0.477	SUBCLONAL	1	TRUE	1	0.328098993711999	2		294	341	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998652	100998652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1345400480	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	242	834	1	ENST00000325455.5:c.1150G>A	p.Ala384Thr	p.A384T	ENST00000325455	NM_001202474.3	384	Gct/Act	1/8	1	2	FACETS	1	0.977	1	1	0.995	1	CLONAL	2	TRUE	1	0.328098993711999	2		835	681	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366501	118366501	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	26	367	0	ENST00000534358.1:c.5450C>T	p.Thr1817Ile	p.T1817I	ENST00000534358	NM_005933.3	1817	aCt/aTt	19/36	1	2	FACETS	0.389	0.308	0.483	0.389	0.308	0.483	SUBCLONAL	1	TRUE	1	0.328098993711999	2		367	407	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445406	49445406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	432	1242	1	ENST00000301067.7:c.2060C>T	p.Ser687Leu	p.S687L	ENST00000301067	NM_003482.3	687	tCa/tTa	10/54	0.0636194786281168	3	FACETS	0.964	0.922	1	1	0.996	1	INDETERMINATE	3	TRUE	1	0.328098993711999	3		1243	1060	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476351	88476351	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	206	714	0	ENST00000360948.2:c.1781A>T	p.Asn594Ile	p.N594I	ENST00000360948	NM_001012338.2	594	aAc/aTc	15/19	1	2	FACETS	1	0.939	1	1	0.994	1	CLONAL	2	TRUE	1	0.328098993711999	2		714	624	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984947	9984947	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	148	507	0	ENST00000330684.3:c.1018A>G	p.Asn340Asp	p.N340D	ENST00000330684	NM_001134407.1	340	Aat/Gat	4/13	1	2	FACETS	1	0.938	1	1	0.992	1	CLONAL	2	TRUE	1	0.328098993711999	2		507	442	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81960706	81960706	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	186	564	0	ENST00000359376.3:c.2437A>G	p.Thr813Ala	p.T813A	ENST00000359376	NM_002661.3	813	Acc/Gcc	23/33	1	2	FACETS	1	0.943	1	1	0.993	1	CLONAL	2	TRUE	1	0.328098993711999	2		564	558	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657690	37657690	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	151	382	0	ENST00000447079.4:c.2607C>A	p.Asn869Lys	p.N869K	ENST00000447079	NM_015083.1	869	aaC/aaA	6/14	1	2	FACETS	1	0.979	1	1	0.993	1	CLONAL	2	TRUE	1	0.328098993711999	2		382	397	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440723	56440723	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	265	714	0	ENST00000407977.2:c.495G>T	p.Trp165Cys	p.W165C	ENST00000407977		165	tgG/tgT	5/10	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.328098993711999	2		714	678	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622201	1622201	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	273	1045	1	ENST00000344749.5:c.674C>T	p.Ala225Val	p.A225V	ENST00000344749	NM_001136139.2	225	gCc/gTc	10/19	1	2	FACETS	1	0.976	1	1	0.996	1	CLONAL	2	TRUE	1	0.328098993711999	2		1046	782	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117135	7117135	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	237	823	0	ENST00000302850.5:c.4081T>C	p.Tyr1361His	p.Y1361H	ENST00000302850	NM_000208.2	1361	Tac/Cac	22/22	1	2	FACETS	1	0.944	1	1	0.995	1	CLONAL	2	TRUE	1	0.328098993711999	2		823	717	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107173	11107173	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765850087	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	257	593	0	ENST00000358026.2:c.1765G>A	p.Ala589Thr	p.A589T	ENST00000358026	NM_001128849.1	589	Gca/Aca	11/36	1	2	FACETS	1	0.98	1	1	0.995	1	CLONAL	2	TRUE	1	0.328098993711999	2		593	716	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18943170	18943170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	58	127	0	ENST00000262803.5:c.152C>T	p.Pro51Leu	p.P51L	ENST00000262803	NM_002911.3	51	cCc/cTc	1/24	1	2	FACETS	1	0.958	1	1	0.983	1	CLONAL	2	TRUE	1	0.328098993711999	2		127	146	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976538	18976538	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	133	1050	0	ENST00000262803.5:c.3188A>T	p.Gln1063Leu	p.Q1063L	ENST00000262803	NM_002911.3	1063	cAg/cTg	22/24	1	2	FACETS	0.91	0.826	0.998	0.91	0.826	0.998	CLONAL	1	TRUE	1	0.328098993711999	2		1050	891	SUCCESS
AXL	558	MSKCC	GRCh37	19	41759556	41759556	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	282	814	1	ENST00000301178.4:c.1979T>C	p.Met660Thr	p.M660T	ENST00000301178	NM_021913.4	660	aTg/aCg	17/20	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.328098993711999	2		815	706	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725167	47725167	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1164583207	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	65	1058	0	ENST00000449228.1:c.577G>A	p.Gly193Arg	p.G193R	ENST00000449228	NM_001127240.2	193	Gga/Aga	4/4	1	2	FACETS	0.403	0.348	0.463	0.403	0.348	0.463	SUBCLONAL	1	TRUE	1	0.328098993711999	2		1058	983	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656919	47656919	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	143	300	0	ENST00000233146.2:c.1115T>C	p.Leu372Ser	p.L372S	ENST00000233146	NM_000251.2	372	tTg/tCg	7/16	1	2	FACETS	1	0.968	1	1	0.992	1	CLONAL	2	TRUE	1	0.328098993711999	2		300	398	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172021	99172021	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	79	548	0	ENST00000074304.5:c.1587A>C	p.Lys529Asn	p.K529N	ENST00000074304	NM_001134224.1	529	aaA/aaC	17/26	1	2	FACETS	0.789	0.695	0.891	0.789	0.695	0.891	SUBCLONAL	1	TRUE	1	0.328098993711999	2		548	610	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873131	136873131	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	28	447	0	ENST00000241393.3:c.367A>G	p.Ser123Gly	p.S123G	ENST00000241393	NM_003467.2	123	Agt/Ggt	2/2	1	2	FACETS	0.379	0.303	0.467	0.379	0.303	0.467	SUBCLONAL	1	TRUE	1	0.328098993711999	2		447	450	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017781	31017781	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	58	877	0	ENST00000375687.4:c.643G>A	p.Ala215Thr	p.A215T	ENST00000375687	NM_015338.5	215	Gct/Act	8/13	1	2	FACETS	0.486	0.417	0.562	0.486	0.417	0.562	SUBCLONAL	1	TRUE	1	0.328098993711999	2		877	727	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514548	41514548	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	40	495	0	ENST00000373198.4:c.113A>G	p.Tyr38Cys	p.Y38C	ENST00000373198	NM_133170.3	38	tAc/tGc	2/32	0.328098993711999	0	FACETS	0.371	0.308	0.44			1	SUBCLONAL	1	TRUE	0	0.328098993711999	0		495	442	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256423	46256423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	154	389	0	ENST00000371998.3:c.651G>A	p.Met217Ile	p.M217I	ENST00000371998		217	atG/atA	7/23	1	2	FACETS	0.978	0.902	1	1	0.992	1	CLONAL	2	TRUE	1	0.328098993711999	2		389	480	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817376	39817376	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	38	628	0	ENST00000288319.7:c.187A>G	p.Arg63Gly	p.R63G	ENST00000288319	NM_182918.3	63	Agg/Ggg	2/10	1	2	FACETS	0.435	0.359	0.52	0.435	0.359	0.52	SUBCLONAL	1	TRUE	1	0.328098993711999	2		628	533	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582171	52582171	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	29	405	0	ENST00000394830.3:c.4657A>G	p.Thr1553Ala	p.T1553A	ENST00000394830	NM_018313.4	1553	Acc/Gcc	30/30	1	2	FACETS	0.347	0.277	0.426	0.347	0.277	0.426	SUBCLONAL	1	TRUE	1	0.328098993711999	2		405	510	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598058	55598058	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	85	421	0	ENST00000288135.5:c.2255T>C	p.Val752Ala	p.V752A	ENST00000288135	NM_000222.2	752	gTg/gCg	16/21	0.328098993711999	1	FACETS	0.841	0.745	0.943	0.841	0.745	0.943	CLONAL	1	TRUE	0	0.328098993711999	1		421	515	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99806113	99806113	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	18	135	0	ENST00000280892.6:c.559A>G	p.Thr187Ala	p.T187A	ENST00000280892	NM_001130678.1	187	Act/Gct	6/7	1	2	FACETS	0.819	0.622	1	0.819	0.622	1	CLONAL	1	TRUE	1	0.328098993711999	2		135	134	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588126	67588126	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs781439997	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	128	307	0	ENST00000274335.5:c.956A>G	p.Asn319Ser	p.N319S	ENST00000274335		319	aAc/aGc	7/15	1	2	FACETS	0.929	0.849	1	1	0.99	1	CLONAL	2	TRUE	1	0.328098993711999	2		307	420	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591276	67591278	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	175	300	0	ENST00000274335.5:c.1777_1779del	p.Lys593del	p.K593del	ENST00000274335		592	AAG/-	13/15	1	2	FACETS	1	0.971	1	1	0.993	1	CLONAL	2	TRUE	1	0.328098993711999	2		300	490	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522600	176522601	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1225914389	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	260	1032	0	ENST00000292408.4:c.1703dup	p.Gly569ArgfsTer13	p.G569Rfs*13	ENST00000292408	NM_213647.1	566	cgc/cgCc	13/18	1	2	FACETS	1	0.964	1	1	0.995	1	CLONAL	2	TRUE	1	0.328098993711999	2		1032	767	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562730	176562730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	204	484	0	ENST00000439151.2:c.626G>A	p.Ser209Asn	p.S209N	ENST00000439151	NM_022455.4	209	aGt/aAt	2/23	1	2	FACETS	0.913	0.85	0.977	1	0.993	1	CLONAL	2	TRUE	1	0.328098993711999	2		484	681	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188370	32188370	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	257	878	0	ENST00000375023.3:c.971del	p.Pro324LeufsTer21	p.P324Lfs*21	ENST00000375023	NM_004557.3	324	cCt/ct	6/30	1	2	FACETS	1	0.976	1	1	0.995	1	CLONAL	2	TRUE	1	0.328098993711999	2		878	731	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161990416	161990416	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	146	459	0	ENST00000366898.1:c.904C>A	p.His302Asn	p.H302N	ENST00000366898	NM_004562.2	302	Cat/Aat	8/12	NA	2	FACETS	0.789	0.724	0.857			1	INDETERMINATE	2	TRUE	NA	0.328098993711999	2		459	564	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140507809	140507809	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	174	409	0	ENST00000288602.6:c.662A>G	p.Glu221Gly	p.E221G	ENST00000288602	NM_004333.4	221	gAa/gGa	5/18	1	2	FACETS	1	0.968	1	1	0.993	1	CLONAL	2	TRUE	1	0.328098993711999	2		409	493	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371820	55371820	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	27	48	0	ENST00000297316.4:c.512del	p.Gly171AlafsTer216	p.G171Afs*216	ENST00000297316	NM_022454.3	170	gaG/ga	2/2	0.253258948158631	4	FACETS	0.918	0.744	1	0.612	0.496	0.74	CLONAL	2	TRUE	1	0.328098993711999	4		48	119	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020506	69020506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1287337314	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	326	580	0	ENST00000288368.4:c.2878G>A	p.Val960Ile	p.V960I	ENST00000288368	NM_024870.2	960	Gtt/Att	24/40	0.305174607844011	3	FACETS	1	0.982	1	1	0.995	1	CLONAL	3	TRUE	1	0.328098993711999	3		580	725	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549369	5549369	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	39	583	0	ENST00000397747.3:c.396G>T	p.Lys132Asn	p.K132N	ENST00000397747	NM_025239.3	132	aaG/aaT	4/7	1	2	FACETS	0.471	0.39	0.561	0.471	0.39	0.561	SUBCLONAL	1	TRUE	1	0.328098993711999	2		583	505	SUCCESS
AR	367	MSKCC	GRCh37	X	66765386	66765386	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	226	831	0	ENST00000374690.3:c.398C>A	p.Pro133Gln	p.P133Q	ENST00000374690	NM_000044.3	133	cCa/cAa	1/8	1	2	FACETS	1	0.982	1	1	0.995	1	CLONAL	2	TRUE	1	0.328098993711999	2		831	612	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342639	70342639	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	52	655	0	ENST00000374080.3:c.1400G>A	p.Ser467Asn	p.S467N	ENST00000374080		467	aGt/aAt	10/45	1	2	FACETS	0.406	0.344	0.474	0.406	0.344	0.474	SUBCLONAL	1	TRUE	1	0.328098993711999	2		655	781	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938711	76938711	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	227	641	0	ENST00000373344.5:c.2037A>C	p.Glu679Asp	p.E679D	ENST00000373344	NM_000489.3	679	gaA/gaC	9/35	1	2	FACETS	1	0.957	1	1	0.995	1	CLONAL	2	TRUE	1	0.328098993711999	2		641	673	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615578	100615578	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	134	513	0	ENST00000308731.7:c.754T>C	p.Trp252Arg	p.W252R	ENST00000308731	NM_000061.2	252	Tgg/Cgg	8/19	1	2	FACETS	0.774	0.706	0.843	1	0.987	1	SUBCLONAL	2	TRUE	1	0.328098993711999	2		513	528	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019601	123019602	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	212	510	0	ENST00000355640.3:c.94dup	p.Thr32AsnfsTer4	p.T32Nfs*4	ENST00000355640		30	tta/ttAa	2/7	1	2	FACETS	0.972	0.907	1	1	0.994	1	CLONAL	2	TRUE	1	0.328098993711999	2		510	665	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845397	42845397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762854045	NA	P-0057245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	71	811	4	ENST00000398585.3:c.865C>T	p.Arg289Cys	p.R289C	ENST00000398585	NM_001135099.1	289	Cgc/Tgc	9/14	1	2	FACETS	0.61	0.531	0.697	0.61	0.531	0.697	SUBCLONAL	1	TRUE	1	0.213430627642035	2		815	1090	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0057245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	119	536	0	ENST00000269305.4:c.673-1G>C		p.X225_splice	ENST00000269305	NM_001126112.2	225			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.213430627642035	2		536	817	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951109	17951109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143038064	NA	P-0057245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	65	719	0	ENST00000458235.1:c.1184G>A	p.Arg395His	p.R395H	ENST00000458235	NM_000215.3	395	cGt/cAt	9/24	0.213430627642035	1	FACETS	0.514	0.444	0.59	0.514	0.444	0.59	SUBCLONAL	1	TRUE	0	0.213430627642035	1		719	1059	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992224	11992224	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	83	488	0	ENST00000396373.4:c.314del	p.Arg105HisfsTer17	p.R105Hfs*17	ENST00000396373	NM_001987.4	105	cGa/ca	3/8	1	2	FACETS	0.958	0.844	1	0.958	0.844	1	CLONAL	1	TRUE	1	0.213430627642035	2		488	812	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164568	36164568	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	57	657	0	ENST00000300305.3:c.1307C>A	p.Ser436Tyr	p.S436Y	ENST00000300305		436	tCc/tAc	8/8	1	2	FACETS	0.618	0.529	0.716	0.618	0.529	0.716	SUBCLONAL	1	TRUE	1	0.213430627642035	2		657	864	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798564	32798564	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs760924428	NA	P-0057245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	147	574	0	ENST00000374899.4:c.1292G>C	p.Gly431Ala	p.G431A	ENST00000374899	NM_018833.2	431	gGg/gCg	8/12	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.213430627642035	2		574	924	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0057254-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	198	144	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.392218521533691	1	FACETS	0.954	0.885	1	0.954	0.885	1	CLONAL	1	TRUE	0	0.392218521533691	1		144	851	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051598	30051598	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057254-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	131	303	0	ENST00000338641.4:c.532C>T	p.Gln178Ter	p.Q178*	ENST00000338641	NM_000268.3	178	Cag/Tag	6/16	0.392218521533691	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.392218521533691	1		303	435	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754352	57754352	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057254-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	105	344	0	ENST00000274289.3:c.499A>G	p.Met167Val	p.M167V	ENST00000274289	NM_006622.3	167	Atg/Gtg	4/14	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.392218521533691	2		344	445	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115892	8115893	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0057256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	121	665	0	ENST00000346208.3:c.1240dup	p.His414ProfsTer93	p.H414Pfs*93	ENST00000346208		413	agc/agCc	6/6	1	2	FACETS	0.969	0.877	1	0.969	0.877	1	CLONAL	1	TRUE	1	0.345298451466992	2		665	723	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539759	187539759	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	85	459	2	ENST00000441802.2:c.7981C>A	p.Leu2661Ile	p.L2661I	ENST00000441802	NM_005245.3	2661	Ctc/Atc	10/27	0.345298451466992	3	FACETS	0.975	0.863	1	0.488	0.431	0.548	CLONAL	1	TRUE	1	0.345298451466992	3		461	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1427441061	NA	P-0057262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	246	329	0	ENST00000269305.4:c.560-2A>G		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.211566421436781	3	FACETS	0.754	0.707	0.803	0.503	0.471	0.536	INDETERMINATE	2	TRUE	0	0.46934172478133	3		329	858	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586404	189586404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908841	NA	P-0057262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	74	210	0	ENST00000264731.3:c.1028G>A	p.Arg343Gln	p.R343Q	ENST00000264731	NM_003722.4	343	cGg/cAg	8/14	1	2	FACETS	0.65	0.571	0.735	0.65	0.571	0.735	SUBCLONAL	1	TRUE	1	0.46934172478133	2		210	485	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0057263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	280	652	1	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.396187472959875	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.410939277870365	3		653	734	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0057263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	140	579	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	0.401626329008895	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.410939277870365	1		579	476	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933311	39933311	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	155	665	0	ENST00000378444.4:c.1288C>G	p.Gln430Glu	p.Q430E	ENST00000378444	NM_001123385.1	430	Cag/Gag	4/15	1	2	FACETS	0.984	0.902	1	0.984	0.902	1	CLONAL	1	TRUE	1	0.410939277870365	2		665	767	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411576	63411576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	84	629	1	ENST00000330258.3:c.1591C>T	p.Arg531Ter	p.R531*	ENST00000330258	NM_152424.3	531	Cga/Tga	2/2	1	2	FACETS	0.806	0.711	0.91	0.806	0.711	0.91	CLONAL	1	TRUE	1	0.21	2		630	992	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097632	27097632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	72	510	0	ENST00000324856.7:c.3221G>A	p.Arg1074Gln	p.R1074Q	ENST00000324856	NM_006015.4	1074	cGg/cAg	12/20	1	2	FACETS	0.879	0.767	1	0.879	0.767	1	CLONAL	1	TRUE	1	0.21	2		510	780	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420661	49420661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555185875	NA	P-0057264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	102	563	0	ENST00000301067.7:c.15088C>T	p.Arg5030Cys	p.R5030C	ENST00000301067	NM_003482.3	5030	Cgt/Tgt	48/54	0.184514364435663	3	FACETS	1	0.96	1	0.58	0.517	0.646	CLONAL	1	TRUE	1	0.21	3		563	926	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579310	7579310	+	splice_donor_variant	Splice_Site	SNP	A	A	C	rs1555526469	NA	P-0057264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	94	470	0	ENST00000269305.4:c.375+2T>G		p.X125_splice	ENST00000269305	NM_001126112.2	125			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.21	2		470	812	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028650	12028650	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	68	363	0	ENST00000353533.5:c.853G>T	p.Asp285Tyr	p.D285Y	ENST00000353533	NM_003010.3	285	Gat/Tat	8/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.21	2		363	579	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0057265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	210	323	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.469866687933472	4	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	2	0.469866687933472	4		323	651	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0057265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	190	278	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	0.316728842492222	3	FACETS	1	0.987	1	0.808	0.757	0.859	CLONAL	2	TRUE	0	0.469866687933472	3		278	412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876658468	NA	P-0057265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	301	582	0	ENST00000269305.4:c.577C>A	p.His193Asn	p.H193N	ENST00000269305	NM_001126112.2	193	Cat/Aat	6/11	0.462203392463037	2	FACETS	0.996	0.947	1	0.996	0.947	1	CLONAL	2	TRUE	0	0.469866687933472	2		582	643	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468218	50468218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	262	511	1	ENST00000331340.3:c.1453G>A	p.Gly485Ser	p.G485S	ENST00000331340	NM_006060.4	485	Ggc/Agc	8/8	0.469866687933472	5	FACETS	0.966	0.906	1	0.644	0.604	0.685	CLONAL	2	TRUE	2	0.469866687933472	5		512	984	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586235	48586235	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0057265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	111	350	0	ENST00000342988.3:c.905-1G>T		p.X302_splice	ENST00000342988	NM_005359.5	302			0.416232537459794	1	FACETS	0.904	0.819	0.992	0.904	0.819	0.992	CLONAL	1	TRUE	0	0.469866687933472	1		350	400	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104671	209104671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	92	376	0	ENST00000345146.2:c.907G>A	p.Val303Ile	p.V303I	ENST00000345146	NM_005896.2	303	Gta/Ata	8/10	0.469866687933472	3	FACETS	0.832	0.741	0.929	0.416	0.37	0.465	CLONAL	1	TRUE	1	0.469866687933472	3		376	581	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0057266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	47	473	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.73	0.619	0.852	0.73	0.619	0.852	SUBCLONAL	1	TRUE	1	0.396135875578867	2		474	325	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231707	66231707	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	65	597	0	ENST00000273854.3:c.1993G>T	p.Glu665Ter	p.E665*	ENST00000273854	NM_004439.5	665	Gaa/Taa	11/18	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.396135875578867	2		597	325	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11269427	11269427	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	144	1018	2	ENST00000361445.4:c.3743G>T	p.Gly1248Val	p.G1248V	ENST00000361445	NM_004958.3	1248	gGa/gTa	25/58	1	2	FACETS	0.828	0.755	0.905	0.828	0.755	0.905	CLONAL	1	TRUE	1	0.396135875578867	2		1020	878	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213852	66213852	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	69	749	0	ENST00000273854.3:c.2578G>T	p.Asp860Tyr	p.D860Y	ENST00000273854	NM_004439.5	860	Gat/Tat	15/18	1	2	FACETS	0.91	0.796	1	0.91	0.796	1	CLONAL	1	TRUE	1	0.396135875578867	2		749	383	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662763	117662763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	53	350	0	ENST00000368508.3:c.4702G>A	p.Val1568Met	p.V1568M	ENST00000368508	NM_002944.2	1568	Gtg/Atg	29/43	1	2	FACETS	0.821	0.704	0.948	0.821	0.704	0.948	CLONAL	1	TRUE	1	0.396135875578867	2		350	326	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841119	15841119	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	118	916	0	ENST00000307771.7:c.1203del	p.His402ThrfsTer?	p.H402Tfs*?	ENST00000307771	NM_005089.3	401	cgT/cg	11/11	1	2	FACETS	0.771	0.695	0.85	0.771	0.695	0.85	SUBCLONAL	1	TRUE	1	0.396135875578867	2		916	773	SUCCESS
AR	367	MSKCC	GRCh37	X	66765214	66765214	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	54	320	0	ENST00000374690.3:c.226C>A	p.Gln76Lys	p.Q76K	ENST00000374690	NM_000044.3	76	Cag/Aag	1/8	1	2	FACETS	0.618	0.529	0.715	0.618	0.529	0.715	SUBCLONAL	1	TRUE	1	0.396135875578867	2		320	441	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778729	76778731	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CCT	CCT	AA	novel	NA	P-0057266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	44	610	2	ENST00000373344.5:c.6848_6849+1delinsTT		p.X2283_splice	ENST00000373344	NM_000489.3	2283		31/35	1	2	FACETS	0.692	0.583	0.812	0.692	0.583	0.812	SUBCLONAL	1	TRUE	1	0.396135875578867	2		612	321	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045888	47045888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782671192	NA	P-0057266-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	74	1160	4	ENST00000377604.3:c.2683C>T	p.Arg895Trp	p.R895W	ENST00000377604	NM_001204468.1	895	Cgg/Tgg	24/24	0.166902560721202	1	FACETS	0.521	0.455	0.593	0.521	0.455	0.593	SUBCLONAL	1	TRUE	0	0.228466761223139	1		1164	1101	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633229	12633229	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs368807126	NA	P-0057266-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	59	1141	1	ENST00000251849.4:c.1171A>T	p.Arg391Trp	p.R391W	ENST00000251849	NM_002880.3	391	Agg/Tgg	11/17	1	2	FACETS	0.57	0.489	0.659	0.57	0.489	0.659	SUBCLONAL	1	TRUE	1	0.228466761223139	2		1142	906	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578242	7578242	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882003	NA	P-0057266-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	113	1248	2	ENST00000269305.4:c.607G>T	p.Val203Leu	p.V203L	ENST00000269305	NM_001126112.2	203	Gtg/Ttg	6/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.228466761223139	2		1250	940	SUCCESS
FH	2271	MSKCC	GRCh37	1	241677004	241677004	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs573311798	NA	P-0057266-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	55	438	0	ENST00000366560.3:c.277A>G	p.Ile93Val	p.I93V	ENST00000366560	NM_000143.3	93	Att/Gtt	3/10	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.228466761223139	2		438	385	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243560	46243560	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0057266-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	28	232	0	ENST00000334344.6:c.1912+1G>T		p.X638_splice	ENST00000334344	NM_152641.2	638			0.203047328915002	1	FACETS	0.89	0.714	1	0.89	0.714	1	CLONAL	1	TRUE	0	0.228466761223139	1		232	244	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654516	29654516	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0057266-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	41	296	0	ENST00000356175.3:c.5206-1G>T		p.X1736_splice	ENST00000356175	NM_000267.3	1736			1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.228466761223139	2		296	291	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244197	5244197	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057266-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	65	1389	7	ENST00000357368.4:c.1285G>T	p.Ala429Ser	p.A429S	ENST00000357368	NM_002850.3	429	Gcg/Tcg	11/38	1	2	FACETS	0.541	0.467	0.621	0.541	0.467	0.621	SUBCLONAL	1	TRUE	1	0.228466761223139	2		1396	1052	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291067	15291067	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057266-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1297	229	1467	10	ENST00000263388.2:c.3143G>T	p.Gly1048Val	p.G1048V	ENST00000263388	NM_000435.2	1048	gGg/gTg	20/33	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.228466761223139	2		1477	1526	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964954	25964954	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057266-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	79	715	0	ENST00000435504.4:c.4252del	p.His1418MetfsTer35	p.H1418Mfs*35	ENST00000435504		1418	Cat/at	13/13	1	2	FACETS	0.908	0.797	1	0.908	0.797	1	CLONAL	1	TRUE	1	0.228466761223139	2		715	762	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050299	128050299	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057266-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	99	728	0	ENST00000285398.2:c.358G>T	p.Ala120Ser	p.A120S	ENST00000285398	NM_000122.1	120	Gcc/Tcc	3/15	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.228466761223139	2		728	867	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530186	212530186	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057266-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	48	471	0	ENST00000342788.4:c.1733C>G	p.Thr578Arg	p.T578R	ENST00000342788	NM_005235.2	578	aCa/aGa	15/28	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.228466761223139	2		471	351	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143326463	143326463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs890780946	NA	P-0057266-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	64	403	0	ENST00000262992.4:c.151G>A	p.Val51Met	p.V51M	ENST00000262992	NM_001101669.1	51	Gtg/Atg	4/24	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.228466761223139	2		403	554	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526255	31526255	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057266-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1373	160	1630	5	ENST00000344624.3:c.785A>T	p.Asp262Val	p.D262V	ENST00000344624		262	gAc/gTc	2/33	1	2	FACETS	0.914	0.835	0.997	0.914	0.835	0.997	CLONAL	1	TRUE	1	0.228466761223139	2		1635	1533	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876478	35876479	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0057266-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	75	912	3	ENST00000303115.3:c.1270_1271delinsCT	p.Gly424Leu	p.G424L	ENST00000303115	NM_002185.3	424	GGa/CTa	8/8	1	2	FACETS	0.706	0.617	0.802	0.706	0.617	0.802	SUBCLONAL	1	TRUE	1	0.228466761223139	2		915	930	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80088593	80088593	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057266-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	31	655	0	ENST00000265081.6:c.2585G>T	p.Gly862Val	p.G862V	ENST00000265081	NM_002439.4	862	gGa/gTa	19/24	0.166902560721202	1	FACETS	0.724	0.587	0.879	0.724	0.587	0.879	SUBCLONAL	1	TRUE	0	0.228466761223139	1		655	332	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32191638	32191638	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057266-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	66	1254	0	ENST00000375023.3:c.68C>A	p.Pro23His	p.P23H	ENST00000375023	NM_004557.3	23	cCc/cAc	1/30	1	2	FACETS	0.478	0.413	0.549	0.478	0.413	0.549	SUBCLONAL	1	TRUE	1	0.228466761223139	2		1254	1208	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931858	68931858	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057266-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	106	952	2	ENST00000288368.4:c.288C>A	p.His96Gln	p.H96Q	ENST00000288368	NM_024870.2	96	caC/caA	3/40	1	2	FACETS	0.78	0.701	0.863	1	0.984	1	SUBCLONAL	2	TRUE	1	0.228466761223139	2		954	595	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911553	39911553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057266-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	47	807	1	ENST00000378444.4:c.5077G>A	p.Ala1693Thr	p.A1693T	ENST00000378444	NM_001123385.1	1693	Gca/Aca	15/15	0.166902560721202	1	FACETS	0.437	0.367	0.514	0.437	0.367	0.514	SUBCLONAL	1	TRUE	0	0.228466761223139	1		808	834	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032530	47032530	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057266-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	62	1234	2	ENST00000377604.3:c.436C>A	p.Arg146Ser	p.R146S	ENST00000377604	NM_001204468.1	146	Cgt/Agt	5/24	0.166902560721202	1	FACETS	0.425	0.365	0.49	0.425	0.365	0.49	SUBCLONAL	1	TRUE	0	0.228466761223139	1		1236	1132	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245342	53245342	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057266-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	70	1041	5	ENST00000375401.3:c.695A>T	p.Glu232Val	p.E232V	ENST00000375401	NM_004187.3	232	gAg/gTg	6/26	0.166902560721202	1	FACETS	0.534	0.464	0.61	0.534	0.464	0.61	SUBCLONAL	1	TRUE	0	0.228466761223139	1		1046	1017	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875893	76875893	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057266-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	35	562	0	ENST00000373344.5:c.5242G>T	p.Gly1748Ter	p.G1748*	ENST00000373344	NM_000489.3	1748	Gga/Tga	20/35	0.166902560721202	1	FACETS	0.603	0.494	0.726	0.603	0.494	0.726	SUBCLONAL	1	TRUE	0	0.228466761223139	1		562	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0057288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	330	789	3	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.358785970611209	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.411576061012984	2		792	798	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952117	178952117	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	81	302	0	ENST00000263967.3:c.3172A>C	p.Ile1058Leu	p.I1058L	ENST00000263967	NM_006218.2	1058	Atc/Ctc	21/21	1	2	FACETS	1	0.924	1	1	0.987	1	CLONAL	2	FALSE	1	0.435900374247537	2		302	181	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696689	47696689	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519972	NA	P-0057289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	160	576	0	ENST00000347630.2:c.259T>A	p.Tyr87Asn	p.Y87N	ENST00000347630	NM_001007230.1	87	Tac/Aac	5/11	1	2	FACETS	0.948	0.881	1	1	0.992	1	CLONAL	2	FALSE	1	0.435900374247537	2		576	387	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195644	102195644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749825246	NA	P-0057289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	112	424	1	ENST00000263464.3:c.404G>A	p.Arg135His	p.R135H	ENST00000263464	NM_001165.4	135	cGt/cAt	2/9	1	2	FACETS	0.859	0.784	0.936	1	0.988	1	CLONAL	2	FALSE	1	0.435900374247537	2		425	299	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440950	56440951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCA	novel	NA	P-0057289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	110	720	0	ENST00000407977.2:c.383_386dup	p.Glu131GlyfsTer2	p.E131Gfs*2	ENST00000407977		129	gcg/gcTGGCg	4/10	1	2	FACETS	0.78	0.702	0.862	0.78	0.702	0.862	SUBCLONAL	1	FALSE	1	0.435900374247537	2		720	647	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528637	89528639	+	frameshift_variant	Frame_Shift_Del	DEL	CCC	CCC	AG	novel	NA	P-0057289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	34	225	1	ENST00000336596.2:c.2937_2939delinsAG	p.Pro980GlufsTer22	p.P980Efs*22	ENST00000336596	NM_005233.5	979	ggCCCa/ggAGa	17/17	1	2	FACETS	0.902	0.746	1	0.902	0.746	1	CLONAL	1	FALSE	1	0.435900374247537	2		226	173	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0057290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	127	323	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	3	FACETS	1	0.918	1			1	INDETERMINATE	2	TRUE	NA	0.240436164465696	3		323	586	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0057290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	105	643	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.240436164465696	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.240436164465696	1		643	610	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974746	21974753	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCTCTA	CTCCTCTA	GTC	novel	NA	P-0057290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	32	344	1	ENST00000304494.5:c.74_81delinsGAC	p.Val25GlyfsTer17	p.V25Gfs*17	ENST00000304494	NM_000077.4	25	gTAGAGGAG/gGAC	1/3	0.240436164465696	1	FACETS	0.874	0.712	1	0.874	0.712	1	CLONAL	1	TRUE	0	0.240436164465696	1		345	268	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057307-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	33	365	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.836	1	1	0.836	1	CLONAL	1	TRUE	1	0.17	2		365	378	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0057307-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	3398	748	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	0.3	19	FACETS	1	0.992	1			1	CLONAL	22	TRUE	NA	0.17	19		748	4432	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070823	30070823	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0057307-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	50	357	0	ENST00000338641.4:c.1341-2A>G		p.X447_splice	ENST00000338641	NM_000268.3	447			1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.17	2		357	587	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183765	10183765	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	129	446	0	ENST00000256474.2:c.234T>G	p.Asn78Lys	p.N78K	ENST00000256474	NM_000551.3	78	aaT/aaG	1/3	0.607581224222484	1	FACETS	0.979	0.902	1	0.979	0.902	1	CLONAL	1	TRUE	0	0.607581224222484	1		446	302	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0057312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	63	410	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.225126882024277	3	FACETS	1	0.963	1	0.668	0.579	0.764	CLONAL	1	TRUE	1	0.225126882024277	3		410	466	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089914	16089914	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	64	303	0	ENST00000268712.3:c.196C>T	p.Arg66Ter	p.R66*	ENST00000268712	NM_006311.3	66	Cga/Tga	3/46	0.225126882024277	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.225126882024277	1		303	448	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858362	27858362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	56	425	0	ENST00000359303.2:c.209G>A	p.Arg70His	p.R70H	ENST00000359303	NM_003535.2	70	cGc/cAc	1/1	0.108246328746087	1	FACETS	0.6	0.513	0.695	0.6	0.513	0.695	INDETERMINATE	1	TRUE	0	0.225126882024277	1		425	736	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732961	30732961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	98	281	0	ENST00000295754.5:c.1574C>T	p.Pro525Leu	p.P525L	ENST00000295754	NM_003242.5	525	cCa/cTa	7/7	1	2	FACETS	0.772	0.69	0.858	1	0.982	1	SUBCLONAL	2	TRUE	1	0.225126882024277	2		281	564	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	92	365	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.7	2		365	262	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0057313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	134	351	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.918	0.842	0.997	0.918	0.842	0.997	CLONAL	1	TRUE	1	0.7	2		351	417	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941654	48941654	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs776534331	NA	P-0057314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	176	169	0	ENST00000267163.4:c.964G>T	p.Glu322Ter	p.E322*	ENST00000267163	NM_000321.2	322	Gaa/Taa	10/27	0.897386803811306	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	FALSE	0	0.897386803811306	2		169	194	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0057314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	386	468	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	0.897386803811306	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	FALSE	0	0.897386803811306	2		468	421	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434325	49434325	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	558	576	1	ENST00000301067.7:c.7228C>T	p.Arg2410Ter	p.R2410*	ENST00000301067	NM_003482.3	2410	Cga/Tga	31/54	0.843903037321732	4	FACETS	0.993	0.957	1	0.993	0.957	1	CLONAL	2	FALSE	2	0.897386803811306	4		577	1188	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188064	11188064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	142	291	0	ENST00000361445.4:c.6030G>A	p.Met2010Ile	p.M2010I	ENST00000361445	NM_004958.3	2010	atG/atA	43/58	0.84552439212748	3	FACETS	1	0.958	1	0.532	0.489	0.576	CLONAL	1	FALSE	1	0.897386803811306	3		291	431	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259367	11259367	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	207	433	0	ENST00000361445.4:c.4201G>C	p.Glu1401Gln	p.E1401Q	ENST00000361445	NM_004958.3	1401	Gaa/Caa	28/58	0.84552439212748	3	FACETS	1	0.954	1	0.514	0.479	0.55	CLONAL	1	FALSE	1	0.897386803811306	3		433	650	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448347	49448347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	427	470	0	ENST00000301067.7:c.364G>A	p.Glu122Lys	p.E122K	ENST00000301067	NM_003482.3	122	Gag/Aag	3/54	0.843903037321732	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	FALSE	2	0.897386803811306	4		470	866	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117539	70117539	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	157	283	0	ENST00000245479.2:c.7C>G	p.Leu3Val	p.L3V	ENST00000245479	NM_000346.3	3	Ctc/Gtc	1/3	0.897386803811306	4	FACETS	0.951	0.874	1	0.476	0.437	0.516	CLONAL	1	FALSE	2	0.897386803811306	4		283	698	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948723	55948723	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	58	352	0	ENST00000263923.4:c.3742G>T	p.Glu1248Ter	p.E1248*	ENST00000263923	NM_002253.2	1248	Gaa/Taa	28/30	0.897386803811306	2	FACETS	0.315	0.271	0.362	0.157	0.135	0.181	SUBCLONAL	1	FALSE	0	0.897386803811306	2		352	411	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0057315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	175	144	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.655618895718376	3	FACETS	0.841	0.794	0.887	0.841	0.794	0.887	CLONAL	3	TRUE	0	0.655618895718376	3		144	281	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0057315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	146	323	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.655618895718376	2		323	435	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591901	48591901	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	158	361	0	ENST00000342988.3:c.1064A>T	p.Asp355Val	p.D355V	ENST00000342988	NM_005359.5	355	gAc/gTc	9/12	0.655618895718376	1	FACETS	0.982	0.915	1	0.982	0.915	1	CLONAL	1	TRUE	0	0.655618895718376	1		361	330	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218488	5218488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1361339357	NA	P-0057315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	277	513	1	ENST00000357368.4:c.3991G>A	p.Ala1331Thr	p.A1331T	ENST00000357368	NM_002850.3	1331	Gcc/Acc	25/38	1	2	FACETS	0.97	0.914	1	0.97	0.914	1	CLONAL	1	TRUE	1	0.655618895718376	2		514	871	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711267	114711268	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	110	263	0	ENST00000543371.1:c.285dup	p.Lys96Ter	p.K96*	ENST00000543371	NM_001198531.1	94	-/T	3/14	1	2	FACETS	0.847	0.768	0.93	0.847	0.768	0.93	CLONAL	1	TRUE	1	0.655618895718376	2		263	396	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554706	63554707	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0057315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	161	350	0	ENST00000307078.5:c.32dup	p.Asp12GlyfsTer8	p.D12Gfs*8	ENST00000307078	NM_004655.3	11	ccg/ccCg	2/11	1	2	FACETS	0.954	0.881	1	0.954	0.881	1	CLONAL	1	TRUE	1	0.655618895718376	2		350	515	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0057316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	81	397	7	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.429392558796053	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.429392558796053	1		404	279	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0057316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	164	646	2	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.429392558796053	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.429392558796053	1		648	569	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0057316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	109	370	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.429392558796053	2		370	448	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566513	41566513	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	139	254	0	ENST00000263253.7:c.4390C>T	p.Gln1464Ter	p.Q1464*	ENST00000263253	NM_001429.3	1464	Cag/Tag	27/31	0.246377924198322	2	FACETS	0.758	0.696	0.822	0.758	0.696	0.822	INDETERMINATE	2	TRUE	0	0.429392558796053	2		254	427	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0057317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	196	351	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.410117138682171	5	FACETS	0.889	0.834	0.945	1	0.986	1	CLONAL	4	TRUE	2	0.410117138682171	5		351	434	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120612003	120612004	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	rs372504208	NA	P-0057317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	13	11	0	ENST00000256646.2:c.17_18del	p.Pro6ArgfsTer27	p.P6Rfs*27	ENST00000256646	NM_024408.3	6	cCC/c	1/34	0.410117138682171	5	FACETS	1	0.845	1	0.427	0.309	0.564	CLONAL	1	TRUE	2	0.410117138682171	5		11	80	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0057317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	547	907	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.399713157474122	4	FACETS	0.937	0.904	0.969	0.937	0.904	0.969	CLONAL	4	TRUE	0	0.410117138682171	4		907	1004	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383338	42383338	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782282654	NA	P-0057317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	98	418	1	ENST00000221972.3:c.358G>A	p.Gly120Ser	p.G120S	ENST00000221972	NM_021601.3	120	Ggc/Agc	2/5	0.410117138682171	1	FACETS	0.669	0.598	0.744	0.669	0.598	0.744	SUBCLONAL	1	TRUE	0	0.410117138682171	1		419	568	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231124	46231124	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	47	299	0	ENST00000334344.6:c.1044T>A	p.Asp348Glu	p.D348E	ENST00000334344	NM_152641.2	348	gaT/gaA	9/21	0.233962383885982	5	FACETS	1	0.854	1	0.336	0.284	0.393	INDETERMINATE	1	TRUE	2	0.410117138682171	5		299	367	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32931999	32931999	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	185	237	0	ENST00000380152.3:c.7738C>G	p.Gln2580Glu	p.Q2580E	ENST00000380152		2580	Cag/Gag	16/27	0.410117138682171	5	FACETS	0.943	0.891	0.995			1	CLONAL	5	TRUE	NA	0.410117138682171	5		237	309	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127363	55127363	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	82	447	0	ENST00000257290.5:c.151G>T	p.Gly51Trp	p.G51W	ENST00000257290	NM_006206.4	51	Ggg/Tgg	3/23	1	2	FACETS	0.528	0.465	0.596	0.528	0.465	0.596	SUBCLONAL	1	TRUE	1	0.410117138682171	2		447	757	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630137	100630137	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	369	243	0	ENST00000308731.7:c.136C>A	p.Arg46Ser	p.R46S	ENST00000308731	NM_000061.2	46	Cgt/Agt	2/19	0.921886871364365	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	1	0.921886871364365	4		243	485	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78435701	78435701	+	splice_acceptor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0057318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	17	160	0	ENST00000370768.2:c.121-2del		p.X41_splice	ENST00000370768	NM_003902.3	41			0.921886871364365	3	FACETS	0.339	0.254	0.438	0.113	0.084	0.146	SUBCLONAL	1	TRUE	0	0.921886871364365	3		160	159	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577093	7577110	+	inframe_deletion	In_Frame_Del	DEL	CGGTCTCTCCCAGGACAG	CGGTCTCTCCCAGGACAG	-	novel	NA	P-0057318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	927	408	1	ENST00000269305.4:c.828_845del	p.Cys277_Arg282del	p.C277_R282del	ENST00000269305	NM_001126112.2	276	gcCTGTCCTGGGAGAGACCGg/gcg	8/11	0.921886871364365	3	FACETS	1	0.999	1	1	0.999	1	CLONAL	3	TRUE	0	0.921886871364365	3		409	936	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272521	15272521	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	502	352	0	ENST00000263388.2:c.5918A>G	p.Glu1973Gly	p.E1973G	ENST00000263388	NM_000435.2	1973	gAg/gGg	33/33	0.921886871364365	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.921886871364365	3		352	790	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280273	1280273	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3089	556	422	0	ENST00000310581.5:c.1950G>T	p.Arg650Ser	p.R650S	ENST00000310581	NM_198253.2	650	agG/agT	4/16	0.921886871364365	10	FACETS	0.776	0.74	0.812	0.194	0.185	0.203	SUBCLONAL	2	TRUE	2	0.921886871364365	10		422	3645	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922770	44922770	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	201	273	0	ENST00000377967.4:c.1631A>G	p.Gln544Arg	p.Q544R	ENST00000377967	NM_021140.2	544	cAg/cGg	16/29	0.921886871364365	4	FACETS	0.936	0.869	1	0.312	0.289	0.336	CLONAL	1	TRUE	1	0.921886871364365	4		273	895	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413566	32413566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121907900	NA	P-0057319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	214	308	1	ENST00000332351.3:c.1384C>T	p.Arg462Trp	p.R462W	ENST00000332351	NM_024426.4	462	Cgg/Tgg	9/10	0.27748689520122	0	FACETS	0.77	0.729	0.809			1	SUBCLONAL	4	TRUE	0	0.27748689520122	0		309	362	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0057320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	182	500	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.825775026833791	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	FALSE	0	0.825775026833791	3		500	195	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874031	123874031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1447464550	NA	P-0057320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	10	23	0	ENST00000330479.4:c.62C>T	p.Ala21Val	p.A21V	ENST00000330479	NM_020382.3	21	gCg/gTg	2/9	0.35987193816566	6	FACETS	0.691	0.472	0.959	0.173	0.118	0.24	INDETERMINATE	1	FALSE	2	0.825775026833791	6		23	93	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953758	48953758	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	64	171	0	ENST00000267163.4:c.1361del	p.Tyr454SerfsTer3	p.Y454Sfs*3	ENST00000267163	NM_000321.2	454	tAc/tc	14/27	0.815836671170937	4	FACETS	1	0.976	1	0.873	0.811	0.929	CLONAL	3	FALSE	0	0.825775026833791	4		171	81	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057321-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	128	365	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.844	0.775	0.913	0.844	0.775	0.913	CLONAL	1	TRUE	1	0.922285670985216	2		365	329	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001091	150001091	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753995655	NA	P-0057321-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	174	326	0	ENST00000253339.5:c.2513G>A	p.Arg838His	p.R838H	ENST00000253339		838	cGt/cAt	4/7	1	2	FACETS	0.95	0.887	1	0.95	0.887	1	CLONAL	1	TRUE	1	0.922285670985216	2		326	397	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	150	365	0				ENST00000310581	NM_198253.2	-/1132			0.244623909161506	6	FACETS	1	0.966	1	1	0.966	1	CLONAL	3	TRUE	3	0.244623909161506	6		365	555	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0057322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	125	410	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.244623909161506	4	FACETS	1	0.978	1	0.826	0.752	0.904	CLONAL	2	TRUE	1	0.244623909161506	4		410	513	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067836	30067836	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315499	NA	P-0057322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	73	372	0	ENST00000338641.4:c.1021C>T	p.Arg341Ter	p.R341*	ENST00000338641	NM_000268.3	341	Cga/Tga	11/16	0.244623909161506	2	FACETS	0.796	0.7	0.898	0.796	0.7	0.898	SUBCLONAL	2	TRUE	0	0.244623909161506	2		372	375	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610311	10610311	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	137	867	1	ENST00000171111.5:c.399G>A	p.Met133Ile	p.M133I	ENST00000171111	NM_203500.1	133	atG/atA	2/6	0.166660157990442	3	FACETS	1	0.98	1	0.646	0.587	0.708	CLONAL	1	TRUE	1	0.244623909161506	3		868	973	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361224	66361224	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	25	246	0	ENST00000273854.3:c.948C>G	p.Ile316Met	p.I316M	ENST00000273854	NM_004439.5	316	atC/atG	4/18	1	2	FACETS	0.584	0.46	0.726	0.584	0.46	0.726	SUBCLONAL	1	TRUE	1	0.244623909161506	2		246	350	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207162	1207162	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs137853076	NA	P-0057340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	376	912	0	ENST00000326873.7:c.250A>T	p.Lys84Ter	p.K84*	ENST00000326873	NM_000455.4	84	Aag/Tag	1/10	0.339245282815642	2	FACETS	0.963	0.915	1	0.963	0.915	1	CLONAL	2	TRUE	0	0.339245282815642	2		912	1151	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0057340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	349	856	0	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	0.301374057622122	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.339245282815642	2		856	922	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792755	33792757	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs746430067	NA	P-0057340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	11	47	0	ENST00000498907.2:c.564_566del	p.Pro189del	p.P189del	ENST00000498907	NM_004364.3	188	ccGCCc/ccc	1/1	0.328337088530668	4	FACETS	0.86	0.6	1	0.43	0.3	0.588	CLONAL	1	TRUE	2	0.339245282815642	4		47	101	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115269657	115269657	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	123	555	0	ENST00000438362.2:c.1549G>T	p.Ala517Ser	p.A517S	ENST00000438362	NM_001242891.1	517	Gct/Tct	13/20	0.339245282815642	3	FACETS	0.995	0.9	1	0.498	0.45	0.548	CLONAL	1	TRUE	1	0.339245282815642	3		555	852	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843682	156843682	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1488	198	1069	0	ENST00000524377.1:c.1108G>T	p.Ala370Ser	p.A370S	ENST00000524377	NM_002529.3	370	Gcc/Tcc	8/17	0.314369709398594	4	FACETS	0.927	0.855	1			1	CLONAL	1	TRUE	NA	0.339245282815642	4		1069	1686	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117765	115117765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	218	349	0	ENST00000257566.3:c.670C>T	p.Pro224Ser	p.P224S	ENST00000257566	NM_016569.3	224	Cca/Tca	3/8	0.339245282815642	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	3	TRUE	0	0.339245282815642	3		349	489	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864727	37864727	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs970583285	NA	P-0057340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	151	721	0	ENST00000269571.5:c.379A>C	p.Thr127Pro	p.T127P	ENST00000269571		127	Acc/Ccc	3/27	0.339245282815642	3	FACETS	1	0.939	1	0.518	0.472	0.565	CLONAL	1	TRUE	1	0.339245282815642	3		721	1006	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602688	10602688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	446	969	1	ENST00000171111.5:c.890G>A	p.Cys297Tyr	p.C297Y	ENST00000171111	NM_203500.1	297	tGc/tAc	3/6	0.339245282815642	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.339245282815642	2		970	1189	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129945	55129945	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	237	601	0	ENST00000257290.5:c.479C>A	p.Thr160Asn	p.T160N	ENST00000257290	NM_006206.4	160	aCc/aAc	4/23	0.339245282815642	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.339245282815642	3		601	765	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161433	55161433	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	203	476	0	ENST00000257290.5:c.3264C>A	p.Phe1088Leu	p.F1088L	ENST00000257290	NM_006206.4	1088	ttC/ttA	23/23	0.339245282815642	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.339245282815642	3		476	655	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439623	140439623	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	111	571	0	ENST00000288602.6:c.2116C>G	p.Leu706Val	p.L706V	ENST00000288602	NM_004333.4	706	Ctc/Gtc	17/18	0.339245282815642	3	FACETS	1	0.955	1	0.554	0.498	0.613	CLONAL	1	TRUE	1	0.339245282815642	3		571	691	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525904	148525904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	68	297	0	ENST00000320356.2:c.553G>T	p.Asp185Tyr	p.D185Y	ENST00000320356	NM_004456.4	185	Gac/Tac	6/20	0.339245282815642	3	FACETS	1	0.886	1	0.509	0.443	0.579	CLONAL	1	TRUE	1	0.339245282815642	3		297	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577535	+	frameshift_variant	Frame_Shift_Del	DEL	GGCC	GGCC	-	novel	NA	P-0057341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	234	516	0	ENST00000269305.4:c.746_749del	p.Arg249ThrfsTer95	p.R249Tfs*95	ENST00000269305	NM_001126112.2	249	aGGCCc/ac	7/11	0.342185217228213	2	FACETS	0.79	0.743	0.838	0.79	0.743	0.838	SUBCLONAL	2	TRUE	0	0.512339350872713	2		516	578	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032100	48032100	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	79	262	0	ENST00000234420.5:c.3490G>A	p.Val1164Met	p.V1164M	ENST00000234420	NM_000179.2	1164	Gtg/Atg	6/10	0.247734455798492	4	FACETS	1	0.938	1	0.365	0.322	0.41	INDETERMINATE	1	TRUE	1	0.512339350872713	4		262	426	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	114	551	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	1	2	FACETS	0.836	0.754	0.923	1	0.986	1	CLONAL	2	TRUE	1	0.21	2		551	649	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680747	88680747	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	57	640	0	ENST00000360948.2:c.510G>T	p.Trp170Cys	p.W170C	ENST00000360948	NM_001012338.2	170	tgG/tgT	6/19	1	2	FACETS	0.773	0.662	0.895	0.773	0.662	0.895	SUBCLONAL	1	TRUE	1	0.21	2		640	702	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0057343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	235	351	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.37079727664818	4	FACETS	0.896	0.847	0.946	1	0.989	1	CLONAL	4	TRUE	1	0.370319790008548	4		351	485	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850705	63850705	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs201178069	NA	P-0057343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	137	316	1	ENST00000279873.7:c.1489del	p.Ile497Ter	p.I497*	ENST00000279873	NM_032199.2	495	Aaa/aa	10/10	0.370319790008548	6	FACETS	1	0.951	1	0.53	0.484	0.579	CLONAL	2	TRUE	2	0.370319790008548	6		317	607	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106915	27106915	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	305	642	0	ENST00000324856.7:c.6526C>T	p.Gln2176Ter	p.Q2176*	ENST00000324856	NM_006015.4	2176	Cag/Tag	20/20	0.37079727664818	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.370319790008548	3		642	836	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877156	89877156	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	95	381	0	ENST00000389301.3:c.481T>C	p.Phe161Leu	p.F161L	ENST00000389301	NM_000135.2	161	Ttc/Ctc	5/43	0.37079727664818	3	FACETS	0.99	0.883	1	0.495	0.441	0.552	CLONAL	1	TRUE	1	0.370319790008548	3		381	614	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542780	187542780	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533979319	NA	P-0057343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	78	351	0	ENST00000441802.2:c.4960C>T	p.Arg1654Cys	p.R1654C	ENST00000441802	NM_005245.3	1654	Cgt/Tgt	10/27	0.37079727664818	3	FACETS	0.973	0.857	1	0.487	0.428	0.549	CLONAL	1	TRUE	1	0.370319790008548	3		351	513	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928978	49928978	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	153	804	0	ENST00000296474.3:c.3388C>G	p.Arg1130Gly	p.R1130G	ENST00000296474	NM_002447.2	1130	Cga/Gga	16/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.370319790008548	2		804	785	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751483	57751483	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	91	369	0	ENST00000274289.3:c.1508G>T	p.Trp503Leu	p.W503L	ENST00000274289	NM_006622.3	503	tGg/tTg	11/14	0.37079727664818	3	FACETS	1	0.948	1	0.555	0.494	0.619	CLONAL	1	TRUE	1	0.370319790008548	3		369	525	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495354	149495354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151236133	NA	P-0057343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	332	822	1	ENST00000261799.4:c.3293G>A	p.Arg1098Gln	p.R1098Q	ENST00000261799	NM_002609.3	1098	cGg/cAg	23/23	0.37079727664818	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.370319790008548	3		823	896	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931846	39931846	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	159	689	0	ENST00000378444.4:c.2753A>C	p.Gln918Pro	p.Q918P	ENST00000378444	NM_001123385.1	918	cAa/cCa	4/15	0.37079727664818	3	FACETS	1	0.976	1	0.586	0.537	0.637	CLONAL	1	TRUE	1	0.370319790008548	3		689	868	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692790	89692790	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554898067	NA	P-0057345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	161	298	0	ENST00000371953.3:c.274G>T	p.Asp92Tyr	p.D92Y	ENST00000371953	NM_000314.4	92	Gac/Tac	5/9	0.705781565625877	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.705781565625877	1		298	293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0057346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	64	179	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		180	839	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952139	178952139	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1560150596	NA	P-0057346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	11	184	0	ENST00000263967.3:c.3194A>T	p.His1065Leu	p.H1065L	ENST00000263967	NM_006218.2	1065	cAt/cTt	21/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		184	253	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs199469672	NA	P-0057346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	38	567	1	ENST00000374080.3:c.131G>C	p.Gly44Ala	p.G44A	ENST00000374080		44	gGt/gCt	2/45	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		568	669	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339230	70339230	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs199469667	NA	P-0057346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	113	546	0	ENST00000374080.3:c.107T>G	p.Leu36Arg	p.L36R	ENST00000374080		36	cTg/cGg	2/45	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		546	619	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0057347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	16	257	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.786	0.58	1	0.786	0.58	1	CLONAL	1	TRUE	1	0.11	2		257	370	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0057347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	34	799	1	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.604	0.491	0.732	0.604	0.491	0.732	SUBCLONAL	1	TRUE	1	0.11	2		800	1024	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0057347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	74	924	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.11	2		924	1047	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0057347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	31	835	2	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.51	0.41	0.624	0.51	0.41	0.624	SUBCLONAL	1	TRUE	1	0.11	2		837	1105	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	30	502	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.776	0.623	0.951	0.776	0.623	0.951	CLONAL	1	TRUE	1	0.11	2		502	703	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	21	508	0	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	1	2	FACETS	0.56	0.429	0.714	0.56	0.429	0.714	SUBCLONAL	1	TRUE	1	0.11	2		508	682	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236086	108236086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782292	NA	P-0057347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	21	475	0	ENST00000278616.4:c.9022C>T	p.Arg3008Cys	p.R3008C	ENST00000278616	NM_000051.3	3008	Cgt/Tgt	63/63	1	2	FACETS	0.527	0.404	0.672	0.527	0.404	0.672	SUBCLONAL	1	TRUE	1	0.11	2		475	725	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs371769427	NA	P-0057347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	9	217	0	ENST00000291552.4:c.101C>A	p.Ser34Tyr	p.S34Y	ENST00000291552	NM_006758.2	34	tCt/tAt	2/8	1	2	FACETS	0.466	0.307	0.67	0.466	0.307	0.67	SUBCLONAL	1	TRUE	1	0.11	2		217	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0057348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	406	1161	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	1	2	FACETS	0.959	0.915	1	0.959	0.915	1	CLONAL	1	TRUE	1	0.856507817059616	2		1161	989	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822008	72822009	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	rs745803083	NA	P-0057348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	171	459	0	ENST00000268489.5:c.10164_10166dup	p.Gln3389dup	p.Q3389dup	ENST00000268489	NM_006885.3	3389	caa/caGCAa	10/10	1	2	FACETS	0.634	0.585	0.684	0.634	0.585	0.684	SUBCLONAL	1	TRUE	1	0.856507817059616	2		459	630	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885315	111885315	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	203	415	0	ENST00000341259.2:c.1203del	p.Tyr401Ter	p.Y401*	ENST00000341259	NM_005475.2	401	taC/ta	6/8	1	2	FACETS	0.848	0.792	0.905	0.848	0.792	0.905	CLONAL	1	TRUE	1	0.856507817059616	2		415	559	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268089	153268090	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTT	novel	NA	P-0057348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	151	253	0	ENST00000281708.4:c.716_718dup	p.Lys239dup	p.K239dup	ENST00000281708	NM_033632.3	239	atg/aAAAtg	4/12	1	2	FACETS	0.86	0.795	0.927	0.86	0.795	0.927	CLONAL	1	TRUE	1	0.856507817059616	2		253	410	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343502	70343502	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	302	599	0	ENST00000374080.3:c.1676C>G	p.Ser559Cys	p.S559C	ENST00000374080		559	tCt/tGt	12/45	1	2	FACETS	0.824	0.779	0.87	0.824	0.779	0.87	CLONAL	1	TRUE	1	0.856507817059616	2		599	856	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0057349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	377	561	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.559969975251253	3	FACETS	0.9	0.86	0.94	0.9	0.86	0.94	CLONAL	2	TRUE	1	0.724115517482364	3		561	788	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871172	35871172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893894	NA	P-0057349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	146	286	3	ENST00000303115.3:c.394C>T	p.Pro132Ser	p.P132S	ENST00000303115	NM_002185.3	132	Cct/Tct	4/8	0.724115517482364	3	FACETS	1	0.966	1	0.548	0.503	0.594	CLONAL	1	TRUE	1	0.724115517482364	3		289	501	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517994	8517994	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	171	404	5	ENST00000356435.5:c.1397G>A	p.Trp466Ter	p.W466*	ENST00000356435		466	tGg/tAg	10/35	1	2	FACETS	0.992	0.921	1	0.992	0.921	1	CLONAL	1	TRUE	1	0.724115517482364	2		409	476	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971121	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	139	360	2	ENST00000304494.5:c.237_238delinsTT	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	79	acCCga/acTTga	2/3	0.724115517482364	1	FACETS	0.972	0.906	1	0.972	0.906	1	CLONAL	1	TRUE	0	0.724115517482364	1		362	252	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876533	35876533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1329173277	NA	P-0057349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	149	518	5	ENST00000303115.3:c.1325G>A	p.Gly442Glu	p.G442E	ENST00000303115	NM_002185.3	442	gGa/gAa	8/8	0.724115517482364	3	FACETS	0.893	0.818	0.97	0.446	0.409	0.485	CLONAL	1	TRUE	1	0.724115517482364	3		523	628	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934362	68934362	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745857499	NA	P-0057349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	194	374	1	ENST00000288368.4:c.428G>A	p.Arg143Gln	p.R143Q	ENST00000288368	NM_024870.2	143	cGg/cAg	4/40	1	2	FACETS	0.967	0.902	1	0.967	0.902	1	CLONAL	1	TRUE	1	0.724115517482364	2		375	554	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347855	347855	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	315	1182	7	ENST00000262320.3:c.1651G>A	p.Glu551Lys	p.E551K	ENST00000262320	NM_003502.3	551	Gag/Aag	6/11	1	2	FACETS	0.974	0.922	1	0.974	0.922	1	CLONAL	1	TRUE	1	0.724115517482364	2		1189	893	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290921	15290921	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765140794	NA	P-0057349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	288	1053	3	ENST00000263388.2:c.3289G>A	p.Gly1097Arg	p.G1097R	ENST00000263388	NM_000435.2	1097	Ggg/Agg	20/33	1	2	FACETS	0.987	0.932	1	0.987	0.932	1	CLONAL	1	TRUE	1	0.724115517482364	2		1056	806	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	25	619	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.168	0.132	0.21	0.168	0.132	0.21	SUBCLONAL	1	TRUE	1	0.568087686918781	2		619	524	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939260	71939260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	58	690	3	ENST00000298229.2:c.209G>A	p.Arg70His	p.R70H	ENST00000298229	NM_001567.3	70	cGc/cAc	2/28	1	2	FACETS	0.25	0.214	0.289	0.25	0.214	0.289	SUBCLONAL	1	TRUE	1	0.568087686918781	2		693	817	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	33	292	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.23	0.186	0.278	0.23	0.186	0.278	SUBCLONAL	1	TRUE	1	0.568087686918781	2		292	506	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	56	775	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.232	0.198	0.269	0.232	0.198	0.269	SUBCLONAL	1	TRUE	1	0.568087686918781	2		778	850	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	36	436	3	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.184	0.151	0.222	0.184	0.151	0.222	SUBCLONAL	1	TRUE	1	0.568087686918781	2		439	687	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	110	304	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.544558683271779	2	FACETS	0.782	0.706	0.862	0.391	0.353	0.431	SUBCLONAL	1	TRUE	0	0.568087686918781	2		304	495	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	398	662	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.805	0.77	0.841	1	0.996	1	CLONAL	2	TRUE	1	0.568087686918781	2		664	870	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138583	2138583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778484981	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	43	637	1	ENST00000219476.3:c.5396C>T	p.Ser1799Leu	p.S1799L	ENST00000219476	NM_000548.3	1799	tCg/tTg	42/42	1	2	FACETS	0.179	0.148	0.212	0.179	0.148	0.212	SUBCLONAL	1	TRUE	1	0.568087686918781	2		638	848	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	45	651	1	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.219	0.183	0.258	0.219	0.183	0.258	SUBCLONAL	1	TRUE	1	0.568087686918781	2		652	725	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746015	162746015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121964865	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	28	263	0	ENST00000367921.3:c.2138C>T	p.Thr713Ile	p.T713I	ENST00000367921	NM_006182.2	713	aCa/aTa	16/18	1	2	FACETS	0.228	0.181	0.28	0.228	0.181	0.28	SUBCLONAL	1	TRUE	1	0.568087686918781	2		263	433	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	10	272	0	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	0.106	0.071	0.15	0.106	0.071	0.15	SUBCLONAL	1	TRUE	1	0.568087686918781	2		272	332	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	73	649	0	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	1	2	FACETS	0.341	0.297	0.388	0.341	0.297	0.388	SUBCLONAL	1	TRUE	1	0.568087686918781	2		649	754	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189412	56189412	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	77	404	0	ENST00000399503.3:c.4444C>T	p.Arg1482Ter	p.R1482*	ENST00000399503	NM_005921.1	1482	Cga/Tga	20/20	1	2	FACETS	0.378	0.331	0.428	0.378	0.331	0.428	SUBCLONAL	1	TRUE	1	0.568087686918781	2		404	717	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368202	45368202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	64	239	0	ENST00000262160.6:c.1400C>T	p.Ser467Leu	p.S467L	ENST00000262160	NM_005901.5	467	tCa/tTa	11/11	1	2	FACETS	0.569	0.495	0.649	0.569	0.495	0.649	SUBCLONAL	1	TRUE	1	0.568087686918781	2		239	396	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026115	14026116	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs769120755	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	45	211	0	ENST00000311895.7:c.1081dup	p.Met361AsnfsTer4	p.M361Nfs*4	ENST00000311895	NM_005236.2	359	gaa/gAaa	6/11	1	2	FACETS	0.421	0.355	0.494	0.421	0.355	0.494	SUBCLONAL	1	TRUE	1	0.568087686918781	2		211	376	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	77	819	0	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.266	0.232	0.302	0.266	0.232	0.302	SUBCLONAL	1	TRUE	1	0.568087686918781	2		819	1021	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	43	243	1	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.336	0.281	0.396	0.336	0.281	0.396	SUBCLONAL	1	TRUE	1	0.568087686918781	2		244	451	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692793	89692793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	212	233	0	ENST00000371953.3:c.277C>T	p.His93Tyr	p.H93Y	ENST00000371953	NM_000314.4	93	Cat/Tat	5/9	0.544558683271779	2	FACETS	0.88	0.829	0.931	0.88	0.829	0.931	CLONAL	2	TRUE	0	0.568087686918781	2		233	424	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	92	343	2	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	1	2	FACETS	0.522	0.465	0.584	0.522	0.465	0.584	SUBCLONAL	1	TRUE	1	0.568087686918781	2		345	620	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346158	89346158	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs878855327	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	17	256	2	ENST00000301030.4:c.6792del	p.Ala2265ProfsTer72	p.A2265Pfs*72	ENST00000301030	NM_001256183.1	2264	ccC/cc	9/13	1	2	FACETS	0.204	0.151	0.265	0.204	0.151	0.265	SUBCLONAL	1	TRUE	1	0.568087686918781	2		258	294	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942053	71942053	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	44	684	0	ENST00000298229.2:c.1322del	p.Asn441ThrfsTer2	p.N441Tfs*2	ENST00000298229	NM_001567.3	439	ccA/cc	12/28	1	2	FACETS	0.177	0.148	0.21	0.177	0.148	0.21	SUBCLONAL	1	TRUE	1	0.568087686918781	2		684	875	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841231	15841236	+	inframe_deletion	In_Frame_Del	DEL	AGCCGG	AGCCGG	-	rs752736259	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	15	195	0	ENST00000307771.7:c.1338_1343del	p.Ser447_Arg448del	p.S447_R448del	ENST00000307771	NM_005089.3	439	AGCCGG/-	11/11	1	2	FACETS	0.196	0.143	0.259	0.196	0.143	0.259	SUBCLONAL	1	TRUE	1	0.568087686918781	2		195	270	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351595	89351595	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	30	637	0	ENST00000301030.4:c.1355del	p.Asn452IlefsTer3	p.N452Ifs*3	ENST00000301030	NM_001256183.1	452	aAt/at	9/13	1	2	FACETS	0.11	0.088	0.135	0.11	0.088	0.135	SUBCLONAL	1	TRUE	1	0.568087686918781	2		637	960	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009413	69009413	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	37	320	0	ENST00000288368.4:c.2530G>T	p.Gly844Cys	p.G844C	ENST00000288368	NM_024870.2	844	Ggt/Tgt	22/40	1	2	FACETS	0.231	0.19	0.278	0.231	0.19	0.278	SUBCLONAL	1	TRUE	1	0.568087686918781	2		320	563	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	197	387	0	ENST00000263967.3:c.278G>C	p.Arg93Pro	p.R93P	ENST00000263967	NM_006218.2	93	cGg/cCg	2/21	1	2	FACETS	0.834	0.773	0.896	0.834	0.773	0.896	CLONAL	1	TRUE	1	0.568087686918781	2		387	832	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	228	758	2	ENST00000227507.2:c.859C>A	p.Pro287Thr	p.P287T	ENST00000227507	NM_053056.2	287	Ccc/Acc	5/5	1	2	FACETS	0.825	0.769	0.883	0.825	0.769	0.883	CLONAL	1	TRUE	1	0.568087686918781	2		760	973	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060955	38060955	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	11	386	0	ENST00000250448.2:c.1034del	p.Gly345AlafsTer5	p.G345Afs*5	ENST00000250448	NM_004496.3	345	gGc/gc	2/2	1	2	FACETS	0.096	0.066	0.134	0.096	0.066	0.134	SUBCLONAL	1	TRUE	1	0.568087686918781	2		386	403	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146945	38146945	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	52	538	0	ENST00000317025.8:c.3197del	p.Asn1066ThrfsTer16	p.N1066Tfs*16	ENST00000317025	NM_023034.1	1066	aAc/ac	18/24	1	2	FACETS	0.193	0.163	0.225	0.193	0.163	0.225	SUBCLONAL	1	TRUE	1	0.568087686918781	2		538	951	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384746	84384747	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	36	221	0	ENST00000321945.7:c.696dup	p.Val233SerfsTer5	p.V233Sfs*5	ENST00000321945	NM_139076.2	232	-/A	8/9	1	2	FACETS	0.325	0.267	0.39	0.325	0.267	0.39	SUBCLONAL	1	TRUE	1	0.568087686918781	2		221	390	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29106023	29106023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782152	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	102	208	0	ENST00000328354.6:c.817G>A	p.Glu273Lys	p.E273K	ENST00000328354	NM_007194.3	273	Gaa/Aaa	7/15	1	2	FACETS	0.935	0.843	1	0.935	0.843	1	CLONAL	1	TRUE	1	0.568087686918781	2		208	384	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781215	3781215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748975160	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	57	811	2	ENST00000262367.5:c.5150G>A	p.Arg1717His	p.R1717H	ENST00000262367	NM_004380.2	1717	cGc/cAc	30/31	1	2	FACETS	0.179	0.153	0.208	0.179	0.153	0.208	SUBCLONAL	1	TRUE	1	0.568087686918781	2		813	1121	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763501	41763501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200271277	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	107	445	0	ENST00000301178.4:c.2300G>A	p.Arg767His	p.R767H	ENST00000301178	NM_021913.4	767	cGc/cAc	19/20	1	2	FACETS	0.681	0.613	0.753	0.681	0.613	0.753	SUBCLONAL	1	TRUE	1	0.568087686918781	2		445	553	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475078	40475078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	38	522	0	ENST00000264657.5:c.1832G>A	p.Ser611Asn	p.S611N	ENST00000264657	NM_139276.2	611	aGt/aAt	20/24	1	2	FACETS	0.181	0.149	0.217	0.181	0.149	0.217	SUBCLONAL	1	TRUE	1	0.568087686918781	2		522	739	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348674	89348674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs963622923	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	67	654	0	ENST00000301030.4:c.4276G>A	p.Glu1426Lys	p.E1426K	ENST00000301030	NM_001256183.1	1426	Gaa/Aaa	9/13	1	2	FACETS	0.244	0.211	0.28	0.244	0.211	0.28	SUBCLONAL	1	TRUE	1	0.568087686918781	2		654	967	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260990	16260990	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	74	453	0	ENST00000375759.3:c.8255G>T	p.Gly2752Val	p.G2752V	ENST00000375759	NM_015001.2	2752	gGt/gTt	11/15	1	2	FACETS	0.429	0.376	0.487	0.429	0.376	0.487	SUBCLONAL	1	TRUE	1	0.568087686918781	2		453	607	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106483	27106483	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	201	570	0	ENST00000324856.7:c.6094G>T	p.Glu2032Ter	p.E2032*	ENST00000324856	NM_006015.4	2032	Gaa/Taa	20/20	1	2	FACETS	0.89	0.827	0.955	0.89	0.827	0.955	CLONAL	1	TRUE	1	0.568087686918781	2		570	795	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653855	206653855	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	51	592	0	ENST00000367120.3:c.1406G>A	p.Ser469Asn	p.S469N	ENST00000367120	NM_014002.3	469	aGc/aAc	13/22	1	2	FACETS	0.198	0.167	0.232	0.198	0.167	0.232	SUBCLONAL	1	TRUE	1	0.568087686918781	2		592	908	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420088	420088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770784292	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	49	361	0	ENST00000399788.2:c.3179C>T	p.Thr1060Met	p.T1060M	ENST00000399788	NM_001042603.1	1060	aCg/aTg	21/28	1	2	FACETS	0.237	0.2	0.278	0.237	0.2	0.278	SUBCLONAL	1	TRUE	1	0.568087686918781	2		361	728	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444920	49444920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370492566	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	41	624	1	ENST00000301067.7:c.2546C>T	p.Ser849Leu	p.S849L	ENST00000301067	NM_003482.3	849	tCg/tTg	10/54	1	2	FACETS	0.19	0.157	0.226	0.19	0.157	0.226	SUBCLONAL	1	TRUE	1	0.568087686918781	2		625	760	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2225396	2225396	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	35	290	0	ENST00000398665.3:c.3610del	p.Ile1204LeufsTer6	p.I1204Lfs*6	ENST00000398665	NM_032482.2	1202	agA/ag	26/28	1	2	FACETS	0.227	0.186	0.274	0.227	0.186	0.274	SUBCLONAL	1	TRUE	1	0.568087686918781	2		290	542	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026120	36026120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	71	810	0	ENST00000358208.4:c.722G>A	p.Cys241Tyr	p.C241Y	ENST00000358208		241	tGc/tAc	7/12	1	2	FACETS	0.255	0.221	0.291	0.255	0.221	0.291	SUBCLONAL	1	TRUE	1	0.568087686918781	2		810	982	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1978259	1978259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	83	692	0	ENST00000382891.5:c.3679C>T	p.Arg1227Trp	p.R1227W	ENST00000382891	NM_133335.3	1227	Cgg/Tgg	21/22	1	2	FACETS	0.293	0.257	0.331	0.293	0.257	0.331	SUBCLONAL	1	TRUE	1	0.568087686918781	2		692	998	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944358	131944358	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554099320	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	16	179	0	ENST00000265335.6:c.2770C>T	p.Gln924Ter	p.Q924*	ENST00000265335		924	Caa/Taa	17/25	1	2	FACETS	0.185	0.136	0.244	0.185	0.136	0.244	SUBCLONAL	1	TRUE	1	0.568087686918781	2		179	304	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481538	20481538	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	88	242	0	ENST00000346618.3:c.607G>A	p.Asp203Asn	p.D203N	ENST00000346618	NM_001949.4	203	Gat/Aat	3/7	1	2	FACETS	0.84	0.75	0.934	0.84	0.75	0.934	CLONAL	1	TRUE	1	0.568087686918781	2		242	369	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197426	26197426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761284557	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	26	296	0	ENST00000356476.2:c.53G>A	p.Arg18His	p.R18H	ENST00000356476		18	cGc/cAc	1/1	1	2	FACETS	0.198	0.156	0.246	0.198	0.156	0.246	SUBCLONAL	1	TRUE	1	0.568087686918781	2		296	462	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324717	31324717	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs41555918	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	28	241	0	ENST00000412585.2:c.91T>C	p.Tyr31His	p.Y31H	ENST00000412585	NM_005514.6	31	Tat/Cat	2/8	1	2	FACETS	0.454	0.365	0.555	0.454	0.365	0.555	SUBCLONAL	1	TRUE	1	0.568087686918781	2		241	217	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545827	106545827	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	27	254	0	ENST00000359195.3:c.3304G>A	p.Ala1102Thr	p.A1102T	ENST00000359195	NM_002649.2	1102	Gcc/Acc	11/11	1	2	FACETS	0.259	0.206	0.32	0.259	0.206	0.32	SUBCLONAL	1	TRUE	1	0.568087686918781	2		254	367	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29197665	29197665	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	55	610	0	ENST00000240100.2:c.529G>T	p.Glu177Ter	p.E177*	ENST00000240100	NM_001394.6	177	Gag/Tag	2/4	1	2	FACETS	0.214	0.182	0.249	0.214	0.182	0.249	SUBCLONAL	1	TRUE	1	0.568087686918781	2		610	905	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98011480	98011480	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	50	409	0	ENST00000289081.3:c.94C>T	p.Gln32Ter	p.Q32*	ENST00000289081	NM_000136.2	32	Caa/Taa	2/15	1	2	FACETS	0.251	0.213	0.294	0.251	0.213	0.294	SUBCLONAL	1	TRUE	1	0.568087686918781	2		409	700	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302843	15302843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	57	823	0	ENST00000263388.2:c.607C>T	p.Pro203Ser	p.P203S	ENST00000263388	NM_000435.2	203	Ccc/Tcc	4/33	1	2	FACETS	0.2	0.17	0.232	0.2	0.17	0.232	SUBCLONAL	1	TRUE	1	0.568087686918781	2		823	1005	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0057352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	130	323	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.242661040507235	5	FACETS	0.977	0.892	1	0.977	0.892	1	CLONAL	3	TRUE	2	0.250681569904525	5		323	487	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041007	47041007	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	114	801	0	ENST00000377604.3:c.1537G>T	p.Glu513Ter	p.E513*	ENST00000377604	NM_001204468.1	513	Gag/Tag	14/24	0.192148539534917	0	FACETS	0.825	0.749	0.904			1	CLONAL	2	TRUE	0	0.250681569904525	0		801	413	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331669	8331669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	171	416	0	ENST00000356435.5:c.5447C>A	p.Ser1816Tyr	p.S1816Y	ENST00000356435		1816	tCc/tAc	33/35	1	2	FACETS	0.842	0.78	0.906	1	0.994	1	CLONAL	3	TRUE	1	0.250681569904525	2		416	540	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526409	31526409	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs202227062	NA	P-0057352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	275	869	0	ENST00000344624.3:c.631C>A	p.Pro211Thr	p.P211T	ENST00000344624		211	Cca/Aca	2/33	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.250681569904525	2		869	930	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465343	120465343	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	132	501	0	ENST00000256646.2:c.4918T>A	p.Phe1640Ile	p.F1640I	ENST00000256646	NM_024408.3	1640	Ttc/Atc	27/34	1	2	FACETS	1	0.933	1	1	0.991	1	CLONAL	2	TRUE	1	0.250681569904525	2		501	513	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423566	88423566	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	71	576	1	ENST00000360948.2:c.2269G>T	p.Gly757Trp	p.G757W	ENST00000360948	NM_001012338.2	757	Ggg/Tgg	18/19	0.250681569904525	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.250681569904525	1		577	439	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015657	27015657	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	110	502	0	ENST00000335756.4:c.244G>T	p.Val82Leu	p.V82L	ENST00000335756	NM_001809.3	82	Gtg/Ttg	3/5	1	2	FACETS	0.826	0.745	0.911	1	0.986	1	CLONAL	2	TRUE	1	0.250681569904525	2		502	531	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958133	2958133	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	159	731	0	ENST00000396946.4:c.2599del	p.Ala867HisfsTer47	p.A867Hfs*47	ENST00000396946	NM_032415.4	867	Gca/ca	19/25	1	2	FACETS	0.996	0.916	1	1	0.992	1	CLONAL	2	TRUE	1	0.250681569904525	2		731	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0057352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	294	770	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.452305356697281	1	FACETS	0.943	0.888	0.999	0.943	0.888	0.999	CLONAL	1	TRUE	0	0.45988297863794	1		770	1044	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112118	115112118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868835900	NA	P-0057352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	243	784	0	ENST00000257566.3:c.1622C>T	p.Pro541Leu	p.P541L	ENST00000257566	NM_016569.3	541	cCc/cTc	7/8	1	2	FACETS	0.871	0.812	0.931	0.871	0.812	0.931	CLONAL	1	TRUE	1	0.45988297863794	2		784	1214	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615171	43615171	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	252	864	0	ENST00000355710.3:c.2585T>C	p.Met862Thr	p.M862T	ENST00000355710	NM_020975.4	862	aTg/aCg	14/20	NA	2	FACETS	0.922	0.862	0.984			1	INDETERMINATE	1	TRUE	NA	0.45988297863794	2		864	1189	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422506	225422506	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	132	441	0	ENST00000264414.4:c.134A>G	p.Gln45Arg	p.Q45R	ENST00000264414	NM_003590.4	45	cAg/cGg	2/16	0.452305356697281	1	FACETS	0.758	0.691	0.829	0.758	0.691	0.829	SUBCLONAL	1	TRUE	0	0.45988297863794	1		441	583	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305307	39305307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	266	645	0	ENST00000373001.3:c.1118C>T	p.Ser373Phe	p.S373F	ENST00000373001	NM_022157.3	373	tCt/tTt	7/7	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.45988297863794	2		645	1089	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441803	49441803	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	106	695	0	ENST00000301067.7:c.4181T>C	p.Leu1394Pro	p.L1394P	ENST00000301067	NM_003482.3	1394	cTc/cCc	14/54	1	2	FACETS	0.401	0.358	0.447	0.401	0.358	0.447	SUBCLONAL	1	TRUE	1	0.45988297863794	2		695	1149	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47108601	47108601	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	115	342	0	ENST00000409792.3:c.6068A>G	p.Tyr2023Cys	p.Y2023C	ENST00000409792	NM_014159.6	2023	tAt/tGt	13/21	0.452305356697281	1	FACETS	0.802	0.727	0.881	0.802	0.727	0.881	CLONAL	1	TRUE	0	0.45988297863794	1		342	480	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638104	176638104	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	206	591	1	ENST00000439151.2:c.2704G>T	p.Glu902Ter	p.E902*	ENST00000439151	NM_022455.4	902	Gaa/Taa	5/23	0.45988297863794	1	FACETS	0.959	0.893	1	0.959	0.893	1	CLONAL	1	TRUE	0	0.45988297863794	1		592	719	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046717	180046717	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	351	951	0	ENST00000261937.6:c.2595C>G	p.Phe865Leu	p.F865L	ENST00000261937	NM_182925.4	865	ttC/ttG	18/30	0.45988297863794	1	FACETS	0.971	0.92	1	0.971	0.92	1	CLONAL	1	TRUE	0	0.45988297863794	1		951	1210	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163621	32163621	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	248	649	0	ENST00000375023.3:c.5605G>T	p.Gly1869Cys	p.G1869C	ENST00000375023	NM_004557.3	1869	Ggc/Tgc	30/30	1	2	FACETS	0.941	0.879	1	0.941	0.879	1	CLONAL	1	TRUE	1	0.45988297863794	2		649	1146	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	127	365	0				ENST00000310581	NM_198253.2	-/1132			0.244416365007732	3	FACETS	0.911	0.838	0.984	0.911	0.838	0.984	INDETERMINATE	2	TRUE	1	0.597673098253413	3		365	303	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721812	49721812	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs142690032	NA	P-0057354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	23	13	1	ENST00000449682.2:c.1951C>T	p.Arg651Ter	p.R651*	ENST00000449682	NM_020998.3	651	Cga/Tga	17/18	0.18878996072678	4	FACETS	1	0.891	1	1	0.891	1	INDETERMINATE	2	TRUE	2	0.597673098253413	4		14	54	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	644	650	1	ENST00000269305.4:c.853G>T	p.Glu285Ter	p.E285*	ENST00000269305	NM_001126112.2	285	Gag/Tag	8/11	0.597673098253413	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.597673098253413	2		651	985	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160488	108160488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730881369	NA	P-0057354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	220	369	0	ENST00000278616.4:c.4396C>T	p.Arg1466Ter	p.R1466*	ENST00000278616	NM_000051.3	1466	Cga/Tga	29/63	0.172709463891701	2	FACETS	1	0.992	1	0.712	0.669	0.756	INDETERMINATE	1	TRUE	0	0.597673098253413	2		369	517	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375990	8375990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142960593	NA	P-0057354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	88	296	0	ENST00000356435.5:c.4607G>A	p.Arg1536His	p.R1536H	ENST00000356435		1536	cGt/cAt	28/35	0.295141852386077	4	FACETS	0.888	0.789	0.993	0.222	0.197	0.249	INDETERMINATE	1	TRUE	0	0.597673098253413	4		296	530	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860556	45860556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	423	765	1	ENST00000391945.4:c.1451C>T	p.Thr484Met	p.T484M	ENST00000391945	NM_000400.3	484	aCg/aTg	15/23	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.597673098253413	2		766	1185	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295411	1295411	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0057354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	37	76	0				ENST00000310581	NM_198253.2	-/1132			0.244416365007732	3	FACETS	0.766	0.649	0.888	0.766	0.649	0.888	INDETERMINATE	2	TRUE	1	0.597673098253413	3		76	105	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619172	37619172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759485356	NA	P-0057354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	287	539	1	ENST00000447079.4:c.848C>T	p.Ser283Leu	p.S283L	ENST00000447079	NM_015083.1	283	tCg/tTg	1/14	0.597673098253413	3	FACETS	1	0.989	1	0.607	0.571	0.643	CLONAL	1	TRUE	1	0.597673098253413	3		540	1028	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910641	29910641	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11539959	NA	P-0057354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1272	546	1188	0	ENST00000376809.5:c.181G>A	p.Asp61Asn	p.D61N	ENST00000376809	NM_002116.7	61	Gac/Aac	2/8	0.597673098253413	3	FACETS	1	0.995	1	0.653	0.625	0.681	CLONAL	1	TRUE	1	0.597673098253413	3		1188	1818	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513574	41513574	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	264	461	0	ENST00000263253.7:c.478C>T	p.Gln160Ter	p.Q160*	ENST00000263253	NM_001429.3	160	Cag/Tag	2/31	0.244416365007732	3	FACETS	0.804	0.757	0.851	0.804	0.757	0.851	INDETERMINATE	2	TRUE	1	0.597673098253413	3		461	714	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247280	153247280	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	140	240	0	ENST00000281708.4:c.1522C>T	p.Gln508Ter	p.Q508*	ENST00000281708	NM_033632.3	508	Caa/Taa	10/12	0.163163064905984	4	FACETS	0.786	0.721	0.853	0.786	0.721	0.853	INDETERMINATE	2	TRUE	2	0.597673098253413	4		240	476	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881415	48881415	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0057354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	84	109	0	ENST00000267163.4:c.138-1G>A		p.X46_splice	ENST00000267163	NM_000321.2	46			0.350208875378883	1	FACETS	1	0.984	1	1	0.984	1	INDETERMINATE	1	TRUE	0	0.597673098253413	1		109	138	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245471	46245471	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	72	271	0	ENST00000334344.6:c.3565C>T	p.Gln1189Ter	p.Q1189*	ENST00000334344	NM_152641.2	1189	Cag/Tag	15/21	0.241791690231933	3	FACETS	0.71	0.622	0.803	0.237	0.207	0.268	INDETERMINATE	1	TRUE	0	0.597673098253413	3		271	441	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128016916	128016916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1192130599	NA	P-0057354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	178	528	0	ENST00000285398.2:c.2173G>A	p.Glu725Lys	p.E725K	ENST00000285398	NM_000122.1	725	Gag/Aag	14/15	0.179328290642772	2	FACETS	0.764	0.705	0.824	0.382	0.352	0.412	INDETERMINATE	1	TRUE	0	0.597673098253413	2		528	780	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659740	227659740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	114	402	0	ENST00000305123.5:c.3715G>A	p.Glu1239Lys	p.E1239K	ENST00000305123	NM_005544.2	1239	Gag/Aag	1/2	0.307615561577603	1	FACETS	0.478	0.432	0.527	0.478	0.432	0.527	INDETERMINATE	1	TRUE	0	0.597673098253413	1		402	559	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29195909	29195909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs918810034	NA	P-0057354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	477	691	1	ENST00000240100.2:c.689C>T	p.Ser230Leu	p.S230L	ENST00000240100	NM_001394.6	230	tCg/tTg	3/4	0.237766432755854	4	FACETS	0.976	0.934	1	0.976	0.934	1	INDETERMINATE	2	TRUE	2	0.597673098253413	4		692	1306	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230889	66230889	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	96	251	0	ENST00000273854.3:c.2082G>C	p.Leu694Phe	p.L694F	ENST00000273854	NM_004439.5	694	ttG/ttC	12/18	0.273215791195595	3	FACETS	1	0.974	1	0.628	0.566	0.694	INDETERMINATE	1	TRUE	1	0.597673098253413	3		251	332	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259766	16259766	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1476917064	NA	P-0057354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	169	399	0	ENST00000375759.3:c.7031C>G	p.Thr2344Arg	p.T2344R	ENST00000375759	NM_015001.2	2344	aCa/aGa	11/15	0.15089344577509	3	FACETS	0.975	0.899	1	0.325	0.299	0.352	INDETERMINATE	1	TRUE	0	0.597673098253413	3		399	753	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715785	18715785	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1250561378	NA	P-0057354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	157	206	0	ENST00000266497.5:c.3616G>A	p.Glu1206Lys	p.E1206K	ENST00000266497		1206	Gaa/Aaa	25/31	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.597673098253413	2		206	356	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487154	56487154	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	136	420	0	ENST00000267101.3:c.1300A>G	p.Lys434Glu	p.K434E	ENST00000267101	NM_001982.3	434	Aag/Gag	12/28	0.241791690231933	3	FACETS	0.9	0.82	0.983	0.3	0.273	0.328	INDETERMINATE	1	TRUE	0	0.597673098253413	3		420	657	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843558	3843558	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	38	401	1	ENST00000262367.5:c.1045del	p.Glu349LysfsTer5	p.E349Kfs*5	ENST00000262367	NM_004380.2	349	Gaa/aa	4/31	0.239716521495498	2	FACETS	0.186	0.153	0.223	0.093	0.076	0.112	INDETERMINATE	1	TRUE	0	0.597673098253413	2		402	684	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075172	16075172	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0057354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	272	269	0	ENST00000268712.3:c.380T>A	p.Leu127Ter	p.L127*	ENST00000268712	NM_006311.3	127	tTg/tAg	4/46	0.597673098253413	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.597673098253413	2		269	424	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546618	9546618	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	130	397	0	ENST00000353224.5:c.1404G>C	p.Glu468Asp	p.E468D	ENST00000353224	NM_177990.2	468	gaG/gaC	5/10	0.323353768024543	1	FACETS	0.516	0.47	0.565	0.516	0.47	0.565	INDETERMINATE	1	TRUE	0	0.597673098253413	1		397	591	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130694	29130694	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	204	292	0	ENST00000328354.6:c.16G>A	p.Asp6Asn	p.D6N	ENST00000328354	NM_007194.3	6	Gat/Aat	2/15	0.244416365007732	3	FACETS	0.815	0.762	0.869	0.815	0.762	0.869	INDETERMINATE	2	TRUE	1	0.597673098253413	3		292	544	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921572	178921572	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	84	182	0	ENST00000263967.3:c.1054G>C	p.Asp352His	p.D352H	ENST00000263967	NM_006218.2	352	Gat/Cat	5/21	0.163163064905984	4	FACETS	0.867	0.777	0.961	0.867	0.777	0.961	INDETERMINATE	2	TRUE	2	0.597673098253413	4		182	259	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38957824	38957824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	111	168	0	ENST00000357387.3:c.2429C>T	p.Ser810Phe	p.S810F	ENST00000357387	NM_152756.3	810	tCc/tTc	25/38	0.244416365007732	3	FACETS	0.9	0.823	0.978	0.9	0.823	0.978	INDETERMINATE	2	TRUE	1	0.597673098253413	3		168	268	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225571	26225571	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	163	511	0	ENST00000360408.1:c.189C>G	p.Ile63Met	p.I63M	ENST00000360408	NM_003532.2	63	atC/atG	1/1	0.597673098253413	3	FACETS	0.809	0.742	0.878	0.404	0.371	0.439	CLONAL	1	TRUE	1	0.597673098253413	3		511	876	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324651	31324651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	35	206	0	ENST00000412585.2:c.157G>A	p.Asp53Asn	p.D53N	ENST00000412585	NM_005514.6	53	Gac/Aac	2/8	0.597673098253413	3	FACETS	0.613	0.506	0.733	0.307	0.253	0.367	SUBCLONAL	1	TRUE	1	0.597673098253413	3		206	248	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945499	151945499	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	208	661	0	ENST00000262189.6:c.2020G>T	p.Glu674Ter	p.E674*	ENST00000262189	NM_170606.2	674	Gaa/Taa	14/59	0.239716521495498	2	FACETS	1	0.985	1	0.594	0.555	0.634	INDETERMINATE	1	TRUE	0	0.597673098253413	2		661	586	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868972	117868972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	190	215	0	ENST00000297338.2:c.727G>A	p.Asp243Asn	p.D243N	ENST00000297338	NM_006265.2	243	Gat/Aat	7/14	0.237766432755854	4	FACETS	1	0.962	1	1	0.962	1	INDETERMINATE	2	TRUE	2	0.597673098253413	4		215	486	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922736	44922736	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	284	174	0	ENST00000377967.4:c.1597del	p.Leu533CysfsTer15	p.L533Cfs*15	ENST00000377967	NM_021140.2	533	Ctg/tg	16/29	0.456360952432532	2	FACETS	0.836	0.805	0.865			1	CLONAL	3	TRUE	NA	0.597673098253413	2		174	379	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835794	68835794	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	275	418	1	ENST00000261769.5:c.385C>T	p.Gln129Ter	p.Q129*	ENST00000261769	NM_004360.3	129	Cag/Tag	3/16	1	2	FACETS	0.946	0.893	1	1	0.995	1	CLONAL	2	FALSE	1	0.395396805514893	2		419	735	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914742	32914742	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	104	302	0	ENST00000380152.3:c.6250G>C	p.Asp2084His	p.D2084H	ENST00000380152		2084	Gat/Cat	11/27	0.395396805514893	0	FACETS	0.893	0.826	0.96			1	CLONAL	2	FALSE	0	0.395396805514893	0		302	178	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831213	72831213	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	277	413	0	ENST00000268489.5:c.5368del	p.Leu1790TyrfsTer24	p.L1790Yfs*24	ENST00000268489	NM_006885.3	1790	Cta/ta	9/10	1	2	FACETS	1	0.969	1	1	0.996	1	CLONAL	2	FALSE	1	0.395396805514893	2		413	676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0057356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	773	964	2	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.821160025399529	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.821160025399529	2		966	930	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212174	36212174	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	461	534	1	ENST00000222270.7:c.1925G>T	p.Arg642Leu	p.R642L	ENST00000222270	NM_014727.1	642	cGg/cTg	3/37	0.73404935564795	5	FACETS	0.984	0.947	1	0.984	0.947	1	CLONAL	3	TRUE	2	0.821160025399529	5		535	849	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55130043	55130043	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774431464	NA	P-0057358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	42	480	1	ENST00000257290.5:c.577G>A	p.Val193Ile	p.V193I	ENST00000257290	NM_006206.4	193	Gtc/Atc	4/23	0.130576556891946	4	FACETS	0.3	0.249	0.356	0.15	0.124	0.178	INDETERMINATE	1	TRUE	2	0.590947461171347	4		481	755	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311643	30311643	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	145	311	0	ENST00000262643.3:c.497T>G	p.Phe166Cys	p.F166C	ENST00000262643	NM_001238.2	166	tTt/tGt	7/12	0.438751422379805	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.590947461171347	1		311	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578234	7578234	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0057359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	210	802	0	ENST00000269305.4:c.615T>G	p.Tyr205Ter	p.Y205*	ENST00000269305	NM_001126112.2	205	taT/taG	6/11	0.0447073603141228	3	FACETS	1	0.948	1			1	INDETERMINATE	2	TRUE	NA	0.235412126166485	3		802	973	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0057362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	108	410	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.758	0.684	0.836	0.758	0.684	0.836	SUBCLONAL	1	TRUE	1	0.6	2		410	475	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0057362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	74	227	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.6	2		228	219	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750825	128750825	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	163	593	0	ENST00000377970.2:c.362T>A	p.Leu121Gln	p.L121Q	ENST00000377970	NM_002467.4	121	cTg/cAg	2/3	1	2	FACETS	0.95	0.877	1	0.95	0.877	1	CLONAL	1	TRUE	1	0.6	2		593	572	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0057363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	139	282	0	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	1	2	FACETS	0.953	0.881	1	1	0.991	1	CLONAL	2	TRUE	1	0.439132417297785	2		282	332	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602359	10602359	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	297	906	0	ENST00000171111.5:c.1219G>C	p.Ala407Pro	p.A407P	ENST00000171111	NM_203500.1	407	Gcc/Ccc	3/6	0.174723963288892	4	FACETS	0.888	0.841	0.935	1	0.993	1	INDETERMINATE	3	TRUE	2	0.439132417297785	4		906	731	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609728	117609728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	160	475	4	ENST00000368508.3:c.6971G>A	p.Cys2324Tyr	p.C2324Y	ENST00000368508	NM_002944.2	2324	tGc/tAc	43/43	0.439132417297785	1	FACETS	0.886	0.843	0.926	1	0.995	1	CLONAL	3	TRUE	0	0.439132417297785	1		479	214	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551439	141551439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	269	595	0	ENST00000220592.5:c.1858G>A	p.Ala620Thr	p.A620T	ENST00000220592	NM_012154.3	620	Gcc/Acc	15/19	0.439132417297785	4	FACETS	1	0.99	1	0.819	0.772	0.866	CLONAL	2	TRUE	1	0.439132417297785	4		595	718	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0057364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	109	473	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.656	0.592	0.723	0.656	0.592	0.723	SUBCLONAL	1	TRUE	1	0.687694713638592	2		474	483	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222006	1222006	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0057364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	388	567	0	ENST00000326873.7:c.920+1G>T		p.X307_splice	ENST00000326873	NM_000455.4	307			0.671881675519511	2	FACETS	0.976	0.942	1	0.976	0.942	1	CLONAL	2	TRUE	0	0.687694713638592	2		567	578	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180273	38180273	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs779805093	NA	P-0057364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	237	726	0	ENST00000396334.3:c.121C>T	p.Arg41Ter	p.R41*	ENST00000396334	NM_002468.4	41	Cga/Tga	1/5	1	2	FACETS	0.925	0.867	0.985	0.925	0.867	0.985	CLONAL	1	TRUE	1	0.687694713638592	2		726	745	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944843	31944843	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	220	651	0	ENST00000340398.3:c.258C>A	p.Ser86Arg	p.S86R	ENST00000340398	NM_001013699.2	86	agC/agA	1/1	1	2	FACETS	0.865	0.807	0.923	0.865	0.807	0.923	CLONAL	1	TRUE	1	0.687694713638592	2		651	740	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587514	29587514	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060500242	NA	P-0057365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	37	355	0	ENST00000356175.3:c.4495C>T	p.Gln1499Ter	p.Q1499*	ENST00000356175	NM_000267.3	1499	Cag/Tag	33/57	0.291584177809128	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		355	258	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0057369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	345	837	1	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.418638878739049	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.418638878739049	1		838	1024	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3645643	3645643	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs372150541	NA	P-0057369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	170	1077	0	ENST00000294008.3:c.1976C>G	p.Ser659Trp	p.S659W	ENST00000294008	NM_032444.2	659	tCg/tGg	9/15	1	2	FACETS	0.62	0.569	0.674	0.62	0.569	0.674	SUBCLONAL	1	TRUE	1	0.418638878739049	2		1077	1309	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95598930	95598937	+	frameshift_variant	Frame_Shift_Del	DEL	GTAGTACT	GTAGTACT	-	novel	NA	P-0057369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	53	418	0	ENST00000393063.1:c.222_229del	p.Val75HisfsTer2	p.V75Hfs*2	ENST00000393063	NM_030621.3	74	gcAGTACTACtc/gctc	4/28	1	2	FACETS	0.448	0.382	0.521	0.448	0.382	0.521	SUBCLONAL	1	TRUE	1	0.418638878739049	2		418	565	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046965	128046965	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	181	602	0	ENST00000285398.2:c.770A>T	p.Lys257Met	p.K257M	ENST00000285398	NM_000122.1	257	aAg/aTg	6/15	1	2	FACETS	0.982	0.906	1	0.982	0.906	1	CLONAL	1	TRUE	1	0.418638878739049	2		602	881	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368527	225368527	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	48	295	0	ENST00000264414.4:c.1219G>A	p.Glu407Lys	p.E407K	ENST00000264414	NM_003590.4	407	Gaa/Aaa	9/16	0.418638878739049	1	FACETS	0.72	0.613	0.834	0.72	0.613	0.834	SUBCLONAL	1	TRUE	0	0.418638878739049	1		295	252	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972714	76972714	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	50	298	0	ENST00000373344.5:c.27C>G	p.Ser9Arg	p.S9R	ENST00000373344	NM_000489.3	9	agC/agG	2/35	1	2	FACETS	0.587	0.499	0.683	0.587	0.499	0.683	SUBCLONAL	1	TRUE	1	0.418638878739049	2		298	407	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732574	190732574	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	31	384	0	ENST00000441310.2:c.2392G>C	p.Asp798His	p.D798H	ENST00000441310	NM_000534.4	798	Gat/Cat	11/13	0.418638878739049	3	FACETS	0.335	0.27	0.408	0.167	0.135	0.204	SUBCLONAL	1	TRUE	1	0.418638878739049	3		384	535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	368	1105	4	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.208327645673242	3	FACETS	1	0.992	1	0.807	0.766	0.85	CLONAL	2	FALSE	0	0.284271590992196	3		1109	1221	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527925	157527925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377877762	NA	P-0057370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	193	570	0	ENST00000346085.5:c.5650C>T	p.Arg1884Trp	p.R1884W	ENST00000346085	NM_020732.3	1884	Cgg/Tgg	20/20	0.284271590992196	3	FACETS	0.987	0.915	1	0.987	0.915	1	CLONAL	2	FALSE	1	0.284271590992196	3		570	786	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600423	43600423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1259626672	NA	P-0057370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	100	839	0	ENST00000355710.3:c.649G>A	p.Ala217Thr	p.A217T	ENST00000355710	NM_020975.4	217	Gcc/Acc	4/20	0.284271590992196	3	FACETS	0.996	0.889	1	0.498	0.444	0.555	CLONAL	1	FALSE	1	0.284271590992196	3		839	807	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858429	9858429	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	56	461	0	ENST00000330684.3:c.2972C>A	p.Ser991Tyr	p.S991Y	ENST00000330684	NM_001134407.1	991	tCc/tAc	13/13	0.284271590992196	6	FACETS	0.887	0.758	1	0.222	0.189	0.257	CLONAL	1	FALSE	2	0.284271590992196	6		461	697	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492796	56492796	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs972986418	NA	P-0057370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	304	531	0	ENST00000407977.2:c.143T>A	p.Ile48Asn	p.I48N	ENST00000407977		48	aTc/aAc	2/10	0.26968360255217	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	FALSE	0	0.284271590992196	3		531	787	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125389	47125389	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	51	343	0	ENST00000409792.3:c.5881G>C	p.Glu1961Gln	p.E1961Q	ENST00000409792	NM_014159.6	1961	Gag/Cag	12/21	0.284271590992196	5	FACETS	1	0.868	1	0.255	0.217	0.298	CLONAL	1	FALSE	1	0.284271590992196	5		343	501	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81941370	81941370	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	56	492	0	ENST00000359376.3:c.1548A>C	p.Glu516Asp	p.E516D	ENST00000359376	NM_002661.3	516	gaA/gaC	16/33	0.284271590992196	6	FACETS	0.795	0.68	0.922	0.199	0.17	0.231	CLONAL	1	FALSE	2	0.284271590992196	6		492	777	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0057371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	123	144	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.503576143261092	2	FACETS	0.814	0.753	0.876	0.814	0.753	0.876	CLONAL	2	TRUE	0	0.609059557925418	2		144	248	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0057371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	354	500	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.532248944464074	1	FACETS	0.811	0.77	0.852	0.811	0.77	0.852	CLONAL	1	TRUE	0	0.609059557925418	1		500	997	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0057371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	214	432	1	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.342806252344771	3	FACETS	0.908	0.852	0.964			1	INDETERMINATE	2	TRUE	NA	0.609059557925418	3		433	505	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0057371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	94	422	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.384985224020898	1	FACETS	0.394	0.351	0.439	0.394	0.351	0.439	SUBCLONAL	1	TRUE	0	0.609059557925418	1		422	545	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247373	153247373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	102	245	0	ENST00000281708.4:c.1429G>A	p.Gly477Ser	p.G477S	ENST00000281708	NM_033632.3	477	Ggt/Agt	10/12	0.384985224020898	1	FACETS	0.7	0.632	0.769	0.7	0.632	0.769	SUBCLONAL	1	TRUE	0	0.609059557925418	1		245	333	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152357799	152357799	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	39	292	0	ENST00000359321.1:c.108T>A	p.Asp36Glu	p.D36E	ENST00000359321	NM_005431.1	36	gaT/gaA	2/3	1	2	FACETS	0.221	0.183	0.264	0.221	0.183	0.264	SUBCLONAL	1	TRUE	1	0.609059557925418	2		292	579	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	74	619	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.209804436431173	2	FACETS	0.848	0.746	0.956	0.424	0.373	0.478	INDETERMINATE	1	TRUE	0	0.43	2		619	406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0057372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	135	1005	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.43	2		1006	621	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971037	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0057372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	127	666	0	ENST00000304494.5:c.321_322del	p.Asp108CysfsTer11	p.D108Cfs*11	ENST00000304494	NM_000077.4	107	cgCGat/cgat	2/3	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.43	2		666	541	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998499	100998499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	62	881	1	ENST00000325455.5:c.1303G>A	p.Gly435Arg	p.G435R	ENST00000325455	NM_001202474.3	435	Ggg/Agg	1/8	0.236986252344991	3	FACETS	0.495	0.427	0.569	0.247	0.213	0.285	INDETERMINATE	1	TRUE	1	0.43	3		882	708	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440938	56440939	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0057372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	158	743	0	ENST00000407977.2:c.398dup	p.Ala134SerfsTer7	p.A134Sfs*7	ENST00000407977		133	gga/ggGa	4/10	0.00750028161814642	3	FACETS	1	0.951	1	0.526	0.482	0.572	INDETERMINATE	1	TRUE	1	0.43	3		743	849	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120479967	120479967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	113	628	0	ENST00000256646.2:c.3460G>A	p.Ala1154Thr	p.A1154T	ENST00000256646	NM_024408.3	1154	Gcg/Acg	21/34	0.566571301761614	1	FACETS	0.193	0.173	0.213	0.193	0.173	0.213	SUBCLONAL	1	TRUE	0	0.889810178807801	1		628	732	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340266	116340266	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	149	236	0	ENST00000397752.3:c.1128G>T	p.Lys376Asn	p.K376N	ENST00000397752	NM_000245.2	376	aaG/aaT	2/21	NA	2	FACETS	0.976	0.906	1			1	INDETERMINATE	1	TRUE	NA	0.889810178807801	2		236	343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1427441061	NA	P-0057377-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	64	329	0	ENST00000269305.4:c.560-2A>G		p.X187_splice	ENST00000269305	NM_001126112.2	187			1	2	FACETS	0.527	0.455	0.604	0.527	0.455	0.604	SUBCLONAL	1	TRUE	1	0.335723193272168	2		329	724	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927989	49927989	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374259168	NA	P-0057377-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	65	877	0	ENST00000296474.3:c.3739G>A	p.Ala1247Thr	p.A1247T	ENST00000296474	NM_002447.2	1247	Gct/Act	18/20	1	2	FACETS	0.487	0.421	0.559	0.487	0.421	0.559	SUBCLONAL	1	TRUE	1	0.335723193272168	2		877	795	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39214727	39214727	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1162412781	NA	P-0057377-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	37	327	0	ENST00000402219.2:c.3397G>C	p.Ala1133Pro	p.A1133P	ENST00000402219	NM_005633.3	1133	Gct/Cct	22/23	1	2	FACETS	0.488	0.402	0.584	0.488	0.402	0.584	SUBCLONAL	1	TRUE	1	0.335723193272168	2		327	452	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47596681	47596682	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0057377-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	54	447	0	ENST00000263735.4:c.37_38insG	p.Leu13ArgfsTer18	p.L13Rfs*18	ENST00000263735	NM_002354.2	13	ctt/cGtt	1/9	1	2	FACETS	0.604	0.516	0.7	0.604	0.516	0.7	SUBCLONAL	1	TRUE	1	0.335723193272168	2		447	533	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0057379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	229	458	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.376395403288418	6	FACETS	1	0.981	1	0.822	0.774	0.871	CLONAL	3	TRUE	2	0.574124439364682	6		458	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	369	735	0	ENST00000269305.4:c.470T>G	p.Val157Gly	p.V157G	ENST00000269305	NM_001126112.2	157	gTc/gGc	5/11	0.574124439364682	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.574124439364682	2		735	643	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163309194	163309194	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	19	458	0	ENST00000271452.3:c.533A>G	p.Glu178Gly	p.E178G	ENST00000271452	NM_145697.2	178	gAa/gGa	8/14	1	2	FACETS	0.328	0.249	0.419	0.328	0.249	0.419	SUBCLONAL	1	TRUE	1	0.574124439364682	2		458	202	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651927	36651928	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0057379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	83	602	1	ENST00000244741.5:c.49_50delinsAT	p.Ala17Ile	p.A17I	ENST00000244741	NM_000389.4	17	GCc/ATc	2/3	0.574124439364682	1	FACETS	0.566	0.503	0.633	0.566	0.503	0.633	SUBCLONAL	1	TRUE	0	0.574124439364682	1		603	364	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650611	48650611	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	34	656	0	ENST00000376670.3:c.581T>A	p.Leu194His	p.L194H	ENST00000376670	NM_002049.3	194	cTc/cAc	3/6	0.496766604622842	1	FACETS	0.241	0.197	0.29	0.241	0.197	0.29	SUBCLONAL	1	TRUE	0	0.574124439364682	1		656	351	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057381-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	38	619	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.939	0.775	1	0.939	0.775	1	CLONAL	1	TRUE	1	0.14	2		619	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519985	NA	P-0057381-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	102	931	0	ENST00000269305.4:c.857A>G	p.Glu286Gly	p.E286G	ENST00000269305	NM_001126112.2	286	gAa/gGa	8/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.14	2		931	1305	SUCCESS
APC	324	MSKCC	GRCh37	5	112164645	112164645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057381-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	25	222	0	ENST00000257430.4:c.1719G>A	p.Met573Ile	p.M573I	ENST00000257430	NM_000038.5	573	atG/atA	14/16	1	2	FACETS	0.834	0.657	1	0.834	0.657	1	CLONAL	1	TRUE	1	0.14	2		222	428	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971113	21971113	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057381-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	48	636	1	ENST00000304494.5:c.245T>A	p.Val82Glu	p.V82E	ENST00000304494	NM_000077.4	82	gTg/gAg	2/3	1	2	FACETS	0.741	0.624	0.871	0.741	0.624	0.871	SUBCLONAL	1	TRUE	1	0.14	2		637	925	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974744	21974744	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057381-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	37	444	0	ENST00000304494.5:c.83T>A	p.Val28Glu	p.V28E	ENST00000304494	NM_000077.4	28	gTg/gAg	1/3	1	2	FACETS	0.844	0.695	1	0.844	0.695	1	CLONAL	1	TRUE	1	0.14	2		444	626	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739903	41739903	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	88	533	0	ENST00000242208.4:c.70C>A	p.Pro24Thr	p.P24T	ENST00000242208	NM_002192.2	24	Cca/Aca	2/3	1	2	FACETS	0.973	0.864	1	0.973	0.864	1	CLONAL	1	TRUE	1	0.341415912321577	2		533	530	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0057411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	41	335	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.44	2		335	169	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441815	49441816	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs756471180	NA	P-0057411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	46	612	0	ENST00000301067.7:c.4168dup	p.Ala1390GlyfsTer42	p.A1390Gfs*42	ENST00000301067	NM_003482.3	1390	gca/gGca	14/54	1	2	FACETS	0.385	0.324	0.453	0.385	0.324	0.453	SUBCLONAL	1	TRUE	1	0.44	2		612	543	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0057411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	52	416	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.853	0.732	0.984	0.853	0.732	0.984	CLONAL	1	TRUE	1	0.44	2		416	277	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412641	139412641	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	138	1341	0	ENST00000277541.6:c.1203del	p.Ser402ArgfsTer229	p.S402Rfs*229	ENST00000277541	NM_017617.3	401	ccC/cc	7/34	1	2	FACETS	0.75	0.683	0.821	0.75	0.683	0.821	SUBCLONAL	1	TRUE	1	0.44	2		1341	836	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371799	55371820	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCCGCGCTGGGCCCCGAG	GGCGGCCGCGCTGGGCCCCGAG	-	novel	NA	P-0057411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	92	369	0	ENST00000297316.4:c.499_520del	p.Leu167TrpfsTer213	p.L167Wfs*213	ENST00000297316	NM_022454.3	163	caGGCGGCCGCGCTGGGCCCCGAG/ca	2/2	1	2	FACETS	0.817	0.737	0.899	1	0.985	1	CLONAL	2	TRUE	1	0.44	2		369	256	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466040	69466040	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	169	1351	1	ENST00000227507.2:c.878T>A	p.Val293Glu	p.V293E	ENST00000227507	NM_053056.2	293	gTg/gAg	5/5	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.44	2		1352	728	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673711	176673711	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs570278338	NA	P-0057411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	61	327	0	ENST00000439151.2:c.4411C>T	p.Arg1471Ter	p.R1471*	ENST00000439151	NM_022455.4	1471	Cga/Tga	10/23	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.44	2		327	273	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431874	49431874	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	35	1033	8	ENST00000301067.7:c.9265del	p.Val3089TrpfsTer30	p.V3089Wfs*30	ENST00000301067	NM_003482.3	3089	Gtg/tg	34/54	1	2	FACETS	0.272	0.222	0.328	0.272	0.222	0.328	SUBCLONAL	1	TRUE	1	0.44	2		1041	585	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220069	36220069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1239076295	NA	P-0057411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	138	1141	2	ENST00000222270.7:c.4789C>T	p.Arg1597Trp	p.R1597W	ENST00000222270	NM_014727.1	1597	Cgg/Tgg	22/37	1	2	FACETS	0.996	0.909	1	0.996	0.909	1	CLONAL	1	TRUE	1	0.44	2		1143	630	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245309	46245309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	34	582	1	ENST00000334344.6:c.3403C>T	p.Pro1135Ser	p.P1135S	ENST00000334344	NM_152641.2	1135	Cca/Tca	15/21	1	2	FACETS	0.388	0.317	0.468	0.388	0.317	0.468	SUBCLONAL	1	TRUE	1	0.44	2		583	398	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645139	86645139	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1175378445	NA	P-0057411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	28	279	0	ENST00000274376.6:c.1211C>T	p.Thr404Met	p.T404M	ENST00000274376	NM_002890.2	404	aCg/aTg	8/25	1	2	FACETS	0.723	0.583	0.879	0.723	0.583	0.879	SUBCLONAL	1	TRUE	1	0.44	2		279	176	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057869	27057870	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0057411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	160	982	0	ENST00000324856.7:c.1579_1580del	p.His527SerfsTer95	p.H527Sfs*95	ENST00000324856	NM_006015.4	526	cCA/c	3/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.44	2		982	664	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624257	89624257	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0057411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	54	302	0	ENST00000371953.3:c.31A>T	p.Arg11Ter	p.R11*	ENST00000371953	NM_000314.4	11	Aga/Tga	1/9	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.44	2		302	228	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692930	89692930	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs1554898161	NA	P-0057411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	114	629	0	ENST00000371953.3:c.414T>G	p.Tyr138Ter	p.Y138*	ENST00000371953	NM_000314.4	138	taT/taG	5/9	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.44	2		629	490	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192075	108192078	+	frameshift_variant	Frame_Shift_Del	DEL	ATTC	ATTC	-	novel	NA	P-0057411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	104	581	1	ENST00000278616.4:c.6500_6503del	p.Tyr2167CysfsTer67	p.Y2167Cfs*67	ENST00000278616	NM_000051.3	2167	tATTCg/tg	45/63	1	2	FACETS	0.979	0.881	1	0.979	0.881	1	CLONAL	1	TRUE	1	0.44	2		582	483	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149656	61149656	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	10	155	0	ENST00000295025.8:c.1851del	p.Gln618LysfsTer13	p.Q618Kfs*13	ENST00000295025	NM_002908.2	616	Ttt/tt	11/11	1	2	FACETS	0.382	0.26	0.533	0.382	0.26	0.533	SUBCLONAL	1	TRUE	1	0.44	2		155	119	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023600	27023601	+	frameshift_variant	Frame_Shift_Ins	INS	GG	GG	CACC	novel	NA	P-0057411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	88	745	0	ENST00000324856.7:c.706_707delinsCACC	p.Gly236HisfsTer128	p.G236Hfs*128	ENST00000324856	NM_006015.4	236	GGt/CACCt	1/20	1	2	FACETS	0.806	0.717	0.901	0.806	0.717	0.901	CLONAL	1	TRUE	1	0.44	2		745	496	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040911	47040911	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs782684857	NA	P-0057412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	894	665	4	ENST00000377604.3:c.1441G>T	p.Glu481Ter	p.E481*	ENST00000377604	NM_001204468.1	481	Gag/Tag	14/24	0.909878257618777	2	FACETS	1	0.998	1			1	CLONAL	2	TRUE	NA	0.909816010943023	2		669	943	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1555525429	NA	P-0057412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	856	722	0	ENST00000269305.4:c.782+1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.909878257618777	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.909816010943023	2		722	915	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073973	8073973	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	182	423	0	ENST00000377482.5:c.686del	p.Asn229MetfsTer18	p.N229Mfs*18	ENST00000377482	NM_018948.3	229	aAt/at	4/4	0.25525964092441	3	FACETS	0.957	0.888	1	0.319	0.296	0.343	INDETERMINATE	1	TRUE	0	0.909816010943023	3		423	608	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435030	18435030	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	196	221	1	ENST00000266497.5:c.15G>T	p.Trp5Cys	p.W5C	ENST00000266497		5	tgG/tgT	1/31	0.643654854594546	4	FACETS	0.968	0.908	1	0.968	0.908	1	CLONAL	2	TRUE	2	0.909816010943023	4		222	425	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425770	49425770	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1281	405	1082	0	ENST00000301067.7:c.12718A>T	p.Thr4240Ser	p.T4240S	ENST00000301067	NM_003482.3	4240	Acc/Tcc	39/54	0.514640712256661	4	FACETS	1	0.956	1	0.504	0.478	0.531	INDETERMINATE	1	TRUE	2	0.909816010943023	4		1082	1686	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526737	106526737	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	184	388	0	ENST00000359195.3:c.3030+1del		p.Q1010fs	ENST00000359195	NM_002649.2	1010	caG/ca	10/11	0.895704676275154	4	FACETS	1	0.952	1	0.346	0.32	0.373	CLONAL	1	TRUE	1	0.909816010943023	4		388	745	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161284203	161284203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142139022	NA	P-0057413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	196	608	1	ENST00000367975.2:c.8C>T	p.Ala3Val	p.A3V	ENST00000367975	NM_003001.3	3	gCg/gTg	1/6	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.38	2		609	771	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615612	43615623	+	inframe_deletion	In_Frame_Del	DEL	AGATGTTTATGA	AGATGTTTATGA	-	rs121913309	NA	P-0057413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	165	507	0	ENST00000355710.3:c.2694_2705del	p.Asp898_Glu901del	p.D898_E901del	ENST00000355710	NM_020975.4	897	cgAGATGTTTATGAa/cga	15/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.38	2		507	754	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597807	43597807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	215	912	1	ENST00000355710.3:c.355C>T	p.Leu119Phe	p.L119F	ENST00000355710	NM_020975.4	119	Ctc/Ttc	3/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.388457652047804	2		913	1062	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413578	32413578	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121907909	NA	P-0057414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	121	425	0	ENST00000332351.3:c.1372C>T	p.Arg458Ter	p.R458*	ENST00000332351	NM_024426.4	458	Cga/Tga	9/10	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.388457652047804	2		425	601	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948755	71948755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773081790	NA	P-0057414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	274	1248	0	ENST00000298229.2:c.3467G>A	p.Arg1156Gln	p.R1156Q	ENST00000298229	NM_001567.3	1156	cGg/cAg	26/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.388457652047804	2		1248	1254	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226090	2226090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316961587	NA	P-0057414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1410	83	1260	2	ENST00000326181.6:c.1787C>T	p.Thr596Met	p.T596M	ENST00000326181	NM_032271.2	596	aCg/aTg	19/21	1	2	FACETS	0.286	0.251	0.324	0.286	0.251	0.324	SUBCLONAL	1	TRUE	1	0.388457652047804	2		1262	1493	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352037	89352037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138353708	NA	P-0057414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	247	894	2	ENST00000301030.4:c.913G>A	p.Ala305Thr	p.A305T	ENST00000301030	NM_001256183.1	305	Gca/Aca	9/13	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.388457652047804	2		896	1188	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831345	89831346	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs878853663	NA	P-0057414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	73	748	5	ENST00000389301.3:c.2730_2731del	p.Trp911AspfsTer31	p.W911Dfs*31	ENST00000389301	NM_000135.2	910	ctCTgg/ctgg	28/43	1	2	FACETS	0.402	0.351	0.458	0.402	0.351	0.458	SUBCLONAL	1	TRUE	1	0.388457652047804	2		753	934	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781371	NA	P-0057414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	303	912	0	ENST00000269305.4:c.328C>T	p.Arg110Cys	p.R110C	ENST00000269305	NM_001126112.2	110	Cgt/Tgt	4/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.388457652047804	2		912	1253	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950311	15950313	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0057414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	149	615	0	ENST00000268712.3:c.6631_6633del	p.Glu2211del	p.E2211del	ENST00000268712	NM_006311.3	2211	GAG/-	42/46	1	2	FACETS	0.999	0.914	1	0.999	0.914	1	CLONAL	1	TRUE	1	0.388457652047804	2		615	768	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612246	1612246	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	233	883	0	ENST00000344749.5:c.1773G>T	p.Gln591His	p.Q591H	ENST00000344749	NM_001136139.2	591	caG/caT	18/19	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.388457652047804	2		883	970	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223252	5223252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763535247	NA	P-0057414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	304	1217	1	ENST00000357368.4:c.2551C>T	p.Arg851Cys	p.R851C	ENST00000357368	NM_002850.3	851	Cgc/Tgc	18/38	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.388457652047804	2		1218	1352	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790090	40790090	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	53	798	2	ENST00000373198.4:c.2641del	p.Arg881GlyfsTer20	p.R881Gfs*20	ENST00000373198	NM_133170.3	881	Cgg/gg	18/32	1	2	FACETS	0.277	0.235	0.323	0.277	0.235	0.323	SUBCLONAL	1	TRUE	1	0.388457652047804	2		800	986	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561861	55561861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201872586	NA	P-0057414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	23	292	0	ENST00000288135.5:c.251C>T	p.Thr84Met	p.T84M	ENST00000288135	NM_000222.2	84	aCg/aTg	2/21	1	2	FACETS	0.275	0.214	0.347	0.275	0.214	0.347	SUBCLONAL	1	TRUE	1	0.388457652047804	2		292	430	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531001	187531001	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754491592	NA	P-0057414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	62	447	0	ENST00000441802.2:c.10022C>T	p.Thr3341Met	p.T3341M	ENST00000441802	NM_005245.3	3341	aCg/aTg	15/27	1	2	FACETS	0.423	0.365	0.487	0.423	0.365	0.487	SUBCLONAL	1	TRUE	1	0.388457652047804	2		447	754	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970923	79970923	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	122	531	0	ENST00000265081.6:c.1151del	p.Gly384AlafsTer31	p.G384Afs*31	ENST00000265081	NM_002439.4	383	aaG/aa	7/24	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.388457652047804	2		531	625	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271560	26271560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285668771	NA	P-0057414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	136	450	0	ENST00000305910.3:c.53G>A	p.Arg18His	p.R18H	ENST00000305910	NM_003534.2	18	cGc/cAc	1/1	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.388457652047804	2		450	582	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467654	50467654	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	169	550	0	ENST00000331340.3:c.889G>A	p.Ala297Thr	p.A297T	ENST00000331340	NM_006060.4	297	Gcc/Acc	8/8	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.388457652047804	2		550	646	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538768	23538769	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACAGGTATGGGTAGTAAGGATAGCTGTTATACACGGAGACCAGGCAGC	novel	NA	P-0057414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	62	428	0	ENST00000380871.4:c.670_671insGCTGCCTGGTCTCCGTGTATAACAGCTATCCTTACTACCCATACCTGT	p.Leu223_Tyr224insCysCysLeuValSerValTyrAsnSerTyrProTyrTyrProTyrLeu	p.L223_Y224insCCLVSVYNSYPYYPYL	ENST00000380871	NM_006167.3	224	tac/tGCTGCCTGGTCTCCGTGTATAACAGCTATCCTTACTACCCATACCTGTac	2/2	1	2	FACETS	0.61	0.528	0.7	0.61	0.528	0.7	SUBCLONAL	1	TRUE	1	0.388457652047804	2		428	523	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27192559	27192559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766717660	NA	P-0057414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	199	501	1	ENST00000380036.4:c.1562G>A	p.Arg521His	p.R521H	ENST00000380036	NM_000459.3	521	cGt/cAt	11/23	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.388457652047804	2		502	848	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430809	47430809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	97	534	2	ENST00000377045.4:c.1774G>A	p.Asp592Asn	p.D592N	ENST00000377045	NM_001654.4	592	Gat/Aat	16/16	1	1	FACETS	0.611	0.545	0.681	0.611	0.545	0.681	SUBCLONAL	1	TRUE	0	0.388457652047804	1		536	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579366	7579366	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0057415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	507	1038	0	ENST00000269305.4:c.321C>G	p.Tyr107Ter	p.Y107*	ENST00000269305	NM_001126112.2	107	taC/taG	4/11	0.727962851527576	2	FACETS	0.822	0.799	0.843	0.822	0.799	0.843	CLONAL	2	TRUE	0	0.912611244207901	2		1038	676	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	100	365	0				ENST00000310581	NM_198253.2	-/1132			0.151371653494146	5	FACETS	0.898	0.801	1	0.299	0.267	0.334	INDETERMINATE	1	TRUE	2	0.374675719300251	5		365	928	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0057416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	505	1261	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	NA	2	FACETS	0.861	0.823	0.899			1	INDETERMINATE	2	TRUE	NA	0.374675719300251	2		1261	1566	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876524	35876524	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	214	625	0	ENST00000303115.3:c.1316C>A	p.Thr439Asn	p.T439N	ENST00000303115	NM_002185.3	439	aCt/aAt	8/8	0.151371653494146	5	FACETS	0.948	0.882	1	0.632	0.588	0.678	INDETERMINATE	2	TRUE	2	0.374675719300251	5		625	941	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974799	21974799	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	128	283	0	ENST00000304494.5:c.28G>T	p.Glu10Ter	p.E10*	ENST00000304494	NM_000077.4	10	Gag/Tag	1/3	0.333184649968336	2	FACETS	0.899	0.823	0.977	0.899	0.823	0.977	CLONAL	2	TRUE	0	0.374675719300251	2		283	380	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523534	106523534	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	106	245	0	ENST00000359195.3:c.2686G>A	p.Val896Met	p.V896M	ENST00000359195	NM_002649.2	896	Gtg/Atg	8/11	0.151371653494146	5	FACETS	0.961	0.866	1	0.64	0.577	0.707	INDETERMINATE	2	TRUE	2	0.374675719300251	5		245	460	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984968	55984968	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0057416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	126	375	0	ENST00000263923.4:c.162-1G>T		p.X54_splice	ENST00000263923	NM_002253.2	54			0.273853879015737	3	FACETS	1	0.977	1	0.62	0.563	0.68	CLONAL	1	TRUE	1	0.374675719300251	3		375	644	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486014	8486014	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs375803455	NA	P-0057416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	185	679	0	ENST00000356435.5:c.2803G>T	p.Val935Phe	p.V935F	ENST00000356435		935	Gtc/Ttc	17/35	0.333184649968336	2	FACETS	1	0.989	1	0.707	0.655	0.761	CLONAL	1	TRUE	0	0.374675719300251	2		679	698	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81534662	81534662	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs755428708	NA	P-0057416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	108	367	0	ENST00000298171.2:c.307G>T	p.Val103Leu	p.V103L	ENST00000298171	NM_000369.2	103	Gtg/Ttg	3/10	0.291463290712359	3	FACETS	0.79	0.714	0.87	0.79	0.714	0.87	SUBCLONAL	2	TRUE	1	0.374675719300251	3		367	433	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506670	103506670	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	34	241	0	ENST00000355739.4:c.413G>T	p.Arg138Leu	p.R138L	ENST00000355739	NM_000123.3	138	cGa/cTa	4/15	1	2	FACETS	0.523	0.428	0.63	0.523	0.428	0.63	SUBCLONAL	1	TRUE	1	0.374675719300251	2		241	347	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846362	128846362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766211091	NA	P-0057416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	354	995	0	ENST00000249373.3:c.1198C>T	p.Arg400Cys	p.R400C	ENST00000249373	NM_005631.4	400	Cgt/Tgt	6/12	0.151371653494146	5	FACETS	1	0.955	1	0.674	0.638	0.712	INDETERMINATE	2	TRUE	2	0.374675719300251	5		995	1459	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552679	18552679	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	192	710	0	ENST00000266497.5:c.2090G>T	p.Ser697Ile	p.S697I	ENST00000266497		697	aGt/aTt	14/31	0.320530312142229	2	FACETS	1	0.991	1	0.746	0.692	0.801	CLONAL	1	TRUE	0	0.374675719300251	2		710	687	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134901	41134901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	76	463	0	ENST00000379561.5:c.727G>A	p.Gly243Ser	p.G243S	ENST00000379561	NM_002015.3	243	Ggt/Agt	2/3	1	2	FACETS	0.662	0.581	0.749	0.662	0.581	0.749	SUBCLONAL	1	TRUE	1	0.374675719300251	2		463	613	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528179	103528179	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs183317723	NA	P-0057416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	77	443	0	ENST00000355739.4:c.3487G>T	p.Val1163Leu	p.V1163L	ENST00000355739	NM_000123.3	1163	Gtg/Ttg	15/15	1	2	FACETS	0.75	0.66	0.847	0.75	0.66	0.847	SUBCLONAL	1	TRUE	1	0.374675719300251	2		443	548	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423578	88423578	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	242	668	0	ENST00000360948.2:c.2257G>T	p.Val753Leu	p.V753L	ENST00000360948	NM_001012338.2	753	Gta/Tta	18/19	0.291463290712359	3	FACETS	0.795	0.743	0.848	0.795	0.743	0.848	SUBCLONAL	2	TRUE	1	0.374675719300251	3		668	965	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144797	11144797	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0057416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	272	690	0	ENST00000358026.2:c.3874-2A>G		p.X1292_splice	ENST00000358026	NM_001128849.1	1292			0.333184649968336	2	FACETS	0.865	0.815	0.917	0.865	0.815	0.917	CLONAL	2	TRUE	0	0.374675719300251	2		690	839	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219925	36219925	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1184	462	1057	1	ENST00000222270.7:c.4727A>T	p.Glu1576Val	p.E1576V	ENST00000222270	NM_014727.1	1576	gAg/gTg	21/37	0.151371653494146	5	FACETS	1	0.992	1	0.78	0.744	0.817	INDETERMINATE	2	TRUE	2	0.374675719300251	5		1058	1646	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917080	50917080	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1731	537	1477	0	ENST00000440232.2:c.2332G>C	p.Ala778Pro	p.A778P	ENST00000440232	NM_002691.3	778	Gcc/Ccc	19/27	0.151371653494146	5	FACETS	0.987	0.943	1	0.658	0.629	0.688	INDETERMINATE	2	TRUE	2	0.374675719300251	5		1477	2268	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52729006	52729006	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	291	706	0	ENST00000322088.6:c.1698G>T	p.Lys566Asn	p.K566N	ENST00000322088	NM_014225.5	566	aaG/aaT	14/15	0.151371653494146	5	FACETS	0.958	0.901	1	0.639	0.6	0.679	INDETERMINATE	2	TRUE	2	0.374675719300251	5		706	1266	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99180027	99180028	+	missense_variant	Missense_Mutation	DNP	TG	TG	AT	novel	NA	P-0057416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1256	190	932	0	ENST00000074304.5:c.1970_1971delinsAT	p.Met657Asn	p.M657N	ENST00000074304	NM_001134224.1	657	aTG/aAT	19/26	0.374675719300251	3	FACETS	0.833	0.767	0.901	0.416	0.383	0.451	CLONAL	1	TRUE	1	0.374675719300251	3		932	1446	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017811	31017811	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1630	330	1209	1	ENST00000375687.4:c.673C>T	p.Gln225Ter	p.Q225*	ENST00000375687	NM_015338.5	225	Cag/Tag	8/13	0.268714137732447	4	FACETS	1	0.99	1	0.412	0.387	0.437	CLONAL	1	TRUE	1	0.374675719300251	4		1210	1960	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40828010	40828010	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	273	596	0	ENST00000373198.4:c.2418G>C	p.Gln806His	p.Q806H	ENST00000373198	NM_133170.3	806	caG/caC	17/32	0.268714137732447	4	FACETS	1	0.983	1	0.747	0.703	0.792	CLONAL	2	TRUE	1	0.374675719300251	4		596	894	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043414	6043414	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	15	108	0	ENST00000265849.7:c.260A>T	p.His87Leu	p.H87L	ENST00000265849	NM_000535.5	87	cAt/cTt	4/15	0.151371653494146	5	FACETS	1	0.738	1	0.334	0.246	0.437	INDETERMINATE	1	TRUE	2	0.374675719300251	5		108	125	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981406	70981407	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751042462	NA	P-0057416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	410	1155	0	ENST00000276594.2:c.689dup	p.Asp231ArgfsTer6	p.D231Rfs*6	ENST00000276594	NM_024504.3	230	cca/ccCa	2/8	0.172076287218249	2	FACETS	0.762	0.724	0.8	0.762	0.724	0.8	INDETERMINATE	2	TRUE	0	0.374675719300251	2		1155	1437	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249588	110249588	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	502	1459	2	ENST00000374672.4:c.1087C>T	p.Leu363Phe	p.L363F	ENST00000374672	NM_004235.4	363	Ctc/Ttc	3/5	0.333184649968336	2	FACETS	0.85	0.813	0.887	0.85	0.813	0.887	CLONAL	2	TRUE	0	0.374675719300251	2		1461	1577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0057418-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	170	641	1	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.516852885689918	1	FACETS	0.877	0.812	0.945	0.877	0.812	0.945	CLONAL	1	TRUE	0	0.516852885689918	1		642	556	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0057418-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	108	227	1				ENST00000310581	NM_198253.2	-/1132			0.270897535349482	3	FACETS	1	0.975	1	0.625	0.564	0.687	INDETERMINATE	1	TRUE	1	0.516852885689918	3		228	421	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0057418-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	290	506	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.516852885689918	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.516852885689918	2		506	521	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933543	36933543	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057419-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	181	1072	0	ENST00000361632.4:c.1744T>G	p.Ser582Ala	p.S582A	ENST00000361632		582	Tcc/Gcc	13/16	1	2	FACETS	0.91	0.84	0.983	0.91	0.84	0.983	CLONAL	1	TRUE	1	0.451162205204932	2		1072	882	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109309783	109309792	+	frameshift_variant	Frame_Shift_Del	DEL	TACATTCTTT	TACATTCTTT	-	novel	NA	P-0057419-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	155	608	0	ENST00000436639.2:c.1523_1532del	p.Lys508MetfsTer21	p.K508Mfs*21	ENST00000436639	NM_014454.2	508	aAAAGAATGTAt/at	9/10	0.451162205204932	1	FACETS	0.88	0.809	0.953	0.88	0.809	0.953	CLONAL	1	TRUE	0	0.451162205204932	1		608	605	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951166	48951166	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0057424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	81	352	0	ENST00000267163.4:c.1328C>G	p.Ser443Ter	p.S443*	ENST00000267163	NM_000321.2	443	tCa/tGa	13/27	0.238542870528204	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.238542870528204	1		352	565	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041896	14041896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	37	433	0	ENST00000311895.7:c.2443G>A	p.Glu815Lys	p.E815K	ENST00000311895	NM_005236.2	815	Gag/Aag	11/11	1	2	FACETS	0.541	0.445	0.649	0.541	0.445	0.649	SUBCLONAL	1	TRUE	1	0.238542870528204	2		433	573	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348450	89348450	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1251	84	1003	0	ENST00000301030.4:c.4500G>C	p.Gln1500His	p.Q1500H	ENST00000301030	NM_001256183.1	1500	caG/caC	9/13	0.238542870528204	1	FACETS	0.465	0.409	0.525	0.465	0.409	0.525	SUBCLONAL	1	TRUE	0	0.238542870528204	1		1003	1335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0057424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	180	1161	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.238542870528204	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.238542870528204	1		1161	1207	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244124	5244124	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1260	71	1016	0	ENST00000357368.4:c.1358C>G	p.Pro453Arg	p.P453R	ENST00000357368	NM_002850.3	453	cCc/cGc	11/38	0.238542870528204	1	FACETS	0.394	0.342	0.45	0.394	0.342	0.45	SUBCLONAL	1	TRUE	0	0.238542870528204	1		1016	1331	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155652	106155652	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1224691808	NA	P-0057424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	43	440	1	ENST00000380013.4:c.553C>T	p.Gln185Ter	p.Q185*	ENST00000380013	NM_001127208.2	185	Cag/Tag	3/11	1	2	FACETS	0.537	0.448	0.636	0.537	0.448	0.636	SUBCLONAL	1	TRUE	1	0.238542870528204	2		441	671	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410981	31410981	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	107	698	0	ENST00000344624.3:c.3539C>G	p.Ser1180Cys	p.S1180C	ENST00000344624		1180	tCt/tGt	28/33	0.238542870528204	3	FACETS	0.837	0.748	0.931	0.279	0.249	0.311	CLONAL	1	TRUE	0	0.238542870528204	3		698	1200	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411887	116411907	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCTCTCTGTTTTAAGATCTG	TTCTCTCTGTTTTAAGATCTG	-	novel	NA	P-0057424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1410	170	980	0	ENST00000397752.3:c.2888-16_2892del		p.X963_splice	ENST00000397752	NM_000245.2	963		14/21	0.238292031009785	3	FACETS	1	0.925	1	0.505	0.462	0.549	CLONAL	1	TRUE	1	0.238542870528204	3		980	1580	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs869320707	NA	P-0057424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	291	866	0	ENST00000397752.3:c.3028+1G>T		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.238292031009785	3	FACETS	0.944	0.886	1	0.944	0.886	1	CLONAL	2	TRUE	1	0.238542870528204	3		866	1446	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845172	128845172	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1254	179	910	0	ENST00000249373.3:c.666C>A	p.Phe222Leu	p.F222L	ENST00000249373	NM_005631.4	222	ttC/ttA	3/12	0.238292031009785	3	FACETS	1	0.978	1	0.586	0.538	0.636	CLONAL	1	TRUE	1	0.238542870528204	3		910	1433	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874398	151874398	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	92	480	0	ENST00000262189.6:c.8140G>C	p.Asp2714His	p.D2714H	ENST00000262189	NM_170606.2	2714	Gat/Cat	38/59	0.238292031009785	3	FACETS	1	0.897	1	0.505	0.448	0.567	CLONAL	1	TRUE	1	0.238542870528204	3		480	854	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040929	47040929	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1432	180	1163	3	ENST00000377604.3:c.1462del	p.Ala488ProfsTer216	p.A488Pfs*216	ENST00000377604	NM_001204468.1	487	Ggg/gg	14/24	1	2	FACETS	0.936	0.86	1	0.936	0.86	1	CLONAL	1	TRUE	1	0.238542870528204	2		1166	1612	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0057434-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	669	646	2	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.759467911521063	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.785708461861112	2		648	847	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435300	110435302	+	inframe_deletion	In_Frame_Del	DEL	GGT	GGT	-	rs765493638	NA	P-0057434-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	15	269	3	ENST00000375856.3:c.3099_3101del	p.Pro1036del	p.P1036del	ENST00000375856	NM_003749.2	1033	ccACCg/ccg	1/2	0.785708461861112	2	FACETS	0.142	0.104	0.189	0.071	0.052	0.095	SUBCLONAL	1	TRUE	0	0.785708461861112	2		272	268	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627485	14627485	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057434-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2439	251	643	0	ENST00000254322.2:c.585G>C	p.Lys195Asn	p.K195N	ENST00000254322	NM_006145.1	195	aaG/aaC	2/3	0.785708461861112	9	FACETS	0.891	0.828	0.956			1	CLONAL	1	TRUE	NA	0.785708461861112	9		643	2690	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627293	14627293	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs779148550	NA	P-0057434-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3853	409	987	0	ENST00000254322.2:c.777G>C	p.Arg259Ser	p.R259S	ENST00000254322	NM_006145.1	259	agG/agC	2/3	0.785708461861112	9	FACETS	0.916	0.866	0.968			1	CLONAL	1	TRUE	NA	0.785708461861112	9		987	4262	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644394	18644397	+	frameshift_variant	Frame_Shift_Del	DEL	AAGA	AAGA	-	rs751944085	NA	P-0057434-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	27	220	0	ENST00000266497.5:c.2578_2581del	p.Glu860LeufsTer4	p.E860Lfs*4	ENST00000266497		858	AAGAaa/aa	18/31	0.785708461861112	6	FACETS	0.459	0.365	0.567	0.115	0.091	0.142	SUBCLONAL	1	TRUE	2	0.785708461861112	6		220	385	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626901	14626901	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057434-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2783	274	723	0	ENST00000254322.2:c.874G>C	p.Gly292Arg	p.G292R	ENST00000254322	NM_006145.1	292	Ggc/Cgc	3/3	0.785708461861112	9	FACETS	0.856	0.798	0.915			1	CLONAL	1	TRUE	NA	0.785708461861112	9		723	3057	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626916	14626916	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057434-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2851	295	692	0	ENST00000254322.2:c.859G>T	p.Asp287Tyr	p.D287Y	ENST00000254322	NM_006145.1	287	Gat/Tat	3/3	0.785708461861112	9	FACETS	0.895	0.837	0.955			1	CLONAL	1	TRUE	NA	0.785708461861112	9		692	3146	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627313	14627313	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057434-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3650	388	932	0	ENST00000254322.2:c.757G>C	p.Asp253His	p.D253H	ENST00000254322	NM_006145.1	253	Gat/Cat	2/3	0.785708461861112	9	FACETS	0.917	0.865	0.971			1	CLONAL	1	TRUE	NA	0.785708461861112	9		932	4038	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627434	14627434	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057434-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2939	283	781	0	ENST00000254322.2:c.636G>T	p.Trp212Cys	p.W212C	ENST00000254322	NM_006145.1	212	tgG/tgT	2/3	0.785708461861112	9	FACETS	0.838	0.783	0.896			1	CLONAL	1	TRUE	NA	0.785708461861112	9		781	3222	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114839	73114839	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057434-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	33	25	0	ENST00000356692.5:c.1220C>A	p.Thr407Lys	p.T407K	ENST00000356692		407	aCa/aAa	9/9	0.785708461861112	3	FACETS	0.836	0.712	0.961	0.557	0.474	0.641	CLONAL	2	TRUE	0	0.785708461861112	3		25	70	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0057436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	1102	740	3	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	NA	2	FACETS	0.848	0.833	0.863			1	INDETERMINATE	3	TRUE	NA	0.604190559373488	2		743	1434	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0057436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	170	345	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.604190559373488	2		345	501	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041714	29041714	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	84	433	0	ENST00000282397.4:c.105T>G	p.Ser35Arg	p.S35R	ENST00000282397	NM_002019.4	35	agT/agG	2/30	0.402333162122605	1	FACETS	0.277	0.244	0.312	0.277	0.244	0.312	SUBCLONAL	1	TRUE	0	0.604190559373488	1		433	700	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934575	NA	P-0057437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	407	841	0	ENST00000269305.4:c.733G>C	p.Gly245Arg	p.G245R	ENST00000269305	NM_001126112.2	245	Ggc/Cgc	7/11	0.364346862738003	2	FACETS	0.943	0.899	0.988	0.943	0.899	0.988	CLONAL	2	TRUE	0	0.372351947299078	2		841	1159	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0057437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	419	875	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	0.364346862738003	2	FACETS	0.952	0.908	0.997	0.952	0.908	0.997	CLONAL	2	TRUE	0	0.372351947299078	2		875	1182	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	78	269	1	ENST00000257430.4:c.3919dup	p.Ile1307AsnfsTer8	p.I1307Nfs*8	ENST00000257430	NM_000038.5	1306	gaa/gAaa	16/16	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.372351947299078	2		270	376	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs770248150	NA	P-0057437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	192	492	0	ENST00000311936.3:c.351A>T	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaT	4/5	0.372351947299078	2	FACETS	0.902	0.848	0.957	1	0.991	1	CLONAL	3	TRUE	0	0.372351947299078	2		492	381	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95599668	95599668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367797765	NA	P-0057437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	201	460	0	ENST00000393063.1:c.128C>T	p.Thr43Met	p.T43M	ENST00000393063	NM_030621.3	43	aCg/aTg	3/28	0.364346862738003	2	FACETS	0.973	0.908	1	0.973	0.908	1	CLONAL	2	TRUE	0	0.372351947299078	2		460	555	SUCCESS
APC	324	MSKCC	GRCh37	5	112175351	112175351	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	112	337	0	ENST00000257430.4:c.4063del	p.Ser1355LeufsTer60	p.S1355Lfs*60	ENST00000257430	NM_000038.5	1354	Ttt/tt	16/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.372351947299078	2		337	516	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0057438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	242	473	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.963	0.904	1	0.963	0.904	1	CLONAL	1	TRUE	1	0.681877975967346	2		474	737	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0057438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	346	418	2	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.681877975967346	1	FACETS	0.853	0.812	0.894	0.853	0.812	0.894	CLONAL	1	TRUE	0	0.681877975967346	1		420	784	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266512	198266512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	139	361	0	ENST00000335508.6:c.2324G>A	p.Arg775Gln	p.R775Q	ENST00000335508	NM_012433.2	775	cGa/cAa	16/25	1	2	FACETS	0.609	0.556	0.665	0.609	0.556	0.665	SUBCLONAL	1	TRUE	1	0.681877975967346	2		361	669	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039405	47039405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	66	763	2	ENST00000377604.3:c.1028G>A	p.Arg343His	p.R343H	ENST00000377604	NM_001204468.1	343	cGc/cAc	10/24	1	2	FACETS	0.198	0.171	0.228	0.198	0.171	0.228	SUBCLONAL	1	TRUE	1	0.681877975967346	2		765	976	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636815	8636815	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	259	489	0	ENST00000356435.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000356435		32	Gat/Tat	2/35	NA	2	FACETS	0.908	0.853	0.964			1	INDETERMINATE	1	TRUE	NA	0.681877975967346	2		489	837	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961791	41961791	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	56	401	1	ENST00000219905.7:c.699C>A	p.Phe233Leu	p.F233L	ENST00000219905	NM_001164273.1	233	ttC/ttA	2/24	0.681877975967346	1	FACETS	0.23	0.197	0.266	0.23	0.197	0.266	SUBCLONAL	1	TRUE	0	0.681877975967346	1		402	470	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248619	8248619	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	358	885	0	ENST00000335790.3:c.268G>T	p.Ala90Ser	p.A90S	ENST00000335790	NM_002315.2	90	Gct/Tct	3/4	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.681877975967346	2		885	1019	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941185	71941185	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	418	985	0	ENST00000298229.2:c.962del	p.Gly321ValfsTer3	p.G321Vfs*3	ENST00000298229	NM_001567.3	320	ctG/ct	9/28	1	2	FACETS	0.976	0.93	1	0.976	0.93	1	CLONAL	1	TRUE	1	0.681877975967346	2		985	1256	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434752	110434752	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	241	396	0	ENST00000375856.3:c.3649G>T	p.Gly1217Cys	p.G1217C	ENST00000375856	NM_003749.2	1217	Ggc/Tgc	1/2	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.681877975967346	2		396	643	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857599	9857599	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	234	541	0	ENST00000330684.3:c.3802C>A	p.Gln1268Lys	p.Q1268K	ENST00000330684	NM_001134407.1	1268	Cag/Aag	13/13	1	2	FACETS	0.976	0.915	1	0.976	0.915	1	CLONAL	1	TRUE	1	0.681877975967346	2		541	703	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602431	10602431	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	300	656	0	ENST00000171111.5:c.1147T>C	p.Ser383Pro	p.S383P	ENST00000171111	NM_203500.1	383	Tcg/Ccg	3/6	0.681877975967346	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.681877975967346	1		656	564	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735541	40735541	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	245	653	0	ENST00000373198.4:c.3332G>C	p.Gly1111Ala	p.G1111A	ENST00000373198	NM_133170.3	1111	gGc/gCc	25/32	NA	2	FACETS	0.965	0.905	1			1	INDETERMINATE	1	TRUE	NA	0.681877975967346	2		653	745	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876421	35876421	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	299	803	1	ENST00000303115.3:c.1213C>A	p.Leu405Met	p.L405M	ENST00000303115	NM_002185.3	405	Ctg/Atg	8/8	1	2	FACETS	0.96	0.906	1	0.96	0.906	1	CLONAL	1	TRUE	1	0.681877975967346	2		804	914	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940410	31940410	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1562687361	NA	P-0057438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	432	849	0	ENST00000375333.2:c.443C>T	p.Ala148Val	p.A148V	ENST00000375333	NM_032454.1	148	gCg/gTg	3/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.681877975967346	2		849	1228	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729268	41729268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	206	427	0	ENST00000242208.4:c.1261G>A	p.Glu421Lys	p.E421K	ENST00000242208	NM_002192.2	421	Gag/Aag	3/3	1	2	FACETS	0.864	0.805	0.925	0.864	0.805	0.925	CLONAL	1	TRUE	1	0.681877975967346	2		427	699	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293618	137293618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	513	1073	0	ENST00000481739.1:c.169C>T	p.Pro57Ser	p.P57S	ENST00000481739	NM_002957.4	57	Ccc/Tcc	2/10	1	2	FACETS	0.967	0.926	1	0.967	0.926	1	CLONAL	1	TRUE	1	0.696400393983163	2		1073	1523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578493	7578493	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1206165503	NA	P-0057441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	711	1392	10	ENST00000269305.4:c.437G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tGg/tAg	5/11	0.86563332325622	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.86563332325622	1		1402	887	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881523	48881523	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0057441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	207	422	0	ENST00000267163.4:c.245C>G	p.Ser82Ter	p.S82*	ENST00000267163	NM_000321.2	82	tCa/tGa	2/27	0.86563332325622	1	FACETS	0.926	0.883	0.966	0.926	0.883	0.966	CLONAL	1	TRUE	0	0.86563332325622	1		422	293	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122513	17122514	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0057441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	529	984	0	ENST00000285071.4:c.881_882del	p.Glu294GlyfsTer9	p.E294Gfs*9	ENST00000285071	NM_144997.5	294	gAG/g	9/14	0.86563332325622	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.86563332325622	1		984	628	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244287	153244287	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	172	429	0	ENST00000281708.4:c.1870C>T	p.Gln624Ter	p.Q624*	ENST00000281708	NM_033632.3	624	Cag/Tag	12/12	0.86563332325622	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.86563332325622	1		429	213	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0057442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	1284	144	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	NA	2	FACETS	1	0.998	1			1	INDETERMINATE	2	TRUE	NA	0.92882636494864	2		144	1341	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033903	49033909	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGACC	CTGGACC	-	novel	NA	P-0057442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	557	89	1	ENST00000267163.4:c.2042_2048del	p.Trp681PhefsTer13	p.W681Ffs*13	ENST00000267163	NM_000321.2	680	atCTGGACC/at	20/27	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.92882636494864	2		90	598	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	182	777	0	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	0.846	0.78	0.915	0.846	0.78	0.915	CLONAL	1	TRUE	1	0.397261478575845	2		777	1083	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0057446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	36	381	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.816	0.676	0.97	0.816	0.676	0.97	CLONAL	1	TRUE	1	0.397261478575845	2		382	222	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717712	89717712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782350	NA	P-0057446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	39	391	2	ENST00000371953.3:c.737C>T	p.Pro246Leu	p.P246L	ENST00000371953	NM_000314.4	246	cCg/cTg	7/9	1	2	FACETS	0.602	0.501	0.715	0.602	0.501	0.715	SUBCLONAL	1	TRUE	1	0.397261478575845	2		393	326	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224536	36224536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	197	914	0	ENST00000222270.7:c.6998G>A	p.Gly2333Glu	p.G2333E	ENST00000222270	NM_014727.1	2333	gGg/gAg	29/37	1	2	FACETS	0.719	0.664	0.776	0.719	0.664	0.776	SUBCLONAL	1	TRUE	1	0.397261478575845	2		914	1380	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434972	49434972	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	189	877	0	ENST00000301067.7:c.6581C>A	p.Pro2194His	p.P2194H	ENST00000301067	NM_003482.3	2194	cCc/cAc	31/54	1	2	FACETS	0.937	0.866	1	0.937	0.866	1	CLONAL	1	TRUE	1	0.397261478575845	2		877	1015	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916933	178916938	+	inframe_deletion	In_Frame_Del	DEL	ACCGTG	ACCGTG	-	novel	NA	P-0057446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	136	395	0	ENST00000263967.3:c.321_326del	p.Asn107_Glu109delinsLys	p.N107_E109delinsK	ENST00000263967	NM_006218.2	107	aACCGTGaa/aaa	2/21	0.397261478575845	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	0	0.397261478575845	2		395	335	SUCCESS
AR	367	MSKCC	GRCh37	X	66942668	66942668	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1064794069	NA	P-0057446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	60	332	0	ENST00000374690.3:c.2450-1G>A		p.X817_splice	ENST00000374690	NM_000044.3	817			1	2	FACETS	0.883	0.765	1	0.883	0.765	1	CLONAL	1	TRUE	1	0.397261478575845	2		332	342	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023782	27023783	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	A	novel	NA	P-0057446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	94	325	1	ENST00000324856.7:c.888_889delinsA	p.Asn296LysfsTer67	p.N296Kfs*67	ENST00000324856	NM_006015.4	296	aaCCaa/aaAaa	1/20	1	2	FACETS	0.775	0.69	0.864	0.775	0.69	0.864	SUBCLONAL	1	TRUE	1	0.397261478575845	2		326	611	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835756	68835828	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGAATACAGTGGGGCACCACCACCGCCCCCCGCCCCATCAGGTATGTTGGCATTTTTCTGAGAAGTTCGCTGT	TGAATACAGTGGGGCACCACCACCGCCCCCCGCCCCATCAGGTATGTTGGCATTTTTCTGAGAAGTTCGCTGT	-	novel	NA	P-0057447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	148	793	0	ENST00000261769.5:c.349_387+34del		p.X117_splice	ENST00000261769	NM_004360.3	117		3/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		793	653	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	147	619	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.447762009646109	2		619	576	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	147	628	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	0.419229826523215	1	FACETS	0.671	0.613	0.731	0.671	0.613	0.731	SUBCLONAL	1	TRUE	0	0.447762009646109	1		628	760	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0057448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	127	549	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.419229826523215	1	FACETS	0.796	0.724	0.871	0.796	0.724	0.871	SUBCLONAL	1	TRUE	0	0.447762009646109	1		549	553	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0057448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	198	548	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.447762009646109	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.447762009646109	1		548	550	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939177	36939177	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs186379741	NA	P-0057448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	274	1177	0	ENST00000361632.4:c.532G>A	p.Val178Met	p.V178M	ENST00000361632		178	Gtg/Atg	5/16	0.419229826523215	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.447762009646109	1		1177	863	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633632	69633632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1450818144	NA	P-0057448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	31	21	0	ENST00000334134.2:c.70C>T	p.Arg24Trp	p.R24W	ENST00000334134	NM_005247.2	24	Cgg/Tgg	1/3	1	2	FACETS	1	0.891	1	1	0.968	1	CLONAL	2	TRUE	1	0.447762009646109	2		21	65	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0057448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	427	828	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.44410533507358	2	FACETS	0.981	0.939	1	0.981	0.939	1	CLONAL	2	TRUE	0	0.447762009646109	2		828	972	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118940	70118941	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	463	1006	0	ENST00000245479.2:c.514dup	p.Tyr172LeufsTer80	p.Y172Lfs*80	ENST00000245479	NM_000346.3	171	gat/gaTt	2/3	0.44410533507358	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.447762009646109	2		1006	997	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091462	193091462	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776558	NA	P-0057448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	178	496	1	ENST00000367435.3:c.131+1G>A		p.X44_splice	ENST00000367435	NM_024529.4	44			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.447762009646109	2		497	691	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266027	41266253	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTA	GGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTA	-	novel	NA	P-0057448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	8	352	0	ENST00000349496.5:c.24_241+9del		p.X8_splice	ENST00000349496	NM_001904.3	8		3/15	0.44410533507358	2	FACETS	0.147	0.094	0.216	0.074	0.047	0.108	SUBCLONAL	1	TRUE	0	0.447762009646109	2		352	243	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061192	38061210	+	frameshift_variant	Frame_Shift_Del	DEL	AAGCGCTTCTGGCGGCGCA	AAGCGCTTCTGGCGGCGCA	-	novel	NA	P-0057450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	168	463	0	ENST00000250448.2:c.779_797del	p.Leu260SerfsTer55	p.L260Sfs*55	ENST00000250448	NM_004496.3	260	tTGCGCCGCCAGAAGCGCTTc/tc	2/2	1	2	FACETS	0.892	0.821	0.965	0.892	0.821	0.965	CLONAL	1	TRUE	1	0.4911413367727	2		463	767	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014089	14014089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1296707814	NA	P-0057450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	217	900	0	ENST00000311895.7:c.67G>A	p.Val23Met	p.V23M	ENST00000311895	NM_005236.2	23	Gtg/Atg	1/11	1	2	FACETS	0.803	0.746	0.862	0.803	0.746	0.862	CLONAL	1	TRUE	1	0.4911413367727	2		900	1101	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719318	190719339	+	frameshift_variant	Frame_Shift_Del	DEL	AATGAGTAATGTATCATGGGAG	AATGAGTAATGTATCATGGGAG	-	novel	NA	P-0057450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	73	325	0	ENST00000441310.2:c.1322_1343del	p.Met441ThrfsTer12	p.M441Tfs*12	ENST00000441310	NM_000534.4	440	tcAATGAGTAATGTATCATGGGAG/tc	9/13	1	2	FACETS	0.745	0.655	0.841	0.745	0.655	0.841	SUBCLONAL	1	TRUE	1	0.4911413367727	2		325	399	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696388	47696403	+	protein_altering_variant	In_Frame_Del	DEL	CTCATCCAAAAGAAAA	CTCATCCAAAAGAAAA	T	novel	NA	P-0057450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	213	556	0	ENST00000347630.2:c.420_435delinsA	p.Asp140_Asp144del	p.D140_D144del	ENST00000347630	NM_001007230.1	140	gaTTTTCTTTTGGATGAG/gaA	6/11	NA	2	FACETS	1	0.941	1			1	INDETERMINATE	1	TRUE	NA	0.4911413367727	2		556	857	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436216	110436216	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1368896620	NA	P-0057451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	183	624	0	ENST00000375856.3:c.2185G>A	p.Ala729Thr	p.A729T	ENST00000375856	NM_003749.2	729	Gcc/Acc	1/2	0.68905046700461	3	FACETS	0.761	0.71	0.814	0.508	0.473	0.543	SUBCLONAL	2	TRUE	0	0.68905046700461	3		624	469	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274259	10274259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	125	449	0	ENST00000330684.3:c.10G>A	p.Val4Met	p.V4M	ENST00000330684	NM_001134407.1	4	Gtg/Atg	2/13	0.68905046700461	2	FACETS	1	0.964	1	0.546	0.501	0.593	CLONAL	1	TRUE	0	0.68905046700461	2		449	332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0057452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	277	750	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.338979723608454	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.338979723608454	3		750	844	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913422	32913422	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555283989	NA	P-0057452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	29	478	0	ENST00000380152.3:c.4930G>C	p.Glu1644Gln	p.E1644Q	ENST00000380152		1644	Gaa/Caa	11/27	0.127382795332647	3	FACETS	0.36	0.288	0.442	0.18	0.144	0.221	INDETERMINATE	1	TRUE	1	0.338979723608454	3		478	556	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275804	38275804	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	97	875	0	ENST00000425967.3:c.1465G>C	p.Ala489Pro	p.A489P	ENST00000425967	NM_001174067.1	489	Gca/Cca	11/19	0.324253472484058	4	FACETS	0.781	0.695	0.873	0.391	0.347	0.437	SUBCLONAL	1	TRUE	2	0.338979723608454	4		875	981	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325358	1325358	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	206	686	0	ENST00000400841.2:c.317T>G	p.Val106Gly	p.V106G	ENST00000400841		106	gTt/gGt	3/6	0.127042327096642	5	FACETS	1	0.967	1	0.711	0.661	0.764	INDETERMINATE	2	TRUE	2	0.338979723608454	5		686	859	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	263	365	0				ENST00000310581	NM_198253.2	-/1132			0.3	5	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	2	0.36	5		365	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578513	7578513	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	418	1016	0	ENST00000269305.4:c.417G>C	p.Lys139Asn	p.K139N	ENST00000269305	NM_001126112.2	139	aaG/aaC	5/11	0.259085192300286	2	FACETS	0.827	0.787	0.868	0.827	0.787	0.868	CLONAL	2	TRUE	0	0.36	2		1016	1404	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0057453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	171	331	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.3	3	FACETS	0.903	0.834	0.973	0.903	0.834	0.973	CLONAL	2	TRUE	1	0.36	3		331	621	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868419	117868419	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	210	548	0	ENST00000297338.2:c.923C>T	p.Pro308Leu	p.P308L	ENST00000297338	NM_006265.2	308	cCt/cTt	8/14	0.207334850890707	5	FACETS	0.913	0.848	0.98	0.609	0.565	0.654	INDETERMINATE	2	TRUE	2	0.36	5		548	984	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16022737	16022738	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	179	422	0	ENST00000268712.3:c.1914dup	p.Gly639ArgfsTer8	p.G639Rfs*8	ENST00000268712	NM_006311.3	638	-/A	17/46	0.259085192300286	2	FACETS	0.818	0.758	0.88	0.818	0.758	0.88	CLONAL	2	TRUE	0	0.36	2		422	608	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448439	49448439	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1242	218	914	1	ENST00000301067.7:c.272G>A	p.Trp91Ter	p.W91*	ENST00000301067	NM_003482.3	91	tGg/tAg	3/54	0.214354959906924	3	FACETS	0.979	0.908	1	0.489	0.454	0.527	INDETERMINATE	1	TRUE	1	0.36	3		915	1460	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412886	49412886	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	104	734	0	ENST00000418115.1:c.137T>C	p.Ile46Thr	p.I46T	ENST00000418115	NM_001664.2	46	aTc/aCc	2/5	0.3	3	FACETS	0.634	0.566	0.706	0.317	0.283	0.353	SUBCLONAL	1	TRUE	1	0.36	3		734	1076	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035962	47035965	+	frameshift_variant	Frame_Shift_Del	DEL	AATG	AATG	-	novel	NA	P-0057453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	321	502	0	ENST00000377604.3:c.641_644del	p.Asn214ArgfsTer51	p.N214Rfs*51	ENST00000377604	NM_001204468.1	214	AATGag/ag	7/24	0.3	2	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.36	2		502	792	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0057454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	553	493	1	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	0.385998802369339	3	FACETS	0.873	0.842	0.903	0.873	0.842	0.903	INDETERMINATE	2	TRUE	1	0.858222542065131	3		494	1055	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664864	138664893	+	inframe_deletion	In_Frame_Del	DEL	GCGGCTGCAGCCGCAGCTGCTGCAGCCGCT	GCGGCTGCAGCCGCAGCTGCTGCAGCCGCT	-	rs387906321	NA	P-0057454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	68	92	0	ENST00000330315.3:c.672_701del	p.Ala225_Ala234del	p.A225_A234del	ENST00000330315	NM_023067.3	224	gcAGCGGCTGCAGCAGCTGCGGCTGCAGCCGCg/gcg	1/1	1	2	FACETS	0.809	0.717	0.904	0.809	0.717	0.904	CLONAL	1	TRUE	1	0.858222542065131	2		92	196	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845871	151845871	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	564	769	0	ENST00000262189.6:c.13141G>T	p.Glu4381Ter	p.E4381*	ENST00000262189	NM_170606.2	4381	Gaa/Taa	52/59	0.385998802369339	3	FACETS	0.819	0.789	0.848	0.819	0.789	0.848	INDETERMINATE	2	TRUE	1	0.858222542065131	3		769	1147	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243852	46243853	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	194	368	0	ENST00000334344.6:c.1950dup	p.Gln651SerfsTer56	p.Q651Sfs*56	ENST00000334344	NM_152641.2	649	cat/caTt	15/21	1	2	FACETS	0.926	0.866	0.988	0.926	0.866	0.988	CLONAL	1	TRUE	1	0.858222542065131	2		368	488	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034962	42034962	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	475	702	0	ENST00000219905.7:c.4804C>G	p.Pro1602Ala	p.P1602A	ENST00000219905	NM_001164273.1	1602	Cct/Gct	15/24	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.858222542065131	2		702	1081	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511638	66511638	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	384	469	0	ENST00000358598.2:c.98A>G	p.Asp33Gly	p.D33G	ENST00000358598	NM_212471.2	33	gAt/gGt	2/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.858222542065131	2		469	861	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228257	53228257	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	532	791	0	ENST00000375401.3:c.2145C>G	p.Phe715Leu	p.F715L	ENST00000375401	NM_004187.3	715	ttC/ttG	15/26	0.858222542065131	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.858222542065131	1		791	698	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0057455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	180	410	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.434443282330075	3	FACETS	0.987	0.918	1	0.987	0.918	1	CLONAL	2	TRUE	1	0.434443282330075	3		410	511	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441974	6441974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	88	642	0	ENST00000356142.4:c.533C>T	p.Ala178Val	p.A178V	ENST00000356142	NM_018890.3	178	gCg/gTg	7/7	1	2	FACETS	0.837	0.744	0.935	0.837	0.744	0.935	CLONAL	1	TRUE	1	0.434443282330075	2		642	484	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227600	36227600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367682204	NA	P-0057455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	58	545	0	ENST00000222270.7:c.7169C>T	p.Ser2390Leu	p.S2390L	ENST00000222270	NM_014727.1	2390	tCg/tTg	31/37	0.434443282330075	1	FACETS	0.792	0.687	0.904	0.792	0.687	0.904	CLONAL	1	TRUE	0	0.434443282330075	1		545	264	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28979931	28979931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	59	503	0	ENST00000282397.4:c.1537G>A	p.Glu513Lys	p.E513K	ENST00000282397	NM_002019.4	513	Gaa/Aaa	11/30	1	2	FACETS	0.617	0.532	0.709	0.617	0.532	0.709	SUBCLONAL	1	TRUE	1	0.434443282330075	2		503	440	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245902	16245902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761996375	NA	P-0057455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	52	319	0	ENST00000375759.3:c.1525G>A	p.Gly509Ser	p.G509S	ENST00000375759	NM_015001.2	509	Ggt/Agt	8/15	1	2	FACETS	0.924	0.794	1	0.924	0.794	1	CLONAL	1	TRUE	1	0.434443282330075	2		319	259	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226566919	226566919	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	66	643	0	ENST00000366794.5:c.1669C>T	p.Leu557Phe	p.L557F	ENST00000366794	NM_001618.3	557	Ctt/Ttt	12/23	0.401231749185924	3	FACETS	0.526	0.456	0.602	0.263	0.228	0.301	SUBCLONAL	1	TRUE	1	0.434443282330075	3		643	703	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244040	46244040	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	72	558	0	ENST00000334344.6:c.2134G>T	p.Glu712Ter	p.E712*	ENST00000334344	NM_152641.2	712	Gaa/Taa	15/21	1	2	FACETS	0.816	0.717	0.923	0.816	0.717	0.923	CLONAL	1	TRUE	1	0.434443282330075	2		558	406	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030893	36030893	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758795351	NA	P-0057455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	33	862	0	ENST00000358208.4:c.1172G>A	p.Arg391His	p.R391H	ENST00000358208		391	cGt/cAt	10/12	1	2	FACETS	0.352	0.287	0.427	0.352	0.287	0.427	SUBCLONAL	1	TRUE	1	0.434443282330075	2		862	431	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73047261	73047261	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	95	429	1	ENST00000356692.5:c.68C>T	p.Pro23Leu	p.P23L	ENST00000356692		23	cCt/cTt	2/9	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.434443282330075	2		430	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934573	NA	P-0057456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	390	758	0	ENST00000269305.4:c.722C>A	p.Ser241Tyr	p.S241Y	ENST00000269305	NM_001126112.2	241	tCc/tAc	7/11	0.476677522883309	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.526411646411048	2		758	741	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930087	68930087	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	66	410	0	ENST00000288368.4:c.148T>G	p.Leu50Val	p.L50V	ENST00000288368	NM_024870.2	50	Tta/Gta	2/40	0.297036772570506	5	FACETS	0.716	0.621	0.818	0.143	0.124	0.164	INDETERMINATE	1	TRUE	0	0.526411646411048	5		410	627	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432587	49432587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1177636600	NA	P-0057456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	412	1037	1	ENST00000301067.7:c.8552G>A	p.Gly2851Asp	p.G2851D	ENST00000301067	NM_003482.3	2851	gGt/gAt	34/54	0.526411646411048	4	FACETS	0.996	0.949	1	0.996	0.949	1	CLONAL	2	TRUE	2	0.526411646411048	4		1038	1199	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005845	69005845	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	64	441	0	ENST00000288368.4:c.2256T>G	p.Asp752Glu	p.D752E	ENST00000288368	NM_024870.2	752	gaT/gaG	21/40	0.297036772570506	5	FACETS	0.843	0.731	0.965	0.169	0.146	0.193	INDETERMINATE	1	TRUE	0	0.526411646411048	5		441	516	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0057457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	112	298	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.875	0.794	0.958	0.875	0.794	0.958	CLONAL	1	TRUE	1	0.684811770984509	2		298	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0057457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	170	740	3	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.684811770984509	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.684811770984509	1		743	322	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357502	89357502	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	184	897	1	ENST00000301030.4:c.316C>T	p.Arg106Ter	p.R106*	ENST00000301030	NM_001256183.1	106	Cga/Tga	5/13	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.684811770984509	2		898	504	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942842	68942842	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	180	711	0	ENST00000288368.4:c.654G>T	p.Met218Ile	p.M218I	ENST00000288368	NM_024870.2	218	atG/atT	6/40	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.684811770984509	2		711	498	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603038	48603039	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCAGCAGCAGGCGGCTACTGCACAAGC	rs876660720	NA	P-0057457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	100	427	0	ENST00000342988.3:c.1349_1376dup	p.Ala460GlyfsTer43	p.A460Gfs*43	ENST00000342988	NM_005359.5	447	atg/aTGCAGCAGCAGGCGGCTACTGCACAAGCtg	11/12	0.684811770984509	1	FACETS	0.612	0.553	0.673	0.612	0.553	0.673	SUBCLONAL	1	TRUE	0	0.684811770984509	1		427	314	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416138	49416138	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0057457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	146	430	0	ENST00000301067.7:c.16339-2A>G		p.X5447_splice	ENST00000301067	NM_003482.3	5447			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.684811770984509	2		430	387	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019589	123019589	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	165	548	0	ENST00000355640.3:c.77A>T	p.Glu26Val	p.E26V	ENST00000355640		26	gAg/gTg	2/7	1	2	FACETS	0.958	0.887	1	0.958	0.887	1	CLONAL	1	TRUE	1	0.684811770984509	2		548	503	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0057458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	139	470	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.393205533937067	3	FACETS	1	0.94	1	0.519	0.473	0.566	CLONAL	1	TRUE	1	0.543728160021699	3		470	627	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0057458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	241	323	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.203216923606434	5	FACETS	1	0.971	1	0.706	0.662	0.751	INDETERMINATE	2	TRUE	2	0.543728160021699	5		323	760	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117799	108117799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202160435	NA	P-0057458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	242	432	0	ENST00000278616.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000278616	NM_000051.3	337	cGt/cAt	8/63	0.529993768408176	3	FACETS	0.931	0.876	0.987	0.931	0.876	0.987	CLONAL	2	TRUE	1	0.543728160021699	3		432	608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519975	NA	P-0057458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	533	1056	0	ENST00000269305.4:c.403T>C	p.Cys135Arg	p.C135R	ENST00000269305	NM_001126112.2	135	Tgc/Cgc	5/11	NA	2	FACETS	0.984	0.949	1			1	INDETERMINATE	2	TRUE	NA	0.543728160021699	2		1056	996	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0057458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	129	354	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.529993768408176	3	FACETS	1	0.939	1	0.52	0.473	0.569	CLONAL	1	TRUE	1	0.543728160021699	3		355	580	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045133	47045133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	163	817	1	ENST00000377604.3:c.2374C>T	p.Arg792Trp	p.R792W	ENST00000377604	NM_001204468.1	792	Cgg/Tgg	21/24	0.543728160021699	3	FACETS	0.891	0.818	0.967	0.445	0.409	0.484	CLONAL	1	TRUE	1	0.543728160021699	3		818	856	SUCCESS
APC	324	MSKCC	GRCh37	5	112175350	112175351	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	154	319	0	ENST00000257430.4:c.4063dup	p.Ser1355PhefsTer20	p.S1355Ffs*20	ENST00000257430	NM_000038.5	1353	-/T	16/16	0.529993768408176	3	FACETS	0.862	0.797	0.928	0.862	0.797	0.928	CLONAL	2	TRUE	1	0.543728160021699	3		319	418	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259416	89259416	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	157	694	0	ENST00000336596.2:c.560G>T	p.Gly187Val	p.G187V	ENST00000336596	NM_005233.5	187	gGt/gTt	3/17	1	2	FACETS	0.758	0.695	0.823	0.758	0.695	0.823	SUBCLONAL	1	TRUE	1	0.543728160021699	2		694	762	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473592	67473593	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	582	868	0	ENST00000327367.4:c.673dup	p.Thr225AsnfsTer86	p.T225Nfs*86	ENST00000327367	NM_005902.3	224	-/A	6/9	0.543728160021699	3	FACETS	0.991	0.961	1	0.991	0.961	1	CLONAL	3	TRUE	0	0.543728160021699	3		868	916	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368268	45368268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	326	564	1	ENST00000262160.6:c.1334C>T	p.Pro445Leu	p.P445L	ENST00000262160	NM_005901.5	445	cCt/cTt	11/11	0.524202754138227	2	FACETS	0.988	0.943	1	0.988	0.943	1	CLONAL	2	TRUE	0	0.543728160021699	2		565	607	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860581	151860581	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	58	745	0	ENST00000262189.6:c.10081A>C	p.Lys3361Gln	p.K3361Q	ENST00000262189	NM_170606.2	3361	Aaa/Caa	43/59	0.493859821597639	4	FACETS	0.324	0.277	0.376	0.162	0.138	0.188	SUBCLONAL	1	TRUE	2	0.543728160021699	4		745	1016	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863224499	NA	P-0057459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	151	859	0	ENST00000269305.4:c.672+1G>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.225433605150319	2	FACETS	0.858	0.785	0.935	0.429	0.392	0.468	INDETERMINATE	1	FALSE	0	0.43119106838422	2		859	816	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945405	71945405	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	139	882	1	ENST00000298229.2:c.2293T>A	p.Phe765Ile	p.F765I	ENST00000298229	NM_001567.3	765	Ttc/Atc	20/28	0.118253400988895	3	FACETS	0.99	0.901	1	0.495	0.45	0.541	INDETERMINATE	1	FALSE	1	0.43119106838422	3		883	792	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380276	+	missense_variant	Missense_Mutation	DNP	TT	TT	AC	novel	NA	P-0057459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	100	652	2	ENST00000311936.3:c.182_183delinsGT	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAA/cGT	3/5	1	2	FACETS	0.666	0.596	0.742	0.666	0.596	0.742	SUBCLONAL	1	FALSE	1	0.43119106838422	2		654	696	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060786	38060803	+	inframe_deletion	In_Frame_Del	DEL	GGAGAACGGGTGGTTGAA	GGAGAACGGGTGGTTGAA	-	novel	NA	P-0057459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	293	1047	0	ENST00000250448.2:c.1186_1203del	p.Phe396_Ser401del	p.F396_S401del	ENST00000250448	NM_004496.3	396	TTCAACCACCCGTTCTCC/-	2/2	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.43119106838422	2		1047	1187	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0057460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	349	795	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.56910917294836	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.56910917294836	1		795	858	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862107	68862107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501244	NA	P-0057460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	297	627	1	ENST00000261769.5:c.2195G>A	p.Arg732Gln	p.R732Q	ENST00000261769	NM_004360.3	732	cGg/cAg	14/16	0.56910917294836	1	FACETS	0.979	0.926	1	0.979	0.926	1	CLONAL	1	TRUE	0	0.56910917294836	1		628	763	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069475	30069475	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	274	741	0	ENST00000338641.4:c.1340G>T	p.Arg447Met	p.R447M	ENST00000338641	NM_000268.3	447	aGg/aTg	12/16	0.56910917294836	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.56910917294836	1		741	674	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472555	88472555	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	274	799	0	ENST00000360948.2:c.2000T>A	p.Met667Lys	p.M667K	ENST00000360948	NM_001012338.2	667	aTg/aAg	16/19	1	2	FACETS	0.927	0.87	0.985	0.927	0.87	0.985	CLONAL	1	TRUE	1	0.56910917294836	2		799	1039	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448391	56448392	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0057460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	349	816	0	ENST00000407977.2:c.255_256del	p.His86ProfsTer9	p.H86Pfs*9	ENST00000407977		85	tcCCac/tcac	3/10	0.56910917294836	1	FACETS	0.987	0.938	1	0.987	0.938	1	CLONAL	1	TRUE	0	0.56910917294836	1		816	889	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	161	619	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.821	0.755	0.891	0.821	0.755	0.891	CLONAL	1	TRUE	1	0.52	2		619	754	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	500	454	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.907	0.872	0.942	1	0.997	1	CLONAL	2	TRUE	1	0.52	2		460	1060	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	233	482	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.888	0.829	0.95	0.888	0.829	0.95	CLONAL	1	TRUE	1	0.52	2		483	1009	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089705	27089706	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1286891446	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	290	779	0	ENST00000324856.7:c.2666dup	p.Met890HisfsTer46	p.M890Hfs*46	ENST00000324856	NM_006015.4	887	-/G	8/20	1	2	FACETS	0.855	0.803	0.908	0.855	0.803	0.908	CLONAL	1	TRUE	1	0.52	2		779	1305	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	247	420	10	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.52	2		430	672	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	137	521	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.597	0.542	0.654	0.597	0.542	0.654	SUBCLONAL	1	TRUE	1	0.52	2		527	883	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	169	351	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.948	0.874	1	0.948	0.874	1	CLONAL	1	TRUE	1	0.52	2		351	686	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	222	422	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.955	0.89	1	0.955	0.89	1	CLONAL	1	TRUE	1	0.52	2		422	894	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	195	364	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.52	2		364	722	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165213	47165213	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	142	314	1	ENST00000409792.3:c.913del	p.Thr305GlnfsTer35	p.T305Qfs*35	ENST00000409792	NM_014159.6	305	Aca/ca	3/21	1	2	FACETS	0.847	0.774	0.923	0.847	0.774	0.923	CLONAL	1	TRUE	1	0.52	2		315	645	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1385	118	812	8	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	1	2	FACETS	0.302	0.271	0.335	0.302	0.271	0.335	SUBCLONAL	1	TRUE	1	0.52	2		820	1503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574026	7574026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	152	685	0	ENST00000269305.4:c.1001G>T	p.Gly334Val	p.G334V	ENST00000269305	NM_001126112.2	334	gGg/gTg	10/11	1	2	FACETS	0.502	0.458	0.548	0.502	0.458	0.548	SUBCLONAL	1	TRUE	1	0.52	2		685	1165	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795103	242795104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768249210	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1341	143	1003	1	ENST00000334409.5:c.105dup	p.Thr36HisfsTer70	p.T36Hfs*70	ENST00000334409	NM_005018.2	35	-/C	2/5	0.3	2	FACETS	0.371	0.336	0.407			1	INDETERMINATE	1	TRUE	NA	0.52	2		1004	1484	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937354	32937355	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs397507952	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	160	336	0	ENST00000380152.3:c.8021dup	p.Ile2675AspfsTer6	p.I2675Dfs*6	ENST00000380152		2672	ata/atAa	18/27	1	2	FACETS	0.836	0.768	0.907	0.836	0.768	0.907	CLONAL	1	TRUE	1	0.52	2		336	736	SUCCESS
APC	324	MSKCC	GRCh37	5	112175273	112175273	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123121	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	124	312	0	ENST00000257430.4:c.3982C>T	p.Gln1328Ter	p.Q1328*	ENST00000257430	NM_000038.5	1328	Cag/Tag	16/16	1	2	FACETS	0.921	0.837	1	0.921	0.837	1	CLONAL	1	TRUE	1	0.52	2		312	518	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715979	52715979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205227	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	354	727	0	ENST00000322088.6:c.544C>T	p.Arg182Trp	p.R182W	ENST00000322088	NM_014225.5	182	Cgg/Tgg	5/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.52	2		727	1282	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139794922	139794922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs551577118	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	299	667	0	ENST00000247668.2:c.316G>A	p.Val106Ile	p.V106I	ENST00000247668	NM_021138.3	106	Gtc/Atc	4/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.52	2		667	1147	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	159	752	0	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	1	2	FACETS	0.522	0.477	0.569	0.522	0.477	0.569	SUBCLONAL	1	TRUE	1	0.52	2		752	1172	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911072	29911072	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1393	454	1367	1	ENST00000376809.5:c.371G>A	p.Gly124Asp	p.G124D	ENST00000376809	NM_002116.7	124	gGc/gAc	3/8	1	2	FACETS	0.945	0.9	0.992	0.945	0.9	0.992	CLONAL	1	TRUE	1	0.52	2		1368	1847	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884218	37884218	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	166	777	0	ENST00000269571.5:c.3694del	p.Ala1232LeufsTer70	p.A1232Lfs*70	ENST00000269571		1230	cGg/cg	27/27	1	2	FACETS	0.483	0.442	0.525	0.483	0.442	0.525	SUBCLONAL	1	TRUE	1	0.52	2		777	1323	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	148	623	2	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.555	0.506	0.606	0.555	0.506	0.606	SUBCLONAL	1	TRUE	1	0.52	2		625	1026	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029445	16029446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	203	465	5	ENST00000268712.3:c.1584dup	p.Glu529ArgfsTer7	p.E529Rfs*7	ENST00000268712	NM_006311.3	528	-/A	15/46	1	2	FACETS	0.859	0.797	0.923	0.859	0.797	0.923	CLONAL	1	TRUE	1	0.52	2		470	909	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120031	70120031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	22	53	0	ENST00000245479.2:c.1037del	p.Pro346ArgfsTer37	p.P346Rfs*37	ENST00000245479	NM_000346.3	345	Ccc/cc	3/3	1	2	FACETS	0.91	0.72	1	0.91	0.72	1	CLONAL	1	TRUE	1	0.52	2		53	93	SUCCESS
APC	324	MSKCC	GRCh37	5	112178033	112178033	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs773874693	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	185	427	0	ENST00000257430.4:c.6747del	p.Gly2250AlafsTer29	p.G2250Afs*29	ENST00000257430	NM_000038.5	2248	Aaa/aa	16/16	1	2	FACETS	0.92	0.852	0.992	0.92	0.852	0.992	CLONAL	1	TRUE	1	0.52	2		427	773	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435312	56435312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139405076	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	399	853	1	ENST00000407977.2:c.1825C>T	p.Arg609Trp	p.R609W	ENST00000407977		609	Cgg/Tgg	9/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.52	2		854	1392	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622211	117622211	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs760646608	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	212	349	0	ENST00000368508.3:c.6659A>T	p.Asn2220Ile	p.N2220I	ENST00000368508	NM_002944.2	2220	aAt/aTt	42/43	0.3	1	FACETS	0.814	0.759	0.871	0.814	0.759	0.871	INDETERMINATE	1	TRUE	0	0.52	1		349	741	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224141	53224141	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	380	811	2	ENST00000375401.3:c.3410C>T	p.Ala1137Val	p.A1137V	ENST00000375401	NM_004187.3	1137	gCg/gTg	22/26	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.52	2		813	1398	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459858	149459858	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566891025	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	364	932	2	ENST00000286301.3:c.349G>A	p.Val117Met	p.V117M	ENST00000286301	NM_005211.3	117	Gtg/Atg	4/22	1	2	FACETS	0.926	0.876	0.977	0.926	0.876	0.977	CLONAL	1	TRUE	1	0.52	2		934	1512	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855024	76855024	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	237	480	0	ENST00000373344.5:c.5812A>G	p.Lys1938Glu	p.K1938E	ENST00000373344	NM_000489.3	1938	Aaa/Gaa	25/35	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.52	2		480	813	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16021243	16021243	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	153	295	1	ENST00000268712.3:c.2014C>T	p.Arg672Ter	p.R672*	ENST00000268712	NM_006311.3	672	Cga/Tga	18/46	1	2	FACETS	0.912	0.837	0.99	0.912	0.837	0.99	CLONAL	1	TRUE	1	0.52	2		296	645	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368388	225368388	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1366667901	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	169	308	0	ENST00000264414.4:c.1358del	p.Asn453ThrfsTer2	p.N453Tfs*2	ENST00000264414	NM_003590.4	453	aAc/ac	9/16	0.3	2	FACETS	0.95	0.876	1			1	INDETERMINATE	1	TRUE	NA	0.52	2		308	684	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521848	157521848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747088591	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	224	539	1	ENST00000346085.5:c.4120C>T	p.Arg1374Cys	p.R1374C	ENST00000346085	NM_020732.3	1374	Cgc/Tgc	18/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.52	2		540	817	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508563	106508563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757016725	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	81	480	0	ENST00000359195.3:c.557C>T	p.Ala186Val	p.A186V	ENST00000359195	NM_002649.2	186	gCg/gTg	2/11	1	2	FACETS	0.393	0.345	0.444	0.393	0.345	0.444	SUBCLONAL	1	TRUE	1	0.52	2		480	793	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534484	187534484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748020206	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	197	351	1	ENST00000441802.2:c.9242C>T	p.Thr3081Met	p.T3081M	ENST00000441802	NM_005245.3	3081	aCg/aTg	13/27	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.52	2		352	669	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495715	56495715	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	241	505	1	ENST00000267101.3:c.3910del	p.His1304MetfsTer7	p.H1304Mfs*7	ENST00000267101	NM_001982.3	1302	gCc/gc	28/28	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.52	2		506	897	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678547	88678547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	98	525	1	ENST00000360948.2:c.989del	p.Pro330HisfsTer84	p.P330Hfs*84	ENST00000360948	NM_001012338.2	330	cCa/ca	9/19	1	2	FACETS	0.442	0.394	0.493	0.442	0.394	0.493	SUBCLONAL	1	TRUE	1	0.52	2		526	853	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433689	49433689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760968358	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	471	1074	0	ENST00000301067.7:c.7864G>A	p.Asp2622Asn	p.D2622N	ENST00000301067	NM_003482.3	2622	Gac/Aac	31/54	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.52	2		1074	1701	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128676	64128676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	364	775	1	ENST00000334205.4:c.533C>T	p.Thr178Met	p.T178M	ENST00000334205	NM_003942.2	178	aCg/aTg	5/17	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.52	2		776	1397	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434958	49434959	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1555192751	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	279	827	0	ENST00000301067.7:c.6594dup	p.Tyr2199LeufsTer3	p.Y2199Lfs*3	ENST00000301067	NM_003482.3	2198	-/C	31/54	1	2	FACETS	0.807	0.757	0.859	0.807	0.757	0.859	CLONAL	1	TRUE	1	0.52	2		827	1330	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468119	31468119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767966111	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	241	580	0	ENST00000344624.3:c.2293G>A	p.Asp765Asn	p.D765N	ENST00000344624		765	Gat/Aat	15/33	1	2	FACETS	0.947	0.885	1	0.947	0.885	1	CLONAL	1	TRUE	1	0.52	2		580	979	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270595	98270595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217844666	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	17	44	0	ENST00000331920.6:c.49G>A	p.Gly17Ser	p.G17S	ENST00000331920	NM_000264.3	17	Ggc/Agc	1/24	1	2	FACETS	0.536	0.404	0.689	0.536	0.404	0.689	SUBCLONAL	1	TRUE	1	0.52	2		44	122	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586144	29586144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555618691	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	121	446	1	ENST00000356175.3:c.4364G>A	p.Arg1455His	p.R1455H	ENST00000356175	NM_000267.3	1455	cGc/cAc	32/57	1	2	FACETS	0.581	0.525	0.64	0.581	0.525	0.64	SUBCLONAL	1	TRUE	1	0.52	2		447	801	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106074	27106074	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	126	547	0	ENST00000324856.7:c.5688del	p.Pro1898HisfsTer25	p.P1898Hfs*25	ENST00000324856	NM_006015.4	1895	gaG/ga	20/20	1	2	FACETS	0.451	0.408	0.497	0.451	0.408	0.497	SUBCLONAL	1	TRUE	1	0.52	2		547	1074	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639649	47639649	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63749832	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	239	448	0	ENST00000233146.2:c.746del	p.Lys249ArgfsTer5	p.K249Rfs*5	ENST00000233146	NM_000251.2	248	Aaa/aa	4/16	1	2	FACETS	0.936	0.875	1	0.936	0.875	1	CLONAL	1	TRUE	1	0.52	2		448	982	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302992	15302992	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755685473	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	404	1027	1	ENST00000263388.2:c.458G>A	p.Arg153His	p.R153H	ENST00000263388	NM_000435.2	153	cGc/cAc	4/33	1	2	FACETS	0.984	0.934	1	0.984	0.934	1	CLONAL	1	TRUE	1	0.52	2		1028	1579	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136258	2136258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45437192	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	388	884	1	ENST00000219476.3:c.4727C>T	p.Thr1576Met	p.T1576M	ENST00000219476	NM_000548.3	1576	aCg/aTg	37/42	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.52	2		885	1392	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278406	39278406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775052125	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	222	478	0	ENST00000402219.2:c.743G>A	p.Arg248His	p.R248H	ENST00000402219	NM_005633.3	248	cGc/cAc	6/23	1	2	FACETS	0.871	0.811	0.933	0.871	0.811	0.933	CLONAL	1	TRUE	1	0.52	2		478	980	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639789	3639789	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373107728	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	392	988	1	ENST00000294008.3:c.3850G>A	p.Val1284Met	p.V1284M	ENST00000294008	NM_032444.2	1284	Gtg/Atg	12/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.52	2		989	1494	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324542	31324543	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1347	310	1072	0	ENST00000412585.2:c.265_266del	p.Gln89AspfsTer9	p.Q89Dfs*9	ENST00000412585	NM_005514.6	89	CAg/g	2/8	1	2	FACETS	0.72	0.676	0.764	0.72	0.676	0.764	SUBCLONAL	1	TRUE	1	0.52	2		1072	1657	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932797	49932797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	347	766	0	ENST00000296474.3:c.3074C>T	p.Ala1025Val	p.A1025V	ENST00000296474	NM_002447.2	1025	gCc/gTc	14/20	1	2	FACETS	0.944	0.892	0.997	0.944	0.892	0.997	CLONAL	1	TRUE	1	0.52	2		766	1414	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138583	2138583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778484981	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	354	637	1	ENST00000219476.3:c.5396C>T	p.Ser1799Leu	p.S1799L	ENST00000219476	NM_000548.3	1799	tCg/tTg	42/42	1	2	FACETS	0.96	0.908	1	0.96	0.908	1	CLONAL	1	TRUE	1	0.52	2		638	1419	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112461	115112461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777764537	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	302	740	2	ENST00000257566.3:c.1279C>T	p.Arg427Trp	p.R427W	ENST00000257566	NM_016569.3	427	Cgg/Tgg	7/8	1	2	FACETS	0.961	0.905	1	0.961	0.905	1	CLONAL	1	TRUE	1	0.52	2		742	1209	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112272	115112272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544562535	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	107	126	0	ENST00000257566.3:c.1468G>A	p.Ala490Thr	p.A490T	ENST00000257566	NM_016569.3	490	Gcc/Acc	7/8	1	2	FACETS	0.813	0.743	0.885	1	0.987	1	CLONAL	2	TRUE	1	0.52	2		126	253	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936678	49936678	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	132	698	1	ENST00000296474.3:c.1249A>G	p.Ser417Gly	p.S417G	ENST00000296474	NM_002447.2	417	Agc/Ggc	2/20	1	2	FACETS	0.393	0.355	0.433	0.393	0.355	0.433	SUBCLONAL	1	TRUE	1	0.52	2		699	1292	SUCCESS
ATR	545	MSKCC	GRCh37	3	142180907	142180907	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751772547	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	72	306	0	ENST00000350721.4:c.7067G>A	p.Arg2356His	p.R2356H	ENST00000350721	NM_001184.3	2356	cGt/cAt	42/47	1	2	FACETS	0.455	0.398	0.518	0.455	0.398	0.518	SUBCLONAL	1	TRUE	1	0.52	2		306	608	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517952	187517952	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	178	539	0	ENST00000441802.2:c.12742del	p.Gln4248ArgfsTer101	p.Q4248Rfs*101	ENST00000441802	NM_005245.3	4248	Cag/ag	25/27	1	2	FACETS	0.658	0.605	0.712	0.658	0.605	0.712	SUBCLONAL	1	TRUE	1	0.52	2		539	1041	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360684	70360684	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	60	230	0	ENST00000374080.3:c.6244C>T	p.Gln2082Ter	p.Q2082*	ENST00000374080		2082	Cag/Tag	42/45	1	2	FACETS	0.599	0.518	0.687	0.599	0.518	0.687	SUBCLONAL	1	TRUE	1	0.52	2		230	385	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305309	65305309	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	136	578	0	ENST00000342505.4:c.2819A>G	p.Tyr940Cys	p.Y940C	ENST00000342505	NM_002227.2	940	tAc/tGc	20/25	1	2	FACETS	0.481	0.436	0.528	0.481	0.436	0.528	SUBCLONAL	1	TRUE	1	0.52	2		578	1087	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699538	117699538	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	154	314	0	ENST00000369458.3:c.103C>G	p.His35Asp	p.H35D	ENST00000369458	NM_024626.3	35	Cac/Gac	3/6	1	2	FACETS	0.955	0.878	1	0.955	0.878	1	CLONAL	1	TRUE	1	0.52	2		314	620	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226566922	226566922	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	62	636	0	ENST00000366794.5:c.1666A>G	p.Thr556Ala	p.T556A	ENST00000366794	NM_001618.3	556	Acc/Gcc	12/23	1	2	FACETS	0.201	0.172	0.232	0.201	0.172	0.232	SUBCLONAL	1	TRUE	1	0.52	2		636	1187	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911540	114911540	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	189	350	0	ENST00000543371.1:c.1058C>A	p.Pro353His	p.P353H	ENST00000543371	NM_001198531.1	353	cCt/cAt	10/14	1	2	FACETS	0.986	0.914	1	0.986	0.914	1	CLONAL	1	TRUE	1	0.52	2		350	737	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962548	100962548	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	121	501	0	ENST00000325455.5:c.1849A>C	p.Lys617Gln	p.K617Q	ENST00000325455	NM_001202474.3	617	Aaa/Caa	3/8	1	2	FACETS	0.501	0.452	0.553	0.501	0.452	0.553	SUBCLONAL	1	TRUE	1	0.52	2		501	929	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999065	100999065	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	125	775	0	ENST00000325455.5:c.737G>T	p.Gly246Val	p.G246V	ENST00000325455	NM_001202474.3	246	gGc/gTc	1/8	1	2	FACETS	0.461	0.416	0.508	0.461	0.416	0.508	SUBCLONAL	1	TRUE	1	0.52	2		775	1044	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377063	118377063	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	104	446	0	ENST00000534358.1:c.10456T>C	p.Phe3486Leu	p.F3486L	ENST00000534358	NM_005933.3	3486	Ttt/Ctt	27/36	1	2	FACETS	0.499	0.446	0.555	0.499	0.446	0.555	SUBCLONAL	1	TRUE	1	0.52	2		446	802	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28903856	28903856	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1490896111	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	227	612	0	ENST00000282397.4:c.2603C>T	p.Thr868Met	p.T868M	ENST00000282397	NM_002019.4	868	aCg/aTg	19/30	1	2	FACETS	0.824	0.767	0.882	0.824	0.767	0.882	CLONAL	1	TRUE	1	0.52	2		612	1060	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571517	95571517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	128	489	1	ENST00000393063.1:c.3160C>T	p.Leu1054Phe	p.L1054F	ENST00000393063	NM_030621.3	1054	Ctc/Ttc	21/28	1	2	FACETS	0.547	0.495	0.602	0.547	0.495	0.602	SUBCLONAL	1	TRUE	1	0.52	2		490	900	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457258	67457258	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1251	197	873	0	ENST00000327367.4:c.232T>C	p.Ser78Pro	p.S78P	ENST00000327367	NM_005902.3	78	Tcc/Ccc	2/9	1	2	FACETS	0.523	0.483	0.565	0.523	0.483	0.565	SUBCLONAL	1	TRUE	1	0.52	2		873	1448	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90633737	90633737	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	328	669	0	ENST00000330062.3:c.347T>C	p.Ile116Thr	p.I116T	ENST00000330062	NM_002168.2	116	aTc/aCc	3/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.52	2		669	1217	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640455	3640455	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569194362	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	448	1031	1	ENST00000294008.3:c.3184C>T	p.Arg1062Cys	p.R1062C	ENST00000294008	NM_032444.2	1062	Cgt/Tgt	12/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.52	2		1032	1576	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67646016	67646016	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	209	473	0	ENST00000264010.4:c.944C>T	p.Thr315Ile	p.T315I	ENST00000264010	NM_006565.3	315	aCa/aTa	4/12	1	2	FACETS	0.925	0.86	0.992	0.925	0.86	0.992	CLONAL	1	TRUE	1	0.52	2		473	869	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771347	68771348	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs587782476	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	139	353	0	ENST00000261769.5:c.44_46dup	p.Leu15dup	p.L15dup	ENST00000261769	NM_004360.3	15	gcg/gcGCTg	1/16	1	2	FACETS	0.703	0.64	0.768	0.703	0.64	0.768	SUBCLONAL	1	TRUE	1	0.52	2		353	761	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579365	7579365	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782461	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	379	867	0	ENST00000269305.4:c.322G>T	p.Gly108Cys	p.G108C	ENST00000269305	NM_001126112.2	108	Ggt/Tgt	4/11	1	2	FACETS	0.995	0.943	1	0.995	0.943	1	CLONAL	1	TRUE	1	0.52	2		867	1465	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912775	50912775	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	385	932	0	ENST00000440232.2:c.2007-1G>T		p.X669_splice	ENST00000440232	NM_002691.3	669			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.52	2		932	1458	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471036	25471036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1215	198	877	0	ENST00000264709.3:c.725C>T	p.Ala242Val	p.A242V	ENST00000264709	NM_175629.2	242	gCc/gTc	7/23	1	2	FACETS	0.539	0.498	0.582	0.539	0.498	0.582	SUBCLONAL	1	TRUE	1	0.52	2		877	1413	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033674	48033675	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	222	244	0	ENST00000234420.5:c.3889dup	p.Ser1297LysfsTer5	p.S1297Kfs*5	ENST00000234420	NM_000179.2	1295	-/A	9/10	1	2	FACETS	0.995	0.94	1	1	0.995	1	CLONAL	2	TRUE	1	0.52	2		244	429	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99154343	99154343	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762110602	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	241	535	0	ENST00000074304.5:c.485G>A	p.Arg162His	p.R162H	ENST00000074304	NM_001134224.1	162	cGt/cAt	8/26	1	2	FACETS	0.94	0.879	1	0.94	0.879	1	CLONAL	1	TRUE	1	0.52	2		535	986	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634653	158634653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	158	386	0	ENST00000263640.3:c.533G>A	p.Ser178Asn	p.S178N	ENST00000263640	NM_001105.4	178	aGc/aAc	5/11	1	2	FACETS	0.9	0.827	0.976	0.9	0.827	0.976	CLONAL	1	TRUE	1	0.52	2		386	675	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378243	225378244	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	127	272	0	ENST00000264414.4:c.651dup	p.Gln218SerfsTer12	p.Q218Sfs*12	ENST00000264414	NM_003590.4	217	-/T	5/16	0.3	2	FACETS	0.869	0.791	0.951			1	INDETERMINATE	1	TRUE	NA	0.52	2		272	562	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309859	30309859	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	345	666	0	ENST00000307677.4:c.163C>A	p.Pro55Thr	p.P55T	ENST00000307677	NM_138578.1	55	Cca/Aca	2/3	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.52	2		666	1302	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42851136	42851136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	194	411	0	ENST00000398585.3:c.757G>A	p.Ala253Thr	p.A253T	ENST00000398585	NM_001135099.1	253	Gcc/Acc	7/14	1	2	FACETS	0.893	0.827	0.96	0.893	0.827	0.96	CLONAL	1	TRUE	1	0.52	2		411	836	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513302	41513302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370355846	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	244	522	1	ENST00000263253.7:c.206G>A	p.Gly69Asp	p.G69D	ENST00000263253	NM_001429.3	69	gGc/gAc	2/31	1	2	FACETS	0.983	0.919	1	0.983	0.919	1	CLONAL	1	TRUE	1	0.52	2		523	955	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390956	89390956	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	169	429	0	ENST00000336596.2:c.1022T>C	p.Val341Ala	p.V341A	ENST00000336596	NM_005233.5	341	gTt/gCt	5/17	0.117973165673563	1	FACETS	0.689	0.635	0.745	0.689	0.635	0.745	INDETERMINATE	1	TRUE	0	0.52	1		429	698	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80057491	80057492	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	111	263	0	ENST00000265081.6:c.1896dup	p.Cys633MetfsTer28	p.C633Mfs*28	ENST00000265081	NM_002439.4	630	-/A	13/24	1	2	FACETS	0.893	0.807	0.983	0.893	0.807	0.983	CLONAL	1	TRUE	1	0.52	2		263	478	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953890	131953890	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs864622571	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	204	336	0	ENST00000265335.6:c.3293G>A	p.Arg1098Gln	p.R1098Q	ENST00000265335		1098	cGg/cAg	21/25	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.52	2		336	773	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839896	27839907	+	inframe_deletion	In_Frame_Del	DEL	TAGCTTCCGGAT	TAGCTTCCGGAT	-	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	136	796	0	ENST00000328488.2:c.187_198del	p.Ile63_Leu66del	p.I63_L66del	ENST00000328488	NM_003533.2	63	ATCCGGAAGCTA/-	1/1	1	2	FACETS	0.411	0.373	0.452	0.411	0.373	0.452	SUBCLONAL	1	TRUE	1	0.52	2		796	1272	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324601	31324604	+	frameshift_variant	Frame_Shift_Del	DEL	CTCT	CTCT	-	rs766427608	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	426	987	0	ENST00000412585.2:c.204_207del	p.Glu69SerfsTer7	p.E69Sfs*7	ENST00000412585	NM_005514.6	68	agAGAG/ag	2/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.52	2		987	1592	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849832	151849832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201883770	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	164	395	0	ENST00000262189.6:c.12484C>T	p.Arg4162Trp	p.R4162W	ENST00000262189	NM_170606.2	4162	Cgg/Tgg	49/59	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.52	2		395	615	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27168568	27168568	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	120	489	0	ENST00000380036.4:c.440T>C	p.Leu147Ser	p.L147S	ENST00000380036	NM_000459.3	147	tTg/tCg	3/23	1	2	FACETS	0.476	0.429	0.526	0.476	0.429	0.526	SUBCLONAL	1	TRUE	1	0.52	2		489	970	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128230293	128230293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772438885	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	336	651	0	ENST00000265960.3:c.1303G>A	p.Asp435Asn	p.D435N	ENST00000265960	NM_001006617.1	435	Gac/Aac	10/12	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.52	2		651	1292	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391220	139391220	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1442	241	1095	0	ENST00000277541.6:c.6971A>G	p.Asn2324Ser	p.N2324S	ENST00000277541	NM_017617.3	2324	aAc/aGc	34/34	1	2	FACETS	0.551	0.512	0.591	0.551	0.512	0.591	SUBCLONAL	1	TRUE	1	0.52	2		1095	1683	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15840950	15840950	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	103	453	0	ENST00000307771.7:c.1034A>T	p.Asp345Val	p.D345V	ENST00000307771	NM_005089.3	345	gAc/gTc	11/11	1	2	FACETS	0.505	0.451	0.561	0.505	0.451	0.561	SUBCLONAL	1	TRUE	1	0.52	2		453	785	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76764094	76764094	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	112	441	0	ENST00000373344.5:c.7214T>C	p.Val2405Ala	p.V2405A	ENST00000373344	NM_000489.3	2405	gTt/gCt	35/35	1	2	FACETS	0.55	0.495	0.609	0.55	0.495	0.609	SUBCLONAL	1	TRUE	1	0.52	2		441	783	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202927	16202927	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	290	477	1	ENST00000375759.3:c.635C>A	p.Pro212His	p.P212H	ENST00000375759	NM_015001.2	212	cCc/cAc	3/15	1	2	FACETS	0.954	0.905	1	0.954	0.905	1	CLONAL	1	TRUE	1	0.932049620384383	2		478	652	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057661	27057661	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	292	553	1	ENST00000324856.7:c.1369C>T	p.Gln457Ter	p.Q457*	ENST00000324856	NM_006015.4	457	Caa/Taa	3/20	1	2	FACETS	0.932	0.884	0.981	0.932	0.884	0.981	CLONAL	1	TRUE	1	0.932049620384383	2		554	672	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092980	27092980	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	215	369	0	ENST00000324856.7:c.2914del	p.Asp972MetfsTer2	p.D972Mfs*2	ENST00000324856	NM_006015.4	971	Ggg/gg	10/20	1	2	FACETS	0.955	0.898	1	0.955	0.898	1	CLONAL	1	TRUE	1	0.932049620384383	2		369	483	SUCCESS
RET	5979	MSKCC	GRCh37	10	43602002	43602002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754859905	NA	P-0057462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	384	787	0	ENST00000355710.3:c.1046C>T	p.Ala349Val	p.A349V	ENST00000355710	NM_020975.4	349	gCg/gTg	5/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.932049620384383	2		787	781	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685300	89685300	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs878853936	NA	P-0057462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	205	277	0	ENST00000371953.3:c.195C>A	p.Tyr65Ter	p.Y65*	ENST00000371953	NM_000314.4	65	taC/taA	3/9	1	2	FACETS	0.916	0.859	0.974	0.916	0.859	0.974	CLONAL	1	TRUE	1	0.932049620384383	2		277	480	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717756	89717756	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730882131	NA	P-0057462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	206	319	0	ENST00000371953.3:c.781C>T	p.Gln261Ter	p.Q261*	ENST00000371953	NM_000314.4	261	Cag/Tag	7/9	1	2	FACETS	0.886	0.83	0.942	0.886	0.83	0.942	CLONAL	1	TRUE	1	0.932049620384383	2		319	499	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77060319	77060319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	196	277	1	ENST00000356341.3:c.850G>A	p.Val284Met	p.V284M	ENST00000356341	NM_002576.4	284	Gtg/Atg	9/15	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.932049620384383	2		278	418	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416952	416953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs771545848	NA	P-0057462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	235	517	9	ENST00000399788.2:c.3597dup	p.Gly1200ArgfsTer7	p.G1200Rfs*7	ENST00000399788	NM_001042603.1	1199	-/A	23/28	1	2	FACETS	0.823	0.773	0.873	0.823	0.773	0.873	CLONAL	1	TRUE	1	0.932049620384383	2		526	613	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0057462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	328	651	1	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.916	0.871	0.962	0.916	0.871	0.962	CLONAL	1	TRUE	1	0.932049620384383	2		652	768	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446069	49446069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs952760497	NA	P-0057462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	148	1015	1	ENST00000301067.7:c.1397G>A	p.Arg466His	p.R466H	ENST00000301067	NM_003482.3	466	cGc/cAc	10/54	1	2	FACETS	0.29	0.264	0.317	0.29	0.264	0.317	SUBCLONAL	1	TRUE	1	0.932049620384383	2		1016	1095	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437757	110437757	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	377	685	0	ENST00000375856.3:c.644G>T	p.Gly215Val	p.G215V	ENST00000375856	NM_003749.2	215	gGg/gTg	1/2	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.932049620384383	2		685	757	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560476	95560476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	327	520	1	ENST00000393063.1:c.5113G>A	p.Glu1705Lys	p.E1705K	ENST00000393063	NM_030621.3	1705	Gaa/Aaa	25/28	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.932049620384383	2		521	649	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562572	95562572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	204	408	0	ENST00000393063.1:c.4685G>A	p.Cys1562Tyr	p.C1562Y	ENST00000393063	NM_030621.3	1562	tGt/tAt	24/28	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.932049620384383	2		408	420	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572556	95572556	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1354833117	NA	P-0057462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	134	215	0	ENST00000393063.1:c.2809C>T	p.Arg937Cys	p.R937C	ENST00000393063	NM_030621.3	937	Cgc/Tgc	19/28	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.932049620384383	2		215	281	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105238745	105238745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143266084	NA	P-0057462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	411	803	1	ENST00000349310.3:c.1217G>A	p.Arg406His	p.R406H	ENST00000349310	NM_001014432.1	406	cGc/cAc	13/15	1	2	FACETS	0.928	0.887	0.97	0.928	0.887	0.97	CLONAL	1	TRUE	1	0.932049620384383	2		804	950	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43700287	43700287	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0057462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	343	595	0	ENST00000382044.4:c.5601-1G>A		p.X1867_splice	ENST00000382044	NM_001141980.1	1867			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.932049620384383	2		595	726	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029251	14029251	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	157	314	0	ENST00000311895.7:c.1467del	p.Lys489AsnfsTer4	p.K489Nfs*4	ENST00000311895	NM_005236.2	488	Aaa/aa	8/11	1	2	FACETS	0.88	0.816	0.944	0.88	0.816	0.944	CLONAL	1	TRUE	1	0.932049620384383	2		314	383	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671655	67671655	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1400980130	NA	P-0057462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	298	501	1	ENST00000264010.4:c.2070del	p.Glu691SerfsTer30	p.E691Sfs*30	ENST00000264010	NM_006565.3	688	gtA/gt	12/12	1	2	FACETS	0.973	0.924	1	0.973	0.924	1	CLONAL	1	TRUE	1	0.932049620384383	2		502	657	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357201	89357201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	381	690	0	ENST00000301030.4:c.433G>A	p.Val145Met	p.V145M	ENST00000301030	NM_001256183.1	145	Gtg/Atg	6/13	1	2	FACETS	0.923	0.88	0.965	0.923	0.88	0.965	CLONAL	1	TRUE	1	0.932049620384383	2		690	886	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687472	37687472	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	260	454	1	ENST00000447079.4:c.4382del	p.Gly1461AlafsTer38	p.G1461Afs*38	ENST00000447079	NM_015083.1	1459	tGg/tg	14/14	1	2	FACETS	0.991	0.938	1	0.991	0.938	1	CLONAL	1	TRUE	1	0.932049620384383	2		455	563	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362446	40362447	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1202978138	NA	P-0057462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	88	537	1	ENST00000293328.3:c.1749dup	p.His584ThrfsTer8	p.H584Tfs*8	ENST00000293328	NM_012448.3	583	-/A	14/19	1	2	FACETS	0.215	0.189	0.242	0.215	0.189	0.242	SUBCLONAL	1	TRUE	1	0.932049620384383	2		538	880	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0057462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	217	350	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.974	0.916	1	0.974	0.916	1	CLONAL	1	TRUE	1	0.932049620384383	2		350	478	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225628	225628	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	252	483	0	ENST00000264932.6:c.407A>C	p.Gln136Pro	p.Q136P	ENST00000264932	NM_004168.2	136	cAg/cCg	4/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.932049620384383	2		483	529	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589223	67589225	+	inframe_deletion	In_Frame_Del	DEL	TAA	TAA	-	novel	NA	P-0057462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	191	369	0	ENST00000274335.5:c.1214_1216del	p.Ile405del	p.I405del	ENST00000274335		404	tTAAta/tta	9/15	1	2	FACETS	0.833	0.778	0.889	0.833	0.778	0.889	CLONAL	1	TRUE	1	0.932049620384383	2		369	492	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515369	149515369	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	84	661	0	ENST00000261799.4:c.113del	p.Pro38ArgfsTer15	p.P38Rfs*15	ENST00000261799	NM_002609.3	38	cCg/cg	3/23	1	2	FACETS	0.207	0.182	0.233	0.207	0.182	0.233	SUBCLONAL	1	TRUE	1	0.932049620384383	2		661	872	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32191659	32191664	+	inframe_deletion	In_Frame_Del	DEL	AGCAGC	AGCAGC	-	rs35795312	NA	P-0057462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	199	713	13	ENST00000375023.3:c.42_47del	p.Leu15_Leu16del	p.L15_L16del	ENST00000375023	NM_004557.3	14	ctGCTGCTa/cta	1/30	1	2	FACETS	0.563	0.523	0.605	0.563	0.523	0.605	SUBCLONAL	1	TRUE	1	0.932049620384383	2		726	758	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100259	157100260	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1554248082	NA	P-0057462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	61	135	2	ENST00000346085.5:c.1202dup	p.Phe402LeufsTer133	p.F402Lfs*133	ENST00000346085	NM_020732.3	399	gcg/gcGg	1/20	1	2	FACETS	0.77	0.678	0.865	0.77	0.678	0.865	SUBCLONAL	1	TRUE	1	0.932049620384383	2		137	170	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946306	2946306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573740263	NA	P-0057462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	417	887	2	ENST00000396946.4:c.3431G>A	p.Arg1144His	p.R1144H	ENST00000396946	NM_032415.4	1144	cGc/cAc	25/25	1	2	FACETS	0.965	0.924	1	0.965	0.924	1	CLONAL	1	TRUE	1	0.932049620384383	2		889	927	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137320979	137320981	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0057462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	270	919	0	ENST00000481739.1:c.938_940del	p.Phe313del	p.F313del	ENST00000481739	NM_002957.4	312	tcCTTc/tcc	7/10	1	2	FACETS	0.818	0.772	0.865	0.818	0.772	0.865	CLONAL	1	TRUE	1	0.932049620384383	2		919	708	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928875	44928876	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0057462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	232	434	0	ENST00000377967.4:c.1982_1983dup	p.Ser662LeufsTer30	p.S662Lfs*30	ENST00000377967	NM_021140.2	659	cct/cCTct	17/29	1	2	FACETS	0.864	0.813	0.917	0.864	0.813	0.917	CLONAL	1	TRUE	1	0.932049620384383	2		434	576	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426635	47426635	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	285	663	0	ENST00000377045.4:c.880C>A	p.Leu294Met	p.L294M	ENST00000377045	NM_001654.4	294	Ctg/Atg	10/16	1	2	FACETS	0.886	0.839	0.934	0.886	0.839	0.934	CLONAL	1	TRUE	1	0.932049620384383	2		663	690	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0057463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	154	227	1				ENST00000310581	NM_198253.2	-/1132			0.3	3	FACETS	1	0.97	1	0.737	0.679	0.797	CLONAL	2	TRUE	0	0.32	3		228	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0057463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	401	673	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.3	3	FACETS	1	0.992	1	0.8	0.761	0.839	CLONAL	2	TRUE	0	0.32	3		673	1212	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161689	56161689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1490957244	NA	P-0057463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	174	547	3	ENST00000399503.3:c.1186C>T	p.Arg396Cys	p.R396C	ENST00000399503	NM_005921.1	396	Cgt/Tgt	6/20	0.265995852770775	2	FACETS	0.819	0.757	0.883	0.819	0.757	0.883	CLONAL	2	TRUE	0	0.32	2		550	664	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042185	42042185	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0057463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	129	595	0	ENST00000219905.7:c.6380C>G	p.Ser2127Ter	p.S2127*	ENST00000219905	NM_001164273.1	2127	tCa/tGa	17/24	0.18865758181345	2	FACETS	1	0.975	1	0.605	0.55	0.663	INDETERMINATE	1	TRUE	0	0.32	2		595	666	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585371	29585371	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555618494	NA	P-0057463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	152	592	0	ENST00000356175.3:c.4120C>T	p.Gln1374Ter	p.Q1374*	ENST00000356175	NM_000267.3	1374	Cag/Tag	31/57	0.3	3	FACETS	1	0.925	1	0.67	0.616	0.726	CLONAL	2	TRUE	0	0.32	3		592	548	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525053	157525053	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	156	479	0	ENST00000346085.5:c.4948G>C	p.Glu1650Gln	p.E1650Q	ENST00000346085	NM_020732.3	1650	Gag/Cag	19/20	0.3	3	FACETS	0.952	0.876	1	0.635	0.584	0.687	CLONAL	2	TRUE	0	0.32	3		479	594	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098921	178098921	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs769685782	NA	P-0057463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	173	516	1	ENST00000397062.3:c.124C>T	p.Arg42Ter	p.R42*	ENST00000397062	NM_006164.4	42	Cga/Tga	2/5	0.205500974201505	3	FACETS	1	0.953	1	0.693	0.641	0.747	CLONAL	2	TRUE	0	0.32	3		517	603	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864417	57864417	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	216	888	0	ENST00000228682.2:c.1894A>T	p.Asn632Tyr	p.N632Y	ENST00000228682	NM_005269.2	632	Aat/Tat	12/12	0.200681844005917	2	FACETS	1	0.984	1	0.598	0.555	0.642	CLONAL	1	TRUE	0	0.32	2		888	1129	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500474	99500474	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	182	1039	0	ENST00000268035.6:c.3907G>T	p.Val1303Phe	p.V1303F	ENST00000268035	NM_000875.3	1303	Gtc/Ttc	21/21	0.18865758181345	2	FACETS	1	0.932	1	0.506	0.466	0.548	INDETERMINATE	1	TRUE	0	0.32	2		1039	1123	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354366	354366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	101	1093	0	ENST00000262320.3:c.1192G>A	p.Ala398Thr	p.A398T	ENST00000262320	NM_003502.3	398	Gct/Act	5/11	0.265995852770775	2	FACETS	0.537	0.479	0.6	0.269	0.239	0.3	SUBCLONAL	1	TRUE	0	0.32	2		1093	1175	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995487	68995487	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	105	576	0	ENST00000288368.4:c.1891G>A	p.Glu631Lys	p.E631K	ENST00000288368	NM_024870.2	631	Gaa/Aaa	18/40	0.3	3	FACETS	0.985	0.882	1	0.328	0.294	0.365	CLONAL	1	TRUE	0	0.32	3		576	773	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611825	100611825	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	232	406	0	ENST00000308731.7:c.1296C>G	p.Ile432Met	p.I432M	ENST00000308731	NM_000061.2	432	atC/atG	14/19	0.3	2	FACETS	0.965	0.91	1			1	CLONAL	3	TRUE	NA	0.32	2		406	501	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0057464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	215	410	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.357926090726313	3	FACETS	0.977	0.913	1	0.977	0.913	1	CLONAL	2	TRUE	1	0.404700452388085	3		410	654	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0057464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	171	227	1				ENST00000310581	NM_198253.2	-/1132			0.357926090726313	3	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	1	0.404700452388085	3		228	499	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956771	68956771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774302685	NA	P-0057464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	324	666	0	ENST00000288368.4:c.889C>T	p.Arg297Cys	p.R297C	ENST00000288368	NM_024870.2	297	Cgt/Tgt	8/40	0.357926090726313	3	FACETS	0.834	0.788	0.881	0.834	0.788	0.881	CLONAL	2	TRUE	1	0.404700452388085	3		666	1154	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892164	9892164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776791010	NA	P-0057464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	142	653	0	ENST00000330684.3:c.2326G>A	p.Asp776Asn	p.D776N	ENST00000330684	NM_001134407.1	776	Gac/Aac	11/13	1	2	FACETS	0.971	0.886	1	0.971	0.886	1	CLONAL	1	TRUE	1	0.404700452388085	2		653	723	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832299	72832299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	148	568	1	ENST00000268489.5:c.4282G>A	p.Ala1428Thr	p.A1428T	ENST00000268489	NM_006885.3	1428	Gcc/Acc	9/10	1	2	FACETS	0.996	0.912	1	0.996	0.912	1	CLONAL	1	TRUE	1	0.404700452388085	2		569	734	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156729	106156729	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1440692352	NA	P-0057464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	102	439	0	ENST00000380013.4:c.1630C>T	p.Arg544Ter	p.R544*	ENST00000380013	NM_001127208.2	544	Cga/Tga	3/11	1	2	FACETS	0.846	0.758	0.939	0.846	0.758	0.939	CLONAL	1	TRUE	1	0.404700452388085	2		439	596	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0057464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	104	461	0	ENST00000304494.5:c.151-1G>A		p.X51_splice	ENST00000304494	NM_000077.4	51			0.404700452388085	1	FACETS	0.919	0.828	1	0.919	0.828	1	CLONAL	1	TRUE	0	0.404700452388085	1		461	446	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935517	13935517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	217	462	0	ENST00000405192.2:c.1339C>T	p.Pro447Ser	p.P447S	ENST00000405192	NM_001163147.1	447	Ccc/Tcc	12/12	0.357926090726313	3	FACETS	0.897	0.837	0.958	0.897	0.837	0.958	CLONAL	2	TRUE	1	0.404700452388085	3		462	719	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748379	43748380	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	121	784	1	ENST00000382044.4:c.2426_2427delinsTT	p.Thr809Ile	p.T809I	ENST00000382044	NM_001141980.1	809	aCC/aTT	12/28	1	2	FACETS	0.797	0.721	0.878	0.797	0.721	0.878	SUBCLONAL	1	TRUE	1	0.404700452388085	2		785	750	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732957	74732958	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	108	408	1	ENST00000359995.5:c.285_286delinsTT	p.Pro96Ser	p.P96S	ENST00000359995	NM_001195427.1	95	ccCCcg/ccTTcg	1/3	0.349201655506749	3	FACETS	1	0.942	1	0.534	0.48	0.591	CLONAL	1	TRUE	1	0.404700452388085	3		409	601	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525029	9525029	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	131	491	0	ENST00000353224.5:c.1856C>T	p.Pro619Leu	p.P619L	ENST00000353224	NM_177990.2	619	cCt/cTt	8/10	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.404700452388085	2		491	642	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924990	49924990	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	133	726	0	ENST00000296474.3:c.3953A>T	p.Gln1318Leu	p.Q1318L	ENST00000296474	NM_002447.2	1318	cAa/cTa	20/20	1	2	FACETS	0.816	0.742	0.895	0.816	0.742	0.895	CLONAL	1	TRUE	1	0.404700452388085	2		726	805	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670814	134670814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	104	578	0	ENST00000398015.3:c.725G>A	p.Gly242Glu	p.G242E	ENST00000398015	NM_004441.4	242	gGg/gAg	3/16	1	2	FACETS	0.764	0.684	0.848	0.764	0.684	0.848	SUBCLONAL	1	TRUE	1	0.404700452388085	2		578	673	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461527	138461527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1248409072	NA	P-0057464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	108	510	0	ENST00000289153.2:c.494G>A	p.Gly165Glu	p.G165E	ENST00000289153	NM_006219.2	165	gGa/gAa	3/22	1	2	FACETS	0.819	0.736	0.906	0.819	0.736	0.906	CLONAL	1	TRUE	1	0.404700452388085	2		510	652	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412905	49412905	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519951	NA	P-0057465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	91	521	0	ENST00000418115.1:c.118G>C	p.Glu40Gln	p.E40Q	ENST00000418115	NM_001664.2	40	Gag/Cag	2/5	1	2	FACETS	0.685	0.607	0.769	0.685	0.607	0.769	SUBCLONAL	1	TRUE	1	0.27	2		521	984	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856113	68856113	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782750	NA	P-0057465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	79	354	0	ENST00000261769.5:c.1921C>T	p.Gln641Ter	p.Q641*	ENST00000261769	NM_004360.3	641	Cag/Tag	12/16	0.284590331649968	1	FACETS	0.868	0.765	0.979	0.868	0.765	0.979	CLONAL	1	TRUE	0	0.27	1		354	583	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692811	89692811	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	45	211	0	ENST00000371953.3:c.295G>T	p.Glu99Ter	p.E99*	ENST00000371953	NM_000314.4	99	Gaa/Taa	5/9	0.284590331649968	1	FACETS	0.915	0.773	1	0.915	0.773	1	CLONAL	1	TRUE	0	0.27	1		211	315	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217617	7217617	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	88	361	0	ENST00000380728.2:c.310G>T	p.Glu104Ter	p.E104*	ENST00000380728		104	Gaa/Taa	4/11	NA	2	FACETS	1	0.954	1			1	INDETERMINATE	1	TRUE	NA	0.27	2		361	570	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178257	56178258	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	43	216	0	ENST00000399503.3:c.3236dup	p.Asn1079LysfsTer2	p.N1079Kfs*2	ENST00000399503	NM_005921.1	1077	tca/tcAa	14/20	1	2	FACETS	0.915	0.768	1	0.915	0.768	1	CLONAL	1	TRUE	1	0.27	2		216	348	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106792	27106793	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	123	545	0	ENST00000324856.7:c.6405dup	p.Leu2136SerfsTer14	p.L2136Sfs*14	ENST00000324856	NM_006015.4	2135	att/aTtt	20/20	1	2	FACETS	0.968	0.875	1	0.968	0.875	1	CLONAL	1	TRUE	1	0.27	2		545	941	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370799	225370799	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	67	265	0	ENST00000264414.4:c.1080C>G	p.Phe360Leu	p.F360L	ENST00000264414	NM_003590.4	360	ttC/ttG	8/16	1	2	FACETS	0.985	0.857	1	0.985	0.857	1	CLONAL	1	TRUE	1	0.27	2		265	504	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239462	123239462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	132	598	0	ENST00000358487.5:c.2375C>T	p.Ser792Leu	p.S792L	ENST00000358487	NM_000141.4	792	tCa/tTa	18/18	0.284590331649968	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.27	1		598	810	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112535	115112536	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0057465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	395	995	0	ENST00000257566.3:c.1204dup	p.Glu402GlyfsTer5	p.E402Gfs*5	ENST00000257566	NM_016569.3	402	gag/gGag	7/8	0.276525107996947	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.27	2		995	1365	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714173	43714173	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	211	810	0	ENST00000382044.4:c.3980C>T	p.Ser1327Leu	p.S1327L	ENST00000382044	NM_001141980.1	1327	tCa/tTa	19/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.27	2		810	1370	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098336	47098336	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0057465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	65	291	0	ENST00000409792.3:c.6938C>G	p.Ser2313Ter	p.S2313*	ENST00000409792	NM_014159.6	2313	tCa/tGa	15/21	1	2	FACETS	0.872	0.757	0.997	0.872	0.757	0.997	CLONAL	1	TRUE	1	0.27	2		291	552	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160643	56160656	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGTGTTAACAAA	GCCGTGTTAACAAA	-	novel	NA	P-0057465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	46	259	0	ENST00000399503.3:c.918_931del	p.Arg307AspfsTer14	p.R307Dfs*14	ENST00000399503	NM_005921.1	306	cGCCGTGTTAACAAA/c	4/20	1	2	FACETS	0.821	0.693	0.962	0.821	0.693	0.962	CLONAL	1	TRUE	1	0.27	2		259	415	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873763	151873763	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	106	360	0	ENST00000262189.6:c.8775G>C	p.Glu2925Asp	p.E2925D	ENST00000262189	NM_170606.2	2925	gaG/gaC	38/59	0.277525703462233	3	FACETS	1	0.971	1	0.617	0.553	0.685	CLONAL	1	TRUE	1	0.27	3		360	722	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873912	151873912	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	85	329	0	ENST00000262189.6:c.8626G>C	p.Asp2876His	p.D2876H	ENST00000262189	NM_170606.2	2876	Gat/Cat	38/59	0.277525703462233	3	FACETS	1	0.908	1	0.516	0.456	0.58	CLONAL	1	TRUE	1	0.27	3		329	693	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891097	151891097	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	106	282	0	ENST00000262189.6:c.4657C>T	p.Gln1553Ter	p.Q1553*	ENST00000262189	NM_170606.2	1553	Cag/Tag	31/59	0.277525703462233	3	FACETS	0.841	0.756	0.929	0.841	0.756	0.929	CLONAL	2	TRUE	1	0.27	3		282	530	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141570511	141570512	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0057465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	125	559	0	ENST00000220592.5:c.616_617del	p.Val206ProfsTer12	p.V206Pfs*12	ENST00000220592	NM_012154.3	206	GTc/c	5/19	1	2	FACETS	0.925	0.836	1	0.925	0.836	1	CLONAL	1	TRUE	1	0.27	2		559	1001	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221897	98221897	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	69	355	0	ENST00000331920.6:c.2872G>C	p.Glu958Gln	p.E958Q	ENST00000331920	NM_000264.3	958	Gaa/Caa	17/24	1	2	FACETS	0.778	0.677	0.887	0.778	0.677	0.887	SUBCLONAL	1	TRUE	1	0.27	2		355	657	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0057471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	8	548	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.236728843719874	3	FACETS	0.3	0.192	0.44	0.15	0.096	0.22	SUBCLONAL	1	FALSE	1	0.236703805946998	3		549	252	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873020	136873020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147198552	NA	P-0057471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	12	542	2	ENST00000241393.3:c.478G>A	p.Val160Ile	p.V160I	ENST00000241393	NM_003467.2	160	Gtc/Atc	2/2	0.166178556996971	3	FACETS	0.623	0.438	0.849	0.312	0.219	0.425	SUBCLONAL	1	FALSE	1	0.236703805946998	3		544	182	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844172	68844172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	8	745	1	ENST00000261769.5:c.760G>A	p.Asp254Asn	p.D254N	ENST00000261769	NM_004360.3	254	Gat/Aat	6/16	0.166178556996971	3	FACETS	0.277	0.177	0.406	0.138	0.088	0.203	SUBCLONAL	1	FALSE	1	0.236703805946998	3		746	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579542	7579542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780728	NA	P-0057471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	9	964	0	ENST00000269305.4:c.145G>A	p.Asp49Asn	p.D49N	ENST00000269305	NM_001126112.2	49	Gat/Aat	4/11	1	2	FACETS	0.209	0.137	0.301	0.209	0.137	0.301	SUBCLONAL	1	FALSE	1	0.236703805946998	2		964	364	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412718	139412718	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1431	994	864	1	ENST00000277541.6:c.1126T>C	p.Cys376Arg	p.C376R	ENST00000277541	NM_017617.3	376	Tgc/Cgc	7/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		865	2425	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	324	834	0	ENST00000322088.6:c.767C>A	p.Ser256Tyr	p.S256Y	ENST00000322088	NM_014225.5	256	tCc/tAc	6/15	0.359705188578169	3	FACETS	0.983	0.929	1	0.983	0.929	1	CLONAL	2	TRUE	1	0.359705188578169	3		834	1081	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346897	91346897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777492549	NA	P-0057473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	71	428	0	ENST00000355112.3:c.3505G>A	p.Ala1169Thr	p.A1169T	ENST00000355112	NM_000057.2	1169	Gct/Act	18/22	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.359705188578169	2		428	282	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672240	86672241	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0057473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	205	373	0	ENST00000274376.6:c.2043_2044del	p.Lys682ArgfsTer6	p.K682Rfs*6	ENST00000274376	NM_002890.2	681	cAG/c	16/25	0.216018943723048	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	3	TRUE	0	0.359705188578169	3		373	437	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106087	27106091	+	frameshift_variant	Frame_Shift_Del	DEL	GATGG	GATGG	C	novel	NA	P-0057473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	545	633	0	ENST00000324856.7:c.5698_5702delinsC	p.Asp1900HisfsTer22	p.D1900Hfs*22	ENST00000324856	NM_006015.4	1900	GATGGa/Ca	20/20	0.359705188578169	3	FACETS	0.953	0.927	0.979	1	0.998	1	CLONAL	5	TRUE	0	0.359705188578169	3		633	750	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0057474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	131	748	1	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.3	1	FACETS	0.982	0.894	1	0.982	0.894	1	CLONAL	1	TRUE	0	0.36	1		749	608	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974792	21974792	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs141798398	NA	P-0057474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	109	312	0	ENST00000304494.5:c.35C>A	p.Ser12Ter	p.S12*	ENST00000304494	NM_000077.4	12	tCg/tAg	1/3	0.3	3	FACETS	1	0.954	1	0.72	0.654	0.788	CLONAL	2	TRUE	0	0.36	3		312	331	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136184	11136184	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	151	697	0	ENST00000358026.2:c.3168G>T	p.Glu1056Asp	p.E1056D	ENST00000358026	NM_001128849.1	1056	gaG/gaT	22/36	0.279536726884685	2	FACETS	0.775	0.713	0.84	0.775	0.713	0.84	SUBCLONAL	2	TRUE	0	0.36	2		697	541	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480330	56480330	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	84	557	1	ENST00000267101.3:c.437G>T	p.Gly146Val	p.G146V	ENST00000267101	NM_001982.3	146	gGt/gTt	4/28	0.3	5	FACETS	1	0.952	1	0.382	0.337	0.43	CLONAL	1	TRUE	2	0.36	5		558	627	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953112	81953112	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	60	418	0	ENST00000359376.3:c.2078G>A	p.Cys693Tyr	p.C693Y	ENST00000359376	NM_002661.3	693	tGt/tAt	20/33	1	2	FACETS	0.654	0.564	0.751	0.654	0.564	0.751	SUBCLONAL	1	TRUE	1	0.36	2		418	510	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969809	81969809	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	96	646	0	ENST00000359376.3:c.2878G>T	p.Glu960Ter	p.E960*	ENST00000359376	NM_002661.3	960	Gag/Tag	27/33	1	2	FACETS	0.759	0.676	0.846	0.759	0.676	0.846	SUBCLONAL	1	TRUE	1	0.36	2		646	703	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221254	1221254	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	198	924	0	ENST00000326873.7:c.777del	p.Asn259LysfsTer28	p.N259Kfs*28	ENST00000326873	NM_000455.4	259	aaC/aa	6/10	0.279536726884685	2	FACETS	1	0.99	1	0.712	0.661	0.765	CLONAL	1	TRUE	0	0.36	2		924	772	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2164186	2164186	+	frameshift_variant,start_lost	Frame_Shift_Del	DEL	G	G	-	rs1268868586	NA	P-0057474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	144	456	1	ENST00000398665.3:c.7del	p.Glu3?	p.E3?	ENST00000398665	NM_032482.2	1	atG/at	1/28	0.279536726884685	2	FACETS	0.846	0.777	0.916	0.846	0.777	0.916	CLONAL	2	TRUE	0	0.36	2		457	473	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602462	10602462	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	237	1117	1	ENST00000171111.5:c.1116del	p.Leu373CysfsTer27	p.L373Cfs*27	ENST00000171111	NM_203500.1	372	ggG/gg	3/6	0.279536726884685	2	FACETS	0.885	0.829	0.942	0.885	0.829	0.942	CLONAL	2	TRUE	0	0.36	2		1118	744	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795117	242795117	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	145	1154	1	ENST00000334409.5:c.92C>A	p.Pro31His	p.P31H	ENST00000334409	NM_005018.2	31	cCc/cAc	2/5	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.36	2		1155	762	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058659	47058665	+	frameshift_variant	Frame_Shift_Del	DEL	GTTTTGT	GTTTTGT	-	novel	NA	P-0057474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	136	683	0	ENST00000409792.3:c.7613_7619del	p.His2538ProfsTer24	p.H2538Pfs*24	ENST00000409792	NM_014159.6	2538	cACAAAACc/cc	21/21	0.142517007754482	3	FACETS	1	0.975	1	0.6	0.546	0.656	INDETERMINATE	1	TRUE	1	0.36	3		683	743	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751506	57751506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1240702031	NA	P-0057474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	103	476	0	ENST00000274289.3:c.1485G>T	p.Glu495Asp	p.E495D	ENST00000274289	NM_006622.3	495	gaG/gaT	11/14	0.3	1	FACETS	0.933	0.838	1	0.933	0.838	1	CLONAL	1	TRUE	0	0.36	1		476	503	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339561	81339561	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0057474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	78	438	0	ENST00000222390.5:c.1445-2A>T		p.X482_splice	ENST00000222390	NM_000601.4	482			0.142517007754482	3	FACETS	0.961	0.846	1	0.481	0.423	0.542	INDETERMINATE	1	TRUE	1	0.36	3		438	532	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	779	888	1	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.87752146768757	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.87752146768757	1		889	947	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575023	64575023	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs794728652	NA	P-0057475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	404	455	0	ENST00000312049.6:c.783+1G>A		p.X261_splice	ENST00000312049	NM_130799.2	261			0.87752146768757	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.87752146768757	1		455	497	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0057476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	283	312	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.530326828193267	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.530326828193267	1		312	609	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0057476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	322	668	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.530326828193267	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.530326828193267	1		668	723	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0057476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	146	422	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.530326828193267	2		422	510	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0057476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	107	274	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.530326828193267	2		274	372	SUCCESS
APC	324	MSKCC	GRCh37	5	112175766	112175766	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	100	303	0	ENST00000257430.4:c.4476del	p.Thr1493ArgfsTer14	p.T1493Rfs*14	ENST00000257430	NM_000038.5	1492	gCc/gc	16/16	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.530326828193267	2		303	367	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057749	27057749	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	443	747	1	ENST00000324856.7:c.1459del	p.Gln487SerfsTer132	p.Q487Sfs*132	ENST00000324856	NM_006015.4	486	tCc/tc	3/20	0.509512209994075	1	FACETS	0.935	0.892	0.978	0.935	0.892	0.978	CLONAL	1	TRUE	0	0.530326828193267	1		748	1313	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006092	22006092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	275	761	0	ENST00000276925.6:c.311C>T	p.Ala104Val	p.A104V	ENST00000276925	NM_004936.3	104	gCg/gTg	2/2	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.530326828193267	2		761	867	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711017	114711017	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	277	340	0	ENST00000543371.1:c.241G>T	p.Glu81Ter	p.E81*	ENST00000543371	NM_001198531.1	81	Gaa/Taa	2/14	0.321177948096303	3	FACETS	0.98	0.927	1	0.98	0.927	1	CLONAL	2	TRUE	1	0.530326828193267	3		340	674	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380277	+	missense_variant	Missense_Mutation	TNP	TTG	TTG	GTC	novel	NA	P-0057476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	161	459	0	ENST00000311936.3:c.181_183delinsGAC	p.Gln61Asp	p.Q61D	ENST00000311936	NM_004985.3	61	CAA/GAC	3/5	0.530326828193267	1	FACETS	0.754	0.695	0.815	0.754	0.695	0.815	SUBCLONAL	1	TRUE	0	0.530326828193267	1		459	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	271	821	0	ENST00000269305.4:c.548C>A	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tAa	5/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.3856288645415	2		821	1355	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95584075	95584075	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	106	362	0	ENST00000393063.1:c.1393G>T	p.Gly465Cys	p.G465C	ENST00000393063	NM_030621.3	465	Ggc/Tgc	10/28	1	2	FACETS	0.804	0.721	0.891	0.804	0.721	0.891	CLONAL	1	TRUE	1	0.3856288645415	2		362	684	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578408	+	inframe_deletion	In_Frame_Del	DEL	CAGCGC	CAGCGC	-	novel	NA	P-0057477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	309	888	0	ENST00000269305.4:c.522_527del	p.Arg174_Cys176delinsSer	p.R174_C176delinsS	ENST00000269305	NM_001126112.2	174	agGCGCTGc/agc	5/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.3856288645415	2		888	1469	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145672	11145672	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	289	982	0	ENST00000358026.2:c.4034C>A	p.Ser1345Ter	p.S1345*	ENST00000358026	NM_001128849.1	1345	tCg/tAg	29/36	0.3856288645415	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.3856288645415	1		982	1091	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219763	36219763	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1201	290	979	0	ENST00000222270.7:c.4662del	p.Gln1555SerfsTer91	p.Q1555Sfs*91	ENST00000222270	NM_014727.1	1554	Ggg/gg	20/37	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.3856288645415	2		979	1491	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140899	37140899	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	176	652	0	ENST00000373509.5:c.735C>G	p.Asp245Glu	p.D245E	ENST00000373509	NM_002648.3	245	gaC/gaG	5/6	1	2	FACETS	0.788	0.724	0.854	0.788	0.724	0.854	SUBCLONAL	1	TRUE	1	0.3856288645415	2		652	1159	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0057478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	880	745	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	1	2	FACETS	1	0.998	1	1	0.999	1	CLONAL	2	TRUE	1	0.942581012579858	2		745	910	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449788	149449788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	672	1247	0	ENST00000286301.3:c.1276del	p.Gln426SerfsTer4	p.Q426Sfs*4	ENST00000286301	NM_005211.3	426	Cag/ag	9/22	1	2	FACETS	0.961	0.928	0.994	0.961	0.928	0.994	CLONAL	1	TRUE	1	0.942581012579858	2		1247	1484	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859018	57859018	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	712	1193	0	ENST00000228682.2:c.514G>T	p.Gly172Ter	p.G172*	ENST00000228682	NM_005269.2	172	Gga/Tga	5/12	0.942581012579858	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.942581012579858	1		1193	766	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607144	189607144	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	620	1056	0	ENST00000264731.3:c.1525del	p.His509ThrfsTer8	p.H509Tfs*8	ENST00000264731	NM_003722.4	508	aCc/ac	12/14	1	2	FACETS	0.994	0.959	1	0.994	0.959	1	CLONAL	1	TRUE	1	0.942581012579858	2		1056	1324	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390715	139390716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGGAGTAGCT	novel	NA	P-0057478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	857	1644	2	ENST00000277541.6:c.7465_7475dup	p.Pro2493AlafsTer100	p.P2493Afs*100	ENST00000277541	NM_017617.3	2492	tcg/tcAGCTACTCCTCg	34/34	0.942581012579858	1	FACETS	0.767	0.749	0.785	0.767	0.749	0.785	SUBCLONAL	1	TRUE	0	0.942581012579858	1		1646	1253	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	98	365	0				ENST00000310581	NM_198253.2	-/1132			NA	3	FACETS	1	0.931	1			1	INDETERMINATE	2	TRUE	NA	0.31	3		365	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0057486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	67	581	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	1	2	FACETS	0.756	0.657	0.862	0.756	0.657	0.862	SUBCLONAL	1	TRUE	1	0.31	2		581	572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0057486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	147	809	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.31	2		809	781	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	21	615	0	ENST00000267101.3:c.273G>A	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atA	3/28	1	2	FACETS	0.204	0.156	0.26	0.204	0.156	0.26	SUBCLONAL	1	TRUE	1	0.31	2		615	664	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923160	48923160	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776789	NA	P-0057486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	42	216	0	ENST00000267163.4:c.607+1G>A		p.X203_splice	ENST00000267163	NM_000321.2	203			0.166598702614618	2	FACETS	1	0.948	1	0.664	0.561	0.776	INDETERMINATE	1	TRUE	0	0.31	2		216	204	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384656	84384656	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	55	466	0	ENST00000321945.7:c.787C>T	p.Gln263Ter	p.Q263*	ENST00000321945	NM_139076.2	263	Cag/Tag	8/9	1	2	FACETS	0.587	0.502	0.681	0.587	0.502	0.681	SUBCLONAL	1	TRUE	1	0.31	2		466	604	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021828	71021828	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0057486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	16	161	0	ENST00000318789.4:c.1531-1G>C		p.X511_splice	ENST00000318789	NM_032682.5	511			1	2	FACETS	0.504	0.373	0.659	0.504	0.373	0.659	SUBCLONAL	1	TRUE	1	0.31	2		161	205	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969399	44969399	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	124	240	0	ENST00000377967.4:c.4081T>C	p.Cys1361Arg	p.C1361R	ENST00000377967	NM_021140.2	1361	Tgt/Cgt	28/29	0.25461979254111	2	FACETS	0.855	0.785	0.926			1	CLONAL	3	TRUE	NA	0.31	2		240	312	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981550	201981551	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0057486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	64	692	0	ENST00000359651.3:c.466_467dup	p.Gly157GlnfsTer98	p.G157Qfs*98	ENST00000359651		155	gac/gaCCc	3/8	1	2	FACETS	0.606	0.524	0.695	0.606	0.524	0.695	SUBCLONAL	1	TRUE	1	0.31	2		692	681	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842627	68842627	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	50	548	0	ENST00000261769.5:c.566del	p.Phe189SerfsTer26	p.F189Sfs*26	ENST00000261769	NM_004360.3	188	gTt/gt	5/16	0.3	1	FACETS	0.532	0.452	0.621	0.532	0.452	0.621	SUBCLONAL	1	TRUE	0	0.31	1		548	512	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649026	37649026	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	43	303	0	ENST00000447079.4:c.2131G>C	p.Glu711Gln	p.E711Q	ENST00000447079	NM_015083.1	711	Gaa/Caa	4/14	1	2	FACETS	0.809	0.679	0.952	0.809	0.679	0.952	CLONAL	1	TRUE	1	0.31	2		303	343	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453110	140453110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	37	317	0	ENST00000288602.6:c.1825C>T	p.Gln609Ter	p.Q609*	ENST00000288602	NM_004333.4	609	Cag/Tag	15/18	0.0732080909614987	3	FACETS	0.594	0.49	0.711	0.297	0.245	0.356	INDETERMINATE	1	TRUE	1	0.31	3		317	464	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760322	133760322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	31	632	0	ENST00000318560.5:c.2645C>T	p.Ser882Phe	p.S882F	ENST00000318560	NM_005157.4	882	tCt/tTt	11/11	1	2	FACETS	0.363	0.293	0.443	0.363	0.293	0.443	SUBCLONAL	1	TRUE	1	0.31	2		632	551	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441815	49441816	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs756471180	NA	P-0057487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	109	612	0	ENST00000301067.7:c.4168dup	p.Ala1390GlyfsTer42	p.A1390Gfs*42	ENST00000301067	NM_003482.3	1390	gca/gGca	14/54	1	2	FACETS	0.786	0.705	0.872	0.786	0.705	0.872	SUBCLONAL	1	TRUE	1	0.293194735550224	2		612	946	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429977	78429978	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1200882279	NA	P-0057487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	61	345	0	ENST00000370768.2:c.901dup	p.Ile301AsnfsTer4	p.I301Nfs*4	ENST00000370768	NM_003902.3	301	ata/aAta	11/20	0.242893851991578	2	FACETS	0.901	0.779	1	0.45	0.389	0.517	CLONAL	1	TRUE	0	0.293194735550224	2		345	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0057487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	282	722	0	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	1	2	FACETS	0.963	0.906	1	1	0.995	1	CLONAL	2	TRUE	1	0.293194735550224	2		722	999	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685281	89685281	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060500116	NA	P-0057487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	27	223	0	ENST00000371953.3:c.176C>G	p.Ser59Ter	p.S59*	ENST00000371953	NM_000314.4	59	tCa/tGa	3/9	0.293194735550224	1	FACETS	0.553	0.441	0.681	0.553	0.441	0.681	SUBCLONAL	1	TRUE	0	0.293194735550224	1		223	284	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301120	65301120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	145	311	1	ENST00000342505.4:c.3328G>A	p.Glu1110Lys	p.E1110K	ENST00000342505	NM_002227.2	1110	Gaa/Aaa	24/25	0.242893851991578	2	FACETS	0.97	0.89	1	0.97	0.89	1	CLONAL	2	TRUE	0	0.293194735550224	2		312	510	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383348	4383348	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	114	731	0	ENST00000261254.3:c.142C>T	p.Gln48Ter	p.Q48*	ENST00000261254	NM_001759.3	48	Cag/Tag	1/5	0.254008760780393	3	FACETS	0.808	0.725	0.895	0.404	0.362	0.448	CLONAL	1	TRUE	1	0.293194735550224	3		731	1104	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228572	36228572	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	170	836	0	ENST00000222270.7:c.7586C>G	p.Ser2529Cys	p.S2529C	ENST00000222270	NM_014727.1	2529	tCc/tGc	34/37	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.293194735550224	2		836	1135	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023726	31023726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768022784	NA	P-0057487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	118	704	0	ENST00000375687.4:c.3211G>A	p.Ala1071Thr	p.A1071T	ENST00000375687	NM_015338.5	1071	Gcg/Acg	13/13	1	2	FACETS	0.844	0.76	0.932	0.844	0.76	0.932	CLONAL	1	TRUE	1	0.293194735550224	2		704	954	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858332	59858333	+	missense_variant	Missense_Mutation	DNP	TC	TC	CA	novel	NA	P-0057487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	27	348	1	ENST00000259008.2:c.1662_1663delinsTG	p.Gln554_Thr555delinsHisAla	p.Q554_T555delinsHA	ENST00000259008	NM_032043.2	554	caGAct/caTGct	12/20	0.278594304515568	1	FACETS	0.299	0.237	0.37	0.299	0.237	0.37	SUBCLONAL	1	TRUE	0	0.293194735550224	1		349	526	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061134	38061202	+	inframe_deletion	In_Frame_Del	DEL	GCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTG	GCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTG	-	novel	NA	P-0057488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	180	338	1	ENST00000250448.2:c.787_855del	p.Gln263_Ser285del	p.Q263_S285del	ENST00000250448	NM_004496.3	263	CAGAAGCGCTTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGC/-	2/2	1	2	FACETS	0.889	0.833	0.946	1	0.993	1	CLONAL	2	FALSE	1	0.538232989578465	2		339	376	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041417	42041417	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	89	580	0	ENST00000219905.7:c.5613del	p.Ser1873LeufsTer5	p.S1873Lfs*5	ENST00000219905	NM_001164273.1	1871	gTt/gt	17/24	0.285262738073121	1	FACETS	0.436	0.387	0.487	0.436	0.387	0.487	INDETERMINATE	1	FALSE	0	0.538232989578465	1		580	555	SUCCESS
APC	324	MSKCC	GRCh37	5	112173701	112173701	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	85	354	0	ENST00000257430.4:c.2411del	p.Asn804IlefsTer16	p.N804Ifs*16	ENST00000257430	NM_000038.5	804	Aat/at	16/16	0.538232989578465	1	FACETS	0.849	0.76	0.941	0.849	0.76	0.941	CLONAL	1	FALSE	0	0.538232989578465	1		354	272	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579312	7579312	+	splice_region_variant,synonymous_variant	Splice_Region	SNP	C	C	T	rs55863639	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	563	613	1	ENST00000269305.4:c.375G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125	acG/acA	4/11	0.697736083956604	2	FACETS	0.975	0.946	1	0.975	0.946	1	CLONAL	2	TRUE	0	0.697736083956604	2		614	828	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453514	138453514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	163	378	0	ENST00000289153.2:c.934C>T	p.Pro312Ser	p.P312S	ENST00000289153	NM_006219.2	312	Cct/Tct	5/22	0.697736083956604	3	FACETS	0.884	0.813	0.957	0.442	0.406	0.479	CLONAL	1	TRUE	1	0.697736083956604	3		378	713	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037966	49037966	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	146	328	0	ENST00000267163.4:c.2206C>T	p.Gln736Ter	p.Q736*	ENST00000267163	NM_000321.2	736	Cag/Tag	21/27	0.697736083956604	1	FACETS	0.97	0.904	1	0.97	0.904	1	CLONAL	1	TRUE	0	0.697736083956604	1		328	281	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066739	5066739	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1340580425	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	128	383	0	ENST00000381652.3:c.1276C>T	p.Arg426Ter	p.R426*	ENST00000381652	NM_004972.3	426	Cga/Tga	10/25	0.697736083956604	1	FACETS	0.979	0.908	1	0.979	0.908	1	CLONAL	1	TRUE	0	0.697736083956604	1		383	244	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665643	86665643	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	139	297	0	ENST00000274376.6:c.1624C>T	p.Gln542Ter	p.Q542*	ENST00000274376	NM_002890.2	542	Cag/Tag	12/25	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.697736083956604	2		297	355	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81528557	81528557	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	109	271	0	ENST00000298171.2:c.236C>T	p.Ser79Phe	p.S79F	ENST00000298171	NM_000369.2	79	tCc/tTc	2/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.697736083956604	2		271	291	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654704	29654704	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	162	403	0	ENST00000356175.3:c.5393C>G	p.Ala1798Gly	p.A1798G	ENST00000356175	NM_000267.3	1798	gCc/gGc	37/57	1	2	FACETS	0.902	0.833	0.972	0.902	0.833	0.972	CLONAL	1	TRUE	1	0.697736083956604	2		403	515	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231295	46231295	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	138	354	0	ENST00000334344.6:c.1135G>T	p.Gly379Ter	p.G379*	ENST00000334344	NM_152641.2	379	Gga/Tga	10/21	1	2	FACETS	0.935	0.859	1	0.935	0.859	1	CLONAL	1	TRUE	1	0.697736083956604	2		354	423	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028115	48028115	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1281207200	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	159	345	0	ENST00000234420.5:c.2993C>T	p.Ser998Phe	p.S998F	ENST00000234420	NM_000179.2	998	tCt/tTt	4/10	1	2	FACETS	0.938	0.866	1	0.938	0.866	1	CLONAL	1	TRUE	1	0.697736083956604	2		345	486	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039555	180039555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375796750	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	470	999	1	ENST00000261937.6:c.3488C>T	p.Ser1163Leu	p.S1163L	ENST00000261937	NM_182925.4	1163	tCg/tTg	26/30	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.697736083956604	2		1000	1255	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920145	76920145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	234	235	0	ENST00000373344.5:c.3932C>T	p.Pro1311Leu	p.P1311L	ENST00000373344	NM_000489.3	1311	cCa/cTa	11/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.697736083956604	1		235	323	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798292	45798293	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	novel	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	329	823	1	ENST00000450313.1:c.643_644delinsAA	p.Val215Lys	p.V215K	ENST00000450313	NM_012222.2	215	GTg/AAg	8/16	1	2	FACETS	0.896	0.848	0.946	0.896	0.848	0.946	CLONAL	1	TRUE	1	0.697736083956604	2		824	1052	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332553	65332553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	149	257	0	ENST00000342505.4:c.986C>T	p.Pro329Leu	p.P329L	ENST00000342505	NM_002227.2	329	cCa/cTa	7/25	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.697736083956604	2		257	423	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480089	120480090	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	195	429	0	ENST00000256646.2:c.3338-1_3338delinsAA		p.X1113_splice	ENST00000256646	NM_024408.3	1113		21/34	1	2	FACETS	0.935	0.87	1	0.935	0.87	1	CLONAL	1	TRUE	1	0.697736083956604	2		429	598	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204507362	204507363	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	170	415	1	ENST00000367182.3:c.437_438delinsTT	p.Ser146Phe	p.S146F	ENST00000367182	NM_001278516.1	146	tCC/tTT	7/11	1	2	FACETS	0.862	0.798	0.929	0.862	0.798	0.929	CLONAL	1	TRUE	1	0.697736083956604	2		416	565	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604642	43604643	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	316	753	0	ENST00000355710.3:c.1227_1228delinsTT	p.Leu410Phe	p.L410F	ENST00000355710	NM_020975.4	409	tcCCtc/tcTTtc	6/20	0.697736083956604	1	FACETS	0.991	0.946	1	0.991	0.946	1	CLONAL	1	TRUE	0	0.697736083956604	1		753	595	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309764	104309764	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	294	690	0	ENST00000369902.3:c.355G>A	p.Glu119Lys	p.E119K	ENST00000369902	NM_016169.3	119	Gag/Aag	3/12	0.697736083956604	1	FACETS	0.944	0.898	0.99	0.944	0.898	0.99	CLONAL	1	TRUE	0	0.697736083956604	1		690	581	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417802	32417803	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	161	356	0	ENST00000332351.3:c.1249_1249+1delinsAA		p.X417_splice	ENST00000332351	NM_024426.4	417		7/10	1	2	FACETS	0.805	0.743	0.87	0.805	0.743	0.87	CLONAL	1	TRUE	1	0.697736083956604	2		356	573	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378669	25378670	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	115	367	0	ENST00000311936.3:c.328_329delinsAT	p.Pro110Ile	p.P110I	ENST00000311936	NM_004985.3	110	CCt/ATt	4/5	0.697736083956604	1	FACETS	0.541	0.491	0.592	0.541	0.491	0.592	SUBCLONAL	1	TRUE	0	0.697736083956604	1		367	397	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378681	25378681	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	105	329	0	ENST00000311936.3:c.317C>A	p.Ser106Tyr	p.S106Y	ENST00000311936	NM_004985.3	106	tCt/tAt	4/5	0.697736083956604	1	FACETS	0.562	0.508	0.617	0.562	0.508	0.617	SUBCLONAL	1	TRUE	0	0.697736083956604	1		329	349	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287289	46287290	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	186	558	1	ENST00000334344.6:c.5234_5235delinsAA	p.Arg1745Lys	p.R1745K	ENST00000334344	NM_152641.2	1745	aGG/aAA	19/21	1	2	FACETS	0.73	0.676	0.786	0.73	0.676	0.786	SUBCLONAL	1	TRUE	1	0.697736083956604	2		559	730	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41021807	41021807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	337	553	0	ENST00000267868.3:c.749G>T	p.Arg250Leu	p.R250L	ENST00000267868	NM_002875.4	250	cGg/cTg	8/10	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.697736083956604	2		553	966	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295176	91295177	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	96	232	0	ENST00000355112.3:c.959_959+1delinsAA		p.X320_splice	ENST00000355112	NM_000057.2	320		4/22	1	2	FACETS	0.893	0.806	0.985	0.893	0.806	0.985	CLONAL	1	TRUE	1	0.697736083956604	2		232	308	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778034	3778035	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	393	989	2	ENST00000262367.5:c.7013_7014delinsTT	p.Ser2338Phe	p.S2338F	ENST00000262367	NM_004380.2	2338	tCC/tTT	31/31	1	2	FACETS	0.897	0.853	0.942	0.897	0.853	0.942	CLONAL	1	TRUE	1	0.697736083956604	2		991	1256	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844211	68844211	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	282	590	0	ENST00000261769.5:c.799T>C	p.Phe267Leu	p.F267L	ENST00000261769	NM_004360.3	267	Ttt/Ctt	6/16	0.697736083956604	1	FACETS	0.96	0.913	1	0.96	0.913	1	CLONAL	1	TRUE	0	0.697736083956604	1		590	548	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554441	63554442	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	309	710	2	ENST00000307078.5:c.297_298delinsAA	p.Glu100Lys	p.E100K	ENST00000307078	NM_004655.3	99	ctGGag/ctAAag	2/11	1	2	FACETS	0.982	0.929	1	0.982	0.929	1	CLONAL	1	TRUE	1	0.697736083956604	2		712	902	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220013	5220014	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	371	859	1	ENST00000357368.4:c.3701_3702delinsAA	p.Arg1234Gln	p.R1234Q	ENST00000357368	NM_002850.3	1234	cGG/cAA	22/38	1	2	FACETS	0.933	0.886	0.981	0.933	0.886	0.981	CLONAL	1	TRUE	1	0.697736083956604	2		860	1140	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955102	17955102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	408	905	0	ENST00000458235.1:c.125C>T	p.Ser42Phe	p.S42F	ENST00000458235	NM_000215.3	42	tCt/tTt	2/24	1	2	FACETS	0.926	0.881	0.971	0.926	0.881	0.971	CLONAL	1	TRUE	1	0.697736083956604	2		905	1263	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645129	86645129	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	132	359	0	ENST00000274376.6:c.1201A>T	p.Ile401Leu	p.I401L	ENST00000274376	NM_002890.2	401	Ata/Tta	8/25	1	2	FACETS	0.948	0.869	1	0.948	0.869	1	CLONAL	1	TRUE	1	0.697736083956604	2		359	399	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020837	26020838	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	162	676	1	ENST00000357647.3:c.120_121delinsTT	p.Arg41Cys	p.R41C	ENST00000357647	NM_003529.2	40	caCCgc/caTTgc	1/1	1	2	FACETS	0.679	0.625	0.735	0.679	0.625	0.735	SUBCLONAL	1	TRUE	1	0.697736083956604	2		677	684	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852024	128852024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	365	897	0	ENST00000249373.3:c.2096G>A	p.Ser699Asn	p.S699N	ENST00000249373	NM_005631.4	699	aGt/aAt	12/12	1	2	FACETS	0.975	0.926	1	0.975	0.926	1	CLONAL	1	TRUE	1	0.697736083956604	2		897	1073	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860171	151860172	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	197	539	1	ENST00000262189.6:c.10490_10491delinsTT	p.Ser3497Phe	p.S3497F	ENST00000262189	NM_170606.2	3497	tCC/tTT	43/59	1	2	FACETS	0.905	0.842	0.969	0.905	0.842	0.969	CLONAL	1	TRUE	1	0.697736083956604	2		540	624	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965728	90965728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	114	344	0	ENST00000265433.3:c.1589C>T	p.Ser530Phe	p.S530F	ENST00000265433	NM_002485.4	530	tCt/tTt	11/16	1	2	FACETS	0.874	0.794	0.956	0.874	0.794	0.956	CLONAL	1	TRUE	1	0.697736083956604	2		344	374	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636702	8636702	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	127	263	0	ENST00000356435.5:c.207T>G	p.Phe69Leu	p.F69L	ENST00000356435		69	ttT/ttG	2/35	0.697736083956604	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.697736083956604	1		263	230	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339319	70339319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	283	299	0	ENST00000374080.3:c.196C>T	p.Pro66Ser	p.P66S	ENST00000374080		66	Cct/Tct	2/45	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.697736083956604	1		299	418	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204507362	204507362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	170	416	0	ENST00000367182.3:c.437C>T	p.Ser146Phe	p.S146F	ENST00000367182	NM_001278516.1	146	tCc/tTc	7/11	1	2	FACETS	0.862	0.798	0.929	0.862	0.798	0.929	CLONAL	1	TRUE	1	0.697736083956604	2		416	565	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	169	365	0				ENST00000310581	NM_198253.2	-/1132			0.472070497926559	4	FACETS	0.994	0.929	1	0.994	0.929	1	CLONAL	3	TRUE	1	0.466986292325214	4		365	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	303	640	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.34158348346969	3	FACETS	0.904	0.861	0.947	0.904	0.861	0.947	CLONAL	3	TRUE	0	0.466986292325214	3		640	590	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363243	40363243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	243	691	1	ENST00000397332.2:c.986C>T	p.Ser329Leu	p.S329L	ENST00000397332	NM_001033082.2	329	tCg/tTg	3/3	0.445560443058194	5	FACETS	1	0.988	1	0.814	0.764	0.865	CLONAL	2	TRUE	2	0.466986292325214	5		692	725	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535283	66535283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs547670481	NA	P-0057491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	131	683	0	ENST00000273854.3:c.178G>A	p.Glu60Lys	p.E60K	ENST00000273854	NM_004439.5	60	Gaa/Aaa	1/18	0.466986292325214	5	FACETS	1	0.948	1	0.356	0.322	0.391	CLONAL	1	TRUE	2	0.466986292325214	5		683	894	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983018	201983019	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0057491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	366	824	1	ENST00000359651.3:c.869_870dup	p.Gly291ArgfsTer4	p.G291Rfs*4	ENST00000359651		289	-/GA	7/8	0.415462111847748	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.466986292325214	3		825	887	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023002	33023002	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	156	593	0	ENST00000300177.4:c.111C>G	p.Asp37Glu	p.D37E	ENST00000300177	NM_001191322.1	37	gaC/gaG	2/2	0.35383951752572	4	FACETS	0.861	0.793	0.932	0.861	0.793	0.932	CLONAL	2	TRUE	2	0.466986292325214	4		593	569	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863656	68863656	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	88	633	0	ENST00000261769.5:c.2395C>G	p.Pro799Ala	p.P799A	ENST00000261769	NM_004360.3	799	Ccc/Gcc	15/16	0.312180129372755	5	FACETS	0.923	0.818	1	0.308	0.272	0.346	CLONAL	1	TRUE	2	0.466986292325214	5		633	694	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18960921	18960921	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	65	743	0	ENST00000262803.5:c.499G>T	p.Glu167Ter	p.E167*	ENST00000262803	NM_002911.3	167	Gag/Tag	4/24	0.466986292325214	6	FACETS	0.566	0.489	0.649			1	SUBCLONAL	1	TRUE	NA	0.466986292325214	6		743	952	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47087991	47087991	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	118	458	1	ENST00000409792.3:c.7084C>A	p.Gln2362Lys	p.Q2362K	ENST00000409792	NM_014159.6	2362	Cag/Aag	16/21	0.476014954821447	3	FACETS	1	0.909	1	0.503	0.454	0.553	CLONAL	1	TRUE	1	0.466986292325214	3		459	620	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779038	135779038	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	208	501	0	ENST00000298552.3:c.2208G>A	p.Met736Ile	p.M736I	ENST00000298552	NM_001162426.1	736	atG/atA	17/23	0.424092280855047	3	FACETS	0.844	0.794	0.894	0.844	0.794	0.894	CLONAL	3	TRUE	0	0.466986292325214	3		501	434	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0057493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	62	554	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.465595087339539	2		554	242	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0057493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	71	470	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.465595087339539	2		470	279	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0057493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	180	857	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	1	2	FACETS	0.948	0.875	1	0.948	0.875	1	CLONAL	1	TRUE	1	0.465595087339539	2		857	816	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577146	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0057493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	250	713	0	ENST00000269305.4:c.792_794del	p.Leu265del	p.L265del	ENST00000269305	NM_001126112.2	264	ctACTg/ctg	8/11	0.357920634667114	3	FACETS	1	0.982	1	0.731	0.689	0.773	CLONAL	2	TRUE	0	0.465595087339539	3		713	604	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710681	114710681	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	64	493	0	ENST00000543371.1:c.166C>T	p.Gln56Ter	p.Q56*	ENST00000543371	NM_001198531.1	56	Caa/Taa	1/14	1	2	FACETS	0.851	0.742	0.967	0.851	0.742	0.967	CLONAL	1	TRUE	1	0.465595087339539	2		493	323	SUCCESS
APC	324	MSKCC	GRCh37	5	112174268	112174268	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0057493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	34	452	0	ENST00000257430.4:c.2977A>T	p.Lys993Ter	p.K993*	ENST00000257430	NM_000038.5	993	Aag/Tag	16/16	0.465595087339539	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.465595087339539	1		452	90	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7120689	7120689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568426700	NA	P-0057493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	174	917	2	ENST00000302850.5:c.3601C>T	p.Arg1201Trp	p.R1201W	ENST00000302850	NM_000208.2	1201	Cgg/Tgg	20/22	1	2	FACETS	0.949	0.875	1	0.949	0.875	1	CLONAL	1	TRUE	1	0.465595087339539	2		919	788	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959106	2959106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs895214237	NA	P-0057493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	170	959	0	ENST00000396946.4:c.2410C>T	p.Arg804Cys	p.R804C	ENST00000396946	NM_032415.4	804	Cgt/Tgt	18/25	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.465595087339539	2		959	668	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115269661	115269664	+	frameshift_variant	Frame_Shift_Del	DEL	AGTC	AGTC	-	novel	NA	P-0057493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	39	747	0	ENST00000438362.2:c.1542_1545del	p.Thr515LeufsTer16	p.T515Lfs*16	ENST00000438362	NM_001242891.1	514	ctGACT/ct	13/20	1	2	FACETS	0.765	0.64	0.902	0.765	0.64	0.902	CLONAL	1	TRUE	1	0.465595087339539	2		747	219	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433843	49433843	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	238	1220	1	ENST00000301067.7:c.7710del	p.Thr2571ProfsTer12	p.T2571Pfs*12	ENST00000301067	NM_003482.3	2570	ccC/cc	31/54	0.327932831237062	4	FACETS	1	0.992	1	0.74	0.691	0.791	CLONAL	1	TRUE	2	0.465595087339539	4		1221	1012	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762189	43762189	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	81	823	0	ENST00000382044.4:c.1256del	p.Pro419GlnfsTer4	p.P419Qfs*4	ENST00000382044	NM_001141980.1	419	cCa/ca	11/28	1	2	FACETS	0.8	0.708	0.898	0.8	0.708	0.898	SUBCLONAL	1	TRUE	1	0.465595087339539	2		823	435	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013715	12013715	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	82	377	0	ENST00000353533.5:c.660del	p.Glu221LysfsTer3	p.E221Kfs*3	ENST00000353533	NM_003010.3	219	ttA/tt	6/11	0.434101527431257	1	FACETS	0.834	0.757	0.911	1	0.985	1	CLONAL	2	TRUE	0	0.465595087339539	1		377	162	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117733	70117750	+	inframe_deletion	In_Frame_Del	DEL	CAAGTTCCCCGTGTGCAT	CAAGTTCCCCGTGTGCAT	-	novel	NA	P-0057493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	708	1034	0	ENST00000245479.2:c.202_219del	p.Lys68_Ile73del	p.K68_I73del	ENST00000245479	NM_000346.3	67	gaCAAGTTCCCCGTGTGCATc/gac	1/3	0.461349209072533	4	FACETS	0.983	0.955	1	0.983	0.955	1	CLONAL	4	TRUE	0	0.465595087339539	4		1034	1134	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296215	15296215	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144163298	NA	P-0057493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	225	1072	0	ENST00000263388.2:c.2149C>T	p.Arg717Cys	p.R717C	ENST00000263388	NM_000435.2	717	Cgc/Tgc	14/33	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.465595087339539	2		1072	913	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129703	47129703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	33	444	0	ENST00000409792.3:c.5177G>A	p.Gly1726Asp	p.G1726D	ENST00000409792	NM_014159.6	1726	gGt/gAt	10/21	1	2	FACETS	0.723	0.594	0.865	0.723	0.594	0.865	SUBCLONAL	1	TRUE	1	0.465595087339539	2		444	196	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045756	26045756	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	118	684	1	ENST00000540144.1:c.118C>A	p.His40Asn	p.H40N	ENST00000540144	NM_003531.2	40	Cat/Aat	1/1	0.465595087339539	3	FACETS	1	0.924	1	0.512	0.463	0.564	CLONAL	1	TRUE	1	0.465595087339539	3		685	610	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412420	63412420	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	317	550	0	ENST00000330258.3:c.747del	p.Thr250LeufsTer32	p.T250Lfs*32	ENST00000330258	NM_152424.3	249	gcT/gc	2/2	0.306823147527123	3	FACETS	1	0.978	1			1	CLONAL	3	TRUE	NA	0.465595087339539	3		550	541	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954198	48954198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123331	NA	P-0057494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	33	305	0	ENST00000267163.4:c.1399C>T	p.Arg467Ter	p.R467*	ENST00000267163	NM_000321.2	467	Cga/Tga	15/27	0.275003930922895	3	FACETS	1	0.861	1	0.354	0.29	0.426	CLONAL	1	FALSE	0	0.275003930922895	3		305	257	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150040	202150040	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs746401108	NA	P-0057494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	9	583	1	ENST00000358485.4:c.1481G>A	p.Arg494Gln	p.R494Q	ENST00000358485	NM_001080125.1	494	cGa/cAa	8/9	0.261933503667415	3	FACETS	0.171	0.112	0.246	0.085	0.056	0.123	SUBCLONAL	1	FALSE	1	0.275003930922895	3		584	436	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156719	20156719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	69	592	0	ENST00000379607.5:c.38G>A	p.Arg13His	p.R13H	ENST00000379607	NM_001412.3	13	cGc/cAc	2/7	0.491784707101096	4	FACETS	1	0.897	1	1	0.897	1	CLONAL	2	TRUE	2	0.585689470542902	4		592	185	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0057496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	91	345	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.664	0.59	0.741	0.664	0.59	0.741	SUBCLONAL	1	TRUE	1	0.485385675885916	2		345	565	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821817	59821817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780235	NA	P-0057496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	63	605	0	ENST00000259008.2:c.2233G>A	p.Ala745Thr	p.A745T	ENST00000259008	NM_032043.2	745	Gca/Aca	15/20	0.187813647025934	1	FACETS	0.235	0.203	0.271	0.235	0.203	0.271	INDETERMINATE	1	TRUE	0	0.485385675885916	1		605	835	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0057496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	267	387	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	0.485385675885916	3	FACETS	0.809	0.761	0.858			1	CLONAL	2	TRUE	NA	0.485385675885916	3		387	845	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577529	7577529	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs730882027	NA	P-0057496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	384	825	0	ENST00000269305.4:c.752T>A	p.Ile251Asn	p.I251N	ENST00000269305	NM_001126112.2	251	aTc/aAc	7/11	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.485385675885916	2		825	1246	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397516435	NA	P-0057496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	151	857	0	ENST00000269305.4:c.586C>G	p.Arg196Gly	p.R196G	ENST00000269305	NM_001126112.2	196	Cga/Gga	6/11	1	2	FACETS	0.489	0.445	0.534	0.489	0.445	0.534	SUBCLONAL	1	TRUE	1	0.485385675885916	2		857	1273	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528730	8528730	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	139	626	0	ENST00000356435.5:c.402G>T	p.Leu134Phe	p.L134F	ENST00000356435		134	ttG/ttT	4/35	0.424234431751861	1	FACETS	0.646	0.59	0.706	0.646	0.59	0.706	SUBCLONAL	1	TRUE	0	0.485385675885916	1		626	671	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813026	76813026	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	201	278	0	ENST00000373344.5:c.6595T>G	p.Phe2199Val	p.F2199V	ENST00000373344	NM_000489.3	2199	Ttt/Gtt	30/35	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.485385675885916	1		278	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0057508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	256	646	2	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.420191669334419	1	FACETS	0.976	0.915	1	0.976	0.915	1	CLONAL	1	TRUE	0	0.433128127802953	1		648	949	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930087	68930087	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	66	410	0	ENST00000288368.4:c.148T>G	p.Leu50Val	p.L50V	ENST00000288368	NM_024870.2	50	Tta/Gta	2/40	0.432813883021046	2	FACETS	0.542	0.471	0.619	0.271	0.235	0.31	SUBCLONAL	1	TRUE	0	0.433128127802953	2		410	562	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344941	118344941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	39	329	0	ENST00000534358.1:c.3067G>A	p.Val1023Ile	p.V1023I	ENST00000534358	NM_005933.3	1023	Gtt/Att	3/36	NA	2	FACETS	0.378	0.313	0.451			1	INDETERMINATE	1	TRUE	NA	0.433128127802953	2		329	476	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636869	158636869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758925804	NA	P-0057508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	84	545	0	ENST00000263640.3:c.311C>T	p.Thr104Met	p.T104M	ENST00000263640	NM_001105.4	104	aCg/aTg	4/11	1	2	FACETS	0.528	0.466	0.594	0.528	0.466	0.594	SUBCLONAL	1	TRUE	1	0.433128127802953	2		545	735	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	251	865	2	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.317365191341859	4	FACETS	1	0.987	1	1	0.995	1	CLONAL	3	FALSE	2	0.317365191341858	4		867	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793881	NA	P-0057509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	141	723	1	ENST00000269305.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGg/gAg	8/11	0.317365191341859	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	FALSE	1	0.317365191341858	3		724	451	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648405	30648405	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	88	734	1	ENST00000295754.5:c.30G>A	p.Trp10Ter	p.W10*	ENST00000295754	NM_003242.5	10	tgG/tgA	1/7	0.317365191341858	6	FACETS	1	0.954	1	0.289	0.256	0.325	CLONAL	1	FALSE	2	0.317365191341858	6		735	784	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717726	89717726	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	24	486	0	ENST00000371953.3:c.752del	p.Gly251ValfsTer5	p.G251Vfs*5	ENST00000371953	NM_000314.4	251	Ggt/gt	7/9	0.317365191341858	3	FACETS	1	0.918	1	0.453	0.36	0.557	CLONAL	1	FALSE	0	0.317365191341858	3		486	129	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857629	9857629	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	86	542	1	ENST00000330684.3:c.3772G>T	p.Gly1258Cys	p.G1258C	ENST00000330684	NM_001134407.1	1258	Ggt/Tgt	13/13	0.317365191341859	3	FACETS	1	0.915	1	1	0.915	1	CLONAL	2	FALSE	1	0.317365191341858	3		543	306	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200750	128200750	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	14	1036	0	ENST00000341105.2:c.1055G>T	p.Cys352Phe	p.C352F	ENST00000341105	NM_032638.4	352	tGt/tTt	5/6	0.313915954972914	5	FACETS	0.208	0.149	0.28	0.069	0.049	0.094	SUBCLONAL	1	FALSE	2	0.317365191341858	5		1036	626	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591234	67591267	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAACTGTTTTTCAGGTGGTTGACTCAAAAAGGTG	AAACTGTTTTTCAGGTGGTTGACTCAAAAAGGTG	-	novel	NA	P-0057509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	82	463	0	ENST00000274335.5:c.1746-14_1765del		p.X582_splice	ENST00000274335		582		13/15	0.317365191341858	9	FACETS	0.962	0.868	1	1	0.964	1	CLONAL	6	FALSE	4	0.317365191341858	9		463	189	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343035	70343035	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	27	785	0	ENST00000374080.3:c.1576G>C	p.Ala526Pro	p.A526P	ENST00000374080		526	Gcc/Ccc	11/45	1	2	FACETS	0.341	0.27	0.422	0.341	0.27	0.422	SUBCLONAL	1	FALSE	1	0.317365191341858	2		785	499	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	242	365	0				ENST00000310581	NM_198253.2	-/1132			0.332383751593115	4	FACETS	0.916	0.862	0.97	1	0.992	1	CLONAL	3	TRUE	2	0.42775592261544	4		365	588	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0057511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	68	326	6	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.229940348013746	2	FACETS	0.517	0.45	0.59	0.258	0.225	0.295	INDETERMINATE	1	TRUE	0	0.42775592261544	2		332	615	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0057511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	113	591	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.323295136786862	3	FACETS	0.501	0.45	0.557	0.251	0.225	0.279	SUBCLONAL	1	TRUE	1	0.42775592261544	3		592	1279	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864313	57864313	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	111	735	0	ENST00000228682.2:c.1790G>A	p.Arg597Lys	p.R597K	ENST00000228682	NM_005269.2	597	aGa/aAa	12/12	0.42775592261544	1	FACETS	0.392	0.351	0.435	0.392	0.351	0.435	SUBCLONAL	1	TRUE	0	0.42775592261544	1		735	1041	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864237	57864237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	81	701	0	ENST00000228682.2:c.1714G>A	p.Glu572Lys	p.E572K	ENST00000228682	NM_005269.2	572	Gag/Aag	12/12	0.42775592261544	1	FACETS	0.303	0.266	0.342	0.303	0.266	0.342	SUBCLONAL	1	TRUE	0	0.42775592261544	1		701	984	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248409	59248409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184098204	NA	P-0057511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	33	559	0	ENST00000371222.2:c.334G>A	p.Glu112Lys	p.E112K	ENST00000371222	NM_002228.3	112	Gag/Aag	1/1	0.240511108062553	3	FACETS	0.2	0.162	0.244	0.1	0.081	0.122	INDETERMINATE	1	TRUE	1	0.42775592261544	3		559	936	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1337	96	905	0	ENST00000326873.7:c.647C>A	p.Ser216Tyr	p.S216Y	ENST00000326873	NM_000455.4	216	tCc/tAc	5/10	1	2	FACETS	0.313	0.278	0.351	0.313	0.278	0.351	SUBCLONAL	1	TRUE	1	0.42775592261544	2		905	1433	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983140	201983141	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0057511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	92	517	0	ENST00000359651.3:c.990_991dup	p.Arg331ProfsTer4	p.R331Pfs*4	ENST00000359651		330	agc/agCCc	7/8	1	2	FACETS	0.468	0.415	0.525	0.468	0.415	0.525	SUBCLONAL	1	TRUE	1	0.42775592261544	2		517	919	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578515	7578515	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1212996409	NA	P-0057511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	657	816	0	ENST00000269305.4:c.415A>G	p.Lys139Glu	p.K139E	ENST00000269305	NM_001126112.2	139	Aag/Gag	5/11	0.42775592261544	1	FACETS	1	0.995	1	1	0.998	1	CLONAL	2	TRUE	0	0.42775592261544	1		816	1079	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739485	145739485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772074149	NA	P-0057511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1440	118	866	0	ENST00000428558.2:c.1885C>T	p.Arg629Trp	p.R629W	ENST00000428558	NM_004260.3	629	Cgg/Tgg	12/22	0.161043877230692	4	FACETS	0.506	0.454	0.56	0.253	0.227	0.28	INDETERMINATE	1	TRUE	2	0.42775592261544	4		866	1558	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519958	NA	P-0057511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	50	832	0	ENST00000481739.1:c.1280C>A	p.Ser427Tyr	p.S427Y	ENST00000481739	NM_002957.4	427	tCc/tAc	10/10	0.286792600702867	1	FACETS	0.157	0.132	0.184	0.157	0.132	0.184	SUBCLONAL	1	TRUE	0	0.42775592261544	1		832	1171	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872559	37872559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293998208	NA	P-0057511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	87	541	0	ENST00000269571.5:c.1519G>A	p.Glu507Lys	p.E507K	ENST00000269571		507	Gag/Aag	13/27	0.323295136786862	3	FACETS	0.487	0.43	0.548	0.243	0.215	0.274	SUBCLONAL	1	TRUE	1	0.42775592261544	3		541	1014	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303656	65303656	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	70	529	0	ENST00000342505.4:c.3099del	p.Glu1033AspfsTer21	p.E1033Dfs*21	ENST00000342505	NM_002227.2	1033	gaG/ga	22/25	0.240511108062553	3	FACETS	0.331	0.287	0.378	0.165	0.143	0.189	INDETERMINATE	1	TRUE	1	0.42775592261544	3		529	1202	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624507	21624507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	74	512	0	ENST00000421138.2:c.1522G>A	p.Glu508Lys	p.E508K	ENST00000421138		508	Gaa/Aaa	14/16	0.356496593733166	2	FACETS	0.404	0.352	0.459	0.202	0.176	0.23	SUBCLONAL	1	TRUE	0	0.42775592261544	2		512	857	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030469	49030475	+	frameshift_variant	Frame_Shift_Del	DEL	ACTGTTT	ACTGTTT	-	novel	NA	P-0057511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	204	280	0	ENST00000267163.4:c.1944_1950del	p.Leu649IlefsTer7	p.L649Ifs*7	ENST00000267163	NM_000321.2	648	tcACTGTTT/tc	19/27	0.226167813112393	0	FACETS	0.711	0.67	0.751			1	INDETERMINATE	2	TRUE	0	0.42775592261544	0		280	384	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67462898	67462898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	80	577	1	ENST00000327367.4:c.614C>T	p.Pro205Leu	p.P205L	ENST00000327367	NM_005902.3	205	cCa/cTa	5/9	0.348238051796527	1	FACETS	0.33	0.29	0.374	0.33	0.29	0.374	SUBCLONAL	1	TRUE	0	0.42775592261544	1		578	890	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472556	88472556	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	357	624	1	ENST00000360948.2:c.1999A>T	p.Met667Leu	p.M667L	ENST00000360948	NM_001012338.2	667	Atg/Ttg	16/19	0.348238051796527	1	FACETS	0.885	0.845	0.926	1	0.996	1	CLONAL	2	TRUE	0	0.42775592261544	1		625	741	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857222	78857222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	94	623	0	ENST00000306801.3:c.1588G>A	p.Glu530Lys	p.E530K	ENST00000306801	NM_020761.2	530	Gaa/Aaa	15/34	0.323295136786862	3	FACETS	0.468	0.415	0.524	0.234	0.207	0.262	SUBCLONAL	1	TRUE	1	0.42775592261544	3		623	1141	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375534	15375534	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1289	169	806	2	ENST00000263377.2:c.893C>T	p.Thr298Ile	p.T298I	ENST00000263377	NM_058243.2	298	aCc/aTc	6/20	1	2	FACETS	0.542	0.496	0.59	0.542	0.496	0.59	SUBCLONAL	1	TRUE	1	0.42775592261544	2		808	1458	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989598	212989598	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	63	315	0	ENST00000342788.4:c.113C>G	p.Ser38Cys	p.S38C	ENST00000342788	NM_005235.2	38	tCt/tGt	2/28	0.348238051796527	1	FACETS	0.496	0.43	0.567	0.496	0.43	0.567	SUBCLONAL	1	TRUE	0	0.42775592261544	1		315	467	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374362	138374362	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1453170251	NA	P-0057511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	34	265	0	ENST00000289153.2:c.3082C>T	p.Leu1028Phe	p.L1028F	ENST00000289153	NM_006219.2	1028	Ctt/Ttt	22/22	0.229940348013746	2	FACETS	0.275	0.224	0.333	0.138	0.112	0.167	INDETERMINATE	1	TRUE	0	0.42775592261544	2		265	578	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151871271	151871271	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	423	399	0	ENST00000262189.6:c.9319A>G	p.Ile3107Val	p.I3107V	ENST00000262189	NM_170606.2	3107	Ata/Gta	39/59	NA	2	FACETS	0.867	0.834	0.901			1	INDETERMINATE	3	TRUE	NA	0.42775592261544	2		399	760	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981563	70981563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1449	105	832	0	ENST00000276594.2:c.533C>T	p.Ser178Leu	p.S178L	ENST00000276594	NM_024504.3	178	tCa/tTa	2/8	0.161043877230692	4	FACETS	0.451	0.402	0.503	0.226	0.201	0.252	INDETERMINATE	1	TRUE	2	0.42775592261544	4		832	1554	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595326	141595326	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1343	127	723	0	ENST00000220592.5:c.107G>A	p.Arg36Lys	p.R36K	ENST00000220592	NM_012154.3	36	aGa/aAa	2/19	0.161043877230692	4	FACETS	0.577	0.52	0.637	0.288	0.26	0.319	INDETERMINATE	1	TRUE	2	0.42775592261544	4		723	1470	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006150	22006150	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253511104	NA	P-0057511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	478	872	0	ENST00000276925.6:c.253C>T	p.His85Tyr	p.H85Y	ENST00000276925	NM_004936.3	85	Cat/Tat	2/2	0.286792600702867	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.42775592261544	1		872	1198	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	166	365	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.983	0.908	1	0.983	0.908	1	CLONAL	1	TRUE	1	0.623350714635431	2		365	542	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs149840192	NA	P-0057512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14500	467	919	0	ENST00000275493.2:c.866C>A	p.Ala289Asp	p.A289D	ENST00000275493	NM_005228.3	289	gCc/gAc	7/28	0.623350714635431	23	FACETS	0.755	0.715	0.797	0.034	0.032	0.037	SUBCLONAL	1	TRUE	1	0.623350714635431	23		919	14967	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590491	67590494	+	frameshift_variant	Frame_Shift_Del	DEL	AGAA	AGAA	-	novel	NA	P-0057512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	55	232	0	ENST00000274335.5:c.1558_1561del	p.Glu520TyrfsTer11	p.E520Yfs*11	ENST00000274335		518	gAGAAa/ga	11/15	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.623350714635431	2		232	172	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439692	51439692	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0057512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	271	485	0	ENST00000262662.1:c.257T>G	p.Leu86Ter	p.L86*	ENST00000262662		86	tTa/tGa	4/4	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.623350714635431	2		485	740	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509827	187509827	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	187	414	0	ENST00000441802.2:c.13686T>A	p.Ser4562Arg	p.S4562R	ENST00000441802	NM_005245.3	4562	agT/agA	27/27	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.623350714635431	2		414	598	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0057513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	332	698	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.309685644061436	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.336937038308623	2		699	924	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947865	178947865	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776932	NA	P-0057513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	58	319	0	ENST00000263967.3:c.2740G>A	p.Gly914Arg	p.G914R	ENST00000263967	NM_006218.2	914	Gga/Aga	19/21	0.21569653825953	2	FACETS	0.644	0.553	0.742	0.322	0.276	0.371	SUBCLONAL	1	TRUE	0	0.336937038308623	2		319	535	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0057513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	143	354	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	0.21569653825953	2	FACETS	1	0.986	1	0.718	0.657	0.781	CLONAL	1	TRUE	0	0.336937038308623	2		354	591	SUCCESS
APC	324	MSKCC	GRCh37	5	112170864	112170864	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0057513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	192	380	0	ENST00000257430.4:c.1958+2T>C		p.X653_splice	ENST00000257430	NM_000038.5	653			0.309685644061436	2	FACETS	0.899	0.835	0.964	0.899	0.835	0.964	CLONAL	2	TRUE	0	0.336937038308623	2		380	634	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977584	2977584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746318779	NA	P-0057513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1523	81	855	1	ENST00000396946.4:c.1100C>T	p.Thr367Met	p.T367M	ENST00000396946	NM_032415.4	367	aCg/aTg	8/25	0.336937038308623	4	FACETS	0.401	0.351	0.454	0.2	0.175	0.227	SUBCLONAL	1	TRUE	2	0.336937038308623	4		856	1604	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170290	119170290	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs112330156	NA	P-0057513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	93	340	0	ENST00000264033.4:c.2520T>G	p.Cys840Trp	p.C840W	ENST00000264033	NM_005188.3	840	tgT/tgG	16/16	0.322322580876401	3	FACETS	1	0.915	1	0.516	0.459	0.576	CLONAL	1	TRUE	1	0.336937038308623	3		340	625	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193728	106193728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	54	281	0	ENST00000380013.4:c.4190C>T	p.Thr1397Ile	p.T1397I	ENST00000380013	NM_001127208.2	1397	aCt/aTt	10/11	1	2	FACETS	0.839	0.719	0.969	0.839	0.719	0.969	CLONAL	1	TRUE	1	0.336937038308623	2		281	382	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913517	NA	P-0057514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	281	431	0	ENST00000288135.5:c.1676T>C	p.Val559Ala	p.V559A	ENST00000288135	NM_000222.2	559	gTt/gCt	11/21	1	2	FACETS	0.966	0.913	1	0.966	0.913	1	CLONAL	1	TRUE	1	0.831452561788105	2		431	700	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992196	72992196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111320371	NA	P-0057514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	501	902	0	ENST00000268489.5:c.1849G>A	p.Val617Ile	p.V617I	ENST00000268489	NM_006885.3	617	Gtt/Att	2/10	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.831452561788105	2		902	1086	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136826	69136826	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	137	420	0	ENST00000288368.4:c.4742del	p.Gly1581GlufsTer55	p.G1581Efs*55	ENST00000288368	NM_024870.2	1580	ttG/tt	39/40	1	2	FACETS	0.491	0.448	0.537	0.491	0.448	0.537	SUBCLONAL	1	TRUE	1	0.831452561788105	2		420	671	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894230	NA	P-0057527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	300	604	0	ENST00000451590.1:c.35G>A	p.Gly12Asp	p.G12D	ENST00000451590	NM_001130442.1	12	gGc/gAc	2/5	0.826133094356093	3	FACETS	1	0.972	1	0.524	0.494	0.554	CLONAL	1	TRUE	1	0.842961541946938	3		604	966	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039340	49039340	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0057527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	573	500	0	ENST00000267163.4:c.2326-1G>A		p.X776_splice	ENST00000267163	NM_000321.2	776			0.839949968063412	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.842961541946938	2		500	666	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356427	66356427	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1321339471	NA	P-0057527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	118	297	0	ENST00000273854.3:c.1070C>A	p.Pro357His	p.P357H	ENST00000273854	NM_004439.5	357	cCc/cAc	5/18	1	2	FACETS	0.897	0.821	0.975	0.897	0.821	0.975	CLONAL	1	TRUE	1	0.842961541946938	2		297	312	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419852	41419852	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	469	488	0	ENST00000373198.4:c.469T>C	p.Trp157Arg	p.W157R	ENST00000373198	NM_133170.3	157	Tgg/Cgg	3/32	0.826133094356093	3	FACETS	0.991	0.956	1	0.991	0.956	1	CLONAL	2	TRUE	1	0.842961541946938	3		488	798	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576873	7576874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	678	640	0	ENST00000269305.4:c.972dup	p.Gly325TrpfsTer12	p.G325Wfs*12	ENST00000269305	NM_001126112.2	324	-/T	9/11	0.842961541946938	2	FACETS	0.968	0.948	0.987	0.968	0.948	0.987	CLONAL	2	TRUE	0	0.842961541946938	2		640	831	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245993	16245993	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	386	338	0	ENST00000375759.3:c.1616G>C	p.Arg539Pro	p.R539P	ENST00000375759	NM_015001.2	539	cGa/cCa	8/15	0.826133094356093	3	FACETS	0.915	0.878	0.953	0.915	0.878	0.953	CLONAL	2	TRUE	1	0.842961541946938	3		338	711	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16174624	16174624	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	455	386	0	ENST00000375759.3:c.62A>G	p.Lys21Arg	p.K21R	ENST00000375759	NM_015001.2	21	aAg/aGg	1/15	0.826133094356093	3	FACETS	0.966	0.931	1	0.966	0.931	1	CLONAL	2	TRUE	1	0.842961541946938	3		386	794	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915534	112915534	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	238	486	0	ENST00000351677.2:c.933+1del		p.M311fs	ENST00000351677	NM_002834.3	311	atG/at	8/16	0.826133094356093	3	FACETS	0.998	0.935	1	0.499	0.467	0.532	CLONAL	1	TRUE	1	0.842961541946938	3		486	804	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599983	10599984	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0057527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	731	784	0	ENST00000171111.5:c.1592_1593delinsCT	p.Leu531Pro	p.L531P	ENST00000171111	NM_203500.1	531	cTG/cCT	5/6	0.376247878474107	5	FACETS	1	0.992	1	0.726	0.701	0.751	INDETERMINATE	2	TRUE	2	0.842961541946938	5		784	1804	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214068	36214068	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4299	1088	972	1	ENST00000222270.7:c.2894G>T	p.Arg965Leu	p.R965L	ENST00000222270	NM_014727.1	965	cGa/cTa	6/37	0.842961541946938	8	FACETS	0.845	0.818	0.873			1	CLONAL	2	TRUE	NA	0.842961541946938	8		973	5387	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185132	99185132	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1392030374	NA	P-0057527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	334	312	0	ENST00000074304.5:c.2533+1G>T		p.X845_splice	ENST00000074304	NM_001134224.1	845			0.842961541946938	3	FACETS	0.94	0.899	0.981	0.94	0.899	0.981	CLONAL	2	TRUE	1	0.842961541946938	3		312	599	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198263210	198263210	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	166	336	0	ENST00000335508.6:c.3109G>T	p.Asp1037Tyr	p.D1037Y	ENST00000335508	NM_012433.2	1037	Gat/Tat	21/25	0.842961541946938	3	FACETS	0.853	0.787	0.922	0.427	0.393	0.461	CLONAL	1	TRUE	1	0.842961541946938	3		336	656	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564823	41564823	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	328	620	0	ENST00000263253.7:c.4124G>A	p.Gly1375Asp	p.G1375D	ENST00000263253	NM_001429.3	1375	gGc/gAc	25/31	NA	2	FACETS	0.969	0.92	1			1	INDETERMINATE	1	TRUE	NA	0.842961541946938	2		620	803	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434213	12434213	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	349	366	0	ENST00000287820.6:c.581G>T	p.Arg194Leu	p.R194L	ENST00000287820	NM_015869.4	194	cGg/cTg	4/7	0.839949968063412	2	FACETS	0.93	0.902	0.957	0.93	0.902	0.957	CLONAL	2	TRUE	0	0.842961541946938	2		366	445	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155566	106155566	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	161	296	0	ENST00000380013.4:c.467A>T	p.Gln156Leu	p.Q156L	ENST00000380013	NM_001127208.2	156	cAa/cTa	3/11	1	2	FACETS	0.979	0.91	1	0.979	0.91	1	CLONAL	1	TRUE	1	0.842961541946938	2		296	390	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508457	106508457	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	259	264	0	ENST00000359195.3:c.451C>T	p.Gln151Ter	p.Q151*	ENST00000359195	NM_002649.2	151	Cag/Tag	2/11	0.839949968063412	2	FACETS	0.979	0.947	1	0.979	0.947	1	CLONAL	2	TRUE	0	0.842961541946938	2		264	314	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151833988	151833988	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	206	396	0	ENST00000262189.6:c.14665G>A	p.Asp4889Asn	p.D4889N	ENST00000262189	NM_170606.2	4889	Gac/Aac	59/59	0.792071669041529	1	FACETS	0.884	0.839	0.927	0.884	0.839	0.927	CLONAL	1	TRUE	0	0.842961541946938	1		396	320	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38188974	38188974	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1302	310	624	0	ENST00000317025.8:c.1040C>A	p.Ala347Asp	p.A347D	ENST00000317025	NM_023034.1	347	gCc/gAc	5/24	0.705283147181942	4	FACETS	0.841	0.791	0.893			1	CLONAL	1	TRUE	NA	0.842961541946938	4		624	1612	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129872	69129872	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	391	288	0	ENST00000288368.4:c.4627del	p.Glu1543SerfsTer23	p.E1543Sfs*23	ENST00000288368	NM_024870.2	1542	ctG/ct	38/40	0.842961541946938	3	FACETS	0.964	0.941	0.985	0.964	0.941	0.985	CLONAL	3	TRUE	0	0.842961541946938	3		288	456	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410042	139410042	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	481	1027	1	ENST00000277541.6:c.1796A>T	p.His599Leu	p.H599L	ENST00000277541	NM_017617.3	599	cAc/cTc	11/34	1	2	FACETS	0.942	0.902	0.982	0.942	0.902	0.982	CLONAL	1	TRUE	1	0.842961541946938	2		1028	1212	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820528	44820528	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0057527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	314	144	0	ENST00000377967.4:c.226-1G>T		p.X76_splice	ENST00000377967	NM_021140.2	76			0.818179442768491	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.842961541946938	2		144	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0057530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	181	771	1	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.275452963253328	3	FACETS	0.756	0.699	0.815	0.756	0.699	0.815	SUBCLONAL	2	TRUE	1	0.378450261748531	3		772	752	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593652	55593652	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	222	405	0	ENST00000288135.5:c.1718C>G	p.Pro573Arg	p.P573R	ENST00000288135	NM_000222.2	573	cCa/cGa	11/21	0.809192028633733	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.809192028633733	2		405	258	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741989	145741989	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188859497	NA	P-0057531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	113	758	0	ENST00000428558.2:c.514C>T	p.Leu172Phe	p.L172F	ENST00000428558	NM_004260.3	172	Ctc/Ttc	5/22	0.549653181766924	3	FACETS	0.671	0.605	0.739	0.335	0.302	0.37	SUBCLONAL	1	TRUE	1	0.809192028633733	3		758	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	154	500	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.294478647577677	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	1	0.294478647577677	4		500	389	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347770	347770	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	64	871	0	ENST00000262320.3:c.1736C>G	p.Ser579Ter	p.S579*	ENST00000262320	NM_003502.3	579	tCa/tGa	6/11	0.289802750774346	3	FACETS	1	0.968	1	0.695	0.605	0.791	CLONAL	1	TRUE	1	0.294478647577677	3		871	359	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587118	189587118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761885185	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	80	337	0	ENST00000264731.3:c.1135C>T	p.Arg379Cys	p.R379C	ENST00000264731	NM_003722.4	379	Cgt/Tgt	9/14	0.281552062097387	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	2	0.294478647577677	4		337	302	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533703	63533703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	48	604	0	ENST00000307078.5:c.1451G>A	p.Gly484Asp	p.G484D	ENST00000307078	NM_004655.3	484	gGt/gAt	6/11	0.281430461260499	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	2	TRUE	0	0.294478647577677	2		604	158	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	34	314	2				ENST00000310581	NM_198253.2	-/1132			0.234376201158495	2	FACETS	1	0.933	1	0.649	0.536	0.772	CLONAL	1	TRUE	0	0.294478647577677	2		316	178	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692901	89692901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786204929	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	31	348	0	ENST00000371953.3:c.385G>A	p.Gly129Arg	p.G129R	ENST00000371953	NM_000314.4	129	Gga/Aga	5/9	0.294478647577677	5	FACETS	0.761	0.615	0.925	0.254	0.205	0.309	CLONAL	1	TRUE	2	0.294478647577677	5		348	399	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534285	534285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894226	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	124	654	0	ENST00000451590.1:c.38G>A	p.Gly13Asp	p.G13D	ENST00000451590	NM_001130442.1	13	gGt/gAt	2/5	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.294478647577677	NA		654	345	SUCCESS
APC	324	MSKCC	GRCh37	5	112116491	112116491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	46	154	0	ENST00000257430.4:c.536C>T	p.Ser179Phe	p.S179F	ENST00000257430	NM_000038.5	179	tCc/tTc	6/16	0.294478647577677	3	FACETS	0.996	0.862	1	0.996	0.862	1	CLONAL	3	TRUE	0	0.294478647577677	3		154	120	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332864	70332864	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	66	583	0	ENST00000373644.4:c.769A>G	p.Thr257Ala	p.T257A	ENST00000373644	NM_030625.2	257	Acc/Gcc	2/12	0.294478647577677	5	FACETS	1	0.89	1	0.68	0.594	0.77	CLONAL	2	TRUE	2	0.294478647577677	5		583	317	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679291	29679291	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555536340	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	39	272	0	ENST00000356175.3:c.7411C>T	p.Gln2471Ter	p.Q2471*	ENST00000356175	NM_000267.3	2471	Cag/Tag	50/57	0.294478647577677	4	FACETS	1	0.954	1	0.493	0.411	0.582	CLONAL	1	TRUE	1	0.294478647577677	4		272	232	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226980	2226980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	63	524	1	ENST00000398665.3:c.4460C>T	p.Ser1487Phe	p.S1487F	ENST00000398665	NM_032482.2	1487	tCc/tTc	27/28	0.294478647577677	3	FACETS	1	0.963	1	0.66	0.573	0.753	CLONAL	1	TRUE	1	0.294478647577677	3		525	372	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923440	9923440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	57	546	2	ENST00000330684.3:c.1847C>T	p.Ser616Phe	p.S616F	ENST00000330684	NM_001134407.1	616	tCc/tTc	9/13	0.289802750774346	3	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	1	0.294478647577677	3		548	191	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721099	61721099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458439158	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	52	414	0	ENST00000401558.2:c.1175C>T	p.Pro392Leu	p.P392L	ENST00000401558	NM_003400.3	392	cCg/cTg	12/25	0.294478647577677	5	FACETS	0.762	0.652	0.882	0.508	0.435	0.588	SUBCLONAL	2	TRUE	2	0.294478647577677	5		414	334	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426751	49426751	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	35	330	0	ENST00000301067.7:c.11737C>T	p.Gln3913Ter	p.Q3913*	ENST00000301067	NM_003482.3	3913	Cag/Tag	39/54	0.294478647577677	6	FACETS	0.944	0.781	1	0.63	0.521	0.749	CLONAL	2	TRUE	3	0.294478647577677	6		330	200	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221270	1221270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	193	726	0	ENST00000326873.7:c.793G>A	p.Glu265Lys	p.E265K	ENST00000326873	NM_000455.4	265	Gag/Aag	6/10	0.294478647577677	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.294478647577677	3		726	684	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194832	30194832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1434470951	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	44	502	1	ENST00000331968.5:c.313C>T	p.Arg105Cys	p.R105C	ENST00000331968	NM_002742.2	105	Cgc/Tgc	2/18	0.289802750774346	3	FACETS	1	0.925	1	0.585	0.493	0.685	CLONAL	1	TRUE	1	0.294478647577677	3		503	293	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324214	31324214	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs281864614	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	59	565	0	ENST00000412585.2:c.349C>G	p.His117Asp	p.H117D	ENST00000412585	NM_005514.6	117	Cac/Gac	3/8	0.294478647577677	6	FACETS	1	0.883	1	0.68	0.589	0.778	CLONAL	2	TRUE	3	0.294478647577677	6		565	312	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457279	67457279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	49	679	1	ENST00000327367.4:c.253C>T	p.His85Tyr	p.H85Y	ENST00000327367	NM_005902.3	85	Cat/Tat	2/9	0.294478647577677	3	FACETS	0.886	0.752	1	0.443	0.376	0.517	CLONAL	1	TRUE	1	0.294478647577677	3		680	431	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223707	36223707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1468457510	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	80	937	1	ENST00000222270.7:c.6257C>T	p.Ser2086Leu	p.S2086L	ENST00000222270	NM_014727.1	2086	tCg/tTg	28/37	0.294478647577677	3	FACETS	1	0.976	1	0.723	0.639	0.812	CLONAL	1	TRUE	1	0.294478647577677	3		938	431	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794089	42794089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	66	492	0	ENST00000575354.2:c.1450C>T	p.Pro484Ser	p.P484S	ENST00000575354	NM_015125.3	484	Cca/Tca	9/20	0.294478647577677	3	FACETS	0.765	0.669	0.868	0.765	0.669	0.868	SUBCLONAL	2	TRUE	1	0.294478647577677	3		492	336	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139762	55139762	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	51	455	0	ENST00000257290.5:c.1423G>A	p.Glu475Lys	p.E475K	ENST00000257290	NM_006206.4	475	Gag/Aag	10/23	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.294478647577677	2		455	289	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144808	11144808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1206010353	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	66	511	1	ENST00000358026.2:c.3883G>A	p.Glu1295Lys	p.E1295K	ENST00000358026	NM_001128849.1	1295	Gag/Aag	28/36	0.294478647577677	3	FACETS	1	0.97	1	0.712	0.622	0.809	CLONAL	1	TRUE	1	0.294478647577677	3		512	361	SUCCESS
ALK	238	MSKCC	GRCh37	2	29420510	29420510	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758127441	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	63	365	1	ENST00000389048.3:c.3971C>T	p.Ser1324Phe	p.S1324F	ENST00000389048	NM_004304.4	1324	tCt/tTt	27/29	0.281430461260499	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	2	TRUE	0	0.294478647577677	2		366	196	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779271	3779271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370704436	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	22	587	1	ENST00000262367.5:c.5777G>A	p.Arg1926Gln	p.R1926Q	ENST00000262367	NM_004380.2	1926	cGg/cAg	31/31	0.289802750774346	3	FACETS	0.849	0.661	1	0.424	0.33	0.532	CLONAL	1	TRUE	1	0.294478647577677	3		588	202	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467670	66467670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	24	311	0	ENST00000273854.3:c.599G>A	p.Arg200Lys	p.R200K	ENST00000273854	NM_004439.5	200	aGa/aAa	3/18	1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	1	0.294478647577677	2		311	150	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519492	176519492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	130	850	2	ENST00000292408.4:c.898C>T	p.Pro300Ser	p.P300S	ENST00000292408	NM_213647.1	300	Ccc/Tcc	7/18	0.294478647577677	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	3	TRUE	0	0.294478647577677	3		852	311	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149498309	149498309	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	99	579	1	ENST00000261799.4:c.2904+1G>A		p.X968_splice	ENST00000261799	NM_002609.3	968			0.281430461260499	2	FACETS	0.963	0.868	1	0.963	0.868	1	CLONAL	2	TRUE	0	0.294478647577677	2		580	349	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126567	2126567	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1378325757	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	34	654	0	ENST00000219476.3:c.2818C>T	p.Leu940Phe	p.L940F	ENST00000219476	NM_000548.3	940	Ctc/Ttc	25/42	0.289802750774346	3	FACETS	0.883	0.724	1	0.442	0.362	0.531	CLONAL	1	TRUE	1	0.294478647577677	3		654	300	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447781	49447781	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	54	514	0	ENST00000301067.7:c.653G>A	p.Ser218Asn	p.S218N	ENST00000301067	NM_003482.3	218	aGt/aAt	5/54	0.294478647577677	6	FACETS	1	0.958	1	0.45	0.385	0.52	CLONAL	1	TRUE	3	0.294478647577677	6		514	432	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412689	139412690	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	116	829	2	ENST00000277541.6:c.1154_1155delinsTT	p.Ser385Phe	p.S385F	ENST00000277541	NM_017617.3	385	tCC/tTT	7/34	0.281552062097387	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	2	0.294478647577677	4		831	469	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234276	39234276	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	37	359	0	ENST00000402219.2:c.2569G>C	p.Glu857Gln	p.E857Q	ENST00000402219	NM_005633.3	857	Gag/Cag	16/23	0.294478647577677	5	FACETS	1	0.941	1	0.451	0.373	0.536	CLONAL	1	TRUE	2	0.294478647577677	5		359	268	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494635	2494635	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	61	609	0	ENST00000355716.4:c.775C>G	p.Gln259Glu	p.Q259E	ENST00000355716	NM_003820.2	259	Cag/Gag	8/8	0.294478647577677	3	FACETS	1	0.968	1			1	CLONAL	1	TRUE	NA	0.294478647577677	3		609	334	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254846	16254846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	52	488	0	ENST00000375759.3:c.2111G>A	p.Arg704Lys	p.R704K	ENST00000375759	NM_015001.2	704	aGa/aAa	11/15	0.294478647577677	13	FACETS	0.931	0.793	1			1	CLONAL	2	TRUE	NA	0.294478647577677	13		488	497	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699408	117699408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	48	495	0	ENST00000369458.3:c.233G>A	p.Gly78Asp	p.G78D	ENST00000369458	NM_024626.3	78	gGc/gAc	3/6	0.294478647577677	3	FACETS	1	0.941	1	0.615	0.523	0.716	CLONAL	1	TRUE	1	0.294478647577677	3		495	304	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61213435	61213435	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	81	338	0	ENST00000301761.2:c.393A>G	p.Ile131Met	p.I131M	ENST00000301761	NM_017841.2	131	atA/atG	4/4	0.294478647577677	6	FACETS	1	0.94	1	0.809	0.722	0.9	CLONAL	3	TRUE	2	0.294478647577677	6		338	270	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124737	108124737	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1060501539	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	37	296	0	ENST00000278616.4:c.2095G>C	p.Glu699Gln	p.E699Q	ENST00000278616	NM_000051.3	699	Gaa/Caa	13/63	0.294478647577677	5	FACETS	0.871	0.725	1	0.581	0.483	0.688	CLONAL	2	TRUE	2	0.294478647577677	5		296	208	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435057	49435058	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	90	605	1	ENST00000301067.7:c.6495_6496delinsTT	p.Gln2166Ter	p.Q2166*	ENST00000301067	NM_003482.3	2165	ccCCag/ccTTag	31/54	0.294478647577677	6	FACETS	0.834	0.746	0.928	0.834	0.746	0.928	CLONAL	3	TRUE	3	0.294478647577677	6		606	388	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885967	111885967	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779973889	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	63	671	0	ENST00000341259.2:c.1589C>T	p.Pro530Leu	p.P530L	ENST00000341259	NM_005475.2	530	cCt/cTt	8/8	0.294478647577677	6	FACETS	0.985	0.857	1	0.657	0.571	0.748	CLONAL	2	TRUE	3	0.294478647577677	6		671	345	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784071	120784071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	79	954	0	ENST00000257552.2:c.914G>A	p.Gly305Glu	p.G305E	ENST00000257552	NM_002442.3	305	gGg/gAg	13/15	1	2	FACETS	0.894	0.795	0.999	1	0.983	1	CLONAL	2	TRUE	1	0.294478647577677	2		954	300	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907177	32907177	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	19	289	0	ENST00000380152.3:c.1562C>T	p.Ser521Leu	p.S521L	ENST00000380152		521	tCa/tTa	10/27	0.294478647577677	4	FACETS	0.699	0.532	0.895	0.233	0.177	0.299	SUBCLONAL	1	TRUE	1	0.294478647577677	4		289	239	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911964	32911964	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555283258	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	25	436	0	ENST00000380152.3:c.3472G>A	p.Glu1158Lys	p.E1158K	ENST00000380152		1158	Gaa/Aaa	11/27	0.294478647577677	4	FACETS	0.811	0.641	1	0.27	0.213	0.336	CLONAL	1	TRUE	1	0.294478647577677	4		436	271	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134081	41134081	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	104	438	0	ENST00000379561.5:c.1547T>C	p.Met516Thr	p.M516T	ENST00000379561	NM_002015.3	516	aTg/aCg	2/3	0.294478647577677	4	FACETS	0.944	0.855	1	0.944	0.855	1	CLONAL	3	TRUE	1	0.294478647577677	4		438	323	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037906	49037934	+	frameshift_variant	Frame_Shift_Del	DEL	AATATAGACCTTAAATTCAAAATCATTGT	AATATAGACCTTAAATTCAAAATCATTGT	-	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	24	271	0	ENST00000267163.4:c.2148_2176del	p.Ile717SerfsTer24	p.I717Sfs*24	ENST00000267163	NM_000321.2	716	AATATAGACCTTAAATTCAAAATCATTGTa/a	21/27	0.294478647577677	4	FACETS	0.756	0.594	0.943	0.252	0.198	0.315	CLONAL	1	TRUE	1	0.294478647577677	4		271	279	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38064126	38064126	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	54	396	1	ENST00000250448.2:c.52T>A	p.Tyr18Asn	p.Y18N	ENST00000250448	NM_004496.3	18	Tac/Aac	1/2	0.289802750774346	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	1	0.294478647577677	3		397	177	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640271	3640271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	44	972	3	ENST00000294008.3:c.3368C>T	p.Ser1123Phe	p.S1123F	ENST00000294008	NM_032444.2	1123	tCt/tTt	12/15	0.289802750774346	3	FACETS	0.87	0.731	1	0.435	0.365	0.512	CLONAL	1	TRUE	1	0.294478647577677	3		975	394	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857971	9857971	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	12	529	0	ENST00000330684.3:c.3430A>T	p.Asn1144Tyr	p.N1144Y	ENST00000330684	NM_001134407.1	1144	Aac/Tac	13/13	0.289802750774346	3	FACETS	0.475	0.334	0.648	0.237	0.167	0.324	SUBCLONAL	1	TRUE	1	0.294478647577677	3		529	197	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875744	56875744	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	26	291	0	ENST00000308159.5:c.2348C>T	p.Ser783Phe	p.S783F	ENST00000308159	NM_014669.4	783	tCt/tTt	21/22	0.289802750774346	3	FACETS	0.718	0.57	0.887	0.359	0.285	0.444	SUBCLONAL	1	TRUE	1	0.294478647577677	3		291	282	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992117	72992117	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	65	648	0	ENST00000268489.5:c.1928C>T	p.Pro643Leu	p.P643L	ENST00000268489	NM_006885.3	643	cCc/cTc	2/10	0.289802750774346	3	FACETS	0.959	0.841	1	0.959	0.841	1	CLONAL	2	TRUE	1	0.294478647577677	3		648	264	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347671	89347671	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	88	686	0	ENST00000301030.4:c.5279T>G	p.Phe1760Cys	p.F1760C	ENST00000301030	NM_001256183.1	1760	tTt/tGt	9/13	0.289802750774346	3	FACETS	1	0.893	1	1	0.893	1	CLONAL	2	TRUE	1	0.294478647577677	3		686	343	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849420	89849420	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768419751	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	93	641	1	ENST00000389301.3:c.1561C>T	p.Leu521Phe	p.L521F	ENST00000389301	NM_000135.2	521	Ctc/Ttc	16/43	0.289802750774346	3	FACETS	0.8	0.715	0.89	0.8	0.715	0.89	SUBCLONAL	2	TRUE	1	0.294478647577677	3		642	453	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587492	29587492	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	58	356	0	ENST00000356175.3:c.4473G>A	p.Trp1491Ter	p.W1491*	ENST00000356175	NM_000267.3	1491	tgG/tgA	33/57	0.294478647577677	4	FACETS	0.777	0.672	0.891	0.518	0.448	0.594	SUBCLONAL	2	TRUE	1	0.294478647577677	4		356	328	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322620	30322620	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	31	410	0	ENST00000322652.5:c.1633G>C	p.Glu545Gln	p.E545Q	ENST00000322652	NM_015355.2	545	Gaa/Caa	14/16	0.294478647577677	4	FACETS	1	0.839	1	0.345	0.28	0.418	CLONAL	1	TRUE	1	0.294478647577677	4		410	263	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40368093	40368093	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	167	564	0	ENST00000293328.3:c.1412A>T	p.His471Leu	p.H471L	ENST00000293328	NM_012448.3	471	cAt/cTt	12/19	0.294478647577677	4	FACETS	1	0.938	1	1	0.938	1	CLONAL	3	TRUE	1	0.294478647577677	4		564	483	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39537545	39537545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	26	240	0	ENST00000262039.4:c.79G>A	p.Glu27Lys	p.E27K	ENST00000262039	NM_002647.2	27	Gaa/Aaa	2/25	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.294478647577677	2		240	122	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968202	18968202	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	122	676	0	ENST00000262803.5:c.2042C>G	p.Ser681Ter	p.S681*	ENST00000262803	NM_002911.3	681	tCa/tGa	15/24	0.294478647577677	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.294478647577677	3		676	398	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256676	19256676	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	47	700	0	ENST00000162023.5:c.1037C>T	p.Ser346Phe	p.S346F	ENST00000162023		346	tCc/tTc	13/13	0.294478647577677	3	FACETS	1	0.94	1	0.614	0.521	0.716	CLONAL	1	TRUE	1	0.294478647577677	3		700	298	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795083	42795084	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	85	909	3	ENST00000575354.2:c.2163_2164delinsTT	p.Pro722Ser	p.P722S	ENST00000575354	NM_015125.3	721	tcCCcg/tcTTcg	10/20	0.294478647577677	3	FACETS	1	0.971	1	0.654	0.58	0.734	CLONAL	1	TRUE	1	0.294478647577677	3		912	506	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921185	50921185	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	47	716	0	ENST00000440232.2:c.3305C>T	p.Pro1102Leu	p.P1102L	ENST00000440232	NM_002691.3	1102	cCt/cTt	27/27	0.294478647577677	3	FACETS	0.992	0.84	1	0.496	0.42	0.58	CLONAL	1	TRUE	1	0.294478647577677	3		716	369	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607403	46607403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	55	818	1	ENST00000263734.3:c.1592C>T	p.Pro531Leu	p.P531L	ENST00000263734	NM_001430.4	531	cCc/cTc	12/16	0.294478647577677	5	FACETS	1	0.951	1	0.422	0.362	0.488	CLONAL	1	TRUE	2	0.294478647577677	5		819	425	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573358	41573358	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	90	764	1	ENST00000263253.7:c.5643T>A	p.Asn1881Lys	p.N1881K	ENST00000263253	NM_001429.3	1881	aaT/aaA	31/31	0.294478647577677	4	FACETS	1	0.922	1	0.692	0.619	0.77	CLONAL	2	TRUE	1	0.294478647577677	4		765	381	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573663	41573663	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1419768039	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	73	677	0	ENST00000263253.7:c.5948G>A	p.Gly1983Glu	p.G1983E	ENST00000263253	NM_001429.3	1983	gGg/gAg	31/31	0.294478647577677	4	FACETS	1	0.921	1	0.704	0.621	0.791	CLONAL	2	TRUE	1	0.294478647577677	4		677	304	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202849	128202849	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	84	594	0	ENST00000341105.2:c.872-1G>A		p.X291_splice	ENST00000341105	NM_032638.4	291			0.27185366721737	0	FACETS	0.867	0.779	0.958			1	CLONAL	2	TRUE	0	0.294478647577677	0		594	232	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268344	142268344	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	18	247	0	ENST00000350721.4:c.3148G>C	p.Glu1050Gln	p.E1050Q	ENST00000350721	NM_001184.3	1050	Gaa/Caa	15/47	0.281552062097387	4	FACETS	0.948	0.718	1	0.474	0.359	0.608	CLONAL	1	TRUE	2	0.294478647577677	4		247	167	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447703	187447703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	52	651	0	ENST00000232014.4:c.490G>A	p.Glu164Lys	p.E164K	ENST00000232014	NM_001130845.1	164	Gag/Aag	5/10	0.281552062097387	4	FACETS	1	0.946	1	0.619	0.529	0.718	CLONAL	1	TRUE	2	0.294478647577677	4		651	369	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197321	106197321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	19	310	0	ENST00000380013.4:c.5654C>T	p.Pro1885Leu	p.P1885L	ENST00000380013	NM_001127208.2	1885	cCt/cTt	11/11	1	2	FACETS	0.872	0.667	1	0.872	0.667	1	CLONAL	1	TRUE	1	0.294478647577677	2		310	148	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549842	187549842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	56	413	0	ENST00000441802.2:c.4399G>A	p.Glu1467Lys	p.E1467K	ENST00000441802	NM_005245.3	1467	Gaa/Aaa	8/27	1	2	FACETS	0.932	0.81	1	1	0.977	1	CLONAL	2	TRUE	1	0.294478647577677	2		413	204	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629283	187629283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	53	518	0	ENST00000441802.2:c.1699C>T	p.Pro567Ser	p.P567S	ENST00000441802	NM_005245.3	567	Cct/Tct	2/27	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.294478647577677	2		518	255	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35857125	35857125	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	33	208	0	ENST00000303115.3:c.46C>T	p.Gln16Ter	p.Q16*	ENST00000303115	NM_002185.3	16	Caa/Taa	1/8	0.294478647577677	10	FACETS	0.955	0.777	1			1	CLONAL	1	TRUE	NA	0.294478647577677	10		208	511	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036966	180036966	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	89	680	0	ENST00000261937.6:c.3746C>T	p.Ser1249Phe	p.S1249F	ENST00000261937	NM_182925.4	1249	tCc/tTc	28/30	0.294478647577677	0	FACETS	0.773	0.703	0.842			1	SUBCLONAL	3	TRUE	0	0.294478647577677	0		680	184	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680433	30680433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	162	553	0	ENST00000376406.3:c.1286G>A	p.Arg429Lys	p.R429K	ENST00000376406	NM_014641.2	429	aGa/aAa	5/15	0.294478647577677	14	FACETS	0.93	0.856	1			1	CLONAL	5	TRUE	NA	0.294478647577677	14		553	655	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181543	32181544	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	68	783	1	ENST00000375023.3:c.2241_2242delinsTT	p.Pro748Ser	p.P748S	ENST00000375023	NM_004557.3	747	agCCct/agTTct	14/30	0.294478647577677	6	FACETS	0.893	0.78	1	0.595	0.52	0.676	CLONAL	2	TRUE	3	0.294478647577677	6		784	411	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005420	150005421	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	59	550	1	ENST00000253339.5:c.804_805delinsAA	p.Trp268_Glu269delinsTer	p.W268_E269delins*	ENST00000253339		268	tgGGaa/tgAAaa	3/7	0.234376201158495	2	FACETS	0.75	0.652	0.856	0.75	0.652	0.856	SUBCLONAL	2	TRUE	0	0.294478647577677	2		551	267	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873468	151873468	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	41	477	0	ENST00000262189.6:c.9070A>T	p.Ser3024Cys	p.S3024C	ENST00000262189	NM_170606.2	3024	Agc/Tgc	38/59	0.234376201158495	2	FACETS	1	0.947	1	0.663	0.558	0.777	CLONAL	1	TRUE	0	0.294478647577677	2		477	210	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27192573	27192573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746958138	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	137	453	0	ENST00000380036.4:c.1576G>A	p.Gly526Arg	p.G526R	ENST00000380036	NM_000459.3	526	Ggg/Agg	11/23	0.234376201158495	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.294478647577677	2		453	402	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221996	98221996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	23	432	0	ENST00000331920.6:c.2773G>A	p.Ala925Thr	p.A925T	ENST00000331920	NM_000264.3	925	Gct/Act	17/24	1	2	FACETS	0.737	0.577	0.92	0.737	0.577	0.92	CLONAL	1	TRUE	1	0.294478647577677	2		432	212	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760808	133760808	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	49	688	0	ENST00000318560.5:c.3131C>T	p.Ser1044Phe	p.S1044F	ENST00000318560	NM_005157.4	1044	tCt/tTt	11/11	0.281552062097387	4	FACETS	1	0.957	1	0.688	0.586	0.799	CLONAL	1	TRUE	2	0.294478647577677	4		688	313	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763876	76763877	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	87	290	0	ENST00000373344.5:c.7431_7432delinsTT	p.Pro2478Ser	p.P2478S	ENST00000373344	NM_000489.3	2477	ccCCca/ccTTca	35/35	0.294478647577677	2	FACETS	1	0.97	1			1	CLONAL	3	TRUE	NA	0.294478647577677	2		290	170	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176493	123176493	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	24	92	0	ENST00000218089.9:c.460G>T	p.Glu154Ter	p.E154*	ENST00000218089	NM_001042749.1	154	Gag/Tag	7/35	0.294478647577677	2	FACETS	1	0.926	1			1	CLONAL	1	TRUE	NA	0.294478647577677	2		92	114	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100549	8100549	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	113	818	0	ENST00000346208.3:c.523T>A	p.Ser175Thr	p.S175T	ENST00000346208		175	Tcg/Acg	3/6	1	2	FACETS	0.919	0.836	1	0.919	0.836	1	CLONAL	1	TRUE	1	0.68873235535831	2		818	357	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69210700	69210700	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1171	151	305	0	ENST00000462284.1:c.284del	p.Pro95GlnfsTer5	p.P95Qfs*5	ENST00000462284	NM_002392.5	95	Cca/ca	4/11	0.68873235535831	19	FACETS	1	0.969	1			1	CLONAL	2	TRUE	NA	0.68873235535831	19		305	1322	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647257	23647257	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	122	539	0	ENST00000261584.4:c.610T>C	p.Ser204Pro	p.S204P	ENST00000261584	NM_024675.3	204	Tct/Cct	4/13	0.192495406334283	6	FACETS	0.998	0.909	1			1	INDETERMINATE	2	TRUE	NA	0.68873235535831	6		539	422	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265262	10265262	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	96	498	0	ENST00000340748.4:c.1784G>C	p.Arg595Thr	p.R595T	ENST00000340748		595	aGg/aCg	20/40	1	2	FACETS	0.992	0.896	1	0.992	0.896	1	CLONAL	1	TRUE	1	0.68873235535831	2		498	281	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39214660	39214660	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	105	509	0	ENST00000402219.2:c.3464C>T	p.Pro1155Leu	p.P1155L	ENST00000402219	NM_005633.3	1155	cCa/cTa	22/23	1	2	FACETS	0.93	0.843	1	0.93	0.843	1	CLONAL	1	TRUE	1	0.68873235535831	2		509	328	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660643	227660643	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	140	599	0	ENST00000305123.5:c.2812A>C	p.Thr938Pro	p.T938P	ENST00000305123	NM_005544.2	938	Act/Cct	1/2	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.68873235535831	2		599	391	SUCCESS
APC	324	MSKCC	GRCh37	5	112154775	112154775	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	89	420	0	ENST00000257430.4:c.1046A>C	p.Gln349Pro	p.Q349P	ENST00000257430	NM_000038.5	349	cAg/cCg	10/16	0.526326277410245	1	FACETS	0.997	0.91	1	0.997	0.91	1	CLONAL	1	TRUE	0	0.68873235535831	1		420	170	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439425	149439425	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	103	537	0	ENST00000286301.3:c.1970G>T	p.Gly657Val	p.G657V	ENST00000286301	NM_005211.3	657	gGc/gTc	15/22	0.669374980350504	3	FACETS	1	0.904	1	0.334	0.301	0.369	CLONAL	1	TRUE	0	0.68873235535831	3		537	401	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561429	9561429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55923311	NA	P-0057535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	67	566	0	ENST00000353224.5:c.353G>A	p.Gly118Asp	p.G118D	ENST00000353224	NM_177990.2	118	gGc/gAc	4/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.224743131687237	2		566	414	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009347	69009347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs190776975	NA	P-0057535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	72	441	0	ENST00000288368.4:c.2464G>A	p.Val822Met	p.V822M	ENST00000288368	NM_024870.2	822	Gtg/Atg	22/40	0.224743131687237	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.224743131687237	1		441	442	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330539	65330539	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	44	467	0	ENST00000342505.4:c.1107C>G	p.Phe369Leu	p.F369L	ENST00000342505	NM_002227.2	369	ttC/ttG	8/25	0.224743131687237	1	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	0	0.224743131687237	1		467	343	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39575933	39575933	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs565363649	NA	P-0057535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	55	319	0	ENST00000262039.4:c.866A>G	p.Asn289Ser	p.N289S	ENST00000262039	NM_002647.2	289	aAt/aGt	8/25	0.224743131687237	1	FACETS	0.76	0.655	0.872	1	0.969	1	SUBCLONAL	2	TRUE	0	0.224743131687237	1		319	286	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158485	26158485	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762757301	NA	P-0057535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	82	639	0	ENST00000289316.2:c.88C>T	p.Arg30Cys	p.R30C	ENST00000289316	NM_138720.2	30	Cgc/Tgc	1/2	0.224743131687237	5	FACETS	0.816	0.72	0.918	0.544	0.48	0.612	CLONAL	2	TRUE	2	0.224743131687237	5		639	598	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874011	123874013	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs780061449	NA	P-0057546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	10	46	0	ENST00000330479.4:c.62_64del	p.Ala21del	p.A21del	ENST00000330479	NM_020382.3	14	gaGGCg/gag	2/9	1	2	FACETS	0.536	0.367	0.743	0.536	0.367	0.743	SUBCLONAL	1	TRUE	1	0.433924747493532	2		46	86	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958063	54958063	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	74	259	0	ENST00000312783.6:c.544G>C	p.Val182Leu	p.V182L	ENST00000312783	NM_198436.1	182	Gta/Cta	6/10	1	2	FACETS	0.963	0.849	1	0.963	0.849	1	CLONAL	1	TRUE	1	0.433924747493532	2		259	354	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0057547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	77	295	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.208401671926328	1	FACETS	0.791	0.706	0.879	0.791	0.706	0.879	INDETERMINATE	1	TRUE	0	0.603773472897852	1		295	225	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0057547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	319	740	3	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.5368075532589	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.603773472897852	2		743	483	SUCCESS
APC	324	MSKCC	GRCh37	5	112175322	112175322	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	48	237	0	ENST00000257430.4:c.4031C>A	p.Ser1344Ter	p.S1344*	ENST00000257430	NM_000038.5	1344	tCa/tAa	16/16	0.603773472897852	2	FACETS	0.883	0.78	0.985	0.883	0.78	0.985	CLONAL	2	TRUE	0	0.603773472897852	2		237	90	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429753	78429753	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	14	245	0	ENST00000370768.2:c.1035T>G	p.Ser345Arg	p.S345R	ENST00000370768	NM_003902.3	345	agT/agG	12/20	0.263138864478343	3	FACETS	0.479	0.349	0.634	0.16	0.116	0.212	INDETERMINATE	1	TRUE	0	0.603773472897852	3		245	126	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245451	153245451	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	245	585	0	ENST00000281708.4:c.1740C>A	p.His580Gln	p.H580Q	ENST00000281708	NM_033632.3	580	caC/caA	11/12	0.348217313390796	3	FACETS	1	0.992	1	1	0.996	1	INDETERMINATE	3	TRUE	1	0.603773472897852	3		585	312	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170171	32170171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	242	1176	2	ENST00000375023.3:c.3437G>A	p.Cys1146Tyr	p.C1146Y	ENST00000375023	NM_004557.3	1146	tGc/tAc	21/30	0.575733129513299	5	FACETS	0.979	0.918	1	0.653	0.612	0.695	CLONAL	2	TRUE	2	0.603773472897852	5		1178	780	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0057550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	48	750	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.774	0.651	0.91	0.774	0.651	0.91	CLONAL	1	TRUE	1	0.11	2		750	1128	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0057550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	31	370	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.859	0.693	1	0.859	0.693	1	CLONAL	1	TRUE	1	0.11	2		370	656	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603030	48603078	+	frameshift_variant	Frame_Shift_Del	DEL	ATCGACAGATGCAGCAGCAGGCGGCTACTGCACAAGCTGCAGCAGCTGC	ATCGACAGATGCAGCAGCAGGCGGCTACTGCACAAGCTGCAGCAGCTGC	GA	novel	NA	P-0057550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	27	325	0	ENST00000342988.3:c.1331_1379delinsGA	p.His444ArgfsTer34	p.H444Rfs*34	ENST00000342988	NM_005359.5	444	cATCGACAGATGCAGCAGCAGGCGGCTACTGCACAAGCTGCAGCAGCTGCc/cGAc	11/12	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.11	2		325	405	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481417	140481417	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913348	NA	P-0057551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	70	393	0	ENST00000288602.6:c.1391G>T	p.Gly464Val	p.G464V	ENST00000288602	NM_004333.4	464	gGa/gTa	11/18	0.182681253602408	0	FACETS	0.77	0.672	0.874			1	SUBCLONAL	1	TRUE	0	0.262544345992269	0		393	511	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0057551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	62	367	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	0.220611074601305	0	FACETS	0.886	0.769	1			1	CLONAL	1	TRUE	0	0.262544345992269	0		367	393	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981483	70981483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	109	1306	0	ENST00000276594.2:c.613G>A	p.Val205Ile	p.V205I	ENST00000276594	NM_024504.3	205	Gtt/Att	2/8	0.245185501366888	0	FACETS	0.536	0.48	0.596			1	SUBCLONAL	1	TRUE	0	0.262544345992269	0		1306	1143	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861139	57861139	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	62	631	0	ENST00000228682.2:c.936C>A	p.Tyr312Ter	p.Y312*	ENST00000228682	NM_005269.2	312	taC/taA	9/12	1	2	FACETS	0.529	0.456	0.61	0.529	0.456	0.61	SUBCLONAL	1	TRUE	1	0.262544345992269	2		631	892	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986485	36986485	+	stop_lost	Nonstop_Mutation	SNP	A	A	T	novel	NA	P-0057551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	187	934	0	ENST00000354822.5:c.1204T>A	p.Ter402ArgextTer63	p.*402Rext*63	ENST00000354822	NM_001079668.2	402	Tga/Aga	3/3	0.231648902982032	0	FACETS	1	0.98	1			1	CLONAL	1	TRUE	0	0.262544345992269	0		934	897	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339474	81339474	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	23	349	0	ENST00000222390.5:c.1530T>A	p.Ser510Arg	p.S510R	ENST00000222390	NM_000601.4	510	agT/agA	13/18	1	2	FACETS	0.439	0.342	0.552	0.439	0.342	0.552	SUBCLONAL	1	TRUE	1	0.262544345992269	2		349	399	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242481	+	inframe_deletion	In_Frame_Del	DEL	AATTAAGAGAAGCAA	AATTAAGAGAAGCAA	-	rs121913425	NA	P-0057552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	50	395	0	ENST00000275493.2:c.2237_2251del	p.Glu746_Thr751delinsAla	p.E746_T751delinsA	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAAca/gca	19/28	1	2	FACETS	0.406	0.344	0.474	0.406	0.344	0.474	SUBCLONAL	1	TRUE	1	0.41	2		395	601	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518171	103518171	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	41	249	0	ENST00000355739.4:c.2109C>G	p.Asp703Glu	p.D703E	ENST00000355739	NM_000123.3	703	gaC/gaG	9/15	1	2	FACETS	0.529	0.441	0.626	0.529	0.441	0.626	SUBCLONAL	1	TRUE	1	0.41	2		249	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0057553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	546	831	1	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.574492175116383	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.574492175116383	2		832	948	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550494	29550497	+	frameshift_variant	Frame_Shift_Del	DEL	TAAC	TAAC	-	rs786202782	NA	P-0057553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	87	98	0	ENST00000356175.3:c.1756_1759del	p.Thr586ValfsTer18	p.T586Vfs*18	ENST00000356175	NM_000267.3	585	tTAACt/tt	16/57	0.574492175116383	1	FACETS	0.972	0.877	1	0.972	0.877	1	CLONAL	1	TRUE	0	0.574492175116383	1		98	222	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0057554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	39	323	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.716	0.593	0.854	0.716	0.593	0.854	SUBCLONAL	1	TRUE	1	0.209787800079824	2		323	519	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247812	59247813	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0057554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	179	871	1	ENST00000371222.2:c.930_931del	p.Lys311SerfsTer6	p.K311Sfs*6	ENST00000371222	NM_002228.3	310	caGAaa/caaa	1/1	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.209787800079824	2		872	1191	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578388	+	frameshift_variant	Frame_Shift_Del	DEL	GAGCAGC	GAGCAGC	-	novel	NA	P-0057554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	141	827	0	ENST00000269305.4:c.542_548del	p.Arg181GlnfsTer64	p.R181Qfs*64	ENST00000269305	NM_001126112.2	181	cGCTGCTCa/ca	5/11	1	2	FACETS	0.803	0.732	0.878	1	0.988	1	CLONAL	2	TRUE	1	0.209787800079824	2		827	837	SUCCESS
APC	324	MSKCC	GRCh37	5	112175706	112175706	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	38	262	0	ENST00000257430.4:c.4415del	p.Val1472GlufsTer35	p.V1472Efs*35	ENST00000257430	NM_000038.5	1472	gTa/ga	16/16	1	2	FACETS	1	0.838	1	1	0.838	1	CLONAL	1	TRUE	1	0.209787800079824	2		262	358	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956723	68956723	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs750933833	NA	P-0057554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	67	470	0	ENST00000288368.4:c.841C>T	p.Arg281Trp	p.R281W	ENST00000288368	NM_024870.2	281	Cgg/Tgg	8/40	1	2	FACETS	0.946	0.822	1	0.946	0.822	1	CLONAL	1	TRUE	1	0.209787800079824	2		470	675	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579366	7579366	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0057555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	424	1038	0	ENST00000269305.4:c.321C>G	p.Tyr107Ter	p.Y107*	ENST00000269305	NM_001126112.2	107	taC/taG	4/11	0.56587718662981	1	FACETS	0.986	0.942	1	0.986	0.942	1	CLONAL	1	TRUE	0	0.56587718662981	1		1038	1090	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437185	52437185	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	357	717	0	ENST00000460680.1:c.1859del	p.Glu620GlyfsTer3	p.E620Gfs*3	ENST00000460680	NM_004656.3	620	gAg/gg	14/17	0.527413703067171	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.56587718662981	1		717	888	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880257	37880257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	19	515	0	ENST00000269571.5:c.2301C>G	p.Ile767Met	p.I767M	ENST00000269571		767	atC/atG	19/27	1	2	FACETS	0.184	0.139	0.238	0.184	0.139	0.238	SUBCLONAL	1	TRUE	1	0.345184645396081	2		515	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0057556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	111	776	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	1	2	FACETS	0.802	0.721	0.888	0.802	0.721	0.888	CLONAL	1	TRUE	1	0.345184645396081	2		776	802	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0057556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	138	797	1	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	1	2	FACETS	0.931	0.847	1	0.931	0.847	1	CLONAL	1	TRUE	1	0.345184645396081	2		798	859	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602413	10602413	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	165	1298	1	ENST00000171111.5:c.1165G>T	p.Asp389Tyr	p.D389Y	ENST00000171111	NM_203500.1	389	Gac/Tac	3/6	0.345184645396081	1	FACETS	0.882	0.81	0.957	0.882	0.81	0.957	CLONAL	1	TRUE	0	0.345184645396081	1		1299	897	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520141	9520141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560752200	NA	P-0057556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	87	456	0	ENST00000353224.5:c.2128G>A	p.Val710Ile	p.V710I	ENST00000353224	NM_177990.2	710	Gtc/Atc	10/10	1	2	FACETS	0.973	0.864	1	0.973	0.864	1	CLONAL	1	TRUE	1	0.345184645396081	2		456	518	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523357	176523357	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	158	1019	0	ENST00000292408.4:c.2014G>T	p.Val672Leu	p.V672L	ENST00000292408	NM_213647.1	672	Gtg/Ttg	15/18	0.264034327335571	1	FACETS	0.976	0.896	1	0.976	0.896	1	CLONAL	1	TRUE	0	0.345184645396081	1		1019	776	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244652	46244652	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	81	573	0	ENST00000334344.6:c.2746C>T	p.Gln916Ter	p.Q916*	ENST00000334344	NM_152641.2	916	Caa/Taa	15/21	1	2	FACETS	0.791	0.698	0.891	0.791	0.698	0.891	SUBCLONAL	1	TRUE	1	0.345184645396081	2		573	593	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725540	162725540	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	48	427	0	ENST00000367921.3:c.652G>C	p.Asp218His	p.D218H	ENST00000367921	NM_006182.2	218	Gat/Cat	7/18	0.23486338536393	3	FACETS	0.627	0.53	0.734	0.314	0.265	0.367	SUBCLONAL	1	TRUE	1	0.345184645396081	3		427	520	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431750	49431750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	83	1022	0	ENST00000301067.7:c.9389C>T	p.Ser3130Phe	p.S3130F	ENST00000301067	NM_003482.3	3130	tCt/tTt	34/54	1	2	FACETS	0.695	0.613	0.783	0.695	0.613	0.783	SUBCLONAL	1	TRUE	1	0.345184645396081	2		1022	692	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155410	106155410	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	36	359	0	ENST00000380013.4:c.311C>G	p.Ser104Cys	p.S104C	ENST00000380013	NM_001127208.2	104	tCt/tGt	3/11	1	2	FACETS	0.42	0.344	0.504	0.42	0.344	0.504	SUBCLONAL	1	TRUE	1	0.345184645396081	2		359	497	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645064	86645064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	59	294	0	ENST00000274376.6:c.1136C>T	p.Ser379Leu	p.S379L	ENST00000274376	NM_002890.2	379	tCa/tTa	8/25	0.200081421438532	2	FACETS	0.95	0.821	1	0.475	0.41	0.544	INDETERMINATE	1	TRUE	0	0.345184645396081	2		294	360	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16174605	16174605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	92	454	1	ENST00000375759.3:c.43G>A	p.Glu15Lys	p.E15K	ENST00000375759	NM_015001.2	15	Gag/Aag	1/15	0.163060090954874	3	FACETS	1	0.96	1	0.584	0.52	0.652	INDETERMINATE	1	TRUE	1	0.345184645396081	3		455	535	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16174625	16174625	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	85	417	0	ENST00000375759.3:c.63G>C	p.Lys21Asn	p.K21N	ENST00000375759	NM_015001.2	21	aaG/aaC	1/15	0.163060090954874	3	FACETS	1	0.964	1	0.609	0.54	0.682	INDETERMINATE	1	TRUE	1	0.345184645396081	3		417	474	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102121	27102121	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	92	576	0	ENST00000324856.7:c.5047G>C	p.Glu1683Gln	p.E1683Q	ENST00000324856	NM_006015.4	1683	Gag/Cag	19/20	1	2	FACETS	0.803	0.714	0.898	0.803	0.714	0.898	CLONAL	1	TRUE	1	0.345184645396081	2		576	664	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46725704	46725704	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	38	632	1	ENST00000371975.4:c.340G>A	p.Glu114Lys	p.E114K	ENST00000371975	NM_003579.3	114	Gaa/Aaa	5/18	1	2	FACETS	0.395	0.326	0.473	0.395	0.326	0.473	SUBCLONAL	1	TRUE	1	0.345184645396081	2		633	557	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344443	118344443	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	41	261	0	ENST00000534358.1:c.2569G>A	p.Glu857Lys	p.E857K	ENST00000534358	NM_005933.3	857	Gag/Aag	3/36	1	2	FACETS	0.822	0.688	0.969	0.822	0.688	0.969	CLONAL	1	TRUE	1	0.345184645396081	2		261	289	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913333	28913333	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	94	597	1	ENST00000282397.4:c.2460G>A	p.Trp820Ter	p.W820*	ENST00000282397	NM_002019.4	820	tgG/tgA	17/30	1	2	FACETS	0.784	0.697	0.875	0.784	0.697	0.875	SUBCLONAL	1	TRUE	1	0.345184645396081	2		598	695	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428326	33428326	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	137	803	1	ENST00000345365.6:c.797G>T	p.Arg266Leu	p.R266L	ENST00000345365	NM_002878.3	266	cGc/cTc	9/10	1	2	FACETS	0.929	0.845	1	0.929	0.845	1	CLONAL	1	TRUE	1	0.345184645396081	2		804	854	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41209077	41209077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224764	NA	P-0057556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	79	665	0	ENST00000357654.3:c.5269G>A	p.Asp1757Asn	p.D1757N	ENST00000357654	NM_007294.3	1757	Gac/Aac	19/23	1	2	FACETS	0.555	0.488	0.629	0.555	0.488	0.629	SUBCLONAL	1	TRUE	1	0.345184645396081	2		665	824	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466772	25466772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	103	724	0	ENST00000264709.3:c.1931C>T	p.Ala644Val	p.A644V	ENST00000264709	NM_175629.2	644	gCt/gTt	16/23	1	2	FACETS	0.918	0.823	1	0.918	0.823	1	CLONAL	1	TRUE	1	0.345184645396081	2		724	650	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027113	48027113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553413355	NA	P-0057556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	51	454	1	ENST00000234420.5:c.1991C>T	p.Ser664Leu	p.S664L	ENST00000234420	NM_000179.2	664	tCa/tTa	4/10	1	2	FACETS	0.608	0.517	0.708	0.608	0.517	0.708	SUBCLONAL	1	TRUE	1	0.345184645396081	2		455	486	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955093	55955093	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	92	508	0	ENST00000263923.4:c.3452C>A	p.Pro1151His	p.P1151H	ENST00000263923	NM_002253.2	1151	cCc/cAc	26/30	1	2	FACETS	0.919	0.818	1	0.919	0.818	1	CLONAL	1	TRUE	1	0.345184645396081	2		508	580	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201767	66201767	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	78	493	0	ENST00000273854.3:c.2735T>A	p.Leu912Gln	p.L912Q	ENST00000273854	NM_004439.5	912	cTg/cAg	16/18	1	2	FACETS	0.859	0.757	0.969	0.859	0.757	0.969	CLONAL	1	TRUE	1	0.345184645396081	2		493	526	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294454	1294454	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	51	942	0	ENST00000310581.5:c.547C>A	p.Gln183Lys	p.Q183K	ENST00000310581	NM_198253.2	183	Cag/Aag	2/16	1	2	FACETS	0.361	0.306	0.422	0.361	0.306	0.422	SUBCLONAL	1	TRUE	1	0.345184645396081	2		942	819	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056119	26056119	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	16	570	0	ENST00000343677.2:c.538G>A	p.Ala180Thr	p.A180T	ENST00000343677	NM_005319.3	180	Gcg/Acg	1/1	1	2	FACETS	0.142	0.104	0.188	0.142	0.104	0.188	SUBCLONAL	1	TRUE	1	0.345184645396081	2		570	651	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275767	38275767	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121909637	NA	P-0057556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	94	704	1	ENST00000425967.3:c.1502G>T	p.Arg501Leu	p.R501L	ENST00000425967	NM_001174067.1	501	cGc/cTc	11/19	0.345184645396081	1	FACETS	0.799	0.713	0.891	0.799	0.713	0.891	SUBCLONAL	1	TRUE	0	0.345184645396081	1		705	564	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401341	139401341	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	177	1243	1	ENST00000277541.6:c.3728C>G	p.Thr1243Ser	p.T1243S	ENST00000277541	NM_017617.3	1243	aCc/aGc	23/34	0.345184645396081	1	FACETS	0.908	0.836	0.982	0.908	0.836	0.982	CLONAL	1	TRUE	0	0.345184645396081	1		1244	935	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793285	139793285	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	52	1020	0	ENST00000247668.2:c.93G>C	p.Lys31Asn	p.K31N	ENST00000247668	NM_021138.3	31	aaG/aaC	2/11	NA	2	FACETS	0.328	0.278	0.383			1	INDETERMINATE	1	TRUE	NA	0.345184645396081	2		1020	918	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186739	11186739	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	85	616	0	ENST00000361445.4:c.6466A>G	p.Ile2156Val	p.I2156V	ENST00000361445	NM_004958.3	2156	Ata/Gta	46/58	1	2	FACETS	0.706	0.624	0.794	0.706	0.624	0.794	SUBCLONAL	1	TRUE	1	0.344458557982718	2		616	699	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70360793	70360793	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0057557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	37	229	0	ENST00000373644.4:c.1968+2T>G		p.X656_splice	ENST00000373644	NM_030625.2	656			1	2	FACETS	0.891	0.74	1	0.891	0.74	1	CLONAL	1	TRUE	1	0.344458557982718	2		229	241	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0057557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	66	375	1	ENST00000311936.3:c.34_35delinsTT	p.Gly12Phe	p.G12F	ENST00000311936	NM_004985.3	12	GGt/TTt	2/5	1	2	FACETS	0.807	0.702	0.92	0.807	0.702	0.92	CLONAL	1	TRUE	1	0.344458557982718	2		376	475	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211499	46211501	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	novel	NA	P-0057557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	49	248	0	ENST00000334344.6:c.465_467del	p.Asn156del	p.N156del	ENST00000334344	NM_152641.2	155	ccAAAt/cct	5/21	1	2	FACETS	0.939	0.8	1	0.939	0.8	1	CLONAL	1	TRUE	1	0.344458557982718	2		248	303	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349278	11349278	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	103	595	0	ENST00000332029.2:c.58del	p.Arg20AspfsTer65	p.R20Dfs*65	ENST00000332029	NM_003745.1	20	Cga/ga	2/2	1	2	FACETS	0.966	0.866	1	0.966	0.866	1	CLONAL	1	TRUE	1	0.344458557982718	2		595	619	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23640540	23640541	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0057557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	79	519	0	ENST00000261584.4:c.2570_2571delinsCT	p.Leu857Ser	p.L857S	ENST00000261584	NM_024675.3	857	tTG/tCT	6/13	1	2	FACETS	0.749	0.66	0.846	0.749	0.66	0.846	SUBCLONAL	1	TRUE	1	0.344458557982718	2		519	612	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740509	58740509	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	100	601	0	ENST00000305921.3:c.1414G>T	p.Glu472Ter	p.E472*	ENST00000305921	NM_003620.3	472	Gaa/Taa	6/6	1	2	FACETS	0.925	0.827	1	0.925	0.827	1	CLONAL	1	TRUE	1	0.344458557982718	2		601	628	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220502	1220502	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	rs121913317	NA	P-0057557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	123	1148	1	ENST00000326873.7:c.595G>T	p.Glu199Ter	p.E199*	ENST00000326873	NM_000455.4	199	Gag/Tag	4/10	0.344458557982718	1	FACETS	0.764	0.691	0.841	0.764	0.691	0.841	SUBCLONAL	1	TRUE	0	0.344458557982718	1		1149	774	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207627	2207627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	179	1164	1	ENST00000398665.3:c.911C>T	p.Ser304Leu	p.S304L	ENST00000398665	NM_032482.2	304	tCg/tTg	11/28	0.344458557982718	1	FACETS	0.885	0.816	0.957	0.885	0.816	0.957	CLONAL	1	TRUE	0	0.344458557982718	1		1165	972	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211135	36211135	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1228	202	1407	0	ENST00000222270.7:c.886G>T	p.Gly296Cys	p.G296C	ENST00000222270	NM_014727.1	296	Ggc/Tgc	3/37	NA	3	FACETS	0.961	0.889	1			1	INDETERMINATE	1	TRUE	NA	0.344458557982718	3		1407	1430	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171751	36171751	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	45	375	0	ENST00000300305.3:c.814C>T	p.Gln272Ter	p.Q272*	ENST00000300305		272	Cag/Tag	7/8	1	2	FACETS	0.689	0.581	0.809	0.689	0.581	0.809	SUBCLONAL	1	TRUE	1	0.344458557982718	2		375	379	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971089	55971090	+	missense_variant	Missense_Mutation	DNP	AC	AC	TA	novel	NA	P-0057557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	91	591	0	ENST00000263923.4:c.1707_1708delinsTA	p.Leu569_Trp570delinsPheArg	p.L569_W570delinsFR	ENST00000263923	NM_002253.2	569	ttGTgg/ttTAgg	13/30	1	2	FACETS	0.839	0.745	0.938	0.839	0.745	0.938	CLONAL	1	TRUE	1	0.344458557982718	2		591	630	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524086	187524086	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	122	641	0	ENST00000441802.2:c.11453G>T	p.Cys3818Phe	p.C3818F	ENST00000441802	NM_005245.3	3818	tGt/tTt	20/27	1	2	FACETS	0.873	0.789	0.962	0.873	0.789	0.962	CLONAL	1	TRUE	1	0.344458557982718	2		641	811	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878962	117878962	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	102	336	0	ENST00000297338.2:c.7T>G	p.Tyr3Asp	p.Y3D	ENST00000297338	NM_006265.2	3	Tac/Gac	2/14	0.295723677971214	3	FACETS	1	0.972	1	0.623	0.559	0.691	CLONAL	1	TRUE	1	0.344458557982718	3		336	557	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0057565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	143	227	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.487936429892379	2		228	563	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560902	9560902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756198440	NA	P-0057565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	146	475	0	ENST00000353224.5:c.880G>A	p.Glu294Lys	p.E294K	ENST00000353224	NM_177990.2	294	Gaa/Aaa	4/10	1	2	FACETS	0.934	0.855	1	0.934	0.855	1	CLONAL	1	TRUE	1	0.487936429892379	2		475	641	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055993	180055993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	217	966	0	ENST00000261937.6:c.992C>T	p.Pro331Leu	p.P331L	ENST00000261937	NM_182925.4	331	cCc/cTc	8/30	1	2	FACETS	0.926	0.861	0.992	0.926	0.861	0.992	CLONAL	1	TRUE	1	0.487936429892379	2		966	961	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895656	28895656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	164	464	0	ENST00000282397.4:c.3118G>A	p.Asp1040Asn	p.D1040N	ENST00000282397	NM_002019.4	1040	Gat/Aat	23/30	1	2	FACETS	0.951	0.875	1	0.951	0.875	1	CLONAL	1	TRUE	1	0.487936429892379	2		464	707	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0057565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	1335	317	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.487936429892379	16	FACETS	0.976	0.962	0.99			1	CLONAL	15	TRUE	NA	0.487936429892379	16		317	1650	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566179	95566179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1566761556	NA	P-0057565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	195	528	1	ENST00000393063.1:c.4144C>T	p.Pro1382Ser	p.P1382S	ENST00000393063	NM_030621.3	1382	Cct/Tct	23/28	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.487936429892379	2		529	789	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213494	27213494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	108	324	0	ENST00000380036.4:c.2890G>A	p.Asp964Asn	p.D964N	ENST00000380036	NM_000459.3	964	Gat/Aat	18/23	0.487936429892379	0	FACETS	0.667	0.605	0.731			1	SUBCLONAL	1	TRUE	0	0.487936429892379	0		324	340	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306621	163306621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	60	244	1	ENST00000271452.3:c.418G>A	p.Glu140Lys	p.E140K	ENST00000271452	NM_145697.2	140	Gaa/Aaa	6/14	1	2	FACETS	0.804	0.698	0.917	0.804	0.698	0.917	CLONAL	1	TRUE	1	0.487936429892379	2		245	306	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034986	42034986	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	194	603	0	ENST00000219905.7:c.4828A>T	p.Thr1610Ser	p.T1610S	ENST00000219905	NM_001164273.1	1610	Act/Tct	15/24	0.487936429892379	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.487936429892379	1		603	596	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	43	365	0				ENST00000310581	NM_198253.2	-/1132			0.244059596993748	5	FACETS	0.892	0.761	1	0.892	0.761	1	CLONAL	3	TRUE	2	0.322225349387258	5		365	148	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0057566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	144	405	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.271941377163395	3	FACETS	0.896	0.827	0.967	0.896	0.827	0.967	CLONAL	3	TRUE	0	0.322225349387258	3		405	386	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720709	89720709	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs863224909	NA	P-0057566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	29	217	0	ENST00000371953.3:c.860C>G	p.Ser287Ter	p.S287*	ENST00000371953	NM_000314.4	287	tCa/tGa	8/9	0.168844091283214	3	FACETS	0.864	0.706	1	0.576	0.471	0.691	INDETERMINATE	2	TRUE	0	0.322225349387258	3		217	121	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248867	133248867	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	69	676	0	ENST00000320574.5:c.1728G>T	p.Lys576Asn	p.K576N	ENST00000320574	NM_006231.2	576	aaG/aaT	16/49	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.322225349387258	2		676	315	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006814	62006814	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs749917008	NA	P-0057566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	32	836	0	ENST00000392795.3:c.574G>C	p.Glu192Gln	p.E192Q	ENST00000392795	NM_001039933.1	192	Gag/Cag	5/6	1	2	FACETS	0.804	0.656	0.969	0.804	0.656	0.969	CLONAL	1	TRUE	1	0.322225349387258	2		836	247	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878106	48878106	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1469887040	NA	P-0057566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	12	137	0	ENST00000267163.4:c.62del	p.Pro21ArgfsTer44	p.P21Rfs*44	ENST00000267163	NM_000321.2	20	Ccc/cc	1/27	0.168844091283214	3	FACETS	1	0.867	1	0.48	0.346	0.637	INDETERMINATE	1	TRUE	0	0.322225349387258	3		137	60	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40789994	40789994	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs746391800	NA	P-0057566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	20	578	0	ENST00000373198.4:c.2737G>A	p.Glu913Lys	p.E913K	ENST00000373198	NM_133170.3	913	Gag/Aag	18/32	0.322225349387258	0	FACETS	0.489	0.376	0.619			1	SUBCLONAL	1	TRUE	0	0.322225349387258	0		578	172	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982143	201982143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	67	1028	1	ENST00000359651.3:c.667G>A	p.Asp223Asn	p.D223N	ENST00000359651		223	Gat/Aat	5/8	0.322225349387258	6	FACETS	0.886	0.774	1	0.443	0.387	0.503	CLONAL	2	TRUE	2	0.322225349387258	6		1029	386	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981162	201981162	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	52	925	0	ENST00000359651.3:c.241G>C	p.Glu81Gln	p.E81Q	ENST00000359651		81	Gag/Cag	2/8	0.322225349387258	6	FACETS	1	0.943	1	0.306	0.26	0.355	CLONAL	1	TRUE	2	0.322225349387258	6		925	434	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69788836	69788836	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	39	257	0	ENST00000352241.4:c.88C>A	p.Gln30Lys	p.Q30K	ENST00000352241	NM_198159.2	30	Caa/Aaa	1/10	0.142806820787552	4	FACETS	0.982	0.826	1	0.982	0.826	1	INDETERMINATE	2	TRUE	2	0.322225349387258	4		257	163	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257943	19257943	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762715467	NA	P-0057566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	40	1245	1	ENST00000162023.5:c.443C>T	p.Pro148Leu	p.P148L	ENST00000162023		148	cCg/cTg	9/13	1	2	FACETS	0.989	0.828	1	0.989	0.828	1	CLONAL	1	TRUE	1	0.322225349387258	2		1246	251	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983111	201983111	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	52	676	0	ENST00000359651.3:c.960G>C	p.Lys320Asn	p.K320N	ENST00000359651		320	aaG/aaC	7/8	0.322225349387258	6	FACETS	1	0.954	1	0.331	0.282	0.384	CLONAL	1	TRUE	2	0.322225349387258	6		676	401	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984450	201984450	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0057566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	48	602	0	ENST00000359651.3:c.1115G>C	p.Ter372SerextTer43	p.*372Sext*43	ENST00000359651		372	tGa/tCa	8/8	0.322225349387258	6	FACETS	1	0.959	1	0.359	0.305	0.419	CLONAL	1	TRUE	2	0.322225349387258	6		602	341	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873688	35873688	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	51	480	0	ENST00000216797.5:c.163G>C	p.Glu55Gln	p.E55Q	ENST00000216797	NM_020529.2	55	Gag/Cag	1/6	0.142806820787552	4	FACETS	1	0.958	1	0.679	0.581	0.786	INDETERMINATE	1	TRUE	2	0.322225349387258	4		480	308	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983130	201983130	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	45	616	0	ENST00000359651.3:c.979G>C	p.Glu327Gln	p.E327Q	ENST00000359651		327	Gag/Cag	7/8	0.322225349387258	6	FACETS	1	0.943	1	0.319	0.269	0.374	CLONAL	1	TRUE	2	0.322225349387258	6		616	360	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056198	27056199	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	63	619	0	ENST00000324856.7:c.1196dup	p.Asn399LysfsTer224	p.N399Kfs*224	ENST00000324856	NM_006015.4	398	-/A	2/20	0.142806820787552	4	FACETS	0.965	0.843	1	0.965	0.843	1	INDETERMINATE	2	TRUE	2	0.322225349387258	4		619	268	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981213	201981213	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	70	1062	0	ENST00000359651.3:c.292G>C	p.Asp98His	p.D98H	ENST00000359651		98	Gat/Cat	2/8	0.322225349387258	6	FACETS	0.757	0.662	0.859	0.378	0.331	0.43	SUBCLONAL	2	TRUE	2	0.322225349387258	6		1062	472	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981500	201981500	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	55	865	0	ENST00000359651.3:c.414G>C	p.Trp138Cys	p.W138C	ENST00000359651		138	tgG/tgC	3/8	0.322225349387258	6	FACETS	0.835	0.718	0.962	0.418	0.359	0.481	CLONAL	2	TRUE	2	0.322225349387258	6		865	336	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129346	64129346	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	44	1042	0	ENST00000334205.4:c.778C>G	p.Pro260Ala	p.P260A	ENST00000334205	NM_003942.2	260	Ccc/Gcc	8/17	0.142806820787552	4	FACETS	0.775	0.656	0.904	0.775	0.656	0.904	INDETERMINATE	2	TRUE	2	0.322225349387258	4		1042	233	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871632	35871632	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs762379232	NA	P-0057566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	35	311	0	ENST00000216797.5:c.874G>C	p.Glu292Gln	p.E292Q	ENST00000216797	NM_020529.2	292	Gag/Cag	5/6	0.142806820787552	4	FACETS	1	0.916	1	0.598	0.494	0.714	INDETERMINATE	1	TRUE	2	0.322225349387258	4		311	240	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873680	35873680	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	48	460	0	ENST00000216797.5:c.171G>T	p.Gln57His	p.Q57H	ENST00000216797	NM_020529.2	57	caG/caT	1/6	0.142806820787552	4	FACETS	1	0.949	1	0.644	0.547	0.749	INDETERMINATE	1	TRUE	2	0.322225349387258	4		460	306	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500459	99500459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	45	936	0	ENST00000268035.6:c.3892G>A	p.Glu1298Lys	p.E1298K	ENST00000268035	NM_000875.3	1298	Gag/Aag	21/21	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.322225349387258	2		936	250	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63537561	63537603	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACTGTACTCACCGGGAAATGAGGTAGAGACACTTGGCCATTG	GACTGTACTCACCGGGAAATGAGGTAGAGACACTTGGCCATTG	-	novel	NA	P-0057566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	38	400	0	ENST00000307078.5:c.1029_1059+12del		p.X343_splice	ENST00000307078	NM_004655.3	343		4/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.322225349387258	2		400	175	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61720109	61720109	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	41	367	0	ENST00000401558.2:c.1325G>C	p.Arg442Thr	p.R442T	ENST00000401558	NM_003400.3	442	aGa/aCa	13/25	0.142806820787552	4	FACETS	1	0.952	1	0.704	0.591	0.827	INDETERMINATE	1	TRUE	2	0.322225349387258	4		367	239	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440906	52440906	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867342588	NA	P-0057566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	32	833	0	ENST00000460680.1:c.598G>A	p.Glu200Lys	p.E200K	ENST00000460680	NM_004656.3	200	Gag/Aag	8/17	0.142806820787552	4	FACETS	0.732	0.594	0.886	0.366	0.297	0.443	INDETERMINATE	1	TRUE	2	0.322225349387258	4		833	359	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720856	176720856	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060501494	NA	P-0057566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	52	494	1	ENST00000439151.2:c.6487C>T	p.Gln2163Ter	p.Q2163*	ENST00000439151	NM_022455.4	2163	Cag/Tag	23/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.322225349387258	2		495	239	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652008	36652008	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	55	1021	0	ENST00000244741.5:c.130G>C	p.Glu44Gln	p.E44Q	ENST00000244741	NM_000389.4	44	Gag/Cag	2/3	0.142806820787552	4	FACETS	1	0.927	1	0.566	0.485	0.653	INDETERMINATE	1	TRUE	2	0.322225349387258	4		1021	399	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771367	68771372	+	splice_donor_variant,intron_variant	Splice_Site	ONP	GTACCC	GTACCC	ATACCT	novel	NA	P-0057566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	29	483	0	ENST00000261769.5:c.48+1_48+6delinsATACCT		p.X16_splice	ENST00000261769	NM_004360.3	16			0.322225349387258	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	0	0.322225349387258	1		483	125	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	287	777	0	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	0.955	0.901	1	0.955	0.901	1	CLONAL	1	TRUE	1	0.695383431047946	2		777	864	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40477038	40477038	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	245	570	0	ENST00000264657.5:c.1407G>C	p.Gln469His	p.Q469H	ENST00000264657	NM_139276.2	469	caG/caC	16/24	1	2	FACETS	0.971	0.911	1	0.971	0.911	1	CLONAL	1	TRUE	1	0.695383431047946	2		570	726	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023213	27023222	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGGCCCTA	GCGGGCCCTA	-	novel	NA	P-0057567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	98	248	0	ENST00000324856.7:c.320_329del	p.Ala107GlyfsTer4	p.A107Gfs*4	ENST00000324856	NM_006015.4	107	GCGGGCCCTAgg/gg	1/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.695383431047946	2		248	244	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	1215	619	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.197245040378556	28	FACETS	1	0.989	1			1	CLONAL	28	TRUE	NA	0.197245040378556	28		619	1558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0057568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	271	500	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.197245040378556	2	FACETS	1	0.971	1	1	0.994	1	CLONAL	3	TRUE	0	0.197245040378556	2		500	872	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874065	151874065	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	107	386	0	ENST00000262189.6:c.8473del	p.Glu2825LysfsTer38	p.E2825Kfs*38	ENST00000262189	NM_170606.2	2825	Gaa/aa	38/59	0.197245040378556	5	FACETS	1	0.961	1	1	0.961	1	CLONAL	3	TRUE	2	0.197245040378556	5		386	417	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44894175	44894175	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0057568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	60	369	0	ENST00000377967.4:c.565-1G>C		p.X189_splice	ENST00000377967	NM_021140.2	189			0.197245040378556	1	FACETS	0.79	0.684	0.904	1	0.972	1	CLONAL	2	TRUE	0	0.197245040378556	1		369	347	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	36	365	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.934	0.767	1	0.934	0.767	1	CLONAL	1	TRUE	1	0.16	2		365	482	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0057569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	27	210	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.130020678826804	3	FACETS	0.967	0.769	1	0.483	0.384	0.597	CLONAL	1	TRUE	1	0.16	3		210	377	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0057569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	104	378	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	1	2	FACETS	1	0.963	1	1	0.989	1	CLONAL	2	TRUE	1	0.16	2		378	561	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494149	140494149	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	179	701	0	ENST00000288602.6:c.1099C>T	p.Pro367Ser	p.P367S	ENST00000288602	NM_004333.4	367	Ccc/Tcc	8/18	1	2	FACETS	1	0.924	1	1	0.992	1	CLONAL	2	TRUE	1	0.16	2		701	1114	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790078	40790078	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	63	834	0	ENST00000373198.4:c.2653C>T	p.Gln885Ter	p.Q885*	ENST00000373198	NM_133170.3	885	Caa/Taa	18/32	1	2	FACETS	0.69	0.595	0.795	0.69	0.595	0.795	SUBCLONAL	1	TRUE	1	0.16	2		834	1141	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797804	42797804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141205881	NA	P-0057569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	81	1147	0	ENST00000575354.2:c.3856C>T	p.Arg1286Cys	p.R1286C	ENST00000575354	NM_015125.3	1286	Cgt/Tgt	16/20	1	2	FACETS	0.79	0.694	0.895	0.79	0.694	0.895	SUBCLONAL	1	TRUE	1	0.16	2		1147	1281	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692887	89692887	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	34	318	0	ENST00000371953.3:c.371G>T	p.Cys124Phe	p.C124F	ENST00000371953	NM_000314.4	124	tGt/tTt	5/9	1	2	FACETS	0.968	0.791	1	0.968	0.791	1	CLONAL	1	TRUE	1	0.16	2		318	439	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448526	49448526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371342351	NA	P-0057569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	53	653	2	ENST00000301067.7:c.185C>T	p.Pro62Leu	p.P62L	ENST00000301067	NM_003482.3	62	cCg/cTg	3/54	1	2	FACETS	0.756	0.643	0.881	0.756	0.643	0.881	SUBCLONAL	1	TRUE	1	0.16	2		655	876	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721370	176721370	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	63	691	0	ENST00000439151.2:c.7001C>G	p.Ser2334Cys	p.S2334C	ENST00000439151	NM_022455.4	2334	tCt/tGt	23/23	1	2	FACETS	0.909	0.785	1	0.909	0.785	1	CLONAL	1	TRUE	1	0.16	2		691	866	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170198	32170199	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1238	70	1283	1	ENST00000375023.3:c.3409_3410delinsTT	p.Pro1137Phe	p.P1137F	ENST00000375023	NM_004557.3	1137	CCc/TTc	21/30	1	2	FACETS	0.669	0.581	0.765	0.669	0.581	0.765	SUBCLONAL	1	TRUE	1	0.16	2		1284	1308	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945486	151945486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	100	1084	0	ENST00000262189.6:c.2033C>T	p.Ser678Phe	p.S678F	ENST00000262189	NM_170606.2	678	tCc/tTc	14/59	1	2	FACETS	0.929	0.827	1	0.929	0.827	1	CLONAL	1	TRUE	1	0.16	2		1084	1345	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372212	55372212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753414463	NA	P-0057569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	62	604	1	ENST00000297316.4:c.902G>A	p.Gly301Asp	p.G301D	ENST00000297316	NM_022454.3	301	gGc/gAc	2/2	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.16	2		605	767	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056425	26056427	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	rs774779034	NA	P-0057570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	122	370	0	ENST00000343677.2:c.230_232del	p.Asn77del	p.N77del	ENST00000343677	NM_005319.3	77	aACAgc/agc	1/1	0.297105597469815	5	FACETS	0.753	0.684	0.824			1	INDETERMINATE	2	TRUE	NA	0.643372300913718	5		370	495	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748114	43748114	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	83	440	0	ENST00000382044.4:c.2692C>A	p.Gln898Lys	p.Q898K	ENST00000382044	NM_001141980.1	898	Caa/Aaa	12/28	1	2	FACETS	0.847	0.746	0.955	0.847	0.746	0.955	CLONAL	1	TRUE	1	0.21664867899709	2		440	905	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934573	NA	P-0057572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	466	758	0	ENST00000269305.4:c.722C>A	p.Ser241Tyr	p.S241Y	ENST00000269305	NM_001126112.2	241	tCc/tAc	7/11	0.656855354382126	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.660196534950738	2		758	686	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419103	419103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	119	295	0	ENST00000399788.2:c.3244G>A	p.Val1082Ile	p.V1082I	ENST00000399788	NM_001042603.1	1082	Gta/Ata	22/28	0.650801935303548	3	FACETS	0.942	0.855	1	0.471	0.427	0.517	CLONAL	1	TRUE	1	0.660196534950738	3		295	509	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0057573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	75	381	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.248438357313811	1	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	0	0.248438357313811	1		382	527	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573229	64573229	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863224807	NA	P-0057573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	157	687	1	ENST00000312049.6:c.1063C>T	p.Arg355Trp	p.R355W	ENST00000312049	NM_130799.2	355	Cgg/Tgg	8/10	0.248438357313811	1	FACETS	0.857	0.783	0.935	0.857	0.783	0.935	CLONAL	1	TRUE	0	0.248438357313811	1		688	1291	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435658	18435658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143896492	NA	P-0057573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	30	197	0	ENST00000266497.5:c.643G>A	p.Gly215Arg	p.G215R	ENST00000266497		215	Gga/Aga	1/31	0.248438357313811	1	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	0	0.248438357313811	1		197	200	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523590	148523590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	36	217	0	ENST00000320356.2:c.863G>A	p.Arg288Gln	p.R288Q	ENST00000320356	NM_004456.4	288	cGa/cAa	8/20	1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	1	0.248438357313811	2		217	282	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22412956	22412956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553196096	NA	P-0057573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	15	112	0	ENST00000344548.3:c.203G>A	p.Arg68Gln	p.R68Q	ENST00000344548	NM_001039802.1	68	cGa/cAa	5/7	0.248438357313811	1	FACETS	0.789	0.582	1	0.789	0.582	1	CLONAL	1	TRUE	0	0.248438357313811	1		112	134	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032572	47032572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	231	426	0	ENST00000377604.3:c.478C>T	p.Arg160Trp	p.R160W	ENST00000377604	NM_001204468.1	160	Cgg/Tgg	5/24	1	1	FACETS	0.821	0.766	0.878	1	0.993	1	CLONAL	2	TRUE	0	0.248438357313811	1		426	992	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041774	42041774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773653972	NA	P-0057573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	64	357	0	ENST00000219905.7:c.5969C>T	p.Thr1990Met	p.T1990M	ENST00000219905	NM_001164273.1	1990	aCg/aTg	17/24	0.248438357313811	1	FACETS	0.817	0.708	0.936	0.817	0.708	0.936	CLONAL	1	TRUE	0	0.248438357313811	1		357	552	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549269	21549269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1278939497	NA	P-0057573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	247	819	0	ENST00000382592.4:c.3007G>A	p.Asp1003Asn	p.D1003N	ENST00000382592	NM_014572.2	1003	Gac/Aac	8/8	0.248438357313811	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.248438357313811	1		819	1410	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954332	48954332	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	45	240	1	ENST00000267163.4:c.1453T>A	p.Ser485Thr	p.S485T	ENST00000267163	NM_000321.2	485	Tct/Act	16/27	0.248438357313811	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.248438357313811	1		241	264	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712820	43712820	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1221	184	767	0	ENST00000382044.4:c.4364C>T	p.Thr1455Ile	p.T1455I	ENST00000382044	NM_001141980.1	1455	aCa/aTa	21/28	0.248438357313811	1	FACETS	0.923	0.85	1	0.923	0.85	1	CLONAL	1	TRUE	0	0.248438357313811	1		767	1405	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2137863	2137863	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0057573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1354	222	1034	1	ENST00000219476.3:c.4990-1G>T		p.X1664_splice	ENST00000219476	NM_000548.3	1664			0.248438357313811	1	FACETS	0.993	0.921	1	0.993	0.921	1	CLONAL	1	TRUE	0	0.248438357313811	1		1035	1576	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119746	70119746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	165	590	1	ENST00000245479.2:c.748G>A	p.Ala250Thr	p.A250T	ENST00000245479	NM_000346.3	250	Gct/Act	3/3	0.248438357313811	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.248438357313811	1		591	1073	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99175926	99175927	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	78	496	0	ENST00000074304.5:c.1840dup	p.Cys614LeufsTer6	p.C614Lfs*6	ENST00000074304	NM_001134224.1	613	cat/caTt	18/26	0.248438357313811	1	FACETS	0.573	0.502	0.649	0.573	0.502	0.649	SUBCLONAL	1	TRUE	0	0.248438357313811	1		496	960	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623262	52623263	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0057573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	57	249	0	ENST00000394830.3:c.2788_2789del	p.Lys930GlufsTer2	p.K930Efs*2	ENST00000394830	NM_018313.4	930	AAg/g	19/30	0.248438357313811	1	FACETS	0.937	0.806	1	0.937	0.806	1	CLONAL	1	TRUE	0	0.248438357313811	1		249	429	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197317	106197317	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	80	369	0	ENST00000380013.4:c.5650A>T	p.Thr1884Ser	p.T1884S	ENST00000380013	NM_001127208.2	1884	Acc/Tcc	11/11	0.248438357313811	1	FACETS	0.923	0.813	1	0.923	0.813	1	CLONAL	1	TRUE	0	0.248438357313811	1		369	611	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681594	30681594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762846533	NA	P-0057573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	122	529	0	ENST00000376406.3:c.503C>T	p.Ser168Leu	p.S168L	ENST00000376406	NM_014641.2	168	tCg/tTg	3/15	1	2	FACETS	0.986	0.89	1	0.986	0.89	1	CLONAL	1	TRUE	1	0.248438357313811	2		529	996	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057579-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	44	619	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.275443126356305	3	FACETS	0.9	0.763	1	0.9	0.763	1	CLONAL	2	TRUE	1	0.275443126356305	3		619	202	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0057579-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	25	359	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	1	0.797	1	1	0.797	1	CLONAL	1	TRUE	1	0.275443126356305	2		359	181	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68984737	68984737	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs951212628	NA	P-0057579-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	13	297	0	ENST00000288368.4:c.1501G>T	p.Asp501Tyr	p.D501Y	ENST00000288368	NM_024870.2	501	Gat/Tat	14/40	0.184069001107859	0	FACETS	0.834	0.604	1			1	CLONAL	1	TRUE	0	0.275443126356305	0		297	82	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0057582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	435	397	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.184421084209787	14	FACETS	1	0.971	1	0.783	0.75	0.817	CLONAL	10	FALSE	1	0.184421084209787	14		397	976	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032302	10032302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	102	519	1	ENST00000330684.3:c.521C>T	p.Thr174Ile	p.T174I	ENST00000330684	NM_001134407.1	174	aCc/aTc	3/13	0.0899825847431761	3	FACETS	0.867	0.776	0.963	0.867	0.776	0.963	INDETERMINATE	2	FALSE	1	0.184421084209787	3		520	697	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040905	47040905	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0057582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	136	387	0	ENST00000377604.3:c.1436-1G>C		p.X479_splice	ENST00000377604	NM_001204468.1	479			0.184421084209787	2	FACETS	0.891	0.814	0.971			1	CLONAL	3	FALSE	NA	0.184421084209787	2		387	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578498	7578499	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	G	novel	NA	P-0057582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	169	791	0	ENST00000269305.4:c.431_432delinsC	p.Gln144ProfsTer26	p.Q144Pfs*26	ENST00000269305	NM_001126112.2	144	cAG/cC	5/11	0.184421084209787	3	FACETS	0.841	0.772	0.914	0.841	0.772	0.914	CLONAL	2	FALSE	1	0.184421084209787	3		791	1190	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0057594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	536	636	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.382555934439952	4	FACETS	1	0.993	1	0.83	0.803	0.858	CLONAL	3	TRUE	0	0.553269896152217	4		636	906	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0057594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	409	361	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.553269896152217	3	FACETS	0.888	0.847	0.929	0.888	0.847	0.929	CLONAL	2	TRUE	1	0.553269896152217	3		361	1063	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557368	187557368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754907142	NA	P-0057594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	88	462	0	ENST00000441802.2:c.3994C>T	p.Arg1332Cys	p.R1332C	ENST00000441802	NM_005245.3	1332	Cgc/Tgc	6/27	0.428137780610605	3	FACETS	0.809	0.719	0.904	0.404	0.359	0.452	CLONAL	1	TRUE	1	0.553269896152217	3		462	502	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439518	220439518	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540215120	NA	P-0057594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	339	849	2	ENST00000243786.2:c.371G>A	p.Arg124His	p.R124H	ENST00000243786	NM_002191.3	124	cGc/cAc	2/2	0.428137780610605	3	FACETS	0.851	0.808	0.895	0.851	0.808	0.895	CLONAL	2	TRUE	1	0.553269896152217	3		851	919	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946463	71946463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367743824	NA	P-0057594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	176	848	0	ENST00000298229.2:c.2627C>T	p.Thr876Met	p.T876M	ENST00000298229	NM_001567.3	876	aCg/aTg	23/28	0.459345667971741	4	FACETS	0.929	0.855	1	0.31	0.285	0.336	CLONAL	1	TRUE	1	0.553269896152217	4		848	1064	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606058	81606058	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	261	505	0	ENST00000298171.2:c.728C>A	p.Ser243Tyr	p.S243Y	ENST00000298171	NM_000369.2	243	tCc/tAc	9/10	0.535013099408591	3	FACETS	0.865	0.815	0.916	0.865	0.815	0.916	CLONAL	2	TRUE	1	0.553269896152217	3		505	696	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434851	56434851	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	336	713	0	ENST00000407977.2:c.2286C>A	p.Cys762Ter	p.C762*	ENST00000407977		762	tgC/tgA	9/10	0.553269896152217	3	FACETS	0.912	0.866	0.958	0.912	0.866	0.958	CLONAL	2	TRUE	1	0.553269896152217	3		713	850	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953255	17953255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs992027786	NA	P-0057594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	413	1132	0	ENST00000458235.1:c.731G>A	p.Arg244Gln	p.R244Q	ENST00000458235	NM_000215.3	244	cGg/cAg	6/24	0.206691673588459	6	FACETS	0.845	0.805	0.886	0.845	0.805	0.886	INDETERMINATE	3	TRUE	3	0.553269896152217	6		1132	1241	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891654	151891654	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0057594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	129	224	0	ENST00000262189.6:c.4379-1G>A		p.X1460_splice	ENST00000262189	NM_170606.2	1460			0.367678535167528	5	FACETS	1	0.98	1	0.813	0.746	0.881	CLONAL	2	TRUE	2	0.553269896152217	5		224	350	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136845	69136845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437834644	NA	P-0057594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	185	287	0	ENST00000288368.4:c.4759C>T	p.Pro1587Ser	p.P1587S	ENST00000288368	NM_024870.2	1587	Cca/Tca	39/40	0.44132088397958	4	FACETS	0.889	0.826	0.954			1	CLONAL	2	TRUE	NA	0.553269896152217	4		287	584	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0057596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	238	458	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.333394838074724	5	FACETS	1	0.962	1	0.776	0.728	0.825	CLONAL	3	TRUE	1	0.333394838074724	5		458	690	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027160	49027160	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0057596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	125	370	0	ENST00000267163.4:c.1727C>G	p.Ser576Ter	p.S576*	ENST00000267163	NM_000321.2	576	tCa/tGa	18/27	0.181874362155973	3	FACETS	0.945	0.861	1	0.63	0.574	0.688	INDETERMINATE	2	TRUE	0	0.333394838074724	3		370	463	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900365	3900365	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750411228	NA	P-0057596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	113	835	0	ENST00000262367.5:c.731C>T	p.Thr244Met	p.T244M	ENST00000262367	NM_004380.2	244	aCg/aTg	2/31	0.205586102947779	3	FACETS	0.725	0.651	0.804	0.362	0.325	0.402	SUBCLONAL	1	TRUE	1	0.333394838074724	3		835	1091	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670438	246670438	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	161	738	1	ENST00000388985.4:c.82G>C	p.Glu28Gln	p.E28Q	ENST00000388985		28	Gag/Cag	1/12	0.333394838074724	4	FACETS	0.949	0.868	1	0.316	0.289	0.345	CLONAL	1	TRUE	1	0.333394838074724	4		739	1357	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784077	120784077	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1493	151	1355	1	ENST00000257552.2:c.908G>T	p.Arg303Leu	p.R303L	ENST00000257552	NM_002442.3	303	cGc/cTc	13/15	0.205586102947779	3	FACETS	0.643	0.585	0.704	0.321	0.292	0.352	SUBCLONAL	1	TRUE	1	0.333394838074724	3		1356	1644	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39240655	39240655	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	41	426	0	ENST00000402219.2:c.2113G>C	p.Glu705Gln	p.E705Q	ENST00000402219	NM_005633.3	705	Gaa/Caa	13/23	0.333394838074724	3	FACETS	0.525	0.436	0.623	0.262	0.218	0.312	SUBCLONAL	1	TRUE	1	0.333394838074724	3		426	547	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027043	48027043	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	84	443	0	ENST00000234420.5:c.1921G>C	p.Glu641Gln	p.E641Q	ENST00000234420	NM_000179.2	641	Gaa/Caa	4/10	0.333394838074724	3	FACETS	0.924	0.817	1	0.462	0.408	0.52	CLONAL	1	TRUE	1	0.333394838074724	3		443	636	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820851	32820851	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1562	127	1123	0	ENST00000354258.4:c.743C>G	p.Ser248Trp	p.S248W	ENST00000354258	NM_000593.5	248	tCg/tGg	1/11	0.23912865971047	5	FACETS	0.677	0.61	0.747	0.226	0.203	0.249	SUBCLONAL	1	TRUE	2	0.333394838074724	5		1123	1689	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0057598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	235	298	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.754	0.706	0.803	1	0.993	1	SUBCLONAL	2	TRUE	1	0.415898598250555	2		298	749	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659675	NA	P-0057598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	205	859	0	ENST00000269305.4:c.764T>C	p.Ile255Thr	p.I255T	ENST00000269305	NM_001126112.2	255	aTc/aCc	7/11	0.415898598250555	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.415898598250555	1		859	741	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479795	67479795	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs757106110	NA	P-0057598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	48	751	0	ENST00000327367.4:c.1102C>T	p.Arg368Ter	p.R368*	ENST00000327367	NM_005902.3	368	Cga/Tga	8/9	1	2	FACETS	0.289	0.243	0.339	0.289	0.243	0.339	SUBCLONAL	1	TRUE	1	0.415898598250555	2		751	800	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166815	32166815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	75	1203	3	ENST00000375023.3:c.4423C>T	p.Arg1475Cys	p.R1475C	ENST00000375023	NM_004557.3	1475	Cgc/Tgc	24/30	1	2	FACETS	0.33	0.288	0.375	0.33	0.288	0.375	SUBCLONAL	1	TRUE	1	0.415898598250555	2		1206	1094	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101062	27101074	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCGGCCCCCAG	AGGCGGCCCCCAG	-	novel	NA	P-0057598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	205	829	0	ENST00000324856.7:c.4345_4357del	p.Gly1449ThrfsTer28	p.G1449Tfs*28	ENST00000324856	NM_006015.4	1448	gcAGGCGGCCCCCAG/gc	18/20	0.348439611614309	1	FACETS	0.977	0.909	1	0.977	0.909	1	CLONAL	1	TRUE	0	0.415898598250555	1		829	799	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139627	202139627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	121	357	0	ENST00000358485.4:c.788G>A	p.Gly263Glu	p.G263E	ENST00000358485	NM_001080125.1	263	gGg/gAg	6/9	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.415898598250555	2		357	486	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	208	619	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.929	0.867	0.992	0.929	0.867	0.992	CLONAL	1	TRUE	1	0.71	2		619	631	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332152	70332153	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1196853334	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	115	245	2	ENST00000373644.4:c.65dup	p.Lys23GlufsTer37	p.K23Efs*37	ENST00000373644	NM_030625.2	19	-/A	2/12	1	2	FACETS	0.956	0.871	1	0.956	0.871	1	CLONAL	1	TRUE	1	0.71	2		247	339	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	261	529	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.71	2		529	705	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	293	312	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.71	2		312	790	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	544	436	3	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	1	0.973	1	1	0.998	1	CLONAL	2	TRUE	1	0.71	2		439	765	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	256	482	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.857	0.805	0.911	0.857	0.805	0.911	CLONAL	1	TRUE	1	0.71	2		483	841	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368388	225368388	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1366667901	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	145	308	0	ENST00000264414.4:c.1358del	p.Asn453ThrfsTer2	p.N453Tfs*2	ENST00000264414	NM_003590.4	453	aAc/ac	9/16	1	2	FACETS	0.977	0.9	1	0.977	0.9	1	CLONAL	1	TRUE	1	0.71	2		308	418	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	233	445	3	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	0.95	0.89	1	0.95	0.89	1	CLONAL	1	TRUE	1	0.71	2		448	691	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	443	868	3	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.71	2		871	1204	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380283	25380283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913528	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	285	459	1	ENST00000311936.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000311936	NM_004985.3	59	Gca/Aca	3/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.71	2		460	739	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168719	56168719	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	221	402	0	ENST00000399503.3:c.1573C>T	p.Gln525Ter	p.Q525*	ENST00000399503	NM_005921.1	525	Cag/Tag	9/20	1	2	FACETS	0.933	0.873	0.995	0.933	0.873	0.995	CLONAL	1	TRUE	1	0.71	2		402	667	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100913	27100913	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	282	667	1	ENST00000324856.7:c.4195C>T	p.Gln1399Ter	p.Q1399*	ENST00000324856	NM_006015.4	1399	Cag/Tag	18/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.71	2		668	772	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	328	566	0	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.71	2		566	825	SUCCESS
APC	324	MSKCC	GRCh37	5	112174412	112174412	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	117	238	0	ENST00000257430.4:c.3121C>T	p.Gln1041Ter	p.Q1041*	ENST00000257430	NM_000038.5	1041	Caa/Taa	16/16	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.71	2		238	321	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589623	67589634	+	inframe_deletion	In_Frame_Del	DEL	ATATGATAGATT	ATATGATAGATT	-	novel	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	60	195	0	ENST00000274335.5:c.1392_1403del	p.Asp464_Tyr467del	p.D464_Y467del	ENST00000274335		462	gaATATGATAGATTa/gaa	10/15	1	2	FACETS	0.65	0.566	0.74	0.65	0.566	0.74	SUBCLONAL	1	TRUE	1	0.71	2		195	260	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	380	869	10	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	1	2	FACETS	0.968	0.92	1	0.968	0.92	1	CLONAL	1	TRUE	1	0.71	2		879	1106	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098975	178098975	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1328994103	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	146	260	0	ENST00000397062.3:c.70T>C	p.Trp24Arg	p.W24R	ENST00000397062	NM_006164.4	24	Tgg/Cgg	2/5	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.71	2		260	382	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274304	5274304	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	382	982	7	ENST00000357368.4:c.143del	p.Gly48ValfsTer17	p.G48Vfs*17	ENST00000357368	NM_002850.3	48	gGt/gt	3/38	1	2	FACETS	0.967	0.919	1	0.967	0.919	1	CLONAL	1	TRUE	1	0.71	2		989	1113	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43730536	43730536	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	276	496	0	ENST00000382044.4:c.3177del	p.Thr1060ProfsTer36	p.T1060Pfs*36	ENST00000382044	NM_001141980.1	1059	ccC/cc	16/28	1	2	FACETS	0.984	0.928	1	0.984	0.928	1	CLONAL	1	TRUE	1	0.71	2		496	790	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	328	982	1	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	1	2	FACETS	0.659	0.622	0.698	0.659	0.622	0.698	SUBCLONAL	1	TRUE	1	0.71	2		983	1402	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748399150	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	405	998	7	ENST00000220592.5:c.1806del	p.Ala603ProfsTer92	p.A603Pfs*92	ENST00000220592	NM_012154.3	602	ccC/cc	14/19	1	2	FACETS	0.855	0.813	0.898	0.855	0.813	0.898	CLONAL	1	TRUE	1	0.71	2		1005	1334	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736511	85736511	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs387906351	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	191	286	6	ENST00000370580.1:c.136del	p.Ile46TyrfsTer24	p.I46Yfs*24	ENST00000370580	NM_003921.4	46	Ata/ta	2/3	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.71	2		292	521	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100975	41100975	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	295	725	0	ENST00000373198.4:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000373198	NM_133170.3	461	Cga/Tga	8/32	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.71	2		725	803	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570305	95570305	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs139786661	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	184	301	0	ENST00000393063.1:c.3428T>C	p.Leu1143Pro	p.L1143P	ENST00000393063	NM_030621.3	1143	cTa/cCa	22/28	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.71	2		301	510	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350611	89350613	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs1163513451	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	465	839	0	ENST00000301030.4:c.2337_2339del	p.Lys779del	p.K779del	ENST00000301030	NM_001256183.1	779	aaGAAt/aat	9/13	1	2	FACETS	0.955	0.912	0.998	0.955	0.912	0.998	CLONAL	1	TRUE	1	0.71	2		839	1372	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564559	55564559	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	260	638	0	ENST00000288135.5:c.450del	p.Cys151AlafsTer10	p.C151Afs*10	ENST00000288135	NM_000222.2	149	aaG/aa	3/21	1	2	FACETS	0.931	0.875	0.987	0.931	0.875	0.987	CLONAL	1	TRUE	1	0.71	2		638	787	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134897	41134897	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	197	378	0	ENST00000379561.5:c.731G>A	p.Gly244Asp	p.G244D	ENST00000379561	NM_002015.3	244	gGc/gAc	2/3	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.71	2		378	527	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941313	71941313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs927834612	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	379	1023	3	ENST00000298229.2:c.1088G>A	p.Arg363His	p.R363H	ENST00000298229	NM_001567.3	363	cGc/cAc	9/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.71	2		1026	1034	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702262	47702262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	146	507	0	ENST00000233146.2:c.1858G>A	p.Val620Ile	p.V620I	ENST00000233146	NM_000251.2	620	Gta/Ata	12/16	1	2	FACETS	0.547	0.5	0.596	0.547	0.5	0.596	SUBCLONAL	1	TRUE	1	0.71	2		507	752	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358526	67358526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	182	438	0	ENST00000327367.4:c.34G>A	p.Val12Met	p.V12M	ENST00000327367	NM_005902.3	12	Gtg/Atg	1/9	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.71	2		438	505	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075436	8075436	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	152	284	0	ENST00000377482.5:c.134T>A	p.Leu45Ter	p.L45*	ENST00000377482	NM_018948.3	45	tTa/tAa	3/4	1	2	FACETS	0.982	0.907	1	0.982	0.907	1	CLONAL	1	TRUE	1	0.71	2		284	436	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363603	40363603	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	291	578	0	ENST00000397332.2:c.626A>G	p.Gln209Arg	p.Q209R	ENST00000397332	NM_001033082.2	209	cAg/cGg	3/3	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.71	2		578	765	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097641	8097641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	147	318	0	ENST00000346208.3:c.23C>T	p.Pro8Leu	p.P8L	ENST00000346208		8	cCg/cTg	2/6	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.71	2		318	399	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170403	119170403	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	167	417	0	ENST00000264033.4:c.2633T>C	p.Leu878Ser	p.L878S	ENST00000264033	NM_005188.3	878	tTg/tCg	16/16	1	2	FACETS	0.831	0.768	0.896	0.831	0.768	0.896	CLONAL	1	TRUE	1	0.71	2		417	566	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023257	1023257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	79	512	0	ENST00000358495.3:c.998C>T	p.Ala333Val	p.A333V	ENST00000358495	NM_134424.2	333	gCt/gTt	11/12	0.3	2	FACETS	0.349	0.307	0.395			1	INDETERMINATE	1	TRUE	NA	0.71	2		512	637	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682456	37682456	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	214	476	0	ENST00000447079.4:c.3647A>G	p.Gln1216Arg	p.Q1216R	ENST00000447079	NM_015083.1	1216	cAg/cGg	13/14	1	2	FACETS	0.991	0.927	1	0.991	0.927	1	CLONAL	1	TRUE	1	0.71	2		476	608	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223066	1223066	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs768144275	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	406	917	0	ENST00000326873.7:c.1003A>G	p.Met335Val	p.M335V	ENST00000326873	NM_000455.4	335	Atg/Gtg	8/10	1	2	FACETS	0.972	0.926	1	0.972	0.926	1	CLONAL	1	TRUE	1	0.71	2		917	1177	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213101	39213101	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	483	914	0	ENST00000402219.2:c.3866G>T	p.Gly1289Val	p.G1289V	ENST00000402219	NM_005633.3	1289	gGg/gTg	23/23	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.71	2		914	1252	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387986	31387986	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	157	281	0	ENST00000328111.2:c.1787T>C	p.Ile596Thr	p.I596T	ENST00000328111	NM_006892.3	596	aTa/aCa	17/23	1	2	FACETS	0.904	0.835	0.976	0.904	0.835	0.976	CLONAL	1	TRUE	1	0.71	2		281	489	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053538	37053538	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	299	516	0	ENST00000231790.2:c.625A>G	p.Asn209Asp	p.N209D	ENST00000231790	NM_000249.3	209	Aat/Gat	8/19	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.71	2		516	836	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43746248	43746248	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	273	581	0	ENST00000523873.1:c.367C>A	p.Leu123Ile	p.L123I	ENST00000523873		123	Cta/Ata	4/8	1	2	FACETS	0.907	0.854	0.961	0.907	0.854	0.961	CLONAL	1	TRUE	1	0.71	2		581	848	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331691	8331691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	247	448	1	ENST00000356435.5:c.5425C>T	p.Pro1809Ser	p.P1809S	ENST00000356435		1809	Cca/Tca	33/35	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.71	2		449	676	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753923	133753923	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	267	536	0	ENST00000318560.5:c.1394del	p.Pro465GlnfsTer55	p.P465Qfs*55	ENST00000318560	NM_005157.4	464	tgC/tg	8/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.71	2		536	737	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223376	53223376	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	246	911	1	ENST00000375401.3:c.3983C>A	p.Pro1328His	p.P1328H	ENST00000375401	NM_004187.3	1328	cCt/cAt	23/26	1	2	FACETS	0.708	0.662	0.755	0.708	0.662	0.755	SUBCLONAL	1	TRUE	1	0.71	2		912	979	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500865	149500865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	97	817	0	ENST00000261799.4:c.2365G>A	p.Ala789Thr	p.A789T	ENST00000261799	NM_002609.3	789	Gca/Aca	17/23	1	2	FACETS	0.617	0.549	0.69	0.617	0.549	0.69	SUBCLONAL	1	TRUE	1	0.310109402563801	2		817	1014	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0057601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	577	351	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.677468246045642	4	FACETS	1	0.995	1			1	CLONAL	3	TRUE	NA	0.677468246045642	4		351	858	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	346	640	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.652987128117925	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.677468246045642	1		640	669	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	793	398	0	ENST00000263967.3:c.3012G>A	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atA	21/21	0.677468246045642	4	FACETS	1	0.997	1			1	CLONAL	3	TRUE	NA	0.677468246045642	4		398	1152	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791024	42791024	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1361309406	NA	P-0057601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	278	851	0	ENST00000575354.2:c.169G>A	p.Glu57Lys	p.E57K	ENST00000575354	NM_015125.3	57	Gag/Aag	2/20	1	2	FACETS	0.694	0.651	0.738	0.694	0.651	0.738	SUBCLONAL	1	TRUE	1	0.677468246045642	2		851	1183	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971124	21971125	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0057601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	240	642	0	ENST00000304494.5:c.233_234del	p.Leu78HisfsTer41	p.L78Hfs*41	ENST00000304494	NM_000077.4	78	cTC/c	2/3	0.677468246045642	1	FACETS	0.874	0.824	0.924	0.874	0.824	0.924	CLONAL	1	TRUE	0	0.677468246045642	1		642	536	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011144	12011144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	123	340	0	ENST00000353533.5:c.551C>T	p.Ser184Leu	p.S184L	ENST00000353533	NM_003010.3	184	tCg/tTg	5/11	0.652987128117925	1	FACETS	0.861	0.792	0.93	0.861	0.792	0.93	CLONAL	1	TRUE	0	0.677468246045642	1		340	279	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008412	71008412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368167189	NA	P-0057601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	149	357	0	ENST00000318789.4:c.2020G>A	p.Glu674Lys	p.E674K	ENST00000318789	NM_032682.5	674	Gag/Aag	21/21	0.652987128117925	1	FACETS	0.983	0.915	1	0.983	0.915	1	CLONAL	1	TRUE	0	0.677468246045642	1		357	296	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054660	5054660	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1466480406	NA	P-0057601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	135	289	0	ENST00000381652.3:c.712C>T	p.Gln238Ter	p.Q238*	ENST00000381652	NM_004972.3	238	Cag/Tag	7/25	0.677468246045642	1	FACETS	0.899	0.832	0.967	0.899	0.832	0.967	CLONAL	1	TRUE	0	0.677468246045642	1		289	293	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331767	68331767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	55	438	0	ENST00000487270.1:c.363G>A	p.Met121Ile	p.M121I	ENST00000487270	NM_133509.3	121	atG/atA	5/11	0.677468246045642	3	FACETS	0.288	0.245	0.334	0.144	0.122	0.167	SUBCLONAL	1	TRUE	1	0.677468246045642	3		438	756	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711032	114711032	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	33	308	0	ENST00000543371.1:c.256G>C	p.Ala86Pro	p.A86P	ENST00000543371	NM_001198531.1	86	Gcg/Ccg	2/14	1	2	FACETS	0.264	0.215	0.319	0.264	0.215	0.319	SUBCLONAL	1	TRUE	1	0.677468246045642	2		308	369	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948196	71948196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	498	1073	0	ENST00000298229.2:c.2908G>A	p.Glu970Lys	p.E970K	ENST00000298229	NM_001567.3	970	Gaa/Aaa	26/28	0.669337629136381	2	FACETS	1	0.961	1	0.502	0.481	0.525	CLONAL	1	TRUE	0	0.677468246045642	2		1073	1463	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217674	7217674	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	268	554	0	ENST00000380728.2:c.253C>T	p.Gln85Ter	p.Q85*	ENST00000380728		85	Cag/Tag	4/11	0.652987128117925	1	FACETS	0.884	0.836	0.931	0.884	0.836	0.931	CLONAL	1	TRUE	0	0.677468246045642	1		554	592	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258578	19258578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	475	1243	0	ENST00000162023.5:c.322G>A	p.Glu108Lys	p.E108K	ENST00000162023		108	Gag/Aag	8/13	1	2	FACETS	0.915	0.874	0.957	0.915	0.874	0.957	CLONAL	1	TRUE	1	0.677468246045642	2		1243	1532	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158655960	158655960	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	103	368	0	ENST00000263640.3:c.46C>A	p.Leu16Ile	p.L16I	ENST00000263640	NM_001105.4	16	Ctc/Atc	3/11	1	2	FACETS	0.597	0.537	0.661	0.597	0.537	0.661	SUBCLONAL	1	TRUE	1	0.677468246045642	2		368	509	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41560073	41560073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	152	297	0	ENST00000263253.7:c.3745G>A	p.Glu1249Lys	p.E1249K	ENST00000263253	NM_001429.3	1249	Gag/Aag	22/31	1	2	FACETS	0.955	0.88	1	0.955	0.88	1	CLONAL	1	TRUE	1	0.677468246045642	2		297	470	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628542	187628542	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	78	781	0	ENST00000441802.2:c.2440G>C	p.Asp814His	p.D814H	ENST00000441802	NM_005245.3	814	Gat/Cat	2/27	0.222755364369148	1	FACETS	0.153	0.134	0.174	0.153	0.134	0.174	INDETERMINATE	1	TRUE	0	0.677468246045642	1		781	993	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862994	117862994	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	183	381	0	ENST00000297338.2:c.1483G>C	p.Glu495Gln	p.E495Q	ENST00000297338	NM_006265.2	495	Gag/Cag	12/14	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.677468246045642	2		381	536	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27192495	27192495	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	198	461	0	ENST00000380036.4:c.1498G>C	p.Glu500Gln	p.E500Q	ENST00000380036	NM_000459.3	500	Gag/Cag	11/23	0.677468246045642	1	FACETS	0.934	0.877	0.991	0.934	0.877	0.991	CLONAL	1	TRUE	0	0.677468246045642	1		461	414	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849182	76849182	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	124	341	0	ENST00000373344.5:c.6094G>A	p.Glu2032Lys	p.E2032K	ENST00000373344	NM_000489.3	2032	Gaa/Aaa	26/35	1	2	FACETS	0.838	0.764	0.914	0.838	0.764	0.914	CLONAL	1	TRUE	1	0.677468246045642	2		341	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0057602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	487	789	3	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.376307433595955	3	FACETS	0.866	0.834	0.899	0.866	0.834	0.899	CLONAL	3	FALSE	0	0.512144670012	3		792	919	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871985	45871985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777095373	NA	P-0057602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	86	655	2	ENST00000391945.4:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000391945	NM_000400.3	88	cGa/cAa	5/23	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.512144670012	NA		657	955	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526439	66526439	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	35	398	0	ENST00000358598.2:c.995A>C	p.Asn332Thr	p.N332T	ENST00000358598	NM_212471.2	332	aAt/aCt	11/11	0.270993206563684	5	FACETS	0.396	0.323	0.477	0.132	0.107	0.159	INDETERMINATE	1	FALSE	2	0.512144670012	5		398	611	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391111	89391111	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	179	612	0	ENST00000336596.2:c.1177A>G	p.Thr393Ala	p.T393A	ENST00000336596	NM_005233.5	393	Acg/Gcg	5/17	0.493233937863105	3	FACETS	0.849	0.789	0.911	0.849	0.789	0.911	CLONAL	2	FALSE	1	0.512144670012	3		612	517	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0057603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	982	351	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.922625264389029	7	FACETS	0.991	0.975	1	0.991	0.975	1	CLONAL	6	TRUE	1	0.922625264389029	7		351	1184	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0057603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	362	668	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.922625264389029	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.922625264389029	1		668	422	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032306	42032306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747008860	NA	P-0057603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	325	701	0	ENST00000219905.7:c.4490C>T	p.Ser1497Leu	p.S1497L	ENST00000219905	NM_001164273.1	1497	tCa/tTa	14/24	0.922625264389029	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.922625264389029	1		701	370	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11194457	11194457	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	360	789	0	ENST00000361445.4:c.5197G>C	p.Ala1733Pro	p.A1733P	ENST00000361445	NM_004958.3	1733	Gct/Cct	37/58	NA	2	FACETS	0.971	0.926	1			1	INDETERMINATE	1	TRUE	NA	0.922625264389029	2		789	804	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0057604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	39	351	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.23	2		351	303	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106648	27106648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553153748	NA	P-0057604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	79	788	0	ENST00000324856.7:c.6259G>A	p.Gly2087Arg	p.G2087R	ENST00000324856	NM_006015.4	2087	Gga/Aga	20/20	1	2	FACETS	0.784	0.688	0.888	0.784	0.688	0.888	SUBCLONAL	1	TRUE	1	0.23	2		788	876	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0057604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	64	304	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.23	2		304	511	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0057604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	65	636	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.981	0.851	1	0.981	0.851	1	CLONAL	1	TRUE	1	0.23	2		636	576	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692948	89692949	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	60	559	0	ENST00000371953.3:c.437dup	p.Leu146PhefsTer34	p.L146Ffs*34	ENST00000371953	NM_000314.4	144	-/T	5/9	1	2	FACETS	0.966	0.833	1	0.966	0.833	1	CLONAL	1	TRUE	1	0.23	2		559	540	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436278	110436278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	39	296	2	ENST00000375856.3:c.2123C>T	p.Ala708Val	p.A708V	ENST00000375856	NM_003749.2	708	gCg/gTg	1/2	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.23	2		298	240	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654651	67654651	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	47	485	0	ENST00000264010.4:c.1138C>T	p.Gln380Ter	p.Q380*	ENST00000264010	NM_006565.3	380	Cag/Tag	6/12	1	2	FACETS	0.586	0.494	0.689	0.586	0.494	0.689	SUBCLONAL	1	TRUE	1	0.23	2		485	697	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023512	27023513	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	49	546	0	ENST00000324856.7:c.620dup	p.Asn209GlnfsTer191	p.N209Qfs*191	ENST00000324856	NM_006015.4	206	-/T	1/20	1	2	FACETS	0.543	0.459	0.637	0.543	0.459	0.637	SUBCLONAL	1	TRUE	1	0.23	2		546	784	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0057607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	183	627	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	0.985	0.911	1	0.985	0.911	1	CLONAL	1	TRUE	1	0.5250784363471	2		627	708	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061208	38061208	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1292426539	NA	P-0057607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	147	721	0	ENST00000250448.2:c.781C>G	p.Arg261Gly	p.R261G	ENST00000250448	NM_004496.3	261	Cgc/Ggc	2/2	1	2	FACETS	0.802	0.734	0.873	0.802	0.734	0.873	CLONAL	1	TRUE	1	0.5250784363471	2		721	698	SUCCESS
APC	324	MSKCC	GRCh37	5	112173747	112173748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0057607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	125	406	0	ENST00000257430.4:c.2457dup	p.Thr820AspfsTer24	p.T820Dfs*24	ENST00000257430	NM_000038.5	819	atg/atGg	16/16	0.5250784363471	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.5250784363471	1		406	303	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934575	NA	P-0057608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	314	841	0	ENST00000269305.4:c.733G>C	p.Gly245Arg	p.G245R	ENST00000269305	NM_001126112.2	245	Ggc/Cgc	7/11	0.769593210471283	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.769593210471283	1		841	466	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376700	118376700	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375852658	NA	P-0057608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	220	456	0	ENST00000534358.1:c.10093G>A	p.Val3365Ile	p.V3365I	ENST00000534358	NM_005933.3	3365	Gtc/Atc	27/36	0.769593210471283	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.769593210471283	1		456	327	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333620	70333620	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	170	471	0	ENST00000373644.4:c.1525C>A	p.Pro509Thr	p.P509T	ENST00000373644	NM_030625.2	509	Cca/Aca	2/12	1	2	FACETS	0.971	0.902	1	0.971	0.902	1	CLONAL	1	TRUE	1	0.769593210471283	2		471	455	SUCCESS
BLM	641	MSKCC	GRCh37	15	91308612	91308612	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	242	441	0	ENST00000355112.3:c.2161G>T	p.Val721Leu	p.V721L	ENST00000355112	NM_000057.2	721	Gta/Tta	9/22	0.769593210471283	4	FACETS	1	0.961	1	0.347	0.324	0.371	CLONAL	1	TRUE	1	0.769593210471283	4		441	1069	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199469672	NA	P-0057610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	248	740	0	ENST00000374080.3:c.131G>T	p.Gly44Val	p.G44V	ENST00000374080		44	gGt/gTt	2/45	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.617458382292661	2		740	743	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266134	41266134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	154	395	0	ENST00000349496.5:c.131C>T	p.Pro44Leu	p.P44L	ENST00000349496	NM_001904.3	44	cCt/cTt	3/15	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.617458382292661	2		395	499	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951071	48951116	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAGAAAGTATACTGAAAAGAGTGAAGGATATAGGATACATCTTT	AAAAGAAAGTATACTGAAAAGAGTGAAGGATATAGGATACATCTTT	-	novel	NA	P-0057611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	118	277	0	ENST00000267163.4:c.1236_1281del	p.Glu413ArgfsTer29	p.E413Rfs*29	ENST00000267163	NM_000321.2	411	ccAAAAGAAAGTATACTGAAAAGAGTGAAGGATATAGGATACATCTTT/cc	13/27	0.59109946772122	1	FACETS	0.931	0.853	1	0.931	0.853	1	CLONAL	1	TRUE	0	0.59109946772122	1		277	302	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257985	19257985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1427	140	1389	0	ENST00000162023.5:c.401C>T	p.Ala134Val	p.A134V	ENST00000162023		134	gCt/gTt	9/13	1	2	FACETS	0.302	0.274	0.332	0.302	0.274	0.332	SUBCLONAL	1	TRUE	1	0.59109946772122	2		1389	1567	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0057612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	165	328	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.65	2		328	472	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0057612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	193	636	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.982	0.913	1	0.982	0.913	1	CLONAL	1	TRUE	1	0.65	2		636	605	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	143	753	1	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	1	2	FACETS	0.531	0.484	0.581	0.531	0.484	0.581	SUBCLONAL	1	TRUE	1	0.65	2		754	828	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653835	89653835	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	84	435	0	ENST00000371953.3:c.133del	p.Val45TyrfsTer9	p.V45Yfs*9	ENST00000371953	NM_000314.4	45	Gta/ta	2/9	1	2	FACETS	0.769	0.685	0.857	0.769	0.685	0.857	SUBCLONAL	1	TRUE	1	0.65	2		435	336	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338671	70338671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	268	942	0	ENST00000374080.3:c.67G>T	p.Asp23Tyr	p.D23Y	ENST00000374080		23	Gat/Tat	1/45	1	2	FACETS	0.956	0.899	1	0.956	0.899	1	CLONAL	1	TRUE	1	0.65	2		942	863	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0057613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	157	227	1				ENST00000310581	NM_198253.2	-/1132			0.368298724717444	5	FACETS	1	0.968	1	0.73	0.673	0.789	CLONAL	2	TRUE	2	0.454954866731612	5		228	530	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244136	153244136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	68	604	0	ENST00000281708.4:c.2021G>A	p.Arg674Gln	p.R674Q	ENST00000281708	NM_033632.3	674	cGg/cAg	12/12	0.390221036715221	3	FACETS	0.602	0.523	0.686	0.301	0.261	0.343	SUBCLONAL	1	TRUE	1	0.454954866731612	3		604	610	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936066	44936067	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs886041899	NA	P-0057613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	123	245	0	ENST00000377967.4:c.2830dup	p.Tyr944LeufsTer5	p.Y944Lfs*5	ENST00000377967	NM_021140.2	943	att/aTtt	18/29	0.182873458292789	3	FACETS	0.988	0.917	1			1	INDETERMINATE	3	TRUE	NA	0.454954866731612	3		245	224	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809254	243809254	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	118	468	0	ENST00000263826.5:c.370C>A	p.Gln124Lys	p.Q124K	ENST00000263826	NM_005465.4	124	Caa/Aaa	4/13	0.132346832709135	6	FACETS	1	0.933	1			1	INDETERMINATE	2	TRUE	NA	0.454954866731612	6		468	479	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900238	101900238	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs201021249	NA	P-0057613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	64	407	0	ENST00000374994.4:c.672G>A	p.Trp224Ter	p.W224*	ENST00000374994	NM_004612.2	224	tgG/tgA	4/9	0.415784630188366	2	FACETS	1	0.916	1	0.531	0.464	0.601	CLONAL	1	TRUE	0	0.454954866731612	2		407	265	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332807	65332807	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	73	468	0	ENST00000342505.4:c.732C>G	p.Phe244Leu	p.F244L	ENST00000342505	NM_002227.2	244	ttC/ttG	7/25	0.39136693438963	3	FACETS	0.916	0.804	1	0.458	0.402	0.518	CLONAL	1	TRUE	1	0.454954866731612	3		468	430	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743359	743359	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	125	470	0	ENST00000314574.4:c.781C>G	p.Gln261Glu	p.Q261E	ENST00000314574	NM_005433.3	261	Cag/Gag	7/12	0.218658893759937	2	FACETS	1	0.982	1	0.659	0.601	0.718	INDETERMINATE	1	TRUE	0	0.454954866731612	2		470	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0057614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	382	500	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.826528179721594	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.826528179721594	1		500	532	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727894	78727894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778029024	NA	P-0057614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	346	758	0	ENST00000306801.3:c.739G>A	p.Glu247Lys	p.E247K	ENST00000306801	NM_020761.2	247	Gag/Aag	6/34	0.826528179721594	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.826528179721594	1		758	468	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	20	365	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.901	0.694	1	0.901	0.694	1	CLONAL	1	TRUE	1	0.275718113642036	2		365	161	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	67	1019	1	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	1	2	FACETS	0.771	0.67	0.881	0.771	0.67	0.881	SUBCLONAL	1	TRUE	1	0.275718113642036	2		1020	630	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607173	189607173	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	64	1020	0	ENST00000264731.3:c.1552G>A	p.Gly518Arg	p.G518R	ENST00000264731	NM_003722.4	518	Gga/Aga	12/14	1	2	FACETS	0.744	0.644	0.852	0.744	0.644	0.852	SUBCLONAL	1	TRUE	1	0.275718113642036	2		1020	624	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437106	110437106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	12	133	1	ENST00000375856.3:c.1295C>T	p.Ser432Phe	p.S432F	ENST00000375856	NM_003749.2	432	tCc/tTc	1/2	NA	2	FACETS	1	0.822	1			1	INDETERMINATE	1	TRUE	NA	0.275718113642036	2		134	71	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858184	9858184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	43	698	1	ENST00000330684.3:c.3217G>A	p.Glu1073Lys	p.E1073K	ENST00000330684	NM_001134407.1	1073	Gaa/Aaa	13/13	0.275718113642036	1	FACETS	0.607	0.508	0.716	0.607	0.508	0.716	SUBCLONAL	1	TRUE	0	0.275718113642036	1		699	443	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872213	45872213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	66	913	0	ENST00000391945.4:c.221C>T	p.Ser74Leu	p.S74L	ENST00000391945	NM_000400.3	74	tCa/tTa	4/23	0.275718113642036	1	FACETS	0.753	0.654	0.86	0.753	0.654	0.86	SUBCLONAL	1	TRUE	0	0.275718113642036	1		913	548	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962530	100962530	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752817186	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	46	543	1	ENST00000325455.5:c.1867C>T	p.Arg623Cys	p.R623C	ENST00000325455	NM_001202474.3	623	Cgc/Tgc	3/8	1	2	FACETS	0.781	0.659	0.916	0.781	0.659	0.916	CLONAL	1	TRUE	1	0.275718113642036	2		544	427	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274851	38274851	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519898	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	33	656	0	ENST00000425967.3:c.1729A>G	p.Asn577Asp	p.N577D	ENST00000425967	NM_001174067.1	577	Aac/Gac	13/19	0.275918576986986	1	FACETS	0.533	0.434	0.644	0.533	0.434	0.644	SUBCLONAL	1	TRUE	0	0.275718113642036	1		656	387	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	24	227	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.951	0.751	1	0.951	0.751	1	CLONAL	1	TRUE	1	0.275718113642036	2		227	183	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs753143066	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	61	684	7	ENST00000295797.4:c.826dup	p.Thr276AsnfsTer16	p.T276Nfs*16	ENST00000295797	NM_002740.5	273	tta/ttAa	9/18	0.275718113642036	1	FACETS	0.807	0.697	0.925	0.807	0.697	0.925	CLONAL	1	TRUE	0	0.275718113642036	1		691	473	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046410	69046410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868582467	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	58	646	0	ENST00000288368.4:c.3883G>A	p.Glu1295Lys	p.E1295K	ENST00000288368	NM_024870.2	1295	Gaa/Aaa	32/40	0.275718113642036	1	FACETS	0.737	0.634	0.849	0.737	0.634	0.849	SUBCLONAL	1	TRUE	0	0.275718113642036	1		646	492	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945055	31945055	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868513155	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	64	989	1	ENST00000340398.3:c.46G>A	p.Ala16Thr	p.A16T	ENST00000340398	NM_001013699.2	16	Gcc/Acc	1/1	1	2	FACETS	0.853	0.74	0.977	0.853	0.74	0.977	CLONAL	1	TRUE	1	0.275718113642036	2		990	544	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945058	151945058	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	32	555	0	ENST00000262189.6:c.2461C>T	p.Pro821Ser	p.P821S	ENST00000262189	NM_170606.2	821	Cca/Tca	14/59	1	2	FACETS	0.563	0.457	0.683	0.563	0.457	0.683	SUBCLONAL	1	TRUE	1	0.275718113642036	2		555	412	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390923	89390923	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	42	397	0	ENST00000336596.2:c.989G>A	p.Arg330Lys	p.R330K	ENST00000336596	NM_005233.5	330	aGa/aAa	5/17	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.275718113642036	2		397	295	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622363	1622363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	44	1190	1	ENST00000344749.5:c.601C>T	p.Pro201Ser	p.P201S	ENST00000344749	NM_001136139.2	201	Ccg/Tcg	9/19	0.275718113642036	1	FACETS	0.517	0.433	0.61	0.517	0.433	0.61	SUBCLONAL	1	TRUE	0	0.275718113642036	1		1191	532	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55962453	55962453	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	52	488	0	ENST00000263923.4:c.2671C>T	p.His891Tyr	p.H891Y	ENST00000263923	NM_002253.2	891	Cat/Tat	19/30	1	2	FACETS	0.982	0.839	1	0.982	0.839	1	CLONAL	1	TRUE	1	0.275718113642036	2		488	384	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746144	162746144	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	32	311	0	ENST00000367921.3:c.2267G>T	p.Trp756Leu	p.W756L	ENST00000367921	NM_006182.2	756	tGg/tTg	16/18	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.275718113642036	2		311	222	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740736	145740736	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	56	1081	0	ENST00000428558.2:c.1364C>T	p.Ser455Phe	p.S455F	ENST00000428558	NM_004260.3	455	tCc/tTc	7/22	1	2	FACETS	0.78	0.668	0.901	0.78	0.668	0.901	CLONAL	1	TRUE	1	0.275718113642036	2		1081	521	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169498	27169498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	55	466	1	ENST00000380036.4:c.499C>T	p.Arg167Trp	p.R167W	ENST00000380036	NM_000459.3	167	Cgg/Tgg	4/23	1	2	FACETS	0.985	0.845	1	0.985	0.845	1	CLONAL	1	TRUE	1	0.275718113642036	2		467	405	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739823	46739823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374567435	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	36	457	0	ENST00000371975.4:c.1624C>T	p.Arg542Cys	p.R542C	ENST00000371975	NM_003579.3	542	Cgc/Tgc	15/18	1	2	FACETS	0.766	0.631	0.916	0.766	0.631	0.916	CLONAL	1	TRUE	1	0.275718113642036	2		457	341	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456642	32456643	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	32	234	0	ENST00000332351.3:c.249_250delinsTT	p.Pro84Ser	p.P84S	ENST00000332351	NM_024426.4	83	gtCCcc/gtTTcc	1/10	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.275718113642036	2		234	179	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445710	49445710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	578	1351	2	ENST00000301067.7:c.1756G>A	p.Glu586Lys	p.E586K	ENST00000301067	NM_003482.3	586	Gaa/Aaa	10/54	0.275718113642036	8	FACETS	1	0.981	1			1	CLONAL	6	TRUE	NA	0.275718113642036	8		1353	1243	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959076	28959076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	39	443	0	ENST00000282397.4:c.2062C>T	p.Pro688Ser	p.P688S	ENST00000282397	NM_002019.4	688	Ccc/Tcc	14/30	1	2	FACETS	0.763	0.633	0.906	0.763	0.633	0.906	CLONAL	1	TRUE	1	0.275718113642036	2		443	371	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066863	30066864	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	46	646	1	ENST00000331968.5:c.2267_2268delinsAA	p.Arg756Lys	p.R756K	ENST00000331968	NM_002742.2	756	aGG/aAA	16/18	1	2	FACETS	0.704	0.593	0.826	0.704	0.593	0.826	SUBCLONAL	1	TRUE	1	0.275718113642036	2		647	474	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029584	14029585	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	28	306	1	ENST00000311895.7:c.1795_1796delinsTT	p.Pro599Phe	p.P599F	ENST00000311895	NM_005236.2	599	CCt/TTt	8/11	0.275718113642036	1	FACETS	0.692	0.555	0.847	0.692	0.555	0.847	SUBCLONAL	1	TRUE	0	0.275718113642036	1		307	253	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118324	17118324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376715412	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	92	936	0	ENST00000285071.4:c.1513G>A	p.Val505Ile	p.V505I	ENST00000285071	NM_144997.5	505	Gtc/Atc	13/14	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.275718113642036	2		936	516	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527559	29527559	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	41	609	0	ENST00000356175.3:c.1008G>A	p.Trp336Ter	p.W336*	ENST00000356175	NM_000267.3	336	tgG/tgA	9/57	1	2	FACETS	0.621	0.517	0.736	0.621	0.517	0.736	SUBCLONAL	1	TRUE	1	0.275718113642036	2		609	479	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29662002	29662002	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876659070	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	55	438	0	ENST00000356175.3:c.5896C>T	p.Gln1966Ter	p.Q1966*	ENST00000356175	NM_000267.3	1966	Cag/Tag	39/57	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.275718113642036	2		438	385	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138516	11138516	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	47	781	0	ENST00000358026.2:c.3272A>C	p.Lys1091Thr	p.K1091T	ENST00000358026	NM_001128849.1	1091	aAa/aCa	24/36	0.275718113642036	1	FACETS	0.624	0.527	0.731	0.624	0.527	0.731	SUBCLONAL	1	TRUE	0	0.275718113642036	1		781	471	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302859	15302860	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	46	1209	1	ENST00000263388.2:c.590_591delinsTT	p.Pro197Leu	p.P197L	ENST00000263388	NM_000435.2	197	cCC/cTT	4/33	0.275718113642036	1	FACETS	0.524	0.441	0.616	0.524	0.441	0.616	SUBCLONAL	1	TRUE	0	0.275718113642036	1		1210	549	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367894	15367894	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	56	1133	0	ENST00000263377.2:c.1432A>G	p.Lys478Glu	p.K478E	ENST00000263377	NM_058243.2	478	Aag/Gag	8/20	0.275718113642036	1	FACETS	0.665	0.57	0.768	0.665	0.57	0.768	SUBCLONAL	1	TRUE	0	0.275718113642036	1		1133	527	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765798	41765798	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	30	609	0	ENST00000301178.4:c.2674G>A	p.Asp892Asn	p.D892N	ENST00000301178	NM_021913.4	892	Gat/Aat	20/20	0.275718113642036	1	FACETS	0.557	0.449	0.678	0.557	0.449	0.678	SUBCLONAL	1	TRUE	0	0.275718113642036	1		609	337	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798810	42798810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	59	1065	0	ENST00000575354.2:c.4382C>T	p.Ser1461Phe	p.S1461F	ENST00000575354	NM_015125.3	1461	tCc/tTc	19/20	0.275718113642036	1	FACETS	0.673	0.579	0.775	0.673	0.579	0.775	SUBCLONAL	1	TRUE	0	0.275718113642036	1		1065	548	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031250	36031250	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	43	818	0	ENST00000358208.4:c.1369G>A	p.Glu457Lys	p.E457K	ENST00000358208		457	Gag/Aag	11/12	1	2	FACETS	0.661	0.553	0.78	0.661	0.553	0.78	SUBCLONAL	1	TRUE	1	0.275718113642036	2		818	472	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660068	12660069	+	missense_variant	Missense_Mutation	DNP	AG	AG	GA	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	52	483	0	ENST00000251849.4:c.152_153delinsTC	p.Pro51Leu	p.P51L	ENST00000251849	NM_002880.3	51	cCT/cTC	2/17	1	2	FACETS	0.865	0.738	1	0.865	0.738	1	CLONAL	1	TRUE	1	0.275718113642036	2		483	436	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438559	52438559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	49	649	0	ENST00000460680.1:c.1160C>T	p.Pro387Leu	p.P387L	ENST00000460680	NM_004656.3	387	cCa/cTa	12/17	1	2	FACETS	0.766	0.649	0.894	0.766	0.649	0.894	SUBCLONAL	1	TRUE	1	0.275718113642036	2		649	464	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502850	186502850	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	62	533	0	ENST00000323963.5:c.308A>G	p.Gln103Arg	p.Q103R	ENST00000323963		103	cAa/cGa	4/11	1	2	FACETS	0.868	0.751	0.995	0.868	0.751	0.995	CLONAL	1	TRUE	1	0.275718113642036	2		533	518	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1255481	1255481	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	37	695	1	ENST00000310581.5:c.3078G>A	p.Trp1026Ter	p.W1026*	ENST00000310581	NM_198253.2	1026	tgG/tgA	14/16	1	2	FACETS	0.729	0.602	0.871	0.729	0.602	0.871	SUBCLONAL	1	TRUE	1	0.275718113642036	2		696	368	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005542	150005542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	57	507	0	ENST00000253339.5:c.683C>T	p.Pro228Leu	p.P228L	ENST00000253339		228	cCt/cTt	3/7	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.275718113642036	2		507	395	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845992	128845993	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	TC	TC	CT	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	32	634	0	ENST00000249373.3:c.922_923delinsCT	p.Ser308Leu	p.S308L	ENST00000249373	NM_005631.4	308	TCc/CTc	5/12	1	2	FACETS	0.54	0.438	0.655	0.54	0.438	0.655	SUBCLONAL	1	TRUE	1	0.275718113642036	2		634	430	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506483	148506483	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	29	244	0	ENST00000320356.2:c.2030-1G>A		p.X677_splice	ENST00000320356	NM_004456.4	677			1	2	FACETS	0.759	0.611	0.927	0.759	0.611	0.927	CLONAL	1	TRUE	1	0.275718113642036	2		244	277	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279455	38279455	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755595684	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	44	588	0	ENST00000425967.3:c.1034C>T	p.Ala345Val	p.A345V	ENST00000425967	NM_001174067.1	345	gCt/gTt	9/19	0.275918576986986	1	FACETS	0.784	0.66	0.921	0.784	0.66	0.921	CLONAL	1	TRUE	0	0.275718113642036	1		588	351	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485247	8485247	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	39	464	0	ENST00000356435.5:c.3133A>G	p.Asn1045Asp	p.N1045D	ENST00000356435		1045	Aac/Gac	18/35	1	2	FACETS	0.799	0.664	0.949	0.799	0.664	0.949	CLONAL	1	TRUE	1	0.275718113642036	2		464	354	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912004	127912004	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	57	430	0	ENST00000373547.4:c.866C>T	p.Pro289Leu	p.P289L	ENST00000373547	NM_002721.4	289	cCa/cTa	7/7	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.275718113642036	2		430	393	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041197	47041197	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	48	1068	1	ENST00000377604.3:c.1625C>T	p.Pro542Leu	p.P542L	ENST00000377604	NM_001204468.1	542	cCt/cTt	15/24	0.275718113642036	1	FACETS	0.523	0.442	0.613	0.523	0.442	0.613	SUBCLONAL	1	TRUE	0	0.275718113642036	1		1069	574	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410829	63410829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	48	846	0	ENST00000330258.3:c.2338G>A	p.Gly780Arg	p.G780R	ENST00000330258	NM_152424.3	780	Ggg/Agg	2/2	0.275718113642036	1	FACETS	0.606	0.513	0.71	0.606	0.513	0.71	SUBCLONAL	1	TRUE	0	0.275718113642036	1		846	495	SUCCESS
AR	367	MSKCC	GRCh37	X	66905958	66905958	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	49	438	0	ENST00000374690.3:c.1875G>A	p.Met625Ile	p.M625I	ENST00000374690	NM_000044.3	625	atG/atA	3/8	0.275718113642036	1	FACETS	0.881	0.749	1	0.881	0.749	1	CLONAL	1	TRUE	0	0.275718113642036	1		438	348	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874635	35874636	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	32	464	0	ENST00000303115.3:c.791_792delinsAA	p.Trp264Ter	p.W264*	ENST00000303115	NM_002185.3	264	tGG/tAA	6/8	1	2	FACETS	0.579	0.47	0.702	0.579	0.47	0.702	SUBCLONAL	1	TRUE	1	0.275718113642036	2		464	401	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139794934	139794936	+	missense_variant	Missense_Mutation	TNP	GAT	GAT	AAA	novel	NA	P-0057628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	41	703	0	ENST00000247668.2:c.328_330delinsAAA	p.Asp110Lys	p.D110K	ENST00000247668	NM_021138.3	110	GAT/AAA	4/11	1	2	FACETS	0.633	0.527	0.75	0.633	0.527	0.75	SUBCLONAL	1	TRUE	1	0.275718113642036	2		703	470	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	46	335	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.693	0.587	0.809	0.693	0.587	0.809	SUBCLONAL	1	TRUE	1	0.45	2		335	295	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	85	295	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.741	0.657	0.83	0.741	0.657	0.83	SUBCLONAL	1	TRUE	1	0.45	2		295	510	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	339	454	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.923	0.878	0.969	1	0.996	1	CLONAL	2	TRUE	1	0.45	2		460	816	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	176	662	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.954	0.88	1	0.954	0.88	1	CLONAL	1	TRUE	1	0.45	2		664	820	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052632	42052632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779811318	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	29	460	0	ENST00000219905.7:c.7303C>T	p.Arg2435Trp	p.R2435W	ENST00000219905	NM_001164273.1	2435	Cgg/Tgg	20/24	0.115307693854542	1	FACETS	0.199	0.159	0.245	0.199	0.159	0.245	INDETERMINATE	1	TRUE	0	0.45	1		460	502	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	127	521	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.962	0.874	1	0.962	0.874	1	CLONAL	1	TRUE	1	0.45	2		527	587	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	136	752	0	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	1	2	FACETS	0.956	0.872	1	0.956	0.872	1	CLONAL	1	TRUE	1	0.45	2		752	632	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	64	334	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.847	0.738	0.963	0.847	0.738	0.963	CLONAL	1	TRUE	1	0.45	2		334	336	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	42	374	4	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	2	FACETS	0.712	0.599	0.837	0.712	0.599	0.837	SUBCLONAL	1	TRUE	1	0.45	2		378	262	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	50	218	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.682	0.581	0.791	0.682	0.581	0.791	SUBCLONAL	1	TRUE	1	0.45	2		218	326	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574678	41574679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs754418509	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	60	1066	0	ENST00000263253.7:c.6970dup	p.His2324ProfsTer55	p.H2324Pfs*55	ENST00000263253	NM_001429.3	2321	-/C	31/31	1	2	FACETS	0.266	0.228	0.308	0.266	0.228	0.308	SUBCLONAL	1	TRUE	1	0.45	2		1066	1001	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003747	45003747	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs1057519877	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	126	611	0	ENST00000558401.1:c.3G>A	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	atG/atA	1/4	0.115307693854542	1	FACETS	1	0.933	1	1	0.933	1	INDETERMINATE	1	TRUE	0	0.45	1		611	423	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821594	72821596	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs374416547	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	14	127	0	ENST00000268489.5:c.10579_10581del	p.Gly3527del	p.G3527del	ENST00000268489	NM_006885.3	3527	GGC/-	10/10	1	2	FACETS	0.604	0.442	0.795	0.604	0.442	0.795	SUBCLONAL	1	TRUE	1	0.45	2		127	103	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102188	27102188	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs61756316	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	109	409	0	ENST00000324856.7:c.5114A>G	p.Asn1705Ser	p.N1705S	ENST00000324856	NM_006015.4	1705	aAc/aGc	19/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.45	2		409	431	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030692	48030692	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs267608092	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	90	394	2	ENST00000234420.5:c.3312del	p.Phe1104LeufsTer11	p.F1104Lfs*11	ENST00000234420	NM_000179.2	1102	acT/ac	5/10	1	2	FACETS	0.832	0.741	0.928	0.832	0.741	0.928	CLONAL	1	TRUE	1	0.45	2		396	481	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205756	108205756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531980488	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	80	371	1	ENST00000278616.4:c.8071C>T	p.Arg2691Cys	p.R2691C	ENST00000278616	NM_000051.3	2691	Cgc/Tgc	55/63	1	2	FACETS	0.829	0.733	0.931	0.829	0.733	0.931	CLONAL	1	TRUE	1	0.45	2		372	429	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511667	38511667	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773956341	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	116	662	3	ENST00000254066.5:c.1165G>A	p.Ala389Thr	p.A389T	ENST00000254066	NM_000964.3	389	Gcc/Acc	8/9	1	2	FACETS	0.908	0.821	0.999	0.908	0.821	0.999	CLONAL	1	TRUE	1	0.45	2		665	568	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751037	128751037	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	107	635	0	ENST00000377970.2:c.574T>C	p.Tyr192His	p.Y192H	ENST00000377970	NM_002467.4	192	Tac/Cac	2/3	1	2	FACETS	0.901	0.811	0.995	0.901	0.811	0.995	CLONAL	1	TRUE	1	0.45	2		635	528	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437606	56437606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886926322	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	100	532	1	ENST00000407977.2:c.856C>T	p.Arg286Trp	p.R286W	ENST00000407977		286	Cgg/Tgg	8/10	1	2	FACETS	0.889	0.797	0.985	0.889	0.797	0.985	CLONAL	1	TRUE	1	0.45	2		533	500	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225365195	225365195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	88	267	0	ENST00000264414.4:c.1495G>A	p.Gly499Ser	p.G499S	ENST00000264414	NM_003590.4	499	Ggt/Agt	11/16	1	2	FACETS	0.956	0.852	1	0.956	0.852	1	CLONAL	1	TRUE	1	0.45	2		267	409	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836623	89836623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137913973	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	212	1039	2	ENST00000389301.3:c.2267G>A	p.Arg756His	p.R756H	ENST00000389301	NM_000135.2	756	cGt/cAt	25/43	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.45	2		1041	866	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165283	47165283	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	100	367	0	ENST00000409792.3:c.843del	p.Glu282LysfsTer19	p.E282Kfs*19	ENST00000409792	NM_014159.6	281	aaA/aa	3/21	1	2	FACETS	0.97	0.871	1	0.97	0.871	1	CLONAL	1	TRUE	1	0.45	2		367	458	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67646013	67646014	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs1470210640	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	46	466	0	ENST00000264010.4:c.950_951del	p.Thr317ArgfsTer91	p.T317Rfs*91	ENST00000264010	NM_006565.3	314	aAC/a	4/12	1	2	FACETS	0.349	0.293	0.41	0.349	0.293	0.41	SUBCLONAL	1	TRUE	1	0.45	2		466	586	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710652	114710652	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	108	518	0	ENST00000543371.1:c.137C>A	p.Ser46Ter	p.S46*	ENST00000543371	NM_001198531.1	46	tCg/tAg	1/14	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.45	2		518	472	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770090	56770090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876659683	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	45	691	0	ENST00000337432.4:c.86C>T	p.Ser29Phe	p.S29F	ENST00000337432	NM_058216.2	29	tCt/tTt	1/9	1	2	FACETS	0.331	0.277	0.39	0.331	0.277	0.39	SUBCLONAL	1	TRUE	1	0.45	2		691	605	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250227	110250227	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	176	866	1	ENST00000374672.4:c.448T>C	p.Phe150Leu	p.F150L	ENST00000374672	NM_004235.4	150	Ttc/Ctc	3/5	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.45	2		867	728	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825519	50825519	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	82	434	2	ENST00000398568.2:c.2156del	p.Asn719MetfsTer13	p.N719Mfs*13	ENST00000398568	NM_001042412.1	717	gAa/ga	14/18	1	2	FACETS	0.813	0.72	0.912	0.813	0.72	0.912	CLONAL	1	TRUE	1	0.45	2		436	448	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551595	150551595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	44	741	0	ENST00000369026.2:c.412C>T	p.Pro138Ser	p.P138S	ENST00000369026	NM_021960.4	138	Ccg/Tcg	1/3	1	2	FACETS	0.256	0.214	0.303	0.256	0.214	0.303	SUBCLONAL	1	TRUE	1	0.45	2		741	764	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383903	15383903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324868843	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	105	508	1	ENST00000263377.2:c.8C>T	p.Ala3Val	p.A3V	ENST00000263377	NM_058243.2	3	gCg/gTg	2/20	1	2	FACETS	0.858	0.771	0.949	0.858	0.771	0.949	CLONAL	1	TRUE	1	0.45	2		509	544	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660775	227660775	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	149	804	1	ENST00000305123.5:c.2680G>T	p.Gly894Trp	p.G894W	ENST00000305123	NM_005544.2	894	Ggg/Tgg	1/2	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.45	2		805	633	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772901	135772901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748845915	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	165	723	0	ENST00000298552.3:c.2722C>T	p.Arg908Trp	p.R908W	ENST00000298552	NM_001162426.1	908	Cgg/Tgg	21/23	1	2	FACETS	0.943	0.867	1	0.943	0.867	1	CLONAL	1	TRUE	1	0.45	2		723	778	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332504	153332504	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	39	446	0	ENST00000281708.4:c.452A>G	p.Asp151Gly	p.D151G	ENST00000281708	NM_033632.3	151	gAc/gGc	2/12	1	2	FACETS	0.316	0.261	0.377	0.316	0.261	0.377	SUBCLONAL	1	TRUE	1	0.45	2		446	549	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225998	53225998	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	235	1288	0	ENST00000375401.3:c.2851C>T	p.Arg951Ter	p.R951*	ENST00000375401	NM_004187.3	951	Cga/Tga	19/26	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.45	2		1288	1005	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522328	157522328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542516057	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	51	879	0	ENST00000346085.5:c.4600C>T	p.Arg1534Cys	p.R1534C	ENST00000346085	NM_020732.3	1534	Cgc/Tgc	18/20	1	2	FACETS	0.266	0.225	0.312	0.266	0.225	0.312	SUBCLONAL	1	TRUE	1	0.45	2		879	851	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110127	8110127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772022668	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	118	644	0	ENST00000585124.1:c.478G>A	p.Gly160Arg	p.G160R	ENST00000585124	NM_004217.3	160	Ggg/Agg	6/9	1	2	FACETS	0.779	0.704	0.858	0.779	0.704	0.858	SUBCLONAL	1	TRUE	1	0.45	2		644	673	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851573	134851573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1281577436	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	102	553	0	ENST00000398015.3:c.979C>T	p.Arg327Cys	p.R327C	ENST00000398015	NM_004441.4	327	Cgc/Tgc	5/16	1	2	FACETS	0.867	0.778	0.96	0.867	0.778	0.96	CLONAL	1	TRUE	1	0.45	2		553	523	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022395	31022395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1162384519	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	150	429	0	ENST00000375687.4:c.1880C>T	p.Ala627Val	p.A627V	ENST00000375687	NM_015338.5	627	gCg/gTg	13/13	0.3	4	FACETS	0.844	0.78	0.908			1	CLONAL	3	TRUE	NA	0.45	4		429	382	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752812	57752812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	84	323	0	ENST00000274289.3:c.1116del	p.Phe372LeufsTer31	p.F372Lfs*31	ENST00000274289	NM_006622.3	372	ttT/tt	8/14	1	2	FACETS	0.975	0.867	1	0.975	0.867	1	CLONAL	1	TRUE	1	0.45	2		323	383	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589636	69589636	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	20	167	0	ENST00000168712.1:c.217G>A	p.Ala73Thr	p.A73T	ENST00000168712	NM_002007.2	73	Gcc/Acc	1/3	1	2	FACETS	0.465	0.357	0.59	0.465	0.357	0.59	SUBCLONAL	1	TRUE	1	0.45	2		167	191	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155727	119155727	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	164	709	2	ENST00000264033.4:c.1484del	p.Pro495ArgfsTer120	p.P495Rfs*120	ENST00000264033	NM_005188.3	494	Ccc/cc	10/16	1	2	FACETS	0.932	0.857	1	0.932	0.857	1	CLONAL	1	TRUE	1	0.45	2		711	782	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279543	18279543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	115	519	0	ENST00000222254.8:c.1816G>A	p.Ala606Thr	p.A606T	ENST00000222254	NM_005027.3	606	Gca/Aca	15/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.45	2		519	428	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028821	47028821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782070362	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	171	1066	0	ENST00000377604.3:c.125G>A	p.Arg42His	p.R42H	ENST00000377604	NM_001204468.1	42	cGt/cAt	3/24	1	2	FACETS	0.882	0.812	0.955	0.882	0.812	0.955	CLONAL	1	TRUE	1	0.45	2		1066	862	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375160	31375160	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	72	1133	0	ENST00000328111.2:c.561del	p.Tyr188ThrfsTer4	p.Y188Tfs*4	ENST00000328111	NM_006892.3	186	aCc/ac	6/23	0.115307693854542	1	FACETS	0.25	0.217	0.285	0.25	0.217	0.285	INDETERMINATE	1	TRUE	0	0.45	1		1133	992	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199422	11199422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	117	579	0	ENST00000361445.4:c.5069C>T	p.Pro1690Leu	p.P1690L	ENST00000361445	NM_004958.3	1690	cCa/cTa	36/58	1	2	FACETS	0.84	0.759	0.925	0.84	0.759	0.925	CLONAL	1	TRUE	1	0.45	2		579	619	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852101	63852101	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	136	664	0	ENST00000279873.7:c.2879T>C	p.Met960Thr	p.M960T	ENST00000279873	NM_032199.2	960	aTg/aCg	10/10	1	2	FACETS	0.914	0.834	0.999	0.914	0.834	0.999	CLONAL	1	TRUE	1	0.45	2		664	661	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120796816	120796816	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1311127832	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	158	919	1	ENST00000257552.2:c.443G>A	p.Arg148Gln	p.R148Q	ENST00000257552	NM_002442.3	148	cGg/cAg	7/15	0.115307693854542	1	FACETS	0.741	0.681	0.805	0.741	0.681	0.805	INDETERMINATE	1	TRUE	0	0.45	1		920	734	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944204	81944204	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	195	961	0	ENST00000359376.3:c.1813C>A	p.Leu605Ile	p.L605I	ENST00000359376	NM_002661.3	605	Ctc/Atc	18/33	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.45	2		961	845	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836575	89836575	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	60	980	0	ENST00000389301.3:c.2315A>G	p.Gln772Arg	p.Q772R	ENST00000389301	NM_000135.2	772	cAg/cGg	25/43	1	2	FACETS	0.35	0.301	0.404	0.35	0.301	0.404	SUBCLONAL	1	TRUE	1	0.45	2		980	761	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110130	8110130	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs531140672	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	117	640	0	ENST00000585124.1:c.475C>T	p.Arg159Cys	p.R159C	ENST00000585124	NM_004217.3	159	Cgc/Tgc	6/9	1	2	FACETS	0.777	0.702	0.857	0.777	0.702	0.857	SUBCLONAL	1	TRUE	1	0.45	2		640	669	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40855799	40855799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	149	592	2	ENST00000428826.2:c.2057G>A	p.Arg686Gln	p.R686Q	ENST00000428826		686	cGa/cAa	19/21	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.45	2		594	660	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936335	78936335	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1198817759	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	64	940	0	ENST00000306801.3:c.3767T>C	p.Leu1256Pro	p.L1256P	ENST00000306801	NM_020761.2	1256	cTg/cCg	32/34	1	2	FACETS	0.386	0.334	0.444	0.386	0.334	0.444	SUBCLONAL	1	TRUE	1	0.45	2		940	736	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39623718	39623718	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178890899	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	38	351	0	ENST00000262039.4:c.2125C>T	p.Pro709Ser	p.P709S	ENST00000262039	NM_002647.2	709	Cca/Tca	20/25	1	2	FACETS	0.366	0.302	0.437	0.366	0.302	0.437	SUBCLONAL	1	TRUE	1	0.45	2		351	462	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350026	15350026	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	75	1161	0	ENST00000263377.2:c.3626A>G	p.His1209Arg	p.H1209R	ENST00000263377	NM_058243.2	1209	cAt/cGt	18/20	1	2	FACETS	0.358	0.313	0.408	0.358	0.313	0.408	SUBCLONAL	1	TRUE	1	0.45	2		1161	930	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277938	18277938	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	105	496	0	ENST00000222254.8:c.1560-2A>G		p.X520_splice	ENST00000222254	NM_005027.3	520			1	2	FACETS	0.935	0.842	1	0.935	0.842	1	CLONAL	1	TRUE	1	0.45	2		496	499	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905751	50905751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	224	1215	0	ENST00000440232.2:c.799G>A	p.Glu267Lys	p.E267K	ENST00000440232	NM_002691.3	267	Gag/Aag	7/27	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.45	2		1215	939	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069455	30069455	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	126	787	0	ENST00000338641.4:c.1320G>T	p.Met440Ile	p.M440I	ENST00000338641	NM_000268.3	440	atG/atT	12/16	1	2	FACETS	0.879	0.798	0.964	0.879	0.798	0.964	CLONAL	1	TRUE	1	0.45	2		787	637	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431010	181431010	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	146	999	0	ENST00000325404.1:c.862G>C	p.Ala288Pro	p.A288P	ENST00000325404	NM_003106.3	288	Gcc/Ccc	1/1	1	2	FACETS	0.804	0.734	0.877	0.804	0.734	0.877	CLONAL	1	TRUE	1	0.45	2		999	807	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953840	55953840	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	114	534	0	ENST00000263923.4:c.3596T>C	p.Val1199Ala	p.V1199A	ENST00000263923	NM_002253.2	1199	gTt/gCt	27/30	1	2	FACETS	0.898	0.812	0.989	0.898	0.812	0.989	CLONAL	1	TRUE	1	0.45	2		534	564	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510240	187510240	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	132	506	0	ENST00000441802.2:c.13273T>C	p.Tyr4425His	p.Y4425H	ENST00000441802	NM_005245.3	4425	Tac/Cac	27/27	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.45	2		506	553	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564795	86564795	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	64	936	0	ENST00000274376.6:c.527C>A	p.Pro176His	p.P176H	ENST00000274376	NM_002890.2	176	cCt/cAt	1/25	1	2	FACETS	0.333	0.288	0.383	0.333	0.288	0.383	SUBCLONAL	1	TRUE	1	0.45	2		936	853	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501541	149501541	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	158	787	0	ENST00000261799.4:c.2246T>C	p.Val749Ala	p.V749A	ENST00000261799	NM_002609.3	749	gTg/gCg	16/23	0.115307693854542	0	FACETS	0.528	0.484	0.573			1	INDETERMINATE	1	TRUE	0	0.45	0		787	732	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722236	176722236	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	44	567	0	ENST00000439151.2:c.7867A>G	p.Ser2623Gly	p.S2623G	ENST00000439151	NM_022455.4	2623	Agt/Ggt	23/23	1	2	FACETS	0.377	0.316	0.445	0.377	0.316	0.445	SUBCLONAL	1	TRUE	1	0.45	2		567	519	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415579	152415579	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs762742833	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	145	722	0	ENST00000206249.3:c.1429C>T	p.Arg477Ter	p.R477*	ENST00000206249	NM_000125.3	477	Cga/Tga	7/8	1	2	FACETS	0.96	0.879	1	0.96	0.879	1	CLONAL	1	TRUE	1	0.45	2		722	671	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864398	151864398	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	106	462	0	ENST00000262189.6:c.9583C>T	p.Gln3195Ter	p.Q3195*	ENST00000262189	NM_170606.2	3195	Cag/Tag	42/59	1	2	FACETS	0.909	0.819	1	0.909	0.819	1	CLONAL	1	TRUE	1	0.45	2		462	518	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542551	141542551	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	40	789	1	ENST00000220592.5:c.2435G>T	p.Arg812Leu	p.R812L	ENST00000220592	NM_012154.3	812	cGg/cTg	18/19	1	2	FACETS	0.258	0.214	0.308	0.258	0.214	0.308	SUBCLONAL	1	TRUE	1	0.45	2		790	688	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98011448	98011448	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	130	580	0	ENST00000289081.3:c.126G>T	p.Gln42His	p.Q42H	ENST00000289081	NM_000136.2	42	caG/caT	2/15	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.45	2		580	575	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933692	39933692	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1284842198	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	120	803	0	ENST00000378444.4:c.907G>A	p.Ala303Thr	p.A303T	ENST00000378444	NM_001123385.1	303	Gcc/Acc	4/15	1	2	FACETS	0.835	0.755	0.918	0.835	0.755	0.918	CLONAL	1	TRUE	1	0.45	2		803	639	SUCCESS
AR	367	MSKCC	GRCh37	X	66766118	66766119	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	152	748	0	ENST00000374690.3:c.1130_1131insA	p.Pro378SerfsTer124	p.P378Sfs*124	ENST00000374690	NM_000044.3	377	cct/ccAt	1/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.45	2		748	628	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	49	365	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.877	0.747	1	0.877	0.747	1	CLONAL	1	TRUE	1	0.356968987914576	2		365	313	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0057630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	155	561	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.356968987914576	2		561	686	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514563	41514563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	130	545	0	ENST00000373198.4:c.98C>T	p.Ser33Phe	p.S33F	ENST00000373198	NM_133170.3	33	tCc/tTc	2/32	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.356968987914576	2		545	488	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159754	20159754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	134	399	0	ENST00000379607.5:c.5C>T	p.Pro2Leu	p.P2L	ENST00000379607	NM_001412.3	2	cCc/cTc	1/7	1	1	FACETS	1	0.974	1	1	0.992	1	CLONAL	2	TRUE	0	0.356968987914576	1		399	276	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267290	41267290	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	109	427	0	ENST00000349496.5:c.874A>G	p.Lys292Glu	p.K292E	ENST00000349496	NM_001904.3	292	Aaa/Gaa	6/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.356968987914576	2		427	511	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873648	35873648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867618621	NA	P-0057630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	59	405	0	ENST00000303115.3:c.604G>A	p.Glu202Lys	p.E202K	ENST00000303115	NM_002185.3	202	Gag/Aag	5/8	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.356968987914576	2		405	322	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381514	81381514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	94	422	0	ENST00000222390.5:c.547G>A	p.Glu183Lys	p.E183K	ENST00000222390	NM_000601.4	183	Gaa/Aaa	5/18	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.356968987914576	2		422	418	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546890	9546890	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	150	664	0	ENST00000353224.5:c.1132C>T	p.His378Tyr	p.H378Y	ENST00000353224	NM_177990.2	378	Cac/Tac	5/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.356968987914576	2		664	595	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755501	39755501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	138	764	0	ENST00000288319.7:c.1264C>T	p.His422Tyr	p.H422Y	ENST00000288319	NM_182918.3	422	Cac/Tac	10/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.356968987914576	2		764	561	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165702	185165702	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	114	475	1	ENST00000265026.3:c.977G>A	p.Arg326Gln	p.R326Q	ENST00000265026	NM_004721.4	326	cGg/cAg	5/14	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.356968987914576	2		476	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578373	7578396	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TCGCTATCTGAGCAGCGCTCATGG	TCGCTATCTGAGCAGCGCTCATGG	-	novel	NA	P-0057630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	22	946	0	ENST00000269305.4:c.534_557del	p.His179_Asp186del	p.H179_D186del	ENST00000269305	NM_001126112.2	178	caCCATGAGCGCTGCTCAGATAGCGAt/cat	5/11	1	2	FACETS	0.159	0.122	0.202	0.159	0.122	0.202	SUBCLONAL	1	TRUE	1	0.356968987914576	2		946	776	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278062	15278062	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	175	901	0	ENST00000263388.2:c.5360C>T	p.Pro1787Leu	p.P1787L	ENST00000263388	NM_000435.2	1787	cCa/cTa	29/33	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.356968987914576	2		901	746	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108307	209108307	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	90	464	0	ENST00000345146.2:c.542G>A	p.Gly181Glu	p.G181E	ENST00000345146	NM_005896.2	181	gGg/gAg	6/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.356968987914576	2		464	426	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164591	47164591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	73	408	0	ENST00000409792.3:c.1535C>T	p.Ser512Leu	p.S512L	ENST00000409792	NM_014159.6	512	tCa/tTa	3/21	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.356968987914576	2		408	339	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960132	134960132	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	139	729	0	ENST00000398015.3:c.2489A>G	p.Asn830Ser	p.N830S	ENST00000398015	NM_004441.4	830	aAc/aGc	13/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.356968987914576	2		729	606	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264627	1264627	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	269	1154	0	ENST00000310581.5:c.2735A>G	p.Glu912Gly	p.E912G	ENST00000310581	NM_198253.2	912	gAg/gGg	11/16	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.356968987914576	2		1154	1044	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856060	151856060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751794784	NA	P-0057630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	144	576	0	ENST00000262189.6:c.11558G>A	p.Arg3853Gln	p.R3853Q	ENST00000262189	NM_170606.2	3853	cGg/cAg	44/59	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.356968987914576	2		576	614	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0057631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	101	529	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.213690886232146	2	FACETS	0.941	0.847	1	1	0.981	1	CLONAL	3	TRUE	0	0.17	2		529	421	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0057631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	63	473	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.806	0.698	0.921	1	0.974	1	CLONAL	2	TRUE	1	0.17	2		474	460	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087961	27087961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	75	562	0	ENST00000324856.7:c.2248C>T	p.Arg750Ter	p.R750*	ENST00000324856	NM_006015.4	750	Cga/Tga	6/20	1	2	FACETS	0.853	0.749	0.965	1	0.98	1	CLONAL	2	TRUE	1	0.17	2		562	517	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645156	67645156	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	70	728	0	ENST00000264010.4:c.421G>T	p.Glu141Ter	p.E141*	ENST00000264010	NM_006565.3	141	Gaa/Taa	3/12	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.17	2		728	759	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398303	25398303	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1296330213	NA	P-0057631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	52	334	0	ENST00000311936.3:c.16C>A	p.Leu6Ile	p.L6I	ENST00000311936	NM_004985.3	6	Ctt/Att	2/5	1	2	FACETS	0.816	0.697	0.945	1	0.969	1	CLONAL	2	TRUE	1	0.17	2		334	375	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705317	43705319	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CCT	CCT	-	novel	NA	P-0057631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	99	806	0	ENST00000382044.4:c.5303_5305del	p.Glu1769del	p.E1769del	ENST00000382044	NM_001141980.1	1768	gAGGaa/gaa	24/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.17	2		806	786	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588982	67588982	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	18	278	0	ENST00000274335.5:c.1073G>C	p.Arg358Pro	p.R358P	ENST00000274335		358	cGa/cCa	8/15	1	2	FACETS	0.882	0.665	1	0.882	0.665	1	CLONAL	1	TRUE	1	0.17	2		278	240	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390669	139390669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	102	1151	0	ENST00000277541.6:c.7522C>T	p.Pro2508Ser	p.P2508S	ENST00000277541	NM_017617.3	2508	Ccc/Tcc	34/34	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.17	2		1151	1007	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874011	123874013	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs780061449	NA	P-0057632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	12	46	0	ENST00000330479.4:c.62_64del	p.Ala21del	p.A21del	ENST00000330479	NM_020382.3	14	gaGGCg/gag	2/9	0.343196165418898	8	FACETS	0.767	0.54	1			1	CLONAL	1	TRUE	NA	0.343196165418898	8		46	185	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285243	212285243	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1332523099	NA	P-0057632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	51	579	0	ENST00000342788.4:c.3058G>A	p.Glu1020Lys	p.E1020K	ENST00000342788	NM_005235.2	1020	Gag/Aag	25/28	NA	2	FACETS	0.539	0.458	0.629			1	INDETERMINATE	1	TRUE	NA	0.343196165418898	2		579	551	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491325	2491325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	245	1500	3	ENST00000355716.4:c.368C>T	p.Pro123Leu	p.P123L	ENST00000355716	NM_003820.2	123	cCa/cTa	4/8	0.343196165418898	1	FACETS	0.876	0.817	0.937	0.876	0.817	0.937	CLONAL	1	TRUE	0	0.343196165418898	1		1503	1350	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49449057	49449785	+	splice_donor_variant,coding_sequence_variant,5_prime_UTR_variant	Splice_Site	DEL	ACCTGCCGGTTCTGAATCTTTATCCTCACCAGCCAGCTTCTGGCTGTCCATCCCTCTCTCCGACTGGGCAGGGCCCTCTCGGGGAGACCTGTTGGTGCCAAGAAAGAGATCTATATGCCTACTAAGTCTTCCCAAGAAGCATTTTTCCCAGAATCCTGGGAAGAAGGCATCCAGACCCTCCAGACATCAGAGCAAAGCCATACTACAAACTCCTATACTGACAAGAAAGTCATTCTCCCTAACCTGTAGGGTCACTTCCTCCCCAGATAAACACATACGCTCTTCTCACACTCTGGAGAGATTCTCAGGGGATCCATTTGACTTTCCCACTTCCAGGCTCCTCTGTAAGAGTTCCTGGGGCCATAGCATCCAACTAGAAGCATATCCATTTGTATCTAATACTGCTCTTTGGCTTGCCTCTGGGTTTTTGGCTTTTGGTGAGCCCTATTCCCACACCTTTCCCTCAAGTCTCAAGTAAGCTCCCATTCTAGAGGCCAGTCTGTGCCAACCCAGGGGTAGTCATGACCCAGGAAGCCTGAGTCCAGCAAAAATCCCTCTCCCAGAGGCAGAGTCTGAGGCACTGCAAGAGATGTAACACACTACTGGAACTACAGCCTAGCTATGGATGGATCTCCCCCACCGCCACTTGTTTCTACGAGGACATCACCATTACAAAAGAAGAAACTCCCTAATTTCCACCCACTTCCAACCCAAATCCAGCTCAGACCA	ACCTGCCGGTTCTGAATCTTTATCCTCACCAGCCAGCTTCTGGCTGTCCATCCCTCTCTCCGACTGGGCAGGGCCCTCTCGGGGAGACCTGTTGGTGCCAAGAAAGAGATCTATATGCCTACTAAGTCTTCCCAAGAAGCATTTTTCCCAGAATCCTGGGAAGAAGGCATCCAGACCCTCCAGACATCAGAGCAAAGCCATACTACAAACTCCTATACTGACAAGAAAGTCATTCTCCCTAACCTGTAGGGTCACTTCCTCCCCAGATAAACACATACGCTCTTCTCACACTCTGGAGAGATTCTCAGGGGATCCATTTGACTTTCCCACTTCCAGGCTCCTCTGTAAGAGTTCCTGGGGCCATAGCATCCAACTAGAAGCATATCCATTTGTATCTAATACTGCTCTTTGGCTTGCCTCTGGGTTTTTGGCTTTTGGTGAGCCCTATTCCCACACCTTTCCCTCAAGTCTCAAGTAAGCTCCCATTCTAGAGGCCAGTCTGTGCCAACCCAGGGGTAGTCATGACCCAGGAAGCCTGAGTCCAGCAAAAATCCCTCTCCCAGAGGCAGAGTCTGAGGCACTGCAAGAGATGTAACACACTACTGGAACTACAGCCTAGCTATGGATGGATCTCCCCCACCGCCACTTGTTTCTACGAGGACATCACCATTACAAAAGAAGAAACTCCCTAATTTCCACCCACTTCCAACCCAAATCCAGCTCAGACCA	-	novel	NA	P-0057632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	44	673	0				ENST00000301067	NM_003482.3	-/5537		1/54	NA	2	FACETS	0.455	0.381	0.538			1	INDETERMINATE	1	TRUE	NA	0.343196165418898	2		673	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0057634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	75	771	1	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.204567029648259	1	FACETS	0.829	0.727	0.939	0.829	0.727	0.939	CLONAL	1	TRUE	0	0.247005407941729	1		772	642	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40476849	40476849	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	55	674	0	ENST00000264657.5:c.1480del	p.Thr494ProfsTer15	p.T494Pfs*15	ENST00000264657	NM_139276.2	494	Acc/cc	17/24	0.247005407941729	0	FACETS	0.754	0.646	0.871			1	SUBCLONAL	1	TRUE	0	0.247005407941729	0		674	445	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061223	38061228	+	inframe_deletion	In_Frame_Del	DEL	TCTCGA	TCTCGA	-	novel	NA	P-0057635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	85	592	0	ENST00000250448.2:c.761_766del	p.Phe254_Asn256delinsTyr	p.F254_N256delinsY	ENST00000250448	NM_004496.3	254	tTCGAGAac/tac	2/2	1	2	FACETS	0.831	0.735	0.934	0.831	0.735	0.934	CLONAL	1	FALSE	1	0.3	2		592	682	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374904	149374904	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	95	621	0	ENST00000360632.3:c.190C>T	p.Gln64Ter	p.Q64*	ENST00000360632	NM_015472.4	64	Cag/Tag	2/7	1	2	FACETS	0.888	0.791	0.992	0.888	0.791	0.992	CLONAL	1	FALSE	1	0.3	2		621	713	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593605	55593610	+	inframe_deletion	In_Frame_Del	DEL	GAAGGT	GAAGGT	-	novel	NA	P-0057636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	205	400	0	ENST00000288135.5:c.1671_1676del	p.Trp557_Val559delinsCys	p.W557_V559delinsC	ENST00000288135	NM_000222.2	557	tgGAAGGTt/tgt	11/21	1	2	FACETS	0.919	0.862	0.976	0.919	0.862	0.976	CLONAL	1	TRUE	1	0.949491536070297	2		400	470	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670882	134670882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200018500	NA	P-0057636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	195	416	0	ENST00000398015.3:c.793G>A	p.Val265Met	p.V265M	ENST00000398015	NM_004441.4	265	Gtg/Atg	3/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.949491536070297	2		416	378	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277035	18277035	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs771075635	NA	P-0057636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	286	551	0	ENST00000222254.8:c.1482G>C	p.Gln494His	p.Q494H	ENST00000222254	NM_005027.3	494	caG/caC	12/16	1	2	FACETS	0.82	0.775	0.865	0.82	0.775	0.865	CLONAL	1	TRUE	1	0.949491536070297	2		551	735	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138382836	138382836	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	203	413	0	ENST00000289153.2:c.2708T>A	p.Leu903Gln	p.L903Q	ENST00000289153	NM_006219.2	903	cTg/cAg	19/22	1	2	FACETS	0.874	0.819	0.93	0.874	0.819	0.93	CLONAL	1	TRUE	1	0.949491536070297	2		413	489	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0057653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	432	542	0	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	0.335631261226958	4	FACETS	1	0.991	1	0.836	0.801	0.872	CLONAL	3	TRUE	0	0.376780852772018	4		542	944	SUCCESS
APC	324	MSKCC	GRCh37	5	112174091	112174094	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1131691143	NA	P-0057653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	47	336	0	ENST00000257430.4:c.2802_2805del	p.Tyr935IlefsTer19	p.Y935Ifs*19	ENST00000257430	NM_000038.5	934	ACTTac/ac	16/16	1	2	FACETS	0.684	0.578	0.799	0.684	0.578	0.799	SUBCLONAL	1	TRUE	1	0.376780852772018	2		336	365	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0057653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	112	673	2	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	1	2	FACETS	0.767	0.69	0.849	0.767	0.69	0.849	SUBCLONAL	1	TRUE	1	0.376780852772018	2		675	775	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721812	49721812	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs142690032	NA	P-0057653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	11	13	1	ENST00000449682.2:c.1951C>T	p.Arg651Ter	p.R651*	ENST00000449682	NM_020998.3	651	Cga/Tga	17/18	0.297796071853693	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	2	TRUE	0	0.376780852772018	2		14	24	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460552	149460552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148727692	NA	P-0057653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	129	815	0	ENST00000286301.3:c.85G>A	p.Glu29Lys	p.E29K	ENST00000286301	NM_005211.3	29	Gag/Aag	3/22	1	2	FACETS	0.739	0.67	0.813	0.739	0.67	0.813	SUBCLONAL	1	TRUE	1	0.376780852772018	2		815	926	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0057654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	188	652	1	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.232067448963399	3	FACETS	1	0.989	1	0.706	0.652	0.762	CLONAL	1	FALSE	1	0.332606372420179	3		653	934	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371708	225371708	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	55	560	1	ENST00000264414.4:c.896T>G	p.Met299Arg	p.M299R	ENST00000264414	NM_003590.4	299	aTg/aGg	7/16	0.252972828026446	3	FACETS	1	0.876	1	0.506	0.438	0.578	INDETERMINATE	1	TRUE	1	0.652770241397365	3		561	221	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561357	9561357	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	100	696	0	ENST00000353224.5:c.425C>G	p.Thr142Arg	p.T142R	ENST00000353224	NM_177990.2	142	aCg/aGg	4/10	1	2	FACETS	0.926	0.836	1	0.926	0.836	1	CLONAL	1	TRUE	1	0.652770241397365	2		696	331	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0057661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	19	410	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.213	0.161	0.275	0.213	0.161	0.275	SUBCLONAL	1	TRUE	1	0.5	2		410	356	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188309	10188309	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	96	428	1	ENST00000256474.2:c.452T>A	p.Ile151Asn	p.I151N	ENST00000256474	NM_000551.3	151	aTc/aAc	2/3	0.345437909493249	2	FACETS	0.899	0.812	0.989	0.899	0.812	0.989	CLONAL	2	TRUE	0	0.374486504594794	2		429	285	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653785	89653785	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	34	233	0	ENST00000371953.3:c.85del	p.Tyr29IlefsTer25	p.Y29Ifs*25	ENST00000371953	NM_000314.4	28	aTt/at	2/9	0.326512565183747	4	FACETS	1	0.933	1	1	0.933	1	CLONAL	2	TRUE	2	0.374486504594794	4		233	101	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46240689	46240689	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	29	207	0	ENST00000334344.6:c.1549G>C	p.Glu517Gln	p.E517Q	ENST00000334344	NM_152641.2	517	Gaa/Caa	12/21	0.374486504594794	4	FACETS	0.872	0.713	1	0.872	0.713	1	CLONAL	2	TRUE	2	0.374486504594794	4		207	122	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144102	11144116	+	inframe_deletion	In_Frame_Del	DEL	TGATCCAGGCCGGCA	TGATCCAGGCCGGCA	-	novel	NA	P-0057662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	218	801	0	ENST00000358026.2:c.3685_3699del	p.Ile1229_Met1233del	p.I1229_M1233del	ENST00000358026	NM_001128849.1	1228	gTGATCCAGGCCGGCAtg/gtg	26/36	0.326512565183747	4	FACETS	0.871	0.811	0.933	0.871	0.811	0.933	CLONAL	2	TRUE	2	0.374486504594794	4		801	919	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99180018	99180018	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	199	570	0	ENST00000074304.5:c.1961T>A	p.Phe654Tyr	p.F654Y	ENST00000074304	NM_001134224.1	654	tTc/tAc	19/26	0.326512565183747	4	FACETS	0.921	0.855	0.989	0.921	0.855	0.989	CLONAL	2	TRUE	2	0.374486504594794	4		570	793	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125214	47125214	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	39	261	0	ENST00000409792.3:c.6056T>C	p.Leu2019Pro	p.L2019P	ENST00000409792	NM_014159.6	2019	cTa/cCa	12/21	0.345437909493249	2	FACETS	0.964	0.822	1	0.964	0.822	1	CLONAL	2	TRUE	0	0.374486504594794	2		261	108	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402685	20402685	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	201	649	0	ENST00000346618.3:c.223del	p.Gln75LysfsTer5	p.Q75Kfs*5	ENST00000346618	NM_001949.4	74	ctC/ct	1/7	0.374486504594794	3	FACETS	0.937	0.872	1	0.937	0.872	1	CLONAL	2	TRUE	1	0.374486504594794	3		649	680	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	77	619	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.216012817811727	2	FACETS	0.819	0.725	0.918	0.819	0.725	0.918	CLONAL	2	TRUE	0	0.288507308173239	2		619	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0057663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	170	770	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.288507308173239	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.288507308173239	1		770	897	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675058	40675058	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs779227895	NA	P-0057663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	73	757	0	ENST00000249776.8:c.22C>A	p.Pro8Thr	p.P8T	ENST00000249776	NM_033286.3	8	Ccc/Acc	1/9	0.288507308173239	1	FACETS	0.601	0.525	0.684	0.601	0.525	0.684	SUBCLONAL	1	TRUE	0	0.288507308173239	1		757	720	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247516	53247516	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	58	504	0	ENST00000375401.3:c.293C>G	p.Ser98Cys	p.S98C	ENST00000375401	NM_004187.3	98	tCc/tGc	3/26	1	2	FACETS	0.174	0.148	0.202	0.174	0.148	0.202	SUBCLONAL	1	TRUE	1	0.662251458721138	2		504	1008	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432409	49432412	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	novel	NA	P-0057664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1258	101	934	0	ENST00000301067.7:c.8727_8730del	p.Ser2910ArgfsTer32	p.S2910Rfs*32	ENST00000301067	NM_003482.3	2909	gtAAGT/gt	34/54	1	2	FACETS	0.224	0.2	0.251	0.224	0.2	0.251	SUBCLONAL	1	TRUE	1	0.662251458721138	2		934	1359	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740376	58740376	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1064797099	NA	P-0057664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	278	327	0	ENST00000305921.3:c.1281G>A	p.Trp427Ter	p.W427*	ENST00000305921	NM_003620.3	427	tgG/tgA	6/6	0.662251458721138	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.662251458721138	3		327	554	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115013	3115013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	465	846	0	ENST00000078429.4:c.548G>A	p.Arg183His	p.R183H	ENST00000078429	NM_002067.2	183	cGc/cAc	4/7	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.662251458721138	2		846	1374	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979515	7979515	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	133	485	1	ENST00000319144.4:c.1510G>T	p.Ala504Ser	p.A504S	ENST00000319144	NM_001139.2	504	Gcg/Tcg	11/15	1	2	FACETS	0.448	0.406	0.492	0.448	0.406	0.492	SUBCLONAL	1	TRUE	1	0.662251458721138	2		486	897	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149739	202149739	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	127	514	0	ENST00000358485.4:c.1180G>A	p.Glu394Lys	p.E394K	ENST00000358485	NM_001080125.1	394	Gag/Aag	8/9	1	2	FACETS	0.506	0.458	0.556	0.506	0.458	0.556	SUBCLONAL	1	TRUE	1	0.662251458721138	2		514	758	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163006	47163006	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	83	259	0	ENST00000409792.3:c.3120del	p.Ser1041LeufsTer80	p.S1041Lfs*80	ENST00000409792	NM_014159.6	1040	ggC/gg	3/21	1	2	FACETS	0.957	0.856	1	0.957	0.856	1	CLONAL	1	TRUE	1	0.662251458721138	2		259	262	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987041	69987041	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	52	469	0	ENST00000394351.3:c.102G>C	p.Gln34His	p.Q34H	ENST00000394351	NM_000248.3	34	caG/caC	2/9	1	2	FACETS	0.183	0.155	0.214	0.183	0.155	0.214	SUBCLONAL	1	TRUE	1	0.662251458721138	2		469	858	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829792	76829797	+	inframe_deletion	In_Frame_Del	DEL	ATAGTC	ATAGTC	-	novel	NA	P-0057664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	46	388	0	ENST00000373344.5:c.6244_6249del	p.Asp2082_Tyr2083del	p.D2082_Y2083del	ENST00000373344	NM_000489.3	2082	GACTAT/-	28/35	0.521466807594977	1	FACETS	0.46	0.392	0.533	0.46	0.392	0.533	SUBCLONAL	1	TRUE	0	0.662251458721138	1		388	202	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	93	640	1	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.231078965181428	1	FACETS	0.682	0.605	0.765	0.682	0.605	0.765	SUBCLONAL	1	TRUE	0	0.231078965181428	1		641	1044	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	26	454	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	0.441	0.348	0.548	0.441	0.348	0.548	SUBCLONAL	1	TRUE	1	0.231078965181428	2		454	510	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	102	310	2	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	1	2	FACETS	0.824	0.739	0.913	1	0.984	1	CLONAL	2	TRUE	1	0.231078965181428	2		312	536	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629035	14629035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764010316	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	147	525	0	ENST00000254322.2:c.127G>A	p.Glu43Lys	p.E43K	ENST00000254322	NM_006145.1	43	Gag/Aag	1/3	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.231078965181428	2		525	876	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183766	10183766	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200885420	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1305	163	834	0	ENST00000256474.2:c.235C>T	p.Arg79Cys	p.R79C	ENST00000256474	NM_000551.3	79	Cgc/Tgc	1/3	0.166059178289754	3	FACETS	1	0.957	1	0.536	0.49	0.584	CLONAL	1	TRUE	1	0.231078965181428	3		834	1468	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539213	187539213	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	85	279	0	ENST00000441802.2:c.8527C>T	p.Gln2843Ter	p.Q2843*	ENST00000441802	NM_005245.3	2843	Caa/Taa	10/27	1	2	FACETS	0.791	0.702	0.886	1	0.98	1	SUBCLONAL	2	TRUE	1	0.231078965181428	2		279	465	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520081	106520081	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	12	148	0	ENST00000359195.3:c.2509G>C	p.Asp837His	p.D837H	ENST00000359195	NM_002649.2	837	Gat/Cat	6/11	1	2	FACETS	0.454	0.318	0.62	0.454	0.318	0.62	SUBCLONAL	1	TRUE	1	0.231078965181428	2		148	229	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093386	30093386	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	49	375	1	ENST00000331968.5:c.1877A>T	p.Gln626Leu	p.Q626L	ENST00000331968	NM_002742.2	626	cAg/cTg	13/18	0.172281603436799	1	FACETS	0.554	0.468	0.649	0.554	0.468	0.649	SUBCLONAL	1	TRUE	0	0.231078965181428	1		376	677	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562912	176562912	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	62	365	0	ENST00000439151.2:c.808C>T	p.Gln270Ter	p.Q270*	ENST00000439151	NM_022455.4	270	Caa/Taa	2/23	1	2	FACETS	0.747	0.645	0.859	0.747	0.645	0.859	SUBCLONAL	1	TRUE	1	0.231078965181428	2		365	718	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17355187	17355187	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	40	410	0	ENST00000375499.3:c.331C>G	p.Leu111Val	p.L111V	ENST00000375499	NM_003000.2	111	Cta/Gta	4/8	1	2	FACETS	0.506	0.419	0.603	0.506	0.419	0.603	SUBCLONAL	1	TRUE	1	0.231078965181428	2		410	684	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858903	78858903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1359463998	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	73	672	1	ENST00000306801.3:c.1938G>A	p.Met646Ile	p.M646I	ENST00000306801	NM_020761.2	646	atG/atA	17/34	1	2	FACETS	0.542	0.472	0.618	0.542	0.472	0.618	SUBCLONAL	1	TRUE	1	0.231078965181428	2		673	1166	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021697	31021697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780823171	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	55	375	0	ENST00000375687.4:c.1696G>A	p.Glu566Lys	p.E566K	ENST00000375687	NM_015338.5	566	Gag/Aag	12/13	0.231078965181428	5	FACETS	0.728	0.621	0.846			1	SUBCLONAL	1	TRUE	NA	0.231078965181428	5		375	880	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252059	226252059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	53	283	0	ENST00000366813.1:c.7C>T	p.Arg3Cys	p.R3C	ENST00000366813		3	Cgt/Tgt	1/3	1	2	FACETS	0.784	0.668	0.911	0.784	0.668	0.911	CLONAL	1	TRUE	1	0.231078965181428	2		283	585	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100619	8100619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	205	875	2	ENST00000346208.3:c.593C>T	p.Ser198Leu	p.S198L	ENST00000346208		198	tCg/tTg	3/6	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.231078965181428	2		877	1358	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983019	201983019	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1236	103	813	1	ENST00000359651.3:c.868G>T	p.Glu290Ter	p.E290*	ENST00000359651		290	Gag/Tag	7/8	1	2	FACETS	0.666	0.594	0.743	0.666	0.594	0.743	SUBCLONAL	1	TRUE	1	0.231078965181428	2		814	1339	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872207	45872207	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	196	581	0	ENST00000391945.4:c.227C>G	p.Thr76Ser	p.T76S	ENST00000391945	NM_000400.3	76	aCt/aGt	4/23	1	2	FACETS	0.806	0.745	0.868	1	0.991	1	CLONAL	2	TRUE	1	0.231078965181428	2		581	1053	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217417	7217417	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	54	456	0	ENST00000380728.2:c.379C>T	p.His127Tyr	p.H127Y	ENST00000380728		127	Cat/Tat	5/11	0.231078965181428	1	FACETS	0.65	0.554	0.755	0.65	0.554	0.755	SUBCLONAL	1	TRUE	0	0.231078965181428	1		456	636	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778836	9778836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	92	676	0	ENST00000377346.4:c.1105C>T	p.Pro369Ser	p.P369S	ENST00000377346	NM_005026.3	369	Ccc/Tcc	9/24	1	2	FACETS	0.748	0.663	0.839	0.748	0.663	0.839	SUBCLONAL	1	TRUE	1	0.231078965181428	2		676	1065	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17355130	17355130	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	41	348	0	ENST00000375499.3:c.388C>G	p.Leu130Val	p.L130V	ENST00000375499	NM_003000.2	130	Ctt/Gtt	4/8	1	2	FACETS	0.546	0.454	0.649	0.546	0.454	0.649	SUBCLONAL	1	TRUE	1	0.231078965181428	2		348	650	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268902	115268903	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	101	357	1	ENST00000438362.2:c.1707_1708delinsTT	p.Ala570Ser	p.A570S	ENST00000438362	NM_001242891.1	569	gtGGca/gtTTca	14/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.231078965181428	2		358	638	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115272893	115272893	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	78	431	1	ENST00000438362.2:c.1480A>G	p.Lys494Glu	p.K494E	ENST00000438362	NM_001242891.1	494	Aaa/Gaa	12/20	1	2	FACETS	0.831	0.729	0.941	0.831	0.729	0.941	CLONAL	1	TRUE	1	0.231078965181428	2		432	812	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771476	112771476	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	177	411	0	ENST00000369452.4:c.1649A>G	p.Asn550Ser	p.N550S	ENST00000369452	NM_007373.3	550	aAc/aGc	9/9	1	2	FACETS	0.954	0.88	1	1	0.992	1	CLONAL	2	TRUE	1	0.231078965181428	2		411	803	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895713	28895713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	78	308	1	ENST00000282397.4:c.3061C>T	p.Arg1021Trp	p.R1021W	ENST00000282397	NM_002019.4	1021	Cgg/Tgg	23/30	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.231078965181428	2		309	524	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881540	48881552	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGGTAAGGATTT	TTGGTAAGGATTT	-	novel	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	36	172	0	ENST00000267163.4:c.263_264+11del		p.X88_splice	ENST00000267163	NM_000321.2	88		2/27	1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	1	0.231078965181428	2		172	302	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105258937	105258937	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs368797346	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	66	737	0	ENST00000349310.3:c.44G>A	p.Arg15Gln	p.R15Q	ENST00000349310	NM_001014432.1	15	cGa/cAa	3/15	0.172281603436799	1	FACETS	0.439	0.38	0.504	0.439	0.38	0.504	SUBCLONAL	1	TRUE	0	0.231078965181428	1		737	1150	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675046	40675046	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	100	607	0	ENST00000249776.8:c.10C>A	p.Pro4Thr	p.P4T	ENST00000249776	NM_033286.3	4	Ccc/Acc	1/9	1	2	FACETS	0.81	0.722	0.905	0.81	0.722	0.905	CLONAL	1	TRUE	1	0.231078965181428	2		607	1068	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467847	99467847	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	34	313	0	ENST00000268035.6:c.2716C>T	p.Gln906Ter	p.Q906*	ENST00000268035	NM_000875.3	906	Cag/Tag	13/21	1	2	FACETS	0.638	0.521	0.77	0.638	0.521	0.77	SUBCLONAL	1	TRUE	1	0.231078965181428	2		313	461	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822675	72822675	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	90	660	0	ENST00000268489.5:c.9500C>T	p.Ser3167Phe	p.S3167F	ENST00000268489	NM_006885.3	3167	tCt/tTt	10/10	1	2	FACETS	0.699	0.618	0.785	0.699	0.618	0.785	SUBCLONAL	1	TRUE	1	0.231078965181428	2		660	1115	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610637	10610637	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	53	562	0	ENST00000171111.5:c.73G>A	p.Glu25Lys	p.E25K	ENST00000171111	NM_203500.1	25	Gag/Aag	2/6	1	2	FACETS	0.491	0.417	0.572	0.491	0.417	0.572	SUBCLONAL	1	TRUE	1	0.231078965181428	2		562	935	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61705969	61705969	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	31	355	0	ENST00000401558.2:c.3202G>C	p.Glu1068Gln	p.E1068Q	ENST00000401558	NM_003400.3	1068	Gaa/Caa	25/25	0.172281603436799	1	FACETS	0.414	0.334	0.505	0.414	0.334	0.505	SUBCLONAL	1	TRUE	0	0.231078965181428	1		355	573	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202122962	202122962	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	92	311	0	ENST00000358485.4:c.8G>A	p.Gly3Glu	p.G3E	ENST00000358485	NM_001080125.1	3	gGa/gAa	1/9	0.172281603436799	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.231078965181428	1		311	559	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54956536	54956536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1198722160	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	182	272	0	ENST00000312783.6:c.658A>G	p.Arg220Gly	p.R220G	ENST00000312783	NM_198436.1	220	Aga/Gga	7/10	0.231078965181428	3	FACETS	0.946	0.877	1	1	0.989	1	CLONAL	3	TRUE	1	0.231078965181428	3		272	619	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721475	49721475	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	265	666	0	ENST00000449682.2:c.2164A>G	p.Met722Val	p.M722V	ENST00000449682	NM_020998.3	722	Atg/Gtg	18/18	0.166059178289754	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.231078965181428	3		666	1078	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280176	142280176	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs377186178	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	119	363	0	ENST00000350721.4:c.1258C>G	p.Leu420Val	p.L420V	ENST00000350721	NM_001184.3	420	Ctc/Gtc	5/47	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.231078965181428	2		363	697	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026756	6026756	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	46	371	0	ENST00000265849.7:c.1640C>G	p.Ser547Ter	p.S547*	ENST00000265849	NM_000535.5	547	tCa/tGa	11/15	1	2	FACETS	0.77	0.648	0.905	0.77	0.648	0.905	CLONAL	1	TRUE	1	0.231078965181428	2		371	517	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339478	116339478	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	31	201	0	ENST00000397752.3:c.340G>C	p.Asp114His	p.D114H	ENST00000397752	NM_000245.2	114	Gat/Cat	2/21	1	2	FACETS	0.76	0.615	0.923	0.76	0.615	0.923	CLONAL	1	TRUE	1	0.231078965181428	2		201	353	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504144	123504144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	50	147	0	ENST00000371139.4:c.320C>T	p.Ser107Leu	p.S107L	ENST00000371139	NM_001114937.2	107	tCa/tTa	3/4	1	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.231078965181428	1		147	291	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937739	44937748	+	protein_altering_variant,splice_region_variant	In_Frame_Del	DEL	CTCTTAAGTT	CTCTTAAGTT	A	novel	NA	P-0057665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	97	200	0	ENST00000377967.4:c.2927_2936delinsA	p.Ala976_Leu979delinsGlu	p.A976_L979delinsE	ENST00000377967	NM_021140.2	976	gCTCTTAAGTTa/gAa	19/29	1	1	FACETS	1	0.957	1	1	0.988	1	CLONAL	2	TRUE	0	0.231078965181428	1		200	333	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171947	32171947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0121604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	34	457	2	ENST00000375023.3:c.3085G>A	p.Ala1029Thr	p.A1029T	ENST00000375023	NM_004557.3	1029	Gcc/Acc	19/30	1	2	FACETS	0.396	0.323	0.479	0.396	0.323	0.479	SUBCLONAL	1	NA	1	0.338479357982266	2		459	507	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619161	37619161	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	209	425	0	ENST00000447079.4:c.837C>A	p.Tyr279Ter	p.Y279*	ENST00000447079	NM_015083.1	279	taC/taA	1/14	0.18808368294909	2	FACETS	1	0.96	1	1	0.995	1	CLONAL	5	FALSE	0	0.18808368294909	2		425	433	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0057668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	45	323	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.209010932765076	2		323	412	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48922000	48922000	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1566187856	NA	P-0057668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	24	204	0	ENST00000267163.4:c.539+1G>A		p.X180_splice	ENST00000267163	NM_000321.2	180			0.209010932765076	1	FACETS	0.759	0.596	0.945	0.759	0.596	0.945	CLONAL	1	TRUE	0	0.209010932765076	1		204	271	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577112	7577112	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1131691029	NA	P-0057668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	115	787	0	ENST00000269305.4:c.826G>C	p.Ala276Pro	p.A276P	ENST00000269305	NM_001126112.2	276	Gcc/Ccc	8/11	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.209010932765076	2		787	1030	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65569055	65569055	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0057668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	54	427	0	ENST00000358664.4:c.3G>A	p.Met1?	p.M1?	ENST00000358664	NM_002382.4	1	atG/atA	1/5	0.209010932765076	1	FACETS	0.98	0.839	1	0.98	0.839	1	CLONAL	1	TRUE	0	0.209010932765076	1		427	472	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778230	27778230	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	85	546	0	ENST00000369163.2:c.379C>G	p.Leu127Val	p.L127V	ENST00000369163	NM_003536.2	127	Ctc/Gtc	1/1	0.209010932765076	3	FACETS	1	0.919	1	0.526	0.464	0.592	CLONAL	1	TRUE	1	0.209010932765076	3		546	854	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101932	11101932	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	162	875	2	ENST00000358026.2:c.1352G>T	p.Arg451Leu	p.R451L	ENST00000358026	NM_001128849.1	451	cGc/cTc	8/36	0.209010932765076	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.209010932765076	1		877	1120	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450382	50450382	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	81	471	0	ENST00000331340.3:c.566C>A	p.Thr189Asn	p.T189N	ENST00000331340	NM_006060.4	189	aCt/aAt	5/8	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.209010932765076	2		471	667	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244150	153244152	+	missense_variant	Missense_Mutation	TNP	CCC	CCC	GCA	novel	NA	P-0057668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	111	424	0	ENST00000281708.4:c.2005_2007delinsTGC	p.Gly669Cys	p.G669C	ENST00000281708	NM_033632.3	669	GGG/TGC	12/12	0.209010932765076	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.209010932765076	1		424	673	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061237	38061243	+	frameshift_variant	Frame_Shift_Del	DEL	CCGGAGT	CCGGAGT	-	novel	NA	P-0057670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	33	869	0	ENST00000250448.2:c.746_752del	p.Asp249AlafsTer70	p.D249Afs*70	ENST00000250448	NM_004496.3	249	gACTCCGGc/gc	2/2	1	2	FACETS	0.516	0.42	0.624	0.516	0.42	0.624	SUBCLONAL	1	TRUE	1	0.318317245612616	2		869	402	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678571	88678571	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	17	358	0	ENST00000360948.2:c.965A>T	p.Glu322Val	p.E322V	ENST00000360948	NM_001012338.2	322	gAg/gTg	9/19	0.188968867790803	1	FACETS	0.945	0.717	1	0.945	0.717	1	INDETERMINATE	1	TRUE	0	0.318317245612616	1		358	95	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0057719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	337	668	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.463049938322638	4	FACETS	0.943	0.921	0.963			1	CLONAL	5	TRUE	NA	0.600452203722448	4		668	381	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205006	123205006	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	21	292	0	ENST00000218089.9:c.2366C>A	p.Thr789Asn	p.T789N	ENST00000218089	NM_001042749.1	789	aCt/aAt	25/35	0.506027791611475	2	FACETS	0.457	0.355	0.574	0.229	0.177	0.287	SUBCLONAL	1	TRUE	0	0.600452203722448	2		292	153	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332132	70332132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745543859	NA	P-0057719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	19	197	0	ENST00000373644.4:c.37G>A	p.Val13Ile	p.V13I	ENST00000373644	NM_030625.2	13	Gtc/Atc	2/12	0.600452203722448	4	FACETS	1	0.796	1	0.345	0.266	0.433	CLONAL	1	TRUE	1	0.600452203722448	4		197	98	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627307	37627307	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	223	1506	0	ENST00000249071.6:c.412A>T	p.Thr138Ser	p.T138S	ENST00000249071	NM_002872.4	138	Acc/Tcc	5/7	0.600452203722448	2	FACETS	1	0.992	1	0.684	0.642	0.726	CLONAL	1	TRUE	0	0.600452203722448	2		1506	543	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259785	142259785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	77	513	0	ENST00000350721.4:c.3542G>A	p.Gly1181Asp	p.G1181D	ENST00000350721	NM_001184.3	1181	gGc/gAc	18/47	0.600452203722448	7	FACETS	1	0.973	1	0.281	0.247	0.317	CLONAL	1	TRUE	2	0.600452203722448	7		513	457	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023254	150023254	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	67	336	0	ENST00000253339.5:c.9G>C	p.Arg3Ser	p.R3S	ENST00000253339		3	agG/agC	1/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.600452203722448	2		336	152	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932468	39932468	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	159	993	1	ENST00000378444.4:c.2131C>A	p.Pro711Thr	p.P711T	ENST00000378444	NM_001123385.1	711	Cca/Aca	4/15	0.360865901038664	3	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.600452203722448	3		994	594	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	20	365	0				ENST00000310581	NM_198253.2	-/1132			0.360268425334652	1	FACETS	1	0.781	1	1	0.781	1	CLONAL	1	FALSE	0	0.360268425334652	1		365	91	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188190	108188190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	39	310	0	ENST00000278616.4:c.6289G>A	p.Glu2097Lys	p.E2097K	ENST00000278616	NM_000051.3	2097	Gaa/Aaa	43/63	1	2	FACETS	0.914	0.763	1	0.914	0.763	1	CLONAL	1	FALSE	1	0.360268425334652	2		310	237	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226002	133226002	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	74	1166	0	ENST00000320574.5:c.3895G>C	p.Glu1299Gln	p.E1299Q	ENST00000320574	NM_006231.2	1299	Gag/Cag	31/49	0.23578237360753	0	FACETS	0.826	0.73	0.929			1	CLONAL	1	FALSE	0	0.360268425334652	0		1166	318	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0057720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	107	640	1	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.329561823544776	0	FACETS	1	0.956	1			1	CLONAL	1	FALSE	0	0.360268425334652	0		641	348	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858524	57858524	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	90	863	0	ENST00000228682.2:c.262C>G	p.Leu88Val	p.L88V	ENST00000228682	NM_005269.2	88	Ctg/Gtg	4/12	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.360268425334652	2		863	433	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270046	198270046	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	53	401	0	ENST00000335508.6:c.1390C>G	p.Leu464Val	p.L464V	ENST00000335508	NM_012433.2	464	Ctt/Gtt	10/25	0.176694259795054	3	FACETS	1	0.88	1	0.515	0.441	0.595	INDETERMINATE	1	FALSE	1	0.360268425334652	3		401	337	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023759	27023763	+	frameshift_variant	Frame_Shift_Del	DEL	CCCAC	CCCAC	-	novel	NA	P-0057720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	55	379	0	ENST00000324856.7:c.866_870del	p.Pro289ArgfsTer109	p.P289Rfs*109	ENST00000324856	NM_006015.4	289	CCCACc/c	1/20	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	FALSE	1	0.360268425334652	2		379	289	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981793	201981794	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0057720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	262	1132	0	ENST00000359651.3:c.505_506dup	p.Leu170CysfsTer85	p.L170Cfs*85	ENST00000359651		168	-/CT	4/8	0.360268425334652	3	FACETS	0.981	0.928	1	1	0.994	1	CLONAL	3	FALSE	1	0.360268425334652	3		1132	583	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188229	108188229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	35	256	0	ENST00000278616.4:c.6328G>A	p.Asp2110Asn	p.D2110N	ENST00000278616	NM_000051.3	2110	Gac/Aac	43/63	1	2	FACETS	0.934	0.772	1	0.934	0.772	1	CLONAL	1	FALSE	1	0.360268425334652	2		256	208	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190746	108190746	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	31	363	0	ENST00000278616.4:c.6413G>T	p.Arg2138Ile	p.R2138I	ENST00000278616	NM_000051.3	2138	aGa/aTa	44/63	1	2	FACETS	0.94	0.768	1	0.94	0.768	1	CLONAL	1	FALSE	1	0.360268425334652	2		363	183	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245858	5245858	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	31	1314	1	ENST00000357368.4:c.917C>A	p.Ser306Ter	p.S306*	ENST00000357368	NM_002850.3	306	tCg/tAg	10/38	0.318632787846475	0	FACETS	0.306	0.247	0.372			1	SUBCLONAL	1	FALSE	0	0.360268425334652	0		1315	360	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602720	10602720	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	91	1107	0	ENST00000171111.5:c.858G>C	p.Gln286His	p.Q286H	ENST00000171111	NM_203500.1	286	caG/caC	3/6	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.360268425334652	2		1107	441	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793146	33793146	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	18	321	0	ENST00000498907.2:c.175G>C	p.Glu59Gln	p.E59Q	ENST00000498907	NM_004364.3	59	Gag/Cag	1/1	1	2	FACETS	0.625	0.473	0.801	0.625	0.473	0.801	SUBCLONAL	1	FALSE	1	0.360268425334652	2		321	160	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149238615	149238615	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	55	521	0	ENST00000360632.3:c.1180G>C	p.Glu394Gln	p.E394Q	ENST00000360632	NM_015472.4	394	Gag/Cag	7/7	1	2	FACETS	0.985	0.848	1	0.985	0.848	1	CLONAL	1	FALSE	1	0.360268425334652	2		521	310	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540110	187540110	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	13	471	0	ENST00000441802.2:c.7630G>A	p.Glu2544Lys	p.E2544K	ENST00000441802	NM_005245.3	2544	Gag/Aag	10/27	1	2	FACETS	0.29	0.206	0.392	0.29	0.206	0.392	SUBCLONAL	1	FALSE	1	0.360268425334652	2		471	249	SUCCESS
APC	324	MSKCC	GRCh37	5	112175448	112175448	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	59	337	0	ENST00000257430.4:c.4157G>C	p.Arg1386Thr	p.R1386T	ENST00000257430	NM_000038.5	1386	aGa/aCa	16/16	0.140881983625983	4	FACETS	0.857	0.745	0.976	0.857	0.745	0.976	INDETERMINATE	2	FALSE	2	0.360268425334652	4		337	260	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522172	157522175	+	frameshift_variant	Frame_Shift_Del	DEL	GGCG	GGCG	-	novel	NA	P-0057720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	93	878	0	ENST00000346085.5:c.4445_4448del	p.Gly1482AlafsTer11	p.G1482Afs*11	ENST00000346085	NM_020732.3	1482	GGCGgc/gc	18/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.360268425334652	2		878	412	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877816	151877816	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs780531989	NA	P-0057720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	46	325	0	ENST00000262189.6:c.7129G>C	p.Asp2377His	p.D2377H	ENST00000262189	NM_170606.2	2377	Gat/Cat	36/59	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	FALSE	1	0.360268425334652	2		325	226	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928839	44928839	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	64	379	0	ENST00000377967.4:c.1939C>T	p.Gln647Ter	p.Q647*	ENST00000377967	NM_021140.2	647	Cag/Tag	17/29	0.329561823544776	0	FACETS	1	0.904	1			1	CLONAL	1	FALSE	0	0.360268425334652	0		379	220	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928921	44928921	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	88	504	0	ENST00000377967.4:c.2021C>G	p.Ser674Cys	p.S674C	ENST00000377967	NM_021140.2	674	tCt/tGt	17/29	0.329561823544776	0	FACETS	0.856	0.765	0.953			1	CLONAL	1	FALSE	0	0.360268425334652	0		504	365	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477837	140477852	+	protein_altering_variant	In_Frame_Del	DEL	TAGGTGCTGTCACATT	TAGGTGCTGTCACATT	G	novel	NA	P-0057720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	60	579	0	ENST00000288602.6:c.1456_1471delinsC	p.Asn486_Thr491delinsPro	p.N486_T491delinsP	ENST00000288602	NM_004333.4	486	AATGTGACAGCACCTAca/Cca	12/18	1	2	FACETS	0.856	0.741	0.981	0.856	0.741	0.981	CLONAL	1	FALSE	1	0.360268425334652	2		579	389	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	65	365	0				ENST00000310581	NM_198253.2	-/1132			0.526778603704173	4	FACETS	1	0.894	1	1	0.894	1	CLONAL	2	TRUE	2	0.677546064304197	4		365	160	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	266	814	1	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	0.273775292048221	6	FACETS	0.878	0.828	0.929	0.878	0.828	0.929	INDETERMINATE	3	TRUE	3	0.677546064304197	6		815	702	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874562	35874562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	195	607	0	ENST00000303115.3:c.718C>T	p.Pro240Ser	p.P240S	ENST00000303115	NM_002185.3	240	Cct/Tct	6/8	0.526778603704173	4	FACETS	0.902	0.842	0.964	0.902	0.842	0.964	CLONAL	2	TRUE	2	0.677546064304197	4		607	535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	380	0	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.677546064304197	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.677546064304197	2		0	534	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261949	16261949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772442954	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	229	695	0	ENST00000375759.3:c.9214C>T	p.His3072Tyr	p.H3072Y	ENST00000375759	NM_015001.2	3072	Cac/Tac	11/15	0.526778603704173	4	FACETS	0.969	0.91	1	0.969	0.91	1	CLONAL	2	TRUE	2	0.677546064304197	4		695	585	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695829	117695829	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	352	812	1	ENST00000369458.3:c.608C>T	p.Ser203Phe	p.S203F	ENST00000369458	NM_024626.3	203	tCt/tTt	4/6	0.526778603704173	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.677546064304197	4		813	793	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166010	118166010	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767827215	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	172	639	0	ENST00000369448.3:c.520C>T	p.Arg174Trp	p.R174W	ENST00000369448	NM_017709.3	174	Cgg/Tgg	2/2	0.526778603704173	4	FACETS	0.822	0.762	0.884	0.822	0.762	0.884	CLONAL	2	TRUE	2	0.677546064304197	4		639	518	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480014	120480014	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173598104	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	319	798	0	ENST00000256646.2:c.3413C>T	p.Pro1138Leu	p.P1138L	ENST00000256646	NM_024408.3	1138	cCc/cTc	21/34	0.526778603704173	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.677546064304197	4		798	740	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054920	176054920	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	186	478	0	ENST00000367669.3:c.1133G>T	p.Arg378Leu	p.R378L	ENST00000367669	NM_022457.5	378	cGt/cTt	10/20	0.532280061323108	3	FACETS	0.886	0.829	0.943	0.886	0.829	0.943	CLONAL	2	TRUE	1	0.677546064304197	3		478	415	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597802	43597802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	299	1116	0	ENST00000355710.3:c.350C>T	p.Pro117Leu	p.P117L	ENST00000355710	NM_020975.4	117	cCc/cTc	3/20	0.526778603704173	4	FACETS	0.927	0.877	0.977	0.927	0.877	0.977	CLONAL	2	TRUE	2	0.677546064304197	4		1116	799	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622140	43622140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	293	834	0	ENST00000355710.3:c.3157C>T	p.Pro1053Ser	p.P1053S	ENST00000355710	NM_020975.4	1053	Cct/Tct	19/20	0.526778603704173	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	2	0.677546064304197	4		834	700	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148958	119148959	+	missense_variant	Missense_Mutation	DNP	TT	TT	GA	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	205	565	1	ENST00000264033.4:c.1178_1179delinsGA	p.Ile393Arg	p.I393R	ENST00000264033	NM_005188.3	393	aTT/aGA	8/16	0.677546064304197	2	FACETS	0.961	0.913	1	0.961	0.913	1	CLONAL	2	TRUE	0	0.677546064304197	2		566	315	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442815	442816	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	169	459	0	ENST00000399788.2:c.1491-1_1491delinsAA		p.X497_splice	ENST00000399788	NM_001042603.1	497		12/28	0.570492847731805	5	FACETS	1	0.983	1	0.789	0.733	0.845	CLONAL	2	TRUE	2	0.677546064304197	5		459	425	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466930	18466930	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	230	413	0	ENST00000266497.5:c.1069A>C	p.Lys357Gln	p.K357Q	ENST00000266497		357	Aaa/Caa	5/31	0.570492847731805	5	FACETS	0.858	0.807	0.909	0.858	0.807	0.909	CLONAL	3	TRUE	2	0.677546064304197	5		413	532	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21626485	21626485	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	244	532	0	ENST00000421138.2:c.1447G>A	p.Ala483Thr	p.A483T	ENST00000421138		483	Gca/Aca	13/16	0.570492847731805	5	FACETS	1	0.972	1	0.705	0.662	0.748	CLONAL	2	TRUE	2	0.677546064304197	5		532	687	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231457	46231457	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	183	403	0	ENST00000334344.6:c.1297T>G	p.Cys433Gly	p.C433G	ENST00000334344	NM_152641.2	433	Tgc/Ggc	10/21	0.570492847731805	5	FACETS	1	0.96	1	0.697	0.648	0.747	CLONAL	2	TRUE	2	0.677546064304197	5		403	521	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420990	49420990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	167	683	1	ENST00000301067.7:c.14759C>T	p.Pro4920Leu	p.P4920L	ENST00000301067	NM_003482.3	4920	cCc/cTc	48/54	0.570492847731805	5	FACETS	0.925	0.856	0.997	0.617	0.57	0.665	CLONAL	2	TRUE	2	0.677546064304197	5		684	537	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432191	121432191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	288	1096	0	ENST00000257555.6:c.938C>T	p.Ser313Phe	p.S313F	ENST00000257555		313	tCc/tTc	4/10	0.67392584222739	2	FACETS	0.984	0.944	1	0.984	0.944	1	CLONAL	2	TRUE	0	0.677546064304197	2		1096	432	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437548	110437548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	359	1099	0	ENST00000375856.3:c.853G>A	p.Glu285Lys	p.E285K	ENST00000375856	NM_003749.2	285	Gag/Aag	1/2	0.532280061323108	3	FACETS	0.991	0.947	1	0.991	0.947	1	CLONAL	2	TRUE	1	0.677546064304197	3		1099	716	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630696	90630696	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	435	799	0	ENST00000330062.3:c.790G>A	p.Asp264Asn	p.D264N	ENST00000330062	NM_002168.2	264	Gac/Aac	6/11	0.677546064304197	5	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	2	0.677546064304197	5		799	837	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122952	2122952	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	272	929	0	ENST00000219476.3:c.2323T>C	p.Ser775Pro	p.S775P	ENST00000219476	NM_000548.3	775	Tct/Cct	21/42	0.635441981132818	3	FACETS	0.941	0.892	0.99	0.941	0.892	0.99	CLONAL	2	TRUE	1	0.677546064304197	3		929	571	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639330	3639330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	374	1359	0	ENST00000294008.3:c.4309C>T	p.Pro1437Ser	p.P1437S	ENST00000294008	NM_032444.2	1437	Ccc/Tcc	12/15	0.635441981132818	3	FACETS	0.989	0.946	1	0.989	0.946	1	CLONAL	2	TRUE	1	0.677546064304197	3		1359	747	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828017	3828017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	287	717	0	ENST00000262367.5:c.2108C>T	p.Pro703Leu	p.P703L	ENST00000262367	NM_004380.2	703	cCt/cTt	10/31	0.635441981132818	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.677546064304197	3		717	545	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56792464	56792464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	225	539	0	ENST00000308159.5:c.194G>A	p.Gly65Glu	p.G65E	ENST00000308159	NM_014669.4	65	gGg/gAg	3/22	0.349850931512386	3	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	2	TRUE	1	0.677546064304197	3		539	417	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831566	72831566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	157	964	0	ENST00000268489.5:c.5015G>A	p.Gly1672Asp	p.G1672D	ENST00000268489	NM_006885.3	1672	gGc/gAc	9/10	0.349850931512386	3	FACETS	1	0.965	1	0.542	0.499	0.587	INDETERMINATE	1	TRUE	1	0.677546064304197	3		964	572	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592318	29592318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	251	628	0	ENST00000356175.3:c.4733C>T	p.Ser1578Phe	p.S1578F	ENST00000356175	NM_000267.3	1578	tCc/tTc	35/57	0.640735094732676	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.677546064304197	2		628	339	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448393	56448393	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	353	1044	1	ENST00000407977.2:c.254C>T	p.Ser85Phe	p.S85F	ENST00000407977		85	tCc/tTc	3/10	0.635115934032406	4	FACETS	0.966	0.918	1	0.966	0.918	1	CLONAL	2	TRUE	2	0.677546064304197	4		1045	905	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872540	136872540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	113	387	0	ENST00000241393.3:c.958G>A	p.Val320Met	p.V320M	ENST00000241393	NM_003467.2	320	Gtg/Atg	2/2	0.532280061323108	3	FACETS	0.818	0.749	0.888	0.818	0.749	0.888	CLONAL	2	TRUE	1	0.677546064304197	3		387	273	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543811	212543811	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	114	551	0	ENST00000342788.4:c.1588A>T	p.Arg530Trp	p.R530W	ENST00000342788	NM_005235.2	530	Agg/Tgg	13/28	0.635441981132818	3	FACETS	1	0.947	1	0.533	0.483	0.584	CLONAL	1	TRUE	1	0.677546064304197	3		551	423	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525129	9525129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	76	479	0	ENST00000353224.5:c.1756G>A	p.Asp586Asn	p.D586N	ENST00000353224	NM_177990.2	586	Gat/Aat	8/10	NA	2	FACETS	0.714	0.632	0.801			1	INDETERMINATE	1	TRUE	NA	0.677546064304197	2		479	314	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101044	41101044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143164081	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	301	996	0	ENST00000373198.4:c.1312G>A	p.Glu438Lys	p.E438K	ENST00000373198	NM_133170.3	438	Gag/Aag	8/32	0.349850931512386	3	FACETS	0.796	0.754	0.839	0.796	0.754	0.839	INDETERMINATE	2	TRUE	1	0.677546064304197	3		996	747	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420106	41420106	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	62	456	0	ENST00000373198.4:c.215G>A	p.Gly72Glu	p.G72E	ENST00000373198	NM_133170.3	72	gGa/gAa	3/32	0.349850931512386	3	FACETS	0.773	0.672	0.88	0.386	0.336	0.44	INDETERMINATE	1	TRUE	1	0.677546064304197	3		456	317	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319054	62319054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	359	1417	3	ENST00000360203.5:c.1412G>A	p.Gly471Asp	p.G471D	ENST00000360203	NM_001283009.1	471	gGc/gAc	17/35	0.273775292048221	6	FACETS	0.867	0.824	0.91	0.867	0.824	0.91	INDETERMINATE	3	TRUE	3	0.677546064304197	6		1420	960	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597493	52597495	+	stop_gained	Nonsense_Mutation	TNP	GAG	GAG	AAA	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	148	420	0	ENST00000394830.3:c.3815_3817delinsTTT	p.Pro1272_Gln1273delinsLeuTer	p.P1272_Q1273delinsL*	ENST00000394830	NM_018313.4	1272	cCTCag/cTTTag	25/30	0.677546064304197	2	FACETS	0.942	0.885	0.996	0.942	0.885	0.996	CLONAL	2	TRUE	0	0.677546064304197	2		420	232	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391081	89391081	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	321	872	0	ENST00000336596.2:c.1147C>T	p.Leu383Phe	p.L383F	ENST00000336596	NM_005233.5	383	Ctc/Ttc	5/17	0.635115934032406	4	FACETS	0.898	0.851	0.946	0.898	0.851	0.946	CLONAL	2	TRUE	2	0.677546064304197	4		872	885	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455542	189455542	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	210	515	0	ENST00000264731.3:c.76C>T	p.Pro26Ser	p.P26S	ENST00000264731	NM_003722.4	26	Cca/Tca	2/14	0.273775292048221	6	FACETS	1	0.988	1	0.829	0.775	0.884	INDETERMINATE	2	TRUE	3	0.677546064304197	6		515	587	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127364	55127364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	148	709	0	ENST00000257290.5:c.152G>A	p.Gly51Glu	p.G51E	ENST00000257290	NM_006206.4	51	gGg/gAg	3/23	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.677546064304197	2		709	418	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593395	55593395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1560416964	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	80	386	0	ENST00000288135.5:c.1552C>T	p.Pro518Ser	p.P518S	ENST00000288135	NM_000222.2	518	Ccc/Tcc	10/21	1	2	FACETS	0.984	0.88	1	0.984	0.88	1	CLONAL	1	TRUE	1	0.677546064304197	2		386	240	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55991405	55991405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	209	1213	0	ENST00000263923.4:c.56C>T	p.Ala19Val	p.A19V	ENST00000263923	NM_002253.2	19	gCc/gTc	1/30	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.677546064304197	2		1213	579	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332699	153332699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780061054	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	134	568	1	ENST00000281708.4:c.257C>T	p.Ser86Leu	p.S86L	ENST00000281708	NM_033632.3	86	tCg/tTg	2/12	0.176876924098897	3	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.677546064304197	3		569	358	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542668	187542668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	104	548	0	ENST00000441802.2:c.5072C>T	p.Ala1691Val	p.A1691V	ENST00000441802	NM_005245.3	1691	gCc/gTc	10/27	0.677546064304197	1	FACETS	0.962	0.883	1	0.962	0.883	1	CLONAL	1	TRUE	0	0.677546064304197	1		548	211	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31504673	31504673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	264	715	0	ENST00000344624.3:c.1657C>T	p.Pro553Ser	p.P553S	ENST00000344624		553	Cct/Tct	8/33	0.526778603704173	4	FACETS	0.964	0.909	1	0.964	0.909	1	CLONAL	2	TRUE	2	0.677546064304197	4		715	678	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915730	131915730	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	132	385	0	ENST00000265335.6:c.728C>T	p.Ser243Phe	p.S243F	ENST00000265335		243	tCc/tTc	5/25	0.526778603704173	4	FACETS	0.931	0.856	1	0.931	0.856	1	CLONAL	2	TRUE	2	0.677546064304197	4		385	351	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131945040	131945040	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	131	256	0	ENST00000265335.6:c.2988G>C	p.Lys996Asn	p.K996N	ENST00000265335		996	aaG/aaC	19/25	0.526778603704173	4	FACETS	0.954	0.877	1	0.954	0.877	1	CLONAL	2	TRUE	2	0.677546064304197	4		256	340	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149511632	149511632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167658274	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	195	689	0	ENST00000261799.4:c.1153C>T	p.Arg385Cys	p.R385C	ENST00000261799	NM_002609.3	385	Cgc/Tgc	8/23	0.15608928533927	6	FACETS	0.872	0.814	0.931	0.872	0.814	0.931	INDETERMINATE	3	TRUE	3	0.677546064304197	6		689	518	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997726	149997726	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	302	452	0	ENST00000253339.5:c.2741C>T	p.Pro914Leu	p.P914L	ENST00000253339		914	cCc/cTc	5/7	0.570492847731805	5	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	TRUE	2	0.677546064304197	5		452	587	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683560	162683560	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	228	681	0	ENST00000366898.1:c.409C>G	p.Pro137Ala	p.P137A	ENST00000366898	NM_004562.2	137	Cca/Gca	3/12	0.570492847731805	5	FACETS	1	0.973	1	0.712	0.668	0.758	CLONAL	2	TRUE	2	0.677546064304197	5		681	635	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983968	2983968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	306	1145	0	ENST00000396946.4:c.562G>A	p.Asp188Asn	p.D188N	ENST00000396946	NM_032415.4	188	Gac/Aac	5/25	0.141009342412373	5	FACETS	1	0.981	1	0.718	0.68	0.758	INDETERMINATE	2	TRUE	2	0.677546064304197	5		1145	845	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467736	50467736	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	237	968	0	ENST00000331340.3:c.972del	p.Glu325SerfsTer90	p.E325Sfs*90	ENST00000331340	NM_006060.4	324	gCc/gc	8/8	0.464130398556305	4	FACETS	0.901	0.846	0.957	0.901	0.846	0.957	CLONAL	2	TRUE	2	0.677546064304197	4		968	651	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214397	55214397	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	252	867	1	ENST00000275493.2:c.523A>G	p.Asn175Asp	p.N175D	ENST00000275493	NM_005228.3	175	Aac/Gac	4/28	0.464130398556305	4	FACETS	0.898	0.845	0.952	0.898	0.845	0.952	CLONAL	2	TRUE	2	0.677546064304197	4		868	695	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339863	116339863	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	265	539	1	ENST00000397752.3:c.725G>A	p.Arg242Lys	p.R242K	ENST00000397752	NM_000245.2	242	aGa/aAa	2/21	0.677546064304197	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	2	0.677546064304197	4		540	630	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439667	140439667	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	190	447	0	ENST00000288602.6:c.2072G>A	p.Arg691Lys	p.R691K	ENST00000288602	NM_004333.4	691	aGa/aAa	17/18	0.677546064304197	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.677546064304197	4		447	449	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836834	151836834	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	262	662	0	ENST00000262189.6:c.14386A>G	p.Met4796Val	p.M4796V	ENST00000262189	NM_170606.2	4796	Atg/Gtg	56/59	0.635115934032406	4	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	2	0.677546064304197	4		662	643	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136827	69136827	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	56	481	1	ENST00000288368.4:c.4741G>A	p.Gly1581Arg	p.G1581R	ENST00000288368	NM_024870.2	1581	Gga/Aga	39/40	0.353935248771951	4	FACETS	0.657	0.564	0.758	0.164	0.141	0.19	INDETERMINATE	1	TRUE	0	0.677546064304197	4		482	422	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117875395	117875395	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	150	427	0	ENST00000297338.2:c.248T>G	p.Ile83Ser	p.I83S	ENST00000297338	NM_006265.2	83	aTt/aGt	3/14	0.611738647776181	4	FACETS	1	0.985	1	0.442	0.406	0.48	CLONAL	1	TRUE	1	0.677546064304197	4		427	560	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341785	8341785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776356704	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	118	738	0	ENST00000356435.5:c.4855G>A	p.Glu1619Lys	p.E1619K	ENST00000356435		1619	Gaa/Aaa	29/35	0.635441981132818	3	FACETS	0.851	0.771	0.935	0.425	0.385	0.468	CLONAL	1	TRUE	1	0.677546064304197	3		738	548	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36846865	36846865	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	199	796	1	ENST00000358127.4:c.1074G>A	p.Trp358Ter	p.W358*	ENST00000358127	NM_001280556.1	358	tgG/tgA	9/10	0.635441981132818	3	FACETS	0.892	0.836	0.947	0.892	0.836	0.947	CLONAL	2	TRUE	1	0.677546064304197	3		797	441	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215835	98215835	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1429444084	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	302	790	0	ENST00000331920.6:c.3374C>T	p.Pro1125Leu	p.P1125L	ENST00000331920	NM_000264.3	1125	cCc/cTc	20/24	0.635441981132818	3	FACETS	0.978	0.931	1	0.978	0.931	1	CLONAL	2	TRUE	1	0.677546064304197	3		790	610	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128230358	128230358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	168	737	0	ENST00000265960.3:c.1238C>T	p.Pro413Leu	p.P413L	ENST00000265960	NM_001006617.1	413	cCt/cTt	10/12	0.635441981132818	3	FACETS	1	0.977	1	0.574	0.531	0.619	CLONAL	1	TRUE	1	0.677546064304197	3		737	578	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786026	135786027	+	missense_variant	Missense_Mutation	DNP	GG	GG	TA	novel	NA	P-0057721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	143	1097	2	ENST00000298552.3:c.1194_1195delinsTA	p.Pro399Thr	p.P399T	ENST00000298552	NM_001162426.1	398	gcCCca/gcTAca	12/23	0.635441981132818	3	FACETS	0.791	0.723	0.863	0.396	0.361	0.432	SUBCLONAL	1	TRUE	1	0.677546064304197	3		1099	714	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	45	365	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.23	2		365	280	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941653	48941653	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0057722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	23	185	0	ENST00000267163.4:c.963C>G	p.Tyr321Ter	p.Y321*	ENST00000267163	NM_000321.2	321	taC/taG	10/27	1	2	FACETS	0.585	0.456	0.734	0.585	0.456	0.734	SUBCLONAL	1	TRUE	1	0.23	2		185	342	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924315	112924315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355732645	NA	P-0057722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	56	995	3	ENST00000351677.2:c.1261C>T	p.Arg421Trp	p.R421W	ENST00000351677	NM_002834.3	421	Cgg/Tgg	11/16	1	2	FACETS	0.449	0.383	0.521	0.449	0.383	0.521	SUBCLONAL	1	TRUE	1	0.23	2		998	1085	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652056	36652057	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGGGT	novel	NA	P-0057722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1440	93	1368	0	ENST00000244741.5:c.179_183dup	p.Asp62ArgfsTer88	p.D62Rfs*88	ENST00000244741	NM_000389.4	60	gag/gAGGGTag	2/3	0.3	3	FACETS	0.588	0.521	0.661			1	SUBCLONAL	1	TRUE	NA	0.23	3		1368	1533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577068	7577069	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1162	90	987	0	ENST00000269305.4:c.869_870insT	p.Lys291GlnfsTer15	p.K291Qfs*15	ENST00000269305	NM_001126112.2	290	cgc/cgTc	8/11	1	2	FACETS	0.625	0.553	0.703	0.625	0.553	0.703	SUBCLONAL	1	TRUE	1	0.23	2		987	1252	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0057723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	481	750	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.798353906135108	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	FALSE	0	0.826010972287934	2		750	572	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0057723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	622	323	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.826010972287934	9	FACETS	0.932	0.903	0.96			1	CLONAL	6	FALSE	NA	0.826010972287934	9		323	1048	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	52	365	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.73	0.631	0.835	0.73	0.631	0.835	SUBCLONAL	1	TRUE	1	0.734576778731751	2		365	194	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717608	89717608	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1564566706	NA	P-0057724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	208	348	0	ENST00000371953.3:c.635-2A>G		p.X212_splice	ENST00000371953	NM_000314.4	212			0.734576778731751	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.734576778731751	1		348	358	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574002	7574002	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs375338359	NA	P-0057724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	321	878	0	ENST00000269305.4:c.1025G>C	p.Arg342Pro	p.R342P	ENST00000269305	NM_001126112.2	342	cGa/cCa	10/11	0.734576778731751	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.734576778731751	1		878	546	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266457	55266457	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775695605	NA	P-0057724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	252	622	1	ENST00000275493.2:c.2749G>A	p.Gly917Arg	p.G917R	ENST00000275493	NM_005228.3	917	Gga/Aga	23/28	1	2	FACETS	0.969	0.911	1	0.969	0.911	1	CLONAL	1	TRUE	1	0.734576778731751	2		623	708	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589498	67589548	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAAATACCTTATCCATTGAATTTATTTTAATCTTTCTAGGATCAAGTTGTC	TAAATACCTTATCCATTGAATTTATTTTAATCTTTCTAGGATCAAGTTGTC	-	novel	NA	P-0057724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	85	106	0	ENST00000274335.5:c.1300-39_1311del		p.X434_splice	ENST00000274335		434		10/15	1	2	FACETS	0.952	0.855	1	0.952	0.855	1	CLONAL	1	TRUE	1	0.734576778731751	2		106	243	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564516	55564516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1174814949	NA	P-0057725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	84	531	1	ENST00000288135.5:c.404G>A	p.Arg135His	p.R135H	ENST00000288135	NM_000222.2	135	cGc/cAc	3/21	0.304613200027749	1	FACETS	0.486	0.43	0.545	0.486	0.43	0.545	INDETERMINATE	1	TRUE	0	0.533728175919206	1		532	475	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579716	7579716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1192416464	NA	P-0057725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	443	611	0	ENST00000269305.4:c.80del	p.Pro27LeufsTer17	p.P27Lfs*17	ENST00000269305	NM_001126112.2	27	cCt/ct	3/11	0.533728175919206	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.533728175919206	2		611	818	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009087	27009087	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	24	91	0	ENST00000335756.4:c.23G>C	p.Arg8Pro	p.R8P	ENST00000335756	NM_001809.3	8	cGa/cCa	1/5	0.511132507458297	2	FACETS	0.848	0.678	1	0.424	0.339	0.519	CLONAL	1	TRUE	0	0.533728175919206	2		91	106	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99154335	99154335	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	149	417	0	ENST00000074304.5:c.477G>C	p.Glu159Asp	p.E159D	ENST00000074304	NM_001134224.1	159	gaG/gaC	8/26	0.533728175919206	2	FACETS	1	0.963	1	0.54	0.496	0.585	CLONAL	1	TRUE	0	0.533728175919206	2		417	517	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645544	215645544	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782475	NA	P-0057725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	167	604	0	ENST00000260947.4:c.1054G>T	p.Val352Leu	p.V352L	ENST00000260947	NM_000465.2	352	Gtg/Ttg	4/11	0.511132507458297	2	FACETS	0.915	0.843	0.989	0.457	0.421	0.495	CLONAL	1	TRUE	0	0.533728175919206	2		604	684	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30664757	30664757	+	intron_variant	Intron	SNP	T	T	G	novel	NA	P-0057725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	41	243	0	ENST00000295754.5:c.94+16288T>G		p.*32*	ENST00000295754	NM_003242.5	54/592			0.170668400381781	4	FACETS	0.647	0.54	0.766			1	INDETERMINATE	1	TRUE	NA	0.533728175919206	4		243	364	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0057726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	331	825	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.580514904541906	2		825	1043	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578218	7578218	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060501198	NA	P-0057726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	300	673	0	ENST00000269305.4:c.631A>G	p.Thr211Ala	p.T211A	ENST00000269305	NM_001126112.2	211	Act/Gct	6/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.580514904541906	2		673	987	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356342	70356342	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	268	720	0	ENST00000374080.3:c.5237C>A	p.Pro1746Gln	p.P1746Q	ENST00000374080		1746	cCa/cAa	37/45	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.580514904541906	2		720	855	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162519	47162557	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGCTCTTCTTGCTGCCTAGAAGGTATTTTGGCTTTCA	GCAGCTCTTCTTGCTGCCTAGAAGGTATTTTGGCTTTCA	CC	novel	NA	P-0057726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	95	366	1	ENST00000409792.3:c.3569_3607delinsGG	p.Val1190GlyfsTer34	p.V1190Gfs*34	ENST00000409792	NM_014159.6	1190	gTGAAAGCCAAAATACCTTCTAGGCAGCAAGAAGAGCTGCca/gGGca	3/21	1	2	FACETS	0.765	0.685	0.849	0.765	0.685	0.849	SUBCLONAL	1	TRUE	1	0.580514904541906	2		367	428	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195677	123195677	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	190	432	0	ENST00000218089.9:c.1591C>T	p.Gln531Ter	p.Q531*	ENST00000218089	NM_001042749.1	531	Caa/Taa	17/35	1	2	FACETS	0.98	0.91	1	0.98	0.91	1	CLONAL	1	TRUE	1	0.580514904541906	2		432	668	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0057727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	254	698	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.47190000965884	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.47190000965884	1		699	706	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591825	48591825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767342	NA	P-0057727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	139	410	0	ENST00000342988.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000342988	NM_005359.5	330	Gaa/Aaa	9/12	0.47190000965884	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.47190000965884	1		410	420	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092947	27092947	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0057727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	169	324	0	ENST00000324856.7:c.2879-1G>A		p.X960_splice	ENST00000324856	NM_006015.4	960			0.432524695994621	2	FACETS	0.965	0.901	1	0.965	0.901	1	CLONAL	2	TRUE	0	0.47190000965884	2		324	371	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076925	41076925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	84	547	0	ENST00000373198.4:c.1495G>A	p.Glu499Lys	p.E499K	ENST00000373198	NM_133170.3	499	Gag/Aag	9/32	0.0961164501109377	4	FACETS	0.702	0.62	0.791	0.351	0.31	0.396	INDETERMINATE	1	TRUE	2	0.47190000965884	4		547	746	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577035	7577035	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	412	669	0	ENST00000269305.4:c.903del	p.Ser303AlafsTer42	p.S303Afs*42	ENST00000269305	NM_001126112.2	301	ccA/cc	8/11	0.757669032591148	2	FACETS	0.998	0.968	1	0.998	0.968	1	CLONAL	2	TRUE	0	0.757669032591148	2		669	545	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067836	30067836	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315499	NA	P-0057730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	119	372	0	ENST00000338641.4:c.1021C>T	p.Arg341Ter	p.R341*	ENST00000338641	NM_000268.3	341	Cga/Tga	11/16	0.27589417038465	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.323430781369968	1		372	561	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712514	52712514	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0057730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	93	478	0	ENST00000394830.3:c.236+2T>A		p.X79_splice	ENST00000394830	NM_018313.4	79			0.323430781369968	1	FACETS	0.891	0.795	0.993	0.891	0.795	0.993	CLONAL	1	TRUE	0	0.323430781369968	1		478	541	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439703	140439703	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	22	398	0	ENST00000288602.6:c.2036G>C	p.Ser679Thr	p.S679T	ENST00000288602	NM_004333.4	679	aGt/aCt	17/18	0.27589417038465	1	FACETS	0.276	0.213	0.349	0.276	0.213	0.349	SUBCLONAL	1	TRUE	0	0.323430781369968	1		398	413	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073805	8073806	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	C	novel	NA	P-0057730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	128	362	1	ENST00000377482.5:c.853_854delinsG	p.Pro285AlafsTer10	p.P285Afs*10	ENST00000377482	NM_018948.3	285	CCc/Gc	4/4	0.274255513087883	2	FACETS	0.925	0.845	1	0.925	0.845	1	CLONAL	2	TRUE	0	0.323430781369968	2		363	428	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0057731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	429	730	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.551158041246995	4	FACETS	0.939	0.908	0.97	0.939	0.908	0.97	CLONAL	4	TRUE	0	0.557542294340415	4		730	638	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106141	27106141	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	181	565	0	ENST00000324856.7:c.5752C>T	p.Arg1918Trp	p.R1918W	ENST00000324856	NM_006015.4	1918	Cgg/Tgg	20/20	0.550169301166556	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.557542294340415	2		565	323	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662128	227662128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775603579	NA	P-0057731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	242	796	0	ENST00000305123.5:c.1327C>T	p.Arg443Cys	p.R443C	ENST00000305123	NM_005544.2	443	Cgc/Tgc	1/2	0.423710510946119	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	2	0.557542294340415	4		796	661	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870846	12870846	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0057731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	80	259	0	ENST00000228872.4:c.73A>T	p.Lys25Ter	p.K25*	ENST00000228872	NM_004064.3	25	Aag/Tag	1/3	0.485312256520714	4	FACETS	0.901	0.805	1	0.901	0.805	1	CLONAL	2	TRUE	2	0.557542294340415	4		259	248	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73992015	73992015	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	121	1116	0	ENST00000318443.5:c.35T>C	p.Val12Ala	p.V12A	ENST00000318443	NM_001024736.1	12	gTg/gCg	2/10	0.557542294340415	5	FACETS	0.705	0.636	0.779	0.176	0.159	0.195	SUBCLONAL	1	TRUE	1	0.557542294340415	5		1116	1130	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2089940	2089944	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCG	GGCCG	-	novel	NA	P-0057731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	72	1023	0	ENST00000219066.1:c.920_924del	p.Pro307ArgfsTer21	p.P307Rfs*21	ENST00000219066	NM_002528.5	307	cCGGCC/c	6/6	0.465636856417768	5	FACETS	0.519	0.452	0.591	0.173	0.15	0.197	SUBCLONAL	1	TRUE	2	0.557542294340415	5		1023	914	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654555	29654558	+	frameshift_variant	Frame_Shift_Del	DEL	AACA	AACA	-	novel	NA	P-0057731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	96	258	0	ENST00000356175.3:c.5246_5249del	p.Thr1749LysfsTer3	p.T1749Kfs*3	ENST00000356175	NM_000267.3	1748	cgAACA/cg	37/57	0.557542294340415	2	FACETS	0.897	0.82	0.973	0.897	0.82	0.973	CLONAL	2	TRUE	0	0.557542294340415	2		258	192	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860293	151860293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765906762	NA	P-0057731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	165	434	0	ENST00000262189.6:c.10369G>A	p.Asp3457Asn	p.D3457N	ENST00000262189	NM_170606.2	3457	Gac/Aac	43/59	0.485312256520714	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.557542294340415	4		434	430	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579529	7579529	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658483	NA	P-0057733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	436	699	0	ENST00000269305.4:c.158G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tGg/tAg	4/11	0.927788664571963	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.928304059390356	2		699	462	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74000769	74000769	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369418465	NA	P-0057733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	396	537	0	ENST00000318443.5:c.1459G>A	p.Val487Met	p.V487M	ENST00000318443	NM_001024736.1	487	Gtg/Atg	7/10	0.705855975916017	4	FACETS	0.976	0.933	1	0.976	0.933	1	CLONAL	2	TRUE	2	0.928304059390356	4		537	843	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436548	110436548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	522	963	0	ENST00000375856.3:c.1853C>T	p.Ala618Val	p.A618V	ENST00000375856	NM_003749.2	618	gCg/gTg	1/2	0.928304059390356	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.928304059390356	2		963	559	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912346	32912350	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAA	AAAAA	-	novel	NA	P-0057733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	114	304	0	ENST00000380152.3:c.3856_3860del	p.Lys1286Ter	p.K1286*	ENST00000380152		1285	gAAAAA/g	11/27	0.928304059390356	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.928304059390356	2		304	119	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127450	17127450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1490236729	NA	P-0057733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	354	608	0	ENST00000285071.4:c.404C>T	p.Pro135Leu	p.P135L	ENST00000285071	NM_144997.5	135	cCt/cTt	6/14	0.927788664571963	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.928304059390356	2		608	378	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805445	46805445	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	412	816	1	ENST00000290295.7:c.511T>A	p.Ser171Thr	p.S171T	ENST00000290295	NM_006361.5	171	Tct/Act	1/2	0.928304059390356	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.928304059390356	2		817	431	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526217	189526217	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	458	701	0	ENST00000264731.3:c.481C>A	p.Pro161Thr	p.P161T	ENST00000264731	NM_003722.4	161	Cca/Aca	4/14	0.705855975916017	4	FACETS	0.939	0.901	0.978	0.939	0.901	0.978	CLONAL	2	TRUE	2	0.928304059390356	4		701	1013	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0057734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	337	837	1	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.65597958679863	2	FACETS	0.958	0.921	0.994	0.958	0.921	0.994	CLONAL	2	TRUE	0	0.689834449617879	2		838	510	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591268	67591322	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCGGCAAAAGAAGTTGAACGAGTGGTTGGGCAATGAAAACACTGAAGAGTAAGT	TTCGGCAAAAGAAGTTGAACGAGTGGTTGGGCAATGAAAACACTGAAGAGTAAGT	-	novel	NA	P-0057734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	47	356	0	ENST00000274335.5:c.1766_1814+6del		p.X589_splice	ENST00000274335		589		13/15	0.671960406324009	2	FACETS	0.927	0.799	1	0.463	0.399	0.531	CLONAL	1	TRUE	0	0.689834449617879	2		356	147	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	109	454	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.336761952679983	2		460	566	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	382	662	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	2	TRUE	1	0.336761952679983	2		664	1004	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737345	145737345	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	264	1038	0	ENST00000428558.2:c.3342G>T	p.Gln1114His	p.Q1114H	ENST00000428558	NM_004260.3	1114	caG/caT	20/22	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.336761952679983	2		1038	1336	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	55	324	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	0.91	0.782	1	0.91	0.782	1	CLONAL	1	TRUE	1	0.336761952679983	2		324	359	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	134	591	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.196156411583654	2	FACETS	1	0.925	1	0.509	0.463	0.558	INDETERMINATE	1	TRUE	0	0.336761952679983	2		591	781	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055897	180055897	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	173	736	1	ENST00000261937.6:c.1088del	p.Pro363ArgfsTer27	p.P363Rfs*27	ENST00000261937	NM_182925.4	363	cCg/cg	8/30	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.336761952679983	2		737	988	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578412	7578412	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519747	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	224	841	0	ENST00000269305.4:c.518T>C	p.Val173Ala	p.V173A	ENST00000269305	NM_001126112.2	173	gTg/gCg	5/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.336761952679983	2		841	1147	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720654	89720654	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	82	453	0	ENST00000371953.3:c.808del	p.Met270CysfsTer6	p.M270Cfs*6	ENST00000371953	NM_000314.4	269	Aaa/aa	8/9	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.336761952679983	2		453	434	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732969	30732969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893810	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	127	421	0	ENST00000295754.5:c.1582C>T	p.Arg528Cys	p.R528C	ENST00000295754	NM_003242.5	528	Cgt/Tgt	7/7	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.336761952679983	2		421	588	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942685	48942685	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913301	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	40	213	0	ENST00000267163.4:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000267163	NM_000321.2	358	Cga/Tga	11/27	1	2	FACETS	0.986	0.825	1	0.986	0.825	1	CLONAL	1	TRUE	1	0.336761952679983	2		213	241	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	244	456	5	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	1	0.336761952679983	2		461	608	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089705	27089706	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1286891446	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	169	779	0	ENST00000324856.7:c.2666dup	p.Met890HisfsTer46	p.M890Hfs*46	ENST00000324856	NM_006015.4	887	-/G	8/20	1	2	FACETS	0.994	0.913	1	0.994	0.913	1	CLONAL	1	TRUE	1	0.336761952679983	2		779	1010	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736510	85736511	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs387906351	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	61	278	1	ENST00000370580.1:c.136dup	p.Ile46AsnfsTer4	p.I46Nfs*4	ENST00000370580	NM_003921.4	46	ata/aAta	2/3	1	2	FACETS	0.971	0.842	1	0.971	0.842	1	CLONAL	1	TRUE	1	0.336761952679983	2		279	373	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262680	16262680	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	122	472	3	ENST00000375759.3:c.9950del	p.Pro3317ArgfsTer83	p.P3317Rfs*83	ENST00000375759	NM_015001.2	3315	caC/ca	11/15	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.336761952679983	2		475	683	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337684	73337684	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771690280	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	35	166	0	ENST00000377767.4:c.2032del	p.Ile678PhefsTer59	p.I678Ffs*59	ENST00000377767	NM_014953.3	678	Att/tt	16/21	1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	1	0.336761952679983	2		166	203	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372093	55372093	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	114	348	1	ENST00000297316.4:c.788del	p.Pro263ArgfsTer124	p.P263Rfs*124	ENST00000297316	NM_022454.3	261	ggC/gg	2/2	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.336761952679983	2		349	662	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5207965	5207965	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	250	980	0	ENST00000357368.4:c.5746C>T	p.Arg1916Ter	p.R1916*	ENST00000357368	NM_002850.3	1916	Cga/Tga	37/38	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.336761952679983	2		980	1350	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971252	15971252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs118021690	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	161	541	0	ENST00000268712.3:c.4697C>T	p.Thr1566Met	p.T1566M	ENST00000268712	NM_006311.3	1566	aCg/aTg	32/46	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.336761952679983	2		541	710	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007741	45007742	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	79	315	0	ENST00000558401.1:c.194_195del	p.Arg65AsnfsTer2	p.R65Nfs*2	ENST00000558401	NM_004048.2	63	gGA/g	2/4	0.196156411583654	2	FACETS	1	0.941	1	0.553	0.489	0.622	INDETERMINATE	1	TRUE	0	0.336761952679983	2		315	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578284	7578284	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	164	743	0	ENST00000269305.4:c.565G>C	p.Ala189Pro	p.A189P	ENST00000269305	NM_001126112.2	189	Gcc/Ccc	6/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.336761952679983	2		743	818	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021366	42021366	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772780139	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	66	298	0	ENST00000219905.7:c.3662G>A	p.Arg1221Gln	p.R1221Q	ENST00000219905	NM_001164273.1	1221	cGg/cAg	11/24	0.196156411583654	2	FACETS	1	0.958	1	0.618	0.541	0.701	INDETERMINATE	1	TRUE	0	0.336761952679983	2		298	317	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035204	6035207	+	frameshift_variant	Frame_Shift_Del	DEL	CTGT	CTGT	-	rs267608154	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	96	357	0	ENST00000265849.7:c.861_864del	p.Arg287SerfsTer19	p.R287Sfs*19	ENST00000265849	NM_000535.5	287	agACAG/ag	8/15	1	2	FACETS	0.899	0.802	1	0.899	0.802	1	CLONAL	1	TRUE	1	0.336761952679983	2		357	634	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525977	41525977	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	95	348	0	ENST00000263253.7:c.1256del	p.Asn419MetfsTer12	p.N419Mfs*12	ENST00000263253	NM_001429.3	418	Aaa/aa	5/31	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.336761952679983	2		348	502	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205092	38205092	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	101	558	1	ENST00000317025.8:c.598del	p.Ser200AlafsTer20	p.S200Afs*20	ENST00000317025	NM_023034.1	200	Agc/gc	2/24	1	2	FACETS	0.745	0.666	0.83	0.745	0.666	0.83	SUBCLONAL	1	TRUE	1	0.336761952679983	2		559	805	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564886	226564886	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	134	430	0	ENST00000366794.5:c.1864del	p.Thr622ProfsTer31	p.T622Pfs*31	ENST00000366794	NM_001618.3	622	Acc/cc	13/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.336761952679983	2		430	652	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391121	89391121	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	121	512	0	ENST00000336596.2:c.1187T>C	p.Val396Ala	p.V396A	ENST00000336596	NM_005233.5	396	gTg/gCg	5/17	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.336761952679983	2		512	714	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309628	30309628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	170	686	0	ENST00000307677.4:c.394C>T	p.Arg132Trp	p.R132W	ENST00000307677	NM_138578.1	132	Cgg/Tgg	2/3	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.336761952679983	2		686	989	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427276	49427276	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	197	733	0	ENST00000301067.7:c.11212C>T	p.Gln3738Ter	p.Q3738*	ENST00000301067	NM_003482.3	3738	Cag/Tag	39/54	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.336761952679983	2		733	866	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657409	29657409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465309384	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	123	499	0	ENST00000356175.3:c.5642C>T	p.Ala1881Val	p.A1881V	ENST00000356175	NM_000267.3	1881	gCc/gTc	38/57	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.336761952679983	2		499	705	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600416	10600416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1021362446	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	216	837	2	ENST00000171111.5:c.1439G>A	p.Gly480Glu	p.G480E	ENST00000171111	NM_203500.1	480	gGg/gAg	4/6	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.336761952679983	2		839	1203	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494317	2494317	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	194	913	1	ENST00000355716.4:c.708G>T	p.Lys236Asn	p.K236N	ENST00000355716	NM_003820.2	236	aaG/aaT	7/8	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.336761952679983	2		914	1094	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782381	9782381	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149376192	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	84	906	0	ENST00000377346.4:c.2314G>A	p.Gly772Ser	p.G772S	ENST00000377346	NM_005026.3	772	Ggc/Agc	18/24	1	2	FACETS	0.417	0.367	0.471	0.417	0.367	0.471	SUBCLONAL	1	TRUE	1	0.336761952679983	2		906	1197	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118368718	118368718	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555044501	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	75	409	0	ENST00000534358.1:c.5732C>T	p.Ala1911Val	p.A1911V	ENST00000534358	NM_005933.3	1911	gCg/gTg	21/36	1	2	FACETS	0.814	0.715	0.921	0.814	0.715	0.921	CLONAL	1	TRUE	1	0.336761952679983	2		409	547	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374639	118374639	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	86	346	0	ENST00000534358.1:c.8032G>A	p.Asp2678Asn	p.D2678N	ENST00000534358	NM_005933.3	2678	Gat/Aat	27/36	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.336761952679983	2		346	478	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438268	110438268	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	43	136	0	ENST00000375856.3:c.133A>G	p.Lys45Glu	p.K45E	ENST00000375856	NM_003749.2	45	Aag/Gag	1/2	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.336761952679983	2		136	251	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99192836	99192836	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	165	525	0	ENST00000268035.6:c.29del	p.Pro10ArgfsTer37	p.P10Rfs*37	ENST00000268035	NM_000875.3	9	tCc/tc	1/21	0.196156411583654	2	FACETS	1	0.981	1	0.609	0.559	0.66	INDETERMINATE	1	TRUE	0	0.336761952679983	2		525	805	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858630	9858630	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1177789326	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	144	504	0	ENST00000330684.3:c.2771T>C	p.Phe924Ser	p.F924S	ENST00000330684	NM_001134407.1	924	tTc/tCc	13/13	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.336761952679983	2		504	679	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101109	41101109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243176969	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	174	763	0	ENST00000373198.4:c.1247G>A	p.Arg416His	p.R416H	ENST00000373198	NM_133170.3	416	cGc/cAc	8/32	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.336761952679983	2		763	1013	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385165	41385165	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753257334	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	221	772	0	ENST00000373198.4:c.796C>T	p.Arg266Cys	p.R266C	ENST00000373198	NM_133170.3	266	Cgc/Tgc	6/32	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.336761952679983	2		772	1014	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431016	181431016	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	229	852	0	ENST00000325404.1:c.868A>G	p.Ser290Gly	p.S290G	ENST00000325404	NM_003106.3	290	Agc/Ggc	1/1	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.336761952679983	2		852	1068	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608586	189608586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747808524	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	126	485	1	ENST00000264731.3:c.1661C>T	p.Ala554Val	p.A554V	ENST00000264731	NM_003722.4	554	gCg/gTg	13/14	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.336761952679983	2		486	732	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217294	66217294	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	54	247	0	ENST00000273854.3:c.2321T>C	p.Val774Ala	p.V774A	ENST00000273854	NM_004439.5	774	gTg/gCg	14/18	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.336761952679983	2		247	307	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157654	106157654	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	60	216	0	ENST00000380013.4:c.2555A>G	p.Glu852Gly	p.E852G	ENST00000380013	NM_001127208.2	852	gAa/gGa	3/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.336761952679983	2		216	259	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056323	26056323	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs770255220	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	125	422	0	ENST00000343677.2:c.334G>T	p.Ala112Ser	p.A112S	ENST00000343677	NM_005319.3	112	Gcc/Tcc	1/1	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.336761952679983	2		422	632	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332070	81332070	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	41	163	0	ENST00000222390.5:c.2014del	p.Asp672IlefsTer13	p.D672Ifs*13	ENST00000222390	NM_000601.4	672	Gat/at	18/18	1	2	FACETS	0.937	0.785	1	0.937	0.785	1	CLONAL	1	TRUE	1	0.336761952679983	2		163	260	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829185	128829185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	87	208	0	ENST00000249373.3:c.193G>A	p.Gly65Ser	p.G65S	ENST00000249373	NM_005631.4	65	Ggc/Agc	1/12	1	2	FACETS	0.833	0.746	0.925	1	0.983	1	CLONAL	2	TRUE	1	0.336761952679983	2		208	310	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738954	145738954	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	169	692	2	ENST00000428558.2:c.2200+1G>A		p.X734_splice	ENST00000428558	NM_004260.3	734			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.336761952679983	2		694	809	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229678	98229678	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	68	238	0	ENST00000331920.6:c.2280G>T	p.Leu760Phe	p.L760F	ENST00000331920	NM_000264.3	760	ttG/ttT	15/24	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.336761952679983	2		238	356	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245258	53245258	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	168	785	0	ENST00000375401.3:c.779A>C	p.Lys260Thr	p.K260T	ENST00000375401	NM_004187.3	260	aAa/aCa	6/26	1	2	FACETS	0.965	0.886	1	0.965	0.886	1	CLONAL	1	TRUE	1	0.336761952679983	2		785	1034	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0057736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	309	680	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.278569828405754	2	FACETS	0.855	0.81	0.901	0.855	0.81	0.901	CLONAL	2	TRUE	0	0.442409556324779	2		680	817	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0057736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	32	692	1	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	0.374628372408473	2	FACETS	0.208	0.168	0.253	0.104	0.084	0.127	SUBCLONAL	1	TRUE	0	0.442409556324779	2		693	696	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579366	7579366	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs770776262	NA	P-0057737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	23	947	0	ENST00000269305.4:c.321C>A	p.Tyr107Ter	p.Y107*	ENST00000269305	NM_001126112.2	107	taC/taA	4/11	1	2	FACETS	0.431	0.334	0.544	0.431	0.334	0.544	SUBCLONAL	1	TRUE	1	0.12	2		947	890	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508389	106508389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758375337	NA	P-0057737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	19	412	0	ENST00000359195.3:c.383C>T	p.Thr128Met	p.T128M	ENST00000359195	NM_002649.2	128	aCg/aTg	2/11	1	2	FACETS	1	0.788	1	1	0.788	1	CLONAL	1	TRUE	1	0.12	2		412	304	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0057739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	827	574	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.545238711333301	9	FACETS	1	0.98	1			1	CLONAL	8	TRUE	NA	0.545238711333301	9		574	1101	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106099	27106100	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	204	642	0	ENST00000324856.7:c.5715dup	p.Arg1906ThrfsTer8	p.R1906Tfs*8	ENST00000324856	NM_006015.4	1904	gaa/gAaa	20/20	0.545238711333301	3	FACETS	0.996	0.934	1	0.996	0.934	1	CLONAL	2	TRUE	1	0.545238711333301	3		642	478	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873835	35873835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs923187160	NA	P-0057739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	25	290	0	ENST00000216797.5:c.16G>A	p.Glu6Lys	p.E6K	ENST00000216797	NM_020529.2	6	Gag/Aag	1/6	0.545238711333301	3	FACETS	0.729	0.581	0.897	0.365	0.29	0.449	SUBCLONAL	1	TRUE	1	0.545238711333301	3		290	160	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0057739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	83	366	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.545238711333301	2		366	284	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978935	25978935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	161	465	0	ENST00000435504.4:c.988G>A	p.Glu330Lys	p.E330K	ENST00000435504		330	Gaa/Aaa	10/13	0.545238711333301	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.545238711333301	3		465	362	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499694	8499694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1202079054	NA	P-0057739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	188	586	1	ENST00000356435.5:c.2275C>T	p.Pro759Ser	p.P759S	ENST00000356435		759	Ccc/Tcc	14/35	0.545238711333301	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.545238711333301	3		587	403	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872374	45872374	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	324	913	0	ENST00000391945.4:c.137C>G	p.Thr46Ser	p.T46S	ENST00000391945	NM_000400.3	46	aCc/aGc	3/23	0.439179620160837	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.545238711333301	4		913	835	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433650	49433650	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs794727549	NA	P-0057739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	454	1365	2	ENST00000301067.7:c.7903C>T	p.Arg2635Ter	p.R2635*	ENST00000301067	NM_003482.3	2635	Cga/Tga	31/54	0.545238711333301	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.545238711333301	4		1367	1189	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250755	26250755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	90	646	0	ENST00000446824.2:c.79C>T	p.Arg27Cys	p.R27C	ENST00000446824	NM_021018.2	27	Cgc/Tgc	1/1	0.545238711333301	3	FACETS	0.884	0.788	0.987			1	CLONAL	1	TRUE	NA	0.545238711333301	3		646	475	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003545	42003545	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	61	347	0	ENST00000219905.7:c.3082C>T	p.Gln1028Ter	p.Q1028*	ENST00000219905	NM_001164273.1	1028	Caa/Taa	8/24	0.496495896138821	4	FACETS	0.985	0.855	1	0.493	0.427	0.563	CLONAL	1	TRUE	2	0.545238711333301	4		347	351	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434123	12434123	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	85	327	0	ENST00000287820.6:c.491G>A	p.Arg164Gln	p.R164Q	ENST00000287820	NM_015869.4	164	cGg/cAg	4/7	0.545238711333301	3	FACETS	1	0.965	1	0.603	0.538	0.671	CLONAL	1	TRUE	1	0.545238711333301	3		327	329	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205025	128205025	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	187	1162	0	ENST00000341105.2:c.416C>T	p.Ser139Phe	p.S139F	ENST00000341105	NM_032638.4	139	tCt/tTt	3/6	0.545238711333301	3	FACETS	1	0.982	1	0.591	0.547	0.636	CLONAL	1	TRUE	1	0.545238711333301	3		1162	739	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121110	3121110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	157	850	0	ENST00000078429.4:c.1013G>A	p.Arg338His	p.R338H	ENST00000078429	NM_002067.2	338	cGc/cAc	7/7	0.545238711333301	3	FACETS	1	0.98	1	0.4	0.368	0.433	CLONAL	1	TRUE	0	0.545238711333301	3		850	611	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257807	16257807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	103	677	1	ENST00000375759.3:c.5072C>T	p.Pro1691Leu	p.P1691L	ENST00000375759	NM_015001.2	1691	cCt/cTt	11/15	0.545238711333301	3	FACETS	1	0.936	1	0.527	0.474	0.583	CLONAL	1	TRUE	1	0.545238711333301	3		678	456	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139177	108139191	+	inframe_deletion	In_Frame_Del	DEL	AGATCTACTTTTCTT	AGATCTACTTTTCTT	-	novel	NA	P-0057739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	109	582	0	ENST00000278616.4:c.2682_2696del	p.Leu895_Asp899del	p.L895_D899del	ENST00000278616	NM_000051.3	893	caAGATCTACTTTTCTTa/caa	18/63	1	2	FACETS	0.973	0.88	1	0.973	0.88	1	CLONAL	1	TRUE	1	0.545238711333301	2		582	411	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112940026	112940026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516797	NA	P-0057739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	293	819	1	ENST00000351677.2:c.1678C>T	p.Leu560Phe	p.L560F	ENST00000351677	NM_002834.3	560	Ctc/Ttc	14/16	0.545238711333301	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	2	0.545238711333301	4		820	797	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562339	95562339	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	81	447	0	ENST00000393063.1:c.4918G>C	p.Gly1640Arg	p.G1640R	ENST00000393063	NM_030621.3	1640	Ggt/Cgt	24/28	0.545238711333301	3	FACETS	1	0.914	1	0.518	0.459	0.58	CLONAL	1	TRUE	1	0.545238711333301	3		447	365	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130325	2130325	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	362	1201	0	ENST00000219476.3:c.3557A>C	p.Tyr1186Ser	p.Y1186S	ENST00000219476	NM_000548.3	1186	tAt/tCt	30/42	0.439179620160837	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.545238711333301	4		1201	973	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857409	9857409	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	206	588	0	ENST00000330684.3:c.3992T>A	p.Val1331Asp	p.V1331D	ENST00000330684	NM_001134407.1	1331	gTc/gAc	13/13	0.439179620160837	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.545238711333301	4		588	486	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619190	37619190	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	139	734	0	ENST00000447079.4:c.866C>T	p.Thr289Ile	p.T289I	ENST00000447079	NM_015083.1	289	aCc/aTc	1/14	0.545238711333301	9	FACETS	1	0.974	1			1	CLONAL	1	TRUE	NA	0.545238711333301	9		734	1238	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39623775	39623790	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGCTGTGGTAAGTTTT	AGCTGTGGTAAGTTTT	-	novel	NA	P-0057739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	61	380	0	ENST00000262039.4:c.2182_2188+9del		p.X728_splice	ENST00000262039	NM_002647.2	728		20/25	0.545238711333301	4	FACETS	0.726	0.628	0.833	0.363	0.314	0.417	SUBCLONAL	1	TRUE	2	0.545238711333301	4		380	476	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212212	5212212	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	297	963	0	ENST00000357368.4:c.4819G>C	p.Glu1607Gln	p.E1607Q	ENST00000357368	NM_002850.3	1607	Gag/Cag	32/38	0.545238711333301	5	FACETS	1	0.982	1	0.437	0.412	0.462	CLONAL	2	TRUE	0	0.545238711333301	5		963	906	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182160	99182160	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1352	102	594	0	ENST00000074304.5:c.2225T>A	p.Val742Glu	p.V742E	ENST00000074304	NM_001134224.1	742	gTg/gAg	21/26	0.545238711333301	12	FACETS	0.959	0.854	1			1	CLONAL	1	TRUE	NA	0.545238711333301	12		594	1454	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309723	30309723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	285	745	0	ENST00000307677.4:c.299G>A	p.Arg100Gln	p.R100Q	ENST00000307677	NM_138578.1	100	cGg/cAg	2/3	0.439179620160837	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.545238711333301	4		745	739	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441266	52441266	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	224	700	0	ENST00000460680.1:c.504C>G	p.Phe168Leu	p.F168L	ENST00000460680	NM_004656.3	168	ttC/ttG	7/17	0.545238711333301	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.545238711333301	3		700	506	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741165	145741165	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	82	864	0	ENST00000428558.2:c.1241C>G	p.Ala414Gly	p.A414G	ENST00000428558	NM_004260.3	414	gCc/gGc	6/22	0.545238711333301	5	FACETS	0.611	0.538	0.69	0.204	0.179	0.23	SUBCLONAL	1	TRUE	2	0.545238711333301	5		864	895	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223601	53223601	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	127	493	0	ENST00000375401.3:c.3758C>G	p.Pro1253Arg	p.P1253R	ENST00000375401	NM_004187.3	1253	cCg/cGg	23/26	0.545238711333301	2	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.545238711333301	2		493	396	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410271	63410271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	322	532	0	ENST00000330258.3:c.2896C>T	p.Leu966Phe	p.L966F	ENST00000330258	NM_152424.3	966	Ctt/Ttt	2/2	0.545238711333301	2	FACETS	0.94	0.909	0.969			1	CLONAL	3	TRUE	NA	0.545238711333301	2		532	419	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0057740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	506	339	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.264772500915572	8	FACETS	0.963	0.932	0.994	1	0.996	1	CLONAL	9	TRUE	1	0.264772500915572	8		339	791	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1976689	1976689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	191	745	0	ENST00000382891.5:c.3472G>A	p.Asp1158Asn	p.D1158N	ENST00000382891	NM_133335.3	1158	Gac/Aac	19/22	0.263684936110447	3	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	1	0.264772500915572	3		745	801	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161970034	161970034	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs756869892	NA	P-0057740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	91	705	0	ENST00000366898.1:c.935A>G	p.Tyr312Cys	p.Y312C	ENST00000366898	NM_004562.2	312	tAc/tGc	9/12	0.230988400124423	4	FACETS	1	0.942	1	0.55	0.487	0.616	CLONAL	1	TRUE	2	0.264772500915572	4		705	791	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	75	619	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	1	0.944	1			1	INDETERMINATE	1	TRUE	NA	0.43895664891746	2		619	307	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0057743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	24	375	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.421	0.329	0.527	0.421	0.329	0.527	SUBCLONAL	1	TRUE	1	0.266435214531539	2		375	428	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0057743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	156	753	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.266435214531539	2	FACETS	1	0.988	1	0.732	0.671	0.796	CLONAL	1	TRUE	0	0.266435214531539	2		753	800	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0057743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	105	423	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.245424668523999	3	FACETS	0.766	0.688	0.848	0.766	0.688	0.848	SUBCLONAL	2	TRUE	1	0.266435214531539	3		423	583	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070877	30070877	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	124	763	0	ENST00000338641.4:c.1393G>C	p.Glu465Gln	p.E465Q	ENST00000338641	NM_000268.3	465	Gag/Cag	13/16	0.219980433460338	3	FACETS	1	0.981	1	0.678	0.613	0.746	CLONAL	1	TRUE	1	0.266435214531539	3		763	778	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336255	80336255	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	49	387	0	ENST00000286548.4:c.1064A>T	p.Glu355Val	p.E355V	ENST00000286548	NM_002072.3	355	gAg/gTg	7/7	1	2	FACETS	0.834	0.707	0.973	0.834	0.707	0.973	CLONAL	1	TRUE	1	0.266435214531539	2		387	441	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195163	123195163	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	46	450	1	ENST00000218089.9:c.1506A>T	p.Leu502Phe	p.L502F	ENST00000218089	NM_001042749.1	502	ttA/ttT	16/35	1	2	FACETS	0.681	0.573	0.8	0.681	0.573	0.8	SUBCLONAL	1	TRUE	1	0.266435214531539	2		451	507	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	39	619	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.18	2		619	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0057745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	58	822	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.3	2	FACETS	0.84	0.72	0.971			1	CLONAL	1	TRUE	NA	0.18	2		822	767	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	54	777	0	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	0.743	0.633	0.865	0.743	0.633	0.865	SUBCLONAL	1	TRUE	1	0.18	2		777	807	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557678	21557679	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	G	novel	NA	P-0057746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	122	696	0	ENST00000382592.4:c.2166_2167delinsC	p.Glu722AspfsTer23	p.E722Dfs*23	ENST00000382592	NM_014572.2	722	gaGGca/gaCca	5/8	0.313519553225003	1	FACETS	0.9	0.814	0.991	0.9	0.814	0.991	CLONAL	1	TRUE	0	0.313519553225003	1		696	729	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141492	11141492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	148	718	0	ENST00000358026.2:c.3469C>T	p.Arg1157Trp	p.R1157W	ENST00000358026	NM_001128849.1	1157	Cgg/Tgg	25/36	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.313519553225003	2		718	888	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258035	123258035	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	104	448	0	ENST00000358487.5:c.1646A>C	p.Asn549Thr	p.N549T	ENST00000358487	NM_000141.4	549	aAt/aCt	12/18	0.313519553225003	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.313519553225003	1		448	477	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141499	11141499	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057746-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	51	613	0	ENST00000358026.2:c.3476G>T	p.Gly1159Val	p.G1159V	ENST00000358026	NM_001128849.1	1159	gGg/gTg	25/36	1	2	FACETS	0.472	0.401	0.551	0.472	0.401	0.551	SUBCLONAL	1	TRUE	1	0.325630355242194	2		613	663	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557678	21557679	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	G	novel	NA	P-0057746-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	80	696	0	ENST00000382592.4:c.2166_2167delinsC	p.Glu722AspfsTer23	p.E722Dfs*23	ENST00000382592	NM_014572.2	722	gaGGca/gaCca	5/8	0.325630355242194	1	FACETS	0.975	0.862	1	0.975	0.862	1	CLONAL	1	TRUE	0	0.325630355242194	1		696	422	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0057747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	39	473	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.671	0.557	0.796	0.671	0.557	0.796	SUBCLONAL	1	TRUE	1	0.336094281683202	2		474	346	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255160	16255160	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	39	360	0	ENST00000375759.3:c.2425A>G	p.Ile809Val	p.I809V	ENST00000375759	NM_015001.2	809	Ata/Gta	11/15	1	2	FACETS	0.669	0.556	0.794	0.669	0.556	0.794	SUBCLONAL	1	TRUE	1	0.336094281683202	2		360	347	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208327	5208327	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	89	894	1	ENST00000357368.4:c.5563G>T	p.Gly1855Cys	p.G1855C	ENST00000357368	NM_002850.3	1855	Ggc/Tgc	36/38	1	2	FACETS	0.666	0.59	0.748	0.666	0.59	0.748	SUBCLONAL	1	TRUE	1	0.336094281683202	2		895	795	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144879	47144879	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	106	411	0	ENST00000409792.3:c.4874G>T	p.Arg1625Leu	p.R1625L	ENST00000409792	NM_014159.6	1625	cGt/cTt	7/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.336094281683202	2		411	423	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499326	89499326	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0057747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	39	352	0	ENST00000336596.2:c.2497-1G>A		p.X833_splice	ENST00000336596	NM_005233.5	833			1	2	FACETS	0.725	0.603	0.86	0.725	0.603	0.86	SUBCLONAL	1	TRUE	1	0.336094281683202	2		352	320	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142949993	142949993	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	60	409	1	ENST00000262992.4:c.2717T>A	p.Met906Lys	p.M906K	ENST00000262992	NM_001101669.1	906	aTg/aAg	24/24	1	2	FACETS	0.915	0.792	1	0.915	0.792	1	CLONAL	1	TRUE	1	0.336094281683202	2		410	390	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499818	8499818	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	26	459	0	ENST00000356435.5:c.2151A>T	p.Lys717Asn	p.K717N	ENST00000356435		717	aaA/aaT	14/35	1	2	FACETS	0.342	0.27	0.424	0.342	0.27	0.424	SUBCLONAL	1	TRUE	1	0.336094281683202	2		459	453	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020662	37020662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	50	444	0	ENST00000358127.4:c.183C>A	p.Ser61Arg	p.S61R	ENST00000358127	NM_001280556.1	61	agC/agA	2/10	1	2	FACETS	0.687	0.584	0.8	0.687	0.584	0.8	SUBCLONAL	1	TRUE	1	0.336094281683202	2		444	433	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	233	619	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.268347218465647	5	FACETS	0.978	0.92	1	0.978	0.92	1	CLONAL	4	TRUE	1	0.31	5		619	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780071	NA	P-0057748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	199	944	0	ENST00000269305.4:c.580C>T	p.Leu194Phe	p.L194F	ENST00000269305	NM_001126112.2	194	Ctt/Ttt	6/11	NA	2	FACETS	0.833	0.773	0.894			1	INDETERMINATE	2	TRUE	NA	0.31	2		944	771	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309006	137309006	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1430081220	NA	P-0057748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	249	974	0	ENST00000481739.1:c.613G>A	p.Val205Met	p.V205M	ENST00000481739	NM_002957.4	205	Gtg/Atg	5/10	1	2	FACETS	0.751	0.703	0.802	1	0.993	1	SUBCLONAL	2	TRUE	1	0.31	2		974	1069	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	125	619	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.512125764041019	3	FACETS	0.889	0.814	0.965	0.889	0.814	0.965	CLONAL	2	TRUE	1	0.512125764041019	3		619	345	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278135	142278135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	68	685	3	ENST00000350721.4:c.1690G>A	p.Asp564Asn	p.D564N	ENST00000350721	NM_001184.3	564	Gat/Aat	7/47	1	2	FACETS	0.942	0.827	1	0.942	0.827	1	CLONAL	1	TRUE	1	0.512125764041019	2		688	282	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604704	48604704	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	131	638	0	ENST00000342988.3:c.1526G>A	p.Trp509Ter	p.W509*	ENST00000342988	NM_005359.5	509	tGg/tAg	12/12	0.512125764041019	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.512125764041019	1		638	369	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610098	43610098	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	43	1586	2	ENST00000355710.3:c.2050C>A	p.Pro684Thr	p.P684T	ENST00000355710	NM_020975.4	684	Ccg/Acg	11/20	1	2	FACETS	0.199	0.166	0.236	0.199	0.166	0.236	SUBCLONAL	1	TRUE	1	0.512125764041019	2		1588	844	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717696	89717696	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	204	435	0	ENST00000371953.3:c.723del	p.Phe241LeufsTer15	p.F241Lfs*15	ENST00000371953	NM_000314.4	241	Ttt/tt	7/9	0.512871937712257	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.512871937712257	2		435	397	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375019	45375019	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	72	379	0	ENST00000262160.6:c.824G>C	p.Cys275Ser	p.C275S	ENST00000262160	NM_005901.5	275	tGt/tCt	8/11	0.512871937712257	2	FACETS	1	0.886	1	0.501	0.443	0.563	CLONAL	1	TRUE	0	0.512871937712257	2		379	280	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991662	25991662	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	85	441	0	ENST00000435504.4:c.580C>G	p.Leu194Val	p.L194V	ENST00000435504		194	Ctc/Gtc	7/13	0.512871937712257	3	FACETS	0.919	0.816	1	0.46	0.408	0.515	CLONAL	1	TRUE	1	0.512871937712257	3		441	453	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38139086	38139086	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	99	380	0	ENST00000317025.8:c.3517G>C	p.Glu1173Gln	p.E1173Q	ENST00000317025	NM_023034.1	1173	Gaa/Caa	20/24	0.512871937712257	9	FACETS	0.907	0.807	1			1	CLONAL	1	TRUE	NA	0.512871937712257	9		380	1190	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0057759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	8	737	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.829065532877137	1	FACETS	0.03	0.019	0.044	0.03	0.019	0.044	SUBCLONAL	1	TRUE	0	0.829065532877137	1		739	378	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692961	89692961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060500122	NA	P-0057759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	59	471	0	ENST00000371953.3:c.445C>T	p.Gln149Ter	p.Q149*	ENST00000371953	NM_000314.4	149	Caa/Taa	5/9	0.829065532877137	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.829065532877137	1		471	78	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432473	49432473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	174	938	0	ENST00000301067.7:c.8666G>A	p.Gly2889Glu	p.G2889E	ENST00000301067	NM_003482.3	2889	gGa/gAa	34/54	0.758718895491515	2	FACETS	0.976	0.936	1	0.976	0.936	1	CLONAL	2	TRUE	0	0.829065532877137	2		938	215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578273	+	missense_variant	Missense_Mutation	DNP	GC	GC	TA	novel	NA	P-0057759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	101	752	1	ENST00000269305.4:c.576_577delinsTA	p.Gln192_His193delinsHisAsn	p.Q192_H193delinsHN	ENST00000269305	NM_001126112.2	192	caGCat/caTAat	6/11	0.829065532877137	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.829065532877137	1		753	130	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0057760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	202	730	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.28354849941982	2	FACETS	0.992	0.923	1	0.992	0.923	1	CLONAL	2	TRUE	0	0.28354849941982	2		730	718	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858210	9858210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756930722	NA	P-0057760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	62	692	1	ENST00000330684.3:c.3191C>T	p.Thr1064Met	p.T1064M	ENST00000330684	NM_001134407.1	1064	aCg/aTg	13/13	1	2	FACETS	0.836	0.723	0.959	0.836	0.723	0.959	CLONAL	1	TRUE	1	0.28354849941982	2		693	523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0057761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	141	740	3	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.246293871683466	3	FACETS	0.844	0.774	0.918	0.563	0.516	0.612	CLONAL	2	FALSE	0	0.37735794489101	3		743	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0057761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	86	668	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.246293871683466	3	FACETS	1	0.964	1	0.403	0.358	0.451	CLONAL	1	FALSE	0	0.37735794489101	3		668	448	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	58	628	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	0.37735794489101	4	FACETS	0.808	0.701	0.922	0.539	0.467	0.615	CLONAL	2	FALSE	1	0.37735794489101	4		628	262	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0057761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	26	257	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.37735794489101	5	FACETS	0.799	0.642	0.974	0.533	0.428	0.649	CLONAL	2	FALSE	2	0.37735794489101	5		257	135	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0057761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	36	403	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	0.37735794489101	4	FACETS	0.755	0.629	0.893	0.503	0.419	0.596	SUBCLONAL	2	FALSE	1	0.37735794489101	4		403	174	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962848	2962848	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41493047	NA	P-0057761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	101	960	0	ENST00000396946.4:c.2060C>T	p.Ala687Val	p.A687V	ENST00000396946	NM_032415.4	687	gCg/gTg	16/25	0.345962265145892	5	FACETS	1	0.96	1	0.751	0.677	0.828	CLONAL	2	FALSE	2	0.37735794489101	5		960	372	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971324	13971324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752431857	NA	P-0057761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	59	464	0	ENST00000405192.2:c.605C>T	p.Thr202Met	p.T202M	ENST00000405192	NM_001163147.1	202	aCg/aTg	8/12	0.345962265145892	5	FACETS	0.894	0.776	1	0.596	0.517	0.68	CLONAL	2	FALSE	2	0.37735794489101	5		464	274	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425644	49425644	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057517992	NA	P-0057761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	113	886	0	ENST00000301067.7:c.12844C>T	p.Arg4282Ter	p.R4282*	ENST00000301067	NM_003482.3	4282	Cga/Tga	39/54	0.37735794489101	7	FACETS	0.995	0.903	1	0.746	0.677	0.817	CLONAL	3	FALSE	3	0.37735794489101	7		886	390	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749592	41749592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1162584880	NA	P-0057761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	103	751	0	ENST00000301178.4:c.1517G>A	p.Arg506His	p.R506H	ENST00000301178	NM_021913.4	506	cGt/cAt	12/20	0.230971751025486	5	FACETS	1	0.957	1	0.74	0.668	0.816	CLONAL	2	FALSE	2	0.37735794489101	5		751	385	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233751	233751	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199844384	NA	P-0057761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	101	683	2	ENST00000264932.6:c.1055G>A	p.Arg352Gln	p.R352Q	ENST00000264932	NM_004168.2	352	cGa/cAa	8/15	0.37735794489101	3	FACETS	0.874	0.788	0.963	0.874	0.788	0.963	CLONAL	2	FALSE	1	0.37735794489101	3		685	364	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946337	2946337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759681668	NA	P-0057761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	134	1043	2	ENST00000396946.4:c.3400G>A	p.Val1134Ile	p.V1134I	ENST00000396946	NM_032415.4	1134	Gtt/Att	25/25	0.345962265145892	5	FACETS	0.856	0.785	0.93	0.856	0.785	0.93	CLONAL	3	FALSE	2	0.37735794489101	5		1045	433	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539870	187539870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	41	408	0	ENST00000441802.2:c.7870G>A	p.Asp2624Asn	p.D2624N	ENST00000441802	NM_005245.3	2624	Gat/Aat	10/27	0.37735794489101	5	FACETS	0.984	0.831	1	0.656	0.554	0.765	CLONAL	2	FALSE	2	0.37735794489101	5		408	173	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946468	71946468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	115	753	1	ENST00000298229.2:c.2632C>T	p.Arg878Cys	p.R878C	ENST00000298229	NM_001567.3	878	Cgc/Tgc	23/28	0.295651342776036	5	FACETS	0.918	0.843	0.994	1	0.979	1	CLONAL	4	FALSE	2	0.37735794489101	5		754	260	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401002	139401002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769908800	NA	P-0057761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	104	917	1	ENST00000277541.6:c.3991G>A	p.Gly1331Arg	p.G1331R	ENST00000277541	NM_017617.3	1331	Ggg/Agg	24/34	0.303348945120252	4	FACETS	0.94	0.848	1	0.94	0.848	1	CLONAL	2	FALSE	2	0.37735794489101	4		918	404	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803738	1803738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774047997	NA	P-0057761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	144	802	0	ENST00000260795.2:c.916G>A	p.Val306Ile	p.V306I	ENST00000260795		306	Gtt/Att	6/17	0.37735794489101	5	FACETS	0.942	0.867	1	0.942	0.867	1	CLONAL	3	FALSE	2	0.37735794489101	5		802	423	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40468879	40468879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293678815	NA	P-0057761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	46	403	1	ENST00000264657.5:c.2185C>T	p.Arg729Cys	p.R729C	ENST00000264657	NM_139276.2	729	Cgc/Tgc	23/24	0.37735794489101	3	FACETS	1	0.898	1	0.539	0.457	0.628	CLONAL	1	FALSE	1	0.37735794489101	3		404	269	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061564	38061564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760564263	NA	P-0057761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	77	176	0	ENST00000250448.2:c.425C>T	p.Ala142Val	p.A142V	ENST00000250448	NM_004496.3	142	gCg/gTg	2/2	0.37735794489101	5	FACETS	1	0.954	1	1	0.983	1	CLONAL	3	FALSE	3	0.37735794489101	5		176	191	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042061	14042061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs562305007	NA	P-0057761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	96	320	0	ENST00000311895.7:c.2608G>A	p.Val870Ile	p.V870I	ENST00000311895	NM_005236.2	870	Gtt/Att	11/11	0.37735794489101	4	FACETS	0.92	0.833	1			1	CLONAL	3	FALSE	NA	0.37735794489101	4		320	254	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357214	70357214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	101	663	3	ENST00000374080.3:c.5729G>A	p.Arg1910His	p.R1910H	ENST00000374080		1910	cGc/cAc	39/45	0.37735794489101	3	FACETS	0.862	0.777	0.95	0.862	0.777	0.95	CLONAL	2	FALSE	1	0.37735794489101	3		666	369	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759904	63759904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	38	348	1	ENST00000279873.7:c.557G>A	p.Arg186Gln	p.R186Q	ENST00000279873	NM_032199.2	186	cGg/cAg	4/10	0.5612642233952	6	FACETS	1	0.893	1			1	CLONAL	1	TRUE	NA	0.5612642233952	6		349	261	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023202	27023202	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	18	112	0	ENST00000324856.7:c.308C>G	p.Ser103Trp	p.S103W	ENST00000324856	NM_006015.4	103	tCg/tGg	1/20	0.5612642233952	3	FACETS	0.74	0.565	0.941	0.247	0.188	0.314	CLONAL	1	TRUE	0	0.5612642233952	3		112	111	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068118	94068118	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	49	197	0	ENST00000369303.4:c.844G>T	p.Gly282Trp	p.G282W	ENST00000369303	NM_004440.3	282	Ggg/Tgg	4/17	0.602346902665762	3	FACETS	0.877	0.75	1	0.439	0.375	0.507	CLONAL	1	TRUE	1	0.613252770947124	3		197	238	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277607	142277607	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	42	284	0	ENST00000350721.4:c.1744T>C	p.Phe582Leu	p.F582L	ENST00000350721	NM_001184.3	582	Ttt/Ctt	8/47	0.497038553851614	4	FACETS	0.795	0.668	0.934	0.397	0.334	0.467	CLONAL	1	TRUE	2	0.613252770947124	4		284	278	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0057764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	354	680	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.568193407506434	2		680	544	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240289	5240289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368361739	NA	P-0057764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	174	1146	0	ENST00000357368.4:c.1625C>T	p.Thr542Met	p.T542M	ENST00000357368	NM_002850.3	542	aCg/aTg	12/38	0.269974316136169	2	FACETS	0.836	0.771	0.902	0.418	0.385	0.451	INDETERMINATE	1	TRUE	0	0.568193407506434	2		1146	733	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465391	99465391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912429	NA	P-0057764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	65	395	0	ENST00000268035.6:c.2216G>A	p.Arg739Gln	p.R739Q	ENST00000268035	NM_000875.3	739	cGg/cAg	11/21	1	2	FACETS	0.982	0.863	1	0.982	0.863	1	CLONAL	1	TRUE	1	0.568193407506434	2		395	233	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0057765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	61	314	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		314	296	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	27	365	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.854	0.683	1	0.854	0.683	1	CLONAL	1	TRUE	1	0.266743595053482	2		365	237	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941653	48941653	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0057767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	23	185	0	ENST00000267163.4:c.963C>G	p.Tyr321Ter	p.Y321*	ENST00000267163	NM_000321.2	321	taC/taG	10/27	0.266743595053482	1	FACETS	0.708	0.555	0.884	0.708	0.555	0.884	SUBCLONAL	1	TRUE	0	0.266743595053482	1		185	211	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073323	8073323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	42	429	1	ENST00000377482.5:c.1336G>A	p.Asp446Asn	p.D446N	ENST00000377482	NM_018948.3	446	Gat/Aat	4/4	1	2	FACETS	0.644	0.537	0.762	0.644	0.537	0.762	SUBCLONAL	1	TRUE	1	0.266743595053482	2		430	489	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097665	27097665	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0057767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	41	652	0	ENST00000324856.7:c.3254C>G	p.Ser1085Ter	p.S1085*	ENST00000324856	NM_006015.4	1085	tCa/tGa	12/20	1	2	FACETS	0.462	0.383	0.549	0.462	0.383	0.549	SUBCLONAL	1	TRUE	1	0.266743595053482	2		652	666	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981298	201981298	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs79918642	NA	P-0057767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	73	926	0	ENST00000359651.3:c.377G>T	p.Arg126Leu	p.R126L	ENST00000359651		126	cGa/cTa	2/8	1	2	FACETS	0.645	0.563	0.734	0.645	0.563	0.734	SUBCLONAL	1	TRUE	1	0.266743595053482	2		926	849	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981767	201981767	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0057767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	86	934	1	ENST00000359651.3:c.479-1G>C		p.X160_splice	ENST00000359651		160			1	2	FACETS	0.735	0.649	0.828	0.735	0.649	0.828	SUBCLONAL	1	TRUE	1	0.266743595053482	2		935	877	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650051	206650051	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs782081148	NA	P-0057767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	62	658	0	ENST00000367120.3:c.571C>T	p.Arg191Ter	p.R191*	ENST00000367120	NM_014002.3	191	Cga/Tga	7/22	1	2	FACETS	0.608	0.525	0.7	0.608	0.525	0.7	SUBCLONAL	1	TRUE	1	0.266743595053482	2		658	764	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70432705	70432705	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	35	456	0	ENST00000373644.4:c.4727C>G	p.Ser1576Cys	p.S1576C	ENST00000373644	NM_030625.2	1576	tCt/tGt	8/12	1	2	FACETS	0.468	0.383	0.564	0.468	0.383	0.564	SUBCLONAL	1	TRUE	1	0.266743595053482	2		456	561	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343963	118343963	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	41	369	0	ENST00000534358.1:c.2089C>G	p.Leu697Val	p.L697V	ENST00000534358	NM_005933.3	697	Ctg/Gtg	3/36	1	2	FACETS	0.835	0.697	0.988	0.835	0.697	0.988	CLONAL	1	TRUE	1	0.266743595053482	2		369	368	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443674	49443674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	71	944	1	ENST00000301067.7:c.3697G>A	p.Glu1233Lys	p.E1233K	ENST00000301067	NM_003482.3	1233	Gag/Aag	11/54	0.266743595053482	3	FACETS	0.651	0.567	0.742	0.325	0.283	0.371	SUBCLONAL	1	TRUE	1	0.266743595053482	3		945	927	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445798	49445799	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0057767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	226	1188	0	ENST00000301067.7:c.1667dup	p.Pro557AlafsTer3	p.P557Afs*3	ENST00000301067	NM_003482.3	556	ccg/ccCg	10/54	0.266743595053482	3	FACETS	0.763	0.709	0.818	0.763	0.709	0.818	SUBCLONAL	2	TRUE	1	0.266743595053482	3		1188	1259	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054471	42054471	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769432234	NA	P-0057767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	29	447	0	ENST00000219905.7:c.7655C>T	p.Ser2552Phe	p.S2552F	ENST00000219905	NM_001164273.1	2552	tCt/tTt	22/24	1	2	FACETS	0.462	0.37	0.566	0.462	0.37	0.566	SUBCLONAL	1	TRUE	1	0.266743595053482	2		447	471	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339582	339582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558178546	NA	P-0057767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	57	912	0	ENST00000262320.3:c.2320G>A	p.Gly774Ser	p.G774S	ENST00000262320	NM_003502.3	774	Ggc/Agc	10/11	1	2	FACETS	0.502	0.43	0.582	0.502	0.43	0.582	SUBCLONAL	1	TRUE	1	0.266743595053482	2		912	851	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832400	72832400	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0057767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	43	491	0	ENST00000268489.5:c.4181C>G	p.Ser1394Ter	p.S1394*	ENST00000268489	NM_006885.3	1394	tCa/tGa	9/10	1	2	FACETS	0.625	0.522	0.738	0.625	0.522	0.738	SUBCLONAL	1	TRUE	1	0.266743595053482	2		491	516	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832468	72832468	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1429363633	NA	P-0057767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	36	503	0	ENST00000268489.5:c.4113C>G	p.Phe1371Leu	p.F1371L	ENST00000268489	NM_006885.3	1371	ttC/ttG	9/10	1	2	FACETS	0.53	0.435	0.637	0.53	0.435	0.637	SUBCLONAL	1	TRUE	1	0.266743595053482	2		503	509	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664539	29664539	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	35	546	0	ENST00000356175.3:c.6518G>C	p.Arg2173Thr	p.R2173T	ENST00000356175	NM_000267.3	2173	aGa/aCa	42/57	0.237384275316613	3	FACETS	0.454	0.371	0.548	0.227	0.185	0.274	SUBCLONAL	1	TRUE	1	0.266743595053482	3		546	655	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0057767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	48	591	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.237384275316613	3	FACETS	0.473	0.399	0.556	0.237	0.199	0.278	SUBCLONAL	1	TRUE	1	0.266743595053482	3		592	862	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857642	59857642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	22	305	0	ENST00000259008.2:c.1915C>T	p.His639Tyr	p.H639Y	ENST00000259008	NM_032043.2	639	Cat/Tat	13/20	0.266743595053482	3	FACETS	0.455	0.352	0.575	0.227	0.176	0.288	SUBCLONAL	1	TRUE	1	0.266743595053482	3		305	411	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775022	73775022	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	43	532	0	ENST00000254810.4:c.151G>C	p.Glu51Gln	p.E51Q	ENST00000254810	NM_005324.3	51	Gag/Cag	3/4	0.237384275316613	3	FACETS	0.587	0.491	0.695	0.294	0.245	0.348	SUBCLONAL	1	TRUE	1	0.266743595053482	3		532	622	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621013	1621013	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1342	111	1241	0	ENST00000344749.5:c.1047C>G	p.Phe349Leu	p.F349L	ENST00000344749	NM_001136139.2	349	ttC/ttG	13/19	0.237384275316613	3	FACETS	0.649	0.581	0.722	0.325	0.29	0.361	SUBCLONAL	1	TRUE	1	0.266743595053482	3		1241	1453	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300176	15300176	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	63	970	0	ENST00000263388.2:c.1100A>G	p.Asp367Gly	p.D367G	ENST00000263388	NM_000435.2	367	gAc/gGc	7/33	0.237384275316613	3	FACETS	0.474	0.408	0.546	0.237	0.204	0.273	SUBCLONAL	1	TRUE	1	0.266743595053482	3		970	1130	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224731	36224731	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1237	79	1173	0	ENST00000222270.7:c.7117C>A	p.Pro2373Thr	p.P2373T	ENST00000222270	NM_014727.1	2373	Ccc/Acc	30/37	0.237384275316613	3	FACETS	0.51	0.447	0.579	0.255	0.223	0.29	SUBCLONAL	1	TRUE	1	0.266743595053482	3		1173	1316	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912813	50912813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758260006	NA	P-0057767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	87	1224	0	ENST00000440232.2:c.2044C>T	p.Arg682Trp	p.R682W	ENST00000440232	NM_002691.3	682	Cgg/Tgg	17/27	0.237384275316613	3	FACETS	0.603	0.531	0.679	0.301	0.265	0.34	SUBCLONAL	1	TRUE	1	0.266743595053482	3		1224	1227	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982458	25982458	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	136	316	0	ENST00000435504.4:c.832C>G	p.Leu278Val	p.L278V	ENST00000435504		278	Ctg/Gtg	9/13	0.266743595053482	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.266743595053482	2		316	412	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606185	47606185	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	32	322	0	ENST00000263735.4:c.649G>C	p.Glu217Gln	p.E217Q	ENST00000263735	NM_002354.2	217	Gaa/Caa	6/9	0.266743595053482	2	FACETS	0.543	0.44	0.659	0.271	0.22	0.33	SUBCLONAL	1	TRUE	0	0.266743595053482	2		322	442	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266828	198266828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs16865307	NA	P-0057767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	44	513	0	ENST00000335508.6:c.2104C>T	p.Arg702Trp	p.R702W	ENST00000335508	NM_012433.2	702	Cgg/Tgg	15/25	0.266743595053482	1	FACETS	0.496	0.416	0.586	0.496	0.416	0.586	SUBCLONAL	1	TRUE	0	0.266743595053482	1		513	576	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023255	31023255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	40	619	0	ENST00000375687.4:c.2740G>A	p.Glu914Lys	p.E914K	ENST00000375687	NM_015338.5	914	Gaa/Aaa	13/13	1	2	FACETS	0.408	0.338	0.487	0.408	0.338	0.487	SUBCLONAL	1	TRUE	1	0.266743595053482	2		619	735	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262267	46262267	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	23	389	0	ENST00000371998.3:c.851C>T	p.Ser284Leu	p.S284L	ENST00000371998		284	tCa/tTa	9/23	1	2	FACETS	0.439	0.341	0.552	0.439	0.341	0.552	SUBCLONAL	1	TRUE	1	0.266743595053482	2		389	393	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70005672	70005672	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1553704841	NA	P-0057767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	30	408	0	ENST00000394351.3:c.701C>G	p.Ser234Ter	p.S234*	ENST00000394351	NM_000248.3	234	tCa/tGa	7/9	1	2	FACETS	0.481	0.387	0.588	0.481	0.387	0.588	SUBCLONAL	1	TRUE	1	0.266743595053482	2		408	468	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178941890	178941890	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	37	357	0	ENST00000263967.3:c.2209G>A	p.Glu737Lys	p.E737K	ENST00000263967	NM_006218.2	737	Gag/Aag	15/21	1	2	FACETS	0.706	0.583	0.844	0.706	0.583	0.844	SUBCLONAL	1	TRUE	1	0.266743595053482	2		357	393	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675562	86675562	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0057767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	27	227	0	ENST00000274376.6:c.2498C>G	p.Ser833Ter	p.S833*	ENST00000274376	NM_002890.2	833	tCa/tGa	19/25	0.237384275316613	3	FACETS	0.755	0.602	0.929	0.377	0.301	0.465	CLONAL	1	TRUE	1	0.266743595053482	3		227	304	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2966382	2966382	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs766156349	NA	P-0057767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	68	757	0	ENST00000396946.4:c.1798G>T	p.Asp600Tyr	p.D600Y	ENST00000396946	NM_032415.4	600	Gat/Tat	14/25	0.237384275316613	3	FACETS	0.69	0.599	0.788	0.345	0.299	0.394	SUBCLONAL	1	TRUE	1	0.266743595053482	3		757	838	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346668	81346668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	23	228	0	ENST00000222390.5:c.1285G>A	p.Glu429Lys	p.E429K	ENST00000222390	NM_000601.4	429	Gaa/Aaa	11/18	0.237384275316613	3	FACETS	0.62	0.484	0.778	0.31	0.242	0.389	SUBCLONAL	1	TRUE	1	0.266743595053482	3		228	315	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483915	212483915	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	154	593	0	ENST00000342788.4:c.2288T>G	p.Val763Gly	p.V763G	ENST00000342788	NM_005235.2	763	gTg/gGg	19/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		593	427	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118934	3118934	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	179	905	1	ENST00000078429.4:c.623del	p.Gly208AlafsTer16	p.G208Afs*16	ENST00000078429	NM_002067.2	206	gtG/gt	5/7	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.477625135276104	2		906	501	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913837	32913837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359507	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	50	407	1	ENST00000380152.3:c.5351del	p.Asn1784ThrfsTer7	p.N1784Tfs*7	ENST00000380152		1782	cAa/ca	11/27	0.477625135276104	2	FACETS	0.784	0.671	0.907	0.392	0.335	0.454	CLONAL	1	TRUE	0	0.477625135276104	2		408	267	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	15	292	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.244	0.178	0.324	0.244	0.178	0.324	SUBCLONAL	1	TRUE	1	0.477625135276104	2		292	257	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	58	300	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.477625135276104	2		300	215	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	14	432	1	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.164	0.118	0.22	0.164	0.118	0.22	SUBCLONAL	1	TRUE	1	0.477625135276104	2		433	358	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	134	973	1	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	0.477625135276104	2	FACETS	1	0.922	1	0.506	0.461	0.552	CLONAL	1	TRUE	0	0.477625135276104	2		974	555	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965666	90965666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	45	346	3	ENST00000265433.3:c.1651del	p.Arg551GlyfsTer8	p.R551Gfs*8	ENST00000265433	NM_002485.4	551	Agg/gg	11/16	0.414529441748181	3	FACETS	0.691	0.583	0.809	0.345	0.291	0.405	SUBCLONAL	1	TRUE	1	0.477625135276104	3		349	338	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278061	18278061	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519801	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	172	870	0	ENST00000222254.8:c.1681A>G	p.Asn561Asp	p.N561D	ENST00000222254	NM_005027.3	561	Aac/Gac	13/16	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.477625135276104	2		870	540	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509085	66509085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	27	276	0	ENST00000273854.3:c.242del	p.Asn81MetfsTer24	p.N81Mfs*24	ENST00000273854	NM_004439.5	81	aAt/at	2/18	1	2	FACETS	0.625	0.501	0.763	0.625	0.501	0.763	SUBCLONAL	1	TRUE	1	0.477625135276104	2		276	181	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	123	1122	17	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	0.358205114800408	1	FACETS	0.671	0.609	0.737	0.671	0.609	0.737	SUBCLONAL	1	TRUE	0	0.477625135276104	1		1139	584	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882049	36882050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs780753361	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	128	834	1	ENST00000358127.4:c.963dup	p.Ala322ArgfsTer19	p.A322Rfs*19	ENST00000358127	NM_001280556.1	321	-/C	8/10	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.477625135276104	2		835	528	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737107	145737109	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs780986647	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	64	777	0	ENST00000428558.2:c.3457_3459del	p.Glu1153del	p.E1153del	ENST00000428558	NM_004260.3	1153	GAG/-	21/22	0.414529441748181	3	FACETS	0.581	0.504	0.666	0.291	0.252	0.333	SUBCLONAL	1	TRUE	1	0.477625135276104	3		777	571	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003779	45003779	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	95	619	0	ENST00000558401.1:c.35T>C	p.Leu12Pro	p.L12P	ENST00000558401	NM_004048.2	12	cTa/cCa	1/4	0.477625135276104	2	FACETS	0.884	0.791	0.982	0.442	0.395	0.491	CLONAL	1	TRUE	0	0.477625135276104	2		619	450	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519505	137519506	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs780346130	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	80	374	9	ENST00000367739.4:c.1132_1133del	p.Ser378PhefsTer6	p.S378Ffs*6	ENST00000367739	NM_000416.2	378	AGt/t	7/7	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.477625135276104	2		383	263	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151290	202151290	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	131	363	0	ENST00000358485.4:c.1596del	p.Lys532AsnfsTer73	p.K532Nfs*73	ENST00000358485	NM_001080125.1	530	agA/ag	9/9	1	2	FACETS	1	0.939	1	1	0.992	1	CLONAL	2	TRUE	1	0.477625135276104	2		363	270	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165282	47165283	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	62	343	0	ENST00000409792.3:c.843dup	p.Glu282ArgfsTer9	p.E282Rfs*9	ENST00000409792	NM_014159.6	281	-/A	3/21	1	2	FACETS	0.987	0.862	1	0.987	0.862	1	CLONAL	1	TRUE	1	0.477625135276104	2		343	263	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991757	72991758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760959844	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	11	318	2	ENST00000268489.5:c.2287dup	p.Glu763GlyfsTer26	p.E763Gfs*26	ENST00000268489	NM_006885.3	763	gag/gGag	2/10	1	2	FACETS	0.271	0.187	0.374	0.271	0.187	0.374	SUBCLONAL	1	TRUE	1	0.477625135276104	2		320	170	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931374	131931374	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	60	406	0	ENST00000265335.6:c.2079G>T	p.Glu693Asp	p.E693D	ENST00000265335		693	gaG/gaT	13/25	1	2	FACETS	0.84	0.73	0.959	0.84	0.73	0.959	CLONAL	1	TRUE	1	0.477625135276104	2		406	299	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332152	70332153	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1196853334	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	32	245	2	ENST00000373644.4:c.65dup	p.Lys23GlufsTer37	p.K23Efs*37	ENST00000373644	NM_030625.2	19	-/A	2/12	1	2	FACETS	0.876	0.721	1	0.876	0.721	1	CLONAL	1	TRUE	1	0.477625135276104	2		247	153	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692892	89692892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554898129	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	87	349	0	ENST00000371953.3:c.376G>A	p.Ala126Thr	p.A126T	ENST00000371953	NM_000314.4	126	Gct/Act	5/9	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.477625135276104	2		349	290	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	82	775	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.675	0.596	0.758	0.675	0.596	0.758	SUBCLONAL	1	TRUE	1	0.477625135276104	2		778	509	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	78	454	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.716	0.632	0.806	0.716	0.632	0.806	SUBCLONAL	1	TRUE	1	0.477625135276104	2		460	456	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546560	9546560	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771840400	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	62	579	0	ENST00000353224.5:c.1462C>T	p.Arg488Ter	p.R488*	ENST00000353224	NM_177990.2	488	Cga/Tga	5/10	1	2	FACETS	0.792	0.688	0.902	0.792	0.688	0.902	CLONAL	1	TRUE	1	0.477625135276104	2		579	328	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	109	754	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.477625135276104	2		754	401	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441815	49441816	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs756471180	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	81	612	0	ENST00000301067.7:c.4168dup	p.Ala1390GlyfsTer42	p.A1390Gfs*42	ENST00000301067	NM_003482.3	1390	gca/gGca	14/54	1	2	FACETS	0.76	0.673	0.854	0.76	0.673	0.854	SUBCLONAL	1	TRUE	1	0.477625135276104	2		612	446	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222961	36222961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	332	1172	2	ENST00000222270.7:c.5590C>T	p.Arg1864Ter	p.R1864*	ENST00000222270	NM_014727.1	1864	Cga/Tga	27/37	0.477625135276104	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.477625135276104	2		1174	660	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481473	20481473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138776759	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	26	393	0	ENST00000346618.3:c.542C>T	p.Thr181Met	p.T181M	ENST00000346618	NM_001949.4	181	aCg/aTg	3/7	0.477625135276104	2	FACETS	0.564	0.45	0.693	0.282	0.225	0.347	SUBCLONAL	1	TRUE	0	0.477625135276104	2		393	193	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2097756	2097756	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	102	590	1	ENST00000219066.1:c.93del	p.Cys32ValfsTer24	p.C32Vfs*24	ENST00000219066	NM_002528.5	31	ggG/gg	1/6	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.477625135276104	2		591	425	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989044	41989044	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	99	583	0	ENST00000219905.7:c.1840del	p.Arg614GlufsTer7	p.R614Efs*7	ENST00000219905	NM_001164273.1	612	ggA/gg	3/24	0.477625135276104	2	FACETS	1	0.976	1	0.634	0.572	0.698	CLONAL	1	TRUE	0	0.477625135276104	2		583	327	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972035	55972035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1487678797	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	93	584	1	ENST00000263923.4:c.1609G>A	p.Gly537Arg	p.G537R	ENST00000263923	NM_002253.2	537	Ggg/Agg	12/30	1	2	FACETS	0.983	0.881	1	0.983	0.881	1	CLONAL	1	TRUE	1	0.477625135276104	2		585	396	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819969	170819971	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	rs767897913	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	46	317	0	ENST00000296930.5:c.519_521del	p.Asp173del	p.D173del	ENST00000296930	NM_002520.6	171	GAT/-	6/11	1	2	FACETS	0.767	0.652	0.893	0.767	0.652	0.893	SUBCLONAL	1	TRUE	1	0.477625135276104	2		317	251	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027014	71027014	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	107	630	0	ENST00000318789.4:c.1313G>A	p.Arg438Gln	p.R438Q	ENST00000318789	NM_032682.5	438	cGg/cAg	15/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.477625135276104	2		630	381	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041405	47041405	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	99	939	0	ENST00000377604.3:c.1753del	p.Gln585ArgfsTer119	p.Q585Rfs*119	ENST00000377604	NM_001204468.1	583	gaC/ga	16/24	NA	2	FACETS	0.818	0.733	0.907			1	INDETERMINATE	1	TRUE	NA	0.477625135276104	2		939	507	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797254	32797254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772061173	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	319	1030	1	ENST00000374899.4:c.1855C>T	p.Arg619Trp	p.R619W	ENST00000374899	NM_018833.2	619	Cgg/Tgg	11/12	0.477625135276104	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.477625135276104	2		1031	622	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217272	11217272	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	116	845	0	ENST00000361445.4:c.4406C>T	p.Thr1469Ile	p.T1469I	ENST00000361445	NM_004958.3	1469	aCc/aTc	30/58	0.477625135276104	2	FACETS	0.947	0.857	1	0.473	0.428	0.52	CLONAL	1	TRUE	0	0.477625135276104	2		845	513	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17380475	17380475	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	239	862	0	ENST00000375499.3:c.40C>T	p.Pro14Ser	p.P14S	ENST00000375499	NM_003000.2	14	Ccg/Tcg	1/8	NA	2	FACETS	0.964	0.91	1			1	INDETERMINATE	2	TRUE	NA	0.477625135276104	2		862	519	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106916	27106917	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	82	718	0	ENST00000324856.7:c.6531_6532dup	p.Asp2178GlyfsTer23	p.D2178Gfs*23	ENST00000324856	NM_006015.4	2176	cag/caGGg	20/20	1	2	FACETS	0.926	0.822	1	0.926	0.822	1	CLONAL	1	TRUE	1	0.477625135276104	2		718	371	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248564	59248564	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	142	929	0	ENST00000371222.2:c.179T>C	p.Leu60Pro	p.L60P	ENST00000371222	NM_002228.3	60	cTc/cCc	1/1	1	2	FACETS	0.968	0.886	1	0.968	0.886	1	CLONAL	1	TRUE	1	0.477625135276104	2		929	614	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838332	156838332	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	124	1033	0	ENST00000524377.1:c.610T>C	p.Ser204Pro	p.S204P	ENST00000524377	NM_002529.3	204	Tcg/Ccg	6/17	1	2	FACETS	0.886	0.804	0.972	0.886	0.804	0.972	CLONAL	1	TRUE	1	0.477625135276104	2		1033	586	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606045	81606045	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	86	542	0	ENST00000298171.2:c.715A>C	p.Thr239Pro	p.T239P	ENST00000298171	NM_000369.2	239	Act/Cct	9/10	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.477625135276104	2		542	338	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832575	72832575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751584946	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	82	410	0	ENST00000268489.5:c.4006G>A	p.Ala1336Thr	p.A1336T	ENST00000268489	NM_006885.3	1336	Gca/Aca	9/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.477625135276104	2		410	260	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349970	89349971	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	33	887	0	ENST00000301030.4:c.2979dup	p.Gly994TrpfsTer24	p.G994Wfs*24	ENST00000301030	NM_001256183.1	993	-/T	9/13	1	2	FACETS	0.241	0.195	0.292	0.241	0.195	0.292	SUBCLONAL	1	TRUE	1	0.477625135276104	2		887	574	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899251	78899251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200161901	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	23	596	0	ENST00000306801.3:c.2890G>A	p.Ala964Thr	p.A964T	ENST00000306801	NM_020761.2	964	Gcc/Acc	24/34	1	2	FACETS	0.26	0.202	0.326	0.26	0.202	0.326	SUBCLONAL	1	TRUE	1	0.477625135276104	2		596	371	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220068	5220068	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	25	896	0	ENST00000357368.4:c.3647T>C	p.Leu1216Pro	p.L1216P	ENST00000357368	NM_002850.3	1216	cTg/cCg	22/38	1	2	FACETS	0.298	0.235	0.371	0.298	0.235	0.371	SUBCLONAL	1	TRUE	1	0.477625135276104	2		896	351	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122890	7122890	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	126	894	1	ENST00000302850.5:c.3369G>T	p.Glu1123Asp	p.E1123D	ENST00000302850	NM_000208.2	1123	gaG/gaT	18/22	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.477625135276104	2		895	431	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267601	7267601	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	152	896	1	ENST00000302850.5:c.407T>C	p.Leu136Pro	p.L136P	ENST00000302850	NM_000208.2	136	cTg/cCg	2/22	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.477625135276104	2		897	522	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523504	41523504	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	74	500	0	ENST00000263253.7:c.923del	p.Pro308ArgfsTer9	p.P308Rfs*9	ENST00000263253	NM_001429.3	307	gCc/gc	4/31	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.477625135276104	2		500	292	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729924	30729924	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	87	447	0	ENST00000295754.5:c.1445C>A	p.Pro482His	p.P482H	ENST00000295754	NM_003242.5	482	cCc/cAc	6/7	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.477625135276104	2		447	312	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940944	49940944	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	93	743	0	ENST00000296474.3:c.99del	p.Tyr34ThrfsTer9	p.Y34Tfs*9	ENST00000296474	NM_002447.2	33	ccC/cc	1/20	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.477625135276104	2		743	387	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931369	131931369	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752824477	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	68	405	0	ENST00000265335.6:c.2074G>A	p.Ala692Thr	p.A692T	ENST00000265335		692	Gct/Act	13/25	1	2	FACETS	0.965	0.847	1	0.965	0.847	1	CLONAL	1	TRUE	1	0.477625135276104	2		405	295	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150407	157150407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750214622	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	95	620	0	ENST00000346085.5:c.1589G>A	p.Gly530Asp	p.G530D	ENST00000346085	NM_020732.3	530	gGc/gAc	2/20	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.477625135276104	2		620	375	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69012025	69012025	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	78	537	0	ENST00000288368.4:c.2662C>A	p.Leu888Ile	p.L888I	ENST00000288368	NM_024870.2	888	Ctt/Att	23/40	0.414529441748181	3	FACETS	0.899	0.793	1	0.45	0.396	0.506	CLONAL	1	TRUE	1	0.477625135276104	3		537	450	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477790	140477791	+	inframe_insertion,splice_region_variant	In_Frame_Ins	INS	-	-	CTGAGTACT	novel	NA	P-0057772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	103	563	0	ENST00000288602.6:c.1509_1517dup	p.Val504_Arg506dup	p.V504_R506dup	ENST00000288602	NM_004333.4	504	agg/agAGTACTCAGg		0.366552057519219	4	FACETS	1	0.982	1	0.724	0.651	0.8	CLONAL	1	TRUE	2	0.443553309044926	4		563	463	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0057773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	84	529	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.249651647645666	3	FACETS	1	0.925	1	0.524	0.467	0.584	INDETERMINATE	1	TRUE	1	0.652145783566316	3		529	326	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0057773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	78	312	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.61	0.539	0.686	0.61	0.539	0.686	SUBCLONAL	1	TRUE	1	0.652145783566316	2		312	392	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0057773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	41	259	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	1	2	FACETS	0.544	0.457	0.639	0.544	0.457	0.639	SUBCLONAL	1	TRUE	1	0.652145783566316	2		259	231	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589584	67589589	+	inframe_deletion	In_Frame_Del	DEL	ACATGA	ACATGA	-	novel	NA	P-0057773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	18	195	0	ENST00000274335.5:c.1348_1353del	p.His450_Glu451del	p.H450_E451del	ENST00000274335		449	ttACATGAa/tta	10/15	1	2	FACETS	0.456	0.347	0.582	0.456	0.347	0.582	SUBCLONAL	1	TRUE	1	0.652145783566316	2		195	121	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370985	55370985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	81	547	0	ENST00000297316.4:c.287C>G	p.Ala96Gly	p.A96G	ENST00000297316	NM_022454.3	96	gCc/gGc	1/2	1	2	FACETS	0.587	0.52	0.659	0.587	0.52	0.659	SUBCLONAL	1	TRUE	1	0.652145783566316	2		547	423	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	33	208	1	ENST00000256196.4:c.68G>A	p.Gly23Asp	p.G23D	ENST00000256196		23	gGc/gAc	1/6	1	2	FACETS	0.569	0.468	0.679	0.569	0.468	0.679	SUBCLONAL	1	TRUE	1	0.652145783566316	2		209	178	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087417	27087417	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	88	712	1	ENST00000324856.7:c.1991del	p.Ser664Ter	p.S664*	ENST00000324856	NM_006015.4	664	tCa/ta	5/20	1	2	FACETS	0.608	0.541	0.679	0.608	0.541	0.679	SUBCLONAL	1	TRUE	1	0.652145783566316	2		713	444	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796517	42796521	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCT	AGGCT	-	novel	NA	P-0057773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	95	963	0	ENST00000575354.2:c.3074_3078del	p.Gln1025ArgfsTer124	p.Q1025Rfs*124	ENST00000575354	NM_015125.3	1025	cAGGCT/c	13/20	1	2	FACETS	0.443	0.394	0.494	0.443	0.394	0.494	SUBCLONAL	1	TRUE	1	0.652145783566316	2		963	658	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447259	187447259	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	102	740	0	ENST00000232014.4:c.934A>C	p.Ile312Leu	p.I312L	ENST00000232014	NM_001130845.1	312	Att/Ctt	5/10	1	2	FACETS	0.565	0.506	0.626	0.565	0.506	0.626	SUBCLONAL	1	TRUE	1	0.652145783566316	2		740	554	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144898	47144898	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	12	497	0	ENST00000409792.3:c.4855C>T	p.Gln1619Ter	p.Q1619*	ENST00000409792	NM_014159.6	1619	Caa/Taa	7/21	0.169116868601715	2	FACETS	0.819	0.58	1	0.41	0.29	0.555	CLONAL	1	TRUE	0	0.242089705007187	2		497	121	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420585	49420585	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	21	838	1	ENST00000301067.7:c.15164A>T	p.Asp5055Val	p.D5055V	ENST00000301067	NM_003482.3	5055	gAc/gTc	48/54	0.169116868601715	2	FACETS	0.986	0.764	1	0.493	0.382	0.62	CLONAL	1	TRUE	0	0.242089705007187	2		839	176	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0057776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	74	351	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.959	0.853	1	1	0.983	1	CLONAL	2	FALSE	1	0.340054340552588	2		351	227	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579369	7579369	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555526581	NA	P-0057776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	225	1163	0	ENST00000269305.4:c.318C>G	p.Ser106Arg	p.S106R	ENST00000269305	NM_001126112.2	106	agC/agG	4/11	0.340054340552588	1	FACETS	1	0.948	1	1	0.995	1	CLONAL	2	FALSE	0	0.340054340552588	1		1163	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0057778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	74	815	1	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			1	2	FACETS	0.933	0.825	1	1	0.982	1	CLONAL	2	TRUE	1	0.273561885503886	2		816	290	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172231	38172232	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	12	520	0	ENST00000317025.8:c.2175dup	p.His726SerfsTer12	p.H726Sfs*12	ENST00000317025	NM_023034.1	725	-/T	12/24	0.273561885503886	1	FACETS	0.399	0.28	0.544	0.399	0.28	0.544	SUBCLONAL	1	TRUE	0	0.273561885503886	1		520	190	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593650	55593651	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCAACACAACTTCCTTATGATCACAAATGGGAGTTT	novel	NA	P-0057812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	88	399	0	ENST00000288135.5:c.1719_1754dup	p.Thr574_Pro585dup	p.T574_P585dup	ENST00000288135	NM_000222.2	574	-/CCAACACAACTTCCTTATGATCACAAATGGGAGTTT	11/21	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.256947532805321	2		399	523	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411285	63411285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1313722059	NA	P-0057878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	133	331	0	ENST00000330258.3:c.1882G>T	p.Ala628Ser	p.A628S	ENST00000330258	NM_152424.3	628	Gcc/Tcc	2/2	1	1	FACETS	0.391	0.357	0.426	0.391	0.357	0.426	SUBCLONAL	1	TRUE	0	0.830370252296592	1		331	479	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850705	63850705	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0057878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	94	296	0	ENST00000279873.7:c.1483A>T	p.Lys495Ter	p.K495*	ENST00000279873	NM_032199.2	495	Aaa/Taa	10/10	1	2	FACETS	0.47	0.419	0.523	0.47	0.419	0.523	SUBCLONAL	1	TRUE	1	0.830370252296592	2		296	482	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805919	89805919	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	177	522	0	ENST00000389301.3:c.3977A>T	p.Gln1326Leu	p.Q1326L	ENST00000389301	NM_000135.2	1326	cAg/cTg	40/43	0.440485924628556	1	FACETS	0.348	0.321	0.375	0.348	0.321	0.375	INDETERMINATE	1	TRUE	0	0.830370252296592	1		522	717	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38139037	38139037	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1313665107	NA	P-0057878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	96	514	1	ENST00000317025.8:c.3566A>G	p.Lys1189Arg	p.K1189R	ENST00000317025	NM_023034.1	1189	aAg/aGg	20/24	0.440485924628556	1	FACETS	0.214	0.19	0.238	0.214	0.19	0.238	INDETERMINATE	1	TRUE	0	0.830370252296592	1		515	633	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0057879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	170	621	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.941	0.869	1	0.941	0.869	1	CLONAL	1	TRUE	1	0.546392835260368	2		622	661	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0057879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	136	311	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	0.390709680480071	1	FACETS	0.889	0.816	0.964	0.889	0.816	0.964	CLONAL	1	TRUE	0	0.546392835260368	1		311	407	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720825	89720825	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	131	280	0	ENST00000371953.3:c.976G>C	p.Asp326His	p.D326H	ENST00000371953	NM_000314.4	326	Gac/Cac	8/9	0.546392835260368	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	0	0.546392835260368	2		280	237	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	77	365	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.98	0.871	1	0.98	0.871	1	CLONAL	1	TRUE	1	0.556986691761337	2		365	282	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717609	89717609	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs876661024	NA	P-0057880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	102	321	0	ENST00000371953.3:c.635-1G>C		p.X212_splice	ENST00000371953	NM_000314.4	212			0.556986691761337	1	FACETS	0.881	0.798	0.966	0.881	0.798	0.966	CLONAL	1	TRUE	0	0.556986691761337	1		321	300	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339576	70339576	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	98	500	0	ENST00000374080.3:c.245G>A	p.Arg82His	p.R82H	ENST00000374080		82	cGt/cAt	3/45	0.37338284840827	3	FACETS	0.684	0.61	0.761	0.342	0.305	0.381	SUBCLONAL	1	TRUE	1	0.556986691761337	3		500	658	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012190	16012190	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	179	482	0	ENST00000268712.3:c.2092C>A	p.Gln698Lys	p.Q698K	ENST00000268712	NM_006311.3	698	Caa/Aaa	19/46	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.556986691761337	2		482	616	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0057881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	89	680	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.18252878357676	1	FACETS	0.93	0.823	1	0.93	0.823	1	CLONAL	1	TRUE	0	0.18252878357676	1		680	953	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936995	48936995	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778842	NA	P-0057881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	38	398	0	ENST00000267163.4:c.763C>T	p.Arg255Ter	p.R255*	ENST00000267163	NM_000321.2	255	Cga/Tga	8/27	0.18252878357676	1	FACETS	0.864	0.714	1	0.864	0.714	1	CLONAL	1	TRUE	0	0.18252878357676	1		398	438	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717713	89717714	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	61	439	0	ENST00000371953.3:c.740dup	p.Leu247PhefsTer6	p.L247Ffs*6	ENST00000371953	NM_000314.4	246	-/T	7/9	0.18252878357676	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.18252878357676	1		439	548	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832445	72832445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753592536	NA	P-0057881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	49	454	0	ENST00000268489.5:c.4136C>T	p.Thr1379Met	p.T1379M	ENST00000268489	NM_006885.3	1379	aCg/aTg	9/10	0.18252878357676	1	FACETS	0.887	0.751	1	0.887	0.751	1	CLONAL	1	TRUE	0	0.18252878357676	1		454	550	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658481	3658481	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140876043	NA	P-0057881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	103	669	0	ENST00000294008.3:c.485C>T	p.Thr162Met	p.T162M	ENST00000294008	NM_032444.2	162	aCg/aTg	2/15	0.18252878357676	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.18252878357676	1		669	989	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050682	30050682	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	50	457	2	ENST00000338641.4:c.488del	p.Leu163TrpfsTer11	p.L163Wfs*11	ENST00000338641	NM_000268.3	162	Ttt/tt	5/16	0.18252878357676	1	FACETS	0.994	0.844	1	0.994	0.844	1	CLONAL	1	TRUE	0	0.18252878357676	1		459	501	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386587	81386587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1032300573	NA	P-0057881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	21	476	0	ENST00000222390.5:c.400C>T	p.Arg134Cys	p.R134C	ENST00000222390	NM_000601.4	134	Cgc/Tgc	4/18	1	2	FACETS	0.549	0.422	0.698	0.549	0.422	0.698	SUBCLONAL	1	TRUE	1	0.18252878357676	2		476	419	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859914	151859914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs546643392	NA	P-0057881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	55	482	0	ENST00000262189.6:c.10748C>T	p.Pro3583Leu	p.P3583L	ENST00000262189	NM_170606.2	3583	cCg/cTg	43/59	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.18252878357676	2		482	550	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261263	115261263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	63	503	0	ENST00000438362.2:c.2458C>T	p.Arg820Cys	p.R820C	ENST00000438362	NM_001242891.1	820	Cgt/Tgt	19/20	0.18252878357676	1	FACETS	0.899	0.776	1	0.899	0.776	1	CLONAL	1	TRUE	0	0.18252878357676	1		503	698	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099262	4099262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730880523	NA	P-0057881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	105	741	0	ENST00000262948.5:c.856G>A	p.Gly286Arg	p.G286R	ENST00000262948	NM_030662.3	286	Ggg/Agg	7/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.18252878357676	2		741	968	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851246	63851246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141236035	NA	P-0057881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	66	687	1	ENST00000279873.7:c.2024C>T	p.Thr675Met	p.T675M	ENST00000279873	NM_032199.2	675	aCg/aTg	10/10	0.18252878357676	1	FACETS	0.882	0.765	1	0.882	0.765	1	CLONAL	1	TRUE	0	0.18252878357676	1		688	745	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124241	2124241	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567474646	NA	P-0057881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	120	802	2	ENST00000219476.3:c.2396G>A	p.Arg799His	p.R799H	ENST00000219476	NM_000548.3	799	cGc/cAc	22/42	0.18252878357676	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.18252878357676	1		804	948	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961208	41961208	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757411884	NA	P-0057881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	48	428	0	ENST00000219905.7:c.116G>A	p.Gly39Glu	p.G39E	ENST00000219905	NM_001164273.1	39	gGa/gAa	2/24	0.18252878357676	1	FACETS	0.943	0.797	1	0.943	0.797	1	CLONAL	1	TRUE	0	0.18252878357676	1		428	507	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828119	3828119	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	92	579	1	ENST00000262367.5:c.2006G>A	p.Arg669Gln	p.R669Q	ENST00000262367	NM_004380.2	669	cGg/cAg	10/31	0.18252878357676	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.18252878357676	1		580	778	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227999	36227999	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751795961	NA	P-0057881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	73	753	0	ENST00000222270.7:c.7385C>T	p.Ala2462Val	p.A2462V	ENST00000222270	NM_014727.1	2462	gCg/gTg	33/37	1	2	FACETS	0.836	0.729	0.951	0.836	0.729	0.951	CLONAL	1	TRUE	1	0.18252878357676	2		753	957	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905261	50905261	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774568050	NA	P-0057881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	110	848	0	ENST00000440232.2:c.469G>A	p.Gly157Arg	p.G157R	ENST00000440232	NM_002691.3	157	Ggg/Agg	5/27	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.18252878357676	2		848	1176	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0057883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	9	323	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.380801140655957	1	FACETS	0.117	0.077	0.168	0.117	0.077	0.168	SUBCLONAL	1	TRUE	0	0.380801140655957	1		323	328	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	182	292	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.895	0.832	0.96	1	0.993	1	CLONAL	2	TRUE	1	0.380801140655957	2		292	534	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0057883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	183	775	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.380801140655957	2		778	793	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0057883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	209	529	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.380801140655957	2	FACETS	0.981	0.927	1	1	0.993	1	CLONAL	3	TRUE	0	0.380801140655957	2		529	373	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0057883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	46	436	3	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.308	0.258	0.363	0.308	0.258	0.363	SUBCLONAL	1	TRUE	1	0.380801140655957	2		439	784	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0057883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	30	482	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.29	0.233	0.355	0.29	0.233	0.355	SUBCLONAL	1	TRUE	1	0.380801140655957	2		483	543	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0057883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	16	328	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.178	0.131	0.235	0.178	0.131	0.235	SUBCLONAL	1	TRUE	1	0.380801140655957	2		328	472	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089730	27089730	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	210	611	0	ENST00000324856.7:c.2686G>T	p.Glu896Ter	p.E896*	ENST00000324856	NM_006015.4	896	Gaa/Taa	8/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.380801140655957	2		611	791	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274794	123274794	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913478	NA	P-0057883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	139	571	0	ENST00000358487.5:c.1124A>G	p.Tyr375Cys	p.Y375C	ENST00000358487	NM_000141.4	375	tAc/tGc	9/18	0.380801140655957	2	FACETS	0.977	0.891	1	0.489	0.445	0.534	CLONAL	1	TRUE	0	0.380801140655957	2		571	747	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0057883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	127	390	0	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.380801140655957	2		390	573	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981861	101981863	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0057883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	221	671	0	ENST00000282441.5:c.286_288del	p.Phe96del	p.F96del	ENST00000282441	NM_001130145.2	94	tcCTTc/tcc	1/9	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.380801140655957	2		671	829	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101750	71101751	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	29	348	0	ENST00000318789.4:c.447dup	p.Gln150ThrfsTer20	p.Q150Tfs*20	ENST00000318789	NM_032682.5	149	-/A	9/21	1	2	FACETS	0.522	0.42	0.637	0.522	0.42	0.637	SUBCLONAL	1	TRUE	1	0.380801140655957	2		348	292	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101895021	101895021	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs867371544	NA	P-0057883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	62	225	1	ENST00000374994.4:c.574G>A	p.Gly192Ser	p.G192S	ENST00000374994	NM_004612.2	192	Ggt/Agt	3/9	1	2	FACETS	0.905	0.797	1	1	0.98	1	CLONAL	2	TRUE	1	0.380801140655957	2		226	180	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	270	864	4	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.380801140655957	2		868	1061	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519757	NA	P-0057883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	56	313	0	ENST00000274335.5:c.1126G>C	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Cga	9/15	1	2	FACETS	0.897	0.784	1	1	0.977	1	CLONAL	2	TRUE	1	0.380801140655957	2		313	164	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850820	63850820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746755575	NA	P-0057883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	208	494	1	ENST00000279873.7:c.1598C>T	p.Ala533Val	p.A533V	ENST00000279873	NM_032199.2	533	gCg/gTg	10/10	0.270715210104303	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.380801140655957	3		495	600	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180318	27180318	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	54	528	0	ENST00000380036.4:c.982G>T	p.Gly328Ter	p.G328*	ENST00000380036	NM_000459.3	328	Gga/Tga	7/23	1	2	FACETS	0.389	0.331	0.452	0.389	0.331	0.452	SUBCLONAL	1	TRUE	1	0.380801140655957	2		528	729	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413115	139413115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	298	729	1	ENST00000277541.6:c.1027G>A	p.Ala343Thr	p.A343T	ENST00000277541	NM_017617.3	343	Gcc/Acc	6/34	1	2	FACETS	0.789	0.744	0.835	1	0.994	1	SUBCLONAL	2	TRUE	1	0.380801140655957	2		730	992	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467545	66467545	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	114	365	0	ENST00000273854.3:c.724G>T	p.Val242Phe	p.V242F	ENST00000273854	NM_004439.5	242	Gtc/Ttc	3/18	1	2	FACETS	0.8	0.728	0.876	1	0.987	1	SUBCLONAL	2	TRUE	1	0.380801140655957	2		365	374	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256430	115256430	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	41	351	1	ENST00000369535.4:c.281A>G	p.Asn94Ser	p.N94S	ENST00000369535	NM_002524.4	94	aAc/aGc	3/7	1	2	FACETS	0.704	0.589	0.83	0.704	0.589	0.83	SUBCLONAL	1	TRUE	1	0.380801140655957	2		352	306	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239530	123239530	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0057883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	552	855	0	ENST00000358487.5:c.2307C>G	p.Tyr769Ter	p.Y769*	ENST00000358487	NM_000141.4	769	taC/taG	18/18	0.380801140655957	2	FACETS	1	0.995	1	1	0.998	1	CLONAL	3	TRUE	0	0.380801140655957	2		855	857	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552716	18552716	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	37	609	1	ENST00000266497.5:c.2127G>A	p.Met709Ile	p.M709I	ENST00000266497		709	atG/atA	14/31	0.380801140655957	1	FACETS	0.429	0.354	0.512	0.429	0.354	0.512	SUBCLONAL	1	TRUE	0	0.380801140655957	1		610	367	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21643131	21643131	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0057883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	28	460	0	ENST00000421138.2:c.394+2T>C		p.X132_splice	ENST00000421138		132			0.380801140655957	1	FACETS	0.463	0.371	0.567	0.463	0.371	0.567	SUBCLONAL	1	TRUE	0	0.380801140655957	1		460	257	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001896	29001899	+	frameshift_variant	Frame_Shift_Del	DEL	AATT	AATT	-	novel	NA	P-0057883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	119	446	0	ENST00000282397.4:c.1266_1269del	p.Ile423SerfsTer3	p.I423Sfs*3	ENST00000282397	NM_002019.4	422	ctAATT/ct	9/30	1	2	FACETS	0.799	0.728	0.873	1	0.987	1	SUBCLONAL	2	TRUE	1	0.380801140655957	2		446	391	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876502	59876502	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	47	505	0	ENST00000259008.2:c.1299A>C	p.Lys433Asn	p.K433N	ENST00000259008	NM_032043.2	433	aaA/aaC	9/20	1	2	FACETS	0.599	0.506	0.701	0.599	0.506	0.701	SUBCLONAL	1	TRUE	1	0.380801140655957	2		505	412	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218428	36218439	+	inframe_deletion	In_Frame_Del	DEL	GAGGCCCTGAGC	GAGGCCCTGAGC	-	novel	NA	P-0057883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	218	765	0	ENST00000222270.7:c.4208_4219del	p.Glu1403_Ser1406del	p.E1403_S1406del	ENST00000222270	NM_014727.1	1403	GAGGCCCTGAGC/-	16/37	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.380801140655957	2		765	814	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047876	180047876	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	254	754	0	ENST00000261937.6:c.2299G>T	p.Gly767Cys	p.G767C	ENST00000261937	NM_182925.4	767	Ggc/Tgc	15/30	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.380801140655957	2		754	991	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859816	151859818	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	novel	NA	P-0057883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	55	420	0	ENST00000262189.6:c.10844_10846del	p.Asp3615del	p.D3615del	ENST00000262189	NM_170606.2	3615	gATGca/gca	43/59	0.285540583999095	3	FACETS	0.764	0.655	0.883	0.382	0.327	0.442	SUBCLONAL	1	TRUE	1	0.380801140655957	3		420	450	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189075	38189075	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	50	611	0	ENST00000317025.8:c.939del	p.Phe313LeufsTer67	p.F313Lfs*67	ENST00000317025	NM_023034.1	313	ttT/tt	5/24	1	2	FACETS	0.554	0.47	0.646	0.554	0.47	0.646	SUBCLONAL	1	TRUE	1	0.380801140655957	2		611	474	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015125	37015125	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	76	679	0	ENST00000358127.4:c.279del	p.Val95TrpfsTer64	p.V95Wfs*64	ENST00000358127	NM_001280556.1	93	ccC/cc	3/10	1	2	FACETS	0.482	0.422	0.547	0.482	0.422	0.547	SUBCLONAL	1	TRUE	1	0.380801140655957	2		679	828	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0057884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	103	500	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.129421907061359	3	FACETS	0.9	0.805	1	0.9	0.805	1	CLONAL	2	FALSE	1	0.157969169470741	3		500	782	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226347	2226347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	65	767	1	ENST00000326181.6:c.1960G>A	p.Gly654Ser	p.G654S	ENST00000326181	NM_032271.2	654	Ggc/Agc	20/21	1	2	FACETS	0.947	0.819	1	0.947	0.819	1	CLONAL	1	FALSE	1	0.157969169470741	2		768	869	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0057885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	106	227	1				ENST00000310581	NM_198253.2	-/1132			0.115103566440722	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.697127205487795	0		228	309	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0057885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	222	648	0	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	1	2	FACETS	0.872	0.815	0.931	0.872	0.815	0.931	CLONAL	1	TRUE	1	0.697127205487795	2		648	730	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913293	NA	P-0057885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	248	480	0	ENST00000371953.3:c.517C>A	p.Arg173Ser	p.R173S	ENST00000371953	NM_000314.4	173	Cgc/Agc	6/9	0.697127205487795	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.697127205487795	1		480	454	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306677	41306677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs724159835	NA	P-0057891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	124	561	3	ENST00000373198.4:c.982C>T	p.Arg328Cys	p.R328C	ENST00000373198	NM_133170.3	328	Cgc/Tgc	7/32	0.544135920749845	3	FACETS	0.738	0.668	0.812	0.369	0.334	0.406	SUBCLONAL	1	TRUE	1	0.543409855409175	3		564	786	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466022	69466022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	349	762	0	ENST00000227507.2:c.860C>T	p.Pro287Leu	p.P287L	ENST00000227507	NM_053056.2	287	cCc/cTc	5/5	0.503514050614936	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	2	0.543409855409175	4		762	969	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588123	69588123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751257747	NA	P-0057891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	295	663	0	ENST00000168712.1:c.575G>A	p.Arg192Gln	p.R192Q	ENST00000168712	NM_002007.2	192	cGa/cAa	3/3	0.503514050614936	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.543409855409175	4		663	781	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453145	140453145	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913366	NA	P-0057891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	112	343	0	ENST00000288602.6:c.1790T>G	p.Leu597Arg	p.L597R	ENST00000288602	NM_004333.4	597	cTa/cGa	15/18	0.544135920749845	4	FACETS	0.872	0.792	0.954	0.872	0.792	0.954	CLONAL	2	TRUE	2	0.543409855409175	4		343	365	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243237	123243237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55774317	NA	P-0057891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	140	686	1	ENST00000358487.5:c.2276G>A	p.Arg759Gln	p.R759Q	ENST00000358487	NM_000141.4	759	cGa/cAa	17/18	1	2	FACETS	0.965	0.883	1	0.965	0.883	1	CLONAL	1	TRUE	1	0.543409855409175	2		687	534	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875904	76875904	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	115	243	0	ENST00000373344.5:c.5231T>A	p.Ile1744Asn	p.I1744N	ENST00000373344	NM_000489.3	1744	aTt/aAt	20/35	0.544135920749845	2	FACETS	0.953	0.88	1			1	CLONAL	2	TRUE	NA	0.543409855409175	2		243	222	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446128	70446128	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1349186385	NA	P-0057891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	92	381	1	ENST00000373644.4:c.5068C>T	p.Arg1690Ter	p.R1690*	ENST00000373644	NM_030625.2	1690	Cga/Tga	11/12	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.543409855409175	2		382	338	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857878	9857878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867464241	NA	P-0057891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	157	629	0	ENST00000330684.3:c.3523G>A	p.Glu1175Lys	p.E1175K	ENST00000330684	NM_001134407.1	1175	Gaa/Aaa	13/13	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.543409855409175	2		629	547	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964333	70964333	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	72	286	0	ENST00000276594.2:c.1695G>A	p.Met565Ile	p.M565I	ENST00000276594	NM_024504.3	565	atG/atA	8/8	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.543409855409175	2		286	242	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437182	52437182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	324	622	0	ENST00000460680.1:c.1862C>T	p.Pro621Leu	p.P621L	ENST00000460680	NM_004656.3	621	cCc/cTc	14/17	0.432594316129471	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.543409855409175	4		622	832	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182179	11182179	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	327	647	1	ENST00000361445.4:c.6667C>T	p.Gln2223Ter	p.Q2223*	ENST00000361445	NM_004958.3	2223	Cag/Tag	48/58	0.544135920749845	4	FACETS	0.983	0.931	1	0.983	0.931	1	CLONAL	2	TRUE	2	0.543409855409175	4		648	945	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089980	16089980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1431286801	NA	P-0057891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	143	302	0	ENST00000268712.3:c.130C>T	p.Arg44Cys	p.R44C	ENST00000268712	NM_006311.3	44	Cgt/Tgt	3/46	0.52485641582287	2	FACETS	0.907	0.843	0.972	0.907	0.843	0.972	CLONAL	2	TRUE	0	0.543409855409175	2		302	290	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790026	40790026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1366458329	NA	P-0057891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	453	568	1	ENST00000373198.4:c.2705G>A	p.Arg902Lys	p.R902K	ENST00000373198	NM_133170.3	902	aGa/aAa	18/32	0.544135920749845	3	FACETS	0.875	0.842	0.907	1	0.996	1	CLONAL	3	TRUE	1	0.543409855409175	3		569	808	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136794	69136794	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs372981486	NA	P-0057891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	73	391	0	ENST00000288368.4:c.4708G>A	p.Gly1570Arg	p.G1570R	ENST00000288368	NM_024870.2	1570	Gga/Aga	39/40	1	2	FACETS	0.728	0.641	0.821	0.728	0.641	0.821	SUBCLONAL	1	TRUE	1	0.543409855409175	2		391	369	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761450	59761450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	122	465	0	ENST00000259008.2:c.2957C>T	p.Ser986Phe	p.S986F	ENST00000259008	NM_032043.2	986	tCc/tTc	20/20	0.544135920749845	3	FACETS	0.915	0.839	0.992	0.915	0.839	0.992	CLONAL	2	TRUE	1	0.543409855409175	3		465	312	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420970	49420970	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1165012136	NA	P-0057891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	302	481	0	ENST00000301067.7:c.14779A>C	p.Ser4927Arg	p.S4927R	ENST00000301067	NM_003482.3	4927	Agt/Cgt	48/54	0.544135920749845	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.543409855409175	4		481	738	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28886156	28886156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	81	467	0	ENST00000282397.4:c.3466G>A	p.Asp1156Asn	p.D1156N	ENST00000282397	NM_002019.4	1156	Gat/Aat	26/30	0.330394621969639	1	FACETS	0.639	0.567	0.714	0.639	0.567	0.714	SUBCLONAL	1	TRUE	0	0.543409855409175	1		467	340	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913691	32913692	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAAAAACAAGATACTTATTTAAGTAACAGTAGCAT	novel	NA	P-0057891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	24	354	0	ENST00000380152.3:c.5201_5235dup	p.Ser1746LysfsTer7	p.S1746Kfs*7	ENST00000380152		1733	-/GAAAAACAAGATACTTATTTAAGTAACAGTAGCAT	11/27	0.544135920749845	3	FACETS	0.455	0.357	0.566	0.227	0.178	0.283	SUBCLONAL	1	TRUE	1	0.543409855409175	3		354	247	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126097	2126097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145258407	NA	P-0057891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	162	773	0	ENST00000219476.3:c.2668C>T	p.His890Tyr	p.H890Y	ENST00000219476	NM_000548.3	890	Cat/Tat	24/42	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.543409855409175	2		773	557	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128015	30128016	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	129	621	0	ENST00000263025.4:c.1113_1114delinsTT	p.Gln372Ter	p.Q372*	ENST00000263025	NM_002746.2	371	ttCCag/ttTTag	8/9	1	2	FACETS	0.881	0.802	0.963	0.881	0.802	0.963	CLONAL	1	TRUE	1	0.543409855409175	2		621	539	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743966	41743966	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201596308	NA	P-0057891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	205	793	0	ENST00000301178.4:c.901C>T	p.Pro301Ser	p.P301S	ENST00000301178	NM_021913.4	301	Cct/Tct	7/20	0.544135920749845	3	FACETS	1	0.969	1	0.539	0.5	0.579	CLONAL	1	TRUE	1	0.543409855409175	3		793	890	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867721	45867722	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	121	794	0	ENST00000391945.4:c.678_679delinsTT	p.Arg227Cys	p.R227C	ENST00000391945	NM_000400.3	226	gcCCgc/gcTTgc	8/23	0.544135920749845	3	FACETS	0.813	0.735	0.894	0.406	0.367	0.447	CLONAL	1	TRUE	1	0.543409855409175	3		794	697	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561450	9561450	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	289	606	0	ENST00000353224.5:c.332G>T	p.Gly111Val	p.G111V	ENST00000353224	NM_177990.2	111	gGa/gTa	4/10	0.544135920749845	3	FACETS	0.882	0.841	0.923	1	0.994	1	CLONAL	3	TRUE	1	0.543409855409175	3		606	511	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624796	9624796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	197	441	0	ENST00000353224.5:c.181C>T	p.Pro61Ser	p.P61S	ENST00000353224	NM_177990.2	61	Ccc/Tcc	3/10	0.544135920749845	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.543409855409175	3		441	373	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376804	31376804	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	119	524	0	ENST00000328111.2:c.799G>T	p.Gly267Cys	p.G267C	ENST00000328111	NM_006892.3	267	Ggc/Tgc	7/23	0.544135920749845	3	FACETS	0.974	0.882	1	0.487	0.441	0.535	CLONAL	1	TRUE	1	0.543409855409175	3		524	572	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164839	36164839	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	178	743	0	ENST00000300305.3:c.1036C>G	p.Arg346Gly	p.R346G	ENST00000300305		346	Cgc/Ggc	8/8	1	2	FACETS	0.9	0.832	0.971	0.9	0.832	0.971	CLONAL	1	TRUE	1	0.543409855409175	2		743	728	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259360	89259361	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	135	470	0	ENST00000336596.2:c.505dup	p.Arg169LysfsTer59	p.R169Kfs*59	ENST00000336596	NM_005233.5	168	-/A	3/17	0.432594316129471	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	2	0.543409855409175	4		470	352	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057101	180057101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	256	613	0	ENST00000261937.6:c.518G>A	p.Ser173Asn	p.S173N	ENST00000261937	NM_182925.4	173	aGc/aAc	5/30	0.40175778622597	6	FACETS	1	0.983	1			1	CLONAL	2	TRUE	NA	0.543409855409175	6		613	873	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93973614	93973614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	93	313	0	ENST00000369303.4:c.1762G>A	p.Ala588Thr	p.A588T	ENST00000369303	NM_004440.3	588	Gct/Act	9/17	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.543409855409175	2		313	269	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553230	106553230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1445424097	NA	P-0057891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	136	594	0	ENST00000369096.4:c.1195C>T	p.Pro399Ser	p.P399S	ENST00000369096	NM_001198.3	399	Ccg/Tcg	5/7	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.543409855409175	2		594	491	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658377	117658377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	92	614	0	ENST00000368508.3:c.5206G>A	p.Gly1736Arg	p.G1736R	ENST00000368508	NM_002944.2	1736	Gga/Aga	31/43	1	2	FACETS	0.979	0.878	1	0.979	0.878	1	CLONAL	1	TRUE	1	0.543409855409175	2		614	346	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752842	128752842	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1479419101	NA	P-0057891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	78	324	0	ENST00000377970.2:c.1003C>A	p.Pro335Thr	p.P335T	ENST00000377970	NM_002467.4	335	Cct/Act	3/3	1	2	FACETS	0.993	0.883	1	0.993	0.883	1	CLONAL	1	TRUE	1	0.543409855409175	2		324	289	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22008850	22008850	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263458730	NA	P-0057891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	244	538	1	ENST00000276925.6:c.103G>A	p.Glu35Lys	p.E35K	ENST00000276925	NM_004936.3	35	Gaa/Aaa	1/2	0.51681188090505	2	FACETS	0.957	0.907	1	0.957	0.907	1	CLONAL	2	TRUE	0	0.543409855409175	2		539	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519999	NA	P-0057892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	251	71	0	ENST00000269305.4:c.716A>G	p.Asn239Ser	p.N239S	ENST00000269305	NM_001126112.2	239	aAc/aGc	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		71	634	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435908	110435908	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	60	53	0	ENST00000375856.3:c.2493del	p.Arg832AlafsTer34	p.R832Afs*34	ENST00000375856	NM_003749.2	831	ggG/gg	1/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		53	1037	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952139	178952139	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1560150596	NA	P-0057892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	205	184	0	ENST00000263967.3:c.3194A>T	p.His1065Leu	p.H1065L	ENST00000263967	NM_006218.2	1065	cAt/cTt	21/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		184	388	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758333	41758333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs537492526	NA	P-0057892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	113	77	0	ENST00000301178.4:c.1789G>A	p.Val597Ile	p.V597I	ENST00000301178	NM_021913.4	597	Gtc/Atc	15/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		77	781	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891599	151891602	+	frameshift_variant	Frame_Shift_Del	DEL	TGAT	TGAT	-	novel	NA	P-0057892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	173	38	0	ENST00000262189.6:c.4430_4433del	p.Asn1477ArgfsTer6	p.N1477Rfs*6	ENST00000262189	NM_170606.2	1477	aATCAg/ag	29/59	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		38	566	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380269	25380269	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	109	55	0	ENST00000311936.3:c.189G>C	p.Glu63Asp	p.E63D	ENST00000311936	NM_004985.3	63	gaG/gaC	3/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		55	851	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143083	7143087	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGC	CCTGC	-	novel	NA	P-0057892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	228	71	0	ENST00000302850.5:c.2282_2286del	p.Arg761LeufsTer37	p.R761Lfs*37	ENST00000302850	NM_000208.2	761	cGCAGG/c	12/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		71	631	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742772	39742776	+	frameshift_variant	Frame_Shift_Del	DEL	AACAA	AACAA	-	novel	NA	P-0057892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	82	54	0	ENST00000361337.2:c.1615_1619del	p.Asn539GlyfsTer4	p.N539Gfs*4	ENST00000361337	NM_003286.2	539	AACAAg/g	15/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		54	711	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590990	67590992	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	novel	NA	P-0057892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	20	20	0	ENST00000274335.5:c.1585_1587del	p.Asp529del	p.D529del	ENST00000274335		528	tATGat/tat	12/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		20	181	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0057893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3989	3053	621	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.260336511459982	49	FACETS	0.988	0.971	1			1	CLONAL	24	TRUE	NA	0.260336511459982	49		622	7042	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0057893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	232	665	0	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.260336511459982	2	FACETS	0.969	0.904	1	0.969	0.904	1	CLONAL	2	TRUE	0	0.260336511459982	2		665	920	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433388	49433388	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555191598	NA	P-0057893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	95	780	1	ENST00000301067.7:c.8059C>T	p.Arg2687Ter	p.R2687*	ENST00000301067	NM_003482.3	2687	Cga/Tga	32/54	1	2	FACETS	0.842	0.749	0.941	0.842	0.749	0.941	CLONAL	1	TRUE	1	0.260336511459982	2		781	867	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161349	185161349	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	141	634	0	ENST00000265026.3:c.776G>A	p.Trp259Ter	p.W259*	ENST00000265026	NM_004721.4	259	tGg/tAg	4/14	0.198255368976148	4	FACETS	0.777	0.708	0.85	0.777	0.708	0.85	SUBCLONAL	2	TRUE	2	0.260336511459982	4		634	878	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459217	120459217	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	51	586	0	ENST00000256646.2:c.6128A>T	p.Asp2043Val	p.D2043V	ENST00000256646	NM_024408.3	2043	gAt/gTt	34/34	1	2	FACETS	0.511	0.433	0.597	0.511	0.433	0.597	SUBCLONAL	1	TRUE	1	0.260336511459982	2		586	767	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162722889	162722889	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	84	490	0	ENST00000367921.3:c.87A>G	p.Ile29Met	p.I29M	ENST00000367921	NM_006182.2	29	atA/atG	4/18	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.260336511459982	2		490	604	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630648	187630648	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	79	687	0	ENST00000441802.2:c.334G>T	p.Val112Leu	p.V112L	ENST00000441802	NM_005245.3	112	Gtg/Ttg	2/27	0.126068647316443	0	FACETS	0.653	0.574	0.738			1	INDETERMINATE	1	TRUE	0	0.260336511459982	0		687	687	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86658395	86658395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	35	178	0	ENST00000274376.6:c.1360G>A	p.Val454Met	p.V454M	ENST00000274376	NM_002890.2	454	Gtg/Atg	10/25	0.260336511459982	2	FACETS	1	0.902	1	0.572	0.472	0.683	CLONAL	1	TRUE	0	0.260336511459982	2		178	235	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967219	93967219	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	60	392	0	ENST00000369303.4:c.2133A>G	p.Ile711Met	p.I711M	ENST00000369303	NM_004440.3	711	atA/atG	12/17	1	2	FACETS	0.952	0.822	1	0.952	0.822	1	CLONAL	1	TRUE	1	0.260336511459982	2		392	484	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940073	76940073	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	82	254	0	ENST00000373344.5:c.675A>T	p.Glu225Asp	p.E225D	ENST00000373344	NM_000489.3	225	gaA/gaT	9/35	0.138867223439809	2	FACETS	0.929	0.826	1			1	INDETERMINATE	2	TRUE	NA	0.260336511459982	2		254	339	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	67	365	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.27	2		365	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	67	630	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	1	2	FACETS	0.787	0.683	0.898	0.787	0.683	0.898	SUBCLONAL	1	TRUE	1	0.27	2		630	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	106	770	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	1	2	FACETS	0.857	0.767	0.953	0.857	0.767	0.953	CLONAL	1	TRUE	1	0.27	2		770	916	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	83	471	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.157255404494483	0	FACETS	0.922	0.816	1			1	INDETERMINATE	1	TRUE	0	0.27	0		471	487	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129160	2129160	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45465195	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	60	769	0	ENST00000219476.3:c.3094C>T	p.Arg1032Ter	p.R1032*	ENST00000219476	NM_000548.3	1032	Cga/Tga	27/42	1	2	FACETS	0.522	0.448	0.602	0.522	0.448	0.602	SUBCLONAL	1	TRUE	1	0.27	2		769	852	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309779	65309779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1456930967	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	177	534	0	ENST00000342505.4:c.2371G>A	p.Glu791Lys	p.E791K	ENST00000342505	NM_002227.2	791	Gag/Aag	17/25	0.259669629932262	3	FACETS	0.945	0.873	1	0.945	0.873	1	CLONAL	2	TRUE	1	0.27	3		534	787	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133561	55133561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs958381664	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	82	502	0	ENST00000257290.5:c.865G>A	p.Glu289Lys	p.E289K	ENST00000257290	NM_006206.4	289	Gaa/Aaa	6/23	1	2	FACETS	0.913	0.806	1	0.913	0.806	1	CLONAL	1	TRUE	1	0.27	2		502	665	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960089	134960089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1224986515	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	84	566	0	ENST00000398015.3:c.2446G>A	p.Glu816Lys	p.E816K	ENST00000398015	NM_004441.4	816	Gaa/Aaa	13/16	1	2	FACETS	0.963	0.851	1	0.963	0.851	1	CLONAL	1	TRUE	1	0.27	2		566	646	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453514	138453514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	42	378	0	ENST00000289153.2:c.934C>T	p.Pro312Ser	p.P312S	ENST00000289153	NM_006219.2	312	Cct/Tct	5/22	1	2	FACETS	0.969	0.812	1	0.969	0.812	1	CLONAL	1	TRUE	1	0.27	2		378	321	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552823	106552823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1042709746	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	89	628	0	ENST00000369096.4:c.788G>A	p.Gly263Glu	p.G263E	ENST00000369096	NM_001198.3	263	gGa/gAa	5/7	0.157255404494483	3	FACETS	0.867	0.768	0.974	0.434	0.384	0.487	INDETERMINATE	1	TRUE	1	0.27	3		628	863	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39644733	39644733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	34	264	0	ENST00000262039.4:c.2462C>T	p.Ser821Phe	p.S821F	ENST00000262039	NM_002647.2	821	tCc/tTc	23/25	1	2	FACETS	0.976	0.802	1	0.976	0.802	1	CLONAL	1	TRUE	1	0.27	2		264	258	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630411	187630411	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	95	672	0	ENST00000441802.2:c.571C>T	p.Arg191Ter	p.R191*	ENST00000441802	NM_005245.3	191	Cga/Tga	2/27	1	2	FACETS	0.903	0.804	1	0.903	0.804	1	CLONAL	1	TRUE	1	0.27	2		672	779	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568555	41568555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555911573	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	67	486	0	ENST00000263253.7:c.4505C>T	p.Pro1502Leu	p.P1502L	ENST00000263253	NM_001429.3	1502	cCt/cTt	28/31	1	2	FACETS	0.985	0.857	1	0.985	0.857	1	CLONAL	1	TRUE	1	0.27	2		486	504	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562641	29562641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854562	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	52	451	1	ENST00000356175.3:c.3721C>T	p.Arg1241Ter	p.R1241*	ENST00000356175	NM_000267.3	1241	Cga/Tga	28/57	1	2	FACETS	0.85	0.725	0.987	0.85	0.725	0.987	CLONAL	1	TRUE	1	0.27	2		452	453	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817464	39817464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	77	542	0	ENST00000288319.7:c.99G>A	p.Met33Ile	p.M33I	ENST00000288319	NM_182918.3	33	atG/atA	2/10	1	2	FACETS	0.807	0.708	0.913	0.807	0.708	0.913	CLONAL	1	TRUE	1	0.27	2		542	707	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412279	139412279	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	80	751	1	ENST00000277541.6:c.1366T>C	p.Cys456Arg	p.C456R	ENST00000277541	NM_017617.3	456	Tgc/Cgc	8/34	1	2	FACETS	0.681	0.598	0.77	0.681	0.598	0.77	SUBCLONAL	1	TRUE	1	0.27	2		752	870	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124437	94124437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	41	425	0	ENST00000369303.4:c.146C>T	p.Ser49Phe	p.S49F	ENST00000369303	NM_004440.3	49	tCc/tTc	2/17	0.157255404494483	3	FACETS	0.976	0.816	1	0.488	0.408	0.577	INDETERMINATE	1	TRUE	1	0.27	3		425	353	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636764	8636764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	68	482	0	ENST00000356435.5:c.145G>A	p.Gly49Arg	p.G49R	ENST00000356435		49	Gga/Aga	2/35	0.157255404494483	0	FACETS	0.649	0.565	0.739			1	INDETERMINATE	1	TRUE	0	0.27	0		482	567	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416710	121416710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373180062	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	46	762	0	ENST00000257555.6:c.139G>A	p.Gly47Arg	p.G47R	ENST00000257555		47	Ggg/Agg	1/10	1	2	FACETS	0.45	0.378	0.53	0.45	0.378	0.53	SUBCLONAL	1	TRUE	1	0.27	2		762	757	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099042	27099043	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	82	535	0	ENST00000324856.7:c.3458_3459delinsTT	p.Ser1153Phe	p.S1153F	ENST00000324856	NM_006015.4	1153	tCC/tTT	13/20	0.259669629932262	3	FACETS	0.93	0.82	1	0.465	0.41	0.525	CLONAL	1	TRUE	1	0.27	3		535	741	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917772	29917772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	111	729	0	ENST00000389048.3:c.896C>T	p.Ser299Phe	p.S299F	ENST00000389048	NM_004304.4	299	tCc/tTc	3/29	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.27	2		729	795	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	58	353	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.999	0.861	1	0.999	0.861	1	CLONAL	1	TRUE	1	0.27	2		353	430	SUCCESS
APC	324	MSKCC	GRCh37	5	112176873	112176873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	41	350	0	ENST00000257430.4:c.5582C>T	p.Ser1861Phe	p.S1861F	ENST00000257430	NM_000038.5	1861	tCt/tTt	16/16	1	2	FACETS	0.868	0.725	1	0.868	0.725	1	CLONAL	1	TRUE	1	0.27	2		350	350	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156585	55156585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779173667	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	94	544	0	ENST00000257290.5:c.2986G>A	p.Glu996Lys	p.E996K	ENST00000257290	NM_006206.4	996	Gag/Aag	22/23	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.27	2		544	672	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981586	101981586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1319669560	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	19	197	0	ENST00000282441.5:c.7C>T	p.Pro3Ser	p.P3S	ENST00000282441	NM_001130145.2	3	Ccc/Tcc	1/9	0.259669629932262	1	FACETS	0.574	0.437	0.734	0.574	0.437	0.734	SUBCLONAL	1	TRUE	0	0.27	1		197	212	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346551	81346551	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444026216	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	25	290	0	ENST00000222390.5:c.1402C>T	p.Arg468Cys	p.R468C	ENST00000222390	NM_000601.4	468	Cgt/Tgt	11/18	1	2	FACETS	0.605	0.477	0.752	0.605	0.477	0.752	SUBCLONAL	1	TRUE	1	0.27	2		290	306	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149244	119149244	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	70	598	0	ENST00000264033.4:c.1252T>A	p.Phe418Ile	p.F418I	ENST00000264033	NM_005188.3	418	Ttc/Atc	9/16	0.259669629932262	1	FACETS	0.82	0.716	0.932	0.82	0.716	0.932	CLONAL	1	TRUE	0	0.27	1		598	547	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271888	15271888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269752929	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	56	746	1	ENST00000263388.2:c.6551C>T	p.Ser2184Leu	p.S2184L	ENST00000263388	NM_000435.2	2184	tCg/tTg	33/33	1	2	FACETS	0.614	0.525	0.711	0.614	0.525	0.711	SUBCLONAL	1	TRUE	1	0.27	2		747	676	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509129	106509129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1463041855	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	70	631	0	ENST00000359195.3:c.1123C>T	p.Arg375Trp	p.R375W	ENST00000359195	NM_002649.2	375	Cgg/Tgg	2/11	1	2	FACETS	0.754	0.657	0.859	0.754	0.657	0.859	SUBCLONAL	1	TRUE	1	0.27	2		631	688	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874562	35874562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	73	607	0	ENST00000303115.3:c.718C>T	p.Pro240Ser	p.P240S	ENST00000303115	NM_002185.3	240	Cct/Tct	6/8	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.27	2		607	512	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955105	93955105	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	31	385	0	ENST00000369303.4:c.2793G>A	p.Trp931Ter	p.W931*	ENST00000369303	NM_004440.3	931	tgG/tgA	16/17	0.157255404494483	3	FACETS	0.807	0.654	0.979	0.403	0.327	0.49	INDETERMINATE	1	TRUE	1	0.27	3		385	323	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40856677	40856677	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs376492983	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	47	371	0	ENST00000428826.2:c.1960C>T	p.Arg654Ter	p.R654*	ENST00000428826		654	Cga/Tga	18/21	1	2	FACETS	0.786	0.664	0.92	0.786	0.664	0.92	CLONAL	1	TRUE	1	0.27	2		371	443	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048749	180048749	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	91	728	0	ENST00000261937.6:c.1813C>T	p.Pro605Ser	p.P605S	ENST00000261937	NM_182925.4	605	Ccg/Tcg	13/30	1	2	FACETS	0.949	0.843	1	0.949	0.843	1	CLONAL	1	TRUE	1	0.27	2		728	710	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169953053	169953053	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	62	468	0	ENST00000295797.4:c.137C>T	p.Ser46Phe	p.S46F	ENST00000295797	NM_002740.5	46	tCc/tTc	2/18	1	2	FACETS	0.965	0.835	1	0.965	0.835	1	CLONAL	1	TRUE	1	0.27	2		468	476	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031889	26031889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	58	336	0	ENST00000244661.2:c.400G>A	p.Glu134Lys	p.E134K	ENST00000244661	NM_003537.3	134	Gaa/Aaa	1/1	0.157255404494483	3	FACETS	1	0.952	1	0.622	0.536	0.715	INDETERMINATE	1	TRUE	1	0.27	3		336	392	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883182	37883182	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs895225081	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	101	742	1	ENST00000269571.5:c.3085G>A	p.Gly1029Ser	p.G1029S	ENST00000269571		1029	Ggc/Agc	25/27	1	2	FACETS	0.861	0.769	0.959	0.861	0.769	0.959	CLONAL	1	TRUE	1	0.27	2		743	869	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956938	2956938	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	60	593	0	ENST00000396946.4:c.2689G>A	p.Gly897Ser	p.G897S	ENST00000396946	NM_032415.4	897	Ggc/Agc	20/25	1	2	FACETS	0.647	0.557	0.745	0.647	0.557	0.745	SUBCLONAL	1	TRUE	1	0.27	2		593	687	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528102	103528102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1233010372	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	33	353	0	ENST00000355739.4:c.3410C>T	p.Pro1137Leu	p.P1137L	ENST00000355739	NM_000123.3	1137	cCc/cTc	15/15	1	2	FACETS	0.515	0.419	0.623	0.515	0.419	0.623	SUBCLONAL	1	TRUE	1	0.27	2		353	475	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970928	70970928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774392514	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	82	571	1	ENST00000276594.2:c.1333G>A	p.Asp445Asn	p.D445N	ENST00000276594	NM_024504.3	445	Gac/Aac	6/8	1	2	FACETS	0.835	0.736	0.942	0.835	0.736	0.942	CLONAL	1	TRUE	1	0.27	2		572	727	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848093	151848093	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	42	296	0	ENST00000262189.6:c.12667-1G>A		p.X4223_splice	ENST00000262189	NM_170606.2	4223			1	2	FACETS	0.92	0.771	1	0.92	0.771	1	CLONAL	1	TRUE	1	0.27	2		296	338	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142949951	142949951	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1310205480	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	43	474	1	ENST00000262992.4:c.2759G>A	p.Gly920Glu	p.G920E	ENST00000262992	NM_001101669.1	920	gGa/gAa	24/24	1	2	FACETS	0.802	0.673	0.946	0.802	0.673	0.946	CLONAL	1	TRUE	1	0.27	2		475	397	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319372	11319372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	114	627	0	ENST00000361445.4:c.95G>A	p.Arg32Gln	p.R32Q	ENST00000361445	NM_004958.3	32	cGg/cAg	2/58	0.259669629932262	3	FACETS	1	0.962	1	0.571	0.513	0.631	CLONAL	1	TRUE	1	0.27	3		627	840	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256402	16256402	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	127	524	0	ENST00000375759.3:c.3667C>T	p.Pro1223Ser	p.P1223S	ENST00000375759	NM_015001.2	1223	Cct/Tct	11/15	0.259669629932262	3	FACETS	0.796	0.722	0.873	0.796	0.722	0.873	SUBCLONAL	2	TRUE	1	0.27	3		524	671	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366961	40366961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	69	602	1	ENST00000397332.2:c.236C>T	p.Pro79Leu	p.P79L	ENST00000397332	NM_001033082.2	79	cCc/cTc	2/3	0.259669629932262	3	FACETS	0.99	0.863	1	0.495	0.431	0.564	CLONAL	1	TRUE	1	0.27	3		603	586	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726225	46726225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	85	471	0	ENST00000371975.4:c.419C>T	p.Pro140Leu	p.P140L	ENST00000371975	NM_003579.3	140	cCt/cTt	6/18	0.259669629932262	3	FACETS	1	0.918	1	0.524	0.463	0.589	CLONAL	1	TRUE	1	0.27	3		471	682	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202597	67202598	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	66	653	0	ENST00000312629.5:c.1406_1407delinsAA	p.Gly469Glu	p.G469E	ENST00000312629	NM_003952.2	469	gGG/gAA	15/15	1	2	FACETS	0.663	0.575	0.759	0.663	0.575	0.759	SUBCLONAL	1	TRUE	1	0.27	2		653	737	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118355602	118355602	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	63	495	0	ENST00000534358.1:c.4244G>A	p.Trp1415Ter	p.W1415*	ENST00000534358	NM_005933.3	1415	tGg/tAg	10/36	0.259669629932262	1	FACETS	0.863	0.748	0.987	0.863	0.748	0.987	CLONAL	1	TRUE	0	0.27	1		495	468	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375063	118375063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	68	433	0	ENST00000534358.1:c.8456C>T	p.Ser2819Phe	p.S2819F	ENST00000534358	NM_005933.3	2819	tCc/tTc	27/36	0.259669629932262	1	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	0	0.27	1		433	419	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	401930	401930	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	37	274	0	ENST00000399788.2:c.4861G>A	p.Asp1621Asn	p.D1621N	ENST00000399788	NM_001042603.1	1621	Gac/Aac	27/28	1	2	FACETS	0.788	0.651	0.94	0.788	0.651	0.94	CLONAL	1	TRUE	1	0.27	2		274	348	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245148	46245148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	59	504	0	ENST00000334344.6:c.3242C>T	p.Ala1081Val	p.A1081V	ENST00000334344	NM_152641.2	1081	gCt/gTt	15/21	1	2	FACETS	0.849	0.731	0.977	0.849	0.731	0.977	CLONAL	1	TRUE	1	0.27	2		504	515	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434556	49434556	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370380369	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	55	739	2	ENST00000301067.7:c.6997C>T	p.Pro2333Ser	p.P2333S	ENST00000301067	NM_003482.3	2333	Cct/Tct	31/54	1	2	FACETS	0.585	0.499	0.678	0.585	0.499	0.678	SUBCLONAL	1	TRUE	1	0.27	2		741	697	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112919953	112919953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	51	289	0	ENST00000351677.2:c.1168G>A	p.Glu390Lys	p.E390K	ENST00000351677	NM_002834.3	390	Gaa/Aaa	10/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.27	2		289	289	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209300	133209300	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879254239	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	52	714	0	ENST00000320574.5:c.6086G>A	p.Gly2029Glu	p.G2029E	ENST00000320574	NM_006231.2	2029	gGg/gAg	44/49	1	2	FACETS	0.546	0.463	0.636	0.546	0.463	0.636	SUBCLONAL	1	TRUE	1	0.27	2		714	706	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004248	29004248	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	66	395	0	ENST00000282397.4:c.1045G>A	p.Gly349Ser	p.G349S	ENST00000282397	NM_002019.4	349	Ggc/Agc	8/30	1	2	FACETS	0.914	0.794	1	0.914	0.794	1	CLONAL	1	TRUE	1	0.27	2		395	535	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656636	3656637	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	104	724	0	ENST00000294008.3:c.598_599delinsTT	p.Pro200Phe	p.P200F	ENST00000294008	NM_032444.2	200	CCc/TTc	3/15	1	2	FACETS	0.868	0.776	0.965	0.868	0.776	0.965	CLONAL	1	TRUE	1	0.27	2		724	888	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56857676	56857676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1209633397	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	94	492	2	ENST00000308159.5:c.712G>A	p.Ala238Thr	p.A238T	ENST00000308159	NM_014669.4	238	Gca/Aca	8/22	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.27	2		494	611	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829179	72829180	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	94	774	0	ENST00000268489.5:c.7401_7402delinsTT	p.Gln2468Ter	p.Q2468*	ENST00000268489	NM_006885.3	2467	ccCCag/ccTTag	9/10	1	2	FACETS	0.799	0.709	0.894	0.799	0.709	0.894	SUBCLONAL	1	TRUE	1	0.27	2		774	872	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89824995	89824995	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	46	475	0	ENST00000389301.3:c.2971T>G	p.Phe991Val	p.F991V	ENST00000389301	NM_000135.2	991	Ttc/Gtc	30/43	1	2	FACETS	0.58	0.488	0.683	0.58	0.488	0.683	SUBCLONAL	1	TRUE	1	0.27	2		475	587	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682116	37682116	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	40	362	0	ENST00000447079.4:c.3308-1G>A		p.X1103_splice	ENST00000447079	NM_015083.1	1103			1	2	FACETS	0.684	0.569	0.813	0.684	0.569	0.813	SUBCLONAL	1	TRUE	1	0.27	2		362	433	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41203080	41203080	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs80357112	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	73	529	0	ENST00000357654.3:c.5332G>A	p.Asp1778Asn	p.D1778N	ENST00000357654	NM_007294.3	1778	Gat/Aat	20/23	1	2	FACETS	0.751	0.656	0.853	0.751	0.656	0.853	SUBCLONAL	1	TRUE	1	0.27	2		529	720	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118897	70118897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	103	585	0	ENST00000245479.2:c.469G>A	p.Glu157Lys	p.E157K	ENST00000245479	NM_000346.3	157	Gag/Aag	2/3	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.27	2		585	600	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094865	11094866	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	43	735	2	ENST00000358026.2:c.38_39delinsAA	p.Arg13Gln	p.R13Q	ENST00000358026	NM_001128849.1	13	cGG/cAA	2/36	1	2	FACETS	0.412	0.343	0.488	0.412	0.343	0.488	SUBCLONAL	1	TRUE	1	0.27	2		737	774	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271835	15271835	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	65	700	0	ENST00000263388.2:c.6604G>T	p.Val2202Phe	p.V2202F	ENST00000263388	NM_000435.2	2202	Gtc/Ttc	33/33	1	2	FACETS	0.746	0.647	0.855	0.746	0.647	0.855	SUBCLONAL	1	TRUE	1	0.27	2		700	645	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748505	40748505	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751752149	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	91	767	1	ENST00000392038.2:c.377C>T	p.Ser126Phe	p.S126F	ENST00000392038	NM_001626.4	126	tCc/tTc	5/14	1	2	FACETS	0.913	0.811	1	0.913	0.811	1	CLONAL	1	TRUE	1	0.27	2		768	738	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022364	26022364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	66	604	0	ENST00000435504.4:c.293C>T	p.Ser98Leu	p.S98L	ENST00000435504		98	tCa/tTa	5/13	1	2	FACETS	0.701	0.608	0.803	0.701	0.608	0.803	SUBCLONAL	1	TRUE	1	0.27	2		604	697	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026588	48026588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	50	456	0	ENST00000234420.5:c.1466C>T	p.Pro489Leu	p.P489L	ENST00000234420	NM_000179.2	489	cCa/cTa	4/10	1	2	FACETS	0.836	0.71	0.974	0.836	0.71	0.974	CLONAL	1	TRUE	1	0.27	2		456	443	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047010	128047010	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237231600	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	89	568	0	ENST00000285398.2:c.725C>T	p.Ser242Phe	p.S242F	ENST00000285398	NM_000122.1	242	tCt/tTt	6/15	1	2	FACETS	0.951	0.844	1	0.951	0.844	1	CLONAL	1	TRUE	1	0.27	2		568	693	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108293	209108293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	33	425	0	ENST00000345146.2:c.556G>A	p.Asp186Asn	p.D186N	ENST00000345146	NM_005896.2	186	Gat/Aat	6/10	1	2	FACETS	0.677	0.552	0.818	0.677	0.552	0.818	SUBCLONAL	1	TRUE	1	0.27	2		425	361	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660961	227660961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	93	643	0	ENST00000305123.5:c.2494C>T	p.Pro832Ser	p.P832S	ENST00000305123	NM_005544.2	832	Ccc/Tcc	1/2	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.27	2		643	678	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944597	40944597	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	43	377	0	ENST00000373198.4:c.1905G>T	p.Lys635Asn	p.K635N	ENST00000373198	NM_133170.3	635	aaG/aaT	12/32	1	2	FACETS	0.669	0.56	0.79	0.669	0.56	0.79	SUBCLONAL	1	TRUE	1	0.27	2		377	476	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42843894	42843894	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	63	426	0	ENST00000398585.3:c.1025C>T	p.Pro342Leu	p.P342L	ENST00000398585	NM_001135099.1	342	cCa/cTa	10/14	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.27	2		426	422	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421279	12421279	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	82	676	0	ENST00000287820.6:c.159G>A	p.Met53Ile	p.M53I	ENST00000287820	NM_015869.4	53	atG/atA	2/7	1	2	FACETS	0.856	0.754	0.964	0.856	0.754	0.964	CLONAL	1	TRUE	1	0.27	2		676	710	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468514	89468514	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	34	355	0	ENST00000336596.2:c.2048T>C	p.Ile683Thr	p.I683T	ENST00000336596	NM_005233.5	683	aTt/aCt	11/17	1	2	FACETS	0.773	0.633	0.929	0.773	0.633	0.929	CLONAL	1	TRUE	1	0.27	2		355	326	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898749	134898749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	37	375	0	ENST00000398015.3:c.1807C>T	p.Pro603Ser	p.P603S	ENST00000398015	NM_004441.4	603	Ccc/Tcc	10/16	1	2	FACETS	0.617	0.509	0.739	0.617	0.509	0.739	SUBCLONAL	1	TRUE	1	0.27	2		375	444	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474673	138474673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	66	453	0	ENST00000289153.2:c.320C>T	p.Pro107Leu	p.P107L	ENST00000289153	NM_006219.2	107	cCa/cTa	2/22	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.27	2		453	430	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937431	178937431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	33	283	0	ENST00000263967.3:c.1819C>T	p.Pro607Ser	p.P607S	ENST00000263967	NM_006218.2	607	Cca/Tca	12/21	1	2	FACETS	0.912	0.746	1	0.912	0.746	1	CLONAL	1	TRUE	1	0.27	2		283	268	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129886	55129887	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	64	502	1	ENST00000257290.5:c.420_421delinsAA	p.Glu141Lys	p.E141K	ENST00000257290	NM_006206.4	140	gtGGag/gtAAag	4/23	1	2	FACETS	0.859	0.744	0.983	0.859	0.744	0.983	CLONAL	1	TRUE	1	0.27	2		503	552	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139858	55139858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	61	437	0	ENST00000257290.5:c.1519C>T	p.Leu507Phe	p.L507F	ENST00000257290	NM_006206.4	507	Ctt/Ttt	10/23	1	2	FACETS	0.907	0.784	1	0.907	0.784	1	CLONAL	1	TRUE	1	0.27	2		437	498	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964904	55964904	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	58	371	0	ENST00000263923.4:c.2333T>A	p.Phe778Tyr	p.F778Y	ENST00000263923	NM_002253.2	778	tTc/tAc	16/30	1	2	FACETS	0.951	0.818	1	0.951	0.818	1	CLONAL	1	TRUE	1	0.27	2		371	452	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143129650	143129650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	28	406	0	ENST00000262992.4:c.1000G>A	p.Glu334Lys	p.E334K	ENST00000262992	NM_001101669.1	334	Gag/Aag	12/24	1	2	FACETS	0.593	0.474	0.728	0.593	0.474	0.728	SUBCLONAL	1	TRUE	1	0.27	2		406	350	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540545	187540561	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTGGCTTCATAAATC	TTCTGGCTTCATAAATC	-	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	39	418	0	ENST00000441802.2:c.7179_7195del	p.Gln2393HisfsTer2	p.Q2393Hfs*2	ENST00000441802	NM_005245.3	2393	caGATTTATGAAGCCAGAAtt/catt	10/27	1	2	FACETS	0.658	0.546	0.783	0.658	0.546	0.783	SUBCLONAL	1	TRUE	1	0.27	2		418	439	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047215	180047215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201205543	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	61	681	2	ENST00000261937.6:c.2500G>A	p.Asp834Asn	p.D834N	ENST00000261937	NM_182925.4	834	Gat/Aat	17/30	1	2	FACETS	0.743	0.641	0.854	0.743	0.641	0.854	SUBCLONAL	1	TRUE	1	0.27	2		683	608	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057798	180057799	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	45	408	0	ENST00000261937.6:c.156_157delinsAA	p.Gly53Arg	p.G53R	ENST00000261937	NM_182925.4	52	agGGga/agAAga	3/30	1	2	FACETS	0.901	0.759	1	0.901	0.759	1	CLONAL	1	TRUE	1	0.27	2		408	370	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394936	394936	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	58	506	0	ENST00000380956.4:c.332T>C	p.Val111Ala	p.V111A	ENST00000380956	NM_001195286.1	111	gTt/gCt	3/9	0.157255404494483	3	FACETS	0.721	0.619	0.833	0.361	0.309	0.417	INDETERMINATE	1	TRUE	1	0.27	3		506	676	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056014	26056015	+	coding_sequence_variant,3_prime_UTR_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	40	284	1	ENST00000343677.2:c.642_*1delinsAA		p.*214*	ENST00000343677	NM_005319.3	214		1/1	0.157255404494483	3	FACETS	0.909	0.757	1	0.454	0.378	0.539	INDETERMINATE	1	TRUE	1	0.27	3		285	370	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250434	26250434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	91	499	0	ENST00000446824.2:c.400G>A	p.Glu134Lys	p.E134K	ENST00000446824	NM_021018.2	134	Gag/Aag	1/1	0.157255404494483	3	FACETS	1	0.97	1	0.635	0.565	0.71	INDETERMINATE	1	TRUE	1	0.27	3		499	602	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64290045	64290045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	59	456	0	ENST00000370651.3:c.488C>T	p.Ser163Phe	p.S163F	ENST00000370651	NM_003463.4	163	tCc/tTc	6/6	0.157255404494483	3	FACETS	0.899	0.773	1	0.449	0.386	0.518	INDETERMINATE	1	TRUE	1	0.27	3		456	552	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554978	106554978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	66	517	0	ENST00000369096.4:c.2095C>T	p.Leu699Phe	p.L699F	ENST00000369096	NM_001198.3	699	Ctc/Ttc	7/7	0.157255404494483	3	FACETS	0.817	0.709	0.935	0.409	0.354	0.468	INDETERMINATE	1	TRUE	1	0.27	3		517	679	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647519	117647519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	39	468	0	ENST00000368508.3:c.5425G>A	p.Gly1809Arg	p.G1809R	ENST00000368508	NM_002944.2	1809	Gga/Aga	33/43	0.157255404494483	3	FACETS	0.874	0.726	1	0.437	0.363	0.52	INDETERMINATE	1	TRUE	1	0.27	3		468	375	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725469	117725469	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	41	402	0	ENST00000368508.3:c.412C>A	p.Leu138Ile	p.L138I	ENST00000368508	NM_002944.2	138	Ctt/Att	5/43	0.157255404494483	3	FACETS	0.754	0.628	0.894	0.377	0.314	0.447	INDETERMINATE	1	TRUE	1	0.27	3		402	457	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983364	149983380	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGTTGATAACCTTTAA	CAGTTGATAACCTTTAA	-	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	42	408	0	ENST00000253339.5:c.2884-6_2894del		p.X962_splice	ENST00000253339		962		7/7	0.157255404494483	3	FACETS	0.781	0.653	0.924	0.391	0.326	0.462	INDETERMINATE	1	TRUE	1	0.27	3		408	452	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874556	151874556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	42	383	0	ENST00000262189.6:c.7982C>T	p.Pro2661Leu	p.P2661L	ENST00000262189	NM_170606.2	2661	cCt/cTt	38/59	1	2	FACETS	0.796	0.666	0.94	0.796	0.666	0.94	CLONAL	1	TRUE	1	0.27	2		383	391	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372211	55372211	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	50	386	0	ENST00000297316.4:c.901G>A	p.Gly301Ser	p.G301S	ENST00000297316	NM_022454.3	301	Ggc/Agc	2/2	1	2	FACETS	0.899	0.764	1	0.899	0.764	1	CLONAL	1	TRUE	1	0.27	2		386	412	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965367	68965367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	34	550	0	ENST00000288368.4:c.979G>A	p.Gly327Arg	p.G327R	ENST00000288368	NM_024870.2	327	Gga/Aga	9/40	1	2	FACETS	0.651	0.532	0.784	0.651	0.532	0.784	SUBCLONAL	1	TRUE	1	0.27	2		550	387	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117870626	117870626	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	25	338	0	ENST00000297338.2:c.446T>C	p.Val149Ala	p.V149A	ENST00000297338	NM_006265.2	149	gTt/gCt	5/14	1	2	FACETS	0.565	0.445	0.702	0.565	0.445	0.702	SUBCLONAL	1	TRUE	1	0.27	2		338	328	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141545606	141545607	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	81	758	0	ENST00000220592.5:c.2231_2232delinsTT	p.Thr744Ile	p.T744I	ENST00000220592	NM_012154.3	744	aCC/aTT	17/19	1	2	FACETS	0.667	0.587	0.754	0.667	0.587	0.754	SUBCLONAL	1	TRUE	1	0.27	2		758	899	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418180	139418180	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	96	685	0	ENST00000277541.6:c.392C>T	p.Pro131Leu	p.P131L	ENST00000277541	NM_017617.3	131	cCc/cTc	3/34	1	2	FACETS	0.894	0.796	0.999	0.894	0.796	0.999	CLONAL	1	TRUE	1	0.27	2		685	795	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15833976	15833976	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	92	277	2	ENST00000307771.7:c.734C>T	p.Pro245Leu	p.P245L	ENST00000307771	NM_005089.3	245	cCc/cTc	8/11	1	1	FACETS	0.996	0.896	1	1	0.987	1	CLONAL	2	TRUE	0	0.27	1		279	296	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229277	123229277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	33	152	0	ENST00000218089.9:c.3761C>T	p.Pro1254Leu	p.P1254L	ENST00000218089	NM_001042749.1	1254	cCa/cTa	34/35	1	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.27	1		152	160	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578435	7578435	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	203	703	0	ENST00000269305.4:c.495del	p.Gln165HisfsTer5	p.Q165Hfs*5	ENST00000269305	NM_001126112.2	165	caG/ca	5/11	0.630869046255769	1	FACETS	0.975	0.915	1	0.975	0.915	1	CLONAL	1	TRUE	0	0.630869046255769	1		703	452	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846090	151846090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756354376	NA	P-0057895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	80	461	0	ENST00000262189.6:c.12922G>A	p.Ala4308Thr	p.A4308T	ENST00000262189	NM_170606.2	4308	Gcc/Acc	52/59	0.630869046255769	3	FACETS	0.536	0.472	0.605	0.268	0.236	0.303	SUBCLONAL	1	TRUE	1	0.630869046255769	3		461	622	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061215	38061231	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGCCGTTCTCGAACA	GCAGCCGTTCTCGAACA	T	novel	NA	P-0057895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	117	451	0	ENST00000250448.2:c.758_774delinsA	p.Met253AsnfsTer63	p.M253Nfs*63	ENST00000250448	NM_004496.3	253	aTGTTCGAGAACGGCTGC/aA	2/2	1	2	FACETS	0.881	0.801	0.965	0.881	0.801	0.965	CLONAL	1	TRUE	1	0.630869046255769	2		451	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587781845	NA	P-0057896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	487	776	0	ENST00000269305.4:c.511G>T	p.Glu171Ter	p.E171*	ENST00000269305	NM_001126112.2	171	Gag/Tag	5/11	0.674666041152667	3	FACETS	0.926	0.898	0.953			1	CLONAL	3	TRUE	NA	0.674666041152667	3		776	695	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110013	115110013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	524	841	1	ENST00000257566.3:c.1865C>T	p.Ser622Leu	p.S622L	ENST00000257566	NM_016569.3	622	tCg/tTg	8/8	0.674666041152667	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	TRUE	1	0.674666041152667	4		842	864	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104268939	104268939	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	98	632	0	ENST00000369902.3:c.196G>A	p.Asp66Asn	p.D66N	ENST00000369902	NM_016169.3	66	Gac/Aac	2/12	0.674666041152667	4	FACETS	0.584	0.52	0.652	0.292	0.26	0.326	SUBCLONAL	1	TRUE	2	0.674666041152667	4		632	833	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104269032	104269032	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	102	534	0	ENST00000369902.3:c.289G>A	p.Asp97Asn	p.D97N	ENST00000369902	NM_016169.3	97	Gat/Aat	2/12	0.674666041152667	4	FACETS	0.643	0.575	0.716	0.322	0.287	0.358	SUBCLONAL	1	TRUE	2	0.674666041152667	4		534	787	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61706032	61706032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	148	578	0	ENST00000401558.2:c.3139G>A	p.Glu1047Lys	p.E1047K	ENST00000401558	NM_003400.3	1047	Gaa/Aaa	25/25	0.522108826648605	3	FACETS	0.859	0.787	0.935	0.43	0.393	0.468	CLONAL	1	TRUE	1	0.674666041152667	3		578	683	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30956831	30956831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	92	460	0	ENST00000375687.4:c.157C>T	p.Leu53Phe	p.L53F	ENST00000375687	NM_015338.5	53	Ctc/Ttc	4/13	0.674666041152667	3	FACETS	0.661	0.588	0.737	0.33	0.294	0.369	SUBCLONAL	1	TRUE	1	0.674666041152667	3		460	552	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573372	41573372	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	284	743	0	ENST00000263253.7:c.5657A>G	p.Tyr1886Cys	p.Y1886C	ENST00000263253	NM_001429.3	1886	tAc/tGc	31/31	0.674666041152667	3	FACETS	1	0.993	1	0.681	0.642	0.72	CLONAL	1	TRUE	1	0.674666041152667	3		743	827	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422973	12422973	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	99	480	0	ENST00000287820.6:c.463G>A	p.Ala155Thr	p.A155T	ENST00000287820	NM_015869.4	155	Gct/Act	3/7	0.674666041152667	4	FACETS	0.674	0.602	0.751	0.225	0.2	0.251	SUBCLONAL	1	TRUE	1	0.674666041152667	4		480	729	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443736	52443736	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	479	739	1	ENST00000460680.1:c.61G>T	p.Asp21Tyr	p.D21Y	ENST00000460680	NM_004656.3	21	Gat/Tat	2/17	0.674666041152667	4	FACETS	0.948	0.914	0.982	0.948	0.914	0.982	CLONAL	3	TRUE	1	0.674666041152667	4		740	836	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510174	187510174	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1423542665	NA	P-0057896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	100	531	0	ENST00000441802.2:c.13339G>A	p.Glu4447Lys	p.E4447K	ENST00000441802	NM_005245.3	4447	Gag/Aag	27/27	NA	2	FACETS	0.72	0.647	0.795			1	INDETERMINATE	1	TRUE	NA	0.674666041152667	2		531	412	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0057965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	52	554	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.982	0.835	1	0.982	0.835	1	CLONAL	1	TRUE	1	0.16	2		554	662	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	15	365	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.788	0.576	1	0.788	0.576	1	CLONAL	1	TRUE	1	0.16	2		365	238	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709505	176709505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	22	303	0	ENST00000439151.2:c.5932G>A	p.Glu1978Lys	p.E1978K	ENST00000439151	NM_022455.4	1978	Gaa/Aaa	19/23	1	2	FACETS	0.899	0.697	1	0.899	0.697	1	CLONAL	1	TRUE	1	0.16	2		303	306	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440372	52440372	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	38	331	0	ENST00000460680.1:c.680G>C	p.Arg227Pro	p.R227P	ENST00000460680	NM_004656.3	227	cGc/cCc	9/17	1	2	FACETS	0.815	0.672	0.974	0.815	0.672	0.974	CLONAL	1	TRUE	1	0.16	2		331	583	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287300	46287300	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0057965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	37	493	0	ENST00000334344.6:c.5245A>T	p.Arg1749Ter	p.R1749*	ENST00000334344	NM_152641.2	1749	Aga/Tga	19/21	1	2	FACETS	0.753	0.62	0.903	0.753	0.62	0.903	CLONAL	1	TRUE	1	0.16	2		493	614	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420607	49420607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123724	NA	P-0057965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	47	837	2	ENST00000301067.7:c.15142C>T	p.Arg5048Cys	p.R5048C	ENST00000301067	NM_003482.3	5048	Cgt/Tgt	48/54	1	2	FACETS	0.766	0.645	0.901	0.766	0.645	0.901	CLONAL	1	TRUE	1	0.16	2		839	767	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427705	49427705	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	38	792	1	ENST00000301067.7:c.10783T>A	p.Tyr3595Asn	p.Y3595N	ENST00000301067	NM_003482.3	3595	Tat/Aat	39/54	1	2	FACETS	0.684	0.564	0.819	0.684	0.564	0.819	SUBCLONAL	1	TRUE	1	0.16	2		793	694	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436780	110436780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373800038	NA	P-0057965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	73	944	1	ENST00000375856.3:c.1621G>A	p.Gly541Arg	p.G541R	ENST00000375856	NM_003749.2	541	Ggg/Agg	1/2	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.16	2		945	810	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17125916	17125916	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	53	710	0	ENST00000285071.4:c.678C>A	p.Phe226Leu	p.F226L	ENST00000285071	NM_144997.5	226	ttC/ttA	7/14	1	2	FACETS	0.892	0.759	1	0.892	0.759	1	CLONAL	1	TRUE	1	0.16	2		710	743	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440378	52440390	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TCGTGGTAGGGCT	TCGTGGTAGGGCT	-	novel	NA	P-0057965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	58	649	0	ENST00000460680.1:c.662_674del	p.Glu221AlafsTer6	p.E221Afs*6	ENST00000460680	NM_004656.3	221	gAGCCCTACCACGAc/gc	9/17	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.16	2		649	548	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032171	26032171	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	40	486	0	ENST00000244661.2:c.118C>A	p.His40Asn	p.H40N	ENST00000244661	NM_003537.3	40	Cac/Aac	1/1	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.16	2		486	477	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904895	101904896	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0057965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	33	338	0	ENST00000374994.4:c.884dup	p.Tyr295Ter	p.Y295*	ENST00000374994	NM_004612.2	295	tac/tAac	5/9	0.211374467560124	1	FACETS	0.958	0.781	1	0.958	0.781	1	CLONAL	1	TRUE	0	0.16	1		338	396	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807891	1807894	+	missense_variant	Missense_Mutation	ONP	GACG	GACG	TGAC	novel	NA	P-0057965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	52	1142	0	ENST00000260795.2:c.1950_1953delinsTGAC	p.Lys650_Thr651delinsAsnAsp	p.K650_T651delinsND	ENST00000260795		650	aaGACG/aaTGAC	13/17	1				0.62	0.852				SUBCLONAL	1	TRUE	1	0.16	2		1142	890	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446374	70446381	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGTGGA	GCAGTGGA	-	novel	NA	P-0057966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	85	498	0	ENST00000373644.4:c.5314_5321del	p.Ala1772LysfsTer12	p.A1772Kfs*12	ENST00000373644	NM_030625.2	1772	GCAGTGGAa/a	11/12	1	2	FACETS	0.362	0.32	0.407	0.362	0.32	0.407	SUBCLONAL	1	TRUE	1	0.68	2		498	691	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0057967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	64	313	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.915	0.795	1	0.915	0.795	1	CLONAL	1	TRUE	1	0.307347026588541	2		313	455	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	44	365	0				ENST00000310581	NM_198253.2	-/1132			0.3	2	FACETS	0.848	0.713	0.995			1	CLONAL	2	TRUE	NA	0.15	2		365	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579312	7579312	+	splice_region_variant,synonymous_variant	Splice_Region	SNP	C	C	T	rs55863639	NA	P-0057980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	46	613	1	ENST00000269305.4:c.375G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125	acG/acA	4/11	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.15	2		614	603	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0057980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	31	741	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.682	0.55	0.832	0.682	0.55	0.832	SUBCLONAL	1	TRUE	1	0.15	2		741	606	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0057980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	19	335	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.898	0.682	1	0.898	0.682	1	CLONAL	1	TRUE	1	0.15	2		335	282	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041211	112041211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140762956	NA	P-0057980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	39	486	0	ENST00000368678.4:c.44C>T	p.Thr15Met	p.T15M	ENST00000368678		15	aCg/aTg	3/13	1	2	FACETS	0.976	0.808	1	0.976	0.808	1	CLONAL	1	TRUE	1	0.15	2		486	533	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508438	29508438	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1057518360	NA	P-0057980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	18	228	0	ENST00000356175.3:c.587-2A>G		p.X196_splice	ENST00000356175	NM_000267.3	196			1	2	FACETS	0.83	0.625	1	0.83	0.625	1	CLONAL	1	TRUE	1	0.15	2		228	289	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100439	8100439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	87	1079	0	ENST00000346208.3:c.413C>T	p.Ser138Phe	p.S138F	ENST00000346208		138	tCc/tTc	3/6	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.15	2		1079	930	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0057981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	45	470	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.327413886821919	4	FACETS	1	0.916	1	1	0.916	1	CLONAL	2	TRUE	2	0.409531025260561	4		470	141	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760703	133760703	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1462634813	NA	P-0057981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	24	962	2	ENST00000318560.5:c.3026G>A	p.Arg1009Gln	p.R1009Q	ENST00000318560	NM_005157.4	1009	cGa/cAa	11/11	1	2	FACETS	1	0.805	1	1	0.805	1	CLONAL	1	TRUE	1	0.409531025260561	2		964	116	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937034	36937034	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	38	503	0	ENST00000361632.4:c.1285G>T	p.Gly429Cys	p.G429C	ENST00000361632		429	Ggc/Tgc	9/16	0.327105382948276	4	FACETS	0.881	0.751	1			1	CLONAL	3	TRUE	NA	0.409531025260561	4		503	99	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579854	7579855	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	33	681	0	ENST00000269305.4:c.58dup	p.Ser20PhefsTer9	p.S20Ffs*9	ENST00000269305	NM_001126112.2	20	tca/tTca	2/11	1	2	FACETS	1	0.851	1	1	0.967	1	CLONAL	2	TRUE	1	0.409531025260561	2		681	80	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593476	215593476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867281641	NA	P-0057981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	11	257	0	ENST00000260947.4:c.2258G>A	p.Gly753Asp	p.G753D	ENST00000260947	NM_000465.2	753	gGc/gAc	11/11	0.322364012656149	1	FACETS	0.657	0.463	0.888	0.657	0.463	0.888	SUBCLONAL	1	TRUE	0	0.409531025260561	1		257	65	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944451	40944451	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	26	440	0	ENST00000373198.4:c.2051A>C	p.Asn684Thr	p.N684T	ENST00000373198	NM_133170.3	684	aAt/aCt	12/32	0.34474982680326	3	FACETS	1	0.934	1	0.722	0.583	0.873	CLONAL	1	TRUE	1	0.409531025260561	3		440	106	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277242	41277242	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	14	300	0	ENST00000349496.5:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000349496	NM_001904.3	571	Gaa/Aaa	11/15	0.162203078654909	3	FACETS	0.886	0.649	1	0.443	0.324	0.582	INDETERMINATE	1	TRUE	1	0.409531025260561	3		300	93	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265587	152265587	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	21	447	0	ENST00000206249.3:c.1040C>G	p.Thr347Ser	p.T347S	ENST00000206249	NM_000125.3	347	aCc/aGc	4/8	0.162203078654909	3	FACETS	0.922	0.718	1	0.461	0.359	0.577	INDETERMINATE	1	TRUE	1	0.409531025260561	3		447	134	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255028	16255028	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	37	312	0	ENST00000375759.3:c.2293A>C	p.Ser765Arg	p.S765R	ENST00000375759	NM_015001.2	765	Agc/Cgc	11/15	0.273765345351484	3	FACETS	0.92	0.761	1	0.46	0.38	0.549	CLONAL	1	TRUE	1	0.273765345351484	3		312	334	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052636	42052636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1054243525	NA	P-0057984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	132	381	3	ENST00000219905.7:c.7307G>A	p.Arg2436His	p.R2436H	ENST00000219905	NM_001164273.1	2436	cGt/cAt	20/24	0.273765345351484	3	FACETS	0.977	0.891	1	0.977	0.891	1	CLONAL	2	TRUE	1	0.273765345351484	3		384	561	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476409	88476409	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0057984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	53	491	0	ENST00000360948.2:c.1723A>T	p.Lys575Ter	p.K575*	ENST00000360948	NM_001012338.2	575	Aag/Tag	15/19	0.273765345351484	3	FACETS	0.925	0.79	1	0.462	0.395	0.536	CLONAL	1	TRUE	1	0.273765345351484	3		491	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0057984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	269	680	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.201597963986296	4	FACETS	1	0.985	1	0.845	0.796	0.894	CLONAL	3	TRUE	0	0.273765345351484	4		680	741	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38504571	38504571	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1410890791	NA	P-0057984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	93	615	2	ENST00000254066.5:c.182T>C	p.Ile61Thr	p.I61T	ENST00000254066	NM_000964.3	61	aTt/aCt	3/9	0.273765345351484	3	FACETS	1	0.948	1	0.556	0.495	0.622	CLONAL	1	TRUE	1	0.273765345351484	3		617	694	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902163	50902163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368033860	NA	P-0057984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	74	895	2	ENST00000440232.2:c.55C>T	p.Arg19Cys	p.R19C	ENST00000440232	NM_002691.3	19	Cgt/Tgt	2/27	0.273765345351484	6	FACETS	0.904	0.79	1	0.226	0.197	0.257	CLONAL	1	TRUE	2	0.273765345351484	6		897	925	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288333	21288333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	81	548	0	ENST00000354336.3:c.578G>A	p.Arg193Lys	p.R193K	ENST00000354336	NM_005207.3	193	aGg/aAg	2/3	0.273765345351484	2	FACETS	1	0.932	1	0.541	0.477	0.609	CLONAL	1	TRUE	0	0.273765345351484	2		548	547	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0057984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	105	314	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.273765345351484	5	FACETS	1	0.967	1	0.781	0.703	0.862	CLONAL	2	TRUE	2	0.273765345351484	5		314	462	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955491	90955491	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	62	407	0	ENST00000265433.3:c.2174A>T	p.Gln725Leu	p.Q725L	ENST00000265433	NM_002485.4	725	cAg/cTg	14/16	0.273765345351484	8	FACETS	0.902	0.777	1	0.129	0.111	0.149	CLONAL	1	TRUE	1	0.273765345351484	8		407	915	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933265	39933290	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGACAAGTCTAGTGGCTTATCTGT	GAAGACAAGTCTAGTGGCTTATCTGT	-	novel	NA	P-0057984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	201	414	3	ENST00000378444.4:c.1309_1334del	p.Thr437Ter	p.T437*	ENST00000378444	NM_001123385.1	437	ACAGATAAGCCACTAGACTTGTCTTCt/t	4/15	0.273765345351484	2	FACETS	1	0.968	1			1	CLONAL	3	TRUE	NA	0.273765345351484	2		417	466	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0057985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	199	254	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.991	0.927	1	1	0.995	1	CLONAL	3	TRUE	1	0.275506458267656	2		254	486	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699360	47699360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	450	365	0	ENST00000347630.2:c.148G>A	p.Glu50Lys	p.E50K	ENST00000347630	NM_001007230.1	50	Gaa/Aaa	4/11	0.275506458267656	2	FACETS	0.994	0.969	1	1	0.998	1	CLONAL	6	TRUE	0	0.275506458267656	2		365	548	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106621	27106621	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	779	668	0	ENST00000324856.7:c.6232G>T	p.Glu2078Ter	p.E2078*	ENST00000324856	NM_006015.4	2078	Gag/Tag	20/20	0.275506458267656	2	FACETS	1	0.992	1	1	0.999	1	CLONAL	6	TRUE	0	0.275506458267656	2		668	925	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466019	69466019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	480	1111	0	ENST00000227507.2:c.857C>A	p.Thr286Lys	p.T286K	ENST00000227507	NM_053056.2	286	aCa/aAa	5/5	1	2	FACETS	0.97	0.929	1	1	0.998	1	CLONAL	3	TRUE	1	0.275506458267656	2		1111	1198	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374828	149374828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	540	325	0	ENST00000360632.3:c.266C>T	p.Ser89Leu	p.S89L	ENST00000360632	NM_015472.4	89	tCg/tTg	2/7	1	2	FACETS	0.93	0.901	0.959	1	0.998	1	CLONAL	5	TRUE	1	0.275506458267656	2		325	843	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121796	108121796	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0057985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	183	253	0	ENST00000278616.4:c.1604C>G	p.Ser535Ter	p.S535*	ENST00000278616	NM_000051.3	535	tCa/tGa	10/63	NA	2	FACETS	0.997	0.931	1			1	INDETERMINATE	3	TRUE	NA	0.275506458267656	2		253	444	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937542	32937542	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	302	483	0	ENST00000380152.3:c.8203C>T	p.Pro2735Ser	p.P2735S	ENST00000380152		2735	Ccc/Tcc	18/27	1	2	FACETS	0.962	0.911	1	1	0.996	1	CLONAL	3	TRUE	1	0.275506458267656	2		483	760	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791385	42791385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	188	893	0	ENST00000575354.2:c.445G>A	p.Asp149Asn	p.D149N	ENST00000575354	NM_015125.3	149	Gat/Aat	3/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.275506458267656	2		893	1113	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0057987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	18	216	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	1	2	FACETS	0.435	0.327	0.562	0.435	0.327	0.562	SUBCLONAL	1	TRUE	1	0.290279968661247	2		216	285	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233208	46233208	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	78	256	0	ENST00000334344.6:c.1429del	p.Met477CysfsTer10	p.M477Cfs*10	ENST00000334344	NM_152641.2	476	cAa/ca	11/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.290279968661247	2		256	422	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74858968	74858968	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519973	NA	P-0057987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	53	264	0	ENST00000284811.8:c.236A>C	p.Tyr79Ser	p.Y79S	ENST00000284811		79	tAc/tCc	4/4	0.290279968661247	1	FACETS	0.969	0.831	1	0.969	0.831	1	CLONAL	1	TRUE	0	0.290279968661247	1		264	322	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0057988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	92	554	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.179160486486879	3	FACETS	1	0.978	1	0.73	0.649	0.818	CLONAL	1	TRUE	1	0.179160486486879	3		554	766	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	42	619	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	0.871	0.727	1			1	INDETERMINATE	1	TRUE	NA	0.179160486486879	2		619	538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0057988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	133	179	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.787	0.714	0.864	1	0.987	1	SUBCLONAL	2	TRUE	1	0.179160486486879	2		180	943	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0057988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	42	144	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.843	0.708	0.991	1	0.964	1	CLONAL	2	TRUE	1	0.179160486486879	2		144	278	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244138	153244138	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	90	445	0	ENST00000281708.4:c.2019G>A	p.Trp673Ter	p.W673*	ENST00000281708	NM_033632.3	673	tgG/tgA	12/12	0.179160486486879	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.179160486486879	1		445	644	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212230	5212230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367918810	NA	P-0057988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	78	750	0	ENST00000357368.4:c.4801G>A	p.Val1601Ile	p.V1601I	ENST00000357368	NM_002850.3	1601	Gtc/Atc	32/38	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.179160486486879	2		750	868	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375037	45375037	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0057988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	31	280	0	ENST00000262160.6:c.806C>G	p.Ser269Ter	p.S269*	ENST00000262160	NM_005901.5	269	tCa/tGa	8/11	1	2	FACETS	0.972	0.787	1	0.972	0.787	1	CLONAL	1	TRUE	1	0.179160486486879	2		280	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0057989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	338	698	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.451395773459208	2	FACETS	0.901	0.856	0.945	0.901	0.856	0.945	CLONAL	2	TRUE	0	0.466245301331706	2		699	805	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746132	162746132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1374086542	NA	P-0057989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	166	266	0	ENST00000367921.3:c.2255G>A	p.Arg752His	p.R752H	ENST00000367921	NM_006182.2	752	cGc/cAc	16/18	0.466245301331706	3	FACETS	0.918	0.851	0.988	0.612	0.567	0.659	CLONAL	2	TRUE	0	0.466245301331706	3		266	478	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972969	68972969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751789846	NA	P-0057989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	58	384	0	ENST00000288368.4:c.1294G>A	p.Val432Met	p.V432M	ENST00000288368	NM_024870.2	432	Gtg/Atg	11/40	NA	2	FACETS	0.41	0.352	0.473			1	INDETERMINATE	1	TRUE	NA	0.466245301331706	2		384	607	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250292	110250292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760546357	NA	P-0057989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1351	141	946	0	ENST00000374672.4:c.383C>T	p.Ala128Val	p.A128V	ENST00000374672	NM_004235.4	128	gCg/gTg	3/5	0.466245301331706	3	FACETS	0.5	0.454	0.549	0.25	0.227	0.275	SUBCLONAL	1	TRUE	1	0.466245301331706	3		946	1492	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999749	100999749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759568940	NA	P-0057989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	64	1076	0	ENST00000325455.5:c.53C>T	p.Pro18Leu	p.P18L	ENST00000325455	NM_001202474.3	18	cCg/cTg	1/8	0.3999315242612	3	FACETS	0.325	0.28	0.374	0.108	0.093	0.125	SUBCLONAL	1	TRUE	0	0.466245301331706	3		1076	1042	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63819048	63819048	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0057989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	40	159	0	ENST00000279873.7:c.1095T>G	p.Tyr365Ter	p.Y365*	ENST00000279873	NM_032199.2	365	taT/taG	7/10	0.436810170264427	2	FACETS	0.566	0.472	0.67	0.283	0.236	0.335	SUBCLONAL	1	TRUE	0	0.466245301331706	2		159	303	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432723	49432723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	164	797	0	ENST00000301067.7:c.8416G>A	p.Gly2806Arg	p.G2806R	ENST00000301067	NM_003482.3	2806	Ggg/Agg	34/54	0.3999315242612	3	FACETS	0.72	0.659	0.783	0.24	0.219	0.261	SUBCLONAL	1	TRUE	0	0.466245301331706	3		797	1205	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181890	56181890	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	62	189	0	ENST00000399503.3:c.4114G>C	p.Gly1372Arg	p.G1372R	ENST00000399503	NM_005921.1	1372	Ggt/Cgt	17/20	1	2	FACETS	0.902	0.785	1	0.902	0.785	1	CLONAL	1	TRUE	1	0.466245301331706	2		189	295	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	131	365	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.540339731773297	2		365	325	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573988	7573988	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	527	736	0	ENST00000269305.4:c.1039G>C	p.Ala347Pro	p.A347P	ENST00000269305	NM_001126112.2	347	Gcc/Ccc	10/11	0.540339731773297	3	FACETS	0.907	0.876	0.937	0.907	0.876	0.937	CLONAL	3	TRUE	0	0.540339731773297	3		736	911	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212892	94212892	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs137852760	NA	P-0057990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	137	243	0	ENST00000323929.3:c.350A>G	p.Asn117Ser	p.N117S	ENST00000323929	NM_005591.3	117	aAc/aGc	5/20	0.501650434898566	2	FACETS	0.883	0.819	0.948	0.883	0.819	0.948	CLONAL	2	TRUE	0	0.540339731773297	2		243	287	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108296	8108296	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1438848669	NA	P-0057990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	158	693	0	ENST00000585124.1:c.928C>G	p.His310Asp	p.H310D	ENST00000585124	NM_004217.3	310	Cat/Gat	9/9	0.540339731773297	3	FACETS	0.789	0.722	0.858	0.263	0.24	0.286	SUBCLONAL	1	TRUE	0	0.540339731773297	3		693	942	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888786	76888786	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	104	448	0	ENST00000373344.5:c.5043A>G	p.Ile1681Met	p.I1681M	ENST00000373344	NM_000489.3	1681	atA/atG	19/35	0.510140146590384	2	FACETS	0.854	0.769	0.942	0.427	0.384	0.471	CLONAL	1	TRUE	0	0.540339731773297	2		448	451	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222339	2222339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771191963	NA	P-0057991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	221	899	0	ENST00000326181.6:c.623G>A	p.Arg208Gln	p.R208Q	ENST00000326181	NM_032271.2	208	cGa/cAa	8/21	1	2	FACETS	0.814	0.763	0.865	1	0.993	1	CLONAL	2	TRUE	1	0.474739421755463	2		899	572	SUCCESS
APC	324	MSKCC	GRCh37	5	112174724	112174724	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	46	195	0	ENST00000257430.4:c.3433G>T	p.Glu1145Ter	p.E1145*	ENST00000257430	NM_000038.5	1145	Gaa/Taa	16/16	1	2	FACETS	0.881	0.75	1	0.881	0.75	1	CLONAL	1	TRUE	1	0.474739421755463	2		195	220	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579446	7579447	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	291	814	0	ENST00000269305.4:c.240dup	p.Thr81TyrfsTer68	p.T81Yfs*68	ENST00000269305	NM_001126112.2	80	-/T	4/11	0.474739421755463	2	FACETS	0.936	0.887	0.985	0.936	0.887	0.985	CLONAL	2	TRUE	0	0.474739421755463	2		814	655	SUCCESS
APC	324	MSKCC	GRCh37	5	112177391	112177391	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	65	223	0	ENST00000257430.4:c.6100T>G	p.Ser2034Ala	p.S2034A	ENST00000257430	NM_000038.5	2034	Tct/Gct	16/16	1	2	FACETS	0.968	0.847	1	0.968	0.847	1	CLONAL	1	TRUE	1	0.474739421755463	2		223	283	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	79	619	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	1	0.949	1			1	INDETERMINATE	1	FALSE	NA	0.294934061425933	2		619	470	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0057993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	13	334	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.24225015720438	3	FACETS	0.301	0.214	0.408	0.151	0.107	0.204	SUBCLONAL	1	FALSE	1	0.294934061425933	3		334	336	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0057993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	234	397	7	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.262980203223703	1	FACETS	0.823	0.77	0.878	1	0.993	1	CLONAL	2	FALSE	0	0.294934061425933	1		404	822	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0057993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	144	858	1	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.209798319778167	2	FACETS	1	0.981	1	0.635	0.58	0.693	CLONAL	1	FALSE	0	0.294934061425933	2		859	769	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306677	41306677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs724159835	NA	P-0057993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	90	561	3	ENST00000373198.4:c.982C>T	p.Arg328Cys	p.R328C	ENST00000373198	NM_133170.3	328	Cgc/Tgc	7/32	0.248014061175214	3	FACETS	0.755	0.668	0.847	0.377	0.334	0.424	SUBCLONAL	1	FALSE	1	0.294934061425933	3		564	928	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129169	64129169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746466314	NA	P-0057993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	112	1076	0	ENST00000334205.4:c.707C>T	p.Ser236Leu	p.S236L	ENST00000334205	NM_003942.2	236	tCg/tTg	7/17	0.248014061175214	3	FACETS	0.757	0.679	0.84	0.379	0.339	0.42	SUBCLONAL	1	FALSE	1	0.294934061425933	3		1076	1151	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056591	26056591	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	30	329	0	ENST00000343677.2:c.66G>C	p.Lys22Asn	p.K22N	ENST00000343677	NM_005319.3	22	aaG/aaC	1/1	0.24225015720438	3	FACETS	0.603	0.486	0.736	0.302	0.243	0.368	SUBCLONAL	1	FALSE	1	0.294934061425933	3		329	387	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456321	32456321	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	192	1018	0	ENST00000332351.3:c.571G>T	p.Gly191Cys	p.G191C	ENST00000332351	NM_024426.4	191	Ggc/Tgc	1/10	0.248014061175214	3	FACETS	1	0.989	1	0.698	0.645	0.753	CLONAL	1	FALSE	1	0.294934061425933	3		1018	1070	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115575	108115575	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	32	349	1	ENST00000278616.4:c.723G>T	p.Lys241Asn	p.K241N	ENST00000278616	NM_000051.3	241	aaG/aaT	7/63	0.248014061175214	3	FACETS	0.583	0.473	0.708	0.292	0.236	0.354	SUBCLONAL	1	FALSE	1	0.294934061425933	3		350	427	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248430	59248430	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	76	678	0	ENST00000371222.2:c.313G>A	p.Asp105Asn	p.D105N	ENST00000371222	NM_002228.3	105	Gat/Aat	1/1	0.209798319778167	2	FACETS	0.646	0.566	0.732	0.323	0.283	0.366	SUBCLONAL	1	FALSE	0	0.294934061425933	2		678	798	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120508099	120508099	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	49	305	0	ENST00000256646.2:c.1658G>T	p.Gly553Val	p.G553V	ENST00000256646	NM_024408.3	553	gGc/gTc	10/34	NA	2	FACETS	0.837	0.711	0.975			1	INDETERMINATE	1	FALSE	NA	0.294934061425933	2		305	397	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274656	123274656	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	50	462	0	ENST00000358487.5:c.1262G>T	p.Arg421Leu	p.R421L	ENST00000358487	NM_000141.4	421	cGt/cTt	9/18	1	2	FACETS	0.695	0.59	0.81	0.695	0.59	0.81	SUBCLONAL	1	FALSE	1	0.294934061425933	2		462	488	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137062	64137062	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	204	842	0	ENST00000334205.4:c.1573G>T	p.Gly525Cys	p.G525C	ENST00000334205	NM_003942.2	525	Ggc/Tgc	13/17	0.248014061175214	3	FACETS	0.851	0.789	0.914	0.851	0.789	0.914	CLONAL	2	FALSE	1	0.294934061425933	3		842	933	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94169033	94169033	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	28	282	0	ENST00000323929.3:c.1959A>T	p.Glu653Asp	p.E653D	ENST00000323929	NM_005591.3	653	gaA/gaT	18/20	0.248014061175214	3	FACETS	0.685	0.548	0.841	0.343	0.274	0.421	SUBCLONAL	1	FALSE	1	0.294934061425933	3		282	318	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944741	31944741	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	23	128	0	ENST00000340398.3:c.360G>T	p.Met120Ile	p.M120I	ENST00000340398	NM_001013699.2	120	atG/atT	1/1	1	2	FACETS	0.912	0.717	1	0.912	0.717	1	CLONAL	1	FALSE	1	0.294934061425933	2		128	171	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201317	133201317	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	74	823	0	ENST00000320574.5:c.6827G>A	p.Trp2276Ter	p.W2276*	ENST00000320574	NM_006231.2	2276	tGg/tAg	49/49	0.248014061175214	3	FACETS	0.66	0.577	0.751	0.33	0.288	0.376	SUBCLONAL	1	FALSE	1	0.294934061425933	3		823	872	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274213	10274213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1302734897	NA	P-0057993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	250	500	0	ENST00000330684.3:c.56G>A	p.Arg19His	p.R19H	ENST00000330684	NM_001134407.1	19	cGc/cAc	2/13	0.214661149061757	4	FACETS	0.898	0.847	0.95	0.898	0.847	0.95	CLONAL	4	FALSE	0	0.294934061425933	4		500	611	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349203	11349232	+	inframe_deletion	In_Frame_Del	DEL	CCGCGGGGCACGGCCGCGGGCGCGCGGGGG	CCGCGGGGCACGGCCGCGGGCGCGCGGGGG	-	rs750807426	NA	P-0057993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	83	109	0	ENST00000332029.2:c.104_133del	p.Ala35_Ala44del	p.A35_A44del	ENST00000332029	NM_003745.1	35	gCCCCCGCGCGCCCGCGGCCGTGCCCCGCGGtc/gtc	2/2	0.214661149061757	4	FACETS	1	0.955	1	0.569	0.507	0.635	CLONAL	2	FALSE	0	0.294934061425933	4		109	320	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349277	11349277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	105	401	3	ENST00000332029.2:c.59G>A	p.Arg20Gln	p.R20Q	ENST00000332029	NM_003745.1	20	cGa/cAa	2/2	0.214661149061757	4	FACETS	1	0.957	1	0.283	0.253	0.315	CLONAL	1	FALSE	0	0.294934061425933	4		404	814	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512280	38512281	+	missense_variant	Missense_Mutation	DNP	GC	GC	CG	novel	NA	P-0057993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1247	103	1124	0	ENST00000254066.5:c.1191_1192delinsCG	p.Leu398Val	p.L398V	ENST00000254066	NM_000964.3	397	acGCtg/acCGtg	9/9	0.144593050805512	4	FACETS	0.67	0.597	0.748	0.335	0.298	0.374	INDETERMINATE	1	FALSE	2	0.294934061425933	4		1124	1350	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610126	10610127	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0057993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	179	869	1	ENST00000171111.5:c.583_584delinsTT	p.Gly195Phe	p.G195F	ENST00000171111	NM_203500.1	195	GGc/TTc	2/6	0.211197152159644	2	FACETS	1	0.984	1	0.634	0.584	0.685	CLONAL	1	FALSE	0	0.294934061425933	2		870	958	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909482	50909482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	128	1102	0	ENST00000440232.2:c.1286C>T	p.Ser429Phe	p.S429F	ENST00000440232	NM_002691.3	429	tCc/tTc	11/27	1	2	FACETS	0.76	0.687	0.837	0.76	0.687	0.837	SUBCLONAL	1	FALSE	1	0.294934061425933	2		1102	1142	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085860	16085860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	56	544	0	ENST00000281043.3:c.1036C>T	p.Pro346Ser	p.P346S	ENST00000281043	NM_005378.4	346	Cca/Tca	3/3	0.181497059236639	3	FACETS	0.732	0.627	0.847	0.366	0.313	0.424	SUBCLONAL	1	FALSE	1	0.294934061425933	3		544	595	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265405	152265405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	60	471	0	ENST00000206249.3:c.858G>A	p.Met286Ile	p.M286I	ENST00000206249	NM_000125.3	286	atG/atA	4/8	0.181497059236639	3	FACETS	0.822	0.708	0.946	0.411	0.354	0.473	CLONAL	1	FALSE	1	0.294934061425933	3		471	568	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339484	81339484	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	158	426	0	ENST00000222390.5:c.1520G>T	p.Trp507Leu	p.W507L	ENST00000222390	NM_000601.4	507	tGg/tTg	13/18	0.24225015720438	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	FALSE	1	0.294934061425933	3		426	529	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29195901	29195901	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	96	920	0	ENST00000240100.2:c.697C>A	p.Pro233Thr	p.P233T	ENST00000240100	NM_001394.6	233	Cca/Aca	3/4	1	2	FACETS	0.588	0.522	0.658	0.588	0.522	0.658	SUBCLONAL	1	FALSE	1	0.294934061425933	2		920	1107	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391593	139391593	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	356	1234	2	ENST00000277541.6:c.6598G>T	p.Val2200Leu	p.V2200L	ENST00000277541	NM_017617.3	2200	Gtg/Ttg	34/34	0.294934061425933	2	FACETS	0.93	0.881	0.98	0.93	0.881	0.98	CLONAL	2	FALSE	0	0.294934061425933	2		1236	1298	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814270	76814270	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	21	281	0	ENST00000373344.5:c.6374A>G	p.Asn2125Ser	p.N2125S	ENST00000373344	NM_000489.3	2125	aAt/aGt	29/35	0.169471114097543	3	FACETS	0.442	0.339	0.561	0.221	0.169	0.281	INDETERMINATE	1	FALSE	1	0.294934061425933	3		281	370	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	174	365	0				ENST00000310581	NM_198253.2	-/1132			0.329656052462418	7	FACETS	1	0.969	1	0.858	0.798	0.919	CLONAL	4	TRUE	2	0.329656052462418	7		365	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0057994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	308	675	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.130563956094445	6	FACETS	0.897	0.849	0.946			1	INDETERMINATE	4	TRUE	NA	0.329656052462418	6		675	864	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044466	47044466	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	180	329	0	ENST00000377604.3:c.1963A>G	p.Met655Val	p.M655V	ENST00000377604	NM_001204468.1	655	Atg/Gtg	18/24	0.130563956094445	3	FACETS	0.961	0.903	1			1	INDETERMINATE	4	TRUE	NA	0.329656052462418	3		329	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs17849781	NA	P-0057994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	187	675	0	ENST00000269305.4:c.832C>G	p.Pro278Ala	p.P278A	ENST00000269305	NM_001126112.2	278	Cct/Gct	8/11	0.130563956094445	6	FACETS	1	0.969	1			1	INDETERMINATE	2	TRUE	NA	0.329656052462418	6		675	864	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066599	94066599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	62	425	1	ENST00000369303.4:c.1160G>A	p.Gly387Glu	p.G387E	ENST00000369303	NM_004440.3	387	gGa/gAa	5/17	0.329656052462418	2	FACETS	1	0.911	1	0.531	0.461	0.606	CLONAL	1	TRUE	0	0.329656052462418	2		426	354	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56809902	56809902	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	87	394	0	ENST00000337432.4:c.1023C>G	p.Ile341Met	p.I341M	ENST00000337432	NM_058216.2	341	atC/atG	8/9	0.123816192509522	4	FACETS	1	0.979	1	0.743	0.661	0.831	INDETERMINATE	1	TRUE	2	0.329656052462418	4		394	472	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539122	23539122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	58	463	0	ENST00000380871.4:c.317C>T	p.Ser106Phe	p.S106F	ENST00000380871	NM_006167.3	106	tCt/tTt	2/2	0.329656052462418	2	FACETS	1	0.928	1	0.557	0.481	0.638	CLONAL	1	TRUE	0	0.329656052462418	2		463	316	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746072	162746072	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	30	322	0	ENST00000367921.3:c.2195G>T	p.Ser732Ile	p.S732I	ENST00000367921	NM_006182.2	732	aGc/aTc	16/18	0.329656052462418	3	FACETS	0.667	0.538	0.812	0.333	0.269	0.406	SUBCLONAL	1	TRUE	1	0.329656052462418	3		322	318	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534741	18534741	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	127	403	0	ENST00000266497.5:c.1799A>G	p.Gln600Arg	p.Q600R	ENST00000266497		600	cAg/cGg	12/31	0.237886959329631	4	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	2	0.329656052462418	4		403	486	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955403	48955409	+	frameshift_variant	Frame_Shift_Del	DEL	GATTCTG	GATTCTG	-	novel	NA	P-0057994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	65	195	0	ENST00000267163.4:c.1521_1527del	p.Asp507GlufsTer10	p.D507Efs*10	ENST00000267163	NM_000321.2	507	GATTCTGga/ga	17/27	0.329656052462418	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	2	TRUE	0	0.329656052462418	2		195	189	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459339	99459339	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	51	428	0	ENST00000268035.6:c.1975C>G	p.Arg659Gly	p.R659G	ENST00000268035	NM_000875.3	659	Cgg/Ggg	9/21	0.329656052462418	3	FACETS	0.912	0.778	1	0.456	0.389	0.53	CLONAL	1	TRUE	1	0.329656052462418	3		428	395	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790408	3790408	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	89	438	0	ENST00000262367.5:c.4125G>T	p.Met1375Ile	p.M1375I	ENST00000262367	NM_004380.2	1375	atG/atT	24/31	0.305548514207246	3	FACETS	0.804	0.718	0.895	0.804	0.718	0.895	CLONAL	2	TRUE	1	0.329656052462418	3		438	391	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990341	81990341	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	73	486	0	ENST00000359376.3:c.3612G>C	p.Arg1204Ser	p.R1204S	ENST00000359376	NM_002661.3	1204	agG/agC	32/33	0.329656052462418	2	FACETS	1	0.957	1	0.598	0.526	0.675	CLONAL	1	TRUE	0	0.329656052462418	2		486	370	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873455	45873455	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	219	682	0	ENST00000391945.4:c.41A>G	p.Tyr14Cys	p.Y14C	ENST00000391945	NM_000400.3	14	tAc/tGc	2/23	0.329656052462418	6	FACETS	1	0.977	1	0.821	0.768	0.876	CLONAL	3	TRUE	2	0.329656052462418	6		682	671	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61753571	61753571	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	124	327	0	ENST00000401558.2:c.212A>G	p.Gln71Arg	p.Q71R	ENST00000401558	NM_003400.3	71	cAg/cGg	3/25	0.329656052462418	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.329656052462418	3		327	374	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309169	137309169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1409447634	NA	P-0057994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	73	785	0	ENST00000481739.1:c.776G>A	p.Ser259Asn	p.S259N	ENST00000481739	NM_002957.4	259	aGc/aAc	5/10	0.329656052462418	3	FACETS	0.945	0.828	1	0.472	0.414	0.536	CLONAL	1	TRUE	1	0.329656052462418	3		785	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0057995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	115	500	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.426609953616387	1	FACETS	0.827	0.748	0.909	0.827	0.748	0.909	CLONAL	1	TRUE	0	0.426609953616387	1		500	513	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675691	30675691	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1469117613	NA	P-0057995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	154	660	0	ENST00000376406.3:c.2665A>G	p.Ser889Gly	p.S889G	ENST00000376406	NM_014641.2	889	Agt/Ggt	8/15	0.426609953616387	2	FACETS	0.849	0.778	0.924	0.425	0.389	0.462	CLONAL	1	TRUE	0	0.426609953616387	2		660	850	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41554505	41554505	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0057995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	107	386	1	ENST00000263253.7:c.3590+1G>A		p.X1197_splice	ENST00000263253	NM_001429.3	1197			0.426609953616387	1	FACETS	0.926	0.837	1	0.926	0.837	1	CLONAL	1	TRUE	0	0.426609953616387	1		387	426	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223064	41223064	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	111	547	0	ENST00000357654.3:c.4867G>T	p.Ala1623Ser	p.A1623S	ENST00000357654	NM_007294.3	1623	Gct/Tct	15/23	0.426609953616387	1	FACETS	0.912	0.825	1	0.912	0.825	1	CLONAL	1	TRUE	0	0.426609953616387	1		547	449	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983006	149983006	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	78	363	0	ENST00000253339.5:c.3252del	p.Phe1084LeufsTer44	p.F1084Lfs*44	ENST00000253339		1084	ttT/tt	7/7	0.426609953616387	1	FACETS	0.956	0.848	1	0.956	0.848	1	CLONAL	1	TRUE	0	0.426609953616387	1		363	301	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0057996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	30	314	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.12564394611704	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		314	261	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0057997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	40	931	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	1	2	FACETS	0.804	0.674	0.946	0.804	0.674	0.946	CLONAL	1	TRUE	1	0.454361855650858	2		931	219	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371972	55371972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	12	447	2	ENST00000297316.4:c.662C>T	p.Thr221Met	p.T221M	ENST00000297316	NM_022454.3	221	aCg/aTg	2/2	0.223959639697075	5	FACETS	0.413	0.29	0.564	0.138	0.096	0.188	INDETERMINATE	1	TRUE	2	0.454361855650858	5		449	215	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183794	10183794	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs119103277	NA	P-0057997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	68	788	0	ENST00000256474.2:c.263G>A	p.Trp88Ter	p.W88*	ENST00000256474	NM_000551.3	88	tGg/tAg	1/3	0.21077863400229	3	FACETS	1	0.966	1	0.434	0.381	0.49	INDETERMINATE	1	TRUE	0	0.454361855650858	3		788	282	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098882	178098882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	83	392	0	ENST00000397062.3:c.163G>A	p.Glu55Lys	p.E55K	ENST00000397062	NM_006164.4	55	Gaa/Aaa	2/5	0.223959639697075	5	FACETS	0.842	0.748	0.94	0.561	0.499	0.627	INDETERMINATE	2	TRUE	2	0.454361855650858	5		392	365	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643401	52643402	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	73	366	0	ENST00000394830.3:c.2494_2495insT	p.Asn832IlefsTer7	p.N832Ifs*7	ENST00000394830	NM_018313.4	832	aat/aTat	17/30	0.442804056170478	2	FACETS	0.868	0.776	0.963	0.868	0.776	0.963	CLONAL	2	TRUE	0	0.454361855650858	2		366	185	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183802	10183805	+	missense_variant	Missense_Mutation	ONP	TTCG	TTCG	CTCT	novel	NA	P-0057997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	68	785	0	ENST00000256474.2:c.271_274delinsCTCT	p.Phe91_Asp92delinsLeuTyr	p.F91_D92delinsLY	ENST00000256474	NM_000551.3	91	TTCGac/CTCTac	1/3	0.21077863400229	3	FACETS	1	0.968	1	0.444	0.39	0.501	INDETERMINATE	1	TRUE	0	0.454361855650858	3		785	276	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0057999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	338	621	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.760121015582153	2		622	886	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0057999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	471	464	1	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.760121015582153	1		465	631	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188078	11188078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	271	457	0	ENST00000361445.4:c.6016G>A	p.Val2006Ile	p.V2006I	ENST00000361445	NM_004958.3	2006	Gtc/Atc	43/58	0.760121015582153	1	FACETS	0.921	0.877	0.965	0.921	0.877	0.965	CLONAL	1	TRUE	0	0.760121015582153	1		457	480	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061462	38061462	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	339	544	0	ENST00000250448.2:c.527T>G	p.Ile176Ser	p.I176S	ENST00000250448	NM_004496.3	176	aTc/aGc	2/2	0.671776892760629	3	FACETS	1	0.955	1			1	CLONAL	1	TRUE	NA	0.760121015582153	3		544	1218	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052519	42052519	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0057999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	173	282	0	ENST00000219905.7:c.7192-2A>G		p.X2398_splice	ENST00000219905	NM_001164273.1	2398			1	2	FACETS	0.946	0.879	1	0.946	0.879	1	CLONAL	1	TRUE	1	0.760121015582153	2		282	481	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127648	2127648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45517275	NA	P-0057999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	305	802	0	ENST00000219476.3:c.2887G>A	p.Val963Met	p.V963M	ENST00000219476	NM_000548.3	963	Gtg/Atg	26/42	1	2	FACETS	0.799	0.754	0.845	0.799	0.754	0.845	SUBCLONAL	1	TRUE	1	0.760121015582153	2		802	1004	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504126	123504126	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	190	197	0	ENST00000371139.4:c.302C>A	p.Pro101Gln	p.P101Q	ENST00000371139	NM_001114937.2	101	cCa/cAa	3/4	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.760121015582153	1		197	259	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061221	38061232	+	inframe_deletion	In_Frame_Del	DEL	GTTCTCGAACAT	GTTCTCGAACAT	-	novel	NA	P-0058000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	70	756	0	ENST00000250448.2:c.757_768del	p.Met253_Asn256del	p.M253_N256del	ENST00000250448	NM_004496.3	253	ATGTTCGAGAAC/-	2/2	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.197205601909749	2		756	618	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550796	150550796	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	50	446	0	ENST00000369026.2:c.860T>A	p.Ile287Asn	p.I287N	ENST00000369026	NM_021960.4	287	aTc/aAc	2/3	1	2	FACETS	0.96	0.815	1	0.96	0.815	1	CLONAL	1	TRUE	1	0.197205601909749	2		446	528	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748263	43748263	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	63	724	0	ENST00000382044.4:c.2543C>G	p.Pro848Arg	p.P848R	ENST00000382044	NM_001141980.1	848	cCt/cGt	12/28	1	2	FACETS	0.891	0.77	1	0.891	0.77	1	CLONAL	1	TRUE	1	0.197205601909749	2		724	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0058001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	110	737	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.74	0.664	0.821	0.74	0.664	0.821	SUBCLONAL	1	FALSE	1	0.292288577718769	2		739	1017	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880257	37880257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	57	515	0	ENST00000269571.5:c.2301C>G	p.Ile767Met	p.I767M	ENST00000269571		767	atC/atG	19/27	1	2	FACETS	0.668	0.573	0.772	0.668	0.573	0.772	SUBCLONAL	1	FALSE	1	0.292288577718769	2		515	584	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0058001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	55	295	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.263945258678502	3	FACETS	0.889	0.762	1	0.445	0.381	0.515	CLONAL	1	FALSE	1	0.292288577718769	3		295	485	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285087	15285087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763870059	NA	P-0058001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	54	871	0	ENST00000263388.2:c.4528C>T	p.Arg1510Cys	p.R1510C	ENST00000263388	NM_000435.2	1510	Cgc/Tgc	25/33	1	2	FACETS	0.386	0.328	0.45	0.386	0.328	0.45	SUBCLONAL	1	FALSE	1	0.292288577718769	2		871	957	SUCCESS
APC	324	MSKCC	GRCh37	5	112173778	112173778	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	20	282	0	ENST00000257430.4:c.2487del	p.Val830CysfsTer12	p.V830Cfs*12	ENST00000257430	NM_000038.5	829	acA/ac	16/16	1	2	FACETS	0.482	0.369	0.614	0.482	0.369	0.614	SUBCLONAL	1	FALSE	1	0.292288577718769	2		282	284	SUCCESS
APC	324	MSKCC	GRCh37	5	112178790	112178790	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	33	370	0	ENST00000257430.4:c.7499A>T	p.Gln2500Leu	p.Q2500L	ENST00000257430	NM_000038.5	2500	cAg/cTg	16/16	1	2	FACETS	0.52	0.423	0.629	0.52	0.423	0.629	SUBCLONAL	1	FALSE	1	0.292288577718769	2		370	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579336	7579336	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	178	779	0	ENST00000269305.4:c.351del	p.Thr118GlnfsTer5	p.T118Qfs*5	ENST00000269305	NM_001126112.2	117	ggG/gg	4/11	0.339142205922878	1	FACETS	0.375	0.345	0.405	0.375	0.345	0.405	INDETERMINATE	1	TRUE	0	0.667775978319053	1		779	948	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717615	89717615	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909227	NA	P-0058002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	184	370	1	ENST00000371953.3:c.640C>T	p.Gln214Ter	p.Q214*	ENST00000371953	NM_000314.4	214	Cag/Tag	7/9	0.667775978319053	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.667775978319053	1		371	359	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974775	21974775	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	192	287	0	ENST00000304494.5:c.52del	p.Thr18ArgfsTer8	p.T18Rfs*8	ENST00000304494	NM_000077.4	18	Acg/cg	1/3	0.629832490948103	2	FACETS	0.824	0.776	0.871	0.824	0.776	0.871	CLONAL	2	TRUE	0	0.667775978319053	2		287	349	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61712945	61712945	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1384560348	NA	P-0058002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	381	380	0	ENST00000401558.2:c.2466A>G	p.Ile822Met	p.I822M	ENST00000401558	NM_003400.3	822	atA/atG	20/25	0.334467194932471	3	FACETS	0.834	0.803	0.865	0.834	0.803	0.865	INDETERMINATE	3	TRUE	0	0.667775978319053	3		380	608	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519920	NA	P-0058002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	131	279	0	ENST00000397062.3:c.85G>A	p.Asp29Asn	p.D29N	ENST00000397062	NM_006164.4	29	Gat/Aat	2/5	0.334568085309827	1	FACETS	0.871	0.804	0.939	0.871	0.804	0.939	INDETERMINATE	1	TRUE	0	0.667775978319053	1		279	300	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434050	49434050	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	525	1024	1	ENST00000301067.7:c.7503del	p.Pro2502GlnfsTer41	p.P2502Qfs*41	ENST00000301067	NM_003482.3	2501	ggG/gg	31/54	0.367400591822749	2	FACETS	1	0.997	1	0.727	0.699	0.754	INDETERMINATE	1	TRUE	0	0.667775978319053	2		1025	1082	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748732	43748732	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	145	802	0	ENST00000382044.4:c.2074G>T	p.Val692Phe	p.V692F	ENST00000382044	NM_001141980.1	692	Gtt/Ttt	12/28	0.334568085309827	1	FACETS	0.331	0.302	0.362	0.331	0.302	0.362	INDETERMINATE	1	TRUE	0	0.667775978319053	1		802	874	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164535	47164535	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	125	332	0	ENST00000409792.3:c.1591del	p.Cys531ValfsTer48	p.C531Vfs*48	ENST00000409792	NM_014159.6	531	Tgt/gt	3/21	0.667775978319053	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.667775978319053	1		332	248	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807363	1807363	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs80053154	NA	P-0058002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	309	850	0	ENST00000260795.2:c.1612A>G	p.Ile538Val	p.I538V	ENST00000260795		538	Atc/Gtc	11/17	0.667775978319053	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.667775978319053	1		850	609	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466019	69466019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	337	1111	0	ENST00000227507.2:c.857C>A	p.Thr286Lys	p.T286K	ENST00000227507	NM_053056.2	286	aCa/aAa	5/5	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.811234927379247	2		1111	826	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0058003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	473	621	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.99	1	1	0.998	1	CLONAL	2	TRUE	1	0.811234927379247	2		622	569	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0058003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	156	282	0	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	1	2	FACETS	0.92	0.852	0.99	0.92	0.852	0.99	CLONAL	1	TRUE	1	0.811234927379247	2		282	418	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229049	36229049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	344	931	0	ENST00000222270.7:c.7829G>A	p.Arg2610His	p.R2610H	ENST00000222270	NM_014727.1	2610	cGc/cAc	36/37	1	2	FACETS	0.998	0.949	1	0.998	0.949	1	CLONAL	1	TRUE	1	0.811234927379247	2		931	850	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730851	40730851	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	240	740	0	ENST00000373198.4:c.3684G>A	p.Met1228Ile	p.M1228I	ENST00000373198	NM_133170.3	1228	atG/atA	27/32	NA	2	FACETS	0.913	0.858	0.969			1	INDETERMINATE	1	TRUE	NA	0.811234927379247	2		740	648	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216886	7216886	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0058003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	262	535	0	ENST00000380728.2:c.634+1G>T		p.X212_splice	ENST00000380728		212			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.811234927379247	2		535	636	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528651	8528651	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	182	356	0	ENST00000356435.5:c.481A>G	p.Lys161Glu	p.K161E	ENST00000356435		161	Aaa/Gaa	4/35	1	2	FACETS	0.982	0.915	1	0.982	0.915	1	CLONAL	1	TRUE	1	0.811234927379247	2		356	457	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468382	89468382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs570346631	NA	P-0058004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	49	182	0	ENST00000336596.2:c.1916G>A	p.Arg639His	p.R639H	ENST00000336596	NM_005233.5	639	cGc/cAc	11/17	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.436064746916934	2		182	216	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225060	NA	P-0058004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	174	523	0	ENST00000263967.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000263967	NM_006218.2	104	cCa/cTa	2/21	0.296333107063776	5	FACETS	1	0.931	1	0.672	0.621	0.724	CLONAL	2	TRUE	2	0.436064746916934	5		523	655	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670715	67670715	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	130	765	3	ENST00000264010.4:c.1960C>T	p.Arg654Ter	p.R654*	ENST00000264010	NM_006565.3	654	Cga/Tga	11/12	1	2	FACETS	0.764	0.694	0.839	0.764	0.694	0.839	SUBCLONAL	1	TRUE	1	0.436064746916934	2		768	780	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294447	1294447	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749187042	NA	P-0058004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	175	669	0	ENST00000310581.5:c.554G>A	p.Arg185Gln	p.R185Q	ENST00000310581	NM_198253.2	185	cGg/cAg	2/16	1	2	FACETS	0.802	0.738	0.869	0.802	0.738	0.869	CLONAL	1	TRUE	1	0.436064746916934	2		669	1001	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526468	31526468	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	170	914	1	ENST00000344624.3:c.572C>T	p.Ser191Phe	p.S191F	ENST00000344624		191	tCt/tTt	2/33	1	2	FACETS	0.827	0.76	0.896	0.827	0.76	0.896	CLONAL	1	TRUE	1	0.436064746916934	2		915	943	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569807	67569807	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	59	275	0	ENST00000274335.5:c.468C>G	p.Ser156Arg	p.S156R	ENST00000274335		156	agC/agG	3/15	1	2	FACETS	0.658	0.568	0.756	0.658	0.568	0.756	SUBCLONAL	1	TRUE	1	0.436064746916934	2		275	411	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0058007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	119	619	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.3	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.17	3		619	609	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0058007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	167	1216	1	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	NA	2	FACETS	0.929	0.853	1			1	INDETERMINATE	2	TRUE	NA	0.17	2		1217	1057	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082749	16082749	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	26	132	0	ENST00000281043.3:c.563A>C	p.Asp188Ala	p.D188A	ENST00000281043	NM_005378.4	188	gAt/gCt	2/3	1	2	FACETS	1	0.825	1	1	0.964	1	CLONAL	3	TRUE	1	0.17	2		132	100	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934148	48934155	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCAGGGG	TTCAGGGG	-	novel	NA	P-0058007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	42	260	0	ENST00000267163.4:c.608-5_610del		p.X203_splice	ENST00000267163	NM_000321.2	203		7/27	0.172808172689445	2	FACETS	0.837	0.703	0.985	0.837	0.703	0.985	CLONAL	2	TRUE	0	0.17	2		260	295	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs864622237	NA	P-0058009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	279	598	0	ENST00000269305.4:c.700T>A	p.Tyr234Asn	p.Y234N	ENST00000269305	NM_001126112.2	234	Tac/Aac	7/11	0.896853950399982	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.896853950399982	1		598	331	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039385	49039385	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs794727372	NA	P-0058009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	330	644	0	ENST00000267163.4:c.2370C>A	p.Tyr790Ter	p.Y790*	ENST00000267163	NM_000321.2	790	taC/taA	23/27	0.896853950399982	1	FACETS	0.971	0.941	1	0.971	0.941	1	CLONAL	1	TRUE	0	0.896853950399982	1		644	418	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778368	3778368	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	285	1016	0	ENST00000262367.5:c.6680G>T	p.Gly2227Val	p.G2227V	ENST00000262367	NM_004380.2	2227	gGg/gTg	31/31	0.549769665998544	1	FACETS	0.546	0.517	0.575	0.546	0.517	0.575	SUBCLONAL	1	TRUE	0	0.896853950399982	1		1016	642	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205196	61205196	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1590764803	NA	P-0058009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	311	494	0	ENST00000301761.2:c.136G>A	p.Asp46Asn	p.D46N	ENST00000301761	NM_017841.2	46	Gac/Aac	2/4	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.896853950399982	2		494	676	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4388025	4388025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs975747044	NA	P-0058009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	235	513	0	ENST00000261254.3:c.511C>T	p.Arg171Trp	p.R171W	ENST00000261254	NM_001759.3	171	Cgg/Tgg	3/5	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.896853950399982	2		513	502	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993079	72993079	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	417	800	0	ENST00000268489.5:c.966C>G	p.Ile322Met	p.I322M	ENST00000268489	NM_006885.3	322	atC/atG	2/10	0.896853950399982	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.896853950399982	1		800	504	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657563	37657563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	197	437	0	ENST00000447079.4:c.2480G>A	p.Gly827Asp	p.G827D	ENST00000447079	NM_015083.1	827	gGt/gAt	6/14	1	2	FACETS	0.921	0.862	0.981	0.921	0.862	0.981	CLONAL	1	TRUE	1	0.896853950399982	2		437	477	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416705	29416705	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs55782189	NA	P-0058009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	236	493	1	ENST00000389048.3:c.4248G>C	p.Lys1416Asn	p.K1416N	ENST00000389048	NM_004304.4	1416	aaG/aaC	29/29	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.896853950399982	2		494	506	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660168	227660168	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	374	983	0	ENST00000305123.5:c.3287G>C	p.Arg1096Pro	p.R1096P	ENST00000305123	NM_005544.2	1096	cGg/cCg	1/2	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.896853950399982	2		983	829	SUCCESS
APC	324	MSKCC	GRCh37	5	112175094	112175094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	81	190	0	ENST00000257430.4:c.3803C>T	p.Pro1268Leu	p.P1268L	ENST00000257430	NM_000038.5	1268	cCa/cTa	16/16	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.896853950399982	2		190	177	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459865	149459865	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs752112146	NA	P-0058009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	353	935	0	ENST00000286301.3:c.342G>T	p.Glu114Asp	p.E114D	ENST00000286301	NM_005211.3	114	gaG/gaT	4/22	0.293988753112219	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.896853950399982	0		935	819	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190784	32190784	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	352	948	0	ENST00000375023.3:c.153C>A	p.Cys51Ter	p.C51*	ENST00000375023	NM_004557.3	51	tgC/tgA	2/30	0.864568689168144	3	FACETS	0.982	0.93	1	0.491	0.465	0.517	CLONAL	1	TRUE	1	0.896853950399982	3		948	1158	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708063	117708063	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	197	366	0	ENST00000368508.3:c.2114G>C	p.Gly705Ala	p.G705A	ENST00000368508	NM_002944.2	705	gGa/gCa	14/43	1	2	FACETS	0.985	0.923	1	0.985	0.923	1	CLONAL	1	TRUE	1	0.896853950399982	2		366	446	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331908	81331908	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1390378476	NA	P-0058009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	113	212	0	ENST00000222390.5:c.2176C>A	p.Pro726Thr	p.P726T	ENST00000222390	NM_000601.4	726	Cca/Aca	18/18	1	2	FACETS	0.826	0.754	0.9	0.826	0.754	0.9	CLONAL	1	TRUE	1	0.896853950399982	2		212	305	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521355	8521355	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0058009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	334	472	0	ENST00000356435.5:c.883A>T	p.Arg295Ter	p.R295*	ENST00000356435		295	Aga/Tga	9/35	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.896853950399982	2		472	673	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750277	133750277	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	277	551	0	ENST00000318560.5:c.1108C>G	p.Leu370Val	p.L370V	ENST00000318560	NM_005157.4	370	Ctg/Gtg	7/11	0.528836791240813	1	FACETS	0.676	0.643	0.708	0.676	0.643	0.708	INDETERMINATE	1	TRUE	0	0.896853950399982	1		551	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0058010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	159	641	1	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.33023341428458	1	FACETS	0.94	0.862	1	0.94	0.862	1	CLONAL	1	TRUE	0	0.337605802720787	1		642	833	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099090	27099091	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0058010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	146	488	0	ENST00000324856.7:c.3510_3511del	p.His1170GlnfsTer22	p.H1170Qfs*22	ENST00000324856	NM_006015.4	1169	cCA/c	13/20	1	2	FACETS	0.938	0.856	1	0.938	0.856	1	CLONAL	1	TRUE	1	0.337605802720787	2		488	922	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343634	343634	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	266	994	2	ENST00000262320.3:c.2040del	p.Thr681ProfsTer24	p.T681Pfs*24	ENST00000262320	NM_003502.3	680	cgG/cg	8/11	0.33023341428458	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.337605802720787	1		996	1292	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0058011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	511	750	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.627054033076893	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.643355045451694	1		750	1048	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380282	25380282	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	226	529	0	ENST00000311936.3:c.176C>G	p.Ala59Gly	p.A59G	ENST00000311936	NM_004985.3	59	gCa/gGa	3/5	1	2	FACETS	0.697	0.649	0.746	0.697	0.649	0.746	SUBCLONAL	1	TRUE	1	0.643355045451694	2		529	1008	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945970	17945970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568403015	NA	P-0058011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1676	91	1186	0	ENST00000458235.1:c.1969C>T	p.Arg657Trp	p.R657W	ENST00000458235	NM_000215.3	657	Cgg/Tgg	15/24	0.289766931512553	1	FACETS	0.109	0.096	0.123	0.109	0.096	0.123	INDETERMINATE	1	TRUE	0	0.643355045451694	1		1186	1767	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216761	2216761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756193932	NA	P-0058011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	484	1162	0	ENST00000398665.3:c.2405C>T	p.Ser802Leu	p.S802L	ENST00000398665	NM_032482.2	802	tCg/tTg	20/28	0.289766931512553	1	FACETS	0.628	0.599	0.657	0.628	0.599	0.657	INDETERMINATE	1	TRUE	0	0.643355045451694	1		1162	1626	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476811	140476811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507479	NA	P-0058011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	263	501	0	ENST00000288602.6:c.1595G>A	p.Cys532Tyr	p.C532Y	ENST00000288602	NM_004333.4	532	tGt/tAt	13/18	0.627054033076893	1	FACETS	0.923	0.872	0.974	0.923	0.872	0.974	CLONAL	1	TRUE	0	0.643355045451694	1		501	601	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562934	29562934	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0058011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	99	431	0	ENST00000356175.3:c.3871-2A>C		p.X1291_splice	ENST00000356175	NM_000267.3	1291			0.627054033076893	1	FACETS	0.367	0.328	0.408	0.367	0.328	0.408	SUBCLONAL	1	TRUE	0	0.643355045451694	1		431	569	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55524195	55524195	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	374	719	0	ENST00000288135.5:c.14G>A	p.Arg5His	p.R5H	ENST00000288135	NM_000222.2	5	cGc/cAc	1/21	0.643355045451694	1	FACETS	0.942	0.899	0.986	0.942	0.899	0.986	CLONAL	1	TRUE	0	0.643355045451694	1		719	837	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101909988	101909992	+	frameshift_variant	Frame_Shift_Del	DEL	ATCAG	ATCAG	-	novel	NA	P-0058011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	27	239	0	ENST00000374994.4:c.1308_1312del	p.Ser437Ter	p.S437*	ENST00000374994	NM_004612.2	436	ccATCAGtt/cctt	8/9	0.486388266203888	1	FACETS	0.183	0.146	0.226	0.183	0.146	0.226	SUBCLONAL	1	TRUE	0	0.643355045451694	1		239	311	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	51	365	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.949	0.807	1	0.949	0.807	1	CLONAL	1	TRUE	1	0.235778964647138	2		365	456	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117084	7117084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	37	774	0	ENST00000302850.5:c.4132C>T	p.Arg1378Trp	p.R1378W	ENST00000302850	NM_000208.2	1378	Cgg/Tgg	22/22	1	2	FACETS	0.438	0.36	0.526	0.438	0.36	0.526	SUBCLONAL	1	TRUE	1	0.235778964647138	2		774	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555526101	NA	P-0058014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	128	1114	0	ENST00000269305.4:c.497C>G	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tGa	5/11	0.235778964647138	1	FACETS	0.919	0.832	1	0.919	0.832	1	CLONAL	1	TRUE	0	0.235778964647138	1		1114	1042	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326695	62326695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140411308	NA	P-0058014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1225	67	1173	0	ENST00000360203.5:c.3514G>A	p.Glu1172Lys	p.E1172K	ENST00000360203	NM_001283009.1	1172	Gag/Aag	34/35	1	2	FACETS	0.44	0.38	0.505	0.44	0.38	0.505	SUBCLONAL	1	TRUE	1	0.235778964647138	2		1173	1292	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104759	69104759	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs139672596	NA	P-0058014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	44	506	1	ENST00000288368.4:c.4603C>T	p.Arg1535Trp	p.R1535W	ENST00000288368	NM_024870.2	1535	Cgg/Tgg	37/40	1	2	FACETS	0.624	0.523	0.737	0.624	0.523	0.737	SUBCLONAL	1	TRUE	1	0.235778964647138	2		507	598	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16056710	16056710	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0058014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	16	247	0	ENST00000268712.3:c.733-1G>A		p.X245_splice	ENST00000268712	NM_006311.3	245			0.235778964647138	1	FACETS	0.468	0.346	0.613	0.468	0.346	0.613	SUBCLONAL	1	TRUE	0	0.235778964647138	1		247	256	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929133	44929133	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	31	354	0	ENST00000377967.4:c.2233G>T	p.Glu745Ter	p.E745*	ENST00000377967	NM_021140.2	745	Gag/Tag	17/29	1	1	FACETS	0.805	0.653	0.976	0.805	0.653	0.976	CLONAL	1	TRUE	0	0.235778964647138	1		354	288	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982336	201982336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1464712552	NA	P-0058014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	69	1087	1	ENST00000359651.3:c.715G>A	p.Asp239Asn	p.D239N	ENST00000359651		239	Gat/Aat	6/8	1	2	FACETS	0.496	0.43	0.567	0.496	0.43	0.567	SUBCLONAL	1	TRUE	1	0.235778964647138	2		1088	1181	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404508	70404508	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0058014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	30	396	0	ENST00000373644.4:c.2022C>A	p.Tyr674Ter	p.Y674*	ENST00000373644	NM_030625.2	674	taC/taA	4/12	0.235778964647138	1	FACETS	0.554	0.446	0.677	0.554	0.446	0.677	SUBCLONAL	1	TRUE	0	0.235778964647138	1		396	405	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413607	32413607	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	52	346	0	ENST00000332351.3:c.1343T>A	p.Val448Glu	p.V448E	ENST00000332351	NM_024426.4	448	gTg/gAg	9/10	0.235778964647138	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	0	0.235778964647138	1		346	358	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441791	49441791	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	88	729	0	ENST00000301067.7:c.4193C>A	p.Ser1398Ter	p.S1398*	ENST00000301067	NM_003482.3	1398	tCg/tAg	14/54	1	2	FACETS	0.879	0.778	0.988	0.879	0.778	0.988	CLONAL	1	TRUE	1	0.235778964647138	2		729	849	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673725	37673725	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	39	540	0	ENST00000447079.4:c.2879G>T	p.Trp960Leu	p.W960L	ENST00000447079	NM_015083.1	960	tGg/tTg	10/14	1	2	FACETS	0.526	0.435	0.628	0.526	0.435	0.628	SUBCLONAL	1	TRUE	1	0.235778964647138	2		540	629	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400292	225400292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	20	199	0	ENST00000264414.4:c.331G>A	p.Asp111Asn	p.D111N	ENST00000264414	NM_003590.4	111	Gat/Aat	3/16	1	2	FACETS	0.597	0.457	0.761	0.597	0.457	0.761	SUBCLONAL	1	TRUE	1	0.235778964647138	2		199	284	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749373	41749373	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	49	392	0	ENST00000226382.2:c.422G>C	p.Arg141Pro	p.R141P	ENST00000226382	NM_003924.3	141	cGa/cCa	2/3	1	2	FACETS	0.848	0.719	0.99	0.848	0.719	0.99	CLONAL	1	TRUE	1	0.235778964647138	2		392	490	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39935747	39935747	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	26	266	0	ENST00000378444.4:c.125G>C	p.Arg42Thr	p.R42T	ENST00000378444	NM_001123385.1	42	aGa/aCa	3/15	1	1	FACETS	0.606	0.48	0.75	0.606	0.48	0.75	SUBCLONAL	1	TRUE	0	0.235778964647138	1		266	321	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038486	47038505	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCCTGTGCCTCACAGTGTG	GGCCTGTGCCTCACAGTGTG	-	novel	NA	P-0058014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	52	419	0	ENST00000377604.3:c.664-15_668del		p.X222_splice	ENST00000377604	NM_001204468.1	222		8/24	1	1	FACETS	0.965	0.824	1	0.965	0.824	1	CLONAL	1	TRUE	0	0.235778964647138	1		419	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0058015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	96	750	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.359432807578406	3	FACETS	0.976	0.87	1	0.488	0.435	0.544	CLONAL	1	FALSE	1	0.359431396877367	3		750	646	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257336	16257336	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0058015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	70	523	0	ENST00000375759.3:c.4601C>G	p.Ser1534Ter	p.S1534*	ENST00000375759	NM_015001.2	1534	tCa/tGa	11/15	0.359432807578406	3	FACETS	1	0.926	1	0.542	0.474	0.614	CLONAL	1	FALSE	1	0.359431396877367	3		523	424	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349146	89349146	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0058015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	140	1076	0	ENST00000301030.4:c.3804del	p.Lys1269SerfsTer49	p.K1269Sfs*49	ENST00000301030	NM_001256183.1	1268	agG/ag	9/13	0.359432807578406	3	FACETS	1	0.981	1	0.643	0.586	0.702	CLONAL	1	FALSE	1	0.359431396877367	3		1076	715	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047034	128047034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1249110579	NA	P-0058015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	69	608	0	ENST00000285398.2:c.701G>A	p.Arg234Gln	p.R234Q	ENST00000285398	NM_000122.1	234	cGa/cAa	6/15	0.266006930519509	5	FACETS	1	0.94	1	0.379	0.33	0.431	CLONAL	1	FALSE	2	0.359431396877367	5		608	520	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885517	111885517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	88	982	2	ENST00000341259.2:c.1294C>T	p.Pro432Ser	p.P432S	ENST00000341259	NM_005475.2	432	Ccc/Tcc	7/8	0.359431396877367	5	FACETS	0.89	0.787	1	0.445	0.393	0.5	CLONAL	1	FALSE	3	0.359431396877367	5		984	847	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813690	50813690	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	84	685	0	ENST00000398568.2:c.1244C>G	p.Ser415Cys	p.S415C	ENST00000398568	NM_001042412.1	415	tCt/tGt	8/18	0.359432807578406	3	FACETS	0.898	0.794	1			1	CLONAL	1	FALSE	NA	0.359431396877367	3		685	614	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229580	5229580	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	11	159	0	ENST00000357368.4:c.2271G>T	p.Gln757His	p.Q757H	ENST00000357368	NM_002850.3	757	caG/caT	15/38	0.359432807578406	1	FACETS	0.261	0.18	0.362	0.261	0.18	0.362	SUBCLONAL	1	FALSE	0	0.359431396877367	1		159	192	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799772	72799772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	53	601	1	ENST00000325599.8:c.1397C>T	p.Ser466Phe	p.S466F	ENST00000325599	NM_018130.2	466	tCt/tTt	11/11	0.158205869680848	3	FACETS	0.716	0.611	0.83	0.239	0.203	0.277	INDETERMINATE	1	FALSE	0	0.359431396877367	3		602	486	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554903	187554903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	47	466	0	ENST00000441802.2:c.4258G>A	p.Glu1420Lys	p.E1420K	ENST00000441802	NM_005245.3	1420	Gaa/Aaa	7/27	0.359431396877367	1	FACETS	0.841	0.716	0.977	0.841	0.716	0.977	CLONAL	1	FALSE	0	0.359431396877367	1		466	255	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192519	138192519	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0058015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	69	347	0	ENST00000237289.4:c.155G>C	p.Arg52Thr	p.R52T	ENST00000237289	NM_001270507.1	52	aGa/aCa	2/9	0.359431396877367	7	FACETS	1	0.918	1			1	CLONAL	1	FALSE	NA	0.359431396877367	7		347	679	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482868	140482868	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	39	605	0	ENST00000288602.6:c.1267C>A	p.Gln423Lys	p.Q423K	ENST00000288602	NM_004333.4	423	Cag/Aag	10/18	0.308615552495079	3	FACETS	0.668	0.555	0.795	0.334	0.277	0.398	SUBCLONAL	1	FALSE	1	0.359431396877367	3		605	383	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562764	29562764	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0058016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	249	402	0	ENST00000356175.3:c.3844del	p.Ser1282ValfsTer3	p.S1282Vfs*3	ENST00000356175	NM_000267.3	1282	Agt/gt	28/57	0.434841997400791	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.434841997400791	2		402	530	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682714	86682714	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0058016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	40	175	0	ENST00000274376.6:c.2919A>T	p.Glu973Asp	p.E973D	ENST00000274376	NM_002890.2	973	gaA/gaT	23/25	1	2	FACETS	0.796	0.667	0.938	0.796	0.667	0.938	CLONAL	1	TRUE	1	0.434841997400791	2		175	231	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917586	94917586	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	61	329	0	ENST00000536441.1:c.935C>T	p.Ser312Leu	p.S312L	ENST00000536441	NM_144665.3	312	tCa/tTa	6/10	1	2	FACETS	0.917	0.794	1	0.917	0.794	1	CLONAL	1	TRUE	1	0.309989020545979	2		329	429	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374129	118374147	+	frameshift_variant	Frame_Shift_Del	DEL	GTAGAAGGATCTGCCAAGG	GTAGAAGGATCTGCCAAGG	-	novel	NA	P-0058017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	71	372	0	ENST00000534358.1:c.7522_7540del	p.Val2508AsnfsTer12	p.V2508Nfs*12	ENST00000534358	NM_005933.3	2508	GTAGAAGGATCTGCCAAGGaa/aa	27/36	1	2	FACETS	0.898	0.786	1	0.898	0.786	1	CLONAL	1	TRUE	1	0.309989020545979	2		372	510	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	103	365	0				ENST00000310581	NM_198253.2	-/1132			0.199956469153248	1	FACETS	0.784	0.703	0.869	0.784	0.703	0.869	INDETERMINATE	1	TRUE	0	0.370962910161119	1		365	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	299	748	1	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.262710005503061	2	FACETS	0.937	0.886	0.99	0.937	0.886	0.99	CLONAL	2	TRUE	0	0.370962910161119	2		749	860	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178253	56178253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	67	292	0	ENST00000399503.3:c.3226C>T	p.Pro1076Ser	p.P1076S	ENST00000399503	NM_005921.1	1076	Ccc/Tcc	14/20	0.212066224241354	2	FACETS	1	0.921	1	0.536	0.469	0.608	INDETERMINATE	1	TRUE	0	0.370962910161119	2		292	337	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246137	46246137	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	125	397	0	ENST00000334344.6:c.4231C>T	p.Gln1411Ter	p.Q1411*	ENST00000334344	NM_152641.2	1411	Caa/Taa	15/21	0.370962910161119	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.370962910161119	1		397	378	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803818	43803818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147938568	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	89	838	0	ENST00000372470.3:c.128G>A	p.Arg43Gln	p.R43Q	ENST00000372470	NM_005373.2	43	cGa/cAa	2/12	0.212066224241354	2	FACETS	0.413	0.365	0.465	0.207	0.182	0.233	INDETERMINATE	1	TRUE	0	0.370962910161119	2		838	1161	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106543577	106543577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	22	219	1	ENST00000369096.4:c.379C>T	p.Pro127Ser	p.P127S	ENST00000369096	NM_001198.3	127	Cct/Tct	3/7	0.160048178416472	2	FACETS	0.448	0.347	0.564	0.224	0.173	0.282	INDETERMINATE	1	TRUE	0	0.370962910161119	2		220	265	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367257	50367257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1245618829	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	99	407	2	ENST00000331340.3:c.64G>A	p.Asp22Asn	p.D22N	ENST00000331340	NM_006060.4	22	Gat/Aat	3/8	1	2	FACETS	0.841	0.751	0.935	0.841	0.751	0.935	CLONAL	1	TRUE	1	0.370962910161119	2		409	635	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622162	1622162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	299	1164	0	ENST00000344749.5:c.713C>T	p.Pro238Leu	p.P238L	ENST00000344749	NM_001136139.2	238	cCc/cTc	10/19	0.319692659219181	1	FACETS	0.986	0.927	1	0.986	0.927	1	CLONAL	1	TRUE	0	0.370962910161119	1		1164	1332	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622539	28622539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	28	328	0	ENST00000241453.7:c.1078G>A	p.Glu360Lys	p.E360K	ENST00000241453	NM_004119.2	360	Gaa/Aaa	9/24	0.319692659219181	1	FACETS	0.425	0.341	0.522	0.425	0.341	0.522	SUBCLONAL	1	TRUE	0	0.370962910161119	1		328	289	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561309	9561309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760330867	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	61	498	0	ENST00000353224.5:c.473C>T	p.Pro158Leu	p.P158L	ENST00000353224	NM_177990.2	158	cCg/cTg	4/10	0.160048178416472	2	FACETS	0.525	0.453	0.604	0.263	0.226	0.302	INDETERMINATE	1	TRUE	0	0.370962910161119	2		498	626	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576027	29576027	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs878853892	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	183	377	0	ENST00000356175.3:c.4000G>T	p.Glu1334Ter	p.E1334*	ENST00000356175	NM_000267.3	1334	Gaa/Taa	30/57	0.262710005503061	2	FACETS	0.975	0.907	1	0.975	0.907	1	CLONAL	2	TRUE	0	0.370962910161119	2		377	506	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622495	158622495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316254232	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	104	490	0	ENST00000263640.3:c.1004G>A	p.Arg335Gln	p.R335Q	ENST00000263640	NM_001105.4	335	cGa/cAa	8/11	1	2	FACETS	0.935	0.839	1	0.935	0.839	1	CLONAL	1	TRUE	1	0.370962910161119	2		490	600	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339799	116339799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	114	439	0	ENST00000397752.3:c.661G>A	p.Glu221Lys	p.E221K	ENST00000397752	NM_000245.2	221	Gaa/Aaa	2/21	0.333024685190713	3	FACETS	1	0.968	1	0.587	0.529	0.647	CLONAL	1	TRUE	1	0.370962910161119	3		439	621	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28963969	28963969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770598745	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	26	374	0	ENST00000282397.4:c.1933G>A	p.Glu645Lys	p.E645K	ENST00000282397	NM_002019.4	645	Gaa/Aaa	13/30	0.319692659219181	1	FACETS	0.272	0.215	0.338	0.272	0.215	0.338	SUBCLONAL	1	TRUE	0	0.370962910161119	1		374	419	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	139	1019	1	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	0.363948997072198	1	FACETS	0.52	0.472	0.571	0.52	0.472	0.571	SUBCLONAL	1	TRUE	0	0.370962910161119	1		1020	1173	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588868	69588868	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	220	1000	0	ENST00000168712.1:c.368G>A	p.Arg123Gln	p.R123Q	ENST00000168712	NM_002007.2	123	cGg/cAg	2/3	1	2	FACETS	0.859	0.797	0.923	0.859	0.797	0.923	CLONAL	1	TRUE	1	0.370962910161119	2		1000	1381	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317623	163317623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747173543	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	25	297	0	ENST00000271452.3:c.1019C>T	p.Ser340Leu	p.S340L	ENST00000271452	NM_145697.2	340	tCg/tTg	12/14	0.199956469153248	1	FACETS	0.495	0.391	0.612	0.495	0.391	0.612	INDETERMINATE	1	TRUE	0	0.370962910161119	1		297	222	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813325	102813325	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1214292132	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	289	645	0	ENST00000307046.8:c.364C>T	p.Arg122Cys	p.R122C	ENST00000307046	NM_001111285.1	122	Cgt/Tgt	3/4	0.370962910161119	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.370962910161119	1		645	894	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339776	116339776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367722737	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	91	405	0	ENST00000397752.3:c.638C>T	p.Ser213Leu	p.S213L	ENST00000397752	NM_000245.2	213	tCg/tTg	2/21	0.333024685190713	3	FACETS	1	0.914	1	0.516	0.459	0.576	CLONAL	1	TRUE	1	0.370962910161119	3		405	564	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675068	40675068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	127	864	0	ENST00000249776.8:c.32G>A	p.Arg11Lys	p.R11K	ENST00000249776	NM_033286.3	11	aGa/aAa	1/9	0.363948997072198	1	FACETS	0.521	0.471	0.574	0.521	0.471	0.574	SUBCLONAL	1	TRUE	0	0.370962910161119	1		864	1070	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228066	53228066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	273	458	1	ENST00000375401.3:c.2248C>T	p.Arg750Trp	p.R750W	ENST00000375401	NM_004187.3	750	Cgg/Tgg	16/26	0.366338641520141	2	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.370962910161119	2		459	625	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858313	9858313	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	124	481	0	ENST00000330684.3:c.3088C>T	p.Pro1030Ser	p.P1030S	ENST00000330684	NM_001134407.1	1030	Cca/Tca	13/13	0.319692659219181	1	FACETS	0.912	0.828	1	0.912	0.828	1	CLONAL	1	TRUE	0	0.370962910161119	1		481	597	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523271	9523271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775109543	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	72	655	1	ENST00000353224.5:c.1966C>T	p.Arg656Trp	p.R656W	ENST00000353224	NM_177990.2	656	Cgg/Tgg	9/10	0.160048178416472	2	FACETS	0.477	0.416	0.543	0.238	0.208	0.272	INDETERMINATE	1	TRUE	0	0.370962910161119	2		656	814	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831834	72831834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139530177	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	237	832	1	ENST00000268489.5:c.4747G>A	p.Gly1583Ser	p.G1583S	ENST00000268489	NM_006885.3	1583	Ggt/Agt	9/10	0.319692659219181	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.370962910161119	1		833	1018	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852503	42852503	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	110	714	0	ENST00000398585.3:c.583C>T	p.Leu195Phe	p.L195F	ENST00000398585	NM_001135099.1	195	Ctt/Ttt	6/14	0.184687797363672	0	FACETS	0.488	0.439	0.541			1	INDETERMINATE	1	TRUE	0	0.370962910161119	0		714	764	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815728	32815728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	326	1000	1	ENST00000354258.4:c.1888C>T	p.Pro630Ser	p.P630S	ENST00000354258	NM_000593.5	630	Ccc/Tcc	8/11	0.160048178416472	2	FACETS	1	0.993	1	0.694	0.655	0.734	INDETERMINATE	1	TRUE	0	0.370962910161119	2		1001	1267	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031679	69031679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1294114324	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	70	379	0	ENST00000288368.4:c.3434C>T	p.Pro1145Leu	p.P1145L	ENST00000288368	NM_024870.2	1145	cCc/cTc	28/40	0.199956469153248	1	FACETS	0.856	0.751	0.968	0.856	0.751	0.968	INDETERMINATE	1	TRUE	0	0.370962910161119	1		379	359	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118806	115118806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754023417	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	203	557	0	ENST00000257566.3:c.535G>A	p.Glu179Lys	p.E179K	ENST00000257566	NM_016569.3	179	Gaa/Aaa	2/8	0.370962910161119	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.370962910161119	1		557	639	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445514	49445514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356632640	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	274	841	0	ENST00000301067.7:c.1952C>T	p.Ser651Leu	p.S651L	ENST00000301067	NM_003482.3	651	tCg/tTg	10/54	0.370962910161119	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.370962910161119	1		841	833	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88671957	88671957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs574695821	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	31	192	0	ENST00000360948.2:c.1213G>A	p.Asp405Asn	p.D405N	ENST00000360948	NM_001012338.2	405	Gat/Aat	10/19	1	2	FACETS	0.682	0.555	0.825	0.682	0.555	0.825	SUBCLONAL	1	TRUE	1	0.370962910161119	2		192	245	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166043	118166043	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	182	476	0	ENST00000369448.3:c.553C>T	p.Gln185Ter	p.Q185*	ENST00000369448	NM_017709.3	185	Caa/Taa	2/2	0.212066224241354	2	FACETS	0.754	0.698	0.811	0.754	0.698	0.811	INDETERMINATE	2	TRUE	0	0.370962910161119	2		476	651	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845935	156845935	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	187	1135	0	ENST00000524377.1:c.1565G>A	p.Gly522Glu	p.G522E	ENST00000524377	NM_002529.3	522	gGg/gAg	13/17	0.199956469153248	1	FACETS	0.71	0.654	0.767	0.71	0.654	0.767	INDETERMINATE	1	TRUE	0	0.370962910161119	1		1135	1157	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906378	50906378	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1235062032	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	282	1255	1	ENST00000440232.2:c.1039C>T	p.Pro347Ser	p.P347S	ENST00000440232	NM_002691.3	347	Ccg/Tcg	9/27	0.319692659219181	1	FACETS	0.878	0.824	0.935	0.878	0.824	0.935	CLONAL	1	TRUE	0	0.370962910161119	1		1256	1410	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486148	8486148	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	229	486	0	ENST00000356435.5:c.2669C>T	p.Ser890Leu	p.S890L	ENST00000356435		890	tCa/tTa	17/35	0.359746835567464	2	FACETS	0.865	0.809	0.921	0.865	0.809	0.921	CLONAL	2	TRUE	0	0.370962910161119	2		486	714	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47643499	47643499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	96	558	0	ENST00000233146.2:c.1007C>T	p.Pro336Leu	p.P336L	ENST00000233146	NM_000251.2	336	cCt/cTt	6/16	1	2	FACETS	0.846	0.755	0.942	0.846	0.755	0.942	CLONAL	1	TRUE	1	0.370962910161119	2		558	612	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166616	118166616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	50	268	0	ENST00000369448.3:c.1126C>T	p.Pro376Ser	p.P376S	ENST00000369448	NM_017709.3	376	Cct/Tct	2/2	0.212066224241354	2	FACETS	0.532	0.451	0.62	0.266	0.225	0.31	INDETERMINATE	1	TRUE	0	0.370962910161119	2		268	507	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834539	156834539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	118	1004	0	ENST00000524377.1:c.307C>T	p.Leu103Phe	p.L103F	ENST00000524377	NM_002529.3	103	Ctc/Ttc	3/17	0.199956469153248	1	FACETS	0.454	0.408	0.503	0.454	0.408	0.503	INDETERMINATE	1	TRUE	0	0.370962910161119	1		1004	1141	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720824	89720825	+	missense_variant	Missense_Mutation	DNP	TG	TG	CT	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	80	378	1	ENST00000371953.3:c.975_976delinsCT	p.Asp326Tyr	p.D326Y	ENST00000371953	NM_000314.4	325	ctTGac/ctCTac	8/9	0.281297399941536	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.370962910161119	1		379	276	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944778	71944780	+	frameshift_variant	Frame_Shift_Del	DEL	CTC	CTC	TT	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	94	857	0	ENST00000298229.2:c.2202_2204delinsTT	p.Lys736ArgfsTer22	p.K736Rfs*22	ENST00000298229	NM_001567.3	734	atCTCc/atTTc	19/28	1	2	FACETS	0.543	0.482	0.608	0.543	0.482	0.608	SUBCLONAL	1	TRUE	1	0.370962910161119	2		857	934	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946378	71946378	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	112	1010	0	ENST00000298229.2:c.2542A>G	p.Thr848Ala	p.T848A	ENST00000298229	NM_001567.3	848	Acg/Gcg	23/28	1	2	FACETS	0.523	0.469	0.581	0.523	0.469	0.581	SUBCLONAL	1	TRUE	1	0.370962910161119	2		1010	1154	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658382	18658382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	91	327	1	ENST00000266497.5:c.3187G>A	p.Gly1063Arg	p.G1063R	ENST00000266497		1063	Gga/Aga	22/31	0.370962910161119	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.370962910161119	1		328	305	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106649	2106649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	193	873	0	ENST00000219476.3:c.653C>T	p.Ser218Phe	p.S218F	ENST00000219476	NM_000548.3	218	tCc/tTc	8/42	0.319692659219181	1	FACETS	0.899	0.832	0.968	0.899	0.832	0.968	CLONAL	1	TRUE	0	0.370962910161119	1		873	943	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639047	3639047	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1352	99	945	0	ENST00000294008.3:c.4592C>T	p.Pro1531Leu	p.P1531L	ENST00000294008	NM_032444.2	1531	cCa/cTa	12/15	0.319692659219181	1	FACETS	0.3	0.266	0.336	0.3	0.266	0.336	SUBCLONAL	1	TRUE	0	0.370962910161119	1		945	1451	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214382	5214382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs977538185	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	129	544	0	ENST00000357368.4:c.4604C>T	p.Ser1535Phe	p.S1535F	ENST00000357368	NM_002850.3	1535	tCt/tTt	30/38	1	2	FACETS	0.91	0.826	0.999	0.91	0.826	0.999	CLONAL	1	TRUE	1	0.370962910161119	2		544	764	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298090	15298090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1269	310	1158	0	ENST00000263388.2:c.1666C>T	p.His556Tyr	p.H556Y	ENST00000263388	NM_000435.2	556	Cat/Tat	11/33	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.370962910161119	2		1158	1579	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256729	19256730	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	252	1011	0	ENST00000162023.5:c.983_984delinsAA	p.Gly328Glu	p.G328E	ENST00000162023		328	gGG/gAA	13/13	1	2	FACETS	0.949	0.886	1	0.949	0.886	1	CLONAL	1	TRUE	1	0.370962910161119	2		1011	1432	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212597	36212597	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	253	1225	2	ENST00000222270.7:c.2348T>A	p.Leu783Ter	p.L783*	ENST00000222270	NM_014727.1	783	tTg/tAg	3/37	0.319692659219181	1	FACETS	0.829	0.774	0.886	0.829	0.774	0.886	CLONAL	1	TRUE	0	0.370962910161119	1		1227	1340	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966507	25966507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	202	658	1	ENST00000435504.4:c.2699C>T	p.Pro900Leu	p.P900L	ENST00000435504		900	cCt/cTt	13/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.370962910161119	2		659	983	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917740	29917740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	187	863	0	ENST00000389048.3:c.928G>A	p.Glu310Lys	p.E310K	ENST00000389048	NM_004304.4	310	Gag/Aag	3/29	1	2	FACETS	0.925	0.853	0.999	0.925	0.853	0.999	CLONAL	1	TRUE	1	0.370962910161119	2		863	1090	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47643501	47643501	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750778	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	103	559	0	ENST00000233146.2:c.1009C>T	p.Gln337Ter	p.Q337*	ENST00000233146	NM_000251.2	337	Caa/Taa	6/16	1	2	FACETS	0.899	0.806	0.997	0.899	0.806	0.997	CLONAL	1	TRUE	1	0.370962910161119	2		559	618	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827951	40827951	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	82	640	0	ENST00000373198.4:c.2477C>T	p.Pro826Leu	p.P826L	ENST00000373198	NM_133170.3	826	cCc/cTc	17/32	0.160048178416472	2	FACETS	0.405	0.356	0.458	0.203	0.178	0.229	INDETERMINATE	1	TRUE	0	0.370962910161119	2		640	1091	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265034	46265034	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	174	454	0	ENST00000371998.3:c.1904C>A	p.Ser635Tyr	p.S635Y	ENST00000371998		635	tCc/tAc	12/23	0.160048178416472	2	FACETS	0.787	0.728	0.847	0.787	0.728	0.847	INDETERMINATE	2	TRUE	0	0.370962910161119	2		454	596	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691853	30691853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1347722182	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	202	360	0	ENST00000295754.5:c.355C>T	p.Pro119Ser	p.P119S	ENST00000295754	NM_003242.5	119	Cca/Tca	3/7	0.359746835567464	2	FACETS	0.967	0.903	1	0.967	0.903	1	CLONAL	2	TRUE	0	0.370962910161119	2		360	563	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1255437	1255437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	100	707	0	ENST00000310581.5:c.3122C>T	p.Ser1041Phe	p.S1041F	ENST00000310581	NM_198253.2	1041	tCc/tTc	14/16	0.199956469153248	1	FACETS	0.47	0.419	0.524	0.47	0.419	0.524	INDETERMINATE	1	TRUE	0	0.370962910161119	1		707	935	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940500	131940500	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	14	264	0	ENST00000265335.6:c.2527T>A	p.Ser843Thr	p.S843T	ENST00000265335		843	Tct/Act	16/25	0.199956469153248	1	FACETS	0.279	0.202	0.373	0.279	0.202	0.373	INDETERMINATE	1	TRUE	0	0.370962910161119	1		264	220	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502629	149502629	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	130	688	0	ENST00000261799.4:c.2159T>G	p.Leu720Arg	p.L720R	ENST00000261799	NM_002609.3	720	cTg/cGg	15/23	0.199956469153248	1	FACETS	0.775	0.703	0.849	0.775	0.703	0.849	INDETERMINATE	1	TRUE	0	0.370962910161119	1		688	737	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673466	30673466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	282	699	1	ENST00000376406.3:c.3494C>T	p.Ala1165Val	p.A1165V	ENST00000376406	NM_014641.2	1165	gCc/gTc	10/15	0.160048178416472	2	FACETS	1	0.992	1	0.669	0.628	0.71	INDETERMINATE	1	TRUE	0	0.370962910161119	2		700	1137	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188307	32188307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1486167088	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1233	129	1091	0	ENST00000375023.3:c.1034G>A	p.Ser345Asn	p.S345N	ENST00000375023	NM_004557.3	345	aGt/aAt	6/30	0.160048178416472	2	FACETS	0.511	0.461	0.563	0.255	0.23	0.282	INDETERMINATE	1	TRUE	0	0.370962910161119	2		1091	1362	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190546	32190546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751511627	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	128	940	1	ENST00000375023.3:c.193C>T	p.Pro65Ser	p.P65S	ENST00000375023	NM_004557.3	65	Cct/Tct	3/30	0.160048178416472	2	FACETS	0.586	0.529	0.646	0.293	0.264	0.323	INDETERMINATE	1	TRUE	0	0.370962910161119	2		941	1178	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956594	93956595	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	41	353	0	ENST00000369303.4:c.2641_2642delinsTT	p.Pro881Leu	p.P881L	ENST00000369303	NM_004440.3	881	CCa/TTa	15/17	0.160048178416472	2	FACETS	0.447	0.372	0.53	0.223	0.186	0.265	INDETERMINATE	1	TRUE	0	0.370962910161119	2		353	495	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271205	38271205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238519686	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	94	729	0	ENST00000425967.3:c.2503G>A	p.Glu835Lys	p.E835K	ENST00000425967	NM_001174067.1	835	Gag/Aag	19/19	0.199956469153248	1	FACETS	0.498	0.442	0.557	0.498	0.442	0.557	INDETERMINATE	1	TRUE	0	0.370962910161119	1		729	829	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978652	70978652	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	71	690	0	ENST00000276594.2:c.1001C>T	p.Pro334Leu	p.P334L	ENST00000276594	NM_024504.3	334	cCc/cTc	5/8	0.199956469153248	1	FACETS	0.392	0.341	0.447	0.392	0.341	0.447	INDETERMINATE	1	TRUE	0	0.370962910161119	1		690	796	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097742	27097742	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	69	396	0	ENST00000324856.7:c.3331G>T	p.Glu1111Ter	p.E1111*	ENST00000324856	NM_006015.4	1111	Gaa/Taa	12/20	1	2	FACETS	0.852	0.742	0.971	0.852	0.742	0.971	CLONAL	1	TRUE	1	0.25	2		396	648	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0058027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	83	719	1	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.896	0.79	1	0.896	0.79	1	CLONAL	1	TRUE	1	0.25	2		720	741	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913250	NA	P-0058027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	71	287	0	ENST00000369535.4:c.34G>T	p.Gly12Cys	p.G12C	ENST00000369535	NM_002524.4	12	Ggt/Tgt	2/7	1	2	FACETS	0.956	0.835	1	0.956	0.835	1	CLONAL	1	TRUE	1	0.25	2		287	594	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699369	117699369	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374822982	NA	P-0058027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	93	408	0	ENST00000369458.3:c.272C>T	p.Ser91Leu	p.S91L	ENST00000369458	NM_024626.3	91	tCg/tTg	3/6	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.25	2		408	681	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748442	162748442	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	63	333	0	ENST00000367921.3:c.2356G>T	p.Glu786Ter	p.E786*	ENST00000367921	NM_006182.2	786	Gaa/Taa	17/18	1	2	FACETS	0.92	0.796	1	0.92	0.796	1	CLONAL	1	TRUE	1	0.25	2		333	548	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0058027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	42	339	1	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.911	0.762	1	0.911	0.762	1	CLONAL	1	TRUE	1	0.25	2		340	369	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692977	89692977	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0058027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	45	352	0	ENST00000371953.3:c.461T>G	p.Phe154Cys	p.F154C	ENST00000371953	NM_000314.4	154	tTc/tGc	5/9	1	2	FACETS	0.9	0.758	1	0.9	0.758	1	CLONAL	1	TRUE	1	0.25	2		352	400	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720870	89720870	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1554825652	NA	P-0058027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	63	282	0	ENST00000371953.3:c.1021T>G	p.Phe341Val	p.F341V	ENST00000371953	NM_000314.4	341	Ttt/Gtt	8/9	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.25	2		282	479	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939260	71939260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	126	690	3	ENST00000298229.2:c.209G>A	p.Arg70His	p.R70H	ENST00000298229	NM_001567.3	70	cGc/cAc	2/28	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.25	2		693	1001	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201966	102201966	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0058027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	31	133	0	ENST00000263464.3:c.1318G>T	p.Glu440Ter	p.E440*	ENST00000263464	NM_001165.4	440	Gaa/Taa	6/9	1	2	FACETS	0.785	0.643	0.941	1	0.949	1	CLONAL	2	TRUE	1	0.25	2		133	158	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115600	108115600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772821016	NA	P-0058027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	41	270	0	ENST00000278616.4:c.748C>T	p.Arg250Ter	p.R250*	ENST00000278616	NM_000051.3	250	Cga/Tga	7/63	1	2	FACETS	0.937	0.783	1	0.937	0.783	1	CLONAL	1	TRUE	1	0.25	2		270	350	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115681	108115681	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs876660933	NA	P-0058027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	14	196	0	ENST00000278616.4:c.829G>T	p.Glu277Ter	p.E277*	ENST00000278616	NM_000051.3	277	Gaa/Taa	7/63	1	2	FACETS	0.455	0.329	0.608	0.455	0.329	0.608	SUBCLONAL	1	TRUE	1	0.25	2		196	246	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864547	57864547	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	131	783	0	ENST00000228682.2:c.2024A>G	p.Asn675Ser	p.N675S	ENST00000228682	NM_005269.2	675	aAc/aGc	12/12	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.25	2		783	1017	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253151	133253151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	60	318	0	ENST00000320574.5:c.890C>T	p.Ser297Phe	p.S297F	ENST00000320574	NM_006231.2	297	tCc/tTc	9/49	1	2	FACETS	0.916	0.79	1	0.916	0.79	1	CLONAL	1	TRUE	1	0.25	2		318	524	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355126	73355126	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	32	259	0	ENST00000377767.4:c.244G>A	p.Asp82Asn	p.D82N	ENST00000377767	NM_014953.3	82	Gac/Aac	2/21	1	2	FACETS	0.773	0.629	0.936	0.773	0.629	0.936	CLONAL	1	TRUE	1	0.25	2		259	331	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125535	7125535	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	74	422	1	ENST00000302850.5:c.3017T>G	p.Phe1006Cys	p.F1006C	ENST00000302850	NM_000208.2	1006	tTt/tGt	17/22	1	2	FACETS	0.975	0.854	1	0.975	0.854	1	CLONAL	1	TRUE	1	0.25	2		423	607	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221667	36221667	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779863547	NA	P-0058027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	123	795	0	ENST00000222270.7:c.5336G>A	p.Arg1779Gln	p.R1779Q	ENST00000222270	NM_014727.1	1779	cGa/cAa	26/37	1	2	FACETS	0.785	0.708	0.867	0.785	0.708	0.867	SUBCLONAL	1	TRUE	1	0.25	2		795	1253	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	48	392	0	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	0.78	0.66	0.913	0.78	0.66	0.913	CLONAL	1	TRUE	1	0.25	2		392	492	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0058027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	25	310	0	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	0.554	0.436	0.689	0.554	0.436	0.689	SUBCLONAL	1	TRUE	1	0.25	2		310	361	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209101857	209101857	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	39	264	0	ENST00000345146.2:c.1191C>A	p.Phe397Leu	p.F397L	ENST00000345146	NM_005896.2	397	ttC/ttA	10/10	1	2	FACETS	0.738	0.612	0.878	0.738	0.612	0.878	SUBCLONAL	1	TRUE	1	0.25	2		264	423	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916921	178916921	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	50	324	0	ENST00000263967.3:c.308A>G	p.Glu103Gly	p.E103G	ENST00000263967	NM_006218.2	103	gAa/gGa	2/21	1	2	FACETS	0.787	0.668	0.918	0.787	0.668	0.918	CLONAL	1	TRUE	1	0.25	2		324	508	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs397517201	NA	P-0058027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	87	453	0	ENST00000263967.3:c.1637A>T	p.Gln546Leu	p.Q546L	ENST00000263967	NM_006218.2	546	cAg/cTg	10/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.25	2		453	607	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430156	181430156	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	19	149	0	ENST00000325404.1:c.8A>C	p.Asn3Thr	p.N3T	ENST00000325404	NM_003106.3	3	aAc/aCc	1/1	1	2	FACETS	1	0.816	1	1	0.816	1	CLONAL	1	TRUE	1	0.25	2		149	141	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515145	31515145	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1202201920	NA	P-0058027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	54	638	0	ENST00000344624.3:c.1240C>T	p.Arg414Ter	p.R414*	ENST00000344624		414	Cga/Tga	5/33	1	2	FACETS	0.452	0.385	0.527	0.452	0.385	0.527	SUBCLONAL	1	TRUE	1	0.25	2		638	955	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575550	67575550	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	45	192	0	ENST00000274335.5:c.623C>A	p.Ser208Tyr	p.S208Y	ENST00000274335		208	tCt/tAt	4/15	1	2	FACETS	0.831	0.7	0.977	0.831	0.7	0.977	CLONAL	1	TRUE	1	0.25	2		192	433	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430668	80430668	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	50	319	0	ENST00000286548.4:c.340C>T	p.Arg114Ter	p.R114*	ENST00000286548	NM_002072.3	114	Cga/Tga	3/7	1	2	FACETS	0.889	0.755	1	0.889	0.755	1	CLONAL	1	TRUE	1	0.25	2		319	450	SUCCESS
AR	367	MSKCC	GRCh37	X	66942692	66942692	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	53	324	0	ENST00000374690.3:c.2473C>A	p.Gln825Lys	p.Q825K	ENST00000374690	NM_000044.3	825	Caa/Aaa	7/8	1	2	FACETS	0.83	0.708	0.963	0.83	0.708	0.963	CLONAL	1	TRUE	1	0.25	2		324	511	SUCCESS
AR	367	MSKCC	GRCh37	X	66942713	66942713	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	30	311	2	ENST00000374690.3:c.2494C>T	p.Arg832Ter	p.R832*	ENST00000374690	NM_000044.3	832	Cga/Tga	7/8	1	2	FACETS	0.428	0.344	0.524	0.428	0.344	0.524	SUBCLONAL	1	TRUE	1	0.25	2		313	561	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217393	123217393	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	37	269	0	ENST00000218089.9:c.3047G>T	p.Arg1016Ile	p.R1016I	ENST00000218089	NM_001042749.1	1016	aGa/aTa	29/35	1	2	FACETS	0.677	0.558	0.81	0.677	0.558	0.81	SUBCLONAL	1	TRUE	1	0.25	2		269	437	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0058029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	10	619	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.607	0.411	0.853	0.607	0.411	0.853	SUBCLONAL	1	TRUE	1	0.18	2		619	183	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672323	86672323	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554049422	NA	P-0058029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	20	341	0	ENST00000274376.6:c.2125C>T	p.Arg709Ter	p.R709*	ENST00000274376	NM_002890.2	709	Cga/Tga	16/25	1	2	FACETS	0.942	0.722	1	0.942	0.722	1	CLONAL	1	TRUE	1	0.18	2		341	236	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982331	201982332	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0058029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	80	1001	0	ENST00000359651.3:c.715dup	p.Asp239GlyfsTer62	p.D239Gfs*62	ENST00000359651		237	aag/aaGg	6/8	1	2	FACETS	0.966	0.849	1	0.966	0.849	1	CLONAL	1	TRUE	1	0.18	2		1001	920	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981167	201981168	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0058029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	76	932	0	ENST00000359651.3:c.248dup	p.Asn83LysfsTer9	p.N83Kfs*9	ENST00000359651		82	-/A	2/8	1	2	FACETS	0.852	0.745	0.968	0.852	0.745	0.968	CLONAL	1	TRUE	1	0.18	2		932	991	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520524	176520524	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763461529	NA	P-0058029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	59	1016	0	ENST00000292408.4:c.1369G>A	p.Asp457Asn	p.D457N	ENST00000292408	NM_213647.1	457	Gac/Aac	10/18	1	2	FACETS	0.811	0.697	0.937	0.811	0.697	0.937	CLONAL	1	TRUE	1	0.18	2		1016	808	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045115	47045115	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	27	350	0	ENST00000377604.3:c.2356C>T	p.Gln786Ter	p.Q786*	ENST00000377604	NM_001204468.1	786	Caa/Taa	21/24	1	1	FACETS	0.993	0.792	1	0.993	0.792	1	CLONAL	1	TRUE	0	0.18	1		350	275	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482859	67482872	+	frameshift_variant	Frame_Shift_Del	DEL	TTCCAGTGTGTCTT	TTCCAGTGTGTCTT	-	novel	NA	P-0058029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	57	532	0	ENST00000327367.4:c.1263_1276del	p.Cys421Ter	p.C421*	ENST00000327367	NM_005902.3	421	tgTTCCAGTGTGTCTTag/tgag	9/9	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.18	2		532	543	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678572	88678572	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0058029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	71	445	0	ENST00000360948.2:c.964G>C	p.Glu322Gln	p.E322Q	ENST00000360948	NM_001012338.2	322	Gag/Cag	9/19	1	2	FACETS	0.869	0.761	0.985	1	0.979	1	CLONAL	2	TRUE	1	0.18	2		445	454	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930281	39930282	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0058029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	56	371	0	ENST00000378444.4:c.3182dup	p.Pro1062AlafsTer17	p.P1062Afs*17	ENST00000378444	NM_001123385.1	1061	aag/aaAg	6/15	1	1	FACETS	0.776	0.667	0.893	1	0.969	1	SUBCLONAL	2	TRUE	0	0.18	1		371	365	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437267	52437267	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1064795638	NA	P-0058031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	50	777	0	ENST00000460680.1:c.1777C>T	p.Gln593Ter	p.Q593*	ENST00000460680	NM_004656.3	593	Cag/Tag	14/17	1	2	FACETS	0.69	0.585	0.804	0.69	0.585	0.804	SUBCLONAL	1	TRUE	1	0.29	2		777	500	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267698	198267698	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	13	266	0	ENST00000335508.6:c.1781G>T	p.Arg594Leu	p.R594L	ENST00000335508	NM_012433.2	594	cGa/cTa	13/25	1	2	FACETS	0.474	0.339	0.639	0.474	0.339	0.639	SUBCLONAL	1	TRUE	1	0.29	2		266	189	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945710	38945710	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	18	223	0	ENST00000357387.3:c.4516A>G	p.Ser1506Gly	p.S1506G	ENST00000357387	NM_152756.3	1506	Agt/Ggt	34/38	1	2	FACETS	0.906	0.689	1	0.906	0.689	1	CLONAL	1	TRUE	1	0.29	2		223	137	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	35	365	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.613	0.502	0.737	0.613	0.502	0.737	SUBCLONAL	1	TRUE	1	0.27	2		365	423	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	74	719	1	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.863	0.756	0.979	0.863	0.756	0.979	CLONAL	1	TRUE	1	0.27	2		720	635	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743742	46743742	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	91	832	0	ENST00000371975.4:c.2034-2A>G		p.X678_splice	ENST00000371975	NM_003579.3	678			1	2	FACETS	0.902	0.801	1	0.902	0.801	1	CLONAL	1	TRUE	1	0.27	2		832	747	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076785	72076785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576347795	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	76	488	0	ENST00000357731.5:c.712G>A	p.Gly238Arg	p.G238R	ENST00000357731	NM_173808.2	238	Gga/Aga	5/7	1	2	FACETS	0.909	0.798	1	0.909	0.798	1	CLONAL	1	TRUE	1	0.27	2		488	619	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596032	43596032	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	87	982	0	ENST00000355710.3:c.199C>A	p.Arg67Ser	p.R67S	ENST00000355710	NM_020975.4	67	Cgc/Agc	2/20	1	2	FACETS	0.886	0.785	0.995	0.886	0.785	0.995	CLONAL	1	TRUE	1	0.27	2		982	727	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852680	63852680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	87	535	0	ENST00000279873.7:c.3458C>T	p.Ser1153Leu	p.S1153L	ENST00000279873	NM_032199.2	1153	tCa/tTa	10/10	1	2	FACETS	0.955	0.846	1	0.955	0.846	1	CLONAL	1	TRUE	1	0.27	2		535	675	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298174	123298174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	67	433	0	ENST00000358487.5:c.680G>A	p.Gly227Glu	p.G227E	ENST00000358487	NM_000141.4	227	gGa/gAa	6/18	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.27	2		433	473	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575497	64575497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	97	932	0	ENST00000312049.6:c.520C>T	p.His174Tyr	p.H174Y	ENST00000312049	NM_130799.2	174	Cac/Tac	3/10	1	2	FACETS	0.963	0.859	1	0.963	0.859	1	CLONAL	1	TRUE	1	0.27	2		932	746	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77069993	77069993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	69	524	0	ENST00000356341.3:c.547G>A	p.Asp183Asn	p.D183N	ENST00000356341	NM_002576.4	183	Gat/Aat	6/15	1	2	FACETS	0.889	0.775	1	0.889	0.775	1	CLONAL	1	TRUE	1	0.27	2		524	575	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373351	118373351	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	58	490	0	ENST00000534358.1:c.6744del	p.His2248GlnfsTer3	p.H2248Qfs*3	ENST00000534358	NM_005933.3	2248	caT/ca	27/36	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.27	2		490	400	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123846	46123846	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	35	385	0	ENST00000334344.6:c.112C>T	p.Pro38Ser	p.P38S	ENST00000334344	NM_152641.2	38	Cct/Tct	2/21	1	2	FACETS	0.67	0.55	0.805	0.67	0.55	0.805	SUBCLONAL	1	TRUE	1	0.27	2		385	387	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242662	46242662	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	41	306	0	ENST00000334344.6:c.1624C>T	p.Arg542Ter	p.R542*	ENST00000334344	NM_152641.2	542	Cga/Tga	13/21	1	2	FACETS	0.858	0.717	1	0.858	0.717	1	CLONAL	1	TRUE	1	0.27	2		306	354	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244118	46244120	+	frameshift_variant	Frame_Shift_Del	DEL	CCT	CCT	TC	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	56	446	0	ENST00000334344.6:c.2212_2214delinsTC	p.Pro738SerfsTer20	p.P738Sfs*20	ENST00000334344	NM_152641.2	738	CCT/TC	15/21	1	2	FACETS	0.932	0.8	1	0.932	0.8	1	CLONAL	1	TRUE	1	0.27	2		446	445	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864817	57864817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1191551029	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	105	933	1	ENST00000228682.2:c.2294C>T	p.Pro765Leu	p.P765L	ENST00000228682	NM_005269.2	765	cCc/cTc	12/12	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.27	2		934	776	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041101	29041101	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	67	538	0	ENST00000282397.4:c.327T>A	p.Tyr109Ter	p.Y109*	ENST00000282397	NM_002019.4	109	taT/taA	3/30	1	2	FACETS	0.812	0.706	0.927	0.812	0.706	0.927	CLONAL	1	TRUE	1	0.27	2		538	611	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557399	95557399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	52	407	0	ENST00000393063.1:c.5575G>A	p.Glu1859Lys	p.E1859K	ENST00000393063	NM_030621.3	1859	Gaa/Aaa	27/28	1	2	FACETS	0.788	0.671	0.915	0.788	0.671	0.915	CLONAL	1	TRUE	1	0.27	2		407	489	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989121	41989121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	52	468	0	ENST00000219905.7:c.1913C>T	p.Ser638Phe	p.S638F	ENST00000219905	NM_001164273.1	638	tCt/tTt	3/24	1	2	FACETS	0.736	0.627	0.856	0.736	0.627	0.856	SUBCLONAL	1	TRUE	1	0.27	2		468	523	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712631	43712631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	130	817	2	ENST00000382044.4:c.4553G>A	p.Gly1518Glu	p.G1518E	ENST00000382044	NM_001141980.1	1518	gGg/gAg	21/28	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.27	2		819	858	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729162	66729162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519732	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	88	636	1	ENST00000307102.5:c.370C>T	p.Pro124Ser	p.P124S	ENST00000307102	NM_002755.3	124	Ccg/Tcg	3/11	1	2	FACETS	0.894	0.792	1	0.894	0.792	1	CLONAL	1	TRUE	1	0.27	2		637	729	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2224030	2224030	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	112	955	0	ENST00000326181.6:c.1244C>T	p.Ser415Phe	p.S415F	ENST00000326181	NM_032271.2	415	tCc/tTc	13/21	1	2	FACETS	0.94	0.844	1	0.94	0.844	1	CLONAL	1	TRUE	1	0.27	2		955	883	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644459	3644459	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	112	774	0	ENST00000294008.3:c.2155C>T	p.Gln719Ter	p.Q719*	ENST00000294008	NM_032444.2	719	Cag/Tag	10/15	1	2	FACETS	0.985	0.886	1	0.985	0.886	1	CLONAL	1	TRUE	1	0.27	2		774	842	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857061	9857061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	30	283	0	ENST00000330684.3:c.4340C>T	p.Ser1447Phe	p.S1447F	ENST00000330684	NM_001134407.1	1447	tCc/tTc	13/13	1	2	FACETS	0.756	0.611	0.92	0.756	0.611	0.92	CLONAL	1	TRUE	1	0.27	2		283	294	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916247	9916247	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753203288	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	56	456	1	ENST00000330684.3:c.2042G>A	p.Arg681Gln	p.R681Q	ENST00000330684	NM_001134407.1	681	cGa/cAa	10/13	1	2	FACETS	0.932	0.8	1	0.932	0.8	1	CLONAL	1	TRUE	1	0.27	2		457	445	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556992	29556992	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	14	158	0	ENST00000356175.3:c.2990G>A	p.Arg997Lys	p.R997K	ENST00000356175	NM_000267.3	997	aGg/aAg	22/57	1	2	FACETS	0.934	0.682	1	0.934	0.682	1	CLONAL	1	TRUE	1	0.27	2		158	111	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664835	29664835	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	27	277	0	ENST00000356175.3:c.6580-2A>T		p.X2194_splice	ENST00000356175	NM_000267.3	2194			0.262754916698575	3	FACETS	0.636	0.506	0.784	0.318	0.253	0.392	SUBCLONAL	1	TRUE	1	0.27	3		277	357	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58701073	58701073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	132	542	0	ENST00000305921.3:c.664C>T	p.Pro222Ser	p.P222S	ENST00000305921	NM_003620.3	222	Ccc/Tcc	2/6	0.262754916698575	3	FACETS	0.814	0.74	0.891	0.814	0.74	0.891	CLONAL	2	TRUE	1	0.27	3		542	682	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775164	73775164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867543814	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	88	875	0	ENST00000254810.4:c.92C>T	p.Pro31Leu	p.P31L	ENST00000254810	NM_005324.3	31	cCc/cTc	2/4	0.262754916698575	3	FACETS	0.815	0.721	0.916	0.407	0.36	0.458	CLONAL	1	TRUE	1	0.27	3		875	908	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221295	1221295	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761164605	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	121	975	0	ENST00000326873.7:c.818C>T	p.Ala273Val	p.A273V	ENST00000326873	NM_000455.4	273	gCc/gTc	6/10	1	2	FACETS	0.997	0.9	1	0.997	0.9	1	CLONAL	1	TRUE	1	0.27	2		975	899	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3114961	3114961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	96	1037	0	ENST00000078429.4:c.496C>T	p.Arg166Cys	p.R166C	ENST00000078429	NM_002067.2	166	Cgc/Tgc	4/7	1	2	FACETS	0.842	0.749	0.94	0.842	0.749	0.94	CLONAL	1	TRUE	1	0.27	2		1037	845	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248560	10248560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	112	1116	0	ENST00000340748.4:c.4193G>A	p.Arg1398Lys	p.R1398K	ENST00000340748		1398	aGg/aAg	35/40	1	2	FACETS	0.87	0.781	0.964	0.87	0.781	0.964	CLONAL	1	TRUE	1	0.27	2		1116	954	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210697	36210697	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	95	840	0	ENST00000222270.7:c.448C>T	p.Arg150Ter	p.R150*	ENST00000222270	NM_014727.1	150	Cga/Tga	3/37	1	2	FACETS	0.863	0.768	0.965	0.863	0.768	0.965	CLONAL	1	TRUE	1	0.27	2		840	815	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467136	25467136	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773048923	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	101	859	1	ENST00000264709.3:c.1739C>T	p.Pro580Leu	p.P580L	ENST00000264709	NM_175629.2	580	cCc/cTc	15/23	1	2	FACETS	0.953	0.852	1	0.953	0.852	1	CLONAL	1	TRUE	1	0.27	2		860	785	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707885	47707885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1198289499	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	43	340	1	ENST00000233146.2:c.2509C>T	p.Pro837Ser	p.P837S	ENST00000233146	NM_000251.2	837	Cct/Tct	15/16	1	2	FACETS	0.866	0.726	1	0.866	0.726	1	CLONAL	1	TRUE	1	0.27	2		341	368	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561352	9561352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773981325	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	56	476	0	ENST00000353224.5:c.430G>A	p.Glu144Lys	p.E144K	ENST00000353224	NM_177990.2	144	Gaa/Aaa	4/10	1	2	FACETS	0.89	0.764	1	0.89	0.764	1	CLONAL	1	TRUE	1	0.27	2		476	466	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624936	9624936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760501160	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	31	447	0	ENST00000353224.5:c.41C>T	p.Pro14Leu	p.P14L	ENST00000353224	NM_177990.2	14	cCg/cTg	3/10	1	2	FACETS	0.633	0.512	0.769	0.633	0.512	0.769	SUBCLONAL	1	TRUE	1	0.27	2		447	363	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100947	41100947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372070542	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	89	706	0	ENST00000373198.4:c.1409G>A	p.Arg470Gln	p.R470Q	ENST00000373198	NM_133170.3	470	cGa/cAa	8/32	1	2	FACETS	0.965	0.856	1	0.965	0.856	1	CLONAL	1	TRUE	1	0.27	2		706	683	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408920	41408920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	56	351	0	ENST00000373198.4:c.506C>T	p.Ser169Leu	p.S169L	ENST00000373198	NM_133170.3	169	tCa/tTa	4/32	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.27	2		351	380	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947808	178947808	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	39	260	0	ENST00000263967.3:c.2683G>T	p.Asp895Tyr	p.D895Y	ENST00000263967	NM_006218.2	895	Gac/Tac	19/21	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.27	2		260	272	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604206	189604206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	52	467	0	ENST00000264731.3:c.1373C>T	p.Ser458Leu	p.S458L	ENST00000264731	NM_003722.4	458	tCa/tTa	11/14	1	2	FACETS	0.786	0.67	0.913	0.786	0.67	0.913	CLONAL	1	TRUE	1	0.27	2		467	490	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607203	189607203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	110	981	1	ENST00000264731.3:c.1582C>T	p.Pro528Ser	p.P528S	ENST00000264731	NM_003722.4	528	Cca/Tca	12/14	1	2	FACETS	0.944	0.848	1	0.944	0.848	1	CLONAL	1	TRUE	1	0.27	2		982	863	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	83	814	1	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	1	2	FACETS	0.971	0.858	1	0.971	0.858	1	CLONAL	1	TRUE	1	0.27	2		815	633	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968142	55968142	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	83	497	0	ENST00000263923.4:c.2188G>A	p.Glu730Lys	p.E730K	ENST00000263923	NM_002253.2	730	Gag/Aag	15/30	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.27	2		497	563	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293565	1293565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	131	1361	0	ENST00000310581.5:c.1436G>A	p.Gly479Asp	p.G479D	ENST00000310581	NM_198253.2	479	gGc/gAc	2/16	1	2	FACETS	0.893	0.808	0.982	0.893	0.808	0.982	CLONAL	1	TRUE	1	0.27	2		1361	1087	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867557	35867557	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	18	225	0	ENST00000303115.3:c.371C>T	p.Thr124Ile	p.T124I	ENST00000303115	NM_002185.3	124	aCc/aTc	3/8	1	2	FACETS	0.494	0.372	0.638	0.494	0.372	0.638	SUBCLONAL	1	TRUE	1	0.27	2		225	270	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876397	35876397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	81	703	0	ENST00000303115.3:c.1189G>A	p.Gly397Arg	p.G397R	ENST00000303115	NM_002185.3	397	Ggg/Agg	8/8	1	2	FACETS	0.877	0.773	0.989	0.877	0.773	0.989	CLONAL	1	TRUE	1	0.27	2		703	684	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457806	149457806	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1561936512	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	64	568	0	ENST00000286301.3:c.598C>T	p.Pro200Ser	p.P200S	ENST00000286301	NM_005211.3	200	Cca/Tca	5/22	1	2	FACETS	0.886	0.768	1	0.886	0.768	1	CLONAL	1	TRUE	1	0.27	2		568	535	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500844	149500844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	92	739	1	ENST00000261799.4:c.2386C>T	p.Pro796Ser	p.P796S	ENST00000261799	NM_002609.3	796	Cca/Tca	17/23	1	2	FACETS	0.893	0.793	1	0.893	0.793	1	CLONAL	1	TRUE	1	0.27	2		740	763	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524540	176524540	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148143006	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	147	1215	0	ENST00000292408.4:c.2272C>T	p.Arg758Cys	p.R758C	ENST00000292408	NM_213647.1	758	Cgc/Tgc	18/18	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.27	2		1215	1078	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057017	180057017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	115	1237	3	ENST00000261937.6:c.602C>T	p.Ala201Val	p.A201V	ENST00000261937	NM_182925.4	201	gCc/gTc	5/30	1	2	FACETS	0.931	0.838	1	0.931	0.838	1	CLONAL	1	TRUE	1	0.27	2		1240	915	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188242	32188242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	121	967	0	ENST00000375023.3:c.1099G>A	p.Gly367Arg	p.G367R	ENST00000375023	NM_004557.3	367	Gga/Aga	6/30	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.27	2		967	875	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106543584	106543584	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	35	226	0	ENST00000369096.4:c.386A>G	p.Asn129Ser	p.N129S	ENST00000369096	NM_001198.3	129	aAc/aGc	3/7	1	2	FACETS	0.943	0.776	1	0.943	0.776	1	CLONAL	1	TRUE	1	0.27	2		226	275	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481412	140481412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913353	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	98	414	1	ENST00000288602.6:c.1396G>A	p.Gly466Arg	p.G466R	ENST00000288602	NM_004333.4	466	Gga/Aga	11/18	0.262754916698575	3	FACETS	0.915	0.821	1	0.915	0.821	1	CLONAL	2	TRUE	1	0.27	3		415	450	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285464	38285464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	81	762	0	ENST00000425967.3:c.689C>T	p.Pro230Leu	p.P230L	ENST00000425967	NM_001174067.1	230	cCt/cTt	6/19	1	2	FACETS	0.749	0.659	0.846	0.749	0.659	0.846	SUBCLONAL	1	TRUE	1	0.27	2		762	801	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912075	56912075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	72	648	1	ENST00000519728.1:c.1303G>A	p.Glu435Lys	p.E435K	ENST00000519728	NM_002350.3	435	Gaa/Aaa	12/13	1	2	FACETS	0.746	0.651	0.848	0.746	0.651	0.848	SUBCLONAL	1	TRUE	1	0.27	2		649	715	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972915	68972915	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs201372935	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	52	307	0	ENST00000288368.4:c.1240G>A	p.Glu414Lys	p.E414K	ENST00000288368	NM_024870.2	414	Gaa/Aaa	11/40	1	2	FACETS	0.89	0.759	1	0.89	0.759	1	CLONAL	1	TRUE	1	0.27	2		307	433	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069613	69069613	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	50	439	0	ENST00000288368.4:c.4288C>T	p.Gln1430Ter	p.Q1430*	ENST00000288368	NM_024870.2	1430	Caa/Taa	35/40	1	2	FACETS	0.715	0.607	0.834	0.715	0.607	0.834	SUBCLONAL	1	TRUE	1	0.27	2		439	518	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636727	8636727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159852	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	45	284	0	ENST00000356435.5:c.182G>A	p.Gly61Glu	p.G61E	ENST00000356435		61	gGa/gAa	2/35	1	2	FACETS	0.972	0.82	1	0.972	0.82	1	CLONAL	1	TRUE	1	0.27	2		284	343	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637126	93637126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	46	407	0	ENST00000375746.1:c.1176G>A	p.Met392Ile	p.M392I	ENST00000375746	NM_001174167.1	392	atG/atA	9/14	1	2	FACETS	0.8	0.675	0.938	0.8	0.675	0.938	CLONAL	1	TRUE	1	0.27	2		407	426	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248156	98248156	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	37	364	0	ENST00000331920.6:c.395T>C	p.Val132Ala	p.V132A	ENST00000331920	NM_000264.3	132	gTt/gCt	3/24	1	2	FACETS	0.743	0.613	0.887	0.743	0.613	0.887	SUBCLONAL	1	TRUE	1	0.27	2		364	369	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730407	133730407	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	66	505	0	ENST00000318560.5:c.473C>T	p.Pro158Leu	p.P158L	ENST00000318560	NM_005157.4	158	cCt/cTt	3/11	1	2	FACETS	0.976	0.849	1	0.976	0.849	1	CLONAL	1	TRUE	1	0.27	2		505	501	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321391	1321391	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	69	481	0	ENST00000400841.2:c.364C>T	p.Pro122Ser	p.P122S	ENST00000400841		122	Ccg/Tcg	4/6	1	1	FACETS	0.987	0.862	1	0.987	0.862	1	CLONAL	1	TRUE	0	0.27	1		481	448	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228054	53228054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	92	387	0	ENST00000375401.3:c.2260G>A	p.Asp754Asn	p.D754N	ENST00000375401	NM_004187.3	754	Gat/Aat	16/26	1	1	FACETS	0.826	0.74	0.915	1	0.984	1	CLONAL	2	TRUE	0	0.27	1		387	357	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354984	70354984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	85	354	0	ENST00000374080.3:c.4906C>T	p.Arg1636Cys	p.R1636C	ENST00000374080		1636	Cgc/Tgc	36/45	1	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.27	1		354	400	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504086	123504086	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0058032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	50	185	0	ENST00000371139.4:c.262C>T	p.Gln88Ter	p.Q88*	ENST00000371139	NM_001114937.2	88	Cag/Tag	3/4	1	1	FACETS	0.752	0.646	0.866	1	0.966	1	SUBCLONAL	2	TRUE	0	0.27	1		185	213	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0058033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	140	410	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.517567854958114	3	FACETS	0.862	0.796	0.928	0.862	0.796	0.928	CLONAL	2	TRUE	1	0.630458308312051	3		410	339	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050644	30050644	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0058033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	154	335	0	ENST00000338641.4:c.448-2A>G		p.X150_splice	ENST00000338641	NM_000268.3	150			0.630458308312051	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.630458308312051	1		335	294	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319887	62319887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371161995	NA	P-0058033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	313	900	0	ENST00000360203.5:c.1729G>A	p.Asp577Asn	p.D577N	ENST00000360203	NM_001283009.1	577	Gac/Aac	21/35	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.630458308312051	2		900	924	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352593	89352593	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0058033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	44	484	0	ENST00000301030.4:c.746T>G	p.Val249Gly	p.V249G	ENST00000301030	NM_001256183.1	249	gTg/gGg	8/13	1	2	FACETS	0.287	0.24	0.338	0.287	0.24	0.338	SUBCLONAL	1	TRUE	1	0.630458308312051	2		484	487	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111995764	111995764	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0058033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	36	406	0	ENST00000368678.4:c.1334A>G	p.Asp445Gly	p.D445G	ENST00000368678		445	gAc/gGc	12/13	1	2	FACETS	0.214	0.175	0.257	0.214	0.175	0.257	SUBCLONAL	1	TRUE	1	0.630458308312051	2		406	534	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0058035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	176	365	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.999	0.926	1	0.999	0.926	1	CLONAL	1	TRUE	1	0.635125664146304	2		365	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0058035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	301	750	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.635125664146304	1	FACETS	0.937	0.889	0.986	0.937	0.889	0.986	CLONAL	1	TRUE	0	0.635125664146304	1		750	690	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0058035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	20	323	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.107	0.081	0.137	0.107	0.081	0.137	SUBCLONAL	1	TRUE	1	0.635125664146304	2		323	591	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0058035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	134	246	0	ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	4/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.635125664146304	2		246	372	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795070	242795070	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0058035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	474	1293	2	ENST00000334409.5:c.139G>A	p.Gly47Arg	p.G47R	ENST00000334409	NM_005018.2	47	Ggg/Agg	2/5	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.635125664146304	2		1295	1384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0058037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	295	1105	4	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.202660378511634	3	FACETS	1	0.991	1	0.832	0.785	0.88	CLONAL	2	TRUE	0	0.29	3		1109	933	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391211	139391211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202065858	NA	P-0058037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	282	1376	0	ENST00000277541.6:c.6980G>A	p.Arg2327Gln	p.R2327Q	ENST00000277541	NM_017617.3	2327	cGg/cAg	34/34	0.296058289172332	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.29	2		1376	837	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124717	108124717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751515818	NA	P-0058037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	91	325	1	ENST00000278616.4:c.2075G>A	p.Arg692His	p.R692H	ENST00000278616	NM_000051.3	692	cGc/cAc	13/63	0.296058289172332	5	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	3	0.29	5		326	398	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	215	694	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.792126083563012	2	FACETS	0.917	0.859	0.976	0.458	0.429	0.488	CLONAL	1	TRUE	0	0.825679390337904	2		694	568	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202313	133202313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756301031	NA	P-0000585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	549	740	0	ENST00000320574.5:c.6575C>T	p.Ala2192Val	p.A2192V	ENST00000320574	NM_006231.2	2192	gCg/gTg	47/49	0.626537132627285	4	FACETS	0.962	0.925	0.999			1	CLONAL	2	TRUE	NA	0.825679390337904	4		740	1262	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0000585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	149	429	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	0.793263599818623	1	FACETS	0.95	0.896	1	0.95	0.896	1	CLONAL	1	TRUE	0	0.825679390337904	1		429	223	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61725918	61725918	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	128	473	0	ENST00000401558.2:c.649C>G	p.Gln217Glu	p.Q217E	ENST00000401558	NM_003400.3	217	Caa/Gaa	9/25	0.825679390337904	3	FACETS	0.799	0.728	0.874			1	SUBCLONAL	1	TRUE	NA	0.825679390337904	3		473	548	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416219	416219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768337054	NA	P-0000585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	175	506	1	ENST00000399788.2:c.3967C>T	p.Arg1323Trp	p.R1323W	ENST00000399788	NM_001042603.1	1323	Cgg/Tgg	24/28	0.825679390337904	4	FACETS	0.964	0.889	1			1	CLONAL	1	TRUE	NA	0.825679390337904	4		507	803	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763976	76763976	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	243	828	0	ENST00000373344.5:c.7332G>C	p.Leu2444Phe	p.L2444F	ENST00000373344	NM_000489.3	2444	ttG/ttC	35/35	0.825679390337904	3	FACETS	0.92	0.861	0.981	0.46	0.43	0.491	CLONAL	1	TRUE	1	0.825679390337904	3		828	904	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589580	67589585	+	inframe_deletion	In_Frame_Del	DEL	AATTAC	AATTAC	-	novel	NA	P-0000585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	230	281	0	ENST00000274335.5:c.1344_1349del	p.Lys448_His450delinsAsn	p.K448_H450delinsN	ENST00000274335		448	aAATTACat/aat	10/15	0.825679390337904	3	FACETS	0.961	0.93	0.99	0.961	0.93	0.99	CLONAL	3	TRUE	0	0.825679390337904	3		281	273	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921807	111921807	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0000585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	166	441	0	ENST00000393256.3:c.596G>C	p.Ter199SerextTer70	p.*199Sext*70	ENST00000393256	NM_006538.4	199	tGa/tCa	4/4	0.735297042724154	4	FACETS	1	0.952	1	0.523	0.481	0.566	CLONAL	1	TRUE	2	0.825679390337904	4		441	702	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119706	108119706	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	83	318	0	ENST00000278616.4:c.1112C>G	p.Thr371Ser	p.T371S	ENST00000278616	NM_000051.3	371	aCt/aGt	9/63	1	2	FACETS	0.922	0.829	1	0.922	0.829	1	CLONAL	1	TRUE	1	0.825679390337904	2		318	218	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100345	8100346	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0000585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	579	887	0	ENST00000346208.3:c.322_323del	p.Thr108ArgfsTer194	p.T108Rfs*194	ENST00000346208		107	CAc/c	3/6	0.816255334485387	4	FACETS	0.913	0.879	0.948	0.913	0.879	0.948	CLONAL	2	TRUE	2	0.825679390337904	4		887	1402	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350600	89350600	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	215	847	0	ENST00000301030.4:c.2350G>C	p.Glu784Gln	p.E784Q	ENST00000301030	NM_001256183.1	784	Gag/Cag	9/13	0.778294088820789	2	FACETS	0.84	0.786	0.896	0.42	0.393	0.448	CLONAL	1	TRUE	0	0.825679390337904	2		847	620	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701051	29701051	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	162	558	0	ENST00000356175.3:c.8335G>T	p.Glu2779Ter	p.E2779*	ENST00000356175	NM_000267.3	2779	Gaa/Taa	57/57	0.816255334485387	4	FACETS	0.928	0.853	1	0.464	0.426	0.503	CLONAL	1	TRUE	2	0.825679390337904	4		558	772	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928332	69928332	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	190	574	0	ENST00000352241.4:c.152C>T	p.Ser51Phe	p.S51F	ENST00000352241	NM_198159.2	51	tCc/tTc	2/10	0.816255334485387	4	FACETS	1	0.94	1	0.509	0.471	0.548	CLONAL	1	TRUE	2	0.825679390337904	4		574	826	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190775	185190775	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	211	717	0	ENST00000265026.3:c.1656G>C	p.Leu552Phe	p.L552F	ENST00000265026	NM_004721.4	552	ttG/ttC	11/14	0.816255334485387	4	FACETS	0.898	0.834	0.965	0.449	0.417	0.483	CLONAL	1	TRUE	2	0.825679390337904	4		717	1039	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155727	56155728	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTTT	novel	NA	P-0000585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	370	393	0	ENST00000399503.3:c.819_820insCTTT	p.Val274LeufsTer28	p.V274Lfs*28	ENST00000399503	NM_005921.1	273	-/CTTT	3/20	0.825679390337904	3	FACETS	0.867	0.84	0.893	0.867	0.84	0.893	CLONAL	3	TRUE	0	0.825679390337904	3		393	487	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513338	106513338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	142	467	0	ENST00000359195.3:c.2242G>A	p.Asp748Asn	p.D748N	ENST00000359195	NM_002649.2	748	Gat/Aat	4/11	0.778294088820789	2	FACETS	0.912	0.841	0.985	0.456	0.42	0.493	CLONAL	1	TRUE	0	0.825679390337904	2		467	377	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741669	145741669	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	350	932	0	ENST00000428558.2:c.834G>C	p.Glu278Asp	p.E278D	ENST00000428558	NM_004260.3	278	gaG/gaC	5/22	0.735297042724154	4	FACETS	1	0.964	1	0.513	0.484	0.542	CLONAL	1	TRUE	2	0.825679390337904	4		932	1510	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604533	43604533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs546866208	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	64	898	1	ENST00000355710.3:c.1118C>T	p.Ala373Val	p.A373V	ENST00000355710	NM_020975.4	373	gCg/gTg	6/20	0.139275353437569	4	FACETS	0.744	0.645	0.852	0.372	0.322	0.426	INDETERMINATE	1	TRUE	2	0.441182089973082	4		899	562	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	53	317	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.403684234840922	3	FACETS	0.418	0.355	0.486	0.209	0.177	0.243	SUBCLONAL	1	TRUE	1	0.441182089973082	3		317	702	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884286	37884286	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs36085723	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	51	455	0	ENST00000269571.5:c.3757G>A	p.Val1253Met	p.V1253M	ENST00000269571		1253	Gtg/Atg	27/27	1	2	FACETS	0.556	0.473	0.646	0.556	0.473	0.646	SUBCLONAL	1	TRUE	1	0.441182089973082	2		455	416	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	44	198	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	0.573	0.482	0.673	0.573	0.482	0.673	SUBCLONAL	1	TRUE	1	0.441182089973082	2		198	348	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021817	71021817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs797045586	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	30	292	0	ENST00000318789.4:c.1541G>A	p.Arg514His	p.R514H	ENST00000318789	NM_032682.5	514	cGt/cAt	18/21	1	2	FACETS	0.496	0.401	0.603	0.496	0.401	0.603	SUBCLONAL	1	TRUE	1	0.441182089973082	2		292	274	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	194	569	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	0.263507737285426	2	FACETS	1	0.964	1	0.532	0.493	0.572	INDETERMINATE	1	TRUE	0	0.441182089973082	2		569	827	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16235967	16235967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	113	549	0	ENST00000375759.3:c.1033C>T	p.Arg345Cys	p.R345C	ENST00000375759	NM_015001.2	345	Cgc/Tgc	4/15	1	2	FACETS	0.658	0.592	0.728	0.658	0.592	0.728	SUBCLONAL	1	TRUE	1	0.441182089973082	2		549	778	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797162	45797162	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	74	1075	0	ENST00000450313.1:c.1253A>G	p.Lys418Arg	p.K418R	ENST00000450313	NM_012222.2	418	aAg/aGg	13/16	1	2	FACETS	0.507	0.443	0.575	0.507	0.443	0.575	SUBCLONAL	1	TRUE	1	0.441182089973082	2		1075	662	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458964	120458964	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	90	950	1	ENST00000256646.2:c.6381G>T	p.Lys2127Asn	p.K2127N	ENST00000256646	NM_024408.3	2127	aaG/aaT	34/34	1	2	FACETS	0.592	0.525	0.663	0.592	0.525	0.663	SUBCLONAL	1	TRUE	1	0.441182089973082	2		951	689	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976508	25976508	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	54	371	1	ENST00000435504.4:c.1037G>A	p.Gly346Asp	p.G346D	ENST00000435504		346	gGt/gAt	11/13	1	2	FACETS	0.564	0.483	0.653	0.564	0.483	0.653	SUBCLONAL	1	TRUE	1	0.441182089973082	2		372	434	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026438	48026438	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786202363	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	78	526	0	ENST00000234420.5:c.1316A>G	p.Asp439Gly	p.D439G	ENST00000234420	NM_000179.2	439	gAt/gGt	4/10	1	2	FACETS	0.538	0.473	0.608	0.538	0.473	0.608	SUBCLONAL	1	TRUE	1	0.441182089973082	2		526	657	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027886	48027886	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779246	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	43	302	0	ENST00000234420.5:c.2764C>T	p.Arg922Ter	p.R922*	ENST00000234420	NM_000179.2	922	Cga/Tga	4/10	1	2	FACETS	0.525	0.441	0.619	0.525	0.441	0.619	SUBCLONAL	1	TRUE	1	0.441182089973082	2		302	371	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437692	52437692	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs201302700	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	76	905	0	ENST00000460680.1:c.1469A>G	p.Asn490Ser	p.N490S	ENST00000460680	NM_004656.3	490	aAt/aGt	13/17	1	2	FACETS	0.537	0.471	0.609	0.537	0.471	0.609	SUBCLONAL	1	TRUE	1	0.441182089973082	2		905	641	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332829	153332829	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	96	625	0	ENST00000281708.4:c.127C>T	p.Gln43Ter	p.Q43*	ENST00000281708	NM_033632.3	43	Cag/Tag	2/12	1	2	FACETS	0.511	0.455	0.572	0.511	0.455	0.572	SUBCLONAL	1	TRUE	1	0.441182089973082	2		625	851	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524993	187524993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371987657	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	78	811	0	ENST00000441802.2:c.10687G>A	p.Val3563Ile	p.V3563I	ENST00000441802	NM_005245.3	3563	Gtc/Atc	19/27	1	2	FACETS	0.541	0.476	0.612	0.541	0.476	0.612	SUBCLONAL	1	TRUE	1	0.441182089973082	2		811	653	SUCCESS
APC	324	MSKCC	GRCh37	5	112174868	112174868	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085128	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	36	286	0	ENST00000257430.4:c.3577C>T	p.Gln1193Ter	p.Q1193*	ENST00000257430	NM_000038.5	1193	Cag/Tag	16/16	1	2	FACETS	0.722	0.598	0.859	0.722	0.598	0.859	SUBCLONAL	1	TRUE	1	0.441182089973082	2		286	226	SUCCESS
APC	324	MSKCC	GRCh37	5	112175141	112175141	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	35	228	0	ENST00000257430.4:c.3850G>T	p.Glu1284Ter	p.E1284*	ENST00000257430	NM_000038.5	1284	Gaa/Taa	16/16	1	2	FACETS	0.752	0.622	0.896	0.752	0.622	0.896	SUBCLONAL	1	TRUE	1	0.441182089973082	2		228	211	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165173	32165173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752105876	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	81	973	1	ENST00000375023.3:c.4955G>A	p.Arg1652His	p.R1652H	ENST00000375023	NM_004557.3	1652	cGc/cAc	27/30	0.139275353437569	4	FACETS	0.724	0.637	0.817	0.362	0.318	0.409	INDETERMINATE	1	TRUE	2	0.441182089973082	4		974	731	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170565	108170565	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	57	500	0	ENST00000278616.4:c.5130G>A	p.Trp1710Ter	p.W1710*	ENST00000278616	NM_000051.3	1710	tgG/tgA	34/63	1	2	FACETS	0.438	0.375	0.506	0.438	0.375	0.506	SUBCLONAL	1	TRUE	1	0.441182089973082	2		500	590	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377264	118377264	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	50	566	0	ENST00000534358.1:c.10657G>T	p.Gly3553Trp	p.G3553W	ENST00000534358	NM_005933.3	3553	Ggg/Tgg	27/36	1	2	FACETS	0.638	0.544	0.742	0.638	0.544	0.742	SUBCLONAL	1	TRUE	1	0.441182089973082	2		566	355	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432289	432289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376128815	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	112	691	0	ENST00000399788.2:c.2234G>A	p.Arg745His	p.R745H	ENST00000399788	NM_001042603.1	745	cGt/cAt	16/28	0.2566053884508	0	FACETS	0.29	0.26	0.322			1	INDETERMINATE	1	TRUE	0	0.441182089973082	0		691	979	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231437	46231437	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	78	280	2	ENST00000334344.6:c.1277C>T	p.Thr426Met	p.T426M	ENST00000334344	NM_152641.2	426	aCg/aTg	10/21	0.403684234840922	3	FACETS	0.675	0.594	0.763	0.338	0.297	0.382	SUBCLONAL	1	TRUE	1	0.441182089973082	3		282	639	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46240657	46240657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757456378	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	79	392	0	ENST00000334344.6:c.1517C>T	p.Ala506Val	p.A506V	ENST00000334344	NM_152641.2	506	gCg/gTg	12/21	0.403684234840922	3	FACETS	0.621	0.546	0.702	0.31	0.273	0.351	SUBCLONAL	1	TRUE	1	0.441182089973082	3		392	704	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225959	133225959	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs949243552	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	69	1087	0	ENST00000320574.5:c.3938C>T	p.Thr1313Met	p.T1313M	ENST00000320574	NM_006231.2	1313	aCg/aTg	31/49	0.152048109657642	0	FACETS	0.275	0.239	0.314			1	INDETERMINATE	1	TRUE	0	0.441182089973082	0		1087	636	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880860	28880860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746322044	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	203	740	0	ENST00000282397.4:c.3770G>A	p.Arg1257His	p.R1257H	ENST00000282397	NM_002019.4	1257	cGc/cAc	29/30	0.373473554257824	4	FACETS	0.916	0.852	0.982	0.611	0.568	0.655	CLONAL	2	TRUE	1	0.441182089973082	4		740	724	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913027	32913027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358685	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	214	699	3	ENST00000380152.3:c.4535G>A	p.Arg1512His	p.R1512H	ENST00000380152		1512	cGt/cAt	11/27	0.373473554257824	4	FACETS	0.92	0.857	0.984	0.613	0.571	0.656	CLONAL	2	TRUE	1	0.441182089973082	4		702	760	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435420	110435420	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1049519615	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	274	757	2	ENST00000375856.3:c.2981C>T	p.Pro994Leu	p.P994L	ENST00000375856	NM_003749.2	994	cCg/cTg	1/2	0.373473554257824	4	FACETS	1	0.989	1	0.801	0.756	0.847	CLONAL	2	TRUE	1	0.441182089973082	4		759	745	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934842	9934842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	106	657	0	ENST00000330684.3:c.1448G>A	p.Gly483Glu	p.G483E	ENST00000330684	NM_001134407.1	483	gGg/gAg	6/13	1	2	FACETS	0.604	0.542	0.671	0.604	0.542	0.671	SUBCLONAL	1	TRUE	1	0.441182089973082	2		657	795	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646867	23646867	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	127	721	0	ENST00000261584.4:c.1000T>C	p.Tyr334His	p.Y334H	ENST00000261584	NM_024675.3	334	Tac/Cac	4/13	1	2	FACETS	0.714	0.647	0.785	0.714	0.647	0.785	SUBCLONAL	1	TRUE	1	0.441182089973082	2		721	806	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849514	68849514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs36087757	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	83	739	1	ENST00000261769.5:c.1417G>A	p.Val473Ile	p.V473I	ENST00000261769	NM_004360.3	473	Gtc/Atc	10/16	1	2	FACETS	0.545	0.48	0.613	0.545	0.48	0.613	SUBCLONAL	1	TRUE	1	0.441182089973082	2		740	691	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098455	11098455	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1361910224	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	44	607	2	ENST00000358026.2:c.973G>A	p.Val325Met	p.V325M	ENST00000358026	NM_001128849.1	325	Gtg/Atg	6/36	1	2	FACETS	0.715	0.603	0.837	0.715	0.603	0.837	SUBCLONAL	1	TRUE	1	0.441182089973082	2		609	279	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132438	11132438	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794284	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	81	973	2	ENST00000358026.2:c.2654G>A	p.Arg885His	p.R885H	ENST00000358026	NM_001128849.1	885	cGc/cAc	19/36	1	2	FACETS	0.729	0.644	0.819	0.729	0.644	0.819	SUBCLONAL	1	TRUE	1	0.441182089973082	2		975	504	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478633	57478633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1131691999	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	65	664	0	ENST00000371085.3:c.305C>T	p.Ala102Val	p.A102V	ENST00000371085	NM_000516.4	102	gCg/gTg	4/13	1	2	FACETS	0.473	0.41	0.541	0.473	0.41	0.541	SUBCLONAL	1	TRUE	1	0.441182089973082	2		664	623	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24135758	24135758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	63	578	0	ENST00000263121.7:c.245C>T	p.Thr82Met	p.T82M	ENST00000263121	NM_003073.3	82	aCg/aTg	3/9	1	2	FACETS	0.575	0.498	0.658	0.575	0.498	0.658	SUBCLONAL	1	TRUE	1	0.441182089973082	2		578	497	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402216	402217	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	121	839	0	ENST00000399788.2:c.4574dup	p.Glu1526GlyfsTer9	p.E1526Gfs*9	ENST00000399788	NM_001042603.1	1525	aag/aaAg	27/28	0.2566053884508	0	FACETS	0.261	0.235	0.288			1	INDETERMINATE	1	TRUE	0	0.441182089973082	0		839	1176	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641389	18641389	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1229278001	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	37	240	0	ENST00000266497.5:c.2393del	p.Asn798MetfsTer16	p.N798Mfs*16	ENST00000266497		796	ctA/ct	17/31	1	2	FACETS	0.621	0.515	0.739	0.621	0.515	0.739	SUBCLONAL	1	TRUE	1	0.441182089973082	2		240	270	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131514	202131514	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	51	267	0	ENST00000358485.4:c.482G>A	p.Arg161Lys	p.R161K	ENST00000358485	NM_001080125.1	161	aGg/aAg	2/9	1	2	FACETS	0.596	0.508	0.692	0.596	0.508	0.692	SUBCLONAL	1	TRUE	1	0.441182089973082	2		267	388	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2229791	2229791	+	stop_lost	Nonstop_Mutation	SNP	G	G	T	novel	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	93	834	0	ENST00000398665.3:c.4614G>T	p.Ter1538TyrextTer63	p.*1538Yext*63	ENST00000398665	NM_032482.2	1538	taG/taT	28/28	1	2	FACETS	0.71	0.632	0.792	0.71	0.632	0.792	SUBCLONAL	1	TRUE	1	0.441182089973082	2		834	594	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	115	889	6	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	1	2	FACETS	0.68	0.612	0.751	0.68	0.612	0.751	SUBCLONAL	1	TRUE	1	0.441182089973082	2		895	767	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966873	25966873	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1271466699	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	58	703	3	ENST00000435504.4:c.2333del	p.Pro778GlnfsTer21	p.P778Qfs*21	ENST00000435504		778	cCa/ca	13/13	1	2	FACETS	0.456	0.391	0.526	0.456	0.391	0.526	SUBCLONAL	1	TRUE	1	0.441182089973082	2		706	577	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845934	72845934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759043061	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	59	510	0	ENST00000268489.5:c.3533C>T	p.Ser1178Leu	p.S1178L	ENST00000268489	NM_006885.3	1178	tCg/tTg	6/10	1	2	FACETS	0.66	0.57	0.758	0.66	0.57	0.758	SUBCLONAL	1	TRUE	1	0.441182089973082	2		510	405	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158525	26158525	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1222808686	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	48	548	0	ENST00000289316.2:c.128A>G	p.Tyr43Cys	p.Y43C	ENST00000289316	NM_138720.2	43	tAc/tGc	1/2	0.441182089973082	5	FACETS	0.486	0.41	0.57			1	SUBCLONAL	1	TRUE	NA	0.441182089973082	5		548	744	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350151	81350151	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	41	388	0	ENST00000222390.5:c.1181G>T	p.Gly394Val	p.G394V	ENST00000222390	NM_000601.4	394	gGg/gTg	10/18	0.403684234840922	3	FACETS	0.396	0.329	0.47	0.198	0.164	0.235	SUBCLONAL	1	TRUE	1	0.441182089973082	3		388	573	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884648	111884648	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1266852479	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	37	629	0	ENST00000341259.2:c.824T>C	p.Phe275Ser	p.F275S	ENST00000341259	NM_005475.2	275	tTt/tCt	3/8	0.403684234840922	3	FACETS	0.431	0.355	0.516	0.216	0.177	0.258	SUBCLONAL	1	TRUE	1	0.441182089973082	3		629	475	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459672	40459672	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1286424849	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	52	900	1	ENST00000345506.4:c.1837G>A	p.Gly613Arg	p.G613R	ENST00000345506	NM_003152.3	613	Ggg/Agg	16/20	1	2	FACETS	0.38	0.323	0.443	0.38	0.323	0.443	SUBCLONAL	1	TRUE	1	0.441182089973082	2		901	620	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78865554	78865554	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	75	605	0	ENST00000306801.3:c.2018A>G	p.Gln673Arg	p.Q673R	ENST00000306801	NM_020761.2	673	cAg/cGg	18/34	1	2	FACETS	0.602	0.528	0.681	0.602	0.528	0.681	SUBCLONAL	1	TRUE	1	0.441182089973082	2		605	565	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966020	18966020	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	29	419	0	ENST00000262803.5:c.1513A>G	p.Ile505Val	p.I505V	ENST00000262803	NM_002911.3	505	Atc/Gtc	11/24	1	2	FACETS	0.36	0.289	0.441	0.36	0.289	0.441	SUBCLONAL	1	TRUE	1	0.441182089973082	2		419	365	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256695	46256695	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773805737	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	115	570	0	ENST00000371998.3:c.751C>T	p.Arg251Cys	p.R251C	ENST00000371998		251	Cgc/Tgc	8/23	1	2	FACETS	0.663	0.597	0.733	0.663	0.597	0.733	SUBCLONAL	1	TRUE	1	0.441182089973082	2		570	786	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495717	72495717	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	120	461	0	ENST00000477973.2:c.355T>G	p.Cys119Gly	p.C119G	ENST00000477973	NM_012234.5	119	Tgc/Ggc	1/4	1	2	FACETS	0.701	0.633	0.773	0.701	0.633	0.773	SUBCLONAL	1	TRUE	1	0.441182089973082	2		461	776	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821005	32821005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1231820574	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	157	1232	2	ENST00000354258.4:c.589C>A	p.Pro197Thr	p.P197T	ENST00000354258	NM_000593.5	197	Cct/Act	1/11	0.139275353437569	4	FACETS	0.865	0.791	0.943	0.432	0.395	0.472	INDETERMINATE	1	TRUE	2	0.441182089973082	4		1234	1186	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553635	106553635	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	19	230	0	ENST00000369096.4:c.1600A>G	p.Thr534Ala	p.T534A	ENST00000369096	NM_001198.3	534	Acc/Gcc	5/7	0.139275353437569	4	FACETS	0.463	0.352	0.594	0.232	0.176	0.297	INDETERMINATE	1	TRUE	2	0.441182089973082	4		230	268	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92300789	92300789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001237-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	45	308	0	ENST00000265734.4:c.598G>A	p.Val200Met	p.V200M	ENST00000265734	NM_001259.6	200	Gtg/Atg	5/8	0.403684234840922	3	FACETS	0.571	0.48	0.671	0.286	0.24	0.336	SUBCLONAL	1	TRUE	1	0.441182089973082	3		308	436	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604533	43604533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs546866208	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	43	898	1	ENST00000355710.3:c.1118C>T	p.Ala373Val	p.A373V	ENST00000355710	NM_020975.4	373	gCg/gTg	6/20	1	2	FACETS	0.916	0.768	1	1	0.967	1	CLONAL	2	TRUE	1	0.12	2		899	391	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	12	317	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.174359356844771	3	FACETS	0.955	0.671	1	0.477	0.335	0.652	CLONAL	1	TRUE	1	0.12	3		317	222	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	10	198	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	1	0.815	1	1	0.815	1	CLONAL	1	TRUE	1	0.12	2		198	125	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021817	71021817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs797045586	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	14	292	0	ENST00000318789.4:c.1541G>A	p.Arg514His	p.R514H	ENST00000318789	NM_032682.5	514	cGt/cAt	18/21	1	2	FACETS	0.926	0.68	1	1	0.931	1	CLONAL	3	TRUE	1	0.12	2		292	84	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	48	569	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	0.905	0.773	1	1	0.981	1	CLONAL	4	TRUE	1	0.12	2		569	221	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16235967	16235967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	27	549	0	ENST00000375759.3:c.1033C>T	p.Arg345Cys	p.R345C	ENST00000375759	NM_015001.2	345	Cgc/Tgc	4/15	1	2	FACETS	0.865	0.691	1	1	0.946	1	CLONAL	2	TRUE	1	0.12	2		549	260	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797162	45797162	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	41	1075	0	ENST00000450313.1:c.1253A>G	p.Lys418Arg	p.K418R	ENST00000450313	NM_012222.2	418	aAg/aGg	13/16	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.12	2		1075	469	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458964	120458964	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	15	950	1	ENST00000256646.2:c.6381G>T	p.Lys2127Asn	p.K2127N	ENST00000256646	NM_024408.3	2127	aaG/aaT	34/34	1	2	FACETS	0.973	0.711	1	0.973	0.711	1	CLONAL	1	TRUE	1	0.12	2		951	257	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976508	25976508	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	13	371	1	ENST00000435504.4:c.1037G>A	p.Gly346Asp	p.G346D	ENST00000435504		346	gGt/gAt	11/13	1	2	FACETS	0.84	0.608	1	1	0.922	1	CLONAL	3	TRUE	1	0.12	2		372	86	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437692	52437692	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs201302700	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	56	905	0	ENST00000460680.1:c.1469A>G	p.Asn490Ser	p.N490S	ENST00000460680	NM_004656.3	490	aAt/aGt	13/17	1	2	FACETS	1	0.94	1	1	0.98	1	CLONAL	2	TRUE	1	0.12	2		905	395	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332829	153332829	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	24	625	0	ENST00000281708.4:c.127C>T	p.Gln43Ter	p.Q43*	ENST00000281708	NM_033632.3	43	Cag/Tag	2/12	1	2	FACETS	0.833	0.656	1	1	0.937	1	CLONAL	2	TRUE	1	0.12	2		625	240	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524993	187524993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371987657	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	25	811	0	ENST00000441802.2:c.10687G>A	p.Val3563Ile	p.V3563I	ENST00000441802	NM_005245.3	3563	Gtc/Atc	19/27	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.12	2		811	281	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165173	32165173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752105876	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	62	973	1	ENST00000375023.3:c.4955G>A	p.Arg1652His	p.R1652H	ENST00000375023	NM_004557.3	1652	cGc/cAc	27/30	0.174359356844771	3	FACETS	1	0.905	1	1	0.905	1	CLONAL	2	TRUE	1	0.12	3		974	517	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170565	108170565	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	12	500	0	ENST00000278616.4:c.5130G>A	p.Trp1710Ter	p.W1710*	ENST00000278616	NM_000051.3	1710	tgG/tgA	34/63	1	2	FACETS	0.794	0.561	1	1	0.875	1	CLONAL	2	TRUE	1	0.12	2		500	126	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377264	118377264	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	27	566	0	ENST00000534358.1:c.10657G>T	p.Gly3553Trp	p.G3553W	ENST00000534358	NM_005933.3	3553	Ggg/Tgg	27/36	1	2	FACETS	0.821	0.655	1	1	0.942	1	CLONAL	2	TRUE	1	0.12	2		566	274	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432289	432289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376128815	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	31	691	0	ENST00000399788.2:c.2234G>A	p.Arg745His	p.R745H	ENST00000399788	NM_001042603.1	745	cGt/cAt	16/28	0.174359356844771	1	FACETS	0.964	0.783	1	1	0.958	1	CLONAL	2	TRUE	0	0.12	1		691	252	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231437	46231437	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	21	280	2	ENST00000334344.6:c.1277C>T	p.Thr426Met	p.T426M	ENST00000334344	NM_152641.2	426	aCg/aTg	10/21	0.291112795048216	3	FACETS	0.847	0.659	1	1	0.891	1	CLONAL	3	TRUE	1	0.12	3		282	146	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46240657	46240657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757456378	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	13	392	0	ENST00000334344.6:c.1517C>T	p.Ala506Val	p.A506V	ENST00000334344	NM_152641.2	506	gCg/gTg	12/21	0.291112795048216	3	FACETS	0.87	0.625	1	0.87	0.625	1	CLONAL	2	TRUE	1	0.12	3		392	132	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225959	133225959	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs949243552	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	55	1087	0	ENST00000320574.5:c.3938C>T	p.Thr1313Met	p.T1313M	ENST00000320574	NM_006231.2	1313	aCg/aTg	31/49	0.174359356844771	1	FACETS	1	0.905	1	1	0.978	1	CLONAL	2	TRUE	0	0.12	1		1087	402	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880860	28880860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746322044	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	86	740	0	ENST00000282397.4:c.3770G>A	p.Arg1257His	p.R1257H	ENST00000282397	NM_002019.4	1257	cGc/cAc	29/30	0.291112795048216	3	FACETS	0.915	0.814	1	1	0.984	1	CLONAL	4	TRUE	1	0.12	3		740	415	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913027	32913027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358685	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	63	699	3	ENST00000380152.3:c.4535G>A	p.Arg1512His	p.R1512H	ENST00000380152		1512	cGt/cAt	11/27	0.291112795048216	3	FACETS	1	0.918	1	1	0.981	1	CLONAL	4	TRUE	1	0.12	3		702	261	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435420	110435420	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1049519615	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	243	757	2	ENST00000375856.3:c.2981C>T	p.Pro994Leu	p.P994L	ENST00000375856	NM_003749.2	994	cCg/cTg	1/2	0.291112795048216	3	FACETS	1	0.943	1	1	0.996	1	CLONAL	6	TRUE	1	0.12	3		759	712	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934842	9934842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	19	657	0	ENST00000330684.3:c.1448G>A	p.Gly483Glu	p.G483E	ENST00000330684	NM_001134407.1	483	gGg/gAg	6/13	1	2	FACETS	0.847	0.646	1	1	0.923	1	CLONAL	2	TRUE	1	0.12	2		657	187	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646867	23646867	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	16	721	0	ENST00000261584.4:c.1000T>C	p.Tyr334His	p.Y334H	ENST00000261584	NM_024675.3	334	Tac/Cac	4/13	1	2	FACETS	0.871	0.648	1	1	0.913	1	CLONAL	2	TRUE	1	0.12	2		721	153	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849514	68849514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs36087757	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	36	739	1	ENST00000261769.5:c.1417G>A	p.Val473Ile	p.V473I	ENST00000261769	NM_004360.3	473	Gtc/Atc	10/16	1	2	FACETS	0.952	0.785	1	1	0.963	1	CLONAL	2	TRUE	1	0.12	2		740	315	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098455	11098455	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1361910224	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	39	607	2	ENST00000358026.2:c.973G>A	p.Val325Met	p.V325M	ENST00000358026	NM_001128849.1	325	Gtg/Atg	6/36	1	2	FACETS	1	0.891	1	1	0.97	1	CLONAL	2	TRUE	1	0.12	2		609	297	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132438	11132438	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794284	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	52	973	2	ENST00000358026.2:c.2654G>A	p.Arg885His	p.R885H	ENST00000358026	NM_001128849.1	885	cGc/cAc	19/36	1	2	FACETS	1	0.931	1	1	0.978	1	CLONAL	2	TRUE	1	0.12	2		975	374	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478633	57478633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1131691999	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	41	664	0	ENST00000371085.3:c.305C>T	p.Ala102Val	p.A102V	ENST00000371085	NM_000516.4	102	gCg/gTg	4/13	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.12	2		664	462	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24135758	24135758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	29	578	0	ENST00000263121.7:c.245C>T	p.Thr82Met	p.T82M	ENST00000263121	NM_003073.3	82	aCg/aTg	3/9	1	2	FACETS	0.806	0.648	0.984	1	0.944	1	CLONAL	2	TRUE	1	0.12	2		578	300	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402216	402217	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	46	839	0	ENST00000399788.2:c.4574dup	p.Glu1526GlyfsTer9	p.E1526Gfs*9	ENST00000399788	NM_001042603.1	1525	aag/aaAg	27/28	0.174359356844771	1	FACETS	1	0.939	1	1	0.976	1	CLONAL	2	TRUE	0	0.12	1		839	293	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2229791	2229791	+	stop_lost	Nonstop_Mutation	SNP	G	G	T	novel	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	48	834	0	ENST00000398665.3:c.4614G>T	p.Ter1538TyrextTer63	p.*1538Yext*63	ENST00000398665	NM_032482.2	1538	taG/taT	28/28	1	2	FACETS	0.897	0.759	1	1	0.97	1	CLONAL	2	TRUE	1	0.12	2		834	446	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966873	25966873	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1271466699	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	39	703	3	ENST00000435504.4:c.2333del	p.Pro778GlnfsTer21	p.P778Qfs*21	ENST00000435504		778	cCa/ca	13/13	1	2	FACETS	1	0.886	1	1	0.969	1	CLONAL	2	TRUE	1	0.12	2		706	300	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845934	72845934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759043061	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	13	510	0	ENST00000268489.5:c.3533C>T	p.Ser1178Leu	p.S1178L	ENST00000268489	NM_006885.3	1178	tCg/tTg	6/10	1	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	TRUE	1	0.12	2		510	167	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884648	111884648	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1266852479	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	34	629	0	ENST00000341259.2:c.824T>C	p.Phe275Ser	p.F275S	ENST00000341259	NM_005475.2	275	tTt/tCt	3/8	0.291112795048216	3	FACETS	0.998	0.818	1	0.998	0.818	1	CLONAL	2	TRUE	1	0.12	3		629	301	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459672	40459672	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1286424849	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	50	900	1	ENST00000345506.4:c.1837G>A	p.Gly613Arg	p.G613R	ENST00000345506	NM_003152.3	613	Ggg/Agg	16/20	1	2	FACETS	0.847	0.719	0.987	1	0.969	1	CLONAL	2	TRUE	1	0.12	2		901	492	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256695	46256695	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773805737	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	27	570	0	ENST00000371998.3:c.751C>T	p.Arg251Cys	p.R251C	ENST00000371998		251	Cgc/Tgc	8/23	1	2	FACETS	1	0.861	1	1	0.957	1	CLONAL	2	TRUE	1	0.12	2		570	205	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821005	32821005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1231820574	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	63	1232	2	ENST00000354258.4:c.589C>A	p.Pro197Thr	p.P197T	ENST00000354258	NM_000593.5	197	Cct/Act	1/11	0.174359356844771	3	FACETS	0.846	0.731	0.971	0.846	0.731	0.971	CLONAL	2	TRUE	1	0.12	3		1234	658	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299832	15299832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465285176	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	79	1085	2	ENST00000263388.2:c.1346G>A	p.Arg449His	p.R449H	ENST00000263388	NM_000435.2	449	cGc/cAc	8/33	1	2	FACETS	1	0.951	1	1	0.985	1	CLONAL	2	TRUE	1	0.12	2		1087	570	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209086	133209086	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	16	579	0	ENST00000320574.5:c.6145A>G	p.Thr2049Ala	p.T2049A	ENST00000320574	NM_006231.2	2049	Acc/Gcc	45/49	0.174359356844771	1	FACETS	0.798	0.594	1	1	0.904	1	CLONAL	2	TRUE	0	0.12	1		579	157	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100399	8100399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs535492085	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	52	1062	0	ENST00000346208.3:c.373G>A	p.Gly125Ser	p.G125S	ENST00000346208		125	Ggc/Agc	3/6	1	2	FACETS	1	0.894	1	1	0.976	1	CLONAL	2	TRUE	1	0.12	2		1062	409	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163768	72163768	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	24	596	0	ENST00000357731.5:c.590A>G	p.Gln197Arg	p.Q197R	ENST00000357731	NM_173808.2	197	cAg/cGg	4/7	1	2	FACETS	1	0.812	1	1	0.949	1	CLONAL	2	TRUE	1	0.12	2		596	194	SUCCESS
FH	2271	MSKCC	GRCh37	1	241672024	241672024	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	14	519	0	ENST00000366560.3:c.617T>C	p.Val206Ala	p.V206A	ENST00000366560	NM_000143.3	206	gTa/gCa	5/10	1	2	FACETS	0.877	0.639	1	1	0.903	1	CLONAL	2	TRUE	1	0.12	2		519	133	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435520	110435520	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	89	769	0	ENST00000375856.3:c.2881G>T	p.Gly961Cys	p.G961C	ENST00000375856	NM_003749.2	961	Ggc/Tgc	1/2	0.291112795048216	3	FACETS	0.888	0.789	0.994	1	0.973	1	CLONAL	3	TRUE	1	0.12	3		769	590	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937188	76937188	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	31	321	0	ENST00000373344.5:c.3560A>G	p.Asn1187Ser	p.N1187S	ENST00000373344	NM_000489.3	1187	aAc/aGc	9/35	0.3	2	FACETS	1	0.831	1	1	0.962	1	CLONAL	4	TRUE	0	0.12	2		321	128	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860136	152860136	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	44	422	0	ENST00000406277.2:c.292T>C	p.Tyr98His	p.Y98H	ENST00000406277	NM_152274.4	98	Tac/Cac	5/7	0.3		FACETS		0.81	1				CLONAL	3	TRUE	0	0.12	2		422	255	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	58	324	0				ENST00000310581	NM_198253.2	-/1132			0.355394293168701	3	FACETS	0.674	0.583	0.772	0.225	0.194	0.258	INDETERMINATE	1	TRUE	0	0.74778954796199	3		324	316	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	360	483	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	0.74778954796199	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.74778954796199	3		483	656	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245759	41245759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55650082	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	158	505	1	ENST00000357654.3:c.1789G>A	p.Glu597Lys	p.E597K	ENST00000357654	NM_007294.3	597	Gaa/Aaa	10/23	0.64422848105928	3	FACETS	0.991	0.912	1			1	CLONAL	1	TRUE	NA	0.74778954796199	3		506	586	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961011	15961011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142717545	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	240	528	2	ENST00000268712.3:c.6209C>T	p.Ser2070Leu	p.S2070L	ENST00000268712	NM_006311.3	2070	tCg/tTg	40/46	0.74778954796199	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.74778954796199	1		530	352	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882319	89882319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	240	702	0	ENST00000389301.3:c.155G>A	p.Arg52Gln	p.R52Q	ENST00000389301	NM_000135.2	52	cGa/cAa	2/43	0.511610169170821	4	FACETS	1	0.969	1	0.355	0.331	0.379	CLONAL	1	TRUE	1	0.74778954796199	4		702	1054	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610503	81610503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137908024	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	94	632	0	ENST00000298171.2:c.2101C>T	p.Arg701Cys	p.R701C	ENST00000298171	NM_000369.2	701	Cgc/Tgc	10/10	0.48617131032752	1	FACETS	0.391	0.35	0.434	0.391	0.35	0.434	SUBCLONAL	1	TRUE	0	0.74778954796199	1		632	403	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781386	135781386	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203549	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	684	982	3	ENST00000298552.3:c.1579C>T	p.Gln527Ter	p.Q527*	ENST00000298552	NM_001162426.1	527	Cag/Tag	15/23	0.74778954796199	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.74778954796199	2		985	887	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005276	150005276	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	186	550	0	ENST00000253339.5:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000253339		317	Cag/Tag	3/7	0.74778954796199	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.74778954796199	1		550	296	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577543	7577543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1019340046	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	358	625	2	ENST00000269305.4:c.738G>A	p.Met246Ile	p.M246I	ENST00000269305	NM_001126112.2	246	atG/atA	7/11	0.74778954796199	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.74778954796199	1		627	511	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11290981	11290981	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	89	524	0	ENST00000361445.4:c.2779+1G>T		p.X927_splice	ENST00000361445	NM_004958.3	927			NA	2	FACETS	0.686	0.613	0.762			1	INDETERMINATE	1	TRUE	NA	0.74778954796199	2		524	347	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245959	16245959	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	107	699	0	ENST00000375759.3:c.1582G>C	p.Val528Leu	p.V528L	ENST00000375759	NM_015001.2	528	Gtg/Ctg	8/15	0.64422848105928	3	FACETS	0.454	0.407	0.504			1	SUBCLONAL	1	TRUE	NA	0.74778954796199	3		699	866	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335035	65335035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	91	529	0	ENST00000342505.4:c.606G>A	p.Met202Ile	p.M202I	ENST00000342505	NM_002227.2	202	atG/atA	6/25	NA	2	FACETS	0.569	0.508	0.633			1	INDETERMINATE	1	TRUE	NA	0.74778954796199	2		529	428	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47709975	47709975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	221	577	0	ENST00000233146.2:c.2692G>A	p.Glu898Lys	p.E898K	ENST00000233146	NM_000251.2	898	Gaa/Aaa	16/16	0.64422848105928	3	FACETS	1	0.99	1			1	CLONAL	1	TRUE	NA	0.74778954796199	3		577	626	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149011	61149011	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	274	555	0	ENST00000295025.8:c.1201C>T	p.His401Tyr	p.H401Y	ENST00000295025	NM_002908.2	401	Cat/Tat	11/11	0.64422848105928	3	FACETS	0.756	0.714	0.798			1	SUBCLONAL	2	TRUE	NA	0.74778954796199	3		555	666	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198264830	198264830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	538	600	0	ENST00000335508.6:c.2962G>A	p.Glu988Lys	p.E988K	ENST00000335508	NM_012433.2	988	Gaa/Aaa	20/25	0.252173072589547	5	FACETS	0.948	0.92	0.976			1	INDETERMINATE	4	TRUE	NA	0.74778954796199	5		600	805	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266484	198266484	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	66	459	0	ENST00000335508.6:c.2352G>C	p.Met784Ile	p.M784I	ENST00000335508	NM_012433.2	784	atG/atC	16/25	0.252173072589547	5	FACETS	0.64	0.556	0.732			1	INDETERMINATE	1	TRUE	NA	0.74778954796199	5		459	585	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732930	30732930	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	540	426	0	ENST00000295754.5:c.1543G>C	p.Glu515Gln	p.E515Q	ENST00000295754	NM_003242.5	515	Gag/Cag	7/7	0.643591741618606	5	FACETS	0.94	0.905	0.974			1	CLONAL	3	TRUE	NA	0.74778954796199	5		426	1087	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643341	52643341	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	302	437	0	ENST00000394830.3:c.2555G>T	p.Arg852Ile	p.R852I	ENST00000394830	NM_018313.4	852	aGa/aTa	17/30	0.526670204734407	2	FACETS	0.821	0.786	0.856	0.821	0.786	0.856	CLONAL	2	TRUE	0	0.74778954796199	2		437	492	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643822	52643822	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1227600181	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	263	462	0	ENST00000394830.3:c.2074G>C	p.Glu692Gln	p.E692Q	ENST00000394830	NM_018313.4	692	Gag/Cag	17/30	0.526670204734407	2	FACETS	0.763	0.726	0.799	0.763	0.726	0.799	SUBCLONAL	2	TRUE	0	0.74778954796199	2		462	461	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643864	52643864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1422119249	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	219	367	0	ENST00000394830.3:c.2032C>T	p.Arg678Cys	p.R678C	ENST00000394830	NM_018313.4	678	Cgc/Tgc	17/30	0.526670204734407	2	FACETS	0.757	0.716	0.797	0.757	0.716	0.797	SUBCLONAL	2	TRUE	0	0.74778954796199	2		367	387	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917612	178917612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	134	450	0	ENST00000263967.3:c.487G>A	p.Ala163Thr	p.A163T	ENST00000263967	NM_006218.2	163	Gca/Aca	3/21	0.503506382964737	5	FACETS	1	0.918	1			1	CLONAL	1	TRUE	NA	0.74778954796199	5		450	753	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808975	1808975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458621673	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	47	387	1	ENST00000260795.2:c.2407G>A	p.Gly803Ser	p.G803S	ENST00000260795		803	Ggc/Agc	17/17	0.525556125899979	2	FACETS	0.274	0.231	0.322	0.137	0.115	0.161	SUBCLONAL	1	TRUE	0	0.74778954796199	2		388	458	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007340	143007340	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	65	348	0	ENST00000262992.4:c.2444C>G	p.Ser815Cys	p.S815C	ENST00000262992	NM_001101669.1	815	tCc/tGc	22/24	0.676996341503866	2	FACETS	0.591	0.517	0.67	0.296	0.258	0.335	SUBCLONAL	1	TRUE	0	0.74778954796199	2		348	294	SUCCESS
APC	324	MSKCC	GRCh37	5	112175517	112175517	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	58	464	0	ENST00000257430.4:c.4226C>G	p.Pro1409Arg	p.P1409R	ENST00000257430	NM_000038.5	1409	cCa/cGa	16/16	0.706888482461665	2	FACETS	0.458	0.395	0.525	0.229	0.197	0.263	SUBCLONAL	1	TRUE	0	0.74778954796199	2		464	339	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515151	149515151	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558122968	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	52	534	1	ENST00000261799.4:c.331G>A	p.Asp111Asn	p.D111N	ENST00000261799	NM_002609.3	111	Gat/Aat	3/23	0.74778954796199	3	FACETS	0.236	0.2	0.275	0.079	0.066	0.092	SUBCLONAL	1	TRUE	0	0.74778954796199	3		535	810	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184781	32184781	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs762081312	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	258	565	0	ENST00000375023.3:c.1802G>C	p.Gly601Ala	p.G601A	ENST00000375023	NM_004557.3	601	gGa/gCa	11/30	0.249567569351671	2	FACETS	0.753	0.716	0.79	0.753	0.716	0.79	INDETERMINATE	2	TRUE	0	0.74778954796199	2		565	458	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112035558	112035558	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	87	651	0	ENST00000368678.4:c.336G>C	p.Leu112Phe	p.L112F	ENST00000368678		112	ttG/ttC	4/13	0.501351803579806	3	FACETS	0.406	0.359	0.456			1	SUBCLONAL	1	TRUE	NA	0.74778954796199	3		651	788	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522418	157522418	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	240	409	0	ENST00000346085.5:c.4690G>C	p.Glu1564Gln	p.E1564Q	ENST00000346085	NM_020732.3	1564	Gag/Cag	18/20	0.74778954796199	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.74778954796199	1		409	381	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224296	55224296	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	102	506	0	ENST00000275493.2:c.1077C>G	p.Phe359Leu	p.F359L	ENST00000275493	NM_005228.3	359	ttC/ttG	9/28	0.477531316742419	4	FACETS	0.614	0.549	0.684			1	SUBCLONAL	1	TRUE	NA	0.74778954796199	4		506	776	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411999	116411999	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	111	489	0	ENST00000397752.3:c.2984T>C	p.Met995Thr	p.M995T	ENST00000397752	NM_000245.2	995	aTg/aCg	14/21	0.290959006122503	4	FACETS	0.83	0.748	0.917	0.415	0.374	0.459	INDETERMINATE	1	TRUE	2	0.74778954796199	4		489	625	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201854	67201854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	181	432	0	ENST00000312629.5:c.1054G>C	p.Glu352Gln	p.E352Q	ENST00000312629	NM_003952.2	352	Gag/Cag	13/15	0.610295629798864	4	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.74778954796199	4		432	669	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988153	85988153	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	250	619	1	ENST00000263360.6:c.1098G>T	p.Met366Ile	p.M366I	ENST00000263360	NM_003797.3	366	atG/atT	10/12	0.355394293168701	3	FACETS	1	0.99	1	0.42	0.394	0.446	INDETERMINATE	1	TRUE	0	0.74778954796199	3		620	729	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343883	118343883	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	73	420	0	ENST00000534358.1:c.2009C>G	p.Ser670Cys	p.S670C	ENST00000534358	NM_005933.3	670	tCt/tGt	3/36	0.355394293168701	3	FACETS	0.488	0.427	0.553	0.163	0.142	0.185	INDETERMINATE	1	TRUE	0	0.74778954796199	3		420	550	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125513776	125513776	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	356	621	0	ENST00000428830.2:c.904C>G	p.Pro302Ala	p.P302A	ENST00000428830	NM_001114121.2	302	Cca/Gca	9/14	0.355394293168701	3	FACETS	1	0.972	1	0.679	0.65	0.708	INDETERMINATE	2	TRUE	0	0.74778954796199	3		621	642	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025527	1025527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	157	630	0	ENST00000358495.3:c.848C>T	p.Ser283Leu	p.S283L	ENST00000358495	NM_134424.2	283	tCa/tTa	9/12	0.64422848105928	3	FACETS	0.66	0.605	0.718			1	SUBCLONAL	1	TRUE	NA	0.74778954796199	3		630	874	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433059	49433059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	286	639	1	ENST00000301067.7:c.8312G>A	p.Arg2771Gln	p.R2771Q	ENST00000301067	NM_003482.3	2771	cGa/cAa	33/54	0.74778954796199	3	FACETS	1	0.981	1	0.548	0.516	0.581	CLONAL	1	TRUE	1	0.74778954796199	3		640	959	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445068	49445068	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	120	242	1	ENST00000301067.7:c.2398C>T	p.Gln800Ter	p.Q800*	ENST00000301067	NM_003482.3	800	Cag/Tag	10/54	0.74778954796199	3	FACETS	1	0.956	1	0.54	0.492	0.59	CLONAL	1	TRUE	1	0.74778954796199	3		243	408	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445649	49445649	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	342	849	0	ENST00000301067.7:c.1817C>G	p.Ser606Cys	p.S606C	ENST00000301067	NM_003482.3	606	tCt/tGt	10/54	0.74778954796199	3	FACETS	0.809	0.764	0.856	0.405	0.382	0.428	CLONAL	1	TRUE	1	0.74778954796199	3		849	1553	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861912	57861912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs925036184	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	271	985	4	ENST00000228682.2:c.1213C>T	p.Arg405Trp	p.R405W	ENST00000228682	NM_005269.2	405	Cgg/Tgg	10/12	0.74778954796199	3	FACETS	0.807	0.756	0.859	0.403	0.378	0.43	CLONAL	1	TRUE	1	0.74778954796199	3		989	1234	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109807	115109807	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	521	518	0	ENST00000257566.3:c.2071G>C	p.Glu691Gln	p.E691Q	ENST00000257566	NM_016569.3	691	Gaa/Caa	8/8	0.74778954796199	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.74778954796199	2		518	646	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895678	28895678	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	178	625	0	ENST00000282397.4:c.3096G>C	p.Glu1032Asp	p.E1032D	ENST00000282397	NM_002019.4	1032	gaG/gaC	23/30	0.741738619846104	2	FACETS	0.914	0.849	0.98	0.457	0.424	0.49	CLONAL	1	TRUE	0	0.74778954796199	2		625	521	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914967	32914967	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398122558	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	695	925	0	ENST00000380152.3:c.6475C>T	p.Gln2159Ter	p.Q2159*	ENST00000380152		2159	Caa/Taa	11/27	0.741738619846104	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.74778954796199	2		925	883	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528021	103528021	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	66	336	0	ENST00000355739.4:c.3329T>C	p.Leu1110Ser	p.L1110S	ENST00000355739	NM_000123.3	1110	tTa/tCa	15/15	0.74778954796199	1	FACETS	0.462	0.406	0.521	0.462	0.406	0.521	SUBCLONAL	1	TRUE	0	0.74778954796199	1		336	239	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872446	35872446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1167027301	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	148	832	3	ENST00000216797.5:c.457G>A	p.Glu153Lys	p.E153K	ENST00000216797	NM_020529.2	153	Gag/Aag	3/6	0.618789085519342	3	FACETS	0.468	0.427	0.512	0.234	0.213	0.256	SUBCLONAL	1	TRUE	1	0.74778954796199	3		835	1161	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609879	81609879	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	59	371	0	ENST00000298171.2:c.1477G>C	p.Gly493Arg	p.G493R	ENST00000298171	NM_000369.2	493	Ggg/Cgg	10/10	0.48617131032752	1	FACETS	0.408	0.355	0.465	0.408	0.355	0.465	SUBCLONAL	1	TRUE	0	0.74778954796199	1		371	242	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95584000	95584000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777894117	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	79	338	0	ENST00000393063.1:c.1468C>T	p.Arg490Cys	p.R490C	ENST00000393063	NM_030621.3	490	Cgc/Tgc	10/28	0.48617131032752	1	FACETS	0.466	0.414	0.52	0.466	0.414	0.52	SUBCLONAL	1	TRUE	0	0.74778954796199	1		338	284	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41001226	41001226	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	261	699	1	ENST00000267868.3:c.347G>A	p.Gly116Glu	p.G116E	ENST00000267868	NM_002875.4	116	gGa/gAa	5/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.74778954796199	2		700	661	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14028072	14028072	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	81	453	0	ENST00000311895.7:c.1126G>C	p.Glu376Gln	p.E376Q	ENST00000311895	NM_005236.2	376	Gaa/Caa	7/11	0.610295629798864	4	FACETS	0.49	0.431	0.553			1	SUBCLONAL	1	TRUE	NA	0.74778954796199	4		453	773	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56866264	56866264	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1374778377	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	185	879	0	ENST00000308159.5:c.1309C>G	p.Leu437Val	p.L437V	ENST00000308159	NM_014669.4	437	Ctc/Gtc	12/22	0.618789085519342	3	FACETS	0.804	0.743	0.867	0.402	0.371	0.434	CLONAL	1	TRUE	1	0.74778954796199	3		879	846	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993491	72993491	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144613545	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	602	872	5	ENST00000268489.5:c.554C>T	p.Ser185Leu	p.S185L	ENST00000268489	NM_006885.3	185	tCg/tTg	2/10	0.618789085519342	3	FACETS	0.954	0.922	0.987	0.954	0.922	0.987	CLONAL	2	TRUE	1	0.74778954796199	3		877	1159	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89880961	89880961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	260	642	0	ENST00000389301.3:c.250G>A	p.Glu84Lys	p.E84K	ENST00000389301	NM_000135.2	84	Gag/Aag	3/43	0.511610169170821	4	FACETS	1	0.966	1	0.349	0.327	0.373	CLONAL	1	TRUE	1	0.74778954796199	4		642	1160	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89880970	89880970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	258	668	3	ENST00000389301.3:c.241G>A	p.Asp81Asn	p.D81N	ENST00000389301	NM_000135.2	81	Gac/Aac	3/43	0.511610169170821	4	FACETS	1	0.943	1	0.336	0.314	0.359	CLONAL	1	TRUE	1	0.74778954796199	4		671	1196	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004580	16004580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	222	359	1	ENST00000268712.3:c.2674G>A	p.Glu892Lys	p.E892K	ENST00000268712	NM_006311.3	892	Gag/Aag	20/46	0.74778954796199	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.74778954796199	1		360	329	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004874	16004874	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	246	549	0	ENST00000268712.3:c.2380G>C	p.Glu794Gln	p.E794Q	ENST00000268712	NM_006311.3	794	Gag/Cag	20/46	0.74778954796199	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.74778954796199	1		549	360	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618619	37618619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	347	493	5	ENST00000447079.4:c.295C>T	p.Arg99Cys	p.R99C	ENST00000447079	NM_015083.1	99	Cgt/Tgt	1/14	0.741575443227311	5	FACETS	1	0.969	1			1	CLONAL	2	TRUE	NA	0.74778954796199	5		498	957	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226534	41226534	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	153	448	0	ENST00000357654.3:c.4489T>C	p.Ser1497Pro	p.S1497P	ENST00000357654	NM_007294.3	1497	Tcc/Ccc	14/23	0.64422848105928	3	FACETS	1	0.96	1			1	CLONAL	1	TRUE	NA	0.74778954796199	3		448	527	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774181	56774181	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	308	665	0	ENST00000337432.4:c.532C>G	p.Gln178Glu	p.Q178E	ENST00000337432	NM_058216.2	178	Cag/Gag	3/9	0.736218102315705	5	FACETS	1	0.951	1	0.67	0.634	0.707	CLONAL	2	TRUE	2	0.74778954796199	5		665	869	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899277	78899277	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	80	323	0	ENST00000306801.3:c.2916G>C	p.Met972Ile	p.M972I	ENST00000306801	NM_020761.2	972	atG/atC	24/34	0.74778954796199	1	FACETS	0.381	0.337	0.426	0.381	0.337	0.426	SUBCLONAL	1	TRUE	0	0.74778954796199	1		323	352	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584560	48584560	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	169	542	0	ENST00000342988.3:c.733C>A	p.Gln245Lys	p.Q245K	ENST00000342988	NM_005359.5	245	Cag/Aag	6/12	1	2	FACETS	0.893	0.828	0.961	0.893	0.828	0.961	CLONAL	1	TRUE	1	0.74778954796199	2		542	506	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798148	42798148	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	249	634	0	ENST00000575354.2:c.4102G>C	p.Glu1368Gln	p.E1368Q	ENST00000575354	NM_015125.3	1368	Gag/Cag	17/20	0.39714985576849	6	FACETS	1	0.992	1	0.355	0.331	0.379	INDETERMINATE	1	TRUE	2	0.74778954796199	6		634	1171	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45864863	45864863	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1426	323	881	0	ENST00000391945.4:c.1156C>G	p.Leu386Val	p.L386V	ENST00000391945	NM_000400.3	386	Ctg/Gtg	12/23	0.39714985576849	6	FACETS	1	0.99	1	0.308	0.29	0.327	INDETERMINATE	1	TRUE	2	0.74778954796199	6		881	1749	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912392	50912392	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	695	782	0	ENST00000440232.2:c.1906C>T	p.Gln636Ter	p.Q636*	ENST00000440232	NM_002691.3	636	Cag/Tag	16/27	0.39714985576849	6	FACETS	0.932	0.904	0.96	0.932	0.904	0.96	INDETERMINATE	4	TRUE	2	0.74778954796199	6		782	1244	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747096	40747096	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	79	488	0	ENST00000373198.4:c.2986C>T	p.Gln996Ter	p.Q996*	ENST00000373198	NM_133170.3	996	Cag/Tag	22/32	0.74778954796199	3	FACETS	0.406	0.357	0.459	0.135	0.119	0.153	SUBCLONAL	1	TRUE	0	0.74778954796199	3		488	715	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980872	40980872	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	99	471	0	ENST00000373198.4:c.1614G>C	p.Gln538His	p.Q538H	ENST00000373198	NM_133170.3	538	caG/caC	10/32	0.74778954796199	3	FACETS	0.515	0.459	0.573	0.172	0.153	0.191	SUBCLONAL	1	TRUE	0	0.74778954796199	3		471	707	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164697	36164697	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	259	645	0	ENST00000300305.3:c.1178G>C	p.Gly393Ala	p.G393A	ENST00000300305		393	gGa/gCa	8/8	0.249567569351671	2	FACETS	0.821	0.771	0.872	0.41	0.385	0.436	INDETERMINATE	1	TRUE	0	0.74778954796199	2		645	844	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252928	36252928	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	157	407	0	ENST00000300305.3:c.434G>C	p.Arg145Thr	p.R145T	ENST00000300305		145	aGa/aCa	4/8	0.249567569351671	2	FACETS	0.758	0.698	0.82	0.379	0.349	0.41	INDETERMINATE	1	TRUE	0	0.74778954796199	2		407	554	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259331	36259331	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	64	257	0	ENST00000300305.3:c.160G>C	p.Glu54Gln	p.E54Q	ENST00000300305		54	Gag/Cag	3/8	0.249567569351671	2	FACETS	0.374	0.324	0.427	0.187	0.162	0.214	INDETERMINATE	1	TRUE	0	0.74778954796199	2		257	458	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288422	21288422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1421511528	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	186	561	0	ENST00000354336.3:c.667C>T	p.Pro223Ser	p.P223S	ENST00000354336	NM_005207.3	223	Cct/Tct	2/3	0.64422848105928	3	FACETS	1	0.948	1			1	CLONAL	1	TRUE	NA	0.74778954796199	3		561	665	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184055	123184055	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	224	357	0	ENST00000218089.9:c.913C>G	p.Arg305Gly	p.R305G	ENST00000218089	NM_001042749.1	305	Cga/Gga	11/35	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.74778954796199	1		357	318	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251885	8251904	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGGAGCCCACCTCGCCCA	GGTGGAGCCCACCTCGCCCA	-	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	33	620	0	ENST00000335790.3:c.173_192del	p.Leu58ProfsTer79	p.L58Pfs*79	ENST00000335790	NM_002315.2	58	cTGGGCGAGGTGGGCTCCACC/c	2/4	0.74778954796199	2	FACETS	0.164	0.133	0.199	0.082	0.066	0.1	SUBCLONAL	1	TRUE	0	0.74778954796199	2		620	538	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344757	118344758	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	111	695	2	ENST00000534358.1:c.2885_2886del	p.Ile962LysfsTer35	p.I962Kfs*35	ENST00000534358	NM_005933.3	961	ctTAta/ctta	3/36	0.355394293168701	3	FACETS	0.514	0.462	0.57	0.171	0.154	0.19	INDETERMINATE	1	TRUE	0	0.74778954796199	3		697	793	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647325	23647341	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTCCTGTTCCTTTAG	TCTTCCTGTTCCTTTAG	-	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	75	478	0	ENST00000261584.4:c.526_542del	p.Leu176AsnfsTer3	p.L176Nfs*3	ENST00000261584	NM_024675.3	176	CTAAAGGAACAGGAAGAa/a	4/13	0.610295629798864	4	FACETS	0.595	0.522	0.674			1	SUBCLONAL	1	TRUE	NA	0.74778954796199	4		478	589	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445293	49445293	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	203	545	0	ENST00000301067.7:c.2173del	p.Leu725CysfsTer205	p.L725Cfs*205	ENST00000301067	NM_003482.3	725	Ctg/tg	10/54	0.74778954796199	3	FACETS	0.71	0.658	0.764	0.355	0.329	0.382	SUBCLONAL	1	TRUE	1	0.74778954796199	3		545	1051	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180049797	180049878	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGCAGACACGTTGGCATTCTGGATCACCAGCTTGCTCACAGTCTGGGAGAGCACAGGCACAAGGATCCATTTCCTGCCCAA	TGGCAGACACGTTGGCATTCTGGATCACCAGCTTGCTCACAGTCTGGGAGAGCACAGGCACAAGGATCCATTTCCTGCCCAA	G	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	55	710	0	ENST00000261937.6:c.1549-39_1591delinsC		p.X517_splice	ENST00000261937	NM_182925.4	517		12/30	NA	2	FACETS	0.266	0.227	0.308			1	INDETERMINATE	1	TRUE	NA	0.74778954796199	2		710	554	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821927	59821952	+	splice_acceptor_variant,frameshift_variant,intron_variant	Splice_Site	INS	CAACGTTCTTTTAATTTTTCTAATAA	CAACGTTCTTTTAATTTTTCTAATAA	TAAAGAGGGGAAAGAAAAAAATGATAAACCAGTAGAGAG	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	76	477	0	ENST00000259008.2:c.2098_2123delinsCTCTCTACTGGTTTATCATTTTTTTCTTTCCCCTCTTTA		p.X700_splice	ENST00000259008	NM_032043.2	700	TTATTAGAAAAATTAAAAGAACGTTGg/CTCTCTACTGGTTTATCATTTTTTTCTTTCCCCTCTTTAg	15/20	0.736218102315705	5	FACETS	0.412	0.36	0.468	0.137	0.12	0.156	SUBCLONAL	1	TRUE	2	0.74778954796199	5		477	1048	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759441	133759501	+	protein_altering_variant	In_Frame_Del	DEL	GCGCCTTCTCCCCAAAGACAAAAAGACCAACTTGTTCAGCGCCTTGATCAAGAAGAAGAAG	GCGCCTTCTCCCCAAAGACAAAAAGACCAACTTGTTCAGCGCCTTGATCAAGAAGAAGAAG	CAGCCCCAACCCCTCCCAA	novel	NA	P-0006124-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	98	892	0	ENST00000318560.5:c.1764_1824delinsCAGCCCCAACCCCTCCCAA	p.Glu588_Lys608delinsAspSerProAsnProSerGln	p.E588_K608delinsDSPNPSQ	ENST00000318560	NM_005157.4	588	gaGCGCCTTCTCCCCAAAGACAAAAAGACCAACTTGTTCAGCGCCTTGATCAAGAAGAAGAAG/gaCAGCCCCAACCCCTCCCAA	11/11	0.74778954796199				0.278	0.349				SUBCLONAL	1	TRUE	0	0.74778954796199	2		892	840	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0006313-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	36	440	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.229424738264263	3	FACETS	0.762	0.626	0.914	0.381	0.313	0.457	CLONAL	1	TRUE	1	0.23	3		440	458	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0006313-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	39	416	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	1	2	FACETS	0.953	0.791	1	0.953	0.791	1	CLONAL	1	TRUE	1	0.23	2		416	356	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858910	243858910	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006313-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	27	355	0	ENST00000263826.5:c.155A>T	p.Asn52Ile	p.N52I	ENST00000263826	NM_005465.4	52	aAc/aTc	2/13	1	2	FACETS	0.755	0.602	0.93	0.755	0.602	0.93	CLONAL	1	TRUE	1	0.23	2		355	311	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118941	115118941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	172	58	0	ENST00000257566.3:c.400C>T	p.Pro134Ser	p.P134S	ENST00000257566	NM_016569.3	134	Cct/Tct	2/8	0.289899145836961	11	FACETS	0.948	0.883	1			1	CLONAL	7	FALSE	NA	0.289899145836961	11		58	412	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966939	25966939	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	123	124	0	ENST00000435504.4:c.2267C>G	p.Thr756Ser	p.T756S	ENST00000435504		756	aCc/aGc	13/13	1	2	FACETS	0.884	0.811	0.959	1	0.992	1	CLONAL	3	FALSE	1	0.289899145836961	2		124	320	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662832	227662832	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009286-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	166	161	0	ENST00000305123.5:c.623T>C	p.Leu208Pro	p.L208P	ENST00000305123	NM_005544.2	208	cTg/cCg	1/2	1	2	FACETS	1	0.979	1	1	0.993	1	CLONAL	2	FALSE	1	0.289899145836961	2		161	496	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	74	330	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.959	0.842	1	0.959	0.842	1	CLONAL	1	TRUE	1	0.331845624576036	2		330	465	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0009613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	69	366	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.331845624576036	2		366	350	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88651982	88651982	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	60	354	0	ENST00000372037.3:c.329G>T	p.Cys110Phe	p.C110F	ENST00000372037	NM_004329.2	110	tGc/tTc	5/13	0.331845624576036	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.331845624576036	1		354	272	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653803	89653803	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554893773	NA	P-0009613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	67	380	0	ENST00000371953.3:c.101C>T	p.Ala34Val	p.A34V	ENST00000371953	NM_000314.4	34	gCt/gTt	2/9	0.331845624576036	1	FACETS	0.999	0.874	1	0.999	0.874	1	CLONAL	1	TRUE	0	0.331845624576036	1		380	337	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610503	81610503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137908024	NA	P-0009613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	85	632	0	ENST00000298171.2:c.2101C>T	p.Arg701Cys	p.R701C	ENST00000298171	NM_000369.2	701	Cgc/Tgc	10/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.331845624576036	2		632	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0009613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	149	824	1	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.331845624576036	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.331845624576036	1		825	554	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733235	40733235	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	249	758	1	ENST00000373198.4:c.3571T>A	p.Ser1191Thr	p.S1191T	ENST00000373198	NM_133170.3	1191	Tcc/Acc	26/32	0.331845624576036	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.331845624576036	3		759	743	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591111	67591112	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAC	novel	NA	P-0009613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	78	362	0	ENST00000274335.5:c.1705_1707dup	p.Asp569dup	p.D569dup	ENST00000274335		569	-/GAC	12/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.331845624576036	2		362	349	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0009613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	43	407	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	1	2	FACETS	0.774	0.65	0.91	0.774	0.65	0.91	CLONAL	1	TRUE	1	0.331845624576036	2		407	335	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923160	48923160	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587776789	NA	P-0013934-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	109	59	0	ENST00000267163.4:c.607+1G>T		p.X203_splice	ENST00000267163	NM_000321.2	203			0.717887942753747	2	FACETS	0.842	0.792	0.889	0.842	0.792	0.889	CLONAL	2	TRUE	0	0.880432410327503	2		59	147	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0013934-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	830	308	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	0.71758791855673	3	FACETS	1	0.998	1	0.827	0.809	0.843	CLONAL	2	TRUE	0	0.880432410327503	3		308	1095	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462772	69462772	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013934-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	165	272	0	ENST00000227507.2:c.585C>A	p.Phe195Leu	p.F195L	ENST00000227507	NM_053056.2	195	ttC/ttA	4/5	0.721547778622433	3	FACETS	0.759	0.699	0.822	0.38	0.349	0.411	SUBCLONAL	1	TRUE	1	0.880432410327503	3		272	711	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870915	12870916	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0013934-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	254	104	0	ENST00000228872.4:c.143_144del	p.His48LeufsTer76	p.H48Lfs*76	ENST00000228872	NM_004064.3	48	CAc/c	1/3	0.721173979167484	2	FACETS	0.846	0.813	0.877	0.846	0.813	0.877	CLONAL	2	TRUE	0	0.880432410327503	2		104	341	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198264998	198264998	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013934-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	98	80	0	ENST00000335508.6:c.2879T>C	p.Val960Ala	p.V960A	ENST00000335508	NM_012433.2	960	gTt/gCt	19/25	0.736516531969112	3	FACETS	0.788	0.708	0.872	0.394	0.354	0.436	SUBCLONAL	1	TRUE	1	0.880432410327503	3		80	407	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468480	89468480	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013934-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	106	63	0	ENST00000336596.2:c.2014A>T	p.Ser672Cys	p.S672C	ENST00000336596	NM_005233.5	672	Agc/Tgc	11/17	0.736516531969112	3	FACETS	0.913	0.825	1	0.456	0.412	0.502	CLONAL	1	TRUE	1	0.880432410327503	3		63	380	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032278	26032278	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013934-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	95	80	0	ENST00000244661.2:c.11C>G	p.Thr4Ser	p.T4S	ENST00000244661	NM_003537.3	4	aCt/aGt	1/1	0.857444695162946	6	FACETS	0.861	0.767	0.961	0.215	0.191	0.241	CLONAL	1	TRUE	2	0.880432410327503	6		80	692	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982478	10982478	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013934-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	57	64	0	ENST00000327064.4:c.101del	p.Gly34AlafsTer91	p.G34Afs*91	ENST00000327064	NM_199141.1	34	Ggc/gc	1/16	0.721547778622433	3	FACETS	0.818	0.727	0.908	0.818	0.727	0.908	CLONAL	2	TRUE	1	0.880432410327503	3		64	114	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78831665	78831665	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013934-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1276	264	249	0	ENST00000306801.3:c.1474G>C	p.Val492Leu	p.V492L	ENST00000306801	NM_020761.2	492	Gtt/Ctt	13/34	0.747820732473497	5	FACETS	0.904	0.845	0.965	0.301	0.281	0.322	CLONAL	1	TRUE	2	0.880432410327503	5		249	1540	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294588	1294588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013934-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1585	189	285	0	ENST00000310581.5:c.413G>A	p.Gly138Glu	p.G138E	ENST00000310581	NM_198253.2	138	gGg/gAg	2/16	0.880432410327503	7	FACETS	0.775	0.713	0.839			1	SUBCLONAL	1	TRUE	NA	0.880432410327503	7		285	1774	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0013935-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	306	754	2	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.98	0.924	1	1	0.996	1	CLONAL	2	TRUE	1	0.28246289338446	2		756	1106	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013935-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	431	881	0	ENST00000397752.3:c.3028G>A	p.Asp1010Asn	p.D1010N	ENST00000397752	NM_000245.2	1010	Gat/Aat	14/21	0.26078055563516	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	0	0.28246289338446	3		881	1106	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149503	61149503	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013935-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	64	453	0	ENST00000295025.8:c.1693T>G	p.Ser565Ala	p.S565A	ENST00000295025	NM_002908.2	565	Tct/Gct	11/11	0.234232706317953	3	FACETS	0.875	0.758	1			1	CLONAL	1	TRUE	NA	0.28246289338446	3		453	591	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285565	46285565	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013935-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	55	352	0	ENST00000334344.6:c.4925G>A	p.Trp1642Ter	p.W1642*	ENST00000334344	NM_152641.2	1642	tGg/tAg	17/21	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.28246289338446	2		352	333	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427533	49427533	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013935-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	119	821	0	ENST00000301067.7:c.10955C>G	p.Ala3652Gly	p.A3652G	ENST00000301067	NM_003482.3	3652	gCc/gGc	39/54	1	2	FACETS	0.898	0.81	0.992	0.898	0.81	0.992	CLONAL	1	TRUE	1	0.28246289338446	2		821	938	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36421193	36421193	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748052737	NA	P-0013935-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	94	432	1	ENST00000300305.3:c.4G>A	p.Ala2Thr	p.A2T	ENST00000300305		2	Gct/Act	1/8	1	2	FACETS	0.943	0.839	1	0.943	0.839	1	CLONAL	1	TRUE	1	0.28246289338446	2		433	706	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045826	143045826	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013935-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	88	669	1	ENST00000262992.4:c.1808C>A	p.Thr603Lys	p.T603K	ENST00000262992	NM_001101669.1	603	aCa/aAa	17/24	1	2	FACETS	0.745	0.659	0.837	0.745	0.659	0.837	SUBCLONAL	1	TRUE	1	0.28246289338446	2		670	836	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0014267-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	451	667	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.274825945351811	4	FACETS	0.987	0.946	1	0.987	0.946	1	INDETERMINATE	2	TRUE	2	0.747150431338146	4		667	1068	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014267-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	429	764	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.747150431338146	2		764	1030	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0014267-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	305	682	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.747150431338146	2		682	739	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544742	65544742	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014267-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	327	569	0	ENST00000358664.4:c.184del	p.Gln62LysfsTer3	p.Q62Kfs*3	ENST00000358664	NM_002382.4	62	Caa/aa	4/5	NA	2	FACETS	0.937	0.903	0.971			1	INDETERMINATE	2	TRUE	NA	0.747150431338146	2		569	467	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874011	123874013	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs780061449	NA	P-0014267-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	10	51	1	ENST00000330479.4:c.62_64del	p.Ala21del	p.A21del	ENST00000330479	NM_020382.3	14	gaGGCg/gag	2/9	1	2	FACETS	0.304	0.208	0.422	0.304	0.208	0.422	SUBCLONAL	1	TRUE	1	0.747150431338146	2		52	88	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856424	111856424	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014267-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	22	133	0	ENST00000341259.2:c.475A>C	p.Thr159Pro	p.T159P	ENST00000341259	NM_005475.2	159	Acc/Ccc	2/8	1	2	FACETS	0.219	0.17	0.276	0.219	0.17	0.276	SUBCLONAL	1	TRUE	1	0.747150431338146	2		133	269	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0014506-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	385	775	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.558556450505069	2	FACETS	0.999	0.958	1	0.999	0.958	1	CLONAL	2	TRUE	0	0.558556450505069	2		775	690	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0014506-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	343	440	1	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	0.558556450505069	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	3	TRUE	1	0.558556450505069	4		441	630	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971097	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0014506-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	257	489	0	ENST00000304494.5:c.261_262delinsAA	p.Glu88Lys	p.E88K	ENST00000304494	NM_000077.4	87	cgGGag/cgAAag	2/3	0.558556450505069	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.558556450505069	2		489	442	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636396	21636396	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014506-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	138	634	0	ENST00000421138.2:c.614A>G	p.Glu205Gly	p.E205G	ENST00000421138		205	gAg/gGg	7/16	0.558556450505069	3	FACETS	0.91	0.829	0.993	0.455	0.414	0.497	CLONAL	1	TRUE	1	0.558556450505069	3		634	695	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166772	32166772	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753820483	NA	P-0014506-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	468	969	2	ENST00000375023.3:c.4466G>A	p.Arg1489Gln	p.R1489Q	ENST00000375023	NM_004557.3	1489	cGa/cAa	24/30	0.558556450505069	4	FACETS	1	0.967	1	0.507	0.484	0.529	CLONAL	2	TRUE	0	0.558556450505069	4		971	1289	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916260	9916260	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014506-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	122	542	0	ENST00000330684.3:c.2029T>G	p.Ser677Ala	p.S677A	ENST00000330684	NM_001134407.1	677	Tcc/Gcc	10/13	0.558556450505069	6	FACETS	1	0.918	1	0.255	0.23	0.281	CLONAL	1	TRUE	2	0.558556450505069	6		542	908	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449569	149449569	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014506-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	174	900	0	ENST00000286301.3:c.1377C>G	p.Ser459Arg	p.S459R	ENST00000286301	NM_005211.3	459	agC/agG	10/22	0.554379510586297	4	FACETS	0.839	0.771	0.91	0.42	0.385	0.455	CLONAL	1	TRUE	2	0.558556450505069	4		900	1157	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564747	139564747	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014506-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	481	1045	1	ENST00000308874.7:c.536A>G	p.Lys179Arg	p.K179R	ENST00000308874		179	aAg/aGg	7/10	0.558556450505069	3	FACETS	0.992	0.951	1	0.992	0.951	1	CLONAL	2	TRUE	1	0.558556450505069	3		1046	1111	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295773	212295773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1299031105	NA	P-0014913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	256	634	0	ENST00000342788.4:c.2540G>A	p.Arg847His	p.R847H	ENST00000342788	NM_005235.2	847	cGt/cAt	21/28	0.573393945690256	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	1	0.625802222333903	3		634	529	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111502	8111503	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	146	719	0	ENST00000346208.3:c.990dup	p.Asn331GlufsTer21	p.N331Efs*21	ENST00000346208		330	agg/aGgg	5/6	0.625802222333903	3	FACETS	0.927	0.848	1			1	CLONAL	1	TRUE	NA	0.625802222333903	3		719	661	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619838	21619838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746455173	NA	P-0014913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	69	545	0	ENST00000382592.4:c.328G>A	p.Ala110Thr	p.A110T	ENST00000382592	NM_014572.2	110	Gca/Aca	2/8	0.573393945690256	3	FACETS	0.704	0.616	0.799	0.352	0.308	0.4	SUBCLONAL	1	TRUE	1	0.625802222333903	3		545	411	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023211	27023227	+	frameshift_variant	Frame_Shift_Del	DEL	ACGCGGGCCCTAGGCCC	ACGCGGGCCCTAGGCCC	CGCGGGCCTA	novel	NA	P-0014913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	64	449	3	ENST00000324856.7:c.317_333delinsCGCGGGCCTA	p.Asn106ThrfsTer4	p.N106Tfs*4	ENST00000324856	NM_006015.4	106	aACGCGGGCCCTAGGCCC/aCGCGGGCCTA	1/20	0.603791803198904	3	FACETS	0.869	0.758	0.987	0.435	0.379	0.494	CLONAL	1	TRUE	1	0.625802222333903	3		452	309	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434384	49434384	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866926540	NA	P-0014913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	143	898	0	ENST00000301067.7:c.7169C>T	p.Pro2390Leu	p.P2390L	ENST00000301067	NM_003482.3	2390	cCg/cTg	31/54	0.625802222333903	4	FACETS	0.743	0.677	0.813	0.186	0.169	0.204	SUBCLONAL	1	TRUE	0	0.625802222333903	4		898	1000	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440867	52440867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	209	899	2	ENST00000460680.1:c.637C>T	p.Arg213Cys	p.R213C	ENST00000460680	NM_004656.3	213	Cgt/Tgt	8/17	0.625802222333903	3	FACETS	1	0.957	1	0.52	0.483	0.558	CLONAL	1	TRUE	1	0.625802222333903	3		901	843	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	49	232	1	ENST00000324856.7:c.1010G>A	p.Trp337Ter	p.W337*	ENST00000324856	NM_006015.4	337	tGg/tAg	1/20	0.603791803198904	3	FACETS	1	0.947	1	0.608	0.524	0.697	CLONAL	1	TRUE	1	0.625802222333903	3		233	169	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865276	57865276	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	172	843	0	ENST00000228682.2:c.2753C>G	p.Ala918Gly	p.A918G	ENST00000228682	NM_005269.2	918	gCc/gGc	12/12	0.625802222333903	4	FACETS	0.865	0.795	0.938	0.216	0.198	0.235	CLONAL	1	TRUE	0	0.625802222333903	4		843	1033	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274848	38274849	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0014913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	76	609	2	ENST00000425967.3:c.1731_1732delinsAT	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaCCtg/aaATtg	13/19	0.588154240694327	2	FACETS	0.649	0.573	0.731	0.325	0.286	0.366	SUBCLONAL	1	TRUE	0	0.625802222333903	2		611	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0016632-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	423	508	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.549764968945734	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.549764968945734	3		508	584	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321690	62321690	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016632-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	243	607	0	ENST00000360203.5:c.2309G>T	p.Gly770Val	p.G770V	ENST00000360203	NM_001283009.1	770	gGa/gTa	26/35	0.549764968945734	3	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.549764968945734	3		607	969	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449764	8449764	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016632-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	462	488	0	ENST00000356435.5:c.3949G>T	p.Asp1317Tyr	p.D1317Y	ENST00000356435		1317	Gac/Tac	23/35	0.549764968945734	6	FACETS	0.924	0.887	0.961	0.739	0.709	0.769	CLONAL	4	TRUE	1	0.549764968945734	6		488	955	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428671	49428671	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016632-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	187	492	0	ENST00000301067.7:c.10279G>T	p.Ala3427Ser	p.A3427S	ENST00000301067	NM_003482.3	3427	Gcc/Tcc	35/54	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.549764968945734	2		492	523	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017752-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	153	597	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.983	0.907	1	0.983	0.907	1	CLONAL	1	TRUE	1	0.669279754121091	2		597	465	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259108	16259108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017752-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	166	814	0	ENST00000375759.3:c.6373G>A	p.Glu2125Lys	p.E2125K	ENST00000375759	NM_015001.2	2125	Gag/Aag	11/15	1	2	FACETS	0.986	0.913	1	0.986	0.913	1	CLONAL	1	TRUE	1	0.669279754121091	2		814	503	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727402	66727443	+	inframe_deletion	In_Frame_Del	DEL	CTAGAGCTTGATGAGCAGCAGCGAAAGCGCCTTGAGGCCTTT	CTAGAGCTTGATGAGCAGCAGCGAAAGCGCCTTGAGGCCTTT	-	novel	NA	P-0017752-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	157	532	0	ENST00000307102.5:c.120_161del	p.Glu41_Leu54del	p.E41_L54del	ENST00000307102	NM_002755.3	40	CTAGAGCTTGATGAGCAGCAGCGAAAGCGCCTTGAGGCCTTT/-	2/11	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.669279754121091	2		532	462	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265667	10265667	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017752-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	156	635	0	ENST00000340748.4:c.1510G>C	p.Glu504Gln	p.E504Q	ENST00000340748		504	Gag/Cag	19/40	1	2	FACETS	0.878	0.809	0.949	0.878	0.809	0.949	CLONAL	1	TRUE	1	0.669279754121091	2		635	531	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876476	35876476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017752-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	201	763	0	ENST00000303115.3:c.1268C>T	p.Ser423Phe	p.S423F	ENST00000303115	NM_002185.3	423	tCt/tTt	8/8	0.626284822351652	4	FACETS	1	0.968	1	0.54	0.5	0.581	CLONAL	1	TRUE	2	0.669279754121091	4		763	929	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100523	157100527	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCG	GCCCG	-	novel	NA	P-0017752-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	128	344	0	ENST00000346085.5:c.1463_1467del	p.Pro488LeufsTer45	p.P488Lfs*45	ENST00000346085	NM_020732.3	487	aGCCCG/a	1/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.669279754121091	2		344	324	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148675	20148675	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017752-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	99	216	0	ENST00000379607.5:c.388C>T	p.Gln130Ter	p.Q130*	ENST00000379607	NM_001412.3	130	Cag/Tag	6/7	0.462716980297535	2	FACETS	1	0.946	1			1	CLONAL	1	TRUE	NA	0.669279754121091	2		216	278	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171464	123171540	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCTGTAAAGGTAAGATATATTTATTTTGAAATCAGCAGCTCTCAAATAGTCACTTCGTTGTTCCACCTAAAGAGAT	GGCTGTAAAGGTAAGATATATTTATTTTGAAATCAGCAGCTCTCAAATAGTCACTTCGTTGTTCCACCTAAAGAGAT	-	novel	NA	P-0017752-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	82	240	0	ENST00000218089.9:c.377_385+68del		p.X126_splice	ENST00000218089	NM_001042749.1	126		6/35	0.462716980297535	2	FACETS	1	0.929	1			1	CLONAL	1	TRUE	NA	0.669279754121091	2		240	234	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0021800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	106	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.371226744521186	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.371226744521186	1		298	411	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867546	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs11466445	NA	P-0021800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	16	8	0	ENST00000374994.4:c.70_78del	p.Ala24_Ala26del	p.A24_A26del	ENST00000374994	NM_004612.2	17	ctGGCGGCGGCg/ctg	1/9	1	2	FACETS	0.937	0.723	1	1	0.929	1	CLONAL	2	TRUE	1	0.371226744521186	2		8	46	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252162	226252162	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	43	31	0	ENST00000366813.1:c.110A>G	p.Lys37Arg	p.K37R	ENST00000366813		37	aAg/aGg	1/3	0.371226744521186	3	FACETS	1	0.933	1	0.602	0.509	0.704	CLONAL	1	TRUE	1	0.371226744521186	3		31	228	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11999000	11999000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	65	53	0	ENST00000353533.5:c.502C>T	p.Leu168Phe	p.L168F	ENST00000353533	NM_003010.3	168	Ctc/Ttc	4/11	0.371226744521186	1	FACETS	0.894	0.781	1	0.894	0.781	1	CLONAL	1	TRUE	0	0.371226744521186	1		53	319	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519337	176519337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758837002	NA	P-0021800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	133	203	0	ENST00000292408.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000292408	NM_213647.1	248	cGg/cAg	7/18	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.371226744521186	2		203	645	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999299	100999299	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	87	243	0	ENST00000325455.5:c.503C>T	p.Ser168Phe	p.S168F	ENST00000325455	NM_001202474.3	168	tCc/tTc	1/8	1	2	FACETS	0.552	0.488	0.621	0.552	0.488	0.621	SUBCLONAL	1	TRUE	1	0.371226744521186	2		243	849	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	301	694	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.523320476285324	3	FACETS	1	0.993	1	0.822	0.784	0.859	CLONAL	2	FALSE	0	0.577519741883978	3		694	545	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041110	180041110	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781402372	NA	P-0022086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	369	1301	0	ENST00000261937.6:c.3289G>A	p.Val1097Met	p.V1097M	ENST00000261937	NM_182925.4	1097	Gtg/Atg	24/30	0.413561480645536	4	FACETS	0.823	0.781	0.866	0.823	0.781	0.866	CLONAL	2	FALSE	2	0.577519741883978	4		1301	1225	SUCCESS
AR	367	MSKCC	GRCh37	X	66765159	66765212	+	inframe_deletion	In_Frame_Del	DEL	GCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA	GCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA	-	novel	NA	P-0022086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	232	479	0	ENST00000374690.3:c.186_239del	p.Gln63_Gln80del	p.Q63_Q80del	ENST00000374690	NM_000044.3	57	ctGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAg/ctg	1/8	0.292432056946277	4	FACETS	0.903	0.853	0.953	1	0.992	1	INDETERMINATE	3	FALSE	2	0.577519741883978	4		479	468	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308047	30308064	+	inframe_deletion	In_Frame_Del	DEL	TGGGACAATAATGCAGTC	TGGGACAATAATGCAGTC	-	novel	NA	P-0022086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	120	494	0	ENST00000262643.3:c.186_203del	p.Trp62_Val67del	p.W62_V67del	ENST00000262643	NM_001238.2	62	TGGGACAATAATGCAGTC/-	5/12	0.585034841073463	4	FACETS	1	0.985	1	0.732	0.665	0.801	CLONAL	1	FALSE	2	0.577519741883978	4		494	448	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043687	6043687	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	238	417	0	ENST00000265849.7:c.166C>A	p.Leu56Ile	p.L56I	ENST00000265849	NM_000535.5	56	Cta/Ata	3/15	0.577519741883978	6	FACETS	1	0.98	1	0.816	0.769	0.864	CLONAL	3	FALSE	2	0.577519741883978	6		417	544	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550797	150550797	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	192	361	0	ENST00000369026.2:c.859A>C	p.Ile287Leu	p.I287L	ENST00000369026	NM_021960.4	287	Atc/Ctc	2/3	0.414737182756532	6	FACETS	0.8	0.74	0.861	0.533	0.493	0.574	SUBCLONAL	2	FALSE	3	0.577519741883978	6		361	896	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911791	32912600	+	inframe_deletion	In_Frame_Del	DEL	ACCATAATTTAACACCTAGCCAAAAGGCAGAAATTACAGAACTTTCTACTATATTAGAAGAATCAGGAAGTCAGTTTGAATTTACTCAGTTTAGAAAACCAAGCTACATATTGCAGAAGAGTACATTTGAAGTGCCTGAAAACCAGATGACTATCTTAAAGACCACTTCTGAGGAATGCAGAGATGCTGATCTTCATGTCATAATGAATGCCCCATCGATTGGTCAGGTAGACAGCAGCAAGCAATTTGAAGGTACAGTTGAAATTAAACGGAAGTTTGCTGGCCTGTTGAAAAATGACTGTAACAAAAGTGCTTCTGGTTATTTAACAGATGAAAATGAAGTGGGGTTTAGGGGCTTTTATTCTGCTCATGGCACAAAACTGAATGTTTCTACTGAAGCTCTGCAAAAAGCTGTGAAACTGTTTAGTGATATTGAGAATATTAGTGAGGAAACTTCTGCAGAGGTACATCCAATAAGTTTATCTTCAAGTAAATGTCATGATTCTGTTGTTTCAATGTTTAAGATAGAAAATCATAATGATAAAACTGTAAGTGAAAAAAATAATAAATGCCAACTGATATTACAAAATAATATTGAAATGACTACTGGCACTTTTGTTGAAGAAATTACTGAAAATTACAAGAGAAATACTGAAAATGAAGATAACAAATATACTGCTGCCAGTAGAAATTCTCATAACTTAGAATTTGATGGCAGTGATTCAAGTAAAAATGATACTGTTTGTATTCATAAAGATGAAACGGACTTGCTATTTACTGATCAGCACAACATATGTCTTAAATTATCTG	ACCATAATTTAACACCTAGCCAAAAGGCAGAAATTACAGAACTTTCTACTATATTAGAAGAATCAGGAAGTCAGTTTGAATTTACTCAGTTTAGAAAACCAAGCTACATATTGCAGAAGAGTACATTTGAAGTGCCTGAAAACCAGATGACTATCTTAAAGACCACTTCTGAGGAATGCAGAGATGCTGATCTTCATGTCATAATGAATGCCCCATCGATTGGTCAGGTAGACAGCAGCAAGCAATTTGAAGGTACAGTTGAAATTAAACGGAAGTTTGCTGGCCTGTTGAAAAATGACTGTAACAAAAGTGCTTCTGGTTATTTAACAGATGAAAATGAAGTGGGGTTTAGGGGCTTTTATTCTGCTCATGGCACAAAACTGAATGTTTCTACTGAAGCTCTGCAAAAAGCTGTGAAACTGTTTAGTGATATTGAGAATATTAGTGAGGAAACTTCTGCAGAGGTACATCCAATAAGTTTATCTTCAAGTAAATGTCATGATTCTGTTGTTTCAATGTTTAAGATAGAAAATCATAATGATAAAACTGTAAGTGAAAAAAATAATAAATGCCAACTGATATTACAAAATAATATTGAAATGACTACTGGCACTTTTGTTGAAGAAATTACTGAAAATTACAAGAGAAATACTGAAAATGAAGATAACAAATATACTGCTGCCAGTAGAAATTCTCATAACTTAGAATTTGATGGCAGTGATTCAAGTAAAAATGATACTGTTTGTATTCATAAAGATGAAACGGACTTGCTATTTACTGATCAGCACAACATATGTCTTAAATTATCTG	-	novel	NA	P-0022086-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	88	411	0	ENST00000380152.3:c.3299_4108del	p.Asn1100_Gly1370delinsSer	p.N1100_G1370delinsS	ENST00000380152		1100	aACCATAATTTAACACCTAGCCAAAAGGCAGAAATTACAGAACTTTCTACTATATTAGAAGAATCAGGAAGTCAGTTTGAATTTACTCAGTTTAGAAAACCAAGCTACATATTGCAGAAGAGTACATTTGAAGTGCCTGAAAACCAGATGACTATCTTAAAGACCACTTCTGAGGAATGCAGAGATGCTGATCTTCATGTCATAATGAATGCCCCATCGATTGGTCAGGTAGACAGCAGCAAGCAATTTGAAGGTACAGTTGAAATTAAACGGAAGTTTGCTGGCCTGTTGAAAAATGACTGTAACAAAAGTGCTTCTGGTTATTTAACAGATGAAAATGAAGTGGGGTTTAGGGGCTTTTATTCTGCTCATGGCACAAAACTGAATGTTTCTACTGAAGCTCTGCAAAAAGCTGTGAAACTGTTTAGTGATATTGAGAATATTAGTGAGGAAACTTCTGCAGAGGTACATCCAATAAGTTTATCTTCAAGTAAATGTCATGATTCTGTTGTTTCAATGTTTAAGATAGAAAATCATAATGATAAAACTGTAAGTGAAAAAAATAATAAATGCCAACTGATATTACAAAATAATATTGAAATGACTACTGGCACTTTTGTTGAAGAAATTACTGAAAATTACAAGAGAAATACTGAAAATGAAGATAACAAATATACTGCTGCCAGTAGAAATTCTCATAACTTAGAATTTGATGGCAGTGATTCAAGTAAAAATGATACTGTTTGTATTCATAAAGATGAAACGGACTTGCTATTTACTGATCAGCACAACATATGTCTTAAATTATCTGgc/agc	11/27	0.585034841073463	2	FACETS	0.886	0.808	0.964	0.886	0.808	0.964	CLONAL	2	FALSE	0	0.577519741883978	2		411	172	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024340-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	179	324	0				ENST00000310581	NM_198253.2	-/1132			0.914524701537955	5	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.914524701537955	5		324	652	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268483	46268483	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs778964948	NA	P-0024340-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	271	260	0	ENST00000371998.3:c.2870C>G	p.Ser957Cys	p.S957C	ENST00000371998		957	tCt/tGt	15/23	0.541651131982841	4	FACETS	0.86	0.821	0.898	0.86	0.821	0.898	INDETERMINATE	3	TRUE	1	0.914524701537955	4		260	440	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981495	201981496	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024340-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	452	790	0	ENST00000359651.3:c.409_410insT	p.Ser137MetfsTer5	p.S137Mfs*5	ENST00000359651		137	agt/aTgt	3/8	0.814588103576824	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.914524701537955	1		790	519	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440530	49440530	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024340-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	514	1026	0	ENST00000301067.7:c.4280G>T	p.Cys1427Phe	p.C1427F	ENST00000301067	NM_003482.3	1427	tGt/tTt	15/54	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.914524701537955	2		1026	1112	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798200	42798200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024340-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	528	1020	0	ENST00000575354.2:c.4154C>A	p.Ala1385Asp	p.A1385D	ENST00000575354	NM_015125.3	1385	gCc/gAc	17/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.914524701537955	2		1020	1134	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967332	25967332	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024340-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	131	266	0	ENST00000435504.4:c.1874G>C	p.Arg625Thr	p.R625T	ENST00000435504		625	aGa/aCa	13/13	1	2	FACETS	0.988	0.913	1	0.988	0.913	1	CLONAL	1	TRUE	1	0.914524701537955	2		266	290	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021799	71021799	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024340-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	109	187	0	ENST00000318789.4:c.1559A>C	p.His520Pro	p.H520P	ENST00000318789	NM_032682.5	520	cAc/cCc	18/21	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.914524701537955	2		187	236	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523095	176523095	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024340-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	440	917	0	ENST00000292408.4:c.1859T>G	p.Val620Gly	p.V620G	ENST00000292408	NM_213647.1	620	gTg/gGg	14/18	NA	2	FACETS	0.954	0.913	0.994			1	INDETERMINATE	1	TRUE	NA	0.914524701537955	2		917	1009	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272822	142272822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024340-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	96	260	0	ENST00000350721.4:c.2377C>T	p.Leu793Phe	p.L793F	ENST00000350721	NM_001184.3	793	Ctt/Ttt	11/47	0.541651131982841	4	FACETS	0.985	0.884	1	0.328	0.294	0.364	INDETERMINATE	1	TRUE	1	0.914524701537955	4		260	408	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751913	57751913	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024340-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	161	397	0	ENST00000274289.3:c.1324G>C	p.Gly442Arg	p.G442R	ENST00000274289	NM_006622.3	442	Ggg/Cgg	10/14	1	2	FACETS	0.804	0.745	0.864	0.804	0.745	0.864	CLONAL	1	TRUE	1	0.914524701537955	2		397	438	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0026363-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	30	473	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.743	0.597	0.909	0.743	0.597	0.909	CLONAL	1	TRUE	1	0.14	2		473	577	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0026363-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	25	346	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	1	2	FACETS	0.854	0.673	1	0.854	0.673	1	CLONAL	1	TRUE	1	0.14	2		346	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0026363-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1184	49	916	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	1	2	FACETS	0.568	0.479	0.667	0.568	0.479	0.667	SUBCLONAL	1	TRUE	1	0.14	2		916	1233	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489785	40489785	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026363-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	42	593	0	ENST00000264657.5:c.641G>C	p.Arg214Pro	p.R214P	ENST00000264657	NM_139276.2	214	cGg/cCg	7/24	1	2	FACETS	0.742	0.617	0.881	0.742	0.617	0.881	SUBCLONAL	1	TRUE	1	0.14	2		593	809	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0026363-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	204	473	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.216691190997766	7	FACETS	0.943	0.883	1	0.943	0.883	1	CLONAL	6	TRUE	1	0.216691190997766	7		473	513	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473722	67473722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs794727798	NA	P-0026363-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	64	177	1	ENST00000327367.4:c.802C>T	p.Arg268Cys	p.R268C	ENST00000327367	NM_005902.3	268	Cgc/Tgc	6/9	0.216691190997766	3	FACETS	1	0.92	1	0.544	0.471	0.623	CLONAL	1	TRUE	1	0.216691190997766	3		178	602	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003496	42003496	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026363-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	120	125	0	ENST00000219905.7:c.3033C>A	p.Tyr1011Ter	p.Y1011*	ENST00000219905	NM_001164273.1	1011	taC/taA	8/24	0.216691190997766	3	FACETS	0.977	0.889	1	0.977	0.889	1	CLONAL	3	TRUE	0	0.216691190997766	3		125	419	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039842	47039846	+	frameshift_variant	Frame_Shift_Del	DEL	TCGCA	TCGCA	-	novel	NA	P-0026363-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	145	202	0	ENST00000377604.3:c.1187_1191del	p.Arg396GlnfsTer45	p.R396Qfs*45	ENST00000377604	NM_001204468.1	395	agTCGCAtc/agtc	12/24	0.156748937079097	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	1	0.216691190997766	3		202	712	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39595507	39595507	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1442062086	NA	P-0026363-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	23	102	0	ENST00000262039.4:c.1393G>T	p.Val465Phe	p.V465F	ENST00000262039	NM_002647.2	465	Gtt/Ttt	12/25	0.156748937079097	3	FACETS	0.916	0.716	1	0.458	0.358	0.573	CLONAL	1	TRUE	1	0.216691190997766	3		102	257	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776393	76776393	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026363-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	39	119	0	ENST00000373344.5:c.7073G>T	p.Trp2358Leu	p.W2358L	ENST00000373344	NM_000489.3	2358	tGg/tTg	34/35	0.156748937079097	3	FACETS	1	0.933	1	0.631	0.525	0.749	CLONAL	1	TRUE	1	0.216691190997766	3		119	316	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0027443-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	85	330	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.773947236640072	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.773947236640072	3		330	122	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22142623	22142624	+	missense_variant	Missense_Mutation	DNP	GC	GC	CT	novel	NA	P-0027443-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	21	286	1	ENST00000215832.6:c.778_779delinsAG	p.Ala260Ser	p.A260S	ENST00000215832	NM_002745.4	260	GCt/AGt	6/9	1	2	FACETS	0.754	0.598	0.923	0.754	0.598	0.923	CLONAL	1	TRUE	1	0.773947236640072	2		287	72	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272144	142272144	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027443-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	30	329	0	ENST00000350721.4:c.2730A>T	p.Glu910Asp	p.E910D	ENST00000350721	NM_001184.3	910	gaA/gaT	13/47	0.16530346403648	3	FACETS	1	0.937	1	0.656	0.546	0.771	INDETERMINATE	1	TRUE	1	0.773947236640072	3		329	82	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027588-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	69	610	0	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	0.261000428736348	1	FACETS	1	0.902	1	1	0.902	1	INDETERMINATE	1	TRUE	0	0.54598891331129	1		610	181	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243859016	243859016	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs397514606	NA	P-0027588-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	26	369	0	ENST00000263826.5:c.49G>A	p.Glu17Lys	p.E17K	ENST00000263826	NM_005465.4	17	Gaa/Aaa	2/13	0.16874237862404	2	FACETS	0.544	0.435	0.667	0.272	0.217	0.334	INDETERMINATE	1	TRUE	0	0.54598891331129	2		369	175	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80109515	80109515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027588-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	24	618	0	ENST00000265081.6:c.2768C>T	p.Pro923Leu	p.P923L	ENST00000265081	NM_002439.4	923	cCt/cTt	20/24	0.294643452978164	1	FACETS	0.372	0.293	0.46	0.372	0.293	0.46	INDETERMINATE	1	TRUE	0	0.54598891331129	1		618	172	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858929	243858929	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027588-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	34	542	0	ENST00000263826.5:c.136G>C	p.Asp46His	p.D46H	ENST00000263826	NM_005465.4	46	Gat/Cat	2/13	0.16874237862404	2	FACETS	0.7	0.578	0.833	0.35	0.289	0.417	INDETERMINATE	1	TRUE	0	0.54598891331129	2		542	178	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0027639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	94	436	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.270567352069076	3	FACETS	1	0.958	1	0.578	0.515	0.646	CLONAL	1	TRUE	1	0.270567352069076	3		436	682	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578446	7578446	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	153	690	0	ENST00000269305.4:c.484A>T	p.Ile162Phe	p.I162F	ENST00000269305	NM_001126112.2	162	Atc/Ttc	5/11	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.270567352069076	2		690	874	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416647	49416647	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	27	438	0	ENST00000301067.7:c.16064T>G	p.Leu5355Arg	p.L5355R	ENST00000301067	NM_003482.3	5355	cTg/cGg	51/54	1	2	FACETS	0.412	0.327	0.509	0.412	0.327	0.509	SUBCLONAL	1	TRUE	1	0.270567352069076	2		438	485	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109867	115109867	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	43	770	2	ENST00000257566.3:c.2011del	p.Asp671ThrfsTer218	p.D671Tfs*218	ENST00000257566	NM_016569.3	671	Gac/ac	8/8	0.270567352069076	1	FACETS	0.369	0.308	0.437	0.369	0.308	0.437	SUBCLONAL	1	TRUE	0	0.270567352069076	1		772	745	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245011	133245011	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	65	731	0	ENST00000320574.5:c.2104G>T	p.Gly702Trp	p.G702W	ENST00000320574	NM_006231.2	702	Ggg/Tgg	19/49	NA	2	FACETS	0.58	0.502	0.666			1	INDETERMINATE	1	TRUE	NA	0.270567352069076	2		731	828	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061004	38061004	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	23	412	0	ENST00000250448.2:c.985G>T	p.Ala329Ser	p.A329S	ENST00000250448	NM_004496.3	329	Gcc/Tcc	2/2	1	2	FACETS	0.39	0.303	0.491	0.39	0.303	0.491	SUBCLONAL	1	TRUE	1	0.270567352069076	2		412	436	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482863	67482863	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	36	389	0	ENST00000327367.4:c.1267A>T	p.Ser423Cys	p.S423C	ENST00000327367	NM_005902.3	423	Agt/Tgt	9/9	1	2	FACETS	0.494	0.405	0.593	0.494	0.405	0.593	SUBCLONAL	1	TRUE	1	0.270567352069076	2		389	539	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134284	2134284	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	42	756	0	ENST00000219476.3:c.4061G>T	p.Gly1354Val	p.G1354V	ENST00000219476	NM_000548.3	1354	gGc/gTc	34/42	NA	2	FACETS	0.39	0.324	0.463			1	INDETERMINATE	1	TRUE	NA	0.270567352069076	2		756	797	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993329	72993329	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	71	761	0	ENST00000268489.5:c.716A>G	p.Lys239Arg	p.K239R	ENST00000268489	NM_006885.3	239	aAa/aGa	2/10	0.178541805650124	2	FACETS	0.538	0.468	0.614	0.269	0.234	0.307	SUBCLONAL	1	TRUE	0	0.270567352069076	2		761	975	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974981	15974981	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0027639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	22	277	0	ENST00000268712.3:c.3896-2A>T		p.X1299_splice	ENST00000268712	NM_006311.3	1299			0.270567352069076	3	FACETS	0.639	0.496	0.805	0.319	0.248	0.403	SUBCLONAL	1	TRUE	1	0.270567352069076	3		277	289	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40761084	40761084	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	104	608	0	ENST00000392038.2:c.268G>T	p.Val90Leu	p.V90L	ENST00000392038	NM_001626.4	90	Gtg/Ttg	4/14	0.270567352069076	1	FACETS	0.995	0.892	1	0.995	0.892	1	CLONAL	1	TRUE	0	0.270567352069076	1		608	668	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858228	27858228	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	91	462	0	ENST00000359303.2:c.343G>C	p.Ala115Pro	p.A115P	ENST00000359303	NM_003535.2	115	Gcc/Ccc	1/1	0.270567352069076	6	FACETS	1	0.977	1	0.358	0.318	0.401	CLONAL	1	TRUE	2	0.270567352069076	6		462	724	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505533	157505533	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	29	261	0	ENST00000346085.5:c.3514A>T	p.Thr1172Ser	p.T1172S	ENST00000346085	NM_020732.3	1172	Acc/Tcc	13/20	1	2	FACETS	0.831	0.67	1	0.831	0.67	1	CLONAL	1	TRUE	1	0.270567352069076	2		261	258	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912011	127912012	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0027639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	32	321	1	ENST00000373547.4:c.858_859delinsTT	p.Ala287Ser	p.A287S	ENST00000373547	NM_002721.4	286	cgGGca/cgTTca	7/7	1	2	FACETS	0.55	0.446	0.668	0.55	0.446	0.668	SUBCLONAL	1	TRUE	1	0.270567352069076	2		322	430	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041029	47041792	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGCTGCCAACAGCCAGGTGAGTGAGCCCTGTGGGTATGTATCCCGGGGAGGCAGGCAGGCGGCAGGGGTGGCATGGGCAGACACTGAGCCCTGTTCTCCTGTCTGGCCCCATGACCAGTCGTATACCATCATGTCACCCGCTGTGCTCAAATCTGAGCTCCAGAGCCCTACCCATCCTAGTTCTGCTCTCCCACCGGCTACCAGCCCCACTGCCCAGGAATCCTACAGCCAGTACCGTGAGTAGCCACAGCCTGTGGGTAGGGGTGGGGAGTTCTTAATAAAGCAGGGAATAGTGTGACCCCGTTCCCCTCACCCCCTAGCTGTTCCCGACGTCTCTACCTACCAGTACGATGAGACCTCCGGCTACTACTATGACCCCCAGACCGGCCTCTACTATGACCCCAACTCCCAGGTAATAGGGCAGCCCAGGGAGGGATGGGATCGGGTCAGGTCGCGTCAGGAACAGCTAGCCCTGCAGGTTCCCTTCACAAGGTCTTCCCTCACATCCCCTCTTCCCTCCTCCTCCCTCAGTATTACTACAATGCTCAGAGCCAGCAGTACCTGTACTGGGATGGGGAGAGGCGGACCTATGTTCCCGCCCTGGAGCAGTCGGCCGACGGACATAAGGAGACAGGGGCACCCTCGAAGGAGGGCAAAGAGAAGAAGGAGAAGCACAAGACCAAGACAGCTCAACAGGTGAACACCAGGGTCCAGCAGTCACTGGCTGGCTGTGTGGTGTCTTCCAGCAACGGCACTCTGTCAG	CTGCTGCCAACAGCCAGGTGAGTGAGCCCTGTGGGTATGTATCCCGGGGAGGCAGGCAGGCGGCAGGGGTGGCATGGGCAGACACTGAGCCCTGTTCTCCTGTCTGGCCCCATGACCAGTCGTATACCATCATGTCACCCGCTGTGCTCAAATCTGAGCTCCAGAGCCCTACCCATCCTAGTTCTGCTCTCCCACCGGCTACCAGCCCCACTGCCCAGGAATCCTACAGCCAGTACCGTGAGTAGCCACAGCCTGTGGGTAGGGGTGGGGAGTTCTTAATAAAGCAGGGAATAGTGTGACCCCGTTCCCCTCACCCCCTAGCTGTTCCCGACGTCTCTACCTACCAGTACGATGAGACCTCCGGCTACTACTATGACCCCCAGACCGGCCTCTACTATGACCCCAACTCCCAGGTAATAGGGCAGCCCAGGGAGGGATGGGATCGGGTCAGGTCGCGTCAGGAACAGCTAGCCCTGCAGGTTCCCTTCACAAGGTCTTCCCTCACATCCCCTCTTCCCTCCTCCTCCCTCAGTATTACTACAATGCTCAGAGCCAGCAGTACCTGTACTGGGATGGGGAGAGGCGGACCTATGTTCCCGCCCTGGAGCAGTCGGCCGACGGACATAAGGAGACAGGGGCACCCTCGAAGGAGGGCAAAGAGAAGAAGGAGAAGCACAAGACCAAGACAGCTCAACAGGTGAACACCAGGGTCCAGCAGTCACTGGCTGGCTGTGTGGTGTCTTCCAGCAACGGCACTCTGTCAG	-	novel	NA	P-0027639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	79	369	0	ENST00000377604.3:c.1561_1950+69del		p.X521_splice	ENST00000377604	NM_001204468.1	521		14-17/24	0.14616881894836	2	FACETS	0.754	0.667	0.847			1	INDETERMINATE	2	TRUE	NA	0.270567352069076	2		369	387	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716098	243716098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	77	671	0	ENST00000263826.5:c.1096C>T	p.Pro366Ser	p.P366S	ENST00000263826	NM_005465.4	366	Cct/Tct	10/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.18	2		671	579	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968251	2968251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377769236	NA	P-0027805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	79	1150	0	ENST00000396946.4:c.1735G>A	p.Glu579Lys	p.E579K	ENST00000396946	NM_032415.4	579	Gag/Aag	13/25	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.18	2		1150	764	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508783	106508783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	42	815	1	ENST00000359195.3:c.777G>A	p.Met259Ile	p.M259I	ENST00000359195	NM_002649.2	259	atG/atA	2/11	0.137665976104741	3	FACETS	0.689	0.574	0.818	0.345	0.287	0.409	SUBCLONAL	1	TRUE	1	0.18	3		816	738	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006496	12006496	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0027805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	43	906	0	ENST00000396373.4:c.463+1G>A		p.X155_splice	ENST00000396373	NM_001987.4	155			1	2	FACETS	0.586	0.489	0.695	0.586	0.489	0.695	SUBCLONAL	1	TRUE	1	0.18	2		906	815	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436429	49436429	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0027805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	33	784	0	ENST00000301067.7:c.5783-1G>A		p.X1928_splice	ENST00000301067	NM_003482.3	1928			1	2	FACETS	0.603	0.49	0.731	0.603	0.49	0.731	SUBCLONAL	1	TRUE	1	0.18	2		784	608	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609817	81609817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	28	636	1	ENST00000298171.2:c.1415C>T	p.Ser472Phe	p.S472F	ENST00000298171	NM_000369.2	472	tCt/tTt	10/10	1	2	FACETS	0.614	0.489	0.756	0.614	0.489	0.756	SUBCLONAL	1	TRUE	1	0.18	2		637	507	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505337	25505337	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	63	1069	1	ENST00000264709.3:c.421G>A	p.Glu141Lys	p.E141K	ENST00000264709	NM_175629.2	141	Gag/Aag	4/23	1	2	FACETS	0.818	0.706	0.94	0.818	0.706	0.94	CLONAL	1	TRUE	1	0.18	2		1070	856	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018095	48018095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	71	893	2	ENST00000234420.5:c.290G>A	p.Trp97Ter	p.W97*	ENST00000234420	NM_000179.2	97	tGg/tAg	2/10	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.18	2		895	736	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755594	39755594	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780042015	NA	P-0027805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	36	916	2	ENST00000288319.7:c.1171G>A	p.Asp391Asn	p.D391N	ENST00000288319	NM_182918.3	391	Gac/Aac	10/10	1	2	FACETS	0.572	0.469	0.689	0.572	0.469	0.689	SUBCLONAL	1	TRUE	1	0.18	2		918	699	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648469	30648470	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0027805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	39	729	1	ENST00000295754.5:c.94_94+1delinsAA		p.X32_splice	ENST00000295754	NM_003242.5	32		1/7	1	2	FACETS	0.747	0.618	0.891	0.747	0.618	0.891	SUBCLONAL	1	TRUE	1	0.18	2		730	580	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459615	149459615	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	34	836	1	ENST00000286301.3:c.592G>A	p.Val198Ile	p.V198I	ENST00000286301	NM_005211.3	198	Gtc/Atc	4/22	1	2	FACETS	0.63	0.513	0.761	0.63	0.513	0.761	SUBCLONAL	1	TRUE	1	0.18	2		837	600	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873694	151873695	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0027805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	59	786	3	ENST00000262189.6:c.8843_8844delinsTT	p.Ser2948Phe	p.S2948F	ENST00000262189	NM_170606.2	2948	tCC/tTT	38/59	1	2	FACETS	0.97	0.834	1	0.97	0.834	1	CLONAL	1	TRUE	1	0.18	2		789	676	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399276	139399276	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	64	1010	2	ENST00000277541.6:c.4867G>T	p.Glu1623Ter	p.E1623*	ENST00000277541	NM_017617.3	1623	Gag/Tag	26/34	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.18	2		1012	698	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0030631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	154	277	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.703299270627269	2		277	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0030631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	306	644	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.703299270627269	1	FACETS	0.999	0.952	1	0.999	0.952	1	CLONAL	1	TRUE	0	0.703299270627269	1		644	565	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0030631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	139	517	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.703299270627269	1	FACETS	0.527	0.483	0.573	0.527	0.483	0.573	SUBCLONAL	1	TRUE	0	0.703299270627269	1		517	486	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249348	110249348	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	667	819	0	ENST00000374672.4:c.1225A>C	p.Lys409Gln	p.K409Q	ENST00000374672	NM_004235.4	409	Aag/Cag	4/5	0.671179825271236	2	FACETS	0.958	0.932	0.983	0.958	0.932	0.983	CLONAL	2	TRUE	0	0.703299270627269	2		819	990	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309866	65309866	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	116	511	0	ENST00000342505.4:c.2284G>C	p.Glu762Gln	p.E762Q	ENST00000342505	NM_002227.2	762	Gag/Cag	17/25	0.335737480505228	1	FACETS	0.372	0.336	0.41	0.372	0.336	0.41	INDETERMINATE	1	TRUE	0	0.703299270627269	1		511	575	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862158	68862168	+	frameshift_variant	Frame_Shift_Del	DEL	GGGACAACGTT	GGGACAACGTT	-	novel	NA	P-0030631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	251	551	0	ENST00000261769.5:c.2246_2256del	p.Arg749LeufsTer4	p.R749Lfs*4	ENST00000261769	NM_004360.3	749	cGGGACAACGTT/c	14/16	0.703299270627269	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.703299270627269	1		551	463	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14015924	14015924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	73	237	0	ENST00000311895.7:c.244G>A	p.Glu82Lys	p.E82K	ENST00000311895	NM_005236.2	82	Gaa/Aaa	2/11	0.297563148672457	3	FACETS	0.638	0.56	0.721	0.319	0.28	0.361	INDETERMINATE	1	TRUE	1	0.703299270627269	3		237	440	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870630	40870630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777571053	NA	P-0030631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	30	447	1	ENST00000428826.2:c.773G>A	p.Arg258Gln	p.R258Q	ENST00000428826		258	cGa/cAa	9/21	0.703299270627269	1	FACETS	0.126	0.101	0.154	0.126	0.101	0.154	SUBCLONAL	1	TRUE	0	0.703299270627269	1		448	440	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919244	48919244	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	39	169	0	ENST00000267163.4:c.409G>C	p.Glu137Gln	p.E137Q	ENST00000267163	NM_000321.2	137	Gaa/Caa	4/27	0.703299270627269	1	FACETS	0.387	0.324	0.454	0.387	0.324	0.454	SUBCLONAL	1	TRUE	0	0.703299270627269	1		169	186	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919294	48919294	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs773642334	NA	P-0030631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	40	212	0	ENST00000267163.4:c.459G>C	p.Lys153Asn	p.K153N	ENST00000267163	NM_000321.2	153	aaG/aaC	4/27	0.703299270627269	1	FACETS	0.353	0.296	0.415	0.353	0.296	0.415	SUBCLONAL	1	TRUE	0	0.703299270627269	1		212	209	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866128	37866128	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4471	509	554	0	ENST00000269571.5:c.637C>T	p.Gln213Ter	p.Q213*	ENST00000269571		213	Cag/Tag	5/27	0.703299270627269	17	FACETS	0.912	0.867	0.958			1	CLONAL	2	TRUE	NA	0.703299270627269	17		554	4980	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40490824	40490824	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555568535	NA	P-0030631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	22	298	0	ENST00000264657.5:c.475G>A	p.Glu159Lys	p.E159K	ENST00000264657	NM_139276.2	159	Gaa/Aaa	6/24	0.703299270627269	1	FACETS	0.14	0.108	0.177	0.14	0.108	0.177	SUBCLONAL	1	TRUE	0	0.703299270627269	1		298	289	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212377	36212377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	175	771	0	ENST00000222270.7:c.2128G>A	p.Val710Met	p.V710M	ENST00000222270	NM_014727.1	710	Gtg/Atg	3/37	1	2	FACETS	0.507	0.466	0.549	0.507	0.466	0.549	SUBCLONAL	1	TRUE	1	0.703299270627269	2		771	982	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015059	71015059	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	62	393	0	ENST00000318789.4:c.1871G>C	p.Arg624Thr	p.R624T	ENST00000318789	NM_032682.5	624	aGa/aCa	20/21	NA	2	FACETS	0.38	0.329	0.435			1	INDETERMINATE	1	TRUE	NA	0.703299270627269	2		393	464	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0031240-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	41	597	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.834	1	1	0.834	1	CLONAL	1	TRUE	1	0.13	2		597	629	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0031240-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	81	667	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.13	2		667	926	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250386	110250386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752786911	NA	P-0031240-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	49	621	0	ENST00000374672.4:c.289G>A	p.Glu97Lys	p.E97K	ENST00000374672	NM_004235.4	97	Gag/Aag	3/5	1	2	FACETS	0.789	0.666	0.926	0.789	0.666	0.926	CLONAL	1	TRUE	1	0.13	2		621	955	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205277	61205277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031240-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	27	0	0	ENST00000301761.2:c.217G>A	p.Glu73Lys	p.E73K	ENST00000301761	NM_017841.2	73	Gag/Aag	2/4	1	2	FACETS	0.496	0.393	0.615	0.496	0.393	0.615	SUBCLONAL	1	TRUE	1	0.13	2		0	838	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300137	137300137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540273274	NA	P-0031240-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	54	650	2	ENST00000481739.1:c.422G>A	p.Arg141His	p.R141H	ENST00000481739	NM_002957.4	141	cGc/cAc	3/10	1	2	FACETS	0.818	0.696	0.952	0.818	0.696	0.952	CLONAL	1	TRUE	1	0.13	2		652	1016	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814825	139814825	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031240-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	46	0	0	ENST00000247668.2:c.818A>C	p.Glu273Ala	p.E273A	ENST00000247668	NM_021138.3	273	gAg/gCg	8/11	1	2	FACETS	0.681	0.571	0.804	0.681	0.571	0.804	SUBCLONAL	1	TRUE	1	0.13	2		0	1039	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333930	70333930	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031240-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	28	334	0	ENST00000373644.4:c.1835G>C	p.Arg612Thr	p.R612T	ENST00000373644	NM_030625.2	612	aGa/aCa	2/12	1	2	FACETS	0.792	0.631	0.976	0.792	0.631	0.976	CLONAL	1	TRUE	1	0.13	2		334	544	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0034085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	108	348	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.239537144361679	3	FACETS	0.853	0.767	0.943	0.853	0.767	0.943	CLONAL	2	FALSE	1	0.239537144361679	3		348	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0034085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	157	556	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.239537144361679	9	FACETS	1	0.927	1			1	CLONAL	4	FALSE	NA	0.239537144361679	9		556	598	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604750	48604750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	8	345	0	ENST00000342988.3:c.1572G>T	p.Trp524Cys	p.W524C	ENST00000342988	NM_005359.5	524	tgG/tgT	12/12	1	2	FACETS	0.281	0.18	0.411	0.281	0.18	0.411	SUBCLONAL	1	FALSE	1	0.239537144361679	2		345	238	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796099	78796122	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGGTGAGGCGCGGGCCGGGCCTT	GGGGTGAGGCGCGGGCCGGGCCTT	-	novel	NA	P-0034085-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	93	491	1	ENST00000306801.3:c.991+2_991+25del		p.X331_splice	ENST00000306801	NM_020761.2	331		8/34	0.239537144361679	7	FACETS	1	0.954	1	0.378	0.336	0.421	CLONAL	2	FALSE	1	0.239537144361679	7		492	548	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034721-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	62	597	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.361394569125218	3	FACETS	0.709	0.614	0.812	0.236	0.204	0.271	SUBCLONAL	1	TRUE	0	0.464268951022912	3		597	464	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0034721-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	89	330	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.464268951022912	1	FACETS	0.68	0.606	0.758	0.68	0.606	0.758	SUBCLONAL	1	TRUE	0	0.464268951022912	1		330	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0034721-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	191	527	1	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.464268951022912	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.464268951022912	1		528	597	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942685	48942685	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913301	NA	P-0034721-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	67	318	0	ENST00000267163.4:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000267163	NM_000321.2	358	Cga/Tga	11/27	0.464268951022912	1	FACETS	0.89	0.783	1	0.89	0.783	1	CLONAL	1	TRUE	0	0.464268951022912	1		318	249	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89815072	89815072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868782409	NA	P-0034721-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	88	455	0	ENST00000389301.3:c.3343G>A	p.Glu1115Lys	p.E1115K	ENST00000389301	NM_000135.2	1115	Gag/Aag	33/43	1	2	FACETS	0.532	0.471	0.597	0.532	0.471	0.597	SUBCLONAL	1	TRUE	1	0.464268951022912	2		455	713	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446161	70446161	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034721-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	62	374	0	ENST00000373644.4:c.5101C>T	p.Gln1701Ter	p.Q1701*	ENST00000373644	NM_030625.2	1701	Caa/Taa	11/12	0.333551497145059	1	FACETS	0.405	0.35	0.464	0.405	0.35	0.464	SUBCLONAL	1	TRUE	0	0.464268951022912	1		374	507	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138122	64138122	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034721-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	49	600	0	ENST00000334205.4:c.2045C>T	p.Ser682Leu	p.S682L	ENST00000334205	NM_003942.2	682	tCg/tTg	16/17	0.280002940465021	1	FACETS	0.206	0.174	0.242	0.206	0.174	0.242	SUBCLONAL	1	TRUE	0	0.464268951022912	1		600	787	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546700	9546700	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034721-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	103	359	0	ENST00000353224.5:c.1322G>T	p.Ser441Ile	p.S441I	ENST00000353224	NM_177990.2	441	aGc/aTc	5/10	0.464268951022912	3	FACETS	0.951	0.853	1	0.475	0.426	0.527	CLONAL	1	TRUE	1	0.464268951022912	3		359	575	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255503	16255503	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034721-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	147	401	0	ENST00000375759.3:c.2768A>C	p.Glu923Ala	p.E923A	ENST00000375759	NM_015001.2	923	gAg/gCg	11/15	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.464268951022912	2		401	632	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276714	115276714	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034721-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	71	265	0	ENST00000438362.2:c.745G>T	p.Gly249Cys	p.G249C	ENST00000438362	NM_001242891.1	249	Ggt/Tgt	8/20	1	2	FACETS	0.816	0.716	0.922	0.816	0.716	0.922	CLONAL	1	TRUE	1	0.464268951022912	2		265	375	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490313	56490313	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034721-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	31	321	0	ENST00000267101.3:c.2082G>C	p.Glu694Asp	p.E694D	ENST00000267101	NM_001982.3	694	gaG/gaC	18/28	1	2	FACETS	0.284	0.229	0.346	0.284	0.229	0.346	SUBCLONAL	1	TRUE	1	0.464268951022912	2		321	470	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33430518	33430518	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034721-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	194	594	0	ENST00000345365.6:c.622G>T	p.Val208Phe	p.V208F	ENST00000345365	NM_002878.3	208	Gtc/Ttc	7/10	1	2	FACETS	0.975	0.903	1	0.975	0.903	1	CLONAL	1	TRUE	1	0.464268951022912	2		594	857	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821829	59821829	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034721-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	118	428	0	ENST00000259008.2:c.2221G>T	p.Val741Leu	p.V741L	ENST00000259008	NM_032043.2	741	Gtg/Ttg	15/20	1	2	FACETS	0.938	0.85	1	0.938	0.85	1	CLONAL	1	TRUE	1	0.464268951022912	2		428	542	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100956	41100956	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034721-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	170	576	0	ENST00000373198.4:c.1400C>G	p.Pro467Arg	p.P467R	ENST00000373198	NM_133170.3	467	cCc/cGc	8/32	0.464268951022912	3	FACETS	0.924	0.849	1	0.462	0.424	0.501	CLONAL	1	TRUE	1	0.464268951022912	3		576	977	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547856	41547856	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034721-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	135	359	0	ENST00000263253.7:c.2837G>T	p.Ser946Ile	p.S946I	ENST00000263253	NM_001429.3	946	aGc/aTc	15/31	0.464268951022912	1	FACETS	0.995	0.911	1	0.995	0.911	1	CLONAL	1	TRUE	0	0.464268951022912	1		359	449	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067061	143067061	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034721-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	68	380	0	ENST00000262992.4:c.1652G>C	p.Gly551Ala	p.G551A	ENST00000262992	NM_001101669.1	551	gGc/gCc	16/24	0.280002940465021	1	FACETS	0.458	0.399	0.522	0.458	0.399	0.522	SUBCLONAL	1	TRUE	0	0.464268951022912	1		380	491	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168483	56168483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034721-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	50	196	0	ENST00000399503.3:c.1439G>A	p.Arg480Lys	p.R480K	ENST00000399503	NM_005921.1	480	aGa/aAa	8/20	1	2	FACETS	0.634	0.54	0.736	0.634	0.54	0.736	SUBCLONAL	1	TRUE	1	0.464268951022912	2		196	340	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043963	180043963	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034721-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	182	646	0	ENST00000261937.6:c.3033G>T	p.Met1011Ile	p.M1011I	ENST00000261937	NM_182925.4	1011	atG/atT	22/30	0.229388029170236	1	FACETS	0.879	0.814	0.946	0.879	0.814	0.946	INDETERMINATE	1	TRUE	0	0.464268951022912	1		646	685	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120660	94120660	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034721-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	105	347	0	ENST00000369303.4:c.391G>T	p.Asp131Tyr	p.D131Y	ENST00000369303	NM_004440.3	131	Gac/Tac	3/17	1	2	FACETS	0.885	0.796	0.979	0.885	0.796	0.979	CLONAL	1	TRUE	1	0.464268951022912	2		347	511	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771211	161771211	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034721-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	302	474	0	ENST00000366898.1:c.1318C>G	p.Gln440Glu	p.Q440E	ENST00000366898	NM_004562.2	440	Cag/Gag	12/12	0.21298906264027	3	FACETS	0.97	0.918	1	0.97	0.918	1	INDETERMINATE	2	TRUE	1	0.464268951022912	3		474	826	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961011	15961011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142717545	NA	P-0035162-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	80	528	2	ENST00000268712.3:c.6209C>T	p.Ser2070Leu	p.S2070L	ENST00000268712	NM_006311.3	2070	tCg/tTg	40/46	1	2	FACETS	0.984	0.887	1	0.984	0.887	1	CLONAL	1	TRUE	1	0.878900507555901	2		530	185	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120363	94120363	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035162-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	73	316	0	ENST00000369303.4:c.688G>T	p.Val230Phe	p.V230F	ENST00000369303	NM_004440.3	230	Gtt/Ttt	3/17	0.824781162120322	3	FACETS	1	0.891	1	0.502	0.446	0.562	CLONAL	1	TRUE	1	0.878900507555901	3		316	238	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411856	116411880	+	intron_variant	Intron	DEL	CCATGATAGCCGTCTTTAACAAGCT	CCATGATAGCCGTCTTTAACAAGCT	-	novel	NA	P-0035162-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	1415	796	0	ENST00000397752.3:c.2888-46_2888-22del		p.*963*	ENST00000397752	NM_000245.2	-/1390			0.878900507555901	12	FACETS	0.983	0.976	0.989			1	CLONAL	12	TRUE	NA	0.878900507555901	12		796	1473	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422702	49422702	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035162-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	81	609	0	ENST00000301067.7:c.14291A>G	p.Glu4764Gly	p.E4764G	ENST00000301067	NM_003482.3	4764	gAg/gGg	45/54	0.824781162120322	3	FACETS	0.861	0.767	0.961	0.431	0.383	0.481	CLONAL	1	TRUE	1	0.878900507555901	3		609	308	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936268	78936268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035162-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	97	544	0	ENST00000306801.3:c.3700G>A	p.Gly1234Arg	p.G1234R	ENST00000306801	NM_020761.2	1234	Gga/Aga	32/34	0.818548420989586	5	FACETS	0.899	0.804	1	0.3	0.268	0.334	CLONAL	1	TRUE	2	0.878900507555901	5		544	569	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960105	134960105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035162-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	34	557	0	ENST00000398015.3:c.2462G>A	p.Gly821Glu	p.G821E	ENST00000398015	NM_004441.4	821	gGa/gAa	13/16	0.568429794933835	6	FACETS	0.464	0.379	0.56	0.155	0.126	0.187	SUBCLONAL	1	TRUE	3	0.878900507555901	6		557	460	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374341	138374341	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035162-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	88	351	0	ENST00000289153.2:c.3103G>A	p.Glu1035Lys	p.E1035K	ENST00000289153	NM_006219.2	1035	Gaa/Aaa	22/22	0.568429794933835	6	FACETS	0.754	0.674	0.839	0.503	0.449	0.56	SUBCLONAL	2	TRUE	3	0.878900507555901	6		351	366	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0036133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	17	463	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.187532987122417	3	FACETS	0.243	0.18	0.318	0.121	0.09	0.159	SUBCLONAL	1	FALSE	1	0.303884345981586	3		463	531	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846036	68846036	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0039376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	117	696	0	ENST00000261769.5:c.1009-2A>G		p.X337_splice	ENST00000261769	NM_004360.3	337			0.240154222514613	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.21	1		696	820	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448387	56448387	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	56	846	0	ENST00000407977.2:c.260C>G	p.Pro87Arg	p.P87R	ENST00000407977		87	cCg/cGg	3/10	1	2	FACETS	0.566	0.483	0.657	0.566	0.483	0.657	SUBCLONAL	1	TRUE	1	0.21	2		846	943	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040533-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	107	324	0				ENST00000310581	NM_198253.2	-/1132			0.293892218097393	1	FACETS	0.584	0.529	0.641	0.584	0.529	0.641	INDETERMINATE	1	TRUE	0	0.680724157661813	1		324	355	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398917	398917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356308443	NA	P-0040533-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	94	495	0	ENST00000380956.4:c.727G>A	p.Glu243Lys	p.E243K	ENST00000380956	NM_001195286.1	243	Gaa/Aaa	6/9	0.40819015174541	1	FACETS	0.441	0.395	0.49	0.441	0.395	0.49	INDETERMINATE	1	TRUE	0	0.680724157661813	1		495	413	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682991	241682991	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1226883651	NA	P-0040533-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	131	532	0	ENST00000366560.3:c.32C>G	p.Ser11Trp	p.S11W	ENST00000366560	NM_000143.3	11	tCg/tGg	1/10	1	2	FACETS	0.679	0.618	0.742	0.679	0.618	0.742	SUBCLONAL	1	TRUE	1	0.680724157661813	2		532	567	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224531	108224531	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040533-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	90	260	0	ENST00000278616.4:c.8710G>C	p.Glu2904Gln	p.E2904Q	ENST00000278616	NM_000051.3	2904	Gag/Cag	60/63	0.680724157661813	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.680724157661813	1		260	166	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511637	46511637	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040533-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	95	446	0	ENST00000262741.5:c.1140C>G	p.Phe380Leu	p.F380L	ENST00000262741	NM_003629.3	380	ttC/ttG	9/10	1	2	FACETS	0.71	0.637	0.787	0.71	0.637	0.787	SUBCLONAL	1	TRUE	1	0.680724157661813	2		446	393	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106271	27106302	+	frameshift_variant	Frame_Shift_Del	DEL	GTAAGGATGAGACCCCACTGTGTACCCTTCTG	GTAAGGATGAGACCCCACTGTGTACCCTTCTG	-	novel	NA	P-0040533-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	198	601	0	ENST00000324856.7:c.5883_5914del	p.Ser1961ArgfsTer27	p.S1961Rfs*27	ENST00000324856	NM_006015.4	1961	aGTAAGGATGAGACCCCACTGTGTACCCTTCTG/a	20/20	0.680724157661813	1	FACETS	0.962	0.904	1	0.962	0.904	1	CLONAL	1	TRUE	0	0.680724157661813	1		601	399	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983018	201983019	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040533-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	310	853	0	ENST00000359651.3:c.868dup	p.Glu290GlyfsTer11	p.E290Gfs*11	ENST00000359651		289	-/G	7/8	1	2	FACETS	0.907	0.857	0.959	0.907	0.857	0.959	CLONAL	1	TRUE	1	0.680724157661813	2		853	1004	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432341	432341	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040533-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	48	298	0	ENST00000399788.2:c.2182C>G	p.Leu728Val	p.L728V	ENST00000399788	NM_001042603.1	728	Ctg/Gtg	16/28	0.236565450619953	1	FACETS	0.394	0.336	0.457	0.394	0.336	0.457	INDETERMINATE	1	TRUE	0	0.680724157661813	1		298	236	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864474	57864474	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040533-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	193	692	0	ENST00000228682.2:c.1951C>G	p.Pro651Ala	p.P651A	ENST00000228682	NM_005269.2	651	Cca/Gca	12/12	0.28508621293822	4	FACETS	0.808	0.752	0.865	0.808	0.752	0.865	INDETERMINATE	2	TRUE	2	0.680724157661813	4		692	590	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355171	15355171	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040533-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	226	878	0	ENST00000263377.2:c.2452G>C	p.Asp818His	p.D818H	ENST00000263377	NM_058243.2	818	Gac/Cac	13/20	0.236565450619953	1	FACETS	0.562	0.525	0.6	0.562	0.525	0.6	INDETERMINATE	1	TRUE	0	0.680724157661813	1		878	779	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582062	189582062	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040533-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	147	400	0	ENST00000264731.3:c.621G>C	p.Lys207Asn	p.K207N	ENST00000264731	NM_003722.4	207	aaG/aaC	5/14	1	2	FACETS	0.847	0.778	0.918	0.847	0.778	0.918	CLONAL	1	TRUE	1	0.680724157661813	2		400	510	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280127	66280127	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040533-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	115	268	0	ENST00000273854.3:c.1562A>C	p.Lys521Thr	p.K521T	ENST00000273854	NM_004439.5	521	aAa/aCa	7/18	0.623126160356833	2	FACETS	0.782	0.723	0.841	0.782	0.723	0.841	SUBCLONAL	2	TRUE	0	0.680724157661813	2		268	216	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29913230	29913230	+	stop_lost,splice_region_variant	Nonstop_Mutation	SNP	T	T	G	novel	NA	P-0040533-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	178	399	0	ENST00000376809.5:c.1096T>G	p.Ter366GlyextTer8	p.*366Gext*8	ENST00000376809	NM_002116.7	366	Tga/Gga	8/8	0.40819015174541	1	FACETS	0.858	0.801	0.915	0.858	0.801	0.915	INDETERMINATE	1	TRUE	0	0.680724157661813	1		399	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579378	7579378	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0040826-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	553	1036	4	ENST00000269305.4:c.309C>G	p.Tyr103Ter	p.Y103*	ENST00000269305	NM_001126112.2	103	taC/taG	4/11	0.425317339756814	2	FACETS	0.982	0.944	1	0.982	0.944	1	CLONAL	2	TRUE	0	0.427092244314166	2		1040	1319	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0042642-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	33	788	4	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.43	2		792	124	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0042642-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	22	1241	4	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	1	2	FACETS	0.853	0.67	1	0.853	0.67	1	CLONAL	1	TRUE	1	0.43	2		1245	120	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807889	1807889	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs78311289	NA	P-0042642-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	23	1417	0	ENST00000260795.2:c.1948A>G	p.Lys650Glu	p.K650E	ENST00000260795		650	Aag/Gag	13/17	1	2	FACETS	0.856	0.677	1	0.856	0.677	1	CLONAL	1	TRUE	1	0.43	2		1417	125	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742463	17742463	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042642-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	29	959	0	ENST00000250003.3:c.650del	p.Pro217ArgfsTer33	p.P217Rfs*33	ENST00000250003	NM_002478.4	215	ggC/gg	2/3	1	2	FACETS	0.977	0.796	1	0.977	0.796	1	CLONAL	1	TRUE	1	0.43	2		959	138	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042642-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	22	1435	2	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.787	0.618	0.978	0.787	0.618	0.978	CLONAL	1	TRUE	1	0.43	2		1437	130	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353819	15353819	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042642-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	30	777	2	ENST00000263377.2:c.3061del	p.His1021IlefsTer47	p.H1021Ifs*47	ENST00000263377	NM_058243.2	1021	Cat/at	14/20	1	2	FACETS	0.581	0.471	0.705	0.581	0.471	0.705	SUBCLONAL	1	TRUE	1	0.43	2		779	240	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955112	17955112	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755706305	NA	P-0042642-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	35	1317	8	ENST00000458235.1:c.115del	p.Gln39SerfsTer108	p.Q39Sfs*108	ENST00000458235	NM_000215.3	39	Cag/ag	2/24	1	2	FACETS	0.92	0.763	1	0.92	0.763	1	CLONAL	1	TRUE	1	0.43	2		1325	177	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1255459	1255459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777672180	NA	P-0042642-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	25	921	1	ENST00000310581.5:c.3100C>T	p.Arg1034Cys	p.R1034C	ENST00000310581	NM_198253.2	1034	Cgc/Tgc	14/16	1	2	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	1	0.43	2		922	108	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0042642-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	31	816	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	1	0.822	1	1	0.822	1	CLONAL	1	TRUE	1	0.43	2		816	144	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0042642-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	30	1180	3	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	1	0.821	1	1	0.821	1	CLONAL	1	TRUE	1	0.43	2		1183	139	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456497	32456497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042642-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	13	345	1	ENST00000332351.3:c.395C>T	p.Pro132Leu	p.P132L	ENST00000332351	NM_024426.4	132	cCg/cTg	1/10	1	2	FACETS	0.695	0.503	0.922	0.695	0.503	0.922	SUBCLONAL	1	TRUE	1	0.43	2		346	87	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300836	137300836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042642-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	30	1202	1	ENST00000481739.1:c.481C>T	p.Arg161Trp	p.R161W	ENST00000481739	NM_002957.4	161	Cgg/Tgg	4/10	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.43	2		1203	127	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100129	27100129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042642-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	25	1071	0	ENST00000324856.7:c.3925C>T	p.Leu1309Phe	p.L1309F	ENST00000324856	NM_006015.4	1309	Ctc/Ttc	16/20	1	2	FACETS	0.953	0.763	1	0.953	0.763	1	CLONAL	1	TRUE	1	0.43	2		1071	122	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090446	37090446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750217	NA	P-0042642-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	10	691	1	ENST00000231790.2:c.2041G>A	p.Ala681Thr	p.A681T	ENST00000231790	NM_000249.3	681	Gct/Act	18/19	1	2	FACETS	1	0.835	1	1	0.835	1	CLONAL	1	TRUE	1	0.43	2		692	35	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051247	128051247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042642-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	19	985	0	ENST00000285398.2:c.76G>A	p.Glu26Lys	p.E26K	ENST00000285398	NM_000122.1	26	Gaa/Aaa	2/15	1	2	FACETS	0.858	0.662	1	0.858	0.662	1	CLONAL	1	TRUE	1	0.43	2		985	103	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287277	46287277	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042642-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	10	721	0	ENST00000334344.6:c.5222T>C	p.Leu1741Pro	p.L1741P	ENST00000334344	NM_152641.2	1741	cTt/cCt	19/21	1	2	FACETS	1	0.775	1	1	0.775	1	CLONAL	1	TRUE	1	0.43	2		721	41	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37856539	37856540	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0042642-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	34	609	0	ENST00000269571.5:c.53_54dup	p.Gly19ProfsTer14	p.G19Pfs*14	ENST00000269571		16	-/CC	1/27	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.43	2		609	146	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52649372	52649372	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042642-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	11	705	0	ENST00000394830.3:c.1919A>G	p.Lys640Arg	p.K640R	ENST00000394830	NM_018313.4	640	aAg/aGg	16/30	1	2	FACETS	0.799	0.582	1	1	0.884	1	CLONAL	2	TRUE	1	0.43	2		705	32	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427621	72427621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042642-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	20	689	0	ENST00000477973.2:c.869C>T	p.Ser290Leu	p.S290L	ENST00000477973	NM_012234.5	290	tCg/tTg	4/4	1	2	FACETS	0.949	0.739	1	0.949	0.739	1	CLONAL	1	TRUE	1	0.43	2		689	98	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249092	55249092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042642-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	12	1060	0	ENST00000275493.2:c.2390G>A	p.Cys797Tyr	p.C797Y	ENST00000275493	NM_005228.3	797	tGc/tAc	20/28	0.220236911507573	1	FACETS	0.456	0.324	0.615	0.456	0.324	0.615	INDETERMINATE	1	TRUE	0	0.43	1		1060	96	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0043580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	115	463	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.922	0.836	1	1	0.988	1	CLONAL	2	FALSE	1	0.272820304674753	2		463	457	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0043580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	67	512	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.84	0.73	0.958	0.84	0.73	0.958	CLONAL	1	FALSE	1	0.272820304674753	2		513	585	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398279	25398279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894365	NA	P-0043580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	10	466	1	ENST00000311936.3:c.40G>A	p.Val14Ile	p.V14I	ENST00000311936	NM_004985.3	14	Gta/Ata	2/5	1	2	FACETS	0.156	0.105	0.221	0.156	0.105	0.221	SUBCLONAL	1	FALSE	1	0.272820304674753	2		467	469	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119932	70119932	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	133	386	0	ENST00000245479.2:c.934C>T	p.Gln312Ter	p.Q312*	ENST00000245479	NM_000346.3	312	Cag/Tag	3/3	1	2	FACETS	1	0.962	1	1	0.991	1	CLONAL	2	FALSE	1	0.272820304674753	2		386	447	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928872	44928872	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs755440519	NA	P-0043580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	12	226	0	ENST00000377967.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000377967	NM_021140.2	658	Cga/Tga	17/29	1	1	FACETS	0.336	0.236	0.459	0.336	0.236	0.459	SUBCLONAL	1	FALSE	0	0.272820304674753	1		226	226	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411576	63411576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	220	376	0	ENST00000330258.3:c.1591C>T	p.Arg531Ter	p.R531*	ENST00000330258	NM_152424.3	531	Cga/Tga	2/2	1	1	FACETS	0.888	0.841	0.935	1	0.996	1	CLONAL	4	FALSE	0	0.272820304674753	1		376	392	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120175	70120175	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	62	379	0	ENST00000245479.2:c.1177C>T	p.Gln393Ter	p.Q393*	ENST00000245479	NM_000346.3	393	Cag/Tag	3/3	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.272820304674753	2		379	363	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474041	29474041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs78723472	NA	P-0043580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	231	758	0	ENST00000389048.3:c.2134G>A	p.Val712Met	p.V712M	ENST00000389048	NM_004304.4	712	Gtg/Atg	12/29	0.154344172843733	2	FACETS	1	0.986	1	1	0.986	1	INDETERMINATE	2	FALSE	0	0.272820304674753	2		758	711	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339230	70339230	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	90	304	0	ENST00000374080.3:c.107T>C	p.Leu36Pro	p.L36P	ENST00000374080		36	cTg/cCg	2/45	1	1	FACETS	0.772	0.69	0.858	1	0.982	1	SUBCLONAL	2	FALSE	0	0.272820304674753	1		304	369	SUCCESS
APC	324	MSKCC	GRCh37	5	112173582	112173582	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0043580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	69	328	0	ENST00000257430.4:c.2291T>G	p.Leu764Ter	p.L764*	ENST00000257430	NM_000038.5	764	tTa/tGa	16/16	1	2	FACETS	0.821	0.721	0.927	1	0.978	1	CLONAL	2	FALSE	1	0.272820304674753	2		328	308	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81954864	81954864	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1345789580	NA	P-0043580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	144	630	0	ENST00000359376.3:c.2297A>G	p.Asn766Ser	p.N766S	ENST00000359376	NM_002661.3	766	aAt/aGt	21/33	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.272820304674753	2		630	718	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89874762	89874762	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	39	534	0	ENST00000389301.3:c.536T>A	p.Leu179His	p.L179H	ENST00000389301	NM_000135.2	179	cTt/cAt	6/43	1	2	FACETS	0.424	0.35	0.506	0.424	0.35	0.506	SUBCLONAL	1	FALSE	1	0.272820304674753	2		534	675	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17117070	17117070	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	82	687	0	ENST00000285071.4:c.1639G>T	p.Val547Phe	p.V547F	ENST00000285071	NM_144997.5	547	Gtc/Ttc	14/14	1	2	FACETS	0.834	0.735	0.94	0.834	0.735	0.94	CLONAL	1	FALSE	1	0.272820304674753	2		687	721	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962456	38962456	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	19	325	0	ENST00000357387.3:c.1676A>G	p.Asn559Ser	p.N559S	ENST00000357387	NM_152756.3	559	aAt/aGt	19/38	1	2	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	FALSE	1	0.272820304674753	2		325	124	SUCCESS
APC	324	MSKCC	GRCh37	5	112175661	112175662	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACCT	novel	NA	P-0043580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	91	355	0	ENST00000257430.4:c.4373_4376dup	p.Ala1460TyrfsTer3	p.A1460Yfs*3	ENST00000257430	NM_000038.5	1457	gca/gcACCTa	16/16	1	2	FACETS	0.808	0.721	0.898	1	0.983	1	CLONAL	2	FALSE	1	0.272820304674753	2		355	413	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938432	44938435	+	frameshift_variant	Frame_Shift_Del	DEL	AATG	AATG	-	novel	NA	P-0043580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	15	293	0	ENST00000377967.4:c.2982_2985del	p.Glu995IlefsTer3	p.E995Ifs*3	ENST00000377967	NM_021140.2	994	AATGaa/aa	20/29	1	1	FACETS	0.383	0.28	0.507	0.383	0.28	0.507	SUBCLONAL	1	FALSE	0	0.272820304674753	1		293	248	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040707	47040707	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	83	379	0	ENST00000377604.3:c.1342C>T	p.Gln448Ter	p.Q448*	ENST00000377604	NM_001204468.1	448	Cag/Tag	13/24	1	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	0	0.272820304674753	1		379	416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578410	7578410	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	113	851	0	ENST00000269305.4:c.520A>T	p.Arg174Trp	p.R174W	ENST00000269305	NM_001126112.2	174	Agg/Tgg	5/11	NA	2	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.215206882610338	2		851	928	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559158	29559158	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	55	400	1	ENST00000356175.3:c.3265G>T	p.Glu1089Ter	p.E1089*	ENST00000356175	NM_000267.3	1089	Gaa/Taa	25/57	1	2	FACETS	0.88	0.752	1	0.88	0.752	1	CLONAL	1	TRUE	1	0.215206882610338	2		401	581	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438208	110438208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	18	130	1	ENST00000375856.3:c.193G>A	p.Gly65Arg	p.G65R	ENST00000375856	NM_003749.2	65	Ggg/Agg	1/2	1	2	FACETS	0.973	0.736	1	0.973	0.736	1	CLONAL	1	TRUE	1	0.215206882610338	2		131	172	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684286	29684286	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0044006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	61	464	0	ENST00000356175.3:c.7807-1G>T		p.X2603_splice	ENST00000356175	NM_000267.3	2603			1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.215206882610338	2		464	511	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46215211	46215211	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	16	215	0	ENST00000334344.6:c.646T>A	p.Ser216Thr	p.S216T	ENST00000334344	NM_152641.2	216	Tcc/Acc	6/21	1	2	FACETS	0.755	0.56	0.986	0.755	0.56	0.986	CLONAL	1	TRUE	1	0.215206882610338	2		215	197	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601309	28601310	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0044006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	56	408	0	ENST00000241453.7:c.2122_2123del	p.Glu708LysfsTer55	p.E708Kfs*55	ENST00000241453	NM_004119.2	708	GAa/a	17/24	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.215206882610338	2		408	476	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176666842	176666842	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	50	381	0	ENST00000439151.2:c.4278G>T	p.Lys1426Asn	p.K1426N	ENST00000439151	NM_022455.4	1426	aaG/aaT	8/23	1	2	FACETS	0.989	0.84	1	0.989	0.84	1	CLONAL	1	TRUE	1	0.215206882610338	2		381	470	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484243	8484243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044006-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	44	541	0	ENST00000356435.5:c.3289C>T	p.His1097Tyr	p.H1097Y	ENST00000356435		1097	Cac/Tac	19/35	0.204484791520496	2	FACETS	0.588	0.492	0.695	0.294	0.246	0.348	SUBCLONAL	1	TRUE	0	0.215206882610338	2		541	695	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	178	346	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.835	0.774	0.898	0.835	0.774	0.898	CLONAL	1	TRUE	1	0.72	2		347	592	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438316	110438317	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	rs532810290	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	71	191	0	ENST00000375856.3:c.82_84dup	p.Asn28dup	p.N28dup	ENST00000375856	NM_003749.2	28	-/AAC	1/2	1	2	FACETS	0.585	0.514	0.661	0.585	0.514	0.661	SUBCLONAL	1	TRUE	1	0.72	2		191	337	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087503	27087503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	436	774	1	ENST00000324856.7:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000324856	NM_006015.4	693	Cga/Tga	5/20	1	2	FACETS	0.962	0.918	1	0.962	0.918	1	CLONAL	1	TRUE	1	0.72	2		775	1259	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	110	819	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.243	0.217	0.27	0.243	0.217	0.27	SUBCLONAL	1	TRUE	1	0.72	2		819	1259	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	138	274	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.852	0.781	0.924	0.852	0.781	0.924	CLONAL	1	TRUE	1	0.72	2		274	450	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630626	158630626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912678	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	147	272	0	ENST00000263640.3:c.617G>A	p.Arg206His	p.R206H	ENST00000263640	NM_001105.4	206	cGc/cAc	6/11	1	2	FACETS	0.975	0.899	1	0.975	0.899	1	CLONAL	1	TRUE	1	0.72	2		272	419	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209616	98209617	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761353734	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	227	662	0	ENST00000331920.6:c.3921dup	p.Arg1308GlnfsTer17	p.R1308Qfs*17	ENST00000331920	NM_000264.3	1307	-/C	23/24	1	2	FACETS	0.757	0.707	0.809	0.757	0.707	0.809	SUBCLONAL	1	TRUE	1	0.72	2		662	833	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	309	521	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.852	0.804	0.9	0.852	0.804	0.9	CLONAL	1	TRUE	1	0.72	2		521	1008	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717769	89717770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	156	321	0	ENST00000371953.3:c.800dup	p.Asp268GlyfsTer30	p.D268Gfs*30	ENST00000371953	NM_000314.4	265	cta/ctAa	7/9	1	2	FACETS	0.84	0.774	0.907	0.84	0.774	0.907	CLONAL	1	TRUE	1	0.72	2		321	516	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	133	332	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	0.743	0.679	0.81	0.743	0.679	0.81	SUBCLONAL	1	TRUE	1	0.72	2		332	497	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138642	55138642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143344944	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	252	543	0	ENST00000257290.5:c.1319C>T	p.Thr440Met	p.T440M	ENST00000257290	NM_006206.4	440	aCg/aTg	9/23	1	2	FACETS	0.894	0.839	0.95	0.894	0.839	0.95	CLONAL	1	TRUE	1	0.72	2		543	783	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	342	703	7	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.943	0.895	0.993	0.943	0.895	0.993	CLONAL	1	TRUE	1	0.72	2		710	1007	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	437	778	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.986	0.941	1	0.986	0.941	1	CLONAL	1	TRUE	1	0.72	2		778	1231	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675571	86675571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1561325048	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	145	209	0	ENST00000274376.6:c.2513del	p.Asn838MetfsTer4	p.N838Mfs*4	ENST00000274376	NM_002890.2	836	gAa/ga	19/25	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.72	2		209	389	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958479	90958480	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs780235686	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	179	321	0	ENST00000265433.3:c.1958dup	p.Leu654AlafsTer5	p.L654Afs*5	ENST00000265433	NM_002485.4	653	aag/aaAg	13/16	1	2	FACETS	0.869	0.806	0.934	0.869	0.806	0.934	CLONAL	1	TRUE	1	0.72	2		321	572	SUCCESS
APC	324	MSKCC	GRCh37	5	112173926	112173926	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060503287	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	214	290	0	ENST00000257430.4:c.2635C>T	p.Gln879Ter	p.Q879*	ENST00000257430	NM_000038.5	879	Cag/Tag	16/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.72	2		290	535	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952049	178952049	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242945375	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	177	332	0	ENST00000263967.3:c.3104C>T	p.Ala1035Val	p.A1035V	ENST00000263967	NM_006218.2	1035	gCt/gTt	21/21	1	2	FACETS	0.924	0.858	0.992	0.924	0.858	0.992	CLONAL	1	TRUE	1	0.72	2		332	532	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623241	52623241	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375764191	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	31	339	0	ENST00000394830.3:c.2810C>T	p.Ala937Val	p.A937V	ENST00000394830	NM_018313.4	937	gCt/gTt	19/30	1	2	FACETS	0.164	0.132	0.201	0.164	0.132	0.201	SUBCLONAL	1	TRUE	1	0.72	2		339	524	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926270	112926270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918457	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	316	545	0	ENST00000351677.2:c.1403C>T	p.Thr468Met	p.T468M	ENST00000351677	NM_002834.3	468	aCg/aTg	12/16	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.72	2		545	870	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223548	53223548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	278	573	1	ENST00000375401.3:c.3811C>T	p.Arg1271Trp	p.R1271W	ENST00000375401	NM_004187.3	1271	Cgg/Tgg	23/26	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.72	2		574	739	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936349	49936349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755080567	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	337	649	1	ENST00000296474.3:c.1499G>A	p.Arg500Gln	p.R500Q	ENST00000296474	NM_002447.2	500	cGg/cAg	3/20	1	2	FACETS	0.965	0.915	1	0.965	0.915	1	CLONAL	1	TRUE	1	0.72	2		650	970	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294598	1294598	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200843534	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	227	405	1	ENST00000310581.5:c.403G>A	p.Gly135Arg	p.G135R	ENST00000310581	NM_198253.2	135	Ggg/Agg	2/16	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.72	2		406	613	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105927	27105928	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	149	545	0	ENST00000324856.7:c.5540dup	p.Gly1848TrpfsTer6	p.G1848Wfs*6	ENST00000324856	NM_006015.4	1846	-/G	20/20	1	2	FACETS	0.524	0.479	0.571	0.524	0.479	0.571	SUBCLONAL	1	TRUE	1	0.72	2		545	790	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394897	394897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	257	422	2	ENST00000380956.4:c.293G>A	p.Arg98Gln	p.R98Q	ENST00000380956	NM_001195286.1	98	cGg/cAg	3/9	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.72	2		424	704	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490289	29490289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149003051	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	285	398	0	ENST00000356175.3:c.374G>A	p.Arg125His	p.R125H	ENST00000356175	NM_000267.3	125	cGt/cAt	4/57	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.72	2		398	755	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585494	29585494	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660428	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	114	248	1	ENST00000356175.3:c.4243G>A	p.Glu1415Lys	p.E1415K	ENST00000356175	NM_000267.3	1415	Gaa/Aaa	31/57	1	2	FACETS	0.838	0.761	0.917	0.838	0.761	0.917	CLONAL	1	TRUE	1	0.72	2		249	378	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101278	27101278	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	306	592	0	ENST00000324856.7:c.4563del	p.Ala1522ProfsTer5	p.A1522Pfs*5	ENST00000324856	NM_006015.4	1520	ggC/gg	18/20	1	2	FACETS	0.982	0.928	1	0.982	0.928	1	CLONAL	1	TRUE	1	0.72	2		592	866	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	329	1241	4	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	1	2	FACETS	0.889	0.841	0.938	0.889	0.841	0.938	CLONAL	1	TRUE	1	0.72	2		1245	1028	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448480	49448480	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	317	586	0	ENST00000301067.7:c.231del	p.His77GlnfsTer53	p.H77Qfs*53	ENST00000301067	NM_003482.3	77	caC/ca	3/54	1	2	FACETS	0.943	0.892	0.994	0.943	0.892	0.994	CLONAL	1	TRUE	1	0.72	2		586	934	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243859002	243859003	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	156	324	0	ENST00000263826.5:c.62dup	p.Asn21LysfsTer19	p.N21Kfs*19	ENST00000263826	NM_005465.4	21	aac/aaAc	2/13	1	2	FACETS	0.957	0.884	1	0.957	0.884	1	CLONAL	1	TRUE	1	0.72	2		324	453	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214871	36214871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	424	885	4	ENST00000222270.7:c.3302del	p.Pro1101LeufsTer81	p.P1101Lfs*81	ENST00000222270	NM_014727.1	1099	ggC/gg	8/37	1	2	FACETS	0.959	0.915	1	0.959	0.915	1	CLONAL	1	TRUE	1	0.72	2		889	1228	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121438916	121438916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1455363200	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	389	838	0	ENST00000257555.6:c.1817G>A	p.Gly606Asp	p.G606D	ENST00000257555		606	gGc/gAc	10/10	1	2	FACETS	0.846	0.803	0.888	0.846	0.803	0.888	CLONAL	1	TRUE	1	0.72	2		838	1278	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564667	86564667	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	329	807	0	ENST00000274376.6:c.402del	p.Pro136LeufsTer38	p.P136Lfs*38	ENST00000274376	NM_002890.2	133	ggT/gg	1/25	1	2	FACETS	0.795	0.752	0.84	0.795	0.752	0.84	SUBCLONAL	1	TRUE	1	0.72	2		807	1149	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180486	94180486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	215	467	0	ENST00000323929.3:c.1682G>A	p.Ser561Asn	p.S561N	ENST00000323929	NM_005591.3	561	aGc/aAc	15/20	1	2	FACETS	0.815	0.76	0.871	0.815	0.76	0.871	CLONAL	1	TRUE	1	0.72	2		467	733	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940077	76940077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	230	482	0	ENST00000373344.5:c.671C>T	p.Ala224Val	p.A224V	ENST00000373344	NM_000489.3	224	gCg/gTg	9/35	1	2	FACETS	0.958	0.898	1	0.958	0.898	1	CLONAL	1	TRUE	1	0.72	2		482	667	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852248	63852248	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	305	528	0	ENST00000279873.7:c.3026C>G	p.Ala1009Gly	p.A1009G	ENST00000279873	NM_032199.2	1009	gCg/gGg	10/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.72	2		528	837	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133247	30133247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	373	602	4	ENST00000263025.4:c.251G>A	p.Arg84His	p.R84H	ENST00000263025	NM_002746.2	84	cGc/cAc	2/9	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.72	2		606	1023	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760927	133760927	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	387	826	1	ENST00000318560.5:c.3250C>T	p.Arg1084Ter	p.R1084*	ENST00000318560	NM_005157.4	1084	Cga/Tga	11/11	1	2	FACETS	0.895	0.851	0.94	0.895	0.851	0.94	CLONAL	1	TRUE	1	0.72	2		827	1201	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945503	17945503	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	330	671	1	ENST00000458235.1:c.2227C>T	p.Gln743Ter	p.Q743*	ENST00000458235	NM_000215.3	743	Cag/Tag	17/24	1	2	FACETS	0.979	0.928	1	0.979	0.928	1	CLONAL	1	TRUE	1	0.72	2		672	936	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257668	16257668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs541126378	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	261	516	0	ENST00000375759.3:c.4933G>A	p.Val1645Ile	p.V1645I	ENST00000375759	NM_015001.2	1645	Gta/Ata	11/15	1	2	FACETS	0.959	0.902	1	0.959	0.902	1	CLONAL	1	TRUE	1	0.72	2		516	756	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49449107	49449107	+	start_lost	Translation_Start_Site	SNP	T	T	A	novel	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	99	436	0	ENST00000301067.7:c.1A>T	p.Met1?	p.M1?	ENST00000301067	NM_003482.3	1	Atg/Ttg	1/54	1	2	FACETS	0.388	0.346	0.432	0.388	0.346	0.432	SUBCLONAL	1	TRUE	1	0.72	2		436	709	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473627	67473627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	375	675	0	ENST00000327367.4:c.707C>T	p.Ser236Phe	p.S236F	ENST00000327367	NM_005902.3	236	tCc/tTc	6/9	1	2	FACETS	0.991	0.943	1	0.991	0.943	1	CLONAL	1	TRUE	1	0.72	2		675	1051	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354499	91354499	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	218	446	2	ENST00000355112.3:c.3939G>T	p.Glu1313Asp	p.E1313D	ENST00000355112	NM_000057.2	1313	gaG/gaT	21/22	1	2	FACETS	0.958	0.896	1	0.958	0.896	1	CLONAL	1	TRUE	1	0.72	2		448	632	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40442030	40442030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777761052	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	392	744	0	ENST00000345506.4:c.275C>T	p.Thr92Met	p.T92M	ENST00000345506	NM_003152.3	92	aCg/aTg	4/20	1	2	FACETS	0.944	0.898	0.99	0.944	0.898	0.99	CLONAL	1	TRUE	1	0.72	2		744	1154	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968250	18968250	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	362	698	1	ENST00000262803.5:c.2090G>A	p.Arg697His	p.R697H	ENST00000262803	NM_002911.3	697	cGc/cAc	15/24	1	2	FACETS	0.974	0.926	1	0.974	0.926	1	CLONAL	1	TRUE	1	0.72	2		699	1032	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229439	36229439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	259	496	0	ENST00000222270.7:c.8129G>A	p.Cys2710Tyr	p.C2710Y	ENST00000222270	NM_014727.1	2710	tGc/tAc	37/37	1	2	FACETS	0.986	0.928	1	0.986	0.928	1	CLONAL	1	TRUE	1	0.72	2		496	730	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702306	47702306	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	264	479	0	ENST00000233146.2:c.1905del	p.Ala636HisfsTer49	p.A636Hfs*49	ENST00000233146	NM_000251.2	634	ttA/tt	12/16	1	2	FACETS	0.975	0.918	1	0.975	0.918	1	CLONAL	1	TRUE	1	0.72	2		479	752	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702376	47702377	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	168	312	0	ENST00000233146.2:c.1977dup	p.Asp660ArgfsTer2	p.D660Rfs*2	ENST00000233146	NM_000251.2	658	gaa/gAaa	12/16	1	2	FACETS	0.939	0.87	1	0.939	0.87	1	CLONAL	1	TRUE	1	0.72	2		312	497	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679909	30679909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	254	468	0	ENST00000376406.3:c.1810G>T	p.Gly604Trp	p.G604W	ENST00000376406	NM_014641.2	604	Ggg/Tgg	5/15	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.72	2		468	694	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553746	106553746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	243	401	0	ENST00000369096.4:c.1711G>A	p.Gly571Ser	p.G571S	ENST00000369096	NM_001198.3	571	Ggc/Agc	5/7	1	2	FACETS	0.947	0.889	1	0.947	0.889	1	CLONAL	1	TRUE	1	0.72	2		401	713	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983162	149983163	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	307	580	0	ENST00000253339.5:c.3095_3096del	p.His1032ProfsTer8	p.H1032Pfs*8	ENST00000253339		1032	cAC/c	7/7	1	2	FACETS	0.889	0.84	0.939	0.889	0.84	0.939	CLONAL	1	TRUE	1	0.72	2		580	959	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055744	152055745	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	248	536	0	ENST00000262189.6:c.177dup	p.Lys60GlufsTer7	p.K60Efs*7	ENST00000262189	NM_170606.2	59	-/G	2/59	1	2	FACETS	0.829	0.777	0.882	0.829	0.777	0.882	CLONAL	1	TRUE	1	0.72	2		536	831	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923772	39923772	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs925770716	NA	P-0044823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	480	852	0	ENST00000378444.4:c.3319G>A	p.Val1107Met	p.V1107M	ENST00000378444	NM_001123385.1	1107	Gtg/Atg	7/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.72	2		852	1303	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044931-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	36	324	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.868	0.713	1	0.868	0.713	1	CLONAL	1	TRUE	1	0.18	2		324	461	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0044931-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	60	754	2	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.877	0.754	1	0.877	0.754	1	CLONAL	1	TRUE	1	0.18	2		756	760	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0044931-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	46	458	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.762	0.64	0.896	0.762	0.64	0.896	SUBCLONAL	1	TRUE	1	0.18	2		458	671	SUCCESS
BLM	641	MSKCC	GRCh37	15	91334069	91334069	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs772671554	NA	P-0044931-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	21	305	0	ENST00000355112.3:c.3014T>C	p.Ile1005Thr	p.I1005T	ENST00000355112	NM_000057.2	1005	aTa/aCa	15/22	1	2	FACETS	0.655	0.504	0.832	0.655	0.504	0.832	SUBCLONAL	1	TRUE	1	0.18	2		305	356	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17380492	17380492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199848267	NA	P-0044931-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1399	140	879	0	ENST00000375499.3:c.23C>T	p.Ser8Phe	p.S8F	ENST00000375499	NM_003000.2	8	tCc/tTc	1/8	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.18	2		879	1539	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610179	81610179	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044931-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	34	424	0	ENST00000298171.2:c.1777G>T	p.Ala593Ser	p.A593S	ENST00000298171	NM_000369.2	593	Gcc/Tcc	10/10	1	2	FACETS	0.618	0.504	0.748	0.618	0.504	0.748	SUBCLONAL	1	TRUE	1	0.18	2		424	611	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528119	29528120	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044931-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	25	432	0	ENST00000356175.3:c.1127_1128insA	p.Met376IlefsTer3	p.M376Ifs*3	ENST00000356175	NM_000267.3	376	atg/atAg	10/57	1	2	FACETS	0.582	0.458	0.726	0.582	0.458	0.726	SUBCLONAL	1	TRUE	1	0.18	2		432	477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578488	7578500	+	frameshift_variant	Frame_Shift_Del	DEL	CAACCCACAGCTG	CAACCCACAGCTG	-	novel	NA	P-0044931-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1307	139	913	1	ENST00000269305.4:c.430_442del	p.Gln144IlefsTer22	p.Q144Ifs*22	ENST00000269305	NM_001126112.2	144	CAGCTGTGGGTTGat/at	5/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.18	2		914	1446	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs730881677	NA	P-0045808-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	154	464	0	ENST00000304494.5:c.151-1G>C		p.X51_splice	ENST00000304494	NM_000077.4	51			0.504042900835413	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.503987764175493	1		464	425	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0045808-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	138	355	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	1	2	FACETS	0.943	0.861	1	0.943	0.861	1	CLONAL	1	TRUE	1	0.503987764175493	2		355	581	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025606	1025606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045808-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	233	743	1	ENST00000358495.3:c.769C>T	p.Arg257Trp	p.R257W	ENST00000358495	NM_134424.2	257	Cgg/Tgg	9/12	0.504042900835413	3	FACETS	1	0.976	1	0.549	0.512	0.588	CLONAL	1	TRUE	1	0.503987764175493	3		744	1054	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158404	26158404	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045808-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	540	835	0	ENST00000289316.2:c.7G>T	p.Glu3Ter	p.E3*	ENST00000289316	NM_138720.2	3	Gaa/Taa	1/2	0.504042900835413	2	FACETS	0.961	0.926	0.996	0.961	0.926	0.996	CLONAL	2	TRUE	0	0.503987764175493	2		835	1115	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813638	50813638	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045808-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	182	638	0	ENST00000398568.2:c.1193del	p.Pro398HisfsTer7	p.P398Hfs*7	ENST00000398568	NM_001042412.1	398	Cca/ca	8/18	0.504042900835413	1	FACETS	0.943	0.875	1	0.943	0.875	1	CLONAL	1	TRUE	0	0.503987764175493	1		638	573	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0045863-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	87	221	1				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.78188152413852	2		222	188	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0045863-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	211	429	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.78188152413852	1	FACETS	0.996	0.947	1	0.996	0.947	1	CLONAL	1	TRUE	0	0.78188152413852	1		429	330	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221743	55221743	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519829	NA	P-0045863-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23894	1391	633	0	ENST00000275493.2:c.787A>C	p.Thr263Pro	p.T263P	ENST00000275493	NM_005228.3	263	Acc/Ccc	7/28	0.78188152413852	52	FACETS	0.964	0.934	0.994			1	CLONAL	3	TRUE	NA	0.78188152413852	52		633	25285	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205286	38205286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045863-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	358	1010	0	ENST00000317025.8:c.404C>T	p.Pro135Leu	p.P135L	ENST00000317025	NM_023034.1	135	cCt/cTt	2/24	1	2	FACETS	0.995	0.947	1	0.995	0.947	1	CLONAL	1	TRUE	1	0.78188152413852	2		1010	920	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683655	162683655	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045863-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	34	690	1	ENST00000366898.1:c.314T>A	p.Val105Glu	p.V105E	ENST00000366898	NM_004562.2	105	gTg/gAg	3/12	0.2982808644534	1	FACETS	0.118	0.096	0.143	0.118	0.096	0.143	INDETERMINATE	1	TRUE	0	0.78188152413852	1		691	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0046106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	539	508	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.920471585719941	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.920471585719941	2		508	550	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661964	29661964	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	464	456	0	ENST00000356175.3:c.5859del	p.Asp1955ThrfsTer3	p.D1955Tfs*3	ENST00000356175	NM_000267.3	1953	aTt/at	39/57	0.920471585719941	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.920471585719941	2		456	484	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0046580-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	48	221	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.17	2		222	530	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41242984	41242984	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs876660601	NA	P-0046580-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	50	449	0	ENST00000357654.3:c.4162C>T	p.Gln1388Ter	p.Q1388*	ENST00000357654	NM_007294.3	1388	Cag/Tag	11/23	1	2	FACETS	0.82	0.695	0.959	0.82	0.695	0.959	CLONAL	1	TRUE	1	0.17	2		449	717	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5206850	5206850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046580-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	27	0	0	ENST00000357368.4:c.5782G>A	p.Glu1928Lys	p.E1928K	ENST00000357368	NM_002850.3	1928	Gag/Aag	38/38	1	2	FACETS	0.424	0.336	0.526	0.424	0.336	0.526	SUBCLONAL	1	TRUE	1	0.17	2		0	749	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145488	58145488	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046580-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	30	431	0	ENST00000257904.6:c.13C>G	p.Arg5Gly	p.R5G	ENST00000257904	NM_000075.3	5	Cga/Gga	2/8	0.275071899820434	3	FACETS	0.815	0.656	0.996	0.407	0.328	0.498	CLONAL	1	TRUE	1	0.17	3		431	470	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513232	44513232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046580-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	40	487	1	ENST00000291552.4:c.703G>A	p.Glu235Lys	p.E235K	ENST00000291552	NM_006758.2	235	Gaa/Aaa	8/8	0.275071899820434	3	FACETS	0.927	0.769	1	0.463	0.384	0.551	CLONAL	1	TRUE	1	0.17	3		488	551	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089755	5089755	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046580-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	10	0	0	ENST00000381652.3:c.2653C>T	p.Gln885Ter	p.Q885*	ENST00000381652	NM_004972.3	885	Cag/Tag	20/25	1	2	FACETS	0.422	0.285	0.595	0.422	0.285	0.595	SUBCLONAL	1	TRUE	1	0.17	2		0	279	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322607	39322607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046580-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	21	0	0	ENST00000373001.3:c.385G>A	p.Asp129Asn	p.D129N	ENST00000373001	NM_022157.3	129	Gac/Aac	2/7	1	2	FACETS	0.35	0.268	0.447	0.35	0.268	0.447	SUBCLONAL	1	TRUE	1	0.17	2		0	705	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73334716	73334716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754234020	NA	P-0046580-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	6	0	0	ENST00000377767.4:c.2744C>T	p.Ser915Leu	p.S915L	ENST00000377767	NM_014953.3	915	tCa/tTa	20/21	1	2	FACETS	0.276	0.164	0.428	0.276	0.164	0.428	SUBCLONAL	1	TRUE	1	0.17	2		0	256	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142949964	142949964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046580-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	11	0	0	ENST00000262992.4:c.2746G>A	p.Glu916Lys	p.E916K	ENST00000262992	NM_001101669.1	916	Gag/Aag	24/24	1	2	FACETS	0.28	0.192	0.39	0.28	0.192	0.39	SUBCLONAL	1	TRUE	1	0.17	2		0	462	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74868196	74868196	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046580-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	4	0	0	ENST00000284811.8:c.98G>C	p.Arg33Thr	p.R33T	ENST00000284811		33	aGa/aCa	3/4	1	2	FACETS	0.432	0.226	0.729	0.432	0.226	0.729	SUBCLONAL	1	TRUE	1	0.17	2		0	109	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0046937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	328	570	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.824418456219862	2	FACETS	0.958	0.931	0.984	0.958	0.931	0.984	CLONAL	2	TRUE	0	0.860123224685219	2		570	398	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885975	111885975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776655476	NA	P-0046937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	201	547	1	ENST00000341259.2:c.1597G>A	p.Glu533Lys	p.E533K	ENST00000341259	NM_005475.2	533	Gaa/Aaa	8/8	0.84601881063177	2	FACETS	0.994	0.932	1	0.497	0.466	0.529	CLONAL	1	TRUE	0	0.860123224685219	2		548	470	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939053	36939053	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	67	619	0	ENST00000361632.4:c.656T>C	p.Leu219Pro	p.L219P	ENST00000361632		219	cTt/cCt	5/16	NA	2	FACETS	0.238	0.206	0.272			1	INDETERMINATE	1	TRUE	NA	0.860123224685219	2		619	655	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89724943	89725083	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCTGCAAAATGGAATAAAAAATCTGTTAAAAATATATTTCACTAAATAGTTTAAGATGAGTCATATTTGTGGGTTTTCATTTTAAATTTTCTTTCTCTAGGTGAAGCTGTACTTCACAAAAACAGTAGAGGAGCCGTCAA	ATCTGCAAAATGGAATAAAAAATCTGTTAAAAATATATTTCACTAAATAGTTTAAGATGAGTCATATTTGTGGGTTTTCATTTTAAATTTTCTTTCTCTAGGTGAAGCTGTACTTCACAAAAACAGTAGAGGAGCCGTCAA	-	novel	NA	P-0046937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	77	89	0	ENST00000371953.3:c.1027-98_1069del		p.X343_splice	ENST00000371953	NM_000314.4	343		9/9	0.839610148243641	2	FACETS	0.904	0.844	0.959	0.904	0.844	0.959	CLONAL	2	TRUE	0	0.860123224685219	2		89	99	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0046981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	300	777	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.425109116286626	2	FACETS	0.785	0.744	0.825	0.785	0.744	0.825	SUBCLONAL	2	TRUE	0	0.557335044729962	2		777	686	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0046981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	140	359	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.557335044729962	6	FACETS	0.763	0.696	0.833			1	SUBCLONAL	2	TRUE	NA	0.557335044729962	6		359	696	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609793	81609793	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	84	356	0	ENST00000298171.2:c.1391G>C	p.Gly464Ala	p.G464A	ENST00000298171	NM_000369.2	464	gGg/gCg	10/10	NA	2	FACETS	0.802	0.713	0.895			1	INDETERMINATE	1	TRUE	NA	0.557335044729962	2		356	376	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568640	41568640	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	147	306	0	ENST00000263253.7:c.4590G>C	p.Glu1530Asp	p.E1530D	ENST00000263253	NM_001429.3	1530	gaG/gaC	28/31	0.450589417722282	3	FACETS	0.86	0.795	0.928	0.574	0.53	0.619	CLONAL	2	TRUE	0	0.557335044729962	3		306	392	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412943	63412943	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	121	715	0	ENST00000330258.3:c.224G>T	p.Gly75Val	p.G75V	ENST00000330258	NM_152424.3	75	gGg/gTg	2/2	0.372801445207244	3	FACETS	0.68	0.614	0.749	0.34	0.307	0.375	SUBCLONAL	1	TRUE	1	0.557335044729962	3		715	817	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608192	100608192	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	71	348	0	ENST00000308731.7:c.1898G>A	p.Cys633Tyr	p.C633Y	ENST00000308731	NM_000061.2	633	tGc/tAc	18/19	0.372801445207244	3	FACETS	0.711	0.623	0.806	0.356	0.311	0.403	SUBCLONAL	1	TRUE	1	0.557335044729962	3		348	458	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645700	215645700	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793050	NA	P-0046981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	116	458	0	ENST00000260947.4:c.898C>T	p.Pro300Ser	p.P300S	ENST00000260947	NM_000465.2	300	Cct/Tct	4/11	0.487407831208097	3	FACETS	0.977	0.884	1	0.488	0.442	0.537	CLONAL	1	TRUE	1	0.557335044729962	3		458	545	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450165	32450165	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs369444006	NA	P-0046981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	41	497	0	ENST00000332351.3:c.647G>A	p.Gly216Asp	p.G216D	ENST00000332351	NM_024426.4	216	gGt/gAt	2/10	0.450589417722282	3	FACETS	0.285	0.237	0.339	0.095	0.079	0.113	SUBCLONAL	1	TRUE	0	0.557335044729962	3		497	660	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202636	67202636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759220531	NA	P-0046981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	98	515	1	ENST00000312629.5:c.1445G>A	p.Arg482His	p.R482H	ENST00000312629	NM_003952.2	482	cGc/cAc	15/15	0.557335044729962	6	FACETS	0.607	0.54	0.679			1	SUBCLONAL	1	TRUE	NA	0.557335044729962	6		516	1225	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793087	33793088	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGG	novel	NA	P-0046981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	66	273	0	ENST00000498907.2:c.231_233dup	p.Leu78dup	p.L78dup	ENST00000498907	NM_004364.3	78	ctg/ctCCTg	1/1	0.557335044729962	4	FACETS	0.773	0.673	0.882			1	SUBCLONAL	1	TRUE	NA	0.557335044729962	4		273	477	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220115	133220115	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047288-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	60	784	0	ENST00000320574.5:c.4322T>A	p.Leu1441Gln	p.L1441Q	ENST00000320574	NM_006231.2	1441	cTg/cAg	34/49	1	2	FACETS	0.859	0.738	0.991	0.859	0.738	0.991	CLONAL	1	TRUE	1	0.16	2		784	873	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988331	36988331	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047288-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	39	377	0	ENST00000354822.5:c.322del	p.Leu108SerfsTer17	p.L108Sfs*17	ENST00000354822	NM_001079668.2	108	Ctc/tc	2/3	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.16	2		377	454	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40458404	40458404	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047288-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	13	153	0	ENST00000345506.4:c.1619A>G	p.Asn540Ser	p.N540S	ENST00000345506	NM_003152.3	540	aAc/aGc	14/20	1	2	FACETS	0.793	0.566	1	0.793	0.566	1	CLONAL	1	TRUE	1	0.16	2		153	205	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988512	36988512	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047288-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	65	648	1	ENST00000354822.5:c.141del	p.Ser48ValfsTer53	p.S48Vfs*53	ENST00000354822	NM_001079668.2	47	ttG/tt	2/3	1	2	FACETS	0.97	0.839	1	0.97	0.839	1	CLONAL	1	TRUE	1	0.16	2		649	838	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790405	3790412	+	frameshift_variant	Frame_Shift_Del	DEL	CTTCATCC	CTTCATCC	-	novel	NA	P-0047288-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	61	547	0	ENST00000262367.5:c.4121_4128del	p.Gly1374ValfsTer11	p.G1374Vfs*11	ENST00000262367	NM_004380.2	1374	gGGATGAAG/g	24/31	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.16	2		547	682	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047863-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	300	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.797671012188192	4	FACETS	0.96	0.911	1	0.96	0.911	1	CLONAL	2	TRUE	2	0.842706638268835	4		298	683	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0047863-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	375	704	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.842706638268835	3	FACETS	0.958	0.919	0.997	0.958	0.919	0.997	CLONAL	2	TRUE	1	0.842706638268835	3		704	660	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0047863-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	354	326	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.842706638268835	3	FACETS	0.993	0.97	1	0.993	0.97	1	CLONAL	3	TRUE	0	0.842706638268835	3		326	401	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0047863-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	348	470	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.842706638268835	3	FACETS	0.998	0.957	1	0.998	0.957	1	CLONAL	2	TRUE	1	0.842706638268835	3		470	588	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0047863-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	440	471	11	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	0.797671012188192	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.842706638268835	4		482	953	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662817	227662817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1273995645	NA	P-0047863-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	764	952	1	ENST00000305123.5:c.638G>A	p.Arg213His	p.R213H	ENST00000305123	NM_005544.2	213	cGc/cAc	1/2	0.788166094560391	3	FACETS	0.982	0.955	1	0.982	0.955	1	CLONAL	2	TRUE	1	0.842706638268835	3		953	1312	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117757	70117758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0047863-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1195	1007	1143	0	ENST00000245479.2:c.227_228dup	p.Val77ArgfsTer34	p.V77Rfs*34	ENST00000245479	NM_000346.3	75	-/GC	1/3	0.842706638268835	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.842706638268835	4		1143	2202	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758765	41758765	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047863-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1509	414	1111	3	ENST00000301178.4:c.1819G>T	p.Gly607Cys	p.G607C	ENST00000301178	NM_021913.4	607	Ggt/Tgt	16/20	0.797671012188192	4	FACETS	0.942	0.893	0.991	0.471	0.446	0.496	CLONAL	1	TRUE	2	0.842706638268835	4		1114	1923	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131084	55131084	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0047863-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	386	506	0	ENST00000257290.5:c.629-2A>T		p.X210_splice	ENST00000257290	NM_006206.4	210			0.842706638268835	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.842706638268835	3		506	648	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964511	70964511	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047863-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	584	812	0	ENST00000276594.2:c.1517C>G	p.Thr506Arg	p.T506R	ENST00000276594	NM_024504.3	506	aCa/aGa	8/8	0.797671012188192	4	FACETS	0.933	0.899	0.969	0.933	0.899	0.969	CLONAL	2	TRUE	2	0.842706638268835	4		812	1368	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039888	47039900	+	frameshift_variant	Frame_Shift_Del	DEL	CAGTGGGCCATCT	CAGTGGGCCATCT	-	novel	NA	P-0047863-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	709	531	0	ENST00000377604.3:c.1233_1245del	p.Gln411HisfsTer70	p.Q411Hfs*70	ENST00000377604	NM_001204468.1	411	CAGTGGGCCATCTca/ca	12/24	0.79479121486022	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.842706638268835	2		531	809	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068307	16068307	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs752892550	NA	P-0047863-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	23	63	0	ENST00000268712.3:c.604C>G	p.Leu202Val	p.L202V	ENST00000268712	NM_006311.3	202	Ctg/Gtg	5/46	0.842706638268835	3	FACETS	0.817	0.651	1	0.408	0.325	0.5	CLONAL	1	TRUE	1	0.842706638268835	3		63	95	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913514	NA	P-0048138-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	117	376	1	ENST00000288135.5:c.2466T>A	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaA	17/21	1	2	FACETS	0.889	0.807	0.975	0.889	0.807	0.975	CLONAL	1	FALSE	1	0.582180017914511	2		377	452	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597885	43597885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1311922451	NA	P-0048138-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	92	1362	2	ENST00000355710.3:c.433G>A	p.Val145Ile	p.V145I	ENST00000355710	NM_020975.4	145	Gta/Ata	3/20	0.285673635683505	1	FACETS	0.184	0.162	0.206	0.184	0.162	0.206	INDETERMINATE	1	FALSE	0	0.582180017914511	1		1364	1221	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028385	42028466	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGGAAGTCTTCCTGCAATGAAGGAGAATCCTCTTCTACTTCTTATATGCATCAGAGGTCACCTGGTGGTCCCACCAAACT	GCTGGAAGTCTTCCTGCAATGAAGGAGAATCCTCTTCTACTTCTTATATGCATCAGAGGTCACCTGGTGGTCCCACCAAACT	-	novel	NA	P-0048138-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	120	209	0	ENST00000219905.7:c.3924_4005del	p.Ser1308ArgfsTer18	p.S1308Rfs*18	ENST00000219905	NM_001164273.1	1308	aGCTGGAAGTCTTCCTGCAATGAAGGAGAATCCTCTTCTACTTCTTATATGCATCAGAGGTCACCTGGTGGTCCCACCAAACTg/ag	13/24	0.582180017914511	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	0	0.582180017914511	1		209	209	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86637138	86637138	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048138-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	31	145	0	ENST00000274376.6:c.1049T>C	p.Ile350Thr	p.I350T	ENST00000274376	NM_002890.2	350	aTa/aCa	6/25	1	2	FACETS	0.745	0.611	0.891	0.745	0.611	0.891	SUBCLONAL	1	FALSE	1	0.582180017914511	2		145	143	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593602	55593612	+	protein_altering_variant	In_Frame_Del	DEL	GTGGAAGGTTG	GTGGAAGGTTG	CT	novel	NA	P-0048138-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	51	317	0	ENST00000288135.5:c.1668_1678delinsCT	p.Gln556_Val560delinsHisPhe	p.Q556_V560delinsHF	ENST00000288135	NM_000222.2	556	caGTGGAAGGTTGtt/caCTtt	11/21	1	2	FACETS	0.539	0.46	0.624	0.539	0.46	0.624	SUBCLONAL	1	FALSE	1	0.582180017914511	2		317	325	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0048370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	73	339	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	0.578	0.507	0.653	0.578	0.507	0.653	SUBCLONAL	1	TRUE	1	0.587817555019048	2		339	430	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164521	36164521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs916623598	NA	P-0048370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	284	694	0	ENST00000300305.3:c.1354G>A	p.Val452Met	p.V452M	ENST00000300305		452	Gtg/Atg	8/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.587817555019048	2		694	858	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149100	61149101	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0048370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	127	468	0	ENST00000295025.8:c.1293_1294del	p.Ser432AsnfsTer7	p.S432Nfs*7	ENST00000295025	NM_002908.2	430	agTTtt/agtt	11/11	1	2	FACETS	0.917	0.837	1	0.917	0.837	1	CLONAL	1	TRUE	1	0.587817555019048	2		468	471	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932911	39932912	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0048370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	171	378	0	ENST00000378444.4:c.1687_1688del	p.Ser563CysfsTer47	p.S563Cfs*47	ENST00000378444	NM_001123385.1	563	AGt/t	4/15	1	1	FACETS	0.842	0.781	0.904	0.842	0.781	0.904	CLONAL	1	TRUE	0	0.587817555019048	1		378	488	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938513	44938513	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	27	257	0	ENST00000377967.4:c.3061T>G	p.Trp1021Gly	p.W1021G	ENST00000377967	NM_021140.2	1021	Tgg/Ggg	20/29	1	1	FACETS	0.267	0.213	0.328	0.267	0.213	0.328	SUBCLONAL	1	TRUE	0	0.587817555019048	1		257	243	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0048491-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	109	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.16926328223028	3	FACETS	0.803	0.733	0.873	0.535	0.489	0.582	INDETERMINATE	2	TRUE	0	0.6856457777177	3		298	266	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488657	212488657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374970657	NA	P-0048491-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	33	348	1	ENST00000342788.4:c.2192C>T	p.Thr731Met	p.T731M	ENST00000342788	NM_005235.2	731	aCg/aTg	18/28	0.294434835564373	1	FACETS	0.472	0.391	0.56	0.472	0.391	0.56	INDETERMINATE	1	TRUE	0	0.6856457777177	1		349	134	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555525585	NA	P-0048491-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	52	478	0	ENST00000269305.4:c.673-2A>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.633443323173641	1	FACETS	0.915	0.807	1	0.915	0.807	1	CLONAL	1	TRUE	0	0.6856457777177	1		478	109	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68292250	68292250	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	279	290	0	ENST00000487270.1:c.154C>G	p.Leu52Val	p.L52V	ENST00000487270	NM_133509.3	52	Ctt/Gtt	3/11	0.262747628906277	6	FACETS	1	0.961	1	1	0.961	1	INDETERMINATE	3	TRUE	3	0.841866344056306	6		290	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578459	7578460	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	746	786	0	ENST00000269305.4:c.470_471insG	p.Arg158ProfsTer23	p.R158Pfs*23	ENST00000269305	NM_001126112.2	157	gtc/gtGc	5/11	0.837121744532837	2	FACETS	0.995	0.976	1	0.995	0.976	1	CLONAL	2	TRUE	0	0.841866344056306	2		786	891	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467712	66467712	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	108	227	0	ENST00000273854.3:c.557T>C	p.Leu186Pro	p.L186P	ENST00000273854	NM_004439.5	186	cTt/cCt	3/18	1	2	FACETS	0.9	0.82	0.982	0.9	0.82	0.982	CLONAL	1	TRUE	1	0.841866344056306	2		227	285	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530164	212530164	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	220	251	1	ENST00000342788.4:c.1755T>A	p.Asp585Glu	p.D585E	ENST00000342788	NM_005235.2	585	gaT/gaA	15/28	0.841866344056306	3	FACETS	0.998	0.947	1	0.998	0.947	1	CLONAL	2	TRUE	1	0.841866344056306	3		252	372	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127257	22127257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2049	546	409	0	ENST00000215832.6:c.871G>C	p.Asp291His	p.D291H	ENST00000215832	NM_002745.4	291	Gac/Cac	7/9	0.841866344056306	11	FACETS	1	0.993	1	0.239	0.228	0.251	CLONAL	2	TRUE	1	0.841866344056306	11		409	2595	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714131	43714131	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049825-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	135	966	0	ENST00000382044.4:c.4022C>A	p.Pro1341Gln	p.P1341Q	ENST00000382044	NM_001141980.1	1341	cCa/cAa	19/28	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.482727909804931	2		966	519	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733142	74733142	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049825-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	66	739	0	ENST00000359995.5:c.101T>C	p.Phe34Ser	p.F34S	ENST00000359995	NM_001195427.1	34	tTc/tCc	1/3	0.482727909804931	3	FACETS	0.6	0.521	0.685	0.3	0.26	0.343	SUBCLONAL	1	TRUE	1	0.482727909804931	3		739	566	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752700	42752700	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049825-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	52	797	0	ENST00000222329.4:c.1564G>T	p.Gly522Trp	p.G522W	ENST00000222329	NM_006494.2	522	Ggg/Tgg	4/4	0.478631499151892	1	FACETS	0.489	0.418	0.566	0.489	0.418	0.566	SUBCLONAL	1	TRUE	0	0.482727909804931	1		797	334	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226042	53226042	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049825-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	121	950	0	ENST00000375401.3:c.2807G>T	p.Arg936Leu	p.R936L	ENST00000375401	NM_004187.3	936	cGc/cTc	19/26	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.482727909804931	2		950	488	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906938	32906938	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	248	417	0	ENST00000380152.3:c.1324del	p.Ser442GlnfsTer18	p.S442Qfs*18	ENST00000380152		441	acT/ac	10/27	0.891864289682825	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.891864289682825	1		417	301	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434569	99434569	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	388	737	0	ENST00000268035.6:c.656G>A	p.Cys219Tyr	p.C219Y	ENST00000268035	NM_000875.3	219	tGt/tAt	3/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.891864289682825	2		737	836	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867697	45867697	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	504	896	0	ENST00000391945.4:c.703G>A	p.Glu235Lys	p.E235K	ENST00000391945	NM_000400.3	235	Gag/Aag	8/23	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.891864289682825	2		896	1126	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549185	87549185	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs778882958	NA	P-0050123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	283	527	0	ENST00000277120.3:c.1742A>G	p.Asp581Gly	p.D581G	ENST00000277120		581	gAc/gGc	15/19	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.891864289682825	2		527	614	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061106	38061107	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0050123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	79	133	0	ENST00000250448.2:c.882dup	p.Lys295GlnfsTer8	p.K295Qfs*8	ENST00000250448	NM_004496.3	294	-/C	2/2	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.891864289682825	2		133	170	SUCCESS
APC	324	MSKCC	GRCh37	5	112176047	112176047	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0050123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	228	363	0	ENST00000257430.4:c.4756A>T	p.Lys1586Ter	p.K1586*	ENST00000257430	NM_000038.5	1586	Aag/Tag	16/16	0.891864289682825	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.891864289682825	1		363	271	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636794	8636794	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	275	614	0	ENST00000356435.5:c.115G>T	p.Gly39Ter	p.G39*	ENST00000356435		39	Gga/Tga	2/35	1	2	FACETS	0.971	0.919	1	0.971	0.919	1	CLONAL	1	TRUE	1	0.891864289682825	2		614	635	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118836	115118836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1430142395	NA	P-0051451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	20	400	0	ENST00000257566.3:c.505C>T	p.Arg169Trp	p.R169W	ENST00000257566	NM_016569.3	169	Cgg/Tgg	2/8	0.234806482242162	1	FACETS	0.482	0.369	0.612	0.482	0.369	0.612	SUBCLONAL	1	FALSE	0	0.31165091975704	1		400	225	SUCCESS
EED	8726	MSKCC	GRCh37	11	85979521	85979521	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	19	245	0	ENST00000263360.6:c.884A>G	p.His295Arg	p.H295R	ENST00000263360	NM_003797.3	295	cAt/cGt	9/12	1	2	FACETS	0.753	0.575	0.958	0.753	0.575	0.958	CLONAL	1	FALSE	1	0.31165091975704	2		245	162	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891714	28891714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779606481	NA	P-0051451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	23	602	0	ENST00000282397.4:c.3307G>A	p.Val1103Ile	p.V1103I	ENST00000282397	NM_002019.4	1103	Gta/Ata	25/30	1	2	FACETS	0.665	0.52	0.83	0.665	0.52	0.83	SUBCLONAL	1	FALSE	1	0.31165091975704	2		602	222	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613069	52613069	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0051451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	24	319	0	ENST00000394830.3:c.3458+1G>C		p.X1153_splice	ENST00000394830	NM_018313.4	1153			0.31165091975704	1	FACETS	0.867	0.687	1	0.867	0.687	1	CLONAL	1	FALSE	0	0.31165091975704	1		319	150	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984784	55984785	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0051451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	29	435	0	ENST00000263923.4:c.344dup	p.Tyr115Ter	p.Y115*	ENST00000263923	NM_002253.2	115	tat/taAt	3/30	1	2	FACETS	0.85	0.686	1	0.85	0.686	1	CLONAL	1	FALSE	1	0.31165091975704	2		435	219	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191468	10191481	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGTGTATACTCTG	CAGTGTATACTCTG	T	novel	NA	P-0051451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	35	365	0	ENST00000256474.2:c.464-3_474delinsT		p.X155_splice	ENST00000256474	NM_000551.3	155		3/3	0.31165091975704	1	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	FALSE	0	0.31165091975704	1		365	186	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0052300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	40	348	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.791	0.657	0.941	0.791	0.657	0.941	CLONAL	1	TRUE	1	0.19	2		348	532	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201475	67201475	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776029111	NA	P-0052300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	69	851	1	ENST00000312629.5:c.916C>T	p.Arg306Trp	p.R306W	ENST00000312629	NM_003952.2	306	Cgg/Tgg	11/15	1	2	FACETS	0.711	0.618	0.813	0.711	0.618	0.813	SUBCLONAL	1	TRUE	1	0.19	2		852	1021	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405851	157405851	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0052300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	35	445	0	ENST00000346085.5:c.2093C>G	p.Ser698Ter	p.S698*	ENST00000346085	NM_020732.3	698	tCa/tGa	6/20	0.141624094645211	1	FACETS	0.736	0.603	0.885	0.736	0.603	0.885	SUBCLONAL	1	TRUE	0	0.19	1		445	453	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27172632	27172632	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	35	487	0	ENST00000380036.4:c.647G>A	p.Trp216Ter	p.W216*	ENST00000380036	NM_000459.3	216	tGg/tAg	5/23	0.192860127994633	1	FACETS	0.647	0.53	0.78	0.647	0.53	0.78	SUBCLONAL	1	TRUE	0	0.19	1		487	515	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0052359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	315	876	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.848557988822758	1	FACETS	0.992	0.956	1	0.992	0.956	1	CLONAL	1	TRUE	0	0.848557988822758	1		876	431	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163325177	163325177	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	262	515	0	ENST00000271452.3:c.1313A>G	p.Glu438Gly	p.E438G	ENST00000271452	NM_145697.2	438	gAa/gGa	14/14	1	2	FACETS	0.924	0.872	0.978	0.924	0.872	0.978	CLONAL	1	TRUE	1	0.848557988822758	2		515	668	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856000	68856000	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs864622612	NA	P-0052359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	286	718	0	ENST00000261769.5:c.1808G>C	p.Cys603Ser	p.C603S	ENST00000261769	NM_004360.3	603	tGt/tCt	12/16	0.848557988822758	1	FACETS	0.942	0.905	0.978	0.942	0.905	0.978	CLONAL	1	TRUE	0	0.848557988822758	1		718	412	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106916	27106917	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0052607-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	36	578	0	ENST00000324856.7:c.6532dup	p.Asp2178GlyfsTer47	p.D2178Gfs*47	ENST00000324856	NM_006015.4	2176	cag/caGg	20/20	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		578	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0052819-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	81	1014	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	1	2	FACETS	0.846	0.744	0.956	0.846	0.744	0.956	CLONAL	1	TRUE	1	0.21	2		1014	912	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586422	189586422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866267914	NA	P-0052819-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	50	408	1	ENST00000264731.3:c.1046G>A	p.Gly349Glu	p.G349E	ENST00000264731	NM_003722.4	349	gGa/gAa	8/14	1	2	FACETS	0.774	0.656	0.904	0.774	0.656	0.904	CLONAL	1	TRUE	1	0.21	2		409	615	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354260	15354260	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052819-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	113	94	0	ENST00000263377.2:c.2620A>G	p.Ser874Gly	p.S874G	ENST00000263377	NM_058243.2	874	Agc/Ggc	14/20	1	2	FACETS	0.871	0.781	0.966	0.871	0.781	0.966	CLONAL	1	TRUE	1	0.21	2		94	1236	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937518	32937518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052819-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	56	53	0	ENST00000380152.3:c.8179G>A	p.Ala2727Thr	p.A2727T	ENST00000380152		2727	Gct/Act	18/27	1	2	FACETS	0.73	0.624	0.846	0.73	0.624	0.846	SUBCLONAL	1	TRUE	1	0.21	2		53	731	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528450	29528450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052819-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	23	30	0	ENST00000356175.3:c.1207C>T	p.Pro403Ser	p.P403S	ENST00000356175	NM_000267.3	403	Cct/Tct	11/57	1	2	FACETS	0.524	0.408	0.659	0.524	0.408	0.659	SUBCLONAL	1	TRUE	1	0.21	2		30	418	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770570	40770570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1468460412	NA	P-0052819-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	39	54	0	ENST00000373198.4:c.2812G>A	p.Gly938Arg	p.G938R	ENST00000373198	NM_133170.3	938	Ggg/Agg	19/32	1	2	FACETS	0.64	0.53	0.764	0.64	0.53	0.764	SUBCLONAL	1	TRUE	1	0.21	2		54	580	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917576	178917576	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052819-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	124	34	0	ENST00000263967.3:c.451G>T	p.Val151Leu	p.V151L	ENST00000263967	NM_006218.2	151	Gtg/Ttg	3/21	0.3	4	FACETS	0.846	0.768	0.927			1	CLONAL	3	TRUE	NA	0.21	4		34	563	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163488	32163488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052819-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	47	52	0	ENST00000375023.3:c.5738G>A	p.Gly1913Asp	p.G1913D	ENST00000375023	NM_004557.3	1913	gGc/gAc	30/30	1	2	FACETS	0.699	0.589	0.821	0.699	0.589	0.821	SUBCLONAL	1	TRUE	1	0.21	2		52	640	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180941	32180941	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052819-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	82	61	0	ENST00000375023.3:c.2409G>C	p.Glu803Asp	p.E803D	ENST00000375023	NM_004557.3	803	gaG/gaC	15/30	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.21	2		61	703	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542217	141542217	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052819-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	87	70	0	ENST00000220592.5:c.2506G>T	p.Gly836Trp	p.G836W	ENST00000220592	NM_012154.3	836	Ggg/Tgg	19/19	0.191581634729564	1	FACETS	0.886	0.783	0.996	0.886	0.783	0.996	CLONAL	1	TRUE	0	0.21	1		70	837	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933127	39933127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052819-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	70	76	0	ENST00000378444.4:c.1472G>C	p.Gly491Ala	p.G491A	ENST00000378444	NM_001123385.1	491	gGa/gCa	4/15	0.3	3	FACETS	0.742	0.645	0.847			1	SUBCLONAL	1	TRUE	NA	0.21	3		76	993	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854890	76854890	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052819-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	47	55	0	ENST00000373344.5:c.5946A>T	p.Lys1982Asn	p.K1982N	ENST00000373344	NM_000489.3	1982	aaA/aaT	25/35	1	2	FACETS	0.698	0.588	0.82	0.698	0.588	0.82	SUBCLONAL	1	TRUE	1	0.21	2		55	641	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0053226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	472	1014	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.851740447460449	1	FACETS	0.964	0.935	0.992	0.964	0.935	0.992	CLONAL	1	TRUE	0	0.851740447460449	1		1014	660	SUCCESS
BLM	641	MSKCC	GRCh37	15	91306247	91306247	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs377563699	NA	P-0053226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	240	370	0	ENST00000355112.3:c.1934A>G	p.Gln645Arg	p.Q645R	ENST00000355112	NM_000057.2	645	cAa/cGa	8/22	0.851740447460449	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.851740447460449	1		370	321	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027394	48027394	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs56371757	NA	P-0053226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	278	451	0	ENST00000234420.5:c.2272C>G	p.Leu758Val	p.L758V	ENST00000234420	NM_000179.2	758	Cta/Gta	4/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.851740447460449	2		451	640	SUCCESS
APC	324	MSKCC	GRCh37	5	112177788	112177788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752091655	NA	P-0053879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	64	245	0	ENST00000257430.4:c.6497G>A	p.Arg2166Gln	p.R2166Q	ENST00000257430	NM_000038.5	2166	cGa/cAa	16/16	1	2	FACETS	0.864	0.756	0.979	0.864	0.756	0.979	CLONAL	1	TRUE	1	0.546756648691343	2		245	271	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0054722-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	27	342	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.383	0.305	0.47	0.383	0.305	0.47	SUBCLONAL	1	TRUE	1	0.548888908436505	2		342	257	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604701	48604701	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054722-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	22	398	0	ENST00000342988.3:c.1523G>T	p.Gly508Val	p.G508V	ENST00000342988	NM_005359.5	508	gGc/gTc	12/12	0.548888908436505	1	FACETS	0.233	0.18	0.293	0.233	0.18	0.293	SUBCLONAL	1	TRUE	0	0.548888908436505	1		398	250	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575103	48575103	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs876660079	NA	P-0054722-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	78	386	0	ENST00000342988.3:c.297G>A	p.Trp99Ter	p.W99*	ENST00000342988	NM_005359.5	99	tgG/tgA	3/12	0.548888908436505	1	FACETS	0.881	0.787	0.979	0.881	0.787	0.979	CLONAL	1	TRUE	0	0.548888908436505	1		386	234	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248998	55248999	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCACGG	novel	NA	P-0054722-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	136	574	0	ENST00000275493.2:c.2302_2303insCGGTGGCCA	p.Ala767_Ser768insThrValAla	p.A767_S768insTVA	ENST00000275493	NM_005228.3	766	atg/aTGGCCACGGtg	20/28	0.416452710422607	5	FACETS	1	0.974	1	0.762	0.701	0.826	CLONAL	2	TRUE	2	0.548888908436505	5		574	395	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480343	89480343	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054722-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	19	294	0	ENST00000336596.2:c.2180T>G	p.Leu727Arg	p.L727R	ENST00000336596	NM_005233.5	727	cTt/cGt	13/17	1	2	FACETS	0.236	0.179	0.304	0.236	0.179	0.304	SUBCLONAL	1	TRUE	1	0.548888908436505	2		294	293	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054784-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	253	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.59005079203272	2	FACETS	0.973	0.928	1	0.973	0.928	1	CLONAL	2	TRUE	0	0.642193994849213	2		298	405	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221318	1221319	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	T	novel	NA	P-0054784-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	436	724	1	ENST00000326873.7:c.841_842delinsT	p.Pro281CysfsTer6	p.P281Cfs*6	ENST00000326873	NM_000455.4	281	CCg/Tg	6/10	NA	2	FACETS	0.842	0.81	0.875			1	INDETERMINATE	2	TRUE	NA	0.642193994849213	2		725	806	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066583	94066583	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054784-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	218	433	0	ENST00000369303.4:c.1176G>T	p.Gln392His	p.Q392H	ENST00000369303	NM_004440.3	392	caG/caT	5/17	0.346468760047354	2	FACETS	0.78	0.736	0.825	0.78	0.736	0.825	INDETERMINATE	2	TRUE	0	0.642193994849213	2		433	435	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11297977	11297977	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054784-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	191	737	0	ENST00000361445.4:c.2131G>A	p.Ala711Thr	p.A711T	ENST00000361445	NM_004958.3	711	Gcc/Acc	13/58	0.220800237818887	3	FACETS	0.911	0.843	0.981			1	INDETERMINATE	1	TRUE	NA	0.642193994849213	3		737	863	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949347	71949347	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054784-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	338	843	0	ENST00000298229.2:c.3727G>C	p.Asp1243His	p.D1243H	ENST00000298229	NM_001567.3	1243	Gac/Cac	28/28	0.285692065055186	3	FACETS	1	0.992	1	0.64	0.606	0.674	INDETERMINATE	1	TRUE	1	0.642193994849213	3		843	1087	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118758	115118758	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054784-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	515	510	0	ENST00000257566.3:c.583G>T	p.Glu195Ter	p.E195*	ENST00000257566	NM_016569.3	195	Gaa/Taa	2/8	0.59005079203272	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.642193994849213	2		510	780	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95596476	95596476	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054784-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	83	258	0	ENST00000393063.1:c.492A>T	p.Leu164Phe	p.L164F	ENST00000393063	NM_030621.3	164	ttA/ttT	6/28	1	2	FACETS	0.933	0.834	1	0.933	0.834	1	CLONAL	1	TRUE	1	0.642193994849213	2		258	277	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95597923	95597923	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054784-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	129	402	0	ENST00000393063.1:c.361G>T	p.Val121Phe	p.V121F	ENST00000393063	NM_030621.3	121	Gtt/Ttt	5/28	1	2	FACETS	0.842	0.769	0.919	0.842	0.769	0.919	CLONAL	1	TRUE	1	0.642193994849213	2		402	477	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274012	10274012	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054784-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	227	916	0	ENST00000330684.3:c.257T>C	p.Val86Ala	p.V86A	ENST00000330684	NM_001134407.1	86	gTg/gCg	2/13	0.272956220548469	2	FACETS	0.966	0.903	1	0.483	0.451	0.515	INDETERMINATE	1	TRUE	0	0.642193994849213	2		916	732	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054784-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	412	592	0	ENST00000269305.4:c.706del	p.Tyr236ThrfsTer11	p.Y236Tfs*11	ENST00000269305	NM_001126112.2	236	Tac/ac	7/11	0.59005079203272	2	FACETS	0.857	0.823	0.89	0.857	0.823	0.89	CLONAL	2	TRUE	0	0.642193994849213	2		592	749	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120437	94120437	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054784-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	57	295	0	ENST00000369303.4:c.614G>T	p.Cys205Phe	p.C205F	ENST00000369303	NM_004440.3	205	tGc/tTc	3/17	0.346468760047354	2	FACETS	0.569	0.491	0.653	0.284	0.245	0.327	INDETERMINATE	1	TRUE	0	0.642193994849213	2		295	312	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135777992	135777992	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054784-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	317	464	0	ENST00000298552.3:c.2391G>C	p.Gln797His	p.Q797H	ENST00000298552	NM_001162426.1	797	caG/caC	18/23	0.60722109385409	2	FACETS	0.863	0.824	0.901	0.863	0.824	0.901	CLONAL	2	TRUE	0	0.642193994849213	2		464	572	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514647	44514647	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054811-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	153	554	0	ENST00000291552.4:c.509A>G	p.Asn170Ser	p.N170S	ENST00000291552	NM_006758.2	170	aAc/aGc	7/8	0.452789650663197	4	FACETS	1	0.984	1	0.43	0.395	0.467	CLONAL	1	TRUE	1	0.567182744578304	4		554	655	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390946	89390946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054811-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	64	408	0	ENST00000336596.2:c.1012G>A	p.Glu338Lys	p.E338K	ENST00000336596	NM_005233.5	338	Gag/Aag	5/17	0.112655875976116	6	FACETS	1	0.963	1			1	INDETERMINATE	1	TRUE	NA	0.567182744578304	6		408	368	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44911033	44911034	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054811-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	115	165	0	ENST00000377967.4:c.735dup	p.Gln247ThrfsTer16	p.Q247Tfs*16	ENST00000377967	NM_021140.2	245	gtc/gtCc	9/29	0.567182744578304	2	FACETS	0.85	0.799	0.898			1	CLONAL	3	TRUE	NA	0.567182744578304	2		165	159	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984350	201984351	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0054811-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	441	768	0	ENST00000359651.3:c.1018dup	p.Glu340GlyfsTer131	p.E340Gfs*131	ENST00000359651		339	cgg/cGgg	8/8	0.52154522765308	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.567182744578304	3		768	965	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849587	68849587	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054811-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	165	766	0	ENST00000261769.5:c.1490A>G	p.Glu497Gly	p.E497G	ENST00000261769	NM_004360.3	497	gAg/gGg	10/16	0.52154522765308	3	FACETS	1	0.955	1	0.527	0.485	0.57	CLONAL	1	TRUE	1	0.567182744578304	3		766	709	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578228	7578228	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054811-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	343	826	0	ENST00000269305.4:c.621del	p.Asp207GlufsTer40	p.D207Efs*40	ENST00000269305	NM_001126112.2	207	gaT/ga	6/11	0.567182744578304	2	FACETS	0.935	0.893	0.976	0.935	0.893	0.976	CLONAL	2	TRUE	0	0.567182744578304	2		826	647	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843420	128843420	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054811-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	222	648	0	ENST00000249373.3:c.528del	p.Gly177AlafsTer125	p.G177Afs*125	ENST00000249373	NM_005631.4	176	gAa/ga	2/12	0.567182744578304	6	FACETS	0.99	0.923	1	0.495	0.461	0.529	CLONAL	2	TRUE	2	0.567182744578304	6		648	844	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955570	55955570	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054811-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	63	515	0	ENST00000263923.4:c.3375G>C	p.Met1125Ile	p.M1125I	ENST00000263923	NM_002253.2	1125	atG/atC	25/30	0.52154522765308	3	FACETS	0.786	0.683	0.896	0.393	0.341	0.448	SUBCLONAL	1	TRUE	1	0.567182744578304	3		515	363	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0055141-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	497	611	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.774832986784448	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.785066304247948	3		611	579	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676174	29676177	+	frameshift_variant	Frame_Shift_Del	DEL	CAGT	CAGT	-	novel	NA	P-0055141-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	158	219	0	ENST00000356175.3:c.7166_7169del	p.Val2389GlufsTer7	p.V2389Efs*7	ENST00000356175	NM_000267.3	2388	aCAGTc/ac	48/57	0.637259674482946	4	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	2	0.785066304247948	4		219	355	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180037003	180037003	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055141-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	300	670	2	ENST00000261937.6:c.3709C>T	p.Pro1237Ser	p.P1237S	ENST00000261937	NM_182925.4	1237	Ccc/Tcc	28/30	0.785066304247948	5	FACETS	0.982	0.929	1	0.655	0.619	0.692	CLONAL	2	TRUE	2	0.785066304247948	5		672	847	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875049	151875049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150994342	NA	P-0055141-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	54	178	0	ENST00000262189.6:c.7489C>T	p.Arg2497Cys	p.R2497C	ENST00000262189	NM_170606.2	2497	Cgc/Tgc	38/59	0.75321890961386	4	FACETS	1	0.913	1	0.269	0.232	0.309	CLONAL	1	TRUE	0	0.785066304247948	4		178	228	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955431	48955431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055418-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	252	376	0	ENST00000267163.4:c.1547G>A	p.Trp516Ter	p.W516*	ENST00000267163	NM_000321.2	516	tGg/tAg	17/27	0.917431734444442	2	FACETS	0.999	0.975	1	0.999	0.975	1	CLONAL	2	TRUE	0	0.917431734444442	2		376	275	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	133	324	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.955	0.879	1	0.955	0.879	1	CLONAL	1	TRUE	1	0.844448564908537	2		324	330	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469672	NA	P-0055505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	333	535	0	ENST00000374080.3:c.131G>A	p.Gly44Asp	p.G44D	ENST00000374080		44	gGt/gAt	2/45	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.844448564908537	2		535	733	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779765	3779768	+	frameshift_variant	Frame_Shift_Del	DEL	TGAC	TGAC	-	novel	NA	P-0055505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	314	778	0	ENST00000262367.5:c.5280_5283del	p.Ser1761ArgfsTer9	p.S1761Rfs*9	ENST00000262367	NM_004380.2	1760	caGTCA/ca	31/31	1	2	FACETS	0.92	0.872	0.969	0.92	0.872	0.969	CLONAL	1	TRUE	1	0.844448564908537	2		778	808	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0055551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	51	296	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.456217685844814	4	FACETS	0.96	0.844	1	0.96	0.844	1	CLONAL	3	FALSE	1	0.456217685844814	4		296	113	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0055551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	21	868	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.423455344858439	3	FACETS	0.215	0.165	0.274	0.072	0.055	0.092	SUBCLONAL	1	FALSE	0	0.456217685844814	3		868	525	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	100	954	0	ENST00000269305.4:c.880del	p.Glu294SerfsTer51	p.E294Sfs*51	ENST00000269305	NM_001126112.2	294	Gag/ag	8/11	0.423455344858439	3	FACETS	0.83	0.742	0.923	0.277	0.247	0.308	CLONAL	1	FALSE	0	0.456217685844814	3		954	649	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221962	1221962	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs398123405	NA	P-0055551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	97	1017	2	ENST00000326873.7:c.877G>T	p.Glu293Ter	p.E293*	ENST00000326873	NM_000455.4	293	Gaa/Taa	7/10	0.432137571794802	2	FACETS	0.579	0.516	0.646	0.289	0.258	0.323	SUBCLONAL	1	FALSE	0	0.456217685844814	2		1019	735	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983136	201983136	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	104	753	0	ENST00000359651.3:c.985C>G	p.Leu329Val	p.L329V	ENST00000359651		329	Ctg/Gtg	7/8	0.1661197702088	2	FACETS	0.717	0.643	0.795	0.358	0.321	0.398	INDETERMINATE	1	FALSE	0	0.456217685844814	2		753	636	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922817	44922824	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGCCTG	CCTGCCTG	-	novel	NA	P-0055551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	136	363	1	ENST00000377967.4:c.1680_1687del	p.Ala561TrpfsTer17	p.A561Wfs*17	ENST00000377967	NM_021140.2	560	CCTGCCTGc/c	16/29	0.419010454414873	2	FACETS	1	0.961	1			1	CLONAL	2	FALSE	NA	0.456217685844814	2		364	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579478	7579496	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGCCTCTGGCATTCTGG	GCAGCCTCTGGCATTCTGG	-	novel	NA	P-0055551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	179	1054	0	ENST00000269305.4:c.191_209del	p.Pro64LeufsTer53	p.P64Lfs*53	ENST00000269305	NM_001126112.2	64	cCCAGAATGCCAGAGGCTGCt/ct	4/11	0.423455344858439	3	FACETS	1	0.99	1	0.487	0.45	0.524	CLONAL	1	FALSE	0	0.456217685844814	3		1054	660	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405967	49405967	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	39	628	0	ENST00000418115.1:c.171G>T	p.Leu57Phe	p.L57F	ENST00000418115	NM_001664.2	57	ttG/ttT	3/5	0.456217685844814	4	FACETS	0.475	0.393	0.567	0.158	0.131	0.189	SUBCLONAL	1	FALSE	1	0.456217685844814	4		628	524	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245456	153245456	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	16	660	0	ENST00000281708.4:c.1735G>T	p.Gly579Trp	p.G579W	ENST00000281708	NM_033632.3	579	Ggg/Tgg	11/12	0.329394232199871	5	FACETS	0.442	0.327	0.581	0.147	0.109	0.194	SUBCLONAL	1	FALSE	2	0.456217685844814	5		660	267	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222528	157222528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554265256	NA	P-0055551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	74	771	1	ENST00000346085.5:c.1795C>T	p.Gln599Ter	p.Q599*	ENST00000346085	NM_020732.3	599	Cag/Tag	4/20	0.423455344858439	3	FACETS	0.7	0.614	0.793	0.233	0.204	0.265	SUBCLONAL	1	FALSE	0	0.456217685844814	3		772	569	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729705	41729705	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	67	849	0	ENST00000242208.4:c.824G>C	p.Gly275Ala	p.G275A	ENST00000242208	NM_002192.2	275	gGt/gCt	3/3	0.456217685844814	4	FACETS	0.662	0.575	0.756	0.331	0.287	0.378	SUBCLONAL	1	FALSE	2	0.456217685844814	4		849	646	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468108	50468108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs750934235	NA	P-0055551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	32	708	0	ENST00000331340.3:c.1343C>A	p.Ala448Glu	p.A448E	ENST00000331340	NM_006060.4	448	gCg/gAg	8/8	0.456217685844814	4	FACETS	0.424	0.343	0.515	0.212	0.171	0.258	SUBCLONAL	1	FALSE	2	0.456217685844814	4		708	482	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5081775	5081775	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	10	374	1	ENST00000381652.3:c.2485G>T	p.Ala829Ser	p.A829S	ENST00000381652	NM_004972.3	829	Gcc/Tcc	19/25	0.456217685844814	2	FACETS	0.783	0.542	1	0.391	0.271	0.535	CLONAL	1	FALSE	0	0.456217685844814	2		375	56	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971041	21971052	+	frameshift_variant	Frame_Shift_Del	DEL	ACGTCCAGCCGC	ACGTCCAGCCGC	G	novel	NA	P-0055551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	10	579	0	ENST00000304494.5:c.306_317delinsC	p.Arg103AlafsTer13	p.R103Afs*13	ENST00000304494	NM_000077.4	102	gcGCGGCTGGACGTg/gcCg	2/3	0.456217685844814	2	FACETS	0.221	0.15	0.312	0.111	0.075	0.156	SUBCLONAL	1	FALSE	0	0.456217685844814	2		579	198	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922817	44922824	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGCCTG	CCTGCCTG	-	novel	NA	P-0055551-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	128	363	1	ENST00000377967.4:c.1680_1687del	p.Ala561TrpfsTer17	p.A561Wfs*17	ENST00000377967	NM_021140.2	560	CCTGCCTGc/c	16/29	0.4314818137442	2	FACETS	0.931	0.858	1			1	CLONAL	2	TRUE	NA	0.459949001652103	2		364	299	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981244	201981290	+	frameshift_variant	Frame_Shift_Del	DEL	AGGAGCTGCGTCTGGTCTTTGGGCCTCTGGGGGACCAACTCCATGCC	AGGAGCTGCGTCTGGTCTTTGGGCCTCTGGGGGACCAACTCCATGCC	-	novel	NA	P-0055551-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	402	1035	0	ENST00000359651.3:c.323_369del	p.Glu108AlafsTer11	p.E108Afs*11	ENST00000359651		108	gAGGAGCTGCGTCTGGTCTTTGGGCCTCTGGGGGACCAACTCCATGCC/g	2/8	0.414911050823449	4	FACETS	0.865	0.826	0.905	0.865	0.826	0.905	CLONAL	3	TRUE	1	0.459949001652103	4		1035	983	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579849	7579853	+	frameshift_variant	Frame_Shift_Del	DEL	GGTCT	GGTCT	-	novel	NA	P-0055551-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	299	927	1	ENST00000269305.4:c.60_64del	p.Asp21MetfsTer6	p.D21Mfs*6	ENST00000269305	NM_001126112.2	20	tcAGACCta/tcta	2/11	0.459949001652103	3	FACETS	1	0.986	1	0.74	0.702	0.78	CLONAL	2	TRUE	0	0.459949001652103	3		928	720	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27205002	27205002	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055551-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	59	696	1	ENST00000380036.4:c.2303T>G	p.Ile768Ser	p.I768S	ENST00000380036	NM_000459.3	768	aTc/aGc	14/23	0.459949001652103	2	FACETS	0.447	0.384	0.515	0.223	0.192	0.258	SUBCLONAL	1	TRUE	0	0.459949001652103	2		697	574	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055643-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	35	324	0				ENST00000310581	NM_198253.2	-/1132			0.154994389102573	3	FACETS	1	0.944	1	0.717	0.588	0.861	CLONAL	1	TRUE	1	0.14	3		324	373	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528441	29528441	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055643-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	32	357	0	ENST00000356175.3:c.1198C>T	p.Gln400Ter	p.Q400*	ENST00000356175	NM_000267.3	400	Cag/Tag	11/57	1	2	FACETS	0.888	0.719	1	0.888	0.719	1	CLONAL	1	TRUE	1	0.14	2		357	515	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416221	29416221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055643-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	37	841	0	ENST00000389048.3:c.4732C>T	p.Pro1578Ser	p.P1578S	ENST00000389048	NM_004304.4	1578	Cct/Tct	29/29	1	2	FACETS	0.812	0.668	0.974	0.812	0.668	0.974	CLONAL	1	TRUE	1	0.14	2		841	651	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495236	212495236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866307465	NA	P-0055643-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	34	547	0	ENST00000342788.4:c.2030G>A	p.Arg677Lys	p.R677K	ENST00000342788	NM_005235.2	677	aGg/aAg	17/28	0.0790209635272706	0	FACETS	0.672	0.547	0.812			1	INDETERMINATE	1	TRUE	0	0.14	0		547	622	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413677	138413677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226099075	NA	P-0055643-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	42	533	0	ENST00000289153.2:c.1843C>T	p.Pro615Ser	p.P615S	ENST00000289153	NM_006219.2	615	Cca/Tca	12/22	1	2	FACETS	0.886	0.738	1	0.886	0.738	1	CLONAL	1	TRUE	1	0.14	2		533	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0055743-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	336	731	2	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.368362516043323	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.368362516043323	2		733	827	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0055743-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	121	257	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.368362516043323	4	FACETS	1	0.926	1	1	0.926	1	CLONAL	3	TRUE	1	0.368362516043323	4		257	297	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183211	56183211	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055743-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	148	286	0	ENST00000399503.3:c.4121A>G	p.Asn1374Ser	p.N1374S	ENST00000399503	NM_005921.1	1374	aAt/aGt	18/20	0.259958975515303	4	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	2	0.368362516043323	4		286	528	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911258	32911258	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055743-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	57	385	0	ENST00000380152.3:c.2766C>G	p.Phe922Leu	p.F922L	ENST00000380152		922	ttC/ttG	11/27	0.368362516043323	5	FACETS	1	0.912	1	0.361	0.31	0.416	CLONAL	1	TRUE	2	0.368362516043323	5		385	444	SUCCESS
APC	324	MSKCC	GRCh37	5	112155043	112155043	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0055743-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	172	344	0	ENST00000257430.4:c.1312+2T>A		p.X438_splice	ENST00000257430	NM_000038.5	438			0.259958975515303	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.368362516043323	4		344	517	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231370	98231370	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145766839	NA	P-0055743-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	256	586	3	ENST00000331920.6:c.1913G>A	p.Arg638His	p.R638H	ENST00000331920	NM_000264.3	638	cGc/cAc	14/24	0.140072686768485	4	FACETS	0.968	0.907	1	0.968	0.907	1	INDETERMINATE	2	TRUE	2	0.368362516043323	4		589	982	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754647	41754647	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs267605498	NA	P-0055743-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	255	595	0	ENST00000301178.4:c.1634-1G>A		p.X545_splice	ENST00000301178	NM_021913.4	545			0.259958975515303	4	FACETS	0.97	0.908	1	0.97	0.908	1	CLONAL	2	TRUE	2	0.368362516043323	4		595	977	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99163126	99163126	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055743-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	80	310	0	ENST00000074304.5:c.1132A>G	p.Lys378Glu	p.K378E	ENST00000074304	NM_001134224.1	378	Aag/Gag	13/26	0.259958975515303	4	FACETS	0.968	0.853	1	0.484	0.426	0.546	CLONAL	1	TRUE	2	0.368362516043323	4		310	614	SUCCESS
APC	324	MSKCC	GRCh37	5	112175021	112175022	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1114167595	NA	P-0055743-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	34	122	0	ENST00000257430.4:c.3734dup	p.Ala1246GlyfsTer10	p.A1246Gfs*10	ENST00000257430	NM_000038.5	1244	caa/cAaa	16/16	0.259958975515303	4	FACETS	1	0.944	1	0.706	0.583	0.84	CLONAL	1	TRUE	2	0.368362516043323	4		122	179	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1327788	1327788	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055743-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	100	458	1	ENST00000400841.2:c.93G>T	p.Gln31His	p.Q31H	ENST00000400841		31	caG/caT	2/6	0.368362516043323	4	FACETS	1	0.935	1	0.354	0.316	0.395	CLONAL	1	TRUE	1	0.368362516043323	4		459	699	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0055797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	63	597	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.841	0.729	0.961	0.841	0.729	0.961	CLONAL	1	TRUE	1	0.346158761543124	2		597	433	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0055797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	126	517	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.346158761543124	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.346158761543124	1		517	555	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0055797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	64	470	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.889	0.773	1	0.889	0.773	1	CLONAL	1	TRUE	1	0.346158761543124	2		470	416	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158610	26158610	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	58	345	0	ENST00000289316.2:c.213C>G	p.Phe71Leu	p.F71L	ENST00000289316	NM_138720.2	71	ttC/ttG	1/2	0.238722800827448	0	FACETS	0.66	0.57	0.757			1	SUBCLONAL	1	TRUE	0	0.346158761543124	0		345	332	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061191	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	40	234	0	ENST00000250448.2:c.798C>G	p.Phe266Leu	p.F266L	ENST00000250448	NM_004496.3	266	ttC/ttG	2/2	1	2	FACETS	0.748	0.624	0.885	0.748	0.624	0.885	SUBCLONAL	1	TRUE	1	0.346158761543124	2		234	309	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733218	74733218	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	73	450	1	ENST00000359995.5:c.25G>A	p.Asp9Asn	p.D9N	ENST00000359995	NM_001195427.1	9	Gat/Aat	1/3	0.195469068326134	4	FACETS	1	0.893	1	0.511	0.447	0.579	INDETERMINATE	1	TRUE	2	0.346158761543124	4		451	556	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606361	93606361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	133	535	0	ENST00000375746.1:c.181G>A	p.Ala61Thr	p.A61T	ENST00000375746	NM_001174167.1	61	Gca/Aca	2/14	0.309151545738876	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.346158761543124	1		535	541	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842414	68842414	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	82	351	0	ENST00000261769.5:c.476del	p.Pro159LeufsTer56	p.P159Lfs*56	ENST00000261769	NM_004360.3	159	Cct/ct	4/16	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.346158761543124	2		351	468	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46715707	46715707	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	34	384	0	ENST00000371975.4:c.126G>C	p.Gln42His	p.Q42H	ENST00000371975	NM_003579.3	42	caG/caC	3/18	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.346158761543124	NA		384	648	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226553703	226553703	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs769447847	NA	P-0055797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	63	270	0	ENST00000366794.5:c.2457G>C	p.Lys819Asn	p.K819N	ENST00000366794	NM_001618.3	819	aaG/aaC	18/23	0.21692523309251	3	FACETS	0.836	0.724	0.957	0.418	0.362	0.479	CLONAL	1	TRUE	1	0.346158761543124	3		270	511	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968837	15968837	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	119	389	0	ENST00000268712.3:c.4913G>C	p.Arg1638Thr	p.R1638T	ENST00000268712	NM_006311.3	1638	aGa/aCa	33/46	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.346158761543124	2		389	486	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40477051	40477051	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	78	291	0	ENST00000264657.5:c.1394C>G	p.Ser465Cys	p.S465C	ENST00000264657	NM_139276.2	465	tCc/tGc	16/24	0.284451488634157	3	FACETS	0.974	0.857	1	0.487	0.428	0.549	CLONAL	1	TRUE	1	0.346158761543124	3		291	543	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391550	84391550	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0055797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	53	463	0	ENST00000321945.7:c.283-1G>A		p.X95_splice	ENST00000321945	NM_139076.2	95			1	2	FACETS	0.8	0.684	0.925	0.8	0.684	0.925	CLONAL	1	TRUE	1	0.346158761543124	2		463	383	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138201312	138201312	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	31	396	0	ENST00000237289.4:c.2011G>C	p.Glu671Gln	p.E671Q	ENST00000237289	NM_001270507.1	671	Gaa/Caa	8/9	0.346158761543124	1	FACETS	0.339	0.274	0.413	0.339	0.274	0.413	SUBCLONAL	1	TRUE	0	0.346158761543124	1		396	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0055805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	190	893	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.573505824610623	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.573505824610623	1		894	437	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245023	133245024	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs752846614	NA	P-0055805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	229	817	1	ENST00000320574.5:c.2091dup	p.Phe699ValfsTer11	p.F699Vfs*11	ENST00000320574	NM_006231.2	697	-/C	19/49	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.573505824610623	2		818	780	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	70	221	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.268602573705771	2		222	424	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026290	48026290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147737737	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	91	387	0	ENST00000234420.5:c.1168G>A	p.Asp390Asn	p.D390N	ENST00000234420	NM_000179.2	390	Gat/Aat	4/10	0.102149414339723	4	FACETS	0.766	0.682	0.856	0.766	0.682	0.856	INDETERMINATE	2	TRUE	2	0.268602573705771	4		387	561	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740665	58740665	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	90	563	0	ENST00000305921.3:c.1570C>T	p.Gln524Ter	p.Q524*	ENST00000305921	NM_003620.3	524	Caa/Taa	6/6	0.228979169893151	3	FACETS	0.985	0.873	1	0.492	0.436	0.552	CLONAL	1	TRUE	1	0.268602573705771	3		563	772	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306632	41306632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	132	721	1	ENST00000373198.4:c.1027C>T	p.Pro343Ser	p.P343S	ENST00000373198	NM_133170.3	343	Ccc/Tcc	7/32	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.268602573705771	2		722	852	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928499	69928499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	109	657	0	ENST00000352241.4:c.319C>T	p.Pro107Ser	p.P107S	ENST00000352241	NM_198159.2	107	Ccc/Tcc	2/10	1	2	FACETS	0.932	0.836	1	0.932	0.836	1	CLONAL	1	TRUE	1	0.268602573705771	2		657	871	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816249	89816249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs964766722	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	105	702	0	ENST00000389301.3:c.3128C>T	p.Ser1043Phe	p.S1043F	ENST00000389301	NM_000135.2	1043	tCc/tTc	32/43	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.268602573705771	2		702	747	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971207	21971208	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	49	474	0	ENST00000304494.5:c.151-1_151delinsAA		p.X51_splice	ENST00000304494	NM_000077.4	51		2/3	0.268602573705771	1	FACETS	0.721	0.612	0.841	0.721	0.612	0.841	SUBCLONAL	1	TRUE	0	0.268602573705771	1		474	438	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032000	10032000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	111	644	0	ENST00000330684.3:c.823G>A	p.Gly275Arg	p.G275R	ENST00000330684	NM_001134407.1	275	Gga/Aga	3/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.268602573705771	2		644	695	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667423	241667423	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913122	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	109	402	0	ENST00000366560.3:c.1027C>T	p.Arg343Ter	p.R343*	ENST00000366560	NM_000143.3	343	Cga/Tga	7/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.268602573705771	2		402	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	161	562	0	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.228979169893151	3	FACETS	1	0.921	1	1	0.921	1	CLONAL	2	TRUE	1	0.268602573705771	3		562	679	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969197	93969197	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	56	264	0	ENST00000369303.4:c.1799T>G	p.Phe600Cys	p.F600C	ENST00000369303	NM_004440.3	600	tTt/tGt	10/17	0.268602573705771	8	FACETS	0.979	0.837	1			1	CLONAL	1	TRUE	NA	0.268602573705771	8		264	769	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559101	29559101	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202023	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	52	179	0	ENST00000356175.3:c.3208C>T	p.Gln1070Ter	p.Q1070*	ENST00000356175	NM_000267.3	1070	Cag/Tag	25/57	0.268602573705771	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.268602573705771	1		179	286	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155953	119155953	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764340189	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	138	703	0	ENST00000264033.4:c.1618C>T	p.Arg540Ter	p.R540*	ENST00000264033	NM_005188.3	540	Cga/Tga	11/16	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.268602573705771	2		703	937	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674155	117674155	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs765733079	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	96	424	0	ENST00000368508.3:c.4319C>T	p.Pro1440Leu	p.P1440L	ENST00000368508	NM_002944.2	1440	cCa/cTa	26/43	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.268602573705771	2		424	610	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523313	9523313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866291709	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	92	534	0	ENST00000353224.5:c.1924C>T	p.Pro642Ser	p.P642S	ENST00000353224	NM_177990.2	642	Ccc/Tcc	9/10	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.268602573705771	2		534	681	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128201272	128201272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779657195	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	75	543	0	ENST00000265960.3:c.1463C>T	p.Ser488Leu	p.S488L	ENST00000265960	NM_001006617.1	488	tCg/tTg	12/12	1	2	FACETS	0.818	0.716	0.927	0.818	0.716	0.927	CLONAL	1	TRUE	1	0.268602573705771	2		543	683	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946257	81946258	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	87	703	1	ENST00000359376.3:c.1990_1991delinsTT	p.Pro664Phe	p.P664F	ENST00000359376	NM_002661.3	664	CCc/TTc	19/33	1	2	FACETS	0.847	0.749	0.951	0.847	0.749	0.951	CLONAL	1	TRUE	1	0.268602573705771	2		704	765	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544630	65544630	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs786203385	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	85	536	0	ENST00000358664.4:c.295+1G>A		p.X99_splice	ENST00000358664	NM_002382.4	99			1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.268602573705771	2		536	612	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029193	26029193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	79	297	0	ENST00000435504.4:c.157C>T	p.Leu53Phe	p.L53F	ENST00000435504		53	Ctt/Ttt	4/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.268602573705771	2		297	497	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350432	89350432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761259443	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	96	766	0	ENST00000301030.4:c.2518C>T	p.Arg840Trp	p.R840W	ENST00000301030	NM_001256183.1	840	Cgg/Tgg	9/13	1	2	FACETS	0.673	0.598	0.753	0.673	0.598	0.753	SUBCLONAL	1	TRUE	1	0.268602573705771	2		766	1062	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964515	70964516	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	102	556	3	ENST00000276594.2:c.1512_1513delinsTT	p.Arg505Cys	p.R505C	ENST00000276594	NM_024504.3	504	ctCCgc/ctTTgc	8/8	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.268602573705771	2		559	733	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134300	11134300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	77	514	1	ENST00000358026.2:c.2966C>T	p.Pro989Leu	p.P989L	ENST00000358026	NM_001128849.1	989	cCc/cTc	20/36	1	2	FACETS	0.98	0.861	1	0.98	0.861	1	CLONAL	1	TRUE	1	0.268602573705771	2		515	585	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650282	48650282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	105	412	0	ENST00000376670.3:c.252G>A	p.Met84Ile	p.M84I	ENST00000376670	NM_002049.3	84	atG/atA	3/6	1	1	FACETS	0.859	0.776	0.946	1	0.986	1	CLONAL	2	TRUE	0	0.268602573705771	1		412	394	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182056	11182056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1468703773	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	90	538	0	ENST00000361445.4:c.6790G>A	p.Glu2264Lys	p.E2264K	ENST00000361445	NM_004958.3	2264	Gag/Aag	48/58	1	2	FACETS	0.98	0.87	1	0.98	0.87	1	CLONAL	1	TRUE	1	0.268602573705771	2		538	684	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932175	36932175	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	112	656	0	ENST00000361632.4:c.2294G>A	p.Gly765Glu	p.G765E	ENST00000361632		765	gGg/gAg	16/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.268602573705771	2		656	696	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743504	46743504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553170121	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	95	508	0	ENST00000371975.4:c.1885G>A	p.Glu629Lys	p.E629K	ENST00000371975	NM_003579.3	629	Gag/Aag	17/18	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.268602573705771	2		508	591	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653278	206653278	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	128	677	0	ENST00000367120.3:c.1248+1G>A		p.X416_splice	ENST00000367120	NM_014002.3	416			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.268602573705771	2		677	862	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944297	206944298	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	89	508	1	ENST00000423557.1:c.332_333delinsTT	p.Ser111Phe	p.S111F	ENST00000423557	NM_000572.2	111	tCC/tTT	3/5	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.268602573705771	2		509	661	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431748	49431748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	122	672	0	ENST00000301067.7:c.9391C>T	p.Pro3131Ser	p.P3131S	ENST00000301067	NM_003482.3	3131	Cct/Tct	34/54	0.268602573705771	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.268602573705771	1		672	617	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937002	48937002	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	65	329	0	ENST00000267163.4:c.770A>T	p.Gln257Leu	p.Q257L	ENST00000267163	NM_000321.2	257	cAg/cTg	8/27	1	2	FACETS	0.872	0.757	0.997	0.872	0.757	0.997	CLONAL	1	TRUE	1	0.268602573705771	2		329	555	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799381	88799381	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	51	271	0	ENST00000360948.2:c.4G>A	p.Asp2Asn	p.D2N	ENST00000360948	NM_001012338.2	2	Gat/Aat	2/19	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.268602573705771	2		271	302	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992214	72992214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	81	797	0	ENST00000268489.5:c.1831G>A	p.Gly611Ser	p.G611S	ENST00000268489	NM_006885.3	611	Ggt/Agt	2/10	1	2	FACETS	0.712	0.626	0.804	0.712	0.626	0.804	SUBCLONAL	1	TRUE	1	0.268602573705771	2		797	847	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946252	81946253	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	86	697	1	ENST00000359376.3:c.1985_1986delinsAA	p.Arg662Lys	p.R662K	ENST00000359376	NM_002661.3	662	aGG/aAA	19/33	1	2	FACETS	0.865	0.765	0.973	0.865	0.765	0.973	CLONAL	1	TRUE	1	0.268602573705771	2		698	740	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579590	7579611	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTGTAGATGGGTGAAAAGAGC	ACTGTAGATGGGTGAAAAGAGC	-	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	61	652	0	ENST00000269305.4:c.97-21_97del		p.X33_splice	ENST00000269305	NM_001126112.2	33		4/11	0.228979169893151	3	FACETS	0.664	0.572	0.765	0.332	0.286	0.383	SUBCLONAL	1	TRUE	1	0.268602573705771	3		652	776	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485993	40485993	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	98	650	0	ENST00000264657.5:c.872T>G	p.Val291Gly	p.V291G	ENST00000264657	NM_139276.2	291	gTt/gGt	9/24	NA	2	FACETS	0.803	0.715	0.896			1	INDETERMINATE	1	TRUE	NA	0.268602573705771	2		650	909	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763293	59763293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	125	613	0	ENST00000259008.2:c.2809G>A	p.Asp937Asn	p.D937N	ENST00000259008	NM_032043.2	937	Gat/Aat	19/20	0.228979169893151	3	FACETS	1	0.971	1	0.592	0.536	0.652	CLONAL	1	TRUE	1	0.268602573705771	3		613	891	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210767	5210768	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	93	783	0	ENST00000357368.4:c.5283_5284delinsAA	p.Glu1762Lys	p.E1762K	ENST00000357368	NM_002850.3	1761	acGGaa/acAAaa	34/38	1	2	FACETS	0.823	0.731	0.922	0.823	0.731	0.922	CLONAL	1	TRUE	1	0.268602573705771	2		783	841	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211990	36211991	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	120	1028	1	ENST00000222270.7:c.1741_1742delinsTT	p.Pro581Phe	p.P581F	ENST00000222270	NM_014727.1	581	CCc/TTc	3/37	1	2	FACETS	0.78	0.702	0.862	0.78	0.702	0.862	SUBCLONAL	1	TRUE	1	0.268602573705771	2		1029	1146	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905712	50905712	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	123	858	0	ENST00000440232.2:c.760T>A	p.Phe254Ile	p.F254I	ENST00000440232	NM_002691.3	254	Ttc/Atc	7/27	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.268602573705771	2		858	849	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718719	190718719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	111	305	0	ENST00000441310.2:c.877C>T	p.Pro293Ser	p.P293S	ENST00000441310	NM_000534.4	293	Cct/Tct	8/13	0.102149414339723	4	FACETS	0.792	0.713	0.875	0.792	0.713	0.875	INDETERMINATE	2	TRUE	2	0.268602573705771	4		305	662	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215633991	215633991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881408	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	97	273	0	ENST00000260947.4:c.1360C>T	p.Pro454Ser	p.P454S	ENST00000260947	NM_000465.2	454	Cca/Tca	5/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.268602573705771	2		273	622	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437354	220437355	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	134	778	2	ENST00000243786.2:c.258_259delinsTT	p.Pro87Ser	p.P87S	ENST00000243786	NM_002191.3	86	ttCCca/ttTTca	1/2	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.268602573705771	2		780	903	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560827	9560827	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	56	530	0	ENST00000353224.5:c.955C>T	p.Pro319Ser	p.P319S	ENST00000353224	NM_177990.2	319	Cct/Tct	4/10	1	2	FACETS	0.607	0.519	0.703	0.607	0.519	0.703	SUBCLONAL	1	TRUE	1	0.268602573705771	2		530	687	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980769	40980770	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	101	510	0	ENST00000373198.4:c.1716_1717delinsAA	p.Gly573Ser	p.G573S	ENST00000373198	NM_133170.3	572	aaGGgc/aaAAgc	10/32	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.268602573705771	2		510	659	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167427	24167428	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	122	690	2	ENST00000263121.7:c.811_812delinsAA	p.Gly271Lys	p.G271K	ENST00000263121	NM_003073.3	271	GGa/AAa	7/9	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.268602573705771	2		692	822	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37091984	37091984	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	80	370	0	ENST00000231790.2:c.2111T>A	p.Val704Glu	p.V704E	ENST00000231790	NM_000249.3	704	gTg/gAg	19/19	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.268602573705771	2		370	534	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468427	89468427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	74	268	0	ENST00000336596.2:c.1961C>T	p.Thr654Ile	p.T654I	ENST00000336596	NM_005233.5	654	aCc/aTc	11/17	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.268602573705771	2		268	465	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952045	178952045	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	64	301	0	ENST00000263967.3:c.3100G>A	p.Glu1034Lys	p.E1034K	ENST00000263967	NM_006218.2	1034	Gag/Aag	21/21	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.268602573705771	2		301	455	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235379	235381	+	frameshift_variant	Frame_Shift_Del	DEL	CAC	CAC	TA	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	103	627	0	ENST00000264932.6:c.1185_1187delinsTA	p.Thr396ArgfsTer27	p.T396Rfs*27	ENST00000264932	NM_004168.2	395	gtCACg/gtTAg	9/15	0.268602573705771	1	FACETS	0.877	0.785	0.975	0.877	0.785	0.975	CLONAL	1	TRUE	0	0.268602573705771	1		627	757	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31464360	31464361	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	118	700	1	ENST00000344624.3:c.2556_2557delinsTT	p.Arg853Cys	p.R853C	ENST00000344624		852	atCCgt/atTTgt	17/33	1	2	FACETS	0.896	0.807	0.99	0.896	0.807	0.99	CLONAL	1	TRUE	1	0.268602573705771	2		701	981	SUCCESS
APC	324	MSKCC	GRCh37	5	112154781	112154781	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	45	465	0	ENST00000257430.4:c.1052G>A	p.Gly351Glu	p.G351E	ENST00000257430	NM_000038.5	351	gGa/gAa	10/16	1	2	FACETS	0.627	0.527	0.739	0.627	0.527	0.739	SUBCLONAL	1	TRUE	1	0.268602573705771	2		465	534	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638755	176638756	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	50	605	1	ENST00000439151.2:c.3355_3356delinsTT	p.Pro1119Phe	p.P1119F	ENST00000439151	NM_022455.4	1119	CCt/TTt	5/23	1	2	FACETS	0.539	0.456	0.63	0.539	0.456	0.63	SUBCLONAL	1	TRUE	1	0.268602573705771	2		606	691	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178623	32178624	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	191	774	1	ENST00000375023.3:c.2770_2771delinsAA	p.Gly924Asn	p.G924N	ENST00000375023	NM_004557.3	924	GGc/AAc	18/30	0.228979169893151	3	FACETS	0.848	0.784	0.914	0.848	0.784	0.914	CLONAL	2	TRUE	1	0.268602573705771	3		775	951	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190509	32190510	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	112	792	0	ENST00000375023.3:c.229_230delinsAA	p.Gly77Lys	p.G77K	ENST00000375023	NM_004557.3	77	GGa/AAa	3/30	0.228979169893151	3	FACETS	0.965	0.867	1	0.483	0.433	0.535	CLONAL	1	TRUE	1	0.268602573705771	3		792	980	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552754	106552754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	75	494	1	ENST00000369096.4:c.719C>T	p.Pro240Leu	p.P240L	ENST00000369096	NM_001198.3	240	cCa/cTa	5/7	0.163782810799628	3	FACETS	0.915	0.802	1			1	CLONAL	1	TRUE	NA	0.268602573705771	3		495	692	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210997	55210997	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	59	358	0	ENST00000275493.2:c.241-1G>A		p.X81_splice	ENST00000275493	NM_005228.3	81			1	2	FACETS	0.968	0.834	1	0.968	0.834	1	CLONAL	1	TRUE	1	0.268602573705771	2		358	454	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194658	29194658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	136	855	2	ENST00000240100.2:c.1070C>T	p.Pro357Leu	p.P357L	ENST00000240100	NM_001394.6	357	cCc/cTc	4/4	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.268602573705771	2		857	932	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274842	38274842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	87	455	0	ENST00000425967.3:c.1738G>A	p.Gly580Arg	p.G580R	ENST00000425967	NM_001174067.1	580	Ggg/Agg	13/19	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.268602573705771	2		455	578	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981340	68981340	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	63	338	1	ENST00000288368.4:c.1412C>T	p.Pro471Leu	p.P471L	ENST00000288368	NM_024870.2	471	cCa/cTa	12/40	1	2	FACETS	0.936	0.811	1	0.936	0.811	1	CLONAL	1	TRUE	1	0.268602573705771	2		339	501	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300140	137300141	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	75	669	0	ENST00000481739.1:c.425_426delinsTT	p.Ser142Phe	p.S142F	ENST00000481739	NM_002957.4	142	tCC/tTT	3/10	1	2	FACETS	0.746	0.653	0.846	0.746	0.653	0.846	SUBCLONAL	1	TRUE	1	0.268602573705771	2		669	749	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401361	139401362	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	97	827	1	ENST00000277541.6:c.3707_3708delinsTT	p.Pro1236Leu	p.P1236L	ENST00000277541	NM_017617.3	1236	cCC/cTT	23/34	1	2	FACETS	0.8	0.712	0.894	0.8	0.712	0.894	SUBCLONAL	1	TRUE	1	0.268602573705771	2		828	903	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410348	63410348	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	104	452	0	ENST00000330258.3:c.2819G>A	p.Trp940Ter	p.W940*	ENST00000330258	NM_152424.3	940	tGg/tAg	2/2	1	1	FACETS	0.834	0.752	0.919	1	0.986	1	CLONAL	2	TRUE	0	0.268602573705771	1		452	402	SUCCESS
AR	367	MSKCC	GRCh37	X	66863214	66863214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	113	265	0	ENST00000374690.3:c.1733G>A	p.Gly578Glu	p.G578E	ENST00000374690	NM_000044.3	578	gGa/gAa	2/8	1	1	FACETS	1	0.928	1	1	0.989	1	CLONAL	2	TRUE	0	0.268602573705771	1		265	356	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0055926-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	686	436	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.534373985651089	4	FACETS	0.943	0.912	0.973	0.943	0.912	0.973	CLONAL	3	TRUE	1	0.533732004332891	4		436	1394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0055926-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	260	569	0	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.533732004332891	1	FACETS	0.996	0.938	1	0.996	0.938	1	CLONAL	1	TRUE	0	0.533732004332891	1		569	717	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023592	27023592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759726621	NA	P-0055926-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	183	337	0	ENST00000324856.7:c.698C>T	p.Ser233Phe	p.S233F	ENST00000324856	NM_006015.4	233	tCc/tTc	1/20	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.533732004332891	2		337	666	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911664	32911664	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs730881521	NA	P-0055926-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	120	252	0	ENST00000380152.3:c.3172A>T	p.Lys1058Ter	p.K1058*	ENST00000380152		1058	Aaa/Taa	11/27	0.534373985651089	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.533732004332891	1		252	301	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127259	55127260	+	splice_acceptor_variant,intron_variant	Splice_Site	DNP	CA	CA	AG	novel	NA	P-0055926-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	137	317	0	ENST00000257290.5:c.50-3_50-2delinsAG		p.X17_splice	ENST00000257290	NM_006206.4	17			1	2	FACETS	0.89	0.813	0.97	0.89	0.813	0.97	CLONAL	1	TRUE	1	0.533732004332891	2		317	577	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0056005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	197	330	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.168984962727719	3	FACETS	1	0.964	1	1	0.964	1	INDETERMINATE	2	FALSE	1	0.3	3		330	714	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199888	108199888	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	55	179	0	ENST00000278616.4:c.7230T>A	p.Phe2410Leu	p.F2410L	ENST00000278616	NM_000051.3	2410	ttT/ttA	49/63	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	FALSE	1	0.3	2		179	318	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495456	56495456	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	123	697	0	ENST00000267101.3:c.3646T>G	p.Ser1216Ala	p.S1216A	ENST00000267101	NM_001982.3	1216	Tcc/Gcc	28/28	0.168984962727719	3	FACETS	0.85	0.767	0.938	0.425	0.383	0.469	INDETERMINATE	1	FALSE	1	0.3	3		697	1109	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533004	63533004	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	65	814	0	ENST00000307078.5:c.1890C>G	p.Ser630Arg	p.S630R	ENST00000307078	NM_004655.3	630	agC/agG	7/11	1	2	FACETS	0.498	0.43	0.571	0.498	0.43	0.571	SUBCLONAL	1	FALSE	1	0.3	2		814	871	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	47	324	0				ENST00000310581	NM_198253.2	-/1132			0.266612811780045	0	FACETS	0.604	0.515	0.7			1	SUBCLONAL	1	FALSE	0	0.407852418000855	0		324	226	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0056007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	49	599	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	1	2	FACETS	0.349	0.295	0.409	0.349	0.295	0.409	SUBCLONAL	1	FALSE	1	0.407852418000855	2		599	688	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021817	71021817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs797045586	NA	P-0056007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	20	292	0	ENST00000318789.4:c.1541G>A	p.Arg514His	p.R514H	ENST00000318789	NM_032682.5	514	cGt/cAt	18/21	1	2	FACETS	0.892	0.692	1	0.892	0.692	1	CLONAL	1	FALSE	1	0.407852418000855	2		292	110	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982141	201982142	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0056007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	240	751	0	ENST00000359651.3:c.666_667dup	p.Asp223ValfsTer32	p.D223Vfs*32	ENST00000359651		222	act/acTGt	5/8	1	2	FACETS	0.821	0.77	0.873	1	0.994	1	CLONAL	2	FALSE	1	0.407852418000855	2		751	717	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281467	198281467	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	17	336	0	ENST00000335508.6:c.664G>C	p.Glu222Gln	p.E222Q	ENST00000335508	NM_012433.2	222	Gag/Cag	6/25	1	2	FACETS	0.259	0.193	0.338	0.259	0.193	0.338	SUBCLONAL	1	FALSE	1	0.407852418000855	2		336	322	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021811	71021811	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	22	221	0	ENST00000318789.4:c.1547A>G	p.Asn516Ser	p.N516S	ENST00000318789	NM_032682.5	516	aAt/aGt	18/21	1	2	FACETS	0.787	0.617	0.98	0.787	0.617	0.98	CLONAL	1	FALSE	1	0.407852418000855	2		221	137	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748198	41748198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	161	606	0	ENST00000226382.2:c.571G>A	p.Asp191Asn	p.D191N	ENST00000226382	NM_003924.3	191	Gac/Aac	3/3	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.407852418000855	2		606	600	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133868	55133868	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	38	300	0	ENST00000257290.5:c.1081del	p.Thr361LeufsTer13	p.T361Lfs*13	ENST00000257290	NM_006206.4	361	Act/ct	7/23	1	2	FACETS	0.896	0.748	1	0.896	0.748	1	CLONAL	1	FALSE	1	0.407852418000855	2		300	208	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249013	55249014	+	protein_altering_variant	In_Frame_Ins	INS	-	-	CAC	rs1554350351	NA	P-0056007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	302	634	0	ENST00000275493.2:c.2311_2312insCAC	p.Asn771delinsThrHis	p.N771delinsTH	ENST00000275493	NM_005228.3	771	aac/aCACac	20/28	0.407852418000855	2	FACETS	0.923	0.881	0.964	1	0.995	1	CLONAL	3	FALSE	0	0.407852418000855	2		634	535	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056007-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	13	324	0				ENST00000310581	NM_198253.2	-/1132			0.378409973499688	1	FACETS	0.446	0.33	0.576	0.446	0.33	0.576	INDETERMINATE	1	TRUE	0	0.775261716556132	1		324	46	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0056007-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	31	599	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	1	2	FACETS	0.53	0.434	0.634	0.53	0.434	0.634	SUBCLONAL	1	TRUE	1	0.775261716556132	2		599	151	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982141	201982142	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0056007-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	63	751	0	ENST00000359651.3:c.666_667dup	p.Asp223ValfsTer32	p.D223Vfs*32	ENST00000359651		222	act/acTGt	5/8	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.775261716556132	2		751	129	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748198	41748198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056007-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	20	606	0	ENST00000226382.2:c.571G>A	p.Asp191Asn	p.D191N	ENST00000226382	NM_003924.3	191	Gac/Aac	3/3	1	2	FACETS	0.759	0.598	0.933	0.759	0.598	0.933	CLONAL	1	TRUE	1	0.775261716556132	2		606	68	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249013	55249014	+	protein_altering_variant	In_Frame_Ins	INS	-	-	CAC	rs1554350351	NA	P-0056007-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	60	634	0	ENST00000275493.2:c.2311_2312insCAC	p.Asn771delinsThrHis	p.N771delinsTH	ENST00000275493	NM_005228.3	771	aac/aCACac	20/28	0.51081441168287	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.775261716556132	2		634	75	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046325	180046325	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056007-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	10	645	1	ENST00000261937.6:c.2689C>A	p.Leu897Ile	p.L897I	ENST00000261937	NM_182925.4	897	Ctc/Atc	19/30	0.378409973499688	1	FACETS	0.14	0.095	0.195	0.14	0.095	0.195	INDETERMINATE	1	TRUE	0	0.775261716556132	1		646	113	SUCCESS
AR	367	MSKCC	GRCh37	X	66766121	66766121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056068-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	35	625	0	ENST00000374690.3:c.1133C>T	p.Pro378Leu	p.P378L	ENST00000374690	NM_000044.3	378	cCg/cTg	1/8	0.128323598951077	6	FACETS	0.364	0.298	0.44	0.121	0.099	0.147	INDETERMINATE	1	TRUE	3	0.704179692785583	6		625	657	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670476	246670476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	16	578	0	ENST00000388985.4:c.44G>A	p.Gly15Glu	p.G15E	ENST00000388985		15	gGa/gAa	1/12	1	2	FACETS	0.575	0.424	0.755	0.575	0.424	0.755	SUBCLONAL	1	FALSE	1	0.188734003285892	2		578	295	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670501	246670501	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	13	546	0	ENST00000388985.4:c.19G>A	p.Glu7Lys	p.E7K	ENST00000388985		7	Gaa/Aaa	1/12	1	2	FACETS	0.54	0.385	0.73	0.54	0.385	0.73	SUBCLONAL	1	FALSE	1	0.188734003285892	2		546	255	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0056178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	70	613	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.167106909581328	2		613	593	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0056178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	51	429	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.167106909581328	2		429	417	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0056178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	90	1029	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.167106909581328	2		1032	747	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720650	89720650	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1257124719	NA	P-0056178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	46	461	0	ENST00000371953.3:c.802-1G>A		p.X268_splice	ENST00000371953	NM_000314.4	268			1	2	FACETS	0.915	0.769	1	0.915	0.769	1	CLONAL	1	FALSE	1	0.167106909581328	2		461	602	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0056178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	80	519	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.757	0.667	0.854	1	0.977	1	SUBCLONAL	2	FALSE	1	0.167106909581328	2		520	632	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0056178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	66	703	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	FALSE	1	0.167106909581328	2		703	715	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0056178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	45	426	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	FALSE	1	0.167106909581328	2		426	441	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141586	202141586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760898260	NA	P-0056178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	10	344	0	ENST00000358485.4:c.874C>T	p.Arg292Trp	p.R292W	ENST00000358485	NM_001080125.1	292	Cgg/Tgg	7/9	1	2	FACETS	0.272	0.183	0.385	0.272	0.183	0.385	SUBCLONAL	1	FALSE	1	0.167106909581328	2		344	440	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755128667	NA	P-0056178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	57	892	1	ENST00000407977.2:c.1976dup	p.Pro660SerfsTer87	p.P660Sfs*87	ENST00000407977		659	ggt/ggGt	9/10	1	2	FACETS	0.887	0.76	1	0.887	0.76	1	CLONAL	1	FALSE	1	0.167106909581328	2		893	769	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	19	642	1	ENST00000397062.3:c.246A>T	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaT	2/5	1	2	FACETS	0.318	0.24	0.41	0.318	0.24	0.41	SUBCLONAL	1	FALSE	1	0.167106909581328	2		643	716	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196880	108196880	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	25	303	2	ENST00000278616.4:c.6908del	p.Lys2303ArgfsTer7	p.K2303Rfs*7	ENST00000278616	NM_000051.3	2301	gcA/gc	47/63	1	2	FACETS	0.697	0.549	0.869	0.697	0.549	0.869	SUBCLONAL	1	FALSE	1	0.167106909581328	2		305	429	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	97	1045	2	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.167106909581328	2		1047	866	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0056178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	24	274	1	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	0.8	0.627	1	0.8	0.627	1	CLONAL	1	FALSE	1	0.167106909581328	2		275	359	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614463	38614463	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	41	411	0	ENST00000299084.4:c.234del	p.Asp79ThrfsTer42	p.D79Tfs*42	ENST00000299084	NM_152594.2	77	Aaa/aa	3/7	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	1	0.167106909581328	2		411	376	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943302	71943302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1175303291	NA	P-0056178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	60	685	0	ENST00000298229.2:c.1634G>A	p.Gly545Asp	p.G545D	ENST00000298229	NM_001567.3	545	gGc/gAc	14/28	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	FALSE	1	0.167106909581328	2		685	717	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026881	48026881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868575342	NA	P-0056178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	40	411	0	ENST00000234420.5:c.1759G>A	p.Ala587Thr	p.A587T	ENST00000234420	NM_000179.2	587	Gca/Aca	4/10	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	FALSE	1	0.167106909581328	2		411	416	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247892	10247892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	80	838	0	ENST00000340748.4:c.4310G>A	p.Arg1437His	p.R1437H	ENST00000340748		1437	cGc/cAc	36/40	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.167106909581328	2		838	736	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39745033	39745033	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0056178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	59	456	0	ENST00000361337.2:c.1822+1G>A		p.X608_splice	ENST00000361337	NM_003286.2	608			0.167106909581328	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	0	0.167106909581328	1		456	522	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199595	11199595	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	43	504	0	ENST00000361445.4:c.4993A>G	p.Arg1665Gly	p.R1665G	ENST00000361445	NM_004958.3	1665	Agg/Ggg	35/58	1	2	FACETS	1	0.838	1	1	0.838	1	CLONAL	1	FALSE	1	0.167106909581328	2		504	514	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097783	27097784	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	50	427	0	ENST00000324856.7:c.3374dup	p.Ser1126ValfsTer67	p.S1126Vfs*67	ENST00000324856	NM_006015.4	1124	-/A	12/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.167106909581328	2		427	452	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864595	57864595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	84	969	0	ENST00000228682.2:c.2072G>A	p.Ser691Asn	p.S691N	ENST00000228682	NM_005269.2	691	aGc/aAc	12/12	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.167106909581328	2		969	805	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973659	15973659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs183518783	NA	P-0056178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	43	495	0	ENST00000268712.3:c.4333C>T	p.Arg1445Cys	p.R1445C	ENST00000268712	NM_006311.3	1445	Cgt/Tgt	31/46	1	2	FACETS	0.957	0.8	1	0.957	0.8	1	CLONAL	1	FALSE	1	0.167106909581328	2		495	538	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245545	41245546	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	novel	NA	P-0056178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	86	821	0	ENST00000357654.3:c.2000_2002dup	p.Gln667dup	p.Q667dup	ENST00000357654	NM_007294.3	667	ctc/cAACtc	10/23	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.167106909581328	2		821	898	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505367	25505367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	46	837	0	ENST00000264709.3:c.391G>A	p.Ala131Thr	p.A131T	ENST00000264709	NM_175629.2	131	Gca/Aca	4/23	1	2	FACETS	0.879	0.74	1	0.879	0.74	1	CLONAL	1	FALSE	1	0.167106909581328	2		837	626	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430699	181430699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	30	613	2	ENST00000325404.1:c.551C>T	p.Pro184Leu	p.P184L	ENST00000325404	NM_003106.3	184	cCg/cTg	1/1	1	2	FACETS	0.65	0.523	0.796	0.65	0.523	0.796	SUBCLONAL	1	FALSE	1	0.167106909581328	2		615	552	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593304	67593304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	34	276	0	ENST00000274335.5:c.2050C>T	p.Pro684Ser	p.P684S	ENST00000274335		684	Ccc/Tcc	15/15	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	FALSE	1	0.167106909581328	2		276	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	22	504	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.428	0.33	0.543	0.428	0.33	0.543	SUBCLONAL	1	TRUE	1	0.16	2		504	642	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	58	613	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.807	0.695	0.929	1	0.972	1	CLONAL	2	TRUE	1	0.16	2		613	449	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	16	268	2	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.784	0.58	1	0.784	0.58	1	CLONAL	1	TRUE	1	0.16	2		270	255	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131412	202131412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339962485	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	33	442	0	ENST00000358485.4:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000358485	NM_001080125.1	127	cGa/cAa	2/9	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.16	2		442	388	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	26	521	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.669	0.529	0.83	0.669	0.529	0.83	SUBCLONAL	1	TRUE	1	0.16	2		521	486	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740668	58740668	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs759850701	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	19	536	0	ENST00000305921.3:c.1573G>T	p.Glu525Ter	p.E525*	ENST00000305921	NM_003620.3	525	Gaa/Taa	6/6	1	2	FACETS	0.529	0.4	0.681	0.529	0.4	0.681	SUBCLONAL	1	TRUE	1	0.16	2		536	449	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169711	11169711	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1375433078	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	24	510	0	ENST00000361445.4:c.7442C>A	p.Ser2481Tyr	p.S2481Y	ENST00000361445	NM_004958.3	2481	tCt/tAt	55/58	1	2	FACETS	0.673	0.526	0.842	0.673	0.526	0.842	SUBCLONAL	1	TRUE	1	0.16	2		510	446	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307755	11307755	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	25	464	0	ENST00000361445.4:c.1152G>T	p.Lys384Asn	p.K384N	ENST00000361445	NM_004958.3	384	aaG/aaT	8/58	1	2	FACETS	0.812	0.639	1	0.812	0.639	1	CLONAL	1	TRUE	1	0.16	2		464	385	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099431	27099431	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768377977	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	24	483	2	ENST00000324856.7:c.3668G>A	p.Arg1223His	p.R1223H	ENST00000324856	NM_006015.4	1223	cGc/cAc	14/20	1	2	FACETS	0.809	0.634	1	0.809	0.634	1	CLONAL	1	TRUE	1	0.16	2		485	371	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428511	78428511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408536007	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	22	386	0	ENST00000370768.2:c.1288C>T	p.Arg430Cys	p.R430C	ENST00000370768	NM_003902.3	430	Cgt/Tgt	14/20	1	2	FACETS	0.689	0.533	0.871	0.689	0.533	0.871	SUBCLONAL	1	TRUE	1	0.16	2		386	399	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165585	118165585	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	17	399	0	ENST00000369448.3:c.95T>G	p.Val32Gly	p.V32G	ENST00000369448	NM_017709.3	32	gTt/gGt	2/2	1	2	FACETS	0.648	0.483	0.844	0.648	0.483	0.844	SUBCLONAL	1	TRUE	1	0.16	2		399	328	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497715	120497715	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782139286	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	28	467	1	ENST00000256646.2:c.2167G>A	p.Glu723Lys	p.E723K	ENST00000256646	NM_024408.3	723	Gaa/Aaa	13/34	1	2	FACETS	0.825	0.659	1	0.825	0.659	1	CLONAL	1	TRUE	1	0.16	2		468	424	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597890	43597890	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	35	838	0	ENST00000355710.3:c.438C>A	p.Tyr146Ter	p.Y146*	ENST00000355710	NM_020975.4	146	taC/taA	3/20	1	2	FACETS	0.703	0.575	0.848	0.703	0.575	0.848	SUBCLONAL	1	TRUE	1	0.16	2		838	622	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615023	43615023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779996040	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	26	771	1	ENST00000355710.3:c.2437C>T	p.Arg813Trp	p.R813W	ENST00000355710	NM_020975.4	813	Cgg/Tgg	14/20	1	2	FACETS	0.689	0.544	0.855	0.689	0.544	0.855	SUBCLONAL	1	TRUE	1	0.16	2		772	472	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63760071	63760071	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751880754	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	12	246	0	ENST00000279873.7:c.724G>A	p.Asp242Asn	p.D242N	ENST00000279873	NM_032199.2	242	Gat/Aat	4/10	1	2	FACETS	0.664	0.466	0.907	0.664	0.466	0.907	SUBCLONAL	1	TRUE	1	0.16	2		246	226	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405743	70405743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	24	389	0	ENST00000373644.4:c.3257C>T	p.Ser1086Leu	p.S1086L	ENST00000373644	NM_030625.2	1086	tCg/tTg	4/12	1	2	FACETS	0.743	0.581	0.929	0.743	0.581	0.929	CLONAL	1	TRUE	1	0.16	2		389	404	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724517	112724517	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	31	466	0	ENST00000369452.4:c.401A>C	p.Lys134Thr	p.K134T	ENST00000369452	NM_007373.3	134	aAa/aCa	2/9	1	2	FACETS	0.999	0.808	1	0.999	0.808	1	CLONAL	1	TRUE	1	0.16	2		466	388	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251941	8251941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	44	863	0	ENST00000335790.3:c.136G>A	p.Glu46Lys	p.E46K	ENST00000335790	NM_002315.2	46	Gaa/Aaa	2/4	1	2	FACETS	0.825	0.69	0.974	0.825	0.69	0.974	CLONAL	1	TRUE	1	0.16	2		863	667	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212851	94212851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368403414	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	17	314	0	ENST00000323929.3:c.391G>A	p.Asp131Asn	p.D131N	ENST00000323929	NM_005591.3	131	Gat/Aat	5/20	1	2	FACETS	0.711	0.53	0.926	0.711	0.53	0.926	CLONAL	1	TRUE	1	0.16	2		314	299	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172385	108172385	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764389018	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	26	316	0	ENST00000278616.4:c.5188C>T	p.Arg1730Ter	p.R1730*	ENST00000278616	NM_000051.3	1730	Cga/Tga	35/63	1	2	FACETS	1	0.821	1	1	0.821	1	CLONAL	1	TRUE	1	0.16	2		316	313	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342391	118342391	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555035511	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	16	232	0	ENST00000534358.1:c.517C>T	p.Arg173Ter	p.R173*	ENST00000534358	NM_005933.3	173	Cga/Tga	3/36	1	2	FACETS	0.98	0.727	1	0.98	0.727	1	CLONAL	1	TRUE	1	0.16	2		232	204	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344566	118344566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	18	369	0	ENST00000534358.1:c.2692G>A	p.Glu898Lys	p.E898K	ENST00000534358	NM_005933.3	898	Gaa/Aaa	3/36	1	2	FACETS	0.664	0.499	0.859	0.664	0.499	0.859	SUBCLONAL	1	TRUE	1	0.16	2		369	339	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636393	21636393	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	25	499	0	ENST00000421138.2:c.617A>C	p.Lys206Thr	p.K206T	ENST00000421138		206	aAa/aCa	7/16	1	2	FACETS	0.718	0.565	0.895	0.718	0.565	0.895	SUBCLONAL	1	TRUE	1	0.16	2		499	435	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287315	46287315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1565642121	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	29	457	0	ENST00000334344.6:c.5260C>T	p.Arg1754Ter	p.R1754*	ENST00000334344	NM_152641.2	1754	Cga/Tga	19/21	1	2	FACETS	0.841	0.675	1	0.841	0.675	1	CLONAL	1	TRUE	1	0.16	2		457	431	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	46	654	0	ENST00000267101.3:c.273G>T	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atT	3/28	1	2	FACETS	0.944	0.794	1	0.944	0.794	1	CLONAL	1	TRUE	1	0.16	2		654	609	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	33	475	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	0.996	0.812	1	0.996	0.812	1	CLONAL	1	TRUE	1	0.16	2		475	414	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975486	26975486	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	28	294	0	ENST00000381527.3:c.1110+2T>C		p.X370_splice	ENST00000381527	NM_001260.1	370			1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.16	2		294	265	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601321	28601321	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	20	340	0	ENST00000241453.7:c.2111G>T	p.Arg704Ile	p.R704I	ENST00000241453	NM_004119.2	704	aGa/aTa	17/24	1	2	FACETS	0.801	0.613	1	0.801	0.613	1	CLONAL	1	TRUE	1	0.16	2		340	312	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915152	32915152	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	23	440	0	ENST00000380152.3:c.6660A>C	p.Glu2220Asp	p.E2220D	ENST00000380152		2220	gaA/gaC	11/27	1	2	FACETS	0.858	0.669	1	0.858	0.669	1	CLONAL	1	TRUE	1	0.16	2		440	335	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337650	73337650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	10	190	0	ENST00000377767.4:c.2066G>A	p.Arg689Gln	p.R689Q	ENST00000377767	NM_014953.3	689	cGa/cAa	16/21	1	2	FACETS	0.698	0.473	0.98	0.698	0.473	0.98	SUBCLONAL	1	TRUE	1	0.16	2		190	179	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435499	110435499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	23	436	0	ENST00000375856.3:c.2902G>A	p.Asp968Asn	p.D968N	ENST00000375856	NM_003749.2	968	Gac/Aac	1/2	1	2	FACETS	0.705	0.549	0.886	0.705	0.549	0.886	SUBCLONAL	1	TRUE	1	0.16	2		436	408	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093441	30093441	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	24	349	1	ENST00000331968.5:c.1822G>T	p.Asp608Tyr	p.D608Y	ENST00000331968	NM_002742.2	608	Gat/Tat	13/18	1	2	FACETS	1	0.817	1	1	0.817	1	CLONAL	1	TRUE	1	0.16	2		350	287	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572447	95572447	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	23	338	0	ENST00000393063.1:c.2918A>C	p.Lys973Thr	p.K973T	ENST00000393063	NM_030621.3	973	aAa/aCa	19/28	1	2	FACETS	0.871	0.679	1	0.871	0.679	1	CLONAL	1	TRUE	1	0.16	2		338	330	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574355	95574355	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs745444772	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	11	256	0	ENST00000393063.1:c.2512T>G	p.Leu838Val	p.L838V	ENST00000393063	NM_030621.3	838	Ttg/Gtg	17/28	1	2	FACETS	0.655	0.452	0.906	0.655	0.452	0.906	SUBCLONAL	1	TRUE	1	0.16	2		256	210	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003192	42003192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764724458	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	26	469	0	ENST00000219905.7:c.2729G>A	p.Arg910Gln	p.R910Q	ENST00000219905	NM_001164273.1	910	cGa/cAa	8/24	1	2	FACETS	0.689	0.544	0.855	0.689	0.544	0.855	SUBCLONAL	1	TRUE	1	0.16	2		469	472	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292667	91292667	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	21	263	0	ENST00000355112.3:c.169A>G	p.Thr57Ala	p.T57A	ENST00000355112	NM_000057.2	57	Aca/Gca	3/22	1	2	FACETS	0.965	0.744	1	0.965	0.744	1	CLONAL	1	TRUE	1	0.16	2		263	272	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112596	2112596	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769147552	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	27	682	1	ENST00000219476.3:c.1356C>A	p.Phe452Leu	p.F452L	ENST00000219476	NM_000548.3	452	ttC/ttA	13/42	1	2	FACETS	0.663	0.526	0.82	0.663	0.526	0.82	SUBCLONAL	1	TRUE	1	0.16	2		683	509	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862767	9862767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1285952756	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	31	617	2	ENST00000330684.3:c.2536C>T	p.Arg846Cys	p.R846C	ENST00000330684	NM_001134407.1	846	Cgc/Tgc	12/13	1	2	FACETS	0.811	0.655	0.987	0.811	0.655	0.987	CLONAL	1	TRUE	1	0.16	2		619	478	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655353	67655353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	21	434	0	ENST00000264010.4:c.1216C>T	p.Pro406Ser	p.P406S	ENST00000264010	NM_006565.3	406	Cct/Tct	7/12	1	2	FACETS	0.702	0.54	0.891	0.702	0.54	0.891	SUBCLONAL	1	TRUE	1	0.16	2		434	374	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832381	72832382	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	24	498	0	ENST00000268489.5:c.4199dup	p.Tyr1401ValfsTer4	p.Y1401Vfs*4	ENST00000268489	NM_006885.3	1400	aag/aaAg	9/10	1	2	FACETS	0.798	0.625	0.997	0.798	0.625	0.997	CLONAL	1	TRUE	1	0.16	2		498	376	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546044	29546044	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778548	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	27	410	0	ENST00000356175.3:c.1549G>A	p.Glu517Lys	p.E517K	ENST00000356175	NM_000267.3	517	Gaa/Aaa	14/57	1	2	FACETS	0.792	0.63	0.978	0.792	0.63	0.978	CLONAL	1	TRUE	1	0.16	2		410	426	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	22	408	0	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	1	2	FACETS	0.703	0.544	0.889	0.703	0.544	0.889	SUBCLONAL	1	TRUE	1	0.16	2		408	391	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59793411	59793411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375082407	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	19	301	0	ENST00000259008.2:c.2393G>A	p.Arg798Gln	p.R798Q	ENST00000259008	NM_032043.2	798	cGa/cAa	17/20	1	2	FACETS	0.965	0.734	1	0.965	0.734	1	CLONAL	1	TRUE	1	0.16	2		301	246	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400757	56400757	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	14	234	0	ENST00000348428.3:c.1351G>T	p.Glu451Ter	p.E451*	ENST00000348428	NM_006785.3	451	Gaa/Taa	11/17	1	2	FACETS	0.758	0.548	1	0.758	0.548	1	CLONAL	1	TRUE	1	0.16	2		234	231	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56409144	56409144	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	20	341	0	ENST00000348428.3:c.1651C>T	p.Arg551Ter	p.R551*	ENST00000348428	NM_006785.3	551	Cga/Tga	14/17	1	2	FACETS	0.877	0.671	1	0.877	0.671	1	CLONAL	1	TRUE	1	0.16	2		341	285	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172323	7172323	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs778989302	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	28	422	0	ENST00000302850.5:c.1246C>T	p.Arg416Ter	p.R416*	ENST00000302850	NM_000208.2	416	Cga/Tga	5/22	1	2	FACETS	0.717	0.572	0.883	0.717	0.572	0.883	SUBCLONAL	1	TRUE	1	0.16	2		422	488	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221279	36221279	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555731976	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	49	851	0	ENST00000222270.7:c.5113C>T	p.Arg1705Ter	p.R1705*	ENST00000222270	NM_014727.1	1705	Cga/Tga	24/37	1	2	FACETS	0.845	0.714	0.989	0.845	0.714	0.989	CLONAL	1	TRUE	1	0.16	2		851	725	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606679	29606679	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs865931787	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	18	501	0	ENST00000389048.3:c.1201C>T	p.Arg401Ter	p.R401*	ENST00000389048	NM_004304.4	401	Cga/Tga	5/29	1	2	FACETS	0.52	0.39	0.674	0.52	0.39	0.674	SUBCLONAL	1	TRUE	1	0.16	2		501	433	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46608817	46608817	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	31	741	0	ENST00000263734.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000263734	NM_001430.4	710	Cga/Tga	13/16	1	2	FACETS	0.763	0.616	0.93	0.763	0.616	0.93	CLONAL	1	TRUE	1	0.16	2		741	508	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026290	48026290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147737737	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	13	387	0	ENST00000234420.5:c.1168G>A	p.Asp390Asn	p.D390N	ENST00000234420	NM_000179.2	390	Gat/Aat	4/10	1	2	FACETS	0.647	0.461	0.875	0.647	0.461	0.875	SUBCLONAL	1	TRUE	1	0.16	2		387	251	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027958	48027958	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1558666905	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	16	280	0	ENST00000234420.5:c.2836G>T	p.Glu946Ter	p.E946*	ENST00000234420	NM_000179.2	946	Gaa/Taa	4/10	1	2	FACETS	0.76	0.562	0.997	0.76	0.562	0.997	CLONAL	1	TRUE	1	0.16	2		280	263	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728698	190728698	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	24	300	0	ENST00000441310.2:c.2086A>C	p.Met696Leu	p.M696L	ENST00000441310	NM_000534.4	696	Atg/Ctg	10/13	1	2	FACETS	1	0.815	1	1	0.815	1	CLONAL	1	TRUE	1	0.16	2		300	288	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262257	46262257	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	18	297	1	ENST00000371998.3:c.841G>T	p.Asp281Tyr	p.D281Y	ENST00000371998		281	Gat/Tat	9/23	1	2	FACETS	0.846	0.637	1	0.846	0.637	1	CLONAL	1	TRUE	1	0.16	2		298	266	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641905	12641905	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs755926381	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	25	272	0	ENST00000251849.4:c.844C>T	p.Arg282Ter	p.R282*	ENST00000251849	NM_002880.3	282	Cga/Tga	8/17	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.16	2		272	251	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686299	30686299	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs767191783	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	26	339	0	ENST00000295754.5:c.155A>C	p.Lys52Thr	p.K52T	ENST00000295754	NM_003242.5	52	aAa/aCa	2/7	1	2	FACETS	0.89	0.705	1	0.89	0.705	1	CLONAL	1	TRUE	1	0.16	2		339	365	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147533	47147533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	19	363	0	ENST00000409792.3:c.4793G>A	p.Arg1598Gln	p.R1598Q	ENST00000409792	NM_014159.6	1598	cGa/cAa	6/21	1	2	FACETS	0.681	0.516	0.875	0.681	0.516	0.875	SUBCLONAL	1	TRUE	1	0.16	2		363	349	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	18	295	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.9	0.679	1	0.9	0.679	1	CLONAL	1	TRUE	1	0.16	2		295	250	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447244	187447244	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542190544	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	34	674	0	ENST00000232014.4:c.949G>A	p.Glu317Lys	p.E317K	ENST00000232014	NM_001130845.1	317	Gag/Aag	5/10	1	2	FACETS	0.708	0.577	0.856	0.708	0.577	0.856	SUBCLONAL	1	TRUE	1	0.16	2		674	600	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136805	55136805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41279521	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	14	274	0	ENST00000257290.5:c.1127G>A	p.Arg376Gln	p.R376Q	ENST00000257290	NM_006206.4	376	cGa/cAa	8/23	1	2	FACETS	0.655	0.473	0.876	0.655	0.473	0.876	SUBCLONAL	1	TRUE	1	0.16	2		274	267	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961080	55961080	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	37	642	0	ENST00000263923.4:c.2860G>T	p.Ala954Ser	p.A954S	ENST00000263923	NM_002253.2	954	Gca/Tca	21/30	1	2	FACETS	0.796	0.655	0.954	0.796	0.655	0.954	CLONAL	1	TRUE	1	0.16	2		642	581	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233140	66233140	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs769393148	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	30	368	1	ENST00000273854.3:c.1859G>A	p.Arg620Gln	p.R620Q	ENST00000273854	NM_004439.5	620	cGg/cAg	10/18	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.16	2		369	301	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045890	143045890	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	24	399	0	ENST00000262992.4:c.1744C>T	p.Pro582Ser	p.P582S	ENST00000262992	NM_001101669.1	582	Ccc/Tcc	17/24	1	2	FACETS	0.882	0.692	1	0.882	0.692	1	CLONAL	1	TRUE	1	0.16	2		399	340	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541803	187541803	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	24	408	0	ENST00000441802.2:c.5937T>G	p.Phe1979Leu	p.F1979L	ENST00000441802	NM_005245.3	1979	ttT/ttG	10/27	1	2	FACETS	0.857	0.672	1	0.857	0.672	1	CLONAL	1	TRUE	1	0.16	2		408	350	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630741	187630741	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs919489407	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	41	567	0	ENST00000441802.2:c.241A>C	p.Asn81His	p.N81H	ENST00000441802	NM_005245.3	81	Aac/Cac	2/27	1	2	FACETS	0.976	0.813	1	0.976	0.813	1	CLONAL	1	TRUE	1	0.16	2		567	525	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685312	86685312	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	12	152	0	ENST00000274376.6:c.3028C>T	p.Arg1010Ter	p.R1010*	ENST00000274376	NM_002890.2	1010	Cga/Tga	24/25	1	2	FACETS	0.987	0.696	1	0.987	0.696	1	CLONAL	1	TRUE	1	0.16	2		152	152	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939624	131939624	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	13	182	0	ENST00000265335.6:c.2410G>T	p.Asp804Tyr	p.D804Y	ENST00000265335		804	Gat/Tat	15/25	1	2	FACETS	0.833	0.595	1	0.833	0.595	1	CLONAL	1	TRUE	1	0.16	2		182	195	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20486949	20486949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188266138	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	18	260	0	ENST00000346618.3:c.914G>A	p.Arg305Gln	p.R305Q	ENST00000346618	NM_001949.4	305	cGa/cAa	5/7	1	2	FACETS	0.789	0.594	1	0.789	0.594	1	CLONAL	1	TRUE	1	0.16	2		260	285	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672422	30672422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148973631	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	50	721	1	ENST00000376406.3:c.4538G>A	p.Arg1513Gln	p.R1513Q	ENST00000376406	NM_014641.2	1513	cGg/cAg	10/15	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.16	2		722	566	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169036	32169036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745902446	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	41	863	0	ENST00000375023.3:c.3997C>T	p.Arg1333Cys	p.R1333C	ENST00000375023	NM_004557.3	1333	Cgt/Tgt	22/30	1	2	FACETS	0.844	0.702	1	0.844	0.702	1	CLONAL	1	TRUE	1	0.16	2		863	607	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185819	32185819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145916093	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	40	781	0	ENST00000375023.3:c.1577C>T	p.Ala526Val	p.A526V	ENST00000375023	NM_004557.3	526	gCg/gTg	9/30	1	2	FACETS	0.87	0.722	1	0.87	0.722	1	CLONAL	1	TRUE	1	0.16	2		781	575	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805604	32805604	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	46	906	0	ENST00000374899.4:c.407T>C	p.Val136Ala	p.V136A	ENST00000374899	NM_018833.2	136	gTc/gCc	2/12	1	2	FACETS	0.784	0.659	0.924	0.784	0.659	0.924	CLONAL	1	TRUE	1	0.16	2		906	733	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818728	32818728	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs55955143	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	31	533	0	ENST00000354258.4:c.1223G>T	p.Trp408Leu	p.W408L	ENST00000354258	NM_000593.5	408	tGg/tTg	4/11	1	2	FACETS	0.799	0.645	0.973	0.799	0.645	0.973	CLONAL	1	TRUE	1	0.16	2		533	485	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679064	117679064	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	20	359	0	ENST00000368508.3:c.3757G>T	p.Asp1253Tyr	p.D1253Y	ENST00000368508	NM_002944.2	1253	Gat/Tat	24/43	1	2	FACETS	0.812	0.621	1	0.812	0.621	1	CLONAL	1	TRUE	1	0.16	2		359	308	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686331	117686331	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	10	232	0	ENST00000368508.3:c.3010A>C	p.Thr1004Pro	p.T1004P	ENST00000368508	NM_002944.2	1004	Act/Cct	20/43	1	2	FACETS	0.672	0.455	0.944	0.672	0.455	0.944	SUBCLONAL	1	TRUE	1	0.16	2		232	186	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527318	137527318	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	72	540	0	ENST00000367739.4:c.328G>T	p.Glu110Ter	p.E110*	ENST00000367739	NM_000416.2	110	Gaa/Taa	3/7	1	2	FACETS	0.789	0.69	0.896	1	0.976	1	SUBCLONAL	2	TRUE	1	0.16	2		540	570	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004840	150004840	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	18	421	0	ENST00000253339.5:c.1385C>A	p.Ser462Ter	p.S462*	ENST00000253339		462	tCa/tAa	3/7	1	2	FACETS	0.743	0.559	0.96	0.743	0.559	0.96	CLONAL	1	TRUE	1	0.16	2		421	303	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005639	150005639	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	18	314	0	ENST00000253339.5:c.586G>T	p.Glu196Ter	p.E196*	ENST00000253339		196	Gaa/Taa	3/7	1	2	FACETS	0.776	0.584	1	0.776	0.584	1	CLONAL	1	TRUE	1	0.16	2		314	290	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14026311	14026311	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	13	216	0	ENST00000405192.2:c.134-1G>T		p.X45_splice	ENST00000405192	NM_001163147.1	45			1	2	FACETS	0.8	0.572	1	0.8	0.572	1	CLONAL	1	TRUE	1	0.16	2		216	203	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509379	106509379	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	28	582	0	ENST00000359195.3:c.1373T>C	p.Val458Ala	p.V458A	ENST00000359195	NM_002649.2	458	gTt/gCt	2/11	1	2	FACETS	0.764	0.61	0.941	0.764	0.61	0.941	CLONAL	1	TRUE	1	0.16	2		582	458	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860613	151860613	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs200124578	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	43	603	0	ENST00000262189.6:c.10049G>T	p.Arg3350Ile	p.R3350I	ENST00000262189	NM_170606.2	3350	aGa/aTa	43/59	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.16	2		603	477	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027813	152027813	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	29	449	0	ENST00000262189.6:c.262C>T	p.Gln88Ter	p.Q88*	ENST00000262189	NM_170606.2	88	Caa/Taa	3/59	1	2	FACETS	0.773	0.619	0.948	0.773	0.619	0.948	CLONAL	1	TRUE	1	0.16	2		449	469	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931862	68931862	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200600940	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	38	523	0	ENST00000288368.4:c.292G>A	p.Glu98Lys	p.E98K	ENST00000288368	NM_024870.2	98	Gaa/Aaa	3/40	1	2	FACETS	0.921	0.76	1	0.921	0.76	1	CLONAL	1	TRUE	1	0.16	2		523	516	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031672	69031672	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	16	329	0	ENST00000288368.4:c.3427G>T	p.Glu1143Ter	p.E1143*	ENST00000288368	NM_024870.2	1143	Gaa/Taa	28/40	1	2	FACETS	0.704	0.52	0.924	0.704	0.52	0.924	CLONAL	1	TRUE	1	0.16	2		329	284	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135777055	135777055	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756514375	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	34	477	1	ENST00000298552.3:c.2423C>T	p.Ala808Val	p.A808V	ENST00000298552	NM_001162426.1	808	gCg/gTg	19/23	1	2	FACETS	0.825	0.673	0.997	0.825	0.673	0.997	CLONAL	1	TRUE	1	0.16	2		478	515	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913517	39913517	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	25	419	1	ENST00000378444.4:c.4811C>A	p.Ser1604Tyr	p.S1604Y	ENST00000378444	NM_001123385.1	1604	tCt/tAt	13/15	1	2	FACETS	0.812	0.639	1	0.812	0.639	1	CLONAL	1	TRUE	1	0.16	2		420	385	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921403	39921403	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	21	403	0	ENST00000378444.4:c.4417C>T	p.Leu1473Phe	p.L1473F	ENST00000378444	NM_001123385.1	1473	Ctt/Ttt	10/15	1	2	FACETS	0.844	0.65	1	0.844	0.65	1	CLONAL	1	TRUE	1	0.16	2		403	311	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732866	44732866	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	26	476	0	ENST00000377967.4:c.69G>T	p.Lys23Asn	p.K23N	ENST00000377967	NM_021140.2	23	aaG/aaT	1/29	1	2	FACETS	0.791	0.626	0.98	0.791	0.626	0.98	CLONAL	1	TRUE	1	0.16	2		476	411	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426296	47426296	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	34	878	0	ENST00000377045.4:c.713G>A	p.Ser238Asn	p.S238N	ENST00000377045	NM_001654.4	238	aGt/aAt	8/16	1	2	FACETS	0.767	0.626	0.927	0.767	0.626	0.927	CLONAL	1	TRUE	1	0.16	2		878	554	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411619	63411619	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	38	764	1	ENST00000330258.3:c.1548G>T	p.Glu516Asp	p.E516D	ENST00000330258	NM_152424.3	516	gaG/gaT	2/2	1	2	FACETS	0.798	0.659	0.955	0.798	0.659	0.955	CLONAL	1	TRUE	1	0.16	2		765	595	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413094	63413094	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	39	760	1	ENST00000330258.3:c.73G>T	p.Ala25Ser	p.A25S	ENST00000330258	NM_152424.3	25	Gca/Tca	2/2	1	2	FACETS	0.78	0.645	0.931	0.78	0.645	0.931	CLONAL	1	TRUE	1	0.16	2		761	625	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344091	70344091	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	36	825	0	ENST00000374080.3:c.1827C>A	p.Phe609Leu	p.F609L	ENST00000374080		609	ttC/ttA	13/45	1	2	FACETS	0.706	0.579	0.85	0.706	0.579	0.85	SUBCLONAL	1	TRUE	1	0.16	2		825	637	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938018	76938018	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	30	525	0	ENST00000373344.5:c.2730G>T	p.Lys910Asn	p.K910N	ENST00000373344	NM_000489.3	910	aaG/aaT	9/35	1	2	FACETS	0.708	0.569	0.865	0.708	0.569	0.865	SUBCLONAL	1	TRUE	1	0.16	2		525	530	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938029	76938029	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	28	524	0	ENST00000373344.5:c.2719C>T	p.Arg907Ter	p.R907*	ENST00000373344	NM_000489.3	907	Cga/Tga	9/35	1	2	FACETS	0.636	0.507	0.784	0.636	0.507	0.784	SUBCLONAL	1	TRUE	1	0.16	2		524	550	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938289	76938289	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	26	502	0	ENST00000373344.5:c.2459A>C	p.Glu820Ala	p.E820A	ENST00000373344	NM_000489.3	820	gAa/gCa	9/35	1	2	FACETS	0.69	0.545	0.856	0.69	0.545	0.856	SUBCLONAL	1	TRUE	1	0.16	2		502	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0056239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	298	845	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.490666236825471	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.489716372986737	2		845	530	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0056239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	77	323	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.490666236825471	3	FACETS	0.974	0.859	1	0.487	0.429	0.548	CLONAL	1	TRUE	1	0.489716372986737	3		323	402	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	101	437	0	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	0.490666236825471	3	FACETS	1	0.951	1	0.549	0.493	0.607	CLONAL	1	TRUE	1	0.489716372986737	3		437	468	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	290	624	0	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	0.490666236825471	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.489716372986737	3		624	604	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562745	21562745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778627422	NA	P-0056239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	325	906	0	ENST00000382592.4:c.1174G>A	p.Ala392Thr	p.A392T	ENST00000382592	NM_014572.2	392	Gcg/Acg	4/8	0.489716372986737	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.489716372986737	4		906	924	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748245	41748245	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	146	876	0	ENST00000226382.2:c.524A>G	p.Lys175Arg	p.K175R	ENST00000226382	NM_003924.3	175	aAg/aGg	3/3	0.490666236825471	3	FACETS	1	0.966	1	0.555	0.507	0.604	CLONAL	1	TRUE	1	0.489716372986737	3		876	669	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967313	25967313	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	88	448	0	ENST00000435504.4:c.1893del	p.His632IlefsTer167	p.H632Ifs*167	ENST00000435504		631	ttT/tt	13/13	0.490666236825471	3	FACETS	0.975	0.867	1	0.487	0.433	0.544	CLONAL	1	TRUE	1	0.489716372986737	3		448	459	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030985	36030985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1459444714	NA	P-0056239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	244	788	0	ENST00000358208.4:c.1264C>T	p.Arg422Trp	p.R422W	ENST00000358208		422	Cgg/Tgg	10/12	0.489716372986737	6	FACETS	0.883	0.825	0.943	0.441	0.412	0.472	CLONAL	2	TRUE	2	0.489716372986737	6		788	1117	SUCCESS
APC	324	MSKCC	GRCh37	5	112175521	112176541	+	frameshift_variant	Frame_Shift_Del	DEL	CAGTGGAATGGTAAGTGGCATTATAAGCCCCAGTGATCTTCCAGATAGCCCTGGACAAACCATGCCACCAAGCAGAAGTAAAACACCTCCACCACCTCCTCAAACAGCTCAAACCAAGCGAGAAGTACCTAAAAATAAAGCACCTACTGCTGAAAAGAGAGAGAGTGGACCTAAGCAAGCTGCAGTAAATGCTGCAGTTCAGAGGGTCCAGGTTCTTCCAGATGCTGATACTTTATTACATTTTGCCACGGAAAGTACTCCAGATGGATTTTCTTGTTCATCCAGCCTGAGTGCTCTGAGCCTCGATGAGCCATTTATACAGAAAGATGTGGAATTAAGAATAATGCCTCCAGTTCAGGAAAATGACAATGGGAATGAAACAGAATCAGAGCAGCCTAAAGAATCAAATGAAAACCAAGAGAAAGAGGCAGAAAAAACTATTGATTCTGAAAAGGACCTATTAGATGATTCAGATGATGATGATATTGAAATACTAGAAGAATGTATTATTTCTGCCATGCCAACAAAGTCATCACGTAAAGCAAAAAAGCCAGCCCAGACTGCTTCAAAATTACCTCCACCTGTGGCAAGGAAACCAAGTCAGCTGCCTGTGTACAAACTTCTACCATCACAAAACAGGTTGCAACCCCAAAAGCATGTTAGTTTTACACCGGGGGATGATATGCCACGGGTGTATTGTGTTGAAGGGACACCTATAAACTTTTCCACAGCTACATCTCTAAGTGATCTAACAATCGAATCCCCTCCAAATGAGTTAGCTGCTGGAGAAGGAGTTAGAGGAGGGGCACAGTCAGGTGAATTTGAAAAACGAGATACCATTCCTACAGAAGGCAGAAGTACAGATGAGGCTCAAGGAGGAAAAACCTCATCTGTAACCATACCTGAATTGGATGACAATAAAGCAGAGGAAGGTGATATTCTTGCAGAATGCATTAATTCTGCTATGCCCAAAGGGAAAAGTCACAAGCCTTTCCGTGTGAAAAAGATAATGGACCAGGTC	CAGTGGAATGGTAAGTGGCATTATAAGCCCCAGTGATCTTCCAGATAGCCCTGGACAAACCATGCCACCAAGCAGAAGTAAAACACCTCCACCACCTCCTCAAACAGCTCAAACCAAGCGAGAAGTACCTAAAAATAAAGCACCTACTGCTGAAAAGAGAGAGAGTGGACCTAAGCAAGCTGCAGTAAATGCTGCAGTTCAGAGGGTCCAGGTTCTTCCAGATGCTGATACTTTATTACATTTTGCCACGGAAAGTACTCCAGATGGATTTTCTTGTTCATCCAGCCTGAGTGCTCTGAGCCTCGATGAGCCATTTATACAGAAAGATGTGGAATTAAGAATAATGCCTCCAGTTCAGGAAAATGACAATGGGAATGAAACAGAATCAGAGCAGCCTAAAGAATCAAATGAAAACCAAGAGAAAGAGGCAGAAAAAACTATTGATTCTGAAAAGGACCTATTAGATGATTCAGATGATGATGATATTGAAATACTAGAAGAATGTATTATTTCTGCCATGCCAACAAAGTCATCACGTAAAGCAAAAAAGCCAGCCCAGACTGCTTCAAAATTACCTCCACCTGTGGCAAGGAAACCAAGTCAGCTGCCTGTGTACAAACTTCTACCATCACAAAACAGGTTGCAACCCCAAAAGCATGTTAGTTTTACACCGGGGGATGATATGCCACGGGTGTATTGTGTTGAAGGGACACCTATAAACTTTTCCACAGCTACATCTCTAAGTGATCTAACAATCGAATCCCCTCCAAATGAGTTAGCTGCTGGAGAAGGAGTTAGAGGAGGGGCACAGTCAGGTGAATTTGAAAAACGAGATACCATTCCTACAGAAGGCAGAAGTACAGATGAGGCTCAAGGAGGAAAAACCTCATCTGTAACCATACCTGAATTGGATGACAATAAAGCAGAGGAAGGTGATATTCTTGCAGAATGCATTAATTCTGCTATGCCCAAAGGGAAAAGTCACAAGCCTTTCCGTGTGAAAAAGATAATGGACCAGGTC	-	novel	NA	P-0056239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	136	338	0	ENST00000257430.4:c.4233_5253del	p.Gly1412LysfsTer14	p.G1412Kfs*14	ENST00000257430	NM_000038.5	1410	tgCAGTGGAATGGTAAGTGGCATTATAAGCCCCAGTGATCTTCCAGATAGCCCTGGACAAACCATGCCACCAAGCAGAAGTAAAACACCTCCACCACCTCCTCAAACAGCTCAAACCAAGCGAGAAGTACCTAAAAATAAAGCACCTACTGCTGAAAAGAGAGAGAGTGGACCTAAGCAAGCTGCAGTAAATGCTGCAGTTCAGAGGGTCCAGGTTCTTCCAGATGCTGATACTTTATTACATTTTGCCACGGAAAGTACTCCAGATGGATTTTCTTGTTCATCCAGCCTGAGTGCTCTGAGCCTCGATGAGCCATTTATACAGAAAGATGTGGAATTAAGAATAATGCCTCCAGTTCAGGAAAATGACAATGGGAATGAAACAGAATCAGAGCAGCCTAAAGAATCAAATGAAAACCAAGAGAAAGAGGCAGAAAAAACTATTGATTCTGAAAAGGACCTATTAGATGATTCAGATGATGATGATATTGAAATACTAGAAGAATGTATTATTTCTGCCATGCCAACAAAGTCATCACGTAAAGCAAAAAAGCCAGCCCAGACTGCTTCAAAATTACCTCCACCTGTGGCAAGGAAACCAAGTCAGCTGCCTGTGTACAAACTTCTACCATCACAAAACAGGTTGCAACCCCAAAAGCATGTTAGTTTTACACCGGGGGATGATATGCCACGGGTGTATTGTGTTGAAGGGACACCTATAAACTTTTCCACAGCTACATCTCTAAGTGATCTAACAATCGAATCCCCTCCAAATGAGTTAGCTGCTGGAGAAGGAGTTAGAGGAGGGGCACAGTCAGGTGAATTTGAAAAACGAGATACCATTCCTACAGAAGGCAGAAGTACAGATGAGGCTCAAGGAGGAAAAACCTCATCTGTAACCATACCTGAATTGGATGACAATAAAGCAGAGGAAGGTGATATTCTTGCAGAATGCATTAATTCTGCTATGCCCAAAGGGAAAAGTCACAAGCCTTTCCGTGTGAAAAAGATAATGGACCAGGTC/tg	16/16	0.490666236825471	3	FACETS	0.982	0.905	1	0.982	0.905	1	CLONAL	2	TRUE	1	0.489716372986737	3		338	352	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346388	152346389	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGTGATAAAGCATTTCTGTTTTT	novel	NA	P-0056239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	58	553	0	ENST00000359321.1:c.159_181dup	p.Leu61GlnfsTer9	p.L61Qfs*9	ENST00000359321	NM_005431.1	61	cta/cAAAAACAGAAATGCTTTATCACCta	3/3	0.489716372986737	4	FACETS	0.526	0.451	0.608	0.263	0.225	0.304	SUBCLONAL	1	TRUE	2	0.489716372986737	4		553	671	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751182	128751182	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	160	681	0	ENST00000377970.2:c.719C>T	p.Ser240Phe	p.S240F	ENST00000377970	NM_002467.4	240	tCc/tTc	2/3	0.490666236825471	4	FACETS	1	0.977	1	0.392	0.36	0.426	CLONAL	1	TRUE	1	0.489716372986737	4		681	827	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0056248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	147	650	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.928	0.851	1	0.928	0.851	1	CLONAL	1	TRUE	1	0.553853856884567	2		650	572	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101199	41101199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368237025	NA	P-0056248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	152	565	0	ENST00000373198.4:c.1157C>T	p.Pro386Leu	p.P386L	ENST00000373198	NM_133170.3	386	cCg/cTg	8/32	0.0753901619128383	3	FACETS	0.827	0.756	0.9			1	INDETERMINATE	1	TRUE	NA	0.553853856884567	3		565	848	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797313	135797313	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	124	248	0	ENST00000298552.3:c.556G>C	p.Ala186Pro	p.A186P	ENST00000298552	NM_001162426.1	186	Gca/Cca	7/23	0.553853856884567	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.553853856884567	1		248	276	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288496	15288496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1162468178	NA	P-0056248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	95	261	0	ENST00000263388.2:c.4243G>A	p.Gly1415Ser	p.G1415S	ENST00000263388	NM_000435.2	1415	Ggc/Agc	24/33	0.553853856884567	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.553853856884567	1		261	216	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0056248-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	63	650	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.968	0.845	1	0.968	0.845	1	CLONAL	1	TRUE	1	0.461455977818386	2		650	282	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101199	41101199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368237025	NA	P-0056248-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	70	565	0	ENST00000373198.4:c.1157C>T	p.Pro386Leu	p.P386L	ENST00000373198	NM_133170.3	386	cCg/cTg	8/32	0.440138170461744	1	FACETS	0.538	0.47	0.61	0.538	0.47	0.61	SUBCLONAL	1	TRUE	0	0.461455977818386	1		565	434	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797313	135797313	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056248-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	69	248	0	ENST00000298552.3:c.556G>C	p.Ala186Pro	p.A186P	ENST00000298552	NM_001162426.1	186	Gca/Cca	7/23	0.461455977818386	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.461455977818386	1		248	192	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288496	15288496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1162468178	NA	P-0056248-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	35	261	0	ENST00000263388.2:c.4243G>A	p.Gly1415Ser	p.G1415S	ENST00000263388	NM_000435.2	1415	Ggc/Agc	24/33	1	2	FACETS	0.998	0.831	1	0.998	0.831	1	CLONAL	1	TRUE	1	0.461455977818386	2		261	152	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152864447	152864447	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	82	89	0	ENST00000406277.2:c.79del	p.Arg27GlufsTer13	p.R27Efs*13	ENST00000406277	NM_152274.4	27	Cga/ga	3/7	NA		FACETS		NA	1				INDETERMINATE	NA	TRUE	NA	0.381411367681351	NA		89	152	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249013	55249013	+	protein_altering_variant	In_Frame_Ins	INS	A	A	GGGT	novel	NA	P-0056275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	425	757	0	ENST00000275493.2:c.2311delinsGGGT	p.Asn771delinsGlyTyr	p.N771delinsGY	ENST00000275493	NM_005228.3	771	Aac/GGGTac	20/28	0.381411367681351	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.381411367681351	3		757	1258	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	51	324	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.521576825253062	2		324	180	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0056276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	521	628	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.506707196415828	5	FACETS	1	0.984	1	1	0.984	1	CLONAL	4	TRUE	1	0.521576825253062	5		628	864	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202710	128202710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	165	783	1	ENST00000341105.2:c.1010G>A	p.Arg337Gln	p.R337Q	ENST00000341105	NM_032638.4	337	cGa/cAa	4/6	1	2	FACETS	0.937	0.864	1	0.937	0.864	1	CLONAL	1	TRUE	1	0.521576825253062	2		784	675	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057193	30057193	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0056276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	90	463	0	ENST00000338641.4:c.676-1G>C		p.X226_splice	ENST00000338641	NM_000268.3	226			0.521576825253062	1	FACETS	0.883	0.793	0.976	0.883	0.793	0.976	CLONAL	1	TRUE	0	0.521576825253062	1		463	289	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270529	98270530	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs751977093	NA	P-0056305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	143	391	2	ENST00000331920.6:c.114dup	p.Leu39AlafsTer51	p.L39Afs*51	ENST00000331920	NM_000264.3	38	-/G	1/24	0.402802164363641	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.402802164363641	1		393	438	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508605	106508605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	232	668	1	ENST00000359195.3:c.599C>T	p.Pro200Leu	p.P200L	ENST00000359195	NM_002649.2	200	cCg/cTg	2/11	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.402802164363641	2		669	848	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651615	206651615	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	140	1040	0	ENST00000367120.3:c.925G>A	p.Val309Ile	p.V309I	ENST00000367120	NM_014002.3	309	Gtt/Att	9/22	0.226762784672005	1	FACETS	0.701	0.639	0.766	0.701	0.639	0.766	INDETERMINATE	1	TRUE	0	0.402802164363641	1		1040	792	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589310	28589310	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	22	391	0	ENST00000241453.7:c.2737T>C	p.Tyr913His	p.Y913H	ENST00000241453	NM_004119.2	913	Tat/Cat	22/24	0.226762784672005	1	FACETS	0.365	0.283	0.459	0.365	0.283	0.459	INDETERMINATE	1	TRUE	0	0.402802164363641	1		391	239	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618920	37618920	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	125	724	0	ENST00000447079.4:c.596A>G	p.Lys199Arg	p.K199R	ENST00000447079	NM_015083.1	199	aAa/aGa	1/14	0.338699978042267	2	FACETS	0.894	0.811	0.982	0.447	0.405	0.491	CLONAL	1	TRUE	0	0.402802164363641	2		724	694	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754492	42754492	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758855122	NA	P-0056305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	83	946	0	ENST00000222329.4:c.248G>A	p.Arg83Gln	p.R83Q	ENST00000222329	NM_006494.2	83	cGg/cAg	2/4	1	2	FACETS	0.357	0.314	0.404	0.357	0.314	0.404	SUBCLONAL	1	TRUE	1	0.402802164363641	2		946	1154	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280317	1280317	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1265160730	NA	P-0056305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	174	1131	0	ENST00000310581.5:c.1906A>G	p.Met636Val	p.M636V	ENST00000310581	NM_198253.2	636	Atg/Gtg	4/16	0.187344343096244	2	FACETS	0.823	0.757	0.892	0.411	0.378	0.446	INDETERMINATE	1	TRUE	0	0.402802164363641	2		1131	1050	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777925	27777925	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	53	689	0	ENST00000369163.2:c.74C>G	p.Ala25Gly	p.A25G	ENST00000369163	NM_003536.2	25	gCg/gGg	1/1	0.261582575452605	5	FACETS	0.477	0.405	0.556	0.159	0.135	0.186	SUBCLONAL	1	TRUE	2	0.402802164363641	5		689	885	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038523	47038523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	271	965	0	ENST00000377604.3:c.685C>T	p.Arg229Cys	p.R229C	ENST00000377604	NM_001204468.1	229	Cgc/Tgc	8/24	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.402802164363641	2		965	1099	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0056309-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	358	683	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.534996792564575	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.534996792564575	1		683	932	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0056309-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	260	473	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.492628708782348	2	FACETS	0.832	0.787	0.878	0.832	0.787	0.878	CLONAL	2	TRUE	0	0.534996792564575	2		473	584	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692790	89692790	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056309-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	168	346	1	ENST00000371953.3:c.274G>C	p.Asp92His	p.D92H	ENST00000371953	NM_000314.4	92	Gac/Cac	5/9	0.534996792564575	1	FACETS	0.977	0.906	1	0.977	0.906	1	CLONAL	1	TRUE	0	0.534996792564575	1		347	471	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724664	43724664	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056309-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	345	859	0	ENST00000382044.4:c.3403G>C	p.Glu1135Gln	p.E1135Q	ENST00000382044	NM_001141980.1	1135	Gaa/Caa	17/28	0.534996792564575	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.534996792564575	1		859	889	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968579	55968579	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056309-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	231	741	1	ENST00000263923.4:c.2084del	p.Pro695LeufsTer14	p.P695Lfs*14	ENST00000263923	NM_002253.2	695	cCt/ct	14/30	0.217832407689668	1	FACETS	0.653	0.609	0.698	0.653	0.609	0.698	INDETERMINATE	1	TRUE	0	0.534996792564575	1		742	969	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838393	156838393	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056309-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1284	365	1181	1	ENST00000524377.1:c.671A>T	p.Gln224Leu	p.Q224L	ENST00000524377	NM_002529.3	224	cAg/cTg	6/17	0.363654154826286	3	FACETS	1	0.974	1	0.524	0.496	0.554	CLONAL	1	TRUE	1	0.534996792564575	3		1182	1649	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050907	49050907	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056309-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	220	573	0	ENST00000267163.4:c.2592del	p.Gly865GlufsTer8	p.G865Efs*8	ENST00000267163	NM_000321.2	864	gAa/ga	25/27	0.534996792564575	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.534996792564575	1		573	565	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467616	66467616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056309-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	157	497	0	ENST00000273854.3:c.653G>A	p.Gly218Asp	p.G218D	ENST00000273854	NM_004439.5	218	gGt/gAt	3/18	0.217832407689668	1	FACETS	0.772	0.711	0.835	0.772	0.711	0.835	INDETERMINATE	1	TRUE	0	0.534996792564575	1		497	557	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7168003	7168003	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056309-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	247	631	0	ENST00000302850.5:c.1586G>T	p.Gly529Val	p.G529V	ENST00000302850	NM_000208.2	529	gGg/gTg	7/22	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.534996792564575	2		631	921	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0056312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	303	219	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.48310434934935	3	FACETS	0.842	0.803	0.881	0.842	0.803	0.881	INDETERMINATE	2	TRUE	1	0.947387729830378	3		219	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578378	7578399	+	frameshift_variant	Frame_Shift_Del	DEL	ATCTGAGCAGCGCTCATGGTGG	ATCTGAGCAGCGCTCATGGTGG	-	novel	NA	P-0056312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	1376	921	0	ENST00000269305.4:c.531_552del	p.His178AlafsTer62	p.H178Afs*62	ENST00000269305	NM_001126112.2	177	ccCCACCATGAGCGCTGCTCAGAT/cc	5/11	0.947387729830378	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.947387729830378	2		921	1428	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506467	148506467	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519833	NA	P-0056323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	107	272	0	ENST00000320356.2:c.2045C>G	p.Ala682Gly	p.A682G	ENST00000320356	NM_004456.4	682	gCa/gGa	18/20	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		272	378	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	129	324	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.987	0.912	1			1	INDETERMINATE	1	TRUE	NA	0.91355059888819	2		324	286	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385240	41385240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	377	716	0	ENST00000373198.4:c.721C>T	p.Arg241Cys	p.R241C	ENST00000373198	NM_133170.3	241	Cgt/Tgt	6/32	0.91355059888819	3	FACETS	1	0.972	1	0.516	0.49	0.543	CLONAL	1	TRUE	1	0.91355059888819	3		716	1164	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244091	153244091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	318	603	0	ENST00000281708.4:c.2066G>A	p.Arg689Gln	p.R689Q	ENST00000281708	NM_033632.3	689	cGg/cAg	12/12	1	2	FACETS	0.955	0.907	1	0.955	0.907	1	CLONAL	1	TRUE	1	0.91355059888819	2		603	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934573	NA	P-0056332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	422	673	0	ENST00000269305.4:c.722C>A	p.Ser241Tyr	p.S241Y	ENST00000269305	NM_001126112.2	241	tCc/tAc	7/11	0.91355059888819	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.91355059888819	1		673	492	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748596	40748596	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754546663	NA	P-0056332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	289	555	2	ENST00000373198.4:c.2920C>T	p.Arg974Trp	p.R974W	ENST00000373198	NM_133170.3	974	Cgg/Tgg	21/32	0.91355059888819	3	FACETS	0.97	0.914	1	0.485	0.457	0.514	CLONAL	1	TRUE	1	0.91355059888819	3		557	950	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374991	45374991	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	48	559	0	ENST00000262160.6:c.852G>C	p.Gln284His	p.Q284H	ENST00000262160	NM_005901.5	284	caG/caC	8/11	0.911567219291845	1	FACETS	0.146	0.123	0.17	0.146	0.123	0.17	SUBCLONAL	1	TRUE	0	0.91355059888819	1		559	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0056333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	66	722	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.14	2		722	885	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716326	52716326	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	39	702	0	ENST00000322088.6:c.770G>T	p.Trp257Leu	p.W257L	ENST00000322088	NM_014225.5	257	tGg/tTg	6/15	1	2	FACETS	0.579	0.478	0.693	0.579	0.478	0.693	SUBCLONAL	1	TRUE	1	0.14	2		702	962	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916942	178916944	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	novel	NA	P-0056333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	33	473	0	ENST00000263967.3:c.330_332del	p.Lys111del	p.K111del	ENST00000263967	NM_006218.2	110	gAAAag/gag	2/21	0.0870490463294082	3	FACETS	0.848	0.689	1	0.424	0.344	0.514	CLONAL	1	TRUE	1	0.14	3		473	595	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	50	324	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.28	NA		324	202	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0056334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	20	597	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.567	0.434	0.722	0.567	0.434	0.722	SUBCLONAL	1	TRUE	1	0.28	2		597	252	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0056334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	50	306	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.28	2		306	356	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0056334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	67	667	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.785	0.682	0.896	0.785	0.682	0.896	SUBCLONAL	1	TRUE	1	0.28	2		667	610	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0056334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	152	816	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	0.821	0.753	0.892	1	0.99	1	CLONAL	2	TRUE	1	0.28	2		816	661	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189856	11189856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139043855	NA	P-0056334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	53	646	1	ENST00000361445.4:c.5653G>A	p.Val1885Ile	p.V1885I	ENST00000361445	NM_004958.3	1885	Gtc/Atc	40/58	1	2	FACETS	0.657	0.56	0.764	0.657	0.56	0.764	SUBCLONAL	1	TRUE	1	0.28	2		647	576	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257797	16257797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	26	615	0	ENST00000375759.3:c.5062G>A	p.Glu1688Lys	p.E1688K	ENST00000375759	NM_015001.2	1688	Gaa/Aaa	11/15	1	2	FACETS	0.359	0.284	0.446	0.359	0.284	0.446	SUBCLONAL	1	TRUE	1	0.28	2		615	517	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105796	27105797	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTCT	novel	NA	P-0056334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	78	584	0	ENST00000324856.7:c.5407_5408insTTCT	p.Glu1803ValfsTer7	p.E1803Vfs*7	ENST00000324856	NM_006015.4	1803	gag/gTTCTag	20/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.28	2		584	462	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598290	28598290	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	76	803	0	ENST00000253063.3:c.262G>A	p.Asp88Asn	p.D88N	ENST00000253063	NM_031459.4	88	Gac/Aac	3/10	1	2	FACETS	0.76	0.666	0.861	0.76	0.666	0.861	SUBCLONAL	1	TRUE	1	0.28	2		803	714	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398262	25398262	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913538	NA	P-0056334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	51	462	0	ENST00000311936.3:c.57G>C	p.Leu19Phe	p.L19F	ENST00000311936	NM_004985.3	19	ttG/ttC	2/5	1	2	FACETS	0.987	0.842	1	0.987	0.842	1	CLONAL	1	TRUE	1	0.28	2		462	369	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210907	133210907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	45	832	0	ENST00000320574.5:c.5869G>A	p.Glu1957Lys	p.E1957K	ENST00000320574	NM_006231.2	1957	Gag/Aag	43/49	1	2	FACETS	0.564	0.473	0.664	0.564	0.473	0.664	SUBCLONAL	1	TRUE	1	0.28	2		832	570	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43773171	43773173	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	novel	NA	P-0056334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	92	659	0	ENST00000382044.4:c.419_421del	p.Lys140_Gly141delinsArg	p.K140_G141delinsR	ENST00000382044	NM_001141980.1	140	aAGGga/aga	5/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.28	2		659	508	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042501	16042501	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0056334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	54	347	0	ENST00000268712.3:c.1174-1G>A		p.X392_splice	ENST00000268712	NM_006311.3	392			1	2	FACETS	0.775	0.668	0.888	1	0.97	1	SUBCLONAL	2	TRUE	1	0.28	2		347	249	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866096	37866096	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	70	808	0	ENST00000269571.5:c.605C>A	p.Ser202Tyr	p.S202Y	ENST00000269571		202	tCc/tAc	5/27	1	2	FACETS	0.812	0.708	0.924	0.812	0.708	0.924	CLONAL	1	TRUE	1	0.28	2		808	616	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866632	37866632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773759626	NA	P-0056334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	59	709	1	ENST00000269571.5:c.799C>T	p.His267Tyr	p.H267Y	ENST00000269571		267	Cac/Tac	7/27	1	2	FACETS	0.745	0.641	0.858	0.745	0.641	0.858	SUBCLONAL	1	TRUE	1	0.28	2		710	566	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367900	15367900	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	56	934	0	ENST00000263377.2:c.1426C>G	p.Pro476Ala	p.P476A	ENST00000263377	NM_058243.2	476	Ccc/Gcc	8/20	1	2	FACETS	0.569	0.487	0.659	0.569	0.487	0.659	SUBCLONAL	1	TRUE	1	0.28	2		934	703	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229363	36229363	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	125	649	0	ENST00000222270.7:c.8053G>C	p.Glu2685Gln	p.E2685Q	ENST00000222270	NM_014727.1	2685	Gag/Cag	37/37	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.28	2		649	637	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024222	31024222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	41	608	0	ENST00000375687.4:c.3707C>T	p.Ser1236Phe	p.S1236F	ENST00000375687	NM_015338.5	1236	tCt/tTt	13/13	1	2	FACETS	0.613	0.51	0.727	0.613	0.51	0.727	SUBCLONAL	1	TRUE	1	0.28	2		608	478	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478835	57478835	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	44	449	0	ENST00000371085.3:c.421G>C	p.Asp141His	p.D141H	ENST00000371085	NM_000516.4	141	Gac/Cac	5/13	1	2	FACETS	0.677	0.568	0.798	0.677	0.568	0.798	SUBCLONAL	1	TRUE	1	0.28	2		449	464	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176683990	176683990	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504055	NA	P-0056334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	53	660	0	ENST00000439151.2:c.4804G>A	p.Asp1602Asn	p.D1602N	ENST00000439151	NM_022455.4	1602	Gat/Aat	13/23	1	2	FACETS	0.65	0.554	0.756	0.65	0.554	0.756	SUBCLONAL	1	TRUE	1	0.28	2		660	582	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176684035	176684035	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	129	707	0	ENST00000439151.2:c.4849G>A	p.Glu1617Lys	p.E1617K	ENST00000439151	NM_022455.4	1617	Gaa/Aaa	13/23	1	2	FACETS	0.762	0.693	0.834	1	0.986	1	SUBCLONAL	2	TRUE	1	0.28	2		707	605	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687130	176687130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	83	493	1	ENST00000439151.2:c.5107G>A	p.Glu1703Lys	p.E1703K	ENST00000439151	NM_022455.4	1703	Gag/Aag	14/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.28	2		494	456	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525053	157525053	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554236623	NA	P-0056334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	79	436	0	ENST00000346085.5:c.4948G>T	p.Glu1650Ter	p.E1650*	ENST00000346085	NM_020732.3	1650	Gag/Tag	19/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.28	2		436	406	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802635	135802635	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203343	NA	P-0056334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	50	406	0	ENST00000298552.3:c.163C>T	p.Gln55Ter	p.Q55*	ENST00000298552	NM_001162426.1	55	Cag/Tag	4/23	1	2	FACETS	0.848	0.721	0.987	0.848	0.721	0.987	CLONAL	1	TRUE	1	0.28	2		406	421	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338683	70338683	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	186	323	0	ENST00000374080.3:c.79C>G	p.Gln27Glu	p.Q27E	ENST00000374080		27	Cag/Gag	1/45	0.3	2	FACETS	1	0.985	1	1	0.993	1	CLONAL	3	TRUE	0	0.28	2		323	381	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200060	123200061	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0056334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	52	198	0	ENST00000218089.9:c.2133dup	p.Asn712Ter	p.N712*	ENST00000218089	NM_001042749.1	711	tgt/tgTt	22/35	0.3	2	FACETS	0.897	0.783	1	1	0.964	1	CLONAL	3	TRUE	0	0.28	2		198	138	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0056343-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	165	330	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.245605124069314	4	FACETS	0.766	0.705	0.829	0.766	0.705	0.829	INDETERMINATE	2	TRUE	2	0.450124013016275	4		330	694	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056343-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	232	473	0	ENST00000304494.5:c.143C>T	p.Pro48Leu	p.P48L	ENST00000304494	NM_000077.4	48	cCg/cTg	1/3	0.450124013016275	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.450124013016275	1		473	667	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578440	7578440	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0056343-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	269	895	0	ENST00000269305.4:c.490A>T	p.Lys164Ter	p.K164*	ENST00000269305	NM_001126112.2	164	Aag/Tag	5/11	0.450124013016275	1	FACETS	0.964	0.905	1	0.964	0.905	1	CLONAL	1	TRUE	0	0.450124013016275	1		895	961	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101441	27101469	+	frameshift_variant	Frame_Shift_Del	DEL	CCACCAAGCATGCAGAATCACATTCCTCA	CCACCAAGCATGCAGAATCACATTCCTCA	-	novel	NA	P-0056343-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	388	679	0	ENST00000324856.7:c.4723_4751del	p.Pro1575GlyfsTer18	p.P1575Gfs*18	ENST00000324856	NM_006015.4	1575	CCACCAAGCATGCAGAATCACATTCCTCAg/g	18/20	0.384291968987363	2	FACETS	0.898	0.856	0.94	0.898	0.856	0.94	CLONAL	2	TRUE	0	0.450124013016275	2		679	960	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593439	48593439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056343-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	199	324	0	ENST00000342988.3:c.1192del	p.Trp398GlyfsTer17	p.W398Gfs*17	ENST00000342988	NM_005359.5	397	gTt/gt	10/12	0.406873400428704	2	FACETS	0.789	0.737	0.843	0.789	0.737	0.843	SUBCLONAL	2	TRUE	0	0.450124013016275	2		324	560	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030580	11030580	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056343-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	147	687	0	ENST00000327064.4:c.1134G>A	p.Met378Ile	p.M378I	ENST00000327064	NM_199141.1	378	atG/atA	10/16	1	2	FACETS	0.546	0.497	0.598	0.546	0.497	0.598	SUBCLONAL	1	TRUE	1	0.450124013016275	2		687	1196	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030815	48030816	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0056343-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	70	216	0	ENST00000234420.5:c.3430_3431del	p.Met1144GlufsTer19	p.M1144Efs*19	ENST00000234420	NM_000179.2	1143	ctTAtg/cttg	5/10	1	2	FACETS	0.795	0.697	0.901	0.795	0.697	0.901	CLONAL	1	TRUE	1	0.450124013016275	2		216	391	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	308	324	0				ENST00000310581	NM_198253.2	-/1132			0.574453898071417	5	FACETS	1	0.988	1	1	0.988	1	CLONAL	4	TRUE	1	0.574453898071417	5		324	464	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350737	89350737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370690185	NA	P-0056361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	218	862	0	ENST00000301030.4:c.2213G>A	p.Arg738His	p.R738H	ENST00000301030	NM_001256183.1	738	cGt/cAt	9/13	0.457242258392393	2	FACETS	0.877	0.817	0.939	0.439	0.408	0.47	CLONAL	1	TRUE	0	0.574453898071417	2		862	865	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31448657	31448657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757002340	NA	P-0056361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	138	422	0	ENST00000344624.3:c.2879C>T	p.Ser960Leu	p.S960L	ENST00000344624		960	tCg/tTg	20/33	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.574453898071417	2		422	461	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192609	94192610	+	missense_variant	Missense_Mutation	DNP	GA	GA	AG	novel	NA	P-0056361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	201	558	0	ENST00000323929.3:c.1464_1465delinsCT	p.His489Tyr	p.H489Y	ENST00000323929	NM_005591.3	488	cgTCat/cgCTat	13/20	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.574453898071417	2		558	473	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986827	36986827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	41	102	0	ENST00000354822.5:c.862G>A	p.Val288Met	p.V288M	ENST00000354822	NM_001079668.2	288	Gtg/Atg	3/3	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.574453898071417	2		102	104	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579545	+	frameshift_variant	Frame_Shift_Del	DEL	CAGTGAACCATTGTTCAATATCGTC	CAGTGAACCATTGTTCAATATCGTC	-	novel	NA	P-0056361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	33	798	0	ENST00000269305.4:c.142_166del	p.Asp48LysfsTer67	p.D48Kfs*67	ENST00000269305	NM_001126112.2	48	GACGATATTGAACAATGGTTCACTGaa/aa	4/11	0.58195717675035	2	FACETS	0.182	0.147	0.221	0.091	0.073	0.111	SUBCLONAL	1	TRUE	0	0.574453898071417	2		798	632	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155180	55155180	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	72	482	0	ENST00000257290.5:c.2779G>C	p.Glu927Gln	p.E927Q	ENST00000257290	NM_006206.4	927	Gag/Cag	21/23	0.492157645135577	3	FACETS	0.747	0.655	0.845			1	SUBCLONAL	1	TRUE	NA	0.574453898071417	3		482	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0056362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	114	504	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.261224379574937	2		504	801	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212182	98212182	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371346118	NA	P-0056363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	53	277	0	ENST00000331920.6:c.3490G>A	p.Val1164Ile	p.V1164I	ENST00000331920	NM_000264.3	1164	Gtt/Att	21/24	0.444404748067597	2	FACETS	0.864	0.743	0.995	0.432	0.371	0.498	CLONAL	1	TRUE	0	0.444404748067597	2		277	276	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627485	14627485	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	40	552	0	ENST00000254322.2:c.585G>C	p.Lys195Asn	p.K195N	ENST00000254322	NM_006145.1	195	aaG/aaC	2/3	1	2	FACETS	0.326	0.27	0.388	0.326	0.27	0.388	SUBCLONAL	1	TRUE	1	0.444404748067597	2		552	552	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319052	62319052	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	100	789	0	ENST00000360203.5:c.1410G>C	p.Gln470His	p.Q470H	ENST00000360203	NM_001283009.1	470	caG/caC	17/35	0.444404748067597	6	FACETS	0.673	0.599	0.752	0.224	0.199	0.251	SUBCLONAL	1	TRUE	3	0.444404748067597	6		789	1264	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551944	150551944	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	97	347	0	ENST00000369026.2:c.63G>C	p.Leu21Phe	p.L21F	ENST00000369026	NM_021960.4	21	ttG/ttC	1/3	0.421934254308311	4	FACETS	0.909	0.81	1	0.454	0.405	0.507	CLONAL	1	TRUE	2	0.444404748067597	4		347	694	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426576	49426596	+	inframe_deletion	In_Frame_Del	DEL	TGCTGCTGCTGTTGAAACTGC	TGCTGCTGCTGTTGAAACTGC	-	novel	NA	P-0056363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	130	792	0	ENST00000301067.7:c.11892_11912del	p.Phe3966_Gln3972del	p.F3966_Q3972del	ENST00000301067	NM_003482.3	3964	caGCAGTTTCAACAGCAGCAGCAa/caa	39/54	0.421934254308311	4	FACETS	0.739	0.669	0.814	0.37	0.334	0.407	SUBCLONAL	1	TRUE	2	0.444404748067597	4		792	1143	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427650	49427655	+	inframe_deletion	In_Frame_Del	DEL	TGCTGT	TGCTGT	-	novel	NA	P-0056363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	101	548	0	ENST00000301067.7:c.10833_10838del	p.Gln3611_Gln3612del	p.Q3611_Q3612del	ENST00000301067	NM_003482.3	3611	caACAGCAc/cac	39/54	0.421934254308311	4	FACETS	1	0.913	1	0.511	0.457	0.568	CLONAL	1	TRUE	2	0.444404748067597	4		548	642	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319034	62319034	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	103	771	0	ENST00000360203.5:c.1392G>T	p.Met464Ile	p.M464I	ENST00000360203	NM_001283009.1	464	atG/atT	17/35	0.444404748067597	6	FACETS	0.674	0.601	0.752	0.225	0.2	0.251	SUBCLONAL	1	TRUE	3	0.444404748067597	6		771	1299	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162923	47162923	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	193	343	0	ENST00000409792.3:c.3203C>G	p.Ser1068Cys	p.S1068C	ENST00000409792	NM_014159.6	1068	tCt/tGt	3/21	0.389784208388017	3	FACETS	1	0.988	1	0.833	0.78	0.885	CLONAL	2	TRUE	0	0.444404748067597	3		343	425	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104007	69104007	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	116	399	0	ENST00000288368.4:c.4397C>T	p.Ala1466Val	p.A1466V	ENST00000288368	NM_024870.2	1466	gCt/gTt	36/40	0.444404748067597	8	FACETS	0.959	0.862	1			1	CLONAL	1	TRUE	NA	0.444404748067597	8		399	1270	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797340	135797340	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	31	249	0	ENST00000298552.3:c.529C>G	p.Leu177Val	p.L177V	ENST00000298552	NM_001162426.1	177	Ctc/Gtc	7/23	0.444707777935569	4	FACETS	0.594	0.481	0.722	0.149	0.12	0.181	SUBCLONAL	1	TRUE	0	0.444404748067597	4		249	339	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0056365-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	24	317	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.787	1	1	0.787	1	CLONAL	1	TRUE	1	0.17	2		317	282	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165228	47165228	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056365-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	17	217	0	ENST00000409792.3:c.898C>G	p.Leu300Val	p.L300V	ENST00000409792	NM_014159.6	300	Ctg/Gtg	3/21	1	2	FACETS	1	0.774	1	1	0.774	1	CLONAL	1	TRUE	1	0.17	2		217	193	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164129	32164129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056365-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	56	564	0	ENST00000375023.3:c.5270G>A	p.Gly1757Glu	p.G1757E	ENST00000375023	NM_004557.3	1757	gGa/gAa	29/30	1	2	FACETS	0.815	0.697	0.945	0.815	0.697	0.945	CLONAL	1	TRUE	1	0.17	2		564	808	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	160	1156	0	ENST00000269305.4:c.403del	p.Cys135AlafsTer35	p.C135Afs*35	ENST00000269305	NM_001126112.2	135	Tgc/gc	5/11	0.207208493728097	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.207208493728097	1		1156	1087	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0056371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	271	728	0	ENST00000397752.3:c.3028+1G>C		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.195974134691327	3	FACETS	0.923	0.866	0.981	0.923	0.866	0.981	CLONAL	3	TRUE	0	0.207208493728097	3		728	1043	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849083	156849083	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	141	1041	0	ENST00000524377.1:c.1975G>T	p.Gly659Cys	p.G659C	ENST00000524377	NM_002529.3	659	Ggc/Tgc	15/17	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.207208493728097	2		1041	954	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639028	176639028	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	43	648	0	ENST00000439151.2:c.3628T>A	p.Ser1210Thr	p.S1210T	ENST00000439151	NM_022455.4	1210	Tca/Aca	5/23	0.207208493728097	2	FACETS	0.597	0.498	0.707	0.299	0.249	0.354	SUBCLONAL	1	TRUE	0	0.207208493728097	2		648	695	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939109	76939110	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0056371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	80	533	1	ENST00000373344.5:c.1638_1639delinsAA	p.Asp547Asn	p.D547N	ENST00000373344	NM_000489.3	546	ggGGat/ggAAat	9/35	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.207208493728097	2		534	642	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420825	49420825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757011865	NA	P-0056372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	31	715	0	ENST00000301067.7:c.14924G>A	p.Arg4975His	p.R4975H	ENST00000301067	NM_003482.3	4975	cGt/cAt	48/54	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		715	551	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0056373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	140	330	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.541787324321647	3	FACETS	0.857	0.79	0.926	0.857	0.79	0.926	CLONAL	2	TRUE	1	0.552917656497567	3		330	377	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518187	103518187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769956023	NA	P-0056373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	23	239	1	ENST00000355739.4:c.2125G>A	p.Asp709Asn	p.D709N	ENST00000355739	NM_000123.3	709	Gac/Aac	9/15	1	2	FACETS	0.307	0.24	0.385	0.307	0.24	0.385	SUBCLONAL	1	TRUE	1	0.552917656497567	2		240	271	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0056374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	27	517	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.172	0.136	0.213	0.172	0.136	0.213	SUBCLONAL	1	TRUE	1	0.530645237029277	2		517	593	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0056374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	155	317	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.530645237029277	2		317	517	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231437	46231437	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	110	280	2	ENST00000334344.6:c.1277C>T	p.Thr426Met	p.T426M	ENST00000334344	NM_152641.2	426	aCg/aTg	10/21	1	2	FACETS	0.949	0.858	1	0.949	0.858	1	CLONAL	1	TRUE	1	0.530645237029277	2		282	437	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572580	141572580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1232302381	NA	P-0056374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	128	537	1	ENST00000220592.5:c.490G>A	p.Val164Met	p.V164M	ENST00000220592	NM_012154.3	164	Gtg/Atg	4/19	0.212018925055093	2	FACETS	0.796	0.724	0.872	0.398	0.362	0.436	INDETERMINATE	1	TRUE	0	0.530645237029277	2		538	606	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980381	7980381	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	211	785	0	ENST00000319144.4:c.1202A>C	p.Glu401Ala	p.E401A	ENST00000319144	NM_001139.2	401	gAg/gCg	9/15	0.385346347599573	1	FACETS	0.859	0.802	0.918	0.859	0.802	0.918	CLONAL	1	TRUE	0	0.530645237029277	1		785	680	SUCCESS
ATR	545	MSKCC	GRCh37	3	142224084	142224084	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	82	421	0	ENST00000350721.4:c.5093C>A	p.Ala1698Glu	p.A1698E	ENST00000350721	NM_001184.3	1698	gCa/gAa	29/47	1	2	FACETS	0.551	0.486	0.62	0.551	0.486	0.62	SUBCLONAL	1	TRUE	1	0.530645237029277	2		421	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578528	7578528	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	525	901	0	ENST00000269305.4:c.402T>G	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	ttT/ttG	5/11	0.722175560129266	2	FACETS	0.845	0.82	0.869	0.845	0.82	0.869	CLONAL	2	TRUE	0	0.828417917008971	2		901	750	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347123	347123	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	238	876	0	ENST00000262320.3:c.1888C>T	p.Gln630Ter	p.Q630*	ENST00000262320	NM_003502.3	630	Cag/Tag	7/11	0.828417917008971	1	FACETS	0.85	0.808	0.891	0.85	0.808	0.891	CLONAL	1	TRUE	0	0.828417917008971	1		876	396	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351208	89351210	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs1431780879	NA	P-0056375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	190	730	1	ENST00000301030.4:c.1740_1742del	p.Ser581del	p.S581del	ENST00000301030	NM_001256183.1	580	tcCTCt/tct	9/13	0.818867783729107	3	FACETS	0.885	0.82	0.952	0.443	0.41	0.476	CLONAL	1	TRUE	1	0.828417917008971	3		731	733	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096617	178096617	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	54	251	0	ENST00000397062.3:c.714A>C	p.Glu238Asp	p.E238D	ENST00000397062	NM_006164.4	238	gaA/gaC	5/5	0.284644712365532	6	FACETS	0.944	0.809	1	0.236	0.202	0.273	INDETERMINATE	1	TRUE	2	0.828417917008971	6		251	367	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0056376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	144	308	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	1	2	FACETS	0.874	0.805	0.945	0.874	0.805	0.945	CLONAL	1	TRUE	1	0.777207255151086	2		308	424	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197462	106197462	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	67	276	0	ENST00000380013.4:c.5795G>T	p.Cys1932Phe	p.C1932F	ENST00000380013	NM_001127208.2	1932	tGt/tTt	11/11	1	2	FACETS	0.434	0.379	0.494	0.434	0.379	0.494	SUBCLONAL	1	TRUE	1	0.777207255151086	2		276	397	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0056377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	270	517	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.91	0.859	0.962	0.91	0.859	0.962	CLONAL	1	TRUE	1	0.839445551698574	2		517	707	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	380	690	0	ENST00000322088.6:c.767C>A	p.Ser256Tyr	p.S256Y	ENST00000322088	NM_014225.5	256	tCc/tAc	6/15	0.839445551698574	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.839445551698574	1		690	514	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239267	105239267	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	377	790	0	ENST00000349310.3:c.1120C>G	p.Pro374Ala	p.P374A	ENST00000349310	NM_001014432.1	374	Ccc/Gcc	12/15	1	2	FACETS	0.866	0.824	0.909	0.866	0.824	0.909	CLONAL	1	TRUE	1	0.839445551698574	2		790	1037	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577086	7577086	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	497	742	0	ENST00000269305.4:c.852del	p.Glu285ArgfsTer60	p.E285Rfs*60	ENST00000269305	NM_001126112.2	284	acA/ac	8/11	0.839445551698574	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.839445551698574	1		742	680	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176700672	176700672	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0056377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	20	283	0	ENST00000439151.2:c.5510-1G>C		p.X1837_splice	ENST00000439151	NM_022455.4	1837			0.839445551698574	1	FACETS	0.134	0.102	0.17	0.134	0.102	0.17	SUBCLONAL	1	TRUE	0	0.839445551698574	1		283	207	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576883	7576883	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	374	602	0	ENST00000269305.4:c.963del	p.Lys321AsnfsTer24	p.K321Nfs*24	ENST00000269305	NM_001126112.2	321	aaA/aa	9/11	0.470004583796825	3	FACETS	0.847	0.813	0.88	0.847	0.813	0.88	CLONAL	3	TRUE	0	0.598639034585741	3		602	639	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17354300	17354495	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CATCCTTCTTCTTCAAATAAGGCTCAATGGATTTGTACTGTGCATAGAAGTTGCTCAAATCCTGTGGTTAAGAGGAAGAAGAAGAAGAAGAAGAAGAAAAGGATCAGATTCCATCATCACCTCAGCTTTATTTACCCCATTTCTTGGACACTGACTACTCGTCCACTCTATGCCAGGCAGAAGCCAGACTCTTTTC	CATCCTTCTTCTTCAAATAAGGCTCAATGGATTTGTACTGTGCATAGAAGTTGCTCAAATCCTGTGGTTAAGAGGAAGAAGAAGAAGAAGAAGAAGAAAAGGATCAGATTCCATCATCACCTCAGCTTTATTTACCCCATTTCTTGGACACTGACTACTCGTCCACTCTATGCCAGGCAGAAGCCAGACTCTTTTC	-	novel	NA	P-0056378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	37	343	0	ENST00000375499.3:c.424-135_484del		p.X142_splice	ENST00000375499	NM_003000.2	142		5/8	0.398134663600066	3	FACETS	0.637	0.529	0.757	0.212	0.176	0.253	SUBCLONAL	1	TRUE	0	0.598639034585741	3		343	252	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466327	120466327	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	72	443	0	ENST00000256646.2:c.4792G>C	p.Ala1598Pro	p.A1598P	ENST00000256646	NM_024408.3	1598	Gct/Cct	26/34	0.489102237343467	3	FACETS	0.599	0.524	0.679	0.299	0.262	0.34	SUBCLONAL	1	TRUE	1	0.598639034585741	3		443	522	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120467950	120467950	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	219	519	1	ENST00000256646.2:c.4489C>T	p.Gln1497Ter	p.Q1497*	ENST00000256646	NM_024408.3	1497	Cag/Tag	25/34	0.489102237343467	3	FACETS	1	0.991	1	0.714	0.667	0.761	CLONAL	1	TRUE	1	0.598639034585741	3		520	666	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743286	162743286	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	29	229	0	ENST00000367921.3:c.1756G>T	p.Glu586Ter	p.E586*	ENST00000367921	NM_006182.2	586	Gaa/Taa	14/18	0.489102237343467	3	FACETS	0.473	0.381	0.577	0.237	0.19	0.289	SUBCLONAL	1	TRUE	1	0.598639034585741	3		229	266	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325024	123325024	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	105	527	0	ENST00000358487.5:c.304T>C	p.Ser102Pro	p.S102P	ENST00000358487	NM_000141.4	102	Tcc/Ccc	3/18	0.496419481660859	2	FACETS	0.645	0.58	0.714	0.322	0.29	0.357	SUBCLONAL	1	TRUE	0	0.598639034585741	2		527	544	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224554	39224554	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	11	287	0	ENST00000402219.2:c.2804C>A	p.Thr935Asn	p.T935N	ENST00000402219	NM_005633.3	935	aCt/aAt	18/23	0.159215553939544	1	FACETS	0.296	0.207	0.404	0.296	0.207	0.404	INDETERMINATE	1	TRUE	0	0.598639034585741	1		287	87	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747107	40747107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	221	430	0	ENST00000373198.4:c.2975G>A	p.Arg992Lys	p.R992K	ENST00000373198	NM_133170.3	992	aGa/aAa	22/32	0.496419481660859	2	FACETS	1	0.983	1	0.574	0.537	0.612	CLONAL	1	TRUE	0	0.598639034585741	2		430	643	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539195	187539195	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	41	345	0	ENST00000441802.2:c.8545G>T	p.Asp2849Tyr	p.D2849Y	ENST00000441802	NM_005245.3	2849	Gat/Tat	10/27	0.496419481660859	2	FACETS	0.481	0.402	0.567	0.24	0.201	0.284	SUBCLONAL	1	TRUE	0	0.598639034585741	2		345	285	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931425	131931425	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	55	304	0	ENST00000265335.6:c.2130T>A	p.Asp710Glu	p.D710E	ENST00000265335		710	gaT/gaA	13/25	0.511764866181077	2	FACETS	0.707	0.61	0.81	0.353	0.305	0.405	SUBCLONAL	1	TRUE	0	0.598639034585741	2		304	260	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178707	32178707	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	144	594	0	ENST00000375023.3:c.2687A>G	p.Asp896Gly	p.D896G	ENST00000375023	NM_004557.3	896	gAc/gGc	18/30	0.598639034585741	4	FACETS	0.987	0.901	1	0.329	0.3	0.359	CLONAL	1	TRUE	1	0.598639034585741	4		594	779	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395497	116395497	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	226	319	0	ENST00000397752.3:c.1790A>C	p.Asp597Ala	p.D597A	ENST00000397752	NM_000245.2	597	gAt/gCt	6/21	0.598639034585741	4	FACETS	0.979	0.927	1	0.979	0.927	1	CLONAL	3	TRUE	1	0.598639034585741	4		319	411	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938932	76938933	+	stop_gained	Nonsense_Mutation	DNP	GA	GA	TT	novel	NA	P-0056378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	45	536	1	ENST00000373344.5:c.1815_1816delinsAA	p.Cys605_Gln606delinsTer	p.C605_Q606delins*	ENST00000373344	NM_000489.3	605	tgTCag/tgAAag	9/35	0.282190947302881	3	FACETS	0.743	0.629	0.867	0.371	0.314	0.434	INDETERMINATE	1	TRUE	1	0.598639034585741	3		537	263	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913250	NA	P-0056379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	127	349	0	ENST00000369535.4:c.34G>A	p.Gly12Ser	p.G12S	ENST00000369535	NM_002524.4	12	Ggt/Agt	2/7	0.441705454788681	3	FACETS	1	0.939	1	0.523	0.474	0.574	CLONAL	1	TRUE	1	0.441269920998509	3		349	672	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0056379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	144	236	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	0.441269920998509	2	FACETS	0.963	0.891	1	0.963	0.891	1	CLONAL	2	TRUE	0	0.441269920998509	2		236	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578206	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs886039484	NA	P-0056379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	558	690	0	ENST00000269305.4:c.643A>G	p.Ser215Gly	p.S215G	ENST00000269305	NM_001126112.2	215	Agt/Ggt	6/11	0.388333074743701	3	FACETS	0.978	0.944	1			1	CLONAL	3	TRUE	NA	0.441269920998509	3		690	1052	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249440	153249440	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	131	456	0	ENST00000281708.4:c.1338G>T	p.Trp446Cys	p.W446C	ENST00000281708	NM_033632.3	446	tgG/tgT	9/12	1	2	FACETS	0.889	0.808	0.973	0.889	0.808	0.973	CLONAL	1	TRUE	1	0.441269920998509	2		456	668	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959240	2959240	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148354898	NA	P-0056379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	281	633	0	ENST00000396946.4:c.2276G>A	p.Arg759Gln	p.R759Q	ENST00000396946	NM_032415.4	759	cGg/cAg	18/25	0.238107284894095	4	FACETS	0.962	0.905	1			1	INDETERMINATE	2	TRUE	NA	0.441269920998509	4		633	954	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913236	39913236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774089771	NA	P-0056379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	290	261	0	ENST00000378444.4:c.4879G>A	p.Asp1627Asn	p.D1627N	ENST00000378444	NM_001123385.1	1627	Gat/Aat	14/15	0.441705454788681	2	FACETS	0.963	0.922	1			1	CLONAL	3	TRUE	NA	0.441269920998509	2		261	455	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119875	70119875	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	108	641	0	ENST00000245479.2:c.877G>T	p.Glu293Ter	p.E293*	ENST00000245479	NM_000346.3	293	Gag/Tag	3/3	0.441269920998509	2	FACETS	0.673	0.604	0.746	0.337	0.302	0.373	SUBCLONAL	1	TRUE	0	0.441269920998509	2		641	727	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16097876	16097876	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223191004	NA	P-0056379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	22	154	0	ENST00000268712.3:c.8G>A	p.Ser3Asn	p.S3N	ENST00000268712	NM_006311.3	3	aGt/aAt	2/46	0.441269920998509	2	FACETS	0.402	0.312	0.506	0.201	0.156	0.253	SUBCLONAL	1	TRUE	0	0.441269920998509	2		154	248	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0056380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	254	731	2	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.457053501837415	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.457053501837415	1		733	671	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106861	27106861	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	278	592	0	ENST00000324856.7:c.6472C>T	p.Arg2158Ter	p.R2158*	ENST00000324856	NM_006015.4	2158	Cga/Tga	20/20	0.448896201333692	2	FACETS	0.927	0.877	0.978	0.927	0.877	0.978	CLONAL	2	TRUE	0	0.457053501837415	2		592	656	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844161	68844161	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	349	546	0	ENST00000261769.5:c.749T>A	p.Ile250Asn	p.I250N	ENST00000261769	NM_004360.3	250	aTc/aAc	6/16	0.448896201333692	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.457053501837415	2		546	748	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844714	156844714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	133	865	0	ENST00000524377.1:c.1268G>A	p.Gly423Asp	p.G423D	ENST00000524377	NM_002529.3	423	gGc/gAc	11/17	0.153944049435644	2	FACETS	0.628	0.57	0.689	0.314	0.285	0.345	INDETERMINATE	1	TRUE	0	0.457053501837415	2		865	927	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325014	123325014	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1434545235	NA	P-0056380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	806	572	3	ENST00000358487.5:c.314A>G	p.Tyr105Cys	p.Y105C	ENST00000358487	NM_000141.4	105	tAt/tGt	3/18	0.457053501837415	6	FACETS	0.918	0.892	0.944	0.765	0.743	0.787	CLONAL	5	TRUE	0	0.457053501837415	6		575	1471	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790162	40790162	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	69	505	1	ENST00000373198.4:c.2569C>A	p.Leu857Ile	p.L857I	ENST00000373198	NM_133170.3	857	Ctt/Att	18/32	0.457053501837415	1	FACETS	0.438	0.382	0.498	0.438	0.382	0.498	SUBCLONAL	1	TRUE	0	0.457053501837415	1		506	532	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513328	106513328	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	30	285	0	ENST00000359195.3:c.2232A>T	p.Lys744Asn	p.K744N	ENST00000359195	NM_002649.2	744	aaA/aaT	4/11	0.195643231307125	3	FACETS	0.402	0.324	0.491	0.201	0.162	0.246	INDETERMINATE	1	TRUE	1	0.457053501837415	3		285	401	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8497250	8497250	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs72694737	NA	P-0056388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	111	209	9	ENST00000356435.5:c.2341A>G	p.Thr781Ala	p.T781A	ENST00000356435		781	Act/Gct	15/35	0.156928604261493	4	FACETS	1	0.956	1	1	0.956	1	INDETERMINATE	2	TRUE	2	0.550861767470034	4		218	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577514	7577514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	412	717	1	ENST00000269305.4:c.767C>T	p.Thr256Ile	p.T256I	ENST00000269305	NM_001126112.2	256	aCa/aTa	7/11	0.550861767470034	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.550861767470034	2		718	711	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577392	64577392	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	245	724	1	ENST00000312049.6:c.190C>T	p.Gln64Ter	p.Q64*	ENST00000312049	NM_130799.2	64	Cag/Tag	2/10	0.842971593683983	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.842971593683983	1		725	334	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101008	41101008	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	268	571	0	ENST00000373198.4:c.1348C>T	p.Arg450Ter	p.R450*	ENST00000373198	NM_133170.3	450	Cga/Tga	8/32	1	2	FACETS	0.867	0.818	0.918	0.867	0.818	0.918	CLONAL	1	TRUE	1	0.842971593683983	2		571	733	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0056390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	111	613	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.363739590866871	1	FACETS	0.902	0.821	0.985	0.902	0.821	0.985	CLONAL	1	TRUE	0	0.553120020605247	1		613	322	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0056390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	95	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.931	0.836	1	0.931	0.836	1	CLONAL	1	TRUE	1	0.553120020605247	2		298	369	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0056390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	62	234	2	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.954	0.835	1	0.954	0.835	1	CLONAL	1	TRUE	1	0.553120020605247	2		236	235	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685314	89685315	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TG	TG	-	rs1564826836	NA	P-0056390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	108	208	0	ENST00000371953.3:c.209+1_209+2del		p.X70_splice	ENST00000371953	NM_000314.4	70		3/9	0.553120020605247	2	FACETS	0.872	0.8	0.943	0.872	0.8	0.943	CLONAL	2	TRUE	0	0.553120020605247	2		208	224	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130342	11130342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	154	606	0	ENST00000358026.2:c.2581G>A	p.Glu861Lys	p.E861K	ENST00000358026	NM_001128849.1	861	Gag/Aag	18/36	NA	2	FACETS	1	0.941	1			1	INDETERMINATE	1	TRUE	NA	0.553120020605247	2		606	542	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	301	567	2	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	0.538965838043511	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.553120020605247	2		569	539	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466040	69466040	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	126	757	0	ENST00000227507.2:c.878T>G	p.Val293Gly	p.V293G	ENST00000227507	NM_053056.2	293	gTg/gGg	5/5	1	2	FACETS	0.943	0.859	1	0.943	0.859	1	CLONAL	1	TRUE	1	0.553120020605247	2		757	483	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191003	185191009	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTTCT	CCCTTCT	-	novel	NA	P-0056390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	157	665	0	ENST00000265026.3:c.1885_1891del	p.Pro629PhefsTer33	p.P629Ffs*33	ENST00000265026	NM_004721.4	628	taCCCTTCT/ta	11/14	1	2	FACETS	0.856	0.787	0.928	0.856	0.787	0.928	CLONAL	1	TRUE	1	0.553120020605247	2		665	663	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060499964	NA	P-0056392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	343	1129	0	ENST00000326873.7:c.667G>A	p.Glu223Lys	p.E223K	ENST00000326873	NM_000455.4	223	Gag/Aag	5/10	0.49004708207664	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.489190777277846	1		1129	1020	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929426	81929426	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1364308657	NA	P-0056392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	150	704	1	ENST00000359376.3:c.1087G>A	p.Gly363Arg	p.G363R	ENST00000359376	NM_002661.3	363	Ggg/Agg	13/33	1	2	FACETS	0.902	0.826	0.98	0.902	0.826	0.98	CLONAL	1	TRUE	1	0.489190777277846	2		705	680	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094488	27094488	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	137	521	0	ENST00000324856.7:c.3196C>T	p.Gln1066Ter	p.Q1066*	ENST00000324856	NM_006015.4	1066	Cag/Tag	11/20	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.489190777277846	2		521	544	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088795	27088795	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	184	734	0	ENST00000324856.7:c.2404C>T	p.Gln802Ter	p.Q802*	ENST00000324856	NM_006015.4	802	Cag/Tag	7/20	1	2	FACETS	0.931	0.861	1	0.931	0.861	1	CLONAL	1	TRUE	1	0.489190777277846	2		734	808	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404501	70404501	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	100	345	0	ENST00000373644.4:c.2015T>C	p.Met672Thr	p.M672T	ENST00000373644	NM_030625.2	672	aTg/aCg	4/12	1	2	FACETS	0.8	0.717	0.887	0.8	0.717	0.887	SUBCLONAL	1	TRUE	1	0.489190777277846	2		345	511	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742818	17742818	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	57	1129	0	ENST00000250003.3:c.726G>T	p.Lys242Asn	p.K242N	ENST00000250003	NM_002478.4	242	aaG/aaT	3/3	1	2	FACETS	0.231	0.197	0.268	0.231	0.197	0.268	SUBCLONAL	1	TRUE	1	0.489190777277846	2		1129	1008	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986877	36986877	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs924707906	NA	P-0056392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	21	361	0	ENST00000354822.5:c.812G>A	p.Gly271Asp	p.G271D	ENST00000354822	NM_001079668.2	271	gGc/gAc	3/3	1	2	FACETS	0.227	0.174	0.289	0.227	0.174	0.289	SUBCLONAL	1	TRUE	1	0.489190777277846	2		361	378	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847276	68847276	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	36	659	0	ENST00000261769.5:c.1198G>C	p.Asp400His	p.D400H	ENST00000261769	NM_004360.3	400	Gat/Cat	9/16	1	2	FACETS	0.215	0.176	0.26	0.215	0.176	0.26	SUBCLONAL	1	TRUE	1	0.489190777277846	2		659	683	SUCCESS
AR	367	MSKCC	GRCh37	X	66765862	66765862	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	245	1323	0	ENST00000374690.3:c.874G>C	p.Gly292Arg	p.G292R	ENST00000374690	NM_000044.3	292	Ggt/Cgt	1/8	1	2	FACETS	0.853	0.797	0.912	0.853	0.797	0.912	CLONAL	1	TRUE	1	0.489190777277846	2		1323	1174	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953126	81953144	+	frameshift_variant	Frame_Shift_Del	DEL	GACGGCCGGCACTTTGTGC	GACGGCCGGCACTTTGTGC	TG	novel	NA	P-0056392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	126	481	1	ENST00000359376.3:c.2092_2110delinsTG	p.Asp698CysfsTer8	p.D698Cfs*8	ENST00000359376	NM_002661.3	698	GACGGCCGGCACTTTGTGCtg/TGtg	20/33	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.489190777277846	2		482	512	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	146	324	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.86246058426376	2		324	331	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0056393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	647	734	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	0.983	0.964	1	1	0.998	1	CLONAL	2	TRUE	1	0.86246058426376	2		735	763	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115874	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752977342	NA	P-0056393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	46	772	0	ENST00000346208.3:c.1220C>T	p.Ser407Leu	p.S407L	ENST00000346208		407	tCg/tTg	6/6	1	2	FACETS	0.129	0.108	0.152	0.129	0.108	0.152	SUBCLONAL	1	TRUE	1	0.86246058426376	2		772	828	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937643	44937643	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0056393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	192	222	0	ENST00000377967.4:c.2833-2A>G		p.X945_splice	ENST00000377967	NM_021140.2	945			1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.86246058426376	1		222	215	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092961	27092961	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	181	356	0	ENST00000324856.7:c.2894del	p.Pro965GlnfsTer3	p.P965Qfs*3	ENST00000324856	NM_006015.4	964	agC/ag	10/20	1	2	FACETS	0.992	0.927	1	0.992	0.927	1	CLONAL	1	TRUE	1	0.86246058426376	2		356	423	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164096	108164096	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0056393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	81	242	0	ENST00000278616.4:c.4668T>A	p.Tyr1556Ter	p.Y1556*	ENST00000278616	NM_000051.3	1556	taT/taA	31/63	1	2	FACETS	0.899	0.808	0.992	0.899	0.808	0.992	CLONAL	1	TRUE	1	0.86246058426376	2		242	209	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832410	72832410	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	208	494	0	ENST00000268489.5:c.4171C>G	p.Leu1391Val	p.L1391V	ENST00000268489	NM_006885.3	1391	Ctg/Gtg	9/10	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.86246058426376	2		494	477	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966670	25966670	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	249	614	0	ENST00000435504.4:c.2536C>G	p.Pro846Ala	p.P846A	ENST00000435504		846	Cct/Gct	13/13	1	2	FACETS	0.906	0.854	0.96	0.906	0.854	0.96	CLONAL	1	TRUE	1	0.86246058426376	2		614	637	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335729	81335729	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	136	318	0	ENST00000222390.5:c.1631A>G	p.Tyr544Cys	p.Y544C	ENST00000222390	NM_000601.4	544	tAt/tGt	15/18	1	2	FACETS	0.964	0.89	1	0.964	0.89	1	CLONAL	1	TRUE	1	0.86246058426376	2		318	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0056394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	232	777	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.369539403149634	1	FACETS	0.933	0.871	0.998	0.933	0.871	0.998	CLONAL	1	TRUE	0	0.395913305028299	1		777	1007	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586422	189586422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866267914	NA	P-0056394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	135	408	1	ENST00000264731.3:c.1046G>A	p.Gly349Glu	p.G349E	ENST00000264731	NM_003722.4	349	gGa/gAa	8/14	0.327015309858548	3	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.395913305028299	3		409	642	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435083	110435083	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	96	829	0	ENST00000375856.3:c.3318G>C	p.Lys1106Asn	p.K1106N	ENST00000375856	NM_003749.2	1106	aaG/aaC	1/2	0.329784119040369	2	FACETS	0.402	0.357	0.45	0.201	0.178	0.225	SUBCLONAL	1	TRUE	0	0.395913305028299	2		829	1207	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098973	178098973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	82	260	0	ENST00000397062.3:c.72G>C	p.Trp24Cys	p.W24C	ENST00000397062	NM_006164.4	24	tgG/tgC	2/5	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.395913305028299	2		260	396	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902604	1902604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	246	781	1	ENST00000382891.5:c.223C>T	p.Pro75Ser	p.P75S	ENST00000382891	NM_133335.3	75	Cca/Tca	2/22	NA	2	FACETS	0.993	0.926	1			1	INDETERMINATE	1	TRUE	NA	0.395913305028299	2		782	1252	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914747	39914747	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	71	442	0	ENST00000378444.4:c.4615G>C	p.Glu1539Gln	p.E1539Q	ENST00000378444	NM_001123385.1	1539	Gag/Cag	12/15	0.395913305028299	3	FACETS	0.485	0.422	0.553	0.242	0.211	0.277	SUBCLONAL	1	TRUE	1	0.395913305028299	3		442	886	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051598	30051598	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	55	293	0	ENST00000338641.4:c.532C>T	p.Gln178Ter	p.Q178*	ENST00000338641	NM_000268.3	178	Cag/Tag	6/16	0.382519127153841	1	FACETS	0.509	0.436	0.588	0.509	0.436	0.588	SUBCLONAL	1	TRUE	0	0.395913305028299	1		293	438	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652282	3652282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	185	690	0	ENST00000294008.3:c.787G>A	p.Glu263Lys	p.E263K	ENST00000294008	NM_032444.2	263	Gag/Aag	4/15	1	2	FACETS	0.869	0.801	0.939	0.869	0.801	0.939	CLONAL	1	TRUE	1	0.395913305028299	2		690	1076	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425853	49425853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772665565	NA	P-0056394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	245	846	0	ENST00000301067.7:c.12635G>A	p.Arg4212Gln	p.R4212Q	ENST00000301067	NM_003482.3	4212	cGg/cAg	39/54	1	2	FACETS	0.978	0.913	1	0.978	0.913	1	CLONAL	1	TRUE	1	0.395913305028299	2		846	1265	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443774	49443775	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0056394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1273	268	1071	0	ENST00000301067.7:c.3596_3597del	p.Leu1199HisfsTer7	p.L1199Hfs*7	ENST00000301067	NM_003482.3	1199	cTC/c	11/54	1	2	FACETS	0.879	0.822	0.937	0.879	0.822	0.937	CLONAL	1	TRUE	1	0.395913305028299	2		1071	1541	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639359	3639359	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1262	142	984	0	ENST00000294008.3:c.4280G>A	p.Cys1427Tyr	p.C1427Y	ENST00000294008	NM_032444.2	1427	tGc/tAc	12/15	1	2	FACETS	0.511	0.464	0.561	0.511	0.464	0.561	SUBCLONAL	1	TRUE	1	0.395913305028299	2		984	1404	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031981	10031981	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	88	690	0	ENST00000330684.3:c.842A>G	p.Tyr281Cys	p.Y281C	ENST00000330684	NM_001134407.1	281	tAc/tGc	3/13	1	2	FACETS	0.448	0.395	0.504	0.448	0.395	0.504	SUBCLONAL	1	TRUE	1	0.395913305028299	2		690	993	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47685247	47685247	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	60	351	1	ENST00000347630.2:c.703G>T	p.Glu235Ter	p.E235*	ENST00000347630	NM_001007230.1	235	Gag/Tag	8/11	0.395913305028299	2	FACETS	0.565	0.487	0.65	0.283	0.243	0.325	SUBCLONAL	1	TRUE	0	0.395913305028299	2		352	536	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225343033	225343033	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	57	391	0	ENST00000264414.4:c.2059G>C	p.Glu687Gln	p.E687Q	ENST00000264414	NM_003590.4	687	Gag/Cag	15/16	1	2	FACETS	0.411	0.352	0.476	0.411	0.352	0.476	SUBCLONAL	1	TRUE	1	0.395913305028299	2		391	700	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572372	41572372	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	248	757	0	ENST00000263253.7:c.4901C>A	p.Ala1634Glu	p.A1634E	ENST00000263253	NM_001429.3	1634	gCa/gAa	30/31	0.382519127153841	1	FACETS	0.952	0.891	1	0.952	0.891	1	CLONAL	1	TRUE	0	0.395913305028299	1		757	1055	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686863	117686863	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	38	277	0	ENST00000368508.3:c.2854C>G	p.Gln952Glu	p.Q952E	ENST00000368508	NM_002944.2	952	Caa/Gaa	19/43	1	2	FACETS	0.449	0.371	0.535	0.449	0.371	0.535	SUBCLONAL	1	TRUE	1	0.395913305028299	2		277	428	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937401	76937401	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	45	358	0	ENST00000373344.5:c.3347C>G	p.Ser1116Cys	p.S1116C	ENST00000373344	NM_000489.3	1116	tCc/tGc	9/35	NA	2	FACETS	0.534	0.449	0.627			1	INDETERMINATE	1	TRUE	NA	0.395913305028299	2		358	426	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0056395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	152	306	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.931	0.857	1	1	0.991	1	CLONAL	2	TRUE	1	0.313259879646332	2		306	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577530	7577530	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	146	659	0	ENST00000269305.4:c.751A>T	p.Ile251Phe	p.I251F	ENST00000269305	NM_001126112.2	251	Atc/Ttc	7/11	0.313259879646332	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.313259879646332	1		659	776	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052630	42052630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372072518	NA	P-0056395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	105	423	0	ENST00000219905.7:c.7301G>A	p.Arg2434Gln	p.R2434Q	ENST00000219905	NM_001164273.1	2434	cGg/cAg	20/24	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.313259879646332	2		423	613	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372446	55372447	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0056395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	155	1103	0	ENST00000297316.4:c.1138dup	p.Gln380ProfsTer4	p.Q380Pfs*4	ENST00000297316	NM_022454.3	379	tac/taCc	2/2	1	2	FACETS	0.859	0.785	0.937	0.859	0.785	0.937	CLONAL	1	TRUE	1	0.313259879646332	2		1103	1152	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271219	26271219	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	111	461	0	ENST00000305910.3:c.394C>A	p.Arg132Ser	p.R132S	ENST00000305910	NM_003534.2	132	Cgt/Agt	1/1	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.313259879646332	2		461	580	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223764	53223764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	188	1015	0	ENST00000375401.3:c.3595G>A	p.Ala1199Thr	p.A1199T	ENST00000375401	NM_004187.3	1199	Gct/Act	23/26	1	2	FACETS	0.992	0.915	1	0.992	0.915	1	CLONAL	1	TRUE	1	0.313259879646332	2		1015	1210	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555525585	NA	P-0056396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	305	478	0	ENST00000269305.4:c.673-2A>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		478	493	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	70	324	0				ENST00000310581	NM_198253.2	-/1132			0.175531405796506	4	FACETS	0.849	0.745	0.961	1	0.963	1	CLONAL	3	TRUE	2	0.175531405796506	4		324	368	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644679	134644679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773064927	NA	P-0056397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	69	408	1	ENST00000398015.3:c.80C>T	p.Thr27Met	p.T27M	ENST00000398015	NM_004441.4	27	aCg/aTg	2/16	1	2	FACETS	0.766	0.668	0.872	1	0.974	1	SUBCLONAL	2	TRUE	1	0.175531405796506	2		409	513	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510064	120510064	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	65	233	0	ENST00000256646.2:c.1445G>C	p.Cys482Ser	p.C482S	ENST00000256646	NM_024408.3	482	tGc/tCc	8/34	0.175531405796506	3	FACETS	0.971	0.845	1	0.971	0.845	1	CLONAL	2	TRUE	1	0.175531405796506	3		233	415	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942656	71942656	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	114	557	0	ENST00000298229.2:c.1612C>A	p.Leu538Met	p.L538M	ENST00000298229	NM_001567.3	538	Ctg/Atg	13/28	0.175531405796506	4	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	2	0.175531405796506	4		557	737	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445361	49445361	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	89	1231	0	ENST00000301067.7:c.2105C>G	p.Pro702Arg	p.P702R	ENST00000301067	NM_003482.3	702	cCt/cGt	10/54	1	2	FACETS	0.859	0.759	0.966	0.859	0.759	0.966	CLONAL	1	TRUE	1	0.175531405796506	2		1231	1181	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030703	48030703	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	41	266	0	ENST00000234420.5:c.3317A>G	p.Asp1106Gly	p.D1106G	ENST00000234420	NM_000179.2	1106	gAt/gGt	5/10	0.175531405796506	3	FACETS	1	0.931	1	0.62	0.517	0.734	CLONAL	1	TRUE	1	0.175531405796506	3		266	410	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539440	187539441	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0056397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	45	298	0	ENST00000441802.2:c.8299_8300del	p.Asp2767SerfsTer2	p.D2767Sfs*2	ENST00000441802	NM_005245.3	2767	GAt/t	10/27	0.175531405796506	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.175531405796506	1		298	407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0056399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	571	642	0	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	0.524560848733389	3	FACETS	0.97	0.94	1	0.97	0.94	1	CLONAL	3	TRUE	0	0.524560848733389	3		642	944	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950111	44950111	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0056399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	23	142	0	ENST00000377967.4:c.3878+2T>G		p.X1293_splice	ENST00000377967	NM_021140.2	1293			0.476959048595943	2	FACETS	0.327	0.255	0.41			1	SUBCLONAL	1	TRUE	NA	0.524560848733389	2		142	268	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846125	68846126	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTGACACCAACGATAATC	novel	NA	P-0056399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	455	680	0	ENST00000261769.5:c.1099_1116dup	p.Asp367_Pro372dup	p.D367_P372dup	ENST00000261769	NM_004360.3	367	act/aCTGACACCAACGATAATCct	8/16	0.490923445873374	5	FACETS	1	0.98	1	0.698	0.666	0.731	CLONAL	2	TRUE	2	0.524560848733389	5		680	1480	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279414	38279414	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	359	602	0	ENST00000425967.3:c.1075T>G	p.Leu359Val	p.L359V	ENST00000425967	NM_001174067.1	359	Tta/Gta	9/19	0.239780645544553	5	FACETS	1	0.991	1	0.794	0.754	0.834	INDETERMINATE	2	TRUE	2	0.524560848733389	5		602	1027	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577518	7577518	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519995	NA	P-0056400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	413	666	0	ENST00000269305.4:c.763A>T	p.Ile255Phe	p.I255F	ENST00000269305	NM_001126112.2	255	Atc/Ttc	7/11	0.195594934759887	4	FACETS	1	0.973	1			1	CLONAL	5	FALSE	NA	0.309398492204853	4		666	690	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466786	57466786	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	46	125	0	ENST00000371085.3:c.5G>A	p.Gly2Asp	p.G2D	ENST00000371085	NM_000516.4	2	gGc/gAc	1/13	0.309398492204853	8	FACETS	0.842	0.716	0.978			1	CLONAL	3	FALSE	NA	0.309398492204853	8		125	227	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168996	11168996	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	264	703	0	ENST00000358026.2:c.4586A>G	p.Tyr1529Cys	p.Y1529C	ENST00000358026	NM_001128849.1	1529	tAc/tGc	32/36	0.309398492204853	5	FACETS	1	0.969	1	1	0.994	1	CLONAL	3	FALSE	3	0.309398492204853	5		703	797	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577586	7577586	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587781589	NA	P-0056401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	236	605	0	ENST00000269305.4:c.695T>C	p.Ile232Thr	p.I232T	ENST00000269305	NM_001126112.2	232	aTc/aCc	7/11	0.634013784358244	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.634013784358244	1		605	481	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547903	41547903	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	182	449	1	ENST00000263253.7:c.2884G>T	p.Val962Leu	p.V962L	ENST00000263253	NM_001429.3	962	Gtg/Ttg	15/31	0.634013784358244	1	FACETS	0.947	0.885	1	0.947	0.885	1	CLONAL	1	TRUE	0	0.634013784358244	1		450	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0056402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	35	893	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		894	358	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052633	42052633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	21	450	0	ENST00000219905.7:c.7304G>A	p.Arg2435Gln	p.R2435Q	ENST00000219905	NM_001164273.1	2435	cGg/cAg	20/24	0.0841427981612538	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		450	296	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18473955	18473956	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	11	299	0	ENST00000266497.5:c.1200dup	p.Val401SerfsTer14	p.V401Sfs*14	ENST00000266497		399	-/A	6/31	0.3	4	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	4		299	214	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050674	69050674	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	16	350	0	ENST00000288368.4:c.4009G>C	p.Asp1337His	p.D1337H	ENST00000288368	NM_024870.2	1337	Gat/Cat	33/40	0.3	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		350	229	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0056403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	866	504	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.792514619235808	3	FACETS	0.983	0.966	0.999	0.983	0.966	0.999	CLONAL	3	TRUE	0	0.792514619235808	3		504	1035	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039164	49039164	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913297	NA	P-0056403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	235	193	0	ENST00000267163.4:c.2242G>T	p.Glu748Ter	p.E748*	ENST00000267163	NM_000321.2	748	Gag/Tag	22/27	0.792514619235808	2	FACETS	0.982	0.945	1	0.982	0.945	1	CLONAL	2	TRUE	0	0.792514619235808	2		193	302	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588124	69588124	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	594	463	0	ENST00000168712.1:c.574del	p.Arg192GlufsTer6	p.R192Efs*6	ENST00000168712	NM_002007.2	192	Cga/ga	3/3	0.792514619235808	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.792514619235808	3		463	1028	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719898	18719898	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs759134545	NA	P-0056403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	232	198	0	ENST00000266497.5:c.3795G>C	p.Trp1265Cys	p.W1265C	ENST00000266497		1265	tgG/tgC	27/31	0.792514619235808	3	FACETS	0.953	0.902	1	0.953	0.902	1	CLONAL	2	TRUE	1	0.792514619235808	3		198	429	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042015	14042015	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	146	224	0	ENST00000311895.7:c.2562A>T	p.Lys854Asn	p.K854N	ENST00000311895	NM_005236.2	854	aaA/aaT	11/11	0.792514619235808	3	FACETS	1	0.948	1	0.521	0.478	0.564	CLONAL	1	TRUE	1	0.792514619235808	3		224	494	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350343	89350343	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	729	510	0	ENST00000301030.4:c.2607G>T	p.Lys869Asn	p.K869N	ENST00000301030	NM_001256183.1	869	aaG/aaT	9/13	0.792514619235808	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.792514619235808	2		510	875	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248390	212248390	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	119	196	0	ENST00000342788.4:c.3877G>A	p.Gly1293Ser	p.G1293S	ENST00000342788	NM_005235.2	1293	Ggc/Agc	28/28	0.792514619235808	2	FACETS	0.966	0.884	1	0.483	0.442	0.525	CLONAL	1	TRUE	0	0.792514619235808	2		196	311	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180388	32180388	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	200	529	0	ENST00000375023.3:c.2543G>C	p.Cys848Ser	p.C848S	ENST00000375023	NM_004557.3	848	tGt/tCt	17/30	0.20693986985308	3	FACETS	0.818	0.759	0.88	0.273	0.253	0.294	INDETERMINATE	1	TRUE	0	0.792514619235808	3		529	861	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069940	5069940	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867553373	NA	P-0056403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	166	129	0	ENST00000381652.3:c.1529T>C	p.Leu510Pro	p.L510P	ENST00000381652	NM_004972.3	510	cTa/cCa	12/25	0.673575666819837	5	FACETS	0.899	0.832	0.968	0.599	0.554	0.645	CLONAL	2	TRUE	2	0.792514619235808	5		129	510	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0056404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	25	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.443	0.349	0.551	0.443	0.349	0.551	SUBCLONAL	1	TRUE	1	0.32	2		298	353	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0056404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	20	198	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	0.546	0.418	0.694	0.546	0.418	0.694	SUBCLONAL	1	TRUE	1	0.32	2		198	229	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	125	660	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.182910972142893	3	FACETS	1	0.911	1	0.504	0.456	0.555	INDETERMINATE	1	TRUE	1	0.32	3		660	899	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577087	7577087	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	188	715	0	ENST00000269305.4:c.851del	p.Thr284LysfsTer61	p.T284Kfs*61	ENST00000269305	NM_001126112.2	284	aCa/aa	8/11	0.161287367576414	4	FACETS	1	0.987	1	0.453	0.417	0.489	INDETERMINATE	1	TRUE	1	0.32	4		715	1142	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	104	324	0				ENST00000310581	NM_198253.2	-/1132			0.426746741814229	1	FACETS	0.528	0.482	0.576	0.528	0.482	0.576	INDETERMINATE	1	TRUE	0	0.873094043770166	1		324	254	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0056405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	81	219	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.449322412428918	1	FACETS	0.399	0.356	0.444	0.399	0.356	0.444	INDETERMINATE	1	TRUE	0	0.873094043770166	1		219	262	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0056405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	1082	960	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	NA	2	FACETS	1	0.998	1			1	INDETERMINATE	2	TRUE	NA	0.873094043770166	2		960	1177	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060673	38060673	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	516	1161	1	ENST00000250448.2:c.1316T>C	p.Leu439Pro	p.L439P	ENST00000250448	NM_004496.3	439	cTa/cCa	2/2	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.873094043770166	2		1162	1151	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330629	65330630	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0056416-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	43	301	0	ENST00000342505.4:c.1016dup	p.Asn339LysfsTer2	p.N339Kfs*2	ENST00000342505	NM_002227.2	339	aat/aaAt	8/25	1	2	FACETS	0.368	0.308	0.435	0.368	0.308	0.435	SUBCLONAL	1	TRUE	1	0.481393331151122	2		301	485	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115975	8115975	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056416-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	147	357	0	ENST00000346208.3:c.1321del	p.Ala441ProfsTer34	p.A441Pfs*34	ENST00000346208		441	Gcc/cc	6/6	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.481393331151122	2		357	445	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217867	7217871	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTT	CTGTT	-	novel	NA	P-0056416-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	74	498	0	ENST00000380728.2:c.140_144del	p.Glu47GlyfsTer48	p.E47Gfs*48	ENST00000380728		47	gAACAG/g	3/11	0.481393331151122	1	FACETS	0.4	0.351	0.454	0.4	0.351	0.454	SUBCLONAL	1	TRUE	0	0.481393331151122	1		498	583	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31511261	31511261	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056416-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	127	503	0	ENST00000344624.3:c.1313C>T	p.Thr438Met	p.T438M	ENST00000344624		438	aCg/aTg	6/33	NA	2	FACETS	0.73	0.662	0.801			1	INDETERMINATE	1	TRUE	NA	0.481393331151122	2		503	723	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0056425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	20	319	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.193706415200855	3	FACETS	0.522	0.398	0.668	0.261	0.199	0.334	SUBCLONAL	1	FALSE	1	0.193706415200855	3		319	434	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0056425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	159	563	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.193706415200855	5	FACETS	1	0.979	1	0.8	0.733	0.869	CLONAL	2	FALSE	2	0.193706415200855	5		563	883	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611920	100611920	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	75	736	0	ENST00000308731.7:c.1201G>A	p.Asp401Asn	p.D401N	ENST00000308731	NM_000061.2	401	Gac/Aac	14/19	0.193706415200855	2	FACETS	0.883	0.772	1	0.441	0.386	0.502	CLONAL	1	FALSE	0	0.193706415200855	2		736	877	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21553838	21553838	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	143	706	0	ENST00000382592.4:c.2764C>G	p.Gln922Glu	p.Q922E	ENST00000382592	NM_014572.2	922	Cag/Gag	7/8	0.145276094799318	3	FACETS	1	0.97	1	0.759	0.693	0.828	CLONAL	2	FALSE	0	0.193706415200855	3		706	711	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129436	30129671	+	splice_donor_variant,splice_acceptor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	TGTGGTCATGCTCAGGATCGGCAATCCGGGCCAGGCCGAAATCACAAATCTGGAATCAGACCTAGCTGCTAAGCTCGGCGCTCAAGGCCTCTGCAGCCTAAGCAGTCACGCCCCCTTGTCTTTGCCTCCACTGTTCCCTTTGCTTGCAATGTTCTCCTGCCCAAGGCTTCTTCTACTGGTCACTGGAAGCCCCAGACCCTGGGGGAGGAGGGGACAGGTGCCCAACCCTCTGACCT	TGTGGTCATGCTCAGGATCGGCAATCCGGGCCAGGCCGAAATCACAAATCTGGAATCAGACCTAGCTGCTAAGCTCGGCGCTCAAGGCCTCTGCAGCCTAAGCAGTCACGCCCCCTTGTCTTTGCCTCCACTGTTCCCTTTGCTTGCAATGTTCTCCTGCCCAAGGCTTCTTCTACTGGTCACTGGAAGCCCCAGACCCTGGGGGAGGAGGGGACAGGTGCCCAACCCTCTGACCT	-	novel	NA	P-0056425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	112	1002	0	ENST00000263025.4:c.542_592del		p.X181_splice	ENST00000263025	NM_002746.2	181	aAGGTCAGAGGGTTGGGCACCTGTCCCCTCCTCCCCCAGGGTCTGGGGCTTCCAGTGACCAGTAGAAGAAGCCTTGGGCAGGAGAACATTGCAAGCAAAGGGAACAGTGGAGGCAAAGACAAGGGGGCGTGACTGCTTAGGCTGCAGAGGCCTTGAGCGCCGAGCTTAGCAGCTAGGTCTGATTCCAGATTTGTGATTTCGGCCTGGCCCGGATTGCCGATCCTGAGCATGACCACAcc/acc	3-4/9	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.193706415200855	2		1002	925	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89833549	89833550	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0056425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	81	358	0	ENST00000389301.3:c.2600dup	p.Phe868ValfsTer18	p.F868Vfs*18	ENST00000389301	NM_000135.2	867	aag/aaAg	27/43	0.193706415200855	3	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	FALSE	1	0.193706415200855	3		358	424	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624876	9624876	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	48	625	1	ENST00000353224.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000353224	NM_177990.2	34	gGc/gTc	3/10	0.188438255982315	3	FACETS	0.707	0.596	0.83	0.353	0.298	0.415	SUBCLONAL	1	FALSE	1	0.193706415200855	3		626	769	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513330	44513330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748212332	NA	P-0056425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	226	880	0	ENST00000291552.4:c.605G>A	p.Arg202His	p.R202H	ENST00000291552	NM_006758.2	202	cGt/cAt	8/8	0.193706415200855	3	FACETS	0.894	0.834	0.957	1	0.99	1	CLONAL	3	FALSE	1	0.193706415200855	3		880	954	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545147	41545147	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	96	691	0	ENST00000263253.7:c.2347G>T	p.Ala783Ser	p.A783S	ENST00000263253	NM_001429.3	783	Gct/Tct	13/31	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.193706415200855	2		691	841	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0056426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	74	463	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.33525092928562	2		463	366	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0056426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	126	913	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	1	2	FACETS	0.872	0.789	0.959	0.872	0.789	0.959	CLONAL	1	TRUE	1	0.33525092928562	2		913	862	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610384	10610384	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	179	1045	1	ENST00000171111.5:c.326C>T	p.Ala109Val	p.A109V	ENST00000171111	NM_203500.1	109	gCc/gTc	2/6	0.33525092928562	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.33525092928562	1		1046	742	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343465	70343466	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0056426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	70	710	1	ENST00000374080.3:c.1639_1640delinsTT	p.Ala547Leu	p.A547L	ENST00000374080		547	GCa/TTa	12/45	1	2	FACETS	0.675	0.588	0.768	0.675	0.588	0.768	SUBCLONAL	1	TRUE	1	0.33525092928562	2		711	619	SUCCESS
APC	324	MSKCC	GRCh37	5	112175621	112175621	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	56	366	0	ENST00000257430.4:c.4330C>T	p.Gln1444Ter	p.Q1444*	ENST00000257430	NM_000038.5	1444	Caa/Taa	16/16	0.22353771375423	2	FACETS	1	0.919	1	0.548	0.472	0.629	CLONAL	1	TRUE	0	0.33525092928562	2		366	305	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090791	5090791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	24	263	0	ENST00000381652.3:c.2939G>A	p.Arg980Lys	p.R980K	ENST00000381652	NM_004972.3	980	aGa/aAa	22/25	1	2	FACETS	0.712	0.562	0.884	0.712	0.562	0.884	SUBCLONAL	1	TRUE	1	0.33525092928562	2		263	201	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0056426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	127	463	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.426674114318458	4	FACETS	0.874	0.797	0.955	0.874	0.797	0.955	CLONAL	2	TRUE	2	0.427435991597565	4		463	485	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668715	52668715	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	186	403	0	ENST00000394830.3:c.1204C>T	p.Gln402Ter	p.Q402*	ENST00000394830	NM_018313.4	402	Cag/Tag	12/30	0.427435991597565	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.427435991597565	2		403	409	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610384	10610384	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	252	1045	1	ENST00000171111.5:c.326C>T	p.Ala109Val	p.A109V	ENST00000171111	NM_203500.1	109	gCc/gTc	2/6	0.427435991597565	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.427435991597565	2		1046	562	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343465	70343466	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0056426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	52	710	1	ENST00000374080.3:c.1639_1640delinsTT	p.Ala547Leu	p.A547L	ENST00000374080		547	GCa/TTa	12/45	0.427435991597565	3	FACETS	0.588	0.501	0.684	0.294	0.25	0.342	SUBCLONAL	1	TRUE	1	0.427435991597565	3		711	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520000	NA	P-0056427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	337	1146	22	ENST00000269305.4:c.452C>A	p.Pro151His	p.P151H	ENST00000269305	NM_001126112.2	151	cCc/cAc	5/11	0.794016292621284	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.794016292621284	1		1168	494	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467617	66467617	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	114	399	1	ENST00000273854.3:c.652G>C	p.Gly218Arg	p.G218R	ENST00000273854	NM_004439.5	218	Ggt/Cgt	3/18	0.103820397064344	4	FACETS	0.795	0.725	0.867	0.795	0.725	0.867	INDETERMINATE	2	TRUE	2	0.794016292621284	4		400	324	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48921986	48921986	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	127	348	8	ENST00000267163.4:c.526C>T	p.Gln176Ter	p.Q176*	ENST00000267163	NM_000321.2	176	Caa/Taa	5/27	0.794016292621284	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.794016292621284	1		356	176	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675445	241675445	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0056427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	121	228	2	ENST00000366560.3:c.379-2A>T		p.X127_splice	ENST00000366560	NM_000143.3	127			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.794016292621284	2		230	269	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120785287	120785287	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	484	832	24	ENST00000257552.2:c.821C>A	p.Ala274Glu	p.A274E	ENST00000257552	NM_002442.3	274	gCg/gAg	12/15	0.142668721790559	4	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.794016292621284	4		856	898	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121438958	121438958	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	221	1150	24	ENST00000257555.6:c.1859C>A	p.Thr620Asn	p.T620N	ENST00000257555		620	aCc/aAc	10/10	0.142668721790559	4	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.794016292621284	4		1174	734	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40457644	40457644	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	242	950	8	ENST00000345506.4:c.1397T>C	p.Val466Ala	p.V466A	ENST00000345506	NM_003152.3	466	gTg/gCg	13/20	1	2	FACETS	0.998	0.939	1	0.998	0.939	1	CLONAL	1	TRUE	1	0.794016292621284	2		958	611	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561437	9561437	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	215	671	12	ENST00000353224.5:c.345C>A	p.His115Gln	p.H115Q	ENST00000353224	NM_177990.2	115	caC/caA	4/10	1	2	FACETS	0.937	0.877	0.998	0.937	0.877	0.998	CLONAL	1	TRUE	1	0.794016292621284	2		683	578	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0056428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	513	348	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.843067362262838	6	FACETS	0.922	0.891	0.954			1	CLONAL	4	TRUE	NA	0.843067362262838	6		348	886	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041074	42041074	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	231	725	0	ENST00000219905.7:c.5452C>T	p.Arg1818Ter	p.R1818*	ENST00000219905	NM_001164273.1	1818	Cga/Tga	16/24	0.835349797805764	3	FACETS	0.888	0.83	0.949	0.444	0.415	0.475	CLONAL	1	TRUE	1	0.843067362262838	3		725	877	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518517	69518517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	297	656	0	ENST00000294312.3:c.128G>A	p.Arg43His	p.R43H	ENST00000294312	NM_005117.2	43	cGc/cAc	1/3	0.835349797805764	3	FACETS	1	0.969	1	0.521	0.491	0.551	CLONAL	1	TRUE	1	0.843067362262838	3		656	962	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998979	100998979	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	557	1065	0	ENST00000325455.5:c.823T>G	p.Phe275Val	p.F275V	ENST00000325455	NM_001202474.3	275	Ttc/Gtc	1/8	0.835349797805764	3	FACETS	0.958	0.926	0.99	0.958	0.926	0.99	CLONAL	2	TRUE	1	0.843067362262838	3		1065	980	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225883	2225883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	606	1046	0	ENST00000326181.6:c.1675G>A	p.Gly559Ser	p.G559S	ENST00000326181	NM_032271.2	559	Ggt/Agt	18/21	0.368671969987728	5	FACETS	0.855	0.825	0.885	0.855	0.825	0.885	INDETERMINATE	3	TRUE	2	0.843067362262838	5		1046	1269	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0056428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	820	809	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.843067362262838	3	FACETS	0.991	0.976	1	0.991	0.976	1	CLONAL	3	TRUE	0	0.843067362262838	3		809	930	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573626	48573627	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0056428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	272	400	0	ENST00000342988.3:c.210_211insG	p.Cys71ValfsTer33	p.C71Vfs*33	ENST00000342988	NM_005359.5	70	-/G	2/12	0.843067362262838	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.843067362262838	2		400	313	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132431	11132431	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	646	1053	0	ENST00000358026.2:c.2647G>C	p.Gly883Arg	p.G883R	ENST00000358026	NM_001128849.1	883	Ggt/Cgt	19/36	0.695675825704208	4	FACETS	0.943	0.909	0.976	0.943	0.909	0.976	CLONAL	2	TRUE	2	0.843067362262838	4		1053	1498	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989623	212989623	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	187	286	0	ENST00000342788.4:c.88G>T	p.Ala30Ser	p.A30S	ENST00000342788	NM_005235.2	30	Gca/Tca	2/28	0.843067362262838	3	FACETS	0.992	0.936	1	0.992	0.936	1	CLONAL	2	TRUE	1	0.843067362262838	3		286	318	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356422	66356423	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0056428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	106	352	0	ENST00000273854.3:c.1074dup	p.Ser359LeufsTer11	p.S359Lfs*11	ENST00000273854	NM_004439.5	358	-/C	5/18	1	2	FACETS	0.852	0.775	0.932	0.852	0.775	0.932	CLONAL	1	TRUE	1	0.843067362262838	2		352	295	SUCCESS
APC	324	MSKCC	GRCh37	5	112174602	112174602	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	279	454	0	ENST00000257430.4:c.3311C>A	p.Ser1104Ter	p.S1104*	ENST00000257430	NM_000038.5	1104	tCa/tAa	16/16	0.842866961230058	2	FACETS	0.927	0.895	0.957	0.927	0.895	0.957	CLONAL	2	TRUE	0	0.843067362262838	2		454	357	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439656	140439656	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	263	337	0	ENST00000288602.6:c.2083G>C	p.Glu695Gln	p.E695Q	ENST00000288602	NM_004333.4	695	Gag/Cag	17/18	0.802790637508589	4	FACETS	0.991	0.938	1	0.991	0.938	1	CLONAL	2	TRUE	2	0.843067362262838	4		337	580	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	251	324	0				ENST00000310581	NM_198253.2	-/1132			0.721021009820211	7	FACETS	0.944	0.884	1	0.378	0.353	0.403	CLONAL	2	TRUE	2	0.721021009820211	7		324	1033	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5246054	5246054	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	216	523	0	ENST00000357368.4:c.721C>T	p.Arg241Cys	p.R241C	ENST00000357368	NM_002850.3	241	Cgc/Tgc	10/38	0.722762101099751	3	FACETS	1	0.99	1	0.654	0.612	0.697	CLONAL	1	TRUE	1	0.721021009820211	3		523	623	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852095	63852095	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	245	738	2	ENST00000279873.7:c.2873C>T	p.Ser958Leu	p.S958L	ENST00000279873	NM_032199.2	958	tCa/tTa	10/10	0.481026916901418	4	FACETS	1	0.991	1	0.442	0.413	0.471	CLONAL	1	TRUE	1	0.721021009820211	4		740	883	SUCCESS
AR	367	MSKCC	GRCh37	X	66766357	66766377	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGCGGCGGCGGCGGC	GGCGGCGGCGGCGGCGGCGGC	-	rs746853821	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	66	84	0	ENST00000374690.3:c.1400_1420del	p.Gly467_Gly473del	p.G467_G473del	ENST00000374690	NM_000044.3	457	GGCGGCGGCGGCGGCGGCGGC/-	1/8	0.722762101099751	2	FACETS	0.663	0.581	0.75			1	SUBCLONAL	1	TRUE	NA	0.721021009820211	2		84	276	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856356	45856356	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	827	1031	0	ENST00000391945.4:c.1816G>C	p.Glu606Gln	p.E606Q	ENST00000391945	NM_000400.3	606	Gag/Cag	19/23	0.616413102714487	5	FACETS	0.965	0.937	0.994	0.965	0.937	0.994	CLONAL	3	TRUE	2	0.721021009820211	5		1031	1649	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882319	89882319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	258	702	0	ENST00000389301.3:c.155G>A	p.Arg52Gln	p.R52Q	ENST00000389301	NM_000135.2	52	cGa/cAa	2/43	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.721021009820211	2		702	628	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032840	48032840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1114167744	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	113	323	0	ENST00000234420.5:c.3640G>A	p.Glu1214Lys	p.E1214K	ENST00000234420	NM_000179.2	1214	Gaa/Aaa	7/10	0.722762101099751	5	FACETS	0.76	0.689	0.835	0.507	0.459	0.557	SUBCLONAL	2	TRUE	2	0.721021009820211	5		323	429	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759824	133759824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	259	888	0	ENST00000318560.5:c.2147C>T	p.Ser716Phe	p.S716F	ENST00000318560	NM_005157.4	716	tCt/tTt	11/11	0.722762101099751	5	FACETS	1	0.981	1	0.281	0.262	0.3	CLONAL	1	TRUE	1	0.721021009820211	5		888	1332	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007712	62007712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1401272877	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	193	531	2	ENST00000392795.3:c.155G>A	p.Arg52His	p.R52H	ENST00000392795	NM_001039933.1	52	cGt/cAt	3/6	0.722762101099751	4	FACETS	1	0.965	1	0.535	0.495	0.576	CLONAL	1	TRUE	2	0.721021009820211	4		533	861	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56809865	56809865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567817363	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	187	523	0	ENST00000337432.4:c.986C>T	p.Ser329Leu	p.S329L	ENST00000337432	NM_058216.2	329	tCa/tTa	8/9	0.722762101099751	4	FACETS	1	0.959	1	0.528	0.488	0.569	CLONAL	1	TRUE	2	0.721021009820211	4		523	846	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024001	27024019	+	frameshift_variant	Frame_Shift_Del	DEL	CGGGGGGCAGCCGCTCGCC	CGGGGGGCAGCCGCTCGCC	-	novel	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	172	143	0	ENST00000324856.7:c.1110_1128del	p.Gly371ProfsTer14	p.G371Pfs*14	ENST00000324856	NM_006015.4	369	ggCGGGGGGCAGCCGCTCGCC/gg	1/20	0.697688920484579	4	FACETS	0.992	0.936	1	1	0.992	1	CLONAL	3	TRUE	2	0.721021009820211	4		143	276	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263312	115263312	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	494	687	0	ENST00000438362.2:c.2038T>C	p.Phe680Leu	p.F680L	ENST00000438362	NM_001242891.1	680	Ttt/Ctt	17/20	0.575147239556284	5	FACETS	1	0.995	1	0.831	0.798	0.865	CLONAL	2	TRUE	2	0.721021009820211	5		687	1144	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740188	162740188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415162860	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	1258	620	0	ENST00000367921.3:c.1390G>A	p.Glu464Lys	p.E464K	ENST00000367921	NM_006182.2	464	Gaa/Aaa	12/18	0.721021009820211	10	FACETS	0.938	0.918	0.958	0.82	0.803	0.838	CLONAL	7	TRUE	2	0.721021009820211	10		620	2065	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226595617	226595617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201256399	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	234	651	1	ENST00000366794.5:c.14C>T	p.Ser5Leu	p.S5L	ENST00000366794	NM_001618.3	5	tCg/tTg	1/23	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.721021009820211	2		652	578	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70412285	70412285	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	120	304	0	ENST00000373644.4:c.4395G>T	p.Arg1465Ser	p.R1465S	ENST00000373644	NM_030625.2	1465	agG/agT	6/12	0.481026916901418	4	FACETS	1	0.982	1	0.449	0.409	0.491	CLONAL	1	TRUE	1	0.721021009820211	4		304	425	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359374	118359374	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	118	463	0	ENST00000534358.1:c.4378T>G	p.Leu1460Val	p.L1460V	ENST00000534358	NM_005933.3	1460	Tta/Gta	11/36	0.29313555436914	3	FACETS	1	0.978	1	0.618	0.564	0.675	INDETERMINATE	1	TRUE	1	0.721021009820211	3		463	360	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118361943	118361943	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	97	269	0	ENST00000534358.1:c.4729G>A	p.Asp1577Asn	p.D1577N	ENST00000534358	NM_005933.3	1577	Gat/Aat	14/36	0.29313555436914	3	FACETS	1	0.984	1	0.744	0.675	0.814	INDETERMINATE	1	TRUE	1	0.721021009820211	3		269	246	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027220	49027244	+	frameshift_variant	Frame_Shift_Del	DEL	TCCAGAATAATCACACTGCAGCAGA	TCCAGAATAATCACACTGCAGCAGA	-	novel	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	204	388	0	ENST00000267163.4:c.1788_1812del	p.Gln597CysfsTer6	p.Q597Cfs*6	ENST00000267163	NM_000321.2	596	cTCCAGAATAATCACACTGCAGCAGAt/ct	18/27	0.722762101099751	5	FACETS	0.854	0.801	0.907	0.854	0.801	0.907	CLONAL	3	TRUE	2	0.721021009820211	5		388	460	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571581	95571581	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	133	377	1	ENST00000393063.1:c.3096A>G	p.Ile1032Met	p.I1032M	ENST00000393063	NM_030621.3	1032	atA/atG	21/28	0.722762101099751	3	FACETS	1	0.933	1	0.512	0.468	0.558	CLONAL	1	TRUE	1	0.721021009820211	3		378	490	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828161	50828161	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	144	438	0	ENST00000398568.2:c.2499C>G	p.Asn833Lys	p.N833K	ENST00000398568	NM_001042412.1	833	aaC/aaG	17/18	NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.721021009820211	2		438	384	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677916	58677936	+	inframe_deletion	In_Frame_Del	DEL	GCCGTTGCCTCCGCGGCCGTC	GCCGTTGCCTCCGCGGCCGTC	-	rs1431633992	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	431	526	0	ENST00000305921.3:c.145_165del	p.Leu49_Pro55del	p.L49_P55del	ENST00000305921	NM_003620.3	47	caGCCGTTGCCTCCGCGGCCGTCg/cag	1/6	0.722762101099751	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.721021009820211	4		526	969	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853925	59853925	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs878855143	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	278	430	0	ENST00000259008.2:c.1936-2A>G		p.X646_splice	ENST00000259008	NM_032043.2	646			0.722762101099751	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.721021009820211	4		430	596	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031415	11031415	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	295	991	0	ENST00000327064.4:c.1415C>G	p.Pro472Arg	p.P472R	ENST00000327064	NM_199141.1	472	cCc/cGc	12/16	0.370773794985956	3	FACETS	1	0.988	1	0.582	0.549	0.616	INDETERMINATE	1	TRUE	1	0.721021009820211	3		991	956	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051587	13051587	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	179	634	0	ENST00000316448.5:c.846C>G	p.Asn282Lys	p.N282K	ENST00000316448	NM_004343.3	282	aaC/aaG	7/9	0.370773794985956	3	FACETS	1	0.98	1	0.58	0.538	0.624	INDETERMINATE	1	TRUE	1	0.721021009820211	3		634	582	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033983	48033983	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1289627423	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	271	388	0	ENST00000234420.5:c.4067T>C	p.Leu1356Ser	p.L1356S	ENST00000234420	NM_000179.2	1356	tTg/tCg	10/10	0.722762101099751	5	FACETS	1	0.958	1	1	0.958	1	CLONAL	3	TRUE	2	0.721021009820211	5		388	517	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872465	136872465	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	87	278	0	ENST00000241393.3:c.1033G>C	p.Glu345Gln	p.E345Q	ENST00000241393	NM_003467.2	345	Gag/Cag	2/2	0.722762101099751	2	FACETS	1	0.912	1	0.507	0.456	0.559	CLONAL	1	TRUE	0	0.721021009820211	2		278	238	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37083757	37083757	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	245	326	1	ENST00000231790.2:c.1668-2A>G		p.X556_splice	ENST00000231790	NM_000249.3	556			0.722762101099751	4	FACETS	0.945	0.889	1	0.945	0.889	1	CLONAL	2	TRUE	2	0.721021009820211	4		327	619	SUCCESS
ATR	545	MSKCC	GRCh37	3	142232360	142232360	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	142	365	0	ENST00000350721.4:c.4624C>T	p.Gln1542Ter	p.Q1542*	ENST00000350721	NM_001184.3	1542	Caa/Taa	26/47	0.722762101099751	5	FACETS	0.779	0.714	0.847	0.52	0.476	0.565	SUBCLONAL	2	TRUE	2	0.721021009820211	5		365	526	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805490	1805491	+	missense_variant	Missense_Mutation	DNP	CG	CG	GA	novel	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1256	246	938	2	ENST00000260795.2:c.1002_1003delinsGA	p.Gly335Arg	p.G335R	ENST00000260795		334	gcCGgg/gcGAgg	7/17	0.722762101099751	4	FACETS	0.782	0.729	0.837			1	SUBCLONAL	1	TRUE	NA	0.721021009820211	4		940	1502	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383678	84383678	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	446	649	0	ENST00000321945.7:c.1174G>C	p.Glu392Gln	p.E392Q	ENST00000321945	NM_139076.2	392	Gaa/Caa	9/9	0.722762101099751	4	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.721021009820211	4		649	986	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31472220	31472220	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	984	714	0	ENST00000344624.3:c.2191C>T	p.Gln731Ter	p.Q731*	ENST00000344624		731	Cag/Tag	14/33	0.721021009820211	7	FACETS	0.941	0.918	0.963	0.941	0.918	0.963	CLONAL	5	TRUE	2	0.721021009820211	7		714	1626	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840086	27840086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	135	462	0	ENST00000328488.2:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000328488	NM_003533.2	3	cGa/cAa	1/1	0.722762101099751	3	FACETS	0.989	0.904	1	0.495	0.452	0.539	CLONAL	1	TRUE	1	0.721021009820211	3		462	515	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821061	32821061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1474299244	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	382	1307	1	ENST00000354258.4:c.533C>T	p.Ser178Leu	p.S178L	ENST00000354258	NM_000593.5	178	tCa/tTa	1/11	0.722762101099751	3	FACETS	1	0.986	1	0.553	0.525	0.582	CLONAL	1	TRUE	1	0.721021009820211	3		1308	1303	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100541	157100542	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCAACAAA	novel	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	227	349	0	ENST00000346085.5:c.1480_1487dup	p.Arg496SerfsTer9	p.R496Sfs*9	ENST00000346085	NM_020732.3	493	gcg/gcGCAACAAAg	1/20	0.722762101099751	3	FACETS	0.927	0.875	0.979	0.927	0.875	0.979	CLONAL	2	TRUE	1	0.721021009820211	3		349	462	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5456122	5456122	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1433541247	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	70	258	0	ENST00000381577.3:c.9A>G	p.Ile3Met	p.I3M	ENST00000381577	NM_014143.3	3	atA/atG	2/7	1	2	FACETS	0.867	0.767	0.97	0.867	0.767	0.97	CLONAL	1	TRUE	1	0.721021009820211	2		258	224	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891457	76891457	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	364	268	0	ENST00000373344.5:c.4648G>C	p.Val1550Leu	p.V1550L	ENST00000373344	NM_000489.3	1550	Gtg/Ctg	16/35	0.722762101099751	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.721021009820211	2		268	434	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209158	36209166	+	inframe_deletion	In_Frame_Del	DEL	CTCCGCCGC	CTCCGCCGC	-	novel	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	33	35	0	ENST00000222270.7:c.240_248del	p.Arg81_Leu83del	p.R81_L83del	ENST00000222270	NM_014727.1	80	CTCCGCCGC/-	1/37	0.721021009820211	7	FACETS	1	0.915	1	0.583	0.486	0.686	CLONAL	2	TRUE	3	0.721021009820211	7		35	110	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874420	76874420	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	19	190	0	ENST00000373344.5:c.5302A>T	p.Asn1768Tyr	p.N1768Y	ENST00000373344	NM_000489.3	1768	Aat/Tat	21/35	0.722762101099751	2	FACETS	0.173	0.131	0.223			1	SUBCLONAL	1	TRUE	NA	0.721021009820211	2		190	304	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850704	63850705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	193	337	0	ENST00000279873.7:c.1489dup	p.Ile497AsnfsTer31	p.I497Nfs*31	ENST00000279873	NM_032199.2	494	-/A	10/10	1	2	FACETS	0.83	0.772	0.889	0.83	0.772	0.889	CLONAL	1	TRUE	1	0.793742775975674	2		337	586	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0056430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	217	342	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.92	0.862	0.98	0.92	0.862	0.98	CLONAL	1	TRUE	1	0.793742775975674	2		342	594	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	326	613	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.869	0.823	0.916	0.869	0.823	0.916	CLONAL	1	TRUE	1	0.793742775975674	2		613	945	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717756	89717756	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730882131	NA	P-0056430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	500	397	0	ENST00000371953.3:c.781C>T	p.Gln261Ter	p.Q261*	ENST00000371953	NM_000314.4	261	Cag/Tag	7/9	0.751271801990974	2	FACETS	0.997	0.972	1	0.997	0.972	1	CLONAL	2	TRUE	0	0.793742775975674	2		397	632	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023724	27023734	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCCCCTCC	GCGGCCCCTCC	-	novel	NA	P-0056430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	330	671	0	ENST00000324856.7:c.836_846del	p.Pro279ArgfsTer117	p.P279Rfs*117	ENST00000324856	NM_006015.4	277	gGCGGCCCCTCC/g	1/20	1	2	FACETS	0.804	0.761	0.848	0.804	0.761	0.848	CLONAL	1	TRUE	1	0.793742775975674	2		671	1034	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852488	63852489	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	405	663	0	ENST00000279873.7:c.3266_3267insA	p.Leu1091ProfsTer70	p.L1091Pfs*70	ENST00000279873	NM_032199.2	1089	tcg/tcAg	10/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.793742775975674	2		663	985	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0056431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	121	463	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	NA	2	FACETS	0.863	0.786	0.944			1	INDETERMINATE	1	TRUE	NA	0.631285069264745	2		463	444	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0056431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	62	303	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.631285069264745	1	FACETS	0.764	0.673	0.858	0.764	0.673	0.858	SUBCLONAL	1	TRUE	0	0.631285069264745	1		303	176	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0056431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	358	570	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.631285069264745	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.631285069264745	1		570	745	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0056431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	363	988	1	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	0.631285069264745	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.631285069264745	1		989	777	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760442	133760442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746334503	NA	P-0056431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	310	971	0	ENST00000318560.5:c.2765C>T	p.Ala922Val	p.A922V	ENST00000318560	NM_005157.4	922	gCg/gTg	11/11	1	2	FACETS	0.965	0.911	1	0.965	0.911	1	CLONAL	1	TRUE	1	0.631285069264745	2		971	1018	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125523731	125523731	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs968420616	NA	P-0056431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	78	248	0	ENST00000428830.2:c.1324C>T	p.Arg442Trp	p.R442W	ENST00000428830	NM_001114121.2	442	Cgg/Tgg	12/14	1	2	FACETS	0.835	0.741	0.933	0.835	0.741	0.933	CLONAL	1	TRUE	1	0.631285069264745	2		248	296	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298026	15298026	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775853385	NA	P-0056431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1380	74	1272	1	ENST00000263388.2:c.1730C>T	p.Thr577Ile	p.T577I	ENST00000263388	NM_000435.2	577	aCa/aTa	11/33	1	2	FACETS	0.161	0.14	0.184	0.161	0.14	0.184	SUBCLONAL	1	TRUE	1	0.631285069264745	2		1273	1454	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271727	38271727	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1679	107	1240	0	ENST00000425967.3:c.2222del	p.Phe741SerfsTer4	p.F741Sfs*4	ENST00000425967	NM_001174067.1	741	tTc/tc	17/19	0.587127413045009	3	FACETS	0.25	0.223	0.279	0.125	0.111	0.14	SUBCLONAL	1	TRUE	1	0.631285069264745	3		1240	1786	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	172	324	0				ENST00000310581	NM_198253.2	-/1132			0.332879165835263	3	FACETS	1	0.988	1	0.722	0.665	0.781	CLONAL	1	TRUE	1	0.332879165835263	3		324	835	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0056432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	296	777	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.197868583758046	2	FACETS	1	0.987	1	0.587	0.551	0.624	INDETERMINATE	1	TRUE	0	0.332879165835263	2		777	1515	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050864	49050864	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886042935	NA	P-0056432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	56	405	0	ENST00000267163.4:c.2548C>T	p.Gln850Ter	p.Q850*	ENST00000267163	NM_000321.2	850	Cag/Tag	25/27	1	2	FACETS	0.558	0.478	0.646	0.558	0.478	0.646	SUBCLONAL	1	TRUE	1	0.332879165835263	2		405	603	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400019	49400019	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	103	704	0	ENST00000418115.1:c.318C>G	p.Phe106Leu	p.F106L	ENST00000418115	NM_001664.2	106	ttC/ttG	4/5	1	2	FACETS	0.529	0.472	0.59	0.529	0.472	0.59	SUBCLONAL	1	TRUE	1	0.332879165835263	2		704	1170	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513348	106513348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528601604	NA	P-0056432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	62	378	0	ENST00000359195.3:c.2252C>T	p.Ser751Leu	p.S751L	ENST00000359195	NM_002649.2	751	tCg/tTg	4/11	1	2	FACETS	0.579	0.5	0.666	0.579	0.5	0.666	SUBCLONAL	1	TRUE	1	0.332879165835263	2		378	643	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988914	41988914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	77	607	0	ENST00000219905.7:c.1706C>T	p.Ser569Leu	p.S569L	ENST00000219905	NM_001164273.1	569	tCa/tTa	3/24	1	2	FACETS	0.479	0.419	0.543	0.479	0.419	0.543	SUBCLONAL	1	TRUE	1	0.332879165835263	2		607	966	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231413	98231413	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	86	742	0	ENST00000331920.6:c.1870C>G	p.Gln624Glu	p.Q624E	ENST00000331920	NM_000264.3	624	Cag/Gag	14/24	1	2	FACETS	0.471	0.415	0.531	0.471	0.415	0.531	SUBCLONAL	1	TRUE	1	0.332879165835263	2		742	1098	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907677	76907677	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	86	329	0	ENST00000373344.5:c.4484A>G	p.Asn1495Ser	p.N1495S	ENST00000373344	NM_000489.3	1495	aAt/aGt	15/35	1	1	FACETS	0.773	0.685	0.867	0.773	0.685	0.867	SUBCLONAL	1	TRUE	0	0.332879165835263	1		329	557	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	104	324	0				ENST00000310581	NM_198253.2	-/1132			0.13367942359962	3	FACETS	0.883	0.79	0.981	0.883	0.79	0.981	CLONAL	2	TRUE	1	0.152790163269018	3		324	830	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874031	123874031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1447464550	NA	P-0056434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	11	55	1	ENST00000330479.4:c.62C>T	p.Ala21Val	p.A21V	ENST00000330479	NM_020382.3	21	gCg/gTg	2/9	1	2	FACETS	1	0.822	1	1	0.822	1	CLONAL	1	TRUE	1	0.152790163269018	2		56	111	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610172	10610172	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1319	114	940	0	ENST00000171111.5:c.538G>A	p.Asp180Asn	p.D180N	ENST00000171111	NM_203500.1	180	Gac/Aac	2/6	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.152790163269018	2		940	1433	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608348	43608348	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1683	140	1222	1	ENST00000355710.3:c.1696C>T	p.Pro566Ser	p.P566S	ENST00000355710	NM_020975.4	566	Ccc/Tcc	9/20	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.152790163269018	2		1223	1823	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348204	348216	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCCCTGGGGGC	CGGCCCTGGGGGC	-	novel	NA	P-0056434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1448	236	1234	0	ENST00000262320.3:c.1290_1302del	p.Pro431ValfsTer45	p.P431Vfs*45	ENST00000262320	NM_003502.3	430	ggGCCCCCAGGGCCG/gg	6/11	1	2	FACETS	0.917	0.853	0.984	1	0.994	1	CLONAL	2	TRUE	1	0.152790163269018	2		1234	1684	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660256	227660257	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1336	102	919	0	ENST00000305123.5:c.3198dup	p.Gly1067TrpfsTer14	p.G1067Wfs*14	ENST00000305123	NM_005544.2	1066	-/T	1/2	1	2	FACETS	0.928	0.827	1	0.928	0.827	1	CLONAL	1	TRUE	1	0.152790163269018	2		919	1438	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139563125	139563125	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	81	802	0	ENST00000308874.7:c.197G>T	p.Arg66Leu	p.R66L	ENST00000308874		66	cGa/cTa	4/10	1	2	FACETS	0.925	0.813	1	0.925	0.813	1	CLONAL	1	TRUE	1	0.152790163269018	2		802	1146	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715778	18715778	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	42	312	0	ENST00000266497.5:c.3609G>T	p.Arg1203Ser	p.R1203S	ENST00000266497		1203	agG/agT	25/31	1	2	FACETS	0.961	0.802	1	0.961	0.802	1	CLONAL	1	TRUE	1	0.152790163269018	2		312	572	SUCCESS
BLM	641	MSKCC	GRCh37	15	91337418	91337418	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	42	319	0	ENST00000355112.3:c.3041A>C	p.His1014Pro	p.H1014P	ENST00000355112	NM_000057.2	1014	cAt/cCt	16/22	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.152790163269018	2		319	518	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0056435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	56	359	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	0.849	0.727	0.983	0.849	0.727	0.983	CLONAL	1	TRUE	1	0.21	2		359	628	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43739588	43739588	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	41	449	0	ENST00000382044.4:c.2812C>T	p.Pro938Ser	p.P938S	ENST00000382044	NM_001141980.1	938	Ccc/Tcc	13/28	1	2	FACETS	0.513	0.426	0.611	0.513	0.426	0.611	SUBCLONAL	1	TRUE	1	0.21	2		449	761	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0056446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	54	463	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.403212527335981	0	FACETS	0.655	0.565	0.751			1	SUBCLONAL	1	FALSE	0	0.403212527335981	0		463	244	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0056446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	186	504	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.322005277392439	3	FACETS	1	0.983	1	1	0.993	1	CLONAL	3	FALSE	1	0.403212527335981	3		504	332	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0056446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	125	618	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	0.403212527335981	0	FACETS	0.587	0.533	0.644			1	SUBCLONAL	1	FALSE	0	0.403212527335981	0		619	630	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339251	70339251	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs199469668	NA	P-0056446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	29	718	0	ENST00000374080.3:c.128A>C	p.Gln43Pro	p.Q43P	ENST00000374080		43	cAa/cCa	2/45	0.403212527335981	0	FACETS	0.084	0.067	0.104			1	SUBCLONAL	1	FALSE	0	0.403212527335981	0		718	1019	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588949	67588949	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	30	256	0	ENST00000274335.5:c.1040T>C	p.Leu347Pro	p.L347P	ENST00000274335		347	cTt/cCt	8/15	0.403212527335981	0	FACETS	0.846	0.698	1			1	CLONAL	1	FALSE	0	0.403212527335981	0		256	105	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023207	27023241	+	frameshift_variant	Frame_Shift_Del	DEL	GGGAACGCGGGCCCTAGGCCCGCCCTGAACAATAA	GGGAACGCGGGCCCTAGGCCCGCCCTGAACAATAA	-	novel	NA	P-0056446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	104	387	0	ENST00000324856.7:c.313_347del	p.Gly105ProfsTer283	p.G105Pfs*283	ENST00000324856	NM_006015.4	105	GGGAACGCGGGCCCTAGGCCCGCCCTGAACAATAAc/c	1/20	0.403212527335981	0	FACETS	0.314	0.28	0.35			1	SUBCLONAL	1	FALSE	0	0.403212527335981	0		387	981	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588966	67588966	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	25	255	0	ENST00000274335.5:c.1059del	p.Thr354ProfsTer19	p.T354Pfs*19	ENST00000274335		353	Ggg/gg	8/15	0.403212527335981	0	FACETS	0.705	0.567	0.857			1	SUBCLONAL	1	FALSE	0	0.403212527335981	0		255	105	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0056447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	138	1167	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	0.81	0.736	0.887	0.81	0.736	0.887	CLONAL	1	FALSE	1	0.359887018778749	2		1167	947	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790072	40790072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753667	NA	P-0056447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	122	952	0	ENST00000373198.4:c.2659G>A	p.Ala887Thr	p.A887T	ENST00000373198	NM_133170.3	887	Gcc/Acc	18/32	1	2	FACETS	0.767	0.693	0.845	0.767	0.693	0.845	SUBCLONAL	1	FALSE	1	0.359887018778749	2		952	884	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068421	26068421	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	24	419	0	ENST00000435504.4:c.69del	p.Lys23AsnfsTer7	p.K23Nfs*7	ENST00000435504		23	aaA/aa	2/13	0.359887018778749	1	FACETS	0.385	0.302	0.48	0.385	0.302	0.48	SUBCLONAL	1	FALSE	0	0.359887018778749	1		419	284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577152	7577154	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	ACC	ACC	-	rs1567548347	NA	P-0056448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	590	726	0	ENST00000269305.4:c.784_786del	p.Gly262del	p.G262del	ENST00000269305	NM_001126112.2	262	GGT/-	8/11	0.663505445006089	4	FACETS	0.883	0.862	0.903			1	CLONAL	4	FALSE	NA	0.795134102266598	4		726	754	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519347	137519347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747857191	NA	P-0056448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	69	358	0	ENST00000367739.4:c.1291C>T	p.Pro431Ser	p.P431S	ENST00000367739	NM_000416.2	431	Ccc/Tcc	7/7	0.788514658092313	2	FACETS	0.909	0.807	1	0.454	0.403	0.507	CLONAL	1	FALSE	0	0.795134102266598	2		358	191	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521594	46521594	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	140	436	0	ENST00000262741.5:c.814G>C	p.Asp272His	p.D272H	ENST00000262741	NM_003629.3	272	Gat/Cat	7/10	0.795134102266598	3	FACETS	0.88	0.806	0.958	0.44	0.403	0.479	CLONAL	1	FALSE	1	0.795134102266598	3		436	559	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900377	32900377	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs81002853	NA	P-0056448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	185	392	1	ENST00000380152.3:c.476-2A>G		p.X159_splice	ENST00000380152		159			0.788514658092313	2	FACETS	0.969	0.928	1	0.969	0.928	1	CLONAL	2	FALSE	0	0.795134102266598	2		393	240	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976100	7976100	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	248	722	0	ENST00000319144.4:c.2095A>G	p.Ile699Val	p.I699V	ENST00000319144	NM_001139.2	699	Att/Gtt	15/15	0.663505445006089	4	FACETS	1	0.988	1			1	CLONAL	1	FALSE	NA	0.795134102266598	4		722	918	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627260	12627260	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	165	510	0	ENST00000251849.4:c.1456G>C	p.Asp486His	p.D486H	ENST00000251849	NM_002880.3	486	Gat/Cat	14/17	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.795134102266598	2		510	403	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741234	145741234	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1482	178	1136	0	ENST00000428558.2:c.1172G>C	p.Gly391Ala	p.G391A	ENST00000428558	NM_004260.3	391	gGg/gCg	6/22	0.795134102266598	6	FACETS	0.699	0.641	0.759	0.175	0.16	0.19	SUBCLONAL	1	FALSE	2	0.795134102266598	6		1136	1660	SUCCESS
AR	367	MSKCC	GRCh37	X	66941790	66941790	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	172	491	0	ENST00000374690.3:c.2434C>A	p.Leu812Ile	p.L812I	ENST00000374690	NM_000044.3	812	Cta/Ata	6/8	0.212208326913255	5	FACETS	0.761	0.704	0.821	0.305	0.281	0.329	INDETERMINATE	2	FALSE	0	0.795134102266598	5		491	623	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008431	70008431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	141	293	0	ENST00000394351.3:c.718C>T	p.Arg240Cys	p.R240C	ENST00000394351	NM_000248.3	240	Cgc/Tgc	8/9	0.419509760558215	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.4377997944977	1		293	440	SUCCESS
APC	324	MSKCC	GRCh37	5	112170770	112170770	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs876658355	NA	P-0056449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	536	661	0	ENST00000257430.4:c.1866C>A	p.Tyr622Ter	p.Y622*	ENST00000257430	NM_000038.5	622	taC/taA	15/16	0.4377997944977	2	FACETS	0.952	0.915	0.99	0.952	0.915	0.99	CLONAL	2	TRUE	0	0.4377997944977	2		661	1286	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732951	30732951	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	175	462	0	ENST00000295754.5:c.1564G>T	p.Asp522Tyr	p.D522Y	ENST00000295754	NM_003242.5	522	Gac/Tac	7/7	0.419509760558215	1	FACETS	0.869	0.802	0.937	0.869	0.802	0.937	CLONAL	1	TRUE	0	0.4377997944977	1		462	719	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006051	22006051	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1385	352	1035	1	ENST00000276925.6:c.352G>T	p.Asp118Tyr	p.D118Y	ENST00000276925	NM_004936.3	118	Gac/Tac	2/2	1	2	FACETS	0.926	0.874	0.979	0.926	0.874	0.979	CLONAL	1	TRUE	1	0.4377997944977	2		1036	1737	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0056450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	84	330	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.313271859234408	3	FACETS	1	0.976	1	0.703	0.624	0.787	CLONAL	1	TRUE	1	0.328744163272755	3		330	423	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593558	48593558	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587781618	NA	P-0056450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	82	205	0	ENST00000342988.3:c.1308+1G>A		p.X436_splice	ENST00000342988	NM_005359.5	436			0.328744163272755	2	FACETS	0.971	0.868	1	0.971	0.868	1	CLONAL	2	TRUE	0	0.328744163272755	2		205	257	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946453	2946453	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368574818	NA	P-0056450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	187	964	1	ENST00000396946.4:c.3284C>T	p.Thr1095Met	p.T1095M	ENST00000396946	NM_032415.4	1095	aCg/aTg	25/25	0.313271859234408	3	FACETS	1	0.978	1	0.582	0.536	0.629	CLONAL	1	TRUE	1	0.328744163272755	3		965	1139	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244185	5244185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774952239	NA	P-0056450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	172	960	2	ENST00000357368.4:c.1297G>A	p.Val433Met	p.V433M	ENST00000357368	NM_002850.3	433	Gtg/Atg	11/38	0.324198487576577	2	FACETS	1	0.968	1	0.55	0.505	0.596	CLONAL	1	TRUE	0	0.328744163272755	2		962	952	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440347	187440347	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1202633041	NA	P-0056450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	126	604	0	ENST00000232014.4:c.2020C>T	p.Arg674Ter	p.R674*	ENST00000232014	NM_001130845.1	674	Cga/Tga	10/10	0.324198487576577	2	FACETS	1	0.938	1	0.523	0.474	0.575	CLONAL	1	TRUE	0	0.328744163272755	2		604	733	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266072	41266253	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTA	TCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTA	-	novel	NA	P-0056450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	50	377	0	ENST00000349496.5:c.70_241+10del		p.X24_splice	ENST00000349496	NM_001904.3	24		3/15	0.324198487576577	2	FACETS	0.836	0.712	0.971	0.418	0.356	0.486	CLONAL	1	TRUE	0	0.328744163272755	2		377	364	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205250	61205250	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	120	481	0	ENST00000301761.2:c.190G>C	p.Glu64Gln	p.E64Q	ENST00000301761	NM_017841.2	64	Gaa/Caa	2/4	0.275745242520681	1	FACETS	0.492	0.443	0.543	0.492	0.443	0.543	SUBCLONAL	1	TRUE	0	0.404499106210209	1		481	963	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205558	61205558	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	163	419	0	ENST00000301761.2:c.343G>A	p.Asp115Asn	p.D115N	ENST00000301761	NM_017841.2	115	Gac/Aac	3/4	0.275745242520681	1	FACETS	0.785	0.721	0.852	0.785	0.721	0.852	SUBCLONAL	1	TRUE	0	0.404499106210209	1		419	819	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205564	61205564	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	158	413	0	ENST00000301761.2:c.349G>C	p.Asp117His	p.D117H	ENST00000301761	NM_017841.2	117	Gat/Cat	3/4	0.275745242520681	1	FACETS	0.788	0.723	0.856	0.788	0.723	0.856	SUBCLONAL	1	TRUE	0	0.404499106210209	1		413	791	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0056458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	150	296	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.577915443223405	3	FACETS	0.904	0.837	0.972	0.904	0.837	0.972	CLONAL	2	TRUE	1	0.577869309542888	3		296	370	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0056458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	149	598	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.577915443223405	4	FACETS	0.996	0.911	1	0.498	0.455	0.543	CLONAL	1	TRUE	2	0.577869309542888	4		598	817	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111498	8111498	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	260	751	0	ENST00000346208.3:c.984G>A	p.Trp328Ter	p.W328*	ENST00000346208		328	tgG/tgA	5/6	0.577915443223405	3	FACETS	0.895	0.844	0.946	0.895	0.844	0.946	CLONAL	2	TRUE	1	0.577869309542888	3		751	648	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15978945	15978945	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	271	522	0	ENST00000268712.3:c.3573del	p.Ile1192LeufsTer52	p.I1192Lfs*52	ENST00000268712	NM_006311.3	1191	ccC/cc	27/46	0.577915443223405	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.577869309542888	2		522	459	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909233	41909233	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	169	820	0	ENST00000372991.4:c.155T>C	p.Ile52Thr	p.I52T	ENST00000372991	NM_001760.3	52	aTc/aCc	1/5	0.577915443223405	3	FACETS	1	0.972	1	0.556	0.513	0.601	CLONAL	1	TRUE	1	0.577869309542888	3		820	678	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109795	115109795	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	CTC	novel	NA	P-0056458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	516	837	0	ENST00000257566.3:c.2083delinsGAG	p.Arg695GlufsTer195	p.R695Efs*195	ENST00000257566	NM_016569.3	695	Cgc/GAGgc	8/8	0.575320486610115	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.577869309542888	3		837	685	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0056460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	83	303	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.517699135087557	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.517699135087557	1		303	218	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870851	12870852	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCGGCCTGCAGGAACCTCT	novel	NA	P-0056460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	50	418	0	ENST00000228872.4:c.85_103dup	p.Pro35LeufsTer96	p.P35Lfs*96	ENST00000228872	NM_004064.3	26	-/TCGGCCTGCAGGAACCTCT	1/3	NA	2	FACETS	0.615	0.525	0.713			1	INDETERMINATE	1	TRUE	NA	0.517699135087557	2		418	314	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205045	123205045	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056460-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	153	268	0	ENST00000218089.9:c.2406del	p.Met803CysfsTer8	p.M803Cfs*8	ENST00000218089	NM_001042749.1	802	aTt/at	25/35	1	1	FACETS	0.916	0.863	0.968	1	0.993	1	CLONAL	2	TRUE	0	0.517699135087557	1		268	239	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0056469-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	142	330	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.963	0.882	1	0.963	0.882	1	CLONAL	1	TRUE	1	0.563059443988608	2		330	524	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0056469-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	84	319	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.959	0.856	1	0.959	0.856	1	CLONAL	1	TRUE	1	0.563059443988608	2		319	311	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578551	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056469-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	326	664	0	ENST00000269305.4:c.379T>A	p.Ser127Thr	p.S127T	ENST00000269305	NM_001126112.2	127	Tcc/Acc	5/11	0.488806405902327	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.563059443988608	1		664	794	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937344	76937344	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056469-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	47	313	0	ENST00000373344.5:c.3404G>A	p.Arg1135Lys	p.R1135K	ENST00000373344	NM_000489.3	1135	aGg/aAg	9/35	0.563059443988608	3	FACETS	0.363	0.306	0.427			1	SUBCLONAL	1	TRUE	NA	0.563059443988608	3		313	589	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620122	21620122	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056469-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	248	437	0	ENST00000382592.4:c.44G>T	p.Ser15Ile	p.S15I	ENST00000382592	NM_014572.2	15	aGc/aTc	2/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.563059443988608	2		437	785	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151213	202151217	+	missense_variant	Missense_Mutation	ONP	GTGAA	GTGAA	CTGAC	novel	NA	P-0056469-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	76	199	0	ENST00000358485.4:c.1513_1517delinsCTGAC	p.Val505_Asn506delinsLeuThr	p.V505_N506delinsLT	ENST00000358485	NM_001080125.1	505	GTGAAc/CTGACc	9/9	0.154070754763405	3	FACETS	1	0.911	1	0.518	0.458	0.582	INDETERMINATE	1	TRUE	1	0.563059443988608	3		199	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0056498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	125	803	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.350485950387041	1	FACETS	0.943	0.856	1	0.943	0.856	1	CLONAL	1	TRUE	0	0.350485950387041	1		803	624	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504585	103504585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747957305	NA	P-0056498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	85	335	0	ENST00000355739.4:c.206G>A	p.Arg69Gln	p.R69Q	ENST00000355739	NM_000123.3	69	cGa/cAa	2/15	0.280343129224421	1	FACETS	0.937	0.832	1	0.937	0.832	1	CLONAL	1	TRUE	0	0.350485950387041	1		335	427	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972883	55972883	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	56	348	0	ENST00000263923.4:c.1507C>T	p.Gln503Ter	p.Q503*	ENST00000263923	NM_002253.2	503	Caa/Taa	11/30	0.147955828057579	2	FACETS	0.496	0.424	0.575	0.248	0.212	0.288	INDETERMINATE	1	TRUE	0	0.350485950387041	2		348	644	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250805	26250805	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	35	445	0	ENST00000446824.2:c.29A>G	p.Lys10Arg	p.K10R	ENST00000446824	NM_021018.2	10	aAg/aGg	1/1	0.246508956749812	2	FACETS	0.412	0.337	0.496	0.206	0.168	0.248	SUBCLONAL	1	TRUE	0	0.350485950387041	2		445	485	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140449166	140449166	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	63	349	0	ENST00000288602.6:c.1913A>T	p.Asp638Val	p.D638V	ENST00000288602	NM_004333.4	638	gAt/gTt	16/18	0.350485950387041	3	FACETS	0.838	0.726	0.96	0.419	0.363	0.48	CLONAL	1	TRUE	1	0.350485950387041	3		349	504	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126340	5126340	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	33	255	0	ENST00000381652.3:c.3185T>G	p.Met1062Arg	p.M1062R	ENST00000381652	NM_004972.3	1062	aTg/aGg	24/25	0.350485950387041	1	FACETS	0.547	0.447	0.659	0.547	0.447	0.659	SUBCLONAL	1	TRUE	0	0.350485950387041	1		255	284	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428266	47428583	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGCCCGGCAGACTGCCCAGGGCATGGAGTGAGCCTCCCAGCCTGGGGAGGGGTGGGGGGAAAGGGTGGGGGAAATGAGGTAACCCCCAGCCAATCCGCCACCTGCCTCCACCCCCACAGCTACCTCCATGCCAAGAACATCATCCACCGAGATCTCAAGTCTAACAGTATCTATCTGTCCCTGGGCTGGGGTTGAGTGGGGGTGTCAAGGGCTTAGAAGGATGCCTCTTGTGGGGGTTCTGGGAATTACAAGGGAGGGGCATGTGTCCCAGAGCTCCTTGCCAGGTGGCAGAGCTGTGGCCAGCCAGGGGGCTTTAA	TGGCCCGGCAGACTGCCCAGGGCATGGAGTGAGCCTCCCAGCCTGGGGAGGGGTGGGGGGAAAGGGTGGGGGAAATGAGGTAACCCCCAGCCAATCCGCCACCTGCCTCCACCCCCACAGCTACCTCCATGCCAAGAACATCATCCACCGAGATCTCAAGTCTAACAGTATCTATCTGTCCCTGGGCTGGGGTTGAGTGGGGGTGTCAAGGGCTTAGAAGGATGCCTCTTGTGGGGGTTCTGGGAATTACAAGGGAGGGGCATGTGTCCCAGAGCTCCTTGCCAGGTGGCAGAGCTGTGGCCAGCCAGGGGGCTTTAA	-	novel	NA	P-0056498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	58	738	0	ENST00000377045.4:c.1230_1300+155del		p.X410_splice	ENST00000377045	NM_001654.4	410		11-12/16	0.232179873306854	0	FACETS	0.347	0.298	0.401			1	SUBCLONAL	1	TRUE	0	0.350485950387041	0		738	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0056499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	410	722	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.465651593220288	2	FACETS	0.926	0.887	0.965	0.926	0.887	0.965	CLONAL	2	TRUE	0	0.523991348704564	2		722	845	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171986	32171986	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	586	847	0	ENST00000375023.3:c.3046C>A	p.His1016Asn	p.H1016N	ENST00000375023	NM_004557.3	1016	Cac/Aac	19/30	0.523991348704564	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	1	0.523991348704564	3		847	1196	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	73	324	0				ENST00000310581	NM_198253.2	-/1132			0.159697991173658	4	FACETS	0.902	0.793	1	0.902	0.793	1	CLONAL	3	TRUE	1	0.159697991173658	4		324	392	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0056500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	127	597	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.968	1	1	0.991	1	CLONAL	2	TRUE	1	0.159697991173658	2		597	691	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0056500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	91	330	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.94	0.836	1	1	0.985	1	CLONAL	2	TRUE	1	0.159697991173658	2		330	606	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0056500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	94	387	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.928	1	1	0.987	1	CLONAL	2	TRUE	1	0.159697991173658	2		388	559	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120232	70120232	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	402	869	1	ENST00000245479.2:c.1234C>T	p.Gln412Ter	p.Q412*	ENST00000245479	NM_000346.3	412	Cag/Tag	3/3	0.159697991173658	4	FACETS	0.925	0.88	0.97	1	0.996	1	CLONAL	5	TRUE	1	0.159697991173658	4		870	1263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876658468	NA	P-0056500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	188	803	0	ENST00000269305.4:c.577C>G	p.His193Asp	p.H193D	ENST00000269305	NM_001126112.2	193	Cat/Gat	6/11	0.159697991173658	1	FACETS	0.892	0.825	0.96	1	0.994	1	CLONAL	3	TRUE	0	0.159697991173658	1		803	810	SUCCESS
APC	324	MSKCC	GRCh37	5	112175706	112175706	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	180	397	0	ENST00000257430.4:c.4415del	p.Val1472GlufsTer35	p.V1472Efs*35	ENST00000257430	NM_000038.5	1472	gTa/ga	16/16	0.159697991173658	4	FACETS	1	0.974	1	1	0.99	1	CLONAL	4	TRUE	1	0.159697991173658	4		397	589	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458482	12458482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	99	767	0	ENST00000287820.6:c.1099G>A	p.Val367Ile	p.V367I	ENST00000287820	NM_015869.4	367	Gtt/Att	6/7	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.159697991173658	2		767	949	SUCCESS
APC	324	MSKCC	GRCh37	5	112174559	112174559	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	91	474	0	ENST00000257430.4:c.3268C>T	p.Gln1090Ter	p.Q1090*	ENST00000257430	NM_000038.5	1090	Caa/Taa	16/16	0.159697991173658	4	FACETS	0.98	0.871	1	0.654	0.581	0.732	CLONAL	2	TRUE	1	0.159697991173658	4		474	674	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057736	27057736	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	221	913	0	ENST00000324856.7:c.1444C>T	p.Gln482Ter	p.Q482*	ENST00000324856	NM_006015.4	482	Cag/Tag	3/20	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.159697991173658	2		913	1121	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456753	32456753	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1212035248	NA	P-0056500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	138	671	0	ENST00000332351.3:c.139G>A	p.Glu47Lys	p.E47K	ENST00000332351	NM_024426.4	47	Gag/Aag	1/10	1	2	FACETS	1	0.959	1	1	0.991	1	CLONAL	2	TRUE	1	0.159697991173658	2		671	793	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998808	100998808	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757746136	NA	P-0056500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	199	858	0	ENST00000325455.5:c.994G>A	p.Gly332Arg	p.G332R	ENST00000325455	NM_001202474.3	332	Ggg/Agg	1/8	0.159697991173658	1	FACETS	0.879	0.815	0.945	1	0.994	1	CLONAL	3	TRUE	0	0.159697991173658	1		858	870	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231174	46231174	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0056500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	102	402	0	ENST00000334344.6:c.1094C>G	p.Ser365Ter	p.S365*	ENST00000334344	NM_152641.2	365	tCa/tGa	9/21	1	2	FACETS	0.869	0.781	0.962	1	0.989	1	CLONAL	3	TRUE	1	0.159697991173658	2		402	490	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918228	50918228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759987234	NA	P-0056500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	226	931	0	ENST00000440232.2:c.2545C>T	p.Arg849Cys	p.R849C	ENST00000440232	NM_002691.3	849	Cgc/Tgc	20/27	1	2	FACETS	0.865	0.805	0.927	1	0.995	1	CLONAL	3	TRUE	1	0.159697991173658	2		931	1091	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445157	49445183	+	inframe_deletion	In_Frame_Del	DEL	AGGTGTGGCTCCTCAGCCTGCGGAGAT	AGGTGTGGCTCCTCAGCCTGCGGAGAT	-	rs375538882	NA	P-0056501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	248	836	0	ENST00000301067.7:c.2283_2309del	p.Ala765_Gln773del	p.A765_Q773del	ENST00000301067	NM_003482.3	761	ctATCTCCGCAGGCTGAGGAGCCACACCTg/ctg	10/54	0.624988986861213	2	FACETS	1	0.989	1	0.607	0.571	0.643	CLONAL	1	TRUE	0	0.627870318023125	2		836	651	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831357	72831358	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTGTTG	rs34918837	NA	P-0056501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	102	473	0	ENST00000268489.5:c.5218_5223dup	p.Gln1740_Gln1741dup	p.Q1740_Q1741dup	ENST00000268489	NM_006885.3	1740	-/CAACAA	9/10	0.624988986861213	2	FACETS	0.812	0.732	0.896	0.406	0.366	0.448	CLONAL	1	TRUE	0	0.627870318023125	2		473	400	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961804	15961806	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	rs148818383	NA	P-0056501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	354	444	0	ENST00000268712.3:c.5989_5991del	p.Val1997del	p.V1997del	ENST00000268712	NM_006311.3	1997	GTT/-	38/46	0.607764446982456	2	FACETS	0.904	0.866	0.941	0.904	0.866	0.941	CLONAL	2	TRUE	0	0.627870318023125	2		444	624	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350520	15350520	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	159	795	0	ENST00000263377.2:c.3395A>T	p.Glu1132Val	p.E1132V	ENST00000263377	NM_058243.2	1132	gAg/gTg	16/20	0.627870318023125	2	FACETS	0.674	0.619	0.732	0.337	0.309	0.366	SUBCLONAL	1	TRUE	0	0.627870318023125	2		795	751	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752974	42752974	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	504	879	0	ENST00000222329.4:c.1290C>G	p.Ile430Met	p.I430M	ENST00000222329	NM_006494.2	430	atC/atG	4/4	0.627870318023125	2	FACETS	0.965	0.932	0.997	0.965	0.932	0.997	CLONAL	2	TRUE	0	0.627870318023125	2		879	832	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350560	15350560	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	188	882	0	ENST00000263377.2:c.3355A>G	p.Ile1119Val	p.I1119V	ENST00000263377	NM_058243.2	1119	Atc/Gtc	16/20	0.627870318023125	2	FACETS	0.724	0.67	0.78	0.362	0.335	0.39	SUBCLONAL	1	TRUE	0	0.627870318023125	2		882	827	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350535	15350536	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0056501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	157	809	0	ENST00000263377.2:c.3379_3380insGG	p.Pro1127ArgfsTer27	p.P1127Rfs*27	ENST00000263377	NM_058243.2	1127	ccc/cGGcc	16/20	0.627870318023125	2	FACETS	0.641	0.588	0.697	0.321	0.294	0.349	SUBCLONAL	1	TRUE	0	0.627870318023125	2		809	780	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350522	15350523	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CG	novel	NA	P-0056501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	155	787	0	ENST00000263377.2:c.3392_3393insCG	p.Glu1132GlyfsTer22	p.E1132Gfs*22	ENST00000263377	NM_058243.2	1131	ccg/ccCGg	16/20	0.627870318023125	2	FACETS	0.659	0.604	0.716	0.33	0.302	0.358	SUBCLONAL	1	TRUE	0	0.627870318023125	2		787	749	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350564	15350565	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGCATG	novel	NA	P-0056501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	176	913	0	ENST00000263377.2:c.3350_3351insCATGCT	p.Ser1117_Pro1118insMetLeu	p.S1117_P1118insML	ENST00000263377	NM_058243.2	1117	tca/tcCATGCTa	16/20	0.627870318023125	2	FACETS	0.663	0.612	0.717	0.332	0.306	0.359	SUBCLONAL	1	TRUE	0	0.627870318023125	2		913	845	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350542	15350554	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGCTCGCTGCG	AGGGCTCGCTGCG	-	novel	NA	P-0056501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	170	826	0	ENST00000263377.2:c.3361_3373del	p.Arg1121SerfsTer28	p.R1121Sfs*28	ENST00000263377	NM_058243.2	1121	CGCAGCGAGCCCTtc/tc	16/20	0.627870318023125	2	FACETS	0.692	0.637	0.748	0.346	0.318	0.374	SUBCLONAL	1	TRUE	0	0.627870318023125	2		826	783	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857532	68857532	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	C	novel	NA	P-0056502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	190	446	0	ENST00000261769.5:c.2164+3A>C		p.X722_splice	ENST00000261769	NM_004360.3	722			0.849806418343405	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.849806418343405	1		446	243	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928065	178928085	+	inframe_deletion	In_Frame_Del	DEL	TACCTCATGGATTAGAAGATT	TACCTCATGGATTAGAAGATT	-	novel	NA	P-0056502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	175	535	0	ENST00000263967.3:c.1344_1364del	p.Pro449_Leu455del	p.P449_L455del	ENST00000263967	NM_006218.2	448	gTACCTCATGGATTAGAAGATTtg/gtg	8/21	1	2	FACETS	0.795	0.738	0.854	0.795	0.738	0.854	SUBCLONAL	1	TRUE	1	0.849806418343405	2		535	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0056503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	636	922	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.890729943650561	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.890729943650561	3		922	674	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942771	44942773	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs398122829	NA	P-0056503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	215	368	0	ENST00000377967.4:c.3354_3356del	p.Leu1119del	p.L1119del	ENST00000377967	NM_021140.2	1117	aaTCTt/aat	23/29	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.890729943650561	1		368	257	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427258	49427258	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	268	1015	0	ENST00000301067.7:c.11230C>T	p.Gln3744Ter	p.Q3744*	ENST00000301067	NM_003482.3	3744	Cag/Tag	39/54	0.850207687704069	4	FACETS	1	0.992	1	0.442	0.415	0.469	CLONAL	1	TRUE	1	0.890729943650561	4		1015	858	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143068	58143068	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	62	986	0	ENST00000257904.6:c.716C>G	p.Pro239Arg	p.P239R	ENST00000257904	NM_000075.3	239	cCt/cGt	7/8	0.790179110340689	4	FACETS	0.261	0.225	0.301	0.087	0.075	0.101	SUBCLONAL	1	TRUE	1	0.890729943650561	4		986	1007	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250961	99250961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121912428	NA	P-0056503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	433	873	1	ENST00000268035.6:c.265C>T	p.Arg89Ter	p.R89*	ENST00000268035	NM_000875.3	89	Cga/Tga	2/21	0.25003962346091	4	FACETS	0.965	0.933	0.996	0.724	0.7	0.747	INDETERMINATE	3	TRUE	0	0.890729943650561	4		874	635	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545981	41545981	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	267	963	0	ENST00000263253.7:c.2597del	p.Pro866LeufsTer80	p.P866Lfs*80	ENST00000263253	NM_001429.3	866	Cct/ct	14/31	1	2	FACETS	0.967	0.914	1	0.967	0.914	1	CLONAL	1	TRUE	1	0.890729943650561	2		963	620	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0056504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	72	221	1				ENST00000310581	NM_198253.2	-/1132			0.484099248493946	1	FACETS	0.835	0.741	0.933	0.835	0.741	0.933	CLONAL	1	TRUE	0	0.552508196878083	1		222	226	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0056504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	95	304	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.552508196878083	2		304	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781504	NA	P-0056504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	191	1036	0	ENST00000269305.4:c.314G>T	p.Gly105Val	p.G105V	ENST00000269305	NM_001126112.2	105	gGc/gTc	4/11	0.505730069989176	1	FACETS	0.979	0.913	1	0.979	0.913	1	CLONAL	1	TRUE	0	0.552508196878083	1		1036	511	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0056504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	17	346	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.552508196878083	1	FACETS	0.119	0.088	0.155	0.119	0.088	0.155	SUBCLONAL	1	TRUE	0	0.552508196878083	1		346	375	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123032	5123032	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	129	421	0	ENST00000381652.3:c.3088A>G	p.Lys1030Glu	p.K1030E	ENST00000381652	NM_004972.3	1030	Aag/Gag	23/25	1	2	FACETS	0.871	0.794	0.952	0.871	0.794	0.952	CLONAL	1	TRUE	1	0.552508196878083	2		421	536	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039215	49039216	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	G	novel	NA	P-0056504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	284	632	0	ENST00000267163.4:c.2293_2294delinsG	p.Lys765GlufsTer45	p.K765Efs*45	ENST00000267163	NM_000321.2	765	AAa/Ga	22/27	0.45499661076558	2	FACETS	0.792	0.75	0.834	0.792	0.75	0.834	SUBCLONAL	2	TRUE	0	0.552508196878083	2		632	649	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519886	NA	P-0056505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	27	414	0	ENST00000349496.5:c.97T>C	p.Ser33Pro	p.S33P	ENST00000349496	NM_001904.3	33	Tct/Cct	3/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		414	126	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778716	3778716	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs149930719	NA	P-0056505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	74	927	0	ENST00000262367.5:c.6332A>G	p.Asn2111Ser	p.N2111S	ENST00000262367	NM_004380.2	2111	aAt/aGt	31/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		927	211	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366437	118366437	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	31	371	0	ENST00000534358.1:c.5386G>T	p.Val1796Leu	p.V1796L	ENST00000534358	NM_005933.3	1796	Gtg/Ttg	19/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		371	126	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243920	46243920	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	20	421	0	ENST00000334344.6:c.2014C>T	p.Gln672Ter	p.Q672*	ENST00000334344	NM_152641.2	672	Caa/Taa	15/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		421	108	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448190	49448190	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	34	739	0	ENST00000301067.7:c.410G>A	p.Trp137Ter	p.W137*	ENST00000301067	NM_003482.3	137	tGg/tAg	4/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		739	160	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223738	36223739	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0056505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	98	1128	0	ENST00000222270.7:c.6292dup	p.Ala2098GlyfsTer10	p.A2098Gfs*10	ENST00000222270	NM_014727.1	2096	-/G	28/37	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1128	300	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711108	61711108	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	20	490	0	ENST00000401558.2:c.2641G>T	p.Ala881Ser	p.A881S	ENST00000401558	NM_003400.3	881	Gct/Tct	21/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		490	116	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098780	178098803	+	inframe_deletion	In_Frame_Del	DEL	CTGGCTGAATTGGGAGAAATTCAC	CTGGCTGAATTGGGAGAAATTCAC	-	novel	NA	P-0056505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	58	658	0	ENST00000397062.3:c.242_265del	p.Gly81_Pro88del	p.G81_P88del	ENST00000397062	NM_006164.4	81	gGTGAATTTCTCCCAATTCAGCCAGcc/gcc	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		658	197	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	43	541	0	ENST00000371085.3:c.602G>C	p.Arg201Pro	p.R201P	ENST00000371085	NM_000516.4	201	cGt/cCt	8/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		541	157	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525654	187525654	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1408225595	NA	P-0056505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	38	516	0	ENST00000441802.2:c.10425del	p.Phe3476SerfsTer6	p.F3476Sfs*6	ENST00000441802	NM_005245.3	3475	ccC/cc	18/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		516	115	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514417	148514417	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	37	492	0	ENST00000320356.2:c.1307A>T	p.Glu436Val	p.E436V	ENST00000320356	NM_004456.4	436	gAg/gTg	11/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		492	132	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0056510-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	512	1109	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	1	2	FACETS	0.939	0.903	0.976	1	0.997	1	CLONAL	2	TRUE	1	0.486269562291884	2		1109	1121	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0056516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	220	871	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.253745250551608	2	FACETS	0.974	0.908	1	0.974	0.908	1	CLONAL	2	TRUE	0	0.253745250551608	2		871	890	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900330	101900330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	60	453	0	ENST00000374994.4:c.764G>A	p.Arg255His	p.R255H	ENST00000374994	NM_004612.2	255	cGt/cAt	4/9	1	2	FACETS	0.961	0.829	1	0.961	0.829	1	CLONAL	1	TRUE	1	0.253745250551608	2		453	492	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604828	48604842	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	TTTAGACTGAGGTCT	TTTAGACTGAGGTCT	-	novel	NA	P-0056516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	11	484	0	ENST00000342988.3:c.1654_*9del		p.*552*	ENST00000342988	NM_005359.5	550		12/12	0.253745250551608	1	FACETS	0.215	0.148	0.299	0.215	0.148	0.299	SUBCLONAL	1	TRUE	0	0.253745250551608	1		484	352	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215661812	215661812	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs748828467	NA	P-0056516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	49	448	0	ENST00000260947.4:c.188T>C	p.Leu63Ser	p.L63S	ENST00000260947	NM_000465.2	63	tTa/tCa	2/11	0.252870440451085	3	FACETS	0.827	0.701	0.967	0.414	0.35	0.484	CLONAL	1	TRUE	1	0.253745250551608	3		448	526	SUCCESS
APC	324	MSKCC	GRCh37	5	112174829	112174829	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	39	292	0	ENST00000257430.4:c.3538del	p.Ser1180ValfsTer2	p.S1180Vfs*2	ENST00000257430	NM_000038.5	1180	Agt/gt	16/16	0.253745250551608	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.253745250551608	1		292	221	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156713	20156713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	73	525	0	ENST00000379607.5:c.44G>A	p.Gly15Asp	p.G15D	ENST00000379607	NM_001412.3	15	gGt/gAt	2/7	1	2	FACETS	0.747	0.652	0.85	0.747	0.652	0.85	SUBCLONAL	1	TRUE	1	0.22	2		525	888	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103396	77103397	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATCGGAAAA	novel	NA	P-0056517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	103	370	0	ENST00000356341.3:c.169_170insTTTTCCGAT	p.Arg56_Ser57insPhePheArg	p.R56_S57insFFR	ENST00000356341	NM_002576.4	57	tcc/tTTTTCCGATcc	2/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.22	2		370	647	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832707	3832707	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	59	592	0	ENST00000262367.5:c.1551del	p.Met518Ter	p.M518*	ENST00000262367	NM_004380.2	517	caG/ca	6/31	1	2	FACETS	0.593	0.509	0.686	0.593	0.509	0.686	SUBCLONAL	1	TRUE	1	0.22	2		592	904	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0056518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	155	597	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.676671126050467	2		597	429	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0056518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	199	330	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.130101356561741	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.676671126050467	0		330	623	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0056518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	116	303	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.991	0.903	1	0.991	0.903	1	CLONAL	1	FALSE	1	0.676671126050467	2		303	346	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0056518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	197	398	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	1	0.676671126050467	2		398	578	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411246	63411246	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	304	876	1	ENST00000330258.3:c.1921C>T	p.Arg641Ter	p.R641*	ENST00000330258	NM_152424.3	641	Cga/Tga	2/2	0.130101356561741	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.676671126050467	0		877	904	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717712	89717712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782350	NA	P-0056518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	28	480	0	ENST00000371953.3:c.737C>T	p.Pro246Leu	p.P246L	ENST00000371953	NM_000314.4	246	cCg/cTg	7/9	1	2	FACETS	0.107	0.085	0.133	0.107	0.085	0.133	SUBCLONAL	1	FALSE	1	0.676671126050467	2		480	773	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117858	70117858	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	320	589	0	ENST00000245479.2:c.326T>C	p.Met109Thr	p.M109T	ENST00000245479	NM_000346.3	109	aTg/aCg	1/3	0.638361980738683	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	0	0.676671126050467	1		589	540	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194904	29194904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372203752	NA	P-0056518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	40	787	0	ENST00000240100.2:c.824G>A	p.Arg275His	p.R275H	ENST00000240100	NM_001394.6	275	cGc/cAc	4/4	0.676671126050467	1	FACETS	0.099	0.082	0.119	0.099	0.082	0.119	SUBCLONAL	1	FALSE	0	0.676671126050467	1		787	789	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591825	48591825	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	264	500	2	ENST00000342988.3:c.988G>T	p.Glu330Ter	p.E330*	ENST00000342988	NM_005359.5	330	Gaa/Taa	9/12	0.934692459532095	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.934692459532095	1		502	288	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216279	2216279	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0056520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	730	643	3	ENST00000398665.3:c.1924-1G>T		p.X642_splice	ENST00000398665	NM_032482.2	642			0.934692459532095	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.934692459532095	2		646	767	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	203	504	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.894	0.828	0.964	1	0.993	1	CLONAL	2	TRUE	1	0.18	2		504	1261	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940455	29940455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138686378	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	101	410	0	ENST00000389048.3:c.776G>A	p.Arg259His	p.R259H	ENST00000389048	NM_004304.4	259	cGc/cAc	2/29	1	2	FACETS	0.929	0.832	1	1	0.986	1	CLONAL	2	TRUE	1	0.18	2		410	604	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637690	52637690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239654517	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	123	515	1	ENST00000394830.3:c.2626C>T	p.Arg876Cys	p.R876C	ENST00000394830	NM_018313.4	876	Cgt/Tgt	18/30	1	2	FACETS	0.777	0.702	0.856	1	0.985	1	SUBCLONAL	2	TRUE	1	0.18	2		516	880	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322698	39322698	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	86	596	0	ENST00000373001.3:c.294G>T	p.Lys98Asn	p.K98N	ENST00000373001	NM_022157.3	98	aaG/aaT	2/7	1	2	FACETS	0.932	0.823	1	0.932	0.823	1	CLONAL	1	TRUE	1	0.18	2		596	1025	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	81	425	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.18	2		425	634	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26974623	26974623	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	113	588	1	ENST00000381527.3:c.967C>T	p.Arg323Ter	p.R323*	ENST00000381527	NM_001260.1	323	Cga/Tga	10/13	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.18	2		589	861	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013719	170013719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388201066	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	99	417	0	ENST00000295797.4:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000295797	NM_002740.5	480	Cgc/Tgc	15/18	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.18	2		417	768	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549883	187549883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs186220887	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	80	551	0	ENST00000441802.2:c.4358G>A	p.Arg1453His	p.R1453H	ENST00000441802	NM_005245.3	1453	cGt/cAt	8/27	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.18	2		551	666	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	169	743	1	ENST00000394830.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000394830	NM_018313.4	710	Cga/Tga	17/30	1	2	FACETS	0.881	0.809	0.956	1	0.991	1	CLONAL	2	TRUE	1	0.18	2		744	1066	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	133	521	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.18	2		521	1050	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	126	426	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.793	0.717	0.872	1	0.986	1	SUBCLONAL	2	TRUE	1	0.18	2		426	883	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778879	9778879	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	159	1028	0	ENST00000377346.4:c.1148A>G	p.Asp383Gly	p.D383G	ENST00000377346	NM_005026.3	383	gAc/gGc	9/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.18	2		1028	1298	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782052	9782052	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	93	947	0	ENST00000377346.4:c.2075T>G	p.Leu692Arg	p.L692R	ENST00000377346	NM_005026.3	692	cTg/cGg	17/24	1	2	FACETS	0.86	0.762	0.965	0.86	0.762	0.965	CLONAL	1	TRUE	1	0.18	2		947	1202	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782391	9782391	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	181	980	1	ENST00000377346.4:c.2324G>A	p.Gly775Asp	p.G775D	ENST00000377346	NM_005026.3	775	gGc/gAc	18/24	1	2	FACETS	0.788	0.725	0.854	1	0.99	1	SUBCLONAL	2	TRUE	1	0.18	2		981	1276	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598336	28598336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769442139	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	224	976	0	ENST00000253063.3:c.308C>T	p.Thr103Met	p.T103M	ENST00000253063	NM_031459.4	103	aCg/aTg	3/10	1	2	FACETS	0.925	0.86	0.993	1	0.993	1	CLONAL	2	TRUE	1	0.18	2		976	1345	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812465	43812465	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs373621350	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	160	685	4	ENST00000372470.3:c.1168C>T	p.Arg390Cys	p.R390C	ENST00000372470	NM_005373.2	390	Cgc/Tgc	8/12	1	2	FACETS	0.884	0.809	0.961	1	0.991	1	CLONAL	2	TRUE	1	0.18	2		689	1006	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332599	65332599	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758451418	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	80	485	0	ENST00000342505.4:c.940G>A	p.Glu314Lys	p.E314K	ENST00000342505	NM_002227.2	314	Gaa/Aaa	7/25	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.18	2		485	616	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256439	115256439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774832953	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	99	491	0	ENST00000369535.4:c.272C>T	p.Ala91Val	p.A91V	ENST00000369535	NM_002524.4	91	gCg/gTg	3/7	1	2	FACETS	0.874	0.782	0.973	1	0.985	1	CLONAL	2	TRUE	1	0.18	2		491	629	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176145105	176145105	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	53	467	0	ENST00000367669.3:c.506G>T	p.Arg169Ile	p.R169I	ENST00000367669	NM_022457.5	169	aGa/aTa	3/20	1	2	FACETS	0.816	0.694	0.949	0.816	0.694	0.949	CLONAL	1	TRUE	1	0.18	2		467	722	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204501343	204501343	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	88	520	0	ENST00000367182.3:c.312G>T	p.Lys104Asn	p.K104N	ENST00000367182	NM_001278516.1	104	aaG/aaT	5/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.18	2		520	734	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518267	204518267	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	97	480	0	ENST00000367182.3:c.930G>T	p.Lys310Asn	p.K310N	ENST00000367182	NM_001278516.1	310	aaG/aaT	11/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.18	2		480	779	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647801	206647801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782361671	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	123	667	3	ENST00000367120.3:c.215C>T	p.Ala72Val	p.A72V	ENST00000367120	NM_014002.3	72	gCg/gTg	4/22	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.18	2		670	942	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653845	206653845	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1195	122	1059	0	ENST00000367120.3:c.1396C>A	p.Leu466Ile	p.L466I	ENST00000367120	NM_014002.3	466	Ctc/Atc	13/22	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.18	2		1059	1317	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63661997	63661997	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	85	623	0	ENST00000279873.7:c.101G>T	p.Arg34Ile	p.R34I	ENST00000279873	NM_032199.2	34	aGa/aTa	2/10	1	2	FACETS	0.945	0.834	1	0.945	0.834	1	CLONAL	1	TRUE	1	0.18	2		623	999	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573220	64573220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	176	909	0	ENST00000312049.6:c.1072G>A	p.Glu358Lys	p.E358K	ENST00000312049	NM_130799.2	358	Gag/Aag	8/10	1	2	FACETS	0.782	0.719	0.849	1	0.99	1	SUBCLONAL	2	TRUE	1	0.18	2		909	1250	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94170355	94170355	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	76	395	0	ENST00000323929.3:c.1914G>T	p.Lys638Asn	p.K638N	ENST00000323929	NM_005591.3	638	aaG/aaT	17/20	1	2	FACETS	0.773	0.679	0.874	1	0.977	1	SUBCLONAL	2	TRUE	1	0.18	2		395	546	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115600	108115600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772821016	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	82	532	1	ENST00000278616.4:c.748C>T	p.Arg250Ter	p.R250*	ENST00000278616	NM_000051.3	250	Cga/Tga	7/63	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.18	2		533	783	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153530	108153530	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	75	461	0	ENST00000278616.4:c.3670C>A	p.Leu1224Ile	p.L1224I	ENST00000278616	NM_000051.3	1224	Ctt/Att	25/63	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.18	2		461	560	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118353197	118353197	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	42	285	0	ENST00000534358.1:c.4073A>C	p.Lys1358Thr	p.K1358T	ENST00000534358	NM_005933.3	1358	aAa/aCa	8/36	1	2	FACETS	0.917	0.765	1	0.917	0.765	1	CLONAL	1	TRUE	1	0.18	2		285	509	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118370033	118370033	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	55	403	0	ENST00000534358.1:c.5977G>T	p.Gly1993Ter	p.G1993*	ENST00000534358	NM_005933.3	1993	Gga/Tga	23/36	1	2	FACETS	0.962	0.823	1	0.962	0.823	1	CLONAL	1	TRUE	1	0.18	2		403	635	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371742	118371742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	89	359	0	ENST00000534358.1:c.6199C>T	p.Arg2067Cys	p.R2067C	ENST00000534358	NM_005933.3	2067	Cgc/Tgc	25/36	1	2	FACETS	0.872	0.775	0.976	1	0.983	1	CLONAL	2	TRUE	1	0.18	2		359	567	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417094	417094	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	104	486	0	ENST00000399788.2:c.3456G>T	p.Met1152Ile	p.M1152I	ENST00000399788	NM_001042603.1	1152	atG/atT	23/28	1	2	FACETS	0.809	0.725	0.899	1	0.984	1	CLONAL	2	TRUE	1	0.18	2		486	714	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435061	18435061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603400	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	92	336	0	ENST00000266497.5:c.46G>A	p.Glu16Lys	p.E16K	ENST00000266497		16	Gaa/Aaa	1/31	1	2	FACETS	0.926	0.825	1	1	0.985	1	CLONAL	2	TRUE	1	0.18	2		336	552	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499670	18499670	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	114	667	0	ENST00000266497.5:c.1525A>C	p.Asn509His	p.N509H	ENST00000266497		509	Aat/Cat	10/31	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.18	2		667	915	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378649	25378649	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	83	512	0	ENST00000311936.3:c.349A>C	p.Lys117Gln	p.K117Q	ENST00000311936	NM_004985.3	117	Aaa/Caa	4/5	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.18	2		512	704	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242710	46242710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777576250	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	83	445	0	ENST00000334344.6:c.1672C>T	p.Arg558Cys	p.R558C	ENST00000334344	NM_152641.2	558	Cgt/Tgt	13/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.18	2		445	667	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246122	46246122	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1565624618	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	110	475	0	ENST00000334344.6:c.4216A>G	p.Thr1406Ala	p.T1406A	ENST00000334344	NM_152641.2	1406	Act/Gct	15/21	1	2	FACETS	0.803	0.722	0.889	1	0.985	1	CLONAL	2	TRUE	1	0.18	2		475	761	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246368	46246368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776372381	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	67	427	0	ENST00000334344.6:c.4462G>A	p.Asp1488Asn	p.D1488N	ENST00000334344	NM_152641.2	1488	Gac/Aac	15/21	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.18	2		427	654	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69210626	69210626	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	68	385	0	ENST00000462284.1:c.209A>C	p.Lys70Thr	p.K70T	ENST00000462284	NM_002392.5	70	aAa/aCa	4/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.18	2		385	597	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114225	115114225	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	183	894	0	ENST00000257566.3:c.992A>C	p.Lys331Thr	p.K331T	ENST00000257566	NM_016569.3	331	aAg/aCg	6/8	1	2	FACETS	0.917	0.845	0.992	1	0.992	1	CLONAL	2	TRUE	1	0.18	2		894	1109	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120675	115120675	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1162	215	1079	0	ENST00000257566.3:c.331G>T	p.Glu111Ter	p.E111*	ENST00000257566	NM_016569.3	111	Gaa/Taa	1/8	1	2	FACETS	0.867	0.804	0.933	1	0.993	1	CLONAL	2	TRUE	1	0.18	2		1079	1377	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123892066	123892066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	98	470	2	ENST00000330479.4:c.875G>A	p.Arg292His	p.R292H	ENST00000330479	NM_020382.3	292	cGc/cAc	8/9	1	2	FACETS	0.798	0.713	0.889	1	0.983	1	SUBCLONAL	2	TRUE	1	0.18	2		472	682	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	113	702	0	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.18	2		702	851	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562052	21562052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1359079402	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1235	133	1131	1	ENST00000382592.4:c.1867C>T	p.Arg623Trp	p.R623W	ENST00000382592	NM_014572.2	623	Cgg/Tgg	4/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.18	2		1132	1368	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959351	26959351	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	101	371	0	ENST00000381527.3:c.518A>G	p.Asp173Gly	p.D173G	ENST00000381527	NM_001260.1	173	gAc/gGc	6/13	1	2	FACETS	0.911	0.816	1	1	0.986	1	CLONAL	2	TRUE	1	0.18	2		371	616	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910439	32910439	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	99	420	1	ENST00000380152.3:c.1947G>T	p.Gln649His	p.Q649H	ENST00000380152		649	caG/caT	11/27	1	2	FACETS	0.87	0.778	0.968	1	0.985	1	CLONAL	2	TRUE	1	0.18	2		421	632	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942686	48942686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767011440	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	66	353	0	ENST00000267163.4:c.1073G>A	p.Arg358Gln	p.R358Q	ENST00000267163	NM_000321.2	358	cGa/cAa	11/27	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.18	2		353	560	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73340141	73340141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753955825	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	104	420	0	ENST00000377767.4:c.1939G>A	p.Asp647Asn	p.D647N	ENST00000377767	NM_014953.3	647	Gat/Aat	15/21	1	2	FACETS	0.943	0.846	1	1	0.987	1	CLONAL	2	TRUE	1	0.18	2		420	613	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347911	73347911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146500302	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	36	348	2	ENST00000377767.4:c.1150C>T	p.Arg384Cys	p.R384C	ENST00000377767	NM_014953.3	384	Cgc/Tgc	8/21	1	2	FACETS	0.68	0.558	0.818	0.68	0.558	0.818	SUBCLONAL	1	TRUE	1	0.18	2		350	588	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347916	73347916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139907646	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	72	335	0	ENST00000377767.4:c.1145G>A	p.Arg382Gln	p.R382Q	ENST00000377767	NM_014953.3	382	cGa/cAa	8/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.18	2		335	561	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73350074	73350074	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	62	351	0	ENST00000377767.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000377767	NM_014953.3	271	Gaa/Taa	5/21	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.18	2		351	551	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560464	95560464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	124	674	0	ENST00000393063.1:c.5125G>A	p.Asp1709Asn	p.D1709N	ENST00000393063	NM_030621.3	1709	Gat/Aat	25/28	1	2	FACETS	0.789	0.713	0.869	1	0.986	1	SUBCLONAL	2	TRUE	1	0.18	2		674	873	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562839	95562839	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	74	411	1	ENST00000393063.1:c.4418C>A	p.Ser1473Ter	p.S1473*	ENST00000393063	NM_030621.3	1473	tCa/tAa	24/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.18	2		412	593	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007743	45007743	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	131	461	1	ENST00000558401.1:c.190G>T	p.Glu64Ter	p.E64*	ENST00000558401	NM_004048.2	64	Gag/Tag	2/4	0.206702711423607	2	FACETS	0.898	0.816	0.986	0.898	0.816	0.986	CLONAL	2	TRUE	0	0.18	2		462	810	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479811	67479811	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500766	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	336	877	0	ENST00000327367.4:c.1118G>A	p.Arg373His	p.R373H	ENST00000327367	NM_005902.3	373	cGc/cAc	8/9	0.206702711423607	2	FACETS	1	0.973	1	1	0.995	1	CLONAL	3	TRUE	0	0.18	2		877	1190	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576112	88576112	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	65	968	0	ENST00000360948.2:c.1561C>T	p.His521Tyr	p.H521Y	ENST00000360948	NM_001012338.2	521	Cac/Tac	13/19	0.3	1	FACETS	0.545	0.47	0.626	0.545	0.47	0.626	SUBCLONAL	1	TRUE	0	0.18	1		968	1206	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857020	9857020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555481892	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	63	332	0	ENST00000330684.3:c.4381G>A	p.Glu1461Lys	p.E1461K	ENST00000330684	NM_001134407.1	1461	Gaa/Aaa	13/13	1	2	FACETS	0.778	0.674	0.889	1	0.972	1	SUBCLONAL	2	TRUE	1	0.18	2		332	450	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637631	23637631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45476495	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	155	757	0	ENST00000261584.4:c.2674G>A	p.Glu892Lys	p.E892K	ENST00000261584	NM_024675.3	892	Gaa/Aaa	7/13	1	2	FACETS	0.767	0.701	0.837	1	0.988	1	SUBCLONAL	2	TRUE	1	0.18	2		757	1122	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647508	23647508	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	129	721	0	ENST00000261584.4:c.359G>T	p.Arg120Ile	p.R120I	ENST00000261584	NM_024675.3	120	aGa/aTa	4/13	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.18	2		721	1052	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50818294	50818294	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	93	474	0	ENST00000398568.2:c.1872G>T	p.Lys624Asn	p.K624N	ENST00000398568	NM_001042412.1	624	aaG/aaT	11/18	1	2	FACETS	0.768	0.683	0.858	1	0.981	1	SUBCLONAL	2	TRUE	1	0.18	2		474	673	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56852609	56852609	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs761156791	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	139	650	0	ENST00000308159.5:c.523C>T	p.Arg175Ter	p.R175*	ENST00000308159	NM_014669.4	175	Cga/Tga	6/22	1	2	FACETS	0.787	0.716	0.862	1	0.987	1	SUBCLONAL	2	TRUE	1	0.18	2		650	981	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868319	56868319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748524706	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	94	414	2	ENST00000308159.5:c.1702C>T	p.Arg568Cys	p.R568C	ENST00000308159	NM_014669.4	568	Cgc/Tgc	15/22	1	2	FACETS	0.794	0.707	0.886	1	0.982	1	SUBCLONAL	2	TRUE	1	0.18	2		416	658	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972500	81972500	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	61	658	0	ENST00000359376.3:c.3293A>C	p.Lys1098Thr	p.K1098T	ENST00000359376	NM_002661.3	1098	aAg/aCg	29/33	1	2	FACETS	0.726	0.625	0.838	0.726	0.625	0.838	SUBCLONAL	1	TRUE	1	0.18	2		658	933	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216403	7216403	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1291	132	1015	1	ENST00000380728.2:c.845C>T	p.Ala282Val	p.A282V	ENST00000380728		282	gCc/gTc	10/11	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.18	2		1016	1423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519996	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	224	1025	0	ENST00000269305.4:c.395A>C	p.Lys132Thr	p.K132T	ENST00000269305	NM_001126112.2	132	aAg/aCg	5/11	1	2	FACETS	0.906	0.841	0.973	1	0.993	1	CLONAL	2	TRUE	1	0.18	2		1025	1374	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998913	11998913	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	66	346	0	ENST00000353533.5:c.415G>T	p.Glu139Ter	p.E139*	ENST00000353533	NM_003010.3	139	Gaa/Taa	4/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.18	2		346	518	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032603	12032603	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	51	621	0	ENST00000353533.5:c.1039T>G	p.Cys347Gly	p.C347G	ENST00000353533	NM_003010.3	347	Tgc/Ggc	9/11	1	2	FACETS	0.661	0.56	0.773	0.661	0.56	0.773	SUBCLONAL	1	TRUE	1	0.18	2		621	857	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12043193	12043193	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	67	397	0	ENST00000353533.5:c.1078G>T	p.Glu360Ter	p.E360*	ENST00000353533	NM_003010.3	360	Gag/Tag	10/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.18	2		397	561	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983343	15983343	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61753151	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	113	512	2	ENST00000268712.3:c.3436C>T	p.Arg1146Trp	p.R1146W	ENST00000268712	NM_006311.3	1146	Cgg/Tgg	26/46	1	2	FACETS	0.778	0.7	0.861	1	0.984	1	SUBCLONAL	2	TRUE	1	0.18	2		514	807	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16021312	16021312	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	41	362	0	ENST00000268712.3:c.1945G>A	p.Ala649Thr	p.A649T	ENST00000268712	NM_006311.3	649	Gca/Aca	18/46	1	2	FACETS	0.708	0.589	0.842	0.708	0.589	0.842	SUBCLONAL	1	TRUE	1	0.18	2		362	643	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049699	16049699	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	117	621	0	ENST00000268712.3:c.1073G>T	p.Arg358Ile	p.R358I	ENST00000268712	NM_006311.3	358	aGa/aTa	10/46	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.18	2		621	888	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527439	29527439	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs587781517	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	79	363	0	ENST00000356175.3:c.889-1G>T		p.X297_splice	ENST00000356175	NM_000267.3	297			1	2	FACETS	0.781	0.688	0.881	1	0.978	1	SUBCLONAL	2	TRUE	1	0.18	2		363	562	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553492	29553492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768638173	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	121	791	1	ENST00000356175.3:c.2041C>T	p.Arg681Ter	p.R681*	ENST00000356175	NM_000267.3	681	Cga/Tga	18/57	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.18	2		792	1062	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40854593	40854593	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	176	887	0	ENST00000428826.2:c.2201C>A	p.Ala734Asp	p.A734D	ENST00000428826		734	gCt/gAt	21/21	1	2	FACETS	0.777	0.714	0.843	1	0.99	1	SUBCLONAL	2	TRUE	1	0.18	2		887	1258	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41276095	41276095	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80356994	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	125	537	2	ENST00000357654.3:c.19C>T	p.Arg7Cys	p.R7C	ENST00000357654	NM_007294.3	7	Cgc/Tgc	2/23	1	2	FACETS	0.776	0.702	0.854	1	0.986	1	SUBCLONAL	2	TRUE	1	0.18	2		539	895	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435825	56435825	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	157	842	0	ENST00000407977.2:c.1312G>A	p.Ala438Thr	p.A438T	ENST00000407977		438	Gcc/Acc	9/10	1	2	FACETS	0.838	0.767	0.913	1	0.99	1	CLONAL	2	TRUE	1	0.18	2		842	1041	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56809870	56809870	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	127	604	0	ENST00000337432.4:c.991A>G	p.Ser331Gly	p.S331G	ENST00000337432	NM_058216.2	331	Agc/Ggc	8/9	1	2	FACETS	0.769	0.696	0.846	1	0.986	1	SUBCLONAL	2	TRUE	1	0.18	2		604	918	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740436	58740436	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs769061997	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	125	613	0	ENST00000305921.3:c.1341G>T	p.Glu447Asp	p.E447D	ENST00000305921	NM_003620.3	447	gaG/gaT	6/6	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.18	2		613	991	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740668	58740668	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs759850701	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	65	536	0	ENST00000305921.3:c.1573G>T	p.Glu525Ter	p.E525*	ENST00000305921	NM_003620.3	525	Gaa/Taa	6/6	1	2	FACETS	0.729	0.63	0.837	0.729	0.63	0.837	SUBCLONAL	1	TRUE	1	0.18	2		536	991	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374881	45374881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	132	583	0	ENST00000262160.6:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000262160	NM_005901.5	321	cGa/cAa	8/11	1	2	FACETS	0.752	0.682	0.826	1	0.986	1	SUBCLONAL	2	TRUE	1	0.18	2		583	975	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375016	45375016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226662382	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	86	444	0	ENST00000262160.6:c.827C>T	p.Ser276Leu	p.S276L	ENST00000262160	NM_005901.5	276	tCg/tTg	8/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.18	2		444	684	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621029	1621029	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1241	213	1257	0	ENST00000344749.5:c.1031A>C	p.His344Pro	p.H344P	ENST00000344749	NM_001136139.2	344	cAc/cCc	13/19	1	2	FACETS	0.814	0.754	0.876	1	0.992	1	CLONAL	2	TRUE	1	0.18	2		1257	1454	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387699	17387699	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	84	709	0	ENST00000359435.4:c.767A>G	p.Glu256Gly	p.E256G	ENST00000359435	NM_001033549.1	256	gAg/gGg	8/9	1	2	FACETS	0.951	0.838	1	0.951	0.838	1	CLONAL	1	TRUE	1	0.18	2		709	981	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271312	18271312	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1297	117	976	2	ENST00000222254.8:c.354C>A	p.Phe118Leu	p.F118L	ENST00000222254	NM_005027.3	118	ttC/ttA	3/16	1	2	FACETS	0.919	0.826	1	0.919	0.826	1	CLONAL	1	TRUE	1	0.18	2		978	1414	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726555	41726555	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	168	805	0	ENST00000301178.4:c.100G>T	p.Glu34Ter	p.E34*	ENST00000301178	NM_021913.4	34	Gaa/Taa	2/20	1	2	FACETS	0.836	0.767	0.908	1	0.99	1	CLONAL	2	TRUE	1	0.18	2		805	1116	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025841	48025841	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542848931	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	48	352	0	ENST00000234420.5:c.719G>A	p.Arg240Gln	p.R240Q	ENST00000234420	NM_000179.2	240	cGa/cAa	4/10	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.18	2		352	500	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095644	178095644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763240080	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	117	559	0	ENST00000397062.3:c.1687G>A	p.Glu563Lys	p.E563K	ENST00000397062	NM_006164.4	563	Gaa/Aaa	5/5	1	2	FACETS	0.779	0.702	0.861	1	0.985	1	SUBCLONAL	2	TRUE	1	0.18	2		559	834	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285292	212285292	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	64	514	0	ENST00000342788.4:c.3009C>A	p.Phe1003Leu	p.F1003L	ENST00000342788	NM_005235.2	1003	ttC/ttA	25/28	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.18	2		514	661	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488706	212488706	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	112	645	0	ENST00000342788.4:c.2143G>T	p.Glu715Ter	p.E715*	ENST00000342788	NM_005235.2	715	Gaa/Taa	18/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.18	2		645	855	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439512	220439512	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755693845	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	202	925	0	ENST00000243786.2:c.365G>A	p.Arg122His	p.R122H	ENST00000243786	NM_002191.3	122	cGc/cAc	2/2	1	2	FACETS	0.909	0.841	0.979	1	0.993	1	CLONAL	2	TRUE	1	0.18	2		925	1235	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378351	225378351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	67	283	0	ENST00000264414.4:c.544G>A	p.Ala182Thr	p.A182T	ENST00000264414	NM_003590.4	182	Gca/Aca	5/16	0.3	2	FACETS	1	0.971	1			1	CLONAL	1	TRUE	NA	0.18	2		283	508	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39713125	39713125	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	43	226	0	ENST00000361337.2:c.531G>T	p.Lys177Asn	p.K177N	ENST00000361337	NM_003286.2	177	aaG/aaT	8/21	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.18	2		226	353	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714491	40714491	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	102	537	0	ENST00000373198.4:c.3906C>A	p.Phe1302Leu	p.F1302L	ENST00000373198	NM_133170.3	1302	ttC/ttA	29/32	0.123781848046056	0	FACETS	1	0.971	1			1	CLONAL	1	TRUE	0	0.18	0		537	748	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21304053	21304053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	141	716	0	ENST00000354336.3:c.832G>A	p.Glu278Lys	p.E278K	ENST00000354336	NM_005207.3	278	Gaa/Aaa	3/3	1	2	FACETS	0.756	0.688	0.828	1	0.987	1	SUBCLONAL	2	TRUE	1	0.18	2		716	1036	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067929	30067929	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	168	847	0	ENST00000338641.4:c.1114G>A	p.Glu372Lys	p.E372K	ENST00000338641	NM_000268.3	372	Gaa/Aaa	11/16	1	2	FACETS	0.879	0.807	0.954	1	0.991	1	CLONAL	2	TRUE	1	0.18	2		847	1062	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537220	41537220	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	172	623	0	ENST00000263253.7:c.2047A>G	p.Thr683Ala	p.T683A	ENST00000263253	NM_001429.3	683	Act/Gct	10/31	1	2	FACETS	0.955	0.878	1	1	0.992	1	CLONAL	2	TRUE	1	0.18	2		623	1001	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564766	41564766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303184977	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	120	776	1	ENST00000263253.7:c.4067G>A	p.Arg1356Gln	p.R1356Q	ENST00000263253	NM_001429.3	1356	cGa/cAa	25/31	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.18	2		777	1137	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572357	41572357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	202	977	2	ENST00000263253.7:c.4886C>T	p.Ala1629Val	p.A1629V	ENST00000263253	NM_001429.3	1629	gCg/gTg	30/31	1	2	FACETS	0.842	0.778	0.908	1	0.992	1	CLONAL	2	TRUE	1	0.18	2		979	1333	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37083811	37083811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	104	491	0	ENST00000231790.2:c.1720C>T	p.Leu574Phe	p.L574F	ENST00000231790	NM_000249.3	574	Ctc/Ttc	15/19	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.18	2		491	813	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127805	47127805	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	118	447	2	ENST00000409792.3:c.5278-1G>T		p.X1760_splice	ENST00000409792	NM_014159.6	1760			1	2	FACETS	0.837	0.755	0.924	1	0.986	1	CLONAL	2	TRUE	1	0.18	2		449	783	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162226	47162226	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	125	596	0	ENST00000409792.3:c.3900G>A	p.Trp1300Ter	p.W1300*	ENST00000409792	NM_014159.6	1300	tgG/tgA	3/21	1	2	FACETS	0.798	0.722	0.879	1	0.986	1	SUBCLONAL	2	TRUE	1	0.18	2		596	870	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162904	47162904	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs757432733	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	125	520	0	ENST00000409792.3:c.3222G>T	p.Lys1074Asn	p.K1074N	ENST00000409792	NM_014159.6	1074	aaG/aaT	3/21	1	2	FACETS	0.84	0.76	0.924	1	0.987	1	CLONAL	2	TRUE	1	0.18	2		520	827	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72842131	72842131	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	46	410	0	ENST00000325599.8:c.1117G>T	p.Asp373Tyr	p.D373Y	ENST00000325599	NM_018130.2	373	Gac/Tac	10/11	1	2	FACETS	0.779	0.655	0.917	0.779	0.655	0.917	CLONAL	1	TRUE	1	0.18	2		410	656	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259627	89259627	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	50	437	0	ENST00000336596.2:c.771T>G	p.Cys257Trp	p.C257W	ENST00000336596	NM_005233.5	257	tgT/tgG	3/17	1	2	FACETS	0.929	0.788	1	0.929	0.788	1	CLONAL	1	TRUE	1	0.18	2		437	598	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498496	89498496	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	65	384	0	ENST00000336596.2:c.2468G>T	p.Arg823Ile	p.R823I	ENST00000336596	NM_005233.5	823	aGa/aTa	14/17	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.18	2		384	555	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119585471	119585471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	102	350	0	ENST00000316626.5:c.914C>T	p.Ser305Leu	p.S305L	ENST00000316626		305	tCg/tTg	9/12	1	2	FACETS	0.907	0.812	1	1	0.986	1	CLONAL	2	TRUE	1	0.18	2		350	625	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200691	128200691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1223	120	1013	0	ENST00000341105.2:c.1114G>A	p.Ala372Thr	p.A372T	ENST00000341105	NM_032638.4	372	Gcc/Acc	5/6	1	2	FACETS	0.993	0.894	1	0.993	0.894	1	CLONAL	1	TRUE	1	0.18	2		1013	1343	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911636	134911636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	95	536	0	ENST00000398015.3:c.2101G>A	p.Glu701Lys	p.E701K	ENST00000398015	NM_004441.4	701	Gag/Aag	11/16	1	2	FACETS	0.795	0.708	0.887	1	0.982	1	SUBCLONAL	2	TRUE	1	0.18	2		536	664	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433425	138433425	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	77	613	0	ENST00000289153.2:c.1187G>A	p.Arg396Lys	p.R396K	ENST00000289153	NM_006219.2	396	aGa/aAa	7/22	1	2	FACETS	0.897	0.785	1	0.897	0.785	1	CLONAL	1	TRUE	1	0.18	2		613	954	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275223	142275223	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	79	319	0	ENST00000350721.4:c.2078+2T>C		p.X693_splice	ENST00000350721	NM_001184.3	693			1	2	FACETS	0.881	0.777	0.992	1	0.981	1	CLONAL	2	TRUE	1	0.18	2		319	498	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278206	142278206	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs371466221	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	75	670	0	ENST00000350721.4:c.1619A>G	p.Tyr540Cys	p.Y540C	ENST00000350721	NM_001184.3	540	tAc/tGc	7/47	1	2	FACETS	0.921	0.805	1	0.921	0.805	1	CLONAL	1	TRUE	1	0.18	2		670	905	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922301	178922301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	98	415	0	ENST00000263967.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000263967	NM_006218.2	357	cGa/cAa	6/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.18	2		415	731	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1952853	1952853	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	174	752	0	ENST00000382891.5:c.1936G>A	p.Glu646Lys	p.E646K	ENST00000382891	NM_133335.3	646	Gaa/Aaa	10/22	1	2	FACETS	0.88	0.809	0.955	1	0.991	1	CLONAL	2	TRUE	1	0.18	2		752	1098	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595548	55595548	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	102	498	0	ENST00000288135.5:c.2038A>C	p.Asn680His	p.N680H	ENST00000288135	NM_000222.2	680	Aat/Cat	14/21	1	2	FACETS	0.86	0.77	0.955	1	0.985	1	CLONAL	2	TRUE	1	0.18	2		498	659	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280083	66280083	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	89	414	0	ENST00000273854.3:c.1606T>G	p.Tyr536Asp	p.Y536D	ENST00000273854	NM_004439.5	536	Tat/Gat	7/18	1	2	FACETS	0.758	0.673	0.85	1	0.979	1	SUBCLONAL	2	TRUE	1	0.18	2		414	652	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84390300	84390300	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	126	585	0	ENST00000321945.7:c.481T>G	p.Phe161Val	p.F161V	ENST00000321945	NM_139076.2	161	Ttt/Gtt	6/9	1	2	FACETS	0.794	0.718	0.873	1	0.986	1	SUBCLONAL	2	TRUE	1	0.18	2		585	882	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244091	153244091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	147	603	0	ENST00000281708.4:c.2066G>A	p.Arg689Gln	p.R689Q	ENST00000281708	NM_033632.3	689	cGg/cAg	12/12	1	2	FACETS	0.829	0.756	0.906	1	0.989	1	CLONAL	2	TRUE	1	0.18	2		603	985	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542504	187542504	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	143	684	0	ENST00000441802.2:c.5236T>C	p.Ser1746Pro	p.S1746P	ENST00000441802	NM_005245.3	1746	Tcc/Ccc	10/27	1	2	FACETS	0.846	0.771	0.925	1	0.989	1	CLONAL	2	TRUE	1	0.18	2		684	939	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	84	346	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	0.924	0.819	1	1	0.983	1	CLONAL	2	TRUE	1	0.18	2		346	505	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590445	67590445	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	52	247	0	ENST00000274335.5:c.1507C>T	p.Arg503Trp	p.R503W	ENST00000274335		503	Cgg/Tgg	11/15	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.18	2		247	419	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593250	67593250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs961235954	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	68	353	0	ENST00000274335.5:c.1996G>A	p.Glu666Lys	p.E666K	ENST00000274335		666	Gaa/Aaa	15/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.18	2		353	527	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80024771	80024771	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	49	421	0	ENST00000265081.6:c.1555C>T	p.Leu519Phe	p.L519F	ENST00000265081	NM_002439.4	519	Ctc/Ttc	10/24	1	2	FACETS	0.821	0.694	0.961	0.821	0.694	0.961	CLONAL	1	TRUE	1	0.18	2		421	663	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	98	323	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.772	0.689	0.861	1	0.982	1	SUBCLONAL	2	TRUE	1	0.18	2		323	705	SUCCESS
APC	324	MSKCC	GRCh37	5	112176051	112176051	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	94	425	0	ENST00000257430.4:c.4760C>A	p.Ser1587Ter	p.S1587*	ENST00000257430	NM_000038.5	1587	tCa/tAa	16/16	1	2	FACETS	0.859	0.765	0.958	1	0.984	1	CLONAL	2	TRUE	1	0.18	2		425	608	SUCCESS
APC	324	MSKCC	GRCh37	5	112177061	112177061	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	54	459	0	ENST00000257430.4:c.5770A>C	p.Lys1924Gln	p.K1924Q	ENST00000257430	NM_000038.5	1924	Aaa/Caa	16/16	1	2	FACETS	0.817	0.697	0.95	0.817	0.697	0.95	CLONAL	1	TRUE	1	0.18	2		459	734	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924513	131924513	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	117	476	0	ENST00000265335.6:c.1186T>G	p.Phe396Val	p.F396V	ENST00000265335		396	Ttt/Gtt	8/25	1	2	FACETS	0.871	0.786	0.961	1	0.987	1	CLONAL	2	TRUE	1	0.18	2		476	746	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131976476	131976476	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	166	569	1	ENST00000265335.6:c.3731C>A	p.Ser1244Tyr	p.S1244Y	ENST00000265335		1244	tCt/tAt	24/25	1	2	FACETS	0.984	0.904	1	1	0.992	1	CLONAL	2	TRUE	1	0.18	2		570	937	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048737	180048737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144803521	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	92	964	2	ENST00000261937.6:c.1825G>A	p.Asp609Asn	p.D609N	ENST00000261937	NM_182925.4	609	Gac/Aac	13/30	0.3	2	FACETS	0.845	0.748	0.949			1	CLONAL	1	TRUE	NA	0.18	2		966	1210	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048881	180048881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751002839	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	189	1131	2	ENST00000261937.6:c.1681G>A	p.Glu561Lys	p.E561K	ENST00000261937	NM_182925.4	561	Gaa/Aaa	13/30	0.3	2	FACETS	0.758	0.699	0.82			1	SUBCLONAL	2	TRUE	NA	0.18	2		1133	1385	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26046038	26046038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867056701	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	66	456	0	ENST00000540144.1:c.400G>A	p.Glu134Lys	p.E134K	ENST00000540144	NM_003531.2	134	Gaa/Aaa	1/1	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.18	2		456	611	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287298	33287298	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	95	743	0	ENST00000374542.5:c.1799T>C	p.Val600Ala	p.V600A	ENST00000374542	NM_001141970.1	600	gTc/gCc	6/8	1	2	FACETS	0.938	0.833	1	0.938	0.833	1	CLONAL	1	TRUE	1	0.18	2		743	1125	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43738988	43738988	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	104	544	0	ENST00000523873.1:c.5A>C	p.Asn2Thr	p.N2T	ENST00000523873		2	aAc/aCc	1/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.18	2		544	784	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663635	117663635	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs755903627	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	43	521	0	ENST00000368508.3:c.4597A>C	p.Lys1533Gln	p.K1533Q	ENST00000368508	NM_002944.2	1533	Aaa/Caa	28/43	0.3	2	FACETS	0.679	0.566	0.804			1	SUBCLONAL	1	TRUE	NA	0.18	2		521	704	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525497	137525497	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	101	587	0	ENST00000367739.4:c.518A>C	p.Asn173Thr	p.N173T	ENST00000367739	NM_000416.2	173	aAt/aCt	4/7	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.18	2		587	942	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151168657	151168657	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	70	553	0	ENST00000262187.5:c.310T>G	p.Leu104Val	p.L104V	ENST00000262187	NM_005614.3	104	Ttg/Gtg	5/8	1	2	FACETS	0.896	0.78	1	0.896	0.78	1	CLONAL	1	TRUE	1	0.18	2		553	868	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874830	151874830	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	117	465	0	ENST00000262189.6:c.7708C>T	p.Gln2570Ter	p.Q2570*	ENST00000262189	NM_170606.2	2570	Caa/Taa	38/59	1	2	FACETS	0.97	0.876	1	1	0.988	1	CLONAL	2	TRUE	1	0.18	2		465	670	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162110	38162110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	106	483	1	ENST00000317025.8:c.2606C>T	p.Ala869Val	p.A869V	ENST00000317025	NM_023034.1	869	gCc/gTc	14/24	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.18	2		484	794	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271227	38271227	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	97	961	0	ENST00000425967.3:c.2481C>A	p.Phe827Leu	p.F827L	ENST00000425967	NM_001174067.1	827	ttC/ttA	19/19	1	2	FACETS	0.883	0.784	0.988	0.883	0.784	0.988	CLONAL	1	TRUE	1	0.18	2		961	1221	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968173	68968173	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	128	635	0	ENST00000288368.4:c.1202G>T	p.Arg401Ile	p.R401I	ENST00000288368	NM_024870.2	401	aGa/aTa	10/40	1	2	FACETS	0.761	0.689	0.837	1	0.985	1	SUBCLONAL	2	TRUE	1	0.18	2		635	935	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072522	5072522	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	84	358	0	ENST00000381652.3:c.1672A>C	p.Lys558Gln	p.K558Q	ENST00000381652	NM_004972.3	558	Aag/Cag	13/25	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.18	2		358	657	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090538	5090538	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	97	392	0	ENST00000381652.3:c.2854A>C	p.Lys952Gln	p.K952Q	ENST00000381652	NM_004972.3	952	Aaa/Caa	21/25	1	2	FACETS	0.901	0.805	1	1	0.985	1	CLONAL	2	TRUE	1	0.18	2		392	598	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	145	473	0	ENST00000304494.5:c.143C>T	p.Pro48Leu	p.P48L	ENST00000304494	NM_000077.4	48	cCg/cTg	1/3	1	2	FACETS	0.927	0.846	1	1	0.99	1	CLONAL	2	TRUE	1	0.18	2		473	869	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97873801	97873801	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	144	952	1	ENST00000289081.3:c.1273C>T	p.Leu425Phe	p.L425F	ENST00000289081	NM_000136.2	425	Ctc/Ttc	13/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.18	2		953	1181	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223016	53223016	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	174	457	1	ENST00000375401.3:c.4056G>T	p.Glu1352Asp	p.E1352D	ENST00000375401	NM_004187.3	1352	gaG/gaT	24/26	1	1	FACETS	0.994	0.92	1	1	0.994	1	CLONAL	3	TRUE	0	0.18	1		458	590	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413161	63413161	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1408167220	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	130	403	0	ENST00000330258.3:c.6G>T	p.Glu2Asp	p.E2D	ENST00000330258	NM_152424.3	2	gaG/gaT	2/2	1	1	FACETS	0.936	0.855	1	1	0.992	1	CLONAL	3	TRUE	0	0.18	1		403	468	SUCCESS
AR	367	MSKCC	GRCh37	X	66765776	66765776	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	211	617	0	ENST00000374690.3:c.788T>G	p.Leu263Arg	p.L263R	ENST00000374690	NM_000044.3	263	cTt/cGt	1/8	1	1	FACETS	0.937	0.873	1	1	0.995	1	CLONAL	3	TRUE	0	0.18	1		617	759	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938995	76938995	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs886044898	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	105	394	0	ENST00000373344.5:c.1753G>T	p.Glu585Ter	p.E585*	ENST00000373344	NM_000489.3	585	Gaa/Taa	9/35	1	1	FACETS	1	0.968	1	1	0.989	1	CLONAL	2	TRUE	0	0.18	1		394	450	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793272	242793272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765748069	NA	P-0056521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	192	1032	1	ENST00000334409.5:c.805G>A	p.Asp269Asn	p.D269N	ENST00000334409	NM_005018.2	269	Gac/Aac	5/5	0.3	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.18	1		1033	1375	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0056522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	181	296	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.987	0.918	1	0.987	0.918	1	CLONAL	1	FALSE	1	0.714756310978912	2		296	513	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306960	65306960	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	209	459	0	ENST00000342505.4:c.2617C>T	p.Arg873Cys	p.R873C	ENST00000342505	NM_002227.2	873	Cgc/Tgc	19/25	0.714756310978912	1	FACETS	0.888	0.837	0.94	0.888	0.837	0.94	CLONAL	1	FALSE	0	0.714756310978912	1		459	423	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0056523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	273	359	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.376413413149689	5	FACETS	1	0.985	1	0.758	0.713	0.803	CLONAL	2	TRUE	2	0.470328246729695	5		359	871	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0056523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	391	686	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.470328246729695	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.470328246729695	2		686	807	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778773	3778773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	60	1040	0	ENST00000262367.5:c.6275C>T	p.Ser2092Leu	p.S2092L	ENST00000262367	NM_004380.2	2092	tCa/tTa	31/31	0.470328246729695	2	FACETS	0.215	0.185	0.249	0.108	0.092	0.125	SUBCLONAL	1	TRUE	0	0.470328246729695	2		1040	1184	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0056524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	157	633	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.229010403522749	5	FACETS	0.938	0.864	1			1	INDETERMINATE	2	FALSE	NA	0.536863049919994	5		633	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0056524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	313	652	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.536863049919994	4	FACETS	1	0.988	1			1	CLONAL	2	FALSE	NA	0.536863049919994	4		652	793	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0056524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	232	554	1	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.536863049919994	4	FACETS	0.889	0.832	0.947			1	CLONAL	2	FALSE	NA	0.536863049919994	4		555	747	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0056524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	60	234	2	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.536863049919994	5	FACETS	0.879	0.776	0.985	0.879	0.776	0.985	CLONAL	3	FALSE	2	0.536863049919994	5		236	153	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828461	72828461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139821312	NA	P-0056524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	28	568	0	ENST00000268489.5:c.8120C>T	p.Ala2707Val	p.A2707V	ENST00000268489	NM_006885.3	2707	gCg/gTg	9/10	0.536863049919994	3	FACETS	0.3	0.239	0.369	0.1	0.079	0.123	SUBCLONAL	1	FALSE	0	0.536863049919994	3		568	441	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519896	NA	P-0056525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	104	400	3	ENST00000281708.4:c.1514G>A	p.Arg505His	p.R505H	ENST00000281708	NM_033632.3	505	cGc/cAc	10/12	0.226168183191739	3	FACETS	1	0.951	1	0.366	0.328	0.406	INDETERMINATE	1	TRUE	0	0.401208786711107	3		403	567	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	259	575	2	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	0.226168183191739	3	FACETS	1	0.977	1	0.717	0.675	0.759	INDETERMINATE	2	TRUE	0	0.401208786711107	3		577	721	SUCCESS
APC	324	MSKCC	GRCh37	5	112175358	112175358	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1554085480	NA	P-0056525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	127	351	0	ENST00000257430.4:c.4067C>G	p.Ser1356Ter	p.S1356*	ENST00000257430	NM_000038.5	1356	tCa/tGa	16/16	0.401208786711107	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.401208786711107	2		351	282	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913315	NA	P-0056525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	23	961	1	ENST00000326873.7:c.580G>A	p.Asp194Asn	p.D194N	ENST00000326873	NM_000455.4	194	Gac/Aac	4/10	0.226168183191739	3	FACETS	0.14	0.108	0.177	0.047	0.036	0.059	INDETERMINATE	1	TRUE	0	0.401208786711107	3		962	985	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978892	25978893	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0056525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	188	435	0	ENST00000435504.4:c.1030_1031del	p.Ser344ArgfsTer3	p.S344Rfs*3	ENST00000435504		344	TCa/a	10/13	0.345005708368131	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	2	0.401208786711107	4		435	633	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577528	7577532	+	protein_altering_variant	In_Frame_Del	DEL	GATGG	GATGG	CC	novel	NA	P-0056525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	601	742	1	ENST00000269305.4:c.749_753delinsGG	p.Pro250_Ile251delinsArg	p.P250_I251delinsR	ENST00000269305	NM_001126112.2	250	cCCATC/cGG	7/11	0.401208786711107	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	4	TRUE	0	0.401208786711107	4		743	1020	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0056526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	138	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.236240100933519	2	FACETS	1	0.963	1	0.553	0.503	0.604	CLONAL	1	TRUE	0	0.326896494967294	2		298	764	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0056526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	169	893	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.326896494967294	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.326896494967294	1		894	845	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974765	21974765	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1329324238	NA	P-0056526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	105	341	2	ENST00000304494.5:c.62C>A	p.Ala21Asp	p.A21D	ENST00000304494	NM_000077.4	21	gCc/gAc	1/3	0.326896494967294	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.326896494967294	1		343	432	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107008	27107008	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	116	639	0	ENST00000324856.7:c.6619C>T	p.Gln2207Ter	p.Q2207*	ENST00000324856	NM_006015.4	2207	Cag/Tag	20/20	0.326896494967294	1	FACETS	0.765	0.69	0.845	0.765	0.69	0.845	SUBCLONAL	1	TRUE	0	0.326896494967294	1		639	776	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954247	32954247	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	107	541	0	ENST00000380152.3:c.9221T>C	p.Leu3074Pro	p.L3074P	ENST00000380152		3074	cTa/cCa	24/27	0.326896494967294	1	FACETS	0.841	0.756	0.932	0.841	0.756	0.932	CLONAL	1	TRUE	0	0.326896494967294	1		541	651	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183565	10183565	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1064794788	NA	P-0056526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	136	758	0	ENST00000256474.2:c.34G>C	p.Glu12Gln	p.E12Q	ENST00000256474	NM_000551.3	12	Gag/Cag	1/3	1	2	FACETS	0.689	0.625	0.757	0.689	0.625	0.757	SUBCLONAL	1	TRUE	1	0.326896494967294	2		758	1208	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73047279	73047279	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	92	428	0	ENST00000356692.5:c.86T>G	p.Leu29Arg	p.L29R	ENST00000356692		29	cTt/cGt	2/9	0.326896494967294	1	FACETS	0.833	0.742	0.93	0.833	0.742	0.93	CLONAL	1	TRUE	0	0.326896494967294	1		428	565	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589179	67589182	+	frameshift_variant	Frame_Shift_Del	DEL	ATAT	ATAT	-	novel	NA	P-0056526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	64	329	2	ENST00000274335.5:c.1167_1170del	p.Tyr390AlafsTer6	p.Y390Afs*6	ENST00000274335		389	aaATAT/aa	9/15	0.238502082592839	3	FACETS	1	0.954	1	0.611	0.531	0.696	CLONAL	1	TRUE	1	0.326896494967294	3		331	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057520000	NA	P-0056527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	134	798	1	ENST00000269305.4:c.452C>G	p.Pro151Arg	p.P151R	ENST00000269305	NM_001126112.2	151	cCc/cGc	5/11	0.783837875668552	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.800113080528016	1		799	186	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40742247	40742247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	94	709	0	ENST00000392038.2:c.877G>A	p.Asp293Asn	p.D293N	ENST00000392038	NM_001626.4	293	Gac/Aac	10/14	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.800113080528016	2		709	219	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265513	198265513	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	67	436	1	ENST00000335508.6:c.2644G>T	p.Ala882Ser	p.A882S	ENST00000335508	NM_012433.2	882	Gca/Tca	18/25	1	2	FACETS	0.859	0.76	0.961	0.859	0.76	0.961	CLONAL	1	TRUE	1	0.800113080528016	2		437	195	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409900	63409900	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1468255983	NA	P-0056527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	55	303	0	ENST00000330258.3:c.3267G>T	p.Arg1089Ser	p.R1089S	ENST00000330258	NM_152424.3	1089	agG/agT	2/2	1	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.800113080528016	1		303	74	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0056528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	322	845	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.323978642851946	2	FACETS	0.773	0.732	0.814	0.773	0.732	0.814	SUBCLONAL	2	TRUE	0	0.477343909356804	2		845	873	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589600	69589600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760825703	NA	P-0056528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	160	336	0	ENST00000168712.1:c.253C>T	p.Arg85Trp	p.R85W	ENST00000168712	NM_002007.2	85	Cgg/Tgg	1/3	0.229137258511608	2	FACETS	1	0.988	1	0.703	0.65	0.757	INDETERMINATE	1	TRUE	0	0.477343909356804	2		336	477	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974762	21974762	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	193	409	0	ENST00000304494.5:c.65G>C	p.Arg22Pro	p.R22P	ENST00000304494	NM_000077.4	22	cGg/cCg	1/3	0.35414648630443	2	FACETS	0.835	0.78	0.891	0.835	0.78	0.891	CLONAL	2	TRUE	0	0.477343909356804	2		409	484	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988691	41988691	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	115	618	0	ENST00000219905.7:c.1483C>T	p.Arg495Ter	p.R495*	ENST00000219905	NM_001164273.1	495	Cga/Tga	3/24	0.245705790281644	3	FACETS	0.906	0.817	0.999	0.453	0.408	0.5	INDETERMINATE	1	TRUE	1	0.477343909356804	3		618	659	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842644	68842644	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	88	792	0	ENST00000261769.5:c.580G>T	p.Gly194Cys	p.G194C	ENST00000261769	NM_004360.3	194	Ggc/Tgc	5/16	1	2	FACETS	0.401	0.354	0.451	0.401	0.354	0.451	SUBCLONAL	1	TRUE	1	0.477343909356804	2		792	920	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691894	30691895	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0056528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	196	489	0	ENST00000295754.5:c.397_398del	p.Phe133LeufsTer6	p.F133Lfs*6	ENST00000295754	NM_003242.5	132	acTTtc/actc	3/7	0.379894746632162	2	FACETS	0.811	0.758	0.866	0.811	0.758	0.866	CLONAL	2	TRUE	0	0.477343909356804	2		489	506	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950087	44950087	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	176	283	0	ENST00000377967.4:c.3857del	p.Pro1286GlnfsTer6	p.P1286Qfs*6	ENST00000377967	NM_021140.2	1286	Cca/ca	26/29	0.320441591712609	2	FACETS	0.973	0.909	1			1	CLONAL	2	TRUE	NA	0.477343909356804	2		283	379	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0056530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	16	325	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.207147123227356	NA		325	363	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0056530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	90	787	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	1	2	FACETS	0.934	0.828	1	0.934	0.828	1	CLONAL	1	FALSE	1	0.207147123227356	2		787	930	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0056531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	45	398	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.335	0.281	0.394	0.335	0.281	0.394	SUBCLONAL	1	TRUE	1	0.478728046567812	2		398	562	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099869	27099869	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	204	693	1	ENST00000324856.7:c.3748C>T	p.Gln1250Ter	p.Q1250*	ENST00000324856	NM_006015.4	1250	Cag/Tag	15/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.478728046567812	2		694	811	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874261	155874261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352822	NA	P-0056531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	399	527	0	ENST00000368323.3:c.270G>A	p.Met90Ile	p.M90I	ENST00000368323	NM_006912.5	90	atG/atA	5/6	0.463813243021547	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.478728046567812	3		527	982	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478878	56478878	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	516	834	0	ENST00000267101.3:c.334G>T	p.Asp112Tyr	p.D112Y	ENST00000267101	NM_001982.3	112	Gat/Tat	3/28	0.463813243021547	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.478728046567812	3		834	1241	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314648	30314648	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	215	620	0	ENST00000262643.3:c.1197C>A	p.Ser399Arg	p.S399R	ENST00000262643	NM_001238.2	399	agC/agA	12/12	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.478728046567812	2		620	849	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25536799	25536799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs959218576	NA	P-0056531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	217	755	1	ENST00000264709.3:c.55C>T	p.Arg19Trp	p.R19W	ENST00000264709	NM_175629.2	19	Cgg/Tgg	2/23	1	2	FACETS	0.96	0.894	1	0.96	0.894	1	CLONAL	1	TRUE	1	0.478728046567812	2		756	944	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098807	178098807	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	56	673	0	ENST00000397062.3:c.238A>G	p.Thr80Ala	p.T80A	ENST00000397062	NM_006164.4	80	Aca/Gca	2/5	0.168705751369412	3	FACETS	0.336	0.287	0.39	0.112	0.095	0.13	INDETERMINATE	1	TRUE	0	0.478728046567812	3		673	863	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098812	178098814	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0056531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	268	680	0	ENST00000397062.3:c.231_233del	p.Asp77del	p.D77del	ENST00000397062	NM_006164.4	77	gaTGAa/gaa	2/5	0.168705751369412	3	FACETS	0.785	0.738	0.833	0.523	0.492	0.555	INDETERMINATE	2	TRUE	0	0.478728046567812	3		680	884	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0056531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	128	359	0	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	0.39502410111061	2	FACETS	0.935	0.863	1	0.935	0.863	1	CLONAL	2	TRUE	0	0.478728046567812	2		359	286	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0056531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	193	416	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	0.39502410111061	2	FACETS	0.814	0.76	0.869	0.814	0.76	0.869	CLONAL	2	TRUE	0	0.478728046567812	2		416	495	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0056531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	10	268	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	0.39502410111061	2	FACETS	0.148	0.099	0.209	0.074	0.049	0.105	SUBCLONAL	1	TRUE	0	0.478728046567812	2		268	283	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371859	55371859	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	56	126	0	ENST00000297316.4:c.552del	p.Glu185SerfsTer202	p.E185Sfs*202	ENST00000297316	NM_022454.3	183	ttC/tt	2/2	1	2	FACETS	0.921	0.797	1	0.921	0.797	1	CLONAL	1	TRUE	1	0.478728046567812	2		126	254	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0056534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	149	306	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.247932044119165	3	FACETS	0.9	0.829	0.973	1	0.986	1	CLONAL	3	TRUE	1	0.26414965123953	3		306	473	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991910	72991910	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	84	752	0	ENST00000268489.5:c.2135G>T	p.Arg712Leu	p.R712L	ENST00000268489	NM_006885.3	712	cGg/cTg	2/10	1	2	FACETS	0.806	0.711	0.908	0.806	0.711	0.908	CLONAL	1	TRUE	1	0.26414965123953	2		752	789	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914046	32914046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358777	NA	P-0056534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	51	574	0	ENST00000380152.3:c.5554G>A	p.Val1852Ile	p.V1852I	ENST00000380152		1852	Gtt/Att	11/27	0.26414965123953	2	FACETS	0.935	0.797	1	0.467	0.398	0.543	CLONAL	1	TRUE	0	0.26414965123953	2		574	413	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429310	78429310	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	149	620	0	ENST00000370768.2:c.1132G>T	p.Glu378Ter	p.E378*	ENST00000370768	NM_003902.3	378	Gaa/Taa	13/20	0.226541917606512	3	FACETS	0.956	0.876	1	0.956	0.876	1	CLONAL	2	TRUE	1	0.26414965123953	3		620	668	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180397	94180397	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1215450873	NA	P-0056534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	173	469	1	ENST00000323929.3:c.1771C>T	p.Gln591Ter	p.Q591*	ENST00000323929	NM_005591.3	591	Caa/Taa	15/20	0.25743879125889	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.26414965123953	2		470	541	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281595	198281595	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	147	542	1	ENST00000335508.6:c.536G>T	p.Gly179Val	p.G179V	ENST00000335508	NM_012433.2	179	gGa/gTa	6/25	0.226541917606512	3	FACETS	0.995	0.912	1	0.995	0.912	1	CLONAL	2	TRUE	1	0.26414965123953	3		543	633	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168716	32168716	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	198	881	0	ENST00000375023.3:c.4207T>C	p.Trp1403Arg	p.W1403R	ENST00000375023	NM_004557.3	1403	Tgg/Cgg	23/30	0.148362441170625	4	FACETS	0.934	0.865	1	0.934	0.865	1	INDETERMINATE	2	TRUE	2	0.26414965123953	4		881	1014	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518189	8518190	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0056534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	62	574	0	ENST00000356435.5:c.1201_1202del	p.Arg401GlyfsTer41	p.R401Gfs*41	ENST00000356435		401	CGg/g	10/35	0.26414965123953	3	FACETS	0.916	0.792	1	0.458	0.396	0.526	CLONAL	1	TRUE	1	0.26414965123953	3		574	580	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524925	8524925	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	91	374	0	ENST00000356435.5:c.679G>T	p.Glu227Ter	p.E227*	ENST00000356435		227	Gag/Tag	7/35	0.26414965123953	3	FACETS	0.894	0.798	0.996	0.894	0.798	0.996	CLONAL	2	TRUE	1	0.26414965123953	3		374	436	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098879	47098879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	152	805	0	ENST00000409792.3:c.6395G>A	p.Arg2132Gln	p.R2132Q	ENST00000409792	NM_014159.6	2132	cGg/cAg	15/21	0.70866677401165	2	FACETS	0.92	0.849	0.992	0.46	0.424	0.496	CLONAL	1	TRUE	0	0.749689100887684	2		805	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0056535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	231	686	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.70866677401165	2	FACETS	0.978	0.938	1	0.978	0.938	1	CLONAL	2	TRUE	0	0.749689100887684	2		686	315	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156936	106156936	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs763386429	NA	P-0056535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	76	481	0	ENST00000380013.4:c.1842del	p.Leu615SerfsTer24	p.L615Sfs*24	ENST00000380013	NM_001127208.2	613	Ggg/gg	3/11	0.285032628614637	3	FACETS	1	0.97	1	0.634	0.565	0.704	INDETERMINATE	1	TRUE	1	0.749689100887684	3		481	220	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31483712	31483712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1561231356	NA	P-0056535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	62	305	0	ENST00000344624.3:c.2020C>T	p.Pro674Ser	p.P674S	ENST00000344624		674	Ccc/Tcc	13/33	0.627463076136125	5	FACETS	0.94	0.816	1	0.313	0.272	0.358	CLONAL	1	TRUE	2	0.749689100887684	5		305	374	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164782	36164782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752616540	NA	P-0056535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	68	952	2	ENST00000300305.3:c.1093G>A	p.Gly365Ser	p.G365S	ENST00000300305		365	Ggc/Agc	8/8	1	2	FACETS	0.413	0.36	0.47	0.413	0.36	0.47	SUBCLONAL	1	TRUE	1	0.749689100887684	2		954	439	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663039	227663039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs529797752	NA	P-0056535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	109	717	0	ENST00000305123.5:c.416G>A	p.Ser139Asn	p.S139N	ENST00000305123	NM_005544.2	139	aGc/aAc	1/2	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.749689100887684	2		717	274	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622216	117622216	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs376903822	NA	P-0056535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	84	483	0	ENST00000368508.3:c.6654C>A	p.Phe2218Leu	p.F2218L	ENST00000368508	NM_002944.2	2218	ttC/ttA	42/43	0.749689100887684	3	FACETS	1	0.896	1	0.502	0.448	0.558	CLONAL	1	TRUE	1	0.749689100887684	3		483	307	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281573	142281573	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	277	634	0	ENST00000350721.4:c.671G>T	p.Arg224Met	p.R224M	ENST00000350721	NM_001184.3	224	aGg/aTg	4/47	0.679632205444761	3	FACETS	0.987	0.955	1	0.987	0.955	1	CLONAL	3	TRUE	0	0.749689100887684	3		634	343	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567832	226567832	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	139	761	0	ENST00000366794.5:c.1334A>G	p.Glu445Gly	p.E445G	ENST00000366794	NM_001618.3	445	gAa/gGa	10/23	0.734044439729594	2	FACETS	0.973	0.896	1	0.487	0.448	0.526	CLONAL	1	TRUE	0	0.749689100887684	2		761	381	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118355000	118355000	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	83	565	1	ENST00000534358.1:c.4189G>T	p.Gly1397Ter	p.G1397*	ENST00000534358	NM_005933.3	1397	Gga/Tga	9/36	0.749689100887684	3	FACETS	0.89	0.792	0.993	0.445	0.396	0.497	CLONAL	1	TRUE	1	0.749689100887684	3		566	342	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934151	48934151	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0056535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	64	348	1	ENST00000267163.4:c.608-2A>T		p.X203_splice	ENST00000267163	NM_000321.2	203			0.609826897955385	1	FACETS	0.962	0.868	1	0.962	0.868	1	CLONAL	1	TRUE	0	0.749689100887684	1		349	111	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135297	30135297	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	90	461	0	ENST00000331968.5:c.521G>T	p.Gly174Val	p.G174V	ENST00000331968	NM_002742.2	174	gGt/gTt	3/18	0.749689100887684	3	FACETS	0.968	0.867	1	0.484	0.433	0.537	CLONAL	1	TRUE	1	0.749689100887684	3		461	341	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304138	91304139	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs367543043	NA	P-0056535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	112	556	7	ENST00000355112.3:c.1544dup	p.Asn515LysfsTer2	p.N515Kfs*2	ENST00000355112	NM_000057.2	512	gga/ggAa	7/22	0.749689100887684	2	FACETS	0.97	0.885	1	0.485	0.442	0.529	CLONAL	1	TRUE	0	0.749689100887684	2		563	308	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104232	2104301	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACTTCTTGGCAGCCGTGTGGGCGACGCTGGCAGGCTCTGCTGATCCTGTGGCTTTTGTCTTTAGGGCGA	GACTTCTTGGCAGCCGTGTGGGCGACGCTGGCAGGCTCTGCTGATCCTGTGGCTTTTGTCTTTAGGGCGA	-	novel	NA	P-0056535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	89	269	0	ENST00000219476.3:c.337-64_342del		p.X113_splice	ENST00000219476	NM_000548.3	113		5/42	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.749689100887684	2		269	185	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2107171	2107171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	171	954	1	ENST00000219476.3:c.840G>A	p.Met280Ile	p.M280I	ENST00000219476	NM_000548.3	280	atG/atA	9/42	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.749689100887684	2		955	454	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152232	11152232	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555788376	NA	P-0056535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	257	589	0	ENST00000358026.2:c.4516G>C	p.Asp1506His	p.D1506H	ENST00000358026	NM_001128849.1	1506	Gac/Cac	31/36	0.734044439729594	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.749689100887684	2		589	327	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812172	212812172	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	61	340	0	ENST00000342788.4:c.404G>C	p.Gly135Ala	p.G135A	ENST00000342788	NM_005235.2	135	gGa/gCa	3/28	1	2	FACETS	0.986	0.87	1	0.986	0.87	1	CLONAL	1	TRUE	1	0.749689100887684	2		340	165	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561549	9561549	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	85	660	0	ENST00000353224.5:c.233A>T	p.Lys78Met	p.K78M	ENST00000353224	NM_177990.2	78	aAg/aTg	4/10	0.475039935217498	6	FACETS	1	0.911	1	0.258	0.228	0.29	CLONAL	1	TRUE	2	0.749689100887684	6		660	549	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359061	81359061	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	97	464	0	ENST00000222390.5:c.900G>T	p.Leu300Phe	p.L300F	ENST00000222390	NM_000601.4	300	ttG/ttT	8/18	0.749689100887684	3	FACETS	1	0.922	1	0.514	0.463	0.568	CLONAL	1	TRUE	1	0.749689100887684	3		464	346	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859875	117859875	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	63	261	0	ENST00000297338.2:c.1760A>G	p.Asn587Ser	p.N587S	ENST00000297338	NM_006265.2	587	aAt/aGt	14/14	0.285032628614637	3	FACETS	1	0.973	1	0.709	0.627	0.793	INDETERMINATE	1	TRUE	1	0.749689100887684	3		261	163	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814737	139814737	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	169	926	0	ENST00000247668.2:c.730C>G	p.Leu244Val	p.L244V	ENST00000247668	NM_021138.3	244	Ctg/Gtg	8/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.749689100887684	2		926	420	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314873	1314873	+	downstream_gene_variant	3'Flank	SNP	G	G	A	novel	NA	P-0056535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	26	391	0				ENST00000400841		-/233			0.744634477609468	3	FACETS	0.686	0.551	0.837	0.343	0.275	0.419	SUBCLONAL	1	TRUE	1	0.749689100887684	3		391	139	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923594	39923594	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	59	790	0	ENST00000378444.4:c.3497C>A	p.Ser1166Tyr	p.S1166Y	ENST00000378444	NM_001123385.1	1166	tCt/tAt	7/15	0.744634477609468	3	FACETS	0.5	0.431	0.574	0.25	0.215	0.287	SUBCLONAL	1	TRUE	1	0.749689100887684	3		790	433	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652498	48652498	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	248	915	0	ENST00000376670.3:c.1169C>A	p.Pro390His	p.P390H	ENST00000376670	NM_002049.3	390	cCc/cAc	6/6	0.744634477609468	3	FACETS	0.887	0.839	0.935	0.887	0.839	0.935	CLONAL	2	TRUE	1	0.749689100887684	3		915	513	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76764100	76764100	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	70	448	0	ENST00000373344.5:c.7208G>T	p.Ser2403Ile	p.S2403I	ENST00000373344	NM_000489.3	2403	aGc/aTc	35/35	0.744634477609468	3	FACETS	0.976	0.861	1	0.488	0.43	0.549	CLONAL	1	TRUE	1	0.749689100887684	3		448	263	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434074	49434076	+	missense_variant	Missense_Mutation	TNP	CCC	CCC	ACG	novel	NA	P-0056535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	117	942	0	ENST00000301067.7:c.7477_7479delinsCGT	p.Gly2493Arg	p.G2493R	ENST00000301067	NM_003482.3	2493	GGG/CGT	31/54	0.70866677401165	2	FACETS	0.9	0.821	0.981	0.45	0.41	0.491	CLONAL	1	TRUE	0	0.749689100887684	2		942	347	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	126	324	0				ENST00000310581	NM_198253.2	-/1132			0.193636969548868	3	FACETS	0.871	0.796	0.949	0.871	0.796	0.949	INDETERMINATE	2	TRUE	1	0.423249252247898	3		324	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	434	762	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.419486665855033	3	FACETS	0.992	0.953	1	0.992	0.953	1	CLONAL	3	TRUE	0	0.423249252247898	3		762	835	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013719	170013719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388201066	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	86	417	0	ENST00000295797.4:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000295797	NM_002740.5	480	Cgc/Tgc	15/18	0.277038253068949	5	FACETS	1	0.973	1	0.447	0.397	0.501	CLONAL	1	TRUE	2	0.423249252247898	5		417	495	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418986	116418986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199763277	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	324	291	0	ENST00000397752.3:c.3497G>A	p.Arg1166Gln	p.R1166Q	ENST00000397752	NM_000245.2	1166	cGa/cAa	17/21	0.423249252247898	6	FACETS	1	0.958	1	1	0.958	1	CLONAL	4	TRUE	2	0.423249252247898	6		291	702	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119585471	119585471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	101	350	0	ENST00000316626.5:c.914C>T	p.Ser305Leu	p.S305L	ENST00000316626		305	tCg/tTg	9/12	0.277038253068949	5	FACETS	0.901	0.81	0.996	0.601	0.54	0.664	CLONAL	2	TRUE	2	0.423249252247898	5		350	433	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504401	8504401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757922864	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	337	446	0	ENST00000356435.5:c.1682G>A	p.Arg561Gln	p.R561Q	ENST00000356435		561	cGa/cAa	12/35	0.419486665855033	3	FACETS	0.914	0.871	0.956	0.914	0.871	0.956	CLONAL	3	TRUE	0	0.423249252247898	3		446	704	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455644	189455644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772867228	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	109	415	0	ENST00000264731.3:c.178G>A	p.Asp60Asn	p.D60N	ENST00000264731	NM_003722.4	60	Gat/Aat	2/14	0.277038253068949	5	FACETS	1	0.983	1	0.499	0.45	0.552	CLONAL	1	TRUE	2	0.423249252247898	5		415	562	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	469	508	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.419486665855033	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.423249252247898	3		508	831	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612083	189612083	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	326	694	0	ENST00000264731.3:c.1835C>T	p.Ser612Phe	p.S612F	ENST00000264731	NM_003722.4	612	tCc/tTc	14/14	0.277038253068949	5	FACETS	1	0.99	1	0.802	0.758	0.846	CLONAL	2	TRUE	2	0.423249252247898	5		694	1047	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561564	9561564	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867333778	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	85	452	0	ENST00000353224.5:c.218G>A	p.Gly73Glu	p.G73E	ENST00000353224	NM_177990.2	73	gGa/gAa	4/10	0.277038253068949	5	FACETS	1	0.947	1	0.374	0.331	0.42	CLONAL	1	TRUE	2	0.423249252247898	5		452	585	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858769	9858769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	142	322	0	ENST00000330684.3:c.2632G>A	p.Glu878Lys	p.E878K	ENST00000330684	NM_001134407.1	878	Gaa/Aaa	13/13	0.394148066771138	2	FACETS	0.984	0.91	1	0.984	0.91	1	CLONAL	2	TRUE	0	0.423249252247898	2		322	341	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306712	41306713	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	268	695	1	ENST00000373198.4:c.946_947delinsAA	p.Gly316Lys	p.G316K	ENST00000373198	NM_133170.3	316	GGg/AAg	7/32	0.277038253068949	5	FACETS	0.982	0.922	1	0.655	0.614	0.696	CLONAL	2	TRUE	2	0.423249252247898	5		696	1054	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453403	40453403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766714643	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	338	898	0	ENST00000345506.4:c.1100C>T	p.Pro367Leu	p.P367L	ENST00000345506	NM_003152.3	367	cCc/cTc	10/20	0.230613588500304	4	FACETS	0.974	0.921	1	0.974	0.921	1	INDETERMINATE	2	TRUE	2	0.423249252247898	4		898	1167	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47735825	47735825	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	163	722	0	ENST00000449228.1:c.35C>T	p.Pro12Leu	p.P12L	ENST00000449228	NM_001127240.2	12	cCa/cTa	1/4	1	2	FACETS	0.878	0.806	0.953	0.878	0.806	0.953	CLONAL	1	TRUE	1	0.423249252247898	2		722	877	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134988	41134988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	112	313	1	ENST00000379561.5:c.640C>T	p.Arg214Cys	p.R214C	ENST00000379561	NM_002015.3	214	Cgt/Tgt	2/3	0.422225179750334	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	2	TRUE	0	0.423249252247898	2		314	263	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141587	202141587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771150445	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	82	406	0	ENST00000358485.4:c.875G>A	p.Arg292Gln	p.R292Q	ENST00000358485	NM_001080125.1	292	cGg/cAg	7/9	0.423821864062792	3	FACETS	0.815	0.72	0.917	0.408	0.36	0.459	CLONAL	1	TRUE	1	0.423249252247898	3		406	576	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623828	28623828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	202	598	1	ENST00000241453.7:c.826C>T	p.His276Tyr	p.H276Y	ENST00000241453	NM_004119.2	276	Cat/Tat	7/24	0.422225179750334	2	FACETS	0.874	0.817	0.933	0.874	0.817	0.933	CLONAL	2	TRUE	0	0.423249252247898	2		599	546	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499354	89499354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	323	444	0	ENST00000336596.2:c.2524C>T	p.Arg842Ter	p.R842*	ENST00000336596	NM_005233.5	842	Cga/Tga	15/17	0.423249252247898	7	FACETS	1	0.963	1			1	CLONAL	3	TRUE	NA	0.423249252247898	7		444	1024	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149241	119149241	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867564832	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	270	590	0	ENST00000264033.4:c.1249C>T	p.Pro417Ser	p.P417S	ENST00000264033	NM_005188.3	417	Cct/Tct	9/16	0.422225179750334	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.423249252247898	2		590	627	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366366	15366366	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	122	607	0	ENST00000263377.2:c.1789C>T	p.Pro597Ser	p.P597S	ENST00000263377	NM_058243.2	597	Ccc/Tcc	10/20	1	2	FACETS	0.843	0.763	0.927	0.843	0.763	0.927	CLONAL	1	TRUE	1	0.423249252247898	2		607	684	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288993	212288993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867944951	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	219	504	0	ENST00000342788.4:c.2753G>A	p.Gly918Glu	p.G918E	ENST00000342788	NM_005235.2	918	gGa/gAa	23/28	0.423821864062792	4	FACETS	1	0.934	1			1	CLONAL	2	TRUE	NA	0.423249252247898	4		504	736	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844777	156844777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56320207	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	157	773	1	ENST00000524377.1:c.1331G>A	p.Arg444Gln	p.R444Q	ENST00000524377	NM_002529.3	444	cGg/cAg	11/17	0.423821864062792	3	FACETS	1	0.936	1	0.512	0.469	0.558	CLONAL	1	TRUE	1	0.423249252247898	3		774	877	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944592	40944592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371723954	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	160	412	0	ENST00000373198.4:c.1910G>A	p.Arg637Gln	p.R637Q	ENST00000373198	NM_133170.3	637	cGg/cAg	12/32	0.277038253068949	5	FACETS	0.986	0.907	1	0.657	0.605	0.711	CLONAL	2	TRUE	2	0.423249252247898	5		412	627	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775629	39775629	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	81	341	0	ENST00000288319.7:c.391C>T	p.Pro131Ser	p.P131S	ENST00000288319	NM_182918.3	131	Cct/Tct	4/10	1	2	FACETS	0.911	0.807	1	0.911	0.807	1	CLONAL	1	TRUE	1	0.423249252247898	2		341	420	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993368	72993368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	363	820	0	ENST00000268489.5:c.677C>T	p.Pro226Leu	p.P226L	ENST00000268489	NM_006885.3	226	cCc/cTc	2/10	0.394148066771138	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.423249252247898	2		820	832	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578317	212578317	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	121	499	0	ENST00000342788.4:c.940G>A	p.Glu314Lys	p.E314K	ENST00000342788	NM_005235.2	314	Gaa/Aaa	8/28	0.423821864062792	4	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.423249252247898	4		499	677	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11204752	11204752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	256	530	1	ENST00000361445.4:c.4825C>T	p.Pro1609Ser	p.P1609S	ENST00000361445	NM_004958.3	1609	Ccc/Tcc	34/58	0.423821864062792	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.423249252247898	3		531	713	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715509	117715509	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	115	298	0	ENST00000368508.3:c.980G>A	p.Gly327Glu	p.G327E	ENST00000368508	NM_002944.2	327	gGa/gAa	10/43	0.423249252247898	2	FACETS	0.818	0.746	0.892	0.818	0.746	0.892	CLONAL	2	TRUE	0	0.423249252247898	2		298	332	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860493	151860493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1380777672	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	629	630	0	ENST00000262189.6:c.10169C>T	p.Pro3390Leu	p.P3390L	ENST00000262189	NM_170606.2	3390	cCc/cTc	43/59	0.423249252247898	8	FACETS	1	0.991	1	0.865	0.834	0.897	CLONAL	4	TRUE	3	0.423249252247898	8		630	1559	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457176	25457176	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149095705	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	142	640	1	ENST00000264709.3:c.2711C>T	p.Pro904Leu	p.P904L	ENST00000264709	NM_175629.2	904	cCg/cTg	23/23	0.423821864062792	3	FACETS	0.891	0.812	0.975	0.446	0.406	0.488	CLONAL	1	TRUE	1	0.423249252247898	3		641	912	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523279	9523279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763590647	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	142	598	2	ENST00000353224.5:c.1958G>A	p.Arg653Gln	p.R653Q	ENST00000353224	NM_177990.2	653	cGg/cAg	9/10	0.277038253068949	5	FACETS	1	0.978	1	0.411	0.374	0.449	CLONAL	1	TRUE	2	0.423249252247898	5		600	890	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058471	69058471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	207	428	0	ENST00000288368.4:c.4115G>A	p.Gly1372Glu	p.G1372E	ENST00000288368	NM_024870.2	1372	gGa/gAa	34/40	0.419486665855033	3	FACETS	0.93	0.875	0.985	0.93	0.875	0.985	CLONAL	3	TRUE	0	0.423249252247898	3		428	425	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518298	8518298	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868403321	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	220	332	0	ENST00000356435.5:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000356435		365	Gaa/Aaa	10/35	0.419486665855033	3	FACETS	0.855	0.804	0.906	0.855	0.804	0.906	CLONAL	3	TRUE	0	0.423249252247898	3		332	491	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284919	15284919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	325	815	2	ENST00000263388.2:c.4696G>A	p.Glu1566Lys	p.E1566K	ENST00000263388	NM_000435.2	1566	Gaa/Aaa	25/33	1	2	FACETS	0.907	0.86	0.954	1	0.996	1	CLONAL	2	TRUE	1	0.423249252247898	2		817	847	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724314	117724314	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	254	604	0	ENST00000368508.3:c.565C>T	p.His189Tyr	p.H189Y	ENST00000368508	NM_002944.2	189	Cat/Tat	6/43	0.423249252247898	2	FACETS	0.909	0.856	0.963	0.909	0.856	0.963	CLONAL	2	TRUE	0	0.423249252247898	2		604	660	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178082	56178082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	88	386	0	ENST00000399503.3:c.3055C>T	p.Pro1019Ser	p.P1019S	ENST00000399503	NM_005921.1	1019	Cct/Tct	14/20	0.193636969548868	3	FACETS	1	0.955	1	0.57	0.507	0.636	INDETERMINATE	1	TRUE	1	0.423249252247898	3		386	442	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271711	15271711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	185	1091	1	ENST00000263388.2:c.6728C>T	p.Pro2243Leu	p.P2243L	ENST00000263388	NM_000435.2	2243	cCt/cTt	33/33	1	2	FACETS	0.816	0.753	0.882	0.816	0.753	0.882	CLONAL	1	TRUE	1	0.423249252247898	2		1092	1071	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543799	212543799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	140	443	0	ENST00000342788.4:c.1600G>A	p.Glu534Lys	p.E534K	ENST00000342788	NM_005235.2	534	Gag/Aag	13/28	0.423821864062792	4	FACETS	1	0.964	1			1	CLONAL	1	TRUE	NA	0.423249252247898	4		443	846	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187527	32187527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1259	336	827	0	ENST00000375023.3:c.1352C>T	p.Ser451Phe	p.S451F	ENST00000375023	NM_004557.3	451	tCc/tTc	8/30	0.423249252247898	6	FACETS	0.919	0.867	0.973	0.46	0.433	0.487	CLONAL	2	TRUE	2	0.423249252247898	6		827	1595	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420193	49420193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	320	723	0	ENST00000301067.7:c.15556C>T	p.His5186Tyr	p.H5186Y	ENST00000301067	NM_003482.3	5186	Cac/Tac	48/54	0.423821864062792	3	FACETS	0.965	0.914	1	0.965	0.914	1	CLONAL	2	TRUE	1	0.423249252247898	3		723	949	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055892	180055892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369919880	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	174	725	1	ENST00000261937.6:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000261937	NM_182925.4	365	Gag/Aag	8/30	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.423249252247898	2		726	650	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434283	49434283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	428	984	1	ENST00000301067.7:c.7270C>T	p.Pro2424Ser	p.P2424S	ENST00000301067	NM_003482.3	2424	Cca/Tca	31/54	0.423821864062792	3	FACETS	0.995	0.949	1	0.995	0.949	1	CLONAL	2	TRUE	1	0.423249252247898	3		985	1232	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557392	29557392	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773578096	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	82	184	0	ENST00000356175.3:c.3105G>A	p.Met1035Ile	p.M1035I	ENST00000356175	NM_000267.3	1035	atG/atA	23/57	0.394148066771138	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	2	TRUE	0	0.423249252247898	2		184	193	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836615	89836615	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145334278	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	361	868	0	ENST00000389301.3:c.2275C>T	p.Pro759Ser	p.P759S	ENST00000389301	NM_000135.2	759	Cct/Tct	25/43	0.423821864062792	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.423249252247898	2		868	826	SUCCESS
APC	324	MSKCC	GRCh37	5	112177073	112177073	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1186128913	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	87	427	0	ENST00000257430.4:c.5782C>T	p.Gln1928Ter	p.Q1928*	ENST00000257430	NM_000038.5	1928	Cag/Tag	16/16	0.193636969548868	3	FACETS	1	0.926	1	0.528	0.469	0.59	INDETERMINATE	1	TRUE	1	0.423249252247898	3		427	472	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381528	81381528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776090604	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	399	358	0	ENST00000222390.5:c.533G>A	p.Arg178Gln	p.R178Q	ENST00000222390	NM_000601.4	178	cGa/cAa	5/18	0.423249252247898	6	FACETS	0.908	0.866	0.949	0.908	0.866	0.949	CLONAL	4	TRUE	2	0.423249252247898	6		358	959	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639025	176639025	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	168	585	0	ENST00000439151.2:c.3625C>T	p.Pro1209Ser	p.P1209S	ENST00000439151	NM_022455.4	1209	Cct/Tct	5/23	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.423249252247898	2		585	684	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209106858	209106858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	227	504	0	ENST00000345146.2:c.710C>T	p.Ser237Phe	p.S237F	ENST00000345146	NM_005896.2	237	tCc/tTc	7/10	0.423821864062792	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.423249252247898	3		504	643	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739622	41739622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	223	439	0	ENST00000242208.4:c.351G>A	p.Met117Ile	p.M117I	ENST00000242208	NM_002192.2	117	atG/atA	2/3	0.243161940794891	5	FACETS	1	0.98	1	0.75	0.7	0.801	INDETERMINATE	2	TRUE	2	0.423249252247898	5		439	766	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1959686	1959686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772239992	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	66	287	0	ENST00000382891.5:c.2908C>T	p.Arg970Cys	p.R970C	ENST00000382891	NM_133335.3	970	Cgt/Tgt	16/22	0.100226812481824	4	FACETS	1	0.937	1			1	INDETERMINATE	1	TRUE	NA	0.423249252247898	4		287	395	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242488	55242488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559717059	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	167	454	0	ENST00000275493.2:c.2258C>T	p.Pro753Leu	p.P753L	ENST00000275493	NM_005228.3	753	cCg/cTg	19/28	0.243161940794891	5	FACETS	1	0.933	1	0.675	0.623	0.729	INDETERMINATE	2	TRUE	2	0.423249252247898	5		454	637	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588644	28588644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	98	427	0	ENST00000241453.7:c.2804C>T	p.Ser935Phe	p.S935F	ENST00000241453	NM_004119.2	935	tCc/tTc	23/24	0.422225179750334	2	FACETS	1	0.901	1	0.502	0.45	0.557	CLONAL	1	TRUE	0	0.423249252247898	2		427	461	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193219826	193219826	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767254478	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	44	295	0	ENST00000367435.3:c.1580C>T	p.Ser527Leu	p.S527L	ENST00000367435	NM_024529.4	527	tCg/tTg	17/17	0.423821864062792	3	FACETS	0.73	0.614	0.857	0.365	0.307	0.429	SUBCLONAL	1	TRUE	1	0.423249252247898	3		295	345	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612094	189612094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	325	695	0	ENST00000264731.3:c.1846C>T	p.Leu616Phe	p.L616F	ENST00000264731	NM_003722.4	616	Ctc/Ttc	14/14	0.277038253068949	5	FACETS	1	0.989	1	0.787	0.744	0.83	CLONAL	2	TRUE	2	0.423249252247898	5		695	1064	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246027122	246027122	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	160	606	1	ENST00000388985.4:c.880G>A	p.Glu294Lys	p.E294K	ENST00000388985		294	Gaa/Aaa	9/12	0.423821864062792	3	FACETS	0.982	0.9	1	0.491	0.45	0.534	CLONAL	1	TRUE	1	0.423249252247898	3		607	933	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371858	116371858	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	216	510	0	ENST00000397752.3:c.1337T>A	p.Ile446Asn	p.I446N	ENST00000397752	NM_000245.2	446	aTt/aAt	3/21	0.423249252247898	6	FACETS	0.884	0.821	0.949	0.442	0.41	0.475	CLONAL	2	TRUE	2	0.423249252247898	6		510	1066	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758815	41758815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	326	849	0	ENST00000301178.4:c.1869G>A	p.Met623Ile	p.M623I	ENST00000301178	NM_021913.4	623	atG/atA	16/20	0.40271295350732	3	FACETS	0.995	0.942	1	0.995	0.942	1	CLONAL	2	TRUE	1	0.423249252247898	3		849	938	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65316545	65316545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	131	584	0	ENST00000342505.4:c.1697C>T	p.Pro566Leu	p.P566L	ENST00000342505	NM_002227.2	566	cCc/cTc	12/25	0.423821864062792	3	FACETS	0.948	0.861	1	0.474	0.43	0.52	CLONAL	1	TRUE	1	0.423249252247898	3		584	791	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115269621	115269621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	117	636	0	ENST00000438362.2:c.1585C>T	p.Pro529Ser	p.P529S	ENST00000438362	NM_001242891.1	529	Cct/Tct	13/20	0.423821864062792	3	FACETS	0.896	0.808	0.988	0.448	0.404	0.494	CLONAL	1	TRUE	1	0.423249252247898	3		636	748	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280169	115280169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372153224	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	239	366	0	ENST00000438362.2:c.463C>T	p.Pro155Ser	p.P155S	ENST00000438362	NM_001242891.1	155	Cct/Tct	5/20	0.423821864062792	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.423249252247898	3		366	663	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458446	120458446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	334	735	0	ENST00000256646.2:c.6899C>T	p.Pro2300Leu	p.P2300L	ENST00000256646	NM_024408.3	2300	cCc/cTc	34/34	0.423821864062792	3	FACETS	0.996	0.944	1	0.996	0.944	1	CLONAL	2	TRUE	1	0.423249252247898	3		735	960	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100300	8100301	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	163	940	1	ENST00000346208.3:c.274_275delinsAA	p.Gly92Lys	p.G92K	ENST00000346208		92	GGa/AAa	3/6	1	2	FACETS	0.846	0.777	0.919	0.846	0.777	0.919	CLONAL	1	TRUE	1	0.423249252247898	2		941	910	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256231	123256231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751077552	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	160	373	0	ENST00000358487.5:c.1678C>T	p.Leu560Phe	p.L560F	ENST00000358487	NM_000141.4	560	Ctc/Ttc	13/18	0.423821864062792	3	FACETS	0.933	0.862	1	0.933	0.862	1	CLONAL	2	TRUE	1	0.423249252247898	3		373	491	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325092	123325117	+	frameshift_variant	Frame_Shift_Del	DEL	AAGTGCACCCCATCCTTAGTCCAACT	AAGTGCACCCCATCCTTAGTCCAACT	-	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	122	752	0	ENST00000358487.5:c.211_236del	p.Ser71GlyfsTer5	p.S71Gfs*5	ENST00000358487	NM_000141.4	71	AGTTGGACTAAGGATGGGGTGCACTTg/g	3/18	0.423821864062792	3	FACETS	0.794	0.717	0.875	0.397	0.358	0.438	SUBCLONAL	1	TRUE	1	0.423249252247898	3		752	880	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285576	46285576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	59	365	0	ENST00000334344.6:c.4936C>T	p.Pro1646Ser	p.P1646S	ENST00000334344	NM_152641.2	1646	Ccc/Tcc	17/21	0.423821864062792	3	FACETS	0.787	0.679	0.904	0.394	0.339	0.452	CLONAL	1	TRUE	1	0.423249252247898	3		365	429	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865306	57865306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	145	787	0	ENST00000228682.2:c.2783C>T	p.Pro928Leu	p.P928L	ENST00000228682	NM_005269.2	928	cCc/cTc	12/12	0.423821864062792	3	FACETS	0.992	0.905	1	0.496	0.452	0.542	CLONAL	1	TRUE	1	0.423249252247898	3		787	837	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256187	133256188	+	missense_variant	Missense_Mutation	DNP	GT	GT	AA	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	216	571	0	ENST00000320574.5:c.473_474delinsTT	p.His158Leu	p.H158L	ENST00000320574	NM_006231.2	158	cAC/cTT	6/49	0.423821864062792	3	FACETS	0.813	0.758	0.869	0.813	0.758	0.869	CLONAL	2	TRUE	1	0.423249252247898	3		571	761	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562716	95562716	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	77	382	0	ENST00000393063.1:c.4541C>T	p.Pro1514Leu	p.P1514L	ENST00000393063	NM_030621.3	1514	cCt/cTt	24/28	NA	2	FACETS	0.786	0.692	0.886			1	INDETERMINATE	1	TRUE	NA	0.423249252247898	2		382	463	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675098	40675098	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	338	819	0	ENST00000249776.8:c.62A>T	p.Glu21Val	p.E21V	ENST00000249776	NM_033286.3	21	gAg/gTg	1/9	0.371646419853523	2	FACETS	0.992	0.943	1	0.992	0.943	1	CLONAL	2	TRUE	0	0.423249252247898	2		819	805	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423523	88423523	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	137	662	0	ENST00000360948.2:c.2312G>A	p.Trp771Ter	p.W771*	ENST00000360948	NM_001012338.2	771	tGg/tAg	18/19	0.423821864062792	3	FACETS	0.806	0.732	0.884	0.403	0.366	0.442	CLONAL	1	TRUE	1	0.423249252247898	3		662	973	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669605	88669605	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	169	335	0	ENST00000360948.2:c.1294-1G>A		p.X432_splice	ENST00000360948	NM_001012338.2	432			0.423821864062792	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.423249252247898	3		335	438	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110740	2110740	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	323	803	0	ENST00000219476.3:c.1045T>C	p.Tyr349His	p.Y349H	ENST00000219476	NM_000548.3	349	Tat/Cat	11/42	0.423821864062792	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.423249252247898	2		803	724	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131364	17131365	+	missense_variant	Missense_Mutation	DNP	GA	GA	AC	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	457	829	2	ENST00000285071.4:c.87_88delinsGT	p.Pro30Ser	p.P30S	ENST00000285071	NM_144997.5	29	ctTCct/ctGTct	4/14	0.419486665855033	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	0	0.423249252247898	3		831	865	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33446575	33446575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555570487	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	261	628	0	ENST00000345365.6:c.58C>T	p.Leu20Phe	p.L20F	ENST00000345365	NM_002878.3	20	Ctc/Ttc	1/10	0.394148066771138	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.423249252247898	2		628	606	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38506169	38506170	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	215	617	0	ENST00000254066.5:c.461_462delinsTT	p.Ser154Phe	p.S154F	ENST00000254066	NM_000964.3	154	tCC/tTT	4/9	0.230613588500304	4	FACETS	0.928	0.865	0.993	0.928	0.865	0.993	INDETERMINATE	2	TRUE	2	0.423249252247898	4		617	779	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740729	58740729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	285	564	0	ENST00000305921.3:c.1634C>T	p.Pro545Leu	p.P545L	ENST00000305921	NM_003620.3	545	cCc/cTc	6/6	0.243161940794891	5	FACETS	1	0.989	1	0.805	0.758	0.852	INDETERMINATE	2	TRUE	2	0.423249252247898	5		564	912	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615701	1615701	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	326	998	0	ENST00000344749.5:c.1570C>T	p.Pro524Ser	p.P524S	ENST00000344749	NM_001136139.2	524	Ccc/Tcc	17/19	1	2	FACETS	0.778	0.736	0.82	1	0.995	1	SUBCLONAL	2	TRUE	1	0.423249252247898	2		998	990	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302560	15302561	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	235	824	0	ENST00000263388.2:c.797_798delinsAT	p.Trp266Tyr	p.W266Y	ENST00000263388	NM_000435.2	266	tGG/tAT	5/33	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.423249252247898	2		824	751	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349196	15349196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	76	470	1	ENST00000263377.2:c.4081C>T	p.Leu1361Phe	p.L1361F	ENST00000263377	NM_058243.2	1361	Ctt/Ttt	20/20	1	2	FACETS	0.813	0.715	0.916	0.813	0.715	0.916	CLONAL	1	TRUE	1	0.423249252247898	2		471	442	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967786	18967786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	186	899	2	ENST00000262803.5:c.1925C>T	p.Thr642Ile	p.T642I	ENST00000262803	NM_002911.3	642	aCc/aTc	14/24	0.40271295350732	3	FACETS	1	0.973	1	0.558	0.515	0.603	CLONAL	1	TRUE	1	0.423249252247898	3		901	954	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753119	42753119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	338	836	1	ENST00000222329.4:c.1145C>T	p.Pro382Leu	p.P382L	ENST00000222329	NM_006494.2	382	cCc/cTc	4/4	0.40271295350732	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.423249252247898	3		837	909	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42788911	42788911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1368159656	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	120	534	0	ENST00000575354.2:c.55C>T	p.Leu19Phe	p.L19F	ENST00000575354	NM_015125.3	19	Ctc/Ttc	1/20	0.40271295350732	3	FACETS	0.917	0.829	1	0.459	0.414	0.506	CLONAL	1	TRUE	1	0.423249252247898	3		534	749	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140314	50140314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756447228	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	131	659	0	ENST00000246792.3:c.227C>T	p.Pro76Leu	p.P76L	ENST00000246792	NM_006270.3	76	cCa/cTa	2/6	1	2	FACETS	0.826	0.751	0.906	0.826	0.751	0.906	CLONAL	1	TRUE	1	0.423249252247898	2		659	749	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967278	25967279	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	186	542	0	ENST00000435504.4:c.1927_1928delinsTT	p.Pro643Leu	p.P643L	ENST00000435504		643	CCa/TTa	13/13	0.423821864062792	3	FACETS	0.921	0.856	0.988	0.921	0.856	0.988	CLONAL	2	TRUE	1	0.423249252247898	3		542	578	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198283264	198283264	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	107	584	0	ENST00000335508.6:c.464T>G	p.Val155Gly	p.V155G	ENST00000335508	NM_012433.2	155	gTa/gGa	5/25	0.423821864062792	3	FACETS	0.912	0.819	1	0.456	0.409	0.505	CLONAL	1	TRUE	1	0.423249252247898	3		584	672	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141691	202141691	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	120	274	1	ENST00000358485.4:c.979G>A	p.Gly327Arg	p.G327R	ENST00000358485	NM_001080125.1	327	Ggg/Agg	7/9	0.423821864062792	3	FACETS	0.931	0.85	1	0.931	0.85	1	CLONAL	2	TRUE	1	0.423249252247898	3		275	369	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488678	212488678	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	224	459	0	ENST00000342788.4:c.2171T>C	p.Leu724Pro	p.L724P	ENST00000342788	NM_005235.2	724	cTt/cCt	18/28	0.423821864062792	4	FACETS	1	0.98	1			1	CLONAL	2	TRUE	NA	0.423249252247898	4		459	676	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980867	40980868	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	272	591	1	ENST00000373198.4:c.1618_1619delinsAA	p.Gly540Lys	p.G540K	ENST00000373198	NM_133170.3	540	GGg/AAg	10/32	0.277038253068949	5	FACETS	1	0.985	1	0.759	0.713	0.805	CLONAL	2	TRUE	2	0.423249252247898	5		592	923	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447581	12447581	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	228	547	0	ENST00000287820.6:c.819+1G>A		p.X273_splice	ENST00000287820	NM_015869.4	273			0.423249252247898	2	FACETS	0.902	0.847	0.959	0.902	0.847	0.959	CLONAL	2	TRUE	0	0.423249252247898	2		547	597	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998049	169998049	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1458333589	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	198	686	0	ENST00000295797.4:c.740C>T	p.Ser247Phe	p.S247F	ENST00000295797	NM_002740.5	247	tCc/tTc	9/18	0.277038253068949	5	FACETS	0.841	0.78	0.905	0.561	0.52	0.604	CLONAL	2	TRUE	2	0.423249252247898	5		686	909	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155297	185155297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767617021	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	300	525	0	ENST00000265026.3:c.538G>A	p.Gly180Arg	p.G180R	ENST00000265026	NM_004721.4	180	Gga/Aga	3/14	0.277038253068949	5	FACETS	0.881	0.832	0.93	0.881	0.832	0.93	CLONAL	3	TRUE	2	0.423249252247898	5		525	877	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191275	185191275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	266	623	0	ENST00000265026.3:c.2156G>A	p.Gly719Asp	p.G719D	ENST00000265026	NM_004721.4	719	gGt/gAt	11/14	0.277038253068949	5	FACETS	1	0.987	1	0.789	0.742	0.838	CLONAL	2	TRUE	2	0.423249252247898	5		623	868	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521364	187521364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	286	633	0	ENST00000441802.2:c.11791C>T	p.His3931Tyr	p.H3931Y	ENST00000441802	NM_005245.3	3931	Cat/Tat	22/27	0.330576461017254	3	FACETS	1	0.988	1	0.773	0.731	0.815	CLONAL	2	TRUE	0	0.423249252247898	3		633	706	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	231100	231100	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1560992565	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	94	393	0	ENST00000264932.6:c.880C>T	p.Gln294Ter	p.Q294*	ENST00000264932	NM_004168.2	294	Cag/Tag	7/15	0.193636969548868	3	FACETS	1	0.901	1	0.505	0.45	0.563	INDETERMINATE	1	TRUE	1	0.423249252247898	3		393	533	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38955761	38955761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	101	419	0	ENST00000357387.3:c.2545G>A	p.Glu849Lys	p.E849K	ENST00000357387	NM_152756.3	849	Gaa/Aaa	26/38	0.193636969548868	3	FACETS	1	0.962	1	0.576	0.517	0.638	INDETERMINATE	1	TRUE	1	0.423249252247898	3		419	502	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958600	38958600	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	63	204	0	ENST00000357387.3:c.2365C>T	p.Gln789Ter	p.Q789*	ENST00000357387	NM_152756.3	789	Cag/Tag	24/38	0.193636969548868	3	FACETS	1	0.957	1	0.618	0.539	0.702	INDETERMINATE	1	TRUE	1	0.423249252247898	3		204	292	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750471	57750471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	111	546	0	ENST00000274289.3:c.1997C>T	p.Ser666Leu	p.S666L	ENST00000274289	NM_006622.3	666	tCa/tTa	14/14	0.193636969548868	3	FACETS	1	0.978	1	0.654	0.591	0.72	INDETERMINATE	1	TRUE	1	0.423249252247898	3		546	486	SUCCESS
APC	324	MSKCC	GRCh37	5	112179642	112179642	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	131	371	0	ENST00000257430.4:c.8351T>C	p.Phe2784Ser	p.F2784S	ENST00000257430	NM_000038.5	2784	tTt/tCt	16/16	0.193636969548868	3	FACETS	1	0.985	1	0.714	0.651	0.78	INDETERMINATE	1	TRUE	1	0.423249252247898	3		371	525	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520318	176520318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs965587225	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	121	598	0	ENST00000292408.4:c.1237C>T	p.Pro413Ser	p.P413S	ENST00000292408	NM_213647.1	413	Cct/Tct	9/18	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.423249252247898	2		598	522	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180600	32180600	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	239	508	0	ENST00000375023.3:c.2526+1G>A		p.X842_splice	ENST00000375023	NM_004557.3	842			0.423249252247898	6	FACETS	1	0.98	1	0.558	0.521	0.595	CLONAL	2	TRUE	2	0.423249252247898	6		508	935	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184844	32184844	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	226	608	0	ENST00000375023.3:c.1739G>A	p.Gly580Asp	p.G580D	ENST00000375023	NM_004557.3	580	gGc/gAc	11/30	0.423249252247898	6	FACETS	0.99	0.922	1	0.495	0.461	0.53	CLONAL	2	TRUE	2	0.423249252247898	6		608	996	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190486	32190486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	361	866	0	ENST00000375023.3:c.253C>T	p.Pro85Ser	p.P85S	ENST00000375023	NM_004557.3	85	Ccc/Tcc	3/30	0.423249252247898	6	FACETS	0.981	0.927	1	0.49	0.463	0.518	CLONAL	2	TRUE	2	0.423249252247898	6		866	1606	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803542	32803542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	309	602	0	ENST00000374899.4:c.617C>T	p.Ser206Phe	p.S206F	ENST00000374899	NM_018833.2	206	tCt/tTt	4/12	0.423249252247898	6	FACETS	1	0.955	1	0.508	0.478	0.539	CLONAL	2	TRUE	2	0.423249252247898	6		602	1327	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139195	37139195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	253	552	0	ENST00000373509.5:c.535C>T	p.Arg179Cys	p.R179C	ENST00000373509	NM_002648.3	179	Cgc/Tgc	4/6	0.423249252247898	6	FACETS	0.889	0.831	0.95	0.445	0.415	0.475	CLONAL	2	TRUE	2	0.423249252247898	6		552	1241	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554952	106554952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528735730	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	275	537	0	ENST00000369096.4:c.2069C>T	p.Ser690Phe	p.S690F	ENST00000369096	NM_001198.3	690	tCc/tTc	7/7	0.423249252247898	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.423249252247898	2		537	633	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017540	112017540	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	200	500	0	ENST00000368678.4:c.973C>T	p.Gln325Ter	p.Q325*	ENST00000368678		325	Cag/Tag	9/13	0.423249252247898	2	FACETS	0.847	0.79	0.904	0.847	0.79	0.904	CLONAL	2	TRUE	0	0.423249252247898	2		500	558	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710675	117710675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	185	376	0	ENST00000368508.3:c.1597G>A	p.Asp533Asn	p.D533N	ENST00000368508	NM_002944.2	533	Gac/Aac	12/43	0.423249252247898	2	FACETS	0.996	0.93	1	0.996	0.93	1	CLONAL	2	TRUE	0	0.423249252247898	2		376	439	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163820	152163820	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	255	563	0	ENST00000206249.3:c.541G>A	p.Glu181Lys	p.E181K	ENST00000206249	NM_000125.3	181	Gag/Aag	2/8	0.423249252247898	2	FACETS	0.946	0.892	1	0.946	0.892	1	CLONAL	2	TRUE	0	0.423249252247898	2		563	637	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976856	2976857	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	220	650	1	ENST00000396946.4:c.1155_1156delinsTT	p.Arg386Ter	p.R386*	ENST00000396946	NM_032415.4	385	tcCCga/tcTTga	9/25	0.350859887781753	5	FACETS	0.86	0.8	0.922	0.573	0.533	0.615	CLONAL	2	TRUE	2	0.423249252247898	5		651	988	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983927	2983927	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	178	742	1	ENST00000396946.4:c.603C>A	p.Asn201Lys	p.N201K	ENST00000396946	NM_032415.4	201	aaC/aaA	5/25	0.350859887781753	5	FACETS	1	0.956	1	0.353	0.325	0.384	CLONAL	1	TRUE	2	0.423249252247898	5		743	1297	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279432	38279432	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	396	555	0	ENST00000425967.3:c.1057G>A	p.Glu353Lys	p.E353K	ENST00000425967	NM_001174067.1	353	Gag/Aag	9/19	0.419486665855033	3	FACETS	0.998	0.957	1	0.998	0.957	1	CLONAL	3	TRUE	0	0.423249252247898	3		555	757	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956741	68956741	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	463	620	0	ENST00000288368.4:c.859G>A	p.Ala287Thr	p.A287T	ENST00000288368	NM_024870.2	287	Gca/Aca	8/40	0.419486665855033	3	FACETS	0.921	0.885	0.958	0.921	0.885	0.958	CLONAL	3	TRUE	0	0.423249252247898	3		620	959	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339236	87339236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	380	450	0	ENST00000277120.3:c.818G>A	p.Gly273Glu	p.G273E	ENST00000277120		273	gGa/gAa	8/19	0.419486665855033	3	FACETS	0.958	0.917	0.999	0.958	0.917	0.999	CLONAL	3	TRUE	0	0.423249252247898	3		450	757	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355565	15355567	+	missense_variant	Missense_Mutation	TNP	GAG	GAG	AAA	novel	NA	P-0056536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	139	672	0	ENST00000263377.2:c.2165_2167delinsTTT	p.Ala722_Pro723delinsValSer	p.A722_P723delinsVS	ENST00000263377	NM_058243.2	722	gCTCcg/gTTTcg	12/20	1	2	FACETS	0.835	0.76	0.912	0.835	0.76	0.912	CLONAL	1	TRUE	1	0.423249252247898	2		672	787	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589537	67589563	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GATCAAGTTGTCAAAGAAGATAATATT	GATCAAGTTGTCAAAGAAGATAATATT	-	novel	NA	P-0056537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	39	199	0	ENST00000274335.5:c.1302_1328del	p.Asp434_Ile442del	p.D434_I442del	ENST00000274335		434	GATCAAGTTGTCAAAGAAGATAATATT/-	10/15	1	2	FACETS	0.819	0.688	0.961	0.819	0.688	0.961	CLONAL	1	TRUE	1	0.535149649914166	2		199	178	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591148	67591149	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGA	novel	NA	P-0056537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	106	376	0	ENST00000274335.5:c.1744_1745+1dup		p.L582_M583dup	ENST00000274335		582	ttg/tTGAtg	12/15	1	2	FACETS	0.876	0.79	0.967	0.876	0.79	0.967	CLONAL	1	TRUE	1	0.535149649914166	2		376	452	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	347	965	3	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.535149649914166	2		968	1251	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265801	16265801	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	243	646	0	ENST00000375759.3:c.10874T>C	p.Val3625Ala	p.V3625A	ENST00000375759	NM_015001.2	3625	gTg/gCg	15/15	1	2	FACETS	0.995	0.931	1	0.995	0.931	1	CLONAL	1	TRUE	1	0.535149649914166	2		646	913	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023253	27023350	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCCGGCGGCGGCGGTGGCGGCAGCAGCGATGGGGTGGGGGCGCCTCCTCACTCAGCCGCGGCCGCCTTGCCGCCCCCAGCCTACGGCTTCGGGCAA	CGCCCGGCGGCGGCGGTGGCGGCAGCAGCGATGGGGTGGGGGCGCCTCCTCACTCAGCCGCGGCCGCCTTGCCGCCCCCAGCCTACGGCTTCGGGCAA	-	novel	NA	P-0056537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	152	230	0	ENST00000324856.7:c.360_457del	p.Pro121LeufsTer246	p.P121Lfs*246	ENST00000324856	NM_006015.4	120	cCGCCCGGCGGCGGCGGTGGCGGCAGCAGCGATGGGGTGGGGGCGCCTCCTCACTCAGCCGCGGCCGCCTTGCCGCCCCCAGCCTACGGCTTCGGGCAA/c	1/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.535149649914166	2		230	389	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023856	27023862	+	frameshift_variant	Frame_Shift_Del	DEL	AGGACGG	AGGACGG	-	novel	NA	P-0056537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	83	270	0	ENST00000324856.7:c.962_968del	p.Gln321ArgfsTer40	p.Q321Rfs*40	ENST00000324856	NM_006015.4	321	cAGGACGGg/cg	1/20	1	2	FACETS	0.789	0.701	0.883	0.789	0.701	0.883	SUBCLONAL	1	TRUE	1	0.535149649914166	2		270	393	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624259	89624259	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	213	279	0	ENST00000371953.3:c.35del	p.Asn12ThrfsTer12	p.N12Tfs*12	ENST00000371953	NM_000314.4	11	agA/ag	1/9	0.535149649914166	2	FACETS	0.993	0.937	1	0.993	0.937	1	CLONAL	2	TRUE	0	0.535149649914166	2		279	401	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188404	32188404	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	215	762	2	ENST00000375023.3:c.937G>T	p.Glu313Ter	p.E313*	ENST00000375023	NM_004557.3	313	Gaa/Taa	6/30	1	2	FACETS	0.994	0.927	1	0.994	0.927	1	CLONAL	1	TRUE	1	0.535149649914166	2		764	808	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349553	70349553	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	225	720	0	ENST00000374080.3:c.3715G>T	p.Gly1239Cys	p.G1239C	ENST00000374080		1239	Ggc/Tgc	27/45	1	2	FACETS	0.967	0.902	1	0.967	0.902	1	CLONAL	1	TRUE	1	0.535149649914166	2		720	870	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0056538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	65	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.0682532075130848	3	FACETS	1	0.967	1	0.689	0.599	0.786	INDETERMINATE	1	FALSE	1	0.227892399932139	3		298	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs878854073	NA	P-0056538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	104	567	0	ENST00000269305.4:c.673-1G>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.227892399932139	2		567	653	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964985	25964985	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	71	638	0	ENST00000435504.4:c.4221G>T	p.Met1407Ile	p.M1407I	ENST00000435504		1407	atG/atT	13/13	1	2	FACETS	0.873	0.761	0.993	0.873	0.761	0.993	CLONAL	1	FALSE	1	0.227892399932139	2		638	714	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573605	48573606	+	frameshift_variant	Frame_Shift_Ins	INS	AA	AA	TAGG	novel	NA	P-0056538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	40	262	0	ENST00000342988.3:c.189_190delinsTAGG	p.Asn64ArgfsTer31	p.N64Rfs*31	ENST00000342988	NM_005359.5	63	acAAat/acTAGGat	2/12	0.172223560578333	2	FACETS	1	0.93	1	0.614	0.512	0.725	CLONAL	1	FALSE	0	0.227892399932139	2		262	286	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0056539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	13	330	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.717464502734512	4	FACETS	0.24	0.17	0.324	0.12	0.085	0.162	SUBCLONAL	1	TRUE	2	0.702339404584062	4		330	263	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482425	56482425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	36	625	1	ENST00000267101.3:c.973G>A	p.Gly325Arg	p.G325R	ENST00000267101	NM_001982.3	325	Gga/Aga	8/28	0.717464502734512	4	FACETS	0.545	0.449	0.652	0.273	0.224	0.326	SUBCLONAL	1	TRUE	2	0.702339404584062	4		626	320	SUCCESS
APC	324	MSKCC	GRCh37	5	112175530	112175530	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	48	390	0	ENST00000257430.4:c.4240del	p.Val1414Ter	p.V1414*	ENST00000257430	NM_000038.5	1413	atG/at	16/16	0.419223786768176	5	FACETS	1	0.944	1	0.41	0.35	0.475	INDETERMINATE	1	TRUE	2	0.702339404584062	5		390	228	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89335006	89335006	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	14	116	0	ENST00000301030.4:c.7872G>A	p.Trp2624Ter	p.W2624*	ENST00000301030	NM_001256183.1	2624	tgG/tgA	13/13	0.275265617851392	2	FACETS	0.699	0.509	0.924	0.349	0.254	0.462	SUBCLONAL	1	FALSE	0	0.323217890959974	2		116	124	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163514	47163532	+	frameshift_variant	Frame_Shift_Del	DEL	TATAAATCATCAAAATGAT	TATAAATCATCAAAATGAT	-	novel	NA	P-0056540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	45	394	0	ENST00000409792.3:c.2594_2612del	p.Asn865IlefsTer20	p.N865Ifs*20	ENST00000409792	NM_014159.6	865	aATCATTTTGATGATTTATAt/at	3/21	1	2	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	FALSE	1	0.323217890959974	2		394	276	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440274	52440274	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs864622592	NA	P-0056540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	55	710	0	ENST00000460680.1:c.778C>T	p.Gln260Ter	p.Q260*	ENST00000460680	NM_004656.3	260	Cag/Tag	9/17	0.323217890959974	1	FACETS	0.524	0.449	0.607	0.524	0.449	0.607	SUBCLONAL	1	FALSE	0	0.323217890959974	1		710	544	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0056541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	47	330	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.0494100734587746	3	FACETS	0.783	0.662	0.916	0.783	0.662	0.916	INDETERMINATE	2	TRUE	1	0.16	3		330	405	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554093	63554093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555583315	NA	P-0056541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	47	810	0	ENST00000307078.5:c.646G>A	p.Gly216Arg	p.G216R	ENST00000307078	NM_004655.3	216	Ggg/Agg	2/11	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.16	2		810	530	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417386	139417386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754236791	NA	P-0056541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	29	920	2	ENST00000277541.6:c.658G>A	p.Val220Met	p.V220M	ENST00000277541	NM_017617.3	220	Gtg/Atg	4/34	1	2	FACETS	0.839	0.673	1	0.839	0.673	1	CLONAL	1	TRUE	1	0.16	2		922	432	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439789	51439789	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	42	527	0	ENST00000262662.1:c.355del	p.Val119TrpfsTer5	p.V119Wfs*5	ENST00000262662		118	gtG/gt	4/4	0.0957589562178178	3	FACETS	1	0.946	1	0.675	0.564	0.798	INDETERMINATE	1	TRUE	1	0.16	3		527	420	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666356	206666356	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	31	811	1	ENST00000367120.3:c.1836G>T	p.Arg612Ser	p.R612S	ENST00000367120	NM_014002.3	612	agG/agT	19/22	1		FACETS		0.61	0.921				CLONAL	1	TRUE	1	0.16	2		812	513	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047146	77047146	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	28	663	0	ENST00000356341.3:c.1398T>G	p.Asn466Lys	p.N466K	ENST00000356341	NM_002576.4	466	aaT/aaG	13/15	1	2	FACETS	0.879	0.703	1	0.879	0.703	1	CLONAL	1	TRUE	1	0.16	2		663	398	SUCCESS
BLM	641	MSKCC	GRCh37	15	91290666	91290666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752755503	NA	P-0056541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	27	493	0	ENST00000355112.3:c.44G>A	p.Arg15His	p.R15H	ENST00000355112	NM_000057.2	15	cGt/cAt	2/22	1	2	FACETS	0.959	0.763	1	0.959	0.763	1	CLONAL	1	TRUE	1	0.16	2		493	352	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445110	89445110	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	13	325	0	ENST00000336596.2:c.1430A>T	p.Lys477Met	p.K477M	ENST00000336596	NM_005233.5	477	aAg/aTg	6/17	0.0957589562178178	3	FACETS	0.716	0.511	0.967	0.358	0.255	0.484	INDETERMINATE	1	TRUE	1	0.16	3		325	245	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0056544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	94	522	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.202996979638402	4	FACETS	1	0.972	1	0.645	0.574	0.721	CLONAL	1	TRUE	2	0.250732743822328	4		522	727	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	52	562	0	ENST00000346208.3:c.878T>A	p.Met293Lys	p.M293K	ENST00000346208		293	aTg/aAg	4/6	NA	2	FACETS	0.566	0.481	0.66			1	INDETERMINATE	1	TRUE	NA	0.250732743822328	2		562	733	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943662	9943662	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560839364	NA	P-0056544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	118	702	0	ENST00000330684.3:c.1279G>A	p.Glu427Lys	p.E427K	ENST00000330684	NM_001134407.1	427	Gag/Aag	5/13	0.202996979638402	4	FACETS	1	0.977	1	0.641	0.577	0.708	CLONAL	1	TRUE	2	0.250732743822328	4		702	919	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017824	31017824	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576523117	NA	P-0056544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	64	814	0	ENST00000375687.4:c.686C>T	p.Pro229Leu	p.P229L	ENST00000375687	NM_015338.5	229	cCg/cTg	8/13	0.110656503282703	3	FACETS	0.589	0.509	0.677	0.295	0.254	0.339	INDETERMINATE	1	TRUE	1	0.250732743822328	3		814	975	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179441	56179441	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	49	257	0	ENST00000399503.3:c.3754G>C	p.Gly1252Arg	p.G1252R	ENST00000399503	NM_005921.1	1252	Gga/Cga	15/20	0.20024377793231	3	FACETS	1	0.935	1	0.596	0.506	0.694	CLONAL	1	TRUE	1	0.250732743822328	3		257	369	SUCCESS
APC	324	MSKCC	GRCh37	5	112173324	112173332	+	inframe_deletion	In_Frame_Del	DEL	GTAATGCAT	GTAATGCAT	-	novel	NA	P-0056544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	30	260	0	ENST00000257430.4:c.2035_2043del	p.Asn679_Cys681del	p.N679_C681del	ENST00000257430	NM_000038.5	678	aGTAATGCATgt/agt	16/16	0.20024377793231	3	FACETS	0.99	0.801	1	0.495	0.4	0.602	CLONAL	1	TRUE	1	0.250732743822328	3		260	272	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0056552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	138	330	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	0.96	0.881	1			1	INDETERMINATE	1	TRUE	NA	0.626149851589612	2		330	459	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11206807	11206807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202187935	NA	P-0056552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	187	577	0	ENST00000361445.4:c.4612C>T	p.Arg1538Trp	p.R1538W	ENST00000361445	NM_004958.3	1538	Cgg/Tgg	32/58	1	2	FACETS	0.997	0.926	1	0.997	0.926	1	CLONAL	1	TRUE	1	0.626149851589612	2		577	599	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	113	324	0				ENST00000310581	NM_198253.2	-/1132			0.437292101134883	3	FACETS	1	0.912	1	0.502	0.456	0.55	INDETERMINATE	1	TRUE	1	0.838467951408385	3		324	381	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894230	NA	P-0056553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	270	587	0	ENST00000451590.1:c.35G>A	p.Gly12Asp	p.G12D	ENST00000451590	NM_001130442.1	12	gGc/gAc	2/5	1	2	FACETS	0.86	0.811	0.91	0.86	0.811	0.91	CLONAL	1	TRUE	1	0.838467951408385	2		587	749	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860568	45860568	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	456	894	0	ENST00000391945.4:c.1439C>A	p.Thr480Asn	p.T480N	ENST00000391945	NM_000400.3	480	aCc/aAc	15/23	1	2	FACETS	0.981	0.939	1	0.981	0.939	1	CLONAL	1	TRUE	1	0.838467951408385	2		894	1109	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370672	225370672	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0056553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	197	264	0	ENST00000264414.4:c.1206+1G>C		p.X402_splice	ENST00000264414	NM_003590.4	402			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.838467951408385	2		264	409	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526225	189526226	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCCATCCCCTCCAACACCGACTACCCAGGCCCG	novel	NA	P-0056553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	258	715	0	ENST00000264731.3:c.490_522dup	p.Ala164_Pro174dup	p.A164_P174dup	ENST00000264731	NM_003722.4	164	-/GCCATCCCCTCCAACACCGACTACCCAGGCCCG	4/14	1	2	FACETS	0.554	0.519	0.591	0.554	0.519	0.591	SUBCLONAL	1	TRUE	1	0.838467951408385	2		715	1110	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249002	55249003	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGTGGA	rs397517109	NA	P-0056553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	279	694	0	ENST00000275493.2:c.2303_2311dup	p.Ser768_Asp770dup	p.S768_D770dup	ENST00000275493	NM_005228.3	768	gcc/gcCAGCGTGGAc	20/28	1	2	FACETS	0.771	0.726	0.817	0.771	0.726	0.817	SUBCLONAL	1	TRUE	1	0.838467951408385	2		694	863	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556886	29556886	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	47	239	0	ENST00000356175.3:c.2884G>T	p.Glu962Ter	p.E962*	ENST00000356175	NM_000267.3	962	Gaa/Taa	22/57	0.47729318841348	1	FACETS	0.931	0.8	1	0.931	0.8	1	CLONAL	1	TRUE	0	0.47729318841348	1		239	161	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857270	9857270	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	144	749	0	ENST00000330684.3:c.4131G>T	p.Leu1377Phe	p.L1377F	ENST00000330684	NM_001134407.1	1377	ttG/ttT	13/13	1	2	FACETS	0.953	0.872	1	0.953	0.872	1	CLONAL	1	TRUE	1	0.47729318841348	2		749	633	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39745008	39745008	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	149	627	0	ENST00000361337.2:c.1798C>T	p.Gln600Ter	p.Q600*	ENST00000361337	NM_003286.2	600	Cag/Tag	17/21	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.47729318841348	2		627	623	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180631	32180631	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	189	775	1	ENST00000375023.3:c.2496C>A	p.Cys832Ter	p.C832*	ENST00000375023	NM_004557.3	832	tgC/tgA	16/30	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.47729318841348	2		776	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577544	7577548	+	protein_altering_variant	In_Frame_Del	DEL	ATGCC	ATGCC	CT	novel	NA	P-0056554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	182	836	3	ENST00000269305.4:c.733_737delinsAG	p.Gly245_Met246delinsArg	p.G245_M246delinsR	ENST00000269305	NM_001126112.2	245	GGCATg/AGg	7/11	0.47729318841348	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.47729318841348	1		839	553	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	153	473	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.409748113779287	5	FACETS	0.807	0.741	0.876	0.538	0.494	0.584	CLONAL	2	TRUE	2	0.527478452240605	5		473	644	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888189	112888189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507511	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	175	623	0	ENST00000351677.2:c.205G>A	p.Glu69Lys	p.E69K	ENST00000351677	NM_002834.3	69	Gag/Aag	3/16	0.346494745038857	4	FACETS	1	0.99	1	0.745	0.689	0.804	CLONAL	1	TRUE	2	0.527478452240605	4		623	680	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250883	153250883	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	127	381	0	ENST00000281708.4:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000281708	NM_033632.3	393	Cga/Tga	8/12	0.41703218743396	3	FACETS	0.816	0.747	0.886	0.816	0.747	0.886	CLONAL	2	TRUE	1	0.527478452240605	3		381	373	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124364	2124364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	151	974	0	ENST00000219476.3:c.2519C>T	p.Ala840Val	p.A840V	ENST00000219476	NM_000548.3	840	gCc/gTc	22/42	1	2	FACETS	0.811	0.743	0.882	0.811	0.743	0.882	CLONAL	1	TRUE	1	0.527478452240605	2		974	706	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980903	40980903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs906977293	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	225	523	1	ENST00000373198.4:c.1583C>T	p.Ser528Leu	p.S528L	ENST00000373198	NM_133170.3	528	tCg/tTg	10/32	0.152196308236062	6	FACETS	0.884	0.828	0.941	0.884	0.828	0.941	INDETERMINATE	3	TRUE	3	0.527478452240605	6		524	661	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679291	29679291	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555536340	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	169	420	0	ENST00000356175.3:c.7411C>T	p.Gln2471Ter	p.Q2471*	ENST00000356175	NM_000267.3	2471	Cag/Tag	50/57	0.346494745038857	4	FACETS	0.956	0.885	1	0.956	0.885	1	CLONAL	2	TRUE	2	0.527478452240605	4		420	512	SUCCESS
APC	324	MSKCC	GRCh37	5	112128185	112128185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779805	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	148	445	0	ENST00000257430.4:c.688C>T	p.Arg230Cys	p.R230C	ENST00000257430	NM_000038.5	230	Cgt/Tgt	7/16	0.346494745038857	4	FACETS	0.816	0.75	0.885	0.816	0.75	0.885	CLONAL	2	TRUE	2	0.527478452240605	4		445	525	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664868	29664868	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1193716348	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	122	414	0	ENST00000356175.3:c.6611G>A	p.Trp2204Ter	p.W2204*	ENST00000356175	NM_000267.3	2204	tGg/tAg	43/57	0.346494745038857	4	FACETS	1	0.985	1	0.739	0.672	0.809	CLONAL	1	TRUE	2	0.527478452240605	4		414	478	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	109	262	1				ENST00000310581	NM_198253.2	-/1132			0.346494745038857	4	FACETS	0.934	0.848	1	0.934	0.848	1	CLONAL	2	TRUE	2	0.527478452240605	4		263	338	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323093	31323093	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	247	1138	0	ENST00000412585.2:c.895+1G>C		p.X299_splice	ENST00000412585	NM_005514.6	299			0.527478452240605	5	FACETS	1	0.989	1	0.434	0.405	0.464	CLONAL	1	TRUE	2	0.527478452240605	5		1138	1288	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745609	162745609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	227	548	0	ENST00000367921.3:c.2024C>T	p.Ser675Phe	p.S675F	ENST00000367921	NM_006182.2	675	tCc/tTc	15/18	0.527478452240605	4	FACETS	0.829	0.774	0.885	0.829	0.774	0.885	CLONAL	2	TRUE	2	0.527478452240605	4		548	793	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157993	27157993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	232	713	0	ENST00000380036.4:c.217G>A	p.Glu73Lys	p.E73K	ENST00000380036	NM_000459.3	73	Gaa/Aaa	2/23	0.426236759158786	2	FACETS	0.828	0.78	0.877	0.828	0.78	0.877	CLONAL	2	TRUE	0	0.527478452240605	2		713	531	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343668	343668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774921991	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	175	1005	4	ENST00000262320.3:c.2006C>T	p.Ser669Phe	p.S669F	ENST00000262320	NM_003502.3	669	tCc/tTc	8/11	1	2	FACETS	0.955	0.882	1	0.955	0.882	1	CLONAL	1	TRUE	1	0.527478452240605	2		1009	695	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633501	3633501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560866356	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	134	810	0	ENST00000294008.3:c.4750C>T	p.Arg1584Cys	p.R1584C	ENST00000294008	NM_032444.2	1584	Cgc/Tgc	14/15	1	2	FACETS	0.762	0.694	0.833	0.762	0.694	0.833	SUBCLONAL	1	TRUE	1	0.527478452240605	2		810	667	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266946	18266946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	85	160	0	ENST00000222254.8:c.257C>T	p.Pro86Leu	p.P86L	ENST00000222254	NM_005027.3	86	cCc/cTc	2/16	0.346494745038857	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	2	0.527478452240605	4		160	213	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244064	46244064	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	161	563	0	ENST00000334344.6:c.2158C>T	p.Gln720Ter	p.Q720*	ENST00000334344	NM_152641.2	720	Cag/Tag	15/21	0.346494745038857	4	FACETS	0.8	0.737	0.864	0.8	0.737	0.864	SUBCLONAL	2	TRUE	2	0.527478452240605	4		563	583	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770557	40770557	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	149	514	0	ENST00000373198.4:c.2825C>T	p.Ser942Phe	p.S942F	ENST00000373198	NM_133170.3	942	tCc/tTc	19/32	0.152196308236062	6	FACETS	1	0.957	1	0.71	0.652	0.77	INDETERMINATE	2	TRUE	3	0.527478452240605	6		514	545	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345765	152345765	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	104	299	0	ENST00000359321.1:c.805T>G	p.Phe269Val	p.F269V	ENST00000359321	NM_005431.1	269	Ttt/Gtt	3/3	0.409748113779287	5	FACETS	1	0.983	1	0.497	0.447	0.549	CLONAL	1	TRUE	2	0.527478452240605	5		299	474	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090363	77090363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	221	544	1	ENST00000356341.3:c.362C>T	p.Pro121Leu	p.P121L	ENST00000356341	NM_002576.4	121	cCg/cTg	4/15	0.152196308236062	6	FACETS	1	0.978	1	0.738	0.689	0.788	INDETERMINATE	2	TRUE	3	0.527478452240605	6		545	778	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926876	112926877	+	missense_variant	Missense_Mutation	DNP	CT	CT	TC	novel	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	183	686	0	ENST00000351677.2:c.1496_1497delinsTC	p.Ser499Phe	p.S499F	ENST00000351677	NM_002834.3	499	tCT/tTC	13/16	0.346494745038857	4	FACETS	1	0.989	1	0.706	0.653	0.76	CLONAL	1	TRUE	2	0.527478452240605	4		686	751	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120805998	120805998	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	247	779	0	ENST00000257552.2:c.179C>T	p.Ser60Phe	p.S60F	ENST00000257552	NM_002442.3	60	tCc/tTc	3/15	0.346494745038857	4	FACETS	0.891	0.835	0.947	0.891	0.835	0.947	CLONAL	2	TRUE	2	0.527478452240605	4		779	803	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042516	42042516	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	77	551	0	ENST00000219905.7:c.6711G>C	p.Leu2237Phe	p.L2237F	ENST00000219905	NM_001164273.1	2237	ttG/ttC	17/24	0.152196308236062	6	FACETS	0.995	0.874	1	0.332	0.291	0.375	INDETERMINATE	1	TRUE	3	0.527478452240605	6		551	603	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678501	88678502	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	171	643	0	ENST00000360948.2:c.1034_1035delinsTT	p.Ser345Phe	p.S345F	ENST00000360948	NM_001012338.2	345	tCC/tTT	9/19	0.152196308236062	6	FACETS	1	0.956	1	0.699	0.646	0.755	INDETERMINATE	2	TRUE	3	0.527478452240605	6		643	635	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923450	9923450	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	85	581	0	ENST00000330684.3:c.1837T>C	p.Phe613Leu	p.F613L	ENST00000330684	NM_001134407.1	613	Ttc/Ctc	9/13	1	2	FACETS	0.646	0.573	0.724	0.646	0.573	0.724	SUBCLONAL	1	TRUE	1	0.527478452240605	2		581	499	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306533	41306533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	219	593	0	ENST00000373198.4:c.1126C>T	p.Pro376Ser	p.P376S	ENST00000373198	NM_133170.3	376	Ccc/Tcc	7/32	0.152196308236062	6	FACETS	0.841	0.787	0.898	0.841	0.787	0.898	INDETERMINATE	3	TRUE	3	0.527478452240605	6		593	676	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46266456	46266456	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	82	508	0	ENST00000371998.3:c.2441A>C	p.Asn814Thr	p.N814T	ENST00000371998		814	aAt/aCt	13/23	0.152196308236062	6	FACETS	1	0.962	1	0.406	0.359	0.457	INDETERMINATE	1	TRUE	3	0.527478452240605	6		508	524	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151562	55151562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	168	457	0	ENST00000257290.5:c.2348C>T	p.Ser783Leu	p.S783L	ENST00000257290	NM_006206.4	783	tCa/tTa	17/23	0.41703218743396	3	FACETS	0.802	0.743	0.862	0.802	0.743	0.862	CLONAL	2	TRUE	1	0.527478452240605	3		457	502	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157507	106157507	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	98	309	0	ENST00000380013.4:c.2408A>G	p.Gln803Arg	p.Q803R	ENST00000380013	NM_001127208.2	803	cAa/cGa	3/11	0.41703218743396	3	FACETS	0.753	0.679	0.828	0.753	0.679	0.828	SUBCLONAL	2	TRUE	1	0.527478452240605	3		309	312	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751121	57751121	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1561215414	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	134	316	0	ENST00000274289.3:c.1746C>A	p.Asn582Lys	p.N582K	ENST00000274289	NM_006622.3	582	aaC/aaA	12/14	0.346494745038857	4	FACETS	0.931	0.853	1	0.931	0.853	1	CLONAL	2	TRUE	2	0.527478452240605	4		316	417	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522446	157522446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	298	771	0	ENST00000346085.5:c.4718C>T	p.Pro1573Leu	p.P1573L	ENST00000346085	NM_020732.3	1573	cCt/cTt	18/20	0.152196308236062	6	FACETS	1	0.991	1	0.829	0.782	0.876	INDETERMINATE	2	TRUE	3	0.527478452240605	6		771	934	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975475	13975475	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	187	417	0	ENST00000405192.2:c.412C>T	p.Pro138Ser	p.P138S	ENST00000405192	NM_001163147.1	138	Ccc/Tcc	7/12	0.409748113779287	5	FACETS	0.969	0.899	1	0.646	0.599	0.695	CLONAL	2	TRUE	2	0.527478452240605	5		417	655	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372703	81372703	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs777970277	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	130	424	0	ENST00000222390.5:c.831C>A	p.His277Gln	p.H277Q	ENST00000222390	NM_000601.4	277	caC/caA	7/18	0.409748113779287	5	FACETS	0.784	0.714	0.857	0.523	0.476	0.572	SUBCLONAL	2	TRUE	2	0.527478452240605	5		424	563	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874519	151874519	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	78	459	0	ENST00000262189.6:c.8019T>G	p.Asp2673Glu	p.D2673E	ENST00000262189	NM_170606.2	2673	gaT/gaG	38/59	0.409748113779287	5	FACETS	0.856	0.752	0.967	0.285	0.25	0.323	CLONAL	1	TRUE	2	0.527478452240605	5		459	619	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202924	27202925	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	81	547	1	ENST00000380036.4:c.2016_2017delinsTT	p.Arg673Cys	p.R673C	ENST00000380036	NM_000459.3	672	atCCgt/atTTgt	13/23	1	2	FACETS	0.792	0.702	0.887	0.792	0.702	0.887	SUBCLONAL	1	TRUE	1	0.527478452240605	2		548	388	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923633	39923633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	304	830	0	ENST00000378444.4:c.3458C>T	p.Pro1153Leu	p.P1153L	ENST00000378444	NM_001123385.1	1153	cCa/cTa	7/15	0.152196308236062	6	FACETS	1	0.988	1	0.779	0.735	0.824	INDETERMINATE	2	TRUE	3	0.527478452240605	6		830	1014	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651646	48651646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	260	873	0	ENST00000376670.3:c.812G>A	p.Arg271Lys	p.R271K	ENST00000376670	NM_002049.3	271	aGa/aAa	5/6	0.152196308236062	6	FACETS	1	0.983	1	0.748	0.702	0.795	INDETERMINATE	2	TRUE	3	0.527478452240605	6		873	903	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341701	8341704	+	missense_variant	Missense_Mutation	ONP	CGAG	CGAG	TGAA	novel	NA	P-0056555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	162	538	0	ENST00000356435.5:c.4936_4939delinsTTCA	p.Leu1646_Glu1647delinsPheLys	p.L1646_E1647delinsFK	ENST00000356435		1646	CTCGaa/TTCAaa	29/35	0.426236759158786	2	FACETS	0.751	0.697	0.806	0.751	0.697	0.806	SUBCLONAL	2	TRUE	0	0.527478452240605	2		538	409	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099315	157099315	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs372726215	NA	P-0056557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	35	504	0	ENST00000346085.5:c.252C>G	p.His84Gln	p.H84Q	ENST00000346085	NM_020732.3	84	caC/caG	1/20	0.38645180135436	3	FACETS	0.756	0.623	0.905	0.378	0.311	0.453	CLONAL	1	TRUE	1	0.406446196548895	3		504	274	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412406	63412406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	34	1074	0	ENST00000330258.3:c.761C>T	p.Ala254Val	p.A254V	ENST00000330258	NM_152424.3	254	gCc/gTc	2/2	0.406446196548895	1	FACETS	0.505	0.414	0.606	0.505	0.414	0.606	SUBCLONAL	1	TRUE	0	0.406446196548895	1		1074	264	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0056558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	70	683	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.16	2		683	843	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7978925	7978925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397514532	NA	P-0056558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	39	442	0	ENST00000319144.4:c.1642C>T	p.Arg548Trp	p.R548W	ENST00000319144	NM_001139.2	548	Cgg/Tgg	12/15	1	2	FACETS	0.871	0.721	1	0.871	0.721	1	CLONAL	1	TRUE	1	0.16	2		442	560	SUCCESS
APC	324	MSKCC	GRCh37	5	112175171	112175171	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085373	NA	P-0056558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	14	201	0	ENST00000257430.4:c.3880C>T	p.Gln1294Ter	p.Q1294*	ENST00000257430	NM_000038.5	1294	Cag/Tag	16/16	1	2	FACETS	0.754	0.545	1	0.754	0.545	1	CLONAL	1	TRUE	1	0.16	2		201	232	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554669	63554669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	68	634	1	ENST00000307078.5:c.70C>T	p.Pro24Ser	p.P24S	ENST00000307078	NM_004655.3	24	Ccc/Tcc	2/11	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.16	2		635	728	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325674	87325674	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	33	458	0	ENST00000277120.3:c.551T>C	p.Ile184Thr	p.I184T	ENST00000277120		184	aTt/aCt	6/19	1	2	FACETS	0.725	0.589	0.879	0.725	0.589	0.879	SUBCLONAL	1	TRUE	1	0.16	2		458	569	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0056563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	248	221	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.819765774548437	2		222	540	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0056563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	514	564	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.819765774548437	3	FACETS	0.997	0.977	1	0.997	0.977	1	CLONAL	3	TRUE	0	0.819765774548437	3		564	591	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0056563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	172	507	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.789184312325066	1	FACETS	0.975	0.924	1	0.975	0.924	1	CLONAL	1	TRUE	0	0.819765774548437	1		507	254	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857436	9857436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	263	812	0	ENST00000330684.3:c.3965G>A	p.Gly1322Glu	p.G1322E	ENST00000330684	NM_001134407.1	1322	gGa/gAa	13/13	1	2	FACETS	0.949	0.895	1	0.949	0.895	1	CLONAL	1	TRUE	1	0.819765774548437	2		812	676	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504590	103504590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1400329743	NA	P-0056563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	123	482	1	ENST00000355739.4:c.211C>T	p.Arg71Cys	p.R71C	ENST00000355739	NM_000123.3	71	Cgt/Tgt	2/15	1	2	FACETS	0.862	0.789	0.937	0.862	0.789	0.937	CLONAL	1	TRUE	1	0.819765774548437	2		483	348	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099351	4099351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	474	1367	0	ENST00000262948.5:c.767C>T	p.Ser256Phe	p.S256F	ENST00000262948	NM_030662.3	256	tCc/tTc	7/11	1	2	FACETS	0.939	0.899	0.98	0.939	0.899	0.98	CLONAL	1	TRUE	1	0.819765774548437	2		1367	1231	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443487	49443487	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	393	878	0	ENST00000301067.7:c.3884C>T	p.Pro1295Leu	p.P1295L	ENST00000301067	NM_003482.3	1295	cCa/cTa	11/54	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.819765774548437	2		878	956	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984079	2984079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	342	853	0	ENST00000396946.4:c.451G>A	p.Glu151Lys	p.E151K	ENST00000396946	NM_032415.4	151	Gag/Aag	5/25	NA	2	FACETS	0.738	0.698	0.778			1	INDETERMINATE	1	TRUE	NA	0.819765774548437	2		853	1131	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167818	185167818	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	201	727	0	ENST00000265026.3:c.1141G>A	p.Gly381Arg	p.G381R	ENST00000265026	NM_004721.4	381	Gga/Aga	6/14	1	2	FACETS	0.892	0.833	0.952	0.892	0.833	0.952	CLONAL	1	TRUE	1	0.819765774548437	2		727	550	SUCCESS
AR	367	MSKCC	GRCh37	X	66766024	66766024	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs777765515	NA	P-0056563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	449	726	0	ENST00000374690.3:c.1036T>C	p.Ser346Pro	p.S346P	ENST00000374690	NM_000044.3	346	Tct/Cct	1/8	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.819765774548437	1		726	613	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154812	2154812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	540	1310	2	ENST00000434045.2:c.409G>A	p.Glu137Lys	p.E137K	ENST00000434045	NM_001127598.1	137	Gag/Aag	4/5	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.819765774548437	2		1312	1268	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180265	32180265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	357	1068	0	ENST00000375023.3:c.2666C>T	p.Ala889Val	p.A889V	ENST00000375023	NM_004557.3	889	gCt/gTt	17/30	1	2	FACETS	0.873	0.829	0.917	0.873	0.829	0.917	CLONAL	1	TRUE	1	0.819765774548437	2		1068	998	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226573372	226573372	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1241257182	NA	P-0056563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	396	793	0	ENST00000366794.5:c.844C>T	p.Arg282Ter	p.R282*	ENST00000366794	NM_001618.3	282	Cga/Tga	7/23	0.459652723690778	3	FACETS	0.799	0.764	0.835	0.799	0.764	0.835	INDETERMINATE	2	TRUE	1	0.819765774548437	3		793	852	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599205	28599206	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0056563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	711	1419	1	ENST00000253063.3:c.651_652delinsTT	p.Pro218Ser	p.P218S	ENST00000253063	NM_031459.4	217	ctCCct/ctTTct	5/10	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	1	TRUE	NA	0.819765774548437	2		1420	1474	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226562001	226562001	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	447	844	0	ENST00000366794.5:c.1996C>T	p.Pro666Ser	p.P666S	ENST00000366794	NM_001618.3	666	Ccc/Tcc	14/23	0.459652723690778	3	FACETS	0.805	0.772	0.838	0.805	0.772	0.838	INDETERMINATE	2	TRUE	1	0.819765774548437	3		844	955	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134544	2134544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201710642	NA	P-0056563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	575	1404	4	ENST00000219476.3:c.4321C>T	p.Pro1441Ser	p.P1441S	ENST00000219476	NM_000548.3	1441	Ccc/Tcc	34/42	1	2	FACETS	0.999	0.961	1	0.999	0.961	1	CLONAL	1	TRUE	1	0.819765774548437	2		1408	1404	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740686	58740686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	285	818	0	ENST00000305921.3:c.1591C>T	p.Pro531Ser	p.P531S	ENST00000305921	NM_003620.3	531	Cca/Tca	6/6	1	2	FACETS	0.978	0.925	1	0.978	0.925	1	CLONAL	1	TRUE	1	0.819765774548437	2		818	711	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866528	78866528	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0056563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	337	945	1	ENST00000306801.3:c.2102-1G>A		p.X701_splice	ENST00000306801	NM_020761.2	701			1	2	FACETS	0.887	0.841	0.933	0.887	0.841	0.933	CLONAL	1	TRUE	1	0.819765774548437	2		946	927	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213996	36213996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	566	1367	0	ENST00000222270.7:c.2822C>T	p.Ser941Phe	p.S941F	ENST00000222270	NM_014727.1	941	tCt/tTt	6/37	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.819765774548437	2		1367	1362	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731545	47731545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	35	31	0	ENST00000449228.1:c.247C>T	p.Arg83Cys	p.R83C	ENST00000449228	NM_001127240.2	83	Cgc/Tgc	2/4	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.819765774548437	2		31	74	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190742133	190742133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	72	458	0	ENST00000441310.2:c.2770C>T	p.His924Tyr	p.H924Y	ENST00000441310	NM_000534.4	924	Cat/Tat	13/13	1	2	FACETS	0.905	0.807	1	0.905	0.807	1	CLONAL	1	TRUE	1	0.819765774548437	2		458	194	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017746	31017746	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	408	981	1	ENST00000375687.4:c.608C>T	p.Ser203Phe	p.S203F	ENST00000375687	NM_015338.5	203	tCc/tTc	8/13	0.819765774548437	3	FACETS	0.953	0.906	1	0.477	0.453	0.501	CLONAL	1	TRUE	1	0.819765774548437	3		982	1472	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165282	47165282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	117	520	0	ENST00000409792.3:c.844G>A	p.Glu282Lys	p.E282K	ENST00000409792	NM_014159.6	282	Gaa/Aaa	3/21	1	2	FACETS	0.903	0.826	0.983	0.903	0.826	0.983	CLONAL	1	TRUE	1	0.819765774548437	2		520	316	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447566	187447567	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0056563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	336	1092	1	ENST00000232014.4:c.626_627delinsTT	p.Ser209Phe	p.S209F	ENST00000232014	NM_001130845.1	209	tCC/tTT	5/10	1	2	FACETS	0.864	0.819	0.909	0.864	0.819	0.909	CLONAL	1	TRUE	1	0.819765774548437	2		1093	949	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521062	187521068	+	frameshift_variant	Frame_Shift_Del	DEL	TGACGGA	TGACGGA	-	novel	NA	P-0056563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	176	637	0	ENST00000441802.2:c.12087_12093del	p.Pro4030LeufsTer14	p.P4030Lfs*14	ENST00000441802	NM_005245.3	4029	aaTCCGTCA/aa	22/27	1	2	FACETS	0.807	0.749	0.867	0.807	0.749	0.867	CLONAL	1	TRUE	1	0.819765774548437	2		637	532	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671669	30671669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	495	1171	1	ENST00000376406.3:c.5291C>T	p.Ala1764Val	p.A1764V	ENST00000376406	NM_014641.2	1764	gCt/gTt	10/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.819765774548437	2		1172	1206	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945099	151945099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219495191	NA	P-0056563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	54	654	1	ENST00000262189.6:c.2420C>T	p.Ser807Phe	p.S807F	ENST00000262189	NM_170606.2	807	tCt/tTt	14/59	0.819765774548437	3	FACETS	0.382	0.327	0.443	0.127	0.108	0.148	SUBCLONAL	1	TRUE	0	0.819765774548437	3		655	486	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27220046	27220046	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0056563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	365	902	0	ENST00000380036.4:c.3104-1G>A		p.X1035_splice	ENST00000380036	NM_000459.3	1035			0.819765774548437	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.819765774548437	1		902	500	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	104	324	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.50120604673116	2		324	340	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0056564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	178	401	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.50120604673116	2		401	575	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533552	533552	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	565	1119	0	ENST00000451590.1:c.351G>C	p.Lys117Asn	p.K117N	ENST00000451590	NM_001130442.1	117	aaG/aaC	4/5	1	2	FACETS	1	0.995	1	1	0.998	1	CLONAL	2	TRUE	1	0.50120604673116	2		1119	959	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372530	118372530	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	70	668	0	ENST00000534358.1:c.6463C>G	p.Pro2155Ala	p.P2155A	ENST00000534358	NM_005933.3	2155	Cca/Gca	26/36	0.50120604673116	1	FACETS	0.362	0.316	0.412	0.362	0.316	0.412	SUBCLONAL	1	TRUE	0	0.50120604673116	1		668	578	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056251	27056251	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	213	797	0	ENST00000324856.7:c.1247G>T	p.Gly416Val	p.G416V	ENST00000324856	NM_006015.4	416	gGg/gTg	2/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.50120604673116	2		797	738	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372396	118372396	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs864309569	NA	P-0056564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	55	518	0	ENST00000534358.1:c.6329C>G	p.Ser2110Ter	p.S2110*	ENST00000534358	NM_005933.3	2110	tCa/tGa	26/36	0.50120604673116	1	FACETS	0.397	0.341	0.459	0.397	0.341	0.459	SUBCLONAL	1	TRUE	0	0.50120604673116	1		518	414	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40371825	40371825	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	203	1000	1	ENST00000293328.3:c.586G>A	p.Glu196Lys	p.E196K	ENST00000293328	NM_012448.3	196	Gag/Aag	6/19	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.50120604673116	2		1001	751	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200258	123200258	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	208	728	0	ENST00000218089.9:c.2237C>G	p.Ala746Gly	p.A746G	ENST00000218089	NM_001042749.1	746	gCt/gGt	23/35	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.50120604673116	2		728	694	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	170	324	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.98	1	1	0.994	1	CLONAL	3	TRUE	1	0.229197583429721	2		324	432	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266107	41266107	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	205	455	0	ENST00000349496.5:c.104T>G	p.Ile35Ser	p.I35S	ENST00000349496	NM_001904.3	35	aTc/aGc	3/15	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	3	TRUE	1	0.229197583429721	2		455	518	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266849	18266851	+	inframe_deletion	In_Frame_Del	DEL	GTG	GTG	-	novel	NA	P-0056565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	285	539	0	ENST00000222254.8:c.161_163del	p.Val54del	p.V54del	ENST00000222254	NM_005027.3	54	GTG/-	2/16	1	2	FACETS	1	0.979	1	1	0.996	1	CLONAL	3	TRUE	1	0.229197583429721	2		539	772	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0056567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	88	597	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.781	0.696	0.871	0.781	0.696	0.871	SUBCLONAL	1	TRUE	1	0.536378359957978	2		597	420	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0056567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	108	463	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.829	0.747	0.914	0.829	0.747	0.914	CLONAL	1	TRUE	1	0.536378359957978	2		463	486	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0056567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	226	504	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.523282742713117	3	FACETS	0.788	0.738	0.84	0.788	0.738	0.84	SUBCLONAL	2	TRUE	1	0.536378359957978	3		504	678	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557629	95557629	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	163	538	0	ENST00000393063.1:c.5438A>G	p.Glu1813Gly	p.E1813G	ENST00000393063	NM_030621.3	1813	gAg/gGg	26/28	1	2	FACETS	0.871	0.801	0.943	0.871	0.801	0.943	CLONAL	1	TRUE	1	0.536378359957978	2		538	698	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023401	27023401	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	130	350	0	ENST00000324856.7:c.508del	p.His170ThrfsTer62	p.H170Tfs*62	ENST00000324856	NM_006015.4	169	ttC/tt	1/20	1	2	FACETS	0.96	0.876	1	0.96	0.876	1	CLONAL	1	TRUE	1	0.536378359957978	2		350	505	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101217	27101218	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCGT	novel	NA	P-0056567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	200	814	0	ENST00000324856.7:c.4500_4503dup	p.Asn1502AlafsTer2	p.N1502Afs*2	ENST00000324856	NM_006015.4	1500	ggg/ggGCGTg	18/20	1	2	FACETS	0.915	0.849	0.983	0.915	0.849	0.983	CLONAL	1	TRUE	1	0.536378359957978	2		814	815	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28601417	28601417	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs752269696	NA	P-0056567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	201	841	0	ENST00000253063.3:c.1102C>T	p.Gln368Ter	p.Q368*	ENST00000253063	NM_031459.4	368	Cag/Tag	8/10	1	2	FACETS	0.939	0.872	1	0.939	0.872	1	CLONAL	1	TRUE	1	0.536378359957978	2		841	798	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	59	324	0				ENST00000310581	NM_198253.2	-/1132			0.280372021894408	1	FACETS	0.561	0.496	0.626	0.561	0.496	0.626	INDETERMINATE	1	TRUE	0	0.872382389517731	1		324	136	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0056574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	110	650	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.872382389517731	2		650	251	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732910	44732910	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	123	309	0	ENST00000377967.4:c.117del	p.Ser40AlafsTer2	p.S40Afs*2	ENST00000377967	NM_021140.2	38	tCc/tc	1/29	0.422538297473973	2	FACETS	0.993	0.951	1			1	INDETERMINATE	2	TRUE	NA	0.872382389517731	2		309	142	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346204	89346204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201043388	NA	P-0056574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	54	419	2	ENST00000301030.4:c.6746G>A	p.Arg2249His	p.R2249H	ENST00000301030	NM_001256183.1	2249	cGc/cAc	9/13	0.117544633179383	4	FACETS	0.816	0.715	0.921	0.816	0.715	0.921	INDETERMINATE	2	TRUE	2	0.872382389517731	4		421	142	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003751	45003751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765817584	NA	P-0056574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	157	526	0	ENST00000558401.1:c.7C>T	p.Arg3Cys	p.R3C	ENST00000558401	NM_004048.2	3	Cgc/Tgc	1/4	0.357506782004757	5	FACETS	1	0.98	1	0.767	0.713	0.822	INDETERMINATE	2	TRUE	2	0.872382389517731	5		526	361	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595786	52595786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	91	496	2	ENST00000394830.3:c.4129G>A	p.Glu1377Lys	p.E1377K	ENST00000394830	NM_018313.4	1377	Gaa/Aaa	26/30	0.470807071584841	4	FACETS	0.892	0.808	0.977	0.892	0.808	0.977	INDETERMINATE	2	TRUE	2	0.872382389517731	4		498	219	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115983	8115984	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0056574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	98	384	0	ENST00000346208.3:c.1330_1331dup	p.Ter444TyrfsTer32	p.*444Yfs*32	ENST00000346208		443	-/TA	6/6	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.872382389517731	2		384	198	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866415	56866415	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	40	493	0	ENST00000519728.1:c.662G>A	p.Arg221Lys	p.R221K	ENST00000519728	NM_002350.3	221	aGa/aAa	8/13	0.477299883315307	1	FACETS	0.389	0.33	0.451	0.389	0.33	0.451	INDETERMINATE	1	TRUE	0	0.872382389517731	1		493	133	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220044	133220044	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	101	727	0	ENST00000320574.5:c.4393C>G	p.Leu1465Val	p.L1465V	ENST00000320574	NM_006231.2	1465	Ctt/Gtt	34/49	0.872382389517731	5	FACETS	1	0.982	1	0.488	0.44	0.538	CLONAL	1	TRUE	2	0.872382389517731	5		727	365	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777912	3777912	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	163	992	1	ENST00000262367.5:c.7136A>T	p.Gln2379Leu	p.Q2379L	ENST00000262367	NM_004380.2	2379	cAg/cTg	31/31	0.117544633179383	4	FACETS	0.964	0.898	1	0.964	0.898	1	INDETERMINATE	2	TRUE	2	0.872382389517731	4		993	363	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492752	56492752	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	181	659	0	ENST00000407977.2:c.187C>A	p.Leu63Ile	p.L63I	ENST00000407977		63	Ctc/Atc	2/10	0.231555248864006	5	FACETS	1	0.986	1	0.806	0.754	0.859	INDETERMINATE	2	TRUE	2	0.872382389517731	5		659	396	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021775	71021775	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	66	332	0	ENST00000318789.4:c.1583del	p.Asn528ThrfsTer12	p.N528Tfs*12	ENST00000318789	NM_032682.5	528	aAc/ac	18/21	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.872382389517731	2		332	147	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866474	56866474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	69	715	0	ENST00000519728.1:c.721G>A	p.Glu241Lys	p.E241K	ENST00000519728	NM_002350.3	241	Gag/Aag	8/13	0.477299883315307	1	FACETS	0.419	0.37	0.469	0.419	0.37	0.469	INDETERMINATE	1	TRUE	0	0.872382389517731	1		715	213	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117861205	117861205	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	108	423	2	ENST00000297338.2:c.1684C>T	p.Gln562Ter	p.Q562*	ENST00000297338	NM_006265.2	562	Cag/Tag	13/14	0.497300571150712	3	FACETS	0.819	0.753	0.886	0.819	0.753	0.886	INDETERMINATE	2	TRUE	1	0.872382389517731	3		425	217	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	294	324	0				ENST00000310581	NM_198253.2	-/1132			0.38698945260234	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.394969954129541	2		324	650	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55272966	55272966	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775345513	NA	P-0056575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	147	557	0	ENST00000275493.2:c.3289G>A	p.Val1097Ile	p.V1097I	ENST00000275493	NM_005228.3	1097	Gtt/Att	28/28	0.166813153065926	0	FACETS	0.57	0.521	0.622			1	INDETERMINATE	1	TRUE	0	0.394969954129541	0		557	790	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0056576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	23	234	2	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.609	0.477	0.759	0.609	0.477	0.759	SUBCLONAL	1	TRUE	1	0.365141405819319	2		236	207	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189448	56189448	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	39	530	1	ENST00000399503.3:c.4480C>T	p.Gln1494Ter	p.Q1494*	ENST00000399503	NM_005921.1	1494	Cag/Tag	20/20	1	2	FACETS	0.512	0.425	0.61	0.512	0.425	0.61	SUBCLONAL	1	TRUE	1	0.365141405819319	2		531	417	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041037	112041037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761032788	NA	P-0056576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	25	578	2	ENST00000368678.4:c.218C>T	p.Thr73Met	p.T73M	ENST00000368678		73	aCg/aTg	3/13	0.240070331743427	1	FACETS	0.277	0.218	0.345	0.277	0.218	0.345	SUBCLONAL	1	TRUE	0	0.365141405819319	1		580	404	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870966	12870966	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	39	407	0	ENST00000228872.4:c.193C>T	p.Gln65Ter	p.Q65*	ENST00000228872	NM_004064.3	65	Cag/Tag	1/3	1	2	FACETS	0.64	0.532	0.759	0.64	0.532	0.759	SUBCLONAL	1	TRUE	1	0.365141405819319	2		407	334	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553356	106553356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	34	520	0	ENST00000369096.4:c.1321C>T	p.Pro441Ser	p.P441S	ENST00000369096	NM_001198.3	441	Ccg/Tcg	5/7	1	2	FACETS	0.568	0.465	0.683	0.568	0.465	0.683	SUBCLONAL	1	TRUE	1	0.365141405819319	2		520	328	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981726	70981726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	398	1060	1	ENST00000276594.2:c.370G>A	p.Ala124Thr	p.A124T	ENST00000276594	NM_024504.3	124	Gcc/Acc	2/8	0.224006243450246	3	FACETS	0.984	0.935	1	0.328	0.311	0.345	INDETERMINATE	1	TRUE	0	0.806714431195512	3		1061	1407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0056579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	127	504	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.22324000334167	2		504	824	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0056579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	67	330	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.22324000334167	2		330	591	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032572	12032572	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	71	504	0	ENST00000353533.5:c.1008C>G	p.Phe336Leu	p.F336L	ENST00000353533	NM_003010.3	336	ttC/ttG	9/11	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.22324000334167	2		504	607	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5029908	5029908	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0056579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	49	408	0	ENST00000381652.3:c.350+2T>A		p.X117_splice	ENST00000381652	NM_004972.3	117			1	2	FACETS	0.984	0.835	1	0.984	0.835	1	CLONAL	1	TRUE	1	0.22324000334167	2		408	446	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250921	153250922	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0056580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	43	268	0	ENST00000281708.4:c.1138dup	p.Asp380GlyfsTer2	p.D380Gfs*2	ENST00000281708	NM_033632.3	380	gat/gGat	8/12	0.314876114683204	2	FACETS	0.883	0.76	1	0.883	0.76	1	CLONAL	2	FALSE	0	0.416022678768115	2		268	117	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104389875	104389875	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	173	556	0	ENST00000369902.3:c.1418T>C	p.Ile473Thr	p.I473T	ENST00000369902	NM_016169.3	473	aTc/aCc	12/12	0.314876114683204	2	FACETS	1	0.989	1	0.726	0.672	0.781	CLONAL	1	FALSE	0	0.416022678768115	2		556	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578459	7578467	+	inframe_deletion	In_Frame_Del	DEL	GACGCGGGT	GACGCGGGT	-	novel	NA	P-0056580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	423	893	0	ENST00000269305.4:c.463_471del	p.Thr155_Val157del	p.T155_V157del	ENST00000269305	NM_001126112.2	155	ACCCGCGTC/-	5/11	0.416022678768115	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	FALSE	0	0.416022678768115	2		893	1000	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865400	40865400	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	253	760	0	ENST00000428826.2:c.1031C>G	p.Ala344Gly	p.A344G	ENST00000428826		344	gCa/gGa	11/21	0.416022678768115	2	FACETS	0.94	0.886	0.995	0.94	0.886	0.995	CLONAL	2	FALSE	0	0.416022678768115	2		760	647	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985635	60985636	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0056580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	41	153	0	ENST00000333681.4:c.264_265delinsTT	p.Val89Leu	p.V89L	ENST00000333681		88	ccGGtg/ccTTtg	2/3	0.421748822765641	3	FACETS	1	0.917	1	1	0.917	1	CLONAL	2	FALSE	1	0.416022678768115	3		153	108	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610535	10610535	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	194	828	0	ENST00000171111.5:c.175C>A	p.His59Asn	p.H59N	ENST00000171111	NM_203500.1	59	Cat/Aat	2/6	0.325568093110646	2	FACETS	1	0.991	1	0.734	0.683	0.787	CLONAL	1	FALSE	0	0.416022678768115	2		828	635	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902109	50902109	+	start_lost,splice_region_variant	Translation_Start_Site	SNP	A	A	T	novel	NA	P-0056580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	131	539	0	ENST00000440232.2:c.1A>T	p.Met1?	p.M1?	ENST00000440232	NM_002691.3	1	Atg/Ttg	2/27	0.421748822765641	4	FACETS	0.857	0.782	0.936	0.857	0.782	0.936	CLONAL	2	FALSE	2	0.416022678768115	4		539	520	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523528	106523528	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	45	264	0	ENST00000359195.3:c.2680A>T	p.Ser894Cys	p.S894C	ENST00000359195	NM_002649.2	894	Agc/Tgc	8/11	0.197000571790481	5	FACETS	1	0.909	1	0.371	0.313	0.434	INDETERMINATE	1	FALSE	2	0.416022678768115	5		264	316	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245086	53245086	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0056580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	188	419	0	ENST00000375401.3:c.854C>G	p.Ser285Ter	p.S285*	ENST00000375401	NM_004187.3	285	tCa/tGa	7/26	0.421748822765641	2	FACETS	0.871	0.82	0.922			1	CLONAL	3	FALSE	NA	0.416022678768115	2		419	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0056600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	259	504	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.25762500776491	2	FACETS	0.971	0.915	1	1	0.993	1	CLONAL	3	FALSE	0	0.25762500776491	2		504	690	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0056600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	43	274	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.25762500776491	3	FACETS	0.841	0.711	0.983	0.841	0.711	0.983	CLONAL	2	FALSE	1	0.25762500776491	3		274	224	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412095	63412095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852217	NA	P-0056600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	403	776	0	ENST00000330258.3:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000330258	NM_152424.3	358	Cga/Tga	2/2	0.25762500776491	4	FACETS	0.905	0.865	0.944	1	0.996	1	CLONAL	5	FALSE	1	0.25762500776491	4		776	870	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1327796	1327798	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs761286705	NA	P-0056600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	70	462	0	ENST00000400841.2:c.83_85del	p.Glu28del	p.E28del	ENST00000400841		28	gAAGga/gga	2/6	0.25762500776491	4	FACETS	1	0.964	1	0.436	0.38	0.495	CLONAL	1	FALSE	1	0.25762500776491	4		462	523	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027023	48027023	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	62	393	0	ENST00000234420.5:c.1901T>C	p.Leu634Ser	p.L634S	ENST00000234420	NM_000179.2	634	tTg/tCg	4/10	0.25762500776491	5	FACETS	0.794	0.688	0.909	0.397	0.344	0.455	CLONAL	2	FALSE	1	0.25762500776491	5		393	420	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023259	31023259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	260	547	0	ENST00000375687.4:c.2744C>T	p.Ser915Phe	p.S915F	ENST00000375687	NM_015338.5	915	tCc/tTc	13/13	0.25762500776491	10	FACETS	0.974	0.913	1	0.557	0.521	0.593	CLONAL	4	FALSE	3	0.25762500776491	10		547	1052	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032182	26032182	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	63	356	0	ENST00000244661.2:c.107T>A	p.Val36Glu	p.V36E	ENST00000244661	NM_003537.3	36	gTg/gAg	1/1	0.25762500776491	6	FACETS	1	0.969	1	0.487	0.422	0.558	CLONAL	1	FALSE	3	0.25762500776491	6		356	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0056602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	133	707	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.22	2		707	955	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0056603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	32	523	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		523	570	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0056605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	107	330	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.805	0.724	0.891	0.805	0.724	0.891	CLONAL	1	TRUE	1	0.44059552251452	2		330	603	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394341	162394341	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146173584	NA	P-0056605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	48	371	0	ENST00000366898.1:c.727G>A	p.Asp243Asn	p.D243N	ENST00000366898	NM_004562.2	243	Gac/Aac	6/12	0.230411762417582	0	FACETS	0.292	0.247	0.342			1	INDETERMINATE	1	TRUE	0	0.44059552251452	0		371	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs530941076	NA	P-0056605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	224	751	0	ENST00000269305.4:c.658T>G	p.Tyr220Asp	p.Y220D	ENST00000269305	NM_001126112.2	220	Tat/Gat	6/11	0.44059552251452	1	FACETS	0.904	0.843	0.967	0.904	0.843	0.967	CLONAL	1	TRUE	0	0.44059552251452	1		751	877	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842725	68842725	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	146	515	1	ENST00000261769.5:c.661G>T	p.Asp221Tyr	p.D221Y	ENST00000261769	NM_004360.3	221	Gat/Tat	5/16	0.44059552251452	1	FACETS	0.686	0.627	0.748	0.686	0.627	0.748	SUBCLONAL	1	TRUE	0	0.44059552251452	1		516	753	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0056606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	87	348	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.906	0.804	1	0.906	0.804	1	CLONAL	1	TRUE	1	0.327589609665682	2		348	586	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129749	108129749	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs780619951	NA	P-0056606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	98	366	0	ENST00000278616.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000278616	NM_000051.3	805	Cga/Tga	16/63	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.327589609665682	2		366	554	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214065	108214074	+	frameshift_variant	Frame_Shift_Del	DEL	TTTCAGTGCC	TTTCAGTGCC	-	rs786202800	NA	P-0056606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	50	264	1	ENST00000278616.4:c.8395_8404del	p.Phe2799LysfsTer4	p.F2799Kfs*4	ENST00000278616	NM_000051.3	2795	gaTTTCAGTGCC/ga	57/63	1	2	FACETS	0.821	0.699	0.954	0.821	0.699	0.954	CLONAL	1	TRUE	1	0.327589609665682	2		265	372	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0056607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	525	794	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.13673992484428	3	FACETS	1	0.996	1	0.745	0.713	0.776	INDETERMINATE	1	TRUE	1	0.609663010741528	3		794	1509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0056607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	360	893	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.13673992484428	3	FACETS	1	0.994	1	0.69	0.654	0.726	INDETERMINATE	1	TRUE	1	0.609663010741528	3		894	1117	SUCCESS
APC	324	MSKCC	GRCh37	5	112174580	112174580	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	126	277	0	ENST00000257430.4:c.3289G>T	p.Glu1097Ter	p.E1097*	ENST00000257430	NM_000038.5	1097	Gaa/Taa	16/16	0.609663010741528	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.609663010741528	1		277	262	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448592	89448592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543425684	NA	P-0056607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	107	453	0	ENST00000336596.2:c.1556C>T	p.Thr519Met	p.T519M	ENST00000336596	NM_005233.5	519	aCg/aTg	7/17	1	2	FACETS	0.706	0.636	0.78	0.706	0.636	0.78	SUBCLONAL	1	TRUE	1	0.609663010741528	2		453	497	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139831	55139831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758137485	NA	P-0056607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	152	416	0	ENST00000257290.5:c.1492G>A	p.Ala498Thr	p.A498T	ENST00000257290	NM_006206.4	498	Gcc/Acc	10/23	0.609663010741528	1	FACETS	0.643	0.591	0.696	0.643	0.591	0.696	SUBCLONAL	1	TRUE	0	0.609663010741528	1		416	539	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93953172	93953172	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs758658280	NA	P-0056607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	31	286	0	ENST00000369303.4:c.2969A>G	p.His990Arg	p.H990R	ENST00000369303	NM_004440.3	990	cAt/cGt	17/17	0.192022430309346	2	FACETS	0.415	0.337	0.502	0.208	0.168	0.251	INDETERMINATE	1	TRUE	0	0.609663010741528	2		286	245	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577095	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519984	NA	P-0056609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	422	789	0	ENST00000269305.4:c.843C>G	p.Asp281Glu	p.D281E	ENST00000269305	NM_001126112.2	281	gaC/gaG	8/11	0.704231824171586	2	FACETS	0.989	0.957	1	0.989	0.957	1	CLONAL	2	TRUE	0	0.705128118146901	2		789	605	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722445	176722445	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	43	341	0	ENST00000439151.2:c.8076A>C	p.Glu2692Asp	p.E2692D	ENST00000439151	NM_022455.4	2692	gaA/gaC	23/23	0.707690754290693	4	FACETS	0.396	0.331	0.468			1	SUBCLONAL	1	TRUE	NA	0.705128118146901	4		341	525	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0056610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	436	1058	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.0853365023595513	6	FACETS	1	0.97	1			1	INDETERMINATE	4	FALSE	NA	0.458927122179037	6		1058	899	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670340	134670340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415689583	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	58	539	0	ENST00000398015.3:c.251G>A	p.Arg84His	p.R84H	ENST00000398015	NM_004441.4	84	cGc/cAc	3/16	1	2	FACETS	0.75	0.645	0.865	0.75	0.645	0.865	SUBCLONAL	1	TRUE	1	0.29	2		539	533	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737052	162737052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765973930	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	110	521	0	ENST00000367921.3:c.1196G>A	p.Arg399Gln	p.R399Q	ENST00000367921	NM_006182.2	399	cGg/cAg	11/18	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.29	2		521	653	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951811	2951811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146334064	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	107	724	3	ENST00000396946.4:c.3139G>A	p.Ala1047Thr	p.A1047T	ENST00000396946	NM_032415.4	1047	Gcc/Acc	23/25	0.3	3	FACETS	1	0.949	1			1	CLONAL	1	TRUE	NA	0.29	3		727	771	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	194	527	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.982	1	1	0.994	1	CLONAL	2	TRUE	1	0.29	2		530	578	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	106	953	6	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	0.78	0.698	0.867	0.78	0.698	0.867	SUBCLONAL	1	TRUE	1	0.29	2		959	937	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	45	860	1	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	1	2	FACETS	0.404	0.338	0.476	0.404	0.338	0.476	SUBCLONAL	1	TRUE	1	0.29	2		861	769	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	64	1215	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.402	0.347	0.463	0.402	0.347	0.463	SUBCLONAL	1	TRUE	1	0.29	2		1216	1097	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	57	387	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.809	0.695	0.933	0.809	0.695	0.933	CLONAL	1	TRUE	1	0.29	2		388	486	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	20	426	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.242	0.184	0.31	0.242	0.184	0.31	SUBCLONAL	1	TRUE	1	0.29	2		426	570	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	56	476	3	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.722	0.619	0.835	0.722	0.619	0.835	SUBCLONAL	1	TRUE	1	0.29	2		479	535	SUCCESS
APC	324	MSKCC	GRCh37	5	112111327	112111327	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	18	164	0	ENST00000257430.4:c.424T>C	p.Ser142Pro	p.S142P	ENST00000257430	NM_000038.5	142	Tca/Cca	5/16	1	2	FACETS	0.762	0.577	0.976	0.762	0.577	0.976	CLONAL	1	TRUE	1	0.29	2		164	163	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131402	17131402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398124537	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	43	852	2	ENST00000285071.4:c.50G>A	p.Arg17His	p.R17H	ENST00000285071	NM_144997.5	17	cGc/cAc	4/14	1	2	FACETS	0.364	0.303	0.431	0.364	0.303	0.431	SUBCLONAL	1	TRUE	1	0.29	2		854	815	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481857	56481857	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519817	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	60	781	0	ENST00000267101.3:c.785C>A	p.Pro262His	p.P262H	ENST00000267101	NM_001982.3	262	cCt/cAt	7/28	1	2	FACETS	0.435	0.374	0.503	0.435	0.374	0.503	SUBCLONAL	1	TRUE	1	0.29	2		781	951	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440943	56440943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786205215	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	140	709	0	ENST00000407977.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000407977		132	Cga/Tga	4/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.29	2		709	748	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	79	376	1	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.29	2		377	475	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934126	39934127	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	54	428	0	ENST00000378444.4:c.472dup	p.Ser158LysfsTer28	p.S158Kfs*28	ENST00000378444	NM_001123385.1	158	agt/aAgt	4/15	1	1	FACETS	0.739	0.632	0.855	0.739	0.632	0.855	SUBCLONAL	1	TRUE	0	0.29	1		428	431	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	141	917	0	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.29	2		917	945	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274911	41274911	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	84	405	0	ENST00000349496.5:c.1161T>G	p.Asn387Lys	p.N387K	ENST00000349496	NM_001904.3	387	aaT/aaG	8/15	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.29	2		405	564	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	43	575	1	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	0.403	0.336	0.478	0.403	0.336	0.478	SUBCLONAL	1	TRUE	1	0.29	2		576	735	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	74	588	4	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.815	0.714	0.924	0.815	0.714	0.924	CLONAL	1	TRUE	1	0.29	2		592	626	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235927	133235927	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149777592	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	92	766	1	ENST00000320574.5:c.3229C>T	p.Arg1077Cys	p.R1077C	ENST00000320574	NM_006231.2	1077	Cgc/Tgc	26/49	1	2	FACETS	0.993	0.883	1	0.993	0.883	1	CLONAL	1	TRUE	1	0.29	2		767	639	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687471	37687472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs760014508	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	75	458	3	ENST00000447079.4:c.4382dup	p.Thr1463AsnfsTer50	p.T1463Nfs*50	ENST00000447079	NM_015083.1	1459	tgg/tGgg	14/14	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.29	2		461	452	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108788	2108788	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	119	835	3	ENST00000219476.3:c.894del	p.Phe298LeufsTer65	p.F298Lfs*65	ENST00000219476	NM_000548.3	297	Ttt/tt	10/42	1	2	FACETS	0.874	0.788	0.965	0.874	0.788	0.965	CLONAL	1	TRUE	1	0.29	2		838	939	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	117	439	0	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	1	1	FACETS	0.884	0.805	0.967	1	0.988	1	CLONAL	2	TRUE	0	0.29	1		439	390	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516905	187516905	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377350329	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	51	619	0	ENST00000441802.2:c.13076G>A	p.Arg4359Gln	p.R4359Q	ENST00000441802	NM_005245.3	4359	cGg/cAg	26/27	1	2	FACETS	0.499	0.423	0.582	0.499	0.423	0.582	SUBCLONAL	1	TRUE	1	0.29	2		619	705	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261555	142261555	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	57	335	0	ENST00000350721.4:c.3402del	p.Phe1134LeufsTer6	p.F1134Lfs*6	ENST00000350721	NM_001184.3	1134	ttT/tt	17/47	1	2	FACETS	0.921	0.792	1	0.921	0.792	1	CLONAL	1	TRUE	1	0.29	2		335	427	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511629	46511629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	37	466	0	ENST00000262741.5:c.1148G>A	p.Arg383His	p.R383H	ENST00000262741	NM_003629.3	383	cGt/cAt	9/10	1	2	FACETS	0.385	0.316	0.462	0.385	0.316	0.462	SUBCLONAL	1	TRUE	1	0.29	2		466	663	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647028	23647028	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1555461597	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	112	787	0	ENST00000261584.4:c.839del	p.Asn280ThrfsTer8	p.N280Tfs*8	ENST00000261584	NM_024675.3	280	aAc/ac	4/13	1	2	FACETS	0.796	0.715	0.883	0.796	0.715	0.883	SUBCLONAL	1	TRUE	1	0.29	2		787	970	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686901	37686901	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	74	648	1	ENST00000447079.4:c.3810del	p.Gly1271AspfsTer23	p.G1271Dfs*23	ENST00000447079	NM_015083.1	1269	Ccc/cc	14/14	1	2	FACETS	0.704	0.616	0.799	0.704	0.616	0.799	SUBCLONAL	1	TRUE	1	0.29	2		649	725	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567646	226567647	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1159330096	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	37	684	1	ENST00000366794.5:c.1519dup	p.Ser507LysfsTer14	p.S507Kfs*14	ENST00000366794	NM_001618.3	507	agc/aAgc	10/23	1	2	FACETS	0.367	0.302	0.441	0.367	0.302	0.441	SUBCLONAL	1	TRUE	1	0.29	2		685	695	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515198	106515198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146675267	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	68	436	0	ENST00000359195.3:c.2341G>A	p.Glu781Lys	p.E781K	ENST00000359195	NM_002649.2	781	Gaa/Aaa	5/11	1	2	FACETS	0.795	0.692	0.906	0.795	0.692	0.906	CLONAL	1	TRUE	1	0.29	2		436	590	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729601	41729601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	91	669	0	ENST00000242208.4:c.928C>T	p.Arg310Trp	p.R310W	ENST00000242208	NM_002192.2	310	Cgg/Tgg	3/3	1	2	FACETS	0.931	0.827	1	0.931	0.827	1	CLONAL	1	TRUE	1	0.29	2		669	674	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56872937	56872937	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	23	381	0	ENST00000308159.5:c.2097del	p.Phe699LeufsTer19	p.F699Lfs*19	ENST00000308159	NM_014669.4	698	Ttt/tt	19/22	1	2	FACETS	0.368	0.286	0.463	0.368	0.286	0.463	SUBCLONAL	1	TRUE	1	0.29	2		381	431	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612209	1612209	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs915880927	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	36	582	0	ENST00000344749.5:c.1810C>T	p.Arg604Ter	p.R604*	ENST00000344749	NM_001136139.2	604	Cga/Tga	18/19	1	2	FACETS	0.47	0.386	0.565	0.47	0.386	0.565	SUBCLONAL	1	TRUE	1	0.29	2		582	528	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856365	111856365	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750857643	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	23	110	0	ENST00000341259.2:c.416G>A	p.Arg139His	p.R139H	ENST00000341259	NM_005475.2	139	cGc/cAc	2/8	1	2	FACETS	0.991	0.78	1	0.991	0.78	1	CLONAL	1	TRUE	1	0.29	2		110	160	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916726	178916726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772110575	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	55	368	0	ENST00000263967.3:c.113G>A	p.Arg38His	p.R38H	ENST00000263967	NM_006218.2	38	cGt/cAt	2/21	1	2	FACETS	0.921	0.79	1	0.921	0.79	1	CLONAL	1	TRUE	1	0.29	2		368	412	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221206	5221206	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200191658	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	162	937	1	ENST00000357368.4:c.3260C>T	p.Thr1087Met	p.T1087M	ENST00000357368	NM_002850.3	1087	aCg/aTg	20/38	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.29	2		938	960	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993013	72993014	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	66	1124	0	ENST00000268489.5:c.1031dup	p.Asn344LysfsTer13	p.N344Kfs*13	ENST00000268489	NM_006885.3	344	aac/aaAc	2/10	1	2	FACETS	0.363	0.313	0.417	0.363	0.313	0.417	SUBCLONAL	1	TRUE	1	0.29	2		1124	1255	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346157	89346158	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs878855327	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	20	469	0	ENST00000301030.4:c.6792dup	p.Ala2265ArgfsTer8	p.A2265Rfs*8	ENST00000301030	NM_001256183.1	2264	-/C	9/13	1	2	FACETS	0.375	0.286	0.479	0.375	0.286	0.479	SUBCLONAL	1	TRUE	1	0.29	2		469	368	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	C	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	57	522	0	ENST00000558401.1:c.1A>C	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Ctg	1/4	1	2	FACETS	0.647	0.554	0.747	0.647	0.554	0.747	SUBCLONAL	1	TRUE	1	0.29	2		522	608	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405201	139405201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767886377	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	59	1099	2	ENST00000277541.6:c.2644G>A	p.Ala882Thr	p.A882T	ENST00000277541	NM_017617.3	882	Gca/Aca	17/34	1	2	FACETS	0.392	0.336	0.454	0.392	0.336	0.454	SUBCLONAL	1	TRUE	1	0.29	2		1101	1038	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526976	31526976	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1485879154	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	144	795	1	ENST00000344624.3:c.64C>T	p.Arg22Ter	p.R22*	ENST00000344624		22	Cga/Tga	2/33	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.29	2		796	890	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124310	2124310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs936484229	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	188	1135	1	ENST00000219476.3:c.2465C>T	p.Ala822Val	p.A822V	ENST00000219476	NM_000548.3	822	gCg/gTg	22/42	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.29	2		1136	1107	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	128	718	4	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.986	0.893	1	0.986	0.893	1	CLONAL	1	TRUE	1	0.29	2		722	895	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832811	3832811	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555484797	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	94	647	1	ENST00000262367.5:c.1447C>T	p.Arg483Ter	p.R483*	ENST00000262367	NM_004380.2	483	Cga/Tga	6/31	1	2	FACETS	0.832	0.74	0.931	0.832	0.74	0.931	CLONAL	1	TRUE	1	0.29	2		648	779	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984559	72984559	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770062973	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	175	1025	2	ENST00000268489.5:c.3025G>A	p.Val1009Met	p.V1009M	ENST00000268489	NM_006885.3	1009	Gtg/Atg	3/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.29	2		1027	1074	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16055259	16055259	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	44	361	0	ENST00000268712.3:c.842+1G>A		p.X281_splice	ENST00000268712	NM_006311.3	281			1	2	FACETS	0.627	0.526	0.739	0.627	0.526	0.739	SUBCLONAL	1	TRUE	1	0.29	2		361	484	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533883	63533884	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	112	662	0	ENST00000307078.5:c.1270_1271del	p.Ser424ProfsTer37	p.S424Pfs*37	ENST00000307078	NM_004655.3	424	TCc/c	6/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.29	2		662	661	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248138	98248138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763774051	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	58	474	0	ENST00000331920.6:c.413G>A	p.Arg138His	p.R138H	ENST00000331920	NM_000264.3	138	cGt/cAt	3/24	1	2	FACETS	0.63	0.541	0.727	0.63	0.541	0.727	SUBCLONAL	1	TRUE	1	0.29	2		474	635	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112323	115112324	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	rs1381943852	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	31	156	0	ENST00000257566.3:c.1416_1417del	p.Leu473ProfsTer218	p.L473Pfs*218	ENST00000257566	NM_016569.3	472	gcGCtc/gctc	7/8	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.29	2		156	197	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356281	66356282	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CA	CA	-	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	75	622	0	ENST00000273854.3:c.1215_1216del	p.Cys405Ter	p.C405*	ENST00000273854	NM_004439.5	405	tgTGag/tgag	5/18	1	2	FACETS	0.804	0.705	0.911	0.804	0.705	0.911	CLONAL	1	TRUE	1	0.29	2		622	643	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448408	49448408	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs797045661	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	46	827	3	ENST00000301067.7:c.303del	p.Ser102AlafsTer28	p.S102Afs*28	ENST00000301067	NM_003482.3	101	ggG/gg	3/54	1	2	FACETS	0.38	0.319	0.448	0.38	0.319	0.448	SUBCLONAL	1	TRUE	1	0.29	2		830	835	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245225	46245225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529386166	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	105	569	0	ENST00000334344.6:c.3319G>A	p.Ala1107Thr	p.A1107T	ENST00000334344	NM_152641.2	1107	Gca/Aca	15/21	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.29	2		569	662	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741586	17741586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	35	342	0	ENST00000250003.3:c.257G>A	p.Gly86Glu	p.G86E	ENST00000250003	NM_002478.4	86	gGg/gAg	1/3	1	2	FACETS	0.632	0.518	0.759	0.632	0.518	0.759	SUBCLONAL	1	TRUE	1	0.29	2		342	382	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248449	212248449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1256468343	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	49	399	0	ENST00000342788.4:c.3818G>A	p.Arg1273Gln	p.R1273Q	ENST00000342788	NM_005235.2	1273	cGg/cAg	28/28	1	2	FACETS	0.758	0.643	0.884	0.758	0.643	0.884	SUBCLONAL	1	TRUE	1	0.29	2		399	446	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564710	55564710	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	56	537	0	ENST00000288135.5:c.598T>A	p.Phe200Ile	p.F200I	ENST00000288135	NM_000222.2	200	Ttc/Atc	3/21	1	2	FACETS	0.657	0.562	0.76	0.657	0.562	0.76	SUBCLONAL	1	TRUE	1	0.29	2		537	588	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110165	8110165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774454455	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	119	689	0	ENST00000585124.1:c.440G>A	p.Arg147Gln	p.R147Q	ENST00000585124	NM_004217.3	147	cGg/cAg	6/9	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.29	2		689	766	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526441	66526441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	34	458	1	ENST00000358598.2:c.997C>T	p.Arg333Cys	p.R333C	ENST00000358598	NM_212471.2	333	Cgt/Tgt	11/11	1	2	FACETS	0.404	0.329	0.488	0.404	0.329	0.488	SUBCLONAL	1	TRUE	1	0.29	2		459	581	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222925	36222925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746346674	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	85	1190	0	ENST00000222270.7:c.5554G>A	p.Ala1852Thr	p.A1852T	ENST00000222270	NM_014727.1	1852	Gcc/Acc	27/37	1	2	FACETS	0.495	0.436	0.559	0.495	0.436	0.559	SUBCLONAL	1	TRUE	1	0.29	2		1190	1184	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604629	55604629	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779103998	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	137	673	0	ENST00000288135.5:c.2837G>A	p.Arg946Gln	p.R946Q	ENST00000288135	NM_000222.2	946	cGa/cAa	21/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.29	2		673	771	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245132	53245133	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	98	425	0	ENST00000375401.3:c.807dup	p.Thr270HisfsTer20	p.T270Hfs*20	ENST00000375401	NM_004187.3	269	-/C	7/26	1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.29	1		425	413	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652243	36652243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs558863376	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	162	877	0	ENST00000244741.5:c.365G>A	p.Arg122His	p.R122H	ENST00000244741	NM_000389.4	122	cGc/cAc	2/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.29	2		877	838	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902657	50902657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141319800	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	54	934	2	ENST00000440232.2:c.232C>T	p.Arg78Cys	p.R78C	ENST00000440232	NM_002691.3	78	Cgc/Tgc	3/27	1	2	FACETS	0.346	0.294	0.403	0.346	0.294	0.403	SUBCLONAL	1	TRUE	1	0.29	2		936	1077	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424740	49424740	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs917419349	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	56	929	0	ENST00000301067.7:c.13607G>A	p.Arg4536Gln	p.R4536Q	ENST00000301067	NM_003482.3	4536	cGa/cAa	40/54	1	2	FACETS	0.392	0.335	0.456	0.392	0.335	0.456	SUBCLONAL	1	TRUE	1	0.29	2		929	984	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225929	133225929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs550525366	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	111	962	1	ENST00000320574.5:c.3968C>T	p.Ala1323Val	p.A1323V	ENST00000320574	NM_006231.2	1323	gCc/gTc	31/49	1	2	FACETS	0.774	0.695	0.859	0.774	0.695	0.859	SUBCLONAL	1	TRUE	1	0.29	2		963	989	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426112	47426112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs923182352	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	55	531	1	ENST00000377045.4:c.632G>A	p.Arg211His	p.R211H	ENST00000377045	NM_001654.4	211	cGc/cAc	7/16	1	1	FACETS	0.602	0.515	0.697	0.602	0.515	0.697	SUBCLONAL	1	TRUE	0	0.29	1		532	539	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262714	16262714	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1022457753	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	96	465	1	ENST00000375759.3:c.9979G>A	p.Ala3327Thr	p.A3327T	ENST00000375759	NM_015001.2	3327	Gcc/Acc	11/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.29	2		466	525	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976638	90976638	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	46	350	0	ENST00000265433.3:c.994G>T	p.Gly332Ter	p.G332*	ENST00000265433	NM_002485.4	332	Gga/Tga	8/16	1	2	FACETS	0.726	0.612	0.851	0.726	0.612	0.851	SUBCLONAL	1	TRUE	1	0.29	2		350	437	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199443	11199443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746116382	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	123	672	0	ENST00000361445.4:c.5048G>A	p.Arg1683Gln	p.R1683Q	ENST00000361445	NM_004958.3	1683	cGg/cAg	36/58	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.29	2		672	691	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094289	27094291	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs759168859	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	44	400	0	ENST00000324856.7:c.3001_3003del	p.Ser1001del	p.S1001del	ENST00000324856	NM_006015.4	999	agTTCt/agt	11/20	1	2	FACETS	0.563	0.472	0.664	0.563	0.472	0.664	SUBCLONAL	1	TRUE	1	0.29	2		400	539	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410643	32410643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	42	668	0	ENST00000332351.3:c.1515G>A	p.Met505Ile	p.M505I	ENST00000332351	NM_024426.4	505	atG/atA	10/10	1	2	FACETS	0.427	0.355	0.506	0.427	0.355	0.506	SUBCLONAL	1	TRUE	1	0.29	2		668	679	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203738	94203738	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1343179190	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	42	292	0	ENST00000323929.3:c.916C>T	p.Gln306Ter	p.Q306*	ENST00000323929	NM_005591.3	306	Cag/Tag	9/20	1	2	FACETS	0.865	0.724	1	0.865	0.724	1	CLONAL	1	TRUE	1	0.29	2		292	335	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434965	110434965	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	56	1009	2	ENST00000375856.3:c.3436C>T	p.Arg1146Cys	p.R1146C	ENST00000375856	NM_003749.2	1146	Cgc/Tgc	1/2	1	2	FACETS	0.396	0.338	0.46	0.396	0.338	0.46	SUBCLONAL	1	TRUE	1	0.29	2		1011	976	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136832	2136832	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs45501091	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	133	909	0	ENST00000219476.3:c.4949A>G	p.Tyr1650Cys	p.Y1650C	ENST00000219476	NM_000548.3	1650	tAc/tGc	38/42	1	2	FACETS	0.903	0.819	0.992	0.903	0.819	0.992	CLONAL	1	TRUE	1	0.29	2		909	1016	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347431	89347431	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139088883	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	51	828	1	ENST00000301030.4:c.5519C>T	p.Ala1840Val	p.A1840V	ENST00000301030	NM_001256183.1	1840	gCg/gTg	9/13	1	2	FACETS	0.392	0.332	0.459	0.392	0.332	0.459	SUBCLONAL	1	TRUE	1	0.29	2		829	897	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805046	89805046	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	58	850	0	ENST00000389301.3:c.4331del	p.Pro1444LeufsTer27	p.P1444Lfs*27	ENST00000389301	NM_000135.2	1444	cCt/ct	43/43	1	2	FACETS	0.396	0.339	0.458	0.396	0.339	0.458	SUBCLONAL	1	TRUE	1	0.29	2		850	1011	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217028	7217028	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762497187	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	40	654	0	ENST00000380728.2:c.493G>A	p.Val165Met	p.V165M	ENST00000380728		165	Gtg/Atg	7/11	1	2	FACETS	0.395	0.327	0.471	0.395	0.327	0.471	SUBCLONAL	1	TRUE	1	0.29	2		654	698	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108547	8108547	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	47	806	1	ENST00000585124.1:c.848G>A	p.Arg283His	p.R283H	ENST00000585124	NM_004217.3	283	cGc/cAc	8/9	1	2	FACETS	0.373	0.313	0.439	0.373	0.313	0.439	SUBCLONAL	1	TRUE	1	0.29	2		807	870	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223303	5223303	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	97	899	0	ENST00000357368.4:c.2500G>T	p.Gly834Cys	p.G834C	ENST00000357368	NM_002850.3	834	Ggc/Tgc	18/38	1	2	FACETS	0.756	0.673	0.844	0.756	0.673	0.844	SUBCLONAL	1	TRUE	1	0.29	2		899	885	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117422	7117422	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	37	590	0	ENST00000302850.5:c.3795-1G>A		p.X1265_splice	ENST00000302850	NM_000208.2	1265			1	2	FACETS	0.393	0.323	0.471	0.393	0.323	0.471	SUBCLONAL	1	TRUE	1	0.29	2		590	650	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145729	11145729	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	100	978	0	ENST00000358026.2:c.4091A>C	p.Glu1364Ala	p.E1364A	ENST00000358026	NM_001128849.1	1364	gAg/gCg	29/36	1	2	FACETS	0.781	0.697	0.871	0.781	0.697	0.871	SUBCLONAL	1	TRUE	1	0.29	2		978	883	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271972	18271972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	44	398	0	ENST00000222254.8:c.575C>T	p.Ala192Val	p.A192V	ENST00000222254	NM_005027.3	192	gCc/gTc	5/16	1	2	FACETS	0.761	0.639	0.895	0.761	0.639	0.895	SUBCLONAL	1	TRUE	1	0.29	2		398	399	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752945	42752945	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	127	1102	0	ENST00000222329.4:c.1319T>C	p.Val440Ala	p.V440A	ENST00000222329	NM_006494.2	440	gTg/gCg	4/4	1	2	FACETS	0.846	0.765	0.932	0.846	0.765	0.932	CLONAL	1	TRUE	1	0.29	2		1102	1035	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637426	47637441	+	frameshift_variant	Frame_Shift_Del	DEL	TTGAGGCTCTCCTCAT	TTGAGGCTCTCCTCAT	-	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	128	678	0	ENST00000233146.2:c.560_575del	p.Leu187ProfsTer22	p.L187Pfs*22	ENST00000233146	NM_000251.2	187	cTTGAGGCTCTCCTCATc/cc	3/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.29	2		678	734	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655273	45655273	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	55	969	0	ENST00000407780.3:c.579G>A	p.Met193Ile	p.M193I	ENST00000407780	NM_001283052.1	193	atG/atA	4/7	1	2	FACETS	0.383	0.326	0.446	0.383	0.326	0.446	SUBCLONAL	1	TRUE	1	0.29	2		969	990	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525977	41525977	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	67	451	0	ENST00000263253.7:c.1252A>G	p.Lys418Glu	p.K418E	ENST00000263253	NM_001429.3	418	Aaa/Gaa	5/31	1	2	FACETS	0.801	0.696	0.914	0.801	0.696	0.914	CLONAL	1	TRUE	1	0.29	2		451	577	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691816	30691816	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	32	465	0	ENST00000295754.5:c.321del	p.Tyr108ThrfsTer16	p.Y108Tfs*16	ENST00000295754	NM_003242.5	106	ctC/ct	3/7	1	2	FACETS	0.361	0.292	0.439	0.361	0.292	0.439	SUBCLONAL	1	TRUE	1	0.29	2		465	612	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933692	49933692	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	110	1156	0	ENST00000296474.3:c.2585del	p.Pro862HisfsTer9	p.P862Hfs*9	ENST00000296474	NM_002447.2	862	cCa/ca	10/20	1	2	FACETS	0.766	0.687	0.85	0.766	0.687	0.85	SUBCLONAL	1	TRUE	1	0.29	2		1156	990	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948061	178948061	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	34	258	0	ENST00000263967.3:c.2835del	p.Phe945LeufsTer12	p.F945Lfs*12	ENST00000263967	NM_006218.2	945	Ttt/tt	20/21	1	2	FACETS	0.639	0.523	0.769	0.639	0.523	0.769	SUBCLONAL	1	TRUE	1	0.29	2		258	367	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612207	189612208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	66	635	0	ENST00000264731.3:c.1963dup	p.Arg655ProfsTer3	p.R655Pfs*3	ENST00000264731	NM_003722.4	653	-/C	14/14	1	2	FACETS	0.702	0.609	0.803	0.702	0.609	0.803	SUBCLONAL	1	TRUE	1	0.29	2		635	648	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751365	57751366	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	21	323	0	ENST00000274289.3:c.1625dup	p.Thr543AsnfsTer21	p.T543Nfs*21	ENST00000274289	NM_006622.3	542	aaa/aaAa		1	2	FACETS	0.381	0.293	0.484	0.381	0.293	0.484	SUBCLONAL	1	TRUE	1	0.29	2		323	380	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911315	29911315	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17185861	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	52	693	0	ENST00000376809.5:c.614G>A	p.Arg205His	p.R205H	ENST00000376809	NM_002116.7	205	cGc/cAc	3/8	1	2	FACETS	0.586	0.498	0.682	0.586	0.498	0.682	SUBCLONAL	1	TRUE	1	0.29	2		693	612	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372254	55372254	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	31	577	0	ENST00000297316.4:c.944C>A	p.Pro315Gln	p.P315Q	ENST00000297316	NM_022454.3	315	cCg/cAg	2/2	1	2	FACETS	0.355	0.286	0.434	0.355	0.286	0.434	SUBCLONAL	1	TRUE	1	0.29	2		577	602	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400980	139400980	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1397249771	NA	P-0056613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	77	663	0	ENST00000277541.6:c.4013C>T	p.Ala1338Val	p.A1338V	ENST00000277541	NM_017617.3	1338	gCg/gTg	24/34	1	2	FACETS	0.836	0.734	0.946	0.836	0.734	0.946	CLONAL	1	TRUE	1	0.29	2		663	635	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035188	42035188	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	374	713	1	ENST00000219905.7:c.5030A>T	p.Lys1677Met	p.K1677M	ENST00000219905	NM_001164273.1	1677	aAg/aTg	15/24	0.624657026118575	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.624657026118575	1		714	804	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016671	12016671	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0056614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	180	263	0	ENST00000353533.5:c.807C>G	p.Tyr269Ter	p.Y269*	ENST00000353533	NM_003010.3	269	taC/taG	7/11	0.614156303005344	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.624657026118575	1		263	349	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883656	37883656	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs768526064	NA	P-0056614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	402	903	0	ENST00000269571.5:c.3268C>G	p.Leu1090Val	p.L1090V	ENST00000269571		1090	Ctg/Gtg	26/27	1	2	FACETS	0.97	0.922	1	0.97	0.922	1	CLONAL	1	TRUE	1	0.624657026118575	2		903	1327	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774776	73774776	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	169	542	0	ENST00000254810.4:c.311T>G	p.Leu104Arg	p.L104R	ENST00000254810	NM_005324.3	104	cTg/cGg	4/4	0.419723199870043	1	FACETS	0.465	0.427	0.503	0.465	0.427	0.503	SUBCLONAL	1	TRUE	0	0.624657026118575	1		542	801	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30664729	30664729	+	intron_variant	Intron	SNP	C	C	G	rs113474008	NA	P-0056614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	61	195	0	ENST00000295754.5:c.94+16260C>G		p.*32*	ENST00000295754	NM_003242.5	45/592			0.379996513821198	3	FACETS	0.413	0.356	0.476	0.138	0.118	0.159	SUBCLONAL	1	TRUE	0	0.624657026118575	3		195	620	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448631	89448631	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0056614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	222	450	0	ENST00000336596.2:c.1594+1G>T		p.X532_splice	ENST00000336596	NM_005233.5	532			0.221884098235583	2	FACETS	0.885	0.826	0.946	0.443	0.413	0.473	INDETERMINATE	1	TRUE	0	0.624657026118575	2		450	803	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144077	55144669	+	splice_acceptor_variant,splice_donor_variant,frameshift_variant,stop_lost,intron_variant	Splice_Site	DEL	AGTGAAAAACAAGCTCTCATGTCTGAACTGAAGATAATGACTCACCTGGGGCCACATTTGAACATTGTAAACTTGCTGGGAGCCTGCACCAAGTCAGGTGGGCTCACTGACCTGGAGTGAGGATTTTCACTGGACACATGTGGTTGTGAAAACTGTTCAATCAGGCTTAAATCCTCCACTCTCCATCCCCACACATGGCAGGGAATAGAAGTCCCTTGAATGGAGCTGACTGGTCCCTTGAATTGATGGAAGCTCATTGGTTTTTGAGCAAAATCTGTTGCCAGTCCAGTCATAGCCATTCATGGCTCTTTATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACTTTTTTGGTATCTTATTTTTTTCTGTGCCATATGGTCTGCAGGACAATTCATGGCTTTTCTGTTCTTCATTTTCATACCCATCTCCTAACGGCTTTTGTCCCCATAGGCCCCATTTACATCATCACAGAGTATTGCTTCTATGGAGATTTGGTCAACTATTTGCATAAGAATAGGGATAGCTTCCTGAGCCACCACCCAGAGAAGCCAAAGAAAGAGCTGGATATCTTTGGATTGAACCCTGCTGATG	AGTGAAAAACAAGCTCTCATGTCTGAACTGAAGATAATGACTCACCTGGGGCCACATTTGAACATTGTAAACTTGCTGGGAGCCTGCACCAAGTCAGGTGGGCTCACTGACCTGGAGTGAGGATTTTCACTGGACACATGTGGTTGTGAAAACTGTTCAATCAGGCTTAAATCCTCCACTCTCCATCCCCACACATGGCAGGGAATAGAAGTCCCTTGAATGGAGCTGACTGGTCCCTTGAATTGATGGAAGCTCATTGGTTTTTGAGCAAAATCTGTTGCCAGTCCAGTCATAGCCATTCATGGCTCTTTATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACTTTTTTGGTATCTTATTTTTTTCTGTGCCATATGGTCTGCAGGACAATTCATGGCTTTTCTGTTCTTCATTTTCATACCCATCTCCTAACGGCTTTTGTCCCCATAGGCCCCATTTACATCATCACAGAGTATTGCTTCTATGGAGATTTGGTCAACTATTTGCATAAGAATAGGGATAGCTTCCTGAGCCACCACCCAGAGAAGCCAAAGAAAGAGCTGGATATCTTTGGATTGAACCCTGCTGATG	-	novel	NA	P-0056614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	35	360	0	ENST00000257290.5:c.1907_2144del		p.X636_splice	ENST00000257290	NM_006206.4	636	AGTGAAAAACAAGCTCTCATGTCTGAACTGAAGATAATGACTCACCTGGGGCCACATTTGAACATTGTAAACTTGCTGGGAGCCTGCACCAAGTCAGGTGGGCTCACTGACCTGGAGTGAGGATTTTCACTGGACACATGTGGTTGTGAAAACTGTTCAATCAGGCTTAAATCCTCCACTCTCCATCCCCACACATGGCAGGGAATAGAAGTCCCTTGAATGGAGCTGACTGGTCCCTTGAATTGATGGAAGCTCATTGGTTTTTGAGCAAAATCTGTTGCCAGTCCAGTCATAGCCATTCATGGCTCTTTATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACTTTTTTGGTATCTTATTTTTTTCTGTGCCATATGGTCTGCAGGACAATTCATGGCTTTTCTGTTCTTCATTTTCATACCCATCTCCTAACGGCTTTTGTCCCCATAGGCCCCATTTACATCATCACAGAGTATTGCTTCTATGGAGATTTGGTCAACTATTTGCATAAGAATAGGGATAGCTTCCTGAGCCACCACCCAGAGAAGCCAAAGAAAGAGCTGGATATCTTTGGATTGAACCCTGCTGATGaa/aa	14-15/23	0.619802603802748	1	FACETS	0.248	0.203	0.297	0.248	0.203	0.297	SUBCLONAL	1	TRUE	0	0.624657026118575	1		360	311	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0056616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	112	613	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.959	0.862	1	0.959	0.862	1	CLONAL	1	TRUE	1	0.28	2		613	834	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0056616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	85	234	2	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.294020355850038	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	2	TRUE	0	0.28	2		236	298	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0056616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	77	405	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.28	2		405	548	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105841	27105841	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	132	495	1	ENST00000324856.7:c.5452C>T	p.Gln1818Ter	p.Q1818*	ENST00000324856	NM_006015.4	1818	Cag/Tag	20/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.28	2		496	776	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692902	89692902	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	18	439	0	ENST00000371953.3:c.386G>T	p.Gly129Val	p.G129V	ENST00000371953	NM_000314.4	129	gGa/gTa	5/9	1	2	FACETS	0.222	0.166	0.288	0.222	0.166	0.288	SUBCLONAL	1	TRUE	1	0.28	2		439	580	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40478189	40478189	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	76	616	0	ENST00000264657.5:c.1310A>G	p.His437Arg	p.H437R	ENST00000264657	NM_139276.2	437	cAc/cGc	15/24	1	2	FACETS	0.536	0.469	0.609	0.536	0.469	0.609	SUBCLONAL	1	TRUE	1	0.28	2		616	1013	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740759	58740760	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0056616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	70	568	0	ENST00000305921.3:c.1664_1665insC	p.Leu555PhefsTer5	p.L555Ffs*5	ENST00000305921	NM_003620.3	555	tta/ttCa	6/6	1	2	FACETS	0.561	0.487	0.64	0.561	0.487	0.64	SUBCLONAL	1	TRUE	1	0.28	2		568	892	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859459	151859459	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	117	501	0	ENST00000262189.6:c.11203A>C	p.Lys3735Gln	p.K3735Q	ENST00000262189	NM_170606.2	3735	Aaa/Caa	43/59	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.28	2		501	829	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0056617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	423	569	0	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.697277583295252	2	FACETS	0.896	0.864	0.928	0.896	0.864	0.928	CLONAL	2	TRUE	0	0.703264458371972	2		569	671	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229284	55229284	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	45	707	0	ENST00000275493.2:c.1591C>T	p.Arg531Ter	p.R531*	ENST00000275493	NM_005228.3	531	Cga/Tga	13/28	0.691013369831553	3	FACETS	0.244	0.204	0.289	0.122	0.102	0.145	SUBCLONAL	1	TRUE	1	0.703264458371972	3		707	708	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056244	26056244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781319824	NA	P-0056617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	55	687	0	ENST00000343677.2:c.413C>T	p.Pro138Leu	p.P138L	ENST00000343677	NM_005319.3	138	cCc/cTc	1/1	0.666699232169907	3	FACETS	0.299	0.255	0.348	0.15	0.127	0.174	SUBCLONAL	1	TRUE	1	0.703264458371972	3		687	706	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31511142	31511142	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	147	745	0	ENST00000344624.3:c.1432G>A	p.Glu478Lys	p.E478K	ENST00000344624		478	Gag/Aag	6/33	0.703264458371972	3	FACETS	0.557	0.508	0.609	0.279	0.254	0.305	SUBCLONAL	1	TRUE	1	0.703264458371972	3		745	1014	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562416	176562416	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	421	681	0	ENST00000439151.2:c.312T>G	p.Asp104Glu	p.D104E	ENST00000439151	NM_022455.4	104	gaT/gaG	2/23	0.697277583295252	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.703264458371972	2		681	587	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874263	155874263	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1557960039	NA	P-0056618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	125	448	0	ENST00000368323.3:c.268A>G	p.Met90Val	p.M90V	ENST00000368323	NM_006912.5	90	Atg/Gtg	5/6	0.263637753144329	3	FACETS	1	0.969	1	0.585	0.529	0.643	CLONAL	1	TRUE	1	0.31579757598644	3		448	784	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023470	27023470	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	146	499	0	ENST00000324856.7:c.577del	p.Glu193SerfsTer39	p.E193Sfs*39	ENST00000324856	NM_006015.4	192	ctG/ct	1/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.31579757598644	2		499	881	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692932	89692932	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0056618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	213	462	0	ENST00000371953.3:c.416T>A	p.Leu139Ter	p.L139*	ENST00000371953	NM_000314.4	139	tTa/tAa	5/9	0.31579757598644	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.31579757598644	2		462	618	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871807	12871810	+	frameshift_variant	Frame_Shift_Del	DEL	CAGA	CAGA	-	novel	NA	P-0056618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	51	205	0	ENST00000228872.4:c.525_528del	p.Asp176ValfsTer48	p.D176Vfs*48	ENST00000228872	NM_004064.3	175	tCAGAc/tc	2/3	0.107031781763677	3	FACETS	0.982	0.837	1	0.491	0.418	0.57	INDETERMINATE	1	TRUE	1	0.31579757598644	3		205	381	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437672	110437672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	152	706	0	ENST00000375856.3:c.729G>A	p.Met243Ile	p.M243I	ENST00000375856	NM_003749.2	243	atG/atA	1/2	1	2	FACETS	0.949	0.867	1	0.949	0.867	1	CLONAL	1	TRUE	1	0.31579757598644	2		706	1014	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15840856	15840856	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	53	328	0	ENST00000307771.7:c.940T>A	p.Leu314Ile	p.L314I	ENST00000307771	NM_005089.3	314	Tta/Ata	11/11	0.298004679658205	3	FACETS	0.638	0.547	0.738	0.213	0.182	0.246	INDETERMINATE	1	TRUE	0	0.63377824315679	3		328	345	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266891	41266891	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	116	371	0	ENST00000349496.5:c.562A>G	p.Ile188Val	p.I188V	ENST00000349496	NM_001904.3	188	Atc/Gtc	5/15	0.749003287187417	2	FACETS	1	0.951	1	0.529	0.484	0.574	CLONAL	1	TRUE	0	0.749003287187417	2		371	293	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048754	180048754	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	105	973	0	ENST00000261937.6:c.1808G>T	p.Gly603Val	p.G603V	ENST00000261937	NM_182925.4	603	gGg/gTg	13/30	0.258515075771355	2	FACETS	0.364	0.325	0.404	0.182	0.162	0.202	INDETERMINATE	1	TRUE	0	0.749003287187417	2		973	771	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877860	151877878	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGTTGGCACAGGTCCAG	GAAGTTGGCACAGGTCCAG	-	novel	NA	P-0056622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	79	422	0	ENST00000262189.6:c.7067_7085del	p.Pro2356GlnfsTer3	p.P2356Qfs*3	ENST00000262189	NM_170606.2	2356	cCTGGACCTGTGCCAACTTCa/ca	36/59	0.421430204828641	3	FACETS	0.777	0.691	0.868	0.777	0.691	0.868	SUBCLONAL	2	TRUE	1	0.419807309602939	3		422	293	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226490	2226490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780810017	NA	P-0056622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	120	1076	0	ENST00000398665.3:c.3970G>A	p.Ala1324Thr	p.A1324T	ENST00000398665	NM_032482.2	1324	Gcg/Acg	27/28	0.421430204828641	2	FACETS	1	0.927	1	0.513	0.465	0.564	CLONAL	1	TRUE	0	0.419807309602939	2		1076	557	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78422340	78422340	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	113	338	0	ENST00000370768.2:c.1622A>G	p.Tyr541Cys	p.Y541C	ENST00000370768	NM_003902.3	541	tAc/tGc	17/20	0.421430204828641	2	FACETS	0.88	0.803	0.958	0.88	0.803	0.958	CLONAL	2	TRUE	0	0.419807309602939	2		338	306	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100446	8100448	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0056622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	510	986	0	ENST00000346208.3:c.420_422del	p.Leu141del	p.L141del	ENST00000346208		140	tcCTTg/tcg	3/6	0.419807309602939	7	FACETS	1	0.983	1	1	0.983	1	CLONAL	4	TRUE	3	0.419807309602939	7		986	1196	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115965	8115966	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	289	458	0	ENST00000346208.3:c.1312dup	p.Met438AsnfsTer69	p.M438Nfs*69	ENST00000346208		437	-/A	6/6	0.419807309602939	7	FACETS	1	0.972	1	1	0.972	1	CLONAL	4	TRUE	3	0.419807309602939	7		458	678	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117508	4117508	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	40	435	0	ENST00000262948.5:c.212A>G	p.Asp71Gly	p.D71G	ENST00000262948	NM_030662.3	71	gAc/gGc	2/11	0.421430204828641	1	FACETS	0.71	0.596	0.835	0.71	0.596	0.835	SUBCLONAL	1	TRUE	0	0.419807309602939	1		435	212	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572986	7572986	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555524156	NA	P-0056623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	297	441	0	ENST00000269305.4:c.1123C>T	p.Gln375Ter	p.Q375*	ENST00000269305	NM_001126112.2	375	Cag/Tag	11/11	0.584528402817754	2	FACETS	0.912	0.869	0.954	0.912	0.869	0.954	CLONAL	2	TRUE	0	0.597480061745353	2		441	545	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916926	178916937	+	inframe_deletion	In_Frame_Del	DEL	GTAGGCAACCGT	GTAGGCAACCGT	-	novel	NA	P-0056623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	765	346	0	ENST00000263967.3:c.314_325del	p.Val105_Arg108del	p.V105_R108del	ENST00000263967	NM_006218.2	105	GTAGGCAACCGT/-	2/21	0.597480061745353	8	FACETS	1	0.988	1	0.878	0.856	0.901	CLONAL	6	TRUE	1	0.597480061745353	8		346	1163	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881495	48881496	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0056623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	166	231	0	ENST00000267163.4:c.218_219insGG	p.Ala74GlufsTer4	p.A74Efs*4	ENST00000267163	NM_000321.2	73	aga/aGGga	2/27	0.584528402817754	2	FACETS	0.871	0.815	0.926	0.871	0.815	0.926	CLONAL	2	TRUE	0	0.597480061745353	2		231	319	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49054170	49054170	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1475201975	NA	P-0056623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	190	182	0	ENST00000267163.4:c.2750A>G	p.Asn917Ser	p.N917S	ENST00000267163	NM_000321.2	917	aAt/aGt	27/27	0.584528402817754	2	FACETS	0.896	0.843	0.948	0.896	0.843	0.948	CLONAL	2	TRUE	0	0.597480061745353	2		182	355	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206729	36206730	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0056623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1671	214	713	0	ENST00000300305.3:c.781_782dup	p.Gln262LeufsTer50	p.Q262Lfs*50	ENST00000300305		261	cct/ccCCt	6/8	0.597480061745353	5	FACETS	0.721	0.667	0.777	0.18	0.166	0.195	SUBCLONAL	1	TRUE	1	0.597480061745353	5		713	1885	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0056624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	55	221	1				ENST00000310581	NM_198253.2	-/1132			0.277223880845299	1	FACETS	1	0.959	1	1	0.982	1	CLONAL	2	FALSE	0	0.3	1		222	127	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0056624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	45	317	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.924	1	1	0.976	1	CLONAL	2	FALSE	1	0.3	2		317	134	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426779	212426779	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	40	453	0	ENST00000342788.4:c.2336A>G	p.His779Arg	p.H779R	ENST00000342788	NM_005235.2	779	cAc/cGc	20/28	0.182126468299109	3	FACETS	1	0.922	1	1	0.922	1	CLONAL	2	FALSE	1	0.3	3		453	134	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0056625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	125	604	0	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	0.525985079187231	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.525985079187231	1		604	346	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448297	56448298	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1567880599	NA	P-0056625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	159	746	2	ENST00000407977.2:c.349dup	p.Arg117ProfsTer8	p.R117Pfs*8	ENST00000407977		117	cgc/cCgc	3/10	0.525985079187231	1	FACETS	0.942	0.871	1	0.942	0.871	1	CLONAL	1	TRUE	0	0.525985079187231	1		748	473	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163376	47163377	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0056625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	45	234	0	ENST00000409792.3:c.2749dup	p.Ser917LysfsTer18	p.S917Kfs*18	ENST00000409792	NM_014159.6	917	agt/aAgt	3/21	1	2	FACETS	0.807	0.686	0.938	0.807	0.686	0.938	CLONAL	1	TRUE	1	0.525985079187231	2		234	212	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522657	67522657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	33	271	0	ENST00000274335.5:c.154G>T	p.Glu52Ter	p.E52*	ENST00000274335		52	Gaa/Taa	1/15	1	2	FACETS	0.477	0.39	0.574	0.477	0.39	0.574	SUBCLONAL	1	TRUE	1	0.525985079187231	2		271	263	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231290	46231290	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	13	289	0	ENST00000334344.6:c.1130T>A	p.Ile377Asn	p.I377N	ENST00000334344	NM_152641.2	377	aTt/aAt	10/21	NA	2	FACETS	0.218	0.155	0.294			1	INDETERMINATE	1	TRUE	NA	0.525985079187231	2		289	227	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12043175	12043175	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0056625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	68	225	0	ENST00000353533.5:c.1060A>T	p.Lys354Ter	p.K354*	ENST00000353533	NM_003010.3	354	Aaa/Taa	10/11	0.525985079187231	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	0	0.525985079187231	1		225	185	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66522027	66522027	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs281864784	NA	P-0056625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	51	184	0	ENST00000358598.2:c.682C>T	p.Arg228Ter	p.R228*	ENST00000358598	NM_212471.2	228	Cga/Tga	7/11	0.525985079187231	1	FACETS	0.831	0.719	0.949	0.831	0.719	0.949	CLONAL	1	TRUE	0	0.525985079187231	1		184	172	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245080	53245080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1428740468	NA	P-0056626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	123	694	0	ENST00000375401.3:c.860C>T	p.Ser287Leu	p.S287L	ENST00000375401	NM_004187.3	287	tCg/tTg	7/26	0.32818546035779	3	FACETS	0.801	0.722	0.883			1	CLONAL	1	TRUE	NA	0.32818546035779	3		694	1090	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579416	7579416	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	476	799	0	ENST00000269305.4:c.271del	p.Trp91GlyfsTer32	p.W91Gfs*32	ENST00000269305	NM_001126112.2	91	Tgg/gg	4/11	0.32818546035779	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	TRUE	0	0.32818546035779	3		799	1114	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856376	111856376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1473658393	NA	P-0056626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	33	148	0	ENST00000341259.2:c.427C>T	p.Arg143Cys	p.R143C	ENST00000341259	NM_005475.2	143	Cgc/Tgc	2/8	0.269938092540453	4	FACETS	1	0.905	1	0.586	0.48	0.703	CLONAL	1	TRUE	2	0.32818546035779	4		148	228	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372741	81372743	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	novel	NA	P-0056626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	51	263	0	ENST00000222390.5:c.791_793del	p.Asp264del	p.D264del	ENST00000222390	NM_000601.4	264	gATGgc/ggc	7/18	0.32818546035779	3	FACETS	0.808	0.687	0.939	0.404	0.343	0.47	CLONAL	1	TRUE	1	0.32818546035779	3		263	448	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0056627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	47	306	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.213003149574964	2		306	378	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520248	9520248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759137045	NA	P-0056627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	42	387	0	ENST00000353224.5:c.2021G>A	p.Arg674Gln	p.R674Q	ENST00000353224	NM_177990.2	674	cGg/cAg	10/10	1	2	FACETS	0.755	0.63	0.895	0.755	0.63	0.895	SUBCLONAL	1	TRUE	1	0.213003149574964	2		387	522	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042388	42042388	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0056627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	84	483	0	ENST00000219905.7:c.6583A>T	p.Lys2195Ter	p.K2195*	ENST00000219905	NM_001164273.1	2195	Aaa/Taa	17/24	0.213003149574964	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.213003149574964	1		483	549	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139862	55139862	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	71	327	2	ENST00000257290.5:c.1523G>T	p.Gly508Val	p.G508V	ENST00000257290	NM_006206.4	508	gGa/gTa	10/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.213003149574964	2		329	467	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041443	47041443	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0056627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	79	574	0	ENST00000377604.3:c.1785+2T>A		p.X595_splice	ENST00000377604	NM_001204468.1	595			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.213003149574964	2		574	614	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928889	49928891	+	missense_variant	Missense_Mutation	TNP	CAC	CAC	AAA	novel	NA	P-0056627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	85	784	2	ENST00000296474.3:c.3475_3477delinsTTT	p.Val1159Phe	p.V1159F	ENST00000296474	NM_002447.2	1159	GTG/TTT	16/20	1	2	FACETS	0.829	0.731	0.934	0.829	0.731	0.934	CLONAL	1	TRUE	1	0.213003149574964	2		786	963	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0056638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	397	670	0	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.563285857897319	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	FALSE	0	0.563285857897319	2		670	661	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265479	152265479	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766779326	NA	P-0056638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	64	499	0	ENST00000206249.3:c.932C>T	p.Thr311Met	p.T311M	ENST00000206249	NM_000125.3	311	aCg/aTg	4/8	0.519809894396545	4	FACETS	0.51	0.441	0.585	0.255	0.22	0.293	SUBCLONAL	1	FALSE	2	0.563285857897319	4		499	696	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958614	38958614	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	244	126	0	ENST00000357387.3:c.2351T>A	p.Leu784His	p.L784H	ENST00000357387	NM_152756.3	784	cTt/cAt	24/38	0.563285857897319	6	FACETS	1	0.985	1			1	CLONAL	4	FALSE	NA	0.563285857897319	6		126	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0056639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	602	718	30	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.43470279098434	3	FACETS	0.901	0.871	0.93	0.901	0.871	0.93	CLONAL	3	TRUE	0	0.506314578083652	3		748	1103	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573631	48573631	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	49	311	1	ENST00000342988.3:c.215T>A	p.Val72Asp	p.V72D	ENST00000342988	NM_005359.5	72	gTt/gAt	2/12	0.461571009127323	1	FACETS	0.719	0.617	0.828	0.719	0.617	0.828	SUBCLONAL	1	TRUE	0	0.506314578083652	1		312	201	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968273	134968273	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	134	622	3	ENST00000398015.3:c.2786G>T	p.Arg929Met	p.R929M	ENST00000398015	NM_004441.4	929	aGg/aTg	15/16	0.464899832715574	2	FACETS	0.78	0.71	0.853	0.39	0.355	0.427	SUBCLONAL	1	TRUE	0	0.506314578083652	2		625	679	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447053	187447053	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1336404127	NA	P-0056639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	415	686	10	ENST00000232014.4:c.1140C>A	p.Phe380Leu	p.F380L	ENST00000232014	NM_001130845.1	380	ttC/ttA	5/10	0.464899832715574	2	FACETS	0.918	0.879	0.957	0.918	0.879	0.957	CLONAL	2	TRUE	0	0.506314578083652	2		696	893	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447652	187447652	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	298	569	14	ENST00000232014.4:c.541G>T	p.Ala181Ser	p.A181S	ENST00000232014	NM_001130845.1	181	Gcc/Tcc	5/10	0.464899832715574	2	FACETS	0.83	0.787	0.874	0.83	0.787	0.874	CLONAL	2	TRUE	0	0.506314578083652	2		583	709	SUCCESS
APC	324	MSKCC	GRCh37	5	112175060	112175060	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	47	122	3	ENST00000257430.4:c.3769del	p.Glu1257LysfsTer8	p.E1257Kfs*8	ENST00000257430	NM_000038.5	1257	Gaa/aa	16/16	0.440254539621107	2	FACETS	0.767	0.666	0.872	0.767	0.666	0.872	SUBCLONAL	2	TRUE	0	0.506314578083652	2		125	121	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0056640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	365	913	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.369622085633929	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.369622085633929	2		913	912	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533054	63533054	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	141	680	0	ENST00000307078.5:c.1840G>C	p.Asp614His	p.D614H	ENST00000307078	NM_004655.3	614	Gac/Cac	7/11	0.276271198853359	2	FACETS	0.893	0.814	0.977	0.447	0.407	0.489	CLONAL	1	TRUE	0	0.369622085633929	2		680	854	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396734	139396734	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771399165	NA	P-0056640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	191	635	1	ENST00000277541.6:c.5374G>A	p.Val1792Met	p.V1792M	ENST00000277541	NM_017617.3	1792	Gtg/Atg	28/34	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.369622085633929	2		636	781	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913396	NA	P-0056641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	165	295	0	ENST00000349496.5:c.95A>T	p.Asp32Val	p.D32V	ENST00000349496	NM_001904.3	32	gAc/gTc	3/15	0.928634140263909	8	FACETS	1	0.95	1			1	CLONAL	1	TRUE	NA	0.928634140263909	8		295	1280	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0056641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	828	502	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.928634140263909	3	FACETS	0.996	0.986	1			1	CLONAL	3	TRUE	NA	0.928634140263909	3		502	874	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0056643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	134	376	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.62535082563019	3	FACETS	0.803	0.73	0.878			1	CLONAL	1	TRUE	NA	0.62535082563019	3		376	701	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438566	52438566	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1553645164	NA	P-0056643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	220	520	1	ENST00000460680.1:c.1153C>T	p.Arg385Ter	p.R385*	ENST00000460680	NM_004656.3	385	Cga/Tga	12/17	0.62535082563019	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.62535082563019	1		521	426	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172124	32172124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61756002	NA	P-0056643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	315	694	0	ENST00000375023.3:c.2908G>A	p.Asp970Asn	p.D970N	ENST00000375023	NM_004557.3	970	Gat/Aat	19/30	1	2	FACETS	0.993	0.938	1	0.993	0.938	1	CLONAL	1	TRUE	1	0.62535082563019	2		694	1015	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948136	178948136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	66	188	0	ENST00000263967.3:c.2908G>A	p.Glu970Lys	p.E970K	ENST00000263967	NM_006218.2	970	Gaa/Aaa	20/21	1	2	FACETS	0.88	0.773	0.991	0.88	0.773	0.991	CLONAL	1	TRUE	1	0.62535082563019	2		188	240	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717609	89717609	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs876661024	NA	P-0056643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	26	276	0	ENST00000371953.3:c.635-1G>C		p.X212_splice	ENST00000371953	NM_000314.4	212			0.62535082563019	3	FACETS	0.208	0.164	0.259			1	SUBCLONAL	1	TRUE	NA	0.62535082563019	3		276	524	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952019	178952019	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1553826166	NA	P-0056643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	130	288	0	ENST00000263967.3:c.3074C>G	p.Thr1025Ser	p.T1025S	ENST00000263967	NM_006218.2	1025	aCc/aGc	21/21	1	2	FACETS	0.954	0.872	1	0.954	0.872	1	CLONAL	1	TRUE	1	0.62535082563019	2		288	436	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763296	59763296	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	56	542	0	ENST00000259008.2:c.2806G>T	p.Glu936Ter	p.E936*	ENST00000259008	NM_032043.2	936	Gaa/Taa	19/20	1	2	FACETS	0.273	0.233	0.316	0.273	0.233	0.316	SUBCLONAL	1	TRUE	1	0.62535082563019	2		542	657	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151209	202151213	+	frameshift_variant	Frame_Shift_Del	DEL	TGAAG	TGAAG	-	rs1193329479	NA	P-0056643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	74	194	0	ENST00000358485.4:c.1513_1517del	p.Val505LeufsTer2	p.V505Lfs*2	ENST00000358485	NM_001080125.1	503	acTGAAGtg/actg	9/9	0.241593117325352	1	FACETS	0.707	0.629	0.789	0.707	0.629	0.789	INDETERMINATE	1	TRUE	0	0.62535082563019	1		194	230	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636933	176636934	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0056643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	54	441	0	ENST00000439151.2:c.1537_1538dup	p.Gly514ArgfsTer23	p.G514Rfs*23	ENST00000439151	NM_022455.4	511	-/AA	5/23	1	2	FACETS	0.271	0.231	0.315	0.271	0.231	0.315	SUBCLONAL	1	TRUE	1	0.62535082563019	2		441	637	SUCCESS
APC	324	MSKCC	GRCh37	5	112174784	112174784	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0056644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	26	228	0	ENST00000257430.4:c.3493A>T	p.Lys1165Ter	p.K1165*	ENST00000257430	NM_000038.5	1165	Aaa/Taa	16/16	1	2	FACETS	0.703	0.566	0.854	0.703	0.566	0.854	SUBCLONAL	1	TRUE	1	0.606250562125953	2		228	122	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0056644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	157	703	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.975	0.899	1	0.975	0.899	1	CLONAL	1	TRUE	1	0.606250562125953	2		703	531	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129884	55129884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs574683248	NA	P-0056644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	106	601	1	ENST00000257290.5:c.418G>A	p.Val140Met	p.V140M	ENST00000257290	NM_006206.4	140	Gtg/Atg	4/23	1	2	FACETS	0.847	0.765	0.932	0.847	0.765	0.932	CLONAL	1	TRUE	1	0.606250562125953	2		602	413	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913237	NA	P-0056644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	104	299	0	ENST00000369535.4:c.35G>T	p.Gly12Val	p.G12V	ENST00000369535	NM_002524.4	12	gGt/gTt	2/7	1	2	FACETS	0.866	0.782	0.955	0.866	0.782	0.955	CLONAL	1	TRUE	1	0.606250562125953	2		299	396	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593504	48593504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	95	245	0	ENST00000342988.3:c.1255G>A	p.Gly419Arg	p.G419R	ENST00000342988	NM_005359.5	419	Ggg/Agg	10/12	0.606250562125953	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.606250562125953	1		245	207	SUCCESS
APC	324	MSKCC	GRCh37	5	112175760	112175761	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs398123122	NA	P-0056644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	49	248	0	ENST00000257430.4:c.4473dup	p.Ala1492CysfsTer22	p.A1492Cfs*22	ENST00000257430	NM_000038.5	1490	cat/caTt	16/16	1	2	FACETS	0.762	0.654	0.879	0.762	0.654	0.879	SUBCLONAL	1	TRUE	1	0.606250562125953	2		248	212	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453150	140453150	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913341	NA	P-0056644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	71	251	0	ENST00000288602.6:c.1785T>G	p.Phe595Leu	p.F595L	ENST00000288602	NM_004333.4	595	ttT/ttG	15/18	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.606250562125953	2		251	233	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170464	108170464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	47	234	0	ENST00000278616.4:c.5029G>A	p.Glu1677Lys	p.E1677K	ENST00000278616	NM_000051.3	1677	Gaa/Aaa	34/63	0.606250562125953	1	FACETS	0.916	0.795	1	0.916	0.795	1	CLONAL	1	TRUE	0	0.606250562125953	1		234	118	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0056645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	244	221	1				ENST00000310581	NM_198253.2	-/1132			0.772648036509619	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.774161080302817	2		222	308	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0056645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	217	317	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.509130820516357	4	FACETS	0.945	0.887	1	0.945	0.887	1	CLONAL	2	TRUE	2	0.774161080302817	4		317	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0056645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	600	762	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.77136793885366	3	FACETS	0.958	0.937	0.979	0.958	0.937	0.979	CLONAL	3	TRUE	0	0.774161080302817	3		762	748	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0056645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	299	523	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.774161080302817	2	FACETS	0.985	0.951	1	0.985	0.951	1	CLONAL	2	TRUE	0	0.774161080302817	2		523	392	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812260	212812260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751175543	NA	P-0056645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	201	256	0	ENST00000342788.4:c.316C>T	p.Arg106Cys	p.R106C	ENST00000342788	NM_005235.2	106	Cgt/Tgt	3/28	0.228429340926322	5	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.774161080302817	5		256	451	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635217	87635217	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746097417	NA	P-0056645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	174	490	0	ENST00000277120.3:c.2269G>A	p.Val757Ile	p.V757I	ENST00000277120		757	Gtc/Atc	18/19	0.638483480349491	3	FACETS	1	0.944	1	0.512	0.473	0.552	CLONAL	1	TRUE	1	0.774161080302817	3		490	609	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615122	100615122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	140	397	0	ENST00000308731.7:c.793C>T	p.Pro265Ser	p.P265S	ENST00000308731	NM_000061.2	265	Cct/Tct	9/19	0.258511454784194	3	FACETS	0.919	0.841	1	0.306	0.28	0.334	INDETERMINATE	1	TRUE	0	0.774161080302817	3		397	546	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084112	47084112	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	246	502	0	ENST00000409792.3:c.7177C>T	p.Pro2393Ser	p.P2393S	ENST00000409792	NM_014159.6	2393	Ccc/Tcc	17/21	0.542540187018551	3	FACETS	0.788	0.744	0.833	0.788	0.744	0.833	SUBCLONAL	2	TRUE	1	0.774161080302817	3		502	559	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114824	108114824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	375	368	0	ENST00000278616.4:c.641C>T	p.Ser214Phe	p.S214F	ENST00000278616	NM_000051.3	214	tCc/tTc	6/63	0.770896487340749	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.774161080302817	2		368	475	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845995	156845995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	160	507	2	ENST00000524377.1:c.1625C>T	p.Ala542Val	p.A542V	ENST00000524377	NM_002529.3	542	gCt/gTt	13/17	0.747707114292591	4	FACETS	1	0.963	1	0.36	0.331	0.39	CLONAL	1	TRUE	1	0.774161080302817	4		509	679	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50811804	50811804	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	139	386	0	ENST00000398568.2:c.1081G>A	p.Asp361Asn	p.D361N	ENST00000398568	NM_001042412.1	361	Gac/Aac	7/18	0.638483480349491	3	FACETS	0.967	0.886	1	0.484	0.443	0.526	CLONAL	1	TRUE	1	0.774161080302817	3		386	515	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902847	1902847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	292	468	0	ENST00000382891.5:c.466G>A	p.Glu156Lys	p.E156K	ENST00000382891	NM_133335.3	156	Gaa/Aaa	2/22	0.772648036509619	2	FACETS	0.943	0.908	0.977	0.943	0.908	0.977	CLONAL	2	TRUE	0	0.774161080302817	2		468	400	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55143648	55143648	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	112	219	0	ENST00000257290.5:c.1880A>G	p.Lys627Arg	p.K627R	ENST00000257290	NM_006206.4	627	aAg/aGg	13/23	0.774161080302817	7	FACETS	1	0.952	1	0.22	0.197	0.244	CLONAL	1	TRUE	2	0.774161080302817	7		219	773	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319909	8319909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	229	286	0	ENST00000356435.5:c.5592G>A	p.Met1864Ile	p.M1864I	ENST00000356435		1864	atG/atA	34/35	0.774161080302817	2	FACETS	0.948	0.909	0.986	0.948	0.909	0.986	CLONAL	2	TRUE	0	0.774161080302817	2		286	312	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359938	87359938	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	184	295	0	ENST00000277120.3:c.1246G>A	p.Glu416Lys	p.E416K	ENST00000277120		416	Gaa/Aaa	11/19	0.638483480349491	3	FACETS	0.837	0.783	0.89	0.837	0.783	0.89	CLONAL	2	TRUE	1	0.774161080302817	3		295	394	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920645	127920645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	124	309	0	ENST00000373547.4:c.254G>A	p.Arg85Lys	p.R85K	ENST00000373547	NM_002721.4	85	aGa/aAa	4/7	0.638483480349491	3	FACETS	1	0.95	1	0.53	0.484	0.579	CLONAL	1	TRUE	1	0.774161080302817	3		309	419	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947596	48947596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1566196458	NA	P-0056646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	180	271	0	ENST00000267163.4:c.1183C>T	p.Gln395Ter	p.Q395*	ENST00000267163	NM_000321.2	395	Caa/Taa	12/27	0.837676557112373	1	FACETS	0.953	0.905	1	0.953	0.905	1	CLONAL	1	TRUE	0	0.837676557112373	1		271	262	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509666	29509666	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	180	394	0	ENST00000356175.3:c.871G>T	p.Glu291Ter	p.E291*	ENST00000356175	NM_000267.3	291	Gaa/Taa	8/57	0.394376581080535	1	FACETS	0.755	0.709	0.8	0.755	0.709	0.8	INDETERMINATE	1	TRUE	0	0.837676557112373	1		394	331	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720813	89720814	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0056646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	74	297	0	ENST00000371953.3:c.964_965insT	p.Lys322IlefsTer3	p.K322Ifs*3	ENST00000371953	NM_000314.4	322	aaa/aTaa	8/9	0.774300504809309	1	FACETS	0.406	0.36	0.454	0.406	0.36	0.454	SUBCLONAL	1	TRUE	0	0.837676557112373	1		297	253	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933217	100933217	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	164	426	0	ENST00000325455.5:c.2173C>G	p.Gln725Glu	p.Q725E	ENST00000325455	NM_001202474.3	725	Caa/Gaa	4/8	1	2	FACETS	0.84	0.778	0.904	0.84	0.778	0.904	CLONAL	1	TRUE	1	0.837676557112373	2		426	466	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416108	49416108	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	216	433	0	ENST00000301067.7:c.16367del	p.Asn5456ThrfsTer5	p.N5456Tfs*5	ENST00000301067	NM_003482.3	5456	aAc/ac	52/54	0.118844733654655	3	FACETS	1	0.99	1	0.656	0.614	0.698	INDETERMINATE	1	TRUE	1	0.837676557112373	3		433	558	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435282	110435282	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	60	188	0	ENST00000375856.3:c.3119A>T	p.Glu1040Val	p.E1040V	ENST00000375856	NM_003749.2	1040	gAg/gTg	1/2	0.118844733654655	3	FACETS	0.764	0.665	0.87	0.382	0.332	0.435	INDETERMINATE	1	TRUE	1	0.837676557112373	3		188	266	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456429	99456432	+	frameshift_variant	Frame_Shift_Del	DEL	GGCT	GGCT	-	novel	NA	P-0056646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	221	477	0	ENST00000268035.6:c.1747_1750del	p.Ala583Ter	p.A583*	ENST00000268035	NM_000875.3	582	aaGGCT/aa	8/21	0.394376581080535	1	FACETS	0.742	0.702	0.783	0.742	0.702	0.783	INDETERMINATE	1	TRUE	0	0.837676557112373	1		477	413	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162140	38162140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	107	407	0	ENST00000317025.8:c.2576C>T	p.Ala859Val	p.A859V	ENST00000317025	NM_023034.1	859	gCt/gTt	14/24	1	2	FACETS	0.46	0.414	0.509	0.46	0.414	0.509	SUBCLONAL	1	TRUE	1	0.837676557112373	2		407	555	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551457	150551457	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	253	729	0	ENST00000369026.2:c.550C>G	p.Arg184Gly	p.R184G	ENST00000369026	NM_021960.4	184	Cgg/Ggg	1/3	1	2	FACETS	0.974	0.911	1	0.974	0.911	1	CLONAL	1	TRUE	1	0.476400449175732	2		729	1091	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670099	29670099	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	177	324	0	ENST00000356175.3:c.7072G>T	p.Gly2358Ter	p.G2358*	ENST00000356175	NM_000267.3	2358	Gga/Tga	47/57	0.464070630733689	2	FACETS	0.958	0.895	1	0.958	0.895	1	CLONAL	2	TRUE	0	0.476400449175732	2		324	388	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361232	66361232	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	70	249	0	ENST00000273854.3:c.940C>A	p.Pro314Thr	p.P314T	ENST00000273854	NM_004439.5	314	Cct/Act	4/18	1	2	FACETS	0.805	0.706	0.911	0.805	0.706	0.911	CLONAL	1	TRUE	1	0.476400449175732	2		249	365	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560460	65560461	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0056647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	207	348	0	ENST00000358664.4:c.136_137del	p.Leu46AlafsTer40	p.L46Afs*40	ENST00000358664	NM_002382.4	46	TTg/g	3/5	0.476400449175732	2	FACETS	0.905	0.849	0.962	0.905	0.849	0.962	CLONAL	2	TRUE	0	0.476400449175732	2		348	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578480	7578498	+	frameshift_variant	Frame_Shift_Del	DEL	TGTGGAATCAACCCACAGC	TGTGGAATCAACCCACAGC	-	novel	NA	P-0056647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	416	736	0	ENST00000269305.4:c.432_450del	p.Gln144HisfsTer20	p.Q144Hfs*20	ENST00000269305	NM_001126112.2	144	caGCTGTGGGTTGATTCCACA/ca	5/11	0.464070630733689	2	FACETS	0.967	0.926	1	0.967	0.926	1	CLONAL	2	TRUE	0	0.476400449175732	2		736	903	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971261	15971261	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	234	378	0	ENST00000268712.3:c.4688A>T	p.His1563Leu	p.H1563L	ENST00000268712	NM_006311.3	1563	cAc/cTc	32/46	0.464070630733689	2	FACETS	0.992	0.936	1	0.992	0.936	1	CLONAL	2	TRUE	0	0.476400449175732	2		378	495	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692895	89692896	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	172	335	0	ENST00000371953.3:c.379_380insA	p.Gly127GlufsTer53	p.G127Efs*53	ENST00000371953	NM_000314.4	127	gga/gAga	5/9	0.476400449175732				0.947	1				CLONAL	2	TRUE	0	0.476400449175732	2		335	356	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836577	89836577	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056658-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	41	789	1	ENST00000389301.3:c.2313C>A	p.His771Gln	p.H771Q	ENST00000389301	NM_000135.2	771	caC/caA	25/43	0.21438083152296	1	FACETS	0.67	0.557	0.795	0.67	0.557	0.795	SUBCLONAL	1	TRUE	0	0.21438083152296	1		790	510	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0056660-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	43	612	1	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	1	2	FACETS	0.563	0.471	0.667	0.563	0.471	0.667	SUBCLONAL	1	TRUE	1	0.26	2		613	587	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729097	66729102	+	inframe_deletion	In_Frame_Del	DEL	AGATCA	AGATCA	-	novel	NA	P-0056660-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	51	497	0	ENST00000307102.5:c.306_311del	p.Ile103_Lys104del	p.I103_K104del	ENST00000307102	NM_002755.3	102	gAGATCAaa/gaa	3/11	1	2	FACETS	0.774	0.658	0.901	0.774	0.658	0.901	CLONAL	1	TRUE	1	0.26	2		497	507	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219359	1219360	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0056660-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	30	740	1	ENST00000326873.7:c.411_412delinsTT	p.Gln137_Glu138delinsHisTer	p.Q137_E138delinsH*	ENST00000326873	NM_000455.4	137	caGGaa/caTTaa	3/10	0.255214907244935	1	FACETS	0.356	0.286	0.436	0.356	0.286	0.436	SUBCLONAL	1	TRUE	0	0.26	1		741	564	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81941372	81941372	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056660-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	49	505	0	ENST00000359376.3:c.1550T>A	p.Val517Glu	p.V517E	ENST00000359376	NM_002661.3	517	gTg/gAg	16/33	1	2	FACETS	0.855	0.725	0.997	0.855	0.725	0.997	CLONAL	1	TRUE	1	0.26	2		505	441	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955220	17955220	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056660-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	29	699	0	ENST00000458235.1:c.7C>T	p.Pro3Ser	p.P3S	ENST00000458235	NM_000215.3	3	Cct/Tct	2/24	1	2	FACETS	0.388	0.31	0.477	0.388	0.31	0.477	SUBCLONAL	1	TRUE	1	0.26	2		699	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0056682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	36	803	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	1	2	FACETS	0.856	0.702	1	0.856	0.702	1	CLONAL	1	TRUE	1	0.14	2		803	601	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711945	89711946	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TAGAC	novel	NA	P-0056682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	14	373	1	ENST00000371953.3:c.564_568dup	p.Pro190LeufsTer11	p.P190Lfs*11	ENST00000371953	NM_000314.4	188	tat/taTAGACt	6/9	1	2	FACETS	0.858	0.621	1	0.858	0.621	1	CLONAL	1	TRUE	1	0.14	2		374	233	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554712	63554712	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	48	443	0	ENST00000307078.5:c.27C>A	p.Cys9Ter	p.C9*	ENST00000307078	NM_004655.3	9	tgC/tgA	2/11	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.14	2		443	576	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	372	324	0				ENST00000310581	NM_198253.2	-/1132			0.560739229553913	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	TRUE	1	0.568660782265324	4		324	672	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	65	463	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.542	0.471	0.618	0.542	0.471	0.618	SUBCLONAL	1	TRUE	1	0.568660782265324	2		463	422	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561263	9561263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769939031	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	170	386	0	ENST00000353224.5:c.519G>A	p.Met173Ile	p.M173I	ENST00000353224	NM_177990.2	173	atG/atA	4/10	0.353145932747519	1	FACETS	0.823	0.762	0.885	0.823	0.762	0.885	CLONAL	1	TRUE	0	0.568660782265324	1		386	520	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716344	18716344	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778895247	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	94	230	0	ENST00000266497.5:c.3691G>A	p.Glu1231Lys	p.E1231K	ENST00000266497		1231	Gaa/Aaa	26/31	1	2	FACETS	0.818	0.733	0.908	0.818	0.733	0.908	CLONAL	1	TRUE	1	0.568660782265324	2		230	404	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115012	3115012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555702147	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	342	660	3	ENST00000078429.4:c.547C>T	p.Arg183Cys	p.R183C	ENST00000078429	NM_002067.2	183	Cgc/Tgc	4/7	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.568660782265324	2		663	973	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37665992	37665992	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	125	265	0	ENST00000447079.4:c.2644C>T	p.Arg882Trp	p.R882W	ENST00000447079	NM_015083.1	882	Cgg/Tgg	7/14	0.353145932747519	1	FACETS	0.828	0.757	0.901	0.828	0.757	0.901	CLONAL	1	TRUE	0	0.568660782265324	1		265	380	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856364	111856364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	44	47	0	ENST00000341259.2:c.415C>T	p.Arg139Cys	p.R139C	ENST00000341259	NM_005475.2	139	Cgc/Tgc	2/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.568660782265324	2		47	113	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577161	64577161	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886039553	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	252	637	1	ENST00000312049.6:c.421C>T	p.Gln141Ter	p.Q141*	ENST00000312049	NM_130799.2	141	Cag/Tag	2/10	0.568660782265324	1	FACETS	0.925	0.87	0.98	0.925	0.87	0.98	CLONAL	1	TRUE	0	0.568660782265324	1		638	686	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760169	133760169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768153649	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	204	557	1	ENST00000318560.5:c.2492C>T	p.Pro831Leu	p.P831L	ENST00000318560	NM_005157.4	831	cCc/cTc	11/11	0.568660782265324	1	FACETS	0.976	0.913	1	0.976	0.913	1	CLONAL	1	TRUE	0	0.568660782265324	1		558	526	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041074	42041074	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	219	725	0	ENST00000219905.7:c.5452C>T	p.Arg1818Ter	p.R1818*	ENST00000219905	NM_001164273.1	1818	Cga/Tga	16/24	0.353145932747519	1	FACETS	0.763	0.713	0.815	0.763	0.713	0.815	SUBCLONAL	1	TRUE	0	0.568660782265324	1		725	722	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989487	212989487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765191737	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	60	232	0	ENST00000342788.4:c.224C>T	p.Ser75Phe	p.S75F	ENST00000342788	NM_005235.2	75	tCc/tTc	2/28	0.353145932747519	1	FACETS	0.436	0.378	0.499	0.436	0.378	0.499	SUBCLONAL	1	TRUE	0	0.568660782265324	1		232	346	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891641	28891641	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371347149	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	196	518	0	ENST00000282397.4:c.3380C>T	p.Pro1127Leu	p.P1127L	ENST00000282397	NM_002019.4	1127	cCt/cTt	25/30	1	2	FACETS	0.953	0.886	1	0.953	0.886	1	CLONAL	1	TRUE	1	0.568660782265324	2		518	723	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517828	187517828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	127	312	0	ENST00000441802.2:c.12866C>T	p.Pro4289Leu	p.P4289L	ENST00000441802	NM_005245.3	4289	cCc/cTc	25/27	1	2	FACETS	0.977	0.892	1	0.977	0.892	1	CLONAL	1	TRUE	1	0.568660782265324	2		312	457	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676149	29676149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	85	184	0	ENST00000356175.3:c.7138C>T	p.Pro2380Ser	p.P2380S	ENST00000356175	NM_000267.3	2380	Cct/Tct	48/57	0.353145932747519	1	FACETS	0.859	0.771	0.95	0.859	0.771	0.95	CLONAL	1	TRUE	0	0.568660782265324	1		184	249	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468522	89468522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	109	217	0	ENST00000336596.2:c.2056G>A	p.Glu686Lys	p.E686K	ENST00000336596	NM_005233.5	686	Gaa/Aaa	11/17	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.568660782265324	2		217	379	SUCCESS
AR	367	MSKCC	GRCh37	X	66863246	66863246	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	155	357	0	ENST00000374690.3:c.1765G>A	p.Glu589Lys	p.E589K	ENST00000374690	NM_000044.3	589	Gaa/Aaa	2/8	1	2	FACETS	0.995	0.916	1	0.995	0.916	1	CLONAL	1	TRUE	1	0.568660782265324	2		357	548	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457251	89457251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867835679	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	74	283	0	ENST00000336596.2:c.1732G>A	p.Glu578Lys	p.E578K	ENST00000336596	NM_005233.5	578	Gaa/Aaa	9/17	1	2	FACETS	0.681	0.6	0.768	0.681	0.6	0.768	SUBCLONAL	1	TRUE	1	0.568660782265324	2		283	382	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505128	149505128	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1483057981	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	192	461	0	ENST00000261799.4:c.1687G>A	p.Glu563Lys	p.E563K	ENST00000261799	NM_002609.3	563	Gag/Aag	12/23	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.568660782265324	2		461	660	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125635	47125635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	129	286	0	ENST00000409792.3:c.5635C>T	p.Arg1879Cys	p.R1879C	ENST00000409792	NM_014159.6	1879	Cgc/Tgc	12/21	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.568660782265324	2		286	452	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934283	68934283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773476490	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	201	319	0	ENST00000288368.4:c.349C>T	p.Arg117Cys	p.R117C	ENST00000288368	NM_024870.2	117	Cgt/Tgt	4/40	0.240190067112982	3	FACETS	0.762	0.71	0.814	0.762	0.71	0.814	INDETERMINATE	2	TRUE	1	0.568660782265324	3		319	596	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593652	55593652	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	132	329	0	ENST00000288135.5:c.1718C>G	p.Pro573Arg	p.P573R	ENST00000288135	NM_000222.2	573	cCa/cGa	11/21	1	2	FACETS	0.898	0.82	0.979	0.898	0.82	0.979	CLONAL	1	TRUE	1	0.568660782265324	2		329	517	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1959680	1959680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868806171	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	68	197	0	ENST00000382891.5:c.2902C>T	p.Arg968Cys	p.R968C	ENST00000382891	NM_133335.3	968	Cgt/Tgt	16/22	0.393922616584409	1	FACETS	0.512	0.449	0.58	0.512	0.449	0.58	SUBCLONAL	1	TRUE	0	0.568660782265324	1		197	334	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734069	58734069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61739281	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	145	423	2	ENST00000305921.3:c.1127C>T	p.Ser376Phe	p.S376F	ENST00000305921	NM_003620.3	376	tCt/tTt	5/6	0.353145932747519	1	FACETS	0.526	0.481	0.573	0.526	0.481	0.573	SUBCLONAL	1	TRUE	0	0.568660782265324	1		425	694	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526122	189526122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193287780	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	223	527	0	ENST00000264731.3:c.386C>T	p.Ser129Leu	p.S129L	ENST00000264731	NM_003722.4	129	tCg/tTg	4/14	1	2	FACETS	0.995	0.929	1	0.995	0.929	1	CLONAL	1	TRUE	1	0.568660782265324	2		527	788	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28624325	28624325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	171	411	0	ENST00000241453.7:c.649G>A	p.Glu217Lys	p.E217K	ENST00000241453	NM_004119.2	217	Gag/Aag	6/24	1	2	FACETS	0.855	0.789	0.924	0.855	0.789	0.924	CLONAL	1	TRUE	1	0.568660782265324	2		411	703	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562729	29562729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	149	386	0	ENST00000356175.3:c.3809C>T	p.Ser1270Phe	p.S1270F	ENST00000356175	NM_000267.3	1270	tCc/tTc	28/57	0.353145932747519	1	FACETS	0.714	0.657	0.774	0.714	0.657	0.774	SUBCLONAL	1	TRUE	0	0.568660782265324	1		386	525	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149250	119149250	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	378	401	0	ENST00000264033.4:c.1258C>G	p.Arg420Gly	p.R420G	ENST00000264033	NM_005188.3	420	Cga/Gga	9/16	0.539862896534909	2	FACETS	0.891	0.853	0.929	0.891	0.853	0.929	CLONAL	2	TRUE	0	0.568660782265324	2		401	746	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119585459	119585459	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	71	221	0	ENST00000316626.5:c.926G>A	p.Gly309Glu	p.G309E	ENST00000316626		309	gGa/gAa	9/12	1	2	FACETS	0.788	0.693	0.888	0.788	0.693	0.888	SUBCLONAL	1	TRUE	1	0.568660782265324	2		221	317	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476351	88476351	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	227	572	0	ENST00000360948.2:c.1781A>G	p.Asn594Ser	p.N594S	ENST00000360948	NM_001012338.2	594	aAc/aGc	15/19	0.353145932747519	1	FACETS	0.739	0.691	0.789	0.739	0.691	0.789	SUBCLONAL	1	TRUE	0	0.568660782265324	1		572	773	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256694	19256694	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	214	630	0	ENST00000162023.5:c.1019C>T	p.Pro340Leu	p.P340L	ENST00000162023		340	cCc/cTc	13/13	1	2	FACETS	0.807	0.75	0.865	0.807	0.75	0.865	CLONAL	1	TRUE	1	0.568660782265324	2		630	933	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812144	43812144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774120606	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	189	336	0	ENST00000372470.3:c.1009G>A	p.Glu337Lys	p.E337K	ENST00000372470	NM_005373.2	337	Gaa/Aaa	7/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.568660782265324	2		336	573	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115272979	115272979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	252	588	0	ENST00000438362.2:c.1394C>T	p.Ser465Leu	p.S465L	ENST00000438362	NM_001242891.1	465	tCa/tTa	12/20	NA	2	FACETS	0.975	0.914	1			1	INDETERMINATE	1	TRUE	NA	0.568660782265324	2		588	909	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471791	120471792	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	66	341	2	ENST00000256646.2:c.3699_3700delinsTT	p.His1234Tyr	p.H1234Y	ENST00000256646	NM_024408.3	1233	ccCCat/ccTTat	23/34	NA	2	FACETS	0.421	0.365	0.48			1	INDETERMINATE	1	TRUE	NA	0.568660782265324	2		343	552	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666666	206666666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	222	541	0	ENST00000367120.3:c.2000C>T	p.Pro667Leu	p.P667L	ENST00000367120	NM_014002.3	667	cCc/cTc	20/22	0.420476965909924	3	FACETS	0.99	0.921	1	0.495	0.46	0.531	CLONAL	1	TRUE	1	0.568660782265324	3		541	1013	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343960	118343960	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	259	236	0	ENST00000534358.1:c.2086C>T	p.Leu696Phe	p.L696F	ENST00000534358	NM_005933.3	696	Ctt/Ttt	3/36	0.539862896534909	2	FACETS	0.969	0.921	1	0.969	0.921	1	CLONAL	2	TRUE	0	0.568660782265324	2		236	470	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418446	49418446	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	75	513	0	ENST00000301067.7:c.15967C>G	p.Arg5323Gly	p.R5323G	ENST00000301067	NM_003482.3	5323	Cgc/Ggc	50/54	1	2	FACETS	0.355	0.31	0.402	0.355	0.31	0.402	SUBCLONAL	1	TRUE	1	0.568660782265324	2		513	744	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431625	49431625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756129096	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	80	633	1	ENST00000301067.7:c.9514C>T	p.Pro3172Ser	p.P3172S	ENST00000301067	NM_003482.3	3172	Cca/Tca	34/54	1	2	FACETS	0.348	0.305	0.393	0.348	0.305	0.393	SUBCLONAL	1	TRUE	1	0.568660782265324	2		634	809	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484072	50484072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	223	456	1	ENST00000394963.4:c.922C>T	p.His308Tyr	p.H308Y	ENST00000394963	NM_003076.4	308	Cat/Tat	8/13	1	2	FACETS	0.89	0.83	0.952	0.89	0.83	0.952	CLONAL	1	TRUE	1	0.568660782265324	2		457	881	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913596	32913597	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	77	243	0	ENST00000380152.3:c.5104_5105delinsTT	p.Pro1702Leu	p.P1702L	ENST00000380152		1702	CCa/TTa	11/27	1	2	FACETS	0.831	0.736	0.931	0.831	0.736	0.931	CLONAL	1	TRUE	1	0.568660782265324	2		243	326	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643774	38643774	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	155	569	0	ENST00000299084.4:c.1244C>T	p.Pro415Leu	p.P415L	ENST00000299084	NM_152594.2	415	cCa/cTa	7/7	0.353145932747519	1	FACETS	0.474	0.434	0.516	0.474	0.434	0.516	SUBCLONAL	1	TRUE	0	0.568660782265324	1		569	823	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729160	66729160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	125	503	1	ENST00000307102.5:c.368C>T	p.Ser123Phe	p.S123F	ENST00000307102	NM_002755.3	123	tCt/tTt	3/11	0.353145932747519	1	FACETS	0.413	0.374	0.455	0.413	0.374	0.455	SUBCLONAL	1	TRUE	0	0.568660782265324	1		504	761	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857490	9857490	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	95	391	0	ENST00000330684.3:c.3911T>G	p.Leu1304Arg	p.L1304R	ENST00000330684	NM_001134407.1	1304	cTt/cGt	13/13	0.353145932747519	1	FACETS	0.492	0.44	0.547	0.492	0.44	0.547	SUBCLONAL	1	TRUE	0	0.568660782265324	1		391	486	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614791	23614791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770692850	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	60	301	0	ENST00000261584.4:c.3550C>T	p.His1184Tyr	p.H1184Y	ENST00000261584	NM_024675.3	1184	Cac/Tac	13/13	0.353145932747519	1	FACETS	0.32	0.276	0.368	0.32	0.276	0.368	SUBCLONAL	1	TRUE	0	0.568660782265324	1		301	472	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348892	89348892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	318	719	0	ENST00000301030.4:c.4058C>T	p.Ser1353Phe	p.S1353F	ENST00000301030	NM_001256183.1	1353	tCc/tTc	9/13	0.353145932747519	1	FACETS	0.81	0.766	0.855	0.81	0.766	0.855	CLONAL	1	TRUE	0	0.568660782265324	1		719	988	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508647	38508647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	260	578	0	ENST00000254066.5:c.695C>T	p.Ser232Phe	p.S232F	ENST00000254066	NM_000964.3	232	tCc/tTc	6/9	0.353145932747519	1	FACETS	0.819	0.77	0.869	0.819	0.77	0.869	CLONAL	1	TRUE	0	0.568660782265324	1		578	799	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252783	10252783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	233	578	1	ENST00000340748.4:c.3182C>T	p.Thr1061Ile	p.T1061I	ENST00000340748		1061	aCc/aTc	29/40	1	2	FACETS	0.973	0.91	1	0.973	0.91	1	CLONAL	1	TRUE	1	0.568660782265324	2		579	842	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311619	30311619	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	120	248	0	ENST00000262643.3:c.473T>G	p.Val158Gly	p.V158G	ENST00000262643	NM_001238.2	158	gTc/gGc	7/12	1	2	FACETS	0.993	0.904	1	0.993	0.904	1	CLONAL	1	TRUE	1	0.568660782265324	2		248	425	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015092	27015092	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	101	355	1	ENST00000335756.4:c.194T>C	p.Leu65Pro	p.L65P	ENST00000335756	NM_001809.3	65	cTg/cCg	2/5	0.353145932747519	1	FACETS	0.481	0.431	0.533	0.481	0.431	0.533	SUBCLONAL	1	TRUE	0	0.568660782265324	1		356	529	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917857	29917857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	157	636	0	ENST00000389048.3:c.811C>T	p.Pro271Ser	p.P271S	ENST00000389048	NM_004304.4	271	Ccc/Tcc	3/29	0.353145932747519	1	FACETS	0.513	0.47	0.557	0.513	0.47	0.557	SUBCLONAL	1	TRUE	0	0.568660782265324	1		636	771	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141129	55141129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444218873	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	122	284	0	ENST00000257290.5:c.1775G>A	p.Gly592Glu	p.G592E	ENST00000257290	NM_006206.4	592	gGa/gAa	12/23	1	2	FACETS	0.935	0.851	1	0.935	0.851	1	CLONAL	1	TRUE	1	0.568660782265324	2		284	459	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561716	55561716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781633384	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	111	255	0	ENST00000288135.5:c.106C>T	p.Pro36Ser	p.P36S	ENST00000288135	NM_000222.2	36	Cca/Tca	2/21	1	2	FACETS	0.925	0.838	1	0.925	0.838	1	CLONAL	1	TRUE	1	0.568660782265324	2		255	422	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871316	35871316	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs777878144	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	28	195	0	ENST00000303115.3:c.537+1G>A		p.X179_splice	ENST00000303115	NM_002185.3	179			0.560739229553913	4	FACETS	0.338	0.27	0.416	0.113	0.09	0.139	SUBCLONAL	1	TRUE	1	0.568660782265324	4		195	457	SUCCESS
APC	324	MSKCC	GRCh37	5	112179183	112179183	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881269	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	82	225	0	ENST00000257430.4:c.7892C>T	p.Ser2631Phe	p.S2631F	ENST00000257430	NM_000038.5	2631	tCc/tTc	16/16	1	2	FACETS	0.955	0.851	1	0.955	0.851	1	CLONAL	1	TRUE	1	0.568660782265324	2		225	302	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515195	149515195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	245	555	0	ENST00000261799.4:c.287G>A	p.Gly96Glu	p.G96E	ENST00000261799	NM_002609.3	96	gGa/gAa	3/23	1	2	FACETS	0.929	0.869	0.99	0.929	0.869	0.99	CLONAL	1	TRUE	1	0.568660782265324	2		555	928	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819816	170819816	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	249	579	0	ENST00000296930.5:c.455C>T	p.Pro152Leu	p.P152L	ENST00000296930	NM_002520.6	152	cCa/cTa	5/11	1	2	FACETS	0.884	0.827	0.942	0.884	0.827	0.942	CLONAL	1	TRUE	1	0.568660782265324	2		579	991	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2966376	2966376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	380	547	0	ENST00000396946.4:c.1804G>A	p.Asp602Asn	p.D602N	ENST00000396946	NM_032415.4	602	Gat/Aat	14/25	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.568660782265324	2		547	1007	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346383	152346383	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	182	388	0	ENST00000359321.1:c.187G>A	p.Ala63Thr	p.A63T	ENST00000359321	NM_005431.1	63	Gca/Aca	3/3	1	2	FACETS	0.96	0.889	1	0.96	0.889	1	CLONAL	1	TRUE	1	0.568660782265324	2		388	667	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273395	38273395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	259	723	0	ENST00000425967.3:c.1940C>T	p.Ser647Phe	p.S647F	ENST00000425967	NM_001174067.1	647	tCc/tTc	14/19	0.353145932747519	1	FACETS	0.71	0.666	0.755	0.71	0.666	0.755	SUBCLONAL	1	TRUE	0	0.568660782265324	1		723	918	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972942	68972942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs902315304	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	168	299	1	ENST00000288368.4:c.1267G>A	p.Gly423Arg	p.G423R	ENST00000288368	NM_024870.2	423	Gga/Aga	11/40	0.240190067112982	3	FACETS	1	0.987	1	0.676	0.625	0.729	INDETERMINATE	1	TRUE	1	0.568660782265324	3		300	561	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970976	70970976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1208665663	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	185	596	0	ENST00000276594.2:c.1285G>A	p.Asp429Asn	p.D429N	ENST00000276594	NM_024504.3	429	Gat/Aat	6/8	0.240190067112982	3	FACETS	0.777	0.716	0.84	0.388	0.358	0.42	INDETERMINATE	1	TRUE	1	0.568660782265324	3		596	1076	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412942	63412943	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	242	698	3	ENST00000330258.3:c.224_225delinsTA	p.Gly75Val	p.G75V	ENST00000330258	NM_152424.3	75	gGG/gTA	2/2	1	2	FACETS	0.841	0.786	0.898	0.841	0.786	0.898	CLONAL	1	TRUE	1	0.568660782265324	2		701	1012	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907606	76907606	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	168	300	0	ENST00000373344.5:c.4555G>A	p.Glu1519Lys	p.E1519K	ENST00000373344	NM_000489.3	1519	Gag/Aag	15/35	1	2	FACETS	0.947	0.874	1	0.947	0.874	1	CLONAL	1	TRUE	1	0.568660782265324	2		300	624	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543662	29543662	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	108	516	0	ENST00000389048.3:c.1501T>G	p.Trp501Gly	p.W501G	ENST00000389048	NM_004304.4	501	Tgg/Ggg	7/29	0.353145932747519	1	FACETS	0.342	0.306	0.38	0.342	0.306	0.38	SUBCLONAL	1	TRUE	0	0.568660782265324	1		516	795	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0056684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	46	340	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.73	0.622	0.846	0.73	0.622	0.846	SUBCLONAL	1	TRUE	1	0.606077787816505	2		340	208	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473711	67473711	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	282	623	0	ENST00000327367.4:c.791C>A	p.Ser264Tyr	p.S264Y	ENST00000327367	NM_005902.3	264	tCc/tAc	6/9	0.163488462736572	1	FACETS	0.675	0.635	0.716	0.675	0.635	0.716	INDETERMINATE	1	TRUE	0	0.606077787816505	1		623	961	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0056684-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	40	296	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.559785176154082	2		296	133	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0056684-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	63	340	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.559785176154082	2		340	187	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473711	67473711	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056684-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	70	623	0	ENST00000327367.4:c.791C>A	p.Ser264Tyr	p.S264Y	ENST00000327367	NM_005902.3	264	tCc/tAc	6/9	0.180519862581514	1	FACETS	0.9	0.8	1	0.9	0.8	1	INDETERMINATE	1	TRUE	0	0.559785176154082	1		623	200	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733335	85733335	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	77	341	0	ENST00000370580.1:c.677G>T	p.Arg226Ile	p.R226I	ENST00000370580	NM_003921.4	226	aGa/aTa	3/3	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.334248475971502	2		341	447	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	56	324	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.2	2		324	552	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397742	49397742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552757	NA	P-0056687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	70	488	1	ENST00000418115.1:c.482C>T	p.Ala161Val	p.A161V	ENST00000418115	NM_001664.2	161	gCa/gTa	5/5	1	2	FACETS	0.772	0.671	0.881	0.772	0.671	0.881	SUBCLONAL	1	TRUE	1	0.2	2		489	907	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128532	30128532	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs748363746	NA	P-0056687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	83	602	0	ENST00000263025.4:c.850C>G	p.Leu284Val	p.L284V	ENST00000263025	NM_002746.2	284	Ctg/Gtg	6/9	1	2	FACETS	0.937	0.825	1	0.937	0.825	1	CLONAL	1	TRUE	1	0.2	2		602	886	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505389	157505389	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	53	397	0	ENST00000346085.5:c.3370G>C	p.Glu1124Gln	p.E1124Q	ENST00000346085	NM_020732.3	1124	Gag/Cag	13/20	1	2	FACETS	0.945	0.806	1	0.945	0.806	1	CLONAL	1	TRUE	1	0.2	2		397	561	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0056688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	101	274	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.55784304571906	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.55784304571906	1		274	247	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989463	7989463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	231	653	2	ENST00000319144.4:c.223G>A	p.Ala75Thr	p.A75T	ENST00000319144	NM_001139.2	75	Gcc/Acc	2/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.55784304571906	2		655	768	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420282	49420291	+	frameshift_variant	Frame_Shift_Del	DEL	TAGACCCGCC	TAGACCCGCC	-	novel	NA	P-0056688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	227	698	0	ENST00000301067.7:c.15458_15467del	p.Arg5153ProfsTer7	p.R5153Pfs*7	ENST00000301067	NM_003482.3	5153	cGGCGGGTCTAc/cc	48/54	1	2	FACETS	0.988	0.922	1	0.988	0.922	1	CLONAL	1	TRUE	1	0.55784304571906	2		698	824	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	98	324	0				ENST00000310581	NM_198253.2	-/1132			0.378985322447483	1	FACETS	0.751	0.672	0.835	0.751	0.672	0.835	SUBCLONAL	1	TRUE	0	0.378985322447483	1		324	558	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562482	21562483	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGGCG	rs550642106	NA	P-0056689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	12	105	1	ENST00000382592.4:c.1431_1436dup	p.Pro479_Ala480dup	p.P479_A480dup	ENST00000382592	NM_014572.2	479	ccg/ccCGCCCCg	4/8	0.280820938761112	2	FACETS	0.379	0.267	0.516	0.19	0.133	0.258	SUBCLONAL	1	TRUE	0	0.378985322447483	2		106	167	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942029	44942030	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	53	288	0	ENST00000377967.4:c.3284dup	p.Trp1096ValfsTer7	p.W1096Vfs*7	ENST00000377967	NM_021140.2	1093	-/A	22/29	0.273466406525103	1	FACETS	0.677	0.58	0.782	0.677	0.58	0.782	SUBCLONAL	1	TRUE	0	0.378985322447483	1		288	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587782272	NA	P-0056689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	184	558	0	ENST00000269305.4:c.994-1G>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.378985322447483	1	FACETS	0.967	0.894	1	0.967	0.894	1	CLONAL	1	TRUE	0	0.378985322447483	1		558	814	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65311254	65311254	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	45	403	0	ENST00000342505.4:c.2057T>G	p.Leu686Arg	p.L686R	ENST00000342505	NM_002227.2	686	cTt/cGt	15/25	0.273466406525103	1	FACETS	0.302	0.253	0.356	0.302	0.253	0.356	SUBCLONAL	1	TRUE	0	0.378985322447483	1		403	638	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429360	78429360	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	125	443	0	ENST00000370768.2:c.1082G>C	p.Arg361Thr	p.R361T	ENST00000370768	NM_003902.3	361	aGa/aCa	13/20	0.273466406525103	1	FACETS	0.731	0.663	0.804	0.731	0.663	0.804	SUBCLONAL	1	TRUE	0	0.378985322447483	1		443	731	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716212	243716212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	65	467	0	ENST00000263826.5:c.982G>A	p.Asp328Asn	p.D328N	ENST00000263826	NM_005465.4	328	Gac/Aac	10/13	0.273466406525103	1	FACETS	0.451	0.391	0.517	0.451	0.391	0.517	SUBCLONAL	1	TRUE	0	0.378985322447483	1		467	616	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160362	108160362	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	26	224	0	ENST00000278616.4:c.4270G>C	p.Glu1424Gln	p.E1424Q	ENST00000278616	NM_000051.3	1424	Gag/Cag	29/63	0.378985322447483	1	FACETS	0.499	0.397	0.614	0.499	0.397	0.614	SUBCLONAL	1	TRUE	0	0.378985322447483	1		224	223	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597606	28597606	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	34	436	0	ENST00000241453.7:c.2299G>C	p.Glu767Gln	p.E767Q	ENST00000241453	NM_004119.2	767	Gaa/Caa	19/24	0.280820938761112	2	FACETS	0.389	0.318	0.47	0.195	0.159	0.235	SUBCLONAL	1	TRUE	0	0.378985322447483	2		436	461	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602402	28602402	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	44	405	0	ENST00000241453.7:c.1966G>C	p.Glu656Gln	p.E656Q	ENST00000241453	NM_004119.2	656	Gag/Cag	16/24	0.280820938761112	2	FACETS	0.453	0.379	0.534	0.226	0.189	0.267	SUBCLONAL	1	TRUE	0	0.378985322447483	2		405	513	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914248	32914248	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	52	360	0	ENST00000380152.3:c.5756A>C	p.Lys1919Thr	p.K1919T	ENST00000380152		1919	aAg/aCg	11/27	0.280820938761112	2	FACETS	0.637	0.543	0.739	0.318	0.271	0.37	SUBCLONAL	1	TRUE	0	0.378985322447483	2		360	431	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778279	3778279	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	81	700	0	ENST00000262367.5:c.6769C>T	p.Gln2257Ter	p.Q2257*	ENST00000262367	NM_004380.2	2257	Cag/Tag	31/31	0.261466226976588	0	FACETS	0.329	0.289	0.371			1	SUBCLONAL	1	TRUE	0	0.378985322447483	0		700	808	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900545	3900545	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	99	767	0	ENST00000262367.5:c.551C>A	p.Thr184Asn	p.T184N	ENST00000262367	NM_004380.2	184	aCc/aAc	2/31	0.261466226976588	0	FACETS	0.356	0.317	0.397			1	SUBCLONAL	1	TRUE	0	0.378985322447483	0		767	912	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78933923	78933923	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	165	746	0	ENST00000306801.3:c.3523G>A	p.Asp1175Asn	p.D1175N	ENST00000306801	NM_020761.2	1175	Gat/Aat	30/34	1	2	FACETS	0.819	0.751	0.89	0.819	0.751	0.89	CLONAL	1	TRUE	1	0.378985322447483	2		746	1063	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214396	36214396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	178	592	0	ENST00000222270.7:c.3050C>T	p.Ala1017Val	p.A1017V	ENST00000222270	NM_014727.1	1017	gCt/gTt	7/37	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.378985322447483	2		592	844	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566523	41566523	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	86	300	0	ENST00000263253.7:c.4400A>C	p.Tyr1467Ser	p.Y1467S	ENST00000263253	NM_001429.3	1467	tAc/tCc	27/31	0.261466226976588	0	FACETS	0.651	0.579	0.727			1	SUBCLONAL	1	TRUE	0	0.378985322447483	0		300	433	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602939	55602939	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	44	364	0	ENST00000288135.5:c.2649C>G	p.Ile883Met	p.I883M	ENST00000288135	NM_000222.2	883	atC/atG	19/21	1	2	FACETS	0.447	0.374	0.527	0.447	0.374	0.527	SUBCLONAL	1	TRUE	1	0.378985322447483	2		364	520	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755629	57755629	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	372	713	1	ENST00000274289.3:c.158C>T	p.Pro53Leu	p.P53L	ENST00000274289	NM_006622.3	53	cCg/cTg	1/14	0.343992794850659	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.378985322447483	1		714	1288	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554797	106554797	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	42	302	0	ENST00000369096.4:c.1914G>T	p.Lys638Asn	p.K638N	ENST00000369096	NM_001198.3	638	aaG/aaT	7/7	1	2	FACETS	0.458	0.382	0.542	0.458	0.382	0.542	SUBCLONAL	1	TRUE	1	0.378985322447483	2		302	484	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577539	64577539	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	45	410	0	ENST00000312049.6:c.43T>C	p.Ser15Pro	p.S15P	ENST00000312049	NM_130799.2	15	Tcc/Ccc	2/10	0.144801677354086	3	FACETS	0.929	0.782	1			1	INDETERMINATE	1	FALSE	NA	0.262997714808041	3		410	417	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197654	106197654	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	23	196	0	ENST00000380013.4:c.5987G>A	p.Gly1996Glu	p.G1996E	ENST00000380013	NM_001127208.2	1996	gGg/gAg	11/11	1	2	FACETS	0.821	0.643	1	0.821	0.643	1	CLONAL	1	FALSE	1	0.262997714808041	2		196	213	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0056712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	323	645	2	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.743516581533175	1	FACETS	0.973	0.931	1	0.973	0.931	1	CLONAL	1	TRUE	0	0.743516581533175	1		647	561	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212252681	212252681	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	84	117	0	ENST00000342788.4:c.3172C>A	p.Pro1058Thr	p.P1058T	ENST00000342788	NM_005235.2	1058	Ccc/Acc	26/28	1	2	FACETS	0.978	0.879	1	0.978	0.879	1	CLONAL	1	TRUE	1	0.743516581533175	2		117	231	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782620	NA	P-0056714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	476	904	0	ENST00000269305.4:c.427G>A	p.Val143Met	p.V143M	ENST00000269305	NM_001126112.2	143	Gtg/Atg	5/11	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	2	TRUE	NA	0.772526241265189	2		904	610	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467865	66467865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs939351025	NA	P-0056714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	130	262	0	ENST00000273854.3:c.404G>A	p.Arg135Gln	p.R135Q	ENST00000273854	NM_004439.5	135	cGg/cAg	3/18	0.728758815341934	4	FACETS	0.988	0.911	1	0.988	0.911	1	CLONAL	2	TRUE	2	0.772526241265189	4		262	302	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857563	9857563	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	201	345	0	ENST00000330684.3:c.3838C>G	p.Gln1280Glu	p.Q1280E	ENST00000330684	NM_001134407.1	1280	Caa/Gaa	13/13	0.382278601840179	5	FACETS	0.909	0.854	0.963	0.909	0.854	0.963	INDETERMINATE	3	TRUE	2	0.772526241265189	5		345	412	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732514	74732514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	52	204	0	ENST00000359995.5:c.395G>A	p.Ser132Asn	p.S132N	ENST00000359995	NM_001195427.1	132	aGt/aAt	2/3	0.757494625569552	3	FACETS	1	0.868	1	0.502	0.434	0.574	CLONAL	1	TRUE	1	0.772526241265189	3		204	186	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858899	78858899	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	206	790	0	ENST00000306801.3:c.1934C>A	p.Ala645Asp	p.A645D	ENST00000306801	NM_020761.2	645	gCc/gAc	17/34	0.757494625569552	3	FACETS	1	0.955	1	0.517	0.481	0.554	CLONAL	1	TRUE	1	0.772526241265189	3		790	715	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750557	128750557	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	68	569	0	ENST00000377970.2:c.94G>C	p.Asp32His	p.D32H	ENST00000377970	NM_002467.4	32	Gac/Cac	2/3	0.772526241265189	7	FACETS	0.433	0.375	0.496	0.087	0.075	0.1	SUBCLONAL	1	TRUE	2	0.772526241265189	7		569	1191	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101966	11101966	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1265247876	NA	P-0056715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	380	737	0	ENST00000358026.2:c.1386C>G	p.Ile462Met	p.I462M	ENST00000358026	NM_001128849.1	462	atC/atG	8/36	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.78	2		737	941	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0056719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	178	488	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.606761893450551	2		488	550	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0056720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	207	722	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.39981892467532	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.39981892467532	1		722	616	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0056720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	100	358	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	0.998	0.896	1	0.998	0.896	1	CLONAL	1	TRUE	1	0.39981892467532	2		358	501	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942685	48942685	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913301	NA	P-0056720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	35	318	0	ENST00000267163.4:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000267163	NM_000321.2	358	Cga/Tga	11/27	1	2	FACETS	0.455	0.373	0.546	0.455	0.373	0.546	SUBCLONAL	1	TRUE	1	0.39981892467532	2		318	385	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716327	52716327	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	193	855	1	ENST00000322088.6:c.771G>T	p.Trp257Cys	p.W257C	ENST00000322088	NM_014225.5	257	tgG/tgT	6/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.39981892467532	2		856	807	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223178	36223178	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377408813	NA	P-0056720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	59	1115	0	ENST00000222270.7:c.5728C>T	p.Pro1910Ser	p.P1910S	ENST00000222270	NM_014727.1	1910	Ccc/Tcc	28/37	1	2	FACETS	0.263	0.225	0.305	0.263	0.225	0.305	SUBCLONAL	1	TRUE	1	0.39981892467532	2		1115	1121	SUCCESS
APC	324	MSKCC	GRCh37	5	112102026	112102027	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0056720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	18	301	0	ENST00000257430.4:c.140dup	p.Leu48ThrfsTer2	p.L48Tfs*2	ENST00000257430	NM_000038.5	47	gta/gTta	3/16	0.352719269183109	1	FACETS	0.239	0.18	0.31	0.239	0.18	0.31	SUBCLONAL	1	TRUE	0	0.39981892467532	1		301	301	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	735	660	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.376070772024245	3	FACETS	1	0.997	1	0.789	0.769	0.809	INDETERMINATE	2	TRUE	0	0.792952402056696	3		660	1094	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880998	37880998	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs144434331	NA	P-0056721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	607	995	1	ENST00000269571.5:c.2327G>T	p.Gly776Val	p.G776V	ENST00000269571		776	gGt/gTt	20/27	0.499102172728502	3	FACETS	0.914	0.884	0.945	0.914	0.884	0.945	CLONAL	2	TRUE	1	0.792952402056696	3		996	1169	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745214	41745214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750029623	NA	P-0056721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	541	758	1	ENST00000301178.4:c.1280G>A	p.Arg427His	p.R427H	ENST00000301178	NM_021913.4	427	cGc/cAc	9/20	0.733082351146883	4	FACETS	0.938	0.901	0.975	0.938	0.901	0.975	CLONAL	2	TRUE	2	0.792952402056696	4		759	1304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579436	7579437	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0056721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	603	958	1	ENST00000269305.4:c.250_251insA	p.Ala84AspfsTer65	p.A84Dfs*65	ENST00000269305	NM_001126112.2	84	gcc/gAcc	4/11	0.751217668781688	2	FACETS	0.923	0.899	0.946	0.923	0.899	0.946	CLONAL	2	TRUE	0	0.792952402056696	2		959	824	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576835	7576858	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTCCCAAGACTTAGTACCTGAAG	GGTCCCAAGACTTAGTACCTGAAG	-	novel	NA	P-0056722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	338	582	0	ENST00000269305.4:c.988_993+18del		p.X330_splice	ENST00000269305	NM_001126112.2	330		9/11	0.668152027865704	2	FACETS	0.932	0.894	0.968	0.932	0.894	0.968	CLONAL	2	TRUE	0	0.668152027865704	2		582	543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576870	7576870	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	385	800	0	ENST00000269305.4:c.976G>C	p.Glu326Gln	p.E326Q	ENST00000269305	NM_001126112.2	326	Gaa/Caa	9/11	0.668152027865704	2	FACETS	0.893	0.859	0.928	0.893	0.859	0.928	CLONAL	2	TRUE	0	0.668152027865704	2		800	645	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245060	41245061	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80357658	NA	P-0056722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	572	839	1	ENST00000357654.3:c.2487dup	p.Lys830Ter	p.K830*	ENST00000357654	NM_007294.3	829	-/T	10/23	0.666649610146449	2	FACETS	0.922	0.893	0.95	0.922	0.893	0.95	CLONAL	2	TRUE	0	0.668152027865704	2		840	929	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0056723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	19	570	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.655	0.497	0.841	0.655	0.497	0.841	SUBCLONAL	1	TRUE	1	0.2	2		570	290	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591892	48591892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767345	NA	P-0056723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	14	559	0	ENST00000342988.3:c.1055G>A	p.Gly352Glu	p.G352E	ENST00000342988	NM_005359.5	352	gGa/gAa	9/12	0.116362238691635	3	FACETS	0.661	0.478	0.882	0.33	0.239	0.441	INDETERMINATE	1	TRUE	1	0.2	3		559	233	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432623	49432623	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555191147	NA	P-0056723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	22	1030	0	ENST00000301067.7:c.8516C>G	p.Ser2839Ter	p.S2839*	ENST00000301067	NM_003482.3	2839	tCa/tGa	34/54	1	2	FACETS	0.603	0.467	0.761	0.603	0.467	0.761	SUBCLONAL	1	TRUE	1	0.2	2		1030	365	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999032	100999032	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	15	1029	0	ENST00000325455.5:c.770C>T	p.Pro257Leu	p.P257L	ENST00000325455	NM_001202474.3	257	cCg/cTg	1/8	1	2	FACETS	0.536	0.391	0.709	0.536	0.391	0.709	SUBCLONAL	1	TRUE	1	0.2	2		1029	280	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238431	98238431	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	21	604	0	ENST00000331920.6:c.1613G>T	p.Gly538Val	p.G538V	ENST00000331920	NM_000264.3	538	gGg/gTg	12/24	1	2	FACETS	0.775	0.598	0.981	0.775	0.598	0.981	CLONAL	1	TRUE	1	0.2	2		604	271	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0056724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	348	517	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.214777912684225	6	FACETS	1	0.978	1			1	CLONAL	4	FALSE	NA	0.214777912684225	6		517	1096	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227019	2227019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	189	839	3	ENST00000398665.3:c.4499C>T	p.Ser1500Phe	p.S1500F	ENST00000398665	NM_032482.2	1500	tCt/tTt	27/28	0.211760910813628	2	FACETS	0.896	0.828	0.967	0.896	0.828	0.967	CLONAL	2	FALSE	0	0.214777912684225	2		842	982	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913381	NA	P-0056724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	56	737	0	ENST00000304494.5:c.322G>A	p.Asp108Asn	p.D108N	ENST00000304494	NM_000077.4	108	Gat/Aat	2/3	0.199728294959544	3	FACETS	0.661	0.564	0.767	0.33	0.282	0.384	SUBCLONAL	1	FALSE	1	0.214777912684225	3		737	874	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259139	36259139	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0056724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	160	781	1	ENST00000300305.3:c.351+1G>T		p.X117_splice	ENST00000300305		117			0.211760910813628	2	FACETS	0.892	0.819	0.969	0.892	0.819	0.969	CLONAL	2	FALSE	0	0.214777912684225	2		782	835	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585494	29585494	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs876660428	NA	P-0056724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	50	262	0	ENST00000356175.3:c.4243G>T	p.Glu1415Ter	p.E1415*	ENST00000356175	NM_000267.3	1415	Gaa/Taa	31/57	0.211760910813628	2	FACETS	0.909	0.778	1	0.909	0.778	1	CLONAL	2	FALSE	0	0.214777912684225	2		262	256	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578462	7578467	+	inframe_deletion	In_Frame_Del	DEL	GCGGGT	GCGGGT	-	rs1555526166	NA	P-0056724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	225	1029	0	ENST00000269305.4:c.463_468del	p.Thr155_Arg156del	p.T155_R156del	ENST00000269305	NM_001126112.2	155	ACCCGC/-	5/11	0.211760910813628	2	FACETS	0.948	0.882	1	0.948	0.882	1	CLONAL	2	FALSE	0	0.214777912684225	2		1029	1105	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781241	135781241	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	89	743	0	ENST00000298552.3:c.1724C>G	p.Ser575Cys	p.S575C	ENST00000298552	NM_001162426.1	575	tCt/tGt	15/23	1	2	FACETS	0.965	0.854	1	0.965	0.854	1	CLONAL	1	FALSE	1	0.214777912684225	2		743	859	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240000	53240011	+	inframe_deletion	In_Frame_Del	DEL	CCGGCATCACAT	CCGGCATCACAT	-	novel	NA	P-0056724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	75	863	0	ENST00000375401.3:c.1430_1441del	p.Asn477_Val481delinsMet	p.N477_V481delinsM	ENST00000375401	NM_004187.3	477	aATGTGATGCCGGtg/atg	11/26	0.214777912684225	1	FACETS	0.758	0.663	0.861	0.758	0.663	0.861	SUBCLONAL	1	FALSE	0	0.214777912684225	1		863	822	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617452	43617452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	47	497	0	ENST00000355710.3:c.2789C>T	p.Thr930Met	p.T930M	ENST00000355710	NM_020975.4	930	aCg/aTg	16/20	0.115596586294496	3	FACETS	1	0.897	1	0.539	0.456	0.63	INDETERMINATE	1	TRUE	1	0.28	3		497	355	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572272	64572272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372468697	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	98	1134	3	ENST00000312049.6:c.1367G>A	p.Arg456His	p.R456H	ENST00000312049	NM_130799.2	456	cGc/cAc	10/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.28	2		1137	553	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662818	227662818	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	68	863	1	ENST00000305123.5:c.637C>T	p.Arg213Cys	p.R213C	ENST00000305123	NM_005544.2	213	Cgc/Tgc	1/2	0.3	2	FACETS	0.896	0.781	1			1	CLONAL	1	TRUE	NA	0.28	2		864	542	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	62	613	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.87	0.753	0.997	0.87	0.753	0.997	CLONAL	1	TRUE	1	0.28	2		613	509	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	33	466	0	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.28	2		466	212	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	69	703	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.862	0.751	0.981	0.862	0.751	0.981	CLONAL	1	TRUE	1	0.28	2		703	572	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129884	55129884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs574683248	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	30	601	1	ENST00000257290.5:c.418G>A	p.Val140Met	p.V140M	ENST00000257290	NM_006206.4	140	Gtg/Atg	4/23	1	2	FACETS	0.604	0.487	0.736	0.604	0.487	0.736	SUBCLONAL	1	TRUE	1	0.28	2		602	355	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041074	42041074	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	57	725	0	ENST00000219905.7:c.5452C>T	p.Arg1818Ter	p.R1818*	ENST00000219905	NM_001164273.1	1818	Cga/Tga	16/24	1	2	FACETS	0.932	0.801	1	0.932	0.801	1	CLONAL	1	TRUE	1	0.28	2		725	437	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075368	8075368	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	18	288	0	ENST00000377482.5:c.202G>T	p.Gly68Trp	p.G68W	ENST00000377482	NM_018948.3	68	Ggg/Tgg	3/4	1	2	FACETS	0.688	0.52	0.884	0.688	0.52	0.884	SUBCLONAL	1	TRUE	1	0.28	2		288	187	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202870	16202870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	66	605	0	ENST00000375759.3:c.578G>A	p.Arg193His	p.R193H	ENST00000375759	NM_015001.2	193	cGc/cAc	3/15	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.28	2		605	464	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256467	16256467	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	57	691	0	ENST00000375759.3:c.3732T>G	p.Asn1244Lys	p.N1244K	ENST00000375759	NM_015001.2	1244	aaT/aaG	11/15	1	2	FACETS	0.768	0.659	0.887	0.768	0.659	0.887	SUBCLONAL	1	TRUE	1	0.28	2		691	530	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105541	27105541	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	42	587	1	ENST00000324856.7:c.5152G>T	p.Glu1718Ter	p.E1718*	ENST00000324856	NM_006015.4	1718	Gaa/Taa	20/20	1	2	FACETS	0.822	0.688	0.97	0.822	0.688	0.97	CLONAL	1	TRUE	1	0.28	2		588	365	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105815	27105815	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	63	624	0	ENST00000324856.7:c.5426T>G	p.Phe1809Cys	p.F1809C	ENST00000324856	NM_006015.4	1809	tTt/tGt	20/20	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.28	2		624	419	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795032	45795032	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768671057	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	60	759	1	ENST00000450313.1:c.1596C>A	p.Phe532Leu	p.F532L	ENST00000450313	NM_012222.2	532	ttC/ttA	16/16	1	2	FACETS	0.878	0.758	1	0.878	0.758	1	CLONAL	1	TRUE	1	0.28	2		760	488	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830924	156830924	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	47	908	0	ENST00000524377.1:c.198G>T	p.Glu66Asp	p.E66D	ENST00000524377	NM_002529.3	66	gaG/gaT	1/17	1	2	FACETS	0.753	0.636	0.881	0.753	0.636	0.881	SUBCLONAL	1	TRUE	1	0.28	2		908	446	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834161	156834161	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	83	947	1	ENST00000524377.1:c.228G>T	p.Gln76His	p.Q76H	ENST00000524377	NM_002529.3	76	caG/caT	2/17	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.28	2		948	570	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163297332	163297332	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1292835761	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	28	418	0	ENST00000271452.3:c.178C>T	p.Arg60Ter	p.R60*	ENST00000271452	NM_145697.2	60	Cga/Tga	3/14	1	2	FACETS	0.952	0.766	1	0.952	0.766	1	CLONAL	1	TRUE	1	0.28	2		418	210	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317622	163317622	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	16	356	0	ENST00000271452.3:c.1018T>G	p.Ser340Ala	p.S340A	ENST00000271452	NM_145697.2	340	Tcg/Gcg	12/14	1	2	FACETS	0.772	0.575	1	0.772	0.575	1	CLONAL	1	TRUE	1	0.28	2		356	148	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054983	176054983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs991566021	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	23	559	1	ENST00000367669.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000367669	NM_022457.5	357	cGa/cAa	10/20	1	2	FACETS	0.775	0.607	0.967	0.775	0.607	0.967	CLONAL	1	TRUE	1	0.28	2		560	212	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094281	193094281	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	40	449	0	ENST00000367435.3:c.171G>T	p.Leu57Phe	p.L57F	ENST00000367435	NM_024529.4	57	ttG/ttT	2/17	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.28	2		449	268	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117022	193117022	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	38	407	0	ENST00000367435.3:c.755T>G	p.Ile252Ser	p.I252S	ENST00000367435	NM_024529.4	252	aTt/aGt	8/17	1	2	FACETS	0.946	0.786	1	0.946	0.786	1	CLONAL	1	TRUE	1	0.28	2		407	287	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193219823	193219823	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	22	300	0	ENST00000367435.3:c.1577A>C	p.Lys526Thr	p.K526T	ENST00000367435	NM_024529.4	526	aAa/aCa	17/17	1	2	FACETS	1	0.837	1	1	0.837	1	CLONAL	1	TRUE	1	0.28	2		300	145	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518460	204518460	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	30	381	0	ENST00000367182.3:c.1123G>T	p.Asp375Tyr	p.D375Y	ENST00000367182	NM_001278516.1	375	Gat/Tat	11/11	1	2	FACETS	0.827	0.669	1	0.827	0.669	1	CLONAL	1	TRUE	1	0.28	2		381	259	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243675668	243675668	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	23	294	0	ENST00000263826.5:c.1312G>T	p.Glu438Ter	p.E438*	ENST00000263826	NM_005465.4	438	Gaa/Taa	12/13	1	2	FACETS	1	0.793	1	1	0.793	1	CLONAL	1	TRUE	1	0.28	2		294	163	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106059	8106059	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	46	700	1	ENST00000346208.3:c.879G>T	p.Met293Ile	p.M293I	ENST00000346208		293	atG/atT	4/6	0.3	2	FACETS	0.716	0.603	0.84			1	SUBCLONAL	1	TRUE	NA	0.28	2		701	459	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332144	70332144	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	15	239	0	ENST00000373644.4:c.49G>T	p.Asp17Tyr	p.D17Y	ENST00000373644	NM_030625.2	17	Gat/Tat	2/12	0.115596586294496	3	FACETS	0.736	0.541	0.968	0.368	0.27	0.484	INDETERMINATE	1	TRUE	1	0.28	3		239	166	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332415	70332415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1419371452	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	56	687	0	ENST00000373644.4:c.320G>A	p.Arg107Gln	p.R107Q	ENST00000373644	NM_030625.2	107	cGa/cAa	2/12	0.115596586294496	3	FACETS	1	0.9	1	0.53	0.455	0.612	INDETERMINATE	1	TRUE	1	0.28	3		687	430	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333858	70333858	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	33	455	1	ENST00000373644.4:c.1763G>T	p.Arg588Ile	p.R588I	ENST00000373644	NM_030625.2	588	aGa/aTa	2/12	0.115596586294496	3	FACETS	0.905	0.739	1	0.452	0.369	0.545	INDETERMINATE	1	TRUE	1	0.28	3		456	297	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692940	89692940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746152219	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	31	646	0	ENST00000371953.3:c.424C>T	p.Arg142Trp	p.R142W	ENST00000371953	NM_000314.4	142	Cgg/Tgg	5/9	1	2	FACETS	0.872	0.708	1	0.872	0.708	1	CLONAL	1	TRUE	1	0.28	2		646	254	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	25	569	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	0.735	0.581	0.91	0.735	0.581	0.91	CLONAL	1	TRUE	1	0.28	2		569	243	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711912	89711912	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	21	538	1	ENST00000371953.3:c.530A>C	p.Tyr177Ser	p.Y177S	ENST00000371953	NM_000314.4	177	tAt/tCt	6/9	1	2	FACETS	0.586	0.452	0.741	0.586	0.452	0.741	SUBCLONAL	1	TRUE	1	0.28	2		539	256	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720858	89720858	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	11	426	0	ENST00000371953.3:c.1009T>A	p.Phe337Ile	p.F337I	ENST00000371953	NM_000314.4	337	Ttt/Att	8/9	1	2	FACETS	0.595	0.413	0.819	0.595	0.413	0.819	SUBCLONAL	1	TRUE	1	0.28	2		426	132	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720871	89720871	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	12	454	0	ENST00000371953.3:c.1022T>G	p.Phe341Cys	p.F341C	ENST00000371953	NM_000314.4	341	tTt/tGt	8/9	1	2	FACETS	0.617	0.435	0.837	0.617	0.435	0.837	SUBCLONAL	1	TRUE	1	0.28	2		454	139	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710613	114710613	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs148876270	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	66	574	0	ENST00000543371.1:c.98A>G	p.Glu33Gly	p.E33G	ENST00000543371	NM_001198531.1	33	gAa/gGa	1/14	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.28	2		574	380	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258070	123258070	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519799	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	37	560	1	ENST00000358487.5:c.1611G>T	p.Met537Ile	p.M537I	ENST00000358487	NM_000141.4	537	atG/atT	12/18	1	2	FACETS	0.864	0.715	1	0.864	0.715	1	CLONAL	1	TRUE	1	0.28	2		561	306	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14303217	14303217	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	50	700	0	ENST00000256196.4:c.458A>G	p.Tyr153Cys	p.Y153C	ENST00000256196		153	tAc/tGc	5/6	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.28	2		700	287	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69456215	69456215	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	67	810	0	ENST00000227507.2:c.134T>G	p.Phe45Cys	p.F45C	ENST00000227507	NM_053056.2	45	tTc/tGc	1/5	1	2	FACETS	0.84	0.73	0.958	0.84	0.73	0.958	CLONAL	1	TRUE	1	0.28	2		810	570	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941456	71941456	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	66	899	0	ENST00000298229.2:c.1141T>C	p.Phe381Leu	p.F381L	ENST00000298229	NM_001567.3	381	Ttt/Ctt	10/28	1	2	FACETS	0.928	0.807	1	0.928	0.807	1	CLONAL	1	TRUE	1	0.28	2		899	508	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189497	94189497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774057024	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	29	378	0	ENST00000323929.3:c.1508G>A	p.Arg503His	p.R503H	ENST00000323929	NM_005591.3	503	cGt/cAt	14/20	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.28	2		378	169	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204753	94204753	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1160887570	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	14	397	0	ENST00000323929.3:c.832G>T	p.Glu278Ter	p.E278*	ENST00000323929	NM_005591.3	278	Gaa/Taa	8/20	1	2	FACETS	0.775	0.565	1	0.775	0.565	1	CLONAL	1	TRUE	1	0.28	2		397	129	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124682	108124682	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	25	561	0	ENST00000278616.4:c.2040C>A	p.Phe680Leu	p.F680L	ENST00000278616	NM_000051.3	680	ttC/ttA	13/63	1	2	FACETS	0.674	0.532	0.835	0.674	0.532	0.835	SUBCLONAL	1	TRUE	1	0.28	2		561	265	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175481	108175481	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1060501568	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	39	421	1	ENST00000278616.4:c.5576G>T	p.Arg1859Ile	p.R1859I	ENST00000278616	NM_000051.3	1859	aGa/aTa	37/63	1	2	FACETS	0.865	0.72	1	0.865	0.72	1	CLONAL	1	TRUE	1	0.28	2		422	322	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180949	108180949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881394	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	20	367	1	ENST00000278616.4:c.5825C>T	p.Ala1942Val	p.A1942V	ENST00000278616	NM_000051.3	1942	gCc/gTc	39/63	1	2	FACETS	0.978	0.755	1	0.978	0.755	1	CLONAL	1	TRUE	1	0.28	2		368	146	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503099	125503099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140276570	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	28	332	0	ENST00000428830.2:c.466C>T	p.Arg156Trp	p.R156W	ENST00000428830	NM_001114121.2	156	Cgg/Tgg	6/14	1	2	FACETS	0.772	0.619	0.945	0.772	0.619	0.945	CLONAL	1	TRUE	1	0.28	2		332	259	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422242	422242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769792722	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	37	705	1	ENST00000399788.2:c.3016G>A	p.Ala1006Thr	p.A1006T	ENST00000399788	NM_001042603.1	1006	Gct/Act	20/28	0.3	2	FACETS	0.645	0.532	0.771			1	SUBCLONAL	1	TRUE	NA	0.28	2		706	410	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472233	472233	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	40	483	0	ENST00000399788.2:c.568G>T	p.Glu190Ter	p.E190*	ENST00000399788	NM_001042603.1	190	Gaa/Taa	5/28	0.3	2	FACETS	1	0.874	1			1	CLONAL	1	TRUE	NA	0.28	2		483	271	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491465	18491465	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	15	359	1	ENST00000266497.5:c.1378C>A	p.Leu460Ile	p.L460I	ENST00000266497		460	Ctt/Att	8/31	1	2	FACETS	0.653	0.48	0.859	0.653	0.48	0.859	SUBCLONAL	1	TRUE	1	0.28	2		360	164	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544119	18544119	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	25	413	0	ENST00000266497.5:c.1936C>A	p.Leu646Ile	p.L646I	ENST00000266497		646	Ctt/Att	13/31	1	2	FACETS	0.888	0.705	1	0.888	0.705	1	CLONAL	1	TRUE	1	0.28	2		413	201	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793451	18793451	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	23	459	0	ENST00000266497.5:c.4148C>A	p.Ser1383Tyr	p.S1383Y	ENST00000266497		1383	tCt/tAt	30/31	1	2	FACETS	0.747	0.585	0.933	0.747	0.585	0.933	CLONAL	1	TRUE	1	0.28	2		459	220	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21630789	21630789	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	41	475	0	ENST00000421138.2:c.815A>G	p.Glu272Gly	p.E272G	ENST00000421138		272	gAa/gGa	8/16	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.28	2		475	272	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443482	49443482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746084513	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	47	753	1	ENST00000301067.7:c.3889C>T	p.Arg1297Cys	p.R1297C	ENST00000301067	NM_003482.3	1297	Cgt/Tgt	11/54	1	2	FACETS	0.617	0.52	0.724	0.617	0.52	0.724	SUBCLONAL	1	TRUE	1	0.28	2		754	544	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480431	50480431	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	31	508	0	ENST00000394963.4:c.393A>C	p.Lys131Asn	p.K131N	ENST00000394963	NM_003076.4	131	aaA/aaC	3/13	1	2	FACETS	0.829	0.673	1	0.829	0.673	1	CLONAL	1	TRUE	1	0.28	2		508	267	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859432	57859432	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	52	874	0	ENST00000228682.2:c.577G>T	p.Glu193Ter	p.E193*	ENST00000228682	NM_005269.2	193	Gaa/Taa	6/12	1	2	FACETS	0.755	0.643	0.877	0.755	0.643	0.877	SUBCLONAL	1	TRUE	1	0.28	2		874	492	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863392	57863392	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759027001	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	84	955	3	ENST00000228682.2:c.1487G>A	p.Arg496His	p.R496H	ENST00000228682	NM_005269.2	496	cGc/cAc	11/12	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.28	2		958	593	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813371	102813371	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	70	725	0	ENST00000307046.8:c.318G>T	p.Glu106Asp	p.E106D	ENST00000307046	NM_001111285.1	106	gaG/gaT	3/4	1	2	FACETS	0.975	0.851	1	0.975	0.851	1	CLONAL	1	TRUE	1	0.28	2		725	513	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120824	115120824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1369545046	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	42	835	0	ENST00000257566.3:c.182C>T	p.Ala61Val	p.A61V	ENST00000257566	NM_016569.3	61	gCc/gTc	1/8	1	2	FACETS	0.699	0.584	0.827	0.699	0.584	0.827	SUBCLONAL	1	TRUE	1	0.28	2		835	429	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214669	133214669	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758619238	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	55	739	3	ENST00000320574.5:c.5609G>A	p.Arg1870His	p.R1870H	ENST00000320574	NM_006231.2	1870	cGc/cAc	41/49	1	2	FACETS	0.773	0.662	0.895	0.773	0.662	0.895	SUBCLONAL	1	TRUE	1	0.28	2		742	508	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249857	133249858	+	missense_variant	Missense_Mutation	DNP	CC	CC	GG	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	27	516	1	ENST00000320574.5:c.1365_1366inv	p.Ala456Pro	p.A456P	ENST00000320574	NM_006231.2	455	ctGGcc/ctCCcc	14/49	1	2	FACETS	0.564	0.449	0.695	0.564	0.449	0.695	SUBCLONAL	1	TRUE	1	0.28	2		517	342	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26978215	26978215	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	59	540	0	ENST00000381527.3:c.1392C>A	p.Tyr464Ter	p.Y464*	ENST00000381527	NM_001260.1	464	taC/taA	13/13	1	2	FACETS	0.992	0.856	1	0.992	0.856	1	CLONAL	1	TRUE	1	0.28	2		540	425	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608225	28608225	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	46	651	0	ENST00000241453.7:c.1831G>T	p.Glu611Ter	p.E611*	ENST00000241453	NM_004119.2	611	Gag/Tag	14/24	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.28	2		651	314	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608499	28608499	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	32	601	0	ENST00000241453.7:c.1643T>G	p.Ile548Ser	p.I548S	ENST00000241453	NM_004119.2	548	aTt/aGt	13/24	1	2	FACETS	0.661	0.537	0.8	0.661	0.537	0.8	SUBCLONAL	1	TRUE	1	0.28	2		601	346	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608524	28608524	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	50	596	0	ENST00000241453.7:c.1618G>A	p.Asp540Asn	p.D540N	ENST00000241453	NM_004119.2	540	Gac/Aac	13/24	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.28	2		596	330	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28971174	28971174	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	26	378	0	ENST00000282397.4:c.1583G>T	p.Arg528Ile	p.R528I	ENST00000282397	NM_002019.4	528	aGa/aTa	12/30	1	2	FACETS	0.807	0.643	0.995	0.807	0.643	0.995	CLONAL	1	TRUE	1	0.28	2		378	230	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008200	29008200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1014160326	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	27	382	0	ENST00000282397.4:c.671G>A	p.Arg224Gln	p.R224Q	ENST00000282397	NM_002019.4	224	cGa/cAa	5/30	1	2	FACETS	0.784	0.626	0.962	0.784	0.626	0.962	CLONAL	1	TRUE	1	0.28	2		382	246	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041148	29041148	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	40	776	0	ENST00000282397.4:c.280T>G	p.Leu94Val	p.L94V	ENST00000282397	NM_002019.4	94	Ttg/Gtg	3/30	1	2	FACETS	0.756	0.629	0.896	0.756	0.629	0.896	SUBCLONAL	1	TRUE	1	0.28	2		776	378	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941657	48941657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1060503077	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	15	204	0	ENST00000267163.4:c.967G>T	p.Glu323Ter	p.E323*	ENST00000267163	NM_000321.2	323	Gaa/Taa	10/27	1	2	FACETS	0.9	0.665	1	0.9	0.665	1	CLONAL	1	TRUE	1	0.28	2		204	119	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103513972	103513972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61749896	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	31	435	2	ENST00000355739.4:c.788G>A	p.Arg263Gln	p.R263Q	ENST00000355739	NM_000123.3	263	cGa/cAa	7/15	1	2	FACETS	0.852	0.692	1	0.852	0.692	1	CLONAL	1	TRUE	1	0.28	2		437	260	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30099992	30099992	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	43	673	1	ENST00000331968.5:c.1628T>A	p.Val543Asp	p.V543D	ENST00000331968	NM_002742.2	543	gTc/gAc	10/18	1	2	FACETS	0.718	0.601	0.846	0.718	0.601	0.846	SUBCLONAL	1	TRUE	1	0.28	2		674	428	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95595882	95595882	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	26	412	0	ENST00000393063.1:c.661G>T	p.Glu221Ter	p.E221*	ENST00000393063	NM_030621.3	221	Gaa/Taa	7/28	1	2	FACETS	0.852	0.678	1	0.852	0.678	1	CLONAL	1	TRUE	1	0.28	2		412	218	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961916	41961916	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1384849789	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	47	411	0	ENST00000219905.7:c.824A>G	p.Asn275Ser	p.N275S	ENST00000219905	NM_001164273.1	275	aAc/aGc	2/24	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.28	2		411	293	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040946	42040946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	49	761	1	ENST00000219905.7:c.5324G>T	p.Arg1775Ile	p.R1775I	ENST00000219905	NM_001164273.1	1775	aGa/aTa	16/24	1	2	FACETS	0.768	0.651	0.896	0.768	0.651	0.896	SUBCLONAL	1	TRUE	1	0.28	2		762	456	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727454	66727454	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519909	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	56	569	0	ENST00000307102.5:c.170A>C	p.Lys57Thr	p.K57T	ENST00000307102	NM_002755.3	57	aAg/aCg	2/11	1	2	FACETS	0.913	0.784	1	0.913	0.784	1	CLONAL	1	TRUE	1	0.28	2		569	438	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420336	88420336	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	46	547	0	ENST00000360948.2:c.2350A>G	p.Thr784Ala	p.T784A	ENST00000360948	NM_001012338.2	784	Acc/Gcc	19/19	1	2	FACETS	0.874	0.738	1	0.874	0.738	1	CLONAL	1	TRUE	1	0.28	2		547	376	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631593	90631593	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs576407061	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	61	785	2	ENST00000330062.3:c.676G>A	p.Glu226Lys	p.E226K	ENST00000330062	NM_002168.2	226	Gag/Aag	5/11	1	2	FACETS	0.939	0.812	1	0.939	0.812	1	CLONAL	1	TRUE	1	0.28	2		787	464	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303987	91303987	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	47	683	0	ENST00000355112.3:c.1384T>C	p.Ser462Pro	p.S462P	ENST00000355112	NM_000057.2	462	Tct/Cct	7/22	1	2	FACETS	0.815	0.689	0.953	0.815	0.689	0.953	CLONAL	1	TRUE	1	0.28	2		683	412	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456457	99456457	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	59	695	2	ENST00000268035.6:c.1774G>T	p.Asp592Tyr	p.D592Y	ENST00000268035	NM_000875.3	592	Gac/Tac	8/21	1	2	FACETS	0.973	0.84	1	0.973	0.84	1	CLONAL	1	TRUE	1	0.28	2		697	433	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900468	3900468	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	75	1001	0	ENST00000262367.5:c.628A>G	p.Asn210Asp	p.N210D	ENST00000262367	NM_004380.2	210	Aat/Gat	2/31	1	2	FACETS	0.896	0.786	1	0.896	0.786	1	CLONAL	1	TRUE	1	0.28	2		1001	598	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041987	14041987	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs377562755	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	57	387	0	ENST00000311895.7:c.2534A>G	p.Asn845Ser	p.N845S	ENST00000311895	NM_005236.2	845	aAt/aGt	11/11	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.28	2		387	361	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50821710	50821710	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	14	403	0	ENST00000398568.2:c.2046C>A	p.Phe682Leu	p.F682L	ENST00000398568	NM_001042412.1	682	ttC/ttA	13/18	1	2	FACETS	0.658	0.478	0.873	0.658	0.478	0.873	SUBCLONAL	1	TRUE	1	0.28	2		403	152	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645069	67645069	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	49	778	0	ENST00000264010.4:c.334G>T	p.Glu112Ter	p.E112*	ENST00000264010	NM_006565.3	112	Gaa/Taa	3/12	1	2	FACETS	0.818	0.694	0.954	0.818	0.694	0.954	CLONAL	1	TRUE	1	0.28	2		778	428	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827991	72827991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	69	1053	1	ENST00000268489.5:c.8590G>A	p.Glu2864Lys	p.E2864K	ENST00000268489	NM_006885.3	2864	Gaa/Aaa	9/10	1	2	FACETS	0.837	0.729	0.953	0.837	0.729	0.953	CLONAL	1	TRUE	1	0.28	2		1054	589	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72863747	72863747	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	58	552	0	ENST00000268489.5:c.3460G>T	p.Glu1154Ter	p.E1154*	ENST00000268489	NM_006885.3	1154	Gaa/Taa	5/10	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.28	2		552	342	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991586	72991586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768340392	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	75	922	0	ENST00000268489.5:c.2459G>A	p.Arg820His	p.R820H	ENST00000268489	NM_006885.3	820	cGc/cAc	2/10	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.28	2		922	534	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993711	72993711	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	75	856	0	ENST00000268489.5:c.334A>G	p.Ser112Gly	p.S112G	ENST00000268489	NM_006885.3	112	Agc/Ggc	2/10	1	2	FACETS	0.978	0.858	1	0.978	0.858	1	CLONAL	1	TRUE	1	0.28	2		856	548	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965130	81965130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	50	663	0	ENST00000359376.3:c.2610G>T	p.Lys870Asn	p.K870N	ENST00000359376	NM_002661.3	870	aaG/aaT	25/33	1	2	FACETS	0.76	0.645	0.885	0.76	0.645	0.885	SUBCLONAL	1	TRUE	1	0.28	2		663	470	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216350	7216350	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	57	768	0	ENST00000380728.2:c.898A>G	p.Lys300Glu	p.K300E	ENST00000380728		300	Aag/Gag	10/11	1	2	FACETS	0.819	0.704	0.945	0.819	0.704	0.945	CLONAL	1	TRUE	1	0.28	2		768	497	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983157	7983157	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1288552418	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	81	996	0	ENST00000319144.4:c.857A>C	p.Lys286Thr	p.K286T	ENST00000319144	NM_001139.2	286	aAg/aCg	7/15	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.28	2		996	570	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961049	15961049	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	27	350	0	ENST00000268712.3:c.6171A>C	p.Gln2057His	p.Q2057H	ENST00000268712	NM_006311.3	2057	caA/caC	40/46	1	2	FACETS	0.765	0.611	0.94	0.765	0.611	0.94	CLONAL	1	TRUE	1	0.28	2		350	252	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325737	30325737	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	15	263	0	ENST00000322652.5:c.1935G>T	p.Gln645His	p.Q645H	ENST00000322652	NM_015355.2	645	caG/caT	16/16	1	2	FACETS	0.638	0.468	0.839	0.638	0.468	0.839	SUBCLONAL	1	TRUE	1	0.28	2		263	168	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375473	40375473	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	72	800	0	ENST00000293328.3:c.477G>T	p.Glu159Asp	p.E159D	ENST00000293328	NM_012448.3	159	gaG/gaT	5/19	1	2	FACETS	0.932	0.815	1	0.932	0.815	1	CLONAL	1	TRUE	1	0.28	2		800	552	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696405	47696405	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	51	633	0	ENST00000347630.2:c.418G>T	p.Asp140Tyr	p.D140Y	ENST00000347630	NM_001007230.1	140	Gat/Tat	6/11	1	2	FACETS	0.925	0.788	1	0.925	0.788	1	CLONAL	1	TRUE	1	0.28	2		633	394	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885829	59885829	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	22	407	0	ENST00000259008.2:c.917A>C	p.Asn306Thr	p.N306T	ENST00000259008	NM_032043.2	306	aAc/aCc	7/20	1	2	FACETS	0.666	0.518	0.837	0.666	0.518	0.837	SUBCLONAL	1	TRUE	1	0.28	2		407	236	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554452	63554452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	61	769	1	ENST00000307078.5:c.287G>A	p.Arg96Gln	p.R96Q	ENST00000307078	NM_004655.3	96	cGa/cAa	2/11	1	2	FACETS	0.871	0.753	1	0.871	0.753	1	CLONAL	1	TRUE	1	0.28	2		770	500	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732446	74732446	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	43	524	0	ENST00000359995.5:c.463T>G	p.Ser155Ala	p.S155A	ENST00000359995	NM_001195427.1	155	Tct/Gct	2/3	1	2	FACETS	0.768	0.644	0.905	0.768	0.644	0.905	CLONAL	1	TRUE	1	0.28	2		524	400	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372045	45372045	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	86	455	0	ENST00000262160.6:c.1124A>C	p.Lys375Thr	p.K375T	ENST00000262160	NM_005901.5	375	aAa/aCa	9/11	1	2	FACETS	0.934	0.834	1	1	0.985	1	CLONAL	2	TRUE	1	0.28	2		455	329	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56377287	56377287	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	13	272	0	ENST00000348428.3:c.908A>C	p.Lys303Thr	p.K303T	ENST00000348428	NM_006785.3	303	aAg/aCg	6/17	1	2	FACETS	0.767	0.552	1	0.767	0.552	1	CLONAL	1	TRUE	1	0.28	2		272	121	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191161	2191161	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	93	1058	0	ENST00000398665.3:c.415A>G	p.Thr139Ala	p.T139A	ENST00000398665	NM_032482.2	139	Acc/Gcc	5/28	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.28	2		1058	653	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217079	2217079	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	58	858	0	ENST00000398665.3:c.2534G>A	p.Ser845Asn	p.S845N	ENST00000398665	NM_032482.2	845	aGc/aAc	21/28	1	2	FACETS	0.869	0.747	1	0.869	0.747	1	CLONAL	1	TRUE	1	0.28	2		858	477	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170638	7170638	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	70	796	1	ENST00000302850.5:c.1393G>T	p.Glu465Ter	p.E465*	ENST00000302850	NM_000208.2	465	Gaa/Taa	6/22	1	2	FACETS	0.992	0.867	1	0.992	0.867	1	CLONAL	1	TRUE	1	0.28	2		797	504	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10273396	10273396	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	52	763	1	ENST00000340748.4:c.907G>T	p.Glu303Ter	p.E303*	ENST00000340748		303	Gaa/Taa	12/40	1	2	FACETS	0.769	0.655	0.893	0.769	0.655	0.893	SUBCLONAL	1	TRUE	1	0.28	2		764	483	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291483	10291483	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	46	779	0	ENST00000340748.4:c.196A>G	p.Thr66Ala	p.T66A	ENST00000340748		66	Acc/Gcc	3/40	1	2	FACETS	0.881	0.744	1	0.881	0.744	1	CLONAL	1	TRUE	1	0.28	2		779	373	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303260	15303260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555729604	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	48	1163	1	ENST00000263388.2:c.268C>T	p.Arg90Cys	p.R90C	ENST00000263388	NM_000435.2	90	Cgt/Tgt	3/33	1	2	FACETS	0.59	0.498	0.691	0.59	0.498	0.691	SUBCLONAL	1	TRUE	1	0.28	2		1164	581	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210688	36210688	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	69	772	3	ENST00000222270.7:c.439C>T	p.Arg147Ter	p.R147*	ENST00000222270	NM_014727.1	147	Cga/Tga	3/37	1	2	FACETS	0.948	0.827	1	0.948	0.827	1	CLONAL	1	TRUE	1	0.28	2		775	520	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211830	36211830	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	89	977	0	ENST00000222270.7:c.1581T>G	p.Phe527Leu	p.F527L	ENST00000222270	NM_014727.1	527	ttT/ttG	3/37	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.28	2		977	592	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229069	36229069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	76	999	0	ENST00000222270.7:c.7849C>T	p.Arg2617Trp	p.R2617W	ENST00000222270	NM_014727.1	2617	Cgg/Tgg	36/37	1	2	FACETS	0.973	0.855	1	0.973	0.855	1	CLONAL	1	TRUE	1	0.28	2		999	558	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727874	41727874	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	91	1105	1	ENST00000301178.4:c.499G>T	p.Glu167Ter	p.E167*	ENST00000301178	NM_021913.4	167	Gag/Tag	4/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.28	2		1106	580	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763424	41763424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	55	717	2	ENST00000301178.4:c.2223G>T	p.Glu741Asp	p.E741D	ENST00000301178	NM_021913.4	741	gaG/gaT	19/20	1	2	FACETS	0.865	0.742	1	0.865	0.742	1	CLONAL	1	TRUE	1	0.28	2		719	454	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868176	45868176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559154781	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	75	1138	2	ENST00000391945.4:c.514G>A	p.Ala172Thr	p.A172T	ENST00000391945	NM_000400.3	172	Gct/Act	7/23	1	2	FACETS	0.976	0.856	1	0.976	0.856	1	CLONAL	1	TRUE	1	0.28	2		1140	549	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416513	29416513	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	97	991	0	ENST00000389048.3:c.4440C>A	p.Phe1480Leu	p.F1480L	ENST00000389048	NM_004304.4	1480	ttC/ttA	29/29	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.28	2		991	564	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234234	39234234	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	32	612	0	ENST00000402219.2:c.2611G>C	p.Val871Leu	p.V871L	ENST00000402219	NM_005633.3	871	Gtc/Ctc	16/23	1	2	FACETS	0.985	0.805	1	0.985	0.805	1	CLONAL	1	TRUE	1	0.28	2		612	232	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018170	48018170	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1558652077	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	77	790	0	ENST00000234420.5:c.365A>G	p.Glu122Gly	p.E122G	ENST00000234420	NM_000179.2	122	gAg/gGg	2/10	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.28	2		790	515	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027244	48027244	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1064795960	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	35	415	0	ENST00000234420.5:c.2122G>T	p.Glu708Ter	p.E708*	ENST00000234420	NM_000179.2	708	Gaa/Taa	4/10	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.28	2		415	230	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027317	48027317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749746725	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	30	380	0	ENST00000234420.5:c.2195G>A	p.Arg732Gln	p.R732Q	ENST00000234420	NM_000179.2	732	cGa/cAa	4/10	1	2	FACETS	0.857	0.694	1	0.857	0.694	1	CLONAL	1	TRUE	1	0.28	2		380	250	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027401	48027401	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	41	559	0	ENST00000234420.5:c.2279A>G	p.Glu760Gly	p.E760G	ENST00000234420	NM_000179.2	760	gAg/gGg	4/10	1	2	FACETS	0.877	0.733	1	0.877	0.733	1	CLONAL	1	TRUE	1	0.28	2		559	334	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030670	48030670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750253	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	37	460	2	ENST00000234420.5:c.3284G>A	p.Arg1095His	p.R1095H	ENST00000234420	NM_000179.2	1095	cGc/cAc	5/10	1	2	FACETS	0.789	0.652	0.941	0.789	0.652	0.941	CLONAL	1	TRUE	1	0.28	2		462	335	SUCCESS
REL	5966	MSKCC	GRCh37	2	61128147	61128147	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1016724251	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	20	253	0	ENST00000295025.8:c.323G>A	p.Arg108Gln	p.R108Q	ENST00000295025	NM_002908.2	108	cGa/cAa	4/11	1	2	FACETS	0.785	0.604	0.994	0.785	0.604	0.994	CLONAL	1	TRUE	1	0.28	2		253	182	SUCCESS
REL	5966	MSKCC	GRCh37	2	61128173	61128173	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	18	260	0	ENST00000295025.8:c.349G>T	p.Glu117Ter	p.E117*	ENST00000295025	NM_002908.2	117	Gaa/Taa	4/11	1	2	FACETS	0.748	0.566	0.959	0.748	0.566	0.959	CLONAL	1	TRUE	1	0.28	2		260	172	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715319	61715319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	22	580	1	ENST00000401558.2:c.2294G>A	p.Arg765Gln	p.R765Q	ENST00000401558	NM_003400.3	765	cGa/cAa	19/25	1	2	FACETS	0.619	0.48	0.778	0.619	0.48	0.778	SUBCLONAL	1	TRUE	1	0.28	2		581	254	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015261	128015261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779748578	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	62	730	1	ENST00000285398.2:c.2260G>A	p.Asp754Asn	p.D754N	ENST00000285398	NM_000122.1	754	Gac/Aac	15/15	1	2	FACETS	0.973	0.843	1	0.973	0.843	1	CLONAL	1	TRUE	1	0.28	2		731	455	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096135	178096135	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	45	600	0	ENST00000397062.3:c.1196C>A	p.Ser399Tyr	p.S399Y	ENST00000397062	NM_006164.4	399	tCt/tAt	5/5	1	2	FACETS	0.753	0.633	0.884	0.753	0.633	0.884	SUBCLONAL	1	TRUE	1	0.28	2		600	427	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190717387	190717387	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1256397998	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	15	363	0	ENST00000441310.2:c.706C>A	p.Leu236Ile	p.L236I	ENST00000441310	NM_000534.4	236	Ctc/Atc	7/13	1	2	FACETS	0.771	0.568	1	0.771	0.568	1	CLONAL	1	TRUE	1	0.28	2		363	139	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131412	202131412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339962485	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	43	442	0	ENST00000358485.4:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000358485	NM_001080125.1	127	cGa/cAa	2/9	1	2	FACETS	0.875	0.735	1	0.875	0.735	1	CLONAL	1	TRUE	1	0.28	2		442	351	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136279	202136279	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	30	604	1	ENST00000358485.4:c.523G>T	p.Glu175Ter	p.E175*	ENST00000358485	NM_001080125.1	175	Gaa/Taa	3/9	1	2	FACETS	0.698	0.564	0.85	0.698	0.564	0.85	SUBCLONAL	1	TRUE	1	0.28	2		605	307	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136284	202136284	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	36	618	1	ENST00000358485.4:c.528G>T	p.Leu176Phe	p.L176F	ENST00000358485	NM_001080125.1	176	ttG/ttT	3/9	1	2	FACETS	0.827	0.682	0.988	0.827	0.682	0.988	CLONAL	1	TRUE	1	0.28	2		619	311	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103903	209103903	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	41	459	0	ENST00000345146.2:c.1046A>G	p.Asn349Ser	p.N349S	ENST00000345146	NM_005896.2	349	aAt/aGt	9/10	1	2	FACETS	0.904	0.756	1	0.904	0.756	1	CLONAL	1	TRUE	1	0.28	2		459	324	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368422	225368422	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	24	425	0	ENST00000264414.4:c.1324A>T	p.Thr442Ser	p.T442S	ENST00000264414	NM_003590.4	442	Aca/Tca	9/16	0.3	2	FACETS	0.836	0.659	1			1	CLONAL	1	TRUE	NA	0.28	2		425	205	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662307	227662307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1446895458	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	81	981	2	ENST00000305123.5:c.1148C>T	p.Ser383Leu	p.S383L	ENST00000305123	NM_005544.2	383	tCg/tTg	1/2	0.3	2	FACETS	0.961	0.848	1			1	CLONAL	1	TRUE	NA	0.28	2		983	602	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546725	9546725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210292896	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	36	548	0	ENST00000353224.5:c.1297C>T	p.Arg433Trp	p.R433W	ENST00000353224	NM_177990.2	433	Cgg/Tgg	5/10	1	2	FACETS	0.693	0.571	0.83	0.693	0.571	0.83	SUBCLONAL	1	TRUE	1	0.28	2		548	371	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31393193	31393193	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	48	485	1	ENST00000328111.2:c.2281G>T	p.Glu761Ter	p.E761*	ENST00000328111	NM_006892.3	761	Gaa/Taa	21/23	1	2	FACETS	0.977	0.829	1	0.977	0.829	1	CLONAL	1	TRUE	1	0.28	2		486	351	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40864896	40864896	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	21	418	0	ENST00000373198.4:c.2372G>T	p.Arg791Ile	p.R791I	ENST00000373198	NM_133170.3	791	aGa/aTa	16/32	1	2	FACETS	0.728	0.563	0.919	0.728	0.563	0.919	CLONAL	1	TRUE	1	0.28	2		418	206	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385260	41385260	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	56	730	0	ENST00000373198.4:c.701A>G	p.Asp234Gly	p.D234G	ENST00000373198	NM_133170.3	234	gAc/gGc	6/32	1	2	FACETS	0.873	0.75	1	0.873	0.75	1	CLONAL	1	TRUE	1	0.28	2		730	458	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37622795	37622795	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	59	1052	0	ENST00000249071.6:c.497A>C	p.Lys166Thr	p.K166T	ENST00000249071	NM_002872.4	166	aAa/aCa	6/7	1	2	FACETS	0.714	0.614	0.823	0.714	0.614	0.823	SUBCLONAL	1	TRUE	1	0.28	2		1052	590	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434198	12434198	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	29	479	1	ENST00000287820.6:c.566A>C	p.Lys189Thr	p.K189T	ENST00000287820	NM_015869.4	189	aAa/aCa	4/7	1	2	FACETS	0.845	0.682	1	0.845	0.682	1	CLONAL	1	TRUE	1	0.28	2		480	245	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475417	12475417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1393014897	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	44	706	1	ENST00000287820.6:c.1291G>A	p.Val431Met	p.V431M	ENST00000287820	NM_015869.4	431	Gtg/Atg	7/7	1	2	FACETS	0.686	0.576	0.808	0.686	0.576	0.808	SUBCLONAL	1	TRUE	1	0.28	2		707	458	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691875	30691875	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	57	405	0	ENST00000295754.5:c.377A>C	p.Lys126Thr	p.K126T	ENST00000295754	NM_003242.5	126	aAa/aCa	3/7	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.28	2		405	275	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715624	30715624	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	35	317	0	ENST00000295754.5:c.1282G>T	p.Glu428Ter	p.E428*	ENST00000295754	NM_003242.5	428	Gaa/Taa	5/7	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.28	2		317	239	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070295	37070295	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	47	445	0	ENST00000231790.2:c.1430C>T	p.Ser477Phe	p.S477F	ENST00000231790	NM_000249.3	477	tCt/tTt	13/19	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.28	2		445	318	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162812	47162812	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	23	461	0	ENST00000409792.3:c.3314G>T	p.Arg1105Ile	p.R1105I	ENST00000409792	NM_014159.6	1105	aGa/aTa	3/21	1	2	FACETS	0.602	0.47	0.754	0.602	0.47	0.754	SUBCLONAL	1	TRUE	1	0.28	2		461	273	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725073	49725073	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	100	1027	0	ENST00000449682.2:c.271G>T	p.Gly91Cys	p.G91C	ENST00000449682	NM_020998.3	91	Ggt/Tgt	3/18	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.28	2		1027	552	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	69	743	1	ENST00000394830.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000394830	NM_018313.4	710	Cga/Tga	17/30	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.28	2		744	443	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259384	89259384	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	42	571	0	ENST00000336596.2:c.528G>T	p.Lys176Asn	p.K176N	ENST00000336596	NM_005233.5	176	aaG/aaT	3/17	1	2	FACETS	0.824	0.69	0.972	0.824	0.69	0.972	CLONAL	1	TRUE	1	0.28	2		571	364	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119721018	119721018	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	62	657	0	ENST00000316626.5:c.157G>T	p.Glu53Ter	p.E53*	ENST00000316626		53	Gaa/Taa	2/12	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.28	2		657	438	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205772	128205772	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	55	966	0	ENST00000341105.2:c.103G>T	p.Glu35Ter	p.E35*	ENST00000341105	NM_032638.4	35	Gaa/Taa	2/6	1	2	FACETS	0.783	0.67	0.905	0.783	0.67	0.905	CLONAL	1	TRUE	1	0.28	2		966	502	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461588	138461588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	36	454	0	ENST00000289153.2:c.433G>A	p.Val145Ile	p.V145I	ENST00000289153	NM_006219.2	145	Gta/Ata	3/22	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.28	2		454	246	SUCCESS
ATR	545	MSKCC	GRCh37	3	142232477	142232477	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs754602382	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	22	331	0	ENST00000350721.4:c.4507C>T	p.Arg1503Ter	p.R1503*	ENST00000350721	NM_001184.3	1503	Cga/Tga	26/47	1	2	FACETS	1	0.84	1	1	0.84	1	CLONAL	1	TRUE	1	0.28	2		331	144	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266671	142266671	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	27	474	0	ENST00000350721.4:c.3253G>T	p.Glu1085Ter	p.E1085*	ENST00000350721	NM_001184.3	1085	Gaa/Taa	16/47	1	2	FACETS	0.824	0.659	1	0.824	0.659	1	CLONAL	1	TRUE	1	0.28	2		474	234	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916624	178916624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749956691	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	26	330	1	ENST00000263967.3:c.11G>A	p.Arg4Gln	p.R4Q	ENST00000263967	NM_006218.2	4	cGa/cAa	2/21	1	2	FACETS	0.833	0.663	1	0.833	0.663	1	CLONAL	1	TRUE	1	0.28	2		331	223	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	39	521	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.838	1	1	0.838	1	CLONAL	1	TRUE	1	0.28	2		521	277	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430614	181430614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	58	872	0	ENST00000325404.1:c.466C>T	p.Arg156Cys	p.R156C	ENST00000325404	NM_003106.3	156	Cgc/Tgc	1/1	1	2	FACETS	0.84	0.723	0.968	0.84	0.723	0.968	CLONAL	1	TRUE	1	0.28	2		872	493	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504951	186504951	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	34	403	0	ENST00000323963.5:c.807G>T	p.Glu269Asp	p.E269D	ENST00000323963		269	gaG/gaT	8/11	0.115596586294496	3	FACETS	0.908	0.744	1	0.454	0.372	0.546	INDETERMINATE	1	TRUE	1	0.28	3		403	305	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444551	187444551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	87	1012	2	ENST00000232014.4:c.1676G>A	p.Gly559Asp	p.G559D	ENST00000232014	NM_001130845.1	559	gGc/gAc	7/10	0.115596586294496	3	FACETS	1	0.958	1	0.587	0.521	0.659	INDETERMINATE	1	TRUE	1	0.28	3		1014	603	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582168	189582168	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121908835	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	57	595	0	ENST00000264731.3:c.727C>T	p.Arg243Trp	p.R243W	ENST00000264731	NM_003722.4	243	Cgg/Tgg	5/14	0.115596586294496	3	FACETS	1	0.862	1	0.501	0.431	0.578	INDETERMINATE	1	TRUE	1	0.28	3		595	463	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133597	55133597	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	58	613	0	ENST00000257290.5:c.901G>T	p.Glu301Ter	p.E301*	ENST00000257290	NM_006206.4	301	Gaa/Taa	6/23	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.28	2		613	389	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144632	55144632	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	41	490	1	ENST00000257290.5:c.2106G>T	p.Lys702Asn	p.K702N	ENST00000257290	NM_006206.4	702	aaG/aaT	15/23	1	2	FACETS	0.924	0.773	1	0.924	0.773	1	CLONAL	1	TRUE	1	0.28	2		491	317	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976604	55976604	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	40	589	0	ENST00000263923.4:c.1221G>T	p.Glu407Asp	p.E407D	ENST00000263923	NM_002253.2	407	gaG/gaT	9/30	1	2	FACETS	0.756	0.629	0.896	0.756	0.629	0.896	SUBCLONAL	1	TRUE	1	0.28	2		589	378	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213909	66213909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	22	419	1	ENST00000273854.3:c.2521C>T	p.Pro841Ser	p.P841S	ENST00000273854	NM_004439.5	841	Cca/Tca	15/18	1	2	FACETS	0.794	0.618	0.995	0.794	0.618	0.995	CLONAL	1	TRUE	1	0.28	2		420	198	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280050	66280050	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	42	359	0	ENST00000273854.3:c.1639G>T	p.Gly547Cys	p.G547C	ENST00000273854	NM_004439.5	547	Ggc/Tgc	7/18	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.28	2		359	282	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244184	153244184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759610249	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	46	528	1	ENST00000281708.4:c.1973G>A	p.Arg658Gln	p.R658Q	ENST00000281708	NM_033632.3	658	cGa/cAa	12/12	1	2	FACETS	0.903	0.763	1	0.903	0.763	1	CLONAL	1	TRUE	1	0.28	2		529	364	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509853	187509853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748762429	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	35	473	1	ENST00000441802.2:c.13660G>A	p.Glu4554Lys	p.E4554K	ENST00000441802	NM_005245.3	4554	Gaa/Aaa	27/27	1	2	FACETS	0.665	0.546	0.799	0.665	0.546	0.799	SUBCLONAL	1	TRUE	1	0.28	2		474	376	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524815	187524815	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778212581	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	80	784	1	ENST00000441802.2:c.10865C>T	p.Thr3622Met	p.T3622M	ENST00000441802	NM_005245.3	3622	aCg/aTg	19/27	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.28	2		785	547	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629223	187629223	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	37	693	0	ENST00000441802.2:c.1759C>T	p.Gln587Ter	p.Q587*	ENST00000441802	NM_005245.3	587	Caa/Taa	2/27	1	2	FACETS	0.695	0.574	0.831	0.695	0.574	0.831	SUBCLONAL	1	TRUE	1	0.28	2		693	380	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271247	1271247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746621306	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	39	444	0	ENST00000310581.5:c.2455C>T	p.Arg819Cys	p.R819C	ENST00000310581	NM_198253.2	819	Cgc/Tgc	8/16	1	2	FACETS	0.954	0.794	1	0.954	0.794	1	CLONAL	1	TRUE	1	0.28	2		444	292	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31407048	31407048	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	34	534	0	ENST00000344624.3:c.3859C>A	p.Leu1287Met	p.L1287M	ENST00000344624		1287	Ctg/Atg	31/33	1	2	FACETS	0.832	0.682	0.999	0.832	0.682	0.999	CLONAL	1	TRUE	1	0.28	2		534	292	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31464402	31464402	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	68	835	0	ENST00000344624.3:c.2515A>G	p.Thr839Ala	p.T839A	ENST00000344624		839	Acg/Gcg	17/33	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.28	2		835	475	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38991178	38991178	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	22	342	0	ENST00000357387.3:c.457-1G>T		p.X153_splice	ENST00000357387	NM_152756.3	153			1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.28	2		342	138	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152446	56152446	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	19	253	0	ENST00000399503.3:c.502G>T	p.Glu168Ter	p.E168*	ENST00000399503	NM_005921.1	168	Gaa/Taa	2/20	1	2	FACETS	0.808	0.617	1	0.808	0.617	1	CLONAL	1	TRUE	1	0.28	2		253	168	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751144	57751144	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	29	379	0	ENST00000274289.3:c.1723T>G	p.Phe575Val	p.F575V	ENST00000274289	NM_006622.3	575	Ttt/Gtt	12/14	1	2	FACETS	0.819	0.66	0.998	0.819	0.66	0.998	CLONAL	1	TRUE	1	0.28	2		379	253	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753027	57753027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1192733931	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	41	403	2	ENST00000274289.3:c.989G>A	p.Arg330Gln	p.R330Q	ENST00000274289	NM_006622.3	330	cGa/cAa	7/14	1	2	FACETS	0.915	0.765	1	0.915	0.765	1	CLONAL	1	TRUE	1	0.28	2		405	320	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649005	86649005	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	15	354	0	ENST00000274376.6:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000274376	NM_002890.2	429	Gaa/Taa	9/25	1	2	FACETS	0.63	0.463	0.83	0.63	0.463	0.83	SUBCLONAL	1	TRUE	1	0.28	2		354	170	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672835	86672835	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	30	323	0	ENST00000274376.6:c.2322T>G	p.Asn774Lys	p.N774K	ENST00000274376	NM_002890.2	774	aaT/aaG	17/25	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.28	2		323	184	SUCCESS
APC	324	MSKCC	GRCh37	5	112170817	112170817	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	32	674	0	ENST00000257430.4:c.1913T>C	p.Ile638Thr	p.I638T	ENST00000257430	NM_000038.5	638	aTa/aCa	15/16	1	2	FACETS	0.651	0.529	0.789	0.651	0.529	0.789	SUBCLONAL	1	TRUE	1	0.28	2		674	351	SUCCESS
APC	324	MSKCC	GRCh37	5	112176873	112176873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	27	371	0	ENST00000257430.4:c.5582C>A	p.Ser1861Tyr	p.S1861Y	ENST00000257430	NM_000038.5	1861	tCt/tAt	16/16	1	2	FACETS	0.846	0.677	1	0.846	0.677	1	CLONAL	1	TRUE	1	0.28	2		371	228	SUCCESS
APC	324	MSKCC	GRCh37	5	112177368	112177368	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	34	358	0	ENST00000257430.4:c.6077C>A	p.Ser2026Tyr	p.S2026Y	ENST00000257430	NM_000038.5	2026	tCt/tAt	16/16	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.28	2		358	222	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931318	131931318	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	47	557	0	ENST00000265335.6:c.2023G>T	p.Asp675Tyr	p.D675Y	ENST00000265335		675	Gac/Tac	13/25	1	2	FACETS	0.9	0.762	1	0.9	0.762	1	CLONAL	1	TRUE	1	0.28	2		557	373	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940689	131940689	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	23	339	0	ENST00000265335.6:c.2716A>G	p.Lys906Glu	p.K906E	ENST00000265335		906	Aag/Gag	16/25	1	2	FACETS	0.842	0.661	1	0.842	0.661	1	CLONAL	1	TRUE	1	0.28	2		339	195	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149452891	149452891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	61	737	0	ENST00000286301.3:c.1055C>A	p.Ala352Asp	p.A352D	ENST00000286301	NM_005211.3	352	gCt/gAt	7/22	1	2	FACETS	0.933	0.807	1	0.933	0.807	1	CLONAL	1	TRUE	1	0.28	2		737	467	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176678730	176678730	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	47	411	1	ENST00000439151.2:c.4642-1G>T		p.X1548_splice	ENST00000439151	NM_022455.4	1548			1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.28	2		412	312	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176710839	176710839	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	42	538	0	ENST00000439151.2:c.6061C>A	p.His2021Asn	p.H2021N	ENST00000439151	NM_022455.4	2021	Cat/Aat	20/23	1	2	FACETS	0.82	0.686	0.967	0.82	0.686	0.967	CLONAL	1	TRUE	1	0.28	2		538	366	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053012	180053012	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	85	1224	0	ENST00000261937.6:c.1278G>T	p.Glu426Asp	p.E426D	ENST00000261937	NM_182925.4	426	gaG/gaT	10/30	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.28	2		1224	560	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398867	398867	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	52	777	0	ENST00000380956.4:c.677C>A	p.Pro226His	p.P226H	ENST00000380956	NM_001195286.1	226	cCt/cAt	6/9	0.3	2	FACETS	0.831	0.709	0.965			1	CLONAL	1	TRUE	NA	0.28	2		777	447	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188583	32188583	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	88	1045	0	ENST00000375023.3:c.872G>A	p.Cys291Tyr	p.C291Y	ENST00000375023	NM_004557.3	291	tGc/tAc	5/30	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.28	2		1045	565	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64290041	64290041	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	40	544	0	ENST00000370651.3:c.484G>T	p.Asp162Tyr	p.D162Y	ENST00000370651	NM_003463.4	162	Gat/Tat	6/6	1	2	FACETS	0.855	0.713	1	0.855	0.713	1	CLONAL	1	TRUE	1	0.28	2		544	334	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536316	106536316	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	47	403	0	ENST00000369096.4:c.283A>G	p.Ser95Gly	p.S95G	ENST00000369096	NM_001198.3	95	Agt/Ggt	2/7	1	2	FACETS	0.965	0.817	1	0.965	0.817	1	CLONAL	1	TRUE	1	0.28	2		403	348	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609759	117609759	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs771164515	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	89	622	0	ENST00000368508.3:c.6940G>T	p.Asp2314Tyr	p.D2314Y	ENST00000368508	NM_002944.2	2314	Gat/Tat	43/43	1	2	FACETS	0.753	0.672	0.839	1	0.98	1	SUBCLONAL	2	TRUE	1	0.28	2		622	422	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662585	117662585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	27	503	1	ENST00000368508.3:c.4880G>A	p.Gly1627Asp	p.G1627D	ENST00000368508	NM_002944.2	1627	gGt/gAt	29/43	1	2	FACETS	0.736	0.588	0.904	0.736	0.588	0.904	CLONAL	1	TRUE	1	0.28	2		504	262	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709028	117709028	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	64	680	0	ENST00000368508.3:c.1929G>T	p.Met643Ile	p.M643I	ENST00000368508	NM_002944.2	643	atG/atT	13/43	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.28	2		680	436	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117739650	117739650	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	21	425	0	ENST00000368508.3:c.143G>T	p.Gly48Val	p.G48V	ENST00000368508	NM_002944.2	48	gGc/gTc	2/43	1	2	FACETS	0.554	0.427	0.701	0.554	0.427	0.701	SUBCLONAL	1	TRUE	1	0.28	2		425	271	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527279	137527279	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	45	607	0	ENST00000367739.4:c.367C>T	p.Arg123Ter	p.R123*	ENST00000367739	NM_000416.2	123	Cga/Tga	3/7	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.28	2		607	275	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138201360	138201360	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	43	627	0	ENST00000237289.4:c.2059C>A	p.His687Asn	p.H687N	ENST00000237289	NM_001270507.1	687	Cat/Aat	8/9	1	2	FACETS	0.802	0.672	0.945	0.802	0.672	0.945	CLONAL	1	TRUE	1	0.28	2		627	383	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023019	150023019	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	35	651	0	ENST00000253339.5:c.244C>T	p.Arg82Ter	p.R82*	ENST00000253339		82	Cga/Tga	1/7	1	2	FACETS	0.853	0.702	1	0.853	0.702	1	CLONAL	1	TRUE	1	0.28	2		651	293	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771139	161771139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	80	812	2	ENST00000366898.1:c.1390G>A	p.Asp464Asn	p.D464N	ENST00000366898	NM_004562.2	464	Gac/Aac	12/12	1	2	FACETS	0.94	0.828	1	0.94	0.828	1	CLONAL	1	TRUE	1	0.28	2		814	608	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978854	13978854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1302857335	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	30	500	2	ENST00000405192.2:c.253C>T	p.Pro85Ser	p.P85S	ENST00000405192	NM_001163147.1	85	Cca/Tca	6/12	1	2	FACETS	0.788	0.637	0.957	0.788	0.637	0.957	CLONAL	1	TRUE	1	0.28	2		502	272	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739642	41739642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	53	621	1	ENST00000242208.4:c.331G>A	p.Ala111Thr	p.A111T	ENST00000242208	NM_002192.2	111	Gca/Aca	2/3	1	2	FACETS	0.862	0.737	0.999	0.862	0.737	0.999	CLONAL	1	TRUE	1	0.28	2		622	439	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444401	50444401	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	44	516	0	ENST00000331340.3:c.331C>T	p.Arg111Ter	p.R111*	ENST00000331340	NM_006060.4	111	Cga/Tga	4/8	1	2	FACETS	0.825	0.693	0.97	0.825	0.693	0.97	CLONAL	1	TRUE	1	0.28	2		516	381	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273297	55273297	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1301373415	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	55	552	0	ENST00000275493.2:c.3620T>G	p.Phe1207Cys	p.F1207C	ENST00000275493	NM_005228.3	1207	tTt/tGt	28/28	1	2	FACETS	0.951	0.816	1	0.951	0.816	1	CLONAL	1	TRUE	1	0.28	2		552	413	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515219	106515219	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	33	469	0	ENST00000359195.3:c.2362G>T	p.Asp788Tyr	p.D788Y	ENST00000359195	NM_002649.2	788	Gat/Tat	5/11	1	2	FACETS	0.845	0.691	1	0.845	0.691	1	CLONAL	1	TRUE	1	0.28	2		469	279	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339981	116339981	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	29	458	0	ENST00000397752.3:c.843C>A	p.Phe281Leu	p.F281L	ENST00000397752	NM_000245.2	281	ttC/ttA	2/21	1	2	FACETS	0.77	0.62	0.939	0.77	0.62	0.939	CLONAL	1	TRUE	1	0.28	2		458	269	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418882	116418882	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	44	406	0	ENST00000397752.3:c.3393G>T	p.Met1131Ile	p.M1131I	ENST00000397752	NM_000245.2	1131	atG/atT	17/21	1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	1	0.28	2		406	312	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845086	128845086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761395599	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	73	971	2	ENST00000249373.3:c.580G>A	p.Glu194Lys	p.E194K	ENST00000249373	NM_005631.4	194	Gaa/Aaa	3/12	1	2	FACETS	0.902	0.79	1	0.902	0.79	1	CLONAL	1	TRUE	1	0.28	2		973	578	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151168528	151168528	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	23	454	0	ENST00000262187.5:c.333-1G>T		p.X111_splice	ENST00000262187	NM_005614.3	111			1	2	FACETS	0.939	0.738	1	0.939	0.738	1	CLONAL	1	TRUE	1	0.28	2		454	175	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845367	151845367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	69	764	0	ENST00000262189.6:c.13645C>T	p.Arg4549Cys	p.R4549C	ENST00000262189	NM_170606.2	4549	Cgc/Tgc	52/59	1	2	FACETS	0.932	0.813	1	0.932	0.813	1	CLONAL	1	TRUE	1	0.28	2		764	529	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874431	151874431	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	36	451	0	ENST00000262189.6:c.8107G>T	p.Asp2703Tyr	p.D2703Y	ENST00000262189	NM_170606.2	2703	Gac/Tac	38/59	1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	1	0.28	2		451	251	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878356	151878356	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	43	706	0	ENST00000262189.6:c.6589C>T	p.Gln2197Ter	p.Q2197*	ENST00000262189	NM_170606.2	2197	Cag/Tag	36/59	1	2	FACETS	0.742	0.622	0.875	0.742	0.622	0.875	SUBCLONAL	1	TRUE	1	0.28	2		706	414	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902277	151902277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1268465923	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	10	229	0	ENST00000262189.6:c.3875G>A	p.Arg1292Gln	p.R1292Q	ENST00000262189	NM_170606.2	1292	cGa/cAa	25/59	1	2	FACETS	0.68	0.464	0.947	0.68	0.464	0.947	SUBCLONAL	1	TRUE	1	0.28	2		229	105	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978677	70978677	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs759502844	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	52	796	0	ENST00000276594.2:c.976T>C	p.Ser326Pro	p.S326P	ENST00000276594	NM_024504.3	326	Tcc/Ccc	5/8	1	2	FACETS	0.846	0.722	0.982	0.846	0.722	0.982	CLONAL	1	TRUE	1	0.28	2		796	439	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982658	90982658	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876658579	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	22	384	0	ENST00000265433.3:c.830A>G	p.Asn277Ser	p.N277S	ENST00000265433	NM_002485.4	277	aAc/aGc	7/16	1	2	FACETS	0.728	0.566	0.913	0.728	0.566	0.913	CLONAL	1	TRUE	1	0.28	2		384	216	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859879	117859879	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	15	296	1	ENST00000297338.2:c.1756C>T	p.Arg586Ter	p.R586*	ENST00000297338	NM_006265.2	586	Cga/Tga	14/14	1	2	FACETS	0.523	0.383	0.69	0.523	0.383	0.69	SUBCLONAL	1	TRUE	1	0.28	2		297	205	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054649	5054649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373174105	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	22	306	0	ENST00000381652.3:c.701G>A	p.Arg234His	p.R234H	ENST00000381652	NM_004972.3	234	cGc/cAc	7/25	1	2	FACETS	1	0.783	1	1	0.783	1	CLONAL	1	TRUE	1	0.28	2		306	157	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054717	5054717	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	22	373	0	ENST00000381652.3:c.769A>C	p.Asn257His	p.N257H	ENST00000381652	NM_004972.3	257	Aat/Cat	7/25	1	2	FACETS	0.859	0.67	1	0.859	0.67	1	CLONAL	1	TRUE	1	0.28	2		373	183	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285871	87285871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408094711	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	41	640	1	ENST00000277120.3:c.208G>A	p.Glu70Lys	p.E70K	ENST00000277120		70	Gaa/Aaa	2/19	1	2	FACETS	0.832	0.695	0.983	0.832	0.695	0.983	CLONAL	1	TRUE	1	0.28	2		641	352	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915951	127915951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	42	496	0	ENST00000373547.4:c.530G>A	p.Arg177Gln	p.R177Q	ENST00000373547	NM_002721.4	177	cGa/cAa	6/7	1	2	FACETS	0.923	0.774	1	0.923	0.774	1	CLONAL	1	TRUE	1	0.28	2		496	325	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391119	139391119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780869345	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	88	1278	3	ENST00000277541.6:c.7072G>A	p.Ala2358Thr	p.A2358T	ENST00000277541	NM_017617.3	2358	Gcc/Acc	34/34	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.28	2		1281	608	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391869	139391869	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780963597	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	68	1226	1	ENST00000277541.6:c.6322G>A	p.Asp2108Asn	p.D2108N	ENST00000277541	NM_017617.3	2108	Gac/Aac	34/34	1	2	FACETS	0.875	0.762	0.997	0.875	0.762	0.997	CLONAL	1	TRUE	1	0.28	2		1227	555	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391968	139391968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs549258808	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	75	1039	1	ENST00000277541.6:c.6223G>A	p.Glu2075Lys	p.E2075K	ENST00000277541	NM_017617.3	2075	Gag/Aag	34/34	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.28	2		1040	531	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317422	1317422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759127718	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	55	708	0	ENST00000400841.2:c.643C>T	p.Arg215Trp	p.R215W	ENST00000400841		215	Cgg/Tgg	5/6	1	2	FACETS	0.877	0.752	1	0.877	0.752	1	CLONAL	1	TRUE	1	0.28	2		708	448	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039844	47039844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	70	982	1	ENST00000377604.3:c.1187G>A	p.Arg396His	p.R396H	ENST00000377604	NM_001204468.1	396	cGc/cAc	12/24	1	2	FACETS	0.887	0.774	1	0.887	0.774	1	CLONAL	1	TRUE	1	0.28	2		983	564	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250079	53250079	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	55	651	2	ENST00000375401.3:c.170C>T	p.Ala57Val	p.A57V	ENST00000375401	NM_004187.3	57	gCt/gTt	2/26	1	2	FACETS	0.803	0.688	0.929	0.803	0.688	0.929	CLONAL	1	TRUE	1	0.28	2		653	489	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412059	63412059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	54	890	0	ENST00000330258.3:c.1108G>A	p.Glu370Lys	p.E370K	ENST00000330258	NM_152424.3	370	Gag/Aag	2/2	1	2	FACETS	0.688	0.587	0.798	0.688	0.587	0.798	SUBCLONAL	1	TRUE	1	0.28	2		890	561	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412510	63412510	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	53	917	0	ENST00000330258.3:c.657G>T	p.Glu219Asp	p.E219D	ENST00000330258	NM_152424.3	219	gaG/gaT	2/2	1	2	FACETS	0.695	0.592	0.807	0.695	0.592	0.807	SUBCLONAL	1	TRUE	1	0.28	2		917	545	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347766	70347766	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	51	617	0	ENST00000374080.3:c.3005A>G	p.Asn1002Ser	p.N1002S	ENST00000374080		1002	aAc/aGc	22/45	1	2	FACETS	0.88	0.75	1	0.88	0.75	1	CLONAL	1	TRUE	1	0.28	2		617	414	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352373	70352373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	43	633	2	ENST00000374080.3:c.4400G>A	p.Arg1467Gln	p.R1467Q	ENST00000374080		1467	cGa/cAa	31/45	1	2	FACETS	0.856	0.718	1	0.856	0.718	1	CLONAL	1	TRUE	1	0.28	2		635	359	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76876001	76876001	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	11	255	0	ENST00000373344.5:c.5135-1G>T		p.X1712_splice	ENST00000373344	NM_000489.3	1712			0.3	1	FACETS	0.609	0.424	0.835	0.609	0.424	0.835	SUBCLONAL	1	TRUE	0	0.28	1		255	111	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907627	76907627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	35	509	2	ENST00000373344.5:c.4534C>T	p.Arg1512Cys	p.R1512C	ENST00000373344	NM_000489.3	1512	Cgt/Tgt	15/35	0.3	1	FACETS	0.7	0.576	0.839	0.7	0.576	0.839	SUBCLONAL	1	TRUE	0	0.28	1		511	307	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937409	76937409	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	21	502	0	ENST00000373344.5:c.3339G>T	p.Glu1113Asp	p.E1113D	ENST00000373344	NM_000489.3	1113	gaG/gaT	9/35	0.3	1	FACETS	0.725	0.562	0.912	0.725	0.562	0.912	CLONAL	1	TRUE	0	0.28	1		502	178	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937673	76937673	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	27	490	0	ENST00000373344.5:c.3075T>G	p.Ile1025Met	p.I1025M	ENST00000373344	NM_000489.3	1025	atT/atG	9/35	0.3	1	FACETS	0.851	0.682	1	0.851	0.682	1	CLONAL	1	TRUE	0	0.28	1		490	195	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937693	76937693	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	27	507	0	ENST00000373344.5:c.3055T>G	p.Leu1019Val	p.L1019V	ENST00000373344	NM_000489.3	1019	Tta/Gta	9/35	0.3	1	FACETS	0.882	0.708	1	0.882	0.708	1	CLONAL	1	TRUE	0	0.28	1		507	188	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939192	76939192	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	20	636	0	ENST00000373344.5:c.1556C>A	p.Ser519Tyr	p.S519Y	ENST00000373344	NM_000489.3	519	tCt/tAt	9/35	0.3	1	FACETS	0.363	0.277	0.464	0.363	0.277	0.464	SUBCLONAL	1	TRUE	0	0.28	1		636	338	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939250	76939250	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	29	731	0	ENST00000373344.5:c.1498G>T	p.Glu500Ter	p.E500*	ENST00000373344	NM_000489.3	500	Gaa/Taa	9/35	0.3	1	FACETS	0.516	0.415	0.632	0.516	0.415	0.632	SUBCLONAL	1	TRUE	0	0.28	1		731	345	SUCCESS
BTK	695	MSKCC	GRCh37	X	100609675	100609675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs128620183	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	41	418	0	ENST00000308731.7:c.1574G>A	p.Arg525Gln	p.R525Q	ENST00000308731	NM_000061.2	525	cGa/cAa	16/19	0.3	2	FACETS	0.807	0.674	0.954			1	CLONAL	1	TRUE	NA	0.28	2		418	363	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123026579	123026579	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	19	470	0	ENST00000355640.3:c.1057-2A>T		p.X353_splice	ENST00000355640		353			0.3	2	FACETS	0.563	0.428	0.721			1	SUBCLONAL	1	TRUE	NA	0.28	2		470	241	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181296	123181296	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	14	350	0	ENST00000218089.9:c.760A>G	p.Lys254Glu	p.K254E	ENST00000218089	NM_001042749.1	254	Aaa/Gaa	9/35	0.3	2	FACETS	0.735	0.535	0.974			1	CLONAL	1	TRUE	NA	0.28	2		350	136	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190069	123190069	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	18	463	2	ENST00000218089.9:c.1288G>T	p.Glu430Ter	p.E430*	ENST00000218089	NM_001042749.1	430	Gaa/Taa	14/35	0.3	2	FACETS	0.636	0.481	0.819			1	SUBCLONAL	1	TRUE	NA	0.28	2		465	202	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205044	123205044	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	21	479	1	ENST00000218089.9:c.2404A>C	p.Ile802Leu	p.I802L	ENST00000218089	NM_001042749.1	802	Att/Ctt	25/35	0.3	2	FACETS	0.909	0.705	1			1	CLONAL	1	TRUE	NA	0.28	2		480	165	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224430	123224430	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	37	482	1	ENST00000218089.9:c.3283G>T	p.Glu1095Ter	p.E1095*	ENST00000218089	NM_001042749.1	1095	Gaa/Taa	31/35	0.3	2	FACETS	0.961	0.796	1			1	CLONAL	1	TRUE	NA	0.28	2		483	275	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224539	123224539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	32	658	0	ENST00000218089.9:c.3392G>T	p.Arg1131Ile	p.R1131I	ENST00000218089	NM_001042749.1	1131	aGa/aTa	31/35	0.3	2	FACETS	0.649	0.528	0.786			1	SUBCLONAL	1	TRUE	NA	0.28	2		658	352	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	46	386	2	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	2	FACETS	0.856	0.727	0.996	1	0.977	1	CLONAL	3	FALSE	1	0.144488896013171	2		388	248	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	244	900	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.972	0.91	1	1	0.996	1	CLONAL	4	FALSE	1	0.144488896013171	2		904	869	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	170	565	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	1	0.969	1	1	0.995	1	CLONAL	4	FALSE	1	0.144488896013171	2		565	542	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589623	67589634	+	inframe_deletion	In_Frame_Del	DEL	ATATGATAGATT	ATATGATAGATT	-	novel	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	67	220	0	ENST00000274335.5:c.1392_1403del	p.Asp464_Tyr467del	p.D464_Y467del	ENST00000274335		462	gaATATGATAGATTa/gaa	10/15	1	2	FACETS	1	0.948	1	1	0.986	1	CLONAL	3	FALSE	1	0.144488896013171	2		220	268	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	160	519	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.971	1	1	0.994	1	CLONAL	3	FALSE	1	0.144488896013171	2		520	659	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801779	3801779	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	174	556	2	ENST00000262367.5:c.3727G>T	p.Glu1243Ter	p.E1243*	ENST00000262367	NM_004380.2	1243	Gag/Tag	20/31	1	2	FACETS	0.951	0.88	1	1	0.995	1	CLONAL	4	FALSE	1	0.144488896013171	2		558	633	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717630	89717630	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554825168	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	150	466	1	ENST00000371953.3:c.655C>T	p.Gln219Ter	p.Q219*	ENST00000371953	NM_000314.4	219	Cag/Tag	7/9	1	2	FACETS	1	0.932	1	1	0.994	1	CLONAL	4	FALSE	1	0.144488896013171	2		467	512	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226064	53226064	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs782405999	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	282	918	2	ENST00000375401.3:c.2785C>T	p.Arg929Ter	p.R929*	ENST00000375401	NM_004187.3	929	Cga/Tga	19/26	1	2	FACETS	1	0.975	1	1	0.997	1	CLONAL	4	FALSE	1	0.144488896013171	2		920	918	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497245	149497245	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	224	851	0	ENST00000261799.4:c.3073del	p.Leu1025CysfsTer20	p.L1025Cfs*20	ENST00000261799	NM_002609.3	1025	Ctg/tg	22/23	1	2	FACETS	1	0.982	1	1	0.995	1	CLONAL	3	FALSE	1	0.144488896013171	2		851	901	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	203	780	1	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.947	0.881	1	1	0.995	1	CLONAL	4	FALSE	1	0.144488896013171	2		781	742	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954272	32954273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359752	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	136	441	2	ENST00000380152.3:c.9253dup	p.Thr3085AsnfsTer26	p.T3085Nfs*26	ENST00000380152		3082	-/A	24/27	1	2	FACETS	0.951	0.87	1	1	0.993	1	CLONAL	4	FALSE	1	0.144488896013171	2		443	495	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930634	32930634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56070345	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	132	447	1	ENST00000380152.3:c.7505G>A	p.Arg2502His	p.R2502H	ENST00000380152		2502	cGc/cAc	15/27	1	2	FACETS	0.946	0.864	1	1	0.993	1	CLONAL	4	FALSE	1	0.144488896013171	2		448	483	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272337	15272337	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs771517374	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	271	1130	11	ENST00000263388.2:c.6102del	p.Gly2035ValfsTer50	p.G2035Vfs*50	ENST00000263388	NM_000435.2	2034	ccC/cc	33/33	1	2	FACETS	0.937	0.88	0.995	1	0.996	1	CLONAL	4	FALSE	1	0.144488896013171	2		1141	1001	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938271	36938271	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	254	1076	0	ENST00000361632.4:c.690del	p.Met231CysfsTer32	p.M231Cfs*32	ENST00000361632		230	ccC/cc	6/16	1	2	FACETS	0.899	0.842	0.957	1	0.996	1	CLONAL	4	FALSE	1	0.144488896013171	2		1076	978	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411695	63411695	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370645786	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	203	913	0	ENST00000330258.3:c.1472G>A	p.Arg491His	p.R491H	ENST00000330258	NM_152424.3	491	cGc/cAc	2/2	1	2	FACETS	1	0.976	1	1	0.995	1	CLONAL	3	FALSE	1	0.144488896013171	2		913	843	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257366	19257366	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	256	1018	0	ENST00000162023.5:c.767del	p.Pro256GlnfsTer?	p.P256Qfs*?	ENST00000162023		256	cCa/ca	11/13	1	2	FACETS	1	0.967	1	1	0.996	1	CLONAL	4	FALSE	1	0.144488896013171	2		1018	847	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097630	27097630	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	155	490	0	ENST00000324856.7:c.3219G>A	p.Trp1073Ter	p.W1073*	ENST00000324856	NM_006015.4	1073	tgG/tgA	12/20	1	2	FACETS	0.933	0.858	1	1	0.994	1	CLONAL	4	FALSE	1	0.144488896013171	2		490	575	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944381	131944382	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs748536322	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	51	178	6	ENST00000265335.6:c.2801dup	p.Asn934LysfsTer10	p.N934Kfs*10	ENST00000265335		931	-/A	17/25	1	2	FACETS	1	0.903	1	1	0.981	1	CLONAL	3	FALSE	1	0.144488896013171	2		184	221	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102196012	102196012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	113	355	0	ENST00000263464.3:c.772C>T	p.Arg258Cys	p.R258C	ENST00000263464	NM_001165.4	258	Cgc/Tgc	2/9	0.144488896013171	2	FACETS	0.933	0.846	1	1	0.988	1	CLONAL	4	FALSE	0	0.144488896013171	2		355	419	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630605	187630605	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	188	641	0	ENST00000441802.2:c.377del	p.Asn126IlefsTer20	p.N126Ifs*20	ENST00000441802	NM_005245.3	126	aAt/at	2/27	1	2	FACETS	0.995	0.923	1	1	0.995	1	CLONAL	4	FALSE	1	0.144488896013171	2		641	654	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196879	108196880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs773570504	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	97	377	0	ENST00000278616.4:c.6908dup	p.Glu2304GlyfsTer69	p.E2304Gfs*69	ENST00000278616	NM_000051.3	2301	gca/gcAa	47/63	1	2	FACETS	0.99	0.888	1	1	0.99	1	CLONAL	3	FALSE	1	0.144488896013171	2		377	452	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599285	55599285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777616126	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	108	475	0	ENST00000288135.5:c.2411G>A	p.Arg804Gln	p.R804Q	ENST00000288135	NM_000222.2	804	cGg/cAg	17/21	1	2	FACETS	1	0.944	1	1	0.991	1	CLONAL	3	FALSE	1	0.144488896013171	2		475	467	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468146	50468146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	174	822	0	ENST00000331340.3:c.1381G>A	p.Val461Met	p.V461M	ENST00000331340	NM_006060.4	461	Gtg/Atg	8/8	1	2	FACETS	1	0.975	1	1	0.994	1	CLONAL	3	FALSE	1	0.144488896013171	2		822	712	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434182	12434182	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776687	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	159	422	1	ENST00000287820.6:c.556del	p.Ser186ValfsTer47	p.S186Vfs*47	ENST00000287820	NM_015869.4	184	Aaa/aa	4/7	1	2	FACETS	1	0.942	1	1	0.994	1	CLONAL	4	FALSE	1	0.144488896013171	2		423	537	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935635	49935635	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	192	774	0	ENST00000296474.3:c.1729del	p.His577ThrfsTer5	p.H577Tfs*5	ENST00000296474	NM_002447.2	577	Cac/ac	5/20	1	2	FACETS	1	0.979	1	1	0.995	1	CLONAL	3	FALSE	1	0.144488896013171	2		774	772	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932068	39932068	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140780988	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	258	822	0	ENST00000378444.4:c.2531C>T	p.Pro844Leu	p.P844L	ENST00000378444	NM_001123385.1	844	cCg/cTg	4/15	1	2	FACETS	0.983	0.923	1	1	0.996	1	CLONAL	4	FALSE	1	0.144488896013171	2		822	908	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37628031	37628031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs578052035	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	212	710	0	ENST00000249071.6:c.229G>A	p.Val77Ile	p.V77I	ENST00000249071	NM_002872.4	77	Gtc/Atc	4/7	1	2	FACETS	0.99	0.923	1	1	0.995	1	CLONAL	4	FALSE	1	0.144488896013171	2		710	741	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325840	65325840	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	180	660	1	ENST00000342505.4:c.1282G>A	p.Ala428Thr	p.A428T	ENST00000342505	NM_002227.2	428	Gcc/Acc	9/25	1	2	FACETS	0.903	0.835	0.972	1	0.995	1	CLONAL	4	FALSE	1	0.144488896013171	2		661	690	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002940	69002940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	112	340	0	ENST00000288368.4:c.2240G>A	p.Arg747Gln	p.R747Q	ENST00000288368	NM_024870.2	747	cGg/cAg	20/40	1	2	FACETS	0.923	0.836	1	1	0.992	1	CLONAL	4	FALSE	1	0.144488896013171	2		340	420	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110127	8110127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772022668	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	208	623	0	ENST00000585124.1:c.478G>A	p.Gly160Arg	p.G160R	ENST00000585124	NM_004217.3	160	Ggg/Agg	6/9	1	2	FACETS	1	0.953	1	1	0.995	1	CLONAL	4	FALSE	1	0.144488896013171	2		623	700	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258735	16258735	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	130	556	1	ENST00000375759.3:c.6005del	p.Asn2002MetfsTer20	p.N2002Mfs*20	ENST00000375759	NM_015001.2	2000	ggA/gg	11/15	1	2	FACETS	0.958	0.872	1	1	0.992	1	CLONAL	3	FALSE	1	0.144488896013171	2		557	626	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753602	42753602	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	270	1107	0	ENST00000222329.4:c.662del	p.Pro221ArgfsTer50	p.P221Rfs*50	ENST00000222329	NM_006494.2	221	cCg/cg	4/4	1	2	FACETS	0.935	0.878	0.994	1	0.996	1	CLONAL	4	FALSE	1	0.144488896013171	2		1107	999	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777062	9777062	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	232	893	0	ENST00000377346.4:c.826A>G	p.Met276Val	p.M276V	ENST00000377346	NM_005026.3	276	Atg/Gtg	7/24	1	2	FACETS	0.995	0.93	1	1	0.996	1	CLONAL	4	FALSE	1	0.144488896013171	2		893	807	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11301655	11301655	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	225	856	0	ENST00000361445.4:c.1496A>C	p.Gln499Pro	p.Q499P	ENST00000361445	NM_004958.3	499	cAg/cCg	10/58	1	2	FACETS	0.921	0.86	0.985	1	0.996	1	CLONAL	4	FALSE	1	0.144488896013171	2		856	845	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260289	16260290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	135	652	0	ENST00000375759.3:c.7559dup	p.Asp2521ArgfsTer6	p.D2521Rfs*6	ENST00000375759	NM_015001.2	2518	-/C	11/15	1	2	FACETS	0.966	0.88	1	1	0.992	1	CLONAL	3	FALSE	1	0.144488896013171	2		652	645	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107137	27107137	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	265	651	0	ENST00000324856.7:c.6748del	p.Glu2250SerfsTer17	p.E2250Sfs*17	ENST00000324856	NM_006015.4	2250	Gag/ag	20/20	1	2	FACETS	0.914	0.86	0.969	1	0.996	1	CLONAL	5	FALSE	1	0.144488896013171	2		651	803	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426247	49426247	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	255	990	2	ENST00000301067.7:c.12241del	p.Gln4081SerfsTer15	p.Q4081Sfs*15	ENST00000301067	NM_003482.3	4081	Cag/ag	39/54	1	2	FACETS	0.889	0.832	0.946	1	0.996	1	CLONAL	4	FALSE	1	0.144488896013171	2		992	993	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490620	56490620	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771899301	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	117	450	0	ENST00000267101.3:c.2264C>T	p.Ala755Val	p.A755V	ENST00000267101	NM_001982.3	755	gCt/gTt	19/28	1	2	FACETS	1	0.967	1	1	0.992	1	CLONAL	3	FALSE	1	0.144488896013171	2		450	471	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112434	115112434	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	64	866	0	ENST00000257566.3:c.1306C>G	p.Arg436Gly	p.R436G	ENST00000257566	NM_016569.3	436	Cgc/Ggc	7/8	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	FALSE	1	0.144488896013171	2		866	854	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619300	23619300	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881878	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	200	584	0	ENST00000261584.4:c.3235G>A	p.Ala1079Thr	p.A1079T	ENST00000261584	NM_024675.3	1079	Gcc/Acc	12/13	1	2	FACETS	0.999	0.929	1	1	0.995	1	CLONAL	4	FALSE	1	0.144488896013171	2		584	693	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127352	17127352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778367	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	231	875	0	ENST00000285071.4:c.502C>T	p.Arg168Cys	p.R168C	ENST00000285071	NM_144997.5	168	Cgc/Tgc	6/14	1	2	FACETS	1	0.963	1	1	0.996	1	CLONAL	4	FALSE	1	0.144488896013171	2		875	767	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883741	37883741	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	320	1030	1	ENST00000269571.5:c.3353T>C	p.Val1118Ala	p.V1118A	ENST00000269571		1118	gTa/gCa	26/27	1	2	FACETS	1	0.98	1	1	0.997	1	CLONAL	4	FALSE	1	0.144488896013171	2		1031	1029	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218598	36218598	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	215	960	1	ENST00000222270.7:c.4303-1G>T		p.X1435_splice	ENST00000222270	NM_014727.1	1435			1	2	FACETS	0.885	0.824	0.947	1	0.995	1	CLONAL	4	FALSE	1	0.144488896013171	2		961	841	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724241	52724241	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	204	551	0	ENST00000322088.6:c.1373T>C	p.Ile458Thr	p.I458T	ENST00000322088	NM_014225.5	458	aTc/aCc	12/15	1	2	FACETS	1	0.972	1	1	0.995	1	CLONAL	4	FALSE	1	0.144488896013171	2		551	653	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249914	39249914	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397517154	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	189	700	0	ENST00000402219.2:c.1655G>A	p.Arg552Lys	p.R552K	ENST00000402219	NM_005633.3	552	aGg/aAg	10/23	1	2	FACETS	0.985	0.914	1	1	0.995	1	CLONAL	4	FALSE	1	0.144488896013171	2		700	664	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193603	99193603	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	204	643	0	ENST00000074304.5:c.2798G>T	p.Arg933Leu	p.R933L	ENST00000074304	NM_001134224.1	933	cGc/cTc	25/26	1	2	FACETS	1	0.979	1	1	0.995	1	CLONAL	4	FALSE	1	0.144488896013171	2		643	629	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663384	227663384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs557991154	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	192	657	0	ENST00000305123.5:c.71G>A	p.Ser24Asn	p.S24N	ENST00000305123	NM_005544.2	24	aGc/aAc	1/2	1	2	FACETS	1	0.942	1	1	0.995	1	CLONAL	4	FALSE	1	0.144488896013171	2		657	654	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37059066	37059067	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs587779047	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	128	489	0	ENST00000231790.2:c.866_867del	p.His289ProfsTer17	p.H289Pfs*17	ENST00000231790	NM_000249.3	287	aAC/a	10/19	1	2	FACETS	0.881	0.803	0.962	1	0.993	1	CLONAL	4	FALSE	1	0.144488896013171	2		489	503	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447708	187447708	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	188	752	0	ENST00000232014.4:c.485T>C	p.Val162Ala	p.V162A	ENST00000232014	NM_001130845.1	162	gTg/gCg	5/10	1	2	FACETS	1	0.979	1	1	0.995	1	CLONAL	3	FALSE	1	0.144488896013171	2		752	756	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213790	66213790	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	115	434	0	ENST00000273854.3:c.2640G>T	p.Trp880Cys	p.W880C	ENST00000273854	NM_004439.5	880	tgG/tgT	15/18	1	2	FACETS	0.948	0.86	1	1	0.992	1	CLONAL	4	FALSE	1	0.144488896013171	2		434	420	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361165	66361165	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	128	362	0	ENST00000273854.3:c.1007G>C	p.Cys336Ser	p.C336S	ENST00000273854	NM_004439.5	336	tGt/tCt	4/18	1	2	FACETS	0.955	0.871	1	1	0.993	1	CLONAL	4	FALSE	1	0.144488896013171	2		362	464	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	231028	231044	+	frameshift_variant	Frame_Shift_Del	DEL	CACACCAGCACTGGCGA	CACACCAGCACTGGCGA	-	novel	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	59	762	0	ENST00000264932.6:c.809_825del	p.His270ArgfsTer45	p.H270Rfs*45	ENST00000264932	NM_004168.2	270	CACACCAGCACTGGCGAc/c	7/15	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	FALSE	1	0.144488896013171	2		762	742	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287200	38287200	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	201	825	0	ENST00000425967.3:c.457G>T	p.Asp153Tyr	p.D153Y	ENST00000425967	NM_001174067.1	153	Gat/Tat	4/19	1	2	FACETS	0.925	0.86	0.992	1	0.995	1	CLONAL	4	FALSE	1	0.144488896013171	2		825	752	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685269	89685269	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0056726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	64	204	0	ENST00000371953.3:c.165del		p.X55_splice	ENST00000371953	NM_000314.4	55			1	2	FACETS	1	0.892	1	1	0.986	1	CLONAL	4	FALSE	1	0.144488896013171	2		204	218	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0056727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	98	418	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.981	0.883	1	0.981	0.883	1	CLONAL	1	TRUE	1	0.555083779114745	2		418	360	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322553	39322553	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	21	403	0	ENST00000373001.3:c.439C>T	p.Gln147Ter	p.Q147*	ENST00000373001	NM_022157.3	147	Cag/Tag	2/7	0.48001345660331	2	FACETS	0.18	0.138	0.229	0.09	0.069	0.115	SUBCLONAL	1	TRUE	0	0.555083779114745	2		403	420	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515192	103515192	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	30	338	0	ENST00000355739.4:c.1693G>C	p.Asp565His	p.D565H	ENST00000355739	NM_000123.3	565	Gat/Cat	8/15	0.48001345660331	2	FACETS	0.334	0.269	0.407	0.167	0.134	0.204	SUBCLONAL	1	TRUE	0	0.555083779114745	2		338	324	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108059	30108059	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	23	400	0	ENST00000331968.5:c.748C>G	p.Gln250Glu	p.Q250E	ENST00000331968	NM_002742.2	250	Caa/Gaa	5/18	1	2	FACETS	0.206	0.16	0.259	0.206	0.16	0.259	SUBCLONAL	1	TRUE	1	0.555083779114745	2		400	403	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738774	43738774	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	96	452	1	ENST00000382044.4:c.2851C>A	p.Pro951Thr	p.P951T	ENST00000382044	NM_001141980.1	951	Cca/Aca	14/28	1	2	FACETS	0.781	0.699	0.866	0.781	0.699	0.866	SUBCLONAL	1	TRUE	1	0.555083779114745	2		453	443	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632768	23632768	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	81	466	0	ENST00000261584.4:c.3028G>T	p.Glu1010Ter	p.E1010*	ENST00000261584	NM_024675.3	1010	Gag/Tag	10/13	1	2	FACETS	0.685	0.606	0.769	0.685	0.606	0.769	SUBCLONAL	1	TRUE	1	0.555083779114745	2		466	426	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40860898	40860898	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	33	475	1	ENST00000428826.2:c.1530G>T	p.Lys510Asn	p.K510N	ENST00000428826		510	aaG/aaT	14/21	1	2	FACETS	0.18	0.146	0.219	0.18	0.146	0.219	SUBCLONAL	1	TRUE	1	0.555083779114745	2		476	660	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945479	17945479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	42	782	0	ENST00000458235.1:c.2251G>A	p.Glu751Lys	p.E751K	ENST00000458235	NM_000215.3	751	Gag/Aag	17/24	1	2	FACETS	0.204	0.17	0.243	0.204	0.17	0.243	SUBCLONAL	1	TRUE	1	0.555083779114745	2		782	741	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912146	50912146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	210	881	0	ENST00000440232.2:c.1880C>T	p.Ala627Val	p.A627V	ENST00000440232	NM_002691.3	627	gCa/gTa	15/27	NA	2	FACETS	0.646	0.599	0.695			1	INDETERMINATE	1	TRUE	NA	0.555083779114745	2		881	1171	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543637	29543637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	159	687	0	ENST00000389048.3:c.1526C>T	p.Ala509Val	p.A509V	ENST00000389048	NM_004304.4	509	gCc/gTc	7/29	1	2	FACETS	0.806	0.74	0.874	0.806	0.74	0.874	CLONAL	1	TRUE	1	0.555083779114745	2		687	711	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537106	41537106	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	40	343	0	ENST00000263253.7:c.1933G>T	p.Glu645Ter	p.E645*	ENST00000263253	NM_001429.3	645	Gaa/Taa	10/31	1	2	FACETS	0.355	0.295	0.422	0.355	0.295	0.422	SUBCLONAL	1	TRUE	1	0.555083779114745	2		343	406	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165246	47165246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	66	323	0	ENST00000409792.3:c.880G>A	p.Asp294Asn	p.D294N	ENST00000409792	NM_014159.6	294	Gat/Aat	3/21	1	2	FACETS	0.723	0.632	0.82	0.723	0.632	0.82	SUBCLONAL	1	TRUE	1	0.555083779114745	2		323	329	SUCCESS
ATR	545	MSKCC	GRCh37	3	142285084	142285084	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	77	332	1	ENST00000350721.4:c.171G>T	p.Lys57Asn	p.K57N	ENST00000350721	NM_001184.3	57	aaG/aaT	3/47	1	2	FACETS	0.71	0.626	0.798	0.71	0.626	0.798	SUBCLONAL	1	TRUE	1	0.555083779114745	2		333	391	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182681688	182681688	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	63	324	0	ENST00000292782.4:c.370G>C	p.Asp124His	p.D124H	ENST00000292782	NM_020640.2	124	Gat/Cat	3/7	1	2	FACETS	0.533	0.462	0.609	0.533	0.462	0.609	SUBCLONAL	1	TRUE	1	0.555083779114745	2		324	426	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164871	106164871	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	32	535	0	ENST00000380013.4:c.3739G>A	p.Glu1247Lys	p.E1247K	ENST00000380013	NM_001127208.2	1247	Gag/Aag	6/11	1	2	FACETS	0.185	0.149	0.225	0.185	0.149	0.225	SUBCLONAL	1	TRUE	1	0.555083779114745	2		535	623	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535488	187535488	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0056727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	19	319	0	ENST00000441802.2:c.9086C>G	p.Ser3029Ter	p.S3029*	ENST00000441802	NM_005245.3	3029	tCa/tGa	12/27	1	2	FACETS	0.196	0.148	0.252	0.196	0.148	0.252	SUBCLONAL	1	TRUE	1	0.555083779114745	2		319	350	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80024675	80024675	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	23	347	0	ENST00000265081.6:c.1459C>G	p.Gln487Glu	p.Q487E	ENST00000265081	NM_002439.4	487	Caa/Gaa	10/24	1	2	FACETS	0.269	0.21	0.338	0.269	0.21	0.338	SUBCLONAL	1	TRUE	1	0.555083779114745	2		347	308	SUCCESS
APC	324	MSKCC	GRCh37	5	112175564	112175564	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	30	396	0	ENST00000257430.4:c.4273G>C	p.Asp1425His	p.D1425H	ENST00000257430	NM_000038.5	1425	Gat/Cat	16/16	1	2	FACETS	0.275	0.221	0.336	0.275	0.221	0.336	SUBCLONAL	1	TRUE	1	0.555083779114745	2		396	393	SUCCESS
APC	324	MSKCC	GRCh37	5	112176351	112176351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779068685	NA	P-0056727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	55	304	0	ENST00000257430.4:c.5060G>A	p.Arg1687Gln	p.R1687Q	ENST00000257430	NM_000038.5	1687	cGa/cAa	16/16	1	2	FACETS	0.667	0.575	0.767	0.667	0.575	0.767	SUBCLONAL	1	TRUE	1	0.555083779114745	2		304	297	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197187	26197187	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	37	643	0	ENST00000356476.2:c.292G>C	p.Glu98Gln	p.E98Q	ENST00000356476		98	Gag/Cag	1/1	0.554661819951814	2	FACETS	0.217	0.179	0.261	0.109	0.089	0.131	SUBCLONAL	1	TRUE	0	0.555083779114745	2		643	613	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197242	26197242	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	44	587	0	ENST00000356476.2:c.237C>G	p.Phe79Leu	p.F79L	ENST00000356476		79	ttC/ttG	1/1	0.554661819951814	2	FACETS	0.292	0.244	0.345	0.146	0.122	0.173	SUBCLONAL	1	TRUE	0	0.555083779114745	2		587	543	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137528174	137528174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	12	289	0	ENST00000367739.4:c.126G>A	p.Met42Ile	p.M42I	ENST00000367739	NM_000416.2	42	atG/atA	2/7	0.549340089763213	1	FACETS	0.139	0.098	0.191	0.139	0.098	0.191	SUBCLONAL	1	TRUE	0	0.555083779114745	1		289	224	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026923	6026923	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	21	77	0	ENST00000265849.7:c.1473G>T	p.Glu491Asp	p.E491D	ENST00000265849	NM_000535.5	491	gaG/gaT	11/15	0.555083779114745	1	FACETS	0.882	0.704	1	0.882	0.704	1	CLONAL	1	TRUE	0	0.555083779114745	1		77	62	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462634	92462634	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	21	295	0	ENST00000265734.4:c.4G>C	p.Glu2Gln	p.E2Q	ENST00000265734	NM_001259.6	2	Gag/Cag	2/8	0.485246192034513	3	FACETS	0.282	0.217	0.358	0.141	0.108	0.179	SUBCLONAL	1	TRUE	1	0.555083779114745	3		295	343	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874913	151874913	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	112	351	0	ENST00000262189.6:c.7625C>A	p.Ser2542Ter	p.S2542*	ENST00000262189	NM_170606.2	2542	tCa/tAa	38/59	0.485246192034513	3	FACETS	0.855	0.771	0.943	0.427	0.385	0.472	CLONAL	1	TRUE	1	0.555083779114745	3		351	603	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274832	38274832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760702592	NA	P-0056727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	28	466	0	ENST00000425967.3:c.1748C>T	p.Thr583Met	p.T583M	ENST00000425967	NM_001174067.1	583	aCg/aTg	13/19	1	2	FACETS	0.216	0.172	0.266	0.216	0.172	0.266	SUBCLONAL	1	TRUE	1	0.555083779114745	2		466	467	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866412	56866412	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	114	539	0	ENST00000519728.1:c.659G>A	p.Arg220Lys	p.R220K	ENST00000519728	NM_002350.3	220	aGa/aAa	8/13	1	2	FACETS	0.737	0.666	0.812	0.737	0.666	0.812	SUBCLONAL	1	TRUE	1	0.555083779114745	2		539	557	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911467	101911467	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	14	222	0	ENST00000374994.4:c.1392G>C	p.Leu464Phe	p.L464F	ENST00000374994	NM_004612.2	464	ttG/ttC	9/9	0.482839568661526	3	FACETS	0.24	0.173	0.321	0.12	0.086	0.161	SUBCLONAL	1	TRUE	1	0.555083779114745	3		222	269	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410982	63410982	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs771682818	NA	P-0056727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	48	338	0	ENST00000330258.3:c.2185G>C	p.Glu729Gln	p.E729Q	ENST00000330258	NM_152424.3	729	Gag/Cag	2/2	1	1	FACETS	0.364	0.309	0.425	0.364	0.309	0.425	SUBCLONAL	1	TRUE	0	0.555083779114745	1		338	343	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0056728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	87	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.289561544892658	3	FACETS	1	0.95	1	0.565	0.5	0.633	CLONAL	1	TRUE	1	0.289561544892658	3		298	609	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138729528	NA	P-0056728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	80	851	0	ENST00000269305.4:c.523C>G	p.Arg175Gly	p.R175G	ENST00000269305	NM_001126112.2	175	Cgc/Ggc	5/11	0.156939999241493	2	FACETS	0.775	0.682	0.875	0.387	0.341	0.438	INDETERMINATE	1	TRUE	0	0.289561544892658	2		851	713	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412095	63412095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852217	NA	P-0056728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	86	776	0	ENST00000330258.3:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000330258	NM_152424.3	358	Cga/Tga	2/2	1	2	FACETS	0.826	0.731	0.928	0.826	0.731	0.928	CLONAL	1	TRUE	1	0.289561544892658	2		776	719	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0056729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	567	508	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.919993270850454	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.919561737486795	1		508	652	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	227	660	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.750139917120773	1	FACETS	0.302	0.281	0.323	0.302	0.281	0.323	SUBCLONAL	1	TRUE	0	0.919561737486795	1		660	884	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0056729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	392	528	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	0.437326994309208	6	FACETS	1	0.993	1	0.813	0.775	0.851	INDETERMINATE	2	TRUE	3	0.919561737486795	6		528	993	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78426150	78426150	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1448786217	NA	P-0056729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	132	702	0	ENST00000370768.2:c.1375C>T	p.Pro459Ser	p.P459S	ENST00000370768	NM_003902.3	459	Ccc/Tcc	15/20	0.467787184138955	1	FACETS	0.292	0.266	0.318	0.292	0.266	0.318	INDETERMINATE	1	TRUE	0	0.919561737486795	1		702	532	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842324	68842348	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAGGCCTCCGTTTCTGGAATCCAAG	TAGGCCTCCGTTTCTGGAATCCAAG	-	novel	NA	P-0056729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	234	603	0	ENST00000261769.5:c.388-3_409del		p.X130_splice	ENST00000261769	NM_004360.3	130		4/16	NA	2	FACETS	0.91	0.857	0.965			1	INDETERMINATE	1	TRUE	NA	0.919561737486795	2		603	559	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0056731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	210	221	1				ENST00000310581	NM_198253.2	-/1132			0.770185116389832	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.770185116389832	1		222	333	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0056731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	217	628	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.909	0.85	0.968	0.909	0.85	0.968	CLONAL	1	TRUE	1	0.770185116389832	2		628	620	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387101	31387101	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1226308460	NA	P-0056731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	335	875	0	ENST00000328111.2:c.1726C>T	p.Arg576Ter	p.R576*	ENST00000328111	NM_006892.3	576	Cga/Tga	16/23	1	2	FACETS	0.995	0.945	1	0.995	0.945	1	CLONAL	1	TRUE	1	0.770185116389832	2		875	874	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243237	123243237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55774317	NA	P-0056731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	305	749	1	ENST00000358487.5:c.2276G>A	p.Arg759Gln	p.R759Q	ENST00000358487	NM_000141.4	759	cGa/cAa	17/18	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.770185116389832	2		750	766	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754304	57754304	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	154	429	2	ENST00000274289.3:c.547C>T	p.Arg183Ter	p.R183*	ENST00000274289	NM_006622.3	183	Cga/Tga	4/14	1	2	FACETS	0.93	0.86	1	0.93	0.86	1	CLONAL	1	TRUE	1	0.770185116389832	2		431	430	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375522	15375522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	435	1109	0	ENST00000263377.2:c.905C>T	p.Pro302Leu	p.P302L	ENST00000263377	NM_058243.2	302	cCc/cTc	6/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.770185116389832	2		1109	1078	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873041	136873041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	222	506	0	ENST00000241393.3:c.457G>A	p.Glu153Lys	p.E153K	ENST00000241393	NM_003467.2	153	Gaa/Aaa	2/2	1	2	FACETS	0.954	0.895	1	0.954	0.895	1	CLONAL	1	TRUE	1	0.770185116389832	2		506	604	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040715	47040716	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1131690789	NA	P-0056731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	30	527	0	ENST00000377604.3:c.1352_1353del	p.Glu451ValfsTer66	p.E451Vfs*66	ENST00000377604	NM_001204468.1	450	acAGag/acag	13/24	1	1	FACETS	0.088	0.07	0.108	0.088	0.07	0.108	SUBCLONAL	1	TRUE	0	0.770185116389832	1		527	543	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106394	27106395	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0056731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	255	675	0	ENST00000324856.7:c.6005_6006delinsTT	p.Ser2002Phe	p.S2002F	ENST00000324856	NM_006015.4	2002	tCC/tTT	20/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.770185116389832	2		675	644	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241899	72241899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	135	360	0	ENST00000357731.5:c.491G>A	p.Gly164Glu	p.G164E	ENST00000357731	NM_173808.2	164	gGg/gAg	3/7	1	2	FACETS	0.881	0.809	0.955	0.881	0.809	0.955	CLONAL	1	TRUE	1	0.770185116389832	2		360	398	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430812	78430812	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	209	519	0	ENST00000370768.2:c.577C>T	p.Pro193Ser	p.P193S	ENST00000370768	NM_003902.3	193	Cca/Tca	8/20	1	2	FACETS	0.884	0.826	0.943	0.884	0.826	0.943	CLONAL	1	TRUE	1	0.770185116389832	2		519	614	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512404	38512405	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0056731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	277	885	2	ENST00000254066.5:c.1315_1316delinsTT	p.Pro439Phe	p.P439F	ENST00000254066	NM_000964.3	439	CCc/TTc	9/9	1	2	FACETS	0.892	0.841	0.945	0.892	0.841	0.945	CLONAL	1	TRUE	1	0.770185116389832	2		887	806	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098498	11098499	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0056731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	278	752	0	ENST00000358026.2:c.1016_1017delinsTT	p.Pro339Leu	p.P339L	ENST00000358026	NM_001128849.1	339	cCC/cTT	6/36	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.770185116389832	2		752	714	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719792	52719793	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0056731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	262	666	3	ENST00000322088.6:c.1004_1005delinsTT	p.Ser335Phe	p.S335F	ENST00000322088	NM_014225.5	335	tCC/tTT	9/15	1	2	FACETS	0.989	0.932	1	0.989	0.932	1	CLONAL	1	TRUE	1	0.770185116389832	2		669	688	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113274	209113275	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0056731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	168	439	0	ENST00000345146.2:c.232_233delinsTT	p.Pro78Phe	p.P78F	ENST00000345146	NM_005896.2	78	CCt/TTt	4/10	1	2	FACETS	0.926	0.859	0.995	0.926	0.859	0.995	CLONAL	1	TRUE	1	0.770185116389832	2		439	471	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225367755	225367755	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	134	462	0	ENST00000264414.4:c.1412A>T	p.Glu471Val	p.E471V	ENST00000264414	NM_003590.4	471	gAa/gTa	10/16	1	2	FACETS	0.879	0.807	0.953	0.879	0.807	0.953	CLONAL	1	TRUE	1	0.770185116389832	2		462	396	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458293	12458293	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	238	634	0	ENST00000287820.6:c.910G>A	p.Glu304Lys	p.E304K	ENST00000287820	NM_015869.4	304	Gag/Aag	6/7	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.770185116389832	2		634	605	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162623	47162623	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	175	418	0	ENST00000409792.3:c.3503T>C	p.Val1168Ala	p.V1168A	ENST00000409792	NM_014159.6	1168	gTt/gCt	3/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.770185116389832	2		418	427	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502241	186502241	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	189	407	0	ENST00000323963.5:c.50G>A	p.Gly17Glu	p.G17E	ENST00000323963		17	gGa/gAa	2/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.770185116389832	2		407	438	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748135	41748135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	130	446	0	ENST00000226382.2:c.634G>A	p.Gly212Arg	p.G212R	ENST00000226382	NM_003924.3	212	Gga/Aga	3/3	1	2	FACETS	0.838	0.767	0.91	0.838	0.767	0.91	CLONAL	1	TRUE	1	0.770185116389832	2		446	403	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196598	106196598	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1335841148	NA	P-0056731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	182	510	0	ENST00000380013.4:c.4931C>T	p.Pro1644Leu	p.P1644L	ENST00000380013	NM_001127208.2	1644	cCa/cTa	11/11	1	2	FACETS	0.949	0.883	1	0.949	0.883	1	CLONAL	1	TRUE	1	0.770185116389832	2		510	498	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514544	149514544	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	208	565	0	ENST00000261799.4:c.400G>C	p.Glu134Gln	p.E134Q	ENST00000261799	NM_002609.3	134	Gaa/Caa	4/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.770185116389832	2		565	524	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166317	32166317	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	379	904	2	ENST00000375023.3:c.4637C>T	p.Pro1546Leu	p.P1546L	ENST00000375023	NM_004557.3	1546	cCc/cTc	26/30	0.737643184089844	4	FACETS	1	0.978	1	0.353	0.334	0.372	CLONAL	1	TRUE	1	0.770185116389832	4		906	1646	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508359	106508359	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	179	524	0	ENST00000359195.3:c.353C>T	p.Thr118Ile	p.T118I	ENST00000359195	NM_002649.2	118	aCt/aTt	2/11	1	2	FACETS	0.867	0.805	0.931	0.867	0.805	0.931	CLONAL	1	TRUE	1	0.770185116389832	2		524	536	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157928	27157928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	276	621	0	ENST00000380036.4:c.152C>T	p.Pro51Leu	p.P51L	ENST00000380036	NM_000459.3	51	cCc/cTc	2/23	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.770185116389832	2		621	708	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537213	80537213	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	168	406	0	ENST00000286548.4:c.185T>G	p.Ile62Ser	p.I62S	ENST00000286548	NM_002072.3	62	aTc/aGc	2/7	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.770185116389832	2		406	435	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0056732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	73	330	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.732	0.645	0.824	0.732	0.645	0.824	SUBCLONAL	1	TRUE	1	0.611818143301768	2		330	326	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660469	67660469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	120	418	1	ENST00000264010.4:c.1369C>T	p.Arg457Ter	p.R457*	ENST00000264010	NM_006565.3	457	Cga/Tga	8/12	1	2	FACETS	0.921	0.838	1	0.921	0.838	1	CLONAL	1	TRUE	1	0.611818143301768	2		419	426	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692790	89692790	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	153	346	1	ENST00000371953.3:c.274G>C	p.Asp92His	p.D92H	ENST00000371953	NM_000314.4	92	Gac/Cac	5/9	0.611818143301768	2	FACETS	0.919	0.861	0.977	0.919	0.861	0.977	CLONAL	2	TRUE	0	0.611818143301768	2		347	272	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0056732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	161	559	0	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	1	2	FACETS	0.933	0.861	1	0.933	0.861	1	CLONAL	1	TRUE	1	0.611818143301768	2		559	564	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630626	158630626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912678	NA	P-0056732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	38	272	0	ENST00000263640.3:c.617G>A	p.Arg206His	p.R206H	ENST00000263640	NM_001105.4	206	cGc/cAc	6/11	1	2	FACETS	0.46	0.382	0.546	0.46	0.382	0.546	SUBCLONAL	1	TRUE	1	0.611818143301768	2		272	270	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165729	108165729	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs762083530	NA	P-0056732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	92	330	1	ENST00000278616.4:c.4852C>T	p.Arg1618Ter	p.R1618*	ENST00000278616	NM_000051.3	1618	Cga/Tga	32/63	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.611818143301768	2		331	296	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106566	27106566	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	218	811	0	ENST00000324856.7:c.6177del	p.Asn2059LysfsTer76	p.N2059Kfs*76	ENST00000324856	NM_006015.4	2059	aaC/aa	20/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.611818143301768	2		811	695	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101477	27101478	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0056732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	172	752	0	ENST00000324856.7:c.4759_4760del	p.Ser1587ProfsTer15	p.S1587Pfs*15	ENST00000324856	NM_006015.4	1587	AGc/c	18/20	1	2	FACETS	0.999	0.925	1	0.999	0.925	1	CLONAL	1	TRUE	1	0.611818143301768	2		752	563	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591092	67591103	+	inframe_deletion	In_Frame_Del	DEL	GTATGAACAGCA	GTATGAACAGCA	-	novel	NA	P-0056732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	63	230	0	ENST00000274335.5:c.1685_1696del	p.Arg562_Ile566delinsLeu	p.R562_I566delinsL	ENST00000274335		562	cGTATGAACAGCAtt/ctt	12/15	1	2	FACETS	0.895	0.785	1	0.895	0.785	1	CLONAL	1	TRUE	1	0.611818143301768	2		230	230	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0056734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	131	317	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		317	395	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720809	89720809	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	25	303	0	ENST00000371953.3:c.961del	p.Thr321GlnfsTer23	p.T321Qfs*23	ENST00000371953	NM_000314.4	320	ttA/tt	8/9	1	2	FACETS	0.532	0.42	0.661	0.532	0.42	0.661	SUBCLONAL	1	TRUE	1	0.305044781987251	2		303	308	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589605	67589607	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0056735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	25	233	0	ENST00000274335.5:c.1368_1370del	p.Phe456_Gln457delinsLeu	p.F456_Q457delinsL	ENST00000274335		456	ttTCAa/tta	10/15	1	2	FACETS	0.495	0.39	0.616	0.495	0.39	0.616	SUBCLONAL	1	TRUE	1	0.305044781987251	2		233	331	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426817	47426817	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	25	559	0	ENST00000377045.4:c.1062G>T	p.Glu354Asp	p.E354D	ENST00000377045	NM_001654.4	354	gaG/gaT	10/16	1	2	FACETS	0.41	0.322	0.51	0.41	0.322	0.51	SUBCLONAL	1	TRUE	1	0.305044781987251	2		559	400	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240184	41240213	+	inframe_deletion	In_Frame_Del	DEL	CCGCGGCGTCGGGGTTGGCAGCCGCGCTGC	CCGCGGCGTCGGGGTTGGCAGCCGCGCTGC	-	novel	NA	P-0056735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	37	123	0	ENST00000379561.5:c.137_166del	p.Gly46_Ala55del	p.G46_A55del	ENST00000379561	NM_002015.3	46	gGCAGCGCGGCTGCCAACCCCGACGCCGCGGcg/gcg	1/3	1	2	FACETS	0.848	0.712	0.995	1	0.962	1	CLONAL	2	TRUE	1	0.305044781987251	2		123	143	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871230	35871230	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	29	347	0	ENST00000216797.5:c.943C>G	p.Leu315Val	p.L315V	ENST00000216797	NM_020529.2	315	Ctg/Gtg	6/6	1	2	FACETS	0.416	0.333	0.51	0.416	0.333	0.51	SUBCLONAL	1	TRUE	1	0.305044781987251	2		347	457	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372528	55372529	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0056735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	66	945	0	ENST00000297316.4:c.1219dup	p.Tyr407LeufsTer7	p.Y407Lfs*7	ENST00000297316	NM_022454.3	406	-/T	2/2	1	2	FACETS	0.494	0.428	0.566	0.494	0.428	0.566	SUBCLONAL	1	TRUE	1	0.305044781987251	2		945	876	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0056736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	93	597	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.877	0.785	0.974	0.877	0.785	0.974	CLONAL	1	TRUE	1	0.517468074108443	2		597	410	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0056736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	95	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.909	0.815	1	0.909	0.815	1	CLONAL	1	TRUE	1	0.517468074108443	2		298	404	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210451	2210451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138206172	NA	P-0056736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	229	1109	1	ENST00000398665.3:c.1058C>T	p.Ala353Val	p.A353V	ENST00000398665	NM_032482.2	353	gCg/gTg	13/28	1	2	FACETS	0.834	0.777	0.893	0.834	0.777	0.893	CLONAL	1	TRUE	1	0.517468074108443	2		1110	1061	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0056736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	135	527	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.517468074108443	2		530	491	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0056736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	124	519	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.925	0.841	1	0.925	0.841	1	CLONAL	1	TRUE	1	0.517468074108443	2		520	518	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435406	110435406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35927012	NA	P-0056736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	171	638	0	ENST00000375856.3:c.2995G>A	p.Val999Met	p.V999M	ENST00000375856	NM_003749.2	999	Gtg/Atg	1/2	1	2	FACETS	0.8	0.737	0.866	0.8	0.737	0.866	SUBCLONAL	1	TRUE	1	0.517468074108443	2		638	826	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209616	98209617	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761353734	NA	P-0056736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	155	662	0	ENST00000331920.6:c.3921dup	p.Arg1308GlnfsTer17	p.R1308Qfs*17	ENST00000331920	NM_000264.3	1307	-/C	23/24	1	2	FACETS	0.687	0.629	0.748	0.687	0.629	0.748	SUBCLONAL	1	TRUE	1	0.517468074108443	2		662	872	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692916	89692918	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	rs1554898152	NA	P-0056736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	63	525	0	ENST00000371953.3:c.402_404del	p.Met134del	p.M134del	ENST00000371953	NM_000314.4	134	ATG/-	5/9	1	2	FACETS	0.667	0.58	0.761	0.667	0.58	0.761	SUBCLONAL	1	TRUE	1	0.517468074108443	2		525	365	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720712	89720712	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	33	219	0	ENST00000371953.3:c.867del	p.Val290Ter	p.V290*	ENST00000371953	NM_000314.4	288	gAa/ga	8/9	1	2	FACETS	0.733	0.604	0.875	0.733	0.604	0.875	SUBCLONAL	1	TRUE	1	0.517468074108443	2		219	174	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753011	57753012	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	64	386	5	ENST00000274289.3:c.1004dup	p.Leu335PhefsTer12	p.L335Ffs*12	ENST00000274289	NM_006622.3	335	ttg/ttTg	7/14	1	2	FACETS	0.695	0.605	0.791	0.695	0.605	0.791	SUBCLONAL	1	TRUE	1	0.517468074108443	2		391	356	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991757	72991758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760959844	NA	P-0056736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	153	711	0	ENST00000268489.5:c.2287dup	p.Glu763GlyfsTer26	p.E763Gfs*26	ENST00000268489	NM_006885.3	763	gag/gGag	2/10	1	2	FACETS	0.829	0.76	0.901	0.829	0.76	0.901	CLONAL	1	TRUE	1	0.517468074108443	2		711	713	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431915	49431915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	203	831	0	ENST00000301067.7:c.9224C>T	p.Ser3075Leu	p.S3075L	ENST00000301067	NM_003482.3	3075	tCg/tTg	34/54	1	2	FACETS	0.843	0.782	0.906	0.843	0.782	0.906	CLONAL	1	TRUE	1	0.517468074108443	2		831	931	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526755	31526755	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	120	549	0	ENST00000344624.3:c.285del	p.Cys96AlafsTer12	p.C96Afs*12	ENST00000344624		95	ccC/cc	2/33	1	2	FACETS	0.74	0.669	0.813	0.74	0.669	0.813	SUBCLONAL	1	TRUE	1	0.517468074108443	2		549	627	SUCCESS
APC	324	MSKCC	GRCh37	5	112178969	112178969	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	81	299	0	ENST00000257430.4:c.7678C>T	p.Arg2560Ter	p.R2560*	ENST00000257430	NM_000038.5	2560	Cga/Tga	16/16	1	2	FACETS	0.935	0.83	1	0.935	0.83	1	CLONAL	1	TRUE	1	0.517468074108443	2		299	335	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015677	112015677	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs751647014	NA	P-0056736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	96	465	1	ENST00000368678.4:c.1165C>T	p.Arg389Ter	p.R389*	ENST00000368678		389	Cga/Tga	11/13	1	2	FACETS	0.744	0.665	0.827	0.744	0.665	0.827	SUBCLONAL	1	TRUE	1	0.517468074108443	2		466	499	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11205104	11205104	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0056736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	45	441	0	ENST00000361445.4:c.4687-2A>C		p.X1563_splice	ENST00000361445	NM_004958.3	1563			1	2	FACETS	0.329	0.276	0.388	0.329	0.276	0.388	SUBCLONAL	1	TRUE	1	0.517468074108443	2		441	528	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106617	27106617	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	186	755	0	ENST00000324856.7:c.6231del	p.Glu2078ArgfsTer57	p.E2078Rfs*57	ENST00000324856	NM_006015.4	2076	taC/ta	20/20	1	2	FACETS	0.864	0.799	0.931	0.864	0.799	0.931	CLONAL	1	TRUE	1	0.517468074108443	2		755	832	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465949	69465949	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	194	909	0	ENST00000227507.2:c.787C>T	p.Gln263Ter	p.Q263*	ENST00000227507	NM_053056.2	263	Cag/Tag	5/5	1	2	FACETS	0.815	0.754	0.878	0.815	0.754	0.878	CLONAL	1	TRUE	1	0.517468074108443	2		909	920	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100405	2100405	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	167	453	0	ENST00000219476.3:c.143T>C	p.Leu48Pro	p.L48P	ENST00000219476	NM_000548.3	48	cTg/cCg	3/42	1	2	FACETS	0.934	0.861	1	0.934	0.861	1	CLONAL	1	TRUE	1	0.517468074108443	2		453	691	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47685237	47685237	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	18	365	1	ENST00000347630.2:c.713del	p.Lys238ArgfsTer17	p.K238Rfs*17	ENST00000347630	NM_001007230.1	238	aAg/ag	8/11	1	2	FACETS	0.209	0.157	0.271	0.209	0.157	0.271	SUBCLONAL	1	TRUE	1	0.517468074108443	2		366	333	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59937201	59937201	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	70	456	0	ENST00000259008.2:c.161T>C	p.Leu54Ser	p.L54S	ENST00000259008	NM_032043.2	54	tTa/tCa	3/20	1	2	FACETS	0.622	0.544	0.705	0.622	0.544	0.705	SUBCLONAL	1	TRUE	1	0.517468074108443	2		456	435	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390928	89390928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	65	344	0	ENST00000336596.2:c.994G>A	p.Val332Ile	p.V332I	ENST00000336596	NM_005233.5	332	Gtt/Att	5/17	1	2	FACETS	0.722	0.63	0.821	0.722	0.63	0.821	SUBCLONAL	1	TRUE	1	0.517468074108443	2		344	348	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801095	135801095	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	112	422	0	ENST00000298552.3:c.242G>T	p.Gly81Val	p.G81V	ENST00000298552	NM_001162426.1	81	gGc/gTc	5/23	1	2	FACETS	0.882	0.797	0.97	0.882	0.797	0.97	CLONAL	1	TRUE	1	0.517468074108443	2		422	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	74	859	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	1	2	FACETS	0.651	0.568	0.741	0.651	0.568	0.741	SUBCLONAL	1	TRUE	1	0.235825231808553	2		859	964	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	80	915	1	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.235825231808553	1	FACETS	0.633	0.555	0.716	0.633	0.555	0.716	SUBCLONAL	1	TRUE	0	0.235825231808553	1		916	946	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934578	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	85	877	1	ENST00000269305.4:c.524G>T	p.Arg175Leu	p.R175L	ENST00000269305	NM_001126112.2	175	cGc/cTc	5/11	1	2	FACETS	0.765	0.675	0.862	0.765	0.675	0.862	SUBCLONAL	1	TRUE	1	0.235825231808553	2		878	942	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488404	20488404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	54	487	1	ENST00000346618.3:c.1060G>A	p.Glu354Lys	p.E354K	ENST00000346618	NM_001949.4	354	Gag/Aag	6/7	0.235825231808553	3	FACETS	0.736	0.627	0.855	0.368	0.313	0.428	SUBCLONAL	1	TRUE	1	0.235825231808553	3		488	696	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030293	180030293	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	175	1106	0	ENST00000261937.6:c.3991G>T	p.Val1331Leu	p.V1331L	ENST00000261937	NM_182925.4	1331	Gtg/Ttg	30/30	0.0652863214050838	3	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.235825231808553	3		1106	1314	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031997	26031997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	40	526	0	ENST00000244661.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000244661	NM_003537.3	98	Gag/Aag	1/1	0.235825231808553	3	FACETS	0.571	0.473	0.681	0.286	0.236	0.341	SUBCLONAL	1	TRUE	1	0.235825231808553	3		526	664	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490319	29490319	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	56	480	0	ENST00000356175.3:c.404G>T	p.Arg135Leu	p.R135L	ENST00000356175	NM_000267.3	135	cGg/cTg	4/57	1	2	FACETS	0.762	0.653	0.882	0.762	0.653	0.882	SUBCLONAL	1	TRUE	1	0.235825231808553	2		480	623	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428208	47428208	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	103	1052	0	ENST00000377045.4:c.1168C>A	p.Leu390Ile	p.L390I	ENST00000377045	NM_001654.4	390	Ctc/Atc	11/16	NA	2	FACETS	0.681	0.607	0.76			1	INDETERMINATE	1	TRUE	NA	0.235825231808553	2		1052	1283	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563036	21563036	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	110	1214	2	ENST00000382592.4:c.883G>T	p.Gly295Ter	p.G295*	ENST00000382592	NM_014572.2	295	Gga/Tga	4/8	1	2	FACETS	0.729	0.653	0.811	0.729	0.653	0.811	SUBCLONAL	1	TRUE	1	0.235825231808553	2		1216	1279	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984850	9984850	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555501093	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	102	548	1	ENST00000330684.3:c.1115G>A	p.Trp372Ter	p.W372*	ENST00000330684	NM_001134407.1	372	tGg/tAg	4/13	0.174155828689166	2	FACETS	1	0.976	1	0.661	0.592	0.735	CLONAL	1	TRUE	0	0.235825231808553	2		549	654	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258568	16258568	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	76	743	0	ENST00000375759.3:c.5833C>G	p.Pro1945Ala	p.P1945A	ENST00000375759	NM_015001.2	1945	Ccc/Gcc	11/15	0.149712987960877	3	FACETS	0.769	0.673	0.873	0.384	0.336	0.437	SUBCLONAL	1	TRUE	1	0.235825231808553	3		743	937	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925601	114925601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749702260	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	311	907	0	ENST00000543371.1:c.1679C>T	p.Pro560Leu	p.P560L	ENST00000543371	NM_001198531.1	560	cCa/cTa	14/14	0.196896807504869	3	FACETS	1	0.991	1	0.826	0.779	0.874	CLONAL	2	TRUE	0	0.235825231808553	3		907	1190	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946975	71946975	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	104	1032	1	ENST00000298229.2:c.2824G>T	p.Gly942Trp	p.G942W	ENST00000298229	NM_001567.3	942	Ggg/Tgg	25/28	0.112052300988244	4	FACETS	0.863	0.77	0.962	0.432	0.385	0.481	INDETERMINATE	1	TRUE	2	0.235825231808553	4		1033	1263	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922234	100922234	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	115	441	0	ENST00000325455.5:c.2278G>T	p.Val760Leu	p.V760L	ENST00000325455	NM_001202474.3	760	Gtg/Ttg	5/8	0.112052300988244	4	FACETS	0.802	0.723	0.886	0.802	0.723	0.886	INDETERMINATE	2	TRUE	2	0.235825231808553	4		441	751	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343008	118343008	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	76	297	0	ENST00000534358.1:c.1134G>T	p.Arg378Ser	p.R378S	ENST00000534358	NM_005933.3	378	agG/agT	3/36	0.112052300988244	4	FACETS	0.937	0.826	1	0.937	0.826	1	INDETERMINATE	2	TRUE	2	0.235825231808553	4		297	425	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202319	133202319	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	88	881	0	ENST00000320574.5:c.6569G>C	p.Cys2190Ser	p.C2190S	ENST00000320574	NM_006231.2	2190	tGt/tCt	47/49	0.235825231808553	3	FACETS	0.73	0.645	0.822	0.365	0.322	0.411	SUBCLONAL	1	TRUE	1	0.235825231808553	3		881	1143	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945173	32945173	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs878853610	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	93	353	1	ENST00000380152.3:c.8568G>T	p.Glu2856Asp	p.E2856D	ENST00000380152		2856	gaG/gaT	20/27	0.174937765211182	2	FACETS	1	0.98	1	0.75	0.669	0.836	CLONAL	1	TRUE	0	0.235825231808553	2		354	526	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100133	30100135	+	missense_variant	Missense_Mutation	TNP	GTA	GTA	AGG	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	122	699	2	ENST00000331968.5:c.1485_1487delinsCCT	p.Thr496Leu	p.T496L	ENST00000331968	NM_002742.2	495	acTACg/acCCTg	10/18	0.174937765211182	2	FACETS	1	0.971	1	0.599	0.541	0.66	CLONAL	1	TRUE	0	0.235825231808553	2		701	864	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986773	36986773	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	31	249	0	ENST00000354822.5:c.916G>T	p.Ala306Ser	p.A306S	ENST00000354822	NM_001079668.2	306	Gcg/Tcg	3/3	0.174937765211182	2	FACETS	0.91	0.738	1	0.455	0.369	0.552	CLONAL	1	TRUE	0	0.235825231808553	2		249	289	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961649	41961650	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	41	462	0	ENST00000219905.7:c.559dup	p.Asp187GlyfsTer46	p.D187Gfs*46	ENST00000219905	NM_001164273.1	186	ctg/ctGg	2/24	1	2	FACETS	0.544	0.452	0.647	0.544	0.452	0.647	SUBCLONAL	1	TRUE	1	0.235825231808553	2		462	639	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726657	88726657	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	79	507	0	ENST00000360948.2:c.387G>T	p.Leu129Phe	p.L129F	ENST00000360948	NM_001012338.2	129	ttG/ttT	4/19	0.235825231808553	4	FACETS	1	0.918	1			1	CLONAL	1	TRUE	NA	0.235825231808553	4		507	782	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2115636	2115636	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	167	963	0	ENST00000219476.3:c.1716G>T	p.Gln572His	p.Q572H	ENST00000219476	NM_000548.3	572	caG/caT	16/42	0.174155828689166	2	FACETS	1	0.987	1	0.698	0.641	0.758	CLONAL	1	TRUE	0	0.235825231808553	2		963	1014	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665816	29665816	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	24	285	1	ENST00000356175.3:c.6852del	p.Asn2285IlefsTer13	p.N2285Ifs*13	ENST00000356175	NM_000267.3	2284	cTt/ct	45/57	1	2	FACETS	0.615	0.482	0.768	0.615	0.482	0.768	SUBCLONAL	1	TRUE	1	0.235825231808553	2		286	331	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39537662	39537662	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	68	381	0	ENST00000262039.4:c.196G>T	p.Glu66Ter	p.E66*	ENST00000262039	NM_002647.2	66	Gaa/Taa	2/25	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.235825231808553	2		381	514	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45423102	45423102	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	21	305	0	ENST00000262160.6:c.26C>A	p.Pro9Gln	p.P9Q	ENST00000262160	NM_005901.5	9	cCg/cAg	2/11	1	2	FACETS	0.546	0.42	0.693	0.546	0.42	0.693	SUBCLONAL	1	TRUE	1	0.235825231808553	2		305	326	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191239	2191239	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	66	699	0	ENST00000398665.3:c.493G>T	p.Gly165Cys	p.G165C	ENST00000398665	NM_032482.2	165	Ggt/Tgt	5/28	0.235825231808553	1	FACETS	0.671	0.581	0.768	0.671	0.581	0.768	SUBCLONAL	1	TRUE	0	0.235825231808553	1		699	736	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134254	11134254	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs797045980	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	64	776	0	ENST00000358026.2:c.2922del	p.Phe975SerfsTer44	p.F975Sfs*44	ENST00000358026	NM_001128849.1	974	Ccc/cc	20/36	0.235825231808553	1	FACETS	0.625	0.54	0.717	0.625	0.54	0.717	SUBCLONAL	1	TRUE	0	0.235825231808553	1		776	766	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212078	36212078	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766234703	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	80	888	3	ENST00000222270.7:c.1829G>A	p.Arg610His	p.R610H	ENST00000222270	NM_014727.1	610	cGc/cAc	3/37	1	2	FACETS	0.664	0.583	0.751	0.664	0.583	0.751	SUBCLONAL	1	TRUE	1	0.235825231808553	2		891	1022	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218352	36218352	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	176	1010	0	ENST00000222270.7:c.4131G>C	p.Glu1377Asp	p.E1377D	ENST00000222270	NM_014727.1	1377	gaG/gaC	16/37	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.235825231808553	2		1010	1108	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224061	36224061	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1314	135	1225	0	ENST00000222270.7:c.6611T>C	p.Met2204Thr	p.M2204T	ENST00000222270	NM_014727.1	2204	aTg/aCg	28/37	1	2	FACETS	0.79	0.716	0.869	0.79	0.716	0.869	SUBCLONAL	1	TRUE	1	0.235825231808553	2		1225	1449	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741869	40741869	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	167	985	0	ENST00000392038.2:c.1103G>T	p.Arg368Leu	p.R368L	ENST00000392038	NM_001626.4	368	cGc/cTc	11/14	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.235825231808553	2		985	1094	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902166	50902166	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	189	1029	0	ENST00000440232.2:c.58G>A	p.Gly20Arg	p.G20R	ENST00000440232	NM_002691.3	20	Ggg/Agg	2/27	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.235825231808553	2		1029	1112	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560932	9560932	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	74	551	0	ENST00000353224.5:c.850C>A	p.Gln284Lys	p.Q284K	ENST00000353224	NM_177990.2	284	Cag/Aag	4/10	1	2	FACETS	0.914	0.799	1	0.914	0.799	1	CLONAL	1	TRUE	1	0.235825231808553	2		551	687	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739075	40739075	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	163	865	0	ENST00000373198.4:c.3209C>A	p.Pro1070His	p.P1070H	ENST00000373198	NM_133170.3	1070	cCt/cAt	24/32	0.112052300988244	4	FACETS	0.776	0.711	0.844	0.776	0.711	0.844	INDETERMINATE	2	TRUE	2	0.235825231808553	4		865	1101	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162624	47162624	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	85	466	0	ENST00000409792.3:c.3502G>T	p.Val1168Phe	p.V1168F	ENST00000409792	NM_014159.6	1168	Gtt/Ttt	3/21	0.149712987960877	3	FACETS	1	0.972	1	0.672	0.594	0.754	CLONAL	1	TRUE	1	0.235825231808553	3		466	600	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851877	134851877	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	56	661	0	ENST00000398015.3:c.1283C>A	p.Thr428Asn	p.T428N	ENST00000398015	NM_004441.4	428	aCc/aAc	5/16	1	2	FACETS	0.625	0.534	0.724	0.625	0.534	0.724	SUBCLONAL	1	TRUE	1	0.235825231808553	2		661	760	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430725	181430725	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	197	1016	1	ENST00000325404.1:c.577C>A	p.Gln193Lys	p.Q193K	ENST00000325404	NM_003106.3	193	Cag/Aag	1/1	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.235825231808553	2		1017	1220	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630592	187630592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	128	728	0	ENST00000441802.2:c.390G>T	p.Glu130Asp	p.E130D	ENST00000441802	NM_005245.3	130	gaG/gaT	2/27	0.174937765211182	2	FACETS	1	0.976	1	0.617	0.559	0.679	CLONAL	1	TRUE	0	0.235825231808553	2		728	879	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518041	176518041	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	155	944	0	ENST00000292408.4:c.539C>A	p.Pro180His	p.P180H	ENST00000292408	NM_213647.1	180	cCc/cAc	5/18	0.174937765211182	2	FACETS	1	0.985	1	0.681	0.623	0.742	CLONAL	1	TRUE	0	0.235825231808553	2		944	965	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30676014	30676014	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	129	654	0	ENST00000376406.3:c.2342del	p.Pro781HisfsTer66	p.P781Hfs*66	ENST00000376406	NM_014641.2	781	cCa/ca	8/15	0.235825231808553	3	FACETS	1	0.982	1	0.684	0.62	0.752	CLONAL	1	TRUE	1	0.235825231808553	3		654	894	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652080	36652080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1337	119	1232	0	ENST00000244741.5:c.202G>A	p.Val68Met	p.V68M	ENST00000244741	NM_000389.4	68	Gtg/Atg	2/3	0.235825231808553	3	FACETS	0.775	0.697	0.858	0.387	0.348	0.429	SUBCLONAL	1	TRUE	1	0.235825231808553	3		1232	1456	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652485	48652485	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	103	1070	0	ENST00000376670.3:c.1156C>A	p.Leu386Ile	p.L386I	ENST00000376670	NM_002049.3	386	Cta/Ata	6/6	NA	2	FACETS	0.717	0.639	0.799			1	INDETERMINATE	1	TRUE	NA	0.235825231808553	2		1070	1219	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245264	53245264	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	98	963	0	ENST00000375401.3:c.773G>T	p.Arg258Leu	p.R258L	ENST00000375401	NM_004187.3	258	cGg/cTg	6/26	NA	2	FACETS	0.686	0.61	0.768			1	INDETERMINATE	1	TRUE	NA	0.235825231808553	2		963	1211	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115272929	115272930	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	A	novel	NA	P-0056737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	139	721	0	ENST00000438362.2:c.1443_1444delinsT	p.Glu481AspfsTer32	p.E481Dfs*32	ENST00000438362	NM_001242891.1	481	gaAGcc/gaTcc	12/20	0.149712987960877	3	FACETS	0.757	0.689	0.829	0.757	0.689	0.829	SUBCLONAL	2	TRUE	1	0.235825231808553	3		721	870	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439887	220439887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751673614	NA	P-0056738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	197	913	2	ENST00000243786.2:c.740G>A	p.Arg247His	p.R247H	ENST00000243786	NM_002191.3	247	cGc/cAc	2/2	0.225827576570217	5	FACETS	0.84	0.781	0.9	0.84	0.781	0.9	CLONAL	3	TRUE	2	0.345763202108279	5		915	687	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441254	52441254	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	125	556	1	ENST00000460680.1:c.516C>A	p.Ser172Arg	p.S172R	ENST00000460680	NM_004656.3	172	agC/agA	7/17	0.303626185323099	2	FACETS	0.954	0.872	1	0.954	0.872	1	CLONAL	2	TRUE	0	0.345763202108279	2		557	379	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484427	57484427	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	102	579	0	ENST00000371085.3:c.608T>C	p.Leu203Pro	p.L203P	ENST00000371085	NM_000516.4	203	cTg/cCg	8/13	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.364790088379144	2		579	541	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813396	102813396	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316717107	NA	P-0056747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	80	607	1	ENST00000307046.8:c.293G>A	p.Arg98Gln	p.R98Q	ENST00000307046	NM_001111285.1	98	cGg/cAg	3/4	1	2	FACETS	0.716	0.629	0.809	0.716	0.629	0.809	SUBCLONAL	1	TRUE	1	0.28	2		608	798	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578285	+	frameshift_variant	Frame_Shift_Del	DEL	TAAGATGCTGAGGAGGGGCC	TAAGATGCTGAGGAGGGGCC	-	novel	NA	P-0056747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	88	682	0	ENST00000269305.4:c.564_583del	p.Ala189ProfsTer13	p.A189Pfs*13	ENST00000269305	NM_001126112.2	188	ctGGCCCCTCCTCAGCATCTTAtc/cttc	6/11	1	2	FACETS	0.606	0.535	0.681	0.606	0.535	0.681	SUBCLONAL	1	TRUE	1	0.28	2		682	1038	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0056747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	203	779	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.0638372344724791	3	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.28	3		779	1221	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222983	1222983	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0056747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	70	594	1	ENST00000326873.7:c.921-1G>A		p.X307_splice	ENST00000326873	NM_000455.4	307			1	2	FACETS	0.627	0.545	0.715	0.627	0.545	0.715	SUBCLONAL	1	TRUE	1	0.28	2		595	798	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272414	15272414	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151322770	NA	P-0056747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1296	123	1075	0	ENST00000263388.2:c.6025C>T	p.Arg2009Trp	p.R2009W	ENST00000263388	NM_000435.2	2009	Cgg/Tgg	33/33	1	2	FACETS	0.619	0.558	0.684	0.619	0.558	0.684	SUBCLONAL	1	TRUE	1	0.28	2		1075	1419	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354010	15354010	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458261626	NA	P-0056747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	33	317	0	ENST00000263377.2:c.2870C>T	p.Pro957Leu	p.P957L	ENST00000263377	NM_058243.2	957	cCc/cTc	14/20	1	2	FACETS	0.508	0.413	0.615	0.508	0.413	0.615	SUBCLONAL	1	TRUE	1	0.28	2		317	464	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228064	36228064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1226047761	NA	P-0056747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	107	810	1	ENST00000222270.7:c.7450C>T	p.Arg2484Cys	p.R2484C	ENST00000222270	NM_014727.1	2484	Cgt/Tgt	33/37	1	2	FACETS	0.609	0.544	0.678	0.609	0.544	0.678	SUBCLONAL	1	TRUE	1	0.28	2		811	1255	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288803	33288803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	43	550	1	ENST00000374542.5:c.749G>A	p.Gly250Asp	p.G250D	ENST00000374542	NM_001141970.1	250	gGc/gAc	3/8	1	2	FACETS	0.406	0.339	0.482	0.406	0.339	0.482	SUBCLONAL	1	TRUE	1	0.28	2		551	756	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0056749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	240	358	7	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	0.650099041398654	4	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.667801247658713	4		365	506	SUCCESS
APC	324	MSKCC	GRCh37	5	112175240	112175240	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	121	215	0	ENST00000257430.4:c.3949G>T	p.Glu1317Ter	p.E1317*	ENST00000257430	NM_000038.5	1317	Gaa/Taa	16/16	0.334683999140153	3	FACETS	0.882	0.812	0.953	0.882	0.812	0.953	INDETERMINATE	2	TRUE	1	0.667801247658713	3		215	274	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27228298	27228298	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	190	433	0	ENST00000380036.4:c.3295C>T	p.Arg1099Ter	p.R1099*	ENST00000380036	NM_000459.3	1099	Cga/Tga	22/23	0.17520030967606	4	FACETS	1	0.946	1	0.676	0.631	0.721	INDETERMINATE	2	TRUE	1	0.667801247658713	4		433	468	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170471	108170471	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794124	NA	P-0056749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	86	300	1	ENST00000278616.4:c.5036G>A	p.Gly1679Asp	p.G1679D	ENST00000278616	NM_000051.3	1679	gGt/gAt	34/63	1	2	FACETS	0.885	0.792	0.982	0.885	0.792	0.982	CLONAL	1	TRUE	1	0.667801247658713	2		301	291	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201102	108201102	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	115	302	0	ENST00000278616.4:c.7469T>G	p.Leu2490Arg	p.L2490R	ENST00000278616	NM_000051.3	2490	cTc/cGc	50/63	1	2	FACETS	0.822	0.746	0.901	0.822	0.746	0.901	CLONAL	1	TRUE	1	0.667801247658713	2		302	419	SUCCESS
APC	324	MSKCC	GRCh37	5	112174165	112174165	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	108	273	0	ENST00000257430.4:c.2874del	p.Arg958SerfsTer7	p.R958Sfs*7	ENST00000257430	NM_000038.5	958	agA/ag	16/16	0.334683999140153	3	FACETS	1	0.948	1	0.537	0.485	0.59	INDETERMINATE	1	TRUE	1	0.667801247658713	3		273	402	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229252	36229252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	372	790	4	ENST00000222270.7:c.7942G>A	p.Ala2648Thr	p.A2648T	ENST00000222270	NM_014727.1	2648	Gcc/Acc	37/37	0.762180999610121	8	FACETS	1	0.975	1			1	CLONAL	2	TRUE	NA	0.762180999610121	8		794	1532	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050770	5050770	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	197	379	0	ENST00000381652.3:c.553G>C	p.Asp185His	p.D185H	ENST00000381652	NM_004972.3	185	Gat/Cat	6/25	0.764586504680101	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.762180999610121	2		379	247	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144488	58144488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	174	353	0	ENST00000257904.6:c.583G>A	p.Val195Met	p.V195M	ENST00000257904	NM_000075.3	195	Gtg/Atg	5/8	0.764586504680101	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.762180999610121	2		353	220	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579357	7579359	+	frameshift_variant	Frame_Shift_Del	DEL	ACG	ACG	CC	novel	NA	P-0056750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	377	758	1	ENST00000269305.4:c.328_330delinsGG	p.Arg110GlyfsTer13	p.R110Gfs*13	ENST00000269305	NM_001126112.2	110	CGT/GG	4/11	0.764586504680101	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.762180999610121	2		759	484	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	274	324	0				ENST00000310581	NM_198253.2	-/1132			0.293689614192887	6	FACETS	1	0.98	1	0.821	0.772	0.871	CLONAL	3	TRUE	2	0.293689614192887	6		324	902	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	230	762	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.214605278302902	3	FACETS	0.87	0.811	0.931	0.87	0.811	0.931	CLONAL	2	TRUE	1	0.293689614192887	3		762	1032	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	97	604	0	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	0.214605278302902	3	FACETS	0.856	0.762	0.956	0.428	0.381	0.478	CLONAL	1	TRUE	1	0.293689614192887	3		604	885	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781629	9781629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	98	558	0	ENST00000377346.4:c.1939C>T	p.Leu647Phe	p.L647F	ENST00000377346	NM_005026.3	647	Ctt/Ttt	15/24	0.214605278302902	3	FACETS	0.848	0.755	0.946	0.424	0.377	0.473	CLONAL	1	TRUE	1	0.293689614192887	3		558	903	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188153	11188153	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	160	482	0	ENST00000361445.4:c.5941A>G	p.Lys1981Glu	p.K1981E	ENST00000361445	NM_004958.3	1981	Aag/Gag	43/58	0.214605278302902	3	FACETS	1	0.987	1	0.713	0.654	0.775	CLONAL	1	TRUE	1	0.293689614192887	3		482	876	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264666	11264666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	76	582	0	ENST00000361445.4:c.3896C>T	p.Ser1299Phe	p.S1299F	ENST00000361445	NM_004958.3	1299	tCc/tTc	26/58	0.214605278302902	3	FACETS	0.665	0.582	0.755	0.333	0.291	0.378	SUBCLONAL	1	TRUE	1	0.293689614192887	3		582	892	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254896	16254896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	147	475	0	ENST00000375759.3:c.2161C>T	p.Pro721Ser	p.P721S	ENST00000375759	NM_015001.2	721	Ccg/Tcg	11/15	0.214605278302902	3	FACETS	1	0.985	1	0.687	0.627	0.749	CLONAL	1	TRUE	1	0.293689614192887	3		475	836	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260725	16260725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	205	541	0	ENST00000375759.3:c.7990C>T	p.Pro2664Ser	p.P2664S	ENST00000375759	NM_015001.2	2664	Ccg/Tcg	11/15	0.214605278302902	3	FACETS	0.875	0.812	0.94	0.875	0.812	0.94	CLONAL	2	TRUE	1	0.293689614192887	3		541	915	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546351	46546351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773957217	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	83	373	0	ENST00000262741.5:c.178C>T	p.Leu60Phe	p.L60F	ENST00000262741	NM_003629.3	60	Ctt/Ttt	2/10	0.214605278302902	3	FACETS	0.774	0.686	0.866	0.774	0.686	0.866	SUBCLONAL	2	TRUE	1	0.293689614192887	3		373	419	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428535	78428535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs988943563	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	56	460	0	ENST00000370768.2:c.1264C>T	p.Pro422Ser	p.P422S	ENST00000370768	NM_003902.3	422	Cct/Tct	14/20	0.214605278302902	3	FACETS	1	0.865	1	0.504	0.432	0.581	CLONAL	1	TRUE	1	0.293689614192887	3		460	434	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165834	118165834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780049033	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	122	438	0	ENST00000369448.3:c.344C>T	p.Ser115Phe	p.S115F	ENST00000369448	NM_017709.3	115	tCc/tTc	2/2	0.214605278302902	3	FACETS	0.797	0.722	0.875	0.797	0.722	0.875	SUBCLONAL	2	TRUE	1	0.293689614192887	3		438	598	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512305	120512305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	77	443	0	ENST00000256646.2:c.937G>A	p.Gly313Ser	p.G313S	ENST00000256646	NM_024408.3	313	Ggc/Agc	6/34	0.214605278302902	3	FACETS	0.786	0.689	0.89	0.393	0.344	0.445	SUBCLONAL	1	TRUE	1	0.293689614192887	3		443	765	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844800	156844800	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs34900547	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	315	628	0	ENST00000524377.1:c.1354C>T	p.Arg452Cys	p.R452C	ENST00000524377	NM_002529.3	452	Cgc/Tgc	11/17	0.205370639652479	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.293689614192887	4		628	1227	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652390	206652390	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	188	604	0	ENST00000367120.3:c.1097C>T	p.Ser366Leu	p.S366L	ENST00000367120	NM_014002.3	366	tCa/tTa	10/22	0.205370639652479	4	FACETS	1	0.988	1	0.692	0.638	0.748	CLONAL	1	TRUE	2	0.293689614192887	4		604	1197	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620418	43620418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1007307889	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	115	431	1	ENST00000355710.3:c.3027G>A	p.Met1009Ile	p.M1009I	ENST00000355710	NM_020975.4	1009	atG/atA	18/20	0.213029643603615	2	FACETS	1	0.972	1	0.607	0.548	0.67	CLONAL	1	TRUE	0	0.293689614192887	2		432	645	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114901028	114901028	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	74	502	0	ENST00000543371.1:c.638C>T	p.Pro213Leu	p.P213L	ENST00000543371	NM_001198531.1	213	cCg/cTg	6/14	0.213029643603615	2	FACETS	0.575	0.502	0.654	0.288	0.251	0.327	SUBCLONAL	1	TRUE	0	0.293689614192887	2		502	876	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8252049	8252049	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	80	514	0	ENST00000335790.3:c.28G>C	p.Val10Leu	p.V10L	ENST00000335790	NM_002315.2	10	Gtg/Ctg	2/4	0.284247329983545	1	FACETS	0.658	0.579	0.743	0.658	0.579	0.743	SUBCLONAL	1	TRUE	0	0.293689614192887	1		514	706	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414262	32414262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144788858	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	114	426	0	ENST00000332351.3:c.1289G>A	p.Arg430Gln	p.R430Q	ENST00000332351	NM_024426.4	430	cGa/cAa	8/10	0.284247329983545	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.293689614192887	1		426	551	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977228	85977228	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	22	277	1	ENST00000263360.6:c.830C>A	p.Ser277Tyr	p.S277Y	ENST00000263360	NM_003797.3	277	tCt/tAt	8/12	1	2	FACETS	0.669	0.52	0.84	0.669	0.52	0.84	SUBCLONAL	1	TRUE	1	0.293689614192887	2		278	224	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149241	119149242	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	71	502	0	ENST00000264033.4:c.1249_1250delinsTT	p.Pro417Phe	p.P417F	ENST00000264033	NM_005188.3	417	CCt/TTt	9/16	1	2	FACETS	0.701	0.611	0.798	0.701	0.611	0.798	SUBCLONAL	1	TRUE	1	0.293689614192887	2		502	690	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503186	125503186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	39	302	0	ENST00000428830.2:c.553C>T	p.His185Tyr	p.H185Y	ENST00000428830	NM_001114121.2	185	Cat/Tat	6/14	1	2	FACETS	0.768	0.638	0.911	0.768	0.638	0.911	CLONAL	1	TRUE	1	0.293689614192887	2		302	346	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472157	472157	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764559792	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	190	438	0	ENST00000399788.2:c.644C>T	p.Pro215Leu	p.P215L	ENST00000399788	NM_001042603.1	215	cCg/cTg	5/28	0.205370639652479	4	FACETS	0.834	0.77	0.899	0.834	0.77	0.899	CLONAL	2	TRUE	2	0.293689614192887	4		438	1004	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398091	4398091	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	227	466	0	ENST00000261254.3:c.655G>A	p.Glu219Lys	p.E219K	ENST00000261254	NM_001759.3	219	Gaa/Aaa	4/5	0.205370639652479	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	2	0.293689614192887	4		466	966	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992172	11992172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	128	426	0	ENST00000396373.4:c.262G>A	p.Glu88Lys	p.E88K	ENST00000396373	NM_001987.4	88	Gaa/Aaa	3/8	0.205370639652479	4	FACETS	1	0.984	1	0.716	0.649	0.786	CLONAL	1	TRUE	2	0.293689614192887	4		426	788	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022768	12022768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	143	439	0	ENST00000396373.4:c.874C>T	p.Leu292Phe	p.L292F	ENST00000396373	NM_001987.4	292	Ctc/Ttc	5/8	0.205370639652479	4	FACETS	0.757	0.69	0.827	0.757	0.69	0.827	SUBCLONAL	2	TRUE	2	0.293689614192887	4		439	832	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435178	18435178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763302534	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	64	296	0	ENST00000266497.5:c.163G>A	p.Glu55Lys	p.E55K	ENST00000266497		55	Gag/Aag	1/31	0.205370639652479	4	FACETS	1	0.96	1	0.645	0.56	0.737	CLONAL	1	TRUE	2	0.293689614192887	4		296	437	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641549	18641549	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	74	320	0	ENST00000266497.5:c.2548G>A	p.Asp850Asn	p.D850N	ENST00000266497		850	Gac/Aac	17/31	0.205370639652479	4	FACETS	0.755	0.663	0.852	0.755	0.663	0.852	SUBCLONAL	2	TRUE	2	0.293689614192887	4		320	432	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644451	18644451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	74	340	0	ENST00000266497.5:c.2629C>T	p.Pro877Ser	p.P877S	ENST00000266497		877	Cct/Tct	18/31	0.205370639652479	4	FACETS	0.811	0.713	0.915	0.811	0.713	0.915	CLONAL	2	TRUE	2	0.293689614192887	4		340	402	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656271	18656271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	63	445	0	ENST00000266497.5:c.2950G>A	p.Gly984Arg	p.G984R	ENST00000266497		984	Gga/Aga	21/31	0.205370639652479	4	FACETS	1	0.921	1	0.545	0.472	0.624	CLONAL	1	TRUE	2	0.293689614192887	4		445	509	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691241	18691241	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	43	236	0	ENST00000266497.5:c.3352G>A	p.Glu1118Lys	p.E1118K	ENST00000266497		1118	Gaa/Aaa	23/31	0.205370639652479	4	FACETS	1	0.93	1	0.603	0.507	0.709	CLONAL	1	TRUE	2	0.293689614192887	4		236	314	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699323	18699323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199904184	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	87	296	0	ENST00000266497.5:c.3424C>T	p.Arg1142Cys	p.R1142C	ENST00000266497		1142	Cgt/Tgt	24/31	0.205370639652479	4	FACETS	0.973	0.867	1	0.973	0.867	1	CLONAL	2	TRUE	2	0.293689614192887	4		296	394	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715647	18715647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	49	234	0	ENST00000266497.5:c.3478G>A	p.Glu1160Lys	p.E1160K	ENST00000266497		1160	Gaa/Aaa	25/31	0.205370639652479	4	FACETS	1	0.957	1	0.69	0.587	0.801	CLONAL	1	TRUE	2	0.293689614192887	4		234	313	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005314	29005314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	50	455	0	ENST00000282397.4:c.947G>A	p.Gly316Glu	p.G316E	ENST00000282397	NM_002019.4	316	gGa/gAa	7/30	0.243868077861272	3	FACETS	0.984	0.837	1	0.328	0.279	0.382	CLONAL	1	TRUE	0	0.293689614192887	3		455	397	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934246	48934246	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	63	411	0	ENST00000267163.4:c.701T>A	p.Leu234Ter	p.L234*	ENST00000267163	NM_000321.2	234	tTg/tAg	7/27	0.243868077861272	3	FACETS	0.826	0.72	0.938	0.55	0.48	0.626	CLONAL	2	TRUE	0	0.293689614192887	3		411	298	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987103	36987103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	132	709	0	ENST00000354822.5:c.586G>A	p.Val196Met	p.V196M	ENST00000354822	NM_001079668.2	196	Gtg/Atg	3/3	0.214605278302902	3	FACETS	0.987	0.895	1	0.494	0.447	0.543	CLONAL	1	TRUE	1	0.293689614192887	3		709	1044	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562317	95562317	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	65	368	0	ENST00000393063.1:c.4940G>A	p.Arg1647Lys	p.R1647K	ENST00000393063	NM_030621.3	1647	aGa/aAa	24/28	0.214605278302902	3	FACETS	0.965	0.838	1	0.483	0.419	0.552	CLONAL	1	TRUE	1	0.293689614192887	3		368	526	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500661	99500661	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370843278	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	73	424	0	ENST00000268035.6:c.4094C>T	p.Ser1365Leu	p.S1365L	ENST00000268035	NM_000875.3	1365	tCg/tTg	21/21	0.214605278302902	3	FACETS	0.876	0.766	0.994	0.438	0.383	0.497	CLONAL	1	TRUE	1	0.293689614192887	3		424	651	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104352	2104352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1487984678	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	124	657	0	ENST00000219476.3:c.392C>T	p.Pro131Leu	p.P131L	ENST00000219476	NM_000548.3	131	cCt/cTt	5/42	1	2	FACETS	0.981	0.887	1	0.981	0.887	1	CLONAL	1	TRUE	1	0.293689614192887	2		657	861	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2111960	2111960	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555501098	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	150	656	0	ENST00000219476.3:c.1208C>T	p.Ser403Phe	p.S403F	ENST00000219476	NM_000548.3	403	tCt/tTt	12/42	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.293689614192887	2		656	935	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790455	3790455	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783490	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	86	500	0	ENST00000262367.5:c.4078C>T	p.Arg1360Ter	p.R1360*	ENST00000262367	NM_004380.2	1360	Cga/Tga	24/31	1	2	FACETS	0.668	0.59	0.752	0.668	0.59	0.752	SUBCLONAL	1	TRUE	1	0.293689614192887	2		500	877	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857172	9857172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555481986	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	75	414	1	ENST00000330684.3:c.4229C>T	p.Ser1410Leu	p.S1410L	ENST00000330684	NM_001134407.1	1410	tCg/tTg	13/13	1	2	FACETS	0.835	0.732	0.945	0.835	0.732	0.945	CLONAL	1	TRUE	1	0.293689614192887	2		415	612	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858066	9858066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	104	584	1	ENST00000330684.3:c.3335C>T	p.Ser1112Phe	p.S1112F	ENST00000330684	NM_001134407.1	1112	tCc/tTc	13/13	1	2	FACETS	0.931	0.833	1	0.931	0.833	1	CLONAL	1	TRUE	1	0.293689614192887	2		585	761	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923415	9923416	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	98	510	1	ENST00000330684.3:c.1871_1872delinsAA	p.Gly624Glu	p.G624E	ENST00000330684	NM_001134407.1	624	gGG/gAA	9/13	1	2	FACETS	0.955	0.852	1	0.955	0.852	1	CLONAL	1	TRUE	1	0.293689614192887	2		511	699	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934560	9934560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	79	452	0	ENST00000330684.3:c.1595G>A	p.Gly532Glu	p.G532E	ENST00000330684	NM_001134407.1	532	gGa/gAa	7/13	1	2	FACETS	0.903	0.795	1	0.903	0.795	1	CLONAL	1	TRUE	1	0.293689614192887	2		452	596	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041833	14041833	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757223070	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	95	439	0	ENST00000311895.7:c.2380C>T	p.His794Tyr	p.H794Y	ENST00000311895	NM_005236.2	794	Cac/Tac	11/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.293689614192887	2		439	595	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347470	89347470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778780920	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	93	606	0	ENST00000301030.4:c.5480C>T	p.Pro1827Leu	p.P1827L	ENST00000301030	NM_001256183.1	1827	cCc/cTc	9/13	1	2	FACETS	0.797	0.708	0.892	0.797	0.708	0.892	SUBCLONAL	1	TRUE	1	0.293689614192887	2		606	795	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350819	89350819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1251812244	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	77	777	0	ENST00000301030.4:c.2131C>T	p.Leu711Phe	p.L711F	ENST00000301030	NM_001256183.1	711	Ctc/Ttc	9/13	1	2	FACETS	0.585	0.513	0.664	0.585	0.513	0.664	SUBCLONAL	1	TRUE	1	0.293689614192887	2		777	896	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89842150	89842150	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1222254954	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	86	467	0	ENST00000389301.3:c.1900G>A	p.Asp634Asn	p.D634N	ENST00000389301	NM_000135.2	634	Gat/Aat	21/43	1	2	FACETS	0.772	0.682	0.868	0.772	0.682	0.868	SUBCLONAL	1	TRUE	1	0.293689614192887	2		467	759	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044470	12044470	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	92	246	0	ENST00000353533.5:c.1093C>T	p.Pro365Ser	p.P365S	ENST00000353533	NM_003010.3	365	Ccc/Tcc	11/11	0.214605278302902	3	FACETS	1	0.911	1	1	0.911	1	CLONAL	2	TRUE	1	0.293689614192887	3		246	353	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	51	268	2	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	0.213029643603615	2	FACETS	1	0.962	1	0.706	0.606	0.814	CLONAL	1	TRUE	0	0.293689614192887	2		270	246	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40486020	40486020	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	170	527	0	ENST00000264657.5:c.845A>G	p.Lys282Arg	p.K282R	ENST00000264657	NM_139276.2	282	aAg/aGg	9/24	0.213029643603615	2	FACETS	1	0.988	1	0.711	0.655	0.77	CLONAL	1	TRUE	0	0.293689614192887	2		527	814	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210733	5210733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779302415	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	108	721	0	ENST00000357368.4:c.5318C>T	p.Ser1773Leu	p.S1773L	ENST00000357368	NM_002850.3	1773	tCg/tTg	34/38	0.214605278302902	3	FACETS	0.79	0.707	0.878	0.395	0.353	0.439	SUBCLONAL	1	TRUE	1	0.293689614192887	3		721	1068	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143073	7143073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774340801	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	183	633	0	ENST00000302850.5:c.2296G>A	p.Asp766Asn	p.D766N	ENST00000302850	NM_000208.2	766	Gat/Aat	12/22	0.214605278302902	3	FACETS	0.755	0.696	0.815	0.755	0.696	0.815	SUBCLONAL	2	TRUE	1	0.293689614192887	3		633	947	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251828	10251828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	162	575	0	ENST00000340748.4:c.3299C>T	p.Pro1100Leu	p.P1100L	ENST00000340748		1100	cCc/cTc	30/40	0.214605278302902	3	FACETS	1	0.988	1	0.729	0.669	0.791	CLONAL	1	TRUE	1	0.293689614192887	3		575	868	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136161	11136161	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	90	626	0	ENST00000358026.2:c.3145C>T	p.Pro1049Ser	p.P1049S	ENST00000358026	NM_001128849.1	1049	Ccc/Tcc	22/36	0.214605278302902	3	FACETS	0.785	0.696	0.882	0.393	0.348	0.441	SUBCLONAL	1	TRUE	1	0.293689614192887	3		626	895	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271793	15271793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	124	826	0	ENST00000263388.2:c.6646G>A	p.Gly2216Arg	p.G2216R	ENST00000263388	NM_000435.2	2216	Gga/Aga	33/33	0.214605278302902	3	FACETS	0.822	0.742	0.907	0.411	0.371	0.454	CLONAL	1	TRUE	1	0.293689614192887	3		826	1178	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303109	15303109	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs771086784	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	224	741	0	ENST00000263388.2:c.341G>A	p.Gly114Asp	p.G114D	ENST00000263388	NM_000435.2	114	gGc/gAc	4/33	0.214605278302902	3	FACETS	0.801	0.745	0.859	0.801	0.745	0.859	CLONAL	2	TRUE	1	0.293689614192887	3		741	1092	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354043	15354043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	81	429	0	ENST00000263377.2:c.2837C>T	p.Pro946Leu	p.P946L	ENST00000263377	NM_058243.2	946	cCt/cTt	14/20	0.214605278302902	3	FACETS	0.979	0.863	1	0.49	0.431	0.552	CLONAL	1	TRUE	1	0.293689614192887	3		429	646	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17949113	17949113	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	104	715	1	ENST00000458235.1:c.1528C>T	p.Gln510Ter	p.Q510*	ENST00000458235	NM_000215.3	510	Cag/Tag	11/24	0.214605278302902	3	FACETS	0.816	0.73	0.909	0.408	0.365	0.455	CLONAL	1	TRUE	1	0.293689614192887	3		716	995	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212411	36212411	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	236	697	0	ENST00000222270.7:c.2162C>T	p.Pro721Leu	p.P721L	ENST00000222270	NM_014727.1	721	cCt/cTt	3/37	0.214605278302902	3	FACETS	0.873	0.814	0.933	0.873	0.814	0.933	CLONAL	2	TRUE	1	0.293689614192887	3		697	1056	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905545	50905545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763249087	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	260	789	2	ENST00000440232.2:c.673C>T	p.Arg225Cys	p.R225C	ENST00000440232	NM_002691.3	225	Cgt/Tgt	6/27	0.214605278302902	3	FACETS	0.928	0.869	0.989	0.928	0.869	0.989	CLONAL	2	TRUE	1	0.293689614192887	3		791	1094	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965983	25965983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200946888	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	194	656	1	ENST00000435504.4:c.3223C>T	p.Arg1075Trp	p.R1075W	ENST00000435504		1075	Cgg/Tgg	13/13	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.293689614192887	2		657	992	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574116	46574116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	225	633	0	ENST00000263734.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000263734	NM_001430.4	44	cCc/cTc	2/16	1	2	FACETS	0.77	0.717	0.824	1	0.992	1	SUBCLONAL	2	TRUE	1	0.293689614192887	2		633	995	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873242	136873242	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	62	330	0	ENST00000241393.3:c.256C>T	p.Leu86Phe	p.L86F	ENST00000241393	NM_003467.2	86	Ctc/Ttc	2/2	1	2	FACETS	0.817	0.706	0.936	0.817	0.706	0.936	CLONAL	1	TRUE	1	0.293689614192887	2		330	517	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257832	198257832	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	93	406	0	ENST00000335508.6:c.3620C>T	p.Ser1207Leu	p.S1207L	ENST00000335508	NM_012433.2	1207	tCg/tTg	24/25	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.293689614192887	2		406	554	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732675	204732675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	110	354	0	ENST00000302823.3:c.10C>T	p.Leu4Phe	p.L4F	ENST00000302823	NM_005214.4	4	Ctt/Ttt	1/4	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.293689614192887	2		354	565	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286760	212286760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763644012	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	47	328	0	ENST00000342788.4:c.2936G>A	p.Arg979Gln	p.R979Q	ENST00000342788	NM_005235.2	979	cGa/cAa	24/28	1	2	FACETS	0.762	0.644	0.892	0.762	0.644	0.892	SUBCLONAL	1	TRUE	1	0.293689614192887	2		328	420	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295699	212295699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776347334	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	42	468	0	ENST00000342788.4:c.2614G>A	p.Glu872Lys	p.E872K	ENST00000342788	NM_005235.2	872	Gaa/Aaa	21/28	1	2	FACETS	0.548	0.457	0.649	0.548	0.457	0.649	SUBCLONAL	1	TRUE	1	0.293689614192887	2		468	522	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295755	212295755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	57	533	1	ENST00000342788.4:c.2558C>T	p.Ser853Phe	p.S853F	ENST00000342788	NM_005235.2	853	tCt/tTt	21/28	1	2	FACETS	0.618	0.53	0.715	0.618	0.53	0.715	SUBCLONAL	1	TRUE	1	0.293689614192887	2		534	628	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812236	212812236	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	37	331	0	ENST00000342788.4:c.340C>T	p.Arg114Ter	p.R114*	ENST00000342788	NM_005235.2	114	Cga/Tga	3/28	1	2	FACETS	0.615	0.507	0.735	0.615	0.507	0.735	SUBCLONAL	1	TRUE	1	0.293689614192887	2		331	410	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440063	220440063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	107	687	0	ENST00000243786.2:c.916C>T	p.Pro306Ser	p.P306S	ENST00000243786	NM_002191.3	306	Cca/Tca	2/2	1	2	FACETS	0.701	0.628	0.78	0.701	0.628	0.78	SUBCLONAL	1	TRUE	1	0.293689614192887	2		687	1039	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560883	9560883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	82	499	0	ENST00000353224.5:c.899G>A	p.Gly300Glu	p.G300E	ENST00000353224	NM_177990.2	300	gGa/gAa	4/10	0.214605278302902	3	FACETS	0.781	0.688	0.881	0.39	0.344	0.441	SUBCLONAL	1	TRUE	1	0.293689614192887	3		499	820	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561396	9561396	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1262495622	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	175	518	0	ENST00000353224.5:c.386C>T	p.Ser129Phe	p.S129F	ENST00000353224	NM_177990.2	129	tCc/tTc	4/10	0.214605278302902	3	FACETS	0.814	0.75	0.88	0.814	0.75	0.88	CLONAL	2	TRUE	1	0.293689614192887	3		518	840	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31025127	31025127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1229055519	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	115	445	0	ENST00000375687.4:c.4612C>T	p.Leu1538Phe	p.L1538F	ENST00000375687	NM_015338.5	1538	Ctt/Ttt	13/13	0.214605278302902	3	FACETS	1	0.981	1	0.693	0.625	0.764	CLONAL	1	TRUE	1	0.293689614192887	3		445	648	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395614	31395614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	212	592	1	ENST00000328111.2:c.2467C>T	p.Arg823Cys	p.R823C	ENST00000328111	NM_006892.3	823	Cgt/Tgt	23/23	0.214605278302902	3	FACETS	0.812	0.754	0.872	0.812	0.754	0.872	CLONAL	2	TRUE	1	0.293689614192887	3		593	1019	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164878	36164878	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1477060839	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	352	704	0	ENST00000300305.3:c.997C>T	p.Pro333Ser	p.P333S	ENST00000300305		333	Ccg/Tcg	8/8	0.205370639652479	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.293689614192887	4		704	1436	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755462	39755462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	143	490	0	ENST00000288319.7:c.1303C>T	p.Pro435Ser	p.P435S	ENST00000288319	NM_182918.3	435	Cct/Tct	10/10	0.205370639652479	4	FACETS	0.779	0.71	0.85	0.779	0.71	0.85	SUBCLONAL	2	TRUE	2	0.293689614192887	4		490	809	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860411	42860411	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	235	559	0	ENST00000398585.3:c.466G>A	p.Glu156Lys	p.E156K	ENST00000398585	NM_001135099.1	156	Gag/Aag	5/14	0.205370639652479	4	FACETS	0.996	0.93	1	0.996	0.93	1	CLONAL	2	TRUE	2	0.293689614192887	4		559	1039	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155369	47155369	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	51	338	0	ENST00000409792.3:c.4712C>T	p.Pro1571Leu	p.P1571L	ENST00000409792	NM_014159.6	1571	cCt/cTt	5/21	0.214605278302902	3	FACETS	0.84	0.715	0.978	0.42	0.357	0.489	CLONAL	1	TRUE	1	0.293689614192887	3		338	474	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163922	47163922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324928449	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	41	346	0	ENST00000409792.3:c.2204C>T	p.Thr735Ile	p.T735I	ENST00000409792	NM_014159.6	735	aCc/aTc	3/21	0.214605278302902	3	FACETS	0.738	0.615	0.874	0.369	0.307	0.437	SUBCLONAL	1	TRUE	1	0.293689614192887	3		346	434	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165543	47165543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	101	540	0	ENST00000409792.3:c.583C>T	p.Pro195Ser	p.P195S	ENST00000409792	NM_014159.6	195	Cca/Tca	3/21	0.214605278302902	3	FACETS	0.917	0.819	1	0.459	0.409	0.511	CLONAL	1	TRUE	1	0.293689614192887	3		540	860	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702549	52702549	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	29	389	1	ENST00000394830.3:c.349C>T	p.Gln117Ter	p.Q117*	ENST00000394830	NM_018313.4	117	Cag/Tag	4/30	0.214605278302902	3	FACETS	0.565	0.453	0.692	0.282	0.226	0.346	SUBCLONAL	1	TRUE	1	0.293689614192887	3		390	401	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890336	72890336	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	44	324	0	ENST00000325599.8:c.346C>T	p.Pro116Ser	p.P116S	ENST00000325599	NM_018130.2	116	Cct/Tct	4/11	0.214605278302902	3	FACETS	0.767	0.644	0.903	0.384	0.322	0.452	CLONAL	1	TRUE	1	0.293689614192887	3		324	448	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670379	134670379	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	65	416	0	ENST00000398015.3:c.290G>A	p.Ser97Asn	p.S97N	ENST00000398015	NM_004441.4	97	aGc/aAc	3/16	0.214605278302902	3	FACETS	0.884	0.767	1	0.442	0.383	0.506	CLONAL	1	TRUE	1	0.293689614192887	3		416	574	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188397	142188397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1169255490	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	42	350	2	ENST00000350721.4:c.6334C>T	p.Arg2112Cys	p.R2112C	ENST00000350721	NM_001184.3	2112	Cgt/Tgt	38/47	0.214605278302902	3	FACETS	1	0.879	1	0.529	0.443	0.623	CLONAL	1	TRUE	1	0.293689614192887	3		352	310	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190873	185190873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144909413	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	249	588	0	ENST00000265026.3:c.1754G>A	p.Arg585Gln	p.R585Q	ENST00000265026	NM_004721.4	585	cGa/cAa	11/14	0.214605278302902	3	FACETS	0.881	0.823	0.94	0.881	0.823	0.94	CLONAL	2	TRUE	1	0.293689614192887	3		588	1104	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191494	185191494	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	96	588	0	ENST00000265026.3:c.2375C>T	p.Thr792Ile	p.T792I	ENST00000265026	NM_004721.4	792	aCc/aTc	11/14	0.214605278302902	3	FACETS	0.718	0.638	0.804	0.359	0.319	0.402	SUBCLONAL	1	TRUE	1	0.293689614192887	3		588	1044	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604249	189604249	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	98	440	1	ENST00000264731.3:c.1416G>A	p.Met472Ile	p.M472I	ENST00000264731	NM_003722.4	472	atG/atA	11/14	0.214605278302902	3	FACETS	0.876	0.78	0.978	0.438	0.39	0.489	CLONAL	1	TRUE	1	0.293689614192887	3		441	874	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948801	55948801	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	16	310	0	ENST00000263923.4:c.3664C>T	p.Gln1222Ter	p.Q1222*	ENST00000263923	NM_002253.2	1222	Cag/Tag	28/30	0.240312720593877	1	FACETS	0.373	0.276	0.49	0.373	0.276	0.49	SUBCLONAL	1	TRUE	0	0.293689614192887	1		310	249	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549725	187549725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199516712	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	30	426	0	ENST00000441802.2:c.4516C>T	p.Arg1506Cys	p.R1506C	ENST00000441802	NM_005245.3	1506	Cgt/Tgt	8/27	0.240312720593877	1	FACETS	0.329	0.264	0.403	0.329	0.264	0.403	SUBCLONAL	1	TRUE	0	0.293689614192887	1		426	530	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876145	35876145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	162	529	0	ENST00000303115.3:c.937G>A	p.Asp313Asn	p.D313N	ENST00000303115	NM_002185.3	313	Gac/Aac	8/8	0.293689614192887	6	FACETS	1	0.937	1	0.512	0.47	0.556	CLONAL	2	TRUE	2	0.293689614192887	6		529	855	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876520	35876520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	179	487	0	ENST00000303115.3:c.1312C>T	p.Leu438Phe	p.L438F	ENST00000303115	NM_002185.3	438	Ctt/Ttt	8/8	0.293689614192887	6	FACETS	1	0.962	1	0.535	0.493	0.578	CLONAL	2	TRUE	2	0.293689614192887	6		487	905	SUCCESS
APC	324	MSKCC	GRCh37	5	112175466	112175466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	131	259	0	ENST00000257430.4:c.4175C>T	p.Ser1392Leu	p.S1392L	ENST00000257430	NM_000038.5	1392	tCa/tTa	16/16	0.293689614192887	4	FACETS	0.988	0.9	1	0.988	0.9	1	CLONAL	2	TRUE	2	0.293689614192887	4		259	584	SUCCESS
APC	324	MSKCC	GRCh37	5	112176309	112176309	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	112	321	1	ENST00000257430.4:c.5018A>T	p.Glu1673Val	p.E1673V	ENST00000257430	NM_000038.5	1673	gAa/gTa	16/16	0.293689614192887	4	FACETS	1	0.983	1	0.731	0.658	0.808	CLONAL	1	TRUE	2	0.293689614192887	4		322	675	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176662905	176662905	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761564636	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	96	341	0	ENST00000439151.2:c.3880C>T	p.Pro1294Ser	p.P1294S	ENST00000439151	NM_022455.4	1294	Cct/Tct	6/23	0.293689614192887	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	2	TRUE	0	0.293689614192887	2		341	323	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045831	26045840	+	frameshift_variant	Frame_Shift_Del	DEL	AAGCTGCCGT	AAGCTGCCGT	-	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	129	535	0	ENST00000540144.1:c.193_202del	p.Lys65SerfsTer23	p.K65Sfs*23	ENST00000540144	NM_003531.2	65	AAGCTGCCGTtc/tc	1/1	0.112051056772655	4	FACETS	1	0.979	1	0.64	0.58	0.703	INDETERMINATE	1	TRUE	2	0.293689614192887	4		535	888	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673725	30673725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs78556678	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	130	555	1	ENST00000376406.3:c.3235C>T	p.Arg1079Cys	p.R1079C	ENST00000376406	NM_014641.2	1079	Cgt/Tgt	10/15	0.112051056772655	4	FACETS	1	0.978	1	0.629	0.57	0.692	INDETERMINATE	1	TRUE	2	0.293689614192887	4		556	910	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169159	32169159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	129	596	0	ENST00000375023.3:c.3874G>A	p.Glu1292Lys	p.E1292K	ENST00000375023	NM_004557.3	1292	Gag/Aag	22/30	0.112051056772655	4	FACETS	1	0.973	1	0.599	0.543	0.659	INDETERMINATE	1	TRUE	2	0.293689614192887	4		596	948	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190459	32190459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	152	752	0	ENST00000375023.3:c.280C>T	p.Pro94Ser	p.P94S	ENST00000375023	NM_004557.3	94	Ccc/Tcc	3/30	0.112051056772655	4	FACETS	1	0.958	1	0.542	0.494	0.592	INDETERMINATE	1	TRUE	2	0.293689614192887	4		752	1236	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288774	33288774	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	118	428	0	ENST00000374542.5:c.778C>T	p.Arg260Cys	p.R260C	ENST00000374542	NM_001141970.1	260	Cgt/Tgt	3/8	0.112051056772655	4	FACETS	1	0.981	1	0.681	0.615	0.751	INDETERMINATE	1	TRUE	2	0.293689614192887	4		428	763	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969117	93969117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	91	353	0	ENST00000369303.4:c.1879G>A	p.Glu627Lys	p.E627K	ENST00000369303	NM_004440.3	627	Gag/Aag	10/17	0.213029643603615	2	FACETS	1	0.974	1	0.656	0.585	0.732	CLONAL	1	TRUE	0	0.293689614192887	2		353	472	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120666	94120666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	62	382	0	ENST00000369303.4:c.385G>A	p.Glu129Lys	p.E129K	ENST00000369303	NM_004440.3	129	Gaa/Aaa	3/17	0.213029643603615	2	FACETS	1	0.927	1	0.553	0.479	0.632	CLONAL	1	TRUE	0	0.293689614192887	2		382	382	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163826	152163826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	112	454	0	ENST00000206249.3:c.547C>T	p.Arg183Cys	p.R183C	ENST00000206249	NM_000125.3	183	Cgc/Tgc	2/8	0.213029643603615	2	FACETS	1	0.975	1	0.626	0.564	0.691	CLONAL	1	TRUE	0	0.293689614192887	2		454	609	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962795	2962795	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146070546	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	395	609	0	ENST00000396946.4:c.2113G>A	p.Gly705Ser	p.G705S	ENST00000396946	NM_032415.4	705	Ggc/Agc	16/25	0.277689830734971	4	FACETS	1	0.953	1	1	0.953	1	CLONAL	3	TRUE	1	0.293689614192887	4		609	1159	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976787	2976787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	492	698	2	ENST00000396946.4:c.1225G>A	p.Glu409Lys	p.E409K	ENST00000396946	NM_032415.4	409	Gag/Aag	9/25	0.277689830734971	4	FACETS	0.984	0.941	1	0.984	0.941	1	CLONAL	3	TRUE	1	0.293689614192887	4		700	1469	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444289	50444289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	55	321	0	ENST00000331340.3:c.219G>A	p.Met73Ile	p.M73I	ENST00000331340	NM_006060.4	73	atG/atA	4/8	0.277689830734971	4	FACETS	0.886	0.758	1	0.295	0.252	0.342	CLONAL	1	TRUE	1	0.293689614192887	4		321	547	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444318	50444318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1427077431	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	181	346	0	ENST00000331340.3:c.248G>A	p.Arg83Gln	p.R83Q	ENST00000331340	NM_006060.4	83	cGa/cAa	4/8	0.277689830734971	4	FACETS	0.931	0.864	1	0.931	0.864	1	CLONAL	3	TRUE	1	0.293689614192887	4		346	571	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381529	81381529	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	58	282	0	ENST00000222390.5:c.532C>T	p.Arg178Ter	p.R178*	ENST00000222390	NM_000601.4	178	Cga/Tga	5/18	0.293689614192887	3	FACETS	0.911	0.784	1	0.456	0.392	0.525	CLONAL	1	TRUE	1	0.293689614192887	3		282	497	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386512	81386512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	34	384	3	ENST00000222390.5:c.475G>A	p.Glu159Lys	p.E159K	ENST00000222390	NM_000601.4	159	Gaa/Aaa	4/18	0.293689614192887	3	FACETS	0.683	0.558	0.822	0.341	0.279	0.411	SUBCLONAL	1	TRUE	1	0.293689614192887	3		387	389	SUCCESS
MET	4233	MSKCC	GRCh37	7	116409732	116409732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	18	227	0	ENST00000397752.3:c.2617G>A	p.Glu873Lys	p.E873K	ENST00000397752	NM_000245.2	873	Gaa/Aaa	12/21	0.293689614192887	3	FACETS	0.611	0.461	0.788	0.306	0.23	0.394	SUBCLONAL	1	TRUE	1	0.293689614192887	3		227	230	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411797	116411797	+	intron_variant	Intron	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	124	927	0	ENST00000397752.3:c.2887+89C>T		p.*963*	ENST00000397752	NM_000245.2	-/1390			0.293689614192887	3	FACETS	0.73	0.658	0.806	0.365	0.329	0.403	SUBCLONAL	1	TRUE	1	0.293689614192887	3		927	1327	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418986	116418986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199763277	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	116	291	0	ENST00000397752.3:c.3497G>A	p.Arg1166Gln	p.R1166Q	ENST00000397752	NM_000245.2	1166	cGa/cAa	17/21	0.293689614192887	3	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	1	0.293689614192887	3		291	428	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055756	152055756	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1283285486	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	46	353	0	ENST00000262189.6:c.166C>T	p.Arg56Ter	p.R56*	ENST00000262189	NM_170606.2	56	Cga/Tga	2/59	0.293689614192887	3	FACETS	0.738	0.621	0.866	0.369	0.31	0.433	SUBCLONAL	1	TRUE	1	0.293689614192887	3		353	487	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372430	55372430	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775790177	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	136	776	0	ENST00000297316.4:c.1120G>A	p.Glu374Lys	p.E374K	ENST00000297316	NM_022454.3	374	Gag/Aag	2/2	1	2	FACETS	0.823	0.747	0.904	0.823	0.747	0.904	CLONAL	1	TRUE	1	0.293689614192887	2		776	1125	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68973000	68973000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1261578482	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	35	333	0	ENST00000288368.4:c.1325G>A	p.Gly442Glu	p.G442E	ENST00000288368	NM_024870.2	442	gGa/gAa	11/40	1	2	FACETS	0.561	0.46	0.674	0.561	0.46	0.674	SUBCLONAL	1	TRUE	1	0.293689614192887	2		333	425	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028040	69028040	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758125979	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	42	470	0	ENST00000288368.4:c.3199G>A	p.Gly1067Ser	p.G1067S	ENST00000288368	NM_024870.2	1067	Ggc/Agc	26/40	1	2	FACETS	0.603	0.504	0.714	0.603	0.504	0.714	SUBCLONAL	1	TRUE	1	0.293689614192887	2		470	474	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069607	69069607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	59	392	0	ENST00000288368.4:c.4282G>A	p.Glu1428Lys	p.E1428K	ENST00000288368	NM_024870.2	1428	Gaa/Aaa	35/40	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.293689614192887	2		392	323	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978524	70978524	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1280479464	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	128	463	0	ENST00000276594.2:c.1129C>T	p.Pro377Ser	p.P377S	ENST00000276594	NM_024504.3	377	Cct/Tct	5/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.293689614192887	2		463	646	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485762	8485762	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	64	255	0	ENST00000356435.5:c.3055G>A	p.Val1019Met	p.V1019M	ENST00000356435		1019	Gtg/Atg	17/35	0.112051056772655	4	FACETS	1	0.971	1	0.744	0.647	0.848	INDETERMINATE	1	TRUE	2	0.293689614192887	4		255	379	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518042	8518042	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	95	444	0	ENST00000356435.5:c.1349G>A	p.Gly450Glu	p.G450E	ENST00000356435		450	gGa/gAa	10/35	0.112051056772655	4	FACETS	1	0.978	1	0.706	0.629	0.787	INDETERMINATE	1	TRUE	2	0.293689614192887	4		444	593	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518412	8518412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1353039582	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	81	216	0	ENST00000356435.5:c.979G>A	p.Gly327Arg	p.G327R	ENST00000356435		327	Gga/Aga	10/35	0.112051056772655	4	FACETS	0.777	0.687	0.873	0.777	0.687	0.873	INDETERMINATE	2	TRUE	2	0.293689614192887	4		216	459	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27173219	27173219	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	126	459	0	ENST00000380036.4:c.761-1G>A		p.X254_splice	ENST00000380036	NM_000459.3	254			0.112051056772655	4	FACETS	0.794	0.72	0.872	0.794	0.72	0.872	INDETERMINATE	2	TRUE	2	0.293689614192887	4		459	699	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185596	27185596	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	161	621	0	ENST00000380036.4:c.1296G>T	p.Met432Ile	p.M432I	ENST00000380036	NM_000459.3	432	atG/atT	9/23	0.112051056772655	4	FACETS	1	0.988	1	0.75	0.687	0.815	INDETERMINATE	1	TRUE	2	0.293689614192887	4		621	946	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197529	27197529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762196494	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	153	512	0	ENST00000380036.4:c.1841G>A	p.Arg614Gln	p.R614Q	ENST00000380036	NM_000459.3	614	cGa/cAa	12/23	0.112051056772655	4	FACETS	1	0.987	1	0.734	0.671	0.8	INDETERMINATE	1	TRUE	2	0.293689614192887	4		512	918	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221941	98221941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	165	510	0	ENST00000331920.6:c.2828C>T	p.Pro943Leu	p.P943L	ENST00000331920	NM_000264.3	943	cCa/cTa	17/24	0.112051056772655	4	FACETS	1	0.988	1	0.72	0.661	0.783	INDETERMINATE	1	TRUE	2	0.293689614192887	4		510	1009	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344833	70344833	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	161	283	0	ENST00000374080.3:c.2063C>T	p.Ser688Phe	p.S688F	ENST00000374080		688	tCc/tTc	15/45	0.293689614192887	2	FACETS	1	0.985	1			1	CLONAL	2	TRUE	NA	0.293689614192887	2		283	440	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348535	70348535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	182	296	0	ENST00000374080.3:c.3442C>T	p.Arg1148Cys	p.R1148C	ENST00000374080		1148	Cgc/Tgc	24/45	0.293689614192887	2	FACETS	1	0.984	1			1	CLONAL	2	TRUE	NA	0.293689614192887	2		296	514	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197861	123197861	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	34	200	0	ENST00000218089.9:c.1985C>G	p.Ala662Gly	p.A662G	ENST00000218089	NM_001042749.1	662	gCa/gGa	20/35	0.293689614192887	2	FACETS	1	0.946	1			1	CLONAL	1	TRUE	NA	0.293689614192887	2		200	163	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	113	324	0				ENST00000310581	NM_198253.2	-/1132			0.289120217689899	3	FACETS	0.796	0.719	0.877	0.796	0.719	0.877	SUBCLONAL	2	TRUE	1	0.289107124846615	3		324	562	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451503	70451503	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	188	483	0	ENST00000373644.4:c.6343G>C	p.Asp2115His	p.D2115H	ENST00000373644	NM_030625.2	2115	Gac/Cac	12/12	0.289120217689899	3	FACETS	0.887	0.821	0.956	0.887	0.821	0.956	CLONAL	2	TRUE	1	0.289107124846615	3		483	839	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0056770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	287	514	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	0.289107124846615	3	FACETS	0.89	0.84	0.941	0.89	0.84	0.941	CLONAL	3	TRUE	0	0.289107124846615	3		514	851	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217458	7217458	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0056770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	129	511	0	ENST00000380728.2:c.338C>G	p.Ser113Ter	p.S113*	ENST00000380728		113	tCa/tGa	5/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.289107124846615	2		511	665	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578227	7578227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	151	509	0	ENST00000269305.4:c.622G>A	p.Asp208Asn	p.D208N	ENST00000269305	NM_001126112.2	208	Gac/Aac	6/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.289107124846615	2		509	833	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676180	29676180	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	31	264	0	ENST00000356175.3:c.7169G>A	p.Arg2390Lys	p.R2390K	ENST00000356175	NM_000267.3	2390	aGa/aAa	48/57	0.205060692449502	4	FACETS	0.638	0.516	0.777	0.319	0.258	0.389	SUBCLONAL	1	TRUE	2	0.289107124846615	4		264	433	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39212966	39212966	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0056770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	51	449	0	ENST00000402219.2:c.4001G>C	p.Ter1334SerextTer31	p.*1334Sext*31	ENST00000402219	NM_005633.3	1334	tGa/tCa	23/23	0.289120217689899	3	FACETS	0.582	0.494	0.679	0.291	0.247	0.34	SUBCLONAL	1	TRUE	1	0.289107124846615	3		449	694	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568527	41568527	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	74	356	0	ENST00000263253.7:c.4477G>C	p.Asp1493His	p.D1493H	ENST00000263253	NM_001429.3	1493	Gat/Cat	28/31	0.141137366999827	4	FACETS	1	0.951	1	0.586	0.514	0.664	INDETERMINATE	1	TRUE	2	0.289107124846615	4		356	563	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568569	41568569	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	88	443	0	ENST00000263253.7:c.4519G>A	p.Asp1507Asn	p.D1507N	ENST00000263253	NM_001429.3	1507	Gat/Aat	28/31	0.141137366999827	4	FACETS	1	0.96	1	0.595	0.527	0.667	INDETERMINATE	1	TRUE	2	0.289107124846615	4		443	660	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164898	106164898	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770335785	NA	P-0056770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	39	349	0	ENST00000380013.4:c.3766G>A	p.Gly1256Ser	p.G1256S	ENST00000380013	NM_001127208.2	1256	Ggc/Agc	6/11	1	2	FACETS	0.54	0.447	0.643	0.54	0.447	0.643	SUBCLONAL	1	TRUE	1	0.289107124846615	2		349	500	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	29	324	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.674	0.54	0.827	0.674	0.54	0.827	SUBCLONAL	1	TRUE	1	0.18	2		324	478	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0056771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	17	317	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.904	0.676	1	0.904	0.676	1	CLONAL	1	TRUE	1	0.18	2		317	209	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95596433	95596433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	20	275	0	ENST00000393063.1:c.535C>T	p.Leu179Phe	p.L179F	ENST00000393063	NM_030621.3	179	Ctt/Ttt	6/28	1	2	FACETS	1	0.775	1	1	0.775	1	CLONAL	1	TRUE	1	0.18	2		275	220	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	164	324	0				ENST00000310581	NM_198253.2	-/1132			0.466886155152707	5	FACETS	0.778	0.715	0.843	0.518	0.477	0.562	SUBCLONAL	2	TRUE	2	0.466886155152707	5		324	768	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163297	32163297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1239036035	NA	P-0056800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	390	851	0	ENST00000375023.3:c.5929G>A	p.Glu1977Lys	p.E1977K	ENST00000375023	NM_004557.3	1977	Gag/Aag	30/30	0.374500072324351	4	FACETS	0.962	0.914	1	0.962	0.914	1	CLONAL	2	TRUE	2	0.466886155152707	4		851	1274	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0056800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	679	755	2	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	0.412542564613851	2	FACETS	0.846	0.821	0.871	1	0.997	1	CLONAL	3	TRUE	0	0.466886155152707	2		757	1146	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246473	46246473	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	121	221	0	ENST00000334344.6:c.4567G>C	p.Asp1523His	p.D1523H	ENST00000334344	NM_152641.2	1523	Gat/Cat	15/21	0.415822157771714	3	FACETS	0.809	0.738	0.883	0.809	0.738	0.883	CLONAL	2	TRUE	1	0.466886155152707	3		221	395	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358517	67358517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	138	309	0	ENST00000327367.4:c.25C>T	p.Pro9Ser	p.P9S	ENST00000327367	NM_005902.3	9	Ccc/Tcc	1/9	0.373951231061298	3	FACETS	0.844	0.775	0.915	0.844	0.775	0.915	CLONAL	2	TRUE	1	0.466886155152707	3		309	432	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918622	44918622	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	225	213	0	ENST00000377967.4:c.1105C>T	p.Gln369Ter	p.Q369*	ENST00000377967	NM_021140.2	369	Cag/Tag	12/29	0.357404382458447	2	FACETS	1	0.987	1			1	CLONAL	2	TRUE	NA	0.466886155152707	2		213	421	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183252	56183252	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	217	362	0	ENST00000399503.3:c.4162G>C	p.Asp1388His	p.D1388H	ENST00000399503	NM_005921.1	1388	Gat/Cat	18/20	0.390703385086214	2	FACETS	0.899	0.844	0.955	0.899	0.844	0.955	CLONAL	2	TRUE	0	0.466886155152707	2		362	517	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554808	106554808	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	149	291	1	ENST00000369096.4:c.1925G>T	p.Ser642Ile	p.S642I	ENST00000369096	NM_001198.3	642	aGc/aTc	7/7	0.374500072324351	4	FACETS	0.911	0.837	0.986	0.911	0.837	0.986	CLONAL	2	TRUE	2	0.466886155152707	4		292	514	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786887	135786887	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554817388	NA	P-0056800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	294	413	0	ENST00000298552.3:c.982C>T	p.Gln328Ter	p.Q328*	ENST00000298552	NM_001162426.1	328	Cag/Tag	10/23	0.466886155152707	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.466886155152707	2		413	585	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904961	101904961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	94	272	0	ENST00000374994.4:c.949C>T	p.His317Tyr	p.H317Y	ENST00000374994	NM_004612.2	317	Cac/Tac	5/9	0.466886155152707	2	FACETS	0.956	0.856	1	0.478	0.428	0.531	CLONAL	1	TRUE	0	0.466886155152707	2		272	421	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797226	45797226	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	281	623	1	ENST00000450313.1:c.1189C>A	p.Leu397Met	p.L397M	ENST00000450313	NM_012222.2	397	Ctg/Atg	13/16	0.373951231061298	3	FACETS	0.926	0.873	0.979	0.926	0.873	0.979	CLONAL	2	TRUE	1	0.466886155152707	3		624	802	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514314	69514314	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	120	523	0	ENST00000294312.3:c.367G>C	p.Glu123Gln	p.E123Q	ENST00000294312	NM_005117.2	123	Gag/Cag	3/3	0.466926684036882	3	FACETS	0.745	0.672	0.822	0.373	0.336	0.411	SUBCLONAL	1	TRUE	1	0.466886155152707	3		523	851	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124587	108124587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786202511	NA	P-0056800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	127	288	0	ENST00000278616.4:c.1945G>A	p.Glu649Lys	p.E649K	ENST00000278616	NM_000051.3	649	Gaa/Aaa	13/63	0.373951231061298	3	FACETS	1	0.983	1	0.679	0.619	0.742	CLONAL	1	TRUE	1	0.466886155152707	3		288	494	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95584060	95584060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	58	353	0	ENST00000393063.1:c.1408G>A	p.Glu470Lys	p.E470K	ENST00000393063	NM_030621.3	470	Gag/Aag	10/28	0.412542564613851	2	FACETS	0.571	0.492	0.657	0.286	0.246	0.329	SUBCLONAL	1	TRUE	0	0.466886155152707	2		353	435	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420000	41420000	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0056800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	160	467	0	ENST00000373198.4:c.321C>G	p.Tyr107Ter	p.Y107*	ENST00000373198	NM_133170.3	107	taC/taG	3/32	0.229145183893306	3	FACETS	1	0.978	1	0.588	0.54	0.638	INDETERMINATE	1	TRUE	1	0.466886155152707	3		467	719	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530425	187530425	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	167	270	1	ENST00000441802.2:c.10118C>A	p.Ser3373Ter	p.S3373*	ENST00000441802	NM_005245.3	3373	tCa/tAa	16/27	0.359598506906108	3	FACETS	1	0.973	1	0.728	0.677	0.78	CLONAL	2	TRUE	0	0.466886155152707	3		271	404	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183238	56183238	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	212	343	0	ENST00000399503.3:c.4148G>C	p.Arg1383Thr	p.R1383T	ENST00000399503	NM_005921.1	1383	aGa/aCa	18/20	0.390703385086214	2	FACETS	0.966	0.908	1	0.966	0.908	1	CLONAL	2	TRUE	0	0.466886155152707	2		343	470	SUCCESS
APC	324	MSKCC	GRCh37	5	112175996	112175996	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660740	NA	P-0056800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	92	204	0	ENST00000257430.4:c.4705G>A	p.Asp1569Asn	p.D1569N	ENST00000257430	NM_000038.5	1569	Gat/Aat	16/16	0.390703385086214	2	FACETS	0.755	0.681	0.831	0.755	0.681	0.831	SUBCLONAL	2	TRUE	0	0.466886155152707	2		204	261	SUCCESS
APC	324	MSKCC	GRCh37	5	112176002	112176002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	96	208	0	ENST00000257430.4:c.4711G>A	p.Asp1571Asn	p.D1571N	ENST00000257430	NM_000038.5	1571	Gat/Aat	16/16	0.390703385086214	2	FACETS	0.773	0.699	0.849	0.773	0.699	0.849	SUBCLONAL	2	TRUE	0	0.466886155152707	2		208	266	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200344	138200344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	282	419	0	ENST00000237289.4:c.1762G>A	p.Ala588Thr	p.A588T	ENST00000237289	NM_001270507.1	588	Gct/Act	7/9	0.374500072324351	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.466886155152707	4		419	840	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864087	97864087	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	253	556	1	ENST00000289081.3:c.1579G>C	p.Asp527His	p.D527H	ENST00000289081	NM_000136.2	527	Gac/Cac	15/15	0.466886155152707	2	FACETS	0.918	0.867	0.971	0.918	0.867	0.971	CLONAL	2	TRUE	0	0.466886155152707	2		557	590	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941837	44941837	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	213	163	0	ENST00000377967.4:c.3161G>C	p.Arg1054Thr	p.R1054T	ENST00000377967	NM_021140.2	1054	aGa/aCa	21/29	0.357404382458447	2	FACETS	1	0.99	1			1	CLONAL	2	TRUE	NA	0.466886155152707	2		163	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0056801-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	93	722	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.306668102872705	1	FACETS	0.965	0.861	1	0.965	0.861	1	CLONAL	1	TRUE	0	0.306668102872705	1		722	532	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0056801-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	46	348	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.993	0.841	1	0.993	0.841	1	CLONAL	1	TRUE	1	0.306668102872705	2		348	302	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604750	48604750	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1568211588	NA	P-0056801-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	71	404	0	ENST00000342988.3:c.1572G>A	p.Trp524Ter	p.W524*	ENST00000342988	NM_005359.5	524	tgG/tgA	12/12	0.293890518186167	1	FACETS	0.952	0.834	1	0.952	0.834	1	CLONAL	1	TRUE	0	0.306668102872705	1		404	412	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244214	153244214	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056801-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	39	445	0	ENST00000281708.4:c.1943T>C	p.Leu648Pro	p.L648P	ENST00000281708	NM_033632.3	648	cTa/cCa	12/12	1	2	FACETS	0.633	0.525	0.753	0.633	0.525	0.753	SUBCLONAL	1	TRUE	1	0.306668102872705	2		445	402	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970969	21970969	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056801-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	78	761	0	ENST00000304494.5:c.389del	p.Leu130ArgfsTer16	p.L130Rfs*16	ENST00000304494	NM_000077.4	130	cTg/cg	2/3	1	2	FACETS	0.949	0.836	1	0.949	0.836	1	CLONAL	1	TRUE	1	0.306668102872705	2		761	536	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007635	45007635	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	47	287	1	ENST00000558401.1:c.82C>T	p.Gln28Ter	p.Q28*	ENST00000558401	NM_004048.2	28	Cag/Tag	2/4	0.234316677352025	3	FACETS	0.636	0.537	0.746	0.212	0.179	0.249	SUBCLONAL	1	FALSE	0	0.358359308085207	3		288	486	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121913370	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	79	236	0	ENST00000288602.6:c.1742A>G	p.Asn581Ser	p.N581S	ENST00000288602	NM_004333.4	581	aAt/aGt	15/18	0.358359308085207	5	FACETS	1	0.973	1	0.464	0.409	0.523	CLONAL	1	FALSE	2	0.358359308085207	5		236	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	580	777	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.358359308085207	5	FACETS	0.974	0.939	1	0.779	0.751	0.808	CLONAL	4	FALSE	0	0.358359308085207	5		777	1277	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	64	455	0	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	0.32885999642973	5	FACETS	0.685	0.592	0.786	0.228	0.197	0.262	SUBCLONAL	1	FALSE	2	0.358359308085207	5		455	802	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520327	176520327	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs762709356	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	116	676	2	ENST00000292408.4:c.1246C>T	p.Arg416Ter	p.R416*	ENST00000292408	NM_213647.1	416	Cga/Tga	9/18	0.357481458484136	4	FACETS	0.99	0.892	1	0.33	0.297	0.365	CLONAL	1	FALSE	1	0.358359308085207	4		678	888	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164591	47164591	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	104	296	0	ENST00000409792.3:c.1535C>G	p.Ser512Ter	p.S512*	ENST00000409792	NM_014159.6	512	tCa/tGa	3/21	0.358385167880537	4	FACETS	0.774	0.696	0.857	0.516	0.464	0.571	SUBCLONAL	2	FALSE	1	0.358359308085207	4		296	509	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945263	54945263	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	79	359	0	ENST00000312783.6:c.1163C>G	p.Ser388Ter	p.S388*	ENST00000312783	NM_198436.1	388	tCa/tGa	10/10	0.358359308085207	6	FACETS	1	0.912	1	0.348	0.306	0.394	CLONAL	1	FALSE	3	0.358359308085207	6		359	724	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007768	45007768	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	120	387	0	ENST00000558401.1:c.215C>G	p.Ser72Ter	p.S72*	ENST00000558401	NM_004048.2	72	tCa/tGa	2/4	0.234316677352025	3	FACETS	1	0.96	1	0.372	0.336	0.41	CLONAL	1	FALSE	0	0.358359308085207	3		387	708	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792825	33792825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755311871	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	76	264	0	ENST00000498907.2:c.496G>A	p.Glu166Lys	p.E166K	ENST00000498907	NM_004364.3	166	Gag/Aag	1/1	0.350021999386699	4	FACETS	1	0.968	1	0.655	0.576	0.738	CLONAL	1	FALSE	2	0.358359308085207	4		264	440	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466006	69466006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	186	918	1	ENST00000227507.2:c.844G>A	p.Asp282Asn	p.D282N	ENST00000227507	NM_053056.2	282	Gac/Aac	5/5	0.102808319470208	6	FACETS	1	0.989	1			1	INDETERMINATE	1	FALSE	NA	0.358359308085207	6		919	1199	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228399	228399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	103	448	0	ENST00000264932.6:c.721G>A	p.Asp241Asn	p.D241N	ENST00000264932	NM_004168.2	241	Gac/Aac	6/15	0.358359308085207	6	FACETS	1	0.917	1	0.344	0.307	0.383	CLONAL	1	FALSE	3	0.358359308085207	6		448	957	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871836	12871836	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	89	289	0	ENST00000228872.4:c.553G>C	p.Glu185Gln	p.E185Q	ENST00000228872	NM_004064.3	185	Gag/Cag	2/3	0.358359308085207	5	FACETS	1	0.96	1	0.592	0.525	0.663	CLONAL	1	FALSE	3	0.358359308085207	5		289	645	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962592	38962592	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	127	361	0	ENST00000357387.3:c.1663C>G	p.Leu555Val	p.L555V	ENST00000357387	NM_152756.3	555	Ctt/Gtt	18/38	0.358359308085207	8	FACETS	0.834	0.755	0.917	0.417	0.377	0.459	CLONAL	2	FALSE	4	0.358359308085207	8		361	882	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913823	32913823	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	311	374	0	ENST00000380152.3:c.5331G>C	p.Lys1777Asn	p.K1777N	ENST00000380152		1777	aaG/aaC	11/27	0.358359308085207	5	FACETS	0.945	0.897	0.993	0.945	0.897	0.993	CLONAL	4	FALSE	1	0.358359308085207	5		374	706	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026622	6026622	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	208	925	0	ENST00000265849.7:c.1774C>G	p.Gln592Glu	p.Q592E	ENST00000265849	NM_000535.5	592	Caa/Gaa	11/15	0.350021999386699	4	FACETS	1	0.973	1	0.553	0.511	0.596	CLONAL	1	FALSE	2	0.358359308085207	4		925	1427	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422465	225422465	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	395	354	0	ENST00000264414.4:c.175A>G	p.Arg59Gly	p.R59G	ENST00000264414	NM_003590.4	59	Aga/Gga	2/16	0.358359308085207	7	FACETS	1	0.981	1			1	CLONAL	4	FALSE	NA	0.358359308085207	7		354	991	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402045	402045	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	138	487	0	ENST00000399788.2:c.4746G>C	p.Lys1582Asn	p.K1582N	ENST00000399788	NM_001042603.1	1582	aaG/aaC	27/28	0.102808319470208	6	FACETS	0.911	0.83	0.995			1	INDETERMINATE	2	FALSE	NA	0.358359308085207	6		487	726	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120805869	120805869	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1283	196	875	1	ENST00000257552.2:c.209A>T	p.Asp70Val	p.D70V	ENST00000257552	NM_002442.3	70	gAc/gTc	4/15	0.358359308085207	5	FACETS	1	0.976	1	0.284	0.262	0.308	CLONAL	1	FALSE	1	0.358359308085207	5		876	1479	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2090220	2090220	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	196	869	0	ENST00000219066.1:c.729C>A	p.His243Gln	p.H243Q	ENST00000219066	NM_002528.5	243	caC/caA	5/6	0.32885999642973	5	FACETS	1	0.989	1	0.469	0.433	0.506	CLONAL	1	FALSE	2	0.358359308085207	5		869	1196	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351506	89351506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	184	777	1	ENST00000301030.4:c.1444G>A	p.Glu482Lys	p.E482K	ENST00000301030	NM_001256183.1	482	Gag/Aag	9/13	0.32885999642973	5	FACETS	1	0.989	1	0.494	0.455	0.534	CLONAL	1	FALSE	2	0.358359308085207	5		778	1065	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3094689	3094689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	36	331	0	ENST00000078429.4:c.40G>A	p.Glu14Lys	p.E14K	ENST00000078429	NM_002067.2	14	Gag/Aag	1/7	0.157034706501226	3	FACETS	0.528	0.434	0.633			1	INDETERMINATE	1	FALSE	NA	0.358359308085207	3		331	449	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225367790	225367790	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	80	268	1	ENST00000264414.4:c.1378-1G>T		p.X460_splice	ENST00000264414	NM_003590.4	460			0.358359308085207	7	FACETS	1	0.97	1			1	CLONAL	1	FALSE	NA	0.358359308085207	7		269	631	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39746816	39746816	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	130	494	0	ENST00000361337.2:c.1830G>C	p.Glu610Asp	p.E610D	ENST00000361337	NM_003286.2	610	gaG/gaC	18/21	0.350021999386699	4	FACETS	1	0.94	1	0.525	0.475	0.577	CLONAL	1	FALSE	2	0.358359308085207	4		494	939	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42870072	42870072	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	164	646	0	ENST00000398585.3:c.100G>T	p.Asp34Tyr	p.D34Y	ENST00000398585	NM_001135099.1	34	Gat/Tat	2/14	0.204511269263881	4	FACETS	0.805	0.74	0.873	0.805	0.74	0.873	INDETERMINATE	2	FALSE	2	0.358359308085207	4		646	772	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426070	138426070	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	99	397	0	ENST00000289153.2:c.1461T>G	p.Asn487Lys	p.N487K	ENST00000289153	NM_006219.2	487	aaT/aaG	9/22	0.358359308085207	5	FACETS	1	0.941	1			1	CLONAL	1	FALSE	NA	0.358359308085207	5		397	786	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801524	1801524	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	176	932	1	ENST00000260795.2:c.430A>T	p.Thr144Ser	p.T144S	ENST00000260795		144	Aca/Tca	3/17	0.350021999386699	4	FACETS	1	0.983	1	0.629	0.579	0.682	CLONAL	1	FALSE	2	0.358359308085207	4		933	1060	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964923	55964924	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	115	338	0	ENST00000263923.4:c.2313_2314delinsTT	p.Ala772Ser	p.A772S	ENST00000263923	NM_002253.2	771	acGGcg/acTTcg	16/30	0.157623600998283	5	FACETS	0.894	0.808	0.984	0.596	0.539	0.656	INDETERMINATE	2	FALSE	2	0.358359308085207	5		338	552	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99806101	99806101	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	51	158	0	ENST00000280892.6:c.571G>C	p.Glu191Gln	p.E191Q	ENST00000280892	NM_001130678.1	191	Gaa/Caa	6/7	0.358359308085207	5	FACETS	0.784	0.671	0.906	0.523	0.447	0.604	CLONAL	2	FALSE	2	0.358359308085207	5		158	279	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418977	116418977	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	75	322	0	ENST00000397752.3:c.3488G>T	p.Gly1163Val	p.G1163V	ENST00000397752	NM_000245.2	1163	gGa/gTa	17/21	0.358359308085207	5	FACETS	1	0.952	1	0.391	0.343	0.442	CLONAL	1	FALSE	2	0.358359308085207	5		322	549	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738798	145738798	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1309	490	1259	0	ENST00000428558.2:c.2267T>C	p.Val756Ala	p.V756A	ENST00000428558	NM_004260.3	756	gTa/gCa	14/22	0.358359308085207	6	FACETS	0.87	0.83	0.91	0.87	0.83	0.91	CLONAL	3	FALSE	3	0.358359308085207	6		1259	1799	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484345	8484345	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	184	366	0	ENST00000356435.5:c.3187G>T	p.Val1063Leu	p.V1063L	ENST00000356435		1063	Gtg/Ttg	19/35	0.265906878101523	3	FACETS	1	0.98	1	0.76	0.707	0.815	CLONAL	2	FALSE	0	0.358359308085207	3		366	531	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325559	87325559	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	153	350	0	ENST00000277120.3:c.436G>T	p.Val146Leu	p.V146L	ENST00000277120		146	Gtg/Ttg	6/19	0.280643775628233	3	FACETS	1	0.968	1	0.728	0.672	0.786	CLONAL	2	FALSE	0	0.358359308085207	3		350	461	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426732	47426732	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1313544010	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	204	423	0	ENST00000377045.4:c.977G>A	p.Arg326Gln	p.R326Q	ENST00000377045	NM_001654.4	326	cGa/cAa	10/16	0.358359308085207	3	FACETS	0.857	0.797	0.919			1	CLONAL	2	FALSE	NA	0.358359308085207	3		423	783	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879732	123879732	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	27	41	0	ENST00000330479.4:c.428C>G	p.Ser143Ter	p.S143*	ENST00000330479	NM_020382.3	143	tCa/tGa	4/9	0.358359308085207	5	FACETS	1	0.888	1	0.827	0.684	0.977	CLONAL	3	FALSE	1	0.358359308085207	5		41	70	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942173	81942174	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	T	novel	NA	P-0056802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	106	634	0	ENST00000359376.3:c.1710_1711delinsT	p.Asn571MetfsTer27	p.N571Mfs*27	ENST00000359376	NM_002661.3	570	ccCAat/ccTat	17/33	0.32885999642973	5	FACETS	1	0.958	1	0.378	0.338	0.42	CLONAL	1	FALSE	2	0.358359308085207	5		634	803	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838389	156838389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1357016517	NA	P-0056812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	61	1472	0	ENST00000524377.1:c.667G>A	p.Glu223Lys	p.E223K	ENST00000524377	NM_002529.3	223	Gag/Aag	6/17	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.16	2		1472	675	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0056813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	54	597	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.241870121372334	2		597	386	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0056813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	45	645	2	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.241870121372334	2		647	270	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160227	22160227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	30	372	0	ENST00000215832.6:c.404G>A	p.Arg135Lys	p.R135K	ENST00000215832	NM_002745.4	135	aGa/aAa	3/9	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.241870121372334	2		372	218	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828782	72828782	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0056813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	32	817	0	ENST00000268489.5:c.7799C>G	p.Ser2600Ter	p.S2600*	ENST00000268489	NM_006885.3	2600	tCa/tGa	9/10	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.241870121372334	2		817	237	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0056813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	32	378	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.241870121372334	2		378	207	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786767	3786767	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587783495	NA	P-0056813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	41	723	2	ENST00000262367.5:c.4444T>G	p.Tyr1482Asp	p.Y1482D	ENST00000262367	NM_004380.2	1482	Tac/Gac	27/31	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.241870121372334	2		725	241	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100403	8100403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	18	1476	1	ENST00000346208.3:c.377C>T	p.Ser126Phe	p.S126F	ENST00000346208		126	tCc/tTc	3/6	0.211434462280909	1	FACETS	0.451	0.339	0.583	0.451	0.339	0.583	SUBCLONAL	1	TRUE	0	0.241870121372334	1		1477	290	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513574	41513574	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	26	753	0	ENST00000263253.7:c.478C>T	p.Gln160Ter	p.Q160*	ENST00000263253	NM_001429.3	160	Cag/Tag	2/31	1	2	FACETS	0.746	0.592	0.922	0.746	0.592	0.922	CLONAL	1	TRUE	1	0.241870121372334	2		753	288	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0056813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	61	221	1				ENST00000310581	NM_198253.2	-/1132			0.22868064873168	4	FACETS	0.91	0.802	1			1	CLONAL	4	TRUE	NA	0.241870121372334	4		222	172	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041576	47041576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	32	622	0	ENST00000377604.3:c.1801C>T	p.Gln601Ter	p.Q601*	ENST00000377604	NM_001204468.1	601	Cag/Tag	17/24	0.175840853296286	2	FACETS	1	0.881	1			1	CLONAL	2	TRUE	NA	0.241870121372334	2		622	122	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427764	72427764	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	25	411	0	ENST00000477973.2:c.726G>C	p.Arg242Ser	p.R242S	ENST00000477973	NM_012234.5	242	agG/agC	4/4	1	2	FACETS	0.837	0.662	1	0.837	0.662	1	CLONAL	1	TRUE	1	0.241870121372334	2		411	247	SUCCESS
CBL	867	MSKCC	GRCh37	11	119158623	119158623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	55	695	1	ENST00000264033.4:c.2003C>T	p.Ser668Leu	p.S668L	ENST00000264033	NM_005188.3	668	tCa/tTa	12/16	0.241870121372334	3	FACETS	1	0.965	1	0.724	0.622	0.834	CLONAL	1	TRUE	1	0.241870121372334	3		696	352	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517446	157517446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761133847	NA	P-0056813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	20	565	2	ENST00000346085.5:c.4010G>A	p.Arg1337Gln	p.R1337Q	ENST00000346085	NM_020732.3	1337	cGa/cAa	16/20	1	2	FACETS	0.742	0.569	0.942	0.742	0.569	0.942	CLONAL	1	TRUE	1	0.241870121372334	2		567	223	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097818	8097818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290396136	NA	P-0056813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	28	1089	1	ENST00000346208.3:c.200C>T	p.Ser67Leu	p.S67L	ENST00000346208		67	tCg/tTg	2/6	0.211434462280909	1	FACETS	0.757	0.607	0.926	0.757	0.607	0.926	CLONAL	1	TRUE	0	0.241870121372334	1		1090	269	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003132	42003132	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1363709175	NA	P-0056813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	43	778	0	ENST00000219905.7:c.2669C>G	p.Ser890Cys	p.S890C	ENST00000219905	NM_001164273.1	890	tCt/tGt	8/24	0.211434462280909	1	FACETS	0.885	0.743	1	0.885	0.743	1	CLONAL	1	TRUE	0	0.241870121372334	1		778	353	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347768	347768	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	56	1557	0	ENST00000262320.3:c.1738G>C	p.Glu580Gln	p.E580Q	ENST00000262320	NM_003502.3	580	Gag/Cag	6/11	1	2	FACETS	0.81	0.699	0.928	1	0.972	1	CLONAL	2	TRUE	1	0.241870121372334	2		1557	286	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639171	3639171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1378182049	NA	P-0056813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	69	1400	1	ENST00000294008.3:c.4468G>A	p.Glu1490Lys	p.E1490K	ENST00000294008	NM_032444.2	1490	Gag/Aag	12/15	1	2	FACETS	0.911	0.8	1	1	0.98	1	CLONAL	2	TRUE	1	0.241870121372334	2		1401	313	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37672051	37672051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	45	546	1	ENST00000447079.4:c.2836G>A	p.Glu946Lys	p.E946K	ENST00000447079	NM_015083.1	946	Gaa/Aaa	9/14	1	2	FACETS	0.974	0.821	1	0.974	0.821	1	CLONAL	1	TRUE	1	0.241870121372334	2		547	382	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865298	40865298	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	53	920	1	ENST00000428826.2:c.1133C>T	p.Ser378Phe	p.S378F	ENST00000428826		378	tCt/tTt	11/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.241870121372334	2		921	340	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220291	5220291	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	22	1074	0	ENST00000357368.4:c.3529G>A	p.Glu1177Lys	p.E1177K	ENST00000357368	NM_002850.3	1177	Gag/Aag	21/38	0.158824430688778	0	FACETS	0.663	0.516	0.832			1	SUBCLONAL	1	TRUE	0	0.241870121372334	0		1074	208	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10244895	10244895	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0056813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	24	1302	0	ENST00000340748.4:c.4814C>G	p.Ser1605Ter	p.S1605*	ENST00000340748		1605	tCa/tGa	39/40	0.158824430688778	0	FACETS	0.579	0.455	0.721			1	SUBCLONAL	1	TRUE	0	0.241870121372334	0		1302	260	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218684	36218684	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	84	1238	0	ENST00000222270.7:c.4388C>T	p.Ser1463Phe	p.S1463F	ENST00000222270	NM_014727.1	1463	tCt/tTt	17/37	0.241870121372334	2	FACETS	0.87	0.779	0.965	1	0.974	1	CLONAL	3	TRUE	0	0.241870121372334	2		1238	266	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940037	49940037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146988970	NA	P-0056813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	21	1392	0	ENST00000296474.3:c.1006G>A	p.Glu336Lys	p.E336K	ENST00000296474	NM_002447.2	336	Gag/Aag	1/20	1	2	FACETS	0.811	0.627	1	0.811	0.627	1	CLONAL	1	TRUE	1	0.241870121372334	2		1392	214	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969386	44969387	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CATTGCCAAGATTGTGCACGAAAAACAAGCGG	novel	NA	P-0056813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	40	282	0	ENST00000377967.4:c.4069_4100dup	p.Asn1368IlefsTer19	p.N1368Ifs*19	ENST00000377967	NM_021140.2	1356	-/CATTGCCAAGATTGTGCACGAAAAACAAGCGG	28/29	0.175840853296286	2	FACETS	1	0.935	1			1	CLONAL	1	TRUE	NA	0.241870121372334	2		282	264	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0056814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	65	613	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.891	0.771	1	0.891	0.771	1	CLONAL	1	TRUE	1	0.18	2		613	811	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560514	65560514	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	94	602	0	ENST00000358664.4:c.83A>G	p.His28Arg	p.H28R	ENST00000358664	NM_002382.4	28	cAt/cGt	3/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.18	2		602	720	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748309	41748309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs894529129	NA	P-0056814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	92	1277	1	ENST00000226382.2:c.460C>T	p.Arg154Cys	p.R154C	ENST00000226382	NM_003924.3	154	Cgc/Tgc	3/3	1	2	FACETS	0.832	0.737	0.935	0.832	0.737	0.935	CLONAL	1	TRUE	1	0.18	2		1278	1228	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845561	63845565	+	frameshift_variant	Frame_Shift_Del	DEL	AACAA	AACAA	-	novel	NA	P-0056814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	26	325	0	ENST00000279873.7:c.1307_1311del	p.Thr436SerfsTer10	p.T436Sfs*10	ENST00000279873	NM_032199.2	434	AACAAa/a	9/10	1	2	FACETS	0.842	0.667	1	0.842	0.667	1	CLONAL	1	TRUE	1	0.18	2		325	343	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100344	27100345	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0056814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	60	1001	0	ENST00000324856.7:c.4058_4059del	p.Pro1353LeufsTer91	p.P1353Lfs*91	ENST00000324856	NM_006015.4	1352	agCCcc/agcc	17/20	1	2	FACETS	0.675	0.579	0.779	0.675	0.579	0.779	SUBCLONAL	1	TRUE	1	0.18	2		1001	988	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685268	89685268	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1085308043	NA	P-0056814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	35	181	0	ENST00000371953.3:c.165-2A>G		p.X55_splice	ENST00000371953	NM_000314.4	55			1	2	FACETS	0.926	0.766	1	1	0.962	1	CLONAL	2	TRUE	1	0.18	2		181	210	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11015733	11015733	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	40	746	0	ENST00000327064.4:c.327C>G	p.Ile109Met	p.I109M	ENST00000327064	NM_199141.1	109	atC/atG	2/16	1	2	FACETS	0.641	0.531	0.764	0.641	0.531	0.764	SUBCLONAL	1	TRUE	1	0.18	2		746	693	SUCCESS
APC	324	MSKCC	GRCh37	5	112173345	112173345	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	57	314	0	ENST00000257430.4:c.2054G>A	p.Trp685Ter	p.W685*	ENST00000257430	NM_000038.5	685	tGg/tAg	16/16	0.479195583873479	3	FACETS	1	0.958	1	0.628	0.547	0.713	CLONAL	1	TRUE	1	0.602451906559233	3		314	196	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913527	NA	P-0056815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	151	510	1	ENST00000311936.3:c.436G>C	p.Ala146Pro	p.A146P	ENST00000311936	NM_004985.3	146	Gca/Cca	4/5	0.296338373883744	4	FACETS	1	0.98	1	0.826	0.777	0.875	INDETERMINATE	3	TRUE	0	0.602451906559233	4		511	243	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739894	41739894	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	73	676	0	ENST00000242208.4:c.79G>A	p.Glu27Lys	p.E27K	ENST00000242208	NM_002192.2	27	Gag/Aag	2/3	0.602451906559233	3	FACETS	0.534	0.468	0.606	0.267	0.234	0.303	SUBCLONAL	1	TRUE	1	0.602451906559233	3		676	590	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169001	11169001	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	514	1112	0	ENST00000358026.2:c.4591G>A	p.Glu1531Lys	p.E1531K	ENST00000358026	NM_001128849.1	1531	Gag/Aag	32/36	0.587172147773436	2	FACETS	0.986	0.953	1	0.986	0.953	1	CLONAL	2	TRUE	0	0.602451906559233	2		1112	865	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165707	118165707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	48	502	0	ENST00000369448.3:c.217G>A	p.Gly73Ser	p.G73S	ENST00000369448	NM_017709.3	73	Ggc/Agc	2/2	0.314930978527538	1	FACETS	0.32	0.271	0.373	0.32	0.271	0.373	INDETERMINATE	1	TRUE	0	0.602451906559233	1		502	348	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912054	32912054	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	64	723	0	ENST00000380152.3:c.3562A>T	p.Ile1188Phe	p.I1188F	ENST00000380152		1188	Att/Ttt	11/27	0.602451906559233	5	FACETS	0.53	0.458	0.608	0.133	0.114	0.152	SUBCLONAL	1	TRUE	1	0.602451906559233	5		723	763	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409436	31409436	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	70	368	0	ENST00000344624.3:c.3671T>G	p.Phe1224Cys	p.F1224C	ENST00000344624		1224	tTt/tGt	29/33	0.479195583873479	3	FACETS	0.911	0.814	1	0.911	0.814	1	CLONAL	2	TRUE	1	0.602451906559233	3		368	166	SUCCESS
APC	324	MSKCC	GRCh37	5	112175531	112175532	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0056815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	141	352	0	ENST00000257430.4:c.4241_4242dup	p.Ser1415Ter	p.S1415*	ENST00000257430	NM_000038.5	1414	gta/gTAta	16/16	0.479195583873479	3	FACETS	0.783	0.721	0.846	0.783	0.721	0.846	SUBCLONAL	2	TRUE	1	0.602451906559233	3		352	389	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0056832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	352	517	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.346964484880314	2	FACETS	0.999	0.948	1	0.999	0.948	1	CLONAL	2	TRUE	0	0.346964484880314	2		517	1016	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060910	38060926	+	frameshift_variant	Frame_Shift_Del	DEL	ATGGGGGGCGCAGTTGA	ATGGGGGGCGCAGTTGA	-	novel	NA	P-0056832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	95	786	1	ENST00000250448.2:c.1063_1079del	p.Ser355LysfsTer54	p.S355Kfs*54	ENST00000250448	NM_004496.3	355	TCAACTGCGCCCCCCATa/a	2/2	0.346964484880314	2	FACETS	0.511	0.453	0.572	0.255	0.226	0.286	SUBCLONAL	1	TRUE	0	0.346964484880314	2		787	1072	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37882814	37882814	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0056832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	175	775	0	ENST00000269571.5:c.2873-1G>C		p.X958_splice	ENST00000269571		958			1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.346964484880314	2		775	974	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610539	215610539	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	67	539	0	ENST00000260947.4:c.1717A>T	p.Ile573Leu	p.I573L	ENST00000260947	NM_000465.2	573	Ata/Tta	8/11	1	2	FACETS	0.569	0.494	0.65	0.569	0.494	0.65	SUBCLONAL	1	TRUE	1	0.346964484880314	2		539	679	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004735	16004743	+	frameshift_variant	Frame_Shift_Del	DEL	TTATCACCT	TTATCACCT	A	novel	NA	P-0056832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	181	740	0	ENST00000268712.3:c.2511_2519delinsT	p.Glu837AspfsTer9	p.E837Dfs*9	ENST00000268712	NM_006311.3	837	gaAGGTGATAAt/gaTt	20/46	0.346964484880314	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.346964484880314	1		740	848	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257524	16257524	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	66	447	1	ENST00000375759.3:c.4789G>T	p.Glu1597Ter	p.E1597*	ENST00000375759	NM_015001.2	1597	Gaa/Taa	11/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.352537925488052	2		448	291	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	45	346	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.79	0.667	0.925	0.79	0.667	0.925	CLONAL	1	TRUE	1	0.352537925488052	2		347	323	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	101	788	4	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.974	0.873	1	0.974	0.873	1	CLONAL	1	TRUE	1	0.352537925488052	2		792	588	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838380	156838380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202030811	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	130	1322	0	ENST00000524377.1:c.658C>T	p.Arg220Trp	p.R220W	ENST00000524377	NM_002529.3	220	Cgg/Tgg	6/17	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.352537925488052	2		1322	660	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604533	43604533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs546866208	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	120	898	1	ENST00000355710.3:c.1118C>T	p.Ala373Val	p.A373V	ENST00000355710	NM_020975.4	373	gCg/gTg	6/20	0.104939638699355	4	FACETS	1	0.984	1	0.733	0.664	0.806	INDETERMINATE	1	TRUE	2	0.352537925488052	4		899	628	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617452	43617452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	68	497	0	ENST00000355710.3:c.2789C>T	p.Thr930Met	p.T930M	ENST00000355710	NM_020975.4	930	aCg/aTg	16/20	0.104939638699355	4	FACETS	1	0.965	1	0.66	0.577	0.75	INDETERMINATE	1	TRUE	2	0.352537925488052	4		497	395	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63662114	63662114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	100	459	0	ENST00000279873.7:c.218C>T	p.Ser73Phe	p.S73F	ENST00000279873	NM_032199.2	73	tCt/tTt	2/10	0.104939638699355	4	FACETS	0.755	0.677	0.837	0.755	0.677	0.837	INDETERMINATE	2	TRUE	2	0.352537925488052	4		459	508	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309777	104309777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745958724	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	101	777	0	ENST00000369902.3:c.368G>A	p.Arg123His	p.R123H	ENST00000369902	NM_016169.3	123	cGt/cAt	3/12	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.352537925488052	2		777	513	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372449	118372451	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	novel	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	48	616	0	ENST00000534358.1:c.6386_6388del	p.Pro2129del	p.P2129del	ENST00000534358	NM_005933.3	2128	CCT/-	26/36	1	2	FACETS	0.612	0.518	0.715	0.612	0.518	0.715	SUBCLONAL	1	TRUE	1	0.352537925488052	2		616	445	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871052	12871053	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1555085575	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	52	515	0	ENST00000228872.4:c.285dup	p.Lys96GlnfsTer29	p.K96Qfs*29	ENST00000228872	NM_004064.3	93	-/C	1/3	1	2	FACETS	0.558	0.475	0.649	0.558	0.475	0.649	SUBCLONAL	1	TRUE	1	0.352537925488052	2		515	529	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871172	12871173	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	72	425	0	ENST00000228872.4:c.400_401del	p.Lys134AspfsTer2	p.K134Dfs*2	ENST00000228872	NM_004064.3	133	ccAAag/ccag	1/3	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.352537925488052	2		425	399	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246417	46246417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778810498	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	63	344	0	ENST00000334344.6:c.4511G>A	p.Arg1504Gln	p.R1504Q	ENST00000334344	NM_152641.2	1504	cGg/cAg	15/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.352537925488052	2		344	310	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012459	29012459	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	42	587	0	ENST00000282397.4:c.412A>T	p.Met138Leu	p.M138L	ENST00000282397	NM_002019.4	138	Atg/Ttg	4/30	1	2	FACETS	0.749	0.628	0.883	0.749	0.628	0.883	SUBCLONAL	1	TRUE	1	0.352537925488052	2		587	318	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068301	30068301	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	49	395	0	ENST00000331968.5:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000331968	NM_002742.2	700	Aaa/Gaa	15/18	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.352537925488052	2		395	265	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222600	2222600	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	28	824	0	ENST00000326181.6:c.794G>T	p.Gly265Val	p.G265V	ENST00000326181	NM_032271.2	265	gGg/gTg	9/21	1	2	FACETS	0.396	0.316	0.487	0.396	0.316	0.487	SUBCLONAL	1	TRUE	1	0.352537925488052	2		824	401	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274018	10274018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1354238435	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	139	1233	0	ENST00000330684.3:c.251C>T	p.Thr84Met	p.T84M	ENST00000330684	NM_001134407.1	84	aCg/aTg	2/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.352537925488052	2		1233	709	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832332	72832332	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	111	676	0	ENST00000268489.5:c.4249C>T	p.Gln1417Ter	p.Q1417*	ENST00000268489	NM_006885.3	1417	Cag/Tag	9/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.352537925488052	2		676	488	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877404	89877404	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	132	772	0	ENST00000389301.3:c.359G>A	p.Ser120Asn	p.S120N	ENST00000389301	NM_000135.2	120	aGc/aAc	4/43	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.352537925488052	2		772	622	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004808	16004808	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs76080188	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	116	773	3	ENST00000268712.3:c.2446G>A	p.Ala816Thr	p.A816T	ENST00000268712	NM_006311.3	816	Gct/Act	20/46	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.352537925488052	2		776	571	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696644	47696644	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	57	558	0	ENST00000347630.2:c.304T>C	p.Phe102Leu	p.F102L	ENST00000347630	NM_001007230.1	102	Ttc/Ctc	5/11	1	2	FACETS	0.84	0.723	0.966	0.84	0.723	0.966	CLONAL	1	TRUE	1	0.352537925488052	2		558	385	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436028	56436028	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	78	729	0	ENST00000407977.2:c.1109del	p.Pro370HisfsTer49	p.P370Hfs*49	ENST00000407977		370	cCa/ca	9/10	0.352537925488052	1	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	0	0.352537925488052	1		729	364	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	119	1208	4	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.352537925488052	2		1212	598	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122996	7122996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377722635	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	122	1053	2	ENST00000302850.5:c.3263G>A	p.Arg1088His	p.R1088H	ENST00000302850	NM_000208.2	1088	cGc/cAc	18/22	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.352537925488052	2		1055	684	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125293	7125293	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	81	782	1	ENST00000302850.5:c.3258+1G>A		p.X1086_splice	ENST00000302850	NM_000208.2	1086			1	2	FACETS	0.936	0.827	1	0.936	0.827	1	CLONAL	1	TRUE	1	0.352537925488052	2		783	491	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754054	42754055	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	98	795	0	ENST00000222329.4:c.297dup	p.Lys100GlufsTer21	p.K100Efs*21	ENST00000222329	NM_006494.2	99	-/G	3/4	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.352537925488052	2		795	547	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641432	47641433	+	inframe_insertion	In_Frame_Ins	INS	-	-	TAATCAAGT	novel	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	79	479	0	ENST00000233146.2:c.819_827dup	p.Lys275_Phe276insLeuIleLys	p.K275_F276insLIK	ENST00000233146	NM_000251.2	273	gta/gTAATCAAGTta	5/16	0.352537925488052	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.352537925488052	1		479	318	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268410	198268410	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	55	483	0	ENST00000335508.6:c.1618A>T	p.Met540Leu	p.M540L	ENST00000335508	NM_012433.2	540	Atg/Ttg	12/25	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.352537925488052	2		483	300	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439988	220439988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1341715949	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	133	1456	0	ENST00000243786.2:c.841G>A	p.Val281Met	p.V281M	ENST00000243786	NM_002191.3	281	Gtg/Atg	2/2	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.352537925488052	2		1456	696	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793340	242793340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201540918	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	142	1352	1	ENST00000334409.5:c.737C>T	p.Thr246Met	p.T246M	ENST00000334409	NM_005018.2	246	aCg/aTg	5/5	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.352537925488052	2		1353	711	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256319	46256319	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	40	306	0	ENST00000371998.3:c.547T>C	p.Trp183Arg	p.W183R	ENST00000371998		183	Tgg/Cgg	7/23	1	2	FACETS	0.978	0.82	1	0.978	0.82	1	CLONAL	1	TRUE	1	0.352537925488052	2		306	232	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274899	41274899	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	42	505	0	ENST00000349496.5:c.1149G>C	p.Trp383Cys	p.W383C	ENST00000349496	NM_001904.3	383	tgG/tgC	8/15	1	2	FACETS	0.722	0.605	0.851	0.722	0.605	0.851	SUBCLONAL	1	TRUE	1	0.352537925488052	2		505	330	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277336	41277336	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	56	325	0	ENST00000349496.5:c.1803+2T>C		p.X601_splice	ENST00000349496	NM_001904.3	601			1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.352537925488052	2		325	293	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55963870	55963870	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	74	504	0	ENST00000263923.4:c.2573A>G	p.Lys858Arg	p.K858R	ENST00000263923	NM_002253.2	858	aAg/aGg	18/30	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.352537925488052	2		504	415	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530398	187530398	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778500047	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	83	393	0	ENST00000441802.2:c.10145C>T	p.Ser3382Leu	p.S3382L	ENST00000441802	NM_005245.3	3382	tCg/tTg	16/27	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.352537925488052	2		393	420	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	63	395	1	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.352537925488052	2		396	299	SUCCESS
APC	324	MSKCC	GRCh37	5	112176740	112176740	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	17	287	0	ENST00000257430.4:c.5453del	p.Asn1818IlefsTer45	p.N1818Ifs*45	ENST00000257430	NM_000038.5	1817	Aaa/aa	16/16	0.352537925488052	1	FACETS	0.563	0.424	0.726	0.563	0.424	0.726	SUBCLONAL	1	TRUE	0	0.352537925488052	1		287	141	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969909	161969909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	113	796	0	ENST00000366898.1:c.1060G>T	p.Gly354Trp	p.G354W	ENST00000366898	NM_004562.2	354	Ggg/Tgg	9/12	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.352537925488052	2		796	614	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846161	128846161	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	115	945	0	ENST00000249373.3:c.1091C>G	p.Thr364Ser	p.T364S	ENST00000249373	NM_005631.4	364	aCc/aGc	5/12	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.352537925488052	2		945	632	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878995	151878995	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	97	652	1	ENST00000262189.6:c.5950C>A	p.Leu1984Ile	p.L1984I	ENST00000262189	NM_170606.2	1984	Cta/Ata	36/59	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.352537925488052	2		653	493	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900141	151900141	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	27	298	0	ENST00000262189.6:c.3970G>T	p.Glu1324Ter	p.E1324*	ENST00000262189	NM_170606.2	1324	Gag/Tag	26/59	1	2	FACETS	1	0.811	1	1	0.811	1	CLONAL	1	TRUE	1	0.352537925488052	2		298	152	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863264	56863264	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	85	689	0	ENST00000519728.1:c.408G>T	p.Arg136Ser	p.R136S	ENST00000519728	NM_002350.3	136	agG/agT	6/13	0.352537925488052	3	FACETS	1	0.954	1	0.574	0.509	0.643	CLONAL	1	TRUE	1	0.352537925488052	3		689	494	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786863	135786863	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs118203483	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	87	490	0	ENST00000298552.3:c.1006C>T	p.Arg336Trp	p.R336W	ENST00000298552	NM_001162426.1	336	Cgg/Tgg	10/23	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.352537925488052	2		490	436	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396860	139396860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368396893	NA	P-0056833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	105	986	2	ENST00000277541.6:c.5248G>A	p.Val1750Met	p.V1750M	ENST00000277541	NM_017617.3	1750	Gtg/Atg	28/34	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.352537925488052	2		988	579	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591931	48591931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	66	463	0	ENST00000342988.3:c.1094G>A	p.Gly365Asp	p.G365D	ENST00000342988	NM_005359.5	365	gGt/gAt	9/12	0.430577075881974	1	FACETS	0.978	0.859	1	0.978	0.859	1	CLONAL	1	TRUE	0	0.430577075881974	1		463	246	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207092	1207092	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555735008	NA	P-0056834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	105	1308	1	ENST00000326873.7:c.180del	p.Tyr60Ter	p.Y60*	ENST00000326873	NM_000455.4	60	taC/ta	1/10	0.430577075881974	1	FACETS	0.882	0.795	0.973	0.882	0.795	0.973	CLONAL	1	TRUE	0	0.430577075881974	1		1309	434	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563532	87563532	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	62	639	0	ENST00000277120.3:c.1920C>A	p.Asp640Glu	p.D640E	ENST00000277120		640	gaC/gaA	16/19	1	2	FACETS	0.809	0.703	0.923	0.809	0.703	0.923	CLONAL	1	TRUE	1	0.430577075881974	2		639	356	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152055	11152055	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs878854224	NA	P-0056835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	674	658	0	ENST00000358026.2:c.4339C>T	p.Arg1447Ter	p.R1447*	ENST00000358026	NM_001128849.1	1447	Cga/Tga	31/36	0.72271089155396	2	FACETS	0.99	0.965	1	0.99	0.965	1	CLONAL	2	TRUE	0	0.72271089155396	2		658	942	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0056835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	548	579	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.72271089155396	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.72271089155396	3		579	1003	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1206992	1206993	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1568689930	NA	P-0056835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	900	992	0	ENST00000326873.7:c.82dup	p.Arg28ProfsTer135	p.R28Pfs*135	ENST00000326873	NM_000455.4	27	cac/caCc	1/10	0.72271089155396	2	FACETS	0.989	0.968	1	0.989	0.968	1	CLONAL	2	TRUE	0	0.72271089155396	2		992	1259	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333579	70333579	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	415	510	0	ENST00000373644.4:c.1484G>T	p.Ser495Ile	p.S495I	ENST00000373644	NM_030625.2	495	aGc/aTc	2/12	0.385226883202134	3	FACETS	0.903	0.865	0.941	0.903	0.865	0.941	INDETERMINATE	2	TRUE	1	0.72271089155396	3		510	866	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610178	10610178	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1568401513	NA	P-0056835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	1010	1056	0	ENST00000171111.5:c.532C>T	p.Gln178Ter	p.Q178*	ENST00000171111	NM_203500.1	178	Cag/Tag	2/6	0.72271089155396	2	FACETS	0.999	0.979	1	0.999	0.979	1	CLONAL	2	TRUE	0	0.72271089155396	2		1056	1399	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023970	31023970	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1417772319	NA	P-0056835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	395	858	0	ENST00000375687.4:c.3455T>C	p.Leu1152Ser	p.L1152S	ENST00000375687	NM_015338.5	1152	tTa/tCa	13/13	0.385226883202134	3	FACETS	1	0.992	1	0.606	0.577	0.637	INDETERMINATE	1	TRUE	1	0.72271089155396	3		858	1227	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49941035	49941035	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	582	949	0	ENST00000296474.3:c.8T>C	p.Leu3Pro	p.L3P	ENST00000296474	NM_002447.2	3	cTc/cCc	1/20	0.671825389530512	2	FACETS	0.904	0.877	0.93	0.904	0.877	0.93	CLONAL	2	TRUE	0	0.72271089155396	2		949	891	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115749	8115750	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCAA	novel	NA	P-0056836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	77	576	1	ENST00000346208.3:c.1136_1137insACGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCA	p.Val378_His379insGlnArgLysMetSerSerLysSerLysLysCysLysLysVal	p.V378_H379insQRKMSSKSKKCKKV	ENST00000346208		365	-/CGAAAAATGTCTAGCAAATCCAAAAAGTGCAAAAAAGTGCAA	6/6	1	2	FACETS	0.552	0.485	0.623	0.552	0.485	0.623	SUBCLONAL	1	TRUE	1	0.545340885578917	2		577	512	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138472	11138472	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0056836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	161	694	0	ENST00000358026.2:c.3228C>G	p.Tyr1076Ter	p.Y1076*	ENST00000358026	NM_001128849.1	1076	taC/taG	24/36	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.545340885578917	2		694	503	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	277	324	0				ENST00000310581	NM_198253.2	-/1132			0.156330568862118	5	FACETS	0.838	0.795	0.882	0.838	0.795	0.882	INDETERMINATE	3	TRUE	2	0.865087256425801	5		324	585	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058033	27058033	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	239	650	1	ENST00000324856.7:c.1741C>T	p.Gln581Ter	p.Q581*	ENST00000324856	NM_006015.4	581	Cag/Tag	3/20	0.209484035515848	3	FACETS	1	0.984	1	0.568	0.533	0.604	INDETERMINATE	1	TRUE	1	0.865087256425801	3		651	697	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779654	3779654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	486	1273	0	ENST00000262367.5:c.5394G>A	p.Met1798Ile	p.M1798I	ENST00000262367	NM_004380.2	1798	atG/atA	31/31	0.196419951408157	3	FACETS	0.845	0.813	0.877	0.845	0.813	0.877	INDETERMINATE	2	TRUE	1	0.865087256425801	3		1273	952	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426022	49426022	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	353	1201	0	ENST00000301067.7:c.12466del	p.Gln4156AsnfsTer5	p.Q4156Nfs*5	ENST00000301067	NM_003482.3	4156	Caa/aa	39/54	0.196419951408157	3	FACETS	1	0.991	1	0.596	0.566	0.627	INDETERMINATE	1	TRUE	1	0.865087256425801	3		1201	980	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087939	27087939	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	408	759	0	ENST00000324856.7:c.2227del	p.Gln743AsnfsTer90	p.Q743Nfs*90	ENST00000324856	NM_006015.4	742	aaC/aa	6/20	0.209484035515848	3	FACETS	0.836	0.801	0.871	0.836	0.801	0.871	INDETERMINATE	2	TRUE	1	0.865087256425801	3		759	808	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467736	50467736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	367	859	0	ENST00000331340.3:c.971C>T	p.Ala324Val	p.A324V	ENST00000331340	NM_006060.4	324	gCc/gTc	8/8	0.198594929364404	5	FACETS	1	0.991	1	0.769	0.733	0.805	INDETERMINATE	2	TRUE	2	0.865087256425801	5		859	845	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860620	45860620	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	491	1285	0	ENST00000391945.4:c.1387C>A	p.Pro463Thr	p.P463T	ENST00000391945	NM_000400.3	463	Ccg/Acg	15/23	0.533074184089586	3	FACETS	1	0.994	1	0.617	0.591	0.644	CLONAL	1	TRUE	1	0.865087256425801	3		1285	1318	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430824	78430824	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	67	659	0	ENST00000370768.2:c.565G>C	p.Glu189Gln	p.E189Q	ENST00000370768	NM_003902.3	189	Gaa/Caa	8/20	0.156330568862118	5	FACETS	0.424	0.368	0.486	0.141	0.122	0.162	INDETERMINATE	1	TRUE	2	0.865087256425801	5		659	839	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755698	57755698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	560	1301	1	ENST00000274289.3:c.89C>T	p.Ser30Leu	p.S30L	ENST00000274289	NM_006622.3	30	tCg/tTg	1/14	0.156330568862118	5	FACETS	1	0.995	1	0.809	0.779	0.839	INDETERMINATE	2	TRUE	2	0.865087256425801	5		1302	1226	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256126	123256126	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	80	808	1	ENST00000358487.5:c.1783G>A	p.Glu595Lys	p.E595K	ENST00000358487	NM_000141.4	595	Gag/Aag	13/18	0.392882776898722	3	FACETS	0.307	0.27	0.348	0.154	0.135	0.174	INDETERMINATE	1	TRUE	1	0.865087256425801	3		809	862	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291048	11291048	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	212	605	0	ENST00000361445.4:c.2713A>G	p.Met905Val	p.M905V	ENST00000361445	NM_004958.3	905	Atg/Gtg	18/58	0.209484035515848	3	FACETS	1	0.982	1	0.571	0.533	0.609	INDETERMINATE	1	TRUE	1	0.865087256425801	3		605	615	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097692	8097692	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1469106968	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	524	806	0	ENST00000346208.3:c.74A>G	p.Asp25Gly	p.D25G	ENST00000346208		25	gAc/gGc	2/6	0.388982504661148	4	FACETS	1	0.996	1	1	0.996	1	INDETERMINATE	2	TRUE	2	0.865087256425801	4		806	927	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575476	64575476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	74	1150	2	ENST00000312049.6:c.541C>T	p.His181Tyr	p.H181Y	ENST00000312049	NM_130799.2	181	Cat/Tat	3/10	1	2	FACETS	0.19	0.165	0.216	0.19	0.165	0.216	SUBCLONAL	1	TRUE	1	0.865087256425801	2		1152	902	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196120	108196120	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	246	552	0	ENST00000278616.4:c.6656T>G	p.Phe2219Cys	p.F2219C	ENST00000278616	NM_000051.3	2219	tTt/tGt	46/63	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.865087256425801	2		552	510	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123841	46123847	+	frameshift_variant	Frame_Shift_Del	DEL	AAATCCC	AAATCCC	-	novel	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	130	425	0	ENST00000334344.6:c.107_113del	p.Lys36MetfsTer20	p.K36Mfs*20	ENST00000334344	NM_152641.2	36	aAAATCCCt/at	2/21	0.196419951408157	3	FACETS	1	0.949	1	0.525	0.48	0.571	INDETERMINATE	1	TRUE	1	0.865087256425801	3		425	410	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481602	56481602	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	83	825	0	ENST00000267101.3:c.637C>T	p.Gln213Ter	p.Q213*	ENST00000267101	NM_001982.3	213	Cag/Tag	6/28	0.196419951408157	3	FACETS	0.33	0.291	0.373	0.165	0.145	0.187	INDETERMINATE	1	TRUE	1	0.865087256425801	3		825	832	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481672	56481672	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	99	1051	0	ENST00000267101.3:c.707C>G	p.Ser236Ter	p.S236*	ENST00000267101	NM_001982.3	236	tCa/tGa	6/28	0.196419951408157	3	FACETS	0.322	0.287	0.36	0.161	0.143	0.18	INDETERMINATE	1	TRUE	1	0.865087256425801	3		1051	1017	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112892384	112892384	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	44	480	0	ENST00000351677.2:c.542T>G	p.Val181Gly	p.V181G	ENST00000351677	NM_002834.3	181	gTt/gGt	5/16	0.33208947698567	1	FACETS	0.136	0.114	0.161	0.136	0.114	0.161	INDETERMINATE	1	TRUE	0	0.865087256425801	1		480	423	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033960	49033960	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	428	401	0	ENST00000267163.4:c.2099del	p.Leu700TrpfsTer5	p.L700Wfs*5	ENST00000267163	NM_000321.2	699	caT/ca	20/27	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.865087256425801	2		401	478	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061568	38061569	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGGCTCATGCACGGGTTCATGGCGGCCGCGTA	novel	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	169	677	0	ENST00000250448.2:c.388_420dup	p.Tyr130_Pro140dup	p.Y130_P140dup	ENST00000250448	NM_004496.3	130	-/TACGCGGCCGCCATGAACCCGTGCATGAGCCCC	2/2	0.156330568862118	5	FACETS	1	0.982	1	0.41	0.377	0.444	INDETERMINATE	1	TRUE	2	0.865087256425801	5		677	730	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003068	42003068	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	59	790	0	ENST00000219905.7:c.2605G>C	p.Asp869His	p.D869H	ENST00000219905	NM_001164273.1	869	Gat/Cat	8/24	0.597482840442531	3	FACETS	0.211	0.181	0.245			1	SUBCLONAL	1	TRUE	NA	0.865087256425801	3		790	924	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035368	42035368	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1436121369	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	210	377	0	ENST00000219905.7:c.5210C>T	p.Pro1737Leu	p.P1737L	ENST00000219905	NM_001164273.1	1737	cCa/cTa	15/24	0.597482840442531	3	FACETS	1	0.992	1			1	CLONAL	1	TRUE	NA	0.865087256425801	3		377	472	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900722	3900722	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	87	932	0	ENST00000262367.5:c.374A>T	p.Gln125Leu	p.Q125L	ENST00000262367	NM_004380.2	125	cAg/cTg	2/31	0.196419951408157	3	FACETS	0.355	0.314	0.4	0.178	0.157	0.2	INDETERMINATE	1	TRUE	1	0.865087256425801	3		932	811	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89883011	89883011	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1204745684	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	242	629	0	ENST00000389301.3:c.13T>C	p.Trp5Arg	p.W5R	ENST00000389301	NM_000135.2	5	Tgg/Cgg	1/43	0.86513630096077	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.865087256425801	1		629	297	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270016	198270016	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	224	393	0	ENST00000335508.6:c.1420T>A	p.Tyr474Asn	p.Y474N	ENST00000335508	NM_012433.2	474	Tac/Aac	10/25	0.263772412380026	2	FACETS	1	0.992	1	0.664	0.629	0.698	INDETERMINATE	1	TRUE	0	0.865087256425801	2		393	390	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202123039	202123039	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	165	519	0	ENST00000358485.4:c.85G>T	p.Glu29Ter	p.E29*	ENST00000358485	NM_001080125.1	29	Gag/Tag	1/9	0.263772412380026	2	FACETS	0.757	0.7	0.815	0.378	0.35	0.408	INDETERMINATE	1	TRUE	0	0.865087256425801	2		519	504	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564739	41564739	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	80	741	0	ENST00000263253.7:c.4040G>A	p.Gly1347Glu	p.G1347E	ENST00000263253	NM_001429.3	1347	gGa/gAa	25/31	0.198594929364404	5	FACETS	0.456	0.4	0.516	0.152	0.133	0.172	INDETERMINATE	1	TRUE	2	0.865087256425801	5		741	932	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164504	47164504	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144677816	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	37	388	0	ENST00000409792.3:c.1622G>A	p.Arg541Gln	p.R541Q	ENST00000409792	NM_014159.6	541	cGa/cAa	3/21	0.390439576756763	5	FACETS	0.357	0.293	0.428	0.119	0.097	0.143	INDETERMINATE	1	TRUE	2	0.865087256425801	5		388	551	SUCCESS
ATR	545	MSKCC	GRCh37	3	142185171	142185171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	35	455	0	ENST00000350721.4:c.6892G>A	p.Asp2298Asn	p.D2298N	ENST00000350721	NM_001184.3	2298	Gat/Aat	40/47	0.390439576756763	5	FACETS	0.336	0.274	0.405	0.112	0.091	0.135	INDETERMINATE	1	TRUE	2	0.865087256425801	5		455	554	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430853	181430853	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	698	1499	0	ENST00000325404.1:c.705G>C	p.Met235Ile	p.M235I	ENST00000325404	NM_003106.3	235	atG/atC	1/1	0.390439576756763	5	FACETS	1	0.993	1	0.738	0.713	0.764	INDETERMINATE	2	TRUE	2	0.865087256425801	5		1499	1674	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155515	106155515	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	108	412	0	ENST00000380013.4:c.416C>G	p.Pro139Arg	p.P139R	ENST00000380013	NM_001127208.2	139	cCa/cGa	3/11	0.263772412380026	2	FACETS	0.655	0.593	0.72	0.328	0.296	0.36	INDETERMINATE	1	TRUE	0	0.865087256425801	2		412	381	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637865	176637865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377684553	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	79	621	1	ENST00000439151.2:c.2465C>T	p.Ser822Phe	p.S822F	ENST00000439151	NM_022455.4	822	tCt/tTt	5/23	0.392882776898722	3	FACETS	0.342	0.3	0.387	0.171	0.15	0.194	INDETERMINATE	1	TRUE	1	0.865087256425801	3		622	765	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5466772	5466772	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	11	115	0	ENST00000381577.3:c.793A>G	p.Arg265Gly	p.R265G	ENST00000381577	NM_014143.3	265	Aga/Gga	6/7	0.392882776898722	3	FACETS	0.258	0.179	0.356	0.129	0.089	0.178	INDETERMINATE	1	TRUE	1	0.865087256425801	3		115	141	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403348	139403348	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	506	1260	2	ENST00000277541.6:c.3145del	p.Gln1049ArgfsTer130	p.Q1049Rfs*130	ENST00000277541	NM_017617.3	1049	Cag/ag	19/34	0.196419951408157	3	FACETS	0.768	0.738	0.798	0.768	0.738	0.798	INDETERMINATE	2	TRUE	1	0.865087256425801	3		1262	1091	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164881	123164881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	33	189	0	ENST00000218089.9:c.194C>T	p.Ser65Phe	p.S65F	ENST00000218089	NM_001042749.1	65	tCt/tTt	5/35	0.484034085114423	2	FACETS	0.313	0.256	0.376			1	INDETERMINATE	1	TRUE	NA	0.865087256425801	2		189	244	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0056838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	619	508	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.379934658474604	5	FACETS	1	0.996	1	0.832	0.801	0.863	INDETERMINATE	2	TRUE	2	0.654754994477656	5		508	1502	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117811	108117811	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	102	377	0	ENST00000278616.4:c.1022T>C	p.Val341Ala	p.V341A	ENST00000278616	NM_000051.3	341	gTc/gCc	8/63	0.655205771981646	3	FACETS	0.795	0.714	0.881	0.398	0.357	0.441	SUBCLONAL	1	TRUE	1	0.654754994477656	3		377	520	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029507	14029507	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	190	435	0	ENST00000311895.7:c.1718T>G	p.Val573Gly	p.V573G	ENST00000311895	NM_005236.2	573	gTg/gGg	8/11	0.655205771981646	3	FACETS	1	0.958	1			1	CLONAL	1	TRUE	NA	0.654754994477656	3		435	735	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578543	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0056838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1379	645	1131	0	ENST00000269305.4:c.387_388del	p.Leu130GlnfsTer18	p.L130Qfs*18	ENST00000269305	NM_001126112.2	129	gcCCtc/gctc	5/11	0.379934658474604	5	FACETS	0.965	0.928	1	0.643	0.618	0.668	INDETERMINATE	2	TRUE	2	0.654754994477656	5		1131	2024	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985451	2985451	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0056838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	32	424	0	ENST00000396946.4:c.358+2T>G		p.X120_splice	ENST00000396946	NM_032415.4	120			0.655205771981646	2	FACETS	0.172	0.139	0.21	0.086	0.069	0.105	SUBCLONAL	1	TRUE	0	0.654754994477656	2		424	568	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115619	108115619	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs907941927	NA	P-0056839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	93	496	0	ENST00000278616.4:c.767A>T	p.Asp256Val	p.D256V	ENST00000278616	NM_000051.3	256	gAt/gTt	7/63	0.300751041497743	2	FACETS	0.864	0.778	0.954	0.864	0.778	0.954	CLONAL	2	TRUE	0	0.361018126188308	2		496	298	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954220	48954220	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	60	321	0	ENST00000267163.4:c.1421G>C	p.Ser474Thr	p.S474T	ENST00000267163	NM_000321.2	474	aGc/aCc	15/27	0.296083226004037	2	FACETS	0.947	0.82	1	0.473	0.41	0.542	CLONAL	1	TRUE	0	0.361018126188308	2		321	351	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440373	52440373	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	91	835	0	ENST00000460680.1:c.679del	p.Arg227AlafsTer4	p.R227Afs*4	ENST00000460680	NM_004656.3	227	Cgc/gc	9/17	0.300751041497743	2	FACETS	1	0.978	1	0.698	0.625	0.775	CLONAL	1	TRUE	0	0.361018126188308	2		835	361	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247306	153247306	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	87	372	0	ENST00000281708.4:c.1496del	p.Gly499ValfsTer25	p.G499Vfs*25	ENST00000281708	NM_033632.3	499	gGt/gt	10/12	0.296083226004037	2	FACETS	0.846	0.758	0.937	0.846	0.758	0.937	CLONAL	2	TRUE	0	0.361018126188308	2		372	285	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0056840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	529	508	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.979	0.953	1			1	CLONAL	7	FALSE	1	0.217769880005596	2		508	709	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0056840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	28	219	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.974	0.801	1	1	0.967	1	CLONAL	3	FALSE	1	0.217769880005596	2		219	88	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969966	81969966	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	108	535	0	ENST00000359376.3:c.3035T>C	p.Leu1012Pro	p.L1012P	ENST00000359376	NM_002661.3	1012	cTc/cCc	27/33	1	2	FACETS	0.984	0.893	1	1	0.991	1	CLONAL	3	FALSE	1	0.217769880005596	2		535	336	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944320	76944320	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	21	154	0	ENST00000373344.5:c.585del	p.Ile196PhefsTer10	p.I196Ffs*10	ENST00000373344	NM_000489.3	195	ctT/ct	7/35	0.217769880005596	2	FACETS	1	0.847	1			1	CLONAL	4	FALSE	NA	0.217769880005596	2		154	46	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0056841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	165	508	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.474651538982338	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	0	0.474651538982338	1		508	485	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933744	49933744	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs750582514	NA	P-0056841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	209	989	0	ENST00000296474.3:c.2533C>T	p.Arg845Ter	p.R845*	ENST00000296474	NM_002447.2	845	Cga/Tga	10/20	0.472365436615462	3	FACETS	1	0.983	1	0.393	0.365	0.422	CLONAL	1	FALSE	0	0.474651538982338	3		989	924	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194784	30194784	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	69	503	0	ENST00000331968.5:c.361A>G	p.Ser121Gly	p.S121G	ENST00000331968	NM_002742.2	121	Agt/Ggt	2/18	0.474651538982338	3	FACETS	0.676	0.59	0.769	0.338	0.295	0.385	SUBCLONAL	1	FALSE	1	0.474651538982338	3		503	532	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409795	139409795	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	215	1311	1	ENST00000277541.6:c.1961C>A	p.Thr654Asn	p.T654N	ENST00000277541	NM_017617.3	654	aCc/aAc	12/34	0.129810464007937	3	FACETS	0.969	0.899	1	0.323	0.299	0.347	INDETERMINATE	1	FALSE	0	0.474651538982338	3		1312	1157	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592119	67592120	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0056842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	87	264	0	ENST00000274335.5:c.1937_1938del	p.Phe646SerfsTer7	p.F646Sfs*7	ENST00000274335		645	acTTtt/actt	14/15	0.394083281216148	1	FACETS	0.59	0.531	0.65	0.59	0.531	0.65	INDETERMINATE	1	TRUE	0	0.763474051793498	1		264	239	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914430	32914430	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	16	432	0	ENST00000380152.3:c.5938A>G	p.Thr1980Ala	p.T1980A	ENST00000380152		1980	Aca/Gca	11/27	0.484204930796649	1	FACETS	0.393	0.298	0.499	0.393	0.298	0.499	SUBCLONAL	1	TRUE	0	0.763474051793498	1		432	66	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068967	30068967	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	80	510	0	ENST00000331968.5:c.1962A>T	p.Arg654Ser	p.R654S	ENST00000331968	NM_002742.2	654	agA/agT	14/18	0.247305090509716	4	FACETS	1	0.934	1	1	0.934	1	INDETERMINATE	2	TRUE	2	0.763474051793498	4		510	177	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061706	38061706	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	310	579	0	ENST00000250448.2:c.283del	p.Ser95AlafsTer2	p.S95Afs*2	ENST00000250448	NM_004496.3	95	Agc/gc	2/2	0.247305090509716	4	FACETS	0.763	0.721	0.805	0.763	0.721	0.805	INDETERMINATE	2	TRUE	2	0.763474051793498	4		579	939	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0056843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	38	278	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	0.362848495928723	3	FACETS	0.881	0.732	1	0.44	0.366	0.523	CLONAL	1	TRUE	1	0.362848495928723	3		278	281	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0056843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	124	400	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.362848495928723	5	FACETS	0.834	0.76	0.91	0.834	0.76	0.91	CLONAL	3	TRUE	2	0.362848495928723	5		400	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0056843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	241	1417	1	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	NA	2	FACETS	0.898	0.842	0.955			1	INDETERMINATE	2	TRUE	NA	0.362848495928723	2		1418	740	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619446	1619446	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	83	1186	0	ENST00000344749.5:c.1195G>T	p.Glu399Ter	p.E399*	ENST00000344749	NM_001136139.2	399	Gag/Tag	15/19	0.350417233814762	2	FACETS	0.698	0.617	0.786	0.349	0.308	0.393	SUBCLONAL	1	TRUE	0	0.362848495928723	2		1186	655	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398652	116398652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	46	337	0	ENST00000397752.3:c.2242C>T	p.His748Tyr	p.H748Y	ENST00000397752	NM_000245.2	748	Cat/Tat	9/21	0.362848495928723	3	FACETS	1	0.939	1	0.609	0.517	0.708	CLONAL	1	TRUE	1	0.362848495928723	3		337	246	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611803	100611803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	99	222	0	ENST00000308731.7:c.1318G>A	p.Asp440Asn	p.D440N	ENST00000308731	NM_000061.2	440	Gat/Aat	14/19	0.362848495928723	2	FACETS	1	0.969	1			1	CLONAL	2	TRUE	NA	0.362848495928723	2		222	237	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138902	64138905	+	missense_variant	Missense_Mutation	ONP	GCCT	GCCT	ACCG	novel	NA	P-0056843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	49	646	0	ENST00000334205.4:c.2269_2272delinsACCG	p.Ala757_Ser758delinsThrAla	p.A757_S758delinsTA	ENST00000334205	NM_003942.2	757	GCCTcc/ACCGcc	17/17	1	2	FACETS	0.667	0.566	0.777	0.667	0.566	0.777	SUBCLONAL	1	TRUE	1	0.362848495928723	2		646	405	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0056844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	13	118	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.259258771256863	1	FACETS	0.434	0.311	0.584	0.434	0.311	0.584	SUBCLONAL	1	TRUE	0	0.315109327031276	1		118	160	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99452077	99452077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1441621301	NA	P-0056844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	42	265	0	ENST00000268035.6:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000268035	NM_000875.3	471	Cgc/Tgc	6/21	1	2	FACETS	0.773	0.647	0.911	0.773	0.647	0.911	CLONAL	1	TRUE	1	0.315109327031276	2		265	345	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281360	49281360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201503697	NA	P-0056844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	199	787	0	ENST00000282018.3:c.407G>A	p.Arg136His	p.R136H	ENST00000282018	NM_020377.2	136	cGt/cAt	1/1	0.220885190954606	2	FACETS	1	0.988	1	0.676	0.627	0.728	CLONAL	1	TRUE	0	0.315109327031276	2		787	934	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579360	7579361	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	124	835	0	ENST00000269305.4:c.326dup	p.Arg110ProfsTer39	p.R110Pfs*39	ENST00000269305	NM_001126112.2	109	ttc/ttTc	4/11	0.259258771256863	1	FACETS	0.78	0.705	0.859	0.78	0.705	0.859	SUBCLONAL	1	TRUE	0	0.315109327031276	1		835	850	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260896	16260896	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	68	510	0	ENST00000375759.3:c.8161G>T	p.Ala2721Ser	p.A2721S	ENST00000375759	NM_015001.2	2721	Gcc/Tcc	11/15	0.259258771256863	1	FACETS	0.713	0.621	0.812	0.713	0.621	0.812	SUBCLONAL	1	TRUE	0	0.315109327031276	1		510	510	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004988	16004988	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	112	642	0	ENST00000268712.3:c.2266A>G	p.Thr756Ala	p.T756A	ENST00000268712	NM_006311.3	756	Acc/Gcc	20/46	0.259258771256863	1	FACETS	0.847	0.763	0.936	0.847	0.763	0.936	CLONAL	1	TRUE	0	0.315109327031276	1		642	707	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566436	41566436	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	56	229	0	ENST00000263253.7:c.4313G>A	p.Cys1438Tyr	p.C1438Y	ENST00000263253	NM_001429.3	1438	tGt/tAt	27/31	0.253407145271442	2	FACETS	1	0.931	1	0.566	0.488	0.65	CLONAL	1	TRUE	0	0.315109327031276	2		229	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0056845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	125	1250	1	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	1	2	FACETS	0.904	0.815	0.997	0.904	0.815	0.997	CLONAL	1	TRUE	1	0.216161530521993	2		1251	1280	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924336	112924336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507536	NA	P-0056847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	362	1238	0	ENST00000351677.2:c.1282G>A	p.Val428Met	p.V428M	ENST00000351677	NM_002834.3	428	Gtg/Atg	11/16	0.155424726149035	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.852039862423446	0		1238	943	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643384	52643384	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	244	561	1	ENST00000394830.3:c.2512G>T	p.Asp838Tyr	p.D838Y	ENST00000394830	NM_018313.4	838	Gat/Tat	17/30	0.852039862423446	1	FACETS	0.967	0.927	1	0.967	0.927	1	CLONAL	1	FALSE	0	0.852039862423446	1		562	340	SUCCESS
APC	324	MSKCC	GRCh37	5	112175549	112175549	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	300	389	0	ENST00000257430.4:c.4258C>G	p.Pro1420Ala	p.P1420A	ENST00000257430	NM_000038.5	1420	Ccc/Gcc	16/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.850618030614317	2		389	691	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650075	206650075	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1451035448	NA	P-0056848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	617	979	0	ENST00000367120.3:c.595G>A	p.Gly199Arg	p.G199R	ENST00000367120	NM_014002.3	199	Ggg/Agg	7/22	1	2	FACETS	0.944	0.909	0.98	0.944	0.909	0.98	CLONAL	1	TRUE	1	0.850618030614317	2		979	1536	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0056849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	36	597	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.74153652144428	2		597	94	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717729	89717729	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	51	273	0	ENST00000371953.3:c.754G>C	p.Asp252His	p.D252H	ENST00000371953	NM_000314.4	252	Gat/Cat	7/9	1	2	FACETS	0.537	0.461	0.62	0.537	0.461	0.62	SUBCLONAL	1	TRUE	1	0.74153652144428	2		273	256	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154282	2154282	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	143	919	1	ENST00000434045.2:c.646G>T	p.Ala216Ser	p.A216S	ENST00000434045	NM_001127598.1	216	Gct/Tct	5/5	0.345352478526142	1	FACETS	0.544	0.5	0.589	0.544	0.5	0.589	INDETERMINATE	1	TRUE	0	0.74153652144428	1		920	446	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154321	2154321	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150866176	NA	P-0056849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	148	1004	0	ENST00000434045.2:c.607G>A	p.Glu203Lys	p.E203K	ENST00000434045	NM_001127598.1	203	Gag/Aag	5/5	0.345352478526142	1	FACETS	0.514	0.472	0.556	0.514	0.472	0.556	INDETERMINATE	1	TRUE	0	0.74153652144428	1		1004	489	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245783	46245783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	57	261	0	ENST00000334344.6:c.3877C>T	p.Leu1293Phe	p.L1293F	ENST00000334344	NM_152641.2	1293	Ctt/Ttt	15/21	0.115515390442154	5	FACETS	1	0.922	1	0.712	0.625	0.802	INDETERMINATE	2	TRUE	2	0.74153652144428	5		261	152	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577500	7577512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TGGAGTCTTCCAG	TGGAGTCTTCCAG	-	novel	NA	P-0056849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	127	534	0	ENST00000269305.4:c.769_781del	p.Leu257ValfsTer84	p.L257Vfs*84	ENST00000269305	NM_001126112.2	257	CTGGAAGACTCCAgt/gt	7/11	0.648984396845889	1	FACETS	0.787	0.726	0.847	0.787	0.726	0.847	SUBCLONAL	1	TRUE	0	0.74153652144428	1		534	274	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562747	29562747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137854556	NA	P-0056849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	50	307	0	ENST00000356175.3:c.3827G>A	p.Arg1276Gln	p.R1276Q	ENST00000356175	NM_000267.3	1276	cGa/cAa	28/57	0.648984396845889	1	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	0	0.74153652144428	1		307	84	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591888	48591888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519739	NA	P-0056849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	51	363	0	ENST00000342988.3:c.1051G>A	p.Asp351Asn	p.D351N	ENST00000342988	NM_005359.5	351	Gat/Aat	9/12	0.68623817346066	1	FACETS	0.766	0.673	0.86	0.766	0.673	0.86	SUBCLONAL	1	TRUE	0	0.74153652144428	1		363	113	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220900	36220902	+	inframe_deletion	In_Frame_Del	DEL	GGT	GGT	-	novel	NA	P-0056849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	73	258	0	ENST00000222270.7:c.4952_4954del	p.Val1651del	p.V1651del	ENST00000222270	NM_014727.1	1650	acGGTg/acg	23/37	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.74153652144428	2		258	182	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743942	41743942	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	184	881	0	ENST00000301178.4:c.877C>G	p.Gln293Glu	p.Q293E	ENST00000301178	NM_021913.4	293	Cag/Gag	7/20	1	2	FACETS	0.896	0.833	0.961	0.896	0.833	0.961	CLONAL	1	TRUE	1	0.74153652144428	2		881	554	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162852	47162852	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	30	287	0	ENST00000409792.3:c.3274C>T	p.Gln1092Ter	p.Q1092*	ENST00000409792	NM_014159.6	1092	Caa/Taa	3/21	0.64507703987856	1	FACETS	0.636	0.531	0.747	0.636	0.531	0.747	SUBCLONAL	1	TRUE	0	0.74153652144428	1		287	80	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955231	1955231	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0056849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	82	403	0	ENST00000382891.5:c.2318C>G	p.Ser773Ter	p.S773*	ENST00000382891	NM_133335.3	773	tCa/tGa	12/22	0.74153652144428	1	FACETS	0.769	0.695	0.844	0.769	0.695	0.844	SUBCLONAL	1	TRUE	0	0.74153652144428	1		403	181	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148507499	148507499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	47	209	0	ENST00000320356.2:c.1955C>T	p.Ser652Phe	p.S652F	ENST00000320356	NM_004456.4	652	tCt/tTt	17/20	0.648984396845889	1	FACETS	0.917	0.809	1	0.917	0.809	1	CLONAL	1	TRUE	0	0.74153652144428	1		209	87	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151834000	151834000	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	67	294	0	ENST00000262189.6:c.14653G>C	p.Asp4885His	p.D4885H	ENST00000262189	NM_170606.2	4885	Gac/Cac	59/59	0.648984396845889	1	FACETS	0.763	0.682	0.845	0.763	0.682	0.845	SUBCLONAL	1	TRUE	0	0.74153652144428	1		294	149	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994146	21994146	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	113	562	0	ENST00000579755.1:c.185G>C	p.Arg62Thr	p.R62T	ENST00000579755		62	aGa/aCa	1/3	0.733805840104308		FACETS		0.629	0.747				SUBCLONAL	1	TRUE	0	0.74153652144428	1		562	279	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411411	63411411	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	31	663	0	ENST00000330258.3:c.1756C>T	p.Arg586Ter	p.R586*	ENST00000330258	NM_152424.3	586	Cga/Tga	2/2	0.74153652144428	1	FACETS	0.198	0.16	0.24	0.198	0.16	0.24	SUBCLONAL	1	TRUE	0	0.74153652144428	1		663	266	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0056851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	791	1005	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	0.775901116608315	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.775901116608315	1		1005	1169	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324681	31324681	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs137854653	NA	P-0056851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	120	658	0	ENST00000412585.2:c.127G>T	p.Glu43Ter	p.E43*	ENST00000412585	NM_005514.6	43	Gag/Tag	2/8	0.1699880470143	2	FACETS	0.351	0.316	0.387	0.175	0.158	0.194	INDETERMINATE	1	TRUE	0	0.775901116608315	2		658	882	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985543	2985543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	285	585	0	ENST00000396946.4:c.268G>T	p.Val90Phe	p.V90F	ENST00000396946	NM_032415.4	90	Gtc/Ttc	4/25	1	2	FACETS	0.766	0.721	0.812	0.766	0.721	0.812	SUBCLONAL	1	TRUE	1	0.775901116608315	2		585	959	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639506	3639506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371580654	NA	P-0056851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	839	1240	0	ENST00000294008.3:c.4133C>T	p.Pro1378Leu	p.P1378L	ENST00000294008	NM_032444.2	1378	cCg/cTg	12/15	0.743976576331322	1	FACETS	0.98	0.955	1	0.98	0.955	1	CLONAL	1	TRUE	0	0.775901116608315	1		1240	1350	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913694	32913724	+	frameshift_variant	Frame_Shift_Del	DEL	AAAACAAGATACTTATTTAAGTAACAGTAGC	AAAACAAGATACTTATTTAAGTAACAGTAGC	-	novel	NA	P-0056851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	38	392	0	ENST00000380152.3:c.5203_5233del	p.Lys1735CysfsTer32	p.K1735Cfs*32	ENST00000380152		1734	gaAAAACAAGATACTTATTTAAGTAACAGTAGC/ga	11/27	0.250730078432516	1	FACETS	0.192	0.159	0.228	0.192	0.159	0.228	INDETERMINATE	1	TRUE	0	0.775901116608315	1		392	313	SUCCESS
APC	324	MSKCC	GRCh37	5	112170753	112170753	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	286	663	0	ENST00000257430.4:c.1849G>C	p.Val617Leu	p.V617L	ENST00000257430	NM_000038.5	617	Gtt/Ctt	15/16	0.775901116608315	1	FACETS	0.883	0.842	0.924	0.883	0.842	0.924	CLONAL	1	TRUE	0	0.775901116608315	1		663	511	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751051	128751066	+	frameshift_variant	Frame_Shift_Del	DEL	GAGCGCCGCCGCCTCA	GAGCGCCGCCGCCTCA	-	novel	NA	P-0056851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1843	458	775	0	ENST00000377970.2:c.591_606del	p.Ala199SerfsTer145	p.A199Sfs*145	ENST00000377970	NM_002467.4	196	ctGAGCGCCGCCGCCTCA/ct	2/3	0.775901116608315	5	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.775901116608315	5		775	2301	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	134	257	2	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	1	2	FACETS	1	0.949	1	1	0.991	1	CLONAL	2	TRUE	1	0.370596950418424	2		259	347	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	344	703	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.951	0.902	1	1	0.996	1	CLONAL	2	TRUE	1	0.370596950418424	2		704	976	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	460	900	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.967	1	1	0.997	1	CLONAL	2	TRUE	1	0.370596950418424	2		904	1226	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	213	317	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.370596950418424	2		317	506	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	192	581	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.755	0.701	0.811	1	0.991	1	SUBCLONAL	2	TRUE	1	0.370596950418424	2		583	686	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263973	104263974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776579	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	246	557	0	ENST00000369902.3:c.71dup	p.Ala25GlyfsTer23	p.A25Gfs*23	ENST00000369902	NM_016169.3	22	gcc/gCcc	1/12	1	2	FACETS	0.816	0.765	0.869	1	0.994	1	CLONAL	2	TRUE	1	0.370596950418424	2		557	813	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	262	519	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.370596950418424	3	FACETS	0.896	0.841	0.953	0.896	0.841	0.953	CLONAL	2	TRUE	1	0.370596950418424	3		520	935	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	195	459	2	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.987	0.921	1	1	0.994	1	CLONAL	2	TRUE	1	0.370596950418424	2		461	533	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509085	66509085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	108	306	0	ENST00000273854.3:c.242del	p.Asn81MetfsTer24	p.N81Mfs*24	ENST00000273854	NM_004439.5	81	aAt/at	2/18	1	2	FACETS	1	0.954	1	1	0.99	1	CLONAL	2	TRUE	1	0.370596950418424	2		306	272	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911143	40911143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370795038	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	156	380	1	ENST00000373198.4:c.2162G>A	p.Arg721His	p.R721H	ENST00000373198	NM_133170.3	721	cGt/cAt	13/32	0.370596950418424	1	FACETS	0.886	0.822	0.952	1	0.992	1	CLONAL	2	TRUE	0	0.370596950418424	1		381	387	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	122	293	0	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	1	2	FACETS	0.799	0.728	0.872	1	0.987	1	SUBCLONAL	2	TRUE	1	0.370596950418424	2		293	412	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222309	53222309	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	459	690	1	ENST00000375401.3:c.4523del	p.Pro1508LeufsTer36	p.P1508Lfs*36	ENST00000375401	NM_004187.3	1508	cCt/ct	26/26	1	1	FACETS	1	0.985	1	1	0.998	1	CLONAL	3	TRUE	0	0.370596950418424	1		691	655	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748120	41748120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759792321	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	149	361	2	ENST00000226382.2:c.649G>A	p.Gly217Arg	p.G217R	ENST00000226382	NM_003924.3	217	Ggg/Agg	3/3	1	2	FACETS	0.865	0.804	0.925	1	0.993	1	CLONAL	3	TRUE	1	0.370596950418424	2		363	310	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510806	157510806	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	332	789	1	ENST00000346085.5:c.3586del	p.Gln1196SerfsTer15	p.Q1196Sfs*15	ENST00000346085	NM_020732.3	1194	aCc/ac	14/20	1	2	FACETS	0.986	0.935	1	1	0.996	1	CLONAL	2	TRUE	1	0.370596950418424	2		790	909	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46733212	46733212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908690	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	370	728	0	ENST00000371975.4:c.973G>A	p.Gly325Arg	p.G325R	ENST00000371975	NM_003579.3	325	Gga/Aga	9/18	1	2	FACETS	1	0.981	1	1	0.997	1	CLONAL	2	TRUE	1	0.370596950418424	2		728	945	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296203	15296204	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CA	CA	-	novel	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	495	1407	2	ENST00000263388.2:c.2160_2161del	p.Cys720Ter	p.C720*	ENST00000263388	NM_000435.2	720	tgTGag/tgag	14/33	1	2	FACETS	0.936	0.896	0.977	1	0.997	1	CLONAL	2	TRUE	1	0.370596950418424	2		1409	1427	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447773	49447773	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	327	694	0	ENST00000301067.7:c.661del	p.Ala221LeufsTer40	p.A221Lfs*40	ENST00000301067	NM_003482.3	221	Gct/ct	5/54	0.185472409692606	3	FACETS	1	0.99	1	1	0.99	1	INDETERMINATE	2	TRUE	1	0.370596950418424	3		694	889	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453468	40453468	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866679330	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	452	1075	0	ENST00000345506.4:c.1165C>T	p.Arg389Cys	p.R389C	ENST00000345506	NM_003152.3	389	Cgc/Tgc	10/20	1	2	FACETS	0.996	0.952	1	1	0.997	1	CLONAL	2	TRUE	1	0.370596950418424	2		1075	1225	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805537	32805539	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	588	1150	0	ENST00000374899.4:c.472_474del	p.Phe158del	p.F158del	ENST00000374899	NM_018833.2	158	TTC/-	2/12	0.185472409692606	3	FACETS	1	0.994	1	1	0.994	1	INDETERMINATE	2	TRUE	1	0.370596950418424	3		1150	1587	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956724	68956724	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs372931548	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	311	579	0	ENST00000288368.4:c.842G>A	p.Arg281Gln	p.R281Q	ENST00000288368	NM_024870.2	281	cGg/cAg	8/40	1	2	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	TRUE	1	0.370596950418424	2		579	701	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907782	76907784	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	rs398123423	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	146	215	6	ENST00000373344.5:c.4377_4379del	p.Glu1464del	p.E1464del	ENST00000373344	NM_000489.3	1459	gaGGAa/gaa	15/35	1	1	FACETS	1	0.955	1	1	0.992	1	CLONAL	2	TRUE	0	0.370596950418424	1		221	309	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120560	2120560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397515296	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	546	1489	1	ENST00000219476.3:c.1820C>T	p.Ala607Val	p.A607V	ENST00000219476	NM_000548.3	607	gCg/gTg	17/42	1	2	FACETS	1	0.968	1	1	0.997	1	CLONAL	2	TRUE	1	0.370596950418424	2		1490	1459	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73047240	73047240	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	196	492	0	ENST00000356692.5:c.51del	p.Lys19ArgfsTer14	p.K19Rfs*14	ENST00000356692		16	aGg/ag	2/9	1	2	FACETS	0.877	0.817	0.939	1	0.993	1	CLONAL	2	TRUE	1	0.370596950418424	2		492	603	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100452	8100452	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1192	78	1369	1	ENST00000346208.3:c.431del	p.Gly144AlafsTer51	p.G144Afs*51	ENST00000346208		142	tcG/tc	3/6	1	2	FACETS	0.331	0.29	0.376	0.331	0.29	0.376	SUBCLONAL	1	TRUE	1	0.370596950418424	2		1370	1270	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477115	67477115	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	381	838	0	ENST00000327367.4:c.922C>A	p.Leu308Ile	p.L308I	ENST00000327367	NM_005902.3	308	Ctc/Atc	7/9	1	2	FACETS	0.935	0.89	0.982	1	0.996	1	CLONAL	2	TRUE	1	0.370596950418424	2		838	1099	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969122	93969122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	163	403	0	ENST00000369303.4:c.1874C>T	p.Ala625Val	p.A625V	ENST00000369303	NM_004440.3	625	gCc/gTc	10/17	1	2	FACETS	0.973	0.902	1	1	0.992	1	CLONAL	2	TRUE	1	0.370596950418424	2		403	452	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928002	49928002	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	203	905	0	ENST00000296474.3:c.3726A>T	p.Gln1242His	p.Q1242H	ENST00000296474	NM_002447.2	1242	caA/caT	18/20	1	2	FACETS	0.967	0.895	1	0.967	0.895	1	CLONAL	1	TRUE	1	0.370596950418424	2		905	1133	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11210197	11210197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	355	680	0	ENST00000361445.4:c.4556C>T	p.Ala1519Val	p.A1519V	ENST00000361445	NM_004958.3	1519	gCt/gTt	31/58	1	2	FACETS	1	0.956	1	1	0.996	1	CLONAL	2	TRUE	1	0.370596950418424	2		680	952	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373764	118373764	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	190	435	0	ENST00000534358.1:c.7157C>G	p.Thr2386Arg	p.T2386R	ENST00000534358	NM_005933.3	2386	aCa/aGa	27/36	0.164309564366468	3	FACETS	1	0.982	1			1	INDETERMINATE	2	TRUE	NA	0.370596950418424	3		435	524	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435219	49435219	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	457	1130	2	ENST00000301067.7:c.6334del	p.Ala2112HisfsTer32	p.A2112Hfs*32	ENST00000301067	NM_003482.3	2112	Gca/ca	31/54	0.185472409692606	3	FACETS	1	0.994	1	1	0.994	1	INDETERMINATE	2	TRUE	1	0.370596950418424	3		1132	1173	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510579	38510579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs948121153	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	424	872	0	ENST00000254066.5:c.833C>T	p.Thr278Met	p.T278M	ENST00000254066	NM_000964.3	278	aCg/aTg	7/9	1	2	FACETS	1	0.985	1	1	0.997	1	CLONAL	2	TRUE	1	0.370596950418424	2		872	1071	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439980	220439980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751753814	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	262	1574	0	ENST00000243786.2:c.833G>A	p.Arg278Gln	p.R278Q	ENST00000243786	NM_002191.3	278	cGg/cAg	2/2	NA	2	FACETS	0.996	0.932	1			1	INDETERMINATE	1	TRUE	NA	0.370596950418424	2		1574	1419	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710643	40710643	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	104	644	0	ENST00000373198.4:c.4208G>T	p.Arg1403Leu	p.R1403L	ENST00000373198	NM_133170.3	1403	cGt/cTt	31/32	0.370596950418424	1	FACETS	0.745	0.668	0.826	0.745	0.668	0.826	SUBCLONAL	1	TRUE	0	0.370596950418424	1		644	614	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125673	47125673	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	268	499	0	ENST00000409792.3:c.5597del	p.Thr1866LysfsTer11	p.T1866Kfs*11	ENST00000409792	NM_014159.6	1866	aCa/aa	12/21	1	2	FACETS	0.993	0.937	1	1	0.995	1	CLONAL	2	TRUE	1	0.370596950418424	2		499	728	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950396	38950396	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	222	498	0	ENST00000357387.3:c.3554T>C	p.Phe1185Ser	p.F1185S	ENST00000357387	NM_152756.3	1185	tTc/tCc	31/38	0.370596950418424	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.370596950418424	3		498	670	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521926	157521926	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554235552	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	335	702	0	ENST00000346085.5:c.4198C>T	p.Gln1400Ter	p.Q1400*	ENST00000346085	NM_020732.3	1400	Cag/Tag	18/20	1	2	FACETS	1	0.98	1	1	0.996	1	CLONAL	2	TRUE	1	0.370596950418424	2		702	851	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27220144	27220144	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	271	661	2	ENST00000380036.4:c.3200+1G>A		p.X1067_splice	ENST00000380036	NM_000459.3	1067			1	2	FACETS	1	0.945	1	1	0.995	1	CLONAL	2	TRUE	1	0.370596950418424	2		663	730	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430364	47430364	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	503	596	0	ENST00000377045.4:c.1639T>C	p.Ser547Pro	p.S547P	ENST00000377045	NM_001654.4	547	Tct/Cct	15/16	1	1	FACETS	1	0.994	1	1	0.998	1	CLONAL	3	TRUE	0	0.370596950418424	1		596	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0056854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	64	652	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.17	2		652	576	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531766	46531766	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	23	389	0	ENST00000262741.5:c.581A>G	p.Glu194Gly	p.E194G	ENST00000262741	NM_003629.3	194	gAg/gGg	5/10	1	2	FACETS	0.641	0.499	0.806	0.641	0.499	0.806	SUBCLONAL	1	TRUE	1	0.17	2		389	422	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0056855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	47	523	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	0.601	0.506	0.706	0.601	0.506	0.706	SUBCLONAL	1	TRUE	1	0.23	2		523	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578281	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGAGG	GAGGAGG	-	novel	NA	P-0056855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	126	1003	0	ENST00000269305.4:c.568_574del	p.Pro190SerfsTer55	p.P190Sfs*55	ENST00000269305	NM_001126112.2	190	CCTCCTCag/ag	6/11	1	2	FACETS	0.972	0.878	1	0.972	0.878	1	CLONAL	1	TRUE	1	0.23	2		1003	1127	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492851	56492852	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0056855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	50	641	0	ENST00000407977.2:c.87_88insAA	p.Leu30AsnfsTer22	p.L30Nfs*22	ENST00000407977		29	-/AA	2/10	1	2	FACETS	0.574	0.485	0.671	0.574	0.485	0.671	SUBCLONAL	1	TRUE	1	0.23	2		641	758	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375045	31375045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745506485	NA	P-0056856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1468	209	827	2	ENST00000328111.2:c.442C>T	p.Arg148Trp	p.R148W	ENST00000328111	NM_006892.3	148	Cgg/Tgg	6/23	0.36412458149581	6	FACETS	0.917	0.848	0.988	0.229	0.212	0.247	CLONAL	1	TRUE	2	0.596227875627663	6		829	1677	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352784	70352784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369442321	NA	P-0056856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	123	434	0	ENST00000374080.3:c.4505C>T	p.Ser1502Phe	p.S1502F	ENST00000374080		1502	tCc/tTc	32/45	0.596227875627663	2	FACETS	0.546	0.494	0.601			1	SUBCLONAL	1	TRUE	NA	0.596227875627663	2		434	756	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275256	115275256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	173	589	0	ENST00000438362.2:c.1157C>T	p.Thr386Ile	p.T386I	ENST00000438362	NM_001242891.1	386	aCa/aTa	10/20	1	2	FACETS	0.857	0.792	0.925	0.857	0.792	0.925	CLONAL	1	TRUE	1	0.596227875627663	2		589	677	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533364	29533400	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CACACCCAGCAATACGAATGGCACCGGTAAGATAAAT	CACACCCAGCAATACGAATGGCACCGGTAAGATAAAT	-	novel	NA	P-0056856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	68	246	0	ENST00000356175.3:c.1370_1392+14del		p.X457_splice	ENST00000356175	NM_000267.3	457		12/57	NA	2	FACETS	0.679	0.595	0.769			1	INDETERMINATE	1	TRUE	NA	0.596227875627663	2		246	336	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752888	42752888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1482244260	NA	P-0056856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1802	190	1343	0	ENST00000222329.4:c.1376C>T	p.Ala459Val	p.A459V	ENST00000222329	NM_006494.2	459	gCc/gTc	4/4	0.479540334948633	3	FACETS	0.415	0.382	0.45	0.208	0.191	0.225	SUBCLONAL	1	TRUE	1	0.596227875627663	3		1343	1992	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437221	220437221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1532	437	1464	0	ENST00000243786.2:c.125G>A	p.Gly42Glu	p.G42E	ENST00000243786	NM_002191.3	42	gGg/gAg	1/2	0.284568459332282	3	FACETS	0.966	0.918	1	0.483	0.459	0.508	INDETERMINATE	1	TRUE	1	0.596227875627663	3		1464	1969	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022836	31022836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1238	229	728	0	ENST00000375687.4:c.2321G>A	p.Arg774Lys	p.R774K	ENST00000375687	NM_015338.5	774	aGa/aAa	13/13	0.36412458149581	6	FACETS	1	0.981	1	0.287	0.266	0.308	CLONAL	1	TRUE	2	0.596227875627663	6		728	1467	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375196	31375196	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770040598	NA	P-0056856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2082	147	1115	1	ENST00000328111.2:c.593G>A	p.Gly198Glu	p.G198E	ENST00000328111	NM_006892.3	198	gGg/gAg	6/23	0.36412458149581	6	FACETS	0.485	0.44	0.532	0.121	0.11	0.133	SUBCLONAL	1	TRUE	2	0.596227875627663	6		1116	2229	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545083	41545083	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	240	599	0	ENST00000263253.7:c.2283G>T	p.Gln761His	p.Q761H	ENST00000263253	NM_001429.3	761	caG/caT	13/31	0.526185167436001	3	FACETS	1	0.987	1	0.401	0.375	0.428	CLONAL	1	TRUE	0	0.596227875627663	3		599	868	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197766	66197766	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	225	458	0	ENST00000273854.3:c.2933A>T	p.Lys978Met	p.K978M	ENST00000273854	NM_004439.5	978	aAg/aTg	17/18	0.557100977943425	2	FACETS	0.86	0.812	0.907	0.86	0.812	0.907	CLONAL	2	TRUE	0	0.596227875627663	2		458	439	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280159	66280159	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	45	237	0	ENST00000273854.3:c.1530C>G	p.Asp510Glu	p.D510E	ENST00000273854	NM_004439.5	510	gaC/gaG	7/18	0.557100977943425	2	FACETS	0.576	0.488	0.672	0.288	0.244	0.336	SUBCLONAL	1	TRUE	0	0.596227875627663	2		237	262	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755601	57755609	+	inframe_deletion	In_Frame_Del	DEL	ATGGTGGTG	ATGGTGGTG	-	rs1561217633	NA	P-0056856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	245	1024	0	ENST00000274289.3:c.178_186del	p.His60_His62del	p.H60_H62del	ENST00000274289	NM_006622.3	60	CACCACCAT/-	1/14	0.5728340131375	2	FACETS	0.786	0.735	0.839	0.393	0.367	0.42	SUBCLONAL	1	TRUE	0	0.596227875627663	2		1024	1045	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790828	89790828	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1595	447	1239	0	ENST00000336032.3:c.215C>T	p.Pro72Leu	p.P72L	ENST00000336032	NM_006813.2	72	cCt/cTt	1/2	0.309815934454659	4	FACETS	1	0.991	1	0.586	0.557	0.616	INDETERMINATE	1	TRUE	2	0.596227875627663	4		1239	2042	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397829	116397829	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0056856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	185	492	0	ENST00000397752.3:c.2102+1G>A		p.X701_splice	ENST00000397752	NM_000245.2	701			0.518027803470017	4	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.596227875627663	4		492	830	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859981	151859981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	149	360	0	ENST00000262189.6:c.10681C>T	p.Pro3561Ser	p.P3561S	ENST00000262189	NM_170606.2	3561	Cct/Tct	43/59	0.547353746174375	3	FACETS	1	0.978	1	0.591	0.543	0.641	CLONAL	1	TRUE	1	0.596227875627663	3		360	549	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282176	38282176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747978107	NA	P-0056856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	286	944	0	ENST00000425967.3:c.880G>A	p.Ala294Thr	p.A294T	ENST00000425967	NM_001174067.1	294	Gcc/Acc	8/19	NA	2	FACETS	0.921	0.866	0.976			1	INDETERMINATE	1	TRUE	NA	0.596227875627663	2		944	1042	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577558	+	frameshift_variant	Frame_Shift_Ins	INS	CAG	CAG	TTCCTGAACAGTTCCT	novel	NA	P-0056856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	477	769	0	ENST00000269305.4:c.723_725delinsAGGAACTGTTCAGGAA	p.Cys242GlyfsTer26	p.C242Gfs*26	ENST00000269305	NM_001126112.2	241	tcCTGc/tcAGGAACTGTTCAGGAAc	7/11	0.583160135082754	2	FACETS	0.85	0.818	0.883	0.85	0.818	0.883	CLONAL	2	TRUE	0	0.596227875627663	2		769	941	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577524	7577524	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	185	919	0	ENST00000269305.4:c.757A>G	p.Thr253Ala	p.T253A	ENST00000269305	NM_001126112.2	253	Acc/Gcc	7/11	0.18088082282001	2	FACETS	0.895	0.825	0.968	0.895	0.825	0.968	CLONAL	2	TRUE	0	0.18088082282001	2		919	1143	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107183	27107183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	96	732	0	ENST00000324856.7:c.6794C>T	p.Pro2265Leu	p.P2265L	ENST00000324856	NM_006015.4	2265	cCg/cTg	20/20	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.18088082282001	2		732	1029	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643583	38643583	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	168	636	0	ENST00000299084.4:c.1053A>T	p.Lys351Asn	p.K351N	ENST00000299084	NM_152594.2	351	aaA/aaT	7/7	0.139885257034754	3	FACETS	0.983	0.903	1	0.983	0.903	1	CLONAL	2	TRUE	1	0.18088082282001	3		636	1030	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934274	68934274	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	51	433	0	ENST00000288368.4:c.340G>T	p.Asp114Tyr	p.D114Y	ENST00000288368	NM_024870.2	114	Gac/Tac	4/40	0.139885257034754	3	FACETS	0.922	0.782	1	0.461	0.391	0.538	CLONAL	1	TRUE	1	0.18088082282001	3		433	667	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0056860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	392	554	1	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.868532521784954	2		555	443	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027127	49027127	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0056860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	108	294	0	ENST00000267163.4:c.1696-2A>T		p.X566_splice	ENST00000267163	NM_000321.2	566			0.854529984716709	2	FACETS	0.908	0.858	0.953	0.908	0.858	0.953	CLONAL	2	TRUE	0	0.868532521784954	2		294	137	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602408	28602408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	271	501	0	ENST00000241453.7:c.1960G>A	p.Glu654Lys	p.E654K	ENST00000241453	NM_004119.2	654	Gaa/Aaa	16/24	0.854529984716709	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.868532521784954	2		501	312	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636196	28636196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	308	574	0	ENST00000241453.7:c.176C>T	p.Ser59Phe	p.S59F	ENST00000241453	NM_004119.2	59	tCc/tTc	3/24	0.854529984716709	2	FACETS	0.996	0.97	1	0.996	0.97	1	CLONAL	2	TRUE	0	0.868532521784954	2		574	356	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95573958	95573958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1256068472	NA	P-0056860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	70	321	0	ENST00000393063.1:c.2791G>A	p.Val931Ile	p.V931I	ENST00000393063	NM_030621.3	931	Gtt/Att	18/28	0.453478008546924	2	FACETS	0.58	0.511	0.653	0.29	0.255	0.327	INDETERMINATE	1	TRUE	0	0.868532521784954	2		321	278	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690810	89690810	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1488857080	NA	P-0056860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	86	327	3	ENST00000371953.3:c.217G>T	p.Glu73Ter	p.E73*	ENST00000371953	NM_000314.4	73	Gaa/Taa	4/9	0.861553546993437	1	FACETS	0.934	0.868	0.995	0.934	0.868	0.995	CLONAL	1	TRUE	0	0.868532521784954	1		330	120	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028383	42028383	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	50	282	0	ENST00000219905.7:c.3921G>C	p.Lys1307Asn	p.K1307N	ENST00000219905	NM_001164273.1	1307	aaG/aaC	13/24	0.863514030524857	1	FACETS	0.53	0.462	0.599	0.53	0.462	0.599	SUBCLONAL	1	TRUE	0	0.868532521784954	1		282	123	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15840928	15840928	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	100	260	0	ENST00000307771.7:c.1012G>C	p.Glu338Gln	p.E338Q	ENST00000307771	NM_005089.3	338	Gaa/Caa	11/11	1	1	FACETS	0.562	0.512	0.612	0.562	0.512	0.612	SUBCLONAL	1	TRUE	0	0.868532521784954	1		260	232	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841331	15841331	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	132	437	0	ENST00000307771.7:c.1415G>C	p.Arg472Thr	p.R472T	ENST00000307771	NM_005089.3	472	aGa/aCa	11/11	1	1	FACETS	0.619	0.572	0.665	0.619	0.572	0.665	SUBCLONAL	1	TRUE	0	0.868532521784954	1		437	278	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0056863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	50	1372	1	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.210933368942983	1	FACETS	0.476	0.403	0.558	0.476	0.403	0.558	SUBCLONAL	1	FALSE	0	0.210933368942983	1		1373	890	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93627350	93627350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756047567	NA	P-0056863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	128	527	1	ENST00000375746.1:c.817C>T	p.Arg273Cys	p.R273C	ENST00000375746	NM_001174167.1	273	Cgt/Tgt	6/14	1	2	FACETS	1	0.975	1	1	0.991	1	CLONAL	2	FALSE	1	0.210933368942983	2		528	507	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0056863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	62	385	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.210933368942983	2		385	480	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256905	16256909	+	frameshift_variant	Frame_Shift_Del	DEL	CCACT	CCACT	-	novel	NA	P-0056863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	74	807	0	ENST00000375759.3:c.4171_4175del	p.His1391ThrfsTer8	p.H1391Tfs*8	ENST00000375759	NM_015001.2	1390	tcCCACTca/tcca	11/15	1	2	FACETS	0.929	0.813	1	0.929	0.813	1	CLONAL	1	FALSE	1	0.210933368942983	2		807	755	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258868	16258869	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0056863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	341	780	0	ENST00000375759.3:c.6134_6135del	p.Arg2045LysfsTer11	p.R2045Kfs*11	ENST00000375759	NM_015001.2	2045	AGa/a	11/15	1	2	FACETS	0.906	0.861	0.952	1	0.997	1	CLONAL	4	FALSE	1	0.210933368942983	2		780	892	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061267	38061267	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1398	295	1199	0	ENST00000250448.2:c.722G>C	p.Gly241Ala	p.G241A	ENST00000250448	NM_004496.3	241	gGc/gCc	2/2	0.191403218529718	3	FACETS	0.913	0.857	0.972	0.913	0.857	0.972	CLONAL	2	FALSE	1	0.210933368942983	3		1199	1693	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191516	10191516	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864321642	NA	P-0056865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	90	543	0	ENST00000256474.2:c.509T>A	p.Val170Asp	p.V170D	ENST00000256474	NM_000551.3	170	gTc/gAc	3/3	0.448381161824331	1	FACETS	0.784	0.701	0.873	0.784	0.701	0.873	SUBCLONAL	1	TRUE	0	0.448381161824331	1		543	397	SUCCESS
APC	324	MSKCC	GRCh37	5	112175720	112175720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	144	333	0	ENST00000257430.4:c.4429C>T	p.Gln1477Ter	p.Q1477*	ENST00000257430	NM_000038.5	1477	Cag/Tag	16/16	0.646534554870809	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.647615690538328	2		333	216	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140165	50140165	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	328	922	0	ENST00000246792.3:c.260A>T	p.Gln87Leu	p.Q87L	ENST00000246792	NM_006270.3	87	cAg/cTg	3/6	0.211081511848047	3	FACETS	1	0.988	1	0.729	0.696	0.762	INDETERMINATE	2	TRUE	0	0.647615690538328	3		922	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0056866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	118	623	0	ENST00000269305.4:c.673-2A>C		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.647615690538328	1	FACETS	0.886	0.814	0.96	0.886	0.814	0.96	CLONAL	1	TRUE	0	0.647615690538328	1		623	278	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200960	108200960	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434220	NA	P-0056866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	60	362	1	ENST00000278616.4:c.7327C>T	p.Arg2443Ter	p.R2443*	ENST00000278616	NM_000051.3	2443	Cga/Tga	50/63	0.61559324725142	3	FACETS	0.947	0.824	1	0.474	0.412	0.539	CLONAL	1	TRUE	1	0.647615690538328	3		363	259	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8252029	8252029	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	323	939	0	ENST00000335790.3:c.48G>T	p.Gln16His	p.Q16H	ENST00000335790	NM_002315.2	16	caG/caT	2/4	0.61559324725142	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.647615690538328	3		939	651	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050415	128050415	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	86	418	0	ENST00000285398.2:c.242A>T	p.Asp81Val	p.D81V	ENST00000285398	NM_000122.1	81	gAt/gTt	3/15	0.647615690538328	3	FACETS	1	0.924	1	0.522	0.465	0.581	CLONAL	1	TRUE	1	0.647615690538328	3		418	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0056867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	403	790	0	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.437047532188133	4	FACETS	0.987	0.951	1	0.987	0.951	1	CLONAL	4	TRUE	0	0.478253590715661	4		790	631	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171442	123171442	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	184	429	0	ENST00000218089.9:c.354C>G	p.Ile118Met	p.I118M	ENST00000218089	NM_001042749.1	118	atC/atG	6/35	0.442619783408787	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.478253590715661	2		429	368	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100988	27100988	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	208	744	0	ENST00000324856.7:c.4270C>T	p.Gln1424Ter	p.Q1424*	ENST00000324856	NM_006015.4	1424	Cag/Tag	18/20	0.44289052056076	4	FACETS	0.936	0.872	1	0.936	0.872	1	CLONAL	2	TRUE	2	0.478253590715661	4		744	687	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842333	68842333	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	118	390	0	ENST00000261769.5:c.394G>C	p.Val132Leu	p.V132L	ENST00000261769	NM_004360.3	132	Gtt/Ctt	4/16	0.203921329079317	5	FACETS	0.957	0.869	1	0.638	0.579	0.698	INDETERMINATE	2	TRUE	2	0.478253590715661	5		390	443	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239418	105239418	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	372	873	0	ENST00000349310.3:c.969C>G	p.Asp323Glu	p.D323E	ENST00000349310	NM_001014432.1	323	gaC/gaG	12/15	0.416421331431065	4	FACETS	0.907	0.871	0.943	0.907	0.871	0.943	CLONAL	4	TRUE	0	0.478253590715661	4		873	634	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900547	3900547	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1445018490	NA	P-0056867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	475	904	0	ENST00000262367.5:c.549G>C	p.Gln183His	p.Q183H	ENST00000262367	NM_004380.2	183	caG/caC	2/31	0.478253590715661	5	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	2	0.478253590715661	5		904	985	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411405	63411405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	151	918	0	ENST00000330258.3:c.1762G>A	p.Ala588Thr	p.A588T	ENST00000330258	NM_152424.3	588	Gct/Act	2/2	0.203858404431488	4	FACETS	0.905	0.832	0.979	0.905	0.832	0.979	INDETERMINATE	2	TRUE	2	0.478253590715661	4		918	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0056868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	227	508	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.461318475757666	1	FACETS	0.999	0.934	1	0.999	0.934	1	CLONAL	1	TRUE	0	0.461318475757666	1		508	758	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0056868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	107	463	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.45427806024594	2	FACETS	0.964	0.869	1	0.482	0.434	0.532	CLONAL	1	TRUE	0	0.461318475757666	2		463	481	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492687	56492687	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	105	484	0	ENST00000407977.2:c.252G>C	p.Gln84His	p.Q84H	ENST00000407977		84	caG/caC	2/10	0.461318475757666	1	FACETS	0.959	0.868	1	0.959	0.868	1	CLONAL	1	TRUE	0	0.461318475757666	1		484	365	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965820	18965820	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	201	1157	0	ENST00000262803.5:c.1398G>T	p.Gln466His	p.Q466H	ENST00000262803	NM_002911.3	466	caG/caT	10/24	NA	2	FACETS	0.917	0.85	0.987			1	INDETERMINATE	1	TRUE	NA	0.461318475757666	2		1157	950	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880869	134880869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	132	675	0	ENST00000398015.3:c.1432G>A	p.Glu478Lys	p.E478K	ENST00000398015	NM_004441.4	478	Gag/Aag	7/16	1	2	FACETS	0.932	0.849	1	0.932	0.849	1	CLONAL	1	TRUE	1	0.461318475757666	2		675	614	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0056869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	68	463	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.119448425075903	8	FACETS	1	0.889	1	0.845	0.742	0.955	CLONAL	5	FALSE	2	0.119448425075903	8		463	305	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0056869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	43	892	1	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.11923568784882	3	FACETS	0.905	0.762	1	1	0.95	1	CLONAL	3	FALSE	1	0.119448425075903	3		893	281	SUCCESS
APC	324	MSKCC	GRCh37	5	112173947	112173947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs755806668	NA	P-0056869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	25	410	0	ENST00000257430.4:c.2656C>T	p.Gln886Ter	p.Q886*	ENST00000257430	NM_000038.5	886	Cag/Tag	16/16	0.119448425075903	8	FACETS	1	0.825	1	0.525	0.414	0.651	CLONAL	2	FALSE	4	0.119448425075903	8		410	271	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924823	49924823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772336656	NA	P-0056869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	25	1418	3	ENST00000296474.3:c.4120C>T	p.Arg1374Cys	p.R1374C	ENST00000296474	NM_002447.2	1374	Cgt/Tgt	20/20	0.119448425075903	6	FACETS	1	0.905	1	0.325	0.256	0.405	CLONAL	1	FALSE	2	0.119448425075903	6		1421	399	SUCCESS
APC	324	MSKCC	GRCh37	5	112176035	112176035	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	20	373	0	ENST00000257430.4:c.4744del	p.Ala1582ProfsTer68	p.A1582Pfs*68	ENST00000257430	NM_000038.5	1582	Gcc/cc	16/16	0.119448425075903	8	FACETS	1	0.779	1	0.508	0.389	0.645	CLONAL	2	FALSE	4	0.119448425075903	8		373	224	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	116	324	0				ENST00000310581	NM_198253.2	-/1132			0.308572005875168	5	FACETS	1	0.971	1	0.766	0.699	0.834	INDETERMINATE	2	FALSE	2	0.575233134722614	5		324	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0056871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	305	504	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.541856047671404	3	FACETS	0.838	0.8	0.876	0.838	0.8	0.876	CLONAL	3	FALSE	0	0.575233134722614	3		504	543	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730802	40730802	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	57	784	0	ENST00000373198.4:c.3733G>T	p.Gly1245Ter	p.G1245*	ENST00000373198	NM_133170.3	1245	Gga/Tga	27/32	NA	2	FACETS	0.442	0.38	0.51			1	INDETERMINATE	1	FALSE	NA	0.575233134722614	2		784	448	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99473487	99473487	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	40	414	0	ENST00000268035.6:c.2909G>A	p.Gly970Glu	p.G970E	ENST00000268035	NM_000875.3	970	gGa/gAa	15/21	0.517626455237298	3	FACETS	0.613	0.512	0.725	0.307	0.256	0.363	SUBCLONAL	1	FALSE	1	0.575233134722614	3		414	292	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227889	123227889	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	104	197	0	ENST00000218089.9:c.3600G>A	p.Met1200Ile	p.M1200I	ENST00000218089	NM_001042749.1	1200	atG/atA	33/35	0.281374351186725	2	FACETS	0.927	0.853	1			1	INDETERMINATE	2	FALSE	NA	0.575233134722614	2		197	195	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030378	49030378	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0056871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	154	351	0	ENST00000267163.4:c.1853C>G	p.Ser618Ter	p.S618*	ENST00000267163	NM_000321.2	618	tCa/tGa	19/27	0.588624300819851	3	FACETS	1	0.972	1			1	CLONAL	2	FALSE	NA	0.575233134722614	3		351	318	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652057	36652058	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0056871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	410	1273	0	ENST00000244741.5:c.182dup	p.Asp62Ter	p.D62*	ENST00000244741	NM_000389.4	60	gag/gaGg	2/3	0.269463902428281	5	FACETS	1	0.981	1	0.626	0.599	0.652	INDETERMINATE	3	FALSE	0	0.575233134722614	5		1273	849	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940181	31940181	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1307450480	NA	P-0056871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	119	1092	0	ENST00000375333.2:c.323C>T	p.Ser108Phe	p.S108F	ENST00000375333	NM_032454.1	108	tCc/tTc	2/8	0.588624300819851	5	FACETS	0.802	0.723	0.886	0.201	0.18	0.222	CLONAL	1	FALSE	1	0.575233134722614	5		1092	961	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319512	62319512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs909417142	NA	P-0056871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	83	1234	0	ENST00000360203.5:c.1616C>T	p.Ser539Phe	p.S539F	ENST00000360203	NM_001283009.1	539	tCc/tTc	19/35	0.361867612286048	5	FACETS	0.584	0.514	0.659	0.195	0.171	0.22	SUBCLONAL	1	FALSE	2	0.575233134722614	5		1234	921	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239590	105239590	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	41	818	0	ENST00000349310.3:c.955G>A	p.Glu319Lys	p.E319K	ENST00000349310	NM_001014432.1	319	Gag/Aag	11/15	0.361867612286048	5	FACETS	0.411	0.341	0.489	0.137	0.113	0.163	SUBCLONAL	1	FALSE	2	0.575233134722614	5		818	646	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425545	49425545	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	214	1221	0	ENST00000301067.7:c.12943C>T	p.Gln4315Ter	p.Q4315*	ENST00000301067	NM_003482.3	4315	Caa/Taa	39/54	0.448075386229807	5	FACETS	1	0.991	1	0.498	0.463	0.534	CLONAL	1	FALSE	2	0.575233134722614	5		1221	928	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43772095	43772095	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	142	798	0	ENST00000382044.4:c.620C>G	p.Ser207Cys	p.S207C	ENST00000382044	NM_001141980.1	207	tCt/tGt	6/28	0.10553331831247	4	FACETS	1	0.986	1	0.693	0.635	0.754	INDETERMINATE	1	FALSE	2	0.575233134722614	4		798	561	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272366	15272366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	90	1390	0	ENST00000263388.2:c.6073G>T	p.Asp2025Tyr	p.D2025Y	ENST00000263388	NM_000435.2	2025	Gat/Tat	33/33	0.308572005875168	5	FACETS	0.739	0.655	0.829	0.246	0.218	0.277	INDETERMINATE	1	FALSE	2	0.575233134722614	5		1390	789	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010443	48010443	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	149	928	0	ENST00000234420.5:c.71C>A	p.Ser24Ter	p.S24*	ENST00000234420	NM_000179.2	24	tCg/tAg	1/10	0.588624300819851	3	FACETS	1	0.973	1	0.569	0.522	0.618	CLONAL	1	FALSE	1	0.575233134722614	3		928	586	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52675985	52675985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	61	612	0	ENST00000394830.3:c.1072G>C	p.Asp358His	p.D358H	ENST00000394830	NM_018313.4	358	Gat/Cat	11/30	0.588624300819851	4	FACETS	0.406	0.349	0.468	0.203	0.174	0.234	SUBCLONAL	1	FALSE	2	0.575233134722614	4		612	823	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064727	80064727	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	44	356	0	ENST00000265081.6:c.2158C>G	p.Gln720Glu	p.Q720E	ENST00000265081	NM_002439.4	720	Caa/Gaa	15/24	0.542563805698532	3	FACETS	0.424	0.355	0.499	0.212	0.177	0.25	SUBCLONAL	1	FALSE	1	0.575233134722614	3		356	465	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672255	30672255	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	455	919	0	ENST00000376406.3:c.4705G>C	p.Glu1569Gln	p.E1569Q	ENST00000376406	NM_014641.2	1569	Gaa/Caa	10/15	0.575233134722614	6	FACETS	1	0.987	1			1	CLONAL	4	FALSE	NA	0.575233134722614	6		919	806	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90949294	90949294	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554554265	NA	P-0056871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	74	236	0	ENST00000265433.3:c.2194C>T	p.Gln732Ter	p.Q732*	ENST00000265433	NM_002485.4	732	Caa/Taa	15/16	0.588624300819851	4	FACETS	1	0.954	1	0.584	0.515	0.657	CLONAL	1	FALSE	2	0.575233134722614	4		236	347	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045190	47045190	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0056871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	306	378	1	ENST00000377604.3:c.2430+1G>A		p.X810_splice	ENST00000377604	NM_001204468.1	810			0.575233134722614	4	FACETS	1	0.966	1			1	CLONAL	4	FALSE	NA	0.575233134722614	4		379	418	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0056872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	339	330	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.503473635174074	6	FACETS	0.967	0.922	1	0.967	0.922	1	CLONAL	4	TRUE	2	0.503473635174074	6		330	699	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252869	36252869	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	169	380	0	ENST00000300305.3:c.493G>C	p.Gly165Arg	p.G165R	ENST00000300305		165	Ggt/Cgt	4/8	0.357504311475655	5	FACETS	0.863	0.801	0.926	0.863	0.801	0.926	CLONAL	3	TRUE	2	0.503473635174074	5		380	455	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105238734	105238734	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146483593	NA	P-0056872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	162	1105	2	ENST00000349310.3:c.1228G>A	p.Gly410Ser	p.G410S	ENST00000349310	NM_001014432.1	410	Ggt/Agt	13/15	0.503473635174074	3	FACETS	0.907	0.832	0.985	0.302	0.277	0.329	CLONAL	1	TRUE	0	0.503473635174074	3		1107	888	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696432	47696432	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519968	NA	P-0056874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	112	546	0	ENST00000347630.2:c.391T>G	p.Trp131Gly	p.W131G	ENST00000347630	NM_001007230.1	131	Tgg/Ggg	6/11	0.141116973604061	3	FACETS	0.815	0.738	0.895	0.815	0.738	0.895	INDETERMINATE	2	TRUE	1	0.379134977466723	3		546	431	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574216	95574216	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0056874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	69	253	0	ENST00000393063.1:c.2650+1G>C		p.X884_splice	ENST00000393063	NM_030621.3	884			0.214696524932876	5	FACETS	1	0.956	1	0.79	0.697	0.887	INDETERMINATE	2	TRUE	2	0.379134977466723	5		253	241	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462609	29462609	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	110	515	0	ENST00000389048.3:c.2292C>G	p.Asn764Lys	p.N764K	ENST00000389048	NM_004304.4	764	aaC/aaG	13/29	1	2	FACETS	0.76	0.691	0.831	1	0.985	1	SUBCLONAL	2	TRUE	1	0.44	2		515	329	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921551	178921551	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056881-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	20	240	0	ENST00000263967.3:c.1033A>T	p.Asn345Tyr	p.N345Y	ENST00000263967	NM_006218.2	345	Aat/Tat	5/21	1	2	FACETS	0.594	0.453	0.76	0.594	0.453	0.76	SUBCLONAL	1	TRUE	1	0.14539297822812	2		240	463	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070577	67070578	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0056881-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	44	207	0	ENST00000412916.2:c.207dup	p.Pro70SerfsTer13	p.P70Sfs*13	ENST00000412916		67	-/T	3/6	0.14539297822812	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.14539297822812	1		207	476	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105586	27105586	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056881-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	85	442	0	ENST00000324856.7:c.5197G>T	p.Glu1733Ter	p.E1733*	ENST00000324856	NM_006015.4	1733	Gag/Tag	20/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.14539297822812	2		442	992	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730831	40730831	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs372700928	NA	P-0056881-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	99	589	0	ENST00000373198.4:c.3704G>T	p.Arg1235Leu	p.R1235L	ENST00000373198	NM_133170.3	1235	cGc/cTc	27/32	0.14539297822812	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.14539297822812	1		589	1194	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061845	38061862	+	inframe_deletion	In_Frame_Del	DEL	CATGTAGGTGTTCATGGA	CATGTAGGTGTTCATGGA	-	novel	NA	P-0056881-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1198	116	644	0	ENST00000250448.2:c.127_144del	p.Ser43_Met48del	p.S43_M48del	ENST00000250448	NM_004496.3	43	TCCATGAACACCTACATG/-	2/2	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.14539297822812	2		644	1314	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122329	2122329	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056881-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1392	69	0	0	ENST00000219476.3:c.2185A>T	p.Ser729Cys	p.S729C	ENST00000219476	NM_000548.3	729	Agt/Tgt	20/42	1	2	FACETS	0.65	0.563	0.744	0.65	0.563	0.744	SUBCLONAL	1	TRUE	1	0.14539297822812	2		0	1461	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856083	68856084	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs1060501224	NA	P-0056881-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	88	496	0	ENST00000261769.5:c.1895_1896del	p.His632ArgfsTer30	p.H632Rfs*30	ENST00000261769	NM_004360.3	631	ACa/a	12/16	0.14539297822812	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.14539297822812	1		496	948	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	62	324	0				ENST00000310581	NM_198253.2	-/1132			0.295729826153752	1	FACETS	0.826	0.723	0.934	0.826	0.723	0.934	INDETERMINATE	1	TRUE	0	0.498639640102297	1		324	226	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0056890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	213	683	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.498639640102297	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.498639640102297	1		683	562	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220154	36220154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	97	965	0	ENST00000222270.7:c.4874C>T	p.Ser1625Phe	p.S1625F	ENST00000222270	NM_014727.1	1625	tCc/tTc	22/37	1	2	FACETS	0.748	0.669	0.832	0.748	0.669	0.832	SUBCLONAL	1	TRUE	1	0.498639640102297	2		965	520	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958571	175958571	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs769230149	NA	P-0056890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	71	389	0	ENST00000367669.3:c.1774A>G	p.Ile592Val	p.I592V	ENST00000367669	NM_022457.5	592	Atc/Gtc	16/20	1	2	FACETS	0.882	0.776	0.994	0.882	0.776	0.994	CLONAL	1	TRUE	1	0.498639640102297	2		389	323	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989699	15989699	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs557813338	NA	P-0056890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	67	357	0	ENST00000268712.3:c.3074C>G	p.Pro1025Arg	p.P1025R	ENST00000268712	NM_006311.3	1025	cCg/cGg	23/46	0.498639640102297	1	FACETS	0.653	0.572	0.739	0.653	0.572	0.739	SUBCLONAL	1	TRUE	0	0.498639640102297	1		357	309	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5258027	5258027	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0056890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	76	466	0	ENST00000357368.4:c.706+1G>A		p.X236_splice	ENST00000357368	NM_002850.3	236			1	2	FACETS	0.947	0.838	1	0.947	0.838	1	CLONAL	1	TRUE	1	0.498639640102297	2		466	322	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599925	10599925	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	202	1021	0	ENST00000171111.5:c.1651A>C	p.Lys551Gln	p.K551Q	ENST00000171111	NM_203500.1	551	Aag/Cag	5/6	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.498639640102297	2		1021	788	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97934394	97934394	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	77	311	0	ENST00000289081.3:c.381T>G	p.Phe127Leu	p.F127L	ENST00000289081	NM_000136.2	127	ttT/ttG	5/15	0.107451582151808	0	FACETS	0.508	0.45	0.569			1	INDETERMINATE	1	TRUE	0	0.498639640102297	0		311	305	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	98	346	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	0.256489093916747	1	FACETS	0.429	0.382	0.478	0.429	0.382	0.478	INDETERMINATE	1	TRUE	0	0.431167282031548	1		347	832	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	123	257	2	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	0.431167282031548	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.431167282031548	1		259	397	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453486	138453486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451809865	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	143	331	0	ENST00000289153.2:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000289153	NM_006219.2	321	cGa/cAa	5/22	1	2	FACETS	0.901	0.823	0.983	0.901	0.823	0.983	CLONAL	1	TRUE	1	0.431167282031548	2		331	736	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894230	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	353	587	0	ENST00000451590.1:c.35G>A	p.Gly12Asp	p.G12D	ENST00000451590	NM_001130442.1	12	gGc/gAc	2/5	0.339953797074252	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.431167282031548	1		587	1284	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1372	372	1025	7	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	0.339953797074252	1	FACETS	0.776	0.734	0.819	0.776	0.734	0.819	SUBCLONAL	1	TRUE	0	0.431167282031548	1		1032	1744	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101155	41101155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1328848371	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1244	341	888	2	ENST00000373198.4:c.1201C>T	p.Arg401Trp	p.R401W	ENST00000373198	NM_133170.3	401	Cgg/Tgg	8/32	1	2	FACETS	0.998	0.942	1	0.998	0.942	1	CLONAL	1	TRUE	1	0.431167282031548	2		890	1585	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557273	187557273	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	250	617	0	ENST00000441802.2:c.4089del	p.Phe1363LeufsTer5	p.F1363Lfs*5	ENST00000441802	NM_005245.3	1363	ttT/tt	6/27	1	2	FACETS	0.995	0.93	1	0.995	0.93	1	CLONAL	1	TRUE	1	0.431167282031548	2		617	1165	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704520	117704520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	77	410	0	ENST00000368508.3:c.2456C>T	p.Ser819Phe	p.S819F	ENST00000368508	NM_002944.2	819	tCc/tTc	16/43	0.256489093916747	1	FACETS	0.361	0.316	0.409	0.361	0.316	0.409	INDETERMINATE	1	TRUE	0	0.431167282031548	1		410	777	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804242	43804242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	166	646	0	ENST00000372470.3:c.242C>T	p.Ser81Phe	p.S81F	ENST00000372470	NM_005373.2	81	tCc/tTc	3/12	0.256489093916747	1	FACETS	0.511	0.468	0.556	0.511	0.468	0.556	INDETERMINATE	1	TRUE	0	0.431167282031548	1		646	1182	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238150	133238150	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	122	592	0	ENST00000320574.5:c.2827C>T	p.Pro943Ser	p.P943S	ENST00000320574	NM_006231.2	943	Cca/Tca	24/49	0.339953797074252	1	FACETS	0.432	0.389	0.477	0.432	0.389	0.477	SUBCLONAL	1	TRUE	0	0.431167282031548	1		592	1028	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041117	42041117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747757361	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	249	585	0	ENST00000219905.7:c.5495G>A	p.Arg1832Gln	p.R1832Q	ENST00000219905	NM_001164273.1	1832	cGg/cAg	16/24	0.256489093916747	1	FACETS	0.814	0.761	0.869	0.814	0.761	0.869	INDETERMINATE	1	TRUE	0	0.431167282031548	1		585	1113	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486068	29486068	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199474729	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	124	324	0	ENST00000356175.3:c.245C>T	p.Ser82Phe	p.S82F	ENST00000356175	NM_000267.3	82	tCt/tTt	3/57	0.431167282031548	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.431167282031548	1		324	442	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519863	29519863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	386	811	0	ENST00000389048.3:c.1708G>A	p.Glu570Lys	p.E570K	ENST00000389048	NM_004304.4	570	Gag/Aag	9/29	0.339953797074252	1	FACETS	0.99	0.939	1	0.99	0.939	1	CLONAL	1	TRUE	0	0.431167282031548	1		811	1419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	405	867	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.431167282031548	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.431167282031548	1		867	1225	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615765	1615767	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs756376945	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1365	423	1073	0	ENST00000344749.5:c.1504_1506del	p.Lys502del	p.K502del	ENST00000344749	NM_001136139.2	502	AAG/-	17/19	0.339953797074252	1	FACETS	0.861	0.818	0.905	0.861	0.818	0.905	CLONAL	1	TRUE	0	0.431167282031548	1		1073	1788	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2492097	2492097	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs772088410	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1555	212	1020	0	ENST00000355716.4:c.500del	p.Pro167ArgfsTer23	p.P167Rfs*23	ENST00000355716	NM_003820.2	165	tgC/tg	5/8	0.256489093916747	1	FACETS	0.437	0.404	0.471	0.437	0.404	0.471	INDETERMINATE	1	TRUE	0	0.431167282031548	1		1020	1767	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299899	15299899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1946	294	1361	2	ENST00000263388.2:c.1279C>T	p.Arg427Cys	p.R427C	ENST00000263388	NM_000435.2	427	Cgc/Tgc	8/33	0.339953797074252	1	FACETS	0.478	0.447	0.509	0.478	0.447	0.509	SUBCLONAL	1	TRUE	0	0.431167282031548	1		1363	2240	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066712	30066712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751618424	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	125	318	0	ENST00000331968.5:c.2419G>A	p.Glu807Lys	p.E807K	ENST00000331968	NM_002742.2	807	Gaa/Aaa	16/18	1	2	FACETS	0.763	0.691	0.839	0.763	0.691	0.839	SUBCLONAL	1	TRUE	1	0.431167282031548	2		318	760	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001305	150001305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568586257	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	261	500	0	ENST00000253339.5:c.2299C>T	p.Arg767Cys	p.R767C	ENST00000253339		767	Cgt/Tgt	4/7	0.256489093916747	1	FACETS	0.872	0.817	0.929	0.872	0.817	0.929	INDETERMINATE	1	TRUE	0	0.431167282031548	1		500	1089	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521688	89521688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1410875132	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	257	537	0	ENST00000336596.2:c.2765G>A	p.Gly922Asp	p.G922D	ENST00000336596	NM_005233.5	922	gGt/gAt	16/17	1	2	FACETS	0.93	0.869	0.992	0.93	0.869	0.992	CLONAL	1	TRUE	1	0.431167282031548	2		537	1282	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962959	2962959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780894425	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1720	454	1134	0	ENST00000396946.4:c.1949G>A	p.Arg650Gln	p.R650Q	ENST00000396946	NM_032415.4	650	cGg/cAg	16/25	1	2	FACETS	0.969	0.921	1	0.969	0.921	1	CLONAL	1	TRUE	1	0.431167282031548	2		1134	2174	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542163	141542163	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324425100	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	309	665	0	ENST00000220592.5:c.2560C>T	p.Arg854Cys	p.R854C	ENST00000220592	NM_012154.3	854	Cgc/Tgc	19/19	1	2	FACETS	0.954	0.897	1	0.954	0.897	1	CLONAL	1	TRUE	1	0.431167282031548	2		665	1503	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123752	11123752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568471266	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1802	161	588	2	ENST00000358026.2:c.2402G>A	p.Arg801His	p.R801H	ENST00000358026	NM_001128849.1	801	cGc/cAc	16/36	0.419156429742897	4	FACETS	0.544	0.497	0.595	0.181	0.165	0.199	SUBCLONAL	1	TRUE	1	0.431167282031548	4		590	1963	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27016062	27016062	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	304	708	0	ENST00000335756.4:c.338C>T	p.Thr113Ile	p.T113I	ENST00000335756	NM_001809.3	113	aCc/aTc	4/5	0.339953797074252	1	FACETS	0.871	0.82	0.923	0.871	0.82	0.923	CLONAL	1	TRUE	0	0.431167282031548	1		708	1270	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937713	17937713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752088869	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	335	748	0	ENST00000458235.1:c.3214G>A	p.Glu1072Lys	p.E1072K	ENST00000458235	NM_000215.3	1072	Gag/Aag	24/24	0.339953797074252	1	FACETS	0.908	0.857	0.959	0.908	0.857	0.959	CLONAL	1	TRUE	0	0.431167282031548	1		748	1343	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189084	32189084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149758111	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	280	637	0	ENST00000375023.3:c.470G>A	p.Arg157Gln	p.R157Q	ENST00000375023	NM_004557.3	157	cGg/cAg	4/30	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.431167282031548	2		637	1260	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37038124	37038124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63751109	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	96	177	0	ENST00000231790.2:c.131C>T	p.Ser44Phe	p.S44F	ENST00000231790	NM_000249.3	44	tCc/tTc	2/19	0.431167282031548	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.431167282031548	1		177	335	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028721	42028721	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	178	617	0	ENST00000219905.7:c.4259C>T	p.Pro1420Leu	p.P1420L	ENST00000219905	NM_001164273.1	1420	cCa/cTa	13/24	0.256489093916747	1	FACETS	0.594	0.547	0.644	0.594	0.547	0.644	INDETERMINATE	1	TRUE	0	0.431167282031548	1		617	1090	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023606	31023606	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	386	683	0	ENST00000375687.4:c.3091A>T	p.Lys1031Ter	p.K1031*	ENST00000375687	NM_015338.5	1031	Aag/Tag	13/13	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.431167282031548	2		683	1512	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970899	21970899	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	552	1102	0	ENST00000304494.5:c.457+2T>C		p.X153_splice	ENST00000304494	NM_000077.4	153			0.431167282031548	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.431167282031548	1		1102	1674	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023901	27023901	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	104	248	0	ENST00000324856.7:c.1007G>T	p.Cys336Phe	p.C336F	ENST00000324856	NM_006015.4	336	tGt/tTt	1/20	0.256489093916747	1	FACETS	0.927	0.837	1	0.927	0.837	1	INDETERMINATE	1	TRUE	0	0.431167282031548	1		248	408	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932101	36932101	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1197	176	892	0	ENST00000361632.4:c.2368C>A	p.Leu790Ile	p.L790I	ENST00000361632		790	Ctc/Atc	16/16	0.256489093916747	1	FACETS	0.466	0.428	0.506	0.466	0.428	0.506	INDETERMINATE	1	TRUE	0	0.431167282031548	1		892	1373	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307256	65307256	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	101	465	0	ENST00000342505.4:c.2432G>T	p.Arg811Met	p.R811M	ENST00000342505	NM_002227.2	811	aGg/aTg	18/25	0.256489093916747	1	FACETS	0.433	0.387	0.483	0.433	0.387	0.483	INDETERMINATE	1	TRUE	0	0.431167282031548	1		465	848	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261260	115261260	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	115	572	0	ENST00000438362.2:c.2461C>T	p.Gln821Ter	p.Q821*	ENST00000438362	NM_001242891.1	821	Cag/Tag	19/20	0.256489093916747	1	FACETS	0.384	0.344	0.425	0.384	0.344	0.425	INDETERMINATE	1	TRUE	0	0.431167282031548	1		572	1091	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201145	108201145	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1350657331	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	104	185	0	ENST00000278616.4:c.7512G>T	p.Met2504Ile	p.M2504I	ENST00000278616	NM_000051.3	2504	atG/atT	50/63	0.371542094055855	5	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.431167282031548	5		185	597	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398029	4398029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	165	591	0	ENST00000261254.3:c.593C>T	p.Pro198Leu	p.P198L	ENST00000261254	NM_001759.3	198	cCa/cTa	4/5	1	2	FACETS	0.74	0.679	0.804	0.74	0.679	0.804	SUBCLONAL	1	TRUE	1	0.431167282031548	2		591	1034	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060821	38060821	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1794	457	1204	0	ENST00000250448.2:c.1168G>A	p.Gly390Arg	p.G390R	ENST00000250448	NM_004496.3	390	Ggg/Agg	2/2	1	2	FACETS	0.942	0.895	0.989	0.942	0.895	0.989	CLONAL	1	TRUE	1	0.431167282031548	2		1204	2251	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041344	42041344	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	342	649	0	ENST00000219905.7:c.5539A>T	p.Lys1847Ter	p.K1847*	ENST00000219905	NM_001164273.1	1847	Aaa/Taa	17/24	0.256489093916747	1	FACETS	0.921	0.871	0.973	0.921	0.871	0.973	INDETERMINATE	1	TRUE	0	0.431167282031548	1		649	1351	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465502	99465502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	253	538	0	ENST00000268035.6:c.2327C>T	p.Pro776Leu	p.P776L	ENST00000268035	NM_000875.3	776	cCt/cTt	11/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.431167282031548	2		538	1163	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532621	63532622	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1819	222	1188	0	ENST00000307078.5:c.1957_1958delinsTT	p.Pro653Leu	p.P653L	ENST00000307078	NM_004655.3	653	CCa/TTa	8/11	0.256489093916747	1	FACETS	0.396	0.366	0.426	0.396	0.366	0.426	INDETERMINATE	1	TRUE	0	0.431167282031548	1		1188	2041	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923258	78923258	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	140	687	0	ENST00000306801.3:c.3281G>A	p.Arg1094Lys	p.R1094K	ENST00000306801	NM_020761.2	1094	aGg/aAg	28/34	0.256489093916747	1	FACETS	0.438	0.398	0.481	0.438	0.398	0.481	INDETERMINATE	1	TRUE	0	0.431167282031548	1		687	1162	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132223	7132223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1528	242	1098	0	ENST00000302850.5:c.2788C>T	p.Leu930Phe	p.L930F	ENST00000302850	NM_000208.2	930	Ctt/Ttt	14/22	0.339953797074252	1	FACETS	0.497	0.463	0.534	0.497	0.463	0.534	SUBCLONAL	1	TRUE	0	0.431167282031548	1		1098	1770	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250860	10250860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757460628	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2278	223	981	1	ENST00000340748.4:c.3620G>A	p.Arg1207His	p.R1207H	ENST00000340748		1207	cGc/cAc	32/40	0.419156429742897	4	FACETS	0.592	0.548	0.638	0.197	0.182	0.213	SUBCLONAL	1	TRUE	1	0.431167282031548	4		982	2501	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107219	11107219	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2112	148	754	1	ENST00000358026.2:c.1811A>G	p.Glu604Gly	p.E604G	ENST00000358026	NM_001128849.1	604	gAg/gGg	11/36	0.419156429742897	4	FACETS	0.435	0.395	0.477	0.145	0.131	0.159	SUBCLONAL	1	TRUE	1	0.431167282031548	4		755	2260	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214893	36214893	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1464	219	1087	0	ENST00000222270.7:c.3319A>G	p.Thr1107Ala	p.T1107A	ENST00000222270	NM_014727.1	1107	Acc/Gcc	8/37	0.339953797074252	1	FACETS	0.473	0.439	0.51	0.473	0.439	0.51	SUBCLONAL	1	TRUE	0	0.431167282031548	1		1087	1683	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39283854	39283854	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	31	402	0	ENST00000402219.2:c.499T>C	p.Cys167Arg	p.C167R	ENST00000402219	NM_005633.3	167	Tgt/Cgt	4/23	0.431167282031548	1	FACETS	0.183	0.147	0.223	0.183	0.147	0.223	SUBCLONAL	1	TRUE	0	0.431167282031548	1		402	618	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257133	198257133	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	171	433	0	ENST00000335508.6:c.3809A>T	p.Asn1270Ile	p.N1270I	ENST00000335508	NM_012433.2	1270	aAc/aTc	25/25	1	2	FACETS	0.885	0.815	0.959	0.885	0.815	0.959	CLONAL	1	TRUE	1	0.431167282031548	2		433	896	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131314	202131315	+	stop_gained	Nonsense_Mutation	DNP	AG	AG	GT	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	229	459	1	ENST00000358485.4:c.282_283delinsGT	p.Glu95Ter	p.E95*	ENST00000358485	NM_001080125.1	94	caAGaa/caGTaa	2/9	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.431167282031548	2		460	1006	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212252707	212252707	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	75	193	0	ENST00000342788.4:c.3146G>A	p.Gly1049Glu	p.G1049E	ENST00000342788	NM_005235.2	1049	gGa/gAa	26/28	1	2	FACETS	0.93	0.82	1	0.93	0.82	1	CLONAL	1	TRUE	1	0.431167282031548	2		193	374	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017181	31017181	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	192	344	0	ENST00000375687.4:c.512G>C	p.Arg171Pro	p.R171P	ENST00000375687	NM_015338.5	171	cGa/cCa	7/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.431167282031548	2		344	806	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46277794	46277794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	191	438	0	ENST00000371998.3:c.3592C>T	p.Pro1198Ser	p.P1198S	ENST00000371998		1198	Cct/Tct	19/23	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.431167282031548	2		438	881	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181432	38181436	+	frameshift_variant	Frame_Shift_Del	DEL	AGCAG	AGCAG	-	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	234	548	0	ENST00000396334.3:c.445_449del	p.Ser149CysfsTer14	p.S149Cfs*14	ENST00000396334	NM_002468.4	149	AGCAGt/t	2/5	0.431167282031548	1	FACETS	0.974	0.91	1	0.974	0.91	1	CLONAL	1	TRUE	0	0.431167282031548	1		548	874	SUCCESS
ATR	545	MSKCC	GRCh37	3	142254961	142254961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	95	228	0	ENST00000350721.4:c.3808G>A	p.Glu1270Lys	p.E1270K	ENST00000350721	NM_001184.3	1270	Gaa/Aaa	20/47	1	2	FACETS	0.861	0.769	0.958	0.861	0.769	0.958	CLONAL	1	TRUE	1	0.431167282031548	2		228	512	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957892	1957892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	317	567	0	ENST00000382891.5:c.2858G>A	p.Gly953Glu	p.G953E	ENST00000382891	NM_133335.3	953	gGg/gAg	15/22	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.431167282031548	2		567	1323	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230824	66230824	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	73	325	0	ENST00000273854.3:c.2147del	p.Lys716SerfsTer7	p.K716Sfs*7	ENST00000273854	NM_004439.5	716	aAg/ag	12/18	1	2	FACETS	0.495	0.433	0.562	0.495	0.433	0.562	SUBCLONAL	1	TRUE	1	0.431167282031548	2		325	684	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542737	187542738	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	178	423	0	ENST00000441802.2:c.5002dup	p.Thr1668AsnfsTer8	p.T1668Nfs*8	ENST00000441802	NM_005245.3	1668	aca/aAca	10/27	1	2	FACETS	0.859	0.792	0.93	0.859	0.792	0.93	CLONAL	1	TRUE	1	0.431167282031548	2		423	961	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80063819	80063820	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	213	492	0	ENST00000265081.6:c.1966dup	p.Ile656AsnfsTer5	p.I656Nfs*5	ENST00000265081	NM_002439.4	655	ata/atAa	14/24	0.431167282031548	1	FACETS	0.96	0.894	1	0.96	0.894	1	CLONAL	1	TRUE	0	0.431167282031548	1		492	807	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80160706	80160706	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	130	664	1	ENST00000265081.6:c.3078del	p.Asn1027IlefsTer33	p.N1027Ifs*33	ENST00000265081	NM_002439.4	1025	gtG/gt	22/24	0.431167282031548	1	FACETS	0.441	0.399	0.485	0.441	0.399	0.485	SUBCLONAL	1	TRUE	0	0.431167282031548	1		665	1073	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32191654	32191654	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1454	441	994	1	ENST00000375023.3:c.52G>T	p.Val18Phe	p.V18F	ENST00000375023	NM_004557.3	18	Gtc/Ttc	1/30	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.431167282031548	2		995	1895	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287590	33287590	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	374	714	0	ENST00000374542.5:c.1507T>C	p.Ser503Pro	p.S503P	ENST00000374542	NM_001141970.1	503	Tcc/Ccc	6/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.431167282031548	2		714	1523	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662738	117662738	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	163	370	0	ENST00000368508.3:c.4727T>A	p.Ile1576Lys	p.I1576K	ENST00000368508	NM_002944.2	1576	aTa/aAa	29/43	0.256489093916747	1	FACETS	0.807	0.742	0.874	0.807	0.742	0.874	INDETERMINATE	1	TRUE	0	0.431167282031548	1		370	735	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001281	150001281	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	223	467	0	ENST00000253339.5:c.2323A>G	p.Lys775Glu	p.K775E	ENST00000253339		775	Aag/Gag	4/7	0.256489093916747	1	FACETS	0.825	0.768	0.883	0.825	0.768	0.883	INDETERMINATE	1	TRUE	0	0.431167282031548	1		467	984	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220357	55220358	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	321	787	0	ENST00000275493.2:c.747_747+1delinsAA		p.X249_splice	ENST00000275493	NM_005228.3	249		6/28	1	2	FACETS	0.983	0.926	1	0.983	0.926	1	CLONAL	1	TRUE	1	0.431167282031548	2		787	1515	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992777	68992777	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	201	625	0	ENST00000288368.4:c.1742A>T	p.His581Leu	p.H581L	ENST00000288368	NM_024870.2	581	cAt/cTt	16/40	1	2	FACETS	0.856	0.793	0.922	0.856	0.793	0.922	CLONAL	1	TRUE	1	0.431167282031548	2		625	1089	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606514	93606515	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1655	533	1146	2	ENST00000375746.1:c.334_335delinsAA	p.Gly112Lys	p.G112K	ENST00000375746	NM_001174167.1	112	GGg/AAg	2/14	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.431167282031548	2		1148	2188	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391949	139391949	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1644	182	1290	0	ENST00000277541.6:c.6242T>C	p.Leu2081Pro	p.L2081P	ENST00000277541	NM_017617.3	2081	cTg/cCg	34/34	0.431167282031548	1	FACETS	0.363	0.333	0.394	0.363	0.333	0.394	SUBCLONAL	1	TRUE	0	0.431167282031548	1		1290	1826	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412672	139412672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1217	592	1188	0	ENST00000277541.6:c.1172C>T	p.Pro391Leu	p.P391L	ENST00000277541	NM_017617.3	391	cCt/cTt	7/34	0.431167282031548	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.431167282031548	1		1188	1809	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0056892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	221	597	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.453312131219469	2	FACETS	1	0.976	1	0.535	0.504	0.567	INDETERMINATE	1	TRUE	0	0.853141008932537	2		597	484	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0056892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	134	306	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.453312131219469	2	FACETS	0.949	0.875	1	0.475	0.437	0.513	INDETERMINATE	1	TRUE	0	0.853141008932537	2		306	331	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	42	513	0	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.209	0.174	0.247	0.209	0.174	0.247	SUBCLONAL	1	TRUE	1	0.853141008932537	2		513	472	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	78	543	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.37	0.326	0.417	0.37	0.326	0.417	SUBCLONAL	1	TRUE	1	0.853141008932537	2		543	494	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325170	123325170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371358242	NA	P-0056892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	47	655	2	ENST00000358487.5:c.158C>T	p.Ala53Val	p.A53V	ENST00000358487	NM_000141.4	53	gCg/gTg	3/18	1	2	FACETS	0.171	0.144	0.202	0.171	0.144	0.202	SUBCLONAL	1	TRUE	1	0.853141008932537	2		657	643	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197307	94197308	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	32	442	0	ENST00000323929.3:c.1196dup	p.Arg400GlnfsTer3	p.R400Qfs*3	ENST00000323929	NM_005591.3	399	ttc/ttTc	11/20	1	2	FACETS	0.175	0.141	0.213	0.175	0.141	0.213	SUBCLONAL	1	TRUE	1	0.853141008932537	2		442	429	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152101	11152101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	60	680	0	ENST00000358026.2:c.4385G>A	p.Ser1462Asn	p.S1462N	ENST00000358026	NM_001128849.1	1462	aGc/aAc	31/36	1	2	FACETS	0.201	0.173	0.232	0.201	0.173	0.232	SUBCLONAL	1	TRUE	1	0.853141008932537	2		680	700	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106194036	106194036	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	20	268	0	ENST00000380013.4:c.4498A>C	p.Lys1500Gln	p.K1500Q	ENST00000380013	NM_001127208.2	1500	Aaa/Caa	10/11	1	2	FACETS	0.144	0.11	0.184	0.144	0.11	0.184	SUBCLONAL	1	TRUE	1	0.853141008932537	2		268	326	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706976	117706976	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	31	510	0	ENST00000368508.3:c.2174A>G	p.Asp725Gly	p.D725G	ENST00000368508	NM_002944.2	725	gAc/gGc	15/43	1	2	FACETS	0.123	0.099	0.151	0.123	0.099	0.151	SUBCLONAL	1	TRUE	1	0.853141008932537	2		510	589	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0056893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	241	613	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.527625049652781	2		613	814	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	108	346	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.972	0.879	1	0.972	0.879	1	CLONAL	1	TRUE	1	0.527625049652781	2		347	421	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0056893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	225	788	4	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.527625049652781	2		792	804	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0056893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	152	463	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.774	0.718	0.832	1	0.99	1	SUBCLONAL	2	TRUE	1	0.527625049652781	2		463	372	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0056893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	95	429	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.527625049652781	2		429	299	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0056893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	99	418	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.527625049652781	2		418	327	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0056893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	52	386	2	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	2	FACETS	0.603	0.516	0.697	0.603	0.516	0.697	SUBCLONAL	1	TRUE	1	0.527625049652781	2		388	327	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0056893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	177	703	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.979	0.906	1	0.979	0.906	1	CLONAL	1	TRUE	1	0.527625049652781	2		704	685	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0056893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	81	358	7	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.936	0.832	1	0.936	0.832	1	CLONAL	1	TRUE	1	0.527625049652781	2		365	328	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0056893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	139	393	5	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.527625049652781	2		398	447	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993336	72993336	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	340	994	4	ENST00000268489.5:c.709C>T	p.Arg237Ter	p.R237*	ENST00000268489	NM_006885.3	237	Cga/Tga	2/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.527625049652781	2		998	1219	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717731	89717732	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1114167661	NA	P-0056893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	119	413	0	ENST00000371953.3:c.757dup	p.Ile253AsnfsTer45	p.I253Nfs*45	ENST00000371953	NM_000314.4	252	-/A	7/9	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.527625049652781	2		413	366	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117854	70117854	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	197	650	0	ENST00000245479.2:c.322C>T	p.Pro108Ser	p.P108S	ENST00000245479	NM_000346.3	108	Ccc/Tcc	1/3	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.527625049652781	2		650	663	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0056893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	68	1029	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.239	0.207	0.274	0.239	0.207	0.274	SUBCLONAL	1	TRUE	1	0.527625049652781	2		1032	1080	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0056893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	367	2623	7	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	1	2	FACETS	0.941	0.891	0.992	0.941	0.891	0.992	CLONAL	1	TRUE	1	0.527625049652781	2		2630	1479	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941004	71941004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1274	106	1238	0	ENST00000298229.2:c.884del	p.Pro295GlnfsTer20	p.P295Qfs*20	ENST00000298229	NM_001567.3	294	Ccc/cc	8/28	1	2	FACETS	0.291	0.26	0.325	0.291	0.26	0.325	SUBCLONAL	1	TRUE	1	0.527625049652781	2		1238	1380	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740726	58740727	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1194694298	NA	P-0056893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	194	531	0	ENST00000305921.3:c.1636dup	p.Leu546ProfsTer6	p.L546Pfs*6	ENST00000305921	NM_003620.3	544	ggc/ggCc	6/6	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.527625049652781	2		531	612	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646980	23646981	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0056893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	123	689	1	ENST00000261584.4:c.886dup	p.Met296AsnfsTer7	p.M296Nfs*7	ENST00000261584	NM_024675.3	296	atg/aAtg	4/13	1	2	FACETS	0.957	0.871	1	0.957	0.871	1	CLONAL	1	TRUE	1	0.527625049652781	2		690	487	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993675	90993676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0056893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	69	291	0	ENST00000265433.3:c.247dup	p.Met83AsnfsTer23	p.M83Nfs*23	ENST00000265433	NM_002485.4	83	atg/aAtg	3/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.527625049652781	2		291	225	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434850	99434850	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1282070639	NA	P-0056893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	205	681	0	ENST00000268035.6:c.937C>T	p.Arg313Cys	p.R313C	ENST00000268035	NM_000875.3	313	Cgc/Tgc	3/21	1	2	FACETS	0.976	0.908	1	0.976	0.908	1	CLONAL	1	TRUE	1	0.527625049652781	2		681	796	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656909	45656909	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1285747758	NA	P-0056893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	352	891	0	ENST00000407780.3:c.247C>T	p.Arg83Ter	p.R83*	ENST00000407780	NM_001283052.1	83	Cga/Tga	3/7	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.527625049652781	2		891	1192	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074055	8074055	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1032815946	NA	P-0056893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	20	318	0	ENST00000377482.5:c.604C>T	p.Arg202Cys	p.R202C	ENST00000377482	NM_018948.3	202	Cgt/Tgt	4/4	1	2	FACETS	0.282	0.215	0.359	0.282	0.215	0.359	SUBCLONAL	1	TRUE	1	0.527625049652781	2		318	269	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920380	114920381	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0056893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	129	448	0	ENST00000543371.1:c.1321_1322del	p.Ala441LysfsTer13	p.A441Kfs*13	ENST00000543371	NM_001198531.1	441	GCa/a	13/14	1	2	FACETS	0.872	0.794	0.953	0.872	0.794	0.953	CLONAL	1	TRUE	1	0.527625049652781	2		448	561	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924729	94924732	+	frameshift_variant	Frame_Shift_Del	DEL	AGTT	AGTT	-	novel	NA	P-0056893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	143	662	0	ENST00000536441.1:c.178_181del	p.Asn60PhefsTer19	p.N60Ffs*19	ENST00000536441	NM_144665.3	60	AACTtt/tt	3/10	1	2	FACETS	0.959	0.879	1	0.959	0.879	1	CLONAL	1	TRUE	1	0.527625049652781	2		662	565	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992965	72992965	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	278	1033	0	ENST00000268489.5:c.1080del	p.Gly361AspfsTer35	p.G361Dfs*35	ENST00000268489	NM_006885.3	360	ccC/cc	2/10	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.527625049652781	2		1033	1045	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346902	89346902	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	11	581	0	ENST00000301030.4:c.6048del	p.Ala2017ProfsTer70	p.A2017Pfs*70	ENST00000301030	NM_001256183.1	2016	ccC/cc	9/13	1	2	FACETS	0.104	0.071	0.145	0.104	0.071	0.145	SUBCLONAL	1	TRUE	1	0.527625049652781	2		581	400	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508267	38508267	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	227	735	3	ENST00000254066.5:c.575G>T	p.Arg192Leu	p.R192L	ENST00000254066	NM_000964.3	192	cGc/cTc	5/9	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.527625049652781	2		738	782	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246767	41246767	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	126	436	0	ENST00000357654.3:c.781T>C	p.Tyr261His	p.Y261H	ENST00000357654	NM_007294.3	261	Tat/Cat	10/23	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.527625049652781	2		436	469	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308312	15308312	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	228	755	0	ENST00000263388.2:c.196C>A	p.Leu66Met	p.L66M	ENST00000263388	NM_000435.2	66	Ctg/Atg	2/33	1	2	FACETS	0.945	0.881	1	0.945	0.881	1	CLONAL	1	TRUE	1	0.527625049652781	2		755	915	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966174	25966174	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199802259	NA	P-0056893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	220	664	0	ENST00000435504.4:c.3032A>G	p.Gln1011Arg	p.Q1011R	ENST00000435504		1011	cAg/cGg	13/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.527625049652781	2		664	762	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975388	13975388	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	194	537	0	ENST00000405192.2:c.499G>T	p.Ala167Ser	p.A167S	ENST00000405192	NM_001163147.1	167	Gct/Tct	7/12	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.527625049652781	2		537	712	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570310	87570310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	251	819	0	ENST00000277120.3:c.2050G>A	p.Ala684Thr	p.A684T	ENST00000277120		684	Gcg/Acg	17/19	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.527625049652781	2		819	920	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0056894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	36	325	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		325	211	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0056896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	28	330	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.25976730566135	3	FACETS	0.832	0.667	1	0.416	0.333	0.509	CLONAL	1	TRUE	1	0.290914136688146	3		330	265	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0056896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	65	1039	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	1	2	FACETS	0.678	0.587	0.776	0.678	0.587	0.776	SUBCLONAL	1	TRUE	1	0.290914136688146	2		1039	659	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141012	55141012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501502	NA	P-0056896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	19	258	0	ENST00000257290.5:c.1658C>T	p.Pro553Leu	p.P553L	ENST00000257290	NM_006206.4	553	cCg/cTg	12/23	0.279467402203279	1	FACETS	0.467	0.355	0.598	0.467	0.355	0.598	SUBCLONAL	1	TRUE	0	0.290914136688146	1		258	239	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0056898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	320	613	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.850907802117213	2		613	735	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0056898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	162	330	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.94	0.873	1	0.94	0.873	1	CLONAL	1	TRUE	1	0.850907802117213	2		330	405	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	372	825	2	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.954	0.908	0.999	0.954	0.908	0.999	CLONAL	1	TRUE	1	0.850907802117213	2		827	917	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0056898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	415	504	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.84862911632954	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.850907802117213	2		504	481	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0056898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	389	900	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.924	0.881	0.968	0.924	0.881	0.968	CLONAL	1	TRUE	1	0.850907802117213	2		904	989	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528105	157528105	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1028186690	NA	P-0056898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	283	649	0	ENST00000346085.5:c.5830C>T	p.Arg1944Ter	p.R1944*	ENST00000346085	NM_020732.3	1944	Cga/Tga	20/20	1	2	FACETS	0.957	0.905	1	0.957	0.905	1	CLONAL	1	TRUE	1	0.850907802117213	2		649	695	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944382	131944382	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs748536322	NA	P-0056898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	81	172	2	ENST00000265335.6:c.2801del	p.Asn934IlefsTer6	p.N934Ifs*6	ENST00000265335		932	Aaa/aa	17/25	1	2	FACETS	0.971	0.875	1	0.971	0.875	1	CLONAL	1	TRUE	1	0.850907802117213	2		174	196	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	272	647	2	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	0.838	0.79	0.887	0.838	0.79	0.887	CLONAL	1	TRUE	1	0.850907802117213	2		649	763	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165216	32165216	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767972771	NA	P-0056898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	74	1117	6	ENST00000375023.3:c.4912del	p.Leu1638CysfsTer68	p.L1638Cfs*68	ENST00000375023	NM_004557.3	1638	Ctg/tg	27/30	1	2	FACETS	0.144	0.125	0.164	0.144	0.125	0.164	SUBCLONAL	1	TRUE	1	0.850907802117213	2		1123	1208	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850704	63850705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	115	337	0	ENST00000279873.7:c.1489dup	p.Ile497AsnfsTer31	p.I497Nfs*31	ENST00000279873	NM_032199.2	494	-/A	10/10	1	2	FACETS	0.788	0.718	0.86	0.788	0.718	0.86	SUBCLONAL	1	TRUE	1	0.850907802117213	2		337	343	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068315	30068315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141649026	NA	P-0056898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	21	319	0	ENST00000331968.5:c.2084G>A	p.Arg695Gln	p.R695Q	ENST00000331968	NM_002742.2	695	cGg/cAg	15/18	1	2	FACETS	0.162	0.124	0.206	0.162	0.124	0.206	SUBCLONAL	1	TRUE	1	0.850907802117213	2		319	305	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591149	67591151	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0056898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	134	286	0	ENST00000274335.5:c.1744_1745+1del		p.LMdel	ENST00000274335		581	tTGAtg/ttg	12/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.850907802117213	2		286	300	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262581	39262581	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs397517180	NA	P-0056898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	174	457	0	ENST00000402219.2:c.925G>T	p.Asp309Tyr	p.D309Y	ENST00000402219	NM_005633.3	309	Gat/Tat	7/23	1	2	FACETS	0.901	0.838	0.965	0.901	0.838	0.965	CLONAL	1	TRUE	1	0.850907802117213	2		457	454	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	530	1174	0	ENST00000227507.2:c.859C>A	p.Pro287Thr	p.P287T	ENST00000227507	NM_053056.2	287	Ccc/Acc	5/5	1	2	FACETS	0.984	0.945	1	0.984	0.945	1	CLONAL	1	TRUE	1	0.850907802117213	2		1174	1266	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49399928	49399928	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0056898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	67	566	0	ENST00000418115.1:c.408+1G>A		p.X136_splice	ENST00000418115	NM_001664.2	136			1	2	FACETS	0.252	0.218	0.288	0.252	0.218	0.288	SUBCLONAL	1	TRUE	1	0.850907802117213	2		566	626	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100399	157100399	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	82	137	0	ENST00000346085.5:c.1337del	p.Pro446ArgfsTer56	p.P446Rfs*56	ENST00000346085	NM_020732.3	446	Ccg/cg	1/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.850907802117213	2		137	175	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141557648	141557648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	531	1244	1	ENST00000220592.5:c.1667C>T	p.Thr556Met	p.T556M	ENST00000220592	NM_012154.3	556	aCg/aTg	13/19	1	2	FACETS	0.931	0.893	0.968	0.931	0.893	0.968	CLONAL	1	TRUE	1	0.850907802117213	2		1245	1341	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101186	27101186	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	442	896	0	ENST00000324856.7:c.4468G>T	p.Glu1490Ter	p.E1490*	ENST00000324856	NM_006015.4	1490	Gag/Tag	18/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.850907802117213	2		896	1006	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777775	3777776	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0056898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	589	1179	0	ENST00000262367.5:c.7272_7273del	p.Ser2425ProfsTer21	p.S2425Pfs*21	ENST00000262367	NM_004380.2	2424	ctGTcc/ctcc	31/31	1	2	FACETS	0.983	0.946	1	0.983	0.946	1	CLONAL	1	TRUE	1	0.850907802117213	2		1179	1409	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925113	81925113	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	269	541	0	ENST00000359376.3:c.904T>C	p.Trp302Arg	p.W302R	ENST00000359376	NM_002661.3	302	Tgg/Cgg	11/33	1	2	FACETS	0.996	0.941	1	0.996	0.941	1	CLONAL	1	TRUE	1	0.850907802117213	2		541	635	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261041	16261041	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	334	637	0	ENST00000375759.3:c.8306C>G	p.Pro2769Arg	p.P2769R	ENST00000375759	NM_015001.2	2769	cCg/cGg	11/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.850907802117213	2		637	732	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512310	120512310	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	271	610	0	ENST00000256646.2:c.932del	p.Asn311MetfsTer85	p.N311Mfs*85	ENST00000256646	NM_024408.3	311	aAt/at	6/34	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.850907802117213	2		610	622	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843473	156843473	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754703492	NA	P-0056898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	255	939	0	ENST00000524377.1:c.899G>A	p.Cys300Tyr	p.C300Y	ENST00000524377	NM_002529.3	300	tGc/tAc	8/17	1	2	FACETS	0.636	0.596	0.677	0.636	0.596	0.677	SUBCLONAL	1	TRUE	1	0.850907802117213	2		939	943	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416066	49416066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	89	741	1	ENST00000301067.7:c.16409C>T	p.Ala5470Val	p.A5470V	ENST00000301067	NM_003482.3	5470	gCc/gTc	52/54	1	2	FACETS	0.224	0.198	0.253	0.224	0.198	0.253	SUBCLONAL	1	TRUE	1	0.850907802117213	2		742	932	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042402	16042402	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	218	562	0	ENST00000268712.3:c.1272G>A	p.Met424Ile	p.M424I	ENST00000268712	NM_006311.3	424	atG/atA	12/46	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.850907802117213	2		562	484	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30302682	30302682	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	162	559	0	ENST00000322652.5:c.773G>C	p.Gly258Ala	p.G258A	ENST00000322652	NM_015355.2	258	gGa/gCa	7/16	1	2	FACETS	0.648	0.597	0.7	0.648	0.597	0.7	SUBCLONAL	1	TRUE	1	0.850907802117213	2		559	588	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952358	38952358	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1177003651	NA	P-0056898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	152	275	0	ENST00000357387.3:c.3067A>G	p.Ser1023Gly	p.S1023G	ENST00000357387	NM_152756.3	1023	Agt/Ggt	30/38	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.850907802117213	2		275	348	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356803	70356803	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	402	875	0	ENST00000374080.3:c.5475C>A	p.Asn1825Lys	p.N1825K	ENST00000374080		1825	aaC/aaA	38/45	1	2	FACETS	0.917	0.875	0.96	0.917	0.875	0.96	CLONAL	1	TRUE	1	0.850907802117213	2		875	1030	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861469	152861469	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	106	320	0	ENST00000406277.2:c.283T>C	p.Ser95Pro	p.S95P	ENST00000406277	NM_152274.4	95	Tcc/Ccc	4/7	1		FACETS		0.625	0.758				SUBCLONAL	1	TRUE	1	0.850907802117213	2		320	361	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0056899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	181	330	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.721062883505864	4	FACETS	0.932	0.879	0.985	0.932	0.879	0.985	CLONAL	3	TRUE	1	0.721062883505864	4		330	309	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0056899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	100	304	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.66119378415639	4	FACETS	0.879	0.809	0.948	0.879	0.809	0.948	CLONAL	3	TRUE	1	0.721062883505864	4		304	181	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0056899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	209	281	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	0.66119378415639	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	3	TRUE	1	0.721062883505864	4		281	330	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870260	44870260	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	131	453	0	ENST00000377967.4:c.439C>T	p.Gln147Ter	p.Q147*	ENST00000377967	NM_021140.2	147	Cag/Tag	5/29	0.721062883505864	7	FACETS	0.836	0.761	0.914	0.418	0.38	0.457	CLONAL	2	TRUE	3	0.721062883505864	7		453	609	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933442	100933443	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0056899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	53	412	0	ENST00000325455.5:c.1947_1948del	p.Arg649SerfsTer16	p.R649Sfs*16	ENST00000325455	NM_001202474.3	649	agAGca/agca	4/8	1	2	FACETS	0.87	0.756	0.99	0.87	0.756	0.99	CLONAL	1	TRUE	1	0.721062883505864	2		412	169	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0056900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	425	722	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.642776382073282	1	FACETS	0.99	0.949	1	0.99	0.949	1	CLONAL	1	TRUE	0	0.642776382073282	1		722	906	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0056900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	342	633	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	NA	2	FACETS	0.888	0.84	0.937			1	INDETERMINATE	1	TRUE	NA	0.642776382073282	2		633	1198	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796472	42796472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367725186	NA	P-0056900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1485	85	1267	5	ENST00000575354.2:c.3029C>T	p.Ala1010Val	p.A1010V	ENST00000575354	NM_015125.3	1010	gCg/gTg	13/20	NA	2	FACETS	0.168	0.148	0.191			1	INDETERMINATE	1	TRUE	NA	0.642776382073282	2		1272	1570	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100312	157100312	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	250	377	0	ENST00000346085.5:c.1249C>G	p.Pro417Ala	p.P417A	ENST00000346085	NM_020732.3	417	Ccg/Gcg	1/20	0.243982215537472	3	FACETS	1	0.993	1	0.72	0.677	0.764	INDETERMINATE	1	TRUE	1	0.642776382073282	3		377	714	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998183	100998183	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	178	495	0	ENST00000325455.5:c.1619C>T	p.Pro540Leu	p.P540L	ENST00000325455	NM_001202474.3	540	cCc/cTc	1/8	0.285195185590612	1	FACETS	0.522	0.482	0.563	0.522	0.482	0.563	INDETERMINATE	1	TRUE	0	0.642776382073282	1		495	720	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818232	43818232	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	314	751	1	ENST00000372470.3:c.1697G>T	p.Ser566Ile	p.S566I	ENST00000372470	NM_005373.2	566	aGc/aTc	12/12	0.506339893276029	1	FACETS	0.75	0.71	0.791	0.75	0.71	0.791	SUBCLONAL	1	TRUE	0	0.642776382073282	1		752	884	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870921	12870921	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0056900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	29	358	0	ENST00000228872.4:c.148A>T	p.Arg50Ter	p.R50*	ENST00000228872	NM_004064.3	50	Aga/Tga	1/3	0.631644697229084	1	FACETS	0.135	0.107	0.165	0.135	0.107	0.165	SUBCLONAL	1	TRUE	0	0.642776382073282	1		358	455	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490366	56490366	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	212	458	0	ENST00000267101.3:c.2135T>G	p.Leu712Arg	p.L712R	ENST00000267101	NM_001982.3	712	cTt/cGt	18/28	0.240242319912465	2	FACETS	1	0.99	1	0.652	0.611	0.693	INDETERMINATE	1	TRUE	0	0.642776382073282	2		458	506	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	87	324	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.906	0.812	1	0.906	0.812	1	CLONAL	1	TRUE	1	0.669219264731945	2		324	287	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0056901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	170	317	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.669219264731945	3	FACETS	0.994	0.93	1	0.994	0.93	1	CLONAL	2	TRUE	1	0.669219264731945	3		317	341	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0056901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	140	463	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.366238875847361	1	FACETS	0.95	0.882	1	0.95	0.882	1	INDETERMINATE	1	TRUE	0	0.669219264731945	1		463	293	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455576	189455576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754361670	NA	P-0056901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	84	433	1	ENST00000264731.3:c.110G>A	p.Arg37Gln	p.R37Q	ENST00000264731	NM_003722.4	37	cGa/cAa	2/14	0.366238875847361	1	FACETS	0.685	0.614	0.757	0.685	0.614	0.757	INDETERMINATE	1	TRUE	0	0.669219264731945	1		434	244	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861646	152861646	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0056901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	153	335	0	ENST00000406277.2:c.107-1G>A		p.X36_splice	ENST00000406277	NM_152274.4	36			1		FACETS		0.99	1				CLONAL	1	TRUE	0	0.669219264731945	1		335	235	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971043	21971044	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCCAGCC	novel	NA	P-0056901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	99	536	0	ENST00000304494.5:c.308_314dup	p.Asp105GlufsTer17	p.D105Efs*17	ENST00000304494	NM_000077.4	105	gac/gaGGCTGGAc	2/3	0.669219264731945	1	FACETS	0.701	0.634	0.769	0.701	0.634	0.769	SUBCLONAL	1	TRUE	0	0.669219264731945	1		536	281	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	239	324	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.911932937450871	2		324	495	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0056904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	647	1167	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.911932937450871	2		1167	1401	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246555	46246565	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCAACAATG	GCGCAACAATG	-	novel	NA	P-0056904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	179	217	0	ENST00000334344.6:c.4650_4660del	p.Ala1551CysfsTer13	p.A1551Cfs*13	ENST00000334344	NM_152641.2	1550	aGCGCAACAATG/a	15/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.911932937450871	2		217	352	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579359	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0056924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	67	940	0	ENST00000269305.4:c.328dup	p.Arg110ProfsTer39	p.R110Pfs*39	ENST00000269305	NM_001126112.2	110	cgt/cCgt	4/11	0.533754639673982	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.533754639673982	1		940	148	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056435	26056435	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs769566015	NA	P-0056924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	32	415	0	ENST00000343677.2:c.222G>C	p.Glu74Asp	p.E74D	ENST00000343677	NM_005319.3	74	gaG/gaC	1/1	0.533754639673982	5	FACETS	1	0.919	1	0.411	0.337	0.493	CLONAL	1	TRUE	2	0.533754639673982	5		415	175	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589027	67589036	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTAAGCCAG	GGTAAGCCAG	-	novel	NA	P-0056924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	13	272	0	ENST00000274335.5:c.1118+2_1118+11del		p.X373_splice	ENST00000274335		373		8/15	0.291911846385042	4	FACETS	1	0.777	1	1	0.777	1	INDETERMINATE	2	TRUE	2	0.533754639673982	4		272	36	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0056925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	95	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.413476146021502	2	FACETS	1	0.942	1	0.538	0.482	0.596	CLONAL	1	TRUE	0	0.444843423002475	2		298	397	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0056925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	185	762	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.44274040290325	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.444843423002475	1		762	615	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0056925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	81	118	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.444843423002475	2	FACETS	0.828	0.742	0.915	0.828	0.742	0.915	CLONAL	2	TRUE	0	0.444843423002475	2		118	220	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	26	488	0	ENST00000263967.3:c.3012G>T	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atT	21/21	1	2	FACETS	0.304	0.24	0.377	0.304	0.24	0.377	SUBCLONAL	1	TRUE	1	0.444843423002475	2		488	385	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106142	27106142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369532498	NA	P-0056925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	121	726	0	ENST00000324856.7:c.5753G>A	p.Arg1918Gln	p.R1918Q	ENST00000324856	NM_006015.4	1918	cGg/cAg	20/20	1	2	FACETS	0.989	0.897	1	0.989	0.897	1	CLONAL	1	TRUE	1	0.444843423002475	2		726	550	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56855488	56855488	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567027753	NA	P-0056925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	116	373	0	ENST00000308159.5:c.637G>A	p.Ala213Thr	p.A213T	ENST00000308159	NM_014669.4	213	Gca/Aca	7/22	0.245642865699593	3	FACETS	1	0.983	1	0.699	0.634	0.767	INDETERMINATE	1	TRUE	1	0.444843423002475	3		373	456	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513310	44513310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs930924689	NA	P-0056925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	187	757	1	ENST00000291552.4:c.625C>T	p.Arg209Cys	p.R209C	ENST00000291552	NM_006758.2	209	Cgt/Tgt	8/8	0.171044888087321	2	FACETS	0.979	0.905	1	0.489	0.452	0.528	INDETERMINATE	1	TRUE	0	0.444843423002475	2		758	859	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0056926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	142	348	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.26927830281068	3	FACETS	1	0.961	1	0.547	0.499	0.597	CLONAL	1	TRUE	1	0.44	3		348	720	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0056926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	78	1039	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	1	2	FACETS	0.388	0.34	0.44	0.388	0.34	0.44	SUBCLONAL	1	TRUE	1	0.44	2		1039	913	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0056926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	49	381	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.3	1	FACETS	0.408	0.346	0.476	0.408	0.346	0.476	SUBCLONAL	1	TRUE	0	0.44	1		381	426	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121076	11121076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1131691371	NA	P-0056926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	48	792	0	ENST00000358026.2:c.2143G>A	p.Asp715Asn	p.D715N	ENST00000358026	NM_001128849.1	715	Gat/Aat	15/36	1	2	FACETS	0.278	0.234	0.327	0.278	0.234	0.327	SUBCLONAL	1	TRUE	1	0.44	2		792	785	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0056929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	197	306	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.267749795727201	3	FACETS	0.76	0.706	0.815	0.76	0.706	0.815	INDETERMINATE	2	TRUE	1	0.452986137156529	3		306	702	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	33	269	0	ENST00000257430.4:c.3925del	p.Glu1309LysfsTer12	p.E1309Kfs*12	ENST00000257430	NM_000038.5	1309	Gaa/aa	16/16	0.227670782524492	2	FACETS	0.406	0.331	0.49	0.203	0.165	0.245	INDETERMINATE	1	TRUE	0	0.452986137156529	2		269	359	SUCCESS
APC	324	MSKCC	GRCh37	5	112174266	112174266	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	173	402	0	ENST00000257430.4:c.2975del	p.Ser992IlefsTer13	p.S992Ifs*13	ENST00000257430	NM_000038.5	992	aGt/at	16/16	0.227670782524492	2	FACETS	0.779	0.723	0.837	0.779	0.723	0.837	INDETERMINATE	2	TRUE	0	0.452986137156529	2		402	490	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114799786	114799786	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0056929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	72	493	0	ENST00000543371.1:c.453T>G	p.Tyr151Ter	p.Y151*	ENST00000543371	NM_001198531.1	151	taT/taG	5/14	0.25639177641093	1	FACETS	0.397	0.347	0.451	0.397	0.347	0.451	INDETERMINATE	1	TRUE	0	0.452986137156529	1		493	619	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200100	67200100	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	236	835	0	ENST00000312629.5:c.487G>C	p.Glu163Gln	p.E163Q	ENST00000312629	NM_003952.2	163	Gag/Cag	6/15	0.309713596009323	1	FACETS	0.902	0.843	0.962	0.902	0.843	0.962	CLONAL	1	TRUE	0	0.452986137156529	1		835	894	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863253	57863253	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	350	799	0	ENST00000228682.2:c.1348A>T	p.Ser450Cys	p.S450C	ENST00000228682	NM_005269.2	450	Agt/Tgt	11/12	0.267749795727201	3	FACETS	0.827	0.783	0.871	0.827	0.783	0.871	INDETERMINATE	2	TRUE	1	0.452986137156529	3		799	1146	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646968	37646968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	185	499	0	ENST00000447079.4:c.2090C>T	p.Pro697Leu	p.P697L	ENST00000447079	NM_015083.1	697	cCa/cTa	3/14	0.25639177641093	1	FACETS	0.89	0.824	0.958	0.89	0.824	0.958	INDETERMINATE	1	TRUE	0	0.452986137156529	1		499	710	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260647	1260647	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	135	796	0	ENST00000310581.5:c.2912G>T	p.Arg971Leu	p.R971L	ENST00000310581	NM_198253.2	971	cGt/cTt	12/16	0.255244777191612	2	FACETS	0.551	0.5	0.605	0.275	0.25	0.303	INDETERMINATE	1	TRUE	0	0.452986137156529	2		796	1082	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128419935	128419935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	203	535	1	ENST00000265960.3:c.493G>T	p.Gly165Cys	p.G165C	ENST00000265960	NM_001006617.1	165	Ggc/Tgc	4/12	0.222727071872103	3	FACETS	1	0.99	1	0.709	0.659	0.761	INDETERMINATE	1	TRUE	1	0.452986137156529	3		536	775	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185001	123185001	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	44	353	0	ENST00000218089.9:c.1048G>A	p.Ala350Thr	p.A350T	ENST00000218089	NM_001042749.1	350	Gct/Act	12/35	0.25639177641093	1	FACETS	0.367	0.308	0.431	0.367	0.308	0.431	INDETERMINATE	1	TRUE	0	0.452986137156529	1		353	410	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023768	27023768	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	60	325	3	ENST00000324856.7:c.874del	p.Thr292ProfsTer71	p.T292Pfs*71	ENST00000324856	NM_006015.4	292	Acc/cc	1/20	1	2	FACETS	0.75	0.647	0.861	0.75	0.647	0.861	SUBCLONAL	1	TRUE	1	0.340423161236763	2		328	470	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112639	115112640	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0056930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	147	811	0	ENST00000257566.3:c.1100_1101del	p.Asp367ValfsTer7	p.D367Vfs*7	ENST00000257566	NM_016569.3	367	gAT/g	7/8	1	2	FACETS	0.889	0.811	0.971	0.889	0.811	0.971	CLONAL	1	TRUE	1	0.340423161236763	2		811	971	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862199	68862199	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs587780787	NA	P-0056930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	148	529	0	ENST00000261769.5:c.2287G>T	p.Glu763Ter	p.E763*	ENST00000261769	NM_004360.3	763	Gag/Tag	14/16	0.340423161236763	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.340423161236763	1		529	634	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0056932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	154	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.199164441348294	5	FACETS	1	0.97	1	0.744	0.684	0.806	INDETERMINATE	2	TRUE	2	0.370109322563975	5		298	580	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220400	1220400	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1359582062	NA	P-0056932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	263	880	0	ENST00000326873.7:c.493G>T	p.Glu165Ter	p.E165*	ENST00000326873	NM_000455.4	165	Gag/Tag	4/10	0.367329534320157	2	FACETS	0.893	0.84	0.947	0.893	0.84	0.947	CLONAL	2	TRUE	0	0.370109322563975	2		880	796	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727487	88727487	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1352987249	NA	P-0056932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	232	723	0	ENST00000360948.2:c.292G>T	p.Asp98Tyr	p.D98Y	ENST00000360948	NM_001012338.2	98	Gac/Tac	3/19	0.22525604594478	3	FACETS	0.989	0.926	1	0.989	0.926	1	CLONAL	2	TRUE	1	0.370109322563975	3		723	751	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106066	8106066	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	157	577	0	ENST00000346208.3:c.886C>A	p.Gln296Lys	p.Q296K	ENST00000346208		296	Cag/Aag	4/6	0.199164441348294	5	FACETS	0.881	0.808	0.956	0.587	0.539	0.638	INDETERMINATE	2	TRUE	2	0.370109322563975	5		577	749	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175777	176175777	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	152	660	0	ENST00000367669.3:c.338G>C	p.Arg113Pro	p.R113P	ENST00000367669	NM_022457.5	113	cGa/cCa	1/20	0.327795260512444	5	FACETS	1	0.986	1	0.353	0.323	0.385	CLONAL	1	TRUE	1	0.370109322563975	5		660	904	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620389	43620389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	161	673	0	ENST00000355710.3:c.2998G>A	p.Asp1000Asn	p.D1000N	ENST00000355710	NM_020975.4	1000	Gac/Aac	18/20	0.199164441348294	5	FACETS	0.895	0.822	0.97	0.597	0.548	0.647	INDETERMINATE	2	TRUE	2	0.370109322563975	5		673	756	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518028	69518028	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0056932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	114	806	0	ENST00000294312.3:c.336+1del		p.X112_splice	ENST00000294312	NM_005117.2	112			1	2	FACETS	0.948	0.855	1	0.948	0.855	1	CLONAL	1	TRUE	1	0.370109322563975	2		806	650	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610223	10610223	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	297	948	1	ENST00000171111.5:c.487C>T	p.Gln163Ter	p.Q163*	ENST00000171111	NM_203500.1	163	Cag/Tag	2/6	0.367329534320157	2	FACETS	0.996	0.941	1	0.996	0.941	1	CLONAL	2	TRUE	0	0.370109322563975	2		949	806	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082931	16082931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1228008742	NA	P-0056932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	34	386	1	ENST00000281043.3:c.745C>T	p.His249Tyr	p.H249Y	ENST00000281043	NM_005378.4	249	Cac/Tac	2/3	0.370109322563975	3	FACETS	0.536	0.438	0.646	0.268	0.219	0.323	SUBCLONAL	1	TRUE	1	0.370109322563975	3		387	406	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739629	41739629	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	69	499	0	ENST00000242208.4:c.344A>G	p.Glu115Gly	p.E115G	ENST00000242208	NM_002192.2	115	gAa/gGa	2/3	0.361724615586399	3	FACETS	0.905	0.79	1	0.453	0.395	0.515	CLONAL	1	TRUE	1	0.370109322563975	3		499	488	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220293	55220293	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	207	869	0	ENST00000275493.2:c.683C>G	p.Pro228Arg	p.P228R	ENST00000275493	NM_005228.3	228	cCc/cGc	6/28	0.361724615586399	3	FACETS	1	0.989	1	0.672	0.623	0.722	CLONAL	1	TRUE	1	0.370109322563975	3		869	987	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0056937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	432	731	2	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.30687616215456	2	FACETS	0.955	0.916	0.995	0.955	0.916	0.995	CLONAL	2	TRUE	0	0.498571393385902	2		733	907	SUCCESS
APC	324	MSKCC	GRCh37	5	112175246	112175246	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1057517558	NA	P-0056937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	113	248	0	ENST00000257430.4:c.3956del	p.Pro1319LeufsTer2	p.P1319Lfs*2	ENST00000257430	NM_000038.5	1319	Cct/ct	16/16	0.429562256531415	2	FACETS	0.882	0.809	0.956	0.882	0.809	0.956	CLONAL	2	TRUE	0	0.498571393385902	2		248	257	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953214	81953214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369516453	NA	P-0056937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	287	454	0	ENST00000359376.3:c.2180G>A	p.Arg727Gln	p.R727Q	ENST00000359376	NM_002661.3	727	cGa/cAa	20/33	0.222442077461138	6	FACETS	0.974	0.92	1	0.974	0.92	1	INDETERMINATE	3	TRUE	3	0.498571393385902	6		454	787	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622148	1622148	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751551556	NA	P-0056937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	287	842	0	ENST00000344749.5:c.727G>A	p.Gly243Ser	p.G243S	ENST00000344749	NM_001136139.2	243	Ggc/Agc	10/19	0.445309823487812	2	FACETS	0.834	0.79	0.879	0.834	0.79	0.879	CLONAL	2	TRUE	0	0.498571393385902	2		842	690	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0056938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	28	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.759	0.605	0.936	0.759	0.605	0.936	CLONAL	1	TRUE	1	0.12	2		298	615	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0056938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	20	512	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.471	0.358	0.604	0.471	0.358	0.604	SUBCLONAL	1	TRUE	1	0.12	2		513	708	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574005	7574006	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	ACATCTCGAAGCGCTCACGCCC	novel	NA	P-0056939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	194	845	2	ENST00000269305.4:c.1000_1021dup	p.Phe341TrpfsTer3	p.F341Wfs*3	ENST00000269305	NM_001126112.2	341	ttc/tGGGCGTGAGCGCTTCGAGATGTtc	10/11	0.696378889597267	1	FACETS	0.633	0.589	0.677	0.633	0.589	0.677	SUBCLONAL	1	TRUE	0	0.696378889597267	1		847	574	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40483527	40483527	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	133	378	0	ENST00000264657.5:c.1072T>G	p.Leu358Val	p.L358V	ENST00000264657	NM_139276.2	358	Ttg/Gtg	11/24	0.696378889597267	1	FACETS	0.892	0.826	0.959	0.892	0.826	0.959	CLONAL	1	TRUE	0	0.696378889597267	1		378	279	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243938	41243938	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	211	702	0	ENST00000357654.3:c.3610del	p.Arg1204GlufsTer6	p.R1204Efs*6	ENST00000357654	NM_007294.3	1204	Aga/ga	10/23	0.696378889597267	1	FACETS	0.936	0.882	0.99	0.936	0.882	0.99	CLONAL	1	TRUE	0	0.696378889597267	1		702	422	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30733045	30733045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs569635708	NA	P-0056939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	53	610	0	ENST00000295754.5:c.1658C>T	p.Ser553Leu	p.S553L	ENST00000295754	NM_003242.5	553	tCg/tTg	7/7	0.252506833887456	4	FACETS	0.332	0.282	0.387			1	INDETERMINATE	1	TRUE	NA	0.696378889597267	4		610	777	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759781	133759781	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764106779	NA	P-0056940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	37	685	0	ENST00000318560.5:c.2104G>A	p.Glu702Lys	p.E702K	ENST00000318560	NM_005157.4	702	Gag/Aag	11/11	1	2	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	TRUE	1	0.14	2		685	518	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967768	18967768	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	43	834	1	ENST00000262803.5:c.1907A>T	p.Asp636Val	p.D636V	ENST00000262803	NM_002911.3	636	gAc/gTc	14/24	1	2	FACETS	0.897	0.749	1	0.897	0.749	1	CLONAL	1	TRUE	1	0.14	2		835	685	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198261022	198261022	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	29	432	0	ENST00000335508.6:c.3297C>G	p.Asn1099Lys	p.N1099K	ENST00000335508	NM_012433.2	1099	aaC/aaG	23/25	1	2	FACETS	0.998	0.801	1	0.998	0.801	1	CLONAL	1	TRUE	1	0.14	2		432	415	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402543	20402543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	17	352	0	ENST00000346618.3:c.80C>A	p.Ala27Asp	p.A27D	ENST00000346618	NM_001949.4	27	gCc/gAc	1/7	1	2	FACETS	0.725	0.54	0.945	0.725	0.54	0.945	CLONAL	1	TRUE	1	0.14	2		352	335	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375317	15375318	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCAA	novel	NA	P-0056941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	102	896	0	ENST00000263377.2:c.1109_1110insTTGC	p.Ala371CysfsTer23	p.A371Cfs*23	ENST00000263377	NM_058243.2	370	gcc/gcTTGCc	6/20	1	2	FACETS	0.694	0.625	0.765	0.694	0.625	0.765	SUBCLONAL	1	TRUE	1	0.75	2		896	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0056943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	404	746	1	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.667421568821976	2	FACETS	0.956	0.922	0.99	0.956	0.922	0.99	CLONAL	2	TRUE	0	0.667421568821976	2		747	633	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298526	11298526	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	228	744	0	ENST00000361445.4:c.1935C>G	p.Ser645Arg	p.S645R	ENST00000361445	NM_004958.3	645	agC/agG	12/58	0.667421568821976	2	FACETS	0.953	0.892	1	0.476	0.446	0.508	CLONAL	1	TRUE	0	0.667421568821976	2		744	717	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645691	215645691	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs375048835	NA	P-0056943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	125	597	0	ENST00000260947.4:c.907G>C	p.Val303Leu	p.V303L	ENST00000260947	NM_000465.2	303	Gtc/Ctc	4/11	0.642953847346667	3	FACETS	0.764	0.693	0.838	0.382	0.346	0.419	SUBCLONAL	1	TRUE	1	0.667421568821976	3		597	654	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394891	394891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	335	604	0	ENST00000380956.4:c.287G>T	p.Arg96Leu	p.R96L	ENST00000380956	NM_001195286.1	96	cGc/cTc	3/9	0.651705364043411	2	FACETS	1	0.988	1	0.565	0.536	0.594	CLONAL	1	TRUE	0	0.667421568821976	2		604	889	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76812979	76812979	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	156	293	0	ENST00000373344.5:c.6642A>C	p.Leu2214Phe	p.L2214F	ENST00000373344	NM_000489.3	2214	ttA/ttC	30/35	1	1	FACETS		NA	1	1	0.993	1	NA	2	TRUE	0	0.667421568821976	1		293	207	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0056944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	215	504	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.154076244924857	3	FACETS	0.815	0.756	0.876	0.543	0.504	0.584	CLONAL	2	TRUE	0	0.230625910672126	3		504	1276	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688715	47688758	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCCACAGTCCTCCTAACTCATCTGCCAGCCGGCACTCAGGAA	CTCCCACAGTCCTCCTAACTCATCTGCCAGCCGGCACTCAGGAA	-	novel	NA	P-0056944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	120	629	0	ENST00000347630.2:c.542_585del	p.Val181GlufsTer31	p.V181Efs*31	ENST00000347630	NM_001007230.1	181	gTTCCTGAGTGCCGGCTGGCAGATGAGTTAGGAGGACTGTGGGAG/g	7/11	0.154076244924857	3	FACETS	1	0.981	1	0.454	0.409	0.5	CLONAL	1	TRUE	0	0.230625910672126	3		629	853	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000039	30000039	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	148	638	1	ENST00000338641.4:c.52C>T	p.Gln18Ter	p.Q18*	ENST00000338641	NM_000268.3	18	Caa/Taa	1/16	0.111897880748312	5	FACETS	0.894	0.816	0.976	0.447	0.408	0.488	INDETERMINATE	2	TRUE	1	0.230625910672126	5		639	966	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0056947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	538	775	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.341240864196062	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	0	0.341240864196062	3		775	1198	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	194	212	0	ENST00000304494.5:c.322G>C	p.Asp108His	p.D108H	ENST00000304494	NM_000077.4	108	Gat/Cat	2/3	0.311120482421881	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.341240864196062	3		212	382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0056947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	496	879	0	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	0.341240864196062	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	TRUE	0	0.341240864196062	3		879	1124	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057764	27057764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	453	978	0	ENST00000324856.7:c.1474del	p.Gln492ArgfsTer127	p.Q492Rfs*127	ENST00000324856	NM_006015.4	491	tCc/tc	3/20	0.341240864196062	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.341240864196062	3		978	1515	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745999	162745999	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	398	429	0	ENST00000367921.3:c.2122C>T	p.His708Tyr	p.H708Y	ENST00000367921	NM_006182.2	708	Cac/Tac	16/18	0.341240864196062	6	FACETS	1	0.96	1	1	0.96	1	CLONAL	5	TRUE	1	0.341240864196062	6		429	783	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226510	41226510	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555582052	NA	P-0056947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	96	505	0	ENST00000357654.3:c.4513G>C	p.Asp1505His	p.D1505H	ENST00000357654	NM_007294.3	1505	Gat/Cat	14/23	0.341240864196062	3	FACETS	1	0.91	1	0.341	0.304	0.38	CLONAL	1	TRUE	0	0.341240864196062	3		505	644	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191571	10191572	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0056947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	104	653	0	ENST00000256474.2:c.564_565delinsTT	p.Glu189Ter	p.E189*	ENST00000256474	NM_000551.3	188	ctGGaa/ctTTaa	3/3	0.341168522748129	4	FACETS	0.839	0.75	0.934	0.28	0.25	0.312	CLONAL	1	TRUE	1	0.341240864196062	4		653	974	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599357	55599357	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1560422319	NA	P-0056947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	35	489	0	ENST00000288135.5:c.2483A>G	p.Asn828Ser	p.N828S	ENST00000288135	NM_000222.2	828	aAc/aGc	17/21	0.341240864196062	1	FACETS	0.577	0.474	0.691	0.577	0.474	0.691	SUBCLONAL	1	TRUE	0	0.341240864196062	1		489	295	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542383	187542383	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	64	483	0	ENST00000441802.2:c.5357C>T	p.Thr1786Ile	p.T1786I	ENST00000441802	NM_005245.3	1786	aCa/aTa	10/27	1	2	FACETS	0.954	0.83	1	0.954	0.83	1	CLONAL	1	TRUE	1	0.341240864196062	2		483	393	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027825	152027825	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0056947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	283	465	0	ENST00000262189.6:c.251-1G>C		p.X84_splice	ENST00000262189	NM_170606.2	84			0.248738749184186	4	FACETS	0.88	0.834	0.926			1	CLONAL	4	TRUE	NA	0.341240864196062	4		465	632	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945194	44945195	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0056947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	176	389	0	ENST00000377967.4:c.3519_3520dup	p.Trp1174SerfsTer5	p.W1174Sfs*5	ENST00000377967	NM_021140.2	1173	tac/taCTc	24/29	0.303351909087331	2	FACETS	0.942	0.882	1			1	CLONAL	3	TRUE	NA	0.341240864196062	2		389	365	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0056948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	98	221	1				ENST00000310581	NM_198253.2	-/1132			0.369136682653767	4	FACETS	1	0.973	1			1	CLONAL	2	TRUE	NA	0.534469791661603	4		222	235	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0056948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	489	317	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.534469791661603	9	FACETS	0.975	0.942	1	0.975	0.942	1	CLONAL	7	TRUE	2	0.534469791661603	9		317	770	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612028	189612028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs900140738	NA	P-0056948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	110	432	0	ENST00000264731.3:c.1780C>T	p.Arg594Ter	p.R594*	ENST00000264731	NM_003722.4	594	Cga/Tga	14/14	0.534469791661603	3	FACETS	0.909	0.819	1	0.454	0.409	0.502	CLONAL	1	TRUE	1	0.534469791661603	3		432	574	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049852	16049853	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0056948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	118	239	0	ENST00000268712.3:c.919dup	p.Ile307AsnfsTer6	p.I307Nfs*6	ENST00000268712	NM_006311.3	307	atc/aAtc	10/46	0.534469791661603	4	FACETS	0.908	0.828	0.991	0.908	0.828	0.991	CLONAL	2	TRUE	2	0.534469791661603	4		239	373	SUCCESS
MET	4233	MSKCC	GRCh37	7	116414965	116414965	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	266	482	0	ENST00000397752.3:c.3059C>T	p.Ser1020Leu	p.S1020L	ENST00000397752	NM_000245.2	1020	tCa/tTa	15/21	0.534469791661603	9	FACETS	1	0.942	1	0.288	0.269	0.307	CLONAL	2	TRUE	2	0.534469791661603	9		482	1419	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42790980	42790980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	435	612	0	ENST00000575354.2:c.125C>T	p.Pro42Leu	p.P42L	ENST00000575354	NM_015125.3	42	cCc/cTc	2/20	0.430080101169054	5	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.534469791661603	5		612	1247	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47108593	47108593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	152	311	0	ENST00000409792.3:c.6076C>T	p.Pro2026Ser	p.P2026S	ENST00000409792	NM_014159.6	2026	Cca/Tca	13/21	0.534469791661603	3	FACETS	0.961	0.89	1	0.961	0.89	1	CLONAL	2	TRUE	1	0.534469791661603	3		311	375	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514058	69514058	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	423	589	0	ENST00000294312.3:c.623C>T	p.Ala208Val	p.A208V	ENST00000294312	NM_005117.2	208	gCc/gTc	3/3	0.534469791661603	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.534469791661603	2		589	707	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333641	70333641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	247	387	0	ENST00000373644.4:c.1546C>T	p.Pro516Ser	p.P516S	ENST00000373644	NM_030625.2	516	Cca/Tca	2/12	0.146437803430705	3	FACETS	0.891	0.847	0.936			1	INDETERMINATE	3	TRUE	NA	0.534469791661603	3		387	438	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121625	108121625	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	225	384	1	ENST00000278616.4:c.1433C>T	p.Ser478Leu	p.S478L	ENST00000278616	NM_000051.3	478	tCa/tTa	10/63	0.534469791661603	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.534469791661603	2		385	378	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561350	9561350	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	241	464	0	ENST00000353224.5:c.432A>T	p.Glu144Asp	p.E144D	ENST00000353224	NM_177990.2	144	gaA/gaT	4/10	0.520745969325684	4	FACETS	0.991	0.931	1	0.991	0.931	1	CLONAL	2	TRUE	2	0.534469791661603	4		464	698	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540998	187540998	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	174	295	0	ENST00000441802.2:c.6742C>G	p.Pro2248Ala	p.P2248A	ENST00000441802	NM_005245.3	2248	Ccg/Gcg	10/27	0.466698632715972	4	FACETS	0.963	0.893	1	0.963	0.893	1	CLONAL	2	TRUE	2	0.534469791661603	4		295	519	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168674	56168674	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	172	306	0	ENST00000399503.3:c.1528G>T	p.Asp510Tyr	p.D510Y	ENST00000399503	NM_005921.1	510	Gat/Tat	9/20	0.534469791661603	4	FACETS	0.844	0.781	0.909	0.844	0.781	0.909	CLONAL	2	TRUE	2	0.534469791661603	4		306	585	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983289	149983289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253121553	NA	P-0056948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	283	440	0	ENST00000253339.5:c.2969G>A	p.Arg990Gln	p.R990Q	ENST00000253339		990	cGa/cAa	7/7	0.532310255695978	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.534469791661603	2		440	481	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439682	140439682	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	389	256	0	ENST00000288602.6:c.2057C>T	p.Pro686Leu	p.P686L	ENST00000288602	NM_004333.4	686	cCa/cTa	17/18	0.534469791661603	9	FACETS	1	0.97	1	1	0.97	1	CLONAL	7	TRUE	2	0.534469791661603	9		256	593	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782197	NA	P-0056949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	360	838	1	ENST00000269305.4:c.434T>C	p.Leu145Pro	p.L145P	ENST00000269305	NM_001126112.2	145	cTg/cCg	5/11	0.363266006541288	2	FACETS	0.803	0.763	0.844	0.803	0.763	0.844	CLONAL	2	TRUE	0	0.432140132110109	2		839	1037	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643770	52643770	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	134	526	0	ENST00000394830.3:c.2126T>A	p.Ile709Asn	p.I709N	ENST00000394830	NM_018313.4	709	aTt/aAt	17/30	0.388169220932659	1	FACETS	0.859	0.784	0.937	0.859	0.784	0.937	CLONAL	1	TRUE	0	0.432140132110109	1		526	566	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650325	48650325	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs184815507	NA	P-0056949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	152	418	0	ENST00000376670.3:c.295G>A	p.Gly99Ser	p.G99S	ENST00000376670	NM_002049.3	99	Ggc/Agc	3/6	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.432140132110109	1		418	400	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227670	53227670	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0056949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	132	276	0	ENST00000375401.3:c.2516+2T>C		p.X839_splice	ENST00000375401	NM_004187.3	839			1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.432140132110109	1		276	331	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183788	10183788	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	123	401	0	ENST00000256474.2:c.257C>A	p.Pro86His	p.P86H	ENST00000256474	NM_000551.3	86	cCc/cAc	1/3	0.388169220932659	1	FACETS	0.903	0.821	0.989	0.903	0.821	0.989	CLONAL	1	TRUE	0	0.432140132110109	1		401	494	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352333	73352333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	165	430	0	ENST00000377767.4:c.572C>T	p.Ala191Val	p.A191V	ENST00000377767	NM_014953.3	191	gCt/gTt	3/21	0.396728846506851	3	FACETS	0.796	0.735	0.86	0.531	0.49	0.573	SUBCLONAL	2	TRUE	0	0.432140132110109	3		430	583	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546711	9546711	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	62	423	0	ENST00000353224.5:c.1311G>C	p.Gln437His	p.Q437H	ENST00000353224	NM_177990.2	437	caG/caC	5/10	NA	2	FACETS	0.73	0.633	0.835			1	INDETERMINATE	1	TRUE	NA	0.432140132110109	2		423	393	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348784	89348784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758148858	NA	P-0056950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	129	898	0	ENST00000301030.4:c.4166C>T	p.Ser1389Phe	p.S1389F	ENST00000301030	NM_001256183.1	1389	tCc/tTc	9/13	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		898	469	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827759	72827759	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1185453374	NA	P-0056951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	321	602	0	ENST00000268489.5:c.8822G>T	p.Gly2941Val	p.G2941V	ENST00000268489	NM_006885.3	2941	gGa/gTa	9/10	1	2	FACETS	0.892	0.843	0.942	0.892	0.843	0.942	CLONAL	1	TRUE	1	0.659287498295771	2		602	1092	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267381	198267381	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	153	439	0	ENST00000335508.6:c.1976A>G	p.Gln659Arg	p.Q659R	ENST00000335508	NM_012433.2	659	cAa/cGa	14/25	1	2	FACETS	0.879	0.809	0.951	0.879	0.809	0.951	CLONAL	1	TRUE	1	0.659287498295771	2		439	528	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131208	55131208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	175	395	0	ENST00000257290.5:c.751G>A	p.Gly251Arg	p.G251R	ENST00000257290	NM_006206.4	251	Gga/Aga	5/23	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.659287498295771	2		395	506	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061194	+	frameshift_variant	Frame_Shift_Del	DEL	GAAG	GAAG	CTT	novel	NA	P-0056951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	385	363	1	ENST00000250448.2:c.795_798delinsAAG	p.Phe266ArgfsTer55	p.F266Rfs*55	ENST00000250448	NM_004496.3	265	cgCTTC/cgAAG	2/2	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.659287498295771	2		364	802	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0056955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	372	762	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.595508249078363	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.595508249078363	1		762	787	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218914	193218914	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	61	337	0	ENST00000367435.3:c.1472A>C	p.Lys491Thr	p.K491T	ENST00000367435	NM_024529.4	491	aAa/aCa	16/17	1	2	FACETS	0.803	0.701	0.913	0.803	0.701	0.913	CLONAL	1	TRUE	1	0.595508249078363	2		337	255	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881418	48881418	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	93	195	0	ENST00000267163.4:c.141del	p.Glu48SerfsTer17	p.E48Sfs*17	ENST00000267163	NM_000321.2	47	cTt/ct	2/27	0.55444293009303	2	FACETS	0.813	0.742	0.885	0.813	0.742	0.885	CLONAL	2	TRUE	0	0.595508249078363	2		195	192	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629718	187629718	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs370104838	NA	P-0056955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	193	723	0	ENST00000441802.2:c.1264A>G	p.Ile422Val	p.I422V	ENST00000441802	NM_005245.3	422	Att/Gtt	2/27	1	2	FACETS	0.904	0.839	0.971	0.904	0.839	0.971	CLONAL	1	TRUE	1	0.595508249078363	2		723	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0056956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	125	1058	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.26443144276708	1	FACETS	0.923	0.835	1	0.923	0.835	1	CLONAL	1	FALSE	0	0.26443144276708	1		1058	889	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713801	30713801	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	60	834	1	ENST00000295754.5:c.1126G>T	p.Val376Leu	p.V376L	ENST00000295754	NM_003242.5	376	Gtg/Ttg	4/7	1	2	FACETS	0.482	0.414	0.557	0.482	0.414	0.557	SUBCLONAL	1	FALSE	1	0.26443144276708	2		835	941	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170313	32170313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201260854	NA	P-0056956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	80	1031	1	ENST00000375023.3:c.3295G>A	p.Gly1099Arg	p.G1099R	ENST00000375023	NM_004557.3	1099	Gga/Aga	21/30	1	2	FACETS	0.652	0.573	0.738	0.652	0.573	0.738	SUBCLONAL	1	FALSE	1	0.26443144276708	2		1032	928	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220371	1220372	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0056956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	53	811	2	ENST00000326873.7:c.465-1_465delinsTT		p.X155_splice	ENST00000326873	NM_000455.4	155		4/10	0.26443144276708	0	FACETS	0.557	0.475	0.647			1	SUBCLONAL	1	FALSE	0	0.26443144276708	0		813	529	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430869	181430869	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	88	1146	0	ENST00000325404.1:c.721G>T	p.Gly241Cys	p.G241C	ENST00000325404	NM_003106.3	241	Ggt/Tgt	1/1	1	2	FACETS	0.533	0.471	0.601	0.533	0.471	0.601	SUBCLONAL	1	FALSE	1	0.26443144276708	2		1146	1248	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729966	41729966	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	63	902	0	ENST00000242208.4:c.563C>A	p.Thr188Lys	p.T188K	ENST00000242208	NM_002192.2	188	aCa/aAa	3/3	0.137083972613353	3	FACETS	0.533	0.459	0.614	0.267	0.229	0.307	INDETERMINATE	1	FALSE	1	0.26443144276708	3		902	1012	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155372	99155372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	49	540	0	ENST00000074304.5:c.598G>A	p.Glu200Lys	p.E200K	ENST00000074304	NM_001134224.1	200	Gag/Aag	9/26	1	2	FACETS	0.518	0.438	0.607	0.518	0.438	0.607	SUBCLONAL	1	FALSE	1	0.26443144276708	2		540	715	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636309	21636309	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0056956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	42	424	0	ENST00000421138.2:c.700+1del		p.X234_splice	ENST00000421138		234			0.0895907240775646	4	FACETS	0.62	0.516	0.735	0.31	0.258	0.368	INDETERMINATE	1	FALSE	2	0.26443144276708	4		424	648	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241001	133241001	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	66	869	4	ENST00000320574.5:c.2516G>T	p.Gly839Val	p.G839V	ENST00000320574	NM_006231.2	839	gGg/gTg	22/49	0.26443144276708	1	FACETS	0.616	0.534	0.705	0.616	0.534	0.705	SUBCLONAL	1	FALSE	0	0.26443144276708	1		873	703	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599910	10599910	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	76	999	0	ENST00000171111.5:c.1666G>C	p.Ala556Pro	p.A556P	ENST00000171111	NM_203500.1	556	Gcc/Ccc	5/6	0.26443144276708	0	FACETS	0.5	0.438	0.568			1	SUBCLONAL	1	FALSE	0	0.26443144276708	0		999	845	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435913	110435913	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	50	766	0	ENST00000375856.3:c.2488G>T	p.Val830Leu	p.V830L	ENST00000375856	NM_003749.2	830	Gtg/Ttg	1/2	1	2	FACETS	0.482	0.407	0.564	0.482	0.407	0.564	SUBCLONAL	1	FALSE	1	0.26443144276708	2		766	785	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	285	504	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.829	0.779	0.88	1	0.994	1	CLONAL	2	TRUE	1	0.307410396627788	2		504	1119	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416710	29416710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	256	450	0	ENST00000389048.3:c.4243C>T	p.Pro1415Ser	p.P1415S	ENST00000389048	NM_004304.4	1415	Ccc/Tcc	29/29	0.307410396627788	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.307410396627788	3		450	786	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934037	39934037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	227	819	2	ENST00000378444.4:c.562C>T	p.Arg188Trp	p.R188W	ENST00000378444	NM_001123385.1	188	Cgg/Tgg	4/15	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.307410396627788	2		821	1019	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076862	41076862	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs750249800	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	104	544	0	ENST00000373198.4:c.1558G>A	p.Glu520Lys	p.E520K	ENST00000373198	NM_133170.3	520	Gag/Aag	9/32	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.307410396627788	2		544	621	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294045	1294045	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1213662764	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	295	1073	1	ENST00000310581.5:c.956C>T	p.Thr319Met	p.T319M	ENST00000310581	NM_198253.2	319	aCg/aTg	2/16	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.307410396627788	2		1074	1312	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087961	27087961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	209	537	0	ENST00000324856.7:c.2248C>T	p.Arg750Ter	p.R750*	ENST00000324856	NM_006015.4	750	Cga/Tga	6/20	1	2	FACETS	0.82	0.763	0.879	1	0.992	1	CLONAL	2	TRUE	1	0.307410396627788	2		537	829	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892299	9892299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs796052549	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	137	517	0	ENST00000330684.3:c.2191G>A	p.Asp731Asn	p.D731N	ENST00000330684	NM_001134407.1	731	Gat/Aat	11/13	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.307410396627788	2		517	599	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418997	116418997	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200754673	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	58	252	0	ENST00000397752.3:c.3508C>T	p.Arg1170Ter	p.R1170*	ENST00000397752	NM_000245.2	1170	Cga/Tga	17/21	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.307410396627788	2		252	358	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720744	89720744	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167674	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	12	242	0	ENST00000371953.3:c.895G>T	p.Glu299Ter	p.E299*	ENST00000371953	NM_000314.4	299	Gaa/Taa	8/9	1	2	FACETS	0.361	0.254	0.494	0.361	0.254	0.494	SUBCLONAL	1	TRUE	1	0.307410396627788	2		242	216	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021428	42021428	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	129	482	0	ENST00000219905.7:c.3724C>T	p.Arg1242Ter	p.R1242*	ENST00000219905	NM_001164273.1	1242	Cga/Tga	11/24	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.307410396627788	2		482	655	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008548	70008548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771113831	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	143	401	0	ENST00000394351.3:c.835C>T	p.Arg279Trp	p.R279W	ENST00000394351	NM_000248.3	279	Cgg/Tgg	8/9	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.307410396627788	2		401	709	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920785	100920785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371165895	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	53	368	0	ENST00000325455.5:c.2363G>A	p.Arg788Gln	p.R788Q	ENST00000325455	NM_001202474.3	788	cGg/cAg	6/8	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.307410396627788	2		368	342	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515141	103515141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770246574	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	79	279	0	ENST00000355739.4:c.1642G>A	p.Glu548Lys	p.E548K	ENST00000355739	NM_000123.3	548	Gaa/Aaa	8/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.307410396627788	2		279	388	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741822	162741822	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs115169993	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	144	535	0	ENST00000367921.3:c.1513G>A	p.Gly505Ser	p.G505S	ENST00000367921	NM_006182.2	505	Ggt/Agt	13/18	1	2	FACETS	0.751	0.687	0.817	1	0.988	1	SUBCLONAL	2	TRUE	1	0.307410396627788	2		535	624	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426776	121426776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150513055	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	223	803	0	ENST00000257555.6:c.467C>T	p.Thr156Met	p.T156M	ENST00000257555		156	aCg/aTg	2/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.307410396627788	2		803	1038	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577569	7577569	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519981	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	216	666	0	ENST00000269305.4:c.712T>C	p.Cys238Arg	p.C238R	ENST00000269305	NM_001126112.2	238	Tgt/Cgt	7/11	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.307410396627788	2		666	943	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637762	176637762	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520339	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	45	665	1	ENST00000439151.2:c.2362C>T	p.Arg788Ter	p.R788*	ENST00000439151	NM_022455.4	788	Cga/Tga	5/23	1	2	FACETS	0.353	0.295	0.417	0.353	0.295	0.417	SUBCLONAL	1	TRUE	1	0.307410396627788	2		666	830	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570213	95570213	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	94	426	0	ENST00000393063.1:c.3520G>T	p.Ala1174Ser	p.A1174S	ENST00000393063	NM_030621.3	1174	Gca/Tca	22/28	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.307410396627788	2		426	505	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592099	67592099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	101	335	0	ENST00000274335.5:c.1915C>T	p.Arg639Ter	p.R639*	ENST00000274335		639	Cga/Tga	14/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.307410396627788	2		335	517	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940455	29940455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138686378	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	68	410	0	ENST00000389048.3:c.776G>A	p.Arg259His	p.R259H	ENST00000389048	NM_004304.4	259	cGc/cAc	2/29	0.307410396627788	3	FACETS	1	0.926	1	0.545	0.475	0.62	CLONAL	1	TRUE	1	0.307410396627788	3		410	468	SUCCESS
APC	324	MSKCC	GRCh37	5	112178000	112178000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768922431	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	104	438	0	ENST00000257430.4:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000257430	NM_000038.5	2237	Cga/Tga	16/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.307410396627788	2		438	565	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545646	106545646	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1461415145	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	130	601	0	ENST00000359195.3:c.3123G>T	p.Gln1041His	p.Q1041H	ENST00000359195	NM_002649.2	1041	caG/caT	11/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.307410396627788	2		601	586	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828772	3828772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	233	667	0	ENST00000262367.5:c.1870C>T	p.Arg624Cys	p.R624C	ENST00000262367	NM_004380.2	624	Cgc/Tgc	9/31	1	2	FACETS	0.762	0.711	0.814	1	0.992	1	SUBCLONAL	2	TRUE	1	0.307410396627788	2		667	995	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118949	115118949	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	63	260	1	ENST00000257566.3:c.392G>A	p.Arg131Gln	p.R131Q	ENST00000257566	NM_016569.3	131	cGa/cAa	2/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.307410396627788	2		261	304	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131895051	131895051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370769989	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	64	345	0	ENST00000265335.6:c.205G>A	p.Asp69Asn	p.D69N	ENST00000265335		69	Gat/Aat	2/25	1	2	FACETS	0.962	0.835	1	0.962	0.835	1	CLONAL	1	TRUE	1	0.307410396627788	2		345	433	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132927	64132927	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145356210	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	187	696	3	ENST00000334205.4:c.1061G>A	p.Arg354Gln	p.R354Q	ENST00000334205	NM_003942.2	354	cGa/cAa	9/17	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.307410396627788	2		699	819	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298226	123298226	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	91	337	0	ENST00000358487.5:c.628C>T	p.Arg210Ter	p.R210*	ENST00000358487	NM_000141.4	210	Cga/Tga	6/18	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.307410396627788	2		337	415	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047314	77047314	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	118	484	0	ENST00000356341.3:c.1230C>A	p.Phe410Leu	p.F410L	ENST00000356341	NM_002576.4	410	ttC/ttA	13/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.307410396627788	2		484	598	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259967	16259967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	215	729	1	ENST00000375759.3:c.7232C>T	p.Ser2411Leu	p.S2411L	ENST00000375759	NM_015001.2	2411	tCg/tTg	11/15	1	2	FACETS	0.754	0.701	0.808	1	0.991	1	SUBCLONAL	2	TRUE	1	0.307410396627788	2		730	928	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627730	14627730	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	191	813	0	ENST00000254322.2:c.340A>G	p.Thr114Ala	p.T114A	ENST00000254322	NM_006145.1	114	Acc/Gcc	2/3	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.307410396627788	2		813	859	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637690	52637690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239654517	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	115	515	1	ENST00000394830.3:c.2626C>T	p.Arg876Cys	p.R876C	ENST00000394830	NM_018313.4	876	Cgt/Tgt	18/30	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.307410396627788	2		516	513	SUCCESS
APC	324	MSKCC	GRCh37	5	112177839	112177839	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	56	356	0	ENST00000257430.4:c.6548C>A	p.Ser2183Tyr	p.S2183Y	ENST00000257430	NM_000038.5	2183	tCt/tAt	16/16	1	2	FACETS	0.959	0.825	1	0.959	0.825	1	CLONAL	1	TRUE	1	0.307410396627788	2		356	380	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249847	133249847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	145	543	0	ENST00000320574.5:c.1376C>T	p.Ser459Phe	p.S459F	ENST00000320574	NM_006231.2	459	tCt/tTt	14/49	1	2	FACETS	0.763	0.699	0.83	1	0.988	1	SUBCLONAL	2	TRUE	1	0.307410396627788	2		543	618	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450397	50450397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	108	574	0	ENST00000331340.3:c.581C>T	p.Thr194Met	p.T194M	ENST00000331340	NM_006060.4	194	aCg/aTg	5/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.307410396627788	2		574	633	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997697	149997697	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs145871963	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	94	417	0	ENST00000253339.5:c.2770C>T	p.Arg924Ter	p.R924*	ENST00000253339		924	Cga/Tga	5/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.307410396627788	2		417	445	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033753	48033753	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1553333707	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	98	366	0	ENST00000234420.5:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000234420	NM_000179.2	1322	Gaa/Taa	9/10	0.307410396627788	3	FACETS	0.796	0.714	0.883	0.796	0.714	0.883	SUBCLONAL	2	TRUE	1	0.307410396627788	3		366	462	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685281	89685281	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	50	228	0	ENST00000371953.3:c.176C>A	p.Ser59Ter	p.S59*	ENST00000371953	NM_000314.4	59	tCa/tAa	3/9	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.307410396627788	2		228	281	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112292	115112292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1282046318	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	27	50	0	ENST00000257566.3:c.1448C>T	p.Thr483Met	p.T483M	ENST00000257566	NM_016569.3	483	aCg/aTg	7/8	1	2	FACETS	0.934	0.762	1	1	0.955	1	CLONAL	2	TRUE	1	0.307410396627788	2		50	94	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224583	108224583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881329	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	102	355	2	ENST00000278616.4:c.8762C>T	p.Thr2921Met	p.T2921M	ENST00000278616	NM_000051.3	2921	aCg/aTg	60/63	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.307410396627788	2		357	497	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412494	80412494	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	120	431	0	ENST00000286548.4:c.547C>T	p.Arg183Ter	p.R183*	ENST00000286548	NM_002072.3	183	Cga/Tga	4/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.307410396627788	2		431	616	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231506	5231506	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1386910242	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	261	898	2	ENST00000357368.4:c.1970G>A	p.Arg657His	p.R657H	ENST00000357368	NM_002850.3	657	cGc/cAc	14/38	1	2	FACETS	0.809	0.758	0.862	1	0.994	1	CLONAL	2	TRUE	1	0.307410396627788	2		900	1049	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979514	7979514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141010860	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	227	724	0	ENST00000319144.4:c.1511C>T	p.Ala504Val	p.A504V	ENST00000319144	NM_001139.2	504	gCg/gTg	11/15	1	2	FACETS	0.8	0.746	0.856	1	0.993	1	SUBCLONAL	2	TRUE	1	0.307410396627788	2		724	923	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539056	23539056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	186	651	1	ENST00000380871.4:c.383G>A	p.Arg128Gln	p.R128Q	ENST00000380871	NM_006167.3	128	cGa/cAa	2/2	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.307410396627788	2		652	847	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873229	136873229	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756830956	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	112	452	0	ENST00000241393.3:c.269C>T	p.Thr90Met	p.T90M	ENST00000241393	NM_003467.2	90	aCg/aTg	2/2	0.307410396627788	3	FACETS	1	0.972	1	0.612	0.551	0.676	CLONAL	1	TRUE	1	0.307410396627788	3		452	687	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118871	61118871	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372213094	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	190	331	0	ENST00000295025.8:c.64C>T	p.Arg22Cys	p.R22C	ENST00000295025	NM_002908.2	22	Cgt/Tgt	2/11	0.307410396627788	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.307410396627788	3		331	593	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672759	86672759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	71	375	0	ENST00000274376.6:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000274376	NM_002890.2	749	cGa/cAa	17/25	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.307410396627788	2		375	405	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808319	99808319	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	74	345	0	ENST00000280892.6:c.370G>T	p.Asp124Tyr	p.D124Y	ENST00000280892	NM_001130678.1	124	Gat/Tat	5/7	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.307410396627788	2		345	417	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466994	18466994	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773615749	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	67	358	0	ENST00000266497.5:c.1133G>A	p.Arg378Gln	p.R378Q	ENST00000266497		378	cGa/cAa	5/31	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.307410396627788	2		358	367	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570469	39570469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1380208670	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	46	289	0	ENST00000262039.4:c.665G>A	p.Arg222Gln	p.R222Q	ENST00000262039	NM_002647.2	222	cGa/cAa	6/25	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.307410396627788	2		289	262	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531829	46531829	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs749759127	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	72	296	0	ENST00000262741.5:c.518A>C	p.Asn173Thr	p.N173T	ENST00000262741	NM_003629.3	173	aAt/aCt	5/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.307410396627788	2		296	361	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850948	63850948	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	170	615	1	ENST00000279873.7:c.1726G>T	p.Glu576Ter	p.E576*	ENST00000279873	NM_032199.2	576	Gaa/Taa	10/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.307410396627788	2		616	837	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970928	21970928	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs116150891	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	248	722	1	ENST00000304494.5:c.430C>T	p.Arg144Cys	p.R144C	ENST00000304494	NM_000077.4	144	Cgc/Tgc	2/3	1	2	FACETS	0.787	0.736	0.84	1	0.993	1	SUBCLONAL	2	TRUE	1	0.307410396627788	2		723	1025	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121756	108121756	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	130	505	1	ENST00000278616.4:c.1564G>T	p.Glu522Ter	p.E522*	ENST00000278616	NM_000051.3	522	Gaa/Taa	10/63	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.307410396627788	2		506	594	SUCCESS
ATR	545	MSKCC	GRCh37	3	142184073	142184073	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	64	321	0	ENST00000350721.4:c.6907C>A	p.Leu2303Ile	p.L2303I	ENST00000350721	NM_001184.3	2303	Ctt/Att	41/47	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.307410396627788	2		321	360	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231233	98231233	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs62637629	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	258	955	2	ENST00000331920.6:c.2050G>A	p.Glu684Lys	p.E684K	ENST00000331920	NM_000264.3	684	Gag/Aag	14/24	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.307410396627788	2		957	1232	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231248	98231248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771882746	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	269	970	2	ENST00000331920.6:c.2035G>A	p.Ala679Thr	p.A679T	ENST00000331920	NM_000264.3	679	Gct/Act	14/24	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.307410396627788	2		972	1236	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251891	153251891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	77	493	0	ENST00000281708.4:c.1115C>A	p.Ser372Tyr	p.S372Y	ENST00000281708	NM_033632.3	372	tCt/tAt	7/12	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.307410396627788	2		493	452	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134405	41134405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772929365	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	166	587	0	ENST00000379561.5:c.1223C>T	p.Ala408Val	p.A408V	ENST00000379561	NM_002015.3	408	gCg/gTg	2/3	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.307410396627788	2		587	859	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611324	28611324	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	103	450	0	ENST00000241453.7:c.1307G>T	p.Arg436Ile	p.R436I	ENST00000241453	NM_004119.2	436	aGa/aTa	10/24	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.307410396627788	2		450	505	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670340	134670340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415689583	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	181	539	0	ENST00000398015.3:c.251G>A	p.Arg84His	p.R84H	ENST00000398015	NM_004441.4	84	cGc/cAc	3/16	1	2	FACETS	0.866	0.802	0.932	1	0.992	1	CLONAL	2	TRUE	1	0.307410396627788	2		539	680	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720857	89720857	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	103	395	0	ENST00000371953.3:c.1008C>A	p.Tyr336Ter	p.Y336*	ENST00000371953	NM_000314.4	336	taC/taA	8/9	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.307410396627788	2		395	516	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945451	151945451	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	206	897	0	ENST00000262189.6:c.2068G>T	p.Glu690Ter	p.E690*	ENST00000262189	NM_170606.2	690	Gaa/Taa	14/59	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.307410396627788	2		897	1032	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856154	111856154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	123	329	0	ENST00000341259.2:c.205G>A	p.Asp69Asn	p.D69N	ENST00000341259	NM_005475.2	69	Gac/Aac	2/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.307410396627788	2		329	589	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027712	48027712	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	56	364	0	ENST00000234420.5:c.2590G>T	p.Gly864Ter	p.G864*	ENST00000234420	NM_000179.2	864	Gga/Tga	4/10	0.307410396627788	3	FACETS	1	0.883	1	0.515	0.442	0.594	CLONAL	1	TRUE	1	0.307410396627788	3		364	408	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791524	42791524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747433677	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	234	957	0	ENST00000575354.2:c.505C>T	p.Arg169Cys	p.R169C	ENST00000575354	NM_015125.3	169	Cgt/Tgt	4/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.307410396627788	2		957	1231	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561762	55561762	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1404387908	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	128	437	0	ENST00000288135.5:c.152G>A	p.Gly51Asp	p.G51D	ENST00000288135	NM_000222.2	51	gGc/gAc	2/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.307410396627788	2		437	612	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048772	180048772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758587669	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	238	1009	2	ENST00000261937.6:c.1790C>T	p.Thr597Met	p.T597M	ENST00000261937	NM_182925.4	597	aCg/aTg	13/30	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.307410396627788	2		1011	1107	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391476	139391476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747504082	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	260	1060	2	ENST00000277541.6:c.6715G>A	p.Asp2239Asn	p.D2239N	ENST00000277541	NM_017617.3	2239	Gac/Aac	34/34	1	2	FACETS	0.776	0.727	0.827	1	0.993	1	SUBCLONAL	2	TRUE	1	0.307410396627788	2		1062	1090	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723053	49723053	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	77	255	0	ENST00000449682.2:c.1363G>A	p.Asp455Asn	p.D455N	ENST00000449682	NM_020998.3	455	Gac/Aac	11/18	1	2	FACETS	0.793	0.702	0.888	1	0.979	1	SUBCLONAL	2	TRUE	1	0.307410396627788	2		255	316	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048760	180048760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754245879	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	263	969	1	ENST00000261937.6:c.1802C>T	p.Ala601Val	p.A601V	ENST00000261937	NM_182925.4	601	gCg/gTg	13/30	1	2	FACETS	0.806	0.756	0.858	1	0.994	1	CLONAL	2	TRUE	1	0.307410396627788	2		970	1061	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344458	118344458	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	101	351	0	ENST00000534358.1:c.2584C>T	p.Arg862Ter	p.R862*	ENST00000534358	NM_005933.3	862	Cga/Tga	3/36	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.307410396627788	2		351	446	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252163	226252163	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	36	158	0	ENST00000366813.1:c.111G>T	p.Lys37Asn	p.K37N	ENST00000366813		37	aaG/aaT	1/3	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.307410396627788	2		158	196	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446447	70446447	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	126	456	0	ENST00000373644.4:c.5387C>T	p.Ser1796Leu	p.S1796L	ENST00000373644	NM_030625.2	1796	tCg/tTg	11/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.307410396627788	2		456	716	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643705	38643705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1345810751	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	234	704	1	ENST00000299084.4:c.1175C>T	p.Ser392Leu	p.S392L	ENST00000299084	NM_152594.2	392	tCg/tTg	7/7	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.307410396627788	2		705	1095	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279569	1279569	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	246	998	0	ENST00000310581.5:c.1967C>T	p.Ser656Leu	p.S656L	ENST00000310581	NM_198253.2	656	tCg/tTg	5/16	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.307410396627788	2		998	1107	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439638	51439638	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750990884	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	148	467	1	ENST00000262662.1:c.203G>A	p.Arg68Gln	p.R68Q	ENST00000262662		68	cGa/cAa	4/4	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.307410396627788	2		468	644	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609957	81609957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756016910	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	132	475	0	ENST00000298171.2:c.1555C>T	p.Arg519Cys	p.R519C	ENST00000298171	NM_000369.2	519	Cgc/Tgc	10/10	1	2	FACETS	0.771	0.703	0.842	1	0.987	1	SUBCLONAL	2	TRUE	1	0.307410396627788	2		475	557	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603020	48603020	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	109	353	0	ENST00000342988.3:c.1321C>T	p.Arg441Cys	p.R441C	ENST00000342988	NM_005359.5	441	Cgt/Tgt	11/12	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.307410396627788	2		353	480	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426725	47426725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773318953	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	227	895	1	ENST00000377045.4:c.970G>A	p.Val324Met	p.V324M	ENST00000377045	NM_001654.4	324	Gtg/Atg	10/16	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.307410396627788	2		896	1066	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020477	14020477	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145402255	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	126	476	2	ENST00000311895.7:c.448C>T	p.Arg150Cys	p.R150C	ENST00000311895	NM_005236.2	150	Cgc/Tgc	3/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.307410396627788	2		478	584	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14028108	14028108	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs199505105	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	65	399	0	ENST00000311895.7:c.1162T>G	p.Leu388Val	p.L388V	ENST00000311895	NM_005236.2	388	Tta/Gta	7/11	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.307410396627788	2		399	401	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261263	115261263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	148	569	1	ENST00000438362.2:c.2458C>T	p.Arg820Cys	p.R820C	ENST00000438362	NM_001242891.1	820	Cgt/Tgt	19/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.307410396627788	2		570	705	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169166	119169166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140725852	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	170	631	0	ENST00000264033.4:c.2350G>A	p.Val784Met	p.V784M	ENST00000264033	NM_005188.3	784	Gtg/Atg	15/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.307410396627788	2		631	899	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945618	54945618	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	102	348	0	ENST00000312783.6:c.952C>A	p.Leu318Ile	p.L318I	ENST00000312783	NM_198436.1	318	Ctt/Att	9/10	1	2	FACETS	0.792	0.713	0.874	1	0.984	1	SUBCLONAL	2	TRUE	1	0.307410396627788	2		348	419	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902934	1902934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	189	649	0	ENST00000382891.5:c.553G>A	p.Glu185Lys	p.E185K	ENST00000382891	NM_133335.3	185	Gaa/Aaa	2/22	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.307410396627788	2		649	912	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265359	152265359	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	131	609	0	ENST00000206249.3:c.812G>T	p.Arg271Ile	p.R271I	ENST00000206249	NM_000125.3	271	aGa/aTa	4/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.307410396627788	2		609	669	SUCCESS
BLM	641	MSKCC	GRCh37	15	91352370	91352370	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	63	318	0	ENST00000355112.3:c.3755C>A	p.Ser1252Tyr	p.S1252Y	ENST00000355112	NM_000057.2	1252	tCt/tAt	20/22	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.307410396627788	2		318	332	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994791	73994791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375871029	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	177	702	2	ENST00000318443.5:c.275G>A	p.Arg92His	p.R92H	ENST00000318443	NM_001024736.1	92	cGc/cAc	3/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.307410396627788	2		704	850	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863449	57863449	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781683841	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	187	687	1	ENST00000228682.2:c.1544G>A	p.Arg515Gln	p.R515Q	ENST00000228682	NM_005269.2	515	cGg/cAg	11/12	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.307410396627788	2		688	935	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89865629	89865629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1010833101	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	190	581	0	ENST00000389301.3:c.838G>A	p.Ala280Thr	p.A280T	ENST00000389301	NM_000135.2	280	Gct/Act	10/43	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.307410396627788	2		581	830	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161298	55161298	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	88	445	0	ENST00000257290.5:c.3129G>T	p.Gln1043His	p.Q1043H	ENST00000257290	NM_006206.4	1043	caG/caT	23/23	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.307410396627788	2		445	556	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619323	1619323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761667569	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	183	691	1	ENST00000344749.5:c.1318G>A	p.Ala440Thr	p.A440T	ENST00000344749	NM_001136139.2	440	Gca/Aca	15/19	1	2	FACETS	0.775	0.717	0.836	1	0.991	1	SUBCLONAL	2	TRUE	1	0.307410396627788	2		692	768	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500519	99500519	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138696883	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	218	903	0	ENST00000268035.6:c.3952G>A	p.Asp1318Asn	p.D1318N	ENST00000268035	NM_000875.3	1318	Gac/Aac	21/21	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.307410396627788	2		903	949	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227872	123227872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	53	320	1	ENST00000218089.9:c.3583C>T	p.Arg1195Cys	p.R1195C	ENST00000218089	NM_001042749.1	1195	Cgt/Tgt	33/35	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.307410396627788	2		321	331	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95592940	95592940	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	76	411	1	ENST00000393063.1:c.880G>T	p.Asp294Tyr	p.D294Y	ENST00000393063	NM_030621.3	294	Gat/Tat	8/28	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.307410396627788	2		412	465	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041169	47041169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782425783	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	200	946	2	ENST00000377604.3:c.1597G>A	p.Ala533Thr	p.A533T	ENST00000377604	NM_001204468.1	533	Gct/Act	15/24	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.307410396627788	2		948	993	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412470	63412470	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs146685042	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	215	996	0	ENST00000330258.3:c.697G>T	p.Asp233Tyr	p.D233Y	ENST00000330258	NM_152424.3	233	Gat/Tat	2/2	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.307410396627788	2		996	1118	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139464	47139464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	172	526	0	ENST00000409792.3:c.5123G>A	p.Arg1708Gln	p.R1708Q	ENST00000409792	NM_014159.6	1708	cGa/cAa	9/21	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.307410396627788	2		526	794	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622622	158622622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	227	544	0	ENST00000263640.3:c.877G>A	p.Asp293Asn	p.D293N	ENST00000263640	NM_001105.4	293	Gac/Aac	8/11	0.307410396627788	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.307410396627788	3		544	697	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243030	105243030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1566818890	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	239	994	1	ENST00000349310.3:c.253G>A	p.Glu85Lys	p.E85K	ENST00000349310	NM_001014432.1	85	Gaa/Aaa	5/15	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.307410396627788	2		995	1153	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56860239	56860239	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	152	568	0	ENST00000519728.1:c.241G>A	p.Asp81Asn	p.D81N	ENST00000519728	NM_002350.3	81	Gac/Aac	4/13	1	2	FACETS	0.76	0.697	0.825	1	0.988	1	SUBCLONAL	2	TRUE	1	0.307410396627788	2		568	651	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665277	176665277	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	36	434	0	ENST00000439151.2:c.3961G>T	p.Gly1321Cys	p.G1321C	ENST00000439151	NM_022455.4	1321	Ggt/Tgt	7/23	1	2	FACETS	0.371	0.304	0.447	0.371	0.304	0.447	SUBCLONAL	1	TRUE	1	0.307410396627788	2		434	631	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021817	71021817	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	69	255	0	ENST00000318789.4:c.1541G>T	p.Arg514Leu	p.R514L	ENST00000318789	NM_032682.5	514	cGt/cTt	18/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.307410396627788	2		255	303	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983971	2983971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	209	810	1	ENST00000396946.4:c.559C>T	p.Arg187Trp	p.R187W	ENST00000396946	NM_032415.4	187	Cgg/Tgg	5/25	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.307410396627788	2		811	1097	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988119	85988119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	56	395	0	ENST00000263360.6:c.1064G>A	p.Arg355Gln	p.R355Q	ENST00000263360	NM_003797.3	355	cGa/cAa	10/12	1	2	FACETS	0.886	0.762	1	0.886	0.762	1	CLONAL	1	TRUE	1	0.307410396627788	2		395	411	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181803	56181803	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	90	340	0	ENST00000399503.3:c.4027G>T	p.Glu1343Ter	p.E1343*	ENST00000399503	NM_005921.1	1343	Gaa/Taa	17/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.307410396627788	2		340	417	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860612	3860612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769798406	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	202	654	0	ENST00000262367.5:c.967C>T	p.Pro323Ser	p.P323S	ENST00000262367	NM_004380.2	323	Cca/Tca	3/31	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.307410396627788	2		654	933	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343502	118343502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1203844881	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	106	514	0	ENST00000534358.1:c.1628C>T	p.Thr543Met	p.T543M	ENST00000534358	NM_005933.3	543	aCg/aTg	3/36	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.307410396627788	2		514	632	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720928	119720928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	152	556	0	ENST00000316626.5:c.247G>A	p.Ala83Thr	p.A83T	ENST00000316626		83	Gcc/Acc	2/12	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.307410396627788	2		556	678	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430354	181430354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	145	455	1	ENST00000325404.1:c.206C>T	p.Ser69Leu	p.S69L	ENST00000325404	NM_003106.3	69	tCg/tTg	1/1	1	2	FACETS	0.794	0.727	0.863	1	0.989	1	SUBCLONAL	2	TRUE	1	0.307410396627788	2		456	594	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278406	39278406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775052125	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	113	559	1	ENST00000402219.2:c.743G>A	p.Arg248His	p.R248H	ENST00000402219	NM_005633.3	248	cGc/cAc	6/23	0.307410396627788	3	FACETS	1	0.98	1	0.676	0.61	0.746	CLONAL	1	TRUE	1	0.307410396627788	3		560	627	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276302	15276302	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	225	865	0	ENST00000263388.2:c.5692G>T	p.Asp1898Tyr	p.D1898Y	ENST00000263388	NM_000435.2	1898	Gac/Tac	31/33	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.307410396627788	2		865	985	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912136	127912136	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	89	327	0	ENST00000373547.4:c.734A>C	p.Lys245Thr	p.K245T	ENST00000373547	NM_002721.4	245	aAa/aCa	7/7	1	2	FACETS	0.793	0.709	0.882	1	0.982	1	SUBCLONAL	2	TRUE	1	0.307410396627788	2		327	365	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378314	225378314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	68	301	0	ENST00000264414.4:c.581G>A	p.Gly194Asp	p.G194D	ENST00000264414	NM_003590.4	194	gGt/gAt	5/16	0.307410396627788	3	FACETS	1	0.916	1	0.533	0.464	0.606	CLONAL	1	TRUE	1	0.307410396627788	3		301	479	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834557	156834557	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	213	1067	0	ENST00000524377.1:c.325G>T	p.Asp109Tyr	p.D109Y	ENST00000524377	NM_002529.3	109	Gat/Tat	3/17	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.307410396627788	2		1067	1107	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027691	48027691	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	72	353	0	ENST00000234420.5:c.2569G>T	p.Asp857Tyr	p.D857Y	ENST00000234420	NM_000179.2	857	Gat/Tat	4/10	0.307410396627788	3	FACETS	1	0.965	1	0.645	0.566	0.73	CLONAL	1	TRUE	1	0.307410396627788	3		353	419	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906944	32906944	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs73169186	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	78	456	0	ENST00000380152.3:c.1329G>T	p.Glu443Asp	p.E443D	ENST00000380152		443	gaG/gaT	10/27	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.307410396627788	2		456	409	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216700	36216700	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376193493	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	215	677	0	ENST00000222270.7:c.3866C>T	p.Thr1289Met	p.T1289M	ENST00000222270	NM_014727.1	1289	aCg/aTg	13/37	1	2	FACETS	0.79	0.735	0.847	1	0.992	1	SUBCLONAL	2	TRUE	1	0.307410396627788	2		677	885	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096334	2096334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139165943	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	83	954	2	ENST00000219066.1:c.173C>T	p.Pro58Leu	p.P58L	ENST00000219066	NM_002528.5	58	cCg/cTg	2/6	1	2	FACETS	0.414	0.364	0.469	0.414	0.364	0.469	SUBCLONAL	1	TRUE	1	0.307410396627788	2		956	1303	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94922974	94922974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1409733830	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	81	460	0	ENST00000536441.1:c.494G>A	p.Arg165Gln	p.R165Q	ENST00000536441	NM_144665.3	165	cGa/cAa	4/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.307410396627788	2		460	446	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665249	138665249	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	284	776	1	ENST00000330315.3:c.316C>A	p.Leu106Ile	p.L106I	ENST00000330315	NM_023067.3	106	Ctc/Atc	1/1	1	2	FACETS	0.826	0.777	0.877	1	0.994	1	CLONAL	2	TRUE	1	0.307410396627788	2		777	1118	SUCCESS
MET	4233	MSKCC	GRCh37	7	116414934	116414934	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	173	694	1	ENST00000397752.3:c.3029-1G>T		p.X1010_splice	ENST00000397752	NM_000245.2	1010			1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.307410396627788	2		695	780	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128305365	128305365	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	175	639	0	ENST00000265960.3:c.931C>T	p.Arg311Ter	p.R311*	ENST00000265960	NM_001006617.1	311	Cga/Tga	7/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.307410396627788	2		639	827	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265106	198265106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1559265118	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	141	419	0	ENST00000335508.6:c.2771G>A	p.Arg924Gln	p.R924Q	ENST00000335508	NM_012433.2	924	cGa/cAa	19/25	0.307410396627788	3	FACETS	1	0.973	1	0.588	0.535	0.643	CLONAL	1	TRUE	1	0.307410396627788	3		419	900	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486277	99486277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201014974	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	170	617	0	ENST00000268035.6:c.3583G>A	p.Val1195Ile	p.V1195I	ENST00000268035	NM_000875.3	1195	Gtc/Atc	19/21	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.307410396627788	2		617	829	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112272	115112272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544562535	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	38	72	0	ENST00000257566.3:c.1468G>A	p.Ala490Thr	p.A490T	ENST00000257566	NM_016569.3	490	Gcc/Acc	7/8	1	2	FACETS	1	0.919	1	1	0.972	1	CLONAL	2	TRUE	1	0.307410396627788	2		72	109	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954976	2954976	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772829458	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	234	827	1	ENST00000396946.4:c.2734C>T	p.Arg912Trp	p.R912W	ENST00000396946	NM_032415.4	912	Cgg/Tgg	21/25	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.307410396627788	2		828	1063	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416137	416137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1449032009	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	113	421	0	ENST00000399788.2:c.4049G>A	p.Arg1350Gln	p.R1350Q	ENST00000399788	NM_001042603.1	1350	cGa/cAa	24/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.307410396627788	2		421	595	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955539	48955539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146236493	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	9	389	0	ENST00000267163.4:c.1655G>A	p.Arg552Gln	p.R552Q	ENST00000267163	NM_000321.2	552	cGa/cAa	17/27	1	2	FACETS	0.146	0.096	0.21	0.146	0.096	0.21	SUBCLONAL	1	TRUE	1	0.307410396627788	2		389	402	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266137	198266137	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	178	420	0	ENST00000335508.6:c.2483G>T	p.Arg828Ile	p.R828I	ENST00000335508	NM_012433.2	828	aGa/aTa	17/25	0.307410396627788	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.307410396627788	3		420	537	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966540	25966540	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	352	773	0	ENST00000435504.4:c.2666C>A	p.Ser889Tyr	p.S889Y	ENST00000435504		889	tCt/tAt	13/13	0.307410396627788	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.307410396627788	3		773	1127	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139414004	139414004	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	229	769	0	ENST00000277541.6:c.756G>T	p.Gln252His	p.Q252H	ENST00000277541	NM_017617.3	252	caG/caT	5/34	1	2	FACETS	0.757	0.706	0.81	1	0.992	1	SUBCLONAL	2	TRUE	1	0.307410396627788	2		769	984	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911954	94911954	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	104	515	0	ENST00000536441.1:c.976C>T	p.Arg326Ter	p.R326*	ENST00000536441	NM_144665.3	326	Cga/Tga	7/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.307410396627788	2		515	555	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319662	62319662	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408202470	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	180	932	0	ENST00000360203.5:c.1645G>A	p.Ala549Thr	p.A549T	ENST00000360203	NM_001283009.1	549	Gcc/Acc	20/35	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.307410396627788	2		932	961	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803501	32803501	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs142794316	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	246	923	1	ENST00000374899.4:c.658C>T	p.Arg220Ter	p.R220*	ENST00000374899	NM_018833.2	220	Cga/Tga	4/12	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.307410396627788	2		924	1183	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169467	11169467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985886104	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	170	702	1	ENST00000358026.2:c.4633C>T	p.Arg1545Cys	p.R1545C	ENST00000358026	NM_001128849.1	1545	Cgc/Tgc	33/36	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.307410396627788	2		703	867	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192672	94192672	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	139	615	0	ENST00000323929.3:c.1402G>T	p.Asp468Tyr	p.D468Y	ENST00000323929	NM_005591.3	468	Gat/Tat	13/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.307410396627788	2		615	676	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914368	32914368	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	83	534	0	ENST00000380152.3:c.5876A>C	p.Lys1959Thr	p.K1959T	ENST00000380152		1959	aAa/aCa	11/27	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.307410396627788	2		534	407	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781414	3781414	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1488071616	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	182	938	1	ENST00000262367.5:c.4951G>A	p.Asp1651Asn	p.D1651N	ENST00000262367	NM_004380.2	1651	Gac/Aac	30/31	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.307410396627788	2		939	1023	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277586	142277586	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	67	386	0	ENST00000350721.4:c.1765G>T	p.Asp589Tyr	p.D589Y	ENST00000350721	NM_001184.3	589	Gat/Tat	8/47	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.307410396627788	2		386	410	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683144	88683144	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	127	527	0	ENST00000372037.3:c.1354G>T	p.Glu452Ter	p.E452*	ENST00000372037	NM_004329.2	452	Gaa/Taa	12/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.307410396627788	2		527	587	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792694	33792694	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	27	98	1	ENST00000498907.2:c.627G>T	p.Gln209His	p.Q209H	ENST00000498907	NM_004364.3	209	caG/caT	1/1	1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	1	0.307410396627788	2		99	165	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322698	39322698	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	112	596	0	ENST00000373001.3:c.294G>T	p.Lys98Asn	p.K98N	ENST00000373001	NM_022157.3	98	aaG/aaT	2/7	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.307410396627788	2		596	643	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777054	9777054	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	189	854	0	ENST00000377346.4:c.818A>G	p.His273Arg	p.H273R	ENST00000377346	NM_005026.3	273	cAc/cGc	7/24	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.307410396627788	2		854	883	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217346	11217346	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	145	600	1	ENST00000361445.4:c.4332G>T	p.Glu1444Asp	p.E1444D	ENST00000361445	NM_004958.3	1444	gaG/gaT	30/58	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.307410396627788	2		601	699	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298533	11298533	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	209	733	0	ENST00000361445.4:c.1928T>G	p.Val643Gly	p.V643G	ENST00000361445	NM_004958.3	643	gTg/gGg	12/58	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.307410396627788	2		733	1016	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257108	16257108	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770452791	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	94	577	0	ENST00000375759.3:c.4373G>A	p.Arg1458His	p.R1458H	ENST00000375759	NM_015001.2	1458	cGt/cAt	11/15	1	2	FACETS	0.911	0.812	1	0.911	0.812	1	CLONAL	1	TRUE	1	0.307410396627788	2		577	671	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258948	16258948	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	239	760	0	ENST00000375759.3:c.6213A>C	p.Lys2071Asn	p.K2071N	ENST00000375759	NM_015001.2	2071	aaA/aaC	11/15	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.307410396627788	2		760	1096	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099374	27099374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	48	666	0	ENST00000324856.7:c.3611C>A	p.Ser1204Tyr	p.S1204Y	ENST00000324856	NM_006015.4	1204	tCc/tAc	14/20	1	2	FACETS	0.41	0.345	0.481	0.41	0.345	0.481	SUBCLONAL	1	TRUE	1	0.307410396627788	2		666	762	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805714	43805714	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs993195285	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	222	780	0	ENST00000372470.3:c.770G>A	p.Arg257His	p.R257H	ENST00000372470	NM_005373.2	257	cGc/cAc	5/12	1	2	FACETS	0.782	0.728	0.837	1	0.992	1	SUBCLONAL	2	TRUE	1	0.307410396627788	2		780	924	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305309	65305309	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	120	649	0	ENST00000342505.4:c.2819A>G	p.Tyr940Cys	p.Y940C	ENST00000342505	NM_002227.2	940	tAc/tGc	20/25	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.307410396627788	2		649	665	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428481	78428481	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1480810494	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	79	469	0	ENST00000370768.2:c.1318C>T	p.Arg440Trp	p.R440W	ENST00000370768	NM_003902.3	440	Cgg/Tgg	14/20	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.307410396627788	2		469	499	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736480	85736480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	98	424	0	ENST00000370580.1:c.167C>T	p.Ser56Phe	p.S56F	ENST00000370580	NM_003921.4	56	tCt/tTt	2/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.307410396627788	2		424	504	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115284200	115284200	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	112	595	3	ENST00000438362.2:c.86C>A	p.Ser29Tyr	p.S29Y	ENST00000438362	NM_001242891.1	29	tCt/tAt	2/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.307410396627788	2		598	608	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837975	156837975	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	292	1106	0	ENST00000524377.1:c.508G>T	p.Val170Leu	p.V170L	ENST00000524377	NM_002529.3	170	Gtg/Ttg	5/17	1	2	FACETS	0.777	0.73	0.824	1	0.994	1	SUBCLONAL	2	TRUE	1	0.307410396627788	2		1106	1223	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156848913	156848913	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	155	656	0	ENST00000524377.1:c.1806-1G>T		p.X602_splice	ENST00000524377	NM_002529.3	602			1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.307410396627788	2		656	683	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176085807	176085807	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	92	425	0	ENST00000367669.3:c.979G>T	p.Asp327Tyr	p.D327Y	ENST00000367669	NM_022457.5	327	Gat/Tat	9/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.307410396627788	2		425	460	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982354	201982354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766561608	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	298	955	0	ENST00000359651.3:c.733C>T	p.Arg245Trp	p.R245W	ENST00000359651		245	Cgg/Tgg	6/8	1	2	FACETS	0.832	0.783	0.882	1	0.995	1	CLONAL	2	TRUE	1	0.307410396627788	2		955	1165	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206661268	206661268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	180	677	1	ENST00000367120.3:c.1634G>A	p.Cys545Tyr	p.C545Y	ENST00000367120	NM_014002.3	545	tGc/tAc	16/22	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.307410396627788	2		678	934	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100702	8100702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1330938980	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	207	981	0	ENST00000346208.3:c.676G>A	p.Val226Met	p.V226M	ENST00000346208		226	Gtg/Atg	3/6	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.307410396627788	2		981	1013	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332457	70332457	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	178	654	0	ENST00000373644.4:c.362T>C	p.Val121Ala	p.V121A	ENST00000373644	NM_030625.2	121	gTc/gCc	2/12	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.307410396627788	2		654	878	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332738	70332738	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	156	585	0	ENST00000373644.4:c.643C>A	p.Pro215Thr	p.P215T	ENST00000373644	NM_030625.2	215	Cct/Act	2/12	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.307410396627788	2		585	731	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333895	70333895	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	100	426	0	ENST00000373644.4:c.1800G>T	p.Lys600Asn	p.K600N	ENST00000373644	NM_030625.2	600	aaG/aaT	2/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.307410396627788	2		426	534	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70360784	70360784	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	59	261	0	ENST00000373644.4:c.1961T>G	p.Val654Gly	p.V654G	ENST00000373644	NM_030625.2	654	gTt/gGt	3/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.307410396627788	2		261	273	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112745385	112745385	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	55	390	0	ENST00000369452.4:c.704-1G>T		p.X235_splice	ENST00000369452	NM_007373.3	235			1	2	FACETS	0.881	0.756	1	0.881	0.756	1	CLONAL	1	TRUE	1	0.307410396627788	2		390	406	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324047	123324047	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	40	672	0	ENST00000358487.5:c.423A>C	p.Glu141Asp	p.E141D	ENST00000358487	NM_000141.4	141	gaA/gaC	4/18	1	2	FACETS	0.33	0.273	0.394	0.33	0.273	0.394	SUBCLONAL	1	TRUE	1	0.307410396627788	2		672	788	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161364	2161364	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	124	516	0	ENST00000434045.2:c.162+1G>A		p.X54_splice	ENST00000434045	NM_001127598.1	54			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.307410396627788	2		516	626	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518070	69518070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	230	878	1	ENST00000294312.3:c.295C>T	p.Arg99Trp	p.R99W	ENST00000294312	NM_005117.2	99	Cgg/Tgg	2/3	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.307410396627788	2		879	1079	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946757	71946757	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	220	871	0	ENST00000298229.2:c.2698A>G	p.Ser900Gly	p.S900G	ENST00000298229	NM_001567.3	900	Agc/Ggc	24/28	1	2	FACETS	0.811	0.756	0.869	1	0.993	1	CLONAL	2	TRUE	1	0.307410396627788	2		871	882	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999140	100999140	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	211	837	0	ENST00000325455.5:c.662T>C	p.Val221Ala	p.V221A	ENST00000325455	NM_001202474.3	221	gTt/gCt	1/8	1	2	FACETS	0.761	0.707	0.816	1	0.991	1	SUBCLONAL	2	TRUE	1	0.307410396627788	2		837	902	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371864	118371864	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	80	431	0	ENST00000534358.1:c.6319+2T>G		p.X2107_splice	ENST00000534358	NM_005933.3	2107			1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.307410396627788	2		431	482	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375351	118375351	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	113	413	0	ENST00000534358.1:c.8744C>A	p.Ser2915Tyr	p.S2915Y	ENST00000534358	NM_005933.3	2915	tCt/tAt	27/36	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.307410396627788	2		413	507	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463269	463269	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	147	508	0	ENST00000399788.2:c.1002C>A	p.Asp334Glu	p.D334E	ENST00000399788	NM_001042603.1	334	gaC/gaA	8/28	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.307410396627788	2		508	700	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435155	18435155	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	116	383	0	ENST00000266497.5:c.140T>G	p.Ile47Ser	p.I47S	ENST00000266497		47	aTc/aGc	1/31	1	2	FACETS	0.789	0.715	0.867	1	0.986	1	SUBCLONAL	2	TRUE	1	0.307410396627788	2		383	478	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716387	18716387	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	110	467	0	ENST00000266497.5:c.3734T>G	p.Leu1245Arg	p.L1245R	ENST00000266497		1245	cTt/cGt	26/31	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.307410396627788	2		467	600	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944829	31944829	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	307	828	1	ENST00000340398.3:c.272C>A	p.Ala91Glu	p.A91E	ENST00000340398	NM_001013699.2	91	gCg/gAg	1/1	1	2	FACETS	0.751	0.707	0.796	1	0.994	1	SUBCLONAL	2	TRUE	1	0.307410396627788	2		829	1330	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46215265	46215265	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771284827	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	55	268	2	ENST00000334344.6:c.700G>A	p.Val234Ile	p.V234I	ENST00000334344	NM_152641.2	234	Gtt/Att	6/21	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.307410396627788	2		270	304	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50482344	50482344	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	151	502	1	ENST00000394963.4:c.695A>C	p.Lys232Thr	p.K232T	ENST00000394963	NM_003076.4	232	aAg/aCg	6/13	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.307410396627788	2		503	689	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491620	56491620	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1565860652	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	160	572	1	ENST00000267101.3:c.2512C>T	p.Arg838Ter	p.R838*	ENST00000267101	NM_001982.3	838	Cga/Tga	21/28	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.307410396627788	2		573	780	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865619	57865619	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	260	955	0	ENST00000228682.2:c.3096G>T	p.Gln1032His	p.Q1032H	ENST00000228682	NM_005269.2	1032	caG/caT	12/12	1	2	FACETS	0.765	0.717	0.815	1	0.993	1	SUBCLONAL	2	TRUE	1	0.307410396627788	2		955	1105	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811750	102811750	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	167	770	1	ENST00000307046.8:c.434A>C	p.Lys145Thr	p.K145T	ENST00000307046	NM_001111285.1	145	aAg/aCg	4/4	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.307410396627788	2		771	992	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431337	121431337	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	116	563	0	ENST00000257555.6:c.541G>T	p.Gly181Trp	p.G181W	ENST00000257555		181	Ggg/Tgg	3/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.307410396627788	2		563	576	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434414	121434414	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1380266144	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	262	1021	1	ENST00000257555.6:c.1178C>A	p.Ser393Tyr	p.S393Y	ENST00000257555		393	tCc/tAc	6/10	1	2	FACETS	0.766	0.717	0.816	1	0.993	1	SUBCLONAL	2	TRUE	1	0.307410396627788	2		1022	1113	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549445	21549445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	171	660	0	ENST00000382592.4:c.2831C>T	p.Ala944Val	p.A944V	ENST00000382592	NM_014572.2	944	gCc/gTc	8/8	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.307410396627788	2		660	754	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608056	28608056	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	166	620	0	ENST00000241453.7:c.1910T>C	p.Val637Ala	p.V637A	ENST00000241453	NM_004119.2	637	gTc/gCc	15/24	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.307410396627788	2		620	777	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041212	29041212	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	166	636	0	ENST00000282397.4:c.216A>C	p.Glu72Asp	p.E72D	ENST00000282397	NM_002019.4	72	gaA/gaC	3/30	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.307410396627788	2		636	781	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907099	32907099	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	82	457	0	ENST00000380152.3:c.1484C>T	p.Ala495Val	p.A495V	ENST00000380152		495	gCt/gTt	10/27	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.307410396627788	2		457	438	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911983	32911983	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	127	588	0	ENST00000380152.3:c.3491T>G	p.Leu1164Arg	p.L1164R	ENST00000380152		1164	cTt/cGt	11/27	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.307410396627788	2		588	605	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912214	32912214	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	156	595	0	ENST00000380152.3:c.3722T>G	p.Phe1241Cys	p.F1241C	ENST00000380152		1241	tTt/tGt	11/27	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.307410396627788	2		595	698	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913105	32913105	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	136	529	0	ENST00000380152.3:c.4613C>A	p.Ser1538Tyr	p.S1538Y	ENST00000380152		1538	tCt/tAt	11/27	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.307410396627788	2		529	664	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914296	32914296	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	64	450	0	ENST00000380152.3:c.5804A>C	p.Asn1935Thr	p.N1935T	ENST00000380152		1935	aAt/aCt	11/27	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.307410396627788	2		450	371	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914766	32914766	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	98	445	0	ENST00000380152.3:c.6274C>A	p.Leu2092Ile	p.L2092I	ENST00000380152		2092	Ctt/Att	11/27	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.307410396627788	2		445	429	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914931	32914931	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	65	451	0	ENST00000380152.3:c.6439C>A	p.His2147Asn	p.H2147N	ENST00000380152		2147	Cac/Aac	11/27	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.307410396627788	2		451	399	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504577	103504578	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	89	418	0	ENST00000355739.4:c.204dup	p.Arg69SerfsTer9	p.R69Sfs*9	ENST00000355739	NM_000123.3	66	-/T	2/15	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.307410396627788	2		418	506	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103510624	103510624	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	45	283	0	ENST00000355739.4:c.529-1G>T		p.X177_splice	ENST00000355739	NM_000123.3	177			1	2	FACETS	0.951	0.803	1	0.951	0.803	1	CLONAL	1	TRUE	1	0.307410396627788	2		283	308	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518250	103518250	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	81	271	0	ENST00000355739.4:c.2188G>T	p.Asp730Tyr	p.D730Y	ENST00000355739	NM_000123.3	730	Gat/Tat	9/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.307410396627788	2		271	390	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436837	110436837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	181	723	2	ENST00000375856.3:c.1564G>A	p.Glu522Lys	p.E522K	ENST00000375856	NM_003749.2	522	Gag/Aag	1/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.307410396627788	2		725	964	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107999	30107999	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	179	633	0	ENST00000331968.5:c.808C>T	p.Pro270Ser	p.P270S	ENST00000331968	NM_002742.2	270	Ccg/Tcg	5/18	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.307410396627788	2		633	807	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872954	35872954	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	193	570	0	ENST00000216797.5:c.278T>G	p.Val93Gly	p.V93G	ENST00000216797	NM_020529.2	93	gTg/gGg	2/6	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.307410396627788	2		570	895	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544721	65544721	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	211	683	1	ENST00000358664.4:c.205G>T	p.Glu69Ter	p.E69*	ENST00000358664	NM_002382.4	69	Gaa/Taa	4/5	1	2	FACETS	0.79	0.735	0.847	1	0.992	1	SUBCLONAL	2	TRUE	1	0.307410396627788	2		684	869	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81574795	81574795	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	89	419	1	ENST00000298171.2:c.691C>A	p.Leu231Met	p.L231M	ENST00000298171	NM_000369.2	231	Ctg/Atg	8/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.307410396627788	2		420	484	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609816	81609816	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	134	501	0	ENST00000298171.2:c.1414T>G	p.Ser472Ala	p.S472A	ENST00000298171	NM_000369.2	472	Tct/Gct	10/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.307410396627788	2		501	629	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032264	42032264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	203	650	1	ENST00000219905.7:c.4448C>T	p.Ala1483Val	p.A1483V	ENST00000219905	NM_001164273.1	1483	gCc/gTc	14/24	1	2	FACETS	0.808	0.751	0.868	1	0.992	1	CLONAL	2	TRUE	1	0.307410396627788	2		651	817	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738605	43738605	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	123	548	0	ENST00000382044.4:c.3020C>A	p.Ser1007Tyr	p.S1007Y	ENST00000382044	NM_001141980.1	1007	tCt/tAt	14/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.307410396627788	2		548	659	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748815	43748815	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	257	784	1	ENST00000382044.4:c.1991C>A	p.Ser664Tyr	p.S664Y	ENST00000382044	NM_001141980.1	664	tCt/tAt	12/28	1	2	FACETS	0.784	0.734	0.835	1	0.993	1	SUBCLONAL	2	TRUE	1	0.307410396627788	2		785	1067	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43771700	43771700	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	202	607	0	ENST00000382044.4:c.683A>C	p.Asn228Thr	p.N228T	ENST00000382044	NM_001141980.1	228	aAc/aCc	7/28	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.307410396627788	2		607	941	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007887	45007887	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	96	405	0	ENST00000558401.1:c.334A>C	p.Ile112Leu	p.I112L	ENST00000558401	NM_004048.2	112	Ata/Cta	2/4	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.307410396627788	2		405	526	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66777489	66777489	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	180	816	0	ENST00000307102.5:c.855G>T	p.Glu285Asp	p.E285D	ENST00000307102	NM_002755.3	285	gaG/gaT	7/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.307410396627788	2		816	897	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251278	99251278	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	181	678	0	ENST00000268035.6:c.582G>T	p.Lys194Asn	p.K194N	ENST00000268035	NM_000875.3	194	aaG/aaT	2/21	1	2	FACETS	0.755	0.698	0.814	1	0.99	1	SUBCLONAL	2	TRUE	1	0.307410396627788	2		678	780	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647621	3647621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145194745	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	75	947	3	ENST00000294008.3:c.1442G>A	p.Arg481Gln	p.R481Q	ENST00000294008	NM_032444.2	481	cGa/cAa	7/15	1	2	FACETS	0.408	0.356	0.464	0.408	0.356	0.464	SUBCLONAL	1	TRUE	1	0.307410396627788	2		950	1197	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862834	9862834	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	190	782	1	ENST00000330684.3:c.2469G>A	p.Met823Ile	p.M823I	ENST00000330684	NM_001134407.1	823	atG/atA	12/13	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.307410396627788	2		783	927	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934895	9934895	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	116	515	0	ENST00000330684.3:c.1395G>T	p.Lys465Asn	p.K465N	ENST00000330684	NM_001134407.1	465	aaG/aaT	6/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.307410396627788	2		515	568	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23652450	23652450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	187	873	0	ENST00000261584.4:c.29G>A	p.Ser10Asn	p.S10N	ENST00000261584	NM_024675.3	10	aGc/aAc	1/13	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.307410396627788	2		873	929	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813617	50813617	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	177	638	1	ENST00000398568.2:c.1171G>T	p.Asp391Tyr	p.D391Y	ENST00000398568	NM_001042412.1	391	Gac/Tac	8/18	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.307410396627788	2		639	855	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828341	50828341	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	127	422	0	ENST00000398568.2:c.2677+2T>C		p.X893_splice	ENST00000398568	NM_001042412.1	893			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.307410396627788	2		422	723	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782304	56782304	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	228	684	0	ENST00000308159.5:c.145A>C	p.Thr49Pro	p.T49P	ENST00000308159	NM_014669.4	49	Aca/Cca	2/22	1	2	FACETS	0.761	0.709	0.814	1	0.992	1	SUBCLONAL	2	TRUE	1	0.307410396627788	2		684	975	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645964	67645964	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	194	598	0	ENST00000264010.4:c.892C>A	p.Leu298Ile	p.L298I	ENST00000264010	NM_006565.3	298	Ctc/Atc	4/12	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.307410396627788	2		598	905	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844141	68844141	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	206	671	0	ENST00000261769.5:c.729G>T	p.Glu243Asp	p.E243D	ENST00000261769	NM_004360.3	243	gaG/gaT	6/16	1	2	FACETS	0.792	0.736	0.85	1	0.992	1	SUBCLONAL	2	TRUE	1	0.307410396627788	2		671	846	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831067	72831067	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	36	608	0	ENST00000268489.5:c.5514G>T	p.Gln1838His	p.Q1838H	ENST00000268489	NM_006885.3	1838	caG/caT	9/10	1	2	FACETS	0.332	0.272	0.4	0.332	0.272	0.4	SUBCLONAL	1	TRUE	1	0.307410396627788	2		608	706	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341539	89341539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777571791	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	191	716	1	ENST00000301030.4:c.7531G>A	p.Val2511Ile	p.V2511I	ENST00000301030	NM_001256183.1	2511	Gtc/Atc	10/13	1	2	FACETS	0.778	0.72	0.837	1	0.991	1	SUBCLONAL	2	TRUE	1	0.307410396627788	2		717	799	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838143	89838143	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs201672093	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	157	667	0	ENST00000389301.3:c.2094G>T	p.Glu698Asp	p.E698D	ENST00000389301	NM_000135.2	698	gaG/gaT	23/43	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.307410396627788	2		667	905	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216755	7216755	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	131	619	0	ENST00000380728.2:c.668C>A	p.Ser223Tyr	p.S223Y	ENST00000380728		223	tCt/tAt	8/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.307410396627788	2		619	694	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989435	7989435	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	170	963	2	ENST00000319144.4:c.251G>A	p.Cys84Tyr	p.C84Y	ENST00000319144	NM_001139.2	84	tGc/tAc	2/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.307410396627788	2		965	956	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004828	16004828	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	178	769	0	ENST00000268712.3:c.2426C>A	p.Ser809Tyr	p.S809Y	ENST00000268712	NM_006311.3	809	tCt/tAt	20/46	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.307410396627788	2		769	866	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685556	29685556	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	100	463	0	ENST00000356175.3:c.7966T>G	p.Leu2656Val	p.L2656V	ENST00000356175	NM_000267.3	2656	Ttg/Gtg	54/57	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.307410396627788	2		463	516	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489460	40489460	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	67	617	1	ENST00000264657.5:c.790G>T	p.Glu264Ter	p.E264*	ENST00000264657	NM_139276.2	264	Gaa/Taa	8/24	1	2	FACETS	0.506	0.438	0.579	0.506	0.438	0.579	SUBCLONAL	1	TRUE	1	0.307410396627788	2		618	862	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243643	41243643	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	197	726	0	ENST00000357654.3:c.3905A>C	p.Glu1302Ala	p.E1302A	ENST00000357654	NM_007294.3	1302	gAa/gCa	10/23	1	2	FACETS	0.809	0.751	0.869	1	0.992	1	CLONAL	2	TRUE	1	0.307410396627788	2		726	792	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770029	56770029	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	152	658	0	ENST00000337432.4:c.25G>A	p.Glu9Lys	p.E9K	ENST00000337432	NM_058216.2	9	Gaa/Aaa	1/9	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.307410396627788	2		658	767	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519896	66519896	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	112	521	0	ENST00000358598.2:c.379G>T	p.Ala127Ser	p.A127S	ENST00000358598	NM_212471.2	127	Gct/Tct	4/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.307410396627788	2		521	560	SUCCESS
YES1	7525	MSKCC	GRCh37	18	747976	747976	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1187206077	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	138	534	0	ENST00000314574.4:c.414G>T	p.Lys138Asn	p.K138N	ENST00000314574	NM_005433.3	138	aaG/aaT	4/12	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.307410396627788	2		534	708	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39576689	39576689	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	63	257	0	ENST00000262039.4:c.979G>T	p.Glu327Ter	p.E327*	ENST00000262039	NM_002647.2	327	Gaa/Taa	9/25	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.307410396627788	2		257	323	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375058	45375058	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	68	311	0	ENST00000262160.6:c.785A>G	p.Asp262Gly	p.D262G	ENST00000262160	NM_005901.5	262	gAt/gGt	8/11	1	2	FACETS	0.796	0.699	0.898	1	0.977	1	SUBCLONAL	2	TRUE	1	0.307410396627788	2		311	278	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390417	56390417	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	89	313	0	ENST00000348428.3:c.1156C>A	p.Leu386Ile	p.L386I	ENST00000348428	NM_006785.3	386	Ctt/Att	10/17	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.307410396627788	2		313	453	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56402497	56402497	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	85	254	0	ENST00000348428.3:c.1539A>C	p.Lys513Asn	p.K513N	ENST00000348428	NM_006785.3	513	aaA/aaC	13/17	1	2	FACETS	0.775	0.69	0.863	1	0.981	1	SUBCLONAL	2	TRUE	1	0.307410396627788	2		254	357	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218498	1218498	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	149	515	0	ENST00000326873.7:c.373A>C	p.Met125Leu	p.M125L	ENST00000326873	NM_000455.4	125	Atg/Ctg	2/10	1	2	FACETS	0.811	0.744	0.88	1	0.989	1	CLONAL	2	TRUE	1	0.307410396627788	2		515	598	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210729	2210729	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	238	867	0	ENST00000398665.3:c.1226G>A	p.Arg409His	p.R409H	ENST00000398665	NM_032482.2	409	cGc/cAc	14/28	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.307410396627788	2		867	1056	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121059	3121059	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	220	886	0	ENST00000078429.4:c.962A>G	p.Asp321Gly	p.D321G	ENST00000078429	NM_002067.2	321	gAc/gGc	7/7	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.307410396627788	2		886	1113	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101037	4101037	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	112	523	0	ENST00000262948.5:c.685G>C	p.Gly229Arg	p.G229R	ENST00000262948	NM_030662.3	229	Ggc/Cgc	6/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.307410396627788	2		523	606	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031776	11031776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776007903	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	239	1040	0	ENST00000327064.4:c.1588G>A	p.Val530Met	p.V530M	ENST00000327064	NM_199141.1	530	Gtg/Atg	14/16	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.307410396627788	2		1040	1068	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096941	11096941	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	249	1004	0	ENST00000358026.2:c.432G>T	p.Gln144His	p.Q144H	ENST00000358026	NM_001128849.1	144	caG/caT	4/36	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.307410396627788	2		1004	1141	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152119	11152119	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	222	682	0	ENST00000358026.2:c.4403A>C	p.Glu1468Ala	p.E1468A	ENST00000358026	NM_001128849.1	1468	gAg/gCg	31/36	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.307410396627788	2		682	1032	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054715	13054715	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	131	482	3	ENST00000316448.5:c.1242G>T	p.Lys414Asn	p.K414N	ENST00000316448	NM_004343.3	414	aaG/aaT	9/9	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.307410396627788	2		485	603	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288775	15288775	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1438155304	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	13	92	0	ENST00000263388.2:c.3964C>T	p.Pro1322Ser	p.P1322S	ENST00000263388	NM_000435.2	1322	Ccc/Tcc	24/33	1	2	FACETS	0.492	0.352	0.661	0.492	0.352	0.661	SUBCLONAL	1	TRUE	1	0.307410396627788	2		92	172	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292471	15292471	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	216	973	0	ENST00000263388.2:c.2708A>G	p.Asp903Gly	p.D903G	ENST00000263388	NM_000435.2	903	gAc/gGc	17/33	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.307410396627788	2		973	1095	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353725	15353725	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	269	916	0	ENST00000263377.2:c.3155A>G	p.Asp1052Gly	p.D1052G	ENST00000263377	NM_058243.2	1052	gAc/gGc	14/20	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.307410396627788	2		916	1256	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946855	17946855	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1208827981	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	156	704	0	ENST00000458235.1:c.1792A>G	p.Met598Val	p.M598V	ENST00000458235	NM_000215.3	598	Atg/Gtg	14/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.307410396627788	2		704	750	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971195	18971195	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	218	817	0	ENST00000262803.5:c.2248G>A	p.Val750Met	p.V750M	ENST00000262803	NM_002911.3	750	Gtg/Atg	16/24	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.307410396627788	2		817	1093	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18975000	18975000	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	175	663	0	ENST00000262803.5:c.2797G>A	p.Ala933Thr	p.A933T	ENST00000262803	NM_002911.3	933	Gcc/Acc	20/24	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.307410396627788	2		663	783	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219005	36219005	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	241	929	0	ENST00000222270.7:c.4504G>T	p.Glu1502Ter	p.E1502*	ENST00000222270	NM_014727.1	1502	Gaa/Taa	19/37	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.307410396627788	2		929	1111	SUCCESS
AXL	558	MSKCC	GRCh37	19	41737138	41737138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	261	1032	0	ENST00000301178.4:c.718G>A	p.Glu240Lys	p.E240K	ENST00000301178	NM_021913.4	240	Gag/Aag	6/20	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.307410396627788	2		1032	1181	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42384754	42384754	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	134	394	0	ENST00000221972.3:c.516G>T	p.Glu172Asp	p.E172D	ENST00000221972	NM_021601.3	172	gaG/gaT	4/5	1	2	FACETS	0.759	0.693	0.829	1	0.987	1	SUBCLONAL	2	TRUE	1	0.307410396627788	2		394	574	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754617	42754617	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	184	951	0	ENST00000222329.4:c.123G>T	p.Glu41Asp	p.E41D	ENST00000222329	NM_006494.2	41	gaG/gaT	2/4	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.307410396627788	2		951	1031	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965760	25965760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	225	793	0	ENST00000435504.4:c.3446G>A	p.Arg1149His	p.R1149H	ENST00000435504		1149	cGt/cAt	13/13	0.307410396627788	3	FACETS	1	0.988	1	0.645	0.599	0.692	CLONAL	1	TRUE	1	0.307410396627788	3		793	1310	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416676	29416676	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	123	610	0	ENST00000389048.3:c.4277T>C	p.Val1426Ala	p.V1426A	ENST00000389048	NM_004304.4	1426	gTc/gCc	29/29	0.307410396627788	3	FACETS	1	0.978	1	0.638	0.578	0.702	CLONAL	1	TRUE	1	0.307410396627788	3		610	723	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451812	29451812	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	131	524	0	ENST00000389048.3:c.2753G>T	p.Arg918Ile	p.R918I	ENST00000389048	NM_004304.4	918	aGa/aTa	16/29	0.307410396627788	3	FACETS	1	0.984	1	0.707	0.643	0.775	CLONAL	1	TRUE	1	0.307410396627788	3		524	695	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030610	48030610	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	291	594	0	ENST00000234420.5:c.3224G>A	p.Cys1075Tyr	p.C1075Y	ENST00000234420	NM_000179.2	1075	tGt/tAt	5/10	0.307410396627788	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.307410396627788	3		594	892	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147756	61147756	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	60	304	0	ENST00000295025.8:c.1066G>T	p.Glu356Ter	p.E356*	ENST00000295025	NM_002908.2	356	Gaa/Taa	10/11	0.307410396627788	3	FACETS	1	0.917	1	0.543	0.469	0.622	CLONAL	1	TRUE	1	0.307410396627788	3		304	415	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61717863	61717863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	235	574	1	ENST00000401558.2:c.1936G>A	p.Asp646Asn	p.D646N	ENST00000401558	NM_003400.3	646	Gat/Aat	17/25	0.307410396627788	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.307410396627788	3		575	839	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051647	128051647	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	158	549	0	ENST00000285398.2:c.11G>T	p.Arg4Ile	p.R4I	ENST00000285398	NM_000122.1	4	aGa/aTa	1/15	0.307410396627788	3	FACETS	1	0.987	1	0.702	0.643	0.763	CLONAL	1	TRUE	1	0.307410396627788	3		549	845	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136300	202136300	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	119	596	0	ENST00000358485.4:c.544C>A	p.Leu182Ile	p.L182I	ENST00000358485	NM_001080125.1	182	Ctt/Att	3/9	0.307410396627788	3	FACETS	1	0.972	1	0.604	0.545	0.665	CLONAL	1	TRUE	1	0.307410396627788	3		596	740	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136346	202136346	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1244888701	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	181	445	0	ENST00000358485.4:c.588+2T>C		p.X196_splice	ENST00000358485	NM_001080125.1	196			0.307410396627788	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.307410396627788	3		445	563	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495276	212495276	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	99	511	0	ENST00000342788.4:c.1990C>A	p.Leu664Met	p.L664M	ENST00000342788	NM_005235.2	664	Ctg/Atg	17/28	0.307410396627788	3	FACETS	1	0.966	1	0.599	0.536	0.667	CLONAL	1	TRUE	1	0.307410396627788	3		511	620	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215609881	215609881	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	85	270	0	ENST00000260947.4:c.1813A>G	p.Thr605Ala	p.T605A	ENST00000260947	NM_000465.2	605	Act/Gct	9/11	0.307410396627788	3	FACETS	1	0.972	1	0.658	0.583	0.737	CLONAL	1	TRUE	1	0.307410396627788	3		270	485	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645399	215645399	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	139	626	0	ENST00000260947.4:c.1199G>T	p.Ser400Ile	p.S400I	ENST00000260947	NM_000465.2	400	aGt/aTt	4/11	0.307410396627788	3	FACETS	1	0.981	1	0.642	0.585	0.703	CLONAL	1	TRUE	1	0.307410396627788	3		626	812	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661053	227661053	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	182	838	0	ENST00000305123.5:c.2402C>A	p.Ala801Asp	p.A801D	ENST00000305123	NM_005544.2	801	gCt/gAt	1/2	0.307410396627788	3	FACETS	1	0.988	1	0.701	0.646	0.757	CLONAL	1	TRUE	1	0.307410396627788	3		838	975	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42843800	42843800	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	178	605	0	ENST00000398585.3:c.1119T>G	p.Asn373Lys	p.N373K	ENST00000398585	NM_001135099.1	373	aaT/aaG	10/14	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.307410396627788	2		605	792	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573636	41573636	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	196	821	0	ENST00000263253.7:c.5921G>T	p.Arg1974Ile	p.R1974I	ENST00000263253	NM_001429.3	1974	aGa/aTa	31/31	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.307410396627788	2		821	894	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574361	41574361	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	192	812	0	ENST00000263253.7:c.6646G>T	p.Gly2216Ter	p.G2216*	ENST00000263253	NM_001429.3	2216	Gga/Tga	31/31	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.307410396627788	2		812	864	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37056019	37056019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	88	348	0	ENST00000231790.2:c.774C>A	p.Phe258Leu	p.F258L	ENST00000231790	NM_000249.3	258	ttC/ttA	9/19	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.307410396627788	2		348	399	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182676	38182676	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	148	558	0	ENST00000396334.3:c.829T>G	p.Phe277Val	p.F277V	ENST00000396334	NM_002468.4	277	Ttc/Gtc	5/5	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.307410396627788	2		558	700	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49929003	49929003	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	169	782	1	ENST00000296474.3:c.3363G>T	p.Glu1121Asp	p.E1121D	ENST00000296474	NM_002447.2	1121	gaG/gaT	16/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.307410396627788	2		783	885	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940121	49940121	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	222	922	1	ENST00000296474.3:c.922C>A	p.Arg308Ser	p.R308S	ENST00000296474	NM_002447.2	308	Cgc/Agc	1/20	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.307410396627788	2		923	992	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610563	52610563	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	27	408	0	ENST00000394830.3:c.3610A>G	p.Ile1204Val	p.I1204V	ENST00000394830	NM_018313.4	1204	Att/Gtt	23/30	1	2	FACETS	0.372	0.295	0.46	0.372	0.295	0.46	SUBCLONAL	1	TRUE	1	0.307410396627788	2		408	472	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696235	52696235	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	54	623	0	ENST00000394830.3:c.442A>G	p.Arg148Gly	p.R148G	ENST00000394830	NM_018313.4	148	Aga/Gga	5/30	1	2	FACETS	0.404	0.344	0.47	0.404	0.344	0.47	SUBCLONAL	1	TRUE	1	0.307410396627788	2		623	870	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987164	69987164	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	151	529	0	ENST00000394351.3:c.225G>T	p.Met75Ile	p.M75I	ENST00000394351	NM_000248.3	75	atG/atT	2/9	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.307410396627788	2		529	784	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188309	142188309	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	63	444	0	ENST00000350721.4:c.6422C>A	p.Ala2141Asp	p.A2141D	ENST00000350721	NM_001184.3	2141	gCt/gAt	38/47	1	2	FACETS	0.878	0.761	1	0.878	0.761	1	CLONAL	1	TRUE	1	0.307410396627788	2		444	467	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280192	142280192	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	119	503	0	ENST00000350721.4:c.1242A>C	p.Gln414His	p.Q414H	ENST00000350721	NM_001184.3	414	caA/caC	5/47	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.307410396627788	2		503	609	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937472	178937472	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	106	498	0	ENST00000263967.3:c.1860A>T	p.Glu620Asp	p.E620D	ENST00000263967	NM_006218.2	620	gaA/gaT	12/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.307410396627788	2		498	604	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185195132	185195132	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	75	285	0	ENST00000265026.3:c.2449G>T	p.Glu817Ter	p.E817*	ENST00000265026	NM_004721.4	817	Gaa/Taa	12/14	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.307410396627788	2		285	339	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447220	187447220	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749366850	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	210	833	0	ENST00000232014.4:c.973C>T	p.Arg325Trp	p.R325W	ENST00000232014	NM_001130845.1	325	Cgg/Tgg	5/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.307410396627788	2		833	971	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449515	187449515	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	135	353	0	ENST00000232014.4:c.365G>T	p.Arg122Leu	p.R122L	ENST00000232014	NM_001130845.1	122	cGg/cTg	4/10	1	2	FACETS	0.812	0.741	0.885	1	0.988	1	CLONAL	2	TRUE	1	0.307410396627788	2		353	541	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1941422	1941422	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	186	626	0	ENST00000382891.5:c.1798C>T	p.Arg600Ter	p.R600*	ENST00000382891	NM_133335.3	600	Cga/Tga	9/22	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.307410396627788	2		626	940	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139714	55139714	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	128	520	0	ENST00000257290.5:c.1375G>T	p.Glu459Ter	p.E459*	ENST00000257290	NM_006206.4	459	Gaa/Taa	10/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.307410396627788	2		520	643	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144551	55144551	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	93	480	0	ENST00000257290.5:c.2025G>T	p.Glu675Asp	p.E675D	ENST00000257290	NM_006206.4	675	gaG/gaT	15/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.307410396627788	2		480	522	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161333	55161333	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	131	526	0	ENST00000257290.5:c.3164G>T	p.Ser1055Ile	p.S1055I	ENST00000257290	NM_006206.4	1055	aGc/aTc	23/23	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.307410396627788	2		526	714	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955605	55955605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	82	463	0	ENST00000263923.4:c.3340G>A	p.Glu1114Lys	p.E1114K	ENST00000263923	NM_002253.2	1114	Gaa/Aaa	25/30	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.307410396627788	2		463	490	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968591	55968591	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	165	655	0	ENST00000263923.4:c.2072C>A	p.Ser691Tyr	p.S691Y	ENST00000263923	NM_002253.2	691	tCt/tAt	14/30	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.307410396627788	2		655	883	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197833	66197833	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	51	304	0	ENST00000273854.3:c.2866T>G	p.Leu956Val	p.L956V	ENST00000273854	NM_004439.5	956	Ttg/Gtg	17/18	1	2	FACETS	0.979	0.836	1	0.979	0.836	1	CLONAL	1	TRUE	1	0.307410396627788	2		304	339	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467631	66467631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	93	420	1	ENST00000273854.3:c.638C>A	p.Ala213Asp	p.A213D	ENST00000273854	NM_004439.5	213	gCt/gAt	3/18	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.307410396627788	2		421	504	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081529	143081529	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	91	512	1	ENST00000262992.4:c.1545C>A	p.Asp515Glu	p.D515E	ENST00000262992	NM_001101669.1	515	gaC/gaA	15/24	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.307410396627788	2		513	568	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081536	143081536	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	129	530	0	ENST00000262992.4:c.1538A>T	p.His513Leu	p.H513L	ENST00000262992	NM_001101669.1	513	cAt/cTt	15/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.307410396627788	2		530	605	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522497	187522497	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	174	624	0	ENST00000441802.2:c.11566A>G	p.Thr3856Ala	p.T3856A	ENST00000441802	NM_005245.3	3856	Acc/Gcc	21/27	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.307410396627788	2		624	793	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181881	56181881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	57	314	0	ENST00000399503.3:c.4105G>A	p.Asp1369Asn	p.D1369N	ENST00000399503	NM_005921.1	1369	Gat/Aat	17/20	1	2	FACETS	0.994	0.857	1	0.994	0.857	1	CLONAL	1	TRUE	1	0.307410396627788	2		314	373	SUCCESS
APC	324	MSKCC	GRCh37	5	112173476	112173476	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	73	331	0	ENST00000257430.4:c.2185C>A	p.Leu729Ile	p.L729I	ENST00000257430	NM_000038.5	729	Ctc/Atc	16/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.307410396627788	2		331	385	SUCCESS
APC	324	MSKCC	GRCh37	5	112175978	112175978	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	77	249	0	ENST00000257430.4:c.4687C>A	p.Leu1563Ile	p.L1563I	ENST00000257430	NM_000038.5	1563	Cta/Ata	16/16	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.307410396627788	2		249	342	SUCCESS
APC	324	MSKCC	GRCh37	5	112177916	112177916	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	89	402	0	ENST00000257430.4:c.6625A>G	p.Ile2209Val	p.I2209V	ENST00000257430	NM_000038.5	2209	Att/Gtt	16/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.307410396627788	2		402	457	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402659	20402659	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	153	377	0	ENST00000346618.3:c.196T>C	p.Ser66Pro	p.S66P	ENST00000346618	NM_001949.4	66	Tcc/Ccc	1/7	1	2	FACETS	0.984	0.906	1	1	0.992	1	CLONAL	2	TRUE	1	0.307410396627788	2		377	506	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225599	26225599	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs556601521	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	164	688	0	ENST00000360408.1:c.217C>T	p.Arg73Ter	p.R73*	ENST00000360408	NM_003532.2	73	Cga/Tga	1/1	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.307410396627788	2		688	871	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324728	31324728	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	228	669	0	ENST00000412585.2:c.80A>C	p.His27Pro	p.H27P	ENST00000412585	NM_005514.6	27	cAc/cCc	2/8	1	2	FACETS	1	0.953	1	1	0.994	1	CLONAL	2	TRUE	1	0.307410396627788	2		669	726	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803551	32803551	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	178	714	1	ENST00000374899.4:c.609-1G>T		p.X203_splice	ENST00000374899	NM_018833.2	203			1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.307410396627788	2		715	878	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816840	32816840	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	204	734	1	ENST00000354258.4:c.1484C>T	p.Thr495Ile	p.T495I	ENST00000354258	NM_000593.5	495	aCc/aTc	6/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.307410396627788	2		735	1038	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286985	33286985	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	143	730	0	ENST00000374542.5:c.1952G>T	p.Arg651Met	p.R651M	ENST00000374542	NM_001141970.1	651	aGg/aTg	7/8	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.307410396627788	2		730	848	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112025289	112025289	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	126	525	2	ENST00000368678.4:c.460C>A	p.Leu154Ile	p.L154I	ENST00000368678		154	Ctt/Att	6/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.307410396627788	2		527	672	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117639383	117639383	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	67	515	1	ENST00000368508.3:c.5973G>T	p.Lys1991Asn	p.K1991N	ENST00000368508	NM_002944.2	1991	aaG/aaT	37/43	1	2	FACETS	0.861	0.75	0.982	0.861	0.75	0.982	CLONAL	1	TRUE	1	0.307410396627788	2		516	506	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663595	117663595	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	137	622	1	ENST00000368508.3:c.4637G>T	p.Gly1546Val	p.G1546V	ENST00000368508	NM_002944.2	1546	gGa/gTa	28/43	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.307410396627788	2		623	621	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674191	117674191	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	154	597	0	ENST00000368508.3:c.4283A>C	p.His1428Pro	p.H1428P	ENST00000368508	NM_002944.2	1428	cAt/cCt	26/43	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.307410396627788	2		597	808	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681511	117681511	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	89	320	1	ENST00000368508.3:c.3439A>T	p.Thr1147Ser	p.T1147S	ENST00000368508	NM_002944.2	1147	Aca/Tca	22/43	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.307410396627788	2		321	443	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715853	117715853	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	85	377	0	ENST00000368508.3:c.905G>A	p.Arg302Lys	p.R302K	ENST00000368508	NM_002944.2	302	aGa/aAa	9/43	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.307410396627788	2		377	441	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519507	137519507	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1488394610	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	98	425	0	ENST00000367739.4:c.1131G>T	p.Glu377Asp	p.E377D	ENST00000367739	NM_000416.2	377	gaG/gaT	7/7	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.307410396627788	2		425	511	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525537	137525537	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774732146	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	125	541	0	ENST00000367739.4:c.478G>A	p.Asp160Asn	p.D160N	ENST00000367739	NM_000416.2	160	Gat/Aat	4/7	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.307410396627788	2		541	631	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528586	157528586	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	201	821	0	ENST00000346085.5:c.6311C>A	p.Pro2104Gln	p.P2104Q	ENST00000346085	NM_020732.3	2104	cCa/cAa	20/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.307410396627788	2		821	916	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985566	2985566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	149	564	0	ENST00000396946.4:c.245C>T	p.Thr82Ile	p.T82I	ENST00000396946	NM_032415.4	82	aCc/aTc	4/25	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.307410396627788	2		564	688	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729771	41729771	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	141	586	0	ENST00000242208.4:c.758G>A	p.Ser253Asn	p.S253N	ENST00000242208	NM_002192.2	253	aGc/aAc	3/3	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.307410396627788	2		586	678	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397786	116397786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	130	616	0	ENST00000397752.3:c.2060C>T	p.Ser687Phe	p.S687F	ENST00000397752	NM_000245.2	687	tCt/tTt	8/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.307410396627788	2		616	594	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829219	128829219	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	115	451	0	ENST00000249373.3:c.227A>G	p.Asn76Ser	p.N76S	ENST00000249373	NM_005631.4	76	aAc/aGc	1/12	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.307410396627788	2		451	524	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846127	128846127	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	216	905	0	ENST00000249373.3:c.1057C>A	p.Leu353Ile	p.L353I	ENST00000249373	NM_005631.4	353	Ctc/Atc	5/12	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.307410396627788	2		905	1133	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148507424	148507424	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	133	406	0	ENST00000320356.2:c.2029+1G>A		p.X677_splice	ENST00000320356	NM_004456.4	677			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.307410396627788	2		406	601	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851226	151851226	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	43	312	0	ENST00000262189.6:c.12145G>T	p.Glu4049Ter	p.E4049*	ENST00000262189	NM_170606.2	4049	Gaa/Taa	48/59	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.307410396627788	2		312	273	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345862	152345862	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	151	568	1	ENST00000359321.1:c.708G>T	p.Lys236Asn	p.K236N	ENST00000359321	NM_005431.1	236	aaG/aaT	3/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.307410396627788	2		569	780	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345987	152345987	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	148	596	0	ENST00000359321.1:c.583A>G	p.Thr195Ala	p.T195A	ENST00000359321	NM_005431.1	195	Aca/Gca	3/3	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.307410396627788	2		596	734	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29195930	29195930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779990842	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	236	893	1	ENST00000240100.2:c.668C>T	p.Thr223Met	p.T223M	ENST00000240100	NM_001394.6	223	aCg/aTg	3/4	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.307410396627788	2		894	1183	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370712	55370712	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	150	367	0	ENST00000297316.4:c.14A>G	p.Asp5Gly	p.D5G	ENST00000297316	NM_022454.3	5	gAt/gGt	1/2	1	2	FACETS	0.823	0.755	0.893	1	0.99	1	CLONAL	2	TRUE	1	0.307410396627788	2		367	593	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56854435	56854436	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	85	426	0	ENST00000519728.1:c.21dup	p.Gly8ArgfsTer7	p.G8Rfs*7	ENST00000519728	NM_002350.3	6	tca/tcAa	2/13	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.307410396627788	2		426	480	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989689	68989689	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	182	582	0	ENST00000288368.4:c.1627G>T	p.Gly543Ter	p.G543*	ENST00000288368	NM_024870.2	543	Gga/Tga	15/40	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.307410396627788	2		582	805	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980478	70980478	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	187	645	0	ENST00000276594.2:c.899C>A	p.Ser300Tyr	p.S300Y	ENST00000276594	NM_024504.3	300	tCt/tAt	4/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.307410396627788	2		645	969	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982024	70982024	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	264	978	0	ENST00000276594.2:c.72G>T	p.Gln24His	p.Q24H	ENST00000276594	NM_024504.3	24	caG/caT	2/8	1	2	FACETS	0.751	0.703	0.8	1	0.993	1	SUBCLONAL	2	TRUE	1	0.307410396627788	2		978	1144	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518087	8518087	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	132	539	0	ENST00000356435.5:c.1304T>G	p.Leu435Trp	p.L435W	ENST00000356435		435	tTg/tGg	10/35	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.307410396627788	2		539	649	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518304	8518304	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	87	365	0	ENST00000356435.5:c.1087T>C	p.Ser363Pro	p.S363P	ENST00000356435		363	Tct/Cct	10/35	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.307410396627788	2		365	431	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22008869	22008869	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	171	624	0	ENST00000276925.6:c.84G>T	p.Glu28Asp	p.E28D	ENST00000276925	NM_004936.3	28	gaG/gaT	1/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.307410396627788	2		624	898	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27183583	27183583	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	117	482	0	ENST00000380036.4:c.1157T>C	p.Val386Ala	p.V386A	ENST00000380036	NM_000459.3	386	gTg/gCg	8/23	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.307410396627788	2		482	593	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27209197	27209197	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	114	526	0	ENST00000380036.4:c.2654T>G	p.Ile885Ser	p.I885S	ENST00000380036	NM_000459.3	885	aTc/aGc	16/23	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.307410396627788	2		526	647	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430667	80430667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1010141343	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	94	442	0	ENST00000286548.4:c.341G>A	p.Arg114Gln	p.R114Q	ENST00000286548	NM_002072.3	114	cGa/cAa	3/7	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.307410396627788	2		442	505	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218641	98218641	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	45	604	0	ENST00000331920.6:c.3223G>T	p.Gly1075Ter	p.G1075*	ENST00000331920	NM_000264.3	1075	Gga/Tga	19/24	1	2	FACETS	0.359	0.301	0.424	0.359	0.301	0.424	SUBCLONAL	1	TRUE	1	0.307410396627788	2		604	815	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904922	101904922	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	120	430	1	ENST00000374994.4:c.910A>T	p.Lys304Ter	p.K304*	ENST00000374994	NM_004612.2	304	Aaa/Taa	5/9	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.307410396627788	2		431	586	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127951935	127951935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	160	752	0	ENST00000373547.4:c.63G>T	p.Glu21Asp	p.E21D	ENST00000373547	NM_002721.4	21	gaG/gaT	1/7	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.307410396627788	2		752	841	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730200	133730200	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764626784	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	107	563	0	ENST00000318560.5:c.266G>A	p.Arg89Gln	p.R89Q	ENST00000318560	NM_005157.4	89	cGg/cAg	3/11	1	2	FACETS	0.993	0.892	1	0.993	0.892	1	CLONAL	1	TRUE	1	0.307410396627788	2		563	701	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922776	44922776	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	163	524	0	ENST00000377967.4:c.1637C>T	p.Ala546Val	p.A546V	ENST00000377967	NM_021140.2	546	gCt/gTt	16/29	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.307410396627788	2		524	771	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038509	47038509	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	206	831	0	ENST00000377604.3:c.671T>C	p.Val224Ala	p.V224A	ENST00000377604	NM_001204468.1	224	gTc/gCc	8/24	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.307410396627788	2		831	999	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410304	63410304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	54	969	0	ENST00000330258.3:c.2863G>A	p.Ala955Thr	p.A955T	ENST00000330258	NM_152424.3	955	Gcc/Acc	2/2	1	2	FACETS	0.376	0.32	0.438	0.376	0.32	0.438	SUBCLONAL	1	TRUE	1	0.307410396627788	2		969	934	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411626	63411626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	214	824	1	ENST00000330258.3:c.1541G>A	p.Ser514Asn	p.S514N	ENST00000330258	NM_152424.3	514	aGc/aAc	2/2	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.307410396627788	2		825	981	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411946	63411946	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	195	898	1	ENST00000330258.3:c.1221A>C	p.Glu407Asp	p.E407D	ENST00000330258	NM_152424.3	407	gaA/gaC	2/2	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.307410396627788	2		899	872	SUCCESS
AR	367	MSKCC	GRCh37	X	66942675	66942675	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	100	420	0	ENST00000374690.3:c.2456T>G	p.Val819Gly	p.V819G	ENST00000374690	NM_000044.3	819	gTg/gGg	7/8	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.307410396627788	2		420	485	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349224	70349224	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	166	808	1	ENST00000374080.3:c.3636G>T	p.Gln1212His	p.Q1212H	ENST00000374080		1212	caG/caT	26/45	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.307410396627788	2		809	960	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912056	76912056	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	72	424	0	ENST00000373344.5:c.4208G>T	p.Arg1403Ile	p.R1403I	ENST00000373344	NM_000489.3	1403	aGa/aTa	13/35	1	2	FACETS	0.903	0.79	1	0.903	0.79	1	CLONAL	1	TRUE	1	0.307410396627788	2		424	519	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937961	76937961	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	140	571	0	ENST00000373344.5:c.2787G>T	p.Gln929His	p.Q929H	ENST00000373344	NM_000489.3	929	caG/caT	9/35	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.307410396627788	2		571	706	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939470	76939470	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	100	677	0	ENST00000373344.5:c.1278G>T	p.Glu426Asp	p.E426D	ENST00000373344	NM_000489.3	426	gaG/gaT	9/35	1	2	FACETS	0.964	0.862	1	0.964	0.862	1	CLONAL	1	TRUE	1	0.307410396627788	2		677	675	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939500	76939500	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	79	638	0	ENST00000373344.5:c.1248G>T	p.Glu416Asp	p.E416D	ENST00000373344	NM_000489.3	416	gaG/gaT	9/35	1	2	FACETS	0.812	0.714	0.917	0.812	0.714	0.917	CLONAL	1	TRUE	1	0.307410396627788	2		638	633	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611779	100611779	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	94	515	0	ENST00000308731.7:c.1342G>T	p.Val448Phe	p.V448F	ENST00000308731	NM_000061.2	448	Gtc/Ttc	14/19	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.307410396627788	2		515	571	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611821	100611821	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	165	655	1	ENST00000308731.7:c.1300G>T	p.Glu434Ter	p.E434*	ENST00000308731	NM_000061.2	434	Gaa/Taa	14/19	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.307410396627788	2		656	756	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034507	123034507	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs750669780	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	102	401	0	ENST00000355640.3:c.1264A>G	p.Met422Val	p.M422V	ENST00000355640		422	Atg/Gtg	6/7	1	2	FACETS	0.805	0.725	0.889	1	0.985	1	CLONAL	2	TRUE	1	0.307410396627788	2		401	412	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176472	123176472	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	83	358	0	ENST00000218089.9:c.439A>C	p.Lys147Gln	p.K147Q	ENST00000218089	NM_001042749.1	147	Aaa/Caa	7/35	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.307410396627788	2		358	431	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179195	123179195	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	84	398	0	ENST00000218089.9:c.644T>C	p.Phe215Ser	p.F215S	ENST00000218089	NM_001042749.1	215	tTt/tCt	8/35	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.307410396627788	2		398	393	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197822	123197822	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	75	450	0	ENST00000218089.9:c.1946G>T	p.Arg649Ile	p.R649I	ENST00000218089	NM_001042749.1	649	aGa/aTa	20/35	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.307410396627788	2		450	419	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504048	123504048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	59	356	0	ENST00000371139.4:c.224G>A	p.Arg75Lys	p.R75K	ENST00000371139	NM_001114937.2	75	aGa/aAa	3/4	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.307410396627788	2		356	339	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504088	123504088	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	74	452	0	ENST00000371139.4:c.264G>T	p.Gln88His	p.Q88H	ENST00000371139	NM_001114937.2	88	caG/caT	3/4	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.307410396627788	2		452	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0056958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	259	1058	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.203373124401239	3	FACETS	0.863	0.809	0.917	0.863	0.809	0.917	CLONAL	3	TRUE	0	0.242353147923827	3		1058	926	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0056959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	20	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.171971422981721	5	FACETS	0.33	0.251	0.422	0.11	0.083	0.141	INDETERMINATE	1	TRUE	2	0.437940510574316	5		298	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0056959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	148	1058	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.279527890084235	2	FACETS	1	0.987	1	0.698	0.642	0.756	CLONAL	1	TRUE	0	0.437940510574316	2		1058	484	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0056959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	103	436	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.843	0.757	0.934	0.843	0.757	0.934	CLONAL	1	TRUE	1	0.437940510574316	2		436	558	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0056959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	41	341	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.282882575274394	3	FACETS	0.625	0.522	0.74	0.208	0.174	0.247	SUBCLONAL	1	TRUE	0	0.437940510574316	3		341	365	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007656	62007656	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs912718113	NA	P-0056959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	192	635	0	ENST00000392795.3:c.211G>A	p.Ala71Thr	p.A71T	ENST00000392795	NM_001039933.1	71	Gcc/Acc	3/6	0.437940510574316	5	FACETS	0.91	0.844	0.979	0.607	0.562	0.653	CLONAL	2	TRUE	2	0.437940510574316	5		635	798	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525018	9525018	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	116	407	0	ENST00000353224.5:c.1867G>T	p.Glu623Ter	p.E623*	ENST00000353224	NM_177990.2	623	Gag/Tag	8/10	0.112178529007945	5	FACETS	1	0.96	1	0.55	0.5	0.602	INDETERMINATE	2	TRUE	1	0.437940510574316	5		407	399	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412542	63412542	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs748480637	NA	P-0056959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	117	746	0	ENST00000330258.3:c.625A>T	p.Ser209Cys	p.S209C	ENST00000330258	NM_152424.3	209	Agc/Tgc	2/2	0.124987542888489	0	FACETS	0.61	0.553	0.67			1	INDETERMINATE	1	TRUE	0	0.437940510574316	0		746	492	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0056960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	78	348	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.122119635535651	3	FACETS	1	0.973	1	0.451	0.4	0.505	INDETERMINATE	1	TRUE	0	0.465686923194012	3		348	305	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0056960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	124	762	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.465686923194012	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.465686923194012	1		762	388	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0056960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	32	523	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.465686923194012	1	FACETS	0.351	0.286	0.425	0.351	0.286	0.425	SUBCLONAL	1	TRUE	0	0.465686923194012	1		523	300	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0056960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	17	724	2	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.406413137546728	1	FACETS	0.324	0.243	0.419	0.324	0.243	0.419	SUBCLONAL	1	TRUE	0	0.465686923194012	1		726	173	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527461	29527461	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786203950	NA	P-0056960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	28	499	0	ENST00000356175.3:c.910C>T	p.Arg304Ter	p.R304*	ENST00000356175	NM_000267.3	304	Cga/Tga	9/57	0.245884264268247	3	FACETS	0.39	0.312	0.48	0.13	0.104	0.16	INDETERMINATE	1	TRUE	0	0.465686923194012	3		499	380	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637555	52637555	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	16	502	0	ENST00000394830.3:c.2761C>T	p.Arg921Ter	p.R921*	ENST00000394830	NM_018313.4	921	Cga/Tga	18/30	0.465686923194012	1	FACETS	0.261	0.193	0.342	0.261	0.193	0.342	SUBCLONAL	1	TRUE	0	0.465686923194012	1		502	202	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060499964	NA	P-0056960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	62	1129	0	ENST00000326873.7:c.667G>A	p.Glu223Lys	p.E223K	ENST00000326873	NM_000455.4	223	Gag/Aag	5/10	NA	2	FACETS	0.564	0.488	0.646			1	INDETERMINATE	1	TRUE	NA	0.465686923194012	2		1129	472	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900209	101900209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	22	456	0	ENST00000374994.4:c.643C>T	p.Arg215Ter	p.R215*	ENST00000374994	NM_004612.2	215	Cga/Tga	4/9	0.406413137546728	1	FACETS	0.29	0.225	0.365	0.29	0.225	0.365	SUBCLONAL	1	TRUE	0	0.465686923194012	1		456	250	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098423	11098423	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs549254467	NA	P-0056960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	23	461	0	ENST00000358026.2:c.941C>T	p.Ala314Val	p.A314V	ENST00000358026	NM_001128849.1	314	gCg/gTg	6/36	0.465686923194012	1	FACETS	0.349	0.273	0.436	0.349	0.273	0.436	SUBCLONAL	1	TRUE	0	0.465686923194012	1		461	217	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922760	44922760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	29	519	0	ENST00000377967.4:c.1621C>T	p.Gln541Ter	p.Q541*	ENST00000377967	NM_021140.2	541	Cag/Tag	16/29	0.465686923194012	1	FACETS	0.31	0.249	0.379	0.31	0.249	0.379	SUBCLONAL	1	TRUE	0	0.465686923194012	1		519	308	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519008	66519008	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555813217	NA	P-0056960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	46	581	1	ENST00000358598.2:c.289C>T	p.Arg97Ter	p.R97*	ENST00000358598	NM_212471.2	97	Cga/Tga	3/11	0.465686923194012	1	FACETS	0.401	0.338	0.47	0.401	0.338	0.47	SUBCLONAL	1	TRUE	0	0.465686923194012	1		582	378	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845580	151845580	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1287135873	NA	P-0056960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	40	753	0	ENST00000262189.6:c.13432C>T	p.Arg4478Ter	p.R4478*	ENST00000262189	NM_170606.2	4478	Cga/Tga	52/59	0.341276419835459	3	FACETS	0.46	0.382	0.547	0.23	0.191	0.274	SUBCLONAL	1	TRUE	1	0.465686923194012	3		753	460	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530184	63530185	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGGCTCTTTGTGACTGAAAATA	novel	NA	P-0056960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	46	560	0	ENST00000307078.5:c.2238-9_2250dup	p.Lys751TyrfsTer20	p.K751Yfs*20	ENST00000307078	NM_004655.3	750	-/TATTTTCAGTCACAAAGAGCCA	10/11	0.465686923194012	1	FACETS	0.695	0.592	0.807	0.695	0.592	0.807	SUBCLONAL	1	TRUE	0	0.465686923194012	1		560	218	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0056961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	583	1029	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.988	1	1	0.998	1	CLONAL	2	TRUE	1	0.522975112958697	2		1032	1068	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11318628	11318628	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375240279	NA	P-0056961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	175	414	0	ENST00000361445.4:c.185G>A	p.Arg62His	p.R62H	ENST00000361445	NM_004958.3	62	cGc/cAc	3/58	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.522975112958697	2		414	649	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105581	27105581	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0056961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	285	551	0	ENST00000324856.7:c.5192T>G	p.Leu1731Ter	p.L1731*	ENST00000324856	NM_006015.4	1731	tTa/tGa	20/20	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.522975112958697	2		551	857	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	71	573	5	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.33	0.287	0.376	0.33	0.287	0.376	SUBCLONAL	1	TRUE	1	0.522975112958697	2		578	823	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0056961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	242	295	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	1	0.986	1	1	0.996	1	CLONAL	2	TRUE	1	0.522975112958697	2		295	417	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911548	114911548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	46	397	0	ENST00000543371.1:c.1066G>A	p.Ala356Thr	p.A356T	ENST00000543371	NM_001198531.1	356	Gca/Aca	10/14	1	2	FACETS	0.309	0.26	0.364	0.309	0.26	0.364	SUBCLONAL	1	TRUE	1	0.522975112958697	2		397	569	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316397	14316397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782457908	NA	P-0056961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	163	425	0	ENST00000256196.4:c.208G>A	p.Ala70Thr	p.A70T	ENST00000256196		70	Gca/Aca	3/6	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.522975112958697	2		425	504	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	43	565	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	0.328	0.274	0.387	0.328	0.274	0.387	SUBCLONAL	1	TRUE	1	0.522975112958697	2		565	502	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200877	67200877	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	106	682	0	ENST00000312629.5:c.870del	p.Tyr291ThrfsTer14	p.Y291Tfs*14	ENST00000312629	NM_003952.2	289	Ccc/cc	10/15	1	2	FACETS	0.432	0.387	0.481	0.432	0.387	0.481	SUBCLONAL	1	TRUE	1	0.522975112958697	2		682	938	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466019	69466019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	303	850	0	ENST00000227507.2:c.857C>T	p.Thr286Ile	p.T286I	ENST00000227507	NM_053056.2	286	aCa/aTa	5/5	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.522975112958697	2		850	1067	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819270	3819270	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	323	673	0	ENST00000262367.5:c.2965G>T	p.Gly989Ter	p.G989*	ENST00000262367	NM_004380.2	989	Gga/Tga	15/31	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.522975112958697	2		673	1004	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857806	9857806	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	192	634	0	ENST00000330684.3:c.3595C>T	p.Pro1199Ser	p.P1199S	ENST00000330684	NM_001134407.1	1199	Ccg/Tcg	13/13	1	2	FACETS	0.911	0.844	0.98	0.911	0.844	0.98	CLONAL	1	TRUE	1	0.522975112958697	2		634	806	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660469	67660469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	183	418	1	ENST00000264010.4:c.1369C>T	p.Arg457Ter	p.R457*	ENST00000264010	NM_006565.3	457	Cga/Tga	8/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.522975112958697	2		419	632	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923723	72923723	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	297	713	0	ENST00000268489.5:c.3355C>T	p.Arg1119Ter	p.R1119*	ENST00000268489	NM_006885.3	1119	Cga/Tga	4/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.522975112958697	2		713	941	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357208	89357208	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	268	606	0	ENST00000301030.4:c.426G>C	p.Gln142His	p.Q142H	ENST00000301030	NM_001256183.1	142	caG/caC	6/13	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.522975112958697	2		606	980	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024365	16024365	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0056961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	45	398	1	ENST00000268712.3:c.1852+1G>A		p.X618_splice	ENST00000268712	NM_006311.3	618			1	2	FACETS	0.301	0.253	0.355	0.301	0.253	0.355	SUBCLONAL	1	TRUE	1	0.522975112958697	2		399	571	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0056961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	169	511	3	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	0.942	0.869	1	0.942	0.869	1	CLONAL	1	TRUE	1	0.522975112958697	2		514	686	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170804	11170804	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1306144699	NA	P-0056961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	103	762	0	ENST00000358026.2:c.4948C>T	p.Arg1650Ter	p.R1650*	ENST00000358026	NM_001128849.1	1650	Cga/Tga	35/36	1	2	FACETS	0.347	0.31	0.388	0.347	0.31	0.388	SUBCLONAL	1	TRUE	1	0.522975112958697	2		762	1134	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0056961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	180	581	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.809	0.747	0.874	0.809	0.747	0.874	CLONAL	1	TRUE	1	0.522975112958697	2		583	851	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390120	89390120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	46	342	0	ENST00000336596.2:c.869G>A	p.Cys290Tyr	p.C290Y	ENST00000336596	NM_005233.5	290	tGc/tAc	4/17	1	2	FACETS	0.334	0.281	0.393	0.334	0.281	0.393	SUBCLONAL	1	TRUE	1	0.522975112958697	2		342	526	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916947	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0056961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	118	320	0	ENST00000263967.3:c.333_334delinsTT	p.Lys111_Ile112delinsAsnPhe	p.K111_I112delinsNF	ENST00000263967	NM_006218.2	111	aaGAtc/aaTTtc	2/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.522975112958697	2		320	393	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265578	152265578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	222	506	0	ENST00000206249.3:c.1031G>A	p.Gly344Asp	p.G344D	ENST00000206249	NM_000125.3	344	gGc/gAc	4/8	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.522975112958697	2		506	814	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984036	2984036	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	78	564	0	ENST00000396946.4:c.494A>G	p.Gln165Arg	p.Q165R	ENST00000396946	NM_032415.4	165	cAg/cGg	5/25	1	2	FACETS	0.381	0.335	0.432	0.381	0.335	0.432	SUBCLONAL	1	TRUE	1	0.522975112958697	2		564	782	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0056961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	271	431	17	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	1	2	FACETS	0.849	0.804	0.895	1	0.995	1	CLONAL	2	TRUE	1	0.522975112958697	2		448	610	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028022	69028022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	48	354	0	ENST00000288368.4:c.3181G>A	p.Glu1061Lys	p.E1061K	ENST00000288368	NM_024870.2	1061	Gaa/Aaa	26/40	1	2	FACETS	0.37	0.313	0.433	0.37	0.313	0.433	SUBCLONAL	1	TRUE	1	0.522975112958697	2		354	496	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347883	128347883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1186797500	NA	P-0056961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	262	710	0	ENST00000265960.3:c.622G>A	p.Gly208Arg	p.G208R	ENST00000265960	NM_001006617.1	208	Ggg/Agg	5/12	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.522975112958697	2		710	995	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759623	133759623	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	249	811	0	ENST00000318560.5:c.1950del	p.Leu651TrpfsTer43	p.L651Wfs*43	ENST00000318560	NM_005157.4	649	aCc/ac	11/11	1	2	FACETS	0.976	0.913	1	0.976	0.913	1	CLONAL	1	TRUE	1	0.522975112958697	2		811	976	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438316	110438317	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	rs532810290	NA	P-0056961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	49	191	0	ENST00000375856.3:c.82_84dup	p.Asn28dup	p.N28dup	ENST00000375856	NM_003749.2	28	-/AAC	1/2	1	2	FACETS	0.635	0.541	0.737	0.635	0.541	0.737	SUBCLONAL	1	TRUE	1	0.522975112958697	2		191	295	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913517	NA	P-0056963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	252	447	0	ENST00000288135.5:c.1676T>A	p.Val559Asp	p.V559D	ENST00000288135	NM_000222.2	559	gTt/gAt	11/21	0.25722216505269	1	FACETS	0.673	0.634	0.712	0.673	0.634	0.712	INDETERMINATE	1	TRUE	0	0.745896933144008	1		447	630	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	105	324	0				ENST00000310581	NM_198253.2	-/1132			0.453932857531365	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.453932857531365	1		324	283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0056965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	377	653	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.453932857531365	3	FACETS	0.952	0.906	1	0.952	0.906	1	CLONAL	2	TRUE	1	0.453932857531365	3		655	1070	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0056965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	197	794	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.453932857531365	3	FACETS	0.806	0.745	0.87	0.403	0.372	0.435	CLONAL	1	TRUE	1	0.453932857531365	3		794	1321	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630683	158630683	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146610930	NA	P-0056965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	131	301	0	ENST00000263640.3:c.560C>T	p.Ser187Leu	p.S187L	ENST00000263640	NM_001105.4	187	tCg/tTg	6/11	0.290529296259576	3	FACETS	0.908	0.832	0.986	0.908	0.832	0.986	CLONAL	2	TRUE	1	0.453932857531365	3		301	390	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495508	56495508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	243	664	1	ENST00000267101.3:c.3698C>T	p.Ala1233Val	p.A1233V	ENST00000267101	NM_001982.3	1233	gCc/gTc	28/28	0.453932857531365	2	FACETS	0.855	0.805	0.907	0.855	0.805	0.907	CLONAL	2	TRUE	0	0.453932857531365	2		665	626	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312810	91312810	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	102	480	0	ENST00000355112.3:c.2549C>G	p.Pro850Arg	p.P850R	ENST00000355112	NM_000057.2	850	cCt/cGt	12/22	0.290529296259576	3	FACETS	0.87	0.779	0.966	0.435	0.389	0.483	CLONAL	1	TRUE	1	0.453932857531365	3		480	634	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	103	324	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.805	0.728	0.883	0.805	0.728	0.883	CLONAL	1	TRUE	1	0.790173818006398	2		324	324	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913384	NA	P-0056990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	164	414	0	ENST00000304494.5:c.262G>T	p.Glu88Ter	p.E88*	ENST00000304494	NM_000077.4	88	Gag/Tag	2/3	0.740531369014901	1	FACETS	0.937	0.882	0.99	0.937	0.882	0.99	CLONAL	1	TRUE	0	0.790173818006398	1		414	268	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376740	118376740	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs782761669	NA	P-0056990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	182	470	0	ENST00000534358.1:c.10133T>C	p.Ile3378Thr	p.I3378T	ENST00000534358	NM_005933.3	3378	aTt/aCt	27/36	1	2	FACETS	0.976	0.909	1	0.976	0.909	1	CLONAL	1	TRUE	1	0.790173818006398	2		470	472	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163764	47163764	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	158	406	0	ENST00000409792.3:c.2362del	p.Thr788ProfsTer10	p.T788Pfs*10	ENST00000409792	NM_014159.6	788	Acc/cc	3/21	1	2	FACETS	0.887	0.82	0.955	0.887	0.82	0.955	CLONAL	1	TRUE	1	0.790173818006398	2		406	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0056991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	118	557	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.461549192418908	1	FACETS	0.727	0.658	0.799	0.727	0.658	0.799	SUBCLONAL	1	TRUE	0	0.461549192418908	1		557	541	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133263	30133263	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	136	668	0	ENST00000263025.4:c.235C>G	p.Gln79Glu	p.Q79E	ENST00000263025	NM_002746.2	79	Cag/Gag	2/9	1	2	FACETS	0.862	0.785	0.942	0.862	0.785	0.942	CLONAL	1	TRUE	1	0.461549192418908	2		668	684	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17354296	17354296	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	81	338	0	ENST00000375499.3:c.488C>A	p.Ser163Tyr	p.S163Y	ENST00000375499	NM_003000.2	163	tCt/tAt	5/8	1	2	FACETS	0.761	0.673	0.855	0.761	0.673	0.855	SUBCLONAL	1	TRUE	1	0.461549192418908	2		338	461	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650115	206650115	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	165	626	0	ENST00000367120.3:c.635A>C	p.Tyr212Ser	p.Y212S	ENST00000367120	NM_014002.3	212	tAc/tCc	7/22	1	2	FACETS	0.874	0.803	0.948	0.874	0.803	0.948	CLONAL	1	TRUE	1	0.461549192418908	2		626	818	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410645	32410645	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1554938534	NA	P-0056991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	136	506	0	ENST00000332351.3:c.1513A>G	p.Met505Val	p.M505V	ENST00000332351	NM_024426.4	505	Atg/Gtg	10/10	0.428720503617335	1	FACETS	0.691	0.63	0.755	0.691	0.63	0.755	SUBCLONAL	1	TRUE	0	0.461549192418908	1		506	656	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517701	176517746	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGCCCCTCTTGGACCTTAGATGCTTCCCTCTGTCCCTGATGTAGA	CTGCCCCTCTTGGACCTTAGATGCTTCCCTCTGTCCCTGATGTAGA	-	novel	NA	P-0056991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	127	745	0	ENST00000292408.4:c.356-43_358del		p.X119_splice	ENST00000292408	NM_213647.1	119		4/18	0.378351152575012	3	FACETS	0.957	0.868	1	0.319	0.289	0.35	CLONAL	1	TRUE	0	0.461549192418908	3		745	708	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649734	48649734	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs781808940	NA	P-0056991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	153	735	0	ENST00000376670.3:c.218C>G	p.Pro73Arg	p.P73R	ENST00000376670	NM_002049.3	73	cCa/cGa	2/6	NA	2	FACETS	0.888	0.813	0.965			1	INDETERMINATE	1	TRUE	NA	0.461549192418908	2		735	747	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0056992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	22	303	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.595	0.462	0.749	0.595	0.462	0.749	SUBCLONAL	1	TRUE	1	0.27	2		303	274	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576890	7576890	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	68	707	0	ENST00000269305.4:c.956del	p.Lys319ArgfsTer26	p.K319Rfs*26	ENST00000269305	NM_001126112.2	319	aAg/ag	9/11	1	2	FACETS	0.608	0.527	0.695	0.608	0.527	0.695	SUBCLONAL	1	TRUE	1	0.27	2		707	829	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013720	170013720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	51	348	0	ENST00000295797.4:c.1439G>A	p.Arg480His	p.R480H	ENST00000295797	NM_002740.5	480	cGc/cAc	15/18	1	2	FACETS	0.739	0.629	0.861	0.739	0.629	0.861	SUBCLONAL	1	TRUE	1	0.27	2		348	511	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266943	18266943	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760416536	NA	P-0056992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	19	204	0	ENST00000222254.8:c.254G>A	p.Arg85Gln	p.R85Q	ENST00000222254	NM_005027.3	85	cGg/cAg	2/16	1	2	FACETS	0.601	0.457	0.77	0.601	0.457	0.77	SUBCLONAL	1	TRUE	1	0.27	2		204	234	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89478289	89478289	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	26	337	0	ENST00000336596.2:c.2108A>C	p.Glu703Ala	p.E703A	ENST00000336596	NM_005233.5	703	gAg/gCg	12/17	1	2	FACETS	0.498	0.394	0.617	0.498	0.394	0.617	SUBCLONAL	1	TRUE	1	0.27	2		337	387	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165176	32165176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157841409	NA	P-0056992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	48	774	1	ENST00000375023.3:c.4952G>A	p.Arg1651His	p.R1651H	ENST00000375023	NM_004557.3	1651	cGc/cAc	27/30	1	2	FACETS	0.419	0.353	0.493	0.419	0.353	0.493	SUBCLONAL	1	TRUE	1	0.27	2		775	848	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93629450	93629450	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	22	253	0	ENST00000375746.1:c.884C>A	p.Ser295Ter	p.S295*	ENST00000375746	NM_001174167.1	295	tCa/tAa	7/14	1	2	FACETS	0.479	0.371	0.605	0.479	0.371	0.605	SUBCLONAL	1	TRUE	1	0.27	2		253	340	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	182	221	1				ENST00000310581	NM_198253.2	-/1132			0.314864510115296	3	FACETS	0.911	0.855	0.968	1	0.993	1	CLONAL	4	TRUE	1	0.314864510115296	3		222	367	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	348	330	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.314864510115296	5	FACETS	1	0.989	1			1	CLONAL	4	TRUE	NA	0.314864510115296	5		330	727	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092966	29092966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	82	433	0	ENST00000328354.6:c.1018G>A	p.Glu340Lys	p.E340K	ENST00000328354	NM_007194.3	340	Gaa/Aaa	10/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.314864510115296	2		433	363	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149817	202149817	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	115	677	0	ENST00000358485.4:c.1258C>T	p.Gln420Ter	p.Q420*	ENST00000358485	NM_001080125.1	420	Cag/Tag	8/9	0.205898847708594	2	FACETS	1	0.984	1	0.726	0.657	0.798	CLONAL	1	TRUE	0	0.314864510115296	2		677	503	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	94	483	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	0.225016627045589	3	FACETS	1	0.971	1	0.629	0.561	0.701	CLONAL	1	TRUE	1	0.314864510115296	3		483	549	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112602	115112602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs865915137	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	165	1006	0	ENST00000257566.3:c.1138G>A	p.Glu380Lys	p.E380K	ENST00000257566	NM_016569.3	380	Gag/Aag	7/8	1	2	FACETS	0.774	0.713	0.837	1	0.99	1	SUBCLONAL	2	TRUE	1	0.314864510115296	2		1006	677	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160488	108160488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730881369	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	83	446	0	ENST00000278616.4:c.4396C>T	p.Arg1466Ter	p.R1466*	ENST00000278616	NM_000051.3	1466	Cga/Tga	29/63	1	2	FACETS	0.93	0.822	1	0.93	0.822	1	CLONAL	1	TRUE	1	0.314864510115296	2		446	567	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023219	27023232	+	frameshift_variant	Frame_Shift_Del	DEL	CCTAGGCCCGCCCT	CCTAGGCCCGCCCT	-	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	32	228	0	ENST00000324856.7:c.325_338del	p.Pro109GlufsTer3	p.P109Efs*3	ENST00000324856	NM_006015.4	109	CCTAGGCCCGCCCTg/g	1/20	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.314864510115296	2		228	170	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075655	8075655	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs772410037	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	87	385	0	ENST00000377482.5:c.25C>T	p.Gln9Ter	p.Q9*	ENST00000377482	NM_018948.3	9	Cag/Tag	2/4	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.314864510115296	2		385	422	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157149	106157149	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1205320001	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	76	441	0	ENST00000380013.4:c.2050C>T	p.Gln684Ter	p.Q684*	ENST00000380013	NM_001127208.2	684	Caa/Taa	3/11	0.225016627045589	3	FACETS	1	0.952	1	0.582	0.512	0.657	CLONAL	1	TRUE	1	0.314864510115296	3		441	480	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117755	70117755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	174	879	0	ENST00000245479.2:c.223G>A	p.Glu75Lys	p.E75K	ENST00000245479	NM_000346.3	75	Gag/Aag	1/3	0.159783631417255	2	FACETS	0.872	0.806	0.939	0.872	0.806	0.939	INDETERMINATE	2	TRUE	0	0.314864510115296	2		879	634	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447507	12447507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	115	620	0	ENST00000287820.6:c.746C>T	p.Ser249Leu	p.S249L	ENST00000287820	NM_015869.4	249	tCa/tTa	5/7	0.314864510115296	4	FACETS	1	0.982	1	0.71	0.641	0.784	CLONAL	1	TRUE	2	0.314864510115296	4		620	676	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619172	37619172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759485356	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	105	736	0	ENST00000447079.4:c.848C>T	p.Ser283Leu	p.S283L	ENST00000447079	NM_015083.1	283	tCg/tTg	1/14	0.225016627045589	3	FACETS	1	0.967	1	0.596	0.534	0.661	CLONAL	1	TRUE	1	0.314864510115296	3		736	648	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227019	2227019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	145	839	3	ENST00000398665.3:c.4499C>T	p.Ser1500Phe	p.S1500F	ENST00000398665	NM_032482.2	1500	tCt/tTt	27/28	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.314864510115296	2		842	633	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820648	3820648	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	95	1120	0	ENST00000262367.5:c.2803C>T	p.Gln935Ter	p.Q935*	ENST00000262367	NM_004380.2	935	Cag/Tag	14/31	1	2	FACETS	0.718	0.638	0.802	0.718	0.638	0.802	SUBCLONAL	1	TRUE	1	0.314864510115296	2		1120	841	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176176047	176176047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752538197	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	39	764	0	ENST00000367669.3:c.68C>T	p.Ser23Leu	p.S23L	ENST00000367669	NM_022457.5	23	tCg/tTg	1/20	1	2	FACETS	0.467	0.386	0.556	0.467	0.386	0.556	SUBCLONAL	1	TRUE	1	0.314864510115296	2		764	531	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242715	16242715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	142	506	0	ENST00000375759.3:c.1336G>A	p.Glu446Lys	p.E446K	ENST00000375759	NM_015001.2	446	Gaa/Aaa	6/15	1	2	FACETS	0.767	0.702	0.835	1	0.988	1	SUBCLONAL	2	TRUE	1	0.314864510115296	2		506	588	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942188	17942188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760901179	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	116	701	0	ENST00000458235.1:c.2827C>T	p.Arg943Cys	p.R943C	ENST00000458235	NM_000215.3	943	Cgc/Tgc	21/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.314864510115296	2		701	569	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129474	152129474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	69	353	0	ENST00000206249.3:c.427G>A	p.Glu143Lys	p.E143K	ENST00000206249	NM_000125.3	143	Gag/Aag	1/8	NA	2	FACETS	0.941	0.831	1			1	INDETERMINATE	2	TRUE	NA	0.314864510115296	2		353	233	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873585	151873585	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	188	622	0	ENST00000262189.6:c.8953C>T	p.Gln2985Ter	p.Q2985*	ENST00000262189	NM_170606.2	2985	Cag/Tag	38/59	0.314864510115296	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.314864510115296	3		622	611	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632297	215632297	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	123	578	0	ENST00000260947.4:c.1477C>T	p.Gln493Ter	p.Q493*	ENST00000260947	NM_000465.2	493	Caa/Taa	6/11	0.205898847708594	2	FACETS	1	0.985	1	0.736	0.668	0.806	CLONAL	1	TRUE	0	0.314864510115296	2		578	531	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112079	115112079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764962945	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	177	1014	0	ENST00000257566.3:c.1661C>T	p.Ser554Leu	p.S554L	ENST00000257566	NM_016569.3	554	tCg/tTg	7/8	1	2	FACETS	0.802	0.741	0.865	1	0.991	1	CLONAL	2	TRUE	1	0.314864510115296	2		1014	701	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061468	38061468	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	66	606	0	ENST00000250448.2:c.521C>T	p.Ser174Leu	p.S174L	ENST00000250448	NM_004496.3	174	tCg/tTg	2/2	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.314864510115296	2		606	405	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375527	118375527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	63	371	0	ENST00000534358.1:c.8920G>A	p.Glu2974Lys	p.E2974K	ENST00000534358	NM_005933.3	2974	Gaa/Aaa	27/36	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.314864510115296	2		371	323	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186666	11186679	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAATGGTCCTTACC	CAATGGTCCTTACC	-	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	30	387	0	ENST00000361445.4:c.6526_6526+13del		p.X2176_splice	ENST00000361445	NM_004958.3	2176		46/58	1	2	FACETS	0.526	0.424	0.642	0.526	0.424	0.642	SUBCLONAL	1	TRUE	1	0.314864510115296	2		387	362	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22408244	22408244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	78	393	0	ENST00000344548.3:c.135G>A	p.Met45Ile	p.M45I	ENST00000344548	NM_001039802.1	45	atG/atA	4/7	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.314864510115296	2		393	387	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818286	43818286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	171	895	1	ENST00000372470.3:c.1751C>T	p.Ser584Phe	p.S584F	ENST00000372470	NM_005373.2	584	tCc/tTc	12/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.314864510115296	2		896	771	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601894	43601894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs77702891	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	85	992	1	ENST00000355710.3:c.938G>A	p.Arg313Gln	p.R313Q	ENST00000355710	NM_020975.4	313	cGg/cAg	5/20	1	2	FACETS	0.809	0.716	0.91	0.809	0.716	0.91	CLONAL	1	TRUE	1	0.314864510115296	2		993	667	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143267	108143267	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	81	299	0	ENST00000278616.4:c.3086C>T	p.Thr1029Ile	p.T1029I	ENST00000278616	NM_000051.3	1029	aCa/aTa	21/63	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.314864510115296	2		299	378	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243535	46243535	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	45	367	0	ENST00000334344.6:c.1888del	p.Val630TyrfsTer17	p.V630Yfs*17	ENST00000334344	NM_152641.2	630	Gta/ta	14/21	0.225016627045589	3	FACETS	1	0.856	1	0.507	0.428	0.594	CLONAL	1	TRUE	1	0.314864510115296	3		367	326	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491597	56491597	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	120	471	0	ENST00000267101.3:c.2489T>C	p.Met830Thr	p.M830T	ENST00000267101	NM_001982.3	830	aTg/aCg	21/28	0.225016627045589	3	FACETS	0.915	0.831	1	0.915	0.831	1	CLONAL	2	TRUE	1	0.314864510115296	3		471	482	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778780	3778780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	128	1117	0	ENST00000262367.5:c.6268C>T	p.Leu2090Phe	p.L2090F	ENST00000262367	NM_004380.2	2090	Ctc/Ttc	31/31	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.314864510115296	2		1117	728	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619250	37619250	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	140	657	0	ENST00000447079.4:c.926G>C	p.Arg309Pro	p.R309P	ENST00000447079	NM_015083.1	309	cGg/cCg	1/14	0.225016627045589	3	FACETS	0.83	0.758	0.905	0.83	0.758	0.905	CLONAL	2	TRUE	1	0.314864510115296	3		657	620	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733138	74733138	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	53	795	0	ENST00000359995.5:c.105G>C	p.Glu35Asp	p.E35D	ENST00000359995	NM_001195427.1	35	gaG/gaC	1/3	0.159783631417255	2	FACETS	0.57	0.485	0.662	0.285	0.242	0.331	INDETERMINATE	1	TRUE	0	0.314864510115296	2		795	591	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733161	74733161	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	51	851	0	ENST00000359995.5:c.82G>A	p.Asp28Asn	p.D28N	ENST00000359995	NM_001195427.1	28	Gac/Aac	1/3	0.159783631417255	2	FACETS	0.484	0.41	0.564	0.242	0.205	0.282	INDETERMINATE	1	TRUE	0	0.314864510115296	2		851	670	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581221	48581221	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	36	495	0	ENST00000342988.3:c.525A>C	p.Glu175Asp	p.E175D	ENST00000342988	NM_005359.5	175	gaA/gaC	5/12	1	2	FACETS	0.474	0.39	0.57	0.474	0.39	0.57	SUBCLONAL	1	TRUE	1	0.314864510115296	2		495	482	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210571	5210571	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749866143	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	73	868	0	ENST00000357368.4:c.5396C>T	p.Ser1799Phe	p.S1799F	ENST00000357368	NM_002850.3	1799	tCt/tTt	35/38	0.230541277451899	1	FACETS	0.724	0.634	0.82	0.724	0.634	0.82	SUBCLONAL	1	TRUE	0	0.314864510115296	1		868	540	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031622	11031622	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	189	1137	0	ENST00000327064.4:c.1537G>A	p.Gly513Arg	p.G513R	ENST00000327064	NM_199141.1	513	Ggg/Agg	13/16	1	2	FACETS	0.76	0.704	0.818	1	0.991	1	SUBCLONAL	2	TRUE	1	0.314864510115296	2		1137	790	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855835	45855835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	176	1071	3	ENST00000391945.4:c.1975C>T	p.His659Tyr	p.H659Y	ENST00000391945	NM_000400.3	659	Cac/Tac	21/23	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.314864510115296	2		1074	805	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966195	25966195	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	134	789	0	ENST00000435504.4:c.3011G>C	p.Arg1004Thr	p.R1004T	ENST00000435504		1004	aGa/aCa	13/13	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.314864510115296	2		789	615	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25990489	25990502	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCAAGCCTAGTA	CCCCAAGCCTAGTA	-	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	73	515	0	ENST00000435504.4:c.725_738del	p.Leu242Ter	p.L242*	ENST00000435504		242	tTACTAGGCTTGGGG/t	8/13	NA	2	FACETS	0.933	0.818	1			1	INDETERMINATE	1	TRUE	NA	0.314864510115296	2		515	497	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12393098	12393098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	209	461	0	ENST00000287820.6:c.7G>A	p.Glu3Lys	p.E3K	ENST00000287820	NM_015869.4	3	Gaa/Aaa	1/7	0.314864510115296	4	FACETS	0.924	0.862	0.986	1	0.991	1	CLONAL	3	TRUE	2	0.314864510115296	4		461	630	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799496	72799496	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747970837	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	91	741	0	ENST00000325599.8:c.1673C>T	p.Thr558Ile	p.T558I	ENST00000325599	NM_018130.2	558	aCc/aTc	11/11	1	2	FACETS	0.912	0.81	1	0.912	0.81	1	CLONAL	1	TRUE	1	0.314864510115296	2		741	634	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169999040	169999040	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	39	231	0	ENST00000295797.4:c.969G>C	p.Gln323His	p.Q323H	ENST00000295797	NM_002740.5	323	caG/caC	10/18	0.314864510115296	3	FACETS	1	0.844	1	0.507	0.422	0.6	CLONAL	1	TRUE	1	0.314864510115296	3		231	283	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196204	106196204	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	57	235	0	ENST00000380013.4:c.4538-1G>A		p.X1513_splice	ENST00000380013	NM_001127208.2	1513			1	2	FACETS	0.787	0.683	0.897	1	0.972	1	SUBCLONAL	2	TRUE	1	0.314864510115296	2		235	230	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196660	106196660	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	78	530	0	ENST00000380013.4:c.4993G>C	p.Asp1665His	p.D1665H	ENST00000380013	NM_001127208.2	1665	Gac/Cac	11/11	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.314864510115296	2		530	474	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628873	187628873	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	92	652	0	ENST00000441802.2:c.2109C>G	p.Phe703Leu	p.F703L	ENST00000441802	NM_005245.3	703	ttC/ttG	2/27	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.314864510115296	2		652	532	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910650	29910669	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGCGAGCCAGAGGATGGA	GCCGCGAGCCAGAGGATGGA	-	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	75	1416	0	ENST00000376809.5:c.196_215del	p.Ser66GlyfsTer26	p.S66Gfs*26	ENST00000376809	NM_002116.7	64	GCCGCGAGCCAGAGGATGGAg/g	2/8	1	2	FACETS	0.562	0.491	0.638	0.562	0.491	0.638	SUBCLONAL	1	TRUE	1	0.314864510115296	2		1416	848	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729412	41729412	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	28	697	0	ENST00000242208.4:c.1117A>C	p.Ile373Leu	p.I373L	ENST00000242208	NM_002192.2	373	Atc/Ctc	3/3	0.314864510115296	1	FACETS	0.285	0.227	0.351	0.285	0.227	0.351	SUBCLONAL	1	TRUE	0	0.314864510115296	1		697	526	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462457	92462457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	54	686	0	ENST00000265734.4:c.181G>A	p.Glu61Lys	p.E61K	ENST00000265734	NM_001259.6	61	Gag/Aag	2/8	0.314864510115296	3	FACETS	0.636	0.543	0.739	0.318	0.271	0.37	SUBCLONAL	1	TRUE	1	0.314864510115296	3		686	624	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965410	68965410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	112	636	1	ENST00000288368.4:c.1022G>A	p.Cys341Tyr	p.C341Y	ENST00000288368	NM_024870.2	341	tGt/tAt	9/40	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.314864510115296	2		637	663	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636236	87636236	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	118	608	0	ENST00000277120.3:c.2401C>A	p.Leu801Met	p.L801M	ENST00000277120		801	Ctg/Atg	19/19	0.314864510115296	1	FACETS	0.774	0.704	0.846	1	0.986	1	SUBCLONAL	2	TRUE	0	0.314864510115296	1		608	408	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918634	44918709	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AAATGCTACTTAAATGCAACTAGAAGCAAAAGTTGTAGTAATACCTCTGCACTTGCAGCACGAATTAAGTATTTAC	AAATGCTACTTAAATGCAACTAGAAGCAAAAGTTGTAGTAATACCTCTGCACTTGCAGCACGAATTAAGTATTTAC	-	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	63	279	0	ENST00000377967.4:c.1118_1193del	p.Lys373ArgfsTer41	p.K373Rfs*41	ENST00000377967	NM_021140.2	373	AAATGCTACTTAAATGCAACTAGAAGCAAAAGTTGTAGTAATACCTCTGCACTTGCAGCACGAATTAAGTATTTACag/ag	12/29	0.181831818600696	2	FACETS	0.837	0.733	0.947			1	INDETERMINATE	2	TRUE	NA	0.314864510115296	2		279	239	SUCCESS
AR	367	MSKCC	GRCh37	X	66863127	66863127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	133	374	0	ENST00000374690.3:c.1646C>T	p.Pro549Leu	p.P549L	ENST00000374690	NM_000044.3	549	cCc/cTc	2/8	0.181831818600696	2	FACETS	0.883	0.814	0.953			1	INDETERMINATE	3	TRUE	NA	0.314864510115296	2		374	319	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200084	123200149	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAATCGAAAATGGAGACATGCCTGAGCAGGTTTTTATTTATTTGCTAGTTACACATTTATCTTTGA	GAATCGAAAATGGAGACATGCCTGAGCAGGTTTTTATTTATTTGCTAGTTACACATTTATCTTTGA	-	novel	NA	P-0056993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	72	285	0	ENST00000218089.9:c.2156_2184+37del		p.X719_splice	ENST00000218089	NM_001042749.1	719		22/35	0.181831818600696	2	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.314864510115296	2		285	320	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0056994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	660	504	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.436401894945407	4	FACETS	0.951	0.923	0.979	0.951	0.923	0.979	CLONAL	4	TRUE	0	0.459687583851509	4		504	1102	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0056994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	74	388	3	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	0.459687583851509	1	FACETS	0.578	0.508	0.653	0.578	0.508	0.653	SUBCLONAL	1	TRUE	0	0.459687583851509	1		391	429	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0056994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	56	296	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.436401894945407	4	FACETS	0.929	0.799	1	0.232	0.199	0.268	CLONAL	1	TRUE	0	0.459687583851509	4		296	383	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	57	433	2	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	0.459687583851509	1	FACETS	0.468	0.403	0.539	0.468	0.403	0.539	SUBCLONAL	1	TRUE	0	0.459687583851509	1		435	408	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729607	41729607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	101	525	0	ENST00000242208.4:c.922C>T	p.Arg308Cys	p.R308C	ENST00000242208	NM_002192.2	308	Cgt/Tgt	3/3	0.163834864795698	2	FACETS	0.692	0.619	0.769	0.346	0.309	0.385	INDETERMINATE	1	TRUE	0	0.459687583851509	2		525	635	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15379801	15379801	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	82	416	0	ENST00000263377.2:c.338G>A	p.Arg113His	p.R113H	ENST00000263377	NM_058243.2	113	cGc/cAc	3/20	0.163834864795698	2	FACETS	0.647	0.572	0.728	0.324	0.286	0.364	INDETERMINATE	1	TRUE	0	0.459687583851509	2		416	551	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441815	49441816	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs756471180	NA	P-0056994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	95	633	0	ENST00000301067.7:c.4168dup	p.Ala1390GlyfsTer42	p.A1390Gfs*42	ENST00000301067	NM_003482.3	1390	gca/gGca	14/54	0.163834864795698	2	FACETS	0.568	0.505	0.634	0.284	0.252	0.317	INDETERMINATE	1	TRUE	0	0.459687583851509	2		633	728	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864125	57864125	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	126	636	1	ENST00000228682.2:c.1607del	p.Pro536GlnfsTer77	p.P536Qfs*77	ENST00000228682	NM_005269.2	534	ggC/gg	12/12	0.163834864795698	2	FACETS	0.674	0.61	0.741	0.337	0.305	0.371	INDETERMINATE	1	TRUE	0	0.459687583851509	2		637	813	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705233	52705233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs949208712	NA	P-0056994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	100	441	2	ENST00000322088.6:c.115G>A	p.Ala39Thr	p.A39T	ENST00000322088	NM_014225.5	39	Gcc/Acc	2/15	0.163834864795698	2	FACETS	0.713	0.638	0.793	0.357	0.319	0.397	INDETERMINATE	1	TRUE	0	0.459687583851509	2		443	610	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978405	2978405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370704955	NA	P-0056994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	168	919	1	ENST00000396946.4:c.925C>T	p.Arg309Cys	p.R309C	ENST00000396946	NM_032415.4	309	Cgc/Tgc	7/25	0.163834864795698	2	FACETS	0.685	0.629	0.744	0.343	0.314	0.372	INDETERMINATE	1	TRUE	0	0.459687583851509	2		920	1067	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420292	49420292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761700549	NA	P-0056994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	116	600	1	ENST00000301067.7:c.15457C>T	p.Arg5153Trp	p.R5153W	ENST00000301067	NM_003482.3	5153	Cgg/Tgg	48/54	0.163834864795698	2	FACETS	0.679	0.612	0.75	0.34	0.306	0.375	INDETERMINATE	1	TRUE	0	0.459687583851509	2		601	743	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857650	78857650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184854653	NA	P-0056994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	109	894	1	ENST00000306801.3:c.1720C>T	p.Arg574Cys	p.R574C	ENST00000306801	NM_020761.2	574	Cgc/Tgc	16/34	0.459687583851509	3	FACETS	0.507	0.454	0.564	0.169	0.151	0.188	SUBCLONAL	1	TRUE	0	0.459687583851509	3		895	1150	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535354	66535354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	217	613	2	ENST00000273854.3:c.107G>A	p.Arg36Gln	p.R36Q	ENST00000273854	NM_004439.5	36	cGa/cAa	1/18	0.459687583851509	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.459687583851509	1		615	555	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243859003	243859003	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	37	235	0	ENST00000263826.5:c.62del	p.Asn21ThrfsTer9	p.N21Tfs*9	ENST00000263826	NM_005465.4	21	aAc/ac	2/13	0.444936619552981	2	FACETS	0.703	0.584	0.834	0.351	0.292	0.417	SUBCLONAL	1	TRUE	0	0.459687583851509	2		235	229	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195903	102195904	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0056994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	59	289	0	ENST00000263464.3:c.664_665del	p.Met222ValfsTer27	p.M222Vfs*27	ENST00000263464	NM_001165.4	221	gcTAtg/gctg	2/9	0.459687583851509	3	FACETS	0.763	0.658	0.876	0.254	0.219	0.292	SUBCLONAL	1	TRUE	0	0.459687583851509	3		289	414	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139322	108139322	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	47	419	0	ENST00000278616.4:c.2824C>A	p.Leu942Ile	p.L942I	ENST00000278616	NM_000051.3	942	Ctc/Atc	18/63	0.459687583851509	3	FACETS	0.473	0.399	0.555	0.158	0.133	0.185	SUBCLONAL	1	TRUE	0	0.459687583851509	3		419	532	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858206	59858206	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	66	331	0	ENST00000259008.2:c.1789G>T	p.Ala597Ser	p.A597S	ENST00000259008	NM_032043.2	597	Gct/Tct	12/20	0.459687583851509	2	FACETS	0.694	0.604	0.79	0.347	0.302	0.395	SUBCLONAL	1	TRUE	0	0.459687583851509	2		331	414	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534429	63534429	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	128	818	0	ENST00000307078.5:c.1092del	p.Val365TrpfsTer10	p.V365Wfs*10	ENST00000307078	NM_004655.3	364	ccC/cc	5/11	0.459687583851509	3	FACETS	0.521	0.47	0.574	0.174	0.156	0.192	SUBCLONAL	1	TRUE	0	0.459687583851509	3		818	1315	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260082	19260082	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	146	853	1	ENST00000162023.5:c.211G>T	p.Glu71Ter	p.E71*	ENST00000162023		71	Gag/Tag	7/13	0.163834864795698	2	FACETS	0.599	0.546	0.655	0.3	0.273	0.328	INDETERMINATE	1	TRUE	0	0.459687583851509	2		854	1060	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543876	41543876	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	80	466	0	ENST00000263253.7:c.2171del	p.Pro724LeufsTer52	p.P724Lfs*52	ENST00000263253	NM_001429.3	723	Ccc/cc	12/31	0.459687583851509	1	FACETS	0.474	0.418	0.535	0.474	0.418	0.535	SUBCLONAL	1	TRUE	0	0.459687583851509	1		466	565	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983367	149983367	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	79	399	0	ENST00000253339.5:c.2891A>T	p.Asn964Ile	p.N964I	ENST00000253339		964	aAc/aTc	7/7	0.459687583851509	1	FACETS	0.635	0.561	0.713	0.635	0.561	0.713	SUBCLONAL	1	TRUE	0	0.459687583851509	1		399	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0056995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	154	1226	0	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	0.809917311324689	1	FACETS	0.324	0.297	0.352	0.324	0.297	0.352	SUBCLONAL	1	TRUE	0	0.809917311324689	1		1226	698	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754268	57754268	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	203	422	0	ENST00000274289.3:c.583T>C	p.Tyr195His	p.Y195H	ENST00000274289	NM_006622.3	195	Tac/Cac	4/14	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.809917311324689	2		422	486	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981815	101981815	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs965501205	NA	P-0056995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	258	889	0	ENST00000282441.5:c.236A>G	p.Asn79Ser	p.N79S	ENST00000282441	NM_001130145.2	79	aAc/aGc	1/9	0.270089127584256	1	FACETS	0.524	0.493	0.556	0.524	0.493	0.556	INDETERMINATE	1	TRUE	0	0.809917311324689	1		889	723	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94908697	94908698	+	stop_gained	Nonsense_Mutation	DNP	CA	CA	AT	novel	NA	P-0056995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	104	540	0	ENST00000536441.1:c.1356_1357delinsAT	p.Tyr452_Asp453delinsTer	p.Y452_D453delins*	ENST00000536441	NM_144665.3	452	taTGat/taATat	9/10	0.270089127584256	1	FACETS	0.375	0.338	0.413	0.375	0.338	0.413	INDETERMINATE	1	TRUE	0	0.809917311324689	1		540	408	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124271	2124277	+	frameshift_variant	Frame_Shift_Del	DEL	CCATCTG	CCATCTG	-	novel	NA	P-0056995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	362	1130	1	ENST00000219476.3:c.2427_2433del	p.Ile810AlafsTer17	p.I810Afs*17	ENST00000219476	NM_000548.3	809	tCCATCTGc/tc	22/42	0.809917311324689	1	FACETS	0.917	0.882	0.952	0.917	0.882	0.952	CLONAL	1	TRUE	0	0.809917311324689	1		1131	580	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124285	2124286	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGATGCCTGACATCATCATCA	novel	NA	P-0056995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	283	1132	0	ENST00000219476.3:c.2443_2463dup	p.Met815_Lys821dup	p.M815_K821dup	ENST00000219476	NM_000548.3	815	gag/gAGATGCCTGACATCATCATCAag	22/42	0.809917311324689	1	FACETS	0.614	0.581	0.648	0.614	0.581	0.648	SUBCLONAL	1	TRUE	0	0.809917311324689	1		1132	677	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	72	330	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.186857317583552	3	FACETS	0.894	0.784	1	0.894	0.784	1	CLONAL	2	TRUE	1	0.2	3		330	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	74	496	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.2	2		496	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0057005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	237	1016	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.381641395164162	3	FACETS	0.982	0.927	1	0.982	0.927	1	CLONAL	3	TRUE	0	0.381641395164162	3		1016	502	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712519	52712519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755035966	NA	P-0057005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	40	594	1	ENST00000394830.3:c.233G>A	p.Arg78Gln	p.R78Q	ENST00000394830	NM_018313.4	78	cGa/cAa	3/30	0.313857160296346	4	FACETS	0.688	0.572	0.817	0.344	0.286	0.409	SUBCLONAL	1	TRUE	2	0.381641395164162	4		595	421	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499796	8499796	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs762547582	NA	P-0057005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	25	663	0	ENST00000356435.5:c.2173T>C	p.Ser725Pro	p.S725P	ENST00000356435		725	Tca/Cca	14/35	0.381641395164162	1	FACETS	0.331	0.261	0.412	0.331	0.261	0.412	SUBCLONAL	1	TRUE	0	0.381641395164162	1		663	320	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591129	67591130	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0057006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	43	291	0	ENST00000274335.5:c.1723_1724del	p.Lys575AspfsTer26	p.K575Dfs*26	ENST00000274335		574	agAAag/agag	12/15	1	2	FACETS	0.434	0.363	0.512	0.434	0.363	0.512	SUBCLONAL	1	TRUE	1	0.450178726408237	2		291	440	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31464410	31464410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	246	718	0	ENST00000344624.3:c.2507G>A	p.Arg836Gln	p.R836Q	ENST00000344624		836	cGa/cAa	17/33	1	2	FACETS	0.881	0.823	0.942	0.881	0.823	0.942	CLONAL	1	TRUE	1	0.450178726408237	2		718	1240	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572387	41572392	+	inframe_deletion	In_Frame_Del	DEL	TGGAGT	TGGAGT	-	novel	NA	P-0057006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	426	819	0	ENST00000263253.7:c.4917_4922del	p.Glu1640_Phe1641del	p.E1640_F1641del	ENST00000263253	NM_001429.3	1639	cTGGAGTtc/ctc	30/31	0.399489138442848	2	FACETS	0.848	0.81	0.887	0.848	0.81	0.887	CLONAL	2	TRUE	0	0.450178726408237	2		819	1116	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591048	67591110	+	inframe_deletion	In_Frame_Del	DEL	AGACTTGAAGAAGCAGGCAGCTGAGTATCGAGAAATTGACAAACGTATGAACAGCATTAAACC	AGACTTGAAGAAGCAGGCAGCTGAGTATCGAGAAATTGACAAACGTATGAACAGCATTAAACC	-	novel	NA	P-0057006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	21	207	0	ENST00000274335.5:c.1645_1707del	p.Lys550_Leu570del	p.K550_L570del	ENST00000274335		547	gaAGACTTGAAGAAGCAGGCAGCTGAGTATCGAGAAATTGACAAACGTATGAACAGCATTAAACCa/gaa	12/15	1	2	FACETS	0.275	0.211	0.35	0.275	0.211	0.35	SUBCLONAL	1	TRUE	1	0.450178726408237	2		207	339	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0057007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	74	348	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.805	0.706	0.911	0.805	0.706	0.911	CLONAL	1	TRUE	1	0.344398469468872	2		348	534	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001410	29001410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771714708	NA	P-0057007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	95	366	0	ENST00000282397.4:c.1322C>T	p.Pro441Leu	p.P441L	ENST00000282397	NM_002019.4	441	cCg/cTg	10/30	1	2	FACETS	0.862	0.768	0.962	0.862	0.768	0.962	CLONAL	1	TRUE	1	0.344398469468872	2		366	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579349	7579349	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1567555667	NA	P-0057007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	242	907	0	ENST00000269305.4:c.338T>G	p.Phe113Cys	p.F113C	ENST00000269305	NM_001126112.2	113	tTc/tGc	4/11	0.344398469468872	1	FACETS	0.999	0.933	1	0.999	0.933	1	CLONAL	1	TRUE	0	0.344398469468872	1		907	1164	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591933	48591933	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060500733	NA	P-0057007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	91	452	0	ENST00000342988.3:c.1096C>T	p.Gln366Ter	p.Q366*	ENST00000342988	NM_005359.5	366	Caa/Taa	9/12	0.344398469468872	1	FACETS	0.832	0.741	0.928	0.832	0.741	0.928	CLONAL	1	TRUE	0	0.344398469468872	1		452	526	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs730881677	NA	P-0057007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	106	464	0	ENST00000304494.5:c.151-1G>C		p.X51_splice	ENST00000304494	NM_000077.4	51			1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.344398469468872	2		464	568	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	143	324	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.89	0.822	0.96	0.89	0.822	0.96	CLONAL	1	TRUE	1	0.88	2		324	365	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0057008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	211	628	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.88	2		628	422	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218084	108218084	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs760955058	NA	P-0057008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	87	289	0	ENST00000278616.4:c.8663T>C	p.Ile2888Thr	p.I2888T	ENST00000278616	NM_000051.3	2888	aTa/aCa	59/63	1	2	FACETS	0.999	0.905	1	0.999	0.905	1	CLONAL	1	TRUE	1	0.88	2		289	198	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186507026	186507027	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0057009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	17	177	0	ENST00000323963.5:c.1193_1194insTA	p.Glu398AspfsTer5	p.E398Dfs*5	ENST00000323963		398	gag/gATag	11/11	1	2	FACETS	0.447	0.334	0.581	0.447	0.334	0.581	SUBCLONAL	1	FALSE	1	0.303088469421661	2		177	251	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207626	29207626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	24	460	0	ENST00000240100.2:c.170G>A	p.Ser57Asn	p.S57N	ENST00000240100	NM_001394.6	57	aGc/aAc	1/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		460	404	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	40	324	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.685	0.573	0.809	0.685	0.573	0.809	SUBCLONAL	1	TRUE	1	0.432372796455216	2		324	270	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587777893	NA	P-0057011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	233	580	0	ENST00000361445.4:c.5930C>A	p.Thr1977Lys	p.T1977K	ENST00000361445	NM_004958.3	1977	aCa/aAa	43/58	0.432372796455216	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.432372796455216	2		580	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579383	7579383	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	174	928	0	ENST00000269305.4:c.304del	p.Thr102ProfsTer21	p.T102Pfs*21	ENST00000269305	NM_001126112.2	102	Acc/cc	4/11	0.432372796455216	1	FACETS	0.84	0.775	0.907	0.84	0.775	0.907	CLONAL	1	TRUE	0	0.432372796455216	1		928	751	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609341	39609341	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	89	343	0	ENST00000262039.4:c.1643T>A	p.Phe548Tyr	p.F548Y	ENST00000262039	NM_002647.2	548	tTt/tAt	15/25	1	2	FACETS	0.955	0.851	1	0.955	0.851	1	CLONAL	1	TRUE	1	0.432372796455216	2		343	431	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872972	136872973	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0057011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	81	430	1	ENST00000241393.3:c.524_525dup	p.Asn176ProfsTer116	p.N176Pfs*116	ENST00000241393	NM_003467.2	175	-/CC	2/2	1	2	FACETS	0.963	0.854	1	0.963	0.854	1	CLONAL	1	TRUE	1	0.432372796455216	2		431	389	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191497	10191497	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs5030819	NA	P-0057011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	98	486	0	ENST00000256474.2:c.490C>T	p.Gln164Ter	p.Q164*	ENST00000256474	NM_000551.3	164	Cag/Tag	3/3	0.432372796455216	1	FACETS	0.858	0.771	0.95	0.858	0.771	0.95	CLONAL	1	TRUE	0	0.432372796455216	1		486	414	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910798	29910798	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs41556317	NA	P-0057011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	139	787	0	ENST00000376809.5:c.338A>G	p.Glu113Gly	p.E113G	ENST00000376809	NM_002116.7	113	gAg/gGg	2/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.432372796455216	2		787	603	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346653	81346653	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	40	247	0	ENST00000222390.5:c.1300A>G	p.Lys434Glu	p.K434E	ENST00000222390	NM_000601.4	434	Aag/Gag	11/18	1	2	FACETS	0.89	0.747	1	0.89	0.747	1	CLONAL	1	TRUE	1	0.432372796455216	2		247	208	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0057012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	353	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.763948107987716	2	FACETS	0.943	0.911	0.974	0.943	0.911	0.974	CLONAL	2	TRUE	0	0.763948107987716	2		298	490	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0057012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	85	425	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.414241469183649	1	FACETS	0.37	0.329	0.413	0.37	0.329	0.413	INDETERMINATE	1	TRUE	0	0.763948107987716	1		425	372	SUCCESS
APC	324	MSKCC	GRCh37	5	112174112	112174112	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	180	358	0	ENST00000257430.4:c.2821G>T	p.Glu941Ter	p.E941*	ENST00000257430	NM_000038.5	941	Gaa/Taa	16/16	0.414241469183649	1	FACETS	0.814	0.763	0.864	0.814	0.763	0.864	INDETERMINATE	1	TRUE	0	0.763948107987716	1		358	358	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578397	7578397	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1555526004	NA	P-0057012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	382	834	1	ENST00000269305.4:c.533A>C	p.His178Pro	p.H178P	ENST00000269305	NM_001126112.2	178	cAc/cCc	5/11	0.763948107987716	1	FACETS	0.998	0.961	1	0.998	0.961	1	CLONAL	1	TRUE	0	0.763948107987716	1		835	619	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372098	55372098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs62642516	NA	P-0057012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	71	449	0	ENST00000297316.4:c.788C>T	p.Pro263Leu	p.P263L	ENST00000297316	NM_022454.3	263	cCg/cTg	2/2	0.423304914255786	1	FACETS	0.235	0.206	0.267	0.235	0.206	0.267	INDETERMINATE	1	TRUE	0	0.763948107987716	1		449	488	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573651	48573651	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	155	372	0	ENST00000342988.3:c.235G>T	p.Asp79Tyr	p.D79Y	ENST00000342988	NM_005359.5	79	Gat/Tat	2/12	0.763948107987716	1	FACETS	0.976	0.917	1	0.976	0.917	1	CLONAL	1	TRUE	0	0.763948107987716	1		372	257	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137219	64137219	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	204	843	0	ENST00000334205.4:c.1651G>T	p.Asp551Tyr	p.D551Y	ENST00000334205	NM_003942.2	551	Gac/Tac	14/17	0.414241469183649	1	FACETS	0.379	0.352	0.408	0.379	0.352	0.408	INDETERMINATE	1	TRUE	0	0.763948107987716	1		843	870	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958791	55958791	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	110	562	0	ENST00000263923.4:c.3062C>A	p.Ser1021Ter	p.S1021*	ENST00000263923	NM_002253.2	1021	tCg/tAg	22/30	0.414241469183649	1	FACETS	0.323	0.291	0.357	0.323	0.291	0.357	INDETERMINATE	1	TRUE	0	0.763948107987716	1		562	551	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411423	63411423	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	361	960	0	ENST00000330258.3:c.1744G>T	p.Glu582Ter	p.E582*	ENST00000330258	NM_152424.3	582	Gag/Tag	2/2	0.71350468218373	3	FACETS	0.993	0.941	1	0.497	0.47	0.524	CLONAL	1	TRUE	1	0.763948107987716	3		960	1315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750600586	NA	P-0057013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	617	1057	1	ENST00000269305.4:c.413C>T	p.Ala138Val	p.A138V	ENST00000269305	NM_001126112.2	138	gCc/gTc	5/11	0.310887033592618	3	FACETS	0.933	0.897	0.968	0.933	0.897	0.968	CLONAL	3	TRUE	0	0.314072982531594	3		1058	1625	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0057013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	49	260	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.281925099287918	3	FACETS	0.86	0.729	1	0.43	0.364	0.501	CLONAL	1	TRUE	1	0.314072982531594	3		260	420	SUCCESS
AR	367	MSKCC	GRCh37	X	66766228	66766228	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	180	216	0	ENST00000374690.3:c.1240C>A	p.Leu414Met	p.L414M	ENST00000374690	NM_000044.3	414	Ctg/Atg	1/8	0.258863291359051	2	FACETS	1	0.984	1			1	CLONAL	3	TRUE	NA	0.314072982531594	2		216	334	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961056	55961056	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1312670638	NA	P-0057013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	136	708	0	ENST00000263923.4:c.2884C>T	p.Arg962Cys	p.R962C	ENST00000263923	NM_002253.2	962	Cgc/Tgc	21/30	0.281925099287918	3	FACETS	1	0.927	1	0.512	0.465	0.561	CLONAL	1	TRUE	1	0.314072982531594	3		708	979	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631824	90631824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	152	674	1	ENST00000330062.3:c.529G>A	p.Asp177Asn	p.D177N	ENST00000330062	NM_002168.2	177	Gac/Aac	4/11	1	2	FACETS	0.979	0.894	1	0.979	0.894	1	CLONAL	1	TRUE	1	0.314072982531594	2		675	989	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559231	141559231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1195	337	765	0	ENST00000220592.5:c.1570G>A	p.Gly524Ser	p.G524S	ENST00000220592	NM_012154.3	524	Ggc/Agc	12/19	0.314072982531594	5	FACETS	1	0.965	1	0.687	0.648	0.727	CLONAL	2	TRUE	2	0.314072982531594	5		765	1532	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316389	14316389	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	2237	501	0	ENST00000256196.4:c.216A>C	p.Gln72His	p.Q72H	ENST00000256196		72	caA/caC	3/6	0.314072982531594	25	FACETS	1	0.993	1			1	CLONAL	24	TRUE	NA	0.314072982531594	25		501	2724	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260749	16260749	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	158	688	0	ENST00000375759.3:c.8014G>T	p.Val2672Leu	p.V2672L	ENST00000375759	NM_015001.2	2672	Gtg/Ttg	11/15	0.314072982531594	3	FACETS	1	0.974	1	0.579	0.53	0.63	CLONAL	1	TRUE	1	0.314072982531594	3		688	1006	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642722	3642722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	327	774	0	ENST00000294008.3:c.2305G>A	p.Glu769Lys	p.E769K	ENST00000294008	NM_032444.2	769	Gag/Aag	11/15	0.314072982531594	2	FACETS	0.953	0.902	1	0.953	0.902	1	CLONAL	2	TRUE	0	0.314072982531594	2		774	1092	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213285	36213285	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1294	390	829	0	ENST00000222270.7:c.2482G>T	p.Glu828Ter	p.E828*	ENST00000222270	NM_014727.1	828	Gag/Tag	4/37	0.302978429506152	4	FACETS	0.969	0.918	1	0.969	0.918	1	CLONAL	2	TRUE	2	0.314072982531594	4		829	1684	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004789	150004789	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	90	483	0	ENST00000253339.5:c.1436C>G	p.Ser479Cys	p.S479C	ENST00000253339		479	tCt/tGt	3/7	0.281925099287918	3	FACETS	0.949	0.842	1	0.474	0.421	0.532	CLONAL	1	TRUE	1	0.314072982531594	3		483	699	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258990	153258995	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGGG	CTGGGG	A	novel	NA	P-0057013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	73	269	0	ENST00000281708.4:c.820_825delinsT	p.Pro274PhefsTer11	p.P274Ffs*11	ENST00000281708	NM_033632.3	274	CCCCAG/T	5/12	0.281925099287918	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.314072982531594	3		269	219	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	246	504	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.708	0.662	0.754	0.708	0.662	0.754	SUBCLONAL	1	TRUE	1	0.75	2		504	927	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123752	11123752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568471266	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	42	588	2	ENST00000358026.2:c.2402G>A	p.Arg801His	p.R801H	ENST00000358026	NM_001128849.1	801	cGc/cAc	16/36	1	2	FACETS	0.146	0.121	0.174	0.146	0.121	0.174	SUBCLONAL	1	TRUE	1	0.75	2		590	768	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515141	103515141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770246574	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	40	279	0	ENST00000355739.4:c.1642G>A	p.Glu548Lys	p.E548K	ENST00000355739	NM_000123.3	548	Gaa/Aaa	8/15	1	2	FACETS	0.296	0.246	0.351	0.296	0.246	0.351	SUBCLONAL	1	TRUE	1	0.75	2		279	360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	337	653	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.963	0.914	1	0.963	0.914	1	CLONAL	1	TRUE	1	0.75	2		655	933	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857650	78857650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184854653	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	254	894	1	ENST00000306801.3:c.1720C>T	p.Arg574Cys	p.R574C	ENST00000306801	NM_020761.2	574	Cgc/Tgc	16/34	1	2	FACETS	0.721	0.676	0.768	0.721	0.676	0.768	SUBCLONAL	1	TRUE	1	0.75	2		895	939	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241895	133241895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483635586	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	44	536	1	ENST00000320574.5:c.2461C>T	p.Arg821Cys	p.R821C	ENST00000320574	NM_006231.2	821	Cgc/Tgc	21/49	1	2	FACETS	0.168	0.14	0.199	0.168	0.14	0.199	SUBCLONAL	1	TRUE	1	0.75	2		537	699	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263973	104263974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776579	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	104	557	0	ENST00000369902.3:c.71dup	p.Ala25GlyfsTer23	p.A25Gfs*23	ENST00000369902	NM_016169.3	22	gcc/gCcc	1/12	1	2	FACETS	0.915	0.831	1	0.915	0.831	1	CLONAL	1	TRUE	1	0.75	2		557	303	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515036	103515036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775996769	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	171	314	0	ENST00000355739.4:c.1537G>A	p.Ala513Thr	p.A513T	ENST00000355739	NM_000123.3	513	Gca/Aca	8/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.75	2		314	372	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	84	441	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	0.509	0.452	0.57	0.509	0.452	0.57	SUBCLONAL	1	TRUE	1	0.75	2		441	440	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	429	893	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.75	2		894	1001	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	48	389	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.399	0.338	0.464	0.399	0.338	0.464	SUBCLONAL	1	TRUE	1	0.75	2		389	321	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955550	48955550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913304	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	19	292	0	ENST00000267163.4:c.1666C>T	p.Arg556Ter	p.R556*	ENST00000267163	NM_000321.2	556	Cga/Tga	17/27	1	2	FACETS	0.18	0.136	0.231	0.18	0.136	0.231	SUBCLONAL	1	TRUE	1	0.75	2		292	282	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215339	5215339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs114545401	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	84	474	0	ENST00000357368.4:c.4279G>A	p.Ala1427Thr	p.A1427T	ENST00000357368	NM_002850.3	1427	Gcc/Acc	28/38	1	2	FACETS	0.286	0.252	0.322	0.286	0.252	0.322	SUBCLONAL	1	TRUE	1	0.75	2		474	784	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332272	70332273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1446158817	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	136	371	0	ENST00000373644.4:c.184dup	p.Thr62AsnfsTer4	p.T62Nfs*4	ENST00000373644	NM_030625.2	59	-/A	2/12	1	2	FACETS	0.885	0.812	0.959	0.885	0.812	0.959	CLONAL	1	TRUE	1	0.75	2		371	410	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027093	71027093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200629338	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	269	583	2	ENST00000318789.4:c.1234G>A	p.Ala412Thr	p.A412T	ENST00000318789	NM_032682.5	412	Gcc/Acc	15/21	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.75	2		585	717	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	83	618	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.36	0.318	0.405	0.36	0.318	0.405	SUBCLONAL	1	TRUE	1	0.75	2		619	615	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437440	52437440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761596789	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	275	640	0	ENST00000460680.1:c.1721C>T	p.Ala574Val	p.A574V	ENST00000460680	NM_004656.3	574	gCg/gTg	13/17	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.75	2		640	726	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168695	32168695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143103753	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	120	876	0	ENST00000375023.3:c.4228C>T	p.Arg1410Cys	p.R1410C	ENST00000375023	NM_004557.3	1410	Cgc/Tgc	23/30	1	2	FACETS	0.318	0.286	0.351	0.318	0.286	0.351	SUBCLONAL	1	TRUE	1	0.75	2		876	1007	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795353	39795353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs187337793	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	115	694	1	ENST00000288319.7:c.367C>T	p.Arg123Cys	p.R123C	ENST00000288319	NM_182918.3	123	Cgc/Tgc	3/10	1	2	FACETS	0.374	0.336	0.413	0.374	0.336	0.413	SUBCLONAL	1	TRUE	1	0.75	2		695	821	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354234	70354234	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	105	758	2	ENST00000374080.3:c.4645C>T	p.Arg1549Cys	p.R1549C	ENST00000374080		1549	Cgc/Tgc	34/45	1	2	FACETS	0.275	0.245	0.306	0.275	0.245	0.306	SUBCLONAL	1	TRUE	1	0.75	2		760	1019	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578341	212578341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1216559792	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	129	370	0	ENST00000342788.4:c.916C>T	p.Arg306Cys	p.R306C	ENST00000342788	NM_005235.2	306	Cgt/Tgt	8/28	1	2	FACETS	0.88	0.806	0.956	0.88	0.806	0.956	CLONAL	1	TRUE	1	0.75	2		370	391	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057281	180057281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142252978	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	182	962	1	ENST00000261937.6:c.457G>A	p.Ala153Thr	p.A153T	ENST00000261937	NM_182925.4	153	Gcc/Acc	4/30	1	2	FACETS	0.537	0.496	0.581	0.537	0.496	0.581	SUBCLONAL	1	TRUE	1	0.75	2		963	903	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333863	70333863	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs750883311	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	23	358	1	ENST00000373644.4:c.1768C>T	p.Arg590Ter	p.R590*	ENST00000373644	NM_030625.2	590	Cga/Tga	2/12	1	2	FACETS	0.146	0.113	0.184	0.146	0.113	0.184	SUBCLONAL	1	TRUE	1	0.75	2		359	421	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575121	64575121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878855197	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	125	616	1	ENST00000312049.6:c.686G>A	p.Arg229His	p.R229H	ENST00000312049	NM_130799.2	229	cGc/cAc	4/10	1	2	FACETS	0.46	0.416	0.505	0.46	0.416	0.505	SUBCLONAL	1	TRUE	1	0.75	2		617	725	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31381362	31381362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113400552	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	39	377	2	ENST00000328111.2:c.1087C>T	p.Arg363Cys	p.R363C	ENST00000328111	NM_006892.3	363	Cgt/Tgt	10/23	1	2	FACETS	0.251	0.208	0.299	0.251	0.208	0.299	SUBCLONAL	1	TRUE	1	0.75	2		379	414	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678076	117678076	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs373090808	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	102	279	0	ENST00000368508.3:c.3857G>A	p.Arg1286His	p.R1286H	ENST00000368508	NM_002944.2	1286	cGc/cAc	25/43	1	2	FACETS	0.907	0.822	0.994	0.907	0.822	0.994	CLONAL	1	TRUE	1	0.75	2		279	300	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936995	48936995	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778842	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	68	322	0	ENST00000267163.4:c.763C>T	p.Arg255Ter	p.R255*	ENST00000267163	NM_000321.2	255	Cga/Tga	8/27	1	2	FACETS	0.526	0.46	0.595	0.526	0.46	0.595	SUBCLONAL	1	TRUE	1	0.75	2		322	345	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143033	47143033	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	180	480	2	ENST00000409792.3:c.4930G>A	p.Gly1644Arg	p.G1644R	ENST00000409792	NM_014159.6	1644	Gga/Aga	8/21	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.75	2		482	476	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10257033	10257033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754990148	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	66	579	1	ENST00000340748.4:c.2840C>T	p.Thr947Met	p.T947M	ENST00000340748		947	aCg/aTg	27/40	1	2	FACETS	0.248	0.215	0.284	0.248	0.215	0.284	SUBCLONAL	1	TRUE	1	0.75	2		580	709	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797278	42797278	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs968289754	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	135	1012	0	ENST00000575354.2:c.3640C>T	p.Arg1214Ter	p.R1214*	ENST00000575354	NM_015125.3	1214	Cga/Tga	15/20	1	2	FACETS	0.327	0.297	0.36	0.327	0.297	0.36	SUBCLONAL	1	TRUE	1	0.75	2		1012	1100	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847351	68847351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs570930882	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	205	565	0	ENST00000261769.5:c.1273G>A	p.Val425Ile	p.V425I	ENST00000261769	NM_004360.3	425	Gtc/Atc	9/16	1	2	FACETS	0.941	0.879	1	0.941	0.879	1	CLONAL	1	TRUE	1	0.75	2		565	581	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78820303	78820303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763716081	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	250	869	2	ENST00000306801.3:c.1243G>A	p.Ala415Thr	p.A415T	ENST00000306801	NM_020761.2	415	Gca/Aca	11/34	1	2	FACETS	0.661	0.618	0.704	0.661	0.618	0.704	SUBCLONAL	1	TRUE	1	0.75	2		871	1009	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290180	15290180	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371437217	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	206	892	0	ENST00000263388.2:c.3455C>T	p.Thr1152Met	p.T1152M	ENST00000263388	NM_000435.2	1152	aCg/aTg	21/33	1	2	FACETS	0.626	0.582	0.673	0.626	0.582	0.673	SUBCLONAL	1	TRUE	1	0.75	2		892	877	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533881	533881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs727503093	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	365	826	1	ENST00000451590.1:c.175G>A	p.Ala59Thr	p.A59T	ENST00000451590	NM_001130442.1	59	Gcc/Acc	3/5	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.75	2		827	960	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24134006	24134006	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	47	411	0	ENST00000263121.7:c.157C>T	p.Arg53Ter	p.R53*	ENST00000263121	NM_003073.3	53	Cga/Tga	2/9	1	2	FACETS	0.268	0.226	0.315	0.268	0.226	0.315	SUBCLONAL	1	TRUE	1	0.75	2		411	467	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953730	48953730	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs3092891	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	54	163	0	ENST00000267163.4:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000267163	NM_000321.2	445	Cga/Tga	14/27	1	2	FACETS	0.727	0.63	0.83	0.727	0.63	0.83	SUBCLONAL	1	TRUE	1	0.75	2		163	198	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	342	864	13	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	0.823	0.779	0.868	0.823	0.779	0.868	CLONAL	1	TRUE	1	0.75	2		877	1108	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485014	57485014	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	78	367	0	ENST00000371085.3:c.848G>A	p.Arg283His	p.R283H	ENST00000371085	NM_000516.4	283	cGc/cAc	11/13	1	2	FACETS	0.565	0.5	0.634	0.565	0.5	0.634	SUBCLONAL	1	TRUE	1	0.75	2		367	368	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206809	36206809	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	281	610	0	ENST00000300305.3:c.703G>A	p.Ala235Thr	p.A235T	ENST00000300305		235	Gcc/Acc	6/8	1	2	FACETS	0.98	0.925	1	0.98	0.925	1	CLONAL	1	TRUE	1	0.75	2		610	765	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219579	133219579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542430685	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	283	660	0	ENST00000320574.5:c.4555C>T	p.Arg1519Cys	p.R1519C	ENST00000320574	NM_006231.2	1519	Cgc/Tgc	36/49	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.75	2		660	683	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991736	25991736	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs530632623	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	88	315	0	ENST00000435504.4:c.506C>T	p.Ala169Val	p.A169V	ENST00000435504		169	gCg/gTg	7/13	1	2	FACETS	0.605	0.539	0.674	0.605	0.539	0.674	SUBCLONAL	1	TRUE	1	0.75	2		315	388	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183540	185183540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	166	310	0	ENST00000265026.3:c.1394C>T	p.Ala465Val	p.A465V	ENST00000265026	NM_004721.4	465	gCg/gTg	9/14	0.299205930568942	3	FACETS	1	0.987	1	0.648	0.6	0.696	INDETERMINATE	1	TRUE	1	0.75	3		310	470	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394896	394896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	126	476	2	ENST00000380956.4:c.292C>T	p.Arg98Trp	p.R98W	ENST00000380956	NM_001195286.1	98	Cgg/Tgg	3/9	1	2	FACETS	0.588	0.535	0.645	0.588	0.535	0.645	SUBCLONAL	1	TRUE	1	0.75	2		478	571	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715979	52715979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205227	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	228	734	0	ENST00000322088.6:c.544C>T	p.Arg182Trp	p.R182W	ENST00000322088	NM_014225.5	182	Cgg/Tgg	5/15	1	2	FACETS	0.72	0.673	0.77	0.72	0.673	0.77	SUBCLONAL	1	TRUE	1	0.75	2		734	844	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223488	53223488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	117	741	1	ENST00000375401.3:c.3871C>T	p.Arg1291Cys	p.R1291C	ENST00000375401	NM_004187.3	1291	Cgc/Tgc	23/26	1	2	FACETS	0.38	0.342	0.419	0.38	0.342	0.419	SUBCLONAL	1	TRUE	1	0.75	2		742	822	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279681	123279681	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	183	369	0	ENST00000358487.5:c.751C>T	p.Arg251Ter	p.R251*	ENST00000358487	NM_000141.4	251	Cga/Tga	7/18	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.75	2		369	457	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098912	47098912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	317	737	0	ENST00000409792.3:c.6362G>A	p.Arg2121His	p.R2121H	ENST00000409792	NM_014159.6	2121	cGc/cAc	15/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.75	2		737	841	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940813	49940813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	139	871	0	ENST00000296474.3:c.230G>A	p.Arg77His	p.R77H	ENST00000296474	NM_002447.2	77	cGc/cAc	1/20	1	2	FACETS	0.365	0.332	0.4	0.365	0.332	0.4	SUBCLONAL	1	TRUE	1	0.75	2		871	1015	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184657	185184657	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs56408536	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	283	374	2	ENST00000265026.3:c.1549C>T	p.Arg517Ter	p.R517*	ENST00000265026	NM_004721.4	517	Cga/Tga	10/14	0.299205930568942	3	FACETS	0.863	0.819	0.908	0.863	0.819	0.908	INDETERMINATE	2	TRUE	1	0.75	3		376	601	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225663	225663	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375576259	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	206	903	0	ENST00000264932.6:c.442G>A	p.Ala148Thr	p.A148T	ENST00000264932	NM_004168.2	148	Gcc/Acc	4/15	1	2	FACETS	0.496	0.459	0.534	0.496	0.459	0.534	SUBCLONAL	1	TRUE	1	0.75	2		903	1108	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349666	15349666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200976853	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	446	987	1	ENST00000263377.2:c.3908C>T	p.Ala1303Val	p.A1303V	ENST00000263377	NM_058243.2	1303	gCg/gTg	19/20	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.75	2		988	1043	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15379802	15379802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	96	488	1	ENST00000263377.2:c.337C>T	p.Arg113Cys	p.R113C	ENST00000263377	NM_058243.2	113	Cgc/Tgc	3/20	1	2	FACETS	0.494	0.442	0.55	0.494	0.442	0.55	SUBCLONAL	1	TRUE	1	0.75	2		489	518	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759443	133759443	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376925416	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	327	728	0	ENST00000318560.5:c.1766G>A	p.Arg589His	p.R589H	ENST00000318560	NM_005157.4	589	cGc/cAc	11/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.75	2		728	786	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264445	16264445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1355879966	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	80	757	3	ENST00000375759.3:c.10648G>A	p.Ala3550Thr	p.A3550T	ENST00000375759	NM_015001.2	3550	Gcc/Acc	13/15	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.75	NA		760	882	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099430	27099430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1227227387	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	62	525	0	ENST00000324856.7:c.3667C>T	p.Arg1223Cys	p.R1223C	ENST00000324856	NM_006015.4	1223	Cgc/Tgc	14/20	1	2	FACETS	0.278	0.24	0.319	0.278	0.24	0.319	SUBCLONAL	1	TRUE	1	0.75	2		525	595	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247836	10247836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	265	964	4	ENST00000340748.4:c.4366C>T	p.Arg1456Trp	p.R1456W	ENST00000340748		1456	Cgg/Tgg	36/40	1	2	FACETS	0.679	0.637	0.723	0.679	0.637	0.723	SUBCLONAL	1	TRUE	1	0.75	2		968	1040	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720650	89720650	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1257124719	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	31	461	0	ENST00000371953.3:c.802-1G>A		p.X268_splice	ENST00000371953	NM_000314.4	268			1	2	FACETS	0.179	0.144	0.219	0.179	0.144	0.219	SUBCLONAL	1	TRUE	1	0.75	2		461	461	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630542	187630542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	310	705	0	ENST00000441802.2:c.440C>T	p.Pro147Leu	p.P147L	ENST00000441802	NM_005245.3	147	cCg/cTg	2/27	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.75	2		705	798	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654857	29654857	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786202112	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	15	221	0	ENST00000356175.3:c.5546G>A	p.Arg1849Gln	p.R1849Q	ENST00000356175	NM_000267.3	1849	cGg/cAg	37/57	1	2	FACETS	0.145	0.106	0.192	0.145	0.106	0.192	SUBCLONAL	1	TRUE	1	0.75	2		221	276	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827732	72827732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241554729	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	187	616	0	ENST00000268489.5:c.8849G>A	p.Arg2950His	p.R2950H	ENST00000268489	NM_006885.3	2950	cGc/cAc	9/10	1	2	FACETS	0.674	0.624	0.725	0.674	0.624	0.725	SUBCLONAL	1	TRUE	1	0.75	2		616	740	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861837	57861837	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs759838377	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	278	618	0	ENST00000228682.2:c.1138C>T	p.Arg380Ter	p.R380*	ENST00000228682	NM_005269.2	380	Cga/Tga	10/12	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.75	2		618	741	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407527	407527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs908661692	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	185	448	0	ENST00000380956.4:c.1285G>A	p.Asp429Asn	p.D429N	ENST00000380956	NM_001195286.1	429	Gat/Aat	9/9	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.75	2		448	429	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93627378	93627378	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs201994789	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	148	432	0	ENST00000375746.1:c.845C>T	p.Ala282Val	p.A282V	ENST00000375746	NM_001174167.1	282	gCg/gTg	6/14	1	2	FACETS	0.914	0.842	0.987	0.914	0.842	0.987	CLONAL	1	TRUE	1	0.75	2		432	432	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164889	36164889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1358657401	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	438	914	0	ENST00000300305.3:c.986C>T	p.Ala329Val	p.A329V	ENST00000300305		329	gCg/gTg	8/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.75	2		914	1088	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057911	27057911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs892173376	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	221	815	1	ENST00000324856.7:c.1619C>T	p.Thr540Met	p.T540M	ENST00000324856	NM_006015.4	540	aCg/aTg	3/20	1	2	FACETS	0.598	0.556	0.641	0.598	0.556	0.641	SUBCLONAL	1	TRUE	1	0.75	2		816	986	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512401	38512402	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs745553450	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	205	793	4	ENST00000254066.5:c.1319dup	p.Pro441AlafsTer5	p.P441Afs*5	ENST00000254066	NM_000964.3	438	gcc/gCcc	9/9	1	2	FACETS	0.653	0.607	0.701	0.653	0.607	0.701	SUBCLONAL	1	TRUE	1	0.75	2		797	837	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443940	18443940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866374517	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	34	241	0	ENST00000266497.5:c.913C>T	p.Pro305Ser	p.P305S	ENST00000266497		305	Cca/Tca	3/31	1	2	FACETS	0.428	0.352	0.511	0.428	0.352	0.511	SUBCLONAL	1	TRUE	1	0.75	2		241	212	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165663	118165663	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776281952	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	130	453	0	ENST00000369448.3:c.173G>A	p.Arg58Gln	p.R58Q	ENST00000369448	NM_017709.3	58	cGg/cAg	2/2	1	2	FACETS	0.657	0.598	0.717	0.657	0.598	0.717	SUBCLONAL	1	TRUE	1	0.75	2		453	528	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142913	7142913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1283504748	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	75	777	2	ENST00000302850.5:c.2456G>A	p.Arg819His	p.R819H	ENST00000302850	NM_000208.2	819	cGc/cAc	12/22	1	2	FACETS	0.222	0.194	0.253	0.222	0.194	0.253	SUBCLONAL	1	TRUE	1	0.75	2		779	900	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813361	102813361	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1280732914	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	173	606	0	ENST00000307046.8:c.328G>A	p.Ala110Thr	p.A110T	ENST00000307046	NM_001111285.1	110	Gca/Aca	3/4	1	2	FACETS	0.605	0.557	0.654	0.605	0.557	0.654	SUBCLONAL	1	TRUE	1	0.75	2		606	763	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136847	55136847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	83	335	0	ENST00000257290.5:c.1169G>A	p.Gly390Asp	p.G390D	ENST00000257290	NM_006206.4	390	gGc/gAc	8/23	1	2	FACETS	0.559	0.496	0.625	0.559	0.496	0.625	SUBCLONAL	1	TRUE	1	0.75	2		335	396	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317015	11317015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759750826	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	245	473	0	ENST00000361445.4:c.479G>A	p.Arg160His	p.R160H	ENST00000361445	NM_004958.3	160	cGc/cAc	4/58	1	2	FACETS	0.999	0.94	1	0.999	0.94	1	CLONAL	1	TRUE	1	0.75	2		473	654	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740264	162740264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756149068	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	170	381	0	ENST00000367921.3:c.1466G>A	p.Arg489Gln	p.R489Q	ENST00000367921	NM_006182.2	489	cGa/cAa	12/18	1	2	FACETS	0.931	0.863	1	0.931	0.863	1	CLONAL	1	TRUE	1	0.75	2		381	487	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931471	131931471	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753002904	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	63	366	0	ENST00000265335.6:c.2176C>T	p.Arg726Cys	p.R726C	ENST00000265335		726	Cgt/Tgt	13/25	1	2	FACETS	0.362	0.314	0.414	0.362	0.314	0.414	SUBCLONAL	1	TRUE	1	0.75	2		366	464	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134687	41134687	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760747458	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	180	418	0	ENST00000379561.5:c.941G>A	p.Arg314His	p.R314H	ENST00000379561	NM_002015.3	314	cGc/cAc	2/3	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.75	2		418	446	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467680	50467680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867719866	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	131	705	0	ENST00000331340.3:c.915G>A	p.Met305Ile	p.M305I	ENST00000331340	NM_006060.4	305	atG/atA	8/8	1	2	FACETS	0.527	0.479	0.577	0.527	0.479	0.577	SUBCLONAL	1	TRUE	1	0.75	2		705	663	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156699	2156699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs975030738	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	366	848	0	ENST00000434045.2:c.223G>A	p.Ala75Thr	p.A75T	ENST00000434045	NM_001127598.1	75	Gcc/Acc	3/5	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.75	2		848	933	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417080	417080	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779176655	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	42	365	0	ENST00000399788.2:c.3470G>A	p.Arg1157His	p.R1157H	ENST00000399788	NM_001042603.1	1157	cGc/cAc	23/28	1	2	FACETS	0.26	0.217	0.308	0.26	0.217	0.308	SUBCLONAL	1	TRUE	1	0.75	2		365	431	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144697	119144697	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	107	420	0	ENST00000264033.4:c.710C>T	p.Ser237Leu	p.S237L	ENST00000264033	NM_005188.3	237	tCg/tTg	4/16	1	2	FACETS	0.548	0.493	0.605	0.548	0.493	0.605	SUBCLONAL	1	TRUE	1	0.75	2		420	521	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574502	41574502	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	319	770	1	ENST00000263253.7:c.6787C>T	p.Arg2263Ter	p.R2263*	ENST00000263253	NM_001429.3	2263	Cga/Tga	31/31	1	2	FACETS	0.972	0.921	1	0.972	0.921	1	CLONAL	1	TRUE	1	0.75	2		771	875	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633320	8633320	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866980874	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	171	440	0	ENST00000356435.5:c.349C>T	p.Arg117Trp	p.R117W	ENST00000356435		117	Cgg/Tgg	3/35	1	2	FACETS	0.905	0.839	0.972	0.905	0.839	0.972	CLONAL	1	TRUE	1	0.75	2		440	504	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799059	42799059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	302	1091	1	ENST00000575354.2:c.4543C>T	p.Arg1515Cys	p.R1515C	ENST00000575354	NM_015125.3	1515	Cgc/Tgc	20/20	1	2	FACETS	0.686	0.646	0.727	0.686	0.646	0.727	SUBCLONAL	1	TRUE	1	0.75	2		1092	1174	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285851	198285851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1360783408	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	20	335	0	ENST00000335508.6:c.202G>A	p.Asp68Asn	p.D68N	ENST00000335508	NM_012433.2	68	Gat/Aat	3/25	1	2	FACETS	0.145	0.11	0.185	0.145	0.11	0.185	SUBCLONAL	1	TRUE	1	0.75	2		335	369	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274102	10274102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	419	853	2	ENST00000330684.3:c.167G>A	p.Gly56Asp	p.G56D	ENST00000330684	NM_001134407.1	56	gGc/gAc	2/13	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.75	2		855	1020	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142446	119142446	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs267602720	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	43	302	0	ENST00000264033.4:c.445C>T	p.Arg149Ter	p.R149*	ENST00000264033	NM_005188.3	149	Cga/Tga	3/16	1	2	FACETS	0.349	0.292	0.41	0.349	0.292	0.41	SUBCLONAL	1	TRUE	1	0.75	2		302	329	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463286	25463286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139293773	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	170	517	1	ENST00000264709.3:c.2207G>A	p.Arg736His	p.R736H	ENST00000264709	NM_175629.2	736	cGc/cAc	19/23	1	2	FACETS	0.675	0.622	0.729	0.675	0.622	0.729	SUBCLONAL	1	TRUE	1	0.75	2		518	672	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540874	187540874	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs562612394	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	142	347	0	ENST00000441802.2:c.6866C>T	p.Ala2289Val	p.A2289V	ENST00000441802	NM_005245.3	2289	gCg/gTg	10/27	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.75	2		347	355	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864491	56864491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746856372	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	82	551	2	ENST00000308159.5:c.979C>T	p.Arg327Cys	p.R327C	ENST00000308159	NM_014669.4	327	Cgc/Tgc	10/22	1	2	FACETS	0.327	0.288	0.369	0.327	0.288	0.369	SUBCLONAL	1	TRUE	1	0.75	2		553	669	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797777	42797777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778206	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	160	946	0	ENST00000575354.2:c.3829C>T	p.Arg1277Cys	p.R1277C	ENST00000575354	NM_015125.3	1277	Cgc/Tgc	16/20	1	2	FACETS	0.383	0.35	0.417	0.383	0.35	0.417	SUBCLONAL	1	TRUE	1	0.75	2		946	1114	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158382	108158382	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781785	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	64	439	0	ENST00000278616.4:c.4049C>T	p.Thr1350Met	p.T1350M	ENST00000278616	NM_000051.3	1350	aCg/aTg	27/63	1	2	FACETS	0.399	0.346	0.455	0.399	0.346	0.455	SUBCLONAL	1	TRUE	1	0.75	2		439	428	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741870	40741870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144444132	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	95	868	0	ENST00000392038.2:c.1102C>T	p.Arg368Cys	p.R368C	ENST00000392038	NM_001626.4	368	Cgc/Tgc	11/14	1	2	FACETS	0.277	0.246	0.31	0.277	0.246	0.31	SUBCLONAL	1	TRUE	1	0.75	2		868	916	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944310	206944310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755490123	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	265	559	0	ENST00000423557.1:c.320C>T	p.Ala107Val	p.A107V	ENST00000423557	NM_000572.2	107	gCg/gTg	3/5	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.75	2		559	654	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240450	98240450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370354759	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	65	418	1	ENST00000331920.6:c.1234G>A	p.Ala412Thr	p.A412T	ENST00000331920	NM_000264.3	412	Gca/Aca	9/24	1	2	FACETS	0.317	0.275	0.363	0.317	0.275	0.363	SUBCLONAL	1	TRUE	1	0.75	2		419	547	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710983	117710983	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	107	241	0	ENST00000368508.3:c.1289G>A	p.Gly430Asp	p.G430D	ENST00000368508	NM_002944.2	430	gGc/gAc	12/43	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.75	2		241	272	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628026	187628026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750746155	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	286	632	1	ENST00000441802.2:c.2956G>A	p.Val986Ile	p.V986I	ENST00000441802	NM_005245.3	986	Gtc/Atc	2/27	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.75	2		633	744	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586101	29586101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876658127	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	54	388	3	ENST00000356175.3:c.4321C>T	p.Arg1441Trp	p.R1441W	ENST00000356175	NM_000267.3	1441	Cgg/Tgg	32/57	1	2	FACETS	0.434	0.372	0.5	0.434	0.372	0.5	SUBCLONAL	1	TRUE	1	0.75	2		391	332	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022422	31022422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370230857	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	171	379	0	ENST00000375687.4:c.1907C>T	p.Ala636Val	p.A636V	ENST00000375687	NM_015338.5	636	gCg/gTg	13/13	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.75	2		379	397	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575594	55575594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs73137716	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	118	304	0	ENST00000288135.5:c.1120G>A	p.Val374Ile	p.V374I	ENST00000288135	NM_000222.2	374	Gta/Ata	7/21	1	2	FACETS	0.928	0.848	1	0.928	0.848	1	CLONAL	1	TRUE	1	0.75	2		304	339	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765753	41765753	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761731744	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	265	585	2	ENST00000301178.4:c.2629G>A	p.Ala877Thr	p.A877T	ENST00000301178	NM_021913.4	877	Gct/Act	20/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.75	2		587	655	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463182	25463182	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs779626155	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	76	565	2	ENST00000264709.3:c.2311C>T	p.Arg771Ter	p.R771*	ENST00000264709	NM_175629.2	771	Cga/Tga	19/23	1	2	FACETS	0.317	0.277	0.359	0.317	0.277	0.359	SUBCLONAL	1	TRUE	1	0.75	2		567	640	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112996	2112996	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45494392	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	239	635	1	ENST00000219476.3:c.1385G>A	p.Arg462His	p.R462H	ENST00000219476	NM_000548.3	462	cGc/cAc	14/42	1	2	FACETS	0.767	0.718	0.817	0.767	0.718	0.817	SUBCLONAL	1	TRUE	1	0.75	2		636	831	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340177	116340177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200074800	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	77	241	0	ENST00000397752.3:c.1039G>A	p.Ala347Thr	p.A347T	ENST00000397752	NM_000245.2	347	Gca/Aca	2/21	1	2	FACETS	0.667	0.591	0.747	0.667	0.591	0.747	SUBCLONAL	1	TRUE	1	0.75	2		241	308	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866710	37866710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258412021	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	40	763	1	ENST00000269571.5:c.877G>A	p.Ala293Thr	p.A293T	ENST00000269571		293	Gcc/Acc	7/27	1	2	FACETS	0.108	0.089	0.129	0.108	0.089	0.129	SUBCLONAL	1	TRUE	1	0.75	2		764	991	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399128	139399128	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372830543	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	407	796	1	ENST00000277541.6:c.5015G>A	p.Arg1672His	p.R1672H	ENST00000277541	NM_017617.3	1672	cGc/cAc	26/34	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.75	2		797	981	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900329	101900329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	77	301	0	ENST00000374994.4:c.763C>T	p.Arg255Cys	p.R255C	ENST00000374994	NM_004612.2	255	Cgt/Tgt	4/9	1	2	FACETS	0.593	0.525	0.666	0.593	0.525	0.666	SUBCLONAL	1	TRUE	1	0.75	2		301	346	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512490	149512490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1443597666	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	62	573	0	ENST00000261799.4:c.950G>A	p.Arg317Gln	p.R317Q	ENST00000261799	NM_002609.3	317	cGg/cAg	7/23	1	2	FACETS	0.271	0.234	0.312	0.271	0.234	0.312	SUBCLONAL	1	TRUE	1	0.75	2		573	610	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265313	10265313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762421501	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	98	727	0	ENST00000340748.4:c.1733C>T	p.Thr578Ile	p.T578I	ENST00000340748		578	aCa/aTa	20/40	1	2	FACETS	0.304	0.27	0.339	0.304	0.27	0.339	SUBCLONAL	1	TRUE	1	0.75	2		727	860	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310859	123310859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759750319	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	270	584	0	ENST00000358487.5:c.569G>A	p.Arg190Gln	p.R190Q	ENST00000358487	NM_000141.4	190	cGg/cAg	5/18	1	2	FACETS	0.985	0.929	1	0.985	0.929	1	CLONAL	1	TRUE	1	0.75	2		584	731	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198177	185198177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs889834349	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	322	552	0	ENST00000265026.3:c.2659G>A	p.Asp887Asn	p.D887N	ENST00000265026	NM_004721.4	887	Gac/Aac	13/14	0.299205930568942	3	FACETS	0.751	0.713	0.79	0.751	0.713	0.79	INDETERMINATE	2	TRUE	1	0.75	3		552	786	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26974623	26974623	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	98	588	1	ENST00000381527.3:c.967C>T	p.Arg323Ter	p.R323*	ENST00000381527	NM_001260.1	323	Cga/Tga	10/13	1	2	FACETS	0.562	0.504	0.623	0.562	0.504	0.623	SUBCLONAL	1	TRUE	1	0.75	2		589	465	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655272	45655272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764295138	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	109	873	1	ENST00000407780.3:c.580C>T	p.Arg194Trp	p.R194W	ENST00000407780	NM_001283052.1	194	Cgg/Tgg	4/7	1	2	FACETS	0.301	0.269	0.334	0.301	0.269	0.334	SUBCLONAL	1	TRUE	1	0.75	2		874	966	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2105507	2105507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45517113	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	121	547	0	ENST00000219476.3:c.586G>A	p.Ala196Thr	p.A196T	ENST00000219476	NM_000548.3	196	Gca/Aca	6/42	1	2	FACETS	0.536	0.485	0.589	0.536	0.485	0.589	SUBCLONAL	1	TRUE	1	0.75	2		547	602	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540977	187540977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200488891	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	52	370	0	ENST00000441802.2:c.6763C>T	p.Arg2255Cys	p.R2255C	ENST00000441802	NM_005245.3	2255	Cgc/Tgc	10/27	1	2	FACETS	0.319	0.272	0.37	0.319	0.272	0.37	SUBCLONAL	1	TRUE	1	0.75	2		370	435	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101690	27101690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1442666063	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	119	852	0	ENST00000324856.7:c.4972C>T	p.Arg1658Trp	p.R1658W	ENST00000324856	NM_006015.4	1658	Cgg/Tgg	18/20	1	2	FACETS	0.32	0.288	0.353	0.32	0.288	0.353	SUBCLONAL	1	TRUE	1	0.75	2		852	993	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194110	94194110	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773469981	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	148	389	0	ENST00000323929.3:c.1318G>A	p.Ala440Thr	p.A440T	ENST00000323929	NM_005591.3	440	Gca/Aca	12/20	1	2	FACETS	0.965	0.891	1	0.965	0.891	1	CLONAL	1	TRUE	1	0.75	2		389	409	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521581	46521581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs552393862	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	166	421	0	ENST00000262741.5:c.827G>A	p.Arg276His	p.R276H	ENST00000262741	NM_003629.3	276	cGt/cAt	7/10	1	2	FACETS	0.878	0.813	0.945	0.878	0.813	0.945	CLONAL	1	TRUE	1	0.75	2		421	504	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123159736	123159736	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1251136516	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	28	314	0	ENST00000218089.9:c.91G>A	p.Glu31Lys	p.E31K	ENST00000218089	NM_001042749.1	31	Gaa/Aaa	4/35	1	2	FACETS	0.281	0.225	0.344	0.281	0.225	0.344	SUBCLONAL	1	TRUE	1	0.75	2		314	266	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719525	61719525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	188	459	0	ENST00000401558.2:c.1658G>A	p.Arg553His	p.R553H	ENST00000401558	NM_003400.3	553	cGt/cAt	15/25	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.75	2		459	443	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256409	46256409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754382773	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	165	379	1	ENST00000371998.3:c.637G>A	p.Ala213Thr	p.A213T	ENST00000371998		213	Gcc/Acc	7/23	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.75	2		380	440	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88677065	88677065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765530074	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	110	663	1	ENST00000372037.3:c.850C>T	p.Arg284Cys	p.R284C	ENST00000372037	NM_004329.2	284	Cgc/Tgc	9/13	1	2	FACETS	0.381	0.342	0.422	0.381	0.342	0.422	SUBCLONAL	1	TRUE	1	0.75	2		664	770	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926872	112926872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507541	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	78	692	1	ENST00000351677.2:c.1492C>T	p.Arg498Trp	p.R498W	ENST00000351677	NM_002834.3	498	Cgg/Tgg	13/16	1	2	FACETS	0.248	0.217	0.281	0.248	0.217	0.281	SUBCLONAL	1	TRUE	1	0.75	2		693	839	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845230	89845230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374968669	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	69	520	2	ENST00000389301.3:c.1805C>T	p.Ala602Val	p.A602V	ENST00000389301	NM_000135.2	602	gCg/gTg	20/43	1	2	FACETS	0.262	0.227	0.299	0.262	0.227	0.299	SUBCLONAL	1	TRUE	1	0.75	2		522	703	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099936	27099936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773264329	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	226	718	1	ENST00000324856.7:c.3815C>T	p.Ala1272Val	p.A1272V	ENST00000324856	NM_006015.4	1272	gCg/gTg	15/20	1	2	FACETS	0.707	0.66	0.756	0.707	0.66	0.756	SUBCLONAL	1	TRUE	1	0.75	2		719	852	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651216	45651216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200793282	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	331	654	2	ENST00000407780.3:c.809C>T	p.Ala270Val	p.A270V	ENST00000407780	NM_001283052.1	270	gCg/gTg	5/7	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.75	2		656	799	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348502	70348502	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1317457286	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	84	561	2	ENST00000374080.3:c.3409G>A	p.Ala1137Thr	p.A1137T	ENST00000374080		1137	Gct/Act	24/45	1	2	FACETS	0.331	0.292	0.373	0.331	0.292	0.373	SUBCLONAL	1	TRUE	1	0.75	2		563	677	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347446	91347446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757088548	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	27	380	0	ENST00000355112.3:c.3608C>T	p.Ala1203Val	p.A1203V	ENST00000355112	NM_000057.2	1203	gCg/gTg	19/22	1	2	FACETS	0.164	0.13	0.203	0.164	0.13	0.203	SUBCLONAL	1	TRUE	1	0.75	2		380	438	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144864	58144864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778185	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	158	465	0	ENST00000257904.6:c.364C>T	p.Arg122Cys	p.R122C	ENST00000257904	NM_000075.3	122	Cgc/Tgc	4/8	1	2	FACETS	0.674	0.62	0.73	0.674	0.62	0.73	SUBCLONAL	1	TRUE	1	0.75	2		465	625	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910394	50910394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	277	933	0	ENST00000440232.2:c.1649G>A	p.Gly550Asp	p.G550D	ENST00000440232	NM_002691.3	550	gGc/gAc	13/27	1	2	FACETS	0.703	0.66	0.747	0.703	0.66	0.747	SUBCLONAL	1	TRUE	1	0.75	2		933	1051	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796484	42796484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780624177	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	492	1125	0	ENST00000575354.2:c.3041C>T	p.Ala1014Val	p.A1014V	ENST00000575354	NM_015125.3	1014	gCg/gTg	13/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.75	2		1125	1252	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226860	2226860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	87	182	1	ENST00000398665.3:c.4340C>T	p.Ala1447Val	p.A1447V	ENST00000398665	NM_032482.2	1447	gCg/gTg	27/28	1	2	FACETS	0.823	0.738	0.911	0.823	0.738	0.911	CLONAL	1	TRUE	1	0.75	2		183	282	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321073	137321073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768721235	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	208	695	0	ENST00000481739.1:c.1030G>A	p.Ala344Thr	p.A344T	ENST00000481739	NM_002957.4	344	Gcc/Acc	7/10	1	2	FACETS	0.721	0.671	0.773	0.721	0.671	0.773	SUBCLONAL	1	TRUE	1	0.75	2		695	769	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215595163	215595163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377227840	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	90	330	0	ENST00000260947.4:c.1973G>A	p.Arg658His	p.R658H	ENST00000260947	NM_000465.2	658	cGc/cAc	10/11	1	2	FACETS	0.945	0.852	1	0.945	0.852	1	CLONAL	1	TRUE	1	0.75	2		330	254	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72873679	72873679	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755799071	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	47	324	0	ENST00000325599.8:c.623C>T	p.Ala208Val	p.A208V	ENST00000325599	NM_018130.2	208	gCg/gTg	6/11	1	2	FACETS	0.379	0.321	0.442	0.379	0.321	0.442	SUBCLONAL	1	TRUE	1	0.75	2		324	331	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967089	18967089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334288478	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	394	860	2	ENST00000262803.5:c.1804G>A	p.Ala602Thr	p.A602T	ENST00000262803	NM_002911.3	602	Gca/Aca	13/24	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.75	2		862	1012	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458536	12458536	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs780238349	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	285	659	0	ENST00000287820.6:c.1153C>T	p.Arg385Ter	p.R385*	ENST00000287820	NM_015869.4	385	Cga/Tga	6/7	1	2	FACETS	0.971	0.917	1	0.971	0.917	1	CLONAL	1	TRUE	1	0.75	2		659	783	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780289	9780289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201282174	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	61	699	0	ENST00000377346.4:c.1459G>A	p.Ala487Thr	p.A487T	ENST00000377346	NM_005026.3	487	Gcc/Acc	11/24	1	2	FACETS	0.226	0.195	0.261	0.226	0.195	0.261	SUBCLONAL	1	TRUE	1	0.75	2		699	719	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149280	119149280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs991981291	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	154	640	0	ENST00000264033.4:c.1288G>A	p.Val430Met	p.V430M	ENST00000264033	NM_005188.3	430	Gtg/Atg	9/16	1	2	FACETS	0.551	0.505	0.599	0.551	0.505	0.599	SUBCLONAL	1	TRUE	1	0.75	2		640	745	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246557	46246557	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161560614	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	38	191	1	ENST00000334344.6:c.4651G>A	p.Ala1551Thr	p.A1551T	ENST00000334344	NM_152641.2	1551	Gca/Aca	15/21	1	2	FACETS	0.48	0.401	0.567	0.48	0.401	0.567	SUBCLONAL	1	TRUE	1	0.75	2		192	211	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108091	30108091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80271647	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	201	490	0	ENST00000331968.5:c.716C>T	p.Ser239Leu	p.S239L	ENST00000331968	NM_002742.2	239	tCg/tTg	5/18	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.75	2		490	510	SUCCESS
APC	324	MSKCC	GRCh37	5	112154771	112154771	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1314843920	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	94	524	0	ENST00000257430.4:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000257430	NM_000038.5	348	Cga/Tga	10/16	1	2	FACETS	0.425	0.378	0.474	0.425	0.378	0.474	SUBCLONAL	1	TRUE	1	0.75	2		524	590	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180441	94180441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139461096	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	84	584	0	ENST00000323929.3:c.1727G>A	p.Arg576Gln	p.R576Q	ENST00000323929	NM_005591.3	576	cGa/cAa	15/20	1	2	FACETS	0.286	0.252	0.322	0.286	0.252	0.322	SUBCLONAL	1	TRUE	1	0.75	2		584	784	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796805	135796805	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203427	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	40	279	1	ENST00000298552.3:c.682C>T	p.Arg228Ter	p.R228*	ENST00000298552	NM_001162426.1	228	Cga/Tga	8/23	1	2	FACETS	0.322	0.268	0.382	0.322	0.268	0.382	SUBCLONAL	1	TRUE	1	0.75	2		280	331	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527508	157527508	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528801298	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	149	454	0	ENST00000346085.5:c.5233G>A	p.Glu1745Lys	p.E1745K	ENST00000346085	NM_020732.3	1745	Gag/Aag	20/20	1	2	FACETS	0.704	0.647	0.764	0.704	0.647	0.764	SUBCLONAL	1	TRUE	1	0.75	2		454	564	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347553	118347553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555037629	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	200	451	0	ENST00000534358.1:c.3190C>T	p.Arg1064Ter	p.R1064*	ENST00000534358	NM_005933.3	1064	Cga/Tga	4/36	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.75	2		451	524	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391832	139391832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766836819	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	471	1040	2	ENST00000277541.6:c.6359G>A	p.Arg2120His	p.R2120H	ENST00000277541	NM_017617.3	2120	cGc/cAc	34/34	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.75	2		1042	1127	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005423	29005423	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	102	331	1	ENST00000282397.4:c.838C>T	p.Arg280Ter	p.R280*	ENST00000282397	NM_002019.4	280	Cga/Tga	7/30	1	2	FACETS	0.883	0.8	0.969	0.883	0.8	0.969	CLONAL	1	TRUE	1	0.75	2		332	308	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911638	114911638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1427214163	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	225	408	0	ENST00000543371.1:c.1156C>T	p.Arg386Trp	p.R386W	ENST00000543371	NM_001198531.1	386	Cgg/Tgg	10/14	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.75	2		408	550	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542455	187542455	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376944386	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	181	459	0	ENST00000441802.2:c.5285C>T	p.Ala1762Val	p.A1762V	ENST00000441802	NM_005245.3	1762	gCg/gTg	10/27	1	2	FACETS	0.958	0.891	1	0.958	0.891	1	CLONAL	1	TRUE	1	0.75	2		459	504	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924403	131924403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1184353235	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	47	269	0	ENST00000265335.6:c.1076G>A	p.Arg359His	p.R359H	ENST00000265335		359	cGc/cAc	8/25	1	2	FACETS	0.395	0.335	0.461	0.395	0.335	0.461	SUBCLONAL	1	TRUE	1	0.75	2		269	317	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127731	64127731	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1455628289	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	126	882	1	ENST00000334205.4:c.224G>A	p.Arg75His	p.R75H	ENST00000334205	NM_003942.2	75	cGc/cAc	3/17	1	2	FACETS	0.327	0.295	0.36	0.327	0.295	0.36	SUBCLONAL	1	TRUE	1	0.75	2		883	1029	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572272	64572272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372468697	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	219	1134	3	ENST00000312049.6:c.1367G>A	p.Arg456His	p.R456H	ENST00000312049	NM_130799.2	456	cGc/cAc	10/10	1	2	FACETS	0.745	0.695	0.796	0.745	0.695	0.796	SUBCLONAL	1	TRUE	1	0.75	2		1137	784	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384014	84384015	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	90	511	0	ENST00000321945.7:c.837dup	p.Leu280SerfsTer13	p.L280Sfs*13	ENST00000321945	NM_139076.2	279	-/T	9/9	1	2	FACETS	0.485	0.432	0.541	0.485	0.432	0.541	SUBCLONAL	1	TRUE	1	0.75	2		511	495	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562756	21562756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs12867400	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	244	371	0	ENST00000382592.4:c.1163C>T	p.Ala388Val	p.A388V	ENST00000382592	NM_014572.2	388	gCg/gTg	4/8	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.75	2		371	582	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662527	227662527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1428460249	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	323	731	0	ENST00000305123.5:c.928G>A	p.Ala310Thr	p.A310T	ENST00000305123	NM_005544.2	310	Gcc/Acc	1/2	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.75	2		731	780	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88676897	88676897	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782682	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	182	591	0	ENST00000372037.3:c.682C>T	p.Arg228Ter	p.R228*	ENST00000372037	NM_004329.2	228	Cga/Tga	9/13	1	2	FACETS	0.635	0.587	0.685	0.635	0.587	0.685	SUBCLONAL	1	TRUE	1	0.75	2		591	764	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28882996	28882996	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867799392	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	188	483	0	ENST00000282397.4:c.3704C>T	p.Ala1235Val	p.A1235V	ENST00000282397	NM_002019.4	1235	gCc/gTc	28/30	1	2	FACETS	0.949	0.884	1	0.949	0.884	1	CLONAL	1	TRUE	1	0.75	2		483	528	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196144	108196144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879254132	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	168	504	0	ENST00000278616.4:c.6680G>A	p.Arg2227His	p.R2227H	ENST00000278616	NM_000051.3	2227	cGc/cAc	46/63	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.75	2		504	441	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6442013	6442013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	107	255	0	ENST00000356142.4:c.572C>T	p.Ala191Val	p.A191V	ENST00000356142	NM_018890.3	191	gCg/gTg	7/7	1	2	FACETS	0.715	0.646	0.787	0.715	0.646	0.787	SUBCLONAL	1	TRUE	1	0.75	2		255	399	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911607	134911607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1384145752	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	204	535	0	ENST00000398015.3:c.2072G>A	p.Arg691Gln	p.R691Q	ENST00000398015	NM_004441.4	691	cGg/cAg	11/16	1	2	FACETS	0.963	0.9	1	0.963	0.9	1	CLONAL	1	TRUE	1	0.75	2		535	565	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28595739	28595739	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1038449460	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	199	798	0	ENST00000253063.3:c.136G>A	p.Ala46Thr	p.A46T	ENST00000253063	NM_031459.4	46	Gcc/Acc	2/10	1	2	FACETS	0.618	0.574	0.665	0.618	0.574	0.665	SUBCLONAL	1	TRUE	1	0.75	2		798	858	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610306	10610306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	161	1018	0	ENST00000171111.5:c.404G>A	p.Arg135His	p.R135H	ENST00000171111	NM_203500.1	135	cGc/cAc	2/6	1	2	FACETS	0.349	0.319	0.38	0.349	0.319	0.38	SUBCLONAL	1	TRUE	1	0.75	2		1018	1230	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78422338	78422338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1244295456	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	191	366	0	ENST00000370768.2:c.1624G>A	p.Ala542Thr	p.A542T	ENST00000370768	NM_003902.3	542	Gct/Act	17/20	1	2	FACETS	0.981	0.915	1	0.981	0.915	1	CLONAL	1	TRUE	1	0.75	2		366	519	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644567	3644567	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115866745	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	103	851	0	ENST00000294008.3:c.2047G>A	p.Ala683Thr	p.A683T	ENST00000294008	NM_032444.2	683	Gcc/Acc	10/15	1	2	FACETS	0.289	0.258	0.323	0.289	0.258	0.323	SUBCLONAL	1	TRUE	1	0.75	2		851	949	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518270	8518270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556357771	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	99	375	1	ENST00000356435.5:c.1121C>T	p.Ala374Val	p.A374V	ENST00000356435		374	gCg/gTg	10/35	1	2	FACETS	0.66	0.593	0.73	0.66	0.593	0.73	SUBCLONAL	1	TRUE	1	0.75	2		376	400	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543671	148543671	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1333628386	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	46	316	0	ENST00000320356.2:c.137G>A	p.Arg46His	p.R46H	ENST00000320356	NM_004456.4	46	cGt/cAt	3/20	1	2	FACETS	0.302	0.255	0.354	0.302	0.255	0.354	SUBCLONAL	1	TRUE	1	0.75	2		316	406	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996765	73996765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558691012	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	67	379	0	ENST00000318443.5:c.1321C>T	p.Arg441Cys	p.R441C	ENST00000318443	NM_001024736.1	441	Cgc/Tgc	6/10	1	2	FACETS	0.383	0.334	0.437	0.383	0.334	0.437	SUBCLONAL	1	TRUE	1	0.75	2		379	466	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451194	70451194	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1202179982	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	213	696	1	ENST00000373644.4:c.6034G>A	p.Ala2012Thr	p.A2012T	ENST00000373644	NM_030625.2	2012	Gca/Aca	12/12	1	2	FACETS	0.683	0.635	0.731	0.683	0.635	0.731	SUBCLONAL	1	TRUE	1	0.75	2		697	832	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1918645	1918645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372805518	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	190	412	0	ENST00000382891.5:c.808G>A	p.Ala270Thr	p.A270T	ENST00000382891	NM_133335.3	270	Gcc/Acc	4/22	1	2	FACETS	0.949	0.884	1	0.949	0.884	1	CLONAL	1	TRUE	1	0.75	2		412	534	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808246	99808246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776434815	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	107	567	0	ENST00000280892.6:c.443G>A	p.Arg148His	p.R148H	ENST00000280892	NM_001130678.1	148	cGc/cAc	5/7	1	2	FACETS	0.469	0.422	0.52	0.469	0.422	0.52	SUBCLONAL	1	TRUE	1	0.75	2		567	608	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403177	116403178	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	72	474	0	ENST00000397752.3:c.2443dup	p.Leu815ProfsTer18	p.L815Pfs*18	ENST00000397752	NM_000245.2	813	ctc/ctCc	11/21	1	2	FACETS	0.375	0.328	0.425	0.375	0.328	0.425	SUBCLONAL	1	TRUE	1	0.75	2		474	512	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63817039	63817039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1269760932	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	88	225	0	ENST00000279873.7:c.1010C>T	p.Thr337Met	p.T337M	ENST00000279873	NM_032199.2	337	aCg/aTg	6/10	1	2	FACETS	0.962	0.866	1	0.962	0.866	1	CLONAL	1	TRUE	1	0.75	2		225	244	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444528	187444528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1438511659	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	223	740	1	ENST00000232014.4:c.1699G>A	p.Val567Ile	p.V567I	ENST00000232014	NM_001130845.1	567	Gtc/Atc	7/10	0.299205930568942	3	FACETS	0.78	0.726	0.836	0.39	0.363	0.418	INDETERMINATE	1	TRUE	1	0.75	3		741	1048	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878749	151878749	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1211949081	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	136	429	0	ENST00000262189.6:c.6196C>T	p.Arg2066Ter	p.R2066*	ENST00000262189	NM_170606.2	2066	Cga/Tga	36/59	1	2	FACETS	0.682	0.623	0.743	0.682	0.623	0.743	SUBCLONAL	1	TRUE	1	0.75	2		429	532	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031691	69031691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748595305	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	41	406	2	ENST00000288368.4:c.3446G>A	p.Arg1149His	p.R1149H	ENST00000288368	NM_024870.2	1149	cGc/cAc	28/40	1	2	FACETS	0.246	0.204	0.291	0.246	0.204	0.291	SUBCLONAL	1	TRUE	1	0.75	2		408	445	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11022898	11022899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	290	895	0	ENST00000327064.4:c.603dup	p.Ala202CysfsTer22	p.A202Cfs*22	ENST00000327064	NM_199141.1	199	-/T	5/16	1	2	FACETS	0.671	0.631	0.712	0.671	0.631	0.712	SUBCLONAL	1	TRUE	1	0.75	2		895	1153	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784573	43784573	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	207	539	0	ENST00000382044.4:c.101G>A	p.Ser34Asn	p.S34N	ENST00000382044	NM_001141980.1	34	aGc/aAc	2/28	1	2	FACETS	0.97	0.907	1	0.97	0.907	1	CLONAL	1	TRUE	1	0.75	2		539	569	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038367	180038367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746879565	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	108	802	0	ENST00000261937.6:c.3650G>A	p.Ser1217Asn	p.S1217N	ENST00000261937	NM_182925.4	1217	aGc/aAc	27/30	1	2	FACETS	0.313	0.28	0.348	0.313	0.28	0.348	SUBCLONAL	1	TRUE	1	0.75	2		802	920	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123880918	123880918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148212570	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	64	371	0	ENST00000330479.4:c.536G>A	p.Arg179His	p.R179H	ENST00000330479	NM_020382.3	179	cGc/cAc	5/9	1	2	FACETS	0.345	0.299	0.395	0.345	0.299	0.395	SUBCLONAL	1	TRUE	1	0.75	2		371	494	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266963	41266963	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770795614	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	212	416	0	ENST00000349496.5:c.634C>T	p.Arg212Cys	p.R212C	ENST00000349496	NM_001904.3	212	Cgt/Tgt	5/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.75	2		416	541	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058423	42058423	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781780633	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	60	419	0	ENST00000219905.7:c.8143C>T	p.Pro2715Ser	p.P2715S	ENST00000219905	NM_001164273.1	2715	Cca/Tca	24/24	1	2	FACETS	0.331	0.286	0.381	0.331	0.286	0.381	SUBCLONAL	1	TRUE	1	0.75	2		419	483	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707969	43707969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140309161	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	145	859	0	ENST00000382044.4:c.4912G>A	p.Val1638Ile	p.V1638I	ENST00000382044	NM_001141980.1	1638	Gtc/Atc	23/28	1	2	FACETS	0.354	0.322	0.387	0.354	0.322	0.387	SUBCLONAL	1	TRUE	1	0.75	2		859	1093	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950000	44950000	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	43	411	0	ENST00000377967.4:c.3769G>A	p.Glu1257Lys	p.E1257K	ENST00000377967	NM_021140.2	1257	Gaa/Aaa	26/29	1	2	FACETS	0.295	0.247	0.348	0.295	0.247	0.348	SUBCLONAL	1	TRUE	1	0.75	2		411	389	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434810	49434810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1228231026	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	276	1081	3	ENST00000301067.7:c.6743G>A	p.Arg2248His	p.R2248H	ENST00000301067	NM_003482.3	2248	cGc/cAc	31/54	1	2	FACETS	0.607	0.57	0.646	0.607	0.57	0.646	SUBCLONAL	1	TRUE	1	0.75	2		1084	1212	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828111	3828111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	190	618	0	ENST00000262367.5:c.2014C>T	p.Arg672Cys	p.R672C	ENST00000262367	NM_004380.2	672	Cgt/Tgt	10/31	1	2	FACETS	0.611	0.566	0.658	0.611	0.566	0.658	SUBCLONAL	1	TRUE	1	0.75	2		618	829	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591092	67591092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554051268	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	105	229	1	ENST00000274335.5:c.1685G>A	p.Arg562His	p.R562H	ENST00000274335		562	cGt/cAt	12/15	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.75	2		230	280	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106846	27106846	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781033223	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	196	701	2	ENST00000324856.7:c.6457C>T	p.Arg2153Cys	p.R2153C	ENST00000324856	NM_006015.4	2153	Cgc/Tgc	20/20	1	2	FACETS	0.618	0.573	0.665	0.618	0.573	0.665	SUBCLONAL	1	TRUE	1	0.75	2		703	846	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053141	180053141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs907068772	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	97	934	0	ENST00000261937.6:c.1228C>T	p.Arg410Cys	p.R410C	ENST00000261937	NM_182925.4	410	Cgc/Tgc	9/30	1	2	FACETS	0.303	0.269	0.338	0.303	0.269	0.338	SUBCLONAL	1	TRUE	1	0.75	2		934	855	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493456	56493456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781502670	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	113	453	0	ENST00000267101.3:c.2864G>A	p.Arg955His	p.R955H	ENST00000267101	NM_001982.3	955	cGc/cAc	24/28	1	2	FACETS	0.553	0.499	0.609	0.553	0.499	0.609	SUBCLONAL	1	TRUE	1	0.75	2		453	545	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219168	133219168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753713315	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	205	885	0	ENST00000320574.5:c.4876C>T	p.Arg1626Cys	p.R1626C	ENST00000320574	NM_006231.2	1626	Cgc/Tgc	37/49	1	2	FACETS	0.575	0.534	0.619	0.575	0.534	0.619	SUBCLONAL	1	TRUE	1	0.75	2		885	950	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31504712	31504712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369576938	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	242	503	0	ENST00000344624.3:c.1618G>A	p.Ala540Thr	p.A540T	ENST00000344624		540	Gca/Aca	8/33	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.75	2		503	585	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522563	176522563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777277309	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	356	880	1	ENST00000292408.4:c.1660G>A	p.Ala554Thr	p.A554T	ENST00000292408	NM_213647.1	554	Gcc/Acc	13/18	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.75	2		881	911	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388073	31388073	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	49	283	0	ENST00000328111.2:c.1874T>C	p.Val625Ala	p.V625A	ENST00000328111	NM_006892.3	625	gTg/gCg	17/23	1	2	FACETS	0.381	0.324	0.443	0.381	0.324	0.443	SUBCLONAL	1	TRUE	1	0.75	2		283	343	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312915	30312915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1411284279	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	146	582	0	ENST00000262643.3:c.718C>T	p.Arg240Cys	p.R240C	ENST00000262643	NM_001238.2	240	Cgt/Tgt	9/12	1	2	FACETS	0.688	0.631	0.747	0.688	0.631	0.747	SUBCLONAL	1	TRUE	1	0.75	2		582	566	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648329	206648329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55721947	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	97	678	0	ENST00000367120.3:c.350G>A	p.Arg117His	p.R117H	ENST00000367120	NM_014002.3	117	cGc/cAc	5/22	1	2	FACETS	0.336	0.299	0.376	0.336	0.299	0.376	SUBCLONAL	1	TRUE	1	0.75	2		678	769	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993366	72993366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140855443	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	317	1008	2	ENST00000268489.5:c.679G>A	p.Val227Ile	p.V227I	ENST00000268489	NM_006885.3	227	Gtc/Atc	2/10	1	2	FACETS	0.703	0.663	0.744	0.703	0.663	0.744	SUBCLONAL	1	TRUE	1	0.75	2		1010	1202	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101119	41101119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755381090	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	120	782	1	ENST00000373198.4:c.1237G>A	p.Ala413Thr	p.A413T	ENST00000373198	NM_133170.3	413	Gcg/Acg	8/32	1	2	FACETS	0.357	0.322	0.394	0.357	0.322	0.394	SUBCLONAL	1	TRUE	1	0.75	2		783	896	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528952	157528952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263114512	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	237	513	0	ENST00000346085.5:c.6677C>T	p.Ser2226Leu	p.S2226L	ENST00000346085	NM_020732.3	2226	tCg/tTg	20/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.75	2		513	605	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685289	89685289	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554897267	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	15	220	0	ENST00000371953.3:c.188del	p.Asn63ThrfsTer36	p.N63Tfs*36	ENST00000371953	NM_000314.4	62	Aaa/aa	3/9	1	2	FACETS	0.146	0.106	0.194	0.146	0.106	0.194	SUBCLONAL	1	TRUE	1	0.75	2		220	274	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806605	1806605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17884368	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	260	968	1	ENST00000260795.2:c.1321G>A	p.Ala441Thr	p.A441T	ENST00000260795		441	Gca/Aca	9/17	1	2	FACETS	0.667	0.625	0.711	0.667	0.625	0.711	SUBCLONAL	1	TRUE	1	0.75	2		969	1039	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100464	2100464	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767626323	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	66	462	1	ENST00000219476.3:c.202G>A	p.Ala68Thr	p.A68T	ENST00000219476	NM_000548.3	68	Gca/Aca	3/42	1	2	FACETS	0.3	0.26	0.343	0.3	0.26	0.343	SUBCLONAL	1	TRUE	1	0.75	2		463	586	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942624	71942624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	69	683	0	ENST00000298229.2:c.1580C>T	p.Thr527Met	p.T527M	ENST00000298229	NM_001567.3	527	aCg/aTg	13/28	1	2	FACETS	0.231	0.201	0.265	0.231	0.201	0.265	SUBCLONAL	1	TRUE	1	0.75	2		683	795	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574157	46574157	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	226	727	1	ENST00000263734.3:c.172C>T	p.Arg58Ter	p.R58*	ENST00000263734	NM_001430.4	58	Cga/Tga	2/16	1	2	FACETS	0.666	0.621	0.712	0.666	0.621	0.712	SUBCLONAL	1	TRUE	1	0.75	2		728	905	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021181	31021181	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs534065676	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	82	673	0	ENST00000375687.4:c.1180C>T	p.Arg394Cys	p.R394C	ENST00000375687	NM_015338.5	394	Cgt/Tgt	12/13	1	2	FACETS	0.314	0.276	0.354	0.314	0.276	0.354	SUBCLONAL	1	TRUE	1	0.75	2		673	697	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806600	1806600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529493162	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	140	934	1	ENST00000260795.2:c.1316G>A	p.Arg439His	p.R439H	ENST00000260795		439	cGc/cAc	9/17	1	2	FACETS	0.357	0.324	0.391	0.357	0.324	0.391	SUBCLONAL	1	TRUE	1	0.75	2		935	1046	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916205	9916205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555491654	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	216	465	0	ENST00000330684.3:c.2084G>A	p.Arg695Gln	p.R695Q	ENST00000330684	NM_001134407.1	695	cGg/cAg	10/13	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.75	2		465	556	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562441	21562441	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1176877473	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	163	390	0	ENST00000382592.4:c.1478C>T	p.Ala493Val	p.A493V	ENST00000382592	NM_014572.2	493	gCg/gTg	4/8	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.75	2		390	420	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106847	27106847	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747780610	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	215	705	2	ENST00000324856.7:c.6458G>A	p.Arg2153His	p.R2153H	ENST00000324856	NM_006015.4	2153	cGc/cAc	20/20	1	2	FACETS	0.675	0.628	0.723	0.675	0.628	0.723	SUBCLONAL	1	TRUE	1	0.75	2		707	850	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352037	89352037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138353708	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	435	799	2	ENST00000301030.4:c.913G>A	p.Ala305Thr	p.A305T	ENST00000301030	NM_001256183.1	305	Gca/Aca	9/13	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.75	2		801	1039	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793517	42793517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560617801	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	259	870	0	ENST00000575354.2:c.1319G>A	p.Arg440His	p.R440H	ENST00000575354	NM_015125.3	440	cGc/cAc	8/20	1	2	FACETS	0.695	0.651	0.74	0.695	0.651	0.74	SUBCLONAL	1	TRUE	1	0.75	2		870	994	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640689	3640689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750906921	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	121	891	0	ENST00000294008.3:c.2950G>A	p.Glu984Lys	p.E984K	ENST00000294008	NM_032444.2	984	Gaa/Aaa	12/15	1	2	FACETS	0.311	0.28	0.344	0.311	0.28	0.344	SUBCLONAL	1	TRUE	1	0.75	2		891	1037	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439742	220439742	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257387062	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	176	1138	1	ENST00000243786.2:c.595C>T	p.Arg199Cys	p.R199C	ENST00000243786	NM_002191.3	199	Cgc/Tgc	2/2	1	2	FACETS	0.371	0.34	0.402	0.371	0.34	0.402	SUBCLONAL	1	TRUE	1	0.75	2		1139	1266	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040892	42040892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463241547	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	79	567	0	ENST00000219905.7:c.5270G>A	p.Arg1757His	p.R1757H	ENST00000219905	NM_001164273.1	1757	cGt/cAt	16/24	1	2	FACETS	0.303	0.266	0.342	0.303	0.266	0.342	SUBCLONAL	1	TRUE	1	0.75	2		567	696	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828787	3828787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1013334018	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	91	570	0	ENST00000262367.5:c.1855G>A	p.Ala619Thr	p.A619T	ENST00000262367	NM_004380.2	619	Gca/Aca	9/31	1	2	FACETS	0.36	0.319	0.403	0.36	0.319	0.403	SUBCLONAL	1	TRUE	1	0.75	2		570	675	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884286	37884286	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs36085723	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	43	455	0	ENST00000269571.5:c.3757G>A	p.Val1253Met	p.V1253M	ENST00000269571		1253	Gtg/Atg	27/27	1	2	FACETS	0.144	0.12	0.172	0.144	0.12	0.172	SUBCLONAL	1	TRUE	1	0.75	2		455	794	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332824	65332824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773295622	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	125	357	1	ENST00000342505.4:c.715C>T	p.Arg239Trp	p.R239W	ENST00000342505	NM_002227.2	239	Cgg/Tgg	7/25	1	2	FACETS	0.98	0.899	1	0.98	0.899	1	CLONAL	1	TRUE	1	0.75	2		358	340	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259759	16259759	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	79	574	0	ENST00000375759.3:c.7024C>T	p.Arg2342Ter	p.R2342*	ENST00000375759	NM_015001.2	2342	Cga/Tga	11/15	0.24244378673329	3	FACETS	0.47	0.414	0.531			1	INDETERMINATE	1	TRUE	NA	0.75	3		574	616	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870501	40870501	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768296055	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	69	567	0	ENST00000428826.2:c.902G>A	p.Arg301His	p.R301H	ENST00000428826		301	cGc/cAc	9/21	1	2	FACETS	0.241	0.21	0.276	0.241	0.21	0.276	SUBCLONAL	1	TRUE	1	0.75	2		567	762	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135804187	135804187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1230244328	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	74	472	0	ENST00000298552.3:c.73G>A	p.Val25Met	p.V25M	ENST00000298552	NM_001162426.1	25	Gtg/Atg	3/23	1	2	FACETS	0.361	0.316	0.409	0.361	0.316	0.409	SUBCLONAL	1	TRUE	1	0.75	2		472	547	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656769	45656769	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	111	625	0	ENST00000407780.3:c.387G>T	p.Glu129Asp	p.E129D	ENST00000407780	NM_001283052.1	129	gaG/gaT	3/7	1	2	FACETS	0.377	0.339	0.418	0.377	0.339	0.418	SUBCLONAL	1	TRUE	1	0.75	2		625	785	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187719	11187719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767904339	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	280	656	2	ENST00000361445.4:c.6178C>T	p.Arg2060Trp	p.R2060W	ENST00000361445	NM_004958.3	2060	Cgg/Tgg	44/58	1	2	FACETS	0.957	0.903	1	0.957	0.903	1	CLONAL	1	TRUE	1	0.75	2		658	780	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118668	11118668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	108	716	0	ENST00000358026.2:c.2092G>A	p.Val698Ile	p.V698I	ENST00000358026	NM_001128849.1	698	Gtc/Atc	14/36	1	2	FACETS	0.33	0.295	0.366	0.33	0.295	0.366	SUBCLONAL	1	TRUE	1	0.75	2		716	873	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023430	31023430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	226	534	1	ENST00000375687.4:c.2915G>A	p.Gly972Asp	p.G972D	ENST00000375687	NM_015338.5	972	gGc/gAc	13/13	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.75	2		535	590	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627983	37627983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375471633	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	356	783	1	ENST00000249071.6:c.277G>A	p.Val93Ile	p.V93I	ENST00000249071	NM_002872.4	93	Gtc/Atc	4/7	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.75	2		784	942	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224792	123224792	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs777611309	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	53	431	0	ENST00000218089.9:c.3556C>T	p.Arg1186Ter	p.R1186*	ENST00000218089	NM_001042749.1	1186	Cga/Tga	32/35	1	2	FACETS	0.288	0.246	0.335	0.288	0.246	0.335	SUBCLONAL	1	TRUE	1	0.75	2		431	490	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136840	69136840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746734356	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	163	353	2	ENST00000288368.4:c.4754G>A	p.Arg1585Gln	p.R1585Q	ENST00000288368	NM_024870.2	1585	cGg/cAg	39/40	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.75	2		355	433	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457360	67457360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770798158	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	202	718	0	ENST00000327367.4:c.334G>A	p.Ala112Thr	p.A112T	ENST00000327367	NM_005902.3	112	Gcc/Acc	2/9	1	2	FACETS	0.634	0.589	0.682	0.634	0.589	0.682	SUBCLONAL	1	TRUE	1	0.75	2		718	849	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803663	1803663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	133	853	1	ENST00000260795.2:c.841G>A	p.Ala281Thr	p.A281T	ENST00000260795		281	Gca/Aca	6/17	1	2	FACETS	0.331	0.3	0.364	0.331	0.3	0.364	SUBCLONAL	1	TRUE	1	0.75	2		854	1071	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28607255	28607255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs988053889	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	257	576	0	ENST00000253063.3:c.1385C>T	p.Ala462Val	p.A462V	ENST00000253063	NM_031459.4	462	gCg/gTg	10/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.75	2		576	660	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652273	3652273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543071212	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	108	701	0	ENST00000294008.3:c.796G>A	p.Ala266Thr	p.A266T	ENST00000294008	NM_032444.2	266	Gct/Act	4/15	1	2	FACETS	0.342	0.306	0.379	0.342	0.306	0.379	SUBCLONAL	1	TRUE	1	0.75	2		701	843	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943658	9943658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	136	702	0	ENST00000330684.3:c.1283C>T	p.Thr428Met	p.T428M	ENST00000330684	NM_001134407.1	428	aCg/aTg	5/13	1	2	FACETS	0.457	0.416	0.501	0.457	0.416	0.501	SUBCLONAL	1	TRUE	1	0.75	2		702	793	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409061	139409061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561126575	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	481	1035	2	ENST00000277541.6:c.2108G>A	p.Arg703His	p.R703H	ENST00000277541	NM_017617.3	703	cGc/cAc	13/34	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.75	2		1037	1156	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843551	3843551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763070109	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	262	485	0	ENST00000262367.5:c.1052G>A	p.Arg351His	p.R351H	ENST00000262367	NM_004380.2	351	cGc/cAc	4/31	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.75	2		485	650	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600363	10600363	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	145	900	0	ENST00000171111.5:c.1492C>T	p.Arg498Ter	p.R498*	ENST00000171111	NM_203500.1	498	Cga/Tga	4/6	1	2	FACETS	0.355	0.323	0.389	0.355	0.323	0.389	SUBCLONAL	1	TRUE	1	0.75	2		900	1088	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466773	25466773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1431156021	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	73	633	0	ENST00000264709.3:c.1930G>A	p.Ala644Thr	p.A644T	ENST00000264709	NM_175629.2	644	Gct/Act	16/23	1	2	FACETS	0.285	0.249	0.325	0.285	0.249	0.325	SUBCLONAL	1	TRUE	1	0.75	2		633	682	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142908	7142908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471585411	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	718	783	1	ENST00000302850.5:c.2461G>A	p.Glu821Lys	p.E821K	ENST00000302850	NM_000208.2	821	Gag/Aag	12/22	1	2	FACETS	1	0.996	1	1	0.998	1	CLONAL	2	TRUE	1	0.75	2		784	897	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161310401	161310401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760572684	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	181	391	0	ENST00000367975.2:c.197C>T	p.Ala66Val	p.A66V	ENST00000367975	NM_003001.3	66	gCg/gTg	4/6	1	2	FACETS	0.914	0.85	0.98	0.914	0.85	0.98	CLONAL	1	TRUE	1	0.75	2		391	528	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996182	73996182	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776412054	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	134	917	1	ENST00000318443.5:c.916G>A	p.Ala306Thr	p.A306T	ENST00000318443	NM_001024736.1	306	Gcc/Acc	5/10	1	2	FACETS	0.338	0.307	0.372	0.338	0.307	0.372	SUBCLONAL	1	TRUE	1	0.75	2		918	1056	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459723	40459723	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	364	600	1	ENST00000345506.4:c.1888G>A	p.Ala630Thr	p.A630T	ENST00000345506	NM_003152.3	630	Gcc/Acc	16/20	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.75	2		601	823	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631207	176631207	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759976291	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	72	465	0	ENST00000439151.2:c.1150G>A	p.Val384Ile	p.V384I	ENST00000439151	NM_022455.4	384	Gtc/Atc	4/23	1	2	FACETS	0.31	0.271	0.353	0.31	0.271	0.353	SUBCLONAL	1	TRUE	1	0.75	2		465	619	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965451	68965451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	228	631	0	ENST00000288368.4:c.1063G>A	p.Ala355Thr	p.A355T	ENST00000288368	NM_024870.2	355	Gct/Act	9/40	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.75	2		631	602	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006078	22006078	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	108	727	1	ENST00000276925.6:c.325C>T	p.Arg109Cys	p.R109C	ENST00000276925	NM_004936.3	109	Cgc/Tgc	2/2	1	2	FACETS	0.309	0.276	0.343	0.309	0.276	0.343	SUBCLONAL	1	TRUE	1	0.75	2		728	933	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335545	73335546	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	115	334	0	ENST00000377767.4:c.2625dup	p.Glu876Ter	p.E876*	ENST00000377767	NM_014953.3	875	-/T	19/21	1	2	FACETS	0.921	0.84	1	0.921	0.84	1	CLONAL	1	TRUE	1	0.75	2		334	333	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161372	2161372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	69	498	0	ENST00000434045.2:c.155C>T	p.Ala52Val	p.A52V	ENST00000434045	NM_001127598.1	52	gCc/gTc	2/5	1	2	FACETS	0.327	0.285	0.372	0.327	0.285	0.372	SUBCLONAL	1	TRUE	1	0.75	2		498	563	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149242	119149242	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	117	623	0	ENST00000264033.4:c.1250C>A	p.Pro417His	p.P417H	ENST00000264033	NM_005188.3	417	cCt/cAt	9/16	1	2	FACETS	0.446	0.402	0.492	0.446	0.402	0.492	SUBCLONAL	1	TRUE	1	0.75	2		623	700	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906627	32906627	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358396	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	124	362	0	ENST00000380152.3:c.1012G>A	p.Ala338Thr	p.A338T	ENST00000380152		338	Gct/Act	10/27	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.75	2		362	325	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933583	39933583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778095	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	312	795	0	ENST00000378444.4:c.1016C>T	p.Pro339Leu	p.P339L	ENST00000378444	NM_001123385.1	339	cCg/cTg	4/15	1	2	FACETS	0.931	0.881	0.982	0.931	0.881	0.982	CLONAL	1	TRUE	1	0.75	2		795	894	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50916701	50916701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878854532	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	189	618	0	ENST00000440232.2:c.2173C>T	p.Arg725Cys	p.R725C	ENST00000440232	NM_002691.3	725	Cgt/Tgt	18/27	1	2	FACETS	0.738	0.685	0.793	0.738	0.685	0.793	SUBCLONAL	1	TRUE	1	0.75	2		618	683	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128268655	128268655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370425781	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	380	796	0	ENST00000265960.3:c.1000G>A	p.Ala334Thr	p.A334T	ENST00000265960	NM_001006617.1	334	Gcc/Acc	8/12	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.75	2		796	979	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298605	11298605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	109	631	0	ENST00000361445.4:c.1856G>A	p.Arg619His	p.R619H	ENST00000361445	NM_004958.3	619	cGc/cAc	12/58	1	2	FACETS	0.391	0.351	0.433	0.391	0.351	0.433	SUBCLONAL	1	TRUE	1	0.75	2		631	744	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176719015	176719015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1321310131	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	47	319	0	ENST00000439151.2:c.6319C>T	p.Arg2107Cys	p.R2107C	ENST00000439151	NM_022455.4	2107	Cgc/Tgc	22/23	1	2	FACETS	0.314	0.265	0.368	0.314	0.265	0.368	SUBCLONAL	1	TRUE	1	0.75	2		319	399	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940370	49940370	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs891415020	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	281	936	0	ENST00000296474.3:c.673G>A	p.Ala225Thr	p.A225T	ENST00000296474	NM_002447.2	225	Gcc/Acc	1/20	1	2	FACETS	0.702	0.66	0.746	0.702	0.66	0.746	SUBCLONAL	1	TRUE	1	0.75	2		936	1067	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348031	348031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765982081	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	413	1067	0	ENST00000262320.3:c.1475G>A	p.Arg492His	p.R492H	ENST00000262320	NM_003502.3	492	cGc/cAc	6/11	1	2	FACETS	0.983	0.938	1	0.983	0.938	1	CLONAL	1	TRUE	1	0.75	2		1067	1120	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629102	86629102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	23	234	2	ENST00000274376.6:c.847C>T	p.Arg283Cys	p.R283C	ENST00000274376	NM_002890.2	283	Cgt/Tgt	4/25	1	2	FACETS	0.246	0.192	0.308	0.246	0.192	0.308	SUBCLONAL	1	TRUE	1	0.75	2		236	249	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849143	156849143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775191394	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	393	822	0	ENST00000524377.1:c.2035G>A	p.Asp679Asn	p.D679N	ENST00000524377	NM_002529.3	679	Gac/Aac	15/17	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.75	2		822	1005	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198851	67198851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373631670	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	141	429	0	ENST00000312629.5:c.322C>T	p.Arg108Cys	p.R108C	ENST00000312629	NM_003952.2	108	Cgc/Tgc	5/15	1	2	FACETS	0.657	0.601	0.715	0.657	0.601	0.715	SUBCLONAL	1	TRUE	1	0.75	2		429	572	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963091	38963091	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	91	294	1	ENST00000357387.3:c.1453C>T	p.Arg485Ter	p.R485*	ENST00000357387	NM_152756.3	485	Cga/Tga	17/38	1	2	FACETS	0.902	0.813	0.995	0.902	0.813	0.995	CLONAL	1	TRUE	1	0.75	2		295	269	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257359	16257359	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	236	515	2	ENST00000375759.3:c.4624C>T	p.Arg1542Ter	p.R1542*	ENST00000375759	NM_015001.2	1542	Cga/Tga	11/15	0.24244378673329	3	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.75	3		517	587	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226574028	226574028	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs201777393	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	71	371	0	ENST00000366794.5:c.833C>T	p.Ala278Val	p.A278V	ENST00000366794	NM_001618.3	278	gCg/gTg	6/23	1	2	FACETS	0.379	0.331	0.43	0.379	0.331	0.43	SUBCLONAL	1	TRUE	1	0.75	2		371	500	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156674	2156674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1356855570	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	276	872	0	ENST00000434045.2:c.248G>A	p.Arg83His	p.R83H	ENST00000434045	NM_001127598.1	83	cGc/cAc	3/5	1	2	FACETS	0.765	0.719	0.812	0.765	0.719	0.812	SUBCLONAL	1	TRUE	1	0.75	2		872	962	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490599	20490599	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749949370	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	154	534	1	ENST00000346618.3:c.1336G>A	p.Asp446Asn	p.D446N	ENST00000346618	NM_001949.4	446	Gat/Aat	7/7	1	2	FACETS	0.61	0.56	0.663	0.61	0.56	0.663	SUBCLONAL	1	TRUE	1	0.75	2		535	673	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276860	15276861	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	83	811	0	ENST00000263388.2:c.5403_5404dup	p.Ala1802GlyfsTer24	p.A1802Gfs*24	ENST00000263388	NM_000435.2	1802	gct/gGGct	30/33	1	2	FACETS	0.264	0.232	0.298	0.264	0.232	0.298	SUBCLONAL	1	TRUE	1	0.75	2		811	839	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052653	42052653	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	79	447	0	ENST00000219905.7:c.7324C>A	p.Leu2442Ile	p.L2442I	ENST00000219905	NM_001164273.1	2442	Ctc/Atc	20/24	1	2	FACETS	0.33	0.29	0.373	0.33	0.29	0.373	SUBCLONAL	1	TRUE	1	0.75	2		447	639	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916875	178916875	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	210	558	0	ENST00000263967.3:c.262C>T	p.Arg88Ter	p.R88*	ENST00000263967	NM_006218.2	88	Cga/Tga	2/21	0.299205930568942	3	FACETS	1	0.983	1	0.579	0.54	0.619	INDETERMINATE	1	TRUE	1	0.75	3		558	665	SUCCESS
AR	367	MSKCC	GRCh37	X	66943633	66943633	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	158	604	1	ENST00000374690.3:c.2713C>T	p.Pro905Ser	p.P905S	ENST00000374690	NM_000044.3	905	Ccc/Tcc	8/8	1	2	FACETS	0.592	0.543	0.642	0.592	0.543	0.642	SUBCLONAL	1	TRUE	1	0.75	2		605	712	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104356918	104356918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775245784	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	96	641	0	ENST00000369902.3:c.778G>A	p.Glu260Lys	p.E260K	ENST00000369902	NM_016169.3	260	Gag/Aag	7/12	1	2	FACETS	0.335	0.298	0.374	0.335	0.298	0.374	SUBCLONAL	1	TRUE	1	0.75	2		641	764	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90970987	90970987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765403660	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	99	368	0	ENST00000265433.3:c.1090G>A	p.Val364Ile	p.V364I	ENST00000265433	NM_002485.4	364	Gta/Ata	9/16	1	2	FACETS	0.642	0.577	0.711	0.642	0.577	0.711	SUBCLONAL	1	TRUE	1	0.75	2		368	411	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928960	49928960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766187988	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	120	864	0	ENST00000296474.3:c.3406C>T	p.Arg1136Cys	p.R1136C	ENST00000296474	NM_002447.2	1136	Cgt/Tgt	16/20	1	2	FACETS	0.367	0.33	0.405	0.367	0.33	0.405	SUBCLONAL	1	TRUE	1	0.75	2		864	873	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36823932	36823932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs945529881	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	341	763	1	ENST00000373129.3:c.250C>T	p.Arg84Trp	p.R84W	ENST00000373129	NM_032017.1	84	Cgg/Tgg	5/12	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.75	2		764	870	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178617	56178617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763984353	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	42	242	0	ENST00000399503.3:c.3590C>T	p.Ala1197Val	p.A1197V	ENST00000399503	NM_005921.1	1197	gCg/gTg	14/20	1	2	FACETS	0.368	0.309	0.434	0.368	0.309	0.434	SUBCLONAL	1	TRUE	1	0.75	2		242	304	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277972	18277972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1193898416	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	206	602	0	ENST00000222254.8:c.1592G>A	p.Arg531His	p.R531H	ENST00000222254	NM_005027.3	531	cGc/cAc	13/16	1	2	FACETS	0.685	0.637	0.735	0.685	0.637	0.735	SUBCLONAL	1	TRUE	1	0.75	2		602	802	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053237	180053237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372947534	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	290	902	1	ENST00000261937.6:c.1132C>T	p.Arg378Cys	p.R378C	ENST00000261937	NM_182925.4	378	Cgc/Tgc	9/30	1	2	FACETS	0.802	0.756	0.85	0.802	0.756	0.85	CLONAL	1	TRUE	1	0.75	2		903	964	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187221	38187222	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	225	790	1	ENST00000317025.8:c.1255dup	p.Thr419AsnfsTer28	p.T419Nfs*28	ENST00000317025	NM_023034.1	419	acc/aAcc	6/24	1	2	FACETS	0.571	0.531	0.612	0.571	0.531	0.612	SUBCLONAL	1	TRUE	1	0.75	2		791	1051	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343121	118343121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	72	312	0	ENST00000534358.1:c.1247C>T	p.Ala416Val	p.A416V	ENST00000534358	NM_005933.3	416	gCt/gTt	3/36	1	2	FACETS	0.553	0.487	0.624	0.553	0.487	0.624	SUBCLONAL	1	TRUE	1	0.75	2		312	347	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118339535	118339535	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555034779	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	193	438	0	ENST00000534358.1:c.478C>T	p.Arg160Ter	p.R160*	ENST00000534358	NM_005933.3	160	Cga/Tga	2/36	1	2	FACETS	0.926	0.862	0.99	0.926	0.862	0.99	CLONAL	1	TRUE	1	0.75	2		438	556	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598362	28598362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770770051	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	357	746	0	ENST00000253063.3:c.334C>T	p.Arg112Cys	p.R112C	ENST00000253063	NM_031459.4	112	Cgc/Tgc	3/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.75	2		746	936	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76931740	76931740	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782344877	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	40	350	1	ENST00000373344.5:c.3790G>A	p.Asp1264Asn	p.D1264N	ENST00000373344	NM_000489.3	1264	Gac/Aac	10/35	1	2	FACETS	0.256	0.212	0.304	0.256	0.212	0.304	SUBCLONAL	1	TRUE	1	0.75	2		351	417	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99812388	99812388	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	85	354	0	ENST00000280892.6:c.281C>T	p.Ala94Val	p.A94V	ENST00000280892	NM_001130678.1	94	gCt/gTt	3/7	1	2	FACETS	0.549	0.488	0.614	0.549	0.488	0.614	SUBCLONAL	1	TRUE	1	0.75	2		354	413	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390123	89390123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355784567	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	56	314	0	ENST00000336596.2:c.872C>T	p.Pro291Leu	p.P291L	ENST00000336596	NM_005233.5	291	cCg/cTg	4/17	1	2	FACETS	0.365	0.313	0.421	0.365	0.313	0.421	SUBCLONAL	1	TRUE	1	0.75	2		314	409	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845389	89845389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769158149	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	127	688	0	ENST00000389301.3:c.1738G>A	p.Val580Met	p.V580M	ENST00000389301	NM_000135.2	580	Gtg/Atg	19/43	1	2	FACETS	0.374	0.338	0.412	0.374	0.338	0.412	SUBCLONAL	1	TRUE	1	0.75	2		688	905	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034983	42034983	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs200022330	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	153	723	0	ENST00000219905.7:c.4825A>G	p.Thr1609Ala	p.T1609A	ENST00000219905	NM_001164273.1	1609	Act/Gct	15/24	1	2	FACETS	0.596	0.546	0.647	0.596	0.546	0.647	SUBCLONAL	1	TRUE	1	0.75	2		723	685	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499063	149499063	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767216776	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	164	677	3	ENST00000261799.4:c.2765G>A	p.Arg922His	p.R922H	ENST00000261799	NM_002609.3	922	cGc/cAc	20/23	1	2	FACETS	0.597	0.55	0.647	0.597	0.55	0.647	SUBCLONAL	1	TRUE	1	0.75	2		680	732	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363268	40363268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201425251	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	94	633	0	ENST00000397332.2:c.961C>T	p.Arg321Cys	p.R321C	ENST00000397332	NM_001033082.2	321	Cgc/Tgc	3/3	1	2	FACETS	0.334	0.297	0.373	0.334	0.297	0.373	SUBCLONAL	1	TRUE	1	0.75	2		633	751	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058651	42058651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	73	251	0	ENST00000219905.7:c.8371G>A	p.Glu2791Lys	p.E2791K	ENST00000219905	NM_001164273.1	2791	Gaa/Aaa	24/24	1	2	FACETS	0.798	0.707	0.892	0.798	0.707	0.892	SUBCLONAL	1	TRUE	1	0.75	2		251	244	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172091	99172091	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776893699	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	311	616	1	ENST00000074304.5:c.1657C>T	p.Arg553Trp	p.R553W	ENST00000074304	NM_001134224.1	553	Cgg/Tgg	17/26	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.75	2		617	723	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514688	103514688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	168	398	0	ENST00000355739.4:c.1189G>A	p.Asp397Asn	p.D397N	ENST00000355739	NM_000123.3	397	Gat/Aat	8/15	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.75	2		398	444	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342656	87342656	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763671078	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	65	550	2	ENST00000277120.3:c.941C>T	p.Ala314Val	p.A314V	ENST00000277120		314	gCg/gTg	9/19	1	2	FACETS	0.27	0.234	0.309	0.27	0.234	0.309	SUBCLONAL	1	TRUE	1	0.75	2		552	642	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325825	65325825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375122732	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	72	532	0	ENST00000342505.4:c.1297G>A	p.Val433Ile	p.V433I	ENST00000342505	NM_002227.2	433	Gtc/Atc	9/25	1	2	FACETS	0.297	0.259	0.338	0.297	0.259	0.338	SUBCLONAL	1	TRUE	1	0.75	2		532	647	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911648	39911648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752359195	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	77	515	0	ENST00000378444.4:c.4982G>A	p.Arg1661Gln	p.R1661Q	ENST00000378444	NM_001123385.1	1661	cGa/cAa	15/15	1	2	FACETS	0.352	0.309	0.398	0.352	0.309	0.398	SUBCLONAL	1	TRUE	1	0.75	2		515	584	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103374	119103374	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	60	358	0	ENST00000264033.4:c.412G>T	p.Glu138Ter	p.E138*	ENST00000264033	NM_005188.3	138	Gaa/Taa	2/16	1	2	FACETS	0.497	0.431	0.568	0.497	0.431	0.568	SUBCLONAL	1	TRUE	1	0.75	2		358	322	SUCCESS
APC	324	MSKCC	GRCh37	5	112116551	112116551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748193367	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	106	284	1	ENST00000257430.4:c.596C>T	p.Ala199Val	p.A199V	ENST00000257430	NM_000038.5	199	gCg/gTg	6/16	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.75	2		285	280	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228415	228415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745309710	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	89	454	1	ENST00000264932.6:c.737G>A	p.Arg246His	p.R246H	ENST00000264932	NM_004168.2	246	cGc/cAc	6/15	1	2	FACETS	0.48	0.427	0.537	0.48	0.427	0.537	SUBCLONAL	1	TRUE	1	0.75	2		455	494	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369291	40369291	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	161	613	1	ENST00000293328.3:c.1267C>T	p.Arg423Ter	p.R423*	ENST00000293328	NM_012448.3	423	Cga/Tga	11/19	1	2	FACETS	0.68	0.626	0.736	0.68	0.626	0.736	SUBCLONAL	1	TRUE	1	0.75	2		614	631	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846280	156846280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs554180226	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	126	912	0	ENST00000524377.1:c.1721G>A	p.Arg574His	p.R574H	ENST00000524377	NM_002529.3	574	cGc/cAc	14/17	1	2	FACETS	0.31	0.28	0.342	0.31	0.28	0.342	SUBCLONAL	1	TRUE	1	0.75	2		912	1085	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335064	65335064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	145	511	1	ENST00000342505.4:c.577G>A	p.Ala193Thr	p.A193T	ENST00000342505	NM_002227.2	193	Gct/Act	6/25	1	2	FACETS	0.592	0.542	0.645	0.592	0.542	0.645	SUBCLONAL	1	TRUE	1	0.75	2		512	653	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664390	29664390	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	33	336	1	ENST00000356175.3:c.6369G>T	p.Glu2123Asp	p.E2123D	ENST00000356175	NM_000267.3	2123	gaG/gaT	42/57	1	2	FACETS	0.221	0.18	0.268	0.221	0.18	0.268	SUBCLONAL	1	TRUE	1	0.75	2		337	398	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926512	59926512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61757643	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	73	555	0	ENST00000259008.2:c.485G>A	p.Arg162Gln	p.R162Q	ENST00000259008	NM_032043.2	162	cGa/cAa	5/20	1	2	FACETS	0.375	0.328	0.425	0.375	0.328	0.425	SUBCLONAL	1	TRUE	1	0.75	2		555	519	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852392	63852392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1300866874	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	214	675	0	ENST00000279873.7:c.3170C>T	p.Ala1057Val	p.A1057V	ENST00000279873	NM_032199.2	1057	gCg/gTg	10/10	1	2	FACETS	0.64	0.595	0.686	0.64	0.595	0.686	SUBCLONAL	1	TRUE	1	0.75	2		675	892	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185223	123185223	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	54	417	0	ENST00000218089.9:c.1175A>C	p.Lys392Thr	p.K392T	ENST00000218089	NM_001042749.1	392	aAa/aCa	13/35	1	2	FACETS	0.37	0.317	0.428	0.37	0.317	0.428	SUBCLONAL	1	TRUE	1	0.75	2		417	389	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169985777	169985777	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	71	465	0	ENST00000295797.4:c.439C>T	p.Arg147Cys	p.R147C	ENST00000295797	NM_002740.5	147	Cgt/Tgt	5/18	0.299205930568942	3	FACETS	0.382	0.333	0.435	0.191	0.166	0.218	INDETERMINATE	1	TRUE	1	0.75	3		465	681	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515148	148515148	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775942317	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	82	467	0	ENST00000320356.2:c.1061G>A	p.Arg354His	p.R354H	ENST00000320356	NM_004456.4	354	cGt/cAt	10/20	1	2	FACETS	0.382	0.337	0.43	0.382	0.337	0.43	SUBCLONAL	1	TRUE	1	0.75	2		467	573	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855837	45855837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762141272	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	130	924	2	ENST00000391945.4:c.1973G>A	p.Arg658His	p.R658H	ENST00000391945	NM_000400.3	658	cGc/cAc	21/23	1	2	FACETS	0.318	0.288	0.35	0.318	0.288	0.35	SUBCLONAL	1	TRUE	1	0.75	2		926	1090	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223334	2223334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757410464	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	391	828	0	ENST00000326181.6:c.946C>T	p.Arg316Cys	p.R316C	ENST00000326181	NM_032271.2	316	Cgc/Tgc	10/21	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.75	2		828	954	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762911	40762911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	337	789	1	ENST00000392038.2:c.97G>A	p.Gly33Ser	p.G33S	ENST00000392038	NM_001626.4	33	Ggc/Agc	3/14	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.75	2		790	897	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448521	49448521	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761525910	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	90	636	1	ENST00000301067.7:c.190C>T	p.Arg64Trp	p.R64W	ENST00000301067	NM_003482.3	64	Cgg/Tgg	3/54	1	2	FACETS	0.302	0.267	0.338	0.302	0.267	0.338	SUBCLONAL	1	TRUE	1	0.75	2		637	796	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288457	21288457	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	156	621	1	ENST00000354336.3:c.702G>T	p.Gln234His	p.Q234H	ENST00000354336	NM_005207.3	234	caG/caT	2/3	1	2	FACETS	0.576	0.529	0.626	0.576	0.529	0.626	SUBCLONAL	1	TRUE	1	0.75	2		622	722	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980527	1980527	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	251	868	0	ENST00000382891.5:c.3989C>A	p.Ala1330Glu	p.A1330E	ENST00000382891	NM_133335.3	1330	gCg/gAg	22/22	1	2	FACETS	0.62	0.58	0.662	0.62	0.58	0.662	SUBCLONAL	1	TRUE	1	0.75	2		868	1079	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981316	68981316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756231722	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	18	273	0	ENST00000288368.4:c.1388G>A	p.Arg463His	p.R463H	ENST00000288368	NM_024870.2	463	cGc/cAc	12/40	1	2	FACETS	0.152	0.114	0.197	0.152	0.114	0.197	SUBCLONAL	1	TRUE	1	0.75	2		273	315	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873100	134873100	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	84	534	0	ENST00000398015.3:c.1404G>T	p.Glu468Asp	p.E468D	ENST00000398015	NM_004441.4	468	gaG/gaT	6/16	1	2	FACETS	0.326	0.287	0.367	0.326	0.287	0.367	SUBCLONAL	1	TRUE	1	0.75	2		534	688	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679558	86679558	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561328441	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	134	375	0	ENST00000274376.6:c.2719C>T	p.Pro907Ser	p.P907S	ENST00000274376	NM_002890.2	907	Cct/Tct	21/25	1	2	FACETS	0.923	0.848	1	0.923	0.848	1	CLONAL	1	TRUE	1	0.75	2		375	387	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186813	142186813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	31	271	0	ENST00000350721.4:c.6650G>A	p.Arg2217His	p.R2217H	ENST00000350721	NM_001184.3	2217	cGc/cAc	39/47	1	2	FACETS	0.356	0.29	0.431	0.356	0.29	0.431	SUBCLONAL	1	TRUE	1	0.75	2		271	232	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313383	30313383	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	75	649	0	ENST00000262643.3:c.983T>C	p.Val328Ala	p.V328A	ENST00000262643	NM_001238.2	328	gTc/gCc	11/12	1	2	FACETS	0.258	0.226	0.294	0.258	0.226	0.294	SUBCLONAL	1	TRUE	1	0.75	2		649	774	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152067	11152067	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374722116	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	168	571	1	ENST00000358026.2:c.4351G>A	p.Ala1451Thr	p.A1451T	ENST00000358026	NM_001128849.1	1451	Gcc/Acc	31/36	1	2	FACETS	0.643	0.592	0.695	0.643	0.592	0.695	SUBCLONAL	1	TRUE	1	0.75	2		572	697	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385240	41385240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	302	716	0	ENST00000373198.4:c.721C>T	p.Arg241Cys	p.R241C	ENST00000373198	NM_133170.3	241	Cgt/Tgt	6/32	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.75	2		716	762	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217233	11217233	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190665412	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	297	624	1	ENST00000361445.4:c.4445G>A	p.Arg1482His	p.R1482H	ENST00000361445	NM_004958.3	1482	cGc/cAc	30/58	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.75	2		625	730	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662818	227662818	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	241	863	1	ENST00000305123.5:c.637C>T	p.Arg213Cys	p.R213C	ENST00000305123	NM_005544.2	213	Cgc/Tgc	1/2	1	2	FACETS	0.682	0.638	0.728	0.682	0.638	0.728	SUBCLONAL	1	TRUE	1	0.75	2		864	942	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073683	8073683	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	246	466	0	ENST00000377482.5:c.976T>G	p.Ser326Ala	p.S326A	ENST00000377482	NM_018948.3	326	Tca/Gca	4/4	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.75	2		466	590	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184640	11184640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	154	489	1	ENST00000361445.4:c.6577C>T	p.Arg2193Cys	p.R2193C	ENST00000361445	NM_004958.3	2193	Cgc/Tgc	47/58	1	2	FACETS	0.642	0.589	0.696	0.642	0.589	0.696	SUBCLONAL	1	TRUE	1	0.75	2		490	640	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189858	11189858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	99	602	1	ENST00000361445.4:c.5651C>T	p.Ala1884Val	p.A1884V	ENST00000361445	NM_004958.3	1884	gCc/gTc	40/58	1	2	FACETS	0.366	0.326	0.408	0.366	0.326	0.408	SUBCLONAL	1	TRUE	1	0.75	2		603	722	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245500	16245500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	143	348	1	ENST00000375759.3:c.1475C>T	p.Ala492Val	p.A492V	ENST00000375759	NM_015001.2	492	gCt/gTt	7/15	0.24244378673329	3	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.75	3		349	354	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254897	16254897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777199627	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	68	546	0	ENST00000375759.3:c.2162C>T	p.Pro721Leu	p.P721L	ENST00000375759	NM_015001.2	721	cCg/cTg	11/15	0.24244378673329	3	FACETS	0.38	0.33	0.434			1	INDETERMINATE	1	TRUE	NA	0.75	3		546	656	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255169	16255170	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	203	403	0	ENST00000375759.3:c.2439dup	p.Val814SerfsTer7	p.V814Sfs*7	ENST00000375759	NM_015001.2	812	gaa/gAaa	11/15	0.24244378673329	3	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.75	3		403	506	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263794	16263794	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	112	717	0	ENST00000375759.3:c.10163T>C	p.Val3388Ala	p.V3388A	ENST00000375759	NM_015001.2	3388	gTg/gCg	12/15	0.24244378673329	3	FACETS	0.489	0.44	0.542			1	INDETERMINATE	1	TRUE	NA	0.75	3		717	839	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089737	27089737	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	109	714	0	ENST00000324856.7:c.2693C>A	p.Ala898Asp	p.A898D	ENST00000324856	NM_006015.4	898	gCt/gAt	8/20	1	2	FACETS	0.389	0.349	0.431	0.389	0.349	0.431	SUBCLONAL	1	TRUE	1	0.75	2		714	748	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937172	36937172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769827020	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	121	897	1	ENST00000361632.4:c.1147G>A	p.Ala383Thr	p.A383T	ENST00000361632		383	Gcc/Acc	9/16	1	2	FACETS	0.29	0.261	0.32	0.29	0.261	0.32	SUBCLONAL	1	TRUE	1	0.75	2		898	1114	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363241	40363241	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1218116984	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	189	626	0	ENST00000397332.2:c.988C>T	p.Arg330Ter	p.R330*	ENST00000397332	NM_001033082.2	330	Cga/Tga	3/3	1	2	FACETS	0.687	0.636	0.739	0.687	0.636	0.739	SUBCLONAL	1	TRUE	1	0.75	2		626	734	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818431	43818431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	181	614	0	ENST00000372470.3:c.1896G>A	p.Trp632Ter	p.W632*	ENST00000372470	NM_005373.2	632	tgG/tgA	12/12	1	2	FACETS	0.652	0.603	0.703	0.652	0.603	0.703	SUBCLONAL	1	TRUE	1	0.75	2		614	740	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797382	45797382	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	120	880	0	ENST00000450313.1:c.1137G>T	p.Gln379His	p.Q379H	ENST00000450313	NM_012222.2	379	caG/caT	12/16	1	2	FACETS	0.335	0.302	0.37	0.335	0.302	0.37	SUBCLONAL	1	TRUE	1	0.75	2		880	956	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521582	46521582	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775105727	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	207	414	0	ENST00000262741.5:c.826C>T	p.Arg276Cys	p.R276C	ENST00000262741	NM_003629.3	276	Cgt/Tgt	7/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.75	2		414	504	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726526	46726526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761573792	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	237	535	0	ENST00000371975.4:c.605G>A	p.Arg202His	p.R202H	ENST00000371975	NM_003579.3	202	cGc/cAc	7/18	1	2	FACETS	0.991	0.931	1	0.991	0.931	1	CLONAL	1	TRUE	1	0.75	2		535	638	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326493	161326493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	267	524	2	ENST00000367975.2:c.268C>A	p.Leu90Met	p.L90M	ENST00000367975	NM_003001.3	90	Ctg/Atg	5/6	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.75	2		526	668	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725496	162725496	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	73	535	1	ENST00000367921.3:c.608T>C	p.Val203Ala	p.V203A	ENST00000367921	NM_006182.2	203	gTa/gCa	7/18	1	2	FACETS	0.295	0.258	0.336	0.295	0.258	0.336	SUBCLONAL	1	TRUE	1	0.75	2		536	659	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163297320	163297320	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	163	392	0	ENST00000271452.3:c.166G>A	p.Val56Ile	p.V56I	ENST00000271452	NM_145697.2	56	Gta/Ata	3/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.75	2		392	380	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317616	163317616	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	13	289	0	ENST00000271452.3:c.1012G>A	p.Glu338Lys	p.E338K	ENST00000271452	NM_145697.2	338	Gaa/Aaa	12/14	1	2	FACETS	0.145	0.103	0.196	0.145	0.103	0.196	SUBCLONAL	1	TRUE	1	0.75	2		289	239	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332931	70332931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	92	662	0	ENST00000373644.4:c.836C>T	p.Ser279Phe	p.S279F	ENST00000373644	NM_030625.2	279	tCt/tTt	2/12	1	2	FACETS	0.328	0.291	0.367	0.328	0.291	0.367	SUBCLONAL	1	TRUE	1	0.75	2		662	748	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333986	70333986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	79	267	0	ENST00000373644.4:c.1891C>T	p.Pro631Ser	p.P631S	ENST00000373644	NM_030625.2	631	Cca/Tca	2/12	1	2	FACETS	0.665	0.59	0.743	0.665	0.59	0.743	SUBCLONAL	1	TRUE	1	0.75	2		267	317	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717754	89717754	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	54	354	0	ENST00000371953.3:c.779A>C	p.Lys260Thr	p.K260T	ENST00000371953	NM_000314.4	260	aAa/aCa	7/9	1	2	FACETS	0.378	0.324	0.437	0.378	0.324	0.437	SUBCLONAL	1	TRUE	1	0.75	2		354	381	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720650	89720650	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	rs587776672	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	32	439	0	ENST00000371953.3:c.802del		p.X268_splice	ENST00000371953	NM_000314.4	268			1	2	FACETS	0.185	0.15	0.225	0.185	0.15	0.225	SUBCLONAL	1	TRUE	1	0.75	2		439	461	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925507	114925507	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	121	854	0	ENST00000543371.1:c.1585C>A	p.Leu529Met	p.L529M	ENST00000543371	NM_001198531.1	529	Ctg/Atg	14/14	1	2	FACETS	0.314	0.283	0.348	0.314	0.283	0.348	SUBCLONAL	1	TRUE	1	0.75	2		854	1026	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154281	2154281	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	398	951	0	ENST00000434045.2:c.647C>A	p.Ala216Asp	p.A216D	ENST00000434045	NM_001127598.1	216	gCt/gAt	5/5	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.75	2		951	979	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200474	67200474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	409	808	0	ENST00000312629.5:c.668G>A	p.Gly223Asp	p.G223D	ENST00000312629	NM_003952.2	223	gGc/gAc	8/15	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.75	2		808	934	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202072	67202072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372739497	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	419	948	0	ENST00000312629.5:c.1175C>T	p.Pro392Leu	p.P392L	ENST00000312629	NM_003952.2	392	cCg/cTg	14/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.75	2		948	1053	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518093	69518093	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	247	914	0	ENST00000294312.3:c.272C>T	p.Ala91Val	p.A91V	ENST00000294312	NM_005117.2	91	gCc/gTc	2/3	1	2	FACETS	0.701	0.656	0.747	0.701	0.656	0.747	SUBCLONAL	1	TRUE	1	0.75	2		914	940	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948646	71948646	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	207	1049	0	ENST00000298229.2:c.3358T>C	p.Ser1120Pro	p.S1120P	ENST00000298229	NM_001567.3	1120	Tcc/Ccc	26/28	1	2	FACETS	0.579	0.537	0.622	0.579	0.537	0.622	SUBCLONAL	1	TRUE	1	0.75	2		1049	954	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103553	77103553	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1214886996	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	48	344	0	ENST00000356341.3:c.13G>A	p.Gly5Ser	p.G5S	ENST00000356341	NM_002576.4	5	Ggc/Agc	2/15	1	2	FACETS	0.344	0.291	0.402	0.344	0.291	0.402	SUBCLONAL	1	TRUE	1	0.75	2		344	372	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94224094	94224094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	17	247	0	ENST00000323929.3:c.58G>A	p.Asp20Asn	p.D20N	ENST00000323929	NM_005591.3	20	Gat/Aat	3/20	1	2	FACETS	0.172	0.128	0.224	0.172	0.128	0.224	SUBCLONAL	1	TRUE	1	0.75	2		247	264	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121507	108121507	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	188	408	0	ENST00000278616.4:c.1315C>A	p.Leu439Ile	p.L439I	ENST00000278616	NM_000051.3	439	Cta/Ata	10/63	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.75	2		408	479	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124551	108124552	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	67	252	0	ENST00000278616.4:c.1914dup	p.Asp639ArgfsTer2	p.D639Rfs*2	ENST00000278616	NM_000051.3	637	caa/cAaa	13/63	1	2	FACETS	0.907	0.803	1	0.907	0.803	1	CLONAL	1	TRUE	1	0.75	2		252	197	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235930	108235930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	81	352	1	ENST00000278616.4:c.8972G>A	p.Cys2991Tyr	p.C2991Y	ENST00000278616	NM_000051.3	2991	tGc/tAc	62/63	1	2	FACETS	0.576	0.511	0.645	0.576	0.511	0.645	SUBCLONAL	1	TRUE	1	0.75	2		353	375	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118368690	118368690	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	100	367	0	ENST00000534358.1:c.5704A>G	p.Thr1902Ala	p.T1902A	ENST00000534358	NM_005933.3	1902	Aca/Gca	21/36	1	2	FACETS	0.586	0.526	0.649	0.586	0.526	0.649	SUBCLONAL	1	TRUE	1	0.75	2		367	455	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374582	118374582	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	115	363	0	ENST00000534358.1:c.7975C>T	p.Arg2659Ter	p.R2659*	ENST00000534358	NM_005933.3	2659	Cga/Tga	27/36	1	2	FACETS	0.691	0.626	0.758	0.691	0.626	0.758	SUBCLONAL	1	TRUE	1	0.75	2		363	444	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155686	119155686	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	127	477	0	ENST00000264033.4:c.1439G>A	p.Arg480Gln	p.R480Q	ENST00000264033	NM_005188.3	480	cGg/cAg	10/16	1	2	FACETS	0.628	0.572	0.687	0.628	0.572	0.687	SUBCLONAL	1	TRUE	1	0.75	2		477	539	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125513750	125513750	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	193	455	0	ENST00000428830.2:c.878A>G	p.His293Arg	p.H293R	ENST00000428830	NM_001114121.2	293	cAc/cGc	9/14	1	2	FACETS	0.994	0.927	1	0.994	0.927	1	CLONAL	1	TRUE	1	0.75	2		455	518	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534717	18534717	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	166	422	0	ENST00000266497.5:c.1775C>A	p.Ser592Tyr	p.S592Y	ENST00000266497		592	tCt/tAt	12/31	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.75	2		422	440	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793409	18793409	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	140	418	0	ENST00000266497.5:c.4106T>G	p.Leu1369Arg	p.L1369R	ENST00000266497		1369	cTt/cGt	30/31	1	2	FACETS	0.96	0.884	1	0.96	0.884	1	CLONAL	1	TRUE	1	0.75	2		418	389	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644488	21644488	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	176	521	0	ENST00000421138.2:c.179A>C	p.Glu60Ala	p.E60A	ENST00000421138		60	gAa/gCa	4/16	1	2	FACETS	0.984	0.915	1	0.984	0.915	1	CLONAL	1	TRUE	1	0.75	2		521	477	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205284	46205284	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	52	406	0	ENST00000334344.6:c.368C>A	p.Pro123His	p.P123H	ENST00000334344	NM_152641.2	123	cCt/cAt	4/21	1	2	FACETS	0.315	0.268	0.366	0.315	0.268	0.366	SUBCLONAL	1	TRUE	1	0.75	2		406	440	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244538	46244538	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs765780561	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	121	510	0	ENST00000334344.6:c.2632G>T	p.Val878Phe	p.V878F	ENST00000334344	NM_152641.2	878	Gtt/Ttt	15/21	1	2	FACETS	0.554	0.502	0.609	0.554	0.502	0.609	SUBCLONAL	1	TRUE	1	0.75	2		510	582	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446470	49446470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168216865	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	130	609	0	ENST00000301067.7:c.1135G>A	p.Asp379Asn	p.D379N	ENST00000301067	NM_003482.3	379	Gat/Aat	9/54	1	2	FACETS	0.566	0.514	0.619	0.566	0.514	0.619	SUBCLONAL	1	TRUE	1	0.75	2		609	613	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489570	56489570	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1377374701	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	73	524	0	ENST00000267101.3:c.2035C>T	p.Arg679Ter	p.R679*	ENST00000267101	NM_001982.3	679	Cga/Tga	17/28	1	2	FACETS	0.327	0.286	0.371	0.327	0.286	0.371	SUBCLONAL	1	TRUE	1	0.75	2		524	595	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856188	111856188	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	200	278	0	ENST00000341259.2:c.239G>A	p.Arg80His	p.R80H	ENST00000341259	NM_005475.2	80	cGc/cAc	2/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.75	2		278	469	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237682	133237682	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	321	807	0	ENST00000320574.5:c.2933A>G	p.Glu978Gly	p.E978G	ENST00000320574	NM_006231.2	978	gAa/gGa	25/49	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.75	2		807	844	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912891	32912891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793495	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	174	384	0	ENST00000380152.3:c.4399C>T	p.His1467Tyr	p.H1467Y	ENST00000380152		1467	Cat/Tat	11/27	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.75	2		384	384	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913873	32913873	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	144	468	0	ENST00000380152.3:c.5381T>C	p.Val1794Ala	p.V1794A	ENST00000380152		1794	gTa/gCa	11/27	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.75	2		468	362	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968994	32968995	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	131	361	0	ENST00000380152.3:c.9430dup	p.Ser3144PhefsTer6	p.S3144Ffs*6	ENST00000380152		3142	gat/gaTt	25/27	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.75	2		361	343	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336172	73336172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	71	231	0	ENST00000377767.4:c.2231C>T	p.Ala744Val	p.A744V	ENST00000377767	NM_014953.3	744	gCc/gTc	17/21	1	2	FACETS	0.664	0.586	0.747	0.664	0.586	0.747	SUBCLONAL	1	TRUE	1	0.75	2		231	285	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347910	73347910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375756603	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	39	248	0	ENST00000377767.4:c.1151G>A	p.Arg384His	p.R384H	ENST00000377767	NM_014953.3	384	cGc/cAc	8/21	1	2	FACETS	0.397	0.331	0.47	0.397	0.331	0.47	SUBCLONAL	1	TRUE	1	0.75	2		248	262	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434833	110434833	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	124	1243	3	ENST00000375856.3:c.3568G>A	p.Val1190Met	p.V1190M	ENST00000375856	NM_003749.2	1190	Gtg/Atg	1/2	1	2	FACETS	0.336	0.303	0.37	0.336	0.303	0.37	SUBCLONAL	1	TRUE	1	0.75	2		1246	985	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571526	95571526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	97	449	0	ENST00000393063.1:c.3151G>A	p.Ala1051Thr	p.A1051T	ENST00000393063	NM_030621.3	1051	Gct/Act	21/28	1	2	FACETS	0.501	0.448	0.557	0.501	0.448	0.557	SUBCLONAL	1	TRUE	1	0.75	2		449	516	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246425	105246425	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	173	663	0	ENST00000349310.3:c.175C>T	p.Gln59Ter	p.Q59*	ENST00000349310	NM_001014432.1	59	Cag/Tag	4/15	1	2	FACETS	0.645	0.595	0.697	0.645	0.595	0.697	SUBCLONAL	1	TRUE	1	0.75	2		663	715	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023147	33023147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	106	593	0	ENST00000300177.4:c.256C>T	p.Arg86Cys	p.R86C	ENST00000300177	NM_001191322.1	86	Cgc/Tgc	2/2	1	2	FACETS	0.407	0.365	0.452	0.407	0.365	0.452	SUBCLONAL	1	TRUE	1	0.75	2		593	694	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358379	91358379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139115275	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	88	586	0	ENST00000355112.3:c.4124G>A	p.Ser1375Asn	p.S1375N	ENST00000355112	NM_000057.2	1375	aGc/aAc	22/22	1	2	FACETS	0.39	0.346	0.437	0.39	0.346	0.437	SUBCLONAL	1	TRUE	1	0.75	2		586	602	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454592	99454592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761469469	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	93	556	1	ENST00000268035.6:c.1511G>A	p.Arg504His	p.R504H	ENST00000268035	NM_000875.3	504	cGc/cAc	7/21	1	2	FACETS	0.328	0.292	0.368	0.328	0.292	0.368	SUBCLONAL	1	TRUE	1	0.75	2		557	755	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454657	99454657	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs750559250	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	138	487	0	ENST00000268035.6:c.1576T>C	p.Tyr526His	p.Y526H	ENST00000268035	NM_000875.3	526	Tac/Cac	7/21	1	2	FACETS	0.607	0.554	0.662	0.607	0.554	0.662	SUBCLONAL	1	TRUE	1	0.75	2		487	606	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347744	347744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771607500	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	375	999	1	ENST00000262320.3:c.1762G>A	p.Ala588Thr	p.A588T	ENST00000262320	NM_003502.3	588	Gcc/Acc	6/11	1	2	FACETS	0.991	0.943	1	0.991	0.943	1	CLONAL	1	TRUE	1	0.75	2		1000	1009	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647734	2647734	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148008907	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	39	652	1	ENST00000342085.4:c.1637G>A	p.Arg546Gln	p.R546Q	ENST00000342085	NM_002613.4	546	cGa/cAa	14/14	1	2	FACETS	0.146	0.121	0.175	0.146	0.121	0.175	SUBCLONAL	1	TRUE	1	0.75	2		653	710	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639300	3639300	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371090786	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	481	985	1	ENST00000294008.3:c.4339G>A	p.Gly1447Ser	p.G1447S	ENST00000294008	NM_032444.2	1447	Ggc/Agc	12/15	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.75	2		986	1126	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790490	3790490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1207183178	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	314	673	0	ENST00000262367.5:c.4043G>A	p.Arg1348His	p.R1348H	ENST00000262367	NM_004380.2	1348	cGc/cAc	24/31	1	2	FACETS	0.943	0.892	0.994	0.943	0.892	0.994	CLONAL	1	TRUE	1	0.75	2		673	888	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026109	14026109	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	91	277	0	ENST00000311895.7:c.1069A>C	p.Ile357Leu	p.I357L	ENST00000311895	NM_005236.2	357	Ata/Cta	6/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.75	2		277	224	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645178	67645178	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	310	598	0	ENST00000264010.4:c.443C>T	p.Ala148Val	p.A148V	ENST00000264010	NM_006565.3	148	gCg/gTg	3/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.75	2		598	777	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842741	68842741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555515292	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	98	416	0	ENST00000261769.5:c.677C>T	p.Ala226Val	p.A226V	ENST00000261769	NM_004360.3	226	gCc/gTc	5/16	1	2	FACETS	0.508	0.455	0.565	0.508	0.455	0.565	SUBCLONAL	1	TRUE	1	0.75	2		416	514	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821664	72821664	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	69	216	0	ENST00000268489.5:c.10511T>C	p.Val3504Ala	p.V3504A	ENST00000268489	NM_006885.3	3504	gTc/gCc	10/10	1	2	FACETS	0.84	0.743	0.941	0.84	0.743	0.941	CLONAL	1	TRUE	1	0.75	2		216	219	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991553	72991553	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	228	733	0	ENST00000268489.5:c.2492A>G	p.Asn831Ser	p.N831S	ENST00000268489	NM_006885.3	831	aAc/aGc	2/10	1	2	FACETS	0.615	0.573	0.658	0.615	0.573	0.658	SUBCLONAL	1	TRUE	1	0.75	2		733	989	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992403	72992403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	309	995	0	ENST00000268489.5:c.1642G>A	p.Ala548Thr	p.A548T	ENST00000268489	NM_006885.3	548	Gct/Act	2/10	1	2	FACETS	0.688	0.648	0.728	0.688	0.648	0.728	SUBCLONAL	1	TRUE	1	0.75	2		995	1198	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216092	7216092	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	185	460	0	ENST00000380728.2:c.967C>T	p.Arg323Ter	p.R323*	ENST00000380728		323	Cga/Tga	11/11	1	2	FACETS	0.917	0.853	0.982	0.917	0.853	0.982	CLONAL	1	TRUE	1	0.75	2		460	538	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984435	7984435	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	114	822	0	ENST00000319144.4:c.423G>T	p.Gln141His	p.Q141H	ENST00000319144	NM_001139.2	141	caG/caT	3/15	1	2	FACETS	0.326	0.293	0.361	0.326	0.293	0.361	SUBCLONAL	1	TRUE	1	0.75	2		822	933	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684056	29684056	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	241	528	0	ENST00000356175.3:c.7754A>G	p.Asp2585Gly	p.D2585G	ENST00000356175	NM_000267.3	2585	gAt/gGt	52/57	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.75	2		528	626	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428309	33428309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458813748	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	108	646	0	ENST00000345365.6:c.814C>T	p.Pro272Ser	p.P272S	ENST00000345365	NM_002878.3	272	Ccc/Tcc	9/10	1	2	FACETS	0.334	0.3	0.372	0.334	0.3	0.372	SUBCLONAL	1	TRUE	1	0.75	2		646	861	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649125	37649125	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	120	294	0	ENST00000447079.4:c.2230G>T	p.Ala744Ser	p.A744S	ENST00000447079	NM_015083.1	744	Gcc/Tcc	4/14	1	2	FACETS	0.958	0.876	1	0.958	0.876	1	CLONAL	1	TRUE	1	0.75	2		294	334	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682248	37682248	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	157	670	0	ENST00000447079.4:c.3439C>T	p.Gln1147Ter	p.Q1147*	ENST00000447079	NM_015083.1	1147	Cag/Tag	13/14	1	2	FACETS	0.574	0.527	0.624	0.574	0.527	0.624	SUBCLONAL	1	TRUE	1	0.75	2		670	729	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699306	47699306	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	133	291	0	ENST00000347630.2:c.200+2T>G		p.X67_splice	ENST00000347630	NM_001007230.1	67			1	2	FACETS	0.977	0.898	1	0.977	0.898	1	CLONAL	1	TRUE	1	0.75	2		291	363	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526179	63526179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755508971	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	58	585	1	ENST00000307078.5:c.2447C>T	p.Ala816Val	p.A816V	ENST00000307078	NM_004655.3	816	gCg/gTg	11/11	1	2	FACETS	0.182	0.155	0.211	0.182	0.155	0.211	SUBCLONAL	1	TRUE	1	0.75	2		586	851	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66525032	66525032	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303569195	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	74	269	0	ENST00000358598.2:c.791G>A	p.Arg264His	p.R264H	ENST00000358598	NM_212471.2	264	cGt/cAt	9/11	1	2	FACETS	0.544	0.479	0.612	0.544	0.479	0.612	SUBCLONAL	1	TRUE	1	0.75	2		269	363	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796992	78796992	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144071963	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	293	564	0	ENST00000306801.3:c.1105C>T	p.Arg369Cys	p.R369C	ENST00000306801	NM_020761.2	369	Cgt/Tgt	9/34	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.75	2		564	682	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78865606	78865606	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	138	567	0	ENST00000306801.3:c.2070G>T	p.Lys690Asn	p.K690N	ENST00000306801	NM_020761.2	690	aaG/aaT	18/34	1	2	FACETS	0.606	0.553	0.661	0.606	0.553	0.661	SUBCLONAL	1	TRUE	1	0.75	2		567	607	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867522	78867522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770546124	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	286	664	1	ENST00000306801.3:c.2258C>T	p.Ala753Val	p.A753V	ENST00000306801	NM_020761.2	753	gCg/gTg	20/34	1	2	FACETS	0.961	0.907	1	0.961	0.907	1	CLONAL	1	TRUE	1	0.75	2		665	794	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348421	56348421	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	27	292	0	ENST00000348428.3:c.229T>G	p.Cys77Gly	p.C77G	ENST00000348428	NM_006785.3	77	Tgt/Ggt	2/17	1	2	FACETS	0.23	0.183	0.284	0.23	0.183	0.284	SUBCLONAL	1	TRUE	1	0.75	2		292	313	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615776	1615776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs182482393	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	237	815	1	ENST00000344749.5:c.1495C>T	p.Arg499Trp	p.R499W	ENST00000344749	NM_001136139.2	499	Cgg/Tgg	17/19	1	2	FACETS	0.678	0.633	0.724	0.678	0.633	0.724	SUBCLONAL	1	TRUE	1	0.75	2		816	932	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212441	5212441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	416	877	0	ENST00000357368.4:c.4676G>A	p.Gly1559Asp	p.G1559D	ENST00000357368	NM_002850.3	1559	gGc/gAc	31/38	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.75	2		877	1035	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267670	7267670	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913153	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	223	690	3	ENST00000302850.5:c.338G>A	p.Arg113Gln	p.R113Q	ENST00000302850	NM_000208.2	113	cGa/cAa	2/22	1	2	FACETS	0.685	0.639	0.733	0.685	0.639	0.733	SUBCLONAL	1	TRUE	1	0.75	2		693	868	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252729	10252729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	159	771	0	ENST00000340748.4:c.3236G>A	p.Gly1079Asp	p.G1079D	ENST00000340748		1079	gGc/gAc	29/40	1	2	FACETS	0.509	0.467	0.553	0.509	0.467	0.553	SUBCLONAL	1	TRUE	1	0.75	2		771	833	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291208	10291208	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	36	635	0	ENST00000340748.4:c.263A>C	p.Lys88Thr	p.K88T	ENST00000340748		88	aAa/aCa	4/40	1	2	FACETS	0.134	0.11	0.162	0.134	0.11	0.162	SUBCLONAL	1	TRUE	1	0.75	2		635	715	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602860	10602860	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1402273110	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1289	70	1079	1	ENST00000171111.5:c.718C>T	p.Arg240Cys	p.R240C	ENST00000171111	NM_203500.1	240	Cgc/Tgc	3/6	1	2	FACETS	0.137	0.119	0.158	0.137	0.119	0.158	SUBCLONAL	1	TRUE	1	0.75	2		1080	1359	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106947	11106947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	146	875	1	ENST00000358026.2:c.1652C>T	p.Ala551Val	p.A551V	ENST00000358026	NM_001128849.1	551	gCc/gTc	10/36	1	2	FACETS	0.376	0.342	0.411	0.376	0.342	0.411	SUBCLONAL	1	TRUE	1	0.75	2		876	1036	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144504	11144504	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1232715199	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	105	707	1	ENST00000358026.2:c.3836C>T	p.Ala1279Val	p.A1279V	ENST00000358026	NM_001128849.1	1279	gCg/gTg	27/36	1	2	FACETS	0.315	0.282	0.35	0.315	0.282	0.35	SUBCLONAL	1	TRUE	1	0.75	2		708	889	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169489	11169489	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	127	763	0	ENST00000358026.2:c.4655G>A	p.Arg1552His	p.R1552H	ENST00000358026	NM_001128849.1	1552	cGc/cAc	33/36	1	2	FACETS	0.375	0.339	0.412	0.375	0.339	0.412	SUBCLONAL	1	TRUE	1	0.75	2		763	904	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170727	11170727	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	251	842	0	ENST00000358026.2:c.4871C>T	p.Ser1624Phe	p.S1624F	ENST00000358026	NM_001128849.1	1624	tCc/tTc	35/36	1	2	FACETS	0.639	0.597	0.681	0.639	0.597	0.681	SUBCLONAL	1	TRUE	1	0.75	2		842	1048	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18960916	18960916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	127	669	0	ENST00000262803.5:c.494G>A	p.Cys165Tyr	p.C165Y	ENST00000262803	NM_002911.3	165	tGc/tAc	4/24	1	2	FACETS	0.384	0.348	0.423	0.384	0.348	0.423	SUBCLONAL	1	TRUE	1	0.75	2		669	881	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976208	18976208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	414	946	1	ENST00000262803.5:c.2968C>T	p.Pro990Ser	p.P990S	ENST00000262803	NM_002911.3	990	Cca/Tca	21/24	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.75	2		947	1092	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976247	18976247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1175515725	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	126	886	0	ENST00000262803.5:c.3007G>A	p.Gly1003Arg	p.G1003R	ENST00000262803	NM_002911.3	1003	Ggg/Agg	21/24	1	2	FACETS	0.353	0.319	0.388	0.353	0.319	0.388	SUBCLONAL	1	TRUE	1	0.75	2		886	953	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793541	42793541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1256145408	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	121	858	0	ENST00000575354.2:c.1343G>A	p.Gly448Glu	p.G448E	ENST00000575354	NM_015125.3	448	gGg/gAg	8/20	1	2	FACETS	0.308	0.278	0.341	0.308	0.278	0.341	SUBCLONAL	1	TRUE	1	0.75	2		858	1047	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794511	42794511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141023382	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	316	998	1	ENST00000575354.2:c.1591G>A	p.Ala531Thr	p.A531T	ENST00000575354	NM_015125.3	531	Gcc/Acc	10/20	1	2	FACETS	0.666	0.628	0.705	0.666	0.628	0.705	SUBCLONAL	1	TRUE	1	0.75	2		999	1265	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723002	52723002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	337	817	2	ENST00000322088.6:c.1187G>A	p.Gly396Asp	p.G396D	ENST00000322088	NM_014225.5	396	gGc/gAc	10/15	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.75	2		819	889	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468900	25468900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566390868	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	130	819	1	ENST00000264709.3:c.1463G>A	p.Arg488Gln	p.R488Q	ENST00000264709	NM_175629.2	488	cGg/cAg	12/23	1	2	FACETS	0.349	0.316	0.385	0.349	0.316	0.385	SUBCLONAL	1	TRUE	1	0.75	2		820	992	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605161	46605161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1445824525	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	189	727	1	ENST00000263734.3:c.1378C>T	p.Pro460Ser	p.P460S	ENST00000263734	NM_001430.4	460	Ccc/Tcc	10/16	1	2	FACETS	0.682	0.632	0.734	0.682	0.632	0.734	SUBCLONAL	1	TRUE	1	0.75	2		728	739	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606914	47606914	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	18	313	0	ENST00000263735.4:c.664G>T	p.Gly222Cys	p.G222C	ENST00000263735	NM_002354.2	222	Ggt/Tgt	7/9	1	2	FACETS	0.137	0.102	0.177	0.137	0.102	0.177	SUBCLONAL	1	TRUE	1	0.75	2		313	351	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99180038	99180038	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	75	764	0	ENST00000074304.5:c.1981G>A	p.Ala661Thr	p.A661T	ENST00000074304	NM_001134224.1	661	Gcg/Acg	19/26	1	2	FACETS	0.232	0.203	0.264	0.232	0.203	0.264	SUBCLONAL	1	TRUE	1	0.75	2		764	861	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193461	99193461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	344	801	0	ENST00000074304.5:c.2656C>T	p.Arg886Cys	p.R886C	ENST00000074304	NM_001134224.1	886	Cgc/Tgc	25/26	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.75	2		801	855	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622508	158622508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	80	487	0	ENST00000263640.3:c.991G>A	p.Ala331Thr	p.A331T	ENST00000263640	NM_001105.4	331	Gcc/Acc	8/11	1	2	FACETS	0.398	0.351	0.448	0.398	0.351	0.448	SUBCLONAL	1	TRUE	1	0.75	2		487	536	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400261	225400261	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	76	172	0	ENST00000264414.4:c.362A>G	p.Asp121Gly	p.D121G	ENST00000264414	NM_003590.4	121	gAc/gGc	3/16	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.75	2		172	180	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661896	227661896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	258	894	0	ENST00000305123.5:c.1559G>A	p.Arg520Gln	p.R520Q	ENST00000305123	NM_005544.2	520	cGg/cAg	1/2	1	2	FACETS	0.702	0.658	0.747	0.702	0.658	0.747	SUBCLONAL	1	TRUE	1	0.75	2		894	980	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661977	227661977	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	336	744	0	ENST00000305123.5:c.1478G>A	p.Arg493His	p.R493H	ENST00000305123	NM_005544.2	493	cGc/cAc	1/2	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.75	2		744	835	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31020763	31020763	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	47	257	0	ENST00000375687.4:c.1060T>G	p.Phe354Val	p.F354V	ENST00000375687	NM_015338.5	354	Ttc/Gtc	11/13	1	2	FACETS	0.432	0.367	0.503	0.432	0.367	0.503	SUBCLONAL	1	TRUE	1	0.75	2		257	290	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385056	31385056	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	84	738	0	ENST00000328111.2:c.1441T>C	p.Cys481Arg	p.C481R	ENST00000328111	NM_006892.3	481	Tgc/Cgc	14/23	1	2	FACETS	0.26	0.229	0.293	0.26	0.229	0.293	SUBCLONAL	1	TRUE	1	0.75	2		738	863	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262365	46262365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766234778	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	124	326	0	ENST00000371998.3:c.949C>T	p.Arg317Cys	p.R317C	ENST00000371998		317	Cgt/Tgt	9/23	1	2	FACETS	0.967	0.886	1	0.967	0.886	1	CLONAL	1	TRUE	1	0.75	2		326	342	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485795	57485795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137854537	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	73	428	0	ENST00000371085.3:c.1096G>A	p.Ala366Thr	p.A366T	ENST00000371085	NM_000516.4	366	Gct/Act	13/13	1	2	FACETS	0.339	0.297	0.385	0.339	0.297	0.385	SUBCLONAL	1	TRUE	1	0.75	2		428	574	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22123603	22123603	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554673521	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	56	414	0	ENST00000215832.6:c.973G>A	p.Ala325Thr	p.A325T	ENST00000215832	NM_002745.4	325	Gcc/Acc	8/9	1	2	FACETS	0.302	0.259	0.349	0.302	0.259	0.349	SUBCLONAL	1	TRUE	1	0.75	2		414	494	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29115416	29115416	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	80	381	0	ENST00000328354.6:c.650G>A	p.Arg217Lys	p.R217K	ENST00000328354	NM_007194.3	217	aGa/aAa	5/15	1	2	FACETS	0.513	0.454	0.576	0.513	0.454	0.576	SUBCLONAL	1	TRUE	1	0.75	2		381	416	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660217	12660217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	190	378	0	ENST00000251849.4:c.4G>A	p.Glu2Lys	p.E2K	ENST00000251849	NM_002880.3	2	Gag/Aag	2/17	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.75	2		378	466	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274839	41274839	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	138	312	0	ENST00000349496.5:c.1089G>A	p.Met363Ile	p.M363I	ENST00000349496	NM_001904.3	363	atG/atA	8/15	1	2	FACETS	0.989	0.911	1	0.989	0.911	1	CLONAL	1	TRUE	1	0.75	2		312	372	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158241	47158241	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	44	289	0	ENST00000409792.3:c.4458G>T	p.Lys1486Asn	p.K1486N	ENST00000409792	NM_014159.6	1486	aaG/aaT	4/21	1	2	FACETS	0.395	0.333	0.463	0.395	0.333	0.463	SUBCLONAL	1	TRUE	1	0.75	2		289	297	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164413	47164414	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	125	295	0	ENST00000409792.3:c.1712dup	p.Asn571LysfsTer10	p.N571Kfs*10	ENST00000409792	NM_014159.6	571	aat/aaAt	3/21	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.75	2		295	322	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164924	47164924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374918549	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	56	257	0	ENST00000409792.3:c.1202G>A	p.Arg401Gln	p.R401Q	ENST00000409792	NM_014159.6	401	cGg/cAg	3/21	1	2	FACETS	0.549	0.474	0.629	0.549	0.474	0.629	SUBCLONAL	1	TRUE	1	0.75	2		257	272	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49724695	49724695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	253	679	0	ENST00000449682.2:c.494G>A	p.Gly165Asp	p.G165D	ENST00000449682	NM_020998.3	165	gGc/gAc	5/18	1	2	FACETS	0.972	0.915	1	0.972	0.915	1	CLONAL	1	TRUE	1	0.75	2		679	694	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643362	52643362	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs774153419	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	142	396	0	ENST00000394830.3:c.2534T>C	p.Phe845Ser	p.F845S	ENST00000394830	NM_018313.4	845	tTt/tCt	17/30	1	2	FACETS	0.928	0.855	1	0.928	0.855	1	CLONAL	1	TRUE	1	0.75	2		396	408	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990397	69990397	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	90	250	0	ENST00000394351.3:c.356T>C	p.Val119Ala	p.V119A	ENST00000394351	NM_000248.3	119	gTa/gCa	4/9	1	2	FACETS	0.941	0.848	1	0.941	0.848	1	CLONAL	1	TRUE	1	0.75	2		250	255	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259196	89259196	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	181	376	0	ENST00000336596.2:c.340G>T	p.Gly114Ter	p.G114*	ENST00000336596	NM_005233.5	114	Gga/Tga	3/17	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.75	2		376	437	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138409875	138409875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1319089813	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	82	411	0	ENST00000289153.2:c.2003G>A	p.Arg668Gln	p.R668Q	ENST00000289153	NM_006219.2	668	cGg/cAg	13/22	1	2	FACETS	0.543	0.481	0.608	0.543	0.481	0.608	SUBCLONAL	1	TRUE	1	0.75	2		411	403	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453566	138453566	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	145	358	0	ENST00000289153.2:c.882A>C	p.Glu294Asp	p.E294D	ENST00000289153	NM_006219.2	294	gaA/gaC	5/22	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.75	2		358	359	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169991092	169991092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	79	318	0	ENST00000295797.4:c.610G>A	p.Asp204Asn	p.D204N	ENST00000295797	NM_002740.5	204	Gat/Aat	7/18	0.299205930568942	3	FACETS	0.54	0.476	0.609	0.27	0.238	0.305	INDETERMINATE	1	TRUE	1	0.75	3		318	536	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928310	178928310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	197	404	0	ENST00000263967.3:c.1496C>T	p.Ser499Phe	p.S499F	ENST00000263967	NM_006218.2	499	tCt/tTt	9/21	0.299205930568942	3	FACETS	1	0.99	1	0.669	0.624	0.714	INDETERMINATE	1	TRUE	1	0.75	3		404	540	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146479	185146479	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	59	433	0	ENST00000265026.3:c.110A>G	p.His37Arg	p.H37R	ENST00000265026	NM_004721.4	37	cAc/cGc	2/14	0.299205930568942	3	FACETS	0.405	0.349	0.467	0.203	0.174	0.234	INDETERMINATE	1	TRUE	1	0.75	3		433	534	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146720	185146720	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs111558473	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	168	600	0	ENST00000265026.3:c.351G>T	p.Lys117Asn	p.K117N	ENST00000265026	NM_004721.4	117	aaG/aaT	2/14	0.299205930568942	3	FACETS	0.655	0.601	0.71	0.327	0.3	0.355	INDETERMINATE	1	TRUE	1	0.75	3		600	941	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803744	1803744	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774929566	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	97	749	1	ENST00000260795.2:c.922G>A	p.Val308Met	p.V308M	ENST00000260795		308	Gtg/Atg	6/17	1	2	FACETS	0.293	0.26	0.328	0.293	0.26	0.328	SUBCLONAL	1	TRUE	1	0.75	2		750	883	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1940202	1940202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	58	233	1	ENST00000382891.5:c.1699G>A	p.Ala567Thr	p.A567T	ENST00000382891	NM_133335.3	567	Gcc/Acc	8/22	1	2	FACETS	0.504	0.436	0.577	0.504	0.436	0.577	SUBCLONAL	1	TRUE	1	0.75	2		234	307	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747985	41747985	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	11	100	0	ENST00000226382.2:c.784G>T	p.Gly262Cys	p.G262C	ENST00000226382	NM_003924.3	262	Ggc/Tgc	3/3	1	2	FACETS	0.299	0.209	0.41	0.299	0.209	0.41	SUBCLONAL	1	TRUE	1	0.75	2		100	98	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197623	106197623	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1413958620	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	95	341	0	ENST00000380013.4:c.5956A>G	p.Thr1986Ala	p.T1986A	ENST00000380013	NM_001127208.2	1986	Aca/Gca	11/11	1	2	FACETS	0.674	0.605	0.746	0.674	0.605	0.746	SUBCLONAL	1	TRUE	1	0.75	2		341	376	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143324200	143324200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	28	246	0	ENST00000262992.4:c.263G>T	p.Arg88Met	p.R88M	ENST00000262992	NM_001101669.1	88	aGg/aTg	5/24	1	2	FACETS	0.276	0.221	0.338	0.276	0.221	0.338	SUBCLONAL	1	TRUE	1	0.75	2		246	271	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244049	153244049	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	174	525	0	ENST00000281708.4:c.2108A>G	p.Asp703Gly	p.D703G	ENST00000281708	NM_033632.3	703	gAt/gGt	12/12	1	2	FACETS	0.915	0.849	0.983	0.915	0.849	0.983	CLONAL	1	TRUE	1	0.75	2		525	507	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541603	187541603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	173	382	0	ENST00000441802.2:c.6137C>T	p.Ala2046Val	p.A2046V	ENST00000441802	NM_005245.3	2046	gCg/gTg	10/27	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.75	2		382	439	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251198	251198	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	151	332	1	ENST00000264932.6:c.1643A>G	p.His548Arg	p.H548R	ENST00000264932	NM_004168.2	548	cAc/cGc	12/15	1	2	FACETS	0.893	0.824	0.964	0.893	0.824	0.964	CLONAL	1	TRUE	1	0.75	2		333	451	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294433	1294433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377016753	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	40	579	1	ENST00000310581.5:c.568G>A	p.Ala190Thr	p.A190T	ENST00000310581	NM_198253.2	190	Gct/Act	2/16	1	2	FACETS	0.136	0.113	0.163	0.136	0.113	0.163	SUBCLONAL	1	TRUE	1	0.75	2		580	782	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409355	31409355	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	21	421	0	ENST00000344624.3:c.3750+2T>C		p.X1250_splice	ENST00000344624		1250			1	2	FACETS	0.137	0.105	0.174	0.137	0.105	0.174	SUBCLONAL	1	TRUE	1	0.75	2		421	409	SUCCESS
APC	324	MSKCC	GRCh37	5	112102997	112102997	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786202322	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	62	408	0	ENST00000257430.4:c.332G>T	p.Ser111Ile	p.S111I	ENST00000257430	NM_000038.5	111	aGt/aTt	4/16	1	2	FACETS	0.315	0.272	0.361	0.315	0.272	0.361	SUBCLONAL	1	TRUE	1	0.75	2		408	525	SUCCESS
APC	324	MSKCC	GRCh37	5	112154671	112154671	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1350080370	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	51	309	0	ENST00000257430.4:c.942G>A	p.Met314Ile	p.M314I	ENST00000257430	NM_000038.5	314	atG/atA	10/16	1	2	FACETS	0.391	0.333	0.453	0.391	0.333	0.453	SUBCLONAL	1	TRUE	1	0.75	2		309	348	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973787	131973787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	49	237	0	ENST00000265335.6:c.3490G>A	p.Glu1164Lys	p.E1164K	ENST00000265335		1164	Gaa/Aaa	23/25	1	2	FACETS	0.465	0.396	0.539	0.465	0.396	0.539	SUBCLONAL	1	TRUE	1	0.75	2		237	281	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515144	149515144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764662524	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	216	773	1	ENST00000261799.4:c.338G>A	p.Arg113Gln	p.R113Q	ENST00000261799	NM_002609.3	113	cGg/cAg	3/23	1	2	FACETS	0.652	0.606	0.698	0.652	0.606	0.698	SUBCLONAL	1	TRUE	1	0.75	2		774	884	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052965	180052965	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367879842	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	134	1076	1	ENST00000261937.6:c.1325C>T	p.Ala442Val	p.A442V	ENST00000261937	NM_182925.4	442	gCc/gTc	10/30	1	2	FACETS	0.318	0.288	0.35	0.318	0.288	0.35	SUBCLONAL	1	TRUE	1	0.75	2		1077	1123	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158762	26158762	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	189	771	0	ENST00000289316.2:c.365A>G	p.Tyr122Cys	p.Y122C	ENST00000289316	NM_138720.2	122	tAc/tGc	1/2	1	2	FACETS	0.612	0.566	0.659	0.612	0.566	0.659	SUBCLONAL	1	TRUE	1	0.75	2		771	824	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839868	27839868	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	325	678	0	ENST00000328488.2:c.226G>A	p.Ala76Thr	p.A76T	ENST00000328488	NM_003533.2	76	Gca/Aca	1/1	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.75	2		678	801	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672888	30672888	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	129	907	0	ENST00000376406.3:c.4072T>C	p.Ser1358Pro	p.S1358P	ENST00000376406	NM_014641.2	1358	Tcc/Ccc	10/15	1	2	FACETS	0.293	0.264	0.322	0.293	0.264	0.322	SUBCLONAL	1	TRUE	1	0.75	2		907	1176	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681678	30681678	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	112	572	0	ENST00000376406.3:c.419T>C	p.Val140Ala	p.V140A	ENST00000376406	NM_014641.2	140	gTc/gCc	3/15	1	2	FACETS	0.404	0.363	0.447	0.404	0.363	0.447	SUBCLONAL	1	TRUE	1	0.75	2		572	739	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64289211	64289211	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	22	409	0	ENST00000370651.3:c.379G>A	p.Glu127Lys	p.E127K	ENST00000370651	NM_003463.4	127	Gaa/Aaa	5/6	1	2	FACETS	0.139	0.107	0.176	0.139	0.107	0.176	SUBCLONAL	1	TRUE	1	0.75	2		409	423	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964379	93964379	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	53	369	0	ENST00000369303.4:c.2518A>G	p.Met840Val	p.M840V	ENST00000369303	NM_004440.3	840	Atg/Gtg	14/17	1	2	FACETS	0.362	0.31	0.42	0.362	0.31	0.42	SUBCLONAL	1	TRUE	1	0.75	2		369	390	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322528	109322528	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1271196492	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	148	570	0	ENST00000436639.2:c.509C>T	p.Pro170Leu	p.P170L	ENST00000436639	NM_014454.2	170	cCg/cTg	3/10	1	2	FACETS	0.586	0.536	0.637	0.586	0.536	0.637	SUBCLONAL	1	TRUE	1	0.75	2		570	674	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2969651	2969651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	369	839	0	ENST00000396946.4:c.1628C>T	p.Pro543Leu	p.P543L	ENST00000396946	NM_032415.4	543	cCc/cTc	12/25	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.75	2		839	926	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509906	106509906	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	266	563	0	ENST00000359195.3:c.1900A>G	p.Asn634Asp	p.N634D	ENST00000359195	NM_002649.2	634	Aac/Gac	2/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.75	2		563	645	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845664	151845664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	165	579	0	ENST00000262189.6:c.13348G>A	p.Val4450Met	p.V4450M	ENST00000262189	NM_170606.2	4450	Gtg/Atg	52/59	1	2	FACETS	0.615	0.566	0.666	0.615	0.566	0.666	SUBCLONAL	1	TRUE	1	0.75	2		579	715	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346290	152346290	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	59	540	0	ENST00000359321.1:c.280A>G	p.Thr94Ala	p.T94A	ENST00000359321	NM_005431.1	94	Aca/Gca	3/3	1	2	FACETS	0.273	0.235	0.315	0.273	0.235	0.315	SUBCLONAL	1	TRUE	1	0.75	2		540	576	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194653	29194654	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	193	888	0	ENST00000240100.2:c.1074dup	p.Thr359HisfsTer91	p.T359Hfs*91	ENST00000240100	NM_001394.6	358	-/C	4/4	1	2	FACETS	0.531	0.491	0.573	0.531	0.491	0.573	SUBCLONAL	1	TRUE	1	0.75	2		888	969	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38186919	38186919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1418991870	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	82	515	1	ENST00000317025.8:c.1558G>A	p.Asp520Asn	p.D520N	ENST00000317025	NM_023034.1	520	Gat/Aat	6/24	1	2	FACETS	0.352	0.31	0.396	0.352	0.31	0.396	SUBCLONAL	1	TRUE	1	0.75	2		516	622	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38283744	38283744	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	169	546	0	ENST00000425967.3:c.734G>A	p.Ser245Asn	p.S245N	ENST00000425967	NM_001174067.1	245	aGc/aAc	7/19	1	2	FACETS	0.686	0.633	0.741	0.686	0.633	0.741	SUBCLONAL	1	TRUE	1	0.75	2		546	657	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978590	70978590	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	250	616	0	ENST00000276594.2:c.1063G>T	p.Glu355Ter	p.E355*	ENST00000276594	NM_024504.3	355	Gag/Tag	5/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.75	2		616	637	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958368	90958368	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	32	244	0	ENST00000265433.3:c.2070G>T	p.Lys690Asn	p.K690N	ENST00000265433	NM_002485.4	690	aaG/aaT	13/16	1	2	FACETS	0.422	0.346	0.508	0.422	0.346	0.508	SUBCLONAL	1	TRUE	1	0.75	2		244	202	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542668	141542668	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1201563583	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	309	716	0	ENST00000220592.5:c.2318G>A	p.Arg773His	p.R773H	ENST00000220592	NM_012154.3	773	cGt/cAt	18/19	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.75	2		716	787	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561522	141561522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764026573	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	163	476	0	ENST00000220592.5:c.1283C>T	p.Ala428Val	p.A428V	ENST00000220592	NM_012154.3	428	gCg/gTg	11/19	1	2	FACETS	0.668	0.615	0.722	0.668	0.615	0.722	SUBCLONAL	1	TRUE	1	0.75	2		476	651	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141582934	141582934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199834249	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	328	710	0	ENST00000220592.5:c.313C>T	p.Pro105Ser	p.P105S	ENST00000220592	NM_012154.3	105	Ccc/Tcc	3/19	1	2	FACETS	0.951	0.901	1	0.951	0.901	1	CLONAL	1	TRUE	1	0.75	2		710	920	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022009	5022009	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	140	368	0	ENST00000381652.3:c.22A>G	p.Met8Val	p.M8V	ENST00000381652	NM_004972.3	8	Atg/Gtg	3/25	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.75	2		368	359	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5070038	5070038	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	38	245	0	ENST00000381652.3:c.1627G>A	p.Glu543Lys	p.E543K	ENST00000381652	NM_004972.3	543	Gaa/Aaa	12/25	1	2	FACETS	0.483	0.402	0.57	0.483	0.402	0.57	SUBCLONAL	1	TRUE	1	0.75	2		245	210	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341268	8341268	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1318648410	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	47	259	0	ENST00000356435.5:c.4948C>T	p.Arg1650Cys	p.R1650C	ENST00000356435		1650	Cgt/Tgt	30/35	1	2	FACETS	0.497	0.423	0.578	0.497	0.423	0.578	SUBCLONAL	1	TRUE	1	0.75	2		259	252	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521398	8521398	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	137	623	0	ENST00000356435.5:c.840T>G	p.Asp280Glu	p.D280E	ENST00000356435		280	gaT/gaG	9/35	1	2	FACETS	0.539	0.491	0.589	0.539	0.491	0.589	SUBCLONAL	1	TRUE	1	0.75	2		623	678	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22008862	22008862	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	290	737	0	ENST00000276925.6:c.91C>T	p.Arg31Ter	p.R31*	ENST00000276925	NM_004936.3	31	Cga/Tga	1/2	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.75	2		737	762	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206620	27206620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	58	433	0	ENST00000380036.4:c.2405C>T	p.Ala802Val	p.A802V	ENST00000380036	NM_000459.3	802	gCc/gTc	15/23	1	2	FACETS	0.331	0.285	0.382	0.331	0.285	0.382	SUBCLONAL	1	TRUE	1	0.75	2		433	467	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87356831	87356831	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	41	351	0	ENST00000277120.3:c.1184T>C	p.Val395Ala	p.V395A	ENST00000277120		395	gTa/gCa	10/19	1	2	FACETS	0.291	0.242	0.344	0.291	0.242	0.344	SUBCLONAL	1	TRUE	1	0.75	2		351	376	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606311	93606311	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	359	916	0	ENST00000375746.1:c.131G>T	p.Ser44Ile	p.S44I	ENST00000375746	NM_001174167.1	44	aGc/aTc	2/14	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.75	2		916	881	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137323827	137323827	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762302539	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	121	831	2	ENST00000481739.1:c.1120G>A	p.Val374Ile	p.V374I	ENST00000481739	NM_002957.4	374	Gtc/Atc	8/10	1	2	FACETS	0.374	0.337	0.413	0.374	0.337	0.413	SUBCLONAL	1	TRUE	1	0.75	2		833	863	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802537	139802537	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373483375	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	360	889	0	ENST00000247668.2:c.382C>T	p.Arg128Cys	p.R128C	ENST00000247668	NM_021138.3	128	Cgc/Tgc	5/11	1	2	FACETS	0.995	0.946	1	0.995	0.946	1	CLONAL	1	TRUE	1	0.75	2		889	965	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156686	20156687	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	51	514	0	ENST00000379607.5:c.70dup	p.Arg24LysfsTer64	p.R24Kfs*64	ENST00000379607	NM_001412.3	24	aga/aAga	2/7	1	2	FACETS	0.238	0.202	0.277	0.238	0.202	0.277	SUBCLONAL	1	TRUE	1	0.75	2		514	572	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936039	44936039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	59	525	0	ENST00000377967.4:c.2800G>A	p.Asp934Asn	p.D934N	ENST00000377967	NM_021140.2	934	Gac/Aac	18/29	1	2	FACETS	0.31	0.267	0.357	0.31	0.267	0.357	SUBCLONAL	1	TRUE	1	0.75	2		525	507	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942757	44942757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367925808	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	124	539	0	ENST00000377967.4:c.3337G>A	p.Val1113Ile	p.V1113I	ENST00000377967	NM_021140.2	1113	Gta/Ata	23/29	1	2	FACETS	0.566	0.514	0.621	0.566	0.514	0.621	SUBCLONAL	1	TRUE	1	0.75	2		539	584	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231049	53231050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	184	699	0	ENST00000375401.3:c.1852dup	p.Cys618LeufsTer4	p.C618Lfs*4	ENST00000375401	NM_004187.3	618	tgc/tTgc	13/26	1	2	FACETS	0.613	0.566	0.661	0.613	0.566	0.661	SUBCLONAL	1	TRUE	1	0.75	2		699	801	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53241078	53241078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556849167	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	75	624	0	ENST00000375401.3:c.1133G>A	p.Arg378Gln	p.R378Q	ENST00000375401	NM_004187.3	378	cGg/cAg	9/26	1	2	FACETS	0.289	0.253	0.328	0.289	0.253	0.328	SUBCLONAL	1	TRUE	1	0.75	2		624	691	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410063	63410063	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	109	815	0	ENST00000330258.3:c.3104A>G	p.Asn1035Ser	p.N1035S	ENST00000330258	NM_152424.3	1035	aAc/aGc	2/2	1	2	FACETS	0.334	0.299	0.371	0.334	0.299	0.371	SUBCLONAL	1	TRUE	1	0.75	2		815	870	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412284	63412284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754747475	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	286	1051	0	ENST00000330258.3:c.883G>A	p.Ala295Thr	p.A295T	ENST00000330258	NM_152424.3	295	Gca/Aca	2/2	1	2	FACETS	0.676	0.635	0.717	0.676	0.635	0.717	SUBCLONAL	1	TRUE	1	0.75	2		1051	1129	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340903	70340904	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	97	686	0	ENST00000374080.3:c.641dup	p.Cys215LeufsTer11	p.C215Lfs*11	ENST00000374080		212	-/G	5/45	1	2	FACETS	0.29	0.258	0.325	0.29	0.258	0.325	SUBCLONAL	1	TRUE	1	0.75	2		686	891	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019598	123019598	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	70	550	0	ENST00000355640.3:c.86G>T	p.Arg29Ile	p.R29I	ENST00000355640		29	aGa/aTa	2/7	1	2	FACETS	0.335	0.292	0.381	0.335	0.292	0.381	SUBCLONAL	1	TRUE	1	0.75	2		550	557	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0057017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	88	221	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.516488284743924	2		222	311	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720857	89720857	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs786201816	NA	P-0057017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	138	382	0	ENST00000371953.3:c.1008C>G	p.Tyr336Ter	p.Y336*	ENST00000371953	NM_000314.4	336	taC/taG	8/9	0.503492964798915	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.516488284743924	1		382	381	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084094	47084094	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	172	493	0	ENST00000409792.3:c.7195C>T	p.Arg2399Ter	p.R2399*	ENST00000409792	NM_014159.6	2399	Cga/Tga	17/21	1	2	FACETS	0.917	0.846	0.991	0.917	0.846	0.991	CLONAL	1	TRUE	1	0.516488284743924	2		493	726	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729775	41729775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	123	436	0	ENST00000242208.4:c.754G>A	p.Ala252Thr	p.A252T	ENST00000242208	NM_002192.2	252	Gcc/Acc	3/3	0.516488284743924	3	FACETS	1	0.941	1	0.525	0.476	0.576	CLONAL	1	TRUE	1	0.516488284743924	3		436	571	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660192	12660192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144637992	NA	P-0057017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	71	370	0	ENST00000251849.4:c.29C>T	p.Thr10Met	p.T10M	ENST00000251849	NM_002880.3	10	aCg/aTg	2/17	1	2	FACETS	0.522	0.456	0.592	0.522	0.456	0.592	SUBCLONAL	1	TRUE	1	0.516488284743924	2		370	527	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340848	70340849	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	137	584	0	ENST00000374080.3:c.582dup	p.Trp195MetfsTer9	p.W195Mfs*9	ENST00000374080		194	tta/ttAa	5/45	1	2	FACETS	0.873	0.796	0.952	0.873	0.796	0.952	CLONAL	1	TRUE	1	0.516488284743924	2		584	608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0057018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	168	949	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.208514438483191	2	FACETS	0.966	0.889	1	0.966	0.889	1	CLONAL	2	TRUE	0	0.221551675987048	2		949	785	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955126	48955472	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGTTTAGGGTATTTAAATCTTTGAAAATTTGAGATCAGCTATAAGTCCTTTCTCTAGGAAAAACACAGATTTGCTTACACTCAAAATTGGAAGGCTATTTCCTATGAGTCCGTAGACTCCAAAATAAAAAATTCTGCTCTAAATAAAAATGGTTTAACCTTTCTACTGTTTTCTTTGTCTGATAATAACTTCCAAAAAAATACCTAGCTCAAGGGTTAATATTTCATAAATAGTTACTTTTTTTTTTCATTTTTAGGAAGTACATCTCAGAATCTTGATTCTGGAACAGATTTGTCTTTCCCATGGATTCTGAATGTGCTTAATTTAAAAGCCTTTGATTTTTACA	AAGTTTAGGGTATTTAAATCTTTGAAAATTTGAGATCAGCTATAAGTCCTTTCTCTAGGAAAAACACAGATTTGCTTACACTCAAAATTGGAAGGCTATTTCCTATGAGTCCGTAGACTCCAAAATAAAAAATTCTGCTCTAAATAAAAATGGTTTAACCTTTCTACTGTTTTCTTTGTCTGATAATAACTTCCAAAAAAATACCTAGCTCAAGGGTTAATATTTCATAAATAGTTACTTTTTTTTTTCATTTTTAGGAAGTACATCTCAGAATCTTGATTCTGGAACAGATTTGTCTTTCCCATGGATTCTGAATGTGCTTAATTTAAAAGCCTTTGATTTTTACA	-	novel	NA	P-0057018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	44	8	0	ENST00000267163.4:c.1499-253_1592del		p.X500_splice	ENST00000267163	NM_000321.2	500		17/27	0.221551675987048	2	FACETS	1	0.868	1	0.519	0.436	0.61	CLONAL	1	TRUE	0	0.221551675987048	2		8	383	SUCCESS
APC	324	MSKCC	GRCh37	5	112173295	112173295	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1380127485	NA	P-0057018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	68	174	0	ENST00000257430.4:c.2004C>G	p.His668Gln	p.H668Q	ENST00000257430	NM_000038.5	668	caC/caG	16/16	0.221551675987048	5	FACETS	0.871	0.764	0.985	0.871	0.764	0.985	CLONAL	3	TRUE	2	0.221551675987048	5		174	313	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087503	27087503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	90	774	1	ENST00000324856.7:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000324856	NM_006015.4	693	Cga/Tga	5/20	1	2	FACETS	0.533	0.472	0.599	0.533	0.472	0.599	SUBCLONAL	1	TRUE	1	0.36	2		775	938	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696730	47696730	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	167	355	0	ENST00000347630.2:c.218C>A	p.Pro73His	p.P73H	ENST00000347630	NM_001007230.1	73	cCc/cAc	5/11	0.265910551527082	3	FACETS	0.993	0.919	1	0.662	0.612	0.714	CLONAL	2	TRUE	0	0.36	3		355	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0057020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	444	893	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.786664066029266	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.788299656357029	1		894	654	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0057020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	179	473	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.788299656357029	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.788299656357029	2		473	226	SUCCESS
APC	324	MSKCC	GRCh37	5	112175908	112175909	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1554086015	NA	P-0057020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	55	242	0	ENST00000257430.4:c.4619_4620del	p.Glu1540AlafsTer3	p.E1540Afs*3	ENST00000257430	NM_000038.5	1539	tcAGag/tcag	16/16	0.754527604513846	1	FACETS	0.89	0.797	0.981	0.89	0.797	0.981	CLONAL	1	TRUE	0	0.788299656357029	1		242	95	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707915	43707915	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	378	921	1	ENST00000382044.4:c.4966C>T	p.Arg1656Ter	p.R1656*	ENST00000382044	NM_001141980.1	1656	Cga/Tga	23/28	1	2	FACETS	0.886	0.843	0.93	0.886	0.843	0.93	CLONAL	1	TRUE	1	0.788299656357029	2		922	1082	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934362	68934362	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745857499	NA	P-0057020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	102	432	0	ENST00000288368.4:c.428G>A	p.Arg143Gln	p.R143Q	ENST00000288368	NM_024870.2	143	cGg/cAg	4/40	1	2	FACETS	0.951	0.864	1	0.951	0.864	1	CLONAL	1	TRUE	1	0.788299656357029	2		432	272	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653425	206653425	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	211	779	1	ENST00000367120.3:c.1309G>T	p.Glu437Ter	p.E437*	ENST00000367120	NM_014002.3	437	Gag/Tag	12/22	1	2	FACETS	0.545	0.506	0.585	0.545	0.506	0.585	SUBCLONAL	1	TRUE	1	0.788299656357029	2		780	983	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028677	12028753	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGATCACATTGGTATGTTTATGCTGATTCAACCTTGCCACAGTAGCGTAACAATAAGAAATTTAGAAGTGAAAGAA	GGGATCACATTGGTATGTTTATGCTGATTCAACCTTGCCACAGTAGCGTAACAATAAGAAATTTAGAAGTGAAAGAA	-	novel	NA	P-0057020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	81	391	0	ENST00000353533.5:c.880_891+65del		p.X294_splice	ENST00000353533	NM_003010.3	294		8/11	0.786664066029266	1	FACETS	0.759	0.688	0.83	0.759	0.688	0.83	SUBCLONAL	1	TRUE	0	0.788299656357029	1		391	164	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0057021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	707	722	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.915813084746004	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.918336603349181	2		722	734	SUCCESS
APC	324	MSKCC	GRCh37	5	112173992	112173992	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1114167559	NA	P-0057021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	232	311	0	ENST00000257430.4:c.2701C>T	p.Gln901Ter	p.Q901*	ENST00000257430	NM_000038.5	901	Cag/Tag	16/16	0.918336603349181	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.918336603349181	2		311	250	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610595	10610595	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0057021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	790	816	0	ENST00000171111.5:c.115A>T	p.Lys39Ter	p.K39*	ENST00000171111	NM_203500.1	39	Aag/Tag	2/6	0.918336603349181	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.918336603349181	2		816	844	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971200	21971201	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	463	411	0	ENST00000304494.5:c.157dup	p.Met53AsnfsTer67	p.M53Nfs*67	ENST00000304494	NM_000077.4	53	atg/aAtg	2/3	0.918336603349181	2	FACETS	0.992	0.975	1	0.992	0.975	1	CLONAL	2	TRUE	0	0.918336603349181	2		411	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0057022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	214	653	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.682958461077133	1	FACETS	0.973	0.918	1	0.973	0.918	1	CLONAL	1	TRUE	0	0.682958461077133	1		655	424	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562294	95562313	+	frameshift_variant	Frame_Shift_Del	DEL	CATCTGGATGATCAAACATA	CATCTGGATGATCAAACATA	-	novel	NA	P-0057022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	30	361	0	ENST00000393063.1:c.4944_4963del	p.Met1649ArgfsTer2	p.M1649Rfs*2	ENST00000393063	NM_030621.3	1648	tgTATGTTTGATCATCCAGATGca/tgca	24/28	1	2	FACETS	0.276	0.223	0.337	0.276	0.223	0.337	SUBCLONAL	1	TRUE	1	0.682958461077133	2		361	318	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602292	10602292	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	91	790	0	ENST00000171111.5:c.1286G>T	p.Gly429Val	p.G429V	ENST00000171111	NM_203500.1	429	gGc/gTc	3/6	1	2	FACETS	0.803	0.711	0.902	0.803	0.711	0.902	CLONAL	1	TRUE	1	0.211026862478623	2		790	1074	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228800	36228800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393734909	NA	P-0057023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	90	823	1	ENST00000222270.7:c.7699C>T	p.Arg2567Cys	p.R2567C	ENST00000222270	NM_014727.1	2567	Cgt/Tgt	35/37	0.0269924225517184	3	FACETS	0.779	0.689	0.876	0.389	0.344	0.438	INDETERMINATE	1	TRUE	1	0.211026862478623	3		824	1211	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577351	64577351	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555166567	NA	P-0057023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	76	699	0	ENST00000312049.6:c.231C>G	p.Tyr77Ter	p.Y77*	ENST00000312049	NM_130799.2	77	taC/taG	2/10	1	2	FACETS	0.784	0.686	0.89	0.784	0.686	0.89	SUBCLONAL	1	TRUE	1	0.211026862478623	2		699	919	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219336	1219344	+	inframe_deletion	In_Frame_Del	DEL	GAGTACTGC	GAGTACTGC	-	novel	NA	P-0057023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	82	695	0	ENST00000326873.7:c.389_397del	p.Glu130_Cys132del	p.E130_C132del	ENST00000326873	NM_000455.4	130	GAGTACTGC/-	3/10	1	2	FACETS	0.772	0.679	0.872	0.772	0.679	0.872	SUBCLONAL	1	TRUE	1	0.211026862478623	2		695	1007	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184457	7184457	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1291755894	NA	P-0057023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	114	774	0	ENST00000302850.5:c.844A>G	p.Asn282Asp	p.N282D	ENST00000302850	NM_000208.2	282	Aac/Gac	3/22	1	2	FACETS	0.994	0.893	1	0.994	0.893	1	CLONAL	1	TRUE	1	0.211026862478623	2		774	1087	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136185	11136185	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0057023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	55	541	0	ENST00000358026.2:c.3168+1G>A		p.X1056_splice	ENST00000358026	NM_001128849.1	1056			1	2	FACETS	0.704	0.601	0.818	0.704	0.601	0.818	SUBCLONAL	1	TRUE	1	0.211026862478623	2		541	740	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15808626	15808626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	63	344	1	ENST00000307771.7:c.8C>T	p.Ala3Val	p.A3V	ENST00000307771	NM_005089.3	3	gCg/gTg	1/11	1	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.211026862478623	1		345	423	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0057024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	125	496	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.336938416920589	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.336938416920589	1		496	534	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567546196	NA	P-0057024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	280	719	0	ENST00000269305.4:c.949del	p.Gln317SerfsTer28	p.Q317Sfs*28	ENST00000269305	NM_001126112.2	317	Cag/ag	9/11	0.296457507878555	2	FACETS	0.902	0.849	0.956	0.902	0.849	0.956	CLONAL	2	TRUE	0	0.336938416920589	2		719	921	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0057024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	51	652	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.296457507878555	2	FACETS	0.363	0.307	0.424	0.181	0.153	0.212	SUBCLONAL	1	TRUE	0	0.336938416920589	2		652	835	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129008	64129008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781669147	NA	P-0057024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	82	809	0	ENST00000334205.4:c.638C>T	p.Thr213Met	p.T213M	ENST00000334205	NM_003942.2	213	aCg/aTg	6/17	0.141883532995443	5	FACETS	0.66	0.58	0.746	0.165	0.145	0.187	INDETERMINATE	1	TRUE	1	0.336938416920589	5		809	1110	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737052	162737052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765973930	NA	P-0057024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	95	521	0	ENST00000367921.3:c.1196G>A	p.Arg399Gln	p.R399Q	ENST00000367921	NM_006182.2	399	cGg/cAg	11/18	0.141883532995443	5	FACETS	1	0.959	1	0.29	0.258	0.325	INDETERMINATE	1	TRUE	1	0.336938416920589	5		521	731	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439905	220439905	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750272026	NA	P-0057024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1256	132	1132	0	ENST00000243786.2:c.758C>T	p.Pro253Leu	p.P253L	ENST00000243786	NM_002191.3	253	cCg/cTg	2/2	0.141883532995443	5	FACETS	0.85	0.769	0.936	0.212	0.192	0.234	INDETERMINATE	1	TRUE	1	0.336938416920589	5		1132	1388	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118882	61118882	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	85	304	1	ENST00000295025.8:c.75C>A	p.Tyr25Ter	p.Y25*	ENST00000295025	NM_002908.2	25	taC/taA	2/11	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.336938416920589	2		305	478	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212615387	212615387	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	73	480	0	ENST00000342788.4:c.599C>T	p.Pro200Leu	p.P200L	ENST00000342788	NM_005235.2	200	cCc/cTc	5/28	0.141883532995443	5	FACETS	1	0.891	1	0.255	0.223	0.29	INDETERMINATE	1	TRUE	1	0.336938416920589	5		480	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0057025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	411	868	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.67335716100363	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.727471045768905	2		868	554	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32438063	32438063	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762688982	NA	P-0057025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	329	535	2	ENST00000332351.3:c.974C>T	p.Ser325Leu	p.S325L	ENST00000332351	NM_024426.4	325	tCa/tTa	5/10	0.727471045768905	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.727471045768905	3		537	609	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272107	15272107	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1724	100	636	0	ENST00000263388.2:c.6332T>G	p.Phe2111Cys	p.F2111C	ENST00000263388	NM_000435.2	2111	tTc/tGc	33/33	0.727471045768905	9	FACETS	0.534	0.475	0.598	0.076	0.067	0.086	SUBCLONAL	1	TRUE	2	0.727471045768905	9		636	1824	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748490	40748490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1209358799	NA	P-0057025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	181	865	3	ENST00000392038.2:c.392C>T	p.Ser131Phe	p.S131F	ENST00000392038	NM_001626.4	131	tCc/tTc	5/14	0.727471045768905	4	FACETS	0.654	0.601	0.709			1	SUBCLONAL	1	TRUE	NA	0.727471045768905	4		868	1315	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0057026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	258	436	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.152879689136331	7	FACETS	1	0.95	1	1	0.95	1	CLONAL	4	TRUE	3	0.152879689136331	7		436	1146	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416668	416668	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	28	300	0	ENST00000399788.2:c.3882G>C	p.Lys1294Asn	p.K1294N	ENST00000399788	NM_001042603.1	1294	aaG/aaC	23/28	0.152879689136331	4	FACETS	0.812	0.648	1	0.406	0.324	0.5	CLONAL	1	TRUE	2	0.152879689136331	4		300	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0057027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	160	722	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.526773354433726	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.526773354433726	1		722	445	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0057027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	95	172	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	0.526773354433726	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	TRUE	0	0.526773354433726	2		172	179	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245912885	245912885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374803671	NA	P-0057027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	70	267	0	ENST00000388985.4:c.1267G>A	p.Ala423Thr	p.A423T	ENST00000388985		423	Gcc/Acc	12/12	1	2	FACETS	0.898	0.79	1	0.898	0.79	1	CLONAL	1	TRUE	1	0.526773354433726	2		267	296	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607643	43607643	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	189	1121	0	ENST00000355710.3:c.1619G>T	p.Arg540Met	p.R540M	ENST00000355710	NM_020975.4	540	aGg/aTg	8/20	1	2	FACETS	0.9	0.834	0.969	0.9	0.834	0.969	CLONAL	1	TRUE	1	0.526773354433726	2		1121	797	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151716	108151731	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTAAGTCCCATAGTG	TTTAAGTCCCATAGTG	-	novel	NA	P-0057027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	35	174	0	ENST00000278616.4:c.3403-6_3412del		p.X1135_splice	ENST00000278616	NM_000051.3	1135		24/63	1	2	FACETS	0.82	0.682	0.971	0.82	0.682	0.971	CLONAL	1	TRUE	1	0.526773354433726	2		174	162	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527988	103527988	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	84	308	0	ENST00000355739.4:c.3296G>T	p.Gly1099Val	p.G1099V	ENST00000355739	NM_000123.3	1099	gGa/gTa	15/15	0.526773354433726	3	FACETS	1	0.943	1	0.547	0.487	0.611	CLONAL	1	TRUE	1	0.526773354433726	3		308	368	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273241	18273241	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	183	656	0	ENST00000222254.8:c.1034G>A	p.Arg345Gln	p.R345Q	ENST00000222254	NM_005027.3	345	cGg/cAg	9/16	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.526773354433726	2		656	678	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022614	36022636	+	frameshift_variant	Frame_Shift_Del	DEL	CGGTTACTGCTCAATGCAGAGAA	CGGTTACTGCTCAATGCAGAGAA	-	novel	NA	P-0057027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	375	712	0	ENST00000358208.4:c.488_510del	p.Arg163ProfsTer11	p.R163Pfs*11	ENST00000358208		163	CGGTTACTGCTCAATGCAGAGAAc/c	5/12	0.468335304222524	5	FACETS	1	0.993	1	0.822	0.782	0.863	CLONAL	2	TRUE	2	0.526773354433726	5		712	1033	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613216	52613217	+	splice_acceptor_variant	Splice_Site	INS	-	-	TGTTGTAAAGAAAACTGGCTGAAGAAAGGTAGT	novel	NA	P-0057027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	83	473	0	ENST00000394830.3:c.3313-34_3313-2dup		p.X1105_splice	ENST00000394830	NM_018313.4	1105			1	2	FACETS	0.608	0.538	0.683	0.608	0.538	0.683	SUBCLONAL	1	TRUE	1	0.526773354433726	2		473	518	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144103	55144103	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	98	420	0	ENST00000257290.5:c.1932A>C	p.Glu644Asp	p.E644D	ENST00000257290	NM_006206.4	644	gaA/gaC	14/23	0.241104733333511	1	FACETS	0.653	0.586	0.723	0.653	0.586	0.723	INDETERMINATE	1	TRUE	0	0.526773354433726	1		420	420	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296155	15296155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754815179	NA	P-0057028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	411	990	0	ENST00000263388.2:c.2209G>A	p.Ala737Thr	p.A737T	ENST00000263388	NM_000435.2	737	Gcc/Acc	14/33	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.778250164637971	2		990	1010	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829549	72829549	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs575480618	NA	P-0057028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	287	593	0	ENST00000268489.5:c.7032C>G	p.Ile2344Met	p.I2344M	ENST00000268489	NM_006885.3	2344	atC/atG	9/10	0.778250164637971	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.778250164637971	1		593	427	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653781	89653781	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs786204914	NA	P-0057028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	33	231	0	ENST00000371953.3:c.80-1G>C		p.X27_splice	ENST00000371953	NM_000314.4	27			0.778250164637971	1	FACETS	0.484	0.404	0.57	0.484	0.404	0.57	SUBCLONAL	1	TRUE	0	0.778250164637971	1		231	107	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874550	35874550	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1055222075	NA	P-0057028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	726	393	0	ENST00000303115.3:c.707-1G>A		p.X236_splice	ENST00000303115	NM_002185.3	236			0.778250164637971	5	FACETS	1	0.987	1	1	0.987	1	CLONAL	4	TRUE	1	0.778250164637971	5		393	996	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981546	201982568	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTAGACCCAGGGCCCTTTGGTGAGAACCCGTTTTCTCCTTCCTTCCCCAGCCTGTCTTGTCCCATCCCTGCCCCTCCACAGAGTGCTAGAGATGACCCCCTCCCCAGACTTCTTCCTCCCTCAATTAGAAAAATTGCAGCAGGTCATCAGACCCATGGGCAGCATCACCTGTCCTGGTCTGGTCCCCTGAGCCCTCTCTGAGTTCTCACCTCCTCTTCCCAGACCAGGGCAGCCCCTTTGCCCAGGAGCTGCTGGACGACGGTCAGCAAGCCAGCCCCTACCACCCCGGCAGCTGTGGCGCAGGAGCCCCCTCCCCTGGCAGCTCTGACGTCTCCACCGCAGGTGAGAGCTCTCTCTGGGCCACAACCTCCCTTCCCCGAAGTGTCCCTTGTTCCCTCTGGCTCCCAGCACCATAACTCAGGCCTTCTGGCAGGAACAGGAACAGGCTGGGAAGTGTGTCCTGAGAGCCAGCAGCGTGGTTGAGCAGAGGGTGGGCCGGCAGGGGACTTACTCTGACCCCGCCCCCCAGGGACTGGTGCTTCTCGGAGCTCCCACTCCTCAGACTCCGGTGGAAGTGACGTGGACCTGGATCCCACTGATGGCAAGCTCTTCCCCAGCGGTGAGTCGAGGGAGGTCCCCAAGAGGGCGTCCCATTTAGCAATGCACAGGGGGCCCGGCTCTTCCTGCAGCCTTTTCCTGTAGAGGGGCTACTCTCCCTAACTCCCCTCTTGCCCCTCCTTGACCTTCCACCACCGTCCCCACAGATGGTTTTCGTGACTGCAAGAAGGGGGATCCCAAGCACGGGAAGCGGAAACGAGGCCGGCCCCGAAAGCTGAGCAAAGAGTACTGGGACTGTCTCGAGGGCAAGAAGAGCAAGCACGGTGAGCTCCGGGGGCACGTGGGTCCTCCCTGCGCCGGGCTGAGCGGCTTCCTGGGGCACTGCGGGTTGTTGCAGGTATCCCTTCTCCCGTTTTCTCTGGCCTCCGCATGGCCTTTGGTAAGGCTGTGCACAAGCTGGGGGCT	CTAGACCCAGGGCCCTTTGGTGAGAACCCGTTTTCTCCTTCCTTCCCCAGCCTGTCTTGTCCCATCCCTGCCCCTCCACAGAGTGCTAGAGATGACCCCCTCCCCAGACTTCTTCCTCCCTCAATTAGAAAAATTGCAGCAGGTCATCAGACCCATGGGCAGCATCACCTGTCCTGGTCTGGTCCCCTGAGCCCTCTCTGAGTTCTCACCTCCTCTTCCCAGACCAGGGCAGCCCCTTTGCCCAGGAGCTGCTGGACGACGGTCAGCAAGCCAGCCCCTACCACCCCGGCAGCTGTGGCGCAGGAGCCCCCTCCCCTGGCAGCTCTGACGTCTCCACCGCAGGTGAGAGCTCTCTCTGGGCCACAACCTCCCTTCCCCGAAGTGTCCCTTGTTCCCTCTGGCTCCCAGCACCATAACTCAGGCCTTCTGGCAGGAACAGGAACAGGCTGGGAAGTGTGTCCTGAGAGCCAGCAGCGTGGTTGAGCAGAGGGTGGGCCGGCAGGGGACTTACTCTGACCCCGCCCCCCAGGGACTGGTGCTTCTCGGAGCTCCCACTCCTCAGACTCCGGTGGAAGTGACGTGGACCTGGATCCCACTGATGGCAAGCTCTTCCCCAGCGGTGAGTCGAGGGAGGTCCCCAAGAGGGCGTCCCATTTAGCAATGCACAGGGGGCCCGGCTCTTCCTGCAGCCTTTTCCTGTAGAGGGGCTACTCTCCCTAACTCCCCTCTTGCCCCTCCTTGACCTTCCACCACCGTCCCCACAGATGGTTTTCGTGACTGCAAGAAGGGGGATCCCAAGCACGGGAAGCGGAAACGAGGCCGGCCCCGAAAGCTGAGCAAAGAGTACTGGGACTGTCTCGAGGGCAAGAAGAGCAAGCACGGTGAGCTCCGGGGGCACGTGGGTCCTCCCTGCGCCGGGCTGAGCGGCTTCCTGGGGCACTGCGGGTTGTTGCAGGTATCCCTTCTCCCGTTTTCTCTGGCCTCCGCATGGCCTTTGGTAAGGCTGTGCACAAGCTGGGGGCT	-	novel	NA	P-0057028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	177	800	0	ENST00000359651.3:c.463_805+145del		p.X155_splice	ENST00000359651		155		3-6/8	1	2	FACETS	0.506	0.466	0.547	0.506	0.466	0.547	SUBCLONAL	1	TRUE	1	0.778250164637971	2		800	899	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916814	48916863	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCACTTTTACTGAGCTACAGAAAAACATAGAAATCAGGTAAAGTTTCTTG	TCACTTTTACTGAGCTACAGAAAAACATAGAAATCAGGTAAAGTTTCTTG	-	novel	NA	P-0057028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	89	308	0	ENST00000267163.4:c.345_380+14del		p.X115_splice	ENST00000267163	NM_000321.2	115		3/27	0.778250164637971	1	FACETS	0.925	0.85	0.999	0.925	0.85	0.999	CLONAL	1	TRUE	0	0.778250164637971	1		308	151	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40828027	40828027	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0057028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	167	384	2	ENST00000373198.4:c.2401A>T	p.Lys801Ter	p.K801*	ENST00000373198	NM_133170.3	801	Aag/Tag	17/32	0.756600175394988	1	FACETS	0.621	0.577	0.666	0.621	0.577	0.666	SUBCLONAL	1	TRUE	0	0.778250164637971	1		386	422	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902191	151902191	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	439	542	0	ENST00000262189.6:c.3961G>C	p.Gly1321Arg	p.G1321R	ENST00000262189	NM_170606.2	1321	Ggc/Cgc	25/59	1	2	FACETS	1	0.981	1	1	0.998	1	CLONAL	2	TRUE	1	0.778250164637971	2		542	558	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0057031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	168	385	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.236476521234934	3	FACETS	1	0.936	1	1	0.936	1	CLONAL	3	TRUE	0	0.236476521234934	3		385	523	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	79	330	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.236476521234934	5	FACETS	1	0.904	1	0.684	0.604	0.769	CLONAL	2	TRUE	2	0.236476521234934	5		330	441	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210451	2210451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138206172	NA	P-0057031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	93	1109	1	ENST00000398665.3:c.1058C>T	p.Ala353Val	p.A353V	ENST00000398665	NM_032482.2	353	gCg/gTg	13/28	0.235461919380076	3	FACETS	0.952	0.845	1	0.476	0.422	0.533	CLONAL	1	TRUE	1	0.236476521234934	3		1110	924	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200097	67200097	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs753125285	NA	P-0057031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	100	655	1	ENST00000312629.5:c.484C>T	p.Arg162Ter	p.R162*	ENST00000312629	NM_003952.2	162	Cga/Tga	6/15	1	2	FACETS	0.866	0.772	0.966	0.866	0.772	0.966	CLONAL	1	TRUE	1	0.236476521234934	2		656	977	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912130	114912130	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0057031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	81	531	0	ENST00000543371.1:c.1200C>G	p.Tyr400Ter	p.Y400*	ENST00000543371	NM_001198531.1	400	taC/taG	11/14	1	2	FACETS	0.933	0.822	1	0.933	0.822	1	CLONAL	1	TRUE	1	0.236476521234934	2		531	734	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158328	108158328	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	37	314	0	ENST00000278616.4:c.3995T>A	p.Ile1332Asn	p.I1332N	ENST00000278616	NM_000051.3	1332	aTt/aAt	27/63	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.236476521234934	2		314	270	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573630	48573630	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	35	333	0	ENST00000342988.3:c.214G>T	p.Val72Phe	p.V72F	ENST00000342988	NM_005359.5	72	Gtt/Ttt	2/12	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.236476521234934	2		333	245	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334750	81334750	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	44	486	0	ENST00000222390.5:c.1966G>T	p.Glu656Ter	p.E656*	ENST00000222390	NM_000601.4	656	Gaa/Taa	17/18	0.236476521234934	4	FACETS	0.81	0.679	0.956	0.27	0.226	0.319	CLONAL	1	TRUE	1	0.236476521234934	4		486	568	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776339	76776339	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	112	541	0	ENST00000373344.5:c.7127G>C	p.Arg2376Thr	p.R2376T	ENST00000373344	NM_000489.3	2376	aGa/aCa	34/35	0.014199972841628	4	FACETS	1	0.926	1	1	0.926	1	INDETERMINATE	2	TRUE	2	0.236476521234934	4		541	568	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264143	46264143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746732554	NA	P-0057032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	104	289	2	ENST00000371998.3:c.1190C>T	p.Ser397Leu	p.S397L	ENST00000371998		397	tCg/tTg	11/23	0.580328515163123	3	FACETS	1	0.98	1	0.665	0.602	0.73	CLONAL	1	TRUE	1	0.611777648473644	3		291	334	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458882	120458882	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	231	705	0	ENST00000256646.2:c.6463G>T	p.Glu2155Ter	p.E2155*	ENST00000256646	NM_024408.3	2155	Gaa/Taa	34/34	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.611777648473644	2		705	660	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842679	68842683	+	frameshift_variant	Frame_Shift_Del	DEL	TATTA	TATTA	-	novel	NA	P-0057032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	219	616	0	ENST00000261769.5:c.616_620del	p.Ile206Ter	p.I206*	ENST00000261769	NM_004360.3	205	ttTATTAtt/tttt	5/16	0.611777648473644	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.611777648473644	1		616	392	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168805	56168805	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0057032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	224	345	0	ENST00000399503.3:c.1659C>G	p.Tyr553Ter	p.Y553*	ENST00000399503	NM_005921.1	553	taC/taG	9/20	0.611777648473644	3	FACETS	0.969	0.925	1	1	0.994	1	CLONAL	3	TRUE	1	0.611777648473644	3		345	329	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0057033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	90	341	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.778049667968019	1	FACETS	0.423	0.379	0.47	0.423	0.379	0.47	SUBCLONAL	1	TRUE	0	0.778049667968019	1		341	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0057033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	952	1096	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.778049667968019	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.778049667968019	2		1096	1221	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117739669	117739669	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	68	284	0	ENST00000368508.3:c.124G>A	p.Gly42Ser	p.G42S	ENST00000368508	NM_002944.2	42	Ggc/Agc	2/43	0.381644586805549	2	FACETS	0.478	0.418	0.542	0.239	0.209	0.271	INDETERMINATE	1	TRUE	0	0.778049667968019	2		284	366	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248737	212248737	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	27	327	0	ENST00000342788.4:c.3530del	p.Asn1177MetfsTer27	p.N1177Mfs*27	ENST00000342788	NM_005235.2	1177	aAt/at	28/28	0.750579355539352	2	FACETS	0.239	0.19	0.294	0.119	0.095	0.147	SUBCLONAL	1	TRUE	0	0.778049667968019	2		327	291	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600006	10600006	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	587	818	0	ENST00000171111.5:c.1570G>T	p.Gly524Cys	p.G524C	ENST00000171111	NM_203500.1	524	Ggc/Tgc	5/6	0.778049667968019	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.778049667968019	1		818	804	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106780	27106780	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	678	648	0	ENST00000324856.7:c.6391A>T	p.Asn2131Tyr	p.N2131Y	ENST00000324856	NM_006015.4	2131	Aat/Tat	20/20	0.778049667968019	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.778049667968019	2		648	850	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77070017	77070017	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	220	456	0	ENST00000356341.3:c.523G>T	p.Glu175Ter	p.E175*	ENST00000356341	NM_002576.4	175	Gaa/Taa	6/15	0.350972908186415	3	FACETS	1	0.975	1	0.363	0.338	0.387	INDETERMINATE	1	TRUE	0	0.778049667968019	3		456	722	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363771	118363771	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0057033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	83	337	0	ENST00000534358.1:c.5005-1G>C		p.X1669_splice	ENST00000534358	NM_005933.3	1669			0.0981073343459496	5	FACETS	0.887	0.785	0.996			1	INDETERMINATE	1	TRUE	NA	0.778049667968019	5		337	521	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220715	1220715	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	412	633	0	ENST00000326873.7:c.733C>G	p.Leu245Val	p.L245V	ENST00000326873	NM_000455.4	245	Ctc/Gtc	5/10	0.778049667968019	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.778049667968019	1		633	579	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030786	48030786	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	40	285	0	ENST00000234420.5:c.3400G>T	p.Gly1134Ter	p.G1134*	ENST00000234420	NM_000179.2	1134	Gga/Tga	5/10	0.0981073343459496	5	FACETS	0.621	0.517	0.736			1	INDETERMINATE	1	TRUE	NA	0.778049667968019	5		285	359	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873426	136873426	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	47	315	0	ENST00000241393.3:c.72G>T	p.Met24Ile	p.M24I	ENST00000241393	NM_003467.2	24	atG/atT	2/2	0.350972908186415	3	FACETS	0.471	0.399	0.551	0.157	0.133	0.184	INDETERMINATE	1	TRUE	0	0.778049667968019	3		315	356	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31372583	31372583	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	113	587	0	ENST00000328111.2:c.224A>G	p.Asp75Gly	p.D75G	ENST00000328111	NM_006892.3	75	gAc/gGc	4/23	0.691366554840333	2	FACETS	0.236	0.211	0.262	0.118	0.105	0.131	SUBCLONAL	1	TRUE	0	0.778049667968019	2		587	1233	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003283	143003283	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	91	407	0	ENST00000262992.4:c.2543G>C	p.Arg848Thr	p.R848T	ENST00000262992	NM_001101669.1	848	aGg/aCg	23/24	0.341996338695399	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.778049667968019	0		407	393	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293982	1293982	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1833	1127	1040	0	ENST00000310581.5:c.1019A>T	p.Gln340Leu	p.Q340L	ENST00000310581	NM_198253.2	340	cAg/cTg	2/16	0.778049667968019	6	FACETS	0.834	0.81	0.857	0.834	0.81	0.857	CLONAL	3	TRUE	3	0.778049667968019	6		1040	2960	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111558	56111558	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	43	18	0	ENST00000399503.3:c.158A>T	p.Glu53Val	p.E53V	ENST00000399503	NM_005921.1	53	gAg/gTg	1/20	0.778049667968019	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.778049667968019	1		18	50	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485918	8485919	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0057033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	157	414	0	ENST00000356435.5:c.2898_2899delinsAA	p.Pro967Thr	p.P967T	ENST00000356435		966	ctCCcg/ctAAcg	17/35	0.778049667968019	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.778049667968019	1		414	235	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0057035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	14	118	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.414387691256396	3	FACETS	0.516	0.375	0.686	0.258	0.187	0.343	SUBCLONAL	1	TRUE	1	0.414387691256396	3		118	158	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	120	251	0	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	0.414387691256396	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	1	0.414387691256396	3		251	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578242	7578242	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882003	NA	P-0057035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	342	654	1	ENST00000269305.4:c.607G>T	p.Val203Leu	p.V203L	ENST00000269305	NM_001126112.2	203	Gtg/Ttg	6/11	0.414387691256396	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.414387691256396	2		655	726	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442715	442715	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	56	462	1	ENST00000399788.2:c.1591G>T	p.Asp531Tyr	p.D531Y	ENST00000399788	NM_001042603.1	531	Gat/Tat	12/28	0.414387691256396	3	FACETS	0.42	0.359	0.487	0.21	0.179	0.244	SUBCLONAL	1	TRUE	1	0.414387691256396	3		463	777	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	94	324	0				ENST00000310581	NM_198253.2	-/1132			0.491918859147749	4	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	2	0.703728446559607	4		324	215	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730799	40730799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	91	601	0	ENST00000373198.4:c.3736G>A	p.Glu1246Lys	p.E1246K	ENST00000373198	NM_133170.3	1246	Gaa/Aaa	27/32	0.703728446559607	1	FACETS	0.461	0.412	0.511	0.461	0.412	0.511	SUBCLONAL	1	TRUE	0	0.703728446559607	1		601	364	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467924	50467924	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	79	452	0	ENST00000331340.3:c.1159G>C	p.Glu387Gln	p.E387Q	ENST00000331340	NM_006060.4	387	Gag/Cag	8/8	0.703728446559607	4	FACETS	1	0.933	1	0.539	0.477	0.604	CLONAL	1	TRUE	2	0.703728446559607	4		452	355	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180641	56180641	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	79	324	0	ENST00000399503.3:c.3970G>A	p.Glu1324Lys	p.E1324K	ENST00000399503	NM_005921.1	1324	Gaa/Aaa	16/20	0.525644648502158	6	FACETS	1	0.955	1	0.391	0.345	0.44	CLONAL	1	TRUE	3	0.703728446559607	6		324	461	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022914	27022948	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCCGCCGCCAGCAGCCTGGGCAACCCGCCGCCG	CCGCCGCCGCCAGCAGCCTGGGCAACCCGCCGCCG	-	novel	NA	P-0057036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	12	26	0	ENST00000324856.7:c.28_62del	p.Ala10LeufsTer89	p.A10Lfs*89	ENST00000324856	NM_006015.4	7	cCCGCCGCCGCCAGCAGCCTGGGCAACCCGCCGCCG/c	1/20	0.703728446559607	3	FACETS	0.941	0.682	1	0.47	0.341	0.618	CLONAL	1	TRUE	1	0.703728446559607	3		26	49	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951811	2951811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146334064	NA	P-0057036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	95	724	3	ENST00000396946.4:c.3139G>A	p.Ala1047Thr	p.A1047T	ENST00000396946	NM_032415.4	1047	Gcc/Acc	23/25	NA	2	FACETS	0.583	0.522	0.648			1	INDETERMINATE	1	TRUE	NA	0.703728446559607	2		727	463	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277601	142277601	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	162	276	0	ENST00000350721.4:c.1750G>T	p.Asp584Tyr	p.D584Y	ENST00000350721	NM_001184.3	584	Gat/Tat	8/47	0.703728446559607	5	FACETS	1	0.961	1	0.704	0.652	0.757	CLONAL	2	TRUE	2	0.703728446559607	5		276	448	SUCCESS
YES1	7525	MSKCC	GRCh37	18	739811	739811	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	67	391	0	ENST00000314574.4:c.1061G>A	p.Gly354Glu	p.G354E	ENST00000314574	NM_005433.3	354	gGa/gAa	9/12	0.703728446559607	4	FACETS	0.769	0.67	0.874	0.384	0.335	0.437	SUBCLONAL	1	TRUE	2	0.703728446559607	4		391	422	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928503	69928503	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	139	668	0	ENST00000352241.4:c.323C>G	p.Ser108Cys	p.S108C	ENST00000352241	NM_198159.2	108	tCt/tGt	2/10	0.703728446559607	3	FACETS	1	0.971	1	0.566	0.519	0.614	CLONAL	1	TRUE	1	0.703728446559607	3		668	472	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244124	153244124	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	132	526	1	ENST00000281708.4:c.2033C>T	p.Ser678Leu	p.S678L	ENST00000281708	NM_033632.3	678	tCa/tTa	12/12	0.703728446559607	2	FACETS	1	0.952	1	0.525	0.483	0.569	CLONAL	1	TRUE	0	0.703728446559607	2		527	357	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501591	149501591	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	101	450	0	ENST00000261799.4:c.2196G>C	p.Leu732Phe	p.L732F	ENST00000261799	NM_002609.3	732	ttG/ttC	16/23	0.703728446559607	3	FACETS	1	0.965	1	0.574	0.518	0.632	CLONAL	1	TRUE	1	0.703728446559607	3		450	338	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553456	106553456	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	71	361	0	ENST00000369096.4:c.1421G>A	p.Gly474Glu	p.G474E	ENST00000369096	NM_001198.3	474	gGa/gAa	5/7	0.703728446559607	2	FACETS	1	0.919	1	0.52	0.463	0.579	CLONAL	1	TRUE	0	0.703728446559607	2		361	194	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534498	140534498	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	118	403	0	ENST00000288602.6:c.415C>A	p.Gln139Lys	p.Q139K	ENST00000288602	NM_004333.4	139	Caa/Aaa	3/18	0.703728446559607	4	FACETS	1	0.968	1	0.577	0.523	0.633	CLONAL	1	TRUE	2	0.703728446559607	4		403	495	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010558	48010560	+	missense_variant	Missense_Mutation	TNP	CTC	CTC	ATT	novel	NA	P-0057036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	155	393	0	ENST00000234420.5:c.186_188delinsATT	p.Ser63Phe	p.S63F	ENST00000234420	NM_000179.2	62	cgCTCc/cgATTc	1/10	0.703728446559607	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.703728446559607	3		393	277	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0057037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	199	628	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.44814932831996	2		628	774	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911807	32911807	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	210	363	0	ENST00000380152.3:c.3315del	p.Ser1106AlafsTer13	p.S1106Afs*13	ENST00000380152		1105	ccT/cc	11/27	0.464100036771091	3	FACETS	0.953	0.9	1			1	CLONAL	3	TRUE	NA	0.464100036771091	3		363	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579552	7579553	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0057038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	158	745	1	ENST00000269305.4:c.133_134dup	p.Ser46CysfsTer78	p.S46Cfs*78	ENST00000269305	NM_001126112.2	45	ctg/ctCTg	4/11	0.442281148785057	2	FACETS	0.862	0.799	0.925	0.862	0.799	0.925	CLONAL	2	TRUE	0	0.464100036771091	2		746	395	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656986	47656986	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	88	276	0	ENST00000233146.2:c.1182T>A	p.Phe394Leu	p.F394L	ENST00000233146	NM_000251.2	394	ttT/ttA	7/16	0.368991357840555	3	FACETS	1	0.973	1	0.645	0.576	0.718	CLONAL	1	TRUE	1	0.464100036771091	3		276	362	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665234	138665234	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	174	778	0	ENST00000330315.3:c.331del	p.Cys111AlafsTer39	p.C111Afs*39	ENST00000330315	NM_023067.3	111	Tgc/gc	1/1	0.464100036771091	4	FACETS	1	0.946	1	0.683	0.633	0.734	CLONAL	2	TRUE	1	0.464100036771091	4		778	536	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7119485	7119485	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	97	687	0	ENST00000302850.5:c.3769C>T	p.Gln1257Ter	p.Q1257*	ENST00000302850	NM_000208.2	1257	Caa/Taa	21/22	0.251154510931597	1	FACETS	0.845	0.753	0.944	0.845	0.753	0.944	CLONAL	1	FALSE	0	0.251154510931597	1		687	799	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691003	NA	P-0057039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	65	621	1	ENST00000269305.4:c.96+1G>T		p.X32_splice	ENST00000269305	NM_001126112.2	32			0.251154510931597	1	FACETS	0.69	0.598	0.79	0.69	0.598	0.79	SUBCLONAL	1	FALSE	0	0.251154510931597	1		622	656	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576105	29576105	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555617368	NA	P-0057039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	84	462	0	ENST00000356175.3:c.4078C>T	p.Gln1360Ter	p.Q1360*	ENST00000356175	NM_000267.3	1360	Caa/Taa	30/57	1	2	FACETS	0.915	0.808	1	0.915	0.808	1	CLONAL	1	FALSE	1	0.251154510931597	2		462	731	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546959	9546959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	64	382	1	ENST00000353224.5:c.1063G>A	p.Ala355Thr	p.A355T	ENST00000353224	NM_177990.2	355	Gcc/Acc	5/10	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	FALSE	1	0.251154510931597	2		383	466	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620388	43620388	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	33	534	0	ENST00000355710.3:c.2998del	p.Asp1000ThrfsTer9	p.D1000Tfs*9	ENST00000355710	NM_020975.4	999	gcG/gc	18/20	1	2	FACETS	0.409	0.332	0.497	0.409	0.332	0.497	SUBCLONAL	1	FALSE	1	0.251154510931597	2		534	642	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437756	49437756	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	101	638	0	ENST00000301067.7:c.5214G>T	p.Glu1738Asp	p.E1738D	ENST00000301067	NM_003482.3	1738	gaG/gaT	22/54	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.251154510931597	2		638	674	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602750	10602750	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	139	852	0	ENST00000171111.5:c.828G>T	p.Leu276Phe	p.L276F	ENST00000171111	NM_203500.1	276	ttG/ttT	3/6	0.251154510931597	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	0	0.251154510931597	1		852	922	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025987	48025987	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	77	394	0	ENST00000234420.5:c.865G>T	p.Gly289Cys	p.G289C	ENST00000234420	NM_000179.2	289	Ggc/Tgc	4/10	0.251154510931597	3	FACETS	1	0.968	1	0.654	0.575	0.738	CLONAL	1	FALSE	1	0.251154510931597	3		394	528	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256737	46256737	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	50	421	0	ENST00000371998.3:c.793G>C	p.Glu265Gln	p.E265Q	ENST00000371998		265	Gag/Cag	8/23	1	2	FACETS	0.537	0.454	0.628	0.537	0.454	0.628	SUBCLONAL	1	FALSE	1	0.251154510931597	2		421	742	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121008	29121008	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	63	579	0	ENST00000328354.6:c.549G>T	p.Leu183Phe	p.L183F	ENST00000328354	NM_007194.3	183	ttG/ttT	4/15	1	2	FACETS	0.592	0.511	0.681	0.592	0.511	0.681	SUBCLONAL	1	FALSE	1	0.251154510931597	2		579	847	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180539	56180539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	33	263	0	ENST00000399503.3:c.3868G>T	p.Ala1290Ser	p.A1290S	ENST00000399503	NM_005921.1	1290	Gca/Tca	16/20	1	2	FACETS	0.688	0.561	0.831	0.688	0.561	0.831	SUBCLONAL	1	FALSE	1	0.251154510931597	2		263	382	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401699	401699	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	97	575	0	ENST00000380956.4:c.1021G>T	p.Ala341Ser	p.A341S	ENST00000380956	NM_001195286.1	341	Gcg/Tcg	7/9	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	1	0.251154510931597	2		575	688	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982053	93982053	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	83	379	1	ENST00000369303.4:c.1412G>T	p.Gly471Val	p.G471V	ENST00000369303	NM_004440.3	471	gGa/gTa	6/17	0.251154510931597	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	0	0.251154510931597	1		380	504	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372037	55372037	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	45	440	0	ENST00000297316.4:c.727G>C	p.Gly243Arg	p.G243R	ENST00000297316	NM_022454.3	243	Ggg/Cgg	2/2	0.251154510931597	1	FACETS	0.724	0.609	0.85	0.724	0.609	0.85	SUBCLONAL	1	FALSE	0	0.251154510931597	1		440	433	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549115	87549115	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	50	498	0	ENST00000277120.3:c.1672A>T	p.Arg558Trp	p.R558W	ENST00000277120		558	Agg/Tgg	15/19	0.166868990230275	0	FACETS	0.499	0.423	0.583			1	SUBCLONAL	1	FALSE	0	0.251154510931597	0		498	597	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0057041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	23	357	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	1	2	FACETS	0.284	0.22	0.357	0.284	0.22	0.357	SUBCLONAL	1	TRUE	1	0.32	2		357	507	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241677	55241677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504256	NA	P-0057041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	71	649	1	ENST00000275493.2:c.2125G>A	p.Glu709Lys	p.E709K	ENST00000275493	NM_005228.3	709	Gaa/Aaa	18/28	1	2	FACETS	0.607	0.529	0.691	0.607	0.529	0.691	SUBCLONAL	1	TRUE	1	0.32	2		650	731	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0057041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	56	558	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	1	2	FACETS	0.525	0.449	0.608	0.525	0.449	0.608	SUBCLONAL	1	TRUE	1	0.32	2		558	667	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974760	21974760	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691186	NA	P-0057041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	18	242	0	ENST00000304494.5:c.67G>T	p.Gly23Cys	p.G23C	ENST00000304494	NM_000077.4	23	Ggt/Tgt	1/3	1	2	FACETS	0.516	0.389	0.665	0.516	0.389	0.665	SUBCLONAL	1	TRUE	1	0.32	2		242	218	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087555	27087555	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1171422700	NA	P-0057041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	68	644	0	ENST00000324856.7:c.2129G>T	p.Arg710Leu	p.R710L	ENST00000324856	NM_006015.4	710	cGc/cTc	5/20	NA	2	FACETS	0.551	0.478	0.629			1	INDETERMINATE	1	TRUE	NA	0.32	2		644	772	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414966	56414966	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	32	465	0	ENST00000348428.3:c.2369del	p.Phe790SerfsTer16	p.F790Sfs*16	ENST00000348428	NM_006785.3	789	agT/ag	17/17	1	2	FACETS	0.347	0.28	0.422	0.347	0.28	0.422	SUBCLONAL	1	TRUE	1	0.32	2		465	577	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625689	1625689	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	65	732	0	ENST00000344749.5:c.385G>T	p.Glu129Ter	p.E129*	ENST00000344749	NM_001136139.2	129	Gag/Tag	7/19	1	2	FACETS	0.523	0.452	0.6	0.523	0.452	0.6	SUBCLONAL	1	TRUE	1	0.32	2		732	777	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035054	37035054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	40	427	0	ENST00000231790.2:c.16G>A	p.Gly6Arg	p.G6R	ENST00000231790	NM_000249.3	6	Ggg/Agg	1/19	1	2	FACETS	0.419	0.348	0.5	0.419	0.348	0.5	SUBCLONAL	1	TRUE	1	0.32	2		427	596	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0057042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	358	418	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.549059692726999	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.549059692726999	2		418	523	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0057042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	100	281	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.936	0.843	1	0.936	0.843	1	CLONAL	1	TRUE	1	0.549059692726999	2		281	389	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087378	27087379	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0057042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	167	525	0	ENST00000324856.7:c.1956dup	p.Thr653AspfsTer23	p.T653Dfs*23	ENST00000324856	NM_006015.4	651	atg/atGg	5/20	1	2	FACETS	0.948	0.874	1	0.948	0.874	1	CLONAL	1	TRUE	1	0.549059692726999	2		525	642	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380346	14380346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	161	316	1	ENST00000256196.4:c.71G>A	p.Gly24Asp	p.G24D	ENST00000256196		24	gGc/gAc	1/6	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.549059692726999	2		317	547	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101585	27101586	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGCC	novel	NA	P-0057042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	248	679	0	ENST00000324856.7:c.4870_4871insCCGC	p.His1624ProfsTer25	p.H1624Pfs*25	ENST00000324856	NM_006015.4	1623	tcg/tCGCCcg	18/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.549059692726999	2		679	900	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193110980	193110980	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	30	135	0	ENST00000367435.3:c.513G>C	p.Arg171Ser	p.R171S	ENST00000367435	NM_024529.4	171	agG/agC	7/17	1	2	FACETS	0.934	0.768	1	0.934	0.768	1	CLONAL	1	TRUE	1	0.549059692726999	2		135	117	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	310	324	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.812927010225263	2		324	643	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0057043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	773	895	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	0.516331670543324	1	FACETS	0.894	0.87	0.918	0.894	0.87	0.918	CLONAL	1	TRUE	0	0.812927010225263	1		895	1263	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	259	406	0	ENST00000335508.6:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000335508	NM_012433.2	902	Gaa/Aaa	18/25	0.811832349787227	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.812927010225263	1		406	343	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942817	44942817	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	662	305	0	ENST00000377967.4:c.3397C>T	p.Gln1133Ter	p.Q1133*	ENST00000377967	NM_021140.2	1133	Caa/Taa	23/29	0.812927010225263	2	FACETS	1	0.998	1			1	CLONAL	2	TRUE	NA	0.812927010225263	2		305	710	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129169	64129169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746466314	NA	P-0057043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	535	841	0	ENST00000334205.4:c.707C>T	p.Ser236Leu	p.S236L	ENST00000334205	NM_003942.2	236	tCg/tTg	7/17	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.812927010225263	2		841	1196	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59934481	59934481	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143615668	NA	P-0057043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	294	387	0	ENST00000259008.2:c.317G>A	p.Arg106His	p.R106H	ENST00000259008	NM_032043.2	106	cGt/cAt	4/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.812927010225263	2		387	700	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166279	118166279	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	283	349	0	ENST00000369448.3:c.789C>G	p.Ile263Met	p.I263M	ENST00000369448	NM_017709.3	263	atC/atG	2/2	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.812927010225263	2		349	625	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662275	67662275	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	158	415	0	ENST00000264010.4:c.1521G>C	p.Glu507Asp	p.E507D	ENST00000264010	NM_006565.3	507	gaG/gaC	9/12	0.374104072484162	1	FACETS	0.478	0.441	0.515	0.478	0.441	0.515	INDETERMINATE	1	TRUE	0	0.812927010225263	1		415	483	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198264978	198264978	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	259	290	0	ENST00000335508.6:c.2899G>C	p.Glu967Gln	p.E967Q	ENST00000335508	NM_012433.2	967	Gag/Cag	19/25	0.811832349787227	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.812927010225263	1		290	317	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089704	27089705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	526	684	0	ENST00000324856.7:c.2661dup	p.Gly888ArgfsTer48	p.G888Rfs*48	ENST00000324856	NM_006015.4	887	cca/ccAa	8/20	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.812927010225263	2		684	1139	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101551	27101551	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	597	826	1	ENST00000324856.7:c.4833G>A	p.Met1611Ile	p.M1611I	ENST00000324856	NM_006015.4	1611	atG/atA	18/20	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.812927010225263	2		827	1312	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981549	201981559	+	frameshift_variant	Frame_Shift_Del	DEL	GACCCAGGGCC	GACCCAGGGCC	-	novel	NA	P-0057043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	492	916	0	ENST00000359651.3:c.463_473del	p.Asp155LeufsTer2	p.D155Lfs*2	ENST00000359651		155	GACCCAGGGCCc/c	3/8	0.583408201047179	3	FACETS	1	0.981	1	0.523	0.499	0.547	CLONAL	1	TRUE	1	0.812927010225263	3		916	1628	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89811455	89811455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372706571	NA	P-0057043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	359	727	2	ENST00000389301.3:c.3538G>A	p.Val1180Met	p.V1180M	ENST00000389301	NM_000135.2	1180	Gtg/Atg	36/43	0.374104072484162	1	FACETS	0.515	0.489	0.541	0.515	0.489	0.541	INDETERMINATE	1	TRUE	0	0.812927010225263	1		729	1018	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265516	198265516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	365	529	0	ENST00000335508.6:c.2641G>A	p.Ala881Thr	p.A881T	ENST00000335508	NM_012433.2	881	Gca/Aca	18/25	0.811832349787227	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.812927010225263	1		529	489	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169999015	169999015	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	244	318	0	ENST00000295797.4:c.944T>C	p.Leu315Pro	p.L315P	ENST00000295797	NM_002740.5	315	cTt/cCt	10/18	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.812927010225263	2		318	528	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950357	38950357	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	371	464	0	ENST00000357387.3:c.3593C>G	p.Thr1198Arg	p.T1198R	ENST00000357387	NM_152756.3	1198	aCa/aGa	31/38	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.812927010225263	2		464	751	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651884	36651885	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0057043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	403	625	0	ENST00000244741.5:c.7dup	p.Glu3GlyfsTer33	p.E3Gfs*33	ENST00000244741	NM_000389.4	2	-/G	2/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.812927010225263	2		625	949	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	124	378	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	1	2	FACETS	0.835	0.762	0.91	0.835	0.762	0.91	CLONAL	1	TRUE	1	0.728171386115131	2		378	408	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11308133	11308133	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	164	444	0	ENST00000361445.4:c.859G>T	p.Glu287Ter	p.E287*	ENST00000361445	NM_004958.3	287	Gaa/Taa	7/58	0.721316012216815	3	FACETS	0.904	0.832	0.978	0.452	0.416	0.489	CLONAL	1	TRUE	1	0.728171386115131	3		444	680	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089618	27089618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	184	565	1	ENST00000324856.7:c.2574G>A	p.Met858Ile	p.M858I	ENST00000324856	NM_006015.4	858	atG/atA	8/20	0.721316012216815	3	FACETS	0.943	0.873	1	0.472	0.436	0.508	CLONAL	1	TRUE	1	0.728171386115131	3		566	731	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195946	102195946	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	26	261	0	ENST00000263464.3:c.706G>C	p.Glu236Gln	p.E236Q	ENST00000263464	NM_001165.4	236	Gaa/Caa	2/9	0.683284909897359	2	FACETS	0.225	0.178	0.278	0.112	0.089	0.139	SUBCLONAL	1	TRUE	0	0.728171386115131	2		261	318	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372495	118372495	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	217	546	0	ENST00000534358.1:c.6428C>G	p.Ser2143Ter	p.S2143*	ENST00000534358	NM_005933.3	2143	tCa/tGa	26/36	0.683284909897359	2	FACETS	0.942	0.881	1	0.471	0.44	0.502	CLONAL	1	TRUE	0	0.728171386115131	2		546	633	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373170	118373170	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555045999	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	143	399	0	ENST00000534358.1:c.6563C>G	p.Ser2188Cys	p.S2188C	ENST00000534358	NM_005933.3	2188	tCt/tGt	27/36	0.683284909897359	2	FACETS	0.916	0.842	0.991	0.458	0.421	0.496	CLONAL	1	TRUE	0	0.728171386115131	2		399	429	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392046	118392046	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	176	392	0	ENST00000534358.1:c.11557G>A	p.Asp3853Asn	p.D3853N	ENST00000534358	NM_005933.3	3853	Gat/Aat	35/36	0.683284909897359	2	FACETS	0.905	0.84	0.972	0.453	0.42	0.486	CLONAL	1	TRUE	0	0.728171386115131	2		392	534	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335867	73335867	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	156	353	0	ENST00000377767.4:c.2428C>G	p.Leu810Val	p.L810V	ENST00000377767	NM_014953.3	810	Ctt/Gtt	18/21	0.689191953784032	2	FACETS	0.88	0.812	0.95	0.44	0.406	0.475	CLONAL	1	TRUE	0	0.728171386115131	2		353	487	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724750	43724750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	204	488	0	ENST00000382044.4:c.3317C>T	p.Ser1106Phe	p.S1106F	ENST00000382044	NM_001141980.1	1106	tCt/tTt	17/28	0.687899291613908	2	FACETS	0.937	0.874	1	0.468	0.437	0.501	CLONAL	1	TRUE	0	0.728171386115131	2		488	598	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994679	73994679	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	172	777	0	ENST00000318443.5:c.163G>C	p.Glu55Gln	p.E55Q	ENST00000318443	NM_001024736.1	55	Gag/Cag	3/10	0.721316012216815	3	FACETS	0.73	0.672	0.79	0.365	0.336	0.395	SUBCLONAL	1	TRUE	1	0.728171386115131	3		777	883	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103427	2103427	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	41	810	0	ENST00000219476.3:c.310C>G	p.Leu104Val	p.L104V	ENST00000219476	NM_000548.3	104	Ctg/Gtg	4/42	1	2	FACETS	0.151	0.125	0.18	0.151	0.125	0.18	SUBCLONAL	1	TRUE	1	0.728171386115131	2		810	744	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658911	3658911	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	191	492	0	ENST00000294008.3:c.55C>T	p.His19Tyr	p.H19Y	ENST00000294008	NM_032444.2	19	Cat/Tat	2/15	1	2	FACETS	0.912	0.849	0.977	0.912	0.849	0.977	CLONAL	1	TRUE	1	0.728171386115131	2		492	575	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632792	23632792	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	121	365	0	ENST00000261584.4:c.3004G>C	p.Glu1002Gln	p.E1002Q	ENST00000261584	NM_024675.3	1002	Gaa/Caa	10/13	1	2	FACETS	0.803	0.731	0.877	0.803	0.731	0.877	CLONAL	1	TRUE	1	0.728171386115131	2		365	414	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348736	89348736	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs977735530	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	65	848	0	ENST00000301030.4:c.4214C>G	p.Ser1405Cys	p.S1405C	ENST00000301030	NM_001256183.1	1405	tCt/tGt	9/13	1	2	FACETS	0.193	0.167	0.222	0.193	0.167	0.222	SUBCLONAL	1	TRUE	1	0.728171386115131	2		848	923	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578233	7578235	+	inframe_deletion	In_Frame_Del	DEL	AAT	AAT	-	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	434	670	0	ENST00000269305.4:c.614_616del	p.Tyr205del	p.Y205del	ENST00000269305	NM_001126112.2	205	tATTtg/ttg	6/11	0.689191953784032	2	FACETS	0.957	0.926	0.987	0.957	0.926	0.987	CLONAL	2	TRUE	0	0.728171386115131	2		670	623	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961026	15961026	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	109	301	0	ENST00000268712.3:c.6194G>C	p.Arg2065Thr	p.R2065T	ENST00000268712	NM_006311.3	2065	aGa/aCa	40/46	0.689191953784032	2	FACETS	0.786	0.712	0.863	0.393	0.356	0.432	SUBCLONAL	1	TRUE	0	0.728171386115131	2		301	381	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968988	15968988	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	134	367	0	ENST00000268712.3:c.4762C>G	p.Gln1588Glu	p.Q1588E	ENST00000268712	NM_006311.3	1588	Cag/Gag	33/46	0.689191953784032	2	FACETS	0.939	0.862	1	0.469	0.431	0.509	CLONAL	1	TRUE	0	0.728171386115131	2		367	392	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733240	74733240	+	start_lost	Translation_Start_Site	SNP	C	C	G	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	116	450	0	ENST00000359995.5:c.3G>C	p.Met1?	p.M1?	ENST00000359995	NM_001195427.1	1	atG/atC	1/3	0.728171386115131	6	FACETS	0.699	0.629	0.774	0.117	0.104	0.13	SUBCLONAL	1	TRUE	0	0.728171386115131	6		450	1119	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222067	2222067	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	196	796	0	ENST00000398665.3:c.2899G>A	p.Glu967Lys	p.E967K	ENST00000398665	NM_032482.2	967	Gag/Aag	24/28	1	2	FACETS	0.78	0.725	0.837	0.78	0.725	0.837	SUBCLONAL	1	TRUE	1	0.728171386115131	2		796	690	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873796	45873796	+	start_lost,splice_region_variant	Translation_Start_Site	SNP	C	C	A	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	135	412	0	ENST00000391945.4:c.3G>T	p.Met1?	p.M1?	ENST00000391945	NM_000400.3	1	atG/atT	1/23	1	2	FACETS	0.866	0.794	0.941	0.866	0.794	0.941	CLONAL	1	TRUE	1	0.728171386115131	2		412	428	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250303	39250303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1212129369	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	259	704	0	ENST00000402219.2:c.1266G>A	p.Met422Ile	p.M422I	ENST00000402219	NM_005633.3	422	atG/atA	10/23	0.728171386115131	3	FACETS	0.889	0.832	0.947	0.444	0.416	0.474	CLONAL	1	TRUE	1	0.728171386115131	3		704	1092	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39294771	39294771	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	106	237	0	ENST00000402219.2:c.211G>C	p.Glu71Gln	p.E71Q	ENST00000402219	NM_005633.3	71	Gag/Cag	2/23	0.728171386115131	3	FACETS	0.807	0.727	0.891	0.404	0.363	0.446	CLONAL	1	TRUE	1	0.728171386115131	3		237	492	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257071	198257071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	161	355	0	ENST00000335508.6:c.3871G>A	p.Asp1291Asn	p.D1291N	ENST00000335508	NM_012433.2	1291	Gat/Aat	25/25	1	2	FACETS	0.841	0.776	0.907	0.841	0.776	0.907	CLONAL	1	TRUE	1	0.728171386115131	2		355	526	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439845	220439845	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	223	746	0	ENST00000243786.2:c.698C>G	p.Ser233Ter	p.S233*	ENST00000243786	NM_002191.3	233	tCa/tGa	2/2	1	2	FACETS	0.902	0.844	0.961	0.902	0.844	0.961	CLONAL	1	TRUE	1	0.728171386115131	2		746	679	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651292	52651292	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	115	375	0	ENST00000394830.3:c.1804G>C	p.Glu602Gln	p.E602Q	ENST00000394830	NM_018313.4	602	Gag/Cag	15/30	0.689191953784032	2	FACETS	0.649	0.587	0.713	0.324	0.293	0.357	SUBCLONAL	1	TRUE	0	0.728171386115131	2		375	487	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52661287	52661287	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	141	300	0	ENST00000394830.3:c.1541+2T>C		p.X514_splice	ENST00000394830	NM_018313.4	514			0.689191953784032	2	FACETS	0.905	0.832	0.98	0.452	0.416	0.49	CLONAL	1	TRUE	0	0.728171386115131	2		300	428	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191223	185191223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	122	376	0	ENST00000265026.3:c.2104G>A	p.Ala702Thr	p.A702T	ENST00000265026	NM_004721.4	702	Gcc/Acc	11/14	0.65033484307472	4	FACETS	0.97	0.879	1	0.485	0.439	0.533	CLONAL	1	TRUE	2	0.728171386115131	4		376	597	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980367	55980367	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1564	135	334	0	ENST00000263923.4:c.724C>G	p.Leu242Val	p.L242V	ENST00000263923	NM_002253.2	242	Ctt/Gtt	6/30	0.728171386115131	9	FACETS	0.774	0.701	0.852			1	SUBCLONAL	1	TRUE	NA	0.728171386115131	9		334	1699	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158049	106158049	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	122	243	0	ENST00000380013.4:c.2950G>T	p.Glu984Ter	p.E984*	ENST00000380013	NM_001127208.2	984	Gaa/Taa	3/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.728171386115131	2		243	302	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931423	131931423	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	186	274	0	ENST00000265335.6:c.2128G>C	p.Asp710His	p.D710H	ENST00000265335		710	Gat/Cat	13/25	0.510733265166787	3	FACETS	1	0.991	1	0.74	0.69	0.79	CLONAL	1	TRUE	1	0.728171386115131	3		274	471	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004232	150004232	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	109	210	0	ENST00000253339.5:c.1993G>C	p.Glu665Gln	p.E665Q	ENST00000253339		665	Gag/Cag	3/7	0.542589438198659	3	FACETS	0.83	0.749	0.915			1	CLONAL	1	TRUE	NA	0.728171386115131	3		210	492	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859299	151859299	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	43	264	0	ENST00000262189.6:c.11363C>G	p.Ser3788Cys	p.S3788C	ENST00000262189	NM_170606.2	3788	tCt/tGt	43/59	0.689191953784032	2	FACETS	0.301	0.252	0.354	0.15	0.126	0.177	SUBCLONAL	1	TRUE	0	0.728171386115131	2		264	393	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187168	38187168	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1305	281	643	0	ENST00000317025.8:c.1309G>C	p.Glu437Gln	p.E437Q	ENST00000317025	NM_023034.1	437	Gag/Cag	6/24	0.728171386115131	4	FACETS	0.841	0.788	0.896			1	CLONAL	1	TRUE	NA	0.728171386115131	4		643	1586	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002888	69002888	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	44	290	0	ENST00000288368.4:c.2188G>T	p.Glu730Ter	p.E730*	ENST00000288368	NM_024870.2	730	Gag/Tag	20/40	1	2	FACETS	0.35	0.294	0.412	0.35	0.294	0.412	SUBCLONAL	1	TRUE	1	0.728171386115131	2		290	345	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009404	69009404	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	53	425	0	ENST00000288368.4:c.2521G>C	p.Glu841Gln	p.E841Q	ENST00000288368	NM_024870.2	841	Gag/Cag	22/40	1	2	FACETS	0.274	0.233	0.318	0.274	0.233	0.318	SUBCLONAL	1	TRUE	1	0.728171386115131	2		425	532	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69012038	69012038	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	84	468	0	ENST00000288368.4:c.2675G>C	p.Arg892Thr	p.R892T	ENST00000288368	NM_024870.2	892	aGa/aCa	23/40	1	2	FACETS	0.37	0.327	0.416	0.37	0.327	0.416	SUBCLONAL	1	TRUE	1	0.728171386115131	2		468	624	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020539	69020539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	67	410	0	ENST00000288368.4:c.2911G>T	p.Asp971Tyr	p.D971Y	ENST00000288368	NM_024870.2	971	Gat/Tat	24/40	1	2	FACETS	0.392	0.341	0.446	0.392	0.341	0.446	SUBCLONAL	1	TRUE	1	0.728171386115131	2		410	470	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028127	69028127	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	65	491	0	ENST00000288368.4:c.3286G>C	p.Asp1096His	p.D1096H	ENST00000288368	NM_024870.2	1096	Gat/Cat	26/40	1	2	FACETS	0.324	0.281	0.371	0.324	0.281	0.371	SUBCLONAL	1	TRUE	1	0.728171386115131	2		491	551	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518223	8518223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	117	320	0	ENST00000356435.5:c.1168G>A	p.Glu390Lys	p.E390K	ENST00000356435		390	Gaa/Aaa	10/35	0.690946345601137	3	FACETS	0.949	0.861	1	0.316	0.287	0.347	CLONAL	1	TRUE	0	0.728171386115131	3		320	462	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123505207	123505207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	143	121	0	ENST00000371139.4:c.353G>A	p.Arg118Lys	p.R118K	ENST00000371139	NM_001114937.2	118	aGa/aAa	4/4	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.728171386115131	1		121	199	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0057045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	134	376	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	0.355174827024004	4	FACETS	0.991	0.905	1	0.991	0.905	1	CLONAL	2	TRUE	2	0.355174827024004	4		376	516	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141549424	141549424	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	108	269	0	ENST00000220592.5:c.2164G>A	p.Glu722Lys	p.E722K	ENST00000220592	NM_012154.3	722	Gag/Aag	16/19	0.192557926599429	5	FACETS	1	0.942	1	0.706	0.638	0.778	INDETERMINATE	2	TRUE	2	0.355174827024004	5		269	440	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422465	225422465	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	73	354	0	ENST00000264414.4:c.175A>G	p.Arg59Gly	p.R59G	ENST00000264414	NM_003590.4	59	Aga/Gga	2/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.670775447643241	2		354	186	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191555	10191555	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs5030823	NA	P-0057046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	113	479	0	ENST00000256474.2:c.548C>A	p.Ser183Ter	p.S183*	ENST00000256474	NM_000551.3	183	tCg/tAg	3/3	0.655718809529965	1	FACETS	0.986	0.909	1	0.986	0.909	1	CLONAL	1	FALSE	0	0.670775447643241	1		479	227	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307316	118307316	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs9332745	NA	P-0057046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	13	0	0	ENST00000534358.1:c.89C>G	p.Ala30Gly	p.A30G	ENST00000534358	NM_005933.3	30	gCc/gGc	1/36	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	FALSE	1	0.670775447643241	2		0	31	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422457	225422461	+	frameshift_variant	Frame_Shift_Del	DEL	TGCAT	TGCAT	-	novel	NA	P-0057046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	41	378	0	ENST00000264414.4:c.179_183del	p.Asn60IlefsTer7	p.N60Ifs*7	ENST00000264414	NM_003590.4	60	aATGCA/a	2/16	1	2	FACETS	0.699	0.59	0.815	0.699	0.59	0.815	SUBCLONAL	1	FALSE	1	0.670775447643241	2		378	175	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131976452	131976452	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	84	446	0	ENST00000265335.6:c.3707A>C	p.Asn1236Thr	p.N1236T	ENST00000265335		1236	aAt/aCt	24/25	1	2	FACETS	0.99	0.887	1	0.99	0.887	1	CLONAL	1	FALSE	1	0.670775447643241	2		446	253	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225160	53225160	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1556836399	NA	P-0057046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	138	279	0	ENST00000375401.3:c.3058C>T	p.Gln1020Ter	p.Q1020*	ENST00000375401	NM_004187.3	1020	Cag/Tag	20/26	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	0	0.670775447643241	1		279	213	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435201	18435202	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1565550462	NA	P-0057048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	63	309	0	ENST00000266497.5:c.192dup	p.Val65CysfsTer16	p.V65Cfs*16	ENST00000266497		62	-/T	1/31	0.16764949083134	3	FACETS	0.862	0.748	0.986	0.862	0.748	0.986	CLONAL	2	FALSE	1	0.169706702411708	3		309	467	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961493	41961493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771815727	NA	P-0057048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	142	579	0	ENST00000219905.7:c.401G>A	p.Arg134His	p.R134H	ENST00000219905	NM_001164273.1	134	cGt/cAt	2/24	1	2	FACETS	1	0.938	1	1	0.991	1	CLONAL	2	FALSE	1	0.169706702411708	2		579	808	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11210254	11210254	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	127	604	1	ENST00000361445.4:c.4499A>G	p.Lys1500Arg	p.K1500R	ENST00000361445	NM_004958.3	1500	aAg/aGg	31/58	1	2	FACETS	0.844	0.764	0.928	1	0.987	1	CLONAL	2	FALSE	1	0.169706702411708	2		605	887	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434872	110434872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	101	908	2	ENST00000375856.3:c.3529G>A	p.Val1177Met	p.V1177M	ENST00000375856	NM_003749.2	1177	Gtg/Atg	1/2	0.172868150798411	0	FACETS	0.966	0.862	1			1	CLONAL	1	FALSE	0	0.169706702411708	0		910	1023	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022325	26022326	+	stop_gained	Nonsense_Mutation	INS	-	-	AACTCTGGGACCATC	novel	NA	P-0057048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	117	615	0	ENST00000435504.4:c.331_332insGATGGTCCCAGAGTT	p.Ser110_Ser111insTer	p.S110_S111ins*	ENST00000435504		111	tct/tGATGGTCCCAGAGTTct	5/13	0.172868150798411	4	FACETS	1	0.981	1	0.47	0.422	0.52	CLONAL	1	FALSE	1	0.169706702411708	4		615	1145	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0057049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	212	728	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.483445049762939	1	FACETS	0.999	0.932	1	0.999	0.932	1	CLONAL	1	TRUE	0	0.483445049762939	1		728	666	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0057049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	193	494	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	1	2	FACETS	0.982	0.91	1	0.982	0.91	1	CLONAL	1	TRUE	1	0.483445049762939	2		494	813	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947596	48947596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1566196458	NA	P-0057049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	98	271	0	ENST00000267163.4:c.1183C>T	p.Gln395Ter	p.Q395*	ENST00000267163	NM_000321.2	395	Caa/Taa	12/27	0.483445049762939	1	FACETS	0.967	0.872	1	0.967	0.872	1	CLONAL	1	TRUE	0	0.483445049762939	1		271	318	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913274	NA	P-0057049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	47	494	0	ENST00000263967.3:c.1634A>C	p.Glu545Ala	p.E545A	ENST00000263967	NM_006218.2	545	gAg/gCg	10/21	0.483445049762939	6	FACETS	0.687	0.579	0.806	0.137	0.115	0.162	SUBCLONAL	1	TRUE	1	0.483445049762939	6		494	557	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152864480	152864481	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	rs782693729	NA	P-0057049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	24	25	0	ENST00000406277.2:c.47dup	p.Ala19GlyfsTer37	p.A19Gfs*37	ENST00000406277	NM_152274.4	16	gag/gaAg	2/7	NA		FACETS		NA	1				INDETERMINATE	NA	TRUE	NA	0.483445049762939	NA		25	44	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545758	106545758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	158	464	0	ENST00000359195.3:c.3235G>A	p.Gly1079Arg	p.G1079R	ENST00000359195	NM_002649.2	1079	Gga/Aga	11/11	1	2	FACETS	0.993	0.913	1	0.993	0.913	1	CLONAL	1	TRUE	1	0.483445049762939	2		464	658	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912821	100912821	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	88	283	0	ENST00000325455.5:c.2501G>T	p.Gly834Val	p.G834V	ENST00000325455	NM_001202474.3	834	gGg/gTg	7/8	1	2	FACETS	0.971	0.866	1	0.971	0.866	1	CLONAL	1	TRUE	1	0.483445049762939	2		283	375	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996800	100996800	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	122	432	0	ENST00000325455.5:c.1727G>A	p.Gly576Asp	p.G576D	ENST00000325455	NM_001202474.3	576	gGc/gAc	2/8	1	2	FACETS	0.918	0.833	1	0.918	0.833	1	CLONAL	1	TRUE	1	0.483445049762939	2		432	550	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378700	25378700	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	23	213	0	ENST00000311936.3:c.298A>G	p.Ile100Val	p.I100V	ENST00000311936	NM_004985.3	100	Att/Gtt	4/5	1	2	FACETS	0.307	0.239	0.385	0.307	0.239	0.385	SUBCLONAL	1	TRUE	1	0.483445049762939	2		213	310	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435384	110435384	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	144	467	0	ENST00000375856.3:c.3017T>C	p.Leu1006Pro	p.L1006P	ENST00000375856	NM_003749.2	1006	cTg/cCg	1/2	1	2	FACETS	0.843	0.77	0.918	0.843	0.77	0.918	CLONAL	1	TRUE	1	0.483445049762939	2		467	707	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670797	134670797	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	118	395	0	ENST00000398015.3:c.708C>G	p.Ile236Met	p.I236M	ENST00000398015	NM_004441.4	236	atC/atG	3/16	0.427974460864224	4	FACETS	0.977	0.882	1	0.326	0.294	0.359	CLONAL	1	TRUE	1	0.483445049762939	4		395	741	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771188	161771188	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	218	591	1	ENST00000366898.1:c.1341G>T	p.Trp447Cys	p.W447C	ENST00000366898	NM_004562.2	447	tgG/tgT	12/12	0.4157707741046	3	FACETS	1	0.982	1	0.578	0.538	0.62	CLONAL	1	TRUE	1	0.483445049762939	3		592	968	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0057050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	84	296	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.38761762023659	2		296	360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0057050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	20	1044	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.38761762023659	1	FACETS	0.092	0.069	0.118	0.092	0.069	0.118	SUBCLONAL	1	TRUE	0	0.38761762023659	1		1044	909	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196808	108196808	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1339794219	NA	P-0057050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	64	267	0	ENST00000278616.4:c.6831A>T	p.Gln2277His	p.Q2277H	ENST00000278616	NM_000051.3	2277	caA/caT	47/63	0.38761762023659	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.38761762023659	1		267	215	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022638	31022638	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	122	652	0	ENST00000375687.4:c.2123A>T	p.Gln708Leu	p.Q708L	ENST00000375687	NM_015338.5	708	cAg/cTg	13/13	1	2	FACETS	0.993	0.9	1	0.993	0.9	1	CLONAL	1	TRUE	1	0.38761762023659	2		652	634	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738449	145738449	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	161	812	3	ENST00000428558.2:c.2536G>A	p.Val846Ile	p.V846I	ENST00000428558	NM_004260.3	846	Gta/Ata	16/22	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.38761762023659	2		815	743	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0057056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	110	597	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.501	0.453	0.551	0.501	0.453	0.551	SUBCLONAL	1	TRUE	1	0.967519556908803	2		597	454	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0057056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	116	517	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.509	0.461	0.559	0.509	0.461	0.559	SUBCLONAL	1	TRUE	1	0.967519556908803	2		517	471	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0057056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	81	398	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.522	0.464	0.583	0.522	0.464	0.583	SUBCLONAL	1	TRUE	1	0.967519556908803	2		398	321	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0057057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	202	754	2	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.933	0.873	0.994	0.933	0.873	0.994	CLONAL	1	FALSE	1	0.847376267435167	2		756	511	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571907	64571907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	618	855	0	ENST00000312049.6:c.1732C>T	p.Gln578Ter	p.Q578*	ENST00000312049	NM_130799.2	578	Caa/Taa	10/10	0.847376267435167	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	0	0.847376267435167	1		855	817	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937626	76937626	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1412505197	NA	P-0057057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	54	342	0	ENST00000373344.5:c.3122A>T	p.Asp1041Val	p.D1041V	ENST00000373344	NM_000489.3	1041	gAt/gTt	9/35	1	2	FACETS	0.782	0.681	0.887	0.782	0.681	0.887	SUBCLONAL	1	FALSE	1	0.847376267435167	2		342	163	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	57	324	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.290934811995151	NA		324	343	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589623	67589634	+	inframe_deletion	In_Frame_Del	DEL	ATATGATAGATT	ATATGATAGATT	-	novel	NA	P-0057058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	25	220	0	ENST00000274335.5:c.1392_1403del	p.Asp464_Tyr467del	p.D464_Y467del	ENST00000274335		462	gaATATGATAGATTa/gaa	10/15	1	2	FACETS	0.567	0.447	0.704	0.567	0.447	0.704	SUBCLONAL	1	TRUE	1	0.290934811995151	2		220	303	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868350	45868350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765679315	NA	P-0057058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	141	664	1	ENST00000391945.4:c.427C>T	p.Arg143Trp	p.R143W	ENST00000391945	NM_000400.3	143	Cgg/Tgg	6/23	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.290934811995151	2		665	941	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653844	89653844	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	156	242	0	ENST00000371953.3:c.143del	p.Asn48ThrfsTer6	p.N48Tfs*6	ENST00000371953	NM_000314.4	48	Aac/ac	2/9	0.290934811995151	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	0	0.290934811995151	2		242	518	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911936	94911936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1202546852	NA	P-0057058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	81	356	0	ENST00000536441.1:c.994G>A	p.Gly332Ser	p.G332S	ENST00000536441	NM_144665.3	332	Ggt/Agt	7/10	1	2	FACETS	0.908	0.801	1	0.908	0.801	1	CLONAL	1	TRUE	1	0.290934811995151	2		356	613	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030593	11030597	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGT	CTGGT	-	novel	NA	P-0057058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	93	472	0	ENST00000327064.4:c.1148_1152del	p.Leu383ProfsTer8	p.L383Pfs*8	ENST00000327064	NM_199141.1	383	CTGGTc/c	10/16	1	2	FACETS	0.975	0.867	1	0.975	0.867	1	CLONAL	1	TRUE	1	0.290934811995151	2		472	656	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023754	31023754	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	79	431	0	ENST00000375687.4:c.3239T>C	p.Leu1080Pro	p.L1080P	ENST00000375687	NM_015338.5	1080	cTa/cCa	13/13	1	2	FACETS	0.752	0.661	0.85	0.752	0.661	0.85	SUBCLONAL	1	TRUE	1	0.290934811995151	2		431	722	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43700210	43700225	+	frameshift_variant	Frame_Shift_Del	DEL	AGAGCTCCAGGAAGTT	AGAGCTCCAGGAAGTT	TG	novel	NA	P-0057058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	90	444	1	ENST00000382044.4:c.5662_5677delinsCA	p.Asn1888GlnfsTer3	p.N1888Qfs*3	ENST00000382044	NM_001141980.1	1888	AACTTCCTGGAGCTCTgg/CAgg	27/28	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.290934811995151	2		445	588	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0057064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	174	317	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.286144960401336	4	FACETS	1	0.952	1	1	0.952	1	CLONAL	3	FALSE	1	0.286144960401336	4		317	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0057064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	100	719	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.233600915450211	1	FACETS	0.77	0.687	0.858	0.77	0.687	0.858	SUBCLONAL	1	FALSE	0	0.286144960401336	1		719	778	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs377767347	NA	P-0057064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	49	402	0	ENST00000342988.3:c.1082G>T	p.Arg361Leu	p.R361L	ENST00000342988	NM_005359.5	361	cGc/cTc	9/12	0.286144960401336	1	FACETS	0.611	0.518	0.714	0.611	0.518	0.714	SUBCLONAL	1	FALSE	0	0.286144960401336	1		402	480	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434967	110434967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	101	627	1	ENST00000375856.3:c.3434G>A	p.Arg1145His	p.R1145H	ENST00000375856	NM_003749.2	1145	cGc/cAc	1/2	1	2	FACETS	0.861	0.769	0.959	0.861	0.769	0.959	CLONAL	1	FALSE	1	0.286144960401336	2		628	820	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555739	21555739	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	108	689	0	ENST00000382592.4:c.2531A>G	p.Asp844Gly	p.D844G	ENST00000382592	NM_014572.2	844	gAt/gGt	6/8	1	2	FACETS	0.844	0.757	0.937	0.844	0.757	0.937	CLONAL	1	FALSE	1	0.286144960401336	2		689	894	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0057065-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	207	508	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.273816460174849	2	FACETS	0.842	0.784	0.9	0.842	0.784	0.9	CLONAL	2	TRUE	0	0.357529579127755	2		508	688	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057065-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	88	330	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.357529579127755	2		330	354	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0057065-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	73	381	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.357529579127755	1	FACETS	0.552	0.483	0.627	0.552	0.483	0.627	SUBCLONAL	1	TRUE	0	0.357529579127755	1		381	607	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs730881677	NA	P-0057065-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	98	464	0	ENST00000304494.5:c.151-1G>C		p.X51_splice	ENST00000304494	NM_000077.4	51			0.357529579127755	1	FACETS	0.97	0.87	1	0.97	0.87	1	CLONAL	1	TRUE	0	0.357529579127755	1		464	464	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178570	32178570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs17604492	NA	P-0057065-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	159	550	0	ENST00000375023.3:c.2824G>A	p.Gly942Arg	p.G942R	ENST00000375023	NM_004557.3	942	Ggg/Agg	18/30	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.357529579127755	2		550	745	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586238	48586238	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057065-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	50	287	0	ENST00000342988.3:c.908del	p.Pro303LeufsTer33	p.P303Lfs*33	ENST00000342988	NM_005359.5	303	Cct/ct	8/12	0.357529579127755	1	FACETS	0.986	0.845	1	0.986	0.845	1	CLONAL	1	TRUE	0	0.357529579127755	1		287	233	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0057078-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	121	597	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.569009497559436	4	FACETS	0.963	0.883	1	0.963	0.883	1	CLONAL	2	TRUE	2	0.670822039134846	4		597	313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587781845	NA	P-0057078-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	463	887	0	ENST00000269305.4:c.511G>T	p.Glu171Ter	p.E171*	ENST00000269305	NM_001126112.2	171	Gag/Tag	5/11	0.670822039134846	1	FACETS	0.998	0.959	1	0.998	0.959	1	CLONAL	1	TRUE	0	0.670822039134846	1		887	919	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789661	3789661	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057078-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	240	483	0	ENST00000262367.5:c.4198G>C	p.Glu1400Gln	p.E1400Q	ENST00000262367	NM_004380.2	1400	Gag/Cag	25/31	0.670822039134846	1	FACETS	0.993	0.939	1	0.993	0.939	1	CLONAL	1	TRUE	0	0.670822039134846	1		483	479	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0057078-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	150	358	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	0.661804271311775	1	FACETS	0.938	0.872	1	0.938	0.872	1	CLONAL	1	TRUE	0	0.670822039134846	1		358	317	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413030	63413030	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057078-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	502	1044	0	ENST00000330258.3:c.137C>T	p.Ser46Leu	p.S46L	ENST00000330258	NM_152424.3	46	tCa/tTa	2/2	1	2	FACETS	0.985	0.943	1	0.985	0.943	1	CLONAL	1	TRUE	1	0.670822039134846	2		1044	1519	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923766	72923766	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057078-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	402	668	0	ENST00000268489.5:c.3312C>G	p.Ile1104Met	p.I1104M	ENST00000268489	NM_006885.3	1104	atC/atG	4/10	0.661804271311775	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.670822039134846	1		668	796	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709524	176709524	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587784169	NA	P-0057078-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	89	219	0	ENST00000439151.2:c.5951G>A	p.Arg1984Gln	p.R1984Q	ENST00000439151	NM_022455.4	1984	cGa/cAa	19/23	0.670822039134846	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.670822039134846	1		219	155	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864023	97864023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881729	NA	P-0057078-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	248	533	0	ENST00000289081.3:c.1643G>A	p.Arg548Gln	p.R548Q	ENST00000289081	NM_000136.2	548	cGa/cAa	15/15	0.670822039134846	2	FACETS	0.88	0.825	0.937	0.44	0.412	0.469	CLONAL	1	TRUE	0	0.670822039134846	2		533	840	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919276	48919277	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057078-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	23	159	0	ENST00000267163.4:c.442dup	p.Met148AsnfsTer9	p.M148Nfs*9	ENST00000267163	NM_000321.2	147	-/A	4/27	0.670822039134846	1	FACETS	0.772	0.628	0.924	0.772	0.628	0.924	CLONAL	1	TRUE	0	0.670822039134846	1		159	59	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946093	13946093	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs767110553	NA	P-0057078-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	125	315	1	ENST00000405192.2:c.1003G>T	p.Gly335Cys	p.G335C	ENST00000405192	NM_001163147.1	335	Ggt/Tgt	10/12	1	2	FACETS	0.907	0.828	0.988	0.907	0.828	0.988	CLONAL	1	TRUE	1	0.670822039134846	2		316	411	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0057090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	64	348	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.21	2		348	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0057090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	80	653	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.756	0.664	0.856	0.756	0.664	0.856	SUBCLONAL	1	TRUE	1	0.21	2		655	1008	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867388	68867388	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	59	689	0	ENST00000261769.5:c.2635G>T	p.Gly879Cys	p.G879C	ENST00000261769	NM_004360.3	879	Ggc/Tgc	16/16	1	2	FACETS	0.845	0.726	0.975	0.845	0.726	0.975	CLONAL	1	TRUE	1	0.21	2		689	665	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436066	56436066	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0057090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	92	957	0	ENST00000407977.2:c.1071C>G	p.Tyr357Ter	p.Y357*	ENST00000407977		357	taC/taG	9/10	1	2	FACETS	0.981	0.871	1	0.981	0.871	1	CLONAL	1	TRUE	1	0.21	2		957	893	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15821881	15821881	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	43	249	0	ENST00000307771.7:c.274A>G	p.Lys92Glu	p.K92E	ENST00000307771	NM_005089.3	92	Aag/Gag	4/11	1	2	FACETS	0.914	0.766	1	0.914	0.766	1	CLONAL	1	TRUE	1	0.21	2		249	448	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0057091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	127	628	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.446490928811152	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	FALSE	1	0.446490928811152	3		628	294	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014298	70014298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142372494	NA	P-0057091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	71	759	0	ENST00000394351.3:c.1159G>A	p.Gly387Ser	p.G387S	ENST00000394351	NM_000248.3	387	Ggt/Agt	9/9	0.146282894033183	4	FACETS	0.762	0.671	0.858	0.762	0.671	0.858	INDETERMINATE	2	FALSE	2	0.446490928811152	4		759	302	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624271	89624271	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1064794096	NA	P-0057091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	69	250	1	ENST00000371953.3:c.45A>T	p.Arg15Ser	p.R15S	ENST00000371953	NM_000314.4	15	agA/agT	1/9	0.446490928811152	2	FACETS	0.928	0.845	1	1	0.98	1	CLONAL	3	FALSE	0	0.446490928811152	2		251	111	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21639508	21639508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138278747	NA	P-0057091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	22	83	0	ENST00000421138.2:c.406G>A	p.Val136Ile	p.V136I	ENST00000421138		136	Gtc/Atc	6/16	0.146282894033183	4	FACETS	1	0.862	1	1	0.862	1	INDETERMINATE	2	FALSE	2	0.446490928811152	4		83	65	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215661786	215661786	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	27	81	0	ENST00000260947.4:c.214A>T	p.Ser72Cys	p.S72C	ENST00000260947	NM_000465.2	72	Agt/Tgt	2/11	0.446490928811152	5	FACETS	0.801	0.648	0.97	0.401	0.324	0.485	CLONAL	2	FALSE	1	0.446490928811152	5		81	126	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204732	128204732	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	63	1210	0	ENST00000341105.2:c.709G>C	p.Gly237Arg	p.G237R	ENST00000341105	NM_032638.4	237	Ggc/Cgc	3/6	0.146282894033183	4	FACETS	1	0.957	1	0.624	0.543	0.711	INDETERMINATE	1	FALSE	2	0.446490928811152	4		1210	327	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971146	21971163	+	frameshift_variant	Frame_Shift_Del	DEL	TTGGGCTCCGCGCCGTGG	TTGGGCTCCGCGCCGTGG	GAGC	novel	NA	P-0057091-T01-IM6	NA	A	A	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	103	768	3	ENST00000304494.5:c.195_212delinsGCTC	p.His66LeufsTer49	p.H66Lfs*49	ENST00000304494	NM_000077.4	65	ctCCACGGCGCGGAGCCCAAc/ctGCTCc	2/3	0.383838972116997	3	FACETS	1	0.921	1	0.677	0.615	0.74	CLONAL	2	FALSE	0	0.446490928811152	3		771	278	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971144	21971162	+	frameshift_variant	Frame_Shift_Del	DEL	AGTTGGGCTCCGCGCCGTG	AGTTGGGCTCCGCGCCGTG	GGAGC	novel	NA	P-0057091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	103	768	3	ENST00000304494.5:c.196_214delinsGCTCC	p.His66AlafsTer49	p.H66Afs*49	ENST00000304494	NM_000077.4	66	CACGGCGCGGAGCCCAACTgc/GCTCCgc	2/3	0.383838972116997	3	FACETS	1	0.921	1	0.677	0.615	0.74	CLONAL	2	FALSE	0	0.446490928811152	3		771	278	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955578	48955578	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0057092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	27	274	0	ENST00000267163.4:c.1694C>G	p.Ser565Ter	p.S565*	ENST00000267163	NM_000321.2	565	tCa/tGa	17/27	1	2	FACETS	0.684	0.545	0.841	0.684	0.545	0.841	SUBCLONAL	1	TRUE	1	0.273244444661569	2		274	289	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453137	140453138	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGT	novel	NA	P-0057092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	82	395	0	ENST00000288602.6:c.1795_1797dup	p.Thr599dup	p.T599dup	ENST00000288602	NM_004333.4	599	-/ACA	15/18	0.237043362521332	3	FACETS	1	0.966	1	0.628	0.555	0.706	CLONAL	1	TRUE	1	0.273244444661569	3		395	543	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106456	27106456	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	74	721	0	ENST00000324856.7:c.6067G>T	p.Glu2023Ter	p.E2023*	ENST00000324856	NM_006015.4	2023	Gaa/Taa	20/20	1	2	FACETS	0.802	0.702	0.91	0.802	0.702	0.91	CLONAL	1	TRUE	1	0.273244444661569	2		721	675	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579503	7579528	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CATCTGGACCTGGGTCTTCAGTGAAC	CATCTGGACCTGGGTCTTCAGTGAAC	-	novel	NA	P-0057092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	101	1074	0	ENST00000269305.4:c.159_184del	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgGTTCACTGAAGACCCAGGTCCAGATGaa/tgaa	4/11	0.273244444661569	1	FACETS	0.817	0.73	0.91	0.817	0.73	0.91	CLONAL	1	TRUE	0	0.273244444661569	1		1074	781	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0057093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	794	628	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.234401395302789	5	FACETS	0.961	0.938	0.984			1	INDETERMINATE	5	TRUE	NA	0.491488883062816	5		628	1168	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983026	149983026	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	390	497	0	ENST00000253339.5:c.3232T>G	p.Phe1078Val	p.F1078V	ENST00000253339		1078	Ttt/Gtt	7/7	0.480904321097351	2	FACETS	1	0.99	1	1	0.997	1	CLONAL	3	TRUE	0	0.491488883062816	2		497	506	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81971404	81971404	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	144	541	0	ENST00000359376.3:c.3094G>T	p.Gly1032Trp	p.G1032W	ENST00000359376	NM_002661.3	1032	Ggg/Tgg	28/33	1	2	FACETS	0.908	0.831	0.989	0.908	0.831	0.989	CLONAL	1	TRUE	1	0.491488883062816	2		541	645	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0057094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	129	613	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.969	0.879	1	0.969	0.879	1	CLONAL	1	TRUE	1	0.32	2		613	832	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058033	27058033	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	97	650	1	ENST00000324856.7:c.1741C>T	p.Gln581Ter	p.Q581*	ENST00000324856	NM_006015.4	581	Cag/Tag	3/20	1	2	FACETS	0.781	0.696	0.872	0.781	0.696	0.872	SUBCLONAL	1	TRUE	1	0.32	2		651	776	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0057094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	52	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.114518331167949	3	FACETS	0.933	0.797	1	0.467	0.398	0.541	INDETERMINATE	1	TRUE	1	0.32	3		298	404	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652158	36652158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1236971182	NA	P-0057094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	150	1028	3	ENST00000244741.5:c.280C>T	p.Arg94Trp	p.R94W	ENST00000244741	NM_000389.4	94	Cgg/Tgg	2/3	1	2	FACETS	0.897	0.819	0.979	0.897	0.819	0.979	CLONAL	1	TRUE	1	0.32	2		1031	1045	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557630	95557630	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	71	557	0	ENST00000393063.1:c.5437G>C	p.Glu1813Gln	p.E1813Q	ENST00000393063	NM_030621.3	1813	Gag/Cag	26/28	1	2	FACETS	0.877	0.767	0.995	0.877	0.767	0.995	CLONAL	1	TRUE	1	0.32	2		557	506	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282115	38282115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554562012	NA	P-0057094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	110	984	3	ENST00000425967.3:c.941C>T	p.Pro314Leu	p.P314L	ENST00000425967	NM_001174067.1	314	cCg/cTg	8/19	0.211612698099899	3	FACETS	0.637	0.571	0.709	0.319	0.285	0.355	SUBCLONAL	1	TRUE	1	0.32	3		987	1251	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572555	95572555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	27	211	0	ENST00000393063.1:c.2810G>A	p.Arg937His	p.R937H	ENST00000393063	NM_030621.3	937	cGc/cAc	19/28	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.32	2		211	154	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101109	27101110	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0057094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	128	900	0	ENST00000324856.7:c.4394_4395del	p.Ser1465CysfsTer25	p.S1465Cfs*25	ENST00000324856	NM_006015.4	1464	gTC/g	18/20	1	2	FACETS	0.888	0.804	0.976	0.888	0.804	0.976	CLONAL	1	TRUE	1	0.32	2		900	901	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348446	89348446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	164	1002	1	ENST00000301030.4:c.4504C>T	p.Pro1502Ser	p.P1502S	ENST00000301030	NM_001256183.1	1502	Ccc/Tcc	9/13	1	2	FACETS	0.803	0.735	0.874	0.803	0.735	0.874	CLONAL	1	TRUE	1	0.32	2		1003	1277	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417499	139417499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	176	1201	2	ENST00000277541.6:c.545G>A	p.Cys182Tyr	p.C182Y	ENST00000277541	NM_017617.3	182	tGt/tAt	4/34	1	2	FACETS	0.855	0.785	0.927	0.855	0.785	0.927	CLONAL	1	TRUE	1	0.32	2		1203	1287	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589590	67589593	+	protein_altering_variant	In_Frame_Del	DEL	ATAT	ATAT	C	novel	NA	P-0057094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	26	219	0	ENST00000274335.5:c.1353_1356delinsC	p.Glu451_Tyr452delinsAsp	p.E451_Y452delinsD	ENST00000274335		451	gaATAT/gaC	10/15	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.32	2		219	118	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	75	324	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.897	0.788	1	0.897	0.788	1	CLONAL	1	TRUE	1	0.33795091540302	2		324	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0057095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	194	504	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.33795091540302	2		504	1081	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0057095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	154	867	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.33795091540302	2		867	896	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0057095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	175	523	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.33795091540302	2		523	745	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106024	27106024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369894428	NA	P-0057095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	107	655	1	ENST00000324856.7:c.5635C>T	p.Arg1879Trp	p.R1879W	ENST00000324856	NM_006015.4	1879	Cgg/Tgg	20/20	0.103148755050087	4	FACETS	1	0.918	1			1	INDETERMINATE	1	TRUE	NA	0.33795091540302	4		656	825	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659982	227659982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1166934768	NA	P-0057095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	171	993	0	ENST00000305123.5:c.3473G>A	p.Gly1158Glu	p.G1158E	ENST00000305123	NM_005544.2	1158	gGa/gAa	1/2	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.33795091540302	2		993	1007	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860333	42860333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758778273	NA	P-0057095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	101	851	2	ENST00000398585.3:c.544G>A	p.Glu182Lys	p.E182K	ENST00000398585	NM_001135099.1	182	Gag/Aag	5/14	0.33795091540302	1	FACETS	0.609	0.544	0.678	0.609	0.544	0.678	SUBCLONAL	1	TRUE	0	0.33795091540302	1		853	816	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541468	29541468	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs1131691131	NA	P-0057095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	19	100	0	ENST00000356175.3:c.1393-1G>C		p.X465_splice	ENST00000356175	NM_000267.3	465			1	2	FACETS	0.986	0.759	1	0.986	0.759	1	CLONAL	1	TRUE	1	0.33795091540302	2		100	114	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254594	1254594	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	166	932	0	ENST00000310581.5:c.3184G>T	p.Ala1062Ser	p.A1062S	ENST00000310581	NM_198253.2	1062	Gcc/Tcc	15/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.33795091540302	2		932	825	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852170	63852171	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0057095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	336	678	0	ENST00000279873.7:c.2948_2949del	p.Leu983ArgfsTer65	p.L983Rfs*65	ENST00000279873	NM_032199.2	983	cTG/c	10/10	0.149407572028563	5	FACETS	0.937	0.887	0.988			1	INDETERMINATE	3	TRUE	NA	0.33795091540302	5		678	1066	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375044	104375044	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1447671524	NA	P-0057095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	85	754	0	ENST00000369902.3:c.1042G>C	p.Glu348Gln	p.E348Q	ENST00000369902	NM_016169.3	348	Gaa/Caa	9/12	0.33795091540302	1	FACETS	0.529	0.467	0.596	0.529	0.467	0.596	SUBCLONAL	1	TRUE	0	0.33795091540302	1		754	790	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203543	108203543	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs773159296	NA	P-0057095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	81	400	0	ENST00000278616.4:c.7843C>G	p.Gln2615Glu	p.Q2615E	ENST00000278616	NM_000051.3	2615	Cag/Gag	53/63	1	2	FACETS	0.94	0.83	1	0.94	0.83	1	CLONAL	1	TRUE	1	0.33795091540302	2		400	510	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273991	10273991	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs753332062	NA	P-0057095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	189	1206	1	ENST00000330684.3:c.278C>A	p.Ala93Glu	p.A93E	ENST00000330684	NM_001134407.1	93	gCa/gAa	2/13	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.33795091540302	2		1207	1076	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541613	187541614	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	AT	novel	NA	P-0057095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	99	469	0	ENST00000441802.2:c.6126_6127delinsAT	p.Gln2043Ter	p.Q2043*	ENST00000441802	NM_005245.3	2042	gaGCag/gaATag	10/27	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.33795091540302	2		469	485	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630163	187630163	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0057095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	93	797	0	ENST00000441802.2:c.819T>G	p.Tyr273Ter	p.Y273*	ENST00000441802	NM_005245.3	273	taT/taG	2/27	1	2	FACETS	0.771	0.685	0.862	0.771	0.685	0.862	SUBCLONAL	1	TRUE	1	0.33795091540302	2		797	714	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80171676	80171676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	49	400	0	ENST00000265081.6:c.3409C>T	p.His1137Tyr	p.H1137Y	ENST00000265081	NM_002439.4	1137	Cat/Tat	24/24	1	2	FACETS	0.794	0.675	0.925	0.794	0.675	0.925	CLONAL	1	TRUE	1	0.33795091540302	2		400	365	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199767	138199767	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs774184566	NA	P-0057095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	160	713	0	ENST00000237289.4:c.1185C>G	p.Phe395Leu	p.F395L	ENST00000237289	NM_001270507.1	395	ttC/ttG	7/9	0.33795091540302	4	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.33795091540302	4		713	939	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978761	13978761	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	127	714	0	ENST00000405192.2:c.346A>G	p.Lys116Glu	p.K116E	ENST00000405192	NM_001163147.1	116	Aag/Gag	6/12	1	2	FACETS	0.921	0.834	1	0.921	0.834	1	CLONAL	1	TRUE	1	0.33795091540302	2		714	816	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14017103	14017103	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs376325638	NA	P-0057095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	63	305	0	ENST00000405192.2:c.184C>G	p.Gln62Glu	p.Q62E	ENST00000405192	NM_001163147.1	62	Cag/Gag	5/12	1	2	FACETS	0.997	0.866	1	0.997	0.866	1	CLONAL	1	TRUE	1	0.33795091540302	2		305	374	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739890	145739890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	172	982	1	ENST00000428558.2:c.1640G>A	p.Cys547Tyr	p.C547Y	ENST00000428558	NM_004260.3	547	tGt/tAt	10/22	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.33795091540302	2		983	992	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	27	330	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.0967674518621271	5	FACETS	0.569	0.451	0.704	0.19	0.15	0.235	INDETERMINATE	1	TRUE	2	0.21012298721673	5		330	594	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	157	1029	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.21012298721673	2		1032	1063	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	538	900	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.21012298721673	2	FACETS	1	0.986	1	1	0.998	1	CLONAL	4	TRUE	0	0.21012298721673	2		904	1217	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	20	296	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.632	0.484	0.807	0.632	0.484	0.807	SUBCLONAL	1	TRUE	1	0.21012298721673	2		296	301	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434833	110434833	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	331	1243	3	ENST00000375856.3:c.3568G>A	p.Val1190Met	p.V1190M	ENST00000375856	NM_003749.2	1190	Gtg/Atg	1/2	0.21012298721673	5	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	2	0.21012298721673	5		1246	1247	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11297916	11297916	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	52	788	1	ENST00000361445.4:c.2192G>A	p.Arg731His	p.R731H	ENST00000361445	NM_004958.3	731	cGc/cAc	13/58	0.180344989415708	0	FACETS	0.465	0.395	0.543			1	SUBCLONAL	1	TRUE	0	0.21012298721673	0		789	840	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17350541	17350541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201900648	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	40	736	0	ENST00000375499.3:c.569C>T	p.Ala190Val	p.A190V	ENST00000375499	NM_003000.2	190	gCc/gTc	6/8	1	2	FACETS	0.484	0.401	0.577	0.484	0.401	0.577	SUBCLONAL	1	TRUE	1	0.21012298721673	2		736	787	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804312	43804313	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	61	932	0	ENST00000372470.3:c.315dup	p.Pro106SerfsTer58	p.P106Sfs*58	ENST00000372470	NM_005373.2	104	-/T	3/12	1	2	FACETS	0.619	0.532	0.714	0.619	0.532	0.714	SUBCLONAL	1	TRUE	1	0.21012298721673	2		932	938	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226589948	226589948	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	121	779	0	ENST00000366794.5:c.253G>T	p.Val85Phe	p.V85F	ENST00000366794	NM_001618.3	85	Gtc/Ttc	2/23	0.21012298721673	5	FACETS	1	0.981	1	0.346	0.311	0.382	CLONAL	1	TRUE	1	0.21012298721673	5		779	1095	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609002	43609003	+	splice_acceptor_variant	Splice_Site	INS	-	-	G	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	86	1032	0	ENST00000355710.3:c.1763dup		p.X588_splice	ENST00000355710	NM_020975.4	588			0.180344989415708	0	FACETS	0.849	0.75	0.954			1	CLONAL	1	TRUE	0	0.21012298721673	0		1032	762	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333987	70333987	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	23	262	0	ENST00000373644.4:c.1892C>A	p.Pro631Gln	p.P631Q	ENST00000373644	NM_030625.2	631	cCa/cAa	2/12	0.0799335520580546	4	FACETS	0.761	0.593	0.956	0.381	0.296	0.478	INDETERMINATE	1	TRUE	2	0.21012298721673	4		262	348	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	150	527	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.21012298721673	1	FACETS	0.952	0.873	1	1	0.991	1	CLONAL	2	TRUE	0	0.21012298721673	1		530	671	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456524	32456524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	41	149	1	ENST00000332351.3:c.368C>T	p.Ala123Val	p.A123V	ENST00000332351	NM_024426.4	123	gCg/gTg	1/10	1	2	FACETS	1	0.852	1	1	0.977	1	CLONAL	3	TRUE	1	0.21012298721673	2		150	130	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138124	64138124	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	144	1121	1	ENST00000334205.4:c.2051del	p.Pro684ArgfsTer36	p.P684Rfs*36	ENST00000334205	NM_003942.2	683	Ccc/cc	16/17	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.21012298721673	2		1122	1088	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114817	108114817	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786204543	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	54	127	0	ENST00000278616.4:c.640del	p.Ser214ProfsTer16	p.S214Pfs*16	ENST00000278616	NM_000051.3	212	Ttt/tt	6/63	0.21012298721673	7	FACETS	0.925	0.792	1			1	CLONAL	2	TRUE	NA	0.21012298721673	7		127	424	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121571	108121571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781841	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	96	358	0	ENST00000278616.4:c.1379C>T	p.Thr460Met	p.T460M	ENST00000278616	NM_000051.3	460	aCg/aTg	10/63	0.21012298721673	7	FACETS	1	0.947	1			1	CLONAL	2	TRUE	NA	0.21012298721673	7		358	633	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363823	118363823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377724112	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	97	546	1	ENST00000534358.1:c.5056C>T	p.Arg1686Cys	p.R1686C	ENST00000534358	NM_005933.3	1686	Cgc/Tgc	16/36	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.21012298721673	2		547	756	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380283	25380283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913528	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	125	348	1	ENST00000311936.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000311936	NM_004985.3	59	Gca/Aca	3/5	0.0967674518621271	5	FACETS	1	0.96	1	0.739	0.67	0.812	INDETERMINATE	2	TRUE	2	0.21012298721673	5		349	706	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211569	46211569	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs896638040	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	57	96	0	ENST00000334344.6:c.535G>A	p.Val179Ile	p.V179I	ENST00000334344	NM_152641.2	179	Gta/Ata	5/21	0.0967674518621271	5	FACETS	1	0.919	1	0.73	0.63	0.837	INDETERMINATE	2	TRUE	2	0.21012298721673	5		96	326	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480447	50480447	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	72	293	0	ENST00000394963.4:c.408+1G>A		p.X136_splice	ENST00000394963	NM_003076.4	136			0.0967674518621271	5	FACETS	0.802	0.701	0.91	0.535	0.467	0.607	INDETERMINATE	2	TRUE	2	0.21012298721673	5		293	562	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481648	56481648	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs774589520	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	420	1109	0	ENST00000267101.3:c.683A>G	p.His228Arg	p.H228R	ENST00000267101	NM_001982.3	228	cAt/cGt	6/28	0.0967674518621271	5	FACETS	0.995	0.948	1	1	0.994	1	INDETERMINATE	4	TRUE	2	0.21012298721673	5		1109	1321	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481814	56481814	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	197	865	0	ENST00000267101.3:c.742C>T	p.His248Tyr	p.H248Y	ENST00000267101	NM_001982.3	248	Cac/Tac	7/28	0.0967674518621271	5	FACETS	1	0.98	1	0.774	0.716	0.834	INDETERMINATE	2	TRUE	2	0.21012298721673	5		865	1062	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494888	56494889	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	191	851	0	ENST00000267101.3:c.3250_3251del	p.Leu1084ThrfsTer21	p.L1084Tfs*21	ENST00000267101	NM_001982.3	1082	gTC/g	27/28	0.0967674518621271	5	FACETS	1	0.978	1	0.766	0.707	0.826	INDETERMINATE	2	TRUE	2	0.21012298721673	5		851	1041	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856226	111856226	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	100	306	0	ENST00000341259.2:c.277G>T	p.Gly93Cys	p.G93C	ENST00000341259	NM_005475.2	93	Ggc/Tgc	2/8	1	2	FACETS	1	0.901	1	1	0.987	1	CLONAL	2	TRUE	1	0.21012298721673	2		306	474	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885607	111885607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs577495609	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	168	1207	1	ENST00000341259.2:c.1384G>A	p.Val462Met	p.V462M	ENST00000341259	NM_005475.2	462	Gtg/Atg	7/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.21012298721673	2		1208	1189	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435325	121435325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	55	1266	0	ENST00000257555.6:c.1358G>A	p.Gly453Asp	p.G453D	ENST00000257555		453	gGc/gAc	7/10	1	2	FACETS	0.539	0.459	0.626	0.539	0.459	0.626	SUBCLONAL	1	TRUE	1	0.21012298721673	2		1266	972	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562933	21562933	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	72	1091	0	ENST00000382592.4:c.986A>G	p.His329Arg	p.H329R	ENST00000382592	NM_014572.2	329	cAt/cGt	4/8	0.21012298721673	3	FACETS	0.628	0.547	0.717	0.314	0.273	0.359	SUBCLONAL	1	TRUE	1	0.21012298721673	3		1091	1205	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913226	32913226	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	166	231	0	ENST00000380152.3:c.4734A>C	p.Leu1578Phe	p.L1578F	ENST00000380152		1578	ttA/ttC	11/27	0.21012298721673	10	FACETS	0.982	0.907	1			1	CLONAL	5	TRUE	NA	0.21012298721673	10		231	592	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434686	110434686	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	69	989	0	ENST00000375856.3:c.3715A>G	p.Met1239Val	p.M1239V	ENST00000375856	NM_003749.2	1239	Atg/Gtg	1/2	0.21012298721673	5	FACETS	0.706	0.612	0.808	0.235	0.204	0.27	SUBCLONAL	1	TRUE	2	0.21012298721673	5		989	1224	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437497	110437497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	63	953	0	ENST00000375856.3:c.904C>T	p.Pro302Ser	p.P302S	ENST00000375856	NM_003749.2	302	Ccg/Tcg	1/2	0.21012298721673	5	FACETS	0.77	0.664	0.886	0.257	0.221	0.296	SUBCLONAL	1	TRUE	2	0.21012298721673	5		953	1024	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060785	38060785	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	220	1387	0	ENST00000250448.2:c.1204A>G	p.Ile402Val	p.I402V	ENST00000250448	NM_004496.3	402	Atc/Gtc	2/2	1	2	FACETS	0.817	0.758	0.877	1	0.992	1	CLONAL	2	TRUE	1	0.21012298721673	2		1387	1282	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293204	91293204	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	28	278	0	ENST00000355112.3:c.706A>G	p.Ile236Val	p.I236V	ENST00000355112	NM_000057.2	236	Att/Gtt	3/22	1	2	FACETS	0.537	0.428	0.662	0.537	0.428	0.662	SUBCLONAL	1	TRUE	1	0.21012298721673	2		278	496	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347983	347983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760961378	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	414	1420	14	ENST00000262320.3:c.1523del	p.Gly508ValfsTer197	p.G508Vfs*197	ENST00000262320	NM_003502.3	508	gGt/gt	6/11	1	2	FACETS	1	0.99	1	1	0.997	1	CLONAL	3	TRUE	1	0.21012298721673	2		1434	1164	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640577	3640577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200842643	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	80	1343	2	ENST00000294008.3:c.3062G>A	p.Arg1021His	p.R1021H	ENST00000294008	NM_032444.2	1021	cGc/cAc	12/15	1	2	FACETS	0.645	0.566	0.731	0.645	0.566	0.731	SUBCLONAL	1	TRUE	1	0.21012298721673	2		1345	1180	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779670	3779670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	165	1209	1	ENST00000262367.5:c.5378C>T	p.Pro1793Leu	p.P1793L	ENST00000262367	NM_004380.2	1793	cCa/cTa	31/31	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.21012298721673	2		1210	1068	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900575	3900575	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	56	1133	0	ENST00000262367.5:c.521G>T	p.Gly174Val	p.G174V	ENST00000262367	NM_004380.2	174	gGt/gTt	2/31	1	2	FACETS	0.493	0.42	0.572	0.493	0.42	0.572	SUBCLONAL	1	TRUE	1	0.21012298721673	2		1133	1082	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041671	14041671	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376688194	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	81	647	0	ENST00000311895.7:c.2218C>T	p.Arg740Cys	p.R740C	ENST00000311895	NM_005236.2	740	Cgc/Tgc	11/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.21012298721673	2		647	664	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619303	23619303	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	120	624	1	ENST00000261584.4:c.3232T>C	p.Cys1078Arg	p.C1078R	ENST00000261584	NM_024675.3	1078	Tgt/Cgt	12/13	1	2	FACETS	0.865	0.783	0.952	1	0.987	1	CLONAL	2	TRUE	1	0.21012298721673	2		625	660	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646981	23646981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	95	272	0	ENST00000261584.4:c.886del	p.Met296Ter	p.M296*	ENST00000261584	NM_024675.3	296	Atg/tg	4/13	1	2	FACETS	0.899	0.803	1	1	0.985	1	CLONAL	2	TRUE	1	0.21012298721673	2		272	503	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56872963	56872963	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	20	126	0	ENST00000308159.5:c.2118T>G	p.His706Gln	p.H706Q	ENST00000308159	NM_014669.4	706	caT/caG	19/22	1	2	FACETS	0.582	0.445	0.743	0.582	0.445	0.743	SUBCLONAL	1	TRUE	1	0.21012298721673	2		126	327	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849631	68849631	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	46	732	0	ENST00000261769.5:c.1534G>T	p.Glu512Ter	p.E512*	ENST00000261769	NM_004360.3	512	Gag/Tag	10/16	1	2	FACETS	0.518	0.434	0.61	0.518	0.434	0.61	SUBCLONAL	1	TRUE	1	0.21012298721673	2		732	846	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	40	531	2	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.627	0.52	0.747	0.627	0.52	0.747	SUBCLONAL	1	TRUE	1	0.21012298721673	2		533	607	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351056	89351057	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	20	826	0	ENST00000301030.4:c.1893dup	p.His632ThrfsTer2	p.H632Tfs*2	ENST00000301030	NM_001256183.1	631	-/A	9/13	1	2	FACETS	0.197	0.149	0.253	0.197	0.149	0.253	SUBCLONAL	1	TRUE	1	0.21012298721673	2		826	968	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89809273	89809273	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	54	834	0	ENST00000389301.3:c.3700A>T	p.Ile1234Phe	p.I1234F	ENST00000389301	NM_000135.2	1234	Att/Ttt	37/43	1	2	FACETS	0.525	0.447	0.611	0.525	0.447	0.611	SUBCLONAL	1	TRUE	1	0.21012298721673	2		834	979	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578397	7578398	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	151	1085	0	ENST00000269305.4:c.532dup	p.His178ProfsTer3	p.H178Pfs*3	ENST00000269305	NM_001126112.2	178	cac/cCac	5/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.21012298721673	2		1085	1035	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	129	1213	3	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.21012298721673	2		1216	1120	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	39	166	0	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	0.947	0.786	1	0.947	0.786	1	CLONAL	1	TRUE	1	0.21012298721673	2		166	392	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682122	37682122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	71	468	0	ENST00000447079.4:c.3313G>A	p.Ala1105Thr	p.A1105T	ENST00000447079	NM_015083.1	1105	Gct/Act	13/14	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.21012298721673	2		468	601	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686931	37686931	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	57	805	0	ENST00000447079.4:c.3839del	p.Pro1280LeufsTer14	p.P1280Lfs*14	ENST00000447079	NM_015083.1	1279	Ccc/cc	14/14	1	2	FACETS	0.588	0.503	0.681	0.588	0.503	0.681	SUBCLONAL	1	TRUE	1	0.21012298721673	2		805	923	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	79	1020	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.701	0.615	0.795	0.701	0.615	0.795	SUBCLONAL	1	TRUE	1	0.21012298721673	2		1020	1072	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40854955	40854955	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	119	726	0	ENST00000428826.2:c.2123G>T	p.Arg708Leu	p.R708L	ENST00000428826		708	cGg/cTg	20/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.21012298721673	2		726	842	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438175	56438175	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1222	74	1129	0	ENST00000407977.2:c.818C>T	p.Ala273Val	p.A273V	ENST00000407977		273	gCc/gTc	7/10	0.21012298721673	2	FACETS	0.543	0.474	0.619	0.272	0.237	0.31	SUBCLONAL	1	TRUE	0	0.21012298721673	2		1129	1296	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532517	63532517	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	400	1281	3	ENST00000307078.5:c.2062del	p.Leu688Ter	p.L688*	ENST00000307078	NM_004655.3	688	Ctg/tg	8/11	0.21012298721673	2	FACETS	1	0.979	1	1	0.996	1	CLONAL	3	TRUE	0	0.21012298721673	2		1284	1207	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774758	73774758	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	113	542	1	ENST00000254810.4:c.329T>G	p.Leu110Arg	p.L110R	ENST00000254810	NM_005324.3	110	cTg/cGg	4/4	0.21012298721673	2	FACETS	0.757	0.682	0.837	0.757	0.682	0.837	SUBCLONAL	2	TRUE	0	0.21012298721673	2		543	710	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394805	45394805	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	48	251	0	ENST00000262160.6:c.544C>T	p.Arg182Ter	p.R182*	ENST00000262160	NM_005901.5	182	Cga/Tga	5/11	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.21012298721673	2		251	404	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1627411	1627411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377688933	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	64	1118	1	ENST00000344749.5:c.313C>T	p.Arg105Trp	p.R105W	ENST00000344749	NM_001136139.2	105	Cgg/Tgg	6/19	1	2	FACETS	0.538	0.464	0.618	0.538	0.464	0.618	SUBCLONAL	1	TRUE	1	0.21012298721673	2		1119	1133	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210754	5210754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768674983	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	43	1204	1	ENST00000357368.4:c.5297G>A	p.Arg1766His	p.R1766H	ENST00000357368	NM_002850.3	1766	cGc/cAc	34/38	0.21012298721673	0	FACETS	0.389	0.324	0.461			1	SUBCLONAL	1	TRUE	0	0.21012298721673	0		1205	832	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214406	5214406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	90	888	1	ENST00000357368.4:c.4580C>T	p.Ala1527Val	p.A1527V	ENST00000357368	NM_002850.3	1527	gCc/gTc	30/38	0.21012298721673	0	FACETS	0.969	0.86	1			1	CLONAL	1	TRUE	0	0.21012298721673	0		889	698	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238958	5238958	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	82	909	0	ENST00000357368.4:c.1821del	p.Val608TrpfsTer30	p.V608Wfs*30	ENST00000357368	NM_002850.3	607	ccC/cc	13/38	0.21012298721673	0	FACETS	0.98	0.865	1			1	CLONAL	1	TRUE	0	0.21012298721673	0		909	629	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260185	10260185	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	60	855	0	ENST00000340748.4:c.2482A>G	p.Ile828Val	p.I828V	ENST00000340748		828	Atc/Gtc	25/40	1	2	FACETS	0.661	0.568	0.763	0.661	0.568	0.763	SUBCLONAL	1	TRUE	1	0.21012298721673	2		855	864	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265027	10265027	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	43	869	0	ENST00000340748.4:c.1913del	p.Lys638ArgfsTer59	p.K638Rfs*59	ENST00000340748		638	aAg/ag	21/40	1	2	FACETS	0.515	0.43	0.611	0.515	0.43	0.611	SUBCLONAL	1	TRUE	1	0.21012298721673	2		869	794	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105645	11105645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	72	929	0	ENST00000358026.2:c.1561C>T	p.Arg521Trp	p.R521W	ENST00000358026	NM_001128849.1	521	Cgg/Tgg	9/36	1	2	FACETS	0.685	0.596	0.78	0.685	0.596	0.78	SUBCLONAL	1	TRUE	1	0.21012298721673	2		929	1001	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272216	15272216	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	53	1119	0	ENST00000263388.2:c.6223C>T	p.Gln2075Ter	p.Q2075*	ENST00000263388	NM_000435.2	2075	Cag/Tag	33/33	1	2	FACETS	0.599	0.509	0.698	0.599	0.509	0.698	SUBCLONAL	1	TRUE	1	0.21012298721673	2		1119	842	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951115	17951115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	167	947	1	ENST00000458235.1:c.1178del	p.Gly393AlafsTer72	p.G393Afs*72	ENST00000458235	NM_000215.3	393	gGc/gc	9/24	1	2	FACETS	0.795	0.73	0.863	1	0.99	1	SUBCLONAL	2	TRUE	1	0.21012298721673	2		948	1000	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266882	18266882	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1374508598	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	46	704	3	ENST00000222254.8:c.193C>T	p.Arg65Trp	p.R65W	ENST00000222254	NM_005027.3	65	Cgg/Tgg	2/16	1	2	FACETS	0.509	0.427	0.599	0.509	0.427	0.599	SUBCLONAL	1	TRUE	1	0.21012298721673	2		707	861	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271956	18271957	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	104	624	0	ENST00000222254.8:c.564dup	p.Glu189ArgfsTer86	p.E189Rfs*86	ENST00000222254	NM_005027.3	187	acc/aCcc	5/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.21012298721673	2		624	715	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	24	807	0	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	1	2	FACETS	0.251	0.196	0.316	0.251	0.196	0.316	SUBCLONAL	1	TRUE	1	0.21012298721673	2		807	909	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18276968	18276968	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1284781492	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	30	429	0	ENST00000222254.8:c.1417-2A>G		p.X473_splice	ENST00000222254	NM_005027.3	473			1	2	FACETS	0.599	0.482	0.732	0.599	0.482	0.732	SUBCLONAL	1	TRUE	1	0.21012298721673	2		429	477	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792755	33792760	+	inframe_deletion	In_Frame_Del	DEL	GGCGGC	GGCGGC	-	rs746430067	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	8	98	0	ENST00000498907.2:c.561_566del	p.Pro188_Pro189del	p.P188_P189del	ENST00000498907	NM_004364.3	187	ccGCCGCCc/ccc	1/1	1	2	FACETS	0.491	0.317	0.717	0.491	0.317	0.717	SUBCLONAL	1	TRUE	1	0.21012298721673	2		98	155	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743960	41743960	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	147	1331	1	ENST00000301178.4:c.895C>A	p.Leu299Ile	p.L299I	ENST00000301178	NM_021913.4	299	Ctc/Atc	7/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.21012298721673	2		1332	1098	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	185	953	6	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	0.945	0.872	1	1	0.992	1	CLONAL	2	TRUE	1	0.21012298721673	2		959	932	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724327	52724327	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	104	917	0	ENST00000322088.6:c.1459T>G	p.Leu487Val	p.L487V	ENST00000322088	NM_014225.5	487	Ttg/Gtg	12/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.21012298721673	2		917	780	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966789	25966789	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	160	977	0	ENST00000435504.4:c.2417T>C	p.Leu806Pro	p.L806P	ENST00000435504		806	cTg/cCg	13/13	0.21012298721673	1	FACETS	0.815	0.748	0.885	1	0.99	1	CLONAL	2	TRUE	0	0.21012298721673	1		977	836	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46588084	46588084	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	67	1014	0	ENST00000263734.3:c.634T>C	p.Cys212Arg	p.C212R	ENST00000263734	NM_001430.4	212	Tgt/Cgt	6/16	0.0588103380012994	4	FACETS	0.713	0.618	0.817	0.357	0.309	0.409	INDETERMINATE	1	TRUE	2	0.21012298721673	4		1014	1082	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609576	46609576	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	78	1126	2	ENST00000263734.3:c.2303del	p.Asn768ThrfsTer3	p.N768Tfs*3	ENST00000263734	NM_001430.4	767	cAa/ca	15/16	0.0588103380012994	4	FACETS	0.743	0.651	0.843	0.372	0.325	0.422	INDETERMINATE	1	TRUE	2	0.21012298721673	4		1128	1209	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149973	202149973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1272714323	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	108	751	1	ENST00000358485.4:c.1414C>T	p.Arg472Ter	p.R472*	ENST00000358485	NM_001080125.1	472	Cga/Tga	8/9	0.0588103380012994	4	FACETS	1	0.979	1	0.691	0.619	0.767	INDETERMINATE	1	TRUE	2	0.21012298721673	4		752	900	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151289	202151290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	59	227	0	ENST00000358485.4:c.1596dup	p.Leu533ThrfsTer6	p.L533Tfs*6	ENST00000358485	NM_001080125.1	530	aga/agAa	9/9	0.0588103380012994	4	FACETS	0.758	0.654	0.872	0.758	0.654	0.872	INDETERMINATE	2	TRUE	2	0.21012298721673	4		227	448	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113331	209113331	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	52	310	0	ENST00000345146.2:c.176A>G	p.Asp59Gly	p.D59G	ENST00000345146	NM_005896.2	59	gAt/gGt	4/10	0.21012298721673	0	FACETS	0.855	0.729	0.993			1	CLONAL	1	TRUE	0	0.21012298721673	0		310	457	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248599	212248599	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	175	650	0	ENST00000342788.4:c.3668A>C	p.Lys1223Thr	p.K1223T	ENST00000342788	NM_005235.2	1223	aAg/aCg	28/28	0.21012298721673	0	FACETS	0.848	0.782	0.916			1	CLONAL	2	TRUE	0	0.21012298721673	0		650	776	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285326	212285326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1390491269	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	53	174	0	ENST00000342788.4:c.2975G>A	p.Arg992His	p.R992H	ENST00000342788	NM_005235.2	992	cGt/cAt	25/28	0.21012298721673	0	FACETS	1	0.938	1			1	CLONAL	1	TRUE	0	0.21012298721673	0		174	338	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660639	227660639	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	131	1105	0	ENST00000305123.5:c.2816A>C	p.Glu939Ala	p.E939A	ENST00000305123	NM_005544.2	939	gAg/gCg	1/2	0.0671715711258128	5	FACETS	0.795	0.72	0.873			1	INDETERMINATE	2	TRUE	NA	0.21012298721673	5		1105	1032	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661267	227661267	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	185	1127	0	ENST00000305123.5:c.2188G>T	p.Gly730Cys	p.G730C	ENST00000305123	NM_005544.2	730	Ggt/Tgt	1/2	0.0671715711258128	5	FACETS	1	0.95	1			1	INDETERMINATE	2	TRUE	NA	0.21012298721673	5		1127	1114	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	64	860	1	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	0.0671715711258128	5	FACETS	0.77	0.665	0.886			1	INDETERMINATE	1	TRUE	NA	0.21012298721673	5		861	1040	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62317172	62317172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770158407	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	272	1361	0	ENST00000360203.5:c.1295G>A	p.Arg432Gln	p.R432Q	ENST00000360203	NM_001283009.1	432	cGg/cAg	16/35	1	2	FACETS	0.971	0.91	1	1	0.995	1	CLONAL	2	TRUE	1	0.21012298721673	2		1361	1333	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37640186	37640186	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1262	69	1592	0	ENST00000249071.6:c.3G>A	p.Met1?	p.M1?	ENST00000249071	NM_002872.4	1	atG/atA	1/7	1	2	FACETS	0.493	0.428	0.565	0.493	0.428	0.565	SUBCLONAL	1	TRUE	1	0.21012298721673	2		1592	1331	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434235	12434235	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	24	154	0	ENST00000287820.6:c.606del	p.Met203CysfsTer30	p.M203Cfs*30	ENST00000287820	NM_015869.4	201	gtG/gt	4/7	1	2	FACETS	0.496	0.388	0.621	0.496	0.388	0.621	SUBCLONAL	1	TRUE	1	0.21012298721673	2		154	461	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098879	47098879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	60	805	0	ENST00000409792.3:c.6395G>A	p.Arg2132Gln	p.R2132Q	ENST00000409792	NM_014159.6	2132	cGg/cAg	15/21	1	2	FACETS	0.518	0.445	0.599	0.518	0.445	0.599	SUBCLONAL	1	TRUE	1	0.21012298721673	2		805	1102	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161939	47161939	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	45	301	0	ENST00000409792.3:c.4187del	p.Asn1396MetfsTer16	p.N1396Mfs*16	ENST00000409792	NM_014159.6	1396	aAt/at	3/21	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.21012298721673	2		301	420	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281339	142281339	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	69	246	0	ENST00000350721.4:c.905T>C	p.Leu302Pro	p.L302P	ENST00000350721	NM_001184.3	302	cTa/cCa	4/47	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.21012298721673	2		246	486	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013719	170013719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388201066	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	52	417	0	ENST00000295797.4:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000295797	NM_002740.5	480	Cgc/Tgc	15/18	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.21012298721673	2		417	440	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	11	704	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.299	0.206	0.416	0.299	0.206	0.416	SUBCLONAL	1	TRUE	1	0.21012298721673	2		704	350	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430396	181430396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	148	943	0	ENST00000325404.1:c.248C>T	p.Ser83Leu	p.S83L	ENST00000325404	NM_003106.3	83	tCg/tTg	1/1	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.21012298721673	2		943	1019	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803571	1803571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs4647924	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	166	1064	2	ENST00000260795.2:c.749C>T	p.Pro250Leu	p.P250L	ENST00000260795		250	cCg/cTg	6/17	1	2	FACETS	1	0.954	1	1	0.992	1	CLONAL	2	TRUE	1	0.21012298721673	2		1066	751	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805497	1805497	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	68	1221	0	ENST00000260795.2:c.1009T>C	p.Tyr337His	p.Y337H	ENST00000260795		337	Tac/Cac	7/17	1	2	FACETS	0.65	0.564	0.744	0.65	0.564	0.744	SUBCLONAL	1	TRUE	1	0.21012298721673	2		1221	995	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749524	41749524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1192207345	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	50	903	0	ENST00000226382.2:c.271G>A	p.Gly91Ser	p.G91S	ENST00000226382	NM_003924.3	91	Ggc/Agc	2/3	1	2	FACETS	0.602	0.509	0.704	0.602	0.509	0.704	SUBCLONAL	1	TRUE	1	0.21012298721673	2		903	791	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213911	66213911	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	79	152	0	ENST00000273854.3:c.2519T>G	p.Ile840Ser	p.I840S	ENST00000273854	NM_004439.5	840	aTt/aGt	15/18	1	2	FACETS	1	0.95	1	1	0.986	1	CLONAL	2	TRUE	1	0.21012298721673	2		152	332	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509084	66509085	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	26	134	0	ENST00000273854.3:c.242dup	p.Asn81LysfsTer8	p.N81Kfs*8	ENST00000273854	NM_004439.5	81	aat/aaAt	2/18	1	2	FACETS	0.952	0.756	1	0.952	0.756	1	CLONAL	1	TRUE	1	0.21012298721673	2		134	260	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106182953	106182953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	38	82	0	ENST00000380013.4:c.3992C>T	p.Thr1331Ile	p.T1331I	ENST00000380013	NM_001127208.2	1331	aCt/aTt	8/11	0.0588103380012994	4	FACETS	0.829	0.689	0.983	0.829	0.689	0.983	INDETERMINATE	2	TRUE	2	0.21012298721673	4		82	264	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271269	153271270	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	18	34	0	ENST00000281708.4:c.508dup	p.Arg170LysfsTer8	p.R170Kfs*8	ENST00000281708	NM_033632.3	170	aga/aAga	3/12	0.0588103380012994	4	FACETS	1	0.891	1	0.682	0.517	0.873	INDETERMINATE	1	TRUE	2	0.21012298721673	4		34	152	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541087	187541087	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	31	516	0	ENST00000441802.2:c.6653T>C	p.Ile2218Thr	p.I2218T	ENST00000441802	NM_005245.3	2218	aTc/aCc	10/27	0.0588103380012994	4	FACETS	0.589	0.475	0.719	0.295	0.237	0.36	INDETERMINATE	1	TRUE	2	0.21012298721673	4		516	606	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294163	1294163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199701877	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	71	1288	0	ENST00000310581.5:c.838G>A	p.Glu280Lys	p.E280K	ENST00000310581	NM_198253.2	280	Gaa/Aaa	2/16	0.180344989415708	0	FACETS	0.514	0.447	0.586			1	SUBCLONAL	1	TRUE	0	0.21012298721673	0		1288	1039	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295101	1295101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	16	114	0	ENST00000310581.5:c.4C>T	p.Pro2Ser	p.P2S	ENST00000310581	NM_198253.2	2	Ccg/Tcg	1/16	0.180344989415708	0	FACETS	0.835	0.622	1			1	CLONAL	1	TRUE	0	0.21012298721673	0		114	144	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449398	31449398	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	64	332	1	ENST00000344624.3:c.2811G>A	p.Met937Ile	p.M937I	ENST00000344624		937	atG/atA	19/33	0.180344989415708	0	FACETS	1	0.884	1			1	CLONAL	1	TRUE	0	0.21012298721673	0		333	472	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31495433	31495433	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	47	584	0	ENST00000344624.3:c.1715del	p.Phe572SerfsTer14	p.F572Sfs*14	ENST00000344624		572	tTc/tc	9/33	0.180344989415708	0	FACETS	0.466	0.392	0.548			1	SUBCLONAL	1	TRUE	0	0.21012298721673	0		584	759	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152428	56152428	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs778331321	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	34	184	0	ENST00000399503.3:c.484C>T	p.Arg162Cys	p.R162C	ENST00000399503	NM_005921.1	162	Cgt/Tgt	2/20	0.0967674518621271	5	FACETS	0.835	0.686	1	0.556	0.457	0.667	INDETERMINATE	2	TRUE	2	0.21012298721673	5		184	255	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149450109	149450109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1315261761	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	81	1130	1	ENST00000286301.3:c.1108C>T	p.Arg370Cys	p.R370C	ENST00000286301	NM_005211.3	370	Cgc/Tgc	8/22	0.180344989415708	0	FACETS	0.52	0.457	0.589			1	SUBCLONAL	1	TRUE	0	0.21012298721673	0		1131	1170	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839736	27839736	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1281167014	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	54	820	0	ENST00000328488.2:c.358A>G	p.Ile120Val	p.I120V	ENST00000328488	NM_003533.2	120	Att/Gtt	1/1	0.0588103380012994	4	FACETS	0.599	0.51	0.698	0.3	0.255	0.349	INDETERMINATE	1	TRUE	2	0.21012298721673	4		820	1038	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323180	31323180	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	139	986	0	ENST00000412585.2:c.809C>T	p.Ala270Val	p.A270V	ENST00000412585	NM_005514.6	270	gCt/gTt	4/8	0.0588103380012994	4	FACETS	0.781	0.71	0.856	0.781	0.71	0.856	INDETERMINATE	2	TRUE	2	0.21012298721673	4		986	1025	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324181	31324181	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	212	1124	0	ENST00000412585.2:c.382G>T	p.Gly128Trp	p.G128W	ENST00000412585	NM_005514.6	128	Ggg/Tgg	3/8	0.0588103380012994	4	FACETS	1	0.982	1	1	0.982	1	INDETERMINATE	2	TRUE	2	0.21012298721673	4		1124	1047	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324573	31324573	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs777906766	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	173	644	0	ENST00000412585.2:c.235G>T	p.Glu79Ter	p.E79*	ENST00000412585	NM_005514.6	79	Gag/Tag	2/8	0.0588103380012994	4	FACETS	1	0.972	1	1	0.991	1	INDETERMINATE	3	TRUE	2	0.21012298721673	4		644	602	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169080	32169080	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	192	1229	0	ENST00000375023.3:c.3953T>G	p.Val1318Gly	p.V1318G	ENST00000375023	NM_004557.3	1318	gTg/gGg	22/30	0.0588103380012994	4	FACETS	0.987	0.912	1	0.987	0.912	1	INDETERMINATE	2	TRUE	2	0.21012298721673	4		1229	1120	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004525	150004525	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	64	692	0	ENST00000253339.5:c.1700A>G	p.Asn567Ser	p.N567S	ENST00000253339		567	aAc/aGc	3/7	0.0588103380012994	4	FACETS	0.731	0.631	0.84	0.365	0.315	0.42	INDETERMINATE	1	TRUE	2	0.21012298721673	4		692	1009	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527474	157527474	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	105	486	0	ENST00000346085.5:c.5199A>C	p.Glu1733Asp	p.E1733D	ENST00000346085	NM_020732.3	1733	gaA/gaC	20/20	0.21012298721673	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.21012298721673	1		486	671	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729498	41729498	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	45	869	0	ENST00000242208.4:c.1031G>T	p.Gly344Val	p.G344V	ENST00000242208	NM_002192.2	344	gGc/gTc	3/3	1	2	FACETS	0.524	0.439	0.619	0.524	0.439	0.619	SUBCLONAL	1	TRUE	1	0.21012298721673	2		869	817	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224508	55224508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	25	278	0	ENST00000275493.2:c.1190C>T	p.Thr397Ile	p.T397I	ENST00000275493	NM_005228.3	397	aCc/aTc	10/28	1	2	FACETS	0.596	0.469	0.743	0.596	0.469	0.743	SUBCLONAL	1	TRUE	1	0.21012298721673	2		278	399	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501317	140501317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1325951163	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	30	141	0	ENST00000288602.6:c.755G>A	p.Arg252Gln	p.R252Q	ENST00000288602	NM_004333.4	252	cGa/cAa	6/18	0.0588103380012994	4	FACETS	1	0.85	1	0.532	0.429	0.648	INDETERMINATE	1	TRUE	2	0.21012298721673	4		141	325	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273413	38273413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	145	1529	0	ENST00000425967.3:c.1922G>A	p.Gly641Asp	p.G641D	ENST00000425967	NM_001174067.1	641	gGc/gAc	14/19	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.21012298721673	2		1529	1258	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	125	943	1	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.21012298721673	2		944	863	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864657	68864657	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	62	407	0	ENST00000288368.4:c.28C>A	p.Arg10Ser	p.R10S	ENST00000288368	NM_024870.2	10	Cgc/Agc	1/40	1	2	FACETS	0.8	0.694	0.913	1	0.974	1	CLONAL	2	TRUE	1	0.21012298721673	2		407	369	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981591	70981591	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	72	1348	0	ENST00000276594.2:c.505T>G	p.Leu169Val	p.L169V	ENST00000276594	NM_024504.3	169	Tta/Gta	2/8	1	2	FACETS	0.574	0.499	0.655	0.574	0.499	0.655	SUBCLONAL	1	TRUE	1	0.21012298721673	2		1348	1194	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866512	117866512	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	21	129	0	ENST00000297338.2:c.1133A>G	p.Gln378Arg	p.Q378R	ENST00000297338	NM_006265.2	378	cAg/cGg	9/14	1	2	FACETS	0.479	0.368	0.609	0.479	0.368	0.609	SUBCLONAL	1	TRUE	1	0.21012298721673	2		129	417	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054591	5054591	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1443023071	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	56	92	0	ENST00000381652.3:c.643C>T	p.Arg215Ter	p.R215*	ENST00000381652	NM_004972.3	215	Cga/Tga	7/25	0.21012298721673	5	FACETS	0.895	0.774	1			1	CLONAL	3	TRUE	NA	0.21012298721673	5		92	261	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974792	21974792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141798398	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	69	370	0	ENST00000304494.5:c.35C>T	p.Ser12Leu	p.S12L	ENST00000304494	NM_000077.4	12	tCg/tTg	1/3	1	2	FACETS	0.833	0.729	0.945	1	0.978	1	CLONAL	2	TRUE	1	0.21012298721673	2		370	394	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639981	93639981	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	88	489	0	ENST00000375746.1:c.1310G>T	p.Gly437Val	p.G437V	ENST00000375746	NM_001174167.1	437	gGg/gTg	10/14	1	2	FACETS	0.805	0.716	0.901	1	0.981	1	CLONAL	2	TRUE	1	0.21012298721673	2		489	520	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390736	139390736	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1195	70	1465	0	ENST00000277541.6:c.7455del	p.Ser2486ArgfsTer103	p.S2486Rfs*103	ENST00000277541	NM_017617.3	2485	ccC/cc	34/34	1	2	FACETS	0.527	0.457	0.602	0.527	0.457	0.602	SUBCLONAL	1	TRUE	1	0.21012298721673	2		1465	1265	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396796	139396796	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	143	1166	0	ENST00000277541.6:c.5312A>C	p.Glu1771Ala	p.E1771A	ENST00000277541	NM_017617.3	1771	gAg/gCg	28/34	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.21012298721673	2		1166	984	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15840957	15840957	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	44	518	0	ENST00000307771.7:c.1041C>A	p.Tyr347Ter	p.Y347*	ENST00000307771	NM_005089.3	347	taC/taA	11/11	1	2	FACETS	0.7	0.586	0.827	0.7	0.586	0.827	SUBCLONAL	1	TRUE	1	0.21012298721673	2		518	598	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932860	39932860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	177	1071	1	ENST00000378444.4:c.1739G>A	p.Gly580Asp	p.G580D	ENST00000378444	NM_001123385.1	580	gGc/gAc	4/15	1	2	FACETS	0.884	0.814	0.956	1	0.992	1	CLONAL	2	TRUE	1	0.21012298721673	2		1072	953	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412746	63412746	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	34	870	0	ENST00000330258.3:c.421T>G	p.Ser141Ala	p.S141A	ENST00000330258	NM_152424.3	141	Tcc/Gcc	2/2	0.21012298721673	1	FACETS	0.476	0.388	0.576	0.476	0.388	0.576	SUBCLONAL	1	TRUE	0	0.21012298721673	1		870	608	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437940	110437940	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	13	57	0	ENST00000375856.3:c.461C>G	p.Pro154Arg	p.P154R	ENST00000375856	NM_003749.2	154	cCc/cGc	1/2	0.21012298721673	5	FACETS	1	0.779	1	0.723	0.525	0.955	CLONAL	2	TRUE	2	0.21012298721673	5		57	75	SUCCESS
AR	367	MSKCC	GRCh37	X	66765205	66765205	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1199988820	NA	P-0057097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	12	422	0	ENST00000374690.3:c.217C>T	p.Gln73Ter	p.Q73*	ENST00000374690	NM_000044.3	73	Cag/Tag	1/8	0.21012298721673	1	FACETS	0.524	0.369	0.715	0.524	0.369	0.715	SUBCLONAL	1	TRUE	0	0.21012298721673	1		422	195	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203436	NA	P-0057102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	125	851	0	ENST00000269305.4:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269305	NM_001126112.2	163	Tac/Cac	5/11	0.454229754447524	1	FACETS	0.915	0.834	0.999	0.915	0.834	0.999	CLONAL	1	TRUE	0	0.454229754447524	1		851	465	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489786	40489786	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	112	545	0	ENST00000264657.5:c.640C>T	p.Arg214Trp	p.R214W	ENST00000264657	NM_139276.2	214	Cgg/Tgg	7/24	0.454229754447524	1	FACETS	0.972	0.882	1	0.972	0.882	1	CLONAL	1	TRUE	0	0.454229754447524	1		545	392	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584605	48584606	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0057102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	96	342	0	ENST00000342988.3:c.779dup	p.Tyr260Ter	p.Y260*	ENST00000342988	NM_005359.5	260	tac/tAac	6/12	0.454229754447524	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.454229754447524	1		342	309	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139440186	139440186	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	23	124	0	ENST00000277541.6:c.53C>T	p.Ala18Val	p.A18V	ENST00000277541	NM_017617.3	18	gCc/gTc	1/34	0.454229754447524	1	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	0	0.454229754447524	1		124	74	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544715	65544722	+	frameshift_variant	Frame_Shift_Del	DEL	TATATTCT	TATATTCT	-	novel	NA	P-0057102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	227	620	0	ENST00000358664.4:c.204_211del	p.Glu69ProfsTer15	p.E69Pfs*15	ENST00000358664	NM_002382.4	68	acAGAATATAtc/actc	4/5	0.454229754447524	2	FACETS	0.931	0.875	0.987	0.931	0.875	0.987	CLONAL	2	TRUE	0	0.454229754447524	2		620	537	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40468910	40468910	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	59	351	0	ENST00000264657.5:c.2154C>A	p.Cys718Ter	p.C718*	ENST00000264657	NM_139276.2	718	tgC/tgA	23/24	0.454229754447524	1	FACETS	0.746	0.648	0.851	0.746	0.648	0.851	SUBCLONAL	1	TRUE	0	0.454229754447524	1		351	269	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149852	202149852	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	126	542	0	ENST00000358485.4:c.1293G>C	p.Glu431Asp	p.E431D	ENST00000358485	NM_001080125.1	431	gaG/gaC	8/9	0.454229754447524	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.454229754447524	1		542	416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578369	7578369	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0057103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	413	669	0	ENST00000269305.4:c.559+2T>G		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.671976019419372	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.720172775672929	3		669	492	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098665	47098665	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0057103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	135	677	0	ENST00000409792.3:c.6609T>A	p.Tyr2203Ter	p.Y2203*	ENST00000409792	NM_014159.6	2203	taT/taA	15/21	0.722784354202744	5	FACETS	1	0.976	1	0.402	0.366	0.44	CLONAL	1	TRUE	2	0.720172775672929	5		677	646	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187084	38187084	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	108	686	0	ENST00000317025.8:c.1393C>A	p.Pro465Thr	p.P465T	ENST00000317025	NM_023034.1	465	Cct/Act	6/24	0.27627200493747	6	FACETS	1	0.978	1	0.331	0.298	0.367	INDETERMINATE	1	TRUE	2	0.720172775672929	6		686	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0057104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	104	504	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.224315629228746	2		504	836	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453149	140453149	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913361	NA	P-0057104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	29	318	0	ENST00000288602.6:c.1786G>C	p.Gly596Arg	p.G596R	ENST00000288602	NM_004333.4	596	Ggt/Cgt	15/18	1	2	FACETS	0.498	0.399	0.612	0.498	0.399	0.612	SUBCLONAL	1	TRUE	1	0.224315629228746	2		318	519	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0057105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	33	221	1				ENST00000310581	NM_198253.2	-/1132			0.214298470869606	1	FACETS	1	0.893	1	1	0.893	1	INDETERMINATE	1	TRUE	0	0.48825069072387	1		222	94	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0057105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	77	317	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.295154052061561	3	FACETS	1	0.977	1	0.732	0.651	0.817	CLONAL	1	TRUE	1	0.48825069072387	3		317	268	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686904	117686904	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	21	271	0	ENST00000368508.3:c.2813G>A	p.Gly938Glu	p.G938E	ENST00000368508	NM_002944.2	938	gGg/gAg	19/43	0.360988221900579	0	FACETS	0.524	0.413	0.647			1	SUBCLONAL	1	TRUE	0	0.48825069072387	0		271	84	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094325	193094325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	44	340	0	ENST00000367435.3:c.215C>T	p.Pro72Leu	p.P72L	ENST00000367435	NM_024529.4	72	cCt/cTt	2/17	0.182211290027595	5	FACETS	1	0.929	1	0.396	0.334	0.463	INDETERMINATE	1	TRUE	2	0.48825069072387	5		340	263	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145655	61145655	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	18	433	0	ENST00000295025.8:c.767C>T	p.Pro256Leu	p.P256L	ENST00000295025	NM_002908.2	256	cCc/cTc	7/11	1	2	FACETS	0.319	0.241	0.412	0.319	0.241	0.412	SUBCLONAL	1	TRUE	1	0.48825069072387	2		433	231	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149290723	149290723	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	111	628	0	ENST00000360632.3:c.496A>T	p.Met166Leu	p.M166L	ENST00000360632	NM_015472.4	166	Atg/Ttg	3/7	0.285822838590656	2	FACETS	0.881	0.807	0.956	0.881	0.807	0.956	INDETERMINATE	2	TRUE	0	0.48825069072387	2		628	258	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1258770	1258770	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	13	627	0	ENST00000310581.5:c.2975A>G	p.Asn992Ser	p.N992S	ENST00000310581	NM_198253.2	992	aAc/aGc	13/16	0.360988221900579	0	FACETS	0.178	0.127	0.239			1	SUBCLONAL	1	TRUE	0	0.48825069072387	0		627	153	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0057114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	461	745	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.500475676468152	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	3	TRUE	0	0.500475676468152	3		745	768	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55524236	55524236	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	166	768	0	ENST00000288135.5:c.55C>G	p.Arg19Gly	p.R19G	ENST00000288135	NM_000222.2	19	Cgc/Ggc	1/21	0.368076901763742	1	FACETS	0.815	0.752	0.88	0.815	0.752	0.88	CLONAL	1	TRUE	0	0.500475676468152	1		768	610	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111794	56111794	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs557606535	NA	P-0057114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	18	19	0	ENST00000399503.3:c.394G>C	p.Asp132His	p.D132H	ENST00000399503	NM_005921.1	132	Gac/Cac	1/20	0.500475676468152	2	FACETS	0.922	0.773	1	1	0.936	1	CLONAL	3	TRUE	0	0.500475676468152	2		19	26	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419997	152419997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	167	768	0	ENST00000206249.3:c.1684G>A	p.Glu562Lys	p.E562K	ENST00000206249	NM_000125.3	562	Gag/Aag	8/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.500475676468152	2		768	636	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141405	11141405	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0057114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	353	745	0	ENST00000358026.2:c.3383-1G>A		p.X1128_splice	ENST00000358026	NM_001128849.1	1128			0.500475676468152	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.500475676468152	2		745	687	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31423003	31423003	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	242	452	0	ENST00000344624.3:c.3310C>G	p.Leu1104Val	p.L1104V	ENST00000344624		1104	Cta/Gta	26/33	0.500475676468152	9	FACETS	0.978	0.911	1	0.279	0.26	0.299	CLONAL	2	TRUE	2	0.500475676468152	9		452	1361	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867458	35867458	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	120	320	0	ENST00000303115.3:c.272T>C	p.Ile91Thr	p.I91T	ENST00000303115	NM_002185.3	91	aTa/aCa	3/8	0.500475676468152	9	FACETS	0.821	0.741	0.905	0.234	0.211	0.259	CLONAL	2	TRUE	2	0.500475676468152	9		320	804	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484160	8484160	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	332	486	0	ENST00000356435.5:c.3372T>G	p.Ile1124Met	p.I1124M	ENST00000356435		1124	atT/atG	19/35	0.494893012055929	3	FACETS	0.944	0.903	0.984	0.944	0.903	0.984	CLONAL	3	TRUE	0	0.500475676468152	3		486	586	SUCCESS
AR	367	MSKCC	GRCh37	X	66765115	66765115	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	135	671	0	ENST00000374690.3:c.127G>T	p.Glu43Ter	p.E43*	ENST00000374690	NM_000044.3	43	Gag/Tag	1/8	1	2	FACETS	0.963	0.88	1	0.963	0.88	1	CLONAL	1	TRUE	1	0.500475676468152	2		671	560	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034422	123034422	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	76	312	0	ENST00000355640.3:c.1179G>T	p.Met393Ile	p.M393I	ENST00000355640		393	atG/atT	6/7	1	2	FACETS	0.868	0.767	0.975	0.868	0.767	0.975	CLONAL	1	TRUE	1	0.500475676468152	2		312	350	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861544	152861544	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	207	732	0	ENST00000406277.2:c.208A>T	p.Ile70Phe	p.I70F	ENST00000406277	NM_152274.4	70	Att/Ttt	4/7	NA		FACETS		0.987	1				INDETERMINATE	1	TRUE	NA	0.500475676468152	2		732	661	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	15	324	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.668	0.489	0.882	0.668	0.489	0.882	SUBCLONAL	1	FALSE	1	0.208832952050546	2		324	215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0057115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	18	928	1	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	1	2	FACETS	0.337	0.252	0.437	0.337	0.252	0.437	SUBCLONAL	1	FALSE	1	0.208832952050546	2		929	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0057115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	23	951	0	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	1	2	FACETS	0.461	0.358	0.58	0.461	0.358	0.58	SUBCLONAL	1	FALSE	1	0.208832952050546	2		951	478	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974679	21974679	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs864622636	NA	P-0057115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	40	697	1	ENST00000304494.5:c.148C>T	p.Gln50Ter	p.Q50*	ENST00000304494	NM_000077.4	50	Cag/Tag	1/3	0.164891614124212	2	FACETS	0.948	0.789	1	0.474	0.394	0.563	CLONAL	1	FALSE	0	0.208832952050546	2		698	404	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233110	46233110	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0057115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	11	248	0	ENST00000334344.6:c.1331-2A>G		p.X444_splice	ENST00000334344	NM_152641.2	444			0.208832952050546	3	FACETS	0.654	0.452	0.903	0.327	0.226	0.452	SUBCLONAL	1	FALSE	1	0.208832952050546	3		248	178	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023625	31023626	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	29	809	1	ENST00000375687.4:c.3110_3111delinsAA	p.Trp1037Ter	p.W1037*	ENST00000375687	NM_015338.5	1037	tGG/tAA	13/13	1	2	FACETS	0.525	0.42	0.645	0.525	0.42	0.645	SUBCLONAL	1	FALSE	1	0.208832952050546	2		810	529	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141821	108141821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	31	430	0	ENST00000278616.4:c.2869G>A	p.Glu957Lys	p.E957K	ENST00000278616	NM_000051.3	957	Gaa/Aaa	19/63	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	FALSE	1	0.208832952050546	2		430	257	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244517	46244517	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	42	550	0	ENST00000334344.6:c.2611C>T	p.Gln871Ter	p.Q871*	ENST00000334344	NM_152641.2	871	Cag/Tag	15/21	0.208832952050546	3	FACETS	1	0.947	1	0.675	0.566	0.796	CLONAL	1	FALSE	1	0.208832952050546	3		550	329	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670777	134670777	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	48	773	0	ENST00000398015.3:c.688G>A	p.Glu230Lys	p.E230K	ENST00000398015	NM_004441.4	230	Gag/Aag	3/16	0.208832952050546	0	FACETS	1	0.88	1			1	CLONAL	1	FALSE	0	0.208832952050546	0		773	349	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425884	49425885	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0057115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	59	1132	1	ENST00000301067.7:c.12603_12604delinsTT	p.Gln4202Ter	p.Q4202*	ENST00000301067	NM_003482.3	4201	ctCCaa/ctTTaa	39/54	0.208832952050546	3	FACETS	1	0.946	1	0.605	0.521	0.696	CLONAL	1	FALSE	1	0.208832952050546	3		1133	516	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495322	56495323	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0057115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	54	730	1	ENST00000267101.3:c.3512_3513delinsTT	p.Ser1171Phe	p.S1171F	ENST00000267101	NM_001982.3	1171	tCC/tTT	28/28	0.208832952050546	3	FACETS	1	0.905	1	0.54	0.461	0.626	CLONAL	1	FALSE	1	0.208832952050546	3		731	529	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40379563	40379563	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	33	847	0	ENST00000293328.3:c.269A>G	p.Tyr90Cys	p.Y90C	ENST00000293328	NM_012448.3	90	tAt/tGt	3/19	1	2	FACETS	0.707	0.575	0.855	0.707	0.575	0.855	SUBCLONAL	1	FALSE	1	0.208832952050546	2		847	447	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2180749	2180749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	32	861	0	ENST00000398665.3:c.119C>T	p.Thr40Ile	p.T40I	ENST00000398665	NM_032482.2	40	aCc/aTc	2/28	1	2	FACETS	0.613	0.497	0.745	0.613	0.497	0.745	SUBCLONAL	1	FALSE	1	0.208832952050546	2		861	500	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593669	215593669	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224671	NA	P-0057115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	15	424	0	ENST00000260947.4:c.2065G>A	p.Asp689Asn	p.D689N	ENST00000260947	NM_000465.2	689	Gac/Aac	11/11	0.103994952576867	0	FACETS	0.441	0.322	0.583			1	INDETERMINATE	1	FALSE	0	0.208832952050546	0		424	258	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259424	89259424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	39	593	0	ENST00000336596.2:c.568G>T	p.Val190Phe	p.V190F	ENST00000336596	NM_005233.5	190	Gtt/Ttt	3/17	0.208832952050546	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	0	0.208832952050546	1		593	270	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381480	81381480	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1338916319	NA	P-0057115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	15	408	0	ENST00000222390.5:c.581C>T	p.Pro194Leu	p.P194L	ENST00000222390	NM_000601.4	194	cCa/cTa	5/18	1	2	FACETS	0.509	0.372	0.675	0.509	0.372	0.675	SUBCLONAL	1	FALSE	1	0.208832952050546	2		408	282	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032237	10032237	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs901580617	NA	P-0057116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	310	702	0	ENST00000330684.3:c.586G>T	p.Val196Leu	p.V196L	ENST00000330684	NM_001134407.1	196	Gtg/Ttg	3/13	0.364864950241774	1	FACETS	0.72	0.681	0.76	0.72	0.681	0.76	INDETERMINATE	1	TRUE	0	0.651588648196788	1		702	891	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695979	117695979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757275063	NA	P-0057116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	246	566	0	ENST00000369458.3:c.458C>T	p.Pro153Leu	p.P153L	ENST00000369458	NM_024626.3	153	cCg/cTg	4/6	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.651588648196788	2		566	735	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709069	117709069	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	263	638	0	ENST00000368508.3:c.1888A>C	p.Ser630Arg	p.S630R	ENST00000368508	NM_002944.2	630	Agt/Cgt	13/43	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.651588648196788	2		638	757	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386529	81386529	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	64	500	0	ENST00000222390.5:c.458G>T	p.Ser153Ile	p.S153I	ENST00000222390	NM_000601.4	153	aGt/aTt	4/18	1	2	FACETS	0.33	0.286	0.378	0.33	0.286	0.378	SUBCLONAL	1	TRUE	1	0.651588648196788	2		500	595	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	30	324	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.497	0.4	0.608	0.497	0.4	0.608	SUBCLONAL	1	TRUE	1	0.247255273962073	2		324	488	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191570	10191570	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1559429824	NA	P-0057117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	77	658	0	ENST00000256474.2:c.563T>C	p.Leu188Pro	p.L188P	ENST00000256474	NM_000551.3	188	cTg/cCg	3/3	0.247255273962073	1	FACETS	0.736	0.645	0.833	0.736	0.645	0.833	SUBCLONAL	1	TRUE	0	0.247255273962073	1		658	742	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254858	16254858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	74	608	0	ENST00000375759.3:c.2123G>A	p.Arg708Lys	p.R708K	ENST00000375759	NM_015001.2	708	aGa/aAa	11/15	1	2	FACETS	0.747	0.653	0.849	0.747	0.653	0.849	SUBCLONAL	1	TRUE	1	0.247255273962073	2		608	801	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	41	330	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.976	0.813	1	0.976	0.813	1	CLONAL	1	TRUE	1	0.16	2		330	525	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876659675	NA	P-0057118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	43	819	0	ENST00000269305.4:c.764T>A	p.Ile255Asn	p.I255N	ENST00000269305	NM_001126112.2	255	aTc/aAc	7/11	1	2	FACETS	0.727	0.607	0.862	0.727	0.607	0.862	SUBCLONAL	1	TRUE	1	0.16	2		819	739	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165677	185165677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753496412	NA	P-0057118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	41	515	1	ENST00000265026.3:c.952G>A	p.Ala318Thr	p.A318T	ENST00000265026	NM_004721.4	318	Gca/Aca	5/14	1	2	FACETS	0.866	0.72	1	0.866	0.72	1	CLONAL	1	TRUE	1	0.16	2		516	592	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366908	15366908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150583855	NA	P-0057118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	64	837	2	ENST00000263377.2:c.1718C>T	p.Thr573Met	p.T573M	ENST00000263377	NM_058243.2	573	aCg/aTg	9/20	1	2	FACETS	0.887	0.766	1	0.887	0.766	1	CLONAL	1	TRUE	1	0.16	2		839	902	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732753	204732753	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	51	599	0	ENST00000302823.3:c.88T>G	p.Phe30Val	p.F30V	ENST00000302823	NM_005214.4	30	Ttc/Gtc	1/4	1	2	FACETS	0.972	0.825	1	0.972	0.825	1	CLONAL	1	TRUE	1	0.16	2		599	656	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0057124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	977	893	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.630796216491584	2		894	1521	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727501	88727501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147992979	NA	P-0057124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1294	101	539	0	ENST00000360948.2:c.278C>T	p.Thr93Met	p.T93M	ENST00000360948	NM_001012338.2	93	aCg/aTg	3/19	0.205036296478312	5	FACETS	0.447	0.398	0.499	0.089	0.079	0.1	INDETERMINATE	1	TRUE	0	0.630796216491584	5		539	1395	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791796	42791796	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	188	875	0	ENST00000575354.2:c.682C>T	p.Arg228Trp	p.R228W	ENST00000575354	NM_015125.3	228	Cgg/Tgg	5/20	0.316427216616497	2	FACETS	0.45	0.414	0.487	0.225	0.207	0.244	INDETERMINATE	1	TRUE	0	0.630796216491584	2		875	1326	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732862	44732862	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	86	568	0	ENST00000377967.4:c.68del	p.Lys23ArgfsTer19	p.K23Rfs*19	ENST00000377967	NM_021140.2	22	gAa/ga	1/29	0.630796216491584	1	FACETS	0.253	0.223	0.284	0.253	0.223	0.284	SUBCLONAL	1	TRUE	0	0.630796216491584	1		568	739	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450166	32450166	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0057124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	489	606	0	ENST00000332351.3:c.647-1G>T		p.X216_splice	ENST00000332351	NM_024426.4	216			0.630796216491584	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.630796216491584	1		606	832	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39573270	39573270	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	35	310	0	ENST00000262039.4:c.751G>C	p.Glu251Gln	p.E251Q	ENST00000262039	NM_002647.2	251	Gaa/Caa	7/25	0.630796216491584	1	FACETS	0.181	0.148	0.218	0.181	0.148	0.218	SUBCLONAL	1	TRUE	0	0.630796216491584	1		310	420	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794812	42794812	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	545	767	0	ENST00000575354.2:c.1892T>C	p.Leu631Pro	p.L631P	ENST00000575354	NM_015125.3	631	cTg/cCg	10/20	0.316427216616497	2	FACETS	1	0.997	1	0.709	0.682	0.736	INDETERMINATE	1	TRUE	0	0.630796216491584	2		767	1219	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239039	98239039	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0057124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	285	304	0	ENST00000331920.6:c.1602+2T>C		p.X534_splice	ENST00000331920	NM_000264.3	534			0.630796216491584	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.630796216491584	1		304	488	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0057125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	299	579	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.350664220235788	3	FACETS	1	0.993	1	0.83	0.79	0.87	CLONAL	2	TRUE	0	0.514208673646351	3		579	587	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0057125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	222	333	1	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.514208673646351	3	FACETS	0.933	0.884	0.981	0.933	0.884	0.981	CLONAL	3	TRUE	0	0.514208673646351	3		334	388	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864368	162864368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	92	512	0	ENST00000366898.1:c.145G>A	p.Glu49Lys	p.E49K	ENST00000366898	NM_004562.2	49	Gag/Aag	2/12	0.514208673646351	3	FACETS	0.887	0.791	0.989	0.444	0.395	0.495	CLONAL	1	TRUE	1	0.514208673646351	3		512	507	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741925	17741925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765066996	NA	P-0057125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	77	396	0	ENST00000250003.3:c.596C>T	p.Ala199Val	p.A199V	ENST00000250003	NM_002478.4	199	gCg/gTg	1/3	0.514208673646351	3	FACETS	1	0.967	1	0.627	0.556	0.702	CLONAL	1	TRUE	1	0.514208673646351	3		396	300	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279907	18279907	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	129	880	0	ENST00000222254.8:c.1990G>A	p.Asp664Asn	p.D664N	ENST00000222254	NM_005027.3	664	Gac/Aac	16/16	0.514208673646351	1	FACETS	0.69	0.629	0.754	0.69	0.629	0.754	SUBCLONAL	1	TRUE	0	0.514208673646351	1		880	540	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40743949	40743949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145907048	NA	P-0057125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	151	891	2	ENST00000392038.2:c.758G>A	p.Arg253Gln	p.R253Q	ENST00000392038	NM_001626.4	253	cGg/cAg	9/14	0.514208673646351	3	FACETS	1	0.95	1	0.525	0.481	0.571	CLONAL	1	TRUE	1	0.514208673646351	3		893	703	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93953157	93953157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755519422	NA	P-0057125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	51	333	0	ENST00000369303.4:c.2984G>A	p.Gly995Asp	p.G995D	ENST00000369303	NM_004440.3	995	gGc/gAc	17/17	0.514208673646351	3	FACETS	0.854	0.731	0.987	0.427	0.365	0.494	CLONAL	1	TRUE	1	0.514208673646351	3		333	292	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953026	2953026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747655872	NA	P-0057125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	126	972	0	ENST00000396946.4:c.2914G>A	p.Glu972Lys	p.E972K	ENST00000396946	NM_032415.4	972	Gag/Aag	22/25	0.363903489473884	0	FACETS	0.472	0.43	0.517			1	SUBCLONAL	1	TRUE	0	0.514208673646351	0		972	504	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395269	139395269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	150	999	2	ENST00000277541.6:c.5669G>A	p.Cys1890Tyr	p.C1890Y	ENST00000277541	NM_017617.3	1890	tGc/tAc	31/34	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.514208673646351	2		1001	529	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248071	59248097	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCTGCAGCCGCGGGTGCTGCACGGG	GGCCTGCAGCCGCGGGTGCTGCACGGG	A	novel	NA	P-0057125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	85	539	2	ENST00000371222.2:c.646_672delinsT	p.Pro216SerfsTer85	p.P216Sfs*85	ENST00000371222	NM_002228.3	216	CCCGTGCAGCACCCGCGGCTGCAGGCC/T	1/1	1	2	FACETS	0.945	0.842	1	0.945	0.842	1	CLONAL	1	TRUE	1	0.514208673646351	2		541	350	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549401	21549401	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	17	673	0	ENST00000382592.4:c.2875C>A	p.Leu959Met	p.L959M	ENST00000382592	NM_014572.2	959	Ctg/Atg	8/8	1	2	FACETS	0.533	0.398	0.694	0.533	0.398	0.694	SUBCLONAL	1	TRUE	1	0.223804826110004	2		673	285	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188315	10188315	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	54	455	0	ENST00000256474.2:c.458T>C	p.Leu153Pro	p.L153P	ENST00000256474	NM_000551.3	153	cTg/cCg	2/3	0.223804826110004	1	FACETS	1	0.902	1	1	0.978	1	CLONAL	2	TRUE	0	0.223804826110004	1		455	204	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556079	29556079	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886041347	NA	P-0057128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	130	201	0	ENST00000356175.3:c.2446C>T	p.Arg816Ter	p.R816*	ENST00000356175	NM_000267.3	816	Cga/Tga	21/57	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.799226592316878	2		201	312	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0057129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	23	504	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.902	0.706	1	0.902	0.706	1	CLONAL	1	TRUE	1	0.219907340073994	2		504	232	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916925	178916930	+	inframe_deletion	In_Frame_Del	DEL	AGTAGG	AGTAGG	-	novel	NA	P-0057129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	56	406	0	ENST00000263967.3:c.312_317del	p.Val105_Gly106del	p.V105_G106del	ENST00000263967	NM_006218.2	104	ccAGTAGGc/ccc	2/21	1	2	FACETS	1	0.884	1	1	0.978	1	CLONAL	2	TRUE	1	0.219907340073994	2		406	249	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109321744	109321744	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	79	626	0	ENST00000436639.2:c.679A>G	p.Asn227Asp	p.N227D	ENST00000436639	NM_014454.2	227	Aac/Gac	4/10	0.219907340073994	3	FACETS	0.987	0.873	1	0.987	0.873	1	CLONAL	2	TRUE	1	0.219907340073994	3		626	404	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0057130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	37	473	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.732	0.604	0.875	0.732	0.604	0.875	SUBCLONAL	1	TRUE	1	0.239544897353179	2		473	422	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602290	10602290	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	55	558	0	ENST00000171111.5:c.1288G>T	p.Gly430Cys	p.G430C	ENST00000171111	NM_203500.1	430	Ggc/Tgc	3/6	0.239544897353179	1	FACETS	0.797	0.683	0.922	0.797	0.683	0.922	CLONAL	1	TRUE	0	0.239544897353179	1		558	507	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375450	15375450	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	86	615	0	ENST00000263377.2:c.977G>T	p.Arg326Leu	p.R326L	ENST00000263377	NM_058243.2	326	cGg/cTg	6/20	0.239544897353179	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.239544897353179	1		615	509	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432494	49432494	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	57	532	0	ENST00000301067.7:c.8645A>T	p.His2882Leu	p.H2882L	ENST00000301067	NM_003482.3	2882	cAc/cTc	34/54	1	2	FACETS	0.973	0.836	1	0.973	0.836	1	CLONAL	1	TRUE	1	0.239544897353179	2		532	489	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913327	32913327	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764834875	NA	P-0057130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	52	341	0	ENST00000380152.3:c.4835C>T	p.Pro1612Leu	p.P1612L	ENST00000380152		1612	cCa/cTa	11/27	0.205555671299584	1	FACETS	0.955	0.816	1	0.955	0.816	1	CLONAL	1	TRUE	0	0.239544897353179	1		341	400	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738586	43738586	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	34	307	0	ENST00000382044.4:c.3039A>C	p.Glu1013Asp	p.E1013D	ENST00000382044	NM_001141980.1	1013	gaA/gaC	14/28	1	2	FACETS	0.719	0.588	0.866	0.719	0.588	0.866	SUBCLONAL	1	TRUE	1	0.239544897353179	2		307	395	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223044	1223057	+	frameshift_variant	Frame_Shift_Del	DEL	CACCAAGGACCGGT	CACCAAGGACCGGT	-	novel	NA	P-0057130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	83	575	0	ENST00000326873.7:c.981_994del	p.Asp327GlufsTer28	p.D327Efs*28	ENST00000326873	NM_000455.4	327	gaCACCAAGGACCGGTgg/gagg	8/10	0.239544897353179	1	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	0	0.239544897353179	1		575	601	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100117	11100117	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	59	402	0	ENST00000358026.2:c.1243C>T	p.Gln415Ter	p.Q415*	ENST00000358026	NM_001128849.1	415	Cag/Tag	7/36	0.239544897353179	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.239544897353179	1		402	375	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410823	63410823	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	55	486	0	ENST00000330258.3:c.2344del	p.Leu782SerfsTer26	p.L782Sfs*26	ENST00000330258	NM_152424.3	782	Ctc/tc	2/2	1	2	FACETS	0.906	0.775	1	0.906	0.775	1	CLONAL	1	TRUE	1	0.239544897353179	2		486	507	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0057131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	136	597	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.702079705071213	4	FACETS	1	0.974	1	0.558	0.517	0.6	CLONAL	2	TRUE	0	0.732609667950882	4		597	288	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1060501197	NA	P-0057131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	379	423	10	ENST00000269305.4:c.716del	p.Asn239ThrfsTer8	p.N239Tfs*8	ENST00000269305	NM_001126112.2	239	aAc/ac	7/11	0.714482149510889	3	FACETS	0.942	0.913	0.97	0.942	0.913	0.97	CLONAL	3	TRUE	0	0.732609667950882	3		433	500	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0057131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	132	286	2	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	0.677930087596755	3	FACETS	0.932	0.883	0.979	0.932	0.883	0.979	CLONAL	3	TRUE	0	0.732609667950882	3		288	176	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534325	63534325	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765865516	NA	P-0057131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	198	589	1	ENST00000307078.5:c.1196G>A	p.Arg399Gln	p.R399Q	ENST00000307078	NM_004655.3	399	cGa/cAa	5/11	0.714482149510889	3	FACETS	0.946	0.878	1	0.315	0.292	0.339	CLONAL	1	TRUE	0	0.732609667950882	3		590	781	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822585	72822586	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs764626362	NA	P-0057131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	55	503	1	ENST00000268489.5:c.9589dup	p.Gln3197ProfsTer42	p.Q3197Pfs*42	ENST00000268489	NM_006885.3	3197	cag/cCag	10/10	0.732609667950882	3	FACETS	0.456	0.39	0.527	0.228	0.195	0.264	SUBCLONAL	1	TRUE	1	0.732609667950882	3		504	450	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820785	3820785	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0057131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	253	782	0	ENST00000262367.5:c.2666C>G	p.Ser889Ter	p.S889*	ENST00000262367	NM_004380.2	889	tCa/tGa	14/31	0.732609667950882	5	FACETS	1	0.981	1	0.375	0.35	0.401	CLONAL	1	TRUE	2	0.732609667950882	5		782	1288	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916840	48916841	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs1566186125	NA	P-0057131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	35	253	0	ENST00000267163.4:c.371_372del	p.Ile124ArgfsTer6	p.I124Rfs*6	ENST00000267163	NM_000321.2	124	ATa/a	3/27	0.732609667950882	1	FACETS	0.688	0.584	0.796	0.688	0.584	0.796	SUBCLONAL	1	TRUE	0	0.732609667950882	1		253	88	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858238	9858238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	80	455	0	ENST00000330684.3:c.3163G>A	p.Glu1055Lys	p.E1055K	ENST00000330684	NM_001134407.1	1055	Gag/Aag	13/13	0.732609667950882	5	FACETS	1	0.962	1	0.402	0.356	0.451	CLONAL	1	TRUE	2	0.732609667950882	5		455	380	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064689	80064689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	59	313	0	ENST00000265081.6:c.2120C>T	p.Ser707Phe	p.S707F	ENST00000265081	NM_002439.4	707	tCt/tTt	15/24	0.732609667950882	2	FACETS	1	0.905	1	0.516	0.454	0.58	CLONAL	1	TRUE	0	0.732609667950882	2		313	156	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981172	55981172	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	56	320	2	ENST00000263923.4:c.527G>C	p.Arg176Thr	p.R176T	ENST00000263923	NM_002253.2	176	aGa/aCa	5/30	0.677930087596755	3	FACETS	1	0.966	1	0.449	0.393	0.507	CLONAL	1	TRUE	0	0.732609667950882	3		322	155	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518160	103518160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	90	247	2	ENST00000355739.4:c.2098C>T	p.Leu700Phe	p.L700F	ENST00000355739	NM_000123.3	700	Ctc/Ttc	9/15	0.315133442025003	5	FACETS	0.758	0.679	0.841			1	INDETERMINATE	2	TRUE	NA	0.732609667950882	5		249	340	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127659	2127659	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	99	573	2	ENST00000219476.3:c.2898C>G	p.Phe966Leu	p.F966L	ENST00000219476	NM_000548.3	966	ttC/ttG	26/42	0.732609667950882	5	FACETS	0.521	0.464	0.582	0.174	0.154	0.194	SUBCLONAL	1	TRUE	2	0.732609667950882	5		575	1089	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266128	198266128	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	37	289	0	ENST00000335508.6:c.2492G>T	p.Arg831Leu	p.R831L	ENST00000335508	NM_012433.2	831	cGa/cTa	17/25	0.318189470896774	3	FACETS	0.914	0.766	1	0.305	0.255	0.358	INDETERMINATE	1	TRUE	0	0.732609667950882	3		289	151	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911161	40911161	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	44	312	0	ENST00000373198.4:c.2144C>G	p.Thr715Ser	p.T715S	ENST00000373198	NM_133170.3	715	aCc/aGc	13/32	0.695312050124677	5	FACETS	0.727	0.611	0.853	0.242	0.203	0.285	SUBCLONAL	1	TRUE	2	0.732609667950882	5		312	347	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31401545	31401545	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	106	380	0	ENST00000344624.3:c.4119G>C	p.Lys1373Asn	p.K1373N	ENST00000344624		1373	aaG/aaC	33/33	0.732609667950882	8	FACETS	1	0.957	1	0.189	0.169	0.21	CLONAL	1	TRUE	2	0.732609667950882	8		380	818	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225672	26225672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	95	543	0	ENST00000360408.1:c.290G>A	p.Cys97Tyr	p.C97Y	ENST00000360408	NM_003532.2	97	tGc/tAc	1/1	0.632553043705477	4	FACETS	0.541	0.481	0.605	0.18	0.16	0.202	SUBCLONAL	1	TRUE	1	0.732609667950882	4		543	831	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14027785	14027785	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	62	218	0	ENST00000405192.2:c.59G>T	p.Arg20Ile	p.R20I	ENST00000405192	NM_001163147.1	20	aGa/aTa	3/12	0.458296526375784	5	FACETS	1	0.964	1	0.439	0.382	0.498	CLONAL	1	TRUE	2	0.732609667950882	5		218	270	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209568	98209568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	156	547	1	ENST00000331920.6:c.3970G>A	p.Glu1324Lys	p.E1324K	ENST00000331920	NM_000264.3	1324	Gaa/Aaa	23/24	0.372409026647192	5	FACETS	1	0.988	1	0.487	0.447	0.528	INDETERMINATE	1	TRUE	2	0.732609667950882	5		548	612	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410481	139410481	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	174	623	2	ENST00000277541.6:c.1621G>T	p.Ala541Ser	p.A541S	ENST00000277541	NM_017617.3	541	Gcc/Tcc	10/34	0.372409026647192	5	FACETS	1	0.982	1	0.404	0.372	0.437	INDETERMINATE	1	TRUE	2	0.732609667950882	5		625	823	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611243	100611243	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	51	208	2	ENST00000308731.7:c.1363G>C	p.Glu455Gln	p.E455Q	ENST00000308731	NM_000061.2	455	Gag/Cag	15/19	0.732609667950882	2	FACETS	0.642	0.552	0.738			1	SUBCLONAL	1	TRUE	NA	0.732609667950882	2		210	217	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0057133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	75	296	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.422986919417153	2		296	323	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0057133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	268	754	2	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.422986919417153	3	FACETS	0.958	0.902	1	0.958	0.902	1	CLONAL	2	TRUE	1	0.422986919417153	3		756	801	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0057133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	106	613	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	0.422986919417153	1	FACETS	0.88	0.794	0.971	0.88	0.794	0.971	CLONAL	1	TRUE	0	0.422986919417153	1		613	449	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	174	690	0	ENST00000322088.6:c.767C>A	p.Ser256Tyr	p.S256Y	ENST00000322088	NM_014225.5	256	tCc/tAc	6/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.422986919417153	2		690	666	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579536	7579536	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567556930	NA	P-0057134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	153	648	0	ENST00000269305.4:c.151G>T	p.Glu51Ter	p.E51*	ENST00000269305	NM_001126112.2	51	Gaa/Taa	4/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.233383211404402	2		648	886	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246543	46246543	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	22	151	0	ENST00000334344.6:c.4637A>G	p.Asn1546Ser	p.N1546S	ENST00000334344	NM_152641.2	1546	aAt/aGt	15/21	0.21581132473497	2	FACETS	0.734	0.57	0.923	0.367	0.285	0.462	CLONAL	1	TRUE	0	0.233383211404402	2		151	257	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143981	11143981	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	69	387	0	ENST00000358026.2:c.3562G>T	p.Asp1188Tyr	p.D1188Y	ENST00000358026	NM_001128849.1	1188	Gac/Tac	26/36	0.175953096351113	2	FACETS	0.884	0.769	1	0.442	0.384	0.504	CLONAL	1	TRUE	0	0.233383211404402	2		387	669	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24129426	24129426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	50	344	1	ENST00000263121.7:c.70G>A	p.Glu24Lys	p.E24K	ENST00000263121	NM_003073.3	24	Gag/Aag	1/9	1	2	FACETS	0.715	0.606	0.835	0.715	0.606	0.835	SUBCLONAL	1	TRUE	1	0.233383211404402	2		345	599	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207510	29207510	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	103	395	0	ENST00000240100.2:c.286C>T	p.Arg96Cys	p.R96C	ENST00000240100	NM_001394.6	96	Cgc/Tgc	1/4	0.233383211404402	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.233383211404402	1		395	598	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097790	27097790	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	52	329	0	ENST00000324856.7:c.3379C>T	p.Gln1127Ter	p.Q1127*	ENST00000324856	NM_006015.4	1127	Cag/Tag	12/20	1	2	FACETS	0.879	0.749	1	0.879	0.749	1	CLONAL	1	TRUE	1	0.233383211404402	2		329	507	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521591	46521591	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	58	398	0	ENST00000262741.5:c.817A>T	p.Ser273Cys	p.S273C	ENST00000262741	NM_003629.3	273	Agc/Tgc	7/10	1	2	FACETS	0.869	0.747	1	0.869	0.747	1	CLONAL	1	TRUE	1	0.233383211404402	2		398	572	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123864	46123864	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	130	286	0	ENST00000334344.6:c.130G>T	p.Glu44Ter	p.E44*	ENST00000334344	NM_152641.2	44	Gag/Tag	2/21	0.21581132473497	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.233383211404402	2		286	498	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240082	41240082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	13	46	0	ENST00000379561.5:c.268G>A	p.Val90Met	p.V90M	ENST00000379561	NM_002015.3	90	Gtg/Atg	1/3	0.175953096351113	2	FACETS	1	0.866	1	0.696	0.505	0.921	CLONAL	1	TRUE	0	0.233383211404402	2		46	80	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556452	29556452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	38	344	0	ENST00000356175.3:c.2819C>T	p.Thr940Ile	p.T940I	ENST00000356175	NM_000267.3	940	aCc/aTc	21/57	0.233383211404402	3	FACETS	0.652	0.538	0.779	0.326	0.269	0.39	SUBCLONAL	1	TRUE	1	0.233383211404402	3		344	558	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40384031	40384031	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	68	318	0	ENST00000293328.3:c.115G>C	p.Glu39Gln	p.E39Q	ENST00000293328	NM_012448.3	39	Gaa/Caa	2/19	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.233383211404402	2		318	455	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249146	10249146	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	75	569	0	ENST00000340748.4:c.4036G>C	p.Asp1346His	p.D1346H	ENST00000340748		1346	Gat/Cat	34/40	0.175953096351113	2	FACETS	0.697	0.609	0.792	0.349	0.304	0.396	SUBCLONAL	1	TRUE	0	0.233383211404402	2		569	922	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953247	17953247	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	89	639	0	ENST00000458235.1:c.739C>G	p.Pro247Ala	p.P247A	ENST00000458235	NM_000215.3	247	Cca/Gca	6/24	0.175953096351113	2	FACETS	0.788	0.697	0.885	0.394	0.348	0.443	SUBCLONAL	1	TRUE	0	0.233383211404402	2		639	968	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42384956	42384956	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	70	471	0	ENST00000221972.3:c.590C>A	p.Ser197Tyr	p.S197Y	ENST00000221972	NM_021601.3	197	tCc/tAc	5/5	0.175953096351113	2	FACETS	0.759	0.661	0.866	0.38	0.33	0.433	SUBCLONAL	1	TRUE	0	0.233383211404402	2		471	790	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47612347	47612347	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	35	306	0	ENST00000263735.4:c.901G>A	p.Glu301Lys	p.E301K	ENST00000263735	NM_002354.2	301	Gag/Aag	8/9	1	2	FACETS	0.735	0.603	0.884	0.735	0.603	0.884	SUBCLONAL	1	TRUE	1	0.233383211404402	2		306	408	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017140	31017140	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0057134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	25	223	2	ENST00000375687.4:c.472-1G>T		p.X158_splice	ENST00000375687	NM_015338.5	158			1	2	FACETS	0.593	0.468	0.738	0.593	0.468	0.738	SUBCLONAL	1	TRUE	1	0.233383211404402	2		225	361	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178041	56178041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	30	294	0	ENST00000399503.3:c.3014G>A	p.Arg1005Lys	p.R1005K	ENST00000399503	NM_005921.1	1005	aGa/aAa	14/20	1	2	FACETS	0.592	0.477	0.724	0.592	0.477	0.724	SUBCLONAL	1	TRUE	1	0.233383211404402	2		294	434	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729670	41729670	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	82	520	0	ENST00000242208.4:c.859C>A	p.Gln287Lys	p.Q287K	ENST00000242208	NM_002192.2	287	Cag/Aag	3/3	0.139768557754473	3	FACETS	0.97	0.854	1	0.485	0.427	0.547	INDETERMINATE	1	TRUE	1	0.233383211404402	3		520	809	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467924	50467924	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	92	424	0	ENST00000331340.3:c.1159G>T	p.Glu387Ter	p.E387*	ENST00000331340	NM_006060.4	387	Gag/Tag	8/8	0.139768557754473	3	FACETS	1	0.971	1	0.641	0.569	0.717	INDETERMINATE	1	TRUE	1	0.233383211404402	3		424	687	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540400	23540400	+	start_lost	Translation_Start_Site	SNP	C	C	A	novel	NA	P-0057134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	50	246	0	ENST00000380871.4:c.3G>T	p.Met1?	p.M1?	ENST00000380871	NM_006167.3	1	atG/atT	1/2	0.233383211404402	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	0	0.233383211404402	1		246	345	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982062	70982062	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	63	478	0	ENST00000276594.2:c.34C>T	p.Gln12Ter	p.Q12*	ENST00000276594	NM_024504.3	12	Cag/Tag	2/8	0.139768557754473	3	FACETS	0.669	0.577	0.77	0.335	0.288	0.385	INDETERMINATE	1	TRUE	1	0.233383211404402	3		478	901	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169501	27169501	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	34	405	0	ENST00000380036.4:c.502C>A	p.His168Asn	p.H168N	ENST00000380036	NM_000459.3	168	Cat/Aat	4/23	0.233383211404402	1	FACETS	0.55	0.449	0.664	0.55	0.449	0.664	SUBCLONAL	1	TRUE	0	0.233383211404402	1		405	468	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570428	87570428	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	121	503	0	ENST00000277120.3:c.2168A>T	p.Tyr723Phe	p.Y723F	ENST00000277120		723	tAc/tTc	17/19	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.233383211404402	2		503	767	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139562812	139562813	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CG	CG	AT	novel	NA	P-0057134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	53	558	0	ENST00000308874.7:c.78_79delinsAT	p.Gly27Cys	p.G27C	ENST00000308874		26	ccCGgc/ccATgc	3/10	1	2	FACETS	0.612	0.521	0.713	0.612	0.521	0.713	SUBCLONAL	1	TRUE	1	0.233383211404402	2		558	742	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003755	45003755	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	TCGTGG	novel	NA	P-0057134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	48	367	0	ENST00000558401.1:c.11delinsTCGTGG	p.Ser4PhefsTer6	p.S4Ffs*6	ENST00000558401	NM_004048.2	4	tCc/tTCGTGGc	1/4	0.233383211404402	1	FACETS	0.532	0.449	0.624	0.532	0.449	0.624	SUBCLONAL	1	TRUE	0	0.233383211404402	1		367	683	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0057135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	187	221	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.747566357606839	2		222	484	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0057135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	93	325	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.925	0.835	1	0.925	0.835	1	CLONAL	1	TRUE	1	0.747566357606839	2		325	269	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0057135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	527	628	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.714142498609293	2	FACETS	0.964	0.937	0.991	0.964	0.937	0.991	CLONAL	2	TRUE	0	0.747566357606839	2		628	731	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858517	9858517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765370528	NA	P-0057135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	208	379	0	ENST00000330684.3:c.2884G>A	p.Glu962Lys	p.E962K	ENST00000330684	NM_001134407.1	962	Gaa/Aaa	13/13	0.736942043629813	2	FACETS	0.956	0.894	1	0.478	0.447	0.51	CLONAL	1	TRUE	0	0.747566357606839	2		379	582	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631322	117631322	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757128233	NA	P-0057135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	167	302	0	ENST00000368508.3:c.6356G>A	p.Gly2119Glu	p.G2119E	ENST00000368508	NM_002944.2	2119	gGg/gAg	40/43	0.747566357606839	1	FACETS	0.885	0.829	0.941	0.885	0.829	0.941	CLONAL	1	TRUE	0	0.747566357606839	1		302	316	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862896	9862896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1198247451	NA	P-0057135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	260	483	1	ENST00000330684.3:c.2407G>A	p.Glu803Lys	p.E803K	ENST00000330684	NM_001134407.1	803	Gag/Aag	12/13	0.736942043629813	2	FACETS	0.893	0.84	0.947	0.446	0.42	0.474	CLONAL	1	TRUE	0	0.747566357606839	2		484	779	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588626	28588626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548609046	NA	P-0057135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	155	270	1	ENST00000241453.7:c.2822C>T	p.Ser941Leu	p.S941L	ENST00000241453	NM_004119.2	941	tCg/tTg	23/24	1	2	FACETS	0.884	0.816	0.954	0.884	0.816	0.954	CLONAL	1	TRUE	1	0.747566357606839	2		271	469	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561352	9561352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773981325	NA	P-0057135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	440	379	0	ENST00000353224.5:c.430G>A	p.Glu144Lys	p.E144K	ENST00000353224	NM_177990.2	144	Gaa/Aaa	4/10	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.747566357606839	2		379	823	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484270	8484270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867884876	NA	P-0057135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	241	359	2	ENST00000356435.5:c.3262C>T	p.Arg1088Cys	p.R1088C	ENST00000356435		1088	Cgt/Tgt	19/35	0.747566357606839	1	FACETS	0.952	0.904	1	0.952	0.904	1	CLONAL	1	TRUE	0	0.747566357606839	1		361	424	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912133	50912133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768773535	NA	P-0057135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	397	549	1	ENST00000440232.2:c.1867C>T	p.Arg623Trp	p.R623W	ENST00000440232	NM_002691.3	623	Cgg/Tgg	15/27	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.747566357606839	2		550	1038	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484163	8484163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781290016	NA	P-0057135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	201	359	0	ENST00000356435.5:c.3369G>A	p.Met1123Ile	p.M1123I	ENST00000356435		1123	atG/atA	19/35	0.747566357606839	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.747566357606839	1		359	333	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498451	89498451	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	155	296	0	ENST00000336596.2:c.2423G>A	p.Trp808Ter	p.W808*	ENST00000336596	NM_005233.5	808	tGg/tAg	14/17	1	2	FACETS	0.947	0.875	1	0.947	0.875	1	CLONAL	1	TRUE	1	0.747566357606839	2		296	438	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902559	1902559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1366552622	NA	P-0057135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	352	494	0	ENST00000382891.5:c.178G>A	p.Gly60Arg	p.G60R	ENST00000382891	NM_133335.3	60	Ggg/Agg	2/22	1	2	FACETS	0.967	0.918	1	0.967	0.918	1	CLONAL	1	TRUE	1	0.747566357606839	2		494	974	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123880945	123880945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	169	235	0	ENST00000330479.4:c.563G>A	p.Arg188Gln	p.R188Q	ENST00000330479	NM_020382.3	188	cGa/cAa	5/9	1	2	FACETS	0.91	0.843	0.978	0.91	0.843	0.978	CLONAL	1	TRUE	1	0.747566357606839	2		235	497	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615096	43615096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	290	533	0	ENST00000355710.3:c.2510C>T	p.Ser837Phe	p.S837F	ENST00000355710	NM_020975.4	837	tCc/tTc	14/20	1	2	FACETS	0.964	0.91	1	0.964	0.91	1	CLONAL	1	TRUE	1	0.747566357606839	2		533	805	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77069944	77069944	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	243	400	0	ENST00000356341.3:c.596C>T	p.Ser199Phe	p.S199F	ENST00000356341	NM_002576.4	199	tCt/tTt	6/15	1	2	FACETS	0.904	0.849	0.961	0.904	0.849	0.961	CLONAL	1	TRUE	1	0.747566357606839	2		400	719	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589316	28589316	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	119	259	0	ENST00000241453.7:c.2731C>T	p.Pro911Ser	p.P911S	ENST00000241453	NM_004119.2	911	Cca/Tca	22/24	1	2	FACETS	0.974	0.89	1	0.974	0.89	1	CLONAL	1	TRUE	1	0.747566357606839	2		259	327	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436485	110436485	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	343	529	1	ENST00000375856.3:c.1916C>T	p.Ser639Phe	p.S639F	ENST00000375856	NM_003749.2	639	tCc/tTc	1/2	1	2	FACETS	0.982	0.933	1	0.982	0.933	1	CLONAL	1	TRUE	1	0.747566357606839	2		530	934	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643751	38643752	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTA	novel	NA	P-0057135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	314	555	0	ENST00000299084.4:c.1223_1225dup	p.Val408dup	p.V408dup	ENST00000299084	NM_152594.2	408	-/GTA	7/7	1	2	FACETS	0.883	0.835	0.932	0.883	0.835	0.932	CLONAL	1	TRUE	1	0.747566357606839	2		555	951	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441994	40441994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	242	545	0	ENST00000345506.4:c.239G>A	p.Gly80Glu	p.G80E	ENST00000345506	NM_003152.3	80	gGg/gAg	4/20	1	2	FACETS	0.78	0.73	0.831	0.78	0.73	0.831	SUBCLONAL	1	TRUE	1	0.747566357606839	2		545	830	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610606	10610606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	291	494	1	ENST00000171111.5:c.104C>T	p.Ser35Phe	p.S35F	ENST00000171111	NM_203500.1	35	tCc/tTc	2/6	1	2	FACETS	0.893	0.842	0.944	0.893	0.842	0.944	CLONAL	1	TRUE	1	0.747566357606839	2		495	872	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749520	41749520	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0057135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	217	289	0	ENST00000301178.4:c.1446-1G>A		p.X482_splice	ENST00000301178	NM_021913.4	482			1	2	FACETS	0.932	0.872	0.993	0.932	0.872	0.993	CLONAL	1	TRUE	1	0.747566357606839	2		289	623	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383306	31383306	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	272	400	0	ENST00000328111.2:c.1218C>G	p.Asn406Lys	p.N406K	ENST00000328111	NM_006892.3	406	aaC/aaG	11/23	1	2	FACETS	0.88	0.828	0.932	0.88	0.828	0.932	CLONAL	1	TRUE	1	0.747566357606839	2		400	827	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294134	1294135	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0057135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	291	578	1	ENST00000310581.5:c.866_867delinsAT	p.Leu289His	p.L289H	ENST00000310581	NM_198253.2	289	cTC/cAT	2/16	1	2	FACETS	0.845	0.797	0.895	0.845	0.797	0.895	CLONAL	1	TRUE	1	0.747566357606839	2		579	921	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945821	38945821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	39	133	0	ENST00000357387.3:c.4405C>T	p.Pro1469Ser	p.P1469S	ENST00000357387	NM_152756.3	1469	Cca/Tca	34/38	1	2	FACETS	0.841	0.714	0.977	0.841	0.714	0.977	CLONAL	1	TRUE	1	0.747566357606839	2		133	124	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952943	2952943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	295	456	0	ENST00000396946.4:c.2997G>A	p.Met999Ile	p.M999I	ENST00000396946	NM_032415.4	999	atG/atA	22/25	1	2	FACETS	0.934	0.882	0.987	0.934	0.882	0.987	CLONAL	1	TRUE	1	0.747566357606839	2		456	845	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372370	55372370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	289	510	0	ENST00000297316.4:c.1060C>T	p.Leu354Phe	p.L354F	ENST00000297316	NM_022454.3	354	Ctc/Ttc	2/2	1	2	FACETS	0.903	0.852	0.955	0.903	0.852	0.955	CLONAL	1	TRUE	1	0.747566357606839	2		510	856	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486278	8486278	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143787300	NA	P-0057135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	201	250	0	ENST00000356435.5:c.2539G>A	p.Val847Met	p.V847M	ENST00000356435		847	Gtg/Atg	17/35	0.747566357606839	1	FACETS	0.988	0.934	1	0.988	0.934	1	CLONAL	1	TRUE	0	0.747566357606839	1		250	341	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971166	21971184	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCAGCAGCTCCGCCACT	CAGCAGCAGCTCCGCCACT	-	novel	NA	P-0057135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	172	303	0	ENST00000304494.5:c.174_192del	p.Val59SerfsTer81	p.V59Sfs*81	ENST00000304494	NM_000077.4	58	cgAGTGGCGGAGCTGCTGCTG/cg	2/3	0.747566357606839	1	FACETS	0.858	0.803	0.912	0.858	0.803	0.912	CLONAL	1	TRUE	0	0.747566357606839	1		303	336	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411128	63411128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	259	469	2	ENST00000330258.3:c.2039G>A	p.Gly680Glu	p.G680E	ENST00000330258	NM_152424.3	680	gGa/gAa	2/2	1	2	FACETS	0.908	0.854	0.963	0.908	0.854	0.963	CLONAL	1	TRUE	1	0.747566357606839	2		471	763	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411162	63411162	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	314	443	0	ENST00000330258.3:c.2005G>T	p.Gly669Trp	p.G669W	ENST00000330258	NM_152424.3	669	Ggg/Tgg	2/2	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.747566357606839	2		443	729	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938781	76938781	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	171	421	1	ENST00000373344.5:c.1967C>T	p.Ser656Phe	p.S656F	ENST00000373344	NM_000489.3	656	tCc/tTc	9/35	1	2	FACETS	0.855	0.792	0.92	0.855	0.792	0.92	CLONAL	1	TRUE	1	0.747566357606839	2		422	535	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954327	48954328	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0057136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	137	219	0	ENST00000267163.4:c.1450_1451del	p.Met484ValfsTer8	p.M484Vfs*8	ENST00000267163	NM_000321.2	483	cAT/c	16/27	0.970762842792104	1	FACETS	0.962	0.929	0.989	0.962	0.929	0.989	CLONAL	1	TRUE	0	0.970762842792104	1		219	151	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925334	114925334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	371	430	0	ENST00000543371.1:c.1412G>A	p.Arg471His	p.R471H	ENST00000543371	NM_001198531.1	471	cGc/cAc	14/14	1	2	FACETS	0.979	0.935	1	0.979	0.935	1	CLONAL	1	TRUE	1	0.970762842792104	2		430	781	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556727	41556727	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0057136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	219	301	1	ENST00000263253.7:c.3671+1G>A		p.X1224_splice	ENST00000263253	NM_001429.3	1224			NA	2	FACETS	0.987	0.93	1			1	INDETERMINATE	1	TRUE	NA	0.970762842792104	2		302	457	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993406	72993406	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	637	570	0	ENST00000268489.5:c.639G>C	p.Gln213His	p.Q213H	ENST00000268489	NM_006885.3	213	caG/caC	2/10	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.970762842792104	2		570	1225	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577113	7577114	+	missense_variant	Missense_Mutation	DNP	AC	AC	GA	novel	NA	P-0057136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	456	526	0	ENST00000269305.4:c.824_825delinsTC	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGT/tTC	8/11	0.970762842792104	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.970762842792104	1		526	471	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007663	62007663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	418	478	0	ENST00000392795.3:c.204G>A	p.Met68Ile	p.M68I	ENST00000392795	NM_001039933.1	68	atG/atA	3/6	1	2	FACETS	0.99	0.948	1	0.99	0.948	1	CLONAL	1	TRUE	1	0.970762842792104	2		478	870	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15273293	15273293	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	518	554	0	ENST00000263388.2:c.5896G>T	p.Asp1966Tyr	p.D1966Y	ENST00000263388	NM_000435.2	1966	Gac/Tac	32/33	1	2	FACETS	0.991	0.954	1	0.991	0.954	1	CLONAL	1	TRUE	1	0.970762842792104	2		554	1077	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313394	30313394	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	352	506	0	ENST00000262643.3:c.994G>T	p.Val332Phe	p.V332F	ENST00000262643	NM_001238.2	332	Gtt/Ttt	11/12	1	2	FACETS	0.993	0.948	1	0.993	0.948	1	CLONAL	1	TRUE	1	0.970762842792104	2		506	730	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55143620	55143620	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3	219	280	0	ENST00000257290.5:c.1852T>A	p.Ser618Thr	p.S618T	ENST00000257290	NM_006206.4	618	Tcc/Acc	13/23	0.970762842792104	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.970762842792104	1		280	222	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524984	8524984	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	241	303	0	ENST00000356435.5:c.620G>T	p.Cys207Phe	p.C207F	ENST00000356435		207	tGt/tTt	7/35	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.970762842792104	2		303	478	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0057137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	563	722	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.82316097047347	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.838883686031189	2		722	659	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720650	89720650	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1257124719	NA	P-0057137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	9	461	0	ENST00000371953.3:c.802-1G>A		p.X268_splice	ENST00000371953	NM_000314.4	268			0.758966589580842	1	FACETS	0.106	0.07	0.15	0.106	0.07	0.15	SUBCLONAL	1	TRUE	0	0.838883686031189	1		461	118	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690847	89690847	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587776667	NA	P-0057137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	41	223	0	ENST00000371953.3:c.253+1G>T		p.X85_splice	ENST00000371953	NM_000314.4	85			0.758966589580842	1	FACETS	0.397	0.337	0.461	0.397	0.337	0.461	SUBCLONAL	1	TRUE	0	0.838883686031189	1		223	143	SUCCESS
APC	324	MSKCC	GRCh37	5	112175925	112175925	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs863225356	NA	P-0057137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	103	150	0	ENST00000257430.4:c.4634C>A	p.Ser1545Ter	p.S1545*	ENST00000257430	NM_000038.5	1545	tCa/tAa	16/16	0.838883686031189	1	FACETS	0.983	0.92	1	0.983	0.92	1	CLONAL	1	TRUE	0	0.838883686031189	1		150	145	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589282	67589285	+	frameshift_variant	Frame_Shift_Del	DEL	TTAC	TTAC	-	novel	NA	P-0057137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	10	199	0	ENST00000274335.5:c.1272_1275del	p.Leu424PhefsTer21	p.L424Ffs*21	ENST00000274335		424	TTACtt/tt	9/15	0.838883686031189	1	FACETS	0.09	0.061	0.127	0.09	0.061	0.127	SUBCLONAL	1	TRUE	0	0.838883686031189	1		199	153	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215339	5215339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs114545401	NA	P-0057139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	32	474	0	ENST00000357368.4:c.4279G>A	p.Ala1427Thr	p.A1427T	ENST00000357368	NM_002850.3	1427	Gcc/Acc	28/38	0.202065463756755	2	FACETS	0.392	0.317	0.477	0.196	0.158	0.239	SUBCLONAL	1	TRUE	0	0.275226959719396	2		474	593	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0057139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	66	754	2	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.275226959719396	3	FACETS	0.763	0.662	0.873	0.382	0.331	0.437	SUBCLONAL	1	TRUE	1	0.275226959719396	3		756	715	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0057139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	58	333	1	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.20703415130519	2	FACETS	1	0.938	1	0.579	0.5	0.665	CLONAL	1	TRUE	0	0.275226959719396	2		334	364	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967186	134967186	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200311306	NA	P-0057139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	48	367	0	ENST00000398015.3:c.2525G>A	p.Arg842Gln	p.R842Q	ENST00000398015	NM_004441.4	842	cGg/cAg	14/16	0.176915440498914	3	FACETS	0.94	0.796	1	0.313	0.265	0.366	CLONAL	1	TRUE	0	0.275226959719396	3		367	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0057139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	213	913	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.202065463756755	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.275226959719396	2		913	669	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90645601	90645601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1328301039	NA	P-0057139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	38	151	0	ENST00000330062.3:c.22G>A	p.Val8Met	p.V8M	ENST00000330062	NM_002168.2	8	Gtg/Atg	1/11	0.208864751481964	3	FACETS	0.805	0.673	0.95	0.805	0.673	0.95	CLONAL	2	TRUE	1	0.275226959719396	3		151	195	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476832	140476832	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs869025340	NA	P-0057139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	140	384	0	ENST00000288602.6:c.1574T>G	p.Leu525Arg	p.L525R	ENST00000288602	NM_004333.4	525	cTg/cGg	13/18	0.19276546664	5	FACETS	1	0.925	1	0.677	0.617	0.739	CLONAL	2	TRUE	2	0.275226959719396	5		384	708	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0057140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	103	440	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.3	6	FACETS	1	0.953	1	1	0.953	1	CLONAL	4	TRUE	2	0.23	6		440	302	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491662	120491663	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs312262800	NA	P-0057140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	13	171	0	ENST00000256646.2:c.2566_2567del	p.Ser856LeufsTer17	p.S856Lfs*17	ENST00000256646	NM_024408.3	856	AGt/t	16/34	1	2	FACETS	0.813	0.583	1	0.813	0.583	1	CLONAL	1	TRUE	1	0.23	2		171	139	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0057140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	36	871	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.3	1	FACETS	0.825	0.687	0.974	1	0.959	1	CLONAL	2	TRUE	0	0.23	1		871	168	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211534	98211534	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	19	469	0	ENST00000331920.6:c.3621C>A	p.Phe1207Leu	p.F1207L	ENST00000331920	NM_000264.3	1207	ttC/ttA	22/24	0.3	1	FACETS	0.706	0.538	0.903	0.706	0.538	0.903	CLONAL	1	TRUE	0	0.23	1		469	207	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0057141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	296	754	2	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.937	0.889	0.986	0.937	0.889	0.986	CLONAL	1	TRUE	1	0.934472565236479	2		756	676	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	265	900	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.937	0.878	0.997	0.937	0.878	0.997	CLONAL	1	TRUE	1	0.537812418832633	2		904	1052	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	205	460	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	0.537187575570262	2	FACETS	0.948	0.881	1	0.474	0.44	0.509	CLONAL	1	TRUE	0	0.537812418832633	2		460	804	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	111	277	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.907	0.821	0.998	0.907	0.821	0.998	CLONAL	1	TRUE	1	0.537812418832633	2		277	455	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	128	268	1	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	1	2	FACETS	0.815	0.741	0.892	0.815	0.741	0.892	CLONAL	1	TRUE	1	0.537812418832633	2		269	584	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578215	28578216	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	194	409	0	ENST00000241453.7:c.2955_2956del	p.Pro986AlafsTer27	p.P986Afs*27	ENST00000241453	NM_004119.2	985	tcTCcg/tccg	24/24	1	2	FACETS	0.904	0.838	0.972	0.904	0.838	0.972	CLONAL	1	TRUE	1	0.537812418832633	2		409	798	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310914	123310914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	231	421	2	ENST00000358487.5:c.514G>A	p.Ala172Thr	p.A172T	ENST00000358487	NM_000141.4	172	Gcc/Acc	5/18	0.537187575570262	2	FACETS	1	0.98	1	0.558	0.522	0.595	CLONAL	1	TRUE	0	0.537812418832633	2		423	770	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	250	621	11	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.886	0.829	0.945	0.886	0.829	0.945	CLONAL	1	TRUE	1	0.537812418832633	2		632	1049	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97897777	97897779	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs3831244	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	108	259	0	ENST00000289081.3:c.692_694del	p.Lys231del	p.K231del	ENST00000289081	NM_000136.2	231	aAGAtt/att	8/15	1	2	FACETS	0.806	0.727	0.89	0.806	0.727	0.89	CLONAL	1	TRUE	1	0.537812418832633	2		259	498	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549883	187549883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs186220887	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	125	551	0	ENST00000441802.2:c.4358G>A	p.Arg1453His	p.R1453H	ENST00000441802	NM_005245.3	1453	cGt/cAt	8/27	1	2	FACETS	0.891	0.81	0.974	0.891	0.81	0.974	CLONAL	1	TRUE	1	0.537812418832633	2		551	522	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	233	467	4	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.993	0.927	1	0.993	0.927	1	CLONAL	1	TRUE	1	0.537812418832633	2		471	873	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933240	49933240	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143096514	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	306	687	1	ENST00000296474.3:c.2870C>T	p.Thr957Met	p.T957M	ENST00000296474	NM_002447.2	957	aCg/aTg	12/20	1	2	FACETS	0.984	0.928	1	0.984	0.928	1	CLONAL	1	TRUE	1	0.537812418832633	2		688	1156	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330610	65330611	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	168	351	1	ENST00000342505.4:c.1035dup	p.Leu346ThrfsTer4	p.L346Tfs*4	ENST00000342505	NM_002227.2	345	-/A	8/25	1	2	FACETS	0.902	0.831	0.975	0.902	0.831	0.975	CLONAL	1	TRUE	1	0.537812418832633	2		352	693	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872175	37872175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs182572604	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	233	548	0	ENST00000269571.5:c.1496G>A	p.Arg499Gln	p.R499Q	ENST00000269571		499	cGg/cAg	12/27	1	2	FACETS	0.987	0.922	1	0.987	0.922	1	CLONAL	1	TRUE	1	0.537812418832633	2		548	878	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538269	187538269	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs748652484	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	193	415	0	ENST00000441802.2:c.8965del	p.Arg2989GlyfsTer20	p.R2989Gfs*20	ENST00000441802	NM_005245.3	2989	Agg/gg	11/27	1	2	FACETS	0.896	0.831	0.964	0.896	0.831	0.964	CLONAL	1	TRUE	1	0.537812418832633	2		415	801	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058052	27058052	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	207	398	0	ENST00000324856.7:c.1762del	p.Gln588SerfsTer31	p.Q588Sfs*31	ENST00000324856	NM_006015.4	587	tCc/tc	3/20	1	2	FACETS	0.955	0.888	1	0.955	0.888	1	CLONAL	1	TRUE	1	0.537812418832633	2		398	806	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354152	15354152	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs868796773	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	68	629	3	ENST00000263377.2:c.2728del	p.Gln910LysfsTer39	p.Q910Kfs*39	ENST00000263377	NM_058243.2	910	Caa/aa	14/20	1	2	FACETS	0.232	0.201	0.266	0.232	0.201	0.266	SUBCLONAL	1	TRUE	1	0.537812418832633	2		632	1089	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245949	5245949	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	315	714	1	ENST00000357368.4:c.826G>A	p.Val276Met	p.V276M	ENST00000357368	NM_002850.3	276	Gtg/Atg	10/38	1	2	FACETS	0.977	0.922	1	0.977	0.922	1	CLONAL	1	TRUE	1	0.537812418832633	2		715	1199	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56401588	56401588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367866327	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	116	261	0	ENST00000348428.3:c.1450G>A	p.Ala484Thr	p.A484T	ENST00000348428	NM_006785.3	484	Gcc/Acc	12/17	1	2	FACETS	0.828	0.75	0.91	0.828	0.75	0.91	CLONAL	1	TRUE	1	0.537812418832633	2		261	521	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445203	49445203	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	364	818	2	ENST00000301067.7:c.2263del	p.Arg755GlyfsTer175	p.R755Gfs*175	ENST00000301067	NM_003482.3	755	Cgg/gg	10/54	1	2	FACETS	0.951	0.9	1	0.951	0.9	1	CLONAL	1	TRUE	1	0.537812418832633	2		820	1424	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210893	36210893	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	303	743	7	ENST00000222270.7:c.649del	p.Arg217GlyfsTer22	p.R217Gfs*22	ENST00000222270	NM_014727.1	215	aCc/ac	3/37	1	2	FACETS	0.878	0.827	0.931	0.878	0.827	0.931	CLONAL	1	TRUE	1	0.537812418832633	2		750	1283	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935417	36935417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1423477405	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	280	662	0	ENST00000361632.4:c.1310C>T	p.Ala437Val	p.A437V	ENST00000361632		437	gCc/gTc	10/16	1	2	FACETS	0.954	0.896	1	0.954	0.896	1	CLONAL	1	TRUE	1	0.537812418832633	2		662	1092	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720703	89720703	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	117	111	0	ENST00000371953.3:c.856del	p.Thr286ProfsTer5	p.T286Pfs*5	ENST00000371953	NM_000314.4	285	gAa/ga	8/9	0.537187575570262	2	FACETS	0.958	0.885	1	0.958	0.885	1	CLONAL	2	TRUE	0	0.537812418832633	2		111	227	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467445	25467445	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	224	530	2	ENST00000264709.3:c.1631G>A	p.Arg544His	p.R544H	ENST00000264709	NM_175629.2	544	cGt/cAt	14/23	1	2	FACETS	0.813	0.757	0.871	0.813	0.757	0.871	CLONAL	1	TRUE	1	0.537812418832633	2		532	1025	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978947	25978947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	138	289	1	ENST00000435504.4:c.976G>A	p.Ala326Thr	p.A326T	ENST00000435504		326	Gcc/Acc	10/13	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.537812418832633	2		290	504	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430546	181430546	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	251	559	0	ENST00000325404.1:c.402del	p.Gly135AlafsTer19	p.G135Afs*19	ENST00000325404	NM_003106.3	133	gCc/gc	1/1	1	2	FACETS	0.887	0.83	0.946	0.887	0.83	0.946	CLONAL	1	TRUE	1	0.537812418832633	2		559	1052	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777092	9777092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146796121	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	75	709	7	ENST00000377346.4:c.856C>T	p.Arg286Trp	p.R286W	ENST00000377346	NM_005026.3	286	Cgg/Tgg	7/24	1	2	FACETS	0.24	0.209	0.274	0.24	0.209	0.274	SUBCLONAL	1	TRUE	1	0.537812418832633	2		716	1161	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797845	45797845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782727	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	268	542	1	ENST00000450313.1:c.926G>A	p.Arg309His	p.R309H	ENST00000450313	NM_012222.2	309	cGc/cAc	10/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.537812418832633	2		543	943	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs749415085	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	122	242	0	ENST00000263967.3:c.112C>A	p.Arg38Ser	p.R38S	ENST00000263967	NM_006218.2	38	Cgt/Agt	2/21	1	2	FACETS	0.928	0.843	1	0.928	0.843	1	CLONAL	1	TRUE	1	0.537812418832633	2		242	489	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713220	30713222	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	134	298	0	ENST00000295754.5:c.553_555del	p.Ile185del	p.I185del	ENST00000295754	NM_003242.5	182	gTCAtc/gtc	4/7	1	2	FACETS	0.919	0.839	1	0.919	0.839	1	CLONAL	1	TRUE	1	0.537812418832633	2		298	542	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056200	27056201	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	214	511	0	ENST00000324856.7:c.1199dup	p.Tyr401IlefsTer222	p.Y401Ifs*222	ENST00000324856	NM_006015.4	399	aac/aaCc	2/20	1	2	FACETS	0.968	0.902	1	0.968	0.902	1	CLONAL	1	TRUE	1	0.537812418832633	2		511	822	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814532	43814532	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	167	367	1	ENST00000372470.3:c.1327G>A	p.Gly443Arg	p.G443R	ENST00000372470	NM_005373.2	443	Ggg/Agg	9/12	1	2	FACETS	0.973	0.898	1	0.973	0.898	1	CLONAL	1	TRUE	1	0.537812418832633	2		368	638	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78426102	78426102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	160	385	0	ENST00000370768.2:c.1423C>T	p.Pro475Ser	p.P475S	ENST00000370768	NM_003902.3	475	Cca/Tca	15/20	1	2	FACETS	0.887	0.816	0.961	0.887	0.816	0.961	CLONAL	1	TRUE	1	0.537812418832633	2		385	671	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459214	120459214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145077404	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	216	444	0	ENST00000256646.2:c.6131G>A	p.Arg2044His	p.R2044H	ENST00000256646	NM_024408.3	2044	cGt/cAt	34/34	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.537812418832633	2		444	792	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466003	69466029	+	inframe_deletion	In_Frame_Del	DEL	GTGGACCTGGCTTGCACACCCACCGAC	GTGGACCTGGCTTGCACACCCACCGAC	-	novel	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	203	716	0	ENST00000227507.2:c.844_870del	p.Asp282_Val290del	p.D282_V290del	ENST00000227507	NM_053056.2	281	GTGGACCTGGCTTGCACACCCACCGAC/-	5/5	1	2	FACETS	0.67	0.62	0.721	0.67	0.62	0.721	SUBCLONAL	1	TRUE	1	0.537812418832633	2		716	1127	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111959635	111959635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	36	315	0	ENST00000375549.3:c.214G>A	p.Val72Ile	p.V72I	ENST00000375549	NM_003002.3	72	Gtc/Atc	3/4	1	2	FACETS	0.205	0.168	0.247	0.205	0.168	0.247	SUBCLONAL	1	TRUE	1	0.537812418832633	2		315	652	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748881	43748881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	273	659	0	ENST00000382044.4:c.1925C>T	p.Ala642Val	p.A642V	ENST00000382044	NM_001141980.1	642	gCa/gTa	12/28	1	2	FACETS	0.915	0.858	0.972	0.915	0.858	0.972	CLONAL	1	TRUE	1	0.537812418832633	2		659	1110	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56867151	56867151	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	223	538	0	ENST00000308159.5:c.1370A>G	p.Gln457Arg	p.Q457R	ENST00000308159	NM_014669.4	457	cAg/cGg	13/22	1	2	FACETS	0.955	0.891	1	0.955	0.891	1	CLONAL	1	TRUE	1	0.537812418832633	2		538	868	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645276	67645276	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	209	506	0	ENST00000264010.4:c.544del	p.Glu182AsnfsTer40	p.E182Nfs*40	ENST00000264010	NM_006565.3	181	Ggg/gg	3/12	1	2	FACETS	0.837	0.777	0.898	0.837	0.777	0.898	CLONAL	1	TRUE	1	0.537812418832633	2		506	929	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366914	15366914	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	256	577	0	ENST00000263377.2:c.1712A>C	p.Lys571Thr	p.K571T	ENST00000263377	NM_058243.2	571	aAa/aCa	9/20	1	2	FACETS	0.935	0.876	0.996	0.935	0.876	0.996	CLONAL	1	TRUE	1	0.537812418832633	2		577	1018	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313408	30313408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	74	452	0	ENST00000262643.3:c.1008G>A	p.Met336Ile	p.M336I	ENST00000262643	NM_001238.2	336	atG/atA	11/12	1	2	FACETS	0.336	0.294	0.383	0.336	0.294	0.383	SUBCLONAL	1	TRUE	1	0.537812418832633	2		452	818	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660796	227660796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	224	494	0	ENST00000305123.5:c.2659C>T	p.Pro887Ser	p.P887S	ENST00000305123	NM_005544.2	887	Cct/Tct	1/2	1	2	FACETS	0.951	0.887	1	0.951	0.887	1	CLONAL	1	TRUE	1	0.537812418832633	2		494	876	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321510	62321510	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	299	726	0	ENST00000360203.5:c.2212T>G	p.Phe738Val	p.F738V	ENST00000360203	NM_001283009.1	738	Ttt/Gtt	25/35	1	2	FACETS	0.911	0.857	0.966	0.911	0.857	0.966	CLONAL	1	TRUE	1	0.537812418832633	2		726	1221	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723602	49723602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774919205	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	29	117	0	ENST00000449682.2:c.1040G>A	p.Arg347Gln	p.R347Q	ENST00000449682	NM_020998.3	347	cGg/cAg	9/18	1	2	FACETS	0.486	0.392	0.591	0.486	0.392	0.591	SUBCLONAL	1	TRUE	1	0.537812418832633	2		117	222	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272565	142272565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	179	365	0	ENST00000350721.4:c.2550G>A	p.Met850Ile	p.M850I	ENST00000350721	NM_001184.3	850	atG/atA	12/47	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.537812418832633	2		365	658	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169953036	169953036	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	83	333	0	ENST00000295797.4:c.123del	p.Phe41LeufsTer28	p.F41Lfs*28	ENST00000295797	NM_002740.5	40	caT/ca	2/18	1	2	FACETS	0.461	0.406	0.519	0.461	0.406	0.519	SUBCLONAL	1	TRUE	1	0.537812418832633	2		333	670	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509592	106509592	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	162	427	0	ENST00000359195.3:c.1586T>C	p.Leu529Pro	p.L529P	ENST00000359195	NM_002649.2	529	cTg/cCg	2/11	1	2	FACETS	0.766	0.704	0.831	0.766	0.704	0.831	SUBCLONAL	1	TRUE	1	0.537812418832633	2		427	786	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517860	8517860	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	51	211	0	ENST00000356435.5:c.1531A>G	p.Thr511Ala	p.T511A	ENST00000356435		511	Act/Gct	10/35	1	2	FACETS	0.453	0.385	0.526	0.453	0.385	0.526	SUBCLONAL	1	TRUE	1	0.537812418832633	2		211	419	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218646	98218646	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	177	325	0	ENST00000331920.6:c.3218T>G	p.Leu1073Arg	p.L1073R	ENST00000331920	NM_000264.3	1073	cTc/cGc	19/24	1	2	FACETS	0.948	0.877	1	0.948	0.877	1	CLONAL	1	TRUE	1	0.537812418832633	2		325	694	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426756	47426756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	313	603	1	ENST00000377045.4:c.1001C>T	p.Ala334Val	p.A334V	ENST00000377045	NM_001654.4	334	gCc/gTc	10/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.537812418832633	2		604	1052	SUCCESS
AR	367	MSKCC	GRCh37	X	66905851	66905851	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0057142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	97	218	0	ENST00000374690.3:c.1769-1G>T		p.X590_splice	ENST00000374690	NM_000044.3	590			1	2	FACETS	0.954	0.858	1	0.954	0.858	1	CLONAL	1	TRUE	1	0.537812418832633	2		218	378	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0057143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	124	221	1				ENST00000310581	NM_198253.2	-/1132			0.319507551746739	3	FACETS	0.956	0.872	1	0.956	0.872	1	CLONAL	2	TRUE	1	0.348504869356792	3		222	437	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0057143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	273	628	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.348504869356792	2		628	649	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	62	243	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.348504869356792	2		243	285	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098975	178098975	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1328994103	NA	P-0057143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	38	188	0	ENST00000397062.3:c.70T>C	p.Trp24Arg	p.W24R	ENST00000397062	NM_006164.4	24	Tgg/Cgg	2/5	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.348504869356792	2		188	192	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771827	135771827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs118203750	NA	P-0057143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	89	523	0	ENST00000298552.3:c.3290G>A	p.Arg1097His	p.R1097H	ENST00000298552	NM_001162426.1	1097	cGt/cAt	23/23	1	2	FACETS	0.967	0.86	1	0.967	0.86	1	CLONAL	1	TRUE	1	0.348504869356792	2		523	528	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141507	11141507	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	108	579	0	ENST00000358026.2:c.3484G>T	p.Gly1162Cys	p.G1162C	ENST00000358026	NM_001128849.1	1162	Ggc/Tgc	25/36	0.348504869356792	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.348504869356792	1		579	480	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855787	45855787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	104	577	0	ENST00000391945.4:c.2023G>T	p.Gly675Cys	p.G675C	ENST00000391945	NM_000400.3	675	Ggc/Tgc	21/23	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.348504869356792	2		577	489	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003747	45003747	+	start_lost	Translation_Start_Site	SNP	G	G	C	novel	NA	P-0057143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	71	396	0	ENST00000558401.1:c.3G>C	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	atG/atC	1/4	0.348504869356792	1	FACETS	0.748	0.655	0.847	0.748	0.655	0.847	SUBCLONAL	1	TRUE	0	0.348504869356792	1		396	450	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545870	41545870	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	154	662	0	ENST00000263253.7:c.2485C>T	p.Gln829Ter	p.Q829*	ENST00000263253	NM_001429.3	829	Cag/Tag	14/31	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.348504869356792	2		662	718	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420532	49420532	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	96	506	0	ENST00000301067.7:c.15217C>T	p.Gln5073Ter	p.Q5073*	ENST00000301067	NM_003482.3	5073	Cag/Tag	48/54	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.348504869356792	2		506	429	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427897	49427897	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0057143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	93	565	0	ENST00000301067.7:c.10693A>T	p.Lys3565Ter	p.K3565*	ENST00000301067	NM_003482.3	3565	Aag/Tag	38/54	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.348504869356792	2		565	514	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832824	3832824	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	94	461	0	ENST00000262367.5:c.1434del	p.Ser479AlafsTer15	p.S479Afs*15	ENST00000262367	NM_004380.2	478	ccC/cc	6/31	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.348504869356792	2		461	379	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610634	10610634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	76	464	0	ENST00000171111.5:c.76G>A	p.Gly26Arg	p.G26R	ENST00000171111	NM_203500.1	26	Ggg/Agg	2/6	0.348504869356792	1	FACETS	0.963	0.85	1	0.963	0.85	1	CLONAL	1	TRUE	0	0.348504869356792	1		464	374	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029186	26029186	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	59	224	0	ENST00000435504.4:c.164G>T	p.Cys55Phe	p.C55F	ENST00000435504		55	tGc/tTc	4/13	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.348504869356792	2		224	297	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47708006	47708006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	49	238	0	ENST00000233146.2:c.2630G>A	p.Arg877Lys	p.R877K	ENST00000233146	NM_000251.2	877	aGa/aAa	15/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.348504869356792	2		238	198	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259181	36259181	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1247386323	NA	P-0057143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	140	628	0	ENST00000300305.3:c.310A>G	p.Thr104Ala	p.T104A	ENST00000300305		104	Acg/Gcg	3/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.348504869356792	2		628	712	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163242	47163242	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	58	277	0	ENST00000409792.3:c.2884G>T	p.Ala962Ser	p.A962S	ENST00000409792	NM_014159.6	962	Gct/Tct	3/21	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.348504869356792	2		277	258	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102855	71102855	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	82	258	0	ENST00000318789.4:c.352C>T	p.Gln118Ter	p.Q118*	ENST00000318789	NM_032682.5	118	Caa/Taa	8/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.348504869356792	2		258	404	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149238699	149238699	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	154	536	0	ENST00000360632.3:c.1096G>C	p.Gly366Arg	p.G366R	ENST00000360632	NM_015472.4	366	Gga/Cga	7/7	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.348504869356792	2		536	683	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503742	186503742	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	77	304	0	ENST00000323963.5:c.419A>C	p.Asn140Thr	p.N140T	ENST00000323963		140	aAt/aCt	5/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.348504869356792	2		304	372	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1795716	1795716	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	33	262	0	ENST00000260795.2:c.55G>A	p.Gly19Ser	p.G19S	ENST00000260795		19	Ggc/Agc	1/17	1	2	FACETS	0.861	0.706	1	0.861	0.706	1	CLONAL	1	TRUE	1	0.348504869356792	2		262	220	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902617	1902617	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	132	607	0	ENST00000382891.5:c.236T>G	p.Leu79Arg	p.L79R	ENST00000382891	NM_133335.3	79	cTg/cGg	2/22	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.348504869356792	2		607	603	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38949863	38949863	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	136	252	0	ENST00000357387.3:c.4087A>T	p.Thr1363Ser	p.T1363S	ENST00000357387	NM_152756.3	1363	Acc/Tcc	31/38	0.319507551746739	3	FACETS	0.861	0.793	0.93	1	0.984	1	CLONAL	3	TRUE	1	0.348504869356792	3		252	355	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131893068	131893068	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1449159448	NA	P-0057143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	173	245	0	ENST00000265335.6:c.52G>A	p.Glu18Lys	p.E18K	ENST00000265335		18	Gag/Aag	1/25	0.344883682272407	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	3	TRUE	0	0.348504869356792	3		245	382	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681129	117681129	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs772324949	NA	P-0057143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	88	283	0	ENST00000368508.3:c.3491T>C	p.Ile1164Thr	p.I1164T	ENST00000368508	NM_002944.2	1164	aTa/aCa	23/43	0.348504869356792	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.348504869356792	1		283	333	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68999973	68999973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	192	398	0	ENST00000288368.4:c.2042C>T	p.Pro681Leu	p.P681L	ENST00000288368	NM_024870.2	681	cCa/cTa	19/40	0.315996418673944	3	FACETS	0.973	0.904	1	0.973	0.904	1	CLONAL	2	TRUE	1	0.348504869356792	3		398	665	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229488	98229488	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	50	278	0	ENST00000331920.6:c.2470A>T	p.Arg824Trp	p.R824W	ENST00000331920	NM_000264.3	824	Agg/Tgg	15/24	1	2	FACETS	0.897	0.765	1	0.897	0.765	1	CLONAL	1	TRUE	1	0.348504869356792	2		278	320	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805553	46805553	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	306	680	0	ENST00000290295.7:c.403G>T	p.Gly135Ter	p.G135*	ENST00000290295	NM_006361.5	135	Gga/Tga	1/2	0.677984680527055	3	FACETS	0.95	0.895	1	0.475	0.447	0.504	CLONAL	1	TRUE	1	0.677984680527055	3		680	1272	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873634	35873634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778404	NA	P-0057145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	17	210	0	ENST00000303115.3:c.590C>T	p.Pro197Leu	p.P197L	ENST00000303115	NM_002185.3	197	cCg/cTg	5/8	1	2	FACETS	0.712	0.531	0.926	0.712	0.531	0.926	CLONAL	1	TRUE	1	0.17	2		210	281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578581	7579597	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGAAAGTCAGGGCACAAGTGAACAGATAAAGCAACTGGAAGACGGCAGCAAAGAAACAAACATGCGTAAGCACCTCCTGCAACCCACTAGCGAGCTAGAGAGAGTTGGCGTCTACACCTCAGGAGCTTTTCTTTTTTTTTTTTTTTTTTGAGATAGGGTCTTGCTCTGTCACTCAGGCTGGAGCACAGTGGTGTGATCACAGCTCACTGCAGCCTCCATCTCCTGGCCTCAAGTGATCTTCCCACCTCAGCCTCCTAAGTGGCTGGGACTATAGGTGTGCACCACCATGCCTGGCTAATTTTTTGTATTTTTTTGTAGAGACGAGGTTTCATCATGTTACCCAGGCTGGTCTTGAACTCCTGGGCTCAGGTGATCTGCCTGCCTTGGCCTCTTTGAGAGTGCTGGGATTGCAGGTGTGAGCCACCAAGCCTGGTCAGGAGCTTATTTTCAAAAGCCAAGGAATACACGTGGATGAAGAAAAAGAAAAGTTCTGCATCCCCAGGAGAGATGCTGAGGGTGTGATGGGATGGATAAAAGCCCAAATTCAAGGGGGGAATATTCAACTTTGGGACAGGAGTCAGAGATCACACATTAAGTGGGTAAACTATAAAAAAACACTGACAGGAAGCCAAAGGGTGAAGAGGAATCCCAAAGTTCCAAACAAAAGAAATGCAGGGGGATACGGCCAGGCATTGAAGTCTCATGGAAGCCAGCCCCTCAGGGCAACTGACCGTGCAAGTCACAGACTTGGCTGTCCCAGAATGCAAGAAGCCCAGACGGAAACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGGACAGAAGATGACAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTGCAGGGGCCACGGGGGGAGCAGCCTCTGGCATTCTGGGAGCTTCATCTGGACCTGGGTCTTCAGTGAACCATTGTTCAATATCGTCCGGGGACAGCATCAAATCATCCATTGCTTGGGACGGCAAGGGGGACTGTAGA	TGAAAGTCAGGGCACAAGTGAACAGATAAAGCAACTGGAAGACGGCAGCAAAGAAACAAACATGCGTAAGCACCTCCTGCAACCCACTAGCGAGCTAGAGAGAGTTGGCGTCTACACCTCAGGAGCTTTTCTTTTTTTTTTTTTTTTTTGAGATAGGGTCTTGCTCTGTCACTCAGGCTGGAGCACAGTGGTGTGATCACAGCTCACTGCAGCCTCCATCTCCTGGCCTCAAGTGATCTTCCCACCTCAGCCTCCTAAGTGGCTGGGACTATAGGTGTGCACCACCATGCCTGGCTAATTTTTTGTATTTTTTTGTAGAGACGAGGTTTCATCATGTTACCCAGGCTGGTCTTGAACTCCTGGGCTCAGGTGATCTGCCTGCCTTGGCCTCTTTGAGAGTGCTGGGATTGCAGGTGTGAGCCACCAAGCCTGGTCAGGAGCTTATTTTCAAAAGCCAAGGAATACACGTGGATGAAGAAAAAGAAAAGTTCTGCATCCCCAGGAGAGATGCTGAGGGTGTGATGGGATGGATAAAAGCCCAAATTCAAGGGGGGAATATTCAACTTTGGGACAGGAGTCAGAGATCACACATTAAGTGGGTAAACTATAAAAAAACACTGACAGGAAGCCAAAGGGTGAAGAGGAATCCCAAAGTTCCAAACAAAAGAAATGCAGGGGGATACGGCCAGGCATTGAAGTCTCATGGAAGCCAGCCCCTCAGGGCAACTGACCGTGCAAGTCACAGACTTGGCTGTCCCAGAATGCAAGAAGCCCAGACGGAAACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGGACAGAAGATGACAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTGCAGGGGCCACGGGGGGAGCAGCCTCTGGCATTCTGGGAGCTTCATCTGGACCTGGGTCTTCAGTGAACCATTGTTCAATATCGTCCGGGGACAGCATCAAATCATCCATTGCTTGGGACGGCAAGGGGGACTGTAGA	-	novel	NA	P-0057145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	62	442	0	ENST00000269305.4:c.97-7_376-27del		p.X33_splice	ENST00000269305	NM_001126112.2	33		4/11	1	2	FACETS	0.794	0.684	0.914	0.794	0.684	0.914	CLONAL	1	TRUE	1	0.17	2		442	919	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs1202793339	NA	P-0057146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	531	586	0	ENST00000269305.4:c.560-1G>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.595827380538024	3	FACETS	0.935	0.907	0.962	0.935	0.907	0.962	CLONAL	3	TRUE	0	0.645593470052053	3		586	776	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436034	110436034	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2046	133	948	0	ENST00000375856.3:c.2367C>A	p.His789Gln	p.H789Q	ENST00000375856	NM_003749.2	789	caC/caA	1/2	0.645593470052053	7	FACETS	0.494	0.446	0.545			1	SUBCLONAL	1	TRUE	NA	0.645593470052053	7		948	2179	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482849	67482849	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	164	461	1	ENST00000327367.4:c.1253G>A	p.Ser418Asn	p.S418N	ENST00000327367	NM_005902.3	418	aGc/aAc	9/9	0.450862247195142	3	FACETS	0.905	0.832	0.98			1	CLONAL	1	TRUE	NA	0.645593470052053	3		462	743	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857784	9857784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145861983	NA	P-0057147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	83	409	0	ENST00000330684.3:c.3617G>A	p.Arg1206Gln	p.R1206Q	ENST00000330684	NM_001134407.1	1206	cGa/cAa	13/13	0.106632537658892	5	FACETS	1	0.972	1	0.338	0.298	0.381	INDETERMINATE	1	TRUE	1	0.232061071465206	5		409	713	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0057147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	109	755	1	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.232061071465206	2		756	755	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085824	16085824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763830786	NA	P-0057147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	82	364	1	ENST00000281043.3:c.1000G>A	p.Ala334Thr	p.A334T	ENST00000281043	NM_005378.4	334	Gcc/Acc	3/3	0.230215339046257	2	FACETS	0.988	0.871	1	0.494	0.435	0.557	CLONAL	1	TRUE	0	0.232061071465206	2		365	715	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870929	12870930	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0057147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	48	218	1	ENST00000228872.4:c.156_157delinsTT	p.Met52_Glu53delinsIleTer	p.M52_E53delinsI*	ENST00000228872	NM_004064.3	52	atGGaa/atTTaa	1/3	1	2	FACETS	0.903	0.764	1	0.903	0.764	1	CLONAL	1	TRUE	1	0.232061071465206	2		219	458	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15984032	15984032	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	42	200	0	ENST00000268712.3:c.3187G>C	p.Gly1063Arg	p.G1063R	ENST00000268712	NM_006311.3	1063	Ggc/Cgc	24/46	1	2	FACETS	0.864	0.722	1	0.864	0.722	1	CLONAL	1	TRUE	1	0.232061071465206	2		200	419	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193489	99193490	+	missense_variant	Missense_Mutation	DNP	GC	GC	CT	novel	NA	P-0057147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	54	491	1	ENST00000074304.5:c.2684_2685delinsCT	p.Cys895Ser	p.C895S	ENST00000074304	NM_001134224.1	895	tGC/tCT	25/26	0.230215339046257	2	FACETS	0.44	0.374	0.513	0.22	0.187	0.257	SUBCLONAL	1	TRUE	0	0.232061071465206	2		492	1057	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161994	47161994	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0057147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	38	277	0	ENST00000409792.3:c.4132A>T	p.Lys1378Ter	p.K1378*	ENST00000409792	NM_014159.6	1378	Aag/Tag	3/21	1	2	FACETS	0.71	0.587	0.848	0.71	0.587	0.848	SUBCLONAL	1	TRUE	1	0.232061071465206	2		277	461	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230769	66230769	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	42	242	0	ENST00000273854.3:c.2202del	p.Asn735ThrfsTer5	p.N735Tfs*5	ENST00000273854	NM_004439.5	734	ccT/cc	12/18	0.106632537658892	5	FACETS	1	0.859	1	0.258	0.215	0.305	INDETERMINATE	1	TRUE	1	0.232061071465206	5		242	473	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044478	47044479	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0057147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	165	439	0	ENST00000377604.3:c.1978dup	p.Arg660ProfsTer13	p.R660Pfs*13	ENST00000377604	NM_001204468.1	659	gcc/gCcc	18/24	0.168136992755647	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.232061071465206	1		439	872	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0057148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	108	239	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.347108258684303	2		239	523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578196	7578196	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	153	576	0	ENST00000269305.4:c.653T>A	p.Val218Glu	p.V218E	ENST00000269305	NM_001126112.2	218	gTg/gAg	6/11	0.326957027871046	1	FACETS	0.88	0.805	0.958	0.88	0.805	0.958	CLONAL	1	TRUE	0	0.347108258684303	1		576	828	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265718	41266423	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGCTTGGTGAAATAGCAAACAAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAG	TGGCTTGGTGAAATAGCAAACAAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAG	-	novel	NA	P-0057148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	91	61	0	ENST00000349496.5:c.13+148_242-20del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	1	2	FACETS	0.878	0.798	0.959	1	0.989	1	CLONAL	3	TRUE	1	0.347108258684303	2		61	199	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0057149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	146	269	2	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.720800707331008	2		271	375	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0057149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	133	326	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.720800707331008	2		326	353	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912149	114912149	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	295	470	6	ENST00000543371.1:c.1219C>T	p.Arg407Ter	p.R407*	ENST00000543371	NM_001198531.1	407	Cga/Tga	11/14	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.720800707331008	2		476	783	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0057149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	324	608	1	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.720800707331008	1	FACETS	0.963	0.92	1	0.963	0.92	1	CLONAL	1	TRUE	0	0.720800707331008	1		609	597	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020351	69020351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201443824	NA	P-0057149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	104	331	2	ENST00000288368.4:c.2723G>A	p.Arg908His	p.R908H	ENST00000288368	NM_024870.2	908	cGt/cAt	24/40	0.294377719799109	2	FACETS	0.646	0.581	0.713	0.323	0.29	0.357	INDETERMINATE	1	TRUE	0	0.720800707331008	2		333	447	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873017	134873017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	141	496	6	ENST00000398015.3:c.1321C>T	p.His441Tyr	p.H441Y	ENST00000398015	NM_004441.4	441	Cac/Tac	6/16	0.22892561100179	1	FACETS	0.399	0.364	0.435	0.399	0.364	0.435	INDETERMINATE	1	TRUE	0	0.720800707331008	1		502	627	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803726	1803726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748261686	NA	P-0057149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	359	855	10	ENST00000260795.2:c.904G>A	p.Gly302Ser	p.G302S	ENST00000260795		302	Ggc/Agc	6/17	0.516121915147391	3	FACETS	0.999	0.946	1			1	CLONAL	1	TRUE	NA	0.720800707331008	3		865	1357	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142966	47142966	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1559720382	NA	P-0057161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	55	358	0	ENST00000409792.3:c.4997A>G	p.Tyr1666Cys	p.Y1666C	ENST00000409792	NM_014159.6	1666	tAt/tGt	8/21	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.14	2		358	714	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188309	10188309	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	64	444	0	ENST00000256474.2:c.452T>A	p.Ile151Asn	p.I151N	ENST00000256474	NM_000551.3	151	aTc/aAc	2/3	1	2	FACETS	0.906	0.782	1	0.906	0.782	1	CLONAL	1	TRUE	1	0.14	2		444	1009	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087461	27087467	+	frameshift_variant	Frame_Shift_Del	DEL	TCTCCTT	TCTCCTT	-	novel	NA	P-0057161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1572	89	699	0	ENST00000324856.7:c.2039_2045del	p.Pro680LeufsTer60	p.P680Lfs*60	ENST00000324856	NM_006015.4	679	TCTCCTTtc/tc	5/20	1	2	FACETS	0.765	0.676	0.862	0.765	0.676	0.862	SUBCLONAL	1	TRUE	1	0.14	2		699	1661	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379485	225379485	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	24	332	0	ENST00000264414.4:c.383G>T	p.Arg128Leu	p.R128L	ENST00000264414	NM_003590.4	128	cGt/cTt	4/16	1	2	FACETS	0.969	0.759	1	0.969	0.759	1	CLONAL	1	TRUE	1	0.14	2		332	354	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0057162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	171	298	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.447795850142198	4	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	2	0.536777263204573	4		298	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0057162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	400	755	1	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	0.536777263204573	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.536777263204573	2		756	702	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856469	111856469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	194	593	1	ENST00000341259.2:c.520G>A	p.Ala174Thr	p.A174T	ENST00000341259	NM_005475.2	174	Gcc/Acc	2/8	0.532325287082751	3	FACETS	1	0.983	1	0.595	0.552	0.64	CLONAL	1	TRUE	1	0.536777263204573	3		594	770	SUCCESS
APC	324	MSKCC	GRCh37	5	112175608	112175608	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	147	322	0	ENST00000257430.4:c.4317del	p.Pro1440HisfsTer33	p.P1440Hfs*33	ENST00000257430	NM_000038.5	1439	ccT/cc	16/16	0.187114146260623	5	FACETS	1	0.979	1	0.785	0.724	0.847	INDETERMINATE	2	TRUE	2	0.536777263204573	5		322	420	SUCCESS
APC	324	MSKCC	GRCh37	5	112174282	112174282	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs864622629	NA	P-0057162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	100	248	0	ENST00000257430.4:c.2991T>G	p.Tyr997Ter	p.Y997*	ENST00000257430	NM_000038.5	997	taT/taG	16/16	0.187114146260623	5	FACETS	1	0.927	1	0.688	0.621	0.757	INDETERMINATE	2	TRUE	2	0.536777263204573	5		248	326	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0057163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	43	418	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.262864766912475	3	FACETS	0.73	0.611	0.863	0.365	0.305	0.432	SUBCLONAL	1	TRUE	1	0.262864766912475	3		418	507	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0057163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	121	473	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.262864766912475	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.262864766912475	3		473	442	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0057163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	123	326	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.262864766912475	2	FACETS	1	0.941	1	1	0.988	1	CLONAL	3	TRUE	0	0.262864766912475	2		326	303	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473705	67473705	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	49	640	0	ENST00000327367.4:c.785A>G	p.Asp262Gly	p.D262G	ENST00000327367	NM_005902.3	262	gAc/gGc	6/9	1	2	FACETS	0.561	0.475	0.657	0.561	0.475	0.657	SUBCLONAL	1	TRUE	1	0.262864766912475	2		640	664	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591101	67591101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	28	197	0	ENST00000274335.5:c.1694G>A	p.Ser565Asn	p.S565N	ENST00000274335		565	aGc/aAc	12/15	0.262864766912475	3	FACETS	0.662	0.529	0.814	0.331	0.264	0.407	SUBCLONAL	1	TRUE	1	0.262864766912475	3		197	364	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0057165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	50	653	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.29063172576947	2		655	337	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589586	67589591	+	inframe_deletion	In_Frame_Del	DEL	ATGAAT	ATGAAT	-	novel	NA	P-0057165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	19	134	0	ENST00000274335.5:c.1351_1356del	p.Glu451_Tyr452del	p.E451_Y452del	ENST00000274335		450	cATGAATat/cat	10/15	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.29063172576947	2		134	101	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528428	29528428	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs876660782	NA	P-0057165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	37	193	0	ENST00000356175.3:c.1186-1G>C		p.X396_splice	ENST00000356175	NM_000267.3	396			1	2	FACETS	0.929	0.781	1	1	0.966	1	CLONAL	2	TRUE	1	0.29063172576947	2		193	137	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250837	10250837	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	37	792	0	ENST00000340748.4:c.3643G>T	p.Gly1215Ter	p.G1215*	ENST00000340748		1215	Gga/Tga	32/40	0.230052923337972	1	FACETS	0.772	0.639	0.918	0.772	0.639	0.918	CLONAL	1	TRUE	0	0.29063172576947	1		792	282	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297923	15297923	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	18	983	0	ENST00000263388.2:c.1833del	p.Thr612ProfsTer4	p.T612Pfs*4	ENST00000263388	NM_000435.2	611	ggG/gg	11/33	0.230052923337972	1	FACETS	0.395	0.297	0.51	0.395	0.297	0.51	SUBCLONAL	1	TRUE	0	0.29063172576947	1		983	268	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138647	55138647	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757211711	NA	P-0057165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	44	419	0	ENST00000257290.5:c.1324C>T	p.Leu442Phe	p.L442F	ENST00000257290	NM_006206.4	442	Ctt/Ttt	9/23	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.29063172576947	2		419	257	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955899	55955899	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	30	404	0	ENST00000263923.4:c.3263T>C	p.Val1088Ala	p.V1088A	ENST00000263923	NM_002253.2	1088	gTc/gCc	24/30	1	2	FACETS	0.988	0.802	1	0.988	0.802	1	CLONAL	1	TRUE	1	0.29063172576947	2		404	209	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630651	187630651	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	45	448	0	ENST00000441802.2:c.331G>C	p.Glu111Gln	p.E111Q	ENST00000441802	NM_005245.3	111	Gaa/Caa	2/27	0.29063172576947	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.29063172576947	1		448	213	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399925	139399925	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	43	1055	0	ENST00000277541.6:c.4423del	p.Asp1475ThrfsTer105	p.D1475Tfs*105	ENST00000277541	NM_017617.3	1475	Gac/ac	25/34	0.29063172576947	1	FACETS	0.742	0.623	0.873	0.742	0.623	0.873	SUBCLONAL	1	TRUE	0	0.29063172576947	1		1055	341	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107236	193107236	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	35	198	0	ENST00000367435.3:c.445G>C	p.Asp149His	p.D149H	ENST00000367435	NM_024529.4	149	Gat/Cat	6/17	0.160033560430392	3	FACETS	0.695	0.57	0.836	0.348	0.285	0.418	INDETERMINATE	1	TRUE	1	0.28	3		198	410	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936168	71936168	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	74	581	0	ENST00000298229.2:c.140G>C	p.Arg47Pro	p.R47P	ENST00000298229	NM_001567.3	47	cGa/cCa	1/28	1	2	FACETS	0.686	0.599	0.779	0.686	0.599	0.779	SUBCLONAL	1	TRUE	1	0.28	2		581	771	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118622	17118622	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	50	421	0	ENST00000285071.4:c.1309G>T	p.Val437Phe	p.V437F	ENST00000285071	NM_144997.5	437	Gtc/Ttc	12/14	0.3	3	FACETS	0.505	0.427	0.591			1	SUBCLONAL	1	TRUE	NA	0.28	3		421	806	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599867	10599867	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0057166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	114	742	0	ENST00000171111.5:c.1708+1G>A		p.X570_splice	ENST00000171111	NM_203500.1	570			0.220722240705328	1	FACETS	0.667	0.599	0.739	0.667	0.599	0.739	SUBCLONAL	1	TRUE	0	0.28	1		742	1050	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095023	11095023	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	132	1050	1	ENST00000358026.2:c.196C>T	p.Gln66Ter	p.Q66*	ENST00000358026	NM_001128849.1	66	Cag/Tag	2/36	0.220722240705328	1	FACETS	0.693	0.628	0.762	0.693	0.628	0.762	SUBCLONAL	1	TRUE	0	0.28	1		1051	1170	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0057168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	58	366	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.767	0.661	0.881	0.767	0.661	0.881	SUBCLONAL	1	TRUE	1	0.400225157864633	2		366	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0057168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	375	734	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.375532106914696	2	FACETS	0.878	0.835	0.922	0.878	0.835	0.922	CLONAL	2	TRUE	0	0.400225157864633	2		734	1067	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944761	31944761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	64	266	0	ENST00000340398.3:c.340G>A	p.Ala114Thr	p.A114T	ENST00000340398	NM_001013699.2	114	Gct/Act	1/1	0.40085313685478	3	FACETS	1	0.895	1	0.516	0.449	0.588	CLONAL	1	TRUE	1	0.400225157864633	3		266	372	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670715	67670715	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	120	497	0	ENST00000264010.4:c.1960C>T	p.Arg654Ter	p.R654*	ENST00000264010	NM_006565.3	654	Cga/Tga	11/12	0.34003312866129	3	FACETS	0.828	0.747	0.914	0.414	0.373	0.457	CLONAL	1	TRUE	1	0.400225157864633	3		497	869	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099315	157099315	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs372726215	NA	P-0057168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	86	504	0	ENST00000346085.5:c.252C>G	p.His84Gln	p.H84Q	ENST00000346085	NM_020732.3	84	caC/caG	1/20	0.40085313685478	3	FACETS	0.669	0.591	0.752	0.334	0.295	0.376	SUBCLONAL	1	TRUE	1	0.400225157864633	3		504	771	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128849141	128849141	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	346	693	0	ENST00000249373.3:c.1369T>C	p.Phe457Leu	p.F457L	ENST00000249373	NM_005631.4	457	Ttc/Ctc	8/12	0.364644204921811	4	FACETS	0.928	0.877	0.979	0.618	0.585	0.653	CLONAL	2	TRUE	1	0.400225157864633	4		693	1305	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0057169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	23	215	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.196738031309289	3	FACETS	0.725	0.565	0.911	0.363	0.282	0.456	CLONAL	1	FALSE	1	0.196738031309289	3		215	354	SUCCESS
ATM	472	MSKCC	GRCh37	11	108213967	108213967	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876659872	NA	P-0057169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	25	247	0	ENST00000278616.4:c.8287C>T	p.Arg2763Ter	p.R2763*	ENST00000278616	NM_000051.3	2763	Cga/Tga	57/63	1	2	FACETS	0.655	0.516	0.815	0.655	0.516	0.815	SUBCLONAL	1	FALSE	1	0.196738031309289	2		247	388	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121561	108121561	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs749036865	NA	P-0057169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	40	406	0	ENST00000278616.4:c.1369C>T	p.Arg457Ter	p.R457*	ENST00000278616	NM_000051.3	457	Cga/Tga	10/63	1	2	FACETS	0.626	0.519	0.745	0.626	0.519	0.745	SUBCLONAL	1	FALSE	1	0.196738031309289	2		406	650	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670256	134670256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	31	442	2	ENST00000398015.3:c.167G>A	p.Arg56His	p.R56H	ENST00000398015	NM_004441.4	56	cGc/cAc	3/16	0.196738031309289	0	FACETS	0.498	0.402	0.607			1	SUBCLONAL	1	FALSE	0	0.196738031309289	0		444	508	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215817	133215817	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	130	623	0	ENST00000320574.5:c.5446A>C	p.Asn1816His	p.N1816H	ENST00000320574	NM_006231.2	1816	Aac/Cac	40/49	1	2	FACETS	1	0.944	1	1	0.99	1	CLONAL	2	FALSE	1	0.196738031309289	2		623	628	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121699	108121699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	45	391	0	ENST00000278616.4:c.1507G>A	p.Glu503Lys	p.E503K	ENST00000278616	NM_000051.3	503	Gaa/Aaa	10/63	1	2	FACETS	0.617	0.517	0.728	0.617	0.517	0.728	SUBCLONAL	1	FALSE	1	0.196738031309289	2		391	741	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013727	12013728	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	45	219	1	ENST00000353533.5:c.673dup	p.Ile225AsnfsTer20	p.I225Nfs*20	ENST00000353533	NM_003010.3	223	-/A	6/11	0.152237177338513	2	FACETS	1	0.858	1	0.511	0.429	0.6	CLONAL	1	FALSE	0	0.196738031309289	2		220	448	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041576	47041576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	110	622	0	ENST00000377604.3:c.1801C>T	p.Gln601Ter	p.Q601*	ENST00000377604	NM_001204468.1	601	Cag/Tag	17/24	0.243141845719034	3	FACETS	1	0.963	1	0.579	0.519	0.642	CLONAL	1	TRUE	1	0.243141845719034	3		622	877	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0057170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	104	436	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.191554145668602	3	FACETS	1	0.978	1	0.678	0.607	0.752	CLONAL	1	TRUE	1	0.243141845719034	3		436	708	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0057178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	102	579	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.363473353634357	3	FACETS	0.87	0.785	0.96	0.87	0.785	0.96	CLONAL	2	FALSE	1	0.363473353634357	3		579	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578537	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs879254214	NA	P-0057178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	446	1203	0	ENST00000269305.4:c.393_395del	p.Asn131del	p.N131del	ENST00000269305	NM_001126112.2	131	aaCAAg/aag	5/11	0.363473353634357	7	FACETS	1	0.988	1	0.903	0.871	0.935	CLONAL	6	FALSE	0	0.363473353634357	7		1203	741	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366709	40366709	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	160	1037	2	ENST00000397332.2:c.488C>A	p.Pro163His	p.P163H	ENST00000397332	NM_001033082.2	163	cCc/cAc	2/3	0.22677917804766	3	FACETS	1	0.965	1	0.718	0.664	0.774	CLONAL	2	FALSE	0	0.363473353634357	3		1039	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0057179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	438	719	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.749317452843063	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.749317452843063	1		719	704	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829029	72829029	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	525	836	0	ENST00000268489.5:c.7552C>T	p.Gln2518Ter	p.Q2518*	ENST00000268489	NM_006885.3	2518	Caa/Taa	9/10	0.749317452843063	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.749317452843063	1		836	867	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560451	65560451	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0057180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	59	347	0	ENST00000358664.4:c.146C>G	p.Ser49Ter	p.S49*	ENST00000358664	NM_002382.4	49	tCa/tGa	3/5	1	2	FACETS	0.879	0.757	1	0.879	0.757	1	CLONAL	1	TRUE	1	0.25	2		347	537	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211611	5211611	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	67	421	0	ENST00000357368.4:c.5224G>C	p.Asp1742His	p.D1742H	ENST00000357368	NM_002850.3	1742	Gat/Cat	33/38	1	2	FACETS	0.918	0.798	1	0.918	0.798	1	CLONAL	1	TRUE	1	0.25	2		421	584	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40993283	40993283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1428987216	NA	P-0057180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	69	297	0	ENST00000267868.3:c.109G>A	p.Asp37Asn	p.D37N	ENST00000267868	NM_002875.4	37	Gat/Aat	3/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.25	2		297	464	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912276	29912276	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0057180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	267	982	0	ENST00000376809.5:c.896-1G>A		p.X299_splice	ENST00000376809	NM_002116.7	299			0.228822067187767	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.25	2		982	1029	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001017	150001017	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	37	260	0	ENST00000253339.5:c.2587C>T	p.Gln863Ter	p.Q863*	ENST00000253339		863	Cag/Tag	4/7	1	2	FACETS	0.955	0.79	1	0.955	0.79	1	CLONAL	1	TRUE	1	0.25	2		260	310	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281022	49281022	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	65	491	0	ENST00000282018.3:c.69C>G	p.Phe23Leu	p.F23L	ENST00000282018	NM_020377.2	23	ttC/ttG	1/1	1	2	FACETS	0.851	0.738	0.974	0.851	0.738	0.974	CLONAL	1	TRUE	1	0.25	2		491	611	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210699	5210699	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	110	824	0	ENST00000357368.4:c.5352G>C	p.Glu1784Asp	p.E1784D	ENST00000357368	NM_002850.3	1784	gaG/gaC	34/38	1	2	FACETS	0.945	0.848	1	0.945	0.848	1	CLONAL	1	TRUE	1	0.25	2		824	931	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149796	202149803	+	frameshift_variant	Frame_Shift_Del	DEL	GTGTTTTT	GTGTTTTT	-	novel	NA	P-0057180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	59	544	0	ENST00000358485.4:c.1237_1244del	p.Val413TyrfsTer8	p.V413Yfs*8	ENST00000358485	NM_001080125.1	413	GTGTTTTTt/t	8/9	1	2	FACETS	0.714	0.614	0.824	0.714	0.614	0.824	SUBCLONAL	1	TRUE	1	0.25	2		544	661	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595825	52595825	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	63	486	0	ENST00000394830.3:c.4090G>T	p.Glu1364Ter	p.E1364*	ENST00000394830	NM_018313.4	1364	Gaa/Taa	26/30	1	2	FACETS	0.715	0.618	0.821	0.715	0.618	0.821	SUBCLONAL	1	TRUE	1	0.25	2		486	705	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197539	106197539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	44	294	0	ENST00000380013.4:c.5872G>A	p.Glu1958Lys	p.E1958K	ENST00000380013	NM_001127208.2	1958	Gaa/Aaa	11/11	1	2	FACETS	0.873	0.734	1	0.873	0.734	1	CLONAL	1	TRUE	1	0.25	2		294	403	SUCCESS
APC	324	MSKCC	GRCh37	5	112111429	112111429	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	35	180	0	ENST00000257430.4:c.526G>A	p.Glu176Lys	p.E176K	ENST00000257430	NM_000038.5	176	Gaa/Aaa	5/16	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.25	2		180	259	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638399	176638399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867210661	NA	P-0057180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	91	639	0	ENST00000439151.2:c.2999C>T	p.Ser1000Phe	p.S1000F	ENST00000439151	NM_022455.4	1000	tCc/tTc	5/23	0.269764589041556	3	FACETS	0.879	0.779	0.986	0.439	0.389	0.493	CLONAL	1	TRUE	1	0.25	3		639	932	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577095	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519984	NA	P-0057181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	129	789	0	ENST00000269305.4:c.843C>G	p.Asp281Glu	p.D281E	ENST00000269305	NM_001126112.2	281	gaC/gaG	8/11	0.226980844751086	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.226980844751086	1		789	977	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	53	324	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.498	0.425	0.577	0.498	0.425	0.577	SUBCLONAL	1	TRUE	1	0.47	2		324	453	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913499	NA	P-0057183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	53	294	2	ENST00000345146.2:c.394C>A	p.Arg132Ser	p.R132S	ENST00000345146	NM_005896.2	132	Cgt/Agt	4/10	1	2	FACETS	0.601	0.515	0.696	0.601	0.515	0.696	SUBCLONAL	1	TRUE	1	0.47	2		296	375	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0057184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	121	306	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.514299632002809	2		306	444	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0057184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	289	1029	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.988	0.929	1	0.988	0.929	1	CLONAL	1	TRUE	1	0.514299632002809	2		1032	1138	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0057184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	602	900	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.989	1	1	0.998	1	CLONAL	2	TRUE	1	0.514299632002809	2		904	1112	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	163	647	2	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	0.871	0.801	0.943	0.871	0.801	0.943	CLONAL	1	TRUE	1	0.514299632002809	2		649	728	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087961	27087961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	191	537	0	ENST00000324856.7:c.2248C>T	p.Arg750Ter	p.R750*	ENST00000324856	NM_006015.4	750	Cga/Tga	6/20	1	2	FACETS	0.993	0.921	1	0.993	0.921	1	CLONAL	1	TRUE	1	0.514299632002809	2		537	748	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0057184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	195	527	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.514299632002809	2	FACETS	1	0.977	1	0.559	0.52	0.6	CLONAL	1	TRUE	0	0.514299632002809	2		530	678	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0057184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	204	531	2	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.514299632002809	2		533	686	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371929	55371930	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	230	719	0	ENST00000297316.4:c.620dup	p.Ser208GlufsTer157	p.S208Efs*157	ENST00000297316	NM_022454.3	207	cag/cAag	2/2	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.514299632002809	2		719	868	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121909229	NA	P-0057184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	263	454	0	ENST00000371953.3:c.389G>C	p.Arg130Pro	p.R130P	ENST00000371953	NM_000314.4	130	cGa/cCa	5/9	0.514299632002809	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.514299632002809	2		454	485	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752960	128752960	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	179	443	0	ENST00000377970.2:c.1121A>G	p.His374Arg	p.H374R	ENST00000377970	NM_002467.4	374	cAc/cGc	3/3	1	2	FACETS	0.954	0.881	1	0.954	0.881	1	CLONAL	1	TRUE	1	0.514299632002809	2		443	730	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770623	40770623	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	150	383	0	ENST00000373198.4:c.2759C>A	p.Thr920Lys	p.T920K	ENST00000373198	NM_133170.3	920	aCa/aAa	19/32	1	2	FACETS	0.997	0.916	1	0.997	0.916	1	CLONAL	1	TRUE	1	0.514299632002809	2		383	585	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499363	89499363	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1317589623	NA	P-0057184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	103	447	0	ENST00000336596.2:c.2538del	p.Met847TrpfsTer10	p.M847Wfs*10	ENST00000336596	NM_005233.5	845	Ccc/cc	15/17	1	2	FACETS	0.62	0.556	0.688	0.62	0.556	0.688	SUBCLONAL	1	TRUE	1	0.514299632002809	2		447	646	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466003	69466038	+	inframe_deletion	In_Frame_Del	DEL	GTGGACCTGGCTTGCACACCCACCGACGTGCGGGAC	GTGGACCTGGCTTGCACACCCACCGACGTGCGGGAC	-	novel	NA	P-0057184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	137	1115	0	ENST00000227507.2:c.847_882del	p.Leu283_Asp294del	p.L283_D294del	ENST00000227507	NM_053056.2	281	GTGGACCTGGCTTGCACACCCACCGACGTGCGGGAC/-	5/5	1	2	FACETS	0.504	0.457	0.553	0.504	0.457	0.553	SUBCLONAL	1	TRUE	1	0.514299632002809	2		1115	1057	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991949	72991949	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs753977275	NA	P-0057184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	240	724	1	ENST00000268489.5:c.2096del	p.Gly699AlafsTer125	p.G699Afs*125	ENST00000268489	NM_006885.3	699	gGc/gc	2/10	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.514299632002809	2		725	923	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922306	178922306	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	82	321	0	ENST00000263967.3:c.1075G>C	p.Gly359Arg	p.G359R	ENST00000263967	NM_006218.2	359	Ggt/Cgt	6/21	1	2	FACETS	0.855	0.759	0.956	0.855	0.759	0.956	CLONAL	1	TRUE	1	0.514299632002809	2		321	373	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	344	1215	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.901	0.851	0.953	0.901	0.851	0.953	CLONAL	1	TRUE	1	0.514299632002809	2		1216	1484	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012564	36012564	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	203	568	0	ENST00000358208.4:c.8G>A	p.Ser3Asn	p.S3N	ENST00000358208		3	aGc/aAc	2/12	1	2	FACETS	0.992	0.922	1	0.992	0.922	1	CLONAL	1	TRUE	1	0.514299632002809	2		568	796	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229011	36229011	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	334	864	0	ENST00000222270.7:c.7795del	p.Glu2599ArgfsTer15	p.E2599Rfs*15	ENST00000222270	NM_014727.1	2597	gcG/gc	36/37	1	2	FACETS	0.995	0.94	1	0.995	0.94	1	CLONAL	1	TRUE	1	0.514299632002809	2		864	1305	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32971074	32971074	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	100	350	0	ENST00000380152.3:c.9541A>G	p.Met3181Val	p.M3181V	ENST00000380152		3181	Atg/Gtg	26/27	1	2	FACETS	0.896	0.805	0.991	0.896	0.805	0.991	CLONAL	1	TRUE	1	0.514299632002809	2		350	434	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166242	118166246	+	frameshift_variant	Frame_Shift_Del	DEL	TTGTG	TTGTG	-	novel	NA	P-0057184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	135	370	0	ENST00000369448.3:c.752_756del	p.Leu251ProfsTer31	p.L251Pfs*31	ENST00000369448	NM_017709.3	251	cTTGTG/c	2/2	1	2	FACETS	0.949	0.867	1	0.949	0.867	1	CLONAL	1	TRUE	1	0.514299632002809	2		370	553	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741857	162741857	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	172	467	0	ENST00000367921.3:c.1552del	p.Val518CysfsTer9	p.V518Cfs*9	ENST00000367921	NM_006182.2	516	gaG/ga	13/18	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.514299632002809	2		467	664	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978906	25978906	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	125	398	0	ENST00000435504.4:c.1017G>C	p.Trp339Cys	p.W339C	ENST00000435504		339	tgG/tgC	10/13	1	2	FACETS	0.976	0.888	1	0.976	0.888	1	CLONAL	1	TRUE	1	0.514299632002809	2		398	498	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42842668	42842668	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	159	593	0	ENST00000398585.3:c.1189C>A	p.Leu397Ile	p.L397I	ENST00000398585	NM_001135099.1	397	Cta/Ata	11/14	1	2	FACETS	0.728	0.668	0.791	0.728	0.668	0.791	SUBCLONAL	1	TRUE	1	0.514299632002809	2		593	849	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89791035	89791035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	48	171	0	ENST00000336032.3:c.422C>T	p.Pro141Leu	p.P141L	ENST00000336032	NM_006813.2	141	cCg/cTg	1/2	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.514299632002809	2		171	169	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	225	324	0				ENST00000310581	NM_198253.2	-/1132			0.408802625643506	3	FACETS	0.983	0.92	1	0.983	0.92	1	CLONAL	2	TRUE	1	0.422832282899969	3		324	656	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413214	139413214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	368	1214	0	ENST00000277541.6:c.928G>A	p.Gly310Arg	p.G310R	ENST00000277541	NM_017617.3	310	Ggg/Agg	6/34	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.422832282899969	2		1214	1407	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250787	26250787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	169	474	0	ENST00000446824.2:c.47C>T	p.Ala16Val	p.A16V	ENST00000446824	NM_021018.2	16	gCc/gTc	1/1	0.300167902966534	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.422832282899969	1		474	526	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218360	36218360	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0057185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	341	1050	0	ENST00000222270.7:c.4139C>G	p.Ser1380Ter	p.S1380*	ENST00000222270	NM_014727.1	1380	tCa/tGa	16/37	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.422832282899969	2		1050	1101	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450120	32450120	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1372808262	NA	P-0057185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	281	891	2	ENST00000332351.3:c.692C>T	p.Thr231Met	p.T231M	ENST00000332351	NM_024426.4	231	aCg/aTg	2/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.422832282899969	2		893	1085	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278162	15278162	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	277	1015	0	ENST00000263388.2:c.5260C>A	p.His1754Asn	p.H1754N	ENST00000263388	NM_000435.2	1754	Cat/Aat	29/33	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.422832282899969	2		1015	1137	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627877	37627877	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	277	675	0	ENST00000447079.4:c.1792C>G	p.Gln598Glu	p.Q598E	ENST00000447079	NM_015083.1	598	Cag/Gag	2/14	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.422832282899969	2		675	909	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166337	118166337	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	69	382	0	ENST00000369448.3:c.847G>A	p.Glu283Lys	p.E283K	ENST00000369448	NM_017709.3	283	Gaa/Aaa	2/2	0.300167902966534	1	FACETS	0.679	0.594	0.769	0.679	0.594	0.769	SUBCLONAL	1	TRUE	0	0.422832282899969	1		382	379	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567848	226567848	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	215	677	0	ENST00000366794.5:c.1318A>G	p.Asn440Asp	p.N440D	ENST00000366794	NM_001618.3	440	Aat/Gat	10/23	0.300167902966534	1	FACETS	0.938	0.873	1	0.938	0.873	1	CLONAL	1	TRUE	0	0.422832282899969	1		677	855	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246091256	246091256	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs566281194	NA	P-0057185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	175	477	0	ENST00000388985.4:c.679C>G	p.Arg227Gly	p.R227G	ENST00000388985		227	Cga/Gga	7/12	0.300167902966534	1	FACETS	0.957	0.884	1	0.957	0.884	1	CLONAL	1	TRUE	0	0.422832282899969	1		477	682	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108194	8108194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201709756	NA	P-0057185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	263	707	0	ENST00000585124.1:c.1030G>A	p.Ala344Thr	p.A344T	ENST00000585124	NM_004217.3	344	Gcc/Acc	9/9	0.422832282899969	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.422832282899969	1		707	676	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229588	5229588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	111	227	0	ENST00000357368.4:c.2263G>A	p.Gly755Ser	p.G755S	ENST00000357368	NM_002850.3	755	Ggc/Agc	15/38	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.422832282899969	2		227	364	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976543	18976581	+	inframe_deletion	In_Frame_Del	DEL	TCCCAGATGAGCCAGCCCGGCCTCTCCCAGCCGGAGCTG	TCCCAGATGAGCCAGCCCGGCCTCTCCCAGCCGGAGCTG	-	novel	NA	P-0057185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	216	1147	0	ENST00000262803.5:c.3199_3237del	p.Met1067_Gln1079del	p.M1067_Q1079del	ENST00000262803	NM_002911.3	1065	TCCCAGATGAGCCAGCCCGGCCTCTCCCAGCCGGAGCTG/-	22/24	1	2	FACETS	0.899	0.834	0.965	0.899	0.834	0.965	CLONAL	1	TRUE	1	0.422832282899969	2		1147	1137	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162727	47162727	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	24	404	0	ENST00000409792.3:c.3399del	p.His1134IlefsTer20	p.H1134Ifs*20	ENST00000409792	NM_014159.6	1133	ctT/ct	3/21	0.422832282899969	1	FACETS	0.227	0.177	0.284	0.227	0.177	0.284	SUBCLONAL	1	TRUE	0	0.422832282899969	1		404	395	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589833	55589833	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	163	431	1	ENST00000288135.5:c.1315G>A	p.Asp439Asn	p.D439N	ENST00000288135	NM_000222.2	439	Gat/Aat	8/21	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.422832282899969	2		432	586	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518942	187518942	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	172	409	0	ENST00000441802.2:c.12262C>T	p.Gln4088Ter	p.Q4088*	ENST00000441802	NM_005245.3	4088	Cag/Tag	24/27	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.422832282899969	2		409	717	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629122	187629123	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	189	512	0	ENST00000441802.2:c.1859dup	p.Asn620LysfsTer56	p.N620Kfs*56	ENST00000441802	NM_005245.3	620	aac/aaAc	2/27	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.422832282899969	2		512	751	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197092	26197095	+	frameshift_variant	Frame_Shift_Del	DEL	GCGA	GCGA	-	novel	NA	P-0057185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	94	569	0	ENST00000356476.2:c.384_387del	p.Arg129AlafsTer?	p.R129Afs*?	ENST00000356476		128	gcTCGC/gc	1/1	0.300167902966534	1	FACETS	0.502	0.446	0.561	0.502	0.446	0.561	SUBCLONAL	1	TRUE	0	0.422832282899969	1		569	699	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371977	55371977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771919828	NA	P-0057185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	287	932	1	ENST00000297316.4:c.667G>A	p.Asp223Asn	p.D223N	ENST00000297316	NM_022454.3	223	Gac/Aac	2/2	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.422832282899969	2		933	1005	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971079	21971079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	251	837	0	ENST00000579755.1:c.322G>A	p.Ala108Thr	p.A108T	ENST00000579755		108	Gct/Act	2/3	0.422832282899969	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.422832282899969	1		837	677	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413093	139413093	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	272	937	0	ENST00000277541.6:c.1049G>T	p.Cys350Phe	p.C350F	ENST00000277541	NM_017617.3	350	tGc/tTc	6/34	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.422832282899969	2		937	1105	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0057186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	246	306	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.616551797790055	2		306	605	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0057186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	182	1096	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.562538666315463	1	FACETS	0.369	0.339	0.399	0.369	0.339	0.399	SUBCLONAL	1	TRUE	0	0.616551797790055	1		1096	1108	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120085	70120085	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	60	69	0	ENST00000245479.2:c.1087C>T	p.Gln363Ter	p.Q363*	ENST00000245479	NM_000346.3	363	Cag/Tag	3/3	0.616551797790055	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.616551797790055	2		69	87	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375019	45375019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	129	397	0	ENST00000262160.6:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000262160	NM_005901.5	275	tGt/tAt	8/11	0.562538666315463	1	FACETS	0.76	0.696	0.825	0.76	0.696	0.825	SUBCLONAL	1	TRUE	0	0.616551797790055	1		397	381	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0057186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	90	355	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	1	2	FACETS	0.626	0.558	0.699	0.626	0.558	0.699	SUBCLONAL	1	TRUE	1	0.616551797790055	2		355	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0057186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	229	829	1	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	0.562538666315463	1	FACETS	0.724	0.677	0.771	0.724	0.677	0.771	SUBCLONAL	1	TRUE	0	0.616551797790055	1		830	710	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473692	67473692	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	482	721	0	ENST00000327367.4:c.772G>A	p.Asp258Asn	p.D258N	ENST00000327367	NM_005902.3	258	Gat/Aat	6/9	0.505878697280997	2	FACETS	0.825	0.793	0.856	0.825	0.793	0.856	CLONAL	2	TRUE	0	0.616551797790055	2		721	948	SUCCESS
APC	324	MSKCC	GRCh37	5	112175302	112175303	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	CT	novel	NA	P-0057186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	178	209	2	ENST00000257430.4:c.4011_4012delinsCT	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1337	ctGCag/ctCTag	16/16	NA	2	FACETS	1	0.974	1			1	INDETERMINATE	2	TRUE	NA	0.616551797790055	2		211	275	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538990	23538990	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775943527	NA	P-0057186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	161	724	2	ENST00000380871.4:c.449C>T	p.Ser150Leu	p.S150L	ENST00000380871	NM_006167.3	150	tCg/tTg	2/2	1	2	FACETS	0.709	0.651	0.768	0.709	0.651	0.768	SUBCLONAL	1	TRUE	1	0.616551797790055	2		726	737	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575188	48575188	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	29	279	0	ENST00000342988.3:c.382G>A	p.Val128Met	p.V128M	ENST00000342988	NM_005359.5	128	Gtg/Atg	3/12	0.562538666315463	1	FACETS	0.174	0.139	0.213	0.174	0.139	0.213	SUBCLONAL	1	TRUE	0	0.616551797790055	1		279	375	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588885	69588885	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	36	794	0	ENST00000168712.1:c.351G>T	p.Glu117Asp	p.E117D	ENST00000168712	NM_002007.2	117	gaG/gaT	2/3	1	2	FACETS	0.183	0.15	0.221	0.183	0.15	0.221	SUBCLONAL	1	TRUE	1	0.616551797790055	2		794	637	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987141	36987141	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	71	1114	0	ENST00000354822.5:c.548T>G	p.Met183Arg	p.M183R	ENST00000354822	NM_001079668.2	183	aTg/aGg	3/3	1	2	FACETS	0.211	0.183	0.241	0.211	0.183	0.241	SUBCLONAL	1	TRUE	1	0.616551797790055	2		1114	1093	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858532	9858533	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	137	551	0	ENST00000330684.3:c.2868dup	p.Gly957TrpfsTer18	p.G957Wfs*18	ENST00000330684	NM_001134407.1	956	-/T	13/13	1	2	FACETS	0.727	0.664	0.794	0.727	0.664	0.794	SUBCLONAL	1	TRUE	1	0.616551797790055	2		551	611	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556046	29556046	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	109	239	0	ENST00000356175.3:c.2413G>A	p.Ala805Thr	p.A805T	ENST00000356175	NM_000267.3	805	Gct/Act	21/57	1	2	FACETS	0.826	0.747	0.909	0.826	0.747	0.909	CLONAL	1	TRUE	1	0.616551797790055	2		239	428	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	99	330	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.876	0.785	0.973	1	0.985	1	CLONAL	2	TRUE	1	0.21	2		330	538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0057187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	116	789	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.21	2		789	813	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740620	145740620	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	167	1004	0	ENST00000428558.2:c.1397C>G	p.Pro466Arg	p.P466R	ENST00000428558	NM_004260.3	466	cCg/cGg	8/22	0.132851476435898	3	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	1	0.21	3		1004	874	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188187	32188187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754712190	NA	P-0057187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	52	685	0	ENST00000375023.3:c.1154G>A	p.Arg385His	p.R385H	ENST00000375023	NM_004557.3	385	cGc/cAc	6/30	1	2	FACETS	0.902	0.768	1	0.902	0.768	1	CLONAL	1	TRUE	1	0.21	2		685	549	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042646	42042647	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	62	490	0	ENST00000219905.7:c.6842dup	p.Gln2282ThrfsTer14	p.Q2282Tfs*14	ENST00000219905	NM_001164273.1	2281	ata/aTta	17/24	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.21	2		490	524	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76953101	76953101	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	40	446	0	ENST00000373344.5:c.212C>G	p.Ser71Cys	p.S71C	ENST00000373344	NM_000489.3	71	tCc/tGc	4/35	1	2	FACETS	0.698	0.579	0.83	0.698	0.579	0.83	SUBCLONAL	1	TRUE	1	0.21	2		446	546	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	65	324	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.556	0.481	0.638	0.556	0.481	0.638	SUBCLONAL	1	TRUE	1	0.272989149688452	2		324	857	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0057189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1340	399	734	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.216904084579895	2	FACETS	0.84	0.797	0.885	0.84	0.797	0.885	CLONAL	2	TRUE	0	0.272989149688452	2		734	1739	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720670	89720670	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786204875	NA	P-0057189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	35	311	0	ENST00000371953.3:c.821G>A	p.Trp274Ter	p.W274*	ENST00000371953	NM_000314.4	274	tGg/tAg	8/9	0.175206136068078	2	FACETS	0.809	0.665	0.969	0.404	0.332	0.485	CLONAL	1	TRUE	0	0.272989149688452	2		311	317	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355326	81355326	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	27	191	0	ENST00000222390.5:c.1048C>T	p.Arg350Ter	p.R350*	ENST00000222390	NM_000601.4	350	Cga/Tga	9/18	0.272989149688452	3	FACETS	0.667	0.531	0.822	0.334	0.265	0.411	SUBCLONAL	1	TRUE	1	0.272989149688452	3		191	337	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033199	69033199	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1032023587	NA	P-0057189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	84	357	1	ENST00000288368.4:c.3639G>T	p.Arg1213Ser	p.R1213S	ENST00000288368	NM_024870.2	1213	agG/agT	30/40	1	2	FACETS	0.841	0.742	0.946	0.841	0.742	0.946	CLONAL	1	TRUE	1	0.272989149688452	2		358	732	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922286	39922286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	102	164	0	ENST00000378444.4:c.3886C>T	p.Leu1296Phe	p.L1296F	ENST00000378444	NM_001123385.1	1296	Ctt/Ttt	9/15	0.117483208967117	2	FACETS	0.961	0.866	1			1	INDETERMINATE	2	TRUE	NA	0.272989149688452	2		164	389	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0057190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	37	473	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.586195482175748	3	FACETS	0.978	0.842	1	1	0.971	1	CLONAL	4	TRUE	1	0.28	3		473	77	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572932	7572932	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	32	452	0	ENST00000269305.4:c.1177G>C	p.Asp393His	p.D393H	ENST00000269305	NM_001126112.2	393	Gac/Cac	11/11	0.34258771692717	3	FACETS	1	0.878	1	1	0.878	1	CLONAL	2	TRUE	1	0.28	3		452	121	SUCCESS
APC	324	MSKCC	GRCh37	5	112174001	112174002	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1554084403	NA	P-0057190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	12	227	0	ENST00000257430.4:c.2711_2712del	p.Arg904LysfsTer7	p.R904Kfs*7	ENST00000257430	NM_000038.5	904	AGa/a	16/16	0.157845125635647	4	FACETS	0.885	0.659	1	1	0.905	1	INDETERMINATE	4	TRUE	2	0.28	4		227	31	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922279	39922289	+	frameshift_variant	Frame_Shift_Del	DEL	GATGAAAGACT	GATGAAAGACT	-	novel	NA	P-0057190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	62	423	0	ENST00000378444.4:c.3883_3893del	p.Ser1295HisfsTer27	p.S1295Hfs*27	ENST00000378444	NM_001123385.1	1295	AGTCTTTCATCc/c	9/15	1	2	FACETS	1	0.927	1	1	0.987	1	CLONAL	4	TRUE	1	0.28	2		423	107	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410811	63410811	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0057190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	10	619	0	ENST00000330258.3:c.2356A>T	p.Met786Leu	p.M786L	ENST00000330258	NM_152424.3	786	Atg/Ttg	2/2	0.34258771692717	0	FACETS	0.779	0.553	1			1	CLONAL	2	TRUE	0	0.28	0		619	33	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782241	56782241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	92	472	0	ENST00000308159.5:c.82C>T	p.His28Tyr	p.H28Y	ENST00000308159	NM_014669.4	28	Cat/Tat	2/22	0.366051139859612	3	FACETS	0.837	0.746	0.933	0.419	0.373	0.467	CLONAL	1	TRUE	1	0.550704525887741	3		472	509	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0057193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	228	633	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.50965326605706	4	FACETS	1	0.959	1	0.348	0.323	0.373	CLONAL	1	TRUE	1	0.550428397424353	4		633	1231	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376300	225376300	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0057193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	150	203	0	ENST00000264414.4:c.655-1G>A		p.X219_splice	ENST00000264414	NM_003590.4	219			0.550428397424353	4	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	2	0.550428397424353	4		203	395	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836803	151836803	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	338	459	0	ENST00000262189.6:c.14417G>T	p.Arg4806Leu	p.R4806L	ENST00000262189	NM_170606.2	4806	cGa/cTa	56/59	0.550428397424353	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.550428397424353	3		459	738	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577527	7577532	+	inframe_deletion	In_Frame_Del	DEL	GGATGG	GGATGG	-	novel	NA	P-0057193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	368	674	0	ENST00000269305.4:c.749_754del	p.Pro250_Ile251del	p.P250_I251del	ENST00000269305	NM_001126112.2	250	cCCATCCtc/ctc	7/11	0.550428397424353	2	FACETS	0.89	0.851	0.93	0.89	0.851	0.93	CLONAL	2	TRUE	0	0.550428397424353	2		674	751	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0057194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	233	359	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.571352197264415	5	FACETS	0.903	0.85	0.957	0.903	0.85	0.957	CLONAL	3	TRUE	2	0.571352197264415	5		359	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0057194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	327	628	0	ENST00000269305.4:c.375+1del		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.571352197264415	2	FACETS	0.995	0.952	1	0.995	0.952	1	CLONAL	2	TRUE	0	0.571352197264415	2		628	575	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539540	187539540	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	120	357	1	ENST00000441802.2:c.8200C>A	p.Leu2734Ile	p.L2734I	ENST00000441802	NM_005245.3	2734	Ctt/Att	10/27	0.571352197264415	2	FACETS	1	0.966	1	0.559	0.509	0.609	CLONAL	1	TRUE	0	0.571352197264415	2		358	376	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293562	1293562	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs776712013	NA	P-0057194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	797	1237	0	ENST00000310581.5:c.1439C>G	p.Ser480Cys	p.S480C	ENST00000310581	NM_198253.2	480	tCc/tGc	2/16	0.510206852929504	5	FACETS	1	0.987	1			1	CLONAL	3	TRUE	NA	0.571352197264415	5		1237	1671	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294000	1294000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1420805598	NA	P-0057194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	975	1241	0	ENST00000310581.5:c.1001C>T	p.Ser334Phe	p.S334F	ENST00000310581	NM_198253.2	334	tCc/tTc	2/16	0.510206852929504	5	FACETS	1	0.996	1			1	CLONAL	3	TRUE	NA	0.571352197264415	5		1241	1857	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294550	1294550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	745	924	0	ENST00000310581.5:c.451C>T	p.His151Tyr	p.H151Y	ENST00000310581	NM_198253.2	151	Cac/Tac	2/16	0.510206852929504	5	FACETS	1	0.99	1			1	CLONAL	3	TRUE	NA	0.571352197264415	5		924	1536	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295417	1295417	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0057194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	155	159	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.997	0.935	1			1	INDETERMINATE	2	TRUE	NA	0.571352197264415	2		159	272	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391859	139391859	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	268	1125	0	ENST00000277541.6:c.6332G>C	p.Arg2111Thr	p.R2111T	ENST00000277541	NM_017617.3	2111	aGg/aCg	34/34	0.571352197264415	3	FACETS	1	0.972	1	0.354	0.331	0.377	CLONAL	1	TRUE	0	0.571352197264415	3		1125	1136	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0057195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	451	330	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.261734971448109	3	FACETS	0.869	0.833	0.904	1	0.995	1	INDETERMINATE	3	TRUE	1	0.438777539656393	3		330	962	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0057195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	800	724	2	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.438777539656393	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.438777539656393	3		726	1382	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0057195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	539	1140	1	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	0.357345526341548	2	FACETS	0.888	0.853	0.924	0.888	0.853	0.924	CLONAL	2	TRUE	0	0.438777539656393	2		1141	1383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577560	7577560	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520002	NA	P-0057195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	289	699	0	ENST00000269305.4:c.721T>G	p.Ser241Ala	p.S241A	ENST00000269305	NM_001126112.2	241	Tcc/Gcc	7/11	0.280445528649923	2	FACETS	1	0.99	1	0.614	0.577	0.651	CLONAL	1	TRUE	0	0.438777539656393	2		699	1073	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0057196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	285	604	0	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	0.3	3	FACETS	0.992	0.933	1	0.662	0.622	0.702	CLONAL	2	FALSE	0	0.3	3		604	1101	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0057196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	362	510	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.3	7	FACETS	1	0.965	1	0.815	0.774	0.857	CLONAL	4	FALSE	2	0.3	7		510	1036	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	119	324	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.798	0.723	0.878	0.798	0.723	0.878	SUBCLONAL	1	TRUE	1	0.503574686841942	2		324	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540652	NA	P-0057197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	323	765	0	ENST00000269305.4:c.743G>C	p.Arg248Pro	p.R248P	ENST00000269305	NM_001126112.2	248	cGg/cCg	7/11	0.475096476119113	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.503574686841942	1		765	929	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0057198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	322	951	0	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.380043988704266	2		951	1468	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533854	533854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	326	887	0	ENST00000451590.1:c.202C>T	p.Arg68Trp	p.R68W	ENST00000451590	NM_001130442.1	68	Cgg/Tgg	3/5	0.190611341408068	1	FACETS	1	0.961	1	1	0.961	1	INDETERMINATE	1	TRUE	0	0.380043988704266	1		887	1357	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719382	190719382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1016802650	NA	P-0057198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	88	224	0	ENST00000441310.2:c.1384G>A	p.Val462Ile	p.V462I	ENST00000441310	NM_000534.4	462	Gtt/Att	9/13	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.380043988704266	2		224	426	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970867	55970867	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	158	456	0	ENST00000263923.4:c.1930G>T	p.Ala644Ser	p.A644S	ENST00000263923	NM_002253.2	644	Gct/Tct	13/30	0.190611341408068	1	FACETS	0.808	0.74	0.878	0.808	0.74	0.878	INDETERMINATE	1	TRUE	0	0.380043988704266	1		456	834	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0057201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	295	650	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.280169761129759	1	FACETS	0.645	0.614	0.676	0.645	0.614	0.676	INDETERMINATE	1	TRUE	0	0.887679403175775	1		650	573	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0057201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	142	531	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.97	0.897	1	0.97	0.897	1	CLONAL	1	TRUE	1	0.887679403175775	2		531	330	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121796	2121796	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	385	1130	0	ENST00000219476.3:c.1958G>C	p.Arg653Thr	p.R653T	ENST00000219476	NM_000548.3	653	aGa/aCa	19/42	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.887679403175775	2		1130	813	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806618	1806618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	303	1038	1	ENST00000260795.2:c.1334C>T	p.Ser445Leu	p.S445L	ENST00000260795		445	tCa/tTa	9/17	0.280169761129759	1	FACETS	0.615	0.585	0.646	0.615	0.585	0.646	INDETERMINATE	1	TRUE	0	0.887679403175775	1		1039	617	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806606	1806606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	310	1030	1	ENST00000260795.2:c.1322C>T	p.Ala441Val	p.A441V	ENST00000260795		441	gCa/gTa	9/17	0.280169761129759	1	FACETS	0.626	0.595	0.656	0.626	0.595	0.656	INDETERMINATE	1	TRUE	0	0.887679403175775	1		1031	621	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845732	151845732	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	297	541	0	ENST00000262189.6:c.13280G>T	p.Trp4427Leu	p.W4427L	ENST00000262189	NM_170606.2	4427	tGg/tTg	52/59	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.887679403175775	2		541	641	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879957	44879958	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	191	185	0	ENST00000377967.4:c.547dup	p.Tyr183LeufsTer2	p.Y183Lfs*2	ENST00000377967	NM_021140.2	182	-/T	6/29	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.887679403175775	1		185	224	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0057209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	216	670	0	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.653353176399112	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	0	0.653353176399112	1		670	382	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271534	26271534	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	80	292	0	ENST00000305910.3:c.79C>T	p.Arg27Trp	p.R27W	ENST00000305910	NM_003534.2	27	Cgg/Tgg	1/1	0.635678140598792	4	FACETS	1	0.974	1			1	CLONAL	1	FALSE	NA	0.653353176399112	4		292	300	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843441	3843441	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	115	374	0	ENST00000262367.5:c.1162A>C	p.Met388Leu	p.M388L	ENST00000262367	NM_004380.2	388	Atg/Ctg	4/31	1	2	FACETS	0.992	0.903	1	0.992	0.903	1	CLONAL	1	FALSE	1	0.653353176399112	2		374	355	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411880	116411897	+	splice_region_variant,intron_variant	Splice_Region	DEL	TCTTTCTTTCTCTCTGTT	TCTTTCTTTCTCTCTGTT	-	novel	NA	P-0057210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	98	954	0	ENST00000397752.3:c.2888-22_2888-5del		p.X963_splice	ENST00000397752	NM_000245.2	963			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		954	647	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	219	504	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	1	0.314019235797354	2		504	585	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	660	900	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.173941924946574	4	FACETS	1	0.987	1	1	0.998	1	INDETERMINATE	6	TRUE	2	0.314019235797354	4		904	905	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	28	388	3	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.367	0.292	0.452	0.367	0.292	0.452	SUBCLONAL	1	TRUE	1	0.314019235797354	2		391	486	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143994	11143994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	44	561	0	ENST00000358026.2:c.3575G>A	p.Arg1192His	p.R1192H	ENST00000358026	NM_001128849.1	1192	cGc/cAc	26/36	1	2	FACETS	0.497	0.416	0.586	0.497	0.416	0.586	SUBCLONAL	1	TRUE	1	0.314019235797354	2		561	564	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	38	793	2	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	0.314019235797354	1	FACETS	0.367	0.303	0.439	0.367	0.303	0.439	SUBCLONAL	1	TRUE	0	0.314019235797354	1		795	556	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	235	390	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	0.173941924946574	4	FACETS	1	0.979	1	1	0.994	1	INDETERMINATE	3	TRUE	2	0.314019235797354	4		390	602	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527809	157527809	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374035954	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	161	412	0	ENST00000346085.5:c.5534G>A	p.Arg1845His	p.R1845H	ENST00000346085	NM_020732.3	1845	cGc/cAc	20/20	1	2	FACETS	1	0.978	1	1	0.993	1	CLONAL	2	TRUE	1	0.314019235797354	2		412	449	SUCCESS
ATR	545	MSKCC	GRCh37	3	142241619	142241619	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1474267384	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	157	427	0	ENST00000350721.4:c.4217C>T	p.Ala1406Val	p.A1406V	ENST00000350721	NM_001184.3	1406	gCg/gTg	23/47	0.128874290008779	3	FACETS	1	0.935	1	1	0.935	1	INDETERMINATE	2	TRUE	1	0.314019235797354	3		427	569	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	17	202	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.523	0.391	0.679	0.523	0.391	0.679	SUBCLONAL	1	TRUE	1	0.314019235797354	2		202	207	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354008	15354008	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	17	306	0	ENST00000263377.2:c.2872del	p.Leu958CysfsTer110	p.L958Cfs*110	ENST00000263377	NM_058243.2	958	Ctg/tg	14/20	1	2	FACETS	0.446	0.333	0.579	0.446	0.333	0.579	SUBCLONAL	1	TRUE	1	0.314019235797354	2		306	243	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	85	336	0	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.314019235797354	2		336	426	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651438	52651438	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	251	492	1	ENST00000394830.3:c.1658del	p.Lys553ArgfsTer16	p.K553Rfs*16	ENST00000394830	NM_018313.4	553	aAg/ag	15/30	0.128874290008779	3	FACETS	0.919	0.865	0.974	1	0.992	1	INDETERMINATE	3	TRUE	1	0.314019235797354	3		493	671	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514998	148515000	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs775039041	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	131	472	1	ENST00000320356.2:c.1209_1211del	p.Glu404del	p.E404del	ENST00000320356	NM_004456.4	403	gaAGAg/gag	10/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.314019235797354	2		473	624	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822563	72822564	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	rs376311468	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	130	648	0	ENST00000268489.5:c.9609_9611dup	p.Gln3204dup	p.Q3204dup	ENST00000268489	NM_006885.3	3204	caa/caGCAa	10/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.314019235797354	2		648	621	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584684	187584684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149295542	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	36	442	0	ENST00000441802.2:c.3349G>A	p.Val1117Met	p.V1117M	ENST00000441802	NM_005245.3	1117	Gtg/Atg	3/27	1	2	FACETS	0.42	0.344	0.505	0.42	0.344	0.505	SUBCLONAL	1	TRUE	1	0.314019235797354	2		442	546	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087513	27087513	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	59	803	0	ENST00000324856.7:c.2090del	p.Pro697ArgfsTer45	p.P697Rfs*45	ENST00000324856	NM_006015.4	696	tCc/tc	5/20	1	2	FACETS	0.438	0.376	0.506	0.438	0.376	0.506	SUBCLONAL	1	TRUE	1	0.314019235797354	2		803	858	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339535	81339535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1192583398	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	47	383	1	ENST00000222390.5:c.1469C>T	p.Thr490Met	p.T490M	ENST00000222390	NM_000601.4	490	aCg/aTg	13/18	1	2	FACETS	0.5	0.421	0.587	0.5	0.421	0.587	SUBCLONAL	1	TRUE	1	0.314019235797354	2		384	599	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	225	519	1	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.945	0.883	1	1	0.994	1	CLONAL	2	TRUE	1	0.314019235797354	2		520	758	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647657	3647657	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs774532876	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	297	941	6	ENST00000294008.3:c.1406del	p.Pro469HisfsTer4	p.P469Hfs*4	ENST00000294008	NM_032444.2	469	cCa/ca	7/15	1	2	FACETS	1	0.984	1	1	0.996	1	CLONAL	2	TRUE	1	0.314019235797354	2		947	852	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	49	819	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.389	0.328	0.456	0.389	0.328	0.456	SUBCLONAL	1	TRUE	1	0.314019235797354	2		819	803	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309037	137309037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs537231520	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	78	944	1	ENST00000481739.1:c.644G>A	p.Arg215Gln	p.R215Q	ENST00000481739	NM_002957.4	215	cGg/cAg	5/10	1	2	FACETS	0.623	0.546	0.705	0.623	0.546	0.705	SUBCLONAL	1	TRUE	1	0.314019235797354	2		945	798	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112326	115112326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1302202171	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	19	327	0	ENST00000257566.3:c.1414G>A	p.Ala472Thr	p.A472T	ENST00000257566	NM_016569.3	472	Gcg/Acg	7/8	1	2	FACETS	0.457	0.347	0.586	0.457	0.347	0.586	SUBCLONAL	1	TRUE	1	0.314019235797354	2		327	265	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282041	38282041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	271	886	0	ENST00000425967.3:c.1015G>A	p.Val339Ile	p.V339I	ENST00000425967	NM_001174067.1	339	Gtc/Atc	8/19	0.128874290008779	3	FACETS	1	0.983	1	1	0.983	1	INDETERMINATE	2	TRUE	1	0.314019235797354	3		886	894	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375783	118375783	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782800112	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	124	414	0	ENST00000534358.1:c.9176C>T	p.Pro3059Leu	p.P3059L	ENST00000534358	NM_005933.3	3059	cCg/cTg	27/36	1	2	FACETS	0.86	0.784	0.94	1	0.988	1	CLONAL	2	TRUE	1	0.314019235797354	2		414	459	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27203007	27203007	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	108	533	0	ENST00000380036.4:c.2099A>G	p.Lys700Arg	p.K700R	ENST00000380036	NM_000459.3	700	aAg/aGg	13/23	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.314019235797354	2		533	567	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221616	36221616	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	282	816	0	ENST00000222270.7:c.5285G>A	p.Arg1762His	p.R1762H	ENST00000222270	NM_014727.1	1762	cGt/cAt	26/37	1	2	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	TRUE	1	0.314019235797354	2		816	729	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101394	27101394	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	42	539	1	ENST00000324856.7:c.4679del	p.Pro1560LeufsTer5	p.P1560Lfs*5	ENST00000324856	NM_006015.4	1559	gCc/gc	18/20	1	2	FACETS	0.501	0.418	0.593	0.501	0.418	0.593	SUBCLONAL	1	TRUE	1	0.314019235797354	2		540	534	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720674	89720675	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	108	234	0	ENST00000371953.3:c.826_827del	p.Asn276TyrfsTer21	p.N276Yfs*21	ENST00000371953	NM_000314.4	275	gtAAat/gtat	8/9	1	2	FACETS	1	0.934	1	1	0.989	1	CLONAL	2	TRUE	1	0.314019235797354	2		234	332	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200076	67200076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1208765540	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	45	577	0	ENST00000312629.5:c.463G>A	p.Glu155Lys	p.E155K	ENST00000312629	NM_003952.2	155	Gag/Aag	6/15	1	2	FACETS	0.487	0.408	0.573	0.487	0.408	0.573	SUBCLONAL	1	TRUE	1	0.314019235797354	2		577	589	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343302	118343303	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	21	324	0	ENST00000534358.1:c.1431_1432del	p.Arg478IlefsTer2	p.R478Ifs*2	ENST00000534358	NM_005933.3	476	tcCTct/tcct	3/36	1	2	FACETS	0.359	0.276	0.456	0.359	0.276	0.456	SUBCLONAL	1	TRUE	1	0.314019235797354	2		324	373	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830455	72830455	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	99	388	0	ENST00000268489.5:c.6126del	p.Pro2044LeufsTer57	p.P2044Lfs*57	ENST00000268489	NM_006885.3	2042	ccT/cc	9/10	1	2	FACETS	0.8	0.72	0.884	1	0.984	1	SUBCLONAL	2	TRUE	1	0.314019235797354	2		388	394	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349641	89349642	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	53	813	0	ENST00000301030.4:c.3308_3309del	p.Lys1103ArgfsTer2	p.K1103Rfs*2	ENST00000301030	NM_001256183.1	1103	aAA/a	9/13	1	2	FACETS	0.396	0.337	0.462	0.396	0.337	0.462	SUBCLONAL	1	TRUE	1	0.314019235797354	2		813	852	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945668	17945668	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	216	742	1	ENST00000458235.1:c.2192C>A	p.Pro731His	p.P731H	ENST00000458235	NM_000215.3	731	cCt/cAt	16/24	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.314019235797354	2		743	593	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753176	42753176	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs538236832	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	244	814	3	ENST00000222329.4:c.1088C>T	p.Ser363Leu	p.S363L	ENST00000222329	NM_006494.2	363	tCg/tTg	4/4	1	2	FACETS	1	0.979	1	1	0.995	1	CLONAL	2	TRUE	1	0.314019235797354	2		817	710	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202767	128202767	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	296	760	0	ENST00000341105.2:c.953C>A	p.Ala318Asp	p.A318D	ENST00000341105	NM_032638.4	318	gCc/gAc	4/6	0.128874290008779	3	FACETS	0.893	0.844	0.943	1	0.993	1	INDETERMINATE	3	TRUE	1	0.314019235797354	3		760	814	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977980	131977980	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs202098299	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	165	370	0	ENST00000265335.6:c.3863G>T	p.Arg1288Met	p.R1288M	ENST00000265335		1288	aGg/aTg	25/25	1	2	FACETS	1	0.982	1	1	0.993	1	CLONAL	2	TRUE	1	0.314019235797354	2		370	442	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31946678	31946680	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGA	AGA	-	novel	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	168	463	0	ENST00000375333.2:c.568_570del		p.X190_splice	ENST00000375333	NM_032454.1	190		4/8	1	2	FACETS	1	0.97	1	1	0.993	1	CLONAL	2	TRUE	1	0.314019235797354	2		463	492	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266417	55266420	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	novel	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	203	442	0	ENST00000275493.2:c.2711_2714del	p.Val904GlyfsTer3	p.V904Gfs*3	ENST00000275493	NM_005228.3	903	acTGTT/ac	23/28	1	2	FACETS	0.881	0.826	0.938	1	0.995	1	CLONAL	3	TRUE	1	0.314019235797354	2		442	489	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994210	21994211	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	101	597	0	ENST00000579755.1:c.120dup	p.Ala41ArgfsTer22	p.A41Rfs*22	ENST00000579755		40	-/C	1/3	1		FACETS		0.855	1				CLONAL	1	TRUE	1	0.314019235797354	2		597	673	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908771	101908771	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1554702207	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	95	272	0	ENST00000374994.4:c.1135A>G	p.Met379Val	p.M379V	ENST00000374994	NM_004612.2	379	Atg/Gtg	7/9	1	2	FACETS	0.917	0.825	1	1	0.986	1	CLONAL	2	TRUE	1	0.314019235797354	2		272	330	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209138	36209153	+	frameshift_variant	Frame_Shift_Del	DEL	TCCGCCGGGGCCTGCG	TCCGCCGGGGCCTGCG	-	novel	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	12	29	0	ENST00000222270.7:c.218_233del	p.Leu73ProfsTer89	p.L73Pfs*89	ENST00000222270	NM_014727.1	73	cTCCGCCGGGGCCTGCGc/cc	1/37	1	2	FACETS	0.98	0.719	1	1	0.908	1	CLONAL	2	TRUE	1	0.314019235797354	2		29	39	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591126	67591129	+	protein_altering_variant	In_Frame_Del	DEL	GAGA	GAGA	T	novel	NA	P-0057211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	109	252	0	ENST00000274335.5:c.1719_1722delinsT	p.Arg574del	p.R574del	ENST00000274335		573	ctGAGA/ctT	12/15	1	2	FACETS	1	0.911	1	1	0.989	1	CLONAL	2	TRUE	1	0.314019235797354	2		252	346	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221785	55221786	+	missense_variant	Missense_Mutation	DNP	AT	AT	GA	novel	NA	P-0057213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	142	624	1	ENST00000275493.2:c.829_830delinsGA	p.Met277Glu	p.M277E	ENST00000275493	NM_005228.3	277	ATg/GAg	7/28	0.615573534219289	3	FACETS	0.766	0.698	0.836	0.255	0.232	0.279	SUBCLONAL	1	FALSE	0	0.627014934669878	3		625	777	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875096	151875097	+	splice_acceptor_variant	Splice_Site	INS	-	-	TT	rs753425356	NA	P-0057213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	16	65	0	ENST00000262189.6:c.7443-3_7443-2dup		p.X2481_splice	ENST00000262189	NM_170606.2	2481			0.615573534219289	3	FACETS	0.664	0.497	0.856	0.221	0.165	0.286	SUBCLONAL	1	FALSE	0	0.627014934669878	3		65	101	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884448	151884448	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773744238	NA	P-0057213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	162	295	0	ENST00000262189.6:c.4907C>T	p.Thr1636Met	p.T1636M	ENST00000262189	NM_170606.2	1636	aCg/aTg	33/59	0.615573534219289	3	FACETS	0.851	0.79	0.912	0.567	0.526	0.608	CLONAL	2	FALSE	0	0.627014934669878	3		295	399	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249413	110249413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	83	957	0	ENST00000374672.4:c.1160C>T	p.Ser387Leu	p.S387L	ENST00000374672	NM_004235.4	387	tCg/tTg	4/5	1	2	FACETS	0.256	0.225	0.289	0.256	0.225	0.289	SUBCLONAL	1	FALSE	1	0.627014934669878	2		957	1034	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225314	2225314	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	61	612	1	ENST00000326181.6:c.1399C>T	p.Gln467Ter	p.Q467*	ENST00000326181	NM_032271.2	467	Cag/Tag	16/21	NA	2	FACETS	0.305	0.263	0.352			1	INDETERMINATE	1	FALSE	NA	0.627014934669878	2		613	637	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627381	37627381	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	229	516	0	ENST00000447079.4:c.1296C>G	p.Asn432Lys	p.N432K	ENST00000447079	NM_015083.1	432	aaC/aaG	2/14	0.618431130370698	3	FACETS	1	0.991	1	0.451	0.422	0.481	CLONAL	1	FALSE	0	0.627014934669878	3		516	709	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519999	NA	P-0057214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	242	577	0	ENST00000269305.4:c.716A>C	p.Asn239Thr	p.N239T	ENST00000269305	NM_001126112.2	239	aAc/aCc	7/11	0.512686246637582	2	FACETS	0.982	0.93	1	0.982	0.93	1	CLONAL	2	TRUE	0	0.527599481369938	2		577	467	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149245729	149245729	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs762463839	NA	P-0057214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	182	523	0	ENST00000360632.3:c.799A>G	p.Met267Val	p.M267V	ENST00000360632	NM_015472.4	267	Atg/Gtg	5/7	0.263495602614014	5	FACETS	1	0.965	1	0.71	0.659	0.763	INDETERMINATE	2	TRUE	2	0.527599481369938	5		523	580	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402705	20402705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	67	531	1	ENST00000346618.3:c.242C>T	p.Ala81Val	p.A81V	ENST00000346618	NM_001949.4	81	gCc/gTc	1/7	0.47146762633813	2	FACETS	0.651	0.568	0.74	0.326	0.284	0.37	SUBCLONAL	1	TRUE	0	0.527599481369938	2		532	390	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205174	123205174	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0057214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	83	152	0	ENST00000218089.9:c.2533+1G>A		p.X845_splice	ENST00000218089	NM_001042749.1	845			0.499532356787765	2	FACETS	0.819	0.74	0.9			1	CLONAL	2	TRUE	NA	0.527599481369938	2		152	192	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574020	7574021	+	inframe_insertion	In_Frame_Ins	INS	-	-	CACGCC	novel	NA	P-0057215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	488	524	0	ENST00000269305.4:c.1001_1006dup	p.Gly334_Arg335dup	p.G334_R335dup	ENST00000269305	NM_001126112.2	334	gag/gGGCGTGag	10/11	0.123715110788723	4	FACETS	1	0.985	1			1	INDETERMINATE	3	TRUE	NA	0.73215424962759	4		524	748	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105258941	105258941	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	171	620	0	ENST00000349310.3:c.40A>G	p.Lys14Glu	p.K14E	ENST00000349310	NM_001014432.1	14	Aaa/Gaa	3/15	0.496605131015103	3	FACETS	0.897	0.828	0.97			1	CLONAL	1	TRUE	NA	0.73215424962759	3		620	711	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416728	121416728	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759053189	NA	P-0057216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	297	832	1	ENST00000257555.6:c.157G>A	p.Gly53Ser	p.G53S	ENST00000257555		53	Ggt/Agt	1/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.787726071550758	2		833	685	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482846	67482846	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	221	516	0	ENST00000327367.4:c.1250C>G	p.Pro417Arg	p.P417R	ENST00000327367	NM_005902.3	417	cCa/cGa	9/9	0.787726071550758	3	FACETS	1	0.942	1	0.505	0.471	0.54	CLONAL	1	TRUE	1	0.787726071550758	3		516	774	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632559	3632559	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	184	804	0	ENST00000294008.3:c.5289G>C	p.Lys1763Asn	p.K1763N	ENST00000294008	NM_032444.2	1763	aaG/aaC	15/15	0.19990837097085	4	FACETS	0.846	0.781	0.914			1	INDETERMINATE	1	TRUE	NA	0.787726071550758	4		804	987	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779209	3779209	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	164	519	0	ENST00000262367.5:c.5839C>G	p.Pro1947Ala	p.P1947A	ENST00000262367	NM_004380.2	1947	Ccc/Gcc	31/31	0.19990837097085	4	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.787726071550758	4		519	529	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41197788	41197788	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	232	577	0	ENST00000357654.3:c.5499del	p.Thr1834ProfsTer9	p.T1834Pfs*9	ENST00000357654	NM_007294.3	1833	gtG/gt	23/23	NA	2	FACETS	0.895	0.84	0.952			1	INDETERMINATE	1	TRUE	NA	0.787726071550758	2		577	658	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736165	204736165	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	126	322	0	ENST00000302823.3:c.522del	p.Leu174PhefsTer13	p.L174Ffs*13	ENST00000302823	NM_005214.4	174	ttG/tt	3/4	1	2	FACETS	0.549	0.498	0.601	0.549	0.498	0.601	SUBCLONAL	1	TRUE	1	0.787726071550758	2		322	583	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180663	32180663	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	260	723	0	ENST00000375023.3:c.2464C>G	p.Gln822Glu	p.Q822E	ENST00000375023	NM_004557.3	822	Cag/Gag	16/30	1	2	FACETS	0.969	0.914	1	0.969	0.914	1	CLONAL	1	TRUE	1	0.787726071550758	2		723	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0057217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	1429	728	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.778895606442447	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.789932452357289	2		728	1693	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039610	180039610	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs202140363	NA	P-0057217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	881	523	3	ENST00000261937.6:c.3433C>T	p.Arg1145Cys	p.R1145C	ENST00000261937	NM_182925.4	1145	Cgc/Tgc	26/30	0.786290321763788	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.789932452357289	2		526	1074	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276653	15276653	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0057217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	1106	693	0	ENST00000263388.2:c.5612C>G	p.Ser1871Ter	p.S1871*	ENST00000263388	NM_000435.2	1871	tCa/tGa	30/33	0.789932452357289	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.789932452357289	3		693	1903	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939047	48939048	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587778828	NA	P-0057217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	93	212	0	ENST00000267163.4:c.884dup	p.Asn295LysfsTer15	p.N295Kfs*15	ENST00000267163	NM_000321.2	293	-/A	9/27	0.764558340725813	3	FACETS	0.897	0.841	0.949	0.897	0.841	0.949	CLONAL	3	TRUE	0	0.789932452357289	3		212	122	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369217	118369217	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	82	236	0	ENST00000534358.1:c.5935C>T	p.Arg1979Ter	p.R1979*	ENST00000534358	NM_005933.3	1979	Cga/Tga	22/36	0.609285892601579	4	FACETS	0.92	0.828	1	0.92	0.828	1	CLONAL	2	TRUE	2	0.789932452357289	4		236	202	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125499320	125499320	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	23	365	0	ENST00000428830.2:c.389A>C	p.Asp130Ala	p.D130A	ENST00000428830	NM_001114121.2	130	gAt/gCt	5/14	0.609285892601579	4	FACETS	0.869	0.688	1	0.434	0.344	0.536	CLONAL	1	TRUE	2	0.789932452357289	4		365	120	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663429	29663429	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	69	369	0	ENST00000356175.3:c.6022G>A	p.Glu2008Lys	p.E2008K	ENST00000356175	NM_000267.3	2008	Gag/Aag	40/57	0.789932452357289	3	FACETS	0.843	0.742	0.951	0.422	0.371	0.476	CLONAL	1	TRUE	1	0.789932452357289	3		369	289	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37856495	37856495	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0057217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	418	330	0	ENST00000269571.5:c.4G>T	p.Glu2Ter	p.E2*	ENST00000269571		2	Gag/Tag	1/27	0.789932452357289	3	FACETS	1	0.98	1	0.527	0.501	0.553	CLONAL	1	TRUE	1	0.789932452357289	3		330	1401	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681677	78681677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	222	371	0	ENST00000306801.3:c.385G>A	p.Glu129Lys	p.E129K	ENST00000306801	NM_020761.2	129	Gaa/Aaa	4/34	0.789932452357289	5	FACETS	0.935	0.868	1	0.312	0.289	0.335	CLONAL	1	TRUE	2	0.789932452357289	5		371	1314	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0057226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	116	398	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.84	0.765	0.918	0.84	0.765	0.918	CLONAL	1	TRUE	1	0.742158567702827	2		398	372	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589589	67589591	+	inframe_deletion	In_Frame_Del	DEL	AAT	AAT	-	novel	NA	P-0057226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	44	188	0	ENST00000274335.5:c.1353_1355del	p.Glu451_Tyr452delinsAsp	p.E451_Y452delinsD	ENST00000274335		451	gAATat/gat	10/15	0.742158567702827	3	FACETS	0.609	0.514	0.712	0.304	0.257	0.356	SUBCLONAL	1	TRUE	1	0.742158567702827	3		188	267	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685315	89685316	+	splice_donor_variant	Splice_Site	INS	-	-	T	rs1064794925	NA	P-0057226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	66	232	0	ENST00000371953.3:c.209+2dup		p.X70_splice	ENST00000371953	NM_000314.4	70			1	2	FACETS	0.835	0.736	0.938	0.835	0.736	0.938	CLONAL	1	TRUE	1	0.742158567702827	2		232	213	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717715	89717715	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519368	NA	P-0057226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	151	388	0	ENST00000371953.3:c.740T>C	p.Leu247Ser	p.L247S	ENST00000371953	NM_000314.4	247	tTa/tCa	7/9	1	2	FACETS	0.908	0.838	0.981	0.908	0.838	0.981	CLONAL	1	TRUE	1	0.742158567702827	2		388	448	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589082	67589132	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCCTTATTCCAAAATGTTAATACCTTTATTTTTATATTGTTTTTACAGGA	TTCCTTATTCCAAAATGTTAATACCTTTATTTTTATATTGTTTTTACAGGA	-	novel	NA	P-0057226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	109	203	0	ENST00000274335.5:c.1119-49_1120del		p.X373_splice	ENST00000274335		373		9/15	0.742158567702827	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.742158567702827	3		203	181	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805404	32805404	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	208	572	0	ENST00000374899.4:c.518C>A	p.Ser173Tyr	p.S173Y	ENST00000374899	NM_018833.2	173	tCt/tAt	3/12	1	2	FACETS	0.861	0.803	0.92	0.861	0.803	0.92	CLONAL	1	TRUE	1	0.742158567702827	2		572	651	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928034	49928034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1449563443	NA	P-0057227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	44	583	2	ENST00000296474.3:c.3694G>A	p.Asp1232Asn	p.D1232N	ENST00000296474	NM_002447.2	1232	Gac/Aac	18/20	1	2	FACETS	0.675	0.564	0.799	0.675	0.564	0.799	SUBCLONAL	1	TRUE	1	0.15	2		585	869	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0057228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	158	845	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.498683414411928	1	FACETS	0.867	0.799	0.936	0.867	0.799	0.936	CLONAL	1	TRUE	0	0.512600409881992	1		845	529	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105588	27105589	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0057228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	130	476	0	ENST00000324856.7:c.5199_5200del	p.Tyr1734Ter	p.Y1734*	ENST00000324856	NM_006015.4	1733	gaGTat/gaat	20/20	0.451057066343828	1	FACETS	0.913	0.836	0.993	0.913	0.836	0.993	CLONAL	1	TRUE	0	0.512600409881992	1		476	413	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320917	30320917	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	83	369	0	ENST00000322652.5:c.1327G>C	p.Glu443Gln	p.E443Q	ENST00000322652	NM_015355.2	443	Gaa/Caa	12/16	1	2	FACETS	0.878	0.78	0.981	0.878	0.78	0.981	CLONAL	1	TRUE	1	0.512600409881992	2		369	369	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755629	57755629	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	174	668	0	ENST00000274289.3:c.158C>G	p.Pro53Arg	p.P53R	ENST00000274289	NM_006622.3	53	cCg/cGg	1/14	1	2	FACETS	0.91	0.84	0.983	0.91	0.84	0.983	CLONAL	1	TRUE	1	0.512600409881992	2		668	746	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875893	76875894	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0057228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	12	169	0	ENST00000373344.5:c.5241_5242del	p.Gly1748AsnfsTer6	p.G1748Nfs*6	ENST00000373344	NM_000489.3	1747	acAGga/acga	20/35	1	1	FACETS	0.225	0.158	0.306	0.225	0.158	0.306	SUBCLONAL	1	TRUE	0	0.512600409881992	1		169	155	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0057229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	326	504	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	NA	2	FACETS	0.76	0.729	0.791			1	INDETERMINATE	2	TRUE	NA	0.812448576999026	2		504	528	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400879	72400879	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs372543475	NA	P-0057229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	60	248	0	ENST00000357731.5:c.292A>G	p.Lys98Glu	p.K98E	ENST00000357731	NM_173808.2	98	Aaa/Gaa	2/7	0.385336315518496	3	FACETS	0.555	0.48	0.636	0.185	0.16	0.212	INDETERMINATE	1	TRUE	0	0.812448576999026	3		248	374	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467836	99467836	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs761602465	NA	P-0057229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	91	312	0	ENST00000268035.6:c.2705C>A	p.Thr902Lys	p.T902K	ENST00000268035	NM_000875.3	902	aCa/aAa	13/21	0.729537166788854	2	FACETS	0.588	0.526	0.653	0.294	0.263	0.327	SUBCLONAL	1	TRUE	0	0.812448576999026	2		312	381	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189585725	189585725	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	19	356	0	ENST00000264731.3:c.986C>G	p.Thr329Ser	p.T329S	ENST00000264731	NM_003722.4	329	aCc/aGc	7/14	0.690083180317462	3	FACETS	0.174	0.132	0.225	0.058	0.044	0.075	SUBCLONAL	1	TRUE	0	0.812448576999026	3		356	377	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867486	35867486	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs771757728	NA	P-0057229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	54	229	0	ENST00000303115.3:c.300A>T	p.Leu100Phe	p.L100F	ENST00000303115	NM_002185.3	100	ttA/ttT	3/8	0.277241439633509	5	FACETS	1	0.928	1	0.225	0.194	0.259	INDETERMINATE	1	TRUE	0	0.812448576999026	5		229	262	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38954859	38955688	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTGAATTATGTTTTTACCTGTACTTCCAACAAATGGCAGCCTGTTTTATGGTGTACTAGTTGTCCATAAAGGTGTATAGGCAGGTAGACGTGAGGACGCTGTAATCTAGTATAATAAAGATGATTACTATATCTCTTGGCTAATTTAAATATGCTAATTAGAACAAAAGAATTTTAATAAATGTTTGATAAATAAAATTAGATACAACTCTCCAGCATAAATAAAAATATGAAAGTAACAAGGAATGAGGATTTCTCAGGTAAAATATAGGCTGGGCTTCCCTAATCCAAAATGATCCAAAATCCAAAACTTTTTGAGCACTGACATGACACTGTAAGTGGAAAATTCCACACATTAGTATTTAATGCAAACTATTTCATACAGAAAATTACTTATAACACTGCATAAAATTATGTTTAGGCTACGTGTATAAGGCGTATATGAAACAGATTAATTTCATGTTTAGACTTGGGTACCATTCCCAAGGTATCTCGTTATATATATGCAAATATTCCAAATCTGAAAAAATCTGAAATGCGAAACATTTCATCATTTTGGATAAGTGATGTTCAACCTGTAACAGTTTATCAGAGCTCAAAGTACTGGTAAGAGAATCTAGGCCTAGAAATACAGACTGGGGTGCCAGCATGGAGTATATGTGAATGCGTTATCAGTAAGGATATTCAACATGCCATGAATGCCACTGAATTTTTGAGCAATTAATGCTGCGCATTAAGATTCTTCCTATATCATGTTAGAAGCAGAATATACAAAAACTCAGAAATGTTAAAAATAATTTATGATGAACTAGTTTTAAATCTGATAACTGG	GTGAATTATGTTTTTACCTGTACTTCCAACAAATGGCAGCCTGTTTTATGGTGTACTAGTTGTCCATAAAGGTGTATAGGCAGGTAGACGTGAGGACGCTGTAATCTAGTATAATAAAGATGATTACTATATCTCTTGGCTAATTTAAATATGCTAATTAGAACAAAAGAATTTTAATAAATGTTTGATAAATAAAATTAGATACAACTCTCCAGCATAAATAAAAATATGAAAGTAACAAGGAATGAGGATTTCTCAGGTAAAATATAGGCTGGGCTTCCCTAATCCAAAATGATCCAAAATCCAAAACTTTTTGAGCACTGACATGACACTGTAAGTGGAAAATTCCACACATTAGTATTTAATGCAAACTATTTCATACAGAAAATTACTTATAACACTGCATAAAATTATGTTTAGGCTACGTGTATAAGGCGTATATGAAACAGATTAATTTCATGTTTAGACTTGGGTACCATTCCCAAGGTATCTCGTTATATATATGCAAATATTCCAAATCTGAAAAAATCTGAAATGCGAAACATTTCATCATTTTGGATAAGTGATGTTCAACCTGTAACAGTTTATCAGAGCTCAAAGTACTGGTAAGAGAATCTAGGCCTAGAAATACAGACTGGGGTGCCAGCATGGAGTATATGTGAATGCGTTATCAGTAAGGATATTCAACATGCCATGAATGCCACTGAATTTTTGAGCAATTAATGCTGCGCATTAAGATTCTTCCTATATCATGTTAGAAGCAGAATATACAAAAACTCAGAAATGTTAAAAATAATTTATGATGAACTAGTTTTAAATCTGATAACTGG	-	novel	NA	P-0057229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	38	140	0	ENST00000357387.3:c.2609+9_2697+17del		p.X870_splice	ENST00000357387	NM_152756.3	870		27/38	0.277241439633509	5	FACETS	1	0.949	1	0.273	0.229	0.32	INDETERMINATE	1	TRUE	0	0.812448576999026	5		140	152	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0057230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	25	466	0	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	0.71	0.561	0.88	0.71	0.561	0.88	SUBCLONAL	1	FALSE	1	0.259870411826846	2		466	271	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821810	72821811	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GACC	novel	NA	P-0057230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	52	474	0	ENST00000268489.5:c.10364_10365insGGTC	p.Phe3456ValfsTer116	p.F3456Vfs*116	ENST00000268489	NM_006885.3	3455	ccc/ccGGTCc	10/10	0.259870411826846	5	FACETS	0.82	0.702	0.949			1	CLONAL	2	FALSE	NA	0.259870411826846	5		474	339	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146524	185146524	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	41	399	0	ENST00000265026.3:c.155T>C	p.Val52Ala	p.V52A	ENST00000265026	NM_004721.4	52	gTa/gCa	2/14	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	FALSE	1	0.259870411826846	2		399	279	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0057231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	59	326	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.514194221607102	2	FACETS	0.841	0.753	0.926	0.841	0.753	0.926	CLONAL	2	TRUE	0	0.655991740772554	2		326	107	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455090	50455090	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0057231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	39	286	0	ENST00000331340.3:c.637C>T	p.Arg213Ter	p.R213*	ENST00000331340	NM_006060.4	213	Cga/Tga	6/8	0.637950379761565	4	FACETS	0.838	0.7	0.989	0.419	0.35	0.495	CLONAL	1	TRUE	2	0.655991740772554	4		286	235	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs760043106	NA	P-0057231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	146	591	0	ENST00000269305.4:c.584T>G	p.Ile195Ser	p.I195S	ENST00000269305	NM_001126112.2	195	aTc/aGc	6/11	0.562053461312708	2	FACETS	0.873	0.816	0.928	0.873	0.816	0.928	CLONAL	2	TRUE	0	0.655991740772554	2		591	255	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120192	70120193	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0057231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	487	441	0	ENST00000245479.2:c.1195_1196dup	p.Glu400ArgfsTer4	p.E400Rfs*4	ENST00000245479	NM_000346.3	398	-/AC	3/3	0.655991740772554	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	4	TRUE	0	0.655991740772554	4		441	600	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998191	169998191	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	57	402	0	ENST00000295797.4:c.882G>T	p.Glu294Asp	p.E294D	ENST00000295797	NM_002740.5	294	gaG/gaT	9/18	0.655991740772554	3	FACETS	0.81	0.7	0.927	0.405	0.35	0.464	CLONAL	1	TRUE	1	0.655991740772554	3		402	285	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805360	32805360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	57	450	0	ENST00000374899.4:c.562G>A	p.Ala188Thr	p.A188T	ENST00000374899	NM_018833.2	188	Gcc/Acc	3/12	0.49765061284365	4	FACETS	0.666	0.573	0.767	0.222	0.191	0.256	SUBCLONAL	1	TRUE	1	0.655991740772554	4		450	432	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0057269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	377	2623	7	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	0.891163114822601	1	FACETS	0.752	0.722	0.781	0.752	0.722	0.781	SUBCLONAL	1	TRUE	0	0.891163114822601	1		2630	624	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0057269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	96	611	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.891163114822601	1	FACETS	0.176	0.157	0.197	0.176	0.157	0.197	SUBCLONAL	1	TRUE	0	0.891163114822601	1		611	678	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0057269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	306	1428	0	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	0.891163114822601	1	FACETS	0.724	0.692	0.756	0.724	0.692	0.756	SUBCLONAL	1	TRUE	0	0.891163114822601	1		1428	526	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112248	115112248	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0057269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	27	1166	1	ENST00000257566.3:c.1492del	p.Leu498CysfsTer134	p.L498Cfs*134	ENST00000257566	NM_016569.3	498	Ctg/tg	7/8	1	2	FACETS	0.205	0.163	0.252	0.205	0.163	0.252	SUBCLONAL	1	TRUE	1	0.891163114822601	2		1167	296	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112380	115112380	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374981272	NA	P-0057269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	34	2570	6	ENST00000257566.3:c.1360C>T	p.Arg454Cys	p.R454C	ENST00000257566	NM_016569.3	454	Cgc/Tgc	7/8	1	2	FACETS	0.118	0.096	0.143	0.118	0.096	0.143	SUBCLONAL	1	TRUE	1	0.891163114822601	2		2576	648	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115272998	115272999	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0057269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	22	1019	0	ENST00000438362.2:c.1374dup	p.Leu459ThrfsTer30	p.L459Tfs*30	ENST00000438362	NM_001242891.1	458	-/A	12/20	0.891163114822601	1	FACETS	0.071	0.055	0.09	0.071	0.055	0.09	SUBCLONAL	1	TRUE	0	0.891163114822601	1		1019	384	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164164	108164164	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0057269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	142	447	3	ENST00000278616.4:c.4741del	p.Ile1581SerfsTer20	p.I1581Sfs*20	ENST00000278616	NM_000051.3	1579	cAa/ca	31/63	0.891163114822601	1	FACETS	0.796	0.748	0.843	0.796	0.748	0.843	SUBCLONAL	1	TRUE	0	0.891163114822601	1		450	222	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755431	39755431	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1183474286	NA	P-0057269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	359	1342	57	ENST00000288319.7:c.1334T>G	p.Phe445Cys	p.F445C	ENST00000288319	NM_182918.3	445	tTt/tGt	10/10	0.109740754146468	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.891163114822601	0		1399	773	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37081758	37081759	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0057269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	281	823	0	ENST00000231790.2:c.1641dup	p.Tyr548IlefsTer9	p.Y548Ifs*9	ENST00000231790	NM_000249.3	547	tta/ttAa	14/19	0.891163114822601	1	FACETS	0.942	0.909	0.975	0.942	0.909	0.975	CLONAL	1	TRUE	0	0.891163114822601	1		823	371	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932575	39932575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	46	876	0	ENST00000378444.4:c.2024G>A	p.Gly675Asp	p.G675D	ENST00000378444	NM_001123385.1	675	gGc/gAc	4/15	1	1	FACETS	0.101	0.085	0.119	0.101	0.085	0.119	SUBCLONAL	1	TRUE	0	0.891163114822601	1		876	566	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620674	52620674	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0057270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	54	251	0	ENST00000394830.3:c.3079C>T	p.Arg1027Ter	p.R1027*	ENST00000394830	NM_018313.4	1027	Cga/Tga	21/30	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.165201777547921	2		251	456	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439862	52439862	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0057270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	64	400	0	ENST00000460680.1:c.850G>T	p.Glu284Ter	p.E284*	ENST00000460680	NM_004656.3	284	Gag/Tag	10/17	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.165201777547921	2		400	641	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188969	142188969	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	57	265	0	ENST00000350721.4:c.6278T>C	p.Leu2093Pro	p.L2093P	ENST00000350721	NM_001184.3	2093	cTa/cCa	37/47	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.165201777547921	2		265	543	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0057271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	189	221	1				ENST00000310581	NM_198253.2	-/1132			0.796521787037776	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.796521787037776	4		222	378	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0057271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	1027	628	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.796521787037776	7	FACETS	0.996	0.979	1			1	CLONAL	6	TRUE	NA	0.796521787037776	7		628	1291	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560902	9560902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756198440	NA	P-0057271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	371	538	0	ENST00000353224.5:c.880G>A	p.Glu294Lys	p.E294K	ENST00000353224	NM_177990.2	294	Gaa/Aaa	4/10	0.796521787037776	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.796521787037776	4		538	801	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911579	134911579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs959853730	NA	P-0057271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	158	486	1	ENST00000398015.3:c.2044C>T	p.Arg682Cys	p.R682C	ENST00000398015	NM_004441.4	682	Cgc/Tgc	11/16	0.796521787037776	4	FACETS	0.94	0.863	1	0.47	0.431	0.511	CLONAL	1	TRUE	2	0.796521787037776	4		487	758	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346589	81346589	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	233	274	0	ENST00000222390.5:c.1364G>A	p.Gly455Glu	p.G455E	ENST00000222390	NM_000601.4	455	gGa/gAa	11/18	0.796521787037776	4	FACETS	0.952	0.896	1	0.952	0.896	1	CLONAL	2	TRUE	2	0.796521787037776	4		274	552	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0057271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	253	414	0	ENST00000304494.5:c.151-1G>A		p.X51_splice	ENST00000304494	NM_000077.4	51			NA	2	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.796521787037776	2		414	291	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509660	106509660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757849968	NA	P-0057271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	360	554	0	ENST00000359195.3:c.1654C>T	p.Arg552Cys	p.R552C	ENST00000359195	NM_002649.2	552	Cgc/Tgc	2/11	0.796521787037776	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.796521787037776	4		554	797	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433847	49433847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	294	1070	0	ENST00000301067.7:c.7706G>A	p.Gly2569Asp	p.G2569D	ENST00000301067	NM_003482.3	2569	gGc/gAc	31/54	0.796521787037776	3	FACETS	1	0.95	1	0.505	0.475	0.535	CLONAL	1	TRUE	1	0.796521787037776	3		1070	1023	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156208	119156208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	375	506	0	ENST00000264033.4:c.1873C>T	p.Pro625Ser	p.P625S	ENST00000264033	NM_005188.3	625	Ccc/Tcc	11/16	0.796521787037776	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.796521787037776	4		506	771	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2105439	2105440	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0057271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	168	595	0	ENST00000219476.3:c.518_519delinsTT	p.Ser173Phe	p.S173F	ENST00000219476	NM_000548.3	173	tCC/tTT	6/42	0.796521787037776	3	FACETS	0.88	0.812	0.951	0.44	0.406	0.476	CLONAL	1	TRUE	1	0.796521787037776	3		595	670	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134508	30134508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	130	348	0	ENST00000263025.4:c.23G>A	p.Gly8Glu	p.G8E	ENST00000263025	NM_002746.2	8	gGg/gAg	1/9	0.796521787037776	3	FACETS	0.947	0.88	1	0.947	0.88	1	CLONAL	2	TRUE	1	0.796521787037776	3		348	241	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906415	50906415	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	538	851	1	ENST00000440232.2:c.1076C>T	p.Pro359Leu	p.P359L	ENST00000440232	NM_002691.3	359	cCc/cTc	9/27	0.796521787037776	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	2	0.796521787037776	4		852	1120	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730851	40730851	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	198	680	0	ENST00000373198.4:c.3684G>A	p.Met1228Ile	p.M1228I	ENST00000373198	NM_133170.3	1228	atG/atA	27/32	0.796521787037776	4	FACETS	0.965	0.894	1	0.482	0.447	0.519	CLONAL	1	TRUE	2	0.796521787037776	4		680	926	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46266488	46266488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	90	347	0	ENST00000371998.3:c.2473G>A	p.Gly825Arg	p.G825R	ENST00000371998		825	Ggg/Agg	13/23	0.796521787037776	4	FACETS	0.835	0.744	0.932	0.418	0.372	0.466	CLONAL	1	TRUE	2	0.796521787037776	4		347	486	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164724	36164724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	243	785	0	ENST00000300305.3:c.1151C>T	p.Pro384Leu	p.P384L	ENST00000300305		384	cCc/cTc	8/8	0.796521787037776	3	FACETS	1	0.944	1	0.504	0.472	0.537	CLONAL	1	TRUE	1	0.796521787037776	3		785	846	SUCCESS
APC	324	MSKCC	GRCh37	5	112179314	112179314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561619997	NA	P-0057271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	243	366	0	ENST00000257430.4:c.8023C>T	p.Pro2675Ser	p.P2675S	ENST00000257430	NM_000038.5	2675	Ccc/Tcc	16/16	0.796521787037776	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.796521787037776	3		366	408	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839895	27839895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	569	596	0	ENST00000328488.2:c.199C>T	p.Pro67Ser	p.P67S	ENST00000328488	NM_003533.2	67	Cct/Tct	1/1	0.796521787037776	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	1	0.796521787037776	4		596	853	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517409	157517409	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554234402	NA	P-0057271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	174	530	1	ENST00000346085.5:c.3973C>T	p.Gln1325Ter	p.Q1325*	ENST00000346085	NM_020732.3	1325	Cag/Tag	16/20	1	2	FACETS	0.971	0.903	1	0.971	0.903	1	CLONAL	1	TRUE	1	0.796521787037776	2		531	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0057272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	432	1058	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.463950342698371	2	FACETS	0.987	0.946	1	0.987	0.946	1	CLONAL	2	TRUE	0	0.479858922819702	2		1058	912	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156848967	156848967	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	181	772	4	ENST00000524377.1:c.1859G>C	p.Gly620Ala	p.G620A	ENST00000524377	NM_002529.3	620	gGc/gCc	15/17	0.479858922819702	3	FACETS	0.879	0.81	0.951	0.44	0.405	0.476	CLONAL	1	TRUE	1	0.479858922819702	3		776	1064	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953759	48953759	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	164	199	0	ENST00000267163.4:c.1363del	p.Arg455GlufsTer2	p.R455Efs*2	ENST00000267163	NM_000321.2	454	taC/ta	14/27	0.190146341228253	5	FACETS	1	0.975	1			1	INDETERMINATE	3	TRUE	NA	0.479858922819702	5		199	357	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628317	90628317	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	203	770	0	ENST00000330062.3:c.1094G>T	p.Ser365Ile	p.S365I	ENST00000330062	NM_002168.2	365	aGc/aTc	9/11	0.234289281529032	3	FACETS	0.843	0.78	0.908			1	INDETERMINATE	1	TRUE	NA	0.479858922819702	3		770	1245	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629841	187629841	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	228	642	1	ENST00000441802.2:c.1141C>A	p.Pro381Thr	p.P381T	ENST00000441802	NM_005245.3	381	Cct/Act	2/27	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.479858922819702	2		643	842	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591113	67591133	+	inframe_deletion	In_Frame_Del	DEL	ACCTTATCCAGCTGAGAAAGA	ACCTTATCCAGCTGAGAAAGA	-	novel	NA	P-0057272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	63	277	0	ENST00000274335.5:c.1706_1726del	p.Asp569_Thr576delinsAla	p.D569_T576delinsA	ENST00000274335		569	gACCTTATCCAGCTGAGAAAGAcg/gcg	12/15	1	2	FACETS	0.668	0.58	0.763	0.668	0.58	0.763	SUBCLONAL	1	TRUE	1	0.479858922819702	2		277	393	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056313	26056313	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0057272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	136	440	0	ENST00000343677.2:c.344A>G	p.Glu115Gly	p.E115G	ENST00000343677	NM_005319.3	115	gAa/gGa	1/1	0.438678152562451	3	FACETS	0.877	0.798	0.961	0.292	0.266	0.321	CLONAL	1	TRUE	0	0.479858922819702	3		440	801	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967984	93967984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	97	338	0	ENST00000369303.4:c.1943G>A	p.Cys648Tyr	p.C648Y	ENST00000369303	NM_004440.3	648	tGc/tAc	11/17	0.479858922819702	3	FACETS	0.971	0.869	1	0.486	0.434	0.54	CLONAL	1	TRUE	1	0.479858922819702	3		338	516	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864663	68864663	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773560075	NA	P-0057272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	60	258	0	ENST00000288368.4:c.34G>A	p.Glu12Lys	p.E12K	ENST00000288368	NM_024870.2	12	Gag/Aag	1/40	0.461643137613195	2	FACETS	0.871	0.757	0.993	0.436	0.378	0.497	CLONAL	1	TRUE	0	0.479858922819702	2		258	287	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0057273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	129	597	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.497033090782024	3	FACETS	0.871	0.791	0.956	0.436	0.395	0.478	CLONAL	1	TRUE	1	0.497033090782024	3		597	744	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0057273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	233	728	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.482397817972653	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.497033090782024	1		728	692	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971116	21971116	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	115	373	0	ENST00000304494.5:c.242C>A	p.Pro81His	p.P81H	ENST00000304494	NM_000077.4	81	cCc/cAc	2/3	0.497033090782024	1	FACETS	0.953	0.867	1	0.953	0.867	1	CLONAL	1	TRUE	0	0.497033090782024	1		373	365	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332591	70332591	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	126	462	0	ENST00000373644.4:c.496C>G	p.Leu166Val	p.L166V	ENST00000373644	NM_030625.2	166	Ctt/Gtt	2/12	1	2	FACETS	0.861	0.782	0.943	0.861	0.782	0.943	CLONAL	1	TRUE	1	0.497033090782024	2		462	589	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251479	10251479	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	187	612	0	ENST00000340748.4:c.3453G>T	p.Leu1151Phe	p.L1151F	ENST00000340748		1151	ttG/ttT	31/40	1	2	FACETS	0.991	0.918	1	0.991	0.918	1	CLONAL	1	TRUE	1	0.497033090782024	2		612	759	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713251	30713251	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	200	365	0	ENST00000295754.5:c.577del	p.Arg193GlyfsTer5	p.R193Gfs*5	ENST00000295754	NM_003242.5	192	aaC/aa	4/7	0.485862075464837	2	FACETS	0.898	0.842	0.955	0.898	0.842	0.955	CLONAL	2	TRUE	0	0.497033090782024	2		365	448	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528627	89528627	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0057273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	54	174	0	ENST00000336596.2:c.2927del	p.Ser976Ter	p.S976*	ENST00000336596	NM_005233.5	976	tCa/ta	17/17	1	2	FACETS	0.866	0.747	0.993	0.866	0.747	0.993	CLONAL	1	TRUE	1	0.497033090782024	2		174	251	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	155	324	0				ENST00000310581	NM_198253.2	-/1132			0.425233453044997	1	FACETS	0.738	0.689	0.787	0.738	0.689	0.787	INDETERMINATE	1	TRUE	0	0.826953802258269	1		324	298	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717695	89717696	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1060500115	NA	P-0057274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	178	407	0	ENST00000371953.3:c.723dup	p.Glu242Ter	p.E242*	ENST00000371953	NM_000314.4	240	-/T	7/9	0.826953802258269	1	FACETS	0.709	0.665	0.754	0.709	0.665	0.754	SUBCLONAL	1	TRUE	0	0.826953802258269	1		407	356	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900499	3900502	+	frameshift_variant	Frame_Shift_Del	DEL	ATTA	ATTA	-	novel	NA	P-0057274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	476	666	0	ENST00000262367.5:c.594_597del	p.Asn199ArgfsTer10	p.N199Rfs*10	ENST00000262367	NM_004380.2	198	atTAAT/at	2/31	1	2	FACETS	0.944	0.904	0.984	0.944	0.904	0.984	CLONAL	1	TRUE	1	0.826953802258269	2		666	1220	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874332	76874332	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	221	456	0	ENST00000373344.5:c.5390T>A	p.Val1797Asp	p.V1797D	ENST00000373344	NM_000489.3	1797	gTc/gAc	21/35	0.484612694578384	1	FACETS	0.384	0.358	0.411	0.384	0.358	0.411	INDETERMINATE	1	TRUE	0	0.826953802258269	1		456	816	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0057275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	287	608	1	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.326786767964731	2	FACETS	1	0.993	1	0.695	0.655	0.736	CLONAL	1	TRUE	0	0.449535479195385	2		609	918	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953760	48953760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913302	NA	P-0057275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	148	192	0	ENST00000267163.4:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000267163	NM_000321.2	455	Cga/Tga	14/27	0.449535479195385	3	FACETS	1	0.973	1	0.739	0.683	0.794	CLONAL	2	TRUE	0	0.449535479195385	3		192	364	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450048	32450048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444869026	NA	P-0057275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	259	543	0	ENST00000332351.3:c.764C>T	p.Ser255Leu	p.S255L	ENST00000332351	NM_024426.4	255	tCg/tTg	2/10	0.170532892429258	5	FACETS	1	0.961	1	0.689	0.646	0.732	INDETERMINATE	2	TRUE	2	0.449535479195385	5		543	934	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295241	1295241	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0057275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	87	228	1				ENST00000310581	NM_198253.2	-/1132			0.289508121345405	4	FACETS	1	0.975	1	0.683	0.608	0.762	CLONAL	1	TRUE	2	0.449535479195385	4		229	411	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410043	63410043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1486040300	NA	P-0057275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	308	645	0	ENST00000330258.3:c.3124C>A	p.Gln1042Lys	p.Q1042K	ENST00000330258	NM_152424.3	1042	Cag/Aag	2/2	0.390715092906013	3	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.449535479195385	3		645	1194	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18576952	18576952	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	187	385	0	ENST00000266497.5:c.2360A>T	p.Gln787Leu	p.Q787L	ENST00000266497		787	cAg/cTg	16/31	0.449535479195385	5	FACETS	0.89	0.823	0.958	0.593	0.549	0.639	CLONAL	2	TRUE	2	0.449535479195385	5		385	783	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132940	30132940	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	46	515	0	ENST00000331968.5:c.661G>C	p.Glu221Gln	p.E221Q	ENST00000331968	NM_002742.2	221	Gaa/Caa	4/18	0.326786767964731	2	FACETS	0.25	0.209	0.294	0.125	0.104	0.147	SUBCLONAL	1	TRUE	0	0.449535479195385	2		515	820	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687249	37687249	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	320	600	0	ENST00000447079.4:c.4153G>A	p.Glu1385Lys	p.E1385K	ENST00000447079	NM_015083.1	1385	Gag/Aag	14/14	0.303448950969529	2	FACETS	0.754	0.714	0.795	0.754	0.714	0.795	SUBCLONAL	2	TRUE	0	0.449535479195385	2		600	944	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096012	11096012	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1247	308	727	0	ENST00000358026.2:c.286A>G	p.Met96Val	p.M96V	ENST00000358026	NM_001128849.1	96	Atg/Gtg	3/36	0.242606536080205	5	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.449535479195385	5		727	1555	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291916	15291916	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1983	513	910	0	ENST00000263388.2:c.2850C>G	p.Cys950Trp	p.C950W	ENST00000263388	NM_000435.2	950	tgC/tgG	18/33	0.449535479195385	7	FACETS	0.971	0.926	1			1	CLONAL	2	TRUE	NA	0.449535479195385	7		910	2496	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223681	36223681	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	403	933	0	ENST00000222270.7:c.6231G>C	p.Gln2077His	p.Q2077H	ENST00000222270	NM_014727.1	2077	caG/caC	28/37	0.282665789957299	3	FACETS	0.754	0.716	0.792	0.754	0.716	0.792	SUBCLONAL	2	TRUE	1	0.449535479195385	3		933	1457	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637344	176637344	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	219	467	0	ENST00000439151.2:c.1944C>G	p.Asp648Glu	p.D648E	ENST00000439151	NM_022455.4	648	gaC/gaG	5/23	0.316315926967115	2	FACETS	1	0.992	1	0.739	0.691	0.788	CLONAL	1	TRUE	0	0.449535479195385	2		467	659	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163524	32163524	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	109	608	0	ENST00000375023.3:c.5702C>G	p.Ser1901Trp	p.S1901W	ENST00000375023	NM_004557.3	1901	tCg/tGg	30/30	0.282665789957299	3	FACETS	0.558	0.499	0.62	0.279	0.249	0.31	SUBCLONAL	1	TRUE	1	0.449535479195385	3		608	1065	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429415	47429415	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	169	498	0	ENST00000377045.4:c.1543C>G	p.Arg515Gly	p.R515G	ENST00000377045	NM_001654.4	515	Cgt/Ggt	14/16	0.390715092906013	3	FACETS	1	0.969	1			1	CLONAL	1	TRUE	NA	0.449535479195385	3		498	835	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0057276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	37	381	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.238341192833715	1	FACETS	0.722	0.596	0.862	0.722	0.596	0.862	SUBCLONAL	1	TRUE	0	0.238341192833715	1		381	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0057276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	89	623	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.238341192833715	2		623	654	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968544	55968544	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	43	436	0	ENST00000263923.4:c.2119C>A	p.Leu707Ile	p.L707I	ENST00000263923	NM_002253.2	707	Ctt/Att	14/30	1	2	FACETS	0.893	0.749	1	0.893	0.749	1	CLONAL	1	TRUE	1	0.238341192833715	2		436	404	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726662	88726662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	52	480	0	ENST00000360948.2:c.382C>T	p.His128Tyr	p.H128Y	ENST00000360948	NM_001012338.2	128	Cat/Tat	4/19	1	2	FACETS	0.887	0.756	1	0.887	0.756	1	CLONAL	1	TRUE	1	0.238341192833715	2		480	492	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596051	43596051	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0057276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	36	702	0	ENST00000355710.3:c.218A>T	p.Tyr73Phe	p.Y73F	ENST00000355710	NM_020975.4	73	tAc/tTc	2/20	0.208643576910317	1	FACETS	0.447	0.367	0.538	0.447	0.367	0.538	SUBCLONAL	1	TRUE	0	0.238341192833715	1		702	595	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633097	3633097	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0057276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	25	540	0	ENST00000294008.3:c.5153+1G>C		p.X1718_splice	ENST00000294008	NM_032444.2	1718			1	2	FACETS	0.468	0.368	0.584	0.468	0.368	0.584	SUBCLONAL	1	TRUE	1	0.238341192833715	2		540	448	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831521	72831521	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs762647934	NA	P-0057276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	87	579	0	ENST00000268489.5:c.5060G>C	p.Ser1687Thr	p.S1687T	ENST00000268489	NM_006885.3	1687	aGt/aCt	9/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.238341192833715	2		579	595	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097664	11097664	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0057276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	103	742	1	ENST00000358026.2:c.844A>T	p.Lys282Ter	p.K282*	ENST00000358026	NM_001128849.1	282	Aag/Tag	5/36	0.238341192833715	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.238341192833715	1		743	660	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456503	29456503	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0057276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	126	628	0	ENST00000389048.3:c.2415C>G	p.Ile805Met	p.I805M	ENST00000389048	NM_004304.4	805	atC/atG	14/29	0.179499490937466	2	FACETS	0.782	0.709	0.858	0.782	0.709	0.858	SUBCLONAL	2	TRUE	0	0.238341192833715	2		628	676	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143235866	143235866	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	18	283	0	ENST00000262992.4:c.422G>C	p.Gly141Ala	p.G141A	ENST00000262992	NM_001101669.1	141	gGg/gCg	6/24	1	2	FACETS	0.51	0.384	0.66	0.51	0.384	0.66	SUBCLONAL	1	TRUE	1	0.238341192833715	2		283	296	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557320	187557320	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0057276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	49	494	0	ENST00000441802.2:c.4042A>T	p.Lys1348Ter	p.K1348*	ENST00000441802	NM_005245.3	1348	Aag/Tag	6/27	0.238341192833715	1	FACETS	0.836	0.71	0.975	0.836	0.71	0.975	CLONAL	1	TRUE	0	0.238341192833715	1		494	433	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358939	81358939	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	32	401	0	ENST00000222390.5:c.1022C>A	p.Pro341His	p.P341H	ENST00000222390	NM_000601.4	341	cCt/cAt	8/18	0.227743292192869	3	FACETS	0.808	0.656	0.979	0.404	0.328	0.49	CLONAL	1	TRUE	1	0.238341192833715	3		401	372	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392129	81392129	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0057276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	38	311	1	ENST00000222390.5:c.148C>A	p.Leu50Ile	p.L50I	ENST00000222390	NM_000601.4	50	Cta/Ata	2/18	0.227743292192869	3	FACETS	1	0.951	1	0.728	0.606	0.863	CLONAL	1	TRUE	1	0.238341192833715	3		312	245	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399299	139399299	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	68	724	0	ENST00000277541.6:c.4844T>G	p.Met1615Arg	p.M1615R	ENST00000277541	NM_017617.3	1615	aTg/aGg	26/34	0.208309275673691	1	FACETS	0.87	0.757	0.991	0.87	0.757	0.991	CLONAL	1	TRUE	0	0.238341192833715	1		724	578	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412627	139412627	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	74	786	0	ENST00000277541.6:c.1217G>T	p.Gly406Val	p.G406V	ENST00000277541	NM_017617.3	406	gGc/gTc	7/34	0.208309275673691	1	FACETS	0.732	0.64	0.831	0.732	0.64	0.831	SUBCLONAL	1	TRUE	0	0.238341192833715	1		786	747	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	39	324	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.74	0.617	0.874	0.74	0.617	0.874	SUBCLONAL	1	FALSE	1	0.430498853355338	2		324	245	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0057278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	111	317	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.430498853355338	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	FALSE	1	0.430498853355338	3		317	289	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444523	49444523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	203	683	1	ENST00000301067.7:c.2848G>A	p.Ala950Thr	p.A950T	ENST00000301067	NM_003482.3	950	Gcc/Acc	11/54	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.430498853355338	2		684	794	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844200	68844200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555515456	NA	P-0057278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	116	551	0	ENST00000261769.5:c.788C>T	p.Thr263Ile	p.T263I	ENST00000261769	NM_004360.3	263	aCc/aTc	6/16	0.430498853355338	1	FACETS	0.934	0.847	1	0.934	0.847	1	CLONAL	1	FALSE	0	0.430498853355338	1		551	453	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276764	15276764	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202027632	NA	P-0057278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	178	768	1	ENST00000263388.2:c.5501G>A	p.Arg1834Gln	p.R1834Q	ENST00000263388	NM_000435.2	1834	cGg/cAg	30/33	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	FALSE	1	0.430498853355338	2		769	818	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604240	189604240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	131	436	0	ENST00000264731.3:c.1407G>A	p.Met469Ile	p.M469I	ENST00000264731	NM_003722.4	469	atG/atA	11/14	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	FALSE	1	0.430498853355338	2		436	575	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0057278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	32	198	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	0.912	0.75	1	0.912	0.75	1	CLONAL	1	FALSE	1	0.430498853355338	2		198	163	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538946	23538946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0057278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	142	687	0	ENST00000380871.4:c.493G>A	p.Glu165Lys	p.E165K	ENST00000380871	NM_006167.3	165	Gag/Aag	2/2	1	2	FACETS	0.938	0.857	1	0.938	0.857	1	CLONAL	1	FALSE	1	0.430498853355338	2		687	703	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995547	68995547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	52	540	0	ENST00000288368.4:c.1951G>A	p.Glu651Lys	p.E651K	ENST00000288368	NM_024870.2	651	Gaa/Aaa	18/40	1	2	FACETS	0.741	0.634	0.857	0.741	0.634	0.857	SUBCLONAL	1	FALSE	1	0.430498853355338	2		540	326	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27209139	27209139	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0057278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	143	401	0	ENST00000380036.4:c.2596C>G	p.His866Asp	p.H866D	ENST00000380036	NM_000459.3	866	Cac/Gac	16/23	0.430498853355338	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	0	0.430498853355338	1		401	447	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189585691	189585691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1205536026	NA	P-0057280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	75	504	0	ENST00000264731.3:c.952C>T	p.Arg318Cys	p.R318C	ENST00000264731	NM_003722.4	318	Cgc/Tgc	7/14	0.333719027314111	4	FACETS	1	0.927	1	0.709	0.628	0.794	CLONAL	2	TRUE	1	0.333719027314111	4		504	282	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776035	9776035	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0057280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	155	816	1	ENST00000377346.4:c.499T>G	p.Phe167Val	p.F167V	ENST00000377346	NM_005026.3	167	Ttc/Gtc	5/24	0.333719027314111	3	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	1	0.333719027314111	3		817	530	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988485	41988485	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0057280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	102	461	0	ENST00000219905.7:c.1277A>C	p.Gln426Pro	p.Q426P	ENST00000219905	NM_001164273.1	426	cAg/cCg	3/24	0.333719027314111	3	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	TRUE	1	0.333719027314111	3		461	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578278	7578279	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0057280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	133	629	0	ENST00000269305.4:c.570_571del	p.Pro191SerfsTer17	p.P191Sfs*17	ENST00000269305	NM_001126112.2	190	ccTCct/ccct	6/11	0.26600160383515	2	FACETS	0.977	0.896	1	0.977	0.896	1	CLONAL	2	TRUE	0	0.333719027314111	2		629	408	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0057281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	77	324	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.942	0.84	1	0.942	0.84	1	CLONAL	1	TRUE	1	0.723690383093335	2		324	226	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0057281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	433	508	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.873	0.843	0.904	1	0.997	1	CLONAL	2	TRUE	1	0.723690383093335	2		508	685	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468020	50468020	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0057281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	181	693	0	ENST00000331340.3:c.1255G>A	p.Ala419Thr	p.A419T	ENST00000331340	NM_006060.4	419	Gcc/Acc	8/8	0.696112627912648	3	FACETS	0.934	0.864	1	0.467	0.432	0.504	CLONAL	1	TRUE	1	0.723690383093335	3		693	729	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104356987	104356987	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554852789	NA	P-0057281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	232	575	1	ENST00000369902.3:c.847G>T	p.Glu283Ter	p.E283*	ENST00000369902	NM_016169.3	283	Gag/Tag	7/12	0.723690383093335	1	FACETS	0.956	0.905	1	0.956	0.905	1	CLONAL	1	TRUE	0	0.723690383093335	1		576	428	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573389	55573389	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0057281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	135	439	0	ENST00000288135.5:c.1051A>G	p.Met351Val	p.M351V	ENST00000288135	NM_000222.2	351	Atg/Gtg	6/21	0.505128367621517	3	FACETS	0.79	0.72	0.863			1	SUBCLONAL	1	TRUE	NA	0.723690383093335	3		439	643	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040110	180040110	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0057281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	171	698	0	ENST00000261937.6:c.3332G>T	p.Gly1111Val	p.G1111V	ENST00000261937	NM_182925.4	1111	gGg/gTg	25/30	1	2	FACETS	0.902	0.836	0.97	0.902	0.836	0.97	CLONAL	1	TRUE	1	0.723690383093335	2		698	524	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474041	29474041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs78723472	NA	P-0001652-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	377	1035	0	ENST00000389048.3:c.2134G>A	p.Val712Met	p.V712M	ENST00000389048	NM_004304.4	712	Gtg/Atg	12/29	0.193375155988051	1	FACETS	1	0.995	1	1	0.995	1	INDETERMINATE	1	TRUE	0	0.439710620909388	1		1035	915	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931683	39931683	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0001652-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	494	681	0	ENST00000378444.4:c.2916C>G	p.Tyr972Ter	p.Y972*	ENST00000378444	NM_001123385.1	972	taC/taG	4/15	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.439710620909388	2		681	1025	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537894	212537894	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001652-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	55	481	0	ENST00000342788.4:c.1711G>A	p.Gly571Arg	p.G571R	ENST00000342788	NM_005235.2	571	Gga/Aga	14/28	1	2	FACETS	0.551	0.472	0.637	0.551	0.472	0.637	SUBCLONAL	1	TRUE	1	0.439710620909388	2		481	454	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426821	121426821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765241951	NA	P-0001652-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	79	563	0	ENST00000257555.6:c.512G>A	p.Arg171Gln	p.R171Q	ENST00000257555		171	cGa/cAa	2/10	0.118260842715953	4	FACETS	0.773	0.68	0.873	0.387	0.34	0.437	INDETERMINATE	1	TRUE	2	0.439710620909388	4		563	669	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001947-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	162	374	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.808654978496204	2		374	392	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188188	32188188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370312303	NA	P-0001947-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	29	409	0	ENST00000375023.3:c.1153C>T	p.Arg385Cys	p.R385C	ENST00000375023	NM_004557.3	385	Cgc/Tgc	6/30	1	2	FACETS	0.144	0.115	0.177	0.144	0.115	0.177	SUBCLONAL	1	TRUE	1	0.808654978496204	2		409	497	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638390	176638390	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001947-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	289	508	0	ENST00000439151.2:c.2990G>T	p.Gly997Val	p.G997V	ENST00000439151	NM_022455.4	997	gGc/gTc	5/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.808654978496204	2		508	691	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578466	7578466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001947-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	47	657	0	ENST00000269305.4:c.464C>T	p.Thr155Ile	p.T155I	ENST00000269305	NM_001126112.2	155	aCc/aTc	5/11	1	2	FACETS	0.127	0.107	0.15	0.127	0.107	0.15	SUBCLONAL	1	TRUE	1	0.808654978496204	2		657	913	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039230	49039230	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001947-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	172	260	0	ENST00000267163.4:c.2308C>T	p.Gln770Ter	p.Q770*	ENST00000267163	NM_000321.2	770	Cag/Tag	22/27	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.808654978496204	2		260	379	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714291	43714291	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1210471024	NA	P-0001947-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	283	423	0	ENST00000382044.4:c.3862T>C	p.Cys1288Arg	p.C1288R	ENST00000382044	NM_001141980.1	1288	Tgt/Cgt	19/28	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.808654978496204	2		423	624	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0002473-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	45	242	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.946	0.8	1	0.946	0.8	1	CLONAL	1	TRUE	1	0.337470139124814	2		242	282	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056280	27056281	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0002473-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	96	579	0	ENST00000324856.7:c.1280dup	p.Gln428AlafsTer195	p.Q428Afs*195	ENST00000324856	NM_006015.4	426	acc/aCcc	2/20	1	2	FACETS	0.72	0.641	0.804	0.72	0.641	0.804	SUBCLONAL	1	TRUE	1	0.337470139124814	2		579	790	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111540	8111541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0002473-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	123	585	0	ENST00000346208.3:c.1029_1030dup	p.Tyr344SerfsTer12	p.Y344Sfs*12	ENST00000346208		342	-/CT	5/6	1	2	FACETS	0.992	0.898	1	0.992	0.898	1	CLONAL	1	TRUE	1	0.337470139124814	2		585	735	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063715	67063717	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TCG	TCG	-	novel	NA	P-0002473-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	57	282	0	ENST00000412916.2:c.165_165+2del		p.X55_splice	ENST00000412916		55		2/6	0.301936778995777	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.337470139124814	1		282	262	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654857	29654857	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002473-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	60	237	0	ENST00000356175.3:c.5546+1del		p.R1849fs	ENST00000356175	NM_000267.3	1849	cGg/cg	37/57	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.337470139124814	2		237	334	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94908662	94908665	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TTTT	TTTT	-	novel	NA	P-0002473-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	75	450	0	ENST00000536441.1:c.1389_1392del	p.Lys464PhefsTer7	p.K464Ffs*7	ENST00000536441	NM_144665.3	463	gaAAAA/ga	9/10	1	2	FACETS	0.932	0.819	1	0.932	0.819	1	CLONAL	1	TRUE	1	0.337470139124814	2		450	477	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2193690	2193690	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002473-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	131	711	1	ENST00000398665.3:c.496G>A	p.Val166Met	p.V166M	ENST00000398665	NM_032482.2	166	Gtg/Atg	6/28	1	2	FACETS	0.907	0.823	0.996	0.907	0.823	0.996	CLONAL	1	TRUE	1	0.337470139124814	2		712	856	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845268	42845268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372563970	NA	P-0002473-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	153	771	0	ENST00000398585.3:c.994G>A	p.Ala332Thr	p.A332T	ENST00000398585	NM_001135099.1	332	Gcc/Acc	9/14	1	2	FACETS	0.973	0.89	1	0.973	0.89	1	CLONAL	1	TRUE	1	0.337470139124814	2		771	932	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620601	52620602	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0005134-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	27	489	0	ENST00000394830.3:c.3151_3152del	p.Trp1051AspfsTer30	p.W1051Dfs*30	ENST00000394830	NM_018313.4	1051	TGg/g	21/30	1	2	FACETS	0.596	0.474	0.734	0.596	0.474	0.734	SUBCLONAL	1	FALSE	1	0.271435941763635	2		489	334	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183730	10183730	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005134-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	23	850	0	ENST00000256474.2:c.200del	p.Asn67ThrfsTer92	p.N67Tfs*92	ENST00000256474	NM_000551.3	67	Aac/ac	1/3	1	2	FACETS	0.428	0.333	0.538	0.428	0.333	0.538	SUBCLONAL	1	FALSE	1	0.271435941763635	2		850	396	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164020	47164021	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0005134-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	14	323	0	ENST00000409792.3:c.2105_2106del	p.Val702AspfsTer23	p.V702Dfs*23	ENST00000409792	NM_014159.6	702	gTG/g	3/21	1	2	FACETS	1	0.732	1	1	0.732	1	CLONAL	1	FALSE	1	0.271435941763635	2		323	103	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037966	49037966	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	189	359	0	ENST00000267163.4:c.2206C>T	p.Gln736Ter	p.Q736*	ENST00000267163	NM_000321.2	736	Cag/Tag	21/27	1	2	FACETS	0.987	0.924	1	0.987	0.924	1	CLONAL	1	TRUE	1	0.900757434928689	2		359	425	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033970	49033970	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0006354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	191	227	0	ENST00000267163.4:c.2106+1G>T		p.X702_splice	ENST00000267163	NM_000321.2	702			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.900757434928689	2		227	403	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458729	120458729	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	70	498	0	ENST00000256646.2:c.6616G>T	p.Glu2206Ter	p.E2206*	ENST00000256646	NM_024408.3	2206	Gaa/Taa	34/34	1	2	FACETS	0.821	0.718	0.931	0.821	0.718	0.931	CLONAL	1	TRUE	1	0.370045900401135	2		498	461	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174418	11174418	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	122	586	0	ENST00000361445.4:c.7257A>T	p.Glu2419Asp	p.E2419D	ENST00000361445	NM_004958.3	2419	gaA/gaT	53/58	0.370045900401135	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.370045900401135	1		586	518	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198269895	198269895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	26	229	0	ENST00000335508.6:c.1444G>A	p.Val482Ile	p.V482I	ENST00000335508	NM_012433.2	482	Gtt/Att	11/25	1	2	FACETS	0.567	0.45	0.699	0.567	0.45	0.699	SUBCLONAL	1	TRUE	1	0.370045900401135	2		229	248	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288535	198288535	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	71	452	0	ENST00000335508.6:c.192A>T	p.Glu64Asp	p.E64D	ENST00000335508	NM_012433.2	64	gaA/gaT	2/25	1	2	FACETS	0.703	0.614	0.798	0.703	0.614	0.798	SUBCLONAL	1	TRUE	1	0.370045900401135	2		452	546	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183863	10183863	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869025631	NA	P-0006510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	82	211	0	ENST00000256474.2:c.332G>A	p.Ser111Asn	p.S111N	ENST00000256474	NM_000551.3	111	aGc/aAc	1/3	0.370045900401135	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.370045900401135	1		211	319	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158197	47158197	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	77	469	1	ENST00000409792.3:c.4502G>T	p.Cys1501Phe	p.C1501F	ENST00000409792	NM_014159.6	1501	tGt/tTt	4/21	0.370045900401135	1	FACETS	0.902	0.797	1	0.902	0.797	1	CLONAL	1	TRUE	0	0.370045900401135	1		470	376	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405929	49405929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	111	585	1	ENST00000418115.1:c.209G>A	p.Arg70Lys	p.R70K	ENST00000418115	NM_001664.2	70	aGg/aAg	3/5	0.370045900401135	1	FACETS	0.928	0.837	1	0.928	0.837	1	CLONAL	1	TRUE	0	0.370045900401135	1		586	527	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152006	55152006	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0006510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	90	384	1	ENST00000257290.5:c.2440-2A>T		p.X814_splice	ENST00000257290	NM_006206.4	814			1	2	FACETS	0.979	0.872	1	0.979	0.872	1	CLONAL	1	TRUE	1	0.370045900401135	2		385	497	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509124	66509124	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	98	460	0	ENST00000273854.3:c.203C>T	p.Thr68Ile	p.T68I	ENST00000273854	NM_004439.5	68	aCt/aTt	2/18	1	2	FACETS	0.953	0.852	1	0.953	0.852	1	CLONAL	1	TRUE	1	0.370045900401135	2		460	556	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615093	43615093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1280808741	NA	P-0006510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	209	610	0	ENST00000355710.3:c.2507G>A	p.Ser836Asn	p.S836N	ENST00000355710	NM_020975.4	836	aGc/aAc	14/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.370045900401135	2		610	949	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186613	108186613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565499041	NA	P-0006510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	84	395	1	ENST00000278616.4:c.6070G>A	p.Gly2024Arg	p.G2024R	ENST00000278616	NM_000051.3	2024	Ggg/Agg	41/63	1	2	FACETS	0.897	0.795	1	0.897	0.795	1	CLONAL	1	TRUE	1	0.370045900401135	2		396	506	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865628	57865628	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	128	720	1	ENST00000228682.2:c.3105C>A	p.Asn1035Lys	p.N1035K	ENST00000228682	NM_005269.2	1035	aaC/aaA	12/12	1	2	FACETS	0.872	0.791	0.958	0.872	0.791	0.958	CLONAL	1	TRUE	1	0.370045900401135	2		721	793	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320351	30320351	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	58	503	0	ENST00000322652.5:c.1292A>T	p.Gln431Leu	p.Q431L	ENST00000322652	NM_015355.2	431	cAg/cTg	11/16	1	2	FACETS	0.687	0.592	0.791	0.687	0.592	0.791	SUBCLONAL	1	TRUE	1	0.370045900401135	2		503	456	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435744	56435744	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	88	346	0	ENST00000407977.2:c.1393G>C	p.Asp465His	p.D465H	ENST00000407977		465	Gac/Cac	9/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.370045900401135	2		346	380	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395769	45395769	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	75	438	0	ENST00000262160.6:c.365G>T	p.Gly122Val	p.G122V	ENST00000262160	NM_005901.5	122	gGa/gTa	4/11	1	2	FACETS	0.801	0.704	0.906	0.801	0.704	0.906	CLONAL	1	TRUE	1	0.370045900401135	2		438	506	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15280902	15280902	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	98	487	2	ENST00000263388.2:c.5194C>A	p.Leu1732Ile	p.L1732I	ENST00000263388	NM_000435.2	1732	Cta/Ata	28/33	1	2	FACETS	0.988	0.884	1	0.988	0.884	1	CLONAL	1	TRUE	1	0.370045900401135	2		489	536	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353734	15353734	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	237	597	1	ENST00000263377.2:c.3146A>T	p.His1049Leu	p.H1049L	ENST00000263377	NM_058243.2	1049	cAc/cTc	14/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.370045900401135	2		598	1103	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004556	150004557	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	169	758	0	ENST00000253339.5:c.1668dup	p.Pro557ThrfsTer22	p.P557Tfs*22	ENST00000253339		556	-/A	3/7	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.370045900401135	2		758	898	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0008676-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	110	487	2	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	0.5108906192381	2	FACETS	0.579	0.52	0.641	0.289	0.26	0.321	SUBCLONAL	1	TRUE	0	0.5108906192381	2		489	744	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030416	49030416	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	342	307	0	ENST00000267163.4:c.1891C>T	p.Gln631Ter	p.Q631*	ENST00000267163	NM_000321.2	631	Caa/Taa	19/27	0.809681896243837	2	FACETS	0.961	0.932	0.987	0.961	0.932	0.987	CLONAL	2	TRUE	0	0.833870400094834	2		307	427	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936995	48936995	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778842	NA	P-0009865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	456	568	0	ENST00000267163.4:c.763C>T	p.Arg255Ter	p.R255*	ENST00000267163	NM_000321.2	255	Cga/Tga	8/27	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.723068635305603	2		568	1098	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030390	49030405	+	frameshift_variant	Frame_Shift_Del	DEL	TAAATTCTACTGCAAA	TAAATTCTACTGCAAA	-	novel	NA	P-0009865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	391	315	0	ENST00000267163.4:c.1866_1881del	p.Asn623GlnfsTer15	p.N623Qfs*15	ENST00000267163	NM_000321.2	622	gTAAATTCTACTGCAAAt/gt	19/27	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.723068635305603	2		315	813	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0010563-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	200	333	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.59803694341674	3	FACETS	0.872	0.816	0.929	0.872	0.816	0.929	CLONAL	2	TRUE	1	0.59803694341674	3		333	498	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934126	39934127	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010563-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	57	296	0	ENST00000378444.4:c.472dup	p.Ser158LysfsTer28	p.S158Kfs*28	ENST00000378444	NM_001123385.1	158	agt/aAgt	4/15	1	1	FACETS	0.363	0.313	0.418	0.363	0.313	0.418	SUBCLONAL	1	TRUE	0	0.59803694341674	1		296	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0010563-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	453	606	0	ENST00000269305.4:c.838A>T	p.Arg280Ter	p.R280*	ENST00000269305	NM_001126112.2	280	Aga/Tga	8/11	0.59803694341674	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.59803694341674	2		606	744	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56367749	56367749	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010563-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	242	330	0	ENST00000348428.3:c.575T>G	p.Val192Gly	p.V192G	ENST00000348428	NM_006785.3	192	gTt/gGt	4/17	0.589085186723684	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.59803694341674	4		330	560	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047495	49047495	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0010563-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	149	260	0	ENST00000267163.4:c.2490-1G>C		p.X830_splice	ENST00000267163	NM_000321.2	830			0.59803694341674	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	0	0.59803694341674	2		260	248	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944379	206944379	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010563-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	102	399	0	ENST00000423557.1:c.251C>G	p.Ser84Cys	p.S84C	ENST00000423557	NM_000572.2	84	tCt/tGt	3/5	0.59803694341674	5	FACETS	0.794	0.71	0.884	0.199	0.177	0.221	SUBCLONAL	1	TRUE	1	0.59803694341674	5		399	815	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111557	56111557	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010563-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	47	63	0	ENST00000399503.3:c.157G>C	p.Glu53Gln	p.E53Q	ENST00000399503	NM_005921.1	53	Gag/Cag	1/20	0.59803694341674	4	FACETS	0.904	0.78	1	0.602	0.52	0.689	CLONAL	2	TRUE	1	0.59803694341674	4		63	139	SUCCESS
APC	324	MSKCC	GRCh37	5	112170671	112170671	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010563-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	71	323	0	ENST00000257430.4:c.1767G>C	p.Leu589Phe	p.L589F	ENST00000257430	NM_000038.5	589	ttG/ttC	15/16	0.59803694341674	4	FACETS	0.77	0.673	0.873	0.257	0.224	0.291	SUBCLONAL	1	TRUE	1	0.59803694341674	4		323	493	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407551	407551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010563-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	278	363	0	ENST00000380956.4:c.1309C>T	p.Pro437Ser	p.P437S	ENST00000380956	NM_001195286.1	437	Cca/Tca	9/9	0.590219631516997	4	FACETS	1	0.981	1			1	CLONAL	2	TRUE	NA	0.59803694341674	4		363	686	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123837	46123837	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0011515-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	20	128	0	ENST00000334344.6:c.103A>T	p.Lys35Ter	p.K35*	ENST00000334344	NM_152641.2	35	Aaa/Taa	2/21	0.237327046926691	3	FACETS	0.364	0.278	0.465	0.182	0.139	0.233	INDETERMINATE	1	TRUE	1	0.430872289225375	3		128	310	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393216	393216	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011515-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	51	357	0	ENST00000380956.4:c.64G>C	p.Gly22Arg	p.G22R	ENST00000380956	NM_001195286.1	22	Ggg/Cgg	2/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.430872289225375	NA		357	535	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21626490	21626490	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011515-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	139	257	0	ENST00000421138.2:c.1442A>G	p.Asp481Gly	p.D481G	ENST00000421138		481	gAc/gGc	13/16	0.237327046926691	3	FACETS	1	0.982	1	0.648	0.592	0.707	INDETERMINATE	1	TRUE	1	0.430872289225375	3		257	605	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941316	71941316	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0011515-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	149	443	0	ENST00000298229.2:c.1090+1G>T		p.X364_splice	ENST00000298229	NM_001567.3	364			NA	2	FACETS	1	0.947	1			1	INDETERMINATE	1	TRUE	NA	0.430872289225375	2		443	662	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577276	64577276	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011515-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	74	482	0	ENST00000312049.6:c.306C>G	p.Asp102Glu	p.D102E	ENST00000312049	NM_130799.2	102	gaC/gaG	2/10	0.237327046926691	3	FACETS	0.422	0.368	0.48	0.211	0.184	0.24	INDETERMINATE	1	TRUE	1	0.430872289225375	3		482	990	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647566	23647566	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs794727654	NA	P-0011515-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	71	356	0	ENST00000261584.4:c.301G>C	p.Asp101His	p.D101H	ENST00000261584	NM_024675.3	101	Gat/Cat	4/13	NA	2	FACETS	0.49	0.428	0.558			1	INDETERMINATE	1	TRUE	NA	0.430872289225375	2		356	672	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445041	89445041	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011515-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	38	292	0	ENST00000336596.2:c.1361C>A	p.Ser454Tyr	p.S454Y	ENST00000336596	NM_005233.5	454	tCt/tAt	6/17	0.17779199737493	2	FACETS	0.336	0.277	0.402	0.168	0.138	0.201	INDETERMINATE	1	TRUE	0	0.430872289225375	2		292	525	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056056	26056056	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011515-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	83	281	0	ENST00000343677.2:c.601A>G	p.Lys201Glu	p.K201E	ENST00000343677	NM_005319.3	201	Aag/Gag	1/1	0.308821226022897	3	FACETS	0.965	0.855	1	0.483	0.427	0.542	CLONAL	1	TRUE	1	0.430872289225375	3		281	485	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740592	145740592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011515-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1601	85	572	0	ENST00000428558.2:c.1425G>T	p.Gln475His	p.Q475H	ENST00000428558	NM_004260.3	475	caG/caT	8/22	0.430872289225375	7	FACETS	0.486	0.427	0.549	0.122	0.106	0.138	SUBCLONAL	1	TRUE	3	0.430872289225375	7		572	1686	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0013550-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	311	181	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.882490283854651	3	FACETS	0.927	0.885	0.968	0.927	0.885	0.968	CLONAL	2	TRUE	1	0.882490283854651	3		181	548	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0013550-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	175	429	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	0.972	0.907	1	0.972	0.907	1	CLONAL	1	TRUE	1	0.882490283854651	2		429	408	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259477	89259477	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200567888	NA	P-0013550-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	234	478	0	ENST00000336596.2:c.621G>T	p.Lys207Asn	p.K207N	ENST00000336596	NM_005233.5	207	aaG/aaT	3/17	1	2	FACETS	0.964	0.908	1	0.964	0.908	1	CLONAL	1	TRUE	1	0.882490283854651	2		478	550	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259236	89259236	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013550-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	184	340	0	ENST00000336596.2:c.380C>G	p.Ser127Cys	p.S127C	ENST00000336596	NM_005233.5	127	tCt/tGt	3/17	1	2	FACETS	0.959	0.895	1	0.959	0.895	1	CLONAL	1	TRUE	1	0.882490283854651	2		340	435	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462400	89462400	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1162005172	NA	P-0013550-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	239	463	0	ENST00000336596.2:c.1872T>A	p.Asp624Glu	p.D624E	ENST00000336596	NM_005233.5	624	gaT/gaA	10/17	1	2	FACETS	0.992	0.935	1	0.992	0.935	1	CLONAL	1	TRUE	1	0.882490283854651	2		463	546	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094304	27094305	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AATG	novel	NA	P-0013550-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	233	405	0	ENST00000324856.7:c.3014_3017dup	p.Lys1007Ter	p.K1007*	ENST00000324856	NM_006015.4	1004	-/AATG	11/20	1	2	FACETS	0.964	0.907	1	0.964	0.907	1	CLONAL	1	TRUE	1	0.882490283854651	2		405	548	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955539	90955539	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013550-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	205	417	0	ENST00000265433.3:c.2126T>A	p.Ile709Lys	p.I709K	ENST00000265433	NM_002485.4	709	aTa/aAa	14/16	0.672541263427866	3	FACETS	1	0.982	1	0.57	0.532	0.609	CLONAL	1	TRUE	1	0.882490283854651	3		417	587	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953730	48953730	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs3092891	NA	P-0013868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	442	202	2	ENST00000267163.4:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000267163	NM_000321.2	445	Cga/Tga	14/27	0.520081061696554	2	FACETS	1	0.993	1	1	0.997	1	CLONAL	3	TRUE	0	0.520081061696554	2		204	540	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81939065	81939065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867345397	NA	P-0013868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	509	1048	2	ENST00000359376.3:c.1420G>A	p.Glu474Lys	p.E474K	ENST00000359376	NM_002661.3	474	Gaa/Aaa	15/33	0.37440217334579	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.520081061696554	1		1050	1062	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932807	39932808	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTGCTGAATAACGGATG	novel	NA	P-0013868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	196	857	0	ENST00000378444.4:c.1775_1791dup	p.Val598HisfsTer77	p.V598Hfs*77	ENST00000378444	NM_001123385.1	597	-/CATCCGTTATTCAGCAC	4/15	1	2	FACETS	0.675	0.624	0.728	0.675	0.624	0.728	SUBCLONAL	1	TRUE	1	0.520081061696554	2		857	1116	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577075	7577075	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013929-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	309	717	0	ENST00000269305.4:c.863del	p.Asn288IlefsTer57	p.N288Ifs*57	ENST00000269305	NM_001126112.2	288	aAt/at	8/11	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	2	TRUE	NA	0.313585217589219	2		717	909	SUCCESS
APC	324	MSKCC	GRCh37	5	112175096	112175097	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs786203760	NA	P-0013929-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	37	162	0	ENST00000257430.4:c.3807_3808del	p.Ile1269MetfsTer6	p.I1269Mfs*6	ENST00000257430	NM_000038.5	1269	ATa/a	16/16	0.307850249376517	2	FACETS	0.761	0.637	0.895	0.761	0.637	0.895	SUBCLONAL	2	TRUE	0	0.313585217589219	2		162	155	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672309	30672309	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013929-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	139	759	0	ENST00000376406.3:c.4651C>G	p.Pro1551Ala	p.P1551A	ENST00000376406	NM_014641.2	1551	Ccc/Gcc	10/15	0.11042926146985	5	FACETS	1	0.972	1	0.39	0.354	0.428	INDETERMINATE	1	TRUE	2	0.313585217589219	5		759	1114	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508424	106508424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751449393	NA	P-0013929-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	29	262	0	ENST00000359195.3:c.418C>T	p.Arg140Trp	p.R140W	ENST00000359195	NM_002649.2	140	Cgg/Tgg	2/11	0.11042926146985	5	FACETS	0.938	0.755	1	0.313	0.251	0.382	INDETERMINATE	1	TRUE	2	0.313585217589219	5		262	290	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599338	55599338	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014184-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	149	411	0	ENST00000288135.5:c.2464A>T	p.Asn822Tyr	p.N822Y	ENST00000288135	NM_000222.2	822	Aat/Tat	17/21	0.134121774100136	4	FACETS	0.83	0.767	0.894	0.83	0.767	0.894	INDETERMINATE	2	TRUE	2	0.830034217724052	4		411	396	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593618	55593662	+	inframe_deletion	In_Frame_Del	DEL	GAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTT	GAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTT	-	novel	NA	P-0014184-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	178	451	0	ENST00000288135.5:c.1684_1728del	p.Glu562_Leu576del	p.E562_L576del	ENST00000288135	NM_000222.2	562	GAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTT/-	11/21	0.134121774100136	4	FACETS	0.776	0.721	0.832	0.776	0.721	0.832	INDETERMINATE	2	TRUE	2	0.830034217724052	4		451	506	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	149	488	0	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.921	0.848	0.996	0.921	0.848	0.996	CLONAL	1	TRUE	1	0.673987076272559	2		488	480	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0014669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	214	562	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.673987076272559	2		562	629	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0014669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	271	657	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.937	0.882	0.994	0.937	0.882	0.994	CLONAL	1	TRUE	1	0.673987076272559	2		660	858	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	251	700	3	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.673987076272559	2		703	658	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170991	56170991	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	178	513	0	ENST00000399503.3:c.1823del	p.Gly608AlafsTer48	p.G608Afs*48	ENST00000399503	NM_005921.1	607	Ggg/gg	10/20	1	2	FACETS	0.991	0.92	1	0.991	0.92	1	CLONAL	1	TRUE	1	0.673987076272559	2		513	533	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201671	66201671	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773217274	NA	P-0014669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	45	582	0	ENST00000273854.3:c.2831C>T	p.Thr944Met	p.T944M	ENST00000273854	NM_004439.5	944	aCg/aTg	16/18	1	2	FACETS	0.201	0.168	0.237	0.201	0.168	0.237	SUBCLONAL	1	TRUE	1	0.673987076272559	2		582	666	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94179032	94179032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148637964	NA	P-0014669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	92	455	0	ENST00000323929.3:c.1811G>A	p.Arg604His	p.R604H	ENST00000323929	NM_005591.3	604	cGt/cAt	16/20	1	2	FACETS	0.472	0.42	0.528	0.472	0.42	0.528	SUBCLONAL	1	TRUE	1	0.673987076272559	2		455	578	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519886	NA	P-0014669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	200	473	0	ENST00000349496.5:c.97T>G	p.Ser33Ala	p.S33A	ENST00000349496	NM_001904.3	33	Tct/Gct	3/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.673987076272559	2		473	540	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720650	89720650	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1257124719	NA	P-0014669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	244	468	0	ENST00000371953.3:c.802-1G>A		p.X268_splice	ENST00000371953	NM_000314.4	268			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.673987076272559	2		468	699	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155721	56155722	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0014669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	176	479	0	ENST00000399503.3:c.816_817del	p.Arg273SerfsTer27	p.R273Sfs*27	ENST00000399503	NM_005921.1	271	agAAaa/agaa	3/20	1	2	FACETS	0.953	0.884	1	0.953	0.884	1	CLONAL	1	TRUE	1	0.673987076272559	2		479	548	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126729	5126729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774469142	NA	P-0014669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	173	547	1	ENST00000381652.3:c.3337C>T	p.Arg1113Cys	p.R1113C	ENST00000381652	NM_004972.3	1113	Cgc/Tgc	25/25	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.673987076272559	2		548	474	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563349	21563349	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	20	1361	1	ENST00000382592.4:c.570del	p.Tyr191ThrfsTer49	p.Y191Tfs*49	ENST00000382592	NM_014572.2	190	ccC/cc	4/8	1	2	FACETS	0.062	0.047	0.08	0.062	0.047	0.08	SUBCLONAL	1	TRUE	1	0.673987076272559	2		1362	953	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350626	15350626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1234699192	NA	P-0014669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	49	1116	1	ENST00000263377.2:c.3289C>T	p.Arg1097Cys	p.R1097C	ENST00000263377	NM_058243.2	1097	Cgt/Tgt	16/20	1	2	FACETS	0.182	0.154	0.214	0.182	0.154	0.214	SUBCLONAL	1	TRUE	1	0.673987076272559	2		1117	798	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0014669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	37	1271	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.149	0.122	0.18	0.149	0.122	0.18	SUBCLONAL	1	TRUE	1	0.673987076272559	2		1275	735	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089592	27089593	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0014669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	285	969	1	ENST00000324856.7:c.2549dup	p.Tyr850Ter	p.Y850*	ENST00000324856	NM_006015.4	850	tat/tAat	8/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.673987076272559	2		970	775	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903690	114903690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369436357	NA	P-0014669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	259	733	1	ENST00000543371.1:c.694C>T	p.Arg232Trp	p.R232W	ENST00000543371	NM_001198531.1	232	Cgg/Tgg	7/14	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.673987076272559	2		734	716	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456660	138456660	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	249	595	4	ENST00000289153.2:c.690del	p.Lys230AsnfsTer3	p.K230Nfs*3	ENST00000289153	NM_006219.2	230	aaA/aa	4/22	0.673987076272559	3	FACETS	1	0.976	1	0.542	0.508	0.578	CLONAL	1	TRUE	1	0.673987076272559	3		599	911	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589576	67589576	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1289537429	NA	P-0014669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	141	243	1	ENST00000274335.5:c.1344del	p.Lys448AsnfsTer32	p.K448Nfs*32	ENST00000274335		447	Aaa/aa	10/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.673987076272559	2		244	391	SUCCESS
APC	324	MSKCC	GRCh37	5	112163705	112163705	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0014669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	136	301	0	ENST00000257430.4:c.1626+2T>A		p.X542_splice	ENST00000257430	NM_000038.5	542			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.673987076272559	2		301	355	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341704	8341704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764664438	NA	P-0014669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	255	585	0	ENST00000356435.5:c.4936C>T	p.Leu1646Phe	p.L1646F	ENST00000356435		1646	Ctc/Ttc	29/35	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.673987076272559	2		585	656	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	272	819	0	ENST00000378444.4:c.4376A>C	p.Asn1459Thr	p.N1459T	ENST00000378444	NM_001123385.1	1459	aAt/aCt	10/15	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.673987076272559	2		819	644	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937041	48937045	+	frameshift_variant	Frame_Shift_Del	DEL	ATACA	ATACA	TAT	novel	NA	P-0014669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	189	422	0	ENST00000267163.4:c.809_813delinsTAT	p.Asp270ValfsTer2	p.D270Vfs*2	ENST00000267163	NM_000321.2	270	gATACA/gTAT	8/27	0.673987076272559	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.673987076272559	1		422	333	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589295	67589339	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TATCCAAATACCAACAGGTAATAAAAACTGAATGAATTATCCAGT	TATCCAAATACCAACAGGTAATAAAAACTGAATGAATTATCCAGT	CAAA	novel	NA	P-0014669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	97	392	1	ENST00000274335.5:c.1283_1299+28delinsCAAA		p.X428_splice	ENST00000274335		428		9/15	1	2	FACETS	0.744	0.668	0.823	0.744	0.668	0.823	SUBCLONAL	1	TRUE	1	0.673987076272559	2		393	387	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961492	41961492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	275	738	0	ENST00000219905.7:c.400C>T	p.Arg134Cys	p.R134C	ENST00000219905	NM_001164273.1	134	Cgt/Tgt	2/24	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.673987076272559	2		738	718	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640689	3640689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750906921	NA	P-0014669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	43	1205	0	ENST00000294008.3:c.2950G>A	p.Glu984Lys	p.E984K	ENST00000294008	NM_032444.2	984	Gaa/Aaa	12/15	1	2	FACETS	0.166	0.138	0.197	0.166	0.138	0.197	SUBCLONAL	1	TRUE	1	0.673987076272559	2		1205	770	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921480	39921480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	170	990	3	ENST00000378444.4:c.4340G>A	p.Arg1447His	p.R1447H	ENST00000378444	NM_001123385.1	1447	cGc/cAc	10/15	1	2	FACETS	0.659	0.607	0.713	0.659	0.607	0.713	SUBCLONAL	1	TRUE	1	0.673987076272559	2		993	765	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219940	36219941	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCA	novel	NA	P-0014669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	256	1090	0	ENST00000222270.7:c.4743_4746dup	p.Leu1583CysfsTer96	p.L1583Cfs*96	ENST00000222270	NM_014727.1	1581	tgt/tgTGCAt	21/37	1	2	FACETS	0.979	0.92	1	0.979	0.92	1	CLONAL	1	TRUE	1	0.673987076272559	2		1090	776	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119545703	119545703	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0014669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	176	436	0	ENST00000316626.5:c.1235-1G>T		p.X412_splice	ENST00000316626		412			0.673987076272559	3	FACETS	1	0.978	1	0.574	0.531	0.618	CLONAL	1	TRUE	1	0.673987076272559	3		436	608	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31947279	31947279	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	127	827	0	ENST00000375333.2:c.764T>C	p.Phe255Ser	p.F255S	ENST00000375333	NM_032454.1	255	tTc/tCc	5/8	1	2	FACETS	0.526	0.477	0.577	0.526	0.477	0.577	SUBCLONAL	1	TRUE	1	0.673987076272559	2		827	717	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201802	102201802	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	52	480	1	ENST00000263464.3:c.1154C>A	p.Ala385Asp	p.A385D	ENST00000263464	NM_001165.4	385	gCc/gAc	6/9	0.889494633152074	2	FACETS	0.266	0.227	0.309	0.133	0.113	0.155	SUBCLONAL	1	TRUE	0	0.889494633152074	2		481	439	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696151	52696151	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	67	650	0	ENST00000394830.3:c.526G>T	p.Gly176Ter	p.G176*	ENST00000394830	NM_018313.4	176	Gga/Tga	5/30	0.345981220658105	2	FACETS	0.168	0.145	0.192	0.084	0.072	0.096	INDETERMINATE	1	TRUE	0	0.889494633152074	2		650	899	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0014891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	126	161	0	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	1	2	FACETS	0.84	0.773	0.908	1	0.989	1	CLONAL	2	TRUE	1	0.4999838921344	2		161	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0017174-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	104	1027	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	0.223709033057568	3	FACETS	0.922	0.824	1	0.461	0.412	0.514	CLONAL	1	TRUE	1	0.223709033057568	3		1027	1121	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0017174-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	50	415	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	0.836	0.709	0.975	0.836	0.709	0.975	CLONAL	1	TRUE	1	0.223709033057568	2		415	535	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30956886	30956889	+	frameshift_variant	Frame_Shift_Del	DEL	TTTA	TTTA	-	novel	NA	P-0017174-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	51	552	0	ENST00000375687.4:c.213_216del	p.Phe71LeufsTer48	p.F71Lfs*48	ENST00000375687	NM_015338.5	71	tTTTAt/tt	4/13	1	2	FACETS	0.737	0.625	0.859	0.737	0.625	0.859	SUBCLONAL	1	TRUE	1	0.223709033057568	2		552	619	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873297	151873297	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017174-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	25	283	0	ENST00000262189.6:c.9241G>C	p.Glu3081Gln	p.E3081Q	ENST00000262189	NM_170606.2	3081	Gaa/Caa	38/59	0.223709033057568	3	FACETS	0.742	0.585	0.922			1	CLONAL	1	TRUE	NA	0.223709033057568	3		283	335	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032579	47032579	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0017174-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	392	436	0	ENST00000377604.3:c.485del	p.Met162SerfsTer104	p.M162Sfs*104	ENST00000377604	NM_001204468.1	162	aTg/ag	5/24	0.223709033057568	4	FACETS	1	0.983	1			1	CLONAL	5	TRUE	NA	0.223709033057568	4		436	815	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862906	9862906	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017174-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	38	669	0	ENST00000330684.3:c.2397C>G	p.Ile799Met	p.I799M	ENST00000330684	NM_001134407.1	799	atC/atG	12/13	1	2	FACETS	0.481	0.396	0.576	0.481	0.396	0.576	SUBCLONAL	1	TRUE	1	0.223709033057568	2		669	707	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020690	37020690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	385	374	1	ENST00000358127.4:c.155G>A	p.Cys52Tyr	p.C52Y	ENST00000358127	NM_001280556.1	52	tGc/tAc	2/10	1	2	FACETS	0.731	0.695	0.768	0.731	0.695	0.768	SUBCLONAL	1	TRUE	1	0.85130839397269	2		375	1237	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932189	39932190	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	706	557	0	ENST00000378444.4:c.2409dup	p.Val804CysfsTer13	p.V804Cfs*13	ENST00000378444	NM_001123385.1	803	-/T	4/15	0.276236662657323	1	FACETS	0.647	0.626	0.668	0.647	0.626	0.668	INDETERMINATE	1	TRUE	0	0.85130839397269	1		557	1473	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936995	48936995	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778842	NA	P-0017290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	458	568	0	ENST00000267163.4:c.763C>T	p.Arg255Ter	p.R255*	ENST00000267163	NM_000321.2	255	Cga/Tga	8/27	1	2	FACETS	0.945	0.904	0.987	0.945	0.904	0.987	CLONAL	1	TRUE	1	0.829623338186325	2		568	1168	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953748	48953755	+	frameshift_variant	Frame_Shift_Del	DEL	CGCTTGTA	CGCTTGTA	-	novel	NA	P-0017290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	191	429	1	ENST00000267163.4:c.1351_1358del	p.Arg451LeufsTer9	p.R451Lfs*9	ENST00000267163	NM_000321.2	451	CGCTTGTAt/t	14/27	1	2	FACETS	0.584	0.541	0.629	0.584	0.541	0.629	SUBCLONAL	1	TRUE	1	0.829623338186325	2		430	788	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017392-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	255	383	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.450681472487902	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.450681472487902	2		383	515	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0017392-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	428	840	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.450681472487902	2	FACETS	0.991	0.949	1	0.991	0.949	1	CLONAL	2	TRUE	0	0.450681472487902	2		843	958	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974813	21974813	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017392-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	46	21	0	ENST00000304494.5:c.14C>G	p.Ala5Gly	p.A5G	ENST00000304494	NM_000077.4	5	gCg/gGg	1/3	0.450681472487902	1	FACETS	0.775	0.676	0.876	1	0.97	1	SUBCLONAL	2	TRUE	0	0.450681472487902	1		21	102	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974819	21974822	+	frameshift_variant	Frame_Shift_Del	DEL	GGCT	GGCT	-	novel	NA	P-0017392-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	38	18	0	ENST00000304494.5:c.5_8del	p.Glu2GlyfsTer23	p.E2Gfs*23	ENST00000304494	NM_000077.4	2	gAGCCg/gg	1/3	0.450681472487902	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.450681472487902	1		18	88	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929235	44929235	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017392-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	204	41	0	ENST00000377967.4:c.2335del	p.Gln779SerfsTer6	p.Q779Sfs*6	ENST00000377967	NM_021140.2	779	Cag/ag	17/29	0.348759262897875	0	FACETS	0.544	0.51	0.578			1	SUBCLONAL	2	TRUE	NA	0.450681472487902	0		41	457	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0018666-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	50	309	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.909	0.773	1	0.909	0.773	1	CLONAL	1	TRUE	1	0.25169747184825	2		310	437	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117870639	117870639	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1360712011	NA	P-0018666-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	69	286	0	ENST00000297338.2:c.433A>C	p.Met145Leu	p.M145L	ENST00000297338	NM_006265.2	145	Atg/Ctg	5/14	0.25169747184825	3	FACETS	1	0.951	1	0.595	0.519	0.677	CLONAL	1	TRUE	1	0.25169747184825	3		286	519	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955550	48955550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913304	NA	P-0018838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	229	237	1	ENST00000267163.4:c.1666C>T	p.Arg556Ter	p.R556*	ENST00000267163	NM_000321.2	556	Cga/Tga	17/27	1	2	FACETS	0.813	0.764	0.862	1	0.994	1	CLONAL	2	TRUE	1	0.512214219451491	2		238	550	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941633	48941633	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	146	197	0	ENST00000267163.4:c.943G>T	p.Glu315Ter	p.E315*	ENST00000267163	NM_000321.2	315	Gaa/Taa	10/27	1	2	FACETS	0.779	0.72	0.839	1	0.99	1	SUBCLONAL	2	TRUE	1	0.512214219451491	2		197	366	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17949096	17949096	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019278-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	198	952	0	ENST00000458235.1:c.1545G>T	p.Lys515Asn	p.K515N	ENST00000458235	NM_000215.3	515	aaG/aaT	11/24	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.741495969165735	2		952	512	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729767	41729767	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019278-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	148	686	0	ENST00000242208.4:c.762G>T	p.Leu254Phe	p.L254F	ENST00000242208	NM_002192.2	254	ttG/ttT	3/3	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.741495969165735	2		686	386	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930283	39930290	+	frameshift_variant	Frame_Shift_Del	DEL	TTTTGTCC	TTTTGTCC	-	novel	NA	P-0019361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	73	627	0	ENST00000378444.4:c.3174_3181del	p.Asp1059AlafsTer17	p.D1059Afs*17	ENST00000378444	NM_001123385.1	1058	caGGACAAAAag/caag	6/15	0.642824986095826	1	FACETS	0.118	0.103	0.135	0.118	0.103	0.135	SUBCLONAL	1	TRUE	0	0.824182700830921	1		627	883	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0019630-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	228	219	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.640659004144019	2	FACETS	0.991	0.944	1	0.991	0.944	1	CLONAL	2	TRUE	0	0.640659004144019	2		219	359	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019630-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	387	374	0				ENST00000310581	NM_198253.2	-/1132			0.640659004144019	5	FACETS	0.984	0.948	1	0.984	0.948	1	CLONAL	4	TRUE	1	0.640659004144019	5		374	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0019630-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	202	470	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.640659004144019	3	FACETS	0.853	0.791	0.918			1	CLONAL	1	TRUE	NA	0.640659004144019	3		471	976	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578187	7578187	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs878854071	NA	P-0019630-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	396	403	0	ENST00000269305.4:c.662del	p.Glu221GlyfsTer26	p.E221Gfs*26	ENST00000269305	NM_001126112.2	221	gAg/gg	6/11	0.640659004144019	3	FACETS	0.942	0.901	0.984			1	CLONAL	2	TRUE	NA	0.640659004144019	3		403	866	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443551	49443551	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019630-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	181	402	0	ENST00000301067.7:c.3820G>C	p.Asp1274His	p.D1274H	ENST00000301067	NM_003482.3	1274	Gat/Cat	11/54	1	2	FACETS	0.872	0.808	0.938	0.872	0.808	0.938	CLONAL	1	TRUE	1	0.640659004144019	2		402	648	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139804372	139804372	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019630-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	162	377	0	ENST00000247668.2:c.529G>A	p.Ala177Thr	p.A177T	ENST00000247668	NM_021138.3	177	Gcg/Acg	6/11	1	2	FACETS	0.903	0.833	0.975	0.903	0.833	0.975	CLONAL	1	TRUE	1	0.640659004144019	2		377	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0019781-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	173	521	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.33150197434686	1	FACETS	0.953	0.877	1	0.953	0.877	1	CLONAL	1	TRUE	0	0.33150197434686	1		521	914	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420209	88420209	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019781-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	89	285	0	ENST00000360948.2:c.2477C>A	p.Ala826Asp	p.A826D	ENST00000360948	NM_001012338.2	826	gCt/gAt	19/19	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.33150197434686	2		285	509	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182580	99182580	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019781-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	79	257	0	ENST00000074304.5:c.2383C>T	p.Gln795Ter	p.Q795*	ENST00000074304	NM_001134224.1	795	Cag/Tag	22/26	1	2	FACETS	0.775	0.682	0.875	0.775	0.682	0.875	SUBCLONAL	1	TRUE	1	0.33150197434686	2		257	615	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0020426-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	749	840	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.622367707925173	2	FACETS	0.979	0.952	1	0.979	0.952	1	CLONAL	2	TRUE	0	0.632944247362055	2		843	1209	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631102	69631102	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121917704	NA	P-0020426-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2539	594	432	0	ENST00000334134.2:c.310C>T	p.Arg104Ter	p.R104*	ENST00000334134	NM_005247.2	104	Cga/Tga	2/3	0.632944247362055	7	FACETS	0.774	0.74	0.808	0.309	0.296	0.324	SUBCLONAL	2	TRUE	2	0.632944247362055	7		432	3133	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867192	68867192	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0020426-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	200	242	0	ENST00000261769.5:c.2440-1G>T		p.X814_splice	ENST00000261769	NM_004360.3	814			0.632944247362055	3	FACETS	0.853	0.791	0.918	0.427	0.395	0.459	CLONAL	1	TRUE	1	0.632944247362055	3		242	975	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280625	41280625	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020426-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	405	352	0	ENST00000349496.5:c.2138A>G	p.Asp713Gly	p.D713G	ENST00000349496	NM_001904.3	713	gAt/gGt	15/15	0.542272374529312	4	FACETS	0.851	0.81	0.892	0.851	0.81	0.892	CLONAL	2	TRUE	2	0.632944247362055	4		352	1228	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932227	39932227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020426-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	823	260	0	ENST00000378444.4:c.2372G>A	p.Trp791Ter	p.W791*	ENST00000378444	NM_001123385.1	791	tGg/tAg	4/15	0.514689568292087	2	FACETS	1	0.998	1			1	CLONAL	2	TRUE	NA	0.632944247362055	2		260	1098	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437328	121437328	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	704	757	0	ENST00000257555.6:c.1666C>G	p.His556Asp	p.H556D	ENST00000257555		556	Cac/Gac	9/10	0.526437703659674	4	FACETS	0.803	0.774	0.831	0.535	0.516	0.554	INDETERMINATE	2	TRUE	1	0.93220487122503	4		757	1818	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198111	185198111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	296	544	0	ENST00000265026.3:c.2593G>T	p.Asp865Tyr	p.D865Y	ENST00000265026	NM_004721.4	865	Gac/Tac	13/14	0.795712873871901	3	FACETS	1	0.977	1	0.533	0.503	0.563	CLONAL	1	TRUE	1	0.93220487122503	3		544	874	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178454	56178456	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0021827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	68	298	0	ENST00000399503.3:c.3427_3429del	p.Ser1143del	p.S1143del	ENST00000399503	NM_005921.1	1143	AGT/-	14/20	1	2	FACETS	0.486	0.427	0.55	0.486	0.427	0.55	SUBCLONAL	1	TRUE	1	0.93220487122503	2		298	300	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178454	56178458	+	protein_altering_variant	In_Frame_Del	DEL	AGTGA	AGTGA	GT	novel	NA	P-0021827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	71	295	3	ENST00000399503.3:c.3427_3431delinsGT	p.Ser1143_Asp1144delinsVal	p.S1143_D1144delinsV	ENST00000399503	NM_005921.1	1143	AGTGAt/GTt	14/20	1	2	FACETS	0.501	0.441	0.565	0.501	0.441	0.565	SUBCLONAL	1	TRUE	1	0.93220487122503	2		298	304	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178458	56178458	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	71	298	0	ENST00000399503.3:c.3431A>T	p.Asp1144Val	p.D1144V	ENST00000399503	NM_005921.1	1144	gAt/gTt	14/20	1	2	FACETS	0.516	0.455	0.581	0.516	0.455	0.581	SUBCLONAL	1	TRUE	1	0.93220487122503	2		298	295	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039435	49039436	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0021827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	245	569	0	ENST00000267163.4:c.2421_2422insTA	p.Pro808TyrfsTer3	p.P808Yfs*3	ENST00000267163	NM_000321.2	807	tca/tcATa	23/27	1	2	FACETS	0.914	0.862	0.967	0.914	0.862	0.967	CLONAL	1	TRUE	1	0.93220487122503	2		569	575	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954222	48954222	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0022386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	171	565	0	ENST00000267163.4:c.1421+2T>C		p.X474_splice	ENST00000267163	NM_000321.2	474			0.676078003969486	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.676078003969486	3		565	203	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922244	39922245	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGGCTGAGCC	novel	NA	P-0022386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	32	323	0	ENST00000378444.4:c.3918_3927dup	p.Ser1310GlyfsTer19	p.S1310Gfs*19	ENST00000378444	NM_001123385.1	1309	-/GGCTCAGCCA	9/15	1	1	FACETS	0.285	0.232	0.343	0.285	0.232	0.343	SUBCLONAL	1	TRUE	0	0.676078003969486	1		323	220	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878175	48878176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTCT	novel	NA	P-0022583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	74	239	0	ENST00000267163.4:c.129_132dup	p.Val45SerfsTer5	p.V45Sfs*5	ENST00000267163	NM_000321.2	43	cct/cCTCTct	1/27	1	2	FACETS	0.653	0.58	0.73	0.653	0.58	0.73	SUBCLONAL	1	TRUE	1	0.939883213706772	2		239	241	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954315	48954317	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	rs587776788	NA	P-0022662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	204	483	0	ENST00000267163.4:c.1439_1441del	p.Asn480del	p.N480del	ENST00000267163	NM_000321.2	479	gACAac/gac	16/27	1	2	FACETS	0.994	0.93	1	0.994	0.93	1	CLONAL	1	TRUE	1	0.767074222031092	2		483	535	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817912	3817912	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0022662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	74	503	0	ENST00000262367.5:c.3061-2A>G		p.X1021_splice	ENST00000262367	NM_004380.2	1021			1	2	FACETS	0.473	0.416	0.534	0.473	0.416	0.534	SUBCLONAL	1	TRUE	1	0.767074222031092	2		503	408	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858638	57858638	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	418	571	0	ENST00000228682.2:c.376A>G	p.Ile126Val	p.I126V	ENST00000228682	NM_005269.2	126	Att/Gtt	4/12	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.857342341832854	2		571	896	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941703	48941703	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	201	482	0	ENST00000267163.4:c.1013del	p.Asp338ValfsTer11	p.D338Vfs*11	ENST00000267163	NM_000321.2	338	gAt/gt	10/27	0.857342341832854	2	FACETS	0.949	0.913	0.982	0.949	0.913	0.982	CLONAL	2	TRUE	0	0.857342341832854	2		482	247	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923751	39923751	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	165	985	0	ENST00000378444.4:c.3340G>T	p.Glu1114Ter	p.E1114*	ENST00000378444	NM_001123385.1	1114	Gag/Tag	7/15	0.158835201558617	0	FACETS	0.324	0.298	0.351			1	INDETERMINATE	1	TRUE	0	0.588712549920316	0		985	712	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953760	48953760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913302	NA	P-0022753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	197	167	0	ENST00000267163.4:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000267163	NM_000321.2	455	Cga/Tga	14/27	0.590760865242872	4	FACETS	1	0.984	1	1	0.995	1	CLONAL	5	FALSE	0	0.590760865242872	4		167	210	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947539	48947539	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1131690892	NA	P-0022929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	378	730	0	ENST00000267163.4:c.1128-2A>G		p.X376_splice	ENST00000267163	NM_000321.2	376			0.854106554538682	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.865774406431186	2		730	432	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932400	39932401	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTGTGTG	novel	NA	P-0022929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	224	488	0	ENST00000378444.4:c.2192_2198dup	p.Pro734ThrfsTer8	p.P734Tfs*8	ENST00000378444	NM_001123385.1	733	acg/acCACACACg	4/15	1	1	FACETS	0.817	0.777	0.857	0.817	0.777	0.857	CLONAL	1	TRUE	0	0.865774406431186	1		488	359	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916758	48916758	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	68	669	0	ENST00000267163.4:c.289del	p.Glu97AsnfsTer14	p.E97Nfs*14	ENST00000267163	NM_000321.2	96	aaG/aa	3/27	1	2	FACETS	0.998	0.874	1	0.998	0.874	1	CLONAL	1	TRUE	1	0.384770776538135	2		669	354	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30095750	30095750	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	48	596	0	ENST00000331968.5:c.1738G>C	p.Val580Leu	p.V580L	ENST00000331968	NM_002742.2	580	Gta/Cta	12/18	1	2	FACETS	0.673	0.57	0.784	0.673	0.57	0.784	SUBCLONAL	1	TRUE	1	0.384770776538135	2		596	371	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897450	78897450	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	237	822	0	ENST00000306801.3:c.2785A>T	p.Met929Leu	p.M929L	ENST00000306801	NM_020761.2	929	Atg/Ttg	23/34	0.286245539276607	3	FACETS	1	0.988	1	0.631	0.588	0.675	CLONAL	1	TRUE	1	0.384770776538135	3		822	1164	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308312	30308312	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0023348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	44	648	0	ENST00000262643.3:c.327-1G>A		p.X109_splice	ENST00000262643	NM_001238.2	109			1	2	FACETS	0.494	0.414	0.582	0.494	0.414	0.582	SUBCLONAL	1	TRUE	1	0.384770776538135	2		648	463	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954198	48954198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123331	NA	P-0023460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	167	526	1	ENST00000267163.4:c.1399C>T	p.Arg467Ter	p.R467*	ENST00000267163	NM_000321.2	467	Cga/Tga	15/27	1	2	FACETS	1	0.974	1	1	0.995	1	CLONAL	4	TRUE	1	0.180049378384511	2		527	421	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953730	48953730	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs3092891	NA	P-0023480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	575	202	2	ENST00000267163.4:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000267163	NM_000321.2	445	Cga/Tga	14/27	0.890248178703514	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.890248178703514	2		204	617	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842269	151842269	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	326	499	0	ENST00000262189.6:c.14143A>G	p.Met4715Val	p.M4715V	ENST00000262189	NM_170606.2	4715	Atg/Gtg	54/59	0.486073873582583	3	FACETS	1	0.993	1	0.645	0.612	0.678	INDETERMINATE	1	TRUE	1	0.890248178703514	3		499	821	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264737	46264737	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	81	422	0	ENST00000371998.3:c.1607C>T	p.Ser536Phe	p.S536F	ENST00000371998		536	tCc/tTc	12/23	1	2	FACETS	0.977	0.882	1	0.977	0.882	1	CLONAL	1	TRUE	1	0.895880487050018	2		422	185	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164853	106164853	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	148	440	0	ENST00000380013.4:c.3721G>T	p.Ala1241Ser	p.A1241S	ENST00000380013	NM_001127208.2	1241	Gct/Tct	6/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.895880487050018	2		440	319	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294412	1294412	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	220	600	0	ENST00000310581.5:c.589C>A	p.Leu197Met	p.L197M	ENST00000310581	NM_198253.2	197	Ctg/Atg	2/16	1	2	FACETS	0.954	0.896	1	0.954	0.896	1	CLONAL	1	TRUE	1	0.895880487050018	2		600	515	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953760	48953760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913302	NA	P-0025171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	187	167	0	ENST00000267163.4:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000267163	NM_000321.2	455	Cga/Tga	14/27	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.909773784355948	2		167	409	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039248	49039248	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs1131690882	NA	P-0025378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	646	534	0	ENST00000267163.4:c.2325+1G>C		p.X775_splice	ENST00000267163	NM_000321.2	775			0.741633812070584	2	FACETS	0.991	0.966	1	0.991	0.966	1	CLONAL	2	TRUE	0	0.741633812070584	2		534	879	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032388	11032388	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	48	641	0	ENST00000327064.4:c.1782del	p.Ser595ArgfsTer105	p.S595Rfs*105	ENST00000327064	NM_199141.1	594	gcG/gc	16/16	1	2	FACETS	0.209	0.176	0.245	0.209	0.176	0.245	SUBCLONAL	1	TRUE	1	0.741633812070584	2		641	619	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783290	9783290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	195	733	1	ENST00000377346.4:c.2534C>T	p.Ala845Val	p.A845V	ENST00000377346	NM_005026.3	845	gCa/gTa	20/24	1	2	FACETS	0.631	0.583	0.68	0.631	0.583	0.68	SUBCLONAL	1	TRUE	1	0.57239867052301	2		734	1080	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922044	39922056	+	frameshift_variant	Frame_Shift_Del	DEL	TCCCCGCCTGGAC	TCCCCGCCTGGAC	-	novel	NA	P-0025404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	150	383	0	ENST00000378444.4:c.4116_4128del	p.Glu1372AspfsTer4	p.E1372Dfs*4	ENST00000378444	NM_001123385.1	1372	gaGTCCAGGCGGGGA/ga	9/15	1	1	FACETS	0.906	0.837	0.977	0.906	0.837	0.977	CLONAL	1	TRUE	0	0.57239867052301	1		383	413	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936995	48936995	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778842	NA	P-0026049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	500	568	0	ENST00000267163.4:c.763C>T	p.Arg255Ter	p.R255*	ENST00000267163	NM_000321.2	255	Cga/Tga	8/27	0.804909202322523	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.804909202322523	2		568	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579409	7579410	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0026374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	278	707	0	ENST00000269305.4:c.277_278del	p.Leu93ValfsTer55	p.L93Vfs*55	ENST00000269305	NM_001126112.2	93	CTg/g	4/11	0.889342068853006	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.889342068853006	1		707	312	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888722	76888725	+	frameshift_variant	Frame_Shift_Del	DEL	TTTC	TTTC	-	novel	NA	P-0026374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	82	389	0	ENST00000373344.5:c.5104_5107del	p.Glu1702TyrfsTer22	p.E1702Yfs*22	ENST00000373344	NM_000489.3	1702	GAAAta/ta	19/35	0.889342068853006	1	FACETS	0.875	0.811	0.936	0.875	0.811	0.936	CLONAL	1	TRUE	0	0.889342068853006	1		389	117	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574235	95574235	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	48	200	0	ENST00000393063.1:c.2632G>T	p.Val878Phe	p.V878F	ENST00000393063	NM_030621.3	878	Gtt/Ttt	17/28	1	2	FACETS	0.915	0.797	1	0.915	0.797	1	CLONAL	1	TRUE	1	0.889342068853006	2		200	118	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451821	29451821	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	194	698	0	ENST00000389048.3:c.2744G>T	p.Trp915Leu	p.W915L	ENST00000389048	NM_004304.4	915	tGg/tTg	16/29	0.889342068853006	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.889342068853006	1		698	233	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57569877	57569878	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	novel	NA	P-0026374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	47	190	0	ENST00000316660.6:c.59_60del		p.X20_splice	ENST00000316660	NM_021127.2	20			1	2	FACETS	0.846	0.733	0.963	0.846	0.733	0.963	CLONAL	1	TRUE	1	0.889342068853006	2		190	125	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579386	7579386	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0027041-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	412	680	0	ENST00000269305.4:c.301A>T	p.Lys101Ter	p.K101*	ENST00000269305	NM_001126112.2	101	Aaa/Taa	4/11	0.75348729412091	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.75348729412091	2		680	532	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420291	88420291	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027041-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	135	415	0	ENST00000360948.2:c.2395G>T	p.Val799Leu	p.V799L	ENST00000360948	NM_001012338.2	799	Gtg/Ttg	19/19	0.746674660093243	3	FACETS	1	0.967	1	0.556	0.509	0.604	CLONAL	1	TRUE	1	0.75348729412091	3		415	444	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938193	36938193	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027041-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	705	744	0	ENST00000361632.4:c.768G>C	p.Trp256Cys	p.W256C	ENST00000361632		256	tgG/tgC	6/16	0.722440108827562	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	4	TRUE	0	0.75348729412091	4		744	817	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068881	30068881	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027041-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	103	481	0	ENST00000331968.5:c.2048C>G	p.Thr683Arg	p.T683R	ENST00000331968	NM_002742.2	683	aCg/aGg	14/18	0.75348729412091	3	FACETS	0.702	0.63	0.778	0.351	0.315	0.389	SUBCLONAL	1	TRUE	1	0.75348729412091	3		481	536	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786036	3786036	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0027041-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	285	606	0	ENST00000262367.5:c.4728+1G>A		p.X1576_splice	ENST00000262367	NM_004380.2	1576			0.75348729412091	3	FACETS	0.932	0.886	0.977	0.932	0.886	0.977	CLONAL	2	TRUE	1	0.75348729412091	3		606	559	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610129	10610129	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027041-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	378	618	0	ENST00000171111.5:c.581T>G	p.Ile194Ser	p.I194S	ENST00000171111	NM_203500.1	194	aTt/aGt	2/6	0.75348729412091	2	FACETS	0.982	0.95	1	0.982	0.95	1	CLONAL	2	TRUE	0	0.75348729412091	2		618	511	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223799	36223799	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027041-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	447	916	1	ENST00000222270.7:c.6349G>T	p.Val2117Leu	p.V2117L	ENST00000222270	NM_014727.1	2117	Gtg/Ttg	28/37	0.75348729412091	3	FACETS	0.98	0.943	1	0.98	0.943	1	CLONAL	2	TRUE	1	0.75348729412091	3		917	833	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343214	118343214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027041-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	47	262	0	ENST00000534358.1:c.1340C>T	p.Pro447Leu	p.P447L	ENST00000534358	NM_005933.3	447	cCg/cTg	3/36	0.75348729412091	3	FACETS	0.516	0.437	0.602	0.258	0.218	0.301	SUBCLONAL	1	TRUE	1	0.75348729412091	3		262	333	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291878	15291878	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1441446913	NA	P-0027041-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	216	847	1	ENST00000263388.2:c.2888C>T	p.Ala963Val	p.A963V	ENST00000263388	NM_000435.2	963	gCa/gTa	18/33	0.75348729412091	2	FACETS	1	0.937	1	0.5	0.468	0.533	CLONAL	1	TRUE	0	0.75348729412091	2		848	573	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910590	50910590	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027041-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	189	739	1	ENST00000440232.2:c.1693C>A	p.His565Asn	p.H565N	ENST00000440232	NM_002691.3	565	Cac/Aac	14/27	0.75348729412091	5	FACETS	0.987	0.911	1			1	CLONAL	1	TRUE	NA	0.75348729412091	5		740	1083	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952167	76952167	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs781943078	NA	P-0027041-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	196	351	0	ENST00000373344.5:c.268G>C	p.Val90Leu	p.V90L	ENST00000373344	NM_000489.3	90	Gta/Cta	5/35	0.644823578563486	3	FACETS	0.918	0.863	0.973			1	CLONAL	2	TRUE	NA	0.75348729412091	3		351	390	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610496	10610496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	65	864	0	ENST00000171111.5:c.214C>T	p.Leu72Phe	p.L72F	ENST00000171111	NM_203500.1	72	Ctc/Ttc	2/6	0.355645830758574	1	FACETS	0.892	0.778	1	0.892	0.778	1	CLONAL	1	TRUE	0	0.355645830758574	1		864	337	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058015	27058015	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	65	668	0	ENST00000324856.7:c.1723C>T	p.Gln575Ter	p.Q575*	ENST00000324856	NM_006015.4	575	Cag/Tag	3/20	0.355645830758574	1	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	0	0.355645830758574	1		668	298	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729689	162729711	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCGGAACGAGAGTGCCACCAA	TGGCGGAACGAGAGTGCCACCAA	-	novel	NA	P-0027097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	41	705	0	ENST00000367921.3:c.779_801del	p.Arg260LeufsTer3	p.R260Lfs*3	ENST00000367921	NM_006182.2	259	TGGCGGAACGAGAGTGCCACCAAt/t	8/18	0.355645830758574	3	FACETS	0.738	0.616	0.873	0.369	0.308	0.437	SUBCLONAL	1	TRUE	1	0.355645830758574	3		705	368	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396863	396863	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	69	955	0	ENST00000262320.3:c.163G>T	p.Glu55Ter	p.E55*	ENST00000262320	NM_003502.3	55	Gag/Tag	2/11	0.355645830758574	1	FACETS	0.879	0.77	0.995	0.879	0.77	0.995	CLONAL	1	TRUE	0	0.355645830758574	1		955	363	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779654	3779654	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	82	939	1	ENST00000262367.5:c.5394G>T	p.Met1798Ile	p.M1798I	ENST00000262367	NM_004380.2	1798	atG/atT	31/31	0.355645830758574	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.355645830758574	1		940	358	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646120	23646594	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCAAATAGTAATTGTTAACTTTCATCATCATCATCATCATCATCAAACACATCTTGATTTACCTTTCACTTGAATAAATAATTTTTCGTGCTGATATTTGTGTGAGGTGACTTCTTCCTTGGACCTGTTAACAATCGACAGGCTAGAAGTTGGCAAAAGTGGTTCACAATGATCTGATGCTGGGGTGCAGGCTGATTTTCTTTTTCCTGTGTATCTTCTACCAGGTGCTTGGGCAACTGCCTTCCTAGACAAGTCATTATCTTCAGTGGGCCCAGCGGGAGAGCTGACTTTAGTTAATGAGAGAAGTTTCTGAGAGGTTCTTGAACTTGGTTGTCCTGTGCATGTGCCAGACATCCTAATTTCACTTTGGTCAGTTTCCTCATTGGAAAGGTTTAAATTTTTACTTGCATCCTTATTTTTATTTTTAAACCCTTTTTTCTTGACATCCAAATGACTCTGAATGACAGCCTCCAC	GGCAAATAGTAATTGTTAACTTTCATCATCATCATCATCATCATCAAACACATCTTGATTTACCTTTCACTTGAATAAATAATTTTTCGTGCTGATATTTGTGTGAGGTGACTTCTTCCTTGGACCTGTTAACAATCGACAGGCTAGAAGTTGGCAAAAGTGGTTCACAATGATCTGATGCTGGGGTGCAGGCTGATTTTCTTTTTCCTGTGTATCTTCTACCAGGTGCTTGGGCAACTGCCTTCCTAGACAAGTCATTATCTTCAGTGGGCCCAGCGGGAGAGCTGACTTTAGTTAATGAGAGAAGTTTCTGAGAGGTTCTTGAACTTGGTTGTCCTGTGCATGTGCCAGACATCCTAATTTCACTTTGGTCAGTTTCCTCATTGGAAAGGTTTAAATTTTTACTTGCATCCTTATTTTTATTTTTAAACCCTTTTTTCTTGACATCCAAATGACTCTGAATGACAGCCTCCAC	-	novel	NA	P-0027097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	24	184	0	ENST00000261584.4:c.1273_1684+63del		p.X425_splice	ENST00000261584	NM_024675.3	425		4/13	0.355645830758574	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.355645830758574	1		184	87	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821880	72821880	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771247982	NA	P-0027097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	42	509	0	ENST00000268489.5:c.10295C>T	p.Ser3432Phe	p.S3432F	ENST00000268489	NM_006885.3	3432	tCc/tTc	10/10	0.335552704796807	1	FACETS	0.786	0.661	0.922	0.786	0.661	0.922	CLONAL	1	TRUE	0	0.355645830758574	1		509	247	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832065	72832094	+	inframe_deletion	In_Frame_Del	DEL	TTGGGCTCTGTTTATCTTCCAAGTCACTCT	TTGGGCTCTGTTTATCTTCCAAGTCACTCT	-	novel	NA	P-0027097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	66	663	0	ENST00000268489.5:c.4487_4516del	p.Glu1496_Thr1506delinsAla	p.E1496_T1506delinsA	ENST00000268489	NM_006885.3	1496	gAGAGTGACTTGGAAGATAAACAGAGCCCAAcg/gcg	9/10	0.335552704796807	1	FACETS	0.809	0.706	0.92	0.809	0.706	0.92	CLONAL	1	TRUE	0	0.355645830758574	1		663	377	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42790784	42791022	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGAGTCCAAGAGGCTCTGGTGTTGGGGGTGGGGGGTAGACAAAAGGGGTGGGGCTACCTCATCTAGGGTGGGGAAGAGCTTGAGTTGGGGTTGGGGCCAGGCTCTCCTGCTGCACAGCTCACCTGGCTCCTTTCCACAGTGTGGACGAATGTGGAACCTCGCTCTGTGGCTGTGTTCCCTTGGCACTCCTTAGTCCCCTTCCTGGCACCCAGCCAGCCTGACCCCTCCGTGCAGCCGAG	CGAGTCCAAGAGGCTCTGGTGTTGGGGGTGGGGGGTAGACAAAAGGGGTGGGGCTACCTCATCTAGGGTGGGGAAGAGCTTGAGTTGGGGTTGGGGCCAGGCTCTCCTGCTGCACAGCTCACCTGGCTCCTTTCCACAGTGTGGACGAATGTGGAACCTCGCTCTGTGGCTGTGTTCCCTTGGCACTCCTTAGTCCCCTTCCTGGCACCCAGCCAGCCTGACCCCTCCGTGCAGCCGAG	-	novel	NA	P-0027097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	54	213	0	ENST00000575354.2:c.68-135_171del		p.X23_splice	ENST00000575354	NM_015125.3	23		2/20	0.355645830758574	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.355645830758574	2		213	131	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825425	134825425	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	27	670	0	ENST00000398015.3:c.941C>A	p.Pro314His	p.P314H	ENST00000398015	NM_004441.4	314	cCt/cAt	4/16	1	2	FACETS	0.43	0.342	0.531	0.43	0.342	0.531	SUBCLONAL	1	TRUE	1	0.355645830758574	2		670	353	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003283	143003283	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	49	481	0	ENST00000262992.4:c.2543G>T	p.Arg848Met	p.R848M	ENST00000262992	NM_001101669.1	848	aGg/aTg	23/24	1	2	FACETS	0.957	0.816	1	0.957	0.816	1	CLONAL	1	TRUE	1	0.355645830758574	2		481	288	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553347	106553347	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	54	628	0	ENST00000369096.4:c.1312G>C	p.Gly438Arg	p.G438R	ENST00000369096	NM_001198.3	438	Ggc/Cgc	5/7	0.355645830758574	3	FACETS	0.922	0.79	1	0.461	0.395	0.533	CLONAL	1	TRUE	1	0.355645830758574	3		628	388	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945483	151945483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs77325966	NA	P-0027097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	27	901	0	ENST00000262189.6:c.2036G>A	p.Arg679Lys	p.R679K	ENST00000262189	NM_170606.2	679	aGa/aAa	14/59	0.355645830758574	1	FACETS	0.409	0.326	0.504	0.409	0.326	0.504	SUBCLONAL	1	TRUE	0	0.355645830758574	1		901	305	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0027634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	620	487	2	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	0.8779069495674	2	FACETS	0.983	0.965	1	0.983	0.965	1	CLONAL	2	TRUE	0	0.882239422360337	2		489	715	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519980	NA	P-0027661-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	401	487	0	ENST00000269305.4:c.528C>G	p.Cys176Trp	p.C176W	ENST00000269305	NM_001126112.2	176	tgC/tgG	5/11	0.431484315604126	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.431484315604126	2		487	891	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163498	108163498	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027661-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	51	476	0	ENST00000278616.4:c.4589A>C	p.Glu1530Ala	p.E1530A	ENST00000278616	NM_000051.3	1530	gAg/gCg	30/63	0.431484315604126	2	FACETS	0.46	0.391	0.536	0.23	0.195	0.268	SUBCLONAL	1	TRUE	0	0.431484315604126	2		476	514	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573567	48573567	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0027661-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	17	255	0	ENST00000342988.3:c.151A>T	p.Lys51Ter	p.K51*	ENST00000342988	NM_005359.5	51	Aaa/Taa	2/12	0.431484315604126	2	FACETS	0.25	0.186	0.326	0.125	0.093	0.163	SUBCLONAL	1	TRUE	0	0.431484315604126	2		255	315	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10257158	10257158	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027661-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	46	601	0	ENST00000340748.4:c.2715A>C	p.Lys905Asn	p.K905N	ENST00000340748		905	aaA/aaC	27/40	0.431484315604126	4	FACETS	0.38	0.318	0.448	0.095	0.079	0.112	SUBCLONAL	1	TRUE	0	0.431484315604126	4		601	804	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659189	86659189	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0027661-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	17	150	0	ENST00000274376.6:c.1478T>G	p.Leu493Ter	p.L493*	ENST00000274376	NM_002890.2	493	tTa/tGa	11/25	0.431484315604126	2	FACETS	0.483	0.363	0.625	0.242	0.181	0.313	SUBCLONAL	1	TRUE	0	0.431484315604126	2		150	163	SUCCESS
APC	324	MSKCC	GRCh37	5	112174415	112174415	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027661-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	15	249	0	ENST00000257430.4:c.3124A>C	p.Ser1042Arg	p.S1042R	ENST00000257430	NM_000038.5	1042	Agt/Cgt	16/16	0.431484315604126	2	FACETS	0.25	0.182	0.331	0.125	0.091	0.166	SUBCLONAL	1	TRUE	0	0.431484315604126	2		249	278	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858004	152858004	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027661-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	16	195	0	ENST00000406277.2:c.611A>G	p.Glu204Gly	p.E204G	ENST00000406277	NM_152274.4	204	gAg/gGg	6/7	0.409999826534736	2	FACETS	0.255	0.188	0.335			1	SUBCLONAL	1	TRUE	NA	0.431484315604126	2		195	291	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78519463	78519463	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	56	384	2	ENST00000306801.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000306801	NM_020761.2	12	Ggc/Tgc	1/34	1	2	FACETS	0.469	0.401	0.543	0.469	0.401	0.543	SUBCLONAL	1	TRUE	1	0.372105238397824	2		386	642	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953730	48953730	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs3092891	NA	P-0028341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	128	202	2	ENST00000267163.4:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000267163	NM_000321.2	445	Cga/Tga	14/27	1	2	FACETS	0.997	0.918	1	1	0.991	1	CLONAL	2	TRUE	1	0.430934710719216	2		204	298	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954327	48954328	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0028341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	84	317	0	ENST00000267163.4:c.1450_1451del	p.Met484ValfsTer8	p.M484Vfs*8	ENST00000267163	NM_000321.2	483	cAT/c	16/27	1	2	FACETS	0.761	0.682	0.843	1	0.981	1	SUBCLONAL	2	TRUE	1	0.430934710719216	2		317	256	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921468	39921477	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCATAG	GGCGGCATAG	-	novel	NA	P-0028341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	213	256	0	ENST00000378444.4:c.4343_4352del	p.Pro1448ArgfsTer33	p.P1448Rfs*33	ENST00000378444	NM_001123385.1	1448	cCTATGCCGCCg/cg	10/15	1	1	FACETS	0.841	0.791	0.892	1	0.994	1	CLONAL	2	TRUE	0	0.430934710719216	1		256	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	110	901	0	ENST00000269305.4:c.379T>C	p.Ser127Pro	p.S127P	ENST00000269305	NM_001126112.2	127	Tcc/Ccc	5/11	0.225857608710578	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.308158284478686	1		901	441	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170479	108170479	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121434217	NA	P-0028805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	33	315	0	ENST00000278616.4:c.5044G>C	p.Asp1682His	p.D1682H	ENST00000278616	NM_000051.3	1682	Gat/Cat	34/63	1	2	FACETS	0.597	0.486	0.72	0.597	0.486	0.72	SUBCLONAL	1	TRUE	1	0.308158284478686	2		315	359	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161285	185161285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	67	556	0	ENST00000265026.3:c.712C>T	p.His238Tyr	p.H238Y	ENST00000265026	NM_004721.4	238	Cat/Tat	4/14	0.225857608710578	1	FACETS	0.84	0.732	0.955	0.84	0.732	0.955	CLONAL	1	TRUE	0	0.308158284478686	1		556	438	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663298	67663305	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAGAATAC	TAGAATAC	-	novel	NA	P-0028805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	29	285	0	ENST00000264010.4:c.1702-3_1706del		p.X568_splice	ENST00000264010	NM_006565.3	568		10/12	0.229517468573541	1	FACETS	0.601	0.484	0.733	0.601	0.484	0.733	SUBCLONAL	1	TRUE	0	0.308158284478686	1		285	265	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551329	29551329	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	31	536	0	ENST00000389048.3:c.1301A>C	p.Lys434Thr	p.K434T	ENST00000389048	NM_004304.4	434	aAg/aCg	6/29	0.273418288224524	0	FACETS	0.497	0.403	0.602			1	SUBCLONAL	1	TRUE	0	0.308158284478686	0		536	280	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643821	52643821	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	35	456	0	ENST00000394830.3:c.2075A>C	p.Glu692Ala	p.E692A	ENST00000394830	NM_018313.4	692	gAg/gCg	17/30	1	2	FACETS	0.577	0.473	0.693	0.577	0.473	0.693	SUBCLONAL	1	TRUE	1	0.308158284478686	2		456	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0029294-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	303	694	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.411162066657768	2	FACETS	0.979	0.927	1	0.979	0.927	1	CLONAL	2	TRUE	0	0.411162066657768	2		694	753	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486211	8486211	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs994861872	NA	P-0029294-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	239	517	0	ENST00000356435.5:c.2606C>A	p.Thr869Asn	p.T869N	ENST00000356435		869	aCt/aAt	17/35	0.411162066657768	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.411162066657768	2		517	542	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058638	72058639	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0029294-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	142	436	1	ENST00000357731.5:c.801_802delinsAA	p.Gln268Lys	p.Q268K	ENST00000357731	NM_173808.2	267	ggCCaa/ggAAaa	6/7	0.243448185332289	5	FACETS	0.956	0.875	1	0.637	0.583	0.694	INDETERMINATE	2	TRUE	2	0.411162066657768	5		437	584	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16052806	16052806	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029294-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	207	376	0	ENST00000268712.3:c.868A>T	p.Ile290Phe	p.I290F	ENST00000268712	NM_006311.3	290	Att/Ttt	9/46	0.411162066657768	2	FACETS	0.952	0.891	1	0.952	0.891	1	CLONAL	2	TRUE	0	0.411162066657768	2		376	529	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220466	1220466	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029294-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	302	795	0	ENST00000326873.7:c.559G>T	p.Gly187Cys	p.G187C	ENST00000326873	NM_000455.4	187	Ggt/Tgt	4/10	0.257570926085349	4	FACETS	0.944	0.89	1	0.944	0.89	1	CLONAL	2	TRUE	2	0.411162066657768	4		795	1098	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45864886	45864886	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029294-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	350	1011	0	ENST00000391945.4:c.1133G>T	p.Arg378Leu	p.R378L	ENST00000391945	NM_000400.3	378	cGc/cTc	12/23	0.257570926085349	4	FACETS	0.909	0.86	0.959	0.909	0.86	0.959	CLONAL	2	TRUE	2	0.411162066657768	4		1011	1321	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149438	61149438	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029294-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	123	418	0	ENST00000295025.8:c.1628G>C	p.Ser543Thr	p.S543T	ENST00000295025	NM_002908.2	543	aGt/aCt	11/11	0.208474268402914	4	FACETS	1	0.985	1	0.49	0.445	0.538	INDETERMINATE	1	TRUE	1	0.411162066657768	4		418	574	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610557	52610557	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029294-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	180	367	2	ENST00000394830.3:c.3616G>T	p.Gly1206Ter	p.G1206*	ENST00000394830	NM_018313.4	1206	Gga/Tga	23/30	0.411162066657768	2	FACETS	0.946	0.881	1	0.946	0.881	1	CLONAL	2	TRUE	0	0.411162066657768	2		369	463	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73047233	73047235	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0029294-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	184	407	0	ENST00000356692.5:c.40_42del	p.Glu14del	p.E14del	ENST00000356692		14	GAG/-	2/9	0.411162066657768	2	FACETS	0.803	0.747	0.862	0.803	0.747	0.862	CLONAL	2	TRUE	0	0.411162066657768	2		407	557	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251152	251152	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029294-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	156	258	2	ENST00000264932.6:c.1597C>T	p.Gln533Ter	p.Q533*	ENST00000264932	NM_004168.2	533	Caa/Taa	12/15	0.317244638019597	6	FACETS	0.939	0.866	1	0.704	0.65	0.76	CLONAL	3	TRUE	2	0.411162066657768	6		260	491	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915820	127915820	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029294-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	161	407	0	ENST00000373547.4:c.661A>G	p.Thr221Ala	p.T221A	ENST00000373547	NM_002721.4	221	Aca/Gca	6/7	0.257570926085349	4	FACETS	0.819	0.753	0.887	0.819	0.753	0.887	CLONAL	2	TRUE	2	0.411162066657768	4		407	675	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0029532-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	42	415	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.206543104913791	2	FACETS	0.75	0.626	0.887	0.375	0.313	0.444	SUBCLONAL	1	TRUE	0	0.25	2		415	448	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0029532-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	14	309	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.206543104913791	2	FACETS	0.345	0.248	0.462	0.172	0.124	0.231	SUBCLONAL	1	TRUE	0	0.25	2		310	325	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0029532-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	47	460	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.987	0.835	1	0.987	0.835	1	CLONAL	1	TRUE	1	0.25	2		460	381	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560493	65560493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029532-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	23	0	0	ENST00000358664.4:c.104G>T	p.Arg35Leu	p.R35L	ENST00000358664	NM_002382.4	35	cGt/cTt	3/5	1	2	FACETS	0.326	0.253	0.411	0.326	0.253	0.411	SUBCLONAL	1	TRUE	1	0.25	2		0	564	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031999	26031999	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1411351920	NA	P-0029532-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	42	640	0	ENST00000244661.2:c.290G>C	p.Cys97Ser	p.C97S	ENST00000244661	NM_003537.3	97	tGt/tCt	1/1	1	2	FACETS	0.512	0.427	0.608	0.512	0.427	0.608	SUBCLONAL	1	TRUE	1	0.25	2		640	656	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165688	47165688	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029532-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	73	656	0	ENST00000409792.3:c.438A>T	p.Lys146Asn	p.K146N	ENST00000409792	NM_014159.6	146	aaA/aaT	3/21	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.25	2		656	533	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017736	31017746	+	protein_altering_variant	In_Frame_Del	DEL	GGCAGCCCGTC	GGCAGCCCGTC	AG	novel	NA	P-0029532-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	36	0	0	ENST00000375687.4:c.598_608delinsAG	p.Gly200_Pro202del	p.G200_P202del	ENST00000375687	NM_015338.5	200	GGCAGCCCGTCc/AGc	8/13	0.292852661389461	3	FACETS	0.369	0.302	0.445	0.185	0.151	0.223	SUBCLONAL	1	TRUE	1	0.25	3		0	878	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163711	32163712	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029532-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	32	394	0	ENST00000375023.3:c.5514_5515insA	p.Pro1839ThrfsTer77	p.P1839Tfs*77	ENST00000375023	NM_004557.3	1838	-/A	30/30	0.120830338675728	4	FACETS	0.729	0.591	0.885	0.364	0.295	0.443	INDETERMINATE	1	TRUE	2	0.25	4		394	439	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151167739	151167739	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0029532-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	7	0	0	ENST00000262187.5:c.381-1G>A		p.X127_splice	ENST00000262187	NM_005614.3	127			NA	2	FACETS	0.265	0.165	0.399			1	INDETERMINATE	1	TRUE	NA	0.25	2		0	211	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0030562-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	55	308	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.293219045904382	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.293219045904382	1		308	219	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28929495	NA	P-0030562-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	219	385	0	ENST00000275493.2:c.2155G>T	p.Gly719Cys	p.G719C	ENST00000275493	NM_005228.3	719	Ggc/Tgc	18/28	0.293219045904382	4	FACETS	0.974	0.916	1	1	0.991	1	CLONAL	4	TRUE	1	0.293219045904382	4		385	496	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0030562-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	171	740	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.293219045904382	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	3	TRUE	1	0.293219045904382	4		740	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578283	7578283	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030562-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	104	397	0	ENST00000269305.4:c.566C>A	p.Ala189Asp	p.A189D	ENST00000269305	NM_001126112.2	189	gCc/gAc	6/11	0.293219045904382	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.293219045904382	2		397	319	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249808	133249808	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030562-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	47	314	0	ENST00000320574.5:c.1415A>C	p.Lys472Thr	p.K472T	ENST00000320574	NM_006231.2	472	aAg/aCg	14/49	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.293219045904382	2		314	299	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131361	17131361	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030562-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	147	506	0	ENST00000285071.4:c.91C>T	p.Gln31Ter	p.Q31*	ENST00000285071	NM_144997.5	31	Caa/Taa	4/14	0.293219045904382	2	FACETS	0.864	0.798	0.931	1	0.985	1	CLONAL	3	TRUE	0	0.293219045904382	2		506	387	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961000	55961000	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030562-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	46	313	0	ENST00000263923.4:c.2940G>T	p.Glu980Asp	p.E980D	ENST00000263923	NM_002253.2	980	gaG/gaT	21/30	0.167782029704428	1	FACETS	1	0.9	1	1	0.9	1	INDETERMINATE	1	TRUE	0	0.293219045904382	1		313	248	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545714	106545714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030562-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	40	405	0	ENST00000359195.3:c.3191C>T	p.Ala1064Val	p.A1064V	ENST00000359195	NM_002649.2	1064	gCt/gTt	11/11	1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	TRUE	1	0.293219045904382	2		405	270	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412614	63412614	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030562-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	68	390	0	ENST00000330258.3:c.553A>G	p.Thr185Ala	p.T185A	ENST00000330258	NM_152424.3	185	Act/Gct	2/2	0.293219045904382	2	FACETS	1	0.964	1	0.65	0.568	0.736	CLONAL	1	TRUE	0	0.293219045904382	2		390	357	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928072	178928098	+	inframe_deletion	In_Frame_Del	DEL	TGGATTAGAAGATTTGCTGAACCCTAT	TGGATTAGAAGATTTGCTGAACCCTAT	-	novel	NA	P-0031647-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	192	512	0	ENST00000263967.3:c.1353_1379del	p.Leu452_Gly460del	p.L452_G460del	ENST00000263967	NM_006218.2	450	caTGGATTAGAAGATTTGCTGAACCCTATt/cat	8/21	0.716452917322285	7	FACETS	1	0.988	1	0.226	0.208	0.244	CLONAL	1	TRUE	1	0.716452917322285	7		512	1104	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615113	100615113	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031647-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	266	479	0	ENST00000308731.7:c.802T>A	p.Tyr268Asn	p.Y268N	ENST00000308731	NM_000061.2	268	Tat/Aat	9/19	0.658835256614004	3	FACETS	0.981	0.931	1			1	CLONAL	2	TRUE	NA	0.716452917322285	3		479	514	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050374	176050377	+	frameshift_variant	Frame_Shift_Del	DEL	GGAC	GGAC	-	novel	NA	P-0031647-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	126	452	0	ENST00000367669.3:c.1188_1191del	p.Lys398LeufsTer10	p.K398Lfs*10	ENST00000367669	NM_022457.5	396	ttGTCC/tt	11/20	0.716452917322285	6	FACETS	0.898	0.812	0.989	0.18	0.162	0.198	CLONAL	1	TRUE	1	0.716452917322285	6		452	953	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373307	118373307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782272214	NA	P-0031647-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	291	511	0	ENST00000534358.1:c.6700G>A	p.Gly2234Arg	p.G2234R	ENST00000534358	NM_005933.3	2234	Ggg/Agg	27/36	0.716452917322285	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.716452917322285	2		511	364	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21626547	21626547	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031647-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	155	432	0	ENST00000421138.2:c.1385T>G	p.Phe462Cys	p.F462C	ENST00000421138		462	tTt/tGt	13/16	0.716452917322285	2	FACETS	1	0.962	1	0.53	0.491	0.571	CLONAL	1	TRUE	0	0.716452917322285	2		432	408	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396479	396479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031647-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	377	835	0	ENST00000262320.3:c.547G>A	p.Asp183Asn	p.D183N	ENST00000262320	NM_003502.3	183	Gac/Aac	2/11	0.716452917322285	6	FACETS	0.911	0.864	0.959	0.456	0.432	0.48	CLONAL	2	TRUE	2	0.716452917322285	6		835	1405	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649137	37649137	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031647-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	95	311	0	ENST00000447079.4:c.2242G>C	p.Asp748His	p.D748H	ENST00000447079	NM_015083.1	748	Gac/Cac	4/14	0.716452917322285	4	FACETS	1	0.895	1	0.5	0.447	0.556	CLONAL	1	TRUE	2	0.716452917322285	4		311	455	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155043	55155043	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031647-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	255	501	0	ENST00000257290.5:c.2752C>A	p.Pro918Thr	p.P918T	ENST00000257290	NM_006206.4	918	Cct/Act	20/23	0.716452917322285	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	2	0.716452917322285	4		501	594	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652011	36652011	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031647-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	126	859	0	ENST00000244741.5:c.133G>T	p.Ala45Ser	p.A45S	ENST00000244741	NM_000389.4	45	Gcc/Tcc	2/3	0.649529422029914	5	FACETS	0.704	0.637	0.776	0.176	0.159	0.194	SUBCLONAL	1	TRUE	1	0.716452917322285	5		859	1036	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865257	57865257	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1253674081	NA	P-0031647-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	186	719	0	ENST00000228682.2:c.2734G>C	p.Gly912Arg	p.G912R	ENST00000228682	NM_005269.2	912	Ggt/Cgt	12/12	0.716452917322285	4	FACETS	1	0.976	1	0.565	0.522	0.609	CLONAL	1	TRUE	2	0.716452917322285	4		719	789	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335062	81335062	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031647-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	101	326	0	ENST00000222390.5:c.1765G>C	p.Val589Leu	p.V589L	ENST00000222390	NM_000601.4	589	Gtc/Ctc	16/18	0.663923223171192	4	FACETS	0.982	0.881	1			1	CLONAL	1	TRUE	NA	0.716452917322285	4		326	493	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724442	43724442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031647-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	197	778	1	ENST00000382044.4:c.3625G>A	p.Glu1209Lys	p.E1209K	ENST00000382044	NM_001141980.1	1209	Gag/Aag	17/28	0.716452917322285	4	FACETS	0.985	0.913	1	0.493	0.456	0.531	CLONAL	1	TRUE	2	0.716452917322285	4		779	958	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261143	16261143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031647-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	54	561	1	ENST00000375759.3:c.8408G>A	p.Gly2803Glu	p.G2803E	ENST00000375759	NM_015001.2	2803	gGg/gAg	11/15	0.716452917322285	3	FACETS	0.369	0.315	0.428	0.184	0.157	0.214	SUBCLONAL	1	TRUE	1	0.716452917322285	3		562	555	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366891	40366891	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031647-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	140	569	0	ENST00000397332.2:c.306A>C	p.Glu102Asp	p.E102D	ENST00000397332	NM_001033082.2	102	gaA/gaC	2/3	0.716452917322285	3	FACETS	0.933	0.853	1	0.466	0.426	0.508	CLONAL	1	TRUE	1	0.716452917322285	3		569	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578199	7578199	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	497	726	0	ENST00000269305.4:c.650T>A	p.Val217Glu	p.V217E	ENST00000269305	NM_001126112.2	217	gTg/gAg	6/11	NA	2	FACETS	0.988	0.954	1			1	INDETERMINATE	2	TRUE	NA	0.605489692907628	2		726	831	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380338	14380339	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCCCACGCC	novel	NA	P-0031858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	89	322	0	ENST00000256196.4:c.70_78dup	p.Gly24_Gly26dup	p.G24_G26dup	ENST00000256196		24	-/GGCGTGGGC	1/6	0.605489692907628	1	FACETS	0.683	0.613	0.757	0.683	0.613	0.757	SUBCLONAL	1	TRUE	0	0.605489692907628	1		322	300	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11269446	11269446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	80	644	0	ENST00000361445.4:c.3724G>A	p.Gly1242Arg	p.G1242R	ENST00000361445	NM_004958.3	1242	Ggg/Agg	25/58	0.399675080919119	1	FACETS	0.305	0.268	0.344	0.305	0.268	0.344	SUBCLONAL	1	TRUE	0	0.605489692907628	1		644	605	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0031960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	306	894	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.59320715145756	2	FACETS	0.848	0.81	0.885	0.848	0.81	0.885	CLONAL	2	TRUE	0	0.679516619454919	2		894	531	SUCCESS
ATM	472	MSKCC	GRCh37	11	108159827	108159827	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	15	112	0	ENST00000278616.4:c.4235del	p.Pro1412LeufsTer39	p.P1412Lfs*39	ENST00000278616	NM_000051.3	1411	agC/ag	28/63	0.19917877298517	6	FACETS	1	0.782	1	0.177	0.131	0.231	INDETERMINATE	1	TRUE	0	0.679516619454919	6		112	98	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433976	49433976	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	117	977	0	ENST00000301067.7:c.7577C>A	p.Ala2526Glu	p.A2526E	ENST00000301067	NM_003482.3	2526	gCa/gAa	31/54	0.357030092078623	4	FACETS	0.98	0.887	1	0.49	0.443	0.54	INDETERMINATE	1	TRUE	2	0.679516619454919	4		977	590	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124322	2124460	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGTGGTGAAGCTCACGCACATCTCAGCCACAGCCAGCATGGCCGTCCCACTGCTGGAGTTCCTGTCCAGTGAGTCCCCGCCCTGCCTGCGCATGCACCCGAGAGGTTCGGGCTGTGTAACCTGTGCGGGCTTCTCTGG	TGGTGGTGAAGCTCACGCACATCTCAGCCACAGCCAGCATGGCCGTCCCACTGCTGGAGTTCCTGTCCAGTGAGTCCCCGCCCTGCCTGCGCATGCACCCGAGAGGTTCGGGCTGTGTAACCTGTGCGGGCTTCTCTGG	-	novel	NA	P-0031960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	105	1030	0	ENST00000219476.3:c.2479_2545+72del		p.X827_splice	ENST00000219476	NM_000548.3	827		22/42	0.418866095302232	4	FACETS	0.685	0.613	0.76	0.342	0.306	0.38	SUBCLONAL	1	TRUE	2	0.679516619454919	4		1030	758	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41209103	41209103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397509243	NA	P-0031960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	416	587	0	ENST00000357654.3:c.5243G>A	p.Gly1748Asp	p.G1748D	ENST00000357654	NM_007294.3	1748	gGt/gAt	19/23	0.6016459287068	3	FACETS	0.895	0.865	0.924	0.895	0.865	0.924	CLONAL	3	TRUE	0	0.679516619454919	3		587	611	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326561	62326589	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCTCCCCAACCAGGTAGGGCACCTGCCT	GGCTCCCCAACCAGGTAGGGCACCTGCCT	-	novel	NA	P-0031960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	172	910	0	ENST00000360203.5:c.3490_3499+19del		p.X1164_splice	ENST00000360203	NM_001283009.1	1164		33/35	0.679516619454919	3	FACETS	1	0.981	1	0.395	0.366	0.426	CLONAL	1	TRUE	0	0.679516619454919	3		910	572	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594228	55594228	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	71	367	0	ENST00000288135.5:c.1931T>G	p.Leu644Arg	p.L644R	ENST00000288135	NM_000222.2	644	cTg/cGg	13/21	0.208950473274709	2	FACETS	0.678	0.597	0.764	0.339	0.298	0.382	INDETERMINATE	1	TRUE	0	0.679516619454919	2		367	308	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602964	55602964	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	53	351	0	ENST00000288135.5:c.2674C>A	p.Pro892Thr	p.P892T	ENST00000288135	NM_000222.2	892	Cct/Act	19/21	0.208950473274709	2	FACETS	0.569	0.489	0.655	0.285	0.244	0.328	INDETERMINATE	1	TRUE	0	0.679516619454919	2		351	274	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914767	39914767	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0031960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	143	369	0	ENST00000378444.4:c.4596-1G>A		p.X1532_splice	ENST00000378444	NM_001123385.1	1532			0.59320715145756	2	FACETS	0.852	0.797	0.906	0.852	0.797	0.906	CLONAL	2	TRUE	0	0.679516619454919	2		369	247	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0032358-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	2192	392	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.3	48	FACETS	1	0.994	1			1	CLONAL	43	FALSE	NA	0.3	48		392	2665	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0032358-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	203	521	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.270962770698355	2	FACETS	0.771	0.715	0.828	0.771	0.715	0.828	SUBCLONAL	2	FALSE	0	0.3	2		521	878	SUCCESS
APC	324	MSKCC	GRCh37	5	112090657	112090657	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs145945630	NA	P-0032358-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	35	292	0	ENST00000257430.4:c.70C>T	p.Arg24Ter	p.R24*	ENST00000257430	NM_000038.5	24	Cga/Tga	2/16	0.3	3	FACETS	0.831	0.683	0.996	0.277	0.227	0.332	CLONAL	1	FALSE	0	0.3	3		292	323	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248526	59248526	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032358-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	170	706	0	ENST00000371222.2:c.217T>G	p.Ser73Ala	p.S73A	ENST00000371222	NM_002228.3	73	Tcg/Gcg	1/1	0.3	4	FACETS	0.798	0.734	0.865	0.798	0.734	0.865	SUBCLONAL	2	FALSE	2	0.3	4		706	923	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037924	49037924	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0032358-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	109	346	0	ENST00000267163.4:c.2167del	p.Ile723SerfsTer3	p.I723Sfs*3	ENST00000267163	NM_000321.2	722	Aaa/aa	21/27	0.270962770698355	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	FALSE	0	0.3	2		346	334	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021290	31021290	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0032358-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	80	540	0	ENST00000375687.4:c.1289C>G	p.Ser430Ter	p.S430*	ENST00000375687	NM_015338.5	430	tCa/tGa	12/13	0.234970031577742	5	FACETS	0.984	0.865	1	0.328	0.288	0.371	CLONAL	1	FALSE	2	0.3	5		540	786	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32790075	32790075	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032358-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	21	180	0	ENST00000374899.4:c.1953G>A	p.Met651Ile	p.M651I	ENST00000374899	NM_018833.2	651	atG/atA	12/12	0.3	6	FACETS	0.723	0.556	0.916	0.181	0.139	0.229	CLONAL	1	FALSE	2	0.3	6		180	310	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502817	186502817	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032358-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	52	440	0	ENST00000323963.5:c.275T>A	p.Leu92Gln	p.L92Q	ENST00000323963		92	cTg/cAg	4/11	0.3	5	FACETS	0.654	0.555	0.762	0.218	0.185	0.254	SUBCLONAL	1	FALSE	2	0.3	5		440	769	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037928	49037955	+	frameshift_variant	Frame_Shift_Del	DEL	TCATTGTAACAGCATACAAGGATCTTCC	TCATTGTAACAGCATACAAGGATCTTCC	-	novel	NA	P-0032430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	49	422	0	ENST00000267163.4:c.2172_2199del	p.Ile724MetfsTer11	p.I724Mfs*11	ENST00000267163	NM_000321.2	723	aTCATTGTAACAGCATACAAGGATCTTCCt/at	21/27	1	2	FACETS	0.421	0.359	0.489	0.421	0.359	0.489	SUBCLONAL	1	TRUE	1	0.833691683604756	2		422	279	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921500	39921518	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGGAACTTGAGCATGGC	AGGGGAACTTGAGCATGGC	-	novel	NA	P-0032430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	411	348	0	ENST00000378444.4:c.4302_4320del	p.Pro1435ArgfsTer43	p.P1435Rfs*43	ENST00000378444	NM_001123385.1	1434	ctGCCATGCTCAAGTTCCCCT/ct	10/15	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.833691683604756	1		348	497	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947630	48947630	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0032441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	134	251	0	ENST00000267163.4:c.1215+2T>A		p.X405_splice	ENST00000267163	NM_000321.2	405			1	2	FACETS	0.988	0.912	1	0.988	0.912	1	CLONAL	1	TRUE	1	0.853132672772456	2		251	318	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127743	47127743	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	362	463	1	ENST00000409792.3:c.5339G>T	p.Trp1780Leu	p.W1780L	ENST00000409792	NM_014159.6	1780	tGg/tTg	11/21	1	2	FACETS	0.99	0.943	1	0.99	0.943	1	CLONAL	1	TRUE	1	0.853132672772456	2		464	857	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90960077	90960077	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	136	292	0	ENST00000265433.3:c.1889C>A	p.Ser630Ter	p.S630*	ENST00000265433	NM_002485.4	630	tCa/tAa	12/16	1	2	FACETS	0.789	0.725	0.855	0.789	0.725	0.855	SUBCLONAL	1	TRUE	1	0.853132672772456	2		292	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0032537-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	130	742	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	0.913	0.828	1	0.913	0.828	1	CLONAL	1	TRUE	1	0.357331862696338	2		742	797	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs869320707	NA	P-0032537-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	157	757	0	ENST00000397752.3:c.3028+1G>T		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.357331862696338	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.357331862696338	1		757	581	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855029	76855029	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1557085898	NA	P-0032537-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	9	518	1	ENST00000373344.5:c.5807A>G	p.Lys1936Arg	p.K1936R	ENST00000373344	NM_000489.3	1936	aAg/aGg	25/35	1	2	FACETS	0.117	0.077	0.169	0.117	0.077	0.169	SUBCLONAL	1	TRUE	1	0.357331862696338	2		519	431	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411380	63411380	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032537-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	143	986	0	ENST00000330258.3:c.1787G>T	p.Arg596Met	p.R596M	ENST00000330258	NM_152424.3	596	aGg/aTg	2/2	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.357331862696338	2		986	790	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514719	103514719	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032537-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	73	461	0	ENST00000355739.4:c.1220A>T	p.Asp407Val	p.D407V	ENST00000355739	NM_000123.3	407	gAt/gTt	8/15	1	2	FACETS	0.933	0.819	1	0.933	0.819	1	CLONAL	1	TRUE	1	0.357331862696338	2		461	438	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021450	42021454	+	frameshift_variant	Frame_Shift_Del	DEL	AGGAC	AGGAC	-	novel	NA	P-0032537-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	113	534	0	ENST00000219905.7:c.3746_3750del	p.Glu1249AlafsTer23	p.E1249Afs*23	ENST00000219905	NM_001164273.1	1249	gAGGAC/g	11/24	0.357331862696338	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.357331862696338	1		534	501	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570062	212570063	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0032537-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	77	467	0	ENST00000342788.4:c.1178_1179delinsTT	p.Arg393Leu	p.R393L	ENST00000342788	NM_005235.2	393	cGG/cTT	10/28	1	2	FACETS	0.889	0.782	1	0.889	0.782	1	CLONAL	1	TRUE	1	0.357331862696338	2		467	485	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125793	47125793	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032537-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	64	385	0	ENST00000409792.3:c.5477G>C	p.Arg1826Pro	p.R1826P	ENST00000409792	NM_014159.6	1826	cGc/cCc	12/21	1	2	FACETS	0.845	0.734	0.964	0.845	0.734	0.964	CLONAL	1	TRUE	1	0.357331862696338	2		385	424	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997830	149997830	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032537-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	105	612	0	ENST00000253339.5:c.2637G>A	p.Trp879Ter	p.W879*	ENST00000253339		879	tgG/tgA	5/7	1	2	FACETS	0.957	0.859	1	0.957	0.859	1	CLONAL	1	TRUE	1	0.357331862696338	2		612	614	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954909	2954909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775400791	NA	P-0032537-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	131	904	1	ENST00000396946.4:c.2801C>T	p.Ser934Leu	p.S934L	ENST00000396946	NM_032415.4	934	tCg/tTg	21/25	0.338198057996488	4	FACETS	0.869	0.787	0.956	0.29	0.262	0.319	CLONAL	1	TRUE	1	0.357331862696338	4		905	1145	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032684-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	60	717	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.440480776096136	2	FACETS	0.386	0.332	0.445	0.193	0.166	0.223	SUBCLONAL	1	TRUE	0	0.446578913959278	2		717	696	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0032775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	100	508	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.474046366321473	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.474046366321473	1		508	251	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600446	10600446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	69	980	1	ENST00000171111.5:c.1409G>A	p.Arg470His	p.R470H	ENST00000171111	NM_203500.1	470	cGt/cAt	4/6	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.474046366321473	2		981	243	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970971	21970971	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0032775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	226	683	0	ENST00000304494.5:c.387C>G	p.Tyr129Ter	p.Y129*	ENST00000304494	NM_000077.4	129	taC/taG	2/3	0.453598943329367	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	TRUE	0	0.474046366321473	3		683	381	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575103	48575103	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	109	465	0	ENST00000342988.3:c.297G>C	p.Trp99Cys	p.W99C	ENST00000342988	NM_005359.5	99	tgG/tgC	3/12	0.474046366321473	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.474046366321473	1		465	236	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608369	43608369	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	75	1259	0	ENST00000355710.3:c.1717G>C	p.Val573Leu	p.V573L	ENST00000355710	NM_020975.4	573	Gtg/Ctg	9/20	0.0869323728853852	4	FACETS	1	0.973	1	0.696	0.615	0.782	INDETERMINATE	1	TRUE	2	0.474046366321473	4		1259	335	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912692	100912692	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	98	465	0	ENST00000325455.5:c.2630T>G	p.Leu877Arg	p.L877R	ENST00000325455	NM_001202474.3	877	cTt/cGt	7/8	0.178921187545752	3	FACETS	0.799	0.721	0.88	0.799	0.721	0.88	INDETERMINATE	2	TRUE	1	0.474046366321473	3		465	320	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89811440	89811440	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1473125013	NA	P-0032775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	69	1074	0	ENST00000389301.3:c.3553T>C	p.Trp1185Arg	p.W1185R	ENST00000389301	NM_000135.2	1185	Tgg/Cgg	36/43	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.474046366321473	2		1074	269	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574025	7574028	+	frameshift_variant	Frame_Shift_Del	DEL	CCCA	CCCA	-	novel	NA	P-0032775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	49	766	0	ENST00000269305.4:c.999_1002del	p.Gly334ValfsTer10	p.G334Vfs*10	ENST00000269305	NM_001126112.2	333	cgTGGG/cg	10/11	0.474046366321473	1	FACETS	0.826	0.71	0.95	0.826	0.71	0.95	CLONAL	1	TRUE	0	0.474046366321473	1		766	191	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0032801-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	36	159	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.271874394358426	1	FACETS	0.887	0.733	1	0.887	0.733	1	CLONAL	1	TRUE	0	0.27	1		159	260	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0032801-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	108	922	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.27	2		922	769	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814548	43814548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1445777626	NA	P-0032801-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	118	657	1	ENST00000372470.3:c.1343C>T	p.Thr448Ile	p.T448I	ENST00000372470	NM_005373.2	448	aCc/aTc	9/12	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.27	2		658	772	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	78	374	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.959451247885852	2		374	148	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267359	198267359	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs377023736	NA	P-0033454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	310	340	0	ENST00000335508.6:c.1998G>T	p.Lys666Asn	p.K666N	ENST00000335508	NM_012433.2	666	aaG/aaT	14/25	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.959451247885852	2		340	632	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380522	31380522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1013448701	NA	P-0033454-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	359	488	1	ENST00000328111.2:c.1012G>A	p.Gly338Arg	p.G338R	ENST00000328111	NM_006892.3	338	Ggg/Agg	9/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.959451247885852	2		489	731	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578441	7578441	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033473-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	13	882	0	ENST00000269305.4:c.489C>A	p.Tyr163Ter	p.Y163*	ENST00000269305	NM_001126112.2	163	taC/taA	5/11	1	2	FACETS	0.055	0.039	0.075	0.055	0.039	0.075	SUBCLONAL	1	TRUE	1	0.820695765801816	2		882	577	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855291	76855291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0033507-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	108	133	0	ENST00000373344.5:c.5698-2A>C		p.X1900_splice	ENST00000373344	NM_000489.3	1900			0.661660122279864	2	FACETS	0.907	0.871	0.937			1	CLONAL	3	TRUE	NA	0.661660122279864	2		133	120	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	532708	532708	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs878854760	NA	P-0033507-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	166	730	1	ENST00000451590.1:c.498C>A	p.His166Gln	p.H166Q	ENST00000451590	NM_001130442.1	166	caC/caA	5/5	0.661660122279864	2	FACETS	0.893	0.825	0.963	0.446	0.412	0.482	CLONAL	1	TRUE	0	0.661660122279864	2		731	562	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922020	39922020	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	35	330	0	ENST00000378444.4:c.4152C>A	p.Tyr1384Ter	p.Y1384*	ENST00000378444	NM_001123385.1	1384	taC/taA	9/15	1	1	FACETS	0.088	0.071	0.106	0.088	0.071	0.106	SUBCLONAL	1	TRUE	0	0.834014863614619	1		330	558	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0033666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	138	161	0	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	0.834014863614619	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.834014863614619	2		161	162	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476265	88476265	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033921-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	267	848	0	ENST00000360948.2:c.1867G>A	p.Gly623Arg	p.G623R	ENST00000360948	NM_001012338.2	623	Gga/Aga	15/19	1	2	FACETS	0.986	0.927	1	0.986	0.927	1	CLONAL	1	TRUE	1	0.637149116490642	2		848	850	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0034768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	494	584	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.721468920728534	2	FACETS	0.894	0.866	0.921	0.894	0.866	0.921	CLONAL	2	TRUE	0	0.758302886490867	2		584	729	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120785318	120785318	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0034768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	189	604	0	ENST00000257552.2:c.791-1G>A		p.X264_splice	ENST00000257552	NM_002442.3	264			0.694172389138238	2	FACETS	0.932	0.868	0.997	0.466	0.434	0.499	CLONAL	1	TRUE	0	0.758302886490867	2		604	535	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720212	43720212	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0034768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	154	542	0	ENST00000382044.4:c.3828+2T>G		p.X1276_splice	ENST00000382044	NM_001141980.1	1276			0.758302886490867	7	FACETS	0.925	0.845	1			1	CLONAL	1	TRUE	NA	0.758302886490867	7		542	1271	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110251303	110251303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	141	685	0	ENST00000374672.4:c.34G>A	p.Val12Ile	p.V12I	ENST00000374672	NM_004235.4	12	Gtc/Atc	2/5	0.758302886490867	3	FACETS	0.688	0.627	0.751	0.344	0.313	0.376	SUBCLONAL	1	TRUE	1	0.758302886490867	3		685	746	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942706	44942706	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	145	618	0	ENST00000377967.4:c.3286T>A	p.Trp1096Arg	p.W1096R	ENST00000377967	NM_021140.2	1096	Tgg/Agg	23/29	0.721680783418944	1	FACETS	0.827	0.77	0.885	0.827	0.77	0.885	CLONAL	1	TRUE	0	0.758302886490867	1		618	287	SUCCESS
AR	367	MSKCC	GRCh37	X	66766411	66766411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	33	161	0	ENST00000374690.3:c.1423G>A	p.Ala475Thr	p.A475T	ENST00000374690	NM_000044.3	475	Gcg/Acg	1/8	0.758302886490867	3	FACETS	0.96	0.798	1	0.48	0.399	0.568	CLONAL	1	TRUE	1	0.758302886490867	3		161	125	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483975	88483975	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035324-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	26	457	0	ENST00000360948.2:c.1595A>G	p.His532Arg	p.H532R	ENST00000360948	NM_001012338.2	532	cAc/cGc	14/19	1	2	FACETS	0.38	0.301	0.471	0.38	0.301	0.471	SUBCLONAL	1	TRUE	1	0.345437691224015	2		457	396	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440002	99440002	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035324-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	54	274	0	ENST00000268035.6:c.970T>A	p.Cys324Ser	p.C324S	ENST00000268035	NM_000875.3	324	Tgt/Agt	4/21	1	2	FACETS	0.965	0.829	1	0.965	0.829	1	CLONAL	1	TRUE	1	0.345437691224015	2		274	324	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969782	81969782	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035324-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	75	420	0	ENST00000359376.3:c.2851G>T	p.Asp951Tyr	p.D951Y	ENST00000359376	NM_002661.3	951	Gac/Tac	27/33	0.316914702339466	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.345437691224015	1		420	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0035324-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	234	614	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.335446237546021	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.345437691224015	2		614	587	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40497608	40497608	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1344978308	NA	P-0035324-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	94	641	1	ENST00000264657.5:c.341G>A	p.Arg114His	p.R114H	ENST00000264657	NM_139276.2	114	cGc/cAc	4/24	0.345437691224015	3	FACETS	1	0.904	1	0.508	0.453	0.567	CLONAL	1	TRUE	1	0.345437691224015	3		642	628	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793352	42793352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776199073	NA	P-0035324-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	225	794	0	ENST00000575354.2:c.1154C>T	p.Ser385Leu	p.S385L	ENST00000575354	NM_015125.3	385	tCg/tTg	8/20	0.345437691224015	4	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	2	0.345437691224015	4		794	856	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368515	225368515	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035324-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	46	325	0	ENST00000264414.4:c.1231A>G	p.Ile411Val	p.I411V	ENST00000264414	NM_003590.4	411	Ata/Gta	9/16	0.291330122428887	3	FACETS	0.777	0.656	0.91	0.388	0.328	0.455	CLONAL	1	TRUE	1	0.345437691224015	3		325	402	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022824	31022824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035324-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	92	528	0	ENST00000375687.4:c.2309C>T	p.Ser770Leu	p.S770L	ENST00000375687	NM_015338.5	770	tCa/tTa	13/13	0.345437691224015	3	FACETS	1	0.918	1	0.519	0.462	0.58	CLONAL	1	TRUE	1	0.345437691224015	3		528	602	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612157	189612157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035324-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	155	564	0	ENST00000264731.3:c.1909C>T	p.Arg637Cys	p.R637C	ENST00000264731	NM_003722.4	637	Cgt/Tgt	14/14	0.345437691224015	3	FACETS	0.867	0.797	0.939	0.578	0.531	0.626	CLONAL	2	TRUE	0	0.345437691224015	3		564	607	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0035324-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	1853	698	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.345437691224015	24	FACETS	0.979	0.965	0.992			1	CLONAL	22	TRUE	NA	0.345437691224015	24		698	2392	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259439	55259439	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs397517126	NA	P-0035324-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	1446	384	0	ENST00000275493.2:c.2497T>G	p.Leu833Val	p.L833V	ENST00000275493	NM_005228.3	833	Ttg/Gtg	21/28	0.345437691224015	24	FACETS	0.994	0.979	1			1	CLONAL	22	TRUE	NA	0.345437691224015	24		384	1837	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0035973-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	1014	501	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.847654856635715	6	FACETS	0.991	0.973	1			1	CLONAL	5	TRUE	NA	0.847654856635715	6		501	1301	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653824	89653824	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035973-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	174	379	0	ENST00000371953.3:c.122G>C	p.Arg41Thr	p.R41T	ENST00000371953	NM_000314.4	41	aGa/aCa	2/9	0.498610866020361	1	FACETS	0.67	0.627	0.713	0.67	0.627	0.713	INDETERMINATE	1	TRUE	0	0.847654856635715	1		379	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579304	7579322	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAACTGACCGTGCAAGTCA	CAACTGACCGTGCAAGTCA	-	novel	NA	P-0035973-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	266	549	0	ENST00000269305.4:c.365_375+8del		p.X122_splice	ENST00000269305	NM_001126112.2	122		4/11	0.847654856635715	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.847654856635715	1		549	326	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251297	99251297	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035973-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	131	588	0	ENST00000268035.6:c.601T>G	p.Tyr201Asp	p.Y201D	ENST00000268035	NM_000875.3	201	Tac/Gac	2/21	0.847654856635715	1	FACETS	0.497	0.457	0.539	0.497	0.457	0.539	SUBCLONAL	1	TRUE	0	0.847654856635715	1		588	358	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035081	30035082	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTGGATCATGATGTTTCAAAGG	novel	NA	P-0035973-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	132	327	0	ENST00000338641.4:c.244_265dup	p.Glu89AlafsTer4	p.E89Afs*4	ENST00000338641	NM_000268.3	81	-/CTGGATCATGATGTTTCAAAGG	3/16	0.847654856635715	1	FACETS	0.696	0.645	0.746	0.696	0.645	0.746	SUBCLONAL	1	TRUE	0	0.847654856635715	1		327	258	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671524	30671524	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035973-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	187	819	0	ENST00000376406.3:c.5436G>C	p.Lys1812Asn	p.K1812N	ENST00000376406	NM_014641.2	1812	aaG/aaC	10/15	0.621266030047193	3	FACETS	0.554	0.511	0.599			1	SUBCLONAL	1	TRUE	NA	0.847654856635715	3		819	1134	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672209	30672209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035973-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	181	825	1	ENST00000376406.3:c.4751G>A	p.Arg1584Lys	p.R1584K	ENST00000376406	NM_014641.2	1584	aGa/aAa	10/15	0.621266030047193	3	FACETS	0.54	0.497	0.585			1	SUBCLONAL	1	TRUE	NA	0.847654856635715	3		826	1126	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397707	139397709	+	missense_variant	Missense_Mutation	TNP	GTC	GTC	ATA	novel	NA	P-0035973-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	141	839	1	ENST00000277541.6:c.5092_5094delinsTAT	p.Asp1698Tyr	p.D1698Y	ENST00000277541	NM_017617.3	1698	GAC/TAT	27/34	0.300248058604075	1	FACETS	0.261	0.238	0.285	0.261	0.238	0.285	INDETERMINATE	1	TRUE	0	0.847654856635715	1		840	735	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579419	7579420	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs587783062	NA	P-0036804-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	138	1100	0	ENST00000269305.4:c.267dup	p.Ser90LeufsTer59	p.S90Lfs*59	ENST00000269305	NM_001126112.2	89	-/C	4/11	0.284328230368768	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	0	0.3	1		1100	704	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0036804-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	48	278	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	0.284647540394583	2	FACETS	1	0.947	1	0.632	0.539	0.733	CLONAL	1	FALSE	0	0.3	2		278	253	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247168	153247168	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1560758208	NA	P-0036911-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	34	218	0	ENST00000281708.4:c.1634A>G	p.Tyr545Cys	p.Y545C	ENST00000281708	NM_033632.3	545	tAt/tGt	10/12	1	2	FACETS	0.745	0.613	0.891	0.745	0.613	0.891	SUBCLONAL	1	TRUE	1	0.41302780431846	2		218	221	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427438	49427438	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036911-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	145	838	0	ENST00000301067.7:c.11050C>T	p.Gln3684Ter	p.Q3684*	ENST00000301067	NM_003482.3	3684	Caa/Taa	39/54	1	2	FACETS	0.912	0.833	0.994	0.912	0.833	0.994	CLONAL	1	TRUE	1	0.41302780431846	2		838	770	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245344	153245345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036911-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	64	413	0	ENST00000281708.4:c.1846dup	p.Thr616AsnfsTer28	p.T616Nfs*28	ENST00000281708	NM_033632.3	616	aca/aAca	11/12	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.41302780431846	2		413	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578201	7578202	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0037368-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	270	581	0	ENST00000269305.4:c.647_648del	p.Val216GlyfsTer5	p.V216Gfs*5	ENST00000269305	NM_001126112.2	216	gTG/g	6/11	0.341675540840489	2	FACETS	0.878	0.827	0.928	0.878	0.827	0.928	CLONAL	2	TRUE	0	0.419190079302502	2		581	734	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480484	57480484	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037368-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	91	276	0	ENST00000371085.3:c.479G>C	p.Arg160Pro	p.R160P	ENST00000371085	NM_000516.4	160	cGt/cCt	6/13	0.20126572857598	5	FACETS	1	0.945	1	0.368	0.327	0.412	INDETERMINATE	1	TRUE	2	0.419190079302502	5		276	640	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	54	374	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.294569999377358	2		374	320	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0038330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	119	501	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.271997950737916	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.294569999377358	3		501	426	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0038330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	83	624	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.294569999377358	2		624	394	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010560	48010560	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587779920	NA	P-0038330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	69	635	0	ENST00000234420.5:c.188C>G	p.Ser63Cys	p.S63C	ENST00000234420	NM_000179.2	63	tCc/tGc	1/10	0.229030657191963	3	FACETS	1	0.955	1	0.404	0.353	0.459	CLONAL	1	TRUE	0	0.294569999377358	3		635	443	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439718	51439718	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	22	290	0	ENST00000262662.1:c.283G>A	p.Asp95Asn	p.D95N	ENST00000262662		95	Gat/Aat	4/4	0.294569999377358	5	FACETS	0.675	0.523	0.851	0.225	0.174	0.284	SUBCLONAL	1	TRUE	2	0.294569999377358	5		290	319	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771504	112771504	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	81	514	0	ENST00000369452.4:c.1677G>C	p.Gln559His	p.Q559H	ENST00000369452	NM_007373.3	559	caG/caC	9/9	0.208778208311352	2	FACETS	1	0.972	1	0.669	0.592	0.75	CLONAL	1	TRUE	0	0.294569999377358	2		514	411	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160488	108160488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730881369	NA	P-0038330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	72	495	0	ENST00000278616.4:c.4396C>T	p.Arg1466Ter	p.R1466*	ENST00000278616	NM_000051.3	1466	Cga/Tga	29/63	0.208778208311352	2	FACETS	1	0.973	1	0.706	0.621	0.797	CLONAL	1	TRUE	0	0.294569999377358	2		495	346	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211548	46211548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	26	238	0	ENST00000334344.6:c.514G>A	p.Glu172Lys	p.E172K	ENST00000334344	NM_152641.2	172	Gaa/Aaa	5/21	0.26809284092006	3	FACETS	0.938	0.747	1			1	CLONAL	1	TRUE	NA	0.294569999377358	3		238	216	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478902	56478902	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	307	794	0	ENST00000267101.3:c.358A>G	p.Met120Val	p.M120V	ENST00000267101	NM_001982.3	120	Atg/Gtg	3/28	0.294569999377358	4	FACETS	0.925	0.878	0.973	0.925	0.878	0.973	CLONAL	4	TRUE	0	0.294569999377358	4		794	729	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26971342	26971342	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	15	206	0	ENST00000381527.3:c.913G>C	p.Asp305His	p.D305H	ENST00000381527	NM_001260.1	305	Gat/Cat	9/13	0.294569999377358	2	FACETS	0.629	0.462	0.827	0.314	0.231	0.414	SUBCLONAL	1	TRUE	0	0.294569999377358	2		206	162	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50818257	50818257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	36	311	0	ENST00000398568.2:c.1835C>G	p.Ser612Cys	p.S612C	ENST00000398568	NM_001042412.1	612	tCt/tGt	11/18	1	2	FACETS	0.974	0.805	1	0.974	0.805	1	CLONAL	1	TRUE	1	0.294569999377358	2		311	251	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78599493	78599493	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	83	346	1	ENST00000306801.3:c.165G>A	p.Met55Ile	p.M55I	ENST00000306801	NM_020761.2	55	atG/atA	2/34	0.271997950737916	3	FACETS	0.891	0.792	0.995	0.891	0.792	0.995	CLONAL	2	TRUE	1	0.294569999377358	3		347	363	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110624	4110624	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	49	645	0	ENST00000262948.5:c.333C>G	p.Ile111Met	p.I111M	ENST00000262948	NM_030662.3	111	atC/atG	3/11	1	2	FACETS	0.741	0.628	0.865	0.741	0.628	0.865	SUBCLONAL	1	TRUE	1	0.294569999377358	2		645	449	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271773	18271773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759830663	NA	P-0038330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	58	715	0	ENST00000222254.8:c.460C>T	p.Arg154Cys	p.R154C	ENST00000222254	NM_005027.3	154	Cgt/Tgt	4/16	1	2	FACETS	0.678	0.582	0.782	0.678	0.582	0.782	SUBCLONAL	1	TRUE	1	0.294569999377358	2		715	581	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749547	41749547	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	96	572	2	ENST00000301178.4:c.1472G>C	p.Arg491Thr	p.R491T	ENST00000301178	NM_021913.4	491	aGa/aCa	12/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.294569999377358	2		574	502	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871990	45871990	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	62	509	0	ENST00000391945.4:c.258G>C	p.Glu86Asp	p.E86D	ENST00000391945	NM_000400.3	86	gaG/gaC	5/23	1	2	FACETS	0.849	0.734	0.973	0.849	0.734	0.973	CLONAL	1	TRUE	1	0.294569999377358	2		509	496	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275399	142275399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202162034	NA	P-0038330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	34	288	0	ENST00000350721.4:c.1904G>A	p.Arg635Gln	p.R635Q	ENST00000350721	NM_001184.3	635	cGa/cAa	9/47	0.271997950737916	3	FACETS	1	0.917	1	0.605	0.498	0.723	CLONAL	1	TRUE	1	0.294569999377358	3		288	219	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184618	185184618	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	78	287	0	ENST00000265026.3:c.1510G>C	p.Glu504Gln	p.E504Q	ENST00000265026	NM_004721.4	504	Gag/Cag	10/14	0.271997950737916	3	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	1	0.294569999377358	3		287	276	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955887	55955887	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	29	403	0	ENST00000263923.4:c.3275G>C	p.Gly1092Ala	p.G1092A	ENST00000263923	NM_002253.2	1092	gGt/gCt	24/30	1	2	FACETS	0.637	0.512	0.779	0.637	0.512	0.779	SUBCLONAL	1	TRUE	1	0.294569999377358	2		403	309	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032230	26032230	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	21	304	0	ENST00000244661.2:c.59A>C	p.Gln20Pro	p.Q20P	ENST00000244661	NM_003537.3	20	cAg/cCg	1/1	0.294569999377358	3	FACETS	0.687	0.531	0.869	0.344	0.265	0.435	SUBCLONAL	1	TRUE	1	0.294569999377358	3		304	238	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048638	6048638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	83	650	0	ENST00000265849.7:c.13G>A	p.Glu5Lys	p.E5K	ENST00000265849	NM_000535.5	5	Gag/Aag	1/15	0.203837889460326	3	FACETS	1	0.971	1	0.661	0.585	0.742	CLONAL	1	TRUE	1	0.294569999377358	3		650	489	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444263	50444263	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	14	257	0	ENST00000331340.3:c.193G>C	p.Glu65Gln	p.E65Q	ENST00000331340	NM_006060.4	65	Gaa/Caa	4/8	0.203837889460326	3	FACETS	0.586	0.425	0.781	0.293	0.212	0.391	SUBCLONAL	1	TRUE	1	0.294569999377358	3		257	186	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412064	116412064	+	intron_variant	Intron	SNP	C	C	G	novel	NA	P-0038330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	73	620	0	ENST00000397752.3:c.3028+21C>G		p.*1010*	ENST00000397752	NM_000245.2	-/1390			0.203837889460326	3	FACETS	0.992	0.869	1	0.496	0.434	0.563	CLONAL	1	TRUE	1	0.294569999377358	3		620	573	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418227	139418228	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0038330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	155	811	0	ENST00000277541.6:c.344dup	p.Thr116HisfsTer27	p.T116Hfs*27	ENST00000277541	NM_017617.3	115	ggc/ggGc	3/34	0.208961840135364	2	FACETS	0.864	0.794	0.936	0.864	0.794	0.936	CLONAL	2	TRUE	0	0.294569999377358	2		811	609	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412634	63412634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753930754	NA	P-0038330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	86	305	0	ENST00000330258.3:c.533G>A	p.Arg178His	p.R178H	ENST00000330258	NM_152424.3	178	cGt/cAt	2/2	0.188855807106459	2	FACETS	1	0.967	1			1	CLONAL	2	TRUE	NA	0.294569999377358	2		305	245	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019595	123019595	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038330-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	16	245	0	ENST00000355640.3:c.83A>T	p.Asn28Ile	p.N28I	ENST00000355640		28	aAt/aTt	2/7	0.188855807106459	2	FACETS	0.442	0.326	0.579			1	SUBCLONAL	1	TRUE	NA	0.294569999377358	2		245	246	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881488	48881489	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0038332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	309	233	0	ENST00000267163.4:c.219_220dup	p.Ala74GlufsTer4	p.A74Efs*4	ENST00000267163	NM_000321.2	70	-/AG	2/27	0.661470682328535	5	FACETS	1	0.992	1	0.882	0.85	0.913	CLONAL	4	TRUE	0	0.661470682328535	5		233	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0038825-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	200	499	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.320191323743439	1	FACETS	0.816	0.76	0.873	1	0.992	1	CLONAL	2	TRUE	0	0.320191323743439	1		499	643	SUCCESS
APC	324	MSKCC	GRCh37	5	112174784	112174784	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0038825-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	66	202	0	ENST00000257430.4:c.3493A>T	p.Lys1165Ter	p.K1165*	ENST00000257430	NM_000038.5	1165	Aaa/Taa	16/16	0.320191323743439	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.320191323743439	1		202	265	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0038825-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	148	459	0	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	1	2	FACETS	0.83	0.762	0.9	1	0.99	1	CLONAL	2	TRUE	1	0.320191323743439	2		459	557	SUCCESS
APC	324	MSKCC	GRCh37	5	112174533	112174533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374380039	NA	P-0038825-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	77	266	0	ENST00000257430.4:c.3242G>A	p.Ser1081Asn	p.S1081N	ENST00000257430	NM_000038.5	1081	aGc/aAc	16/16	0.320191323743439	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.320191323743439	1		266	298	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0038941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	88	161	0	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	1	2	FACETS	0.774	0.697	0.852	1	0.983	1	SUBCLONAL	2	TRUE	1	0.481914390039928	2		161	236	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953760	48953760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913302	NA	P-0038941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	151	167	0	ENST00000267163.4:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000267163	NM_000321.2	455	Cga/Tga	14/27	1	2	FACETS	0.89	0.826	0.955	1	0.992	1	CLONAL	2	TRUE	1	0.481914390039928	2		167	352	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445825	49445826	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1246	284	1132	0	ENST00000301067.7:c.1640dup	p.Pro548ThrfsTer3	p.P548Tfs*3	ENST00000301067	NM_003482.3	547	cca/ccCa	10/54	1	2	FACETS	0.472	0.442	0.502	0.472	0.442	0.502	SUBCLONAL	1	TRUE	1	0.787329026140923	2		1132	1530	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039356-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	45	215	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.63	0.528	0.742	0.63	0.528	0.742	SUBCLONAL	1	TRUE	1	0.227929420016155	2		215	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0039356-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	115	626	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.921	0.827	1	0.921	0.827	1	CLONAL	1	TRUE	1	0.227929420016155	2		626	1096	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231357	5231357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039356-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	64	932	0	ENST00000357368.4:c.2119G>A	p.Glu707Lys	p.E707K	ENST00000357368	NM_002850.3	707	Gag/Aag	14/38	1	2	FACETS	0.526	0.454	0.605	0.526	0.454	0.605	SUBCLONAL	1	TRUE	1	0.227929420016155	2		932	1067	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039600-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	139	717	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.427957570674921	1	FACETS	0.906	0.829	0.986	0.906	0.829	0.986	CLONAL	1	TRUE	0	0.440485873608763	1		717	543	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925131	81925131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1382212475	NA	P-0039600-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	128	598	2	ENST00000359376.3:c.922G>A	p.Ala308Thr	p.A308T	ENST00000359376	NM_002661.3	308	Gcg/Acg	11/33	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.440485873608763	2		600	546	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023174	48023174	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs63751077	NA	P-0039600-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	240	589	0	ENST00000234420.5:c.599C>G	p.Ser200Ter	p.S200*	ENST00000234420	NM_000179.2	200	tCa/tGa	3/10	0.440485873608763	3	FACETS	0.946	0.888	1	0.946	0.888	1	CLONAL	2	TRUE	1	0.440485873608763	3		589	703	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505632	186505632	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039600-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	78	305	0	ENST00000323963.5:c.1040A>G	p.Asn347Ser	p.N347S	ENST00000323963		347	aAt/aGt	10/11	0.340034951750409	5	FACETS	1	0.935	1	0.364	0.321	0.411	CLONAL	1	TRUE	2	0.440485873608763	5		305	538	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514780	44514780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769567889	NA	P-0039631-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	91	463	2	ENST00000291552.4:c.467G>A	p.Arg156His	p.R156H	ENST00000291552	NM_006758.2	156	cGt/cAt	6/8	0.402052991896564	3	FACETS	0.802	0.712	0.897	0.401	0.356	0.449	CLONAL	1	TRUE	1	0.402052991896564	3		465	678	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138548	11138548	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039631-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	362	608	0	ENST00000358026.2:c.3304T>C	p.Phe1102Leu	p.F1102L	ENST00000358026	NM_001128849.1	1102	Ttc/Ctc	24/36	0.401577408313426	4	FACETS	0.912	0.868	0.957	0.912	0.868	0.957	CLONAL	3	TRUE	1	0.402052991896564	4		608	923	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552934	106552934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039631-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	62	741	0	ENST00000369096.4:c.899C>T	p.Pro300Leu	p.P300L	ENST00000369096	NM_001198.3	300	cCc/cTc	5/7	0.402052991896564	5	FACETS	0.554	0.477	0.638	0.185	0.159	0.213	SUBCLONAL	1	TRUE	2	0.402052991896564	5		741	892	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107043	27107043	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	219	544	0	ENST00000324856.7:c.6654del	p.Met2218IlefsTer13	p.M2218Ifs*13	ENST00000324856	NM_006015.4	2218	atG/at	20/20	0.895865296887967	1	FACETS	0.878	0.84	0.914	0.878	0.84	0.914	CLONAL	1	TRUE	0	0.90804372522777	1		544	300	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446359	49446359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1411463611	NA	P-0039850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	51	766	1	ENST00000301067.7:c.1246G>A	p.Ala416Thr	p.A416T	ENST00000301067	NM_003482.3	416	Gcc/Acc	9/54	1	2	FACETS	0.126	0.106	0.147	0.126	0.106	0.147	SUBCLONAL	1	TRUE	1	0.90804372522777	2		767	894	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237641	133237641	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115193764	NA	P-0039850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	317	684	1	ENST00000320574.5:c.2974G>A	p.Ala992Thr	p.A992T	ENST00000320574	NM_006231.2	992	Gcc/Acc	25/49	1	2	FACETS	0.795	0.753	0.838	0.795	0.753	0.838	SUBCLONAL	1	TRUE	1	0.90804372522777	2		685	878	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039473	49039494	+	frameshift_variant	Frame_Shift_Del	DEL	CCAACACCAACAAAAATGACTC	CCAACACCAACAAAAATGACTC	-	novel	NA	P-0039850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	411	502	4	ENST00000267163.4:c.2459_2480del	p.Pro820GlnfsTer6	p.P820Qfs*6	ENST00000267163	NM_000321.2	820	CCAACACCAACAAAAATGACTCca/ca	23/27	0.870885554870433	2	FACETS	0.849	0.825	0.873	0.849	0.825	0.873	CLONAL	2	TRUE	0	0.90804372522777	2		506	533	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936659	49936659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376534011	NA	P-0039850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	169	633	1	ENST00000296474.3:c.1268G>A	p.Arg423His	p.R423H	ENST00000296474	NM_002447.2	423	cGc/cAc	2/20	1	2	FACETS	0.469	0.432	0.508	0.469	0.432	0.508	SUBCLONAL	1	TRUE	1	0.90804372522777	2		634	793	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519277	187519277	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	194	430	0	ENST00000441802.2:c.12106T>A	p.Tyr4036Asn	p.Y4036N	ENST00000441802	NM_005245.3	4036	Tat/Aat	23/27	1	2	FACETS	0.73	0.68	0.782	0.73	0.68	0.782	SUBCLONAL	1	TRUE	1	0.90804372522777	2		430	585	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78933932	78933932	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	602	918	1	ENST00000306801.3:c.3532C>A	p.Arg1178Ser	p.R1178S	ENST00000306801	NM_020761.2	1178	Cgc/Agc	30/34	0.523514870214321	3	FACETS	1	0.992	1	0.561	0.538	0.583	INDETERMINATE	1	TRUE	1	0.90405669982457	3		919	1725	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0040200-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	182	219	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.981	0.914	1	0.981	0.914	1	CLONAL	1	TRUE	1	0.815701122905692	2		219	455	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040200-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	332	461	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.815701122905692	2		461	788	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577045	7577045	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040200-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	407	541	0	ENST00000269305.4:c.893del	p.Glu298GlyfsTer47	p.E298Gfs*47	ENST00000269305	NM_001126112.2	298	gAg/gg	8/11	0.815701122905692	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.815701122905692	1		541	575	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922196	39922196	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040200-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	226	441	1	ENST00000378444.4:c.3976G>T	p.Glu1326Ter	p.E1326*	ENST00000378444	NM_001123385.1	1326	Gaa/Taa	9/15	0.203740224440156	1	FACETS	0.439	0.41	0.468	0.439	0.41	0.468	INDETERMINATE	1	TRUE	0	0.815701122905692	1		442	748	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971155	21971155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501260	NA	P-0040200-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	242	261	0	ENST00000304494.5:c.203C>T	p.Ala68Val	p.A68V	ENST00000304494	NM_000077.4	68	gCg/gTg	2/3	0.815701122905692	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.815701122905692	1		261	337	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0040256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	58	215	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.205093637619561	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		215	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0040256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	42	694	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		694	761	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92247418	92247418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	18	257	0	ENST00000265734.4:c.802G>A	p.Asp268Asn	p.D268N	ENST00000265734	NM_001259.6	268	Gat/Aat	7/8	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		257	298	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0040350-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	97	415	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.295294957391314	3	FACETS	0.925	0.832	1	0.925	0.832	1	CLONAL	2	TRUE	1	0.32	3		415	380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0040350-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	146	977	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	0.268858393560264	2	FACETS	0.816	0.749	0.886	0.816	0.749	0.886	CLONAL	2	TRUE	0	0.32	2		977	559	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483964	212483964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040350-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	39	470	0	ENST00000342788.4:c.2239C>T	p.Pro747Ser	p.P747S	ENST00000342788	NM_005235.2	747	Cct/Tct	19/28	0.256867059562388	2	FACETS	0.776	0.654	0.908	0.776	0.654	0.908	CLONAL	2	TRUE	0	0.32	2		470	157	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0040655-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	59	226	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.898	0.778	1	1	0.976	1	CLONAL	2	TRUE	1	0.21	2		226	313	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254728	46254728	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040655-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	45	237	0	ENST00000334344.6:c.4918A>G	p.Lys1640Glu	p.K1640E	ENST00000334344	NM_152641.2	1640	Aaa/Gaa	16/21	1	2	FACETS	0.818	0.692	0.954	1	0.965	1	CLONAL	2	TRUE	1	0.21	2		237	262	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112580	115112581	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0040655-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	62	780	1	ENST00000257566.3:c.1159_1160delinsAA	p.Pro387Asn	p.P387N	ENST00000257566	NM_016569.3	387	CCc/AAc	7/8	1	2	FACETS	0.559	0.481	0.644	0.559	0.481	0.644	SUBCLONAL	1	TRUE	1	0.21	2		781	1056	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959073	28959073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761475937	NA	P-0040655-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	49	358	0	ENST00000282397.4:c.2065G>A	p.Glu689Lys	p.E689K	ENST00000282397	NM_002019.4	689	Gag/Aag	14/30	0.257693982114873	1	FACETS	0.971	0.824	1	0.971	0.824	1	CLONAL	1	TRUE	0	0.21	1		358	430	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040655-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	84	825	1	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	1	2	FACETS	0.804	0.708	0.907	0.804	0.708	0.907	CLONAL	1	TRUE	1	0.21	2		826	995	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145589	11145589	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0040655-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	62	593	0	ENST00000358026.2:c.3952-1G>A		p.X1318_splice	ENST00000358026	NM_001128849.1	1318			1	2	FACETS	0.968	0.836	1	0.968	0.836	1	CLONAL	1	TRUE	1	0.21	2		593	610	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660280	227660280	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040655-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	48	586	0	ENST00000305123.5:c.3175C>A	p.Leu1059Met	p.L1059M	ENST00000305123	NM_005544.2	1059	Ctg/Atg	1/2	1	2	FACETS	0.724	0.612	0.849	0.724	0.612	0.849	SUBCLONAL	1	TRUE	1	0.21	2		586	631	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098556	47098562	+	frameshift_variant	Frame_Shift_Del	DEL	ACTGGGA	ACTGGGA	-	novel	NA	P-0040655-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	36	478	0	ENST00000409792.3:c.6712_6718del	p.Ser2238MetfsTer8	p.S2238Mfs*8	ENST00000409792	NM_014159.6	2238	TCCCAGTat/at	15/21	1	2	FACETS	0.682	0.56	0.819	0.682	0.56	0.819	SUBCLONAL	1	TRUE	1	0.21	2		478	503	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729248	41729248	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0040655-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	32	361	0	ENST00000242208.4:c.1281G>C	p.Ter427TyrextTer29	p.*427Yext*29	ENST00000242208	NM_002192.2	427	taG/taC	3/3	1	2	FACETS	0.731	0.593	0.886	0.731	0.593	0.886	SUBCLONAL	1	TRUE	1	0.21	2		361	417	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879391	56879391	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040655-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	47	684	0	ENST00000519728.1:c.908T>C	p.Val303Ala	p.V303A	ENST00000519728	NM_002350.3	303	gTg/gCg	9/13	1	2	FACETS	0.549	0.462	0.646	0.549	0.462	0.646	SUBCLONAL	1	TRUE	1	0.21	2		684	815	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964388	70964388	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040655-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	63	381	0	ENST00000276594.2:c.1640C>A	p.Ser547Ter	p.S547*	ENST00000276594	NM_024504.3	547	tCa/tAa	8/8	0.3	5	FACETS	1	0.967	1	0.475	0.411	0.544	CLONAL	1	TRUE	2	0.21	5		381	554	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039883	47039883	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040655-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	70	720	1	ENST00000377604.3:c.1226C>A	p.Ala409Glu	p.A409E	ENST00000377604	NM_001204468.1	409	gCg/gAg	12/24	0.169382599241653	3	FACETS	0.823	0.716	0.939	0.412	0.358	0.47	CLONAL	1	TRUE	1	0.21	3		721	895	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239294	105239294	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040655-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	28	0	0	ENST00000349310.3:c.1093G>T	p.Glu365Ter	p.E365*	ENST00000349310	NM_001014432.1	365	Gag/Tag	12/15	1	2	FACETS	0.33	0.263	0.408	0.33	0.263	0.408	SUBCLONAL	1	TRUE	1	0.21	2		0	807	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988182	85988182	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0040655-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	12	0	0	ENST00000263360.6:c.1125+2T>C		p.X375_splice	ENST00000263360	NM_003797.3	375			1	2	FACETS	0.411	0.288	0.563	0.411	0.288	0.563	SUBCLONAL	1	TRUE	1	0.21	2		0	278	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0040730-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	121	415	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.884269061109566	4	FACETS	0.832	0.754	0.915			1	CLONAL	1	TRUE	NA	0.880166341683723	4		415	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0040730-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	758	779	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.884269061109566	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.880166341683723	2		779	837	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724437	112724450	+	frameshift_variant	Frame_Shift_Del	DEL	ATCCAAGAGATCTA	ATCCAAGAGATCTA	-	novel	NA	P-0040730-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	154	449	0	ENST00000369452.4:c.321_334del	p.Leu107PhefsTer22	p.L107Ffs*22	ENST00000369452	NM_007373.3	107	ttATCCAAGAGATCTAta/ttta	2/9	1	2	FACETS	0.87	0.806	0.936	0.87	0.806	0.936	CLONAL	1	TRUE	1	0.880166341683723	2		449	402	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458335	12458335	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs72551362	NA	P-0040730-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	501	576	2	ENST00000287820.6:c.952G>A	p.Val318Met	p.V318M	ENST00000287820	NM_015869.4	318	Gtg/Atg	6/7	0.884269061109566	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.880166341683723	2		578	545	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467421	66467421	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040730-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	127	198	0	ENST00000273854.3:c.848T>G	p.Leu283Arg	p.L283R	ENST00000273854	NM_004439.5	283	cTg/cGg	3/18	0.614964985873331	3	FACETS	0.831	0.77	0.892			1	CLONAL	2	TRUE	NA	0.880166341683723	3		198	250	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910375	29910401	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GGCCCTGGCCCTGACCCAGACCTGGGC	GGCCCTGGCCCTGACCCAGACCTGGGC	-	novel	NA	P-0040730-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	921	1228	0	ENST00000376809.5:c.47_73del	p.Ala16_Ala24del	p.A16_A24del	ENST00000376809	NM_002116.7	15	ggGGCCCTGGCCCTGACCCAGACCTGGGCg/ggg	1/8	0.710160568566268	6	FACETS	0.98	0.952	1	0.98	0.952	1	CLONAL	3	TRUE	3	0.880166341683723	6		1228	1964	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866647	117866647	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040730-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	274	393	0	ENST00000297338.2:c.998A>T	p.Asp333Val	p.D333V	ENST00000297338	NM_006265.2	333	gAt/gTt	9/14	0.880166341683723	7	FACETS	0.826	0.775	0.879	0.275	0.258	0.293	CLONAL	2	TRUE	1	0.880166341683723	7		393	1206	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942146	17942146	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040730-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1274	69	893	0	ENST00000458235.1:c.2869G>C	p.Val957Leu	p.V957L	ENST00000458235	NM_000215.3	957	Gtg/Ctg	21/24	0.884269061109566	3	FACETS	0.168	0.145	0.193	0.084	0.072	0.097	SUBCLONAL	1	TRUE	1	0.880166341683723	3		893	1343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0040913-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	210	708	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.405066652980646	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.405066652980646	3		708	532	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523727	176523727	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs780050403	NA	P-0040913-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	96	638	0	ENST00000292408.4:c.2138A>G	p.His713Arg	p.H713R	ENST00000292408	NM_213647.1	713	cAc/cGc	16/18	1	2	FACETS	0.915	0.818	1	0.915	0.818	1	CLONAL	1	TRUE	1	0.405066652980646	2		638	518	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	49	461	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	0.841	0.713	0.983	0.841	0.713	0.983	CLONAL	1	TRUE	1	0.232522127959365	2		461	501	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0041022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	92	573	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.159090875704554	2	FACETS	0.856	0.764	0.954	0.856	0.764	0.954	CLONAL	2	TRUE	0	0.232522127959365	2		573	462	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508955	106508955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759136884	NA	P-0041022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	25	388	0	ENST00000359195.3:c.949G>A	p.Glu317Lys	p.E317K	ENST00000359195	NM_002649.2	317	Gag/Aag	2/11	0.144815214141492	3	FACETS	0.583	0.459	0.726	0.291	0.229	0.363	SUBCLONAL	1	TRUE	1	0.232522127959365	3		388	412	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115751	8115751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	13	354	0	ENST00000346208.3:c.1097G>A	p.Arg366Gln	p.R366Q	ENST00000346208		366	cGa/cAa	6/6	1	2	FACETS	0.291	0.207	0.395	0.291	0.207	0.395	SUBCLONAL	1	TRUE	1	0.232522127959365	2		354	384	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248401	212248401	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1365124530	NA	P-0041022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	14	222	0	ENST00000342788.4:c.3866C>T	p.Ser1289Phe	p.S1289F	ENST00000342788	NM_005235.2	1289	tCc/tTc	28/28	1	2	FACETS	0.533	0.385	0.711	0.533	0.385	0.711	SUBCLONAL	1	TRUE	1	0.232522127959365	2		222	226	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883959	37883959	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138611862	NA	P-0041022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	99	601	0	ENST00000269571.5:c.3430G>C	p.Asp1144His	p.D1144H	ENST00000269571		1144	Gat/Cat	27/27	0.162509433250552	2	FACETS	1	0.979	1	0.699	0.625	0.778	CLONAL	1	TRUE	0	0.232522127959365	2		601	609	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210474	2210474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	53	567	0	ENST00000398665.3:c.1081G>A	p.Glu361Lys	p.E361K	ENST00000398665	NM_032482.2	361	Gag/Aag	13/28	1	2	FACETS	0.781	0.665	0.907	0.781	0.665	0.907	CLONAL	1	TRUE	1	0.232522127959365	2		567	584	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033959	48033959	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	13	293	0	ENST00000234420.5:c.4043A>G	p.Glu1348Gly	p.E1348G	ENST00000234420	NM_000179.2	1348	gAa/gGa	10/10	0.144815214141492	3	FACETS	0.486	0.346	0.656	0.243	0.173	0.328	SUBCLONAL	1	TRUE	1	0.232522127959365	3		293	257	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160564	56160564	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	33	167	0	ENST00000399503.3:c.838C>A	p.Gln280Lys	p.Q280K	ENST00000399503	NM_005921.1	280	Cag/Aag	4/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.232522127959365	2		167	202	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178367	56178400	+	frameshift_variant	Frame_Shift_Del	DEL	ACCCCAGTAGAGGAGAAATGCAGATTAGATGTCA	ACCCCAGTAGAGGAGAAATGCAGATTAGATGTCA	-	novel	NA	P-0041022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	12	245	0	ENST00000399503.3:c.3341_3374del	p.Thr1114IlefsTer23	p.T1114Ifs*23	ENST00000399503	NM_005921.1	1114	ACCCCAGTAGAGGAGAAATGCAGATTAGATGTCAat/at	14/20	1	2	FACETS	0.447	0.314	0.611	0.447	0.314	0.611	SUBCLONAL	1	TRUE	1	0.232522127959365	2		245	231	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140500172	140500172	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	69	662	1	ENST00000288602.6:c.970G>T	p.Asp324Tyr	p.D324Y	ENST00000288602	NM_004333.4	324	Gac/Tac	7/18	0.144815214141492	3	FACETS	0.913	0.794	1	0.456	0.397	0.521	CLONAL	1	TRUE	1	0.232522127959365	3		663	726	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937006	48937012	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGAGT	CAGGAGT	-	novel	NA	P-0041375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	201	392	0	ENST00000267163.4:c.774_780del	p.Asn258LysfsTer4	p.N258Kfs*4	ENST00000267163	NM_000321.2	258	aaCAGGAGT/aa	8/27	0.932839876003525	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.932839876003525	1		392	213	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0041635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	51	161	0	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	0.560706038892536	2	FACETS	0.834	0.734	0.935	0.834	0.734	0.935	CLONAL	2	TRUE	0	0.560706038892536	2		161	109	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0041905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	726	684	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.520508957931253	5	FACETS	0.951	0.929	0.973	0.951	0.929	0.973	CLONAL	5	TRUE	0	0.572643315219945	5		684	991	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260707	16260707	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	306	651	0	ENST00000375759.3:c.7972G>T	p.Val2658Leu	p.V2658L	ENST00000375759	NM_015001.2	2658	Gtg/Ttg	11/15	0.572767331802931	3	FACETS	0.999	0.949	1	0.999	0.949	1	CLONAL	2	TRUE	1	0.572643315219945	3		651	688	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660472	67660472	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	202	372	0	ENST00000264010.4:c.1372A>G	p.Lys458Glu	p.K458E	ENST00000264010	NM_006565.3	458	Aag/Gag	8/12	0.5112826920752	5	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.572643315219945	5		372	525	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56402502	56402502	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0041905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	136	218	0	ENST00000348428.3:c.1544T>A	p.Leu515Ter	p.L515*	ENST00000348428	NM_006785.3	515	tTa/tAa	13/17	0.572643315219945	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.572643315219945	2		218	198	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231825	36231825	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	122	591	0	ENST00000300305.3:c.559G>T	p.Ala187Ser	p.A187S	ENST00000300305		187	Gcc/Tcc	5/8	0.198948036538093	2	FACETS	0.764	0.693	0.838	0.382	0.346	0.419	INDETERMINATE	1	TRUE	0	0.572643315219945	2		591	558	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610695	52610695	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	143	327	0	ENST00000394830.3:c.3478C>T	p.Arg1160Ter	p.R1160*	ENST00000394830	NM_018313.4	1160	Cga/Tga	23/30	0.572643315219945	2	FACETS	0.995	0.93	1	0.995	0.93	1	CLONAL	2	TRUE	0	0.572643315219945	2		327	251	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280085	66280085	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	69	261	1	ENST00000273854.3:c.1604T>A	p.Val535Asp	p.V535D	ENST00000273854	NM_004439.5	535	gTt/gAt	7/18	0.572643315219945	2	FACETS	0.945	0.833	1	0.473	0.416	0.532	CLONAL	1	TRUE	0	0.572643315219945	2		262	255	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0041976-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6954	303	392	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.949616172657831	30	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.949616172657831	30		392	7257	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0041976-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	209	840	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.949616172657831	2	FACETS	0.974	0.95	0.994	0.974	0.95	0.994	CLONAL	2	TRUE	0	0.949616172657831	2		843	226	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973548	15973548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1000518180	NA	P-0041976-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	59	372	4	ENST00000268712.3:c.4444C>T	p.Arg1482Trp	p.R1482W	ENST00000268712	NM_006311.3	1482	Cgg/Tgg	31/46	0.949616172657831	2	FACETS	0.675	0.592	0.763	0.338	0.296	0.382	SUBCLONAL	1	TRUE	0	0.949616172657831	2		376	184	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163476	47163476	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041976-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	33	298	0	ENST00000409792.3:c.2650C>T	p.Gln884Ter	p.Q884*	ENST00000409792	NM_014159.6	884	Cag/Tag	3/21	0.475113464680025	1	FACETS	0.225	0.186	0.269	0.225	0.186	0.269	INDETERMINATE	1	TRUE	0	0.949616172657831	1		298	162	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771199	161771199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041976-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	75	717	0	ENST00000366898.1:c.1330G>A	p.Glu444Lys	p.E444K	ENST00000366898	NM_004562.2	444	Gag/Aag	12/12	0.471597720976121	3	FACETS	0.605	0.533	0.682	0.202	0.177	0.228	INDETERMINATE	1	TRUE	0	0.949616172657831	3		717	385	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472553	88472553	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041976-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	90	680	0	ENST00000360948.2:c.2002G>C	p.Val668Leu	p.V668L	ENST00000360948	NM_001012338.2	668	Gtg/Ctg	16/19	0.949616172657831	1	FACETS	0.47	0.425	0.515	0.47	0.425	0.515	SUBCLONAL	1	TRUE	0	0.949616172657831	1		680	212	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748585	43748585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752153816	NA	P-0041976-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	160	479	0	ENST00000523873.1:c.539G>A	p.Gly180Asp	p.G180D	ENST00000523873		180	gGc/gAc	6/8	0.949616172657831	2	FACETS	0.991	0.966	1	0.991	0.966	1	CLONAL	2	TRUE	0	0.949616172657831	2		479	170	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680713	30680713	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041976-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	50	594	0	ENST00000376406.3:c.1006G>C	p.Glu336Gln	p.E336Q	ENST00000376406	NM_014641.2	336	Gag/Cag	5/15	0.949616172657831	2	FACETS	0.387	0.331	0.448	0.194	0.165	0.224	SUBCLONAL	1	TRUE	0	0.949616172657831	2		594	272	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110669	8110669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041976-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	72	591	0	ENST00000585124.1:c.223G>A	p.Asp75Asn	p.D75N	ENST00000585124	NM_004217.3	75	Gat/Aat	5/9	0.949616172657831	2	FACETS	0.59	0.522	0.662	0.295	0.261	0.331	SUBCLONAL	1	TRUE	0	0.949616172657831	2		591	257	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62316884	62316884	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041976-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	29	998	0	ENST00000360203.5:c.1200C>G	p.Phe400Leu	p.F400L	ENST00000360203	NM_001283009.1	400	ttC/ttG	15/35	NA	2	FACETS	0.113	0.09	0.139			1	INDETERMINATE	1	TRUE	NA	0.949616172657831	2		998	541	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24135807	24135807	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041976-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	88	508	0	ENST00000263121.7:c.294G>C	p.Glu98Asp	p.E98D	ENST00000263121	NM_003073.3	98	gaG/gaC	3/9	0.458782628211964	1	FACETS	0.255	0.227	0.284	0.255	0.227	0.284	INDETERMINATE	1	TRUE	0	0.949616172657831	1		508	382	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162156	47162156	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041976-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	36	417	0	ENST00000409792.3:c.3970C>G	p.Gln1324Glu	p.Q1324E	ENST00000409792	NM_014159.6	1324	Caa/Gaa	3/21	0.475113464680025	1	FACETS	0.184	0.152	0.219	0.184	0.152	0.219	INDETERMINATE	1	TRUE	0	0.949616172657831	1		417	216	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162695	47162695	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041976-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	16	395	1	ENST00000409792.3:c.3431C>A	p.Ser1144Tyr	p.S1144Y	ENST00000409792	NM_014159.6	1144	tCt/tAt	3/21	0.475113464680025	1	FACETS	0.128	0.095	0.167	0.128	0.095	0.167	INDETERMINATE	1	TRUE	0	0.949616172657831	1		396	138	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163010	47163010	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041976-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	32	337	0	ENST00000409792.3:c.3116C>G	p.Ser1039Cys	p.S1039C	ENST00000409792	NM_014159.6	1039	tCt/tGt	3/21	0.475113464680025	1	FACETS	0.212	0.174	0.254	0.212	0.174	0.254	INDETERMINATE	1	TRUE	0	0.949616172657831	1		337	167	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165543	47165543	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041976-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	28	600	0	ENST00000409792.3:c.583C>G	p.Pro195Ala	p.P195A	ENST00000409792	NM_014159.6	195	Cca/Gca	3/21	0.475113464680025	1	FACETS	0.187	0.15	0.227	0.187	0.15	0.227	INDETERMINATE	1	TRUE	0	0.949616172657831	1		600	166	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912172	29912172	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041976-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	16	230	0	ENST00000376809.5:c.893G>C	p.Trp298Ser	p.W298S	ENST00000376809	NM_002116.7	298	tGg/tCg	4/8	0.867563719194497	1	FACETS	0.347	0.266	0.435	0.347	0.266	0.435	SUBCLONAL	1	TRUE	0	0.949616172657831	1		230	51	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955571	48955571	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	41	228	0	ENST00000267163.4:c.1687T>C	p.Trp563Arg	p.W563R	ENST00000267163	NM_000321.2	563	Tgg/Cgg	17/27	0.461645454187518	2	FACETS	0.529	0.442	0.624	0.264	0.221	0.312	SUBCLONAL	1	TRUE	0	0.523849317974772	2		228	296	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934189	48934189	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0042639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	180	479	0	ENST00000267163.4:c.644C>G	p.Ser215Ter	p.S215*	ENST00000267163	NM_000321.2	215	tCa/tGa	7/27	0.635290991957565	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.635290991957565	2		479	282	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0042809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	618	573	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.84076509341894	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.84076509341894	2		573	731	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	377	717	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.84076509341894	2		717	854	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037877	49037877	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913295	NA	P-0042809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	46	328	0	ENST00000267163.4:c.2117G>T	p.Cys706Phe	p.C706F	ENST00000267163	NM_000321.2	706	tGt/tTt	21/27	0.84076509341894	1	FACETS	0.255	0.216	0.297	0.255	0.216	0.297	SUBCLONAL	1	TRUE	0	0.84076509341894	1		328	249	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22412956	22412956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553196096	NA	P-0042809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	76	147	0	ENST00000344548.3:c.203G>A	p.Arg68Gln	p.R68Q	ENST00000344548	NM_001039802.1	68	cGa/cAa	5/7	1	2	FACETS	0.972	0.872	1	0.972	0.872	1	CLONAL	1	TRUE	1	0.84076509341894	2		147	186	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874937	151874937	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	214	372	0	ENST00000262189.6:c.7601del	p.Pro2534GlnfsTer28	p.P2534Qfs*28	ENST00000262189	NM_170606.2	2534	cCa/ca	38/59	1	2	FACETS	0.998	0.937	1	0.998	0.937	1	CLONAL	1	TRUE	1	0.84076509341894	2		372	510	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878136	48878136	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	20	90	0	ENST00000267163.4:c.88G>T	p.Glu30Ter	p.E30*	ENST00000267163	NM_000321.2	30	Gag/Tag	1/27	0.84076509341894	1	FACETS	0.332	0.26	0.413	0.332	0.26	0.413	SUBCLONAL	1	TRUE	0	0.84076509341894	1		90	83	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872613	37872613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043322-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1197	136	1154	1	ENST00000269571.5:c.1573C>T	p.Pro525Ser	p.P525S	ENST00000269571		525	Ccc/Tcc	13/27	0.283659273947619	5	FACETS	1	0.927	1	0.342	0.31	0.376	CLONAL	1	TRUE	2	0.283659273947619	5		1155	1333	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168939	11168939	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043322-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	80	591	0	ENST00000358026.2:c.4529G>C	p.Gly1510Ala	p.G1510A	ENST00000358026	NM_001128849.1	1510	gGa/gCa	32/36	0.252032047565374	4	FACETS	1	0.882	1	0.501	0.441	0.566	CLONAL	1	TRUE	2	0.283659273947619	4		591	722	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631934	90631934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913502	NA	P-0043428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	11	573	0	ENST00000330062.3:c.419G>A	p.Arg140Gln	p.R140Q	ENST00000330062	NM_002168.2	140	cGg/cAg	4/11	0.146245669368909	4	FACETS	0.105	0.071	0.146	0.052	0.035	0.073	INDETERMINATE	1	TRUE	2	0.731481942887793	4		573	498	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544748	65544748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	8	394	0	ENST00000358664.4:c.178C>T	p.Arg60Trp	p.R60W	ENST00000358664	NM_002382.4	60	Cgg/Tgg	4/5	1	2	FACETS	0.073	0.047	0.108	0.073	0.047	0.108	SUBCLONAL	1	TRUE	1	0.731481942887793	2		394	299	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916840	48916841	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs1566186125	NA	P-0043428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	213	242	0	ENST00000267163.4:c.371_372del	p.Ile124ArgfsTer6	p.I124Rfs*6	ENST00000267163	NM_000321.2	124	ATa/a	3/27	0.731481942887793	3	FACETS	0.978	0.94	1	0.978	0.94	1	CLONAL	3	TRUE	0	0.731481942887793	3		242	271	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992630	72992630	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1189486286	NA	P-0043668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	28	585	0	ENST00000268489.5:c.1415C>A	p.Ala472Glu	p.A472E	ENST00000268489	NM_006885.3	472	gCg/gAg	2/10	1	2	FACETS	0.543	0.433	0.669	0.543	0.433	0.669	SUBCLONAL	1	FALSE	1	0.224148736137207	2		585	460	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434477	49434477	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	71	978	0	ENST00000301067.7:c.7076C>T	p.Ala2359Val	p.A2359V	ENST00000301067	NM_003482.3	2359	gCa/gTa	31/54	1	2	FACETS	0.897	0.783	1	0.897	0.783	1	CLONAL	1	FALSE	1	0.224148736137207	2		978	706	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0044388-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	46	550	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.611	0.513	0.719	0.611	0.513	0.719	SUBCLONAL	1	TRUE	1	0.19	2		550	793	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0044388-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	140	309	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.3	3	FACETS	0.88	0.805	0.959	1	0.983	1	CLONAL	3	TRUE	1	0.19	3		310	611	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170774	11170774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568565786	NA	P-0044388-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	59	788	1	ENST00000358026.2:c.4918C>T	p.Arg1640Trp	p.R1640W	ENST00000358026	NM_001128849.1	1640	Cgg/Tgg	35/36	0.204207185208849	3	FACETS	0.61	0.523	0.706	0.305	0.261	0.353	SUBCLONAL	1	TRUE	1	0.19	3		789	1115	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578260	7578260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204041	NA	P-0044388-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	244	720	2	ENST00000269305.4:c.589G>A	p.Val197Met	p.V197M	ENST00000269305	NM_001126112.2	197	Gtg/Atg	6/11	0.257199832039028	2	FACETS	0.986	0.924	1	1	0.992	1	CLONAL	3	TRUE	0	0.19	2		722	868	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291812	15291812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779592020	NA	P-0044388-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	139	1016	3	ENST00000263388.2:c.2954G>A	p.Arg985His	p.R985H	ENST00000263388	NM_000435.2	985	cGc/cAc	18/33	0.204207185208849	3	FACETS	1	0.981	1	0.658	0.598	0.722	CLONAL	1	TRUE	1	0.19	3		1019	1217	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405724	139405724	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0044388-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	115	801	1	ENST00000277541.6:c.2468-1G>A		p.X823_splice	ENST00000277541	NM_017617.3	823			0.3	3	FACETS	1	0.974	1	0.625	0.561	0.692	CLONAL	1	TRUE	1	0.19	3		802	1061	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962566	100962566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749564230	NA	P-0044388-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	78	445	1	ENST00000325455.5:c.1831G>A	p.Val611Ile	p.V611I	ENST00000325455	NM_001202474.3	611	Gtt/Att	3/8	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.19	2		446	658	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636367	21636367	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs376839517	NA	P-0044388-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	197	539	0	ENST00000421138.2:c.643C>T	p.Arg215Ter	p.R215*	ENST00000421138		215	Cga/Tga	7/16	0.3	3	FACETS	0.946	0.878	1	1	0.99	1	CLONAL	3	TRUE	1	0.19	3		539	800	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368291	45368291	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044388-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	86	400	0	ENST00000262160.6:c.1311G>T	p.Trp437Cys	p.W437C	ENST00000262160	NM_005901.5	437	tgG/tgT	11/11	0.3	1	FACETS	0.834	0.741	0.934	1	0.982	1	CLONAL	2	TRUE	0	0.19	1		400	491	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143087	30143087	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756273623	NA	P-0044388-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	79	694	0	ENST00000389048.3:c.439G>A	p.Glu147Lys	p.E147K	ENST00000389048	NM_004304.4	147	Gag/Aag	1/29	1	2	FACETS	0.909	0.798	1	0.909	0.798	1	CLONAL	1	TRUE	1	0.19	2		694	915	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277145	38277145	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044388-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	107	728	0	ENST00000425967.3:c.1283A>G	p.Tyr428Cys	p.Y428C	ENST00000425967	NM_001174067.1	428	tAc/tGc	10/19	0.282032158467787	2	FACETS	1	0.98	1	0.705	0.632	0.782	CLONAL	1	TRUE	0	0.19	2		728	799	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738211	133738211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370646520	NA	P-0045156-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	412	512	0	ENST00000318560.5:c.611C>T	p.Thr204Met	p.T204M	ENST00000318560	NM_005157.4	204	aCg/aTg	4/11	0.535173507844424	4	FACETS	0.993	0.949	1	0.993	0.949	1	CLONAL	2	TRUE	2	0.81560116311162	4		512	924	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632414	3632414	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867187228	NA	P-0045156-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1449	100	894	1	ENST00000294008.3:c.5434G>A	p.Ala1812Thr	p.A1812T	ENST00000294008	NM_032444.2	1812	Gcc/Acc	15/15	0.81560116311162	4	FACETS	0.287	0.255	0.322	0.096	0.085	0.108	SUBCLONAL	1	TRUE	1	0.81560116311162	4		895	1549	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0045808-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	82	1025	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.722603085811707	3	FACETS	0.292	0.257	0.33	0.146	0.128	0.165	SUBCLONAL	1	TRUE	1	0.802557495778206	3		1025	980	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0045808-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	149	375	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	1	2	FACETS	0.94	0.869	1	0.94	0.869	1	CLONAL	1	TRUE	1	0.802557495778206	2		375	395	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50811826	50811826	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs886040872	NA	P-0045808-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	159	394	1	ENST00000398568.2:c.1103C>A	p.Ser368Ter	p.S368*	ENST00000398568	NM_001042412.1	368	tCa/tAa	7/18	0.802557495778206	1	FACETS	0.93	0.876	0.983	0.93	0.876	0.983	CLONAL	1	TRUE	0	0.802557495778206	1		395	255	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025606	1025606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045808-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	294	761	2	ENST00000358495.3:c.769C>T	p.Arg257Trp	p.R257W	ENST00000358495	NM_134424.2	257	Cgg/Tgg	9/12	0.802557495778206	3	FACETS	0.97	0.914	1			1	CLONAL	1	TRUE	NA	0.802557495778206	3		763	1058	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40460212	40460212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045808-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	284	586	0	ENST00000345506.4:c.1923G>A	p.Trp641Ter	p.W641*	ENST00000345506	NM_003152.3	641	tgG/tgA	17/20	0.722603085811707	3	FACETS	1	0.983	1	0.553	0.521	0.586	CLONAL	1	TRUE	1	0.802557495778206	3		586	897	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158404	26158404	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045808-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	798	769	0	ENST00000289316.2:c.7G>T	p.Glu3Ter	p.E3*	ENST00000289316	NM_138720.2	3	Gaa/Taa	1/2	0.789150455898214	2	FACETS	0.997	0.978	1	0.997	0.978	1	CLONAL	2	TRUE	0	0.802557495778206	2		769	997	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0046201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	505	850	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.629539906415312	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.629539906415312	2		850	791	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012389	29012389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161996687	NA	P-0046201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	170	574	0	ENST00000282397.4:c.482C>T	p.Thr161Met	p.T161M	ENST00000282397	NM_002019.4	161	aCg/aTg	4/30	0.478417229508281	6	FACETS	1	0.94	1	0.343	0.314	0.373	CLONAL	1	TRUE	3	0.629539906415312	6		574	1186	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849054	156849054	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786205449	NA	P-0046201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	63	961	0	ENST00000524377.1:c.1946G>A	p.Arg649Gln	p.R649Q	ENST00000524377	NM_002529.3	649	cGg/cAg	15/17	0.629539906415312	3	FACETS	0.23	0.197	0.265	0.115	0.098	0.133	SUBCLONAL	1	TRUE	1	0.629539906415312	3		961	1146	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436026	56436026	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771831816	NA	P-0046201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	384	678	0	ENST00000407977.2:c.1111C>T	p.Arg371Ter	p.R371*	ENST00000407977		371	Cga/Tga	9/10	0.629539906415312	2	FACETS	0.961	0.924	0.997	0.961	0.924	0.997	CLONAL	2	TRUE	0	0.629539906415312	2		678	635	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929371	44929371	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0046201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	31	414	0	ENST00000377967.4:c.2471C>G	p.Ser824Ter	p.S824*	ENST00000377967	NM_021140.2	824	tCa/tGa	17/29	0.629539906415312	2	FACETS	0.182	0.147	0.223			1	SUBCLONAL	1	TRUE	NA	0.629539906415312	2		414	540	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870882	12870882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	72	437	0	ENST00000228872.4:c.109G>A	p.Asp37Asn	p.D37N	ENST00000228872	NM_004064.3	37	Gac/Aac	1/3	0.372158250021221	2	FACETS	0.449	0.392	0.509	0.224	0.196	0.255	INDETERMINATE	1	TRUE	0	0.629539906415312	2		437	510	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916120	9916120	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0046201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	278	488	0	ENST00000330684.3:c.2168+1G>A		p.X723_splice	ENST00000330684	NM_001134407.1	723			0.629539906415312	2	FACETS	0.95	0.906	0.992	0.95	0.906	0.992	CLONAL	2	TRUE	0	0.629539906415312	2		488	465	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64289166	64289166	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	260	448	2	ENST00000370651.3:c.334C>T	p.Pro112Ser	p.P112S	ENST00000370651	NM_003463.4	112	Cca/Tca	5/6	0.546464333324208	3	FACETS	0.959	0.908	1	0.959	0.908	1	CLONAL	2	TRUE	1	0.629539906415312	3		450	566	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476327	88476327	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	47	797	0	ENST00000360948.2:c.1805A>C	p.Lys602Thr	p.K602T	ENST00000360948	NM_001012338.2	602	aAg/aCg	15/19	0.629539906415312	2	FACETS	0.195	0.163	0.229	0.097	0.081	0.115	SUBCLONAL	1	TRUE	0	0.629539906415312	2		797	767	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735356	204735356	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	41	474	0	ENST00000302823.3:c.157A>G	p.Ile53Val	p.I53V	ENST00000302823	NM_005214.4	53	Atc/Gtc	2/4	0.413002931843612	3	FACETS	0.338	0.281	0.402			1	SUBCLONAL	1	TRUE	NA	0.629539906415312	3		474	506	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98011447	98011447	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	40	560	0	ENST00000289081.3:c.127G>C	p.Glu43Gln	p.E43Q	ENST00000289081	NM_000136.2	43	Gag/Cag	2/15	1	2	FACETS	0.216	0.179	0.257	0.216	0.179	0.257	SUBCLONAL	1	TRUE	1	0.629539906415312	2		560	589	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027156	49027159	+	frameshift_variant	Frame_Shift_Del	DEL	CAAT	CAAT	-	novel	NA	P-0046319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	344	271	0	ENST00000267163.4:c.1726_1729del	p.Ser576ArgfsTer34	p.S576Rfs*34	ENST00000267163	NM_000321.2	575	CAATca/ca	18/27	0.856273471043661	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.856273471043661	2		271	390	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39321543	39321543	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	225	308	0	ENST00000373001.3:c.478A>C	p.Thr160Pro	p.T160P	ENST00000373001	NM_022157.3	160	Act/Cct	3/7	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.856273471043661	2		308	514	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919888	50919888	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	368	988	1	ENST00000440232.2:c.2975A>T	p.Lys992Met	p.K992M	ENST00000440232	NM_002691.3	992	aAg/aTg	24/27	0.191005686624138	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.856273471043661	0		989	841	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628736	187628736	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs369161430	NA	P-0046319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	295	529	0	ENST00000441802.2:c.2246A>G	p.Asn749Ser	p.N749S	ENST00000441802	NM_005245.3	749	aAt/aGt	2/27	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.856273471043661	2		529	688	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931610	39931610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	308	200	0	ENST00000378444.4:c.2989del	p.Ala997HisfsTer24	p.A997Hfs*24	ENST00000378444	NM_001123385.1	997	Gca/ca	4/15	0.510336195437361	2	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.856273471043661	2		200	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577115	7577115	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519983	NA	P-0046511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	461	869	0	ENST00000269305.4:c.823T>C	p.Cys275Arg	p.C275R	ENST00000269305	NM_001126112.2	275	Tgt/Cgt	8/11	0.342719350973172	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.377947615036363	3		869	929	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426688	212426688	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	90	668	0	ENST00000342788.4:c.2427C>G	p.His809Gln	p.H809Q	ENST00000342788	NM_005235.2	809	caC/caG	20/28	0.232647125318117	3	FACETS	0.892	0.792	0.998	0.446	0.396	0.499	CLONAL	1	TRUE	1	0.377947615036363	3		668	635	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056241	26056241	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs149712381	NA	P-0046511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	120	708	0	ENST00000343677.2:c.416A>C	p.Lys139Thr	p.K139T	ENST00000343677	NM_005319.3	139	aAg/aCg	1/1	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.377947615036363	2		708	603	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046758-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	61	374	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.939	1			1	INDETERMINATE	1	TRUE	NA	0.581670171223407	2		374	188	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400019	49400019	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046758-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	101	498	0	ENST00000418115.1:c.318C>G	p.Phe106Leu	p.F106L	ENST00000418115	NM_001664.2	106	ttC/ttG	4/5	0.581670171223407	3	FACETS	0.743	0.666	0.826	0.372	0.333	0.413	SUBCLONAL	1	TRUE	1	0.581670171223407	3		498	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1555525367	NA	P-0046758-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	225	625	0	ENST00000269305.4:c.783-1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.581670171223407	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.581670171223407	1		625	423	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741363	17741363	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046758-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	291	586	0	ENST00000250003.3:c.34G>C	p.Asp12His	p.D12H	ENST00000250003	NM_002478.4	12	Gac/Cac	1/3	0.581670171223407	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.581670171223407	1		586	566	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378607	25378607	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046758-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	91	419	0	ENST00000311936.3:c.391C>A	p.Gln131Lys	p.Q131K	ENST00000311936	NM_004985.3	131	Cag/Aag	4/5	0.581670171223407	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.581670171223407	1		419	170	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416137	49416137	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0046758-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	161	325	0	ENST00000301067.7:c.16339-1G>C		p.X5447_splice	ENST00000301067	NM_003482.3	5447			0.581670171223407	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.581670171223407	1		325	319	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42050023	42050023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046758-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	11	283	0	ENST00000219905.7:c.7177G>A	p.Glu2393Lys	p.E2393K	ENST00000219905	NM_001164273.1	2393	Gaa/Aaa	19/24	0.474266162287323	1	FACETS	0.197	0.137	0.272	0.197	0.137	0.272	SUBCLONAL	1	TRUE	0	0.581670171223407	1		283	136	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197821	123197822	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0046758-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	56	189	0	ENST00000218089.9:c.1947_1948del	p.Arg649SerfsTer11	p.R649Sfs*11	ENST00000218089	NM_001042749.1	649	AGa/a	20/35	0.379650630014808	0	FACETS	0.588	0.517	0.66			1	SUBCLONAL	1	TRUE	NA	0.581670171223407	0		189	137	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474605	138474605	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046758-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	28	329	0	ENST00000289153.2:c.388A>G	p.Ile130Val	p.I130V	ENST00000289153	NM_006219.2	130	Ata/Gta	2/22	0.581670171223407	3	FACETS	0.328	0.262	0.403	0.164	0.131	0.202	SUBCLONAL	1	TRUE	1	0.581670171223407	3		329	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0046906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	14	795	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	1	2	FACETS	0.093	0.067	0.126	0.093	0.067	0.126	SUBCLONAL	1	TRUE	1	0.368185391019551	2		795	814	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212518	36212518	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	22	0	0	ENST00000222270.7:c.2269C>T	p.Gln757Ter	p.Q757*	ENST00000222270	NM_014727.1	757	Cag/Tag	3/37	1	2	FACETS	0.121	0.093	0.154	0.121	0.093	0.154	SUBCLONAL	1	TRUE	1	0.368185391019551	2		0	990	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0046936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	418	584	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.572905398575256	3	FACETS	0.916	0.886	0.945	0.916	0.886	0.945	CLONAL	3	TRUE	0	0.675111428060159	3		584	603	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238542	142238542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148064542	NA	P-0046936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	38	216	0	ENST00000350721.4:c.4351C>T	p.Arg1451Trp	p.R1451W	ENST00000350721	NM_001184.3	1451	Cgg/Tgg	24/47	0.589850909554565	3	FACETS	0.81	0.677	0.954	0.405	0.338	0.477	CLONAL	1	TRUE	1	0.675111428060159	3		216	186	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1956917	1956917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761204359	NA	P-0046936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	204	652	1	ENST00000382891.5:c.2368G>A	p.Val790Ile	p.V790I	ENST00000382891	NM_133335.3	790	Gtt/Att	13/22	0.530720606849151	3	FACETS	0.846	0.793	0.899	0.564	0.528	0.6	CLONAL	2	TRUE	0	0.675111428060159	3		653	478	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	66	685	0	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	0.224924341694946	1	FACETS	0.942	0.818	1	0.942	0.818	1	CLONAL	1	TRUE	0	0.224924341694946	1		685	553	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933342	39933342	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	81	736	0	ENST00000378444.4:c.1257A>C	p.Lys419Asn	p.K419N	ENST00000378444	NM_001123385.1	419	aaA/aaC	4/15	NA	2	FACETS	0.903	0.794	1			1	INDETERMINATE	1	TRUE	NA	0.224924341694946	2		736	798	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532742	46532742	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	34	315	0	ENST00000262741.5:c.336A>T	p.Leu112Phe	p.L112F	ENST00000262741	NM_003629.3	112	ttA/ttT	4/10	1	2	FACETS	0.942	0.772	1	0.942	0.772	1	CLONAL	1	TRUE	1	0.224924341694946	2		315	321	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557285	29557285	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	22	239	0	ENST00000356175.3:c.2998C>G	p.Arg1000Gly	p.R1000G	ENST00000356175	NM_000267.3	1000	Cgt/Ggt	23/57	0.224924341694946	1	FACETS	0.965	0.753	1	0.965	0.753	1	CLONAL	1	TRUE	0	0.224924341694946	1		239	180	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0047506-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	332	758	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	1	2	FACETS	1	0.99	1	1	0.997	1	CLONAL	3	FALSE	1	0.251040772530776	2		758	765	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253753	153253754	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047506-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	77	250	0	ENST00000281708.4:c.979_980insT	p.Glu327ValfsTer5	p.E327Vfs*5	ENST00000281708	NM_033632.3	327	gaa/gTaa	6/12	0.116648309721745	4	FACETS	0.914	0.824	1	1	0.987	1	INDETERMINATE	5	FALSE	2	0.251040772530776	4		250	168	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44896907	44896917	+	frameshift_variant	Frame_Shift_Del	DEL	TCACATTGCCC	TCACATTGCCC	-	novel	NA	P-0047506-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	31	411	0	ENST00000377967.4:c.627_637del	p.Phe209LeufsTer4	p.F209Lfs*4	ENST00000377967	NM_021140.2	209	ttTCACATTGCCCac/ttac	8/29	0.251040772530776	1	FACETS	0.956	0.79	1	1	0.961	1	CLONAL	2	FALSE	0	0.251040772530776	1		411	113	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442777	99442777	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047506-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	171	548	0	ENST00000268035.6:c.1174C>G	p.His392Asp	p.H392D	ENST00000268035	NM_000875.3	392	Cat/Gat	5/21	1	2	FACETS	0.94	0.872	1	1	0.994	1	CLONAL	3	FALSE	1	0.251040772530776	2		548	483	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478224	99478225	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAG	novel	NA	P-0047506-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	43	318	0	ENST00000268035.6:c.3131_3133dup	p.Arg1044dup	p.R1044dup	ENST00000268035	NM_000875.3	1044	gag/gaGAGg	16/21	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	FALSE	1	0.251040772530776	2		318	282	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164861	36164862	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0047506-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	290	948	0	ENST00000300305.3:c.1013_1014insCT	p.Leu339CysfsTer256	p.L339Cfs*256	ENST00000300305		338	gcg/gcCTg	8/8	1	2	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	FALSE	1	0.251040772530776	2		948	927	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80343449	80343449	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047506-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	20	294	0	ENST00000286548.4:c.870C>G	p.Asp290Glu	p.D290E	ENST00000286548	NM_002072.3	290	gaC/gaG	6/7	1	2	FACETS	0.954	0.735	1	0.954	0.735	1	CLONAL	1	FALSE	1	0.251040772530776	2		294	167	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0047747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	335	1199	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.637491348632275	1	FACETS	0.948	0.903	0.994	0.948	0.903	0.994	CLONAL	1	TRUE	0	0.64978943024719	1		1199	734	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149516579	149516579	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	268	939	1	ENST00000261799.4:c.32C>A	p.Ala11Asp	p.A11D	ENST00000261799	NM_002609.3	11	gCc/gAc	2/23	1	2	FACETS	0.844	0.793	0.897	0.844	0.793	0.897	CLONAL	1	TRUE	1	0.64978943024719	2		940	977	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444777	49444777	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	362	1116	2	ENST00000301067.7:c.2689G>T	p.Glu897Ter	p.E897*	ENST00000301067	NM_003482.3	897	Gag/Tag	10/54	0.238390535904821	3	FACETS	1	0.994	1	0.665	0.631	0.7	INDETERMINATE	1	TRUE	1	0.64978943024719	3		1118	1110	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864803	57864803	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	303	958	0	ENST00000228682.2:c.2280C>A	p.Asn760Lys	p.N760K	ENST00000228682	NM_005269.2	760	aaC/aaA	12/12	0.238390535904821	3	FACETS	1	0.992	1	0.637	0.601	0.673	INDETERMINATE	1	TRUE	1	0.64978943024719	3		958	970	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040675	16040675	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	160	434	1	ENST00000268712.3:c.1459T>C	p.Tyr487His	p.Y487H	ENST00000268712	NM_006311.3	487	Tat/Cat	14/46	0.637491348632275	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.64978943024719	1		435	312	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273276	18273276	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	248	720	0	ENST00000222254.8:c.1069G>T	p.Ala357Ser	p.A357S	ENST00000222254	NM_005027.3	357	Gct/Tct	9/16	1	2	FACETS	0.946	0.887	1	0.946	0.887	1	CLONAL	1	TRUE	1	0.64978943024719	2		720	807	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797798	42797798	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	278	1125	0	ENST00000575354.2:c.3850G>T	p.Glu1284Ter	p.E1284*	ENST00000575354	NM_015125.3	1284	Gag/Tag	16/20	0.637491348632275	1	FACETS	0.953	0.903	1	0.953	0.903	1	CLONAL	1	TRUE	0	0.64978943024719	1		1125	606	SUCCESS
REL	5966	MSKCC	GRCh37	2	61121590	61121590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	121	437	2	ENST00000295025.8:c.212C>T	p.Pro71Leu	p.P71L	ENST00000295025	NM_002908.2	71	cCa/cTa	3/11	0.64978943024719	2	FACETS	0.943	0.86	1	0.471	0.43	0.515	CLONAL	1	TRUE	0	0.64978943024719	2		439	395	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46271081	46271081	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	191	538	0	ENST00000371998.3:c.3205C>G	p.Leu1069Val	p.L1069V	ENST00000371998		1069	Ctg/Gtg	17/23	0.64978943024719	3	FACETS	0.951	0.881	1			1	CLONAL	1	TRUE	NA	0.64978943024719	3		538	819	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048807	180048807	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	304	1170	1	ENST00000261937.6:c.1755C>A	p.Tyr585Ter	p.Y585*	ENST00000261937	NM_182925.4	585	taC/taA	13/30	0.64978943024719	3	FACETS	0.9	0.847	0.955	0.45	0.423	0.478	CLONAL	1	TRUE	1	0.64978943024719	3		1171	1377	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020939	26020939	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	190	635	0	ENST00000357647.3:c.222G>C	p.Glu74Asp	p.E74D	ENST00000357647	NM_003529.2	74	gaG/gaC	1/1	1	2	FACETS	0.934	0.868	1	0.934	0.868	1	CLONAL	1	TRUE	1	0.64978943024719	2		635	626	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056067	26056288	+	inframe_deletion	In_Frame_Del	DEL	GCCTTGGGCTTCACAGCCTTAGCAGCACTTTTGGCAGCTTTCTTGGGCTTCGCAACCTTGGCCTTCTTTGGGCTCTTAGCCACTTTCTTGGTTACAGTGGCCGCGGCCGGCTTCTTCGCTTTCTTCGGTGTTTTCTTAGCGCTCTTCTTCGGAGTTGCGCCGCCAGCCGCCTTCTTGGGCTTCTTGGCTGCCCCAACTGGCTTCTTAGGTTTGGTTCCGCCC	GCCTTGGGCTTCACAGCCTTAGCAGCACTTTTGGCAGCTTTCTTGGGCTTCGCAACCTTGGCCTTCTTTGGGCTCTTAGCCACTTTCTTGGTTACAGTGGCCGCGGCCGGCTTCTTCGCTTTCTTCGGTGTTTTCTTAGCGCTCTTCTTCGGAGTTGCGCCGCCAGCCGCCTTCTTGGGCTTCTTGGCTGCCCCAACTGGCTTCTTAGGTTTGGTTCCGCCC	-	novel	NA	P-0047747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	15	593	0	ENST00000343677.2:c.369_590del	p.Gly124_Ala197del	p.G124_A197del	ENST00000343677	NM_005319.3	123	gcGGGCGGAACCAAACCTAAGAAGCCAGTTGGGGCAGCCAAGAAGCCCAAGAAGGCGGCTGGCGGCGCAACTCCGAAGAAGAGCGCTAAGAAAACACCGAAGAAAGCGAAGAAGCCGGCCGCGGCCACTGTAACCAAGAAAGTGGCTAAGAGCCCAAAGAAGGCCAAGGTTGCGAAGCCCAAGAAAGCTGCCAAAAGTGCTGCTAAGGCTGTGAAGCCCAAGGCc/gcc	1/1	1	2	FACETS	0.077	0.055	0.102	0.077	0.055	0.102	SUBCLONAL	1	TRUE	1	0.64978943024719	2		593	603	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92300830	92300830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	194	504	0	ENST00000265734.4:c.557G>A	p.Arg186Lys	p.R186K	ENST00000265734	NM_001259.6	186	aGa/aAa	5/8	0.64978943024719	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.64978943024719	1		504	388	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32191705	32191705	+	start_lost	Translation_Start_Site	SNP	T	T	G	novel	NA	P-0047747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	143	887	1	ENST00000375023.3:c.1A>C	p.Met1?	p.M1?	ENST00000375023	NM_004557.3	1	Atg/Ctg	1/30	1	2	FACETS	0.575	0.525	0.628	0.575	0.525	0.628	SUBCLONAL	1	TRUE	1	0.64978943024719	2		888	765	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578179	7578179	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048099-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	379	1029	1	ENST00000269305.4:c.670G>T	p.Glu224Ter	p.E224*	ENST00000269305	NM_001126112.2	224	Gag/Tag	6/11	0.237372898616042	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.239465250321002	2		1030	1348	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489534	56489534	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048099-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	170	782	1	ENST00000267101.3:c.1999C>A	p.Arg667Ser	p.R667S	ENST00000267101	NM_001982.3	667	Cgt/Agt	17/28	0.19463218505802	3	FACETS	0.807	0.742	0.875	0.807	0.742	0.875	CLONAL	2	TRUE	1	0.239465250321002	3		783	985	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257270	133257270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048099-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	79	544	0	ENST00000320574.5:c.208G>A	p.Glu70Lys	p.E70K	ENST00000320574	NM_006231.2	70	Gag/Aag	3/49	0.239465250321002	3	FACETS	0.979	0.86	1	0.489	0.43	0.553	CLONAL	1	TRUE	1	0.239465250321002	3		544	755	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743949	46743949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149441991	NA	P-0048099-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	78	637	0	ENST00000371975.4:c.2239C>T	p.Arg747Cys	p.R747C	ENST00000371975	NM_003579.3	747	Cgc/Tgc	18/18	0.211422999764532	3	FACETS	0.823	0.722	0.933	0.412	0.361	0.467	CLONAL	1	TRUE	1	0.239465250321002	3		637	886	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933842	39933842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745720817	NA	P-0048099-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1376	127	1251	2	ENST00000378444.4:c.757G>A	p.Val253Ile	p.V253I	ENST00000378444	NM_001123385.1	253	Gtc/Atc	4/15	0.19463218505802	3	FACETS	0.79	0.713	0.872	0.395	0.356	0.436	SUBCLONAL	1	TRUE	1	0.239465250321002	3		1253	1503	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462933	120462933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1450649026	NA	P-0048099-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	107	760	3	ENST00000256646.2:c.5398C>T	p.Arg1800Cys	p.R1800C	ENST00000256646	NM_024408.3	1800	Cgt/Tgt	30/34	0.239465250321002	6	FACETS	1	0.94	1	0.269	0.24	0.299	CLONAL	1	TRUE	2	0.239465250321002	6		763	1230	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464362	120464362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048099-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1614	138	944	0	ENST00000256646.2:c.5284G>A	p.Glu1762Lys	p.E1762K	ENST00000256646	NM_024408.3	1762	Gaa/Aaa	29/34	0.239465250321002	6	FACETS	0.973	0.882	1	0.243	0.22	0.268	CLONAL	1	TRUE	2	0.239465250321002	6		944	1752	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204499896	204499896	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048099-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1345	73	633	0	ENST00000367182.3:c.238C>A	p.Leu80Ile	p.L80I	ENST00000367182	NM_001278516.1	80	Ctt/Att	4/11	0.239465250321002	9	FACETS	0.79	0.688	0.901			1	CLONAL	1	TRUE	NA	0.239465250321002	9		633	1418	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350577	89350579	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs766042947	NA	P-0048099-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	126	831	0	ENST00000301030.4:c.2371_2373del	p.Lys791del	p.K791del	ENST00000301030	NM_001256183.1	791	AAG/-	9/13	0.231580743439133	2	FACETS	0.971	0.877	1	0.485	0.438	0.535	CLONAL	1	TRUE	0	0.239465250321002	2		831	1084	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936385	49936385	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048099-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1339	133	1140	0	ENST00000296474.3:c.1463A>G	p.Asn488Ser	p.N488S	ENST00000296474	NM_002447.2	488	aAc/aGc	3/20	0.239465250321002	3	FACETS	0.845	0.765	0.93	0.422	0.382	0.465	CLONAL	1	TRUE	1	0.239465250321002	3		1140	1472	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635236	87635236	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048099-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	94	794	1	ENST00000277120.3:c.2288T>C	p.Phe763Ser	p.F763S	ENST00000277120		763	tTc/tCc	18/19	1	2	FACETS	0.799	0.71	0.895	0.799	0.71	0.895	SUBCLONAL	1	TRUE	1	0.239465250321002	2		795	982	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352781	70352781	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048099-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1181	91	983	0	ENST00000374080.3:c.4502C>T	p.Thr1501Ile	p.T1501I	ENST00000374080		1501	aCc/aTc	32/45	0.19463218505802	3	FACETS	0.669	0.592	0.752	0.335	0.296	0.376	SUBCLONAL	1	TRUE	1	0.239465250321002	3		983	1272	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76919037	76919037	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048099-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	35	391	0	ENST00000373344.5:c.3954T>G	p.Asn1318Lys	p.N1318K	ENST00000373344	NM_000489.3	1318	aaT/aaG	12/35	0.19463218505802	3	FACETS	0.734	0.601	0.883	0.367	0.3	0.442	SUBCLONAL	1	TRUE	1	0.239465250321002	3		391	446	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820668	3820668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768030911	NA	P-0048103-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	123	889	0	ENST00000262367.5:c.2783C>T	p.Pro928Leu	p.P928L	ENST00000262367	NM_004380.2	928	cCg/cTg	14/31	0.14821732164893	4	FACETS	1	0.982	1	0.684	0.619	0.753	INDETERMINATE	1	FALSE	2	0.319015867435166	4		889	743	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579346	7579348	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs764486868	NA	P-0048103-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	120	693	0	ENST00000269305.4:c.339_341del	p.Phe113del	p.F113del	ENST00000269305	NM_001126112.2	113	ttCTTg/ttg	4/11	0.220436091912617	2	FACETS	1	0.98	1	0.66	0.598	0.725	CLONAL	1	FALSE	0	0.319015867435166	2		693	570	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0048103-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	62	325	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.221066972784975	2	FACETS	1	0.969	1	0.709	0.618	0.806	CLONAL	1	FALSE	0	0.319015867435166	2		325	274	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032071	26032071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048103-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	49	527	0	ENST00000244661.2:c.218G>A	p.Arg73Gln	p.R73Q	ENST00000244661	NM_003537.3	73	cGa/cAa	1/1	0.319015867435166	3	FACETS	0.629	0.533	0.736	0.21	0.177	0.246	SUBCLONAL	1	FALSE	0	0.319015867435166	3		527	566	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	117	374	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.489273081003525	2		374	476	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	71	181	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.782	0.687	0.884	0.782	0.687	0.884	SUBCLONAL	1	TRUE	1	0.489273081003525	2		181	371	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0048720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	171	226	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.478890866673177	3	FACETS	0.933	0.867	1	0.933	0.867	1	CLONAL	2	TRUE	1	0.489273081003525	3		226	466	SUCCESS
APC	324	MSKCC	GRCh37	5	112175561	112175561	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	92	215	0	ENST00000257430.4:c.4271del	p.Pro1424GlnfsTer49	p.P1424Qfs*49	ENST00000257430	NM_000038.5	1424	Cca/ca	16/16	0.386803226757131	1	FACETS	0.848	0.761	0.939	0.848	0.761	0.939	CLONAL	1	TRUE	0	0.489273081003525	1		215	335	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41526008	41526008	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0048720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	137	155	0	ENST00000263253.7:c.1282+1G>A		p.X428_splice	ENST00000263253	NM_001429.3	428			0.489273081003525	2	FACETS	0.924	0.855	0.994	0.924	0.855	0.994	CLONAL	2	TRUE	0	0.489273081003525	2		155	303	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092711	27092711	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0048720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	115	233	0	ENST00000324856.7:c.2733-1G>C		p.X911_splice	ENST00000324856	NM_006015.4	911			1	2	FACETS	0.977	0.885	1	0.977	0.885	1	CLONAL	1	TRUE	1	0.489273081003525	2		233	481	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29099491	29099492	+	splice_donor_variant	Splice_Site	INS	-	-	CAATTCC	novel	NA	P-0048720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	90	149	0	ENST00000328354.6:c.903_908+1dup		p.X301_splice	ENST00000328354	NM_007194.3	301			NA	2	FACETS	0.868	0.786	0.95			1	INDETERMINATE	2	TRUE	NA	0.489273081003525	2		149	212	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424957	49424957	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1225433147	NA	P-0048720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	157	783	1	ENST00000301067.7:c.13530+1G>A		p.X4510_splice	ENST00000301067	NM_003482.3	4510			0.478890866673177	3	FACETS	0.675	0.617	0.736	0.337	0.308	0.368	SUBCLONAL	1	TRUE	1	0.489273081003525	3		784	1184	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	37	374	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.963	0.798	1	0.963	0.798	1	CLONAL	1	TRUE	1	0.293318582044718	2		374	262	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	74	181	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.114504822127051	3	FACETS	1	0.941	1	0.562	0.493	0.636	INDETERMINATE	1	TRUE	1	0.293318582044718	3		181	515	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0048720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	123	226	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.193688889800986	4	FACETS	1	0.966	1	0.753	0.685	0.824	CLONAL	2	TRUE	1	0.293318582044718	4		226	480	SUCCESS
APC	324	MSKCC	GRCh37	5	112175561	112175561	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	38	215	0	ENST00000257430.4:c.4271del	p.Pro1424GlnfsTer49	p.P1424Qfs*49	ENST00000257430	NM_000038.5	1424	Cca/ca	16/16	1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	1	0.293318582044718	2		215	254	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41526008	41526008	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0048720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	117	155	0	ENST00000263253.7:c.1282+1G>A		p.X428_splice	ENST00000263253	NM_001429.3	428			0.293318582044718	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.293318582044718	2		155	336	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25462032	25462032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774100557	NA	P-0048720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	93	531	1	ENST00000264709.3:c.2375G>A	p.Arg792His	p.R792H	ENST00000264709	NM_175629.2	792	cGc/cAc	20/23	0.176683938057406	0	FACETS	0.802	0.714	0.894			1	CLONAL	1	TRUE	0	0.293318582044718	0		532	559	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092711	27092711	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0048720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	59	233	0	ENST00000324856.7:c.2733-1G>C		p.X911_splice	ENST00000324856	NM_006015.4	911			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.293318582044718	2		233	315	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29099491	29099492	+	splice_donor_variant	Splice_Site	INS	-	-	CAATTCC	novel	NA	P-0048720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	77	149	0	ENST00000328354.6:c.903_908+1dup		p.X301_splice	ENST00000328354	NM_007194.3	301			0.293318582044718	2	FACETS	0.924	0.821	1	0.924	0.821	1	CLONAL	2	TRUE	0	0.293318582044718	2		149	284	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0048746-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	183	897	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.866	0.801	0.933	0.866	0.801	0.933	CLONAL	1	TRUE	1	0.574941868962007	2		898	735	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242474	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGA	GAATTAAGA	-	rs121913436	NA	P-0048746-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	185	489	0	ENST00000275493.2:c.2239_2247del	p.Leu747_Glu749del	p.L747_E749del	ENST00000275493	NM_005228.3	746	GAATTAAGA/-	19/28	0.574941868962007	3	FACETS	0.771	0.718	0.827	0.771	0.718	0.827	SUBCLONAL	2	TRUE	1	0.574941868962007	3		489	537	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419043	419043	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048746-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	151	513	0	ENST00000399788.2:c.3304G>A	p.Glu1102Lys	p.E1102K	ENST00000399788	NM_001042603.1	1102	Gaa/Aaa	22/28	NA	2	FACETS	0.967	0.889	1			1	INDETERMINATE	1	TRUE	NA	0.574941868962007	2		513	543	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023376	27023385	+	frameshift_variant	Frame_Shift_Del	DEL	TCGCCGCCGC	TCGCCGCCGC	-	novel	NA	P-0048746-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	99	203	0	ENST00000324856.7:c.482_491del	p.Val161AlafsTer68	p.V161Afs*68	ENST00000324856	NM_006015.4	161	gTCGCCGCCGCc/gc	1/20	1	2	FACETS	0.765	0.698	0.834	1	0.985	1	SUBCLONAL	2	TRUE	1	0.574941868962007	2		203	225	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43773221	43773221	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0048746-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	125	417	0	ENST00000382044.4:c.372-1G>T		p.X124_splice	ENST00000382044	NM_001141980.1	124			1	2	FACETS	0.977	0.891	1	0.977	0.891	1	CLONAL	1	TRUE	1	0.574941868962007	2		417	445	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048773-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	254	374	0				ENST00000310581	NM_198253.2	-/1132			0.687573313026888	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.783002039499727	4		374	540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0048773-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	1145	795	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.704945253431043	4	FACETS	0.989	0.976	1			1	CLONAL	4	TRUE	NA	0.783002039499727	4		795	1318	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481806	56481806	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048773-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	528	603	0	ENST00000267101.3:c.734C>T	p.Ala245Val	p.A245V	ENST00000267101	NM_001982.3	245	gCc/gTc	7/28	0.783002039499727	3	FACETS	0.975	0.941	1	0.975	0.941	1	CLONAL	2	TRUE	1	0.783002039499727	3		603	962	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923093	48923094	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0048773-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	173	278	0	ENST00000267163.4:c.543_544del	p.Ser182TyrfsTer2	p.S182Yfs*2	ENST00000267163	NM_000321.2	181	ATa/a	6/27	0.783002039499727	3	FACETS	0.896	0.839	0.953	0.896	0.839	0.953	CLONAL	2	TRUE	1	0.783002039499727	3		278	343	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037866	49037866	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0048773-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	88	229	0	ENST00000267163.4:c.2107-1G>T		p.X703_splice	ENST00000267163	NM_000321.2	703			0.783002039499727	3	FACETS	0.965	0.864	1	0.483	0.432	0.536	CLONAL	1	TRUE	1	0.783002039499727	3		229	324	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464961	120464961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764895571	NA	P-0048773-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	192	470	0	ENST00000256646.2:c.5111G>A	p.Arg1704His	p.R1704H	ENST00000256646	NM_024408.3	1704	cGt/cAt	28/34	1	2	FACETS	0.96	0.895	1	0.96	0.895	1	CLONAL	1	TRUE	1	0.783002039499727	2		470	511	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350517	15350517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048773-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	364	911	0	ENST00000263377.2:c.3398C>T	p.Pro1133Leu	p.P1133L	ENST00000263377	NM_058243.2	1133	cCc/cTc	16/20	0.687573313026888	4	FACETS	1	0.984	1	0.549	0.519	0.579	CLONAL	1	TRUE	2	0.783002039499727	4		911	1510	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50816350	50816350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868852255	NA	P-0048773-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	217	298	0	ENST00000398568.2:c.1790C>T	p.Ser597Phe	p.S597F	ENST00000398568	NM_001042412.1	597	tCt/tTt	10/18	0.779715383713504	2	FACETS	0.883	0.842	0.922	0.883	0.842	0.922	CLONAL	2	TRUE	0	0.783002039499727	2		298	314	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856422	111856422	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048773-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	14	181	2	ENST00000341259.2:c.473A>C	p.His158Pro	p.H158P	ENST00000341259	NM_005475.2	158	cAc/cCc	2/8	0.467343458134687	3	FACETS	0.234	0.169	0.312	0.078	0.056	0.104	INDETERMINATE	1	TRUE	0	0.783002039499727	3		183	213	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748081	72748081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048773-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	214	645	1	ENST00000357731.5:c.97C>T	p.Pro33Ser	p.P33S	ENST00000357731	NM_173808.2	33	Ccg/Tcg	1/7	1	2	FACETS	0.954	0.893	1	0.954	0.893	1	CLONAL	1	TRUE	1	0.783002039499727	2		646	573	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717685	89717708	+	inframe_deletion	In_Frame_Del	DEL	AGTTCATGTACTTTGAGTTCCCTC	AGTTCATGTACTTTGAGTTCCCTC	-	novel	NA	P-0048773-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	274	421	0	ENST00000371953.3:c.712_735del	p.Phe238_Gln245del	p.F238_Q245del	ENST00000371953	NM_000314.4	237	aAGTTCATGTACTTTGAGTTCCCTCag/aag	7/9	0.774026633494251	2	FACETS	0.89	0.855	0.925	0.89	0.855	0.925	CLONAL	2	TRUE	0	0.783002039499727	2		421	393	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574748	95574748	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048773-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	149	361	0	ENST00000393063.1:c.2349T>G	p.Asp783Glu	p.D783E	ENST00000393063	NM_030621.3	783	gaT/gaG	16/28	1	2	FACETS	0.951	0.879	1	0.951	0.879	1	CLONAL	1	TRUE	1	0.783002039499727	2		361	400	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349738	15349738	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048773-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	639	892	0	ENST00000263377.2:c.3836C>G	p.Ala1279Gly	p.A1279G	ENST00000263377	NM_058243.2	1279	gCa/gGa	19/20	0.687573313026888	4	FACETS	0.98	0.945	1	0.98	0.945	1	CLONAL	2	TRUE	2	0.783002039499727	4		892	1485	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147720	61147735	+	frameshift_variant	Frame_Shift_Del	DEL	GAGAGACCAAGACCTG	GAGAGACCAAGACCTG	-	novel	NA	P-0048773-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	172	232	0	ENST00000295025.8:c.1031_1046del	p.Glu344ValfsTer25	p.E344Vfs*25	ENST00000295025	NM_002908.2	344	GAGAGACCAAGACCTGgt/gt	10/11	0.779715383713504	2	FACETS	0.943	0.898	0.985	0.943	0.898	0.985	CLONAL	2	TRUE	0	0.783002039499727	2		232	233	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513586	41513586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148575477	NA	P-0048773-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	256	603	0	ENST00000263253.7:c.490G>A	p.Gly164Arg	p.G164R	ENST00000263253	NM_001429.3	164	Gga/Aga	2/31	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.783002039499727	2		603	650	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935631	13935631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048773-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	430	465	0	ENST00000405192.2:c.1225C>A	p.Pro409Thr	p.P409T	ENST00000405192	NM_001163147.1	409	Cca/Aca	12/12	0.783002039499727	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.783002039499727	3		465	758	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798773	135798773	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048773-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	210	217	0	ENST00000298552.3:c.470T>G	p.Ile157Ser	p.I157S	ENST00000298552	NM_001162426.1	157	aTt/aGt	6/23	0.783002039499727	3	FACETS	0.917	0.865	0.969	0.917	0.865	0.969	CLONAL	2	TRUE	1	0.783002039499727	3		217	407	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519432	176519432	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048773-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1291	69	1008	0	ENST00000292408.4:c.838C>T	p.His280Tyr	p.H280Y	ENST00000292408	NM_213647.1	280	Cac/Tac	7/18	0.783002039499727	3	FACETS	0.18	0.156	0.207	0.09	0.078	0.104	SUBCLONAL	1	TRUE	1	0.783002039499727	3		1008	1360	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706885	117706885	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048773-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	44	393	0	ENST00000368508.3:c.2265G>T	p.Trp755Cys	p.W755C	ENST00000368508	NM_002944.2	755	tgG/tgT	15/43	0.783002039499727	4	FACETS	0.24	0.2	0.284	0.06	0.05	0.071	SUBCLONAL	1	TRUE	0	0.783002039499727	4		393	835	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219175	94219175	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs779269083	NA	P-0049138-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	22	291	1	ENST00000323929.3:c.229G>T	p.Glu77Ter	p.E77*	ENST00000323929	NM_005591.3	77	Gag/Tag	4/20	0.171008484374034	3	FACETS	0.591	0.458	0.746	0.296	0.229	0.373	SUBCLONAL	1	TRUE	1	0.239404768075417	3		292	348	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703691	47703691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049138-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	41	294	0	ENST00000233146.2:c.2191G>A	p.Glu731Lys	p.E731K	ENST00000233146	NM_000251.2	731	Gaa/Aaa	13/16	0.171008484374034	3	FACETS	0.832	0.693	0.986	0.416	0.346	0.493	CLONAL	1	TRUE	1	0.239404768075417	3		294	461	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888198	112888198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121918453	NA	P-0049154-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	274	811	0	ENST00000351677.2:c.214G>A	p.Ala72Thr	p.A72T	ENST00000351677	NM_002834.3	72	Gcc/Acc	3/16	1	2	FACETS	0.855	0.808	0.903	0.855	0.808	0.903	CLONAL	1	TRUE	1	0.923538904322722	2		811	694	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300446	11300446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049154-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	449	954	0	ENST00000361445.4:c.1700C>T	p.Ser567Phe	p.S567F	ENST00000361445	NM_004958.3	567	tCt/tTt	11/58	0.923538904322722	1	FACETS	0.986	0.963	1	0.986	0.963	1	CLONAL	1	TRUE	0	0.923538904322722	1		954	531	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958162	2958162	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049154-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	474	1092	0	ENST00000396946.4:c.2570A>C	p.Glu857Ala	p.E857A	ENST00000396946	NM_032415.4	857	gAg/gCg	19/25	0.923538904322722	3	FACETS	0.886	0.846	0.928	0.443	0.423	0.464	CLONAL	1	TRUE	1	0.923538904322722	3		1092	1693	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0049427-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	202	231	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.772876936656219	4	FACETS	0.934	0.888	0.979	0.934	0.888	0.979	CLONAL	3	FALSE	1	0.896641791695179	4		231	305	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579468	7579472	+	frameshift_variant	Frame_Shift_Del	DEL	CACGG	CACGG	-	novel	NA	P-0049427-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	232	696	0	ENST00000269305.4:c.215_219del	p.Pro72ArgfsTer75	p.P72Rfs*75	ENST00000269305	NM_001126112.2	72	cCCGTG/c	4/11	0.712794038571759	2	FACETS	0.86	0.826	0.891	0.86	0.826	0.891	CLONAL	2	FALSE	0	0.896641791695179	2		696	301	SUCCESS
AR	367	MSKCC	GRCh37	X	66764992	66764992	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049427-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1890	182	319	0	ENST00000374690.3:c.4G>C	p.Glu2Gln	p.E2Q	ENST00000374690	NM_000044.3	2	Gaa/Caa	1/8	0.896641791695179	14	FACETS	1	0.983	1			1	CLONAL	1	FALSE	NA	0.896641791695179	14		319	2072	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	238	374	0				ENST00000310581	NM_198253.2	-/1132			0.892421106584733	5	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	2	0.892421106584733	5		374	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0050889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	89	783	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	NA	2	FACETS	0.34	0.302	0.381			1	INDETERMINATE	1	TRUE	NA	0.892421106584733	2		783	586	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636973	176636973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1215568879	NA	P-0050889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	13	643	0	ENST00000439151.2:c.1573C>T	p.Arg525Trp	p.R525W	ENST00000439151	NM_022455.4	525	Cgg/Tgg	5/23	0.887315131654848	2	FACETS	0.146	0.104	0.198	0.073	0.052	0.099	SUBCLONAL	1	TRUE	0	0.892421106584733	2		643	199	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881512	48881512	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	143	305	0	ENST00000267163.4:c.234G>A	p.Trp78Ter	p.W78*	ENST00000267163	NM_000321.2	78	tgG/tgA	2/27	0.826602600560522	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.892421106584733	3		305	150	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774771	73774771	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	110	472	1	ENST00000254810.4:c.316G>A	p.Glu106Lys	p.E106K	ENST00000254810	NM_005324.3	106	Gaa/Aaa	4/4	0.458827979018765	4	FACETS	0.885	0.799	0.976	0.443	0.399	0.488	INDETERMINATE	1	TRUE	2	0.892421106584733	4		473	527	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830288	72830288	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	24	490	0	ENST00000268489.5:c.6293C>T	p.Ser2098Leu	p.S2098L	ENST00000268489	NM_006885.3	2098	tCg/tTg	9/10	0.887315131654848	2	FACETS	0.306	0.241	0.379	0.153	0.12	0.19	SUBCLONAL	1	TRUE	0	0.892421106584733	2		490	176	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941916	71941916	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0050889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	175	868	0	ENST00000298229.2:c.1274C>G	p.Ser425Ter	p.S425*	ENST00000298229	NM_001567.3	425	tCa/tGa	11/28	0.493847283467828	3	FACETS	0.944	0.874	1	0.472	0.437	0.508	INDETERMINATE	1	TRUE	1	0.892421106584733	3		868	601	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953811	55953811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	89	636	0	ENST00000263923.4:c.3625G>A	p.Asp1209Asn	p.D1209N	ENST00000263923	NM_002253.2	1209	Gac/Aac	27/30	0.493847283467828	3	FACETS	1	0.916	1	0.511	0.459	0.566	INDETERMINATE	1	TRUE	1	0.892421106584733	3		636	282	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732894	44732894	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	59	282	0	ENST00000377967.4:c.97G>A	p.Glu33Lys	p.E33K	ENST00000377967	NM_021140.2	33	Gag/Aag	1/29	0.365405016299321	2	FACETS	0.501	0.435	0.571			1	INDETERMINATE	1	TRUE	NA	0.892421106584733	2		282	264	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245954	16245954	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	19	432	1	ENST00000375759.3:c.1577C>T	p.Ser526Leu	p.S526L	ENST00000375759	NM_015001.2	526	tCg/tTg	8/15	1	2	FACETS	0.333	0.255	0.422	0.333	0.255	0.422	SUBCLONAL	1	TRUE	1	0.892421106584733	2		433	128	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726714	88726714	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	86	495	0	ENST00000360948.2:c.330C>G	p.Ile110Met	p.I110M	ENST00000360948	NM_001012338.2	110	atC/atG	4/19	0.153222365395052	3	FACETS	1	0.949	1	0.364	0.327	0.403	INDETERMINATE	1	TRUE	0	0.892421106584733	3		495	255	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765534	41765534	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	174	756	0	ENST00000301178.4:c.2410G>A	p.Glu804Lys	p.E804K	ENST00000301178	NM_021913.4	804	Gag/Aag	20/20	0.534272401736826	6	FACETS	0.858	0.793	0.924	0.572	0.529	0.616	INDETERMINATE	2	TRUE	3	0.892421106584733	6		756	633	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589823	55589823	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	21	471	0	ENST00000288135.5:c.1305G>T	p.Glu435Asp	p.E435D	ENST00000288135	NM_000222.2	435	gaG/gaT	8/21	0.493847283467828	3	FACETS	0.215	0.165	0.273	0.107	0.082	0.137	INDETERMINATE	1	TRUE	1	0.892421106584733	3		471	317	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651918	36651925	+	frameshift_variant	Frame_Shift_Del	DEL	GGCAGCAA	GGCAGCAA	-	novel	NA	P-0050889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	369	859	0	ENST00000244741.5:c.43_50del	p.Ser15LeufsTer18	p.S15Lfs*18	ENST00000244741	NM_000389.4	14	GGCAGCAAg/g	2/3	0.701028239551004	3	FACETS	0.763	0.728	0.797	0.763	0.728	0.797	SUBCLONAL	2	TRUE	1	0.892421106584733	3		859	784	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443695	29443695	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863225281	NA	P-0051231-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	42	604	0	ENST00000389048.3:c.3522C>G	p.Phe1174Leu	p.F1174L	ENST00000389048	NM_004304.4	1174	ttC/ttG	23/29	0.217030030400141	0	FACETS	0.437	0.363	0.518			1	SUBCLONAL	1	FALSE	0	0.217030030400141	0		604	694	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023895	27023895	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051231-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	12	136	0	ENST00000324856.7:c.1001C>G	p.Ser334Trp	p.S334W	ENST00000324856	NM_006015.4	334	tCg/tGg	1/20	1	2	FACETS	0.614	0.432	0.837	0.614	0.432	0.837	SUBCLONAL	1	FALSE	1	0.217030030400141	2		136	180	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023696	27023696	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051231-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	23	0	0	ENST00000324856.7:c.802C>T	p.Gln268Ter	p.Q268*	ENST00000324856	NM_006015.4	268	Cag/Tag	1/20	1	2	FACETS	0.371	0.288	0.468	0.371	0.288	0.468	SUBCLONAL	1	FALSE	1	0.217030030400141	2		0	571	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023676	27023676	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051231-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	19	0	0	ENST00000324856.7:c.782C>G	p.Ser261Trp	p.S261W	ENST00000324856	NM_006015.4	261	tCg/tGg	1/20	1	2	FACETS	0.322	0.244	0.416	0.322	0.244	0.416	SUBCLONAL	1	FALSE	1	0.217030030400141	2		0	543	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443589	29443589	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051231-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	37	0	0	ENST00000389048.3:c.3628G>A	p.Glu1210Lys	p.E1210K	ENST00000389048	NM_004304.4	1210	Gag/Aag	23/29	0.217030030400141	0	FACETS	0.301	0.247	0.362			1	SUBCLONAL	1	FALSE	0	0.217030030400141	0		0	888	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651983	36651984	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0051231-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	101	844	0	ENST00000244741.5:c.106dup	p.Ala36GlyfsTer12	p.A36Gfs*12	ENST00000244741	NM_000389.4	35	-/G	2/3	1	2	FACETS	0.831	0.741	0.928	0.831	0.741	0.928	CLONAL	1	FALSE	1	0.217030030400141	2		844	1120	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0051453-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	494	550	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.716949118357565	2	FACETS	0.968	0.939	0.996	0.968	0.939	0.996	CLONAL	2	TRUE	0	0.716949118357565	2		550	712	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754823	29754823	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051453-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	213	531	0	ENST00000389048.3:c.1112C>T	p.Ala371Val	p.A371V	ENST00000389048	NM_004304.4	371	gCt/gTt	4/29	0.262809001618364	6	FACETS	1	0.99	1	0.461	0.428	0.496	INDETERMINATE	1	TRUE	3	0.716949118357565	6		531	1045	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0052299-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	1300	573	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.699025884371664	8	FACETS	1	0.998	1			1	CLONAL	7	TRUE	NA	0.699025884371664	8		573	1549	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041150	29041150	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052299-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	167	624	0	ENST00000282397.4:c.278C>A	p.Thr93Asn	p.T93N	ENST00000282397	NM_002019.4	93	aCc/aAc	3/30	0.698411275002188	3	FACETS	1	0.929	1	0.504	0.464	0.544	CLONAL	1	TRUE	1	0.699025884371664	3		624	640	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89883001	89883001	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs757468756	NA	P-0052299-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	148	323	0	ENST00000389301.3:c.23A>G	p.Asn8Ser	p.N8S	ENST00000389301	NM_000135.2	8	aAc/aGc	1/43	0.695690294014937	4	FACETS	0.784	0.722	0.847			1	SUBCLONAL	2	TRUE	NA	0.699025884371664	4		323	459	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59924461	59924461	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs587780833	NA	P-0052299-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	269	271	3	ENST00000259008.2:c.627+1G>A		p.X209_splice	ENST00000259008	NM_032043.2	209			0.699025884371664	4	FACETS	0.942	0.909	0.974	0.942	0.909	0.974	CLONAL	4	TRUE	0	0.699025884371664	4		274	347	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475492	12475517	+	frameshift_variant	Frame_Shift_Del	DEL	TCCTCACAGCTGTTTGCCAAGCTGCT	TCCTCACAGCTGTTTGCCAAGCTGCT	-	novel	NA	P-0052299-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	293	621	0	ENST00000287820.6:c.1366_1391del	p.Ser456ProfsTer67	p.S456Pfs*67	ENST00000287820	NM_015869.4	456	TCCTCACAGCTGTTTGCCAAGCTGCTc/c	7/7	0.699025884371664	6	FACETS	0.829	0.779	0.879			1	CLONAL	2	TRUE	NA	0.699025884371664	6		621	1213	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052618-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	203	303	0	ENST00000256196.4:c.68G>T	p.Gly23Val	p.G23V	ENST00000256196		23	gGc/gTc	1/6	0.664860025830468	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.664860025830468	1		303	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793881	NA	P-0052618-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	453	497	0	ENST00000269305.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGg/gAg	8/11	0.664860025830468	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.664860025830468	2		497	661	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966760	18966760	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052618-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	248	607	0	ENST00000262803.5:c.1571A>G	p.Asn524Ser	p.N524S	ENST00000262803	NM_002911.3	524	aAc/aGc	12/24	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.664860025830468	2		607	720	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539055	187539055	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052618-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	187	358	0	ENST00000441802.2:c.8685G>C	p.Lys2895Asn	p.K2895N	ENST00000441802	NM_005245.3	2895	aaG/aaC	10/27	0.244131795907635	3	FACETS	1	0.99	1	0.715	0.666	0.766	INDETERMINATE	1	TRUE	1	0.664860025830468	3		358	524	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0052760-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	17	573	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.34	0.252	0.445	0.34	0.252	0.445	SUBCLONAL	1	TRUE	1	0.17	2		573	588	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0052760-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	51	315	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	0.926	0.786	1	0.926	0.786	1	CLONAL	1	TRUE	1	0.17	2		315	648	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971151	21971152	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGGA	novel	NA	P-0052760-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	25	496	0	ENST00000304494.5:c.206_207insTCCG	p.Glu69AspfsTer52	p.E69Dfs*52	ENST00000304494	NM_000077.4	69	gag/gaTCCGg	2/3	1	2	FACETS	0.661	0.52	0.824	0.661	0.52	0.824	SUBCLONAL	1	TRUE	1	0.17	2		496	445	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0052819-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	98	511	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.226705126818679	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.233963205133486	1		511	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577505	7577505	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs745425759	NA	P-0052819-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	145	665	0	ENST00000269305.4:c.776A>T	p.Asp259Val	p.D259V	ENST00000269305	NM_001126112.2	259	gAc/gTc	7/11	0.226705126818679	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.233963205133486	1		665	868	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981498	70981498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052819-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	190	1039	1	ENST00000276594.2:c.598G>A	p.Glu200Lys	p.E200K	ENST00000276594	NM_024504.3	200	Gag/Aag	2/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.233963205133486	2		1040	1286	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189388	99189388	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052819-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	69	598	0	ENST00000074304.5:c.2644G>C	p.Glu882Gln	p.E882Q	ENST00000074304	NM_001134224.1	882	Gag/Cag	24/26	1	2	FACETS	0.736	0.64	0.841	0.736	0.64	0.841	SUBCLONAL	1	TRUE	1	0.233963205133486	2		598	801	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161323	185161323	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052819-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	96	584	0	ENST00000265026.3:c.750G>T	p.Lys250Asn	p.K250N	ENST00000265026	NM_004721.4	250	aaG/aaT	4/14	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.233963205133486	2		584	805	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747876	41747876	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052819-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	91	332	0	ENST00000226382.2:c.893T>C	p.Leu298Pro	p.L298P	ENST00000226382	NM_003924.3	298	cTc/cCc	3/3	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.233963205133486	2		332	631	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046504	69046504	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052819-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	93	532	0	ENST00000288368.4:c.3977C>A	p.Pro1326Gln	p.P1326Q	ENST00000288368	NM_024870.2	1326	cCa/cAa	32/40	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.233963205133486	2		532	661	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815662	139815663	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0052819-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	98	619	1	ENST00000247668.2:c.1133_1134delinsTT	p.Ser378Phe	p.S378F	ENST00000247668	NM_021138.3	378	tCC/tTT	9/11	NA	2	FACETS	1	0.96	1			1	INDETERMINATE	1	TRUE	NA	0.233963205133486	2		620	723	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0053170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	37	394	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	0.126648922588156	3	FACETS	1	0.892	1	0.372	0.306	0.444	CLONAL	1	TRUE	0	0.18	3		394	402	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164863	36164863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	67	983	1	ENST00000300305.3:c.1012G>A	p.Ala338Thr	p.A338T	ENST00000300305		338	Gcg/Acg	8/8	1	2	FACETS	0.752	0.651	0.861	0.752	0.651	0.861	SUBCLONAL	1	TRUE	1	0.18	2		984	990	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40451798	40451798	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1314655783	NA	P-0053170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	89	976	0	ENST00000345506.4:c.580C>A	p.Pro194Thr	p.P194T	ENST00000345506	NM_003152.3	194	Ccc/Acc	7/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.18	2		976	782	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058685	47058686	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCCA	novel	NA	P-0053170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	44	531	0	ENST00000409792.3:c.7589_7592dup	p.Glu2531AspfsTer5	p.E2531Dfs*5	ENST00000409792	NM_014159.6	2531	gag/gaTGGAg	21/21	1	2	FACETS	0.931	0.781	1	0.931	0.781	1	CLONAL	1	TRUE	1	0.18	2		531	525	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0053279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	112	310	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.614010737478213	3	FACETS	1	0.954	1	0.543	0.492	0.596	CLONAL	1	TRUE	1	0.680908049176431	3		310	406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0053279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	593	680	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.672628180024805	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.680908049176431	3		680	752	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40789994	40789994	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs746391800	NA	P-0053279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	80	663	0	ENST00000373198.4:c.2737G>A	p.Glu913Lys	p.E913K	ENST00000373198	NM_133170.3	913	Gag/Aag	18/32	0.467286895171922	3	FACETS	0.418	0.367	0.472	0.209	0.183	0.236	SUBCLONAL	1	TRUE	1	0.680908049176431	3		663	754	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426859	49426859	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	282	679	0	ENST00000301067.7:c.11629C>T	p.Gln3877Ter	p.Q3877*	ENST00000301067	NM_003482.3	3877	Cag/Tag	39/54	0.407259794576426	3	FACETS	0.816	0.772	0.861	0.816	0.772	0.861	INDETERMINATE	2	TRUE	1	0.680908049176431	3		679	680	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464433	120464433	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0053279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	112	402	0	ENST00000256646.2:c.5214-1G>C		p.X1738_splice	ENST00000256646	NM_024408.3	1738			0.516700823362984	3	FACETS	1	0.951	1	0.538	0.487	0.59	CLONAL	1	TRUE	1	0.680908049176431	3		402	410	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518487	69518487	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	157	399	0	ENST00000294312.3:c.158A>T	p.His53Leu	p.H53L	ENST00000294312	NM_005117.2	53	cAc/cTc	1/3	0.680908049176431	6	FACETS	0.962	0.88	1	0.241	0.22	0.263	CLONAL	1	TRUE	2	0.680908049176431	6		399	1132	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628255	90628255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	80	1122	0	ENST00000330062.3:c.1156G>T	p.Asp386Tyr	p.D386Y	ENST00000330062	NM_002168.2	386	Gat/Tat	9/11	0.467286895171922	3	FACETS	0.302	0.265	0.342	0.151	0.132	0.171	SUBCLONAL	1	TRUE	1	0.680908049176431	3		1122	1043	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100593	67100593	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	180	491	0	ENST00000412916.2:c.291G>C	p.Leu97Phe	p.L97F	ENST00000412916		97	ttG/ttC	4/6	0.279112304258345	4	FACETS	0.82	0.761	0.88	0.82	0.761	0.88	INDETERMINATE	2	TRUE	2	0.680908049176431	4		491	542	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100641	67100641	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	220	661	1	ENST00000412916.2:c.339G>A	p.Trp113Ter	p.W113*	ENST00000412916		113	tgG/tgA	4/6	0.279112304258345	4	FACETS	1	0.992	1	0.747	0.698	0.798	INDETERMINATE	1	TRUE	2	0.680908049176431	4		662	727	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322767	30322767	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	70	315	0	ENST00000322652.5:c.1780G>C	p.Glu594Gln	p.E594Q	ENST00000322652	NM_015355.2	594	Gaa/Caa	14/16	0.467286895171922	3	FACETS	0.913	0.803	1	0.456	0.401	0.515	CLONAL	1	TRUE	1	0.680908049176431	3		315	302	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144125	11144125	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	316	985	0	ENST00000358026.2:c.3706C>T	p.Gln1236Ter	p.Q1236*	ENST00000358026	NM_001128849.1	1236	Cag/Tag	26/36	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.680908049176431	2		985	792	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630400	47630400	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779976	NA	P-0053279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	364	1046	0	ENST00000233146.2:c.70C>T	p.Gln24Ter	p.Q24*	ENST00000233146	NM_000251.2	24	Cag/Tag	1/16	0.339815853999605	3	FACETS	0.881	0.841	0.922	0.881	0.841	0.922	INDETERMINATE	2	TRUE	1	0.680908049176431	3		1046	813	SUCCESS
APC	324	MSKCC	GRCh37	5	112102057	112102057	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	105	235	0	ENST00000257430.4:c.170A>G	p.Asp57Gly	p.D57G	ENST00000257430	NM_000038.5	57	gAt/gGt	3/16	0.448571980671433	2	FACETS	1	0.986	1	0.741	0.681	0.802	CLONAL	1	TRUE	0	0.680908049176431	2		235	208	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553054	106553054	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	46	925	0	ENST00000369096.4:c.1019G>C	p.Arg340Thr	p.R340T	ENST00000369096	NM_001198.3	340	aGa/aCa	5/7	0.467286895171922	3	FACETS	0.226	0.189	0.266	0.113	0.094	0.133	SUBCLONAL	1	TRUE	1	0.680908049176431	3		925	802	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696689	47696689	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519972	NA	P-0053644-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	18	317	0	ENST00000347630.2:c.259T>A	p.Tyr87Asn	p.Y87N	ENST00000347630	NM_001007230.1	87	Tac/Aac	5/11	1	2	FACETS	0.639	0.481	0.825	0.639	0.481	0.825	SUBCLONAL	1	TRUE	1	0.211818303707921	2		317	266	SUCCESS
APC	324	MSKCC	GRCh37	5	112175799	112175799	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053644-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	16	131	0	ENST00000257430.4:c.4508C>A	p.Ser1503Ter	p.S1503*	ENST00000257430	NM_000038.5	1503	tCa/tAa	16/16	0.211818303707921	1	FACETS	0.986	0.735	1	0.986	0.735	1	CLONAL	1	TRUE	0	0.211818303707921	1		131	137	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427951	49427951	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053644-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	28	488	2	ENST00000301067.7:c.10639C>T	p.Arg3547Cys	p.R3547C	ENST00000301067	NM_003482.3	3547	Cgc/Tgc	38/54	1	2	FACETS	0.577	0.461	0.711	0.577	0.461	0.711	SUBCLONAL	1	TRUE	1	0.211818303707921	2		490	458	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061114	38061190	+	protein_altering_variant	In_Frame_Del	DEL	TCAGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTT	TCAGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTT	GCGGG	novel	NA	P-0053644-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	38	334	2	ENST00000250448.2:c.799_875delinsCCCGC	p.Lys267_Glu292delinsProAla	p.K267_E292delinsPA	ENST00000250448	NM_004496.3	267	AAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGGCGCCAAGGGCGGCCCTGAg/CCCGCg	2/2	1	2	FACETS	0.983	0.814	1	0.983	0.814	1	CLONAL	1	TRUE	1	0.211818303707921	2		336	365	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054137-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	22	383	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.94	0.729	1	0.94	0.729	1	CLONAL	1	TRUE	1	0.15	2		383	312	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098892	47098892	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054137-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	42	820	0	ENST00000409792.3:c.6382G>T	p.Glu2128Ter	p.E2128*	ENST00000409792	NM_014159.6	2128	Gag/Tag	15/21	1	2	FACETS	0.81	0.675	0.961	0.81	0.675	0.961	CLONAL	1	TRUE	1	0.15	2		820	691	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045527	47045527	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054137-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	36	932	1	ENST00000377604.3:c.2494G>T	p.Glu832Ter	p.E832*	ENST00000377604	NM_001204468.1	832	Gag/Tag	22/24	0.136034261910105	0	FACETS	0.925	0.761	1			1	CLONAL	1	TRUE	0	0.15	0		933	441	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323146	31323146	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054137-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	45	996	0	ENST00000412585.2:c.843C>A	p.Tyr281Ter	p.Y281*	ENST00000412585	NM_005514.6	281	taC/taA	4/8	0.192687038776777	3	FACETS	0.928	0.778	1	0.464	0.389	0.547	CLONAL	1	TRUE	1	0.15	3		996	695	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240816	53240816	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054137-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	20	701	0	ENST00000375401.3:c.1264G>T	p.Glu422Ter	p.E422*	ENST00000375401	NM_004187.3	422	Gag/Tag	10/26	0.136034261910105	0	FACETS	0.571	0.436	0.73			1	SUBCLONAL	1	TRUE	0	0.15	0		701	397	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442676	442676	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs759749431	NA	P-0054137-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	32	677	0	ENST00000399788.2:c.1630G>T	p.Val544Leu	p.V544L	ENST00000399788	NM_001042603.1	544	Gtg/Ttg	12/28	0.3	2	FACETS	0.853	0.692	1			1	CLONAL	1	TRUE	NA	0.15	2		677	500	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127310	17127310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749368513	NA	P-0054137-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	36	843	0	ENST00000285071.4:c.544C>T	p.Leu182Phe	p.L182F	ENST00000285071	NM_144997.5	182	Ctc/Ttc	6/14	1	2	FACETS	0.986	0.81	1	0.986	0.81	1	CLONAL	1	TRUE	1	0.15	2		843	487	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125238	47125249	+	inframe_deletion	In_Frame_Del	DEL	TTGGTGGCCAAA	TTGGTGGCCAAA	-	novel	NA	P-0054137-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	21	556	0	ENST00000409792.3:c.6021_6032del	p.Asp2007_Lys2011delinsGlu	p.D2007_K2011delinsE	ENST00000409792	NM_014159.6	2007	gaTTTGGCCACCAAa/gaa	12/21	1	2	FACETS	0.676	0.52	0.86	0.676	0.52	0.86	SUBCLONAL	1	TRUE	1	0.15	2		556	414	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066534	94066534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1402331883	NA	P-0054137-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	27	462	0	ENST00000369303.4:c.1225G>T	p.Ala409Ser	p.A409S	ENST00000369303	NM_004440.3	409	Gct/Tct	5/17	1	2	FACETS	1	0.817	1	1	0.817	1	CLONAL	1	TRUE	1	0.15	2		462	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578476	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTGCCGGGCGG	GGGTGCCGGGCGG	-	rs876659215	NA	P-0054139-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	1054	761	1	ENST00000269305.4:c.454_466del	p.Pro152AlafsTer14	p.P152Afs*14	ENST00000269305	NM_001126112.2	152	CCGCCCGGCACCCgc/gc	5/11	0.931281661416966	3	FACETS	0.953	0.942	0.964	0.953	0.942	0.964	CLONAL	3	TRUE	0	0.931281661416966	3		762	1160	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458315	120458315	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054139-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	526	574	0	ENST00000256646.2:c.7030G>T	p.Glu2344Ter	p.E2344*	ENST00000256646	NM_024408.3	2344	Gaa/Taa	34/34	0.400025767315789	6	FACETS	0.941	0.905	0.977	0.941	0.905	0.977	INDETERMINATE	3	TRUE	3	0.931281661416966	6		574	1146	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217811	7217812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054139-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	611	584	0	ENST00000380728.2:c.199_200insT	p.Glu67ValfsTer30	p.E67Vfs*30	ENST00000380728		67	gaa/gTaa	3/11	0.931281661416966	3	FACETS	0.941	0.912	0.97	0.627	0.608	0.647	CLONAL	2	TRUE	0	0.931281661416966	3		584	1022	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933056	39933056	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054139-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	343	719	1	ENST00000378444.4:c.1543A>T	p.Ser515Cys	p.S515C	ENST00000378444	NM_001123385.1	515	Agt/Tgt	4/15	NA	2	FACETS	1	0.962	1			1	INDETERMINATE	1	TRUE	NA	0.931281661416966	2		720	729	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0054161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	102	306	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		306	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0054426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	261	584	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.628794335513363	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.644350809480956	1		584	540	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0054426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	196	390	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.644350809480956	2	FACETS	0.9	0.85	0.949	0.9	0.85	0.949	CLONAL	2	TRUE	0	0.644350809480956	2		390	338	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912186	114912186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	122	518	1	ENST00000543371.1:c.1256C>T	p.Ala419Val	p.A419V	ENST00000543371	NM_001198531.1	419	gCg/gTg	11/14	0.316072543610033	1	FACETS	0.384	0.348	0.423	0.384	0.348	0.423	INDETERMINATE	1	TRUE	0	0.644350809480956	1		519	668	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265989	41266510	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACAT	TAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACAT	-	novel	NA	P-0054426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	83	135	0	ENST00000349496.5:c.14-26_309del		p.X5_splice	ENST00000349496	NM_001904.3	5		3-4/15	0.628794335513363	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.644350809480956	1		135	139	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277955	41277955	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	143	322	0	ENST00000349496.5:c.1919T>C	p.Leu640Pro	p.L640P	ENST00000349496	NM_001904.3	640	cTg/cCg	12/15	0.628794335513363	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.644350809480956	1		322	293	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251883	153251883	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0054426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	126	337	0	ENST00000281708.4:c.1122+1G>T		p.X374_splice	ENST00000281708	NM_033632.3	374			0.628794335513363	1	FACETS	0.94	0.867	1	0.94	0.867	1	CLONAL	1	TRUE	0	0.644350809480956	1		337	282	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683156	88683156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	149	417	0	ENST00000372037.3:c.1366C>T	p.Pro456Ser	p.P456S	ENST00000372037	NM_004329.2	456	Cca/Tca	12/13	0.316072543610033	1	FACETS	0.766	0.708	0.827	0.766	0.708	0.827	INDETERMINATE	1	TRUE	0	0.644350809480956	1		417	409	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656849	45656849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199766847	NA	P-0054430-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	138	596	1	ENST00000407780.3:c.307G>A	p.Val103Ile	p.V103I	ENST00000407780	NM_001283052.1	103	Gtc/Atc	3/7	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.24	2		597	1012	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344973	70344973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756039521	NA	P-0054430-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	108	649	0	ENST00000374080.3:c.2203G>A	p.Ala735Thr	p.A735T	ENST00000374080		735	Gcc/Acc	15/45	1	2	FACETS	0.905	0.81	1	0.905	0.81	1	CLONAL	1	TRUE	1	0.24	2		649	995	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996161	73996161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1223303121	NA	P-0054430-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1303	151	1004	0	ENST00000318443.5:c.895G>A	p.Glu299Lys	p.E299K	ENST00000318443	NM_001024736.1	299	Gaa/Aaa	5/10	1	2	FACETS	0.865	0.789	0.947	0.865	0.789	0.947	CLONAL	1	TRUE	1	0.24	2		1004	1454	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458503	120458503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054430-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	116	591	2	ENST00000256646.2:c.6842G>A	p.Gly2281Asp	p.G2281D	ENST00000256646	NM_024408.3	2281	gGc/gAc	34/34	1	2	FACETS	0.978	0.88	1	0.978	0.88	1	CLONAL	1	TRUE	1	0.24	2		593	988	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938641	76938641	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054430-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	53	545	0	ENST00000373344.5:c.2107T>A	p.Ser703Thr	p.S703T	ENST00000373344	NM_000489.3	703	Tct/Act	9/35	1	2	FACETS	0.648	0.551	0.753	0.648	0.551	0.753	SUBCLONAL	1	TRUE	1	0.24	2		545	682	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509421	149509421	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054716-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	242	789	3	ENST00000261799.4:c.1478G>T	p.Ser493Ile	p.S493I	ENST00000261799	NM_002609.3	493	aGc/aTc	10/23	1	2	FACETS	0.615	0.574	0.657	0.615	0.574	0.657	SUBCLONAL	1	TRUE	1	0.717872428759126	2		792	1096	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033778	48033791	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TACGATTATTTCGG	TACGATTATTTCGG	-	novel	NA	P-0054716-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	111	160	0	ENST00000234420.5:c.3991_4001+3del		p.X1331_splice	ENST00000234420	NM_000179.2	1331		9/10	1	2	FACETS	0.931	0.847	1	0.931	0.847	1	CLONAL	1	TRUE	1	0.717872428759126	2		160	332	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161778	47161778	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs898862144	NA	P-0054716-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	30	301	0	ENST00000409792.3:c.4348G>A	p.Val1450Ile	p.V1450I	ENST00000409792	NM_014159.6	1450	Gtc/Atc	3/21	1	2	FACETS	0.153	0.123	0.188	0.153	0.123	0.188	SUBCLONAL	1	TRUE	1	0.717872428759126	2		301	545	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955534	90955534	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780333168	NA	P-0054716-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	217	326	0	ENST00000265433.3:c.2131C>T	p.His711Tyr	p.H711Y	ENST00000265433	NM_002485.4	711	Cat/Tat	14/16	0.717872428759126	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.717872428759126	1		326	377	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937091	48937091	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054801-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	178	156	0	ENST00000267163.4:c.859G>T	p.Glu287Ter	p.E287*	ENST00000267163	NM_000321.2	287	Gag/Tag	8/27	0.815237617700038	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	0	0.815237617700038	3		156	201	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176662926	176662926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054801-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	160	238	1	ENST00000439151.2:c.3901G>A	p.Val1301Ile	p.V1301I	ENST00000439151	NM_022455.4	1301	Gta/Ata	6/23	0.656394197893942	5	FACETS	0.938	0.877	0.999	0.938	0.877	0.999	CLONAL	3	TRUE	2	0.815237617700038	5		239	310	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0054856-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	357	427	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.936357432749804	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.936357432749804	1		429	399	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236087	108236087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781894	NA	P-0054856-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	374	610	0	ENST00000278616.4:c.9023G>A	p.Arg3008His	p.R3008H	ENST00000278616	NM_000051.3	3008	cGt/cAt	63/63	0.936357432749804	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.936357432749804	1		610	412	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436149	56436149	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054856-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	1343	772	1	ENST00000407977.2:c.988C>T	p.Arg330Ter	p.R330*	ENST00000407977		330	Cga/Tga	9/10	0.936357432749804	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.936357432749804	3		773	1396	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513202	149513202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374864774	NA	P-0054856-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	529	947	3	ENST00000261799.4:c.881C>T	p.Thr294Met	p.T294M	ENST00000261799	NM_002609.3	294	aCg/aTg	6/23	0.50001543783558	1	FACETS	0.681	0.659	0.704	0.681	0.659	0.704	INDETERMINATE	1	TRUE	0	0.936357432749804	1		950	882	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519996	NA	P-0054856-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	724	986	0	ENST00000269305.4:c.395A>C	p.Lys132Thr	p.K132T	ENST00000269305	NM_001126112.2	132	aAg/aCg	5/11	0.936357432749804	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.936357432749804	1		986	805	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390914	89390914	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054856-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	219	345	0	ENST00000336596.2:c.980C>G	p.Ser327Cys	p.S327C	ENST00000336596	NM_005233.5	327	tCt/tGt	5/17	0.179237820792105	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.936357432749804	0		345	476	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40857139	40857139	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054856-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	508	493	0	ENST00000428826.2:c.1902G>T	p.Gln634His	p.Q634H	ENST00000428826		634	caG/caT	17/21	0.936357432749804	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.936357432749804	2		493	542	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180076529	180076529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054856-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	19	72	2	ENST00000261937.6:c.17C>T	p.Ala6Val	p.A6V	ENST00000261937	NM_182925.4	6	gCg/gTg	1/30	0.44250234557214	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.936357432749804	0		74	51	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380279	25380279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054869-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	187	641	0	ENST00000311936.3:c.179G>A	p.Gly60Asp	p.G60D	ENST00000311936	NM_004985.3	60	gGt/gAt	3/5	0.0865518966176126	3	FACETS	0.925	0.856	0.996	1	0.989	1	INDETERMINATE	3	TRUE	1	0.19	3		641	777	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192026	108192026	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs539978799	NA	P-0054869-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	54	447	1	ENST00000278616.4:c.6453-2A>G		p.X2151_splice	ENST00000278616	NM_000051.3	2151			1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.19	2		448	529	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984340	201984340	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0054869-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	64	871	0	ENST00000359651.3:c.1005C>G	p.Tyr335Ter	p.Y335*	ENST00000359651		335	taC/taG	8/8	1	2	FACETS	0.866	0.749	0.994	0.866	0.749	0.994	CLONAL	1	TRUE	1	0.19	2		871	778	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202225	108202225	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs769142993	NA	P-0054869-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	38	484	0	ENST00000278616.4:c.7570G>C	p.Ala2524Pro	p.A2524P	ENST00000278616	NM_000051.3	2524	Gct/Cct	51/63	1	2	FACETS	0.862	0.713	1	0.862	0.713	1	CLONAL	1	TRUE	1	0.19	2		484	464	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0055018-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	20	309	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.792	0.608	1	0.792	0.608	1	CLONAL	1	TRUE	1	0.233824165254151	2		310	216	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624296	89624296	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786201995	NA	P-0055018-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	54	439	0	ENST00000371953.3:c.70G>T	p.Asp24Tyr	p.D24Y	ENST00000371953	NM_000314.4	24	Gac/Tac	1/9	0.233824165254151	1	FACETS	0.822	0.703	0.953	0.822	0.703	0.953	CLONAL	1	TRUE	0	0.233824165254151	1		439	496	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248535	10248540	+	inframe_deletion	In_Frame_Del	DEL	CTGGTA	CTGGTA	-	novel	NA	P-0055018-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	97	744	0	ENST00000340748.4:c.4213_4218del	p.Tyr1405_Gln1406del	p.Y1405_Q1406del	ENST00000340748		1405	TACCAG/-	35/40	1	2	FACETS	0.903	0.804	1	0.903	0.804	1	CLONAL	1	TRUE	1	0.233824165254151	2		744	919	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845271	151845271	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055018-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	69	504	0	ENST00000262189.6:c.13741del	p.Glu4581LysfsTer45	p.E4581Kfs*45	ENST00000262189	NM_170606.2	4581	Gaa/aa	52/59	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.233824165254151	2		504	557	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89354973	89354973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778367008	NA	P-0055023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	353	701	0	ENST00000301030.4:c.707C>T	p.Thr236Met	p.T236M	ENST00000301030	NM_001256183.1	236	aCg/aTg	7/13	0.855665510827226	3	FACETS	0.987	0.935	1	0.493	0.467	0.52	CLONAL	1	TRUE	1	0.855665510827226	3		701	1194	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	304	509	3	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	0.722775321470772	4	FACETS	1	0.994	1	0.744	0.702	0.787	CLONAL	1	TRUE	2	0.722775321470772	4		512	974	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	228	464	0	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	0.722775321470772	3	FACETS	0.902	0.851	0.954	0.902	0.851	0.954	CLONAL	2	TRUE	1	0.722775321470772	3		464	476	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	395	406	2	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	0.315910013920197	6	FACETS	1	0.988	1	1	0.996	1	INDETERMINATE	4	TRUE	3	0.722775321470772	6		408	630	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212456	5212456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1191088838	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	577	832	1	ENST00000357368.4:c.4661C>T	p.Ala1554Val	p.A1554V	ENST00000357368	NM_002850.3	1554	gCg/gTg	31/38	0.54822910124557	4	FACETS	0.958	0.921	0.995	0.958	0.921	0.995	CLONAL	2	TRUE	2	0.722775321470772	4		833	1436	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797258	135797258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514834	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	84	290	0	ENST00000298552.3:c.611G>A	p.Arg204His	p.R204H	ENST00000298552	NM_001162426.1	204	cGt/cAt	7/23	0.703363819648195	2	FACETS	0.884	0.791	0.98	0.442	0.395	0.49	CLONAL	1	TRUE	0	0.722775321470772	2		290	263	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	289	1014	3	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	0.722775321470772	3	FACETS	0.836	0.785	0.888	0.418	0.392	0.444	CLONAL	1	TRUE	1	0.722775321470772	3		1017	1303	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	192	726	3	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	0.54822910124557	4	FACETS	0.997	0.923	1	0.499	0.461	0.537	CLONAL	1	TRUE	2	0.722775321470772	4		729	918	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056425	26056427	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	rs774779034	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	132	357	0	ENST00000343677.2:c.230_232del	p.Asn77del	p.N77del	ENST00000343677	NM_005319.3	77	aACAgc/agc	1/1	0.722775321470772	3	FACETS	0.866	0.79	0.946	0.433	0.395	0.473	CLONAL	1	TRUE	1	0.722775321470772	3		357	574	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	228	654	6	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	0.722775321470772	3	FACETS	0.982	0.916	1	0.491	0.458	0.525	CLONAL	1	TRUE	1	0.722775321470772	3		660	875	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562345	21562345	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1204055851	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	268	801	0	ENST00000382592.4:c.1574G>A	p.Arg525His	p.R525H	ENST00000382592	NM_014572.2	525	cGc/cAc	4/8	1	2	FACETS	0.952	0.897	1	0.952	0.897	1	CLONAL	1	TRUE	1	0.722775321470772	2		801	779	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101170	41101170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41279256	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	413	783	1	ENST00000373198.4:c.1186G>A	p.Val396Ile	p.V396I	ENST00000373198	NM_133170.3	396	Gta/Ata	8/32	0.39503368872461	4	FACETS	0.906	0.865	0.949			1	INDETERMINATE	2	TRUE	NA	0.722775321470772	4		784	1086	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926270	112926270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918457	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	366	518	3	ENST00000351677.2:c.1403C>T	p.Thr468Met	p.T468M	ENST00000351677	NM_002834.3	468	aCg/aTg	12/16	0.722775321470772	3	FACETS	0.872	0.832	0.911	0.872	0.832	0.911	CLONAL	2	TRUE	1	0.722775321470772	3		521	791	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564680	86564680	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	567	911	0	ENST00000274376.6:c.416del	p.Pro139LeufsTer35	p.P139Lfs*35	ENST00000274376	NM_002890.2	138	Ccc/cc	1/25	0.701455648049633	2	FACETS	0.91	0.883	0.937	0.91	0.883	0.937	CLONAL	2	TRUE	0	0.722775321470772	2		911	862	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459777	149459777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1214590308	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	548	912	0	ENST00000286301.3:c.430C>T	p.Arg144Cys	p.R144C	ENST00000286301	NM_005211.3	144	Cgt/Tgt	4/22	0.54822910124557	4	FACETS	0.899	0.863	0.935	0.899	0.863	0.935	CLONAL	2	TRUE	2	0.722775321470772	4		912	1453	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	199	657	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.701455648049633	2	FACETS	0.94	0.876	1	0.47	0.438	0.503	CLONAL	1	TRUE	0	0.722775321470772	2		660	586	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466004	69466004	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	307	869	1	ENST00000227507.2:c.842T>A	p.Val281Glu	p.V281E	ENST00000227507	NM_053056.2	281	gTg/gAg	5/5	0.703312164804915	3	FACETS	0.936	0.882	0.992	0.468	0.441	0.496	CLONAL	1	TRUE	1	0.722775321470772	3		870	1235	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409060	4409060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781695497	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	423	380	2	ENST00000261254.3:c.755C>T	p.Ala252Val	p.A252V	ENST00000261254	NM_001759.3	252	gCg/gTg	5/5	0.722775321470772	3	FACETS	0.971	0.944	0.997	0.971	0.944	0.997	CLONAL	3	TRUE	0	0.722775321470772	3		382	547	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	364	901	2	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.722775321470772	3	FACETS	0.987	0.935	1	0.494	0.467	0.521	CLONAL	1	TRUE	1	0.722775321470772	3		903	1389	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371824	55371824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	22	34	0	ENST00000297316.4:c.514G>A	p.Gly172Ser	p.G172S	ENST00000297316	NM_022454.3	172	Ggc/Agc	2/2	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.722775321470772	2		34	42	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830109	72830109	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	494	683	0	ENST00000268489.5:c.6472C>T	p.Arg2158Ter	p.R2158*	ENST00000268489	NM_006885.3	2158	Cga/Tga	9/10	0.634721996421983	4	FACETS	0.981	0.941	1	0.981	0.941	1	CLONAL	2	TRUE	2	0.722775321470772	4		683	1200	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152170	11152170	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	217	682	0	ENST00000358026.2:c.4454C>A	p.Pro1485His	p.P1485H	ENST00000358026	NM_001128849.1	1485	cCt/cAt	31/36	0.54822910124557	4	FACETS	0.851	0.79	0.914	0.425	0.395	0.457	CLONAL	1	TRUE	2	0.722775321470772	4		682	1216	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610705	52610706	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	231	379	0	ENST00000394830.3:c.3467_3468del	p.Lys1156SerfsTer24	p.K1156Sfs*24	ENST00000394830	NM_018313.4	1156	aAA/a	23/30	0.701455648049633	2	FACETS	0.954	0.912	0.995	0.954	0.912	0.995	CLONAL	2	TRUE	0	0.722775321470772	2		379	335	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411950	116411950	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	603	840	0	ENST00000397752.3:c.2935C>G	p.His979Asp	p.H979D	ENST00000397752	NM_000245.2	979	Cat/Gat	14/21	0.315910013920197	6	FACETS	0.953	0.918	0.989	0.953	0.918	0.989	INDETERMINATE	3	TRUE	3	0.722775321470772	6		840	1427	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16235926	16235926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	180	455	0	ENST00000375759.3:c.992C>T	p.Pro331Leu	p.P331L	ENST00000375759	NM_015001.2	331	cCc/cTc	4/15	0.701455648049633	2	FACETS	0.984	0.915	1	0.492	0.457	0.528	CLONAL	1	TRUE	0	0.722775321470772	2		455	506	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248484	59248484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs76768281	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	252	695	0	ENST00000371222.2:c.259C>T	p.His87Tyr	p.H87Y	ENST00000371222	NM_002228.3	87	Cac/Tac	1/1	0.701455648049633	2	FACETS	0.886	0.832	0.941	0.443	0.416	0.471	CLONAL	1	TRUE	0	0.722775321470772	2		695	787	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612840	228612840	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	285	838	0	ENST00000366696.1:c.187A>G	p.Ile63Val	p.I63V	ENST00000366696	NM_003493.2	63	Atc/Gtc	1/1	0.634721996421983	4	FACETS	0.985	0.924	1	0.492	0.462	0.524	CLONAL	1	TRUE	2	0.722775321470772	4		838	1380	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435229	110435229	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1443489792	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	128	358	0	ENST00000375856.3:c.3172G>A	p.Ala1058Thr	p.A1058T	ENST00000375856	NM_003749.2	1058	Gcc/Acc	1/2	1	2	FACETS	0.915	0.838	0.995	0.915	0.838	0.995	CLONAL	1	TRUE	1	0.722775321470772	2		358	387	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72834005	72834005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	177	477	1	ENST00000268489.5:c.3888G>A	p.Met1296Ile	p.M1296I	ENST00000268489	NM_006885.3	1296	atG/atA	8/10	0.634721996421983	4	FACETS	0.936	0.863	1	0.468	0.431	0.507	CLONAL	1	TRUE	2	0.722775321470772	4		478	901	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991890	72991890	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	489	733	0	ENST00000268489.5:c.2155T>C	p.Tyr719His	p.Y719H	ENST00000268489	NM_006885.3	719	Tac/Cac	2/10	0.634721996421983	4	FACETS	0.966	0.926	1	0.966	0.926	1	CLONAL	2	TRUE	2	0.722775321470772	4		733	1206	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218410	36218410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	577	762	1	ENST00000222270.7:c.4189G>A	p.Ala1397Thr	p.A1397T	ENST00000222270	NM_014727.1	1397	Gcg/Acg	16/37	0.54822910124557	4	FACETS	0.967	0.93	1	0.967	0.93	1	CLONAL	2	TRUE	2	0.722775321470772	4		763	1422	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557818	187557818	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	168	466	0	ENST00000441802.2:c.3893G>C	p.Gly1298Ala	p.G1298A	ENST00000441802	NM_005245.3	1298	gGc/gCc	5/27	0.701455648049633	2	FACETS	0.897	0.831	0.966	0.449	0.415	0.483	CLONAL	1	TRUE	0	0.722775321470772	2		466	518	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524254	148524254	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	96	328	0	ENST00000320356.2:c.728+2T>C		p.X243_splice	ENST00000320356	NM_004456.4	243			0.315910013920197	6	FACETS	1	0.977	1	0.449	0.402	0.499	INDETERMINATE	1	TRUE	3	0.722775321470772	6		328	482	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372197	55372197	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	88	257	0	ENST00000297316.4:c.887A>T	p.Tyr296Phe	p.Y296F	ENST00000297316	NM_022454.3	296	tAc/tTc	2/2	1	2	FACETS	0.892	0.801	0.986	0.892	0.801	0.986	CLONAL	1	TRUE	1	0.722775321470772	2		257	273	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753800	133753800	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	387	572	0	ENST00000318560.5:c.1271-2A>G		p.X424_splice	ENST00000318560	NM_005157.4	424			0.703363819648195	2	FACETS	0.963	0.93	0.995	0.963	0.93	0.995	CLONAL	2	TRUE	0	0.722775321470772	2		572	556	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972697	76972697	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	143	206	0	ENST00000373344.5:c.44T>C	p.Val15Ala	p.V15A	ENST00000373344	NM_000489.3	15	gTg/gCg	2/35	0.650559611445467	2	FACETS	0.972	0.896	1			1	CLONAL	1	TRUE	NA	0.722775321470772	2		206	407	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955525	48955525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	24	341	0	ENST00000267163.4:c.1644del	p.Lys548AsnfsTer3	p.K548Nfs*3	ENST00000267163	NM_000321.2	547	atA/at	17/27	1	2	FACETS	0.221	0.173	0.276	0.221	0.173	0.276	SUBCLONAL	1	TRUE	1	0.722775321470772	2		341	301	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224229	98224229	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055024-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	24	384	0	ENST00000331920.6:c.2612A>G	p.Asn871Ser	p.N871S	ENST00000331920	NM_000264.3	871	aAc/aGc	16/24	0.703363819648195	2	FACETS	0.164	0.128	0.206	0.082	0.064	0.103	SUBCLONAL	1	TRUE	0	0.722775321470772	2		384	404	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955550	48955550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913304	NA	P-0055029-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	90	237	1	ENST00000267163.4:c.1666C>T	p.Arg556Ter	p.R556*	ENST00000267163	NM_000321.2	556	Cga/Tga	17/27	1	2	FACETS	0.998	0.906	1	0.998	0.906	1	CLONAL	1	TRUE	1	0.888103961417307	2		238	203	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937006	48937018	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGAGTGCACGG	CAGGAGTGCACGG	-	novel	NA	P-0055029-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	86	306	0	ENST00000267163.4:c.774_786del	p.Asn258LysfsTer2	p.N258Kfs*2	ENST00000267163	NM_000321.2	258	aaCAGGAGTGCACGG/aa	8/27	1	2	FACETS	0.687	0.615	0.761	0.687	0.615	0.761	SUBCLONAL	1	TRUE	1	0.888103961417307	2		306	282	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479292	50479293	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCTGT	novel	NA	P-0055029-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	105	691	0	ENST00000394963.4:c.141_145dup	p.Tyr49CysfsTer23	p.Y49Cfs*23	ENST00000394963	NM_003076.4	47	ggg/ggGCTGTg	1/13	1	2	FACETS	0.357	0.32	0.396	0.357	0.32	0.396	SUBCLONAL	1	TRUE	1	0.888103961417307	2		691	663	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0055110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	58	907	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.363231305946313	2	FACETS	0.751	0.655	0.853	0.751	0.655	0.853	SUBCLONAL	2	TRUE	0	0.37651297738301	2		907	205	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624275	89624275	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204910	NA	P-0055110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	13	401	2	ENST00000371953.3:c.49C>T	p.Gln17Ter	p.Q17*	ENST00000371953	NM_000314.4	17	Caa/Taa	1/9	0.37651297738301	0	FACETS	0.414	0.298	0.552			1	SUBCLONAL	1	TRUE	0	0.37651297738301	0		403	104	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099103	27099103	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	62	525	0	ENST00000324856.7:c.3524del	p.Pro1175HisfsTer5	p.P1175Hfs*5	ENST00000324856	NM_006015.4	1173	atC/at	13/20	0.160525274974047	2	FACETS	1	0.971	1	0.719	0.629	0.814	INDETERMINATE	1	TRUE	0	0.37651297738301	2		525	229	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793406	18793406	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	22	430	0	ENST00000266497.5:c.4103A>T	p.Tyr1368Phe	p.Y1368F	ENST00000266497		1368	tAt/tTt	30/31	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.37651297738301	2		430	78	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133814	55133814	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	22	473	0	ENST00000257290.5:c.1027C>A	p.Pro343Thr	p.P343T	ENST00000257290	NM_006206.4	343	Cca/Aca	7/23	0.209776533133858	2	FACETS	0.721	0.564	0.901	0.361	0.282	0.451	INDETERMINATE	1	TRUE	0	0.37651297738301	2		473	162	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971201	21971214	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCATGACCTGCCAG	TCATGACCTGCCAG	-	novel	NA	P-0055110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	28	428	0	ENST00000304494.5:c.151-7_157del		p.X51_splice	ENST00000304494	NM_000077.4	51		2/3	0.37651297738301	1	FACETS	0.85	0.689	1	0.85	0.689	1	CLONAL	1	TRUE	0	0.37651297738301	1		428	142	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0055245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	164	251	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	0.928839559176565	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.928839559176565	1		251	188	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579533	7579533	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	758	992	0	ENST00000269305.4:c.154C>T	p.Gln52Ter	p.Q52*	ENST00000269305	NM_001126112.2	52	Caa/Taa	4/11	0.928839559176565	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.928839559176565	2		992	805	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740620	145740620	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	273	1035	0	ENST00000428558.2:c.1397C>G	p.Pro466Arg	p.P466R	ENST00000428558	NM_004260.3	466	cCg/cGg	8/22	NA	2	FACETS	0.486	0.456	0.518			1	INDETERMINATE	1	TRUE	NA	0.928839559176565	2		1035	1209	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478194	99478195	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAC	novel	NA	P-0055245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	446	525	1	ENST00000268035.6:c.3100_3102dup	p.Thr1034dup	p.T1034dup	ENST00000268035	NM_000875.3	1034	aaa/aaAACa	16/21	0.928839559176565	2	FACETS	0.943	0.924	0.962	0.943	0.924	0.962	CLONAL	2	TRUE	0	0.928839559176565	2		526	509	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408865	41408865	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	131	559	0	ENST00000373198.4:c.561T>G	p.His187Gln	p.H187Q	ENST00000373198	NM_133170.3	187	caT/caG	4/32	0.190961808930865	5	FACETS	0.838	0.76	0.919	0.168	0.152	0.184	INDETERMINATE	1	TRUE	0	0.928839559176565	5		559	806	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738805	145738806	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCC	novel	NA	P-0055245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	265	1209	0	ENST00000428558.2:c.2259_2260insGGG	p.Arg753_Arg754insGly	p.R753_R754insG	ENST00000428558	NM_004260.3	753	-/GGG	14/22	NA	2	FACETS	0.412	0.385	0.439			1	INDETERMINATE	1	TRUE	NA	0.928839559176565	2		1209	1386	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0055288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	842	727	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.435098162515084	5	FACETS	0.904	0.88	0.928	1	0.996	1	CLONAL	5	TRUE	1	0.435098162515084	5		727	1415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs967461896	NA	P-0055288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	444	850	0	ENST00000269305.4:c.526T>C	p.Cys176Arg	p.C176R	ENST00000269305	NM_001126112.2	176	Tgc/Cgc	5/11	0.435098162515084	2	FACETS	0.975	0.933	1	0.975	0.933	1	CLONAL	2	TRUE	0	0.435098162515084	2		850	1047	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687400	117687400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146570171	NA	P-0055288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	37	391	0	ENST00000368508.3:c.2651C>T	p.Ser884Phe	p.S884F	ENST00000368508	NM_002944.2	884	tCc/tTc	18/43	0.294629801281264	3	FACETS	0.374	0.308	0.449	0.125	0.102	0.15	SUBCLONAL	1	TRUE	0	0.435098162515084	3		391	553	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941715	48941716	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0055288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	14	279	0	ENST00000267163.4:c.1027_1028del	p.Leu343SerfsTer3	p.L343Sfs*3	ENST00000267163	NM_000321.2	342	aCT/a	10/27	0.435098162515084	1	FACETS	0.188	0.135	0.252	0.188	0.135	0.252	SUBCLONAL	1	TRUE	0	0.435098162515084	1		279	268	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339602	116339602	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	40	413	0	ENST00000397752.3:c.464A>C	p.Gln155Pro	p.Q155P	ENST00000397752	NM_000245.2	155	cAg/cCg	2/21	0.435098162515084	5	FACETS	0.392	0.325	0.468	0.098	0.081	0.117	SUBCLONAL	1	TRUE	1	0.435098162515084	5		413	775	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519980	NA	P-0055302-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	161	487	0	ENST00000269305.4:c.528C>G	p.Cys176Trp	p.C176W	ENST00000269305	NM_001126112.2	176	tgC/tgG	5/11	0.262145799162664	2	FACETS	0.849	0.781	0.921	0.849	0.781	0.921	CLONAL	2	TRUE	0	0.262145799162664	2		487	723	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265535	152265535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571716552	NA	P-0055302-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	151	418	0	ENST00000206249.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000206249	NM_000125.3	330	Gag/Aag	4/8	0.262145799162664	2	FACETS	0.943	0.865	1	0.943	0.865	1	CLONAL	2	TRUE	0	0.262145799162664	2		418	611	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391982	139391982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751048658	NA	P-0055302-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	42	574	0	ENST00000277541.6:c.6209G>A	p.Arg2070Gln	p.R2070Q	ENST00000277541	NM_017617.3	2070	cGg/cAg	34/34	0.262145799162664	2	FACETS	0.409	0.34	0.485	0.204	0.17	0.243	SUBCLONAL	1	TRUE	0	0.262145799162664	2		574	784	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739135	46739135	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1487464723	NA	P-0055302-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	70	429	0	ENST00000371975.4:c.1484C>T	p.Ser495Leu	p.S495L	ENST00000371975	NM_003579.3	495	tCa/tTa	13/18	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.262145799162664	2		429	517	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690810	89690810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055302-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	88	224	1	ENST00000371953.3:c.217G>A	p.Glu73Lys	p.E73K	ENST00000371953	NM_000314.4	73	Gaa/Aaa	4/9	0.262145799162664	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.262145799162664	2		225	295	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732404	74732404	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055302-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	148	378	0	ENST00000359995.5:c.505T>G	p.Ser169Ala	p.S169A	ENST00000359995	NM_001195427.1	169	Tcc/Gcc	2/3	0.262145799162664	2	FACETS	0.873	0.799	0.949	0.873	0.799	0.949	CLONAL	2	TRUE	0	0.262145799162664	2		378	647	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030213	180030213	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055302-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	87	465	0	ENST00000261937.6:c.4071C>G	p.Phe1357Leu	p.F1357L	ENST00000261937	NM_182925.4	1357	ttC/ttG	30/30	0.262145799162664	2	FACETS	1	0.942	1	0.549	0.487	0.616	CLONAL	1	TRUE	0	0.262145799162664	2		465	604	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38153313	38153313	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0055302-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	43	326	0	ENST00000317025.8:c.2915+1G>T		p.X972_splice	ENST00000317025	NM_023034.1	972			0.238123208398193	4	FACETS	0.799	0.669	0.944	0.4	0.334	0.472	CLONAL	1	TRUE	2	0.262145799162664	4		326	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0055305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	393	920	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.271315178539191	6	FACETS	0.931	0.888	0.974			1	CLONAL	5	TRUE	NA	0.271315178539191	6		920	960	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286205	66286205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777851171	NA	P-0055305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	21	372	0	ENST00000273854.3:c.1481G>A	p.Arg494His	p.R494H	ENST00000273854	NM_004439.5	494	cGt/cAt	6/18	0.183874736752726	3	FACETS	0.465	0.357	0.591	0.233	0.178	0.296	SUBCLONAL	1	TRUE	1	0.271315178539191	3		372	378	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220433	1220433	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	151	965	0	ENST00000326873.7:c.526G>T	p.Asp176Tyr	p.D176Y	ENST00000326873	NM_000455.4	176	Gac/Tac	4/10	0.189824694150662	2	FACETS	1	0.986	1	0.713	0.652	0.776	CLONAL	1	TRUE	0	0.271315178539191	2		965	781	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143964	11143964	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0055305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	94	628	0	ENST00000358026.2:c.3547-2A>G		p.X1183_splice	ENST00000358026	NM_001128849.1	1183			0.189824694150662	2	FACETS	1	0.976	1	0.678	0.605	0.755	CLONAL	1	TRUE	0	0.271315178539191	2		628	511	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610097	10610097	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	117	901	0	ENST00000171111.5:c.613G>T	p.Glu205Ter	p.E205*	ENST00000171111	NM_203500.1	205	Gag/Tag	2/6	0.189824694150662	2	FACETS	1	0.976	1	0.628	0.567	0.692	CLONAL	1	TRUE	0	0.271315178539191	2		901	687	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137075	64137075	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	51	572	1	ENST00000334205.4:c.1586G>T	p.Arg529Leu	p.R529L	ENST00000334205	NM_003942.2	529	cGc/cTc	13/17	0.271315178539191	3	FACETS	0.824	0.701	0.96	0.412	0.35	0.48	CLONAL	1	TRUE	1	0.271315178539191	3		573	518	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110040	115110040	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	110	938	1	ENST00000257566.3:c.1838C>A	p.Ala613Asp	p.A613D	ENST00000257566	NM_016569.3	613	gCc/gAc	8/8	0.183874736752726	3	FACETS	1	0.979	1	0.67	0.603	0.742	CLONAL	1	TRUE	1	0.271315178539191	3		939	687	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094915	143094915	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	94	571	0	ENST00000262992.4:c.1229C>A	p.Ala410Glu	p.A410E	ENST00000262992	NM_001101669.1	410	gCa/gAa	14/24	0.183874736752726	3	FACETS	1	0.976	1	0.677	0.604	0.755	CLONAL	1	TRUE	1	0.271315178539191	3		571	581	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30668366	30668366	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	78	708	0	ENST00000376406.3:c.6146G>C	p.Cys2049Ser	p.C2049S	ENST00000376406	NM_014641.2	2049	tGc/tCc	15/15	0.224883587609951	4	FACETS	1	0.925	1	0.537	0.471	0.607	CLONAL	1	TRUE	2	0.271315178539191	4		708	681	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978632	70978632	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	92	681	1	ENST00000276594.2:c.1021G>T	p.Ala341Ser	p.A341S	ENST00000276594	NM_024504.3	341	Gct/Tct	5/8	0.271315178539191	3	FACETS	1	0.964	1	0.602	0.535	0.673	CLONAL	1	TRUE	1	0.271315178539191	3		682	640	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662754	227662754	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	108	931	0	ENST00000305123.5:c.701G>T	p.Gly234Val	p.G234V	ENST00000305123	NM_005544.2	234	gGg/gTg	1/2	0.224883587609951	4	FACETS	1	0.973	1	0.629	0.565	0.698	CLONAL	1	TRUE	2	0.271315178539191	4		931	804	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0055311-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	89	215	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.189022214120784	4	FACETS	0.855	0.759	0.957	0.855	0.759	0.957	CLONAL	2	TRUE	2	0.213299619517055	4		215	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0055311-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	191	632	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.188568182736066	2	FACETS	0.86	0.795	0.928	0.86	0.795	0.928	CLONAL	2	TRUE	0	0.213299619517055	2		632	1041	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462643	29462643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187200776	NA	P-0055311-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	223	930	0	ENST00000389048.3:c.2258G>A	p.Arg753Gln	p.R753Q	ENST00000389048	NM_004304.4	753	cGg/cAg	13/29	0.197627803500547	3	FACETS	0.933	0.867	1	0.933	0.867	1	CLONAL	2	TRUE	1	0.213299619517055	3		930	1240	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	655	511	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.218366037294141	5	FACETS	1	0.993	1			1	INDETERMINATE	4	TRUE	NA	0.652522545264365	5		511	941	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	273	374	0				ENST00000310581	NM_198253.2	-/1132			0.304831947641902	5	FACETS	0.834	0.788	0.88	0.834	0.788	0.88	INDETERMINATE	3	TRUE	2	0.652522545264365	5		374	662	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561263	9561263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769939031	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	97	334	0	ENST00000353224.5:c.519G>A	p.Met173Ile	p.M173I	ENST00000353224	NM_177990.2	173	atG/atA	4/10	NA	2	FACETS	0.652	0.584	0.723			1	INDETERMINATE	1	TRUE	NA	0.652522545264365	2		334	456	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628235	187628235	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	123	574	1	ENST00000441802.2:c.2747C>T	p.Ser916Leu	p.S916L	ENST00000441802	NM_005245.3	916	tCa/tTa	2/27	0.280203358064577	1	FACETS	0.487	0.442	0.533	0.487	0.442	0.533	INDETERMINATE	1	TRUE	0	0.652522545264365	1		575	522	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956220	55956220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190050670	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	79	344	0	ENST00000263923.4:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000263923	NM_002253.2	1032	cGa/cAa	23/30	0.509034972653995	1	FACETS	0.535	0.475	0.598	0.535	0.475	0.598	SUBCLONAL	1	TRUE	0	0.652522545264365	1		344	305	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467675	50467675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759124417	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	235	476	1	ENST00000331340.3:c.910G>A	p.Glu304Lys	p.E304K	ENST00000331340	NM_006060.4	304	Gaa/Aaa	8/8	0.304831947641902	5	FACETS	1	0.952	1	0.679	0.636	0.722	INDETERMINATE	2	TRUE	2	0.652522545264365	5		477	700	SUCCESS
AXL	558	MSKCC	GRCh37	19	41736901	41736901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201799923	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	214	761	1	ENST00000301178.4:c.616G>A	p.Glu206Lys	p.E206K	ENST00000301178	NM_021913.4	206	Gaa/Aaa	5/20	1	2	FACETS	0.712	0.662	0.764	0.712	0.662	0.764	SUBCLONAL	1	TRUE	1	0.652522545264365	2		762	921	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791758	42791758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1380826096	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	220	678	1	ENST00000575354.2:c.644G>A	p.Arg215Gln	p.R215Q	ENST00000575354	NM_015125.3	215	cGg/cAg	5/20	1	2	FACETS	0.727	0.677	0.779	0.727	0.677	0.779	SUBCLONAL	1	TRUE	1	0.652522545264365	2		679	927	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248486	212248486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178525913	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	199	400	0	ENST00000342788.4:c.3781G>A	p.Glu1261Lys	p.E1261K	ENST00000342788	NM_005235.2	1261	Gag/Aag	28/28	0.363008805325606	1	FACETS	1	0.975	1	1	0.975	1	INDETERMINATE	1	TRUE	0	0.652522545264365	1		400	386	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858306	9858306	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	89	364	0	ENST00000330684.3:c.3095C>T	p.Ser1032Phe	p.S1032F	ENST00000330684	NM_001134407.1	1032	tCc/tTc	13/13	0.363008805325606	1	FACETS	0.605	0.542	0.67	0.605	0.542	0.67	INDETERMINATE	1	TRUE	0	0.652522545264365	1		364	304	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562641	29562641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854562	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	203	380	0	ENST00000356175.3:c.3721C>T	p.Arg1241Ter	p.R1241*	ENST00000356175	NM_000267.3	1241	Cga/Tga	28/57	0.554861615160612	2	FACETS	0.79	0.744	0.835	0.79	0.744	0.835	SUBCLONAL	2	TRUE	0	0.652522545264365	2		380	394	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957133	81957133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1476399695	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	159	426	0	ENST00000359376.3:c.2351G>A	p.Arg784Gln	p.R784Q	ENST00000359376	NM_002661.3	784	cGa/cAa	22/33	1	2	FACETS	0.864	0.796	0.934	0.864	0.796	0.934	CLONAL	1	TRUE	1	0.652522545264365	2		426	564	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155953	119155953	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764340189	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	190	629	1	ENST00000264033.4:c.1618C>T	p.Arg540Ter	p.R540*	ENST00000264033	NM_005188.3	540	Cga/Tga	11/16	0.652522545264365	3	FACETS	0.748	0.691	0.807			1	SUBCLONAL	1	TRUE	NA	0.652522545264365	3		630	1033	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944983	31944983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1175067252	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	695	892	0	ENST00000340398.3:c.118C>T	p.Arg40Cys	p.R40C	ENST00000340398	NM_001013699.2	40	Cgc/Tgc	1/1	0.564348889245924	3	FACETS	1	0.997	1	0.822	0.798	0.845	CLONAL	2	TRUE	0	0.652522545264365	3		892	1146	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577540	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	rs1555525498	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	375	626	1	ENST00000269305.4:c.741_742delinsTT	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	247	aaCCgg/aaTTgg	7/11	0.554861615160612	2	FACETS	1	0.996	1	0.743	0.711	0.776	CLONAL	1	TRUE	0	0.652522545264365	2		627	773	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723473	52723473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	137	419	0	ENST00000322088.6:c.1334C>T	p.Ser445Phe	p.S445F	ENST00000322088	NM_014225.5	445	tCc/tTc	11/15	1	2	FACETS	0.762	0.696	0.83	0.762	0.696	0.83	SUBCLONAL	1	TRUE	1	0.652522545264365	2		419	551	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123199756	123199756	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	35	216	0	ENST00000218089.9:c.2056C>T	p.Gln686Ter	p.Q686*	ENST00000218089	NM_001042749.1	686	Cag/Tag	21/35	0.224084977183824	3	FACETS	0.737	0.61	0.876	0.246	0.203	0.292	INDETERMINATE	1	TRUE	0	0.652522545264365	3		216	193	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757422	40757422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	159	530	0	ENST00000373198.4:c.2876C>T	p.Ser959Phe	p.S959F	ENST00000373198	NM_133170.3	959	tCt/tTt	20/32	NA	2	FACETS	0.732	0.673	0.793			1	INDETERMINATE	1	TRUE	NA	0.652522545264365	2		530	666	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321324	1321324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	236	497	0	ENST00000400841.2:c.431G>A	p.Gly144Glu	p.G144E	ENST00000400841		144	gGg/gAg	4/6	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.652522545264365	2		497	600	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371770	116371770	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs369705803	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	151	281	0	ENST00000397752.3:c.1249C>T	p.Arg417Ter	p.R417*	ENST00000397752	NM_000245.2	417	Cga/Tga	3/21	0.304831947641902	5	FACETS	0.918	0.845	0.993	0.612	0.563	0.662	INDETERMINATE	2	TRUE	2	0.652522545264365	5		281	499	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785524	50785524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201836260	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	146	416	1	ENST00000398568.2:c.514C>T	p.Arg172Cys	p.R172C	ENST00000398568	NM_001042412.1	172	Cgt/Tgt	4/18	NA	2	FACETS	0.848	0.778	0.919			1	INDETERMINATE	1	TRUE	NA	0.652522545264365	2		417	528	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969162	93969162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	153	288	0	ENST00000369303.4:c.1834G>A	p.Glu612Lys	p.E612K	ENST00000369303	NM_004440.3	612	Gaa/Aaa	10/17	0.224084977183824	3	FACETS	0.85	0.788	0.912	0.566	0.525	0.608	INDETERMINATE	2	TRUE	0	0.652522545264365	3		288	366	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120867	94120867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	171	308	0	ENST00000369303.4:c.184G>A	p.Asp62Asn	p.D62N	ENST00000369303	NM_004440.3	62	Gat/Aat	3/17	0.224084977183824	3	FACETS	0.891	0.831	0.952	0.594	0.554	0.635	INDETERMINATE	2	TRUE	0	0.652522545264365	3		308	390	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885467	23885467	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	124	359	0	ENST00000374561.5:c.344G>A	p.Arg115Lys	p.R115K	ENST00000374561	NM_002167.4	115	aGg/aAg	2/3	0.63009057578923	3	FACETS	0.922	0.837	1	0.461	0.418	0.505	CLONAL	1	TRUE	1	0.652522545264365	3		359	547	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759850	63759850	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	142	224	0	ENST00000279873.7:c.503G>A	p.Gly168Glu	p.G168E	ENST00000279873	NM_032199.2	168	gGg/gAg	4/10	0.63009057578923	3	FACETS	0.834	0.771	0.898	0.834	0.771	0.898	CLONAL	2	TRUE	1	0.652522545264365	3		224	346	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362576	118362576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	214	337	0	ENST00000534358.1:c.4937C>T	p.Ser1646Phe	p.S1646F	ENST00000534358	NM_005933.3	1646	tCt/tTt	15/36	0.652522545264365	3	FACETS	0.805	0.755	0.857			1	CLONAL	2	TRUE	NA	0.652522545264365	3		337	540	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148891	119148891	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	114	246	0	ENST00000264033.4:c.1111T>G	p.Tyr371Asp	p.Y371D	ENST00000264033	NM_005188.3	371	Tac/Gac	8/16	0.652522545264365	3	FACETS	0.785	0.718	0.854			1	SUBCLONAL	2	TRUE	NA	0.652522545264365	3		246	295	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120975	115120975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	351	453	0	ENST00000257566.3:c.31C>T	p.Pro11Ser	p.P11S	ENST00000257566	NM_016569.3	11	Cct/Tct	1/8	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.652522545264365	NA		453	714	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432097	121432097	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	645	788	2	ENST00000257555.6:c.844G>A	p.Ala282Thr	p.A282T	ENST00000257555		282	Gcc/Acc	4/10	0.652522545264365	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.652522545264365	3		790	1197	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953630	32953630	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs886040801	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	82	304	0	ENST00000380152.3:c.8931T>A	p.Tyr2977Ter	p.Y2977*	ENST00000380152		2977	taT/taA	22/27	1	2	FACETS	0.728	0.648	0.814	0.728	0.648	0.814	SUBCLONAL	1	TRUE	1	0.652522545264365	2		304	345	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134450	41134450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	116	414	0	ENST00000379561.5:c.1178C>T	p.Ser393Phe	p.S393F	ENST00000379561	NM_002015.3	393	tCc/tTc	2/3	1	2	FACETS	0.758	0.687	0.832	0.758	0.687	0.832	SUBCLONAL	1	TRUE	1	0.652522545264365	2		414	469	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335577	73335578	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	60	253	0	ENST00000377767.4:c.2593_2594delinsTT	p.Pro865Leu	p.P865L	ENST00000377767	NM_014953.3	865	CCa/TTa	19/21	1	2	FACETS	0.783	0.682	0.889	0.783	0.682	0.889	SUBCLONAL	1	TRUE	1	0.652522545264365	2		253	235	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131720	2131721	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	220	966	1	ENST00000219476.3:c.3735_3736delinsAA	p.Asp1246Asn	p.D1246N	ENST00000219476	NM_000548.3	1245	cgGGac/cgAAac	31/42	1	2	FACETS	0.745	0.694	0.798	0.745	0.694	0.798	SUBCLONAL	1	TRUE	1	0.652522545264365	2		967	905	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642711	3642712	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	188	602	0	ENST00000294008.3:c.2315_2316delinsTT	p.Ser772Phe	p.S772F	ENST00000294008	NM_032444.2	772	tCC/tTT	11/15	1	2	FACETS	0.79	0.732	0.85	0.79	0.732	0.85	SUBCLONAL	1	TRUE	1	0.652522545264365	2		602	729	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817881	3817882	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	119	439	0	ENST00000262367.5:c.3089_3090delinsTT	p.Ser1030Phe	p.S1030F	ENST00000262367	NM_004380.2	1030	tCC/tTT	16/31	1	2	FACETS	0.773	0.702	0.847	0.773	0.702	0.847	SUBCLONAL	1	TRUE	1	0.652522545264365	2		439	472	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832879	3832879	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	152	447	0	ENST00000262367.5:c.1379T>C	p.Val460Ala	p.V460A	ENST00000262367	NM_004380.2	460	gTt/gCt	6/31	1	2	FACETS	0.991	0.914	1	0.991	0.914	1	CLONAL	1	TRUE	1	0.652522545264365	2		447	470	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351504	89351504	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	187	737	1	ENST00000301030.4:c.1446del	p.Ser483AlafsTer27	p.S483Afs*27	ENST00000301030	NM_001256183.1	482	gaG/ga	9/13	1	2	FACETS	0.771	0.714	0.83	0.771	0.714	0.83	SUBCLONAL	1	TRUE	1	0.652522545264365	2		738	743	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831300	89831300	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	159	430	0	ENST00000389301.3:c.2776C>T	p.His926Tyr	p.H926Y	ENST00000389301	NM_000135.2	926	Cac/Tac	28/43	1	2	FACETS	0.789	0.726	0.854	0.789	0.726	0.854	SUBCLONAL	1	TRUE	1	0.652522545264365	2		430	618	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226206	2226207	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	344	1168	2	ENST00000398665.3:c.3686_3687delinsTT	p.Pro1229Leu	p.P1229L	ENST00000398665	NM_032482.2	1229	cCC/cTT	27/28	1	2	FACETS	0.894	0.847	0.943	0.894	0.847	0.943	CLONAL	1	TRUE	1	0.652522545264365	2		1170	1179	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7119503	7119503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	168	567	0	ENST00000302850.5:c.3751G>A	p.Asp1251Asn	p.D1251N	ENST00000302850	NM_000208.2	1251	Gat/Aat	21/22	1	2	FACETS	0.715	0.659	0.774	0.715	0.659	0.774	SUBCLONAL	1	TRUE	1	0.652522545264365	2		567	720	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296110	15296110	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377521258	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	425	1168	0	ENST00000263388.2:c.2254G>A	p.Asp752Asn	p.D752N	ENST00000263388	NM_000435.2	752	Gat/Aat	14/33	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.652522545264365	2		1168	1205	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302855	15302855	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	275	997	0	ENST00000263388.2:c.595G>A	p.Val199Met	p.V199M	ENST00000263388	NM_000435.2	199	Gtg/Atg	4/33	1	2	FACETS	0.798	0.75	0.848	0.798	0.75	0.848	SUBCLONAL	1	TRUE	1	0.652522545264365	2		997	1056	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873028	136873028	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	231	362	0	ENST00000241393.3:c.470A>T	p.Tyr157Phe	p.Y157F	ENST00000241393	NM_003467.2	157	tAt/tTt	2/2	0.569850079531574	2	FACETS	0.831	0.787	0.875	0.831	0.787	0.875	CLONAL	2	TRUE	0	0.652522545264365	2		362	426	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251683	212251683	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	145	337	0	ENST00000342788.4:c.3376C>T	p.Gln1126Ter	p.Q1126*	ENST00000342788	NM_005235.2	1126	Cag/Tag	27/28	0.363008805325606	1	FACETS	1	0.942	1	1	0.942	1	INDETERMINATE	1	TRUE	0	0.652522545264365	1		337	295	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662619	227662619	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	420	586	0	ENST00000305123.5:c.836C>T	p.Pro279Leu	p.P279L	ENST00000305123	NM_005544.2	279	cCc/cTc	1/2	0.569850079531574	2	FACETS	0.887	0.853	0.92	0.887	0.853	0.92	CLONAL	2	TRUE	0	0.652522545264365	2		586	726	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101077	41101077	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	250	564	1	ENST00000373198.4:c.1279C>T	p.Gln427Ter	p.Q427*	ENST00000373198	NM_133170.3	427	Cag/Tag	8/32	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.652522545264365	2		565	641	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866300	42866300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	344	660	0	ENST00000398585.3:c.332G>A	p.Gly111Glu	p.G111E	ENST00000398585	NM_001135099.1	111	gGg/gAg	3/14	0.552720029300997	2	FACETS	0.891	0.853	0.927	0.891	0.853	0.927	CLONAL	2	TRUE	0	0.652522545264365	2		660	592	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475438	12475438	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	142	435	0	ENST00000287820.6:c.1312C>T	p.Gln438Ter	p.Q438*	ENST00000287820	NM_015869.4	438	Caa/Taa	7/7	0.63009057578923	3	FACETS	0.832	0.76	0.907	0.416	0.38	0.454	CLONAL	1	TRUE	1	0.652522545264365	3		435	694	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191283	185191283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1304712037	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	304	457	0	ENST00000265026.3:c.2164G>A	p.Gly722Ser	p.G722S	ENST00000265026	NM_004721.4	722	Ggc/Agc	11/14	0.63009057578923	3	FACETS	0.951	0.903	0.998	0.951	0.903	0.998	CLONAL	2	TRUE	1	0.652522545264365	3		457	650	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264550	1264550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	263	495	0	ENST00000310581.5:c.2812C>T	p.Arg938Trp	p.R938W	ENST00000310581	NM_198253.2	938	Cgg/Tgg	11/16	0.304831947641902	5	FACETS	0.973	0.915	1	0.648	0.61	0.688	INDETERMINATE	2	TRUE	2	0.652522545264365	5		495	820	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053230	180053230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1222091667	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	462	1009	2	ENST00000261937.6:c.1139G>A	p.Ser380Asn	p.S380N	ENST00000261937	NM_182925.4	380	aGt/aAt	9/30	NA	2	FACETS	0.856	0.824	0.888			1	INDETERMINATE	2	TRUE	NA	0.652522545264365	2		1011	827	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864472	162864473	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	90	328	1	ENST00000366898.1:c.40_41delinsTT	p.Pro14Leu	p.P14L	ENST00000366898	NM_004562.2	14	CCa/TTa	2/12	0.224084977183824	3	FACETS	0.882	0.787	0.981	0.294	0.262	0.327	INDETERMINATE	1	TRUE	0	0.652522545264365	3		329	415	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92244534	92244534	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	187	283	0	ENST00000265734.4:c.901C>T	p.Gln301Ter	p.Q301*	ENST00000265734	NM_001259.6	301	Cag/Tag	8/8	0.304831947641902	5	FACETS	1	0.973	1	0.726	0.676	0.777	INDETERMINATE	2	TRUE	2	0.652522545264365	5		283	521	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69039642	69039642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	53	298	0	ENST00000288368.4:c.3754C>T	p.Leu1252Phe	p.L1252F	ENST00000288368	NM_024870.2	1252	Ctt/Ttt	31/40	0.652522545264365	6	FACETS	0.633	0.539	0.735	0.127	0.107	0.147	SUBCLONAL	1	TRUE	1	0.652522545264365	6		298	592	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981681	70981681	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140792769	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	1622	1175	0	ENST00000276594.2:c.415G>A	p.Glu139Lys	p.E139K	ENST00000276594	NM_024504.3	139	Gag/Aag	2/8	0.652522545264365	6	FACETS	0.988	0.971	1	0.988	0.971	1	CLONAL	5	TRUE	1	0.652522545264365	6		1175	2320	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955491	90955491	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	82	327	0	ENST00000265433.3:c.2174A>T	p.Gln725Leu	p.Q725L	ENST00000265433	NM_002485.4	725	cAg/cTg	14/16	1	2	FACETS	0.788	0.701	0.879	0.788	0.701	0.879	SUBCLONAL	1	TRUE	1	0.652522545264365	2		327	319	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932124	39932124	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	156	773	0	ENST00000378444.4:c.2475C>G	p.Ser825Arg	p.S825R	ENST00000378444	NM_001123385.1	825	agC/agG	4/15	0.340924377669844	3	FACETS	0.596	0.545	0.65			1	INDETERMINATE	1	TRUE	NA	0.652522545264365	3		773	1064	SUCCESS
AR	367	MSKCC	GRCh37	X	66931462	66931462	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555995851	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	125	513	1	ENST00000374690.3:c.2104C>T	p.Leu702Phe	p.L702F	ENST00000374690	NM_000044.3	702	Ctc/Ttc	4/8	0.224084977183824	3	FACETS	0.737	0.668	0.81	0.246	0.222	0.27	INDETERMINATE	1	TRUE	0	0.652522545264365	3		514	689	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891475	76891475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	89	467	0	ENST00000373344.5:c.4630G>A	p.Glu1544Lys	p.E1544K	ENST00000373344	NM_000489.3	1544	Gaa/Aaa	16/35	0.224084977183824	3	FACETS	0.675	0.6	0.755	0.225	0.2	0.252	INDETERMINATE	1	TRUE	0	0.652522545264365	3		467	536	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123022495	123022495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	348	624	1	ENST00000355640.3:c.904C>T	p.His302Tyr	p.H302Y	ENST00000355640		302	Cac/Tac	3/7	0.224084977183824	3	FACETS	0.951	0.907	0.995	0.634	0.604	0.664	INDETERMINATE	2	TRUE	0	0.652522545264365	3		625	744	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191752	123191752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	74	284	0	ENST00000218089.9:c.1341G>A	p.Met447Ile	p.M447I	ENST00000218089	NM_001042749.1	447	atG/atA	15/35	0.224084977183824	3	FACETS	0.817	0.72	0.921	0.272	0.24	0.307	INDETERMINATE	1	TRUE	0	0.652522545264365	3		284	368	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0055342-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	26	215	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.221588485544098	2	FACETS	0.956	0.761	1	0.478	0.38	0.589	CLONAL	1	FALSE	0	0.246135488730906	2		215	221	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0055342-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	138	827	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	1	2	FACETS	0.968	0.878	1	0.968	0.878	1	CLONAL	1	FALSE	1	0.246135488730906	2		827	1159	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890135	76890135	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055342-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	18	414	0	ENST00000373344.5:c.4759G>T	p.Gly1587Cys	p.G1587C	ENST00000373344	NM_000489.3	1587	Ggt/Tgt	17/35	1	2	FACETS	0.571	0.43	0.737	0.571	0.43	0.737	SUBCLONAL	1	FALSE	1	0.246135488730906	2		414	256	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989042	41989042	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055342-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	31	455	0	ENST00000219905.7:c.1834G>T	p.Gly612Ter	p.G612*	ENST00000219905	NM_001164273.1	612	Gga/Tga	3/24	1	2	FACETS	0.884	0.717	1	0.884	0.717	1	CLONAL	1	FALSE	1	0.246135488730906	2		455	285	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042673	42042673	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055342-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	16	459	0	ENST00000219905.7:c.6870del	p.Arg2291GlufsTer44	p.R2291Efs*44	ENST00000219905	NM_001164273.1	2290	Ggg/gg	17/24	1	2	FACETS	0.508	0.375	0.666	0.508	0.375	0.666	SUBCLONAL	1	FALSE	1	0.246135488730906	2		459	256	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471043	25471043	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055342-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	154	718	0	ENST00000264709.3:c.718G>C	p.Glu240Gln	p.E240Q	ENST00000264709	NM_175629.2	240	Gag/Cag	7/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.246135488730906	2		718	1050	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989557	212989557	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055342-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	61	329	0	ENST00000342788.4:c.154T>A	p.Tyr52Asn	p.Y52N	ENST00000342788	NM_005235.2	52	Tac/Aac	2/28	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	FALSE	1	0.246135488730906	2		329	435	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31486624	31486624	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055342-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	29	319	0	ENST00000344624.3:c.1888C>A	p.His630Asn	p.H630N	ENST00000344624		630	Cat/Aat	11/33	0.146631038279675	3	FACETS	1	0.871	1	0.554	0.446	0.674	INDETERMINATE	1	FALSE	1	0.246135488730906	3		319	239	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502665	149502665	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055342-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	55	686	0	ENST00000261799.4:c.2123G>C	p.Arg708Pro	p.R708P	ENST00000261799	NM_002609.3	708	cGc/cCc	15/23	0.146631038279675	3	FACETS	0.497	0.424	0.578	0.249	0.212	0.289	INDETERMINATE	1	FALSE	1	0.246135488730906	3		686	1009	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578537	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs879254214	NA	P-0055343-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	225	911	3	ENST00000269305.4:c.393_395del	p.Asn131del	p.N131del	ENST00000269305	NM_001126112.2	131	aaCAAg/aag	5/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		914	1234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1555525367	NA	P-0055349-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	38	625	0	ENST00000269305.4:c.783-1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		625	485	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650270	48650270	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055349-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	58	882	0	ENST00000376670.3:c.240G>T	p.Leu80Phe	p.L80F	ENST00000376670	NM_002049.3	80	ttG/ttT	3/6	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		882	684	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939964	76939964	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055349-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	77	744	0	ENST00000373344.5:c.784del	p.Gln262AsnfsTer26	p.Q262Nfs*26	ENST00000373344	NM_000489.3	262	Caa/aa	9/35	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		744	865	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0055380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	216	840	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.522285540451134	1	FACETS	0.841	0.786	0.898	0.841	0.786	0.898	CLONAL	1	TRUE	0	0.552897207964529	1		843	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0055428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	22	893	1	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.397730618482529	1	FACETS	0.118	0.091	0.151	0.118	0.091	0.151	SUBCLONAL	1	TRUE	0	0.397730618482529	1		894	748	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0055428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	355	1033	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.386595628794447	2	FACETS	0.822	0.78	0.865	0.822	0.78	0.865	CLONAL	2	TRUE	0	0.397730618482529	2		1033	1086	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0055428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	148	788	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	0.397730618482529	1	FACETS	0.913	0.836	0.993	0.913	0.836	0.993	CLONAL	1	TRUE	0	0.397730618482529	1		788	653	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63810718	63810718	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	104	479	0	ENST00000279873.7:c.805A>C	p.Lys269Gln	p.K269Q	ENST00000279873	NM_032199.2	269	Aag/Cag	5/10	0.38067189080059	1	FACETS	0.981	0.884	1	0.981	0.884	1	CLONAL	1	TRUE	0	0.397730618482529	1		479	427	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466829	57466829	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	47	431	0	ENST00000371085.3:c.48G>C	p.Glu16Asp	p.E16D	ENST00000371085	NM_000516.4	16	gaG/gaC	1/13	1	2	FACETS	0.473	0.399	0.554	0.473	0.399	0.554	SUBCLONAL	1	TRUE	1	0.397730618482529	2		431	500	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067904	30067904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	41	886	0	ENST00000338641.4:c.1089G>A	p.Met363Ile	p.M363I	ENST00000338641	NM_000268.3	363	atG/atA	11/16	0.246116885270808	0	FACETS	0.152	0.126	0.181			1	SUBCLONAL	1	TRUE	0	0.397730618482529	0		886	817	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588851	29588851	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0055434-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	80	234	0	ENST00000356175.3:c.4637C>G	p.Ser1546Ter	p.S1546*	ENST00000356175	NM_000267.3	1546	tCa/tGa	34/57	1	2	FACETS	0.788	0.706	0.872	0.788	0.706	0.872	SUBCLONAL	1	TRUE	1	0.936047599042764	2		234	217	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562740	29562745	+	inframe_deletion	In_Frame_Del	DEL	CTCTTC	CTCTTC	-	novel	NA	P-0055434-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	97	366	0	ENST00000356175.3:c.3821_3826del	p.Leu1274_Phe1275del	p.L1274_F1275del	ENST00000356175	NM_000267.3	1274	CTCTTC/-	28/57	1	2	FACETS	0.878	0.798	0.96	0.878	0.798	0.96	CLONAL	1	TRUE	1	0.936047599042764	2		366	236	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46603685	46603685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055434-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	75	473	0	ENST00000263734.3:c.1042G>A	p.Glu348Lys	p.E348K	ENST00000263734	NM_001430.4	348	Gag/Aag	9/16	0.822311955440283	3	FACETS	0.524	0.461	0.592	0.262	0.23	0.296	SUBCLONAL	1	TRUE	1	0.936047599042764	3		473	449	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131375	202131375	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055499-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	73	569	0	ENST00000358485.4:c.343G>A	p.Glu115Lys	p.E115K	ENST00000358485	NM_001080125.1	115	Gaa/Aaa	2/9	1	2	FACETS	0.914	0.799	1	0.914	0.799	1	CLONAL	1	TRUE	1	0.246480085589408	2		569	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0055500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	271	584	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.280852449160305	2	FACETS	0.865	0.812	0.919	0.865	0.812	0.919	CLONAL	2	TRUE	0	0.31	2		584	1011	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913558	32913559	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359479	NA	P-0055500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	74	408	1	ENST00000380152.3:c.5073dup	p.Trp1692MetfsTer3	p.W1692Mfs*3	ENST00000380152		1689	gca/gcAa	11/27	0.268302538699693	2	FACETS	0.929	0.824	1	0.929	0.824	1	CLONAL	2	TRUE	0	0.31	2		409	257	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910570	29910570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199474358	NA	P-0055500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	221	805	0	ENST00000376809.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000376809	NM_002116.7	37	tCc/tTc	2/8	0.120382518134236	3	FACETS	1	0.98	1	0.577	0.535	0.62	INDETERMINATE	1	TRUE	1	0.31	3		805	1428	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106456	27106456	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	189	569	0	ENST00000324856.7:c.6067G>C	p.Glu2023Gln	p.E2023Q	ENST00000324856	NM_006015.4	2023	Gaa/Caa	20/20	0.281864434696265	3	FACETS	1	0.989	1	0.711	0.656	0.767	CLONAL	1	TRUE	1	0.31	3		569	991	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220701	1220701	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730881976	NA	P-0055500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	144	814	0	ENST00000326873.7:c.719C>G	p.Ser240Trp	p.S240W	ENST00000326873	NM_000455.4	240	tCg/tGg	5/10	0.289494264178267	1	FACETS	0.794	0.723	0.868	0.794	0.723	0.868	SUBCLONAL	1	TRUE	0	0.31	1		814	989	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134491	30134491	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	88	475	0	ENST00000263025.4:c.40C>A	p.Pro14Thr	p.P14T	ENST00000263025	NM_002746.2	14	Ccc/Acc	1/9	0.268302538699693	2	FACETS	0.688	0.609	0.773	0.344	0.304	0.387	SUBCLONAL	1	TRUE	0	0.31	2		475	825	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662315	117662315	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	49	541	0	ENST00000368508.3:c.5062del	p.Trp1688GlyfsTer42	p.W1688Gfs*42	ENST00000368508	NM_002944.2	1688	Tgg/gg	30/43	0.171906820244156	0	FACETS	0.576	0.489	0.67			1	INDETERMINATE	1	TRUE	0	0.31	0		541	379	SUCCESS
BTK	695	MSKCC	GRCh37	X	100609618	100609618	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	58	428	1	ENST00000308731.7:c.1631G>A	p.Arg544Lys	p.R544K	ENST00000308731	NM_000061.2	544	aGg/aAg	16/19	0.120382518134236	3	FACETS	0.69	0.593	0.797	0.345	0.296	0.399	INDETERMINATE	1	TRUE	1	0.31	3		429	626	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0055503-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	272	585	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.933	0.879	0.988	0.933	0.879	0.988	CLONAL	1	TRUE	1	0.734020493345089	2		585	794	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0055503-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	666	920	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.734020493345089	2	FACETS	0.999	0.975	1	0.999	0.975	1	CLONAL	2	TRUE	0	0.734020493345089	2		920	908	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720803	89720804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs786204892	NA	P-0055503-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	84	309	0	ENST00000371953.3:c.955dup	p.Thr319AsnfsTer6	p.T319Nfs*6	ENST00000371953	NM_000314.4	318	-/A	8/9	1	2	FACETS	0.556	0.493	0.621	0.556	0.493	0.621	SUBCLONAL	1	TRUE	1	0.734020493345089	2		309	412	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591085	67591085	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519839	NA	P-0055542-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	246	239	0	ENST00000274335.5:c.1678G>T	p.Asp560Tyr	p.D560Y	ENST00000274335		560	Gac/Tac	12/15	0.593241491090029	4	FACETS	0.942	0.895	0.988	0.942	0.895	0.988	CLONAL	3	TRUE	1	0.693752594399821	4		239	425	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263850	133263850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055542-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	47	188	0	ENST00000320574.5:c.52G>A	p.Glu18Lys	p.E18K	ENST00000320574	NM_006231.2	18	Gag/Aag	1/49	0.693752594399821	4	FACETS	1	0.908	1	0.363	0.309	0.42	CLONAL	1	TRUE	1	0.693752594399821	4		188	211	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481478	20481478	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055542-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	77	312	0	ENST00000346618.3:c.547C>G	p.Leu183Val	p.L183V	ENST00000346618	NM_001949.4	183	Ctt/Gtt	3/7	0.639154252824806	4	FACETS	0.959	0.847	1			1	CLONAL	1	TRUE	NA	0.693752594399821	4		312	392	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212488	5212488	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055542-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	47	590	0	ENST00000357368.4:c.4629G>C	p.Glu1543Asp	p.E1543D	ENST00000357368	NM_002850.3	1543	gaG/gaC	31/38	0.603004062865443	4	FACETS	0.341	0.287	0.401	0.171	0.143	0.201	SUBCLONAL	1	TRUE	2	0.693752594399821	4		590	673	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309790	30309790	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374460634	NA	P-0055542-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	62	578	2	ENST00000307677.4:c.232C>T	p.Arg78Trp	p.R78W	ENST00000307677	NM_138578.1	78	Cgg/Tgg	2/3	0.541366608635444	4	FACETS	0.436	0.376	0.501	0.218	0.188	0.251	SUBCLONAL	1	TRUE	2	0.693752594399821	4		580	695	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910239	50910239	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0055542-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	82	482	0	ENST00000440232.2:c.1495-1G>A		p.X499_splice	ENST00000440232	NM_002691.3	499			NA	2	FACETS	0.642	0.57	0.718			1	INDETERMINATE	1	TRUE	NA	0.693752594399821	2		482	368	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169887	32169887	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055542-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	50	752	0	ENST00000375023.3:c.3721G>C	p.Asp1241His	p.D1241H	ENST00000375023	NM_004557.3	1241	Gat/Cat	21/30	0.455393554866625	4	FACETS	0.312	0.264	0.365			1	SUBCLONAL	1	TRUE	NA	0.693752594399821	4		752	783	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870376	155870376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055542-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	118	432	0	ENST00000368323.3:c.463G>A	p.Glu155Lys	p.E155K	ENST00000368323	NM_006912.5	155	Gaa/Aaa	6/6	0.693752594399821	5	FACETS	0.83	0.749	0.917	0.277	0.249	0.306	CLONAL	1	TRUE	2	0.693752594399821	5		432	836	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650348	12650348	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055542-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	105	469	0	ENST00000251849.4:c.498G>C	p.Gln166His	p.Q166H	ENST00000251849	NM_002880.3	166	caG/caC	5/17	0.397748117579702	6	FACETS	0.981	0.879	1			1	INDETERMINATE	1	TRUE	NA	0.693752594399821	6		469	737	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291438	11291438	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055542-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	62	505	1	ENST00000361445.4:c.2568G>T	p.Glu856Asp	p.E856D	ENST00000361445	NM_004958.3	856	gaG/gaT	17/58	0.196537919556603	1	FACETS	0.294	0.255	0.336	0.294	0.255	0.336	INDETERMINATE	1	TRUE	0	0.693752594399821	1		506	397	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727917	78727917	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055542-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	46	589	0	ENST00000306801.3:c.762G>A	p.Met254Ile	p.M254I	ENST00000306801	NM_020761.2	254	atG/atA	6/34	0.605142234486695	2	FACETS	0.384	0.325	0.45	0.192	0.162	0.225	SUBCLONAL	1	TRUE	0	0.693752594399821	2		589	345	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224235	55224235	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055542-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	44	470	0	ENST00000275493.2:c.1016G>C	p.Gly339Ala	p.G339A	ENST00000275493	NM_005228.3	339	gGa/gCa	9/28	0.404577461788863	4	FACETS	0.434	0.364	0.512	0.217	0.182	0.256	INDETERMINATE	1	TRUE	2	0.693752594399821	4		470	495	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56854435	56854435	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055542-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	40	364	0	ENST00000519728.1:c.17C>T	p.Ser6Leu	p.S6L	ENST00000519728	NM_002350.3	6	tCa/tTa	2/13	0.663742006954194	5	FACETS	0.386	0.32	0.46	0.129	0.106	0.154	SUBCLONAL	1	TRUE	2	0.693752594399821	5		364	609	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0055545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	83	277	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.314615265169845	5	FACETS	0.841	0.749	0.936	0.841	0.749	0.936	CLONAL	3	TRUE	2	0.314615265169845	5		278	308	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303880	91303880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768127491	NA	P-0055545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	58	364	0	ENST00000355112.3:c.1277C>T	p.Ser426Leu	p.S426L	ENST00000355112	NM_000057.2	426	tCa/tTa	7/22	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.314615265169845	2		364	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0055545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	81	565	1	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.314615265169845	2		566	473	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102198850	102198850	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	507	237	0	ENST00000263464.3:c.1021C>G	p.Leu341Val	p.L341V	ENST00000263464	NM_001165.4	341	Cta/Gta	4/9	0.314615265169845	24	FACETS	1	0.975	1			1	CLONAL	19	TRUE	NA	0.314615265169845	24		237	752	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136825	2136825	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs749554579	NA	P-0055545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	88	640	0	ENST00000219476.3:c.4942A>G	p.Ile1648Val	p.I1648V	ENST00000219476	NM_000548.3	1648	Att/Gtt	38/42	0.234206285643386	4	FACETS	1	0.925	1	0.528	0.468	0.593	CLONAL	1	TRUE	2	0.314615265169845	4		640	696	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993702	72993702	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	95	531	0	ENST00000268489.5:c.343G>T	p.Asp115Tyr	p.D115Y	ENST00000268489	NM_006885.3	115	Gac/Tac	2/10	0.148920305723896	3	FACETS	0.763	0.683	0.848	0.763	0.683	0.848	INDETERMINATE	2	TRUE	1	0.314615265169845	3		531	458	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89811424	89811424	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1450954823	NA	P-0055545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	31	626	0	ENST00000389301.3:c.3569A>G	p.Gln1190Arg	p.Q1190R	ENST00000389301	NM_000135.2	1190	cAg/cGg	36/43	0.148920305723896	3	FACETS	0.376	0.303	0.459	0.188	0.151	0.23	INDETERMINATE	1	TRUE	1	0.314615265169845	3		626	607	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437633	52437633	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs746878681	NA	P-0055545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	60	544	0	ENST00000460680.1:c.1528C>A	p.Pro510Thr	p.P510T	ENST00000460680	NM_004656.3	510	Cct/Act	13/17	1	2	FACETS	0.679	0.585	0.781	0.679	0.585	0.781	SUBCLONAL	1	TRUE	1	0.314615265169845	2		544	562	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55269449	55269449	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	126	590	0	ENST00000275493.2:c.3136A>T	p.Thr1046Ser	p.T1046S	ENST00000275493	NM_005228.3	1046	Acc/Tcc	26/28	0.314615265169845	4	FACETS	1	0.976	1	0.623	0.564	0.685	CLONAL	1	TRUE	2	0.314615265169845	4		590	845	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	51	897	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.402451212208553	4	FACETS	0.562	0.477	0.656	0.281	0.238	0.328	SUBCLONAL	1	FALSE	2	0.402451212208553	4		898	632	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	57	374	0				ENST00000310581	NM_198253.2	-/1132			0.276577931493732	5	FACETS	1	0.927	1	1	0.927	1	CLONAL	3	FALSE	2	0.402451212208553	5		374	141	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	256	193	1	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.402451212208553	2	FACETS	1	0.992	1	1	0.996	1	CLONAL	3	FALSE	0	0.402451212208553	2		194	365	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801065	135801065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs118203361	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	36	106	0	ENST00000298552.3:c.272C>T	p.Ser91Leu	p.S91L	ENST00000298552	NM_001162426.1	91	tCg/tTg	5/23	0.402044756315204	3	FACETS	0.762	0.629	0.909	0.381	0.314	0.455	CLONAL	1	FALSE	1	0.402451212208553	3		106	282	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789627	3789627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201186078	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	280	163	1	ENST00000262367.5:c.4232G>A	p.Gly1411Glu	p.G1411E	ENST00000262367	NM_004380.2	1411	gGa/gAa	25/31	0.402451212208553	5	FACETS	1	0.983	1	1	0.994	1	CLONAL	5	FALSE	1	0.402451212208553	5		164	424	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759873	63759873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141049493	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	29	77	0	ENST00000279873.7:c.526G>A	p.Val176Met	p.V176M	ENST00000279873	NM_032199.2	176	Gtg/Atg	4/10	0.402451212208553	2	FACETS	0.655	0.529	0.797	0.328	0.264	0.399	SUBCLONAL	1	FALSE	0	0.402451212208553	2		77	220	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982387	201982387	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	106	318	0	ENST00000359651.3:c.766G>T	p.Glu256Ter	p.E256*	ENST00000359651		256	Gag/Tag	6/8	0.402451212208553	3	FACETS	0.884	0.793	0.98	0.442	0.396	0.49	CLONAL	1	FALSE	1	0.402451212208553	3		318	716	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131355	17131355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	59	267	1	ENST00000285071.4:c.97G>A	p.Asp33Asn	p.D33N	ENST00000285071	NM_144997.5	33	Gat/Aat	4/14	0.402451212208553	2	FACETS	0.774	0.668	0.887	0.387	0.334	0.444	SUBCLONAL	1	FALSE	0	0.402451212208553	2		268	379	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984428	201984428	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	80	243	0	ENST00000359651.3:c.1093G>C	p.Glu365Gln	p.E365Q	ENST00000359651		365	Gag/Cag	8/8	0.402451212208553	3	FACETS	0.818	0.721	0.922	0.409	0.36	0.461	CLONAL	1	FALSE	1	0.402451212208553	3		243	584	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882030	36882030	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	36	249	0	ENST00000358127.4:c.983C>G	p.Ser328Ter	p.S328*	ENST00000358127	NM_001280556.1	328	tCa/tGa	8/10	0.402451212208553	3	FACETS	0.46	0.378	0.552	0.23	0.189	0.276	SUBCLONAL	1	FALSE	1	0.402451212208553	3		249	467	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881415	48881415	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	32	37	0	ENST00000267163.4:c.138-1G>A		p.X46_splice	ENST00000267163	NM_000321.2	46			0.313642116175171	1	FACETS	1	0.898	1	1	0.976	1	CLONAL	3	FALSE	0	0.402451212208553	1		37	42	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073947	8073947	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs994703930	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	18	94	0	ENST00000377482.5:c.712C>T	p.Pro238Ser	p.P238S	ENST00000377482	NM_018948.3	238	Cct/Tct	4/4	0.00873090660061937	4	FACETS	0.35	0.263	0.454			1	INDETERMINATE	1	FALSE	NA	0.402451212208553	4		94	358	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562603	176562603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	169	181	0	ENST00000439151.2:c.499G>A	p.Glu167Lys	p.E167K	ENST00000439151	NM_022455.4	167	Gaa/Aaa	2/23	0.402451212208553	6	FACETS	0.987	0.92	1			1	CLONAL	4	FALSE	NA	0.402451212208553	6		181	384	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022540	12022540	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	53	230	0	ENST00000396373.4:c.646G>A	p.Glu216Lys	p.E216K	ENST00000396373	NM_001987.4	216	Gag/Aag	5/8	0.402451212208553	8	FACETS	1	0.881	1			1	CLONAL	1	FALSE	NA	0.402451212208553	8		230	560	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743928	46743928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	135	204	0	ENST00000371975.4:c.2218C>T	p.His740Tyr	p.H740Y	ENST00000371975	NM_003579.3	740	Cat/Tat	18/18	0.402451212208553	5	FACETS	0.918	0.838	1	0.918	0.838	1	CLONAL	2	FALSE	3	0.402451212208553	5		204	586	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659606	88659606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	114	119	0	ENST00000372037.3:c.389G>A	p.Cys130Tyr	p.C130Y	ENST00000372037	NM_004329.2	130	tGt/tAt	6/13	0.402451212208553	2	FACETS	0.951	0.897	1	1	0.992	1	CLONAL	4	FALSE	0	0.402451212208553	2		119	149	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200115	67200115	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	73	295	0	ENST00000312629.5:c.502G>T	p.Glu168Ter	p.E168*	ENST00000312629	NM_003952.2	168	Gaa/Taa	6/15	0.402451212208553	5	FACETS	0.919	0.804	1			1	CLONAL	1	FALSE	NA	0.402451212208553	5		295	633	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369244	118369244	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	102	67	0	ENST00000534358.1:c.5961+1G>A		p.X1987_splice	ENST00000534358	NM_005933.3	1987			0.402451212208553	3	FACETS	1	0.971	1			1	CLONAL	3	FALSE	NA	0.402451212208553	3		67	181	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914312	32914312	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	33	92	0	ENST00000380152.3:c.5820G>C	p.Glu1940Asp	p.E1940D	ENST00000380152		1940	gaG/gaC	11/27	0.402451212208553	7	FACETS	1	0.926	1			1	CLONAL	1	FALSE	NA	0.402451212208553	7		92	257	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724685	43724685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	57	159	0	ENST00000382044.4:c.3382G>A	p.Asp1128Asn	p.D1128N	ENST00000382044	NM_001141980.1	1128	Gat/Aat	17/28	0.402451212208553	4	FACETS	1	0.923	1	0.553	0.477	0.636	CLONAL	1	FALSE	2	0.402451212208553	4		159	359	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128244	30128244	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs778983958	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	51	276	0	ENST00000263025.4:c.988C>G	p.Leu330Val	p.L330V	ENST00000263025	NM_002746.2	330	Ctg/Gtg	7/9	0.320730968115386	5	FACETS	0.51	0.432	0.596			1	SUBCLONAL	1	FALSE	NA	0.402451212208553	5		276	797	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184589	7184589	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761203947	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	59	153	1	ENST00000302850.5:c.712G>A	p.Glu238Lys	p.E238K	ENST00000302850	NM_000208.2	238	Gag/Aag	3/22	0.402451212208553	6	FACETS	1	0.863	1	0.334	0.287	0.385	CLONAL	1	FALSE	3	0.402451212208553	6		154	528	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726665	41726666	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGGGATGG	novel	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	26	280	0	ENST00000301178.4:c.211_218dup	p.Gln74GlyfsTer27	p.Q74Gfs*27	ENST00000301178	NM_021913.4	70	-/CGGGATGG	2/20	0.402451212208553	5	FACETS	0.425	0.335	0.527	0.106	0.083	0.132	SUBCLONAL	1	FALSE	1	0.402451212208553	5		280	488	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966463	25966463	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	49	181	0	ENST00000435504.4:c.2743C>G	p.Pro915Ala	p.P915A	ENST00000435504		915	Cca/Gca	13/13	0.320730968115386	5	FACETS	0.996	0.846	1			1	CLONAL	1	FALSE	NA	0.402451212208553	5		181	392	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966600	25966600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1005263447	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	30	169	0	ENST00000435504.4:c.2606C>T	p.Ser869Leu	p.S869L	ENST00000435504		869	tCa/tTa	13/13	0.320730968115386	5	FACETS	0.854	0.69	1			1	CLONAL	1	FALSE	NA	0.402451212208553	5		169	280	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877415	40877415	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	30	188	0	ENST00000373198.4:c.2281G>T	p.Asp761Tyr	p.D761Y	ENST00000373198	NM_133170.3	761	Gac/Tac	15/32	0.402451212208553	6	FACETS	0.683	0.55	0.833	0.137	0.11	0.167	SUBCLONAL	1	FALSE	1	0.402451212208553	6		188	394	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288152	21288152	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	86	132	0	ENST00000354336.3:c.397G>C	p.Asp133His	p.D133H	ENST00000354336	NM_005207.3	133	Gat/Cat	2/3	0.402451212208553	3	FACETS	0.82	0.733	0.911	0.547	0.488	0.608	CLONAL	2	FALSE	0	0.402451212208553	3		132	313	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374364	138374364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	97	82	0	ENST00000289153.2:c.3080C>T	p.Ser1027Phe	p.S1027F	ENST00000289153	NM_006219.2	1027	tCt/tTt	22/22	0.402451212208553	8	FACETS	1	0.953	1	0.721	0.654	0.789	CLONAL	4	FALSE	2	0.402451212208553	8		82	246	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916941	178916941	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	21	101	0	ENST00000263967.3:c.328G>C	p.Glu110Gln	p.E110Q	ENST00000263967	NM_006218.2	110	Gaa/Caa	2/21	0.402451212208553	8	FACETS	0.805	0.621	1	0.134	0.103	0.17	CLONAL	1	FALSE	2	0.402451212208553	8		101	286	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198096	185198096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	18	146	0	ENST00000265026.3:c.2578G>C	p.Glu860Gln	p.E860Q	ENST00000265026	NM_004721.4	860	Gag/Cag	13/14	0.402451212208553	8	FACETS	0.582	0.438	0.754	0.097	0.073	0.126	SUBCLONAL	1	FALSE	2	0.402451212208553	8		146	339	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127504	55127504	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	17	120	0	ENST00000257290.5:c.292T>C	p.Tyr98His	p.Y98H	ENST00000257290	NM_006206.4	98	Tac/Cac	3/23	1	2	FACETS	0.388	0.29	0.503	0.388	0.29	0.503	SUBCLONAL	1	FALSE	1	0.402451212208553	2		120	218	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235345	235345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	36	151	0	ENST00000264932.6:c.1151C>T	p.Ser384Leu	p.S384L	ENST00000264932	NM_004168.2	384	tCa/tTa	9/15	0.276577931493732	5	FACETS	0.551	0.452	0.662	0.184	0.15	0.221	SUBCLONAL	1	FALSE	2	0.402451212208553	5		151	521	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562387	176562387	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	168	193	0	ENST00000439151.2:c.283G>A	p.Glu95Lys	p.E95K	ENST00000439151	NM_022455.4	95	Gaa/Aaa	2/23	0.402451212208553	6	FACETS	1	0.965	1			1	CLONAL	4	FALSE	NA	0.402451212208553	6		193	358	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030206	180030206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	28	235	0	ENST00000261937.6:c.4078G>A	p.Asp1360Asn	p.D1360N	ENST00000261937	NM_182925.4	1360	Gac/Aac	30/30	0.402451212208553	0	FACETS	0.365	0.293	0.446			1	SUBCLONAL	1	FALSE	0	0.402451212208553	0		235	228	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64288841	64288841	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	29	125	0	ENST00000370651.3:c.237G>C	p.Gln79His	p.Q79H	ENST00000370651	NM_003463.4	79	caG/caC	4/6	0.402451212208553	9	FACETS	0.775	0.621	0.95	0.129	0.103	0.159	CLONAL	1	FALSE	3	0.402451212208553	9		125	448	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001017	150001017	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	14	87	0	ENST00000253339.5:c.2587C>G	p.Gln863Glu	p.Q863E	ENST00000253339		863	Cag/Gag	4/7	0.402451212208553	4	FACETS	0.485	0.351	0.647	0.243	0.175	0.324	SUBCLONAL	1	FALSE	2	0.402451212208553	4		87	201	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439656	140439656	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	13	77	0	ENST00000288602.6:c.2083G>T	p.Glu695Ter	p.E695*	ENST00000288602	NM_004333.4	695	Gag/Tag	17/18	0.402451212208553	8	FACETS	0.859	0.615	1			1	CLONAL	1	FALSE	NA	0.402451212208553	8		77	166	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859351	151859351	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	46	115	0	ENST00000262189.6:c.11311G>C	p.Asp3771His	p.D3771H	ENST00000262189	NM_170606.2	3771	Gac/Cac	43/59	0.402451212208553	6	FACETS	1	0.95	1			1	CLONAL	1	FALSE	NA	0.402451212208553	6		115	312	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336347	80336347	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1297612239	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	37	98	0	ENST00000286548.4:c.972C>G	p.Ile324Met	p.I324M	ENST00000286548	NM_002072.3	324	atC/atG	7/7	0.402451212208553	3	FACETS	0.792	0.656	0.942	0.396	0.328	0.471	CLONAL	1	FALSE	1	0.402451212208553	3		98	279	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411714	63411714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	20	244	0	ENST00000330258.3:c.1453G>A	p.Glu485Lys	p.E485K	ENST00000330258	NM_152424.3	485	Gag/Aag	2/2	0.34572267117234	0	FACETS	0.279	0.214	0.354			1	SUBCLONAL	1	FALSE	0	0.402451212208553	0		244	213	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0055562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	466	897	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.759954856170983	3	FACETS	1	0.986	1	0.697	0.672	0.722	CLONAL	2	TRUE	0	0.759954856170983	3		898	809	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	505	374	0				ENST00000310581	NM_198253.2	-/1132			0.759954856170983	12	FACETS	1	0.988	1	1	0.988	1	CLONAL	9	TRUE	3	0.759954856170983	12		374	689	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873620	37873620	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	579	1083	1	ENST00000269571.5:c.1785C>A	p.Phe595Leu	p.F595L	ENST00000269571		595	ttC/ttA	15/27	0.759954856170983	3	FACETS	1	0.987	1	0.693	0.671	0.716	CLONAL	2	TRUE	0	0.759954856170983	3		1084	1011	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562226	95562226	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	99	428	0	ENST00000393063.1:c.5031C>G	p.Phe1677Leu	p.F1677L	ENST00000393063	NM_030621.3	1677	ttC/ttG	24/28	0.759954856170983	4	FACETS	0.822	0.736	0.913	0.411	0.368	0.457	CLONAL	1	TRUE	2	0.759954856170983	4		428	558	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981167	201981168	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0055562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	281	1190	0	ENST00000359651.3:c.248dup	p.Asn83LysfsTer9	p.N83Kfs*9	ENST00000359651		82	-/A	2/8	0.757406141268512	3	FACETS	0.992	0.933	1	0.496	0.466	0.526	CLONAL	1	TRUE	1	0.759954856170983	3		1190	1029	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89334990	89334990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	24	23	0	ENST00000301030.4:c.7888G>A	p.Glu2630Lys	p.E2630K	ENST00000301030	NM_001256183.1	2630	Gaa/Aaa	13/13	0.759954856170983	4	FACETS	0.95	0.805	1	1	0.948	1	CLONAL	3	TRUE	2	0.759954856170983	4		23	39	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162014	22162014	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	170	554	0	ENST00000215832.6:c.241G>A	p.Glu81Lys	p.E81K	ENST00000215832	NM_002745.4	81	Gag/Aag	2/9	0.759954856170983	3	FACETS	1	0.964	1	0.536	0.495	0.578	CLONAL	1	TRUE	1	0.759954856170983	3		554	576	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828872	26828872	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	230	427	0	ENST00000381527.3:c.94T>G	p.Tyr32Asp	p.Y32D	ENST00000381527	NM_001260.1	32	Tat/Gat	1/13	0.408154504317789	5	FACETS	0.892	0.842	0.943	0.892	0.842	0.943	INDETERMINATE	3	TRUE	2	0.759954856170983	5		427	484	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045001	47045001	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	1015	612	4	ENST00000377604.3:c.2327G>A	p.Arg776Gln	p.R776Q	ENST00000377604	NM_001204468.1	776	cGg/cAg	20/24	0.759954856170983	4	FACETS	1	0.998	1			1	CLONAL	4	TRUE	NA	0.759954856170983	4		616	1087	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633412	3633412	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	297	1163	1	ENST00000294008.3:c.4839G>T	p.Glu1613Asp	p.E1613D	ENST00000294008	NM_032444.2	1613	gaG/gaT	14/15	0.757406141268512	3	FACETS	0.955	0.899	1	0.477	0.449	0.506	CLONAL	1	TRUE	1	0.759954856170983	3		1164	1130	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813747	50813747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	219	872	0	ENST00000398568.2:c.1301C>T	p.Pro434Leu	p.P434L	ENST00000398568	NM_001042412.1	434	cCa/cTa	8/18	0.759954856170983	4	FACETS	0.941	0.875	1	0.47	0.437	0.505	CLONAL	1	TRUE	2	0.759954856170983	4		872	1078	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578543	7578551	+	inframe_deletion	In_Frame_Del	DEL	GGCAGGGGA	GGCAGGGGA	-	novel	NA	P-0055562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	445	1080	0	ENST00000269305.4:c.379_387del	p.Ser127_Ala129del	p.S127_A129del	ENST00000269305	NM_001126112.2	127	TCCCCTGCC/-	5/11	0.759954856170983	2	FACETS	0.965	0.936	0.993	0.965	0.936	0.993	CLONAL	2	TRUE	0	0.759954856170983	2		1080	607	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740786	58740787	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0055562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	549	678	0	ENST00000305921.3:c.1691_1692del	p.Ala564GlufsTer13	p.A564Efs*13	ENST00000305921	NM_003620.3	564	gCA/g	6/6	0.759954856170983	4	FACETS	1	0.979	1	0.76	0.736	0.782	CLONAL	3	TRUE	0	0.759954856170983	4		678	837	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007572	62007572	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	290	1090	0	ENST00000392795.3:c.295G>C	p.Glu99Gln	p.E99Q	ENST00000392795	NM_001039933.1	99	Gag/Cag	3/6	0.759954856170983	4	FACETS	1	0.955	1	0.255	0.239	0.271	CLONAL	1	TRUE	0	0.759954856170983	4		1090	1318	SUCCESS
YES1	7525	MSKCC	GRCh37	18	746003	746003	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	84	317	0	ENST00000314574.4:c.519G>C	p.Leu173Phe	p.L173F	ENST00000314574	NM_005433.3	173	ttG/ttC	5/12	0.759954856170983	4	FACETS	0.664	0.587	0.746			1	SUBCLONAL	1	TRUE	NA	0.759954856170983	4		317	586	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021756	71021756	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	158	439	0	ENST00000318789.4:c.1602G>A	p.Trp534Ter	p.W534*	ENST00000318789	NM_032682.5	534	tgG/tgA	18/21	0.72177057901648	3	FACETS	1	0.99	1	0.739	0.686	0.794	CLONAL	1	TRUE	1	0.759954856170983	3		439	388	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279582	1279582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1228165704	NA	P-0055562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	2399	1139	0	ENST00000310581.5:c.1954G>A	p.Glu652Lys	p.E652K	ENST00000310581	NM_198253.2	652	Gag/Aag	5/16	0.759954856170983	12	FACETS	1	0.99	1	1	0.99	1	CLONAL	9	TRUE	3	0.759954856170983	12		1139	3354	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53254068	53254068	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	435	433	0	ENST00000375401.3:c.4G>T	p.Glu2Ter	p.E2*	ENST00000375401	NM_004187.3	2	Gag/Tag	1/26	0.759954856170983	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.759954856170983	2		433	515	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0055562-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	168	383	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.944	0.878	1	0.944	0.878	1	CLONAL	1	TRUE	1	0.839021109608526	2		383	424	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055562-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	87	374	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.91	0.82	1	0.91	0.82	1	CLONAL	1	TRUE	1	0.839021109608526	2		374	228	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055562-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	16	648	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	1	2	FACETS	0.065	0.048	0.087	0.065	0.048	0.087	SUBCLONAL	1	TRUE	1	0.839021109608526	2		648	584	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259580	16259580	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055562-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	234	579	0	ENST00000375759.3:c.6845C>G	p.Ser2282Cys	p.S2282C	ENST00000375759	NM_015001.2	2282	tCt/tGt	11/15	1	2	FACETS	0.901	0.846	0.957	0.901	0.846	0.957	CLONAL	1	TRUE	1	0.839021109608526	2		579	619	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710681	114710681	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055562-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	257	411	0	ENST00000543371.1:c.166C>T	p.Gln56Ter	p.Q56*	ENST00000543371	NM_001198531.1	56	Caa/Taa	1/14	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.839021109608526	2		411	605	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256126	123256126	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055562-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	323	633	1	ENST00000358487.5:c.1783G>A	p.Glu595Lys	p.E595K	ENST00000358487	NM_000141.4	595	Gag/Aag	13/18	1	2	FACETS	0.972	0.923	1	0.972	0.923	1	CLONAL	1	TRUE	1	0.839021109608526	2		634	792	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481406	56481406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055562-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	354	660	0	ENST00000267101.3:c.593G>A	p.Gly198Glu	p.G198E	ENST00000267101	NM_001982.3	198	gGa/gAa	5/28	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.839021109608526	2		660	833	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43766921	43766921	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055562-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	173	231	0	ENST00000382044.4:c.1130C>G	p.Ser377Cys	p.S377C	ENST00000382044	NM_001141980.1	377	tCt/tGt	10/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.839021109608526	2		231	365	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354437	91354437	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055562-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	152	342	0	ENST00000355112.3:c.3877G>C	p.Glu1293Gln	p.E1293Q	ENST00000355112	NM_000057.2	1293	Gaa/Caa	21/22	1	2	FACETS	0.936	0.867	1	0.936	0.867	1	CLONAL	1	TRUE	1	0.839021109608526	2		342	387	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640569	3640569	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055562-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	653	824	0	ENST00000294008.3:c.3070C>A	p.Pro1024Thr	p.P1024T	ENST00000294008	NM_032444.2	1024	Ccc/Acc	12/15	0.670819381803227	3	FACETS	0.93	0.901	0.959	0.93	0.901	0.959	CLONAL	2	TRUE	1	0.839021109608526	3		824	1188	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435552	56435552	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs62636625	NA	P-0055562-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	661	753	1	ENST00000407977.2:c.1585C>T	p.Arg529Trp	p.R529W	ENST00000407977		529	Cgg/Tgg	9/10	0.769305573293956	3	FACETS	0.965	0.935	0.994	0.965	0.935	0.994	CLONAL	2	TRUE	1	0.839021109608526	3		754	1159	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400019	49400019	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055562-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	45	498	0	ENST00000418115.1:c.318C>G	p.Phe106Leu	p.F106L	ENST00000418115	NM_001664.2	106	ttC/ttG	4/5	1	2	FACETS	0.134	0.112	0.158	0.134	0.112	0.158	SUBCLONAL	1	TRUE	1	0.839021109608526	2		498	802	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557746	187557746	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1560955858	NA	P-0055562-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	170	274	0	ENST00000441802.2:c.3965T>C	p.Ile1322Thr	p.I1322T	ENST00000441802	NM_005245.3	1322	aTt/aCt	5/27	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.839021109608526	2		274	394	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630726	187630726	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055562-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	40	527	0	ENST00000441802.2:c.256G>T	p.Glu86Ter	p.E86*	ENST00000441802	NM_005245.3	86	Gaa/Taa	2/27	1	2	FACETS	0.13	0.108	0.156	0.13	0.108	0.156	SUBCLONAL	1	TRUE	1	0.839021109608526	2		527	731	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181758	56181758	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0055562-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	26	214	0	ENST00000399503.3:c.3983-1G>A		p.X1328_splice	ENST00000399503	NM_005921.1	1328			1	2	FACETS	0.185	0.146	0.229	0.185	0.146	0.229	SUBCLONAL	1	TRUE	1	0.839021109608526	2		214	335	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528335	157528335	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055562-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	328	701	0	ENST00000346085.5:c.6060G>C	p.Leu2020Phe	p.L2020F	ENST00000346085	NM_020732.3	2020	ttG/ttC	20/20	1	2	FACETS	0.9	0.853	0.947	0.9	0.853	0.947	CLONAL	1	TRUE	1	0.839021109608526	2		701	869	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444326	50444326	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055562-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	24	359	0	ENST00000331340.3:c.256G>T	p.Asp86Tyr	p.D86Y	ENST00000331340	NM_006060.4	86	Gat/Tat	4/8	1	2	FACETS	0.132	0.103	0.165	0.132	0.103	0.165	SUBCLONAL	1	TRUE	1	0.839021109608526	2		359	434	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782690	135782690	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	rs118203512	NA	P-0055562-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	96	386	0	ENST00000298552.3:c.1331C>G	p.Ser444Ter	p.S444*	ENST00000298552	NM_001162426.1	444	tCa/tGa	13/23	0.839021109608526	1	FACETS	0.359	0.322	0.397	0.359	0.322	0.397	SUBCLONAL	1	TRUE	0	0.839021109608526	1		386	370	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918259	44918259	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0055562-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	186	188	0	ENST00000377967.4:c.884C>G	p.Ser295Ter	p.S295*	ENST00000377967	NM_021140.2	295	tCa/tGa	11/29	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.839021109608526	1		188	226	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220428	123220428	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055562-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	293	235	0	ENST00000218089.9:c.3085C>T	p.Gln1029Ter	p.Q1029*	ENST00000218089	NM_001042749.1	1029	Cag/Tag	30/35	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.839021109608526	1		235	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587780070	NA	P-0055563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	149	787	0	ENST00000269305.4:c.535C>A	p.His179Asn	p.H179N	ENST00000269305	NM_001126112.2	179	Cat/Aat	5/11	0.404646731211416	1	FACETS	0.702	0.641	0.765	0.702	0.641	0.765	SUBCLONAL	1	FALSE	0	0.404646731211416	1		787	837	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724605	162724605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756942296	NA	P-0055563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	128	537	0	ENST00000367921.3:c.377G>A	p.Gly126Asp	p.G126D	ENST00000367921	NM_006182.2	126	gGc/gAc	5/18	1	2	FACETS	0.879	0.797	0.964	0.879	0.797	0.964	CLONAL	1	FALSE	1	0.404646731211416	2		537	720	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424741	49424741	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783692	NA	P-0055563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	216	822	1	ENST00000301067.7:c.13606C>T	p.Arg4536Ter	p.R4536*	ENST00000301067	NM_003482.3	4536	Cga/Tga	40/54	1	2	FACETS	0.976	0.907	1	0.976	0.907	1	CLONAL	1	FALSE	1	0.404646731211416	2		823	1094	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420273	88420273	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	115	564	1	ENST00000360948.2:c.2413G>A	p.Gly805Arg	p.G805R	ENST00000360948	NM_001012338.2	805	Ggg/Agg	19/19	1	2	FACETS	0.786	0.709	0.868	0.786	0.709	0.868	SUBCLONAL	1	FALSE	1	0.404646731211416	2		565	723	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524693	106524694	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	55	215	0	ENST00000359195.3:c.2856dup	p.Met953TyrfsTer12	p.M953Yfs*12	ENST00000359195	NM_002649.2	952	att/aTtt	9/11	1	2	FACETS	0.712	0.611	0.821	0.712	0.611	0.821	SUBCLONAL	1	FALSE	1	0.404646731211416	2		215	382	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0055564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	49	181	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.814	0.689	0.952	0.814	0.689	0.952	CLONAL	1	TRUE	1	0.2	2		181	602	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0055564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	87	787	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.825	0.729	0.929	0.825	0.729	0.929	CLONAL	1	TRUE	1	0.2	2		787	1054	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023622	27023634	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCGGCGGCTGC	CGGCGGCGGCTGC	-	novel	NA	P-0055564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	85	140	0	ENST00000324856.7:c.732_744del	p.Ala245ProfsTer114	p.A245Pfs*114	ENST00000324856	NM_006015.4	243	gCGGCGGCGGCTGCc/gc	1/20	1	2	FACETS	0.914	0.816	1	1	0.988	1	CLONAL	3	TRUE	1	0.2	2		140	310	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843613	156843613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561243137	NA	P-0055564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	84	919	1	ENST00000524377.1:c.1039C>T	p.Arg347Cys	p.R347C	ENST00000524377	NM_002529.3	347	Cgc/Tgc	8/17	1	2	FACETS	0.757	0.666	0.854	0.757	0.666	0.854	SUBCLONAL	1	TRUE	1	0.2	2		920	1110	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913396	NA	P-0055564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	19	428	0	ENST00000349496.5:c.95A>G	p.Asp32Gly	p.D32G	ENST00000349496	NM_001904.3	32	gAc/gGc	3/15	1	2	FACETS	0.317	0.239	0.409	0.317	0.239	0.409	SUBCLONAL	1	TRUE	1	0.2	2		428	600	SUCCESS
AR	367	MSKCC	GRCh37	X	66765382	66765382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770661499	NA	P-0055564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	60	813	3	ENST00000374690.3:c.394G>A	p.Val132Ile	p.V132I	ENST00000374690	NM_000044.3	132	Gtc/Atc	1/8	1	2	FACETS	0.647	0.556	0.747	0.647	0.556	0.747	SUBCLONAL	1	TRUE	1	0.2	2		816	927	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0055565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	369	840	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.47737579154137	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.47737579154137	1		843	1071	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	131	374	0				ENST00000310581	NM_198253.2	-/1132			0.476403607900196	3	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	1	0.47737579154137	3		374	337	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138376610	138376610	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	158	407	0	ENST00000289153.2:c.2864G>A	p.Arg955Gln	p.R955Q	ENST00000289153	NM_006219.2	955	cGa/cAa	20/22	1	2	FACETS	0.928	0.853	1	0.928	0.853	1	CLONAL	1	TRUE	1	0.47737579154137	2		407	713	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793296	139793296	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	331	706	0	ENST00000247668.2:c.104C>G	p.Ser35Cys	p.S35C	ENST00000247668	NM_021138.3	35	tCc/tGc	2/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.47737579154137	2		706	1367	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0055566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	45	30	0				ENST00000310581	NM_198253.2	-/1132			0.155479706128203	2	FACETS	0.836	0.716	0.964	1	0.947	1	CLONAL	3	TRUE	0	0.23	2		30	156	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397710	49397710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	38	134	0	ENST00000418115.1:c.514G>A	p.Glu172Lys	p.E172K	ENST00000418115	NM_001664.2	172	Gaa/Aaa	5/5	1	2	FACETS	0.767	0.634	0.915	0.767	0.634	0.915	CLONAL	1	TRUE	1	0.23	2		134	431	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509403	46509403	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	40	147	0	ENST00000262741.5:c.1328C>T	p.Ser443Phe	p.S443F	ENST00000262741	NM_003629.3	443	tCc/tTc	10/10	1	2	FACETS	0.75	0.623	0.891	0.75	0.623	0.891	SUBCLONAL	1	TRUE	1	0.23	2		147	464	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100093	30100093	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	24	178	0	ENST00000331968.5:c.1527T>A	p.Asn509Lys	p.N509K	ENST00000331968	NM_002742.2	509	aaT/aaA	10/18	0.170581091781944	2	FACETS	0.486	0.381	0.609	0.243	0.19	0.305	SUBCLONAL	1	TRUE	0	0.23	2		178	429	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829803	72829803	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	29	187	0	ENST00000268489.5:c.6778T>G	p.Phe2260Val	p.F2260V	ENST00000268489	NM_006885.3	2260	Ttc/Gtc	9/10	1	2	FACETS	0.5	0.401	0.614	0.5	0.401	0.614	SUBCLONAL	1	TRUE	1	0.23	2		187	504	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0055566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	44	30	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.238843474951304	2		30	262	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509403	46509403	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	125	147	0	ENST00000262741.5:c.1328C>T	p.Ser443Phe	p.S443F	ENST00000262741	NM_003629.3	443	tCc/tTc	10/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.238843474951304	2		147	916	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812567	43812567	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	94	179	0	ENST00000372470.3:c.1270C>T	p.Gln424Ter	p.Q424*	ENST00000372470	NM_005373.2	424	Caa/Taa	8/12	1	2	FACETS	0.92	0.817	1	0.92	0.817	1	CLONAL	1	TRUE	1	0.238843474951304	2		179	856	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032047	26032047	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	87	137	0	ENST00000244661.2:c.242C>A	p.Thr81Asn	p.T81N	ENST00000244661	NM_003537.3	81	aCc/aAc	1/1	1	2	FACETS	0.966	0.855	1	0.966	0.855	1	CLONAL	1	TRUE	1	0.238843474951304	2		137	754	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0055567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	28	674	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	0.846	0.684	1	1	0.949	1	CLONAL	2	TRUE	1	0.213521282684507	2		674	155	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424176	49424177	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0055567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	33	441	0	ENST00000301067.7:c.13885_13886insG	p.Thr4629SerfsTer18	p.T4629Sfs*18	ENST00000301067	NM_003482.3	4629	acc/aGcc	42/54	0.213521282684507	6	FACETS	1	0.858	1	1	0.945	1	CLONAL	4	TRUE	3	0.213521282684507	6		441	107	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0055574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	224	215	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.966	1	1	0.995	1	CLONAL	2	TRUE	1	0.35210560780667	2		215	608	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0055574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	66	264	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.234769543298566	1	FACETS	0.835	0.728	0.949	0.835	0.728	0.949	CLONAL	1	TRUE	0	0.35210560780667	1		264	370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579328	7579328	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	144	762	0	ENST00000269305.4:c.359A>G	p.Lys120Arg	p.K120R	ENST00000269305	NM_001126112.2	120	aAg/aGg	4/11	0.35210560780667	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.35210560780667	1		762	613	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462178	120462178	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	53	657	0	ENST00000256646.2:c.5538T>G	p.Asp1846Glu	p.D1846E	ENST00000256646	NM_024408.3	1846	gaT/gaG	31/34	0.35210560780667	1	FACETS	0.411	0.35	0.478	0.411	0.35	0.478	SUBCLONAL	1	TRUE	0	0.35210560780667	1		657	604	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040675	47040680	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	ACTACC	ACTACC	-	novel	NA	P-0055574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	122	486	0	ENST00000377604.3:c.1311_1316del	p.Tyr437_Gln439delinsTer	p.Y437_Q439delins*	ENST00000377604	NM_001204468.1	437	tACTACCaa/taa	13/24	1	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.35210560780667	1		486	433	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0055577-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	46	378	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.785	0.663	0.92	0.785	0.663	0.92	CLONAL	1	TRUE	1	0.293611201665565	2		378	399	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392668	118392668	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055577-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	70	307	0	ENST00000534358.1:c.11700G>T	p.Met3900Ile	p.M3900I	ENST00000534358	NM_005933.3	3900	atG/atT	36/36	0.293611201665565	4	FACETS	1	0.908	1			1	CLONAL	1	TRUE	NA	0.293611201665565	4		307	587	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912238	32912238	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055577-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	73	553	0	ENST00000380152.3:c.3746A>G	p.Glu1249Gly	p.E1249G	ENST00000380152		1249	gAg/gGg	11/27	1	2	FACETS	0.807	0.706	0.916	0.807	0.706	0.916	CLONAL	1	TRUE	1	0.293611201665565	2		553	616	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207162	1207162	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs137853076	NA	P-0055577-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	253	354	0	ENST00000326873.7:c.250A>T	p.Lys84Ter	p.K84*	ENST00000326873	NM_000455.4	84	Aag/Tag	1/10	0.293611201665565	5	FACETS	1	0.97	1			1	CLONAL	2	TRUE	NA	0.293611201665565	5		354	1169	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597490	10597491	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0055577-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	152	239	0	ENST00000171111.5:c.1712_1713delinsTT	p.Gly571Val	p.G571V	ENST00000171111	NM_203500.1	571	gGC/gTT	6/6	0.293611201665565	6	FACETS	1	0.976	1	0.588	0.539	0.639	CLONAL	2	TRUE	2	0.293611201665565	6		239	699	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843252	128843252	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055577-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	115	527	0	ENST00000249373.3:c.359C>G	p.Ala120Gly	p.A120G	ENST00000249373	NM_005631.4	120	gCa/gGa	2/12	1	2	FACETS	0.831	0.747	0.919	0.831	0.747	0.919	CLONAL	1	TRUE	1	0.293611201665565	2		527	943	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181227	123181227	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055577-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	70	156	0	ENST00000218089.9:c.691G>A	p.Val231Met	p.V231M	ENST00000218089	NM_001042749.1	231	Gtg/Atg	9/35	0.240006480426832	2	FACETS	0.987	0.883	1			1	CLONAL	3	TRUE	NA	0.293611201665565	2		156	161	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522551	176522551	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	259	865	0	ENST00000292408.4:c.1648G>C	p.Val550Leu	p.V550L	ENST00000292408	NM_213647.1	550	Gtg/Ctg	13/18	0.552487705127135	3	FACETS	1	0.99	1	0.641	0.601	0.682	CLONAL	1	TRUE	1	0.552487705127135	3		865	933	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244302	153244302	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0055580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	70	210	0	ENST00000281708.4:c.1856-1G>C		p.X619_splice	ENST00000281708	NM_033632.3	619			1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.552487705127135	2		210	248	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671672	30671672	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	326	730	0	ENST00000376406.3:c.5288C>A	p.Ala1763Glu	p.A1763E	ENST00000376406	NM_014641.2	1763	gCa/gAa	10/15	0.451798049493119	3	FACETS	0.967	0.918	1	0.967	0.918	1	CLONAL	2	TRUE	1	0.552487705127135	3		730	779	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674236	117674236	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	169	506	0	ENST00000368508.3:c.4238del	p.Gly1413GlufsTer9	p.G1413Efs*9	ENST00000368508	NM_002944.2	1413	gGa/ga	26/43	1	2	FACETS	0.727	0.669	0.788	0.727	0.669	0.788	SUBCLONAL	1	TRUE	1	0.552487705127135	2		506	841	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0055587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	97	215	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.284346378376761	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.284346378376761	1		215	494	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885835	59885836	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0055587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	75	434	0	ENST00000259008.2:c.910_911delinsTT	p.Gly304Leu	p.G304L	ENST00000259008	NM_032043.2	304	GGg/TTg	7/20	1	2	FACETS	0.917	0.805	1	0.917	0.805	1	CLONAL	1	TRUE	1	0.284346378376761	2		434	575	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214408	55214408	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	118	640	0	ENST00000275493.2:c.534G>T	p.Met178Ile	p.M178I	ENST00000275493	NM_005228.3	178	atG/atT	4/28	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.284346378376761	2		640	744	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135777003	135777003	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	355	517	0	ENST00000298552.3:c.2475G>T	p.Glu825Asp	p.E825D	ENST00000298552	NM_001162426.1	825	gaG/gaT	19/23	0.254709126804552	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	0	0.284346378376761	3		517	891	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0055599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	175	550	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.470752213951843	2		550	704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0055599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	216	684	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.470752213951843	1	FACETS	0.972	0.907	1	0.972	0.907	1	CLONAL	1	TRUE	0	0.470752213951843	1		685	722	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696462	47696462	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	103	376	0	ENST00000347630.2:c.361C>G	p.Arg121Gly	p.R121G	ENST00000347630	NM_001007230.1	121	Cgg/Ggg	6/11	0.470752213951843	1	FACETS	0.917	0.828	1	0.917	0.828	1	CLONAL	1	TRUE	0	0.470752213951843	1		376	365	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0055599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	54	310	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.726	0.624	0.836	0.726	0.624	0.836	SUBCLONAL	1	TRUE	1	0.470752213951843	2		310	316	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944258	81944258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750403828	NA	P-0055599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	219	659	0	ENST00000359376.3:c.1867C>T	p.Arg623Cys	p.R623C	ENST00000359376	NM_002661.3	623	Cgc/Tgc	18/33	0.470752213951843	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.470752213951843	1		659	700	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916947	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATCCTCAATCGAGAA	novel	NA	P-0055599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	76	341	0	ENST00000263967.3:c.336_350dup	p.Leu113_Ile117dup	p.L113_I117dup	ENST00000263967	NM_006218.2	113	-/ATCCTCAATCGAGAA	2/21	0.187559223931436	4	FACETS	1	0.932	1	0.543	0.478	0.613	INDETERMINATE	1	TRUE	2	0.470752213951843	4		341	437	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713823	30713823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	55	672	1	ENST00000295754.5:c.1148C>T	p.Ser383Phe	p.S383F	ENST00000295754	NM_003242.5	383	tCc/tTc	4/7	1	2	FACETS	0.957	0.817	1	0.957	0.817	1	CLONAL	1	TRUE	1	0.14	2		673	821	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750566	57750568	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	rs764901947	NA	P-0055600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	27	373	0	ENST00000274289.3:c.1900_1902del	p.Ile634del	p.I634del	ENST00000274289	NM_006622.3	634	ATC/-	14/14	1	2	FACETS	0.738	0.585	0.912	0.738	0.585	0.912	CLONAL	1	TRUE	1	0.14	2		373	523	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146404	185146404	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	25	322	0	ENST00000265026.3:c.35C>G	p.Ser12Cys	p.S12C	ENST00000265026	NM_004721.4	12	tCt/tGt	2/14	1	2	FACETS	1	0.806	1	1	0.806	1	CLONAL	1	TRUE	1	0.14	2		322	349	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566054	141566054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	45	689	0	ENST00000220592.5:c.1210G>A	p.Glu404Lys	p.E404K	ENST00000220592	NM_012154.3	404	Gag/Aag	10/19	1	2	FACETS	0.865	0.725	1	0.865	0.725	1	CLONAL	1	TRUE	1	0.14	2		689	743	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0055602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	388	550	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.578459781817778	2	FACETS	0.845	0.81	0.88	0.845	0.81	0.88	CLONAL	2	TRUE	0	0.633903803780545	2		550	724	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0055602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	102	390	1				ENST00000310581	NM_198253.2	-/1132			0.313094585317664	1	FACETS	0.555	0.5	0.613	0.555	0.5	0.613	INDETERMINATE	1	TRUE	0	0.633903803780545	1		391	396	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955489	90955489	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1421870412	NA	P-0055602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	177	447	0	ENST00000265433.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000265433	NM_002485.4	726	Gaa/Aaa	14/16	0.313094585317664	1	FACETS	0.757	0.703	0.812	0.757	0.703	0.812	INDETERMINATE	1	TRUE	0	0.633903803780545	1		447	504	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546655	9546655	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	227	485	0	ENST00000353224.5:c.1367G>A	p.Gly456Glu	p.G456E	ENST00000353224	NM_177990.2	456	gGg/gAg	5/10	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.633903803780545	2		485	706	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918195	50918195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	383	996	1	ENST00000440232.2:c.2512C>T	p.Pro838Ser	p.P838S	ENST00000440232	NM_002691.3	838	Ccc/Tcc	20/27	0.313094585317664	1	FACETS	0.821	0.782	0.861	0.821	0.782	0.861	INDETERMINATE	1	TRUE	0	0.633903803780545	1		997	1005	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486155	8486155	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	199	465	0	ENST00000356435.5:c.2662G>A	p.Gly888Arg	p.G888R	ENST00000356435		888	Gga/Aga	17/35	0.632111911860099	1	FACETS	0.949	0.889	1	0.949	0.889	1	CLONAL	1	TRUE	0	0.633903803780545	1		465	452	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152054	55152054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	154	605	0	ENST00000257290.5:c.2486G>A	p.Gly829Glu	p.G829E	ENST00000257290	NM_006206.4	829	gGa/gAa	18/23	0.313094585317664	1	FACETS	0.469	0.43	0.509	0.469	0.43	0.509	INDETERMINATE	1	TRUE	0	0.633903803780545	1		605	708	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212484000	212484000	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1369649105	NA	P-0055602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	50	354	0	ENST00000342788.4:c.2203G>A	p.Gly735Ser	p.G735S	ENST00000342788	NM_005235.2	735	Ggt/Agt	19/28	0.313094585317664	1	FACETS	0.306	0.26	0.356	0.306	0.26	0.356	INDETERMINATE	1	TRUE	0	0.633903803780545	1		354	352	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832062	72832062	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	377	602	1	ENST00000268489.5:c.4519G>A	p.Gly1507Ser	p.G1507S	ENST00000268489	NM_006885.3	1507	Ggc/Agc	9/10	0.249876752057262	3	FACETS	0.817	0.778	0.856			1	INDETERMINATE	2	TRUE	NA	0.633903803780545	3		603	959	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8246257	8246257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	189	433	0	ENST00000335790.3:c.377G>A	p.Gly126Glu	p.G126E	ENST00000335790	NM_002315.2	126	gGa/gAa	4/4	0.313094585317664	1	FACETS	0.878	0.82	0.937	0.878	0.82	0.937	INDETERMINATE	1	TRUE	0	0.633903803780545	1		433	464	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631614	119631614	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	154	330	1	ENST00000316626.5:c.652T>G	p.Cys218Gly	p.C218G	ENST00000316626		218	Tgt/Ggt	6/12	0.604362072631878	1	FACETS	0.93	0.863	0.997	0.93	0.863	0.997	CLONAL	1	TRUE	0	0.633903803780545	1		331	357	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673394	30673394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	405	765	1	ENST00000376406.3:c.3566G>A	p.Gly1189Glu	p.G1189E	ENST00000376406	NM_014641.2	1189	gGa/gAa	10/15	0.313094585317664	1	FACETS	0.822	0.784	0.86	0.822	0.784	0.86	INDETERMINATE	1	TRUE	0	0.633903803780545	1		766	1062	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	10	264	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.85	0.577	1	0.85	0.577	1	CLONAL	1	TRUE	1	0.14	2		264	168	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	15	427	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.719	0.525	0.953	0.719	0.525	0.953	CLONAL	1	TRUE	1	0.14	2		429	298	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176540	56176540	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1305030339	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	30	405	0	ENST00000399503.3:c.2090G>A	p.Arg697His	p.R697H	ENST00000399503	NM_005921.1	697	cGc/cAc	12/20	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.14	2		405	369	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261155	16261155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1032279699	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	43	512	0	ENST00000375759.3:c.8420G>A	p.Arg2807His	p.R2807H	ENST00000375759	NM_015001.2	2807	cGt/cAt	11/15	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.14	2		512	556	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606679	29606679	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs865931787	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	27	521	1	ENST00000389048.3:c.1201C>T	p.Arg401Ter	p.R401*	ENST00000389048	NM_004304.4	401	Cga/Tga	5/29	1	2	FACETS	0.622	0.493	0.77	0.622	0.493	0.77	SUBCLONAL	1	TRUE	1	0.14	2		522	620	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	75	629	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.955	0.838	1	1	0.982	1	CLONAL	2	TRUE	1	0.14	2		629	561	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193205453	193205453	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1199579887	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	25	388	1	ENST00000367435.3:c.1384C>T	p.Pro462Ser	p.P462S	ENST00000367435	NM_024529.4	462	Cct/Tct	15/17	1	2	FACETS	0.729	0.573	0.909	0.729	0.573	0.909	CLONAL	1	TRUE	1	0.14	2		389	490	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	40	484	1	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	0.94	0.78	1	0.94	0.78	1	CLONAL	1	TRUE	1	0.14	2		485	608	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	17	338	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	1	0.756	1	1	0.756	1	CLONAL	1	TRUE	1	0.14	2		338	240	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030232	180030232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371358529	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	45	803	0	ENST00000261937.6:c.4052C>T	p.Pro1351Leu	p.P1351L	ENST00000261937	NM_182925.4	1351	cCg/cTg	30/30	1	2	FACETS	0.804	0.673	0.948	0.804	0.673	0.948	CLONAL	1	TRUE	1	0.14	2		803	800	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332915	153332915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200698994	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	24	413	0	ENST00000281708.4:c.41G>A	p.Arg14Gln	p.R14Q	ENST00000281708	NM_033632.3	14	cGa/cAa	2/12	1	2	FACETS	0.803	0.629	1	0.803	0.629	1	CLONAL	1	TRUE	1	0.14	2		413	427	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	39	488	1	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.14	2		489	400	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584500	189584500	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	15	335	1	ENST00000264731.3:c.796C>T	p.Arg266Ter	p.R266*	ENST00000264731	NM_003722.4	266	Cga/Tga	6/14	1	2	FACETS	0.864	0.632	1	0.864	0.632	1	CLONAL	1	TRUE	1	0.14	2		336	248	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	8	325	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.534	0.343	0.782	0.534	0.343	0.782	SUBCLONAL	1	TRUE	1	0.14	2		325	214	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258036	123258036	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519045	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	8	508	0	ENST00000358487.5:c.1645A>C	p.Asn549His	p.N549H	ENST00000358487	NM_000141.4	549	Aat/Cat	12/18	1	2	FACETS	0.325	0.208	0.477	0.325	0.208	0.477	SUBCLONAL	1	TRUE	1	0.14	2		508	352	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10267124	10267124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751093624	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	41	535	1	ENST00000340748.4:c.1294G>A	p.Glu432Lys	p.E432K	ENST00000340748		432	Gaa/Aaa	17/40	1	2	FACETS	0.921	0.766	1	0.921	0.766	1	CLONAL	1	TRUE	1	0.14	2		536	636	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259389	89259389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	17	471	0	ENST00000336596.2:c.533G>A	p.Gly178Glu	p.G178E	ENST00000336596	NM_005233.5	178	gGa/gAa	3/17	1	2	FACETS	0.738	0.55	0.962	0.738	0.55	0.962	CLONAL	1	TRUE	1	0.14	2		471	329	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993828	72993828	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371922710	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	21	565	0	ENST00000268489.5:c.217G>A	p.Glu73Lys	p.E73K	ENST00000268489	NM_006885.3	73	Gag/Aag	2/10	1	2	FACETS	0.787	0.606	1	0.787	0.606	1	CLONAL	1	TRUE	1	0.14	2		565	381	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476382	88476382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	28	561	0	ENST00000360948.2:c.1750G>A	p.Asp584Asn	p.D584N	ENST00000360948	NM_001012338.2	584	Gat/Aat	15/19	1	2	FACETS	0.729	0.581	0.898	0.729	0.581	0.898	SUBCLONAL	1	TRUE	1	0.14	2		561	549	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156729	106156729	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1440692352	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	21	361	2	ENST00000380013.4:c.1630C>T	p.Arg544Ter	p.R544*	ENST00000380013	NM_001127208.2	544	Cga/Tga	3/11	1	2	FACETS	0.779	0.599	0.99	0.779	0.599	0.99	CLONAL	1	TRUE	1	0.14	2		363	385	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155467	106155467	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773565437	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	17	362	0	ENST00000380013.4:c.368G>A	p.Arg123His	p.R123H	ENST00000380013	NM_001127208.2	123	cGt/cAt	3/11	1	2	FACETS	0.87	0.65	1	0.87	0.65	1	CLONAL	1	TRUE	1	0.14	2		362	279	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	47	734	1	ENST00000267101.3:c.273G>T	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atT	3/28	1	2	FACETS	0.9	0.758	1	0.9	0.758	1	CLONAL	1	TRUE	1	0.14	2		735	746	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692940	89692940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746152219	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	17	533	0	ENST00000371953.3:c.424C>T	p.Arg142Trp	p.R142W	ENST00000371953	NM_000314.4	142	Cgg/Tgg	5/9	1	2	FACETS	0.719	0.535	0.937	0.719	0.535	0.937	CLONAL	1	TRUE	1	0.14	2		533	338	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796804	135796804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223799508	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	13	303	0	ENST00000298552.3:c.683G>A	p.Arg228Gln	p.R228Q	ENST00000298552	NM_001162426.1	228	cGa/cAa	8/23	1	2	FACETS	0.731	0.521	0.988	0.731	0.521	0.988	CLONAL	1	TRUE	1	0.14	2		303	254	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260624	1260624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199422305	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	53	689	1	ENST00000310581.5:c.2935C>T	p.Arg979Trp	p.R979W	ENST00000310581	NM_198253.2	979	Cgg/Tgg	12/16	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.14	2		690	735	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175871	24175871	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	37	547	0	ENST00000263121.7:c.1099G>A	p.Asp367Asn	p.D367N	ENST00000263121	NM_003073.3	367	Gac/Aac	8/9	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.14	2		547	494	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157635	106157635	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	13	250	0	ENST00000380013.4:c.2536G>T	p.Glu846Ter	p.E846*	ENST00000380013	NM_001127208.2	846	Gaa/Taa	3/11	1	2	FACETS	1	0.827	1	1	0.827	1	CLONAL	1	TRUE	1	0.14	2		250	150	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557912	21557912	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757472527	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	20	483	1	ENST00000382592.4:c.1933C>T	p.Arg645Trp	p.R645W	ENST00000382592	NM_014572.2	645	Cgg/Tgg	5/8	1	2	FACETS	0.807	0.617	1	0.807	0.617	1	CLONAL	1	TRUE	1	0.14	2		484	354	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317623	163317623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747173543	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	20	266	0	ENST00000271452.3:c.1019C>T	p.Ser340Leu	p.S340L	ENST00000271452	NM_145697.2	340	tCg/tTg	12/14	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.14	2		266	210	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59793411	59793411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375082407	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	18	407	0	ENST00000259008.2:c.2393G>A	p.Arg798Gln	p.R798Q	ENST00000259008	NM_032043.2	798	cGa/cAa	17/20	1	2	FACETS	1	0.763	1	1	0.763	1	CLONAL	1	TRUE	1	0.14	2		407	254	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395478	116395478	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45602940	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	16	440	0	ENST00000397752.3:c.1771C>T	p.Arg591Trp	p.R591W	ENST00000397752	NM_000245.2	591	Cgg/Tgg	6/21	1	2	FACETS	0.735	0.543	0.965	0.735	0.543	0.965	CLONAL	1	TRUE	1	0.14	2		440	311	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021818	71021818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869025203	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	13	199	0	ENST00000318789.4:c.1540C>T	p.Arg514Cys	p.R514C	ENST00000318789	NM_032682.5	514	Cgt/Tgt	18/21	1	2	FACETS	1	0.718	1	1	0.718	1	CLONAL	1	TRUE	1	0.14	2		199	185	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395569	116395569	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs375951814	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	17	378	0	ENST00000397752.3:c.1862C>T	p.Thr621Ile	p.T621I	ENST00000397752	NM_000245.2	621	aCa/aTa	6/21	1	2	FACETS	0.995	0.744	1	0.995	0.744	1	CLONAL	1	TRUE	1	0.14	2		378	244	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2090156	2090156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148474733	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	53	922	4	ENST00000219066.1:c.793G>A	p.Ala265Thr	p.A265T	ENST00000219066	NM_002528.5	265	Gcc/Acc	5/6	1	2	FACETS	0.861	0.732	1	0.861	0.732	1	CLONAL	1	TRUE	1	0.14	2		926	879	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41962101	41962101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	15	390	0	ENST00000219905.7:c.1009G>A	p.Asp337Asn	p.D337N	ENST00000219905	NM_001164273.1	337	Gat/Aat	2/24	1	2	FACETS	0.785	0.574	1	0.785	0.574	1	CLONAL	1	TRUE	1	0.14	2		390	273	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349196	15349196	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	21	377	0	ENST00000263377.2:c.4081C>A	p.Leu1361Ile	p.L1361I	ENST00000263377	NM_058243.2	1361	Ctt/Att	20/20	1	2	FACETS	0.826	0.636	1	0.826	0.636	1	CLONAL	1	TRUE	1	0.14	2		377	363	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860908	151860908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	13	309	0	ENST00000262189.6:c.9754C>T	p.Arg3252Cys	p.R3252C	ENST00000262189	NM_170606.2	3252	Cgt/Tgt	43/59	1	2	FACETS	0.957	0.684	1	0.957	0.684	1	CLONAL	1	TRUE	1	0.14	2		309	194	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457674	67457674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749178459	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	39	677	2	ENST00000327367.4:c.484G>A	p.Glu162Lys	p.E162K	ENST00000327367	NM_005902.3	162	Gaa/Aaa	3/9	1	2	FACETS	0.757	0.626	0.904	0.757	0.626	0.904	CLONAL	1	TRUE	1	0.14	2		679	736	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281756	49281756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	37	742	0	ENST00000282018.3:c.803C>T	p.Thr268Ile	p.T268I	ENST00000282018	NM_020377.2	268	aCc/aTc	1/1	1	2	FACETS	0.822	0.676	0.986	0.822	0.676	0.986	CLONAL	1	TRUE	1	0.14	2		742	643	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257889	19257889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1482048547	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	44	988	1	ENST00000162023.5:c.497G>A	p.Arg166His	p.R166H	ENST00000162023		166	cGc/cAc	9/13	1	2	FACETS	0.748	0.625	0.885	0.748	0.625	0.885	SUBCLONAL	1	TRUE	1	0.14	2		989	840	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752361	57752361	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	17	414	0	ENST00000274289.3:c.1212G>T	p.Lys404Asn	p.K404N	ENST00000274289	NM_006622.3	404	aaG/aaT	9/14	1	2	FACETS	1	0.818	1	1	0.818	1	CLONAL	1	TRUE	1	0.14	2		414	217	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38616972	38616972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764823722	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	10	317	1	ENST00000299084.4:c.385G>A	p.Glu129Lys	p.E129K	ENST00000299084	NM_152594.2	129	Gaa/Aaa	4/7	1	2	FACETS	0.725	0.491	1	0.725	0.491	1	CLONAL	1	TRUE	1	0.14	2		318	197	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206852	102206852	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	16	332	0	ENST00000263464.3:c.1480G>T	p.Glu494Ter	p.E494*	ENST00000263464	NM_001165.4	494	Gaa/Taa	7/9	1	2	FACETS	0.859	0.635	1	0.859	0.635	1	CLONAL	1	TRUE	1	0.14	2		332	266	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43730553	43730553	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	36	530	0	ENST00000382044.4:c.3160C>T	p.Arg1054Ter	p.R1054*	ENST00000382044	NM_001141980.1	1054	Cga/Tga	16/28	1	2	FACETS	0.915	0.751	1	0.915	0.751	1	CLONAL	1	TRUE	1	0.14	2		530	562	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158369	106158369	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	13	263	0	ENST00000380013.4:c.3270G>T	p.Lys1090Asn	p.K1090N	ENST00000380013	NM_001127208.2	1090	aaG/aaT	3/11	1	2	FACETS	0.837	0.597	1	0.837	0.597	1	CLONAL	1	TRUE	1	0.14	2		263	222	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351577	89351577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778960311	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	52	903	0	ENST00000301030.4:c.1373G>A	p.Arg458Gln	p.R458Q	ENST00000301030	NM_001256183.1	458	cGa/cAa	9/13	1	2	FACETS	0.76	0.644	0.887	0.76	0.644	0.887	SUBCLONAL	1	TRUE	1	0.14	2		903	978	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073826	8073826	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	11	313	0	ENST00000377482.5:c.833A>G	p.Glu278Gly	p.E278G	ENST00000377482	NM_018948.3	278	gAa/gGa	4/4	1	2	FACETS	0.759	0.524	1	0.759	0.524	1	CLONAL	1	TRUE	1	0.14	2		313	207	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812597	43812597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754296556	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	24	576	1	ENST00000372470.3:c.1300G>A	p.Asp434Asn	p.D434N	ENST00000372470	NM_005373.2	434	Gac/Aac	8/12	1	2	FACETS	0.719	0.562	0.9	0.719	0.562	0.9	SUBCLONAL	1	TRUE	1	0.14	2		577	477	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63662043	63662043	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	27	412	0	ENST00000279873.7:c.147G>T	p.Lys49Asn	p.K49N	ENST00000279873	NM_032199.2	49	aaG/aaT	2/10	1	2	FACETS	0.799	0.634	0.987	0.799	0.634	0.987	CLONAL	1	TRUE	1	0.14	2		412	483	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624270	89624271	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	18	375	0	ENST00000371953.3:c.47_48dup	p.Gln17IlefsTer8	p.Q17Ifs*8	ENST00000371953	NM_000314.4	15	aga/agATa	1/9	1	2	FACETS	0.777	0.584	1	0.777	0.584	1	CLONAL	1	TRUE	1	0.14	2		375	331	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741439	17741439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369671991	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	52	818	1	ENST00000250003.3:c.110C>T	p.Ser37Phe	p.S37F	ENST00000250003	NM_002478.4	37	tCc/tTc	1/3	1	2	FACETS	0.914	0.776	1	0.914	0.776	1	CLONAL	1	TRUE	1	0.14	2		819	813	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505413	125505413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1255118863	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	14	315	0	ENST00000428830.2:c.703G>A	p.Asp235Asn	p.D235N	ENST00000428830	NM_001114121.2	235	Gat/Aat	7/14	1	2	FACETS	0.93	0.673	1	0.93	0.673	1	CLONAL	1	TRUE	1	0.14	2		315	215	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50481150	50481150	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	21	360	0	ENST00000394963.4:c.536A>G	p.Lys179Arg	p.K179R	ENST00000394963	NM_003076.4	179	aAa/aGa	5/13	1	2	FACETS	0.723	0.556	0.919	0.723	0.556	0.919	CLONAL	1	TRUE	1	0.14	2		360	415	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235923	133235923	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	29	625	0	ENST00000320574.5:c.3233A>G	p.Tyr1078Cys	p.Y1078C	ENST00000320574	NM_006231.2	1078	tAc/tGc	26/49	1	2	FACETS	0.717	0.574	0.88	0.717	0.574	0.88	SUBCLONAL	1	TRUE	1	0.14	2		625	578	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950818	32950818	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	19	305	0	ENST00000380152.3:c.8644A>C	p.Lys2882Gln	p.K2882Q	ENST00000380152		2882	Aaa/Caa	21/27	1	2	FACETS	0.862	0.654	1	0.862	0.654	1	CLONAL	1	TRUE	1	0.14	2		305	315	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134885	41134885	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	27	434	0	ENST00000379561.5:c.743A>C	p.Lys248Thr	p.K248T	ENST00000379561	NM_002015.3	248	aAa/aCa	2/3	1	2	FACETS	1	0.799	1	1	0.799	1	CLONAL	1	TRUE	1	0.14	2		434	384	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582112	95582112	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	14	323	0	ENST00000393063.1:c.1799A>G	p.Asp600Gly	p.D600G	ENST00000393063	NM_030621.3	600	gAc/gGc	12/28	1	2	FACETS	0.743	0.537	0.994	0.743	0.537	0.994	CLONAL	1	TRUE	1	0.14	2		323	269	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95599690	95599690	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	17	361	0	ENST00000393063.1:c.106G>T	p.Ala36Ser	p.A36S	ENST00000393063	NM_030621.3	36	Gca/Tca	3/28	1	2	FACETS	0.723	0.539	0.942	0.723	0.539	0.942	CLONAL	1	TRUE	1	0.14	2		361	336	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135019	2135019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1468281970	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	46	801	0	ENST00000219476.3:c.4561C>T	p.Pro1521Ser	p.P1521S	ENST00000219476	NM_000548.3	1521	Ccc/Tcc	35/42	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.14	2		801	619	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984572	72984572	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	48	904	1	ENST00000268489.5:c.3012G>T	p.Lys1004Asn	p.K1004N	ENST00000268489	NM_006885.3	1004	aaG/aaT	3/10	1	2	FACETS	0.785	0.661	0.921	0.785	0.661	0.921	CLONAL	1	TRUE	1	0.14	2		905	874	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234585	41234585	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs761640584	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	19	457	0	ENST00000357654.3:c.4193A>G	p.Asp1398Gly	p.D1398G	ENST00000357654	NM_007294.3	1398	gAt/gGt	12/23	1	2	FACETS	0.765	0.58	0.983	0.765	0.58	0.983	CLONAL	1	TRUE	1	0.14	2		457	355	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47700169	47700169	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	29	370	0	ENST00000347630.2:c.4T>C	p.Ser2Pro	p.S2P	ENST00000347630	NM_001007230.1	2	Tca/Cca	3/11	1	2	FACETS	0.771	0.618	0.947	0.771	0.618	0.947	CLONAL	1	TRUE	1	0.14	2		370	537	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761462	59761462	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	19	432	0	ENST00000259008.2:c.2945A>C	p.Lys982Thr	p.K982T	ENST00000259008	NM_032043.2	982	aAa/aCa	20/20	1	2	FACETS	0.838	0.636	1	0.838	0.636	1	CLONAL	1	TRUE	1	0.14	2		432	324	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2214495	2214495	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	41	768	0	ENST00000398665.3:c.1823A>C	p.Gln608Pro	p.Q608P	ENST00000398665	NM_032482.2	608	cAg/cCg	19/28	1	2	FACETS	0.786	0.653	0.935	0.786	0.653	0.935	CLONAL	1	TRUE	1	0.14	2		768	745	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630351	47630351	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	33	629	0	ENST00000233146.2:c.21G>T	p.Glu7Asp	p.E7D	ENST00000233146	NM_000251.2	7	gaG/gaT	1/16	1	2	FACETS	0.773	0.628	0.937	0.773	0.628	0.937	CLONAL	1	TRUE	1	0.14	2		629	610	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622678	158622678	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	11	342	0	ENST00000263640.3:c.821A>C	p.His274Pro	p.H274P	ENST00000263640	NM_001105.4	274	cAc/cCc	8/11	1	2	FACETS	0.763	0.527	1	0.763	0.527	1	CLONAL	1	TRUE	1	0.14	2		342	206	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958153	54958153	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	25	443	0	ENST00000312783.6:c.454G>T	p.Glu152Ter	p.E152*	ENST00000312783	NM_198436.1	152	Gaa/Taa	6/10	1	2	FACETS	0.825	0.649	1	0.825	0.649	1	CLONAL	1	TRUE	1	0.14	2		443	433	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574637	41574637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145312648	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	48	915	2	ENST00000263253.7:c.6922C>T	p.Arg2308Cys	p.R2308C	ENST00000263253	NM_001429.3	2308	Cgc/Tgc	31/31	1	2	FACETS	0.784	0.66	0.92	0.784	0.66	0.92	CLONAL	1	TRUE	1	0.14	2		917	875	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940495	49940495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	57	838	0	ENST00000296474.3:c.548G>A	p.Gly183Asp	p.G183D	ENST00000296474	NM_002447.2	183	gGc/gAc	1/20	1	2	FACETS	0.988	0.846	1	0.988	0.846	1	CLONAL	1	TRUE	1	0.14	2		838	824	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946209	55946209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	29	407	0	ENST00000263923.4:c.3970G>A	p.Ala1324Thr	p.A1324T	ENST00000263923	NM_002253.2	1324	Gca/Aca	30/30	1	2	FACETS	0.819	0.656	1	0.819	0.656	1	CLONAL	1	TRUE	1	0.14	2		407	506	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542839	187542839	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	19	431	0	ENST00000441802.2:c.4901A>G	p.Asp1634Gly	p.D1634G	ENST00000441802	NM_005245.3	1634	gAt/gGt	10/27	1	2	FACETS	0.956	0.726	1	0.956	0.726	1	CLONAL	1	TRUE	1	0.14	2		431	284	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549319	187549319	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763980330	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	42	522	0	ENST00000441802.2:c.4799C>T	p.Ser1600Leu	p.S1600L	ENST00000441802	NM_005245.3	1600	tCg/tTg	9/27	1	2	FACETS	0.98	0.817	1	0.98	0.817	1	CLONAL	1	TRUE	1	0.14	2		522	612	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627950	187627950	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	36	625	0	ENST00000441802.2:c.3032C>A	p.Ser1011Tyr	p.S1011Y	ENST00000441802	NM_005245.3	1011	tCt/tAt	2/27	1	2	FACETS	0.89	0.73	1	0.89	0.73	1	CLONAL	1	TRUE	1	0.14	2		625	578	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294020	1294020	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	71	1017	1	ENST00000310581.5:c.981G>T	p.Glu327Asp	p.E327D	ENST00000310581	NM_198253.2	327	gaG/gaT	2/16	1	2	FACETS	0.996	0.867	1	0.996	0.867	1	CLONAL	1	TRUE	1	0.14	2		1018	1018	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923646	131923646	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1441242803	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	11	238	0	ENST00000265335.6:c.916G>T	p.Asp306Tyr	p.D306Y	ENST00000265335		306	Gac/Tac	7/25	1	2	FACETS	0.935	0.648	1	0.935	0.648	1	CLONAL	1	TRUE	1	0.14	2		238	168	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519650	137519650	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs372635142	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	25	325	0	ENST00000367739.4:c.988A>G	p.Thr330Ala	p.T330A	ENST00000367739	NM_000416.2	330	Aca/Gca	7/7	1	2	FACETS	1	0.826	1	1	0.826	1	CLONAL	1	TRUE	1	0.14	2		325	339	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192483	138192483	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs749663550	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	21	329	0	ENST00000237289.4:c.119T>G	p.Phe40Cys	p.F40C	ENST00000237289	NM_001270507.1	40	tTt/tGt	2/9	1	2	FACETS	0.826	0.636	1	0.826	0.636	1	CLONAL	1	TRUE	1	0.14	2		329	363	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334783	81334783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	16	373	0	ENST00000222390.5:c.1933C>T	p.His645Tyr	p.H645Y	ENST00000222390	NM_000601.4	645	Cat/Tat	17/18	1	2	FACETS	0.754	0.557	0.991	0.754	0.557	0.991	CLONAL	1	TRUE	1	0.14	2		373	303	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285474	38285474	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	52	657	0	ENST00000425967.3:c.679G>T	p.Glu227Ter	p.E227*	ENST00000425967	NM_001174067.1	227	Gaa/Taa	6/19	1	2	FACETS	0.9	0.765	1	0.9	0.765	1	CLONAL	1	TRUE	1	0.14	2		657	825	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793256	139793256	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	44	818	0	ENST00000247668.2:c.64A>G	p.Thr22Ala	p.T22A	ENST00000247668	NM_021138.3	22	Acc/Gcc	2/11	1	2	FACETS	0.784	0.655	0.927	0.784	0.655	0.927	CLONAL	1	TRUE	1	0.14	2		818	802	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937106	39937106	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	42	745	0	ENST00000378444.4:c.77G>A	p.Ser26Asn	p.S26N	ENST00000378444	NM_001123385.1	26	aGc/aAc	2/15	1	2	FACETS	0.733	0.61	0.87	0.733	0.61	0.87	SUBCLONAL	1	TRUE	1	0.14	2		745	819	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845338	76845338	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs782333013	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	15	372	0	ENST00000373344.5:c.6183G>T	p.Lys2061Asn	p.K2061N	ENST00000373344	NM_000489.3	2061	aaG/aaT	27/35	1	2	FACETS	1	0.744	1	1	0.744	1	CLONAL	1	TRUE	1	0.14	2		372	211	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938419	76938419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	20	594	1	ENST00000373344.5:c.2329G>T	p.Gly777Ter	p.G777*	ENST00000373344	NM_000489.3	777	Gga/Tga	9/35	1	2	FACETS	0.803	0.613	1	0.803	0.613	1	CLONAL	1	TRUE	1	0.14	2		595	356	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0055604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	18	219	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.751	0.577	0.947	1	0.912	1	CLONAL	2	TRUE	1	0.278775372483595	2		219	86	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0055604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	8	391	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.709	0.461	1	0.709	0.461	1	CLONAL	1	TRUE	1	0.278775372483595	2		391	81	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024574	14024574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143479220	NA	P-0055604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	12	271	0	ENST00000311895.7:c.800G>A	p.Arg267His	p.R267H	ENST00000311895	NM_005236.2	267	cGc/cAc	5/11	0.157867496828157	3	FACETS	0.925	0.656	1	0.308	0.218	0.417	INDETERMINATE	1	TRUE	0	0.278775372483595	3		271	106	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160660	56160661	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	76	351	0	ENST00000399503.3:c.935dup	p.Met312IlefsTer14	p.M312Ifs*14	ENST00000399503	NM_005921.1	312	atg/aTtg	4/20	0.278775372483595	5	FACETS	1	0.96	1	1	0.96	1	CLONAL	3	TRUE	2	0.278775372483595	5		351	221	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176620	56176621	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0055604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	21	320	0	ENST00000399503.3:c.2171_2172dup	p.Lys725Ter	p.K725*	ENST00000399503	NM_005921.1	724	cta/cTAta	12/20	0.278775372483595	5	FACETS	0.862	0.672	1	0.574	0.448	0.717	CLONAL	2	TRUE	2	0.278775372483595	5		320	124	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0055605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	40	319	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	1	0.92	1	1	0.972	1	CLONAL	2	TRUE	1	0.13	2		319	262	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63816929	63816930	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0055605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	15	196	1	ENST00000279873.7:c.906dup	p.Val303SerfsTer4	p.V303Sfs*4	ENST00000279873	NM_032199.2	300	-/A	6/10	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.13	2		197	157	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0055605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	33	532	2	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.958	0.784	1	1	0.96	1	CLONAL	2	TRUE	1	0.13	2		534	265	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	52	385	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	0.376351076692616	1	FACETS	0.921	0.795	1	1	0.983	1	CLONAL	4	TRUE	0	0.13	1		385	203	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0055605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	29	392	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.86	0.697	1	1	0.964	1	CLONAL	3	TRUE	1	0.13	2		392	173	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0055605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	67	776	2	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.895	0.781	1	1	0.984	1	CLONAL	3	TRUE	1	0.13	2		778	384	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114817	108114817	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786204543	NA	P-0055605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	74	513	0	ENST00000278616.4:c.640del	p.Ser214ProfsTer16	p.S214Pfs*16	ENST00000278616	NM_000051.3	212	Ttt/tt	6/63	1	2	FACETS	1	0.954	1	1	0.985	1	CLONAL	2	TRUE	1	0.13	2		513	481	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106434	27106434	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	129	602	0	ENST00000324856.7:c.6046del	p.Leu2016CysfsTer14	p.L2016Cfs*14	ENST00000324856	NM_006015.4	2015	atC/at	20/20	0.376351076692616	1	FACETS	0.966	0.889	1	1	0.993	1	CLONAL	6	TRUE	0	0.13	1		602	320	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502190	157502190	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs387907144	NA	P-0055605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	39	552	0	ENST00000346085.5:c.3223C>T	p.Arg1075Ter	p.R1075*	ENST00000346085	NM_020732.3	1075	Cga/Tga	12/20	1	2	FACETS	1	0.886	1	1	0.969	1	CLONAL	2	TRUE	1	0.13	2		552	277	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466027	69466035	+	inframe_deletion	In_Frame_Del	DEL	GACGTGCGG	GACGTGCGG	-	novel	NA	P-0055605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	74	959	0	ENST00000227507.2:c.871_879del	p.Arg291_Val293del	p.R291_V293del	ENST00000227507	NM_053056.2	289	GACGTGCGG/-	5/5	1	2	FACETS	1	0.954	1	1	0.985	1	CLONAL	2	TRUE	1	0.13	2		959	479	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445041	49445041	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	51	768	5	ENST00000301067.7:c.2425del	p.Gln809ArgfsTer121	p.Q809Rfs*121	ENST00000301067	NM_003482.3	809	Cag/ag	10/54	1	2	FACETS	0.988	0.842	1	1	0.974	1	CLONAL	2	TRUE	1	0.13	2		773	397	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383774	15383774	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	77	762	5	ENST00000263377.2:c.137del	p.Pro46ArgfsTer47	p.P46Rfs*47	ENST00000263377	NM_058243.2	46	cCg/cg	2/20	1	2	FACETS	0.893	0.787	1	1	0.986	1	CLONAL	3	TRUE	1	0.13	2		767	442	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520202	176520202	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763979974	NA	P-0055605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	75	993	1	ENST00000292408.4:c.1121C>T	p.Ala374Val	p.A374V	ENST00000292408	NM_213647.1	374	gCg/gTg	9/18	1	2	FACETS	1	0.957	1	1	0.985	1	CLONAL	2	TRUE	1	0.13	2		994	479	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155731	119155731	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373989524	NA	P-0055605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	76	678	0	ENST00000264033.4:c.1484C>T	p.Pro495Leu	p.P495L	ENST00000264033	NM_005188.3	495	cCg/cTg	10/16	1	2	FACETS	0.9	0.793	1	1	0.986	1	CLONAL	3	TRUE	1	0.13	2		678	433	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905041	50905041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs577686721	NA	P-0055605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	51	615	0	ENST00000440232.2:c.323C>T	p.Ala108Val	p.A108V	ENST00000440232	NM_002691.3	108	gCg/gTg	4/27	1	2	FACETS	0.98	0.839	1	1	0.981	1	CLONAL	3	TRUE	1	0.13	2		615	267	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164835	106164835	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	40	623	0	ENST00000380013.4:c.3703G>T	p.Gly1235Ter	p.G1235*	ENST00000380013	NM_001127208.2	1235	Gga/Tga	6/11	1	2	FACETS	1	0.868	1	1	0.969	1	CLONAL	2	TRUE	1	0.13	2		623	294	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331813	68331813	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	47	540	0	ENST00000487270.1:c.409G>A	p.Ala137Thr	p.A137T	ENST00000487270	NM_133509.3	137	Gct/Act	5/11	1	2	FACETS	1	0.855	1	1	0.973	1	CLONAL	2	TRUE	1	0.13	2		540	358	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647656	3647657	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs774532876	NA	P-0055605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	57	1071	0	ENST00000294008.3:c.1406dup	p.Leu470IlefsTer8	p.L470Ifs*8	ENST00000294008	NM_032444.2	469	cca/ccCa	7/15	1	2	FACETS	0.753	0.646	0.87	1	0.967	1	SUBCLONAL	2	TRUE	1	0.13	2		1071	582	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338663	70338663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	80	790	0	ENST00000374080.3:c.59G>A	p.Gly20Glu	p.G20E	ENST00000374080		20	gGg/gAg	1/45	0.152273087882189	1	FACETS	1	0.898	1	1	0.988	1	CLONAL	3	TRUE	0	0.13	1		790	378	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711878	89711879	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TAAC	novel	NA	P-0055605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	22	481	0	ENST00000371953.3:c.499_502dup	p.Ile168AsnfsTer13	p.I168Nfs*13	ENST00000371953	NM_000314.4	166	gta/gTAACta	6/9	1	2	FACETS	0.877	0.683	1	1	0.936	1	CLONAL	2	TRUE	1	0.13	2		481	193	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941881	71941882	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0055605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	39	813	1	ENST00000298229.2:c.1241dup	p.His415AlafsTer51	p.H415Afs*51	ENST00000298229	NM_001567.3	413	-/A	11/28	1	2	FACETS	0.85	0.706	1	1	0.961	1	CLONAL	2	TRUE	1	0.13	2		814	353	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433345	49433345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	39	781	1	ENST00000301067.7:c.8102G>A	p.Arg2701Gln	p.R2701Q	ENST00000301067	NM_003482.3	2701	cGg/cAg	32/54	1	2	FACETS	1	0.883	1	1	0.969	1	CLONAL	2	TRUE	1	0.13	2		782	279	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606034	81606034	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	32	485	0	ENST00000298171.2:c.706del	p.Thr236ProfsTer14	p.T236Pfs*14	ENST00000298171	NM_000369.2	235	cAa/ca	9/10	1	2	FACETS	0.969	0.791	1	1	0.959	1	CLONAL	2	TRUE	1	0.13	2		485	254	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3795303	3795303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057521558	NA	P-0055605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	44	444	0	ENST00000262367.5:c.3889C>T	p.His1297Tyr	p.H1297Y	ENST00000262367	NM_004380.2	1297	Cac/Tac	22/31	1	2	FACETS	1	0.886	1	1	0.972	1	CLONAL	2	TRUE	1	0.13	2		444	318	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56878443	56878444	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	42	508	0	ENST00000308159.5:c.2385dup	p.Ala796CysfsTer47	p.A796Cfs*47	ENST00000308159	NM_014669.4	794	-/T	22/22	1	2	FACETS	1	0.861	1	1	0.97	1	CLONAL	2	TRUE	1	0.13	2		508	314	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919963	50919963	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	44	753	0	ENST00000440232.2:c.3050C>G	p.Thr1017Arg	p.T1017R	ENST00000440232	NM_002691.3	1017	aCa/aGa	24/27	1	2	FACETS	0.912	0.767	1	1	0.968	1	CLONAL	2	TRUE	1	0.13	2		753	371	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672714	47672714	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	35	567	0	ENST00000233146.2:c.1308del	p.Phe436LeufsTer2	p.F436Lfs*2	ENST00000233146	NM_000251.2	435	gTt/gt	8/16	1	2	FACETS	1	0.834	1	1	0.834	1	CLONAL	1	TRUE	1	0.13	2		567	528	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380522	31380522	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs773216636	NA	P-0055605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	72	784	2	ENST00000328111.2:c.1016del	p.Gly339AlafsTer32	p.G339Afs*32	ENST00000328111	NM_006892.3	338	Ggg/gg	9/23	0.152273087882189	0	FACETS	0.837	0.735	0.945			1	CLONAL	3	TRUE	0	0.13	0		786	384	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928097	178928098	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	20	543	0	ENST00000263967.3:c.1377dup	p.Gly460TrpfsTer9	p.G460Wfs*9	ENST00000263967	NM_006218.2	459	att/aTtt	8/21	1	2	FACETS	0.974	0.745	1	0.974	0.745	1	CLONAL	1	TRUE	1	0.13	2		543	316	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589530	67589592	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTCTAGGATCAAGTTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATTACATGAATA	TTTCTAGGATCAAGTTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATTACATGAATA	-	novel	NA	P-0055605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	16	177	0	ENST00000274335.5:c.1300-6_1356del		p.X434_splice	ENST00000274335		434		10/15	1	2	FACETS	0.947	0.706	1	1	0.92	1	CLONAL	2	TRUE	1	0.13	2		177	130	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903692	41903692	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	60	816	1	ENST00000372991.4:c.865G>A	p.Ala289Thr	p.A289T	ENST00000372991	NM_001760.3	289	Gcc/Acc	5/5	1	2	FACETS	0.959	0.831	1	1	0.983	1	CLONAL	3	TRUE	1	0.13	2		817	321	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338671	70338671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	118	795	0	ENST00000374080.3:c.67G>A	p.Asp23Asn	p.D23N	ENST00000374080		23	Gat/Aat	1/45	0.152273087882189	1	FACETS	0.956	0.872	1	1	0.993	1	CLONAL	5	TRUE	0	0.13	1		795	355	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0055610-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	87	383	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.857	0.766	0.952	0.857	0.766	0.952	CLONAL	1	TRUE	1	0.636407027275847	2		383	319	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94926620	94926620	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0055610-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	119	380	0	ENST00000536441.1:c.144+1G>A		p.X48_splice	ENST00000536441	NM_144665.3	48			1	2	FACETS	0.954	0.869	1	0.954	0.869	1	CLONAL	1	TRUE	1	0.636407027275847	2		380	392	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784646	43784646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055610-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	119	377	0	ENST00000382044.4:c.28G>A	p.Gly10Arg	p.G10R	ENST00000382044	NM_001141980.1	10	Gga/Aga	2/28	1	2	FACETS	0.888	0.808	0.971	0.888	0.808	0.971	CLONAL	1	TRUE	1	0.636407027275847	2		377	421	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245798	41245816	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTCGTTTTGAAAGCAGA	CTTTCGTTTTGAAAGCAGA	-	novel	NA	P-0055610-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	116	571	0	ENST00000357654.3:c.1732_1750del	p.Ser578LeufsTer4	p.S578Lfs*4	ENST00000357654	NM_007294.3	578	TCTGCTTTCAAAACGAAAGct/ct	10/23	1	2	FACETS	0.905	0.822	0.99	0.905	0.822	0.99	CLONAL	1	TRUE	1	0.636407027275847	2		571	403	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0055610-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	243	670	2	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.636407027275847	1	FACETS	0.996	0.94	1	0.996	0.94	1	CLONAL	1	TRUE	0	0.636407027275847	1		672	523	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602613	10602613	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055610-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	272	873	0	ENST00000171111.5:c.965C>T	p.Pro322Leu	p.P322L	ENST00000171111	NM_203500.1	322	cCc/cTc	3/6	0.636407027275847	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.636407027275847	1		873	514	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136125	11136125	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055610-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	256	688	0	ENST00000358026.2:c.3109A>T	p.Asn1037Tyr	p.N1037Y	ENST00000358026	NM_001128849.1	1037	Aac/Tac	22/36	0.636407027275847	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.636407027275847	1		688	522	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288401	15288487	+	inframe_deletion	In_Frame_Del	DEL	GCAGGCGGGGTCGCAGCGGCTGTTGTTGAAGAGGCGCCAGCACTGCAGCGCCTCGCATTGCCGCCAGGGGTCGCCCACGCTCAGCGA	GCAGGCGGGGTCGCAGCGGCTGTTGTTGAAGAGGCGCCAGCACTGCAGCGCCTCGCATTGCCGCCAGGGGTCGCCCACGCTCAGCGA	-	novel	NA	P-0055610-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	199	677	0	ENST00000263388.2:c.4252_4338del	p.Leu1419_Ser1447del	p.L1419_S1447del	ENST00000263388	NM_000435.2	1418	TCGCTGAGCGTGGGCGACCCCTGGCGGCAATGCGAGGCGCTGCAGTGCTGGCGCCTCTTCAACAACAGCCGCTGCGACCCCGCCTGC/-	24/33	0.636407027275847	1	FACETS	0.969	0.909	1	0.969	0.909	1	CLONAL	1	TRUE	0	0.636407027275847	1		677	440	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525974	41525974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055610-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	72	355	0	ENST00000263253.7:c.1249C>T	p.Leu417Phe	p.L417F	ENST00000263253	NM_001429.3	417	Ctc/Ttc	5/31	1	2	FACETS	0.718	0.633	0.809	0.718	0.633	0.809	SUBCLONAL	1	TRUE	1	0.636407027275847	2		355	315	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022211	5022211	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055610-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	68	368	0	ENST00000381652.3:c.224G>A	p.Cys75Tyr	p.C75Y	ENST00000381652	NM_004972.3	75	tGt/tAt	3/25	0.636407027275847	1	FACETS	0.691	0.611	0.774	0.691	0.611	0.774	SUBCLONAL	1	TRUE	0	0.636407027275847	1		368	211	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040773	47040773	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055610-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	251	411	0	ENST00000377604.3:c.1408G>T	p.Gly470Ter	p.G470*	ENST00000377604	NM_001204468.1	470	Gga/Tga	13/24	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.636407027275847	1		411	370	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0055617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	244	543	1	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.660556325578643	2		544	731	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442453	52442499	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCCCACCCTCCAAACAAAGCACAGAGTCCAGCAGACCTGGTGGGCA	ATCCCACCCTCCAAACAAAGCACAGAGTCCAGCAGACCTGGTGGGCA	-	novel	NA	P-0055617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	90	154	0	ENST00000460680.1:c.246_255+37del		p.X82_splice	ENST00000460680	NM_004656.3	82		4/17	0.660556325578643	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.660556325578643	1		154	179	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0055618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	86	215	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.856	0.761	0.956	0.856	0.761	0.956	CLONAL	1	TRUE	1	0.485380812571417	2		215	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0055618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	177	314	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.485380812571417	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.485380812571417	1		314	550	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662610	227662610	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	94	396	1	ENST00000305123.5:c.845T>C	p.Val282Ala	p.V282A	ENST00000305123	NM_005544.2	282	gTc/gCc	1/2	0.265044053987675	1	FACETS	0.45	0.4	0.502	0.45	0.4	0.502	INDETERMINATE	1	TRUE	0	0.485380812571417	1		397	652	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928010	178928010	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	79	198	0	ENST00000263967.3:c.1288T>C	p.Phe430Leu	p.F430L	ENST00000263967	NM_006218.2	430	Ttt/Ctt	8/21	1	2	FACETS	0.917	0.812	1	0.917	0.812	1	CLONAL	1	TRUE	1	0.485380812571417	2		198	355	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256287	16256287	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	73	301	0	ENST00000375759.3:c.3552G>A	p.Met1184Ile	p.M1184I	ENST00000375759	NM_015001.2	1184	atG/atA	11/15	0.265044053987675	1	FACETS	0.416	0.364	0.471	0.416	0.364	0.471	INDETERMINATE	1	TRUE	0	0.485380812571417	1		301	548	SUCCESS
CBL	867	MSKCC	GRCh37	11	119167696	119167696	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	140	339	0	ENST00000264033.4:c.2105C>A	p.Thr702Asn	p.T702N	ENST00000264033	NM_005188.3	702	aCt/aAt	13/16	0.343649434373727	1	FACETS	0.84	0.769	0.913	0.84	0.769	0.913	CLONAL	1	TRUE	0	0.485380812571417	1		339	520	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820734	3820734	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	272	587	0	ENST00000262367.5:c.2717T>C	p.Val906Ala	p.V906A	ENST00000262367	NM_004380.2	906	gTg/gCg	14/31	0.265044053987675	1	FACETS	0.871	0.819	0.925	0.871	0.819	0.925	INDETERMINATE	1	TRUE	0	0.485380812571417	1		587	974	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858019	9858019	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	80	320	0	ENST00000330684.3:c.3382T>G	p.Phe1128Val	p.F1128V	ENST00000330684	NM_001134407.1	1128	Ttc/Gtc	13/13	0.265044053987675	1	FACETS	0.43	0.379	0.485	0.43	0.379	0.485	INDETERMINATE	1	TRUE	0	0.485380812571417	1		320	580	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195665	123195665	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	116	115	0	ENST00000218089.9:c.1579T>G	p.Cys527Gly	p.C527G	ENST00000218089	NM_001042749.1	527	Tgt/Ggt	17/35	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.485380812571417	1		115	244	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0055619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	50	219	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.330711461099468	2		219	227	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246445	105246445	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	90	423	0	ENST00000349310.3:c.155T>G	p.Leu52Arg	p.L52R	ENST00000349310	NM_001014432.1	52	cTc/cGc	4/15	0.146207062838311	3	FACETS	0.797	0.712	0.887	0.797	0.712	0.887	INDETERMINATE	2	TRUE	1	0.330711461099468	3		423	398	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835780	68835781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0055619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	97	397	0	ENST00000261769.5:c.377dup	p.Pro127AlafsTer41	p.P127Afs*41	ENST00000261769	NM_004360.3	124	cgc/cgCc	3/16	0.330711461099468	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.330711461099468	1		397	327	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717733	89717733	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	78	269	0	ENST00000371953.3:c.758T>C	p.Ile253Thr	p.I253T	ENST00000371953	NM_000314.4	253	aTc/aCc	7/9	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.330711461099468	2		269	360	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205131	123205131	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	46	277	0	ENST00000218089.9:c.2491G>A	p.Asp831Asn	p.D831N	ENST00000218089	NM_001042749.1	831	Gat/Aat	25/35	1	2	FACETS	0.777	0.656	0.909	0.777	0.656	0.909	CLONAL	1	TRUE	1	0.330711461099468	2		277	358	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0055620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	121	392	1	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.238890288929955	2	FACETS	0.983	0.894	1	0.983	0.894	1	CLONAL	2	TRUE	0	0.266459029464057	2		393	462	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30946592	30946594	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs752094508	NA	P-0055620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	113	216	1	ENST00000375687.4:c.25_27del	p.Lys9del	p.K9del	ENST00000375687	NM_015338.5	5	cAGAag/cag	1/13	0.266459029464057	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.266459029464057	3		217	392	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62312043	62312043	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762108489	NA	P-0055620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	158	539	0	ENST00000360203.5:c.1162G>A	p.Gly388Arg	p.G388R	ENST00000360203	NM_001283009.1	388	Gga/Aga	14/35	0.266459029464057	3	FACETS	0.913	0.838	0.991	0.913	0.838	0.991	CLONAL	2	TRUE	1	0.266459029464057	3		539	736	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326538	62326538	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149145821	NA	P-0055620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	67	532	0	ENST00000360203.5:c.3463G>A	p.Val1155Met	p.V1155M	ENST00000360203	NM_001283009.1	1155	Gtg/Atg	33/35	0.266459029464057	3	FACETS	0.793	0.688	0.906	0.396	0.344	0.453	CLONAL	1	TRUE	1	0.266459029464057	3		532	719	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293164	91293164	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	34	207	0	ENST00000355112.3:c.667del	p.Glu223AsnfsTer9	p.E223Nfs*9	ENST00000355112	NM_000057.2	222	gaG/ga	3/22	0.238890288929955	2	FACETS	0.959	0.788	1	0.48	0.394	0.575	CLONAL	1	TRUE	0	0.266459029464057	2		207	266	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880257	37880257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	51	423	0	ENST00000269571.5:c.2301C>G	p.Ile767Met	p.I767M	ENST00000269571		767	atC/atG	19/27	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.22	2		423	451	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052636	42052636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1054243525	NA	P-0055621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	99	387	0	ENST00000219905.7:c.7307G>A	p.Arg2436His	p.R2436H	ENST00000219905	NM_001164273.1	2436	cGt/cAt	20/24	0.216899678021186	2	FACETS	0.808	0.723	0.897	0.808	0.723	0.897	CLONAL	2	TRUE	0	0.22	2		387	557	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426526	49426526	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	45	796	0	ENST00000301067.7:c.11962C>T	p.Gln3988Ter	p.Q3988*	ENST00000301067	NM_003482.3	3988	Cag/Tag	39/54	1	2	FACETS	0.45	0.376	0.531	0.45	0.376	0.531	SUBCLONAL	1	TRUE	1	0.22	2		796	910	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883753	37883753	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	124	817	0	ENST00000269571.5:c.3365C>T	p.Ser1122Phe	p.S1122F	ENST00000269571		1122	tCt/tTt	26/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.22	2		817	845	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025558	1025558	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1467957407	NA	P-0055621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	93	667	0	ENST00000358495.3:c.817G>A	p.Glu273Lys	p.E273K	ENST00000358495	NM_134424.2	273	Gag/Aag	9/12	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.22	2		667	807	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880991	37880992	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCTG	novel	NA	P-0055621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	83	606	0	ENST00000269571.5:c.2321_2326dup	p.Ala775_Gly776insValAla	p.A775_G776insVA	ENST00000269571		774	atg/aTGGCTGtg	20/27	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.22	2		606	733	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883636	37883636	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	97	663	0	ENST00000269571.5:c.3248C>G	p.Ser1083Cys	p.S1083C	ENST00000269571		1083	tCc/tGc	26/27	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.22	2		663	690	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896460	151896460	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780537762	NA	P-0055621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	51	276	0	ENST00000262189.6:c.4177C>T	p.Leu1393Phe	p.L1393F	ENST00000262189	NM_170606.2	1393	Ctt/Ttt	27/59	0.3	5	FACETS	1	0.944	1	0.415	0.353	0.484	CLONAL	1	TRUE	2	0.22	5		276	495	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880257	37880257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055621-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	62	423	0	ENST00000269571.5:c.2301C>G	p.Ile767Met	p.I767M	ENST00000269571		767	atC/atG	19/27	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.27981076327937	2		423	392	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052636	42052636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1054243525	NA	P-0055621-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	75	387	0	ENST00000219905.7:c.7307G>A	p.Arg2436His	p.R2436H	ENST00000219905	NM_001164273.1	2436	cGt/cAt	20/24	0.266938737571282	2	FACETS	1	0.967	1	0.651	0.573	0.734	CLONAL	1	TRUE	0	0.27981076327937	2		387	412	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426526	49426526	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055621-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	55	796	0	ENST00000301067.7:c.11962C>T	p.Gln3988Ter	p.Q3988*	ENST00000301067	NM_003482.3	3988	Cag/Tag	39/54	1	2	FACETS	0.498	0.425	0.579	0.498	0.425	0.579	SUBCLONAL	1	TRUE	1	0.27981076327937	2		796	789	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883753	37883753	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055621-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	120	817	0	ENST00000269571.5:c.3365C>T	p.Ser1122Phe	p.S1122F	ENST00000269571		1122	tCt/tTt	26/27	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.27981076327937	2		817	640	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025558	1025558	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1467957407	NA	P-0055621-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	99	667	0	ENST00000358495.3:c.817G>A	p.Glu273Lys	p.E273K	ENST00000358495	NM_134424.2	273	Gag/Aag	9/12	0.233310713342232	1	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	0	0.27981076327937	1		667	593	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880991	37880992	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCTG	novel	NA	P-0055621-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	100	606	0	ENST00000269571.5:c.2321_2326dup	p.Ala775_Gly776insValAla	p.A775_G776insVA	ENST00000269571		774	atg/aTGGCTGtg	20/27	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.27981076327937	2		606	590	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883636	37883636	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055621-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	106	663	0	ENST00000269571.5:c.3248C>G	p.Ser1083Cys	p.S1083C	ENST00000269571		1083	tCc/tGc	26/27	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.27981076327937	2		663	517	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896460	151896460	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780537762	NA	P-0055621-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	57	276	0	ENST00000262189.6:c.4177C>T	p.Leu1393Phe	p.L1393F	ENST00000262189	NM_170606.2	1393	Ctt/Ttt	27/59	0.27981076327937	4	FACETS	1	0.946	1	0.608	0.523	0.7	CLONAL	1	TRUE	2	0.27981076327937	4		276	429	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696450	47696450	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	53	389	0	ENST00000347630.2:c.373T>C	p.Phe125Leu	p.F125L	ENST00000347630	NM_001007230.1	125	Ttt/Ctt	6/11	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.23	2		389	447	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866605	117866605	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs749183142	NA	P-0055634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	59	421	0	ENST00000297338.2:c.1040T>C	p.Ile347Thr	p.I347T	ENST00000297338	NM_006265.2	347	aTt/aCt	9/14	1	2	FACETS	0.985	0.848	1	0.985	0.848	1	CLONAL	1	TRUE	1	0.23	2		421	521	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240469	98240469	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1564051834	NA	P-0055634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	41	273	0	ENST00000331920.6:c.1216-1G>A		p.X406_splice	ENST00000331920	NM_000264.3	406			1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.23	2		273	326	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40371810	40371810	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	295	523	4	ENST00000293328.3:c.601G>T	p.Glu201Ter	p.E201*	ENST00000293328	NM_012448.3	201	Gag/Tag	6/19	0.618890046250497	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.618890046250497	4		527	694	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831357	72831358	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTG	rs34918837	NA	P-0055635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	94	347	2	ENST00000268489.5:c.5221_5223dup	p.Gln1741dup	p.Q1741dup	ENST00000268489	NM_006885.3	1741	-/CAA	9/10	0.327407949240935	5	FACETS	1	0.961	1	0.389	0.347	0.433	INDETERMINATE	1	TRUE	2	0.618890046250497	5		349	502	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125789	47125789	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	195	332	2	ENST00000409792.3:c.5481G>T	p.Trp1827Cys	p.W1827C	ENST00000409792	NM_014159.6	1827	tgG/tgT	12/21	0.618890046250497	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.618890046250497	2		334	293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0055635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	608	719	3	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.618890046250497	3	FACETS	1	0.991	1	1	0.998	1	CLONAL	3	TRUE	1	0.618890046250497	3		722	826	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910801	114910801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1336546841	NA	P-0055635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	162	518	3	ENST00000543371.1:c.920C>T	p.Thr307Met	p.T307M	ENST00000543371	NM_001198531.1	307	aCg/aTg	9/14	0.618890046250497	3	FACETS	1	0.953	1	0.525	0.483	0.568	CLONAL	1	TRUE	1	0.618890046250497	3		521	653	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200991	108200991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781361	NA	P-0055635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	90	335	1	ENST00000278616.4:c.7358G>A	p.Arg2453His	p.R2453H	ENST00000278616	NM_000051.3	2453	cGt/cAt	50/63	0.618890046250497	5	FACETS	0.903	0.802	1	0.301	0.267	0.337	CLONAL	1	TRUE	2	0.618890046250497	5		336	621	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510164	120510164	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	244	424	7	ENST00000256646.2:c.1345G>T	p.Ala449Ser	p.A449S	ENST00000256646	NM_024408.3	449	Gca/Tca	8/34	0.618890046250497	4	FACETS	0.957	0.899	1	0.957	0.899	1	CLONAL	2	TRUE	2	0.618890046250497	4		431	667	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741471	17741471	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs761828232	NA	P-0055635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	221	770	3	ENST00000250003.3:c.142C>A	p.Pro48Thr	p.P48T	ENST00000250003	NM_002478.4	48	Ccg/Acg	1/3	0.618890046250497	3	FACETS	1	0.979	1	0.559	0.521	0.598	CLONAL	1	TRUE	1	0.618890046250497	3		773	836	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398065	4398065	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	155	546	4	ENST00000261254.3:c.629C>T	p.Ala210Val	p.A210V	ENST00000261254	NM_001759.3	210	gCc/gTc	4/5	0.618890046250497	4	FACETS	1	0.917	1	0.501	0.458	0.545	CLONAL	1	TRUE	2	0.618890046250497	4		550	810	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491370	18491370	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	36	202	0	ENST00000266497.5:c.1283A>G	p.Tyr428Cys	p.Y428C	ENST00000266497		428	tAt/tGt	8/31	0.618890046250497	4	FACETS	0.703	0.581	0.838	0.351	0.29	0.419	SUBCLONAL	1	TRUE	2	0.618890046250497	4		202	268	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656340	18656340	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	168	291	0	ENST00000266497.5:c.3019G>C	p.Asp1007His	p.D1007H	ENST00000266497		1007	Gat/Cat	21/31	0.618890046250497	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.618890046250497	4		291	418	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424969	49424970	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0055635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	374	698	4	ENST00000301067.7:c.13518_13519insT	p.Ser4507Ter	p.S4507*	ENST00000301067	NM_003482.3	4506	-/T	39/54	0.618890046250497	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.618890046250497	3		702	790	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133234531	133234531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	97	446	2	ENST00000320574.5:c.3301G>A	p.Ala1101Thr	p.A1101T	ENST00000320574	NM_006231.2	1101	Gca/Aca	27/49	0.618890046250497	4	FACETS	0.739	0.659	0.824	0.369	0.329	0.412	SUBCLONAL	1	TRUE	2	0.618890046250497	4		448	687	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023011	33023011	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	197	418	1	ENST00000300177.4:c.120G>T	p.Gln40His	p.Q40H	ENST00000300177	NM_001191322.1	40	caG/caT	2/2	0.618890046250497	3	FACETS	0.867	0.811	0.923	0.867	0.811	0.923	CLONAL	2	TRUE	1	0.618890046250497	3		419	481	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374431	31374431	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	314	513	7	ENST00000328111.2:c.430A>T	p.Arg144Trp	p.R144W	ENST00000328111	NM_006892.3	144	Agg/Tgg	5/23	0.618890046250497	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.618890046250497	4		520	782	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420032	41420032	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	204	432	3	ENST00000373198.4:c.289G>C	p.Glu97Gln	p.E97Q	ENST00000373198	NM_133170.3	97	Gag/Cag	3/32	0.618890046250497	4	FACETS	0.944	0.882	1	0.944	0.882	1	CLONAL	2	TRUE	2	0.618890046250497	4		435	565	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539743	187539743	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	116	322	0	ENST00000441802.2:c.7997A>T	p.Asn2666Ile	p.N2666I	ENST00000441802	NM_005245.3	2666	aAt/aTt	10/27	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.618890046250497	2		322	360	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553111	106553111	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	276	616	4	ENST00000369096.4:c.1076C>A	p.Thr359Lys	p.T359K	ENST00000369096	NM_001198.3	359	aCg/aAg	5/7	0.618890046250497	4	FACETS	0.879	0.829	0.931	0.879	0.829	0.931	CLONAL	2	TRUE	2	0.618890046250497	4		620	821	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221750	55221750	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748627278	NA	P-0055635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	289	625	0	ENST00000275493.2:c.794C>T	p.Pro265Leu	p.P265L	ENST00000275493	NM_005228.3	265	cCc/cTc	7/28	0.618890046250497	4	FACETS	0.925	0.874	0.978	0.925	0.874	0.978	CLONAL	2	TRUE	2	0.618890046250497	4		625	817	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335665	81335666	+	missense_variant	Missense_Mutation	DNP	GA	GA	TG	novel	NA	P-0055635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	182	506	3	ENST00000222390.5:c.1694_1695delinsCA	p.Leu565Pro	p.L565P	ENST00000222390	NM_000601.4	565	cTC/cCA	15/18	0.618890046250497	4	FACETS	0.872	0.81	0.935	0.872	0.81	0.935	CLONAL	2	TRUE	2	0.618890046250497	4		509	546	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033237	69033237	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	246	489	3	ENST00000288368.4:c.3677C>A	p.Pro1226His	p.P1226H	ENST00000288368	NM_024870.2	1226	cCc/cAc	30/40	0.618890046250497	4	FACETS	0.982	0.924	1	0.982	0.924	1	CLONAL	2	TRUE	2	0.618890046250497	4		492	655	SUCCESS
BTK	695	MSKCC	GRCh37	X	100604931	100604931	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	73	373	0	ENST00000308731.7:c.1922G>T	p.Arg641Leu	p.R641L	ENST00000308731	NM_000061.2	641	cGt/cTt	19/19	0.618890046250497	3	FACETS	0.809	0.711	0.912	0.404	0.355	0.456	CLONAL	1	TRUE	1	0.618890046250497	3		373	382	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220516	123220516	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	109	523	2	ENST00000218089.9:c.3173C>A	p.Ser1058Ter	p.S1058*	ENST00000218089	NM_001042749.1	1058	tCa/tAa	30/35	0.618890046250497	3	FACETS	0.771	0.694	0.853	0.386	0.347	0.427	SUBCLONAL	1	TRUE	1	0.618890046250497	3		525	598	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224715	123224715	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	90	369	0	ENST00000218089.9:c.3479C>A	p.Thr1160Lys	p.T1160K	ENST00000218089	NM_001042749.1	1160	aCa/aAa	32/35	0.618890046250497	3	FACETS	0.886	0.79	0.987	0.443	0.395	0.494	CLONAL	1	TRUE	1	0.618890046250497	3		369	430	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0055636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	49	632	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	0.916	0.774	1	0.916	0.774	1	CLONAL	1	TRUE	1	0.16	2		632	669	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874836	151874836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs992402398	NA	P-0055636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	17	267	0	ENST00000262189.6:c.7702G>A	p.Gly2568Arg	p.G2568R	ENST00000262189	NM_170606.2	2568	Gga/Aga	38/59	1	2	FACETS	0.756	0.564	0.984	0.756	0.564	0.984	CLONAL	1	TRUE	1	0.16	2		267	281	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484229	120484229	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	26	452	0	ENST00000256646.2:c.2901del	p.Tyr967Ter	p.Y967*	ENST00000256646	NM_024408.3	967	taC/ta	18/34	1	2	FACETS	0.632	0.5	0.785	0.632	0.5	0.785	SUBCLONAL	1	TRUE	1	0.16	2		452	514	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509609	29509610	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	35	373	0	ENST00000356175.3:c.816dup	p.Leu273SerfsTer18	p.L273Sfs*18	ENST00000356175	NM_000267.3	272	att/aTtt	8/57	1	2	FACETS	1	0.828	1	1	0.828	1	CLONAL	1	TRUE	1	0.16	2		373	433	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0055637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	34	490	1	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	1	2	FACETS	0.952	0.777	1	0.952	0.777	1	CLONAL	1	TRUE	1	0.14	2		491	510	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881488	48881489	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0055637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	18	233	0	ENST00000267163.4:c.219_220dup	p.Ala74GlufsTer4	p.A74Efs*4	ENST00000267163	NM_000321.2	70	-/AG	2/27	1	2	FACETS	0.993	0.748	1	0.993	0.748	1	CLONAL	1	TRUE	1	0.14	2		233	259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577557	7577558	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGAACT	novel	NA	P-0055637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	45	515	0	ENST00000269305.4:c.718_723dup	p.Ser240_Ser241dup	p.S240_S241dup	ENST00000269305	NM_001126112.2	240	-/AGTTCC	7/11	1	2	FACETS	0.885	0.742	1	0.885	0.742	1	CLONAL	1	TRUE	1	0.14	2		515	726	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66525100	66525100	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	52	279	0	ENST00000358598.2:c.859G>A	p.Glu287Lys	p.E287K	ENST00000358598	NM_212471.2	287	Gaa/Aaa	9/11	0.3	3	FACETS	0.814	0.694	0.946	0.814	0.694	0.946	CLONAL	2	TRUE	1	0.14	3		279	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579331	7579331	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	150	637	0	ENST00000269305.4:c.356C>G	p.Ala119Gly	p.A119G	ENST00000269305	NM_001126112.2	119	gCc/gGc	4/11	0.533329400355748	1	FACETS	0.946	0.873	1	0.946	0.873	1	CLONAL	1	TRUE	0	0.533329400355748	1		637	436	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912248	32912248	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	149	484	0	ENST00000380152.3:c.3756del	p.Ala1253GlnfsTer6	p.A1253Qfs*6	ENST00000380152		1252	tcT/tc	11/27	0.533329400355748	1	FACETS	0.942	0.869	1	0.942	0.869	1	CLONAL	1	TRUE	0	0.533329400355748	1		484	435	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	74	374	0				ENST00000310581	NM_198253.2	-/1132			0.254206776522323	1	FACETS	1	0.914	1	1	0.914	1	INDETERMINATE	1	TRUE	0	0.508023791538987	1		374	211	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0055639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	45	309	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.163378834536905	3	FACETS	1	0.875	1	0.517	0.439	0.601	INDETERMINATE	1	TRUE	1	0.508023791538987	3		310	215	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204726	128204726	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	60	821	0	ENST00000341105.2:c.715C>T	p.Gln239Ter	p.Q239*	ENST00000341105	NM_032638.4	239	Cag/Tag	3/6	0.354233591862025	0	FACETS	0.409	0.355	0.467			1	SUBCLONAL	1	TRUE	0	0.508023791538987	0		821	284	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868658	56868658	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	28	327	0	ENST00000308159.5:c.1750C>T	p.Leu584Phe	p.L584F	ENST00000308159	NM_014669.4	584	Ctt/Ttt	16/22	0.163378834536905	3	FACETS	0.614	0.494	0.75	0.307	0.247	0.375	INDETERMINATE	1	TRUE	1	0.508023791538987	3		327	225	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715746	18715746	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1191317818	NA	P-0055639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	34	273	0	ENST00000266497.5:c.3577C>T	p.Pro1193Ser	p.P1193S	ENST00000266497		1193	Cct/Tct	25/31	0.508023791538987	1	FACETS	0.78	0.65	0.92	0.78	0.65	0.92	CLONAL	1	TRUE	0	0.508023791538987	1		273	128	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29195879	29195879	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs767641023	NA	P-0055639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	61	747	0	ENST00000240100.2:c.719A>G	p.Tyr240Cys	p.Y240C	ENST00000240100	NM_001394.6	240	tAt/tGt	3/4	1	2	FACETS	0.671	0.582	0.767	0.671	0.582	0.767	SUBCLONAL	1	TRUE	1	0.508023791538987	2		747	358	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814553	43814553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	38	472	0	ENST00000372470.3:c.1348G>A	p.Glu450Lys	p.E450K	ENST00000372470	NM_005373.2	450	Gag/Aag	9/12	1	2	FACETS	0.556	0.462	0.66	0.556	0.462	0.66	SUBCLONAL	1	TRUE	1	0.508023791538987	2		472	269	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416962	416963	+	missense_variant	Missense_Mutation	DNP	GG	GG	TA	novel	NA	P-0055639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	40	355	1	ENST00000399788.2:c.3587_3588delinsTA	p.Ser1196Leu	p.S1196L	ENST00000399788	NM_001042603.1	1196	tCC/tTA	23/28	NA	2	FACETS	0.653	0.547	0.77			1	INDETERMINATE	1	TRUE	NA	0.508023791538987	2		356	241	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37863394	37863395	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0055639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	75	668	1	ENST00000269571.5:c.225_225+1delinsAA		p.X75_splice	ENST00000269571		75		2/27	1	2	FACETS	0.946	0.837	1	0.946	0.837	1	CLONAL	1	TRUE	1	0.508023791538987	2		669	312	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292735	62292736	+	missense_variant	Missense_Mutation	DNP	CT	CT	TA	novel	NA	P-0055639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	111	585	2	ENST00000360203.5:c.187_188delinsTA	p.Leu63Tyr	p.L63Y	ENST00000360203	NM_001283009.1	63	CTc/TAc	3/35	0.383866395922955	3	FACETS	1	0.981	1	0.678	0.614	0.744	CLONAL	1	TRUE	1	0.508023791538987	3		587	404	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221936	98221936	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1064794260	NA	P-0055645-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	43	667	2	ENST00000331920.6:c.2833C>T	p.Arg945Ter	p.R945*	ENST00000331920	NM_000264.3	945	Cga/Tga	17/24	1	2	FACETS	0.257	0.214	0.305	0.257	0.214	0.305	SUBCLONAL	1	TRUE	1	0.406390720548983	2		669	822	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115931	8115931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	80	539	0	ENST00000346208.3:c.1277C>T	p.Ser426Phe	p.S426F	ENST00000346208		426	tCc/tTc	6/6	0.343501343191087	5	FACETS	1	0.965	1	0.42	0.37	0.473	CLONAL	1	TRUE	2	0.376894496359704	5		539	528	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0055657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	57	525	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.245734543900847	5	FACETS	1	0.884	1	0.344	0.295	0.397	CLONAL	1	TRUE	2	0.376894496359704	5		526	459	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254510	1254510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918664	NA	P-0055657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	107	1054	0	ENST00000310581.5:c.3268G>A	p.Val1090Met	p.V1090M	ENST00000310581	NM_198253.2	1090	Gtg/Atg	15/16	0.37737514198727	3	FACETS	1	0.952	1	0.55	0.495	0.609	CLONAL	1	TRUE	1	0.376894496359704	3		1054	613	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831491	72831491	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs369392504	NA	P-0055657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	95	687	0	ENST00000268489.5:c.5090T>C	p.Ile1697Thr	p.I1697T	ENST00000268489	NM_006885.3	1697	aTt/aCt	9/10	0.366707244168572	1	FACETS	0.938	0.84	1	0.938	0.84	1	CLONAL	1	TRUE	0	0.376894496359704	1		687	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576851	7576851	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0055657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	54	637	0	ENST00000269305.4:c.993+2T>C		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.37737514198727	1	FACETS	0.794	0.683	0.913	0.794	0.683	0.913	CLONAL	1	TRUE	0	0.376894496359704	1		637	293	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948006	17948006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	86	829	0	ENST00000458235.1:c.1718C>T	p.Ala573Val	p.A573V	ENST00000458235	NM_000215.3	573	gCg/gTg	13/24	0.126362733918297	5	FACETS	1	0.97	1	0.324	0.287	0.364	INDETERMINATE	1	TRUE	1	0.376894496359704	5		829	551	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324660	31324660	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	52	222	0	ENST00000412585.2:c.148G>T	p.Gly50Cys	p.G50C	ENST00000412585	NM_005514.6	50	Ggc/Tgc	2/8	0.146801633295943	2	FACETS	0.893	0.79	0.996	1	0.968	1	INDETERMINATE	3	TRUE	0	0.376894496359704	2		222	103	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263894	133263894	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	18	330	0	ENST00000320574.5:c.8T>C	p.Leu3Pro	p.L3P	ENST00000320574	NM_006231.2	3	cTg/cCg	1/49	0.37737514198727	3	FACETS	0.428	0.323	0.553	0.214	0.161	0.277	SUBCLONAL	1	TRUE	1	0.376894496359704	3		330	265	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831579	72831579	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	67	645	1	ENST00000268489.5:c.5002C>T	p.Pro1668Ser	p.P1668S	ENST00000268489	NM_006885.3	1668	Cca/Tca	9/10	0.366707244168572	1	FACETS	0.692	0.604	0.787	0.692	0.604	0.787	SUBCLONAL	1	TRUE	0	0.376894496359704	1		646	417	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62298901	62298901	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	72	617	0	ENST00000360203.5:c.694G>T	p.Ala232Ser	p.A232S	ENST00000360203	NM_001283009.1	232	Gcc/Tcc	8/35	0.37737514198727	5	FACETS	0.972	0.85	1	0.324	0.283	0.369	CLONAL	1	TRUE	2	0.376894496359704	5		617	615	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826617	50826617	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0055658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	50	217	0	ENST00000398568.2:c.2341+1G>C		p.X781_splice	ENST00000398568	NM_001042412.1	781			0.561824836581506	1	FACETS	0.901	0.783	1	0.901	0.783	1	CLONAL	1	TRUE	0	0.561824836581506	1		217	142	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542327	187542327	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	78	389	0	ENST00000441802.2:c.5413G>A	p.Ala1805Thr	p.A1805T	ENST00000441802	NM_005245.3	1805	Gct/Act	10/27	1	2	FACETS	0.954	0.848	1	0.954	0.848	1	CLONAL	1	TRUE	1	0.561824836581506	2		389	291	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287374	33287374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	99	573	2	ENST00000374542.5:c.1723C>T	p.Pro575Ser	p.P575S	ENST00000374542	NM_001141970.1	575	Ccc/Tcc	6/8	1	2	FACETS	0.504	0.45	0.561	0.504	0.45	0.561	SUBCLONAL	1	TRUE	1	0.580623242404603	2		575	677	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690813	89690813	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1554897861	NA	P-0055659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	86	292	0	ENST00000371953.3:c.220A>T	p.Arg74Ter	p.R74*	ENST00000371953	NM_000314.4	74	Aga/Tga	4/9	0.580623242404603	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.580623242404603	1		292	195	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589614	67589634	+	inframe_deletion	In_Frame_Del	DEL	AAGTCGAGAATATGATAGATT	AAGTCGAGAATATGATAGATT	-	novel	NA	P-0055659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	32	218	0	ENST00000274335.5:c.1378_1398del	p.Ser460_Leu466del	p.S460_L466del	ENST00000274335		459	aaAAGTCGAGAATATGATAGATTa/aaa	10/15	0.580623242404603	1	FACETS	0.631	0.522	0.749	0.631	0.522	0.749	SUBCLONAL	1	TRUE	0	0.580623242404603	1		218	124	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054965	176054965	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	122	488	0	ENST00000367669.3:c.1088A>C	p.His363Pro	p.H363P	ENST00000367669	NM_022457.5	363	cAt/cCt	10/20	1	2	FACETS	0.971	0.884	1	0.971	0.884	1	CLONAL	1	TRUE	1	0.580623242404603	2		488	433	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446408	49446408	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	142	728	0	ENST00000301067.7:c.1197del	p.His400ThrfsTer2	p.H400Tfs*2	ENST00000301067	NM_003482.3	399	ggG/gg	9/54	1	2	FACETS	0.468	0.426	0.513	0.468	0.426	0.513	SUBCLONAL	1	TRUE	1	0.580623242404603	2		728	1045	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579552	7579571	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCATCAAATCATCCATTG	CAGCATCAAATCATCCATTG	-	novel	NA	P-0055659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	225	811	0	ENST00000269305.4:c.116_135del	p.Ala39ValfsTer6	p.A39Vfs*6	ENST00000269305	NM_001126112.2	39	gCAATGGATGATTTGATGCTG/g	4/11	0.580623242404603	1	FACETS	0.884	0.829	0.941	0.884	0.829	0.941	CLONAL	1	TRUE	0	0.580623242404603	1		811	622	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094784	143094784	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0055659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	20	261	0	ENST00000262992.4:c.1359+1G>C		p.X453_splice	ENST00000262992	NM_001101669.1	453			0.580623242404603	1	FACETS	0.251	0.192	0.318	0.251	0.192	0.318	SUBCLONAL	1	TRUE	0	0.580623242404603	1		261	195	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557629	95557629	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	95	539	0	ENST00000393063.1:c.5438A>G	p.Glu1813Gly	p.E1813G	ENST00000393063	NM_030621.3	1813	gAg/gGg	26/28	1	2	FACETS	0.99	0.89	1	0.99	0.89	1	CLONAL	1	TRUE	1	0.58	2		539	331	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94209531	94209531	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	111	401	0	ENST00000323929.3:c.583A>C	p.Asn195His	p.N195H	ENST00000323929	NM_005591.3	195	Aat/Cat	7/20	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.58	2		401	379	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95563005	95563005	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	61	444	0	ENST00000393063.1:c.4252G>T	p.Glu1418Ter	p.E1418*	ENST00000393063	NM_030621.3	1418	Gag/Tag	24/28	1	2	FACETS	0.907	0.792	1	0.907	0.792	1	CLONAL	1	TRUE	1	0.58	2		444	232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0055662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	200	975	0	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	0.336094632156359	1	FACETS	0.958	0.889	1	0.958	0.889	1	CLONAL	1	TRUE	0	0.382381786017835	1		975	883	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0055663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	627	740	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.545041235073835	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	1	0.545041235073835	4		740	1062	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0055663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	105	310	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.917	0.828	1	0.917	0.828	1	CLONAL	1	TRUE	1	0.545041235073835	2		310	420	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0055663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	663	698	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.545041235073835	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	1	0.545041235073835	4		698	1146	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049819	16049819	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	147	394	0	ENST00000268712.3:c.953G>C	p.Trp318Ser	p.W318S	ENST00000268712	NM_006311.3	318	tGg/tCg	10/46	1	2	FACETS	0.924	0.847	1	0.924	0.847	1	CLONAL	1	TRUE	1	0.545041235073835	2		394	584	SUCCESS
MET	4233	MSKCC	GRCh37	7	116399458	116399458	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	207	476	0	ENST00000397752.3:c.2278A>T	p.Ile760Leu	p.I760L	ENST00000397752	NM_000245.2	760	Ata/Tta	10/21	0.545041235073835	4	FACETS	1	0.968	1	0.359	0.333	0.387	CLONAL	1	TRUE	1	0.545041235073835	4		476	1089	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223445	53223445	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	175	933	0	ENST00000375401.3:c.3914T>C	p.Leu1305Ser	p.L1305S	ENST00000375401	NM_004187.3	1305	tTg/tCg	23/26	1	2	FACETS	0.802	0.739	0.866	0.802	0.739	0.866	CLONAL	1	TRUE	1	0.545041235073835	2		933	801	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0055665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	86	695	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.663	0.586	0.747	0.663	0.586	0.747	SUBCLONAL	1	TRUE	1	0.287097566954551	2		695	903	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	89	415	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.287097566954551	2		415	586	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102084	27102084	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	69	601	0	ENST00000324856.7:c.5010G>A	p.Trp1670Ter	p.W1670*	ENST00000324856	NM_006015.4	1670	tgG/tgA	19/20	1	2	FACETS	0.697	0.606	0.795	0.697	0.606	0.795	SUBCLONAL	1	TRUE	1	0.287097566954551	2		601	690	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200469	67200469	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	101	737	0	ENST00000312629.5:c.663T>G	p.His221Gln	p.H221Q	ENST00000312629	NM_003952.2	221	caT/caG	8/15	0.287097566954551	1	FACETS	0.661	0.59	0.737	0.661	0.59	0.737	SUBCLONAL	1	TRUE	0	0.287097566954551	1		737	911	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207186	1207186	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	78	825	0	ENST00000326873.7:c.274G>T	p.Glu92Ter	p.E92*	ENST00000326873	NM_000455.4	92	Gag/Tag	1/10	NA	3	FACETS	0.717	0.629	0.812			1	INDETERMINATE	1	TRUE	NA	0.287097566954551	3		825	867	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579330	7579330	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055667-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	219	910	1	ENST00000269305.4:c.357del	p.Lys120SerfsTer3	p.K120Sfs*3	ENST00000269305	NM_001126112.2	119	gcC/gc	4/11	0.601173547105223	1	FACETS	0.954	0.896	1	0.954	0.896	1	CLONAL	1	TRUE	0	0.611881320547669	1		911	521	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444650	187444650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1246753673	NA	P-0055667-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	157	683	1	ENST00000232014.4:c.1577G>A	p.Arg526His	p.R526H	ENST00000232014	NM_001130845.1	526	cGc/cAc	7/10	1	2	FACETS	0.943	0.869	1	0.943	0.869	1	CLONAL	1	TRUE	1	0.611881320547669	2		684	544	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628542	187628542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157383372	NA	P-0055667-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	218	845	0	ENST00000441802.2:c.2440G>A	p.Asp814Asn	p.D814N	ENST00000441802	NM_005245.3	814	Gat/Aat	2/27	1	2	FACETS	0.995	0.929	1	0.995	0.929	1	CLONAL	1	TRUE	1	0.611881320547669	2		845	716	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0055670-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	45	215	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	0.79	0.664	0.929			1	INDETERMINATE	1	TRUE	NA	0.237373554800071	2		215	480	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0055670-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	49	328	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.924	0.783	1	0.924	0.783	1	CLONAL	1	TRUE	1	0.237373554800071	2		329	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578541	7578541	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055670-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	83	752	0	ENST00000269305.4:c.389T>A	p.Leu130His	p.L130H	ENST00000269305	NM_001126112.2	130	cTc/cAc	5/11	0.237373554800071	1	FACETS	0.765	0.674	0.862	0.765	0.674	0.862	SUBCLONAL	1	TRUE	0	0.237373554800071	1		752	806	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591885	48591885	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055670-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	60	446	0	ENST00000342988.3:c.1048G>T	p.Val350Phe	p.V350F	ENST00000342988	NM_005359.5	350	Gtt/Ttt	9/12	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.237373554800071	2		446	501	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29002008	29002008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141378173	NA	P-0055670-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	58	397	0	ENST00000282397.4:c.1157G>A	p.Arg386His	p.R386H	ENST00000282397	NM_002019.4	386	cGt/cAt	9/30	1	2	FACETS	0.953	0.819	1	0.953	0.819	1	CLONAL	1	TRUE	1	0.237373554800071	2		397	513	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215817	133215817	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055670-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	121	693	0	ENST00000320574.5:c.5446A>C	p.Asn1816His	p.N1816H	ENST00000320574	NM_006231.2	1816	Aac/Cac	40/49	1	2	FACETS	0.768	0.695	0.844	1	0.985	1	SUBCLONAL	2	TRUE	1	0.237373554800071	2		693	664	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218514	5218514	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055670-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	108	689	0	ENST00000357368.4:c.3965A>G	p.Lys1322Arg	p.K1322R	ENST00000357368	NM_002850.3	1322	aAa/aGa	25/38	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.237373554800071	2		689	885	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519920	NA	P-0055679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	115	199	0	ENST00000397062.3:c.85G>T	p.Asp29Tyr	p.D29Y	ENST00000397062	NM_006164.4	29	Gat/Tat	2/5	NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.65274612746946	2		199	331	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023258	27023258	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	101	150	0	ENST00000324856.7:c.365del	p.Gly122AlafsTer110	p.G122Afs*110	ENST00000324856	NM_006015.4	122	Ggc/gc	1/20	0.65274612746946	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.65274612746946	1		150	161	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100459	8100459	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	367	807	0	ENST00000346208.3:c.433C>T	p.His145Tyr	p.H145Y	ENST00000346208		145	Cac/Tac	3/6	0.65274612746946	3	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.65274612746946	3		807	1303	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	91	374	0				ENST00000310581	NM_198253.2	-/1132			0.251437962796766	2	FACETS	0.865	0.778	0.955	0.865	0.778	0.955	CLONAL	2	TRUE	0	0.366594484519211	2		374	287	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112553	115112553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	140	910	0	ENST00000257566.3:c.1187C>T	p.Ser396Phe	p.S396F	ENST00000257566	NM_016569.3	396	tCc/tTc	7/8	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.366594484519211	2		910	529	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45649965	45649965	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	76	662	0	ENST00000407780.3:c.870G>A	p.Trp290Ter	p.W290*	ENST00000407780	NM_001283052.1	290	tgG/tgA	6/7	0.124037365083778	0	FACETS	0.589	0.518	0.664			1	INDETERMINATE	1	TRUE	0	0.366594484519211	0		662	446	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944607	40944607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766880457	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	37	420	0	ENST00000373198.4:c.1895G>A	p.Arg632Gln	p.R632Q	ENST00000373198	NM_133170.3	632	cGa/cAa	12/32	0.366594484519211	0	FACETS	0.649	0.54	0.768			1	SUBCLONAL	1	TRUE	0	0.366594484519211	0		420	197	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521711	89521711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	57	550	0	ENST00000336596.2:c.2788G>A	p.Glu930Lys	p.E930K	ENST00000336596	NM_005233.5	930	Gaa/Aaa	16/17	1	2	FACETS	0.791	0.681	0.91	0.791	0.681	0.91	CLONAL	1	TRUE	1	0.366594484519211	2		550	393	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514563	41514563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	65	472	1	ENST00000373198.4:c.98C>T	p.Ser33Phe	p.S33F	ENST00000373198	NM_133170.3	33	tCc/tTc	2/32	0.366594484519211	0	FACETS	0.783	0.685	0.887			1	SUBCLONAL	1	TRUE	0	0.366594484519211	0		473	287	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957171	81957171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	97	665	0	ENST00000359376.3:c.2389C>T	p.His797Tyr	p.H797Y	ENST00000359376	NM_002661.3	797	Cac/Tac	22/33	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.366594484519211	2		665	459	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2137925	2137958	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCTGCAGTGCAGGAAAGGTAGGGCCGGGTGGGG	CCCTGCAGTGCAGGAAAGGTAGGGCCGGGTGGGG	-	rs137854209	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	36	980	2	ENST00000219476.3:c.5068+27_5069-47del		p.X1690_splice	ENST00000219476	NM_000548.3	1690		39/42	1	2	FACETS	0.363	0.298	0.436	0.363	0.298	0.436	SUBCLONAL	1	TRUE	1	0.366594484519211	2		982	541	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849863	156849863	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747855434	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	105	741	0	ENST00000524377.1:c.2119G>A	p.Glu707Lys	p.E707K	ENST00000524377	NM_002529.3	707	Gag/Aag	16/17	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.366594484519211	2		741	513	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586056	29586056	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1135402857	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	16	344	0	ENST00000356175.3:c.4276C>T	p.Gln1426Ter	p.Q1426*	ENST00000356175	NM_000267.3	1426	Cag/Tag	32/57	1	2	FACETS	0.891	0.668	1	0.891	0.668	1	CLONAL	1	TRUE	1	0.366594484519211	2		344	98	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633406	8633406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	30	476	0	ENST00000356435.5:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000356435		88	cGg/cAg	3/35	0.352433362482236	1	FACETS	0.488	0.394	0.593	0.488	0.394	0.593	SUBCLONAL	1	TRUE	0	0.366594484519211	1		476	274	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191141	2191141	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	104	830	1	ENST00000398665.3:c.395C>T	p.Ser132Phe	p.S132F	ENST00000398665	NM_032482.2	132	tCc/tTc	5/28	0.352433362482236	1	FACETS	0.802	0.72	0.888	0.802	0.72	0.888	CLONAL	1	TRUE	0	0.366594484519211	1		831	578	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046410	69046410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868582467	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	62	601	0	ENST00000288368.4:c.3883G>A	p.Glu1295Lys	p.E1295K	ENST00000288368	NM_024870.2	1295	Gaa/Aaa	32/40	0.270970978076842	0	FACETS	0.544	0.471	0.622			1	SUBCLONAL	1	TRUE	0	0.366594484519211	0		601	394	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231359	5231359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1340279963	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	101	802	0	ENST00000357368.4:c.2117C>T	p.Pro706Leu	p.P706L	ENST00000357368	NM_002850.3	706	cCc/cTc	14/38	0.352433362482236	1	FACETS	0.835	0.749	0.926	0.835	0.749	0.926	CLONAL	1	TRUE	0	0.366594484519211	1		802	539	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609394	39609394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1360571803	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	39	413	0	ENST00000262039.4:c.1696C>T	p.Arg566Cys	p.R566C	ENST00000262039	NM_002647.2	566	Cgt/Tgt	15/25	1	2	FACETS	0.716	0.596	0.849	0.716	0.596	0.849	SUBCLONAL	1	TRUE	1	0.366594484519211	2		413	297	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125533	7125533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867354196	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	66	591	0	ENST00000302850.5:c.3019C>T	p.Pro1007Ser	p.P1007S	ENST00000302850	NM_000208.2	1007	Cca/Tca	17/22	0.352433362482236	1	FACETS	0.752	0.656	0.855	0.752	0.656	0.855	SUBCLONAL	1	TRUE	0	0.366594484519211	1		591	391	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790003	40790003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	71	604	0	ENST00000373198.4:c.2728G>A	p.Glu910Lys	p.E910K	ENST00000373198	NM_133170.3	910	Gag/Aag	18/32	0.366594484519211	0	FACETS	0.697	0.612	0.787			1	SUBCLONAL	1	TRUE	0	0.366594484519211	0		604	352	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129904	69129904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	50	464	0	ENST00000288368.4:c.4658G>A	p.Gly1553Glu	p.G1553E	ENST00000288368	NM_024870.2	1553	gGa/gAa	38/40	0.270970978076842	0	FACETS	0.527	0.449	0.611			1	SUBCLONAL	1	TRUE	0	0.366594484519211	0		464	328	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211656	46211656	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	19	259	0	ENST00000334344.6:c.625del	p.Val209CysfsTer6	p.V209Cfs*6	ENST00000334344	NM_152641.2	208	Ggg/gg	5/21	0.184812019491522	3	FACETS	0.915	0.702	1	0.458	0.351	0.58	INDETERMINATE	1	TRUE	1	0.366594484519211	3		259	134	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3120990	3120990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1259650887	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	88	684	1	ENST00000078429.4:c.893C>T	p.Pro298Leu	p.P298L	ENST00000078429	NM_002067.2	298	cCc/cTc	7/7	0.352433362482236	1	FACETS	0.914	0.814	1	0.914	0.814	1	CLONAL	1	TRUE	0	0.366594484519211	1		685	429	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804269	43804269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766638870	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	87	683	0	ENST00000372470.3:c.269G>A	p.Arg90Gln	p.R90Q	ENST00000372470	NM_005373.2	90	cGa/cAa	3/12	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.366594484519211	2		683	474	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468128	31468128	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	38	596	0	ENST00000344624.3:c.2284T>C	p.Phe762Leu	p.F762L	ENST00000344624		762	Ttc/Ctc	15/33	0.202036838632932	3	FACETS	0.68	0.563	0.809			1	INDETERMINATE	1	TRUE	NA	0.366594484519211	3		596	361	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81954867	81954867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757834798	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	59	661	0	ENST00000359376.3:c.2300C>T	p.Pro767Leu	p.P767L	ENST00000359376	NM_002661.3	767	cCg/cTg	21/33	1	2	FACETS	0.879	0.76	1	0.879	0.76	1	CLONAL	1	TRUE	1	0.366594484519211	2		661	366	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347677	89347678	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	111	947	0	ENST00000301030.4:c.5272_5273delinsTT	p.Pro1758Phe	p.P1758F	ENST00000301030	NM_001256183.1	1758	CCc/TTc	9/13	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.366594484519211	2		947	582	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287412	46287412	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	27	362	0	ENST00000334344.6:c.5272-1G>A		p.X1758_splice	ENST00000334344	NM_152641.2	1758			0.184812019491522	3	FACETS	1	0.805	1	0.501	0.402	0.611	INDETERMINATE	1	TRUE	1	0.366594484519211	3		362	174	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739887	46739887	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1420879628	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	65	412	0	ENST00000371975.4:c.1688C>T	p.Ser563Leu	p.S563L	ENST00000371975	NM_003579.3	563	tCg/tTg	15/18	1	2	FACETS	0.988	0.861	1	0.988	0.861	1	CLONAL	1	TRUE	1	0.366594484519211	2		412	359	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344820	65344820	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	51	292	0	ENST00000342505.4:c.217C>T	p.Leu73Phe	p.L73F	ENST00000342505	NM_002227.2	73	Ctt/Ttt	4/25	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.366594484519211	2		292	226	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123245023	123245023	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	52	570	0	ENST00000358487.5:c.2081G>A	p.Trp694Ter	p.W694*	ENST00000358487	NM_000141.4	694	tGg/tAg	16/18	0.249582000540106	0	FACETS	0.585	0.501	0.676			1	SUBCLONAL	1	TRUE	0	0.366594484519211	0		570	307	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572216	64572216	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	81	614	0	ENST00000312049.6:c.1423G>A	p.Ala475Thr	p.A475T	ENST00000312049	NM_130799.2	475	Gcc/Acc	10/10	1	2	FACETS	0.893	0.789	1	0.893	0.789	1	CLONAL	1	TRUE	1	0.366594484519211	2		614	495	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103489	77103489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1048521	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	73	433	0	ENST00000356341.3:c.77C>T	p.Ala26Val	p.A26V	ENST00000356341	NM_002576.4	26	gCc/gTc	2/15	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.366594484519211	2		433	350	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216544	108216545	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	14	382	1	ENST00000278616.4:c.8493_8494delinsTT	p.Arg2832Cys	p.R2832C	ENST00000278616	NM_000051.3	2831	ttCCgt/ttTTgt	58/63	0.364667530101227	1	FACETS	0.533	0.389	0.704	0.533	0.389	0.704	SUBCLONAL	1	TRUE	0	0.366594484519211	1		383	117	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691198	18691198	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	31	397	0	ENST00000266497.5:c.3309T>A	p.Tyr1103Ter	p.Y1103*	ENST00000266497		1103	taT/taA	23/31	0.366594484519211	1	FACETS	0.987	0.811	1	0.987	0.811	1	CLONAL	1	TRUE	0	0.366594484519211	1		397	140	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120994	115120995	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	93	551	0	ENST00000257566.3:c.11_12delinsTT	p.Ser4Phe	p.S4F	ENST00000257566	NM_016569.3	4	tCC/tTT	1/8	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.366594484519211	2		551	463	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252774	133252774	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs767060387	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	52	508	0	ENST00000320574.5:c.926A>G	p.Asn309Ser	p.N309S	ENST00000320574	NM_006231.2	309	aAc/aGc	10/49	1	2	FACETS	0.915	0.784	1	0.915	0.784	1	CLONAL	1	TRUE	1	0.366594484519211	2		508	310	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562726	21562726	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	92	544	0	ENST00000382592.4:c.1193C>T	p.Pro398Leu	p.P398L	ENST00000382592	NM_014572.2	398	cCt/cTt	4/8	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.366594484519211	2		544	419	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912514	32912514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	16	425	0	ENST00000380152.3:c.4022C>T	p.Ser1341Leu	p.S1341L	ENST00000380152		1341	tCa/tTa	11/27	0.366594484519211	1	FACETS	0.54	0.402	0.701	0.54	0.402	0.701	SUBCLONAL	1	TRUE	0	0.366594484519211	1		425	132	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779851	3779851	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	95	901	0	ENST00000262367.5:c.5197T>C	p.Tyr1733His	p.Y1733H	ENST00000262367	NM_004380.2	1733	Tat/Cat	31/31	1	2	FACETS	0.932	0.832	1	0.932	0.832	1	CLONAL	1	TRUE	1	0.366594484519211	2		901	556	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843561	3843561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	84	619	0	ENST00000262367.5:c.1042C>T	p.Pro348Ser	p.P348S	ENST00000262367	NM_004380.2	348	Cct/Tct	4/31	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.366594484519211	2		619	451	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56866244	56866244	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543658965	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	87	446	0	ENST00000308159.5:c.1289C>T	p.Ser430Phe	p.S430F	ENST00000308159	NM_014669.4	430	tCc/tTc	12/22	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.366594484519211	2		446	370	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831063	72831063	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	77	532	0	ENST00000268489.5:c.5518C>T	p.Gln1840Ter	p.Q1840*	ENST00000268489	NM_006885.3	1840	Cag/Tag	9/10	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.366594484519211	2		532	396	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226434	2226434	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	129	1052	0	ENST00000398665.3:c.3914G>A	p.Gly1305Glu	p.G1305E	ENST00000398665	NM_032482.2	1305	gGa/gAa	27/28	0.352433362482236	1	FACETS	0.847	0.769	0.928	0.847	0.769	0.928	CLONAL	1	TRUE	0	0.366594484519211	1		1052	679	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051130	128051130	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	111	735	0	ENST00000285398.2:c.193A>T	p.Met65Leu	p.M65L	ENST00000285398	NM_000122.1	65	Atg/Ttg	2/15	1	2	FACETS	0.939	0.846	1	0.939	0.846	1	CLONAL	1	TRUE	1	0.366594484519211	2		735	645	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872931	136872931	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	56	458	0	ENST00000241393.3:c.567C>G	p.Phe189Leu	p.F189L	ENST00000241393	NM_003467.2	189	ttC/ttG	2/2	1	2	FACETS	0.888	0.765	1	0.888	0.765	1	CLONAL	1	TRUE	1	0.366594484519211	2		458	344	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546961	9546961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	49	501	0	ENST00000353224.5:c.1061C>T	p.Pro354Leu	p.P354L	ENST00000353224	NM_177990.2	354	cCt/cTt	5/10	1	2	FACETS	0.876	0.747	1	0.876	0.747	1	CLONAL	1	TRUE	1	0.366594484519211	2		501	305	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62305292	62305292	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	92	816	0	ENST00000360203.5:c.766-1G>A		p.X256_splice	ENST00000360203	NM_001283009.1	256			0.366594484519211	3	FACETS	0.881	0.783	0.985	0.441	0.391	0.493	CLONAL	1	TRUE	1	0.366594484519211	3		816	674	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326825	62326825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568726633	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	134	1108	0	ENST00000360203.5:c.3644C>T	p.Ser1215Phe	p.S1215F	ENST00000360203	NM_001283009.1	1215	tCt/tTt	34/35	0.366594484519211	3	FACETS	1	0.951	1	0.535	0.486	0.586	CLONAL	1	TRUE	1	0.366594484519211	3		1108	809	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000069	30000069	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	124	688	0	ENST00000338641.4:c.82A>G	p.Thr28Ala	p.T28A	ENST00000338641	NM_000268.3	28	Acc/Gcc	1/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.366594484519211	2		688	597	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390200	89390200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	34	396	0	ENST00000336596.2:c.949C>T	p.Pro317Ser	p.P317S	ENST00000336596	NM_005233.5	317	Cct/Tct	4/17	1	2	FACETS	0.535	0.437	0.643	0.535	0.437	0.643	SUBCLONAL	1	TRUE	1	0.366594484519211	2		396	347	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958810	55958810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	54	545	0	ENST00000263923.4:c.3043G>A	p.Gly1015Ser	p.G1015S	ENST00000263923	NM_002253.2	1015	Ggc/Agc	22/30	0.352433362482236	1	FACETS	0.665	0.57	0.767	0.665	0.57	0.767	SUBCLONAL	1	TRUE	0	0.366594484519211	1		545	362	SUCCESS
APC	324	MSKCC	GRCh37	5	112174041	112174041	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	52	412	1	ENST00000257430.4:c.2750A>T	p.Asp917Val	p.D917V	ENST00000257430	NM_000038.5	917	gAt/gTt	16/16	0.169956014222837	3	FACETS	0.927	0.803	1	0.618	0.535	0.706	INDETERMINATE	2	TRUE	0	0.366594484519211	3		413	181	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977660	2977660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	49	720	0	ENST00000396946.4:c.1024G>A	p.Glu342Lys	p.E342K	ENST00000396946	NM_032415.4	342	Gag/Aag	8/25	0.274748937171858	0	FACETS	0.409	0.347	0.477			1	SUBCLONAL	1	TRUE	0	0.366594484519211	0		720	414	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523551	148523551	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	34	208	0	ENST00000320356.2:c.902A>C	p.Asn301Thr	p.N301T	ENST00000320356	NM_004456.4	301	aAt/aCt	8/20	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.366594484519211	2		208	146	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148526909	148526909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	27	354	1	ENST00000320356.2:c.395C>T	p.Pro132Leu	p.P132L	ENST00000320356	NM_004456.4	132	cCt/cTt	5/20	1	2	FACETS	0.957	0.77	1	0.957	0.77	1	CLONAL	1	TRUE	1	0.366594484519211	2		355	154	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741776	145741776	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1345625725	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	128	944	0	ENST00000428558.2:c.727C>T	p.Gln243Ter	p.Q243*	ENST00000428558	NM_004260.3	243	Caa/Taa	5/22	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.366594484519211	2		944	679	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428249	47428249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760360817	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	90	904	0	ENST00000377045.4:c.1209G>A	p.Met403Ile	p.M403I	ENST00000377045	NM_001654.4	403	atG/atA	11/16	0.366594484519211	1	FACETS	0.706	0.628	0.789	0.706	0.628	0.789	SUBCLONAL	1	TRUE	0	0.366594484519211	1		904	568	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940453	76940453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	23	474	0	ENST00000373344.5:c.640G>A	p.Asp214Asn	p.D214N	ENST00000373344	NM_000489.3	214	Gat/Aat	8/35	0.366594484519211	1	FACETS	0.637	0.501	0.791	0.637	0.501	0.791	SUBCLONAL	1	TRUE	0	0.366594484519211	1		474	161	SUCCESS
BTK	695	MSKCC	GRCh37	X	100624991	100624991	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	25	504	0	ENST00000308731.7:c.386A>T	p.Lys129Ile	p.K129I	ENST00000308731	NM_000061.2	129	aAa/aTa	5/19	0.366594484519211	1	FACETS	0.541	0.429	0.668	0.541	0.429	0.668	SUBCLONAL	1	TRUE	0	0.366594484519211	1		504	206	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528145	29528147	+	frameshift_variant	Frame_Shift_Del	DEL	CGT	CGT	TG	novel	NA	P-0055680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	45	644	1	ENST00000356175.3:c.1153_1155delinsTG	p.Arg385Ter	p.R385*	ENST00000356175	NM_000267.3	385	CGT/TG	10/57	1	2	FACETS	0.944	0.799	1	0.944	0.799	1	CLONAL	1	TRUE	1	0.366594484519211	2		645	260	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149516579	149516579	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	143	939	1	ENST00000261799.4:c.32C>A	p.Ala11Asp	p.A11D	ENST00000261799	NM_002609.3	11	gCc/gAc	2/23	1	2	FACETS	0.936	0.859	1	0.936	0.859	1	CLONAL	1	TRUE	1	0.61373091954721	2		940	498	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458270	12458270	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	82	642	4	ENST00000287820.6:c.892del	p.Leu298CysfsTer38	p.L298Cfs*38	ENST00000287820	NM_015869.4	296	aCc/ac	6/7	1	2	FACETS	0.854	0.76	0.952	0.854	0.76	0.952	CLONAL	1	TRUE	1	0.61373091954721	2		646	313	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437612	56437612	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	58	497	1	ENST00000407977.2:c.850G>T	p.Glu284Ter	p.E284*	ENST00000407977		284	Gag/Tag	8/10	1	2	FACETS	0.626	0.542	0.716	0.626	0.542	0.716	SUBCLONAL	1	TRUE	1	0.61373091954721	2		498	302	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196282	106196282	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs866214403	NA	P-0055681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	75	455	0	ENST00000380013.4:c.4615C>T	p.Gln1539Ter	p.Q1539*	ENST00000380013	NM_001127208.2	1539	Cag/Tag	11/11	1	2	FACETS	0.947	0.841	1	0.947	0.841	1	CLONAL	1	TRUE	1	0.61373091954721	2		455	258	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685554	29685555	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs772757623	NA	P-0055681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	69	528	0	ENST00000356175.3:c.7967dup	p.Leu2656PhefsTer16	p.L2656Ffs*16	ENST00000356175	NM_000267.3	2655	aat/aaTt	54/57	1	2	FACETS	0.91	0.803	1	0.91	0.803	1	CLONAL	1	TRUE	1	0.61373091954721	2		528	247	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926501	59926501	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	62	691	0	ENST00000259008.2:c.496A>G	p.Thr166Ala	p.T166A	ENST00000259008	NM_032043.2	166	Act/Gct	5/20	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.61373091954721	2		691	195	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157722	106157722	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0055681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	52	317	0	ENST00000380013.4:c.2623A>T	p.Lys875Ter	p.K875*	ENST00000380013	NM_001127208.2	875	Aag/Tag	3/11	1	2	FACETS	0.873	0.755	0.999	0.873	0.755	0.999	CLONAL	1	TRUE	1	0.61373091954721	2		317	194	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628158	187628158	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs768948260	NA	P-0055681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	120	815	0	ENST00000441802.2:c.2824G>C	p.Glu942Gln	p.E942Q	ENST00000441802	NM_005245.3	942	Gaa/Caa	2/27	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.61373091954721	2		815	374	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324675	31324675	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	48	1032	0	ENST00000412585.2:c.133del	p.Arg45AlafsTer14	p.R45Afs*14	ENST00000412585	NM_005514.6	45	Cgc/gc	2/8	1	2	FACETS	0.373	0.316	0.436	0.373	0.316	0.436	SUBCLONAL	1	TRUE	1	0.61373091954721	2		1032	419	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730186	133730186	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0055681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	148	553	1	ENST00000318560.5:c.254-2A>T		p.X85_splice	ENST00000318560	NM_005157.4	85			0.3713767375092	3	FACETS	0.985	0.915	1	0.985	0.915	1	CLONAL	2	TRUE	1	0.61373091954721	3		554	320	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608200	100608200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	71	525	0	ENST00000308731.7:c.1890G>T	p.Met630Ile	p.M630I	ENST00000308731	NM_000061.2	630	atG/atT	18/19	1	2	FACETS	0.893	0.789	1	0.893	0.789	1	CLONAL	1	TRUE	1	0.61373091954721	2		525	259	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0055682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	489	727	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.377837953007697	5	FACETS	0.926	0.889	0.963	0.926	0.889	0.963	CLONAL	4	TRUE	1	0.377837953007697	5		727	1095	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966608	36966608	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766774692	NA	P-0055682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	75	823	3	ENST00000358127.4:c.718G>A	p.Val240Met	p.V240M	ENST00000358127	NM_001280556.1	240	Gtg/Atg	6/10	NA	2	FACETS	0.454	0.397	0.516			1	INDETERMINATE	1	TRUE	NA	0.377837953007697	2		826	874	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579316	7579316	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	256	701	0	ENST00000269305.4:c.371del	p.Cys124SerfsTer46	p.C124Sfs*46	ENST00000269305	NM_001126112.2	124	tGc/tc	4/11	0.288529597873319	3	FACETS	1	0.986	1	0.764	0.719	0.81	CLONAL	2	TRUE	0	0.377837953007697	3		701	703	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0055683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	39	181	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.668	0.554	0.796	0.668	0.554	0.796	SUBCLONAL	1	TRUE	1	0.25	2		181	467	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913355	NA	P-0055683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	34	385	0	ENST00000288602.6:c.1406G>T	p.Gly469Val	p.G469V	ENST00000288602	NM_004333.4	469	gGa/gTa	11/18	1	2	FACETS	0.557	0.455	0.673	0.557	0.455	0.673	SUBCLONAL	1	TRUE	1	0.25	2		385	488	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	66	889	0	ENST00000227507.2:c.859C>G	p.Pro287Ala	p.P287A	ENST00000227507	NM_053056.2	287	Ccc/Gcc	5/5	1	2	FACETS	0.522	0.451	0.599	0.522	0.451	0.599	SUBCLONAL	1	TRUE	1	0.25	2		889	1012	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107096	27107096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	51	617	0	ENST00000324856.7:c.6707G>C	p.Arg2236Pro	p.R2236P	ENST00000324856	NM_006015.4	2236	cGc/cCc	20/20	1	2	FACETS	0.533	0.451	0.622	0.533	0.451	0.622	SUBCLONAL	1	TRUE	1	0.25	2		617	766	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120370	70120370	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555629443	NA	P-0055683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	161	1045	1	ENST00000245479.2:c.1372C>T	p.Gln458Ter	p.Q458*	ENST00000245479	NM_000346.3	458	Cag/Tag	3/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.25	2		1046	1127	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653807	89653807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554893782	NA	P-0055683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	49	356	0	ENST00000371953.3:c.105G>A	p.Met35Ile	p.M35I	ENST00000371953	NM_000314.4	35	atG/atA	2/9	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.25	2		356	358	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225600	26225600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771825902	NA	P-0055683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	53	656	0	ENST00000360408.1:c.218G>A	p.Arg73Gln	p.R73Q	ENST00000360408	NM_003532.2	73	cGa/cAa	1/1	1	2	FACETS	0.473	0.402	0.552	0.473	0.402	0.552	SUBCLONAL	1	TRUE	1	0.25	2		656	896	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099026	27099026	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	66	621	0	ENST00000324856.7:c.3442C>T	p.Gln1148Ter	p.Q1148*	ENST00000324856	NM_006015.4	1148	Cag/Tag	13/20	1	2	FACETS	0.629	0.544	0.72	0.629	0.544	0.72	SUBCLONAL	1	TRUE	1	0.25	2		621	840	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821875	72821875	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	49	570	2	ENST00000268489.5:c.10300del	p.Leu3434SerfsTer51	p.L3434Sfs*51	ENST00000268489	NM_006885.3	3434	Ctc/tc	10/10	1	2	FACETS	0.506	0.427	0.593	0.506	0.427	0.593	SUBCLONAL	1	TRUE	1	0.25	2		572	775	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112235	115112235	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	29	325	0	ENST00000257566.3:c.1505G>A	p.Gly502Asp	p.G502D	ENST00000257566	NM_016569.3	502	gGc/gAc	7/8	1	2	FACETS	0.598	0.48	0.732	0.598	0.48	0.732	SUBCLONAL	1	TRUE	1	0.25	2		325	388	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62008713	62008713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1350196178	NA	P-0055683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	84	893	0	ENST00000392795.3:c.103C>T	p.Arg35Trp	p.R35W	ENST00000392795	NM_001039933.1	35	Cgg/Tgg	2/6	1	2	FACETS	0.673	0.593	0.76	0.673	0.593	0.76	SUBCLONAL	1	TRUE	1	0.25	2		893	998	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681655	30681657	+	inframe_deletion	In_Frame_Del	DEL	CTA	CTA	-	novel	NA	P-0055683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	45	553	0	ENST00000376406.3:c.440_442del	p.Val147del	p.V147del	ENST00000376406	NM_014641.2	147	gTAGaa/gaa	3/15	1	2	FACETS	0.495	0.415	0.584	0.495	0.415	0.584	SUBCLONAL	1	TRUE	1	0.25	2		553	727	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005270	150005271	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0055683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	45	553	0	ENST00000253339.5:c.954_955del	p.Gly319HisfsTer2	p.G319Hfs*2	ENST00000253339		318	agAGgc/aggc	3/7	1	2	FACETS	0.56	0.47	0.66	0.56	0.47	0.66	SUBCLONAL	1	TRUE	1	0.25	2		553	643	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249017	55249018	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCACGT	novel	NA	P-0055683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	50	675	0	ENST00000275493.2:c.2316_2321dup	p.His773_Val774dup	p.H773_V774dup	ENST00000275493	NM_005228.3	773	ccc/ccCCACGTc	20/28	1	2	FACETS	0.455	0.384	0.532	0.455	0.384	0.532	SUBCLONAL	1	TRUE	1	0.25	2		675	880	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133748330	133748330	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	46	680	0	ENST00000318560.5:c.992del	p.Asn331ThrfsTer5	p.N331Tfs*5	ENST00000318560	NM_005157.4	331	Aac/ac	6/11	1	2	FACETS	0.406	0.341	0.479	0.406	0.341	0.479	SUBCLONAL	1	TRUE	1	0.25	2		680	906	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120376	70120376	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	CACGG	novel	NA	P-0055683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	147	1026	0	ENST00000245479.2:c.1378delinsCACGG	p.Thr460HisfsTer119	p.T460Hfs*119	ENST00000245479	NM_000346.3	460	Acc/CACGGcc	3/3	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.25	2		1026	1118	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0055684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	388	336	0	ENST00000374690.3:c.2105T>A	p.Leu702His	p.L702H	ENST00000374690	NM_000044.3	702	cTc/cAc	4/8	0.857599150217498	2	FACETS	1	0.968	1			1	CLONAL	1	TRUE	NA	0.857599150217498	2		336	889	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692792	89692792	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs779530981	NA	P-0055684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	176	372	0	ENST00000371953.3:c.276C>A	p.Asp92Glu	p.D92E	ENST00000371953	NM_000314.4	92	gaC/gaA	5/9	0.857599150217498	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.857599150217498	1		372	226	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754325	57754325	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	214	398	0	ENST00000274289.3:c.526G>T	p.Val176Leu	p.V176L	ENST00000274289	NM_006622.3	176	Gtg/Ttg	4/14	0.437065207747688	1	FACETS	0.707	0.668	0.747	0.707	0.668	0.747	INDETERMINATE	1	TRUE	0	0.857599150217498	1		398	403	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729917	47729917	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	139	502	0	ENST00000449228.1:c.472C>T	p.Pro158Ser	p.P158S	ENST00000449228	NM_001127240.2	158	Ccc/Tcc	3/4	0.525121050179798	1	FACETS	0.376	0.345	0.409	0.376	0.345	0.409	SUBCLONAL	1	TRUE	0	0.857599150217498	1		502	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578231	7578245	+	inframe_deletion	In_Frame_Del	DEL	CAAATACTCCACACG	CAAATACTCCACACG	-	novel	NA	P-0055684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	340	746	0	ENST00000269305.4:c.604_618del	p.Arg202_Leu206del	p.R202_L206del	ENST00000269305	NM_001126112.2	202	CGTGTGGAGTATTTG/-	6/11	0.857599150217498	1	FACETS	0.897	0.863	0.93	0.897	0.863	0.93	CLONAL	1	TRUE	0	0.857599150217498	1		746	505	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533735	63533735	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	358	848	0	ENST00000307078.5:c.1419C>G	p.His473Gln	p.H473Q	ENST00000307078	NM_004655.3	473	caC/caG	6/11	1	2	FACETS	0.931	0.886	0.976	0.931	0.886	0.976	CLONAL	1	TRUE	1	0.857599150217498	2		848	897	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47079248	47079248	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	274	509	0	ENST00000409792.3:c.7258C>G	p.Pro2420Ala	p.P2420A	ENST00000409792	NM_014159.6	2420	Cct/Gct	18/21	1	2	FACETS	0.941	0.889	0.994	0.941	0.889	0.994	CLONAL	1	TRUE	1	0.857599150217498	2		509	679	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169999729	169999729	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	39	390	0	ENST00000295797.4:c.1040A>G	p.Gln347Arg	p.Q347R	ENST00000295797	NM_002740.5	347	cAa/cGa	11/18	1	2	FACETS	0.196	0.162	0.234	0.196	0.162	0.234	SUBCLONAL	1	TRUE	1	0.857599150217498	2		390	463	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031963	26031963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	274	533	0	ENST00000244661.2:c.326del	p.Asn109ThrfsTer10	p.N109Tfs*10	ENST00000244661	NM_003537.3	109	aAc/ac	1/1	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.857599150217498	2		533	639	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508366	106508366	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	226	474	0	ENST00000359195.3:c.360C>G	p.Asp120Glu	p.D120E	ENST00000359195	NM_002649.2	120	gaC/gaG	2/11	0.253202927564348	6	FACETS	0.773	0.72	0.827	0.258	0.24	0.276	INDETERMINATE	2	TRUE	0	0.857599150217498	6		474	926	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339432	116339432	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0055684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	218	405	0	ENST00000397752.3:c.294T>A	p.Cys98Ter	p.C98*	ENST00000397752	NM_000245.2	98	tgT/tgA	2/21	0.253202927564348	6	FACETS	0.861	0.802	0.92	0.287	0.267	0.307	INDETERMINATE	2	TRUE	0	0.857599150217498	6		405	802	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934576	NA	P-0055685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	340	817	0	ENST00000269305.4:c.818G>C	p.Arg273Pro	p.R273P	ENST00000269305	NM_001126112.2	273	cGt/cCt	8/11	0.534518938368429	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.534518938368429	1		817	865	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033245	69033245	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530869739	NA	P-0055685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	220	574	1	ENST00000288368.4:c.3685G>A	p.Val1229Ile	p.V1229I	ENST00000288368	NM_024870.2	1229	Gtc/Atc	30/40	0.534518938368429	3	FACETS	0.955	0.888	1	0.478	0.444	0.513	CLONAL	1	TRUE	1	0.534518938368429	3		575	1092	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244574	41244574	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	195	602	0	ENST00000357654.3:c.2974del	p.Thr992LeufsTer8	p.T992Lfs*8	ENST00000357654	NM_007294.3	992	Act/ct	10/23	0.534518938368429	1	FACETS	0.831	0.773	0.891	0.831	0.773	0.891	CLONAL	1	TRUE	0	0.534518938368429	1		602	643	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665179	138665179	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	250	810	0	ENST00000330315.3:c.386C>G	p.Thr129Arg	p.T129R	ENST00000330315	NM_023067.3	129	aCg/aGg	1/1	1	2	FACETS	0.804	0.752	0.859	0.804	0.752	0.859	CLONAL	1	TRUE	1	0.534518938368429	2		810	1163	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	217	677	4	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.917	0.853	0.983	0.917	0.853	0.983	CLONAL	1	TRUE	1	0.487971570540049	2		681	970	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	280	782	11	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.487971570540049	2		793	1101	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	110	251	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.487971570540049	2		251	450	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	307	901	2	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.947	0.891	1	0.947	0.891	1	CLONAL	1	TRUE	1	0.487971570540049	2		903	1329	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	253	700	3	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.979	0.916	1	0.979	0.916	1	CLONAL	1	TRUE	1	0.487971570540049	2		703	1059	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	23	523	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.112	0.086	0.142	0.112	0.086	0.142	SUBCLONAL	1	TRUE	1	0.487971570540049	2		523	843	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	355	707	6	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.487971570540049	2		713	1077	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	236	776	2	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.925	0.863	0.989	0.925	0.863	0.989	CLONAL	1	TRUE	1	0.487971570540049	2		778	1046	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101402	27101402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	181	480	1	ENST00000324856.7:c.4689del	p.Met1564Ter	p.M1564*	ENST00000324856	NM_006015.4	1562	Ccc/cc	18/20	1	2	FACETS	0.97	0.896	1	0.97	0.896	1	CLONAL	1	TRUE	1	0.487971570540049	2		481	765	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	238	617	2	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.487971570540049	2		619	890	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405953	49405953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	227	558	1	ENST00000418115.1:c.185G>A	p.Gly62Glu	p.G62E	ENST00000418115	NM_001664.2	62	gGg/gAg	3/5	1	2	FACETS	0.908	0.846	0.972	0.908	0.846	0.972	CLONAL	1	TRUE	1	0.487971570540049	2		559	1025	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	203	382	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.487971570540049	2		382	572	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	120	451	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.847	0.767	0.93	0.847	0.767	0.93	CLONAL	1	TRUE	1	0.487971570540049	2		453	581	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992196	72992196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111320371	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	274	795	0	ENST00000268489.5:c.1849G>A	p.Val617Ile	p.V617I	ENST00000268489	NM_006885.3	617	Gtt/Att	2/10	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.487971570540049	2		795	1100	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	129	400	5	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	0.953	0.867	1	0.953	0.867	1	CLONAL	1	TRUE	1	0.487971570540049	2		405	555	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681119	117681120	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs748436511	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	132	468	0	ENST00000368508.3:c.3500dup	p.Leu1167PhefsTer26	p.L1167Ffs*26	ENST00000368508	NM_002944.2	1167	tta/ttTa	23/43	1	2	FACETS	0.823	0.749	0.901	0.823	0.749	0.901	CLONAL	1	TRUE	1	0.487971570540049	2		468	657	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	159	486	5	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.792	0.726	0.86	0.792	0.726	0.86	SUBCLONAL	1	TRUE	1	0.487971570540049	2		491	823	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434182	12434182	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776687	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	136	422	0	ENST00000287820.6:c.556del	p.Ser186ValfsTer47	p.S186Vfs*47	ENST00000287820	NM_015869.4	184	Aaa/aa	4/7	1	2	FACETS	0.931	0.849	1	0.931	0.849	1	CLONAL	1	TRUE	1	0.487971570540049	2		422	599	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879672	151879672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	52	219	0	ENST00000262189.6:c.5273G>A	p.Arg1758His	p.R1758H	ENST00000262189	NM_170606.2	1758	cGt/cAt	36/59	1	2	FACETS	0.65	0.556	0.751	0.65	0.556	0.751	SUBCLONAL	1	TRUE	1	0.487971570540049	2		219	328	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982557	10982557	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	44	161	0	ENST00000327064.4:c.179T>C	p.Val60Ala	p.V60A	ENST00000327064	NM_199141.1	60	gTg/gCg	1/16	1	2	FACETS	0.73	0.617	0.853	0.73	0.617	0.853	SUBCLONAL	1	TRUE	1	0.487971570540049	2		161	247	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430410	181430410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	327	692	0	ENST00000325404.1:c.262C>T	p.Arg88Trp	p.R88W	ENST00000325404	NM_003106.3	88	Cgg/Tgg	1/1	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.487971570540049	2		692	1121	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345760	152345760	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	86	235	0	ENST00000359321.1:c.810del	p.Phe270LeufsTer27	p.F270Lfs*27	ENST00000359321	NM_005431.1	270	ttT/tt	3/3	1	2	FACETS	0.783	0.696	0.876	0.783	0.696	0.876	SUBCLONAL	1	TRUE	1	0.487971570540049	2		235	450	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682809	190682810	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587778609	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	88	315	1	ENST00000441310.2:c.492dup	p.Cys165MetfsTer2	p.C165Mfs*2	ENST00000441310	NM_000534.4	162	gca/gcAa	5/13	1	2	FACETS	0.769	0.684	0.859	0.769	0.684	0.859	SUBCLONAL	1	TRUE	1	0.487971570540049	2		316	469	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925436	114925436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766219492	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	189	554	0	ENST00000543371.1:c.1514G>A	p.Arg505Gln	p.R505Q	ENST00000543371	NM_001198531.1	505	cGa/cAa	14/14	1	2	FACETS	0.966	0.894	1	0.966	0.894	1	CLONAL	1	TRUE	1	0.487971570540049	2		554	802	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646279	3646279	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749277750	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	287	922	1	ENST00000294008.3:c.1799C>T	p.Pro600Leu	p.P600L	ENST00000294008	NM_032444.2	600	cCg/cTg	8/15	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.487971570540049	2		923	1159	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372338	55372338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	230	802	1	ENST00000297316.4:c.1028G>A	p.Arg343Gln	p.R343Q	ENST00000297316	NM_022454.3	343	cGg/cAg	2/2	0.487971570540049	3	FACETS	0.977	0.91	1	0.489	0.455	0.524	CLONAL	1	TRUE	1	0.487971570540049	3		803	1200	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830885	72830885	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	235	730	2	ENST00000268489.5:c.5696del	p.Gly1899GlufsTer15	p.G1899Efs*15	ENST00000268489	NM_006885.3	1899	gGa/ga	9/10	1	2	FACETS	0.923	0.861	0.986	0.923	0.861	0.986	CLONAL	1	TRUE	1	0.487971570540049	2		732	1044	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578260	7578260	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786204041	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	37	677	0	ENST00000269305.4:c.589G>T	p.Val197Leu	p.V197L	ENST00000269305	NM_001126112.2	197	Gtg/Ttg	6/11	1	2	FACETS	0.151	0.123	0.181	0.151	0.123	0.181	SUBCLONAL	1	TRUE	1	0.487971570540049	2		677	1007	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099940	27099940	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	271	754	0	ENST00000324856.7:c.3819G>T	p.Met1273Ile	p.M1273I	ENST00000324856	NM_006015.4	1273	atG/atT	15/20	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.487971570540049	2		754	1104	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431413	121431413	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	220	747	1	ENST00000257555.6:c.620del	p.Gly207AlafsTer26	p.G207Afs*26	ENST00000257555		206	tGg/tg	3/10	1	2	FACETS	0.895	0.833	0.96	0.895	0.833	0.96	CLONAL	1	TRUE	1	0.487971570540049	2		748	1007	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250198	133250198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775340163	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	249	724	0	ENST00000320574.5:c.1322C>T	p.Pro441Leu	p.P441L	ENST00000320574	NM_006231.2	441	cCg/cTg	13/49	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.487971570540049	2		724	972	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562514	21562514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	10	31	0	ENST00000382592.4:c.1405C>T	p.Pro469Ser	p.P469S	ENST00000382592	NM_014572.2	469	Cct/Tct	4/8	1	2	FACETS	0.759	0.526	1	0.759	0.526	1	CLONAL	1	TRUE	1	0.487971570540049	2		31	54	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43766874	43766874	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	88	217	0	ENST00000382044.4:c.1177C>T	p.Gln393Ter	p.Q393*	ENST00000382044	NM_001141980.1	393	Caa/Taa	10/28	1	2	FACETS	0.847	0.754	0.944	0.847	0.754	0.944	CLONAL	1	TRUE	1	0.487971570540049	2		217	426	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274094	10274094	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	257	790	0	ENST00000330684.3:c.175C>A	p.Gln59Lys	p.Q59K	ENST00000330684	NM_001134407.1	59	Cag/Aag	2/13	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.487971570540049	2		790	1037	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348694	89348694	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	312	850	0	ENST00000301030.4:c.4256C>A	p.Thr1419Asn	p.T1419N	ENST00000301030	NM_001256183.1	1419	aCc/aAc	9/13	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.487971570540049	2		850	1273	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976159	7976159	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514528	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	314	827	2	ENST00000319144.4:c.2036G>A	p.Arg679His	p.R679H	ENST00000319144	NM_001139.2	679	cGc/cAc	15/15	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.487971570540049	2		829	1274	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609302	39609302	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	97	260	0	ENST00000262039.4:c.1604T>C	p.Val535Ala	p.V535A	ENST00000262039	NM_002647.2	535	gTc/gCc	15/25	1	2	FACETS	0.833	0.746	0.925	0.833	0.746	0.925	CLONAL	1	TRUE	1	0.487971570540049	2		260	477	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223983	36223983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760774396	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	315	946	0	ENST00000222270.7:c.6533G>A	p.Gly2178Asp	p.G2178D	ENST00000222270	NM_014727.1	2178	gGc/gAc	28/37	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.487971570540049	2		946	1276	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095952	178095952	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	172	465	0	ENST00000397062.3:c.1379G>T	p.Arg460Met	p.R460M	ENST00000397062	NM_006164.4	460	aGg/aTg	5/5	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.487971570540049	2		465	674	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723503	49723503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	23	66	0	ENST00000449682.2:c.1139G>A	p.Arg380Gln	p.R380Q	ENST00000449682	NM_020998.3	380	cGg/cAg	9/18	1	2	FACETS	0.982	0.782	1	0.982	0.782	1	CLONAL	1	TRUE	1	0.487971570540049	2		66	96	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651277	52651277	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	122	412	0	ENST00000394830.3:c.1818+1G>A		p.X606_splice	ENST00000394830	NM_018313.4	606			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.487971570540049	2		412	475	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591146	67591146	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	95	301	0	ENST00000274335.5:c.1739A>G	p.Tyr580Cys	p.Y580C	ENST00000274335		580	tAc/tGc	12/15	1	2	FACETS	0.841	0.752	0.934	0.841	0.752	0.934	CLONAL	1	TRUE	1	0.487971570540049	2		301	463	SUCCESS
APC	324	MSKCC	GRCh37	5	112176308	112176308	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs587779796	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	106	371	2	ENST00000257430.4:c.5017G>T	p.Glu1673Ter	p.E1673*	ENST00000257430	NM_000038.5	1673	Gaa/Taa	16/16	1	2	FACETS	0.799	0.718	0.883	0.799	0.718	0.883	SUBCLONAL	1	TRUE	1	0.487971570540049	2		373	544	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149434901	149434901	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	76	450	0	ENST00000286301.3:c.2555-2A>C		p.X852_splice	ENST00000286301	NM_005211.3	852			1	2	FACETS	0.434	0.38	0.492	0.434	0.38	0.492	SUBCLONAL	1	TRUE	1	0.487971570540049	2		450	718	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469813	157469816	+	frameshift_variant	Frame_Shift_Del	DEL	CCCA	CCCA	-	novel	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	182	698	0	ENST00000346085.5:c.2607_2610del	p.Pro870GlyfsTer43	p.P870Gfs*43	ENST00000346085	NM_020732.3	869	ggCCCA/gg	9/20	1	2	FACETS	0.709	0.653	0.767	0.709	0.653	0.767	SUBCLONAL	1	TRUE	1	0.487971570540049	2		698	1052	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188086	151188086	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	147	454	0	ENST00000262187.5:c.67A>G	p.Thr23Ala	p.T23A	ENST00000262187	NM_005614.3	23	Acg/Gcg	2/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.487971570540049	2		454	532	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371745	55371746	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	162	535	0	ENST00000297316.4:c.437dup	p.Arg147AlafsTer15	p.R147Afs*15	ENST00000297316	NM_022454.3	145	-/A	2/2	0.487971570540049	3	FACETS	1	0.954	1	0.528	0.485	0.573	CLONAL	1	TRUE	1	0.487971570540049	3		535	782	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8501018	8501018	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	145	370	0	ENST00000356435.5:c.1864A>C	p.Ser622Arg	p.S622R	ENST00000356435		622	Agt/Cgt	13/35	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.487971570540049	2		370	585	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528699	8528699	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	161	462	0	ENST00000356435.5:c.433A>G	p.Met145Val	p.M145V	ENST00000356435		145	Atg/Gtg	4/35	1	2	FACETS	0.913	0.839	0.989	0.913	0.839	0.989	CLONAL	1	TRUE	1	0.487971570540049	2		462	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578554	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CTTGTTGAGGGCAGGGGAGTA	CTTGTTGAGGGCAGGGGAGTA	-	novel	NA	P-0055687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	2187	925	0	ENST00000269305.4:c.376_396del	p.Tyr126_Lys132del	p.Y126_K132del	ENST00000269305	NM_001126112.2	126	TACTCCCCTGCCCTCAACAAG/-	5/11	0.834308099742847	5	FACETS	0.972	0.964	0.98			1	CLONAL	5	TRUE	NA	0.834308099742847	5		925	2428	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503133	125503133	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	182	351	0	ENST00000428830.2:c.500T>C	p.Met167Thr	p.M167T	ENST00000428830	NM_001114121.2	167	aTg/aCg	6/14	0.834308099742847	3	FACETS	0.933	0.864	1	0.466	0.432	0.502	CLONAL	1	TRUE	1	0.834308099742847	3		351	663	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973508	15973508	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	212	356	0	ENST00000268712.3:c.4484G>T	p.Gly1495Val	p.G1495V	ENST00000268712	NM_006311.3	1495	gGc/gTc	31/46	NA	2	FACETS	0.979	0.918	1			1	INDETERMINATE	1	TRUE	NA	0.834308099742847	2		356	519	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484793	57484793	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1261	149	664	0	ENST00000371085.3:c.773G>C	p.Arg258Pro	p.R258P	ENST00000371085	NM_000516.4	258	cGg/cCg	10/13	0.49664422283835	4	FACETS	0.465	0.423	0.509	0.232	0.211	0.255	INDETERMINATE	1	TRUE	2	0.834308099742847	4		664	1410	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0055688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	118	573	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.342632865996855	2		573	625	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0055688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	115	598	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.951	0.857	1	0.951	0.857	1	CLONAL	1	TRUE	1	0.342632865996855	2		598	706	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591085	67591085	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519839	NA	P-0055688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	63	239	0	ENST00000274335.5:c.1678G>T	p.Asp560Tyr	p.D560Y	ENST00000274335		560	Gac/Tac	12/15	1	2	FACETS	0.917	0.796	1	0.917	0.796	1	CLONAL	1	TRUE	1	0.342632865996855	2		239	401	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074064	8074064	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	83	378	0	ENST00000377482.5:c.595C>T	p.Arg199Ter	p.R199*	ENST00000377482	NM_018948.3	199	Cga/Tga	4/4	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.342632865996855	2		378	470	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672291	86672291	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0055688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	98	386	0	ENST00000274376.6:c.2093T>G	p.Leu698Ter	p.L698*	ENST00000274376	NM_002890.2	698	tTa/tGa	16/25	1	2	FACETS	0.985	0.88	1	0.985	0.88	1	CLONAL	1	TRUE	1	0.342632865996855	2		386	581	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073929	8073929	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	85	476	0	ENST00000377482.5:c.730C>T	p.Arg244Ter	p.R244*	ENST00000377482	NM_018948.3	244	Cga/Tga	4/4	1	2	FACETS	0.889	0.788	0.998	0.889	0.788	0.998	CLONAL	1	TRUE	1	0.342632865996855	2		476	558	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239969	53239969	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	150	692	0	ENST00000375401.3:c.1472A>G	p.Asn491Ser	p.N491S	ENST00000375401	NM_004187.3	491	aAt/aGt	11/26	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.342632865996855	2		692	844	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553357	106553357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	113	523	0	ENST00000369096.4:c.1322C>T	p.Pro441Leu	p.P441L	ENST00000369096	NM_001198.3	441	cCg/cTg	5/7	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.342632865996855	2		523	619	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653844	89653844	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	109	290	0	ENST00000371953.3:c.143del	p.Asn48ThrfsTer6	p.N48Tfs*6	ENST00000371953	NM_000314.4	48	Aac/ac	2/9	0.342632865996855	2	FACETS	0.86	0.779	0.943	0.86	0.779	0.943	CLONAL	2	TRUE	0	0.342632865996855	2		290	370	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098914	178098964	+	inframe_deletion	In_Frame_Del	DEL	TTCCGTCGCTGACTGAAGTCAAATACTTCTCGACTTACTCCAAGATCTATA	TTCCGTCGCTGACTGAAGTCAAATACTTCTCGACTTACTCCAAGATCTATA	-	novel	NA	P-0055688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	78	387	0	ENST00000397062.3:c.81_131del	p.Asp27_Lys44delinsGlu	p.D27_K44delinsE	ENST00000397062	NM_006164.4	27	gaTATAGATCTTGGAGTAAGTCGAGAAGTATTTGACTTCAGTCAGCGACGGAAa/gaa	2/5	1	2	FACETS	0.876	0.771	0.987	0.876	0.771	0.987	CLONAL	1	TRUE	1	0.342632865996855	2		387	520	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588182	67588202	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCTCGAGGTAAGGCTACAGA	ATCTCGAGGTAAGGCTACAGA	-	novel	NA	P-0055688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	50	245	0	ENST00000274335.5:c.1013_1019+14del		p.X338_splice	ENST00000274335		338		7/15	1	2	FACETS	0.748	0.637	0.87	0.748	0.637	0.87	SUBCLONAL	1	TRUE	1	0.342632865996855	2		245	390	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682692	86682693	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	47	184	0	ENST00000274376.6:c.2898dup	p.Met967TyrfsTer7	p.M967Yfs*7	ENST00000274376	NM_002890.2	966	cgt/cgTt	23/25	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.342632865996855	2		184	222	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577573	7577573	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0055689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	984	629	0	ENST00000269305.4:c.708C>G	p.Tyr236Ter	p.Y236*	ENST00000269305	NM_001126112.2	236	taC/taG	7/11	0.911305813657731	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.911305813657731	3		629	1045	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921460	39921460	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs967564648	NA	P-0055689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	440	354	0	ENST00000378444.4:c.4360C>T	p.Arg1454Trp	p.R1454W	ENST00000378444	NM_001123385.1	1454	Cgg/Tgg	10/15	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.911305813657731	1		354	474	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462024	120462024	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	302	681	0	ENST00000256646.2:c.5692G>T	p.Asp1898Tyr	p.D1898Y	ENST00000256646	NM_024408.3	1898	Gat/Tat	31/34	0.911305813657731	3	FACETS	0.879	0.829	0.931	0.44	0.414	0.466	CLONAL	1	TRUE	1	0.911305813657731	3		681	1097	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402795	139402795	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780582836	NA	P-0055689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	525	986	1	ENST00000277541.6:c.3214G>A	p.Gly1072Ser	p.G1072S	ENST00000277541	NM_017617.3	1072	Ggc/Agc	20/34	0.911305813657731	3	FACETS	0.979	0.936	1	0.326	0.312	0.341	CLONAL	1	TRUE	0	0.911305813657731	3		987	1714	SUCCESS
AR	367	MSKCC	GRCh37	X	66942711	66942711	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	196	252	0	ENST00000374690.3:c.2492T>C	p.Leu831Pro	p.L831P	ENST00000374690	NM_000044.3	831	cTt/cCt	7/8	1	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.911305813657731	1		252	227	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467826	66467826	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	146	316	0	ENST00000273854.3:c.443A>C	p.Lys148Thr	p.K148T	ENST00000273854	NM_004439.5	148	aAg/aCg	3/18	0.266985969907896	3	FACETS	1	0.978	1	0.582	0.536	0.628	INDETERMINATE	1	TRUE	1	0.911305813657731	3		316	401	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2220110	2220110	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	110	725	0	ENST00000398665.3:c.2695A>C	p.Ser899Arg	p.S899R	ENST00000398665	NM_032482.2	899	Agc/Cgc	23/28	0.911305813657731	2	FACETS	0.266	0.239	0.296	0.133	0.119	0.148	SUBCLONAL	1	TRUE	0	0.911305813657731	2		725	906	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170432	11170432	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	718	692	0	ENST00000358026.2:c.4735T>C	p.Tyr1579His	p.Y1579H	ENST00000358026	NM_001128849.1	1579	Tat/Cat	34/36	0.911305813657731	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.911305813657731	2		692	770	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294676	1294676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	407	540	0	ENST00000310581.5:c.325G>A	p.Gly109Arg	p.G109R	ENST00000310581	NM_198253.2	109	Ggg/Agg	2/16	0.879986261485341	3	FACETS	1	0.988	1	0.552	0.526	0.579	CLONAL	1	TRUE	1	0.911305813657731	3		540	1177	SUCCESS
APC	324	MSKCC	GRCh37	5	112116585	112116585	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	112	335	0	ENST00000257430.4:c.631del	p.Glu211LysfsTer8	p.E211Kfs*8	ENST00000257430	NM_000038.5	210	atG/at	6/16	0.911305813657731	1	FACETS	0.863	0.811	0.913	0.863	0.811	0.913	CLONAL	1	TRUE	0	0.911305813657731	1		335	155	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0055690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	120	264	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.269089399120545	1	FACETS	0.919	0.84	0.999	0.919	0.84	0.999	INDETERMINATE	1	TRUE	0	0.560993532371107	1		264	335	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988508	36988508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	278	663	1	ENST00000354822.5:c.145C>T	p.Pro49Ser	p.P49S	ENST00000354822	NM_001079668.2	49	Ccc/Tcc	2/3	0.560993532371107	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.560993532371107	1		664	663	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613073	52613073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	163	384	1	ENST00000394830.3:c.3455G>A	p.Gly1152Asp	p.G1152D	ENST00000394830	NM_018313.4	1152	gGc/gAc	22/30	0.560993532371107	1	FACETS	0.959	0.889	1	0.959	0.889	1	CLONAL	1	TRUE	0	0.560993532371107	1		385	436	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0055691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	139	383	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.326403273273216	1	FACETS	0.737	0.675	0.802	0.737	0.675	0.802	SUBCLONAL	1	TRUE	0	0.539851269066611	1		383	510	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682399	52682400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	190	288	0	ENST00000394830.3:c.773dup	p.Asn258LysfsTer6	p.N258Kfs*6	ENST00000394830	NM_018313.4	258	aat/aaAt	8/30	0.493929751191008	2	FACETS	0.898	0.842	0.953	0.898	0.842	0.953	CLONAL	2	TRUE	0	0.539851269066611	2		288	392	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508328	106508328	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769318398	NA	P-0055691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	370	560	0	ENST00000359195.3:c.322G>A	p.Glu108Lys	p.E108K	ENST00000359195	NM_002649.2	108	Gag/Aag	2/11	0.384162168757766	3	FACETS	0.88	0.837	0.923	0.88	0.837	0.923	CLONAL	2	TRUE	1	0.539851269066611	3		560	989	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864772	68864772	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0055691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	310	655	0	ENST00000288368.4:c.141+2T>C		p.X47_splice	ENST00000288368	NM_024870.2	47			0.147666643315745	0	FACETS	0.49	0.462	0.518			1	INDETERMINATE	1	TRUE	0	0.539851269066611	0		655	1079	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0055693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	328	680	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.370663709914139	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.370663709914139	2		680	832	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0055693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	279	528	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.370663709914139	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.370663709914139	3		528	787	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0055693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	131	242	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.370663709914139	3	FACETS	1	0.933	1	1	0.933	1	CLONAL	2	TRUE	1	0.370663709914139	3		242	410	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910617	29910617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199474377	NA	P-0055693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1631	92	1344	1	ENST00000376809.5:c.157G>A	p.Asp53Asn	p.D53N	ENST00000376809	NM_002116.7	53	Gac/Aac	2/8	0.234295251639774	3	FACETS	0.342	0.302	0.384	0.114	0.1	0.128	SUBCLONAL	1	TRUE	0	0.370663709914139	3		1345	1723	SUCCESS
APC	324	MSKCC	GRCh37	5	112174759	112174760	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs786203020	NA	P-0055693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	52	238	0	ENST00000257430.4:c.3473_3474del	p.Arg1158ThrfsTer5	p.R1158Tfs*5	ENST00000257430	NM_000038.5	1156	gaAGag/gaag	16/16	0.370663709914139	3	FACETS	0.875	0.748	1	0.438	0.374	0.507	CLONAL	1	TRUE	1	0.370663709914139	3		238	380	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226553741	226553741	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	35	434	0	ENST00000366794.5:c.2419G>A	p.Asp807Asn	p.D807N	ENST00000366794	NM_001618.3	807	Gat/Aat	18/23	0.370663709914139	3	FACETS	0.446	0.365	0.537	0.223	0.182	0.269	SUBCLONAL	1	TRUE	1	0.370663709914139	3		434	502	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965123	15965123	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	44	497	0	ENST00000268712.3:c.5473G>C	p.Val1825Leu	p.V1825L	ENST00000268712	NM_006311.3	1825	Gtg/Ctg	37/46	0.370663709914139	2	FACETS	0.408	0.341	0.482	0.204	0.17	0.241	SUBCLONAL	1	TRUE	0	0.370663709914139	2		497	582	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306736	41306736	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	293	688	0	ENST00000373198.4:c.923A>C	p.Lys308Thr	p.K308T	ENST00000373198	NM_133170.3	308	aAg/aCg	7/32	0.370663709914139	5	FACETS	0.926	0.87	0.984			1	CLONAL	2	TRUE	NA	0.370663709914139	5		688	1328	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117717424	117717424	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	35	326	0	ENST00000368508.3:c.783T>G	p.Phe261Leu	p.F261L	ENST00000368508	NM_002944.2	261	ttT/ttG	8/43	0.234295251639774	3	FACETS	0.527	0.432	0.633	0.176	0.144	0.211	SUBCLONAL	1	TRUE	0	0.370663709914139	3		326	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587780070	NA	P-0055694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	78	751	0	ENST00000269305.4:c.535C>G	p.His179Asp	p.H179D	ENST00000269305	NM_001126112.2	179	Cat/Gat	5/11	0.259397130849546	1	FACETS	0.568	0.498	0.644	0.568	0.498	0.644	SUBCLONAL	1	TRUE	0	0.259397130849546	1		751	921	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829167	128829167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	38	191	0	ENST00000249373.3:c.175C>T	p.Pro59Ser	p.P59S	ENST00000249373	NM_005631.4	59	Ccg/Tcg	1/12	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.259397130849546	2		191	259	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32439136	32439136	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	19	531	0	ENST00000332351.3:c.937G>T	p.Ala313Ser	p.A313S	ENST00000332351	NM_024426.4	313	Gcc/Tcc	4/10	0.214945991370334	4	FACETS	1	0.876	1	0.63	0.48	0.804	CLONAL	1	TRUE	2	0.19	4		531	189	SUCCESS
YES1	7525	MSKCC	GRCh37	18	732951	732951	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs761347968	NA	P-0055695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	25	500	0	ENST00000314574.4:c.1306A>G	p.Ile436Val	p.I436V	ENST00000314574	NM_005433.3	436	Atc/Gtc	11/12	0.194286794960935	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.19	1		500	179	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812259	212812259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs991337964	NA	P-0055695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	16	340	0	ENST00000342788.4:c.317G>A	p.Arg106His	p.R106H	ENST00000342788	NM_005235.2	106	cGt/cAt	3/28	0.214945991370334	4	FACETS	0.821	0.608	1	0.411	0.304	0.538	CLONAL	1	TRUE	2	0.19	4		340	244	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183871	10183871	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	42	613	0	ENST00000256474.2:c.340+1del		p.G114fs	ENST00000256474	NM_000551.3	114	Ggt/gt	1/3	0.301321350460278	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	0	0.19	2		613	180	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125824	47125824	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	13	275	0	ENST00000409792.3:c.5446G>T	p.Glu1816Ter	p.E1816*	ENST00000409792	NM_014159.6	1816	Gag/Tag	12/21	0.301321350460278	2	FACETS	1	0.862	1	0.691	0.499	0.92	CLONAL	1	TRUE	0	0.19	2		275	99	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443880	52443880	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	79	749	0	ENST00000460680.1:c.15del	p.Trp5CysfsTer67	p.W5Cfs*67	ENST00000460680	NM_004656.3	5	tgG/tg	1/17	0.301321350460278	2	FACETS	1	0.909	1	1	0.98	1	CLONAL	3	TRUE	0	0.19	2		749	271	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0055698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	49	215	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.884	0.749	1	0.884	0.749	1	CLONAL	1	TRUE	1	0.23	2		215	482	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584513	48584514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs377767334	NA	P-0055698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	43	396	0	ENST00000342988.3:c.692dup	p.Ser232GlnfsTer3	p.S232Qfs*3	ENST00000342988	NM_005359.5	229	ctg/ctGg	6/12	0.3	1	FACETS	0.707	0.592	0.835	0.707	0.592	0.835	SUBCLONAL	1	TRUE	0	0.23	1		396	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578175	7578175	+	splice_donor_variant	Splice_Site	SNP	A	A	T	rs1555525703	NA	P-0055698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	79	685	0	ENST00000269305.4:c.672+2T>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.3	1	FACETS	0.69	0.606	0.781	0.69	0.606	0.781	SUBCLONAL	1	TRUE	0	0.23	1		685	881	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0055699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	31	383	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		383	637	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850704	63850705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0055700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	135	353	1	ENST00000279873.7:c.1489dup	p.Ile497AsnfsTer31	p.I497Nfs*31	ENST00000279873	NM_032199.2	494	-/A	10/10	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.606950571122564	2		354	434	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0055700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	283	776	2	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.963	0.907	1	0.963	0.907	1	CLONAL	1	TRUE	1	0.606950571122564	2		778	968	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0055700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	129	454	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	0.842	0.767	0.919	0.842	0.767	0.919	CLONAL	1	TRUE	1	0.606950571122564	2		454	505	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0055700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	130	423	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.935	0.855	1	0.935	0.855	1	CLONAL	1	TRUE	1	0.606950571122564	2		423	458	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164505	47164505	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	131	390	0	ENST00000409792.3:c.1621C>T	p.Arg541Ter	p.R541*	ENST00000409792	NM_014159.6	541	Cga/Tga	3/21	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.606950571122564	2		390	420	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589558	67589575	+	inframe_deletion	In_Frame_Del	DEL	AATATTGAAGCTGTAGGG	AATATTGAAGCTGTAGGG	-	novel	NA	P-0055700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	57	202	0	ENST00000274335.5:c.1323_1340del	p.Asn441_Gly446del	p.N441_G446del	ENST00000274335		441	AATATTGAAGCTGTAGGG/-	10/15	1	2	FACETS	0.899	0.782	1	0.899	0.782	1	CLONAL	1	TRUE	1	0.606950571122564	2		202	209	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0055701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	320	215	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.464783735779896	3	FACETS	0.946	0.896	0.997			1	CLONAL	2	TRUE	NA	0.464783735779896	3		215	897	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577527	7577542	+	frameshift_variant	Frame_Shift_Del	DEL	GGATGGGCCTCCGGTT	GGATGGGCCTCCGGTT	-	novel	NA	P-0055701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	228	916	0	ENST00000269305.4:c.739_754del	p.Asn247SerfsTer93	p.N247Sfs*93	ENST00000269305	NM_001126112.2	247	AACCGGAGGCCCATCCtc/tc	7/11	0.464783735779896	1	FACETS	0.969	0.906	1	0.969	0.906	1	CLONAL	1	TRUE	0	0.464783735779896	1		916	777	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938593	44938594	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0055701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	129	197	0	ENST00000377967.4:c.3144_3144+1del		p.LR1047fs	ENST00000377967	NM_021140.2	1047	ttGAga/ttga	20/29	1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.464783735779896	1		197	346	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390416	118390416	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520053	NA	P-0055702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	386	679	0	ENST00000534358.1:c.11230C>T	p.Arg3744Ter	p.R3744*	ENST00000534358	NM_005933.3	3744	Cga/Tga	32/36	0.667947027619747	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.667947027619747	1		679	751	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410555	63410555	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	433	874	0	ENST00000330258.3:c.2612G>T	p.Arg871Leu	p.R871L	ENST00000330258	NM_152424.3	871	cGa/cTa	2/2	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.667947027619747	2		874	1284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0055703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1506	41	840	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.226	0.187	0.27	0.226	0.187	0.27	SUBCLONAL	1	FALSE	1	0.234575738671163	2		843	1547	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0055703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1604	92	884	5	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	0.104945626197322	5	FACETS	0.625	0.553	0.703	0.208	0.184	0.235	INDETERMINATE	1	FALSE	2	0.234575738671163	5		889	1696	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100728	8100728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs771019738	NA	P-0055703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1522	94	898	4	ENST00000346208.3:c.708del	p.Ser237AlafsTer28	p.S237Afs*28	ENST00000346208		234	ttC/tt	3/6	1	2	FACETS	0.496	0.439	0.557	0.496	0.439	0.557	SUBCLONAL	1	FALSE	1	0.234575738671163	2		902	1616	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440904	56440904	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1458799446	NA	P-0055703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1319	134	798	0	ENST00000407977.2:c.433C>T	p.Arg145Ter	p.R145*	ENST00000407977		145	Cga/Tga	4/10	1	2	FACETS	0.786	0.712	0.865	0.786	0.712	0.865	SUBCLONAL	1	FALSE	1	0.234575738671163	2		798	1453	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953748	48953748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759079385	NA	P-0055703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	18	215	0	ENST00000267163.4:c.1351C>T	p.Arg451Cys	p.R451C	ENST00000267163	NM_000321.2	451	Cgc/Tgc	14/27	0.234575738671163	1	FACETS	0.505	0.381	0.653	0.505	0.381	0.653	SUBCLONAL	1	FALSE	0	0.234575738671163	1		215	268	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612900	228612900	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	60	789	0	ENST00000366696.1:c.127C>T	p.Arg43Trp	p.R43W	ENST00000366696	NM_003493.2	43	Cgg/Tgg	1/1	1	2	FACETS	0.447	0.384	0.517	0.447	0.384	0.517	SUBCLONAL	1	FALSE	1	0.234575738671163	2		789	1144	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579547	7579547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567557016	NA	P-0055703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1366	93	811	0	ENST00000269305.4:c.140del	p.Pro47ArgfsTer76	p.P47Rfs*76	ENST00000269305	NM_001126112.2	47	cCg/cg	4/11	1	2	FACETS	0.543	0.481	0.611	0.543	0.481	0.611	SUBCLONAL	1	FALSE	1	0.234575738671163	2		811	1459	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446040	49446040	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064210	NA	P-0055703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1946	138	1087	5	ENST00000301067.7:c.1426G>A	p.Ala476Thr	p.A476T	ENST00000301067	NM_003482.3	476	Gca/Aca	10/54	0.104945626197322	5	FACETS	0.763	0.691	0.84	0.254	0.23	0.28	INDETERMINATE	1	FALSE	2	0.234575738671163	5		1092	2084	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226561931	226561931	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	32	397	0	ENST00000366794.5:c.2066A>G	p.Tyr689Cys	p.Y689C	ENST00000366794	NM_001618.3	689	tAt/tGt	14/23	1	2	FACETS	0.545	0.441	0.662	0.545	0.441	0.662	SUBCLONAL	1	FALSE	1	0.234575738671163	2		397	501	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860582	45860582	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1693	121	1023	0	ENST00000391945.4:c.1425del	p.Val476SerfsTer8	p.V476Sfs*8	ENST00000391945	NM_000400.3	475	ccC/cc	15/23	0.0441192285846426	3	FACETS	0.635	0.571	0.704	0.318	0.285	0.352	INDETERMINATE	1	FALSE	1	0.234575738671163	3		1023	1814	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439866	51439866	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	44	473	0	ENST00000262662.1:c.431C>T	p.Ala144Val	p.A144V	ENST00000262662		144	gCc/gTc	4/4	0.028286922282069	3	FACETS	0.477	0.398	0.564	0.238	0.199	0.282	INDETERMINATE	1	FALSE	1	0.234575738671163	3		473	879	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36931992	36931992	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1332794856	NA	P-0055703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1308	69	850	0	ENST00000361632.4:c.2477G>A	p.Arg826Gln	p.R826Q	ENST00000361632		826	cGg/cAg	16/16	0.028286922282069	3	FACETS	0.477	0.414	0.547	0.239	0.207	0.274	INDETERMINATE	1	FALSE	1	0.234575738671163	3		850	1377	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879640	123879640	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	36	337	0	ENST00000330479.4:c.336G>T	p.Glu112Asp	p.E112D	ENST00000330479	NM_020382.3	112	gaG/gaT	4/9	1	2	FACETS	0.484	0.397	0.582	0.484	0.397	0.582	SUBCLONAL	1	FALSE	1	0.234575738671163	2		337	634	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712769	43712769	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	82	790	0	ENST00000382044.4:c.4415T>C	p.Phe1472Ser	p.F1472S	ENST00000382044	NM_001141980.1	1472	tTc/tCc	21/28	1	2	FACETS	0.617	0.542	0.697	0.617	0.542	0.697	SUBCLONAL	1	FALSE	1	0.234575738671163	2		790	1134	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472529	88472529	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	83	680	1	ENST00000360948.2:c.2026G>T	p.Val676Leu	p.V676L	ENST00000360948	NM_001012338.2	676	Gtg/Ttg	16/19	1	2	FACETS	0.644	0.567	0.728	0.644	0.567	0.728	SUBCLONAL	1	FALSE	1	0.234575738671163	2		681	1098	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533099	63533099	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	119	784	0	ENST00000307078.5:c.1795del	p.Ala599ProfsTer90	p.A599Pfs*90	ENST00000307078	NM_004655.3	599	Gcc/cc	7/11	1	2	FACETS	0.888	0.8	0.982	0.888	0.8	0.982	CLONAL	1	FALSE	1	0.234575738671163	2		784	1142	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372422	55372422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1235	88	901	1	ENST00000297316.4:c.1112G>A	p.Cys371Tyr	p.C371Y	ENST00000297316	NM_022454.3	371	tGc/tAc	2/2	1	2	FACETS	0.567	0.5	0.639	0.567	0.5	0.639	SUBCLONAL	1	FALSE	1	0.234575738671163	2		902	1323	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24135817	24135817	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	309	516	0	ENST00000263121.7:c.305del	p.Gly102AlafsTer41	p.G102Afs*41	ENST00000263121	NM_003073.3	102	Ggc/gc	3/9	0.375275548753269	2	FACETS	0.928	0.878	0.979	0.928	0.878	0.979	CLONAL	2	TRUE	0	0.382716705247565	2		516	870	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0055705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	374	309	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.840998922116708	3	FACETS	0.901	0.863	0.939	0.901	0.863	0.939	CLONAL	2	TRUE	1	0.840998922116708	3		310	701	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905324	50905324	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	456	1067	1	ENST00000440232.2:c.537del	p.Arg180GlyfsTer3	p.R180Gfs*3	ENST00000440232	NM_002691.3	178	Ggg/gg	5/27	1	2	FACETS	0.924	0.884	0.964	0.924	0.884	0.964	CLONAL	1	TRUE	1	0.840998922116708	2		1068	1174	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965472	68965472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200682883	NA	P-0055705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	114	655	1	ENST00000288368.4:c.1084C>T	p.Arg362Trp	p.R362W	ENST00000288368	NM_024870.2	362	Cgg/Tgg	9/40	0.840998922116708	2	FACETS	0.39	0.351	0.431	0.195	0.175	0.216	SUBCLONAL	1	TRUE	0	0.840998922116708	2		656	695	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625218	69625218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168737490	NA	P-0055705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7758	834	1063	11	ENST00000334134.2:c.575G>A	p.Arg192Gln	p.R192Q	ENST00000334134	NM_005247.2	192	cGg/cAg	3/3	0.840998922116708	15	FACETS	1	0.997	1			1	CLONAL	1	TRUE	NA	0.840998922116708	15		1074	8592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577097	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1567547661	NA	P-0055705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	829	763	2	ENST00000269305.4:c.841_842del	p.Asp281ProfsTer24	p.D281Pfs*24	ENST00000269305	NM_001126112.2	281	GAc/c	8/11	0.840998922116708	2	FACETS	0.972	0.954	0.989	0.972	0.954	0.989	CLONAL	2	TRUE	0	0.840998922116708	2		765	1014	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286277	66286277	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	97	303	0	ENST00000273854.3:c.1409C>A	p.Ser470Tyr	p.S470Y	ENST00000273854	NM_004439.5	470	tCt/tAt	6/18	NA	2	FACETS	0.779	0.704	0.857			1	INDETERMINATE	1	TRUE	NA	0.840998922116708	2		303	296	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630407	187630407	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	407	673	4	ENST00000441802.2:c.575C>T	p.Thr192Ile	p.T192I	ENST00000441802	NM_005245.3	192	aCa/aTa	2/27	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.840998922116708	2		677	962	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413270	139413270	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	814	884	5	ENST00000277541.6:c.872A>G	p.Tyr291Cys	p.Y291C	ENST00000277541	NM_017617.3	291	tAc/tGc	6/34	0.840998922116708	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.840998922116708	2		889	941	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0055706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	78	383	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.318332969199722	1	FACETS	0.943	0.832	1	0.943	0.832	1	CLONAL	1	TRUE	0	0.318332969199722	1		383	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	150	756	0	ENST00000269305.4:c.542G>C	p.Arg181Pro	p.R181P	ENST00000269305	NM_001126112.2	181	cGc/cCc	5/11	0.318332969199722	1	FACETS	0.943	0.863	1	0.943	0.863	1	CLONAL	1	TRUE	0	0.318332969199722	1		756	840	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0055707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	169	977	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	0.319180343326635	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.319180343326635	1		977	678	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182641	38182641	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs387907272	NA	P-0055707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	17	481	0	ENST00000396334.3:c.794T>C	p.Leu265Pro	p.L265P	ENST00000396334	NM_002468.4	265	cTg/cCg	5/5	1	2	FACETS	0.213	0.158	0.278	0.213	0.158	0.278	SUBCLONAL	1	TRUE	1	0.319180343326635	2		481	501	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805604	46805604	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369403058	NA	P-0055712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	93	1115	0	ENST00000290295.7:c.352G>A	p.Glu118Lys	p.E118K	ENST00000290295	NM_006361.5	118	Gaa/Aaa	1/2	1	2	FACETS	0.479	0.424	0.538	0.479	0.424	0.538	SUBCLONAL	1	TRUE	1	0.34	2		1115	1142	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863224683	NA	P-0055712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	95	953	0	ENST00000269305.4:c.388C>T	p.Leu130Phe	p.L130F	ENST00000269305	NM_001126112.2	130	Ctc/Ttc	5/11	1	2	FACETS	0.506	0.449	0.567	0.506	0.449	0.567	SUBCLONAL	1	TRUE	1	0.34	2		953	1104	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474492	40474492	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113994139	NA	P-0055712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	41	492	0	ENST00000264657.5:c.1909G>A	p.Val637Met	p.V637M	ENST00000264657	NM_139276.2	637	Gtg/Atg	21/24	1	2	FACETS	0.377	0.313	0.449	0.377	0.313	0.449	SUBCLONAL	1	TRUE	1	0.34	2		492	639	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274638	198274638	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	120	664	0	ENST00000335508.6:c.760T>C	p.Trp254Arg	p.W254R	ENST00000335508	NM_012433.2	254	Tgg/Cgg	7/25	1	2	FACETS	0.802	0.724	0.885	0.802	0.724	0.885	CLONAL	1	TRUE	1	0.34	2		664	880	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0055714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	863	899	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.858266805650511	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.858266805650511	2		899	955	SUCCESS
AR	367	MSKCC	GRCh37	X	66765112	66765112	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	253	639	0	ENST00000374690.3:c.124C>A	p.Pro42Thr	p.P42T	ENST00000374690	NM_000044.3	42	Cca/Aca	1/8	0.634031639498768	3	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.858266805650511	3		639	752	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246570	46246570	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	121	214	0	ENST00000334344.6:c.4664C>A	p.Ala1555Asp	p.A1555D	ENST00000334344	NM_152641.2	1555	gCt/gAt	15/21	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.858266805650511	2		214	195	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99482451	99482451	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	250	518	0	ENST00000268035.6:c.3319C>G	p.Pro1107Ala	p.P1107A	ENST00000268035	NM_000875.3	1107	Cca/Gca	18/21	0.847317711140562	4	FACETS	1	0.987	1	0.299	0.28	0.318	CLONAL	1	TRUE	0	0.858266805650511	4		518	906	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311667	15311667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	10	16	0	ENST00000263388.2:c.50C>T	p.Pro17Leu	p.P17L	ENST00000263388	NM_000435.2	17	cCg/cTg	1/33	0.858266805650511	2	FACETS	1	0.824	1	0.583	0.431	0.734	CLONAL	1	TRUE	0	0.858266805650511	2		16	20	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319108	62319627	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCTGGAGATGCAGATGTACGGGCCACCCCTGCCAGGGCCTGAGCACCGGTGACACCTCTGACATCAGCGGGGTGGAAGTGGTGGGGGTCCCCATGAGCCGGGTGCTGGGGGTCTCGGGCCTCGAGGGCTAAAGGGGTGCTGGTGCACTTCCCCACTGTCTGCTCCCTCTGGCCACGCTCAGCCCTTTCCCAGTCTGCCTGGAGAACCCACACATCATCGACAAGCACCAGATCTGGGTGGGGGTCGTCCCCAGAGGCCCCGATGGAGCCCAGTTGAGCTCCGCGTTTGACAGACGGTGAGGGCCTGTCCCTGGGCCCTGCTGGGGTGGGAGGTGGGGGAGCACTGAGGCCTGAGGTCCTGAGCAGTGGCCTCTCCGGCTCTAGGTTTTCCGAGGAGTGCTTATCCTCCCTGGGGAAGGCTCTGGGTGAGTGCCCTGAATGCCCCAGCTGTGCCCATCCTGGATCCTGGACCCCTGCTCCCAAGAGCTGGTAGGGAACCCTGCAGACATCCTGCCCCTGC	CTCTGGAGATGCAGATGTACGGGCCACCCCTGCCAGGGCCTGAGCACCGGTGACACCTCTGACATCAGCGGGGTGGAAGTGGTGGGGGTCCCCATGAGCCGGGTGCTGGGGGTCTCGGGCCTCGAGGGCTAAAGGGGTGCTGGTGCACTTCCCCACTGTCTGCTCCCTCTGGCCACGCTCAGCCCTTTCCCAGTCTGCCTGGAGAACCCACACATCATCGACAAGCACCAGATCTGGGTGGGGGTCGTCCCCAGAGGCCCCGATGGAGCCCAGTTGAGCTCCGCGTTTGACAGACGGTGAGGGCCTGTCCCTGGGCCCTGCTGGGGTGGGAGGTGGGGGAGCACTGAGGCCTGAGGTCCTGAGCAGTGGCCTCTCCGGCTCTAGGTTTTCCGAGGAGTGCTTATCCTCCCTGGGGAAGGCTCTGGGTGAGTGCCCTGAATGCCCCAGCTGTGCCCATCCTGGATCCTGGACCCCTGCTCCCAAGAGCTGGTAGGGAACCCTGCAGACATCCTGCCCCTGC	-	novel	NA	P-0055714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1332	229	964	0	ENST00000360203.5:c.1468_1637-25del		p.X490_splice	ENST00000360203	NM_001283009.1	490		17-19/35	0.528950636920116	4	FACETS	0.635	0.59	0.682	0.212	0.196	0.228	SUBCLONAL	1	TRUE	1	0.858266805650511	4		964	1561	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674303	117674303	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	185	343	0	ENST00000368508.3:c.4171G>C	p.Asp1391His	p.D1391H	ENST00000368508	NM_002944.2	1391	Gat/Cat	26/43	0.837853007913725	3	FACETS	0.992	0.921	1	0.496	0.46	0.533	CLONAL	1	TRUE	1	0.858266805650511	3		343	621	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566507	41566507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	214	355	1	ENST00000263253.7:c.4384C>T	p.Arg1462Ter	p.R1462*	ENST00000263253	NM_001429.3	1462	Cga/Tga	27/31	0.701656823861492	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.701656823861492	1		356	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577095	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519984	NA	P-0055716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	413	773	0	ENST00000269305.4:c.843C>G	p.Asp281Glu	p.D281E	ENST00000269305	NM_001126112.2	281	gaC/gaG	8/11	0.701656823861492	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.701656823861492	1		773	739	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111493	8111494	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0055716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	334	741	0	ENST00000346208.3:c.981_982del	p.Trp328GlufsTer23	p.W328Efs*23	ENST00000346208		327	CTc/c	5/6	1	2	FACETS	0.932	0.882	0.982	0.932	0.882	0.982	CLONAL	1	TRUE	1	0.701656823861492	2		741	1022	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492725	56492725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1478237679	NA	P-0055716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1526	508	564	0	ENST00000407977.2:c.214G>A	p.Val72Ile	p.V72I	ENST00000407977		72	Gtt/Att	2/10	0.511998927820392	5	FACETS	1	0.996	1			1	CLONAL	1	TRUE	NA	0.701656823861492	5		564	2034	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367306	50367306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	116	513	0	ENST00000331340.3:c.113C>T	p.Ser38Phe	p.S38F	ENST00000331340	NM_006060.4	38	tCc/tTc	3/8	1	2	FACETS	0.47	0.424	0.519	0.47	0.424	0.519	SUBCLONAL	1	TRUE	1	0.701656823861492	2		513	703	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	118	374	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.892	0.818	0.967	0.892	0.818	0.967	CLONAL	1	TRUE	1	0.9348167846512	2		374	283	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	416	648	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.9348167846512	2		648	890	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	1247	696	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.9348167846512	4	FACETS	0.992	0.974	1			1	CLONAL	3	TRUE	NA	0.9348167846512	4		696	1735	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216546	108216546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529296539	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	227	387	0	ENST00000278616.4:c.8495G>A	p.Arg2832His	p.R2832H	ENST00000278616	NM_000051.3	2832	cGt/cAt	58/63	1	2	FACETS	0.962	0.906	1	0.962	0.906	1	CLONAL	1	TRUE	1	0.9348167846512	2		387	505	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325482	1325482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766121638	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	349	558	0	ENST00000400841.2:c.193G>A	p.Asp65Asn	p.D65N	ENST00000400841		65	Gat/Aat	3/6	1	1	FACETS	0.495	0.471	0.519	0.495	0.471	0.519	SUBCLONAL	1	TRUE	0	0.9348167846512	1		558	804	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978935	25978935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	287	486	0	ENST00000435504.4:c.988G>A	p.Glu330Lys	p.E330K	ENST00000435504		330	Gaa/Aaa	10/13	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.9348167846512	2		486	614	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241873	72241873	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1252345844	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	222	380	2	ENST00000357731.5:c.517C>T	p.Arg173Ter	p.R173*	ENST00000357731	NM_173808.2	173	Cga/Tga	3/7	1	2	FACETS	0.937	0.881	0.993	0.937	0.881	0.993	CLONAL	1	TRUE	1	0.9348167846512	2		382	507	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167740	185167740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	337	565	0	ENST00000265026.3:c.1063G>A	p.Asp355Asn	p.D355N	ENST00000265026	NM_004721.4	355	Gat/Aat	6/14	1	2	FACETS	0.93	0.885	0.976	0.93	0.885	0.976	CLONAL	1	TRUE	1	0.9348167846512	2		565	775	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010560	48010560	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587779920	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	221	635	0	ENST00000234420.5:c.188C>G	p.Ser63Cys	p.S63C	ENST00000234420	NM_000179.2	63	tCc/tGc	1/10	1	2	FACETS	0.948	0.891	1	0.948	0.891	1	CLONAL	1	TRUE	1	0.9348167846512	2		635	499	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805705	46805705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138213197	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	608	1140	0	ENST00000290295.7:c.251G>A	p.Gly84Glu	p.G84E	ENST00000290295	NM_006361.5	84	gGa/gAa	1/2	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.9348167846512	2		1140	1292	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447410	12447410	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	447	669	0	ENST00000287820.6:c.649G>C	p.Glu217Gln	p.E217Q	ENST00000287820	NM_015869.4	217	Gag/Cag	5/7	0.655752487768146	4	FACETS	1	0.994	1			1	CLONAL	1	TRUE	NA	0.9348167846512	4		669	1453	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300039	137300040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755912201	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	513	1072	7	ENST00000481739.1:c.331dup	p.Leu111ProfsTer70	p.L111Pfs*70	ENST00000481739	NM_002957.4	108	-/C	3/10	1	2	FACETS	0.865	0.83	0.9	0.865	0.83	0.9	CLONAL	1	TRUE	1	0.9348167846512	2		1079	1269	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907638	111907638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	264	401	0	ENST00000393256.3:c.412G>A	p.Glu138Lys	p.E138K	ENST00000393256	NM_006538.4	138	Gaa/Aaa	3/4	1	2	FACETS	0.964	0.912	1	0.964	0.912	1	CLONAL	1	TRUE	1	0.9348167846512	2		401	586	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797180	45797180	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781533	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	580	1055	1	ENST00000450313.1:c.1235C>T	p.Ser412Leu	p.S412L	ENST00000450313	NM_012222.2	412	tCa/tTa	13/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.9348167846512	2		1056	1198	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864717	68864717	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	257	545	0	ENST00000288368.4:c.88G>A	p.Glu30Lys	p.E30K	ENST00000288368	NM_024870.2	30	Gag/Aag	1/40	1	2	FACETS	0.966	0.913	1	0.966	0.913	1	CLONAL	1	TRUE	1	0.9348167846512	2		545	569	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794756	120794756	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	546	1038	1	ENST00000257552.2:c.601C>T	p.Arg201Ter	p.R201*	ENST00000257552	NM_002442.3	201	Cga/Tga	9/15	1	2	FACETS	0.976	0.939	1	0.976	0.939	1	CLONAL	1	TRUE	1	0.9348167846512	2		1039	1197	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686229	117686229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	217	328	0	ENST00000368508.3:c.3112G>A	p.Glu1038Lys	p.E1038K	ENST00000368508	NM_002944.2	1038	Gaa/Aaa	20/43	1	2	FACETS	0.982	0.924	1	0.982	0.924	1	CLONAL	1	TRUE	1	0.9348167846512	2		328	473	SUCCESS
APC	324	MSKCC	GRCh37	5	112178100	112178100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878853466	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	270	444	0	ENST00000257430.4:c.6809C>T	p.Ser2270Phe	p.S2270F	ENST00000257430	NM_000038.5	2270	tCt/tTt	16/16	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.9348167846512	2		444	576	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618799	37618799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1206	404	668	1	ENST00000447079.4:c.475G>A	p.Asp159Asn	p.D159N	ENST00000447079	NM_015083.1	159	Gat/Aat	1/14	0.743039938910756	4	FACETS	1	0.974	1			1	CLONAL	1	TRUE	NA	0.9348167846512	4		669	1610	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947618	48947618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	160	272	0	ENST00000267163.4:c.1205C>T	p.Ser402Phe	p.S402F	ENST00000267163	NM_000321.2	402	tCc/tTc	12/27	1	2	FACETS	0.93	0.865	0.996	0.93	0.865	0.996	CLONAL	1	TRUE	1	0.9348167846512	2		272	368	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218029	108218029	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	169	294	0	ENST00000278616.4:c.8608G>C	p.Asp2870His	p.D2870H	ENST00000278616	NM_000051.3	2870	Gat/Cat	59/63	1	2	FACETS	0.908	0.846	0.972	0.908	0.846	0.972	CLONAL	1	TRUE	1	0.9348167846512	2		294	398	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447443	12447443	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	987	716	1	ENST00000287820.6:c.682G>A	p.Asp228Asn	p.D228N	ENST00000287820	NM_015869.4	228	Gat/Aat	5/7	0.655752487768146	4	FACETS	0.888	0.868	0.909			1	CLONAL	3	TRUE	NA	0.9348167846512	4		717	1533	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186729	11186729	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	321	638	0	ENST00000361445.4:c.6476C>T	p.Ser2159Phe	p.S2159F	ENST00000361445	NM_004958.3	2159	tCt/tTt	46/58	1	2	FACETS	0.901	0.856	0.947	0.901	0.856	0.947	CLONAL	1	TRUE	1	0.9348167846512	2		638	762	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021823	246021823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1435733310	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	435	802	1	ENST00000388985.4:c.1051G>A	p.Gly351Ser	p.G351S	ENST00000388985		351	Ggt/Agt	10/12	1	2	FACETS	0.959	0.919	1	0.959	0.919	1	CLONAL	1	TRUE	1	0.9348167846512	2		803	970	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100343	8100343	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	644	1267	1	ENST00000346208.3:c.317A>G	p.His106Arg	p.H106R	ENST00000346208		106	cAc/cGc	3/6	1	2	FACETS	0.941	0.908	0.974	0.941	0.908	0.974	CLONAL	1	TRUE	1	0.9348167846512	2		1268	1464	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307254	118307254	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555138458	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	98	159	0	ENST00000534358.1:c.30del	p.Ala11ProfsTer17	p.A11Pfs*17	ENST00000534358	NM_005933.3	9	ttC/tt	1/36	1	2	FACETS	0.94	0.857	1	0.94	0.857	1	CLONAL	1	TRUE	1	0.9348167846512	2		159	223	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344615	118344615	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	341	541	0	ENST00000534358.1:c.2741A>T	p.Glu914Val	p.E914V	ENST00000534358	NM_005933.3	914	gAg/gTg	3/36	1	2	FACETS	0.957	0.912	1	0.957	0.912	1	CLONAL	1	TRUE	1	0.9348167846512	2		541	762	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230562	46230562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	275	429	1	ENST00000334344.6:c.811C>T	p.His271Tyr	p.H271Y	ENST00000334344	NM_152641.2	271	Cat/Tat	8/21	1	2	FACETS	0.961	0.91	1	0.961	0.91	1	CLONAL	1	TRUE	1	0.9348167846512	2		430	612	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416447	49416447	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	457	757	0	ENST00000301067.7:c.16264A>G	p.Met5422Val	p.M5422V	ENST00000301067	NM_003482.3	5422	Atg/Gtg	51/54	1	2	FACETS	0.96	0.92	0.999	0.96	0.92	0.999	CLONAL	1	TRUE	1	0.9348167846512	2		757	1019	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028859	42028859	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	366	641	0	ENST00000219905.7:c.4397A>T	p.Lys1466Ile	p.K1466I	ENST00000219905	NM_001164273.1	1466	aAa/aTa	13/24	1	2	FACETS	0.99	0.945	1	0.99	0.945	1	CLONAL	1	TRUE	1	0.9348167846512	2		641	791	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303904	91303904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	380	592	0	ENST00000355112.3:c.1301C>T	p.Ser434Leu	p.S434L	ENST00000355112	NM_000057.2	434	tCa/tTa	7/22	1	2	FACETS	0.972	0.929	1	0.972	0.929	1	CLONAL	1	TRUE	1	0.9348167846512	2		592	836	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777988	3777988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	673	1259	0	ENST00000262367.5:c.7060C>T	p.Pro2354Ser	p.P2354S	ENST00000262367	NM_004380.2	2354	Ccc/Tcc	31/31	1	2	FACETS	0.957	0.925	0.99	0.957	0.925	0.99	CLONAL	1	TRUE	1	0.9348167846512	2		1259	1504	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129029	30129029	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	450	918	0	ENST00000263025.4:c.737C>G	p.Pro246Arg	p.P246R	ENST00000263025	NM_002746.2	246	cCt/cGt	5/9	1	2	FACETS	0.983	0.943	1	0.983	0.943	1	CLONAL	1	TRUE	1	0.9348167846512	2		918	979	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40857122	40857122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	328	582	0	ENST00000428826.2:c.1919C>T	p.Ser640Phe	p.S640F	ENST00000428826		640	tCt/tTt	17/21	1	2	FACETS	0.972	0.925	1	0.972	0.925	1	CLONAL	1	TRUE	1	0.9348167846512	2		582	722	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727866	78727866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	454	779	1	ENST00000306801.3:c.711G>A	p.Met237Ile	p.M237I	ENST00000306801	NM_020761.2	237	atG/atA	6/34	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.9348167846512	2		780	965	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300145	15300145	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	624	1049	1	ENST00000263388.2:c.1131C>A	p.Cys377Ter	p.C377*	ENST00000263388	NM_000435.2	377	tgC/tgA	7/33	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.9348167846512	2		1050	1323	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860629	45860629	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	559	1136	0	ENST00000391945.4:c.1378A>G	p.Thr460Ala	p.T460A	ENST00000391945	NM_000400.3	460	Aca/Gca	15/23	1	2	FACETS	0.991	0.954	1	0.991	0.954	1	CLONAL	1	TRUE	1	0.9348167846512	2		1136	1207	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902708	50902708	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	624	1033	2	ENST00000440232.2:c.283A>G	p.Ile95Val	p.I95V	ENST00000440232	NM_002691.3	95	Atc/Gtc	3/27	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.9348167846512	2		1035	1265	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724303	52724303	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	442	836	0	ENST00000322088.6:c.1435C>G	p.His479Asp	p.H479D	ENST00000322088	NM_014225.5	479	Cat/Gat	12/15	1	2	FACETS	0.948	0.908	0.989	0.948	0.908	0.989	CLONAL	1	TRUE	1	0.9348167846512	2		836	997	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250227	39250227	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	524	786	0	ENST00000402219.2:c.1342G>C	p.Gly448Arg	p.G448R	ENST00000402219	NM_005633.3	448	Gga/Cga	10/23	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.9348167846512	2		786	1075	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485399	57485402	+	frameshift_variant	Frame_Shift_Del	DEL	GCCC	GCCC	-	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	250	341	0	ENST00000371085.3:c.982_985del	p.Pro328GlufsTer6	p.P328Efs*6	ENST00000371085	NM_000516.4	327	gaGCCC/ga	12/13	1	2	FACETS	0.992	0.938	1	0.992	0.938	1	CLONAL	1	TRUE	1	0.9348167846512	2		341	539	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755407	39755407	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	427	769	0	ENST00000288319.7:c.1358G>A	p.Trp453Ter	p.W453*	ENST00000288319	NM_182918.3	453	tGg/tAg	10/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.9348167846512	2		769	902	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091732	29091732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766191039	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	131	173	0	ENST00000328354.6:c.1225G>A	p.Asp409Asn	p.D409N	ENST00000328354	NM_007194.3	409	Gac/Aac	11/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.9348167846512	2		173	263	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074302	30074302	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	252	482	0	ENST00000338641.4:c.1564G>C	p.Glu522Gln	p.E522Q	ENST00000338641	NM_000268.3	522	Gag/Cag	14/16	1	2	FACETS	0.949	0.896	1	0.949	0.896	1	CLONAL	1	TRUE	1	0.9348167846512	2		482	568	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556680	41556680	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	340	550	0	ENST00000263253.7:c.3625C>T	p.Gln1209Ter	p.Q1209*	ENST00000263253	NM_001429.3	1209	Caa/Taa	20/31	1	2	FACETS	0.961	0.915	1	0.961	0.915	1	CLONAL	1	TRUE	1	0.9348167846512	2		550	757	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456717	138456717	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	242	424	0	ENST00000289153.2:c.633C>G	p.Ser211Arg	p.S211R	ENST00000289153	NM_006219.2	211	agC/agG	4/22	1	2	FACETS	0.904	0.851	0.956	0.904	0.851	0.956	CLONAL	1	TRUE	1	0.9348167846512	2		424	573	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215909	142215909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	301	498	0	ENST00000350721.4:c.5684G>A	p.Arg1895Lys	p.R1895K	ENST00000350721	NM_001184.3	1895	aGa/aAa	33/47	1	2	FACETS	0.951	0.903	1	0.951	0.903	1	CLONAL	1	TRUE	1	0.9348167846512	2		498	677	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217247	66217247	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1232544378	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	253	428	0	ENST00000273854.3:c.2368T>A	p.Tyr790Asn	p.Y790N	ENST00000273854	NM_004439.5	790	Tac/Aac	14/18	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.9348167846512	2		428	536	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562652	176562652	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	387	635	0	ENST00000439151.2:c.548T>A	p.Ile183Asn	p.I183N	ENST00000439151	NM_022455.4	183	aTc/aAc	2/23	1	2	FACETS	0.971	0.927	1	0.971	0.927	1	CLONAL	1	TRUE	1	0.9348167846512	2		635	853	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287547	33287547	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	570	807	0	ENST00000374542.5:c.1550C>A	p.Ser517Tyr	p.S517Y	ENST00000374542	NM_001141970.1	517	tCt/tAt	6/8	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.9348167846512	2		807	1128	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510844	157510844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	511	779	0	ENST00000346085.5:c.3619C>T	p.Pro1207Ser	p.P1207S	ENST00000346085	NM_020732.3	1207	Cca/Tca	14/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.9348167846512	2		779	1085	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880240	151880240	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	268	339	0	ENST00000262189.6:c.5084A>T	p.Gln1695Leu	p.Q1695L	ENST00000262189	NM_170606.2	1695	cAa/cTa	35/59	1	2	FACETS	0.983	0.931	1	0.983	0.931	1	CLONAL	1	TRUE	1	0.9348167846512	2		339	583	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955531	90955531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	291	486	1	ENST00000265433.3:c.2134C>T	p.His712Tyr	p.H712Y	ENST00000265433	NM_002485.4	712	Cat/Tat	14/16	1	2	FACETS	0.943	0.894	0.993	0.943	0.894	0.993	CLONAL	1	TRUE	1	0.9348167846512	2		487	660	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117861207	117861207	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	279	467	0	ENST00000297338.2:c.1682A>G	p.Gln561Arg	p.Q561R	ENST00000297338	NM_006265.2	561	cAg/cGg	13/14	1	2	FACETS	0.918	0.869	0.968	0.918	0.869	0.968	CLONAL	1	TRUE	1	0.9348167846512	2		467	650	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868414	117868414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	317	469	0	ENST00000297338.2:c.928G>A	p.Asp310Asn	p.D310N	ENST00000297338	NM_006265.2	310	Gat/Aat	8/14	1	2	FACETS	0.933	0.886	0.98	0.933	0.886	0.98	CLONAL	1	TRUE	1	0.9348167846512	2		469	727	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090810	5090810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs55873896	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	156	281	0	ENST00000381652.3:c.2958C>G	p.Asn986Lys	p.N986K	ENST00000381652	NM_004972.3	986	aaC/aaG	22/25	NA	2	FACETS	0.862	0.8	0.926			1	INDETERMINATE	1	TRUE	NA	0.9348167846512	2		281	387	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376626	8376626	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	273	467	0	ENST00000356435.5:c.4487G>C	p.Arg1496Pro	p.R1496P	ENST00000356435		1496	cGa/cCa	27/35	1	2	FACETS	0.923	0.873	0.973	0.923	0.873	0.973	CLONAL	1	TRUE	1	0.9348167846512	2		467	633	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249711	110249711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	562	1161	1	ENST00000374672.4:c.964G>A	p.Glu322Lys	p.E322K	ENST00000374672	NM_004235.4	322	Gag/Aag	3/5	1	2	FACETS	0.947	0.912	0.983	0.947	0.912	0.983	CLONAL	1	TRUE	1	0.9348167846512	2		1162	1269	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969392	44969392	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	368	265	0	ENST00000377967.4:c.4074C>A	p.Cys1358Ter	p.C1358*	ENST00000377967	NM_021140.2	1358	tgC/tgA	28/29	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.9348167846512	1		265	391	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0055748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	274	219	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.246055676932286	6	FACETS	0.931	0.882	0.98	0.931	0.882	0.98	CLONAL	6	TRUE	0	0.246055676932286	6		219	595	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519980	NA	P-0055748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	214	487	0	ENST00000269305.4:c.528C>G	p.Cys176Trp	p.C176W	ENST00000269305	NM_001126112.2	176	tgC/tgG	5/11	0.227252257874975	2	FACETS	0.966	0.899	1	0.966	0.899	1	CLONAL	2	TRUE	0	0.246055676932286	2		487	900	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016635	12016636	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0055748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	85	402	0	ENST00000353533.5:c.772_773del	p.Ile258CysfsTer9	p.I258Cfs*9	ENST00000353533	NM_003010.3	257	tcTAtt/tctt	7/11	0.227252257874975	2	FACETS	0.909	0.809	1	0.909	0.809	1	CLONAL	2	TRUE	0	0.246055676932286	2		402	380	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120806013	120806013	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	123	990	0	ENST00000257552.2:c.164C>G	p.Pro55Arg	p.P55R	ENST00000257552	NM_002442.3	55	cCc/cGc	3/15	0.246055676932286	5	FACETS	1	0.952	1	0.363	0.327	0.401	CLONAL	1	TRUE	2	0.246055676932286	5		990	1256	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569690	41569690	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	63	249	0	ENST00000263253.7:c.4681A>T	p.Ser1561Cys	p.S1561C	ENST00000263253	NM_001429.3	1561	Agc/Tgc	29/31	0.244443717816333	4	FACETS	0.896	0.779	1	0.896	0.779	1	CLONAL	2	TRUE	2	0.246055676932286	4		249	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs786201838	NA	P-0055749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	1038	886	0	ENST00000269305.4:c.578A>C	p.His193Pro	p.H193P	ENST00000269305	NM_001126112.2	193	cAt/cCt	6/11	0.808111973902869	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.808111973902869	3		886	1160	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623569	43623569	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	174	359	0	ENST00000355710.3:c.3197A>C	p.Asp1066Ala	p.D1066A	ENST00000355710	NM_020975.4	1066	gAc/gCc	20/20	0.685358991988656	3	FACETS	0.983	0.91	1	0.492	0.454	0.53	CLONAL	1	TRUE	1	0.808111973902869	3		359	615	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139203	108139203	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	262	712	0	ENST00000278616.4:c.2705A>T	p.Lys902Met	p.K902M	ENST00000278616	NM_000051.3	902	aAg/aTg	18/63	0.808111973902869	3	FACETS	1	0.961	1	0.515	0.483	0.547	CLONAL	1	TRUE	1	0.808111973902869	3		712	884	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833942	44833949	+	frameshift_variant	Frame_Shift_Del	DEL	ACAGTCTG	ACAGTCTG	-	novel	NA	P-0055749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	279	302	0	ENST00000377967.4:c.368_375del	p.Gln123LeufsTer19	p.Q123Lfs*19	ENST00000377967	NM_021140.2	122	ttACAGTCTGac/ttac	4/29	0.808111973902869	2	FACETS	1	0.99	1			1	CLONAL	2	TRUE	NA	0.808111973902869	2		302	329	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107088	27107089	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0055750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	21	770	1	ENST00000324856.7:c.6699_6700delinsCT	p.Ala2234Ser	p.A2234S	ENST00000324856	NM_006015.4	2233	cgGGct/cgCTct	20/20	0.381582469359607	1	FACETS	0.222	0.17	0.282	0.222	0.17	0.282	SUBCLONAL	1	TRUE	0	0.381582469359607	1		771	402	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52661289	52661290	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	34	427	0	ENST00000394830.3:c.1540dup	p.Ser514LysfsTer2	p.S514Kfs*2	ENST00000394830	NM_018313.4	514	agt/aAgt	14/30	0.381582469359607	1	FACETS	0.434	0.355	0.523	0.434	0.355	0.523	SUBCLONAL	1	TRUE	0	0.381582469359607	1		427	332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0055752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	143	1065	2	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.0617709935559398	3	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.20480342220532	3		1067	1030	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0055752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	23	464	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.20480342220532	1	FACETS	0.471	0.366	0.593	0.471	0.366	0.593	SUBCLONAL	1	TRUE	0	0.20480342220532	1		464	428	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942968	15943753	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTGAAAGAGAATCAAAAACATTTCCACTTATTTCTGAAAGGCCAATCAGGAAACAAACATGCATTGCCCCATCAGCCCACTGAATACACACAGCACTTGGCAAGTGACCTAGAACAATACCAGGACCCACCACACAGAGACCTTTTTTTTTGGAGACAGAGTCTCTCTCTGTCGCACCCAGGCTGGAGTGCAGTGGCGCGATCTTGGCTCACTGCAACCTCCGCCTCCCAGATTCAAGGGATTCTCCTACCTCAGTCTCCCAAGTAGCTGGGACTACAGGCACCCACCACCACACCAGGCTAATTTTTTGTATTTTTAGGAGATGGGGTTTCACCATATTGGTCAGGCTGATCTCGAATTCCGAACCTCAGGTGATCCGCCCGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCACCCAGCCCAGAGACCATCTTAATCCACAGATAACTCCTTAAGGAAATTTGTTTCCCAAGTGAATCAGTCACCCACACTTCTATTAAAGTTACTCAACAATTTTCTCAGTTCCCTAGTTTTGACAGTGTTCTTTAATAGTTTCATTCTTTTTGTTCATTTATCTTTTCAATAGGTATTTACTGGATCTCAGTTCCTTTCTGTGCTACTGGGTAAACCTTCCTTCACTAAATTATTTATTTATTTTTCCATATTAGAGCAGTCACTCCCCTGGTATACAGTTGGTACTCAGTACATATTTGTTGGACTGACTACTGCTGTGCCAATTTTGTATTGGTAAATAATGTCTTTTCAATCTTA	CCTGAAAGAGAATCAAAAACATTTCCACTTATTTCTGAAAGGCCAATCAGGAAACAAACATGCATTGCCCCATCAGCCCACTGAATACACACAGCACTTGGCAAGTGACCTAGAACAATACCAGGACCCACCACACAGAGACCTTTTTTTTTGGAGACAGAGTCTCTCTCTGTCGCACCCAGGCTGGAGTGCAGTGGCGCGATCTTGGCTCACTGCAACCTCCGCCTCCCAGATTCAAGGGATTCTCCTACCTCAGTCTCCCAAGTAGCTGGGACTACAGGCACCCACCACCACACCAGGCTAATTTTTTGTATTTTTAGGAGATGGGGTTTCACCATATTGGTCAGGCTGATCTCGAATTCCGAACCTCAGGTGATCCGCCCGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCACCCAGCCCAGAGACCATCTTAATCCACAGATAACTCCTTAAGGAAATTTGTTTCCCAAGTGAATCAGTCACCCACACTTCTATTAAAGTTACTCAACAATTTTCTCAGTTCCCTAGTTTTGACAGTGTTCTTTAATAGTTTCATTCTTTTTGTTCATTTATCTTTTCAATAGGTATTTACTGGATCTCAGTTCCTTTCTGTGCTACTGGGTAAACCTTCCTTCACTAAATTATTTATTTATTTTTCCATATTAGAGCAGTCACTCCCCTGGTATACAGTTGGTACTCAGTACATATTTGTTGGACTGACTACTGCTGTGCCAATTTTGTATTGGTAAATAATGTCTTTTCAATCTTA	-	novel	NA	P-0055752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	23	492	0	ENST00000268712.3:c.6733+2_6734del		p.X2245_splice	ENST00000268712	NM_006311.3	2245		44/46	0.20480342220532	1	FACETS	0.451	0.351	0.568	0.451	0.351	0.568	SUBCLONAL	1	TRUE	0	0.20480342220532	1		492	447	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943682	17943682	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	67	1269	0	ENST00000458235.1:c.2407T>C	p.Trp803Arg	p.W803R	ENST00000458235	NM_000215.3	803	Tgg/Cgg	18/24	0.20480342220532	1	FACETS	0.61	0.529	0.699	0.61	0.529	0.699	SUBCLONAL	1	TRUE	0	0.20480342220532	1		1269	962	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204693	128204693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs78245253	NA	P-0055752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	84	1288	0	ENST00000341105.2:c.748C>T	p.Pro250Ser	p.P250S	ENST00000341105	NM_032638.4	250	Ccc/Tcc	3/6	0.20480342220532	1	FACETS	0.72	0.635	0.813	0.72	0.635	0.813	SUBCLONAL	1	TRUE	0	0.20480342220532	1		1288	1022	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479158	50479159	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	C	novel	NA	P-0055752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	37	781	0	ENST00000394963.4:c.6_7delinsC	p.Ala3ProfsTer67	p.A3Pfs*67	ENST00000394963	NM_003076.4	2	gcGGcc/gcCcc	1/13	1	2	FACETS	0.607	0.5	0.728	0.607	0.5	0.728	SUBCLONAL	1	TRUE	1	0.20480342220532	2		781	595	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	41	1023	0	ENST00000267101.3:c.273G>A	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atA	3/28	0.400972466200343	4	FACETS	0.671	0.559	0.795	0.335	0.279	0.398	SUBCLONAL	1	FALSE	2	0.381305602776886	4		1023	443	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100426	8100426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	100	1528	0	ENST00000346208.3:c.400C>T	p.Pro134Ser	p.P134S	ENST00000346208		134	Ccc/Tcc	3/6	0.240915281610885	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	0	0.381305602776886	1		1528	399	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732617	190732617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375020232	NA	P-0055753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	23	561	1	ENST00000441310.2:c.2435G>A	p.Arg812His	p.R812H	ENST00000441310	NM_000534.4	812	cGt/cAt	11/13	0.257368125666596	4	FACETS	0.575	0.448	0.72	0.287	0.224	0.36	SUBCLONAL	1	FALSE	2	0.381305602776886	4		562	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579398	+	frameshift_variant	Frame_Shift_Del	DEL	GGGAAGGGAC	GGGAAGGGAC	-	novel	NA	P-0055753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	45	1341	1	ENST00000269305.4:c.289_298del	p.Val97ArgfsTer23	p.V97Rfs*23	ENST00000269305	NM_001126112.2	97	GTCCCTTCCCag/ag	4/11	0.238520124605488	4	FACETS	0.872	0.735	1			1	CLONAL	1	FALSE	NA	0.381305602776886	4		1342	374	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502211	157502211	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	21	803	0	ENST00000346085.5:c.3244G>A	p.Glu1082Lys	p.E1082K	ENST00000346085	NM_020732.3	1082	Gag/Aag	12/20	NA	2	FACETS	0.299	0.229	0.379			1	INDETERMINATE	1	FALSE	NA	0.381305602776886	2		803	369	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117863003	117863003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	34	455	0	ENST00000297338.2:c.1474C>T	p.Gln492Ter	p.Q492*	ENST00000297338	NM_006265.2	492	Cag/Tag	12/14	0.247828721395231	5	FACETS	1	0.859	1	0.351	0.288	0.422	CLONAL	1	FALSE	2	0.381305602776886	5		455	266	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929459	44929462	+	frameshift_variant	Frame_Shift_Del	DEL	AATT	AATT	-	novel	NA	P-0055753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	37	406	0	ENST00000377967.4:c.2562_2565del	p.Ile854MetfsTer12	p.I854Mfs*12	ENST00000377967	NM_021140.2	853	acAATT/ac	17/29	0.238520124605488	2	FACETS	0.975	0.812	1			1	CLONAL	1	FALSE	NA	0.381305602776886	2		406	199	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	124	374	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.879	0.802	0.958	0.879	0.802	0.958	CLONAL	1	TRUE	1	0.702178270388277	2		374	402	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0055754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	679	1117	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	0.587890355144909	2	FACETS	0.917	0.891	0.942	0.917	0.891	0.942	CLONAL	2	TRUE	0	0.702178270388277	2		1117	1055	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108053	30108053	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	185	441	1	ENST00000331968.5:c.754T>A	p.Tyr252Asn	p.Y252N	ENST00000331968	NM_002742.2	252	Tac/Aac	5/18	1	2	FACETS	0.836	0.776	0.899	0.836	0.776	0.899	CLONAL	1	TRUE	1	0.702178270388277	2		442	630	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108085	30108085	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	100	445	0	ENST00000331968.5:c.722T>C	p.Ile241Thr	p.I241T	ENST00000331968	NM_002742.2	241	aTt/aCt	5/18	1	2	FACETS	0.552	0.495	0.612	0.552	0.495	0.612	SUBCLONAL	1	TRUE	1	0.702178270388277	2		445	516	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217870	7217871	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0055754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	253	664	0	ENST00000380728.2:c.140_141del	p.Glu47AlafsTer49	p.E47Afs*49	ENST00000380728		47	gAA/g	3/11	0.678646109686154	1	FACETS	0.864	0.817	0.912	0.864	0.817	0.912	CLONAL	1	TRUE	0	0.702178270388277	1		664	541	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547954	41547954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	229	564	0	ENST00000263253.7:c.2935G>A	p.Glu979Lys	p.E979K	ENST00000263253	NM_001429.3	979	Gag/Aag	15/31	1	2	FACETS	0.892	0.835	0.951	0.892	0.835	0.951	CLONAL	1	TRUE	1	0.702178270388277	2		564	731	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548276	41548276	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	131	337	1	ENST00000263253.7:c.3064G>T	p.Glu1022Ter	p.E1022*	ENST00000263253	NM_001429.3	1022	Gaa/Taa	16/31	1	2	FACETS	0.888	0.813	0.966	0.888	0.813	0.966	CLONAL	1	TRUE	1	0.702178270388277	2		338	420	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469898	157469898	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs794727977	NA	P-0055754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	49	775	2	ENST00000346085.5:c.2692C>T	p.Arg898Ter	p.R898*	ENST00000346085	NM_020732.3	898	Cga/Tga	9/20	1	2	FACETS	0.166	0.14	0.195	0.166	0.14	0.195	SUBCLONAL	1	TRUE	1	0.702178270388277	2		777	839	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060782	38060784	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0055770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	1240	1114	2	ENST00000250448.2:c.1205_1207del	p.Ile402del	p.I402del	ENST00000250448	NM_004496.3	402	aTCAac/aac	2/2	0.37304977057835	6	FACETS	1	0.997	1	1	0.997	1	CLONAL	4	TRUE	2	0.552943952649805	6		1116	2129	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562577	21562577	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395329857	NA	P-0055770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	52	162	0	ENST00000382592.4:c.1342C>T	p.Arg448Cys	p.R448C	ENST00000382592	NM_014572.2	448	Cgt/Tgt	4/8	0.556356511575902	3	FACETS	0.98	0.843	1			1	CLONAL	1	TRUE	NA	0.552943952649805	3		162	245	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720700	89720849	+	inframe_deletion	In_Frame_Del	DEL	AGGAAACCTCAGAAAAAGTAGAAAATGGAAGTCTATGTGATCAAGAAATCGATAGCATTTGCAGTATAGAGCGTGCAGATAATGACAAGGAATATCTAGTACTTACTTTAACAAAAAATGATCTTGACAAAGCAAATAAAGACAAAGCCA	AGGAAACCTCAGAAAAAGTAGAAAATGGAAGTCTATGTGATCAAGAAATCGATAGCATTTGCAGTATAGAGCGTGCAGATAATGACAAGGAATATCTAGTACTTACTTTAACAAAAAATGATCTTGACAAAGCAAATAAAGACAAAGCCA	-	novel	NA	P-0055770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	97	260	0	ENST00000371953.3:c.852_1001del	p.Glu284_Asn334delinsAsp	p.E284_N334delinsD	ENST00000371953	NM_000314.4	284	gAGGAAACCTCAGAAAAAGTAGAAAATGGAAGTCTATGTGATCAAGAAATCGATAGCATTTGCAGTATAGAGCGTGCAGATAATGACAAGGAATATCTAGTACTTACTTTAACAAAAAATGATCTTGACAAAGCAAATAAAGACAAAGCCAac/gac	8/9	0.446560227401939	3	FACETS	1	0.982	1	0.491	0.443	0.541	CLONAL	1	TRUE	0	0.552943952649805	3		260	304	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910761	32910761	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs886040419	NA	P-0055770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	169	303	0	ENST00000380152.3:c.2269A>T	p.Lys757Ter	p.K757*	ENST00000380152		757	Aaa/Taa	11/27	NA	2	FACETS	0.921	0.862	0.979			1	INDETERMINATE	2	TRUE	NA	0.552943952649805	2		303	332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576893	7576897	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTG	GGCTG	-	novel	NA	P-0055770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	400	786	1	ENST00000269305.4:c.949_953del	p.Gln317LysfsTer18	p.Q317Kfs*18	ENST00000269305	NM_001126112.2	317	CAGCCa/a	9/11	0.421190955169274	3	FACETS	1	0.979	1			1	CLONAL	2	TRUE	NA	0.552943952649805	3		787	888	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924820	49924820	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	346	1050	0	ENST00000296474.3:c.4123C>G	p.Pro1375Ala	p.P1375A	ENST00000296474	NM_002447.2	1375	Cca/Gca	20/20	0.489595236469206	4	FACETS	1	0.994	1	0.711	0.672	0.751	CLONAL	1	TRUE	2	0.552943952649805	4		1050	1367	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323150	31323174	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTGCTCTTCTCCAGAAGGCACCA	CTCTGCTCTTCTCCAGAAGGCACCA	-	novel	NA	P-0055770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1215	191	867	0	ENST00000412585.2:c.815_839del	p.Val272AspfsTer17	p.V272Dfs*17	ENST00000412585	NM_005514.6	272	gTGGTGCCTTCTGGAGAAGAGCAGAGa/ga	4/8	0.556356511575902	4	FACETS	0.763	0.703	0.825	0.382	0.351	0.413	SUBCLONAL	1	TRUE	2	0.552943952649805	4		867	1406	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793780	89793780	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	85	411	0	ENST00000336032.3:c.849G>C	p.Lys283Asn	p.K283N	ENST00000336032	NM_006813.2	283	aaG/aaC	2/2	0.472551197462189	3	FACETS	0.804	0.713	0.901			1	CLONAL	1	TRUE	NA	0.552943952649805	3		411	488	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249755	110249756	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0055770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	211	1015	0	ENST00000374672.4:c.919dup	p.Leu307ProfsTer16	p.L307Pfs*16	ENST00000374672	NM_004235.4	307	ctg/cCtg	3/5	0.412822195460308	4	FACETS	0.925	0.858	0.996			1	CLONAL	1	TRUE	NA	0.552943952649805	4		1015	1281	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918580	44918583	+	frameshift_variant	Frame_Shift_Del	DEL	TGGA	TGGA	-	novel	NA	P-0055770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	331	229	0	ENST00000377967.4:c.1067_1070del	p.Met356ThrfsTer2	p.M356Tfs*2	ENST00000377967	NM_021140.2	355	TGGAtg/tg	12/29	0.552943952649805	4	FACETS	0.937	0.901	0.972			1	CLONAL	4	TRUE	NA	0.552943952649805	4		229	496	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061127	38061199	+	protein_altering_variant	In_Frame_Del	DEL	TGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTT	TGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTT	GGGGGCCGGCGGCGGGGGC	novel	NA	P-0055770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	610	165	0	ENST00000250448.2:c.790_862delinsGCCCCCGCCGCCGGCCCCC	p.Lys264_Lys288delinsAlaProAlaAlaGlyProGln	p.K264_K288delinsAPAAGPQ	ENST00000250448	NM_004496.3	264	AAGCGCTTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGGCGCCAag/GCCCCCGCCGCCGGCCCCCag	2/2	0.37304977057835	6	FACETS	1	0.994	1	1	0.998	1	CLONAL	6	TRUE	2	0.552943952649805	6		165	740	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACAACCCCC	rs397517115	NA	P-0055773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	846	1004	0	ENST00000275493.2:c.2311_2319dup	p.Asn771_His773dup	p.N771_H773dup	ENST00000275493	NM_005228.3	771	gac/gACAACCCCCac	20/28	0.370919660030328	8	FACETS	0.947	0.917	0.977	0.789	0.764	0.814	CLONAL	5	TRUE	2	0.370919660030328	8		1004	2036	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577131	7577131	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	155	949	0	ENST00000269305.4:c.807del	p.Phe270LeufsTer75	p.F270Lfs*75	ENST00000269305	NM_001126112.2	269	agC/ag	8/11	0.361528415099567	1	FACETS	0.845	0.774	0.918	0.845	0.774	0.918	CLONAL	1	TRUE	0	0.370919660030328	1		949	806	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0055774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	60	309	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.0964782965607021	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		310	208	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159754	20159754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	160	845	0	ENST00000379607.5:c.5C>T	p.Pro2Leu	p.P2L	ENST00000379607	NM_001412.3	2	cCc/cTc	1/7	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		845	464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	350	766	1	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	2	TRUE	NA	0.571591348363348	2		767	598	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177839	56177839	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	66	432	1	ENST00000399503.3:c.2812C>T	p.Pro938Ser	p.P938S	ENST00000399503	NM_005921.1	938	Cct/Tct	14/20	0.577222185731649	3	FACETS	0.746	0.65	0.849	0.373	0.325	0.425	SUBCLONAL	1	TRUE	1	0.571591348363348	3		433	398	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005260	150005260	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	57	587	0	ENST00000253339.5:c.965C>G	p.Ser322Cys	p.S322C	ENST00000253339		322	tCt/tGt	3/7	0.428648965283821	4	FACETS	0.649	0.557	0.748	0.324	0.278	0.374	SUBCLONAL	1	TRUE	2	0.571591348363348	4		587	483	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	65	374	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.992	0.861	1	0.992	0.861	1	CLONAL	1	FALSE	1	0.262195437819268	2		374	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0055776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	57	1199	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	1	2	FACETS	0.369	0.315	0.428	0.369	0.315	0.428	SUBCLONAL	1	FALSE	1	0.262195437819268	2		1199	1178	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0055776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	36	378	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.0213655381191042	3	FACETS	0.792	0.652	0.949	0.396	0.326	0.475	INDETERMINATE	1	FALSE	1	0.262195437819268	3		378	392	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972927	55972927	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	26	621	0	ENST00000263923.4:c.1463T>A	p.Val488Glu	p.V488E	ENST00000263923	NM_002253.2	488	gTg/gAg	11/30	1	2	FACETS	0.543	0.43	0.673	0.543	0.43	0.673	SUBCLONAL	1	FALSE	1	0.262195437819268	2		621	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577562	7577563	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGT	novel	NA	P-0055778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	208	886	0	ENST00000269305.4:c.716_718dup	p.Asn239dup	p.N239dup	ENST00000269305	NM_001126112.2	239	agt/aACAgt	7/11	0.652150901654614	1	FACETS	0.683	0.638	0.73	0.683	0.638	0.73	SUBCLONAL	1	TRUE	0	0.652150901654614	1		886	629	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425603	49425609	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTCCT	GGCTCCT	-	novel	NA	P-0055778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1215	408	1427	0	ENST00000301067.7:c.12879_12885del	p.Gly4294TyrfsTer88	p.G4294Yfs*88	ENST00000301067	NM_003482.3	4293	ccAGGAGCC/cc	39/54	1	2	FACETS	0.771	0.732	0.811	0.771	0.732	0.811	SUBCLONAL	1	TRUE	1	0.652150901654614	2		1427	1623	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604724	48604725	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGAG	rs377767373	NA	P-0055778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	242	585	0	ENST00000342988.3:c.1547_1550dup	p.Ser517ArgfsTer11	p.S517Rfs*11	ENST00000342988	NM_005359.5	516	cag/cAGAGag	12/12	0.652150901654614	1	FACETS	0.906	0.854	0.958	0.906	0.854	0.958	CLONAL	1	TRUE	0	0.652150901654614	1		585	552	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266464	198266464	+	splice_donor_variant	Splice_Site	DEL	A	A	-	novel	NA	P-0055778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	166	394	0	ENST00000335508.6:c.2370+2del		p.X790_splice	ENST00000335508	NM_012433.2	790			1	2	FACETS	0.994	0.92	1	0.994	0.92	1	CLONAL	1	TRUE	1	0.652150901654614	2		394	512	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019731	123019746	+	frameshift_variant	Frame_Shift_Del	DEL	GCAATATGGAGACTCA	GCAATATGGAGACTCA	-	novel	NA	P-0055778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	318	420	0	ENST00000355640.3:c.222_237del	p.Tyr75LeufsTer50	p.Y75Lfs*50	ENST00000355640		73	tgGCAATATGGAGACTCA/tg	2/7	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.652150901654614	1		420	564	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984334	201984347	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGGTACTACTACA	CAGGTACTACTACA	TGG	novel	NA	P-0055778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	241	1015	2	ENST00000359651.3:c.1002-3_1012delinsTGG		p.X334_splice	ENST00000359651		334		8/8	0.390830557263732	1	FACETS	0.398	0.37	0.426	0.398	0.37	0.426	INDETERMINATE	1	TRUE	0	0.652150901654614	1		1017	1253	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0055779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	36	315	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		316	228	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719731	61719731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	27	729	0	ENST00000401558.2:c.1537G>A	p.Glu513Lys	p.E513K	ENST00000401558	NM_003400.3	513	Gaa/Aaa	14/25	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		729	444	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0055798-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	101	215	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.261689246968746	2	FACETS	1	0.981	1	0.72	0.646	0.798	CLONAL	1	TRUE	0	0.27412985943772	2		215	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579579	7579580	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCAA	novel	NA	P-0055798-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	116	745	0	ENST00000269305.4:c.103_107dup	p.Ser37CysfsTer9	p.S37Cfs*9	ENST00000269305	NM_001126112.2	36	ccg/ccTTGCCg	4/11	0.196424200538052	3	FACETS	0.949	0.86	1	0.633	0.573	0.695	CLONAL	2	TRUE	0	0.27412985943772	3		745	507	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0055803-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	54	378	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.264740854473765	3	FACETS	1	0.934	1	0.581	0.498	0.671	CLONAL	1	FALSE	1	0.277219506693774	3		378	382	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443938	18443938	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055803-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	15	287	0	ENST00000266497.5:c.911T>G	p.Met304Arg	p.M304R	ENST00000266497		304	aTg/aGg	3/31	0.264740854473765	3	FACETS	0.97	0.716	1	0.485	0.358	0.635	CLONAL	1	FALSE	1	0.277219506693774	3		287	127	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0055807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	94	219	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.151384908731881	2	FACETS	1	0.927	1	1	0.983	1	CLONAL	3	TRUE	0	0.151384908731881	2		219	397	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0055807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	163	603	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.151384908731881	1	FACETS	1	0.964	1	1	0.992	1	CLONAL	2	TRUE	0	0.151384908731881	1		603	914	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482438	56482438	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	180	556	0	ENST00000267101.3:c.986A>C	p.Lys329Thr	p.K329T	ENST00000267101	NM_001982.3	329	aAa/aCa	8/28	0.125218526157151	3	FACETS	0.892	0.825	0.961	1	0.981	1	CLONAL	4	TRUE	0	0.151384908731881	3		556	717	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879794	37879794	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	319	571	0	ENST00000269571.5:c.2089G>T	p.Val697Leu	p.V697L	ENST00000269571		697	Gtg/Ttg	18/27	0.125218526157151	3	FACETS	0.947	0.898	0.996	1	0.996	1	CLONAL	6	TRUE	0	0.151384908731881	3		571	798	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058045	27058045	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	126	499	0	ENST00000324856.7:c.1753C>T	p.Gln585Ter	p.Q585*	ENST00000324856	NM_006015.4	585	Cag/Tag	3/20	0.151384908731881	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.151384908731881	3		499	731	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856030	68856030	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555516860	NA	P-0055807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	122	543	0	ENST00000261769.5:c.1838A>G	p.Asn613Ser	p.N613S	ENST00000261769	NM_004360.3	613	aAc/aGc	12/16	1	2	FACETS	1	0.957	1	1	0.99	1	CLONAL	2	TRUE	1	0.151384908731881	2		543	731	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260206	19260206	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	62	614	0	ENST00000162023.5:c.87G>C	p.Met29Ile	p.M29I	ENST00000162023		29	atG/atC	7/13	0.0811078639369365	3	FACETS	0.867	0.747	0.999	0.434	0.373	0.5	INDETERMINATE	1	TRUE	1	0.151384908731881	3		614	1016	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398890	398890	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	87	534	0	ENST00000380956.4:c.700C>A	p.Pro234Thr	p.P234T	ENST00000380956	NM_001195286.1	234	Ccc/Acc	6/9	1	2	FACETS	0.807	0.714	0.906	1	0.981	1	CLONAL	2	TRUE	1	0.151384908731881	2		534	712	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467981	50467981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	84	641	0	ENST00000331340.3:c.1216G>A	p.Glu406Lys	p.E406K	ENST00000331340	NM_006060.4	406	Gag/Aag	8/8	1	2	FACETS	0.818	0.723	0.921	1	0.98	1	CLONAL	2	TRUE	1	0.151384908731881	2		641	678	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0055808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	121	30	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.665447606217398	2		30	340	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0055808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	213	356	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.665447606217398	2		356	636	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0055808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	12	391	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.064	0.044	0.089	0.064	0.044	0.089	SUBCLONAL	1	TRUE	1	0.665447606217398	2		391	562	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0055808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	359	1117	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.665447606217398	2		1117	1045	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111965602	111965602	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	69	112	0	ENST00000375549.3:c.388G>T	p.Ala130Ser	p.A130S	ENST00000375549	NM_003002.3	130	Gca/Tca	4/4	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.665447606217398	2		112	179	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427900	49427900	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	367	755	0	ENST00000301067.7:c.10690C>T	p.Leu3564Phe	p.L3564F	ENST00000301067	NM_003482.3	3564	Ctc/Ttc	38/54	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.665447606217398	2		755	1047	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637437	176637438	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0055808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	181	447	0	ENST00000439151.2:c.2042dup	p.Asn681LysfsTer2	p.N681Kfs*2	ENST00000439151	NM_022455.4	679	-/A	5/23	1	2	FACETS	0.78	0.722	0.841	0.78	0.722	0.841	SUBCLONAL	1	TRUE	1	0.665447606217398	2		447	697	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696730	176696730	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784148	NA	P-0055808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	181	439	0	ENST00000439151.2:c.5431C>T	p.Arg1811Ter	p.R1811*	ENST00000439151	NM_022455.4	1811	Cga/Tga	16/23	1	2	FACETS	0.786	0.727	0.847	0.786	0.727	0.847	SUBCLONAL	1	TRUE	1	0.665447606217398	2		439	692	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913138	44913139	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	308	290	0	ENST00000377967.4:c.814dup	p.Tyr272LeufsTer11	p.Y272Lfs*11	ENST00000377967	NM_021140.2	271	-/T	10/29	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.665447606217398	1		290	451	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185018	123185018	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0055808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	188	242	0	ENST00000218089.9:c.1065T>G	p.Tyr355Ter	p.Y355*	ENST00000218089	NM_001042749.1	355	taT/taG	12/35	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.665447606217398	1		242	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574030	7574030	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	118	860	0	ENST00000269305.4:c.997del	p.Arg333ValfsTer12	p.R333Vfs*12	ENST00000269305	NM_001126112.2	333	Cgt/gt	10/11	1	2	FACETS	0.801	0.723	0.883	1	0.986	1	CLONAL	2	TRUE	1	0.197067907750929	2		860	748	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242737	66242737	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	34	291	0	ENST00000273854.3:c.1835T>C	p.Val612Ala	p.V612A	ENST00000273854	NM_004439.5	612	gTt/gCt	9/18	1	2	FACETS	0.686	0.56	0.828	0.686	0.56	0.828	SUBCLONAL	1	TRUE	1	0.197067907750929	2		291	503	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0055811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	53	378	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.16	2		378	619	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307529	118307529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	36	416	1	ENST00000534358.1:c.302C>T	p.Ser101Leu	p.S101L	ENST00000534358	NM_005933.3	101	tCa/tTa	1/36	1	2	FACETS	0.753	0.617	0.905	0.753	0.617	0.905	CLONAL	1	TRUE	1	0.16	2		417	598	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233459	69233459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	50	452	0	ENST00000462284.1:c.1324G>A	p.Glu442Lys	p.E442K	ENST00000462284	NM_002392.5	442	Gaa/Aaa	11/11	1	2	FACETS	0.962	0.815	1	0.962	0.815	1	CLONAL	1	TRUE	1	0.16	2		452	650	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544735	65544735	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	48	545	0	ENST00000358664.4:c.191T>G	p.Leu64Arg	p.L64R	ENST00000358664	NM_002382.4	64	cTa/cGa	4/5	0.143110879464313	1	FACETS	0.795	0.671	0.933	0.795	0.671	0.933	CLONAL	1	TRUE	0	0.16	1		545	694	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311688	30311688	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	60	514	0	ENST00000262643.3:c.542A>G	p.Glu181Gly	p.E181G	ENST00000262643	NM_001238.2	181	gAa/gGa	7/12	1	2	FACETS	0.992	0.853	1	0.992	0.853	1	CLONAL	1	TRUE	1	0.16	2		514	756	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341107	8341107	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1354653576	NA	P-0055811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	45	423	0	ENST00000356435.5:c.5109T>A	p.Ser1703Arg	p.S1703R	ENST00000356435		1703	agT/agA	30/35	0.186903876391497	1	FACETS	0.938	0.787	1	0.938	0.787	1	CLONAL	1	TRUE	0	0.16	1		423	552	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0055812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	73	30	0				ENST00000310581	NM_198253.2	-/1132			0.487653089045333	1	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	0	0.487653089045333	1		30	223	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230641	46230641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	125	519	0	ENST00000334344.6:c.890C>T	p.Ser297Phe	p.S297F	ENST00000334344	NM_152641.2	297	tCc/tTc	8/21	1	2	FACETS	0.919	0.835	1	0.919	0.835	1	CLONAL	1	TRUE	1	0.487653089045333	2		519	558	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0055812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	222	1158	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	1	2	FACETS	0.865	0.805	0.928	0.865	0.805	0.928	CLONAL	1	TRUE	1	0.487653089045333	2		1158	1052	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357487	89357487	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	175	885	2	ENST00000301030.4:c.331C>T	p.Leu111Phe	p.L111F	ENST00000301030	NM_001256183.1	111	Ctc/Ttc	5/13	1	2	FACETS	0.947	0.874	1	0.947	0.874	1	CLONAL	1	TRUE	1	0.487653089045333	2		887	758	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049724	16049724	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	302	562	0	ENST00000268712.3:c.1048C>T	p.Arg350Ter	p.R350*	ENST00000268712	NM_006311.3	350	Cga/Tga	10/46	0.425888418006685	3	FACETS	0.93	0.88	0.981	0.93	0.88	0.981	CLONAL	2	TRUE	1	0.487653089045333	3		562	828	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543826	212543826	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775988789	NA	P-0055812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	151	490	0	ENST00000342788.4:c.1573C>T	p.Arg525Cys	p.R525C	ENST00000342788	NM_005235.2	525	Cgc/Tgc	13/28	1	2	FACETS	0.981	0.901	1	0.981	0.901	1	CLONAL	1	TRUE	1	0.487653089045333	2		490	631	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505554	157505554	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554231904	NA	P-0055812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	83	350	0	ENST00000346085.5:c.3535C>T	p.Gln1179Ter	p.Q1179*	ENST00000346085	NM_020732.3	1179	Cag/Tag	13/20	1	2	FACETS	0.933	0.829	1	0.933	0.829	1	CLONAL	1	TRUE	1	0.487653089045333	2		350	365	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223978	2223978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	193	954	0	ENST00000326181.6:c.1192C>T	p.Pro398Ser	p.P398S	ENST00000326181	NM_032271.2	398	Cct/Tct	13/21	1	2	FACETS	0.894	0.828	0.963	0.894	0.828	0.963	CLONAL	1	TRUE	1	0.487653089045333	2		954	885	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110605	4110605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756646033	NA	P-0055812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	202	872	0	ENST00000262948.5:c.352G>A	p.Glu118Lys	p.E118K	ENST00000262948	NM_030662.3	118	Gag/Aag	3/11	1	2	FACETS	0.875	0.811	0.941	0.875	0.811	0.941	CLONAL	1	TRUE	1	0.487653089045333	2		872	947	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715643	18715643	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	56	306	0	ENST00000266497.5:c.3474A>G	p.Ile1158Met	p.I1158M	ENST00000266497		1158	atA/atG	25/31	1	2	FACETS	0.682	0.587	0.784	0.682	0.587	0.784	SUBCLONAL	1	TRUE	1	0.487653089045333	2		306	337	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868179	45868179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	156	1080	0	ENST00000391945.4:c.511C>T	p.Pro171Ser	p.P171S	ENST00000391945	NM_000400.3	171	Ccc/Tcc	7/23	1	2	FACETS	0.789	0.723	0.858	0.789	0.723	0.858	SUBCLONAL	1	TRUE	1	0.487653089045333	2		1080	811	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11308006	11308006	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753248955	NA	P-0055812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	173	807	0	ENST00000361445.4:c.986C>T	p.Ala329Val	p.A329V	ENST00000361445	NM_004958.3	329	gCc/gTc	7/58	1	2	FACETS	0.882	0.813	0.954	0.882	0.813	0.954	CLONAL	1	TRUE	1	0.487653089045333	2		807	804	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099976	27099976	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0055812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	183	905	0	ENST00000324856.7:c.3855T>A	p.Tyr1285Ter	p.Y1285*	ENST00000324856	NM_006015.4	1285	taT/taA	15/20	1	2	FACETS	0.912	0.843	0.984	0.912	0.843	0.984	CLONAL	1	TRUE	1	0.487653089045333	2		905	823	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101270	27101271	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	159	893	0	ENST00000324856.7:c.4552_4553delinsTT	p.Pro1518Phe	p.P1518F	ENST00000324856	NM_006015.4	1518	CCc/TTc	18/20	1	2	FACETS	0.896	0.823	0.972	0.896	0.823	0.972	CLONAL	1	TRUE	1	0.487653089045333	2		893	728	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659632	88659632	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	180	597	0	ENST00000372037.3:c.415C>G	p.Pro139Ala	p.P139A	ENST00000372037	NM_004329.2	139	Ccc/Gcc	6/13	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.487653089045333	2		597	672	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885810	111885811	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	160	768	1	ENST00000341259.2:c.1432_1433delinsTT	p.Pro478Phe	p.P478F	ENST00000341259	NM_005475.2	478	CCt/TTt	8/8	1	2	FACETS	0.757	0.694	0.822	0.757	0.694	0.822	SUBCLONAL	1	TRUE	1	0.487653089045333	2		769	867	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865875	56865875	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	84	416	1	ENST00000308159.5:c.1207C>T	p.Gln403Ter	p.Q403*	ENST00000308159	NM_014669.4	403	Cag/Tag	11/22	1	2	FACETS	0.676	0.598	0.758	0.676	0.598	0.758	SUBCLONAL	1	TRUE	1	0.487653089045333	2		417	510	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262103	10262104	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0055812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	147	768	2	ENST00000340748.4:c.2187_2188delinsAA	p.Asn729_Arg730delinsLysSer	p.N729_R730delinsKS	ENST00000340748		729	aaTCgc/aaAAgc	23/40	1	2	FACETS	0.7	0.639	0.764	0.7	0.639	0.764	SUBCLONAL	1	TRUE	1	0.487653089045333	2		770	861	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795374	39795374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	171	777	0	ENST00000288319.7:c.346C>T	p.Pro116Ser	p.P116S	ENST00000288319	NM_182918.3	116	Cca/Tca	3/10	1	2	FACETS	0.916	0.844	0.99	0.916	0.844	0.99	CLONAL	1	TRUE	1	0.487653089045333	2		777	766	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590694	189590695	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	126	508	1	ENST00000264731.3:c.1259_1260delinsTT	p.Ser420Phe	p.S420F	ENST00000264731	NM_003722.4	420	tCC/tTT	10/14	0.487653089045333	1	FACETS	0.774	0.704	0.846	0.774	0.704	0.846	SUBCLONAL	1	TRUE	0	0.487653089045333	1		509	505	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858263	27858263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	174	825	1	ENST00000359303.2:c.308G>A	p.Gly103Asp	p.G103D	ENST00000359303	NM_003535.2	103	gGt/gAt	1/1	1	2	FACETS	0.869	0.801	0.94	0.869	0.801	0.94	CLONAL	1	TRUE	1	0.487653089045333	2		826	821	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969188	93969188	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	93	354	0	ENST00000369303.4:c.1808C>T	p.Pro603Leu	p.P603L	ENST00000369303	NM_004440.3	603	cCa/cTa	10/17	1	2	FACETS	0.937	0.839	1	0.937	0.839	1	CLONAL	1	TRUE	1	0.487653089045333	2		354	407	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109321705	109321705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	159	698	0	ENST00000436639.2:c.718G>A	p.Glu240Lys	p.E240K	ENST00000436639	NM_014454.2	240	Gaa/Aaa	4/10	1	2	FACETS	0.839	0.77	0.911	0.839	0.77	0.911	CLONAL	1	TRUE	1	0.487653089045333	2		698	777	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128432180	128432180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	120	315	0	ENST00000265960.3:c.266G>A	p.Arg89Lys	p.R89K	ENST00000265960	NM_001006617.1	89	aGa/aAa	3/12	0.487653089045333	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.487653089045333	1		315	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520000	NA	P-0055814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	754	935	0	ENST00000269305.4:c.452C>A	p.Pro151His	p.P151H	ENST00000269305	NM_001126112.2	151	cCc/cAc	5/11	0.610601195565951	2	FACETS	0.952	0.927	0.976	0.952	0.927	0.976	CLONAL	2	TRUE	0	0.686806218363018	2		935	1153	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10274009	10274009	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148831705	NA	P-0055814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	116	578	0	ENST00000340748.4:c.871A>G	p.Lys291Glu	p.K291E	ENST00000340748		291	Aaa/Gaa	11/40	0.152057767305043	3	FACETS	0.533	0.48	0.589	0.266	0.24	0.295	INDETERMINATE	1	TRUE	1	0.686806218363018	3		578	852	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793407	242793407	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	78	919	1	ENST00000334409.5:c.670G>A	p.Gly224Arg	p.G224R	ENST00000334409	NM_005018.2	224	Ggg/Agg	5/5	NA	2	FACETS	0.233	0.204	0.265			1	INDETERMINATE	1	TRUE	NA	0.686806218363018	2		920	974	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0055816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	81	383	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.169227994633059	3	FACETS	1	0.924	1	0.695	0.621	0.773	INDETERMINATE	2	TRUE	0	0.355882350407505	3		383	257	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0055816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	154	763	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.355882350407505	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.355882350407505	1		763	589	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4095414	4095414	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	161	805	0	ENST00000262948.5:c.1018C>T	p.Pro340Ser	p.P340S	ENST00000262948	NM_030662.3	340	Ccc/Tcc	9/11	0.355882350407505	0	FACETS	0.858	0.79	0.93			1	CLONAL	1	TRUE	0	0.355882350407505	0		805	679	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753425	42753425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	49	929	2	ENST00000222329.4:c.839C>T	p.Ser280Leu	p.S280L	ENST00000222329	NM_006494.2	280	tCg/tTg	4/4	0.169227994633059	3	FACETS	0.431	0.364	0.506	0.144	0.121	0.169	INDETERMINATE	1	TRUE	0	0.355882350407505	3		931	752	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52725424	52725424	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339473268	NA	P-0055816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	142	685	0	ENST00000322088.6:c.1591G>A	p.Asp531Asn	p.D531N	ENST00000322088	NM_014225.5	531	Gac/Aac	13/15	0.169227994633059	3	FACETS	1	0.976	1	0.398	0.363	0.435	INDETERMINATE	1	TRUE	0	0.355882350407505	3		685	787	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52725471	52725471	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	108	632	1	ENST00000322088.6:c.1638G>T	p.Lys546Asn	p.K546N	ENST00000322088	NM_014225.5	546	aaG/aaT	13/15	0.169227994633059	3	FACETS	1	0.951	1	0.366	0.328	0.405	INDETERMINATE	1	TRUE	0	0.355882350407505	3		633	652	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52725487	52725487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1475762998	NA	P-0055816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	93	553	0	ENST00000322088.6:c.1654G>A	p.Asp552Asn	p.D552N	ENST00000322088	NM_014225.5	552	Gac/Aac	13/15	0.169227994633059	3	FACETS	1	0.947	1	0.368	0.328	0.411	INDETERMINATE	1	TRUE	0	0.355882350407505	3		553	557	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907051	101907051	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	17	275	0	ENST00000374994.4:c.1011G>T	p.Lys337Asn	p.K337N	ENST00000374994	NM_004612.2	337	aaG/aaT	6/9	0.231156587300812	3	FACETS	0.549	0.411	0.712			1	SUBCLONAL	1	TRUE	NA	0.355882350407505	3		275	205	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0055817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	252	673	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.448105367909305	1	FACETS	0.896	0.839	0.953	0.896	0.839	0.953	CLONAL	1	TRUE	0	0.468780724866578	1		673	919	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0055817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	145	429	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.468780724866578	2		429	618	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242486	+	inframe_deletion	In_Frame_Del	DEL	TTAAGAGAAGCAACATCT	TTAAGAGAAGCAACATCT	-	rs121913440	NA	P-0055817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	85	470	0	ENST00000275493.2:c.2239_2256del	p.Leu747_Ser752del	p.L747_S752del	ENST00000275493	NM_005228.3	747	TTAAGAGAAGCAACATCT/-	19/28	1	2	FACETS	0.591	0.522	0.663	0.591	0.522	0.663	SUBCLONAL	1	TRUE	1	0.468780724866578	2		470	614	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711242	61711242	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0055817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	91	420	0	ENST00000401558.2:c.2509-2A>T		p.X837_splice	ENST00000401558	NM_003400.3	837			1	2	FACETS	0.878	0.784	0.978	0.878	0.784	0.978	CLONAL	1	TRUE	1	0.468780724866578	2		420	442	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0055818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	86	727	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.882655993138799	6	FACETS	1	0.905	1	0.505	0.452	0.559	CLONAL	2	TRUE	2	0.882655993138799	6		727	267	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0055818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1	65	790	1	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	0.882655993138799	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.882655993138799	2		791	66	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025984	1025984	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	22	497	0	ENST00000358495.3:c.546G>T	p.Leu182Phe	p.L182F	ENST00000358495	NM_134424.2	182	ttG/ttT	8/12	0.882655993138799	2	FACETS	0.767	0.616	0.928	0.383	0.308	0.464	CLONAL	1	TRUE	0	0.882655993138799	2		497	65	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44527586	44527586	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	20	449	0	ENST00000291552.4:c.19T>G	p.Ser7Ala	p.S7A	ENST00000291552	NM_006758.2	7	Tcc/Gcc	1/8	0.882655993138799	2	FACETS	1	0.831	1	0.515	0.416	0.616	CLONAL	1	TRUE	0	0.882655993138799	2		449	44	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0055822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	103	383	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.272543630413319	5	FACETS	1	0.93	1	0.776	0.702	0.853	CLONAL	3	FALSE	1	0.272543630413319	5		383	343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0055822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	219	933	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	0.263223157539482	5	FACETS	0.911	0.857	0.966	1	0.984	1	CLONAL	5	FALSE	1	0.272543630413319	5		933	497	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325683	87325683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	48	533	0	ENST00000277120.3:c.560C>T	p.Ala187Val	p.A187V	ENST00000277120		187	gCa/gTa	6/19	1	2	FACETS	0.793	0.678	0.917	1	0.967	1	CLONAL	2	FALSE	1	0.272543630413319	2		533	222	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023069	27023069	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	26	64	0	ENST00000324856.7:c.175G>T	p.Glu59Ter	p.E59*	ENST00000324856	NM_006015.4	59	Gag/Tag	1/20	0.272543630413319	3	FACETS	0.951	0.778	1	1	0.938	1	CLONAL	3	FALSE	1	0.272543630413319	3		64	76	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941242	36941242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	31	1016	0	ENST00000361632.4:c.97G>A	p.Ala33Thr	p.A33T	ENST00000361632		33	Gcc/Acc	3/16	0.272543630413319	3	FACETS	0.891	0.723	1	0.446	0.361	0.54	CLONAL	1	FALSE	1	0.272543630413319	3		1016	290	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784078	120784078	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	31	1223	1	ENST00000257552.2:c.907C>T	p.Arg303Cys	p.R303C	ENST00000257552	NM_002442.3	303	Cgc/Tgc	13/15	0.272543630413319	5	FACETS	0.805	0.651	0.979	0.201	0.162	0.245	CLONAL	1	FALSE	1	0.272543630413319	5		1224	398	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193198	11193198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1220892340	NA	P-0055822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	30	848	0	ENST00000361445.4:c.5303C>T	p.Thr1768Ile	p.T1768I	ENST00000361445	NM_004958.3	1768	aCa/aTa	38/58	0.272543630413319	1	FACETS	0.63	0.508	0.766	0.63	0.508	0.766	SUBCLONAL	1	FALSE	0	0.272543630413319	1		848	302	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690826	89690826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	48	381	0	ENST00000371953.3:c.233C>T	p.Thr78Ile	p.T78I	ENST00000371953	NM_000314.4	78	aCc/aTc	4/9	0.272543630413319	3	FACETS	1	0.944	1	0.625	0.531	0.728	CLONAL	1	FALSE	1	0.272543630413319	3		381	320	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909952	100909953	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0055822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	36	508	0	ENST00000325455.5:c.2696_2697delinsTT	p.Arg899Leu	p.R899L	ENST00000325455	NM_001202474.3	899	cGG/cTT	8/8	0.272543630413319	3	FACETS	1	0.927	1	0.623	0.515	0.741	CLONAL	1	FALSE	1	0.272543630413319	3		508	241	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858546	57858546	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	27	898	0	ENST00000228682.2:c.284T>A	p.Leu95Gln	p.L95Q	ENST00000228682	NM_005269.2	95	cTg/cAg	4/12	0.272543630413319	5	FACETS	0.674	0.536	0.833	0.169	0.134	0.209	SUBCLONAL	1	FALSE	1	0.272543630413319	5		898	414	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222872	36222872	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	42	1110	2	ENST00000222270.7:c.5501G>T	p.Arg1834Leu	p.R1834L	ENST00000222270	NM_014727.1	1834	cGc/cTc	27/37	0.24851992026233	3	FACETS	1	0.92	1	0.582	0.488	0.685	CLONAL	1	FALSE	1	0.272543630413319	3		1112	301	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546599	9546599	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	25	723	0	ENST00000353224.5:c.1423G>T	p.Val475Phe	p.V475F	ENST00000353224	NM_177990.2	475	Gtt/Ttt	5/10	0.183060400115317	3	FACETS	0.688	0.543	0.854	0.229	0.181	0.285	SUBCLONAL	1	FALSE	0	0.272543630413319	3		723	303	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617667	100617667	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	34	616	0	ENST00000308731.7:c.402C>A	p.Tyr134Ter	p.Y134*	ENST00000308731	NM_000061.2	134	taC/taA	6/19	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	FALSE	1	0.272543630413319	2		616	206	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228217	53228217	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	AA	novel	NA	P-0055822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	31	867	0	ENST00000375401.3:c.2185delinsTT	p.Val729PhefsTer8	p.V729Ffs*8	ENST00000375401	NM_004187.3	729	Gtc/TTtc	15/26	1	2	FACETS	0.914	0.743	1	0.914	0.743	1	CLONAL	1	FALSE	1	0.272543630413319	2		867	249	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421807	49421807	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	146	1087	0	ENST00000301067.7:c.14500del	p.Glu4834LysfsTer24	p.E4834Kfs*24	ENST00000301067	NM_003482.3	4834	Gaa/aa	46/54	1	2	FACETS	0.508	0.463	0.555	0.508	0.463	0.555	SUBCLONAL	1	TRUE	1	0.540434323487758	2		1087	1064	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	49	374	0				ENST00000310581	NM_198253.2	-/1132			0.280140634425981	3	FACETS	0.948	0.814	1	0.948	0.814	1	CLONAL	2	TRUE	1	0.29	3		374	204	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0055824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	131	309	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.210255242434519	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.29	4		310	477	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426847	70426847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	52	472	2	ENST00000373644.4:c.4507C>T	p.Arg1503Trp	p.R1503W	ENST00000373644	NM_030625.2	1503	Cgg/Tgg	7/12	1	2	FACETS	0.757	0.645	0.879	0.757	0.645	0.879	SUBCLONAL	1	TRUE	1	0.29	2		474	474	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892182	9892182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	155	820	0	ENST00000330684.3:c.2308C>T	p.Pro770Ser	p.P770S	ENST00000330684	NM_001134407.1	770	Cct/Tct	11/13	0.210255242434519	4	FACETS	0.839	0.768	0.912	0.839	0.768	0.912	CLONAL	2	TRUE	2	0.29	4		820	822	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068025	94068025	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	30	324	0	ENST00000369303.4:c.937G>A	p.Glu313Lys	p.E313K	ENST00000369303	NM_004440.3	313	Gaa/Aaa	4/17	1	2	FACETS	0.706	0.57	0.859	0.706	0.57	0.859	SUBCLONAL	1	TRUE	1	0.29	2		324	293	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912094	127912094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	94	393	0	ENST00000373547.4:c.776C>T	p.Pro259Leu	p.P259L	ENST00000373547	NM_002721.4	259	cCt/cTt	7/7	0.299937633843641	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.29	2		393	294	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462324	89462324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	91	546	0	ENST00000336596.2:c.1796C>T	p.Pro599Leu	p.P599L	ENST00000336596	NM_005233.5	599	cCa/cTa	10/17	0.175823121764167	4	FACETS	0.84	0.749	0.936	0.84	0.749	0.936	CLONAL	2	TRUE	2	0.29	4		546	482	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970967	55970967	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	103	661	0	ENST00000263923.4:c.1830G>A	p.Trp610Ter	p.W610*	ENST00000263923	NM_002253.2	610	tgG/tgA	13/30	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.29	2		661	579	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446807	49446807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	97	835	0	ENST00000301067.7:c.1003C>T	p.Pro335Ser	p.P335S	ENST00000301067	NM_003482.3	335	Ccc/Tcc	8/54	0.267855309454603	3	FACETS	0.928	0.827	1	0.464	0.413	0.519	CLONAL	1	TRUE	1	0.29	3		835	825	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436344	110436344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	74	368	0	ENST00000375856.3:c.2057C>T	p.Pro686Leu	p.P686L	ENST00000375856	NM_003749.2	686	cCc/cTc	1/2	0.175823121764167	4	FACETS	0.866	0.763	0.976	0.866	0.763	0.976	CLONAL	2	TRUE	2	0.29	4		368	380	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14028102	14028102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	57	438	1	ENST00000311895.7:c.1156G>A	p.Glu386Lys	p.E386K	ENST00000311895	NM_005236.2	386	Gaa/Aaa	7/11	0.210255242434519	4	FACETS	1	0.958	1	0.659	0.567	0.758	CLONAL	1	TRUE	2	0.29	4		439	385	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244175	41244175	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	105	602	0	ENST00000357654.3:c.3373T>G	p.Ser1125Ala	p.S1125A	ENST00000357654	NM_007294.3	1125	Tct/Gct	10/23	0.299937633843641	2	FACETS	0.989	0.895	1	0.989	0.895	1	CLONAL	2	TRUE	0	0.29	2		602	366	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790147	40790147	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	90	803	0	ENST00000373198.4:c.2584C>T	p.Leu862Phe	p.L862F	ENST00000373198	NM_133170.3	862	Ctc/Ttc	18/32	0.280140634425981	3	FACETS	0.916	0.812	1	0.458	0.406	0.514	CLONAL	1	TRUE	1	0.29	3		803	776	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106534435	106534435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	37	276	0	ENST00000369096.4:c.7G>A	p.Asp3Asn	p.D3N	ENST00000369096	NM_001198.3	3	Gat/Aat	1/7	1	2	FACETS	0.859	0.711	1	0.859	0.711	1	CLONAL	1	TRUE	1	0.29	2		276	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0055826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	114	694	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.235993368832079	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.235993368832079	1		694	699	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0055827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	225	650	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	0.314448494610448	2	FACETS	0.989	0.925	1	0.989	0.925	1	CLONAL	2	TRUE	0	0.31774733665535	2		650	716	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983445	90983445	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659811	NA	P-0055827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	20	329	3	ENST00000265433.3:c.658C>G	p.Gln220Glu	p.Q220E	ENST00000265433	NM_002485.4	220	Caa/Gaa	6/16	0.31774733665535	3	FACETS	0.414	0.316	0.529			1	SUBCLONAL	1	TRUE	NA	0.31774733665535	3		332	352	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	73	374	0				ENST00000310581	NM_198253.2	-/1132			0.270858080925022	3	FACETS	0.987	0.888	1	1	0.975	1	CLONAL	4	TRUE	0	0.270858080925022	3		374	155	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0055829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	253	959	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.203384424401672	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	0	0.270858080925022	3		959	670	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652134	36652135	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0055829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	74	970	0	ENST00000244741.5:c.259dup	p.Asp87GlyfsTer2	p.D87Gfs*2	ENST00000244741	NM_000389.4	86	cgg/cGgg	2/3	0.270858080925022	7	FACETS	1	0.961	1	0.314	0.275	0.357	CLONAL	1	TRUE	3	0.270858080925022	7		970	729	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347895	89347895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	64	850	0	ENST00000301030.4:c.5055G>A	p.Met1685Ile	p.M1685I	ENST00000301030	NM_001256183.1	1685	atG/atA	9/13	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.270858080925022	2		850	408	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120785258	120785258	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1389547060	NA	P-0055829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	56	824	0	ENST00000257552.2:c.850C>T	p.Arg284Ter	p.R284*	ENST00000257552	NM_002442.3	284	Cga/Tga	12/15	0.270858080925022	1	FACETS	0.748	0.642	0.864	0.748	0.642	0.864	SUBCLONAL	1	TRUE	0	0.270858080925022	1		824	478	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590665	95590665	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	91	378	0	ENST00000393063.1:c.1244C>G	p.Ser415Cys	p.S415C	ENST00000393063	NM_030621.3	415	tCt/tGt	9/28	0.221561140264612	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.270858080925022	3		378	328	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348563	89348563	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	117	930	0	ENST00000301030.4:c.4387G>C	p.Glu1463Gln	p.E1463Q	ENST00000301030	NM_001256183.1	1463	Gag/Cag	9/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.270858080925022	2		930	581	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348701	89348701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	108	864	1	ENST00000301030.4:c.4249G>A	p.Asp1417Asn	p.D1417N	ENST00000301030	NM_001256183.1	1417	Gat/Aat	9/13	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.270858080925022	2		865	594	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348707	89348707	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	110	872	1	ENST00000301030.4:c.4243G>A	p.Glu1415Lys	p.E1415K	ENST00000301030	NM_001256183.1	1415	Gag/Aag	9/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.270858080925022	2		873	615	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348752	89348752	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	125	941	0	ENST00000301030.4:c.4198G>T	p.Asp1400Tyr	p.D1400Y	ENST00000301030	NM_001256183.1	1400	Gat/Tat	9/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.270858080925022	2		941	637	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348926	89348926	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	118	880	0	ENST00000301030.4:c.4024G>T	p.Glu1342Ter	p.E1342*	ENST00000301030	NM_001256183.1	1342	Gag/Tag	9/13	1	2	FACETS	0.854	0.774	0.938	1	0.987	1	CLONAL	2	TRUE	1	0.270858080925022	2		880	510	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349282	89349282	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	135	1090	0	ENST00000301030.4:c.3668G>C	p.Arg1223Thr	p.R1223T	ENST00000301030	NM_001256183.1	1223	aGa/aCa	9/13	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.270858080925022	2		1090	676	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349574	89349574	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1302188767	NA	P-0055829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	132	933	2	ENST00000301030.4:c.3376G>A	p.Asp1126Asn	p.D1126N	ENST00000301030	NM_001256183.1	1126	Gac/Aac	9/13	1	2	FACETS	0.789	0.718	0.862	1	0.987	1	SUBCLONAL	2	TRUE	1	0.270858080925022	2		935	618	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349809	89349809	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs776520817	NA	P-0055829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	95	924	0	ENST00000301030.4:c.3141G>T	p.Gln1047His	p.Q1047H	ENST00000301030	NM_001256183.1	1047	caG/caT	9/13	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.270858080925022	2		924	654	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349874	89349874	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1401051885	NA	P-0055829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	115	1017	0	ENST00000301030.4:c.3076G>C	p.Glu1026Gln	p.E1026Q	ENST00000301030	NM_001256183.1	1026	Gaa/Caa	9/13	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.270858080925022	2		1017	640	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351104	89351104	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	97	870	0	ENST00000301030.4:c.1846G>T	p.Glu616Ter	p.E616*	ENST00000301030	NM_001256183.1	616	Gag/Tag	9/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.270858080925022	2		870	538	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215609817	215609817	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587781443	NA	P-0055829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	47	403	0	ENST00000260947.4:c.1877A>G	p.Asn626Ser	p.N626S	ENST00000260947	NM_000465.2	626	aAt/aGt	9/11	0.237321375729472	3	FACETS	0.849	0.717	0.995	0.425	0.358	0.498	CLONAL	1	TRUE	1	0.270858080925022	3		403	464	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183701	10183701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764755691	NA	P-0055829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	69	517	0	ENST00000256474.2:c.170G>A	p.Gly57Glu	p.G57E	ENST00000256474	NM_000551.3	57	gGg/gAg	1/3	0.0694356052492111	4	FACETS	1	0.972	1	0.726	0.634	0.824	INDETERMINATE	1	TRUE	2	0.270858080925022	4		517	446	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923050	44923051	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0055829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	144	310	0	ENST00000377967.4:c.1911_1912insTA	p.Asn638Ter	p.N638*	ENST00000377967	NM_021140.2	637	-/TA	16/29	0.248635977385415	2	FACETS	0.974	0.9	1			1	CLONAL	3	TRUE	NA	0.270858080925022	2		310	364	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366379	15366379	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	30	595	1	ENST00000263377.2:c.1776G>C	p.Lys592Asn	p.K592N	ENST00000263377	NM_058243.2	592	aaG/aaC	10/20	1	2	FACETS	0.619	0.499	0.755	0.619	0.499	0.755	SUBCLONAL	1	TRUE	1	0.270858080925022	2		596	358	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	62	374	0				ENST00000310581	NM_198253.2	-/1132			0.3	3	FACETS	0.897	0.777	1	1	0.963	1	CLONAL	3	TRUE	1	0.11	3		374	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0055829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	75	959	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.11	2		959	1182	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652134	36652135	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0055829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	33	970	0	ENST00000244741.5:c.259dup	p.Asp87GlyfsTer2	p.D87Gfs*2	ENST00000244741	NM_000389.4	86	cgg/cGgg	2/3	1	2	FACETS	0.655	0.531	0.796	0.655	0.531	0.796	SUBCLONAL	1	TRUE	1	0.11	2		970	916	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347895	89347895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	21	850	0	ENST00000301030.4:c.5055G>A	p.Met1685Ile	p.M1685I	ENST00000301030	NM_001256183.1	1685	atG/atA	9/13	1	2	FACETS	0.536	0.411	0.684	0.536	0.411	0.684	SUBCLONAL	1	TRUE	1	0.11	2		850	712	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120785258	120785258	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1389547060	NA	P-0055829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	75	824	0	ENST00000257552.2:c.850C>T	p.Arg284Ter	p.R284*	ENST00000257552	NM_002442.3	284	Cga/Tga	12/15	1	2	FACETS	0.889	0.778	1	1	0.98	1	CLONAL	2	TRUE	1	0.11	2		824	767	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590665	95590665	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	36	378	0	ENST00000393063.1:c.1244C>G	p.Ser415Cys	p.S415C	ENST00000393063	NM_030621.3	415	tCt/tGt	9/28	1	2	FACETS	0.814	0.67	0.976	1	0.955	1	CLONAL	2	TRUE	1	0.11	2		378	402	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348563	89348563	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	46	930	0	ENST00000301030.4:c.4387G>C	p.Glu1463Gln	p.E1463Q	ENST00000301030	NM_001256183.1	1463	Gag/Cag	9/13	1	2	FACETS	0.816	0.684	0.962	0.816	0.684	0.962	CLONAL	1	TRUE	1	0.11	2		930	1025	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348701	89348701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	30	864	1	ENST00000301030.4:c.4249G>A	p.Asp1417Asn	p.D1417N	ENST00000301030	NM_001256183.1	1417	Gat/Aat	9/13	1	2	FACETS	0.549	0.44	0.673	0.549	0.44	0.673	SUBCLONAL	1	TRUE	1	0.11	2		865	994	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348707	89348707	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	29	872	1	ENST00000301030.4:c.4243G>A	p.Glu1415Lys	p.E1415K	ENST00000301030	NM_001256183.1	1415	Gag/Aag	9/13	1	2	FACETS	0.533	0.426	0.657	0.533	0.426	0.657	SUBCLONAL	1	TRUE	1	0.11	2		873	989	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348752	89348752	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	39	941	0	ENST00000301030.4:c.4198G>T	p.Asp1400Tyr	p.D1400Y	ENST00000301030	NM_001256183.1	1400	Gat/Tat	9/13	1	2	FACETS	0.693	0.572	0.829	0.693	0.572	0.829	SUBCLONAL	1	TRUE	1	0.11	2		941	1023	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348926	89348926	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	19	880	0	ENST00000301030.4:c.4024G>T	p.Glu1342Ter	p.E1342*	ENST00000301030	NM_001256183.1	1342	Gag/Tag	9/13	1	2	FACETS	0.453	0.342	0.585	0.453	0.342	0.585	SUBCLONAL	1	TRUE	1	0.11	2		880	763	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349282	89349282	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	27	1090	0	ENST00000301030.4:c.3668G>C	p.Arg1223Thr	p.R1223T	ENST00000301030	NM_001256183.1	1223	aGa/aCa	9/13	1	2	FACETS	0.419	0.331	0.52	0.419	0.331	0.52	SUBCLONAL	1	TRUE	1	0.11	2		1090	1173	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349574	89349574	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1302188767	NA	P-0055829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	29	933	2	ENST00000301030.4:c.3376G>A	p.Asp1126Asn	p.D1126N	ENST00000301030	NM_001256183.1	1126	Gac/Aac	9/13	1	2	FACETS	0.568	0.454	0.7	0.568	0.454	0.7	SUBCLONAL	1	TRUE	1	0.11	2		935	928	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349809	89349809	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs776520817	NA	P-0055829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	34	924	0	ENST00000301030.4:c.3141G>T	p.Gln1047His	p.Q1047H	ENST00000301030	NM_001256183.1	1047	caG/caT	9/13	1	2	FACETS	0.534	0.434	0.648	0.534	0.434	0.648	SUBCLONAL	1	TRUE	1	0.11	2		924	1157	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349874	89349874	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1401051885	NA	P-0055829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	26	1017	0	ENST00000301030.4:c.3076G>C	p.Glu1026Gln	p.E1026Q	ENST00000301030	NM_001256183.1	1026	Gaa/Caa	9/13	1	2	FACETS	0.385	0.303	0.48	0.385	0.303	0.48	SUBCLONAL	1	TRUE	1	0.11	2		1017	1229	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351104	89351104	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	15	870	0	ENST00000301030.4:c.1846G>T	p.Glu616Ter	p.E616*	ENST00000301030	NM_001256183.1	616	Gag/Tag	9/13	1	2	FACETS	0.318	0.231	0.424	0.318	0.231	0.424	SUBCLONAL	1	TRUE	1	0.11	2		870	858	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215609817	215609817	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587781443	NA	P-0055829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	10	403	0	ENST00000260947.4:c.1877A>G	p.Asn626Ser	p.N626S	ENST00000260947	NM_000465.2	626	aAt/aGt	9/11	1	2	FACETS	0.344	0.231	0.487	0.344	0.231	0.487	SUBCLONAL	1	TRUE	1	0.11	2		403	529	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183701	10183701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764755691	NA	P-0055829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	26	517	0	ENST00000256474.2:c.170G>A	p.Gly57Glu	p.G57E	ENST00000256474	NM_000551.3	57	gGg/gAg	1/3	1	2	FACETS	0.604	0.476	0.751	0.604	0.476	0.751	SUBCLONAL	1	TRUE	1	0.11	2		517	783	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923050	44923051	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0055829-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	73	310	0	ENST00000377967.4:c.1911_1912insTA	p.Asn638Ter	p.N638*	ENST00000377967	NM_021140.2	637	-/TA	16/29	0.173025760432964	2	FACETS	1	0.904	1			1	CLONAL	3	TRUE	NA	0.11	2		310	428	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774795	73774795	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	402	567	0	ENST00000254810.4:c.292G>A	p.Glu98Lys	p.E98K	ENST00000254810	NM_005324.3	98	Gaa/Aaa	4/4	1	2	FACETS	0.772	0.734	0.81	1	0.996	1	SUBCLONAL	2	TRUE	1	0.418040498536289	2		567	1246	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0055838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	122	392	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.299097163531254	4	FACETS	0.801	0.726	0.881	0.801	0.726	0.881	CLONAL	2	TRUE	2	0.315948372189329	4		392	634	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0055838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	44	319	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.315948372189329	1	FACETS	0.8	0.675	0.938	0.8	0.675	0.938	CLONAL	1	TRUE	0	0.315948372189329	1		319	293	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0055838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	85	327	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	0.315948372189329	2	FACETS	0.975	0.863	1	0.487	0.431	0.547	CLONAL	1	TRUE	0	0.315948372189329	2		327	552	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047965	180047965	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370847176	NA	P-0055838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1370	183	1008	1	ENST00000261937.6:c.2210G>A	p.Arg737His	p.R737H	ENST00000261937	NM_182925.4	737	cGc/cAc	15/30	0.315948372189329	5	FACETS	1	0.968	1	0.275	0.252	0.298	CLONAL	1	TRUE	1	0.315948372189329	5		1009	1553	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956203	175956203	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	143	402	0	ENST00000367669.3:c.2009G>T	p.Gly670Val	p.G670V	ENST00000367669	NM_022457.5	670	gGa/gTa	18/20	0.315948372189329	5	FACETS	0.924	0.844	1	0.616	0.562	0.672	CLONAL	2	TRUE	2	0.315948372189329	5		402	722	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135008	2135008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1279603512	NA	P-0055838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	163	890	0	ENST00000219476.3:c.4550C>T	p.Pro1517Leu	p.P1517L	ENST00000219476	NM_000548.3	1517	cCa/cTa	35/42	0.190481990885367	4	FACETS	1	0.959	1	0.539	0.493	0.587	CLONAL	1	TRUE	2	0.315948372189329	4		890	1259	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955959	55955959	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	70	500	0	ENST00000263923.4:c.3203C>A	p.Pro1068His	p.P1068H	ENST00000263923	NM_002253.2	1068	cCt/cAt	24/30	0.315948372189329	3	FACETS	0.858	0.748	0.976	0.429	0.374	0.488	CLONAL	1	TRUE	1	0.315948372189329	3		500	598	SUCCESS
APC	324	MSKCC	GRCh37	5	112162905	112162905	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	89	449	0	ENST00000257430.4:c.1509G>A	p.Met503Ile	p.M503I	ENST00000257430	NM_000038.5	503	atG/atA	12/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.315948372189329	2		449	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0055839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	395	673	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.659046331038258	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.659046331038258	2		673	530	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0055839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	86	383	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.659046331038258	3	FACETS	0.826	0.746	0.908	0.826	0.746	0.908	CLONAL	2	TRUE	1	0.659046331038258	3		383	210	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161293	55161293	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	105	436	0	ENST00000257290.5:c.3124T>A	p.Ser1042Thr	p.S1042T	ENST00000257290	NM_006206.4	1042	Tcg/Acg	23/23	0.65359691788222	2	FACETS	1	0.974	1	0.599	0.546	0.653	CLONAL	1	TRUE	0	0.659046331038258	2		436	266	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0055839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	67	338	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.642004074617808	3	FACETS	0.926	0.812	1	0.463	0.406	0.523	CLONAL	1	TRUE	1	0.659046331038258	3		338	292	SUCCESS
APC	324	MSKCC	GRCh37	5	112175642	112175642	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	125	328	0	ENST00000257430.4:c.4351del	p.Glu1451LysfsTer22	p.E1451Kfs*22	ENST00000257430	NM_000038.5	1451	Gaa/aa	16/16	0.642004074617808	3	FACETS	0.897	0.827	0.969	0.897	0.827	0.969	CLONAL	2	TRUE	1	0.659046331038258	3		328	281	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31939922	31939922	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	137	522	1	ENST00000375333.2:c.149C>A	p.Pro50His	p.P50H	ENST00000375333	NM_032454.1	50	cCc/cAc	1/8	0.659046331038258	5	FACETS	0.987	0.898	1	0.329	0.299	0.36	CLONAL	1	TRUE	2	0.659046331038258	5		523	838	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0055841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	264	501	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.645739048606004	5	FACETS	0.939	0.882	0.996	0.626	0.588	0.664	CLONAL	2	TRUE	2	0.649391196469749	5		501	855	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0055841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	340	616	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.645739048606004	5	FACETS	0.96	0.909	1	0.64	0.606	0.674	CLONAL	2	TRUE	2	0.649391196469749	5		616	1077	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0055841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	215	383	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.649391196469749	3	FACETS	0.91	0.855	0.965	0.91	0.855	0.965	CLONAL	2	TRUE	1	0.649391196469749	3		383	482	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465606	99465606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	397	723	0	ENST00000268035.6:c.2431G>A	p.Glu811Lys	p.E811K	ENST00000268035	NM_000875.3	811	Gag/Aag	11/21	0.454870753404871	5	FACETS	0.836	0.798	0.875	0.627	0.598	0.656	CLONAL	3	TRUE	1	0.649391196469749	5		723	962	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999654	100999654	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11571143	NA	P-0055841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	596	1297	1	ENST00000325455.5:c.148G>A	p.Ala50Thr	p.A50T	ENST00000325455	NM_001202474.3	50	Gcc/Acc	1/8	0.649391196469749	3	FACETS	0.99	0.955	1	0.99	0.955	1	CLONAL	2	TRUE	1	0.649391196469749	3		1298	1228	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149440464	149440464	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371692872	NA	P-0055841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	236	921	0	ENST00000286301.3:c.1930G>A	p.Glu644Lys	p.E644K	ENST00000286301	NM_005211.3	644	Gag/Aag	14/22	1	2	FACETS	0.965	0.904	1	0.965	0.904	1	CLONAL	1	TRUE	1	0.649391196469749	2		921	753	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5206802	5206802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	241	790	2	ENST00000357368.4:c.5830G>A	p.Asp1944Asn	p.D1944N	ENST00000357368	NM_002850.3	1944	Gac/Aac	38/38	0.62657343756468	4	FACETS	0.935	0.872	1	0.468	0.436	0.501	CLONAL	1	TRUE	2	0.649391196469749	4		792	1309	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856313	111856313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747913408	NA	P-0055841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	23	36	0	ENST00000341259.2:c.364G>A	p.Glu122Lys	p.E122K	ENST00000341259	NM_005475.2	122	Gag/Aag	2/8	0.649391196469749	3	FACETS	1	0.919	1	0.661	0.532	0.799	CLONAL	1	TRUE	1	0.649391196469749	3		36	71	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795001	42795001	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs373041068	NA	P-0055841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	612	1230	0	ENST00000575354.2:c.2081C>G	p.Ser694Cys	p.S694C	ENST00000575354	NM_015125.3	694	tCt/tGt	10/20	0.62657343756468	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.649391196469749	4		1230	1505	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305228	39305228	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	200	716	0	ENST00000373001.3:c.1197C>G	p.Ile399Met	p.I399M	ENST00000373001	NM_022157.3	399	atC/atG	7/7	0.649391196469749	3	FACETS	0.999	0.927	1	0.499	0.463	0.537	CLONAL	1	TRUE	1	0.649391196469749	3		716	817	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490616	56490616	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	298	510	0	ENST00000267101.3:c.2260C>A	p.Gln754Lys	p.Q754K	ENST00000267101	NM_001982.3	754	Caa/Aaa	19/28	0.649391196469749	3	FACETS	0.985	0.936	1	0.985	0.936	1	CLONAL	2	TRUE	1	0.649391196469749	3		510	617	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857532	57857532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767782645	NA	P-0055841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	249	971	0	ENST00000228682.2:c.58C>T	p.Arg20Trp	p.R20W	ENST00000228682	NM_005269.2	20	Cgg/Tgg	2/12	0.649391196469749	3	FACETS	0.968	0.906	1	0.484	0.453	0.517	CLONAL	1	TRUE	1	0.649391196469749	3		971	1049	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034951	42034951	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	215	878	0	ENST00000219905.7:c.4793C>G	p.Thr1598Ser	p.T1598S	ENST00000219905	NM_001164273.1	1598	aCt/aGt	15/24	0.649391196469749	3	FACETS	1	0.945	1	0.509	0.473	0.545	CLONAL	1	TRUE	1	0.649391196469749	3		878	862	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657562	37657562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	157	668	0	ENST00000447079.4:c.2479G>A	p.Gly827Ser	p.G827S	ENST00000447079	NM_015083.1	827	Ggt/Agt	6/14	1	2	FACETS	0.889	0.819	0.961	0.889	0.819	0.961	CLONAL	1	TRUE	1	0.649391196469749	2		668	544	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657603	37657603	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	183	657	0	ENST00000447079.4:c.2520G>T	p.Met840Ile	p.M840I	ENST00000447079	NM_015083.1	840	atG/atT	6/14	1	2	FACETS	0.93	0.863	0.999	0.93	0.863	0.999	CLONAL	1	TRUE	1	0.649391196469749	2		657	606	SUCCESS
YES1	7525	MSKCC	GRCh37	18	739761	739761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762678626	NA	P-0055841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	169	576	1	ENST00000314574.4:c.1111C>T	p.Pro371Ser	p.P371S	ENST00000314574	NM_005433.3	371	Cca/Tca	9/12	0.649391196469749	3	FACETS	0.955	0.88	1	0.477	0.44	0.517	CLONAL	1	TRUE	1	0.649391196469749	3		577	722	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18276970	18276970	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	276	405	0	ENST00000222254.8:c.1417G>A	p.Glu473Lys	p.E473K	ENST00000222254	NM_005027.3	473	Gag/Aag	12/16	0.62657343756468	4	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	2	0.649391196469749	4		405	685	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794752	42794752	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	474	1105	0	ENST00000575354.2:c.1832C>T	p.Pro611Leu	p.P611L	ENST00000575354	NM_015125.3	611	cCa/cTa	10/20	0.62657343756468	4	FACETS	0.9	0.861	0.94	0.9	0.861	0.94	CLONAL	2	TRUE	2	0.649391196469749	4		1105	1337	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912835	50912835	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146530638	NA	P-0055841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	524	1226	0	ENST00000440232.2:c.2066G>A	p.Arg689Gln	p.R689Q	ENST00000440232	NM_002691.3	689	cGg/cAg	17/27	0.62657343756468	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.649391196469749	4		1226	1279	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633230	12633230	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	409	786	0	ENST00000251849.4:c.1170del	p.Phe390LeufsTer14	p.F390Lfs*14	ENST00000251849	NM_002880.3	390	ttC/tt	11/17	0.62657343756468	4	FACETS	0.931	0.888	0.975	0.931	0.888	0.975	CLONAL	2	TRUE	2	0.649391196469749	4		786	1116	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55597510	55597510	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	129	550	0	ENST00000288135.5:c.2158G>C	p.Glu720Gln	p.E720Q	ENST00000288135	NM_000222.2	720	Gag/Cag	15/21	0.649391196469749	3	FACETS	0.853	0.776	0.934	0.426	0.388	0.467	CLONAL	1	TRUE	1	0.649391196469749	3		550	617	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860708	151860709	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0055841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	475	682	0	ENST00000262189.6:c.9953_9954del	p.Thr3318SerfsTer7	p.T3318Sfs*7	ENST00000262189	NM_170606.2	3318	aCA/a	43/59	0.649391196469749	4	FACETS	0.919	0.885	0.953	0.919	0.885	0.953	CLONAL	3	TRUE	1	0.649391196469749	4		682	875	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74859044	74859044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	156	514	0	ENST00000284811.8:c.160G>A	p.Glu54Lys	p.E54K	ENST00000284811		54	Gag/Aag	4/4	0.625369444893477	5	FACETS	1	0.958	1	0.358	0.327	0.389	CLONAL	1	TRUE	2	0.649391196469749	5		514	884	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0055842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	578	889	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.806566531127999	2		889	1296	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524525	187524525	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35670235	NA	P-0055842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	359	725	0	ENST00000441802.2:c.11155G>A	p.Val3719Met	p.V3719M	ENST00000441802	NM_005245.3	3719	Gtg/Atg	19/27	1	2	FACETS	0.897	0.853	0.943	0.897	0.853	0.943	CLONAL	1	TRUE	1	0.806566531127999	2		725	992	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507426	8507426	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	22	417	1	ENST00000356435.5:c.1552C>A	p.Gln518Lys	p.Q518K	ENST00000356435		518	Cag/Aag	11/35	1	2	FACETS	0.135	0.104	0.171	0.135	0.104	0.171	SUBCLONAL	1	TRUE	1	0.806566531127999	2		418	404	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123875232	123875232	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	18	216	0	ENST00000330479.4:c.188G>T	p.Cys63Phe	p.C63F	ENST00000330479	NM_020382.3	63	tGc/tTc	3/9	0.263498605971287	1	FACETS	0.085	0.063	0.11	0.085	0.063	0.11	INDETERMINATE	1	TRUE	0	0.806566531127999	1		216	315	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216619	2216619	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs557983259	NA	P-0055842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	83	1173	2	ENST00000398665.3:c.2263G>A	p.Val755Ile	p.V755I	ENST00000398665	NM_032482.2	755	Gtc/Atc	20/28	0.806566531127999	1	FACETS	0.127	0.111	0.144	0.127	0.111	0.144	SUBCLONAL	1	TRUE	0	0.806566531127999	1		1175	967	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289911	15289911	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	620	1172	0	ENST00000263388.2:c.3643C>A	p.His1215Asn	p.H1215N	ENST00000263388	NM_000435.2	1215	Cac/Aac	22/33	1	2	FACETS	0.972	0.936	1	0.972	0.936	1	CLONAL	1	TRUE	1	0.806566531127999	2		1172	1581	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909369	41909369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	162	207	0	ENST00000372991.4:c.19G>A	p.Glu7Lys	p.E7K	ENST00000372991	NM_001760.3	7	Gaa/Aaa	1/5	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.806566531127999	2		207	307	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856124	151856125	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0055842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	41	498	0	ENST00000262189.6:c.11493dup	p.Gly3832TrpfsTer14	p.G3832Wfs*14	ENST00000262189	NM_170606.2	3831	-/T	44/59	0.806566531127999	1	FACETS	0.13	0.108	0.155	0.13	0.108	0.155	SUBCLONAL	1	TRUE	0	0.806566531127999	1		498	465	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400293	139400293	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	411	717	0	ENST00000277541.6:c.4055G>T	p.Cys1352Phe	p.C1352F	ENST00000277541	NM_017617.3	1352	tGc/tTc	25/34	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.806566531127999	2		717	976	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0055843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	18	219	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.827	1	1	0.827	1	CLONAL	1	TRUE	1	0.11	2		219	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	15	797	0	ENST00000269305.4:c.672G>C	p.Glu224Asp	p.E224D	ENST00000269305	NM_001126112.2	224	gaG/gaC	6/11	1	2	FACETS	0.545	0.397	0.725	0.545	0.397	0.725	SUBCLONAL	1	TRUE	1	0.11	2		797	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0055844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	101	1025	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.159971286007325	2	FACETS	1	0.977	1	0.679	0.606	0.756	CLONAL	1	TRUE	0	0.188422347588977	2		1025	790	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0055844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	99	501	1	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	0.188422347588977	3	FACETS	1	0.968	1	0.802	0.719	0.889	CLONAL	2	TRUE	0	0.188422347588977	3		502	478	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134988	41134988	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	31	430	0	ENST00000379561.5:c.640C>A	p.Arg214Ser	p.R214S	ENST00000379561	NM_002015.3	214	Cgt/Agt	2/3	1	2	FACETS	0.924	0.748	1	0.924	0.748	1	CLONAL	1	TRUE	1	0.188422347588977	2		430	356	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94211978	94211978	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0055844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	30	695	0	ENST00000323929.3:c.467C>G	p.Ser156Ter	p.S156*	ENST00000323929	NM_005591.3	156	tCa/tGa	6/20	0.188422347588977	2	FACETS	0.62	0.498	0.758	0.31	0.249	0.379	SUBCLONAL	1	TRUE	0	0.188422347588977	2		695	514	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964239	28964239	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	18	291	0	ENST00000282397.4:c.1663G>A	p.Val555Met	p.V555M	ENST00000282397	NM_002019.4	555	Gtg/Atg	13/30	1	2	FACETS	0.708	0.533	0.914	0.708	0.533	0.914	CLONAL	1	TRUE	1	0.188422347588977	2		291	270	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796754	135796754	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203434	NA	P-0055855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	15	200	0	ENST00000298552.3:c.733C>T	p.Arg245Ter	p.R245*	ENST00000298552	NM_001162426.1	245	Cga/Tga	8/23	0.541962320037288	1	FACETS	0.275	0.202	0.361	0.275	0.202	0.361	SUBCLONAL	1	TRUE	0	0.541962320037288	1		200	147	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778090	135778090	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203673	NA	P-0055855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	60	503	0	ENST00000298552.3:c.2293C>T	p.Gln765Ter	p.Q765*	ENST00000298552	NM_001162426.1	765	Cag/Tag	18/23	0.541962320037288	1	FACETS	0.416	0.36	0.477	0.416	0.36	0.477	SUBCLONAL	1	TRUE	0	0.541962320037288	1		503	388	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437265	220437265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1224525818	NA	P-0055855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	326	1454	0	ENST00000243786.2:c.169C>T	p.Arg57Trp	p.R57W	ENST00000243786	NM_002191.3	57	Cgg/Tgg	1/2	0.541962320037288	3	FACETS	1	0.989	1	0.393	0.37	0.416	CLONAL	1	TRUE	0	0.541962320037288	3		1454	1298	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610511	10610528	+	inframe_deletion	In_Frame_Del	DEL	TGATGCCAAAGGCCTGCT	TGATGCCAAAGGCCTGCT	-	novel	NA	P-0055855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	305	876	0	ENST00000171111.5:c.182_199del	p.Lys61_Ile66del	p.K61_I66del	ENST00000171111	NM_203500.1	61	aAGCAGGCCTTTGGCATCAtg/atg	2/6	0.541962320037288	2	FACETS	0.902	0.858	0.946	0.902	0.858	0.946	CLONAL	2	TRUE	0	0.541962320037288	2		876	624	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752909	57752909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151304321	NA	P-0055855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	24	323	0	ENST00000274289.3:c.1019C>T	p.Pro340Leu	p.P340L	ENST00000274289	NM_006622.3	340	cCg/cTg	8/14	0.541962320037288	2	FACETS	0.3	0.235	0.375	0.15	0.117	0.188	SUBCLONAL	1	TRUE	0	0.541962320037288	2		323	295	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0055856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	733	973	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.537839969426234	2	FACETS	0.934	0.905	0.963	0.934	0.905	0.963	CLONAL	2	TRUE	0	0.537839969426234	2		973	1459	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	174	303	0	ENST00000256196.4:c.68G>T	p.Gly23Val	p.G23V	ENST00000256196		23	gGc/gTc	1/6	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.537839969426234	2		303	545	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376352	15376352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776261114	NA	P-0055856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1888	935	1455	1	ENST00000263377.2:c.662C>T	p.Thr221Met	p.T221M	ENST00000263377	NM_058243.2	221	aCg/aTg	5/20	0.428731918995951	4	FACETS	0.947	0.917	0.977			1	CLONAL	2	TRUE	NA	0.537839969426234	4		1456	2823	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39233631	39233631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	101	375	0	ENST00000402219.2:c.2713C>A	p.His905Asn	p.H905N	ENST00000402219	NM_005633.3	905	Cat/Aat	17/23	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.537839969426234	2		375	357	SUCCESS
APC	324	MSKCC	GRCh37	5	112174096	112174096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs137854575	NA	P-0055858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	45	201	0	ENST00000257430.4:c.2805C>A	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	taC/taA	16/16	1	2	FACETS	0.932	0.801	1	0.932	0.801	1	CLONAL	1	TRUE	1	0.704813535514777	2		201	137	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0055858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	401	567	0	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	0.681360733039617	3	FACETS	0.99	0.961	1	0.99	0.961	1	CLONAL	3	TRUE	0	0.704813535514777	3		567	518	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0055858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	35	146	0	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.704813535514777	2		146	98	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107023	27107024	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0055858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	126	358	0	ENST00000324856.7:c.6635dup	p.Ala2213GlyfsTer12	p.A2213Gfs*12	ENST00000324856	NM_006015.4	2212	cag/cAag	20/20	0.704813535514777	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.704813535514777	1		358	215	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925629	114925630	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0055858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	217	716	0	ENST00000543371.1:c.1708_1709del	p.Ser570IlefsTer38	p.S570Ifs*38	ENST00000543371	NM_001198531.1	569	tcCTca/tcca	14/14	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.704813535514777	2		716	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577101	7577101	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	558	747	0	ENST00000269305.4:c.837del	p.Arg280GlufsTer65	p.R280Efs*65	ENST00000269305	NM_001126112.2	279	ggG/gg	8/11	0.593561963304345	4	FACETS	0.878	0.854	0.902	0.878	0.854	0.902	CLONAL	4	TRUE	0	0.684561769700636	4		747	782	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36808970	36808970	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	111	570	0	ENST00000373129.3:c.1084C>T	p.Gln362Ter	p.Q362*	ENST00000373129	NM_032017.1	362	Cag/Tag	11/12	0.595259046083449	4	FACETS	0.793	0.713	0.877	0.396	0.356	0.439	SUBCLONAL	1	TRUE	2	0.684561769700636	4		570	689	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417084	417084	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	81	231	0	ENST00000399788.2:c.3466G>C	p.Asp1156His	p.D1156H	ENST00000399788	NM_001042603.1	1156	Gac/Cac	23/28	0.589365717825718	3	FACETS	1	0.97	1	0.419	0.374	0.465	CLONAL	1	TRUE	0	0.684561769700636	3		231	253	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955548	48955692	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCGAATCATGGAATCCCTTGCATGGCTCTCAGTAAGTAGCTAAATAATTGAAGAAATTCATTCATGTGCATATGGCTAACAAATTATTGTTAGTGAGAGGTGTTTCTTAACATCTACCTCAAGAACATATAGGGAATTTAATGA	ATCGAATCATGGAATCCCTTGCATGGCTCTCAGTAAGTAGCTAAATAATTGAAGAAATTCATTCATGTGCATATGGCTAACAAATTATTGTTAGTGAGAGGTGTTTCTTAACATCTACCTCAAGAACATATAGGGAATTTAATGA	-	novel	NA	P-0055860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	49	201	0	ENST00000267163.4:c.1666_1695+115del		p.X556_splice	ENST00000267163	NM_000321.2	556		17/27	NA	2	FACETS	1	0.873	1			1	INDETERMINATE	1	TRUE	NA	0.684561769700636	2		201	142	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245293	41245293	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0055860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	476	701	0	ENST00000357654.3:c.2255T>G	p.Leu752Ter	p.L752*	ENST00000357654	NM_007294.3	752	tTa/tGa	10/23	0.626346396165952	3	FACETS	0.914	0.886	0.941	0.914	0.886	0.941	CLONAL	3	TRUE	0	0.684561769700636	3		701	681	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561271	9561271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	69	369	0	ENST00000353224.5:c.511C>T	p.His171Tyr	p.H171Y	ENST00000353224	NM_177990.2	171	Cac/Tac	4/10	0.595259046083449	4	FACETS	0.807	0.705	0.915	0.403	0.352	0.458	CLONAL	1	TRUE	2	0.684561769700636	4		369	421	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55232988	55232988	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	82	307	0	ENST00000275493.2:c.1738A>G	p.Ile580Val	p.I580V	ENST00000275493	NM_005228.3	580	Atc/Gtc	15/28	0.651727164971832	3	FACETS	0.927	0.824	1	0.463	0.412	0.518	CLONAL	1	TRUE	1	0.684561769700636	3		307	347	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865320	57865320	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	134	823	0	ENST00000228682.2:c.2797G>A	p.Gly933Ser	p.G933S	ENST00000228682	NM_005269.2	933	Ggt/Agt	12/12	0.684561769700636	4	FACETS	0.831	0.755	0.91	0.415	0.377	0.455	CLONAL	1	TRUE	2	0.684561769700636	4		823	794	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0055861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	32	310	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.842	0.687	1	0.842	0.687	1	CLONAL	1	FALSE	1	0.30904235194209	2		310	246	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0055861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	101	546	1	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.0328315558715184	3	FACETS	1	0.977	1			1	INDETERMINATE	1	FALSE	NA	0.30904235194209	3		547	567	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089736	27089736	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	103	486	1	ENST00000324856.7:c.2692G>A	p.Ala898Thr	p.A898T	ENST00000324856	NM_006015.4	898	Gct/Act	8/20	1	2	FACETS	0.995	0.891	1	0.995	0.891	1	CLONAL	1	FALSE	1	0.30904235194209	2		487	670	SUCCESS
APC	324	MSKCC	GRCh37	5	112177350	112177350	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	30	192	0	ENST00000257430.4:c.6059del	p.Cys2020PhefsTer24	p.C2020Ffs*24	ENST00000257430	NM_000038.5	2020	tGt/tt	16/16	1	2	FACETS	1	0.837	1	1	0.837	1	CLONAL	1	FALSE	1	0.30904235194209	2		192	188	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0055861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	55	310	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.503290539840354	2		310	203	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0055861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	176	546	1	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.503290539840354	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.503290539840354	1		547	486	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089736	27089736	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	149	486	1	ENST00000324856.7:c.2692G>A	p.Ala898Thr	p.A898T	ENST00000324856	NM_006015.4	898	Gct/Act	8/20	1	2	FACETS	0.957	0.877	1	0.957	0.877	1	CLONAL	1	TRUE	1	0.503290539840354	2		487	619	SUCCESS
APC	324	MSKCC	GRCh37	5	112177350	112177350	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	63	192	0	ENST00000257430.4:c.6059del	p.Cys2020PhefsTer24	p.C2020Ffs*24	ENST00000257430	NM_000038.5	2020	tGt/tt	16/16	0.503290539840354	1	FACETS	0.991	0.873	1	0.991	0.873	1	CLONAL	1	TRUE	0	0.503290539840354	1		192	189	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0055866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	95	644	0	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	0.168114689724684	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.205303167094677	1		644	756	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989592	212989592	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	66	268	0	ENST00000342788.4:c.119C>G	p.Ser40Cys	p.S40C	ENST00000342788	NM_005235.2	40	tCt/tGt	2/28	0.0944501727246296	3	FACETS	1	0.899	1	1	0.899	1	INDETERMINATE	2	TRUE	1	0.205303167094677	3		268	343	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742876	17742876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs930939009	NA	P-0055866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	98	758	0	ENST00000250003.3:c.784G>A	p.Glu262Lys	p.E262K	ENST00000250003	NM_002478.4	262	Gag/Aag	3/3	0.205303167094677	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.205303167094677	1		758	790	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514530	41514530	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	56	462	0	ENST00000373198.4:c.131G>T	p.Ser44Ile	p.S44I	ENST00000373198	NM_133170.3	44	aGt/aTt	2/32	1	2	FACETS	0.911	0.78	1	0.911	0.78	1	CLONAL	1	TRUE	1	0.205303167094677	2		462	599	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251634	212251634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3748961	NA	P-0055868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	189	429	0	ENST00000342788.4:c.3425G>A	p.Arg1142Gln	p.R1142Q	ENST00000342788	NM_005235.2	1142	cGa/cAa	27/28	1	2	FACETS	0.869	0.808	0.931	0.869	0.808	0.931	CLONAL	1	TRUE	1	0.75669530419905	2		429	575	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	22	313	0	ENST00000397062.3:c.101G>A	p.Arg34Gln	p.R34Q	ENST00000397062	NM_006164.4	34	cGa/cAa	2/5	1	2	FACETS	0.105	0.081	0.133	0.105	0.081	0.133	SUBCLONAL	1	TRUE	1	0.75669530419905	2		313	554	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998975	100998975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	285	752	0	ENST00000325455.5:c.827C>T	p.Ser276Leu	p.S276L	ENST00000325455	NM_001202474.3	276	tCa/tTa	1/8	0.75669530419905	1	FACETS	0.897	0.854	0.94	0.897	0.854	0.94	CLONAL	1	TRUE	0	0.75669530419905	1		752	522	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188847	32188847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	736	781	0	ENST00000375023.3:c.707G>A	p.Gly236Glu	p.G236E	ENST00000375023	NM_004557.3	236	gGa/gAa	4/30	0.694090468420936	3	FACETS	0.979	0.949	1	0.979	0.949	1	CLONAL	2	TRUE	1	0.75669530419905	3		781	1370	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760786	133760786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1330364358	NA	P-0055868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	386	776	0	ENST00000318560.5:c.3109G>A	p.Glu1037Lys	p.E1037K	ENST00000318560	NM_005157.4	1037	Gag/Aag	11/11	1	2	FACETS	0.908	0.864	0.953	0.908	0.864	0.953	CLONAL	1	TRUE	1	0.75669530419905	2		776	1123	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319853	8319853	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	121	306	1	ENST00000356435.5:c.5648G>A	p.Arg1883Gln	p.R1883Q	ENST00000356435		1883	cGa/cAa	34/35	0.75669530419905	1	FACETS	0.768	0.707	0.828	0.768	0.707	0.828	SUBCLONAL	1	TRUE	0	0.75669530419905	1		307	259	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573765	64573765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565644005	NA	P-0055868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	66	756	0	ENST00000312049.6:c.988C>T	p.Arg330Cys	p.R330C	ENST00000312049	NM_130799.2	330	Cgc/Tgc	7/10	1	2	FACETS	0.147	0.126	0.169	0.147	0.126	0.169	SUBCLONAL	1	TRUE	1	0.75669530419905	2		756	1190	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211449	98211449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779844193	NA	P-0055868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	256	662	0	ENST00000331920.6:c.3706G>A	p.Glu1236Lys	p.E1236K	ENST00000331920	NM_000264.3	1236	Gag/Aag	22/24	1	2	FACETS	0.748	0.701	0.795	0.748	0.701	0.795	SUBCLONAL	1	TRUE	1	0.75669530419905	2		662	905	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983019	201983019	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149307595	NA	P-0055868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1226	103	921	1	ENST00000359651.3:c.868G>A	p.Glu290Lys	p.E290K	ENST00000359651		290	Gag/Aag	7/8	1	2	FACETS	0.205	0.182	0.229	0.205	0.182	0.229	SUBCLONAL	1	TRUE	1	0.75669530419905	2		922	1329	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101586	27101586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1420328983	NA	P-0055868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	347	879	0	ENST00000324856.7:c.4868C>T	p.Ser1623Leu	p.S1623L	ENST00000324856	NM_006015.4	1623	tCg/tTg	18/20	1	2	FACETS	0.69	0.652	0.728	0.69	0.652	0.728	SUBCLONAL	1	TRUE	1	0.75669530419905	2		879	1330	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667843	37667843	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	203	442	0	ENST00000447079.4:c.2728G>T	p.Glu910Ter	p.E910*	ENST00000447079	NM_015083.1	910	Gag/Tag	8/14	1	2	FACETS	0.796	0.741	0.852	0.796	0.741	0.852	SUBCLONAL	1	TRUE	1	0.75669530419905	2		442	674	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117639414	117639414	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	97	322	0	ENST00000368508.3:c.5942C>A	p.Thr1981Asn	p.T1981N	ENST00000368508	NM_002944.2	1981	aCt/aAt	37/43	0.114992681135575	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.75669530419905	0		322	371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0055870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	61	578	2	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.818	0.706	0.941	0.818	0.706	0.941	CLONAL	1	TRUE	1	0.240483453726726	2		580	620	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0055870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	36	304	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	1	2	FACETS	0.764	0.628	0.915	0.764	0.628	0.915	CLONAL	1	TRUE	1	0.240483453726726	2		304	392	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0055870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	125	520	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.191247719720843	2	FACETS	0.819	0.743	0.898	0.819	0.743	0.898	CLONAL	2	TRUE	0	0.240483453726726	2		520	635	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258744	115258744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434596	NA	P-0055870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	85	350	0	ENST00000369535.4:c.38G>A	p.Gly13Asp	p.G13D	ENST00000369535	NM_002524.4	13	gGt/gAt	2/7	0.191247719720843	2	FACETS	1	0.977	1	0.718	0.637	0.805	CLONAL	1	TRUE	0	0.240483453726726	2		350	492	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974744	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAGCAGCGCCCGCA	CCTCCAGCAGCGCCCGCA	-	novel	NA	P-0055870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	29	385	0	ENST00000304494.5:c.83_100del	p.Val28_Glu33del	p.V28_E33del	ENST00000304494	NM_000077.4	28	gTGCGGGCGCTGCTGGAGGcg/gcg	1/3	0.240483453726726	1	FACETS	0.547	0.439	0.67	0.547	0.439	0.67	SUBCLONAL	1	TRUE	0	0.240483453726726	1		385	388	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736302	243736302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	46	342	0	ENST00000263826.5:c.745C>T	p.Arg249Cys	p.R249C	ENST00000263826	NM_005465.4	249	Cgt/Tgt	8/13	1	2	FACETS	0.744	0.627	0.874	0.744	0.627	0.874	SUBCLONAL	1	TRUE	1	0.240483453726726	2		342	514	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	79	219	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.827	0.733	0.926	1	0.981	1	CLONAL	2	TRUE	1	0.278449354465573	2		219	343	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	78	215	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.862	0.764	0.965	1	0.982	1	CLONAL	2	TRUE	1	0.278449354465573	2		215	325	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	187	758	2	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.278449354465573	2		760	1039	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	129	507	0	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.278449354465573	2		507	702	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	58	726	3	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.435	0.373	0.504	0.435	0.373	0.504	SUBCLONAL	1	TRUE	1	0.278449354465573	2		729	957	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	124	532	2	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.278449354465573	2		534	730	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	23	372	2	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	0.416	0.324	0.523	0.416	0.324	0.523	SUBCLONAL	1	TRUE	1	0.278449354465573	2		374	397	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736238	243736238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	43	291	2	ENST00000263826.5:c.809G>A	p.Arg270His	p.R270H	ENST00000263826	NM_005465.4	270	cGt/cAt	8/13	1	2	FACETS	0.796	0.667	0.938	0.796	0.667	0.938	CLONAL	1	TRUE	1	0.278449354465573	2		293	388	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149107	61149107	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs140572082	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	36	400	0	ENST00000295025.8:c.1297A>G	p.Thr433Ala	p.T433A	ENST00000295025	NM_002908.2	433	Aca/Gca	11/11	1	2	FACETS	0.499	0.41	0.6	0.499	0.41	0.6	SUBCLONAL	1	TRUE	1	0.278449354465573	2		400	518	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970967	21970967	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755927351	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	229	726	1	ENST00000304494.5:c.391C>T	p.Arg131Cys	p.R131C	ENST00000304494	NM_000077.4	131	Cgc/Tgc	2/3	1	2	FACETS	0.75	0.699	0.804	1	0.992	1	SUBCLONAL	2	TRUE	1	0.278449354465573	2		727	1096	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	112	289	2	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.849	0.767	0.933	1	0.987	1	CLONAL	2	TRUE	1	0.278449354465573	2		291	474	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476310	88476310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760692815	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	160	615	0	ENST00000360948.2:c.1822G>A	p.Gly608Ser	p.G608S	ENST00000360948	NM_001012338.2	608	Ggc/Agc	15/19	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.278449354465573	2		615	910	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119781	70119781	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1274036689	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	55	596	0	ENST00000245479.2:c.788del	p.Gly263AlafsTer16	p.G263Afs*16	ENST00000245479	NM_000346.3	261	gaG/ga	3/3	1	2	FACETS	0.482	0.411	0.56	0.482	0.411	0.56	SUBCLONAL	1	TRUE	1	0.278449354465573	2		596	819	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992316	72992316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs62640001	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	281	989	2	ENST00000268489.5:c.1729G>A	p.Val577Ile	p.V577I	ENST00000268489	NM_006885.3	577	Gtc/Atc	2/10	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.278449354465573	2		991	1351	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109935	115109935	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	221	888	0	ENST00000257566.3:c.1943C>T	p.Pro648Leu	p.P648L	ENST00000257566	NM_016569.3	648	cCg/cTg	8/8	1	2	FACETS	0.804	0.748	0.862	1	0.992	1	CLONAL	2	TRUE	1	0.278449354465573	2		888	987	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795364	42795364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	57	726	1	ENST00000575354.2:c.2444C>T	p.Ala815Val	p.A815V	ENST00000575354	NM_015125.3	815	gCc/gTc	10/20	1	2	FACETS	0.516	0.442	0.598	0.516	0.442	0.598	SUBCLONAL	1	TRUE	1	0.278449354465573	2		727	793	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186742	108186742	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs532480170	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	32	356	1	ENST00000278616.4:c.6100C>T	p.Arg2034Ter	p.R2034*	ENST00000278616	NM_000051.3	2034	Cga/Tga	42/63	1	2	FACETS	0.472	0.382	0.573	0.472	0.382	0.573	SUBCLONAL	1	TRUE	1	0.278449354465573	2		357	487	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512401	38512401	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1441911200	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	55	720	0	ENST00000254066.5:c.1312G>C	p.Ala438Pro	p.A438P	ENST00000254066	NM_000964.3	438	Gcc/Ccc	9/9	1	2	FACETS	0.465	0.396	0.54	0.465	0.396	0.54	SUBCLONAL	1	TRUE	1	0.278449354465573	2		720	850	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402605	20402605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775788562	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	34	486	0	ENST00000346618.3:c.142G>A	p.Ala48Thr	p.A48T	ENST00000346618	NM_001949.4	48	Gcc/Acc	1/7	1	2	FACETS	0.386	0.315	0.468	0.386	0.315	0.468	SUBCLONAL	1	TRUE	1	0.278449354465573	2		486	632	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163217	32163217	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	62	837	0	ENST00000375023.3:c.6009del	p.Lys2003AsnfsTer13	p.K2003Nfs*13	ENST00000375023	NM_004557.3	2003	aaA/aa	30/30	1	2	FACETS	0.396	0.34	0.457	0.396	0.34	0.457	SUBCLONAL	1	TRUE	1	0.278449354465573	2		837	1125	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599271	28599271	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs770146088	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	83	925	0	ENST00000253063.3:c.722del	p.Pro241GlnfsTer6	p.P241Qfs*6	ENST00000253063	NM_031459.4	239	agC/ag	5/10	1	2	FACETS	0.511	0.45	0.578	0.511	0.45	0.578	SUBCLONAL	1	TRUE	1	0.278449354465573	2		925	1166	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661664	227661665	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	133	616	0	ENST00000305123.5:c.1790_1791del	p.Gly597AlafsTer13	p.G597Afs*13	ENST00000305123	NM_005544.2	597	gGG/g	1/2	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.278449354465573	2		616	700	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912079	127912079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	13	311	2	ENST00000373547.4:c.791G>A	p.Arg264His	p.R264H	ENST00000373547	NM_002721.4	264	cGt/cAt	7/7	1	2	FACETS	0.242	0.172	0.328	0.242	0.172	0.328	SUBCLONAL	1	TRUE	1	0.278449354465573	2		313	386	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090471	37090471	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs63750702	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	34	398	0	ENST00000231790.2:c.2066A>G	p.Gln689Arg	p.Q689R	ENST00000231790	NM_000249.3	689	cAg/cGg	18/19	1	2	FACETS	0.395	0.321	0.477	0.395	0.321	0.477	SUBCLONAL	1	TRUE	1	0.278449354465573	2		398	619	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725059	89725059	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	62	174	0	ENST00000371953.3:c.1042A>C	p.Thr348Pro	p.T348P	ENST00000371953	NM_000314.4	348	Aca/Cca	9/9	0.278449354465573	2	FACETS	0.9	0.795	1	1	0.97	1	CLONAL	3	TRUE	0	0.278449354465573	2		174	165	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622410	1622410	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	43	568	0	ENST00000344749.5:c.554A>G	p.Tyr185Cys	p.Y185C	ENST00000344749	NM_001136139.2	185	tAc/tGc	9/19	1	2	FACETS	0.401	0.334	0.475	0.401	0.334	0.475	SUBCLONAL	1	TRUE	1	0.278449354465573	2		568	770	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032092	10032092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201674066	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	42	618	0	ENST00000330684.3:c.731G>A	p.Arg244His	p.R244H	ENST00000330684	NM_001134407.1	244	cGc/cAc	3/13	1	2	FACETS	0.375	0.312	0.445	0.375	0.312	0.445	SUBCLONAL	1	TRUE	1	0.278449354465573	2		618	805	SUCCESS
EED	8726	MSKCC	GRCh37	11	85966331	85966331	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	14	256	0	ENST00000263360.6:c.426+2T>C		p.X142_splice	ENST00000263360	NM_003797.3	142			1	2	FACETS	0.459	0.332	0.613	0.459	0.332	0.613	SUBCLONAL	1	TRUE	1	0.278449354465573	2		256	219	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426730	49426735	+	inframe_deletion	In_Frame_Del	DEL	GCTGCT	GCTGCT	-	rs576788910	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	63	348	0	ENST00000301067.7:c.11753_11758del	p.Gln3918_Gln3919del	p.Q3918_Q3919del	ENST00000301067	NM_003482.3	3918	cAGCAGCta/cta	39/54	1	2	FACETS	0.975	0.845	1	0.975	0.845	1	CLONAL	1	TRUE	1	0.278449354465573	2		348	464	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137452	202137452	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	38	404	0	ENST00000358485.4:c.680A>T	p.Asn227Ile	p.N227I	ENST00000358485	NM_001080125.1	227	aAc/aTc	4/9	1	2	FACETS	0.532	0.439	0.636	0.532	0.439	0.636	SUBCLONAL	1	TRUE	1	0.278449354465573	2		404	513	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245112	41245112	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	53	795	0	ENST00000357654.3:c.2436G>T	p.Lys812Asn	p.K812N	ENST00000357654	NM_007294.3	812	aaG/aaT	10/23	1	2	FACETS	0.432	0.367	0.504	0.432	0.367	0.504	SUBCLONAL	1	TRUE	1	0.278449354465573	2		795	881	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341473	70341473	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1157525906	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	196	781	0	ENST00000374080.3:c.908G>A	p.Arg303Gln	p.R303Q	ENST00000374080		303	cGg/cAg	7/45	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.278449354465573	2		781	978	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543301	65543301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779789251	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	50	503	0	ENST00000358664.4:c.376G>A	p.Ala126Thr	p.A126T	ENST00000358664	NM_002382.4	126	Gcc/Acc	5/5	1	2	FACETS	0.494	0.418	0.578	0.494	0.418	0.578	SUBCLONAL	1	TRUE	1	0.278449354465573	2		503	727	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918181	50918181	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	220	889	1	ENST00000440232.2:c.2498G>A	p.Arg833His	p.R833H	ENST00000440232	NM_002691.3	833	cGc/cAc	20/27	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.278449354465573	2		890	1063	SUCCESS
APC	324	MSKCC	GRCh37	5	112176831	112176831	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371686531	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	55	305	1	ENST00000257430.4:c.5540C>T	p.Thr1847Met	p.T1847M	ENST00000257430	NM_000038.5	1847	aCg/aTg	16/16	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.278449354465573	2		306	374	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433888	78433888	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	40	288	0	ENST00000370768.2:c.212-1G>T		p.X71_splice	ENST00000370768	NM_003902.3	71			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.278449354465573	2		288	206	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451156	70451156	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	97	662	0	ENST00000373644.4:c.5996A>G	p.His1999Arg	p.H1999R	ENST00000373644	NM_030625.2	1999	cAc/cGc	12/12	1	2	FACETS	0.789	0.702	0.881	0.789	0.702	0.881	SUBCLONAL	1	TRUE	1	0.278449354465573	2		662	883	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625411	69625411	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	179	800	0	ENST00000334134.2:c.382A>T	p.Thr128Ser	p.T128S	ENST00000334134	NM_005247.2	128	Acg/Tcg	3/3	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.278449354465573	2		800	1010	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205791	108205791	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	19	336	0	ENST00000278616.4:c.8106A>G	p.Ile2702Met	p.I2702M	ENST00000278616	NM_000051.3	2702	atA/atG	55/63	1	2	FACETS	0.419	0.317	0.538	0.419	0.317	0.538	SUBCLONAL	1	TRUE	1	0.278449354465573	2		336	326	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366501	118366501	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	34	309	0	ENST00000534358.1:c.5450C>G	p.Thr1817Ser	p.T1817S	ENST00000534358	NM_005933.3	1817	aCt/aGt	19/36	1	2	FACETS	0.43	0.35	0.52	0.43	0.35	0.52	SUBCLONAL	1	TRUE	1	0.278449354465573	2		309	568	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149391	119149391	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	33	356	0	ENST00000264033.4:c.1399C>T	p.Leu467Phe	p.L467F	ENST00000264033	NM_005188.3	467	Ctc/Ttc	9/16	1	2	FACETS	0.471	0.383	0.571	0.471	0.383	0.571	SUBCLONAL	1	TRUE	1	0.278449354465573	2		356	503	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125507371	125507371	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	40	361	0	ENST00000428830.2:c.746A>G	p.Asn249Ser	p.N249S	ENST00000428830	NM_001114121.2	249	aAt/aGt	8/14	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.278449354465573	2		361	234	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422273	422273	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	40	503	0	ENST00000399788.2:c.2985A>C	p.Lys995Asn	p.K995N	ENST00000399788	NM_001042603.1	995	aaA/aaC	20/28	1	2	FACETS	0.425	0.352	0.507	0.425	0.352	0.507	SUBCLONAL	1	TRUE	1	0.278449354465573	2		503	676	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418359	49418359	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	33	408	0	ENST00000301067.7:c.16052+2T>C		p.X5351_splice	ENST00000301067	NM_003482.3	5351			1	2	FACETS	0.386	0.313	0.468	0.386	0.313	0.468	SUBCLONAL	1	TRUE	1	0.278449354465573	2		408	614	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518246	103518246	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	56	184	1	ENST00000355739.4:c.2184G>A	p.Trp728Ter	p.W728*	ENST00000355739	NM_000123.3	728	tgG/tgA	9/15	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.278449354465573	2		185	308	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251189	99251189	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	50	647	0	ENST00000268035.6:c.493T>C	p.Ser165Pro	p.S165P	ENST00000268035	NM_000875.3	165	Tcc/Ccc	2/21	1	2	FACETS	0.426	0.36	0.499	0.426	0.36	0.499	SUBCLONAL	1	TRUE	1	0.278449354465573	2		647	843	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343618	343618	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	73	911	0	ENST00000262320.3:c.2056T>C	p.Ser686Pro	p.S686P	ENST00000262320	NM_003502.3	686	Tcc/Ccc	8/11	1	2	FACETS	0.472	0.411	0.537	0.472	0.411	0.537	SUBCLONAL	1	TRUE	1	0.278449354465573	2		911	1112	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56857662	56857662	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	40	529	0	ENST00000308159.5:c.698T>C	p.Val233Ala	p.V233A	ENST00000308159	NM_014669.4	233	gTg/gCg	8/22	1	2	FACETS	0.416	0.344	0.496	0.416	0.344	0.496	SUBCLONAL	1	TRUE	1	0.278449354465573	2		529	691	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819694	81819694	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	62	589	0	ENST00000359376.3:c.100C>A	p.Arg34Ser	p.R34S	ENST00000359376	NM_002661.3	34	Cgc/Agc	2/33	1	2	FACETS	0.511	0.44	0.589	0.511	0.44	0.589	SUBCLONAL	1	TRUE	1	0.278449354465573	2		589	871	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969944	81969944	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	105	481	0	ENST00000359376.3:c.3013T>C	p.Cys1005Arg	p.C1005R	ENST00000359376	NM_002661.3	1005	Tgc/Cgc	27/33	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.278449354465573	2		481	646	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273923	18273923	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	56	615	0	ENST00000222254.8:c.1256C>G	p.Thr419Arg	p.T419R	ENST00000222254	NM_005027.3	419	aCa/aGa	10/16	1	2	FACETS	0.469	0.4	0.544	0.469	0.4	0.544	SUBCLONAL	1	TRUE	1	0.278449354465573	2		615	858	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214870	36214871	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	185	845	0	ENST00000222270.7:c.3296_3297del	p.Gly1099AlafsTer13	p.G1099Afs*13	ENST00000222270	NM_014727.1	1099	gGC/g	8/37	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.278449354465573	2		845	1099	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440078	220440078	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	147	999	0	ENST00000243786.2:c.935del	p.Pro312LeufsTer24	p.P312Lfs*24	ENST00000243786	NM_002191.3	311	Ccc/cc	2/2	1	2	FACETS	0.924	0.842	1	0.924	0.842	1	CLONAL	1	TRUE	1	0.278449354465573	2		999	1143	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026234	36026234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	82	958	5	ENST00000358208.4:c.836G>A	p.Gly279Asp	p.G279D	ENST00000358208		279	gGc/gAc	7/12	1	2	FACETS	0.492	0.432	0.557	0.492	0.432	0.557	SUBCLONAL	1	TRUE	1	0.278449354465573	2		963	1197	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933166	49933166	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs557923113	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	37	617	0	ENST00000296474.3:c.2944T>C	p.Trp982Arg	p.W982R	ENST00000296474	NM_002447.2	982	Tgg/Cgg	12/20	1	2	FACETS	0.423	0.348	0.508	0.423	0.348	0.508	SUBCLONAL	1	TRUE	1	0.278449354465573	2		617	628	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851741	134851741	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	59	577	0	ENST00000398015.3:c.1147C>T	p.Gln383Ter	p.Q383*	ENST00000398015	NM_004441.4	383	Cag/Tag	5/16	1	2	FACETS	0.55	0.472	0.636	0.55	0.472	0.636	SUBCLONAL	1	TRUE	1	0.278449354465573	2		577	770	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215333	142215333	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	128	384	0	ENST00000350721.4:c.5768G>A	p.Cys1923Tyr	p.C1923Y	ENST00000350721	NM_001184.3	1923	tGc/tAc	34/47	1	2	FACETS	0.799	0.727	0.875	1	0.987	1	SUBCLONAL	2	TRUE	1	0.278449354465573	2		384	575	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435853	149435853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs991336822	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	68	704	0	ENST00000286301.3:c.2371G>A	p.Val791Met	p.V791M	ENST00000286301	NM_005211.3	791	Gtg/Atg	18/22	1	2	FACETS	0.5	0.433	0.572	0.5	0.433	0.572	SUBCLONAL	1	TRUE	1	0.278449354465573	2		704	977	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503906	149503906	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1472863128	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	138	566	0	ENST00000261799.4:c.1930G>A	p.Glu644Lys	p.E644K	ENST00000261799	NM_002609.3	644	Gag/Aag	14/23	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.278449354465573	2		566	711	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910642	29910642	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	77	1143	0	ENST00000376809.5:c.182A>G	p.Asp61Gly	p.D61G	ENST00000376809	NM_002116.7	61	gAc/gGc	2/8	1	2	FACETS	0.448	0.391	0.509	0.448	0.391	0.509	SUBCLONAL	1	TRUE	1	0.278449354465573	2		1143	1235	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157256712	157256712	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	17	176	0	ENST00000346085.5:c.2037+2T>C		p.X679_splice	ENST00000346085	NM_020732.3	679			1	2	FACETS	0.427	0.318	0.556	0.427	0.318	0.556	SUBCLONAL	1	TRUE	1	0.278449354465573	2		176	286	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976771	2976771	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	59	752	0	ENST00000396946.4:c.1241A>G	p.Asn414Ser	p.N414S	ENST00000396946	NM_032415.4	414	aAc/aGc	9/25	1	2	FACETS	0.403	0.345	0.467	0.403	0.345	0.467	SUBCLONAL	1	TRUE	1	0.278449354465573	2		752	1051	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738252	145738252	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	57	908	0	ENST00000428558.2:c.2733G>T	p.Gln911His	p.Q911H	ENST00000428558	NM_004260.3	911	caG/caT	16/22	1	2	FACETS	0.397	0.339	0.461	0.397	0.339	0.461	SUBCLONAL	1	TRUE	1	0.278449354465573	2		908	1031	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185574	27185574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774742672	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	79	592	0	ENST00000380036.4:c.1274G>A	p.Ser425Asn	p.S425N	ENST00000380036	NM_000459.3	425	aGt/aAt	9/23	1	2	FACETS	0.661	0.581	0.748	0.661	0.581	0.748	SUBCLONAL	1	TRUE	1	0.278449354465573	2		592	858	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93626901	93626901	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	29	388	0	ENST00000375746.1:c.748G>T	p.Gly250Cys	p.G250C	ENST00000375746	NM_001174167.1	250	Ggt/Tgt	5/14	1	2	FACETS	0.373	0.298	0.458	0.373	0.298	0.458	SUBCLONAL	1	TRUE	1	0.278449354465573	2		388	559	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760246	133760246	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	111	537	0	ENST00000318560.5:c.2569G>A	p.Ala857Thr	p.A857T	ENST00000318560	NM_005157.4	857	Gca/Aca	11/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.278449354465573	2		537	639	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360634	70360634	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	52	462	0	ENST00000374080.3:c.6194A>C	p.Gln2065Pro	p.Q2065P	ENST00000374080		2065	cAg/cCg	42/45	1	2	FACETS	0.618	0.526	0.72	0.618	0.526	0.72	SUBCLONAL	1	TRUE	1	0.278449354465573	2		462	604	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849190	76849190	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	18	341	0	ENST00000373344.5:c.6086T>G	p.Met2029Arg	p.M2029R	ENST00000373344	NM_000489.3	2029	aTg/aGg	26/35	1	2	FACETS	0.454	0.341	0.586	0.454	0.341	0.586	SUBCLONAL	1	TRUE	1	0.278449354465573	2		341	285	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435885	56435887	+	frameshift_variant	Frame_Shift_Del	DEL	GTC	GTC	TT	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	116	469	0	ENST00000407977.2:c.1250_1252delinsAA	p.Gly417GlufsTer2	p.G417Efs*2	ENST00000407977		417	gGACtg/gAAtg	9/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.278449354465573	2		469	560	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106969	27106971	+	frameshift_variant	Frame_Shift_Del	DEL	AAC	AAC	G	novel	NA	P-0055871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	119	492	0	ENST00000324856.7:c.6580_6582delinsG	p.Asn2194AlafsTer30	p.N2194Afs*30	ENST00000324856	NM_006015.4	2194	AAC/G	20/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.278449354465573	2		492	655	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073509	8073509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	39	416	0	ENST00000377482.5:c.1150G>T	p.Glu384Ter	p.E384*	ENST00000377482	NM_018948.3	384	Gaa/Taa	4/4	0.257102786602173	1	FACETS	0.203	0.167	0.242	0.203	0.167	0.242	INDETERMINATE	1	TRUE	0	0.504979566690881	1		416	570	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0055872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	80	327	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	0.257102786602173	1	FACETS	0.535	0.472	0.601	0.535	0.472	0.601	INDETERMINATE	1	TRUE	0	0.504979566690881	1		327	443	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002816	69002816	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	35	207	0	ENST00000288368.4:c.2116A>G	p.Thr706Ala	p.T706A	ENST00000288368	NM_024870.2	706	Act/Gct	20/40	0.298181875613307	5	FACETS	0.59	0.484	0.709	0.197	0.161	0.237	INDETERMINATE	1	TRUE	2	0.504979566690881	5		207	413	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612908	228612908	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	52	553	1	ENST00000366696.1:c.119A>T	p.His40Leu	p.H40L	ENST00000366696	NM_003493.2	40	cAc/cTc	1/1	0.496632219963929	3	FACETS	0.284	0.24	0.331	0.142	0.12	0.166	SUBCLONAL	1	TRUE	1	0.496632219963929	3		554	922	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs587781702	NA	P-0055877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	11	1116	0	ENST00000269305.4:c.920-1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		1116	513	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0055878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	191	407	1	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	1	2	FACETS	0.892	0.828	0.957	0.892	0.828	0.957	CLONAL	1	TRUE	1	0.642323594901647	2		408	667	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602619	10602619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	325	737	3	ENST00000171111.5:c.959G>A	p.Arg320Gln	p.R320Q	ENST00000171111	NM_203500.1	320	cGg/cAg	3/6	0.642323594901647	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.642323594901647	1		740	598	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221293	1221293	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	298	709	0	ENST00000326873.7:c.816C>A	p.Tyr272Ter	p.Y272*	ENST00000326873	NM_000455.4	272	taC/taA	6/10	0.642323594901647	1	FACETS	0.989	0.939	1	0.989	0.939	1	CLONAL	1	TRUE	0	0.642323594901647	1		709	637	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023228	27023261	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCTGAACAATAACCTCACGGAGCCGCCCGGCG	GCCCTGAACAATAACCTCACGGAGCCGCCCGGCG	-	novel	NA	P-0055878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	58	189	0	ENST00000324856.7:c.336_369del	p.Leu113AlafsTer108	p.L113Afs*108	ENST00000324856	NM_006015.4	112	GCCCTGAACAATAACCTCACGGAGCCGCCCGGCGgc/gc	1/20	0.642323594901647	1	FACETS	0.771	0.677	0.868	0.771	0.677	0.868	SUBCLONAL	1	TRUE	0	0.642323594901647	1		189	159	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225915	133225915	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	252	681	0	ENST00000320574.5:c.3982G>T	p.Asp1328Tyr	p.D1328Y	ENST00000320574	NM_006231.2	1328	Gac/Tac	31/49	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.642323594901647	2		681	754	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29196018	29196018	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	446	653	0	ENST00000240100.2:c.580G>T	p.Gly194Trp	p.G194W	ENST00000240100	NM_001394.6	194	Ggg/Tgg	3/4	0.599548319893759	2	FACETS	0.992	0.958	1	0.992	0.958	1	CLONAL	2	TRUE	0	0.642323594901647	2		653	700	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039327	47039345	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGGGCCCTGGCACCCTA	TGGGGGCCCTGGCACCCTA	-	novel	NA	P-0055878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	282	372	0	ENST00000377604.3:c.950_968del	p.Leu317ProfsTer12	p.L317Pfs*12	ENST00000377604	NM_001204468.1	317	cTGGGGGCCCTGGCACCCTAc/cc	10/24	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.642323594901647	1		372	448	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	72	374	0				ENST00000310581	NM_198253.2	-/1132			0.396782705340017	1	FACETS	0.884	0.779	0.996	0.884	0.779	0.996	CLONAL	1	TRUE	0	0.396782705340017	1		374	329	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	285	550	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.396782705340017	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.396782705340017	3		550	782	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	208	684	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.396782705340017	2		685	893	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857679	9857679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886042648	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	167	568	0	ENST00000330684.3:c.3722G>A	p.Arg1241Gln	p.R1241Q	ENST00000330684	NM_001134407.1	1241	cGg/cAg	13/13	0.396782705340017	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.396782705340017	1		568	486	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939048	36939048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	121	737	0	ENST00000361632.4:c.661C>T	p.Pro221Ser	p.P221S	ENST00000361632		221	Ccc/Tcc	5/16	0.396782705340017	3	FACETS	0.799	0.721	0.881	0.399	0.36	0.441	SUBCLONAL	1	TRUE	1	0.396782705340017	3		737	915	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13949269	13949269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	46	240	0	ENST00000405192.2:c.859G>A	p.Glu287Lys	p.E287K	ENST00000405192	NM_001163147.1	287	Gaa/Aaa	9/12	0.10595418830686	3	FACETS	0.85	0.719	0.993	0.425	0.359	0.497	INDETERMINATE	1	TRUE	1	0.396782705340017	3		240	327	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134995	2134995	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767449740	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	355	829	1	ENST00000219476.3:c.4537G>A	p.Glu1513Lys	p.E1513K	ENST00000219476	NM_000548.3	1513	Gag/Aag	35/42	0.396782705340017	1	FACETS	0.777	0.739	0.816	1	0.995	1	SUBCLONAL	2	TRUE	0	0.396782705340017	1		830	923	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743942	40743942	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868489194	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	114	496	0	ENST00000373198.4:c.3053G>A	p.Arg1018Gln	p.R1018Q	ENST00000373198	NM_133170.3	1018	cGa/cAa	23/32	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.396782705340017	2		496	570	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955074	93955074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	85	359	0	ENST00000369303.4:c.2824G>A	p.Asp942Asn	p.D942N	ENST00000369303	NM_004440.3	942	Gat/Aat	16/17	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.396782705340017	2		359	392	SUCCESS
APC	324	MSKCC	GRCh37	5	112178781	112178781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141010008	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	97	477	0	ENST00000257430.4:c.7490C>T	p.Ser2497Leu	p.S2497L	ENST00000257430	NM_000038.5	2497	tCg/tTg	16/16	0.396782705340017	1	FACETS	0.82	0.734	0.91	0.82	0.734	0.91	CLONAL	1	TRUE	0	0.396782705340017	1		477	478	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68999972	68999972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	119	638	0	ENST00000288368.4:c.2041C>T	p.Pro681Ser	p.P681S	ENST00000288368	NM_024870.2	681	Cca/Tca	19/40	1	2	FACETS	0.926	0.837	1	0.926	0.837	1	CLONAL	1	TRUE	1	0.396782705340017	2		638	648	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449462	31449462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	143	467	1	ENST00000344624.3:c.2747C>T	p.Ser916Leu	p.S916L	ENST00000344624		916	tCa/tTa	19/33	0.396782705340017	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.396782705340017	1		468	513	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110608	4110608	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749389113	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	186	834	0	ENST00000262948.5:c.349C>T	p.Arg117Cys	p.R117C	ENST00000262948	NM_030662.3	117	Cgc/Tgc	3/11	1	2	FACETS	0.917	0.847	0.991	0.917	0.847	0.991	CLONAL	1	TRUE	1	0.396782705340017	2		834	1022	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644451	18644451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	93	413	0	ENST00000266497.5:c.2629C>T	p.Pro877Ser	p.P877S	ENST00000266497		877	Cct/Tct	18/31	1	2	FACETS	0.914	0.815	1	0.914	0.815	1	CLONAL	1	TRUE	1	0.396782705340017	2		413	513	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980488	70980488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267601982	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	149	765	2	ENST00000276594.2:c.889G>A	p.Gly297Arg	p.G297R	ENST00000276594	NM_024504.3	297	Gga/Aga	4/8	1	2	FACETS	0.808	0.737	0.881	0.808	0.737	0.881	CLONAL	1	TRUE	1	0.396782705340017	2		767	930	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784475	9784475	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	206	431	0	ENST00000377346.4:c.2860G>A	p.Glu954Lys	p.E954K	ENST00000377346	NM_005026.3	954	Gaa/Aaa	22/24	0.396782705340017	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	1	0.396782705340017	3		431	600	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935367	36935367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	114	876	2	ENST00000361632.4:c.1360C>T	p.Pro454Ser	p.P454S	ENST00000361632		454	Cca/Tca	10/16	0.396782705340017	3	FACETS	0.651	0.585	0.722	0.326	0.292	0.361	SUBCLONAL	1	TRUE	1	0.396782705340017	3		878	1057	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805212	43805212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	114	704	0	ENST00000372470.3:c.662G>A	p.Gly221Glu	p.G221E	ENST00000372470	NM_005373.2	221	gGa/gAa	4/12	0.396782705340017	3	FACETS	0.806	0.725	0.892	0.403	0.362	0.446	CLONAL	1	TRUE	1	0.396782705340017	3		704	854	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828179	243828179	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	73	374	0	ENST00000263826.5:c.179A>T	p.Gln60Leu	p.Q60L	ENST00000263826	NM_005465.4	60	cAg/cTg	3/13	1	2	FACETS	0.807	0.708	0.913	0.807	0.708	0.913	CLONAL	1	TRUE	1	0.396782705340017	2		374	456	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658298	18658298	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	79	500	0	ENST00000266497.5:c.3103C>T	p.His1035Tyr	p.H1035Y	ENST00000266497		1035	Cac/Tac	22/31	1	2	FACETS	0.899	0.794	1	0.899	0.794	1	CLONAL	1	TRUE	1	0.396782705340017	2		500	443	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608255	28608255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	126	554	0	ENST00000241453.7:c.1801C>T	p.Leu601Phe	p.L601F	ENST00000241453	NM_004119.2	601	Ctc/Ttc	14/24	0.396782705340017	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.396782705340017	1		554	480	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239722	41239722	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	202	778	0	ENST00000379561.5:c.628A>G	p.Lys210Glu	p.K210E	ENST00000379561	NM_002015.3	210	Aag/Gag	1/3	0.396782705340017	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.396782705340017	1		778	806	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714132	43714132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202077092	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	146	901	0	ENST00000382044.4:c.4021C>T	p.Pro1341Ser	p.P1341S	ENST00000382044	NM_001141980.1	1341	Cca/Tca	19/28	1	2	FACETS	0.704	0.642	0.77	0.704	0.642	0.77	SUBCLONAL	1	TRUE	1	0.396782705340017	2		901	1045	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347659	89347660	+	missense_variant	Missense_Mutation	DNP	AA	AA	CC	novel	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	203	875	2	ENST00000301030.4:c.5290_5291delinsGG	p.Phe1764Gly	p.F1764G	ENST00000301030	NM_001256183.1	1764	TTc/GGc	9/13	0.396782705340017	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.396782705340017	1		877	732	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665062	29665062	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	114	546	0	ENST00000356175.3:c.6661C>T	p.Pro2221Ser	p.P2221S	ENST00000356175	NM_000267.3	2221	Cca/Tca	44/57	1	2	FACETS	0.933	0.842	1	0.933	0.842	1	CLONAL	1	TRUE	1	0.396782705340017	2		546	616	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866666	78866666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	74	524	0	ENST00000306801.3:c.2239G>A	p.Glu747Lys	p.E747K	ENST00000306801	NM_020761.2	747	Gaa/Aaa	19/34	1	2	FACETS	0.704	0.617	0.797	0.704	0.617	0.797	SUBCLONAL	1	TRUE	1	0.396782705340017	2		524	530	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210761	36210761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	167	970	0	ENST00000222270.7:c.512C>T	p.Pro171Leu	p.P171L	ENST00000222270	NM_014727.1	171	cCt/cTt	3/37	1	2	FACETS	0.785	0.721	0.853	0.785	0.721	0.853	SUBCLONAL	1	TRUE	1	0.396782705340017	2		970	1072	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222917	36222917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	244	1028	0	ENST00000222270.7:c.5546C>T	p.Ser1849Leu	p.S1849L	ENST00000222270	NM_014727.1	1849	tCa/tTa	27/37	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.396782705340017	2		1028	1155	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523256	9523256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	146	600	1	ENST00000353224.5:c.1981C>T	p.Pro661Ser	p.P661S	ENST00000353224	NM_177990.2	661	Cca/Tca	9/10	1	2	FACETS	0.92	0.84	1	0.92	0.84	1	CLONAL	1	TRUE	1	0.396782705340017	2		601	800	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655376	45655376	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	175	979	0	ENST00000407780.3:c.476C>A	p.Thr159Lys	p.T159K	ENST00000407780	NM_001283052.1	159	aCa/aAa	4/7	1	2	FACETS	0.808	0.743	0.876	0.808	0.743	0.876	CLONAL	1	TRUE	1	0.396782705340017	2		979	1092	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259034	89259034	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	57	271	0	ENST00000336596.2:c.178G>A	p.Glu60Lys	p.E60K	ENST00000336596	NM_005233.5	60	Gaa/Aaa	3/17	1	2	FACETS	0.909	0.785	1	0.909	0.785	1	CLONAL	1	TRUE	1	0.396782705340017	2		271	316	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169953088	169953088	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	129	505	0	ENST00000295797.4:c.172T>G	p.Cys58Gly	p.C58G	ENST00000295797	NM_002740.5	58	Tgt/Ggt	2/18	1	2	FACETS	0.921	0.836	1	0.921	0.836	1	CLONAL	1	TRUE	1	0.396782705340017	2		505	706	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957738	1957738	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	174	753	0	ENST00000382891.5:c.2704A>G	p.Lys902Glu	p.K902E	ENST00000382891	NM_133335.3	902	Aaa/Gaa	15/22	0.396782705340017	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.396782705340017	1		753	700	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524567	176524568	+	missense_variant	Missense_Mutation	DNP	TC	TC	GT	novel	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	206	1052	0	ENST00000292408.4:c.2299_2300delinsGT	p.Ser767Val	p.S767V	ENST00000292408	NM_213647.1	767	TCt/GTt	18/18	1	2	FACETS	0.936	0.868	1	0.936	0.868	1	CLONAL	1	TRUE	1	0.396782705340017	2		1052	1109	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672411	30672411	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	214	881	0	ENST00000376406.3:c.4549G>A	p.Gly1517Arg	p.G1517R	ENST00000376406	NM_014641.2	1517	Gga/Aga	10/15	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.396782705340017	2		881	1032	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687382	117687382	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1248261976	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	109	358	0	ENST00000368508.3:c.2669A>G	p.Tyr890Cys	p.Y890C	ENST00000368508	NM_002944.2	890	tAc/tGc	18/43	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.396782705340017	2		358	479	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117717405	117717405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	114	366	0	ENST00000368508.3:c.802G>A	p.Glu268Lys	p.E268K	ENST00000368508	NM_002944.2	268	Gaa/Aaa	8/43	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.396782705340017	2		366	505	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157524979	157525002	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTGTTCTTCCCCATCTTCAGTTA	CTTGTTCTTCCCCATCTTCAGTTA	-	novel	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	94	315	0	ENST00000346085.5:c.4895-19_4899del		p.X1632_splice	ENST00000346085	NM_020732.3	1632		19/20	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.396782705340017	2		315	466	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528899	157528900	+	missense_variant	Missense_Mutation	DNP	GG	GG	AC	novel	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	147	636	1	ENST00000346085.5:c.6624_6625delinsAC	p.Asp2209His	p.D2209H	ENST00000346085	NM_020732.3	2208	gtGGac/gtACac	20/20	1	2	FACETS	0.929	0.848	1	0.929	0.848	1	CLONAL	1	TRUE	1	0.396782705340017	2		637	798	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434422	140434422	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	121	513	0	ENST00000288602.6:c.2276G>T	p.Gly759Val	p.G759V	ENST00000288602	NM_004333.4	759	gGa/gTa	18/18	0.10595418830686	3	FACETS	0.966	0.873	1	0.483	0.436	0.532	INDETERMINATE	1	TRUE	1	0.396782705340017	3		513	757	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835909	151835909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	110	444	0	ENST00000262189.6:c.14615C>T	p.Ser4872Phe	p.S4872F	ENST00000262189	NM_170606.2	4872	tCc/tTc	58/59	0.10595418830686	3	FACETS	1	0.953	1	0.55	0.495	0.608	INDETERMINATE	1	TRUE	1	0.396782705340017	3		444	604	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518019	8518019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	103	495	0	ENST00000356435.5:c.1372G>A	p.Asp458Asn	p.D458N	ENST00000356435		458	Gat/Aat	10/35	0.396782705340017	1	FACETS	0.977	0.88	1	0.977	0.88	1	CLONAL	1	TRUE	0	0.396782705340017	1		495	426	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412305	139412305	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	225	1032	0	ENST00000277541.6:c.1340C>T	p.Pro447Leu	p.P447L	ENST00000277541	NM_017617.3	447	cCc/cTc	8/34	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.396782705340017	2		1032	984	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0055882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	698	899	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.573374972034785	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.573374972034785	2		899	1021	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911177	29911177	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80300804	NA	P-0055882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	118	702	0	ENST00000376809.5:c.476C>T	p.Ala159Val	p.A159V	ENST00000376809	NM_002116.7	159	gCg/gTg	3/8	0.573374972034785	3	FACETS	0.474	0.426	0.525	0.237	0.213	0.263	SUBCLONAL	1	TRUE	1	0.573374972034785	3		702	1117	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0055883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	49	383	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.86	0.73	1	0.86	0.73	1	CLONAL	1	TRUE	1	0.28	2		383	407	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0055883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	74	430	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.28	2		430	521	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0055883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	80	322	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	0.3	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.28	1		322	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0055883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	104	625	0	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	1	2	FACETS	0.998	0.894	1	0.998	0.894	1	CLONAL	1	TRUE	1	0.28	2		625	744	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651631	48651631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	124	681	0	ENST00000376670.3:c.797C>T	p.Thr266Met	p.T266M	ENST00000376670	NM_002049.3	266	aCg/aTg	5/6	1	2	FACETS	0.946	0.855	1	0.946	0.855	1	CLONAL	1	TRUE	1	0.28	2		681	936	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857275	9857275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426934537	NA	P-0055883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	80	572	0	ENST00000330684.3:c.4126C>T	p.Arg1376Cys	p.R1376C	ENST00000330684	NM_001134407.1	1376	Cgc/Tgc	13/13	1	2	FACETS	0.804	0.707	0.907	0.804	0.707	0.907	CLONAL	1	TRUE	1	0.28	2		572	711	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	163	374	0				ENST00000310581	NM_198253.2	-/1132			0.368564674886039	1	FACETS	0.647	0.601	0.693	0.647	0.601	0.693	INDETERMINATE	1	TRUE	0	0.792443939114455	1		374	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0055884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	721	710	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.78322617775586	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.792443939114455	2		711	890	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273534	5273534	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1397380294	NA	P-0055884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	398	741	0	ENST00000357368.4:c.298C>T	p.Arg100Trp	p.R100W	ENST00000357368	NM_002850.3	100	Cgg/Tgg	4/38	1	2	FACETS	0.993	0.947	1	0.993	0.947	1	CLONAL	1	TRUE	1	0.792443939114455	2		741	1012	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1485	47	670	1	ENST00000269571.5:c.829G>T	p.Asp277Tyr	p.D277Y	ENST00000269571		277	Gac/Tac	7/27	0.250490438576051	4	FACETS	0.139	0.116	0.164	0.069	0.058	0.082	INDETERMINATE	1	TRUE	2	0.792443939114455	4		671	1532	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984448	201984449	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	757	612	0	ENST00000359651.3:c.1114dup	p.Ter372LeufsTer99	p.*372Lfs*99	ENST00000359651		371	-/T	8/8	0.663802112477877	3	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.792443939114455	3		612	1148	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021535	31021535	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs757832294	NA	P-0055884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	524	612	0	ENST00000375687.4:c.1534C>T	p.Gln512Ter	p.Q512*	ENST00000375687	NM_015338.5	512	Cag/Tag	12/13	NA	2	FACETS	0.784	0.759	0.81			1	INDETERMINATE	2	TRUE	NA	0.792443939114455	2		612	843	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849299	89849299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374490484	NA	P-0055884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	279	536	1	ENST00000389301.3:c.1594G>A	p.Glu532Lys	p.E532K	ENST00000389301	NM_000135.2	532	Gag/Aag	17/43	1	2	FACETS	0.948	0.895	1	0.948	0.895	1	CLONAL	1	TRUE	1	0.792443939114455	2		537	743	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100566	8100566	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	253	859	0	ENST00000346208.3:c.540G>C	p.Glu180Asp	p.E180D	ENST00000346208		180	gaG/gaC	3/6	0.493972669397713	1	FACETS	0.41	0.384	0.436	0.41	0.384	0.436	SUBCLONAL	1	TRUE	0	0.792443939114455	1		859	941	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927054	131927054	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770012364	NA	P-0055884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	169	281	0	ENST00000265335.6:c.1591C>T	p.His531Tyr	p.H531Y	ENST00000265335		531	Cat/Tat	10/25	0.663802112477877	3	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.792443939114455	3		281	454	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678039	117678039	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	241	421	0	ENST00000368508.3:c.3894G>C	p.Gln1298His	p.Q1298H	ENST00000368508	NM_002944.2	1298	caG/caC	25/43	0.367557520635601	1	FACETS	0.722	0.681	0.762	0.722	0.681	0.762	INDETERMINATE	1	TRUE	0	0.792443939114455	1		421	509	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133710840	133710840	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	294	428	0	ENST00000318560.5:c.7G>C	p.Glu3Gln	p.E3Q	ENST00000318560	NM_005157.4	3	Gag/Cag	1/11	0.792443939114455	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.792443939114455	1		428	388	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929074	44929074	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0055884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	318	266	0	ENST00000377967.4:c.2174T>A	p.Leu725Ter	p.L725*	ENST00000377967	NM_021140.2	725	tTg/tAg	17/29	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.792443939114455	1		266	396	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226573235	226573248	+	frameshift_variant	Frame_Shift_Del	DEL	TGTCTGTGTCTTGA	TGTCTGTGTCTTGA	C	novel	NA	P-0055884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	64	684	0	ENST00000366794.5:c.968_981delinsG	p.Val323GlyfsTer8	p.V323Gfs*8	ENST00000366794	NM_001618.3	323	gTCAAGACACAGACA/gG	7/23	0.368564674886039	1	FACETS	0.102	0.088	0.118	0.102	0.088	0.118	INDETERMINATE	1	TRUE	0	0.792443939114455	1		684	952	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0055885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	57	215	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.927	0.795	1	0.927	0.795	1	CLONAL	1	TRUE	1	0.22827441322852	2		215	539	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0055885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	120	626	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.22827441322852	2		626	1003	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575080	48575080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	29	300	0	ENST00000342988.3:c.274C>T	p.His92Tyr	p.H92Y	ENST00000342988	NM_005359.5	92	Cat/Tat	3/12	0.22827441322852	1	FACETS	0.514	0.412	0.63	0.514	0.412	0.63	SUBCLONAL	1	TRUE	0	0.22827441322852	1		300	438	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880980	134880980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771555643	NA	P-0055885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	84	506	0	ENST00000398015.3:c.1543G>A	p.Gly515Ser	p.G515S	ENST00000398015	NM_004441.4	515	Ggc/Agc	7/16	1	2	FACETS	0.814	0.718	0.918	0.814	0.718	0.918	CLONAL	1	TRUE	1	0.22827441322852	2		506	904	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0055900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	178	490	1	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	0.185704718870391	5	FACETS	1	0.957	1	1	0.957	1	CLONAL	3	FALSE	2	0.251452260900792	5		491	621	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100327	27100327	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	608	489	0	ENST00000324856.7:c.4040del	p.Gly1347AlafsTer134	p.G1347Afs*134	ENST00000324856	NM_006015.4	1347	Ggc/gc	17/20	0.185704718870391	5	FACETS	0.962	0.933	0.991	1	0.998	1	CLONAL	7	FALSE	2	0.251452260900792	5		489	989	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420399	49420399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	207	520	0	ENST00000301067.7:c.15350G>A	p.Cys5117Tyr	p.C5117Y	ENST00000301067	NM_003482.3	5117	tGt/tAt	48/54	0.10613205197027	4	FACETS	0.966	0.905	1	1	0.994	1	INDETERMINATE	4	FALSE	2	0.251452260900792	4		520	533	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881323	37881323	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	276	542	0	ENST00000269571.5:c.2515G>A	p.Val839Met	p.V839M	ENST00000269571		839	Gtg/Atg	21/27	1	2	FACETS	1	0.984	1	1	0.996	1	CLONAL	3	FALSE	1	0.251452260900792	2		542	662	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696432	47696432	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519968	NA	P-0055904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	79	379	0	ENST00000347630.2:c.391T>G	p.Trp131Gly	p.W131G	ENST00000347630	NM_001007230.1	131	Tgg/Ggg	6/11	1	2	FACETS	0.872	0.769	0.981	0.872	0.769	0.981	CLONAL	1	TRUE	1	0.3744133899509	2		379	484	SUCCESS
APC	324	MSKCC	GRCh37	5	112177374	112177374	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	32	209	0	ENST00000257430.4:c.6083G>C	p.Ser2028Thr	p.S2028T	ENST00000257430	NM_000038.5	2028	aGt/aCt	16/16	NA	2	FACETS	0.788	0.644	0.947			1	INDETERMINATE	1	TRUE	NA	0.3744133899509	2		209	217	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940099	31940099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759072198	NA	P-0055904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	171	854	1	ENST00000375333.2:c.241G>A	p.Val81Ile	p.V81I	ENST00000375333	NM_032454.1	81	Gta/Ata	2/8	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.3744133899509	2		855	910	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0055906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	333	30	0				ENST00000310581	NM_198253.2	-/1132			0.817413652263623	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.817413652263623	1		30	413	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0055906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	546	894	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.785286989344097	2	FACETS	0.919	0.895	0.942	0.919	0.895	0.942	CLONAL	2	TRUE	0	0.817413652263623	2		894	727	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21652489	21652489	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	98	517	0	ENST00000421138.2:c.16G>T	p.Ala6Ser	p.A6S	ENST00000421138		6	Gct/Tct	3/16	0.405913287085962	2	FACETS	0.409	0.366	0.455	0.205	0.183	0.228	INDETERMINATE	1	TRUE	0	0.817413652263623	2		517	586	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061715	38061715	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754657304	NA	P-0055906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	113	471	0	ENST00000250448.2:c.274G>A	p.Ala92Thr	p.A92T	ENST00000250448	NM_004496.3	92	Gcc/Acc	2/2	0.53850178662908	1	FACETS	0.454	0.413	0.497	0.454	0.413	0.497	SUBCLONAL	1	TRUE	0	0.817413652263623	1		471	360	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621149	1621149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376498623	NA	P-0055906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	242	1089	1	ENST00000344749.5:c.997G>A	p.Gly333Ser	p.G333S	ENST00000344749	NM_001136139.2	333	Ggc/Agc	12/19	0.410516084445867	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.817413652263623	0		1090	667	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413010	49413010	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519952	NA	P-0055906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	297	506	1	ENST00000418115.1:c.13C>T	p.Arg5Trp	p.R5W	ENST00000418115	NM_001664.2	5	Cgg/Tgg	2/5	0.817413652263623	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.817413652263623	1		507	400	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341913	8341913	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	216	340	0	ENST00000356435.5:c.4727A>G	p.Glu1576Gly	p.E1576G	ENST00000356435		1576	gAa/gGa	29/35	NA	2	FACETS	0.982	0.946	1			1	INDETERMINATE	2	TRUE	NA	0.817413652263623	2		340	269	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391785	139392344	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACAGGGTGGGCGTGCCCCCCAGCGGGGCTCCGTGCAGCTGCGGGCTGCGCACCAGGTTGTACTCGTCCAGCAGCCTCACGATGTCGTGATGCATGCGCTCCTGTGCGATGTCGCGCGGCAGGCGGTCCATATGATCCGTGATGTCCCGGTTGGCAAAGTGGTCCAGCAGCACCTTGGCGGTCTCGTAGCTGCCCTCCCGGGCGGCCAGAAACAGGGGTGTCTCCTCCTGGGGGATGAGGGCGGGGGCCGGTGAGGGGGGCCAGGCCAGGCGTGGGGACCCTCCCCAAGGTTCCATCACCAGAGGAAGCAGCAGTACAACCTCCTCCGCGGGGTGGGGGCAGGCAGGCTGCTCCTCAGGACCCCACCCCAGCGTCCTGCAACCACCTAGCCTGACTCTTGTTAAATGTTAAGGCTTTGATACATCTTCTGAAACCCACCCAGAGAGGGGATCTGTGCAGTCCTCTACCCTAGATCAGCGGGGCTCCACCTCTATGGGGGGGTCACAGACCCCACTGAAAATCTAACCAACTGCAGGCCCTCTTCCCTGCCCCCAATAAGGC	ACAGGGTGGGCGTGCCCCCCAGCGGGGCTCCGTGCAGCTGCGGGCTGCGCACCAGGTTGTACTCGTCCAGCAGCCTCACGATGTCGTGATGCATGCGCTCCTGTGCGATGTCGCGCGGCAGGCGGTCCATATGATCCGTGATGTCCCGGTTGGCAAAGTGGTCCAGCAGCACCTTGGCGGTCTCGTAGCTGCCCTCCCGGGCGGCCAGAAACAGGGGTGTCTCCTCCTGGGGGATGAGGGCGGGGGCCGGTGAGGGGGGCCAGGCCAGGCGTGGGGACCCTCCCCAAGGTTCCATCACCAGAGGAAGCAGCAGTACAACCTCCTCCGCGGGGTGGGGGCAGGCAGGCTGCTCCTCAGGACCCCACCCCAGCGTCCTGCAACCACCTAGCCTGACTCTTGTTAAATGTTAAGGCTTTGATACATCTTCTGAAACCCACCCAGAGAGGGGATCTGTGCAGTCCTCTACCCTAGATCAGCGGGGCTCCACCTCTATGGGGGGGTCACAGACCCCACTGAAAATCTAACCAACTGCAGGCCCTCTTCCCTGCCCCCAATAAGGC	-	novel	NA	P-0055906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	380	883	0	ENST00000277541.6:c.6181-334_6406del		p.X2061_splice	ENST00000277541	NM_017617.3	2061		34/34	0.80118543209076	2	FACETS	0.8	0.771	0.829	0.8	0.771	0.829	SUBCLONAL	2	TRUE	0	0.817413652263623	2		883	581	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204992	128204992	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	325	797	0	ENST00000341105.2:c.449G>A	p.Gly150Glu	p.G150E	ENST00000341105	NM_032638.4	150	gGa/gAa	3/6	1	2	FACETS	1	0.987	1	1	0.997	1	CLONAL	3	TRUE	1	0.254660258314791	2		797	765	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533721	63533721	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	55	649	0	ENST00000307078.5:c.1433A>T	p.His478Leu	p.H478L	ENST00000307078	NM_004655.3	478	cAc/cTc	6/11	0.254660258314791	5	FACETS	0.797	0.68	0.925	0.199	0.17	0.232	CLONAL	1	TRUE	1	0.254660258314791	5		649	749	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751177	57751177	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1320708077	NA	P-0055907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	53	254	0	ENST00000274289.3:c.1690C>A	p.Gln564Lys	p.Q564K	ENST00000274289	NM_006622.3	564	Caa/Aaa	12/14	0.394878375604527	3	FACETS	0.982	0.846	1	0.982	0.846	1	CLONAL	2	TRUE	1	0.254660258314791	3		254	239	SUCCESS
ALK	238	MSKCC	GRCh37	2	29450509	29450509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774004991	NA	P-0055908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	195	902	0	ENST00000389048.3:c.2845G>A	p.Glu949Lys	p.E949K	ENST00000389048	NM_004304.4	949	Gaa/Aaa	17/29	0.677853379418252	3	FACETS	0.812	0.752	0.874	0.406	0.376	0.437	CLONAL	1	TRUE	1	0.759256054137176	3		902	873	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855601	45855601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144277365	NA	P-0055908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	132	734	0	ENST00000391945.4:c.2056C>T	p.Arg686Cys	p.R686C	ENST00000391945	NM_000400.3	686	Cgt/Tgt	22/23	0.676283055526925	3	FACETS	0.765	0.696	0.837	0.383	0.348	0.419	SUBCLONAL	1	TRUE	1	0.759256054137176	3		734	627	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712692	43712692	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	195	751	0	ENST00000382044.4:c.4492G>C	p.Ala1498Pro	p.A1498P	ENST00000382044	NM_001141980.1	1498	Gcc/Ccc	21/28	0.626087708869279	2	FACETS	0.804	0.748	0.862	0.402	0.374	0.431	CLONAL	1	TRUE	0	0.759256054137176	2		751	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579480	7579481	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0055908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	391	750	0	ENST00000269305.4:c.206dup	p.Ala70CysfsTer79	p.A70Cfs*79	ENST00000269305	NM_001126112.2	69	gct/gcCt	4/11	0.626087708869279	2	FACETS	0.831	0.8	0.861	0.831	0.8	0.861	CLONAL	2	TRUE	0	0.759256054137176	2		750	620	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627787	37627787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	386	674	0	ENST00000447079.4:c.1702C>A	p.Pro568Thr	p.P568T	ENST00000447079	NM_015083.1	568	Cct/Act	2/14	0.626087708869279	2	FACETS	0.872	0.841	0.903	0.872	0.841	0.903	CLONAL	2	TRUE	0	0.759256054137176	2		674	583	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560875	9560875	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	194	404	0	ENST00000353224.5:c.907G>T	p.Ala303Ser	p.A303S	ENST00000353224	NM_177990.2	303	Gca/Tca	4/10	0.164796575830278	6	FACETS	1	0.98	1			1	INDETERMINATE	2	TRUE	NA	0.759256054137176	6		404	565	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120612007	120612007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1234964366	NA	P-0055908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	19	41	0	ENST00000256646.2:c.14G>A	p.Arg5His	p.R5H	ENST00000256646	NM_024408.3	5	cGc/cAc	1/34	0.454094914402173	4	FACETS	1	0.877	1	0.603	0.47	0.75	INDETERMINATE	1	TRUE	2	0.759256054137176	4		41	73	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030486	49030486	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0055910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	37	157	0	ENST00000267163.4:c.1960+1G>A		p.X654_splice	ENST00000267163	NM_000321.2	654			0.372724824164839	1	FACETS	0.939	0.785	1	0.939	0.785	1	CLONAL	1	TRUE	0	0.372724824164839	1		157	172	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499420	89499420	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	69	323	0	ENST00000336596.2:c.2590G>T	p.Asp864Tyr	p.D864Y	ENST00000336596	NM_005233.5	864	Gac/Tac	15/17	1	2	FACETS	0.907	0.794	1	0.907	0.794	1	CLONAL	1	TRUE	1	0.372724824164839	2		323	408	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81534655	81534655	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	41	204	0	ENST00000298171.2:c.300G>C	p.Leu100Phe	p.L100F	ENST00000298171	NM_000369.2	100	ttG/ttC	3/10	1	2	FACETS	0.887	0.744	1	0.887	0.744	1	CLONAL	1	TRUE	1	0.372724824164839	2		204	248	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396290	396290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	170	695	1	ENST00000262320.3:c.736G>A	p.Glu246Lys	p.E246K	ENST00000262320	NM_003502.3	246	Gaa/Aaa	2/11	0.372724824164839	1	FACETS	0.694	0.637	0.753	0.694	0.637	0.753	SUBCLONAL	1	TRUE	0	0.372724824164839	1		696	1070	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579325	7579326	+	stop_gained	Nonsense_Mutation	INS	-	-	ACT	novel	NA	P-0055910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	127	531	0	ENST00000269305.4:c.359_361dup	p.Lys120_Ser121insTer	p.K120_S121ins*	ENST00000269305	NM_001126112.2	121	tct/tAGTct	4/11	0.372724824164839	1	FACETS	0.886	0.805	0.971	0.886	0.805	0.971	CLONAL	1	TRUE	0	0.372724824164839	1		531	626	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912435	50912435	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	157	845	0	ENST00000440232.2:c.1949C>A	p.Ser650Ter	p.S650*	ENST00000440232	NM_002691.3	650	tCa/tAa	16/27	1	2	FACETS	0.849	0.777	0.925	0.849	0.777	0.925	CLONAL	1	TRUE	1	0.372724824164839	2		845	992	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422821	12422821	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	51	222	0	ENST00000287820.6:c.311G>T	p.Ser104Ile	p.S104I	ENST00000287820	NM_015869.4	104	aGt/aTt	3/7	0.372724824164839	1	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	0	0.372724824164839	1		222	222	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114674	73114674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	71	274	0	ENST00000356692.5:c.1055C>T	p.Ser352Phe	p.S352F	ENST00000356692		352	tCt/tTt	9/9	0.204203044837947	4	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.372724824164839	4		274	390	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190828	106190828	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	92	317	0	ENST00000380013.4:c.4106C>A	p.Ser1369Ter	p.S1369*	ENST00000380013	NM_001127208.2	1369	tCa/tAa	9/11	0.372724824164839	1	FACETS	0.994	0.889	1	0.994	0.889	1	CLONAL	1	TRUE	0	0.372724824164839	1		317	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0055911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	320	673	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.462866995594325	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.462866995594325	2		673	662	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0055911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	131	501	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.462866995594325	3	FACETS	0.936	0.85	1	0.468	0.425	0.513	CLONAL	1	TRUE	1	0.462866995594325	3		501	745	SUCCESS
APC	324	MSKCC	GRCh37	5	112175350	112175351	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	114	144	0	ENST00000257430.4:c.4063dup	p.Ser1355PhefsTer20	p.S1355Ffs*20	ENST00000257430	NM_000038.5	1353	-/T	16/16	0.453342688092702	3	FACETS	0.868	0.799	0.937	0.868	0.799	0.937	CLONAL	3	TRUE	0	0.462866995594325	3		144	233	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288474	21288474	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	131	487	0	ENST00000354336.3:c.719C>G	p.Ala240Gly	p.A240G	ENST00000354336	NM_005207.3	240	gCg/gGg	2/3	1	2	FACETS	0.983	0.895	1	0.983	0.895	1	CLONAL	1	TRUE	1	0.462866995594325	2		487	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0055912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	190	632	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.330597213427116	2	FACETS	0.809	0.755	0.863	0.809	0.755	0.863	CLONAL	2	TRUE	0	0.495682078493064	2		632	474	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	89	374	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.495682078493064	2		374	305	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316310	14316310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	11	393	0	ENST00000256196.4:c.295G>A	p.Gly99Ser	p.G99S	ENST00000256196		99	Ggc/Agc	3/6	0.150780152993337	0	FACETS	0.102	0.07	0.141			1	INDETERMINATE	1	TRUE	0	0.495682078493064	0		393	220	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955577	48955580	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TCAG	TCAG	-	novel	NA	P-0055912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	32	170	0	ENST00000267163.4:c.1694_1695+2del		p.X565_splice	ENST00000267163	NM_000321.2	565		17/27	0.495682078493064	1	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	0	0.495682078493064	1		170	89	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562641	29562642	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGT	novel	NA	P-0055912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	91	345	0	ENST00000356175.3:c.3722_3725dup	p.Leu1243SerfsTer7	p.L1243Sfs*7	ENST00000356175	NM_000267.3	1241	cga/cGAGTga	28/57	0.330597213427116	2	FACETS	0.771	0.697	0.848	0.771	0.697	0.848	SUBCLONAL	2	TRUE	0	0.495682078493064	2		345	238	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685315	89685315	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1554897280	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	161	229	0	ENST00000371953.3:c.209+1G>A		p.X70_splice	ENST00000371953	NM_000314.4	70			0.883463902199428	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.883463902199428	1		229	183	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519985	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	649	729	0	ENST00000269305.4:c.857A>G	p.Glu286Gly	p.E286G	ENST00000269305	NM_001126112.2	286	gAa/gGa	8/11	0.883463902199428	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.883463902199428	1		729	767	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435300	110435302	+	inframe_deletion	In_Frame_Del	DEL	GGT	GGT	-	rs765493638	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	17	125	1	ENST00000375856.3:c.3099_3101del	p.Pro1036del	p.P1036del	ENST00000375856	NM_003749.2	1033	ccACCg/ccg	1/2	1	2	FACETS	0.123	0.092	0.161	0.123	0.092	0.161	SUBCLONAL	1	TRUE	1	0.883463902199428	2		126	312	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225556	2225556	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	517	871	0	ENST00000326181.6:c.1559A>G	p.Asn520Ser	p.N520S	ENST00000326181	NM_032271.2	520	aAc/aGc	17/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.883463902199428	2		871	1145	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210481	5210481	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	360	473	0	ENST00000357368.4:c.5486G>T	p.Arg1829Leu	p.R1829L	ENST00000357368	NM_002850.3	1829	cGg/cTg	35/38	1	2	FACETS	0.964	0.919	1	0.964	0.919	1	CLONAL	1	TRUE	1	0.883463902199428	2		473	845	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021361	42021361	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	177	271	0	ENST00000219905.7:c.3658-1G>T		p.X1220_splice	ENST00000219905	NM_001164273.1	1220			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.883463902199428	2		271	371	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	543	645	0	ENST00000267101.3:c.273G>C	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atC	3/28	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.883463902199428	2		645	1123	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561571	9561571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758518559	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	262	365	0	ENST00000353224.5:c.211G>A	p.Val71Ile	p.V71I	ENST00000353224	NM_177990.2	71	Gtt/Att	4/10	1	2	FACETS	0.957	0.904	1	0.957	0.904	1	CLONAL	1	TRUE	1	0.883463902199428	2		365	620	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851802	134851802	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs200876961	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	1361	675	1	ENST00000398015.3:c.1208C>A	p.Thr403Asn	p.T403N	ENST00000398015	NM_004441.4	403	aCc/aAc	5/16	0.883463902199428	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.883463902199428	3		676	1452	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037406	12037406	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	500	653	0	ENST00000396373.4:c.1037A>G	p.Tyr346Cys	p.Y346C	ENST00000396373	NM_001987.4	346	tAt/tGt	6/8	0.15325151545621	4	FACETS	0.947	0.909	0.984	0.947	0.909	0.984	INDETERMINATE	2	TRUE	2	0.883463902199428	4		653	1126	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135977	64135977	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	714	841	0	ENST00000334205.4:c.1238G>T	p.Arg413Leu	p.R413L	ENST00000334205	NM_003942.2	413	cGg/cTg	11/17	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.883463902199428	2		841	1499	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172322	7172322	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	309	387	0	ENST00000302850.5:c.1247G>T	p.Arg416Leu	p.R416L	ENST00000302850	NM_000208.2	416	cGa/cTa	5/22	1	2	FACETS	0.883	0.837	0.93	0.883	0.837	0.93	CLONAL	1	TRUE	1	0.883463902199428	2		387	792	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444386	50444386	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	265	338	0	ENST00000331340.3:c.316G>T	p.Gly106Ter	p.G106*	ENST00000331340	NM_006060.4	106	Gga/Tga	4/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.883463902199428	2		338	596	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189827	11189827	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	868	536	0	ENST00000361445.4:c.5682G>T	p.Leu1894Phe	p.L1894F	ENST00000361445	NM_004958.3	1894	ttG/ttT	40/58	0.715409973811136	3	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.883463902199428	3		536	1393	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105929	27105930	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	386	555	0	ENST00000324856.7:c.5541dup	p.Gly1848TrpfsTer6	p.G1848Wfs*6	ENST00000324856	NM_006015.4	1847	ggt/ggTt	20/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.883463902199428	2		555	859	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163315514	163315514	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	206	391	0	ENST00000271452.3:c.854G>T	p.Cys285Phe	p.C285F	ENST00000271452	NM_145697.2	285	tGc/tTc	11/14	1	2	FACETS	0.897	0.84	0.955	0.897	0.84	0.955	CLONAL	1	TRUE	1	0.883463902199428	2		391	520	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099311	193099311	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	120	240	0	ENST00000367435.3:c.245A>G	p.Asn82Ser	p.N82S	ENST00000367435	NM_024529.4	82	aAt/aGt	3/17	0.883463902199428	3	FACETS	0.768	0.697	0.842	0.384	0.348	0.421	SUBCLONAL	1	TRUE	1	0.883463902199428	3		240	510	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977125	85977125	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	179	259	0	ENST00000263360.6:c.727G>T	p.Asp243Tyr	p.D243Y	ENST00000263360	NM_003797.3	243	Gat/Tat	8/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.883463902199428	2		259	384	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342536	118342536	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	31	212	0	ENST00000534358.1:c.662A>G	p.Lys221Arg	p.K221R	ENST00000534358	NM_005933.3	221	aAg/aGg	3/36	1	2	FACETS	0.236	0.191	0.287	0.236	0.191	0.287	SUBCLONAL	1	TRUE	1	0.883463902199428	2		212	297	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409156	4409156	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs777786993	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	375	448	0	ENST00000261254.3:c.851T>C	p.Val284Ala	p.V284A	ENST00000261254	NM_001759.3	284	gTg/gCg	5/5	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.883463902199428	2		448	819	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446383	49446384	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	457	774	0	ENST00000301067.7:c.1221_1222delinsTT	p.Lys407_Glu408delinsAsnTer	p.K407_E408delinsN*	ENST00000301067	NM_003482.3	407	aaGGaa/aaTTaa	9/54	1	2	FACETS	0.933	0.893	0.973	0.933	0.893	0.973	CLONAL	1	TRUE	1	0.883463902199428	2		774	1109	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033860	49033877	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	GTGAACGCCTTCTGTCTG	GTGAACGCCTTCTGTCTG	-	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	214	286	0	ENST00000267163.4:c.1997_2014del	p.Cys666_Glu672delinsTer	p.C666_E672delins*	ENST00000267163	NM_000321.2	666	tGTGAACGCCTTCTGTCTGag/tag	20/27	0.883463902199428	1	FACETS	0.998	0.959	1	0.998	0.959	1	CLONAL	1	TRUE	0	0.883463902199428	1		286	271	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335954	73335954	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	182	291	0	ENST00000377767.4:c.2343-2A>G		p.X781_splice	ENST00000377767	NM_014953.3	781			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.883463902199428	2		291	405	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871760	35871760	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	389	673	0	ENST00000216797.5:c.746A>G	p.Gln249Arg	p.Q249R	ENST00000216797	NM_020529.2	249	cAg/cGg	5/6	1	2	FACETS	0.921	0.879	0.964	0.921	0.879	0.964	CLONAL	1	TRUE	1	0.883463902199428	2		673	956	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265586	10265586	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1269876059	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	340	511	0	ENST00000340748.4:c.1591A>T	p.Ile531Phe	p.I531F	ENST00000340748		531	Atc/Ttc	19/40	1	2	FACETS	0.992	0.944	1	0.992	0.944	1	CLONAL	1	TRUE	1	0.883463902199428	2		511	776	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292528	15292528	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	555	937	1	ENST00000263388.2:c.2651G>A	p.Cys884Tyr	p.C884Y	ENST00000263388	NM_000435.2	884	tGc/tAc	17/33	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.883463902199428	2		938	1213	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470956	25470956	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	595	782	0	ENST00000264709.3:c.805G>A	p.Ala269Thr	p.A269T	ENST00000264709	NM_175629.2	269	Gct/Act	7/23	0.883463902199428	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.883463902199428	1		782	713	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439455	220439455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	296	550	0	ENST00000243786.2:c.308C>T	p.Ala103Val	p.A103V	ENST00000243786	NM_002191.3	103	gCc/gTc	2/2	1	2	FACETS	0.96	0.91	1	0.96	0.91	1	CLONAL	1	TRUE	1	0.883463902199428	2		550	698	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422539	225422539	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	199	277	0	ENST00000264414.4:c.101G>A	p.Trp34Ter	p.W34*	ENST00000264414	NM_003590.4	34	tGg/tAg	2/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.883463902199428	2		277	432	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480453	89480453	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	254	289	1	ENST00000336596.2:c.2290G>A	p.Asp764Asn	p.D764N	ENST00000336596	NM_005233.5	764	Gat/Aat	13/17	0.883463902199428	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.883463902199428	1		290	296	SUCCESS
APC	324	MSKCC	GRCh37	5	112154882	112154882	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	415	584	0	ENST00000257430.4:c.1153G>C	p.Ala385Pro	p.A385P	ENST00000257430	NM_000038.5	385	Gca/Cca	10/16	1	2	FACETS	0.995	0.952	1	0.995	0.952	1	CLONAL	1	TRUE	1	0.883463902199428	2		584	944	SUCCESS
APC	324	MSKCC	GRCh37	5	112175705	112175705	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	165	259	0	ENST00000257430.4:c.4414G>T	p.Val1472Leu	p.V1472L	ENST00000257430	NM_000038.5	1472	Gta/Tta	16/16	1	2	FACETS	0.885	0.822	0.949	0.885	0.822	0.949	CLONAL	1	TRUE	1	0.883463902199428	2		259	422	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180379	32180379	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	903	760	0	ENST00000375023.3:c.2552A>T	p.Lys851Met	p.K851M	ENST00000375023	NM_004557.3	851	aAg/aTg	17/30	0.883463902199428	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.883463902199428	2		760	994	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552782	106552782	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs372836043	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	677	557	0	ENST00000369096.4:c.747C>G	p.Ser249Arg	p.S249R	ENST00000369096	NM_001198.3	249	agC/agG	5/7	0.883463902199428	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.883463902199428	2		557	737	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161990391	161990391	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	459	316	0	ENST00000366898.1:c.929A>G	p.Glu310Gly	p.E310G	ENST00000366898	NM_004562.2	310	gAg/gGg	8/12	0.883463902199428	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.883463902199428	2		316	504	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439611	140439611	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	268	471	0	ENST00000288602.6:c.2127+1G>T		p.X709_splice	ENST00000288602	NM_004333.4	709			1	2	FACETS	0.879	0.83	0.93	0.879	0.83	0.93	CLONAL	1	TRUE	1	0.883463902199428	2		471	690	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370765	55370765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	377	462	0	ENST00000297316.4:c.67G>A	p.Val23Met	p.V23M	ENST00000297316	NM_022454.3	23	Gtg/Atg	1/2	0.883463902199428	2	FACETS	0.955	0.91	0.999	0.477	0.455	0.5	CLONAL	1	TRUE	0	0.883463902199428	2		462	894	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595405	141595405	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	869	634	0	ENST00000220592.5:c.28G>T	p.Ala10Ser	p.A10S	ENST00000220592	NM_012154.3	10	Gca/Tca	2/19	0.883463902199428	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.883463902199428	2		634	932	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404654	8404654	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	139	197	0	ENST00000356435.5:c.4093G>C	p.Asp1365His	p.D1365H	ENST00000356435		1365	Gac/Cac	25/35	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.883463902199428	2		197	295	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412663	139412663	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	1171	968	0	ENST00000277541.6:c.1181del	p.Gly394AlafsTer237	p.G394Afs*237	ENST00000277541	NM_017617.3	394	gGc/gc	7/34	0.883463902199428	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.883463902199428	2		968	1301	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127743	64127743	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	509	828	0	ENST00000334205.4:c.236A>G	p.Gln79Arg	p.Q79R	ENST00000334205	NM_003942.2	79	cAa/cGa	3/17	1	2	FACETS	0.991	0.952	1	0.991	0.952	1	CLONAL	1	TRUE	1	0.883463902199428	2		828	1163	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356283	66356285	+	missense_variant	Missense_Mutation	TNP	CAC	CAC	AAA	novel	NA	P-0055922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	313	483	1	ENST00000273854.3:c.1212_1214delinsTTT	p.Cys405Phe	p.C405F	ENST00000273854	NM_004439.5	404	gtGTGt/gtTTTt	5/18	0.883463902199428	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.883463902199428	1		484	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0055925-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	494	584	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.592198038300472	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.592198038300472	2		584	791	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0055925-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	266	266	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.249639686531051	3	FACETS	0.917	0.866	0.968			1	INDETERMINATE	2	TRUE	NA	0.592198038300472	3		266	635	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524486	44524486	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055925-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	82	220	0	ENST00000291552.4:c.71T>C	p.Ile24Thr	p.I24T	ENST00000291552	NM_006758.2	24	aTt/aCt	2/8	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.592198038300472	2		220	277	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134290	2134290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747104864	NA	P-0055925-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1355	280	867	0	ENST00000219476.3:c.4067G>A	p.Gly1356Asp	p.G1356D	ENST00000219476	NM_000548.3	1356	gGc/gAc	34/42	0.552710699475908	5	FACETS	1	0.978	1	0.364	0.341	0.388	CLONAL	1	TRUE	2	0.592198038300472	5		867	1635	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435269	49435269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374216845	NA	P-0055925-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	235	872	2	ENST00000301067.7:c.6284G>A	p.Arg2095His	p.R2095H	ENST00000301067	NM_003482.3	2095	cGt/cAt	31/54	1	2	FACETS	0.928	0.868	0.99	0.928	0.868	0.99	CLONAL	1	TRUE	1	0.592198038300472	2		874	855	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222546	2222546	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055925-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	703	788	0	ENST00000326181.6:c.740T>G	p.Leu247Arg	p.L247R	ENST00000326181	NM_032271.2	247	cTg/cGg	9/21	0.552710699475908	5	FACETS	0.998	0.965	1	0.998	0.965	1	CLONAL	3	TRUE	2	0.592198038300472	5		788	1498	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439921	56439921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055925-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	411	581	0	ENST00000407977.2:c.671C>T	p.Pro224Leu	p.P224L	ENST00000407977		224	cCc/cTc	6/10	0.592198038300472	2	FACETS	0.99	0.952	1	0.99	0.952	1	CLONAL	2	TRUE	0	0.592198038300472	2		581	701	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155400	106155400	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs781201899	NA	P-0055927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	48	351	0	ENST00000380013.4:c.301C>A	p.Pro101Thr	p.P101T	ENST00000380013	NM_001127208.2	101	Cct/Act	3/11	0.374084883870498	3	FACETS	0.618	0.523	0.723	0.309	0.261	0.362	SUBCLONAL	1	TRUE	1	0.372975654402436	3		351	494	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347819	347819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746435850	NA	P-0055927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	122	1078	0	ENST00000262320.3:c.1687G>A	p.Ala563Thr	p.A563T	ENST00000262320	NM_003502.3	563	Gcc/Acc	6/11	0.343927676735168	3	FACETS	0.811	0.732	0.895	0.406	0.366	0.448	CLONAL	1	TRUE	1	0.372975654402436	3		1078	957	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	275	927	0	ENST00000269305.4:c.469G>C	p.Val157Leu	p.V157L	ENST00000269305	NM_001126112.2	157	Gtc/Ctc	5/11	0.294292168299239	2	FACETS	0.817	0.769	0.867	0.817	0.769	0.867	CLONAL	2	TRUE	0	0.372975654402436	2		927	902	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149234	119149234	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	175	534	0	ENST00000264033.4:c.1242G>T	p.Gln414His	p.Q414H	ENST00000264033	NM_005188.3	414	caG/caT	9/16	0.343927676735168	3	FACETS	0.849	0.785	0.915	0.849	0.785	0.915	CLONAL	2	TRUE	1	0.372975654402436	3		534	656	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219151	94219151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	40	417	0	ENST00000323929.3:c.253G>A	p.Gly85Ser	p.G85S	ENST00000323929	NM_005591.3	85	Ggt/Agt	4/20	0.343927676735168	3	FACETS	0.408	0.339	0.487	0.204	0.169	0.244	SUBCLONAL	1	TRUE	1	0.372975654402436	3		417	623	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56402442	56402442	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	44	236	0	ENST00000348428.3:c.1484G>T	p.Gly495Val	p.G495V	ENST00000348428	NM_006785.3	495	gGa/gTa	13/17	1	2	FACETS	0.786	0.663	0.922	0.786	0.663	0.922	CLONAL	1	TRUE	1	0.372975654402436	2		236	300	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123672	11123672	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	161	688	0	ENST00000358026.2:c.2322C>A	p.Asn774Lys	p.N774K	ENST00000358026	NM_001128849.1	774	aaC/aaA	16/36	0.30026933780385	2	FACETS	1	0.988	1	0.702	0.646	0.759	CLONAL	1	TRUE	0	0.372975654402436	2		688	615	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872615	136872615	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	59	421	0	ENST00000241393.3:c.883T>A	p.Cys295Ser	p.C295S	ENST00000241393	NM_003467.2	295	Tgt/Agt	2/2	0.298180828076917	4	FACETS	0.806	0.694	0.928	0.269	0.231	0.31	CLONAL	1	TRUE	1	0.372975654402436	4		421	539	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961123	55961123	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0055927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	212	558	0	ENST00000263923.4:c.2818-1G>T		p.X940_splice	ENST00000263923	NM_002253.2	940			0.206202560720084	3	FACETS	1	0.965	1			1	INDETERMINATE	2	TRUE	NA	0.372975654402436	3		558	642	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539452	187539452	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	55	411	0	ENST00000441802.2:c.8288A>G	p.Glu2763Gly	p.E2763G	ENST00000441802	NM_005245.3	2763	gAg/gGg	10/27	0.374084883870498	3	FACETS	0.723	0.619	0.836	0.361	0.309	0.418	SUBCLONAL	1	TRUE	1	0.372975654402436	3		411	484	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0055928-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	62	264	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.207713368409449	1	FACETS	0.773	0.673	0.88	0.773	0.673	0.88	INDETERMINATE	1	TRUE	0	0.425099794961647	1		264	297	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024001	27024002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0055928-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	32	120	0	ENST00000324856.7:c.1113dup	p.Gln372AlafsTer28	p.Q372Afs*28	ENST00000324856	NM_006015.4	369	-/G	1/20	0.425099794961647	1	FACETS	0.823	0.679	0.981	0.823	0.679	0.981	CLONAL	1	TRUE	0	0.425099794961647	1		120	144	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073884	8073885	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	GTTA	novel	NA	P-0055928-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	24	412	0	ENST00000377482.5:c.771_774dup	p.Lys259Ter	p.K259*	ENST00000377482	NM_018948.3	258	-/TAAC	4/4	0.425099794961647	1	FACETS	0.221	0.173	0.277	0.221	0.173	0.277	SUBCLONAL	1	TRUE	0	0.425099794961647	1		412	402	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620478	52620481	+	frameshift_variant	Frame_Shift_Del	DEL	TCTG	TCTG	-	novel	NA	P-0055928-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	118	391	0	ENST00000394830.3:c.3272_3275del	p.Ser1091TrpfsTer42	p.S1091Wfs*42	ENST00000394830	NM_018313.4	1091	tCAGAg/tg	21/30	0.425099794961647	1	FACETS	0.938	0.852	1	0.938	0.852	1	CLONAL	1	TRUE	0	0.425099794961647	1		391	466	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	155	573	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.182805458950212	2	FACETS	0.943	0.863	1	0.472	0.431	0.514	INDETERMINATE	1	TRUE	0	0.350019052917146	2		573	939	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	167	436	0	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	2	FACETS	0.8	0.733	0.87	0.8	0.733	0.87	SUBCLONAL	1	TRUE	1	0.350019052917146	2		436	1193	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229473	98229473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201125580	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	92	366	0	ENST00000331920.6:c.2485G>A	p.Val829Met	p.V829M	ENST00000331920	NM_000264.3	829	Gtg/Atg	15/24	1	2	FACETS	0.847	0.753	0.946	0.847	0.753	0.946	CLONAL	1	TRUE	1	0.350019052917146	2		366	621	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781146	161781146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531247345	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	158	547	0	ENST00000366898.1:c.1259G>A	p.Arg420His	p.R420H	ENST00000366898	NM_004562.2	420	cGc/cAc	11/12	1	2	FACETS	0.969	0.887	1	0.969	0.887	1	CLONAL	1	TRUE	1	0.350019052917146	2		547	932	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388045	31388045	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754182982	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	87	349	0	ENST00000328111.2:c.1846G>A	p.Val616Met	p.V616M	ENST00000328111	NM_006892.3	616	Gtg/Atg	17/23	0.266192568645178	3	FACETS	0.939	0.832	1	0.47	0.416	0.527	CLONAL	1	TRUE	1	0.350019052917146	3		349	622	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	61	695	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.325	0.279	0.375	0.325	0.279	0.375	SUBCLONAL	1	TRUE	1	0.350019052917146	2		695	1074	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	194	501	2	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.350019052917146	2		503	930	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022819	12022819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465114480	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	155	560	1	ENST00000396373.4:c.925C>T	p.Arg309Trp	p.R309W	ENST00000396373	NM_001987.4	309	Cgg/Tgg	5/8	0.148718290544144	4	FACETS	1	0.98	1	0.614	0.561	0.669	INDETERMINATE	1	TRUE	2	0.350019052917146	4		561	974	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	94	753	0	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	1	2	FACETS	0.453	0.401	0.508	0.453	0.401	0.508	SUBCLONAL	1	TRUE	1	0.350019052917146	2		753	1186	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	101	488	0	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.805	0.72	0.895	0.805	0.72	0.895	CLONAL	1	TRUE	1	0.350019052917146	2		488	717	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223018	5223018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61729778	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	54	555	0	ENST00000357368.4:c.2785C>T	p.Arg929Cys	p.R929C	ENST00000357368	NM_002850.3	929	Cgt/Tgt	18/38	1	2	FACETS	0.349	0.297	0.406	0.349	0.297	0.406	SUBCLONAL	1	TRUE	1	0.350019052917146	2		555	885	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	196	758	2	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	1	2	FACETS	0.979	0.905	1	0.979	0.905	1	CLONAL	1	TRUE	1	0.350019052917146	2		760	1144	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675571	86675571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1561325048	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	37	214	0	ENST00000274376.6:c.2513del	p.Asn838MetfsTer4	p.N838Mfs*4	ENST00000274376	NM_002890.2	836	gAa/ga	19/25	1	2	FACETS	0.675	0.559	0.805	0.675	0.559	0.805	SUBCLONAL	1	TRUE	1	0.350019052917146	2		214	313	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	165	677	4	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.884	0.81	0.96	0.884	0.81	0.96	CLONAL	1	TRUE	1	0.350019052917146	2		681	1067	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843535	156843535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369367198	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	155	685	0	ENST00000524377.1:c.961G>A	p.Val321Met	p.V321M	ENST00000524377	NM_002529.3	321	Gtg/Atg	8/17	0.15719811699679	3	FACETS	0.953	0.871	1			1	INDETERMINATE	1	TRUE	NA	0.350019052917146	3		685	1092	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	106	507	0	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.350019052917146	2		507	581	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867149	45867149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1322620921	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	186	723	0	ENST00000391945.4:c.970C>T	p.Arg324Cys	p.R324C	ENST00000391945	NM_000400.3	324	Cgc/Tgc	11/23	1	2	FACETS	0.976	0.9	1	0.976	0.9	1	CLONAL	1	TRUE	1	0.350019052917146	2		723	1089	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120219	94120219	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs2278106	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	66	290	0	ENST00000369303.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000369303	NM_004440.3	278	Ccc/Tcc	3/17	0.302623026030102	1	FACETS	0.806	0.703	0.917	0.806	0.703	0.917	CLONAL	1	TRUE	0	0.350019052917146	1		290	386	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	132	484	5	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	0.961	0.873	1	0.961	0.873	1	CLONAL	1	TRUE	1	0.350019052917146	2		489	785	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715979	52715979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205227	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	171	669	1	ENST00000322088.6:c.544C>T	p.Arg182Trp	p.R182W	ENST00000322088	NM_014225.5	182	Cgg/Tgg	5/15	NA	2	FACETS	0.915	0.841	0.993			1	INDETERMINATE	1	TRUE	NA	0.350019052917146	2		670	1068	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741837	17741837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199584989	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	76	179	0	ENST00000250003.3:c.508G>A	p.Ala170Thr	p.A170T	ENST00000250003	NM_002478.4	170	Gcg/Acg	1/3	0.130050226914826	0	FACETS	0.938	0.831	1			1	INDETERMINATE	1	TRUE	0	0.350019052917146	0		179	301	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828914	72828914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147043604	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	151	638	0	ENST00000268489.5:c.7667C>T	p.Ala2556Val	p.A2556V	ENST00000268489	NM_006885.3	2556	gCg/gTg	9/10	1	2	FACETS	0.971	0.887	1	0.971	0.887	1	CLONAL	1	TRUE	1	0.350019052917146	2		638	889	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942154	81942154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	135	604	0	ENST00000359376.3:c.1691G>A	p.Arg564Gln	p.R564Q	ENST00000359376	NM_002661.3	564	cGg/cAg	17/33	1	2	FACETS	0.952	0.866	1	0.952	0.866	1	CLONAL	1	TRUE	1	0.350019052917146	2		604	810	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532710	187532710	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1010116749	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	149	424	0	ENST00000441802.2:c.9683del	p.Pro3228LeufsTer42	p.P3228Lfs*42	ENST00000441802	NM_005245.3	3228	cCt/ct	14/27	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.350019052917146	2		424	725	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156534	55156534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778597	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	102	580	0	ENST00000257290.5:c.2935C>T	p.Arg979Cys	p.R979C	ENST00000257290	NM_006206.4	979	Cgc/Tgc	22/23	0.130050226914826	0	FACETS	0.451	0.403	0.502			1	INDETERMINATE	1	TRUE	0	0.350019052917146	0		580	840	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301111	65301111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370434553	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	51	306	2	ENST00000342505.4:c.3337C>T	p.Arg1113Cys	p.R1113C	ENST00000342505	NM_002227.2	1113	Cgc/Tgc	24/25	1	2	FACETS	0.592	0.504	0.689	0.592	0.504	0.689	SUBCLONAL	1	TRUE	1	0.350019052917146	2		308	492	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151254	202151254	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	106	354	0	ENST00000358485.4:c.1557del	p.Lys520AsnfsTer10	p.K520Nfs*10	ENST00000358485	NM_001080125.1	518	atG/at	9/9	0.350019052917146	2	FACETS	1	0.913	1	0.509	0.457	0.564	CLONAL	1	TRUE	0	0.350019052917146	2		354	595	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275254	41275254	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1553631860	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	113	373	0	ENST00000349496.5:c.1420C>T	p.Arg474Ter	p.R474*	ENST00000349496	NM_001904.3	474	Cga/Tga	9/15	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.350019052917146	2		373	646	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28979946	28979946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764045713	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	115	481	0	ENST00000282397.4:c.1522C>T	p.Arg508Cys	p.R508C	ENST00000282397	NM_002019.4	508	Cgc/Tgc	11/30	1	2	FACETS	0.976	0.881	1	0.976	0.881	1	CLONAL	1	TRUE	1	0.350019052917146	2		481	673	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259480	16259480	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	121	522	1	ENST00000375759.3:c.6750del	p.Ala2251GlnfsTer102	p.A2251Qfs*102	ENST00000375759	NM_015001.2	2249	Ccc/cc	11/15	0.257045436499489	3	FACETS	1	0.91	1			1	CLONAL	1	TRUE	NA	0.350019052917146	3		523	806	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004349	150004349	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	92	367	0	ENST00000253339.5:c.1876C>T	p.Arg626Ter	p.R626*	ENST00000253339		626	Cga/Tga	3/7	0.15719811699679	3	FACETS	1	0.908	1			1	INDETERMINATE	1	TRUE	NA	0.350019052917146	3		367	604	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562820	21562820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1379487930	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	119	479	0	ENST00000382592.4:c.1099G>A	p.Val367Ile	p.V367I	ENST00000382592	NM_014572.2	367	Gtc/Atc	4/8	1	2	FACETS	0.938	0.847	1	0.938	0.847	1	CLONAL	1	TRUE	1	0.350019052917146	2		479	725	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845883	72845883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756387925	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	107	497	0	ENST00000268489.5:c.3584G>A	p.Arg1195His	p.R1195H	ENST00000268489	NM_006885.3	1195	cGc/cAc	6/10	1	2	FACETS	0.747	0.67	0.83	0.747	0.67	0.83	SUBCLONAL	1	TRUE	1	0.350019052917146	2		497	818	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197187	26197187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	156	614	0	ENST00000356476.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000356476		98	Gag/Aag	1/1	1	2	FACETS	0.822	0.751	0.895	0.822	0.751	0.895	CLONAL	1	TRUE	1	0.350019052917146	2		614	1085	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538979	23538979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771028824	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	167	685	1	ENST00000380871.4:c.460C>T	p.Arg154Trp	p.R154W	ENST00000380871	NM_006167.3	154	Cgg/Tgg	2/2	1	2	FACETS	0.941	0.864	1	0.941	0.864	1	CLONAL	1	TRUE	1	0.350019052917146	2		686	1014	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	218	851	0	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.887	0.823	0.954	0.887	0.823	0.954	CLONAL	1	TRUE	1	0.350019052917146	2		851	1404	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998128	169998128	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs753143066	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	155	518	9	ENST00000295797.4:c.826del	p.Thr276GlnfsTer7	p.T276Qfs*7	ENST00000295797	NM_002740.5	273	ttA/tt	9/18	1	2	FACETS	0.959	0.877	1	0.959	0.877	1	CLONAL	1	TRUE	1	0.350019052917146	2		527	924	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218429	133218430	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	108	615	0	ENST00000320574.5:c.5180_5181dup	p.Glu1728TrpfsTer34	p.E1728Wfs*34	ENST00000320574	NM_006231.2	1727	-/TG	39/49	1	2	FACETS	0.704	0.632	0.782	0.704	0.632	0.782	SUBCLONAL	1	TRUE	1	0.350019052917146	2		615	876	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953142	38953142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs569163921	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	33	210	0	ENST00000357387.3:c.2842G>A	p.Val948Met	p.V948M	ENST00000357387	NM_152756.3	948	Gtg/Atg	29/38	1	2	FACETS	0.776	0.636	0.932	0.776	0.636	0.932	CLONAL	1	TRUE	1	0.350019052917146	2		210	243	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210734	2210734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	171	681	0	ENST00000398665.3:c.1231C>T	p.Arg411Cys	p.R411C	ENST00000398665	NM_032482.2	411	Cgc/Tgc	14/28	1	2	FACETS	0.854	0.784	0.927	0.854	0.784	0.927	CLONAL	1	TRUE	1	0.350019052917146	2		681	1144	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43730536	43730536	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	42	442	2	ENST00000382044.4:c.3177del	p.Thr1060ProfsTer36	p.T1060Pfs*36	ENST00000382044	NM_001141980.1	1059	ccC/cc	16/28	1	2	FACETS	0.322	0.268	0.382	0.322	0.268	0.382	SUBCLONAL	1	TRUE	1	0.350019052917146	2		444	746	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008324	29008324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770377283	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	27	244	0	ENST00000282397.4:c.547C>T	p.Arg183Cys	p.R183C	ENST00000282397	NM_002019.4	183	Cgc/Tgc	5/30	1	2	FACETS	0.374	0.297	0.461	0.374	0.297	0.461	SUBCLONAL	1	TRUE	1	0.350019052917146	2		244	413	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18962981	18962981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763818930	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	203	789	0	ENST00000262803.5:c.848C>T	p.Pro283Leu	p.P283L	ENST00000262803	NM_002911.3	283	cCg/cTg	6/24	1	2	FACETS	0.974	0.902	1	0.974	0.902	1	CLONAL	1	TRUE	1	0.350019052917146	2		789	1191	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191069	2191069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746714270	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	168	573	2	ENST00000398665.3:c.323G>A	p.Arg108His	p.R108H	ENST00000398665	NM_032482.2	108	cGc/cAc	5/28	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.350019052917146	2		575	951	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339827	116339827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780740	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	114	417	0	ENST00000397752.3:c.689C>T	p.Thr230Met	p.T230M	ENST00000397752	NM_000245.2	230	aCg/aTg	2/21	0.266192568645178	3	FACETS	0.997	0.898	1	0.498	0.449	0.551	CLONAL	1	TRUE	1	0.350019052917146	3		417	768	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211082	36211082	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1285	253	889	0	ENST00000222270.7:c.837del	p.Arg280GlyfsTer25	p.R280Gfs*25	ENST00000222270	NM_014727.1	278	aCc/ac	3/37	1	2	FACETS	0.94	0.877	1	0.94	0.877	1	CLONAL	1	TRUE	1	0.350019052917146	2		889	1538	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921558	39921558	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779671180	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	197	668	2	ENST00000378444.4:c.4262G>A	p.Arg1421His	p.R1421H	ENST00000378444	NM_001123385.1	1421	cGc/cAc	10/15	NA	2	FACETS	1	0.942	1			1	INDETERMINATE	1	TRUE	NA	0.350019052917146	2		670	1102	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294123	1294123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1309920442	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	205	891	0	ENST00000310581.5:c.878G>A	p.Arg293His	p.R293H	ENST00000310581	NM_198253.2	293	cGc/cAc	2/16	1	2	FACETS	0.966	0.895	1	0.966	0.895	1	CLONAL	1	TRUE	1	0.350019052917146	2		891	1212	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012245	152012245	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	189	398	0	ENST00000262189.6:c.568C>T	p.Arg190Ter	p.R190*	ENST00000262189	NM_170606.2	190	Cga/Tga	4/59	0.266192568645178	3	FACETS	0.845	0.783	0.909	0.845	0.783	0.909	CLONAL	2	TRUE	1	0.350019052917146	3		398	751	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331979	81331979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763933267	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	46	271	0	ENST00000222390.5:c.2105G>A	p.Arg702His	p.R702H	ENST00000222390	NM_000601.4	702	cGt/cAt	18/18	0.266192568645178	3	FACETS	0.671	0.566	0.788	0.336	0.283	0.394	SUBCLONAL	1	TRUE	1	0.350019052917146	3		271	460	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712824	43712824	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1201648831	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	193	655	0	ENST00000382044.4:c.4360C>T	p.Arg1454Ter	p.R1454*	ENST00000382044	NM_001141980.1	1454	Cga/Tga	21/28	1	2	FACETS	0.996	0.921	1	0.996	0.921	1	CLONAL	1	TRUE	1	0.350019052917146	2		655	1107	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164650	36164650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1569002104	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	182	652	1	ENST00000300305.3:c.1225G>A	p.Ala409Thr	p.A409T	ENST00000300305		409	Gcc/Acc	8/8	1	2	FACETS	0.878	0.809	0.951	0.878	0.809	0.951	CLONAL	1	TRUE	1	0.350019052917146	2		653	1184	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242854	98242854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs925067209	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	92	350	0	ENST00000331920.6:c.763C>T	p.Arg255Trp	p.R255W	ENST00000331920	NM_000264.3	255	Cgg/Tgg	6/24	1	2	FACETS	0.858	0.763	0.958	0.858	0.763	0.958	CLONAL	1	TRUE	1	0.350019052917146	2		350	613	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214866	36214866	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768047932	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	202	765	0	ENST00000222270.7:c.3292G>A	p.Gly1098Arg	p.G1098R	ENST00000222270	NM_014727.1	1098	Ggg/Agg	8/37	1	2	FACETS	0.843	0.779	0.909	0.843	0.779	0.909	CLONAL	1	TRUE	1	0.350019052917146	2		765	1369	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809512	36809512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748294638	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	204	705	1	ENST00000373129.3:c.953G>A	p.Arg318His	p.R318H	ENST00000373129	NM_032017.1	318	cGc/cAc	10/12	1	2	FACETS	0.948	0.877	1	0.948	0.877	1	CLONAL	1	TRUE	1	0.350019052917146	2		706	1230	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311605	15311605	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1445073298	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	40	143	0	ENST00000263388.2:c.112del	p.Ala38LeufsTer198	p.A38Lfs*198	ENST00000263388	NM_000435.2	38	Gct/ct	1/33	1	2	FACETS	0.85	0.71	1	0.85	0.71	1	CLONAL	1	TRUE	1	0.350019052917146	2		143	269	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224110	36224111	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	107	598	1	ENST00000222270.7:c.6666dup	p.Thr2223HisfsTer80	p.T2223Hfs*80	ENST00000222270	NM_014727.1	2220	-/C	28/37	1	2	FACETS	0.636	0.57	0.707	0.636	0.57	0.707	SUBCLONAL	1	TRUE	1	0.350019052917146	2		599	961	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094473	27094473	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	143	469	0	ENST00000324856.7:c.3181A>G	p.Ile1061Val	p.I1061V	ENST00000324856	NM_006015.4	1061	Att/Gtt	11/20	1	2	FACETS	0.959	0.874	1	0.959	0.874	1	CLONAL	1	TRUE	1	0.350019052917146	2		469	852	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653797	206653797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1336309654	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	161	653	0	ENST00000367120.3:c.1348C>T	p.Leu450Phe	p.L450F	ENST00000367120	NM_014002.3	450	Ctc/Ttc	13/22	1	2	FACETS	0.869	0.796	0.945	0.869	0.796	0.945	CLONAL	1	TRUE	1	0.350019052917146	2		653	1059	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226558215	226558215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755524804	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	127	471	0	ENST00000366794.5:c.2074G>A	p.Asp692Asn	p.D692N	ENST00000366794	NM_001618.3	692	Gac/Aac	15/23	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.350019052917146	2		471	709	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118353210	118353210	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	49	169	0	ENST00000534358.1:c.4086G>T	p.Lys1362Asn	p.K1362N	ENST00000534358	NM_005933.3	1362	aaG/aaT	8/36	1	2	FACETS	0.859	0.731	0.998	0.859	0.731	0.998	CLONAL	1	TRUE	1	0.350019052917146	2		169	326	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066912	30066912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752897300	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	64	470	0	ENST00000331968.5:c.2219G>A	p.Arg740Gln	p.R740Q	ENST00000331968	NM_002742.2	740	cGg/cAg	16/18	0.182805458950212	2	FACETS	0.514	0.444	0.589	0.257	0.222	0.295	INDETERMINATE	1	TRUE	0	0.350019052917146	2		470	712	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304345	91304345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	99	413	0	ENST00000355112.3:c.1742C>T	p.Thr581Ile	p.T581I	ENST00000355112	NM_000057.2	581	aCa/aTa	7/22	1	2	FACETS	0.86	0.768	0.957	0.86	0.768	0.957	CLONAL	1	TRUE	1	0.350019052917146	2		413	658	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132677	67132677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200416354	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	101	430	2	ENST00000412916.2:c.560G>A	p.Arg187His	p.R187H	ENST00000412916		187	cGt/cAt	6/6	1	2	FACETS	0.849	0.759	0.944	0.849	0.759	0.944	CLONAL	1	TRUE	1	0.350019052917146	2		432	680	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671661	67671662	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	105	439	0	ENST00000264010.4:c.2072_2073del	p.Glu691AlafsTer4	p.E691Afs*4	ENST00000264010	NM_006565.3	690	aaAGag/aaag	12/12	1	2	FACETS	0.843	0.755	0.935	0.843	0.755	0.935	CLONAL	1	TRUE	1	0.350019052917146	2		439	712	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528152	29528152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555611025	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	101	509	0	ENST00000356175.3:c.1160G>A	p.Ser387Asn	p.S387N	ENST00000356175	NM_000267.3	387	aGc/aAc	10/57	1	2	FACETS	0.788	0.705	0.877	0.788	0.705	0.877	SUBCLONAL	1	TRUE	1	0.350019052917146	2		509	732	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511672	38511672	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	144	529	0	ENST00000254066.5:c.1170G>T	p.Lys390Asn	p.K390N	ENST00000254066	NM_000964.3	390	aaG/aaT	8/9	1	2	FACETS	0.812	0.74	0.888	0.812	0.74	0.888	CLONAL	1	TRUE	1	0.350019052917146	2		529	1013	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385184	41385184	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	129	643	0	ENST00000373198.4:c.777G>C	p.Gln259His	p.Q259H	ENST00000373198	NM_133170.3	259	caG/caC	6/32	0.350019052917146	1	FACETS	0.563	0.509	0.62	0.563	0.509	0.62	SUBCLONAL	1	TRUE	0	0.350019052917146	1		643	1080	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548340	41548340	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	75	280	0	ENST00000263253.7:c.3128A>G	p.Gln1043Arg	p.Q1043R	ENST00000263253	NM_001429.3	1043	cAg/cGg	16/31	1	2	FACETS	0.754	0.662	0.854	0.754	0.662	0.854	SUBCLONAL	1	TRUE	1	0.350019052917146	2		280	568	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037191	71037191	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	113	476	0	ENST00000318789.4:c.1100C>T	p.Thr367Ile	p.T367I	ENST00000318789	NM_032682.5	367	aCc/aTc	14/21	1	2	FACETS	0.842	0.758	0.931	0.842	0.758	0.931	CLONAL	1	TRUE	1	0.350019052917146	2		476	767	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961424	1961424	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	145	529	0	ENST00000382891.5:c.3212A>G	p.Asp1071Gly	p.D1071G	ENST00000382891	NM_133335.3	1071	gAt/gGt	17/22	NA	2	FACETS	0.905	0.825	0.988			1	INDETERMINATE	1	TRUE	NA	0.350019052917146	2		529	916	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187558062	187558062	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	56	270	0	ENST00000441802.2:c.3649G>A	p.Val1217Met	p.V1217M	ENST00000441802	NM_005245.3	1217	Gtg/Atg	5/27	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.350019052917146	2		270	308	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167761	56167761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	105	341	0	ENST00000399503.3:c.1326G>A	p.Met442Ile	p.M442I	ENST00000399503	NM_005921.1	442	atG/atA	7/20	1	2	FACETS	0.982	0.882	1	0.982	0.882	1	CLONAL	1	TRUE	1	0.350019052917146	2		341	611	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043943	180043943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	144	706	0	ENST00000261937.6:c.3053G>A	p.Ser1018Asn	p.S1018N	ENST00000261937	NM_182925.4	1018	aGc/aAc	22/30	0.169900893844887	0	FACETS	0.542	0.494	0.593			1	INDETERMINATE	1	TRUE	0	0.350019052917146	0		706	986	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401514	401514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	89	485	0	ENST00000380956.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000380956	NM_001195286.1	279	gGa/gAa	7/9	1	2	FACETS	0.805	0.714	0.901	0.805	0.714	0.901	CLONAL	1	TRUE	1	0.350019052917146	2		485	632	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021059	26021059	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	55	568	0	ENST00000357647.3:c.342del	p.His114GlnfsTer?	p.H114Qfs*?	ENST00000357647	NM_003529.2	114	caC/ca	1/1	1	2	FACETS	0.3	0.256	0.349	0.3	0.256	0.349	SUBCLONAL	1	TRUE	1	0.350019052917146	2		568	1047	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675973	30675973	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	173	622	1	ENST00000376406.3:c.2383G>T	p.Val795Phe	p.V795F	ENST00000376406	NM_014641.2	795	Gtt/Ttt	8/15	1	2	FACETS	0.886	0.814	0.961	0.886	0.814	0.961	CLONAL	1	TRUE	1	0.350019052917146	2		623	1116	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793497	89793497	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	58	257	0	ENST00000336032.3:c.566C>A	p.Ser189Ter	p.S189*	ENST00000336032	NM_006813.2	189	tCg/tAg	2/2	1	2	FACETS	0.719	0.619	0.828	0.719	0.619	0.828	SUBCLONAL	1	TRUE	1	0.350019052917146	2		257	461	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636223	87636223	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	38	552	1	ENST00000277120.3:c.2388G>T	p.Gln796His	p.Q796H	ENST00000277120		796	caG/caT	19/19	1	2	FACETS	0.319	0.263	0.382	0.319	0.263	0.382	SUBCLONAL	1	TRUE	1	0.350019052917146	2		553	681	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030526	47030526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	173	817	0	ENST00000377604.3:c.301G>A	p.Asp101Asn	p.D101N	ENST00000377604	NM_001204468.1	101	Gac/Aac	4/24	1	2	FACETS	0.846	0.778	0.918	0.846	0.778	0.918	CLONAL	1	TRUE	1	0.350019052917146	2		817	1168	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339957	70339957	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	42	467	0	ENST00000374080.3:c.490T>C	p.Cys164Arg	p.C164R	ENST00000374080		164	Tgt/Cgt	4/45	1	2	FACETS	0.295	0.245	0.35	0.295	0.245	0.35	SUBCLONAL	1	TRUE	1	0.350019052917146	2		467	814	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191805	123191805	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	66	323	0	ENST00000218089.9:c.1394T>C	p.Val465Ala	p.V465A	ENST00000218089	NM_001042749.1	465	gTt/gCt	15/35	1	2	FACETS	0.768	0.668	0.876	0.768	0.668	0.876	SUBCLONAL	1	TRUE	1	0.350019052917146	2		323	491	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	160	374	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.913	0.848	0.979	1	0.992	1	CLONAL	2	TRUE	1	0.461082427145308	2		374	380	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0055935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	249	585	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.95	1	1	0.995	1	CLONAL	2	TRUE	1	0.461082427145308	2		585	537	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148726	20148726	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0055935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	105	163	0	ENST00000379607.5:c.338-1G>C		p.X113_splice	ENST00000379607	NM_001412.3	113			1	1	FACETS	1	0.989	1	1	0.993	1	CLONAL	3	TRUE	0	0.461082427145308	1		163	110	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	150	374	0				ENST00000310581	NM_198253.2	-/1132			0.437451031079693	5	FACETS	0.834	0.769	0.901			1	CLONAL	3	TRUE	NA	0.437451031079693	5		374	454	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311619	15311621	+	inframe_deletion	In_Frame_Del	DEL	AGC	AGC	-	rs746497955	NA	P-0055936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	10	115	1	ENST00000263388.2:c.96_98del	p.Leu33del	p.L33del	ENST00000263388	NM_000435.2	32	ctGCTa/cta	1/33	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.437451031079693	NA		116	122	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577530	7577530	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	270	688	0	ENST00000269305.4:c.751A>T	p.Ile251Phe	p.I251F	ENST00000269305	NM_001126112.2	251	Atc/Ttc	7/11	0.437451031079693	3	FACETS	0.931	0.877	0.986			1	CLONAL	2	TRUE	NA	0.437451031079693	3		688	808	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622458	28622458	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	230	474	0	ENST00000241453.7:c.1159C>T	p.Arg387Ter	p.R387*	ENST00000241453	NM_004119.2	387	Cga/Tga	9/24	NA	2	FACETS	1	0.963	1			1	INDETERMINATE	2	TRUE	NA	0.437451031079693	2		474	511	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060817	38060818	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0055936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	205	1013	0	ENST00000250448.2:c.1171dup	p.Asp391GlyfsTer24	p.D391Gfs*24	ENST00000250448	NM_004496.3	391	gac/gGac	2/2	0.437451031079693	3	FACETS	0.922	0.854	0.993	0.461	0.427	0.497	CLONAL	1	TRUE	1	0.437451031079693	3		1013	1239	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100451	2100451	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	114	490	0	ENST00000219476.3:c.189G>C	p.Gln63His	p.Q63H	ENST00000219476	NM_000548.3	63	caG/caC	3/42	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.437451031079693	2		490	479	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983920	15983920	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0055936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	99	334	0	ENST00000268712.3:c.3298+1G>T		p.X1100_splice	ENST00000268712	NM_006311.3	1100			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.437451031079693	2		334	392	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46588079	46588088	+	protein_altering_variant	In_Frame_Del	DEL	GTCTGTGTGG	GTCTGTGTGG	CAGA	novel	NA	P-0055936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	179	678	1	ENST00000263734.3:c.629_638delinsCAGA	p.Ser210_Gly213delinsThrAsp	p.S210_G213delinsTD	ENST00000263734	NM_001430.4	210	aGTCTGTGTGGc/aCAGAc	6/16	0.437451031079693	6	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.437451031079693	6		679	1339	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652803	212652803	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200302763	NA	P-0055936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	187	402	0	ENST00000342788.4:c.503G>A	p.Arg168Gln	p.R168Q	ENST00000342788	NM_005235.2	168	cGg/cAg	4/28	0.437451031079693	3	FACETS	0.985	0.917	1	0.657	0.611	0.703	CLONAL	2	TRUE	0	0.437451031079693	3		402	529	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131103	55131103	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs766847405	NA	P-0055936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	225	431	0	ENST00000257290.5:c.646C>A	p.Leu216Ile	p.L216I	ENST00000257290	NM_006206.4	216	Cta/Ata	5/23	0.437451031079693	3	FACETS	0.995	0.932	1	0.995	0.932	1	CLONAL	2	TRUE	1	0.437451031079693	3		431	630	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294652	1294652	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	274	473	0	ENST00000310581.5:c.349A>T	p.Thr117Ser	p.T117S	ENST00000310581	NM_198253.2	117	Acc/Tcc	2/16	0.437451031079693	5	FACETS	0.912	0.86	0.965			1	CLONAL	3	TRUE	NA	0.437451031079693	5		473	758	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449510	31449510	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	47	274	0	ENST00000344624.3:c.2699C>G	p.Pro900Arg	p.P900R	ENST00000344624		900	cCa/cGa	19/33	0.246098399967326	5	FACETS	0.881	0.745	1	0.294	0.248	0.344	INDETERMINATE	1	TRUE	2	0.437451031079693	5		274	404	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135780967	135780967	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs118203610	NA	P-0055936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	349	491	0	ENST00000298552.3:c.1997+1G>A		p.X666_splice	ENST00000298552	NM_001162426.1	666			0.437451031079693	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	0	0.437451031079693	3		491	632	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949966	44949966	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0055936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	234	125	0	ENST00000377967.4:c.3737-2A>T		p.X1246_splice	ENST00000377967	NM_021140.2	1246			0.437451031079693	3	FACETS	0.959	0.916	1			1	CLONAL	4	TRUE	NA	0.437451031079693	3		125	340	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38964982	38964982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	96	168	0	ENST00000357387.3:c.1312C>T	p.Leu438Phe	p.L438F	ENST00000357387	NM_152756.3	438	Ctt/Ttt	16/38	0.324548732235128	1	FACETS	0.709	0.649	0.769	0.709	0.649	0.769	INDETERMINATE	1	TRUE	0	0.834620370628848	1		168	189	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523702	148523702	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	78	215	0	ENST00000320356.2:c.751C>T	p.Gln251Ter	p.Q251*	ENST00000320356	NM_004456.4	251	Cag/Tag	8/20	0.301194040200779	3	FACETS	0.838	0.743	0.938	0.279	0.247	0.313	INDETERMINATE	1	TRUE	0	0.834620370628848	3		215	316	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	20	374	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.68	0.523	0.861	0.68	0.523	0.861	SUBCLONAL	1	TRUE	1	0.330471837708652	2		374	178	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038526	47038526	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	67	866	1	ENST00000377604.3:c.688C>T	p.Arg230Ter	p.R230*	ENST00000377604	NM_001204468.1	230	Cga/Tga	8/24	0.231733914082607	0	FACETS	0.76	0.665	0.863			1	SUBCLONAL	1	TRUE	0	0.330471837708652	0		867	357	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098800	178098800	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	95	718	0	ENST00000397062.3:c.245A>G	p.Glu82Gly	p.E82G	ENST00000397062	NM_006164.4	82	gAa/gGa	2/5	1	2	FACETS	0.841	0.749	0.938	0.841	0.749	0.938	CLONAL	1	TRUE	1	0.330471837708652	2		718	684	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037144	71037144	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0055938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	44	328	0	ENST00000318789.4:c.1146+1G>A		p.X382_splice	ENST00000318789	NM_032682.5	382			1	2	FACETS	0.551	0.462	0.65	0.551	0.462	0.65	SUBCLONAL	1	TRUE	1	0.330471837708652	2		328	483	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971209	21971209	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0055938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	108	420	0	ENST00000304494.5:c.151-2A>T		p.X51_splice	ENST00000304494	NM_000077.4	51			0.330471837708652	1	FACETS	0.85	0.772	0.93	1	0.987	1	CLONAL	2	TRUE	0	0.330471837708652	1		420	321	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589591	67589592	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATA	novel	NA	P-0055938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	24	230	0	ENST00000274335.5:c.1356_1358dup	p.Asn453dup	p.N453dup	ENST00000274335		453	tat/tATAat	10/15	1	2	FACETS	0.802	0.634	0.994	0.802	0.634	0.994	CLONAL	1	TRUE	1	0.330471837708652	2		230	181	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545772	63545772	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	39	421	0	ENST00000307078.5:c.822C>G	p.Phe274Leu	p.F274L	ENST00000307078	NM_004655.3	274	ttC/ttG	3/11	1	2	FACETS	0.82	0.683	0.971	0.82	0.683	0.971	CLONAL	1	TRUE	1	0.330471837708652	2		421	288	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400691	56400691	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	15	315	0	ENST00000348428.3:c.1285G>C	p.Asp429His	p.D429H	ENST00000348428	NM_006785.3	429	Gat/Cat	11/17	1	2	FACETS	0.308	0.224	0.408	0.308	0.224	0.408	SUBCLONAL	1	TRUE	1	0.330471837708652	2		315	295	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220667	1220667	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	99	1133	0	ENST00000326873.7:c.685G>C	p.Asp229His	p.D229H	ENST00000326873	NM_000455.4	229	Gac/Cac	5/10	1	2	FACETS	0.844	0.754	0.94	0.844	0.754	0.94	CLONAL	1	TRUE	1	0.330471837708652	2		1133	710	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164642	36164643	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0055938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	74	819	0	ENST00000300305.3:c.1232_1233del	p.Ala411GlyfsTer188	p.A411Gfs*188	ENST00000300305		411	gCC/g	8/8	1	2	FACETS	0.816	0.715	0.924	0.816	0.715	0.924	CLONAL	1	TRUE	1	0.330471837708652	2		819	549	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628248	187628248	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	64	688	0	ENST00000441802.2:c.2734del	p.Val912LeufsTer2	p.V912Lfs*2	ENST00000441802	NM_005245.3	912	Gtt/tt	2/27	1	2	FACETS	0.712	0.617	0.815	0.712	0.617	0.815	SUBCLONAL	1	TRUE	1	0.330471837708652	2		688	544	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910668	29910668	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs199474400	NA	P-0055938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	145	1556	0	ENST00000376809.5:c.208G>T	p.Glu70Ter	p.E70*	ENST00000376809	NM_002116.7	70	Gag/Tag	2/8	0.330471837708652	3	FACETS	0.769	0.703	0.837	0.769	0.703	0.837	SUBCLONAL	2	TRUE	1	0.330471837708652	3		1556	665	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357063	70357063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	28	970	1	ENST00000374080.3:c.5578C>T	p.Pro1860Ser	p.P1860S	ENST00000374080		1860	Cct/Tct	39/45	0.231733914082607	0	FACETS	0.254	0.203	0.313			1	SUBCLONAL	1	TRUE	0	0.330471837708652	0		971	446	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0055946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	248	727	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.549399852955857	2		727	866	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0055947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	394	742	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.772482116099432	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.772482116099432	2		742	488	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380346	14380346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	175	218	0	ENST00000256196.4:c.71G>A	p.Gly24Asp	p.G24D	ENST00000256196		24	gGc/gAc	1/6	0.689675096630783	4	FACETS	1	0.97	1			1	CLONAL	2	TRUE	NA	0.772482116099432	4		218	377	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023257	1023257	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	256	448	0	ENST00000358495.3:c.998C>A	p.Ala333Asp	p.A333D	ENST00000358495	NM_134424.2	333	gCt/gAt	11/12	0.596937938413273	4	FACETS	0.85	0.8	0.901			1	CLONAL	2	TRUE	NA	0.772482116099432	4		448	691	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0055948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	26	215	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.587	0.466	0.724	0.587	0.466	0.724	SUBCLONAL	1	FALSE	1	0.340709102942327	2		215	260	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577035	7577036	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0055948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	79	899	0	ENST00000269305.4:c.902dup	p.Gly302ArgfsTer4	p.G302Rfs*4	ENST00000269305	NM_001126112.2	301	cca/ccCa	8/11	1	2	FACETS	0.604	0.53	0.683	0.604	0.53	0.683	SUBCLONAL	1	FALSE	1	0.340709102942327	2		899	768	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92247483	92247483	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	15	333	0	ENST00000265734.4:c.737A>G	p.Asp246Gly	p.D246G	ENST00000265734	NM_001259.6	246	gAt/gGt	7/8	1	2	FACETS	0.321	0.235	0.426	0.321	0.235	0.426	SUBCLONAL	1	FALSE	1	0.340709102942327	2		333	274	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0055949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	59	255	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.564	0.485	0.65	0.564	0.485	0.65	SUBCLONAL	1	TRUE	1	0.357126565994075	2		255	586	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0055949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	127	266	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.127444545530814	4	FACETS	1	0.971	1	0.591	0.536	0.65	INDETERMINATE	1	TRUE	2	0.357126565994075	4		266	816	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391488	84391488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	78	149	0	ENST00000321945.7:c.344G>A	p.Arg115Lys	p.R115K	ENST00000321945	NM_139076.2	115	aGg/aAg	5/9	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.357126565994075	2		149	413	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620610	52620610	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	76	270	0	ENST00000394830.3:c.3143T>A	p.Ile1048Asn	p.I1048N	ENST00000394830	NM_018313.4	1048	aTt/aAt	21/30	1	2	FACETS	0.578	0.507	0.656	0.578	0.507	0.656	SUBCLONAL	1	TRUE	1	0.357126565994075	2		270	736	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0055950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	142	458	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	0.128437424951022	1	FACETS	0.524	0.486	0.562	0.524	0.486	0.562	INDETERMINATE	1	FALSE	0	0.939548182708277	1		458	306	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0055950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	130	305	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	1	0.939548182708277	2		305	270	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981687	70981687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	232	995	2	ENST00000276594.2:c.409G>A	p.Asp137Asn	p.D137N	ENST00000276594	NM_024504.3	137	Gac/Aac	2/8	0.335664774028465	2	FACETS	0.691	0.647	0.736	0.345	0.323	0.368	INDETERMINATE	1	FALSE	0	0.939548182708277	2		997	715	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0055951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	170	532	2	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.876	0.815	0.937	0.876	0.815	0.937	CLONAL	1	TRUE	1	0.947180074428965	2		534	410	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397639	139397639	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	336	877	0	ENST00000277541.6:c.5162T>G	p.Val1721Gly	p.V1721G	ENST00000277541	NM_017617.3	1721	gTg/gGg	27/34	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.947180074428965	2		877	656	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107014	27107014	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	376	598	0	ENST00000324856.7:c.6625C>T	p.Gln2209Ter	p.Q2209*	ENST00000324856	NM_006015.4	2209	Cag/Tag	20/20	0.947180074428965	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.947180074428965	2		598	383	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848086	151848086	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	116	284	0	ENST00000262189.6:c.12673C>T	p.Arg4225Ter	p.R4225*	ENST00000262189	NM_170606.2	4225	Cga/Tga	51/59	1	2	FACETS	0.897	0.823	0.973	0.897	0.823	0.973	CLONAL	1	TRUE	1	0.947180074428965	2		284	273	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390794	139390797	+	frameshift_variant	Frame_Shift_Del	DEL	GTGG	GTGG	-	novel	NA	P-0055951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	285	1048	0	ENST00000277541.6:c.7394_7397del	p.Pro2465ArgfsTer11	p.P2465Rfs*11	ENST00000277541	NM_017617.3	2465	cCCACg/cg	34/34	1	2	FACETS	0.879	0.831	0.926	0.879	0.831	0.926	CLONAL	1	TRUE	1	0.947180074428965	2		1048	685	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874986	151874988	+	frameshift_variant	Frame_Shift_Ins	INS	CTG	CTG	TGCAT	novel	NA	P-0055951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	78	231	0	ENST00000262189.6:c.7550_7552delinsATGCA	p.Ser2517TyrfsTer5	p.S2517Yfs*5	ENST00000262189	NM_170606.2	2517	tCAGta/tATGCAta	38/59	1	2	FACETS	0.862	0.774	0.952	0.862	0.774	0.952	CLONAL	1	TRUE	1	0.947180074428965	2		231	191	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1188	53	901	0	ENST00000269305.4:c.379T>C	p.Ser127Pro	p.S127P	ENST00000269305	NM_001126112.2	127	Tcc/Ccc	5/11	1	2	FACETS	0.61	0.518	0.712	0.61	0.518	0.712	SUBCLONAL	1	TRUE	1	0.14	2		901	1241	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0055952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	41	215	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.971	0.808	1	0.971	0.808	1	CLONAL	1	TRUE	1	0.14	2		215	603	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	57	374	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.902	1			1	INDETERMINATE	1	TRUE	NA	0.2	2		374	535	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477853	140477853	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs180177036	NA	P-0055953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	24	207	0	ENST00000288602.6:c.1455G>C	p.Leu485Phe	p.L485F	ENST00000288602	NM_004333.4	485	ttG/ttC	12/18	1	2	FACETS	0.38	0.296	0.477	0.38	0.296	0.477	SUBCLONAL	1	TRUE	1	0.2	2		207	632	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287404	33287404	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	8	291	0	ENST00000374542.5:c.1693C>G	p.Gln565Glu	p.Q565E	ENST00000374542	NM_001141970.1	565	Cag/Gag	6/8	1	2	FACETS	0.116	0.074	0.171	0.116	0.074	0.171	SUBCLONAL	1	TRUE	1	0.2	2		291	692	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061226	38061226	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	64	388	0	ENST00000250448.2:c.763G>C	p.Glu255Gln	p.E255Q	ENST00000250448	NM_004496.3	255	Gag/Cag	2/2	1	2	FACETS	0.749	0.647	0.86	0.749	0.647	0.86	SUBCLONAL	1	TRUE	1	0.2	2		388	855	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004505	150004505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201128649	NA	P-0055953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	29	411	1	ENST00000253339.5:c.1720G>A	p.Glu574Lys	p.E574K	ENST00000253339		574	Gag/Aag	3/7	1	2	FACETS	0.313	0.249	0.385	0.313	0.249	0.385	SUBCLONAL	1	TRUE	1	0.2	2		412	928	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115279476	115279476	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	71	255	0	ENST00000438362.2:c.541G>A	p.Glu181Lys	p.E181K	ENST00000438362	NM_001242891.1	181	Gaa/Aaa	6/20	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.2	2		255	621	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482374	56482374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	92	316	0	ENST00000267101.3:c.922G>A	p.Asp308Asn	p.D308N	ENST00000267101	NM_001982.3	308	Gac/Aac	8/28	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.2	2		316	777	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641556	23641556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	80	328	1	ENST00000261584.4:c.1919C>T	p.Ser640Leu	p.S640L	ENST00000261584	NM_024675.3	640	tCa/tTa	5/13	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.2	2		329	769	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651904	36651926	+	frameshift_variant	Frame_Shift_Del	DEL	GTCAGAACCCATGCGGCAGCAAG	GTCAGAACCCATGCGGCAGCAAG	-	novel	NA	P-0055953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	76	402	0	ENST00000244741.5:c.27_49del	p.Gln10LeufsTer18	p.Q10Lfs*18	ENST00000244741	NM_000389.4	9	cGTCAGAACCCATGCGGCAGCAAG/c	2/3	1	2	FACETS	0.951	0.833	1	0.951	0.833	1	CLONAL	1	TRUE	1	0.2	2		402	799	SUCCESS
BLM	641	MSKCC	GRCh37	15	91341562	91341562	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	20	281	0	ENST00000355112.3:c.3353T>C	p.Phe1118Ser	p.F1118S	ENST00000355112	NM_000057.2	1118	tTc/tCc	17/22	1	2	FACETS	0.311	0.237	0.399	0.311	0.237	0.399	SUBCLONAL	1	TRUE	1	0.2	2		281	643	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661734	227661734	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	11	313	0	ENST00000305123.5:c.1721C>A	p.Ser574Tyr	p.S574Y	ENST00000305123	NM_005544.2	574	tCc/tAc	1/2	1	2	FACETS	0.163	0.112	0.228	0.163	0.112	0.228	SUBCLONAL	1	TRUE	1	0.2	2		313	673	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277466	142277466	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	13	136	0	ENST00000350721.4:c.1885T>C	p.Ser629Pro	p.S629P	ENST00000350721	NM_001184.3	629	Tca/Cca	8/47	1	2	FACETS	0.349	0.248	0.474	0.349	0.248	0.474	SUBCLONAL	1	TRUE	1	0.2	2		136	372	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055953-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	54	374	0				ENST00000310581	NM_198253.2	-/1132			0.206723170081462	3	FACETS	1	0.966	1			1	CLONAL	1	TRUE	NA	0.221073425764298	3		374	365	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477853	140477853	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs180177036	NA	P-0055953-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	59	207	0	ENST00000288602.6:c.1455G>C	p.Leu485Phe	p.L485F	ENST00000288602	NM_004333.4	485	ttG/ttC	12/18	0.198184710526059	3	FACETS	1	0.924	1	0.556	0.479	0.64	CLONAL	1	TRUE	1	0.221073425764298	3		207	533	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287404	33287404	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055953-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	42	291	0	ENST00000374542.5:c.1693C>G	p.Gln565Glu	p.Q565E	ENST00000374542	NM_001141970.1	565	Cag/Gag	6/8	0.197099654685341	2	FACETS	0.636	0.53	0.754	0.318	0.265	0.377	SUBCLONAL	1	TRUE	0	0.221073425764298	2		291	597	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061226	38061226	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055953-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	52	388	0	ENST00000250448.2:c.763G>C	p.Glu255Gln	p.E255Q	ENST00000250448	NM_004496.3	255	Gag/Cag	2/2	1	2	FACETS	0.718	0.611	0.837	0.718	0.611	0.837	SUBCLONAL	1	TRUE	1	0.221073425764298	2		388	655	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004505	150004505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201128649	NA	P-0055953-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	56	411	1	ENST00000253339.5:c.1720G>A	p.Glu574Lys	p.E574K	ENST00000253339		574	Gag/Aag	3/7	1	2	FACETS	0.672	0.574	0.779	0.672	0.574	0.779	SUBCLONAL	1	TRUE	1	0.221073425764298	2		412	754	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115279476	115279476	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055953-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	71	255	0	ENST00000438362.2:c.541G>A	p.Glu181Lys	p.E181K	ENST00000438362	NM_001242891.1	181	Gaa/Aaa	6/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.221073425764298	2		255	518	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482374	56482374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055953-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	195	316	0	ENST00000267101.3:c.922G>A	p.Asp308Asn	p.D308N	ENST00000267101	NM_001982.3	308	Gac/Aac	8/28	0.206723170081462	3	FACETS	0.895	0.831	0.961			1	CLONAL	3	TRUE	NA	0.221073425764298	3		316	730	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641556	23641556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055953-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	166	328	1	ENST00000261584.4:c.1919C>T	p.Ser640Leu	p.S640L	ENST00000261584	NM_024675.3	640	tCa/tTa	5/13	1	2	FACETS	1	0.963	1	1	0.993	1	CLONAL	2	TRUE	1	0.221073425764298	2		329	697	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651904	36651926	+	frameshift_variant	Frame_Shift_Del	DEL	GTCAGAACCCATGCGGCAGCAAG	GTCAGAACCCATGCGGCAGCAAG	-	novel	NA	P-0055953-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	110	402	0	ENST00000244741.5:c.27_49del	p.Gln10LeufsTer18	p.Q10Lfs*18	ENST00000244741	NM_000389.4	9	cGTCAGAACCCATGCGGCAGCAAG/c	2/3	0.197099654685341	2	FACETS	1	0.98	1	0.69	0.62	0.764	CLONAL	1	TRUE	0	0.221073425764298	2		402	721	SUCCESS
BLM	641	MSKCC	GRCh37	15	91341562	91341562	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055953-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	34	281	0	ENST00000355112.3:c.3353T>C	p.Phe1118Ser	p.F1118S	ENST00000355112	NM_000057.2	1118	tTc/tCc	17/22	1	2	FACETS	0.589	0.481	0.712	0.589	0.481	0.712	SUBCLONAL	1	TRUE	1	0.221073425764298	2		281	522	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661734	227661734	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055953-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	38	313	0	ENST00000305123.5:c.1721C>A	p.Ser574Tyr	p.S574Y	ENST00000305123	NM_005544.2	574	tCc/tAc	1/2	1	2	FACETS	0.599	0.494	0.716	0.599	0.494	0.716	SUBCLONAL	1	TRUE	1	0.221073425764298	2		313	574	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277466	142277466	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055953-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	19	136	0	ENST00000350721.4:c.1885T>C	p.Ser629Pro	p.S629P	ENST00000350721	NM_001184.3	629	Tca/Cca	8/47	0.198184710526059	3	FACETS	0.614	0.466	0.788	0.307	0.233	0.394	SUBCLONAL	1	TRUE	1	0.221073425764298	3		136	311	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216455	2216455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754139005	NA	P-0055953-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	49	491	0	ENST00000398665.3:c.2099C>T	p.Ser700Leu	p.S700L	ENST00000398665	NM_032482.2	700	tCg/tTg	20/28	1	2	FACETS	0.511	0.431	0.599	0.511	0.431	0.599	SUBCLONAL	1	TRUE	1	0.221073425764298	2		491	868	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845621	63845621	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055953-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	14	157	0	ENST00000279873.7:c.1360del	p.Glu454LysfsTer25	p.E454Kfs*25	ENST00000279873	NM_032199.2	454	Gaa/aa	9/10	NA	2	FACETS	0.507	0.366	0.677			1	INDETERMINATE	1	TRUE	NA	0.221073425764298	2		157	250	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247367	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747241612	NA	P-0055973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	17	278	0	ENST00000281708.4:c.1435C>G	p.Arg479Gly	p.R479G	ENST00000281708	NM_033632.3	479	Cga/Gga	10/12	0.302083133332354	1	FACETS	0.443	0.332	0.575	0.443	0.332	0.575	SUBCLONAL	1	TRUE	0	0.31	1		278	209	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579433	7579433	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1064793279	NA	P-0055973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	149	973	0	ENST00000269305.4:c.254del	p.Pro85LeufsTer38	p.P85Lfs*38	ENST00000269305	NM_001126112.2	85	cCt/ct	4/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.31	2		973	734	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974676	21974676	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0055973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	111	586	0	ENST00000304494.5:c.150+1G>A		p.X50_splice	ENST00000304494	NM_000077.4	50			0.302083133332354	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.31	1		586	504	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0055974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	893	431	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.744179864132343	8	FACETS	0.932	0.913	0.951	1	0.997	1	CLONAL	7	TRUE	2	0.744179864132343	8		431	1189	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577523	7577523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	673	850	0	ENST00000269305.4:c.758C>T	p.Thr253Ile	p.T253I	ENST00000269305	NM_001126112.2	253	aCc/aTc	7/11	0.555333177988584	4	FACETS	0.91	0.882	0.937	0.91	0.882	0.937	CLONAL	3	TRUE	1	0.744179864132343	4		850	1156	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791286	42791286	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs61741480	NA	P-0055974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	756	1130	0	ENST00000575354.2:c.346G>T	p.Val116Leu	p.V116L	ENST00000575354	NM_015125.3	116	Gtg/Ttg	3/20	0.749738268216379	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	2	0.744179864132343	4		1130	1621	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998382	100998382	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	123	182	0	ENST00000325455.5:c.1420C>A	p.Pro474Thr	p.P474T	ENST00000325455	NM_001202474.3	474	Ccg/Acg	1/8	0.749738268216379	4	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	2	0.744179864132343	4		182	277	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101064	4101064	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs727504363	NA	P-0055974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	312	510	0	ENST00000262948.5:c.658A>G	p.Ile220Val	p.I220V	ENST00000262948	NM_030662.3	220	Atc/Gtc	6/11	0.749738268216379	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.744179864132343	2		510	376	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132565	11132568	+	frameshift_variant	Frame_Shift_Del	DEL	CCTG	CCTG	-	novel	NA	P-0055974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	709	1037	0	ENST00000358026.2:c.2782_2785del	p.Leu928CysfsTer21	p.L928Cfs*21	ENST00000358026	NM_001128849.1	927	ttCCTG/tt	19/36	0.749738268216379	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.744179864132343	2		1037	840	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259388	89259388	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	141	502	0	ENST00000336596.2:c.532G>T	p.Gly178Ter	p.G178*	ENST00000336596	NM_005233.5	178	Gga/Tga	3/17	0.374115715172032	3	FACETS	0.949	0.869	1			1	INDETERMINATE	1	TRUE	NA	0.744179864132343	3		502	548	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231111	142231111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	234	449	0	ENST00000350721.4:c.4843G>A	p.Asp1615Asn	p.D1615N	ENST00000350721	NM_001184.3	1615	Gac/Aac	27/47	0.555333177988584	4	FACETS	0.776	0.727	0.826	0.517	0.484	0.551	SUBCLONAL	2	TRUE	1	0.744179864132343	4		449	707	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161990442	161990442	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	110	467	0	ENST00000366898.1:c.878G>T	p.Cys293Phe	p.C293F	ENST00000366898	NM_004562.2	293	tGt/tTt	8/12	NA	2	FACETS	0.678	0.613	0.746			1	INDETERMINATE	1	TRUE	NA	0.744179864132343	2		467	436	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450319	50450320	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0055974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	199	742	1	ENST00000331340.3:c.503_504delinsAA	p.Ser168Ter	p.S168*	ENST00000331340	NM_006060.4	168	tCC/tAA	5/8	0.555333177988584	4	FACETS	1	0.974	1	0.368	0.341	0.396	CLONAL	1	TRUE	1	0.744179864132343	4		743	845	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375964	8375964	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs144763077	NA	P-0055974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	117	394	0	ENST00000356435.5:c.4633G>T	p.Asp1545Tyr	p.D1545Y	ENST00000356435		1545	Gat/Tat	28/35	0.749738268216379	3	FACETS	0.904	0.82	0.992	0.452	0.41	0.496	CLONAL	1	TRUE	1	0.744179864132343	3		394	477	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002710	37002710	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	542	875	0	ENST00000358127.4:c.539C>A	p.Ser180Tyr	p.S180Y	ENST00000358127	NM_001280556.1	180	tCc/tAc	5/10	0.749738268216379	3	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.744179864132343	3		875	893	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039668	47039668	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	257	1053	0	ENST00000377604.3:c.1120G>C	p.Gly374Arg	p.G374R	ENST00000377604	NM_001204468.1	374	Ggc/Cgc	11/24	0.207273191662704	1	FACETS	0.57	0.536	0.605	0.57	0.536	0.605	INDETERMINATE	1	TRUE	0	0.744179864132343	1		1053	761	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412245	63412245	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	255	1239	0	ENST00000330258.3:c.922C>G	p.Pro308Ala	p.P308A	ENST00000330258	NM_152424.3	308	Cca/Gca	2/2	0.207273191662704	1	FACETS	0.592	0.557	0.628	0.592	0.557	0.628	INDETERMINATE	1	TRUE	0	0.744179864132343	1		1239	727	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0055975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	281	840	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.250134284632457	1	FACETS	0.769	0.722	0.818	1	0.994	1	SUBCLONAL	2	FALSE	0	0.250134284632457	1		843	1278	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591825	48591825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767342	NA	P-0055975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	50	536	0	ENST00000342988.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000342988	NM_005359.5	330	Gaa/Aaa	9/12	1	2	FACETS	0.814	0.691	0.949	0.814	0.691	0.949	CLONAL	1	FALSE	1	0.250134284632457	2		536	491	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046507	69046507	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	38	584	0	ENST00000288368.4:c.3980A>C	p.Asn1327Thr	p.N1327T	ENST00000288368	NM_024870.2	1327	aAc/aCc	32/40	0.170609066896964	5	FACETS	0.556	0.458	0.667	0.139	0.114	0.167	SUBCLONAL	1	FALSE	1	0.250134284632457	5		584	751	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417815	32417815	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	73	651	0	ENST00000332351.3:c.1237A>G	p.Arg413Gly	p.R413G	ENST00000332351	NM_024426.4	413	Agg/Ggg	7/10	1	2	FACETS	0.827	0.723	0.939	0.827	0.723	0.939	CLONAL	1	FALSE	1	0.250134284632457	2		651	706	SUCCESS
AR	367	MSKCC	GRCh37	X	66905943	66905943	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0055975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	43	287	0	ENST00000374690.3:c.1860T>A	p.Cys620Ter	p.C620*	ENST00000374690	NM_000044.3	620	tgT/tgA	3/8	1	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	0	0.250134284632457	1		287	251	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0055976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	142	584	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.368578616494368	1	FACETS	0.865	0.79	0.942	0.865	0.79	0.942	CLONAL	1	TRUE	0	0.405849979183419	1		584	645	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0055976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	49	215	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.762	0.648	0.885	0.762	0.648	0.885	SUBCLONAL	1	TRUE	1	0.405849979183419	2		215	317	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs371769427	NA	P-0055976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	11	244	0	ENST00000291552.4:c.101C>A	p.Ser34Tyr	p.S34Y	ENST00000291552	NM_006758.2	34	tCt/tAt	2/8	0.286332251921691	1	FACETS	0.174	0.119	0.241	0.174	0.119	0.241	SUBCLONAL	1	TRUE	0	0.405849979183419	1		244	249	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15943758	15943758	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	23	291	0	ENST00000268712.3:c.6730T>G	p.Ser2244Ala	p.S2244A	ENST00000268712	NM_006311.3	2244	Tca/Gca	43/46	1	2	FACETS	0.38	0.297	0.477	0.38	0.297	0.477	SUBCLONAL	1	TRUE	1	0.405849979183419	2		291	298	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0055977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	33	878	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	1	2	FACETS	0.605	0.492	0.733	0.605	0.492	0.733	SUBCLONAL	1	FALSE	1	0.218173550106381	2		878	500	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692920	89692921	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0055977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	28	649	0	ENST00000371953.3:c.405_406insAA	p.Cys136AsnfsTer12	p.C136Nfs*12	ENST00000371953	NM_000314.4	135	ata/atAAa	5/9	1	2	FACETS	0.778	0.622	0.955	0.778	0.622	0.955	CLONAL	1	FALSE	1	0.218173550106381	2		649	330	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609952	43609952	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	81	1345	0	ENST00000355710.3:c.1904G>C	p.Arg635Pro	p.R635P	ENST00000355710	NM_020975.4	635	cGc/cCc	11/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.218173550106381	2		1345	593	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285582	46285582	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	15	375	0	ENST00000334344.6:c.4942C>T	p.Gln1648Ter	p.Q1648*	ENST00000334344	NM_152641.2	1648	Cag/Tag	17/21	1	2	FACETS	0.543	0.397	0.719	0.543	0.397	0.719	SUBCLONAL	1	FALSE	1	0.218173550106381	2		375	253	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	82	374	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.781	0.693	0.875	0.781	0.693	0.875	SUBCLONAL	1	TRUE	1	0.521033855586219	2		374	403	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631837	90631837	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519736	NA	P-0055978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	264	881	0	ENST00000330062.3:c.516G>C	p.Arg172Ser	p.R172S	ENST00000330062	NM_002168.2	172	agG/agC	4/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.521033855586219	2		881	978	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519874	NA	P-0055978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	136	456	0	ENST00000356142.4:c.85C>A	p.Pro29Thr	p.P29T	ENST00000356142	NM_018890.3	29	Cct/Act	2/7	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.521033855586219	2		456	435	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244268	98244268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	215	598	0	ENST00000331920.6:c.709del	p.Glu237LysfsTer13	p.E237Kfs*13	ENST00000331920	NM_000264.3	237	Gaa/aa	5/24	0.521033855586219	2	FACETS	0.909	0.856	0.962	0.909	0.856	0.962	CLONAL	2	TRUE	0	0.521033855586219	2		598	454	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0055979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	111	644	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	1	2	FACETS	0.848	0.762	0.939	0.848	0.762	0.939	CLONAL	1	TRUE	1	0.343130043919845	2		644	763	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346387	73346387	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	133	329	0	ENST00000377767.4:c.1413G>T	p.Arg471Ser	p.R471S	ENST00000377767	NM_014953.3	471	agG/agT	10/21	0.343130043919845	3	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	1	0.343130043919845	3		329	439	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0055981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	182	277	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.831858132737103	2	FACETS	0.91	0.847	0.973	0.455	0.423	0.487	CLONAL	1	TRUE	0	0.831858132737103	2		278	481	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870831	12870831	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	187	169	2	ENST00000228872.4:c.58C>T	p.Gln20Ter	p.Q20*	ENST00000228872	NM_004064.3	20	Cag/Tag	1/3	0.871928635202409	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.871928635202409	2		171	205	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183752	10183752	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs5030803	NA	P-0055984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	286	1048	0	ENST00000256474.2:c.221T>A	p.Val74Asp	p.V74D	ENST00000256474	NM_000551.3	74	gTc/gAc	1/3	0.477920210459617	1	FACETS	0.784	0.739	0.831	0.784	0.739	0.831	SUBCLONAL	1	TRUE	0	0.554366032061364	1		1048	951	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11227528	11227528	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	371	649	0	ENST00000361445.4:c.4300G>C	p.Glu1434Gln	p.E1434Q	ENST00000361445	NM_004958.3	1434	Gaa/Caa	29/58	0.517824855380143	3	FACETS	0.92	0.876	0.964			1	CLONAL	2	TRUE	NA	0.554366032061364	3		649	929	SUCCESS
CBL	867	MSKCC	GRCh37	11	119077153	119077153	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs772525018	NA	P-0055984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	198	736	0	ENST00000264033.4:c.26C>A	p.Ser9Tyr	p.S9Y	ENST00000264033	NM_005188.3	9	tCt/tAt	1/16	1	2	FACETS	0.837	0.777	0.9	0.837	0.777	0.9	CLONAL	1	TRUE	1	0.554366032061364	2		736	853	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421715	49421715	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0055984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	249	871	0	ENST00000301067.7:c.14516-2A>T		p.X4839_splice	ENST00000301067	NM_003482.3	4839			1	2	FACETS	0.857	0.802	0.914	0.857	0.802	0.914	CLONAL	1	TRUE	1	0.554366032061364	2		871	1048	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578290	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGATGCTGAGGAGGGGCCAGACC	AGATGCTGAGGAGGGGCCAGACC	-	novel	NA	P-0055984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	195	889	0	ENST00000269305.4:c.560-1_581del		p.X187_splice	ENST00000269305	NM_001126112.2	187		6/11	0.477920210459617	1	FACETS	0.685	0.636	0.736	0.685	0.636	0.736	SUBCLONAL	1	TRUE	0	0.554366032061364	1		889	742	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17389654	17389654	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	186	700	0	ENST00000359435.4:c.787G>A	p.Asp263Asn	p.D263N	ENST00000359435	NM_001033549.1	263	Gat/Aat	9/9	1	2	FACETS	0.808	0.747	0.871	0.808	0.747	0.871	CLONAL	1	TRUE	1	0.554366032061364	2		700	831	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436422	52436445	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTTGGCCAGCATGCCTGCGAAG	AGGTTGGCCAGCATGCCTGCGAAG	-	novel	NA	P-0055984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	170	808	0	ENST00000460680.1:c.2057-8_2072del		p.X686_splice	ENST00000460680	NM_004656.3	686		17/17	0.477920210459617	1	FACETS	0.636	0.586	0.687	0.636	0.586	0.687	SUBCLONAL	1	TRUE	0	0.554366032061364	1		808	697	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593337	67593337	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	121	386	1	ENST00000274335.5:c.2083G>T	p.Val695Leu	p.V695L	ENST00000274335		695	Gtg/Ttg	15/15	0.554366032061364	3	FACETS	1	0.923	1	0.51	0.462	0.559	CLONAL	1	TRUE	1	0.554366032061364	3		387	547	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606515	93606515	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	247	1059	0	ENST00000375746.1:c.335G>C	p.Gly112Ala	p.G112A	ENST00000375746	NM_001174167.1	112	gGg/gCg	2/14	1	2	FACETS	0.749	0.699	0.8	0.749	0.699	0.8	SUBCLONAL	1	TRUE	1	0.554366032061364	2		1059	1190	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53254067	53254084	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	TCCATGGTGGGCCCGAGG	TCCATGGTGGGCCCGAGG	-	novel	NA	P-0055984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	148	411	0	ENST00000375401.3:c.-13_5del		p.*5*	ENST00000375401	NM_004187.3	?-2/1560		1/26	1	1	FACETS	0.932	0.86	1	0.932	0.86	1	CLONAL	1	TRUE	0	0.554366032061364	1		411	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	191	1015	0	ENST00000269305.4:c.470T>G	p.Val157Gly	p.V157G	ENST00000269305	NM_001126112.2	157	gTc/gGc	5/11	0.165373753566466	2	FACETS	1	0.979	1	0.583	0.538	0.63	INDETERMINATE	1	TRUE	0	0.28	2		1015	1170	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939890	71939890	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	155	1009	1	ENST00000298229.2:c.517A>G	p.Ser173Gly	p.S173G	ENST00000298229	NM_001567.3	173	Agt/Ggt	4/28	0.290669724322355	3	FACETS	0.797	0.73	0.866	0.797	0.73	0.866	SUBCLONAL	2	TRUE	1	0.28	3		1010	792	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134512	2134512	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs45507198	NA	P-0055985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	75	1136	1	ENST00000219476.3:c.4289G>A	p.Trp1430Ter	p.W1430*	ENST00000219476	NM_000548.3	1430	tGg/tAg	34/42	0.210046012774708	3	FACETS	0.565	0.494	0.643	0.283	0.247	0.322	SUBCLONAL	1	TRUE	1	0.28	3		1137	1080	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782177	NA	P-0055986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	483	785	0	ENST00000269305.4:c.644G>T	p.Ser215Ile	p.S215I	ENST00000269305	NM_001126112.2	215	aGt/aTt	6/11	0.774317001653314	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.775487449597258	2		785	594	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999053	100999053	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	116	818	1	ENST00000325455.5:c.749G>T	p.Gly250Val	p.G250V	ENST00000325455	NM_001202474.3	250	gGa/gTa	1/8	0.775487449597258	3	FACETS	0.678	0.613	0.747	0.339	0.306	0.374	SUBCLONAL	1	TRUE	1	0.775487449597258	3		819	612	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411327	63411327	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	570	986	2	ENST00000330258.3:c.1840C>A	p.His614Asn	p.H614N	ENST00000330258	NM_152424.3	614	Cac/Aac	2/2	0.34513544924348	6	FACETS	1	0.994	1	1	0.994	1	INDETERMINATE	3	TRUE	3	0.775487449597258	6		988	1109	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615008	43615008	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1372786615	NA	P-0055986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	388	798	0	ENST00000355710.3:c.2422A>G	p.Lys808Glu	p.K808E	ENST00000355710	NM_020975.4	808	Aaa/Gaa	14/20	0.76444827425833	2	FACETS	0.939	0.908	0.968	0.939	0.908	0.968	CLONAL	2	TRUE	0	0.775487449597258	2		798	533	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288379	15288379	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	470	823	0	ENST00000263388.2:c.4360G>C	p.Asp1454His	p.D1454H	ENST00000263388	NM_000435.2	1454	Gac/Cac	24/33	0.76444827425833	2	FACETS	0.99	0.963	1	0.99	0.963	1	CLONAL	2	TRUE	0	0.775487449597258	2		823	612	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037515	12037515	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	53	312	0	ENST00000396373.4:c.1146C>A	p.Asn382Lys	p.N382K	ENST00000396373	NM_001987.4	382	aaC/aaA	6/8	0.775487449597258	6	FACETS	0.844	0.722	0.978	0.169	0.144	0.196	CLONAL	1	TRUE	1	0.775487449597258	6		312	413	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037866	49037867	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GA	GA	TG	novel	NA	P-0055986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	56	235	1	ENST00000267163.4:c.2107-1_2107delinsTG		p.X703_splice	ENST00000267163	NM_000321.2	703		21/27	0.76444827425833	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	0	0.775487449597258	2		236	71	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260571	10260571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	137	566	0	ENST00000340748.4:c.2291C>T	p.Ser764Phe	p.S764F	ENST00000340748		764	tCt/tTt	24/40	0.76444827425833	2	FACETS	1	0.939	1	0.511	0.471	0.551	CLONAL	1	TRUE	0	0.775487449597258	2		566	346	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215622	36215622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1047662710	NA	P-0055986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	210	799	3	ENST00000222270.7:c.3419G>A	p.Arg1140His	p.R1140H	ENST00000222270	NM_014727.1	1140	cGc/cAc	9/37	0.775487449597258	5	FACETS	0.926	0.858	0.997	0.232	0.214	0.25	CLONAL	1	TRUE	1	0.775487449597258	5		802	1265	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359072	81359072	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	157	333	0	ENST00000222390.5:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000222390	NM_000601.4	297	Gat/Tat	8/18	0.76291859300613	3	FACETS	0.943	0.881	1	0.943	0.881	1	CLONAL	2	TRUE	1	0.775487449597258	3		333	298	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5070043	5070043	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	14	183	0	ENST00000381652.3:c.1632T>G	p.Asp544Glu	p.D544E	ENST00000381652	NM_004972.3	544	gaT/gaG	12/25	0.775487449597258	3	FACETS	0.404	0.294	0.535	0.202	0.147	0.268	SUBCLONAL	1	TRUE	1	0.775487449597258	3		183	124	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253790	153253790	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	29	322	0	ENST00000281708.4:c.943G>C	p.Ala315Pro	p.A315P	ENST00000281708	NM_033632.3	315	Gct/Cct	6/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		322	413	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032767	30032785	+	protein_altering_variant	In_Frame_Del	DEL	GATTTGGTGTGCCGGACTC	GATTTGGTGTGCCGGACTC	CATT	novel	NA	P-0055988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	29	395	3	ENST00000338641.4:c.142_160delinsCATT	p.Asp48_Thr53delinsHis	p.D48_T53delinsH	ENST00000338641	NM_000268.3	48	GATTTGGTGTGCCGGACTCtg/CATTtg	2/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		398	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0055989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	81	673	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.778	0.685	0.878	1	0.978	1	SUBCLONAL	2	FALSE	1	0.137346589056115	2		673	758	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736160	204736160	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	35	288	0	ENST00000302823.3:c.517G>T	p.Gly173Trp	p.G173W	ENST00000302823	NM_005214.4	173	Ggg/Tgg	3/4	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	FALSE	1	0.137346589056115	2		288	452	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447676	187447676	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	72	602	0	ENST00000232014.4:c.517C>G	p.Pro173Ala	p.P173A	ENST00000232014	NM_001130845.1	173	Cct/Gct	5/10	0.137633124273397	3	FACETS	1	0.969	1	0.697	0.608	0.793	CLONAL	1	FALSE	1	0.137346589056115	3		602	804	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0055992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	59	181	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.698	0.601	0.804	0.698	0.601	0.804	SUBCLONAL	1	TRUE	1	0.32	2		181	528	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0055992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	72	460	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.789	0.69	0.896	0.789	0.69	0.896	SUBCLONAL	1	TRUE	1	0.32	2		460	570	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511172	148511172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554486390	NA	P-0055992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	142	480	0	ENST00000320356.2:c.1730C>T	p.Pro577Leu	p.P577L	ENST00000320356	NM_004456.4	577	cCg/cTg	15/20	1	2	FACETS	0.897	0.817	0.982	0.897	0.817	0.982	CLONAL	1	TRUE	1	0.32	2		480	989	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466022	69466022	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1292	218	1022	0	ENST00000227507.2:c.860C>G	p.Pro287Arg	p.P287R	ENST00000227507	NM_053056.2	287	cCc/cGc	5/5	1	2	FACETS	0.902	0.837	0.971	0.902	0.837	0.971	CLONAL	1	TRUE	1	0.32	2		1022	1510	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720679	89720679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123329	NA	P-0055992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	65	359	0	ENST00000371953.3:c.830C>T	p.Thr277Ile	p.T277I	ENST00000371953	NM_000314.4	277	aCa/aTa	8/9	1	2	FACETS	0.954	0.83	1	0.954	0.83	1	CLONAL	1	TRUE	1	0.32	2		359	426	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023622	27023634	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCGGCGGCTGC	CGGCGGCGGCTGC	-	novel	NA	P-0055992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	185	140	0	ENST00000324856.7:c.732_744del	p.Ala245ProfsTer114	p.A245Pfs*114	ENST00000324856	NM_006015.4	243	gCGGCGGCGGCTGCc/gc	1/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.32	2		140	945	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148883	119148883	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	140	243	0	ENST00000264033.4:c.1103A>G	p.Tyr368Cys	p.Y368C	ENST00000264033	NM_005188.3	368	tAt/tGt	8/16	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.900831704780149	2		243	310	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125676	47125676	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	235	466	0	ENST00000409792.3:c.5594del	p.Ser1865ThrfsTer12	p.S1865Tfs*12	ENST00000409792	NM_014159.6	1865	aGc/ac	12/21	0.437619333123419	1	FACETS	0.589	0.556	0.622	0.589	0.556	0.622	INDETERMINATE	1	TRUE	0	0.900831704780149	1		466	487	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593662	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCCTTATGATCC	novel	NA	P-0055993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	209	417	0	ENST00000288135.5:c.1738_1739insCTCCTTATGATC	p.Asp579_His580insProProTyrAsp	p.D579_H580insPPYD	ENST00000288135	NM_000222.2	576	ctt/ctTCCTTATGATCCt	11/21	1	2	FACETS	0.732	0.683	0.782	0.732	0.683	0.782	SUBCLONAL	1	TRUE	1	0.900831704780149	2		417	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0055994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	344	840	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.551399736838468	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.551399736838468	1		843	898	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0055994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	108	508	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.28610806670708	1	FACETS	0.793	0.718	0.869	0.793	0.718	0.869	INDETERMINATE	1	TRUE	0	0.551399736838468	1		508	358	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611137	100611137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	261	642	1	ENST00000308731.7:c.1469G>A	p.Arg490His	p.R490H	ENST00000308731	NM_000061.2	490	cGc/cAc	15/19	0.551399736838468	1	FACETS	0.932	0.877	0.987	0.932	0.877	0.987	CLONAL	1	TRUE	0	0.551399736838468	1		643	736	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938099	76938100	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0055995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	218	601	0	ENST00000373344.5:c.2648_2649del	p.Gln883ArgfsTer13	p.Q883Rfs*13	ENST00000373344	NM_000489.3	883	cAA/c	9/35	1	2	FACETS	0.853	0.796	0.912	0.853	0.796	0.912	CLONAL	1	TRUE	1	0.654499975899903	2		601	781	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0055995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	488	863	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.654499975899903	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.654499975899903	1		863	920	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561923	55561923	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	111	258	0	ENST00000288135.5:c.313A>T	p.Asn105Tyr	p.N105Y	ENST00000288135	NM_000222.2	105	Aat/Tat	2/21	1	2	FACETS	0.983	0.894	1	0.983	0.894	1	CLONAL	1	TRUE	1	0.654499975899903	2		258	345	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188074	151188074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	98	372	1	ENST00000262187.5:c.79G>A	p.Val27Ile	p.V27I	ENST00000262187	NM_005614.3	27	Gtt/Att	2/8	0.270795003520316	1	FACETS	0.558	0.502	0.616	0.558	0.502	0.616	INDETERMINATE	1	TRUE	0	0.654499975899903	1		373	361	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	226	374	0				ENST00000310581	NM_198253.2	-/1132			0.502062717883157	4	FACETS	0.78	0.728	0.834	0.78	0.728	0.834	SUBCLONAL	2	TRUE	2	0.502062717883157	4		374	867	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0055996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	287	226	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.502062717883157	3	FACETS	0.85	0.808	0.892	0.85	0.808	0.892	CLONAL	3	TRUE	0	0.502062717883157	3		226	561	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188183	11188183	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057524049	NA	P-0055996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	170	555	0	ENST00000361445.4:c.5911G>A	p.Ala1971Thr	p.A1971T	ENST00000361445	NM_004958.3	1971	Gcc/Acc	43/58	0.117327578853644	4	FACETS	0.811	0.749	0.875	0.811	0.749	0.875	INDETERMINATE	2	TRUE	2	0.502062717883157	4		555	627	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600567	43600567	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	235	1109	1	ENST00000355710.3:c.793G>A	p.Glu265Lys	p.E265K	ENST00000355710	NM_020975.4	265	Gag/Aag	4/20	0.462343250055925	3	FACETS	0.927	0.863	0.992	0.463	0.431	0.496	CLONAL	1	TRUE	1	0.502062717883157	3		1110	1264	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877474	28877474	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	120	555	0	ENST00000282397.4:c.3847G>T	p.Gly1283Trp	p.G1283W	ENST00000282397	NM_002019.4	1283	Ggg/Tgg	30/30	1	2	FACETS	0.921	0.836	1	0.921	0.836	1	CLONAL	1	TRUE	1	0.502062717883157	2		555	519	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872961	35872961	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs758681852	NA	P-0055996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	85	638	0	ENST00000216797.5:c.271A>C	p.Met91Leu	p.M91L	ENST00000216797	NM_020529.2	91	Atg/Ctg	2/6	0.502062717883157	3	FACETS	0.406	0.358	0.458	0.203	0.179	0.229	SUBCLONAL	1	TRUE	1	0.502062717883157	3		638	1043	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003763	45003763	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	381	695	0	ENST00000558401.1:c.20del	p.Leu7Ter	p.L7*	ENST00000558401	NM_004048.2	7	Tta/ta	1/4	0.435943690035393	2	FACETS	0.974	0.932	1	0.974	0.932	1	CLONAL	2	TRUE	0	0.502062717883157	2		695	779	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574026	7574026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	433	837	2	ENST00000269305.4:c.1001G>T	p.Gly334Val	p.G334V	ENST00000269305	NM_001126112.2	334	gGg/gTg	10/11	0.435943690035393	2	FACETS	0.973	0.934	1	0.973	0.934	1	CLONAL	2	TRUE	0	0.502062717883157	2		839	886	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051225	13051225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1490417226	NA	P-0055996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	140	781	0	ENST00000316448.5:c.661G>A	p.Glu221Lys	p.E221K	ENST00000316448	NM_004343.3	221	Gag/Aag	5/9	1	2	FACETS	0.602	0.548	0.659	0.602	0.548	0.659	SUBCLONAL	1	TRUE	1	0.502062717883157	2		781	926	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210890	36210890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767027293	NA	P-0055996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	430	1389	0	ENST00000222270.7:c.641C>T	p.Ser214Phe	p.S214F	ENST00000222270	NM_014727.1	214	tCc/tTc	3/37	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.502062717883157	2		1389	1309	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47612318	47612318	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	100	449	0	ENST00000263735.4:c.872A>C	p.Lys291Thr	p.K291T	ENST00000263735	NM_002354.2	291	aAg/aCg	8/9	0.502062717883157	3	FACETS	0.923	0.827	1	0.461	0.413	0.512	CLONAL	1	TRUE	1	0.502062717883157	3		449	540	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251780	212251781	+	missense_variant	Missense_Mutation	DNP	CA	CA	AC	novel	NA	P-0055996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	89	445	1	ENST00000342788.4:c.3278_3279delinsGT	p.Val1093Gly	p.V1093G	ENST00000342788	NM_005235.2	1093	gTG/gGT	27/28	0.16156073653771	3	FACETS	0.968	0.863	1	0.323	0.287	0.36	INDETERMINATE	1	TRUE	0	0.502062717883157	3		446	458	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439821	220439821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	218	1268	0	ENST00000243786.2:c.674G>A	p.Ser225Asn	p.S225N	ENST00000243786	NM_002191.3	225	aGt/aAt	2/2	0.16156073653771	3	FACETS	0.858	0.797	0.922	0.286	0.265	0.308	INDETERMINATE	1	TRUE	0	0.502062717883157	3		1268	1266	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293719	1293719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1400139919	NA	P-0055996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1445	476	1435	1	ENST00000310581.5:c.1282C>T	p.Arg428Trp	p.R428W	ENST00000310581	NM_198253.2	428	Cgg/Tgg	2/16	0.502062717883157	4	FACETS	1	0.996	1	0.741	0.706	0.777	CLONAL	1	TRUE	2	0.502062717883157	4		1436	1921	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722122	176722122	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	272	767	0	ENST00000439151.2:c.7753G>T	p.Gly2585Ter	p.G2585*	ENST00000439151	NM_022455.4	2585	Gga/Tga	23/23	0.338121815722376	4	FACETS	0.876	0.824	0.93	0.876	0.824	0.93	CLONAL	2	TRUE	2	0.502062717883157	4		767	929	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031962	26031962	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	197	569	0	ENST00000244661.2:c.327C>G	p.Asn109Lys	p.N109K	ENST00000244661	NM_003537.3	109	aaC/aaG	1/1	0.188269316533947	5	FACETS	1	0.976	1	0.737	0.686	0.79	INDETERMINATE	2	TRUE	2	0.502062717883157	5		569	622	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163720	32163720	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	83	1001	0	ENST00000375023.3:c.5506G>C	p.Glu1836Gln	p.E1836Q	ENST00000375023	NM_004557.3	1836	Gag/Cag	30/30	0.188269316533947	5	FACETS	0.497	0.437	0.561	0.166	0.145	0.187	INDETERMINATE	1	TRUE	2	0.502062717883157	5		1001	1167	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609967	117609967	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0055996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	161	314	0	ENST00000368508.3:c.6734-2A>G		p.X2245_splice	ENST00000368508	NM_002944.2	2245			0.502062717883157	2	FACETS	0.954	0.89	1	0.954	0.89	1	CLONAL	2	TRUE	0	0.502062717883157	2		314	336	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350067	81350067	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0055996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	176	343	0	ENST00000222390.5:c.1265T>A	p.Leu422Ter	p.L422*	ENST00000222390	NM_000601.4	422	tTa/tAa	10/18	0.315776885898306	6	FACETS	1	0.969	1	0.727	0.673	0.784	CLONAL	2	TRUE	3	0.502062717883157	6		343	644	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411421	63411421	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	69	1114	0	ENST00000330258.3:c.1746G>T	p.Glu582Asp	p.E582D	ENST00000330258	NM_152424.3	582	gaG/gaT	2/2	0.435943690035393	2	FACETS	0.282	0.245	0.323	0.141	0.122	0.162	SUBCLONAL	1	TRUE	0	0.502062717883157	2		1114	975	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0055997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	24	521	1	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	1	2	FACETS	1	0.835	1	1	0.835	1	CLONAL	1	TRUE	1	0.06	2		522	738	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928086	178928088	+	inframe_deletion	In_Frame_Del	DEL	TGC	TGC	-	novel	NA	P-0055997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	21	468	0	ENST00000263967.3:c.1366_1368del	p.Leu456del	p.L456del	ENST00000263967	NM_006218.2	455	tTGCtg/ttg	8/21	1	2	FACETS	1	0.818	1	1	0.818	1	CLONAL	1	TRUE	1	0.06	2		468	648	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916638	178916667	+	inframe_deletion	In_Frame_Del	DEL	GAACTGTGGGGCATCCACTTGATGCCCCCA	GAACTGTGGGGCATCCACTTGATGCCCCCA	-	novel	NA	P-0055997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	12	303	0	ENST00000263967.3:c.25_54del	p.Glu9_Pro18del	p.E9_P18del	ENST00000263967	NM_006218.2	9	GAACTGTGGGGCATCCACTTGATGCCCCCA/-	2/21	1	2	FACETS	0.932	0.653	1	0.932	0.653	1	CLONAL	1	TRUE	1	0.06	2		303	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577514	7577515	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	243	683	0	ENST00000269305.4:c.766dup	p.Thr256AsnfsTer8	p.T256Nfs*8	ENST00000269305	NM_001126112.2	256	aca/aAca	7/11	0.197279414118794	2	FACETS	1	0.985	1	0.597	0.557	0.639	CLONAL	1	TRUE	0	0.312930276763606	2		683	1300	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41197776	41197776	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs80356914	NA	P-0055999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	349	739	0	ENST00000357654.3:c.5511G>T	p.Trp1837Cys	p.W1837C	ENST00000357654	NM_007294.3	1837	tgG/tgT	23/23	0.197279414118794	2	FACETS	0.831	0.786	0.877	0.831	0.786	0.877	CLONAL	2	TRUE	0	0.312930276763606	2		739	1342	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787716	135787716	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	102	438	1	ENST00000298552.3:c.866C>A	p.Ser289Ter	p.S289*	ENST00000298552	NM_001162426.1	289	tCa/tAa	9/23	0.312930276763606	1	FACETS	0.704	0.629	0.783	0.704	0.629	0.783	SUBCLONAL	1	TRUE	0	0.312930276763606	1		439	781	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411048	63411048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	103	700	0	ENST00000330258.3:c.2119G>A	p.Gly707Arg	p.G707R	ENST00000330258	NM_152424.3	707	Gga/Aga	2/2	1	2	FACETS	0.655	0.585	0.73	0.655	0.585	0.73	SUBCLONAL	1	TRUE	1	0.312930276763606	2		700	1005	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913492	NA	P-0056000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	117	535	0	ENST00000286548.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000286548	NM_002072.3	209	cAa/cTa	5/7	1	2	FACETS	0.933	0.845	1	0.933	0.845	1	CLONAL	1	TRUE	1	0.467088922314908	2		535	537	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442567	52442567	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1253151209	NA	P-0056000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	123	614	0	ENST00000460680.1:c.178C>T	p.Arg60Ter	p.R60*	ENST00000460680	NM_004656.3	60	Cga/Tga	4/17	0.467088922314908	1	FACETS	0.757	0.688	0.83	0.757	0.688	0.83	SUBCLONAL	1	TRUE	0	0.467088922314908	1		614	533	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823904	3823904	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	90	899	3	ENST00000262367.5:c.2311C>T	p.Gln771Ter	p.Q771*	ENST00000262367	NM_004380.2	771	Cag/Tag	13/31	1	2	FACETS	0.361	0.319	0.406	0.361	0.319	0.406	SUBCLONAL	1	TRUE	1	0.467088922314908	2		902	1068	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752903	42752903	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	321	1227	0	ENST00000222329.4:c.1361T>G	p.Phe454Cys	p.F454C	ENST00000222329	NM_006494.2	454	tTc/tGc	4/4	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.467088922314908	2		1227	1356	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0056002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	121	219	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.381151970987248	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.458384800291402	3		219	262	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0056002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	409	1025	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	3	TRUE	NA	0.458384800291402	2		1025	551	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0056002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	66	315	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.813	0.721	0.909	1	0.979	1	CLONAL	2	TRUE	1	0.458384800291402	2		316	177	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888210	112888210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121918464	NA	P-0056002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	9	646	0	ENST00000351677.2:c.226G>A	p.Glu76Lys	p.E76K	ENST00000351677	NM_002834.3	76	Gag/Aag	3/16	1	2	FACETS	0.096	0.063	0.139	0.096	0.063	0.139	SUBCLONAL	1	TRUE	1	0.458384800291402	2		646	409	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974703	21974703	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	132	597	1	ENST00000304494.5:c.124A>T	p.Asn42Tyr	p.N42Y	ENST00000304494	NM_000077.4	42	Aat/Tat	1/3	0.362078897840763	0	FACETS	0.639	0.594	0.684			1	SUBCLONAL	2	TRUE	0	0.458384800291402	0		598	244	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030338	11030340	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0056002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	143	672	0	ENST00000327064.4:c.1091_1093del	p.Glu364del	p.E364del	ENST00000327064	NM_199141.1	363	aAAGaa/aaa	9/16	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.458384800291402	2		672	457	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347422	91347422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	167	366	1	ENST00000355112.3:c.3584C>T	p.Ser1195Phe	p.S1195F	ENST00000355112	NM_000057.2	1195	tCc/tTc	19/22	0.458384800291402	7	FACETS	1	0.979	1			1	CLONAL	3	TRUE	NA	0.458384800291402	7		367	454	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0056003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	71	378	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.520783258642865	4	FACETS	0.96	0.879	1	0.96	0.879	1	CLONAL	4	TRUE	0	0.520783258642865	4		378	108	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0056003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	110	785	1	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.520783258642865	3	FACETS	0.959	0.89	1	0.959	0.89	1	CLONAL	3	TRUE	0	0.520783258642865	3		786	185	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62325761	62325761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750539539	NA	P-0056003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	77	936	0	ENST00000360203.5:c.3029C>T	p.Thr1010Met	p.T1010M	ENST00000360203	NM_001283009.1	1010	aCg/aTg	31/35	0.520783258642865	6	FACETS	1	0.902	1	0.343	0.301	0.388	CLONAL	1	TRUE	3	0.520783258642865	6		936	586	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500554	149500554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	80	900	3	ENST00000261799.4:c.2483C>T	p.Ala828Val	p.A828V	ENST00000261799	NM_002609.3	828	gCg/gTg	18/23	0.49343126363211	3	FACETS	1	0.957	1	0.583	0.518	0.652	CLONAL	1	TRUE	1	0.520783258642865	3		903	332	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106375	27106375	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	75	669	1	ENST00000324856.7:c.5987del	p.Gly1996AlafsTer19	p.G1996Afs*19	ENST00000324856	NM_006015.4	1996	Ggc/gc	20/20	0.520783258642865	3	FACETS	1	0.96	1	0.601	0.532	0.674	CLONAL	1	TRUE	1	0.520783258642865	3		670	302	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911713	32911713	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	16	526	0	ENST00000380152.3:c.3221G>C	p.Ser1074Thr	p.S1074T	ENST00000380152		1074	aGt/aCt	11/27	0.520783258642865	4	FACETS	1	0.813	1	0.275	0.207	0.353	CLONAL	1	TRUE	0	0.520783258642865	4		526	85	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881459	48881459	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	69	248	0	ENST00000267163.4:c.181del	p.Cys61ValfsTer4	p.C61Vfs*4	ENST00000267163	NM_000321.2	61	Tgt/gt	2/27	0.520783258642865	4	FACETS	1	0.953	1	1	0.953	1	CLONAL	4	TRUE	0	0.520783258642865	4		248	96	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0056004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	117	840	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.23539351717423	1	FACETS	0.439	0.396	0.485	0.439	0.396	0.485	INDETERMINATE	1	TRUE	0	0.497719957300511	1		843	804	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	172	374	0				ENST00000310581	NM_198253.2	-/1132			0.232557644423987	2	FACETS	1	0.989	1	0.695	0.645	0.747	INDETERMINATE	1	TRUE	0	0.497719957300511	2		374	497	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510560	38510560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	602	677	0	ENST00000254066.5:c.814C>T	p.Arg272Trp	p.R272W	ENST00000254066	NM_000964.3	272	Cgg/Tgg	7/9	0.497719957300511	5	FACETS	0.902	0.871	0.933			1	CLONAL	4	TRUE	NA	0.497719957300511	5		677	1171	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981543	201981544	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0056004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	378	940	0	ENST00000359651.3:c.460dup	p.Leu154ProfsTer7	p.L154Pfs*7	ENST00000359651		153	gcc/gCcc	3/8	0.212389404257682	2	FACETS	1	0.995	1	0.694	0.659	0.728	INDETERMINATE	1	TRUE	0	0.497719957300511	2		940	1095	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576953	7577153	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAAGTGAATCTGAGGCATAACTGCACCCTTGGTCTCCTCCACCGCTTCTTGTCCTGCTTGCTTACCTCGCTTAGTGCTCCCTGGGGGCAGCTCGTGGTGAGGCTCCCCTTTCTTGCGGAGATTCTCTTCCTCTGTGCGCCGGTCTCTCCCAGGACAGGCACAAACACGCACCTCAAAGCTGTTCCGTCCCAGTAGATTAC	AAAAGTGAATCTGAGGCATAACTGCACCCTTGGTCTCCTCCACCGCTTCTTGTCCTGCTTGCTTACCTCGCTTAGTGCTCCCTGGGGGCAGCTCGTGGTGAGGCTCCCCTTTCTTGCGGAGATTCTCTTCCTCTGTGCGCCGGTCTCTCCCAGGACAGGCACAAACACGCACCTCAAAGCTGTTCCGTCCCAGTAGATTAC	-	novel	NA	P-0056004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	147	712	0	ENST00000269305.4:c.785_920-27del		p.X262_splice	ENST00000269305	NM_001126112.2	262		8/11	0.23539351717423	1	FACETS	0.714	0.655	0.777	0.714	0.655	0.777	INDETERMINATE	1	TRUE	0	0.497719957300511	1		712	621	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057021	180057022	+	missense_variant	Missense_Mutation	DNP	CG	CG	AT	novel	NA	P-0056004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	120	1147	1	ENST00000261937.6:c.597_598delinsAT	p.His199_Asp200delinsGlnTyr	p.H199_D200delinsQY	ENST00000261937	NM_182925.4	199	caCGat/caATat	5/30	0.232557644423987	2	FACETS	0.48	0.432	0.53	0.24	0.216	0.265	INDETERMINATE	1	TRUE	0	0.497719957300511	2		1148	1005	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853332	151853332	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	222	433	0	ENST00000262189.6:c.11770G>A	p.Glu3924Lys	p.E3924K	ENST00000262189	NM_170606.2	3924	Gaa/Aaa	45/59	0.238639552325252	2	FACETS	0.765	0.717	0.813	0.765	0.717	0.813	INDETERMINATE	2	TRUE	0	0.497719957300511	2		433	583	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981990	70981990	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1229	143	1209	0	ENST00000276594.2:c.106T>C	p.Tyr36His	p.Y36H	ENST00000276594	NM_024504.3	36	Tat/Cat	2/8	0.406536927162272	3	FACETS	0.523	0.475	0.574	0.262	0.237	0.287	SUBCLONAL	1	TRUE	1	0.497719957300511	3		1209	1372	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486069	8486069	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs747803106	NA	P-0056004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	41	619	0	ENST00000356435.5:c.2748A>C	p.Glu916Asp	p.E916D	ENST00000356435		916	gaA/gaC	17/35	0.363709574304733	1	FACETS	0.267	0.222	0.317	0.267	0.222	0.317	SUBCLONAL	1	TRUE	0	0.497719957300511	1		619	463	SUCCESS
AR	367	MSKCC	GRCh37	X	66937454	66937454	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	70	617	1	ENST00000374690.3:c.2308G>A	p.Val770Ile	p.V770I	ENST00000374690	NM_000044.3	770	Gtt/Att	5/8	0.318597745483854	1	FACETS	0.364	0.318	0.415	0.364	0.318	0.415	SUBCLONAL	1	TRUE	0	0.497719957300511	1		618	580	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593609	55593611	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	rs121913685	NA	P-0056006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	733	332	0	ENST00000288135.5:c.1679_1681del	p.Val560del	p.V560del	ENST00000288135	NM_000222.2	559	GTT/-	11/21	0.825556596995988	6	FACETS	0.898	0.872	0.925			1	CLONAL	4	TRUE	NA	0.825556596995988	6		332	1310	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267491	198267491	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs763149798	NA	P-0056006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	388	262	0	ENST00000335508.6:c.1866G>C	p.Glu622Asp	p.E622D	ENST00000335508	NM_012433.2	622	gaG/gaC	14/25	0.825556596995988	4	FACETS	0.917	0.874	0.959	0.917	0.874	0.959	CLONAL	2	TRUE	2	0.825556596995988	4		262	936	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722201	49722201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	269	344	1	ENST00000449682.2:c.1739G>A	p.Gly580Asp	p.G580D	ENST00000449682	NM_020998.3	580	gGc/gAc	15/18	0.536718890100631	3	FACETS	1	0.95	1			1	CLONAL	1	TRUE	NA	0.825556596995988	3		345	910	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	67	374	0				ENST00000310581	NM_198253.2	-/1132			0.42355192568222	1	FACETS	0.326	0.286	0.369	0.326	0.286	0.369	INDETERMINATE	1	TRUE	0	0.851457879797812	1		374	277	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0056007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	230	719	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	1	2	FACETS	0.508	0.473	0.544	0.508	0.473	0.544	SUBCLONAL	1	TRUE	1	0.851457879797812	2		719	1063	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021817	71021817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs797045586	NA	P-0056007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	67	177	0	ENST00000318789.4:c.1541G>A	p.Arg514His	p.R514H	ENST00000318789	NM_032682.5	514	cGt/cAt	18/21	0.42355192568222	1	FACETS	0.345	0.303	0.389	0.345	0.303	0.389	INDETERMINATE	1	TRUE	0	0.851457879797812	1		177	262	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982141	201982142	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0056007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	560	846	0	ENST00000359651.3:c.666_667dup	p.Asp223ValfsTer32	p.D223Vfs*32	ENST00000359651		222	act/acTGt	5/8	1	2	FACETS	0.993	0.955	1	0.993	0.955	1	CLONAL	1	TRUE	1	0.851457879797812	2		846	1325	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281467	198281467	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	156	381	0	ENST00000335508.6:c.664G>C	p.Glu222Gln	p.E222Q	ENST00000335508	NM_012433.2	222	Gag/Cag	6/25	1	2	FACETS	0.559	0.514	0.607	0.559	0.514	0.607	SUBCLONAL	1	TRUE	1	0.851457879797812	2		381	655	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021811	71021811	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	78	199	0	ENST00000318789.4:c.1547A>G	p.Asn516Ser	p.N516S	ENST00000318789	NM_032682.5	516	aAt/aGt	18/21	0.42355192568222	1	FACETS	0.381	0.339	0.426	0.381	0.339	0.426	INDETERMINATE	1	TRUE	0	0.851457879797812	1		199	276	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748198	41748198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	387	686	1	ENST00000226382.2:c.571G>A	p.Asp191Asn	p.D191N	ENST00000226382	NM_003924.3	191	Gac/Aac	3/3	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.851457879797812	2		687	889	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133868	55133868	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	114	332	0	ENST00000257290.5:c.1081del	p.Thr361LeufsTer13	p.T361Lfs*13	ENST00000257290	NM_006206.4	361	Act/ct	7/23	1	2	FACETS	0.461	0.416	0.508	0.461	0.416	0.508	SUBCLONAL	1	TRUE	1	0.851457879797812	2		332	581	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249013	55249014	+	protein_altering_variant	In_Frame_Ins	INS	-	-	CAC	rs1554350351	NA	P-0056007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	581	585	0	ENST00000275493.2:c.2311_2312insCAC	p.Asn771delinsThrHis	p.N771delinsTH	ENST00000275493	NM_005228.3	771	aac/aCACac	20/28	0.832319432782972	2	FACETS	0.937	0.916	0.958	0.937	0.916	0.958	CLONAL	2	TRUE	0	0.851457879797812	2		585	728	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs17849781	NA	P-0056009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	278	751	0	ENST00000269305.4:c.832C>A	p.Pro278Thr	p.P278T	ENST00000269305	NM_001126112.2	278	Cct/Act	8/11	0.389897106796833	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.397288637287641	1		751	843	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711355	114711356	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCGCC	novel	NA	P-0056009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	18	198	0	ENST00000543371.1:c.372_376dup	p.Arg126ProfsTer31	p.R126Pfs*31	ENST00000543371	NM_001198531.1	124	acc/aCCGCCcc	3/14	0.295657874390402	1	FACETS	0.295	0.222	0.381	0.295	0.222	0.381	SUBCLONAL	1	TRUE	0	0.397288637287641	1		198	246	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118902	70118902	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	267	770	0	ENST00000245479.2:c.475del	p.Glu159SerfsTer24	p.E159Sfs*24	ENST00000245479	NM_000346.3	158	gcG/gc	2/3	0.261261953803164	2	FACETS	0.793	0.746	0.842	0.793	0.746	0.842	SUBCLONAL	2	TRUE	0	0.397288637287641	2		770	847	SUCCESS
APC	324	MSKCC	GRCh37	5	112173560	112173561	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	39	259	0	ENST00000257430.4:c.2274dup	p.Ala759SerfsTer16	p.A759Sfs*16	ENST00000257430	NM_000038.5	757	caa/cAaa	16/16	1	2	FACETS	0.811	0.677	0.958	0.811	0.677	0.958	CLONAL	1	TRUE	1	0.397288637287641	2		259	242	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0056010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	371	632	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.431211785480359	3	FACETS	0.842	0.806	0.878	0.842	0.806	0.878	CLONAL	3	FALSE	0	0.518056923970244	3		632	714	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436414	52436414	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	600	746	0	ENST00000460680.1:c.2080C>T	p.Gln694Ter	p.Q694*	ENST00000460680	NM_004656.3	694	Cag/Tag	17/17	0.518056923970244	4	FACETS	0.924	0.897	0.952	0.924	0.897	0.952	CLONAL	4	FALSE	0	0.518056923970244	4		746	951	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106916	27106917	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0056010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	102	698	0	ENST00000324856.7:c.6527_6528del	p.Gln2176ArgfsTer48	p.Q2176Rfs*48	ENST00000324856	NM_006015.4	2176	cAG/c	20/20	0.518056923970244	4	FACETS	0.655	0.585	0.729	0.327	0.292	0.365	SUBCLONAL	1	FALSE	2	0.518056923970244	4		698	913	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142134	108142134	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs192810283	NA	P-0056010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	100	375	0	ENST00000278616.4:c.3077+1G>A		p.X1026_splice	ENST00000278616	NM_000051.3	1026			0.156873987845161	2	FACETS	1	0.929	1	0.519	0.467	0.573	INDETERMINATE	1	FALSE	0	0.518056923970244	2		375	372	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424062	49424062	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs886041779	NA	P-0056010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	405	1016	0	ENST00000301067.7:c.13999+1G>A		p.X4667_splice	ENST00000301067	NM_003482.3	4667			0.518056923970244	4	FACETS	0.956	0.91	1	0.956	0.91	1	CLONAL	2	FALSE	2	0.518056923970244	4		1016	1242	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981084	201981084	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0056010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	362	615	0	ENST00000359651.3:c.164-1G>A		p.X55_splice	ENST00000359651		55			0.518056923970244	3	FACETS	0.905	0.867	0.943	0.905	0.867	0.943	CLONAL	3	FALSE	0	0.518056923970244	3		615	648	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201067	108201074	+	frameshift_variant	Frame_Shift_Del	DEL	AGAACATG	AGAACATG	-	novel	NA	P-0056010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	38	353	0	ENST00000278616.4:c.7435_7442del	p.Glu2479TyrfsTer12	p.E2479Yfs*12	ENST00000278616	NM_000051.3	2478	gaAGAACATGat/gaat	50/63	0.156873987845161	2	FACETS	0.422	0.349	0.502	0.211	0.174	0.251	INDETERMINATE	1	FALSE	0	0.518056923970244	2		353	348	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41558725	41558725	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0056010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	181	327	0	ENST00000263253.7:c.3672-2A>G		p.X1224_splice	ENST00000263253	NM_001429.3	1224			0.430285849208768	3	FACETS	1	0.987	1	0.803	0.753	0.854	CLONAL	2	FALSE	0	0.518056923970244	3		327	365	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191812	123191812	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	TG	novel	NA	P-0056010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	118	212	0	ENST00000218089.9:c.1401delinsTG	p.Phe468ValfsTer5	p.F468Vfs*5	ENST00000218089	NM_001042749.1	467	ttC/ttTG	15/35	0.410081394872599	2	FACETS	0.969	0.895	1			1	CLONAL	2	FALSE	NA	0.518056923970244	2		212	235	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0056011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	89	215	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.843	0.753	0.939	0.843	0.753	0.939	CLONAL	1	TRUE	1	0.535825626630088	2		215	394	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0056011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	114	419	0	ENST00000288602.6:c.1397G>T	p.Gly466Val	p.G466V	ENST00000288602	NM_004333.4	466	gGa/gTa	11/18	1	2	FACETS	0.886	0.803	0.974	0.886	0.803	0.974	CLONAL	1	TRUE	1	0.535825626630088	2		419	480	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665135	138665135	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	141	675	0	ENST00000330315.3:c.430del	p.Arg144GlyfsTer6	p.R144Gfs*6	ENST00000330315	NM_023067.3	144	Cgg/gg	1/1	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.535825626630088	2		675	520	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	118	406	0	ENST00000397752.3:c.3028G>A	p.Asp1010Asn	p.D1010N	ENST00000397752	NM_000245.2	1010	Gat/Aat	14/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		406	895	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0056013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1215	176	656	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	0.367576251118005	6	FACETS	1	0.979	1	0.239	0.219	0.26	CLONAL	1	FALSE	1	0.367576251118005	6		656	1391	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508727	148508727	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs267601394	NA	P-0056013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	13	303	0	ENST00000320356.2:c.1937A>T	p.Tyr646Phe	p.Y646F	ENST00000320356	NM_004456.4	646	tAc/tTc	16/20	0.369002974027105	4	FACETS	0.189	0.133	0.256	0.063	0.044	0.086	SUBCLONAL	1	FALSE	1	0.367576251118005	4		303	513	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	78	374	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.974	0.867	1	0.974	0.867	1	CLONAL	1	TRUE	1	0.615893070720762	2		374	260	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0056014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	7245	434	0	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.615893070720762	37	FACETS	1	0.999	1			1	CLONAL	36	TRUE	NA	0.615893070720762	37		434	7635	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690819	89690820	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0056014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	85	298	1	ENST00000371953.3:c.227_228del	p.Tyr76Ter	p.Y76*	ENST00000371953	NM_000314.4	76	TAt/t	4/9	0.615893070720762	1	FACETS	0.893	0.805	0.982	0.893	0.805	0.982	CLONAL	1	TRUE	0	0.615893070720762	1		299	214	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242800933	242800933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866653159	NA	P-0056014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	238	790	2	ENST00000334409.5:c.58C>T	p.Arg20Trp	p.R20W	ENST00000334409	NM_005018.2	20	Cgg/Tgg	1/5	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.615893070720762	2		792	755	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0056015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	179	219	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.469609443869349	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.469609443869349	3		219	396	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650858	48650858	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782632688	NA	P-0056015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	153	675	0	ENST00000376670.3:c.727C>T	p.Arg243Trp	p.R243W	ENST00000376670	NM_002049.3	243	Cgg/Tgg	4/6	0.335052958782598	4	FACETS	0.783	0.715	0.855	0.391	0.357	0.428	SUBCLONAL	1	TRUE	2	0.469609443869349	4		675	1223	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025621	1025621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763842232	NA	P-0056015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	221	592	0	ENST00000358495.3:c.754G>A	p.Glu252Lys	p.E252K	ENST00000358495	NM_134424.2	252	Gag/Aag	9/12	0.469609443869349	3	FACETS	1	0.983	1	0.586	0.545	0.628	CLONAL	1	TRUE	1	0.469609443869349	3		592	992	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	368	554	0	ENST00000269305.4:c.734del	p.Gly245AlafsTer2	p.G245Afs*2	ENST00000269305	NM_001126112.2	245	gGc/gc	7/11	0.469609443869349	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.469609443869349	2		554	723	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225533	26225533	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	123	465	0	ENST00000360408.1:c.151G>C	p.Glu51Gln	p.E51Q	ENST00000360408	NM_003532.2	51	Gag/Cag	1/1	0.335052958782598	4	FACETS	0.814	0.735	0.897	0.407	0.367	0.449	CLONAL	1	TRUE	2	0.469609443869349	4		465	946	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0056016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	69	219	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.919	0.805	1	1	0.98	1	CLONAL	2	TRUE	1	0.19	2		219	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578529	7578529	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs780442292	NA	P-0056016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	143	945	0	ENST00000269305.4:c.401T>G	p.Phe134Cys	p.F134C	ENST00000269305	NM_001126112.2	134	tTt/tGt	5/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.19	2		945	1293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577100	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCGGTCTCT	CGCCGGTCTCT	-	novel	NA	P-0056016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	105	782	0	ENST00000269305.4:c.838_848del	p.Arg280HisfsTer22	p.R280Hfs*22	ENST00000269305	NM_001126112.2	280	AGAGACCGGCGc/c	8/11	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.19	2		782	1082	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673866	30673867	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	T	novel	NA	P-0056019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	48	240	0	ENST00000376406.3:c.3093_3094delinsA	p.Glu1032AsnfsTer84	p.E1032Nfs*84	ENST00000376406	NM_014641.2	1031	caGGaa/caAaa	10/15	0.437213113426943	3	FACETS	0.408	0.344	0.479	0.136	0.114	0.16	SUBCLONAL	1	TRUE	0	0.439594642597438	3		240	653	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099406	157099426	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAA	CAGCAGCAGCAGCAGCAGCAA	-	rs762617219	NA	P-0056021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	33	150	0	ENST00000346085.5:c.363_383del	p.Gln125_Gln131del	p.Q125_Q131del	ENST00000346085	NM_020732.3	115	CAGCAGCAGCAGCAGCAGCAA/-	1/20	1	2	FACETS	0.641	0.528	0.767	0.641	0.528	0.767	SUBCLONAL	1	TRUE	1	0.547259617328859	2		150	188	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	103	374	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.922	1	1	0.99	1	CLONAL	2	TRUE	1	0.547259617328859	2		374	188	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755823	39755823	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	32	210	1	ENST00000288319.7:c.942G>A	p.Trp314Ter	p.W314*	ENST00000288319	NM_182918.3	314	tgG/tgA	10/10	1	2	FACETS	0.594	0.486	0.713	0.594	0.486	0.713	SUBCLONAL	1	TRUE	1	0.547259617328859	2		211	197	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994158	21994158	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	63	387	0	ENST00000579755.1:c.173A>G	p.Gln58Arg	p.Q58R	ENST00000579755		58	cAg/cGg	1/3	1		FACETS		0.525	0.69				SUBCLONAL	1	TRUE	1	0.547259617328859	2		387	381	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0056023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	29	159	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.172883360883173	0	FACETS	0.816	0.675	0.965			1	CLONAL	4	FALSE	0	0.172883360883173	0		159	85	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0056023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	89	360	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.172883360883173	0	FACETS	0.873	0.793	0.955			1	CLONAL	5	FALSE	0	0.172883360883173	0		360	195	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0056023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	122	501	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.172883360883173	3	FACETS	0.989	0.908	1	1	0.992	1	CLONAL	5	FALSE	1	0.172883360883173	3		501	310	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593388	48593388	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1555686594	NA	P-0056023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	21	331	1	ENST00000342988.3:c.1140-1G>A		p.X380_splice	ENST00000342988	NM_005359.5	380			0.172883360883173	0	FACETS	0.75	0.584	0.938			1	CLONAL	2	FALSE	0	0.172883360883173	0		332	134	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31421385	31421385	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	36	356	0	ENST00000344624.3:c.3519C>G	p.His1173Gln	p.H1173Q	ENST00000344624		1173	caC/caG	27/33	0.149983172316075	2	FACETS	0.841	0.701	0.994	1	0.933	1	CLONAL	3	FALSE	0	0.172883360883173	2		356	165	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876107	35876107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	66	433	0	ENST00000303115.3:c.899C>T	p.Pro300Leu	p.P300L	ENST00000303115	NM_002185.3	300	cCt/cTt	8/8	0.149983172316075	2	FACETS	0.975	0.856	1	1	0.973	1	CLONAL	3	FALSE	0	0.172883360883173	2		433	261	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347913	70347913	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	296	699	0	ENST00000374080.3:c.3152A>G	p.Tyr1051Cys	p.Y1051C	ENST00000374080		1051	tAc/tGc	22/45	0.172883360883173	3	FACETS	1	0.957	1	1	0.996	1	CLONAL	6	FALSE	0	0.172883360883173	3		699	615	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0056024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	9	501	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.298	0.196	0.429	0.298	0.196	0.429	SUBCLONAL	1	TRUE	1	0.15	2		501	403	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0056024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	29	242	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.15	2		242	268	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0056024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	62	550	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.15	2		550	818	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105551	27105551	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	43	352	0	ENST00000324856.7:c.5162G>C	p.Arg1721Pro	p.R1721P	ENST00000324856	NM_006015.4	1721	cGa/cCa	20/20	1	2	FACETS	0.809	0.675	0.958	0.809	0.675	0.958	CLONAL	1	TRUE	1	0.15	2		352	709	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023815	27023815	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	41	241	0	ENST00000324856.7:c.921del	p.Tyr308ThrfsTer55	p.Y308Tfs*55	ENST00000324856	NM_006015.4	307	ggC/gg	1/20	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.15	2		241	487	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984390	201984390	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	71	481	0	ENST00000359651.3:c.1055A>G	p.Tyr352Cys	p.Y352C	ENST00000359651		352	tAc/tGc	8/8	1	2	FACETS	0.987	0.859	1	0.987	0.859	1	CLONAL	1	TRUE	1	0.15	2		481	959	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645038	67645038	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	52	464	0	ENST00000264010.4:c.305del	p.Asn102IlefsTer7	p.N102Ifs*7	ENST00000264010	NM_006565.3	101	gtA/gt	3/12	1	2	FACETS	0.877	0.744	1	0.877	0.744	1	CLONAL	1	TRUE	1	0.15	2		464	791	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99163063	99163063	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	35	284	0	ENST00000074304.5:c.1069A>G	p.Ile357Val	p.I357V	ENST00000074304	NM_001134224.1	357	Atc/Gtc	13/26	1	2	FACETS	0.896	0.733	1	0.896	0.733	1	CLONAL	1	TRUE	1	0.15	2		284	521	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0056025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	8	262	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.34	0.219	0.499	0.34	0.219	0.499	SUBCLONAL	1	TRUE	1	0.2	2		262	235	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0056025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	40	1027	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	1	2	FACETS	0.488	0.404	0.583	0.488	0.404	0.583	SUBCLONAL	1	TRUE	1	0.2	2		1027	819	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028616	12028616	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	22	275	0	ENST00000353533.5:c.819A>C	p.Glu273Asp	p.E273D	ENST00000353533	NM_003010.3	273	gaA/gaC	8/11	1	2	FACETS	0.748	0.58	0.943	0.748	0.58	0.943	CLONAL	1	TRUE	1	0.2	2		275	294	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792694	33792694	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	23	93	0	ENST00000498907.2:c.627G>T	p.Gln209His	p.Q209H	ENST00000498907	NM_004364.3	209	caG/caT	1/1	0.20469387720134	1	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	0	0.2	1		93	170	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0056079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	43	574	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	1	2	FACETS	0.779	0.65	0.922	0.779	0.65	0.922	CLONAL	1	TRUE	1	0.14	2		574	789	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0056079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	60	598	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.14	2		598	761	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936983	48936983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690863	NA	P-0056079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	16	332	0	ENST00000267163.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000267163	NM_000321.2	251	Cga/Tga	8/27	1	2	FACETS	0.481	0.354	0.634	0.481	0.354	0.634	SUBCLONAL	1	TRUE	1	0.14	2		332	475	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0056079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	46	193	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.17660611677151	2	FACETS	0.993	0.84	1	0.993	0.84	1	CLONAL	2	TRUE	0	0.14	2		193	331	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560514	65560514	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	29	410	0	ENST00000358664.4:c.83A>G	p.His28Arg	p.H28R	ENST00000358664	NM_002382.4	28	cAt/cGt	3/5	1	2	FACETS	0.629	0.503	0.773	0.629	0.503	0.773	SUBCLONAL	1	TRUE	1	0.14	2		410	659	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143044482	143044482	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	29	352	0	ENST00000262992.4:c.1980del	p.Leu661Ter	p.L661*	ENST00000262992	NM_001101669.1	660	ggG/gg	18/24	1	2	FACETS	0.832	0.667	1	0.832	0.667	1	CLONAL	1	TRUE	1	0.14	2		352	498	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182574	99182574	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	42	472	0	ENST00000074304.5:c.2377C>T	p.Arg793Ter	p.R793*	ENST00000074304	NM_001134224.1	793	Cga/Tga	22/26	1	2	FACETS	0.963	0.803	1	0.963	0.803	1	CLONAL	1	TRUE	1	0.14	2		472	623	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374702	118374702	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587783680	NA	P-0056079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	36	396	1	ENST00000534358.1:c.8095C>T	p.Arg2699Ter	p.R2699*	ENST00000534358	NM_005933.3	2699	Cga/Tga	27/36	1	2	FACETS	0.937	0.769	1	0.937	0.769	1	CLONAL	1	TRUE	1	0.14	2		397	549	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361787	70361787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	47	573	1	ENST00000374080.3:c.6463G>A	p.Val2155Ile	p.V2155I	ENST00000374080		2155	Gtc/Atc	44/45	1	2	FACETS	0.741	0.623	0.872	0.741	0.623	0.872	SUBCLONAL	1	TRUE	1	0.14	2		574	906	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268340	142268340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770645649	NA	P-0056079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	23	232	0	ENST00000350721.4:c.3152G>A	p.Arg1051His	p.R1051H	ENST00000350721	NM_001184.3	1051	cGt/cAt	15/47	1	2	FACETS	0.947	0.738	1	0.947	0.738	1	CLONAL	1	TRUE	1	0.14	2		232	347	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683589	29683589	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	27	232	0	ENST00000356175.3:c.7664A>T	p.Asp2555Val	p.D2555V	ENST00000356175	NM_000267.3	2555	gAt/gTt	51/57	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.14	2		232	349	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212506	36212506	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	50	655	1	ENST00000222270.7:c.2257C>A	p.Leu753Ile	p.L753I	ENST00000222270	NM_014727.1	753	Cta/Ata	3/37	1	2	FACETS	0.747	0.632	0.875	0.747	0.632	0.875	SUBCLONAL	1	TRUE	1	0.14	2		656	956	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845874	151845874	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	55	479	1	ENST00000262189.6:c.13138G>A	p.Asp4380Asn	p.D4380N	ENST00000262189	NM_170606.2	4380	Gat/Aat	52/59	1	2	FACETS	0.978	0.835	1	0.978	0.835	1	CLONAL	1	TRUE	1	0.14	2		480	803	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0056080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	66	309	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.784	0.68	0.896	0.784	0.68	0.896	SUBCLONAL	1	FALSE	1	0.272911877385305	2		310	617	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0056080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	95	893	1	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.272911877385305	1	FACETS	0.787	0.7	0.879	0.787	0.7	0.879	SUBCLONAL	1	FALSE	0	0.272911877385305	1		894	764	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145430	58145430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894340	NA	P-0056080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	70	632	0	ENST00000257904.6:c.71G>A	p.Arg24His	p.R24H	ENST00000257904	NM_000075.3	24	cGt/cAt	2/8	1	2	FACETS	0.799	0.697	0.91	0.799	0.697	0.91	CLONAL	1	FALSE	1	0.272911877385305	2		632	642	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0056080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	17	273	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.433	0.323	0.563	0.433	0.323	0.563	SUBCLONAL	1	FALSE	1	0.272911877385305	2		274	288	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264899	46264899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	67	516	0	ENST00000371998.3:c.1769G>A	p.Arg590Lys	p.R590K	ENST00000371998		590	aGa/aAa	12/23	1	2	FACETS	0.874	0.76	0.997	0.874	0.76	0.997	CLONAL	1	FALSE	1	0.272911877385305	2		516	562	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264490	16264490	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	73	669	1	ENST00000375759.3:c.10693C>T	p.Arg3565Ter	p.R3565*	ENST00000375759	NM_015001.2	3565	Cga/Tga	13/15	1	2	FACETS	0.657	0.574	0.748	0.657	0.574	0.748	SUBCLONAL	1	FALSE	1	0.272911877385305	2		670	814	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486253	8486253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1256737547	NA	P-0056080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	29	486	0	ENST00000356435.5:c.2564G>A	p.Gly855Asp	p.G855D	ENST00000356435		855	gGc/gAc	17/35	0.272911877385305	1	FACETS	0.369	0.296	0.453	0.369	0.296	0.453	SUBCLONAL	1	FALSE	0	0.272911877385305	1		486	497	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199925	108199925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555122245	NA	P-0056080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	26	275	0	ENST00000278616.4:c.7267G>A	p.Glu2423Lys	p.E2423K	ENST00000278616	NM_000051.3	2423	Gaa/Aaa	49/63	1	2	FACETS	0.532	0.421	0.659	0.532	0.421	0.659	SUBCLONAL	1	FALSE	1	0.272911877385305	2		275	358	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951873	2951873	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	74	807	0	ENST00000396946.4:c.3077C>T	p.Ser1026Phe	p.S1026F	ENST00000396946	NM_032415.4	1026	tCc/tTc	23/25	1	2	FACETS	0.681	0.595	0.774	0.681	0.595	0.774	SUBCLONAL	1	FALSE	1	0.272911877385305	2		807	796	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295265	1295265	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0056080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	42	327	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.802	0.671	0.946	0.802	0.671	0.946	CLONAL	1	FALSE	1	0.272911877385305	2		327	384	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622575	28622575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	26	317	0	ENST00000241453.7:c.1042G>A	p.Gly348Arg	p.G348R	ENST00000241453	NM_004119.2	348	Gga/Aga	9/24	1	2	FACETS	0.528	0.418	0.654	0.528	0.418	0.654	SUBCLONAL	1	FALSE	1	0.272911877385305	2		317	361	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972524	32972524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660917	NA	P-0056080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	45	713	0	ENST00000380152.3:c.9874C>T	p.Pro3292Ser	p.P3292S	ENST00000380152		3292	Ccg/Tcg	27/27	1	2	FACETS	0.452	0.379	0.534	0.452	0.379	0.534	SUBCLONAL	1	FALSE	1	0.272911877385305	2		713	729	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520204	9520204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1433508693	NA	P-0056080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	59	621	1	ENST00000353224.5:c.2065G>A	p.Ala689Thr	p.A689T	ENST00000353224	NM_177990.2	689	Gca/Aca	10/10	1	2	FACETS	0.668	0.574	0.771	0.668	0.574	0.771	SUBCLONAL	1	FALSE	1	0.272911877385305	2		622	647	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805446	1805446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	52	817	0	ENST00000260795.2:c.958G>A	p.Glu320Lys	p.E320K	ENST00000260795		320	Gag/Aag	7/17	1	2	FACETS	0.532	0.452	0.62	0.532	0.452	0.62	SUBCLONAL	1	FALSE	1	0.272911877385305	2		817	716	SUCCESS
APC	324	MSKCC	GRCh37	5	112170793	112170793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1350471118	NA	P-0056080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	62	729	0	ENST00000257430.4:c.1889C>T	p.Ala630Val	p.A630V	ENST00000257430	NM_000038.5	630	gCc/gTc	15/16	1	2	FACETS	0.555	0.478	0.639	0.555	0.478	0.639	SUBCLONAL	1	FALSE	1	0.272911877385305	2		729	819	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860073	151860073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	41	522	0	ENST00000262189.6:c.10589C>T	p.Ser3530Phe	p.S3530F	ENST00000262189	NM_170606.2	3530	tCt/tTt	43/59	1	2	FACETS	0.549	0.457	0.652	0.549	0.457	0.652	SUBCLONAL	1	FALSE	1	0.272911877385305	2		522	547	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449827	8449827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	33	502	0	ENST00000356435.5:c.3886G>A	p.Glu1296Lys	p.E1296K	ENST00000356435		1296	Gag/Aag	23/35	0.272911877385305	1	FACETS	0.359	0.291	0.435	0.359	0.291	0.435	SUBCLONAL	1	FALSE	0	0.272911877385305	1		502	582	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252690	133252690	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	94	617	0	ENST00000320574.5:c.1010A>C	p.Glu337Ala	p.E337A	ENST00000320574	NM_006231.2	337	gAa/gCa	10/49	0.256394807030785	8	FACETS	1	0.939	1	0.848	0.763	0.936	CLONAL	4	FALSE	3	0.256394807030785	8		617	306	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39317400	39317401	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0056081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	37	546	0	ENST00000373001.3:c.785_786del	p.Phe262Ter	p.F262*	ENST00000373001	NM_022157.3	262	tTT/t	5/7	0.256394807030785	4	FACETS	0.925	0.771	1	0.617	0.514	0.729	CLONAL	2	FALSE	1	0.256394807030785	4		546	196	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0056082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	556	578	2	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.633179137940536	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.633179137940536	2		580	862	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0056082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	98	325	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	0.661	0.593	0.734	0.661	0.593	0.734	SUBCLONAL	1	TRUE	1	0.633179137940536	2		325	468	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575121	48575122	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	153	395	1	ENST00000342988.3:c.320dup	p.Asn107LysfsTer2	p.N107Kfs*2	ENST00000342988	NM_005359.5	105	-/A	3/12	0.633179137940536	1	FACETS	0.737	0.681	0.795	0.737	0.681	0.795	SUBCLONAL	1	TRUE	0	0.633179137940536	1		396	448	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494187	140494187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1158980679	NA	P-0056082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	339	794	0	ENST00000288602.6:c.1061G>A	p.Arg354Gln	p.R354Q	ENST00000288602	NM_004333.4	354	cGa/cAa	8/18	0.633179137940536	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.633179137940536	1		794	682	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346565	89346565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	195	632	0	ENST00000301030.4:c.6385G>A	p.Asp2129Asn	p.D2129N	ENST00000301030	NM_001256183.1	2129	Gac/Aac	9/13	0.177116924766319	3	FACETS	1	0.972	1	0.364	0.338	0.392	INDETERMINATE	1	TRUE	0	0.633179137940536	3		632	742	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112154	115112154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370487115	NA	P-0056082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	149	615	0	ENST00000257566.3:c.1586G>A	p.Gly529Asp	p.G529D	ENST00000257566	NM_016569.3	529	gGc/gAc	7/8	1	2	FACETS	0.712	0.652	0.774	0.712	0.652	0.774	SUBCLONAL	1	TRUE	1	0.633179137940536	2		615	661	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029439	16029439	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	206	611	0	ENST00000268712.3:c.1591G>C	p.Glu531Gln	p.E531Q	ENST00000268712	NM_006311.3	531	Gaa/Caa	15/46	0.633179137940536	2	FACETS	0.77	0.716	0.826	0.385	0.358	0.413	SUBCLONAL	1	TRUE	0	0.633179137940536	2		611	845	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376230	15376230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1483781735	NA	P-0056082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	169	550	0	ENST00000263377.2:c.784G>A	p.Ala262Thr	p.A262T	ENST00000263377	NM_058243.2	262	Gct/Act	5/20	0.177116924766319	3	FACETS	1	0.935	1	0.339	0.312	0.366	INDETERMINATE	1	TRUE	0	0.633179137940536	3		550	692	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47600690	47600690	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	201	524	0	ENST00000263735.4:c.165T>A	p.Asn55Lys	p.N55K	ENST00000263735	NM_002354.2	55	aaT/aaA	2/9	1	2	FACETS	0.851	0.791	0.913	0.851	0.791	0.913	CLONAL	1	TRUE	1	0.633179137940536	2		524	746	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728691	190728691	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	120	420	0	ENST00000441310.2:c.2079T>A	p.Asn693Lys	p.N693K	ENST00000441310	NM_000534.4	693	aaT/aaA	10/13	1	2	FACETS	0.783	0.711	0.858	0.783	0.711	0.858	SUBCLONAL	1	TRUE	1	0.633179137940536	2		420	484	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947499	38947499	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	131	312	0	ENST00000357387.3:c.4181T>C	p.Leu1394Ser	p.L1394S	ENST00000357387	NM_152756.3	1394	tTa/tCa	32/38	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.633179137940536	2		312	397	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460559	8460559	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	23	491	0	ENST00000356435.5:c.3727A>G	p.Thr1243Ala	p.T1243A	ENST00000356435		1243	Acc/Gcc	22/35	0.633179137940536	1	FACETS	0.138	0.107	0.173	0.138	0.107	0.173	SUBCLONAL	1	TRUE	0	0.633179137940536	1		491	361	SUCCESS
APC	324	MSKCC	GRCh37	5	112174580	112174580	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	68	467	0	ENST00000257430.4:c.3289G>T	p.Glu1097Ter	p.E1097*	ENST00000257430	NM_000038.5	1097	Gaa/Taa	16/16	1	2	FACETS	0.936	0.816	1	0.936	0.816	1	CLONAL	1	TRUE	1	0.279273094292901	2		467	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0056083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	287	801	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	0.267824302063746	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.279273094292901	2		801	1005	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956778	68956778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746227590	NA	P-0056083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	77	667	0	ENST00000288368.4:c.896G>A	p.Arg299Gln	p.R299Q	ENST00000288368	NM_024870.2	299	cGg/cAg	8/40	0.272042625965692	3	FACETS	0.677	0.593	0.768	0.339	0.296	0.384	SUBCLONAL	1	TRUE	1	0.279273094292901	3		667	928	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584461	39584461	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	60	431	0	ENST00000262039.4:c.1126G>A	p.Val376Met	p.V376M	ENST00000262039	NM_002647.2	376	Gtg/Atg	10/25	0.261896151326849	2	FACETS	0.761	0.655	0.875	0.38	0.327	0.438	SUBCLONAL	1	TRUE	0	0.279273094292901	2		431	565	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259343	89259343	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	43	490	0	ENST00000336596.2:c.487A>G	p.Lys163Glu	p.K163E	ENST00000336596	NM_005233.5	163	Aag/Gag	3/17	0.272042625965692	3	FACETS	0.571	0.477	0.675	0.285	0.238	0.338	SUBCLONAL	1	TRUE	1	0.279273094292901	3		490	615	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760199	133760199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	87	621	0	ENST00000318560.5:c.2522C>T	p.Ala841Val	p.A841V	ENST00000318560	NM_005157.4	841	gCc/gTc	11/11	1	2	FACETS	0.781	0.69	0.878	0.781	0.69	0.878	SUBCLONAL	1	TRUE	1	0.279273094292901	2		621	798	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	37	219	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.653	0.543	0.774	0.653	0.543	0.774	SUBCLONAL	1	TRUE	1	0.52719445400953	2		219	215	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	53	436	0	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	1	FACETS	0.425	0.364	0.492	0.425	0.364	0.492	SUBCLONAL	1	TRUE	0	0.52719445400953	1		436	348	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	57	277	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.647	0.558	0.743	0.647	0.558	0.743	SUBCLONAL	1	TRUE	1	0.52719445400953	2		278	334	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	56	782	11	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.212765744556536	2	FACETS	0.372	0.318	0.431	0.186	0.159	0.216	INDETERMINATE	1	TRUE	0	0.52719445400953	2		793	571	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	23	464	0	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.408	0.319	0.509	0.408	0.319	0.509	SUBCLONAL	1	TRUE	1	0.52719445400953	2		464	214	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	79	901	2	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.43	0.378	0.486	0.43	0.378	0.486	SUBCLONAL	1	TRUE	1	0.52719445400953	2		903	697	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	42	700	3	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.3	0.25	0.356	0.3	0.25	0.356	SUBCLONAL	1	TRUE	1	0.52719445400953	2		703	531	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296358	15296358	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	84	928	3	ENST00000263388.2:c.2084del	p.Pro695ArgfsTer165	p.P695Rfs*165	ENST00000263388	NM_000435.2	695	cCg/cg	13/33	1	2	FACETS	0.447	0.394	0.503	0.447	0.394	0.503	SUBCLONAL	1	TRUE	1	0.52719445400953	2		931	713	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	105	523	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.909	0.82	1	0.909	0.82	1	CLONAL	1	TRUE	1	0.52719445400953	2		523	438	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	18	787	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.093	0.07	0.122	0.093	0.07	0.122	SUBCLONAL	1	TRUE	1	0.52719445400953	2		787	731	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	18	321	1	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	0.19	0.143	0.247	0.19	0.143	0.247	SUBCLONAL	1	TRUE	1	0.52719445400953	2		322	359	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937164	39937164	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	118	459	1	ENST00000378444.4:c.19del	p.Leu7CysfsTer9	p.L7Cfs*9	ENST00000378444	NM_001123385.1	7	Ctg/tg	2/15	1	1	FACETS	0.872	0.795	0.952	0.872	0.795	0.952	CLONAL	1	TRUE	0	0.52719445400953	1		460	378	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045000	47045000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556782020	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	221	496	1	ENST00000377604.3:c.2326C>T	p.Arg776Trp	p.R776W	ENST00000377604	NM_001204468.1	776	Cgg/Tgg	20/24	1	1	FACETS	0.762	0.721	0.803	1	0.994	1	SUBCLONAL	2	TRUE	0	0.52719445400953	1		497	405	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	42	847	2	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.34	0.283	0.402	0.34	0.283	0.402	SUBCLONAL	1	TRUE	1	0.52719445400953	2		849	469	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217234	11217234	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1031980569	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	40	620	1	ENST00000361445.4:c.4444C>T	p.Arg1482Cys	p.R1482C	ENST00000361445	NM_004958.3	1482	Cgc/Tgc	30/58	1	2	FACETS	0.26	0.215	0.31	0.26	0.215	0.31	SUBCLONAL	1	TRUE	1	0.52719445400953	2		621	584	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508182	38508184	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs751811710	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	33	610	3	ENST00000254066.5:c.499_501del	p.Lys167del	p.K167del	ENST00000254066	NM_000964.3	164	AAG/-	5/9	1	2	FACETS	0.25	0.203	0.304	0.25	0.203	0.304	SUBCLONAL	1	TRUE	1	0.52719445400953	2		613	500	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925150	81925150	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	32	666	0	ENST00000359376.3:c.941T>C	p.Met314Thr	p.M314T	ENST00000359376	NM_002661.3	314	aTg/aCg	11/33	1	2	FACETS	0.217	0.175	0.264	0.217	0.175	0.264	SUBCLONAL	1	TRUE	1	0.52719445400953	2		666	560	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446270	187446270	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	58	820	5	ENST00000232014.4:c.1418del	p.Pro473ArgfsTer117	p.P473Rfs*117	ENST00000232014	NM_001130845.1	473	cCg/cg	6/10	1	2	FACETS	0.36	0.308	0.415	0.36	0.308	0.415	SUBCLONAL	1	TRUE	1	0.52719445400953	2		825	612	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542110	187542110	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	19	506	1	ENST00000441802.2:c.5630del	p.Pro1877LeufsTer20	p.P1877Lfs*20	ENST00000441802	NM_005245.3	1877	cCt/ct	10/27	1	2	FACETS	0.311	0.236	0.398	0.311	0.236	0.398	SUBCLONAL	1	TRUE	1	0.52719445400953	2		507	232	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233090	69233090	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746910913	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	23	406	2	ENST00000462284.1:c.961del	p.Leu321PhefsTer52	p.L321Ffs*52	ENST00000462284	NM_002392.5	319	Ccc/cc	11/11	1	2	FACETS	0.355	0.277	0.444	0.355	0.277	0.444	SUBCLONAL	1	TRUE	1	0.52719445400953	2		408	246	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231773	36231773	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1569061762	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	69	745	0	ENST00000300305.3:c.611G>A	p.Arg204Gln	p.R204Q	ENST00000300305		204	cGa/cAa	5/8	1	2	FACETS	0.564	0.493	0.641	0.564	0.493	0.641	SUBCLONAL	1	TRUE	1	0.52719445400953	2		745	464	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199945	138199945	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	42	589	2	ENST00000237289.4:c.1368del	p.Pro457LeufsTer20	p.P457Lfs*20	ENST00000237289	NM_001270507.1	455	Ggg/gg	7/9	1	2	FACETS	0.35	0.292	0.414	0.35	0.292	0.414	SUBCLONAL	1	TRUE	1	0.52719445400953	2		591	455	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526126	63526126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854728	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	211	778	1	ENST00000307078.5:c.2500C>T	p.Arg834Trp	p.R834W	ENST00000307078	NM_004655.3	834	Cgg/Tgg	11/11	0.212765744556536	2	FACETS	1	0.983	1	0.583	0.544	0.624	INDETERMINATE	1	TRUE	0	0.52719445400953	2		779	686	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088681	27088682	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	69	872	2	ENST00000324856.7:c.2296dup	p.Gln766ProfsTer51	p.Q766Pfs*51	ENST00000324856	NM_006015.4	764	tcc/tCcc	7/20	1	2	FACETS	0.374	0.325	0.427	0.374	0.325	0.427	SUBCLONAL	1	TRUE	1	0.52719445400953	2		874	700	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748850	41748850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138698106	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	76	886	2	ENST00000301178.4:c.1375G>A	p.Val459Met	p.V459M	ENST00000301178	NM_021913.4	459	Gtg/Atg	11/20	1	2	FACETS	0.372	0.326	0.422	0.372	0.326	0.422	SUBCLONAL	1	TRUE	1	0.52719445400953	2		888	775	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745962	745963	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	22	602	0	ENST00000314574.4:c.559_560del	p.Ser187Ter	p.S187*	ENST00000314574	NM_005433.3	187	AGt/t	5/12	1	2	FACETS	0.464	0.362	0.58	0.464	0.362	0.58	SUBCLONAL	1	TRUE	1	0.52719445400953	2		602	180	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066883	77066883	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	24	370	0	ENST00000356341.3:c.602A>G	p.Tyr201Cys	p.Y201C	ENST00000356341	NM_002576.4	201	tAc/tGc	7/15	1	2	FACETS	0.323	0.253	0.403	0.323	0.253	0.403	SUBCLONAL	1	TRUE	1	0.52719445400953	2		370	282	SUCCESS
ATM	472	MSKCC	GRCh37	11	108225590	108225590	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	26	417	0	ENST00000278616.4:c.8839A>G	p.Thr2947Ala	p.T2947A	ENST00000278616	NM_000051.3	2947	Acc/Gcc	61/63	1	2	FACETS	0.488	0.389	0.6	0.488	0.389	0.6	SUBCLONAL	1	TRUE	1	0.52719445400953	2		417	202	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615765	1615767	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs756376945	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	62	900	0	ENST00000344749.5:c.1504_1506del	p.Lys502del	p.K502del	ENST00000344749	NM_001136139.2	502	AAG/-	17/19	1	2	FACETS	0.318	0.274	0.366	0.318	0.274	0.366	SUBCLONAL	1	TRUE	1	0.52719445400953	2		900	739	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40469200	40469200	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1064794957	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	20	433	0	ENST00000264657.5:c.2144C>T	p.Pro715Leu	p.P715L	ENST00000264657	NM_139276.2	715	cCa/cTa	22/24	1	2	FACETS	0.226	0.172	0.289	0.226	0.172	0.289	SUBCLONAL	1	TRUE	1	0.52719445400953	2		433	336	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118391565	118391565	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	31	429	0	ENST00000534358.1:c.11483del	p.Lys3828ArgfsTer31	p.K3828Rfs*31	ENST00000534358	NM_005933.3	3826	ttA/tt	34/36	1	2	FACETS	0.36	0.291	0.437	0.36	0.291	0.437	SUBCLONAL	1	TRUE	1	0.52719445400953	2		429	327	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	52	707	6	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.31	0.263	0.362	0.31	0.263	0.362	SUBCLONAL	1	TRUE	1	0.52719445400953	2		713	636	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879673	151879673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	38	287	1	ENST00000262189.6:c.5272C>T	p.Arg1758Cys	p.R1758C	ENST00000262189	NM_170606.2	1758	Cgt/Tgt	36/59	1	2	FACETS	0.918	0.771	1	0.918	0.771	1	CLONAL	1	TRUE	1	0.52719445400953	2		288	157	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110566	4110566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397517413	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	42	795	0	ENST00000262948.5:c.391G>A	p.Val131Met	p.V131M	ENST00000262948	NM_030662.3	131	Gtg/Atg	3/11	1	2	FACETS	0.23	0.191	0.274	0.23	0.191	0.274	SUBCLONAL	1	TRUE	1	0.52719445400953	2		795	692	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15975514	15975514	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	71	547	0	ENST00000268712.3:c.3840del	p.Ser1281ValfsTer16	p.S1281Vfs*16	ENST00000268712	NM_006311.3	1280	ggG/gg	29/46	1	2	FACETS	0.955	0.842	1	0.955	0.842	1	CLONAL	1	TRUE	1	0.52719445400953	2		547	282	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621912	1621914	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs748560717	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	180	922	0	ENST00000344749.5:c.878_880del	p.Phe293del	p.F293del	ENST00000344749	NM_001136139.2	293	tTCTcc/tcc	11/19	1	2	FACETS	0.984	0.91	1	0.984	0.91	1	CLONAL	1	TRUE	1	0.52719445400953	2		922	694	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573318	41573318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781609478	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	55	965	0	ENST00000263253.7:c.5603C>T	p.Thr1868Met	p.T1868M	ENST00000263253	NM_001429.3	1868	aCg/aTg	31/31	1	2	FACETS	0.284	0.242	0.33	0.284	0.242	0.33	SUBCLONAL	1	TRUE	1	0.52719445400953	2		965	735	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17350557	17350557	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1045881797	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	25	558	0	ENST00000375499.3:c.553G>A	p.Glu185Lys	p.E185K	ENST00000375499	NM_003000.2	185	Gag/Aag	6/8	1	2	FACETS	0.23	0.18	0.286	0.23	0.18	0.286	SUBCLONAL	1	TRUE	1	0.52719445400953	2		558	413	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56792460	56792460	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	49	601	0	ENST00000308159.5:c.190C>A	p.Leu64Ile	p.L64I	ENST00000308159	NM_014669.4	64	Ctc/Atc	3/22	1	2	FACETS	0.434	0.368	0.507	0.434	0.368	0.507	SUBCLONAL	1	TRUE	1	0.52719445400953	2		601	428	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349910	15349910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200078058	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	166	798	0	ENST00000263377.2:c.3742G>A	p.Ala1248Thr	p.A1248T	ENST00000263377	NM_058243.2	1248	Gct/Act	18/20	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.52719445400953	2		798	621	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911108	29911108	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199474502	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	48	724	0	ENST00000376809.5:c.407G>T	p.Gly136Val	p.G136V	ENST00000376809	NM_002116.7	136	gGg/gTg	3/8	0.0769688137621614	4	FACETS	0.458	0.387	0.537	0.229	0.193	0.269	INDETERMINATE	1	TRUE	2	0.52719445400953	4		724	607	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258709	115258709	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	29	451	0	ENST00000369535.4:c.73C>T	p.Gln25Ter	p.Q25*	ENST00000369535	NM_002524.4	25	Cag/Tag	2/7	1	2	FACETS	0.256	0.205	0.315	0.256	0.205	0.315	SUBCLONAL	1	TRUE	1	0.52719445400953	2		451	429	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729683	162729683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	31	725	1	ENST00000367921.3:c.769G>A	p.Val257Met	p.V257M	ENST00000367921	NM_006182.2	257	Gtg/Atg	8/18	1	2	FACETS	0.205	0.165	0.25	0.205	0.165	0.25	SUBCLONAL	1	TRUE	1	0.52719445400953	2		726	574	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104359217	104359217	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	59	573	0	ENST00000369902.3:c.938G>T	p.Arg313Met	p.R313M	ENST00000369902	NM_016169.3	313	aGg/aTg	8/12	1	2	FACETS	0.446	0.384	0.513	0.446	0.384	0.513	SUBCLONAL	1	TRUE	1	0.52719445400953	2		573	502	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769475	112769475	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	66	500	0	ENST00000369452.4:c.1427T>C	p.Leu476Ser	p.L476S	ENST00000369452	NM_007373.3	476	tTa/tCa	8/9	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.52719445400953	2		500	218	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143477	108143477	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	70	551	0	ENST00000278616.4:c.3182T>G	p.Leu1061Arg	p.L1061R	ENST00000278616	NM_000051.3	1061	cTt/cGt	22/63	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.52719445400953	2		551	219	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256580	133256581	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	40	525	0	ENST00000320574.5:c.382dup	p.Ile128AsnfsTer76	p.I128Nfs*76	ENST00000320574	NM_006231.2	128	att/aAtt	5/49	1	2	FACETS	0.4	0.333	0.475	0.4	0.333	0.475	SUBCLONAL	1	TRUE	1	0.52719445400953	2		525	379	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528128	103528128	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	31	452	0	ENST00000355739.4:c.3436A>G	p.Ser1146Gly	p.S1146G	ENST00000355739	NM_000123.3	1146	Agc/Ggc	15/15	1	2	FACETS	0.307	0.248	0.374	0.307	0.248	0.374	SUBCLONAL	1	TRUE	1	0.52719445400953	2		452	383	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643771	38643771	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	52	855	0	ENST00000299084.4:c.1241T>C	p.Val414Ala	p.V414A	ENST00000299084	NM_152594.2	414	gTa/gCa	7/7	1	2	FACETS	0.299	0.254	0.348	0.299	0.254	0.348	SUBCLONAL	1	TRUE	1	0.52719445400953	2		855	660	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003231	42003231	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	36	676	0	ENST00000219905.7:c.2768T>C	p.Val923Ala	p.V923A	ENST00000219905	NM_001164273.1	923	gTt/gCt	8/24	1	2	FACETS	0.349	0.287	0.419	0.349	0.287	0.419	SUBCLONAL	1	TRUE	1	0.52719445400953	2		676	391	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576237	88576237	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	24	689	0	ENST00000360948.2:c.1436G>A	p.Ser479Asn	p.S479N	ENST00000360948	NM_001012338.2	479	aGc/aAc	13/19	1	2	FACETS	0.193	0.151	0.242	0.193	0.151	0.242	SUBCLONAL	1	TRUE	1	0.52719445400953	2		689	472	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116138	67116138	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	36	514	0	ENST00000412916.2:c.422A>C	p.Gln141Pro	p.Q141P	ENST00000412916		141	cAg/cCg	5/6	1	2	FACETS	0.342	0.281	0.41	0.342	0.281	0.41	SUBCLONAL	1	TRUE	1	0.52719445400953	2		514	399	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934356	81934356	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	47	659	0	ENST00000359376.3:c.1333A>G	p.Ser445Gly	p.S445G	ENST00000359376	NM_002661.3	445	Agc/Ggc	14/33	1	2	FACETS	0.325	0.274	0.381	0.325	0.274	0.381	SUBCLONAL	1	TRUE	1	0.52719445400953	2		659	549	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249247	10249247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	56	660	0	ENST00000340748.4:c.3935G>A	p.Arg1312Gln	p.R1312Q	ENST00000340748		1312	cGg/cAg	34/40	1	2	FACETS	0.385	0.33	0.445	0.385	0.33	0.445	SUBCLONAL	1	TRUE	1	0.52719445400953	2		660	552	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252745	10252745	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	77	832	0	ENST00000340748.4:c.3220G>A	p.Val1074Met	p.V1074M	ENST00000340748		1074	Gtg/Atg	29/40	1	2	FACETS	0.415	0.364	0.47	0.415	0.364	0.47	SUBCLONAL	1	TRUE	1	0.52719445400953	2		832	704	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602698	10602698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145222481	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	219	930	0	ENST00000171111.5:c.880G>A	p.Asp294Asn	p.D294N	ENST00000171111	NM_203500.1	294	Gac/Aac	3/6	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.52719445400953	2		930	754	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136161	11136161	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	35	752	1	ENST00000358026.2:c.3145C>A	p.Pro1049Thr	p.P1049T	ENST00000358026	NM_001128849.1	1049	Ccc/Acc	22/36	1	2	FACETS	0.214	0.174	0.258	0.214	0.174	0.258	SUBCLONAL	1	TRUE	1	0.52719445400953	2		753	621	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152067	11152067	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374722116	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	56	649	0	ENST00000358026.2:c.4351G>A	p.Ala1451Thr	p.A1451T	ENST00000358026	NM_001128849.1	1451	Gcc/Acc	31/36	1	2	FACETS	0.409	0.351	0.473	0.409	0.351	0.473	SUBCLONAL	1	TRUE	1	0.52719445400953	2		649	519	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050900	13050900	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	51	581	0	ENST00000316448.5:c.431T>C	p.Val144Ala	p.V144A	ENST00000316448	NM_004343.3	144	gTt/gCt	4/9	1	2	FACETS	0.343	0.291	0.4	0.343	0.291	0.4	SUBCLONAL	1	TRUE	1	0.52719445400953	2		581	564	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921202	50921202	+	stop_lost	Nonstop_Mutation	SNP	T	T	C	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	57	812	0	ENST00000440232.2:c.3322T>C	p.Ter1108ArgextTer?	p.*1108Rext*?	ENST00000440232	NM_002691.3	1108	Tga/Cga	27/27	1	2	FACETS	0.335	0.287	0.388	0.335	0.287	0.388	SUBCLONAL	1	TRUE	1	0.52719445400953	2		812	645	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027490	48027490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	35	454	0	ENST00000234420.5:c.2368G>A	p.Asp790Asn	p.D790N	ENST00000234420	NM_000179.2	790	Gat/Aat	4/10	1	2	FACETS	0.402	0.33	0.483	0.402	0.33	0.483	SUBCLONAL	1	TRUE	1	0.52719445400953	2		454	330	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371645	225371645	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs772510228	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	53	663	0	ENST00000264414.4:c.959A>G	p.Tyr320Cys	p.Y320C	ENST00000264414	NM_003590.4	320	tAt/tGt	7/16	1	2	FACETS	0.689	0.591	0.794	0.689	0.591	0.794	SUBCLONAL	1	TRUE	1	0.52719445400953	2		663	292	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371705	225371705	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	76	605	0	ENST00000264414.4:c.899A>G	p.Tyr300Cys	p.Y300C	ENST00000264414	NM_003590.4	300	tAc/tGc	7/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.52719445400953	2		605	257	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42861458	42861458	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	145	620	0	ENST00000398585.3:c.412G>A	p.Ala138Thr	p.A138T	ENST00000398585	NM_001135099.1	138	Gcc/Acc	4/14	1	2	FACETS	0.889	0.814	0.967	0.889	0.814	0.967	CLONAL	1	TRUE	1	0.52719445400953	2		620	619	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170011234	170011234	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	46	750	0	ENST00000295797.4:c.1355C>A	p.Pro452Gln	p.P452Q	ENST00000295797	NM_002740.5	452	cCa/cAa	14/18	1	2	FACETS	0.338	0.284	0.397	0.338	0.284	0.397	SUBCLONAL	1	TRUE	1	0.52719445400953	2		750	517	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55991417	55991417	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	74	790	0	ENST00000263923.4:c.44T>C	p.Val15Ala	p.V15A	ENST00000263923	NM_002253.2	15	gTg/gCg	1/30	1	2	FACETS	0.429	0.376	0.487	0.429	0.376	0.487	SUBCLONAL	1	TRUE	1	0.52719445400953	2		790	654	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538284	187538284	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	34	680	1	ENST00000441802.2:c.8950C>A	p.Leu2984Ile	p.L2984I	ENST00000441802	NM_005245.3	2984	Cta/Ata	11/27	1	2	FACETS	0.43	0.352	0.517	0.43	0.352	0.517	SUBCLONAL	1	TRUE	1	0.52719445400953	2		681	300	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178002	56178002	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	40	575	1	ENST00000399503.3:c.2975C>A	p.Ser992Tyr	p.S992Y	ENST00000399503	NM_005921.1	992	tCt/tAt	14/20	1	2	FACETS	0.496	0.414	0.587	0.496	0.414	0.587	SUBCLONAL	1	TRUE	1	0.52719445400953	2		576	306	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517598	176517598	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	66	972	0	ENST00000292408.4:c.299T>C	p.Leu100Pro	p.L100P	ENST00000292408	NM_213647.1	100	cTc/cCc	3/18	1	2	FACETS	0.352	0.305	0.403	0.352	0.305	0.403	SUBCLONAL	1	TRUE	1	0.52719445400953	2		972	712	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322910	31322910	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	80	906	0	ENST00000412585.2:c.986C>A	p.Ala329Asp	p.A329D	ENST00000412585	NM_005514.6	329	gCt/gAt	5/8	0.0769688137621614	4	FACETS	0.62	0.546	0.701	0.31	0.273	0.351	INDETERMINATE	1	TRUE	2	0.52719445400953	4		906	747	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909321	41909321	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	57	507	1	ENST00000372991.4:c.67G>T	p.Gly23Trp	p.G23W	ENST00000372991	NM_001760.3	23	Ggg/Tgg	1/5	0.0769688137621614	4	FACETS	0.648	0.556	0.747	0.324	0.278	0.374	INDETERMINATE	1	TRUE	2	0.52719445400953	4		508	510	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2969704	2969704	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	38	772	1	ENST00000396946.4:c.1575G>T	p.Lys525Asn	p.K525N	ENST00000396946	NM_032415.4	525	aaG/aaT	12/25	1	2	FACETS	0.231	0.19	0.277	0.231	0.19	0.277	SUBCLONAL	1	TRUE	1	0.52719445400953	2		773	624	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835903	151835903	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	25	485	0	ENST00000262189.6:c.14621G>T	p.Arg4874Leu	p.R4874L	ENST00000262189	NM_170606.2	4874	cGg/cTg	58/59	1	2	FACETS	0.234	0.184	0.291	0.234	0.184	0.291	SUBCLONAL	1	TRUE	1	0.52719445400953	2		485	406	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845642	151845642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	131	715	0	ENST00000262189.6:c.13370G>A	p.Gly4457Asp	p.G4457D	ENST00000262189	NM_170606.2	4457	gGc/gAc	52/59	1	2	FACETS	0.986	0.9	1	0.986	0.9	1	CLONAL	1	TRUE	1	0.52719445400953	2		715	504	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38148026	38148026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	71	781	0	ENST00000317025.8:c.3085G>T	p.Gly1029Trp	p.G1029W	ENST00000317025	NM_023034.1	1029	Ggg/Tgg	17/24	1	2	FACETS	0.577	0.505	0.654	0.577	0.505	0.654	SUBCLONAL	1	TRUE	1	0.52719445400953	2		781	467	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409883	63409883	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	40	276	0	ENST00000330258.3:c.3284C>A	p.Pro1095His	p.P1095H	ENST00000330258	NM_152424.3	1095	cCc/cAc	2/2	1	1	FACETS	0.522	0.438	0.614	0.522	0.438	0.614	SUBCLONAL	1	TRUE	0	0.52719445400953	1		276	214	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412835	63412835	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	54	443	0	ENST00000330258.3:c.332G>A	p.Ser111Asn	p.S111N	ENST00000330258	NM_152424.3	111	aGt/aAt	2/2	1	1	FACETS	0.488	0.419	0.562	0.488	0.419	0.562	SUBCLONAL	1	TRUE	0	0.52719445400953	1		443	309	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	91	374	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.695097317208503	2		374	236	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86667971	86667971	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770599456	NA	P-0056086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	88	437	1	ENST00000274376.6:c.1735C>T	p.Arg579Trp	p.R579W	ENST00000274376	NM_002890.2	579	Cgg/Tgg	13/25	1	2	FACETS	0.817	0.731	0.906	0.817	0.731	0.906	CLONAL	1	TRUE	1	0.695097317208503	2		438	310	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913396	NA	P-0056092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	47	268	0	ENST00000349496.5:c.95A>T	p.Asp32Val	p.D32V	ENST00000349496	NM_001904.3	32	gAc/gTc	3/15	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	FALSE	1	0.442884236581802	2		268	187	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0056092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	52	674	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.442884236581802	2		674	179	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254713	46254724	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTGGCAGTCT	CTGTGGCAGTCT	AAATATG	novel	NA	P-0056093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	194	347	0	ENST00000334344.6:c.4903_4914delinsAAATATG	p.Leu1635LysfsTer4	p.L1635Kfs*4	ENST00000334344	NM_152641.2	1635	CTGTGGCAGTCT/AAATATG	16/21	NA	2	FACETS	0.844	0.787	0.902			1	INDETERMINATE	1	FALSE	NA	0.848074966762374	2		347	542	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs1057519842	NA	P-0056094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	16	354	0	ENST00000274335.5:c.1727_1729del	p.Thr576del	p.T576del	ENST00000274335		575	aaGACg/aag	12/15	1	2	FACETS	0.849	0.627	1	0.849	0.627	1	CLONAL	1	TRUE	1	0.13	2		354	290	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692911	89692911	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121909241	NA	P-0056094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	26	544	0	ENST00000371953.3:c.395G>T	p.Gly132Val	p.G132V	ENST00000371953	NM_000314.4	132	gGt/gTt	5/9	1	2	FACETS	0.913	0.722	1	0.913	0.722	1	CLONAL	1	TRUE	1	0.13	2		544	438	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0056094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	26	277	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.13	2		278	359	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821890	72821890	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	37	575	0	ENST00000268489.5:c.10285del	p.Arg3429ValfsTer56	p.R3429Vfs*56	ENST00000268489	NM_006885.3	3429	Cgt/gt	10/10	1	2	FACETS	0.892	0.734	1	0.892	0.734	1	CLONAL	1	TRUE	1	0.13	2		575	638	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413565	32413565	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121907903	NA	P-0056094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	28	556	0	ENST00000332351.3:c.1385G>A	p.Arg462Gln	p.R462Q	ENST00000332351	NM_024426.4	462	cGg/cAg	9/10	1	2	FACETS	0.639	0.509	0.789	0.639	0.509	0.789	SUBCLONAL	1	TRUE	1	0.13	2		556	674	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980007	7980007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147992320	NA	P-0056094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	51	929	3	ENST00000319144.4:c.1330G>A	p.Val444Ile	p.V444I	ENST00000319144	NM_001139.2	444	Gtt/Att	10/15	1	2	FACETS	0.807	0.684	0.944	0.807	0.684	0.944	CLONAL	1	TRUE	1	0.13	2		932	972	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0056094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	51	939	9	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.944	0.8	1	0.944	0.8	1	CLONAL	1	TRUE	1	0.13	2		948	831	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155402	106155403	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0056094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	27	549	0	ENST00000380013.4:c.311_312dup	p.Gly105LeufsTer9	p.G105Lfs*9	ENST00000380013	NM_001127208.2	101	-/TC	3/11	1	2	FACETS	0.836	0.664	1	0.836	0.664	1	CLONAL	1	TRUE	1	0.13	2		549	497	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692932	89692932	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs1085308048	NA	P-0056094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	35	674	0	ENST00000371953.3:c.416T>G	p.Leu139Ter	p.L139*	ENST00000371953	NM_000314.4	139	tTa/tGa	5/9	1	2	FACETS	1	0.828	1	1	0.828	1	CLONAL	1	TRUE	1	0.13	2		674	532	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918593	94918593	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	28	601	0	ENST00000536441.1:c.589C>A	p.Leu197Met	p.L197M	ENST00000536441	NM_144665.3	197	Ctg/Atg	5/10	1	2	FACETS	0.905	0.722	1	0.905	0.722	1	CLONAL	1	TRUE	1	0.13	2		601	476	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829809	72829809	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	52	948	0	ENST00000268489.5:c.6772C>T	p.Gln2258Ter	p.Q2258*	ENST00000268489	NM_006885.3	2258	Cag/Tag	9/10	1	2	FACETS	0.857	0.728	1	0.857	0.728	1	CLONAL	1	TRUE	1	0.13	2		948	933	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389093	31389093	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	33	553	0	ENST00000328111.2:c.2006G>A	p.Gly669Asp	p.G669D	ENST00000328111	NM_006892.3	669	gGc/gAc	19/23	1	2	FACETS	0.878	0.714	1	0.878	0.714	1	CLONAL	1	TRUE	1	0.13	2		553	578	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361154	66361154	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	20	419	0	ENST00000273854.3:c.1018A>G	p.Lys340Glu	p.K340E	ENST00000273854	NM_004439.5	340	Aag/Gag	4/18	1	2	FACETS	0.857	0.655	1	0.857	0.655	1	CLONAL	1	TRUE	1	0.13	2		419	359	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0056095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1182	87	782	11	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.626	0.552	0.705	0.626	0.552	0.705	SUBCLONAL	1	TRUE	1	0.219131902801579	2		793	1269	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0056095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	208	432	2	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.219131902801579	4	FACETS	1	0.961	1	0.785	0.731	0.841	CLONAL	3	TRUE	0	0.219131902801579	4		434	737	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714396	117714396	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	33	387	0	ENST00000368508.3:c.1253C>T	p.Ser418Leu	p.S418L	ENST00000368508	NM_002944.2	418	tCa/tTa	11/43	1	2	FACETS	0.481	0.391	0.584	0.481	0.391	0.584	SUBCLONAL	1	TRUE	1	0.219131902801579	2		387	626	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991141	41991141	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0056095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	65	554	0	ENST00000219905.7:c.2092+2T>C		p.X698_splice	ENST00000219905	NM_001164273.1	698			0.188865080841933	3	FACETS	0.685	0.592	0.786	0.342	0.296	0.393	SUBCLONAL	1	TRUE	1	0.219131902801579	3		554	961	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246532	41246532	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357569	NA	P-0056095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	81	678	2	ENST00000357654.3:c.1016del	p.Lys339ArgfsTer2	p.K339Rfs*2	ENST00000357654	NM_007294.3	339	aAg/ag	10/23	1	2	FACETS	0.818	0.719	0.924	0.818	0.719	0.924	CLONAL	1	TRUE	1	0.219131902801579	2		680	904	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543871	212543871	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1361402584	NA	P-0056095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	49	489	0	ENST00000342788.4:c.1528G>A	p.Asp510Asn	p.D510N	ENST00000342788	NM_005235.2	510	Gat/Aat	13/28	1	2	FACETS	0.608	0.513	0.712	0.608	0.513	0.712	SUBCLONAL	1	TRUE	1	0.219131902801579	2		489	736	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022314	31022314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754774849	NA	P-0056095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	46	545	0	ENST00000375687.4:c.1799C>T	p.Thr600Ile	p.T600I	ENST00000375687	NM_015338.5	600	aCc/aTc	13/13	1	2	FACETS	0.516	0.433	0.609	0.516	0.433	0.609	SUBCLONAL	1	TRUE	1	0.219131902801579	2		545	813	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966020	18966020	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	89	775	2	ENST00000262803.5:c.1513A>G	p.Ile505Val	p.I505V	ENST00000262803	NM_002911.3	505	Atc/Gtc	11/24	1	2	FACETS	0.73	0.645	0.821	0.73	0.645	0.821	SUBCLONAL	1	TRUE	1	0.219131902801579	2		777	1113	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922020	39922020	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	37	330	0	ENST00000378444.4:c.4152C>A	p.Tyr1384Ter	p.Y1384*	ENST00000378444	NM_001123385.1	1384	taC/taA	9/15	1	1	FACETS	0.492	0.405	0.59	0.492	0.405	0.59	SUBCLONAL	1	TRUE	0	0.219131902801579	1		330	611	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182901	123182901	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	40	155	0	ENST00000218089.9:c.866T>C	p.Phe289Ser	p.F289S	ENST00000218089	NM_001042749.1	289	tTt/tCt	10/35	1	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	0	0.219131902801579	1		155	289	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174383	11174383	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057524044	NA	P-0056095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	70	644	0	ENST00000361445.4:c.7292T>C	p.Leu2431Pro	p.L2431P	ENST00000361445	NM_004958.3	2431	cTg/cCg	53/58	0.151859534379765	2	FACETS	0.709	0.617	0.809	0.355	0.308	0.405	SUBCLONAL	1	TRUE	0	0.219131902801579	2		644	901	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097698	27097698	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	98	593	0	ENST00000324856.7:c.3287A>G	p.Tyr1096Cys	p.Y1096C	ENST00000324856	NM_006015.4	1096	tAt/tGt	12/20	0.151859534379765	2	FACETS	0.994	0.885	1	0.497	0.442	0.555	CLONAL	1	TRUE	0	0.219131902801579	2		593	900	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65316510	65316510	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	59	489	0	ENST00000342505.4:c.1732A>G	p.Ile578Val	p.I578V	ENST00000342505	NM_002227.2	578	Atc/Gtc	12/25	0.151859534379765	2	FACETS	0.747	0.642	0.862	0.373	0.321	0.431	SUBCLONAL	1	TRUE	0	0.219131902801579	2		489	721	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506384	120506385	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0056095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	115	511	1	ENST00000256646.2:c.1727_1728delinsTT	p.Pro576Leu	p.P576L	ENST00000256646	NM_024408.3	576	cCC/cTT	11/34	0.219131902801579	3	FACETS	1	0.978	1	0.665	0.598	0.735	CLONAL	1	TRUE	1	0.219131902801579	3		512	876	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466040	69466040	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	81	860	0	ENST00000227507.2:c.878T>C	p.Val293Ala	p.V293A	ENST00000227507	NM_053056.2	293	gTg/gCg	5/5	1	2	FACETS	0.623	0.547	0.706	0.623	0.547	0.706	SUBCLONAL	1	TRUE	1	0.219131902801579	2		860	1186	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948737	71948737	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	104	1026	1	ENST00000298229.2:c.3449T>C	p.Leu1150Pro	p.L1150P	ENST00000298229	NM_001567.3	1150	cTg/cCg	26/28	1	2	FACETS	0.712	0.635	0.794	0.712	0.635	0.794	SUBCLONAL	1	TRUE	1	0.219131902801579	2		1027	1334	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420576	49420576	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1152	101	924	1	ENST00000301067.7:c.15173T>C	p.Val5058Ala	p.V5058A	ENST00000301067	NM_003482.3	5058	gTg/gCg	48/54	1	2	FACETS	0.736	0.655	0.822	0.736	0.655	0.822	SUBCLONAL	1	TRUE	1	0.219131902801579	2		925	1253	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058379	42058379	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	51	445	0	ENST00000219905.7:c.8099G>A	p.Arg2700Lys	p.R2700K	ENST00000219905	NM_001164273.1	2700	aGa/aAa	24/24	0.188865080841933	3	FACETS	0.721	0.612	0.842	0.361	0.306	0.421	SUBCLONAL	1	TRUE	1	0.219131902801579	3		445	716	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655485	67655485	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	63	463	0	ENST00000264010.4:c.1348A>G	p.Ser450Gly	p.S450G	ENST00000264010	NM_006565.3	450	Agt/Ggt	7/12	1	2	FACETS	0.79	0.682	0.907	0.79	0.682	0.907	CLONAL	1	TRUE	1	0.219131902801579	2		463	728	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993821	72993821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	94	745	2	ENST00000268489.5:c.224C>T	p.Ala75Val	p.A75V	ENST00000268489	NM_006885.3	75	gCc/gTc	2/10	1	2	FACETS	0.856	0.76	0.959	0.856	0.76	0.959	CLONAL	1	TRUE	1	0.219131902801579	2		747	1002	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375160	31375160	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1213	101	955	0	ENST00000328111.2:c.561del	p.Tyr188ThrfsTer4	p.Y188Tfs*4	ENST00000328111	NM_006892.3	186	aCc/ac	6/23	1	2	FACETS	0.702	0.625	0.784	0.702	0.625	0.784	SUBCLONAL	1	TRUE	1	0.219131902801579	2		955	1314	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090425	37090426	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	53	505	0	ENST00000231790.2:c.2023dup	p.Ser675LysfsTer4	p.S675Kfs*4	ENST00000231790	NM_000249.3	674	gaa/gAaa	18/19	0.152845073249652	1	FACETS	0.596	0.507	0.693	0.596	0.507	0.693	SUBCLONAL	1	TRUE	0	0.219131902801579	1		505	723	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584491	189584491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866404340	NA	P-0056095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	101	399	0	ENST00000264731.3:c.787C>T	p.His263Tyr	p.H263Y	ENST00000264731	NM_003722.4	263	Cat/Tat	6/14	0.188865080841933	3	FACETS	0.809	0.724	0.899	0.809	0.724	0.899	CLONAL	2	TRUE	1	0.219131902801579	3		399	632	SUCCESS
APC	324	MSKCC	GRCh37	5	112174016	112174016	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs878853430	NA	P-0056095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	45	411	0	ENST00000257430.4:c.2725A>G	p.Thr909Ala	p.T909A	ENST00000257430	NM_000038.5	909	Acc/Gcc	16/16	1	2	FACETS	0.654	0.549	0.771	0.654	0.549	0.771	SUBCLONAL	1	TRUE	1	0.219131902801579	2		411	628	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835899	151835899	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	49	397	0	ENST00000262189.6:c.14625A>C	p.Arg4875Ser	p.R4875S	ENST00000262189	NM_170606.2	4875	agA/agC	58/59	0.219131902801579	4	FACETS	0.695	0.587	0.815	0.174	0.146	0.204	SUBCLONAL	1	TRUE	0	0.219131902801579	4		397	784	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38153472	38153472	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0056095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	52	444	0	ENST00000317025.8:c.2759-2A>G		p.X920_splice	ENST00000317025	NM_023034.1	920			1	2	FACETS	0.688	0.585	0.802	0.688	0.585	0.802	SUBCLONAL	1	TRUE	1	0.219131902801579	2		444	690	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058557	69058557	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	77	610	1	ENST00000288368.4:c.4203del	p.Phe1401LeufsTer12	p.F1401Lfs*12	ENST00000288368	NM_024870.2	1401	Ttt/tt	34/40	1	2	FACETS	0.789	0.691	0.894	0.789	0.691	0.894	SUBCLONAL	1	TRUE	1	0.219131902801579	2		611	891	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0056096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	234	215	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.474609914653604	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.474609914653604	3		215	598	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857770	78857770	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	175	675	2	ENST00000306801.3:c.1840G>A	p.Glu614Lys	p.E614K	ENST00000306801	NM_020761.2	614	Gag/Aag	16/34	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.474609914653604	2		677	673	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652296	36652296	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775743777	NA	P-0056096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	189	632	1	ENST00000244741.5:c.418C>T	p.Arg140Ter	p.R140*	ENST00000244741	NM_000389.4	140	Cga/Tga	2/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.474609914653604	2		633	717	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0056098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	37	159	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.871	0.719	1	0.871	0.719	1	CLONAL	1	TRUE	1	0.217220963492606	2		159	391	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0056098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	120	336	0	ENST00000374690.3:c.2105T>A	p.Leu702His	p.L702H	ENST00000374690	NM_000044.3	702	cTc/cAc	4/8	0.083686748651052	2	FACETS	0.772	0.697	0.85			1	INDETERMINATE	2	TRUE	NA	0.217220963492606	2		336	716	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916957	178916957	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200018596	NA	P-0056098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	51	324	0	ENST00000263967.3:c.344G>T	p.Arg115Leu	p.R115L	ENST00000263967	NM_006218.2	115	cGa/cTa	2/21	1	2	FACETS	0.756	0.642	0.882	0.756	0.642	0.882	SUBCLONAL	1	TRUE	1	0.217220963492606	2		324	621	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625374	69625374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782226740	NA	P-0056098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1282	100	870	0	ENST00000334134.2:c.419C>T	p.Thr140Met	p.T140M	ENST00000334134	NM_005247.2	140	aCg/aTg	3/3	1	2	FACETS	0.666	0.593	0.745	0.666	0.593	0.745	SUBCLONAL	1	TRUE	1	0.217220963492606	2		870	1382	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544646	65544646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	97	585	0	ENST00000358664.4:c.280C>T	p.Leu94Phe	p.L94F	ENST00000358664	NM_002382.4	94	Ctt/Ttt	4/5	0.217220963492606	1	FACETS	0.752	0.669	0.842	0.752	0.669	0.842	SUBCLONAL	1	TRUE	0	0.217220963492606	1		585	1058	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253784	153253785	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0056098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	65	311	0	ENST00000281708.4:c.948dup	p.Asp317ArgfsTer15	p.D317Rfs*15	ENST00000281708	NM_033632.3	316	-/A	6/12	1	2	FACETS	0.811	0.702	0.929	0.811	0.702	0.929	CLONAL	1	TRUE	1	0.217220963492606	2		311	738	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456961	149456961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200702302	NA	P-0056098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	91	497	1	ENST00000286301.3:c.767G>A	p.Arg256His	p.R256H	ENST00000286301	NM_005211.3	256	cGt/cAt	6/22	1	2	FACETS	0.858	0.761	0.963	0.858	0.761	0.963	CLONAL	1	TRUE	1	0.217220963492606	2		498	976	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	111	374	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.859	0.791	0.927			1	INDETERMINATE	3	TRUE	NA	0.393428157064488	2		374	219	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174458	11174458	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	210	689	0	ENST00000361445.4:c.7217T>G	p.Val2406Gly	p.V2406G	ENST00000361445	NM_004958.3	2406	gTg/gGg	53/58	0.154252155604538	2	FACETS	0.972	0.91	1	0.972	0.91	1	INDETERMINATE	2	TRUE	0	0.393428157064488	2		689	549	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11194430	11194430	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	147	625	0	ENST00000361445.4:c.5224G>A	p.Glu1742Lys	p.E1742K	ENST00000361445	NM_004958.3	1742	Gaa/Aaa	37/58	0.154252155604538	2	FACETS	0.827	0.761	0.894	0.827	0.761	0.894	INDETERMINATE	2	TRUE	0	0.393428157064488	2		625	452	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272521	11272521	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	103	455	0	ENST00000361445.4:c.3409G>C	p.Glu1137Gln	p.E1137Q	ENST00000361445	NM_004958.3	1137	Gag/Cag	23/58	0.154252155604538	2	FACETS	0.816	0.738	0.895	0.816	0.738	0.895	INDETERMINATE	2	TRUE	0	0.393428157064488	2		455	321	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726673	46726673	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	86	553	0	ENST00000371975.4:c.752T>C	p.Ile251Thr	p.I251T	ENST00000371975	NM_003579.3	251	aTa/aCa	7/18	0.154252155604538	2	FACETS	1	0.94	1	0.542	0.483	0.606	INDETERMINATE	1	TRUE	0	0.393428157064488	2		553	403	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280645	115280645	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	201	558	0	ENST00000438362.2:c.386T>A	p.Ile129Asn	p.I129N	ENST00000438362	NM_001242891.1	129	aTt/aAt	4/20	0.154252155604538	2	FACETS	0.921	0.86	0.983	0.921	0.86	0.983	INDETERMINATE	2	TRUE	0	0.393428157064488	2		558	555	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682973	241682973	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	58	630	0	ENST00000366560.3:c.50C>G	p.Ala17Gly	p.A17G	ENST00000366560	NM_000143.3	17	gCt/gGt	1/10	0.393428157064488	8	FACETS	1	0.9	1			1	CLONAL	1	TRUE	NA	0.393428157064488	8		630	606	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809248	243809248	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	75	499	0	ENST00000263826.5:c.376G>C	p.Asp126His	p.D126H	ENST00000263826	NM_005465.4	126	Gat/Cat	4/13	0.393428157064488	8	FACETS	0.788	0.688	0.896			1	SUBCLONAL	1	TRUE	NA	0.393428157064488	8		499	1055	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63760018	63760018	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	104	481	0	ENST00000279873.7:c.671A>C	p.Tyr224Ser	p.Y224S	ENST00000279873	NM_032199.2	224	tAc/tCc	4/10	0.196278109327608	3	FACETS	0.801	0.723	0.882			1	INDETERMINATE	2	TRUE	NA	0.393428157064488	3		481	395	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413560	32413560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28941778	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	113	542	1	ENST00000332351.3:c.1390G>A	p.Asp464Asn	p.D464N	ENST00000332351	NM_024426.4	464	Gac/Aac	9/10	0.393428157064488	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.393428157064488	1		543	333	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589639	69589639	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	233	220	0	ENST00000168712.1:c.214G>T	p.Gly72Cys	p.G72C	ENST00000168712	NM_002007.2	72	Ggc/Tgc	1/3	0.393428157064488	5	FACETS	0.918	0.877	0.958	1	0.994	1	CLONAL	6	TRUE	1	0.393428157064488	5		220	342	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942102	71942102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	93	904	1	ENST00000298229.2:c.1366G>A	p.Asp456Asn	p.D456N	ENST00000298229	NM_001567.3	456	Gac/Aac	12/28	0.393428157064488	5	FACETS	0.937	0.833	1	0.234	0.208	0.263	CLONAL	1	TRUE	1	0.393428157064488	5		905	802	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285666	46285666	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	126	446	0	ENST00000334344.6:c.5026C>T	p.Gln1676Ter	p.Q1676*	ENST00000334344	NM_152641.2	1676	Cag/Tag	17/21	0.156349972265296	4	FACETS	1	0.97	1	0.755	0.69	0.822	INDETERMINATE	2	TRUE	1	0.393428157064488	4		446	394	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446428	49446428	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	116	792	0	ENST00000301067.7:c.1177C>T	p.Gln393Ter	p.Q393*	ENST00000301067	NM_003482.3	393	Caa/Taa	9/54	0.156349972265296	4	FACETS	0.913	0.828	1	0.609	0.552	0.668	INDETERMINATE	2	TRUE	1	0.393428157064488	4		792	450	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490577	56490577	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	122	528	0	ENST00000267101.3:c.2221A>G	p.Ile741Val	p.I741V	ENST00000267101	NM_001982.3	741	Att/Gtt	19/28	0.156349972265296	4	FACETS	1	0.968	1	0.752	0.687	0.82	INDETERMINATE	2	TRUE	1	0.393428157064488	4		528	383	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623541	28623541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	93	472	0	ENST00000241453.7:c.1016C>T	p.Ser339Leu	p.S339L	ENST00000241453	NM_004119.2	339	tCa/tTa	8/24	0.393428157064488	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.393428157064488	1		472	296	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434530	110434530	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	104	595	0	ENST00000375856.3:c.3871G>C	p.Gly1291Arg	p.G1291R	ENST00000375856	NM_003749.2	1291	Ggg/Cgg	1/2	0.24643173195466	2	FACETS	0.905	0.822	0.991	0.905	0.822	0.991	CLONAL	2	TRUE	0	0.393428157064488	2		595	292	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628303	90628303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	77	1001	3	ENST00000330062.3:c.1108G>A	p.Ala370Thr	p.A370T	ENST00000330062	NM_002168.2	370	Gcc/Acc	9/11	1	2	FACETS	0.882	0.777	0.993	0.882	0.777	0.993	CLONAL	1	TRUE	1	0.393428157064488	2		1004	444	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459257	99459257	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	103	791	1	ENST00000268035.6:c.1893G>A	p.Trp631Ter	p.W631*	ENST00000268035	NM_000875.3	631	tgG/tgA	9/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.393428157064488	2		792	383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	112	732	1	ENST00000269305.4:c.580C>A	p.Leu194Ile	p.L194I	ENST00000269305	NM_001126112.2	194	Ctt/Att	6/11	0.393428157064488	1	FACETS	0.757	0.691	0.825	1	0.986	1	SUBCLONAL	2	TRUE	0	0.393428157064488	1		733	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	110	654	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.393428157064488	1	FACETS	0.756	0.689	0.825	1	0.986	1	SUBCLONAL	2	TRUE	0	0.393428157064488	1		654	297	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004811	16004811	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	192	715	0	ENST00000268712.3:c.2443C>A	p.Pro815Thr	p.P815T	ENST00000268712	NM_006311.3	815	Ccc/Acc	20/46	0.393428157064488	1	FACETS	0.918	0.86	0.977	1	0.994	1	CLONAL	2	TRUE	0	0.393428157064488	1		715	427	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068436	16068436	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs754924127	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	22	86	0	ENST00000268712.3:c.475C>G	p.Pro159Ala	p.P159A	ENST00000268712	NM_006311.3	159	Cca/Gca	5/46	0.393428157064488	1	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	0	0.393428157064488	1		86	81	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701088	29701088	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	160	503	0	ENST00000356175.3:c.8372G>A	p.Arg2791Gln	p.R2791Q	ENST00000356175	NM_000267.3	2791	cGa/cAa	57/57	1	2	FACETS	0.926	0.858	0.996	1	0.992	1	CLONAL	2	TRUE	1	0.393428157064488	2		503	439	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492817	56492817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	92	646	0	ENST00000407977.2:c.122C>T	p.Ser41Leu	p.S41L	ENST00000407977		41	tCa/tTa	2/10	1	2	FACETS	0.939	0.838	1	0.939	0.838	1	CLONAL	1	TRUE	1	0.393428157064488	2		646	498	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732409	74732409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326283685	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	152	566	2	ENST00000359995.5:c.500G>A	p.Arg167Gln	p.R167Q	ENST00000359995	NM_001195427.1	167	cGa/cAa	2/3	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.393428157064488	2		568	551	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097122	11097122	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	97	1059	0	ENST00000358026.2:c.613C>T	p.Gln205Ter	p.Q205*	ENST00000358026	NM_001128849.1	205	Cag/Tag	4/36	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.393428157064488	2		1059	417	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129655	11129655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	149	809	1	ENST00000358026.2:c.2461G>A	p.Glu821Lys	p.E821K	ENST00000358026	NM_001128849.1	821	Gag/Aag	17/36	1	2	FACETS	0.791	0.728	0.855	1	0.989	1	SUBCLONAL	2	TRUE	1	0.393428157064488	2		810	479	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860619	45860619	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	350	978	0	ENST00000391945.4:c.1388C>A	p.Pro463Gln	p.P463Q	ENST00000391945	NM_000400.3	463	cCg/cAg	15/23	0.393428157064488	5	FACETS	0.982	0.938	1	1	0.994	1	CLONAL	4	TRUE	2	0.393428157064488	5		978	720	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920329	50920329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763951036	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	142	1074	0	ENST00000440232.2:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000440232	NM_002691.3	1032	cGg/cAg	25/27	NA	2	FACETS	0.778	0.714	0.843			1	INDETERMINATE	2	TRUE	NA	0.393428157064488	2		1074	464	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241979	39241979	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	110	305	0	ENST00000402219.2:c.1867T>A	p.Phe623Ile	p.F623I	ENST00000402219	NM_005633.3	623	Ttt/Att	11/23	0.154252155604538	2	FACETS	0.827	0.752	0.905	0.827	0.752	0.905	INDETERMINATE	2	TRUE	0	0.393428157064488	2		305	338	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400264	225400264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	44	232	0	ENST00000264414.4:c.359G>A	p.Arg120Lys	p.R120K	ENST00000264414	NM_003590.4	120	aGa/aAa	3/16	0.393428157064488	1	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	0	0.393428157064488	1		232	174	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206728	36206728	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	65	824	1	ENST00000300305.3:c.784C>T	p.Gln262Ter	p.Q262*	ENST00000300305		262	Cag/Tag	6/8	1	2	FACETS	0.739	0.643	0.843	0.739	0.643	0.843	SUBCLONAL	1	TRUE	1	0.393428157064488	2		825	447	SUCCESS
ATR	545	MSKCC	GRCh37	3	142222243	142222243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	119	388	0	ENST00000350721.4:c.5249C>T	p.Ser1750Phe	p.S1750F	ENST00000350721	NM_001184.3	1750	tCt/tTt	30/47	NA	2	FACETS	0.772	0.703	0.843			1	INDETERMINATE	2	TRUE	NA	0.393428157064488	2		388	392	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374909	149374909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	75	667	0	ENST00000360632.3:c.185C>T	p.Ser62Leu	p.S62L	ENST00000360632	NM_015472.4	62	tCg/tTg	2/7	0.346014449395767	3	FACETS	1	0.916	1	0.526	0.462	0.593	CLONAL	1	TRUE	1	0.393428157064488	3		667	434	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675202	30675202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	45	616	0	ENST00000376406.3:c.3043G>A	p.Glu1015Lys	p.E1015K	ENST00000376406	NM_014641.2	1015	Gag/Aag	9/15	0.173322457969578	3	FACETS	0.567	0.476	0.667	0.189	0.158	0.223	INDETERMINATE	1	TRUE	0	0.393428157064488	3		616	483	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164162	32164162	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	185	746	0	ENST00000375023.3:c.5237A>G	p.Asn1746Ser	p.N1746S	ENST00000375023	NM_004557.3	1746	aAc/aGc	29/30	0.173322457969578	3	FACETS	1	0.976	1	0.737	0.686	0.789	INDETERMINATE	2	TRUE	0	0.393428157064488	3		746	509	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017596	112017596	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	115	561	0	ENST00000368678.4:c.917A>G	p.Glu306Gly	p.E306G	ENST00000368678		306	gAa/gGa	9/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.393428157064488	2		561	447	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157520015	157520015	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	127	691	0	ENST00000346085.5:c.4084C>T	p.Gln1362Ter	p.Q1362*	ENST00000346085	NM_020732.3	1362	Cag/Tag	17/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.393428157064488	2		691	471	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524663	106524663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	86	317	0	ENST00000359195.3:c.2824C>T	p.Leu942Phe	p.L942F	ENST00000359195	NM_002649.2	942	Ctt/Ttt	9/11	0.24643173195466	2	FACETS	0.892	0.802	0.985	0.892	0.802	0.985	CLONAL	2	TRUE	0	0.393428157064488	2		317	245	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002719	37002719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757277825	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	76	727	0	ENST00000358127.4:c.530C>T	p.Ser177Leu	p.S177L	ENST00000358127	NM_001280556.1	177	tCg/tTg	5/10	0.393428157064488	0	FACETS	0.721	0.638	0.809			1	SUBCLONAL	1	TRUE	0	0.393428157064488	0		727	325	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933101	39933101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	62	435	0	ENST00000378444.4:c.1498G>A	p.Glu500Lys	p.E500K	ENST00000378444	NM_001123385.1	500	Gaa/Aaa	4/15	0.150973883627583	2	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.393428157064488	2		435	228	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833949	44833949	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	157	253	0	ENST00000377967.4:c.373G>A	p.Asp125Asn	p.D125N	ENST00000377967	NM_021140.2	125	Gac/Aac	4/29	0.150973883627583	2	FACETS	0.921	0.861	0.979			1	INDETERMINATE	3	TRUE	NA	0.393428157064488	2		253	289	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339663	70339663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	170	374	0	ENST00000374080.3:c.332G>A	p.Ser111Asn	p.S111N	ENST00000374080		111	aGt/aAt	3/45	0.235459895925394	2	FACETS	0.865	0.81	0.92			1	INDETERMINATE	3	TRUE	NA	0.393428157064488	2		374	333	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164909	123164909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	65	204	0	ENST00000218089.9:c.222C>A	p.His74Gln	p.H74Q	ENST00000218089	NM_001042749.1	74	caC/caA	5/35	0.393428157064488	0	FACETS	0.737	0.659	0.815			1	SUBCLONAL	2	TRUE	NA	0.393428157064488	0		204	136	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191479	10191479	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1559429613	NA	P-0056100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	240	492	0	ENST00000256474.2:c.472C>G	p.Leu158Val	p.L158V	ENST00000256474	NM_000551.3	158	Ctg/Gtg	3/3	0.605824244627264	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.605824244627264	1		492	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0056100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	283	708	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.605824244627264	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.605824244627264	1		708	497	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692902	89692902	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	253	529	0	ENST00000371953.3:c.386G>T	p.Gly129Val	p.G129V	ENST00000371953	NM_000314.4	129	gGa/gTa	5/9	0.605824244627264	2	FACETS	0.967	0.92	1	0.967	0.92	1	CLONAL	2	TRUE	0	0.605824244627264	2		529	432	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059122	47059132	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGTACCTTGC	GAGTACCTTGC	-	novel	NA	P-0056100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	159	492	0	ENST00000409792.3:c.7529_7533+6del		p.X2510_splice	ENST00000409792	NM_014159.6	2510		20/21	0.605824244627264	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.605824244627264	1		492	366	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589817	55589817	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	132	454	0	ENST00000288135.5:c.1299C>A	p.Phe433Leu	p.F433L	ENST00000288135	NM_000222.2	433	ttC/ttA	8/21	1	2	FACETS	0.958	0.876	1	0.958	0.876	1	CLONAL	1	TRUE	1	0.605824244627264	2		454	455	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193846	106193863	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGAAAAAACGGAGTGG	GGAGAAAAAACGGAGTGG	A	novel	NA	P-0056100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	108	413	0	ENST00000380013.4:c.4308_4325delinsA	p.Glu1437CysfsTer35	p.E1437Cfs*35	ENST00000380013	NM_001127208.2	1436	gaGGAGAAAAAACGGAGTGGt/gaAt	10/11	1	2	FACETS	0.839	0.758	0.923	0.839	0.758	0.923	CLONAL	1	TRUE	1	0.605824244627264	2		413	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577066	7577066	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	823	689	0	ENST00000269305.4:c.872del	p.Lys291ArgfsTer54	p.K291Rfs*54	ENST00000269305	NM_001126112.2	291	aAg/ag	8/11	0.782622750561131	2	FACETS	0.989	0.972	1	0.989	0.972	1	CLONAL	2	FALSE	0	0.847120104231654	2		689	982	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618875	37618875	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	302	523	0	ENST00000447079.4:c.552del	p.Arg185GlyfsTer6	p.R185Gfs*6	ENST00000447079	NM_015083.1	184	aCc/ac	1/14	0.847120104231654	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	0	0.847120104231654	1		523	386	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535385	66535385	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	215	443	0	ENST00000273854.3:c.76G>T	p.Ala26Ser	p.A26S	ENST00000273854	NM_004439.5	26	Gcg/Tcg	1/18	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.847120104231654	2		443	460	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86648993	86648993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	80	278	0	ENST00000274376.6:c.1273C>T	p.His425Tyr	p.H425Y	ENST00000274376	NM_002890.2	425	Cac/Tac	9/25	1	2	FACETS	0.855	0.766	0.946	0.855	0.766	0.946	CLONAL	1	FALSE	1	0.847120104231654	2		278	221	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138321	2138321	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45517414	NA	P-0056103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	188	907	0	ENST00000219476.3:c.5254C>T	p.Gln1752Ter	p.Q1752*	ENST00000219476	NM_000548.3	1752	Cag/Tag	41/42	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.511692483699884	2		907	718	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641143	117641143	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	116	706	0	ENST00000368508.3:c.5828A>G	p.Glu1943Gly	p.E1943G	ENST00000368508	NM_002944.2	1943	gAa/gGa	36/43	0.511692483699884	3	FACETS	0.562	0.506	0.622			1	SUBCLONAL	1	TRUE	NA	0.511692483699884	3		706	1013	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0056104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	211	574	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.6402237185639	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.6402237185639	1		574	443	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0056104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	174	362	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.6402237185639	2		362	484	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814930	139814930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371121908	NA	P-0056104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	108	636	1	ENST00000247668.2:c.923G>A	p.Arg308Gln	p.R308Q	ENST00000247668	NM_021138.3	308	cGg/cAg	8/11	0.401096679618068	1	FACETS	0.425	0.382	0.469	0.425	0.382	0.469	SUBCLONAL	1	TRUE	0	0.6402237185639	1		637	540	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061317	38061317	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	286	663	0	ENST00000250448.2:c.672C>A	p.Phe224Leu	p.F224L	ENST00000250448	NM_004496.3	224	ttC/ttA	2/2	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.6402237185639	2		663	693	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680598	241680598	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	112	335	0	ENST00000366560.3:c.151C>G	p.Arg51Gly	p.R51G	ENST00000366560	NM_000143.3	51	Cgg/Ggg	2/10	NA	2	FACETS	1	0.914	1			1	INDETERMINATE	1	TRUE	NA	0.6402237185639	2		335	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0056105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	365	847	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.509368666641618	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.541516374112965	1		847	973	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103513879	103513879	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	114	294	0	ENST00000355739.4:c.695A>T	p.Tyr232Phe	p.Y232F	ENST00000355739	NM_000123.3	232	tAc/tTc	7/15	1	2	FACETS	0.804	0.727	0.884	0.804	0.727	0.884	CLONAL	1	TRUE	1	0.541516374112965	2		294	524	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682443	37682443	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	218	464	0	ENST00000447079.4:c.3634G>C	p.Val1212Leu	p.V1212L	ENST00000447079	NM_015083.1	1212	Gtt/Ctt	13/14	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.541516374112965	2		464	748	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244669	41244669	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	252	659	0	ENST00000357654.3:c.2879del	p.Gly960AlafsTer40	p.G960Afs*40	ENST00000357654	NM_007294.3	960	gGc/gc	10/23	1	2	FACETS	0.947	0.887	1	0.947	0.887	1	CLONAL	1	TRUE	1	0.541516374112965	2		659	983	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681752	78681763	+	inframe_deletion	In_Frame_Del	DEL	GGGGTGCCCCGG	GGGGTGCCCCGG	-	novel	NA	P-0056105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	270	692	0	ENST00000306801.3:c.460_471del	p.Gly154_Arg157del	p.G154_R157del	ENST00000306801	NM_020761.2	154	GGGGTGCCCCGG/-	4/34	1	2	FACETS	0.992	0.932	1	0.992	0.932	1	CLONAL	1	TRUE	1	0.541516374112965	2		692	1005	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182630	99182630	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	144	473	0	ENST00000074304.5:c.2433G>T	p.Glu811Asp	p.E811D	ENST00000074304	NM_001134224.1	811	gaG/gaT	22/26	1	2	FACETS	0.852	0.78	0.928	0.852	0.78	0.928	CLONAL	1	TRUE	1	0.541516374112965	2		473	624	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46255846	46255846	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	149	364	0	ENST00000371998.3:c.458T>C	p.Val153Ala	p.V153A	ENST00000371998		153	gTt/gCt	6/23	1	2	FACETS	0.917	0.841	0.996	0.917	0.841	0.996	CLONAL	1	TRUE	1	0.541516374112965	2		364	600	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527299	157527299	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0056105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	109	266	0	ENST00000346085.5:c.5026-2A>T		p.X1676_splice	ENST00000346085	NM_020732.3	1676			0.541516374112965	1	FACETS	0.866	0.786	0.948	0.866	0.786	0.948	CLONAL	1	TRUE	0	0.541516374112965	1		266	339	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0056106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	19	383	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.238839169231002	2	FACETS	1	0.833	1	0.537	0.421	0.664	INDETERMINATE	1	TRUE	0	0.561122822965572	2		383	63	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0056106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	175	840	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.531264841466057	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	0	0.561122822965572	2		843	311	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250996	10250996	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs776723837	NA	P-0056106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	10	650	0	ENST00000340748.4:c.3484G>C	p.Asp1162His	p.D1162H	ENST00000340748		1162	Gac/Cac	32/40	0.527450108317013	2	FACETS	0.211	0.143	0.296	0.105	0.071	0.148	SUBCLONAL	1	TRUE	0	0.561122822965572	2		650	169	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6045628	6045628	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs573374779	NA	P-0056106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	13	142	0	ENST00000265849.7:c.58C>G	p.Arg20Gly	p.R20G	ENST00000265849	NM_000535.5	20	Cgg/Ggg	2/15	0.462618731060236	1	FACETS	0.877	0.656	1	0.877	0.656	1	CLONAL	1	TRUE	0	0.561122822965572	1		142	38	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248544	8248544	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	109	593	0	ENST00000335790.3:c.343G>T	p.Ala115Ser	p.A115S	ENST00000335790	NM_002315.2	115	Gcc/Tcc	3/4	0.263208185436449	2	FACETS	0.639	0.574	0.709	0.32	0.287	0.355	SUBCLONAL	1	TRUE	0	0.417955381484586	2		593	816	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934038	49934038	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	55	671	0	ENST00000296474.3:c.2374C>G	p.His792Asp	p.H792D	ENST00000296474	NM_002447.2	792	Cat/Gat	9/20	0.392834200318504	1	FACETS	0.309	0.264	0.359	0.309	0.264	0.359	SUBCLONAL	1	TRUE	0	0.417955381484586	1		671	674	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0056109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	383	1199	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.74532701296727	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.74532701296727	1		1199	623	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0056109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	490	315	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.74532701296727	3	FACETS	0.986	0.95	1	0.986	0.95	1	CLONAL	2	TRUE	1	0.74532701296727	3		315	915	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563311	21563311	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs77919685	NA	P-0056127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	558	1124	0	ENST00000382592.4:c.608C>T	p.Ala203Val	p.A203V	ENST00000382592	NM_014572.2	203	gCg/gTg	4/8	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.807630178299924	2		1124	1292	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	287	387	0	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	0.40402019338204	1	FACETS	0.727	0.69	0.763	0.727	0.69	0.763	INDETERMINATE	1	TRUE	0	0.807630178299924	1		387	583	SUCCESS
APC	324	MSKCC	GRCh37	5	112175524	112175524	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	92	440	0	ENST00000257430.4:c.4233del	p.Ser1411ArgfsTer4	p.S1411Rfs*4	ENST00000257430	NM_000038.5	1411	agT/ag	16/16	0.43078572086921	1	FACETS	0.353	0.315	0.392	0.353	0.315	0.392	INDETERMINATE	1	TRUE	0	0.807630178299924	1		440	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578528	7578528	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	642	1059	0	ENST00000269305.4:c.402T>A	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	ttT/ttA	5/11	0.807630178299924	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.807630178299924	1		1059	860	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067449	37067449	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	159	651	0	ENST00000231790.2:c.1360G>A	p.Gly454Arg	p.G454R	ENST00000231790	NM_000249.3	454	Ggg/Agg	12/19	1	2	FACETS	0.519	0.477	0.564	0.519	0.477	0.564	SUBCLONAL	1	TRUE	1	0.807630178299924	2		651	758	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906774	32906774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869320791	NA	P-0056127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	135	706	0	ENST00000380152.3:c.1159G>A	p.Val387Ile	p.V387I	ENST00000380152		387	Gtt/Att	10/27	1	2	FACETS	0.408	0.371	0.447	0.408	0.371	0.447	SUBCLONAL	1	TRUE	1	0.807630178299924	2		706	819	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683207	88683207	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	99	459	0	ENST00000372037.3:c.1417G>T	p.Val473Phe	p.V473F	ENST00000372037	NM_004329.2	473	Gtt/Ttt	12/13	0.807630178299924	3	FACETS	0.567	0.507	0.631	0.283	0.253	0.316	SUBCLONAL	1	TRUE	1	0.807630178299924	3		459	607	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418360	49418360	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0056127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	42	507	0	ENST00000301067.7:c.16052+1G>T		p.X5351_splice	ENST00000301067	NM_003482.3	5351			0.416760490207249	2	FACETS	0.163	0.135	0.193	0.081	0.067	0.097	INDETERMINATE	1	TRUE	0	0.807630178299924	2		507	640	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972413	32972413	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	127	656	0	ENST00000380152.3:c.9763G>T	p.Gly3255Trp	p.G3255W	ENST00000380152		3255	Ggg/Tgg	27/27	1	2	FACETS	0.454	0.412	0.498	0.454	0.412	0.498	SUBCLONAL	1	TRUE	1	0.807630178299924	2		656	693	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350652	89350652	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	189	1002	0	ENST00000301030.4:c.2298G>T	p.Lys766Asn	p.K766N	ENST00000301030	NM_001256183.1	766	aaG/aaT	9/13	0.413205733030099	3	FACETS	0.529	0.487	0.572	0.176	0.162	0.191	INDETERMINATE	1	TRUE	0	0.807630178299924	3		1002	1243	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15280930	15280930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1427867146	NA	P-0056127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	49	1034	0	ENST00000263388.2:c.5166G>A	p.Met1722Ile	p.M1722I	ENST00000263388	NM_000435.2	1722	atG/atA	28/33	0.795789100602189	2	FACETS	0.132	0.111	0.155	0.066	0.055	0.078	SUBCLONAL	1	TRUE	0	0.807630178299924	2		1034	920	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033615	48033615	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	115	507	0	ENST00000234420.5:c.3826G>A	p.Glu1276Lys	p.E1276K	ENST00000234420	NM_000179.2	1276	Gaa/Aaa	9/10	0.375794111509636	3	FACETS	0.561	0.505	0.619	0.187	0.168	0.207	INDETERMINATE	1	TRUE	0	0.807630178299924	3		507	713	SUCCESS
APC	324	MSKCC	GRCh37	5	112174622	112174622	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	213	465	0	ENST00000257430.4:c.3331G>T	p.Glu1111Ter	p.E1111*	ENST00000257430	NM_000038.5	1111	Gaa/Taa	16/16	0.43078572086921	1	FACETS	0.742	0.699	0.784	0.742	0.699	0.784	INDETERMINATE	1	TRUE	0	0.807630178299924	1		465	424	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2949786	2949787	+	missense_variant	Missense_Mutation	DNP	AG	AG	CT	novel	NA	P-0056127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	141	775	1	ENST00000396946.4:c.3157_3158inv	p.Leu1053Arg	p.L1053R	ENST00000396946	NM_032415.4	1053	CTg/AGg	24/25	0.348706951184957	2	FACETS	0.382	0.347	0.418	0.191	0.173	0.209	INDETERMINATE	1	TRUE	0	0.807630178299924	2		776	915	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339547	81339547	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	83	477	0	ENST00000222390.5:c.1457C>G	p.Ser486Cys	p.S486C	ENST00000222390	NM_000601.4	486	tCt/tGt	13/18	0.348706951184957	2	FACETS	0.372	0.329	0.419	0.186	0.164	0.21	INDETERMINATE	1	TRUE	0	0.807630178299924	2		477	552	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931687	39931687	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	192	405	0	ENST00000378444.4:c.2912G>T	p.Gly971Val	p.G971V	ENST00000378444	NM_001123385.1	971	gGt/gTt	4/15	1	1	FACETS	0.53	0.494	0.567	0.53	0.494	0.567	SUBCLONAL	1	TRUE	0	0.807630178299924	1		405	535	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040715	47040716	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1131690789	NA	P-0056127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	220	522	0	ENST00000377604.3:c.1352_1353del	p.Glu451ValfsTer66	p.E451Vfs*66	ENST00000377604	NM_001204468.1	450	acAGag/acag	13/24	1	1	FACETS	0.604	0.567	0.641	0.604	0.567	0.641	SUBCLONAL	1	TRUE	0	0.807630178299924	1		522	538	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165306	47165306	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs869025571	NA	P-0056129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	101	468	0	ENST00000409792.3:c.820C>T	p.Gln274Ter	p.Q274*	ENST00000409792	NM_014159.6	274	Caa/Taa	3/21	0.588604459552614	1	FACETS	0.917	0.834	1	0.917	0.834	1	CLONAL	1	TRUE	0	0.588604459552614	1		468	264	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	256470	256470	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	8	520	0	ENST00000264932.6:c.1930G>T	p.Val644Leu	p.V644L	ENST00000264932	NM_004168.2	644	Gtg/Ttg	15/15	1	2	FACETS	0.121	0.077	0.179	0.121	0.077	0.179	SUBCLONAL	1	TRUE	1	0.346856384866968	2		520	380	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021360	42021360	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0056130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	11	340	0	ENST00000219905.7:c.3658-2A>G		p.X1220_splice	ENST00000219905	NM_001164273.1	1220			1	2	FACETS	0.492	0.341	0.676	0.492	0.341	0.676	SUBCLONAL	1	TRUE	1	0.346856384866968	2		340	129	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432717	49432717	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	32	778	1	ENST00000301067.7:c.8422del	p.Leu2808CysfsTer43	p.L2808Cfs*43	ENST00000301067	NM_003482.3	2808	Ctg/tg	34/54	1	2	FACETS	0.347	0.281	0.422	0.347	0.281	0.422	SUBCLONAL	1	TRUE	1	0.346856384866968	2		779	532	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	13	290	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	0.369213794518456	3	FACETS	1	0.83	1	0.601	0.439	0.788	CLONAL	1	TRUE	1	0.422307484528074	3		290	62	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537975	212537975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267599192	NA	P-0056131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	34	376	0	ENST00000342788.4:c.1630C>T	p.Arg544Trp	p.R544W	ENST00000342788	NM_005235.2	544	Cgg/Tgg	14/28	0.28046338829585	5	FACETS	1	0.897	1	0.737	0.615	0.867	CLONAL	2	TRUE	2	0.422307484528074	5		376	119	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604748	48604748	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	36	443	0	ENST00000342988.3:c.1570T>A	p.Trp524Arg	p.W524R	ENST00000342988	NM_005359.5	524	Tgg/Agg	12/12	0.356002918171128	2	FACETS	0.991	0.845	1	0.991	0.845	1	CLONAL	2	TRUE	0	0.422307484528074	2		443	86	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0056131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	24	684	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.422307484528074	1	FACETS	1	0.818	1	1	0.818	1	CLONAL	1	TRUE	0	0.422307484528074	1		684	88	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576256	88576256	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	31	599	0	ENST00000360948.2:c.1417G>A	p.Gly473Ser	p.G473S	ENST00000360948	NM_001012338.2	473	Ggt/Agt	13/19	0.369213794518456	3	FACETS	1	0.843	1	1	0.843	1	CLONAL	2	TRUE	1	0.422307484528074	3		599	88	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129002	30129002	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	27	623	0	ENST00000263025.4:c.764A>C	p.Asn255Thr	p.N255T	ENST00000263025	NM_002746.2	255	aAc/aCc	5/9	0.15215976346211	3	FACETS	0.956	0.769	1	0.478	0.384	0.583	INDETERMINATE	1	TRUE	1	0.422307484528074	3		623	162	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438178	56438178	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	46	908	0	ENST00000407977.2:c.815G>A	p.Cys272Tyr	p.C272Y	ENST00000407977		272	tGt/tAt	7/10	0.422307484528074	1	FACETS	0.868	0.758	0.979	1	0.974	1	CLONAL	2	TRUE	0	0.422307484528074	1		908	99	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38314931	38314931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1563627828	NA	P-0056131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	15	681	0	ENST00000425967.3:c.133G>A	p.Val45Met	p.V45M	ENST00000425967	NM_001174067.1	45	Gtg/Atg	3/19	0.275702847295154	4	FACETS	0.783	0.578	1	0.392	0.289	0.513	CLONAL	1	TRUE	2	0.422307484528074	4		681	129	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0056132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	200	624	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.995	0.926	1	0.995	0.926	1	CLONAL	1	TRUE	1	0.611961709753455	2		624	657	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692849	89692849	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554898097	NA	P-0056132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	8	171	0	ENST00000371953.3:c.333G>A	p.Trp111Ter	p.W111*	ENST00000371953	NM_000314.4	111	tgG/tgA	5/9	0.432968252285702	1	FACETS	0.103	0.066	0.151	0.103	0.066	0.151	SUBCLONAL	1	TRUE	0	0.611961709753455	1		171	176	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0056132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	13	465	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	0.432968252285702	1	FACETS	0.085	0.06	0.116	0.085	0.06	0.116	SUBCLONAL	1	TRUE	0	0.611961709753455	1		465	346	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653815	89653815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	10	375	0	ENST00000371953.3:c.113C>T	p.Pro38Leu	p.P38L	ENST00000371953	NM_000314.4	38	cCt/cTt	2/9	0.432968252285702	1	FACETS	0.077	0.052	0.11	0.077	0.052	0.11	SUBCLONAL	1	TRUE	0	0.611961709753455	1		375	293	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0056132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	107	30	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.611961709753455	2		30	332	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425638	49425638	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	256	842	0	ENST00000301067.7:c.12850C>T	p.Gln4284Ter	p.Q4284*	ENST00000301067	NM_003482.3	4284	Cag/Tag	39/54	1	2	FACETS	0.964	0.905	1	0.964	0.905	1	CLONAL	1	TRUE	1	0.611961709753455	2		842	868	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961493	41961493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771815727	NA	P-0056132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	211	591	1	ENST00000219905.7:c.401G>A	p.Arg134His	p.R134H	ENST00000219905	NM_001164273.1	134	cGt/cAt	2/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.611961709753455	2		592	643	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426205	49426205	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	296	936	0	ENST00000301067.7:c.12283C>G	p.Leu4095Val	p.L4095V	ENST00000301067	NM_003482.3	4095	Ctg/Gtg	39/54	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.611961709753455	2		936	934	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569978	95569978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	173	537	0	ENST00000393063.1:c.3755C>T	p.Ser1252Leu	p.S1252L	ENST00000393063	NM_030621.3	1252	tCa/tTa	22/28	1	2	FACETS	0.97	0.898	1	0.97	0.898	1	CLONAL	1	TRUE	1	0.611961709753455	2		537	583	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456457	99456457	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376607968	NA	P-0056132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	185	527	0	ENST00000268035.6:c.1774G>A	p.Asp592Asn	p.D592N	ENST00000268035	NM_000875.3	592	Gac/Aac	8/21	1	2	FACETS	0.883	0.818	0.949	0.883	0.818	0.949	CLONAL	1	TRUE	1	0.611961709753455	2		527	685	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723052	52723052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	262	730	0	ENST00000322088.6:c.1237G>A	p.Glu413Lys	p.E413K	ENST00000322088	NM_014225.5	413	Gag/Aag	10/15	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.611961709753455	2		730	854	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73110208	73110208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373009608	NA	P-0056132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	89	450	0	ENST00000356692.5:c.416C>T	p.Ser139Leu	p.S139L	ENST00000356692		139	tCa/tTa	5/9	1	2	FACETS	0.761	0.68	0.847	0.761	0.68	0.847	SUBCLONAL	1	TRUE	1	0.611961709753455	2		450	382	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920436	134920436	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	199	667	0	ENST00000398015.3:c.2251C>G	p.Leu751Val	p.L751V	ENST00000398015	NM_004441.4	751	Ctg/Gtg	12/16	1	2	FACETS	0.906	0.842	0.971	0.906	0.842	0.971	CLONAL	1	TRUE	1	0.611961709753455	2		667	718	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534470	187534470	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	149	412	0	ENST00000441802.2:c.9256G>C	p.Asp3086His	p.D3086H	ENST00000441802	NM_005245.3	3086	Gat/Cat	13/27	1	2	FACETS	0.942	0.866	1	0.942	0.866	1	CLONAL	1	TRUE	1	0.611961709753455	2		412	517	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859453	151859453	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	426	567	0	ENST00000262189.6:c.11209G>T	p.Glu3737Ter	p.E3737*	ENST00000262189	NM_170606.2	3737	Gag/Tag	43/59	0.286394899883146	3	FACETS	1	0.994	1	0.802	0.771	0.832	INDETERMINATE	2	TRUE	0	0.611961709753455	3		567	756	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217400	123217401	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0056132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	108	196	0	ENST00000218089.9:c.3053+2dup		p.X1018_splice	ENST00000218089	NM_001042749.1	1018			1	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.611961709753455	1		196	214	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420481	49420499	+	frameshift_variant	Frame_Shift_Del	DEL	TTAGCAGTCCTCGGTGCAG	TTAGCAGTCCTCGGTGCAG	CA	novel	NA	P-0056132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	266	792	2	ENST00000301067.7:c.15250_15268delinsTG	p.Leu5084CysfsTer48	p.L5084Cfs*48	ENST00000301067	NM_003482.3	5084	CTGCACCGAGGACTGCTAAcc/TGcc	48/54	1	2	FACETS	0.98	0.921	1	0.98	0.921	1	CLONAL	1	TRUE	1	0.611961709753455	2		794	887	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0056134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	403	840	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.769978233490552	1	FACETS	0.962	0.926	0.998	0.962	0.926	0.998	CLONAL	1	TRUE	0	0.769978233490552	1		843	669	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	102	374	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.769978233490552	2		374	246	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247585	123247585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	188	522	1	ENST00000358487.5:c.1906G>A	p.Glu636Lys	p.E636K	ENST00000358487	NM_000141.4	636	Gaa/Aaa	14/18	1	2	FACETS	0.87	0.81	0.933	0.87	0.81	0.933	CLONAL	1	TRUE	1	0.769978233490552	2		523	561	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247514	123247514	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	188	504	0	ENST00000358487.5:c.1977G>C	p.Lys659Asn	p.K659N	ENST00000358487	NM_000141.4	659	aaG/aaC	14/18	1	2	FACETS	0.852	0.792	0.913	0.852	0.792	0.913	CLONAL	1	TRUE	1	0.769978233490552	2		504	573	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033844	49033844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853294	NA	P-0056134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	190	528	0	ENST00000267163.4:c.1981C>T	p.Arg661Trp	p.R661W	ENST00000267163	NM_000321.2	661	Cgg/Tgg	20/27	0.769978233490552	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.769978233490552	1		528	288	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621035	1621035	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747273925	NA	P-0056134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	360	985	0	ENST00000344749.5:c.1025C>T	p.Pro342Leu	p.P342L	ENST00000344749	NM_001136139.2	342	cCg/cTg	13/19	1	2	FACETS	0.906	0.861	0.952	0.906	0.861	0.952	CLONAL	1	TRUE	1	0.769978233490552	2		985	1032	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0056134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	831	817	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.767691629924748	2	FACETS	0.971	0.95	0.991	0.971	0.95	0.991	CLONAL	2	TRUE	0	0.769978233490552	2		817	1112	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923034	44923034	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	339	288	0	ENST00000377967.4:c.1895G>A	p.Trp632Ter	p.W632*	ENST00000377967	NM_021140.2	632	tGg/tAg	16/29	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.769978233490552	1		288	452	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981172	201981173	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0056134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	399	866	1	ENST00000359651.3:c.251_252insT	p.Lys84AsnfsTer8	p.K84Nfs*8	ENST00000359651		84	aag/aaTg	2/8	1	2	FACETS	0.995	0.948	1	0.995	0.948	1	CLONAL	1	TRUE	1	0.769978233490552	2		867	1042	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247543	123247543	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	204	571	0	ENST00000358487.5:c.1948G>C	p.Asp650His	p.D650H	ENST00000358487	NM_000141.4	650	Gat/Cat	14/18	1	2	FACETS	0.836	0.779	0.894	0.836	0.779	0.894	CLONAL	1	TRUE	1	0.769978233490552	2		571	634	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172201	99172201	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	311	740	1	ENST00000074304.5:c.1767C>A	p.Phe589Leu	p.F589L	ENST00000074304	NM_001134224.1	589	ttC/ttA	17/26	0.390857047827922	3	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.769978233490552	3		741	1053	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564809	41564809	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	307	678	0	ENST00000263253.7:c.4111del	p.Leu1371CysfsTer39	p.L1371Cfs*39	ENST00000263253	NM_001429.3	1370	gaC/ga	25/31	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.769978233490552	2		678	790	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412639	139412639	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	842	885	0	ENST00000277541.6:c.1205C>G	p.Ser402Trp	p.S402W	ENST00000277541	NM_017617.3	402	tCg/tGg	7/34	0.767691629924748	2	FACETS	0.958	0.937	0.978	0.958	0.937	0.978	CLONAL	2	TRUE	0	0.769978233490552	2		885	1142	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176332	24176346	+	frameshift_variant	Frame_Shift_Del	DEL	ATGAGGCGTCTTGCC	ATGAGGCGTCTTGCC	T	novel	NA	P-0056134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	317	882	0	ENST00000263121.7:c.1123_1137delinsT	p.Met375Ter	p.M375*	ENST00000263121	NM_003073.3	375	ATGAGGCGTCTTGCC/T	9/9	1	2	FACETS	0.892	0.844	0.941	0.892	0.844	0.941	CLONAL	1	TRUE	1	0.769978233490552	2		882	923	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426788	121426788	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	945	621	1	ENST00000257555.6:c.479C>A	p.Ala160Asp	p.A160D	ENST00000257555		160	gCc/gAc	2/10	0.927106489049918	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.927106489049918	3		622	1480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912657	NA	P-0056138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	427	617	0	ENST00000269305.4:c.814G>C	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ctg	8/11	0.927106489049918	1	FACETS	0.956	0.932	0.978	0.956	0.932	0.978	CLONAL	1	TRUE	0	0.927106489049918	1		617	517	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472499	88472499	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	750	567	4	ENST00000360948.2:c.2056C>A	p.Leu686Met	p.L686M	ENST00000360948	NM_001012338.2	686	Ctg/Atg	16/19	0.830572374858197	3	FACETS	0.956	0.93	0.983	0.956	0.93	0.983	CLONAL	2	TRUE	1	0.927106489049918	3		571	1238	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463509	25463509	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	373	563	0	ENST00000264709.3:c.2173G>T	p.Glu725Ter	p.E725*	ENST00000264709	NM_175629.2	725	Gag/Tag	18/23	NA	2	FACETS	0.856	0.815	0.897			1	INDETERMINATE	1	TRUE	NA	0.927106489049918	2		563	940	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15273288	15273288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs373866355	NA	P-0056138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	503	558	3	ENST00000263388.2:c.5901G>T	p.Met1967Ile	p.M1967I	ENST00000263388	NM_000435.2	1967	atG/atT	32/33	0.927106489049918	3	FACETS	0.991	0.947	1	0.495	0.473	0.518	CLONAL	1	TRUE	1	0.927106489049918	3		561	1603	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1253854	1253854	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	790	548	0	ENST00000310581.5:c.3388A>G	p.Ile1130Val	p.I1130V	ENST00000310581	NM_198253.2	1130	Atc/Gtc	16/16	0.78339991126988	4	FACETS	0.971	0.941	1			1	CLONAL	2	TRUE	NA	0.927106489049918	4		548	1691	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944881	131944881	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	114	159	2	ENST00000265335.6:c.2902G>T	p.Gly968Trp	p.G968W	ENST00000265335		968	Ggg/Tgg	18/25	1	2	FACETS	0.828	0.757	0.901	0.828	0.757	0.901	CLONAL	1	TRUE	1	0.927106489049918	2		161	297	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323345	31323346	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0056138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	244	319	3	ENST00000412585.2:c.643dup	p.His215ProfsTer6	p.H215Pfs*6	ENST00000412585	NM_005514.6	215	cac/cCac	4/8	0.88797927266078	4	FACETS	0.977	0.913	1	0.326	0.304	0.348	CLONAL	1	TRUE	1	0.927106489049918	4		322	1038	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411131	63411131	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	436	322	2	ENST00000330258.3:c.2036G>T	p.Arg679Leu	p.R679L	ENST00000330258	NM_152424.3	679	cGg/cTg	2/2	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.927106489049918	1		324	457	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405954	49405954	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	63	694	0	ENST00000418115.1:c.184G>A	p.Gly62Arg	p.G62R	ENST00000418115	NM_001664.2	62	Ggg/Agg	3/5	0.0872221986019532	3	FACETS	1	0.914	1	0.538	0.465	0.617	INDETERMINATE	1	TRUE	1	0.219380270786654	3		694	592	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998684	100998684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	34	1004	0	ENST00000325455.5:c.1118C>T	p.Ala373Val	p.A373V	ENST00000325455	NM_001202474.3	373	gCg/gTg	1/8	1	2	FACETS	0.636	0.519	0.768	0.636	0.519	0.768	SUBCLONAL	1	TRUE	1	0.219380270786654	2		1004	487	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844172	68844172	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1555515445	NA	P-0056140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	128	873	0	ENST00000261769.5:c.760G>T	p.Asp254Tyr	p.D254Y	ENST00000261769	NM_004360.3	254	Gat/Tat	6/16	0.219380270786654	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	0	0.219380270786654	2		873	571	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074435	8074435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs980250925	NA	P-0056140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	63	494	0	ENST00000377482.5:c.224C>T	p.Pro75Leu	p.P75L	ENST00000377482	NM_018948.3	75	cCg/cTg	4/4	1	2	FACETS	0.823	0.716	0.938	1	0.975	1	CLONAL	2	TRUE	1	0.219380270786654	2		494	349	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653799	89653799	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	54	447	0	ENST00000371953.3:c.97A>G	p.Ile33Val	p.I33V	ENST00000371953	NM_000314.4	33	Att/Gtt	2/9	0.0872221986019532	3	FACETS	1	0.948	1	0.624	0.534	0.722	INDETERMINATE	1	TRUE	1	0.219380270786654	3		447	438	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959944	38959944	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	18	414	0	ENST00000357387.3:c.1988T>A	p.Ile663Asn	p.I663N	ENST00000357387	NM_152756.3	663	aTt/aAt	21/38	1	2	FACETS	0.542	0.407	0.7	0.542	0.407	0.7	SUBCLONAL	1	TRUE	1	0.219380270786654	2		414	303	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0056141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	39	562	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.18	2		562	370	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692887	89692887	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	22	340	0	ENST00000371953.3:c.371G>C	p.Cys124Ser	p.C124S	ENST00000371953	NM_000314.4	124	tGt/tCt	5/9	1	2	FACETS	0.929	0.722	1	0.929	0.722	1	CLONAL	1	TRUE	1	0.18	2		340	263	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0056141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	41	231	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.9	0.75	1	0.9	0.75	1	CLONAL	1	TRUE	1	0.18	2		231	506	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921567	178921567	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553821144	NA	P-0056141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	9	252	0	ENST00000263967.3:c.1049A>G	p.Asp350Gly	p.D350G	ENST00000263967	NM_006218.2	350	gAc/gGc	5/21	1	2	FACETS	0.518	0.343	0.742	0.518	0.343	0.742	SUBCLONAL	1	TRUE	1	0.18	2		252	193	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519896	NA	P-0056141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	47	368	1	ENST00000281708.4:c.1514G>T	p.Arg505Leu	p.R505L	ENST00000281708	NM_033632.3	505	cGc/cTc	10/12	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.18	2		369	487	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850704	63850705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	31	353	1	ENST00000279873.7:c.1489dup	p.Ile497AsnfsTer31	p.I497Nfs*31	ENST00000279873	NM_032199.2	494	-/A	10/10	1	2	FACETS	0.801	0.648	0.975	0.801	0.648	0.975	CLONAL	1	TRUE	1	0.18	2		354	430	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097801	27097801	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	42	467	0	ENST00000324856.7:c.3391del	p.Gln1131SerfsTer30	p.Q1131Sfs*30	ENST00000324856	NM_006015.4	1130	atC/at	12/20	1	2	FACETS	0.822	0.685	0.973	0.822	0.685	0.973	CLONAL	1	TRUE	1	0.18	2		467	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0056142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	500	695	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.61710220039598	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.61710220039598	2		695	784	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0056180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	158	644	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	1	2	FACETS	0.965	0.888	1	0.965	0.888	1	CLONAL	1	TRUE	1	0.532438716013576	2		644	615	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0056180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	42	319	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.657	0.553	0.771	0.657	0.553	0.771	SUBCLONAL	1	TRUE	1	0.532438716013576	2		319	240	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0056180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	283	884	5	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.532438716013576	2		889	929	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370236	40370236	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs761761205	NA	P-0056180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	132	804	8	ENST00000293328.3:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000293328	NM_012448.3	368	Cag/ag	9/19	1	2	FACETS	0.666	0.606	0.73	0.666	0.606	0.73	SUBCLONAL	1	TRUE	1	0.532438716013576	2		812	744	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959064	2959064	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	207	731	0	ENST00000396946.4:c.2452C>T	p.Arg818Trp	p.R818W	ENST00000396946	NM_032415.4	818	Cgg/Tgg	18/25	1	2	FACETS	0.998	0.929	1	0.998	0.929	1	CLONAL	1	TRUE	1	0.532438716013576	2		731	779	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577519	7577527	+	inframe_deletion	In_Frame_Del	DEL	GATGGTGAG	GATGGTGAG	-	novel	NA	P-0056180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	189	665	0	ENST00000269305.4:c.754_762del	p.Leu252_Ile254del	p.L252_I254del	ENST00000269305	NM_001126112.2	252	CTCACCATC/-	7/11	1	2	FACETS	0.966	0.895	1	0.966	0.895	1	CLONAL	1	TRUE	1	0.532438716013576	2		665	735	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830807	72830807	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	209	661	0	ENST00000268489.5:c.5774del	p.Gly1925ValfsTer72	p.G1925Vfs*72	ENST00000268489	NM_006885.3	1925	gGt/gt	9/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.532438716013576	2		661	738	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748399150	NA	P-0056180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	256	972	4	ENST00000220592.5:c.1806del	p.Ala603ProfsTer92	p.A603Pfs*92	ENST00000220592	NM_012154.3	602	ccC/cc	14/19	1	2	FACETS	0.928	0.869	0.989	0.928	0.869	0.989	CLONAL	1	TRUE	1	0.532438716013576	2		976	1036	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222433	2222433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs930481759	NA	P-0056180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	182	532	0	ENST00000398665.3:c.3265C>T	p.Arg1089Trp	p.R1089W	ENST00000398665	NM_032482.2	1089	Cgg/Tgg	24/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.532438716013576	2		532	594	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980402	201980402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	237	770	1	ENST00000359651.3:c.142del	p.Gln48ArgfsTer107	p.Q48Rfs*107	ENST00000359651		46	aaC/aa	1/8	0.532438716013576	4	FACETS	0.97	0.903	1	0.323	0.301	0.347	CLONAL	1	TRUE	1	0.532438716013576	4		771	1407	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257788	133257788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1161199196	NA	P-0056180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	92	539	0	ENST00000320574.5:c.140G>A	p.Arg47Gln	p.R47Q	ENST00000320574	NM_006231.2	47	cGg/cAg	2/49	1	2	FACETS	0.474	0.421	0.531	0.474	0.421	0.531	SUBCLONAL	1	TRUE	1	0.532438716013576	2		539	729	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717636	89717636	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1554825174	NA	P-0056180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	88	408	0	ENST00000371953.3:c.661A>T	p.Lys221Ter	p.K221*	ENST00000371953	NM_000314.4	221	Aag/Tag	7/9	1	2	FACETS	0.863	0.77	0.961	0.863	0.77	0.961	CLONAL	1	TRUE	1	0.532438716013576	2		408	383	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200654	67200655	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0056180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	267	853	0	ENST00000312629.5:c.765_766insT	p.Gly256TrpfsTer25	p.G256Wfs*25	ENST00000312629	NM_003952.2	255	-/T	9/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.532438716013576	2		853	871	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941933	71941933	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	181	753	0	ENST00000298229.2:c.1291T>C	p.Trp431Arg	p.W431R	ENST00000298229	NM_001567.3	431	Tgg/Cgg	11/28	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.532438716013576	2		753	663	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944175	71944175	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	190	761	0	ENST00000298229.2:c.2008A>C	p.Thr670Pro	p.T670P	ENST00000298229	NM_001567.3	670	Aca/Cca	17/28	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.532438716013576	2		761	703	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230685	46230685	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	76	377	0	ENST00000334344.6:c.934T>C	p.Cys312Arg	p.C312R	ENST00000334344	NM_152641.2	312	Tgt/Cgt	8/21	1	2	FACETS	0.909	0.805	1	0.909	0.805	1	CLONAL	1	TRUE	1	0.532438716013576	2		377	314	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082734	16082734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	37	40	0	ENST00000281043.3:c.548C>T	p.Ala183Val	p.A183V	ENST00000281043	NM_005378.4	183	gCc/gTc	2/3	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.532438716013576	2		40	107	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591153	67591154	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0056180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	52	286	0	ENST00000274335.5:c.1745+2dup		p.X582_splice	ENST00000274335		582			1	2	FACETS	0.842	0.725	0.967	0.842	0.725	0.967	CLONAL	1	TRUE	1	0.532438716013576	2		286	232	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27209124	27209124	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	97	401	0	ENST00000380036.4:c.2581G>A	p.Ala861Thr	p.A861T	ENST00000380036	NM_000459.3	861	Gcc/Acc	16/23	1	2	FACETS	0.934	0.839	1	0.934	0.839	1	CLONAL	1	TRUE	1	0.532438716013576	2		401	390	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249797	110249797	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	224	784	0	ENST00000374672.4:c.878del	p.Pro293LeufsTer33	p.P293Lfs*33	ENST00000374672	NM_004235.4	293	cCt/ct	3/5	1	2	FACETS	0.982	0.916	1	0.982	0.916	1	CLONAL	1	TRUE	1	0.532438716013576	2		784	857	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0056183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	45	215	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.171654309916189	2		215	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782197	NA	P-0056183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	83	914	0	ENST00000269305.4:c.434T>C	p.Leu145Pro	p.L145P	ENST00000269305	NM_001126112.2	145	cTg/cCg	5/11	0.166990776713619	1	FACETS	0.825	0.726	0.931	0.825	0.726	0.931	CLONAL	1	TRUE	0	0.171654309916189	1		914	1072	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974744	21974775	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTCCTCTACCCGACCCCGGGCCGCGGCCGT	ACCTCCTCTACCCGACCCCGGGCCGCGGCCGT	-	novel	NA	P-0056183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	30	338	0	ENST00000304494.5:c.52_83del	p.Thr18AlafsTer15	p.T18Afs*15	ENST00000304494	NM_000077.4	18	ACGGCCGCGGCCCGGGGTCGGGTAGAGGAGGTg/g	1/3	0.171654309916189	1	FACETS	0.766	0.617	0.936	0.766	0.617	0.936	CLONAL	1	TRUE	0	0.171654309916189	1		338	417	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134270	11134270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs797045981	NA	P-0056183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	66	630	1	ENST00000358026.2:c.2936G>A	p.Arg979Gln	p.R979Q	ENST00000358026	NM_001128849.1	979	cGa/cAa	20/36	1	2	FACETS	0.922	0.799	1	0.922	0.799	1	CLONAL	1	TRUE	1	0.171654309916189	2		631	834	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870205	44870205	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0056183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	32	298	0	ENST00000377967.4:c.385-1G>T		p.X129_splice	ENST00000377967	NM_021140.2	129			0.171654309916189	1	FACETS	0.775	0.628	0.94	0.775	0.628	0.94	CLONAL	1	TRUE	0	0.171654309916189	1		298	440	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28901619	28901619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	33	328	0	ENST00000282397.4:c.2776G>A	p.Asp926Asn	p.D926N	ENST00000282397	NM_002019.4	926	Gac/Aac	20/30	1	2	FACETS	0.868	0.707	1	0.868	0.707	1	CLONAL	1	TRUE	1	0.171654309916189	2		328	443	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10267094	10267094	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	48	426	0	ENST00000340748.4:c.1324A>G	p.Ile442Val	p.I442V	ENST00000340748		442	Atc/Gtc	17/40	1	2	FACETS	0.845	0.713	0.991	0.845	0.713	0.991	CLONAL	1	TRUE	1	0.171654309916189	2		426	662	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732925	30732925	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	75	362	0	ENST00000295754.5:c.1538T>G	p.Val513Gly	p.V513G	ENST00000295754	NM_003242.5	513	gTg/gGg	7/7	0.171654309916189	2	FACETS	0.894	0.785	1	0.894	0.785	1	CLONAL	2	TRUE	0	0.171654309916189	2		362	489	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111499	8111500	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0056184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	142	606	0	ENST00000346208.3:c.987dup	p.Arg330GlufsTer22	p.R330Efs*22	ENST00000346208		329	agg/aGgg	5/6	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.31	2		606	791	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056199	27056199	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	158	579	0	ENST00000324856.7:c.1196del	p.Asn399ThrfsTer34	p.N399Tfs*34	ENST00000324856	NM_006015.4	399	Aac/ac	2/20	0.273862964271474	2	FACETS	0.753	0.692	0.816	0.753	0.692	0.816	SUBCLONAL	2	TRUE	0	0.31	2		579	677	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839730	27839730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	90	591	0	ENST00000328488.2:c.364C>T	p.Pro122Ser	p.P122S	ENST00000328488	NM_003533.2	122	Cct/Tct	1/1	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.31	NA		591	857	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709156	117709156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	49	369	0	ENST00000368508.3:c.1801G>A	p.Gly601Ser	p.G601S	ENST00000368508	NM_002944.2	601	Ggc/Agc	13/43	0.267556335124406	1	FACETS	0.763	0.649	0.888	0.763	0.649	0.888	SUBCLONAL	1	TRUE	0	0.31	1		369	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0056185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	582	779	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.575759779049162	2	FACETS	0.845	0.816	0.873	0.845	0.816	0.873	CLONAL	2	TRUE	0	0.625329734519019	2		779	1102	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782006	NA	P-0056185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	591	737	1	ENST00000269305.4:c.859G>A	p.Glu287Lys	p.E287K	ENST00000269305	NM_001126112.2	287	Gag/Aag	8/11	0.575759779049162	2	FACETS	0.826	0.798	0.854	0.826	0.798	0.854	CLONAL	2	TRUE	0	0.625329734519019	2		738	1144	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0056185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	470	802	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.295141161776716	1	FACETS	0.809	0.774	0.845	0.809	0.774	0.845	INDETERMINATE	1	TRUE	0	0.625329734519019	1		802	1277	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061450	38061450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	257	470	0	ENST00000250448.2:c.539C>T	p.Thr180Ile	p.T180I	ENST00000250448	NM_004496.3	180	aCc/aTc	2/2	1	2	FACETS	0.982	0.922	1	0.982	0.922	1	CLONAL	1	TRUE	1	0.625329734519019	2		470	837	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575069	64575069	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	339	540	1	ENST00000312049.6:c.738del	p.Ile247LeufsTer34	p.I247Lfs*34	ENST00000312049	NM_130799.2	246	tcC/tc	4/10	0.561023772519607	1	FACETS	0.949	0.903	0.996	0.949	0.903	0.996	CLONAL	1	TRUE	0	0.625329734519019	1		541	785	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576870	7576873	+	frameshift_variant	Frame_Shift_Del	DEL	CTCC	CTCC	TCT	novel	NA	P-0056185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	464	679	2	ENST00000269305.4:c.973_976delinsAGA	p.Gly325ArgfsTer20	p.G325Rfs*20	ENST00000269305	NM_001126112.2	325	GGAGaa/AGAaa	9/11	0.575759779049162	2	FACETS	0.773	0.742	0.804	0.773	0.742	0.804	SUBCLONAL	2	TRUE	0	0.625329734519019	2		681	960	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	56	374	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.781	0.68	0.887	0.781	0.68	0.887	SUBCLONAL	1	FALSE	1	0.762962424310483	2		374	188	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717776	89717776	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	rs1060500110	NA	P-0056186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	73	328	0	ENST00000371953.3:c.801+1del		p.K267fs	ENST00000371953	NM_000314.4	267	aaG/aa	7/9	0.762962424310483	1	FACETS	0.925	0.84	1	0.925	0.84	1	CLONAL	1	FALSE	0	0.762962424310483	1		328	128	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0056187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	660	626	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.657334173855736	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.680917872503371	2		626	964	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0056187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	102	234	1	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.331615423338826	1	FACETS	0.711	0.645	0.778	0.711	0.645	0.778	INDETERMINATE	1	TRUE	0	0.680917872503371	1		235	278	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953017	2953017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064795307	NA	P-0056187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1743	122	806	0	ENST00000396946.4:c.2923C>T	p.Arg975Trp	p.R975W	ENST00000396946	NM_032415.4	975	Cgg/Tgg	22/25	0.237754897871167	6	FACETS	0.454	0.408	0.503			1	INDETERMINATE	1	TRUE	NA	0.680917872503371	6		806	1865	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332611	65332611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568014073	NA	P-0056187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	166	316	0	ENST00000342505.4:c.928G>A	p.Val310Ile	p.V310I	ENST00000342505	NM_002227.2	310	Gtt/Att	7/25	0.331615423338826	1	FACETS	0.792	0.736	0.849	0.792	0.736	0.849	INDETERMINATE	1	TRUE	0	0.680917872503371	1		316	406	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133057	30133057	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	302	331	2	ENST00000331968.5:c.544C>A	p.Leu182Met	p.L182M	ENST00000331968	NM_002742.2	182	Ctg/Atg	4/18	0.66440699240479	2	FACETS	0.922	0.883	0.96	0.922	0.883	0.96	CLONAL	2	TRUE	0	0.680917872503371	2		333	481	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544717	65544717	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	81	613	0	ENST00000358664.4:c.209A>G	p.Tyr70Cys	p.Y70C	ENST00000358664	NM_002382.4	70	tAt/tGt	4/5	0.66440699240479	2	FACETS	0.254	0.223	0.288	0.127	0.111	0.144	SUBCLONAL	1	TRUE	0	0.680917872503371	2		613	936	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643579	38643580	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0056187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	149	544	3	ENST00000299084.4:c.1052_1053dup	p.Cys352AsnfsTer55	p.C352Nfs*55	ENST00000299084	NM_152594.2	350	gga/ggAAa	7/7	0.415713283373992	1	FACETS	0.498	0.457	0.54	0.498	0.457	0.54	SUBCLONAL	1	TRUE	0	0.680917872503371	1		547	580	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530109	63530109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793454	NA	P-0056187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	585	571	10	ENST00000307078.5:c.2326C>T	p.Pro776Ser	p.P776S	ENST00000307078	NM_004655.3	776	Cca/Tca	10/11	0.657334173855736	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.680917872503371	2		581	846	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119937	70119938	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACCTA	novel	NA	P-0056187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	458	503	5	ENST00000245479.2:c.940_944dup	p.Tyr315Ter	p.Y315*	ENST00000245479	NM_000346.3	313	-/ACCTA	3/3	0.657334173855736	2	FACETS	0.994	0.962	1	0.994	0.962	1	CLONAL	2	TRUE	0	0.680917872503371	2		508	677	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573639	48573639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	150	311	0	ENST00000342988.3:c.223C>T	p.Gln75Ter	p.Q75*	ENST00000342988	NM_005359.5	75	Cag/Tag	2/12	0.680917872503371	1	FACETS	0.959	0.893	1	0.959	0.893	1	CLONAL	1	TRUE	0	0.680917872503371	1		311	303	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758769	41758769	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	345	854	0	ENST00000301178.4:c.1823C>G	p.Ser608Cys	p.S608C	ENST00000301178	NM_021913.4	608	tCt/tGt	16/20	1	2	FACETS	0.947	0.898	0.997	0.947	0.898	0.997	CLONAL	1	TRUE	1	0.680917872503371	2		854	1070	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73108216	73108216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	27	63	0	ENST00000356692.5:c.316G>A	p.Glu106Lys	p.E106K	ENST00000356692		106	Gaa/Aaa	4/9	0.351029249987199	1	FACETS	0.513	0.417	0.617	0.513	0.417	0.617	INDETERMINATE	1	TRUE	0	0.680917872503371	1		63	102	SUCCESS
APC	324	MSKCC	GRCh37	5	112175073	112175074	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0056187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	31	137	0	ENST00000257430.4:c.3784dup	p.Tyr1262LeufsTer14	p.Y1262Lfs*14	ENST00000257430	NM_000038.5	1261	act/acTt	16/16	0.331615423338826	1	FACETS	0.293	0.238	0.354	0.293	0.238	0.354	INDETERMINATE	1	TRUE	0	0.680917872503371	1		137	205	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0056188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	230	684	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.373738970761599	1	FACETS	0.84	0.784	0.898	0.84	0.784	0.898	CLONAL	1	TRUE	0	0.443393255011993	1		685	961	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020768	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs926053251	NA	P-0056188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	174	511	0	ENST00000358127.4:c.77T>G	p.Val26Gly	p.V26G	ENST00000358127	NM_001280556.1	26	gTt/gGt	2/10	0.443393255011993	1	FACETS	0.856	0.79	0.924	0.856	0.79	0.924	CLONAL	1	TRUE	0	0.443393255011993	1		511	714	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247373	153247373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	61	218	2	ENST00000281708.4:c.1429G>A	p.Gly477Ser	p.G477S	ENST00000281708	NM_033632.3	477	Ggt/Agt	10/12	0.150776442940348	1	FACETS	0.61	0.529	0.697	0.61	0.529	0.697	INDETERMINATE	1	TRUE	0	0.443393255011993	1		220	351	SUCCESS
APC	324	MSKCC	GRCh37	5	112175358	112175358	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	130	214	0	ENST00000257430.4:c.4067C>A	p.Ser1356Ter	p.S1356*	ENST00000257430	NM_000038.5	1356	tCa/tAa	16/16	NA	2	FACETS	0.88	0.81	0.953			1	INDETERMINATE	2	TRUE	NA	0.443393255011993	2		214	333	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247172	153247172	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	67	240	0	ENST00000281708.4:c.1630G>T	p.Val544Phe	p.V544F	ENST00000281708	NM_033632.3	544	Gtc/Ttc	10/12	0.150776442940348	1	FACETS	0.538	0.469	0.613	0.538	0.469	0.613	INDETERMINATE	1	TRUE	0	0.443393255011993	1		240	437	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224214	36224214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774855256	NA	P-0056188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	188	604	0	ENST00000222270.7:c.6764C>T	p.Pro2255Leu	p.P2255L	ENST00000222270	NM_014727.1	2255	cCg/cTg	28/37	1	2	FACETS	0.835	0.772	0.902	0.835	0.772	0.902	CLONAL	1	TRUE	1	0.443393255011993	2		604	1015	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109702	115109702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1218875641	NA	P-0056188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	262	878	1	ENST00000257566.3:c.2176C>T	p.Arg726Trp	p.R726W	ENST00000257566	NM_016569.3	726	Cgg/Tgg	8/8	1	2	FACETS	0.893	0.835	0.952	0.893	0.835	0.952	CLONAL	1	TRUE	1	0.443393255011993	2		879	1324	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405131	405131	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0056188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	159	485	0	ENST00000380956.4:c.1212+1G>A		p.X404_splice	ENST00000380956	NM_001195286.1	404			NA	2	FACETS	0.87	0.798	0.945			1	INDETERMINATE	1	TRUE	NA	0.443393255011993	2		485	824	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891259	101891259	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	47	395	0	ENST00000374994.4:c.220G>T	p.Glu74Ter	p.E74*	ENST00000374994	NM_004612.2	74	Gaa/Taa	2/9	0.373738970761599	1	FACETS	0.28	0.235	0.329	0.28	0.235	0.329	SUBCLONAL	1	TRUE	0	0.443393255011993	1		395	590	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0056189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	123	234	0	ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	4/10	0.41394491971241	1	FACETS	0.981	0.898	1	0.981	0.898	1	CLONAL	1	TRUE	0	0.544843785530333	1		234	335	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356269	66356269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200754741	NA	P-0056189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	199	500	0	ENST00000273854.3:c.1228G>A	p.Gly410Ser	p.G410S	ENST00000273854	NM_004439.5	410	Ggt/Agt	5/18	0.310669758354811	1	FACETS	0.907	0.846	0.97	0.907	0.846	0.97	INDETERMINATE	1	TRUE	0	0.544843785530333	1		500	586	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073803	8073804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0056189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	126	320	0	ENST00000377482.5:c.855dup	p.Arg286GlnfsTer7	p.R286Qfs*7	ENST00000377482	NM_018948.3	285	-/C	4/4	0.544843785530333	1	FACETS	0.984	0.902	1	0.984	0.902	1	CLONAL	1	TRUE	0	0.544843785530333	1		320	342	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808400	1808400	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	148	1023	0	ENST00000260795.2:c.2158A>T	p.Thr720Ser	p.T720S	ENST00000260795		720	Aca/Tca	15/17	0.310669758354811	1	FACETS	0.402	0.366	0.439	0.402	0.366	0.439	INDETERMINATE	1	TRUE	0	0.544843785530333	1		1023	984	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0056190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	64	159	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.893	0.781	1	0.893	0.781	1	CLONAL	1	TRUE	1	0.534828868083276	2		159	268	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0056190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	104	277	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.997	0.9	1	0.997	0.9	1	CLONAL	1	TRUE	1	0.534828868083276	2		278	390	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411366	63411366	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	240	769	0	ENST00000330258.3:c.1801C>T	p.Arg601Ter	p.R601*	ENST00000330258	NM_152424.3	601	Cga/Tga	2/2	0.403308189191188	4	FACETS	1	0.97	1	0.357	0.333	0.382	CLONAL	1	TRUE	1	0.534828868083276	4		769	1286	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589255	67589255	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	68	309	0	ENST00000274335.5:c.1243C>T	p.Gln415Ter	p.Q415*	ENST00000274335		415	Cag/Tag	9/15	1	2	FACETS	0.997	0.878	1	0.997	0.878	1	CLONAL	1	TRUE	1	0.534828868083276	2		309	255	SUCCESS
APC	324	MSKCC	GRCh37	5	112173817	112173820	+	frameshift_variant	Frame_Shift_Del	DEL	TAGT	TAGT	-	rs879254091	NA	P-0056190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	102	286	0	ENST00000257430.4:c.2527_2530del	p.Ser843LeufsTer17	p.S843Lfs*17	ENST00000257430	NM_000038.5	842	gaTAGT/ga	16/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.534828868083276	2		286	351	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129851	55129851	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	125	491	0	ENST00000257290.5:c.385G>C	p.Val129Leu	p.V129L	ENST00000257290	NM_006206.4	129	Gta/Cta	4/23	1	2	FACETS	0.966	0.879	1	0.966	0.879	1	CLONAL	1	TRUE	1	0.534828868083276	2		491	484	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163808	152163808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1461174228	NA	P-0056190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	159	403	1	ENST00000206249.3:c.529G>A	p.Glu177Lys	p.E177K	ENST00000206249	NM_000125.3	177	Gaa/Aaa	2/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.534828868083276	2		404	532	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90960093	90960093	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	18	243	0	ENST00000265433.3:c.1873G>T	p.Glu625Ter	p.E625*	ENST00000265433	NM_002485.4	625	Gaa/Taa	12/16	1	2	FACETS	0.216	0.162	0.28	0.216	0.162	0.28	SUBCLONAL	1	TRUE	1	0.534828868083276	2		243	311	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0056191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	157	383	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.415135481198721	3	FACETS	0.864	0.799	0.931	0.864	0.799	0.931	CLONAL	2	TRUE	1	0.500133041883073	3		383	454	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435269	49435269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374216845	NA	P-0056191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	223	872	2	ENST00000301067.7:c.6284G>A	p.Arg2095His	p.R2095H	ENST00000301067	NM_003482.3	2095	cGt/cAt	31/54	0.415135481198721	3	FACETS	0.95	0.883	1	0.475	0.441	0.51	CLONAL	1	TRUE	1	0.500133041883073	3		874	1174	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962846	2962846	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	500	876	0	ENST00000396946.4:c.2062C>T	p.Arg688Ter	p.R688*	ENST00000396946	NM_032415.4	688	Cga/Tga	16/25	0.489964658147178	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.500133041883073	3		876	1180	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577508	7577508	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060501201	NA	P-0056191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	371	686	0	ENST00000269305.4:c.773A>G	p.Glu258Gly	p.E258G	ENST00000269305	NM_001126112.2	258	gAa/gGa	7/11	0.452200684065255	2	FACETS	0.874	0.833	0.914	0.874	0.833	0.914	CLONAL	2	TRUE	0	0.500133041883073	2		686	849	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591246	67591246	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0056191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	9	333	0	ENST00000274335.5:c.1746-2A>T		p.X582_splice	ENST00000274335		582			0.452200684065255	2	FACETS	0.105	0.069	0.151	0.052	0.034	0.076	SUBCLONAL	1	TRUE	0	0.500133041883073	2		333	344	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480594	50480594	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	231	427	0	ENST00000394963.4:c.464G>T	p.Arg155Met	p.R155M	ENST00000394963	NM_003076.4	155	aGg/aTg	4/13	0.415135481198721	3	FACETS	0.892	0.837	0.949	0.892	0.837	0.949	CLONAL	2	TRUE	1	0.500133041883073	3		427	647	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554735	63554736	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0056191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	107	433	0	ENST00000307078.5:c.2_3dup	p.Ser2Ter	p.S2*	ENST00000307078	NM_004655.3	1	-/TG	2/11	0.489964658147178	3	FACETS	0.911	0.819	1	0.456	0.409	0.504	CLONAL	1	TRUE	1	0.500133041883073	3		433	587	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032405	11032405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536915842	NA	P-0056191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	228	909	0	ENST00000327064.4:c.1799C>T	p.Pro600Leu	p.P600L	ENST00000327064	NM_199141.1	600	cCg/cTg	16/16	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.500133041883073	2		909	897	SUCCESS
APC	324	MSKCC	GRCh37	5	112174694	112174694	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	109	268	0	ENST00000257430.4:c.3403del	p.Tyr1135MetfsTer30	p.Y1135Mfs*30	ENST00000257430	NM_000038.5	1135	Tat/at	16/16	0.452200684065255	2	FACETS	0.882	0.808	0.958	0.882	0.808	0.958	CLONAL	2	TRUE	0	0.500133041883073	2		268	247	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0056192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	142	584	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.387579542679732	1	FACETS	0.98	0.896	1	0.98	0.896	1	CLONAL	1	TRUE	0	0.387579542679732	1		584	603	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519927	NA	P-0056192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	169	409	0	ENST00000263967.3:c.1625A>G	p.Glu542Gly	p.E542G	ENST00000263967	NM_006218.2	542	gAa/gGa	10/21	0.387579542679732	4	FACETS	1	0.978	1			1	CLONAL	2	TRUE	NA	0.387579542679732	4		409	528	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696462	47696462	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	183	376	0	ENST00000347630.2:c.361C>G	p.Arg121Gly	p.R121G	ENST00000347630	NM_001007230.1	121	Cgg/Ggg	6/11	0.386714759357263	2	FACETS	0.978	0.911	1	0.978	0.911	1	CLONAL	2	TRUE	0	0.387579542679732	2		376	483	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428055	33428055	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	48	473	0	ENST00000345365.6:c.904C>T	p.Pro302Ser	p.P302S	ENST00000345365	NM_002878.3	302	Cca/Tca	10/10	0.386714759357263	2	FACETS	0.444	0.375	0.52	0.222	0.187	0.26	SUBCLONAL	1	TRUE	0	0.387579542679732	2		473	558	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045851	143045851	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	76	484	0	ENST00000262992.4:c.1783G>C	p.Val595Leu	p.V595L	ENST00000262992	NM_001101669.1	595	Gtg/Ctg	17/24	0.249514538148793	1	FACETS	0.58	0.51	0.656	0.58	0.51	0.656	SUBCLONAL	1	TRUE	0	0.387579542679732	1		484	545	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638346	117638346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777342450	NA	P-0056192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	74	320	0	ENST00000368508.3:c.6095G>A	p.Gly2032Glu	p.G2032E	ENST00000368508	NM_002944.2	2032	gGa/gAa	38/43	1	2	FACETS	0.922	0.811	1	0.922	0.811	1	CLONAL	1	TRUE	1	0.387579542679732	2		320	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0056193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	576	1025	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.794616792750917	2	FACETS	0.968	0.944	0.991	0.968	0.944	0.991	CLONAL	2	TRUE	0	0.798861039938418	2		1025	745	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056648	26056648	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs755438887	NA	P-0056193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	53	223	0	ENST00000343677.2:c.9G>C	p.Glu3Asp	p.E3D	ENST00000343677	NM_005319.3	3	gaG/gaC	1/1	0.262586242403425	3	FACETS	0.638	0.548	0.735	0.319	0.274	0.368	INDETERMINATE	1	TRUE	1	0.798861039938418	3		223	291	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039399	49039399	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0056193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	657	634	0	ENST00000267163.4:c.2384C>G	p.Ser795Ter	p.S795*	ENST00000267163	NM_000321.2	795	tCa/tGa	23/27	0.798861039938418	2	FACETS	0.988	0.967	1	0.988	0.967	1	CLONAL	2	TRUE	0	0.798861039938418	2		634	832	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733543	85733543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	183	431	0	ENST00000370580.1:c.469G>A	p.Glu157Lys	p.E157K	ENST00000370580	NM_003921.4	157	Gaa/Aaa	3/3	0.426100324340147	3	FACETS	0.976	0.904	1	0.325	0.301	0.35	INDETERMINATE	1	TRUE	0	0.798861039938418	3		431	657	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076683	102076683	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	91	505	0	ENST00000282441.5:c.862C>T	p.Gln288Ter	p.Q288*	ENST00000282441	NM_001130145.2	288	Cag/Tag	5/9	0.782336031371496	3	FACETS	0.355	0.314	0.399	0.178	0.157	0.2	SUBCLONAL	1	TRUE	1	0.798861039938418	3		505	898	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102094427	102094430	+	frameshift_variant	Frame_Shift_Del	DEL	GATG	GATG	ATT	novel	NA	P-0056193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	79	479	1	ENST00000282441.5:c.1107_1110delinsATT	p.Met370PhefsTer5	p.M370Ffs*5	ENST00000282441	NM_001130145.2	369	ggGATG/ggATT	7/9	0.782336031371496	3	FACETS	0.297	0.26	0.336	0.148	0.13	0.168	SUBCLONAL	1	TRUE	1	0.798861039938418	3		480	933	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102098217	102098217	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	75	403	0	ENST00000282441.5:c.1181G>C	p.Arg394Pro	p.R394P	ENST00000282441	NM_001130145.2	394	cGa/cCa	8/9	0.782336031371496	3	FACETS	0.373	0.326	0.423	0.186	0.163	0.212	SUBCLONAL	1	TRUE	1	0.798861039938418	3		403	705	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195535	102195535	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	76	427	0	ENST00000263464.3:c.295C>G	p.Leu99Val	p.L99V	ENST00000263464	NM_001165.4	99	Cta/Gta	2/9	0.782336031371496	3	FACETS	0.349	0.305	0.396	0.174	0.152	0.198	SUBCLONAL	1	TRUE	1	0.798861039938418	3		427	763	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023159	1023159	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	237	717	0	ENST00000358495.3:c.1096A>G	p.Thr366Ala	p.T366A	ENST00000358495	NM_134424.2	366	Acc/Gcc	11/12	0.268417010864085	4	FACETS	0.974	0.909	1	0.487	0.454	0.521	INDETERMINATE	1	TRUE	2	0.798861039938418	4		717	1096	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914401	32914401	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs80358824	NA	P-0056193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	205	520	0	ENST00000380152.3:c.5909C>G	p.Ser1970Ter	p.S1970*	ENST00000380152		1970	tCa/tGa	11/27	0.798861039938418	2	FACETS	0.764	0.712	0.817	0.382	0.356	0.409	SUBCLONAL	1	TRUE	0	0.798861039938418	2		520	672	SUCCESS
BLM	641	MSKCC	GRCh37	15	91308570	91308570	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	93	530	1	ENST00000355112.3:c.2119C>A	p.Pro707Thr	p.P707T	ENST00000355112	NM_000057.2	707	Cct/Act	9/22	0.539125861830249	2	FACETS	0.322	0.286	0.36	0.161	0.143	0.18	SUBCLONAL	1	TRUE	0	0.798861039938418	2		531	724	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428276	33428276	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	115	576	0	ENST00000345365.6:c.847G>T	p.Gly283Ter	p.G283*	ENST00000345365	NM_002878.3	283	Gga/Tga	9/10	0.367185046237634	3	FACETS	0.504	0.454	0.557	0.168	0.151	0.186	INDETERMINATE	1	TRUE	0	0.798861039938418	3		576	799	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030712	48030712	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	211	319	0	ENST00000234420.5:c.3326T>C	p.Ile1109Thr	p.I1109T	ENST00000234420	NM_000179.2	1109	aTt/aCt	5/10	0.297264536827194	4	FACETS	0.858	0.803	0.913	0.858	0.803	0.913	INDETERMINATE	2	TRUE	2	0.798861039938418	4		319	554	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543904	212543904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	71	314	0	ENST00000342788.4:c.1495G>A	p.Glu499Lys	p.E499K	ENST00000342788	NM_005235.2	499	Gaa/Aaa	13/28	0.181432552105291	6	FACETS	0.731	0.638	0.831	0.122	0.106	0.139	INDETERMINATE	1	TRUE	0	0.798861039938418	6		314	632	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223633	53223633	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1910	147	890	0	ENST00000375401.3:c.3726C>G	p.Phe1242Leu	p.F1242L	ENST00000375401	NM_004187.3	1242	ttC/ttG	23/26	0.798861039938418	4	FACETS	0.322	0.292	0.353			1	SUBCLONAL	1	TRUE	NA	0.798861039938418	4		890	2057	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224247	53224247	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1639	131	719	0	ENST00000375401.3:c.3304C>G	p.Leu1102Val	p.L1102V	ENST00000375401	NM_004187.3	1102	Ctc/Gtc	22/26	0.798861039938418	4	FACETS	0.333	0.301	0.368			1	SUBCLONAL	1	TRUE	NA	0.798861039938418	4		719	1770	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937824	76937824	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	405	563	1	ENST00000373344.5:c.2924A>T	p.Asp975Val	p.D975V	ENST00000373344	NM_000489.3	975	gAt/gTt	9/35	0.163886042425463	3	FACETS	0.915	0.878	0.953	0.61	0.585	0.635	INDETERMINATE	2	TRUE	0	0.798861039938418	3		564	775	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52692233	52692233	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	102	331	0	ENST00000394830.3:c.627del	p.Lys210AsnfsTer14	p.K210Nfs*14	ENST00000394830	NM_018313.4	209	caG/ca	6/30	1	2	FACETS	0.79	0.709	0.876	0.79	0.709	0.876	SUBCLONAL	1	TRUE	1	0.489793620743958	2		331	527	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52692246	52692246	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	146	358	0	ENST00000394830.3:c.614G>T	p.Ser205Ile	p.S205I	ENST00000394830	NM_018313.4	205	aGc/aTc	6/30	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.489793620743958	2		358	590	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453137	140453138	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTG	novel	NA	P-0056194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	194	338	0	ENST00000288602.6:c.1797_1798insCAC	p.Thr599_Val600insHis	p.T599_V600insH	ENST00000288602	NM_004333.4	599	-/CAC	15/18	0.489793620743958	3	FACETS	0.819	0.762	0.877	0.819	0.762	0.877	CLONAL	2	TRUE	1	0.489793620743958	3		338	602	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937745	44937745	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	184	481	0	ENST00000377967.4:c.2933A>T	p.Lys978Met	p.K978M	ENST00000377967	NM_021140.2	978	aAg/aTg	19/29	0.489793620743958	1	FACETS	0.958	0.89	1	0.958	0.89	1	CLONAL	1	TRUE	0	0.489793620743958	1		481	592	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	64	461	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	0.799	0.697	0.907	1	0.975	1	CLONAL	2	TRUE	1	0.259232863671766	2		461	309	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0056195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	58	378	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.259232863671766	5	FACETS	1	0.948	1	0.797	0.691	0.909	CLONAL	2	TRUE	2	0.259232863671766	5		378	260	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0056195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	76	344	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	0.184289371193308	4	FACETS	0.902	0.8	1	0.902	0.8	1	CLONAL	3	TRUE	1	0.259232863671766	4		344	273	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699360	47699360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	33	340	0	ENST00000347630.2:c.148G>A	p.Glu50Lys	p.E50K	ENST00000347630	NM_001007230.1	50	Gaa/Aaa	4/11	0.235508809125484	3	FACETS	0.773	0.636	0.924	0.515	0.424	0.616	CLONAL	2	TRUE	0	0.259232863671766	3		340	186	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0056196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	21	277	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.268144796746694	1	FACETS	0.658	0.511	0.827	0.658	0.511	0.827	SUBCLONAL	1	TRUE	0	0.339463275866828	1		278	156	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0056196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	196	470	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.216515251063103	3	FACETS	1	0.981	1	0.766	0.713	0.819	CLONAL	2	TRUE	0	0.339463275866828	3		471	588	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0056196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	25	303	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	0.712	0.564	0.879	0.712	0.564	0.879	SUBCLONAL	1	TRUE	1	0.339463275866828	2		303	207	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945382	151945382	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	27	405	0	ENST00000262189.6:c.2137del	p.Glu713AsnfsTer5	p.E713Nfs*5	ENST00000262189	NM_170606.2	713	Gaa/aa	14/59	0.339463275866828	3	FACETS	0.854	0.693	1	0.854	0.693	1	CLONAL	2	TRUE	1	0.339463275866828	3		405	109	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016633	12016633	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	52	321	0	ENST00000353533.5:c.769T>A	p.Ser257Thr	p.S257T	ENST00000353533	NM_003010.3	257	Tct/Act	7/11	0.216515251063103	3	FACETS	1	0.889	1	0.687	0.595	0.783	CLONAL	2	TRUE	0	0.339463275866828	3		321	174	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289025	33289025	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	90	648	0	ENST00000374542.5:c.527C>T	p.Ser176Phe	p.S176F	ENST00000374542	NM_001141970.1	176	tCt/tTt	3/8	0.196344467043507	5	FACETS	1	0.976	1	0.459	0.408	0.514	INDETERMINATE	1	TRUE	2	0.339463275866828	5		648	581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0056197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	125	1025	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.663484699744721	1	FACETS	0.856	0.788	0.926	0.856	0.788	0.926	CLONAL	1	TRUE	0	0.663484699744721	1		1025	294	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244808	41244808	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs80357419	NA	P-0056197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	144	653	0	ENST00000357654.3:c.2740G>T	p.Glu914Ter	p.E914*	ENST00000357654	NM_007294.3	914	Gag/Tag	10/23	0.663484699744721	1	FACETS	0.987	0.917	1	0.987	0.917	1	CLONAL	1	TRUE	0	0.663484699744721	1		653	294	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943307	71943307	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	113	699	1	ENST00000298229.2:c.1639T>C	p.Ser547Pro	p.S547P	ENST00000298229	NM_001567.3	547	Tcc/Ccc	14/28	0.663484699744721	1	FACETS	0.879	0.806	0.953	0.879	0.806	0.953	CLONAL	1	TRUE	0	0.663484699744721	1		700	259	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851362	63851362	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	264	608	0	ENST00000279873.7:c.2140C>A	p.Pro714Thr	p.P714T	ENST00000279873	NM_032199.2	714	Ccc/Acc	10/10	1	2	FACETS	1	0.984	1	1	0.996	1	CLONAL	2	TRUE	1	0.663484699744721	2		608	378	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800579	32800599	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TCCTGGATCTCCCGAAGCACT	TCCTGGATCTCCCGAAGCACT	-	novel	NA	P-0056197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	145	862	0	ENST00000374899.4:c.948_968del	p.Glu316_Gln322del	p.E316_Q322del	ENST00000374899	NM_018833.2	316	gaAGTGCTTCGGGAGATCCAGGAt/gat	6/12	1	2	FACETS	0.751	0.688	0.816	0.751	0.688	0.816	SUBCLONAL	1	TRUE	1	0.663484699744721	2		862	582	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0056199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	1157	840	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.609063869438224	4	FACETS	0.95	0.933	0.967	0.95	0.933	0.967	CLONAL	4	FALSE	0	0.663667697262072	4		843	1526	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022499	12022499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200351280	NA	P-0056199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1354	280	917	1	ENST00000396373.4:c.605G>A	p.Arg202Gln	p.R202Q	ENST00000396373	NM_001987.4	202	cGg/cAg	5/8	0.663667697262072	6	FACETS	1	0.987	1	0.3	0.281	0.321	CLONAL	1	FALSE	2	0.663667697262072	6		918	1634	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143023	47143023	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	289	176	0	ENST00000409792.3:c.4940G>T	p.Arg1647Met	p.R1647M	ENST00000409792	NM_014159.6	1647	aGg/aTg	8/21	0.304242071621739	6	FACETS	1	0.971	1	0.776	0.736	0.817	INDETERMINATE	3	FALSE	2	0.663667697262072	6		176	653	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870210	155870210	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	85	208	0	ENST00000368323.3:c.629C>T	p.Pro210Leu	p.P210L	ENST00000368323	NM_006912.5	210	cCa/cTa	6/6	0.331654272680177	6	FACETS	0.708	0.625	0.797	0.177	0.156	0.2	INDETERMINATE	1	FALSE	2	0.663667697262072	6		208	842	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118866	115118866	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	97	233	0	ENST00000257566.3:c.475G>A	p.Asp159Asn	p.D159N	ENST00000257566	NM_016569.3	159	Gat/Aat	2/8	0.64481568440022	4	FACETS	0.762	0.68	0.849	0.254	0.226	0.283	SUBCLONAL	1	FALSE	1	0.663667697262072	4		233	638	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1977026	1977026	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	150	521	0	ENST00000382891.5:c.3520G>C	p.Glu1174Gln	p.E1174Q	ENST00000382891	NM_133335.3	1174	Gag/Cag	20/22	0.138043251183632	3	FACETS	0.762	0.697	0.83	0.254	0.232	0.277	INDETERMINATE	1	FALSE	0	0.663667697262072	3		521	790	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542456	187542456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371394820	NA	P-0056200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	61	472	0	ENST00000441802.2:c.5284G>A	p.Ala1762Thr	p.A1762T	ENST00000441802	NM_005245.3	1762	Gcg/Acg	10/27	0.222877907489331	1	FACETS	0.67	0.577	0.771	0.67	0.577	0.771	SUBCLONAL	1	TRUE	0	0.2378256971763	1		472	675	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175996825	175996825	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0056200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	68	348	0	ENST00000367669.3:c.1613-1G>A		p.X538_splice	ENST00000367669	NM_022457.5	538			1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.2378256971763	2		348	550	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188158	108188167	+	frameshift_variant	Frame_Shift_Del	DEL	ATGAAAATAA	ATGAAAATAA	-	novel	NA	P-0056200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	54	300	0	ENST00000278616.4:c.6258_6267del	p.Tyr2086Ter	p.Y2086*	ENST00000278616	NM_000051.3	2086	tATGAAAATAAa/ta	43/63	0.2378256971763	1	FACETS	0.924	0.791	1	0.924	0.791	1	CLONAL	1	TRUE	0	0.2378256971763	1		300	433	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038548	47038575	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCGTGCCCAAGTCAGGTGAGGCCCACCT	GCGTGCCCAAGTCAGGTGAGGCCCACCT	CCTA	novel	NA	P-0056200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	116	427	2	ENST00000377604.3:c.710_724+13delinsCCTA		p.X237_splice	ENST00000377604	NM_001204468.1	237		8/24	1	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.2378256971763	1		429	580	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	57	277	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.925	0.795	1	0.925	0.795	1	CLONAL	1	TRUE	1	0.25	2		278	493	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	69	411	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.25	2		412	523	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	46	289	0	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.25	2		289	324	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99180039	99180039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767987854	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	90	659	0	ENST00000074304.5:c.1982C>T	p.Ala661Val	p.A661V	ENST00000074304	NM_001134224.1	661	gCg/gTg	19/26	1	2	FACETS	0.988	0.876	1	0.988	0.876	1	CLONAL	1	TRUE	1	0.25	2		659	729	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907692	111907692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775080943	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	62	345	0	ENST00000393256.3:c.466G>A	p.Gly156Arg	p.G156R	ENST00000393256	NM_006538.4	156	Gga/Aga	3/4	1	2	FACETS	0.952	0.823	1	0.952	0.823	1	CLONAL	1	TRUE	1	0.25	2		345	521	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	82	479	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.929	0.819	1	0.929	0.819	1	CLONAL	1	TRUE	1	0.25	2		479	706	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852248	63852248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145564601	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	100	531	0	ENST00000279873.7:c.3026C>T	p.Ala1009Val	p.A1009V	ENST00000279873	NM_032199.2	1009	gCg/gTg	10/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.25	2		531	689	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721622	49721622	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs200268600	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	8	32	0	ENST00000449682.2:c.2017G>A	p.Gly673Ser	p.G673S	ENST00000449682	NM_020998.3	673	Ggt/Agt	18/18	1	2	FACETS	1	0.792	1	1	0.792	1	CLONAL	1	TRUE	1	0.25	2		32	48	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412110	63412110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852216	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	113	785	1	ENST00000330258.3:c.1057C>T	p.Arg353Ter	p.R353*	ENST00000330258	NM_152424.3	353	Cga/Tga	2/2	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.25	2		786	891	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535442	66535442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	47	189	1	ENST00000273854.3:c.19C>T	p.Arg7Trp	p.R7W	ENST00000273854	NM_004439.5	7	Cgg/Tgg	1/18	1	2	FACETS	1	0.882	1	1	0.975	1	CLONAL	2	TRUE	1	0.25	2		190	182	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779343	3779343	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1369215188	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	110	838	0	ENST00000262367.5:c.5705C>T	p.Thr1902Met	p.T1902M	ENST00000262367	NM_004380.2	1902	aCg/aTg	31/31	1	2	FACETS	0.914	0.82	1	0.914	0.82	1	CLONAL	1	TRUE	1	0.25	2		838	963	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375495	15375495	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45500091	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	151	881	0	ENST00000263377.2:c.932C>T	p.Pro311Leu	p.P311L	ENST00000263377	NM_058243.2	311	cCg/cTg	6/20	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.25	2		881	1195	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526163	189526163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	125	607	1	ENST00000264731.3:c.427G>A	p.Val143Ile	p.V143I	ENST00000264731	NM_003722.4	143	Gtc/Atc	4/14	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.25	2		608	904	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696461	47696461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	119	386	0	ENST00000347630.2:c.362G>A	p.Arg121Gln	p.R121Q	ENST00000347630	NM_001007230.1	121	cGg/cAg	6/11	0.256353411801202	2	FACETS	0.864	0.783	0.949	0.864	0.783	0.949	CLONAL	2	TRUE	0	0.25	2		386	551	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528705	8528705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370111525	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	78	417	0	ENST00000356435.5:c.427G>A	p.Ala143Thr	p.A143T	ENST00000356435		143	Gcc/Acc	4/35	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.25	2		417	562	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212056	5212056	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1314953096	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	124	745	0	ENST00000357368.4:c.4975C>T	p.Arg1659Cys	p.R1659C	ENST00000357368	NM_002850.3	1659	Cgc/Tgc	32/38	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.25	2		745	863	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907687	111907687	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373945451	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	64	357	0	ENST00000393256.3:c.461G>A	p.Arg154His	p.R154H	ENST00000393256	NM_006538.4	154	cGt/cAt	3/4	1	2	FACETS	0.938	0.813	1	0.938	0.813	1	CLONAL	1	TRUE	1	0.25	2		357	546	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434235	49434235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375114492	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	162	970	1	ENST00000301067.7:c.7318G>A	p.Val2440Ile	p.V2440I	ENST00000301067	NM_003482.3	2440	Gtt/Att	31/54	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.25	2		971	1295	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533584	63533584	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	72	928	0	ENST00000307078.5:c.1570G>A	p.Val524Ile	p.V524I	ENST00000307078	NM_004655.3	524	Gtc/Atc	6/11	0.256353411801202	2	FACETS	0.526	0.457	0.599	0.263	0.228	0.3	SUBCLONAL	1	TRUE	0	0.25	2		928	1096	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610165	81610165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs185776618	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	57	376	0	ENST00000298171.2:c.1763C>T	p.Thr588Met	p.T588M	ENST00000298171	NM_000369.2	588	aCg/aTg	10/10	1	2	FACETS	0.829	0.712	0.957	0.829	0.712	0.957	CLONAL	1	TRUE	1	0.25	2		376	550	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099941	27099941	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	98	634	0	ENST00000324856.7:c.3820G>T	p.Gly1274Ter	p.G1274*	ENST00000324856	NM_006015.4	1274	Gga/Tga	15/20	1	2	FACETS	0.911	0.811	1	0.911	0.811	1	CLONAL	1	TRUE	1	0.25	2		634	861	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948208	71948208	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	127	899	0	ENST00000298229.2:c.2920G>C	p.Ala974Pro	p.A974P	ENST00000298229	NM_001567.3	974	Gcc/Ccc	26/28	1	2	FACETS	0.983	0.889	1	0.983	0.889	1	CLONAL	1	TRUE	1	0.25	2		899	1034	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598910	28598910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758133085	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	102	804	0	ENST00000253063.3:c.470G>A	p.Arg157His	p.R157H	ENST00000253063	NM_031459.4	157	cGc/cAc	4/10	1	2	FACETS	0.797	0.711	0.888	0.797	0.711	0.888	SUBCLONAL	1	TRUE	1	0.25	2		804	1024	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430868	181430868	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	51	989	0	ENST00000325404.1:c.720G>A	p.Met240Ile	p.M240I	ENST00000325404	NM_003106.3	240	atG/atA	1/1	1	2	FACETS	0.404	0.341	0.472	0.404	0.341	0.472	SUBCLONAL	1	TRUE	1	0.25	2		989	1011	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149917	202149917	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	94	511	0	ENST00000358485.4:c.1358C>A	p.Pro453Gln	p.P453Q	ENST00000358485	NM_001080125.1	453	cCg/cAg	8/9	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.25	2		511	740	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817418	39817418	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	60	490	0	ENST00000288319.7:c.145C>A	p.Pro49Thr	p.P49T	ENST00000288319	NM_182918.3	49	Cca/Aca	2/10	1	2	FACETS	0.805	0.694	0.927	0.805	0.694	0.927	CLONAL	1	TRUE	1	0.25	2		490	596	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373238	118373238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782789725	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	73	408	2	ENST00000534358.1:c.6631C>T	p.Arg2211Trp	p.R2211W	ENST00000534358	NM_005933.3	2211	Cgg/Tgg	27/36	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.25	2		410	565	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658568	206658568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199623162	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	71	528	1	ENST00000367120.3:c.1541C>T	p.Thr514Met	p.T514M	ENST00000367120	NM_014002.3	514	aCg/aTg	15/22	1	2	FACETS	0.904	0.79	1	0.904	0.79	1	CLONAL	1	TRUE	1	0.25	2		529	628	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645435	67645435	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	80	323	0	ENST00000264010.4:c.700G>T	p.Glu234Ter	p.E234*	ENST00000264010	NM_006565.3	234	Gag/Tag	3/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.25	2		323	499	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199526	16199526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146693537	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	56	432	1	ENST00000375759.3:c.299G>A	p.Arg100His	p.R100H	ENST00000375759	NM_015001.2	100	cGt/cAt	2/15	1	2	FACETS	0.816	0.699	0.944	0.816	0.699	0.944	CLONAL	1	TRUE	1	0.25	2		433	549	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43817930	43817930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148784027	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	105	689	1	ENST00000372470.3:c.1609C>T	p.Arg537Trp	p.R537W	ENST00000372470	NM_005373.2	537	Cgg/Tgg	11/12	1	2	FACETS	0.986	0.883	1	0.986	0.883	1	CLONAL	1	TRUE	1	0.25	2		690	852	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195242	102195242	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	35	228	0	ENST00000263464.3:c.2T>C	p.Met1?	p.M1?	ENST00000263464	NM_001165.4	1	aTg/aCg	2/9	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.25	2		228	264	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372400	118372400	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	88	401	0	ENST00000534358.1:c.6333A>C	p.Lys2111Asn	p.K2111N	ENST00000534358	NM_005933.3	2111	aaA/aaC	26/36	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.25	2		401	608	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066873	30066873	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	90	508	0	ENST00000331968.5:c.2258A>G	p.Glu753Gly	p.E753G	ENST00000331968	NM_002742.2	753	gAg/gGg	16/18	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.25	2		508	703	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122285	2122285	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	116	731	0	ENST00000219476.3:c.2141C>A	p.Pro714His	p.P714H	ENST00000219476	NM_000548.3	714	cCt/cAt	20/42	1	2	FACETS	0.96	0.864	1	0.96	0.864	1	CLONAL	1	TRUE	1	0.25	2		731	967	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347518	89347518	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	89	656	0	ENST00000301030.4:c.5432G>T	p.Arg1811Met	p.R1811M	ENST00000301030	NM_001256183.1	1811	aGg/aTg	9/13	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.25	2		656	678	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349622	89349622	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	52	698	0	ENST00000301030.4:c.3328G>T	p.Glu1110Ter	p.E1110*	ENST00000301030	NM_001256183.1	1110	Gag/Tag	9/13	1	2	FACETS	0.416	0.353	0.486	0.416	0.353	0.486	SUBCLONAL	1	TRUE	1	0.25	2		698	1000	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56798132	56798132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	109	365	0	ENST00000337432.4:c.863C>T	p.Thr288Ile	p.T288I	ENST00000337432	NM_058216.2	288	aCa/aTa	6/9	0.256353411801202	2	FACETS	0.944	0.852	1	0.944	0.852	1	CLONAL	2	TRUE	0	0.25	2		365	462	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662968	227662968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	106	688	0	ENST00000305123.5:c.487G>A	p.Val163Ile	p.V163I	ENST00000305123	NM_005544.2	163	Gtc/Atc	1/2	1	2	FACETS	0.967	0.866	1	0.967	0.866	1	CLONAL	1	TRUE	1	0.25	2		688	877	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430642	181430642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	79	496	1	ENST00000325404.1:c.494G>A	p.Gly165Asp	p.G165D	ENST00000325404	NM_003106.3	165	gGc/gAc	1/1	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.25	2		497	487	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230759	66230759	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	21	259	0	ENST00000273854.3:c.2212C>A	p.His738Asn	p.H738N	ENST00000273854	NM_004439.5	738	Cat/Aat	12/18	1	2	FACETS	0.553	0.426	0.701	0.553	0.426	0.701	SUBCLONAL	1	TRUE	1	0.25	2		259	304	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589623	67589624	+	inframe_insertion	In_Frame_Ins	INS	-	-	TATGAT	novel	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	46	219	0	ENST00000274335.5:c.1387_1392dup	p.Tyr463_Asp464dup	p.Y463_D464dup	ENST00000274335		463	-/TATGAT	10/15	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.25	2		219	271	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456848	149456848	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371848144	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	118	624	0	ENST00000286301.3:c.880C>T	p.Arg294Trp	p.R294W	ENST00000286301	NM_005211.3	294	Cgg/Tgg	6/22	0.3	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	0	0.25	1		624	823	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858494	27858494	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188857118	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	76	416	0	ENST00000359303.2:c.77C>T	p.Ala26Val	p.A26V	ENST00000359303	NM_003535.2	26	gCg/gTg	1/1	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.25	2		416	494	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69027987	69027987	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	22	263	0	ENST00000288368.4:c.3147-1G>A		p.X1049_splice	ENST00000288368	NM_024870.2	1049			1	2	FACETS	0.669	0.52	0.842	0.669	0.52	0.842	SUBCLONAL	1	TRUE	1	0.25	2		263	263	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341745	8341745	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	43	490	0	ENST00000356435.5:c.4895T>C	p.Leu1632Pro	p.L1632P	ENST00000356435		1632	cTg/cCg	29/35	1	2	FACETS	0.457	0.381	0.541	0.457	0.381	0.541	SUBCLONAL	1	TRUE	1	0.25	2		490	753	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030473	47030473	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	133	779	1	ENST00000377604.3:c.248G>A	p.Arg83Gln	p.R83Q	ENST00000377604	NM_001204468.1	83	cGg/cAg	4/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.25	2		780	929	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0056202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	203	710	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.392924065340367	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.409769701595861	1		711	741	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686365	117686365	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1287346255	NA	P-0056202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	37	169	0	ENST00000368508.3:c.2976C>A	p.Phe992Leu	p.F992L	ENST00000368508	NM_002944.2	992	ttC/ttA	20/43	0.409769701595861	1	FACETS	0.662	0.55	0.784	0.662	0.55	0.784	SUBCLONAL	1	TRUE	0	0.409769701595861	1		169	217	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254582	46254582	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0056202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	99	328	0	ENST00000334344.6:c.4774-2A>C		p.X1592_splice	ENST00000334344	NM_152641.2	1592			1	2	FACETS	0.982	0.881	1	0.982	0.881	1	CLONAL	1	TRUE	1	0.409769701595861	2		328	492	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937447	178937447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	62	416	0	ENST00000263967.3:c.1835G>A	p.Arg612Gln	p.R612Q	ENST00000263967	NM_006218.2	612	cGa/cAa	12/21	0.289574443984644	3	FACETS	0.626	0.541	0.719			1	SUBCLONAL	1	TRUE	NA	0.409769701595861	3		416	582	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210225	123210225	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	98	253	0	ENST00000218089.9:c.2577C>G	p.His859Gln	p.H859Q	ENST00000218089	NM_001042749.1	859	caC/caG	26/35	1	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.409769701595861	1		253	347	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246680	46246680	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0056202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	30	125	0	ENST00000334344.6:c.4773+1G>T		p.X1591_splice	ENST00000334344	NM_152641.2	1591			1	2	FACETS	0.832	0.677	1	0.832	0.677	1	CLONAL	1	TRUE	1	0.409769701595861	2		125	176	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0056203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	310	584	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.438343051960513	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.438343051960513	2		584	620	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690835	89690835	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs876661177	NA	P-0056203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	88	295	0	ENST00000371953.3:c.242T>G	p.Phe81Cys	p.F81C	ENST00000371953	NM_000314.4	81	tTt/tGt	4/9	0.438343051960513	1	FACETS	0.633	0.563	0.708	0.633	0.563	0.708	SUBCLONAL	1	TRUE	0	0.438343051960513	1		295	495	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685289	89685289	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554897267	NA	P-0056203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	54	174	0	ENST00000371953.3:c.188del	p.Asn63ThrfsTer36	p.N63Tfs*36	ENST00000371953	NM_000314.4	62	Aaa/aa	3/9	0.438343051960513	1	FACETS	0.517	0.443	0.597	0.517	0.443	0.597	SUBCLONAL	1	TRUE	0	0.438343051960513	1		174	372	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103508418	103508418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	68	151	1	ENST00000355739.4:c.484G>A	p.Glu162Lys	p.E162K	ENST00000355739	NM_000123.3	162	Gaa/Aaa	5/15	0.347982195149038	3	FACETS	1	0.969	1	0.449	0.394	0.506	CLONAL	1	TRUE	0	0.438343051960513	3		152	281	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211361	98211361	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	148	730	0	ENST00000331920.6:c.3794C>G	p.Ala1265Gly	p.A1265G	ENST00000331920	NM_000264.3	1265	gCc/gGc	22/24	0.438343051960513	2	FACETS	1	0.959	1	0.538	0.493	0.584	CLONAL	1	TRUE	0	0.438343051960513	2		730	628	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401202	139401202	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	153	896	0	ENST00000277541.6:c.3867T>G	p.Asn1289Lys	p.N1289K	ENST00000277541	NM_017617.3	1289	aaT/aaG	23/34	0.438343051960513	2	FACETS	1	0.917	1	0.5	0.458	0.543	CLONAL	1	TRUE	0	0.438343051960513	2		896	698	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0056204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	115	181	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.0394856798868013	4	FACETS	1	0.953	1	1	0.953	1	INDETERMINATE	2	TRUE	2	0.152431030518084	4		181	793	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0056204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	78	378	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.146951127341977	3	FACETS	0.924	0.813	1	0.924	0.813	1	CLONAL	2	TRUE	1	0.152431030518084	3		378	596	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911622	114911622	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	45	559	0	ENST00000543371.1:c.1140C>G	p.Ile380Met	p.I380M	ENST00000543371	NM_001198531.1	380	atC/atG	10/14	1	2	FACETS	0.927	0.778	1	0.927	0.778	1	CLONAL	1	TRUE	1	0.152431030518084	2		559	637	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186745	108186745	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	74	424	0	ENST00000278616.4:c.6103A>C	p.Thr2035Pro	p.T2035P	ENST00000278616	NM_000051.3	2035	Aca/Cca	42/63	0.149700716816999	2	FACETS	0.838	0.735	0.95	0.838	0.735	0.95	CLONAL	2	TRUE	0	0.152431030518084	2		424	579	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120886	94120886	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	45	371	1	ENST00000369303.4:c.165G>T	p.Trp55Cys	p.W55C	ENST00000369303	NM_004440.3	55	tgG/tgT	3/17	0.149700716816999	2	FACETS	1	0.953	1	0.696	0.586	0.818	CLONAL	1	TRUE	0	0.152431030518084	2		372	424	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974182	2974182	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	120	854	0	ENST00000396946.4:c.1423G>T	p.Asp475Tyr	p.D475Y	ENST00000396946	NM_032415.4	475	Gac/Tac	10/25	0.146951127341977	3	FACETS	0.896	0.808	0.989	0.896	0.808	0.989	CLONAL	2	TRUE	1	0.152431030518084	3		854	946	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	164	677	4	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	0.245924231052501	1	FACETS	1	0.954	1	1	0.993	1	CLONAL	2	TRUE	0	0.245924231052501	1		681	559	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	135	360	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.132792591218357	3	FACETS	0.919	0.842	0.999	1	0.985	1	INDETERMINATE	3	TRUE	1	0.245924231052501	3		360	447	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161907	47161907	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	88	325	1	ENST00000409792.3:c.4219del	p.Arg1407GlyfsTer5	p.R1407Gfs*5	ENST00000409792	NM_014159.6	1407	Agg/gg	3/21	0.245924231052501	3	FACETS	1	0.962	1	0.779	0.696	0.865	CLONAL	2	TRUE	0	0.245924231052501	3		326	344	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	150	360	0	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	0.835	0.769	0.903	1	0.993	1	CLONAL	3	TRUE	1	0.245924231052501	2		360	487	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	208	306	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.245924231052501	3	FACETS	0.918	0.87	0.965	1	0.995	1	CLONAL	6	TRUE	0	0.245924231052501	3		306	345	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	89	229	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	1	0.941	1	1	0.987	1	CLONAL	2	TRUE	1	0.245924231052501	2		229	336	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223796	53223796	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	191	920	1	ENST00000375401.3:c.3563G>C	p.Cys1188Ser	p.C1188S	ENST00000375401	NM_004187.3	1188	tGt/tCt	23/26	0.245924231052501	1	FACETS	1	0.969	1	1	0.994	1	CLONAL	2	TRUE	0	0.245924231052501	1		921	632	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	155	685	8	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	0.245924231052501	1	FACETS	1	0.966	1	1	0.992	1	CLONAL	2	TRUE	0	0.245924231052501	1		693	509	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	144	397	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.245924231052501	0	FACETS	0.796	0.735	0.858			1	SUBCLONAL	3	TRUE	0	0.245924231052501	0		397	370	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	71	225	0	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	0.245924231052501	1	FACETS	1	0.931	1	1	0.984	1	CLONAL	2	TRUE	0	0.245924231052501	1		225	236	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435256	18435256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	85	274	0	ENST00000266497.5:c.241G>A	p.Ala81Thr	p.A81T	ENST00000266497		81	Gca/Aca	1/31	1	2	FACETS	0.914	0.821	1	1	0.988	1	CLONAL	3	TRUE	1	0.245924231052501	2		274	252	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287469	46287469	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	114	316	0	ENST00000334344.6:c.5333del	p.Asn1778IlefsTer13	p.N1778Ifs*13	ENST00000334344	NM_152641.2	1776	ttA/tt	20/21	0.132792591218357	3	FACETS	0.967	0.88	1	1	0.985	1	INDETERMINATE	3	TRUE	1	0.245924231052501	3		316	359	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	140	318	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	0.93	0.856	1	1	0.993	1	CLONAL	3	TRUE	1	0.245924231052501	2		318	408	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636729	8636729	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	110	308	0	ENST00000356435.5:c.180del	p.Gly61GlufsTer11	p.G61Efs*11	ENST00000356435		60	aaA/aa	2/35	1	2	FACETS	0.923	0.84	1	1	0.991	1	CLONAL	3	TRUE	1	0.245924231052501	2		308	323	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593507	48593507	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1367209662	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	91	260	2	ENST00000342988.3:c.1258C>T	p.Arg420Cys	p.R420C	ENST00000342988	NM_005359.5	420	Cgt/Tgt	10/12	1	2	FACETS	1	0.97	1	1	0.988	1	CLONAL	2	TRUE	1	0.245924231052501	2		262	303	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	123	426	7	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.972	0.89	1	1	0.992	1	CLONAL	3	TRUE	1	0.245924231052501	2		433	343	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348151	89348151	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs891050032	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	193	819	0	ENST00000301030.4:c.4799G>A	p.Arg1600Gln	p.R1600Q	ENST00000301030	NM_001256183.1	1600	cGg/cAg	9/13	0.245924231052501	1	FACETS	0.837	0.78	0.896	1	0.994	1	CLONAL	3	TRUE	0	0.245924231052501	1		819	548	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630605	187630605	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	204	573	1	ENST00000441802.2:c.377del	p.Asn126IlefsTer20	p.N126Ifs*20	ENST00000441802	NM_005245.3	126	aAt/at	2/27	0.0602344168660436	3	FACETS	0.995	0.928	1	1	0.992	1	INDETERMINATE	3	TRUE	1	0.245924231052501	3		574	624	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348998	11348998	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	138	398	1	ENST00000332029.2:c.338del	p.Phe113SerfsTer5	p.F113Sfs*5	ENST00000332029	NM_003745.1	113	tTc/tc	2/2	0.245924231052501	1	FACETS	1	0.963	1	1	0.992	1	CLONAL	2	TRUE	0	0.245924231052501	1		399	452	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323352	31323352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1428341966	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	116	510	0	ENST00000412585.2:c.637G>A	p.Val213Met	p.V213M	ENST00000412585	NM_005514.6	213	Gtg/Atg	4/8	0.0602344168660436	3	FACETS	0.883	0.803	0.966	1	0.981	1	INDETERMINATE	3	TRUE	1	0.245924231052501	3		510	400	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224533	36224533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758088530	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	224	934	1	ENST00000222270.7:c.6995G>A	p.Arg2332His	p.R2332H	ENST00000222270	NM_014727.1	2332	cGt/cAt	29/37	0.245924231052501	1	FACETS	0.892	0.837	0.948	1	0.995	1	CLONAL	3	TRUE	0	0.245924231052501	1		935	597	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218451	36218451	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs34078597	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	101	671	0	ENST00000222270.7:c.4235del	p.Gly1412AlafsTer10	p.G1412Afs*10	ENST00000222270	NM_014727.1	1410	caG/ca	16/37	0.245924231052501	1	FACETS	0.984	0.888	1	1	0.988	1	CLONAL	2	TRUE	0	0.245924231052501	1		671	366	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187222	38187222	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	253	799	1	ENST00000317025.8:c.1255del	p.Thr419ProfsTer8	p.T419Pfs*8	ENST00000317025	NM_023034.1	419	Acc/cc	6/24	1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	1	0.245924231052501	2		800	871	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806605	1806605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17884368	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	175	808	0	ENST00000260795.2:c.1321G>A	p.Ala441Thr	p.A441T	ENST00000260795		441	Gca/Aca	9/17	0.245924231052501	1	FACETS	0.863	0.802	0.926	1	0.994	1	CLONAL	3	TRUE	0	0.245924231052501	1		808	482	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101453	27101453	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	190	706	1	ENST00000324856.7:c.4735C>T	p.Gln1579Ter	p.Q1579*	ENST00000324856	NM_006015.4	1579	Cag/Tag	18/20	1	2	FACETS	0.913	0.85	0.978	1	0.994	1	CLONAL	3	TRUE	1	0.245924231052501	2		707	564	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900353	3900353	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	160	626	0	ENST00000262367.5:c.743del	p.Pro248ArgfsTer3	p.P248Rfs*3	ENST00000262367	NM_004380.2	248	cCg/cg	2/31	0.245924231052501	1	FACETS	1	0.954	1	1	0.992	1	CLONAL	2	TRUE	0	0.245924231052501	1		626	545	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2097756	2097756	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	159	605	0	ENST00000219066.1:c.93del	p.Cys32ValfsTer24	p.C32Vfs*24	ENST00000219066	NM_002528.5	31	ggG/gg	1/6	0.245924231052501	1	FACETS	1	0.977	1	1	0.993	1	CLONAL	2	TRUE	0	0.245924231052501	1		605	495	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229205	36229205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	101	575	1	ENST00000222270.7:c.7895G>A	p.Arg2632His	p.R2632H	ENST00000222270	NM_014727.1	2632	cGc/cAc	37/37	0.245924231052501	1	FACETS	0.984	0.888	1	1	0.988	1	CLONAL	2	TRUE	0	0.245924231052501	1		576	366	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660270	227660270	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	28	617	0	ENST00000305123.5:c.3185del	p.Gly1062AlafsTer8	p.G1062Afs*8	ENST00000305123	NM_005544.2	1062	gGc/gc	1/2	0.132792591218357	3	FACETS	0.508	0.405	0.626	0.254	0.202	0.313	INDETERMINATE	1	TRUE	1	0.245924231052501	3		617	503	SUCCESS
ATM	472	MSKCC	GRCh37	11	108126975	108126975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs565622131	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	211	571	0	ENST00000278616.4:c.2158C>T	p.Arg720Cys	p.R720C	ENST00000278616	NM_000051.3	720	Cgt/Tgt	14/63	1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	1	0.245924231052501	2		571	698	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993348	72993348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759852645	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	200	776	0	ENST00000268489.5:c.697G>A	p.Val233Met	p.V233M	ENST00000268489	NM_006885.3	233	Gtg/Atg	2/10	0.245924231052501	1	FACETS	1	0.986	1	1	0.994	1	CLONAL	2	TRUE	0	0.245924231052501	1		776	588	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252856	10252856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370786558	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	154	692	1	ENST00000340748.4:c.3109G>A	p.Ala1037Thr	p.A1037T	ENST00000340748		1037	Gca/Aca	29/40	0.245924231052501	1	FACETS	1	0.937	1	1	0.992	1	CLONAL	2	TRUE	0	0.245924231052501	1		693	538	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97887408	97887408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745910444	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	165	488	0	ENST00000289081.3:c.956C>T	p.Thr319Met	p.T319M	ENST00000289081	NM_000136.2	319	aCg/aTg	10/15	1	2	FACETS	0.893	0.826	0.961	1	0.994	1	CLONAL	3	TRUE	1	0.245924231052501	2		488	501	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683208	88683209	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	117	424	0	ENST00000372037.3:c.1426_1427dup	p.Lys477SerfsTer22	p.K477Sfs*22	ENST00000372037	NM_004329.2	473	gtt/gtTGt	12/13	1	2	FACETS	1	0.973	1	1	0.991	1	CLONAL	2	TRUE	1	0.245924231052501	2		424	400	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63816929	63816930	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	65	196	1	ENST00000279873.7:c.906dup	p.Val303SerfsTer4	p.V303Sfs*4	ENST00000279873	NM_032199.2	300	-/A	6/10	1	2	FACETS	1	0.884	1	1	0.981	1	CLONAL	2	TRUE	1	0.245924231052501	2		197	262	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259405	16259405	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	17	403	0	ENST00000375759.3:c.6670A>G	p.Asn2224Asp	p.N2224D	ENST00000375759	NM_015001.2	2224	Aat/Gat	11/15	1	2	FACETS	0.472	0.352	0.615	0.472	0.352	0.615	SUBCLONAL	1	TRUE	1	0.245924231052501	2		403	293	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814636	43814636	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	138	495	0	ENST00000372470.3:c.1431G>C	p.Trp477Cys	p.W477C	ENST00000372470	NM_005373.2	477	tgG/tgC	9/12	1	2	FACETS	0.897	0.824	0.972	1	0.993	1	CLONAL	3	TRUE	1	0.245924231052501	2		495	417	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70442644	70442644	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	178	502	0	ENST00000373644.4:c.4966C>T	p.Arg1656Cys	p.R1656C	ENST00000373644	NM_030625.2	1656	Cgt/Tgt	10/12	1	2	FACETS	0.963	0.895	1	1	0.994	1	CLONAL	3	TRUE	1	0.245924231052501	2		502	501	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114901035	114901035	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	28	546	0	ENST00000543371.1:c.647del	p.Pro216HisfsTer9	p.P216Hfs*9	ENST00000543371	NM_001198531.1	215	aaC/aa	6/14	1	2	FACETS	0.412	0.328	0.508	0.412	0.328	0.508	SUBCLONAL	1	TRUE	1	0.245924231052501	2		546	553	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911020	94911020	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	165	545	0	ENST00000536441.1:c.1110C>A	p.Asp370Glu	p.D370E	ENST00000536441	NM_144665.3	370	gaC/gaA	8/10	1	2	FACETS	1	0.981	1	1	0.993	1	CLONAL	2	TRUE	1	0.245924231052501	2		545	559	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246374	46246374	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1174556277	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	101	312	0	ENST00000334344.6:c.4468G>T	p.Gly1490Ter	p.G1490*	ENST00000334344	NM_152641.2	1490	Gga/Tga	15/21	0.132792591218357	3	FACETS	0.94	0.85	1	1	0.982	1	INDETERMINATE	3	TRUE	1	0.245924231052501	3		312	327	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907487	32907487	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	79	214	0	ENST00000380152.3:c.1875del	p.Phe625LeufsTer19	p.F625Lfs*19	ENST00000380152		624	gcT/gc	10/27	1	2	FACETS	0.996	0.892	1	1	0.988	1	CLONAL	3	TRUE	1	0.245924231052501	2		214	215	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73340142	73340145	+	frameshift_variant	Frame_Shift_Del	DEL	GTGA	GTGA	-	novel	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	87	253	0	ENST00000377767.4:c.1935_1938del	p.His646IlefsTer3	p.H646Ifs*3	ENST00000377767	NM_014953.3	645	acTCAC/ac	15/21	1	2	FACETS	1	0.921	1	1	0.986	1	CLONAL	2	TRUE	1	0.245924231052501	2		253	341	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226048	2226048	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	36	727	1	ENST00000326181.6:c.1747-2A>G		p.X583_splice	ENST00000326181	NM_032271.2	583			0.245924231052501	1	FACETS	0.481	0.395	0.578	0.481	0.395	0.578	SUBCLONAL	1	TRUE	0	0.245924231052501	1		728	534	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348949	89348949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765151001	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	158	842	0	ENST00000301030.4:c.4001C>T	p.Pro1334Leu	p.P1334L	ENST00000301030	NM_001256183.1	1334	cCg/cTg	9/13	0.245924231052501	1	FACETS	0.97	0.893	1	1	0.992	1	CLONAL	2	TRUE	0	0.245924231052501	1		842	581	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512389	38512389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1055195329	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	160	621	0	ENST00000254066.5:c.1300G>A	p.Gly434Arg	p.G434R	ENST00000254066	NM_000964.3	434	Ggg/Agg	9/9	1	2	FACETS	1	0.97	1	1	0.994	1	CLONAL	3	TRUE	1	0.245924231052501	2		621	399	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677763	47677763	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761155742	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	136	401	0	ENST00000347630.2:c.1102C>T	p.Arg368Cys	p.R368C	ENST00000347630	NM_001007230.1	368	Cgc/Tgc	11/11	1	2	FACETS	0.859	0.788	0.933	1	0.992	1	CLONAL	3	TRUE	1	0.245924231052501	2		401	429	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258551	19258551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	168	879	1	ENST00000162023.5:c.349G>A	p.Ala117Thr	p.A117T	ENST00000162023		117	Gca/Aca	8/13	0.245924231052501	1	FACETS	0.954	0.881	1	1	0.992	1	CLONAL	2	TRUE	0	0.245924231052501	1		880	628	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149689	202149689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	153	503	0	ENST00000358485.4:c.1130G>A	p.Gly377Glu	p.G377E	ENST00000358485	NM_001080125.1	377	gGa/gAa	8/9	0.132792591218357	3	FACETS	0.93	0.857	1	1	0.987	1	INDETERMINATE	3	TRUE	1	0.245924231052501	3		503	501	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067499	37067499	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs267607825	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	248	447	0	ENST00000231790.2:c.1409+1G>C		p.X470_splice	ENST00000231790	NM_000249.3	470			0.245924231052501	3	FACETS	1	0.984	1	1	0.995	1	CLONAL	5	TRUE	0	0.245924231052501	3		447	419	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125583	47125583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750289124	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	23	361	0	ENST00000409792.3:c.5687C>T	p.Ala1896Val	p.A1896V	ENST00000409792	NM_014159.6	1896	gCa/gTa	12/21	0.245924231052501	3	FACETS	0.644	0.502	0.808	0.215	0.167	0.27	SUBCLONAL	1	TRUE	0	0.245924231052501	3		361	326	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146698	185146698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	217	542	1	ENST00000265026.3:c.329C>T	p.Thr110Ile	p.T110I	ENST00000265026	NM_004721.4	110	aCa/aTa	2/14	1	2	FACETS	0.944	0.883	1	1	0.995	1	CLONAL	3	TRUE	1	0.245924231052501	2		543	623	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595596	55595596	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781588289	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	75	222	0	ENST00000288135.5:c.2086G>A	p.Asp696Asn	p.D696N	ENST00000288135	NM_000222.2	696	Gat/Aat	14/21	0.245924231052501	1	FACETS	1	0.966	1	1	0.986	1	CLONAL	2	TRUE	0	0.245924231052501	1		222	218	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514319	149514319	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	94	380	0	ENST00000261799.4:c.625C>T	p.Leu209Phe	p.L209F	ENST00000261799	NM_002609.3	209	Ctc/Ttc	4/23	0.245924231052501	1	FACETS	1	0.972	1	1	0.989	1	CLONAL	2	TRUE	0	0.245924231052501	1		380	276	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519393	176519393	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201913502	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	144	708	1	ENST00000292408.4:c.799G>A	p.Val267Met	p.V267M	ENST00000292408	NM_213647.1	267	Gtg/Atg	7/18	0.245924231052501	1	FACETS	1	0.973	1	1	0.992	1	CLONAL	2	TRUE	0	0.245924231052501	1		709	453	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931612	39931612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	133	446	1	ENST00000378444.4:c.2987G>A	p.Arg996Gln	p.R996Q	ENST00000378444	NM_001123385.1	996	cGg/cAg	4/15	0.245924231052501	1	FACETS	1	0.961	1	1	0.991	1	CLONAL	2	TRUE	0	0.245924231052501	1		447	437	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034427	123034427	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	71	310	0	ENST00000355640.3:c.1189del	p.Ile397PhefsTer18	p.I397Ffs*18	ENST00000355640		395	gAa/ga	6/7	0.245924231052501	1	FACETS	0.879	0.775	0.989	1	0.98	1	CLONAL	2	TRUE	0	0.245924231052501	1		310	288	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857872	9857872	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	204	395	0	ENST00000330684.3:c.3529G>C	p.Gly1177Arg	p.G1177R	ENST00000330684	NM_001134407.1	1177	Ggg/Cgg	13/13	0.575184710014713	3	FACETS	0.914	0.848	0.983	0.457	0.424	0.492	CLONAL	1	TRUE	1	0.575184710014713	3		395	999	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118584	11118584	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	115	241	1	ENST00000358026.2:c.2008G>T	p.Glu670Ter	p.E670*	ENST00000358026	NM_001128849.1	670	Gag/Tag	14/36	1	2	FACETS	0.86	0.779	0.944	0.86	0.779	0.944	CLONAL	1	TRUE	1	0.575184710014713	2		242	465	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183725	10183726	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	180	428	0	ENST00000256474.2:c.194_195insA	p.Val66GlyfsTer66	p.V66Gfs*66	ENST00000256474	NM_000551.3	65	tcg/tcAg	1/3	0.575184710014713	1	FACETS	0.971	0.905	1	0.971	0.905	1	CLONAL	1	TRUE	0	0.575184710014713	1		428	459	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098373	47098373	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0056208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	147	322	0	ENST00000409792.3:c.6901del	p.Thr2301HisfsTer8	p.T2301Hfs*8	ENST00000409792	NM_014159.6	2301	Aca/ca	15/21	0.575184710014713	1	FACETS	0.963	0.89	1	0.963	0.89	1	CLONAL	1	TRUE	0	0.575184710014713	1		322	378	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52661306	52661307	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0056208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	136	272	0	ENST00000394830.3:c.1523dup	p.Ser509Ter	p.S509*	ENST00000394830	NM_018313.4	508	ggt/ggGt	14/30	0.575184710014713	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.575184710014713	1		272	323	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0056209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	35	215	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.985	0.812	1	0.985	0.812	1	CLONAL	1	TRUE	1	0.277482235740197	2		215	256	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0056209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	16	181	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.403	0.298	0.529	0.403	0.298	0.529	SUBCLONAL	1	TRUE	1	0.277482235740197	2		181	286	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102121	27102121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	21	584	0	ENST00000324856.7:c.5047G>A	p.Glu1683Lys	p.E1683K	ENST00000324856	NM_006015.4	1683	Gag/Aag	19/20	1	2	FACETS	0.456	0.351	0.579	0.456	0.351	0.579	SUBCLONAL	1	TRUE	1	0.277482235740197	2		584	332	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983130	201983130	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	26	562	0	ENST00000359651.3:c.979G>C	p.Glu327Gln	p.E327Q	ENST00000359651		327	Gag/Cag	7/8	0.277482235740197	3	FACETS	0.606	0.48	0.751	0.202	0.16	0.251	SUBCLONAL	1	TRUE	0	0.277482235740197	3		562	352	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034822	42034822	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs776608268	NA	P-0056209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	17	450	0	ENST00000219905.7:c.4664G>C	p.Gly1555Ala	p.G1555A	ENST00000219905	NM_001164273.1	1555	gGa/gCa	15/24	1	2	FACETS	0.375	0.279	0.489	0.375	0.279	0.489	SUBCLONAL	1	TRUE	1	0.277482235740197	2		450	327	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40379687	40379687	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	20	545	0	ENST00000293328.3:c.145G>C	p.Asp49His	p.D49H	ENST00000293328	NM_012448.3	49	Gat/Cat	3/19	1	2	FACETS	0.459	0.351	0.586	0.459	0.351	0.586	SUBCLONAL	1	TRUE	1	0.277482235740197	2		545	314	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287875	33287875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754198630	NA	P-0056209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	46	687	0	ENST00000374542.5:c.1378G>A	p.Asp460Asn	p.D460N	ENST00000374542	NM_001141970.1	460	Gat/Aat	5/8	1	2	FACETS	0.73	0.615	0.857	0.73	0.615	0.857	SUBCLONAL	1	TRUE	1	0.277482235740197	2		687	454	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039642	47039642	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	47	361	0	ENST00000377604.3:c.1096del	p.Leu366CysfsTer119	p.L366Cfs*119	ENST00000377604	NM_001204468.1	365	gCc/gc	11/24	1	1	FACETS	0.776	0.664	0.895	1	0.966	1	SUBCLONAL	2	TRUE	0	0.277482235740197	1		361	188	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750945	128750945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	89	407	0	ENST00000377970.2:c.482C>T	p.Ser161Leu	p.S161L	ENST00000377970	NM_002467.4	161	tCa/tTa	2/3	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.330820359786388	2		407	491	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487277	56487277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035001455	NA	P-0056212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	58	486	0	ENST00000267101.3:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000267101	NM_001982.3	475	Cgg/Tgg	12/28	1	2	FACETS	0.657	0.566	0.756	0.657	0.566	0.756	SUBCLONAL	1	TRUE	1	0.433651416831205	2		486	407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577147	7577147	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	163	425	0	ENST00000269305.4:c.791del	p.Leu264HisfsTer81	p.L264Hfs*81	ENST00000269305	NM_001126112.2	264	cTa/ca	8/11	0.367923796553039	2	FACETS	0.858	0.796	0.922	0.858	0.796	0.922	CLONAL	2	TRUE	0	0.433651416831205	2		425	438	SUCCESS
APC	324	MSKCC	GRCh37	5	112175039	112175040	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs1114167583	NA	P-0056212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	39	166	0	ENST00000257430.4:c.3749_3750del	p.Lys1250SerfsTer5	p.K1250Sfs*5	ENST00000257430	NM_000038.5	1250	AAa/a	16/16	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.433651416831205	2		166	151	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912189	114912189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867720073	NA	P-0056212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	85	513	0	ENST00000543371.1:c.1259G>A	p.Arg420Gln	p.R420Q	ENST00000543371	NM_001198531.1	420	cGg/cAg	11/14	1	2	FACETS	0.978	0.869	1	0.978	0.869	1	CLONAL	1	TRUE	1	0.433651416831205	2		513	401	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897021	28897021	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	91	414	0	ENST00000282397.4:c.2859G>T	p.Lys953Asn	p.K953N	ENST00000282397	NM_002019.4	953	aaG/aaT	21/30	0.433651416831205	6	FACETS	0.83	0.736	0.931	0.208	0.184	0.233	CLONAL	1	TRUE	2	0.433651416831205	6		414	944	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791543	42791544	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0056212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	178	674	1	ENST00000575354.2:c.525dup	p.Ala176CysfsTer11	p.A176Cfs*11	ENST00000575354	NM_015125.3	175	agt/agTt	4/20	0.348167807352722	3	FACETS	0.817	0.757	0.88	0.545	0.505	0.587	CLONAL	2	TRUE	0	0.433651416831205	3		675	611	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416200	29416200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	129	507	1	ENST00000389048.3:c.4753G>T	p.Gly1585Cys	p.G1585C	ENST00000389048	NM_004304.4	1585	Ggc/Tgc	29/29	0.363583846675613	2	FACETS	0.798	0.731	0.866	0.798	0.731	0.866	SUBCLONAL	2	TRUE	0	0.433651416831205	2		508	373	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248394	212248394	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	36	264	1	ENST00000342788.4:c.3873G>T	p.Lys1291Asn	p.K1291N	ENST00000342788	NM_005235.2	1291	aaG/aaT	28/28	0.358157964437471	3	FACETS	0.716	0.592	0.855	0.358	0.296	0.428	SUBCLONAL	1	TRUE	1	0.433651416831205	3		265	282	SUCCESS
APC	324	MSKCC	GRCh37	5	112175375	112175475	+	frameshift_variant	Frame_Shift_Del	DEL	TCCAAAAGTGGTGCTCAGACACCCAAAAGTCCACCTGAACACTATGTTCAGGAGACCCCACTCATGTTTAGCAGATGTACTTCTGTCAGTTCACTTGATAG	TCCAAAAGTGGTGCTCAGACACCCAAAAGTCCACCTGAACACTATGTTCAGGAGACCCCACTCATGTTTAGCAGATGTACTTCTGTCAGTTCACTTGATAG	-	novel	NA	P-0056212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	32	201	0	ENST00000257430.4:c.4085_4185del	p.Ser1362PhefsTer2	p.S1362Ffs*2	ENST00000257430	NM_000038.5	1362	TCCAAAAGTGGTGCTCAGACACCCAAAAGTCCACCTGAACACTATGTTCAGGAGACCCCACTCATGTTTAGCAGATGTACTTCTGTCAGTTCACTTGATAGt/t	16/16	1	2	FACETS	0.72	0.589	0.865	0.72	0.589	0.865	SUBCLONAL	1	TRUE	1	0.433651416831205	2		201	205	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216652	36216652	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1205441044	NA	P-0056213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	33	532	0	ENST00000222270.7:c.3818A>G	p.His1273Arg	p.H1273R	ENST00000222270	NM_014727.1	1273	cAt/cGt	13/37	1	2	FACETS	0.868	0.705	1	0.868	0.705	1	CLONAL	1	TRUE	1	0.12	2		532	634	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375040	45375040	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	16	229	0	ENST00000262160.6:c.803A>C	p.Tyr268Ser	p.Y268S	ENST00000262160	NM_005901.5	268	tAc/tCc	8/11	1	2	FACETS	0.966	0.714	1	0.966	0.714	1	CLONAL	1	TRUE	1	0.12	2		229	276	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274851	38274851	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519898	NA	P-0056214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	136	347	0	ENST00000425967.3:c.1729A>G	p.Asn577Asp	p.N577D	ENST00000425967	NM_001174067.1	577	Aac/Gac	13/19	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.557458434826303	2		347	339	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0056215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	17	215	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.701	0.522	0.915	0.701	0.522	0.915	CLONAL	1	TRUE	1	0.12	2		215	404	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021365	42021365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs984878518	NA	P-0056215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	22	180	0	ENST00000219905.7:c.3661C>T	p.Arg1221Trp	p.R1221W	ENST00000219905	NM_001164273.1	1221	Cgg/Tgg	11/24	1	2	FACETS	1	0.837	1	1	0.837	1	CLONAL	1	TRUE	1	0.12	2		180	333	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713485	30713486	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0056215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	28	305	0	ENST00000295754.5:c.813dup	p.Glu272Ter	p.E272*	ENST00000295754	NM_003242.5	270	-/T	4/7	1	2	FACETS	0.884	0.705	1	0.884	0.705	1	CLONAL	1	TRUE	1	0.12	2		305	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0056216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	629	763	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.624193246336539	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.626309402733243	3		763	852	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278106	41278106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	188	277	0	ENST00000349496.5:c.1982G>A	p.Arg661Gln	p.R661Q	ENST00000349496	NM_001904.3	661	cGa/cAa	13/15	0.626309402733243	3	FACETS	0.976	0.914	1	0.976	0.914	1	CLONAL	2	TRUE	1	0.626309402733243	3		277	404	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430770	47430770	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	404	360	3	ENST00000377045.4:c.1735C>T	p.Arg579Trp	p.R579W	ENST00000377045	NM_001654.4	579	Cgg/Tgg	16/16	0.626309402733243	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.626309402733243	2		363	530	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110034	115110050	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGCGGCCGCCGCTGC	GAGGCGGCCGCCGCTGC	-	novel	NA	P-0056216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	158	689	0	ENST00000257566.3:c.1828_1844del	p.Ala610LeufsTer76	p.A610Lfs*76	ENST00000257566	NM_016569.3	610	GCAGCGGCGGCCGCCTCc/c	8/8	0.580057884494387	3	FACETS	0.812	0.745	0.882	0.406	0.372	0.441	CLONAL	1	TRUE	1	0.626309402733243	3		689	816	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265754	41266209	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGG	ATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGG	-	novel	NA	P-0056216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	63	59	0	ENST00000349496.5:c.13+184_208del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.626309402733243	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.626309402733243	3		59	111	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752413	57752413	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	20	159	0	ENST00000274289.3:c.1160G>T	p.Arg387Ile	p.R387I	ENST00000274289	NM_006622.3	387	aGa/aTa	9/14	0.626309402733243	3	FACETS	0.413	0.317	0.525	0.207	0.158	0.263	SUBCLONAL	1	TRUE	1	0.626309402733243	3		159	203	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	64	387	0	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	1	2	FACETS	0.835	0.726	0.951	0.835	0.726	0.951	CLONAL	1	TRUE	1	0.41	2		387	374	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	20	397	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.305	0.233	0.389	0.305	0.233	0.389	SUBCLONAL	1	TRUE	1	0.41	2		397	320	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920227	76920227	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	40	276	0	ENST00000373344.5:c.3850C>A	p.Leu1284Ile	p.L1284I	ENST00000373344	NM_000489.3	1284	Ctt/Att	11/35	1	2	FACETS	0.81	0.678	0.954	0.81	0.678	0.954	CLONAL	1	TRUE	1	0.41	2		276	241	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426123	138426123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217537873	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	30	216	0	ENST00000289153.2:c.1408G>A	p.Glu470Lys	p.E470K	ENST00000289153	NM_006219.2	470	Gaa/Aaa	9/22	1	2	FACETS	0.887	0.723	1	0.887	0.723	1	CLONAL	1	TRUE	1	0.41	2		216	165	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73343019	73343019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	31	169	0	ENST00000377767.4:c.1787G>T	p.Arg596Ile	p.R596I	ENST00000377767	NM_014953.3	596	aGa/aTa	14/21	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.41	2		169	133	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509723	106509723	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	57	404	0	ENST00000359195.3:c.1717G>T	p.Glu573Ter	p.E573*	ENST00000359195	NM_002649.2	573	Gaa/Taa	2/11	1	2	FACETS	0.921	0.796	1	0.921	0.796	1	CLONAL	1	TRUE	1	0.41	2		404	302	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573894	18573894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759658584	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	36	252	0	ENST00000266497.5:c.2212C>T	p.Arg738Cys	p.R738C	ENST00000266497		738	Cgt/Tgt	15/31	1	2	FACETS	0.981	0.816	1	0.981	0.816	1	CLONAL	1	TRUE	1	0.41	2		252	179	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699369	47699369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	34	283	1	ENST00000347630.2:c.139G>A	p.Glu47Lys	p.E47K	ENST00000347630	NM_001007230.1	47	Gaa/Aaa	4/11	1	2	FACETS	0.846	0.698	1	0.846	0.698	1	CLONAL	1	TRUE	1	0.41	2		284	196	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383746	84383746	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755313466	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	52	439	0	ENST00000321945.7:c.1106G>A	p.Arg369Gln	p.R369Q	ENST00000321945	NM_139076.2	369	cGa/cAa	9/9	1	2	FACETS	0.778	0.666	0.9	0.778	0.666	0.9	SUBCLONAL	1	TRUE	1	0.41	2		439	326	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325762	30325762	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs771704089	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	24	162	0	ENST00000322652.5:c.1960C>T	p.Arg654Ter	p.R654*	ENST00000322652	NM_015355.2	654	Cga/Tga	16/16	1	2	FACETS	0.922	0.733	1	0.922	0.733	1	CLONAL	1	TRUE	1	0.41	2		162	127	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70355083	70355083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779481901	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	126	600	1	ENST00000374080.3:c.5005G>A	p.Asp1669Asn	p.D1669N	ENST00000374080		1669	Gat/Aat	36/45	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.41	2		601	588	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560097	29560097	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	23	233	0	ENST00000356175.3:c.3574G>T	p.Glu1192Ter	p.E1192*	ENST00000356175	NM_000267.3	1192	Gaa/Taa	27/57	1	2	FACETS	0.606	0.476	0.755	0.606	0.476	0.755	SUBCLONAL	1	TRUE	1	0.41	2		233	185	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915943	127915943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781486938	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	58	348	0	ENST00000373547.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000373547	NM_002721.4	180	Gaa/Aaa	6/7	1	2	FACETS	0.993	0.86	1	0.993	0.86	1	CLONAL	1	TRUE	1	0.41	2		348	285	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	72	176	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	1	0.963	1	1	0.986	1	CLONAL	2	TRUE	1	0.41	2		176	151	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765576	41765576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763066660	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	81	479	0	ENST00000301178.4:c.2452G>A	p.Glu818Lys	p.E818K	ENST00000301178	NM_021913.4	818	Gaa/Aaa	20/20	1	2	FACETS	0.896	0.793	1	0.896	0.793	1	CLONAL	1	TRUE	1	0.41	2		479	441	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72866457	72866457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375075276	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	41	216	0	ENST00000325599.8:c.806G>A	p.Arg269His	p.R269H	ENST00000325599	NM_018130.2	269	cGt/cAt	7/11	1	2	FACETS	0.909	0.764	1	0.909	0.764	1	CLONAL	1	TRUE	1	0.41	2		216	220	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212216	98212216	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	29	162	0	ENST00000331920.6:c.3456C>A	p.Phe1152Leu	p.F1152L	ENST00000331920	NM_000264.3	1152	ttC/ttA	21/24	1	2	FACETS	0.863	0.7	1	0.863	0.7	1	CLONAL	1	TRUE	1	0.41	2		162	164	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624245	89624245	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554890335	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	38	162	0	ENST00000371953.3:c.19G>T	p.Glu7Ter	p.E7*	ENST00000371953	NM_000314.4	7	Gag/Tag	1/9	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.41	2		162	167	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059183	27059183	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	53	283	0	ENST00000324856.7:c.1820C>A	p.Ser607Ter	p.S607*	ENST00000324856	NM_006015.4	607	tCa/tAa	4/20	1	2	FACETS	0.767	0.657	0.886	0.767	0.657	0.886	SUBCLONAL	1	TRUE	1	0.41	2		283	337	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649005	86649005	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	33	210	0	ENST00000274376.6:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000274376	NM_002890.2	429	Gaa/Taa	9/25	1	2	FACETS	0.953	0.785	1	0.953	0.785	1	CLONAL	1	TRUE	1	0.41	2		210	169	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710657	117710657	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	31	198	0	ENST00000368508.3:c.1615G>T	p.Glu539Ter	p.E539*	ENST00000368508	NM_002944.2	539	Gaa/Taa	12/43	1	2	FACETS	0.84	0.686	1	0.84	0.686	1	CLONAL	1	TRUE	1	0.41	2		198	180	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137487	202137487	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	87	311	0	ENST00000358485.4:c.715G>T	p.Glu239Ter	p.E239*	ENST00000358485	NM_001080125.1	239	Gaa/Taa	4/9	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.41	2		311	304	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249857	133249857	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1565972665	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	39	272	0	ENST00000320574.5:c.1366G>C	p.Ala456Pro	p.A456P	ENST00000320574	NM_006231.2	456	Gcc/Ccc	14/49	1	2	FACETS	0.799	0.668	0.944	0.799	0.668	0.944	CLONAL	1	TRUE	1	0.41	2		272	238	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961363	41961363	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	61	313	0	ENST00000219905.7:c.271C>T	p.Arg91Ter	p.R91*	ENST00000219905	NM_001164273.1	91	Cga/Tga	2/24	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.41	2		313	253	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942155	71942155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	91	706	0	ENST00000298229.2:c.1419G>T	p.Glu473Asp	p.E473D	ENST00000298229	NM_001567.3	473	gaG/gaT	12/28	1	2	FACETS	0.76	0.676	0.849	0.76	0.676	0.849	SUBCLONAL	1	TRUE	1	0.41	2		706	584	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020225	123020225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	59	461	1	ENST00000355640.3:c.713G>A	p.Arg238Gln	p.R238Q	ENST00000355640		238	cGa/cAa	2/7	1	2	FACETS	0.888	0.769	1	0.888	0.769	1	CLONAL	1	TRUE	1	0.41	2		462	324	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720857	89720857	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	62	245	0	ENST00000371953.3:c.1008C>A	p.Tyr336Ter	p.Y336*	ENST00000371953	NM_000314.4	336	taC/taA	8/9	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.41	2		245	249	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128036895	128036895	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	87	377	0	ENST00000285398.2:c.1584G>T	p.Lys528Asn	p.K528N	ENST00000285398	NM_000122.1	528	aaG/aaT	10/15	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.41	2		377	392	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759967	133759967	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773883545	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	124	656	0	ENST00000318560.5:c.2290C>T	p.Arg764Trp	p.R764W	ENST00000318560	NM_005157.4	764	Cgg/Tgg	11/11	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.41	2		656	587	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112892416	112892416	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1488672907	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	39	313	0	ENST00000351677.2:c.574G>T	p.Asp192Tyr	p.D192Y	ENST00000351677	NM_002834.3	192	Gat/Tat	5/16	1	2	FACETS	0.675	0.562	0.799	0.675	0.562	0.799	SUBCLONAL	1	TRUE	1	0.41	2		313	282	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724329	117724329	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	64	392	0	ENST00000368508.3:c.550C>T	p.Pro184Ser	p.P184S	ENST00000368508	NM_002944.2	184	Ccc/Tcc	6/43	1	2	FACETS	0.932	0.812	1	0.932	0.812	1	CLONAL	1	TRUE	1	0.41	2		392	335	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341701	8341701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766088715	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	57	347	0	ENST00000356435.5:c.4939G>A	p.Glu1647Lys	p.E1647K	ENST00000356435		1647	Gaa/Aaa	29/35	1	2	FACETS	0.912	0.788	1	0.912	0.788	1	CLONAL	1	TRUE	1	0.41	2		347	305	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614469	38614469	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	32	281	0	ENST00000299084.4:c.235G>T	p.Asp79Tyr	p.D79Y	ENST00000299084	NM_152594.2	79	Gac/Tac	3/7	1	2	FACETS	0.75	0.614	0.902	0.75	0.614	0.902	CLONAL	1	TRUE	1	0.41	2		281	208	SUCCESS
APC	324	MSKCC	GRCh37	5	112177377	112177377	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	34	216	0	ENST00000257430.4:c.6086C>A	p.Ser2029Tyr	p.S2029Y	ENST00000257430	NM_000038.5	2029	tCt/tAt	16/16	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.41	2		216	155	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937185	76937185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	34	474	0	ENST00000373344.5:c.3563C>T	p.Ser1188Phe	p.S1188F	ENST00000373344	NM_000489.3	1188	tCc/tTc	9/35	1	2	FACETS	0.568	0.466	0.682	0.568	0.466	0.682	SUBCLONAL	1	TRUE	1	0.41	2		474	292	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117340	115117340	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	30	234	0	ENST00000257566.3:c.834C>A	p.Phe278Leu	p.F278L	ENST00000257566	NM_016569.3	278	ttC/ttA	4/8	1	2	FACETS	0.71	0.577	0.86	0.71	0.577	0.86	SUBCLONAL	1	TRUE	1	0.41	2		234	206	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240738	53240738	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	189	516	0	ENST00000375401.3:c.1342G>T	p.Glu448Ter	p.E448*	ENST00000375401	NM_004187.3	448	Gaa/Taa	10/26	1	2	FACETS	1	0.984	1	1	0.994	1	CLONAL	2	TRUE	1	0.41	2		516	402	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251634	212251634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3748961	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	64	429	0	ENST00000342788.4:c.3425G>A	p.Arg1142Gln	p.R1142Q	ENST00000342788	NM_005235.2	1142	cGa/cAa	27/28	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.41	2		429	292	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29197723	29197723	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs774219516	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	123	641	0	ENST00000240100.2:c.471C>A	p.Phe157Leu	p.F157L	ENST00000240100	NM_001394.6	157	ttC/ttA	2/4	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.41	2		641	538	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725558	117725558	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	53	270	0	ENST00000368508.3:c.323C>A	p.Ser108Tyr	p.S108Y	ENST00000368508	NM_002944.2	108	tCt/tAt	5/43	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.41	2		270	255	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244612	41244612	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80356985	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	55	490	1	ENST00000357654.3:c.2936G>A	p.Arg979His	p.R979H	ENST00000357654	NM_007294.3	979	cGt/cAt	10/23	1	2	FACETS	0.808	0.695	0.93	0.808	0.695	0.93	CLONAL	1	TRUE	1	0.41	2		491	332	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073509	8073509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	45	416	0	ENST00000377482.5:c.1150G>T	p.Glu384Ter	p.E384*	ENST00000377482	NM_018948.3	384	Gaa/Taa	4/4	1	2	FACETS	0.798	0.675	0.932	0.798	0.675	0.932	CLONAL	1	TRUE	1	0.41	2		416	275	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955517	48955517	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	21	229	0	ENST00000267163.4:c.1633G>T	p.Glu545Ter	p.E545*	ENST00000267163	NM_000321.2	545	Gaa/Taa	17/27	1	2	FACETS	0.545	0.422	0.687	0.545	0.422	0.687	SUBCLONAL	1	TRUE	1	0.41	2		229	188	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515193	149515193	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	91	580	1	ENST00000261799.4:c.289G>T	p.Glu97Ter	p.E97*	ENST00000261799	NM_002609.3	97	Gaa/Taa	3/23	1	2	FACETS	0.929	0.828	1	0.929	0.828	1	CLONAL	1	TRUE	1	0.41	2		581	478	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117816	108117816	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	44	223	0	ENST00000278616.4:c.1027G>T	p.Glu343Ter	p.E343*	ENST00000278616	NM_000051.3	343	Gaa/Taa	8/63	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.41	2		223	197	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624568	21624568	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	43	347	0	ENST00000421138.2:c.1461G>T	p.Lys487Asn	p.K487N	ENST00000421138		487	aaG/aaT	14/16	1	2	FACETS	0.81	0.682	0.949	0.81	0.682	0.949	CLONAL	1	TRUE	1	0.41	2		347	259	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190069	123190069	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	23	276	0	ENST00000218089.9:c.1288G>T	p.Glu430Ter	p.E430*	ENST00000218089	NM_001042749.1	430	Gaa/Taa	14/35	1	2	FACETS	0.545	0.427	0.68	0.545	0.427	0.68	SUBCLONAL	1	TRUE	1	0.41	2		276	206	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162426	47162426	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	53	293	1	ENST00000409792.3:c.3700G>T	p.Glu1234Ter	p.E1234*	ENST00000409792	NM_014159.6	1234	Gaa/Taa	3/21	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.41	2		294	248	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950665	38950665	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1249602445	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	32	257	0	ENST00000357387.3:c.3285G>T	p.Lys1095Asn	p.K1095N	ENST00000357387	NM_152756.3	1095	aaG/aaT	31/38	1	2	FACETS	0.872	0.715	1	0.872	0.715	1	CLONAL	1	TRUE	1	0.41	2		257	179	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073434	8073434	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	21	380	0	ENST00000377482.5:c.1225A>C	p.Lys409Gln	p.K409Q	ENST00000377482	NM_018948.3	409	Aaa/Caa	4/4	1	2	FACETS	0.318	0.245	0.404	0.318	0.245	0.404	SUBCLONAL	1	TRUE	1	0.41	2		380	322	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199435	11199435	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	68	469	1	ENST00000361445.4:c.5056G>T	p.Asp1686Tyr	p.D1686Y	ENST00000361445	NM_004958.3	1686	Gac/Tac	36/58	1	2	FACETS	0.885	0.774	1	0.885	0.774	1	CLONAL	1	TRUE	1	0.41	2		470	375	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746060	162746060	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	30	301	0	ENST00000367921.3:c.2183A>C	p.Asp728Ala	p.D728A	ENST00000367921	NM_006182.2	728	gAc/gCc	16/18	0.208254745166201	3	FACETS	0.683	0.553	0.83	0.342	0.276	0.415	INDETERMINATE	1	TRUE	1	0.41	3		301	258	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63662080	63662080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	48	309	0	ENST00000279873.7:c.184G>A	p.Glu62Lys	p.E62K	ENST00000279873	NM_032199.2	62	Gaa/Aaa	2/10	1	2	FACETS	0.83	0.707	0.965	0.83	0.707	0.965	CLONAL	1	TRUE	1	0.41	2		309	282	SUCCESS
EED	8726	MSKCC	GRCh37	11	85968617	85968617	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	29	167	0	ENST00000263360.6:c.613C>A	p.Leu205Ile	p.L205I	ENST00000263360	NM_003797.3	205	Ctt/Att	6/12	1	2	FACETS	0.863	0.7	1	0.863	0.7	1	CLONAL	1	TRUE	1	0.41	2		167	164	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344681	118344681	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	15	225	0	ENST00000534358.1:c.2807C>A	p.Ser936Tyr	p.S936Y	ENST00000534358	NM_005933.3	936	tCt/tAt	3/36	1	2	FACETS	0.331	0.242	0.438	0.331	0.242	0.438	SUBCLONAL	1	TRUE	1	0.41	2		225	221	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906699	32906699	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	54	384	0	ENST00000380152.3:c.1084G>T	p.Asp362Tyr	p.D362Y	ENST00000380152		362	Gat/Tat	10/27	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.41	2		384	236	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910647	32910647	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	34	276	0	ENST00000380152.3:c.2155A>C	p.Asn719His	p.N719H	ENST00000380152		719	Aat/Cat	11/27	1	2	FACETS	0.829	0.684	0.99	0.829	0.684	0.99	CLONAL	1	TRUE	1	0.41	2		276	200	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911823	32911823	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	45	401	0	ENST00000380152.3:c.3331A>C	p.Ile1111Leu	p.I1111L	ENST00000380152		1111	Att/Ctt	11/27	1	2	FACETS	0.765	0.647	0.894	0.765	0.647	0.894	SUBCLONAL	1	TRUE	1	0.41	2		401	287	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954024	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	25	305	0	ENST00000380152.3:c.9090_9091insC	p.Lys3031GlnfsTer13	p.K3031Qfs*13	ENST00000380152		3030	-/C	23/27	1	2	FACETS	0.598	0.474	0.738	0.598	0.474	0.738	SUBCLONAL	1	TRUE	1	0.41	2		305	204	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968832	32968832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80359193	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	30	170	0	ENST00000380152.3:c.9263C>T	p.Ala3088Val	p.A3088V	ENST00000380152		3088	gCc/gTc	25/27	1	2	FACETS	1	0.819	1	1	0.819	1	CLONAL	1	TRUE	1	0.41	2		170	146	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987023	36987023	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	57	417	0	ENST00000354822.5:c.666G>T	p.Glu222Asp	p.E222D	ENST00000354822	NM_001079668.2	222	gaG/gaT	3/3	1	2	FACETS	0.903	0.78	1	0.903	0.78	1	CLONAL	1	TRUE	1	0.41	2		417	308	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673804	37673804	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	55	355	0	ENST00000447079.4:c.2958C>A	p.Phe986Leu	p.F986L	ENST00000447079	NM_015083.1	986	ttC/ttA	10/14	1	2	FACETS	0.717	0.616	0.827	0.717	0.616	0.827	SUBCLONAL	1	TRUE	1	0.41	2		355	374	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221323	36221323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	124	638	0	ENST00000222270.7:c.5157C>A	p.Phe1719Leu	p.F1719L	ENST00000222270	NM_014727.1	1719	ttC/ttA	24/37	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.41	2		638	540	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451883	29451883	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	93	598	0	ENST00000389048.3:c.2682A>C	p.Lys894Asn	p.K894N	ENST00000389048	NM_004304.4	894	aaA/aaC	16/29	1	2	FACETS	0.861	0.768	0.959	0.861	0.768	0.959	CLONAL	1	TRUE	1	0.41	2		598	527	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919851	96919851	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	56	257	0	ENST00000258439.3:c.412C>A	p.Leu138Met	p.L138M	ENST00000258439	NM_001193304.2	138	Ctg/Atg	4/4	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.41	2		257	259	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257771	198257771	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	50	314	0	ENST00000335508.6:c.3681T>G	p.Ile1227Met	p.I1227M	ENST00000335508	NM_012433.2	1227	atT/atG	24/25	1	2	FACETS	0.9	0.77	1	0.9	0.77	1	CLONAL	1	TRUE	1	0.41	2		314	271	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265072	46265072	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	45	309	0	ENST00000371998.3:c.1942G>T	p.Glu648Ter	p.E648*	ENST00000371998		648	Gaa/Taa	12/23	1	2	FACETS	0.911	0.772	1	0.911	0.772	1	CLONAL	1	TRUE	1	0.41	2		309	241	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911512	134911512	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	94	413	0	ENST00000398015.3:c.1977G>T	p.Glu659Asp	p.E659D	ENST00000398015	NM_004441.4	659	gaG/gaT	11/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.41	2		413	400	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169953104	169953104	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	73	313	0	ENST00000295797.4:c.188A>G	p.Glu63Gly	p.E63G	ENST00000295797	NM_002740.5	63	gAa/gGa	2/18	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.41	2		313	328	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185195175	185195175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749182070	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	26	220	0	ENST00000265026.3:c.2492G>A	p.Arg831Gln	p.R831Q	ENST00000265026	NM_004721.4	831	cGa/cAa	12/14	1	2	FACETS	0.622	0.495	0.764	0.622	0.495	0.764	SUBCLONAL	1	TRUE	1	0.41	2		220	204	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55963889	55963889	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	18	265	0	ENST00000263923.4:c.2554G>T	p.Asp852Tyr	p.D852Y	ENST00000263923	NM_002253.2	852	Gat/Tat	18/30	1	2	FACETS	0.264	0.198	0.341	0.264	0.198	0.341	SUBCLONAL	1	TRUE	1	0.41	2		265	333	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630847	187630847	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	84	353	0	ENST00000441802.2:c.135G>T	p.Glu45Asp	p.E45D	ENST00000441802	NM_005245.3	45	gaG/gaT	2/27	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.41	2		353	403	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873598	35873598	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1188286965	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	31	165	0	ENST00000303115.3:c.554G>T	p.Ser185Ile	p.S185I	ENST00000303115	NM_002185.3	185	aGc/aTc	5/8	1	2	FACETS	0.995	0.816	1	0.995	0.816	1	CLONAL	1	TRUE	1	0.41	2		165	152	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168494	56168494	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	17	207	0	ENST00000399503.3:c.1450G>T	p.Glu484Ter	p.E484*	ENST00000399503	NM_005921.1	484	Gaa/Taa	8/20	1	2	FACETS	0.58	0.436	0.748	0.58	0.436	0.748	SUBCLONAL	1	TRUE	1	0.41	2		207	143	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638679	176638679	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	96	526	0	ENST00000439151.2:c.3279A>G	p.Ile1093Met	p.I1093M	ENST00000439151	NM_022455.4	1093	atA/atG	5/23	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.41	2		526	440	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910382	29910382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	84	605	0	ENST00000376809.5:c.52G>A	p.Ala18Thr	p.A18T	ENST00000376809	NM_002116.7	18	Gcc/Acc	1/8	1	2	FACETS	0.925	0.821	1	0.925	0.821	1	CLONAL	1	TRUE	1	0.41	2		605	443	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979375	93979375	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	27	220	0	ENST00000369303.4:c.1453C>A	p.Gln485Lys	p.Q485K	ENST00000369303	NM_004440.3	485	Caa/Aaa	7/17	1	2	FACETS	0.866	0.698	1	0.866	0.698	1	CLONAL	1	TRUE	1	0.41	2		220	152	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683887	117683887	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	27	370	0	ENST00000368508.3:c.3260A>C	p.Asn1087Thr	p.N1087T	ENST00000368508	NM_002944.2	1087	aAt/aCt	21/43	1	2	FACETS	0.54	0.431	0.663	0.54	0.431	0.663	SUBCLONAL	1	TRUE	1	0.41	2		370	244	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099266	157099266	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	74	381	0	ENST00000346085.5:c.203A>C	p.Lys68Thr	p.K68T	ENST00000346085	NM_020732.3	68	aAa/aCa	1/20	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.41	2		381	346	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729749	41729749	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	57	398	0	ENST00000242208.4:c.780G>T	p.Lys260Asn	p.K260N	ENST00000242208	NM_002192.2	260	aaG/aaT	3/3	1	2	FACETS	0.785	0.677	0.902	0.785	0.677	0.902	CLONAL	1	TRUE	1	0.41	2		398	354	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56860221	56860221	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	70	346	0	ENST00000519728.1:c.223G>T	p.Asp75Tyr	p.D75Y	ENST00000519728	NM_002350.3	75	Gat/Tat	4/13	1	2	FACETS	0.923	0.809	1	0.923	0.809	1	CLONAL	1	TRUE	1	0.41	2		346	370	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27109610	27109610	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	63	467	0	ENST00000380036.4:c.22G>A	p.Val8Ile	p.V8I	ENST00000380036	NM_000459.3	8	Gtt/Att	1/23	1	2	FACETS	0.753	0.654	0.86	0.753	0.654	0.86	SUBCLONAL	1	TRUE	1	0.41	2		467	408	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202835	27202835	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	43	269	0	ENST00000380036.4:c.1927G>T	p.Glu643Ter	p.E643*	ENST00000380036	NM_000459.3	643	Gaa/Taa	13/23	1	2	FACETS	0.829	0.699	0.971	0.829	0.699	0.971	CLONAL	1	TRUE	1	0.41	2		269	253	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849262	76849262	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	49	345	0	ENST00000373344.5:c.6014T>G	p.Phe2005Cys	p.F2005C	ENST00000373344	NM_000489.3	2005	tTt/tGt	26/35	1	2	FACETS	0.833	0.71	0.966	0.833	0.71	0.966	CLONAL	1	TRUE	1	0.41	2		345	287	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615134	100615134	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	39	308	0	ENST00000308731.7:c.781G>T	p.Glu261Ter	p.E261*	ENST00000308731	NM_000061.2	261	Gaa/Taa	9/19	1	2	FACETS	0.723	0.603	0.856	0.723	0.603	0.856	SUBCLONAL	1	TRUE	1	0.41	2		308	263	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202501	123202501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	32	257	0	ENST00000218089.9:c.2353G>A	p.Glu785Lys	p.E785K	ENST00000218089	NM_001042749.1	785	Gaa/Aaa	24/35	1	2	FACETS	0.78	0.639	0.937	0.78	0.639	0.937	CLONAL	1	TRUE	1	0.41	2		257	200	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710657	117710660	+	stop_gained	Nonsense_Mutation	ONP	CTTC	CTTC	ATTA	novel	NA	P-0056217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	21	199	0	ENST00000368508.3:c.1612_1615delinsTAAT	p.Glu538_Glu539delinsTer	p.E538_E539delins*	ENST00000368508	NM_002944.2	538	GAAGaa/TAATaa	12/43	1	2	FACETS	0.569	0.441	0.717	0.569	0.441	0.717	SUBCLONAL	1	TRUE	1	0.41	2		199	180	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528109	157528113	+	frameshift_variant	Frame_Shift_Del	DEL	GCATC	GCATC	-	novel	NA	P-0056218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	109	466	0	ENST00000346085.5:c.5834_5838del	p.Cys1945LeufsTer8	p.C1945Lfs*8	ENST00000346085	NM_020732.3	1945	tGCATC/t	20/20	0.628199756462779	3	FACETS	0.727	0.655	0.803	0.364	0.327	0.402	SUBCLONAL	1	TRUE	1	0.734211395788686	3		466	558	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0056219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	83	242	1	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.997	0.893	1	0.997	0.893	1	CLONAL	1	TRUE	1	0.660894611925478	2		243	252	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418624	49418624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1459471282	NA	P-0056219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	159	447	1	ENST00000301067.7:c.15890C>T	p.Thr5297Met	p.T5297M	ENST00000301067	NM_003482.3	5297	aCg/aTg	49/54	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.660894611925478	2		448	461	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180586	56180588	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	rs1357146419	NA	P-0056219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	209	251	0	ENST00000399503.3:c.3918_3920del	p.Ile1307del	p.I1307del	ENST00000399503	NM_005921.1	1305	aaCATc/aac	16/20	0.660894611925478	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	1	0.660894611925478	3		251	412	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995200	15995219	+	frameshift_variant	Frame_Shift_Del	DEL	TTGGATGTGCCACATGGACT	TTGGATGTGCCACATGGACT	-	novel	NA	P-0056219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	119	446	0	ENST00000268712.3:c.2974_2993del	p.Ser992GlufsTer19	p.S992Efs*19	ENST00000268712	NM_006311.3	992	AGTCCATGTGGCACATCCAAg/g	22/46	0.660894611925478	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.660894611925478	1		446	237	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170009717	170009717	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	93	196	0	ENST00000295797.4:c.1279G>A	p.Gly427Arg	p.G427R	ENST00000295797	NM_002740.5	427	Gga/Aga	13/18	1	2	FACETS	0.967	0.871	1	0.967	0.871	1	CLONAL	1	TRUE	1	0.660894611925478	2		196	291	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	86	374	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.702881219941555	2		374	199	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584495	48584495	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs774334251	NA	P-0056222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	151	259	0	ENST00000342988.3:c.668G>A	p.Ser223Asn	p.S223N	ENST00000342988	NM_005359.5	223	aGt/aAt	6/12	1	2	FACETS	0.916	0.844	0.99	0.916	0.844	0.99	CLONAL	1	TRUE	1	0.702881219941555	2		259	469	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606376	93606376	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	281	630	0	ENST00000375746.1:c.196A>T	p.Ile66Phe	p.I66F	ENST00000375746	NM_001174167.1	66	Atc/Ttc	2/14	0.150822472144058	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.702881219941555	0		630	871	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0056223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	47	159	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.329968576621529	2		159	281	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0056223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	128	383	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.329968576621529	3	FACETS	0.872	0.795	0.953	0.872	0.795	0.953	CLONAL	2	TRUE	1	0.329968576621529	3		383	518	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0056223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	57	345	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	0.715	0.614	0.825	0.715	0.614	0.825	SUBCLONAL	1	TRUE	1	0.329968576621529	2		345	483	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0056223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	136	255	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	0.288582471607982	4	FACETS	1	0.979	1	0.814	0.746	0.884	CLONAL	2	TRUE	1	0.329968576621529	4		255	449	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0056223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	67	295	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.951	0.829	1	0.951	0.829	1	CLONAL	1	TRUE	1	0.329968576621529	2		295	427	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411783	63411783	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	334	763	1	ENST00000330258.3:c.1384G>T	p.Glu462Ter	p.E462*	ENST00000330258	NM_152424.3	462	Gaa/Taa	2/2	0.329968576621529	3	FACETS	0.953	0.901	1	0.953	0.901	1	CLONAL	2	TRUE	1	0.329968576621529	3		764	1237	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779816	135779816	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768189353	NA	P-0056223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	109	332	0	ENST00000298552.3:c.2023G>A	p.Asp675Asn	p.D675N	ENST00000298552	NM_001162426.1	675	Gac/Aac	16/23	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.329968576621529	2		332	564	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235377	235377	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748683825	NA	P-0056223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	132	578	1	ENST00000264932.6:c.1183G>A	p.Val395Ile	p.V395I	ENST00000264932	NM_004168.2	395	Gtc/Atc	9/15	0.329968576621529	3	FACETS	0.999	0.906	1	0.5	0.453	0.549	CLONAL	1	TRUE	1	0.329968576621529	3		579	933	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631935	90631935	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs267606870	NA	P-0056223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	130	555	0	ENST00000330062.3:c.418C>G	p.Arg140Gly	p.R140G	ENST00000330062	NM_002168.2	140	Cgg/Ggg	4/11	1	2	FACETS	0.916	0.831	1	0.916	0.831	1	CLONAL	1	TRUE	1	0.329968576621529	2		555	860	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584506	48584507	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0056223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	86	265	0	ENST00000342988.3:c.680dup	p.Ser227ArgfsTer8	p.S227Rfs*8	ENST00000342988	NM_005359.5	227	agt/aGgt	6/12	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.329968576621529	2		265	429	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057616	180057616	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	196	772	0	ENST00000261937.6:c.339C>A	p.Tyr113Ter	p.Y113*	ENST00000261937	NM_182925.4	113	taC/taA	3/30	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.329968576621529	2		772	1060	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0056224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	607	632	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.645594748369762	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.645594748369762	3		632	804	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435649	110435649	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1441639943	NA	P-0056224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	112	382	0	ENST00000375856.3:c.2752G>A	p.Glu918Lys	p.E918K	ENST00000375856	NM_003749.2	918	Gag/Aag	1/2	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.645594748369762	2		382	290	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	102	374	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.97	2		374	210	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0056225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	23	242	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.137	0.106	0.172	0.137	0.106	0.172	SUBCLONAL	1	TRUE	1	0.97	2		242	347	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0056225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	463	814	1	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	0.967	0.928	1	0.967	0.928	1	CLONAL	1	TRUE	1	0.97	2		815	987	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246445	105246445	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	25	423	0	ENST00000349310.3:c.155T>G	p.Leu52Arg	p.L52R	ENST00000349310	NM_001014432.1	52	cTc/cGc	4/15	1	2	FACETS	0.061	0.047	0.076	0.061	0.047	0.076	SUBCLONAL	1	TRUE	1	0.97	2		423	852	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340838	70340838	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	194	262	0	ENST00000374080.3:c.571A>G	p.Thr191Ala	p.T191A	ENST00000374080		191	Acc/Gcc	5/45	1	1	FACETS	0.552	0.519	0.585	0.552	0.519	0.585	SUBCLONAL	1	TRUE	0	0.97	1		262	373	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0056226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	11	30	0				ENST00000310581	NM_198253.2	-/1132			0.201020323537091	5	FACETS	1	0.773	1	1	0.919	1	CLONAL	5	TRUE	3	0.201020323537091	5		30	27	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0056226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	34	959	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.201020323537091	3	FACETS	1	0.909	1	1	0.975	1	CLONAL	7	TRUE	0	0.201020323537091	3		959	51	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133849	55133893	+	inframe_deletion	In_Frame_Del	DEL	GACTCTGATTGAAAATCTCACTGAGATCACCACTGATGTGGAAAA	GACTCTGATTGAAAATCTCACTGAGATCACCACTGATGTGGAAAA	-	novel	NA	P-0056226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	218	384	0	ENST00000257290.5:c.1064_1108del	p.Thr355_Lys369del	p.T355_K369del	ENST00000257290	NM_006206.4	354	ctGACTCTGATTGAAAATCTCACTGAGATCACCACTGATGTGGAAAAg/ctg	7/23	0.201020323537091	65	FACETS	1	0.95	1			1	CLONAL	25	TRUE	NA	0.201020323537091	65		384	625	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0056227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	32	181	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.106893098221406	3	FACETS	0.907	0.744	1	0.907	0.744	1	INDETERMINATE	2	TRUE	1	0.22	3		181	178	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652097	36652098	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0056227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	54	627	0	ENST00000244741.5:c.222dup	p.Lys75GlnfsTer14	p.K75Qfs*14	ENST00000244741	NM_000389.4	73	-/C	2/3	0.407379285180872	3	FACETS	1	0.96	1	0.686	0.588	0.793	CLONAL	1	TRUE	1	0.22	3		627	397	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101089	26101089	+	start_lost	Translation_Start_Site	SNP	C	C	T	rs1559535727	NA	P-0056227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	23	433	0	ENST00000435504.4:c.3G>A	p.Met1?	p.M1?	ENST00000435504		1	atG/atA	1/13	1	2	FACETS	0.619	0.482	0.776	0.619	0.482	0.776	SUBCLONAL	1	TRUE	1	0.22	2		433	338	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867774	45867774	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	47	659	0	ENST00000391945.4:c.626A>G	p.Tyr209Cys	p.Y209C	ENST00000391945	NM_000400.3	209	tAc/tGc	8/23	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.22	2		659	372	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661536	227661536	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	23	665	0	ENST00000305123.5:c.1919T>G	p.Val640Gly	p.V640G	ENST00000305123	NM_005544.2	640	gTa/gGa	1/2	1	2	FACETS	0.596	0.464	0.748	0.596	0.464	0.748	SUBCLONAL	1	TRUE	1	0.22	2		665	351	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165605	47165605	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	31	439	0	ENST00000409792.3:c.521C>A	p.Pro174Gln	p.P174Q	ENST00000409792	NM_014159.6	174	cCa/cAa	3/21	0.106893098221406	3	FACETS	0.852	0.69	1	0.426	0.345	0.518	INDETERMINATE	1	TRUE	1	0.22	3		439	367	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588954	67588954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	11	176	0	ENST00000274335.5:c.1045G>A	p.Asp349Asn	p.D349N	ENST00000274335		349	Gat/Aat	8/15	0.326924987117497	3	FACETS	0.661	0.457	0.912	0.33	0.228	0.456	SUBCLONAL	1	TRUE	1	0.22	3		176	168	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164780	32164780	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	50	501	0	ENST00000375023.3:c.5122G>T	p.Ala1708Ser	p.A1708S	ENST00000375023	NM_004557.3	1708	Gct/Tct	28/30	0.158380837681865	4	FACETS	1	0.948	1	0.64	0.544	0.746	CLONAL	1	TRUE	2	0.22	4		501	433	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739362	145739362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1484366007	NA	P-0056227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	44	583	2	ENST00000428558.2:c.2008G>A	p.Val670Ile	p.V670I	ENST00000428558	NM_004260.3	670	Gtt/Att	12/22	0.326924987117497	3	FACETS	1	0.88	1	0.529	0.444	0.622	CLONAL	1	TRUE	1	0.22	3		585	420	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806092	1806099	+	missense_variant	Missense_Mutation	ONP	AGTGTGTA	AGTGTGTA	GGAGTGTG	novel	NA	P-0056227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	35	645	0	ENST00000260795.2:c.1111_1118delinsGGAGTGTG	p.Ser371_Tyr373delinsGlyValCys	p.S371_Y373delinsGVC	ENST00000260795		371	AGTGTGTAt/GGAGTGTGt	8/17	1	2	FACETS	0.833	0.683	1	0.833	0.683	1	CLONAL	1	TRUE	1	0.22	2		645	382	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0056228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	58	508	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.898	0.773	1	0.898	0.773	1	CLONAL	1	TRUE	1	0.261932353031828	2		508	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0056228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	85	783	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.261932353031828	2		783	582	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557277	29557277	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs1060500273	NA	P-0056228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	24	201	0	ENST00000356175.3:c.2991-1G>C		p.X997_splice	ENST00000356175	NM_000267.3	997			1	2	FACETS	0.681	0.535	0.849	0.681	0.535	0.849	SUBCLONAL	1	TRUE	1	0.261932353031828	2		201	269	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828166	3828166	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	48	325	0	ENST00000262367.5:c.1959A>T	p.Leu653Phe	p.L653F	ENST00000262367	NM_004380.2	653	ttA/ttT	10/31	0.261932353031828	1	FACETS	0.849	0.72	0.991	0.849	0.72	0.991	CLONAL	1	TRUE	0	0.261932353031828	1		325	375	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857079	9857079	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	34	247	0	ENST00000330684.3:c.4322C>T	p.Thr1441Ile	p.T1441I	ENST00000330684	NM_001134407.1	1441	aCc/aTc	13/13	0.261932353031828	1	FACETS	0.96	0.79	1	0.96	0.79	1	CLONAL	1	TRUE	0	0.261932353031828	1		247	235	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805923	89805923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	53	650	2	ENST00000389301.3:c.3973G>A	p.Asp1325Asn	p.D1325N	ENST00000389301	NM_000135.2	1325	Gat/Aat	40/43	0.261932353031828	1	FACETS	0.696	0.594	0.808	0.696	0.594	0.808	SUBCLONAL	1	TRUE	0	0.261932353031828	1		652	505	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180303	38180303	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0056228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	57	655	0	ENST00000396334.3:c.151A>C	p.Asn51His	p.N51H	ENST00000396334	NM_002468.4	51	Aac/Cac	1/5	1	2	FACETS	0.766	0.657	0.885	0.766	0.657	0.885	SUBCLONAL	1	TRUE	1	0.261932353031828	2		655	568	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0056234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	12	501	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.189107624590148	5	FACETS	1	0.777	1	0.815	0.59	1	CLONAL	3	FALSE	1	0.189107624590148	5		501	50	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0056234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	17	654	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.189107624590148	3	FACETS	1	0.798	1	1	0.915	1	CLONAL	3	FALSE	1	0.189107624590148	3		654	63	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	18	310	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	0.189107624590148	5	FACETS	0.926	0.711	1	0.694	0.533	0.877	CLONAL	3	FALSE	1	0.189107624590148	5		310	88	SUCCESS
MET	4233	MSKCC	GRCh37	7	116409781	116409781	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	84	254	0	ENST00000397752.3:c.2666C>G	p.Ser889Cys	p.S889C	ENST00000397752	NM_000245.2	889	tCt/tGt	12/21	0.308381874130007	3	FACETS	0.883	0.786	0.985			1	INDETERMINATE	1	TRUE	NA	0.73225503020616	3		254	355	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412905	49412905	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519951	NA	P-0056235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	188	502	0	ENST00000418115.1:c.118G>C	p.Glu40Gln	p.E40Q	ENST00000418115	NM_001664.2	40	Gag/Cag	2/5	0.73225503020616	1	FACETS	0.82	0.768	0.871	0.82	0.768	0.871	CLONAL	1	TRUE	0	0.73225503020616	1		502	397	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858600	57858600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756282060	NA	P-0056235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	205	603	0	ENST00000228682.2:c.338G>A	p.Arg113Gln	p.R113Q	ENST00000228682	NM_005269.2	113	cGa/cAa	4/12	1	2	FACETS	0.868	0.809	0.928	0.868	0.809	0.928	CLONAL	1	TRUE	1	0.73225503020616	2		603	645	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016634	12016634	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	115	257	0	ENST00000353533.5:c.770C>G	p.Ser257Cys	p.S257C	ENST00000353533	NM_003010.3	257	tCt/tGt	7/11	0.715337392221872	1	FACETS	0.981	0.909	1	0.981	0.909	1	CLONAL	1	TRUE	0	0.73225503020616	1		257	203	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878235	151878235	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0056235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	150	534	0	ENST00000262189.6:c.6710C>G	p.Ser2237Ter	p.S2237*	ENST00000262189	NM_170606.2	2237	tCa/tGa	36/59	0.658895152611463	3	FACETS	0.75	0.687	0.817	0.375	0.343	0.409	SUBCLONAL	1	TRUE	1	0.73225503020616	3		534	746	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147564	47147564	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	100	267	0	ENST00000409792.3:c.4762G>C	p.Glu1588Gln	p.E1588Q	ENST00000409792	NM_014159.6	1588	Gag/Cag	6/21	0.73225503020616	1	FACETS	0.813	0.743	0.883	0.813	0.743	0.883	CLONAL	1	TRUE	0	0.73225503020616	1		267	213	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759881	133759881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1310633113	NA	P-0056235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	196	733	1	ENST00000318560.5:c.2204C>T	p.Thr735Met	p.T735M	ENST00000318560	NM_005157.4	735	aCg/aTg	11/11	1	2	FACETS	0.793	0.737	0.851	0.793	0.737	0.851	SUBCLONAL	1	TRUE	1	0.73225503020616	2		734	675	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878973	151878973	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	158	461	1	ENST00000262189.6:c.5972C>T	p.Ser1991Leu	p.S1991L	ENST00000262189	NM_170606.2	1991	tCa/tTa	36/59	0.658895152611463	3	FACETS	0.883	0.811	0.957	0.441	0.405	0.479	CLONAL	1	TRUE	1	0.73225503020616	3		462	668	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258971	16258971	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	190	552	0	ENST00000375759.3:c.6236G>C	p.Arg2079Thr	p.R2079T	ENST00000375759	NM_015001.2	2079	aGa/aCa	11/15	0.73225503020616	1	FACETS	0.843	0.791	0.896	0.843	0.791	0.896	CLONAL	1	TRUE	0	0.73225503020616	1		552	390	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259654	16259654	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	148	388	0	ENST00000375759.3:c.6919G>T	p.Glu2307Ter	p.E2307*	ENST00000375759	NM_015001.2	2307	Gaa/Taa	11/15	0.73225503020616	1	FACETS	0.89	0.829	0.95	0.89	0.829	0.95	CLONAL	1	TRUE	0	0.73225503020616	1		388	288	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204513756	204513756	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	144	234	0	ENST00000367182.3:c.766G>A	p.Glu256Lys	p.E256K	ENST00000367182	NM_001278516.1	256	Gaa/Aaa	9/11	0.686787655993166	4	FACETS	0.906	0.836	0.977	0.604	0.557	0.651	CLONAL	2	TRUE	1	0.73225503020616	4		234	376	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999468	100999468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	274	798	0	ENST00000325455.5:c.334G>A	p.Asp112Asn	p.D112N	ENST00000325455	NM_001202474.3	112	Gac/Aac	1/8	1	2	FACETS	0.902	0.849	0.955	0.902	0.849	0.955	CLONAL	1	TRUE	1	0.73225503020616	2		798	830	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897053	28897053	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	135	355	0	ENST00000282397.4:c.2827G>C	p.Glu943Gln	p.E943Q	ENST00000282397	NM_002019.4	943	Gaa/Caa	21/30	0.73225503020616	1	FACETS	0.92	0.856	0.984	0.92	0.856	0.984	CLONAL	1	TRUE	0	0.73225503020616	1		355	254	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43700267	43700267	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	188	524	0	ENST00000382044.4:c.5620T>C	p.Phe1874Leu	p.F1874L	ENST00000382044	NM_001141980.1	1874	Ttc/Ctc	27/28	1	2	FACETS	0.974	0.907	1	0.974	0.907	1	CLONAL	1	TRUE	1	0.73225503020616	2		524	527	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016554	12016554	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	101	190	0	ENST00000353533.5:c.690C>G	p.Ile230Met	p.I230M	ENST00000353533	NM_003010.3	230	atC/atG	7/11	0.715337392221872	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.73225503020616	1		190	170	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592039	67592039	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	99	209	0	ENST00000274335.5:c.1855C>T	p.His619Tyr	p.H619Y	ENST00000274335		619	Cat/Tat	14/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.73225503020616	2		209	226	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845835	151845835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536013179	NA	P-0056235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	400	566	0	ENST00000262189.6:c.13177G>A	p.Asp4393Asn	p.D4393N	ENST00000262189	NM_170606.2	4393	Gat/Aat	52/59	0.658895152611463	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.73225503020616	3		566	714	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846238	151846238	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0056235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	239	307	0	ENST00000262189.6:c.12775-1G>A		p.X4259_splice	ENST00000262189	NM_170606.2	4259			0.658895152611463	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.73225503020616	3		307	408	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878094	151878094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	126	402	0	ENST00000262189.6:c.6851C>T	p.Ser2284Leu	p.S2284L	ENST00000262189	NM_170606.2	2284	tCa/tTa	36/59	0.658895152611463	3	FACETS	0.771	0.7	0.845	0.385	0.35	0.423	SUBCLONAL	1	TRUE	1	0.73225503020616	3		402	610	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0056236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	162	308	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.678883740026924	2		308	450	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0056236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	163	181	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.949	0.877	1	0.949	0.877	1	CLONAL	1	TRUE	1	0.678883740026924	2		181	506	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717615	89717615	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909227	NA	P-0056236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	152	325	0	ENST00000371953.3:c.640C>T	p.Gln214Ter	p.Q214*	ENST00000371953	NM_000314.4	214	Cag/Tag	7/9	1	2	FACETS	0.921	0.849	0.996	0.921	0.849	0.996	CLONAL	1	TRUE	1	0.678883740026924	2		325	486	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0056236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	128	281	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.678883740026924	2		281	374	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180680	32180680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1331335302	NA	P-0056236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	303	681	0	ENST00000375023.3:c.2447G>A	p.Arg816Lys	p.R816K	ENST00000375023	NM_004557.3	816	aGg/aAg	16/30	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.678883740026924	2		681	879	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406295	70406295	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762257556	NA	P-0056236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	250	502	1	ENST00000373644.4:c.3809C>T	p.Thr1270Met	p.T1270M	ENST00000373644	NM_030625.2	1270	aCg/aTg	4/12	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.678883740026924	2		503	696	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258346	16258521	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGCAGAGAAGATTACAAGGACTGCTTCTAAAAACTCTGCTGCAGACCTTGAACATCCCGAACCAAGTTTGCCTCTCAGCCGAACAAGGCGCCGGAATGTAAGGAGCGTCTATGCAACCATGGGTGACCATGAAAACCGCTCTCCTGTCAAAGAGCCCGTTGAGCAACCAAGAGT	GAGGCAGAGAAGATTACAAGGACTGCTTCTAAAAACTCTGCTGCAGACCTTGAACATCCCGAACCAAGTTTGCCTCTCAGCCGAACAAGGCGCCGGAATGTAAGGAGCGTCTATGCAACCATGGGTGACCATGAAAACCGCTCTCCTGTCAAAGAGCCCGTTGAGCAACCAAGAGT	-	novel	NA	P-0056236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	27	503	0	ENST00000375759.3:c.5613_5788del	p.Glu1871AspfsTer33	p.E1871Dfs*33	ENST00000375759	NM_015001.2	1871	GAGGCAGAGAAGATTACAAGGACTGCTTCTAAAAACTCTGCTGCAGACCTTGAACATCCCGAACCAAGTTTGCCTCTCAGCCGAACAAGGCGCCGGAATGTAAGGAGCGTCTATGCAACCATGGGTGACCATGAAAACCGCTCTCCTGTCAAAGAGCCCGTTGAGCAACCAAGAGTg/g	11/15	0.678883740026924	1	FACETS	0.113	0.09	0.14	0.113	0.09	0.14	SUBCLONAL	1	TRUE	0	0.678883740026924	1		503	464	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396616	396641	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTTCTCCTCGTTCGAGTCACAGGG	CTCTTCTCCTCGTTCGAGTCACAGGG	-	novel	NA	P-0056236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	245	531	0	ENST00000262320.3:c.385_410del	p.Pro129AlafsTer14	p.P129Afs*14	ENST00000262320	NM_003502.3	129	CCCTGTGACTCGAACGAGGAGAAGAGg/g	2/11	0.678883740026924	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.678883740026924	1		531	462	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197349	26197349	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	58	435	0	ENST00000356476.2:c.130C>A	p.Pro44Thr	p.P44T	ENST00000356476		44	Ccc/Acc	1/1	1	2	FACETS	0.309	0.265	0.357	0.309	0.265	0.357	SUBCLONAL	1	TRUE	1	0.678883740026924	2		435	553	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097741	27097753	+	frameshift_variant	Frame_Shift_Del	DEL	AGAAGACCCTCCC	AGAAGACCCTCCC	-	novel	NA	P-0056237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	67	447	0	ENST00000324856.7:c.3330_3342del	p.Glu1111GlnfsTer46	p.E1111Qfs*46	ENST00000324856	NM_006015.4	1110	ggAGAAGACCCTCCC/gg	12/20	1	2	FACETS	0.927	0.806	1	0.927	0.806	1	CLONAL	1	TRUE	1	0.256281892755794	2		447	564	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032799	30032799	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	72	390	0	ENST00000338641.4:c.174A>T	p.Glu58Asp	p.E58D	ENST00000338641	NM_000268.3	58	gaA/gaT	2/16	1	2	FACETS	0.886	0.774	1	0.886	0.774	1	CLONAL	1	TRUE	1	0.256281892755794	2		390	634	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143330	108143342	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGAGGTGAGTTT	TTGAGGTGAGTTT	-	novel	NA	P-0056237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	24	324	0	ENST00000278616.4:c.3152_3153+11del		p.X1051_splice	ENST00000278616	NM_000051.3	1051		21/63	0.256281892755794	1	FACETS	0.469	0.368	0.586	0.469	0.368	0.586	SUBCLONAL	1	TRUE	0	0.256281892755794	1		324	348	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0056238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	499	550	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.876703870638955	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.876703870638955	2		550	568	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0056238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	60	30	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.76	0.691	0.825			1	INDETERMINATE	2	TRUE	NA	0.876703870638955	2		30	90	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074379	8074380	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0056238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	284	352	1	ENST00000377482.5:c.279_280delinsTT	p.Pro94Ser	p.P94S	ENST00000377482	NM_018948.3	93	ccCCct/ccTTct	4/4	0.876703870638955	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.876703870638955	2		353	320	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691100	18691100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372642230	NA	P-0056238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	201	337	0	ENST00000266497.5:c.3211C>T	p.Pro1071Ser	p.P1071S	ENST00000266497		1071	Cct/Tct	23/31	1	2	FACETS	0.959	0.899	1	0.959	0.899	1	CLONAL	1	TRUE	1	0.876703870638955	2		337	478	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11022923	11022923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	202	781	1	ENST00000327064.4:c.622C>T	p.Arg208Trp	p.R208W	ENST00000327064	NM_199141.1	208	Cgg/Tgg	5/16	0.228023680112888	3	FACETS	0.839	0.78	0.9	0.28	0.259	0.3	INDETERMINATE	1	TRUE	0	0.876703870638955	3		782	790	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099406	157099426	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAA	CAGCAGCAGCAGCAGCAGCAA	-	rs762617219	NA	P-0056240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	70	150	0	ENST00000346085.5:c.363_383del	p.Gln125_Gln131del	p.Q125_Q131del	ENST00000346085	NM_020732.3	115	CAGCAGCAGCAGCAGCAGCAA/-	1/20	0.29126881517337	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.29126881517337	1		150	331	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989608	212989608	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	51	250	0	ENST00000342788.4:c.103A>G	p.Lys35Glu	p.K35E	ENST00000342788	NM_005235.2	35	Aaa/Gaa	2/28	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.29126881517337	2		250	276	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191480	10191480	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913346	NA	P-0056240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	52	352	0	ENST00000256474.2:c.473T>C	p.Leu158Pro	p.L158P	ENST00000256474	NM_000551.3	158	cTg/cCg	3/3	0.29126881517337	1	FACETS	0.872	0.745	1	0.872	0.745	1	CLONAL	1	TRUE	0	0.29126881517337	1		352	350	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084151	47084152	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0056240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	47	476	0	ENST00000409792.3:c.7137_7138del	p.Pro2381LeufsTer47	p.P2381Lfs*47	ENST00000409792	NM_014159.6	2379	ccGCcc/cccc	17/21	0.29126881517337	1	FACETS	0.809	0.685	0.944	0.809	0.685	0.944	CLONAL	1	TRUE	0	0.29126881517337	1		476	341	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441234	52441235	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0056240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	82	453	0	ENST00000460680.1:c.535dup	p.Arg179ProfsTer4	p.R179Pfs*4	ENST00000460680	NM_004656.3	179	cgg/cCgg	7/17	0.29126881517337	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.29126881517337	1		453	419	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52649469	52649469	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	58	411	0	ENST00000394830.3:c.1822del	p.Tyr608IlefsTer34	p.Y608Ifs*34	ENST00000394830	NM_018313.4	608	Tat/at	16/30	0.29126881517337	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.29126881517337	1		411	303	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0056274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	177	277	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.768	0.714	0.824	1	0.991	1	SUBCLONAL	2	TRUE	1	0.477858972421645	2		278	482	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758858	41758858	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746561913	NA	P-0056274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	66	737	1	ENST00000301178.4:c.1912G>A	p.Gly638Arg	p.G638R	ENST00000301178	NM_021913.4	638	Ggg/Agg	16/20	0.477858972421645	3	FACETS	0.291	0.251	0.334	0.145	0.125	0.167	SUBCLONAL	1	TRUE	1	0.477858972421645	3		738	1178	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87322773	87322773	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	142	470	0	ENST00000277120.3:c.374A>G	p.Asn125Ser	p.N125S	ENST00000277120		125	aAc/aGc	5/19	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.477858972421645	2		470	533	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903682	114903682	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	223	566	0	ENST00000543371.1:c.686G>T	p.Gly229Val	p.G229V	ENST00000543371	NM_001198531.1	229	gGa/gTa	7/14	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.477858972421645	2		566	744	SUCCESS
APC	324	MSKCC	GRCh37	5	112164656	112164656	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0056274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	139	248	0	ENST00000257430.4:c.1730T>G	p.Leu577Ter	p.L577*	ENST00000257430	NM_000038.5	577	tTa/tGa	14/16	1	2	FACETS	0.765	0.705	0.827	1	0.989	1	SUBCLONAL	2	TRUE	1	0.477858972421645	2		248	380	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710966	117710966	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	26	353	0	ENST00000368508.3:c.1306C>T	p.Leu436Phe	p.L436F	ENST00000368508	NM_002944.2	436	Ctt/Ttt	12/43	1	2	FACETS	0.248	0.196	0.308	0.248	0.196	0.308	SUBCLONAL	1	TRUE	1	0.477858972421645	2		353	438	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080540	5080540	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	53	308	0	ENST00000381652.3:c.2292del	p.Gln764HisfsTer17	p.Q764Hfs*17	ENST00000381652	NM_004972.3	764	cAa/ca	18/25	1	2	FACETS	0.588	0.503	0.681	0.588	0.503	0.681	SUBCLONAL	1	TRUE	1	0.477858972421645	2		308	377	SUCCESS
APC	324	MSKCC	GRCh37	5	112175775	112175775	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	144	381	0	ENST00000257430.4:c.4484del	p.Ser1495IlefsTer12	p.S1495Ifs*12	ENST00000257430	NM_000038.5	1495	aGt/at	16/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.477858972421645	2		381	463	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0056277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	83	573	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.807	0.711	0.91	0.807	0.711	0.91	CLONAL	1	TRUE	1	0.233252041437277	2		573	882	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0056277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	110	771	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.233252041437277	1	FACETS	0.882	0.791	0.978	0.882	0.791	0.978	CLONAL	1	TRUE	0	0.233252041437277	1		771	945	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609570	81609570	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	85	570	0	ENST00000298171.2:c.1168T>C	p.Cys390Arg	p.C390R	ENST00000298171	NM_000369.2	390	Tgt/Cgt	10/10	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.233252041437277	2		570	719	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2225409	2225409	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	58	482	0	ENST00000398665.3:c.3619A>T	p.Ile1207Phe	p.I1207F	ENST00000398665	NM_032482.2	1207	Atc/Ttc	26/28	1	2	FACETS	0.801	0.688	0.924	0.801	0.688	0.924	CLONAL	1	TRUE	1	0.233252041437277	2		482	621	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437338	220437338	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	118	1018	0	ENST00000243786.2:c.242C>G	p.Ser81Cys	p.S81C	ENST00000243786	NM_002191.3	81	tCc/tGc	1/2	1	2	FACETS	0.933	0.84	1	0.933	0.84	1	CLONAL	1	TRUE	1	0.233252041437277	2		1018	1084	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077518	30077518	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	70	492	0	ENST00000338641.4:c.1665G>C	p.Glu555Asp	p.E555D	ENST00000338641	NM_000268.3	555	gaG/gaC	15/16	0.217421604781683	3	FACETS	1	0.908	1	0.526	0.458	0.599	CLONAL	1	TRUE	1	0.233252041437277	3		492	637	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568518	41568518	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	63	422	0	ENST00000263253.7:c.4468G>C	p.Ala1490Pro	p.A1490P	ENST00000263253	NM_001429.3	1490	Gct/Cct	28/31	0.217421604781683	3	FACETS	0.826	0.718	0.942	0.826	0.718	0.942	CLONAL	2	TRUE	1	0.233252041437277	3		422	365	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55603443	55603443	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	84	280	0	ENST00000288135.5:c.2799T>G	p.Asn933Lys	p.N933K	ENST00000288135	NM_000222.2	933	aaT/aaG	20/21	0.186038561207043	1	FACETS	1	0.92	1	1	0.986	1	CLONAL	2	TRUE	0	0.233252041437277	1		280	307	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92244497	92244497	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	68	455	0	ENST00000265734.4:c.938A>C	p.His313Pro	p.H313P	ENST00000265734	NM_001259.6	313	cAc/cCc	8/8	1	2	FACETS	0.793	0.689	0.906	0.793	0.689	0.906	CLONAL	1	TRUE	1	0.233252041437277	2		455	735	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0056278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	58	374	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.764	0.659	0.876	0.764	0.659	0.876	SUBCLONAL	1	TRUE	1	0.4128288659721	2		374	368	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397800	49397800	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	91	494	0	ENST00000418115.1:c.424G>A	p.Glu142Lys	p.E142K	ENST00000418115	NM_001664.2	142	Gaa/Aaa	5/5	1	2	FACETS	0.542	0.48	0.607	0.542	0.48	0.607	SUBCLONAL	1	TRUE	1	0.4128288659721	2		494	814	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0056278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	155	181	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.4128288659721	2		181	617	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243484	46243484	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	200	508	0	ENST00000334344.6:c.1837C>T	p.Gln613Ter	p.Q613*	ENST00000334344	NM_152641.2	613	Cag/Tag	14/21	1	2	FACETS	0.991	0.927	1	1	0.994	1	CLONAL	2	TRUE	1	0.4128288659721	2		508	489	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028790	47028790	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	185	621	0	ENST00000377604.3:c.94C>T	p.Arg32Ter	p.R32*	ENST00000377604	NM_001204468.1	32	Cga/Tga	3/24	0.243860137250679	0	FACETS	0.931	0.866	0.999			1	INDETERMINATE	1	TRUE	NA	0.4128288659721	0		621	565	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397678	139397678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778830490	NA	P-0056278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	149	1029	0	ENST00000277541.6:c.5123C>T	p.Ser1708Leu	p.S1708L	ENST00000277541	NM_017617.3	1708	tCg/tTg	27/34	0.277312802294057	2	FACETS	0.558	0.508	0.611	0.279	0.254	0.306	SUBCLONAL	1	TRUE	0	0.4128288659721	2		1029	1293	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528596	8528596	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	118	443	0	ENST00000356435.5:c.536G>T	p.Arg179Leu	p.R179L	ENST00000356435		179	cGa/cTa	4/35	1	2	FACETS	0.986	0.892	1	0.986	0.892	1	CLONAL	1	TRUE	1	0.4128288659721	2		443	580	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691003	NA	P-0056278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	229	603	0	ENST00000269305.4:c.96+1G>T		p.X32_splice	ENST00000269305	NM_001126112.2	32			0.355186311251061	2	FACETS	0.847	0.794	0.901	0.847	0.794	0.901	CLONAL	2	TRUE	0	0.4128288659721	2		603	655	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096291	178096291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	178	693	0	ENST00000397062.3:c.1040C>T	p.Ser347Leu	p.S347L	ENST00000397062	NM_006164.4	347	tCa/tTa	5/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.4128288659721	2		693	739	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462300	89462300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	37	447	2	ENST00000336596.2:c.1772C>T	p.Pro591Leu	p.P591L	ENST00000336596	NM_005233.5	591	cCa/cTa	10/17	1	2	FACETS	0.38	0.313	0.455	0.38	0.313	0.455	SUBCLONAL	1	TRUE	1	0.4128288659721	2		449	472	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610564	10610564	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	140	996	0	ENST00000171111.5:c.146A>G	p.Asn49Ser	p.N49S	ENST00000171111	NM_203500.1	49	aAc/aGc	2/6	0.192967069076696	2	FACETS	0.592	0.538	0.649	0.296	0.269	0.325	INDETERMINATE	1	TRUE	0	0.4128288659721	2		996	1146	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073337	8073337	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0056278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	97	614	0	ENST00000377482.5:c.1322C>G	p.Ser441Ter	p.S441*	ENST00000377482	NM_018948.3	441	tCa/tGa	4/4	0.217029934105105	1	FACETS	0.519	0.462	0.579	0.519	0.462	0.579	INDETERMINATE	1	TRUE	0	0.4128288659721	1		614	719	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105784	27105784	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	65	610	0	ENST00000324856.7:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000324856	NM_006015.4	1799	Gag/Aag	20/20	0.217029934105105	1	FACETS	0.451	0.391	0.516	0.451	0.391	0.516	INDETERMINATE	1	TRUE	0	0.4128288659721	1		610	554	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137313	64137313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	313	855	0	ENST00000334205.4:c.1745C>T	p.Ala582Val	p.A582V	ENST00000334205	NM_003942.2	582	gCg/gTg	14/17	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.4128288659721	2		855	1034	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444145	49444145	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	129	1064	0	ENST00000301067.7:c.3226G>A	p.Glu1076Lys	p.E1076K	ENST00000301067	NM_003482.3	1076	Gag/Aag	11/54	1	2	FACETS	0.595	0.539	0.655	0.595	0.539	0.655	SUBCLONAL	1	TRUE	1	0.4128288659721	2		1064	1050	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494884	56494884	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	193	693	0	ENST00000267101.3:c.3241C>A	p.Pro1081Thr	p.P1081T	ENST00000267101	NM_001982.3	1081	Cca/Aca	27/28	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.4128288659721	2		693	816	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023027	33023027	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	105	602	0	ENST00000300177.4:c.136C>T	p.Gln46Ter	p.Q46*	ENST00000300177	NM_001191322.1	46	Cag/Tag	2/2	0.311721374459873	1	FACETS	0.706	0.634	0.781	0.706	0.634	0.781	SUBCLONAL	1	TRUE	0	0.4128288659721	1		602	572	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023094	33023094	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	79	615	0	ENST00000300177.4:c.203T>C	p.Met68Thr	p.M68T	ENST00000300177	NM_001191322.1	68	aTg/aCg	2/2	0.311721374459873	1	FACETS	0.538	0.473	0.606	0.538	0.473	0.606	SUBCLONAL	1	TRUE	0	0.4128288659721	1		615	565	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872381	45872381	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0056278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	115	777	0	ENST00000391945.4:c.130T>C	p.Ser44Pro	p.S44P	ENST00000391945	NM_000400.3	44	Tca/Cca	3/23	NA	2	FACETS	0.583	0.525	0.646			1	INDETERMINATE	1	TRUE	NA	0.4128288659721	2		777	955	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082548	16082548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1357629501	NA	P-0056278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	112	673	0	ENST00000281043.3:c.362C>T	p.Ser121Phe	p.S121F	ENST00000281043	NM_005378.4	121	tCc/tTc	2/3	0.30501396000251	1	FACETS	0.62	0.558	0.685	0.62	0.558	0.685	SUBCLONAL	1	TRUE	0	0.4128288659721	1		673	695	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416719	29416719	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	180	615	0	ENST00000389048.3:c.4234C>A	p.Pro1412Thr	p.P1412T	ENST00000389048	NM_004304.4	1412	Cct/Act	29/29	0.30501396000251	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.4128288659721	1		615	684	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400316	225400316	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	41	300	0	ENST00000264414.4:c.307C>T	p.Gln103Ter	p.Q103*	ENST00000264414	NM_003590.4	103	Caa/Taa	3/16	0.202249039074563	0	FACETS	0.349	0.292	0.413			1	INDETERMINATE	1	TRUE	0	0.4128288659721	0		300	334	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389193	31389193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	183	636	0	ENST00000328111.2:c.2106G>A	p.Met702Ile	p.M702I	ENST00000328111	NM_006892.3	702	atG/atA	19/23	1	2	FACETS	0.932	0.86	1	0.932	0.86	1	CLONAL	1	TRUE	1	0.4128288659721	2		636	951	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542734	187542734	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0056278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	150	523	0	ENST00000441802.2:c.5006C>G	p.Ser1669Ter	p.S1669*	ENST00000441802	NM_005245.3	1669	tCa/tGa	10/27	0.4128288659721	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.4128288659721	1		523	548	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323250	31323250	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	136	843	0	ENST00000412585.2:c.739G>C	p.Asp247His	p.D247H	ENST00000412585	NM_005514.6	247	Gac/Cac	4/8	0.355186311251061	2	FACETS	0.705	0.641	0.773	0.353	0.32	0.387	SUBCLONAL	1	TRUE	0	0.4128288659721	2		843	934	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141545571	141545571	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	105	862	0	ENST00000220592.5:c.2267T>A	p.Ile756Asn	p.I756N	ENST00000220592	NM_012154.3	756	aTc/aAc	17/19	0.217029934105105	1	FACETS	0.422	0.377	0.47	0.422	0.377	0.47	INDETERMINATE	1	TRUE	0	0.4128288659721	1		862	956	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396523	139396523	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0056278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	118	877	0	ENST00000277541.6:c.5402C>G	p.Ser1801Ter	p.S1801*	ENST00000277541	NM_017617.3	1801	tCa/tGa	29/34	0.277312802294057	2	FACETS	0.482	0.433	0.534	0.241	0.216	0.267	SUBCLONAL	1	TRUE	0	0.4128288659721	2		877	1186	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400081	139400081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1253	129	1086	1	ENST00000277541.6:c.4267C>T	p.Leu1423Phe	p.L1423F	ENST00000277541	NM_017617.3	1423	Ctc/Ttc	25/34	0.277312802294057	2	FACETS	0.452	0.408	0.499	0.226	0.204	0.25	SUBCLONAL	1	TRUE	0	0.4128288659721	2		1087	1382	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923751	39923751	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs757991049	NA	P-0056278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	212	484	0	ENST00000378444.4:c.3340G>C	p.Glu1114Gln	p.E1114Q	ENST00000378444	NM_001123385.1	1114	Gag/Cag	7/15	0.243860137250679	0	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.4128288659721	0		484	568	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928860	44928860	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	69	264	0	ENST00000377967.4:c.1961del	p.Pro654LeufsTer37	p.P654Lfs*37	ENST00000377967	NM_021140.2	654	Cct/ct	17/29	0.243860137250679	0	FACETS	0.861	0.761	0.965			1	INDETERMINATE	1	TRUE	NA	0.4128288659721	0		264	228	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0056279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	351	508	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.685889651069603	4	FACETS	0.937	0.898	0.976	0.937	0.898	0.976	CLONAL	3	TRUE	1	0.685889651069603	4		508	614	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	585	831	0	ENST00000269305.4:c.383del	p.Pro128LeufsTer42	p.P128Lfs*42	ENST00000269305	NM_001126112.2	128	cCt/ct	5/11	0.622196526115877	3	FACETS	0.868	0.843	0.892	0.868	0.843	0.892	CLONAL	3	TRUE	0	0.685889651069603	3		831	880	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755128667	NA	P-0056279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	473	858	1	ENST00000407977.2:c.1976dup	p.Pro660SerfsTer87	p.P660Sfs*87	ENST00000407977		659	ggt/ggGt	9/10	NA	2	FACETS	0.822	0.792	0.852			1	INDETERMINATE	2	TRUE	NA	0.685889651069603	2		859	839	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098823	178098823	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	391	651	0	ENST00000397062.3:c.222A>C	p.Leu74Phe	p.L74F	ENST00000397062	NM_006164.4	74	ttA/ttC	2/5	0.503633106997419	5	FACETS	1	0.989	1	0.744	0.708	0.779	CLONAL	2	TRUE	2	0.685889651069603	5		651	1037	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115873	8115874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0056282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	410	568	0	ENST00000346208.3:c.1220dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tCcg	6/6	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.882745779479281	2		568	910	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057826	27057826	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	435	621	0	ENST00000324856.7:c.1534C>T	p.Gln512Ter	p.Q512*	ENST00000324856	NM_006015.4	512	Cag/Tag	3/20	1	2	FACETS	0.95	0.909	0.992	0.95	0.909	0.992	CLONAL	1	TRUE	1	0.882745779479281	2		621	1037	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352585	118352585	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555039343	NA	P-0056282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	341	411	0	ENST00000534358.1:c.3790C>T	p.Arg1264Ter	p.R1264*	ENST00000534358	NM_005933.3	1264	Cga/Tga	7/36	0.882745779479281	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.882745779479281	1		411	414	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508666	38508666	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1298	171	591	0	ENST00000254066.5:c.714G>T	p.Lys238Asn	p.K238N	ENST00000254066	NM_000964.3	238	aaG/aaT	6/9	0.513472392259021	4	FACETS	0.497	0.455	0.54	0.166	0.151	0.18	INDETERMINATE	1	TRUE	1	0.882745779479281	4		591	1469	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149982960	149982960	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	48	410	0	ENST00000253339.5:c.3298G>T	p.Glu1100Ter	p.E1100*	ENST00000253339		1100	Gaa/Taa	7/7	1	2	FACETS	0.177	0.149	0.207	0.177	0.149	0.207	SUBCLONAL	1	TRUE	1	0.882745779479281	2		410	616	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428213	47428213	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	65	446	0	ENST00000377045.4:c.1173C>A	p.Tyr391Ter	p.Y391*	ENST00000377045	NM_001654.4	391	taC/taA	11/16	1	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.22516408272894	1		446	347	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156098	106156099	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCTCCTGCAGAAAATAACATCCAGGGAACCAC	novel	NA	P-0056283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	17	337	0	ENST00000380013.4:c.1000_1031dup	p.Lys345LeufsTer13	p.K345Lfs*13	ENST00000380013	NM_001127208.2	333	-/TCTCCTGCAGAAAATAACATCCAGGGAACCAC	3/11	0.0838074378914904	3	FACETS	0.545	0.407	0.711	0.273	0.203	0.356	INDETERMINATE	1	TRUE	1	0.22516408272894	3		337	308	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156994	106156994	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	41	468	0	ENST00000380013.4:c.1897del	p.Met633CysfsTer6	p.M633Cfs*6	ENST00000380013	NM_001127208.2	632	cAa/ca	3/11	0.0838074378914904	3	FACETS	1	0.868	1	0.523	0.437	0.62	INDETERMINATE	1	TRUE	1	0.22516408272894	3		468	387	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483136	29483136	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	25	260	0	ENST00000356175.3:c.197del	p.Asn66ThrfsTer3	p.N66Tfs*3	ENST00000356175	NM_000267.3	66	Aac/ac	2/57	1	2	FACETS	0.405	0.32	0.504	0.405	0.32	0.504	SUBCLONAL	1	TRUE	1	0.419419437618097	2		260	294	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411770	63411770	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	56	944	0	ENST00000330258.3:c.1397A>T	p.Asn466Ile	p.N466I	ENST00000330258	NM_152424.3	466	aAt/aTt	2/2	0.419419437618097	3	FACETS	0.331	0.283	0.385	0.166	0.141	0.193	SUBCLONAL	1	TRUE	1	0.419419437618097	3		944	975	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0056293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	79	219	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.215351672521873	3	FACETS	0.952	0.847	1	0.952	0.847	1	CLONAL	2	TRUE	1	0.339369470278813	3		219	286	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0056293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	124	538	0	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	0.215351672521873	3	FACETS	1	0.983	1	0.704	0.639	0.773	CLONAL	1	TRUE	1	0.339369470278813	3		538	607	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856196	111856196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	66	238	0	ENST00000341259.2:c.247C>T	p.Arg83Trp	p.R83W	ENST00000341259	NM_005475.2	83	Cgg/Tgg	2/8	0.15584942772825	3	FACETS	1	0.925	1	0.363	0.316	0.413	INDETERMINATE	1	TRUE	0	0.339369470278813	3		238	418	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690618	88690618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149623569	NA	P-0056293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	76	474	0	ENST00000360948.2:c.412C>T	p.Arg138Trp	p.R138W	ENST00000360948	NM_001012338.2	138	Cgg/Tgg	5/19	1	2	FACETS	0.811	0.713	0.917	0.811	0.713	0.917	CLONAL	1	TRUE	1	0.339369470278813	2		474	552	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099343	27099343	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	91	705	0	ENST00000324856.7:c.3580G>T	p.Gly1194Ter	p.G1194*	ENST00000324856	NM_006015.4	1194	Gga/Tga	14/20	1	2	FACETS	0.858	0.763	0.96	0.858	0.763	0.96	CLONAL	1	TRUE	1	0.339369470278813	2		705	625	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578205	226578205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765820369	NA	P-0056293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	118	624	0	ENST00000366794.5:c.523G>A	p.Glu175Lys	p.E175K	ENST00000366794	NM_001618.3	175	Gag/Aag	4/23	0.340694898174124	3	FACETS	0.879	0.792	0.971	0.44	0.396	0.486	CLONAL	1	TRUE	1	0.339369470278813	3		624	925	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917722	94917722	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	84	392	0	ENST00000536441.1:c.799del	p.Glu267LysfsTer3	p.E267Kfs*3	ENST00000536441	NM_144665.3	267	Gaa/aa	6/10	0.340694898174124	3	FACETS	0.844	0.752	0.941	0.844	0.752	0.941	CLONAL	2	TRUE	1	0.339369470278813	3		392	343	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349588	15349588	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	226	1026	0	ENST00000263377.2:c.3986G>T	p.Arg1329Leu	p.R1329L	ENST00000263377	NM_058243.2	1329	cGg/cTg	19/20	0.205935283787746	3	FACETS	1	0.987	1	0.42	0.39	0.451	CLONAL	1	TRUE	0	0.339369470278813	3		1026	1237	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907689	111907708	+	frameshift_variant	Frame_Shift_Del	DEL	ATTGGAGACGAGTTTAACGC	ATTGGAGACGAGTTTAACGC	-	novel	NA	P-0056293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	59	508	0	ENST00000393256.3:c.463_482del	p.Ile155LeufsTer10	p.I155Lfs*10	ENST00000393256	NM_006538.4	155	ATTGGAGACGAGTTTAACGCt/t	3/4	0.339369470278813	3	FACETS	0.547	0.469	0.631	0.182	0.156	0.211	SUBCLONAL	1	TRUE	0	0.339369470278813	3		508	744	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0056294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	166	219	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.657757419750599	2		219	453	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0056294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	116	30	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.657757419750599	2		30	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0056294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	398	926	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.657757419750599	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.657757419750599	1		926	674	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087558	27087558	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0056294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	362	991	0	ENST00000324856.7:c.2132C>G	p.Ser711Ter	p.S711*	ENST00000324856	NM_006015.4	711	tCa/tGa	5/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.657757419750599	2		991	949	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873425	45873425	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	242	1059	0	ENST00000391945.4:c.71A>G	p.Tyr24Cys	p.Y24C	ENST00000391945	NM_000400.3	24	tAc/tGc	2/23	1	2	FACETS	0.996	0.934	1	0.996	0.934	1	CLONAL	1	TRUE	1	0.657757419750599	2		1059	739	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954299	48954299	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0056294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	118	188	0	ENST00000267163.4:c.1422-2A>G		p.X474_splice	ENST00000267163	NM_000321.2	474			1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.657757419750599	2		188	347	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642754	3642754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747563780	NA	P-0056294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	338	1073	1	ENST00000294008.3:c.2273C>T	p.Ala758Val	p.A758V	ENST00000294008	NM_032444.2	758	gCg/gTg	11/15	0.657757419750599	3	FACETS	0.954	0.901	1	0.477	0.45	0.504	CLONAL	1	TRUE	1	0.657757419750599	3		1074	1432	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125513713	125513713	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0056294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	156	395	0	ENST00000428830.2:c.841G>T	p.Gly281Cys	p.G281C	ENST00000428830	NM_001114121.2	281	Ggt/Tgt	9/14	1	2	FACETS	0.98	0.905	1	0.98	0.905	1	CLONAL	1	TRUE	1	0.657757419750599	2		395	484	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871210	12871219	+	frameshift_variant	Frame_Shift_Del	DEL	AGCAATGCGC	AGCAATGCGC	-	novel	NA	P-0056294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	81	377	0	ENST00000228872.4:c.439_448del	p.Gln147GlufsTer2	p.Q147Efs*2	ENST00000228872	NM_004064.3	146	gAGCAATGCGCa/ga	1/3	1	2	FACETS	0.88	0.784	0.979	0.88	0.784	0.979	CLONAL	1	TRUE	1	0.657757419750599	2		377	280	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448671	49448685	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAAACAAGCTACCTG	CAAACAAGCTACCTG	-	novel	NA	P-0056294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	158	583	0	ENST00000301067.7:c.174_176+12del		p.X58_splice	ENST00000301067	NM_003482.3	58		2/54	1	2	FACETS	0.949	0.876	1	0.949	0.876	1	CLONAL	1	TRUE	1	0.657757419750599	2		583	506	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256548	133256548	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	168	451	0	ENST00000320574.5:c.415C>G	p.Leu139Val	p.L139V	ENST00000320574	NM_006231.2	139	Ctg/Gtg	5/49	1	2	FACETS	0.949	0.878	1	0.949	0.878	1	CLONAL	1	TRUE	1	0.657757419750599	2		451	538	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033848	49033848	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	194	364	0	ENST00000267163.4:c.1985T>G	p.Leu662Arg	p.L662R	ENST00000267163	NM_000321.2	662	cTa/cGa	20/27	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.657757419750599	2		364	541	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49280958	49280958	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1331069467	NA	P-0056294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	36	311	0	ENST00000282018.3:c.5A>G	p.Glu2Gly	p.E2G	ENST00000282018	NM_020377.2	2	gAg/gGg	1/1	1	2	FACETS	0.251	0.206	0.301	0.251	0.206	0.301	SUBCLONAL	1	TRUE	1	0.657757419750599	2		311	436	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061661	38061661	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	101	310	0	ENST00000250448.2:c.328C>G	p.Pro110Ala	p.P110A	ENST00000250448	NM_004496.3	110	Ccg/Gcg	2/2	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.657757419750599	2		310	291	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273919	10273919	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	365	1128	0	ENST00000330684.3:c.350C>T	p.Ser117Phe	p.S117F	ENST00000330684	NM_001134407.1	117	tCc/tTc	2/13	0.657757419750599	3	FACETS	1	0.987	1	0.561	0.531	0.591	CLONAL	1	TRUE	1	0.657757419750599	3		1128	1315	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961609	18961609	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	309	1053	0	ENST00000262803.5:c.742G>T	p.Glu248Ter	p.E248*	ENST00000262803	NM_002911.3	248	Gag/Tag	5/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.657757419750599	2		1053	912	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47604188	47604188	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0056294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	213	313	1	ENST00000263735.4:c.527T>A	p.Leu176Gln	p.L176Q	ENST00000263735	NM_002354.2	176	cTg/cAg	5/9	0.160999467750298	3	FACETS	1	0.992	1	0.743	0.696	0.792	INDETERMINATE	1	TRUE	1	0.657757419750599	3		314	579	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116249	209116250	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAACCGCCACT	novel	NA	P-0056294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	72	235	0	ENST00000345146.2:c.16_26dup	p.Val11AlafsTer5	p.V11Afs*5	ENST00000345146	NM_005896.2	9	tct/tcAGTGGCGGTTCt	3/10	1	2	FACETS	0.556	0.488	0.628	0.556	0.488	0.628	SUBCLONAL	1	TRUE	1	0.657757419750599	2		235	394	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098628	47098628	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs774347385	NA	P-0056294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	217	866	0	ENST00000409792.3:c.6646C>A	p.Pro2216Thr	p.P2216T	ENST00000409792	NM_014159.6	2216	Ccc/Acc	15/21	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.657757419750599	2		866	656	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721551	49721551	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	228	695	0	ENST00000449682.2:c.2088C>G	p.Asn696Lys	p.N696K	ENST00000449682	NM_020998.3	696	aaC/aaG	18/18	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.657757419750599	2		695	639	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540739	187540739	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs756957772	NA	P-0056294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	304	453	0	ENST00000441802.2:c.7001A>C	p.His2334Pro	p.H2334P	ENST00000441802	NM_005245.3	2334	cAt/cCt	10/27	0.655384618205081	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.657757419750599	2		453	440	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540173	23540192	+	frameshift_variant	Frame_Shift_Del	DEL	CTCAGCTGGTCGTTCTGCGC	CTCAGCTGGTCGTTCTGCGC	-	novel	NA	P-0056294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	46	358	0	ENST00000380871.4:c.211_230del	p.Ala71HisfsTer30	p.A71Hfs*30	ENST00000380871	NM_006167.3	71	GCGCAGAACGACCAGCTGAGc/c	1/2	1	2	FACETS	0.553	0.469	0.644	0.553	0.469	0.644	SUBCLONAL	1	TRUE	1	0.657757419750599	2		358	253	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29195861	29195861	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	334	1093	2	ENST00000240100.2:c.737C>T	p.Pro246Leu	p.P246L	ENST00000240100	NM_001394.6	246	cCa/cTa	3/4	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.657757419750599	2		1095	1013	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926885	112926885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507544	NA	P-0056296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	26	674	0	ENST00000351677.2:c.1505C>T	p.Ser502Leu	p.S502L	ENST00000351677	NM_002834.3	502	tCa/tTa	13/16	1	2	FACETS	0.614	0.485	0.764	0.614	0.485	0.764	SUBCLONAL	1	TRUE	1	0.13	2		674	651	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	43	648	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	0.194565206515508	4	FACETS	1	0.878	1	0.532	0.444	0.63	CLONAL	1	TRUE	2	0.13	4		648	703	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0056296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	17	390	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.863	0.644	1	0.863	0.644	1	CLONAL	1	TRUE	1	0.13	2		391	303	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482426	56482426	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	41	686	0	ENST00000267101.3:c.974G>C	p.Gly325Ala	p.G325A	ENST00000267101	NM_001982.3	325	gGa/gCa	8/28	0.194565206515508	4	FACETS	0.903	0.75	1	0.452	0.375	0.538	CLONAL	1	TRUE	2	0.13	4		686	789	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512233	120512233	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0056296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	43	676	0	ENST00000256646.2:c.1009G>T	p.Glu337Ter	p.E337*	ENST00000256646	NM_024408.3	337	Gag/Tag	6/34	1	2	FACETS	0.907	0.757	1	0.907	0.757	1	CLONAL	1	TRUE	1	0.13	2		676	729	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199925	108199925	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0056296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	32	249	0	ENST00000278616.4:c.7267G>T	p.Glu2423Ter	p.E2423*	ENST00000278616	NM_000051.3	2423	Gaa/Taa	49/63	1	2	FACETS	0.784	0.638	0.948	1	0.947	1	CLONAL	2	TRUE	1	0.13	2		249	314	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135777994	135777994	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs397514862	NA	P-0056296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	40	628	0	ENST00000298552.3:c.2389C>T	p.Gln797Ter	p.Q797*	ENST00000298552	NM_001162426.1	797	Cag/Tag	18/23	0.194565206515508	1	FACETS	0.908	0.753	1	0.908	0.753	1	CLONAL	1	TRUE	0	0.13	1		628	634	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226180	53226180	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	50	463	0	ENST00000375401.3:c.2669C>G	p.Ala890Gly	p.A890G	ENST00000375401	NM_004187.3	890	gCc/gGc	19/26	1	1	FACETS	0.873	0.742	1	1	0.97	1	CLONAL	2	TRUE	0	0.13	1		463	412	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039340	49039341	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0056297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	153	531	0	ENST00000267163.4:c.2330dup	p.Thr778TyrfsTer17	p.T778Yfs*17	ENST00000267163	NM_000321.2	775	-/C		1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.784817258325022	2		531	389	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637569	23637569	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555459925	NA	P-0056297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	163	523	0	ENST00000261584.4:c.2736G>C	p.Trp912Cys	p.W912C	ENST00000261584	NM_024675.3	912	tgG/tgC	7/13	1	2	FACETS	0.882	0.816	0.949	0.882	0.816	0.949	CLONAL	1	TRUE	1	0.784817258325022	2		523	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579492	7579493	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CTGGGAGCTTCATCTGGAC	novel	NA	P-0056297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	280	916	0	ENST00000269305.4:c.176_194dup	p.Met66SerfsTer3	p.M66Sfs*3	ENST00000269305	NM_001126112.2	65	aga/agGTCCAGATGAAGCTCCCAGa	4/11	0.784817258325022	1	FACETS	0.66	0.624	0.696	0.66	0.624	0.696	SUBCLONAL	1	TRUE	0	0.784817258325022	1		916	657	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652065	36652065	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	467	1018	0	ENST00000244741.5:c.187T>G	p.Phe63Val	p.F63V	ENST00000244741	NM_000389.4	63	Ttc/Gtc	2/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.784817258325022	2		1018	1123	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0056298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	72	458	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	0.637	0.557	0.722	0.637	0.557	0.722	SUBCLONAL	1	TRUE	1	0.453317033070459	2		458	499	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39237789	39237789	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	78	439	0	ENST00000402219.2:c.2446A>G	p.Ile816Val	p.I816V	ENST00000402219	NM_005633.3	816	Att/Gtt	15/23	1	2	FACETS	0.712	0.628	0.803	0.712	0.628	0.803	SUBCLONAL	1	TRUE	1	0.453317033070459	2		439	483	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439242	52439260	+	frameshift_variant	Frame_Shift_Del	DEL	GCTTGGGTTTGTTGGGAGG	GCTTGGGTTTGTTGGGAGG	-	novel	NA	P-0056298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	111	910	0	ENST00000460680.1:c.982_1000del	p.Pro328Ter	p.P328*	ENST00000460680	NM_004656.3	328	CCTCCCAACAAACCCAAGCta/ta	11/17	0.389943289572609	1	FACETS	0.49	0.44	0.543	0.49	0.44	0.543	SUBCLONAL	1	TRUE	0	0.453317033070459	1		910	773	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900198	101900198	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	61	391	0	ENST00000374994.4:c.632T>C	p.Ile211Thr	p.I211T	ENST00000374994	NM_004612.2	211	aTt/aCt	4/9	1	2	FACETS	0.57	0.493	0.654	0.57	0.493	0.654	SUBCLONAL	1	TRUE	1	0.453317033070459	2		391	472	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0056301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	574	585	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.537271592850279	4	FACETS	0.974	0.94	1			1	CLONAL	3	FALSE	NA	0.537271592850279	4		585	1124	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781504	NA	P-0056301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	325	1294	0	ENST00000269305.4:c.314G>T	p.Gly105Val	p.G105V	ENST00000269305	NM_001126112.2	105	gGc/gTc	4/11	1	2	FACETS	0.962	0.908	1	0.962	0.908	1	CLONAL	1	FALSE	1	0.537271592850279	2		1294	1258	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166319	118166319	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	88	464	0	ENST00000369448.3:c.829G>A	p.Asp277Asn	p.D277N	ENST00000369448	NM_017709.3	277	Gac/Aac	2/2	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.537271592850279	NA		464	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578279	7578280	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0056301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	145	1030	0	ENST00000269305.4:c.569dup	p.Pro191SerfsTer18	p.P191Sfs*18	ENST00000269305	NM_001126112.2	190	cct/ccCt	6/11	1	2	FACETS	0.542	0.494	0.593	0.542	0.494	0.593	SUBCLONAL	1	FALSE	1	0.537271592850279	2		1030	996	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872018	35872018	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs779399614	NA	P-0056301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	254	680	0	ENST00000216797.5:c.595G>T	p.Val199Leu	p.V199L	ENST00000216797	NM_020529.2	199	Gtg/Ttg	4/6	0.537271592850279	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	0	0.537271592850279	1		680	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0056302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	156	673	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.320153819210548	1	FACETS	0.979	0.898	1	0.979	0.898	1	CLONAL	1	TRUE	0	0.338471059051311	1		673	782	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0056302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	37	242	1	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.338471059051311	3	FACETS	0.858	0.71	1	0.429	0.355	0.511	CLONAL	1	TRUE	1	0.338471059051311	3		243	298	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0056307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	364	897	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.271473327002008	2	FACETS	0.987	0.937	1	0.987	0.937	1	CLONAL	2	TRUE	0	0.317522266246372	2		898	1161	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0056307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	324	695	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.317522266246372	2	FACETS	0.962	0.909	1	0.962	0.909	1	CLONAL	2	TRUE	0	0.317522266246372	2		695	1061	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028790	47028790	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	341	621	0	ENST00000377604.3:c.94C>T	p.Arg32Ter	p.R32*	ENST00000377604	NM_001204468.1	32	Cga/Tga	3/24	0.185019094271664	2	FACETS	0.965	0.919	1			1	INDETERMINATE	3	TRUE	NA	0.317522266246372	2		621	742	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854945	76854945	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0056307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	132	227	0	ENST00000373344.5:c.5891del	p.Gly1964GlufsTer18	p.G1964Efs*18	ENST00000373344	NM_000489.3	1964	gGa/ga	25/35	0.185019094271664	2	FACETS	0.987	0.904	1			1	INDETERMINATE	2	TRUE	NA	0.317522266246372	2		227	421	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246467	46246467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	37	361	0	ENST00000334344.6:c.4561G>A	p.Asp1521Asn	p.D1521N	ENST00000334344	NM_152641.2	1521	Gat/Aat	15/21	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.317522266246372	NA		361	498	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132558	11132558	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0056307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	385	1374	0	ENST00000358026.2:c.2774T>G	p.Leu925Arg	p.L925R	ENST00000358026	NM_001128849.1	925	cTc/cGc	19/36	0.317522266246372	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.317522266246372	2		1374	1166	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624818	9624818	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	45	761	0	ENST00000353224.5:c.159G>C	p.Met53Ile	p.M53I	ENST00000353224	NM_177990.2	53	atG/atC	3/10	0.146429477984066	4	FACETS	0.495	0.415	0.585	0.248	0.207	0.293	INDETERMINATE	1	TRUE	2	0.317522266246372	4		761	754	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228054	53228054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	52	603	0	ENST00000375401.3:c.2260G>A	p.Asp754Asn	p.D754N	ENST00000375401	NM_004187.3	754	Gat/Aat	16/26	0.185019094271664	2	FACETS	0.552	0.47	0.643			1	INDETERMINATE	1	TRUE	NA	0.317522266246372	2		603	593	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0056309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	106	378	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.434574674588457	2	FACETS	0.874	0.797	0.952	0.874	0.797	0.952	CLONAL	2	TRUE	0	0.462991694632901	2		378	262	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0056309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	362	470	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.392168236061472	2	FACETS	0.867	0.825	0.909	0.867	0.825	0.909	CLONAL	2	TRUE	0	0.462991694632901	2		471	902	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692790	89692790	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	82	394	0	ENST00000371953.3:c.274G>C	p.Asp92His	p.D92H	ENST00000371953	NM_000314.4	92	Gac/Cac	5/9	0.392168236061472	2	FACETS	0.922	0.832	1	0.922	0.832	1	CLONAL	2	TRUE	0	0.462991694632901	2		394	192	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724664	43724664	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	263	804	0	ENST00000382044.4:c.3403G>C	p.Glu1135Gln	p.E1135Q	ENST00000382044	NM_001141980.1	1135	Gaa/Caa	17/28	0.425490014729666	2	FACETS	0.907	0.857	0.958	0.907	0.857	0.958	CLONAL	2	TRUE	0	0.462991694632901	2		804	626	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968579	55968579	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0056309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	125	628	0	ENST00000263923.4:c.2084del	p.Pro695LeufsTer14	p.P695Lfs*14	ENST00000263923	NM_002253.2	695	cCt/ct	14/30	1	2	FACETS	0.817	0.741	0.897	0.817	0.741	0.897	CLONAL	1	TRUE	1	0.462991694632901	2		628	661	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838393	156838393	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0056309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1223	441	1015	0	ENST00000524377.1:c.671A>T	p.Gln224Leu	p.Q224L	ENST00000524377	NM_002529.3	224	cAg/cTg	6/17	0.384397562708153	5	FACETS	0.97	0.923	1	0.647	0.615	0.679	CLONAL	2	TRUE	2	0.462991694632901	5		1015	1664	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050907	49050907	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0056309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	140	524	0	ENST00000267163.4:c.2592del	p.Gly865GlufsTer8	p.G865Efs*8	ENST00000267163	NM_000321.2	864	gAa/ga	25/27	0.425490014729666	2	FACETS	0.847	0.781	0.914	0.847	0.781	0.914	CLONAL	2	TRUE	0	0.462991694632901	2		524	357	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465531	99465531	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	249	668	0	ENST00000268035.6:c.2356G>C	p.Glu786Gln	p.E786Q	ENST00000268035	NM_000875.3	786	Gag/Cag	11/21	0.156775867423403	5	FACETS	1	0.969	1	0.702	0.658	0.748	INDETERMINATE	2	TRUE	2	0.462991694632901	5		668	865	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437286	52437286	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	345	963	0	ENST00000460680.1:c.1758C>G	p.Ile586Met	p.I586M	ENST00000460680	NM_004656.3	586	atC/atG	14/17	0.452355458952877	2	FACETS	0.905	0.861	0.95	0.905	0.861	0.95	CLONAL	2	TRUE	0	0.462991694632901	2		963	823	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439152	52439152	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	325	906	0	ENST00000460680.1:c.1090C>G	p.His364Asp	p.H364D	ENST00000460680	NM_004656.3	364	Cac/Gac	11/17	0.452355458952877	2	FACETS	0.791	0.75	0.833	0.791	0.75	0.833	SUBCLONAL	2	TRUE	0	0.462991694632901	2		906	887	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467616	66467616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	78	413	0	ENST00000273854.3:c.653G>A	p.Gly218Asp	p.G218D	ENST00000273854	NM_004439.5	218	gGt/gAt	3/18	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.462991694632901	2		413	319	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347939	70347939	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868804661	NA	P-0056309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	337	782	0	ENST00000374080.3:c.3178C>T	p.His1060Tyr	p.H1060Y	ENST00000374080		1060	Cac/Tac	22/45	0.425490014729666	2	FACETS	0.833	0.791	0.875	0.833	0.791	0.875	CLONAL	2	TRUE	0	0.462991694632901	2		782	874	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0056310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	249	501	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.922761982735856	4	FACETS	1	0.972	1	0.52	0.492	0.548	CLONAL	2	TRUE	0	0.922761982735856	4		501	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659675	NA	P-0056310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	1228	716	0	ENST00000269305.4:c.764T>C	p.Ile255Thr	p.I255T	ENST00000269305	NM_001126112.2	255	aTc/aCc	7/11	0.922761982735856	4	FACETS	1	0.998	1	1	0.998	1	CLONAL	4	TRUE	0	0.922761982735856	4		716	1265	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063317	67063317	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	183	174	0	ENST00000412916.2:c.7C>T	p.Arg3Cys	p.R3C	ENST00000412916		3	Cgc/Tgc	1/6	0.922761982735856	3	FACETS	1	0.98	1	0.71	0.674	0.746	CLONAL	2	TRUE	0	0.922761982735856	3		174	272	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736254	243736254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772090769	NA	P-0056310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	164	400	2	ENST00000263826.5:c.793G>A	p.Gly265Arg	p.G265R	ENST00000263826	NM_005465.4	265	Gga/Aga	8/13	0.922761982735856	4	FACETS	1	0.94	1	0.342	0.314	0.37	CLONAL	1	TRUE	1	0.922761982735856	4		402	667	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972993	25972993	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368088924	NA	P-0056310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	194	482	0	ENST00000435504.4:c.1432C>T	p.Leu478Phe	p.L478F	ENST00000435504		478	Ctt/Ttt	12/13	0.922761982735856	2	FACETS	0.885	0.828	0.944	0.443	0.414	0.472	CLONAL	1	TRUE	0	0.922761982735856	2		482	475	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973025	25973025	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	226	523	0	ENST00000435504.4:c.1400C>T	p.Ser467Leu	p.S467L	ENST00000435504		467	tCa/tTa	12/13	0.922761982735856	2	FACETS	0.922	0.868	0.978	0.461	0.434	0.489	CLONAL	1	TRUE	0	0.922761982735856	2		523	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0056311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	443	1053	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.444224615047633	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.444224615047633	2		1053	965	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852546	63852546	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0056311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	113	578	0	ENST00000279873.7:c.3324C>G	p.Asn1108Lys	p.N1108K	ENST00000279873	NM_032199.2	1108	aaC/aaG	10/10	0.1731369364348	5	FACETS	1	0.975	1	0.42	0.378	0.464	INDETERMINATE	1	TRUE	2	0.444224615047633	5		578	673	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69998298	69998298	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs779202378	NA	P-0056311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	129	639	0	ENST00000394351.3:c.538A>G	p.Asn180Asp	p.N180D	ENST00000394351	NM_000248.3	180	Aac/Gac	5/9	1	2	FACETS	0.973	0.885	1	0.973	0.885	1	CLONAL	1	TRUE	1	0.444224615047633	2		639	597	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0056313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	222	231	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.705533457768218	2		231	537	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0056313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	260	378	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.525823808727955	3	FACETS	0.867	0.82	0.914	0.867	0.82	0.914	CLONAL	2	TRUE	1	0.705533457768218	3		378	575	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0056313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	108	251	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.841	0.762	0.923	0.841	0.762	0.923	CLONAL	1	TRUE	1	0.705533457768218	2		251	364	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107135	27107136	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0056313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	319	797	0	ENST00000324856.7:c.6747dup	p.Glu2250ArgfsTer28	p.E2250Rfs*28	ENST00000324856	NM_006015.4	2249	tca/tcAa	20/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.705533457768218	2		797	866	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017142	31017142	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1259109293	NA	P-0056313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	139	338	0	ENST00000375687.4:c.473C>T	p.Ala158Val	p.A158V	ENST00000375687	NM_015338.5	158	gCg/gTg	7/13	1	2	FACETS	0.934	0.858	1	0.934	0.858	1	CLONAL	1	TRUE	1	0.705533457768218	2		338	422	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720679	89720679	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs398123329	NA	P-0056313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	82	309	0	ENST00000371953.3:c.830C>G	p.Thr277Arg	p.T277R	ENST00000371953	NM_000314.4	277	aCa/aGa	8/9	1	2	FACETS	0.941	0.842	1	0.941	0.842	1	CLONAL	1	TRUE	1	0.705533457768218	2		309	247	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056217	27056217	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0056313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	279	864	0	ENST00000324856.7:c.1213C>T	p.Gln405Ter	p.Q405*	ENST00000324856	NM_006015.4	405	Cag/Tag	2/20	1	2	FACETS	0.952	0.897	1	0.952	0.897	1	CLONAL	1	TRUE	1	0.705533457768218	2		864	831	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164160	108164160	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs746499337	NA	P-0056313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	110	304	1	ENST00000278616.4:c.4732C>T	p.Gln1578Ter	p.Q1578*	ENST00000278616	NM_000051.3	1578	Cag/Tag	31/63	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.705533457768218	2		305	265	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188120	108188121	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0056313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	95	332	0	ENST00000278616.4:c.6220dup	p.Cys2074LeufsTer14	p.C2074Lfs*14	ENST00000278616	NM_000051.3	2073	-/T	43/63	1	2	FACETS	0.797	0.716	0.88	0.797	0.716	0.88	SUBCLONAL	1	TRUE	1	0.705533457768218	2		332	338	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15379846	15379846	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	143	434	0	ENST00000263377.2:c.293A>G	p.Tyr98Cys	p.Y98C	ENST00000263377	NM_058243.2	98	tAt/tGt	3/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.705533457768218	2		434	377	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463588	25463588	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0056313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	540	808	0	ENST00000264709.3:c.2094G>T	p.Trp698Cys	p.W698C	ENST00000264709	NM_175629.2	698	tgG/tgT	18/23	0.525823808727955	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.705533457768218	3		808	1002	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47607095	47607095	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	207	632	0	ENST00000263735.4:c.845G>C	p.Gly282Ala	p.G282A	ENST00000263735	NM_002354.2	282	gGa/gCa	7/9	0.525823808727955	3	FACETS	0.978	0.909	1	0.489	0.454	0.524	CLONAL	1	TRUE	1	0.705533457768218	3		632	812	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0056316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	45	719	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		719	876	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0056318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	55	452	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.166636952554679	3	FACETS	0.868	0.742	1	0.868	0.742	1	CLONAL	2	TRUE	1	0.11	3		452	608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578206	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs886039484	NA	P-0056318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	69	760	0	ENST00000269305.4:c.643A>G	p.Ser215Gly	p.S215G	ENST00000269305	NM_001126112.2	215	Agt/Ggt	6/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.11	2		760	1003	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341925	8341925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0056318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	28	415	0	ENST00000356435.5:c.4715G>A	p.Arg1572Lys	p.R1572K	ENST00000356435		1572	aGa/aAa	29/35	0.3	2	FACETS	1	0.841	1			1	CLONAL	1	TRUE	NA	0.11	2		415	479	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401646	401646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0056320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	66	640	0	ENST00000380956.4:c.968G>A	p.Gly323Glu	p.G323E	ENST00000380956	NM_001195286.1	323	gGg/gAg	7/9	1	2	FACETS	0.852	0.739	0.974	0.852	0.739	0.974	CLONAL	1	TRUE	1	0.23	2		640	674	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878176	151878176	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0056320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	99	655	0	ENST00000262189.6:c.6769C>T	p.Arg2257Ter	p.R2257*	ENST00000262189	NM_170606.2	2257	Cga/Tga	36/59	0.145497692930539	3	FACETS	1	0.971	1	0.631	0.563	0.703	CLONAL	1	TRUE	1	0.23	3		655	761	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422846	49422846	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0056320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	82	680	0	ENST00000301067.7:c.14249C>G	p.Pro4750Arg	p.P4750R	ENST00000301067	NM_003482.3	4750	cCa/cGa	44/54	1	2	FACETS	0.994	0.877	1	0.994	0.877	1	CLONAL	1	TRUE	1	0.23	2		680	717	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265448	152265448	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0056320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	77	572	0	ENST00000206249.3:c.901T>C	p.Ser301Pro	p.S301P	ENST00000206249	NM_000125.3	301	Tct/Cct	4/8	1	2	FACETS	0.93	0.816	1	0.93	0.816	1	CLONAL	1	TRUE	1	0.23	2		572	720	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941684	48941684	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000828-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	18	189	0	ENST00000267163.4:c.994G>C	p.Asp332His	p.D332H	ENST00000267163	NM_000321.2	332	Gat/Cat	10/27	0.450086167240538	1	FACETS	0.912	0.706	1	0.912	0.706	1	CLONAL	1	TRUE	0	0.450086167240538	1		189	68	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578281	7578336	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGCCAGACCTAAGAGCAATCAGTGAGGAATCAGAGGCCTGGGGACCCTGGGCAAC	GGGCCAGACCTAAGAGCAATCAGTGAGGAATCAGAGGCCTGGGGACCCTGGGCAAC	-	novel	NA	P-0000828-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	275	645	0	ENST00000269305.4:c.559+35_568del		p.X187_splice	ENST00000269305	NM_001126112.2	187		6/11	NA	2	FACETS	0.949	0.898	1			1	INDETERMINATE	2	TRUE	NA	0.450086167240538	2		645	644	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0001921-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	533	644	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.228035149521534	7	FACETS	1	0.972	1	1	0.997	1	CLONAL	7	TRUE	2	0.228035149521534	7		646	1039	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0001921-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	292	575	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.228035149521534	7	FACETS	0.945	0.89	1	0.756	0.712	0.801	CLONAL	4	TRUE	2	0.228035149521534	7		575	1064	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0001921-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	63	368	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.216092485821754	2	FACETS	0.847	0.738	0.965	0.847	0.738	0.965	CLONAL	2	TRUE	0	0.228035149521534	2		368	326	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361135	66361135	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001921-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	64	473	0	ENST00000273854.3:c.1037A>G	p.Glu346Gly	p.E346G	ENST00000273854	NM_004439.5	346	gAg/gGg	4/18	0.140779247414381	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.228035149521534	1		473	391	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730080	41730080	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001921-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	50	644	0	ENST00000242208.4:c.449T>C	p.Val150Ala	p.V150A	ENST00000242208	NM_002192.2	150	gTg/gCg	3/3	0.140779247414381	1	FACETS	0.688	0.583	0.803	0.688	0.583	0.803	SUBCLONAL	1	TRUE	0	0.228035149521534	1		644	565	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814319	76814319	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0001921-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	142	176	0	ENST00000373344.5:c.6327-2A>G		p.X2109_splice	ENST00000373344	NM_000489.3	2109			0.123846730877375	2	FACETS	1	0.964	1			1	INDETERMINATE	6	TRUE	NA	0.228035149521534	2		176	202	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0002311-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	60	610	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.374768803044183	4	FACETS	0.936	0.82	1			1	CLONAL	2	FALSE	NA	0.464649745188268	4		610	202	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057988	27057988	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002311-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	123	689	0	ENST00000324856.7:c.1696C>T	p.Gln566Ter	p.Q566*	ENST00000324856	NM_006015.4	566	Cag/Tag	3/20	0.273625186591826	5	FACETS	1	0.975	1	0.786	0.718	0.856	INDETERMINATE	2	FALSE	2	0.464649745188268	5		689	381	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624301	89624301	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002311-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	137	608	0	ENST00000371953.3:c.75G>C	p.Leu25Phe	p.L25F	ENST00000371953	NM_000314.4	25	ttG/ttC	1/9	0.273625186591826	5	FACETS	0.968	0.885	1	0.645	0.59	0.702	INDETERMINATE	2	FALSE	2	0.464649745188268	5		608	517	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214089	108214089	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002311-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	53	291	0	ENST00000278616.4:c.8409G>C	p.Lys2803Asn	p.K2803N	ENST00000278616	NM_000051.3	2803	aaG/aaC	57/63	0.357856736309673	4	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	FALSE	2	0.464649745188268	4		291	148	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12043942	12043942	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002311-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	65	418	1	ENST00000396373.4:c.1321G>A	p.Glu441Lys	p.E441K	ENST00000396373	NM_001987.4	441	Gag/Aag	8/8	0.464649745188268	6	FACETS	1	0.923	1			1	CLONAL	2	FALSE	NA	0.464649745188268	6		419	252	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17129492	17129492	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002311-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	71	693	1	ENST00000285071.4:c.394G>A	p.Glu132Lys	p.E132K	ENST00000285071	NM_144997.5	132	Gag/Aag	5/14	0.464649745188268	4	FACETS	0.965	0.854	1	0.965	0.854	1	CLONAL	2	FALSE	2	0.464649745188268	4		694	232	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762959	40762959	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs387906659	NA	P-0002311-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	69	601	0	ENST00000392038.2:c.49G>A	p.Glu17Lys	p.E17K	ENST00000392038	NM_001626.4	17	Gaa/Aaa	3/14	0.273625186591826	5	FACETS	1	0.885	1	0.669	0.59	0.753	INDETERMINATE	2	FALSE	2	0.464649745188268	5		601	251	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067374	37067374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002311-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	79	472	0	ENST00000231790.2:c.1285G>A	p.Glu429Lys	p.E429K	ENST00000231790	NM_000249.3	429	Gag/Aag	12/19	0.273625186591826	5	FACETS	1	0.936	1	0.715	0.637	0.797	INDETERMINATE	2	FALSE	2	0.464649745188268	5		472	269	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161718	47161718	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002311-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	43	315	0	ENST00000409792.3:c.4408C>T	p.Pro1470Ser	p.P1470S	ENST00000409792	NM_014159.6	1470	Cca/Tca	3/21	0.273625186591826	5	FACETS	0.831	0.704	0.967	0.554	0.469	0.645	INDETERMINATE	2	FALSE	2	0.464649745188268	5		315	189	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281551	142281551	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002311-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	68	670	0	ENST00000350721.4:c.693G>C	p.Gln231His	p.Q231H	ENST00000350721	NM_001184.3	231	caG/caC	4/47	0.273625186591826	5	FACETS	1	0.961	1	0.808	0.715	0.904	INDETERMINATE	2	FALSE	2	0.464649745188268	5		670	205	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665487	176665487	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002311-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	82	438	0	ENST00000439151.2:c.4171G>T	p.Glu1391Ter	p.E1391*	ENST00000439151	NM_022455.4	1391	Gaa/Taa	7/23	0.255772267843032	2	FACETS	0.806	0.724	0.89	0.806	0.724	0.89	INDETERMINATE	2	FALSE	0	0.464649745188268	2		438	219	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651970	36651980	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGCGACTGT	GCCGCGACTGT	-	novel	NA	P-0002311-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	149	775	0	ENST00000244741.5:c.93_103del	p.Ser31ArgfsTer13	p.S31Rfs*13	ENST00000244741	NM_000389.4	31	aGCCGCGACTGT/a	2/3	0.464649745188268	4	FACETS	0.964	0.888	1	0.964	0.888	1	CLONAL	2	FALSE	2	0.464649745188268	4		775	487	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978788	13978788	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002311-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	57	646	3	ENST00000405192.2:c.319C>T	p.Gln107Ter	p.Q107*	ENST00000405192	NM_001163147.1	107	Cag/Tag	6/12	0.324223062825117	6	FACETS	1	0.964	1	0.35	0.302	0.402	CLONAL	1	FALSE	2	0.464649745188268	6		649	338	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918502	44918502	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002311-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	48	205	0	ENST00000377967.4:c.985C>T	p.Gln329Ter	p.Q329*	ENST00000377967	NM_021140.2	329	Cag/Tag	12/29	0.374768803044183	2	FACETS	0.861	0.767	0.952			1	CLONAL	3	FALSE	NA	0.464649745188268	2		205	80	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0002828-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	2382	715	2	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	0.769685945103122	9	FACETS	1	0.998	1			1	CLONAL	7	TRUE	NA	0.769685945103122	9		717	3086	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391114	89391114	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002828-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	199	826	0	ENST00000336596.2:c.1180G>T	p.Val394Leu	p.V394L	ENST00000336596	NM_005233.5	394	Gtg/Ttg	5/17	NA	2	FACETS	0.732	0.681	0.785			1	INDETERMINATE	1	TRUE	NA	0.769685945103122	2		826	706	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311727	30311727	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002828-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	111	502	0	ENST00000262643.3:c.581C>A	p.Ser194Ter	p.S194*	ENST00000262643	NM_001238.2	194	tCa/tAa	7/12	0.424635326860711	3	FACETS	0.501	0.45	0.554	0.25	0.225	0.277	INDETERMINATE	1	TRUE	1	0.769685945103122	3		502	798	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15280923	15280923	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002828-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1375	255	1151	0	ENST00000263388.2:c.5173G>C	p.Glu1725Gln	p.E1725Q	ENST00000263388	NM_000435.2	1725	Gag/Cag	28/33	0.424635326860711	3	FACETS	0.563	0.525	0.602	0.281	0.262	0.301	INDETERMINATE	1	TRUE	1	0.769685945103122	3		1151	1630	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845648	151845658	+	frameshift_variant	Frame_Shift_Del	DEL	CTCAGAGCTAG	CTCAGAGCTAG	-	novel	NA	P-0002828-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	193	838	0	ENST00000262189.6:c.13354_13364del	p.Leu4452GlufsTer17	p.L4452Efs*17	ENST00000262189	NM_170606.2	4452	CTAGCTCTGAGg/g	52/59	0.383429944116389	1	FACETS	0.393	0.365	0.423	0.393	0.365	0.423	INDETERMINATE	1	TRUE	0	0.769685945103122	1		838	784	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0004189-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	391	644	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.708141720044433	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.708141720044433	1		644	687	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459187	120459187	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004189-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	265	573	0	ENST00000256646.2:c.6158G>C	p.Arg2053Pro	p.R2053P	ENST00000256646	NM_024408.3	2053	cGc/cCc	34/34	1	2	FACETS	0.945	0.889	1	0.945	0.889	1	CLONAL	1	TRUE	1	0.708141720044433	2		573	792	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436592	49436592	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004189-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	335	707	0	ENST00000301067.7:c.5714A>G	p.Gln1905Arg	p.Q1905R	ENST00000301067	NM_003482.3	1905	cAg/cGg	26/54	1	2	FACETS	0.849	0.803	0.895	0.849	0.803	0.895	CLONAL	1	TRUE	1	0.708141720044433	2		707	1115	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953769	48953769	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1131690884	NA	P-0004189-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	74	163	0	ENST00000267163.4:c.1372G>T	p.Glu458Ter	p.E458*	ENST00000267163	NM_000321.2	458	Gaa/Taa	14/27	0.708141720044433	1	FACETS	0.804	0.722	0.887	0.804	0.722	0.887	CLONAL	1	TRUE	0	0.708141720044433	1		163	168	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633370	8633370	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004189-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	248	467	0	ENST00000356435.5:c.299C>A	p.Ala100Asp	p.A100D	ENST00000356435		100	gCc/gAc	3/35	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.708141720044433	2		467	675	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0006194-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	247	354	1				ENST00000310581	NM_198253.2	-/1132			0.579034617571309	5	FACETS	0.943	0.892	0.995	0.943	0.892	0.995	CLONAL	3	TRUE	2	0.668224908698641	5		355	523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0006194-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	314	715	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	NA	2	FACETS	0.996	0.956	1			1	INDETERMINATE	2	TRUE	NA	0.668224908698641	2		715	472	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490346	29490346	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006194-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	143	389	0	ENST00000356175.3:c.431C>G	p.Ser144Cys	p.S144C	ENST00000356175	NM_000267.3	144	tCt/tGt	4/57	0.595931179738613	4	FACETS	1	0.959	1	0.54	0.494	0.589	CLONAL	1	TRUE	2	0.668224908698641	4		389	661	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097233	178097233	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006194-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	268	406	0	ENST00000397062.3:c.481C>G	p.Gln161Glu	p.Q161E	ENST00000397062	NM_006164.4	161	Cag/Gag	4/5	0.668224908698641	3	FACETS	0.954	0.904	1	0.636	0.602	0.669	CLONAL	2	TRUE	0	0.668224908698641	3		406	561	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346669	225346669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006194-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	182	329	1	ENST00000264414.4:c.1969C>T	p.His657Tyr	p.H657Y	ENST00000264414	NM_003590.4	657	Cat/Tat	14/16	0.663459834245482	2	FACETS	0.956	0.904	1	0.956	0.904	1	CLONAL	2	TRUE	0	0.668224908698641	2		330	285	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423365	116423365	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1261418076	NA	P-0006194-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	78	277	0	ENST00000397752.3:c.3640G>A	p.Glu1214Lys	p.E1214K	ENST00000397752	NM_000245.2	1214	Gaa/Aaa	19/21	0.668224908698641	4	FACETS	1	0.908	1	0.515	0.455	0.579	CLONAL	1	TRUE	2	0.668224908698641	4		277	378	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876941	151876941	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1315727898	NA	P-0006194-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	72	319	0	ENST00000262189.6:c.7420G>A	p.Gly2474Arg	p.G2474R	ENST00000262189	NM_170606.2	2474	Ggg/Agg	37/59	0.595931179738613	4	FACETS	1	0.899	1	0.512	0.45	0.578	CLONAL	1	TRUE	2	0.668224908698641	4		319	351	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342818	87342818	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006194-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	107	397	0	ENST00000277120.3:c.1103G>A	p.Gly368Glu	p.G368E	ENST00000277120		368	gGg/gAg	9/19	0.654862051731897	3	FACETS	1	0.957	1	0.367	0.332	0.404	CLONAL	1	TRUE	0	0.668224908698641	3		397	388	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797271	135797272	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0006194-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	172	238	0	ENST00000298552.3:c.597dup	p.Val200ArgfsTer18	p.V200Rfs*18	ENST00000298552	NM_001162426.1	199	-/C	7/23	0.654862051731897	3	FACETS	0.836	0.789	0.881	0.836	0.789	0.881	CLONAL	3	TRUE	0	0.668224908698641	3		238	274	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137313580	137313580	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006194-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	581	883	1	ENST00000481739.1:c.839T>A	p.Val280Glu	p.V280E	ENST00000481739	NM_002957.4	280	gTg/gAg	6/10	0.654862051731897	3	FACETS	0.98	0.955	1	0.98	0.955	1	CLONAL	3	TRUE	0	0.668224908698641	3		884	789	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279858	46279866	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAA	CAGCAGCAA	-	rs749960421	NA	P-0006883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	20	302	3	ENST00000371998.3:c.3789_3797del	p.Gln1274_Gln1276del	p.Q1274_Q1276del	ENST00000371998		1262	CAGCAGCAA/-	20/23	0.611641002652687	4	FACETS	0.365	0.279	0.465	0.122	0.093	0.155	SUBCLONAL	1	TRUE	1	0.611641002652687	4		305	289	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0006883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	2292	362	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	0.611641002652687	37	FACETS	1	0.997	1			1	CLONAL	35	TRUE	NA	0.611641002652687	37		362	2487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576849	7576855	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTACCTG	GTACCTG	-	novel	NA	P-0006883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	204	483	0	ENST00000269305.4:c.991_993+4del		p.X331_splice	ENST00000269305	NM_001126112.2	331		9/11	0.398175793765655	2	FACETS	0.901	0.851	0.951	0.901	0.851	0.951	CLONAL	2	TRUE	0	0.611641002652687	2		483	370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577578	7577578	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	145	516	0	ENST00000269305.4:c.703A>G	p.Asn235Asp	p.N235D	ENST00000269305	NM_001126112.2	235	Aac/Gac	7/11	0.281861622099605	2	FACETS	0.99	0.91	1	0.99	0.91	1	CLONAL	2	TRUE	0	0.306273306089928	2		516	478	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738151	133738151	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	123	451	0	ENST00000318560.5:c.551T>G	p.Leu184Arg	p.L184R	ENST00000318560	NM_005157.4	184	cTc/cGc	4/11	0.267869063505498	4	FACETS	0.867	0.786	0.952	0.867	0.786	0.952	CLONAL	2	TRUE	2	0.306273306089928	4		451	605	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430767	47430767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	228	864	1	ENST00000377045.4:c.1732G>A	p.Glu578Lys	p.E578K	ENST00000377045	NM_001654.4	578	Gag/Aag	16/16	0.263338352674836	3	FACETS	0.753	0.701	0.807	0.753	0.701	0.807	SUBCLONAL	2	TRUE	1	0.306273306089928	3		865	1140	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519980	NA	P-0015976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	133	577	0	ENST00000269305.4:c.528C>G	p.Cys176Trp	p.C176W	ENST00000269305	NM_001126112.2	176	tgC/tgG	5/11	NA	2	FACETS	0.914	0.842	0.988			1	INDETERMINATE	3	TRUE	NA	0.287776244160366	2		577	337	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719535	190719535	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	46	364	0	ENST00000441310.2:c.1537G>A	p.Glu513Lys	p.E513K	ENST00000441310	NM_000534.4	513	Gaa/Aaa	9/13	0.191622442332118	3	FACETS	0.96	0.81	1	0.48	0.405	0.562	CLONAL	1	TRUE	1	0.287776244160366	3		364	381	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0016549-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	293	635	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.538337084041129	3	FACETS	0.974	0.923	1	0.974	0.923	1	CLONAL	2	TRUE	1	0.538337084041129	3		635	709	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016549-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	240	421	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.513062515741527	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.538337084041129	2		423	445	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088759	27088759	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016549-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	343	607	1	ENST00000324856.7:c.2368C>T	p.Gln790Ter	p.Q790*	ENST00000324856	NM_006015.4	790	Cag/Tag	7/20	0.520638081608585	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.538337084041129	2		608	600	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406235	70406235	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016549-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	168	547	0	ENST00000373644.4:c.3749C>T	p.Ser1250Leu	p.S1250L	ENST00000373644	NM_030625.2	1250	tCa/tTa	4/12	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.538337084041129	2		547	597	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592301	29592301	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016549-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	112	324	0	ENST00000356175.3:c.4716del	p.Tyr1573ThrfsTer30	p.Y1573Tfs*30	ENST00000356175	NM_000267.3	1572	ttC/tt	35/57	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.538337084041129	2		324	416	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944358	206944358	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016549-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	58	471	0	ENST00000423557.1:c.272T>C	p.Leu91Pro	p.L91P	ENST00000423557	NM_000572.2	91	cTg/cCg	3/5	0.538337084041129	3	FACETS	0.427	0.366	0.493	0.213	0.183	0.247	SUBCLONAL	1	TRUE	1	0.538337084041129	3		471	641	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0017434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	70	550	1	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.320304127262651	0	FACETS	0.677	0.598	0.761			1	SUBCLONAL	1	TRUE	0	0.447731025216028	0		551	255	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808332	1808332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	9	769	0	ENST00000260795.2:c.2090G>A	p.Gly697Asp	p.G697D	ENST00000260795		697	gGc/gAc	15/17	0.44692468945646	2	FACETS	0.099	0.064	0.142	0.049	0.032	0.071	SUBCLONAL	1	TRUE	0	0.447731025216028	2		769	408	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0017752-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	171	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.427342999694718	3	FACETS	0.792	0.734	0.851	0.792	0.734	0.851	SUBCLONAL	2	TRUE	1	0.533180556865013	3		622	513	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727402	66727443	+	inframe_deletion	In_Frame_Del	DEL	CTAGAGCTTGATGAGCAGCAGCGAAAGCGCCTTGAGGCCTTT	CTAGAGCTTGATGAGCAGCAGCGAAAGCGCCTTGAGGCCTTT	-	novel	NA	P-0017752-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	211	489	0	ENST00000307102.5:c.120_161del	p.Glu41_Leu54del	p.E41_L54del	ENST00000307102	NM_002755.3	40	CTAGAGCTTGATGAGCAGCAGCGAAAGCGCCTTGAGGCCTTT/-	2/11	0.344734361556	3	FACETS	0.781	0.729	0.834	0.781	0.729	0.834	SUBCLONAL	2	TRUE	1	0.533180556865013	3		489	642	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876476	35876476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017752-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	193	652	0	ENST00000303115.3:c.1268C>T	p.Ser423Phe	p.S423F	ENST00000303115	NM_002185.3	423	tCt/tTt	8/8	0.302092576735391	3	FACETS	1	0.97	1	0.363	0.336	0.391	INDETERMINATE	1	TRUE	0	0.533180556865013	3		652	843	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100523	157100527	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCG	GCCCG	-	novel	NA	P-0017752-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	36	145	0	ENST00000346085.5:c.1463_1467del	p.Pro488LeufsTer45	p.P488Lfs*45	ENST00000346085	NM_020732.3	487	aGCCCG/a	1/20	1	2	FACETS	0.813	0.678	0.961	0.813	0.678	0.961	CLONAL	1	TRUE	1	0.533180556865013	2		145	166	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437361	121437361	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751368921	NA	P-0017752-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	190	950	1	ENST00000257555.6:c.1699G>A	p.Val567Ile	p.V567I	ENST00000257555		567	Gtc/Atc	9/10	0.344734361556	3	FACETS	0.876	0.809	0.945	0.438	0.404	0.473	CLONAL	1	TRUE	1	0.533180556865013	3		951	1031	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265667	10265667	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017752-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	263	726	0	ENST00000340748.4:c.1510G>C	p.Glu504Gln	p.E504Q	ENST00000340748		504	Gag/Cag	19/40	0.344734361556	3	FACETS	1	0.993	1	0.713	0.67	0.758	CLONAL	1	TRUE	1	0.533180556865013	3		726	876	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435717	49435717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017752-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	336	845	1	ENST00000301067.7:c.6166G>A	p.Asp2056Asn	p.D2056N	ENST00000301067	NM_003482.3	2056	Gac/Aac	29/54	0.344734361556	3	FACETS	1	0.994	1	0.709	0.671	0.748	CLONAL	1	TRUE	1	0.533180556865013	3		846	1126	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435962	49435962	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764256829	NA	P-0017752-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	376	924	0	ENST00000301067.7:c.6019G>C	p.Glu2007Gln	p.E2007Q	ENST00000301067	NM_003482.3	2007	Gag/Cag	28/54	0.344734361556	3	FACETS	0.788	0.748	0.828	0.788	0.748	0.828	SUBCLONAL	2	TRUE	1	0.533180556865013	3		924	1134	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203436	NA	P-0017787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	167	519	0	ENST00000269305.4:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269305	NM_001126112.2	163	Tac/Cac	5/11	0.662120482548792	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.662120482548792	1		519	328	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495752	72495752	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	72	355	0	ENST00000477973.2:c.318del	p.Pro107LeufsTer29	p.P107Lfs*29	ENST00000477973	NM_012234.5	107	cCt/ct	1/4	0.662120482548792	1	FACETS	0.791	0.706	0.878	0.791	0.706	0.878	SUBCLONAL	1	TRUE	0	0.662120482548792	1		355	184	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339524	81339524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	99	488	0	ENST00000222390.5:c.1480C>T	p.Arg494Ter	p.R494*	ENST00000222390	NM_000601.4	494	Cga/Tga	13/18	1	2	FACETS	0.564	0.505	0.627	0.564	0.505	0.627	SUBCLONAL	1	TRUE	1	0.662120482548792	2		488	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0018045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	804	689	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.882810375799264	4	FACETS	0.972	0.959	0.983	0.972	0.959	0.983	CLONAL	4	TRUE	0	0.896647330667389	4		690	875	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232145	98232145	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	287	845	0	ENST00000331920.6:c.1797T>A	p.Asp599Glu	p.D599E	ENST00000331920	NM_000264.3	599	gaT/gaA	13/24	0.896647330667389	3	FACETS	0.961	0.905	1	0.32	0.301	0.34	CLONAL	1	TRUE	0	0.896647330667389	3		845	965	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0018212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	98	535	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.796977997940281	4	FACETS	1	0.938	1	0.354	0.318	0.392	CLONAL	1	TRUE	1	0.799960273661919	4		535	415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	723	572	2	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.776324624921099	5	FACETS	0.978	0.963	0.993			1	CLONAL	5	TRUE	NA	0.799960273661919	5		574	813	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946089	13946089	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	28	784	0	ENST00000405192.2:c.1007G>C	p.Arg336Pro	p.R336P	ENST00000405192	NM_001163147.1	336	cGa/cCa	10/12	1	2	FACETS	0.407	0.328	0.495	0.407	0.328	0.495	SUBCLONAL	1	TRUE	1	0.799960273661919	2		784	172	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873765	151873765	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	125	588	0	ENST00000262189.6:c.8773G>T	p.Glu2925Ter	p.E2925*	ENST00000262189	NM_170606.2	2925	Gag/Tag	38/59	0.799960273661919	3	FACETS	0.904	0.837	0.97	0.904	0.837	0.97	CLONAL	2	TRUE	1	0.799960273661919	3		588	242	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187251	38187251	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	156	1121	0	ENST00000317025.8:c.1226G>A	p.Ser409Asn	p.S409N	ENST00000317025	NM_023034.1	409	aGt/aAt	6/24	0.678632236850439	5	FACETS	1	0.965	1			1	CLONAL	1	TRUE	NA	0.799960273661919	5		1121	781	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182146	11182146	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018235-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	321	579	0	ENST00000361445.4:c.6700T>C	p.Ser2234Pro	p.S2234P	ENST00000361445	NM_004958.3	2234	Tcg/Ccg	48/58	1	2	FACETS	0.927	0.881	0.973	0.927	0.881	0.973	CLONAL	1	TRUE	1	0.962026871003337	2		579	720	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597450	10597451	+	stop_gained	Nonsense_Mutation	DNP	CG	CG	TT	novel	NA	P-0018235-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	337	737	0	ENST00000171111.5:c.1752_1753delinsAA	p.Tyr584_Asp585delinsTer	p.Y584_D585delins*	ENST00000171111	NM_203500.1	584	taCGac/taAAac	6/6	1	2	FACETS	0.87	0.827	0.914	0.87	0.827	0.914	CLONAL	1	TRUE	1	0.962026871003337	2		737	805	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0018312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	155	774	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.864	0.79	0.942	0.864	0.79	0.942	CLONAL	1	TRUE	1	0.34	2		776	1055	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649095	37649096	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0018312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	108	559	0	ENST00000447079.4:c.2200_2201delinsTT	p.Gly734Leu	p.G734L	ENST00000447079	NM_015083.1	734	GGa/TTa	4/14	0.177761075057574	4	FACETS	0.791	0.713	0.874			1	INDETERMINATE	2	TRUE	NA	0.34	4		559	538	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244725	41244725	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	72	691	0	ENST00000357654.3:c.2823T>A	p.Asn941Lys	p.N941K	ENST00000357654	NM_007294.3	941	aaT/aaA	10/23	0.191371622760903	2	FACETS	0.819	0.717	0.929	0.41	0.358	0.465	INDETERMINATE	1	TRUE	0	0.34	2		691	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578552	7578552	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	rs1567554500	NA	P-0018996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	492	878	0	ENST00000269305.4:c.378C>G	p.Tyr126Ter	p.Y126*	ENST00000269305	NM_001126112.2	126	taC/taG	5/11	0.599742270593499	3	FACETS	0.977	0.946	1	0.977	0.946	1	CLONAL	3	FALSE	0	0.599635685850337	3		878	728	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741913	17741913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1250046314	NA	P-0018996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	44	313	0	ENST00000250003.3:c.584G>A	p.Gly195Asp	p.G195D	ENST00000250003	NM_002478.4	195	gGc/gAc	1/3	0.599742270593499	3	FACETS	0.988	0.84	1	0.494	0.42	0.574	CLONAL	1	FALSE	1	0.599635685850337	3		313	193	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797108	42797108	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	135	862	0	ENST00000575354.2:c.3470C>G	p.Ala1157Gly	p.A1157G	ENST00000575354	NM_015125.3	1157	gCa/gGa	15/20	0.505023904757498	5	FACETS	0.882	0.801	0.967	0.294	0.267	0.323	CLONAL	1	FALSE	2	0.599635685850337	5		862	970	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36265224	36265224	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	125	623	0	ENST00000300305.3:c.95A>G	p.His32Arg	p.H32R	ENST00000300305		32	cAc/cGc	2/8	0.554646251034162	4	FACETS	0.811	0.734	0.893			1	CLONAL	1	FALSE	NA	0.599635685850337	4		623	822	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920010	1920010	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	120	774	0	ENST00000382891.5:c.1070C>T	p.Pro357Leu	p.P357L	ENST00000382891	NM_133335.3	357	cCt/cTt	5/22	0.315284091134457	5	FACETS	1	0.914	1	0.202	0.183	0.223	INDETERMINATE	1	FALSE	0	0.599635685850337	5		774	751	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914100	32914114	+	frameshift_variant	Frame_Shift_Del	DEL	TTCAGTAAAGTAATT	TTCAGTAAAGTAATT	A	novel	NA	P-0018996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	287	696	1	ENST00000380152.3:c.5608_5622delinsA	p.Phe1870LysfsTer7	p.F1870Kfs*7	ENST00000380152		1870	TTCAGTAAAGTAATT/A	11/27	0.599635685850337	2	FACETS	0.935	0.891	0.978	0.935	0.891	0.978	CLONAL	2	FALSE	0	0.599635685850337	2		697	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0019325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	592	915	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.782871689419188	3	FACETS	0.991	0.97	1	0.991	0.97	1	CLONAL	3	TRUE	0	0.782871689419188	3		915	708	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011182	12011182	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	44	485	0	ENST00000353533.5:c.589G>C	p.Asp197His	p.D197H	ENST00000353533	NM_003010.3	197	Gat/Cat	5/11	0.782871689419188	3	FACETS	1	0.89	1	0.35	0.299	0.404	CLONAL	1	TRUE	0	0.782871689419188	3		485	149	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546883	9546883	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	84	526	0	ENST00000353224.5:c.1139C>A	p.Ala380Asp	p.A380D	ENST00000353224	NM_177990.2	380	gCc/gAc	5/10	0.636846046050359	4	FACETS	1	0.962	1	0.59	0.526	0.658	CLONAL	1	TRUE	2	0.782871689419188	4		526	324	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532710	187532710	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1010116749	NA	P-0019325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	80	596	0	ENST00000441802.2:c.9683del	p.Pro3228LeufsTer42	p.P3228Lfs*42	ENST00000441802	NM_005245.3	3228	cCt/ct	14/27	0.7283702841468	3	FACETS	1	0.921	1	0.347	0.309	0.387	CLONAL	1	TRUE	0	0.782871689419188	3		596	273	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55228017	55228017	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	35	436	0	ENST00000275493.2:c.1484G>C	p.Gly495Ala	p.G495A	ENST00000275493	NM_005228.3	495	gGt/gCt	12/28	0.206629464051632	3	FACETS	0.957	0.8	1	0.479	0.4	0.563	INDETERMINATE	1	TRUE	1	0.782871689419188	3		436	130	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345999	152345999	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	65	590	0	ENST00000359321.1:c.571C>G	p.Leu191Val	p.L191V	ENST00000359321	NM_005431.1	191	Ctt/Gtt	3/3	0.51870030513997	4	FACETS	1	0.913	1	0.527	0.461	0.597	CLONAL	1	TRUE	2	0.782871689419188	4		590	281	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914655	39914655	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	89	725	1	ENST00000378444.4:c.4707G>A	p.Met1569Ile	p.M1569I	ENST00000378444	NM_001123385.1	1569	atG/atA	12/15	0.755415604162506	1	FACETS	0.961	0.885	1	0.961	0.885	1	CLONAL	1	TRUE	0	0.782871689419188	1		726	144	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578421	7578422	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCA	novel	NA	P-0019383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	200	744	0	ENST00000269305.4:c.506_508dup	p.Met169dup	p.M169dup	ENST00000269305	NM_001126112.2	169	acg/aTGAcg	5/11	0.619454358917426	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.619454358917426	1		744	417	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716328	52716328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1343613316	NA	P-0019383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	153	552	3	ENST00000322088.6:c.772C>T	p.Arg258Cys	p.R258C	ENST00000322088	NM_014225.5	258	Cgc/Tgc	6/15	0.619454358917426	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.619454358917426	1		555	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	378	945	1	ENST00000269305.4:c.166G>T	p.Glu56Ter	p.E56*	ENST00000269305	NM_001126112.2	56	Gaa/Taa	4/11	0.891442690427572	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.891442690427572	1		946	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0019454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	553	915	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.84648935111005	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.84648935111005	1		915	732	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0019908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	275	744	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.652521924521103	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.652521924521103	1		744	562	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624564	21624564	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs146077019	NA	P-0019908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	237	590	0	ENST00000421138.2:c.1465A>G	p.Ile489Val	p.I489V	ENST00000421138		489	Ata/Gta	14/16	1	2	FACETS	0.978	0.916	1	0.978	0.916	1	CLONAL	1	TRUE	1	0.652521924521103	2		590	743	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528157	29528157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	47	728	0	ENST00000356175.3:c.1165C>T	p.His389Tyr	p.H389Y	ENST00000356175	NM_000267.3	389	Cac/Tac	10/57	0.652521924521103	1	FACETS	0.176	0.148	0.207	0.176	0.148	0.207	SUBCLONAL	1	TRUE	0	0.652521924521103	1		728	550	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244508	41244508	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	477	752	0	ENST00000357654.3:c.3040del	p.Met1014TrpfsTer10	p.M1014Wfs*10	ENST00000357654	NM_007294.3	1014	Atg/tg	10/23	NA	2	FACETS	0.987	0.954	1			1	INDETERMINATE	2	TRUE	NA	0.652521924521103	2		752	741	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183632	185183632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746343770	NA	P-0019908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	194	531	1	ENST00000265026.3:c.1486C>T	p.Arg496Trp	p.R496W	ENST00000265026	NM_004721.4	496	Cgg/Tgg	9/14	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.652521924521103	2		532	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0019941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	984	804	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.61343791292601	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.61343791292601	3		804	1373	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0019941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	442	830	2	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.61343791292601	3	FACETS	1	0.958	1	0.666	0.639	0.694	CLONAL	2	TRUE	0	0.61343791292601	3		832	942	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951110	48951110	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	389	513	0	ENST00000267163.4:c.1272C>A	p.Tyr424Ter	p.Y424*	ENST00000267163	NM_000321.2	424	taC/taA	13/27	0.598121058166838	3	FACETS	0.979	0.946	1	0.979	0.946	1	CLONAL	3	TRUE	0	0.61343791292601	3		513	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0020006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	152	937	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	NA	2	FACETS	0.825	0.757	0.894			1	INDETERMINATE	2	TRUE	NA	0.309822352617302	2		937	595	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70441195	70441195	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	68	726	3	ENST00000373644.4:c.4864C>T	p.Arg1622Ter	p.R1622*	ENST00000373644	NM_030625.2	1622	Cga/Tga	9/12	0.273579563177116	3	FACETS	0.761	0.662	0.869			1	SUBCLONAL	1	TRUE	NA	0.309822352617302	3		729	666	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246455	105246455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	68	695	0	ENST00000349310.3:c.145G>A	p.Glu49Lys	p.E49K	ENST00000349310	NM_001014432.1	49	Gag/Aag	4/15	1	2	FACETS	0.619	0.538	0.707	0.619	0.538	0.707	SUBCLONAL	1	TRUE	1	0.309822352617302	2		695	709	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196162	108196162	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	54	702	0	ENST00000278616.4:c.6698T>C	p.Ile2233Thr	p.I2233T	ENST00000278616	NM_000051.3	2233	aTc/aCc	46/63	0.233983858014477	1	FACETS	0.655	0.56	0.758	0.655	0.56	0.758	SUBCLONAL	1	TRUE	0	0.309822352617302	1		702	450	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495394	149495394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	65	747	0	ENST00000261799.4:c.3253G>A	p.Glu1085Lys	p.E1085K	ENST00000261799	NM_002609.3	1085	Gag/Aag	23/23	1	2	FACETS	0.68	0.589	0.778	0.68	0.589	0.778	SUBCLONAL	1	TRUE	1	0.309822352617302	2		747	617	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39347503	39347503	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs771423136	NA	P-0020006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	58	581	0	ENST00000402219.2:c.61G>C	p.Gly21Arg	p.G21R	ENST00000402219	NM_005633.3	21	Gga/Cga	1/23	1	2	FACETS	0.756	0.651	0.871	0.756	0.651	0.871	SUBCLONAL	1	TRUE	1	0.309822352617302	2		581	495	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375177	31375177	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	86	750	0	ENST00000328111.2:c.574G>A	p.Ala192Thr	p.A192T	ENST00000328111	NM_006892.3	192	Gcc/Acc	6/23	0.309822352617302	3	FACETS	0.731	0.646	0.823	0.366	0.323	0.412	SUBCLONAL	1	TRUE	1	0.309822352617302	3		750	877	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49724585	49724585	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772304481	NA	P-0020006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	39	497	1	ENST00000449682.2:c.604G>A	p.Glu202Lys	p.E202K	ENST00000449682	NM_020998.3	202	Gag/Aag	5/18	0.309822352617302	3	FACETS	0.562	0.466	0.671			1	SUBCLONAL	1	TRUE	NA	0.309822352617302	3		498	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0020118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	294	794	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.267311350337823	2	FACETS	0.879	0.829	0.931	0.879	0.829	0.931	CLONAL	2	TRUE	0	0.336990788161495	2		794	992	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439724	220439724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201577506	NA	P-0020118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	104	968	1	ENST00000243786.2:c.577G>A	p.Val193Ile	p.V193I	ENST00000243786	NM_002191.3	193	Gtc/Atc	2/2	0.285229415737746	3	FACETS	0.742	0.663	0.826	0.371	0.331	0.413	SUBCLONAL	1	TRUE	1	0.336990788161495	3		969	972	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0020236-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	158	635	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.159867780985291	3	FACETS	1	0.952	1	1	0.989	1	CLONAL	3	TRUE	1	0.159867780985291	3		635	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578260	7578260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204041	NA	P-0020236-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	13	677	1	ENST00000269305.4:c.589G>A	p.Val197Met	p.V197M	ENST00000269305	NM_001126112.2	197	Gtg/Atg	6/11	1	2	FACETS	0.253	0.179	0.344	0.253	0.179	0.344	SUBCLONAL	1	TRUE	1	0.159867780985291	2		678	643	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001231	150001231	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020236-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	105	509	0	ENST00000253339.5:c.2373G>C	p.Met791Ile	p.M791I	ENST00000253339		791	atG/atC	4/7	0.159867780985291	3	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	1	0.159867780985291	3		509	684	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0020298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	248	845	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.807636340236932	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.807636340236932	1		845	328	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611845	1611845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1301102408	NA	P-0020298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	156	590	0	ENST00000344749.5:c.1817G>A	p.Arg606Gln	p.R606Q	ENST00000344749	NM_001136139.2	606	cGg/cAg	19/19	0.807636340236932	1	FACETS	0.828	0.776	0.88	0.828	0.776	0.88	CLONAL	1	TRUE	0	0.807636340236932	1		590	278	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128268675	128268675	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	36	697	0	ENST00000265960.3:c.980A>C	p.Lys327Thr	p.K327T	ENST00000265960	NM_001006617.1	327	aAg/aCg	8/12	0.807636340236932	1	FACETS	0.171	0.141	0.205	0.171	0.141	0.205	SUBCLONAL	1	TRUE	0	0.807636340236932	1		697	310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0020458-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	292	896	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.447221643407454	1	FACETS	0.982	0.925	1	0.982	0.925	1	CLONAL	1	TRUE	0	0.461676001511971	1		896	991	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566049	141566049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020458-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	149	718	2	ENST00000220592.5:c.1215G>A	p.Met405Ile	p.M405I	ENST00000220592	NM_012154.3	405	atG/atA	10/19	0.461676001511971	3	FACETS	0.78	0.711	0.851	0.26	0.237	0.284	SUBCLONAL	1	TRUE	0	0.461676001511971	3		720	1019	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0021272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	309	644	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.608932157628978	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.608932157628978	1		646	613	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376293	225376293	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	49	296	0	ENST00000264414.4:c.661A>G	p.Ser221Gly	p.S221G	ENST00000264414	NM_003590.4	221	Agc/Ggc	6/16	0.279240679515348	2	FACETS	1	0.96	1	0.649	0.565	0.735	INDETERMINATE	1	TRUE	0	0.608932157628978	2		296	124	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475061	40475063	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0021315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	272	1006	1	ENST00000264657.5:c.1847_1849del	p.Glu616del	p.E616del	ENST00000264657	NM_139276.2	616	gAAGga/gga	20/24	0.244801533704839	5	FACETS	1	0.96	1	0.685	0.643	0.728	INDETERMINATE	2	TRUE	2	0.441925971775312	5		1007	996	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726666	41726666	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778883675	NA	P-0021315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	293	1090	1	ENST00000301178.4:c.211C>T	p.Arg71Trp	p.R71W	ENST00000301178	NM_021913.4	71	Cgg/Tgg	2/20	0.16990195783034	4	FACETS	0.93	0.876	0.985	0.93	0.876	0.985	INDETERMINATE	2	TRUE	2	0.441925971775312	4		1091	1028	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0021315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	64	812	4	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	0.16990195783034	4	FACETS	0.61	0.527	0.699	0.305	0.263	0.35	INDETERMINATE	1	TRUE	2	0.441925971775312	4		816	685	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0021315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	15	243	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	0.441925971775312	3	FACETS	0.395	0.289	0.521	0.132	0.096	0.174	SUBCLONAL	1	TRUE	0	0.441925971775312	3		243	210	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974721	21974721	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	128	586	0	ENST00000304494.5:c.106del	p.Ala36ArgfsTer17	p.A36Rfs*17	ENST00000304494	NM_000077.4	36	Gcg/cg	1/3	0.441925971775312	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.441925971775312	1		586	348	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542109	187542110	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1560943587	NA	P-0021315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	115	597	0	ENST00000441802.2:c.5630dup	p.Val1878CysfsTer8	p.V1878Cfs*8	ENST00000441802	NM_005245.3	1877	cct/ccCt	10/27	0.441925971775312	2	FACETS	0.756	0.689	0.826	0.756	0.689	0.826	SUBCLONAL	2	TRUE	0	0.441925971775312	2		597	344	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61729435	61729435	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	31	758	2	ENST00000401558.2:c.312del	p.Lys104AsnfsTer17	p.K104Nfs*17	ENST00000401558	NM_003400.3	104	aaA/aa	5/25	0.16990195783034	4	FACETS	0.348	0.281	0.425	0.174	0.14	0.213	INDETERMINATE	1	TRUE	2	0.441925971775312	4		760	581	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511185	148511185	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	74	807	0	ENST00000320356.2:c.1717A>G	p.Thr573Ala	p.T573A	ENST00000320356	NM_004456.4	573	Acc/Gcc	15/20	0.244801533704839	5	FACETS	0.633	0.553	0.72	0.211	0.184	0.24	INDETERMINATE	1	TRUE	2	0.441925971775312	5		807	880	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610163	28610163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770571247	NA	P-0021315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	44	724	1	ENST00000241453.7:c.1327G>A	p.Ala443Thr	p.A443T	ENST00000241453	NM_004119.2	443	Gca/Aca	11/24	1	2	FACETS	0.34	0.284	0.401	0.34	0.284	0.401	SUBCLONAL	1	TRUE	1	0.441925971775312	2		725	586	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149751	202149751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	286	945	1	ENST00000358485.4:c.1192C>T	p.Gln398Ter	p.Q398*	ENST00000358485	NM_001080125.1	398	Cag/Tag	8/9	0.16990195783034	4	FACETS	1	0.966	1	1	0.966	1	INDETERMINATE	2	TRUE	2	0.441925971775312	4		946	902	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763489	41763489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201238916	NA	P-0021315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	210	913	1	ENST00000301178.4:c.2288G>A	p.Arg763His	p.R763H	ENST00000301178	NM_021913.4	763	cGc/cAc	19/20	0.16990195783034	4	FACETS	0.859	0.799	0.92	0.859	0.799	0.92	INDETERMINATE	2	TRUE	2	0.441925971775312	4		914	798	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530198	212530198	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	86	514	0	ENST00000342788.4:c.1721C>A	p.Pro574His	p.P574H	ENST00000342788	NM_005235.2	574	cCt/cAt	15/28	0.16990195783034	4	FACETS	1	0.979	1	0.738	0.658	0.824	INDETERMINATE	1	TRUE	2	0.441925971775312	4		514	380	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396851	139396851	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	512	929	0	ENST00000277541.6:c.5257G>A	p.Gly1753Arg	p.G1753R	ENST00000277541	NM_017617.3	1753	Ggg/Agg	28/34	0.441925971775312	5	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	2	0.441925971775312	5		929	1245	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263216	115263216	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	264	1080	0	ENST00000438362.2:c.2134A>G	p.Met712Val	p.M712V	ENST00000438362	NM_001242891.1	712	Atg/Gtg	17/20	0.238243348990095	3	FACETS	1	0.992	1	0.695	0.651	0.739	INDETERMINATE	1	TRUE	1	0.441925971775312	3		1080	1050	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468265	120468265	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	197	887	0	ENST00000256646.2:c.4174C>G	p.Gln1392Glu	p.Q1392E	ENST00000256646	NM_024408.3	1392	Cag/Gag	25/34	0.238243348990095	3	FACETS	0.798	0.742	0.856	0.798	0.742	0.856	INDETERMINATE	2	TRUE	1	0.441925971775312	3		887	682	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426905	49426906	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	rs748986705	NA	P-0021315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	113	727	0	ENST00000301067.7:c.11580_11582dup	p.Gln3863dup	p.Q3863dup	ENST00000301067	NM_003482.3	3863	caa/caGCAa	39/54	0.238243348990095	3	FACETS	1	0.967	1	0.581	0.525	0.64	INDETERMINATE	1	TRUE	1	0.441925971775312	3		727	537	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433773	49433773	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs35050033	NA	P-0021315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	239	1330	1	ENST00000301067.7:c.7780del	p.Leu2594TrpfsTer97	p.L2594Wfs*97	ENST00000301067	NM_003482.3	2594	Ctg/tg	31/54	0.238243348990095	3	FACETS	1	0.99	1	0.664	0.62	0.71	INDETERMINATE	1	TRUE	1	0.441925971775312	3		1331	994	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348565	89348565	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	272	1524	1	ENST00000301030.4:c.4385del	p.Arg1462LysfsTer69	p.R1462Kfs*69	ENST00000301030	NM_001256183.1	1462	aGa/aa	9/13	0.238243348990095	3	FACETS	1	0.991	1	0.648	0.607	0.689	INDETERMINATE	1	TRUE	1	0.441925971775312	3		1525	1160	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371649	89371649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750217123	NA	P-0021315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	302	1001	1	ENST00000301030.4:c.191C>T	p.Ala64Val	p.A64V	ENST00000301030	NM_001256183.1	64	gCg/gTg	4/13	0.238243348990095	3	FACETS	1	0.956	1	1	0.956	1	INDETERMINATE	2	TRUE	1	0.441925971775312	3		1002	825	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118501	17118501	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs748878853	NA	P-0021315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	306	982	5	ENST00000285071.4:c.1430G>A	p.Arg477Gln	p.R477Q	ENST00000285071	NM_144997.5	477	cGa/cAa	12/14	0.441925971775312	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.441925971775312	2		987	630	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257570	19257570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368120349	NA	P-0021315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	235	970	3	ENST00000162023.5:c.656G>A	p.Arg219Gln	p.R219Q	ENST00000162023		219	cGa/cAa	10/13	0.16990195783034	4	FACETS	0.883	0.826	0.943	0.883	0.826	0.943	INDETERMINATE	2	TRUE	2	0.441925971775312	4		973	868	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919959	50919959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371667262	NA	P-0021315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	145	987	0	ENST00000440232.2:c.3046C>T	p.Arg1016Cys	p.R1016C	ENST00000440232	NM_002691.3	1016	Cgc/Tgc	24/27	1	2	FACETS	0.846	0.772	0.922	0.846	0.772	0.922	CLONAL	1	TRUE	1	0.441925971775312	2		987	776	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035049	37035052	+	frameshift_variant	Frame_Shift_Del	DEL	TGGC	TGGC	-	novel	NA	P-0021315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	186	661	0	ENST00000231790.2:c.11_14del	p.Val4GlufsTer12	p.V4Efs*12	ENST00000231790	NM_000249.3	4	gTGGCa/ga	1/19	0.441925971775312	2	FACETS	0.803	0.748	0.86	0.803	0.748	0.86	CLONAL	2	TRUE	0	0.441925971775312	2		661	524	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443569	52443569	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0021315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	261	724	0	ENST00000460680.1:c.122+1del		p.X41_splice	ENST00000460680	NM_004656.3	41			0.441925971775312	2	FACETS	0.94	0.888	0.994	0.94	0.888	0.994	CLONAL	2	TRUE	0	0.441925971775312	2		724	628	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430891	181430891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1418197359	NA	P-0021315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	349	1258	1	ENST00000325404.1:c.743C>T	p.Ala248Val	p.A248V	ENST00000325404	NM_003106.3	248	gCc/gTc	1/1	0.244801533704839	5	FACETS	1	0.97	1	0.69	0.653	0.728	INDETERMINATE	2	TRUE	2	0.441925971775312	5		1259	1268	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183611	185183611	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	278	852	2	ENST00000265026.3:c.1465A>G	p.Ile489Val	p.I489V	ENST00000265026	NM_004721.4	489	Atc/Gtc	9/14	0.244801533704839	5	FACETS	0.878	0.828	0.929	0.878	0.828	0.929	INDETERMINATE	3	TRUE	2	0.441925971775312	5		854	794	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564667	86564667	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	379	1064	1	ENST00000274376.6:c.402del	p.Pro136LeufsTer38	p.P136Lfs*38	ENST00000274376	NM_002890.2	133	ggT/gg	1/25	0.441925971775312	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.441925971775312	2		1065	819	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528375	157528375	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs869312697	NA	P-0021315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	234	985	0	ENST00000346085.5:c.6100C>T	p.Gln2034Ter	p.Q2034*	ENST00000346085	NM_020732.3	2034	Cag/Tag	20/20	0.16990195783034	4	FACETS	0.834	0.779	0.891	0.834	0.779	0.891	INDETERMINATE	2	TRUE	2	0.441925971775312	4		985	915	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508371	106508371	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	31	466	0	ENST00000359195.3:c.365T>G	p.Leu122Arg	p.L122R	ENST00000359195	NM_002649.2	122	cTg/cGg	2/11	0.244801533704839	5	FACETS	0.598	0.484	0.728	0.199	0.161	0.243	INDETERMINATE	1	TRUE	2	0.441925971775312	5		466	390	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781482	135781482	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	156	660	0	ENST00000298552.3:c.1483G>C	p.Glu495Gln	p.E495Q	ENST00000298552	NM_001162426.1	495	Gag/Cag	15/23	0.441925971775312	5	FACETS	0.768	0.705	0.835	0.512	0.47	0.557	SUBCLONAL	2	TRUE	2	0.441925971775312	5		660	764	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399536	139399536	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	305	884	2	ENST00000277541.6:c.4607G>A	p.Cys1536Tyr	p.C1536Y	ENST00000277541	NM_017617.3	1536	tGc/tAc	26/34	0.441925971775312	5	FACETS	0.928	0.874	0.983	0.619	0.582	0.656	CLONAL	2	TRUE	2	0.441925971775312	5		886	1237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578381	7578382	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	C	novel	NA	P-0021315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	299	927	0	ENST00000269305.4:c.548_549delinsG	p.Ser183TrpfsTer64	p.S183Wfs*64	ENST00000269305	NM_001126112.2	183	tCA/tG	5/11	0.441925971775312	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.441925971775312	2		927	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0021359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	157	773	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	0.276905674792495	3	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.275441450689071	3		773	938	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29007963	29007963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	29	275	0	ENST00000282397.4:c.806C>T	p.Pro269Leu	p.P269L	ENST00000282397	NM_002019.4	269	cCt/cTt	6/30	NA	2	FACETS	0.59	0.474	0.722			1	INDETERMINATE	1	TRUE	NA	0.275441450689071	2		275	357	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669522	88669522	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	78	540	1	ENST00000360948.2:c.1376G>T	p.Arg459Leu	p.R459L	ENST00000360948	NM_001012338.2	459	cGg/cTg	12/19	0.227469642751976	1	FACETS	0.904	0.796	1	0.904	0.796	1	CLONAL	1	TRUE	0	0.275441450689071	1		541	540	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786056	3786056	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	83	774	1	ENST00000262367.5:c.4709C>A	p.Ala1570Glu	p.A1570E	ENST00000262367	NM_004380.2	1570	gCa/gAa	28/31	0.194681581096674	3	FACETS	0.654	0.575	0.738	0.327	0.287	0.369	SUBCLONAL	1	TRUE	1	0.275441450689071	3		775	1049	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41199721	41199721	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs80358029	NA	P-0021359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	57	615	0	ENST00000357654.3:c.5407-1G>C		p.X1803_splice	ENST00000357654	NM_007294.3	1803			0.276905674792495	3	FACETS	0.542	0.463	0.628	0.271	0.231	0.314	SUBCLONAL	1	TRUE	1	0.275441450689071	3		615	869	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519383	137519383	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	31	244	0	ENST00000367739.4:c.1255C>G	p.Leu419Val	p.L419V	ENST00000367739	NM_000416.2	419	Ctg/Gtg	7/7	0.275441450689071	5	FACETS	0.657	0.531	0.801			1	SUBCLONAL	1	TRUE	NA	0.275441450689071	5		244	484	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934362	68934362	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745857499	NA	P-0021359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	50	550	0	ENST00000288368.4:c.428G>A	p.Arg143Gln	p.R143Q	ENST00000288368	NM_024870.2	143	cGg/cAg	4/40	1	2	FACETS	0.423	0.358	0.495	0.423	0.358	0.495	SUBCLONAL	1	TRUE	1	0.275441450689071	2		550	858	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0021524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	194	575	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	NA	2	FACETS	0.818	0.768	0.868			1	INDETERMINATE	2	TRUE	NA	0.589970604472456	2		575	402	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200988	108200988	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	94	611	0	ENST00000278616.4:c.7355T>A	p.Leu2452Gln	p.L2452Q	ENST00000278616	NM_000051.3	2452	cTg/cAg	50/63	1	2	FACETS	0.821	0.736	0.911	0.821	0.736	0.911	CLONAL	1	TRUE	1	0.589970604472456	2		611	388	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845349	42845349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770738725	NA	P-0021524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	122	775	2	ENST00000398585.3:c.913C>T	p.Pro305Ser	p.P305S	ENST00000398585	NM_001135099.1	305	Ccc/Tcc	9/14	1	2	FACETS	0.94	0.856	1	0.94	0.856	1	CLONAL	1	TRUE	1	0.589970604472456	2		777	440	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163903	32163903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	102	580	1	ENST00000375023.3:c.5323G>A	p.Ala1775Thr	p.A1775T	ENST00000375023	NM_004557.3	1775	Gcg/Acg	30/30	1	2	FACETS	0.88	0.793	0.97	0.88	0.793	0.97	CLONAL	1	TRUE	1	0.589970604472456	2		581	393	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920242	76920242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	88	701	0	ENST00000373344.5:c.3835G>A	p.Glu1279Lys	p.E1279K	ENST00000373344	NM_000489.3	1279	Gaa/Aaa	11/35	0.589970604472456	1	FACETS	0.831	0.748	0.917	0.831	0.748	0.917	CLONAL	1	TRUE	0	0.589970604472456	1		701	253	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717766	89717766	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	73	490	0	ENST00000371953.3:c.791T>C	p.Met264Thr	p.M264T	ENST00000371953	NM_000314.4	264	aTg/aCg	7/9	1	2	FACETS	0.786	0.693	0.884	0.786	0.693	0.884	SUBCLONAL	1	TRUE	1	0.589970604472456	2		490	315	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637593	23637593	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781457	NA	P-0021524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	66	800	0	ENST00000261584.4:c.2712G>A	p.Trp904Ter	p.W904*	ENST00000261584	NM_024675.3	904	tgG/tgA	7/13	0.558544087220961	1	FACETS	0.478	0.418	0.542	0.478	0.418	0.542	SUBCLONAL	1	TRUE	0	0.589970604472456	1		800	330	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115040	3115040	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	71	1251	1	ENST00000078429.4:c.575A>T	p.Tyr192Phe	p.Y192F	ENST00000078429	NM_002067.2	192	tAc/tTc	4/7	0.575215751058994	1	FACETS	0.371	0.324	0.42	0.371	0.324	0.42	SUBCLONAL	1	TRUE	0	0.589970604472456	1		1252	458	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446125	70446125	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs769808628	NA	P-0021524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	22	619	0	ENST00000373644.4:c.5065A>G	p.Thr1689Ala	p.T1689A	ENST00000373644	NM_030625.2	1689	Act/Gct	11/12	1	2	FACETS	0.194	0.15	0.246	0.194	0.15	0.246	SUBCLONAL	1	TRUE	1	0.589970604472456	2		619	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0021932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	363	575	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.634357068140803	2	FACETS	0.907	0.871	0.943	0.907	0.871	0.943	CLONAL	2	TRUE	0	0.658099940757994	2		575	608	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067884	30067884	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	189	670	0	ENST00000338641.4:c.1069G>T	p.Glu357Ter	p.E357*	ENST00000338641	NM_000268.3	357	Gag/Tag	11/16	0.658099940757994	1	FACETS	0.952	0.892	1	0.952	0.892	1	CLONAL	1	TRUE	0	0.658099940757994	1		670	405	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2215893	2215893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370203279	NA	P-0021932-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	212	714	1	ENST00000326181.6:c.95C>T	p.Thr32Met	p.T32M	ENST00000326181	NM_032271.2	32	aCg/aTg	3/21	0.658930496006709	3	FACETS	0.817	0.759	0.878	0.409	0.379	0.439	CLONAL	1	TRUE	1	0.658099940757994	3		715	1048	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0022191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	792	517	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.554844464775009	5	FACETS	0.91	0.887	0.932			1	CLONAL	4	TRUE	NA	0.784294631030606	5		517	1208	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070877	30070877	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	247	621	0	ENST00000338641.4:c.1393G>T	p.Glu465Ter	p.E465*	ENST00000338641	NM_000268.3	465	Gag/Tag	13/16	0.784294631030606	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.784294631030606	1		621	366	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022387-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	98	115	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.714389367783367	2		115	254	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587780070	NA	P-0022387-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	63	899	0	ENST00000269305.4:c.535C>A	p.His179Asn	p.H179N	ENST00000269305	NM_001126112.2	179	Cat/Aat	5/11	1	2	FACETS	0.159	0.137	0.184	0.159	0.137	0.184	SUBCLONAL	1	TRUE	1	0.714389367783367	2		899	1107	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692775	89692775	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554898053	NA	P-0022387-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	10	338	0	ENST00000371953.3:c.259C>T	p.Gln87Ter	p.Q87*	ENST00000371953	NM_000314.4	87	Caa/Taa	5/9	0.714389367783367	1	FACETS	0.096	0.065	0.136	0.096	0.065	0.136	SUBCLONAL	1	TRUE	0	0.714389367783367	1		338	187	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942124	81942124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781434235	NA	P-0022387-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	268	726	0	ENST00000359376.3:c.1661C>T	p.Thr554Met	p.T554M	ENST00000359376	NM_002661.3	554	aCg/aTg	17/33	1	2	FACETS	0.909	0.856	0.964	0.909	0.856	0.964	CLONAL	1	TRUE	1	0.714389367783367	2		726	825	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121856	2121856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745897413	NA	P-0022387-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	427	1100	0	ENST00000219476.3:c.2018C>T	p.Ala673Val	p.A673V	ENST00000219476	NM_000548.3	673	gCg/gTg	19/42	1	2	FACETS	0.95	0.905	0.994	0.95	0.905	0.994	CLONAL	1	TRUE	1	0.714389367783367	2		1100	1259	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281904	39281904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886041241	NA	P-0022387-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	147	401	0	ENST00000402219.2:c.571G>A	p.Glu191Lys	p.E191K	ENST00000402219	NM_005633.3	191	Gaa/Aaa	5/23	1	2	FACETS	0.812	0.746	0.88	0.812	0.746	0.88	CLONAL	1	TRUE	1	0.714389367783367	2		401	507	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63662157	63662157	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022387-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	173	365	0	ENST00000279873.7:c.261T>G	p.Asn87Lys	p.N87K	ENST00000279873	NM_032199.2	87	aaT/aaG	2/10	0.714389367783367	1	FACETS	0.9	0.842	0.957	0.9	0.842	0.957	CLONAL	1	TRUE	0	0.714389367783367	1		365	346	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631112	69631112	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022387-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	251	721	0	ENST00000334134.2:c.300C>A	p.Asn100Lys	p.N100K	ENST00000334134	NM_005247.2	100	aaC/aaA	2/3	1	2	FACETS	0.822	0.771	0.874	0.822	0.771	0.874	CLONAL	1	TRUE	1	0.714389367783367	2		721	855	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579378	7579378	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	192	1025	1	ENST00000269305.4:c.309C>A	p.Tyr103Ter	p.Y103*	ENST00000269305	NM_001126112.2	103	taC/taA	4/11	0.324456376355923	2	FACETS	0.87	0.808	0.934	0.87	0.808	0.934	CLONAL	2	TRUE	0	0.324456376355923	2		1026	680	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276723	15276723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1031506714	NA	P-0022397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	100	991	0	ENST00000263388.2:c.5542C>T	p.Arg1848Cys	p.R1848C	ENST00000263388	NM_000435.2	1848	Cgt/Tgt	30/33	0.324456376355923	4	FACETS	0.982	0.877	1	0.491	0.438	0.548	CLONAL	1	TRUE	2	0.324456376355923	4		991	831	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76777829	76777829	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	206	870	1	ENST00000373344.5:c.6887A>T	p.Asn2296Ile	p.N2296I	ENST00000373344	NM_000489.3	2296	aAt/aTt	32/35	0.314037230767328	2	FACETS	0.977	0.911	1	0.977	0.911	1	CLONAL	2	TRUE	0	0.324456376355923	2		871	650	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0022483-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	52	341	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.224510500082125	2		341	444	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028895	47028895	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0022483-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	53	82	0	ENST00000377604.3:c.199G>T	p.Glu67Ter	p.E67*	ENST00000377604	NM_001204468.1	67	Gag/Tag	3/24	1	1	FACETS	0.825	0.71	0.948	1	0.971	1	CLONAL	2	TRUE	0	0.224510500082125	1		82	254	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602878	10602878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022483-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	70	244	0	ENST00000171111.5:c.700C>T	p.Arg234Trp	p.R234W	ENST00000171111	NM_203500.1	234	Cgg/Tgg	3/6	0.183176844901926	1	FACETS	0.693	0.603	0.79	0.693	0.603	0.79	SUBCLONAL	1	TRUE	0	0.224510500082125	1		244	799	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176085773	176085773	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022483-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	40	64	0	ENST00000367669.3:c.1013G>T	p.Ser338Ile	p.S338I	ENST00000367669	NM_022457.5	338	aGt/aTt	9/20	1	2	FACETS	0.867	0.721	1	0.867	0.721	1	CLONAL	1	TRUE	1	0.224510500082125	2		64	411	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347456	89347456	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022483-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	59	348	0	ENST00000301030.4:c.5494A>T	p.Arg1832Trp	p.R1832W	ENST00000301030	NM_001256183.1	1832	Agg/Tgg	9/13	1	2	FACETS	0.776	0.667	0.896	0.776	0.667	0.896	SUBCLONAL	1	TRUE	1	0.224510500082125	2		348	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576853	7576858	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CTGAAG	CTGAAG	-	novel	NA	P-0022483-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	70	172	0	ENST00000269305.4:c.988_993del	p.Leu330_Gln331del	p.L330_Q331del	ENST00000269305	NM_001126112.2	330	CTTCAG/-	9/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.224510500082125	2		172	543	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559776	29559810	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCAAACAGGTGGCAGGAAACGTGGCATGTCTCG	GCGCAAACAGGTGGCAGGAAACGTGGCATGTCTCG	-	novel	NA	P-0022483-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	27	48	0	ENST00000356175.3:c.3374_3408del	p.Ala1125GlufsTer58	p.A1125Efs*58	ENST00000356175	NM_000267.3	1125	GCGCAAACAGGTGGCAGGAAACGTGGCATGTCTCGg/g	26/57	1	2	FACETS	0.666	0.53	0.822	0.666	0.53	0.822	SUBCLONAL	1	TRUE	1	0.224510500082125	2		48	361	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45423019	45423019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022483-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	23	66	0	ENST00000262160.6:c.109G>A	p.Glu37Lys	p.E37K	ENST00000262160	NM_005901.5	37	Gaa/Aaa	2/11	0.130007962916917	1	FACETS	0.466	0.363	0.586	0.466	0.363	0.586	INDETERMINATE	1	TRUE	0	0.224510500082125	1		66	390	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091801	29091801	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022483-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	31	111	0	ENST00000328354.6:c.1156G>C	p.Gly386Arg	p.G386R	ENST00000328354	NM_007194.3	386	Gga/Cga	11/15	1	2	FACETS	0.522	0.421	0.637	0.522	0.421	0.637	SUBCLONAL	1	TRUE	1	0.224510500082125	2		111	529	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138197196	138197196	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022483-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	40	82	0	ENST00000237289.4:c.698A>G	p.Tyr233Cys	p.Y233C	ENST00000237289	NM_001270507.1	233	tAc/tGc	5/9	0.224510500082125	1	FACETS	0.722	0.6	0.858	0.722	0.6	0.858	SUBCLONAL	1	TRUE	0	0.224510500082125	1		82	438	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971202	13971202	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs977319524	NA	P-0022483-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	55	67	0	ENST00000405192.2:c.727G>T	p.Gly243Cys	p.G243C	ENST00000405192	NM_001163147.1	243	Ggc/Tgc	8/12	0.224510500082125	3	FACETS	1	0.908	1	0.541	0.463	0.626	CLONAL	1	TRUE	1	0.224510500082125	3		67	504	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230764	53230764	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022483-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	93	68	0	ENST00000375401.3:c.2029G>T	p.Glu677Ter	p.E677*	ENST00000375401	NM_004187.3	677	Gag/Tag	14/26	1	1	FACETS	0.968	0.867	1	1	0.986	1	CLONAL	2	TRUE	0	0.224510500082125	1		68	380	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253136	133253136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	42	660	0	ENST00000320574.5:c.905G>A	p.Gly302Asp	p.G302D	ENST00000320574	NM_006231.2	302	gGc/gAc	9/49	0.358168477482799	2	FACETS	0.389	0.325	0.46	0.194	0.162	0.23	SUBCLONAL	1	TRUE	0	0.532178874607633	2		660	406	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476387	88476387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202056599	NA	P-0022507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	153	737	0	ENST00000360948.2:c.1745G>A	p.Arg582Gln	p.R582Q	ENST00000360948	NM_001012338.2	582	cGg/cAg	15/19	0.532178874607633	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.532178874607633	1		737	341	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1555525429	NA	P-0022507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	361	890	0	ENST00000269305.4:c.782+1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.532178874607633	3	FACETS	1	0.969	1			1	CLONAL	3	TRUE	NA	0.532178874607633	3		890	568	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781645	9781645	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	58	814	0	ENST00000377346.4:c.1955G>C	p.Arg652Pro	p.R652P	ENST00000377346	NM_005026.3	652	cGc/cCc	15/24	0.357973015302092	3	FACETS	0.587	0.505	0.676	0.196	0.168	0.226	SUBCLONAL	1	TRUE	0	0.532178874607633	3		814	470	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505526	25505526	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	270	903	1	ENST00000264709.3:c.232A>G	p.Met78Val	p.M78V	ENST00000264709	NM_175629.2	78	Atg/Gtg	4/23	0.532178874607633	3	FACETS	0.856	0.807	0.906	0.856	0.807	0.906	CLONAL	2	TRUE	1	0.532178874607633	3		904	750	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354956	70354956	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	40	797	0	ENST00000374080.3:c.4878G>C	p.Glu1626Asp	p.E1626D	ENST00000374080		1626	gaG/gaC	36/45	0.386669595316101	1	FACETS	0.265	0.22	0.314	0.265	0.22	0.314	SUBCLONAL	1	TRUE	0	0.532178874607633	1		797	417	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188309	10188309	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs869025655	NA	P-0022757-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	282	1122	0	ENST00000256474.2:c.452T>G	p.Ile151Ser	p.I151S	ENST00000256474	NM_000551.3	151	aTc/aGc	2/3	0.50953216163816	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.50953216163816	2		1122	536	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	22	658	1	ENST00000397752.3:c.3028G>T	p.Asp1010Tyr	p.D1010Y	ENST00000397752	NM_000245.2	1010	Gat/Tat	14/21	0.231947925244487	1	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	0	0.314874154870241	1		659	100	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578483	7578483	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	19	918	0	ENST00000269305.4:c.447del	p.Thr150HisfsTer20	p.T150Hfs*20	ENST00000269305	NM_001126112.2	149	tcC/tc	5/11	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.314874154870241	2		918	111	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279235	142279235	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	15	464	1	ENST00000350721.4:c.1411G>A	p.Glu471Lys	p.E471K	ENST00000350721	NM_001184.3	471	Gaa/Aaa	6/47	1	2	FACETS	0.794	0.586	1	0.794	0.586	1	CLONAL	1	TRUE	1	0.314874154870241	2		465	120	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293660	137293660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	16	911	0	ENST00000481739.1:c.211C>T	p.Pro71Ser	p.P71S	ENST00000481739	NM_002957.4	71	Ccc/Tcc	2/10	0.231947925244487	1	FACETS	0.771	0.577	0.997	0.771	0.577	0.997	CLONAL	1	TRUE	0	0.314874154870241	1		911	111	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325345	1325345	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	12	553	0	ENST00000400841.2:c.330T>A	p.Ser110Arg	p.S110R	ENST00000400841		110	agT/agA	3/6	0.314874154870241	0	FACETS	0.36	0.254	0.489			1	SUBCLONAL	1	TRUE	NA	0.314874154870241	0		553	145	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514458	41514459	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0023023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	11	493	1	ENST00000373198.4:c.202_203delinsTT	p.Ala68Leu	p.A68L	ENST00000373198	NM_133170.3	68	GCa/TTa	2/32	1	2	FACETS	0.448	0.31	0.618	0.448	0.31	0.618	SUBCLONAL	1	TRUE	1	0.314874154870241	2		494	156	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0023189-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	79	937	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.16	2		937	963	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729962	30729962	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs104893819	NA	P-0023189-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	13	535	0	ENST00000295754.5:c.1483C>T	p.Arg495Ter	p.R495*	ENST00000295754	NM_003242.5	495	Cga/Tga	6/7	1	2	FACETS	0.25	0.177	0.341	0.25	0.177	0.341	SUBCLONAL	1	TRUE	1	0.16	2		535	649	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842746	68842746	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023189-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	53	495	0	ENST00000261769.5:c.682T>A	p.Tyr228Asn	p.Y228N	ENST00000261769	NM_004360.3	228	Tac/Aac	5/16	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.16	2		495	643	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115884	8115909	+	frameshift_variant	Frame_Shift_Del	DEL	CCACTCCAGCCACATGCTGACCACGC	CCACTCCAGCCACATGCTGACCACGC	-	novel	NA	P-0023256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	312	721	1	ENST00000346208.3:c.1234_1259del	p.Ser412AlafsTer86	p.S412Afs*86	ENST00000346208		410	agCCACTCCAGCCACATGCTGACCACGCcc/agcc	6/6	1	2	FACETS	0.977	0.922	1	0.977	0.922	1	CLONAL	1	TRUE	1	0.614885320678257	2		722	1039	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0023415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	381	535	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.52793635552966	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.52793635552966	3		535	820	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs786201057	NA	P-0023415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	173	559	0	ENST00000269305.4:c.374C>G	p.Thr125Arg	p.T125R	ENST00000269305	NM_001126112.2	125	aCg/aGg	4/11	0.52793635552966	1	FACETS	0.94	0.872	1	0.94	0.872	1	CLONAL	1	TRUE	0	0.52793635552966	1		559	513	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921737	111921737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1170116948	NA	P-0023415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	177	445	1	ENST00000393256.3:c.526G>A	p.Glu176Lys	p.E176K	ENST00000393256	NM_006538.4	176	Gaa/Aaa	4/4	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.52793635552966	2		446	590	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519721	137519721	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0023415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	23	355	0	ENST00000367739.4:c.917C>G	p.Ser306Ter	p.S306*	ENST00000367739	NM_000416.2	306	tCa/tGa	7/7	1	2	FACETS	0.205	0.16	0.259	0.205	0.16	0.259	SUBCLONAL	1	TRUE	1	0.52793635552966	2		355	424	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233726	133233726	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	114	569	0	ENST00000320574.5:c.3578G>C	p.Arg1193Thr	p.R1193T	ENST00000320574	NM_006231.2	1193	aGa/aCa	29/49	1	2	FACETS	0.687	0.619	0.757	0.687	0.619	0.757	SUBCLONAL	1	TRUE	1	0.52793635552966	2		569	629	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057874	27057883	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCAGTCCC	CAGCAGTCCC	-	novel	NA	P-0023415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	309	848	2	ENST00000324856.7:c.1583_1592del	p.Gln528ArgfsTer88	p.Q528Rfs*88	ENST00000324856	NM_006015.4	528	CAGCAGTCCCcg/cg	3/20	1	2	FACETS	0.999	0.942	1	0.999	0.942	1	CLONAL	1	TRUE	1	0.52793635552966	2		850	1172	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105716	27105742	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAAGAAGAGGAAGTAGTTGAAAATG	AAGAAGAAGAGGAAGTAGTTGAAAATG	CAGA	novel	NA	P-0023415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	125	376	2	ENST00000324856.7:c.5327_5353delinsCAGA	p.Glu1776AlafsTer3	p.E1776Afs*3	ENST00000324856	NM_006015.4	1776	gAAGAAGAAGAGGAAGTAGTTGAAAATGat/gCAGAat	20/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.52793635552966	2		378	450	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127380	17127380	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	223	826	2	ENST00000285071.4:c.474C>G	p.Ile158Met	p.I158M	ENST00000285071	NM_144997.5	158	atC/atG	6/14	1	2	FACETS	0.752	0.699	0.806	0.752	0.699	0.806	SUBCLONAL	1	TRUE	1	0.52793635552966	2		828	1124	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585385	29585385	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	163	636	0	ENST00000356175.3:c.4134G>C	p.Gln1378His	p.Q1378H	ENST00000356175	NM_000267.3	1378	caG/caC	31/57	0.445537572392867	3	FACETS	0.79	0.724	0.859			1	SUBCLONAL	1	TRUE	NA	0.52793635552966	3		636	988	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511592	38511592	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	62	715	0	ENST00000254066.5:c.1090C>G	p.Arg364Gly	p.R364G	ENST00000254066	NM_000964.3	364	Cgg/Ggg	8/9	NA	2	FACETS	0.245	0.211	0.282			1	INDETERMINATE	1	TRUE	NA	0.52793635552966	2		715	959	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430730	181430736	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGCCC	GCAGCCC	-	novel	NA	P-0023415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	192	673	0	ENST00000325404.1:c.582_588del	p.Met194IlefsTer7	p.M194Ifs*7	ENST00000325404	NM_003106.3	194	atGCAGCCC/at	1/1	0.52793635552966	3	FACETS	0.945	0.874	1	0.472	0.437	0.51	CLONAL	1	TRUE	1	0.52793635552966	3		673	973	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050711	5050711	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	183	469	0	ENST00000381652.3:c.494G>C	p.Trp165Ser	p.W165S	ENST00000381652	NM_004972.3	165	tGg/tCg	6/25	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.52793635552966	2		469	603	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249416	110249416	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	397	992	5	ENST00000374672.4:c.1157G>A	p.Arg386Gln	p.R386Q	ENST00000374672	NM_004235.4	386	cGa/cAa	4/5	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.52793635552966	2		997	1355	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0023560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	150	890	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.456149674811525	1	FACETS	0.965	0.888	1	0.965	0.888	1	CLONAL	1	TRUE	0	0.478712017933484	1		893	494	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472634	88472634	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	45	444	0	ENST00000360948.2:c.1921G>T	p.Asp641Tyr	p.D641Y	ENST00000360948	NM_001012338.2	641	Gat/Tat	16/19	1	2	FACETS	0.57	0.481	0.667	0.57	0.481	0.667	SUBCLONAL	1	TRUE	1	0.478712017933484	2		444	330	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678488	88678488	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	61	702	1	ENST00000360948.2:c.1048G>T	p.Val350Leu	p.V350L	ENST00000360948	NM_001012338.2	350	Gtg/Ttg	9/19	1	2	FACETS	0.549	0.475	0.63	0.549	0.475	0.63	SUBCLONAL	1	TRUE	1	0.478712017933484	2		703	464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0023632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	326	689	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.763833536318953	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.763833536318953	2		690	402	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	370	641	1	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.763833536318953	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.763833536318953	3		642	430	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988692	41988692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753241568	NA	P-0023632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	79	524	1	ENST00000219905.7:c.1484G>A	p.Arg495Gln	p.R495Q	ENST00000219905	NM_001164273.1	495	cGa/cAa	3/24	1	2	FACETS	0.841	0.75	0.935	0.841	0.75	0.935	CLONAL	1	TRUE	1	0.763833536318953	2		525	246	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958281	11958281	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs758381870	NA	P-0023632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	103	437	0	ENST00000353533.5:c.191A>G	p.Asn64Ser	p.N64S	ENST00000353533	NM_003010.3	64	aAt/aGt	2/11	0.763833536318953	2	FACETS	0.876	0.815	0.933	0.876	0.815	0.933	CLONAL	2	TRUE	0	0.763833536318953	2		437	154	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690206	47690206	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	100	635	0	ENST00000233146.2:c.1423G>C	p.Asp475His	p.D475H	ENST00000233146	NM_000251.2	475	Gat/Cat	9/16	0.763833536318953	3	FACETS	0.905	0.814	0.999	0.452	0.407	0.5	CLONAL	1	TRUE	1	0.763833536318953	3		635	400	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321460	62321460	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746024103	NA	P-0023632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	287	774	0	ENST00000360203.5:c.2162G>A	p.Arg721Lys	p.R721K	ENST00000360203	NM_001283009.1	721	aGa/aAa	25/35	0.583609296924659	6	FACETS	0.878	0.831	0.926	0.878	0.831	0.926	CLONAL	3	TRUE	3	0.763833536318953	6		774	721	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271265	153271266	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	125	374	0	ENST00000281708.4:c.512dup	p.Leu172ValfsTer6	p.L172Vfs*6	ENST00000281708	NM_033632.3	171	aag/aaAg	3/12	0.652897186424127	4	FACETS	0.877	0.805	0.951	0.877	0.805	0.951	CLONAL	2	TRUE	2	0.763833536318953	4		374	329	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271460	26271460	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023712-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	169	692	0	ENST00000305910.3:c.153G>C	p.Glu51Asp	p.E51D	ENST00000305910	NM_003534.2	51	gaG/gaC	1/1	1	2	FACETS	0.886	0.82	0.954	0.886	0.82	0.954	CLONAL	1	TRUE	1	0.702711502355778	2		692	543	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354353	354353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142097791	NA	P-0023712-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	201	844	3	ENST00000262320.3:c.1205C>T	p.Thr402Met	p.T402M	ENST00000262320	NM_003502.3	402	aCg/aTg	5/11	1	2	FACETS	0.946	0.882	1	0.946	0.882	1	CLONAL	1	TRUE	1	0.702711502355778	2		847	605	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188257	10188257	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023712-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	273	783	0	ENST00000256474.2:c.400del	p.Glu134AsnfsTer25	p.E134Nfs*25	ENST00000256474	NM_000551.3	134	Gaa/aa	2/3	0.702711502355778	1	FACETS	0.977	0.928	1	0.977	0.928	1	CLONAL	1	TRUE	0	0.702711502355778	1		783	516	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436410	52436410	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0023712-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	183	796	0	ENST00000460680.1:c.2084del	p.Asn695ThrfsTer41	p.N695Tfs*41	ENST00000460680	NM_004656.3	695	aAc/ac	17/17	0.702711502355778	1	FACETS	0.916	0.859	0.973	0.916	0.859	0.973	CLONAL	1	TRUE	0	0.702711502355778	1		796	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0023767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	98	915	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.563592455201961	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.563592455201961	1		915	248	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164772	106164772	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761811530	NA	P-0023767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	50	293	0	ENST00000380013.4:c.3640C>T	p.Arg1214Trp	p.R1214W	ENST00000380013	NM_001127208.2	1214	Cgg/Tgg	6/11	1	2	FACETS	0.556	0.474	0.645	0.556	0.474	0.645	SUBCLONAL	1	TRUE	1	0.563592455201961	2		293	319	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051642	30051642	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	59	227	0	ENST00000338641.4:c.576C>A	p.Tyr192Ter	p.Y192*	ENST00000338641	NM_000268.3	192	taC/taA	6/16	0.563592455201961	1	FACETS	0.726	0.634	0.823	0.726	0.634	0.823	SUBCLONAL	1	TRUE	0	0.563592455201961	1		227	207	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397678	139397678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778830490	NA	P-0023767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	42	387	0	ENST00000277541.6:c.5123C>T	p.Ser1708Leu	p.S1708L	ENST00000277541	NM_017617.3	1708	tCg/tTg	27/34	0.366487180410937	3	FACETS	0.567	0.475	0.668	0.283	0.237	0.334	SUBCLONAL	1	TRUE	1	0.563592455201961	3		387	337	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371712	55371713	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0023767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	48	274	0	ENST00000297316.4:c.403dup	p.Tyr135LeufsTer27	p.Y135Lfs*27	ENST00000297316	NM_022454.3	134	-/T	2/2	1	2	FACETS	0.448	0.38	0.523	0.448	0.38	0.523	SUBCLONAL	1	TRUE	1	0.563592455201961	2		274	380	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046641	42046642	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0023767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	84	241	0	ENST00000219905.7:c.7018_7019del	p.Val2340ArgfsTer4	p.V2340Rfs*4	ENST00000219905	NM_001164273.1	2339	TGt/t	18/24	0.563592455201961	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.563592455201961	1		241	204	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254905	16254905	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs949668986	NA	P-0023767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	50	330	0	ENST00000375759.3:c.2170C>T	p.Arg724Ter	p.R724*	ENST00000375759	NM_015001.2	724	Cga/Tga	11/15	0.131202780704438	5	FACETS	0.846	0.72	0.984			1	INDETERMINATE	1	TRUE	NA	0.563592455201961	5		330	387	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2105493	2105504	+	inframe_deletion	In_Frame_Del	DEL	TCGACGAGTACA	TCGACGAGTACA	-	novel	NA	P-0023767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	94	343	0	ENST00000219476.3:c.575_586del	p.Asp192_Ile195del	p.D192_I195del	ENST00000219476	NM_000548.3	191	cTCGACGAGTACAtc/ctc	6/42	0.508694488636071	0	FACETS	0.697	0.634	0.76			1	SUBCLONAL	1	TRUE	0	0.563592455201961	0		343	209	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216558	7216570	+	frameshift_variant	Frame_Shift_Del	DEL	AGCATGTTCCATC	AGCATGTTCCATC	-	novel	NA	P-0023767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	103	327	0	ENST00000380728.2:c.765_777del	p.Met256ThrfsTer85	p.M256Tfs*85	ENST00000380728		255	caGATGGAACATGCT/ca	9/11	0.563592455201961	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.563592455201961	1		327	242	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050334	128050334	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	93	307	0	ENST00000285398.2:c.323G>A	p.Cys108Tyr	p.C108Y	ENST00000285398	NM_000122.1	108	tGc/tAc	3/15	1	2	FACETS	0.985	0.885	1	0.985	0.885	1	CLONAL	1	TRUE	1	0.563592455201961	2		307	335	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331941	81331941	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	83	241	0	ENST00000222390.5:c.2143T>C	p.Trp715Arg	p.W715R	ENST00000222390	NM_000601.4	715	Tgg/Cgg	18/18	0.289264240243633	3	FACETS	0.767	0.688	0.85	0.767	0.688	0.85	INDETERMINATE	2	TRUE	1	0.563592455201961	3		241	246	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873483	151873483	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	154	319	0	ENST00000262189.6:c.9055C>T	p.Gln3019Ter	p.Q3019*	ENST00000262189	NM_170606.2	3019	Cag/Tag	38/59	0.289264240243633	3	FACETS	0.896	0.83	0.963	0.896	0.83	0.963	INDETERMINATE	2	TRUE	1	0.563592455201961	3		319	391	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667868	37667868	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	253	296	0	ENST00000447079.4:c.2753A>G	p.Asp918Gly	p.D918G	ENST00000447079	NM_015083.1	918	gAt/gGt	8/14	0.485685571337767	4	FACETS	1	0.989	1			1	CLONAL	3	TRUE	NA	0.485685571337767	4		296	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577519	7577527	+	inframe_deletion	In_Frame_Del	DEL	GATGGTGAG	GATGGTGAG	-	novel	NA	P-0023834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	190	306	0	ENST00000269305.4:c.754_762del	p.Leu252_Ile254del	p.L252_I254del	ENST00000269305	NM_001126112.2	252	CTCACCATC/-	7/11	0.485685571337767	3	FACETS	1	0.984	1	0.774	0.724	0.823	CLONAL	2	TRUE	0	0.485685571337767	3		306	419	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636031	28636031	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	83	347	0	ENST00000241453.7:c.341G>A	p.Cys114Tyr	p.C114Y	ENST00000241453	NM_004119.2	114	tGc/tAc	3/24	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	1	TRUE	NA	0.485685571337767	2		347	280	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774204	66774204	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	104	521	0	ENST00000307102.5:c.680G>T	p.Arg227Met	p.R227M	ENST00000307102	NM_002755.3	227	aGg/aTg	6/11	0.379985810217439	3	FACETS	0.844	0.757	0.936	0.422	0.378	0.468	CLONAL	1	TRUE	1	0.485685571337767	3		521	631	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045910	180045910	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	42	289	0	ENST00000261937.6:c.2861C>A	p.Pro954His	p.P954H	ENST00000261937	NM_182925.4	954	cCc/cAc	21/30	0.155459029825579	6	FACETS	1	0.943	1	0.323	0.271	0.38	INDETERMINATE	1	TRUE	2	0.485685571337767	6		289	264	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004345	150004345	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs970337024	NA	P-0023834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	66	319	0	ENST00000253339.5:c.1880G>A	p.Arg627Lys	p.R627K	ENST00000253339		627	aGg/aAg	3/7	0.33048866651494	2	FACETS	0.863	0.755	0.978	0.431	0.377	0.489	CLONAL	1	TRUE	0	0.485685571337767	2		319	315	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867291	45867291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199863965	NA	P-0023840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	288	408	2	ENST00000391945.4:c.902C>T	p.Thr301Met	p.T301M	ENST00000391945	NM_000400.3	301	aCg/aTg	10/23	0.405215525483044	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.405215525483044	3		410	711	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342788	118342788	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	76	368	0	ENST00000534358.1:c.914G>C	p.Arg305Thr	p.R305T	ENST00000534358	NM_005933.3	305	aGg/aCg	3/36	0.405215525483044	3	FACETS	0.904	0.795	1	0.452	0.397	0.511	CLONAL	1	TRUE	1	0.405215525483044	3		368	499	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965180	15965180	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	15	201	0	ENST00000268712.3:c.5416A>T	p.Ser1806Cys	p.S1806C	ENST00000268712	NM_006311.3	1806	Agc/Tgc	37/46	1	2	FACETS	0.275	0.201	0.365	0.275	0.201	0.365	SUBCLONAL	1	TRUE	1	0.405215525483044	2		201	269	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937989	76937989	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	44	437	1	ENST00000373344.5:c.2759G>T	p.Gly920Val	p.G920V	ENST00000373344	NM_000489.3	920	gGt/gTt	9/35	0.369967922319883	4	FACETS	0.411	0.344	0.486	0.206	0.172	0.243	SUBCLONAL	1	TRUE	2	0.405215525483044	4		438	742	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0024019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	120	503	0	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	0.644011749862748	1	FACETS	0.946	0.871	1	0.946	0.871	1	CLONAL	1	TRUE	0	0.644011749862748	1		503	267	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211745	36211745	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1453375558	NA	P-0024019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	76	571	0	ENST00000222270.7:c.1496C>A	p.Pro499His	p.P499H	ENST00000222270	NM_014727.1	499	cCc/cAc	3/37	0.431722947840577	3	FACETS	0.515	0.452	0.583	0.257	0.226	0.292	SUBCLONAL	1	TRUE	1	0.644011749862748	3		571	606	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0024115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	42	285	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.166699998697776	5	FACETS	0.992	0.827	1	0.331	0.275	0.392	CLONAL	1	FALSE	2	0.166699998697776	5		285	635	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0024115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	93	662	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.0566674908661018	1	FACETS	0.926	0.826	1	1	0.985	1	INDETERMINATE	2	FALSE	0	0.166699998697776	1		662	552	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0024115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	64	545	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	0.986	0.852	1	0.986	0.852	1	CLONAL	1	FALSE	1	0.166699998697776	2		545	779	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981827	101981827	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1232067606	NA	P-0024115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	29	545	0	ENST00000282441.5:c.248C>G	p.Thr83Ser	p.T83S	ENST00000282441	NM_001130145.2	83	aCc/aGc	1/9	0.124120850884556	4	FACETS	0.713	0.571	0.876	0.357	0.285	0.438	SUBCLONAL	1	FALSE	2	0.166699998697776	4		545	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577493	7577497	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CCTGA	CCTGA	-	rs1567548832	NA	P-0024115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	43	562	0	ENST00000269305.4:c.782+2_782+6del		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.166699998697776	1	FACETS	0.836	0.698	0.988	0.836	0.698	0.988	CLONAL	1	FALSE	0	0.166699998697776	1		562	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0024337-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	142	796	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.340202925592004	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.340202925592004	1		796	684	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182057	38182057	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024337-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	108	601	0	ENST00000396334.3:c.681G>C	p.Lys227Asn	p.K227N	ENST00000396334	NM_002468.4	227	aaG/aaC	3/5	0.332009829553981	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.340202925592004	1		601	515	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927983	178927988	+	inframe_deletion	In_Frame_Del	DEL	CCATTG	CCATTG	-	novel	NA	P-0024337-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	45	361	0	ENST00000263967.3:c.1261_1266del	p.Pro421_Leu422del	p.P421_L422del	ENST00000263967	NM_006218.2	421	CCATTG/-	8/21	1	2	FACETS	0.962	0.814	1	0.962	0.814	1	CLONAL	1	TRUE	1	0.340202925592004	2		361	275	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0024365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	332	644	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.323004008600705	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	TRUE	0	0.376913176756703	3		644	685	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784000	120784000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	100	610	0	ENST00000257552.2:c.985G>A	p.Val329Ile	p.V329I	ENST00000257552	NM_002442.3	329	Gtc/Atc	13/15	0.149104055209074	2	FACETS	0.996	0.892	1	0.498	0.446	0.553	INDETERMINATE	1	TRUE	0	0.376913176756703	2		610	533	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758301	41758301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1352416510	NA	P-0024365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	66	613	0	ENST00000301178.4:c.1757C>T	p.Ala586Val	p.A586V	ENST00000301178	NM_021913.4	586	gCg/gTg	15/20	0.198175812434783	5	FACETS	0.945	0.821	1	0.315	0.273	0.36	INDETERMINATE	1	TRUE	2	0.376913176756703	5		613	580	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0024723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	89	585	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.614085840505371	2	FACETS	0.947	0.849	1	0.474	0.424	0.525	CLONAL	1	TRUE	0	0.614085840505371	2		585	306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578538	7578538	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1131691037	NA	P-0024723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	290	903	0	ENST00000269305.4:c.392A>T	p.Asn131Ile	p.N131I	ENST00000269305	NM_001126112.2	131	aAc/aTc	5/11	0.609983747673318	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.614085840505371	2		903	401	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983137	201983137	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1403955742	NA	P-0024723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	174	657	1	ENST00000359651.3:c.986T>C	p.Leu329Pro	p.L329P	ENST00000359651		329	cTg/cCg	7/8	0.614085840505371	3	FACETS	1	0.99	1	0.732	0.679	0.786	CLONAL	1	TRUE	1	0.614085840505371	3		658	506	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435125	18435125	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	41	459	1	ENST00000266497.5:c.110G>T	p.Ser37Ile	p.S37I	ENST00000266497		37	aGt/aTt	1/31	0.610488449306169	1	FACETS	0.984	0.85	1	0.984	0.85	1	CLONAL	1	TRUE	0	0.614085840505371	1		460	94	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113091	209113091	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0024723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	31	223	0	ENST00000345146.2:c.414+2T>A		p.X138_splice	ENST00000345146	NM_005896.2	138			0.342361027717887	6	FACETS	1	0.88	1	0.369	0.301	0.446	INDETERMINATE	1	TRUE	3	0.614085840505371	6		223	203	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430896	181430896	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	165	912	0	ENST00000325404.1:c.748T>G	p.Ser250Ala	p.S250A	ENST00000325404	NM_003106.3	250	Tcc/Gcc	1/1	0.614085840505371	7	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.614085840505371	7		912	936	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502249	186502249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	84	307	0	ENST00000323963.5:c.58C>T	p.Pro20Ser	p.P20S	ENST00000323963		20	Ccc/Tcc	2/11	0.614085840505371	7	FACETS	1	0.967	1			1	CLONAL	1	TRUE	NA	0.614085840505371	7		307	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0024726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	420	689	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.632634743677138	5	FACETS	1	0.994	1	0.874	0.85	0.897	CLONAL	4	TRUE	0	0.786065588666021	5		690	533	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274248	5274282	+	frameshift_variant	Frame_Shift_Del	DEL	TCCAGGTCACTCGTGGCTTGGGGTCACCCGTGGCC	TCCAGGTCACTCGTGGCTTGGGGTCACCCGTGGCC	-	novel	NA	P-0024726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	311	1045	0	ENST00000357368.4:c.165_199del	p.Ala56GlnfsTer12	p.A56Qfs*12	ENST00000357368	NM_002850.3	55	caGGCCACGGGTGACCCCAAGCCACGAGTGACCTGGAac/caac	3/38	0.662054183216503	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.786065588666021	3		1045	537	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252793	10252793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	183	720	0	ENST00000340748.4:c.3172G>A	p.Gly1058Ser	p.G1058S	ENST00000340748		1058	Ggc/Agc	29/40	0.662054183216503	3	FACETS	0.879	0.824	0.934	0.879	0.824	0.934	CLONAL	2	TRUE	1	0.786065588666021	3		720	369	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314919	1314919	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	28	528	0	ENST00000400841.2:c.742C>T	p.Leu248Phe	p.L248F	ENST00000400841		248	Ctt/Ttt	6/6	NA	2	FACETS	0.261	0.209	0.32			1	INDETERMINATE	1	TRUE	NA	0.786065588666021	2		528	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0024738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	142	629	3	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.0963396603285913	3	FACETS	1	0.944	1			1	INDETERMINATE	2	TRUE	NA	0.349832898334248	3		632	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578502	7578502	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	300	277	0	ENST00000269305.4:c.428T>C	p.Val143Ala	p.V143A	ENST00000269305	NM_001126112.2	143	gTg/gCg	5/11	0.650671342877531	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.65	1		277	453	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609003	43609003	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0024740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	118	70	0	ENST00000355710.3:c.1760-1G>T		p.X587_splice	ENST00000355710	NM_020975.4	587			0.650671342877531	5	FACETS	0.899	0.826	0.972			1	CLONAL	3	TRUE	NA	0.65	5		70	266	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409093	4409093	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	71	95	0	ENST00000261254.3:c.788A>G	p.Gln263Arg	p.Q263R	ENST00000261254	NM_001759.3	263	cAg/cGg	5/5	0.650671342877531	5	FACETS	0.7	0.611	0.796			1	SUBCLONAL	1	TRUE	NA	0.65	5		95	616	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913239	32913239	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs56072130	NA	P-0024740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	166	85	0	ENST00000380152.3:c.4747A>T	p.Ile1583Phe	p.I1583F	ENST00000380152		1583	Att/Ttt	11/27	0.579202391137171	4	FACETS	0.898	0.833	0.966	0.449	0.416	0.483	CLONAL	2	TRUE	0	0.65	4		85	469	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794428	242794428	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	198	151	0	ENST00000334409.5:c.514G>C	p.Gly172Arg	p.G172R	ENST00000334409	NM_005018.2	172	Ggt/Cgt	3/5	0.579202391137171	2	FACETS	1	0.992	1	0.73	0.686	0.775	CLONAL	1	TRUE	0	0.65	2		151	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0024870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	71	915	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.27	2		915	370	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250883	153250883	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	13	73	0	ENST00000281708.4:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000281708	NM_033632.3	393	Cga/Tga	8/12	1	2	FACETS	0.655	0.469	0.879	0.655	0.469	0.879	SUBCLONAL	1	TRUE	1	0.27	2		73	147	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0024971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	986	640	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.545180600616104	4	FACETS	1	0.997	1	1	0.997	1	CLONAL	4	TRUE	0	0.542420274315299	4		640	1264	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735497	40735497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1453093376	NA	P-0024971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	200	570	0	ENST00000373198.4:c.3376G>A	p.Glu1126Lys	p.E1126K	ENST00000373198	NM_133170.3	1126	Gaa/Aaa	25/32	0.396758134239821	5	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.542420274315299	5		570	1189	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861257	57861257	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	197	497	0	ENST00000228682.2:c.1054C>A	p.Gln352Lys	p.Q352K	ENST00000228682	NM_005269.2	352	Cag/Aag	9/12	0.545180600616104	4	FACETS	1	0.977	1	0.378	0.35	0.408	CLONAL	1	TRUE	1	0.542420274315299	4		497	987	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123889436	123889436	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	132	394	0	ENST00000330479.4:c.663C>A	p.Asp221Glu	p.D221E	ENST00000330479	NM_020382.3	221	gaC/gaA	7/9	0.420572214953984	4	FACETS	0.967	0.879	1	0.484	0.439	0.53	CLONAL	1	TRUE	2	0.542420274315299	4		394	776	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0025026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	241	513	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.739282093145852	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.739282093145852	1		513	395	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921567	178921567	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553821144	NA	P-0025026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	54	362	0	ENST00000263967.3:c.1049A>G	p.Asp350Gly	p.D350G	ENST00000263967	NM_006218.2	350	gAc/gGc	5/21	0.344927035056687	2	FACETS	0.667	0.577	0.763	0.334	0.288	0.382	INDETERMINATE	1	TRUE	0	0.739282093145852	2		362	219	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201277	133201287	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	GGCTGGCTAAT	GGCTGGCTAAT	-	novel	NA	P-0025026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	144	310	0	ENST00000320574.5:c.6857_*6del		p.*2286*	ENST00000320574	NM_006231.2	2286		49/49	0.437081607599552	1	FACETS	0.838	0.779	0.897	0.838	0.779	0.897	INDETERMINATE	1	TRUE	0	0.739282093145852	1		310	293	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968237	18968237	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	207	525	1	ENST00000262803.5:c.2077A>G	p.Ile693Val	p.I693V	ENST00000262803	NM_002911.3	693	Atc/Gtc	15/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.739282093145852	2		526	527	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891420	76891420	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	134	494	0	ENST00000373344.5:c.4685C>T	p.Pro1562Leu	p.P1562L	ENST00000373344	NM_000489.3	1562	cCc/cTc	16/35	0.739282093145852	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.739282093145852	1		494	207	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576865	7576866	+	stop_gained	Nonsense_Mutation	INS	-	-	TAT	novel	NA	P-0025946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	291	529	0	ENST00000269305.4:c.978_980dup	p.Glu326_Tyr327insTer	p.E326_Y327ins*	ENST00000269305	NM_001126112.2	327	tat/taATAt	9/11	0.684197640032018	1	FACETS	0.947	0.9	0.994	0.947	0.9	0.994	CLONAL	1	TRUE	0	0.684197640032018	1		529	591	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001159	150001159	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	202	469	0	ENST00000253339.5:c.2445del	p.Val816LeufsTer20	p.V816Lfs*20	ENST00000253339		815	gcA/gc	4/7	0.684197640032018	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.684197640032018	1		469	356	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410486	63410487	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	T	novel	NA	P-0025946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	268	560	0	ENST00000330258.3:c.2680_2681delinsA	p.Arg894ThrfsTer82	p.R894Tfs*82	ENST00000330258	NM_152424.3	894	CGc/Ac	2/2	1	2	FACETS	0.937	0.882	0.994	0.937	0.882	0.994	CLONAL	1	TRUE	1	0.684197640032018	2		560	836	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0025949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	225	744	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.61326979564202	2	FACETS	0.96	0.911	1	0.96	0.911	1	CLONAL	2	TRUE	0	0.61326979564202	2		744	382	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115284260	115284260	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0025949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	141	493	0	ENST00000438362.2:c.26C>G	p.Ser9Ter	p.S9*	ENST00000438362	NM_001242891.1	9	tCa/tGa	2/20	0.508579427954387	4	FACETS	0.918	0.845	0.993	0.918	0.845	0.993	CLONAL	2	TRUE	2	0.61326979564202	4		493	404	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035101	42035101	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	199	710	0	ENST00000219905.7:c.4943C>G	p.Ser1648Cys	p.S1648C	ENST00000219905	NM_001164273.1	1648	tCt/tGt	15/24	0.508579427954387	4	FACETS	0.995	0.93	1	0.995	0.93	1	CLONAL	2	TRUE	2	0.61326979564202	4		710	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	421	552	1	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.721375529789758	1	FACETS	0.99	0.951	1	0.99	0.951	1	CLONAL	1	TRUE	0	0.721375529789758	1		553	754	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0026943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	123	652	1	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	1	2	FACETS	0.958	0.865	1	0.958	0.865	1	CLONAL	1	TRUE	1	0.244818063468555	2		653	1049	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0026976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	169	459	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.562331430443145	2		459	539	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220443	1220443	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	225	606	0	ENST00000326873.7:c.536C>G	p.Pro179Arg	p.P179R	ENST00000326873	NM_000455.4	179	cCg/cGg	4/10	1	2	FACETS	0.941	0.879	1	0.941	0.879	1	CLONAL	1	TRUE	1	0.562331430443145	2		606	850	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880998	37880998	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs144434331	NA	P-0026976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	225	567	0	ENST00000269571.5:c.2327G>T	p.Gly776Val	p.G776V	ENST00000269571		776	gGt/gTt	20/27	1	2	FACETS	0.961	0.897	1	0.961	0.897	1	CLONAL	1	TRUE	1	0.562331430443145	2		567	833	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971053	21971053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137854598	NA	P-0026976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	143	421	0	ENST00000304494.5:c.305C>T	p.Ala102Val	p.A102V	ENST00000304494	NM_000077.4	102	gCg/gTg	2/3	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.562331430443145	2		421	461	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220633	1220633	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	219	665	0	ENST00000326873.7:c.652del	p.Ala218LeufsTer69	p.A218Lfs*69	ENST00000326873	NM_000455.4	217	ccG/cc	5/10	1	2	FACETS	0.9	0.839	0.964	0.9	0.839	0.964	CLONAL	1	TRUE	1	0.562331430443145	2		665	865	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482392	56482392	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	1633	512	2	ENST00000267101.3:c.940A>G	p.Lys314Glu	p.K314E	ENST00000267101	NM_001982.3	314	Aaa/Gaa	8/28	0.562331430443145	10	FACETS	0.953	0.938	0.967			1	CLONAL	9	TRUE	NA	0.562331430443145	10		514	2201	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774121	66774121	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	222	776	0	ENST00000307102.5:c.597C>G	p.Asn199Lys	p.N199K	ENST00000307102	NM_002755.3	199	aaC/aaG	6/11	0.278178646614878	3	FACETS	1	0.99	1	0.649	0.609	0.69	INDETERMINATE	1	TRUE	1	0.881473102259313	3		776	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577098	7577099	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0027262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	494	648	0	ENST00000269305.4:c.839_840delinsTT	p.Arg280Ile	p.R280I	ENST00000269305	NM_001126112.2	280	aGA/aTT	8/11	0.881473102259313	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.881473102259313	3		648	525	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246029	41246029	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	509	715	0	ENST00000357654.3:c.1519del	p.Arg507AspfsTer25	p.R507Dfs*25	ENST00000357654	NM_007294.3	507	Aga/ga	10/23	0.881473102259313	3	FACETS	0.999	0.983	1	0.999	0.983	1	CLONAL	3	TRUE	0	0.881473102259313	3		715	555	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651379	52651379	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	294	674	0	ENST00000394830.3:c.1717C>G	p.His573Asp	p.H573D	ENST00000394830	NM_018313.4	573	Cat/Gat	15/30	0.855552820054467	4	FACETS	0.93	0.881	0.978	0.62	0.587	0.652	CLONAL	2	TRUE	1	0.881473102259313	4		674	675	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0027959-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	57	937	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.469349626973465	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.469349626973465	1		937	146	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0027959-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	57	328	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.271553400850784	3	FACETS	0.815	0.712	0.923	0.815	0.712	0.923	INDETERMINATE	2	TRUE	1	0.469349626973465	3		328	184	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835596	68835596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587783047	NA	P-0027959-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	69	421	1	ENST00000261769.5:c.187C>T	p.Arg63Ter	p.R63*	ENST00000261769	NM_004360.3	63	Cga/Tga	3/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.469349626973465	2		422	231	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435201	18435202	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1565550462	NA	P-0027959-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	21	252	1	ENST00000266497.5:c.192dup	p.Val65CysfsTer16	p.V65Cfs*16	ENST00000266497		62	-/T	1/31	1	2	FACETS	0.639	0.497	0.801	0.639	0.497	0.801	SUBCLONAL	1	TRUE	1	0.469349626973465	2		253	140	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573430	48573430	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027959-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	21	151	0	ENST00000342988.3:c.14C>G	p.Ser5Cys	p.S5C	ENST00000342988	NM_005359.5	5	tCt/tGt	2/12	0.450192177844538	1	FACETS	0.978	0.777	1	0.978	0.777	1	CLONAL	1	TRUE	0	0.469349626973465	1		151	70	SUCCESS
APC	324	MSKCC	GRCh37	5	112177073	112177073	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027959-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	27	347	0	ENST00000257430.4:c.5782del	p.Gln1928ArgfsTer42	p.Q1928Rfs*42	ENST00000257430	NM_000038.5	1928	Cag/ag	16/16	0.271553400850784	3	FACETS	0.821	0.66	1	0.411	0.33	0.501	INDETERMINATE	1	TRUE	1	0.469349626973465	3		347	173	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430247	181430247	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027959-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	46	325	0	ENST00000325404.1:c.99C>A	p.Asn33Lys	p.N33K	ENST00000325404	NM_003106.3	33	aaC/aaA	1/1	0.271553400850784	3	FACETS	1	0.962	1	0.725	0.62	0.835	INDETERMINATE	1	TRUE	1	0.469349626973465	3		325	167	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528109	157528110	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0027959-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	88	503	0	ENST00000346085.5:c.5835dup	p.Ile1946HisfsTer9	p.I1946Hfs*9	ENST00000346085	NM_020732.3	1945	tgc/tgCc	20/20	0.469349626973465	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.469349626973465	2		503	177	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0028108-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	337	689	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.746095975897761	2	FACETS	0.957	0.923	0.99	0.957	0.923	0.99	CLONAL	2	TRUE	0	0.746095975897761	2		690	472	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0028108-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	111	346	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.746095975897761	3	FACETS	1	0.966	1	0.569	0.517	0.623	CLONAL	1	TRUE	1	0.746095975897761	3		346	359	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0028108-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	248	378	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.715957242744884	5	FACETS	0.892	0.837	0.948	0.594	0.558	0.632	CLONAL	2	TRUE	2	0.746095975897761	5		378	790	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604673	48604673	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060500738	NA	P-0028108-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	256	328	0	ENST00000342988.3:c.1495T>C	p.Cys499Arg	p.C499R	ENST00000342988	NM_005359.5	499	Tgc/Cgc	12/12	0.735813459144303	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.746095975897761	2		328	337	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453987	140453987	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs180177040	NA	P-0028108-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	67	227	0	ENST00000288602.6:c.1741A>C	p.Asn581His	p.N581H	ENST00000288602	NM_004333.4	581	Aat/Cat	14/18	0.746095975897761	3	FACETS	0.945	0.83	1	0.472	0.415	0.533	CLONAL	1	TRUE	1	0.746095975897761	3		227	261	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94922987	94922987	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028108-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	120	398	0	ENST00000536441.1:c.481C>A	p.Leu161Met	p.L161M	ENST00000536441	NM_144665.3	161	Ctg/Atg	4/10	0.746095975897761	2	FACETS	0.86	0.785	0.938	0.43	0.392	0.469	CLONAL	1	TRUE	0	0.746095975897761	2		398	374	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748584	40748584	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028108-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	114	465	0	ENST00000373198.4:c.2932G>A	p.Ala978Thr	p.A978T	ENST00000373198	NM_133170.3	978	Gcg/Acg	21/32	0.477779840986846	5	FACETS	0.947	0.854	1			1	CLONAL	1	TRUE	NA	0.746095975897761	5		465	684	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620600	52620600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028108-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	372	535	0	ENST00000394830.3:c.3153G>A	p.Trp1051Ter	p.W1051*	ENST00000394830	NM_018313.4	1051	tgG/tgA	21/30	0.735813459144303	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.746095975897761	2		535	497	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964505	93964505	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs770305987	NA	P-0028108-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	139	377	0	ENST00000369303.4:c.2392A>C	p.Ile798Leu	p.I798L	ENST00000369303	NM_004440.3	798	Att/Ctt	14/17	0.746095975897761	3	FACETS	0.98	0.897	1	0.49	0.448	0.533	CLONAL	1	TRUE	1	0.746095975897761	3		377	522	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939192	76939192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028108-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	183	314	0	ENST00000373344.5:c.1556C>T	p.Ser519Phe	p.S519F	ENST00000373344	NM_000489.3	519	tCt/tTt	9/35	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.746095975897761	1		314	251	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0028696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	404	890	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.782886421600948	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.794120868892601	2		893	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0028809-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	33	590	1	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	1	2	FACETS	0.459	0.374	0.554	0.459	0.374	0.554	SUBCLONAL	1	TRUE	1	0.41	2		591	351	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932045	39932045	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028809-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	27	724	0	ENST00000378444.4:c.2554T>G	p.Phe852Val	p.F852V	ENST00000378444	NM_001123385.1	852	Ttc/Gtc	4/15	1	2	FACETS	0.364	0.289	0.449	0.364	0.289	0.449	SUBCLONAL	1	TRUE	1	0.41	2		724	362	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024019	27024020	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	T	novel	NA	P-0028809-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	11	154	0	ENST00000324856.7:c.1125_1126delinsT	p.Arg376GlyfsTer15	p.R376Gfs*15	ENST00000324856	NM_006015.4	375	gcCCgg/gcTgg	1/20	1	2	FACETS	0.479	0.333	0.657	0.479	0.333	0.657	SUBCLONAL	1	TRUE	1	0.41	2		154	112	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375090	104375094	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGG	CGCGG	-	novel	NA	P-0029145-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	17	508	0	ENST00000369902.3:c.1089_1093del	p.Arg364AlafsTer2	p.R364Afs*2	ENST00000369902	NM_016169.3	363	aCGCGG/a	9/12	0.82666468029019	1	FACETS	0.287	0.218	0.365	0.287	0.218	0.365	SUBCLONAL	1	FALSE	0	0.82666468029019	1		508	84	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264373	46264373	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029145-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	63	337	0	ENST00000371998.3:c.1420G>T	p.Ala474Ser	p.A474S	ENST00000371998		474	Gcc/Tcc	11/23	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	FALSE	1	0.82666468029019	2		337	146	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0029267-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	283	644	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.795181052320775	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.787166345976471	1		644	356	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032279	10032279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029267-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	187	649	0	ENST00000330684.3:c.544G>A	p.Glu182Lys	p.E182K	ENST00000330684	NM_001134407.1	182	Gaa/Aaa	3/13	0.396366345381637	2	FACETS	1	0.974	1	0.541	0.506	0.577	INDETERMINATE	1	TRUE	0	0.787166345976471	2		649	439	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348076	348076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781377815	NA	P-0029267-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	266	819	1	ENST00000262320.3:c.1430G>A	p.Arg477His	p.R477H	ENST00000262320	NM_003502.3	477	cGt/cAt	6/11	0.181443122819862	5	FACETS	0.909	0.855	0.963			1	INDETERMINATE	2	TRUE	NA	0.787166345976471	5		820	811	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246091312	246091312	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029267-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	290	547	0	ENST00000388985.4:c.623G>T	p.Cys208Phe	p.C208F	ENST00000388985		208	tGt/tTt	7/12	NA	2	FACETS	0.791	0.756	0.824			1	INDETERMINATE	2	TRUE	NA	0.787166345976471	2		547	466	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988037	85988037	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs947096920	NA	P-0029267-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	32	236	0	ENST00000263360.6:c.982A>G	p.Ile328Val	p.I328V	ENST00000263360	NM_003797.3	328	Att/Gtt	10/12	0.587180865411115	4	FACETS	0.568	0.463	0.685	0.142	0.115	0.172	SUBCLONAL	1	TRUE	0	0.787166345976471	4		236	256	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133065	30133065	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029267-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	31	418	0	ENST00000331968.5:c.536G>A	p.Gly179Glu	p.G179E	ENST00000331968	NM_002742.2	179	gGg/gAg	4/18	0.482728186751619	1	FACETS	0.258	0.21	0.311	0.258	0.21	0.311	SUBCLONAL	1	TRUE	0	0.787166345976471	1		418	185	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590683	95590683	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029267-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	46	378	0	ENST00000393063.1:c.1226A>C	p.Tyr409Ser	p.Y409S	ENST00000393063	NM_030621.3	409	tAt/tCt	9/28	0.795181052320775	1	FACETS	0.627	0.544	0.712	0.627	0.544	0.712	SUBCLONAL	1	TRUE	0	0.787166345976471	1		378	113	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647653	2647653	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029267-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	150	596	0	ENST00000342085.4:c.1556C>G	p.Pro519Arg	p.P519R	ENST00000342085	NM_002613.4	519	cCt/cGt	14/14	0.396366345381637	2	FACETS	0.71	0.652	0.769	0.355	0.326	0.385	INDETERMINATE	1	TRUE	0	0.787166345976471	2		596	537	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598036	55598036	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0029267-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	24	388	0	ENST00000288135.5:c.2234-1G>T		p.X745_splice	ENST00000288135	NM_000222.2	745			0.260615748064169	1	FACETS	0.183	0.144	0.228	0.183	0.144	0.228	INDETERMINATE	1	TRUE	0	0.787166345976471	1		388	202	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534504	140534504	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029267-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	46	548	0	ENST00000288602.6:c.409G>C	p.Val137Leu	p.V137L	ENST00000288602	NM_004333.4	137	Gtt/Ctt	3/18	0.438276025161598	3	FACETS	0.371	0.313	0.435	0.124	0.104	0.145	INDETERMINATE	1	TRUE	0	0.787166345976471	3		548	439	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123011	5123011	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029267-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	26	354	0	ENST00000381652.3:c.3067C>T	p.Pro1023Ser	p.P1023S	ENST00000381652	NM_004972.3	1023	Cca/Tca	23/25	0.795181052320775	2	FACETS	0.342	0.273	0.421	0.171	0.136	0.211	SUBCLONAL	1	TRUE	0	0.787166345976471	2		354	193	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220611	123220611	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029267-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	62	464	0	ENST00000218089.9:c.3268C>G	p.Leu1090Val	p.L1090V	ENST00000218089	NM_001042749.1	1090	Ctt/Gtt	30/35	0.795181052320775	1	FACETS	0.406	0.355	0.461	0.406	0.355	0.461	SUBCLONAL	1	TRUE	0	0.787166345976471	1		464	235	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274734	123274734	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029327-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	233	580	0	ENST00000358487.5:c.1184T>A	p.Val395Asp	p.V395D	ENST00000358487	NM_000141.4	395	gTc/gAc	9/18	0.27620068405139	6	FACETS	0.99	0.933	1			1	CLONAL	5	TRUE	NA	0.27620068405139	6		580	529	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362446	40362447	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1202978138	NA	P-0029327-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	98	481	0	ENST00000293328.3:c.1749dup	p.His584ThrfsTer8	p.H584Tfs*8	ENST00000293328	NM_012448.3	583	-/A	14/19	0.27620068405139	4	FACETS	1	0.901	1	1	0.901	1	CLONAL	2	TRUE	2	0.27620068405139	4		481	451	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245350	41245350	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029327-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	41	651	0	ENST00000357654.3:c.2198A>G	p.Glu733Gly	p.E733G	ENST00000357654	NM_007294.3	733	gAg/gGg	10/23	0.27620068405139	4	FACETS	0.846	0.705	1	0.423	0.352	0.501	CLONAL	1	TRUE	2	0.27620068405139	4		651	448	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163641	32163641	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029327-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	77	440	0	ENST00000375023.3:c.5585G>T	p.Arg1862Leu	p.R1862L	ENST00000375023	NM_004557.3	1862	cGg/cTg	30/30	0.27620068405139	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.27620068405139	3		440	271	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390280	139390774	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	CAGAATAGATAAAAGTTTCTACCTGGGGCCAGATAAAACAGTACATATAAATAAAAAGGCAGTGTTTCTGTGTAAAATAAAAGTACATAAATAAATACTAAAAAAAATTAAAATCCTCGTTCTTATTTTGTATAAAAACATGTGTTTTAAAAAGGCTCCTCTGGTCGGCCCTGGCATCCACAGAGCGCACACAGACGCCCGAAGGCTTGGGAAAGGAAGCCGGGGTCTCGTGGGGCGCGCCGTTTACTTGAAGGCCTCCGGAATGCGGGCGATCTGGGACTGCATGCTGGTGGGAGGGCTGGAGACGCCCTCGGACCAGTCGGAGACGTTGGAATGCGGGGACGAGCTGGACCACTGGTCAGGGGACTCAGGGGACGGGGTGAGGAAGGGGTGCTCAGGCACCTGTAGCTGGTGGCTGGGGGTGTTGTCCACAGGCGAGGAGTAGCTGTGCTGCGAGGGGGGCGTCAGGAACTGGGCTGCGGTCACGGGTGGGAC	CAGAATAGATAAAAGTTTCTACCTGGGGCCAGATAAAACAGTACATATAAATAAAAAGGCAGTGTTTCTGTGTAAAATAAAAGTACATAAATAAATACTAAAAAAAATTAAAATCCTCGTTCTTATTTTGTATAAAAACATGTGTTTTAAAAAGGCTCCTCTGGTCGGCCCTGGCATCCACAGAGCGCACACAGACGCCCGAAGGCTTGGGAAAGGAAGCCGGGGTCTCGTGGGGCGCGCCGTTTACTTGAAGGCCTCCGGAATGCGGGCGATCTGGGACTGCATGCTGGTGGGAGGGCTGGAGACGCCCTCGGACCAGTCGGAGACGTTGGAATGCGGGGACGAGCTGGACCACTGGTCAGGGGACTCAGGGGACGGGGTGAGGAAGGGGTGCTCAGGCACCTGTAGCTGGTGGCTGGGGGTGTTGTCCACAGGCGAGGAGTAGCTGTGCTGCGAGGGGGGCGTCAGGAACTGGGCTGCGGTCACGGGTGGGAC	-	novel	NA	P-0029327-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	262	42	0	ENST00000277541.6:c.7417_*243del		p.*2473*	ENST00000277541	NM_017617.3	2473		34/34	0.27620068405139	7	FACETS	0.972	0.945	0.996	1	0.996	1	CLONAL	11	TRUE	1	0.27620068405139	7		42	300	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397717	139397717	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029327-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	225	723	0	ENST00000277541.6:c.5084G>T	p.Ser1695Ile	p.S1695I	ENST00000277541	NM_017617.3	1695	aGt/aTt	27/34	0.27620068405139	7	FACETS	1	0.981	1	0.744	0.697	0.791	CLONAL	4	TRUE	1	0.27620068405139	7		723	617	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399125	139399125	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029327-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	41	603	0	ENST00000277541.6:c.5018G>T	p.Gly1673Val	p.G1673V	ENST00000277541	NM_017617.3	1673	gGc/gTc	26/34	0.27620068405139	7	FACETS	0.96	0.799	1	0.16	0.133	0.19	CLONAL	1	TRUE	1	0.27620068405139	7		603	523	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505637	186505652	+	frameshift_variant	Frame_Shift_Del	DEL	GATCTACCTACCAATC	GATCTACCTACCAATC	-	novel	NA	P-0029327-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	14	264	0	ENST00000323963.5:c.1046_1061del	p.Asp349ValfsTer21	p.D349Vfs*21	ENST00000323963		349	GATCTACCTACCAATCgt/gt	10/11	0.27620068405139	4	FACETS	0.526	0.38	0.703	0.263	0.19	0.352	SUBCLONAL	1	TRUE	2	0.27620068405139	4		264	246	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382152	152382154	+	inframe_deletion	In_Frame_Del	DEL	TGG	TGG	-	novel	NA	P-0029736-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	135	287	0	ENST00000206249.3:c.1265_1267del	p.Val422del	p.V422del	ENST00000206249	NM_000125.3	421	aTGGtg/atg	6/8	0.650580440593713	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.652800612806037	1		287	259	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256715	16256721	+	frameshift_variant	Frame_Shift_Del	DEL	AACTATC	AACTATC	-	novel	NA	P-0029736-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	332	439	0	ENST00000375759.3:c.3980_3986del	p.Lys1327MetfsTer3	p.K1327Mfs*3	ENST00000375759	NM_015001.2	1327	aAACTATCt/at	11/15	1	2	FACETS	1	0.966	1	1	0.997	1	CLONAL	2	TRUE	1	0.652800612806037	2		439	506	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1040453	1040453	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029736-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	177	584	0	ENST00000358495.3:c.119A>T	p.Gln40Leu	p.Q40L	ENST00000358495	NM_134424.2	40	cAg/cTg	3/12	NA	2	FACETS	1	0.936	1			1	INDETERMINATE	1	TRUE	NA	0.652800612806037	2		584	537	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435402	110435402	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029736-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	133	447	0	ENST00000375856.3:c.2999G>C	p.Gly1000Ala	p.G1000A	ENST00000375856	NM_003749.2	1000	gGc/gCc	1/2	NA	2	FACETS	0.748	0.682	0.816			1	INDETERMINATE	1	TRUE	NA	0.652800612806037	2		447	545	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430870	181430870	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029736-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	200	670	0	ENST00000325404.1:c.722G>T	p.Gly241Val	p.G241V	ENST00000325404	NM_003106.3	241	gGt/gTt	1/1	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.652800612806037	2		670	592	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180640	56180643	+	frameshift_variant	Frame_Shift_Del	DEL	TGAA	TGAA	-	novel	NA	P-0029736-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	110	331	0	ENST00000399503.3:c.3971_3974del	p.Glu1324GlyfsTer11	p.E1324Gfs*11	ENST00000399503	NM_005921.1	1323	atTGAA/at	16/20	0.650580440593713	1	FACETS	0.887	0.812	0.963	0.887	0.812	0.963	CLONAL	1	TRUE	0	0.652800612806037	1		331	256	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589575	67589608	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAAAATTACATGAATATAACACTCAGTTTCAA	GAAAAAATTACATGAATATAACACTCAGTTTCAA	-	novel	NA	P-0029736-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	83	185	0	ENST00000274335.5:c.1345_1378del	p.Leu449ValfsTer20	p.L449Vfs*20	ENST00000274335		446	ggGAAAAAATTACATGAATATAACACTCAGTTTCAA/gg	10/15	0.650580440593713	1	FACETS	0.902	0.814	0.99	0.902	0.814	0.99	CLONAL	1	TRUE	0	0.652800612806037	1		185	190	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0029844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	288	517	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.864352923589639	2		517	608	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28901639	28901639	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	213	379	0	ENST00000282397.4:c.2756A>G	p.Asn919Ser	p.N919S	ENST00000282397	NM_002019.4	919	aAc/aGc	20/30	1	2	FACETS	0.966	0.907	1	0.966	0.907	1	CLONAL	1	TRUE	1	0.864352923589639	2		379	510	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057584	180057584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	338	576	0	ENST00000261937.6:c.371C>T	p.Thr124Met	p.T124M	ENST00000261937	NM_182925.4	124	aCg/aTg	3/30	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.864352923589639	2		576	773	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693007	89693008	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0029844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	239	305	0	ENST00000371953.3:c.492+1dup		p.K164fs	ENST00000371953	NM_000314.4	164	aag/aaGg	5/9	0.857755459417952	2	FACETS	0.967	0.935	0.996	0.967	0.935	0.996	CLONAL	2	TRUE	0	0.864352923589639	2		305	286	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252333	133252333	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	247	363	0	ENST00000320574.5:c.1094A>G	p.Asp365Gly	p.D365G	ENST00000320574	NM_006231.2	365	gAc/gGc	11/49	1	2	FACETS	0.967	0.912	1	0.967	0.912	1	CLONAL	1	TRUE	1	0.864352923589639	2		363	591	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281295	49281295	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	288	563	1	ENST00000282018.3:c.342G>C	p.Met114Ile	p.M114I	ENST00000282018	NM_020377.2	114	atG/atC	1/1	1	2	FACETS	0.995	0.942	1	0.995	0.942	1	CLONAL	1	TRUE	1	0.864352923589639	2		564	670	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785180	135786202	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACAGAACACTCAACTTTTAAAATTTTTTAGTTTTTATTGTTTTTAATGGAGAGAAGATGTCAGGGAAGAATGCAAGGCCTCTTGGGATAGGACACTTCAATGCCTGCCTTGATTCAGGCTAAGTTGCCACCATTTCACCCCCCGTCGTATTTGTGCCATCATTGCAGATGCCAATGCAGTGGGAAGGGCAAATGACAGCTTAGTGTTACTATGAAGGTGGGTTTGGTCAGGTGTGGTGGCTCAAACCTGTAATCCCAGGATTTTGGGAGGCCCAGGTAGGAGGATCGTTTGAGTCCAGGAGTTTAAGACTAGCCTGGGCAACATAGTGAGACCTCATCTCCACCAAAAAAAAAAAAAACTTAGCCAGGCATCATGGCACATGCCTGTAGTCCCAGCTACTAGCGAGGCTGATGCAGGAGGATTGCATGAGTCTGGGAGGTCAAGGCTGCAGTGAGCCATGATCGTGCCACTGCACTCCACCCTGGGCGACAGAGCAAGACCCTGTCTCCAAAAAAAAAAAAAAAAAAAAAATCAAGAGAGTAGGTTTGACCTGCTGGGTTCCCCACAAGAGTTCTGCCAAAGCAGAGTTTTGGAACCACCCAGGGGTCGGCAGATCACACCTTGAGAGCAGCTTGTTAGTCCATTTTCAATTATTCTGATTCAAACCCATTGCATTTTAGGTCAGAATTCTATCTGGCATAATTAGGCTTCTCAAAGTGAGGCTTGCAAGTGAGTCACTGTGCCTGGGCAGAGGGATAGCAGACGAGCTGGATCGCACCTTCCTGGGGGGTGTGACTGTGGCCTGGGGGAGTGAAATGTGCACGTAGTCATCCGAATGACAGAGTGGGGCTGGAGGAGGAGAGGTTGCTGGGGTTCCCAGAGGAGTTCCTTTTCCACCTGCTTAGAGACAAGGGCAGAACATATATGAACACTGAGCCCAACTATTAGAAAAACTGCCGATTTTTTTTCAGCCTATAACTATTACTATAAATAAAGCTGCTAGAGTTAACTTTCTGGGGATCT	ACAGAACACTCAACTTTTAAAATTTTTTAGTTTTTATTGTTTTTAATGGAGAGAAGATGTCAGGGAAGAATGCAAGGCCTCTTGGGATAGGACACTTCAATGCCTGCCTTGATTCAGGCTAAGTTGCCACCATTTCACCCCCCGTCGTATTTGTGCCATCATTGCAGATGCCAATGCAGTGGGAAGGGCAAATGACAGCTTAGTGTTACTATGAAGGTGGGTTTGGTCAGGTGTGGTGGCTCAAACCTGTAATCCCAGGATTTTGGGAGGCCCAGGTAGGAGGATCGTTTGAGTCCAGGAGTTTAAGACTAGCCTGGGCAACATAGTGAGACCTCATCTCCACCAAAAAAAAAAAAAACTTAGCCAGGCATCATGGCACATGCCTGTAGTCCCAGCTACTAGCGAGGCTGATGCAGGAGGATTGCATGAGTCTGGGAGGTCAAGGCTGCAGTGAGCCATGATCGTGCCACTGCACTCCACCCTGGGCGACAGAGCAAGACCCTGTCTCCAAAAAAAAAAAAAAAAAAAAAATCAAGAGAGTAGGTTTGACCTGCTGGGTTCCCCACAAGAGTTCTGCCAAAGCAGAGTTTTGGAACCACCCAGGGGTCGGCAGATCACACCTTGAGAGCAGCTTGTTAGTCCATTTTCAATTATTCTGATTCAAACCCATTGCATTTTAGGTCAGAATTCTATCTGGCATAATTAGGCTTCTCAAAGTGAGGCTTGCAAGTGAGTCACTGTGCCTGGGCAGAGGGATAGCAGACGAGCTGGATCGCACCTTCCTGGGGGGTGTGACTGTGGCCTGGGGGAGTGAAATGTGCACGTAGTCATCCGAATGACAGAGTGGGGCTGGAGGAGGAGAGGTTGCTGGGGTTCCCAGAGGAGTTCCTTTTCCACCTGCTTAGAGACAAGGGCAGAACATATATGAACACTGAGCCCAACTATTAGAAAAACTGCCGATTTTTTTTCAGCCTATAACTATTACTATAAATAAAGCTGCTAGAGTTAACTTTCTGGGGATCT	-	novel	NA	P-0029844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3	147	0	0	ENST00000298552.3:c.1142-122_1263+779del		p.X381_splice	ENST00000298552	NM_001162426.1	381		12/23	1	2	FACETS	1	0.994	1	1	0.995	1	CLONAL	2	TRUE	1	0.864352923589639	2		0	150	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0029844-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	235	314	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.445273523793856	3	FACETS	0.809	0.76	0.86	0.809	0.76	0.86	CLONAL	2	TRUE	1	0.58669186936008	3		314	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578238	7578255	+	inframe_deletion	In_Frame_Del	DEL	TCCACACGCAAATTTCCT	TCCACACGCAAATTTCCT	-	rs1567551704	NA	P-0029844-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	375	828	1	ENST00000269305.4:c.594_611del	p.Gly199_Glu204del	p.G199_E204del	ENST00000269305	NM_001126112.2	198	gaAGGAAATTTGCGTGTGGAg/gag	6/11	0.58669186936008	2	FACETS	0.946	0.907	0.984	0.946	0.907	0.984	CLONAL	2	TRUE	0	0.58669186936008	2		829	676	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519938	NA	P-0029844-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	240	394	0	ENST00000263967.3:c.1034A>C	p.Asn345Thr	p.N345T	ENST00000263967	NM_006218.2	345	aAt/aCt	5/21	0.58669186936008	3	FACETS	0.971	0.915	1	0.971	0.915	1	CLONAL	2	TRUE	1	0.58669186936008	3		394	545	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214058	36214058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1385766471	NA	P-0029844-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	521	928	1	ENST00000222270.7:c.2884C>T	p.Arg962Cys	p.R962C	ENST00000222270	NM_014727.1	962	Cgc/Tgc	6/37	0.353124045521736	5	FACETS	0.907	0.871	0.943	0.907	0.871	0.943	CLONAL	3	TRUE	2	0.58669186936008	5		929	1227	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056336	27056336	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029844-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	237	526	1	ENST00000324856.7:c.1333del	p.Leu445SerfsTer174	p.L445Sfs*174	ENST00000324856	NM_006015.4	444	ggC/gg	2/20	0.570098956611347	3	FACETS	0.986	0.929	1	0.986	0.929	1	CLONAL	2	TRUE	1	0.58669186936008	3		527	530	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039405	49039406	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029844-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	384	708	0	ENST00000267163.4:c.2391dup	p.Arg798ThrfsTer17	p.R798Tfs*17	ENST00000267163	NM_000321.2	797	tta/ttAa	23/27	0.58669186936008	2	FACETS	0.981	0.942	1	0.981	0.942	1	CLONAL	2	TRUE	0	0.58669186936008	2		708	667	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220388	1220389	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029844-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	397	826	1	ENST00000326873.7:c.483dup	p.Asp162Ter	p.D162*	ENST00000326873	NM_000455.4	161	att/aTtt	4/10	0.58669186936008	2	FACETS	0.957	0.919	0.995	0.957	0.919	0.995	CLONAL	2	TRUE	0	0.58669186936008	2		827	707	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221340	36221340	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029844-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	464	816	0	ENST00000222270.7:c.5174C>T	p.Pro1725Leu	p.P1725L	ENST00000222270	NM_014727.1	1725	cCc/cTc	24/37	0.353124045521736	5	FACETS	1	0.994	1	0.804	0.769	0.839	CLONAL	2	TRUE	2	0.58669186936008	5		816	1233	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217329	11217329	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030397-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	42	710	0	ENST00000361445.4:c.4349A>G	p.Tyr1450Cys	p.Y1450C	ENST00000361445	NM_004958.3	1450	tAt/tGt	30/58	1	2	FACETS	0.426	0.359	0.499	0.426	0.359	0.499	SUBCLONAL	1	TRUE	1	0.907962643392396	2		710	217	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660732	227660732	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030397-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	140	897	0	ENST00000305123.5:c.2723A>T	p.Tyr908Phe	p.Y908F	ENST00000305123	NM_005544.2	908	tAc/tTc	1/2	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.907962643392396	2		897	288	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0030569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	168	890	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.485563110890255	2	FACETS	0.846	0.788	0.904	0.846	0.788	0.904	CLONAL	2	TRUE	0	0.515966218699541	2		893	385	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964430	55964430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564385300	NA	P-0030569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	52	353	0	ENST00000263923.4:c.2383G>A	p.Gly795Arg	p.G795R	ENST00000263923	NM_002253.2	795	Ggg/Agg	17/30	0.21220845674678	3	FACETS	0.829	0.71	0.957	0.276	0.236	0.319	INDETERMINATE	1	TRUE	0	0.515966218699541	3		353	306	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111102	193111102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	51	284	0	ENST00000367435.3:c.635G>A	p.Ser212Asn	p.S212N	ENST00000367435	NM_024529.4	212	aGt/aAt	7/17	0.455923327985343	3	FACETS	0.78	0.666	0.903	0.39	0.333	0.452	CLONAL	1	TRUE	1	0.515966218699541	3		284	319	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858234	9858234	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1221693782	NA	P-0030569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	62	368	0	ENST00000330684.3:c.3167T>C	p.Met1056Thr	p.M1056T	ENST00000330684	NM_001134407.1	1056	aTg/aCg	13/13	0.49147092737319	1	FACETS	0.878	0.771	0.991	0.878	0.771	0.991	CLONAL	1	TRUE	0	0.515966218699541	1		368	203	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127389	55127389	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	61	520	0	ENST00000257290.5:c.180del	p.Met61CysfsTer22	p.M61Cfs*22	ENST00000257290	NM_006206.4	59	taC/ta	3/23	0.21220845674678	3	FACETS	0.715	0.619	0.819	0.238	0.206	0.273	INDETERMINATE	1	TRUE	0	0.515966218699541	3		520	416	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056292	26056292	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	88	391	0	ENST00000343677.2:c.365A>G	p.Lys122Arg	p.K122R	ENST00000343677	NM_005319.3	122	aAg/aGg	1/1	0.515966218699541	3	FACETS	0.954	0.849	1	0.477	0.424	0.532	CLONAL	1	TRUE	1	0.515966218699541	3		391	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578259	7578259	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	512	742	0	ENST00000269305.4:c.590T>G	p.Val197Gly	p.V197G	ENST00000269305	NM_001126112.2	197	gTg/gGg	6/11	0.810074112170579	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	FALSE	0	0.810074112170579	3		742	584	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012392	176012392	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	258	392	0	ENST00000367669.3:c.1542G>T	p.Lys514Asn	p.K514N	ENST00000367669	NM_022457.5	514	aaG/aaT	14/20	0.589443508812035	6	FACETS	0.925	0.88	0.97	0.925	0.88	0.97	CLONAL	4	FALSE	2	0.810074112170579	6		392	451	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56862985	56863000	+	frameshift_variant	Frame_Shift_Del	DEL	GAACATTAAACTGCCA	GAACATTAAACTGCCA	-	novel	NA	P-0030836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	79	498	0	ENST00000308159.5:c.892_907del	p.Asn298LeufsTer19	p.N298Lfs*19	ENST00000308159	NM_014669.4	297	ctGAACATTAAACTGCCA/ct	9/22	0.810074112170579	3	FACETS	0.597	0.527	0.672	0.299	0.263	0.336	SUBCLONAL	1	FALSE	1	0.810074112170579	3		498	459	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805555	1805555	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	136	574	1	ENST00000260795.2:c.1067T>C	p.Val356Ala	p.V356A	ENST00000260795		356	gTg/gCg	7/17	0.810074112170579	3	FACETS	0.92	0.841	1	0.46	0.42	0.501	CLONAL	1	FALSE	1	0.810074112170579	3		575	513	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	71	422	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.393856178717952	2		422	340	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610405	10610405	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	90	637	0	ENST00000171111.5:c.305C>A	p.Ser102Ter	p.S102*	ENST00000171111	NM_203500.1	102	tCa/tAa	2/6	0.388558398051028	1	FACETS	0.882	0.787	0.982	0.882	0.787	0.982	CLONAL	1	TRUE	0	0.393856178717952	1		637	416	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178655	108178656	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587781730	NA	P-0031437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	50	274	0	ENST00000278616.4:c.5712dup	p.Ser1905IlefsTer25	p.S1905Ifs*25	ENST00000278616	NM_000051.3	1902	-/A	38/63	0.302120361187848	2	FACETS	1	0.941	1	0.596	0.512	0.686	CLONAL	1	TRUE	0	0.393856178717952	2		274	213	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0032261-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	679	635	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.562971300319799	4	FACETS	0.881	0.855	0.907	0.881	0.855	0.907	CLONAL	3	TRUE	1	0.783716645311921	4		635	1169	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0032261-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	590	593	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.772374870740227	2	FACETS	0.975	0.951	0.998	0.975	0.951	0.998	CLONAL	2	TRUE	0	0.783716645311921	2		593	772	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260241	10260241	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555690467	NA	P-0032261-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	112	706	1	ENST00000340748.4:c.2426C>T	p.Ser809Leu	p.S809L	ENST00000340748		809	tCg/tTg	25/40	0.783716645311921	2	FACETS	0.314	0.282	0.349	0.157	0.141	0.175	SUBCLONAL	1	TRUE	0	0.783716645311921	2		707	909	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829665	72829665	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032261-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1229	328	674	0	ENST00000268489.5:c.6916G>A	p.Glu2306Lys	p.E2306K	ENST00000268489	NM_006885.3	2306	Gag/Aag	9/10	0.783716645311921	4	FACETS	0.959	0.904	1	0.32	0.301	0.339	CLONAL	1	TRUE	1	0.783716645311921	4		674	1557	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757393	40757393	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0032261-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	398	602	0	ENST00000373198.4:c.2904+1G>C		p.X968_splice	ENST00000373198	NM_133170.3	968			0.54561128402029	5	FACETS	0.961	0.915	1	0.64	0.61	0.672	CLONAL	2	TRUE	2	0.783716645311921	5		602	1150	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0032525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	543	797	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.495299144896212	4	FACETS	0.92	0.891	0.948	0.92	0.891	0.948	CLONAL	4	TRUE	0	0.531939108983398	4		797	850	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1272334	1272334	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	73	781	0	ENST00000310581.5:c.2348C>G	p.Thr783Ser	p.T783S	ENST00000310581	NM_198253.2	783	aCc/aGc	7/16	0.483010629345846	2	FACETS	0.711	0.625	0.803	0.356	0.312	0.402	SUBCLONAL	1	TRUE	0	0.531939108983398	2		781	386	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0032659-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	509	620	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.855254457064844	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.855254457064844	2		620	562	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0032659-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	352	186	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	2	TRUE	NA	0.855254457064844	2		186	408	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069097	5069099	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs1371743120	NA	P-0032659-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	174	200	0	ENST00000381652.3:c.1407_1409del	p.Lys469del	p.K469del	ENST00000381652	NM_004972.3	468	AAG/-	11/25	0.855254457064844	2	FACETS	0.976	0.909	1	0.488	0.454	0.522	CLONAL	1	TRUE	0	0.855254457064844	2		200	417	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168953	11168953	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032659-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	451	242	0	ENST00000358026.2:c.4543G>T	p.Glu1515Ter	p.E1515*	ENST00000358026	NM_001128849.1	1515	Gag/Tag	32/36	0.855254457064844	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.855254457064844	2		242	514	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	64	632	1	ENST00000394830.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000394830	NM_018313.4	710	Cga/Tga	17/30	0.286167333272364	1	FACETS	0.743	0.644	0.85	0.743	0.644	0.85	SUBCLONAL	1	TRUE	0	0.286167333272364	1		633	516	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0032999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	65	483	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.894	0.777	1	0.894	0.777	1	CLONAL	1	TRUE	1	0.286167333272364	2		483	508	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0032999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	78	396	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.286167333272364	2		396	498	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105574	27105585	+	frameshift_variant	Frame_Shift_Del	DEL	GGCATTTTAAAG	GGCATTTTAAAG	T	novel	NA	P-0032999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	56	535	0	ENST00000324856.7:c.5185_5196delinsT	p.Gly1729Ter	p.G1729*	ENST00000324856	NM_006015.4	1729	GGCATTTTAAAG/T	20/20	0.286167333272364	0	FACETS	0.659	0.566	0.76			1	SUBCLONAL	1	TRUE	0	0.286167333272364	0		535	424	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0033322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	415	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.738069644657144	5	FACETS	0.996	0.95	1	0.664	0.633	0.696	CLONAL	2	TRUE	2	0.738069644657144	5		622	1189	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	171	557	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.620720583074368	4	FACETS	0.936	0.862	1	0.468	0.431	0.507	CLONAL	1	TRUE	2	0.738069644657144	4		557	860	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019279	31019279	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	151	411	0	ENST00000375687.4:c.874G>C	p.Asp292His	p.D292H	ENST00000375687	NM_015338.5	292	Gac/Cac	9/13	0.675480531744497	3	FACETS	0.981	0.901	1	0.491	0.45	0.532	CLONAL	1	TRUE	1	0.738069644657144	3		411	571	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134479	30134479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	180	406	0	ENST00000263025.4:c.52G>A	p.Glu18Lys	p.E18K	ENST00000263025	NM_002746.2	18	Gag/Aag	1/9	0.703469323265683	4	FACETS	1	0.968	1	0.544	0.503	0.587	CLONAL	1	TRUE	2	0.738069644657144	4		406	779	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845926	72845926	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	136	463	3	ENST00000268489.5:c.3541C>T	p.Gln1181Ter	p.Q1181*	ENST00000268489	NM_006885.3	1181	Caa/Taa	6/10	0.675480531744497	3	FACETS	0.997	0.912	1	0.499	0.456	0.543	CLONAL	1	TRUE	1	0.738069644657144	3		466	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0034519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	584	644	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.413946447204677	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	4	TRUE	0	0.437570257252039	4		646	915	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034519-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	118	115	0				ENST00000310581	NM_198253.2	-/1132			0.437570257252039	3	FACETS	0.981	0.896	1	0.981	0.896	1	CLONAL	2	TRUE	1	0.437570257252039	3		115	335	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034906-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	67	115	0				ENST00000310581	NM_198253.2	-/1132			0.765373855993054	7	FACETS	0.627	0.543	0.717	0.104	0.09	0.12	SUBCLONAL	1	TRUE	1	0.765373855993054	7		115	814	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0034906-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	112	629	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.680497315070928	1	FACETS	0.769	0.707	0.831	0.769	0.707	0.831	SUBCLONAL	1	TRUE	0	0.765373855993054	1		630	235	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013691	12013691	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0034906-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	54	349	0	ENST00000353533.5:c.634-1G>C		p.X212_splice	ENST00000353533	NM_003010.3	212			0.680497315070928	1	FACETS	0.822	0.729	0.914	0.822	0.729	0.914	CLONAL	1	TRUE	0	0.765373855993054	1		349	106	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785992	135785992	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0034906-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	144	675	0	ENST00000298552.3:c.1229C>G	p.Ser410Ter	p.S410*	ENST00000298552	NM_001162426.1	410	tCa/tGa	12/23	0.765373855993054	1	FACETS	0.922	0.862	0.981	0.922	0.862	0.981	CLONAL	1	TRUE	0	0.765373855993054	1		675	252	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983140	201983141	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034906-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	175	530	0	ENST00000359651.3:c.991dup	p.Arg331ProfsTer140	p.R331Pfs*140	ENST00000359651		330	agc/agCc	7/8	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.765373855993054	2		530	451	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288499	15288499	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393495970	NA	P-0034906-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	92	234	1	ENST00000263388.2:c.4240G>A	p.Gly1414Ser	p.G1414S	ENST00000263388	NM_000435.2	1414	Ggc/Agc	24/33	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.765373855993054	2		235	222	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249029	55249029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs483352806	NA	P-0034906-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	9	669	3	ENST00000275493.2:c.2327G>A	p.Arg776His	p.R776H	ENST00000275493	NM_005228.3	776	cGc/cAc	20/28	1	2	FACETS	0.054	0.035	0.079	0.054	0.035	0.079	SUBCLONAL	1	TRUE	1	0.765373855993054	2		672	432	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264275	30264275	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034906-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	14	67	0	ENST00000322652.5:c.10C>G	p.Gln4Glu	p.Q4E	ENST00000322652	NM_015355.2	4	Cag/Gag	1/16	0.765373855993054	3	FACETS	0.581	0.427	0.762	0.291	0.213	0.381	SUBCLONAL	1	TRUE	1	0.765373855993054	3		67	87	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151947965	151947965	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1205516959	NA	P-0034906-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	17	501	0	ENST00000262189.6:c.1708G>C	p.Glu570Gln	p.E570Q	ENST00000262189	NM_170606.2	570	Gag/Cag	12/59	1	2	FACETS	0.152	0.113	0.198	0.152	0.113	0.198	SUBCLONAL	1	TRUE	1	0.765373855993054	2		501	293	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034906-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	43	115	0				ENST00000310581	NM_198253.2	-/1132			0.634162904634076	7	FACETS	0.708	0.593	0.837	0.118	0.098	0.14	SUBCLONAL	1	FALSE	1	0.634162904634076	7		115	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0034906-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	48	629	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.557764726447344	1	FACETS	0.591	0.507	0.679	0.591	0.507	0.679	SUBCLONAL	1	FALSE	0	0.634162904634076	1		630	175	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013691	12013691	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0034906-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	29	349	0	ENST00000353533.5:c.634-1G>C		p.X212_splice	ENST00000353533	NM_003010.3	212			0.557764726447344	1	FACETS	0.664	0.548	0.789	0.664	0.548	0.789	SUBCLONAL	1	FALSE	0	0.634162904634076	1		349	94	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785992	135785992	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0034906-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	126	675	0	ENST00000298552.3:c.1229C>G	p.Ser410Ter	p.S410*	ENST00000298552	NM_001162426.1	410	tCa/tGa	12/23	0.622823348625791	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	0	0.634162904634076	1		675	252	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242035	105242035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034906-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	16	1046	2	ENST00000349310.3:c.389G>A	p.Gly130Glu	p.G130E	ENST00000349310	NM_001014432.1	130	gGg/gAg	6/15	0.557764726447344	1	FACETS	0.125	0.092	0.164	0.125	0.092	0.164	SUBCLONAL	1	FALSE	0	0.634162904634076	1		1048	276	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983140	201983141	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034906-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	100	530	0	ENST00000359651.3:c.991dup	p.Arg331ProfsTer140	p.R331Pfs*140	ENST00000359651		330	agc/agCc	7/8	1	2	FACETS	0.928	0.837	1	0.928	0.837	1	CLONAL	1	FALSE	1	0.634162904634076	2		530	340	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288499	15288499	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393495970	NA	P-0034906-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	37	234	1	ENST00000263388.2:c.4240G>A	p.Gly1414Ser	p.G1414S	ENST00000263388	NM_000435.2	1414	Ggc/Agc	24/33	1	2	FACETS	0.663	0.553	0.782	0.663	0.553	0.782	SUBCLONAL	1	FALSE	1	0.634162904634076	2		235	176	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907255	32907255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80358449	NA	P-0034906-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	12	495	0	ENST00000380152.3:c.1640C>T	p.Ser547Leu	p.S547L	ENST00000380152		547	tCa/tTa	10/27	1	2	FACETS	0.263	0.185	0.357	0.263	0.185	0.357	SUBCLONAL	1	FALSE	1	0.634162904634076	2		495	144	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246388	41246388	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034906-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	17	736	0	ENST00000357654.3:c.1160C>A	p.Ser387Tyr	p.S387Y	ENST00000357654	NM_007294.3	387	tCc/tAc	10/23	0.634162904634076	3	FACETS	0.26	0.193	0.338	0.13	0.096	0.169	SUBCLONAL	1	FALSE	1	0.634162904634076	3		736	272	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217270	66217270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457386561	NA	P-0034906-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	11	395	0	ENST00000273854.3:c.2345G>A	p.Arg782Lys	p.R782K	ENST00000273854	NM_004439.5	782	aGa/aAa	14/18	0.557764726447344	1	FACETS	0.275	0.192	0.376	0.275	0.192	0.376	SUBCLONAL	1	FALSE	0	0.634162904634076	1		395	86	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0034995-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	210	915	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.282553619298557	2	FACETS	0.924	0.863	0.987	0.924	0.863	0.987	CLONAL	2	TRUE	0	0.358895209474577	2		915	633	SUCCESS
BLM	641	MSKCC	GRCh37	15	91290672	91290672	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0034995-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	1212	290	0	ENST00000355112.3:c.50C>G	p.Ser17Ter	p.S17*	ENST00000355112	NM_000057.2	17	tCa/tGa	2/22	1	2	FACETS	0.99	0.972	1			1	CLONAL	4	TRUE	1	0.358895209474577	2		290	1705	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0035774-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	301	591	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.464365746264308	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.478314638027655	2		591	575	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936995	48936995	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778842	NA	P-0035774-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	164	276	0	ENST00000267163.4:c.763C>T	p.Arg255Ter	p.R255*	ENST00000267163	NM_000321.2	255	Cga/Tga	8/27	0.344148799374945	3	FACETS	1	0.974	1	0.734	0.682	0.786	CLONAL	2	TRUE	0	0.478314638027655	3		276	386	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909232	41909232	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035774-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	134	639	1	ENST00000372991.4:c.156C>G	p.Ile52Met	p.I52M	ENST00000372991	NM_001760.3	52	atC/atG	1/5	0.334996366466838	5	FACETS	1	0.984	1	0.279	0.254	0.305	CLONAL	1	TRUE	0	0.478314638027655	5		640	690	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367346	50367346	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035774-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	68	378	0	ENST00000331340.3:c.153A>T	p.Arg51Ser	p.R51S	ENST00000331340	NM_006060.4	51	agA/agT	3/8	0.478314638027655	5	FACETS	1	0.913	1	0.353	0.308	0.402	CLONAL	1	TRUE	2	0.478314638027655	5		378	461	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556370	29556370	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035774-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	129	438	0	ENST00000356175.3:c.2737A>G	p.Ile913Val	p.I913V	ENST00000356175	NM_000267.3	913	Ata/Gta	21/57	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.478314638027655	2		438	535	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411887	116411888	+	intron_variant	Intron	INS	-	-	AG	novel	NA	P-0035774-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	490	830	0	ENST00000397752.3:c.2888-16_2888-15insAG		p.*963*	ENST00000397752	NM_000245.2	-/1390			0.37615104569771	3	FACETS	1	0.994	1	0.804	0.772	0.835	CLONAL	2	TRUE	0	0.478314638027655	3		830	1053	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108025	30108025	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs921106234	NA	P-0035774-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	135	532	0	ENST00000331968.5:c.782A>G	p.Lys261Arg	p.K261R	ENST00000331968	NM_002742.2	261	aAg/aGg	5/18	0.148401734300619	3	FACETS	1	0.967	1	0.561	0.512	0.613	INDETERMINATE	1	TRUE	1	0.478314638027655	3		532	623	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38194897	38194897	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035774-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	174	625	0	ENST00000317025.8:c.836G>T	p.Gly279Val	p.G279V	ENST00000317025	NM_023034.1	279	gGa/gTa	4/24	0.464365746264308	2	FACETS	0.999	0.922	1	0.5	0.461	0.54	CLONAL	1	TRUE	0	0.478314638027655	2		625	728	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38194906	38194906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035774-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	170	616	0	ENST00000317025.8:c.827C>T	p.Ser276Phe	p.S276F	ENST00000317025	NM_023034.1	276	tCc/tTc	4/24	0.464365746264308	2	FACETS	1	0.929	1	0.504	0.465	0.545	CLONAL	1	TRUE	0	0.478314638027655	2		616	705	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0036677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	358	406	0	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.697320127498647	1		406	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs786201838	NA	P-0036677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	235	718	0	ENST00000269305.4:c.578A>C	p.His193Pro	p.H193P	ENST00000269305	NM_001126112.2	193	cAt/cCt	6/11	0.697320127498647	1	FACETS	0.934	0.883	0.985	0.934	0.883	0.985	CLONAL	1	TRUE	0	0.697320127498647	1		718	470	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434795	49434795	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	330	782	0	ENST00000301067.7:c.6758A>G	p.Asp2253Gly	p.D2253G	ENST00000301067	NM_003482.3	2253	gAt/gGt	31/54	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.697320127498647	2		782	917	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821152	72821152	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	237	563	0	ENST00000268489.5:c.11023C>G	p.Pro3675Ala	p.P3675A	ENST00000268489	NM_006885.3	3675	Ccg/Gcg	10/10	1	2	FACETS	0.897	0.84	0.955	0.897	0.84	0.955	CLONAL	1	TRUE	1	0.697320127498647	2		563	758	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553203	106553203	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	202	593	0	ENST00000369096.4:c.1168C>A	p.Pro390Thr	p.P390T	ENST00000369096	NM_001198.3	390	Cct/Act	5/7	1	2	FACETS	0.954	0.89	1	0.954	0.89	1	CLONAL	1	TRUE	1	0.697320127498647	2		593	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0036869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	492	700	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.772997304795861	2	FACETS	0.912	0.887	0.937	0.912	0.887	0.937	CLONAL	2	TRUE	0	0.822043652558528	2		700	656	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120789171	120789171	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	162	388	0	ENST00000257552.2:c.766G>T	p.Ala256Ser	p.A256S	ENST00000257552	NM_002442.3	256	Gcc/Tcc	11/15	1	2	FACETS	0.952	0.883	1	0.952	0.883	1	CLONAL	1	TRUE	1	0.822043652558528	2		388	414	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864585	37864585	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	134	464	0	ENST00000269571.5:c.237G>C	p.Glu79Asp	p.E79D	ENST00000269571		79	gaG/gaC	3/27	0.822043652558528	2	FACETS	0.605	0.552	0.66	0.302	0.276	0.33	SUBCLONAL	1	TRUE	0	0.822043652558528	2		464	539	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967783	18967783	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	243	744	0	ENST00000262803.5:c.1922C>G	p.Ala641Gly	p.A641G	ENST00000262803	NM_002911.3	641	gCc/gGc	14/24	0.393121540906237	4	FACETS	1	0.937	1	0.501	0.468	0.536	INDETERMINATE	1	TRUE	2	0.822043652558528	4		744	1074	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127321	55127321	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0036869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	152	493	0	ENST00000257290.5:c.109A>T	p.Lys37Ter	p.K37*	ENST00000257290	NM_006206.4	37	Aag/Tag	3/23	0.353081829165515	3	FACETS	1	0.959	1	0.354	0.326	0.383	INDETERMINATE	1	TRUE	0	0.822043652558528	3		493	491	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0037253-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	634	314	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.876298268280133	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.876298268280133	2		314	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0037253-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	973	774	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.876298268280133	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.876298268280133	2		776	1065	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953760	48953760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913302	NA	P-0037253-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	207	180	0	ENST00000267163.4:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000267163	NM_000321.2	455	Cga/Tga	14/27	0.876298268280133	2	FACETS	0.993	0.961	1	0.993	0.961	1	CLONAL	2	TRUE	0	0.876298268280133	2		180	238	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38954953	38954953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037253-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	46	230	1	ENST00000357387.3:c.2620C>T	p.Pro874Ser	p.P874S	ENST00000357387	NM_152756.3	874	Cct/Tct	27/38	0.67527206058967	4	FACETS	0.758	0.643	0.882	0.379	0.321	0.441	SUBCLONAL	1	TRUE	2	0.876298268280133	4		231	260	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578537	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs879254214	NA	P-0037553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	349	851	0	ENST00000269305.4:c.393_395del	p.Asn131del	p.N131del	ENST00000269305	NM_001126112.2	131	aaCAAg/aag	5/11	NA	2	FACETS	0.977	0.933	1			1	INDETERMINATE	2	TRUE	NA	0.513299071647858	2		851	696	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595991	43595991	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	93	859	0	ENST00000355710.3:c.158T>C	p.Val53Ala	p.V53A	ENST00000355710	NM_020975.4	53	gTc/gCc	2/20	1	2	FACETS	0.619	0.552	0.691	0.619	0.552	0.691	SUBCLONAL	1	TRUE	1	0.513299071647858	2		859	585	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627838	37627838	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	196	760	0	ENST00000447079.4:c.1757del	p.Pro586LeufsTer24	p.P586Lfs*24	ENST00000447079	NM_015083.1	585	Ccc/cc	2/14	0.513299071647858	1	FACETS	0.987	0.92	1	0.987	0.92	1	CLONAL	1	TRUE	0	0.513299071647858	1		760	575	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519966	NA	P-0037933-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	33	547	0	ENST00000347630.2:c.397T>A	p.Phe133Ile	p.F133I	ENST00000347630	NM_001007230.1	133	Ttc/Atc	6/11	0.119080927056704	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		547	433	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0038049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	162	341	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.156847666627166	2	FACETS	0.768	0.713	0.823	0.768	0.713	0.823	INDETERMINATE	2	TRUE	0	0.526239545173586	2		341	401	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0038049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	160	651	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.526239545173586	2		651	599	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021658	31021658	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1569326367	NA	P-0038049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	156	569	1	ENST00000375687.4:c.1657G>T	p.Glu553Ter	p.E553*	ENST00000375687	NM_015338.5	553	Gaa/Taa	12/13	1	2	FACETS	0.909	0.836	0.986	0.909	0.836	0.986	CLONAL	1	TRUE	1	0.526239545173586	2		570	652	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004254	29004254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143093353	NA	P-0038097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	67	344	0	ENST00000282397.4:c.1039G>A	p.Val347Ile	p.V347I	ENST00000282397	NM_002019.4	347	Gta/Ata	8/30	0.132223024068423	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.886302839011424	0		344	175	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514305	69514305	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs760883667	NA	P-0038097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	103	600	0	ENST00000294312.3:c.376A>G	p.Ile126Val	p.I126V	ENST00000294312	NM_005117.2	126	Atc/Gtc	3/3	0.191348323333541	5	FACETS	1	0.932	1	0.686	0.624	0.749	INDETERMINATE	2	TRUE	2	0.886302839011424	5		600	263	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244578	46244578	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	119	538	0	ENST00000334344.6:c.2672T>A	p.Val891Glu	p.V891E	ENST00000334344	NM_152641.2	891	gTa/gAa	15/21	0.886302839011424	6	FACETS	1	0.977	1	0.252	0.227	0.277	CLONAL	1	TRUE	1	0.886302839011424	6		538	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578483	7578488	+	inframe_deletion	In_Frame_Del	DEL	GGAATC	GGAATC	-	novel	NA	P-0038097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	470	841	2	ENST00000269305.4:c.442_447del	p.Asp148_Ser149del	p.D148_S149del	ENST00000269305	NM_001126112.2	148	GATTCC/-	5/11	0.873332723387015	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.886302839011424	2		843	504	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873619	35873619	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1345734622	NA	P-0038097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	49	232	0	ENST00000303115.3:c.575A>G	p.Gln192Arg	p.Q192R	ENST00000303115	NM_002185.3	192	cAg/cGg	5/8	0.853290971297453	4	FACETS	0.966	0.827	1	0.322	0.275	0.372	CLONAL	1	TRUE	1	0.886302839011424	4		232	216	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650747	48650747	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	92	655	0	ENST00000376670.3:c.616A>G	p.Asn206Asp	p.N206D	ENST00000376670	NM_002049.3	206	Aac/Gac	4/6	0.754837482543858	1	FACETS	0.709	0.651	0.767	0.709	0.651	0.767	SUBCLONAL	1	TRUE	0	0.886302839011424	1		655	163	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0038144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	319	620	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.267907552946691	2		620	1085	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057911	27057911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs892173376	NA	P-0038144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	95	782	1	ENST00000324856.7:c.1619C>T	p.Thr540Met	p.T540M	ENST00000324856	NM_006015.4	540	aCg/aTg	3/20	1	2	FACETS	0.751	0.668	0.841	0.751	0.668	0.841	SUBCLONAL	1	TRUE	1	0.267907552946691	2		783	944	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183740	10183748	+	inframe_deletion	In_Frame_Del	DEL	AGCCCTCCC	AGCCCTCCC	-	novel	NA	P-0038229-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	75	637	0	ENST00000256474.2:c.211_219del	p.Pro71_Gln73del	p.P71_Q73del	ENST00000256474	NM_000551.3	70	gAGCCCTCCCag/gag	1/3	0.325968305158269	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	0	0.325968305158269	1		637	325	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957481	1957481	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038229-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	70	708	0	ENST00000382891.5:c.2580C>G	p.Ile860Met	p.I860M	ENST00000382891	NM_133335.3	860	atC/atG	14/22	0.116717111557289	3	FACETS	1	0.965	1	0.649	0.568	0.734	INDETERMINATE	1	FALSE	1	0.325968305158269	3		708	385	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038330-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	94	115	0				ENST00000310581	NM_198253.2	-/1132			0.799869626517543	3	FACETS	0.919	0.842	0.996	0.919	0.842	0.996	CLONAL	2	TRUE	1	0.799869626517543	3		115	179	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0038330-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	304	610	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.490430074738913	3	FACETS	0.89	0.847	0.932	0.89	0.847	0.932	CLONAL	2	TRUE	1	0.799869626517543	3		610	598	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0038330-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	122	535	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.799869626517543	4	FACETS	0.939	0.851	1	0.313	0.283	0.344	CLONAL	1	TRUE	1	0.799869626517543	4		535	585	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749547	41749547	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038330-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	646	589	0	ENST00000301178.4:c.1472G>C	p.Arg491Thr	p.R491T	ENST00000301178	NM_021913.4	491	aGa/aCa	12/20	0.291234513217207	5	FACETS	0.971	0.946	0.995			1	INDETERMINATE	4	TRUE	NA	0.799869626517543	5		589	915	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048638	6048638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038330-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	613	682	0	ENST00000265849.7:c.13G>A	p.Glu5Lys	p.E5K	ENST00000265849	NM_000535.5	5	Gag/Aag	1/15	0.236456266433913	4	FACETS	0.943	0.915	0.971	0.707	0.686	0.728	INDETERMINATE	3	TRUE	0	0.799869626517543	4		682	975	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275399	142275399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202162034	NA	P-0038330-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	124	384	0	ENST00000350721.4:c.1904G>A	p.Arg635Gln	p.R635Q	ENST00000350721	NM_001184.3	635	cGa/cAa	9/47	0.799869626517543	4	FACETS	0.938	0.851	1	0.313	0.283	0.343	CLONAL	1	TRUE	1	0.799869626517543	4		384	595	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160488	108160488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730881369	NA	P-0038330-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	262	511	0	ENST00000278616.4:c.4396C>T	p.Arg1466Ter	p.R1466*	ENST00000278616	NM_000051.3	1466	Cga/Tga	29/63	0.471507977203354	2	FACETS	0.795	0.759	0.83	0.795	0.759	0.83	INDETERMINATE	2	TRUE	0	0.799869626517543	2		511	412	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010560	48010560	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587779920	NA	P-0038330-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	62	337	0	ENST00000234420.5:c.188C>G	p.Ser63Cys	p.S63C	ENST00000234420	NM_000179.2	63	tCc/tGc	1/10	0.535440055762403	3	FACETS	0.476	0.412	0.545	0.159	0.137	0.182	SUBCLONAL	1	TRUE	0	0.799869626517543	3		337	456	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478902	56478902	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038330-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	696	818	0	ENST00000267101.3:c.358A>G	p.Met120Val	p.M120V	ENST00000267101	NM_001982.3	120	Atg/Gtg	3/28	0.799869626517543	2	FACETS	0.998	0.977	1	0.998	0.977	1	CLONAL	2	TRUE	0	0.799869626517543	2		818	872	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412634	63412634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753930754	NA	P-0038330-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	249	386	3	ENST00000330258.3:c.533G>A	p.Arg178His	p.R178H	ENST00000330258	NM_152424.3	178	cGt/cAt	2/2	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.799869626517543	1		389	334	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771504	112771504	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038330-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	170	566	0	ENST00000369452.4:c.1677G>C	p.Gln559His	p.Q559H	ENST00000369452	NM_007373.3	559	caG/caC	9/9	0.240016357066173	2	FACETS	0.612	0.565	0.662	0.306	0.282	0.331	INDETERMINATE	1	TRUE	0	0.799869626517543	2		566	694	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701248	43701248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773338141	NA	P-0038330-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	356	569	0	ENST00000382044.4:c.5447G>A	p.Arg1816Gln	p.R1816Q	ENST00000382044	NM_001141980.1	1816	cGa/cAa	26/28	0.136912946014006	6	FACETS	1	0.963	1			1	INDETERMINATE	3	TRUE	NA	0.799869626517543	6		569	763	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50818257	50818257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038330-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	55	367	0	ENST00000398568.2:c.1835C>G	p.Ser612Cys	p.S612C	ENST00000398568	NM_001042412.1	612	tCt/tGt	11/18	NA	2	FACETS	0.619	0.536	0.708			1	INDETERMINATE	1	TRUE	NA	0.799869626517543	2		367	222	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110624	4110624	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038330-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	161	825	0	ENST00000262948.5:c.333C>G	p.Ile111Met	p.I111M	ENST00000262948	NM_030662.3	111	atC/atG	3/11	0.372963719443836	2	FACETS	0.468	0.429	0.509	0.234	0.214	0.255	INDETERMINATE	1	TRUE	0	0.799869626517543	2		825	860	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871990	45871990	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038330-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	148	630	0	ENST00000391945.4:c.258G>C	p.Glu86Asp	p.E86D	ENST00000391945	NM_000400.3	86	gaG/gaC	5/23	0.352182788550668	5	FACETS	0.863	0.788	0.942			1	INDETERMINATE	1	TRUE	NA	0.799869626517543	5		630	943	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412064	116412064	+	intron_variant	Intron	SNP	C	C	G	novel	NA	P-0038330-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	448	710	0	ENST00000397752.3:c.3028+21C>G		p.*1010*	ENST00000397752	NM_000245.2	-/1390			0.799869626517543	3	FACETS	0.954	0.918	0.99	0.954	0.918	0.99	CLONAL	2	TRUE	1	0.799869626517543	3		710	822	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418227	139418228	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0038330-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	570	1011	0	ENST00000277541.6:c.344dup	p.Thr116HisfsTer27	p.T116Hfs*27	ENST00000277541	NM_017617.3	115	ggc/ggGc	3/34	0.739739139852515	2	FACETS	0.847	0.823	0.871	0.847	0.823	0.871	CLONAL	2	TRUE	0	0.799869626517543	2		1011	841	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123875307	123875307	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038330-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	86	432	0	ENST00000330479.4:c.263T>C	p.Leu88Ser	p.L88S	ENST00000330479	NM_020382.3	88	tTa/tCa	3/9	0.794964800664494	2	FACETS	0.45	0.399	0.504	0.225	0.199	0.252	SUBCLONAL	1	TRUE	0	0.799869626517543	2		432	478	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795412	42795412	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038330-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2360	160	831	0	ENST00000575354.2:c.2492C>G	p.Thr831Arg	p.T831R	ENST00000575354	NM_015125.3	831	aCg/aGg	10/20	0.799869626517543	8	FACETS	0.54	0.492	0.59			1	SUBCLONAL	1	TRUE	NA	0.799869626517543	8		831	2520	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356400	66356400	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0038330-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	74	441	0	ENST00000273854.3:c.1097C>G	p.Ser366Ter	p.S366*	ENST00000273854	NM_004439.5	366	tCa/tGa	5/18	0.28428185127334	3	FACETS	0.595	0.523	0.673	0.198	0.174	0.225	INDETERMINATE	1	TRUE	0	0.799869626517543	3		441	435	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323150	31323150	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038330-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	116	818	0	ENST00000412585.2:c.839G>C	p.Arg280Thr	p.R280T	ENST00000412585	NM_005514.6	280	aGa/aCa	4/8	0.485563576336511	3	FACETS	0.454	0.408	0.502	0.227	0.204	0.251	SUBCLONAL	1	TRUE	1	0.799869626517543	3		818	895	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0038499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	377	689	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.87536009700197	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.87536009700197	1		690	473	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953730	48953730	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs3092891	NA	P-0038499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	98	160	0	ENST00000267163.4:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000267163	NM_000321.2	445	Cga/Tga	14/27	0.87536009700197	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.87536009700197	1		160	117	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541543	29541546	+	frameshift_variant	Frame_Shift_Del	DEL	TAAG	TAAG	-	rs1135402811	NA	P-0038499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	90	361	0	ENST00000356175.3:c.1469_1472del	p.Lys490IlefsTer7	p.K490Ifs*7	ENST00000356175	NM_000267.3	489	taTAAG/ta	13/57	0.87536009700197	1	FACETS	0.948	0.885	1	0.948	0.885	1	CLONAL	1	TRUE	0	0.87536009700197	1		361	122	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933786	36933786	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs756719784	NA	P-0038649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	34	697	0	ENST00000361632.4:c.1613T>C	p.Ile538Thr	p.I538T	ENST00000361632		538	aTt/aCt	12/16	0.193879901590116	2	FACETS	0.321	0.262	0.388	0.161	0.131	0.194	INDETERMINATE	1	TRUE	0	0.378829422325005	2		697	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578271	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	novel	NA	P-0038649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	124	708	0	ENST00000269305.4:c.578_580del	p.His193del	p.H193del	ENST00000269305	NM_001126112.2	193	cATCtt/ctt	6/11	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.378829422325005	2		708	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	533	572	2	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	NA	2	FACETS	0.965	0.945	0.983			1	INDETERMINATE	2	TRUE	NA	0.884125592266012	2		574	625	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292531	15292531	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs572814447	NA	P-0038960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	611	855	1	ENST00000263388.2:c.2648G>A	p.Arg883Gln	p.R883Q	ENST00000263388	NM_000435.2	883	cGa/cAa	17/33	0.529078819431693	2	FACETS	1	0.996	1	0.601	0.581	0.621	INDETERMINATE	1	TRUE	0	0.884125592266012	2		856	1150	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217303	123217303	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	136	507	0	ENST00000218089.9:c.2957A>T	p.Asn986Ile	p.N986I	ENST00000218089	NM_001042749.1	986	aAt/aTt	29/35	0.742524281396195	3	FACETS	0.518	0.47	0.567	0.259	0.235	0.284	SUBCLONAL	1	TRUE	1	0.884125592266012	3		507	857	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577518	7577518	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519995	NA	P-0039012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	261	572	0	ENST00000269305.4:c.763A>T	p.Ile255Phe	p.I255F	ENST00000269305	NM_001126112.2	255	Atc/Ttc	7/11	0.746535529791365	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.746535529791365	1		572	436	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119234	3119234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775040372	NA	P-0039012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	11	606	0	ENST00000078429.4:c.766C>T	p.Arg256Trp	p.R256W	ENST00000078429	NM_002067.2	256	Cgg/Tgg	6/7	0.746535529791365	1	FACETS	0.039	0.027	0.055	0.039	0.027	0.055	SUBCLONAL	1	TRUE	0	0.746535529791365	1		606	470	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954022	32954023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs397507419	NA	P-0039012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	65	416	8	ENST00000380152.3:c.9097dup	p.Thr3033AsnfsTer11	p.T3033Nfs*11	ENST00000380152		3030	aca/acAa	23/27	0.743380076440479	1	FACETS	0.797	0.712	0.882	0.797	0.712	0.882	SUBCLONAL	1	TRUE	0	0.746535529791365	1		424	137	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599968	28599968	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	273	641	3	ENST00000253063.3:c.850G>T	p.Glu284Ter	p.E284*	ENST00000253063	NM_031459.4	284	Gag/Tag	6/10	0.155997702782048	4	FACETS	1	0.993	1	0.726	0.683	0.77	INDETERMINATE	1	TRUE	2	0.746535529791365	4		644	880	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953768	48953768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	121	215	0	ENST00000267163.4:c.1371G>A	p.Met457Ile	p.M457I	ENST00000267163	NM_000321.2	457	atG/atA	14/27	0.725515234933387	2	FACETS	0.932	0.875	0.986	0.932	0.875	0.986	CLONAL	2	TRUE	0	0.746535529791365	2		215	174	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562684	95562684	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	73	309	0	ENST00000393063.1:c.4573G>A	p.Val1525Met	p.V1525M	ENST00000393063	NM_030621.3	1525	Gtg/Atg	24/28	0.73122663636062	2	FACETS	0.785	0.696	0.879	0.393	0.348	0.44	SUBCLONAL	1	TRUE	0	0.746535529791365	2		309	249	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039109-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	51	115	0				ENST00000310581	NM_198253.2	-/1132			0.331161397129151	6	FACETS	1	0.913	1	0.718	0.621	0.821	INDETERMINATE	2	TRUE	3	0.589864703237975	6		115	175	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652198	36652199	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039109-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	374	761	0	ENST00000244741.5:c.322dup	p.Glu108GlyfsTer21	p.E108Gfs*21	ENST00000244741	NM_000389.4	107	gag/gaGg	2/3	0.331161397129151	6	FACETS	1	0.985	1	1	0.985	1	INDETERMINATE	3	TRUE	3	0.589864703237975	6		761	860	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539091	187539092	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0039109-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	221	470	0	ENST00000441802.2:c.8648dup	p.Tyr2883Ter	p.Y2883*	ENST00000441802	NM_005245.3	2883	tac/taAc	10/27	0.547794396339028	5	FACETS	1	0.97	1	0.708	0.662	0.755	CLONAL	2	TRUE	2	0.589864703237975	5		470	665	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171627	36171628	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039109-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	138	316	0	ENST00000300305.3:c.937dup	p.Leu313ProfsTer287	p.L313Pfs*287	ENST00000300305		313	ctc/cCtc	7/8	0.27912792744584	5	FACETS	1	0.975	1	0.766	0.704	0.828	INDETERMINATE	2	TRUE	2	0.589864703237975	5		316	384	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224448	123224448	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	CATGC	novel	NA	P-0039109-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	204	220	0	ENST00000218089.9:c.3301delinsCATGC	p.Ser1101HisfsTer36	p.S1101Hfs*36	ENST00000218089	NM_001042749.1	1101	Agt/CATGCgt	31/35	0.589864703237975	2	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.589864703237975	2		220	291	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050954	49050954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	21	294	0	ENST00000267163.4:c.2638G>A	p.Glu880Lys	p.E880K	ENST00000267163	NM_000321.2	880	Gaa/Aaa	25/27	0.531993899405169	2	FACETS	0.24	0.184	0.305	0.12	0.092	0.153	SUBCLONAL	1	TRUE	0	0.531993899405169	2		294	329	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683976	29683976	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0039468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	191	430	0	ENST00000356175.3:c.7676-2A>G		p.X2559_splice	ENST00000356175	NM_000267.3	2559			0.531993899405169	2	FACETS	0.968	0.91	1	0.968	0.91	1	CLONAL	2	TRUE	0	0.531993899405169	2		430	371	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861842	57861842	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	268	622	0	ENST00000228682.2:c.1143A>T	p.Lys381Asn	p.K381N	ENST00000228682	NM_005269.2	381	aaA/aaT	10/12	0.499660131877737	4	FACETS	0.902	0.848	0.956	0.902	0.848	0.956	CLONAL	2	TRUE	2	0.531993899405169	4		622	856	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923110	48923144	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTGCATTGGTGCTAAAAGTTTCTTGGATCACAT	TTCTGCATTGGTGCTAAAAGTTTCTTGGATCACAT	-	novel	NA	P-0039468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	15	218	0	ENST00000267163.4:c.560_594del	p.Ser187PhefsTer4	p.S187Ffs*4	ENST00000267163	NM_000321.2	186	aaTTCTGCATTGGTGCTAAAAGTTTCTTGGATCACATtt/aatt	6/27	0.531993899405169	2	FACETS	0.43	0.317	0.564	0.215	0.158	0.282	SUBCLONAL	1	TRUE	0	0.531993899405169	2		218	131	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577587	7577592	+	inframe_deletion	In_Frame_Del	DEL	TGGTGG	TGGTGG	-	novel	NA	P-0039468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	214	592	0	ENST00000269305.4:c.689_694del	p.Thr230_Thr231del	p.T230_T231del	ENST00000269305	NM_001126112.2	230	aCCACCAtc/atc	7/11	0.531993899405169	2	FACETS	0.84	0.789	0.891	0.84	0.789	0.891	CLONAL	2	TRUE	0	0.531993899405169	2		592	479	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245198	41245198	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	294	612	0	ENST00000357654.3:c.2350del	p.Ser784ArgfsTer8	p.S784Rfs*8	ENST00000357654	NM_007294.3	784	Tcg/cg	10/23	0.531993899405169	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.531993899405169	2		612	552	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998189	169998189	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	219	443	0	ENST00000295797.4:c.880G>A	p.Glu294Lys	p.E294K	ENST00000295797	NM_002740.5	294	Gag/Aag	9/18	0.531993899405169	8	FACETS	0.912	0.847	0.979			1	CLONAL	2	TRUE	NA	0.531993899405169	8		443	1172	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228159	53228159	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	153	361	0	ENST00000375401.3:c.2243G>A	p.Arg748Gln	p.R748Q	ENST00000375401	NM_004187.3	748	cGg/cAg	15/26	NA	2	FACETS	1	0.937	1			1	INDETERMINATE	1	TRUE	NA	0.743512789590948	2		361	406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876658468	NA	P-0039685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	349	354	0	ENST00000269305.4:c.577C>G	p.His193Asp	p.H193D	ENST00000269305	NM_001126112.2	193	Cat/Gat	6/11	0.743512789590948	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.743512789590948	2		354	462	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39690066	39690066	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	83	327	1	ENST00000361337.2:c.91C>T	p.Arg31Ter	p.R31*	ENST00000361337	NM_003286.2	31	Cga/Tga	3/21	0.349009917552858	5	FACETS	0.904	0.798	1	0.301	0.266	0.339	CLONAL	1	FALSE	2	0.571420246228787	5		328	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0039798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	541	492	0	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.466292245829587	3	FACETS	1	0.995	1	0.786	0.758	0.813	CLONAL	2	FALSE	0	0.571420246228787	3		492	1033	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061570	38061581	+	inframe_deletion	In_Frame_Del	DEL	GGGCTCATGCAC	GGGCTCATGCAC	-	novel	NA	P-0039798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	15	79	0	ENST00000250448.2:c.408_419del	p.Cys137_Pro140del	p.C137_P140del	ENST00000250448	NM_004496.3	136	ccGTGCATGAGCCCc/ccc	2/2	0.337543465934513	3	FACETS	0.427	0.314	0.562	0.214	0.157	0.281	INDETERMINATE	1	FALSE	1	0.571420246228787	3		79	158	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061594	38061596	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	novel	NA	P-0039798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	15	90	0	ENST00000250448.2:c.393_395del	p.Ala133del	p.A133del	ENST00000250448	NM_004496.3	131	gcGGCc/gcc	2/2	0.337543465934513	3	FACETS	0.519	0.383	0.68	0.26	0.191	0.34	INDETERMINATE	1	FALSE	1	0.571420246228787	3		90	130	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980831	40980831	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1623	332	736	0	ENST00000373198.4:c.1655T>A	p.Leu552His	p.L552H	ENST00000373198	NM_133170.3	552	cTc/cAc	10/32	0.349009917552858	5	FACETS	1	0.982	1	0.368	0.346	0.39	CLONAL	1	FALSE	2	0.571420246228787	5		736	1955	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271227	153271227	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	10	312	0	ENST00000281708.4:c.551G>T	p.Gly184Val	p.G184V	ENST00000281708	NM_033632.3	184	gGa/gTa	3/12	0.542772332708226	2	FACETS	0.197	0.133	0.276	0.098	0.066	0.138	SUBCLONAL	1	FALSE	0	0.571420246228787	2		312	178	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	240490	240490	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1224049828	NA	P-0039798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	28	174	0	ENST00000264932.6:c.1450A>G	p.Ile484Val	p.I484V	ENST00000264932	NM_004168.2	484	Att/Gtt	11/15	0.571420246228787	5	FACETS	0.636	0.51	0.78	0.212	0.17	0.26	SUBCLONAL	1	FALSE	2	0.571420246228787	5		174	286	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244406	5244406	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039860-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	54	726	0	ENST00000357368.4:c.1076C>A	p.Pro359His	p.P359H	ENST00000357368	NM_002850.3	359	cCt/cAt	11/38	0.261728912805537	3	FACETS	0.948	0.835	1	1	0.979	1	CLONAL	4	TRUE	1	0.261728912805537	3		726	123	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828051	3828051	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039860-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	21	574	0	ENST00000262367.5:c.2074C>A	p.Pro692Thr	p.P692T	ENST00000262367	NM_004380.2	692	Ccc/Acc	10/31	0.261728912805537	0	FACETS	0.769	0.609	0.945			1	CLONAL	2	TRUE	0	0.261728912805537	0		574	77	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31466297	31466297	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039860-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	23	619	0	ENST00000344624.3:c.2458C>T	p.Gln820Ter	p.Q820*	ENST00000344624		820	Cag/Tag	16/33	0.222697730948294	2	FACETS	0.814	0.646	1	0.814	0.646	1	CLONAL	2	TRUE	0	0.261728912805537	2		619	108	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812260	212812260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751175543	NA	P-0040038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	46	286	0	ENST00000342788.4:c.316C>T	p.Arg106Cys	p.R106C	ENST00000342788	NM_005235.2	106	Cgt/Tgt	3/28	0.384827091776493	3	FACETS	0.525	0.445	0.613	0.263	0.222	0.307	INDETERMINATE	1	TRUE	1	0.878275526820255	3		286	287	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578234	7578234	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs786202222	NA	P-0040038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	1784	656	0	ENST00000269305.4:c.615T>A	p.Tyr205Ter	p.Y205*	ENST00000269305	NM_001126112.2	205	taT/taA	6/11	0.666703594504052	6	FACETS	0.979	0.971	0.986			1	CLONAL	6	TRUE	NA	0.878275526820255	6		656	1907	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061727	38061727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374795877	NA	P-0040038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	152	490	0	ENST00000250448.2:c.262G>A	p.Gly88Ser	p.G88S	ENST00000250448	NM_004496.3	88	Ggc/Agc	2/2	0.433632351678678	3	FACETS	0.891	0.819	0.965	0.297	0.273	0.322	INDETERMINATE	1	TRUE	0	0.878275526820255	3		490	559	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227972	55227972	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	60	364	0	ENST00000275493.2:c.1439T>C	p.Leu480Pro	p.L480P	ENST00000275493	NM_005228.3	480	cTg/cCg	12/28	0.470855900811845	6	FACETS	0.746	0.643	0.857	0.186	0.16	0.215	INDETERMINATE	1	TRUE	2	0.878275526820255	6		364	505	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0040206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	106	610	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.171547215331547	4	FACETS	0.957	0.863	1	0.957	0.863	1	INDETERMINATE	2	TRUE	2	0.335509916847996	4		610	441	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0040206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	47	578	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.335509916847996	2		579	270	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789661	3789661	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	48	478	0	ENST00000262367.5:c.4198G>C	p.Glu1400Gln	p.E1400Q	ENST00000262367	NM_004380.2	1400	Gag/Cag	25/31	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.335509916847996	2		478	263	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438535	52438535	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0040206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	47	675	0	ENST00000460680.1:c.1184C>G	p.Ser395Ter	p.S395*	ENST00000460680	NM_004656.3	395	tCa/tGa	12/17	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.335509916847996	2		675	269	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437315	52437315	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0040206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	45	710	0	ENST00000460680.1:c.1730-1G>C		p.X577_splice	ENST00000460680	NM_004656.3	577			1	2	FACETS	0.979	0.828	1	0.979	0.828	1	CLONAL	1	TRUE	1	0.335509916847996	2		710	274	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427900	49427900	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	41	853	0	ENST00000301067.7:c.10690C>G	p.Leu3564Val	p.L3564V	ENST00000301067	NM_003482.3	3564	Ctc/Gtc	38/54	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.335509916847996	2		853	239	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936802	32936802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	19	322	0	ENST00000380152.3:c.7948G>A	p.Glu2650Lys	p.E2650K	ENST00000380152		2650	Gaa/Aaa	17/27	0.255398402310697	3	FACETS	1	0.91	1	0.719	0.556	0.902	CLONAL	1	TRUE	1	0.335509916847996	3		322	92	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216786	7216786	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs748835899	NA	P-0040206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	24	494	0	ENST00000380728.2:c.637C>T	p.Pro213Ser	p.P213S	ENST00000380728		213	Cct/Tct	8/11	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.335509916847996	2		494	105	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137650	202137650	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	26	297	0	ENST00000358485.4:c.757G>C	p.Asp253His	p.D253H	ENST00000358485	NM_001080125.1	253	Gat/Cat	5/9	1	2	FACETS	1	0.811	1	1	0.811	1	CLONAL	1	TRUE	1	0.335509916847996	2		297	153	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610510	215610511	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	47	411	0	ENST00000260947.4:c.1745dup	p.Lys583GlufsTer5	p.K583Efs*5	ENST00000260947	NM_000465.2	582	cag/caAg	8/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.335509916847996	2		411	199	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339015	225339015	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	21	392	0	ENST00000264414.4:c.2254G>A	p.Glu752Lys	p.E752K	ENST00000264414	NM_003590.4	752	Gaa/Aaa	16/16	1	2	FACETS	0.894	0.696	1	0.894	0.696	1	CLONAL	1	TRUE	1	0.335509916847996	2		392	140	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339021	225339021	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	22	395	0	ENST00000264414.4:c.2248G>C	p.Glu750Gln	p.E750Q	ENST00000264414	NM_003590.4	750	Gag/Cag	16/16	1	2	FACETS	0.937	0.734	1	0.937	0.734	1	CLONAL	1	TRUE	1	0.335509916847996	2		395	140	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091126	29091126	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	134	915	0	ENST00000328354.6:c.1364T>G	p.Val455Gly	p.V455G	ENST00000328354	NM_007194.3	455	gTc/gGc	12/15	0.236166046356512	3	FACETS	1	0.943	1	0.692	0.634	0.753	CLONAL	2	TRUE	0	0.335509916847996	3		915	449	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547882	41547882	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	55	449	0	ENST00000263253.7:c.2863C>A	p.Pro955Thr	p.P955T	ENST00000263253	NM_001429.3	955	Cca/Aca	15/31	0.236166046356512	3	FACETS	0.938	0.825	1	0.938	0.825	1	CLONAL	3	TRUE	0	0.335509916847996	3		449	136	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565509	41565509	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	31	302	0	ENST00000263253.7:c.4175G>C	p.Arg1392Thr	p.R1392T	ENST00000263253	NM_001429.3	1392	aGa/aCa	26/31	0.236166046356512	3	FACETS	1	0.912	1	0.773	0.644	0.911	CLONAL	2	TRUE	0	0.335509916847996	3		302	93	SUCCESS
ATR	545	MSKCC	GRCh37	3	142234351	142234351	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	20	304	0	ENST00000350721.4:c.4389G>C	p.Lys1463Asn	p.K1463N	ENST00000350721	NM_001184.3	1463	aaG/aaC	25/47	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.335509916847996	2		304	100	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155701	56155701	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	20	312	0	ENST00000399503.3:c.793G>C	p.Glu265Gln	p.E265Q	ENST00000399503	NM_005921.1	265	Gaa/Caa	3/20	1	2	FACETS	0.817	0.63	1	0.817	0.63	1	CLONAL	1	TRUE	1	0.335509916847996	2		312	146	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300403	11300404	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0040206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	29	558	0	ENST00000361445.4:c.1742_1743delinsTT	p.Ser581Ile	p.S581I	ENST00000361445	NM_004958.3	581	aGC/aTT	11/58	1	2	FACETS	0.945	0.765	1	0.945	0.765	1	CLONAL	1	TRUE	1	0.335509916847996	2		558	183	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0040655-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	150	331	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.280599775211765	3	FACETS	1	0.961	1	0.697	0.649	0.744	INDETERMINATE	2	TRUE	0	0.651781897303038	3		331	292	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040655-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	678	909	0	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.651781897303038	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.651781897303038	2		909	1001	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959073	28959073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761475937	NA	P-0040655-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	115	325	0	ENST00000282397.4:c.2065G>A	p.Glu689Lys	p.E689K	ENST00000282397	NM_002019.4	689	Gag/Aag	14/30	NA	2	FACETS	1	0.916	1			1	INDETERMINATE	1	TRUE	NA	0.651781897303038	2		325	351	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658503	3658503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040655-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	149	757	0	ENST00000294008.3:c.463G>A	p.Glu155Lys	p.E155K	ENST00000294008	NM_032444.2	155	Gaa/Aaa	2/15	0.280599775211765	3	FACETS	0.637	0.581	0.695	0.212	0.193	0.232	INDETERMINATE	1	TRUE	0	0.651781897303038	3		757	952	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145589	11145589	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0040655-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	415	726	0	ENST00000358026.2:c.3952-1G>A		p.X1318_splice	ENST00000358026	NM_001128849.1	1318			0.651781897303038	2	FACETS	0.935	0.9	0.969	0.935	0.9	0.969	CLONAL	2	TRUE	0	0.651781897303038	2		726	681	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254728	46254728	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040655-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	161	265	0	ENST00000334344.6:c.4918A>G	p.Lys1640Glu	p.K1640E	ENST00000334344	NM_152641.2	1640	Aaa/Gaa	16/21	0.280599775211765	3	FACETS	1	0.956	1	0.687	0.641	0.732	INDETERMINATE	2	TRUE	0	0.651781897303038	3		265	318	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112580	115112581	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0040655-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	439	840	1	ENST00000257566.3:c.1159_1160delinsAA	p.Pro387Asn	p.P387N	ENST00000257566	NM_016569.3	387	CCc/AAc	7/8	0.238986150568957	3	FACETS	0.921	0.882	0.96	0.614	0.588	0.64	INDETERMINATE	2	TRUE	0	0.651781897303038	3		841	970	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748889	41748889	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040655-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	221	713	0	ENST00000301178.4:c.1414G>T	p.Val472Phe	p.V472F	ENST00000301178	NM_021913.4	472	Gtc/Ttc	11/20	0.651781897303038	3	FACETS	0.983	0.915	1	0.491	0.457	0.526	CLONAL	1	TRUE	1	0.651781897303038	3		713	915	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964388	70964388	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040655-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	253	479	0	ENST00000276594.2:c.1640C>A	p.Ser547Ter	p.S547*	ENST00000276594	NM_024504.3	547	tCa/tAa	8/8	0.651781897303038	8	FACETS	0.799	0.746	0.854	0.266	0.248	0.285	SUBCLONAL	2	TRUE	2	0.651781897303038	8		479	1436	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039883	47039883	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040655-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	467	812	1	ENST00000377604.3:c.1226C>A	p.Ala409Glu	p.A409E	ENST00000377604	NM_001204468.1	409	gCg/gAg	12/24	0.43921906694202	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	2	0.651781897303038	4		813	1068	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988182	85988182	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0040655-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	63	283	0	ENST00000263360.6:c.1125+2T>C		p.X375_splice	ENST00000263360	NM_003797.3	375			0.521191244691644	4	FACETS	0.92	0.801	1			1	CLONAL	1	TRUE	NA	0.651781897303038	4		283	347	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239294	105239294	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040655-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	198	812	0	ENST00000349310.3:c.1093G>T	p.Glu365Ter	p.E365*	ENST00000349310	NM_001014432.1	365	Gag/Tag	12/15	1	2	FACETS	0.915	0.851	0.98	0.915	0.851	0.98	CLONAL	1	TRUE	1	0.651781897303038	2		812	664	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660280	227660280	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040655-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	392	743	0	ENST00000305123.5:c.3175C>A	p.Leu1059Met	p.L1059M	ENST00000305123	NM_005544.2	1059	Ctg/Atg	1/2	0.127185932889247	4	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.651781897303038	4		743	816	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098556	47098562	+	frameshift_variant	Frame_Shift_Del	DEL	ACTGGGA	ACTGGGA	-	novel	NA	P-0040655-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	163	536	0	ENST00000409792.3:c.6712_6718del	p.Ser2238MetfsTer8	p.S2238Mfs*8	ENST00000409792	NM_014159.6	2238	TCCCAGTat/at	15/21	1	2	FACETS	0.893	0.824	0.964	0.893	0.824	0.964	CLONAL	1	TRUE	1	0.651781897303038	2		536	560	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879391	56879391	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040655-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	197	608	0	ENST00000519728.1:c.908T>C	p.Val303Ala	p.V303A	ENST00000519728	NM_002350.3	303	gTg/gCg	9/13	0.189543857899204	5	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.651781897303038	5		608	1002	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729248	41729248	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0040655-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	98	347	0	ENST00000242208.4:c.1281G>C	p.Ter427TyrextTer29	p.*427Yext*29	ENST00000242208	NM_002192.2	427	taG/taC	3/3	0.651781897303038	3	FACETS	0.836	0.749	0.927	0.418	0.374	0.464	CLONAL	1	TRUE	1	0.651781897303038	3		347	477	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	41	602	2	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	0.516	0.429	0.612	0.516	0.429	0.612	SUBCLONAL	1	TRUE	1	0.28	2		604	568	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424970	49424970	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783691	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	132	759	1	ENST00000301067.7:c.13518del	p.Ser4507AlafsTer12	p.S4507Afs*12	ENST00000301067	NM_003482.3	4506	ccC/cc	39/54	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.28	2		760	929	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570292	87570292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463968979	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	98	606	0	ENST00000277120.3:c.2032G>A	p.Ala678Thr	p.A678T	ENST00000277120		678	Gcg/Acg	17/19	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.28	2		606	698	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052632	42052632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779811318	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	98	535	1	ENST00000219905.7:c.7303C>T	p.Arg2435Trp	p.R2435W	ENST00000219905	NM_001164273.1	2435	Cgg/Tgg	20/24	0.144579224338336	1	FACETS	0.941	0.84	1	0.941	0.84	1	INDETERMINATE	1	TRUE	0	0.28	1		536	640	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	119	811	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.28	2		815	831	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	103	478	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.28	2		478	678	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963988	2963988	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755527825	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	84	668	0	ENST00000396946.4:c.1819G>A	p.Glu607Lys	p.E607K	ENST00000396946	NM_032415.4	607	Gaa/Aaa	15/25	1	2	FACETS	0.786	0.694	0.886	0.786	0.694	0.886	SUBCLONAL	1	TRUE	1	0.28	2		668	763	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	131	409	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.28	2		409	633	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	108	919	2	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.797	0.714	0.885	0.797	0.714	0.885	SUBCLONAL	1	TRUE	1	0.28	2		921	968	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	62	370	1	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	1	2	FACETS	0.959	0.83	1	0.959	0.83	1	CLONAL	1	TRUE	1	0.28	2		371	462	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	59	378	1	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.943	0.813	1	0.943	0.813	1	CLONAL	1	TRUE	1	0.28	2		379	447	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	71	505	8	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	0.765	0.667	0.87	0.765	0.667	0.87	SUBCLONAL	1	TRUE	1	0.28	2		513	663	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968322	2968323	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762770988	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	98	772	0	ENST00000396946.4:c.1663dup	p.Arg555ProfsTer38	p.R555Pfs*38	ENST00000396946	NM_032415.4	555	cgg/cCgg	13/25	1	2	FACETS	0.71	0.632	0.793	0.71	0.632	0.793	SUBCLONAL	1	TRUE	1	0.28	2		772	986	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144049	11144051	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	142	795	1	ENST00000358026.2:c.3634_3636del	p.Glu1212del	p.E1212del	ENST00000358026	NM_001128849.1	1210	gtGGAg/gtg	26/36	1	2	FACETS	0.967	0.88	1	0.967	0.88	1	CLONAL	1	TRUE	1	0.28	2		796	1049	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042043	14042043	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778284	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	364	59	0	ENST00000311895.7:c.2590C>T	p.Arg864Cys	p.R864C	ENST00000311895	NM_005236.2	864	Cgc/Tgc	11/11	1	2	FACETS	1	0.99	1	1	0.997	1	CLONAL	3	TRUE	1	0.28	2		59	768	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349641	89349641	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs772267579	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	140	877	6	ENST00000301030.4:c.3309del	p.Asp1104MetfsTer214	p.D1104Mfs*214	ENST00000301030	NM_001256183.1	1103	aaA/aa	9/13	1	2	FACETS	0.903	0.82	0.989	0.903	0.82	0.989	CLONAL	1	TRUE	1	0.28	2		883	1108	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149917	202149917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	129	668	1	ENST00000358485.4:c.1358C>T	p.Pro453Leu	p.P453L	ENST00000358485	NM_001080125.1	453	cCg/cTg	8/9	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.28	2		669	852	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257366	19257366	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	105	797	1	ENST00000162023.5:c.767del	p.Pro256GlnfsTer?	p.P256Qfs*?	ENST00000162023		256	cCa/ca	11/13	1	2	FACETS	0.889	0.796	0.988	0.889	0.796	0.988	CLONAL	1	TRUE	1	0.28	2		798	844	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989406	7989406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs8077661	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	888	151	0	ENST00000319144.4:c.280G>A	p.Gly94Ser	p.G94S	ENST00000319144	NM_001139.2	94	Ggc/Agc	2/15	1	2	FACETS	0.916	0.89	0.942	1	0.999	1	CLONAL	4	TRUE	1	0.28	2		151	1731	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245795	5245795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368461283	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	133	794	0	ENST00000357368.4:c.980C>T	p.Thr327Met	p.T327M	ENST00000357368	NM_002850.3	327	aCg/aTg	10/38	1	2	FACETS	0.918	0.832	1	0.918	0.832	1	CLONAL	1	TRUE	1	0.28	2		794	1035	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89335037	89335037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	262	45	0	ENST00000301030.4:c.7841C>T	p.Ala2614Val	p.A2614V	ENST00000301030	NM_001256183.1	2614	gCg/gTg	13/13	1	2	FACETS	1	0.979	1	1	0.996	1	CLONAL	3	TRUE	1	0.28	2		45	583	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755427	39755427	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	69	616	2	ENST00000288319.7:c.1338del	p.Phe446LeufsTer59	p.F446Lfs*59	ENST00000288319	NM_182918.3	446	ttT/tt	10/10	1	2	FACETS	0.678	0.59	0.774	0.678	0.59	0.774	SUBCLONAL	1	TRUE	1	0.28	2		618	727	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554356	63554357	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	109	678	0	ENST00000307078.5:c.382_383del	p.Leu128ThrfsTer12	p.L128Tfs*12	ENST00000307078	NM_004655.3	128	TTa/a	2/11	1	2	FACETS	0.874	0.784	0.969	0.874	0.784	0.969	CLONAL	1	TRUE	1	0.28	2		678	891	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656969	47656969	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779075	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	56	400	0	ENST00000233146.2:c.1165C>T	p.Arg389Ter	p.R389*	ENST00000233146	NM_000251.2	389	Cga/Tga	7/16	1	2	FACETS	0.749	0.642	0.866	0.749	0.642	0.866	SUBCLONAL	1	TRUE	1	0.28	2		400	534	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954975	2954975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368119340	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	123	764	0	ENST00000396946.4:c.2735G>A	p.Arg912Gln	p.R912Q	ENST00000396946	NM_032415.4	912	cGg/cAg	21/25	1	2	FACETS	0.934	0.843	1	0.934	0.843	1	CLONAL	1	TRUE	1	0.28	2		764	941	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564755	139564755	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	124	884	1	ENST00000308874.7:c.549del	p.Arg184GlyfsTer13	p.R184Gfs*13	ENST00000308874		182	Ccc/cc	7/10	1	2	FACETS	0.868	0.784	0.957	0.868	0.784	0.957	CLONAL	1	TRUE	1	0.28	2		885	1020	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288998	33288998	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761103937	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	93	601	1	ENST00000374542.5:c.554G>A	p.Arg185Gln	p.R185Q	ENST00000374542	NM_001141970.1	185	cGg/cAg	3/8	1	2	FACETS	0.825	0.733	0.924	0.825	0.733	0.924	CLONAL	1	TRUE	1	0.28	2		602	805	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120529603	120529603	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782452794	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	91	542	2	ENST00000256646.2:c.854G>A	p.Arg285His	p.R285H	ENST00000256646	NM_024408.3	285	cGc/cAc	5/34	1	2	FACETS	0.869	0.771	0.973	0.869	0.771	0.973	CLONAL	1	TRUE	1	0.28	2		544	748	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628072	90628072	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781481805	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	129	860	6	ENST00000330062.3:c.1247C>T	p.Ala416Val	p.A416V	ENST00000330062	NM_002168.2	416	gCg/gTg	10/11	0.144579224338336	1	FACETS	0.781	0.707	0.86	0.781	0.707	0.86	INDETERMINATE	1	TRUE	0	0.28	1		866	1014	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445500	49445500	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs886042284	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	114	919	1	ENST00000301067.7:c.1966del	p.Leu656CysfsTer274	p.L656Cfs*274	ENST00000301067	NM_003482.3	656	Ctg/tg	10/54	1	2	FACETS	0.74	0.664	0.82	0.74	0.664	0.82	SUBCLONAL	1	TRUE	1	0.28	2		920	1101	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468398	89468398	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1467832547	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	30	285	0	ENST00000336596.2:c.1938del	p.Glu647ArgfsTer9	p.E647Rfs*9	ENST00000336596	NM_005233.5	644	tcA/tc	11/17	1	2	FACETS	0.638	0.514	0.777	0.638	0.514	0.777	SUBCLONAL	1	TRUE	1	0.28	2		285	336	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	148	968	5	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.889	0.81	0.972	0.889	0.81	0.972	CLONAL	1	TRUE	1	0.28	2		973	1189	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795061	242795061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1203794937	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	137	1045	2	ENST00000334409.5:c.148G>A	p.Ala50Thr	p.A50T	ENST00000334409	NM_005018.2	50	Gcc/Acc	2/5	1	2	FACETS	0.856	0.777	0.94	0.856	0.777	0.94	CLONAL	1	TRUE	1	0.28	2		1047	1143	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982767	7982767	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	129	790	0	ENST00000319144.4:c.1018del	p.Leu340SerfsTer12	p.L340Sfs*12	ENST00000319144	NM_001139.2	340	Ctc/tc	8/15	1	2	FACETS	0.946	0.857	1	0.946	0.857	1	CLONAL	1	TRUE	1	0.28	2		790	974	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007752	45007753	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	67	376	1	ENST00000558401.1:c.204dup	p.Val69SerfsTer21	p.V69Sfs*21	ENST00000558401	NM_004048.2	67	gaa/gAaa	2/4	0.144579224338336	1	FACETS	0.878	0.765	0.999	0.878	0.765	0.999	INDETERMINATE	1	TRUE	0	0.28	1		377	469	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185045	99185045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778972642	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	60	447	1	ENST00000074304.5:c.2447C>T	p.Thr816Met	p.T816M	ENST00000074304	NM_001134224.1	816	aCg/aTg	23/26	1	2	FACETS	0.797	0.687	0.916	0.797	0.687	0.916	CLONAL	1	TRUE	1	0.28	2		448	538	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437711	49437713	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs886049482	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	100	767	0	ENST00000301067.7:c.5257_5259del	p.Lys1753del	p.K1753del	ENST00000301067	NM_003482.3	1753	AAG/-	22/54	1	2	FACETS	0.709	0.632	0.791	0.709	0.632	0.791	SUBCLONAL	1	TRUE	1	0.28	2		767	1008	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478548	99478548	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	53	325	0	ENST00000268035.6:c.3190C>T	p.Arg1064Ter	p.R1064*	ENST00000268035	NM_000875.3	1064	Cga/Tga	17/21	0.144579224338336	1	FACETS	0.773	0.661	0.896	0.773	0.661	0.896	INDETERMINATE	1	TRUE	0	0.28	1		325	421	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874166	155874166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777520196	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	85	673	0	ENST00000368323.3:c.365G>A	p.Arg122Gln	p.R122Q	ENST00000368323	NM_006912.5	122	cGa/cAa	5/6	1	2	FACETS	0.576	0.508	0.65	0.576	0.508	0.65	SUBCLONAL	1	TRUE	1	0.28	2		673	1054	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169985727	169985727	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369872734	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	99	511	0	ENST00000295797.4:c.389G>A	p.Arg130His	p.R130H	ENST00000295797	NM_002740.5	130	cGc/cAc	5/18	1	2	FACETS	0.862	0.769	0.962	0.862	0.769	0.962	CLONAL	1	TRUE	1	0.28	2		511	820	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122996	7122996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377722635	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	127	790	1	ENST00000302850.5:c.3263G>A	p.Arg1088His	p.R1088H	ENST00000302850	NM_000208.2	1088	cGc/cAc	18/22	1	2	FACETS	0.873	0.79	0.961	0.873	0.79	0.961	CLONAL	1	TRUE	1	0.28	2		791	1039	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859930	117859930	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1363929252	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	25	218	0	ENST00000297338.2:c.1705C>T	p.Arg569Cys	p.R569C	ENST00000297338	NM_006265.2	569	Cgt/Tgt	14/14	1	2	FACETS	0.635	0.502	0.788	0.635	0.502	0.788	SUBCLONAL	1	TRUE	1	0.28	2		218	281	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267470	7267470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1240458376	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	114	641	0	ENST00000302850.5:c.538G>A	p.Glu180Lys	p.E180K	ENST00000302850	NM_000208.2	180	Gag/Aag	2/22	1	2	FACETS	0.986	0.887	1	0.986	0.887	1	CLONAL	1	TRUE	1	0.28	2		641	826	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630906	187630906	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	99	544	0	ENST00000441802.2:c.76C>T	p.Arg26Ter	p.R26*	ENST00000441802	NM_005245.3	26	Cga/Tga	2/27	1	2	FACETS	0.974	0.87	1	0.974	0.87	1	CLONAL	1	TRUE	1	0.28	2		544	726	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229336	36229336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777603343	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	93	663	1	ENST00000222270.7:c.8026G>A	p.Ala2676Thr	p.A2676T	ENST00000222270	NM_014727.1	2676	Gcc/Acc	37/37	1	2	FACETS	0.851	0.756	0.952	0.851	0.756	0.952	CLONAL	1	TRUE	1	0.28	2		664	781	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40709549	40709549	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	71	558	1	ENST00000373198.4:c.4353G>T	p.Glu1451Asp	p.E1451D	ENST00000373198	NM_133170.3	1451	gaG/gaT	32/32	1	2	FACETS	0.815	0.712	0.927	0.815	0.712	0.927	CLONAL	1	TRUE	1	0.28	2		559	622	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701242	43701242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368366606	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	91	638	0	ENST00000382044.4:c.5453G>A	p.Arg1818Gln	p.R1818Q	ENST00000382044	NM_001141980.1	1818	cGg/cAg	26/28	0.144579224338336	1	FACETS	0.764	0.678	0.855	0.764	0.678	0.855	INDETERMINATE	1	TRUE	0	0.28	1		638	732	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551418	141551418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	78	660	0	ENST00000220592.5:c.1879G>A	p.Ala627Thr	p.A627T	ENST00000220592	NM_012154.3	627	Gcc/Acc	15/19	1	2	FACETS	0.678	0.595	0.768	0.678	0.595	0.768	SUBCLONAL	1	TRUE	1	0.28	2		660	822	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17117006	17117006	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781733528	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	95	700	2	ENST00000285071.4:c.1703C>T	p.Thr568Met	p.T568M	ENST00000285071	NM_144997.5	568	aCg/aTg	14/14	1	2	FACETS	0.777	0.691	0.869	0.777	0.691	0.869	SUBCLONAL	1	TRUE	1	0.28	2		702	873	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868219	37868219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775294491	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	126	696	0	ENST00000269571.5:c.940G>A	p.Val314Ile	p.V314I	ENST00000269571		314	Gtc/Atc	8/27	1	2	FACETS	0.997	0.902	1	0.997	0.902	1	CLONAL	1	TRUE	1	0.28	2		696	903	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456593	40456593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	131	781	1	ENST00000345506.4:c.1303G>A	p.Val435Met	p.V435M	ENST00000345506	NM_003152.3	435	Gtg/Atg	12/20	1	2	FACETS	0.904	0.819	0.994	0.904	0.819	0.994	CLONAL	1	TRUE	1	0.28	2		782	1035	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40468878	40468878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	71	393	1	ENST00000264657.5:c.2186G>A	p.Arg729His	p.R729H	ENST00000264657	NM_139276.2	729	cGc/cAc	23/24	1	2	FACETS	0.786	0.686	0.894	0.786	0.686	0.894	SUBCLONAL	1	TRUE	1	0.28	2		394	645	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554128	63554128	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	755	112	0	ENST00000307078.5:c.611del	p.Gly204GlufsTer7	p.G204Efs*7	ENST00000307078	NM_004655.3	204	gGa/ga	2/11	1	2	FACETS	1	0.994	1	1	0.998	1	CLONAL	3	TRUE	1	0.28	2		112	1615	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11151999	11151999	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1262500025	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	70	572	0	ENST00000358026.2:c.4283C>T	p.Thr1428Met	p.T1428M	ENST00000358026	NM_001128849.1	1428	aCg/aTg	31/36	1	2	FACETS	0.759	0.661	0.864	0.759	0.661	0.864	SUBCLONAL	1	TRUE	1	0.28	2		572	659	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152170	11152170	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	105	730	0	ENST00000358026.2:c.4454C>A	p.Pro1485His	p.P1485H	ENST00000358026	NM_001128849.1	1485	cCt/cAt	31/36	1	2	FACETS	0.763	0.682	0.849	0.763	0.682	0.849	SUBCLONAL	1	TRUE	1	0.28	2		730	983	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971731	18971731	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	747	158	1	ENST00000262803.5:c.2397G>T	p.Gln799His	p.Q799H	ENST00000262803	NM_002911.3	799	caG/caT	17/24	1	2	FACETS	1	0.995	1	1	0.998	1	CLONAL	3	TRUE	1	0.28	2		159	1570	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855888	45855888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747476170	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	158	845	1	ENST00000391945.4:c.1922G>A	p.Arg641Gln	p.R641Q	ENST00000391945	NM_000400.3	641	cGg/cAg	21/23	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.28	2		846	1039	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994394	25994394	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs565110158	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	62	325	0	ENST00000435504.4:c.419C>T	p.Pro140Leu	p.P140L	ENST00000435504		140	cCg/cTg	6/13	1	2	FACETS	0.936	0.81	1	0.936	0.81	1	CLONAL	1	TRUE	1	0.28	2		325	473	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561397	9561397	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	570	58	0	ENST00000353224.5:c.385T>A	p.Ser129Thr	p.S129T	ENST00000353224	NM_177990.2	129	Tcc/Acc	4/10	1	2	FACETS	1	0.994	1	1	0.998	1	CLONAL	3	TRUE	1	0.28	2		58	1199	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012606	36012606	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	71	424	0	ENST00000358208.4:c.50G>T	p.Ser17Ile	p.S17I	ENST00000358208		17	aGc/aTc	2/12	1	2	FACETS	0.919	0.803	1	0.919	0.803	1	CLONAL	1	TRUE	1	0.28	2		424	552	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499430	89499430	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	69	513	1	ENST00000336596.2:c.2600A>G	p.Asn867Ser	p.N867S	ENST00000336596	NM_005233.5	867	aAc/aGc	15/17	1	2	FACETS	0.681	0.592	0.777	0.681	0.592	0.777	SUBCLONAL	1	TRUE	1	0.28	2		514	724	SUCCESS
ATR	545	MSKCC	GRCh37	3	142257375	142257375	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	82	511	0	ENST00000350721.4:c.3674T>C	p.Ile1225Thr	p.I1225T	ENST00000350721	NM_001184.3	1225	aTc/aCc	19/47	1	2	FACETS	0.989	0.874	1	0.989	0.874	1	CLONAL	1	TRUE	1	0.28	2		511	592	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183639	185183641	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	81	402	0	ENST00000265026.3:c.1495_1497del	p.Glu499del	p.E499del	ENST00000265026	NM_004721.4	498	aAGGag/aag	9/14	1	2	FACETS	0.963	0.849	1	0.963	0.849	1	CLONAL	1	TRUE	1	0.28	2		402	601	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518873	187518873	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755592521	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	92	572	0	ENST00000441802.2:c.12331G>A	p.Ala4111Thr	p.A4111T	ENST00000441802	NM_005245.3	4111	Gcc/Acc	24/27	1	2	FACETS	0.794	0.704	0.889	0.794	0.704	0.889	SUBCLONAL	1	TRUE	1	0.28	2		572	828	SUCCESS
APC	324	MSKCC	GRCh37	5	112102098	112102098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767741687	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	29	288	0	ENST00000257430.4:c.211C>T	p.Arg71Cys	p.R71C	ENST00000257430	NM_000038.5	71	Cgt/Tgt	3/16	1	2	FACETS	0.709	0.571	0.866	0.709	0.571	0.866	SUBCLONAL	1	TRUE	1	0.28	2		288	292	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056387	26056387	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	67	427	0	ENST00000343677.2:c.270G>T	p.Lys90Asn	p.K90N	ENST00000343677	NM_005319.3	90	aaG/aaT	1/1	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.28	2		427	470	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023181	150023181	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs191160444	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	64	627	0	ENST00000253339.5:c.82C>T	p.Arg28Trp	p.R28W	ENST00000253339		28	Cgg/Tgg	1/7	1	2	FACETS	0.67	0.58	0.769	0.67	0.58	0.769	SUBCLONAL	1	TRUE	1	0.28	2		627	682	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850934	128850934	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	672	101	0	ENST00000249373.3:c.1781T>C	p.Val594Ala	p.V594A	ENST00000249373	NM_005631.4	594	gTg/gCg	10/12	1	2	FACETS	0.885	0.856	0.914	1	0.998	1	CLONAL	4	TRUE	1	0.28	2		101	1356	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140500178	140500178	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762305547	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	168	879	1	ENST00000288602.6:c.964G>A	p.Ala322Thr	p.A322T	ENST00000288602	NM_004333.4	322	Gcc/Acc	7/18	1	2	FACETS	0.934	0.856	1	0.934	0.856	1	CLONAL	1	TRUE	1	0.28	2		880	1285	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859843	151859845	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	49	392	0	ENST00000262189.6:c.10817_10819del	p.Arg3606del	p.R3606del	ENST00000262189	NM_170606.2	3606	aGAAca/aca	43/59	1	2	FACETS	0.843	0.716	0.983	0.843	0.716	0.983	CLONAL	1	TRUE	1	0.28	2		392	415	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38194865	38194865	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	721	103	0	ENST00000317025.8:c.868A>C	p.Ser290Arg	p.S290R	ENST00000317025	NM_023034.1	290	Agt/Cgt	4/24	1	2	FACETS	1	0.995	1	1	0.998	1	CLONAL	3	TRUE	1	0.28	2		103	1518	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38194927	38194927	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs770072974	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	742	133	2	ENST00000317025.8:c.806A>G	p.Gln269Arg	p.Q269R	ENST00000317025	NM_023034.1	269	cAg/cGg	4/24	1	2	FACETS	1	0.992	1	1	0.998	1	CLONAL	3	TRUE	1	0.28	2		135	1638	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779093	135779093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060503207	NA	P-0040678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	88	490	1	ENST00000298552.3:c.2153G>A	p.Arg718Gln	p.R718Q	ENST00000298552	NM_001162426.1	718	cGg/cAg	17/23	1	2	FACETS	0.969	0.859	1	0.969	0.859	1	CLONAL	1	TRUE	1	0.28	2		491	649	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0040937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	57	830	2	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.138164267922977	3	FACETS	1	0.919	1	1	0.973	1	CLONAL	3	TRUE	1	0.122	3		832	303	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591898	48591898	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	18	553	0	ENST00000342988.3:c.1061T>G	p.Val354Gly	p.V354G	ENST00000342988	NM_005359.5	354	gTg/gGg	9/12	0.20638432051422	4	FACETS	1	0.77	1	0.513	0.385	0.663	CLONAL	1	TRUE	2	0.122	4		553	323	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041380	47041380	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	16	877	0	ENST00000377604.3:c.1724A>T	p.Asp575Val	p.D575V	ENST00000377604	NM_001204468.1	575	gAt/gTt	16/24	0.138164267922977	0	FACETS	1	0.757	1			1	CLONAL	1	TRUE	0	0.122	0		877	225	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0041277-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	305	341	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.332061608870612	NA		341	713	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141986	108141986	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660628	NA	P-0041277-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	88	404	0	ENST00000278616.4:c.2930G>T	p.Cys977Phe	p.C977F	ENST00000278616	NM_000051.3	977	tGt/tTt	20/63	0.332061608870612	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.332061608870612	1		404	338	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282709	1282709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768398955	NA	P-0041277-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1174	114	639	2	ENST00000310581.5:c.1604G>A	p.Arg535His	p.R535H	ENST00000310581	NM_198253.2	535	cGt/cAt	3/16	0.332061608870612	9	FACETS	1	0.962	1	0.165	0.147	0.183	CLONAL	1	TRUE	2	0.332061608870612	9		641	1288	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427524	49427524	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs768831474	NA	P-0041277-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	246	816	0	ENST00000301067.7:c.10964T>G	p.Leu3655Arg	p.L3655R	ENST00000301067	NM_003482.3	3655	cTt/cGt	39/54	0.231928475164184	5	FACETS	0.863	0.809	0.919			1	CLONAL	3	TRUE	NA	0.332061608870612	5		816	857	SUCCESS
AR	367	MSKCC	GRCh37	X	66766510	66766510	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041277-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	264	574	0	ENST00000374690.3:c.1522A>T	p.Met508Leu	p.M508L	ENST00000374690	NM_000044.3	508	Atg/Ttg	1/8	0.332061608870612	2	FACETS	1	0.952	1			1	CLONAL	3	TRUE	NA	0.332061608870612	2		574	528	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940041	76940041	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041277-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	196	281	0	ENST00000373344.5:c.707A>T	p.His236Leu	p.H236L	ENST00000373344	NM_000489.3	236	cAt/cTt	9/35	0.332061608870612	2	FACETS	1	0.979	1			1	CLONAL	3	TRUE	NA	0.332061608870612	2		281	364	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245273	46245273	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041277-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	149	518	0	ENST00000334344.6:c.3367G>T	p.Gly1123Trp	p.G1123W	ENST00000334344	NM_152641.2	1123	Ggg/Tgg	15/21	0.267721358721116	3	FACETS	1	0.928	1			1	CLONAL	2	TRUE	NA	0.332061608870612	3		518	518	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362422	40362422	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041277-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	181	638	0	ENST00000293328.3:c.1774G>T	p.Gly592Trp	p.G592W	ENST00000293328	NM_012448.3	592	Ggg/Tgg	14/19	0.332061608870612	3	FACETS	0.949	0.878	1	0.949	0.878	1	CLONAL	2	TRUE	1	0.332061608870612	3		638	670	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274695	198274695	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041277-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	82	489	0	ENST00000335508.6:c.703A>G	p.Thr235Ala	p.T235A	ENST00000335508	NM_012433.2	235	Aca/Gca	7/25	0.332061608870612	3	FACETS	1	0.886	1	0.502	0.443	0.565	CLONAL	1	TRUE	1	0.332061608870612	3		489	574	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629788	187629788	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041277-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	233	738	0	ENST00000441802.2:c.1194G>T	p.Leu398Phe	p.L398F	ENST00000441802	NM_005245.3	398	ttG/ttT	2/27	0.224106109855362	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.332061608870612	3		738	760	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041988-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	42	115	0				ENST00000310581	NM_198253.2	-/1132			0.269166160189843	3	FACETS	0.837	0.706	0.979	0.837	0.706	0.979	CLONAL	2	TRUE	1	0.27	3		115	211	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048638	6048638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041988-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	133	682	0	ENST00000265849.7:c.13G>A	p.Glu5Lys	p.E5K	ENST00000265849	NM_000535.5	5	Gag/Aag	1/15	0.181845354119654	4	FACETS	0.993	0.904	1	0.993	0.904	1	CLONAL	2	TRUE	2	0.27	4		682	630	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0041988-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	184	662	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.066472945401377	4	FACETS	1	0.976	1	1	0.976	1	INDETERMINATE	2	TRUE	2	0.27	4		662	764	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0041988-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	17	342	0	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	0.298389672697437	6	FACETS	0.782	0.584	1	0.195	0.146	0.254	CLONAL	1	TRUE	2	0.27	6		342	248	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041988-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	73	445	2	ENST00000335508.6:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000335508	NM_012433.2	902	Gaa/Aaa	18/25	0.193038360514252	3	FACETS	0.849	0.753	0.949	0.849	0.753	0.949	CLONAL	3	TRUE	0	0.27	3		447	241	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879925	44879925	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs189751539	NA	P-0041988-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	87	301	0	ENST00000377967.4:c.514C>T	p.Arg172Ter	p.R172*	ENST00000377967	NM_021140.2	172	Cga/Tga	6/29	0.165566961027252	2	FACETS	0.963	0.869	1			1	CLONAL	3	TRUE	NA	0.27	2		301	223	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158439	108158439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041988-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	42	414	0	ENST00000278616.4:c.4106C>T	p.Ser1369Leu	p.S1369L	ENST00000278616	NM_000051.3	1369	tCa/tTa	27/63	0.269166160189843	3	FACETS	1	0.949	1	0.679	0.571	0.797	CLONAL	1	TRUE	1	0.27	3		414	260	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340440	8340440	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041988-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	78	469	0	ENST00000356435.5:c.5156G>A	p.Gly1719Glu	p.G1719E	ENST00000356435		1719	gGg/gAg	31/35	0.298389672697437	9	FACETS	1	0.971	1	0.196	0.172	0.222	CLONAL	1	TRUE	2	0.27	9		469	819	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274548	198274548	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	152	783	1	ENST00000335508.6:c.850G>T	p.Ala284Ser	p.A284S	ENST00000335508	NM_012433.2	284	Gca/Tca	7/25	0.521764111206556	3	FACETS	0.935	0.857	1	0.468	0.428	0.509	CLONAL	1	TRUE	1	0.533277201356415	3		784	772	SUCCESS
APC	324	MSKCC	GRCh37	5	112175925	112175925	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs863225356	NA	P-0042887-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	25	258	0	ENST00000257430.4:c.4634C>A	p.Ser1545Ter	p.S1545*	ENST00000257430	NM_000038.5	1545	tCa/tAa	16/16	1	2	FACETS	0.723	0.571	0.896	0.723	0.571	0.896	SUBCLONAL	1	TRUE	1	0.255280384150092	2		258	271	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0042887-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	56	344	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.255280384150092	2		344	404	SUCCESS
APC	324	MSKCC	GRCh37	5	112174405	112174405	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042887-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	19	254	0	ENST00000257430.4:c.3114del	p.Gly1039GlufsTer17	p.G1039Efs*17	ENST00000257430	NM_000038.5	1038	tcT/tc	16/16	1	2	FACETS	0.73	0.556	0.932	0.73	0.556	0.932	CLONAL	1	TRUE	1	0.255280384150092	2		254	204	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980844	40980844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043094-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	109	750	0	ENST00000373198.4:c.1642G>A	p.Glu548Lys	p.E548K	ENST00000373198	NM_133170.3	548	Gaa/Aaa	10/32	1	2	FACETS	0.837	0.752	0.927	0.837	0.752	0.927	CLONAL	1	TRUE	1	0.379649790837279	2		750	686	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0043094-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	71	354	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.804	0.704	0.912	0.804	0.704	0.912	CLONAL	1	TRUE	1	0.379649790837279	2		355	465	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0043094-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	82	327	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.365966748223516	3	FACETS	0.973	0.87	1	0.973	0.87	1	CLONAL	2	TRUE	1	0.379649790837279	3		327	264	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812260	212812260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751175543	NA	P-0043094-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	57	286	0	ENST00000342788.4:c.316C>T	p.Arg106Cys	p.R106C	ENST00000342788	NM_005235.2	106	Cgt/Tgt	3/28	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.379649790837279	2		286	273	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720803	89720804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs786204892	NA	P-0043094-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	13	399	0	ENST00000371953.3:c.955dup	p.Thr319AsnfsTer6	p.T319Nfs*6	ENST00000371953	NM_000314.4	318	-/A	8/9	0.379649790837279	1	FACETS	0.523	0.377	0.698	0.523	0.377	0.698	SUBCLONAL	1	TRUE	0	0.379649790837279	1		399	106	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0043094-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	343	1204	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	0.356173236647893	3	FACETS	0.945	0.895	0.997	0.945	0.895	0.997	CLONAL	2	TRUE	1	0.379649790837279	3		1204	1137	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716366	18716366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs935135637	NA	P-0043094-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	51	412	0	ENST00000266497.5:c.3713C>T	p.Ser1238Leu	p.S1238L	ENST00000266497		1238	tCa/tTa	26/31	1	2	FACETS	0.832	0.711	0.963	0.832	0.711	0.963	CLONAL	1	TRUE	1	0.379649790837279	2		412	323	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955149	93955149	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043094-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	31	500	0	ENST00000369303.4:c.2749C>T	p.Gln917Ter	p.Q917*	ENST00000369303	NM_004440.3	917	Caa/Taa	16/17	1	2	FACETS	0.883	0.721	1	0.883	0.721	1	CLONAL	1	TRUE	1	0.379649790837279	2		500	185	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93640037	93640037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043094-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	50	377	0	ENST00000375746.1:c.1366C>T	p.Leu456Phe	p.L456F	ENST00000375746	NM_001174167.1	456	Ctc/Ttc	10/14	1	2	FACETS	0.736	0.627	0.855	0.736	0.627	0.855	SUBCLONAL	1	TRUE	1	0.379649790837279	2		377	358	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139721	55139721	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043094-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	90	574	0	ENST00000257290.5:c.1382C>T	p.Ser461Phe	p.S461F	ENST00000257290	NM_006206.4	461	tCc/tTc	10/23	1	2	FACETS	0.958	0.853	1	0.958	0.853	1	CLONAL	1	TRUE	1	0.379649790837279	2		574	495	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073655	8073656	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0043094-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	72	537	1	ENST00000377482.5:c.1003_1004delinsTT	p.Pro335Phe	p.P335F	ENST00000377482	NM_018948.3	335	CCc/TTc	4/4	1	2	FACETS	0.745	0.652	0.845	0.745	0.652	0.845	SUBCLONAL	1	TRUE	1	0.379649790837279	2		538	509	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243102	105243102	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043094-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	184	1205	0	ENST00000349310.3:c.181C>T	p.Gln61Ter	p.Q61*	ENST00000349310	NM_001014432.1	61	Cag/Tag	5/15	1	2	FACETS	0.944	0.871	1	0.944	0.871	1	CLONAL	1	TRUE	1	0.379649790837279	2		1205	1027	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99163051	99163051	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043094-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	61	384	0	ENST00000074304.5:c.1057C>T	p.Gln353Ter	p.Q353*	ENST00000074304	NM_001134224.1	353	Cag/Tag	13/26	1	2	FACETS	0.843	0.731	0.965	0.843	0.731	0.965	CLONAL	1	TRUE	1	0.379649790837279	2		384	381	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728857	190728857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043094-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	33	364	0	ENST00000441310.2:c.2245C>T	p.Pro749Ser	p.P749S	ENST00000441310	NM_000534.4	749	Cca/Tca	10/13	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.379649790837279	2		364	162	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520219	9520219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867360779	NA	P-0043094-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	102	519	0	ENST00000353224.5:c.2050G>A	p.Glu684Lys	p.E684K	ENST00000353224	NM_177990.2	684	Gag/Aag	10/10	1	2	FACETS	0.982	0.881	1	0.982	0.881	1	CLONAL	1	TRUE	1	0.379649790837279	2		519	547	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566516	41566516	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043094-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	77	439	0	ENST00000263253.7:c.4393G>A	p.Glu1465Lys	p.E1465K	ENST00000263253	NM_001429.3	1465	Gaa/Aaa	27/31	1	2	FACETS	0.932	0.822	1	0.932	0.822	1	CLONAL	1	TRUE	1	0.379649790837279	2		439	435	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090558	71090558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369057936	NA	P-0043094-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	84	521	0	ENST00000318789.4:c.790C>T	p.Pro264Ser	p.P264S	ENST00000318789	NM_032682.5	264	Cct/Tct	11/21	1	2	FACETS	0.948	0.84	1	0.948	0.84	1	CLONAL	1	TRUE	1	0.379649790837279	2		521	467	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665387	117665387	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043094-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	51	367	0	ENST00000368508.3:c.4360C>G	p.Pro1454Ala	p.P1454A	ENST00000368508	NM_002944.2	1454	Cca/Gca	27/43	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.379649790837279	2		367	255	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709191	117709191	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043094-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	35	351	0	ENST00000368508.3:c.1766T>A	p.Ile589Asn	p.I589N	ENST00000368508	NM_002944.2	589	aTc/aAc	13/43	1	2	FACETS	0.74	0.61	0.885	0.74	0.61	0.885	SUBCLONAL	1	TRUE	1	0.379649790837279	2		351	249	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005563	150005563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043094-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	67	459	0	ENST00000253339.5:c.662C>T	p.Ser221Leu	p.S221L	ENST00000253339		221	tCa/tTa	3/7	1	2	FACETS	0.989	0.864	1	0.989	0.864	1	CLONAL	1	TRUE	1	0.379649790837279	2		459	357	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043146-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	65	115	0				ENST00000310581	NM_198253.2	-/1132			0.45460649227383	3	FACETS	0.978	0.866	1	0.978	0.866	1	CLONAL	2	TRUE	1	0.468862631233937	3		115	175	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0043146-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	113	327	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.847	0.765	0.934	0.847	0.765	0.934	CLONAL	1	TRUE	1	0.468862631233937	2		327	569	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577266	64577273	+	frameshift_variant	Frame_Shift_Del	DEL	AGAGGGAC	AGAGGGAC	-	novel	NA	P-0043146-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	280	1064	0	ENST00000312049.6:c.309_316del	p.Leu105SerfsTer9	p.L105Sfs*9	ENST00000312049	NM_130799.2	103	ctGTCCCTCTat/ctat	2/10	0.448946863890129	1	FACETS	0.94	0.884	0.997	0.94	0.884	0.997	CLONAL	1	TRUE	0	0.468862631233937	1		1064	973	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272121	142272121	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043146-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	157	560	1	ENST00000350721.4:c.2753A>T	p.Lys918Ile	p.K918I	ENST00000350721	NM_001184.3	918	aAa/aTa	13/47	1	2	FACETS	0.942	0.865	1	0.942	0.865	1	CLONAL	1	TRUE	1	0.468862631233937	2		561	711	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872613	37872613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043322-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1881	464	944	1	ENST00000269571.5:c.1573C>T	p.Pro525Ser	p.P525S	ENST00000269571		525	Ccc/Tcc	13/27	0.784844094786507	5	FACETS	1	0.987	1	0.366	0.348	0.385	CLONAL	1	TRUE	2	0.784844094786507	5		945	2345	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168939	11168939	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043322-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	305	546	0	ENST00000358026.2:c.4529G>C	p.Gly1510Ala	p.G1510A	ENST00000358026	NM_001128849.1	1510	gGa/gCa	32/36	0.784844094786507	4	FACETS	1	0.953	1	0.507	0.477	0.538	CLONAL	1	TRUE	2	0.784844094786507	4		546	1368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0043364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	72	629	3	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.284945902704442	2	FACETS	1	0.96	1	0.615	0.54	0.695	CLONAL	1	TRUE	0	0.308738229560537	2		632	379	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0043364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	92	454	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.284945902704442	2	FACETS	0.94	0.844	1	0.94	0.844	1	CLONAL	2	TRUE	0	0.308738229560537	2		454	317	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110332	3110332	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0043364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	56	425	0	ENST00000078429.4:c.321+1G>A		p.X107_splice	ENST00000078429	NM_002067.2	107			0.218948778791116	2	FACETS	1	0.961	1	0.667	0.576	0.764	CLONAL	1	TRUE	0	0.308738229560537	2		425	272	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0043550-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	444	513	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.650971782195877	2	FACETS	0.99	0.956	1	0.99	0.956	1	CLONAL	2	TRUE	0	0.650971782195877	2		513	689	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622047	43622047	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1207742610	NA	P-0043550-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	78	380	0	ENST00000355710.3:c.3064A>G	p.Thr1022Ala	p.T1022A	ENST00000355710	NM_020975.4	1022	Act/Gct	19/20	0.650971782195877	3	FACETS	0.52	0.457	0.587	0.26	0.228	0.294	SUBCLONAL	1	TRUE	1	0.650971782195877	3		380	611	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107183	27107183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043550-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	101	487	0	ENST00000324856.7:c.6794C>T	p.Pro2265Leu	p.P2265L	ENST00000324856	NM_006015.4	2265	cCg/cTg	20/20	0.276364489776073	5	FACETS	0.784	0.701	0.873	0.261	0.233	0.291	INDETERMINATE	1	TRUE	2	0.650971782195877	5		487	782	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527935	103527935	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043550-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	30	240	1	ENST00000355739.4:c.3243G>T	p.Lys1081Asn	p.K1081N	ENST00000355739	NM_000123.3	1081	aaG/aaT	15/15	0.420859966158278	2	FACETS	0.293	0.236	0.357	0.146	0.118	0.179	SUBCLONAL	1	TRUE	0	0.650971782195877	2		241	315	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968604	55968604	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043550-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	100	423	0	ENST00000263923.4:c.2059T>C	p.Ser687Pro	p.S687P	ENST00000263923	NM_002253.2	687	Tca/Cca	14/30	0.650971782195877	3	FACETS	0.43	0.383	0.479	0.215	0.191	0.24	SUBCLONAL	1	TRUE	1	0.650971782195877	3		423	948	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0043588-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	232	550	1	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.574157155181792	2	FACETS	0.991	0.94	1	0.991	0.94	1	CLONAL	2	TRUE	0	0.56806375170053	2		551	412	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0043588-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	164	374	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	0.574157155181792	3	FACETS	1	0.98	1	0.397	0.365	0.429	CLONAL	1	TRUE	0	0.56806375170053	3		374	623	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052915	180052915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043588-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	69	1191	1	ENST00000261937.6:c.1375C>T	p.His459Tyr	p.H459Y	ENST00000261937	NM_182925.4	459	Cac/Tac	10/30	0.574157155181792	3	FACETS	0.365	0.317	0.417	0.183	0.158	0.209	SUBCLONAL	1	TRUE	1	0.56806375170053	3		1192	854	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0043597-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	254	671	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	0.492319787288612	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.492319787288612	1		671	637	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646949	37646949	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1159844816	NA	P-0043597-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	188	482	0	ENST00000447079.4:c.2071A>G	p.Ile691Val	p.I691V	ENST00000447079	NM_015083.1	691	Atc/Gtc	3/14	0.492319787288612	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.492319787288612	1		482	456	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326258	62326258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755300600	NA	P-0043597-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	161	806	0	ENST00000360203.5:c.3274C>T	p.Leu1092Phe	p.L1092F	ENST00000360203	NM_001283009.1	1092	Ctc/Ttc	32/35	1	2	FACETS	0.872	0.801	0.946	0.872	0.801	0.946	CLONAL	1	TRUE	1	0.492319787288612	2		806	750	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304417	91304417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043597-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	37	264	1	ENST00000355112.3:c.1814C>T	p.Thr605Ile	p.T605I	ENST00000355112	NM_000057.2	605	aCa/aTa	7/22	0.492319787288612	3	FACETS	0.576	0.476	0.687	0.288	0.238	0.344	SUBCLONAL	1	TRUE	1	0.492319787288612	3		265	325	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955106	93955106	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043597-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	49	348	0	ENST00000369303.4:c.2792G>T	p.Trp931Leu	p.W931L	ENST00000369303	NM_004440.3	931	tGg/tTg	16/17	1	2	FACETS	0.516	0.438	0.601	0.516	0.438	0.601	SUBCLONAL	1	TRUE	1	0.492319787288612	2		348	386	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033281	69033281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043597-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	53	284	0	ENST00000288368.4:c.3721G>A	p.Glu1241Lys	p.E1241K	ENST00000288368	NM_024870.2	1241	Gaa/Aaa	30/40	0.338184731627626	1	FACETS	0.458	0.392	0.53	0.458	0.392	0.53	SUBCLONAL	1	TRUE	0	0.492319787288612	1		284	354	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0043653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	176	314	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.499440394734417	3	FACETS	0.926	0.861	0.991	0.926	0.861	0.991	CLONAL	2	TRUE	1	0.521086533609149	3		314	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0043653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	435	890	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.520519929356185	2	FACETS	0.993	0.953	1	0.993	0.953	1	CLONAL	2	TRUE	0	0.521086533609149	2		893	841	SUCCESS
APC	324	MSKCC	GRCh37	5	112175772	112175772	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	168	299	0	ENST00000257430.4:c.4483del	p.Ser1495ValfsTer12	p.S1495Vfs*12	ENST00000257430	NM_000038.5	1494	gAa/ga	16/16	0.520519929356185	2	FACETS	0.98	0.917	1	0.98	0.917	1	CLONAL	2	TRUE	0	0.521086533609149	2		299	329	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577591	7577591	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	614	591	0	ENST00000269305.4:c.690del	p.Thr231ProfsTer16	p.T231Pfs*16	ENST00000269305	NM_001126112.2	230	acC/ac	7/11	0.328376839034209	4	FACETS	0.933	0.906	0.959			1	CLONAL	4	TRUE	NA	0.536773952989184	4		591	942	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258079	16258079	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	289	494	0	ENST00000375759.3:c.5344G>A	p.Asp1782Asn	p.D1782N	ENST00000375759	NM_015001.2	1782	Gat/Aat	11/15	0.536773952989184	4	FACETS	0.94	0.887	0.995	0.47	0.443	0.498	CLONAL	2	TRUE	0	0.536773952989184	4		494	880	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249141	10249141	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	207	838	0	ENST00000340748.4:c.4041C>G	p.Asp1347Glu	p.D1347E	ENST00000340748		1347	gaC/gaG	34/40	0.410315453852403	4	FACETS	1	0.958	1	0.524	0.485	0.563	CLONAL	1	TRUE	2	0.536773952989184	4		838	1132	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151868351	151868351	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	116	441	0	ENST00000262189.6:c.9451C>T	p.Gln3151Ter	p.Q3151*	ENST00000262189	NM_170606.2	3151	Cag/Tag	40/59	0.536773952989184	5	FACETS	0.832	0.749	0.92	0.277	0.249	0.307	CLONAL	1	TRUE	2	0.536773952989184	5		441	938	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0044445-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	150	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.912	0.839	0.989	0.912	0.839	0.989	CLONAL	1	TRUE	1	0.61	2		622	539	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0044445-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	44	325	1				ENST00000310581	NM_198253.2	-/1132			0.3	0	FACETS	0.38	0.325	0.439			1	INDETERMINATE	1	TRUE	0	0.61	0		326	148	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0044445-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	153	827	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.118539220472613	0	FACETS	0.36	0.331	0.39			1	INDETERMINATE	1	TRUE	0	0.61	0		827	544	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0044445-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	94	387	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	1	2	FACETS	0.978	0.88	1	0.978	0.88	1	CLONAL	1	TRUE	1	0.61	2		387	315	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56377265	56377265	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044445-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	47	299	0	ENST00000348428.3:c.886C>T	p.Arg296Ter	p.R296*	ENST00000348428	NM_006785.3	296	Cga/Tga	6/17	0.0783635225138886	0	FACETS	0.261	0.222	0.303			1	INDETERMINATE	1	TRUE	0	0.61	0		299	230	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416623	121416623	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044445-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	138	789	0	ENST00000257555.6:c.52G>C	p.Glu18Gln	p.E18Q	ENST00000257555		18	Gag/Cag	1/10	0.0783635225138886	0	FACETS	0.351	0.321	0.382			1	INDETERMINATE	1	TRUE	0	0.61	0		789	503	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651906	36651906	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044445-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	137	704	1	ENST00000244741.5:c.28C>T	p.Gln10Ter	p.Q10*	ENST00000244741	NM_000389.4	10	Cag/Tag	2/3	0.118539220472613	3	FACETS	1	0.949	1	0.527	0.482	0.575	INDETERMINATE	1	TRUE	1	0.61	3		705	556	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645693	12645693	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397516827	NA	P-0044445-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	106	321	0	ENST00000251849.4:c.776C>G	p.Ser259Cys	p.S259C	ENST00000251849	NM_002880.3	259	tCc/tGc	7/17	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.61	2		321	334	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256524	115256524	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044445-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	144	686	2	ENST00000369535.4:c.187G>A	p.Glu63Lys	p.E63K	ENST00000369535	NM_002524.4	63	Gag/Aag	3/7	1	2	FACETS	0.791	0.724	0.86	0.791	0.724	0.86	SUBCLONAL	1	TRUE	1	0.61	2		688	597	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100093	157100120	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCGGCGGCGGCAGCAGCAGGAGGCG	GCGGCGGCGGCGGCAGCAGCAGGAGGCG	-	rs1554247989	NA	P-0044445-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	22	20	0	ENST00000346085.5:c.1044_1071del	p.Ala349MetfsTer11	p.A349Mfs*11	ENST00000346085	NM_020732.3	344	GCGGCGGCGGCGGCAGCAGCAGGAGGCGgc/gc	1/20	0.118539220472613	3	FACETS	1	0.838	1	1	0.838	1	INDETERMINATE	2	TRUE	1	0.61	3		20	46	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89809327	89809327	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1262639465	NA	P-0044445-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	132	514	0	ENST00000389301.3:c.3646G>A	p.Ala1216Thr	p.A1216T	ENST00000389301	NM_000135.2	1216	Gcc/Acc	37/43	0.0783635225138886	0	FACETS	0.399	0.365	0.434			1	INDETERMINATE	1	TRUE	0	0.61	0		514	423	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569760	41569760	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044445-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	73	264	0	ENST00000263253.7:c.4751T>G	p.Leu1584Arg	p.L1584R	ENST00000263253	NM_001429.3	1584	cTa/cGa	29/31	0.0783635225138886	0	FACETS	0.348	0.308	0.391			1	INDETERMINATE	1	TRUE	0	0.61	0		264	268	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446798	49446798	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044445-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	183	637	0	ENST00000301067.7:c.1012G>C	p.Glu338Gln	p.E338Q	ENST00000301067	NM_003482.3	338	Gag/Cag	8/54	0.218272416826181	4	FACETS	0.788	0.731	0.847	0.788	0.731	0.847	INDETERMINATE	2	TRUE	2	0.61	4		637	613	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029533	14029533	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044445-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	84	457	0	ENST00000311895.7:c.1744G>T	p.Asp582Tyr	p.D582Y	ENST00000311895	NM_005236.2	582	Gac/Tac	8/11	0.0783635225138886	0	FACETS	0.314	0.279	0.35			1	INDETERMINATE	1	TRUE	0	0.61	0		457	342	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827300	72827300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044445-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	93	740	2	ENST00000268489.5:c.9281C>T	p.Ala3094Val	p.A3094V	ENST00000268489	NM_006885.3	3094	gCa/gTa	9/10	0.0783635225138886	0	FACETS	0.213	0.19	0.238			1	INDETERMINATE	1	TRUE	0	0.61	0		742	557	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747825	41747825	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0044445-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	70	264	0	ENST00000226382.2:c.944G>C	p.Ter315SerextTer41	p.*315Sext*41	ENST00000226382	NM_003924.3	315	tGa/tCa	3/3	1	2	FACETS	0.964	0.853	1	0.964	0.853	1	CLONAL	1	TRUE	1	0.61	2		264	238	SUCCESS
APC	324	MSKCC	GRCh37	5	112164570	112164570	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044445-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	55	273	0	ENST00000257430.4:c.1644G>C	p.Leu548Phe	p.L548F	ENST00000257430	NM_000038.5	548	ttG/ttC	14/16	1	2	FACETS	0.855	0.741	0.975	0.855	0.741	0.975	CLONAL	1	TRUE	1	0.61	2		273	211	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637607	176637607	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1562208147	NA	P-0044445-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	90	593	0	ENST00000439151.2:c.2207C>G	p.Ser736Cys	p.S736C	ENST00000439151	NM_022455.4	736	tCt/tGt	5/23	1	2	FACETS	0.729	0.65	0.811	0.729	0.65	0.811	SUBCLONAL	1	TRUE	1	0.61	2		593	405	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637631	176637631	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0044445-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	85	617	0	ENST00000439151.2:c.2231C>G	p.Ser744Ter	p.S744*	ENST00000439151	NM_022455.4	744	tCa/tGa	5/23	1	2	FACETS	0.697	0.619	0.778	0.697	0.619	0.778	SUBCLONAL	1	TRUE	1	0.61	2		617	400	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289046	33289046	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044445-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	156	797	0	ENST00000374542.5:c.506C>G	p.Thr169Arg	p.T169R	ENST00000374542	NM_001141970.1	169	aCa/aGa	3/8	0.118539220472613	3	FACETS	0.941	0.864	1	0.471	0.432	0.511	INDETERMINATE	1	TRUE	1	0.61	3		797	709	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652179	36652179	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044445-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	187	779	0	ENST00000244741.5:c.301C>G	p.Leu101Val	p.L101V	ENST00000244741	NM_000389.4	101	Ctg/Gtg	2/3	0.118539220472613	3	FACETS	1	0.988	1	0.655	0.608	0.703	INDETERMINATE	1	TRUE	1	0.61	3		779	611	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652267	36652267	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044445-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	171	720	0	ENST00000244741.5:c.389C>A	p.Ser130Tyr	p.S130Y	ENST00000244741	NM_000389.4	130	tCc/tAc	2/3	0.118539220472613	3	FACETS	1	0.984	1	0.616	0.569	0.664	INDETERMINATE	1	TRUE	1	0.61	3		720	594	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017585	112017585	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044445-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	120	652	0	ENST00000368678.4:c.928G>C	p.Glu310Gln	p.E310Q	ENST00000368678		310	Gag/Cag	9/13	0.118539220472613	3	FACETS	1	0.908	1	0.5	0.454	0.549	INDETERMINATE	1	TRUE	1	0.61	3		652	513	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170020914	170020914	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0044445-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	11	45	0	ENST00000295797.4:c.1790G>C	p.Ter597SerextTer18	p.*597Sext*18	ENST00000295797	NM_002740.5	597	tGa/tCa	18/18	1	2	FACETS	1	0.828	1	1	0.828	1	CLONAL	1	TRUE	1	0.61	2		45	30	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	936	824	2	ENST00000269305.4:c.472del	p.Arg158AlafsTer12	p.R158Afs*12	ENST00000269305	NM_001126112.2	158	Cgc/gc	5/11	0.765958084066372	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.765958084066372	3		826	1118	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027764	48027764	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	114	335	0	ENST00000234420.5:c.2642G>A	p.Gly881Asp	p.G881D	ENST00000234420	NM_000179.2	881	gGt/gAt	4/10	0.765958084066372	6	FACETS	0.91	0.819	1	0.228	0.204	0.252	CLONAL	1	TRUE	2	0.765958084066372	6		335	828	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295133	15295133	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	295	823	0	ENST00000263388.2:c.2539G>C	p.Asp847His	p.D847H	ENST00000263388	NM_000435.2	847	Gat/Cat	16/33	0.439053280225872	4	FACETS	1	0.992	1	0.446	0.42	0.472	INDETERMINATE	1	TRUE	1	0.765958084066372	4		823	1017	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148507480	148507480	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	142	371	1	ENST00000320356.2:c.1974A>T	p.Arg658Ser	p.R658S	ENST00000320356	NM_004456.4	658	agA/agT	17/20	0.765958084066372	4	FACETS	0.957	0.874	1	0.319	0.291	0.348	CLONAL	1	TRUE	1	0.765958084066372	4		372	684	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755554	39755554	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044759-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	246	519	2	ENST00000288319.7:c.1211del	p.Pro404ArgfsTer25	p.P404Rfs*25	ENST00000288319	NM_182918.3	404	cCg/cg	10/10	0.128419287971393	5	FACETS	0.964	0.906	1	0.723	0.679	0.768	INDETERMINATE	3	TRUE	1	0.378207433148587	5		521	705	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041518	14041518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149364215	NA	P-0044759-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	85	435	0	ENST00000311895.7:c.2065C>T	p.Arg689Cys	p.R689C	ENST00000311895	NM_005236.2	689	Cgt/Tgt	11/11	0.37113256871216	3	FACETS	0.977	0.866	1	0.489	0.433	0.548	CLONAL	1	TRUE	1	0.378207433148587	3		435	547	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489535	56489535	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044759-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	387	552	0	ENST00000267101.3:c.2000G>T	p.Arg667Leu	p.R667L	ENST00000267101	NM_001982.3	667	cGt/cTt	17/28	0.378207433148587	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	1	0.378207433148587	4		552	877	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456630	32456630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044759-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	148	256	0	ENST00000332351.3:c.262G>A	p.Gly88Ser	p.G88S	ENST00000332351	NM_024426.4	88	Ggc/Agc	1/10	0.378207433148587	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.378207433148587	4		256	450	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396651	30396651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044759-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	12	63	2	ENST00000331968.5:c.68C>T	p.Ala23Val	p.A23V	ENST00000331968	NM_002742.2	23	gCg/gTg	1/18	1	2	FACETS	1	0.735	1	1	0.735	1	CLONAL	1	TRUE	1	0.378207433148587	2		65	62	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610567	81610567	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044759-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	72	397	0	ENST00000298171.2:c.2165A>G	p.Gln722Arg	p.Q722R	ENST00000298171	NM_000369.2	722	cAa/cGa	10/10	1	2	FACETS	0.949	0.834	1	0.949	0.834	1	CLONAL	1	TRUE	1	0.378207433148587	2		397	401	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812223	212812223	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044759-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	66	335	1	ENST00000342788.4:c.353C>A	p.Ala118Glu	p.A118E	ENST00000342788	NM_005235.2	118	gCa/gAa	3/28	0.105364729897032	4	FACETS	1	0.94	1	0.57	0.496	0.649	INDETERMINATE	1	TRUE	2	0.378207433148587	4		336	422	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081548	143081548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775054204	NA	P-0044759-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	187	478	0	ENST00000262992.4:c.1526C>T	p.Ser509Phe	p.S509F	ENST00000262992	NM_001101669.1	509	tCc/tTc	15/24	0.378207433148587	3	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	1	0.378207433148587	3		478	585	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969088	93969088	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044759-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	114	314	0	ENST00000369303.4:c.1908G>T	p.Glu636Asp	p.E636D	ENST00000369303	NM_004440.3	636	gaG/gaT	10/17	0.378207433148587	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	0	0.378207433148587	2		314	294	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	81	115	0				ENST00000310581	NM_198253.2	-/1132			0.492722893440592	5	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	FALSE	3	0.492722893440592	5		115	247	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0045300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	4191	662	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.492722893440592	44	FACETS	0.993	0.987	0.999			1	CLONAL	42	FALSE	NA	0.492722893440592	44		662	4627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0045300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	353	872	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.492722893440592	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	3	FALSE	0	0.492722893440592	2		872	456	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913381	NA	P-0045300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	160	740	0	ENST00000304494.5:c.322G>A	p.Asp108Asn	p.D108N	ENST00000304494	NM_000077.4	108	Gat/Aat	2/3	0.405154495885868	0	FACETS	0.71	0.672	0.747			1	SUBCLONAL	2	FALSE	0	0.492722893440592	0		740	232	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106696	2106696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	348	1090	1	ENST00000219476.3:c.700G>A	p.Glu234Lys	p.E234K	ENST00000219476	NM_000548.3	234	Gag/Aag	8/42	0.492722893440592	2	FACETS	1	0.978	1	1	0.997	1	CLONAL	3	FALSE	0	0.492722893440592	2		1091	464	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742733	39742733	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	255	578	0	ENST00000361337.2:c.1576G>C	p.Glu526Gln	p.E526Q	ENST00000361337	NM_003286.2	526	Gag/Cag	15/21	0.492722893440592	4	FACETS	0.913	0.863	0.964	1	0.993	1	CLONAL	3	FALSE	2	0.492722893440592	4		578	564	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591035	67591035	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1367776221	NA	P-0045300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	85	279	1	ENST00000274335.5:c.1628G>A	p.Arg543Lys	p.R543K	ENST00000274335		543	aGa/aAa	12/15	0.492722893440592	2	FACETS	0.966	0.898	1	1	0.986	1	CLONAL	3	FALSE	0	0.492722893440592	2		280	119	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481417	140481417	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913348	NA	P-0045300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	201	462	0	ENST00000288602.6:c.1391G>C	p.Gly464Ala	p.G464A	ENST00000288602	NM_004333.4	464	gGa/gCa	11/18	0.492722893440592	6	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	FALSE	3	0.492722893440592	6		462	492	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919203	178919203	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1482313267	NA	P-0045300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	55	237	0	ENST00000263967.3:c.688C>G	p.Arg230Gly	p.R230G	ENST00000263967	NM_006218.2	230	Cga/Gga	4/21	0.492722893440592	5	FACETS	1	0.966	1	0.481	0.415	0.552	CLONAL	1	FALSE	2	0.492722893440592	5		237	269	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977198	85977198	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0045300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	204	420	0	ENST00000263360.6:c.800C>G	p.Ser267Ter	p.S267*	ENST00000263360	NM_003797.3	267	tCa/tGa	8/12	0.492722893440592	10	FACETS	0.949	0.885	1			1	CLONAL	4	FALSE	NA	0.492722893440592	10		420	648	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44910953	44910953	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0045300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	52	149	0	ENST00000377967.4:c.655-1G>C		p.X219_splice	ENST00000377967	NM_021140.2	219			1	1	FACETS	1	0.949	1	1	0.983	1	CLONAL	2	FALSE	0	0.492722893440592	1		149	74	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335148	65335148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	171	440	0	ENST00000342505.4:c.493G>A	p.Asp165Asn	p.D165N	ENST00000342505	NM_002227.2	165	Gat/Aat	6/25	0.492722893440592	5	FACETS	0.908	0.844	0.973	0.908	0.844	0.973	CLONAL	3	FALSE	2	0.492722893440592	5		440	443	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600594	43600594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	157	828	4	ENST00000355710.3:c.820G>A	p.Ala274Thr	p.A274T	ENST00000355710	NM_020975.4	274	Gcg/Acg	4/20	0.255434226751821	5	FACETS	1	0.974	1	0.751	0.693	0.81	INDETERMINATE	2	FALSE	2	0.492722893440592	5		832	492	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426373	49426373	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	360	1107	0	ENST00000301067.7:c.12115G>C	p.Glu4039Gln	p.E4039Q	ENST00000301067	NM_003482.3	4039	Gag/Cag	39/54	0.492722893440592	6	FACETS	0.895	0.854	0.937	1	0.992	1	CLONAL	4	FALSE	3	0.492722893440592	6		1107	810	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716298	52716298	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	436	948	0	ENST00000322088.6:c.742C>G	p.Leu248Val	p.L248V	ENST00000322088	NM_014225.5	248	Ctg/Gtg	6/15	0.492722893440592	6	FACETS	1	0.99	1	1	0.99	1	CLONAL	4	FALSE	2	0.492722893440592	6		948	812	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098775	178098775	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	134	689	0	ENST00000397062.3:c.270G>C	p.Gln90His	p.Q90H	ENST00000397062	NM_006164.4	90	caG/caC	2/5	0.282971523196445	3	FACETS	0.758	0.694	0.824	0.758	0.694	0.824	INDETERMINATE	2	FALSE	1	0.492722893440592	3		689	447	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742637	39742637	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	143	404	0	ENST00000361337.2:c.1480G>C	p.Glu494Gln	p.E494Q	ENST00000361337	NM_003286.2	494	Gag/Cag	15/21	0.492722893440592	4	FACETS	0.889	0.823	0.955	1	0.987	1	CLONAL	3	FALSE	2	0.492722893440592	4		404	325	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430248	181430248	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	108	599	0	ENST00000325404.1:c.100C>G	p.Gln34Glu	p.Q34E	ENST00000325404	NM_003106.3	34	Cag/Gag	1/1	0.492722893440592	5	FACETS	0.851	0.768	0.937	0.567	0.512	0.625	CLONAL	2	FALSE	2	0.492722893440592	5		599	448	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659239	86659239	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	134	298	0	ENST00000274376.6:c.1528G>A	p.Glu510Lys	p.E510K	ENST00000274376	NM_002890.2	510	Gaa/Aaa	11/25	0.492722893440592	2	FACETS	0.996	0.942	1	1	0.992	1	CLONAL	3	FALSE	0	0.492722893440592	2		298	182	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683989	117683989	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	224	504	0	ENST00000368508.3:c.3158C>G	p.Pro1053Arg	p.P1053R	ENST00000368508	NM_002944.2	1053	cCa/cGa	21/43	0.492722893440592	2	FACETS	0.981	0.939	1	1	0.995	1	CLONAL	3	FALSE	0	0.492722893440592	2		504	309	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031732	69031732	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	245	631	0	ENST00000288368.4:c.3487G>C	p.Glu1163Gln	p.E1163Q	ENST00000288368	NM_024870.2	1163	Gag/Cag	28/40	0.492722893440592	5	FACETS	0.984	0.927	1	0.984	0.927	1	CLONAL	3	FALSE	2	0.492722893440592	5		631	586	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152038	11152038	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	122	654	0	ENST00000358026.2:c.4322C>T	p.Ser1441Leu	p.S1441L	ENST00000358026	NM_001128849.1	1441	tCa/tTa	31/36	0.492722893440592	4	FACETS	1	0.982	1	0.674	0.612	0.74	CLONAL	1	FALSE	2	0.492722893440592	4		654	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0045411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	75	804	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.303997907933571	3	FACETS	1	0.975	1	0.491	0.432	0.553	CLONAL	1	FALSE	0	0.303997907933571	3		804	386	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391007	89391007	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	10	362	0	ENST00000336596.2:c.1074del	p.Phe359SerfsTer12	p.F359Sfs*12	ENST00000336596	NM_005233.5	358	aCc/ac	5/17	0.303997907933571	5	FACETS	0.602	0.409	0.845	0.201	0.136	0.282	SUBCLONAL	1	FALSE	2	0.303997907933571	5		362	159	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579472	7579473	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	C	novel	NA	P-0045432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	323	949	1	ENST00000269305.4:c.214_215delinsG	p.Pro72AlafsTer51	p.P72Afs*51	ENST00000269305	NM_001126112.2	72	CCc/Gc	4/11	0.387281381838848	2	FACETS	0.953	0.903	1	0.953	0.903	1	CLONAL	2	FALSE	0	0.390065810951747	2		950	869	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475061	40475063	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0045544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	189	1006	1	ENST00000264657.5:c.1847_1849del	p.Glu616del	p.E616del	ENST00000264657	NM_139276.2	616	gAAGga/gga	20/24	0.72070819412639	4	FACETS	1	0.95	1	0.258	0.239	0.279	CLONAL	1	TRUE	0	0.72070819412639	4		1007	873	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs967461896	NA	P-0045544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	273	624	0	ENST00000269305.4:c.526T>C	p.Cys176Arg	p.C176R	ENST00000269305	NM_001126112.2	176	Tgc/Cgc	5/11	0.72070819412639	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.72070819412639	1		624	402	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041509	14041509	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	136	345	1	ENST00000311895.7:c.2056G>T	p.Val686Leu	p.V686L	ENST00000311895	NM_005236.2	686	Gtg/Ttg	11/11	0.72070819412639	3	FACETS	0.982	0.898	1	0.491	0.449	0.535	CLONAL	1	TRUE	1	0.72070819412639	3		346	523	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147727	61147727	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	86	210	0	ENST00000295025.8:c.1037C>G	p.Pro346Arg	p.P346R	ENST00000295025	NM_002908.2	346	cCa/cGa	10/11	0.72070819412639	7	FACETS	0.763	0.674	0.859			1	SUBCLONAL	1	TRUE	NA	0.72070819412639	7		210	876	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624773	9624773	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	379	342	0	ENST00000353224.5:c.204G>T	p.Lys68Asn	p.K68N	ENST00000353224	NM_177990.2	68	aaG/aaT	3/10	0.395878631834345	3	FACETS	0.935	0.905	0.964	0.935	0.905	0.964	INDETERMINATE	3	TRUE	0	0.72070819412639	3		342	510	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199901	108199901	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046178-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	108	181	0	ENST00000278616.4:c.7243G>C	p.Ala2415Pro	p.A2415P	ENST00000278616	NM_000051.3	2415	Gct/Cct	49/63	0.817945532860057	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.818496644711022	1		181	150	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572140	64572153	+	frameshift_variant	Frame_Shift_Del	DEL	AGTGCTGGCTTCTT	AGTGCTGGCTTCTT	-	novel	NA	P-0046178-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	276	817	0	ENST00000312049.6:c.1486_1499del	p.Lys496GlyfsTer30	p.K496Gfs*30	ENST00000312049	NM_130799.2	496	AAGAAGCCAGCACTg/g	10/10	0.818496644711022	1	FACETS	0.953	0.913	0.992	0.953	0.913	0.992	CLONAL	1	TRUE	0	0.818496644711022	1		817	418	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046461-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	175	115	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		115	479	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0046583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	54	378	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.3	3	FACETS	1	0.924	1	1	0.972	1	CLONAL	3	TRUE	1	0.13	3		378	265	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0046583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	64	890	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.89	0.768	1	0.89	0.768	1	CLONAL	1	TRUE	1	0.13	2		893	1106	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0046583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	31	317	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.838	1	1	0.838	1	CLONAL	1	TRUE	1	0.13	2		317	458	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155689	119155689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	39	451	0	ENST00000264033.4:c.1442C>T	p.Pro481Leu	p.P481L	ENST00000264033	NM_005188.3	481	cCg/cTg	10/16	1	2	FACETS	0.993	0.822	1	0.993	0.822	1	CLONAL	1	TRUE	1	0.13	2		451	604	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469672	NA	P-0046583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	42	550	0	ENST00000374080.3:c.131G>A	p.Gly44Asp	p.G44D	ENST00000374080		44	gGt/gAt	2/45	1	2	FACETS	0.86	0.716	1	0.86	0.716	1	CLONAL	1	TRUE	1	0.13	2		550	751	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266111	41266493	+	splice_donor_variant,splice_acceptor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	TTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGC	TTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGC	-	novel	NA	P-0047365-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	98	350	0	ENST00000349496.5:c.109_291del		p.X37_splice	ENST00000349496	NM_001904.3	37	caTTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCt/cat	3-4/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		350	437	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047438-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	89	115	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.756341663570113	2		115	201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0047438-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	117	693	0	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	0.162481900552264	4	FACETS	0.927	0.849	1	0.927	0.849	1	INDETERMINATE	2	TRUE	2	0.756341663570113	4		693	293	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963988	2963988	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755527825	NA	P-0047438-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	161	668	0	ENST00000396946.4:c.1819G>A	p.Glu607Lys	p.E607K	ENST00000396946	NM_032415.4	607	Gaa/Aaa	15/25	0.756341663570113	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.756341663570113	2		668	212	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101309	27101309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772281669	NA	P-0047438-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	183	714	0	ENST00000324856.7:c.4591G>A	p.Glu1531Lys	p.E1531K	ENST00000324856	NM_006015.4	1531	Gaa/Aaa	18/20	0.162481900552264	4	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	2	TRUE	2	0.756341663570113	4		714	387	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983129	201983129	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047438-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	38	640	0	ENST00000359651.3:c.978C>A	p.Tyr326Ter	p.Y326*	ENST00000359651		326	taC/taA	7/8	0.756341663570113	1	FACETS	0.182	0.15	0.217	0.182	0.15	0.217	SUBCLONAL	1	TRUE	0	0.756341663570113	1		640	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577527	+	frameshift_variant	Frame_Shift_Del	DEL	AGTGTGATGATGGTGAG	AGTGTGATGATGGTGAG	-	novel	NA	P-0047438-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	140	628	0	ENST00000269305.4:c.754_770del	p.Leu252GlyfsTer6	p.L252Gfs*6	ENST00000269305	NM_001126112.2	252	CTCACCATCATCACACTg/g	7/11	0.162481900552264	4	FACETS	0.856	0.788	0.924	0.856	0.788	0.924	INDETERMINATE	2	TRUE	2	0.756341663570113	4		628	380	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136998	11136998	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047438-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	185	691	0	ENST00000358026.2:c.3191G>A	p.Gly1064Glu	p.G1064E	ENST00000358026	NM_001128849.1	1064	gGg/gAg	23/36	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.756341663570113	2		691	433	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727101	40727101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1302171855	NA	P-0047438-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	40	562	0	ENST00000373198.4:c.3863G>A	p.Cys1288Tyr	p.C1288Y	ENST00000373198	NM_133170.3	1288	tGc/tAc	28/32	0.522650594309945	1	FACETS	0.387	0.326	0.453	0.387	0.326	0.453	SUBCLONAL	1	TRUE	0	0.756341663570113	1		562	170	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448542	89448542	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047438-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	68	505	0	ENST00000336596.2:c.1506C>A	p.Asp502Glu	p.D502E	ENST00000336596	NM_005233.5	502	gaC/gaA	7/17	0.162481900552264	4	FACETS	0.877	0.78	0.978	0.877	0.78	0.978	INDETERMINATE	2	TRUE	2	0.756341663570113	4		505	180	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041442	47041442	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0047438-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	104	325	0	ENST00000377604.3:c.1785+1G>A		p.X595_splice	ENST00000377604	NM_001204468.1	595			0.50650702144275	2	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.756341663570113	2		325	119	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551451	141551451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047621-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	194	489	0	ENST00000220592.5:c.1846G>A	p.Gly616Ser	p.G616S	ENST00000220592	NM_012154.3	616	Ggc/Agc	15/19	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.553594135340447	2		489	658	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347786	89347786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750529678	NA	P-0047621-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	179	684	1	ENST00000301030.4:c.5164C>T	p.Pro1722Ser	p.P1722S	ENST00000301030	NM_001256183.1	1722	Ccc/Tcc	9/13	0.122404277275992	0	FACETS	0.448	0.415	0.483			1	INDETERMINATE	1	TRUE	0	0.553594135340447	0		685	644	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966350	25966350	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047621-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	150	703	0	ENST00000435504.4:c.2856A>C	p.Leu952Phe	p.L952F	ENST00000435504		952	ttA/ttC	13/13	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.553594135340447	2		703	443	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188201	10188201	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs5030812	NA	P-0047621-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	139	436	0	ENST00000256474.2:c.344A>G	p.His115Arg	p.H115R	ENST00000256474	NM_000551.3	115	cAc/cGc	2/3	0.553594135340447	1	FACETS	0.974	0.897	1	0.974	0.897	1	CLONAL	1	TRUE	0	0.553594135340447	1		436	373	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047752-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	148	115	0				ENST00000310581	NM_198253.2	-/1132			0.250890709328885	4	FACETS	0.907	0.833	0.983	0.907	0.833	0.983	CLONAL	3	TRUE	1	0.255277449184066	4		115	535	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0047752-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	149	341	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.25111911686055	3	FACETS	0.895	0.824	0.969	0.895	0.824	0.969	CLONAL	3	TRUE	0	0.255277449184066	3		341	490	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035169	30035169	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047752-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	172	468	0	ENST00000338641.4:c.331C>T	p.Gln111Ter	p.Q111*	ENST00000338641	NM_000268.3	111	Cag/Tag	3/16	0.243328180185092	2	FACETS	0.944	0.871	1	0.944	0.871	1	CLONAL	2	TRUE	0	0.255277449184066	2		468	714	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041247	47041247	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047752-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	158	794	0	ENST00000377604.3:c.1675G>T	p.Glu559Ter	p.E559*	ENST00000377604	NM_001204468.1	559	Gaa/Taa	15/24	0.255277449184066	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.255277449184066	1		794	1018	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361088	70361088	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047752-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	129	369	1	ENST00000374080.3:c.6276G>T	p.Gln2092His	p.Q2092H	ENST00000374080		2092	caG/caT	43/45	0.255277449184066	3	FACETS	0.982	0.894	1	0.982	0.894	1	CLONAL	2	TRUE	1	0.255277449184066	3		370	580	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504332	8504332	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs139581216	NA	P-0047752-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	82	485	0	ENST00000356435.5:c.1751G>T	p.Arg584Leu	p.R584L	ENST00000356435		584	cGt/cTt	12/35	0.255277449184066	3	FACETS	0.949	0.837	1	0.475	0.418	0.536	CLONAL	1	TRUE	1	0.255277449184066	3		485	763	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17380483	17380483	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047752-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	136	704	1	ENST00000375499.3:c.32G>T	p.Arg11Leu	p.R11L	ENST00000375499	NM_003000.2	11	cGc/cTc	1/8	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.255277449184066	2		705	1055	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041166	47041166	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047752-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	130	711	0	ENST00000377604.3:c.1594C>T	p.Pro532Ser	p.P532S	ENST00000377604	NM_001204468.1	532	Ccc/Tcc	15/24	0.255277449184066	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.255277449184066	1		711	837	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041256	47041256	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047752-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	139	760	0	ENST00000377604.3:c.1684A>C	p.Ser562Arg	p.S562R	ENST00000377604	NM_001204468.1	562	Agc/Cgc	15/24	0.255277449184066	1	FACETS	0.985	0.896	1	0.985	0.896	1	CLONAL	1	TRUE	0	0.255277449184066	1		760	964	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205006	123205006	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047752-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	67	212	0	ENST00000218089.9:c.2366C>A	p.Thr789Asn	p.T789N	ENST00000218089	NM_001042749.1	789	aCt/aAt	25/35	0.255277449184066	3	FACETS	0.809	0.707	0.918	0.809	0.707	0.918	CLONAL	2	TRUE	1	0.255277449184066	3		212	366	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257347	16257347	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	154	450	0	ENST00000375759.3:c.4612C>T	p.Gln1538Ter	p.Q1538*	ENST00000375759	NM_015001.2	1538	Caa/Taa	11/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.535280147259733	2		450	511	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115734	8115735	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	128	361	0	ENST00000346208.3:c.1081dup	p.Ile361AsnfsTer10	p.I361Nfs*10	ENST00000346208		360	-/A	6/6	NA	2	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.535280147259733	2		361	393	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396651	30396651	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	12	23	0	ENST00000331968.5:c.68C>G	p.Ala23Gly	p.A23G	ENST00000331968	NM_002742.2	23	gCg/gGg	1/18	NA	2	FACETS	1	0.845	1			1	INDETERMINATE	1	TRUE	NA	0.535280147259733	2		23	36	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858432	27858448	+	frameshift_variant	Frame_Shift_Del	DEL	CGGTGCCTGGCCTGTAG	CGGTGCCTGGCCTGTAG	-	novel	NA	P-0047756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	126	518	0	ENST00000359303.2:c.123_139del	p.Tyr42GlyfsTer4	p.Y42Gfs*4	ENST00000359303	NM_003535.2	41	cgCTACAGGCCAGGCACCGtg/cgtg	1/1	0.535280147259733	3	FACETS	0.828	0.75	0.909	0.414	0.375	0.455	CLONAL	1	TRUE	1	0.535280147259733	3		518	721	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0048030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	247	629	3	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.84621930789985	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.84621930789985	2		632	273	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790072	40790072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753667	NA	P-0048030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	178	868	4	ENST00000373198.4:c.2659G>A	p.Ala887Thr	p.A887T	ENST00000373198	NM_133170.3	887	Gcc/Acc	18/32	0.840402365598758	4	FACETS	0.95	0.876	1	0.317	0.292	0.342	CLONAL	1	TRUE	1	0.84621930789985	4		872	818	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332617	153332617	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769623850	NA	P-0048030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	97	550	0	ENST00000281708.4:c.339G>T	p.Glu113Asp	p.E113D	ENST00000281708	NM_033632.3	113	gaG/gaT	2/12	0.84621930789985	2	FACETS	0.997	0.907	1	0.498	0.453	0.544	CLONAL	1	TRUE	0	0.84621930789985	2		550	230	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95598907	95598907	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048030-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	102	534	0	ENST00000393063.1:c.252G>T	p.Gln84His	p.Q84H	ENST00000393063	NM_030621.3	84	caG/caT	4/28	0.84621930789985	3	FACETS	0.983	0.888	1	0.328	0.296	0.361	CLONAL	1	TRUE	0	0.84621930789985	3		534	349	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913514	NA	P-0048138-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	147	630	0	ENST00000288135.5:c.2466T>A	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaA	17/21	1	2	FACETS	0.97	0.896	1	0.97	0.896	1	CLONAL	1	TRUE	1	0.76157712591024	2		630	398	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028385	42028466	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGGAAGTCTTCCTGCAATGAAGGAGAATCCTCTTCTACTTCTTATATGCATCAGAGGTCACCTGGTGGTCCCACCAAACT	GCTGGAAGTCTTCCTGCAATGAAGGAGAATCCTCTTCTACTTCTTATATGCATCAGAGGTCACCTGGTGGTCCCACCAAACT	-	novel	NA	P-0048138-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	95	327	0	ENST00000219905.7:c.3924_4005del	p.Ser1308ArgfsTer18	p.S1308Rfs*18	ENST00000219905	NM_001164273.1	1308	aGCTGGAAGTCTTCCTGCAATGAAGGAGAATCCTCTTCTACTTCTTATATGCATCAGAGGTCACCTGGTGGTCCCACCAAACTg/ag	13/24	0.723956243938773	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.76157712591024	1		327	149	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86637138	86637138	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048138-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	36	353	0	ENST00000274376.6:c.1049T>C	p.Ile350Thr	p.I350T	ENST00000274376	NM_002890.2	350	aTa/aCa	6/25	1	2	FACETS	0.587	0.49	0.693	0.587	0.49	0.693	SUBCLONAL	1	TRUE	1	0.76157712591024	2		353	161	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593602	55593612	+	protein_altering_variant	In_Frame_Del	DEL	GTGGAAGGTTG	GTGGAAGGTTG	CT	novel	NA	P-0048138-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	102	585	0	ENST00000288135.5:c.1668_1678delinsCT	p.Gln556_Val560delinsHisPhe	p.Q556_V560delinsHF	ENST00000288135	NM_000222.2	556	caGTGGAAGGTTGtt/caCTtt	11/21	1	2	FACETS	0.759	0.685	0.835	0.759	0.685	0.835	SUBCLONAL	1	TRUE	1	0.76157712591024	2		585	353	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0048237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	186	280	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.986	0.919	1	0.986	0.919	1	CLONAL	1	TRUE	1	0.744053993390209	2		280	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519999	NA	P-0048237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	333	540	0	ENST00000269305.4:c.716A>G	p.Asn239Ser	p.N239S	ENST00000269305	NM_001126112.2	239	aAc/aGc	7/11	0.695171268181189	1	FACETS	0.908	0.868	0.948	0.908	0.868	0.948	CLONAL	1	TRUE	0	0.744053993390209	1		540	619	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729114	66729114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1298033161	NA	P-0048237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	247	434	0	ENST00000307102.5:c.322C>T	p.Arg108Trp	p.R108W	ENST00000307102	NM_002755.3	108	Cgg/Tgg	3/11	1	2	FACETS	0.931	0.875	0.989	0.931	0.875	0.989	CLONAL	1	TRUE	1	0.744053993390209	2		434	713	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791974	42791974	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	520	726	0	ENST00000575354.2:c.778C>A	p.His260Asn	p.H260N	ENST00000575354	NM_015125.3	260	Cac/Aac	6/20	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.744053993390209	2		726	1321	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50138634	50138890	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	GGTGGGGACAGGAGGCGTTGGCAGAAGGCACACAGTGGCAGTAGCCCAGAAGAGGCCAGGAAGTAAGGGTGGGTATGTGATGTGTCCTGGGAGACCCAGATGAGGAAATTGAGGCTCAGTGAGGGCCTCAGGTCACACAGCAAGGTGCGAAGGCAGCTAGTCCCGAGAGCTTGTGGTGGTTGCTTCTCTCTTGCCTGGGCTACAGGAGGACGCAGGGGCAGCCCCCGCCCTTCTTCCTGGGGGCACTGGGAGGGCTC	GGTGGGGACAGGAGGCGTTGGCAGAAGGCACACAGTGGCAGTAGCCCAGAAGAGGCCAGGAAGTAAGGGTGGGTATGTGATGTGTCCTGGGAGACCCAGATGAGGAAATTGAGGCTCAGTGAGGGCCTCAGGTCACACAGCAAGGTGCGAAGGCAGCTAGTCCCGAGAGCTTGTGGTGGTTGCTTCTCTCTTGCCTGGGCTACAGGAGGACGCAGGGGCAGCCCCCGCCCTTCTTCCTGGGGGCACTGGGAGGGCTC	-	novel	NA	P-0048237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	264	116	0	ENST00000246792.3:c.600_*199del		p.*200*	ENST00000246792	NM_006270.3	200		6/6	NA	2	FACETS	0.994	0.956	1			1	INDETERMINATE	2	TRUE	NA	0.744053993390209	2		116	357	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469564	25469564	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs796065342	NA	P-0048470-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	184	755	2	ENST00000264709.3:c.1204C>T	p.Gln402Ter	p.Q402*	ENST00000264709	NM_175629.2	402	Cag/Tag	10/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		757	799	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562982	21562982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048470-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	85	732	1	ENST00000382592.4:c.937G>A	p.Val313Met	p.V313M	ENST00000382592	NM_014572.2	313	Gtg/Atg	4/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		733	487	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25536802	25536802	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048470-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	140	761	0	ENST00000264709.3:c.52G>T	p.Glu18Ter	p.E18*	ENST00000264709	NM_175629.2	18	Gag/Tag	2/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		761	768	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361239	66361239	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048470-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	28	310	0	ENST00000273854.3:c.933A>T	p.Lys311Asn	p.K311N	ENST00000273854	NM_004439.5	311	aaA/aaT	4/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		310	320	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0048508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	36	513	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.246137230114426	1	FACETS	0.737	0.607	0.881	0.737	0.607	0.881	SUBCLONAL	1	TRUE	0	0.26	1		513	327	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692892	89692892	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554898129	NA	P-0048897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	178	294	0	ENST00000371953.3:c.376G>T	p.Ala126Ser	p.A126S	ENST00000371953	NM_000314.4	126	Gct/Tct	5/9	0.531214751327772	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	0	0.531214751327772	2		294	335	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589599	67589604	+	inframe_deletion	In_Frame_Del	DEL	TCAGTT	TCAGTT	-	novel	NA	P-0048897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	81	252	0	ENST00000274335.5:c.1365_1370del	p.Phe456_Gln457del	p.F456_Q457del	ENST00000274335		454	acTCAGTTt/act	10/15	1	2	FACETS	0.82	0.727	0.918	0.82	0.727	0.918	CLONAL	1	TRUE	1	0.531214751327772	2		252	372	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021708	31021708	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	182	462	0	ENST00000375687.4:c.1709del	p.Pro570ArgfsTer133	p.P570Rfs*133	ENST00000375687	NM_015338.5	569	gtC/gt	12/13	1	2	FACETS	0.939	0.868	1	0.939	0.868	1	CLONAL	1	TRUE	1	0.531214751327772	2		462	730	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0049333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	225	662	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.17833527073928	3	FACETS	1	0.983	1	0.591	0.549	0.634	INDETERMINATE	1	TRUE	1	0.36180629010828	3		662	1243	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0049333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	228	622	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.36180629010828	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.36180629010828	1		622	890	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980415	201980416	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGGAGGGTACAGG	novel	NA	P-0049333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	231	658	0	ENST00000359651.3:c.155_163+4dup		p.L51fs	ENST00000359651		51	ttg/tTGGAGGGTACAGGtg	1/8	0.203176346380912	2	FACETS	1	0.987	1	0.613	0.571	0.656	INDETERMINATE	1	TRUE	0	0.36180629010828	2		658	1042	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023769	27023769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	337	402	0	ENST00000324856.7:c.879del	p.Thr294ProfsTer69	p.T294Pfs*69	ENST00000324856	NM_006015.4	292	aCc/ac	1/20	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.587518745678719	2		402	834	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	238	368	0	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	0.175683722833085	3	FACETS	0.924	0.87	0.979	0.924	0.87	0.979	INDETERMINATE	2	TRUE	1	0.587518745678719	3		368	567	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	356	699	7	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.587518745678719	2		706	947	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	356	633	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	0.22523733321128	3	FACETS	0.903	0.86	0.947	0.903	0.86	0.947	INDETERMINATE	2	TRUE	1	0.587518745678719	3		633	868	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	228	439	0	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.587518745678719	2		439	739	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	16	410	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.175683722833085	3	FACETS	0.128	0.094	0.169	0.064	0.047	0.085	INDETERMINATE	1	TRUE	1	0.587518745678719	3		410	552	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612175	189612175	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1560311554	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	355	560	0	ENST00000264731.3:c.1927C>T	p.Arg643Ter	p.R643*	ENST00000264731	NM_003722.4	643	Cga/Tga	14/14	0.175683722833085	3	FACETS	0.919	0.874	0.963	0.919	0.874	0.963	INDETERMINATE	2	TRUE	1	0.587518745678719	3		560	851	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857910	9857910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	180	532	0	ENST00000330684.3:c.3491C>T	p.Thr1164Met	p.T1164M	ENST00000330684	NM_001134407.1	1164	aCg/aTg	13/13	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.587518745678719	2		532	463	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670606	30670606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1371318631	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	298	481	0	ENST00000376406.3:c.5914G>A	p.Asp1972Asn	p.D1972N	ENST00000376406	NM_014641.2	1972	Gac/Aac	13/15	0.148782733361179	4	FACETS	1	0.985	1	1	0.985	1	INDETERMINATE	2	TRUE	2	0.587518745678719	4		481	732	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	45	663	2	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	0.175683722833085	3	FACETS	0.231	0.193	0.273	0.115	0.096	0.137	INDETERMINATE	1	TRUE	1	0.587518745678719	3		665	859	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284979	15284979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774475688	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	365	585	0	ENST00000263388.2:c.4636C>T	p.Arg1546Cys	p.R1546C	ENST00000263388	NM_000435.2	1546	Cgc/Tgc	25/33	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.587518745678719	2		585	844	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026984	71026984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763413735	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	342	424	1	ENST00000318789.4:c.1343C>T	p.Ser448Leu	p.S448L	ENST00000318789	NM_032682.5	448	tCg/tTg	15/21	NA	2	FACETS	0.796	0.759	0.834			1	INDETERMINATE	2	TRUE	NA	0.587518745678719	2		425	731	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570292	87570292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463968979	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	235	606	0	ENST00000277120.3:c.2032G>A	p.Ala678Thr	p.A678T	ENST00000277120		678	Gcg/Acg	17/19	1	2	FACETS	0.759	0.715	0.803	1	0.993	1	SUBCLONAL	2	TRUE	1	0.587518745678719	2		606	527	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733513	85733513	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs387906350	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	239	562	4	ENST00000370580.1:c.499del	p.Ser167LeufsTer6	p.S167Lfs*6	ENST00000370580	NM_003921.4	167	Tct/ct	3/3	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.587518745678719	2		566	594	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442808	99442809	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	340	492	0	ENST00000268035.6:c.1211dup	p.Asn404LysfsTer66	p.N404Kfs*66	ENST00000268035	NM_000875.3	402	cta/ctAa	5/21	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.587518745678719	2		492	819	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536193	41536193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	313	469	0	ENST00000263253.7:c.1810C>T	p.Arg604Trp	p.R604W	ENST00000263253	NM_001429.3	604	Cgg/Tgg	9/31	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.587518745678719	2		469	775	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470498	25470498	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747448117	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	424	624	0	ENST00000264709.3:c.976C>T	p.Arg326Cys	p.R326C	ENST00000264709	NM_175629.2	326	Cgc/Tgc	8/23	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.587518745678719	2		624	974	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972525	32972525	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56121817	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	285	491	0	ENST00000380152.3:c.9875C>T	p.Pro3292Leu	p.P3292L	ENST00000380152		3292	cCg/cTg	27/27	0.175683722833085	3	FACETS	1	0.966	1	1	0.966	1	INDETERMINATE	2	TRUE	1	0.587518745678719	3		491	613	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494170	140494170	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	336	639	1	ENST00000288602.6:c.1078C>T	p.Arg360Ter	p.R360*	ENST00000288602	NM_004333.4	360	Cga/Tga	8/18	0.22523733321128	3	FACETS	0.908	0.863	0.953	0.908	0.863	0.953	INDETERMINATE	2	TRUE	1	0.587518745678719	3		640	815	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217240	11217240	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148486930	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	335	509	0	ENST00000361445.4:c.4438C>T	p.Arg1480Cys	p.R1480C	ENST00000361445	NM_004958.3	1480	Cgc/Tgc	30/58	0.571600312116014	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.587518745678719	1		509	751	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166547	118166547	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs74114325	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	282	382	1	ENST00000369448.3:c.1057G>A	p.Val353Ile	p.V353I	ENST00000369448	NM_017709.3	353	Gtc/Atc	2/2	1	2	FACETS	0.814	0.772	0.855	1	0.995	1	CLONAL	2	TRUE	1	0.587518745678719	2		383	590	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246550	105246550	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	33	442	1	ENST00000349310.3:c.50A>G	p.Glu17Gly	p.E17G	ENST00000349310	NM_001014432.1	17	gAg/gGg	4/15	1	2	FACETS	0.161	0.131	0.196	0.161	0.131	0.196	SUBCLONAL	1	TRUE	1	0.587518745678719	2		443	696	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191118	185191118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564401067	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	297	499	0	ENST00000265026.3:c.1999G>A	p.Ala667Thr	p.A667T	ENST00000265026	NM_004721.4	667	Gcc/Acc	11/14	0.175683722833085	3	FACETS	1	0.975	1	1	0.975	1	INDETERMINATE	2	TRUE	1	0.587518745678719	3		499	627	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	620	571	5	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	1	2	FACETS	0.877	0.857	0.897	1	0.998	1	CLONAL	3	TRUE	1	0.587518745678719	2		576	802	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433388	49433388	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555191598	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	375	588	0	ENST00000301067.7:c.8059C>T	p.Arg2687Ter	p.R2687*	ENST00000301067	NM_003482.3	2687	Cga/Tga	32/54	1	2	FACETS	0.757	0.722	0.792	1	0.996	1	SUBCLONAL	2	TRUE	1	0.587518745678719	2		588	843	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431874	49431874	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	380	584	1	ENST00000301067.7:c.9265del	p.Val3089TrpfsTer30	p.V3089Wfs*30	ENST00000301067	NM_003482.3	3089	Gtg/tg	34/54	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.587518745678719	2		585	901	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671005	30671005	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1344945241	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	380	635	0	ENST00000376406.3:c.5741del	p.Gly1914GlufsTer57	p.G1914Efs*57	ENST00000376406	NM_014641.2	1914	gGa/ga	12/15	0.148782733361179	4	FACETS	1	0.984	1	1	0.984	1	INDETERMINATE	2	TRUE	2	0.587518745678719	4		635	959	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81891943	81891943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771121259	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	283	475	0	ENST00000359376.3:c.413C>T	p.Thr138Met	p.T138M	ENST00000359376	NM_002661.3	138	aCg/aTg	4/33	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.587518745678719	2		475	668	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290030	15290030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752282553	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	375	684	1	ENST00000263388.2:c.3524G>A	p.Arg1175Gln	p.R1175Q	ENST00000263388	NM_000435.2	1175	cGg/cAg	22/33	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.587518745678719	2		685	939	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658535	206658535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1281179215	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	206	402	0	ENST00000367120.3:c.1508C>T	p.Ala503Val	p.A503V	ENST00000367120	NM_014002.3	503	gCg/gTg	15/22	1	2	FACETS	0.815	0.767	0.864	1	0.993	1	CLONAL	2	TRUE	1	0.587518745678719	2		402	430	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268525	46268525	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199688314	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	29	343	0	ENST00000371998.3:c.2912C>T	p.Ala971Val	p.A971V	ENST00000371998		971	gCg/gTg	15/23	1	2	FACETS	0.224	0.179	0.275	0.224	0.179	0.275	SUBCLONAL	1	TRUE	1	0.587518745678719	2		343	441	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534318	534318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1447218022	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	191	355	1	ENST00000451590.1:c.5C>T	p.Thr2Met	p.T2M	ENST00000451590	NM_001130442.1	2	aCg/aTg	2/5	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.587518745678719	2		356	451	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006463	12006463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	372	596	1	ENST00000396373.4:c.431C>T	p.Pro144Leu	p.P144L	ENST00000396373	NM_001987.4	144	cCg/cTg	4/8	0.148782733361179	4	FACETS	1	0.993	1	1	0.993	1	INDETERMINATE	2	TRUE	2	0.587518745678719	4		597	813	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562552	21562552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	79	108	0	ENST00000382592.4:c.1367C>T	p.Thr456Met	p.T456M	ENST00000382592	NM_014572.2	456	aCg/aTg	4/8	NA	2	FACETS	0.796	0.719	0.873			1	INDETERMINATE	2	TRUE	NA	0.587518745678719	2		108	169	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849994	151849994	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	172	338	0	ENST00000262189.6:c.12322C>T	p.Arg4108Ter	p.R4108*	ENST00000262189	NM_170606.2	4108	Cga/Tga	49/59	0.22523733321128	3	FACETS	0.9	0.838	0.963	0.9	0.838	0.963	INDETERMINATE	2	TRUE	1	0.587518745678719	3		338	421	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028642	42028642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367727094	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	303	563	1	ENST00000219905.7:c.4180C>T	p.Arg1394Cys	p.R1394C	ENST00000219905	NM_001164273.1	1394	Cgt/Tgt	13/24	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.587518745678719	2		564	725	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707900	47707900	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	239	353	0	ENST00000233146.2:c.2524G>T	p.Glu842Ter	p.E842*	ENST00000233146	NM_000251.2	842	Gag/Tag	15/16	0.22523733321128	3	FACETS	0.989	0.933	1	0.989	0.933	1	INDETERMINATE	2	TRUE	1	0.587518745678719	3		353	532	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46597034	46597034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767899036	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	341	504	2	ENST00000263734.3:c.848C>T	p.Ala283Val	p.A283V	ENST00000263734	NM_001430.4	283	gCg/gTg	7/16	0.22523733321128	3	FACETS	0.939	0.893	0.985	0.939	0.893	0.985	INDETERMINATE	2	TRUE	1	0.587518745678719	3		506	800	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604707	48604707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs377767371	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	231	370	0	ENST00000342988.3:c.1529G>T	p.Gly510Val	p.G510V	ENST00000342988	NM_005359.5	510	gGa/gTa	12/12	0.175683722833085	3	FACETS	0.965	0.909	1	0.965	0.909	1	INDETERMINATE	2	TRUE	1	0.587518745678719	3		370	527	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367315	50367315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751092583	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	192	415	0	ENST00000331340.3:c.122C>T	p.Ser41Leu	p.S41L	ENST00000331340	NM_006060.4	41	tCg/tTg	3/8	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.587518745678719	2		415	484	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854949	76854949	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	372	287	0	ENST00000373344.5:c.5887C>T	p.Arg1963Trp	p.R1963W	ENST00000373344	NM_000489.3	1963	Cgg/Tgg	25/35	1	1	FACETS	1	0.995	1	1	0.997	1	CLONAL	2	TRUE	0	0.587518745678719	1		287	413	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217225	11217225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	295	470	0	ENST00000361445.4:c.4453G>A	p.Glu1485Lys	p.E1485K	ENST00000361445	NM_004958.3	1485	Gag/Aag	30/58	0.571600312116014	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.587518745678719	1		470	681	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216310	2216310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780465036	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	396	596	2	ENST00000398665.3:c.1954C>T	p.Arg652Trp	p.R652W	ENST00000398665	NM_032482.2	652	Cgg/Tgg	20/28	1	2	FACETS	0.84	0.805	0.876	1	0.996	1	CLONAL	2	TRUE	1	0.587518745678719	2		598	802	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596063	43596063	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs570176656	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	282	582	0	ENST00000355710.3:c.230G>A	p.Arg77His	p.R77H	ENST00000355710	NM_020975.4	77	cGc/cAc	2/20	0.455149083313978	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.587518745678719	1		582	588	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598946	28598946	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1003343893	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	419	656	1	ENST00000253063.3:c.506G>T	p.Arg169Leu	p.R169L	ENST00000253063	NM_031459.4	169	cGg/cTg	4/10	1	2	FACETS	0.8	0.766	0.834	1	0.996	1	SUBCLONAL	2	TRUE	1	0.587518745678719	2		657	891	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11301671	11301671	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	375	561	0	ENST00000361445.4:c.1480G>T	p.Gly494Trp	p.G494W	ENST00000361445	NM_004958.3	494	Ggg/Tgg	10/58	0.571600312116014	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.587518745678719	1		561	801	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518658	204518658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	166	300	0	ENST00000367182.3:c.1321G>A	p.Glu441Lys	p.E441K	ENST00000367182	NM_001278516.1	441	Gag/Aag	11/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.587518745678719	2		300	406	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109992	115109992	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	491	623	0	ENST00000257566.3:c.1886T>C	p.Leu629Pro	p.L629P	ENST00000257566	NM_016569.3	629	cTc/cCc	8/8	1	2	FACETS	0.751	0.721	0.781	1	0.997	1	SUBCLONAL	2	TRUE	1	0.587518745678719	2		623	1113	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544660	65544660	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	342	586	0	ENST00000358664.4:c.266A>G	p.Lys89Arg	p.K89R	ENST00000358664	NM_002382.4	89	aAg/aGg	4/5	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.587518745678719	2		586	853	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781372	3781372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	390	646	0	ENST00000262367.5:c.4993G>A	p.Asp1665Asn	p.D1665N	ENST00000262367	NM_004380.2	1665	Gac/Aac	30/31	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.587518745678719	2		646	914	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796993	78796993	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376501662	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	311	476	0	ENST00000306801.3:c.1106G>A	p.Arg369His	p.R369H	ENST00000306801	NM_020761.2	369	cGt/cAt	9/34	0.175683722833085	3	FACETS	0.943	0.895	0.992	0.943	0.895	0.992	INDETERMINATE	2	TRUE	1	0.587518745678719	3		476	726	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4094473	4094473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201110543	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	387	678	1	ENST00000262948.5:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000262948	NM_030662.3	357	cGg/cAg	10/11	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.587518745678719	2		679	886	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224087	36224087	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	364	598	0	ENST00000222270.7:c.6641del	p.Pro2214GlnfsTer2	p.P2214Qfs*2	ENST00000222270	NM_014727.1	2213	Ccc/cc	28/37	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.587518745678719	2		598	907	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023499	31023499	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	215	440	0	ENST00000375687.4:c.2984A>G	p.His995Arg	p.H995R	ENST00000375687	NM_015338.5	995	cAc/cGc	13/13	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.587518745678719	2		440	516	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839867	27839867	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334849705	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	387	545	1	ENST00000328488.2:c.227C>T	p.Ala76Val	p.A76V	ENST00000328488	NM_003533.2	76	gCa/gTa	1/1	0.148782733361179	4	FACETS	1	0.993	1	1	0.993	1	INDETERMINATE	2	TRUE	2	0.587518745678719	4		546	870	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798402	32798402	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	289	552	0	ENST00000374899.4:c.1454T>C	p.Val485Ala	p.V485A	ENST00000374899	NM_018833.2	485	gTg/gCg	8/12	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.587518745678719	2		552	704	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399408	139399409	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAC	novel	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	276	649	0	ENST00000277541.6:c.4732_4734dup	p.Val1578dup	p.V1578dup	ENST00000277541	NM_017617.3	1578	-/GTG	26/34	1	2	FACETS	0.94	0.883	0.997	0.94	0.883	0.997	CLONAL	1	TRUE	1	0.587518745678719	2		649	1000	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814897	139814897	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	367	554	1	ENST00000247668.2:c.890C>T	p.Ala297Val	p.A297V	ENST00000247668	NM_021138.3	297	gCc/gTc	8/11	1	2	FACETS	0.766	0.73	0.801	1	0.996	1	SUBCLONAL	2	TRUE	1	0.587518745678719	2		555	816	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938603	76938603	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	243	231	0	ENST00000373344.5:c.2145A>T	p.Lys715Asn	p.K715N	ENST00000373344	NM_000489.3	715	aaA/aaT	9/35	1	1	FACETS	1	0.986	1	1	0.996	1	CLONAL	2	TRUE	0	0.587518745678719	1		231	283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0049826-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	314	890	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.284738266495386	2	FACETS	0.921	0.871	0.971	0.921	0.871	0.971	CLONAL	2	TRUE	0	0.37932548444835	2		893	899	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444815	49444815	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049826-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	394	909	0	ENST00000301067.7:c.2651del	p.Pro884LeufsTer46	p.P884Lfs*46	ENST00000301067	NM_003482.3	884	cCt/ct	10/54	0.333681514124393	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.37932548444835	3		909	1218	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606596	29606596	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0049826-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	70	455	0	ENST00000389048.3:c.1282+2T>G		p.X428_splice	ENST00000389048	NM_004304.4	428			0.382274538670094	3	FACETS	0.833	0.728	0.947	0.417	0.364	0.474	CLONAL	1	TRUE	1	0.37932548444835	3		455	527	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740867	58740867	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049833-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	220	490	0	ENST00000305921.3:c.1772G>C	p.Gly591Ala	p.G591A	ENST00000305921	NM_003620.3	591	gGa/gCa	6/6	1	2	FACETS	0.952	0.888	1	0.952	0.888	1	CLONAL	1	TRUE	1	0.608358025057771	2		490	760	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339373	116339373	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049833-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	137	441	0	ENST00000397752.3:c.235C>T	p.Gln79Ter	p.Q79*	ENST00000397752	NM_000245.2	79	Cag/Tag	2/21	1	2	FACETS	0.868	0.794	0.945	0.868	0.794	0.945	CLONAL	1	TRUE	1	0.608358025057771	2		441	519	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593613	55593613	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913521	NA	P-0050110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	206	385	0	ENST00000288135.5:c.1679T>A	p.Val560Asp	p.V560D	ENST00000288135	NM_000222.2	560	gTt/gAt	11/21	1	2	FACETS	0.909	0.85	0.968	0.909	0.85	0.968	CLONAL	1	TRUE	1	0.858889203567756	2		385	528	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913514	NA	P-0050110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	41	630	0	ENST00000288135.5:c.2466T>A	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaA	17/21	1	2	FACETS	0.16	0.133	0.191	0.16	0.133	0.191	SUBCLONAL	1	TRUE	1	0.858889203567756	2		630	596	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913514	NA	P-0050110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	195	396	0	ENST00000288135.5:c.2466T>G	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaG	17/21	1	2	FACETS	0.762	0.709	0.816	0.762	0.709	0.816	SUBCLONAL	1	TRUE	1	0.858889203567756	2		396	596	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599333	55599333	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913682	NA	P-0050110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	26	409	0	ENST00000288135.5:c.2459A>G	p.Asp820Gly	p.D820G	ENST00000288135	NM_000222.2	820	gAt/gGt	17/21	1	2	FACETS	0.096	0.076	0.12	0.096	0.076	0.12	SUBCLONAL	1	TRUE	1	0.858889203567756	2		409	628	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280672	115280672	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	290	400	0	ENST00000438362.2:c.359C>A	p.Ser120Ter	p.S120*	ENST00000438362	NM_001242891.1	120	tCa/tAa	4/20	0.858889203567756	1	FACETS	0.937	0.901	0.972	0.937	0.901	0.972	CLONAL	1	TRUE	0	0.858889203567756	1		400	411	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602900	55602900	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0050110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	242	357	0	ENST00000288135.5:c.2610T>G	p.Tyr870Ter	p.Y870*	ENST00000288135	NM_000222.2	870	taT/taG	19/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.858889203567756	2		357	544	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541343	187541343	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	25	329	0	ENST00000441802.2:c.6397G>A	p.Gly2133Ser	p.G2133S	ENST00000441802	NM_005245.3	2133	Ggt/Agt	10/27	1	2	FACETS	0.122	0.095	0.152	0.122	0.095	0.152	SUBCLONAL	1	TRUE	1	0.858889203567756	2		329	478	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0050182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	101	872	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.205595080703437	1	FACETS	0.966	0.863	1	0.966	0.863	1	CLONAL	1	TRUE	0	0.225181064544327	1		872	824	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0050182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	91	462	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.225181064544327	2		462	732	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575183	48575183	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	67	312	0	ENST00000342988.3:c.377T>G	p.Val126Gly	p.V126G	ENST00000342988	NM_005359.5	126	gTc/gGc	3/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.225181064544327	2		312	407	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942773	44942773	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	86	281	0	ENST00000377967.4:c.3353T>G	p.Leu1118Arg	p.L1118R	ENST00000377967	NM_021140.2	1118	cTt/cGt	23/29	1	1	FACETS	0.841	0.748	0.939	1	0.982	1	CLONAL	2	TRUE	0	0.225181064544327	1		281	403	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0050193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2308	825	1620	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	0.15304078683689	6	FACETS	1	0.994	1	1	0.997	1	CLONAL	4	FALSE	3	0.15304078683689	6		1620	3133	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431319	49431319	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	164	650	0	ENST00000301067.7:c.9820C>T	p.Gln3274Ter	p.Q3274*	ENST00000301067	NM_003482.3	3274	Cag/Tag	34/54	0.15304078683689	1	FACETS	0.949	0.874	1	1	0.994	1	CLONAL	3	FALSE	0	0.15304078683689	1		650	695	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433053	49433062	+	frameshift_variant	Frame_Shift_Del	DEL	GAGAGTCGGT	GAGAGTCGGT	-	novel	NA	P-0050193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	277	1222	0	ENST00000301067.7:c.8309_8318del	p.Asp2770AlafsTer14	p.D2770Afs*14	ENST00000301067	NM_003482.3	2770	gACCGACTCTCc/gc	33/54	0.15304078683689	1	FACETS	0.844	0.791	0.899	1	0.996	1	CLONAL	3	FALSE	0	0.15304078683689	1		1222	1320	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048714	180048714	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1655	520	1201	0	ENST00000261937.6:c.1848C>A	p.Phe616Leu	p.F616L	ENST00000261937	NM_182925.4	616	ttC/ttA	13/30	0.152880952275787	4	FACETS	0.901	0.86	0.942	1	0.997	1	CLONAL	4	FALSE	2	0.15304078683689	4		1201	2175	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184086	123184086	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	10	205	0	ENST00000218089.9:c.944G>A	p.Trp315Ter	p.W315*	ENST00000218089	NM_001042749.1	315	tGg/tAg	11/35	0.303362824549729	2	FACETS	0.871	0.606	1			1	CLONAL	3	FALSE	NA	0.15304078683689	2		205	50	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050225-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	54	421	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.196801736462372	4	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	2	0.17	4		423	310	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970927	21970928	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0050225-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	14	922	0	ENST00000304494.5:c.430dup	p.Arg144ProfsTer21	p.R144Pfs*21	ENST00000304494	NM_000077.4	144	cgc/cCgc	2/3	0.127390572577447	0	FACETS	0.616	0.445	0.822			1	SUBCLONAL	1	TRUE	0	0.17	0		922	222	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0050398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	84	915	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.18	2		915	789	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0050398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	38	349	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	0.606	0.499	0.725	0.606	0.499	0.725	SUBCLONAL	1	TRUE	1	0.18	2		349	697	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481620	56481620	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	92	591	0	ENST00000267101.3:c.655T>A	p.Phe219Ile	p.F219I	ENST00000267101	NM_001982.3	219	Ttt/Att	6/28	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.18	2		591	827	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495523	56495534	+	inframe_deletion	In_Frame_Del	DEL	CACAGAGTTGCC	CACAGAGTTGCC	-	novel	NA	P-0050398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	105	533	0	ENST00000267101.3:c.3716_3727del	p.Gln1239_Pro1242del	p.Q1239_P1242del	ENST00000267101	NM_001982.3	1238	aCACAGAGTTGCCca/aca	28/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.18	2		533	789	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910665	32910665	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs431825294	NA	P-0050398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	59	390	0	ENST00000380152.3:c.2173A>G	p.Lys725Glu	p.K725E	ENST00000380152		725	Aaa/Gaa	11/27	1	2	FACETS	0.957	0.822	1	0.957	0.822	1	CLONAL	1	TRUE	1	0.18	2		390	685	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0050545-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	29	830	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.314	0.251	0.387	0.314	0.251	0.387	SUBCLONAL	1	TRUE	1	0.21	2		830	879	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17359601	17359601	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050545-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	28	400	0	ENST00000375499.3:c.240G>C	p.Lys80Asn	p.K80N	ENST00000375499	NM_003000.2	80	aaG/aaC	3/8	1	2	FACETS	0.548	0.437	0.674	0.548	0.437	0.674	SUBCLONAL	1	TRUE	1	0.21	2		400	487	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738308	190738308	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1238956903	NA	P-0050545-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	19	296	0	ENST00000441310.2:c.2560C>G	p.Leu854Val	p.L854V	ENST00000441310	NM_000534.4	854	Ctt/Gtt	12/13	1	2	FACETS	0.52	0.394	0.668	0.52	0.394	0.668	SUBCLONAL	1	TRUE	1	0.21	2		296	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0050765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	416	774	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.296775432511654	3	FACETS	0.964	0.92	1	0.964	0.92	1	CLONAL	3	TRUE	0	0.315420651022189	3		776	1056	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0050765-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	177	915	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.113456070662345	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	0	0.113456070662345	3		915	969	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21630888	21630888	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050765-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	66	476	0	ENST00000421138.2:c.716G>T	p.Gly239Val	p.G239V	ENST00000421138		239	gGt/gTt	8/16	0.113456070662345	9	FACETS	1	0.967	1	0.237	0.205	0.273	CLONAL	1	TRUE	3	0.113456070662345	9		476	1141	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430458	181430458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1260218988	NA	P-0050765-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	62	910	1	ENST00000325404.1:c.310G>A	p.Glu104Lys	p.E104K	ENST00000325404	NM_003106.3	104	Gag/Aag	1/1	0.113456070662345	7	FACETS	1	0.968	1	0.296	0.254	0.341	CLONAL	1	TRUE	2	0.113456070662345	7		911	949	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586122	29586122	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050865-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	232	494	0	ENST00000356175.3:c.4345del	p.Ser1449AlafsTer13	p.S1449Afs*13	ENST00000356175	NM_000267.3	1448	Aaa/aa	32/57	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.815600322525578	2		494	556	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553703	29553703	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1555613843	NA	P-0050865-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	237	473	0	ENST00000356175.3:c.2251+1G>A		p.X751_splice	ENST00000356175	NM_000267.3	751			1	2	FACETS	0.983	0.924	1	0.983	0.924	1	CLONAL	1	TRUE	1	0.78	2		473	618	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593619	55593659	+	protein_altering_variant	In_Frame_Del	DEL	AGATAAATGGAAACAATTATGTTTACATAGACCCAACACAA	AGATAAATGGAAACAATTATGTTTACATAGACCCAACACAA	GT	novel	NA	P-0050865-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	188	504	2	ENST00000288135.5:c.1685_1725delinsGT	p.Glu562_Gln575delinsGly	p.E562_Q575delinsG	ENST00000288135	NM_000222.2	562	gAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAA/gGT	11/21	1	2	FACETS	0.788	0.732	0.845	0.788	0.732	0.845	SUBCLONAL	1	TRUE	1	0.78	2		506	612	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050903-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	176	314	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.493604739214049	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.493604739214049	2		314	324	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0050903-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	99	285	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.493604739214049	2		285	363	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932981	39932981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050903-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	177	751	0	ENST00000378444.4:c.1618C>T	p.Arg540Trp	p.R540W	ENST00000378444	NM_001123385.1	540	Cgg/Tgg	4/15	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.493604739214049	2		751	712	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967027	25967027	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050903-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	199	765	1	ENST00000435504.4:c.2179C>T	p.Pro727Ser	p.P727S	ENST00000435504		727	Ccc/Tcc	13/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.493604739214049	2		766	735	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370730	55370730	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050903-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	127	673	0	ENST00000297316.4:c.32A>G	p.Asp11Gly	p.D11G	ENST00000297316	NM_022454.3	11	gAc/gGc	1/2	0.268680463899949	6	FACETS	1	0.963	1			1	INDETERMINATE	1	TRUE	NA	0.493604739214049	6		673	907	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0050936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	56	915	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	NA	2	FACETS	0.32	0.273	0.371			1	INDETERMINATE	1	TRUE	NA	0.506969814435855	2		915	691	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350062	70350062	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1160145619	NA	P-0050936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	38	480	0	ENST00000374080.3:c.4045C>T	p.Gln1349Ter	p.Q1349*	ENST00000374080		1349	Cag/Tag	28/45	1	2	FACETS	0.296	0.244	0.354	0.296	0.244	0.354	SUBCLONAL	1	TRUE	1	0.506969814435855	2		480	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0051066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	268	796	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.394775642919588	2	FACETS	1	0.992	1	0.678	0.639	0.718	CLONAL	1	TRUE	0	0.537785457794443	2		796	735	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15975498	15975498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	80	512	0	ENST00000268712.3:c.3856C>T	p.Leu1286Phe	p.L1286F	ENST00000268712	NM_006311.3	1286	Ctc/Ttc	29/46	0.394775642919588	2	FACETS	0.789	0.699	0.884	0.395	0.349	0.442	SUBCLONAL	1	TRUE	0	0.537785457794443	2		512	377	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180542	56180542	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	48	312	0	ENST00000399503.3:c.3871C>G	p.Leu1291Val	p.L1291V	ENST00000399503	NM_005921.1	1291	Cta/Gta	16/20	0.436131482763246	3	FACETS	1	0.927	1	0.379	0.325	0.438	CLONAL	1	TRUE	0	0.537785457794443	3		312	199	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843416	3843431	+	frameshift_variant	Frame_Shift_Del	DEL	GTCATGTGATTCAAAA	GTCATGTGATTCAAAA	CACATT	novel	NA	P-0051066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	79	432	1	ENST00000262367.5:c.1172_1187delinsAATGTG	p.Val391GlufsTer40	p.V391Efs*40	ENST00000262367	NM_004380.2	391	gTTTTGAATCACATGACg/gAATGTGg	4/31	0.393505919563292	3	FACETS	0.641	0.564	0.723	0.32	0.282	0.362	SUBCLONAL	1	TRUE	1	0.537785457794443	3		433	582	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874011	123874013	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs780061449	NA	P-0051160-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	13	26	0	ENST00000330479.4:c.62_64del	p.Ala21del	p.A21del	ENST00000330479	NM_020382.3	14	gaGGCg/gag	2/9	1	2	FACETS	1	0.773	1	1	0.773	1	CLONAL	1	TRUE	1	0.17	2		26	140	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0051160-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	6	341	4	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	1	2	FACETS	0.458	0.274	0.708	0.458	0.274	0.708	SUBCLONAL	1	TRUE	1	0.17	2		345	154	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0051160-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	7	435	1	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.132678387433859	3	FACETS	0.369	0.229	0.555	0.185	0.114	0.278	SUBCLONAL	1	TRUE	1	0.17	3		436	242	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176330	24176330	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1057517825	NA	P-0051160-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	9	921	0	ENST00000263121.7:c.1121G>A	p.Arg374Gln	p.R374Q	ENST00000263121	NM_003073.3	374	cGg/cAg	9/9	1	2	FACETS	0.253	0.166	0.364	0.253	0.166	0.364	SUBCLONAL	1	TRUE	1	0.17	2		921	419	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300570	11300570	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764486955	NA	P-0051160-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	8	0	0	ENST00000361445.4:c.1576C>T	p.Arg526Cys	p.R526C	ENST00000361445	NM_004958.3	526	Cgt/Tgt	11/58	1	2	FACETS	0.363	0.233	0.533	0.363	0.233	0.533	SUBCLONAL	1	TRUE	1	0.17	2		0	259	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392700	118392700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051160-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	4	0	0	ENST00000534358.1:c.11732C>T	p.Ser3911Leu	p.S3911L	ENST00000534358	NM_005933.3	3911	tCg/tTg	36/36	1	2	FACETS	0.31	0.162	0.525	0.31	0.162	0.525	SUBCLONAL	1	TRUE	1	0.17	2		0	152	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206933	162206933	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777074432	NA	P-0051160-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	4	0	0	ENST00000366898.1:c.742G>A	p.Val248Ile	p.V248I	ENST00000366898	NM_004562.2	248	Gtc/Atc	7/12	1	2	FACETS	0.413	0.216	0.697	0.413	0.216	0.697	SUBCLONAL	1	TRUE	1	0.17	2		0	114	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50481242	50481242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051160-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	4	0	0	ENST00000394963.4:c.628C>T	p.Arg210Trp	p.R210W	ENST00000394963	NM_003076.4	210	Cgg/Tgg	5/13	1	2	FACETS	0.256	0.133	0.434	0.256	0.133	0.434	SUBCLONAL	1	TRUE	1	0.17	2		0	184	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412311	139412311	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752919688	NA	P-0051160-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	13	0	0	ENST00000277541.6:c.1334C>T	p.Thr445Met	p.T445M	ENST00000277541	NM_017617.3	445	aCg/aTg	8/34	1	2	FACETS	0.31	0.22	0.42	0.31	0.22	0.42	SUBCLONAL	1	TRUE	1	0.17	2		0	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0051377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	272	764	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.448403869122948	3	FACETS	0.976	0.928	1	0.976	0.928	1	CLONAL	3	FALSE	0	0.448403869122948	3		764	507	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0051410-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	22	341	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.566	0.438	0.715	0.566	0.438	0.715	SUBCLONAL	1	TRUE	1	0.21	2		341	370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555526101	NA	P-0051410-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	77	851	0	ENST00000269305.4:c.497C>G	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tGa	5/11	1	2	FACETS	0.944	0.828	1	0.944	0.828	1	CLONAL	1	TRUE	1	0.21	2		851	777	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183788	10183788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882034	NA	P-0051410-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	73	725	3	ENST00000256474.2:c.257C>T	p.Pro86Leu	p.P86L	ENST00000256474	NM_000551.3	86	cCc/cTc	1/3	0.0516838890916385	3	FACETS	1	0.919	1	0.534	0.467	0.607	INDETERMINATE	1	TRUE	1	0.21	3		728	719	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845885	156845885	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051410-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	89	948	0	ENST00000524377.1:c.1515C>G	p.Ile505Met	p.I505M	ENST00000524377	NM_002529.3	505	atC/atG	13/17	1	2	FACETS	0.923	0.817	1	0.923	0.817	1	CLONAL	1	TRUE	1	0.21	2		948	918	SUCCESS
APC	324	MSKCC	GRCh37	5	112176254	112176254	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs759441332	NA	P-0051410-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	24	511	0	ENST00000257430.4:c.4963A>G	p.Thr1655Ala	p.T1655A	ENST00000257430	NM_000038.5	1655	Aca/Gca	16/16	1	2	FACETS	0.494	0.386	0.618	0.494	0.386	0.618	SUBCLONAL	1	TRUE	1	0.21	2		511	463	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044906	47044907	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0051410-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	72	428	0	ENST00000377604.3:c.2237dup	p.Glu748Ter	p.E748*	ENST00000377604	NM_001204468.1	744	-/G	20/24	0.0786192691533865	2	FACETS	0.781	0.685	0.884			1	INDETERMINATE	2	TRUE	NA	0.21	2		428	439	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115269008	115269008	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0051410-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	25	349	0	ENST00000438362.2:c.1603-1G>T		p.X535_splice	ENST00000438362	NM_001242891.1	535			1	2	FACETS	0.623	0.491	0.776	0.623	0.491	0.776	SUBCLONAL	1	TRUE	1	0.21	2		349	382	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571907	64571907	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051410-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	61	990	0	ENST00000312049.6:c.1732C>A	p.Gln578Lys	p.Q578K	ENST00000312049	NM_130799.2	578	Caa/Aaa	10/10	1	2	FACETS	0.579	0.498	0.668	0.579	0.498	0.668	SUBCLONAL	1	TRUE	1	0.21	2		990	1003	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029002	14029002	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0051410-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	14	277	1	ENST00000311895.7:c.1214-1G>T		p.X405_splice	ENST00000311895	NM_005236.2	405			1	2	FACETS	0.585	0.423	0.781	0.585	0.423	0.781	SUBCLONAL	1	TRUE	1	0.21	2		278	228	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842333	68842333	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051410-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	27	492	0	ENST00000261769.5:c.394G>C	p.Val132Leu	p.V132L	ENST00000261769	NM_004360.3	132	Gtt/Ctt	4/16	0.197549539122825	3	FACETS	0.559	0.444	0.692	0.28	0.222	0.346	SUBCLONAL	1	TRUE	1	0.21	3		492	508	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830088	72830088	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051410-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	37	0	0	ENST00000268489.5:c.6493G>C	p.Asp2165His	p.D2165H	ENST00000268489	NM_006885.3	2165	Gac/Cac	9/10	0.197549539122825	3	FACETS	0.489	0.401	0.587	0.244	0.2	0.294	SUBCLONAL	1	TRUE	1	0.21	3		0	797	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830278	72830278	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1456428565	NA	P-0051410-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	10	0	0	ENST00000268489.5:c.6303G>A	p.Met2101Ile	p.M2101I	ENST00000268489	NM_006885.3	2101	atG/atA	9/10	0.197549539122825	3	FACETS	0.276	0.186	0.391	0.138	0.093	0.196	SUBCLONAL	1	TRUE	1	0.21	3		0	381	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830823	72830823	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051410-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	36	0	0	ENST00000268489.5:c.5758G>C	p.Glu1920Gln	p.E1920Q	ENST00000268489	NM_006885.3	1920	Gag/Cag	9/10	0.197549539122825	3	FACETS	0.464	0.38	0.559	0.232	0.19	0.28	SUBCLONAL	1	TRUE	1	0.21	3		0	816	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441443	40441443	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051410-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	20	0	0	ENST00000345506.4:c.14T>G	p.Ile5Ser	p.I5S	ENST00000345506	NM_003152.3	5	aTc/aGc	3/20	1	2	FACETS	0.4	0.305	0.512	0.4	0.305	0.512	SUBCLONAL	1	TRUE	1	0.21	2		0	476	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603113	48603113	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051410-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	28	0	0	ENST00000342988.3:c.1414C>T	p.Pro472Ser	p.P472S	ENST00000342988	NM_005359.5	472	Cca/Tca	11/12	1	2	FACETS	0.423	0.336	0.521	0.423	0.336	0.521	SUBCLONAL	1	TRUE	1	0.21	2		0	631	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213367	36213368	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0051410-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	71	873	2	ENST00000222270.7:c.2564_2565delinsTT	p.Arg855Leu	p.R855L	ENST00000222270	NM_014727.1	855	cGG/cTT	4/37	1	2	FACETS	0.874	0.761	0.995	0.874	0.761	0.995	CLONAL	1	TRUE	1	0.21	2		875	774	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467194	25467194	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051410-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	32	601	0	ENST00000264709.3:c.1681G>A	p.Glu561Lys	p.E561K	ENST00000264709	NM_175629.2	561	Gag/Aag	15/23	0.291443861323589	1	FACETS	0.578	0.468	0.702	0.578	0.468	0.702	SUBCLONAL	1	TRUE	0	0.21	1		601	472	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721197	39721197	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051410-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	29	550	0	ENST00000361337.2:c.700C>G	p.Leu234Val	p.L234V	ENST00000361337	NM_003286.2	234	Ctt/Gtt	9/21	1	2	FACETS	0.526	0.421	0.646	0.526	0.421	0.646	SUBCLONAL	1	TRUE	1	0.21	2		550	525	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158202	47158202	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0051410-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	58	432	0	ENST00000409792.3:c.4497T>A	p.Cys1499Ter	p.C1499*	ENST00000409792	NM_014159.6	1499	tgT/tgA	4/21	0.0516838890916385	3	FACETS	1	0.956	1	0.645	0.555	0.743	INDETERMINATE	1	TRUE	1	0.21	3		432	473	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467548	66467548	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051410-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	35	406	0	ENST00000273854.3:c.721G>C	p.Ala241Pro	p.A241P	ENST00000273854	NM_004439.5	241	Gct/Cct	3/18	1	2	FACETS	0.868	0.712	1	0.868	0.712	1	CLONAL	1	TRUE	1	0.21	2		406	384	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517826	187517826	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051410-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	49	403	0	ENST00000441802.2:c.12868G>T	p.Glu4290Ter	p.E4290*	ENST00000441802	NM_005245.3	4290	Gag/Tag	25/27	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.21	2		403	423	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818324	170818324	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051410-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	56	522	1	ENST00000296930.5:c.154G>A	p.Gly52Ser	p.G52S	ENST00000296930	NM_002520.6	52	Ggt/Agt	3/11	1	2	FACETS	0.847	0.725	0.98	0.847	0.725	0.98	CLONAL	1	TRUE	1	0.21	2		523	630	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370846	55370846	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775715316	NA	P-0051410-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	82	675	3	ENST00000297316.4:c.148G>A	p.Ala50Thr	p.A50T	ENST00000297316	NM_022454.3	50	Gcg/Acg	1/2	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.21	2		678	574	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0051420-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	207	662	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	1	2	FACETS	0.995	0.927	1	1	0.994	1	CLONAL	2	FALSE	1	0.306532679700598	2		662	679	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410538	63410538	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051420-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	194	403	0	ENST00000330258.3:c.2629G>C	p.Gly877Arg	p.G877R	ENST00000330258	NM_152424.3	877	Ggc/Cgc	2/2	1	1	FACETS	1	0.975	1	1	0.995	1	CLONAL	3	FALSE	0	0.306532679700598	1		403	337	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443697	29443697	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs281864719	NA	P-0051667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	111	647	0	ENST00000389048.3:c.3520T>C	p.Phe1174Leu	p.F1174L	ENST00000389048	NM_004304.4	1174	Ttc/Ctc	23/29	1	2	FACETS	0.501	0.451	0.554	0.501	0.451	0.554	SUBCLONAL	1	TRUE	1	0.713578405891679	2		647	621	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953942	17953942	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	62	1295	0	ENST00000458235.1:c.460C>G	p.Leu154Val	p.L154V	ENST00000458235	NM_000215.3	154	Ctc/Gtc	5/24	0.493806022022342	1	FACETS	0.159	0.137	0.184	0.159	0.137	0.184	SUBCLONAL	1	TRUE	0	0.713578405891679	1		1295	701	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907696	76907697	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0051667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	64	569	0	ENST00000373344.5:c.4464dup	p.Leu1489ThrfsTer10	p.L1489Tfs*10	ENST00000373344	NM_000489.3	1488	-/A	15/35	0.431933674545794	0	FACETS		NA	1			1	NA	1	TRUE	0	0.713578405891679	0		569	301	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579346	7579348	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs764486868	NA	P-0051819-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	186	771	0	ENST00000269305.4:c.339_341del	p.Phe113del	p.F113del	ENST00000269305	NM_001126112.2	113	ttCTTg/ttg	4/11	0.498904595405453	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.498904595405453	1		771	558	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971138	21971138	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs760640852	NA	P-0051819-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	179	616	0	ENST00000304494.5:c.220G>T	p.Asp74Tyr	p.D74Y	ENST00000304494	NM_000077.4	74	Gac/Tac	2/3	0.498904595405453	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.498904595405453	1		616	402	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844143	68844143	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1064794231	NA	P-0051819-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	50	549	0	ENST00000261769.5:c.731A>G	p.Asp244Gly	p.D244G	ENST00000261769	NM_004360.3	244	gAt/gGt	6/16	1	2	FACETS	0.305	0.258	0.356	0.305	0.258	0.356	SUBCLONAL	1	TRUE	1	0.498904595405453	2		549	658	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88671966	88671966	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0051819-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	49	181	0	ENST00000360948.2:c.1205-1G>A		p.X402_splice	ENST00000360948	NM_001012338.2	402			1	2	FACETS	0.761	0.65	0.881	0.761	0.65	0.881	SUBCLONAL	1	TRUE	1	0.498904595405453	2		181	258	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156870	106156870	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1365072838	NA	P-0051819-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	190	479	0	ENST00000380013.4:c.1771C>T	p.Gln591Ter	p.Q591*	ENST00000380013	NM_001127208.2	591	Cag/Tag	3/11	0.492832039441689	2	FACETS	0.982	0.921	1	0.982	0.921	1	CLONAL	2	TRUE	0	0.498904595405453	2		479	388	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713129	30713129	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0051819-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	57	253	0	ENST00000295754.5:c.455-1G>A		p.X152_splice	ENST00000295754	NM_003242.5	152			0.498904595405453	1	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	0	0.498904595405453	1		253	171	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212923	94212923	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051819-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	85	279	0	ENST00000323929.3:c.319C>T	p.Pro107Ser	p.P107S	ENST00000323929	NM_005591.3	107	Cca/Tca	5/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.498904595405453	2		279	258	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895689	28895689	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051819-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	165	472	0	ENST00000282397.4:c.3085del	p.Leu1029PhefsTer8	p.L1029Ffs*8	ENST00000282397	NM_002019.4	1029	Ctt/tt	23/30	0.498904595405453	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.498904595405453	1		472	438	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250390	10250390	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051819-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	128	555	0	ENST00000340748.4:c.3862G>T	p.Val1288Phe	p.V1288F	ENST00000340748		1288	Gtc/Ttc	33/40	1	2	FACETS	0.947	0.862	1	0.947	0.862	1	CLONAL	1	TRUE	1	0.498904595405453	2		555	542	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307245	65307245	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051819-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	51	412	0	ENST00000342505.4:c.2443C>G	p.Pro815Ala	p.P815A	ENST00000342505	NM_002227.2	815	Cca/Gca	18/25	1	2	FACETS	0.439	0.373	0.511	0.439	0.373	0.511	SUBCLONAL	1	TRUE	1	0.498904595405453	2		412	466	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324868	31324868	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051819-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	32	572	0	ENST00000412585.2:c.68G>A	p.Trp23Ter	p.W23*	ENST00000412585	NM_005514.6	23	tGg/tAg	1/8	0.498904595405453	1	FACETS	0.34	0.277	0.411	0.34	0.277	0.411	SUBCLONAL	1	TRUE	0	0.498904595405453	1		572	283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0051863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	473	915	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.849649979365305	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.854603241445445	2		915	544	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215927	36215927	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs372271044	NA	P-0051968-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	23	683	0	ENST00000222270.7:c.3467A>G	p.Asn1156Ser	p.N1156S	ENST00000222270	NM_014727.1	1156	aAt/aGt	10/37	0.175754744839461	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		683	421	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715979	52715979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205227	NA	P-0052035-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	115	569	0	ENST00000322088.6:c.544C>T	p.Arg182Trp	p.R182W	ENST00000322088	NM_014225.5	182	Cgg/Tgg	5/15	0.218548244445971	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	0	0.27980429311363	1		569	493	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743885	41743885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780282463	NA	P-0052196-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	137	934	0	ENST00000301178.4:c.820G>A	p.Gly274Arg	p.G274R	ENST00000301178	NM_021913.4	274	Gga/Aga	7/20	1	2	FACETS	0.274	0.249	0.302	0.274	0.249	0.302	SUBCLONAL	1	TRUE	1	0.846652493292009	2		934	1179	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161970019	161970019	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052196-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	99	694	0	ENST00000366898.1:c.950A>T	p.Gln317Leu	p.Q317L	ENST00000366898	NM_004562.2	317	cAg/cTg	9/12	1	2	FACETS	0.236	0.21	0.264	0.236	0.21	0.264	SUBCLONAL	1	TRUE	1	0.846652493292009	2		694	989	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950528	68950528	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0052196-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	33	251	0	ENST00000288368.4:c.839+1G>C		p.X280_splice	ENST00000288368	NM_024870.2	280			1	2	FACETS	0.229	0.186	0.276	0.229	0.186	0.276	SUBCLONAL	1	TRUE	1	0.846652493292009	2		251	341	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391747	139391747	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052196-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1652	157	1053	0	ENST00000277541.6:c.6444C>A	p.Ser2148Arg	p.S2148R	ENST00000277541	NM_017617.3	2148	agC/agA	34/34	0.846652493292009	3	FACETS	0.292	0.266	0.319	0.146	0.133	0.16	SUBCLONAL	1	TRUE	1	0.846652493292009	3		1053	1809	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	166	590	1	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.562973758741969	6	FACETS	0.916	0.85	0.984	0.916	0.85	0.984	CLONAL	3	FALSE	3	0.562973758741969	6		591	456	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115284260	115284260	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	21	493	0	ENST00000438362.2:c.26C>G	p.Ser9Ter	p.S9*	ENST00000438362	NM_001242891.1	9	tCa/tGa	2/20	0.562973758741969	4	FACETS	0.47	0.363	0.595	0.157	0.121	0.199	SUBCLONAL	1	FALSE	1	0.562973758741969	4		493	248	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254962	16254962	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	38	429	0	ENST00000375759.3:c.2227C>G	p.Gln743Glu	p.Q743E	ENST00000375759	NM_015001.2	743	Cag/Gag	11/15	0.516355188290964	5	FACETS	1	0.897	1			1	CLONAL	1	FALSE	NA	0.562973758741969	5		429	225	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650934	37650934	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	30	437	0	ENST00000447079.4:c.2406C>G	p.Phe802Leu	p.F802L	ENST00000447079	NM_015083.1	802	ttC/ttG	5/14	0.562973758741969	6	FACETS	0.917	0.743	1	0.306	0.247	0.371	CLONAL	1	FALSE	3	0.562973758741969	6		437	247	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69229651	69229651	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	54	397	0	ENST00000462284.1:c.727G>C	p.Asp243His	p.D243H	ENST00000462284	NM_002392.5	243	Gat/Cat	9/11	0.562973758741969	11	FACETS	1	0.963	1	0.131	0.112	0.152	CLONAL	1	FALSE	0	0.562973758741969	11		397	470	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620683	52620683	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	40	334	0	ENST00000394830.3:c.3070G>C	p.Glu1024Gln	p.E1024Q	ENST00000394830	NM_018313.4	1024	Gaa/Caa	21/30	0.270628775378613	6	FACETS	0.927	0.782	1	0.463	0.391	0.541	INDETERMINATE	2	FALSE	2	0.562973758741969	6		334	163	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602760	10602760	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	230	925	0	ENST00000171111.5:c.818G>C	p.Cys273Ser	p.C273S	ENST00000171111	NM_203500.1	273	tGc/tCc	3/6	0.562973758741969	3	FACETS	0.975	0.929	1	0.975	0.929	1	CLONAL	3	FALSE	0	0.562973758741969	3		925	358	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480568	123480568	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	65	600	0	ENST00000371139.4:c.76G>A	p.Asp26Asn	p.D26N	ENST00000371139	NM_001114937.2	26	Gat/Aat	1/4	0.562973758741969	1	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	FALSE	0	0.562973758741969	1		600	165	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119789	70119789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778047936	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	48	627	0	ENST00000245479.2:c.791G>A	p.Arg264Lys	p.R264K	ENST00000245479	NM_000346.3	264	aGa/aAa	3/3	0.363947904180596	6	FACETS	1	0.927	1	0.386	0.328	0.449	CLONAL	1	FALSE	3	0.562973758741969	6		627	313	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259169	89259169	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	75	389	0	ENST00000336596.2:c.313G>A	p.Asp105Asn	p.D105N	ENST00000336596	NM_005233.5	105	Gac/Aac	3/17	0.270628775378613	6	FACETS	0.957	0.865	1	0.957	0.865	1	INDETERMINATE	4	FALSE	2	0.562973758741969	6		389	148	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099340	27099340	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	72	580	0	ENST00000324856.7:c.3577G>A	p.Asp1193Asn	p.D1193N	ENST00000324856	NM_006015.4	1193	Gat/Aat	14/20	0.516355188290964	5	FACETS	0.797	0.703	0.896			1	SUBCLONAL	2	FALSE	NA	0.562973758741969	5		580	296	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347725	89347725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759287339	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	57	735	0	ENST00000301030.4:c.5225C>T	p.Ser1742Leu	p.S1742L	ENST00000301030	NM_001256183.1	1742	tCg/tTg	9/13	0.562973758741969	3	FACETS	0.892	0.771	1	0.446	0.385	0.511	CLONAL	1	FALSE	1	0.562973758741969	3		735	291	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590660	189590660	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	18	370	0	ENST00000264731.3:c.1225G>C	p.Glu409Gln	p.E409Q	ENST00000264731	NM_003722.4	409	Gag/Cag	10/14	0.562973758741969	7	FACETS	0.59	0.444	0.761	0.098	0.074	0.127	SUBCLONAL	1	FALSE	1	0.562973758741969	7		370	261	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675551	30675551	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	96	810	0	ENST00000376406.3:c.2805G>C	p.Glu935Asp	p.E935D	ENST00000376406	NM_014641.2	935	gaG/gaC	8/15	0.562973758741969	7	FACETS	0.794	0.71	0.883	0.318	0.284	0.354	SUBCLONAL	2	FALSE	2	0.562973758741969	7		810	517	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258935	16258935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs546998631	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	60	727	0	ENST00000375759.3:c.6200C>T	p.Pro2067Leu	p.P2067L	ENST00000375759	NM_015001.2	2067	cCg/cTg	11/15	0.516355188290964	5	FACETS	1	0.964	1			1	CLONAL	1	FALSE	NA	0.562973758741969	5		727	290	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058645	42058645	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	26	236	0	ENST00000219905.7:c.8365G>C	p.Glu2789Gln	p.E2789Q	ENST00000219905	NM_001164273.1	2789	Gag/Cag	24/24	0.498826146455062	4	FACETS	1	0.922	1	0.662	0.535	0.802	CLONAL	1	FALSE	2	0.562973758741969	4		236	109	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259578	89259578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	77	399	0	ENST00000336596.2:c.722G>A	p.Arg241Lys	p.R241K	ENST00000336596	NM_005233.5	241	aGg/aAg	3/17	0.270628775378613	6	FACETS	0.914	0.826	1	0.914	0.826	1	INDETERMINATE	4	FALSE	2	0.562973758741969	6		399	159	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476376	88476376	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	36	631	0	ENST00000360948.2:c.1756C>A	p.Gln586Lys	p.Q586K	ENST00000360948	NM_001012338.2	586	Cag/Aag	15/19	0.498826146455062	4	FACETS	0.826	0.684	0.983	0.413	0.342	0.492	CLONAL	1	FALSE	2	0.562973758741969	4		631	242	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41021774	41021774	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	65	471	0	ENST00000267868.3:c.716C>T	p.Ser239Leu	p.S239L	ENST00000267868	NM_002875.4	239	tCa/tTa	8/10	0.498826146455062	4	FACETS	1	0.942	1	0.571	0.499	0.648	CLONAL	1	FALSE	2	0.562973758741969	4		471	316	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467918	50467918	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	30	469	1	ENST00000331340.3:c.1153G>A	p.Glu385Lys	p.E385K	ENST00000331340	NM_006060.4	385	Gag/Aag	8/8	0.363947904180596	6	FACETS	0.925	0.749	1	0.308	0.249	0.374	CLONAL	1	FALSE	3	0.562973758741969	6		470	245	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971194	21971194	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	91	312	0	ENST00000304494.5:c.164del	p.Gly55AlafsTer91	p.G55Afs*91	ENST00000304494	NM_000077.4	55	gGc/gc	2/3	0.503016696166104	2	FACETS	0.908	0.829	0.987	0.908	0.829	0.987	CLONAL	2	FALSE	0	0.562973758741969	2		312	178	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944463	40944463	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	64	556	1	ENST00000373198.4:c.2039C>A	p.Thr680Lys	p.T680K	ENST00000373198	NM_133170.3	680	aCa/aAa	12/32	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	FALSE	NA	0.562973758741969	2		557	156	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170016852	170016852	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	42	548	1	ENST00000295797.4:c.1657G>A	p.Asp553Asn	p.D553N	ENST00000295797	NM_002740.5	553	Gat/Aat	17/18	0.562973758741969	7	FACETS	0.973	0.815	1	0.162	0.135	0.192	CLONAL	1	FALSE	1	0.562973758741969	7		549	369	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94906474	94906474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1173588660	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	32	398	2	ENST00000536441.1:c.1424G>A	p.Arg475Gln	p.R475Q	ENST00000536441	NM_144665.3	475	cGa/cAa	10/10	0.420702131375283	5	FACETS	1	0.836	1	0.341	0.279	0.41	CLONAL	1	FALSE	2	0.562973758741969	5		400	205	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937145	36937145	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	78	743	0	ENST00000361632.4:c.1174G>C	p.Glu392Gln	p.E392Q	ENST00000361632		392	Gag/Cag	9/16	0.416450651018207	4	FACETS	1	0.956	1	0.587	0.519	0.659	CLONAL	1	FALSE	2	0.562973758741969	4		743	369	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40874858	40874858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	52	604	0	ENST00000428826.2:c.442G>A	p.Glu148Lys	p.E148K	ENST00000428826		148	Gag/Aag	6/21	0.562973758741969	6	FACETS	0.949	0.81	1	0.316	0.27	0.367	CLONAL	1	FALSE	3	0.562973758741969	6		604	414	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350822	15350822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200902225	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	65	686	0	ENST00000263377.2:c.3181G>A	p.Glu1061Lys	p.E1061K	ENST00000263377	NM_058243.2	1061	Gaa/Aaa	15/20	0.562973758741969	7	FACETS	0.762	0.664	0.866	0.381	0.332	0.433	SUBCLONAL	2	FALSE	3	0.562973758741969	7		686	365	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485307	8485307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	23	424	0	ENST00000356435.5:c.3073C>T	p.His1025Tyr	p.H1025Y	ENST00000356435		1025	Cat/Tat	18/35	0.503016696166104	2	FACETS	0.717	0.568	0.883	0.358	0.284	0.442	SUBCLONAL	1	FALSE	0	0.562973758741969	2		424	114	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713864	30713864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223845	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	56	598	0	ENST00000295754.5:c.1189G>A	p.Asp397Asn	p.D397N	ENST00000295754	NM_003242.5	397	Gac/Aac	4/7	0.270628775378613	6	FACETS	1	0.91	1	0.27	0.232	0.311	INDETERMINATE	1	FALSE	2	0.562973758741969	6		598	392	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591070	67591070	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	22	234	0	ENST00000274335.5:c.1663G>C	p.Glu555Gln	p.E555Q	ENST00000274335		555	Gag/Cag	12/15	0.365108218950951	3	FACETS	1	0.835	1	0.355	0.281	0.437	CLONAL	1	FALSE	0	0.562973758741969	3		234	94	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535355	66535355	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	24	521	1	ENST00000273854.3:c.106C>T	p.Arg36Ter	p.R36*	ENST00000273854	NM_004439.5	36	Cga/Tga	1/18	0.562973758741969	5	FACETS	0.971	0.768	1	0.243	0.192	0.3	CLONAL	1	FALSE	1	0.562973758741969	5		522	162	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721789	176721789	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	43	471	1	ENST00000439151.2:c.7420C>T	p.Gln2474Ter	p.Q2474*	ENST00000439151	NM_022455.4	2474	Cag/Tag	23/23	0.365108218950951	3	FACETS	1	0.933	1	0.395	0.336	0.459	CLONAL	1	FALSE	0	0.562973758741969	3		472	165	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799155	88799155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	37	538	0	ENST00000360948.2:c.230C>T	p.Ser77Leu	p.S77L	ENST00000360948	NM_001012338.2	77	tCa/tTa	2/19	0.498826146455062	4	FACETS	1	0.874	1	0.529	0.441	0.626	CLONAL	1	FALSE	2	0.562973758741969	4		538	194	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673804	37673804	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	50	466	0	ENST00000447079.4:c.2958C>G	p.Phe986Leu	p.F986L	ENST00000447079	NM_015083.1	986	ttC/ttG	10/14	0.562973758741969	6	FACETS	0.899	0.764	1	0.3	0.254	0.349	CLONAL	1	FALSE	3	0.562973758741969	6		466	420	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38504705	38504705	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	70	608	1	ENST00000254066.5:c.316G>A	p.Glu106Lys	p.E106K	ENST00000254066	NM_000964.3	106	Gag/Aag	3/9	0.562973758741969	6	FACETS	1	0.929	1	0.365	0.319	0.415	CLONAL	1	FALSE	3	0.562973758741969	6		609	483	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288812	33288812	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	58	430	0	ENST00000374542.5:c.740C>T	p.Ser247Leu	p.S247L	ENST00000374542	NM_001141970.1	247	tCa/tTa	3/8	0.562973758741969	7	FACETS	0.914	0.785	1	0.183	0.157	0.211	CLONAL	1	FALSE	2	0.562973758741969	7		430	543	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462628	40462628	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	61	602	0	ENST00000345506.4:c.2326G>C	p.Asp776His	p.D776H	ENST00000345506	NM_003152.3	776	Gac/Cac	20/20	0.562973758741969	6	FACETS	0.853	0.737	0.98	0.284	0.245	0.327	CLONAL	1	FALSE	3	0.562973758741969	6		602	540	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876296	35876296	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	18	512	0	ENST00000303115.3:c.1088G>T	p.Arg363Ile	p.R363I	ENST00000303115	NM_002185.3	363	aGa/aTa	8/8	0.562973758741969	6	FACETS	0.555	0.418	0.716			1	SUBCLONAL	1	FALSE	NA	0.562973758741969	6		512	245	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026084	48026084	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	101	386	0	ENST00000234420.5:c.962C>A	p.Ser321Ter	p.S321*	ENST00000234420	NM_000179.2	321	tCa/tAa	4/10	0.562973758741969	6	FACETS	1	0.95	1	0.798	0.727	0.87	CLONAL	3	FALSE	2	0.562973758741969	6		386	239	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098808	178098808	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	53	616	0	ENST00000397062.3:c.237G>C	p.Glu79Asp	p.E79D	ENST00000397062	NM_006164.4	79	gaG/gaC	2/5	0.383199395211129	5	FACETS	0.89	0.762	1	0.178	0.152	0.206	CLONAL	1	FALSE	0	0.562973758741969	5		616	390	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871714	37871714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	64	756	4	ENST00000269571.5:c.1238C>T	p.Ser413Leu	p.S413L	ENST00000269571		413	tCa/tTa	11/27	0.562973758741969	6	FACETS	1	0.894	1	0.345	0.299	0.394	CLONAL	1	FALSE	3	0.562973758741969	6		760	467	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733512	85733512	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	42	407	0	ENST00000370580.1:c.500C>G	p.Ser167Cys	p.S167C	ENST00000370580	NM_003921.4	167	tCt/tGt	3/3	0.562973758741969	8	FACETS	1	0.91	1			1	CLONAL	1	FALSE	NA	0.562973758741969	8		407	354	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325023	123325023	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	42	644	0	ENST00000358487.5:c.305C>G	p.Ser102Cys	p.S102C	ENST00000358487	NM_000141.4	102	tCc/tGc	3/18	0.562973758741969	3	FACETS	0.79	0.665	0.927	0.263	0.221	0.309	CLONAL	1	FALSE	0	0.562973758741969	3		644	242	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875655	56875655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	48	563	0	ENST00000308159.5:c.2259G>A	p.Met753Ile	p.M753I	ENST00000308159	NM_014669.4	753	atG/atA	21/22	0.562973758741969	3	FACETS	0.63	0.534	0.734	0.315	0.267	0.367	SUBCLONAL	1	FALSE	1	0.562973758741969	3		563	347	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371774	45371774	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	68	385	0	ENST00000262160.6:c.1217A>G	p.Tyr406Cys	p.Y406C	ENST00000262160	NM_005901.5	406	tAt/tGt	10/11	0.420702131375283	5	FACETS	1	0.953	1	0.766	0.679	0.856	CLONAL	2	FALSE	2	0.562973758741969	5		385	194	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211614	46211614	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	11	279	0	ENST00000334344.6:c.580G>A	p.Glu194Lys	p.E194K	ENST00000334344	NM_152641.2	194	Gaa/Aaa	5/21	0.516024327080376	5	FACETS	0.477	0.331	0.658	0.095	0.066	0.132	SUBCLONAL	1	FALSE	0	0.562973758741969	5		279	151	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162861	47162861	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763434646	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	25	444	0	ENST00000409792.3:c.3265C>T	p.Arg1089Trp	p.R1089W	ENST00000409792	NM_014159.6	1089	Cgg/Tgg	3/21	0.270628775378613	6	FACETS	1	0.861	1	0.278	0.22	0.342	INDETERMINATE	1	FALSE	2	0.562973758741969	6		444	170	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467545	66467545	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	67	284	0	ENST00000273854.3:c.724G>T	p.Val242Phe	p.V242F	ENST00000273854	NM_004439.5	242	Gtc/Ttc	3/18	0.562973758741969	5	FACETS	0.944	0.842	1	0.708	0.632	0.786	CLONAL	3	FALSE	1	0.562973758741969	5		284	155	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187180	11187180	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	23	639	0	ENST00000361445.4:c.6238G>C	p.Glu2080Gln	p.E2080Q	ENST00000361445	NM_004958.3	2080	Gag/Cag	45/58	0.545070179783172	3	FACETS	0.602	0.473	0.749	0.301	0.236	0.375	SUBCLONAL	1	FALSE	1	0.562973758741969	3		639	174	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307709	11307709	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	26	478	0	ENST00000361445.4:c.1198G>C	p.Ala400Pro	p.A400P	ENST00000361445	NM_004958.3	400	Gct/Cct	8/58	0.545070179783172	3	FACETS	0.759	0.608	0.928	0.379	0.304	0.464	CLONAL	1	FALSE	1	0.562973758741969	3		478	156	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414974	78414974	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	32	354	0	ENST00000370768.2:c.1792C>A	p.Pro598Thr	p.P598T	ENST00000370768	NM_003902.3	598	Cct/Act	19/20	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.562973758741969	NA		354	436	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733431	85733431	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	44	423	0	ENST00000370580.1:c.581G>C	p.Arg194Thr	p.R194T	ENST00000370580	NM_003921.4	194	aGa/aCa	3/3	0.562973758741969	8	FACETS	1	0.944	1			1	CLONAL	1	FALSE	NA	0.562973758741969	8		423	325	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733483	85733483	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	28	400	0	ENST00000370580.1:c.529C>G	p.Leu177Val	p.L177V	ENST00000370580	NM_003921.4	177	Cta/Gta	3/3	0.562973758741969	8	FACETS	0.836	0.669	1			1	CLONAL	1	FALSE	NA	0.562973758741969	8		400	320	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85742008	85742008	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	47	669	0	ENST00000370580.1:c.28G>C	p.Glu10Gln	p.E10Q	ENST00000370580	NM_003921.4	10	Gag/Cag	1/3	0.562973758741969	8	FACETS	0.672	0.566	0.79			1	SUBCLONAL	1	FALSE	NA	0.562973758741969	8		669	668	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844186	156844186	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs767630555	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	42	846	0	ENST00000524377.1:c.1189C>A	p.Pro397Thr	p.P397T	ENST00000524377	NM_002529.3	397	Ccg/Acg	9/17	0.562973758741969	4	FACETS	0.821	0.689	0.966	0.274	0.229	0.322	CLONAL	1	FALSE	1	0.562973758741969	4		846	284	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981228	201981228	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	78	860	0	ENST00000359651.3:c.307T>G	p.Cys103Gly	p.C103G	ENST00000359651		103	Tgc/Ggc	2/8	0.562973758741969	7	FACETS	1	0.972	1			1	CLONAL	1	FALSE	NA	0.562973758741969	7		860	488	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617393	43617394	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	CT	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	40	405	0	ENST00000355710.3:c.2731-1_2731delinsCT		p.X911_splice	ENST00000355710	NM_020975.4	911		16/20	0.383589707917951	6	FACETS	1	0.955	1	0.365	0.306	0.429	CLONAL	1	FALSE	2	0.562973758741969	6		405	207	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405706	70405706	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	24	511	0	ENST00000373644.4:c.3220G>A	p.Glu1074Lys	p.E1074K	ENST00000373644	NM_030625.2	1074	Gag/Aag	4/12	0.383589707917951	6	FACETS	0.934	0.737	1	0.234	0.184	0.29	CLONAL	1	FALSE	2	0.562973758741969	6		511	194	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61197629	61197629	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs778449586	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	40	511	0	ENST00000301761.2:c.11C>G	p.Ser4Cys	p.S4C	ENST00000301761	NM_017841.2	4	tCt/tGt	1/4	0.562973758741969	6	FACETS	0.577	0.479	0.686			1	SUBCLONAL	1	FALSE	NA	0.562973758741969	6		511	524	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135692	64135692	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	120	789	0	ENST00000334205.4:c.1160G>T	p.Arg387Leu	p.R387L	ENST00000334205	NM_003942.2	387	cGg/cTg	10/17	0.562973758741969	6	FACETS	1	0.968	1			1	CLONAL	2	FALSE	NA	0.562973758741969	6		789	399	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948448	71948448	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	50	1068	0	ENST00000298229.2:c.3160C>T	p.Pro1054Ser	p.P1054S	ENST00000298229	NM_001567.3	1054	Cca/Tca	26/28	0.420702131375283	5	FACETS	0.908	0.773	1	0.303	0.257	0.352	CLONAL	1	FALSE	2	0.562973758741969	5		1068	361	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103161	119103161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	59	409	0	ENST00000264033.4:c.199G>A	p.Val67Met	p.V67M	ENST00000264033	NM_005188.3	67	Gtg/Atg	2/16	0.562973758741969	7	FACETS	0.76	0.658	0.87			1	SUBCLONAL	2	FALSE	NA	0.562973758741969	7		409	332	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409082	4409082	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	46	404	0	ENST00000261254.3:c.777G>T	p.Gln259His	p.Q259H	ENST00000261254	NM_001759.3	259	caG/caT	5/5	0.491102111845087	3	FACETS	1	0.89	1	0.351	0.299	0.406	CLONAL	1	FALSE	0	0.562973758741969	3		404	199	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246437	46246437	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1390057319	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	28	289	0	ENST00000334344.6:c.4531G>C	p.Glu1511Gln	p.E1511Q	ENST00000334344	NM_152641.2	1511	Gaa/Caa	15/21	0.516024327080376	5	FACETS	1	0.9	1	0.238	0.192	0.289	CLONAL	1	FALSE	0	0.562973758741969	5		289	154	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420356	49420356	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	208	707	0	ENST00000301067.7:c.15393G>T	p.Met5131Ile	p.M5131I	ENST00000301067	NM_003482.3	5131	atG/atT	48/54	0.516024327080376	5	FACETS	1	0.96	1	0.811	0.77	0.852	CLONAL	4	FALSE	0	0.562973758741969	5		707	336	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420682	49420682	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	55	622	0	ENST00000301067.7:c.15067G>C	p.Asp5023His	p.D5023H	ENST00000301067	NM_003482.3	5023	Gac/Cac	48/54	0.516024327080376	5	FACETS	1	0.907	1	0.215	0.184	0.247	CLONAL	1	FALSE	0	0.562973758741969	5		622	336	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446787	49446787	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	45	580	0	ENST00000301067.7:c.1023G>C	p.Glu341Asp	p.E341D	ENST00000301067	NM_003482.3	341	gaG/gaC	8/54	0.516024327080376	5	FACETS	0.772	0.65	0.906	0.154	0.13	0.182	CLONAL	1	FALSE	0	0.562973758741969	5		580	382	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865353	57865353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	48	882	0	ENST00000228682.2:c.2830C>T	p.Pro944Ser	p.P944S	ENST00000228682	NM_005269.2	944	Cca/Tca	12/12	0.562973758741969	11	FACETS	1	0.869	1	0.094	0.079	0.11	CLONAL	1	FALSE	0	0.562973758741969	11		882	584	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865804	57865804	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	41	674	0	ENST00000228682.2:c.3281C>G	p.Ser1094Cys	p.S1094C	ENST00000228682	NM_005269.2	1094	tCc/tGc	12/12	0.562973758741969	11	FACETS	1	0.858	1	0.094	0.078	0.112	CLONAL	1	FALSE	0	0.562973758741969	11		674	498	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69229690	69229690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	49	404	0	ENST00000462284.1:c.766G>A	p.Glu256Lys	p.E256K	ENST00000462284	NM_002392.5	256	Gaa/Aaa	9/11	0.562973758741969	11	FACETS	1	0.962	1	0.136	0.115	0.159	CLONAL	1	FALSE	0	0.562973758741969	11		404	412	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118881	115118881	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	14	393	0	ENST00000257566.3:c.460G>T	p.Asp154Tyr	p.D154Y	ENST00000257566	NM_016569.3	154	Gac/Tac	2/8	1	2	FACETS	0.572	0.42	0.749	0.572	0.42	0.749	SUBCLONAL	1	FALSE	1	0.562973758741969	2		393	87	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597615	28597615	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	19	399	0	ENST00000241453.7:c.2291-1G>C		p.X764_splice	ENST00000241453	NM_004119.2	764			0.562973758741969	3	FACETS	0.721	0.554	0.912	0.24	0.184	0.304	CLONAL	1	FALSE	0	0.562973758741969	3		399	120	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912247	32912247	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1361496246	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	21	507	0	ENST00000380152.3:c.3755C>T	p.Ser1252Phe	p.S1252F	ENST00000380152		1252	tCt/tTt	11/27	0.562973758741969	7	FACETS	0.655	0.505	0.83	0.109	0.084	0.139	SUBCLONAL	1	FALSE	1	0.562973758741969	7		507	274	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944603	32944603	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397507982	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	36	586	0	ENST00000380152.3:c.8396G>C	p.Arg2799Thr	p.R2799T	ENST00000380152		2799	aGa/aCa	19/27	0.562973758741969	7	FACETS	0.865	0.712	1	0.144	0.118	0.173	CLONAL	1	FALSE	1	0.562973758741969	7		586	356	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108055	30108055	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	29	644	1	ENST00000331968.5:c.752C>T	p.Ser251Leu	p.S251L	ENST00000331968	NM_002742.2	251	tCa/tTa	5/18	0.270628775378613	6	FACETS	1	0.903	1	0.299	0.242	0.363	INDETERMINATE	1	FALSE	2	0.562973758741969	6		645	183	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40685688	40685688	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	65	465	0	ENST00000249776.8:c.841G>C	p.Glu281Gln	p.E281Q	ENST00000249776	NM_033286.3	281	Gag/Cag	9/9	0.498826146455062	4	FACETS	1	0.973	1	0.74	0.649	0.835	CLONAL	1	FALSE	2	0.562973758741969	4		465	244	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042786	42042786	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	32	356	0	ENST00000219905.7:c.6981G>C	p.Gln2327His	p.Q2327H	ENST00000219905	NM_001164273.1	2327	caG/caC	17/24	0.498826146455062	4	FACETS	0.95	0.779	1	0.475	0.389	0.57	CLONAL	1	FALSE	2	0.562973758741969	4		356	187	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104408	2104408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	75	765	0	ENST00000219476.3:c.448G>A	p.Gly150Arg	p.G150R	ENST00000219476	NM_000548.3	150	Ggg/Agg	5/42	0.562973758741969	3	FACETS	1	0.901	1	0.511	0.451	0.575	CLONAL	1	FALSE	1	0.562973758741969	3		765	334	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781378	3781379	+	missense_variant	Missense_Mutation	DNP	CA	CA	AT	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	63	863	1	ENST00000262367.5:c.4986_4987delinsAT	p.Asp1662_Gly1663delinsGluTrp	p.D1662_G1663delinsEW	ENST00000262367	NM_004380.2	1662	gaTGgg/gaATgg	30/31	0.562973758741969	3	FACETS	1	0.913	1	0.529	0.462	0.6	CLONAL	1	FALSE	1	0.562973758741969	3		864	271	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934581	9934581	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	20	499	0	ENST00000330684.3:c.1574C>G	p.Ser525Cys	p.S525C	ENST00000330684	NM_001134407.1	525	tCt/tGt	7/13	0.562973758741969	3	FACETS	0.615	0.475	0.777	0.308	0.237	0.389	SUBCLONAL	1	FALSE	1	0.562973758741969	3		499	148	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634434	23634434	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	29	384	0	ENST00000261584.4:c.2852C>G	p.Ser951Cys	p.S951C	ENST00000261584	NM_024675.3	951	tCt/tGt	9/13	0.562973758741969	3	FACETS	0.936	0.762	1	0.468	0.381	0.564	CLONAL	1	FALSE	1	0.562973758741969	3		384	141	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50784027	50784027	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	37	638	0	ENST00000398568.2:c.418G>C	p.Glu140Gln	p.E140Q	ENST00000398568	NM_001042412.1	140	Gaa/Caa	3/18	0.562973758741969	3	FACETS	0.619	0.513	0.737	0.31	0.256	0.369	SUBCLONAL	1	FALSE	1	0.562973758741969	3		638	272	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813889	50813889	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	63	619	0	ENST00000398568.2:c.1443C>G	p.Phe481Leu	p.F481L	ENST00000398568	NM_001042412.1	481	ttC/ttG	8/18	0.562973758741969	3	FACETS	1	0.941	1	0.567	0.496	0.642	CLONAL	1	FALSE	1	0.562973758741969	3		619	253	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822322	72822322	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	107	804	1	ENST00000268489.5:c.9853C>T	p.Pro3285Ser	p.P3285S	ENST00000268489	NM_006885.3	3285	Cct/Tct	10/10	0.562973758741969	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	FALSE	1	0.562973758741969	3		805	231	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934238	81934238	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs746020068	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	83	598	0	ENST00000359376.3:c.1215C>G	p.Ile405Met	p.I405M	ENST00000359376	NM_002661.3	405	atC/atG	14/33	0.562973758741969	3	FACETS	0.879	0.791	0.969	0.879	0.791	0.969	CLONAL	2	FALSE	1	0.562973758741969	3		598	215	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349970	89349970	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	62	813	0	ENST00000301030.4:c.2980G>T	p.Gly994Trp	p.G994W	ENST00000301030	NM_001256183.1	994	Ggg/Tgg	9/13	0.562973758741969	3	FACETS	0.932	0.811	1	0.466	0.405	0.53	CLONAL	1	FALSE	1	0.562973758741969	3		813	303	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264407	30264407	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	100	344	1	ENST00000322652.5:c.142G>T	p.Gly48Trp	p.G48W	ENST00000322652	NM_015355.2	48	Ggg/Tgg	1/16	0.562973758741969	6	FACETS	1	0.971	1	0.797	0.72	0.876	CLONAL	2	FALSE	3	0.562973758741969	6		345	316	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881127	37881127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	77	821	0	ENST00000269571.5:c.2456C>T	p.Ser819Phe	p.S819F	ENST00000269571		819	tCc/tTc	20/27	0.562973758741969	6	FACETS	1	0.967	1	0.428	0.377	0.482	CLONAL	1	FALSE	3	0.562973758741969	6		821	453	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246454	41246454	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	45	667	0	ENST00000357654.3:c.1094G>C	p.Arg365Thr	p.R365T	ENST00000357654	NM_007294.3	365	aGa/aCa	10/23	0.562973758741969	6	FACETS	1	0.848	1	0.335	0.282	0.393	CLONAL	1	FALSE	3	0.562973758741969	6		667	338	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246489	41246489	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs80356935	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	33	667	1	ENST00000357654.3:c.1059G>A	p.Trp353Ter	p.W353*	ENST00000357654	NM_007294.3	353	tgG/tgA	10/23	0.562973758741969	6	FACETS	0.683	0.557	0.825	0.228	0.185	0.275	SUBCLONAL	1	FALSE	3	0.562973758741969	6		668	365	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56787344	56787344	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	27	390	0	ENST00000337432.4:c.830G>C	p.Arg277Thr	p.R277T	ENST00000337432	NM_058216.2	277	aGa/aCa	5/9	0.363947904180596	6	FACETS	0.98	0.785	1	0.327	0.261	0.4	CLONAL	1	FALSE	3	0.562973758741969	6		390	208	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876501	59876501	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	16	448	0	ENST00000259008.2:c.1300G>C	p.Asp434His	p.D434H	ENST00000259008	NM_032043.2	434	Gat/Cat	9/20	0.363947904180596	6	FACETS	0.549	0.407	0.719	0.183	0.135	0.24	SUBCLONAL	1	FALSE	3	0.562973758741969	6		448	220	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926597	59926597	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	26	427	0	ENST00000259008.2:c.400C>G	p.Leu134Val	p.L134V	ENST00000259008	NM_032043.2	134	Ctg/Gtg	5/20	0.363947904180596	6	FACETS	1	0.843	1	0.356	0.284	0.437	CLONAL	1	FALSE	3	0.562973758741969	6		427	184	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743299	743299	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	129	581	0	ENST00000314574.4:c.841G>C	p.Val281Leu	p.V281L	ENST00000314574	NM_005433.3	281	Gtt/Ctt	7/12	0.420702131375283	5	FACETS	1	0.98	1	0.814	0.748	0.882	CLONAL	2	FALSE	2	0.562973758741969	5		581	346	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110146	3110146	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	63	451	0	ENST00000078429.4:c.137-1G>T		p.X46_splice	ENST00000078429	NM_002067.2	46			0.562973758741969	3	FACETS	1	0.898	1	0.673	0.599	0.749	CLONAL	2	FALSE	0	0.562973758741969	3		451	142	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7141690	7141690	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	66	530	0	ENST00000302850.5:c.2680G>C	p.Glu894Gln	p.E894Q	ENST00000302850	NM_000208.2	894	Gag/Cag	13/22	0.562973758741969	3	FACETS	1	0.885	1	0.337	0.295	0.382	CLONAL	1	FALSE	0	0.562973758741969	3		530	297	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982585	10982585	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	24	37	0	ENST00000327064.4:c.207C>G	p.Ile69Met	p.I69M	ENST00000327064	NM_199141.1	69	atC/atG	1/16	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.562973758741969	NA		37	174	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354140	15354140	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1192169871	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	49	615	1	ENST00000263377.2:c.2740G>A	p.Glu914Lys	p.E914K	ENST00000263377	NM_058243.2	914	Gag/Aag	14/20	0.562973758741969	7	FACETS	1	0.937	1	0.301	0.256	0.351	CLONAL	1	FALSE	3	0.562973758741969	7		616	348	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224698	36224698	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	45	1005	0	ENST00000222270.7:c.7084C>A	p.Pro2362Thr	p.P2362T	ENST00000222270	NM_014727.1	2362	Ccg/Acg	30/37	0.562973758741969	4	FACETS	0.626	0.527	0.735	0.157	0.131	0.184	SUBCLONAL	1	FALSE	0	0.562973758741969	4		1005	399	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234276	39234276	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	18	461	0	ENST00000402219.2:c.2569G>C	p.Glu857Gln	p.E857Q	ENST00000402219	NM_005633.3	857	Gag/Cag	16/23	0.562973758741969	3	FACETS	0.381	0.288	0.491	0.191	0.144	0.246	SUBCLONAL	1	FALSE	1	0.562973758741969	3		461	215	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018106	48018106	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	91	640	0	ENST00000234420.5:c.301G>C	p.Glu101Gln	p.E101Q	ENST00000234420	NM_000179.2	101	Gag/Cag	2/10	0.562973758741969	6	FACETS	0.999	0.895	1	0.499	0.447	0.554	CLONAL	2	FALSE	2	0.562973758741969	6		640	344	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149626	61149626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	22	243	0	ENST00000295025.8:c.1816G>A	p.Glu606Lys	p.E606K	ENST00000295025	NM_002908.2	606	Gag/Aag	11/11	0.562973758741969	6	FACETS	0.752	0.585	0.944	0.188	0.146	0.236	CLONAL	1	FALSE	2	0.562973758741969	6		243	221	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61720128	61720128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	59	409	0	ENST00000401558.2:c.1306G>A	p.Asp436Asn	p.D436N	ENST00000401558	NM_003400.3	436	Gat/Aat	13/25	0.562973758741969	6	FACETS	1	0.949	1	0.304	0.263	0.349	CLONAL	1	FALSE	2	0.562973758741969	6		409	366	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538328	9538329	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	62	492	0	ENST00000353224.5:c.1669_1670del	p.Ser557LeufsTer4	p.S557Lfs*4	ENST00000353224	NM_177990.2	557	TCc/c	7/10	0.420702131375283	5	FACETS	1	0.912	1	0.698	0.613	0.786	CLONAL	2	FALSE	2	0.562973758741969	5		492	194	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560943	9560943	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	84	461	0	ENST00000353224.5:c.839C>A	p.Pro280His	p.P280H	ENST00000353224	NM_177990.2	280	cCc/cAc	4/10	0.420702131375283	5	FACETS	0.895	0.807	0.985	0.895	0.807	0.985	CLONAL	3	FALSE	2	0.562973758741969	5		461	205	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561454	9561454	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	47	580	0	ENST00000353224.5:c.328C>T	p.Gln110Ter	p.Q110*	ENST00000353224	NM_177990.2	110	Cag/Tag	4/10	0.420702131375283	5	FACETS	1	0.925	1	0.383	0.325	0.446	CLONAL	1	FALSE	2	0.562973758741969	5		580	268	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36028625	36028625	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	35	746	0	ENST00000358208.4:c.967G>T	p.Glu323Ter	p.E323*	ENST00000358208		323	Gag/Tag	8/12	0.420702131375283	5	FACETS	0.796	0.655	0.953	0.265	0.218	0.318	CLONAL	1	FALSE	2	0.562973758741969	5		746	288	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39726938	39726938	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	24	266	0	ENST00000361337.2:c.936G>C	p.Gln312His	p.Q312H	ENST00000361337	NM_003286.2	312	caG/caC	11/21	0.420702131375283	5	FACETS	0.894	0.706	1	0.298	0.235	0.369	CLONAL	1	FALSE	2	0.562973758741969	5		266	176	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54963225	54963225	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	16	425	0	ENST00000312783.6:c.29C>G	p.Ser10Ter	p.S10*	ENST00000312783	NM_198436.1	10	tCa/tGa	3/10	0.562973758741969	5	FACETS	0.454	0.336	0.595			1	SUBCLONAL	1	FALSE	NA	0.562973758741969	5		425	231	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29099518	29099518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	41	297	0	ENST00000328354.6:c.883G>A	p.Glu295Lys	p.E295K	ENST00000328354	NM_007194.3	295	Gaa/Aaa	8/15	0.562973758741969	5	FACETS	1	0.954	1	0.471	0.397	0.551	CLONAL	1	FALSE	2	0.562973758741969	5		297	190	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564798	41564798	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	47	605	0	ENST00000263253.7:c.4099G>C	p.Asp1367His	p.D1367H	ENST00000263253	NM_001429.3	1367	Gat/Cat	25/31	0.562973758741969	5	FACETS	0.677	0.572	0.793	0.226	0.19	0.265	SUBCLONAL	1	FALSE	2	0.562973758741969	5		605	455	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933819	49933819	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	49	643	0	ENST00000296474.3:c.2458G>C	p.Glu820Gln	p.E820Q	ENST00000296474	NM_002447.2	820	Gag/Cag	10/20	0.270628775378613	6	FACETS	1	0.96	1	0.353	0.301	0.409	INDETERMINATE	1	FALSE	2	0.562973758741969	6		643	262	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259598	89259598	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	76	371	0	ENST00000336596.2:c.742G>T	p.Gly248Cys	p.G248C	ENST00000336596	NM_005233.5	248	Ggc/Tgc	3/17	0.270628775378613	6	FACETS	0.963	0.872	1	0.963	0.872	1	INDETERMINATE	4	FALSE	2	0.562973758741969	6		371	149	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390128	89390128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	22	301	0	ENST00000336596.2:c.877C>T	p.His293Tyr	p.H293Y	ENST00000336596	NM_005233.5	293	Cac/Tac	4/17	0.270628775378613	6	FACETS	0.944	0.737	1	0.236	0.184	0.296	INDETERMINATE	1	FALSE	2	0.562973758741969	6		301	176	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390191	89390191	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	17	326	0	ENST00000336596.2:c.940G>T	p.Asp314Tyr	p.D314Y	ENST00000336596	NM_005233.5	314	Gac/Tac	4/17	0.270628775378613	6	FACETS	0.702	0.526	0.908	0.175	0.131	0.227	INDETERMINATE	1	FALSE	2	0.562973758741969	6		326	183	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119642282	119642282	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	41	473	0	ENST00000316626.5:c.415G>T	p.Val139Leu	p.V139L	ENST00000316626		139	Gta/Tta	4/12	0.562973758741969	9	FACETS	1	0.9	1			1	CLONAL	1	FALSE	NA	0.562973758741969	9		473	389	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920506	134920506	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	40	591	0	ENST00000398015.3:c.2321C>G	p.Ser774Ter	p.S774*	ENST00000398015	NM_004441.4	774	tCa/tGa	12/16	0.492689720640556	4	FACETS	0.874	0.732	1			1	CLONAL	1	FALSE	NA	0.562973758741969	4		591	254	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277508	142277508	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	181	354	1	ENST00000350721.4:c.1843G>T	p.Ala615Ser	p.A615S	ENST00000350721	NM_001184.3	615	Gct/Tct	8/47	0.562973758741969	7	FACETS	1	0.973	1	1	0.973	1	CLONAL	6	FALSE	1	0.562973758741969	7		355	250	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447612	187447612	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	47	673	0	ENST00000232014.4:c.581C>G	p.Ser194Cys	p.S194C	ENST00000232014	NM_001130845.1	194	tCt/tGt	5/10	0.562973758741969	7	FACETS	0.882	0.745	1	0.147	0.124	0.172	CLONAL	1	FALSE	1	0.562973758741969	7		673	456	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157900	106157900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1406291692	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	92	270	0	ENST00000380013.4:c.2801G>A	p.Gly934Glu	p.G934E	ENST00000380013	NM_001127208.2	934	gGa/gAa	3/11	0.562973758741969	5	FACETS	0.913	0.838	0.988	0.913	0.838	0.988	CLONAL	4	FALSE	1	0.562973758741969	5		270	165	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1253881	1253881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	56	784	0	ENST00000310581.5:c.3361C>T	p.Pro1121Ser	p.P1121S	ENST00000310581	NM_198253.2	1121	Ccg/Tcg	16/16	0.416450651018207	4	FACETS	1	0.924	1	0.553	0.478	0.634	CLONAL	1	FALSE	2	0.562973758741969	4		784	281	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1255456	1255456	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs374968697	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	75	599	2	ENST00000310581.5:c.3103G>T	p.Val1035Phe	p.V1035F	ENST00000310581	NM_198253.2	1035	Gtc/Ttc	14/16	0.416450651018207	4	FACETS	0.801	0.711	0.895	0.801	0.711	0.895	CLONAL	2	FALSE	2	0.562973758741969	4		601	260	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264556	1264556	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	32	601	0	ENST00000310581.5:c.2806G>C	p.Asp936His	p.D936H	ENST00000310581	NM_198253.2	936	Gat/Cat	11/16	0.416450651018207	4	FACETS	0.846	0.692	1	0.423	0.346	0.509	CLONAL	1	FALSE	2	0.562973758741969	4		601	210	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944564	38944564	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	34	329	1	ENST00000357387.3:c.4897G>A	p.Glu1633Lys	p.E1633K	ENST00000357387	NM_152756.3	1633	Gag/Aag	36/38	0.562973758741969	6	FACETS	1	0.908	1			1	CLONAL	1	FALSE	NA	0.562973758741969	6		330	219	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665715	86665715	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	24	297	0	ENST00000274376.6:c.1696G>T	p.Glu566Ter	p.E566*	ENST00000274376	NM_002890.2	566	Gag/Tag	12/25	0.365108218950951	3	FACETS	1	0.808	1	0.337	0.269	0.413	CLONAL	1	FALSE	0	0.562973758741969	3		297	108	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271297	26271297	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	68	590	0	ENST00000305910.3:c.316G>C	p.Glu106Gln	p.E106Q	ENST00000305910	NM_003534.2	106	Gag/Cag	1/1	0.562973758741969	14	FACETS	0.954	0.831	1	0.212	0.184	0.242	CLONAL	2	FALSE	5	0.562973758741969	14		590	554	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839904	27839904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	157	544	0	ENST00000328488.2:c.190C>T	p.Arg64Trp	p.R64W	ENST00000328488	NM_003533.2	64	Cgg/Tgg	1/1	0.562973758741969	14	FACETS	0.969	0.891	1	0.431	0.396	0.467	CLONAL	4	FALSE	5	0.562973758741969	14		544	630	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681461	30681461	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	39	449	0	ENST00000376406.3:c.551C>G	p.Ser184Ter	p.S184*	ENST00000376406	NM_014641.2	184	tCa/tGa	4/15	0.562973758741969	7	FACETS	0.849	0.704	1	0.17	0.14	0.202	CLONAL	1	FALSE	2	0.562973758741969	7		449	393	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322261	31322261	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	18	247	0	ENST00000412585.2:c.1088G>C	p.Ter363SerextTer3	p.*363Sext*3	ENST00000412585	NM_005514.6	363	tGa/tCa	7/8	0.562973758741969	7	FACETS	0.815	0.616	1	0.163	0.123	0.21	CLONAL	1	FALSE	2	0.562973758741969	7		247	189	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169259	32169259	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	160	686	0	ENST00000375023.3:c.3774C>A	p.Tyr1258Ter	p.Y1258*	ENST00000375023	NM_004557.3	1258	taC/taA	22/30	0.562973758741969	7	FACETS	0.903	0.839	0.967	0.722	0.671	0.774	CLONAL	4	FALSE	2	0.562973758741969	7		686	379	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190365	32190365	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	42	826	1	ENST00000375023.3:c.374C>A	p.Ser125Tyr	p.S125Y	ENST00000375023	NM_004557.3	125	tCc/tAc	3/30	0.562973758741969	7	FACETS	0.923	0.772	1	0.185	0.154	0.218	CLONAL	1	FALSE	2	0.562973758741969	7		827	389	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997461	149997461	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	39	532	0	ENST00000253339.5:c.2818C>G	p.Leu940Val	p.L940V	ENST00000253339		940	Ctt/Gtt	6/7	0.164764404112803	5	FACETS	0.765	0.643	0.897	0.51	0.429	0.598	INDETERMINATE	2	FALSE	2	0.562973758741969	5		532	167	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505476	157505476	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	43	373	0	ENST00000346085.5:c.3457G>C	p.Glu1153Gln	p.E1153Q	ENST00000346085	NM_020732.3	1153	Gag/Cag	13/20	0.164764404112803	5	FACETS	0.933	0.795	1	0.622	0.53	0.72	INDETERMINATE	2	FALSE	2	0.562973758741969	5		373	151	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963972	2963972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	48	730	0	ENST00000396946.4:c.1835G>A	p.Gly612Glu	p.G612E	ENST00000396946	NM_032415.4	612	gGa/gAa	15/25	0.363947904180596	6	FACETS	1	0.963	1	0.493	0.421	0.572	CLONAL	1	FALSE	3	0.562973758741969	6		730	245	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985495	2985495	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	39	484	0	ENST00000396946.4:c.316G>C	p.Val106Leu	p.V106L	ENST00000396946	NM_032415.4	106	Gtg/Ctg	4/25	0.363947904180596	6	FACETS	1	0.837	1	0.335	0.279	0.397	CLONAL	1	FALSE	3	0.562973758741969	6		484	293	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739959	41739959	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	51	413	0	ENST00000242208.4:c.14G>T	p.Trp5Leu	p.W5L	ENST00000242208	NM_002192.2	5	tGg/tTg	2/3	0.363947904180596	6	FACETS	1	0.931	1	0.751	0.65	0.858	CLONAL	2	FALSE	3	0.562973758741969	6		413	171	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392060	81392060	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	41	343	0	ENST00000222390.5:c.217A>G	p.Arg73Gly	p.R73G	ENST00000222390	NM_000601.4	73	Aga/Gga	2/18	0.363947904180596	6	FACETS	1	0.863	1	0.679	0.576	0.79	CLONAL	2	FALSE	3	0.562973758741969	6		343	152	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509186	106509186	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	31	643	0	ENST00000359195.3:c.1180C>G	p.Leu394Val	p.L394V	ENST00000359195	NM_002649.2	394	Ctt/Gtt	2/11	0.363947904180596	6	FACETS	0.861	0.699	1	0.287	0.233	0.348	CLONAL	1	FALSE	3	0.562973758741969	6		643	272	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873549	151873549	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	45	585	0	ENST00000262189.6:c.8989C>T	p.Gln2997Ter	p.Q2997*	ENST00000262189	NM_170606.2	2997	Caa/Taa	38/59	0.363947904180596	6	FACETS	1	0.956	1	0.468	0.397	0.546	CLONAL	1	FALSE	3	0.562973758741969	6		585	242	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012293	152012293	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	54	529	0	ENST00000262189.6:c.520G>C	p.Asp174His	p.D174H	ENST00000262189	NM_170606.2	174	Gat/Cat	4/59	0.363947904180596	6	FACETS	1	0.964	1	0.475	0.409	0.547	CLONAL	1	FALSE	3	0.562973758741969	6		529	286	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021833	69021833	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	23	531	0	ENST00000288368.4:c.3121G>T	p.Glu1041Ter	p.E1041*	ENST00000288368	NM_024870.2	1041	Gag/Tag	25/40	0.562973758741969	2	FACETS	0.483	0.38	0.601	0.242	0.19	0.301	SUBCLONAL	1	FALSE	0	0.562973758741969	2		531	169	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965854	90965854	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1060503472	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	18	329	0	ENST00000265433.3:c.1463C>G	p.Ser488Cys	p.S488C	ENST00000265433	NM_002485.4	488	tCt/tGt	11/16	0.562973758741969	5	FACETS	0.674	0.51	0.865			1	SUBCLONAL	1	FALSE	NA	0.562973758741969	5		329	175	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878834	117878834	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	33	290	0	ENST00000297338.2:c.135C>G	p.Ile45Met	p.I45M	ENST00000297338	NM_006265.2	45	atC/atG	2/14	0.365108218950951	3	FACETS	0.884	0.728	1	0.295	0.242	0.352	CLONAL	1	FALSE	0	0.562973758741969	3		290	170	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471059	8471059	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	31	367	1	ENST00000356435.5:c.3440T>C	p.Leu1147Ser	p.L1147S	ENST00000356435		1147	tTg/tCg	20/35	0.503016696166104	2	FACETS	0.765	0.644	0.888	0.765	0.644	0.888	SUBCLONAL	2	FALSE	0	0.562973758741969	2		368	72	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395070	139395070	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	43	793	0	ENST00000277541.6:c.5868C>G	p.Ile1956Met	p.I1956M	ENST00000277541	NM_017617.3	1956	atC/atG	31/34	0.491102111845087	3	FACETS	0.862	0.728	1	0.287	0.242	0.336	CLONAL	1	FALSE	0	0.562973758741969	3		793	227	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045178	47045178	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs782064788	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	141	661	0	ENST00000377604.3:c.2419A>G	p.Asn807Asp	p.N807D	ENST00000377604	NM_001204468.1	807	Aat/Gat	21/24	0.562973758741969	3	FACETS	1	0.984	1	0.801	0.746	0.856	CLONAL	2	FALSE	0	0.562973758741969	3		661	267	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227740	53227740	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1556839520	NA	P-0052304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	57	661	0	ENST00000375401.3:c.2448G>C	p.Lys816Asn	p.K816N	ENST00000375401	NM_004187.3	816	aaG/aaC	17/26	0.562973758741969	3	FACETS	1	0.956	1	0.416	0.362	0.473	CLONAL	1	FALSE	0	0.562973758741969	3		661	208	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	79	366	1				ENST00000310581	NM_198253.2	-/1132			0.253258753664643	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.326631278205092	2		367	199	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950442	17950442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200836500	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	145	840	0	ENST00000458235.1:c.1285C>T	p.Leu429Phe	p.L429F	ENST00000458235	NM_000215.3	429	Ctc/Ttc	10/24	0.1697685276218	3	FACETS	0.78	0.714	0.849	0.78	0.714	0.849	INDETERMINATE	2	TRUE	1	0.326631278205092	3		840	662	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	139	774	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.20589111192906	4	FACETS	1	0.986	1	0.746	0.68	0.815	CLONAL	1	TRUE	2	0.326631278205092	4		776	757	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510207	187510207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	98	576	0	ENST00000441802.2:c.13306C>T	p.Pro4436Ser	p.P4436S	ENST00000441802	NM_005245.3	4436	Cct/Tct	27/27	0.203600104660336	2	FACETS	0.802	0.722	0.886	0.802	0.722	0.886	CLONAL	2	TRUE	0	0.326631278205092	2		576	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203436	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	146	519	0	ENST00000269305.4:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269305	NM_001126112.2	163	Tac/Cac	5/11	0.20589111192906	4	FACETS	1	0.981	1	0.641	0.585	0.7	CLONAL	1	TRUE	2	0.326631278205092	4		519	925	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021785	71021785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs112795301	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	39	323	0	ENST00000318789.4:c.1573C>T	p.Arg525Ter	p.R525*	ENST00000318789	NM_032682.5	525	Cga/Tga	18/21	0.20589111192906	4	FACETS	0.981	0.816	1	0.49	0.408	0.582	CLONAL	1	TRUE	2	0.326631278205092	4		323	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579395	7579395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	151	1057	0	ENST00000269305.4:c.292C>T	p.Pro98Ser	p.P98S	ENST00000269305	NM_001126112.2	98	Cct/Tct	4/11	0.20589111192906	4	FACETS	1	0.987	1	0.728	0.665	0.793	CLONAL	1	TRUE	2	0.326631278205092	4		1057	843	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260597	1260597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	40	712	0	ENST00000310581.5:c.2962G>A	p.Asp988Asn	p.D988N	ENST00000310581	NM_198253.2	988	Gat/Aat	12/16	0.253258753664643	2	FACETS	0.426	0.353	0.507	0.213	0.176	0.254	SUBCLONAL	1	TRUE	0	0.326631278205092	2		712	575	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309776	104309776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202247756	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	101	700	0	ENST00000369902.3:c.367C>T	p.Arg123Cys	p.R123C	ENST00000369902	NM_016169.3	123	Cgt/Tgt	3/12	0.203600104660336	2	FACETS	1	0.963	1	0.581	0.521	0.645	CLONAL	1	TRUE	0	0.326631278205092	2		700	532	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045804	26045804	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1415819059	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	86	791	0	ENST00000540144.1:c.166C>T	p.Gln56Ter	p.Q56*	ENST00000540144	NM_003531.2	56	Cag/Tag	1/1	0.20589111192906	4	FACETS	1	0.94	1	0.548	0.485	0.616	CLONAL	1	TRUE	2	0.326631278205092	4		791	637	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983495	90983495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	38	274	1	ENST00000265433.3:c.608C>T	p.Pro203Leu	p.P203L	ENST00000265433	NM_002485.4	203	cCa/cTa	6/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.326631278205092	2		275	160	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149683	202149683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762734568	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	58	549	1	ENST00000358485.4:c.1124C>T	p.Ser375Phe	p.S375F	ENST00000358485	NM_001080125.1	375	tCc/tTc	8/9	0.286001599512684	4	FACETS	1	0.883	1			1	CLONAL	1	TRUE	NA	0.326631278205092	4		550	458	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143079	7143079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138897740	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	94	782	1	ENST00000302850.5:c.2290C>T	p.Leu764Phe	p.L764F	ENST00000302850	NM_000208.2	764	Ctt/Ttt	12/22	0.250717560387347	2	FACETS	1	0.958	1	0.574	0.513	0.64	CLONAL	1	TRUE	0	0.326631278205092	2		783	501	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528553	89528553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	13	216	0	ENST00000336596.2:c.2853G>A	p.Met951Ile	p.M951I	ENST00000336596	NM_005233.5	951	atG/atA	17/17	0.241414059667339	1	FACETS	0.533	0.383	0.713	0.533	0.383	0.713	SUBCLONAL	1	TRUE	0	0.326631278205092	1		216	125	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523678	176523678	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	63	1116	0	ENST00000292408.4:c.2089G>A	p.Glu697Lys	p.E697K	ENST00000292408	NM_213647.1	697	Gag/Aag	16/18	0.1697685276218	3	FACETS	0.603	0.521	0.693	0.302	0.26	0.347	INDETERMINATE	1	TRUE	1	0.326631278205092	3		1116	744	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866465	42866465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	153	997	0	ENST00000398585.3:c.167G>A	p.Gly56Glu	p.G56E	ENST00000398585	NM_001135099.1	56	gGa/gAa	3/14	0.253258753664643	2	FACETS	1	0.987	1	0.714	0.655	0.775	CLONAL	1	TRUE	0	0.326631278205092	2		997	656	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180050984	180050984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	149	1117	0	ENST00000261937.6:c.1499C>T	p.Pro500Leu	p.P500L	ENST00000261937	NM_182925.4	500	cCc/cTc	11/30	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.326631278205092	2		1117	638	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938922	178938922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	53	741	0	ENST00000263967.3:c.2164G>A	p.Glu722Lys	p.E722K	ENST00000263967	NM_006218.2	722	Gag/Aag	14/21	0.312250253086778	3	FACETS	1	0.947	1	0.617	0.529	0.712	CLONAL	1	TRUE	1	0.326631278205092	3		741	306	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177960	56177960	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	37	469	0	ENST00000399503.3:c.2933T>G	p.Leu978Ter	p.L978*	ENST00000399503	NM_005921.1	978	tTa/tGa	14/20	0.286042638958814	4	FACETS	0.755	0.623	0.903	0.378	0.311	0.452	CLONAL	1	TRUE	2	0.326631278205092	4		469	398	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295725	212295725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	33	634	1	ENST00000342788.4:c.2588G>A	p.Gly863Glu	p.G863E	ENST00000342788	NM_005235.2	863	gGg/gAg	21/28	1	2	FACETS	0.748	0.612	0.9	0.748	0.612	0.9	SUBCLONAL	1	TRUE	1	0.326631278205092	2		635	270	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159098	143159098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1321044670	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	28	364	0	ENST00000262992.4:c.755G>A	p.Arg252Gln	p.R252Q	ENST00000262992	NM_001101669.1	252	cGa/cAa	10/24	0.203600104660336	2	FACETS	1	0.856	1	0.536	0.433	0.65	CLONAL	1	TRUE	0	0.326631278205092	2		364	160	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143461	30143461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	64	185	0	ENST00000389048.3:c.65G>A	p.Gly22Glu	p.G22E	ENST00000389048	NM_004304.4	22	gGg/gAg	1/29	0.1697685276218	3	FACETS	1	0.924	1	1	0.924	1	INDETERMINATE	2	TRUE	1	0.326631278205092	3		185	213	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46603747	46603747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61757375	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	215	755	0	ENST00000263734.3:c.1104G>A	p.Met368Ile	p.M368I	ENST00000263734	NM_001430.4	368	atG/atA	9/16	0.326631278205092	5	FACETS	0.844	0.786	0.903	0.844	0.786	0.903	CLONAL	3	TRUE	2	0.326631278205092	5		755	775	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256713	19256713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	137	855	0	ENST00000162023.5:c.1000C>T	p.Pro334Ser	p.P334S	ENST00000162023		334	Cct/Tct	13/13	0.1697685276218	3	FACETS	1	0.986	1	0.727	0.663	0.794	INDETERMINATE	1	TRUE	1	0.326631278205092	3		855	671	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156321	106156321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	50	315	0	ENST00000380013.4:c.1222C>T	p.Pro408Ser	p.P408S	ENST00000380013	NM_001127208.2	408	Ccc/Tcc	3/11	0.326631278205092	1	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	0	0.326631278205092	1		315	237	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350072	89350072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	147	999	0	ENST00000301030.4:c.2878G>A	p.Glu960Lys	p.E960K	ENST00000301030	NM_001256183.1	960	Gag/Aag	9/13	0.312250253086778	3	FACETS	1	0.984	1	0.678	0.62	0.739	CLONAL	1	TRUE	1	0.326631278205092	3		999	772	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131486	202131486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	75	463	0	ENST00000358485.4:c.454C>T	p.Pro152Ser	p.P152S	ENST00000358485	NM_001080125.1	152	Cca/Tca	2/9	0.286001599512684	4	FACETS	1	0.974	1			1	CLONAL	1	TRUE	NA	0.326631278205092	4		463	426	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15827390	15827390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770397614	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	65	237	0	ENST00000307771.7:c.506G>A	p.Arg169Gln	p.R169Q	ENST00000307771	NM_005089.3	169	cGa/cAa	7/11	0.208573521639504	2	FACETS	1	0.95	1			1	CLONAL	2	TRUE	NA	0.326631278205092	2		237	175	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194858	30194858	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771807174	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	118	486	0	ENST00000331968.5:c.287G>A	p.Gly96Glu	p.G96E	ENST00000331968	NM_002742.2	96	gGa/gAa	2/18	0.286042638958814	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.326631278205092	4		486	404	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873020	134873020	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	51	627	0	ENST00000398015.3:c.1324C>T	p.Gln442Ter	p.Q442*	ENST00000398015	NM_004441.4	442	Caa/Taa	6/16	NA	2	FACETS	0.773	0.659	0.898			1	INDETERMINATE	1	TRUE	NA	0.326631278205092	2		627	404	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639878	3639878	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750580998	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	135	1074	2	ENST00000294008.3:c.3761C>T	p.Ser1254Leu	p.S1254L	ENST00000294008	NM_032444.2	1254	tCg/tTg	12/15	0.203600104660336	2	FACETS	1	0.984	1	0.688	0.627	0.751	CLONAL	1	TRUE	0	0.326631278205092	2		1076	601	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445311	49445311	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	147	1267	1	ENST00000301067.7:c.2155C>T	p.Pro719Ser	p.P719S	ENST00000301067	NM_003482.3	719	Ccg/Tcg	10/54	0.247225815987131	4	FACETS	1	0.983	1	0.662	0.604	0.723	CLONAL	1	TRUE	2	0.326631278205092	4		1268	902	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967835	93967835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138518092	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	44	505	0	ENST00000369303.4:c.2092G>A	p.Glu698Lys	p.E698K	ENST00000369303	NM_004440.3	698	Gaa/Aaa	11/17	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.326631278205092	2		505	250	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250430	26250431	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs778901635	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	29	620	0	ENST00000446824.2:c.403_404del	p.Arg135GlyfsTer?	p.R135Gfs*?	ENST00000446824	NM_021018.2	135	AGg/g	1/1	0.20589111192906	4	FACETS	0.431	0.345	0.53	0.216	0.172	0.265	SUBCLONAL	1	TRUE	2	0.326631278205092	4		620	546	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197333	106197333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1327529544	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	45	377	0	ENST00000380013.4:c.5666C>T	p.Pro1889Leu	p.P1889L	ENST00000380013	NM_001127208.2	1889	cCc/cTc	11/11	0.326631278205092	1	FACETS	0.957	0.811	1	0.957	0.811	1	CLONAL	1	TRUE	0	0.326631278205092	1		377	241	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676333	37676333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1302109388	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	80	547	0	ENST00000447079.4:c.3088C>T	p.Pro1030Ser	p.P1030S	ENST00000447079	NM_015083.1	1030	Cct/Tct	11/14	0.20589111192906	4	FACETS	1	0.967	1	0.637	0.562	0.717	CLONAL	1	TRUE	2	0.326631278205092	4		547	510	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095005	11095005	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1307434805	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	78	1266	1	ENST00000358026.2:c.178G>A	p.Gly60Arg	p.G60R	ENST00000358026	NM_001128849.1	60	Ggg/Agg	2/36	0.225472518443553	3	FACETS	0.649	0.569	0.735	0.216	0.189	0.245	SUBCLONAL	1	TRUE	0	0.326631278205092	3		1267	856	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973797	131973797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	40	302	0	ENST00000265335.6:c.3500C>T	p.Ser1167Phe	p.S1167F	ENST00000265335		1167	tCt/tTt	23/25	0.1697685276218	3	FACETS	1	0.934	1	0.619	0.519	0.729	INDETERMINATE	1	TRUE	1	0.326631278205092	3		302	230	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226558140	226558140	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1458089304	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	44	600	0	ENST00000366794.5:c.2149C>T	p.Gln717Ter	p.Q717*	ENST00000366794	NM_001618.3	717	Cag/Tag	15/23	1	2	FACETS	0.528	0.443	0.623	0.528	0.443	0.623	SUBCLONAL	1	TRUE	1	0.326631278205092	2		600	510	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931700	39931700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	55	390	1	ENST00000378444.4:c.2899G>A	p.Ala967Thr	p.A967T	ENST00000378444	NM_001123385.1	967	Gcc/Acc	4/15	0.208573521639504	2	FACETS	0.923	0.793	1			1	CLONAL	1	TRUE	NA	0.326631278205092	2		391	365	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111597	56111597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886480221	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	31	185	0	ENST00000399503.3:c.197G>A	p.Arg66Gln	p.R66Q	ENST00000399503	NM_005921.1	66	cGg/cAg	1/20	0.286042638958814	4	FACETS	1	0.923	1	0.639	0.521	0.77	CLONAL	1	TRUE	2	0.326631278205092	4		185	197	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761450	59761450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	76	469	0	ENST00000259008.2:c.2957C>T	p.Ser986Phe	p.S986F	ENST00000259008	NM_032043.2	986	tCc/tTc	20/20	0.20589111192906	4	FACETS	0.938	0.83	1	0.938	0.83	1	CLONAL	2	TRUE	2	0.326631278205092	4		469	329	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968303	134968303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	102	707	0	ENST00000398015.3:c.2816C>T	p.Ser939Phe	p.S939F	ENST00000398015	NM_004441.4	939	tCc/tTc	15/16	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.326631278205092	2		707	458	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657596	37657596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748453656	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	62	515	0	ENST00000447079.4:c.2513C>T	p.Ser838Leu	p.S838L	ENST00000447079	NM_015083.1	838	tCg/tTg	6/14	0.20589111192906	4	FACETS	1	0.96	1	0.646	0.56	0.738	CLONAL	1	TRUE	2	0.326631278205092	4		515	390	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433716	49433716	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	181	1363	1	ENST00000301067.7:c.7837C>T	p.Pro2613Ser	p.P2613S	ENST00000301067	NM_003482.3	2613	Ccg/Tcg	31/54	0.247225815987131	4	FACETS	0.807	0.745	0.872	0.807	0.745	0.872	CLONAL	2	TRUE	2	0.326631278205092	4		1364	911	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389236	8389236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	53	433	0	ENST00000356435.5:c.4382C>T	p.Ser1461Leu	p.S1461L	ENST00000356435		1461	tCa/tTa	26/35	0.312250253086778	3	FACETS	1	0.956	1	0.658	0.565	0.758	CLONAL	1	TRUE	1	0.326631278205092	3		433	287	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359065	81359065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760721822	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	50	395	0	ENST00000222390.5:c.896C>T	p.Pro299Leu	p.P299L	ENST00000222390	NM_000601.4	299	cCt/cTt	8/18	0.208573521639504	4	FACETS	0.836	0.716	0.965			1	CLONAL	2	TRUE	NA	0.326631278205092	4		395	243	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093410	30093410	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771285195	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	94	499	0	ENST00000331968.5:c.1853G>A	p.Arg618Gln	p.R618Q	ENST00000331968	NM_002742.2	618	cGa/cAa	13/18	0.286042638958814	4	FACETS	0.854	0.769	0.942	1	0.975	1	CLONAL	3	TRUE	2	0.326631278205092	4		499	298	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073802	8073802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	63	340	0	ENST00000377482.5:c.857G>A	p.Arg286Lys	p.R286K	ENST00000377482	NM_018948.3	286	aGa/aAa	4/4	0.18664470322714	3	FACETS	0.75	0.654	0.853			1	INDETERMINATE	2	TRUE	NA	0.326631278205092	3		340	299	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11177088	11177088	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	81	434	0	ENST00000361445.4:c.6989T>C	p.Val2330Ala	p.V2330A	ENST00000361445	NM_004958.3	2330	gTt/gCt	50/58	0.18664470322714	3	FACETS	0.773	0.686	0.866			1	INDETERMINATE	2	TRUE	NA	0.326631278205092	3		434	373	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11297967	11297967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	90	703	0	ENST00000361445.4:c.2141C>T	p.Thr714Ile	p.T714I	ENST00000361445	NM_004958.3	714	aCt/aTt	13/58	0.18664470322714	3	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.326631278205092	3		703	549	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300459	11300459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	117	856	0	ENST00000361445.4:c.1687C>T	p.His563Tyr	p.H563Y	ENST00000361445	NM_004958.3	563	Cat/Tat	11/58	0.18664470322714	3	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.326631278205092	3		856	573	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36814416	36814417	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	50	769	0	ENST00000373129.3:c.624-1_624delinsAA		p.X208_splice	ENST00000373129	NM_032017.1	208		8/12	0.312250253086778	3	FACETS	0.595	0.504	0.694	0.297	0.252	0.347	SUBCLONAL	1	TRUE	1	0.326631278205092	3		769	599	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551525	150551525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs945056615	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	92	1003	0	ENST00000369026.2:c.482C>T	p.Pro161Leu	p.P161L	ENST00000369026	NM_021960.4	161	cCc/cTc	1/3	0.326631278205092	3	FACETS	0.647	0.573	0.726	0.323	0.286	0.363	SUBCLONAL	1	TRUE	1	0.326631278205092	3		1003	1013	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845913	156845913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	207	1187	0	ENST00000524377.1:c.1543G>A	p.Glu515Lys	p.E515K	ENST00000524377	NM_002529.3	515	Gag/Aag	13/17	0.326631278205092	3	FACETS	0.917	0.853	0.983	0.917	0.853	0.983	CLONAL	2	TRUE	1	0.326631278205092	3		1187	804	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162722984	162722984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	25	516	0	ENST00000367921.3:c.182G>A	p.Gly61Glu	p.G61E	ENST00000367921	NM_006182.2	61	gGa/gAa	4/18	0.326631278205092	3	FACETS	0.464	0.365	0.577	0.232	0.182	0.289	SUBCLONAL	1	TRUE	1	0.326631278205092	3		516	384	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243675682	243675682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	11	300	1	ENST00000263826.5:c.1298G>A	p.Arg433Lys	p.R433K	ENST00000263826	NM_005465.4	433	aGa/aAa	12/13	1	2	FACETS	0.36	0.249	0.498	0.36	0.249	0.498	SUBCLONAL	1	TRUE	1	0.326631278205092	2		301	187	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946766	71946766	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778009547	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	106	910	0	ENST00000298229.2:c.2707C>T	p.Pro903Ser	p.P903S	ENST00000298229	NM_001567.3	903	Ccc/Tcc	24/28	0.312250253086778	3	FACETS	1	0.93	1	0.524	0.469	0.581	CLONAL	1	TRUE	1	0.326631278205092	3		910	721	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948752	71948752	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	163	1220	1	ENST00000298229.2:c.3464C>T	p.Pro1155Leu	p.P1155L	ENST00000298229	NM_001567.3	1155	cCc/cTc	26/28	0.312250253086778	3	FACETS	1	0.985	1	0.658	0.604	0.715	CLONAL	1	TRUE	1	0.326631278205092	3		1221	882	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198390	108198390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762427092	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	48	390	0	ENST00000278616.4:c.6994C>T	p.Leu2332Phe	p.L2332F	ENST00000278616	NM_000051.3	2332	Ctt/Ttt	48/63	0.184388354077155	3	FACETS	1	0.944	1			1	INDETERMINATE	1	TRUE	NA	0.326631278205092	3		390	275	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362000	118362000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	46	342	1	ENST00000534358.1:c.4786C>T	p.His1596Tyr	p.H1596Y	ENST00000534358	NM_005933.3	1596	Cat/Tat	14/36	0.286001599512684	4	FACETS	1	0.953	1			1	CLONAL	1	TRUE	NA	0.326631278205092	4		343	277	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022415	12022415	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	146	1027	0	ENST00000396373.4:c.521C>T	p.Pro174Leu	p.P174L	ENST00000396373	NM_001987.4	174	cCc/cTc	5/8	0.326631278205092	5	FACETS	0.839	0.766	0.915	0.839	0.766	0.915	CLONAL	2	TRUE	3	0.326631278205092	5		1027	794	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427579	49427580	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	86	832	0	ENST00000301067.7:c.10908_10909delinsTT	p.Pro3637Ser	p.P3637S	ENST00000301067	NM_003482.3	3636	ctCCct/ctTTct	39/54	0.247225815987131	4	FACETS	1	0.911	1	0.517	0.458	0.581	CLONAL	1	TRUE	2	0.326631278205092	4		832	675	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431229	49431229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	133	845	0	ENST00000301067.7:c.9910C>T	p.Pro3304Ser	p.P3304S	ENST00000301067	NM_003482.3	3304	Ccc/Tcc	34/54	0.247225815987131	4	FACETS	0.832	0.758	0.91	0.832	0.758	0.91	CLONAL	2	TRUE	2	0.326631278205092	4		845	649	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432199	121432199	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	100	831	0	ENST00000257555.6:c.946A>T	p.Lys316Ter	p.K316*	ENST00000257555		316	Aag/Tag	4/10	0.1697685276218	3	FACETS	1	0.972	1	0.628	0.562	0.698	INDETERMINATE	1	TRUE	1	0.326631278205092	3		831	567	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209256	133209256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500801	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	124	889	0	ENST00000320574.5:c.6130C>T	p.Leu2044Phe	p.L2044F	ENST00000320574	NM_006231.2	2044	Ctt/Ttt	44/49	0.1697685276218	3	FACETS	1	0.977	1	0.629	0.57	0.691	INDETERMINATE	1	TRUE	1	0.326631278205092	3		889	702	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250268	133250268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	83	714	0	ENST00000320574.5:c.1252C>T	p.Pro418Ser	p.P418S	ENST00000320574	NM_006231.2	418	Cct/Tct	13/49	0.1697685276218	3	FACETS	1	0.924	1	0.53	0.468	0.595	INDETERMINATE	1	TRUE	1	0.326631278205092	3		714	558	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893598	28893598	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	59	497	0	ENST00000282397.4:c.3248G>A	p.Trp1083Ter	p.W1083*	ENST00000282397	NM_002019.4	1083	tGg/tAg	24/30	0.250717560387347	2	FACETS	1	0.948	1	0.598	0.518	0.684	CLONAL	1	TRUE	0	0.326631278205092	2		497	302	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346401	73346401	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	26	238	0	ENST00000377767.4:c.1399C>G	p.Arg467Gly	p.R467G	ENST00000377767	NM_014953.3	467	Cga/Gga	10/21	NA	2	FACETS	1	0.923	1			1	INDETERMINATE	1	TRUE	NA	0.326631278205092	2		238	119	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435154	110435154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	91	752	0	ENST00000375856.3:c.3247C>T	p.Pro1083Ser	p.P1083S	ENST00000375856	NM_003749.2	1083	Ccg/Tcg	1/2	NA	2	FACETS	1	0.961	1			1	INDETERMINATE	1	TRUE	NA	0.326631278205092	2		752	476	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30103746	30103746	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	53	415	0	ENST00000331968.5:c.1192C>T	p.Pro398Ser	p.P398S	ENST00000331968	NM_002742.2	398	Cca/Tca	8/18	0.286042638958814	4	FACETS	1	0.935	1	0.585	0.501	0.677	CLONAL	1	TRUE	2	0.326631278205092	4		415	368	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331732	68331733	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	41	236	0	ENST00000487270.1:c.328_329delinsTT	p.Pro110Leu	p.P110L	ENST00000487270	NM_133509.3	110	CCa/TTa	5/11	0.326631278205092	7	FACETS	1	0.891	1			1	CLONAL	2	TRUE	NA	0.326631278205092	7		236	212	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348212	348212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1164434521	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	138	1186	0	ENST00000262320.3:c.1294C>T	p.Pro432Ser	p.P432S	ENST00000262320	NM_003502.3	432	Cca/Tca	6/11	0.203600104660336	2	FACETS	1	0.982	1	0.648	0.591	0.707	CLONAL	1	TRUE	0	0.326631278205092	2		1186	652	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993902	72993902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777812986	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	97	833	0	ENST00000268489.5:c.143G>A	p.Gly48Glu	p.G48E	ENST00000268489	NM_006885.3	48	gGg/gAg	2/10	0.312250253086778	3	FACETS	1	0.943	1	0.544	0.485	0.606	CLONAL	1	TRUE	1	0.326631278205092	3		833	635	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687707	29687707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567628713	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	63	550	0	ENST00000356175.3:c.8300C>T	p.Ser2767Phe	p.S2767F	ENST00000356175	NM_000267.3	2767	tCc/tTc	56/57	0.326631278205092	5	FACETS	1	0.956	1	0.417	0.362	0.478	CLONAL	1	TRUE	2	0.326631278205092	5		550	459	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435321	56435321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	118	935	0	ENST00000407977.2:c.1816C>T	p.Pro606Ser	p.P606S	ENST00000407977		606	Cct/Tct	9/10	0.20589111192906	4	FACETS	1	0.983	1	0.716	0.647	0.789	CLONAL	1	TRUE	2	0.326631278205092	4		935	669	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119797	70119797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	130	859	0	ENST00000245479.2:c.799C>T	p.Pro267Ser	p.P267S	ENST00000245479	NM_000346.3	267	Cct/Tct	3/3	0.20589111192906	4	FACETS	0.794	0.722	0.87	0.794	0.722	0.87	SUBCLONAL	2	TRUE	2	0.326631278205092	4		859	665	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791518	42791519	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	155	1032	0	ENST00000575354.2:c.499_500delinsAA	p.Gly167Lys	p.G167K	ENST00000575354	NM_015125.3	167	GGa/AAa	4/20	0.1697685276218	3	FACETS	1	0.985	1	0.68	0.623	0.739	INDETERMINATE	1	TRUE	1	0.326631278205092	3		1032	812	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867270	45867270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	74	815	0	ENST00000391945.4:c.923C>T	p.Pro308Leu	p.P308L	ENST00000391945	NM_000400.3	308	cCc/cTc	10/23	0.1697685276218	3	FACETS	0.871	0.763	0.988	0.436	0.381	0.494	INDETERMINATE	1	TRUE	1	0.326631278205092	3		815	605	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443595	29443595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	132	862	0	ENST00000389048.3:c.3622C>T	p.Leu1208Phe	p.L1208F	ENST00000389048	NM_004304.4	1208	Ctc/Ttc	23/29	0.1697685276218	3	FACETS	1	0.983	1	0.675	0.614	0.74	INDETERMINATE	1	TRUE	1	0.326631278205092	3		862	696	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449864	29449864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	175	1028	0	ENST00000389048.3:c.2991G>A	p.Met997Ile	p.M997I	ENST00000389048	NM_004304.4	997	atG/atA	18/29	0.1697685276218	3	FACETS	1	0.989	1	0.748	0.69	0.809	INDETERMINATE	1	TRUE	1	0.326631278205092	3		1028	833	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249788	39249788	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	65	478	0	ENST00000402219.2:c.1781C>T	p.Pro594Leu	p.P594L	ENST00000402219	NM_005633.3	594	cCc/cTc	10/23	0.326631278205092	5	FACETS	0.797	0.695	0.907	0.531	0.463	0.605	CLONAL	2	TRUE	2	0.326631278205092	5		478	372	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46597016	46597016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764569499	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	98	506	0	ENST00000263734.3:c.830C>T	p.Ala277Val	p.A277V	ENST00000263734	NM_001430.4	277	gCc/gTc	7/16	0.326631278205092	5	FACETS	1	0.981	1	0.496	0.443	0.552	CLONAL	1	TRUE	2	0.326631278205092	5		506	601	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703508	47703508	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1558519495	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	112	492	0	ENST00000233146.2:c.2008C>T	p.Pro670Ser	p.P670S	ENST00000233146	NM_000251.2	670	Ccc/Tcc	13/16	0.326631278205092	5	FACETS	0.858	0.778	0.941	0.858	0.778	0.941	CLONAL	3	TRUE	2	0.326631278205092	5		492	397	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719223	190719223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868155651	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	27	294	0	ENST00000441310.2:c.1225C>T	p.His409Tyr	p.H409Y	ENST00000441310	NM_000534.4	409	Cac/Tac	9/13	1	2	FACETS	0.908	0.729	1	0.908	0.729	1	CLONAL	1	TRUE	1	0.326631278205092	2		294	182	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661669	227661670	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	99	810	1	ENST00000305123.5:c.1785_1786delinsAA	p.Gly596Arg	p.G596R	ENST00000305123	NM_005544.2	595	cgGGgg/cgAAgg	1/2	0.307693740962551	3	FACETS	1	0.956	1			1	CLONAL	1	TRUE	NA	0.326631278205092	3		811	623	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794969	242794970	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	102	1190	2	ENST00000334409.5:c.239_240delinsTT	p.Ala80Val	p.A80V	ENST00000334409	NM_005018.2	80	gCC/gTT	2/5	0.307693740962551	3	FACETS	1	0.954	1			1	CLONAL	1	TRUE	NA	0.326631278205092	3		1192	650	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623099	52623099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	59	494	1	ENST00000394830.3:c.2952G>A	p.Trp984Ter	p.W984*	ENST00000394830	NM_018313.4	984	tgG/tgA	19/30	0.20589111192906	4	FACETS	1	0.952	1	0.619	0.535	0.71	CLONAL	1	TRUE	2	0.326631278205092	4		495	387	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462368	89462368	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs772013090	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	48	536	0	ENST00000336596.2:c.1840A>G	p.Lys614Glu	p.K614E	ENST00000336596	NM_005233.5	614	Aag/Gag	10/17	0.241414059667339	1	FACETS	0.918	0.782	1	0.918	0.782	1	CLONAL	1	TRUE	0	0.326631278205092	1		536	268	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528609	89528609	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	26	246	0	ENST00000336596.2:c.2909A>G	p.Lys970Arg	p.K970R	ENST00000336596	NM_005233.5	970	aAa/aGa	17/17	0.241414059667339	1	FACETS	0.753	0.601	0.923	0.753	0.601	0.923	CLONAL	1	TRUE	0	0.326631278205092	1		246	177	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260249	149260249	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	119	978	1	ENST00000360632.3:c.644C>T	p.Pro215Leu	p.P215L	ENST00000360632	NM_015472.4	215	cCc/cTc	4/7	0.312250253086778	3	FACETS	1	0.957	1	0.553	0.499	0.61	CLONAL	1	TRUE	1	0.326631278205092	3		979	766	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937438	178937438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	32	420	0	ENST00000263967.3:c.1826C>T	p.Pro609Leu	p.P609L	ENST00000263967	NM_006218.2	609	cCt/cTt	12/21	0.312250253086778	3	FACETS	1	0.91	1	0.597	0.489	0.716	CLONAL	1	TRUE	1	0.326631278205092	3		420	191	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509086	66509086	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	12	290	0	ENST00000273854.3:c.241A>G	p.Asn81Asp	p.N81D	ENST00000273854	NM_004439.5	81	Aat/Gat	2/18	0.326631278205092	1	FACETS	0.615	0.436	0.829	0.615	0.436	0.829	SUBCLONAL	1	TRUE	0	0.326631278205092	1		290	100	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041033	112041034	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	53	510	1	ENST00000368678.4:c.221_222delinsAA	p.Gly74Glu	p.G74E	ENST00000368678		74	gGG/gAA	3/13	0.208573521639504	4	FACETS	0.932	0.796	1			1	CLONAL	1	TRUE	NA	0.326631278205092	4		511	462	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622161	117622161	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	20	314	0	ENST00000368508.3:c.6709G>A	p.Gly2237Arg	p.G2237R	ENST00000368508	NM_002944.2	2237	Gga/Aga	42/43	NA	2	FACETS	0.869	0.671	1			1	INDETERMINATE	1	TRUE	NA	0.326631278205092	2		314	141	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679055	117679055	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	41	395	0	ENST00000368508.3:c.3766C>T	p.Leu1256Phe	p.L1256F	ENST00000368508	NM_002944.2	1256	Ctt/Ttt	24/43	NA	2	FACETS	1	0.933	1			1	INDETERMINATE	1	TRUE	NA	0.326631278205092	2		395	206	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545581	106545581	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	45	396	0	ENST00000359195.3:c.3058C>T	p.Leu1020Phe	p.L1020F	ENST00000359195	NM_002649.2	1020	Ctt/Ttt	11/11	0.215804372979461	2	FACETS	1	0.944	1	0.629	0.534	0.732	CLONAL	1	TRUE	0	0.326631278205092	2		396	219	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753112	128753112	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	54	366	0	ENST00000377970.2:c.1273G>A	p.Glu425Lys	p.E425K	ENST00000377970	NM_002467.4	425	Gag/Aag	3/3	1	2	FACETS	0.999	0.858	1	0.999	0.858	1	CLONAL	1	TRUE	1	0.326631278205092	2		366	331	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5563168	5563168	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	102	388	1	ENST00000397747.3:c.773C>A	p.Thr258Lys	p.T258K	ENST00000397747	NM_025239.3	258	aCa/aAa	6/7	0.312250253086778	3	FACETS	1	0.922	1	1	0.922	1	CLONAL	2	TRUE	1	0.326631278205092	3		389	355	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528756	8528756	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	49	472	0	ENST00000356435.5:c.376C>T	p.Pro126Ser	p.P126S	ENST00000356435		126	Cct/Tct	4/35	NA	2	FACETS	0.84	0.714	0.978			1	INDETERMINATE	1	TRUE	NA	0.326631278205092	2		472	357	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244415	98244416	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	63	500	1	ENST00000331920.6:c.654_654+1delinsAA		p.X218_splice	ENST00000331920	NM_000264.3	218		4/24	0.253258753664643	2	FACETS	1	0.96	1	0.634	0.553	0.721	CLONAL	1	TRUE	0	0.326631278205092	2		501	304	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566377	139566377	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	131	777	0	ENST00000308874.7:c.637-1G>A		p.X213_splice	ENST00000308874		213			0.253258753664643	2	FACETS	0.802	0.732	0.875	0.802	0.732	0.875	CLONAL	2	TRUE	0	0.326631278205092	2		777	500	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349996	70349996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	135	375	0	ENST00000374080.3:c.3979C>T	p.Pro1327Ser	p.P1327S	ENST00000374080		1327	Cca/Tca	28/45	0.208573521639504	2	FACETS	1	0.954	1			1	CLONAL	2	TRUE	NA	0.326631278205092	2		375	391	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874297	76874297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	46	287	0	ENST00000373344.5:c.5425G>A	p.Glu1809Lys	p.E1809K	ENST00000373344	NM_000489.3	1809	Gag/Aag	21/35	0.208573521639504	2	FACETS	0.945	0.812	1			1	CLONAL	2	TRUE	NA	0.326631278205092	2		287	149	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637014	93637015	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0052339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	55	518	0	ENST00000375746.1:c.1064_1065delinsTT	p.Pro355Leu	p.P355L	ENST00000375746	NM_001174167.1	355	cCC/cTT	9/14	0.253258753664643	2	FACETS	0.999	0.859	1	0.5	0.429	0.576	CLONAL	1	TRUE	0	0.326631278205092	2		518	337	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435252	56435252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs538022572	NA	P-0052411-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	109	921	0	ENST00000407977.2:c.1885G>A	p.Ala629Thr	p.A629T	ENST00000407977		629	Gcc/Acc	9/10	0.495073272872034	3	FACETS	0.517	0.463	0.574	0.258	0.231	0.287	SUBCLONAL	1	TRUE	1	0.495073272872034	3		921	1063	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360550	70360550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052411-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	212	773	0	ENST00000374080.3:c.6110G>A	p.Gly2037Asp	p.G2037D	ENST00000374080		2037	gGc/gAc	42/45	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.495073272872034	2		773	768	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780805	9780807	+	inframe_deletion	In_Frame_Del	DEL	GCA	GCA	-	novel	NA	P-0052411-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	32	748	0	ENST00000377346.4:c.1529_1531del	p.Gln510del	p.Q510del	ENST00000377346	NM_005026.3	509	ctGCAg/ctg	13/24	0.37073661683127	1	FACETS	0.163	0.131	0.198	0.163	0.131	0.198	SUBCLONAL	1	TRUE	0	0.495073272872034	1		748	598	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0052465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	70	1205	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	1	2	FACETS	0.688	0.599	0.784	0.688	0.599	0.784	SUBCLONAL	1	TRUE	1	0.267547266201382	2		1205	761	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128676	64128676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	59	710	1	ENST00000334205.4:c.533C>T	p.Thr178Met	p.T178M	ENST00000334205	NM_003942.2	178	aCg/aTg	5/17	1	2	FACETS	0.677	0.582	0.781	0.677	0.582	0.781	SUBCLONAL	1	TRUE	1	0.267547266201382	2		711	651	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0052609-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	43	286	1	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.703658673132569	2		287	108	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0052609-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	58	469	1	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.676391390213347	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.703658673132569	1		470	75	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0052609-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	29	571	0	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.703658673132569	2		571	79	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063718	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0052609-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	22	185	0	ENST00000412916.2:c.165+2dup		p.X55_splice	ENST00000412916		55			0.703658673132569	1	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	0	0.703658673132569	1		185	37	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519989	NA	P-0052609-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	31	475	0	ENST00000269305.4:c.730G>C	p.Gly244Arg	p.G244R	ENST00000269305	NM_001126112.2	244	Ggc/Cgc	7/11	0.676391390213347	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.703658673132569	1		475	52	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100988	27100988	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052609-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	41	573	0	ENST00000324856.7:c.4270C>T	p.Gln1424Ter	p.Q1424*	ENST00000324856	NM_006015.4	1424	Cag/Tag	18/20	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.703658673132569	2		573	99	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482556	56482556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052609-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	41	440	0	ENST00000267101.3:c.1013G>A	p.Ser338Asn	p.S338N	ENST00000267101	NM_001982.3	338	aGc/aAc	9/28	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.703658673132569	2		440	115	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847219	68847220	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0052609-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	41	382	0	ENST00000261769.5:c.1141_1142del	p.Lys381GlyfsTer5	p.K381Gfs*5	ENST00000261769	NM_004360.3	381	AAg/g	9/16	0.703658673132569	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.703658673132569	1		382	62	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115267935	115267935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052609-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	34	338	0	ENST00000438362.2:c.1798G>A	p.Asp600Asn	p.D600N	ENST00000438362	NM_001242891.1	600	Gat/Aat	15/20	1	2	FACETS	0.879	0.736	1	0.879	0.736	1	CLONAL	1	TRUE	1	0.703658673132569	2		338	110	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380546	31380546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052609-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	28	615	1	ENST00000328111.2:c.1036G>A	p.Glu346Lys	p.E346K	ENST00000328111	NM_006892.3	346	Gag/Aag	9/23	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.703658673132569	2		616	76	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176516	142176516	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052609-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	35	321	0	ENST00000350721.4:c.7585G>C	p.Glu2529Gln	p.E2529Q	ENST00000350721	NM_001184.3	2529	Gag/Cag	45/47	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.703658673132569	2		321	81	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0052669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	111	396	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.334727395048169	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.334727395048169	2		396	313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0052669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	114	567	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.33460699393752	1	FACETS	0.852	0.768	0.94	0.852	0.768	0.94	CLONAL	1	TRUE	0	0.334727395048169	1		567	666	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604790	48604790	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1568211615	NA	P-0052669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	74	355	0	ENST00000342988.3:c.1612G>T	p.Glu538Ter	p.E538*	ENST00000342988	NM_005359.5	538	Gaa/Taa	12/12	0.281167940762612	1	FACETS	0.916	0.806	1	0.916	0.806	1	CLONAL	1	TRUE	0	0.334727395048169	1		355	402	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105807	27105807	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	87	469	1	ENST00000324856.7:c.5418del	p.Ser1807ValfsTer8	p.S1807Vfs*8	ENST00000324856	NM_006015.4	1806	atC/at	20/20	1	2	FACETS	0.949	0.842	1	0.949	0.842	1	CLONAL	1	TRUE	1	0.334727395048169	2		470	548	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	160	115	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.84	2		115	307	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439918	56439918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367688879	NA	P-0052745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	334	675	0	ENST00000407977.2:c.674G>A	p.Arg225His	p.R225H	ENST00000407977		225	cGc/cAc	6/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.84	2		675	750	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934352	39934352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1420747737	NA	P-0052745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	301	774	2	ENST00000378444.4:c.247C>T	p.Arg83Trp	p.R83W	ENST00000378444	NM_001123385.1	83	Cgg/Tgg	4/15	1	2	FACETS	0.984	0.933	1	0.984	0.933	1	CLONAL	1	TRUE	1	0.84	2		776	728	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148504799	148504799	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0052745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	212	419	0	ENST00000320356.2:c.2196-1G>C		p.X732_splice	ENST00000320356	NM_004456.4	732			1	2	FACETS	0.994	0.932	1	0.994	0.932	1	CLONAL	1	TRUE	1	0.84	2		419	508	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138825	64138825	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	270	585	0	ENST00000334205.4:c.2192G>C	p.Arg731Pro	p.R731P	ENST00000334205	NM_003942.2	731	cGg/cCg	17/17	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.84	2		585	564	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42851184	42851184	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	243	490	0	ENST00000398585.3:c.709A>G	p.Ile237Val	p.I237V	ENST00000398585	NM_001135099.1	237	Ata/Gta	7/14	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.84	2		490	574	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579328	7579329	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0052796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	87	635	0	ENST00000269305.4:c.358_359del	p.Lys120ValfsTer28	p.K120Vfs*28	ENST00000269305	NM_001126112.2	120	AAg/g	4/11	0.351259483819374	1	FACETS	0.873	0.776	0.975	0.873	0.776	0.975	CLONAL	1	TRUE	0	0.351259483819374	1		635	468	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858973	57858973	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	122	780	0	ENST00000228682.2:c.469C>A	p.His157Asn	p.H157N	ENST00000228682	NM_005269.2	157	Cat/Aat	5/12	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.351259483819374	2		780	683	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183867	10183867	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs751232153	NA	P-0052796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	76	561	0	ENST00000256474.2:c.336C>G	p.Tyr112Ter	p.Y112*	ENST00000256474	NM_000551.3	112	taC/taG	1/3	0.351259483819374	1	FACETS	0.912	0.805	1	0.912	0.805	1	CLONAL	1	TRUE	0	0.351259483819374	1		561	391	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052810-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	67	115	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.470436084048461	2		115	254	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0052810-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	104	563	2	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.470436084048461	2		565	434	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052810-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	33	419	0	ENST00000263967.3:c.3012G>A	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atA	21/21	1	2	FACETS	0.298	0.242	0.361	0.298	0.242	0.361	SUBCLONAL	1	TRUE	1	0.470436084048461	2		419	471	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806089	1806089	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913479	NA	P-0052810-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	414	773	1	ENST00000260795.2:c.1108G>T	p.Gly370Cys	p.G370C	ENST00000260795		370	Ggc/Tgc	8/17	0.404911658601258	4	FACETS	0.889	0.85	0.929	0.889	0.85	0.929	CLONAL	3	TRUE	1	0.470436084048461	4		774	970	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951994	178951994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052810-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	92	385	0	ENST00000263967.3:c.3049G>A	p.Asp1017Asn	p.D1017N	ENST00000263967	NM_006218.2	1017	Gat/Aat	21/21	1	2	FACETS	0.922	0.824	1	0.922	0.824	1	CLONAL	1	TRUE	1	0.470436084048461	2		385	424	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971138	21971142	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CGGCG	CGGCG	-	novel	NA	P-0052810-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	78	413	0	ENST00000304494.5:c.216_220del	p.Cys72Ter	p.C72*	ENST00000304494	NM_000077.4	72	tgCGCCGac/tgac	2/3	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.470436084048461	2		413	311	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828056	3828057	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0052810-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	291	602	0	ENST00000262367.5:c.2068dup	p.Ala690GlyfsTer36	p.A690Gfs*36	ENST00000262367	NM_004380.2	690	gct/gGct	10/31	0.470436084048461	3	FACETS	0.931	0.879	0.983	0.931	0.879	0.983	CLONAL	2	TRUE	1	0.470436084048461	3		602	821	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937713	44937714	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACA	novel	NA	P-0052810-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	134	236	0	ENST00000377967.4:c.2902_2904dup	p.Thr968dup	p.T968dup	ENST00000377967	NM_021140.2	968	-/ACA	19/29	1	1	FACETS	0.77	0.713	0.827	1	0.989	1	SUBCLONAL	2	TRUE	0	0.470436084048461	1		236	283	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888198	112888198	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121918453	NA	P-0052810-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	20	578	0	ENST00000351677.2:c.214G>C	p.Ala72Pro	p.A72P	ENST00000351677	NM_002834.3	72	Gcc/Ccc	3/16	1	2	FACETS	0.163	0.124	0.209	0.163	0.124	0.209	SUBCLONAL	1	TRUE	1	0.470436084048461	2		578	521	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098980	178098981	+	protein_altering_variant	In_Frame_Ins	INS	-	-	ACT	novel	NA	P-0052810-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	176	229	0	ENST00000397062.3:c.64_65insAGT	p.Ile22delinsLysLeu	p.I22delinsKL	ENST00000397062	NM_006164.4	22	ata/aAGTta	2/5	0.470436084048461	3	FACETS	0.945	0.888	1	0.945	0.888	1	CLONAL	3	TRUE	0	0.470436084048461	3		229	326	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040038	180040038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1176433163	NA	P-0052810-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	155	918	0	ENST00000261937.6:c.3404G>A	p.Arg1135Lys	p.R1135K	ENST00000261937	NM_182925.4	1135	aGg/aAg	25/30	1	2	FACETS	0.984	0.903	1	0.984	0.903	1	CLONAL	1	TRUE	1	0.470436084048461	2		918	670	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196988	123196999	+	inframe_deletion	In_Frame_Del	DEL	TGACTAACTTGT	TGACTAACTTGT	-	novel	NA	P-0052810-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	93	185	0	ENST00000218089.9:c.1756_1767del	p.Thr586_Leu589del	p.T586_L589del	ENST00000218089	NM_001042749.1	585	gTGACTAACTTGTtg/gtg	19/35	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.470436084048461	1		185	219	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026835	71026835	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1233328410	NA	P-0052868-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	10	249	0	ENST00000318789.4:c.1387G>T	p.Glu463Ter	p.E463*	ENST00000318789	NM_032682.5	463	Gaa/Taa	16/21	0.172112803407472	3	FACETS	1	0.834	1	0.689	0.478	0.94	INDETERMINATE	1	FALSE	1	0.310360729717406	3		249	54	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374837	149374837	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052868-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	26	312	0	ENST00000360632.3:c.257G>C	p.Arg86Pro	p.R86P	ENST00000360632	NM_015472.4	86	cGc/cCc	2/7	0.172112803407472	3	FACETS	1	0.857	1	1	0.948	1	INDETERMINATE	3	FALSE	1	0.310360729717406	3		312	62	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	326	665	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.724474805555594	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.724474805555594	1		665	561	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653805	89653805	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659443	NA	P-0053214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	192	352	0	ENST00000371953.3:c.103A>G	p.Met35Val	p.M35V	ENST00000371953	NM_000314.4	35	Atg/Gtg	2/9	0.724474805555594	1	FACETS	0.969	0.913	1	0.969	0.913	1	CLONAL	1	TRUE	0	0.724474805555594	1		352	349	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021728	71021728	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1559602356	NA	P-0053214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	216	350	1	ENST00000318789.4:c.1630C>T	p.Arg544Ter	p.R544*	ENST00000318789	NM_032682.5	544	Cga/Tga	18/21	0.724474805555594	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.724474805555594	1		351	366	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115818	8115831	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCTCGTTTAACC	CAGCTCGTTTAACC	-	novel	NA	P-0053214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	261	557	0	ENST00000346208.3:c.1165_1178del	p.Ser389GlyfsTer113	p.S389Gfs*113	ENST00000346208		388	aaCAGCTCGTTTAACCcg/aacg	6/6	NA	2	FACETS	0.86	0.808	0.913			1	INDETERMINATE	1	TRUE	NA	0.724474805555594	2		557	838	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941404	71941404	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0053214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	39	797	0	ENST00000298229.2:c.1091-2A>C		p.X364_splice	ENST00000298229	NM_001567.3	364			0.724474805555594	1	FACETS	0.099	0.081	0.119	0.099	0.081	0.119	SUBCLONAL	1	TRUE	0	0.724474805555594	1		797	694	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77043774	77043774	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0053214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	262	445	0	ENST00000356341.3:c.1551+1G>T		p.X517_splice	ENST00000356341	NM_002576.4	517			0.423988805784295	6	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.724474805555594	6		445	1220	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053434-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	49	421	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.705	0.599	0.821	0.705	0.599	0.821	SUBCLONAL	1	TRUE	1	0.386034045650865	2		423	360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053434-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	123	552	1	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	NA	2	FACETS	1	0.915	1			1	INDETERMINATE	1	TRUE	NA	0.386034045650865	2		553	631	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106261	27106261	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053434-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	59	762	1	ENST00000324856.7:c.5872G>A	p.Glu1958Lys	p.E1958K	ENST00000324856	NM_006015.4	1958	Gaa/Aaa	20/20	0.292111963264541	3	FACETS	0.53	0.455	0.612			1	SUBCLONAL	1	TRUE	NA	0.386034045650865	3		763	688	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185169080	185169080	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053434-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	78	466	0	ENST00000265026.3:c.1175G>C	p.Ser392Thr	p.S392T	ENST00000265026	NM_004721.4	392	aGt/aCt	7/14	0.381347605850626	3	FACETS	1	0.949	1	0.569	0.502	0.64	CLONAL	1	TRUE	1	0.386034045650865	3		466	424	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971025	21971026	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0053434-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	81	544	0	ENST00000304494.5:c.331_332dup	p.Arg112AlafsTer35	p.R112Afs*35	ENST00000304494	NM_000077.4	111	ggc/ggGGc	2/3	0.261152019279691	3	FACETS	1	0.915	1			1	CLONAL	1	TRUE	NA	0.386034045650865	3		544	480	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50830399	50830399	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053434-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	34	559	0	ENST00000398568.2:c.2842A>G	p.Thr948Ala	p.T948A	ENST00000398568	NM_001042412.1	948	Aca/Gca	18/18	0.306373311285355	4	FACETS	0.527	0.43	0.636			1	SUBCLONAL	1	TRUE	NA	0.386034045650865	4		559	463	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0053601-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	93	327	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.91	0.814	1	0.91	0.814	1	CLONAL	1	TRUE	1	0.45	2		327	454	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696689	47696689	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519972	NA	P-0053644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	82	538	0	ENST00000347630.2:c.259T>A	p.Tyr87Asn	p.Y87N	ENST00000347630	NM_001007230.1	87	Tac/Aac	5/11	1	2	FACETS	0.839	0.751	0.93	0.839	0.751	0.93	CLONAL	1	TRUE	1	0.782173491427351	2		538	250	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246961	10246961	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs768764350	NA	P-0053644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	30	707	0	ENST00000340748.4:c.4444G>A	p.Gly1482Ser	p.G1482S	ENST00000340748		1482	Ggc/Agc	37/40	1	2	FACETS	0.219	0.176	0.267	0.219	0.176	0.267	SUBCLONAL	1	TRUE	1	0.782173491427351	2		707	351	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061114	38061190	+	protein_altering_variant	In_Frame_Del	DEL	TCAGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTT	TCAGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTT	GCGGG	novel	NA	P-0053644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	100	401	2	ENST00000250448.2:c.799_875delinsCCCGC	p.Lys267_Glu292delinsProAla	p.K267_E292delinsPA	ENST00000250448	NM_004496.3	267	AAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGGCGCCAAGGGCGGCCCTGAg/CCCGCg	2/2	0.152388976859796	3	FACETS	0.77	0.702	0.839	0.77	0.702	0.839	INDETERMINATE	2	TRUE	1	0.782173491427351	3		403	231	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358670	67358670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	32	0	0	ENST00000327367.4:c.178G>A	p.Val60Ile	p.V60I	ENST00000327367	NM_005902.3	60	Gtc/Atc	1/9	1	2	FACETS	0.551	0.446	0.671	0.551	0.446	0.671	SUBCLONAL	1	TRUE	1	0.15	2		0	774	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821752	72821752	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs764957994	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	30	0	0	ENST00000268489.5:c.10423A>G	p.Ser3475Gly	p.S3475G	ENST00000268489	NM_006885.3	3475	Agc/Ggc	10/10	1	2	FACETS	0.637	0.512	0.78	0.637	0.512	0.78	SUBCLONAL	1	TRUE	1	0.15	2		0	628	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792669	33792669	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1378898437	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	23	158	0	ENST00000498907.2:c.652A>G	p.Met218Val	p.M218V	ENST00000498907	NM_004364.3	218	Atg/Gtg	1/1	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.15	2		158	221	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437610	110437610	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1287695683	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	64	856	2	ENST00000375856.3:c.791T>C	p.Val264Ala	p.V264A	ENST00000375856	NM_003749.2	264	gTc/gCc	1/2	1	2	FACETS	0.814	0.703	0.936	0.814	0.703	0.936	CLONAL	1	TRUE	1	0.15	2		858	1048	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95599774	95599774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748788519	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	20	0	0	ENST00000393063.1:c.22C>T	p.Pro8Ser	p.P8S	ENST00000393063	NM_030621.3	8	Ccc/Tcc	3/28	1	2	FACETS	0.5	0.381	0.641	0.5	0.381	0.641	SUBCLONAL	1	TRUE	1	0.15	2		0	533	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821520	72821521	+	missense_variant	Missense_Mutation	DNP	AA	AA	GG	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	27	0	0	ENST00000268489.5:c.10654_10655delinsCC	p.Leu3552Pro	p.L3552P	ENST00000268489	NM_006885.3	3552	TTg/CCg	10/10	1	2	FACETS	0.563	0.446	0.697	0.563	0.446	0.697	SUBCLONAL	1	TRUE	1	0.15	2		0	640	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821653	72821653	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760410635	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	19	175	1	ENST00000268489.5:c.10522G>A	p.Gly3508Ser	p.G3508S	ENST00000268489	NM_006885.3	3508	Ggc/Agc	10/10	1	2	FACETS	1	0.79	1	1	0.79	1	CLONAL	1	TRUE	1	0.15	2		176	243	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821691	72821691	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	34	365	0	ENST00000268489.5:c.10484T>C	p.Val3495Ala	p.V3495A	ENST00000268489	NM_006885.3	3495	gTg/gCg	10/10	1	2	FACETS	0.916	0.748	1	0.916	0.748	1	CLONAL	1	TRUE	1	0.15	2		365	495	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120412	70120412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1336660139	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	72	995	0	ENST00000245479.2:c.1414G>A	p.Ala472Thr	p.A472T	ENST00000245479	NM_000346.3	472	Gct/Act	3/3	1	2	FACETS	0.786	0.684	0.896	0.786	0.684	0.896	SUBCLONAL	1	TRUE	1	0.15	2		995	1222	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792679	33792680	+	missense_variant	Missense_Mutation	DNP	GC	GC	CG	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	23	161	2	ENST00000498907.2:c.641_642delinsCG	p.Gly214Ala	p.G214A	ENST00000498907	NM_004364.3	214	gGC/gCG	1/1	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.15	2		163	223	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793064	33793065	+	missense_variant	Missense_Mutation	DNP	CG	CG	TT	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	34	380	0	ENST00000498907.2:c.256_257delinsAA	p.Arg86Lys	p.R86K	ENST00000498907	NM_004364.3	86	CGg/AAg	1/1	1	2	FACETS	0.873	0.713	1	0.873	0.713	1	CLONAL	1	TRUE	1	0.15	2		380	519	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466791	57466791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	21	167	0	ENST00000371085.3:c.10C>T	p.Leu4Phe	p.L4F	ENST00000371085	NM_000516.4	4	Ctc/Ttc	1/13	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.15	2		167	228	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24129419	24129419	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	32	498	0	ENST00000263121.7:c.63C>G	p.Asp21Glu	p.D21E	ENST00000263121	NM_003073.3	21	gaC/gaG	1/9	1	2	FACETS	0.671	0.543	0.816	0.671	0.543	0.816	SUBCLONAL	1	TRUE	1	0.15	2		498	636	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572876	41572876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	79	764	0	ENST00000263253.7:c.5161G>A	p.Ala1721Thr	p.A1721T	ENST00000263253	NM_001429.3	1721	Gct/Act	31/31	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.15	2		764	939	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572882	41572882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	76	754	1	ENST00000263253.7:c.5167G>A	p.Ala1723Thr	p.A1723T	ENST00000263253	NM_001429.3	1723	Gcc/Acc	31/31	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.15	2		755	946	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665307	138665309	+	missense_variant	Missense_Mutation	TNP	CGC	CGC	GCT	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	58	951	4	ENST00000330315.3:c.256_258delinsAGC	p.Ala86Ser	p.A86S	ENST00000330315	NM_023067.3	86	GCG/AGC	1/1	1	2	FACETS	0.672	0.575	0.778	0.672	0.575	0.778	SUBCLONAL	1	TRUE	1	0.15	2		955	1151	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430704	181430704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	61	916	0	ENST00000325404.1:c.556C>T	p.Leu186Phe	p.L186F	ENST00000325404	NM_003106.3	186	Ctc/Ttc	1/1	1	2	FACETS	0.767	0.659	0.884	0.767	0.659	0.884	SUBCLONAL	1	TRUE	1	0.15	2		916	1061	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430716	181430717	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	65	939	1	ENST00000325404.1:c.568_569delinsAA	p.Gly190Asn	p.G190N	ENST00000325404	NM_003106.3	190	GGc/AAc	1/1	1	2	FACETS	0.825	0.713	0.948	0.825	0.713	0.948	CLONAL	1	TRUE	1	0.15	2		940	1050	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100369	157100369	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1371755731	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	25	219	0	ENST00000346085.5:c.1306A>G	p.Ser436Gly	p.S436G	ENST00000346085	NM_020732.3	436	Agc/Ggc	1/20	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.15	2		219	275	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100371	157100371	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	24	212	0	ENST00000346085.5:c.1308C>A	p.Ser436Arg	p.S436R	ENST00000346085	NM_020732.3	436	agC/agA	1/20	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.15	2		212	267	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371638	55371638	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	65	754	0	ENST00000297316.4:c.328A>T	p.Thr110Ser	p.T110S	ENST00000297316	NM_022454.3	110	Acg/Tcg	2/2	1	2	FACETS	0.96	0.83	1	0.96	0.83	1	CLONAL	1	TRUE	1	0.15	2		754	903	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371762	55371762	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	30	455	0	ENST00000297316.4:c.452T>C	p.Val151Ala	p.V151A	ENST00000297316	NM_022454.3	151	gTg/gCg	2/2	1	2	FACETS	0.752	0.605	0.92	0.752	0.605	0.92	CLONAL	1	TRUE	1	0.15	2		455	532	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732824	44732825	+	missense_variant	Missense_Mutation	DNP	TA	TA	CG	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	39	343	0	ENST00000377967.4:c.27_28delinsCG	p.Thr10Ala	p.T10A	ENST00000377967	NM_021140.2	9	gcTAcc/gcCGcc	1/29	1	1	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	0	0.15	1		343	453	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732894	44732894	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	22	349	0	ENST00000377967.4:c.97G>C	p.Glu33Gln	p.E33Q	ENST00000377967	NM_021140.2	33	Gag/Cag	1/29	1	1	FACETS	0.675	0.522	0.853	0.675	0.522	0.853	SUBCLONAL	1	TRUE	0	0.15	1		349	402	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922674	44922674	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	20	177	0	ENST00000377967.4:c.1535C>A	p.Pro512Gln	p.P512Q	ENST00000377967	NM_021140.2	512	cCa/cAa	16/29	1	1	FACETS	1	0.812	1	1	0.812	1	CLONAL	1	TRUE	0	0.15	1		177	231	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922772	44922772	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	26	235	0	ENST00000377967.4:c.1633C>G	p.Leu545Val	p.L545V	ENST00000377967	NM_021140.2	545	Ctt/Gtt	16/29	1	1	FACETS	0.927	0.734	1	0.927	0.734	1	CLONAL	1	TRUE	0	0.15	1		235	346	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922883	44922883	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	26	303	0	ENST00000377967.4:c.1744T>G	p.Ser582Ala	p.S582A	ENST00000377967	NM_021140.2	582	Tca/Gca	16/29	1	1	FACETS	0.851	0.674	1	0.851	0.674	1	CLONAL	1	TRUE	0	0.15	1		303	377	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922895	44922895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	26	267	0	ENST00000377967.4:c.1756G>A	p.Gly586Arg	p.G586R	ENST00000377967	NM_021140.2	586	Gga/Aga	16/29	1	1	FACETS	0.824	0.653	1	0.824	0.653	1	CLONAL	1	TRUE	0	0.15	1		267	389	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922938	44922938	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	42	251	0	ENST00000377967.4:c.1799G>A	p.Gly600Glu	p.G600E	ENST00000377967	NM_021140.2	600	gGa/gAa	16/29	1	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.15	1		251	402	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922974	44922974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs973676174	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	44	288	0	ENST00000377967.4:c.1835G>A	p.Arg612Gln	p.R612Q	ENST00000377967	NM_021140.2	612	cGa/cAa	16/29	1	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.15	1		288	420	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922985	44922985	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	40	294	0	ENST00000377967.4:c.1846A>T	p.Thr616Ser	p.T616S	ENST00000377967	NM_021140.2	616	Act/Tct	16/29	1	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.15	1		294	416	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928852	44928852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750754452	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	26	197	0	ENST00000377967.4:c.1952C>T	p.Ser651Leu	p.S651L	ENST00000377967	NM_021140.2	651	tCg/tTg	17/29	1	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	0	0.15	1		197	253	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928914	44928914	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	33	256	0	ENST00000377967.4:c.2014G>T	p.Ala672Ser	p.A672S	ENST00000377967	NM_021140.2	672	Gct/Tct	17/29	1	1	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	0	0.15	1		256	355	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928920	44928920	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	35	256	0	ENST00000377967.4:c.2020T>A	p.Ser674Thr	p.S674T	ENST00000377967	NM_021140.2	674	Tct/Act	17/29	1	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.15	1		256	354	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928949	44928950	+	missense_variant	Missense_Mutation	DNP	CA	CA	TG	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	26	290	0	ENST00000377967.4:c.2049_2050inv	p.Thr684Ala	p.T684A	ENST00000377967	NM_021140.2	683	ccCAcc/ccTGcc	17/29	1	1	FACETS	0.879	0.696	1	0.879	0.696	1	CLONAL	1	TRUE	0	0.15	1		290	365	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928953	44928954	+	missense_variant	Missense_Mutation	DNP	CT	CT	AC	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	26	287	0	ENST00000377967.4:c.2053_2054delinsAC	p.Leu685Thr	p.L685T	ENST00000377967	NM_021140.2	685	CTg/ACg	17/29	1	1	FACETS	0.874	0.692	1	0.874	0.692	1	CLONAL	1	TRUE	0	0.15	1		287	367	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929071	44929071	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs749563708	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	45	270	0	ENST00000377967.4:c.2171T>C	p.Ile724Thr	p.I724T	ENST00000377967	NM_021140.2	724	aTa/aCa	17/29	1	1	FACETS	0.821	0.693	0.962	1	0.965	1	CLONAL	2	TRUE	0	0.15	1		270	338	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929074	44929076	+	missense_variant	Missense_Mutation	TNP	TGA	TGA	CAG	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	41	282	0	ENST00000377967.4:c.2174_2176delinsCAG	p.Leu725_Thr726delinsSerAla	p.L725_T726delinsSA	ENST00000377967	NM_021140.2	725	tTGAcg/tCAGcg	17/29	1	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.15	1		282	365	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929099	44929100	+	missense_variant	Missense_Mutation	DNP	CA	CA	TT	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	44	288	2	ENST00000377967.4:c.2199_2200delinsTT	p.Thr734Ser	p.T734S	ENST00000377967	NM_021140.2	733	caCAct/caTTct	17/29	1	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.15	1		290	399	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929127	44929127	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	51	318	0	ENST00000377967.4:c.2227A>G	p.Ser743Gly	p.S743G	ENST00000377967	NM_021140.2	743	Agt/Ggt	17/29	1	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.15	1		318	446	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929160	44929160	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	49	369	0	ENST00000377967.4:c.2260A>G	p.Met754Val	p.M754V	ENST00000377967	NM_021140.2	754	Atg/Gtg	17/29	1	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.15	1		369	502	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929179	44929180	+	missense_variant	Missense_Mutation	DNP	GC	GC	CT	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	38	366	0	ENST00000377967.4:c.2279_2280delinsCT	p.Cys760Ser	p.C760S	ENST00000377967	NM_021140.2	760	tGC/tCT	17/29	1	1	FACETS	0.9	0.743	1	0.9	0.743	1	CLONAL	1	TRUE	0	0.15	1		366	521	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763858	76763858	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	10	0	0	ENST00000373344.5:c.7450C>G	p.Pro2484Ala	p.P2484A	ENST00000373344	NM_000489.3	2484	Cca/Gca	35/35	1	1	FACETS	0.305	0.205	0.431	0.305	0.205	0.431	SUBCLONAL	1	TRUE	0	0.15	1		0	405	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929450	44929452	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	22	325	0	ENST00000377967.4:c.2550_2552del	p.Leu851del	p.L851del	ENST00000377967	NM_021140.2	850	ggGCTa/gga	17/29	1	1	FACETS	0.622	0.481	0.787	0.622	0.481	0.787	SUBCLONAL	1	TRUE	0	0.15	1		325	436	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100380	157100380	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1385126607	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	14	188	0	ENST00000346085.5:c.1317G>C	p.Glu439Asp	p.E439D	ENST00000346085	NM_020732.3	439	gaG/gaC	1/20	1	2	FACETS	0.83	0.6	1	0.83	0.6	1	CLONAL	1	TRUE	1	0.15	2		188	225	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741827	17741827	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs561153957	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	24	325	0	ENST00000250003.3:c.498C>G	p.Asp166Glu	p.D166E	ENST00000250003	NM_002478.4	166	gaC/gaG	1/3	1	2	FACETS	0.804	0.63	1	0.804	0.63	1	CLONAL	1	TRUE	1	0.15	2		325	398	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821746	72821746	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs145105101	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	31	0	0	ENST00000268489.5:c.10429G>C	p.Glu3477Gln	p.E3477Q	ENST00000268489	NM_006885.3	3477	Gag/Cag	10/10	1	2	FACETS	0.644	0.519	0.786	0.644	0.519	0.786	SUBCLONAL	1	TRUE	1	0.15	2		0	642	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982529	10982530	+	missense_variant	Missense_Mutation	DNP	GC	GC	CA	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	6	0	0	ENST00000327064.4:c.151_152delinsCA	p.Ala51Gln	p.A51Q	ENST00000327064	NM_199141.1	51	GCg/CAg	1/16	1	2	FACETS	0.289	0.172	0.448	0.289	0.172	0.448	SUBCLONAL	1	TRUE	1	0.15	2		0	277	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792698	33792698	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	18	156	0	ENST00000498907.2:c.623T>A	p.Phe208Tyr	p.F208Y	ENST00000498907	NM_004364.3	208	tTc/tAc	1/1	1	2	FACETS	1	0.79	1	1	0.79	1	CLONAL	1	TRUE	1	0.15	2		156	228	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393287	393287	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	41	614	0	ENST00000380956.4:c.135G>T	p.Glu45Asp	p.E45D	ENST00000380956	NM_001195286.1	45	gaG/gaT	2/9	1	2	FACETS	0.739	0.614	0.879	0.739	0.614	0.879	SUBCLONAL	1	TRUE	1	0.15	2		614	740	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300948	137300949	+	missense_variant	Missense_Mutation	DNP	TG	TG	GC	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	87	845	2	ENST00000481739.1:c.593_594delinsGC	p.Met198Ser	p.M198S	ENST00000481739	NM_002957.4	198	aTG/aGC	4/10	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.15	2		847	1085	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300957	137300957	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	78	787	0	ENST00000481739.1:c.602A>G	p.Lys201Arg	p.K201R	ENST00000481739	NM_002957.4	201	aAg/aGg	4/10	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.15	2		787	1018	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821730	72821733	+	frameshift_variant	Frame_Shift_Del	DEL	CTCC	CTCC	-	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	31	452	0	ENST00000268489.5:c.10442_10445del	p.Arg3481ThrfsTer3	p.R3481Tfs*3	ENST00000268489	NM_006885.3	3481	aGGAGc/ac	10/10	1	2	FACETS	0.676	0.546	0.825	0.676	0.546	0.825	SUBCLONAL	1	TRUE	1	0.15	2		452	611	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992497	72992497	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	48	0	0	ENST00000268489.5:c.1548del	p.Ser517ValfsTer19	p.S517Vfs*19	ENST00000268489	NM_006885.3	516	ggT/gg	2/10	1	2	FACETS	0.621	0.523	0.73	0.621	0.523	0.73	SUBCLONAL	1	TRUE	1	0.15	2		0	1030	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821738	72821739	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCC	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	30	0	0	ENST00000268489.5:c.10436_10437insGGCC	p.Arg3481SerfsTer91	p.R3481Sfs*91	ENST00000268489	NM_006885.3	3479	gca/gcGGCCa	10/10	1	2	FACETS	0.643	0.517	0.787	0.643	0.517	0.787	SUBCLONAL	1	TRUE	1	0.15	2		0	622	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100384	157100384	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1307907368	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	14	176	0	ENST00000346085.5:c.1321A>G	p.Ser441Gly	p.S441G	ENST00000346085	NM_020732.3	441	Agc/Ggc	1/20	1	2	FACETS	0.924	0.669	1	0.924	0.669	1	CLONAL	1	TRUE	1	0.15	2		176	202	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100387	157100387	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	12	164	0	ENST00000346085.5:c.1324A>G	p.Ser442Gly	p.S442G	ENST00000346085	NM_020732.3	442	Agc/Ggc	1/20	1	2	FACETS	0.851	0.599	1	0.851	0.599	1	CLONAL	1	TRUE	1	0.15	2		164	188	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100393	157100393	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	10	132	0	ENST00000346085.5:c.1330A>G	p.Ser444Gly	p.S444G	ENST00000346085	NM_020732.3	444	Agc/Ggc	1/20	1	2	FACETS	0.844	0.573	1	0.844	0.573	1	CLONAL	1	TRUE	1	0.15	2		132	158	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528275	157528275	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	51	696	0	ENST00000346085.5:c.6000T>G	p.Asp2000Glu	p.D2000E	ENST00000346085	NM_020732.3	2000	gaT/gaG	20/20	1	2	FACETS	0.8	0.678	0.935	0.8	0.678	0.935	CLONAL	1	TRUE	1	0.15	2		696	850	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371767	55371767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	26	426	0	ENST00000297316.4:c.457G>A	p.Gly153Ser	p.G153S	ENST00000297316	NM_022454.3	153	Ggc/Agc	2/2	1	2	FACETS	0.685	0.541	0.851	0.685	0.541	0.851	SUBCLONAL	1	TRUE	1	0.15	2		426	506	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413198	139413198	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs761318281	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	82	1024	0	ENST00000277541.6:c.944C>A	p.Thr315Asn	p.T315N	ENST00000277541	NM_017617.3	315	aCc/aAc	6/34	1	2	FACETS	0.91	0.799	1	0.91	0.799	1	CLONAL	1	TRUE	1	0.15	2		1024	1202	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732836	44732846	+	missense_variant	Missense_Mutation	ONP	TGCCGCCGCCG	TGCCGCCGCCG	CTCTGCTGCTC	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	25	332	1	ENST00000377967.4:c.39_49delinsCTCTGCTGCTC	p.Ala14_Ala17delinsSerAlaAlaPro	p.A14_A17delinsSAAP	ENST00000377967	NM_021140.2	13	gcTGCCGCCGCCGct/gcCTCTGCTGCTCct	1/29	1	1	FACETS	0.676	0.532	0.843	0.676	0.532	0.843	SUBCLONAL	1	TRUE	0	0.15	1		333	456	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922856	44922868	+	missense_variant	Missense_Mutation	ONP	TCTGCAGGCCATG	TCTGCAGGCCATG	CCAGCAGGCCCTA	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	21	312	1	ENST00000377967.4:c.1717_1729delinsCCAGCAGGCCCTA	p.Ser573_Val577delinsProAlaGlyProIle	p.S573_V577delinsPAGPI	ENST00000377967	NM_021140.2	573	TCTGCAGGCCATGtt/CCAGCAGGCCCTAtt	16/29	1	1	FACETS	0.696	0.535	0.884	0.696	0.535	0.884	SUBCLONAL	1	TRUE	0	0.15	1		313	372	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922866	44922866	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	21	306	0	ENST00000377967.4:c.1727A>C	p.His576Pro	p.H576P	ENST00000377967	NM_021140.2	576	cAt/cCt	16/29	1	1	FACETS	0.71	0.546	0.901	0.71	0.546	0.901	CLONAL	1	TRUE	0	0.15	1		306	365	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922868	44922868	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	21	307	0	ENST00000377967.4:c.1729G>A	p.Val577Ile	p.V577I	ENST00000377967	NM_021140.2	577	Gtt/Att	16/29	1	1	FACETS	0.696	0.535	0.884	0.696	0.535	0.884	SUBCLONAL	1	TRUE	0	0.15	1		307	372	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0054044-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	962	785	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.399566886839788	3	FACETS	0.974	0.951	0.997			1	CLONAL	3	TRUE	NA	0.560385051749496	3		785	1504	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41022125	41022126	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs34091239	NA	P-0054044-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	159	664	1	ENST00000267868.3:c.855dup	p.Pro286ThrfsTer37	p.P286Tfs*37	ENST00000267868	NM_002875.4	283	-/A	9/10	0.560483567561483	3	FACETS	0.899	0.825	0.976	0.45	0.412	0.488	CLONAL	1	TRUE	1	0.560385051749496	3		665	808	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0054044-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	326	546	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.509535899784531	4	FACETS	0.796	0.752	0.84	0.796	0.752	0.84	SUBCLONAL	2	TRUE	2	0.560385051749496	4		546	1141	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0054044-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	95	324	1	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	0.558317614054596	2	FACETS	0.819	0.734	0.908	0.409	0.367	0.454	CLONAL	1	TRUE	0	0.560385051749496	2		325	414	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513547	41513547	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs780440242	NA	P-0054044-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	396	684	0	ENST00000263253.7:c.451A>G	p.Thr151Ala	p.T151A	ENST00000263253	NM_001429.3	151	Aca/Gca	2/31	0.137117385217357	6	FACETS	1	0.987	1			1	INDETERMINATE	3	TRUE	NA	0.560385051749496	6		684	924	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439793	51439793	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054044-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	169	495	0	ENST00000262662.1:c.358G>C	p.Glu120Gln	p.E120Q	ENST00000262662		120	Gag/Cag	4/4	0.560483567561483	4	FACETS	0.923	0.848	1	0.461	0.424	0.501	CLONAL	1	TRUE	2	0.560385051749496	4		495	1020	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73340119	73340119	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054044-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	49	324	0	ENST00000377767.4:c.1961A>C	p.Lys654Thr	p.K654T	ENST00000377767	NM_014953.3	654	aAg/aCg	15/21	0.553945002621741	3	FACETS	1	0.899	1	0.531	0.455	0.612	CLONAL	1	TRUE	1	0.560385051749496	3		324	211	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790126	40790126	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054044-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1215	249	777	0	ENST00000373198.4:c.2605T>C	p.Tyr869His	p.Y869H	ENST00000373198	NM_133170.3	869	Tac/Cac	18/32	0.509535899784531	4	FACETS	0.947	0.883	1	0.474	0.441	0.507	CLONAL	1	TRUE	2	0.560385051749496	4		777	1464	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516889	187516889	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054044-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	174	521	0	ENST00000441802.2:c.13092A>C	p.Glu4364Asp	p.E4364D	ENST00000441802	NM_005245.3	4364	gaA/gaC	26/27	NA	2	FACETS	0.932	0.862	1			1	INDETERMINATE	1	TRUE	NA	0.560385051749496	2		521	666	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250346	110250346	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1277713044	NA	P-0054044-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	251	955	0	ENST00000374672.4:c.329C>G	p.Ser110Cys	p.S110C	ENST00000374672	NM_004235.4	110	tCc/tGc	3/5	0.560483567561483	3	FACETS	0.924	0.863	0.987	0.462	0.431	0.494	CLONAL	1	TRUE	1	0.560385051749496	3		955	1241	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855264	76855275	+	inframe_deletion	In_Frame_Del	DEL	TCCATACTGTCT	TCCATACTGTCT	-	novel	NA	P-0054044-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	30	439	0	ENST00000373344.5:c.5712_5723del	p.Glu1904_Met1907del	p.E1904_M1907del	ENST00000373344	NM_000489.3	1904	gaAGACAGTATGGAt/gat	24/35	0.393990734335187	4	FACETS	1	0.933	1	0.668	0.548	0.799	CLONAL	1	TRUE	2	0.560385051749496	4		439	125	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371987	55371987	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1563871654	NA	P-0054077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	18	478	0	ENST00000297316.4:c.677C>G	p.Pro226Arg	p.P226R	ENST00000297316	NM_022454.3	226	cCg/cGg	2/2	1	2	FACETS	0.815	0.617	1	0.815	0.617	1	CLONAL	1	TRUE	1	0.24	2		478	184	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888165	112888165	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507510	NA	P-0121474-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	166	597	0	ENST00000351677.2:c.181G>A	p.Asp61Asn	p.D61N	ENST00000351677	NM_002834.3	61	Gat/Aat	3/16	1	2	FACETS	0.721	0.665	0.778	0.721	0.665	0.778	SUBCLONAL	1	NA	1	0.758672341181946	2		597	607	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106078	27106079	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCCA	novel	NA	P-0121474-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	144	487	1	ENST00000324856.7:c.5692_5696dup	p.Asp1900HisfsTer25	p.D1900Hfs*25	ENST00000324856	NM_006015.4	1897	ccc/cCCCCAcc	20/20	1	2	FACETS	0.64	0.586	0.696	0.64	0.586	0.696	SUBCLONAL	1	NA	1	0.758672341181946	2		488	593	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579359	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587780066	NA	P-0054117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	441	629	0	ENST00000269305.4:c.328del	p.Arg110ValfsTer13	p.R110Vfs*13	ENST00000269305	NM_001126112.2	110	Cgt/gt	4/11	0.533094090840944	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.533094090840944	2		629	819	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857325	68857325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054117-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	115	347	0	ENST00000261769.5:c.1960C>T	p.Pro654Ser	p.P654S	ENST00000261769	NM_004360.3	654	Cca/Tca	13/16	0.533094090840944	3	FACETS	1	0.943	1	0.529	0.479	0.582	CLONAL	1	TRUE	1	0.533094090840944	3		347	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0054258-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	364	644	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	NA	2	FACETS	0.985	0.956	1			1	INDETERMINATE	2	TRUE	NA	0.797880163782361	2		646	463	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881489	48881490	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs587778862	NA	P-0054258-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	160	284	0	ENST00000267163.4:c.219_220del	p.Arg73SerfsTer36	p.R73Sfs*36	ENST00000267163	NM_000321.2	71	AGa/a	2/27	0.779659821732089	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.797880163782361	2		284	194	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206914	162206914	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs139600787	NA	P-0054258-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	230	390	0	ENST00000366898.1:c.761A>G	p.Asn254Ser	p.N254S	ENST00000366898	NM_004562.2	254	aAc/aGc	7/12	0.61464881452664	4	FACETS	0.881	0.828	0.936	0.881	0.828	0.936	CLONAL	2	TRUE	2	0.797880163782361	4		390	588	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0054265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	227	749	0	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		749	782	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877139	151877140	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054439-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	314	596	0	ENST00000262189.6:c.7221dup	p.Ser2408ValfsTer22	p.S2408Vfs*22	ENST00000262189	NM_170606.2	2407	-/G	37/59	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		596	759	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578276	7578277	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGAG	novel	NA	P-0054566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	97	761	0	ENST00000269305.4:c.569_572dup	p.Gln192SerfsTer18	p.Q192Sfs*18	ENST00000269305	NM_001126112.2	191	cct/ccCTCCt	6/11	0.413911969229049	0	FACETS	0.334	0.299	0.371			1	SUBCLONAL	1	TRUE	0	0.559787079322823	0		761	457	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683483	182683483	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	156	463	0	ENST00000292782.4:c.62C>G	p.Ser21Cys	p.S21C	ENST00000292782	NM_020640.2	21	tCt/tGt	2/7	1	2	FACETS	0.909	0.836	0.985	0.909	0.836	0.985	CLONAL	1	TRUE	1	0.559787079322823	2		463	613	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0054624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	170	334	13	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	1	0.976	1	1	0.993	1	CLONAL	2	TRUE	1	0.36	2		347	424	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236203	108236203	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434219	NA	P-0054624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	45	585	0	ENST00000278616.4:c.9139C>T	p.Arg3047Ter	p.R3047*	ENST00000278616	NM_000051.3	3047	Cga/Tga	63/63	1	2	FACETS	0.293	0.245	0.346	0.293	0.245	0.346	SUBCLONAL	1	TRUE	1	0.36	2		585	854	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023151	27023179	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	-	novel	NA	P-0054624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	52	41	0	ENST00000324856.7:c.267_295del	p.Ser90ProfsTer11	p.S90Pfs*11	ENST00000324856	NM_006015.4	86	gGCGGAGCCGGCAGCGGCGGCGGGCCCGGC/g	1/20	1	2	FACETS	0.963	0.854	1	1	0.983	1	CLONAL	3	TRUE	1	0.36	2		41	100	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266611	198266611	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs755415626	NA	P-0054624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	45	369	0	ENST00000335508.6:c.2225G>A	p.Gly742Asp	p.G742D	ENST00000335508	NM_012433.2	742	gGt/gAt	16/25	1	2	FACETS	0.572	0.481	0.672	0.572	0.481	0.672	SUBCLONAL	1	TRUE	1	0.36	2		369	437	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052636	42052636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1054243525	NA	P-0054624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	63	556	0	ENST00000219905.7:c.7307G>A	p.Arg2436His	p.R2436H	ENST00000219905	NM_001164273.1	2436	cGt/cAt	20/24	1	2	FACETS	0.481	0.416	0.553	0.481	0.416	0.553	SUBCLONAL	1	TRUE	1	0.36	2		556	727	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464505	25464506	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs753637583	NA	P-0054624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	117	733	0	ENST00000264709.3:c.2007dup	p.Ile670HisfsTer43	p.I670Hfs*43	ENST00000264709	NM_175629.2	669	-/C	17/23	1	2	FACETS	0.719	0.648	0.795	0.719	0.648	0.795	SUBCLONAL	1	TRUE	1	0.36	2		733	904	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114769	108114769	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0054624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	47	564	0	ENST00000278616.4:c.586A>T	p.Lys196Ter	p.K196*	ENST00000278616	NM_000051.3	196	Aaa/Taa	6/63	1	2	FACETS	0.404	0.34	0.475	0.404	0.34	0.475	SUBCLONAL	1	TRUE	1	0.36	2		564	646	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528657	157528657	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554238072	NA	P-0054624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	85	676	2	ENST00000346085.5:c.6382C>T	p.Arg2128Ter	p.R2128*	ENST00000346085	NM_020732.3	2128	Cga/Tga	20/20	1	2	FACETS	0.581	0.513	0.654	0.581	0.513	0.654	SUBCLONAL	1	TRUE	1	0.36	2		678	813	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	51	421	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.234424528892637	2	FACETS	0.901	0.766	1	0.45	0.383	0.524	CLONAL	1	TRUE	0	0.234424528892637	2		423	483	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	37	239	0	ENST00000288602.6:c.1742A>T	p.Asn581Ile	p.N581I	ENST00000288602	NM_004333.4	581	aAt/aTt	15/18	0.234424528892637	2	FACETS	1	0.935	1	0.644	0.535	0.765	CLONAL	1	TRUE	0	0.234424528892637	2		239	245	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448297	56448298	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1567880599	NA	P-0054639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	191	533	1	ENST00000407977.2:c.349dup	p.Arg117ProfsTer8	p.R117Pfs*8	ENST00000407977		117	cgc/cCgc	3/10	0.234424528892637	2	FACETS	0.992	0.919	1	0.992	0.919	1	CLONAL	2	TRUE	0	0.234424528892637	2		534	821	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634731	158634731	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748791232	NA	P-0054639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	32	353	0	ENST00000263640.3:c.455G>A	p.Arg152His	p.R152H	ENST00000263640	NM_001105.4	152	cGc/cAc	5/11	0.234424528892637	2	FACETS	0.492	0.398	0.598	0.246	0.199	0.299	SUBCLONAL	1	TRUE	0	0.234424528892637	2		353	555	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0054677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	12	316	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	1	2	FACETS	0.295	0.207	0.402	0.295	0.207	0.402	SUBCLONAL	1	TRUE	1	0.45	2		316	181	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0054677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	101	887	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	1	2	FACETS	0.884	0.793	0.979	0.884	0.793	0.979	CLONAL	1	TRUE	1	0.45	2		887	508	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790000	40790000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159843	NA	P-0054677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	52	628	0	ENST00000373198.4:c.2731G>A	p.Glu911Lys	p.E911K	ENST00000373198	NM_133170.3	911	Gaa/Aaa	18/32	1	2	FACETS	0.535	0.456	0.621	0.535	0.456	0.621	SUBCLONAL	1	TRUE	1	0.45	2		628	432	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	140	421	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.680979149110765	3	FACETS	0.84	0.777	0.904	0.84	0.777	0.904	CLONAL	2	TRUE	1	0.680979149110765	3		423	328	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913708	32913708	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	65	311	0	ENST00000380152.3:c.5216A>G	p.Tyr1739Cys	p.Y1739C	ENST00000380152		1739	tAt/tGt	11/27	1	2	FACETS	0.841	0.739	0.948	0.841	0.739	0.948	CLONAL	1	TRUE	1	0.680979149110765	2		311	227	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054808-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	79	115	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.819	0.725	0.919			1	INDETERMINATE	2	TRUE	NA	0.249223392486843	2		115	387	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0054808-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	126	535	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.166076449233876	3	FACETS	0.839	0.761	0.92	0.839	0.761	0.92	CLONAL	2	TRUE	1	0.249223392486843	3		535	678	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356359	66356359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199650353	NA	P-0054808-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	33	511	0	ENST00000273854.3:c.1138C>T	p.Pro380Ser	p.P380S	ENST00000273854	NM_004439.5	380	Cct/Tct	5/18	0.249223392486843	1	FACETS	0.405	0.329	0.491	0.405	0.329	0.491	SUBCLONAL	1	TRUE	0	0.249223392486843	1		511	572	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087907	27087907	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054808-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	225	716	0	ENST00000324856.7:c.2194C>T	p.Gln732Ter	p.Q732*	ENST00000324856	NM_006015.4	732	Cag/Tag	6/20	1	2	FACETS	1	0.965	1	1	0.994	1	CLONAL	2	TRUE	1	0.249223392486843	2		716	857	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752888	42752888	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054808-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	97	1077	0	ENST00000222329.4:c.1376C>G	p.Ala459Gly	p.A459G	ENST00000222329	NM_006494.2	459	gCc/gGc	4/4	1	2	FACETS	0.914	0.814	1	0.914	0.814	1	CLONAL	1	TRUE	1	0.249223392486843	2		1077	852	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456701	32456701	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054808-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	28	523	0	ENST00000332351.3:c.191C>G	p.Ser64Cys	p.S64C	ENST00000332351	NM_024426.4	64	tCt/tGt	1/10	1	2	FACETS	0.515	0.411	0.634	0.515	0.411	0.634	SUBCLONAL	1	TRUE	1	0.249223392486843	2		523	436	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74000697	74000697	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054808-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	47	820	0	ENST00000318443.5:c.1387C>A	p.Pro463Thr	p.P463T	ENST00000318443	NM_001024736.1	463	Ccc/Acc	7/10	1	2	FACETS	0.483	0.406	0.568	0.483	0.406	0.568	SUBCLONAL	1	TRUE	1	0.249223392486843	2		820	781	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733358	40733358	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054808-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	49	454	0	ENST00000373198.4:c.3448G>A	p.Glu1150Lys	p.E1150K	ENST00000373198	NM_133170.3	1150	Gag/Aag	26/32	1	2	FACETS	0.846	0.717	0.987	0.846	0.717	0.987	CLONAL	1	TRUE	1	0.249223392486843	2		454	465	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0054862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	152	341	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.844820892033495	2		341	342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0054862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	300	615	0	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	0.844820892033495	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.844820892033495	1		615	380	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159748	20159748	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	193	462	1	ENST00000379607.5:c.11A>G	p.Asn4Ser	p.N4S	ENST00000379607	NM_001412.3	4	aAt/aGt	1/7	0.48017636004232	1	FACETS	0.783	0.739	0.827	0.783	0.739	0.827	INDETERMINATE	1	TRUE	0	0.844820892033495	1		463	337	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054868-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	159	115	0				ENST00000310581	NM_198253.2	-/1132			0.378950016992694	6	FACETS	0.888	0.818	0.959	0.666	0.614	0.719	CLONAL	3	TRUE	2	0.378950016992694	6		115	554	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303035	15303035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777257132	NA	P-0054868-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	223	1168	1	ENST00000263388.2:c.415G>A	p.Asp139Asn	p.D139N	ENST00000263388	NM_000435.2	139	Gat/Aat	4/33	0.174533960999109	5	FACETS	1	0.99	1	0.476	0.442	0.511	INDETERMINATE	1	TRUE	2	0.378950016992694	5		1169	1294	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0054868-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1252	141	662	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.378950016992694	7	FACETS	1	0.937	1			1	CLONAL	1	TRUE	NA	0.378950016992694	7		662	1393	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343475	118343475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054868-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	19	422	0	ENST00000534358.1:c.1601C>T	p.Ser534Leu	p.S534L	ENST00000534358	NM_005933.3	534	tCg/tTg	3/36	0.378950016992694	2	FACETS	0.317	0.24	0.408	0.159	0.12	0.204	SUBCLONAL	1	TRUE	0	0.378950016992694	2		422	316	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222759	53222759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054868-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	44	518	0	ENST00000375401.3:c.4177G>A	p.Glu1393Lys	p.E1393K	ENST00000375401	NM_004187.3	1393	Gag/Aag	25/26	0.254891054552681	2	FACETS	0.366	0.306	0.432			1	SUBCLONAL	1	TRUE	NA	0.378950016992694	2		518	635	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61709516	61709516	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054868-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	24	243	0	ENST00000401558.2:c.2971G>A	p.Asp991Asn	p.D991N	ENST00000401558	NM_003400.3	991	Gat/Aat	23/25	1	2	FACETS	0.471	0.37	0.587	0.471	0.37	0.587	SUBCLONAL	1	TRUE	1	0.378950016992694	2		243	269	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962804	2962804	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054868-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	177	960	0	ENST00000396946.4:c.2104G>T	p.Glu702Ter	p.E702*	ENST00000396946	NM_032415.4	702	Gag/Tag	16/25	0.0766242014044711	3	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.378950016992694	3		960	1000	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433544	49433544	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054868-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	341	1143	0	ENST00000301067.7:c.8009C>G	p.Ser2670Cys	p.S2670C	ENST00000301067	NM_003482.3	2670	tCc/tGc	31/54	1	2	FACETS	0.777	0.735	0.82	1	0.995	1	SUBCLONAL	2	TRUE	1	0.378950016992694	2		1143	1158	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793483	18793483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603405	NA	P-0054868-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	12	261	0	ENST00000266497.5:c.4180G>A	p.Glu1394Lys	p.E1394K	ENST00000266497		1394	Gaa/Aaa	30/31	0.256222774010765	5	FACETS	0.29	0.203	0.398	0.097	0.067	0.133	SUBCLONAL	1	TRUE	2	0.378950016992694	5		261	342	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106862	27106862	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142069738	NA	P-0054868-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	93	712	0	ENST00000324856.7:c.6473G>A	p.Arg2158Gln	p.R2158Q	ENST00000324856	NM_006015.4	2158	cGa/cAa	20/20	0.254891054552681	4	FACETS	0.843	0.749	0.943			1	CLONAL	1	TRUE	NA	0.378950016992694	4		712	803	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435583	18435583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746276290	NA	P-0054868-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	44	237	0	ENST00000266497.5:c.568G>A	p.Glu190Lys	p.E190K	ENST00000266497		190	Gaa/Aaa	1/31	0.256222774010765	5	FACETS	1	0.937	1	0.412	0.347	0.482	CLONAL	1	TRUE	2	0.378950016992694	5		237	295	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306549	163306549	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753469318	NA	P-0054868-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	46	306	0	ENST00000271452.3:c.346C>T	p.Arg116Trp	p.R116W	ENST00000271452	NM_145697.2	116	Cgg/Tgg	6/14	0.378950016992694	10	FACETS	1	0.871	1	0.13	0.109	0.153	CLONAL	1	TRUE	2	0.378950016992694	10		306	587	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542708	187542708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054868-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	45	413	0	ENST00000441802.2:c.5032G>A	p.Glu1678Lys	p.E1678K	ENST00000441802	NM_005245.3	1678	Gaa/Aaa	10/27	0.295239316530081	2	FACETS	0.711	0.6	0.833	0.356	0.3	0.417	SUBCLONAL	1	TRUE	0	0.378950016992694	2		413	334	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733140	74733140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054868-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	121	885	0	ENST00000359995.5:c.103G>A	p.Glu35Lys	p.E35K	ENST00000359995	NM_001195427.1	35	Gag/Aag	1/3	0.312725947102681	6	FACETS	0.945	0.851	1	0.236	0.212	0.261	CLONAL	1	TRUE	2	0.378950016992694	6		885	1188	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480099	20480099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054868-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	15	349	0	ENST00000346618.3:c.416G>A	p.Gly139Glu	p.G139E	ENST00000346618	NM_001949.4	139	gGa/gAa	2/7	0.378950016992694	7	FACETS	0.232	0.168	0.309			1	SUBCLONAL	1	TRUE	NA	0.378950016992694	7		349	665	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088731	27088731	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054868-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	164	614	0	ENST00000324856.7:c.2340G>C	p.Gln780His	p.Q780H	ENST00000324856	NM_006015.4	780	caG/caC	7/20	0.254891054552681	4	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.378950016992694	4		614	908	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590602	95590602	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054868-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	11	254	0	ENST00000393063.1:c.1307C>A	p.Ser436Tyr	p.S436Y	ENST00000393063	NM_030621.3	436	tCt/tAt	9/28	0.175348168317717	3	FACETS	0.263	0.181	0.365	0.088	0.06	0.122	INDETERMINATE	1	TRUE	0	0.378950016992694	3		254	263	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590606	95590606	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054868-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	11	257	0	ENST00000393063.1:c.1303C>A	p.Pro435Thr	p.P435T	ENST00000393063	NM_030621.3	435	Cct/Act	9/28	0.175348168317717	3	FACETS	0.256	0.176	0.355	0.085	0.058	0.119	INDETERMINATE	1	TRUE	0	0.378950016992694	3		257	270	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100961	27100961	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054868-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	108	648	0	ENST00000324856.7:c.4243C>A	p.Gln1415Lys	p.Q1415K	ENST00000324856	NM_006015.4	1415	Cag/Aag	18/20	0.254891054552681	4	FACETS	0.975	0.875	1			1	CLONAL	1	TRUE	NA	0.378950016992694	4		648	806	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39746841	39746841	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054868-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	27	388	0	ENST00000361337.2:c.1855T>C	p.Tyr619His	p.Y619H	ENST00000361337	NM_003286.2	619	Tat/Cat	18/21	0.285076009892383	3	FACETS	0.349	0.277	0.432	0.116	0.092	0.144	SUBCLONAL	1	TRUE	0	0.378950016992694	3		388	485	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421355	12421355	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054868-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	99	594	0	ENST00000287820.6:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000287820	NM_015869.4	79	Gaa/Caa	2/7	0.174533960999109	5	FACETS	0.819	0.729	0.914	0.273	0.243	0.305	INDETERMINATE	1	TRUE	2	0.378950016992694	5		594	1001	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421394	12421394	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369959243	NA	P-0054868-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	79	472	0	ENST00000287820.6:c.274G>A	p.Asp92Asn	p.D92N	ENST00000287820	NM_015869.4	92	Gat/Aat	2/7	0.174533960999109	5	FACETS	0.835	0.734	0.944	0.278	0.244	0.315	INDETERMINATE	1	TRUE	2	0.378950016992694	5		472	783	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422983	12422983	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054868-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	61	389	0	ENST00000287820.6:c.473G>C	p.Gly158Ala	p.G158A	ENST00000287820	NM_015869.4	158	gGa/gCa	3/7	0.174533960999109	5	FACETS	0.883	0.762	1	0.294	0.254	0.338	INDETERMINATE	1	TRUE	2	0.378950016992694	5		389	572	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127687	47127687	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054868-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	65	354	0	ENST00000409792.3:c.5395G>C	p.Glu1799Gln	p.E1799Q	ENST00000409792	NM_014159.6	1799	Gag/Cag	11/21	0.174533960999109	5	FACETS	0.989	0.858	1	0.33	0.286	0.377	INDETERMINATE	1	TRUE	2	0.378950016992694	5		354	544	SUCCESS
ATR	545	MSKCC	GRCh37	3	142232471	142232471	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054868-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	19	273	0	ENST00000350721.4:c.4513G>A	p.Asp1505Asn	p.D1505N	ENST00000350721	NM_001184.3	1505	Gat/Aat	26/47	0.174533960999109	5	FACETS	0.617	0.469	0.79	0.206	0.156	0.264	INDETERMINATE	1	TRUE	2	0.378950016992694	5		273	255	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876547	35876547	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054868-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	231	466	0	ENST00000303115.3:c.1339G>C	p.Glu447Gln	p.E447Q	ENST00000303115	NM_002185.3	447	Gaa/Caa	8/8	0.378950016992694	6	FACETS	1	0.988	1	0.618	0.577	0.66	CLONAL	2	TRUE	2	0.378950016992694	6		466	867	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288815	33288815	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054868-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	73	493	0	ENST00000374542.5:c.737C>G	p.Ser246Cys	p.S246C	ENST00000374542	NM_001141970.1	246	tCt/tGt	3/8	0.158316423537569	4	FACETS	0.893	0.781	1	0.446	0.39	0.507	INDETERMINATE	1	TRUE	2	0.378950016992694	4		493	595	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547185	106547185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054868-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	17	240	0	ENST00000369096.4:c.422G>A	p.Arg141Lys	p.R141K	ENST00000369096	NM_001198.3	141	aGa/aAa	4/7	0.185905634224857	2	FACETS	0.39	0.291	0.507	0.195	0.145	0.254	INDETERMINATE	1	TRUE	0	0.378950016992694	2		240	230	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112029144	112029144	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054868-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	17	325	0	ENST00000368678.4:c.424G>T	p.Asp142Tyr	p.D142Y	ENST00000368678		142	Gac/Tac	5/13	0.185905634224857	2	FACETS	0.296	0.221	0.386	0.148	0.11	0.193	INDETERMINATE	1	TRUE	0	0.378950016992694	2		325	303	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054868-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	31	115	0				ENST00000310581	NM_198253.2	-/1132			0.286186383080063	5	FACETS	0.977	0.792	1	0.244	0.198	0.297	CLONAL	1	TRUE	1	0.286186383080063	5		115	317	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303035	15303035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777257132	NA	P-0054868-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	51	1168	1	ENST00000263388.2:c.415G>A	p.Asp139Asn	p.D139N	ENST00000263388	NM_000435.2	139	Gat/Aat	4/33	1	2	FACETS	0.389	0.329	0.455	0.389	0.329	0.455	SUBCLONAL	1	TRUE	1	0.286186383080063	2		1169	917	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0054868-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	58	662	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.0910519446670788	3	FACETS	0.612	0.525	0.708	0.306	0.262	0.354	INDETERMINATE	1	TRUE	1	0.286186383080063	3		662	757	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343475	118343475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054868-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	21	422	0	ENST00000534358.1:c.1601C>T	p.Ser534Leu	p.S534L	ENST00000534358	NM_005933.3	534	tCg/tTg	3/36	1	2	FACETS	0.356	0.274	0.453	0.356	0.274	0.453	SUBCLONAL	1	TRUE	1	0.286186383080063	2		422	412	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222759	53222759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054868-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	31	518	0	ENST00000375401.3:c.4177G>A	p.Glu1393Lys	p.E1393K	ENST00000375401	NM_004187.3	1393	Gag/Aag	25/26	0.0734154708254113	2	FACETS	0.489	0.395	0.596			1	INDETERMINATE	1	TRUE	NA	0.286186383080063	2		518	443	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432863	432863	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054868-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	28	550	0	ENST00000399788.2:c.2053C>G	p.Leu685Val	p.L685V	ENST00000399788	NM_001042603.1	685	Ctc/Gtc	15/28	1	2	FACETS	0.352	0.28	0.434	0.352	0.28	0.434	SUBCLONAL	1	TRUE	1	0.286186383080063	2		550	556	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61709516	61709516	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054868-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	164	243	0	ENST00000401558.2:c.2971G>A	p.Asp991Asn	p.D991N	ENST00000401558	NM_003400.3	991	Gat/Aat	23/25	0.286186383080063	5	FACETS	1	0.969	1			1	CLONAL	3	TRUE	NA	0.286186383080063	5		243	501	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962804	2962804	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054868-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	52	960	0	ENST00000396946.4:c.2104G>T	p.Glu702Ter	p.E702*	ENST00000396946	NM_032415.4	702	Gag/Tag	16/25	0.0910519446670788	3	FACETS	0.515	0.437	0.601	0.258	0.218	0.301	INDETERMINATE	1	TRUE	1	0.286186383080063	3		960	806	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590602	95590606	+	missense_variant	Missense_Mutation	ONP	GAAGG	GAAGG	TAAGT	novel	NA	P-0054868-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	9	0	0	ENST00000393063.1:c.1303_1307delinsACTTA	p.Pro435_Ser436delinsThrTyr	p.P435_S436delinsTY	ENST00000393063	NM_030621.3	435	CCTTCt/ACTTAt	9/28	1	2	FACETS	0.189	0.124	0.272	0.189	0.124	0.272	SUBCLONAL	1	TRUE	1	0.286186383080063	2		0	333	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433544	49433544	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054868-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	64	1143	0	ENST00000301067.7:c.8009C>G	p.Ser2670Cys	p.S2670C	ENST00000301067	NM_003482.3	2670	tCc/tGc	31/54	1	2	FACETS	0.44	0.379	0.506	0.44	0.379	0.506	SUBCLONAL	1	TRUE	1	0.286186383080063	2		1143	1017	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885856	23885856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054868-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	26	795	0	ENST00000374561.5:c.62G>A	p.Ser21Asn	p.S21N	ENST00000374561	NM_002167.4	21	aGt/aAt	1/3	0.0602230290042653	3	FACETS	0.405	0.32	0.503	0.202	0.16	0.252	INDETERMINATE	1	TRUE	1	0.286186383080063	3		795	513	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0054872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	91	400	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.797	0.709	0.891	0.797	0.709	0.891	SUBCLONAL	1	TRUE	1	0.381089516732704	2		400	599	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0054872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	176	341	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.38100940989503	2	FACETS	0.995	0.926	1	0.995	0.926	1	CLONAL	2	TRUE	0	0.381089516732704	2		341	464	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778738	3778738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1489860615	NA	P-0054872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	173	821	0	ENST00000262367.5:c.6310C>T	p.Arg2104Cys	p.R2104C	ENST00000262367	NM_004380.2	2104	Cgc/Tgc	31/31	1	2	FACETS	0.857	0.787	0.929	0.857	0.787	0.929	CLONAL	1	TRUE	1	0.381089516732704	2		821	1060	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775601	39775601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146705250	NA	P-0054872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	87	321	0	ENST00000288319.7:c.419G>A	p.Arg140Gln	p.R140Q	ENST00000288319	NM_182918.3	140	cGg/cAg	4/10	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.381089516732704	2		321	448	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460389	149460389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761230419	NA	P-0054872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	127	510	2	ENST00000286301.3:c.248G>A	p.Arg83His	p.R83H	ENST00000286301	NM_005211.3	83	cGc/cAc	3/22	1	2	FACETS	0.834	0.756	0.917	0.834	0.756	0.917	CLONAL	1	TRUE	1	0.381089516732704	2		512	799	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124240	2124240	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1366556255	NA	P-0054872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	193	671	2	ENST00000219476.3:c.2395C>T	p.Arg799Cys	p.R799C	ENST00000219476	NM_000548.3	799	Cgc/Tgc	22/42	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.381089516732704	2		673	967	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732946	30732946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	77	304	0	ENST00000295754.5:c.1559G>T	p.Cys520Phe	p.C520F	ENST00000295754	NM_003242.5	520	tGc/tTc	7/7	1	2	FACETS	0.99	0.874	1	0.99	0.874	1	CLONAL	1	TRUE	1	0.381089516732704	2		304	408	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349494	89349494	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	147	695	0	ENST00000301030.4:c.3456G>T	p.Lys1152Asn	p.K1152N	ENST00000301030	NM_001256183.1	1152	aaG/aaT	9/13	1	2	FACETS	0.893	0.815	0.974	0.893	0.815	0.974	CLONAL	1	TRUE	1	0.381089516732704	2		695	864	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440703	56440703	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	249	555	0	ENST00000407977.2:c.515T>C	p.Leu172Pro	p.L172P	ENST00000407977		172	cTg/cCg	5/10	0.38100940989503	2	FACETS	0.91	0.855	0.966	0.91	0.855	0.966	CLONAL	2	TRUE	0	0.381089516732704	2		555	718	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715603	30715603	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs886038787	NA	P-0054872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	46	184	0	ENST00000295754.5:c.1261A>G	p.Thr421Ala	p.T421A	ENST00000295754	NM_003242.5	421	Act/Gct	5/7	1	2	FACETS	0.865	0.733	1	0.865	0.733	1	CLONAL	1	TRUE	1	0.381089516732704	2		184	279	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250875	153250893	+	frameshift_variant	Frame_Shift_Del	DEL	AACTATTCGGTTACCACAA	AACTATTCGGTTACCACAA	-	novel	NA	P-0054872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	66	330	0	ENST00000281708.4:c.1167_1185del	p.Phe389LeufsTer9	p.F389Lfs*9	ENST00000281708	NM_033632.3	389	ttTTGTGGTAACCGAATAGTT/tt	8/12	1	2	FACETS	0.794	0.692	0.905	0.794	0.692	0.905	CLONAL	1	TRUE	1	0.381089516732704	2		330	436	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27192620	27192620	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	73	444	0	ENST00000380036.4:c.1623C>G	p.Ile541Met	p.I541M	ENST00000380036	NM_000459.3	541	atC/atG	11/23	0.202256298605194	3	FACETS	0.942	0.83	1			1	INDETERMINATE	1	TRUE	NA	0.581677555103672	3		444	344	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637690	52637690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239654517	NA	P-0054881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	13	380	1	ENST00000394830.3:c.2626C>T	p.Arg876Cys	p.R876C	ENST00000394830	NM_018313.4	876	Cgt/Tgt	18/30	0.112387869644944	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		381	199	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106210	27106210	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	37	475	0	ENST00000324856.7:c.5823del	p.Phe1941LeufsTer15	p.F1941Lfs*15	ENST00000324856	NM_006015.4	1941	Ttt/tt	20/20	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		475	593	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046753	42046753	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	26	340	0	ENST00000219905.7:c.7127C>A	p.Ser2376Ter	p.S2376*	ENST00000219905	NM_001164273.1	2376	tCa/tAa	18/24	0.112387869644944	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		340	482	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562533	176562534	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs1345337658	NA	P-0054881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	27	469	0	ENST00000439151.2:c.430_431del	p.Lys144AspfsTer10	p.K144Dfs*10	ENST00000439151	NM_022455.4	143	acAAag/acag	2/23	0.112387869644944	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		469	352	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0054899-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	332	472	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	0.685543406807201	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.685543406807201	3		472	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572986	7572986	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555524156	NA	P-0054899-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	105	374	1	ENST00000269305.4:c.1123C>T	p.Gln375Ter	p.Q375*	ENST00000269305	NM_001126112.2	375	Cag/Tag	11/11	0.685543406807201	3	FACETS	0.984	0.888	1	0.492	0.444	0.542	CLONAL	1	TRUE	1	0.685543406807201	3		375	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578247	+	inframe_deletion	In_Frame_Del	DEL	ACTCCACACGCA	ACTCCACACGCA	-	novel	NA	P-0054899-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	268	597	2	ENST00000269305.4:c.602_613del	p.Leu201_Glu204del	p.L201_E204del	ENST00000269305	NM_001126112.2	201	tTGCGTGTGGAGTat/tat	6/11	0.685543406807201	3	FACETS	0.916	0.868	0.965	0.916	0.868	0.965	CLONAL	2	TRUE	1	0.685543406807201	3		599	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0054905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	281	773	2	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.252955121291869	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.252955121291869	2		775	964	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0054905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	174	396	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.228653658597711	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	0	0.252955121291869	3		396	448	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188977	32188977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760997487	NA	P-0054905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	116	804	2	ENST00000375023.3:c.577C>T	p.Arg193Cys	p.R193C	ENST00000375023	NM_004557.3	193	Cgt/Tgt	4/30	0.219295450978272	3	FACETS	1	0.968	1	0.59	0.531	0.652	CLONAL	1	TRUE	1	0.252955121291869	3		806	876	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246308	41246308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	84	565	0	ENST00000357654.3:c.1240G>A	p.Asp414Asn	p.D414N	ENST00000357654	NM_007294.3	414	Gac/Aac	10/23	0.252955121291869	3	FACETS	1	0.942	1	0.555	0.49	0.624	CLONAL	1	TRUE	1	0.252955121291869	3		565	674	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262430	39262430	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	76	493	0	ENST00000402219.2:c.997G>T	p.Glu333Ter	p.E333*	ENST00000402219	NM_005633.3	333	Gaa/Taa	8/23	0.252955121291869	2	FACETS	1	0.933	1	0.547	0.481	0.619	CLONAL	1	TRUE	0	0.252955121291869	2		493	549	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509397	106509397	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	75	616	0	ENST00000359195.3:c.1391T>C	p.Val464Ala	p.V464A	ENST00000359195	NM_002649.2	464	gTg/gCg	2/11	0.19223066058047	4	FACETS	1	0.885	1	0.505	0.442	0.574	CLONAL	1	TRUE	2	0.252955121291869	4		616	735	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556687	41556691	+	frameshift_variant	Frame_Shift_Del	DEL	AGAGC	AGAGC	CTCT	novel	NA	P-0054905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	61	474	0	ENST00000263253.7:c.3632_3636delinsCTCT	p.Glu1211AlafsTer16	p.E1211Afs*16	ENST00000263253	NM_001429.3	1211	gAGAGC/gCTCT	20/31	0.252955121291869	3	FACETS	0.926	0.799	1	0.463	0.399	0.532	CLONAL	1	TRUE	1	0.252955121291869	3		474	587	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	124	314	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.897	0.816	0.981	0.897	0.816	0.981	CLONAL	1	TRUE	1	0.553191549012096	2		314	500	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0054906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	28	34	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.553191549012096	2		34	87	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560493	65560493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	171	430	0	ENST00000358664.4:c.104G>T	p.Arg35Leu	p.R35L	ENST00000358664	NM_002382.4	35	cGt/cTt	3/5	0.553191549012096	1	FACETS	0.946	0.878	1	0.946	0.878	1	CLONAL	1	TRUE	0	0.553191549012096	1		430	473	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665096	138665096	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs758370933	NA	P-0054906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	76	186	0	ENST00000330315.3:c.469C>G	p.Pro157Ala	p.P157A	ENST00000330315	NM_023067.3	157	Ccc/Gcc	1/1	1	2	FACETS	0.907	0.803	1	0.907	0.803	1	CLONAL	1	TRUE	1	0.553191549012096	2		186	303	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032542	47032542	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886044718	NA	P-0054906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	242	319	0	ENST00000377604.3:c.448C>T	p.Gln150Ter	p.Q150*	ENST00000377604	NM_001204468.1	150	Cag/Tag	5/24	1	1	FACETS	0.752	0.714	0.789	1	0.994	1	SUBCLONAL	2	TRUE	0	0.553191549012096	1		319	421	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415622	49415622	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	143	353	1	ENST00000301067.7:c.16555G>T	p.Asp5519Tyr	p.D5519Y	ENST00000301067	NM_003482.3	5519	Gat/Tat	54/54	1	2	FACETS	0.966	0.886	1	0.966	0.886	1	CLONAL	1	TRUE	1	0.553191549012096	2		354	535	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246493817	246493817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	142	327	1	ENST00000388985.4:c.359C>T	p.Ser120Leu	p.S120L	ENST00000388985		120	tCa/tTa	4/12	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.553191549012096	2		328	486	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992756	72992756	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	54	618	0	ENST00000268489.5:c.1289C>G	p.Ser430Cys	p.S430C	ENST00000268489	NM_006885.3	430	tCc/tGc	2/10	1	2	FACETS	0.195	0.166	0.228	0.195	0.166	0.228	SUBCLONAL	1	TRUE	1	0.553191549012096	2		618	999	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673691	37673691	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0054906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	177	421	0	ENST00000447079.4:c.2847-2A>T		p.X949_splice	ENST00000447079	NM_015083.1	949			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.553191549012096	2		421	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0054911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	278	708	0	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	0.211806716905802	2	FACETS	1	0.992	1	0.689	0.646	0.732	CLONAL	1	TRUE	0	0.342427530254718	2		708	1179	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681757	30681757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779352833	NA	P-0054911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	65	640	0	ENST00000376406.3:c.340C>T	p.Arg114Cys	p.R114C	ENST00000376406	NM_014641.2	114	Cgt/Tgt	3/15	1	2	FACETS	0.326	0.281	0.375	0.326	0.281	0.375	SUBCLONAL	1	TRUE	1	0.342427530254718	2		640	1164	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918870	76918870	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0054911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	180	298	0	ENST00000373344.5:c.4120+1G>A		p.X1374_splice	ENST00000373344	NM_000489.3	1374			1	1	FACETS	0.779	0.723	0.837	1	0.991	1	SUBCLONAL	2	TRUE	0	0.342427530254718	1		298	559	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200005	128200005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1392	272	830	1	ENST00000341105.2:c.1300G>A	p.Ala434Thr	p.A434T	ENST00000341105	NM_032638.4	434	Gct/Act	6/6	0.248288085572415	3	FACETS	1	0.981	1	0.559	0.523	0.597	CLONAL	1	TRUE	1	0.342427530254718	3		831	1664	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729187	66729187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	309	558	0	ENST00000307102.5:c.395C>T	p.Ala132Val	p.A132V	ENST00000307102	NM_002755.3	132	gCg/gTg	3/11	0.109828226099374	4	FACETS	1	0.953	1	0.506	0.477	0.537	INDETERMINATE	2	TRUE	0	0.342427530254718	4		558	1196	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243913	41243913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	171	650	0	ENST00000357654.3:c.3635C>T	p.Ser1212Leu	p.S1212L	ENST00000357654	NM_007294.3	1212	tCa/tTa	10/23	NA	2	FACETS	0.905	0.832	0.983			1	INDETERMINATE	1	TRUE	NA	0.342427530254718	2		650	1103	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226568877	226568877	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	71	548	0	ENST00000366794.5:c.1192C>G	p.Leu398Val	p.L398V	ENST00000366794	NM_001618.3	398	Ctc/Gtc	9/23	0.248288085572415	3	FACETS	0.423	0.368	0.484	0.212	0.184	0.242	SUBCLONAL	1	TRUE	1	0.342427530254718	3		548	1147	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246078846	246078846	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	251	685	0	ENST00000388985.4:c.799C>G	p.Gln267Glu	p.Q267E	ENST00000388985		267	Caa/Gaa	8/12	0.248288085572415	3	FACETS	1	0.99	1	0.658	0.615	0.704	CLONAL	1	TRUE	1	0.342427530254718	3		685	1304	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442533	49442533	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	66	404	0	ENST00000301067.7:c.4040C>G	p.Ser1347Cys	p.S1347C	ENST00000301067	NM_003482.3	1347	tCt/tGt	13/54	1	2	FACETS	0.463	0.401	0.531	0.463	0.401	0.531	SUBCLONAL	1	TRUE	1	0.342427530254718	2		404	832	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445707	49445707	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs199980307	NA	P-0054911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2074	164	1305	0	ENST00000301067.7:c.1759G>C	p.Glu587Gln	p.E587Q	ENST00000301067	NM_003482.3	587	Gag/Cag	10/54	1	2	FACETS	0.428	0.391	0.467	0.428	0.391	0.467	SUBCLONAL	1	TRUE	1	0.342427530254718	2		1305	2238	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811747	102811747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1198	155	880	0	ENST00000307046.8:c.437C>T	p.Ser146Phe	p.S146F	ENST00000307046	NM_001111285.1	146	tCt/tTt	4/4	1	2	FACETS	0.669	0.611	0.731	0.669	0.611	0.731	SUBCLONAL	1	TRUE	1	0.342427530254718	2		880	1353	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99452105	99452105	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	41	345	0	ENST00000268035.6:c.1439G>T	p.Arg480Met	p.R480M	ENST00000268035	NM_000875.3	480	aGg/aTg	6/21	NA	2	FACETS	0.356	0.295	0.423			1	INDETERMINATE	1	TRUE	NA	0.342427530254718	2		345	673	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243707	41243707	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs80356866	NA	P-0054911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	141	579	0	ENST00000357654.3:c.3841C>T	p.Gln1281Ter	p.Q1281*	ENST00000357654	NM_007294.3	1281	Cag/Tag	10/23	NA	2	FACETS	0.745	0.677	0.816			1	INDETERMINATE	1	TRUE	NA	0.342427530254718	2		579	1106	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222080	2222080	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1533	116	843	0	ENST00000398665.3:c.2912C>G	p.Ser971Cys	p.S971C	ENST00000398665	NM_032482.2	971	tCt/tGt	24/28	0.247469727243416	3	FACETS	0.481	0.432	0.534	0.16	0.144	0.178	SUBCLONAL	1	TRUE	0	0.342427530254718	3		843	1649	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474694	138474694	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	258	506	0	ENST00000289153.2:c.299G>T	p.Cys100Phe	p.C100F	ENST00000289153	NM_006219.2	100	tGt/tTt	2/22	0.342427530254718	3	FACETS	0.831	0.778	0.885			1	CLONAL	2	TRUE	NA	0.342427530254718	3		506	1062	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361202	66361202	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	137	359	0	ENST00000273854.3:c.970C>A	p.Pro324Thr	p.P324T	ENST00000273854	NM_004439.5	324	Cct/Act	4/18	0.342427530254718	3	FACETS	1	0.966	1	0.563	0.512	0.617	CLONAL	1	TRUE	1	0.342427530254718	3		359	832	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549427	187549427	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	117	576	0	ENST00000441802.2:c.4691C>A	p.Ala1564Asp	p.A1564D	ENST00000441802	NM_005245.3	1564	gCt/gAt	9/27	0.261734817652667	0	FACETS	0.567	0.511	0.626			1	SUBCLONAL	1	TRUE	0	0.342427530254718	0		576	793	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280274	1280274	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	887	864	0	ENST00000310581.5:c.1949G>T	p.Arg650Met	p.R650M	ENST00000310581	NM_198253.2	650	aGg/aTg	4/16	0.342427530254718	5	FACETS	0.934	0.906	0.963			1	CLONAL	4	TRUE	NA	0.342427530254718	5		864	2098	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420078	152420078	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	46	463	0	ENST00000206249.3:c.1765G>C	p.Glu589Gln	p.E589Q	ENST00000206249	NM_000125.3	589	Gag/Cag	8/8	1	2	FACETS	0.353	0.296	0.416	0.353	0.296	0.416	SUBCLONAL	1	TRUE	1	0.342427530254718	2		463	762	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391547	139391547	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1401419952	NA	P-0054912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	157	787	0	ENST00000277541.6:c.6644C>T	p.Ser2215Leu	p.S2215L	ENST00000277541	NM_017617.3	2215	tCg/tTg	34/34	1	2	FACETS	0.727	0.665	0.792	0.727	0.665	0.792	SUBCLONAL	1	TRUE	1	0.420176152289697	2		787	1028	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0054912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	119	285	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.377347891640518	3	FACETS	1	0.984	1	0.714	0.648	0.783	CLONAL	1	TRUE	1	0.420176152289697	3		285	480	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844175	68844175	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	144	588	1	ENST00000261769.5:c.763C>T	p.Gln255Ter	p.Q255*	ENST00000261769	NM_004360.3	255	Cag/Tag	6/16	0.420176152289697	1	FACETS	0.854	0.781	0.93	0.854	0.781	0.93	CLONAL	1	TRUE	0	0.420176152289697	1		589	634	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061243	38061243	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	126	533	0	ENST00000250448.2:c.746A>T	p.Asp249Val	p.D249V	ENST00000250448	NM_004496.3	249	gAc/gTc	2/2	1	2	FACETS	0.804	0.729	0.883	0.804	0.729	0.883	CLONAL	1	TRUE	1	0.420176152289697	2		533	746	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8246269	8246269	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0054912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	45	319	0	ENST00000335790.3:c.366-1G>C		p.X122_splice	ENST00000335790	NM_002315.2	122			0.282995477245575	1	FACETS	0.455	0.383	0.534	0.455	0.383	0.534	SUBCLONAL	1	TRUE	0	0.420176152289697	1		319	372	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94201056	94201056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	35	237	0	ENST00000323929.3:c.1021G>A	p.Glu341Lys	p.E341K	ENST00000323929	NM_005591.3	341	Gaa/Aaa	10/20	0.357544165937095	1	FACETS	0.58	0.478	0.692	0.58	0.478	0.692	SUBCLONAL	1	TRUE	0	0.420176152289697	1		237	227	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658231	18658231	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	92	390	0	ENST00000266497.5:c.3036G>C	p.Leu1012Phe	p.L1012F	ENST00000266497		1012	ttG/ttC	22/31	0.357544165937095	1	FACETS	0.71	0.634	0.791	0.71	0.634	0.791	SUBCLONAL	1	TRUE	0	0.420176152289697	1		390	487	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448693	49448693	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	113	455	0	ENST00000301067.7:c.166C>A	p.Gln56Lys	p.Q56K	ENST00000301067	NM_003482.3	56	Cag/Aag	2/54	1	2	FACETS	0.812	0.732	0.897	0.812	0.732	0.897	CLONAL	1	TRUE	1	0.420176152289697	2		455	662	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481623	56481623	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	152	680	0	ENST00000267101.3:c.658G>C	p.Gly220Arg	p.G220R	ENST00000267101	NM_001982.3	220	Ggg/Cgg	6/28	1	2	FACETS	0.739	0.675	0.806	0.739	0.675	0.806	SUBCLONAL	1	TRUE	1	0.420176152289697	2		680	979	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347093	347093	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	211	761	0	ENST00000262320.3:c.1918G>C	p.Glu640Gln	p.E640Q	ENST00000262320	NM_003502.3	640	Gaa/Caa	7/11	NA	2	FACETS	0.989	0.919	1			1	INDETERMINATE	1	TRUE	NA	0.420176152289697	2		761	1015	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557353	29557353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	55	224	0	ENST00000356175.3:c.3066G>A	p.Met1022Ile	p.M1022I	ENST00000356175	NM_000267.3	1022	atG/atA	23/57	1	2	FACETS	0.811	0.697	0.933	0.811	0.697	0.933	CLONAL	1	TRUE	1	0.420176152289697	2		224	323	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943723	17943723	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0054912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	79	561	0	ENST00000458235.1:c.2366C>G	p.Ser789Ter	p.S789*	ENST00000458235	NM_000215.3	789	tCa/tGa	18/24	0.16046104273563	2	FACETS	0.499	0.439	0.565	0.25	0.219	0.283	INDETERMINATE	1	TRUE	0	0.420176152289697	2		561	753	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451912	29451912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs925802421	NA	P-0054912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	109	649	0	ENST00000389048.3:c.2653G>A	p.Asp885Asn	p.D885N	ENST00000389048	NM_004304.4	885	Gat/Aat	16/29	0.420176152289697	1	FACETS	0.565	0.507	0.625	0.565	0.507	0.625	SUBCLONAL	1	TRUE	0	0.420176152289697	1		649	726	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177845	142177845	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	57	281	0	ENST00000350721.4:c.7458G>C	p.Leu2486Phe	p.L2486F	ENST00000350721	NM_001184.3	2486	ttG/ttC	44/47	0.377347891640518	3	FACETS	0.829	0.714	0.954	0.415	0.357	0.477	CLONAL	1	TRUE	1	0.420176152289697	3		281	396	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447270	187447270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369445234	NA	P-0054912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	253	636	0	ENST00000232014.4:c.923C>T	p.Ser308Leu	p.S308L	ENST00000232014	NM_001130845.1	308	tCg/tTg	5/10	0.377347891640518	3	FACETS	1	0.992	1	0.712	0.667	0.759	CLONAL	1	TRUE	1	0.420176152289697	3		636	1023	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751896	57751896	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	128	455	0	ENST00000274289.3:c.1341G>T	p.Met447Ile	p.M447I	ENST00000274289	NM_006622.3	447	atG/atT	10/14	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.420176152289697	2		455	596	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750960	128750960	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777980347	NA	P-0054912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	127	463	0	ENST00000377970.2:c.497C>T	p.Ser166Phe	p.S166F	ENST00000377970	NM_002467.4	166	tCc/tTc	2/3	1	2	FACETS	0.8	0.725	0.878	0.8	0.725	0.878	SUBCLONAL	1	TRUE	1	0.420176152289697	2		463	756	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453145	140453145	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913366	NA	P-0054917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	129	376	0	ENST00000288602.6:c.1790T>A	p.Leu597Gln	p.L597Q	ENST00000288602	NM_004333.4	597	cTa/cAa	15/18	1	2	FACETS	0.964	0.887	1	0.964	0.887	1	CLONAL	1	TRUE	1	0.85	2		376	315	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575079	64575088	+	frameshift_variant	Frame_Shift_Del	DEL	ATGGCACACA	ATGGCACACA	-	novel	NA	P-0054917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	267	646	0	ENST00000312049.6:c.719_728del	p.Val240AlafsTer38	p.V240Afs*38	ENST00000312049	NM_130799.2	240	gTGTGTGCCATc/gc	4/10	1	2	FACETS	0.891	0.84	0.943	0.891	0.84	0.943	CLONAL	1	TRUE	1	0.85	2		646	705	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0054920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	144	585	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.468392632971219	2		585	536	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165321	47165321	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	48	454	0	ENST00000409792.3:c.805C>T	p.Gln269Ter	p.Q269*	ENST00000409792	NM_014159.6	269	Caa/Taa	3/21	1	2	FACETS	0.45	0.381	0.527	0.45	0.381	0.527	SUBCLONAL	1	TRUE	1	0.468392632971219	2		454	455	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761283	59761283	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	33	740	0	ENST00000259008.2:c.3124G>C	p.Glu1042Gln	p.E1042Q	ENST00000259008	NM_032043.2	1042	Gaa/Caa	20/20	1	2	FACETS	0.226	0.183	0.274	0.226	0.183	0.274	SUBCLONAL	1	TRUE	1	0.468392632971219	2		740	624	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682895	190682895	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	54	413	0	ENST00000441310.2:c.571G>C	p.Val191Leu	p.V191L	ENST00000441310	NM_000534.4	191	Gta/Cta	5/13	1	2	FACETS	0.501	0.429	0.58	0.501	0.429	0.58	SUBCLONAL	1	TRUE	1	0.468392632971219	2		413	460	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	52	392	3	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.2	2		395	516	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	41	316	2	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	1	2	FACETS	0.81	0.675	0.961	0.81	0.675	0.961	CLONAL	1	TRUE	1	0.2	2		318	506	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	111	435	1	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.877	0.79	0.969	1	0.987	1	CLONAL	2	TRUE	1	0.2	2		436	633	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	50	483	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.718	0.608	0.84	0.718	0.608	0.84	SUBCLONAL	1	TRUE	1	0.2	2		483	696	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	19	328	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.451	0.342	0.581	0.451	0.342	0.581	SUBCLONAL	1	TRUE	1	0.2	2		328	421	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	48	401	0	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.678	0.572	0.795	0.678	0.572	0.795	SUBCLONAL	1	TRUE	1	0.2	2		401	708	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	27	432	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.453	0.359	0.561	0.453	0.359	0.561	SUBCLONAL	1	TRUE	1	0.2	2		432	596	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	46	409	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.816	0.686	0.959	0.816	0.686	0.959	CLONAL	1	TRUE	1	0.2	2		409	564	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200387	138200387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760531232	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	93	616	0	ENST00000237289.4:c.1805C>T	p.Thr602Met	p.T602M	ENST00000237289	NM_001270507.1	602	aCg/aTg	7/9	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.2	2		616	861	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	20	340	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	1	2	FACETS	0.45	0.343	0.576	0.45	0.343	0.576	SUBCLONAL	1	TRUE	1	0.2	2		340	444	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131418	17131418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751171641	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	89	615	0	ENST00000285071.4:c.34G>A	p.Glu12Lys	p.E12K	ENST00000285071	NM_144997.5	12	Gag/Aag	4/14	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.2	2		615	816	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110228	3110228	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769019097	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	79	694	1	ENST00000078429.4:c.218G>A	p.Arg73His	p.R73H	ENST00000078429	NM_002067.2	73	cGc/cAc	2/7	1	2	FACETS	0.791	0.694	0.896	0.791	0.694	0.896	SUBCLONAL	1	TRUE	1	0.2	2		695	999	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350470	15350470	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs779348570	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	71	675	0	ENST00000263377.2:c.3445C>T	p.Arg1149Trp	p.R1149W	ENST00000263377	NM_058243.2	1149	Cgg/Tgg	16/20	1	2	FACETS	0.863	0.752	0.983	0.863	0.752	0.983	CLONAL	1	TRUE	1	0.2	2		675	823	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043349	6043349	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781716	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	40	268	0	ENST00000265849.7:c.325del	p.Glu109LysfsTer3	p.E109Kfs*3	ENST00000265849	NM_000535.5	109	Gaa/aa	4/15	1	2	FACETS	0.868	0.721	1	0.868	0.721	1	CLONAL	1	TRUE	1	0.2	2		268	461	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910626	29910626	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	114	1176	1	ENST00000376809.5:c.166C>T	p.Gln56Ter	p.Q56*	ENST00000376809	NM_002116.7	56	Cag/Tag	2/8	1	2	FACETS	0.866	0.777	0.96	0.866	0.777	0.96	CLONAL	1	TRUE	1	0.2	2		1177	1317	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396482	139396482	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	107	792	1	ENST00000277541.6:c.5443del	p.Asp1815ThrfsTer72	p.D1815Tfs*72	ENST00000277541	NM_017617.3	1815	Gac/ac	29/34	1	2	FACETS	0.973	0.87	1	0.973	0.87	1	CLONAL	1	TRUE	1	0.2	2		793	1100	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486050	29486050	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1438566555	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	29	294	0	ENST00000356175.3:c.233del	p.Asn78IlefsTer7	p.N78Ifs*7	ENST00000356175	NM_000267.3	76	gAa/ga	3/57	1	2	FACETS	0.633	0.507	0.777	0.633	0.507	0.777	SUBCLONAL	1	TRUE	1	0.2	2		294	458	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396839	396839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145608130	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	82	684	0	ENST00000262320.3:c.187C>T	p.Arg63Cys	p.R63C	ENST00000262320	NM_003502.3	63	Cgc/Tgc	2/11	1	2	FACETS	0.918	0.808	1	0.918	0.808	1	CLONAL	1	TRUE	1	0.2	2		684	893	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813674	50813674	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	90	702	0	ENST00000398568.2:c.1228G>A	p.Glu410Lys	p.E410K	ENST00000398568	NM_001042412.1	410	Gag/Aag	8/18	1	2	FACETS	0.826	0.731	0.928	0.826	0.731	0.928	CLONAL	1	TRUE	1	0.2	2		702	1090	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162868	38162868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201879366	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	126	601	0	ENST00000317025.8:c.2338C>T	p.Arg780Cys	p.R780C	ENST00000317025	NM_023034.1	780	Cgc/Tgc	13/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.2	2		601	1082	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096132	2096133	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs763525759	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	84	707	1	ENST00000219066.1:c.374dup	p.Val127GlyfsTer43	p.V127Gfs*43	ENST00000219066	NM_002528.5	125	cca/ccCa	2/6	1	2	FACETS	0.898	0.792	1	0.898	0.792	1	CLONAL	1	TRUE	1	0.2	2		708	935	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022502	12022502	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1232497641	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	102	785	5	ENST00000396373.4:c.613del	p.Leu205TrpfsTer4	p.L205Wfs*4	ENST00000396373	NM_001987.4	203	tCc/tc	5/8	0.3	3	FACETS	1	0.959	1			1	CLONAL	1	TRUE	NA	0.2	3		790	972	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434005	49434005	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	76	799	0	ENST00000301067.7:c.7548del	p.Asn2517IlefsTer26	p.N2517Ifs*26	ENST00000301067	NM_003482.3	2516	ccC/cc	31/54	1	2	FACETS	0.755	0.661	0.858	0.755	0.661	0.858	SUBCLONAL	1	TRUE	1	0.2	2		799	1006	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231449	5231449	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	84	718	3	ENST00000357368.4:c.2027del	p.Pro676ArgfsTer134	p.P676Rfs*134	ENST00000357368	NM_002850.3	676	cCg/cg	14/38	1	2	FACETS	0.711	0.626	0.803	0.711	0.626	0.803	SUBCLONAL	1	TRUE	1	0.2	2		721	1182	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345760	152345760	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	37	269	0	ENST00000359321.1:c.810del	p.Phe270LeufsTer27	p.F270Lfs*27	ENST00000359321	NM_005431.1	270	ttT/tt	3/3	1	2	FACETS	0.961	0.793	1	0.961	0.793	1	CLONAL	1	TRUE	1	0.2	2		269	385	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608363	43608363	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750958377	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	97	993	0	ENST00000355710.3:c.1711G>A	p.Asp571Asn	p.D571N	ENST00000355710	NM_020975.4	571	Gat/Aat	9/20	1	2	FACETS	0.833	0.741	0.933	0.833	0.741	0.933	CLONAL	1	TRUE	1	0.2	2		993	1164	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161807897	161807897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56092260	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	50	374	1	ENST00000366898.1:c.1096C>T	p.Arg366Trp	p.R366W	ENST00000366898	NM_004562.2	366	Cgg/Tgg	10/12	1	2	FACETS	0.888	0.753	1	0.888	0.753	1	CLONAL	1	TRUE	1	0.2	2		375	563	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974701	21974701	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	44	447	0	ENST00000304494.5:c.126T>A	p.Asn42Lys	p.N42K	ENST00000304494	NM_000077.4	42	aaT/aaA	1/3	1	2	FACETS	0.76	0.637	0.897	0.76	0.637	0.897	SUBCLONAL	1	TRUE	1	0.2	2		447	579	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993624	72993624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs997674247	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	86	712	0	ENST00000268489.5:c.421G>A	p.Ala141Thr	p.A141T	ENST00000268489	NM_006885.3	141	Gcg/Acg	2/10	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.2	2		712	849	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158637068	158637069	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CA	CA	-	rs141073095	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	88	675	3	ENST00000263640.3:c.111_112del	p.Cys37Ter	p.C37*	ENST00000263640	NM_001105.4	37	tgTGaa/tgaa	4/11	1	2	FACETS	0.93	0.823	1	0.93	0.823	1	CLONAL	1	TRUE	1	0.2	2		678	946	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38954947	38954947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771642192	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	26	240	0	ENST00000357387.3:c.2626G>A	p.Val876Ile	p.V876I	ENST00000357387	NM_152756.3	876	Gtc/Atc	27/38	1	2	FACETS	0.813	0.644	1	0.813	0.644	1	CLONAL	1	TRUE	1	0.2	2		240	320	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133234459	133234459	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs139603739	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	46	419	1	ENST00000320574.5:c.3373C>T	p.Arg1125Ter	p.R1125*	ENST00000320574	NM_006231.2	1125	Cga/Tga	27/49	1	2	FACETS	0.632	0.531	0.744	0.632	0.531	0.744	SUBCLONAL	1	TRUE	1	0.2	2		420	728	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24129410	24129410	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	52	335	0	ENST00000263121.7:c.54G>C	p.Gln18His	p.Q18H	ENST00000263121	NM_003073.3	18	caG/caC	1/9	1	2	FACETS	0.996	0.848	1	0.996	0.848	1	CLONAL	1	TRUE	1	0.2	2		335	522	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214894	36214894	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555729827	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	92	730	2	ENST00000222270.7:c.3325del	p.Arg1109GlufsTer73	p.R1109Efs*73	ENST00000222270	NM_014727.1	1107	aCc/ac	8/37	1	2	FACETS	0.871	0.772	0.978	0.871	0.772	0.978	CLONAL	1	TRUE	1	0.2	2		732	1056	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188524	11188524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316157865	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	43	418	0	ENST00000361445.4:c.5897G>A	p.Arg1966Gln	p.R1966Q	ENST00000361445	NM_004958.3	1966	cGg/cAg	42/58	1	2	FACETS	0.626	0.522	0.741	0.626	0.522	0.741	SUBCLONAL	1	TRUE	1	0.2	2		418	687	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023082	27023083	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	20	83	0	ENST00000324856.7:c.192dup	p.Pro65AlafsTer46	p.P65Afs*46	ENST00000324856	NM_006015.4	63	gtg/gtGg	1/20	1	2	FACETS	0.781	0.604	0.983	1	0.921	1	CLONAL	2	TRUE	1	0.2	2		83	128	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094368	27094368	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367844043	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	90	522	0	ENST00000324856.7:c.3076C>T	p.Arg1026Cys	p.R1026C	ENST00000324856	NM_006015.4	1026	Cgt/Tgt	11/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.2	2		522	808	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115279437	115279437	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	52	472	0	ENST00000438362.2:c.580G>T	p.Gly194Trp	p.G194W	ENST00000438362	NM_001242891.1	194	Ggg/Tgg	6/20	1	2	FACETS	0.576	0.489	0.672	0.576	0.489	0.672	SUBCLONAL	1	TRUE	1	0.2	2		472	903	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193110985	193110988	+	frameshift_variant	Frame_Shift_Del	DEL	TGTC	TGTC	-	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	17	168	0	ENST00000367435.3:c.520_523del	p.Ser174LysfsTer27	p.S174Kfs*27	ENST00000367435	NM_024529.4	173	tTGTCt/tt	7/17	1	2	FACETS	0.783	0.586	1	0.783	0.586	1	CLONAL	1	TRUE	1	0.2	2		168	217	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100414	8100414	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	102	888	0	ENST00000346208.3:c.388C>A	p.Leu130Ile	p.L130I	ENST00000346208		130	Ctc/Atc	3/6	1	2	FACETS	0.965	0.861	1	0.965	0.861	1	CLONAL	1	TRUE	1	0.2	2		888	1057	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8105982	8105982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	70	504	0	ENST00000346208.3:c.802G>A	p.Ala268Thr	p.A268T	ENST00000346208		268	Gca/Aca	4/6	1	2	FACETS	0.962	0.838	1	0.962	0.838	1	CLONAL	1	TRUE	1	0.2	2		504	728	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136976	64136976	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	65	564	2	ENST00000334205.4:c.1487G>A	p.Arg496His	p.R496H	ENST00000334205	NM_003942.2	496	cGc/cAc	13/17	1	2	FACETS	0.783	0.678	0.898	0.783	0.678	0.898	SUBCLONAL	1	TRUE	1	0.2	2		566	830	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164132	108164134	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	27	262	0	ENST00000278616.4:c.4708_4710del	p.Val1570del	p.V1570del	ENST00000278616	NM_000051.3	1568	caTGTt/cat	31/63	1	2	FACETS	0.596	0.473	0.737	0.596	0.473	0.737	SUBCLONAL	1	TRUE	1	0.2	2		262	453	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914176	32914176	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	33	409	0	ENST00000380152.3:c.5684A>G	p.Glu1895Gly	p.E1895G	ENST00000380152		1895	gAg/gGg	11/27	1	2	FACETS	0.608	0.494	0.736	0.608	0.494	0.736	SUBCLONAL	1	TRUE	1	0.2	2		409	543	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73350086	73350086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	32	331	0	ENST00000377767.4:c.799G>A	p.Gly267Ser	p.G267S	ENST00000377767	NM_014953.3	267	Ggc/Agc	5/21	1	2	FACETS	0.697	0.565	0.846	0.697	0.565	0.846	SUBCLONAL	1	TRUE	1	0.2	2		331	459	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68934892	68934892	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	42	369	1	ENST00000487270.1:c.961C>A	p.Leu321Ile	p.L321I	ENST00000487270	NM_133509.3	321	Ctt/Att	10/11	1	2	FACETS	0.714	0.595	0.847	0.714	0.595	0.847	SUBCLONAL	1	TRUE	1	0.2	2		370	588	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99491883	99491883	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373732310	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	93	636	0	ENST00000268035.6:c.3668G>A	p.Arg1223His	p.R1223H	ENST00000268035	NM_000875.3	1223	cGc/cAc	20/21	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.2	2		636	913	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823883	3823883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	87	698	1	ENST00000262367.5:c.2332G>A	p.Ala778Thr	p.A778T	ENST00000262367	NM_004380.2	778	Gca/Aca	13/31	1	2	FACETS	0.864	0.763	0.972	0.864	0.763	0.972	CLONAL	1	TRUE	1	0.2	2		699	1007	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50815245	50815245	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	73	552	0	ENST00000398568.2:c.1598T>C	p.Leu533Pro	p.L533P	ENST00000398568	NM_001042412.1	533	cTg/cCg	9/18	1	2	FACETS	0.737	0.642	0.839	0.737	0.642	0.839	SUBCLONAL	1	TRUE	1	0.2	2		552	991	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116197	67116197	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753789494	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	64	478	1	ENST00000412916.2:c.481C>T	p.Arg161Trp	p.R161W	ENST00000412916		161	Cgg/Tgg	5/6	1	2	FACETS	0.799	0.691	0.917	0.799	0.691	0.917	CLONAL	1	TRUE	1	0.2	2		479	801	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81927318	81927318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	106	691	1	ENST00000359376.3:c.991C>T	p.Leu331Phe	p.L331F	ENST00000359376	NM_002661.3	331	Ctt/Ttt	12/33	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.2	2		692	1025	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486095	29486097	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	27	300	0	ENST00000356175.3:c.274_276del	p.Lys92del	p.K92del	ENST00000356175	NM_000267.3	91	gAAAaa/gaa	3/57	1	2	FACETS	0.563	0.447	0.695	0.563	0.447	0.695	SUBCLONAL	1	TRUE	1	0.2	2		300	480	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657619	37657619	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	60	523	0	ENST00000447079.4:c.2536G>T	p.Gly846Ter	p.G846*	ENST00000447079	NM_015083.1	846	Gga/Tga	6/14	1	2	FACETS	0.704	0.605	0.813	0.704	0.605	0.813	SUBCLONAL	1	TRUE	1	0.2	2		523	852	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119060	70119060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	45	487	0	ENST00000245479.2:c.632C>T	p.Ser211Leu	p.S211L	ENST00000245479	NM_000346.3	211	tCg/tTg	2/3	1	2	FACETS	0.841	0.707	0.99	0.841	0.707	0.99	CLONAL	1	TRUE	1	0.2	2		487	535	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223041	5223041	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	77	676	0	ENST00000357368.4:c.2762T>G	p.Leu921Arg	p.L921R	ENST00000357368	NM_002850.3	921	cTg/cGg	18/38	1	2	FACETS	0.921	0.807	1	0.921	0.807	1	CLONAL	1	TRUE	1	0.2	2		676	836	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355152	15355152	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	102	905	1	ENST00000263377.2:c.2471C>T	p.Thr824Ile	p.T824I	ENST00000263377	NM_058243.2	824	aCc/aTc	13/20	1	2	FACETS	0.909	0.811	1	0.909	0.811	1	CLONAL	1	TRUE	1	0.2	2		906	1122	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951053	17951053	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	84	602	0	ENST00000458235.1:c.1240A>C	p.Thr414Pro	p.T414P	ENST00000458235	NM_000215.3	414	Act/Cct	9/24	1	2	FACETS	0.898	0.792	1	0.898	0.792	1	CLONAL	1	TRUE	1	0.2	2		602	935	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753378	42753378	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745501213	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	105	906	0	ENST00000222329.4:c.886G>A	p.Gly296Ser	p.G296S	ENST00000222329	NM_006494.2	296	Ggc/Agc	4/4	1	2	FACETS	0.932	0.833	1	0.932	0.833	1	CLONAL	1	TRUE	1	0.2	2		906	1127	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573120	41573120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1200588584	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	84	877	3	ENST00000263253.7:c.5405C>T	p.Pro1802Leu	p.P1802L	ENST00000263253	NM_001429.3	1802	cCg/cTg	31/31	1	2	FACETS	0.845	0.745	0.953	0.845	0.745	0.953	CLONAL	1	TRUE	1	0.2	2		880	994	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648377	30648377	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	52	391	0	ENST00000295754.5:c.2T>C	p.Met1?	p.M1?	ENST00000295754	NM_003242.5	1	aTg/aCg	1/7	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.2	2		391	486	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71050173	71050173	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	29	347	0	ENST00000318789.4:c.1012A>T	p.Thr338Ser	p.T338S	ENST00000318789	NM_032682.5	338	Aca/Tca	13/21	1	2	FACETS	0.529	0.424	0.65	0.529	0.424	0.65	SUBCLONAL	1	TRUE	1	0.2	2		347	548	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664799	138664799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	51	158	0	ENST00000330315.3:c.766G>A	p.Gly256Arg	p.G256R	ENST00000330315	NM_023067.3	256	Ggg/Agg	1/1	1	2	FACETS	0.754	0.644	0.874	1	0.965	1	SUBCLONAL	2	TRUE	1	0.2	2		158	338	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129992	55129992	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	82	621	0	ENST00000257290.5:c.526C>T	p.Gln176Ter	p.Q176*	ENST00000257290	NM_006206.4	176	Cag/Tag	4/23	1	2	FACETS	0.94	0.828	1	0.94	0.828	1	CLONAL	1	TRUE	1	0.2	2		621	872	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155173	106155173	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	61	371	0	ENST00000380013.4:c.74G>A	p.Cys25Tyr	p.C25Y	ENST00000380013	NM_001127208.2	25	tGc/tAc	3/11	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.2	2		371	534	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156735	106156735	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs746451522	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	42	413	0	ENST00000380013.4:c.1636A>G	p.Lys546Glu	p.K546E	ENST00000380013	NM_001127208.2	546	Aag/Gag	3/11	1	2	FACETS	0.791	0.66	0.937	0.791	0.66	0.937	CLONAL	1	TRUE	1	0.2	2		413	531	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512331	149512331	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1399784936	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	81	552	0	ENST00000261799.4:c.1109G>A	p.Arg370His	p.R370H	ENST00000261799	NM_002609.3	370	cGc/cAc	7/23	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.2	2		552	737	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517585	176517585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1292799769	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	108	896	1	ENST00000292408.4:c.286G>A	p.Ala96Thr	p.A96T	ENST00000292408	NM_213647.1	96	Gct/Act	3/18	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.2	2		897	1073	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323221	31323223	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	73	720	0	ENST00000412585.2:c.766_768del	p.Glu256del	p.E256del	ENST00000412585	NM_005514.6	256	GAG/-	4/8	1	2	FACETS	0.771	0.672	0.878	0.771	0.672	0.878	SUBCLONAL	1	TRUE	1	0.2	2		720	947	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874474	151874474	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	39	375	0	ENST00000262189.6:c.8064del	p.Lys2688AsnfsTer9	p.K2688Nfs*9	ENST00000262189	NM_170606.2	2688	aaA/aa	38/59	1	2	FACETS	0.734	0.608	0.876	0.734	0.608	0.876	SUBCLONAL	1	TRUE	1	0.2	2		375	531	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285555	38285555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	76	589	2	ENST00000425967.3:c.598C>T	p.Pro200Ser	p.P200S	ENST00000425967	NM_001174067.1	200	Ccg/Tcg	6/19	1	2	FACETS	0.886	0.776	1	0.886	0.776	1	CLONAL	1	TRUE	1	0.2	2		591	858	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69039625	69039625	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	39	421	0	ENST00000288368.4:c.3737G>T	p.Arg1246Met	p.R1246M	ENST00000288368	NM_024870.2	1246	aGg/aTg	31/40	1	2	FACETS	0.549	0.453	0.655	0.549	0.453	0.655	SUBCLONAL	1	TRUE	1	0.2	2		421	711	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006081	22006081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202221094	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	149	673	0	ENST00000276925.6:c.322G>A	p.Val108Met	p.V108M	ENST00000276925	NM_004936.3	108	Gtg/Atg	2/2	1	2	FACETS	1	0.954	1	1	0.992	1	CLONAL	2	TRUE	1	0.2	2		673	702	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044874	47044874	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	90	817	0	ENST00000377604.3:c.2203del	p.Glu735ArgfsTer67	p.E735Rfs*67	ENST00000377604	NM_001204468.1	734	Ggg/gg	20/24	1	2	FACETS	0.86	0.761	0.966	0.86	0.761	0.966	CLONAL	1	TRUE	1	0.2	2		817	1047	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430356	47430356	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771396364	NA	P-0054929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	68	816	0	ENST00000377045.4:c.1631G>A	p.Arg544His	p.R544H	ENST00000377045	NM_001654.4	544	cGc/cAc	15/16	1	2	FACETS	0.686	0.595	0.785	0.686	0.595	0.785	SUBCLONAL	1	TRUE	1	0.2	2		816	991	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174817	56174818	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	64	296	0	ENST00000399503.3:c.1977dup	p.Ala660SerfsTer37	p.A660Sfs*37	ENST00000399503	NM_005921.1	659	aga/agAa	11/20	0.526002131977062	1	FACETS	0.915	0.806	1	0.915	0.806	1	CLONAL	1	TRUE	0	0.526002131977062	1		296	196	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554276	29554284	+	inframe_deletion	In_Frame_Del	DEL	GCGCATTGA	GCGCATTGA	-	novel	NA	P-0054972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	42	495	0	ENST00000356175.3:c.2294_2302del	p.Arg765_Glu767del	p.R765_E767del	ENST00000356175	NM_000267.3	764	agGCGCATTGAg/agg	19/57	1	2	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	TRUE	1	0.13	2		495	637	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495701	72495706	+	inframe_deletion	In_Frame_Del	DEL	CTGTTT	CTGTTT	-	novel	NA	P-0054972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	33	374	0	ENST00000477973.2:c.364_369del	p.Arg122_Asn123del	p.R122_N123del	ENST00000477973	NM_012234.5	122	agAAACAGt/agt	1/4	1	2	FACETS	0.973	0.791	1	0.973	0.791	1	CLONAL	1	TRUE	1	0.13	2		374	522	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239893	98239893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	49	472	0	ENST00000331920.6:c.1439C>T	p.Ser480Leu	p.S480L	ENST00000331920	NM_000264.3	480	tCa/tTa	10/24	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.13	2		472	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	148	575	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.946	0.868	1	0.946	0.868	1	CLONAL	1	TRUE	1	0.549069379966353	2		575	570	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	97	325	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.864	0.775	0.957	0.864	0.775	0.957	CLONAL	1	TRUE	1	0.549069379966353	2		326	409	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548886	29548886	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs953440640	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	71	532	0	ENST00000356175.3:c.1660C>T	p.Gln554Ter	p.Q554*	ENST00000356175	NM_000267.3	554	Cag/Tag	15/57	1	2	FACETS	0.593	0.519	0.672	0.593	0.519	0.672	SUBCLONAL	1	TRUE	1	0.549069379966353	2		532	436	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133889	41133889	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	98	340	0	ENST00000379561.5:c.1739C>T	p.Ser580Phe	p.S580F	ENST00000379561	NM_002015.3	580	tCc/tTc	2/3	1	2	FACETS	0.85	0.763	0.941	0.85	0.763	0.941	CLONAL	1	TRUE	1	0.549069379966353	2		340	420	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983275	149983275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	216	507	1	ENST00000253339.5:c.2983C>T	p.Arg995Cys	p.R995C	ENST00000253339		995	Cgc/Tgc	7/7	0.426880709376088	3	FACETS	0.853	0.806	0.899	0.853	0.806	0.899	CLONAL	3	TRUE	0	0.549069379966353	3		508	392	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584486	187584486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1035563944	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	51	354	0	ENST00000441802.2:c.3547C>T	p.Pro1183Ser	p.P1183S	ENST00000441802	NM_005245.3	1183	Cca/Tca	3/27	1	2	FACETS	0.92	0.792	1	0.92	0.792	1	CLONAL	1	TRUE	1	0.549069379966353	2		354	202	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008201	29008201	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	32	317	0	ENST00000282397.4:c.670C>T	p.Arg224Ter	p.R224*	ENST00000282397	NM_002019.4	224	Cga/Tga	5/30	1	2	FACETS	0.563	0.461	0.677	0.563	0.461	0.677	SUBCLONAL	1	TRUE	1	0.549069379966353	2		317	207	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268985	142268985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs911751877	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	72	305	0	ENST00000350721.4:c.2965C>T	p.Arg989Cys	p.R989C	ENST00000350721	NM_001184.3	989	Cgt/Tgt	14/47	1	2	FACETS	0.857	0.756	0.964	0.857	0.756	0.964	CLONAL	1	TRUE	1	0.549069379966353	2		305	306	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459188	120459188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772005110	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	211	537	0	ENST00000256646.2:c.6157C>T	p.Arg2053Cys	p.R2053C	ENST00000256646	NM_024408.3	2053	Cgc/Tgc	34/34	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.549069379966353	2		537	649	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856031	111856031	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	194	483	0	ENST00000341259.2:c.82G>A	p.Glu28Lys	p.E28K	ENST00000341259	NM_005475.2	28	Gag/Aag	2/8	0.14130812851462	4	FACETS	0.789	0.732	0.847	0.789	0.732	0.847	INDETERMINATE	2	TRUE	2	0.549069379966353	4		483	694	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925397	114925397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773530340	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	217	576	1	ENST00000543371.1:c.1475C>T	p.Ser492Leu	p.S492L	ENST00000543371	NM_001198531.1	492	tCg/tTg	14/14	0.48424294432854	0	FACETS	0.741	0.697	0.786			1	SUBCLONAL	1	TRUE	0	0.549069379966353	0		577	481	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518246	8518246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	89	289	0	ENST00000356435.5:c.1145G>A	p.Gly382Glu	p.G382E	ENST00000356435		382	gGa/gAa	10/35	1	2	FACETS	0.937	0.838	1	0.937	0.838	1	CLONAL	1	TRUE	1	0.549069379966353	2		289	346	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845679	68845679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	180	619	0	ENST00000261769.5:c.925C>T	p.Pro309Ser	p.P309S	ENST00000261769	NM_004360.3	309	Cct/Tct	7/16	1	2	FACETS	0.942	0.872	1	0.942	0.872	1	CLONAL	1	TRUE	1	0.549069379966353	2		619	696	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024150	31024150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542568224	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	103	560	1	ENST00000375687.4:c.3635C>T	p.Ser1212Phe	p.S1212F	ENST00000375687	NM_015338.5	1212	tCc/tTc	13/13	1	2	FACETS	0.761	0.684	0.842	0.761	0.684	0.842	SUBCLONAL	1	TRUE	1	0.549069379966353	2		561	493	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665280	176665280	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784107	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	81	326	0	ENST00000439151.2:c.3964C>T	p.Arg1322Ter	p.R1322*	ENST00000439151	NM_022455.4	1322	Cga/Tga	7/23	1	2	FACETS	0.732	0.649	0.821	0.732	0.649	0.821	SUBCLONAL	1	TRUE	1	0.549069379966353	2		326	403	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346963	89346963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768652993	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	123	348	0	ENST00000301030.4:c.5987C>T	p.Pro1996Leu	p.P1996L	ENST00000301030	NM_001256183.1	1996	cCc/cTc	9/13	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.549069379966353	2		348	371	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087515	27087515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866476464	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	315	697	0	ENST00000324856.7:c.2089C>T	p.Pro697Ser	p.P697S	ENST00000324856	NM_006015.4	697	Ccg/Tcg	5/20	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.549069379966353	2		697	941	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755769	39755769	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	153	460	0	ENST00000288319.7:c.996G>A	p.Trp332Ter	p.W332*	ENST00000288319	NM_182918.3	332	tgG/tgA	10/10	0.549069379966353	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.549069379966353	1		460	389	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510817	120510817	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs312262795	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	106	370	0	ENST00000256646.2:c.1147C>T	p.Pro383Ser	p.P383S	ENST00000256646	NM_024408.3	383	Cct/Tct	7/34	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.549069379966353	2		370	353	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420108	49420108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123729	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	181	510	0	ENST00000301067.7:c.15641G>A	p.Arg5214His	p.R5214H	ENST00000301067	NM_003482.3	5214	cGc/cAc	48/54	0.14130812851462	4	FACETS	0.788	0.73	0.848	0.788	0.73	0.848	INDETERMINATE	2	TRUE	2	0.549069379966353	4		510	648	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432459	49432459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	202	692	1	ENST00000301067.7:c.8680C>T	p.Pro2894Ser	p.P2894S	ENST00000301067	NM_003482.3	2894	Ccg/Tcg	34/54	0.14130812851462	4	FACETS	1	0.99	1	0.72	0.668	0.772	INDETERMINATE	1	TRUE	2	0.549069379966353	4		693	792	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230828	66230828	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	60	347	0	ENST00000273854.3:c.2143G>A	p.Glu715Lys	p.E715K	ENST00000273854	NM_004439.5	715	Gaa/Aaa	12/18	1	2	FACETS	0.867	0.755	0.986	0.867	0.755	0.986	CLONAL	1	TRUE	1	0.549069379966353	2		347	252	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828282	72828282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs967750771	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	121	607	0	ENST00000268489.5:c.8299G>A	p.Gly2767Arg	p.G2767R	ENST00000268489	NM_006885.3	2767	Gga/Aga	9/10	1	2	FACETS	0.809	0.734	0.887	0.809	0.734	0.887	CLONAL	1	TRUE	1	0.549069379966353	2		607	545	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340396	8340396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	127	490	0	ENST00000356435.5:c.5200G>A	p.Glu1734Lys	p.E1734K	ENST00000356435		1734	Gaa/Aaa	31/35	1	2	FACETS	0.734	0.667	0.805	0.734	0.667	0.805	SUBCLONAL	1	TRUE	1	0.549069379966353	2		490	630	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082318	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	215	843	1	ENST00000281043.3:c.131_132delinsTT	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCC/cTT	2/3	1	2	FACETS	0.936	0.871	1	0.936	0.871	1	CLONAL	1	TRUE	1	0.549069379966353	2		844	837	SUCCESS
APC	324	MSKCC	GRCh37	5	112174853	112174853	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	38	183	0	ENST00000257430.4:c.3562C>T	p.Pro1188Ser	p.P1188S	ENST00000257430	NM_000038.5	1188	Cct/Tct	16/16	1	2	FACETS	0.975	0.821	1	0.975	0.821	1	CLONAL	1	TRUE	1	0.549069379966353	2		183	142	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162735832	162735832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	92	394	0	ENST00000367921.3:c.1141C>T	p.Pro381Ser	p.P381S	ENST00000367921	NM_006182.2	381	Cct/Tct	10/18	1	2	FACETS	0.755	0.674	0.84	0.755	0.674	0.84	SUBCLONAL	1	TRUE	1	0.549069379966353	2		394	444	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864748	37864748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754295165	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	185	442	0	ENST00000269571.5:c.400C>T	p.Pro134Ser	p.P134S	ENST00000269571		134	Cca/Tca	3/27	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.549069379966353	2		442	583	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248369	212248369	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1325370392	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	60	264	0	ENST00000342788.4:c.3898C>T	p.Pro1300Ser	p.P1300S	ENST00000342788	NM_005235.2	1300	Cct/Tct	28/28	1	2	FACETS	0.871	0.758	0.99	0.871	0.758	0.99	CLONAL	1	TRUE	1	0.549069379966353	2		264	251	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133968	41133968	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767908809	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	151	511	0	ENST00000379561.5:c.1660C>T	p.Arg554Cys	p.R554C	ENST00000379561	NM_002015.3	554	Cgc/Tgc	2/3	1	2	FACETS	0.849	0.778	0.922	0.849	0.778	0.922	CLONAL	1	TRUE	1	0.549069379966353	2		511	648	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526418	31526418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	218	899	1	ENST00000344624.3:c.622C>T	p.Pro208Ser	p.P208S	ENST00000344624		208	Cct/Tct	2/33	1	2	FACETS	0.878	0.818	0.941	0.878	0.818	0.941	CLONAL	1	TRUE	1	0.549069379966353	2		900	904	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932395	36932395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376317083	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	179	658	0	ENST00000361632.4:c.2074C>T	p.Pro692Ser	p.P692S	ENST00000361632		692	Ccc/Tcc	16/16	1	2	FACETS	0.917	0.848	0.988	0.917	0.848	0.988	CLONAL	1	TRUE	1	0.549069379966353	2		658	711	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563270	21563271	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	169	735	2	ENST00000382592.4:c.648_649delinsTT	p.Pro217Ser	p.P217S	ENST00000382592	NM_014572.2	216	ttCCcc/ttTTcc	4/8	1	2	FACETS	0.815	0.751	0.882	0.815	0.751	0.882	CLONAL	1	TRUE	1	0.549069379966353	2		737	755	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783814	50783814	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	91	514	0	ENST00000398568.2:c.205C>T	p.Gln69Ter	p.Q69*	ENST00000398568	NM_001042412.1	69	Cag/Tag	3/18	1	2	FACETS	0.787	0.703	0.876	0.787	0.703	0.876	SUBCLONAL	1	TRUE	1	0.549069379966353	2		514	421	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647482	23647482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1174443228	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	129	523	1	ENST00000261584.4:c.385C>T	p.Pro129Ser	p.P129S	ENST00000261584	NM_024675.3	129	Ccc/Tcc	4/13	1	2	FACETS	0.977	0.891	1	0.977	0.891	1	CLONAL	1	TRUE	1	0.549069379966353	2		524	481	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445878	49445878	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334315280	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	290	919	0	ENST00000301067.7:c.1588C>T	p.Pro530Ser	p.P530S	ENST00000301067	NM_003482.3	530	Cct/Tct	10/54	0.14130812851462	4	FACETS	0.755	0.71	0.8	0.755	0.71	0.8	INDETERMINATE	2	TRUE	2	0.549069379966353	4		919	1084	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576853	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	95	565	0	ENST00000269305.4:c.993_993+1delinsAA		p.X331_splice	ENST00000269305	NM_001126112.2	331		9/11	1	2	FACETS	0.736	0.658	0.818	0.736	0.658	0.818	SUBCLONAL	1	TRUE	1	0.549069379966353	2		565	470	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354155	15354155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1477636105	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	232	611	0	ENST00000263377.2:c.2725C>T	p.Pro909Ser	p.P909S	ENST00000263377	NM_058243.2	909	Ccc/Tcc	14/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.549069379966353	2		611	661	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291365	11291365	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	139	418	0	ENST00000361445.4:c.2641C>G	p.Arg881Gly	p.R881G	ENST00000361445	NM_004958.3	881	Cgc/Ggc	17/58	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.549069379966353	2		418	458	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11308006	11308006	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753248955	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	168	534	0	ENST00000361445.4:c.986C>T	p.Ala329Val	p.A329V	ENST00000361445	NM_004958.3	329	gCc/gTc	7/58	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.549069379966353	2		534	595	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748030	72748030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457410051	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	188	652	0	ENST00000357731.5:c.148G>A	p.Val50Ile	p.V50I	ENST00000357731	NM_173808.2	50	Gtc/Atc	1/7	1	2	FACETS	0.988	0.916	1	0.988	0.916	1	CLONAL	1	TRUE	1	0.549069379966353	2		652	693	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430399	78430399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	101	374	1	ENST00000370768.2:c.769G>A	p.Asp257Asn	p.D257N	ENST00000370768	NM_003902.3	257	Gat/Aat	10/20	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.549069379966353	2		375	367	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733568	85733569	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	95	417	1	ENST00000370580.1:c.443_444delinsAA	p.Arg148Lys	p.R148K	ENST00000370580	NM_003921.4	148	aGG/aAA	3/3	1	2	FACETS	0.92	0.826	1	0.92	0.826	1	CLONAL	1	TRUE	1	0.549069379966353	2		418	376	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981552	201981552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	226	795	0	ENST00000359651.3:c.466C>T	p.Pro156Ser	p.P156S	ENST00000359651		156	Cca/Tca	3/8	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.549069379966353	2		795	814	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623581	43623581	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	95	338	1	ENST00000355710.3:c.3209C>T	p.Pro1070Leu	p.P1070L	ENST00000355710	NM_020975.4	1070	cCt/cTt	20/20	1	2	FACETS	0.948	0.851	1	0.948	0.851	1	CLONAL	1	TRUE	1	0.549069379966353	2		339	365	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406378	70406378	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	175	640	0	ENST00000373644.4:c.3892C>T	p.Pro1298Ser	p.P1298S	ENST00000373644	NM_030625.2	1298	Cct/Tct	4/12	1	2	FACETS	0.935	0.864	1	0.935	0.864	1	CLONAL	1	TRUE	1	0.549069379966353	2		640	682	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104352456	104352456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	177	585	0	ENST00000369902.3:c.572C>T	p.Pro191Leu	p.P191L	ENST00000369902	NM_016169.3	191	cCc/cTc	4/12	1	2	FACETS	0.93	0.86	1	0.93	0.86	1	CLONAL	1	TRUE	1	0.549069379966353	2		585	693	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588117	69588117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763955342	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	138	625	0	ENST00000168712.1:c.581C>T	p.Ser194Leu	p.S194L	ENST00000168712	NM_002007.2	194	tCg/tTg	3/3	1	2	FACETS	0.874	0.799	0.953	0.874	0.799	0.953	CLONAL	1	TRUE	1	0.549069379966353	2		625	575	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090315	77090315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	125	419	1	ENST00000356341.3:c.410C>T	p.Ser137Phe	p.S137F	ENST00000356341	NM_002576.4	137	tCc/tTc	4/15	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.549069379966353	2		420	429	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432332	432332	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	70	336	0	ENST00000399788.2:c.2191G>A	p.Gly731Ser	p.G731S	ENST00000399788	NM_001042603.1	731	Ggt/Agt	16/28	NA	2	FACETS	0.911	0.802	1			1	INDETERMINATE	1	TRUE	NA	0.549069379966353	2		336	280	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022544	12022544	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	207	615	0	ENST00000396373.4:c.650G>A	p.Arg217Lys	p.R217K	ENST00000396373	NM_001987.4	217	aGa/aAa	5/8	0.172855294044687	4	FACETS	1	0.991	1	0.745	0.693	0.798	INDETERMINATE	1	TRUE	2	0.549069379966353	4		615	784	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244214	46244214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	39	352	0	ENST00000334344.6:c.2308C>T	p.Pro770Ser	p.P770S	ENST00000334344	NM_152641.2	770	Cca/Tca	15/21	0.14130812851462	4	FACETS	0.884	0.738	1	0.442	0.369	0.522	INDETERMINATE	1	TRUE	2	0.549069379966353	4		352	249	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967551	26967551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754765308	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	52	356	0	ENST00000381527.3:c.694C>T	p.Pro232Ser	p.P232S	ENST00000381527	NM_001260.1	232	Cca/Tca	7/13	1	2	FACETS	0.779	0.67	0.897	0.779	0.67	0.897	SUBCLONAL	1	TRUE	1	0.549069379966353	2		356	243	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912486	32912486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224588	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	35	379	1	ENST00000380152.3:c.3994C>T	p.His1332Tyr	p.H1332Y	ENST00000380152		1332	Cat/Tat	11/27	1	2	FACETS	0.664	0.55	0.789	0.664	0.55	0.789	SUBCLONAL	1	TRUE	1	0.549069379966353	2		380	192	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066847	30066847	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771765508	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	137	493	0	ENST00000331968.5:c.2284C>T	p.Arg762Cys	p.R762C	ENST00000331968	NM_002742.2	762	Cgc/Tgc	16/18	1	2	FACETS	0.926	0.846	1	0.926	0.846	1	CLONAL	1	TRUE	1	0.549069379966353	2		493	539	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30103659	30103659	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	116	552	0	ENST00000331968.5:c.1279G>A	p.Gly427Arg	p.G427R	ENST00000331968	NM_002742.2	427	Gga/Aga	8/18	1	2	FACETS	0.751	0.679	0.826	0.751	0.679	0.826	SUBCLONAL	1	TRUE	1	0.549069379966353	2		552	563	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961933	41961933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	82	389	0	ENST00000219905.7:c.841G>A	p.Gly281Arg	p.G281R	ENST00000219905	NM_001164273.1	281	Ggg/Agg	2/24	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.549069379966353	2		389	284	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343710	343710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	209	797	0	ENST00000262320.3:c.1964G>A	p.Gly655Glu	p.G655E	ENST00000262320	NM_003502.3	655	gGg/gAg	8/11	1	2	FACETS	0.958	0.891	1	0.958	0.891	1	CLONAL	1	TRUE	1	0.549069379966353	2		797	795	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830931	72830931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763043942	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	121	474	0	ENST00000268489.5:c.5650G>A	p.Glu1884Lys	p.E1884K	ENST00000268489	NM_006885.3	1884	Gaa/Aaa	9/10	1	2	FACETS	0.938	0.853	1	0.938	0.853	1	CLONAL	1	TRUE	1	0.549069379966353	2		474	470	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973572	15973572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	123	384	0	ENST00000268712.3:c.4420G>A	p.Gly1474Arg	p.G1474R	ENST00000268712	NM_006311.3	1474	Ggg/Agg	31/46	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.549069379966353	2		384	434	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663698	29663698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	71	439	2	ENST00000356175.3:c.6130C>T	p.Pro2044Ser	p.P2044S	ENST00000356175	NM_000267.3	2044	Cca/Tca	41/57	1	2	FACETS	0.892	0.786	1	0.892	0.786	1	CLONAL	1	TRUE	1	0.549069379966353	2		441	290	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55704604	55704604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757147876	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	94	630	0	ENST00000284073.2:c.667G>A	p.Val223Met	p.V223M	ENST00000284073	NM_138962.2	223	Gtg/Atg	10/14	1	2	FACETS	0.439	0.39	0.491	0.439	0.39	0.491	SUBCLONAL	1	TRUE	1	0.549069379966353	2		630	780	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734032	58734032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1316246346	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	159	435	0	ENST00000305921.3:c.1090C>T	p.Arg364Ter	p.R364*	ENST00000305921	NM_003620.3	364	Cga/Tga	5/6	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.549069379966353	2		435	497	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796098	78796098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773914053	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	153	418	0	ENST00000306801.3:c.988C>T	p.Arg330Trp	p.R330W	ENST00000306801	NM_020761.2	330	Cgg/Tgg	8/34	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.549069379966353	2		418	517	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11027380	11027380	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	210	801	0	ENST00000327064.4:c.947C>A	p.Pro316Gln	p.P316Q	ENST00000327064	NM_199141.1	316	cCa/cAa	8/16	1	2	FACETS	0.984	0.917	1	0.984	0.917	1	CLONAL	1	TRUE	1	0.549069379966353	2		801	777	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098417	11098417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767826277	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	192	419	2	ENST00000358026.2:c.935C>T	p.Ser312Phe	p.S312F	ENST00000358026	NM_001128849.1	312	tCc/tTc	6/36	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.549069379966353	2		421	582	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271692	15271693	+	missense_variant	Missense_Mutation	DNP	GG	GG	TA	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	236	901	1	ENST00000263388.2:c.6746_6747delinsTA	p.Pro2249Leu	p.P2249L	ENST00000263388	NM_000435.2	2249	cCC/cTA	33/33	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.549069379966353	2		902	804	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302248	15302249	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	190	596	1	ENST00000263388.2:c.1022_1023delinsTT	p.Pro341Leu	p.P341L	ENST00000263388	NM_000435.2	341	cCC/cTT	6/33	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.549069379966353	2		597	687	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384938	17384938	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	230	777	2	ENST00000359435.4:c.488C>T	p.Pro163Leu	p.P163L	ENST00000359435	NM_001033549.1	163	cCc/cTc	5/9	1	2	FACETS	0.991	0.926	1	0.991	0.926	1	CLONAL	1	TRUE	1	0.549069379966353	2		779	845	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216184	36216184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1263085346	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	197	595	0	ENST00000222270.7:c.3592G>A	p.Gly1198Arg	p.G1198R	ENST00000222270	NM_014727.1	1198	Ggg/Agg	11/37	1	2	FACETS	0.993	0.922	1	0.993	0.922	1	CLONAL	1	TRUE	1	0.549069379966353	2		595	723	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278326	39278326	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	75	562	0	ENST00000402219.2:c.823C>T	p.Pro275Ser	p.P275S	ENST00000402219	NM_005633.3	275	Ccc/Tcc	6/23	1	2	FACETS	0.697	0.614	0.785	0.697	0.614	0.785	SUBCLONAL	1	TRUE	1	0.549069379966353	2		562	392	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41542820	41542820	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	159	292	0	ENST00000263253.7:c.2131G>A	p.Gly711Ser	p.G711S	ENST00000263253	NM_001429.3	711	Ggt/Agt	11/31	0.195091551139436	2	FACETS	0.928	0.867	0.989	0.928	0.867	0.989	INDETERMINATE	2	TRUE	0	0.549069379966353	2		292	312	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884830	134884830	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	164	403	0	ENST00000398015.3:c.1606A>G	p.Arg536Gly	p.R536G	ENST00000398015	NM_004441.4	536	Agg/Ggg	8/16	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.549069379966353	2		403	564	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189936	66189936	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	56	244	0	ENST00000273854.3:c.3010G>A	p.Asp1004Asn	p.D1004N	ENST00000273854	NM_004439.5	1004	Gat/Aat	18/18	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.549069379966353	2		244	190	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217148	66217148	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747385140	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	99	469	0	ENST00000273854.3:c.2467C>T	p.Arg823Trp	p.R823W	ENST00000273854	NM_004439.5	823	Cgg/Tgg	14/18	1	2	FACETS	0.855	0.768	0.946	0.855	0.768	0.946	CLONAL	1	TRUE	1	0.549069379966353	2		469	422	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280161	66280161	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	53	205	0	ENST00000273854.3:c.1528G>A	p.Asp510Asn	p.D510N	ENST00000273854	NM_004439.5	510	Gac/Aac	7/18	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.549069379966353	2		205	193	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142949951	142949951	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1310205480	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	84	464	0	ENST00000262992.4:c.2759G>A	p.Gly920Glu	p.G920E	ENST00000262992	NM_001101669.1	920	gGa/gAa	24/24	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.549069379966353	2		464	284	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539990	187539990	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	85	400	0	ENST00000441802.2:c.7750G>T	p.Val2584Phe	p.V2584F	ENST00000441802	NM_005245.3	2584	Gtc/Ttc	10/27	1	2	FACETS	0.844	0.751	0.941	0.844	0.751	0.941	CLONAL	1	TRUE	1	0.549069379966353	2		400	367	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584596	187584596	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	78	425	0	ENST00000441802.2:c.3437C>T	p.Pro1146Leu	p.P1146L	ENST00000441802	NM_005245.3	1146	cCa/cTa	3/27	1	2	FACETS	0.841	0.745	0.942	0.841	0.745	0.942	CLONAL	1	TRUE	1	0.549069379966353	2		425	338	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750809	57750809	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1275409138	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	71	375	0	ENST00000274289.3:c.1795C>T	p.Arg599Trp	p.R599W	ENST00000274289	NM_006622.3	599	Cgg/Tgg	13/14	1	2	FACETS	0.94	0.83	1	0.94	0.83	1	CLONAL	1	TRUE	1	0.549069379966353	2		375	275	SUCCESS
APC	324	MSKCC	GRCh37	5	112174518	112174518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766394131	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	46	288	0	ENST00000257430.4:c.3227C>T	p.Pro1076Leu	p.P1076L	ENST00000257430	NM_000038.5	1076	cCt/cTt	16/16	1	2	FACETS	0.71	0.603	0.825	0.71	0.603	0.825	SUBCLONAL	1	TRUE	1	0.549069379966353	2		288	236	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675371	30675372	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	140	512	1	ENST00000376406.3:c.2984_2985delinsTT	p.Ser995Phe	p.S995F	ENST00000376406	NM_014641.2	995	tCC/tTT	8/15	1	2	FACETS	0.901	0.824	0.981	0.901	0.824	0.981	CLONAL	1	TRUE	1	0.549069379966353	2		513	566	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170144	32170144	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	198	772	0	ENST00000375023.3:c.3464C>T	p.Pro1155Leu	p.P1155L	ENST00000375023	NM_004557.3	1155	cCa/cTa	21/30	1	2	FACETS	0.964	0.896	1	0.964	0.896	1	CLONAL	1	TRUE	1	0.549069379966353	2		772	748	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976681	2976681	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	108	445	0	ENST00000396946.4:c.1331A>G	p.Asn444Ser	p.N444S	ENST00000396946	NM_032415.4	444	aAc/aGc	9/25	1	2	FACETS	0.851	0.769	0.938	0.851	0.769	0.938	CLONAL	1	TRUE	1	0.549069379966353	2		445	462	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14027788	14027788	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	62	238	0	ENST00000405192.2:c.56G>A	p.Gly19Glu	p.G19E	ENST00000405192	NM_001163147.1	19	gGg/gAg	3/12	1	2	FACETS	0.809	0.706	0.92	0.809	0.706	0.92	CLONAL	1	TRUE	1	0.549069379966353	2		238	279	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359039	81359039	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	102	465	0	ENST00000222390.5:c.922G>A	p.Gly308Ser	p.G308S	ENST00000222390	NM_000601.4	308	Ggt/Agt	8/18	1	2	FACETS	0.975	0.88	1	0.975	0.88	1	CLONAL	1	TRUE	1	0.549069379966353	2		465	381	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381504	81381505	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	75	336	0	ENST00000222390.5:c.556_557delinsAA	p.Gly186Lys	p.G186K	ENST00000222390	NM_000601.4	186	GGa/AAa	5/18	1	2	FACETS	0.905	0.8	1	0.905	0.8	1	CLONAL	1	TRUE	1	0.549069379966353	2		336	302	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851576	128851576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	173	611	0	ENST00000249373.3:c.1901C>T	p.Pro634Leu	p.P634L	ENST00000249373	NM_005631.4	634	cCc/cTc	11/12	1	2	FACETS	0.982	0.907	1	0.982	0.907	1	CLONAL	1	TRUE	1	0.549069379966353	2		611	642	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325623	87325623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	57	420	0	ENST00000277120.3:c.500C>T	p.Ser167Phe	p.S167F	ENST00000277120		167	tCc/tTc	6/19	0.549069379966353	1	FACETS	0.78	0.681	0.886	0.78	0.681	0.886	SUBCLONAL	1	TRUE	0	0.549069379966353	1		420	193	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248001	98248002	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	161	419	1	ENST00000331920.6:c.549_550delinsTT	p.Gln184Ter	p.Q184*	ENST00000331920	NM_000264.3	183	ctCCag/ctTTag	3/24	0.549069379966353	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.549069379966353	1		420	401	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293556	137293557	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0054973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	307	904	1	ENST00000481739.1:c.107_108delinsTT	p.Ser36Phe	p.S36F	ENST00000481739	NM_002957.4	36	tCC/tTT	2/10	0.549069379966353	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.549069379966353	1		905	719	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0054974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	167	629	3	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.613268177356084	1	FACETS	0.914	0.852	0.977	0.914	0.852	0.977	CLONAL	1	TRUE	0	0.653887847602505	1		632	376	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	99	421	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.993	0.897	1	0.993	0.897	1	CLONAL	1	TRUE	1	0.653887847602505	2		423	305	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5073770	5073770	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs77375493	NA	P-0054974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	8	362	1	ENST00000381652.3:c.1849G>T	p.Val617Phe	p.V617F	ENST00000381652	NM_004972.3	617	Gtc/Ttc	14/25	0.653887847602505	1	FACETS	0.075	0.048	0.11	0.075	0.048	0.11	SUBCLONAL	1	TRUE	0	0.653887847602505	1		363	220	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581304	48581305	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	134	466	0	ENST00000342988.3:c.609dup	p.Ser204IlefsTer2	p.S204Ifs*2	ENST00000342988	NM_005359.5	203	cca/ccAa	5/12	0.613268177356084	1	FACETS	0.862	0.795	0.93	0.862	0.795	0.93	CLONAL	1	TRUE	0	0.653887847602505	1		466	320	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619805	1619805	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	195	713	0	ENST00000344749.5:c.1141A>G	p.Ser381Gly	p.S381G	ENST00000344749	NM_001136139.2	381	Agc/Ggc	14/19	1	2	FACETS	0.992	0.924	1	0.992	0.924	1	CLONAL	1	TRUE	1	0.653887847602505	2		713	601	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485418	57485418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	97	353	0	ENST00000371085.3:c.1000G>A	p.Val334Met	p.V334M	ENST00000371085	NM_000516.4	334	Gtg/Atg	12/13	0.620046660614827	3	FACETS	0.605	0.54	0.675	0.303	0.27	0.338	SUBCLONAL	1	TRUE	1	0.620046660614827	3		353	677	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	33	421	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.636	0.518	0.77	0.636	0.518	0.77	SUBCLONAL	1	TRUE	1	0.231478662890723	2		423	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0054976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	76	937	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	NA	2	FACETS	1	0.936	1			1	INDETERMINATE	1	TRUE	NA	0.231478662890723	2		937	594	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356152	66356152	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370633345	NA	P-0054976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	55	507	0	ENST00000273854.3:c.1345G>A	p.Asp449Asn	p.D449N	ENST00000273854	NM_004439.5	449	Gac/Aac	5/18	0.231478662890723	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.231478662890723	1		507	370	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260571	10260571	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	26	511	0	ENST00000340748.4:c.2291C>A	p.Ser764Tyr	p.S764Y	ENST00000340748		764	tCt/tAt	24/40	0.231478662890723	1	FACETS	0.412	0.326	0.512	0.412	0.326	0.512	SUBCLONAL	1	TRUE	0	0.231478662890723	1		511	482	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0054977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	116	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.95	1	1	0.99	1	CLONAL	2	FALSE	1	0.215928637755025	2		622	500	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0054978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	90	347	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.40211205455327	2		347	372	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0054978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	156	354	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.781	0.72	0.843	1	0.99	1	SUBCLONAL	2	TRUE	1	0.40211205455327	2		355	497	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0054978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	247	662	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.40211205455327	2		662	928	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0054978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	346	644	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	0.921	0.875	0.968	1	0.996	1	CLONAL	2	TRUE	1	0.40211205455327	2		644	934	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236087	108236087	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	127	476	0	ENST00000278616.4:c.9023G>T	p.Arg3008Leu	p.R3008L	ENST00000278616	NM_000051.3	3008	cGt/cTt	63/63	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.40211205455327	2		476	588	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088726	27088726	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	255	694	0	ENST00000324856.7:c.2335G>T	p.Gly779Ter	p.G779*	ENST00000324856	NM_006015.4	779	Gga/Tga	7/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.40211205455327	2		694	974	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855787	45855787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	219	635	0	ENST00000391945.4:c.2023G>T	p.Gly675Cys	p.G675C	ENST00000391945	NM_000400.3	675	Ggc/Tgc	21/23	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.40211205455327	2		635	821	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024242	31024242	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	140	518	1	ENST00000375687.4:c.3727C>T	p.Gln1243Ter	p.Q1243*	ENST00000375687	NM_015338.5	1243	Cag/Tag	13/13	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.40211205455327	2		519	550	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131212	202131212	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	39	307	0	ENST00000358485.4:c.180G>T	p.Met60Ile	p.M60I	ENST00000358485	NM_001080125.1	60	atG/atT	2/9	1	2	FACETS	0.477	0.395	0.567	0.477	0.395	0.567	SUBCLONAL	1	TRUE	1	0.40211205455327	2		307	407	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494286	2494311	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTGTCTGTGTATTGCAGGTGATGTA	TGTGTCTGTGTATTGCAGGTGATGTA	-	novel	NA	P-0054978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	196	690	0	ENST00000355716.4:c.695-18_702del		p.X232_splice	ENST00000355716	NM_003820.2	232		7/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.40211205455327	2		690	847	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981202	201981202	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	109	812	0	ENST00000359651.3:c.281G>C	p.Arg94Pro	p.R94P	ENST00000359651		94	cGa/cCa	2/8	1	2	FACETS	0.491	0.439	0.545	0.491	0.439	0.545	SUBCLONAL	1	TRUE	1	0.40211205455327	2		812	1105	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720835	89720836	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0054978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	85	333	0	ENST00000371953.3:c.987_988del	p.Asn329LysfsTer13	p.N329Kfs*13	ENST00000371953	NM_000314.4	329	aAT/a	8/9	0.327416397104353	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.40211205455327	1		333	234	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142105	108142105	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730881388	NA	P-0054978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	93	426	0	ENST00000278616.4:c.3049C>T	p.Gln1017Ter	p.Q1017*	ENST00000278616	NM_000051.3	1017	Cag/Tag	20/63	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.40211205455327	2		426	393	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134386	30134386	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	196	615	0	ENST00000263025.4:c.145G>C	p.Gly49Arg	p.G49R	ENST00000263025	NM_002746.2	49	Ggc/Cgc	1/9	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.40211205455327	2		615	792	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957163	81957163	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	162	513	0	ENST00000359376.3:c.2381C>G	p.Ala794Gly	p.A794G	ENST00000359376	NM_002661.3	794	gCc/gGc	22/33	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.40211205455327	2		513	720	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350349	89350349	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	251	717	0	ENST00000301030.4:c.2601C>G	p.Asp867Glu	p.D867E	ENST00000301030	NM_001256183.1	867	gaC/gaG	9/13	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.40211205455327	2		717	1038	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362275	40362275	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	80	487	0	ENST00000293328.3:c.1820T>C	p.Leu607Pro	p.L607P	ENST00000293328	NM_012448.3	607	cTc/cCc	15/19	1	2	FACETS	0.566	0.498	0.639	0.566	0.498	0.639	SUBCLONAL	1	TRUE	1	0.40211205455327	2		487	703	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510335	187510335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	79	272	0	ENST00000441802.2:c.13178C>T	p.Pro4393Leu	p.P4393L	ENST00000441802	NM_005245.3	4393	cCt/cTt	27/27	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.40211205455327	2		272	362	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562655	176562655	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	167	503	0	ENST00000439151.2:c.551T>G	p.Phe184Cys	p.F184C	ENST00000439151	NM_022455.4	184	tTt/tGt	2/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.40211205455327	2		503	700	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162146	38162146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	121	380	0	ENST00000317025.8:c.2570C>T	p.Ser857Phe	p.S857F	ENST00000317025	NM_023034.1	857	tCt/tTt	14/24	0.40211205455327	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.40211205455327	1		380	407	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90971059	90971059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	166	249	0	ENST00000265433.3:c.1018C>T	p.Pro340Ser	p.P340S	ENST00000265433	NM_002485.4	340	Cca/Tca	9/16	0.40211205455327	3	FACETS	0.984	0.911	1	0.984	0.911	1	CLONAL	2	TRUE	1	0.40211205455327	3		249	504	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820602	44820602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	88	216	0	ENST00000377967.4:c.299G>A	p.Gly100Asp	p.G100D	ENST00000377967	NM_021140.2	100	gGt/gAt	3/29	1	1	FACETS	0.888	0.805	0.971	1	0.986	1	CLONAL	2	TRUE	0	0.40211205455327	1		216	197	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433313	49433323	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCAGCTGCT	CTGCAGCTGCT	A	novel	NA	P-0054978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	157	645	0	ENST00000301067.7:c.8124_8134delinsT	p.Ala2709GlufsTer21	p.A2709Efs*21	ENST00000301067	NM_003482.3	2708	gcAGCAGCTGCAGga/gcTga	32/54	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.40211205455327	2		645	684	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0054980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	748	785	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.942448620422653	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.942448620422653	2		785	783	SUCCESS
BLM	641	MSKCC	GRCh37	15	91333901	91333901	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	97	272	0	ENST00000355112.3:c.2846T>C	p.Phe949Ser	p.F949S	ENST00000355112	NM_000057.2	949	tTt/tCt	15/22	0.504990198551273	4	FACETS	0.662	0.591	0.737	0.221	0.197	0.246	INDETERMINATE	1	TRUE	1	0.942448620422653	4		272	604	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293168	212293168	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	120	150	0	ENST00000342788.4:c.2684G>A	p.Arg895Lys	p.R895K	ENST00000342788	NM_005235.2	895	aGg/aAg	22/28	NA	2	FACETS	0.976	0.899	1			1	INDETERMINATE	1	TRUE	NA	0.942448620422653	2		150	261	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117645507	117645507	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs147114498	NA	P-0054980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	352	149	0	ENST00000368508.3:c.5629C>A	p.Pro1877Thr	p.P1877T	ENST00000368508	NM_002944.2	1877	Cca/Aca	34/43	0.514162424018938	6	FACETS	0.992	0.947	1	0.992	0.947	1	INDETERMINATE	3	TRUE	3	0.942448620422653	6		149	724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0054981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	250	890	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.290610068987836	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.290610068987836	2		893	780	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0054981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	115	421	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.290610068987836	3	FACETS	0.857	0.775	0.942	0.857	0.775	0.942	CLONAL	2	TRUE	1	0.290610068987836	3		421	529	SUCCESS
APC	324	MSKCC	GRCh37	5	112173578	112173578	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	95	242	0	ENST00000257430.4:c.2287G>T	p.Glu763Ter	p.E763*	ENST00000257430	NM_000038.5	763	Gaa/Taa	16/16	0.290610068987836	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	0	0.290610068987836	2		242	315	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296181	15296181	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144935367	NA	P-0054981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	57	808	0	ENST00000263388.2:c.2183G>A	p.Arg728His	p.R728H	ENST00000263388	NM_000435.2	728	cGc/cAc	14/33	0.290610068987836	3	FACETS	0.427	0.365	0.496	0.214	0.182	0.248	SUBCLONAL	1	TRUE	1	0.290610068987836	3		808	1051	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981823	201981824	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	130	769	0	ENST00000359651.3:c.535dup	p.Tyr179LeufsTer17	p.Y179Lfs*17	ENST00000359651		178	-/T	4/8	0.290610068987836	3	FACETS	0.921	0.833	1	0.46	0.416	0.507	CLONAL	1	TRUE	1	0.290610068987836	3		769	1113	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201897	67201897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200633410	NA	P-0054981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	214	671	1	ENST00000312629.5:c.1097C>T	p.Thr366Met	p.T366M	ENST00000312629	NM_003952.2	366	aCg/aTg	13/15	0.161383182917948	5	FACETS	1	0.966	1	0.709	0.659	0.761	INDETERMINATE	2	TRUE	2	0.290610068987836	5		672	994	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446368	29446368	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	107	745	0	ENST00000389048.3:c.3199C>A	p.Gln1067Lys	p.Q1067K	ENST00000389048	NM_004304.4	1067	Caa/Aaa	20/29	1	2	FACETS	0.851	0.763	0.945	0.851	0.763	0.945	CLONAL	1	TRUE	1	0.290610068987836	2		745	865	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971054	21971054	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	270	292	0	ENST00000304494.5:c.304G>C	p.Ala102Pro	p.A102P	ENST00000304494	NM_000077.4	102	Gcg/Ccg	2/3	0.931430962723581	2	FACETS	0.988	0.966	1	0.988	0.966	1	CLONAL	2	TRUE	0	0.933050780409534	2		292	293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	470	569	0	ENST00000269305.4:c.542G>C	p.Arg181Pro	p.R181P	ENST00000269305	NM_001126112.2	181	cGc/cCc	5/11	0.918403162981008	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.933050780409534	2		569	487	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179197	123179197	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	218	172	1	ENST00000218089.9:c.646C>T	p.Arg216Ter	p.R216*	ENST00000218089	NM_001042749.1	216	Cga/Tga	8/35	0.8428415868986	2	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.933050780409534	2		173	228	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870260	44870260	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	249	178	0	ENST00000377967.4:c.439C>T	p.Gln147Ter	p.Q147*	ENST00000377967	NM_021140.2	147	Cag/Tag	5/29	0.8428415868986	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.933050780409534	2		178	255	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949069	151949069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776295921	NA	P-0054982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	158	434	0	ENST00000262189.6:c.1576C>T	p.Arg526Cys	p.R526C	ENST00000262189	NM_170606.2	526	Cgt/Tgt	11/59	1	2	FACETS	0.97	0.903	1	0.97	0.903	1	CLONAL	1	TRUE	1	0.933050780409534	2		434	349	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778461	3778461	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	498	795	0	ENST00000262367.5:c.6587A>T	p.Gln2196Leu	p.Q2196L	ENST00000262367	NM_004380.2	2196	cAg/cTg	31/31	0.933050780409534	2	FACETS	0.988	0.973	1	0.988	0.973	1	CLONAL	2	TRUE	0	0.933050780409534	2		795	540	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218482	1218482	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	162	446	0	ENST00000326873.7:c.357C>G	p.Asn119Lys	p.N119K	ENST00000326873	NM_000455.4	119	aaC/aaG	2/10	0.933050780409534	2	FACETS	0.877	0.815	0.94	0.438	0.407	0.47	CLONAL	1	TRUE	0	0.933050780409534	2		446	396	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92300823	92300824	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0054982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	112	318	1	ENST00000265734.4:c.563_564delinsAA	p.Pro188Gln	p.P188Q	ENST00000265734	NM_001259.6	188	cCC/cAA	5/8	0.477554904982172	4	FACETS	1	0.958	1	0.367	0.333	0.404	INDETERMINATE	1	TRUE	1	0.933050780409534	4		319	421	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778441	3778453	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	GCTGCTGCTGCTG	GCTGCTGCTGCTG	CA	novel	NA	P-0054982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	371	772	2	ENST00000262367.5:c.6595_6607delinsTG	p.Gln2199Ter	p.Q2199*	ENST00000262367	NM_004380.2	2199	CAGCAGCAGCAGCaa/TGaa	31/31	0.933050780409534	2	FACETS	0.803	0.778	0.828	0.803	0.778	0.828	CLONAL	2	TRUE	0	0.933050780409534	2		774	495	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	36	314	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.938	0.772	1	0.938	0.772	1	CLONAL	1	TRUE	1	0.19	2		314	404	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602619	10602619	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1239985410	NA	P-0054983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	100	641	0	ENST00000171111.5:c.959G>T	p.Arg320Leu	p.R320L	ENST00000171111	NM_203500.1	320	cGg/cTg	3/6	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.19	2		641	785	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413085	139413085	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1300110216	NA	P-0054983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	75	585	0	ENST00000277541.6:c.1057C>T	p.Arg353Cys	p.R353C	ENST00000277541	NM_017617.3	353	Cgt/Tgt	6/34	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.19	2		585	764	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143257	108143257	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0054983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	23	244	0	ENST00000278616.4:c.3078-2A>T		p.X1026_splice	ENST00000278616	NM_000051.3	1026			1	2	FACETS	0.799	0.624	1	0.799	0.624	1	CLONAL	1	TRUE	1	0.19	2		244	303	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272263	15272263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	73	609	1	ENST00000263388.2:c.6176G>A	p.Gly2059Glu	p.G2059E	ENST00000263388	NM_000435.2	2059	gGg/gAg	33/33	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.19	2		610	673	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375471	15375471	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	102	686	0	ENST00000263377.2:c.956G>T	p.Gly319Val	p.G319V	ENST00000263377	NM_058243.2	319	gGc/gTc	6/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.19	2		686	924	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961375	1961375	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	61	504	1	ENST00000382891.5:c.3163C>T	p.Gln1055Ter	p.Q1055*	ENST00000382891	NM_133335.3	1055	Cag/Tag	17/22	0.143119928357501	3	FACETS	0.929	0.8	1	0.464	0.4	0.535	CLONAL	1	TRUE	1	0.19	3		505	757	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115952	8115953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	114	430	0	ENST00000346208.3:c.1300dup	p.His434ProfsTer73	p.H434Pfs*73	ENST00000346208		433	cac/caCc	6/6	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.466264367540528	2		430	436	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038427	180038427	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	174	730	0	ENST00000261937.6:c.3590G>C	p.Gly1197Ala	p.G1197A	ENST00000261937	NM_182925.4	1197	gGc/gCc	27/30	1	2	FACETS	0.983	0.907	1	0.983	0.907	1	CLONAL	1	TRUE	1	0.466264367540528	2		730	759	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0054985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	205	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.747569656847266	3	FACETS	1	0.973	1	0.544	0.507	0.582	CLONAL	1	TRUE	1	0.777846976885674	3		622	673	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628824	187628824	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	289	600	0	ENST00000441802.2:c.2158C>G	p.Leu720Val	p.L720V	ENST00000441802	NM_005245.3	720	Ctt/Gtt	2/27	1	2	FACETS	0.964	0.911	1	0.964	0.911	1	CLONAL	1	TRUE	1	0.777846976885674	2		600	771	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024332	31024332	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778060	NA	P-0054985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	304	583	0	ENST00000375687.4:c.3817C>T	p.Arg1273Cys	p.R1273C	ENST00000375687	NM_015338.5	1273	Cgt/Tgt	13/13	1	2	FACETS	0.95	0.899	1	0.95	0.899	1	CLONAL	1	TRUE	1	0.777846976885674	2		583	823	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443601	52443601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	311	490	0	ENST00000460680.1:c.91G>A	p.Glu31Lys	p.E31K	ENST00000460680	NM_004656.3	31	Gag/Aag	3/17	0.777846976885674	1	FACETS	0.979	0.938	1	0.979	0.938	1	CLONAL	1	TRUE	0	0.777846976885674	1		490	499	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340429	8340429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	271	447	1	ENST00000356435.5:c.5167G>A	p.Glu1723Lys	p.E1723K	ENST00000356435		1723	Gag/Aag	31/35	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.777846976885674	2		448	649	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244235	153244235	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0054985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	204	373	0	ENST00000281708.4:c.1922C>G	p.Ser641Ter	p.S641*	ENST00000281708	NM_033632.3	641	tCa/tGa	12/12	0.750817101741387	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.777846976885674	1		373	317	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123876	46123876	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	190	270	0	ENST00000334344.6:c.142C>A	p.His48Asn	p.H48N	ENST00000334344	NM_152641.2	48	Cac/Aac	2/21	1	2	FACETS	0.999	0.932	1	0.999	0.932	1	CLONAL	1	TRUE	1	0.777846976885674	2		270	489	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435089	49435089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776944266	NA	P-0054985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	353	622	0	ENST00000301067.7:c.6464C>T	p.Ser2155Leu	p.S2155L	ENST00000301067	NM_003482.3	2155	tCg/tTg	31/54	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.777846976885674	2		622	888	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733044	74733044	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	358	536	0	ENST00000359995.5:c.199G>C	p.Asp67His	p.D67H	ENST00000359995	NM_001195427.1	67	Gac/Cac	1/3	0.777846976885674	1	FACETS	0.973	0.935	1	0.973	0.935	1	CLONAL	1	TRUE	0	0.777846976885674	1		536	578	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106918	11106927	+	frameshift_variant	Frame_Shift_Del	DEL	CATCGACCAG	CATCGACCAG	-	novel	NA	P-0054985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	379	700	1	ENST00000358026.2:c.1623_1632del	p.Ile542ArgfsTer68	p.I542Rfs*68	ENST00000358026	NM_001128849.1	541	ctCATCGACCAG/ct	10/36	1	2	FACETS	0.944	0.899	0.99	0.944	0.899	0.99	CLONAL	1	TRUE	1	0.777846976885674	2		701	1032	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936080	178936080	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	169	470	0	ENST00000263967.3:c.1622C>G	p.Ser541Cys	p.S541C	ENST00000263967	NM_006218.2	541	tCt/tGt	10/21	0.747569656847266	3	FACETS	1	0.967	1	0.54	0.499	0.582	CLONAL	1	TRUE	1	0.777846976885674	3		470	559	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912048	127912048	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	206	369	0	ENST00000373547.4:c.822C>G	p.Phe274Leu	p.F274L	ENST00000373547	NM_002721.4	274	ttC/ttG	7/7	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.777846976885674	2		369	513	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76812927	76812927	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	239	264	0	ENST00000373344.5:c.6694C>A	p.Pro2232Thr	p.P2232T	ENST00000373344	NM_000489.3	2232	Cca/Aca	30/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.777846976885674	1		264	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579366	7579366	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs770776262	NA	P-0054986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	458	564	0	ENST00000269305.4:c.321C>A	p.Tyr107Ter	p.Y107*	ENST00000269305	NM_001126112.2	107	taC/taA	4/11	0.736390947136378	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.736390947136378	1		564	760	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519132	187519132	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	241	301	0	ENST00000441802.2:c.12251G>T	p.Gly4084Val	p.G4084V	ENST00000441802	NM_005245.3	4084	gGt/gTt	23/27	0.736390947136378	1	FACETS	0.987	0.937	1	0.987	0.937	1	CLONAL	1	TRUE	0	0.736390947136378	1		301	419	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685187	89685323	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTCTTGATAGTATTAATGTAATTTCAAATGTTAGCTCATTTTTGTTAATGGTGGCTTTTTGTTTGTTTGTTTTGTTTTAAGGTTTTTGGATTCAAAGCATAAAAACCATTACAAGATATACAATCTGTAAGTATG	TTTTCTTGATAGTATTAATGTAATTTCAAATGTTAGCTCATTTTTGTTAATGGTGGCTTTTTGTTTGTTTGTTTTGTTTTAAGGTTTTTGGATTCAAAGCATAAAAACCATTACAAGATATACAATCTGTAAGTATG	-	novel	NA	P-0054986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	25	44	0	ENST00000371953.3:c.165-76_209+16del		p.X55_splice	ENST00000371953	NM_000314.4	55		3/9	0.736390947136378	1	FACETS	0.703	0.579	0.833	0.703	0.579	0.833	SUBCLONAL	1	TRUE	0	0.736390947136378	1		44	61	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959070	2959070	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	378	498	0	ENST00000396946.4:c.2446T>C	p.Cys816Arg	p.C816R	ENST00000396946	NM_032415.4	816	Tgc/Cgc	18/25	0.736390947136378	3	FACETS	0.967	0.917	1	0.484	0.458	0.51	CLONAL	1	TRUE	1	0.736390947136378	3		498	1452	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869598	117869636	+	inframe_deletion	In_Frame_Del	DEL	GTGCTCTGTTCAGACTCTAATAGGAGGTTAGAAGTAGTA	GTGCTCTGTTCAGACTCTAATAGGAGGTTAGAAGTAGTA	-	novel	NA	P-0054986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	96	267	0	ENST00000297338.2:c.558_596del	p.Thr187_Thr199del	p.T187_T199del	ENST00000297338	NM_006265.2	186	acTACTACTTCTAACCTCCTATTAGAGTCTGAACAGAGCACc/acc	6/14	0.736390947136378	3	FACETS	0.495	0.441	0.552	0.247	0.22	0.276	SUBCLONAL	1	TRUE	1	0.736390947136378	3		267	721	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861553	152861567	+	inframe_deletion	In_Frame_Del	DEL	GGTCATAGGCGTCCA	GGTCATAGGCGTCCA	-	novel	NA	P-0054986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1457	137	530	0	ENST00000406277.2:c.185_199del	p.Leu62_Asp66del	p.L62_D66del	ENST00000406277	NM_152274.4	62	cTGGACGCCTATGACCct/cct	4/7	0.736390947136378		FACETS		0.289	0.351				SUBCLONAL	1	TRUE	NA	0.736390947136378	3		530	1594	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579383	7579383	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	321	640	0	ENST00000269305.4:c.304del	p.Thr102ProfsTer21	p.T102Pfs*21	ENST00000269305	NM_001126112.2	102	Acc/cc	4/11	0.443632113623502	2	FACETS	0.943	0.896	0.991	0.943	0.896	0.991	CLONAL	2	TRUE	0	0.443632113623502	2		640	767	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519380	137519380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1470644923	NA	P-0054987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	119	212	1	ENST00000367739.4:c.1258G>A	p.Glu420Lys	p.E420K	ENST00000367739	NM_000416.2	420	Gaa/Aaa	7/7	0.429520873537192	3	FACETS	0.953	0.87	1	0.953	0.87	1	CLONAL	2	TRUE	1	0.443632113623502	3		213	344	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	42	421	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.257690219941896	3	FACETS	0.783	0.659	0.918	0.783	0.659	0.918	CLONAL	2	FALSE	1	0.257690219941896	3		423	235	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0054989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	148	349	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	0.96	0.894	1	1	0.994	1	CLONAL	4	FALSE	1	0.257690219941896	2		349	299	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0054989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	9	396	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	0.386	0.255	0.552	0.386	0.255	0.552	SUBCLONAL	1	FALSE	1	0.257690219941896	2		396	181	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	133	836	0	ENST00000269305.4:c.398T>A	p.Met133Lys	p.M133K	ENST00000269305	NM_001126112.2	133	aTg/aAg	5/11	0.257690219941896	3	FACETS	0.879	0.805	0.955	1	0.983	1	CLONAL	3	FALSE	1	0.257690219941896	3		836	442	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606030	81606030	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	15	433	0	ENST00000298171.2:c.700T>A	p.Ser234Thr	p.S234T	ENST00000298171	NM_000369.2	234	Tct/Act	9/10	0.14057172556905	4	FACETS	0.823	0.604	1	0.411	0.302	0.542	INDETERMINATE	1	FALSE	2	0.257690219941896	4		433	178	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241677	55241677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504256	NA	P-0054995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	122	655	0	ENST00000275493.2:c.2125G>A	p.Glu709Lys	p.E709K	ENST00000275493	NM_005228.3	709	Gaa/Aaa	18/28	0.149788217903378	3	FACETS	1	0.977	1	0.427	0.385	0.471	CLONAL	1	TRUE	0	0.243726009708698	3		655	877	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0054995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	118	573	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.149788217903378	3	FACETS	1	0.983	1	0.482	0.434	0.531	CLONAL	1	TRUE	0	0.243726009708698	3		573	752	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0054996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	240	890	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.710949094290879	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.710949094290879	1		893	407	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	445	421	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.710949094290879	6	FACETS	0.91	0.88	0.94			1	CLONAL	5	TRUE	NA	0.710949094290879	6		423	666	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027164	49027165	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GACC	novel	NA	P-0054996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	99	390	0	ENST00000267163.4:c.1734_1737dup	p.Glu580ProfsTer6	p.E580Pfs*6	ENST00000267163	NM_000321.2	577	-/GACC	18/27	0.710949094290879	1	FACETS	0.816	0.744	0.888	0.816	0.744	0.888	CLONAL	1	TRUE	0	0.710949094290879	1		390	220	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	70	115	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.317527961299948	2		115	412	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589586	67589591	+	inframe_deletion	In_Frame_Del	DEL	ATGAAT	ATGAAT	-	novel	NA	P-0054997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	19	197	0	ENST00000274335.5:c.1351_1356del	p.Glu451_Tyr452del	p.E451_Y452del	ENST00000274335		450	cATGAATat/cat	10/15	1	2	FACETS	0.942	0.723	1	0.942	0.723	1	CLONAL	1	TRUE	1	0.317527961299948	2		197	127	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0054998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	134	396	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.30314158626641	3	FACETS	0.957	0.874	1	0.957	0.874	1	CLONAL	2	TRUE	1	0.30314158626641	3		396	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579388	7579389	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0054998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	192	802	0	ENST00000269305.4:c.298dup	p.Gln100ProfsTer49	p.Q100Pfs*49	ENST00000269305	NM_001126112.2	100	cag/cCag	4/11	0.23629259475845	2	FACETS	0.775	0.718	0.834	0.775	0.718	0.834	SUBCLONAL	2	TRUE	0	0.30314158626641	2		802	817	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057766	27057766	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	194	706	2	ENST00000324856.7:c.1474C>T	p.Gln492Ter	p.Q492*	ENST00000324856	NM_006015.4	492	Cag/Tag	3/20	0.239906292265993	3	FACETS	0.763	0.706	0.822	0.763	0.706	0.822	SUBCLONAL	2	TRUE	1	0.30314158626641	3		708	966	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950689	38950689	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	103	323	0	ENST00000357387.3:c.3261C>G	p.Phe1087Leu	p.F1087L	ENST00000357387	NM_152756.3	1087	ttC/ttG	31/38	0.30314158626641	4	FACETS	0.809	0.727	0.897	0.809	0.727	0.897	CLONAL	2	TRUE	2	0.30314158626641	4		323	547	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994932	73994932	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs865951188	NA	P-0054998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	14	230	0	ENST00000318443.5:c.416C>T	p.Ala139Val	p.A139V	ENST00000318443	NM_001024736.1	139	gCc/gTc	3/10	0.239906292265993	3	FACETS	0.384	0.277	0.514	0.192	0.138	0.257	SUBCLONAL	1	TRUE	1	0.30314158626641	3		230	277	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829526	72829526	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	146	610	0	ENST00000268489.5:c.7055A>G	p.Tyr2352Cys	p.Y2352C	ENST00000268489	NM_006885.3	2352	tAc/tGc	9/10	0.186368480429119	4	FACETS	1	0.986	1	0.728	0.664	0.795	CLONAL	1	TRUE	2	0.30314158626641	4		610	862	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0054999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	93	380	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	1	2	FACETS	0.777	0.693	0.866	0.777	0.693	0.866	SUBCLONAL	1	TRUE	1	0.473069931004836	2		380	506	SUCCESS
APC	324	MSKCC	GRCh37	5	112175419	112175419	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0054999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	98	307	0	ENST00000257430.4:c.4128T>G	p.Tyr1376Ter	p.Y1376*	ENST00000257430	NM_000038.5	1376	taT/taG	16/16	0.473069931004836	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.473069931004836	1		307	305	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942125	81942125	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	151	584	0	ENST00000359376.3:c.1667del	p.Gly556AlafsTer42	p.G556Afs*42	ENST00000359376	NM_002661.3	554	acG/ac	17/33	0.173123329958793	3	FACETS	0.907	0.83	0.989	0.302	0.276	0.33	INDETERMINATE	1	TRUE	0	0.473069931004836	3		584	870	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242494	55242494	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	90	329	0	ENST00000275493.2:c.2264C>A	p.Ala755Asp	p.A755D	ENST00000275493	NM_005228.3	755	gCc/gAc	19/28	1	2	FACETS	0.875	0.78	0.974	0.875	0.78	0.974	CLONAL	1	TRUE	1	0.473069931004836	2		329	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0055000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	194	613	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.501640122717567	2	FACETS	0.972	0.915	1	0.972	0.915	1	CLONAL	2	TRUE	0	0.539258820301899	2		614	370	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0055000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	54	347	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.378686133506111	3	FACETS	0.782	0.672	0.902	0.391	0.336	0.451	CLONAL	1	TRUE	1	0.539258820301899	3		347	325	SUCCESS
APC	324	MSKCC	GRCh37	5	112164646	112164646	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	53	244	0	ENST00000257430.4:c.1720G>T	p.Glu574Ter	p.E574*	ENST00000257430	NM_000038.5	574	Gaa/Taa	14/16	1	2	FACETS	0.862	0.744	0.989	0.862	0.744	0.989	CLONAL	1	TRUE	1	0.539258820301899	2		244	228	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570070	212570070	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745408040	NA	P-0055000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	189	394	0	ENST00000342788.4:c.1171G>A	p.Val391Ile	p.V391I	ENST00000342788	NM_005235.2	391	Gtc/Atc	10/28	0.539258820301899	2	FACETS	0.874	0.819	0.929	0.874	0.819	0.929	CLONAL	2	TRUE	0	0.539258820301899	2		394	401	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245399	153245399	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	403	495	0	ENST00000281708.4:c.1792A>C	p.Asn598His	p.N598H	ENST00000281708	NM_033632.3	598	Aat/Cat	11/12	0.288104734269723	4	FACETS	0.916	0.883	0.948	1	0.997	1	INDETERMINATE	4	TRUE	2	0.539258820301899	4		495	628	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576096	88576096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371590703	NA	P-0055000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	109	653	0	ENST00000360948.2:c.1577C>T	p.Pro526Leu	p.P526L	ENST00000360948	NM_001012338.2	526	cCg/cTg	13/19	0.137513567400827	3	FACETS	0.896	0.807	0.989	0.299	0.269	0.33	INDETERMINATE	1	TRUE	0	0.539258820301899	3		653	573	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039290	47039290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	127	649	1	ENST00000377604.3:c.913C>T	p.Arg305Cys	p.R305C	ENST00000377604	NM_001204468.1	305	Cgc/Tgc	10/24	1	2	FACETS	0.929	0.846	1	0.929	0.846	1	CLONAL	1	TRUE	1	0.539258820301899	2		650	507	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967216	93967216	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	108	308	0	ENST00000369303.4:c.2136G>T	p.Glu712Asp	p.E712D	ENST00000369303	NM_004440.3	712	gaG/gaT	12/17	0.288104734269723	4	FACETS	0.797	0.721	0.875	0.797	0.721	0.875	INDETERMINATE	2	TRUE	2	0.539258820301899	4		308	387	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628105	90628105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	118	686	0	ENST00000330062.3:c.1214C>T	p.Thr405Met	p.T405M	ENST00000330062	NM_002168.2	405	aCg/aTg	10/11	0.137513567400827	3	FACETS	0.899	0.813	0.989	0.3	0.271	0.33	INDETERMINATE	1	TRUE	0	0.539258820301899	3		686	618	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436383	52436383	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	219	653	0	ENST00000460680.1:c.2111T>C	p.Val704Ala	p.V704A	ENST00000460680	NM_004656.3	704	gTc/gCc	17/17	0.53967541333639	3	FACETS	0.962	0.903	1	0.962	0.903	1	CLONAL	2	TRUE	1	0.539258820301899	3		653	536	SUCCESS
APC	324	MSKCC	GRCh37	5	112162804	112162804	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0055000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	57	319	0	ENST00000257430.4:c.1412del		p.X471_splice	ENST00000257430	NM_000038.5	471			1	2	FACETS	0.923	0.802	1	0.923	0.802	1	CLONAL	1	TRUE	1	0.539258820301899	2		319	229	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	283	115	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.946358010035836	2		115	515	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0055001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	446	472	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	1	2	FACETS	0.975	0.934	1	0.975	0.934	1	CLONAL	1	TRUE	1	0.946358010035836	2		472	967	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164855	36164855	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	524	690	0	ENST00000300305.3:c.1020del	p.Ser341ProfsTer253	p.S341Pfs*253	ENST00000300305		340	ccC/cc	8/8	0.365133877869002	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.946358010035836	0		690	579	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717715	89717716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587782341	NA	P-0055002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	103	437	0	ENST00000371953.3:c.741dup	p.Pro248ThrfsTer5	p.P248Tfs*5	ENST00000371953	NM_000314.4	247	tta/ttAa	7/9	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.354080560878071	2		437	497	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188197	10188197	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0055002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	125	523	0	ENST00000256474.2:c.341-1G>T		p.X114_splice	ENST00000256474	NM_000551.3	114			0.354080560878071	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.354080560878071	1		523	534	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692798	89692798	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	34	337	0	ENST00000371953.3:c.284del	p.Pro95HisfsTer4	p.P95Hfs*4	ENST00000371953	NM_000314.4	94	aaC/aa	5/9	1	2	FACETS	0.797	0.655	0.954	0.797	0.655	0.954	CLONAL	1	TRUE	1	0.354080560878071	2		337	241	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161748	47161748	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	32	356	0	ENST00000409792.3:c.4378T>G	p.Trp1460Gly	p.W1460G	ENST00000409792	NM_014159.6	1460	Tgg/Ggg	3/21	0.354080560878071	1	FACETS	0.454	0.369	0.549	0.454	0.369	0.549	SUBCLONAL	1	TRUE	0	0.354080560878071	1		356	328	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588771	52588772	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0055002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	168	619	0	ENST00000394830.3:c.4256dup	p.Val1420CysfsTer89	p.V1420Cfs*89	ENST00000394830	NM_018313.4	1419	ggt/ggGt	27/30	0.354080560878071	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.354080560878071	1		619	631	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239879	53239890	+	inframe_deletion	In_Frame_Del	DEL	TAACTCCAGTGA	TAACTCCAGTGA	-	novel	NA	P-0055002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	122	321	0	ENST00000375401.3:c.1551_1562del	p.His518_Tyr521del	p.H518_Y521del	ENST00000375401	NM_004187.3	517	gaTCACTGGAGTTAc/gac	11/26	1	1	FACETS	0.909	0.834	0.986	1	0.99	1	CLONAL	2	TRUE	0	0.354080560878071	1		321	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578415	7578415	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	589	749	0	ENST00000269305.4:c.515T>A	p.Val172Asp	p.V172D	ENST00000269305	NM_001126112.2	172	gTt/gAt	5/11	0.810106312307731	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.810106312307731	2		749	705	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0055005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	202	688	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.711612462882332	1	FACETS	0.937	0.883	0.991	0.937	0.883	0.991	CLONAL	1	TRUE	0	0.720113488450959	1		688	383	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390688	118390688	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	111	393	0	ENST00000534358.1:c.11338A>C	p.Met3780Leu	p.M3780L	ENST00000534358	NM_005933.3	3780	Atg/Ctg	33/36	1	2	FACETS	0.738	0.668	0.81	0.738	0.668	0.81	SUBCLONAL	1	TRUE	1	0.720113488450959	2		393	418	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600418	10600418	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	209	691	0	ENST00000171111.5:c.1437C>A	p.Asp479Glu	p.D479E	ENST00000171111	NM_203500.1	479	gaC/gaA	4/6	0.704146906750272	4	FACETS	0.94	0.872	1	0.313	0.29	0.337	CLONAL	1	TRUE	1	0.720113488450959	4		691	1062	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637387	47637387	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147346837	NA	P-0055005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	123	584	0	ENST00000233146.2:c.521G>A	p.Gly174Glu	p.G174E	ENST00000233146	NM_000251.2	174	gGa/gAa	3/16	1	2	FACETS	0.536	0.486	0.589	0.536	0.486	0.589	SUBCLONAL	1	TRUE	1	0.720113488450959	2		584	637	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450264	50450312	+	frameshift_variant	Frame_Shift_Del	DEL	TGCGGGGCCTCATTCACCCAGAAGGGCAACCTGCTCCGGCACATCAAGC	TGCGGGGCCTCATTCACCCAGAAGGGCAACCTGCTCCGGCACATCAAGC	-	novel	NA	P-0055005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	123	544	0	ENST00000331340.3:c.451_499del	p.Gly151IlefsTer26	p.G151Ifs*26	ENST00000331340	NM_006060.4	150	TGCGGGGCCTCATTCACCCAGAAGGGCAACCTGCTCCGGCACATCAAGCtg/tg	5/8	1	2	FACETS	0.841	0.768	0.918	0.841	0.768	0.918	CLONAL	1	TRUE	1	0.720113488450959	2		544	406	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247055	53247055	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	191	590	0	ENST00000375401.3:c.445A>C	p.Ile149Leu	p.I149L	ENST00000375401	NM_004187.3	149	Att/Ctt	4/26	NA	2	FACETS	0.902	0.839	0.967			1	INDETERMINATE	1	TRUE	NA	0.720113488450959	2		590	588	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073640	8073640	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	80	335	0	ENST00000377482.5:c.1019C>A	p.Ser340Tyr	p.S340Y	ENST00000377482	NM_018948.3	340	tCt/tAt	4/4	0.338106839448819	4	FACETS	0.989	0.871	1			1	CLONAL	1	TRUE	NA	0.339928259427729	4		335	638	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440049	49440049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	41	613	0	ENST00000301067.7:c.4577G>A	p.Cys1526Tyr	p.C1526Y	ENST00000301067	NM_003482.3	1526	tGt/tAt	16/54	1	2	FACETS	0.322	0.268	0.384	0.322	0.268	0.384	SUBCLONAL	1	TRUE	1	0.339928259427729	2		613	748	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216556	7216878	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTAGCATGTTCCATCTGCTTTTGCAAGGACAGGGCACCACCAGGCTGGAGGAAACCTAGGTGGGGAAGAGGGGCATGTGAGATGAGAATGAAACAGGGAGGGGAGGACCTGAGAGCTAGAGCTCCTGCATGGGATGTTATCACCTGTCTGAGTGGGCTGAAAGTGGCCATGCACAGCATAGGGCTGTGGCTGTGGCTGAGATAGGTACTGCACTGCAGGGAATGCCGAAGGAGCTGAGAAAGGAAAAGACAGAGCCATTAAAATCTTTTACTGAATGGCATTCCTCCTTTGACCTTGAGGAAGGCCAAGCCCCATCCCTCCTA	TTAGCATGTTCCATCTGCTTTTGCAAGGACAGGGCACCACCAGGCTGGAGGAAACCTAGGTGGGGAAGAGGGGCATGTGAGATGAGAATGAAACAGGGAGGGGAGGACCTGAGAGCTAGAGCTCCTGCATGGGATGTTATCACCTGTCTGAGTGGGCTGAAAGTGGCCATGCACAGCATAGGGCTGTGGCTGTGGCTGAGATAGGTACTGCACTGCAGGGAATGCCGAAGGAGCTGAGAAAGGAAAAGACAGAGCCATTAAAATCTTTTACTGAATGGCATTCCTCCTTTGACCTTGAGGAAGGCCAAGCCCCATCCCTCCTA	-	novel	NA	P-0055009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	114	460	0	ENST00000380728.2:c.634+9_779del		p.X212_splice	ENST00000380728		212		8-9/11	0.339928259427729	1	FACETS	0.98	0.885	1	0.98	0.885	1	CLONAL	1	TRUE	0	0.339928259427729	1		460	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576871	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CCTGAAGGGTGAAATATTCT	CCTGAAGGGTGAAATATTCT	-	novel	NA	P-0055009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	102	463	0	ENST00000269305.4:c.975_993+1del		p.X325_splice	ENST00000269305	NM_001126112.2	325		9/11	0.339928259427729	1	FACETS	0.894	0.802	0.992	0.894	0.802	0.992	CLONAL	1	TRUE	0	0.339928259427729	1		463	557	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650918	37650937	+	frameshift_variant	Frame_Shift_Del	DEL	AAGATGCACTGGATTTCAAG	AAGATGCACTGGATTTCAAG	-	novel	NA	P-0055009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	59	403	0	ENST00000447079.4:c.2393_2412del	p.Asp798GlyfsTer10	p.D798Gfs*10	ENST00000447079	NM_015083.1	797	cAAGATGCACTGGATTTCAAG/c	5/14	1	2	FACETS	0.592	0.509	0.683	0.592	0.509	0.683	SUBCLONAL	1	TRUE	1	0.339928259427729	2		403	586	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729943	39729943	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs770954982	NA	P-0055009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	42	477	0	ENST00000361337.2:c.1258A>G	p.Ile420Val	p.I420V	ENST00000361337	NM_003286.2	420	Atc/Gtc	13/21	1	2	FACETS	0.35	0.291	0.415	0.35	0.291	0.415	SUBCLONAL	1	TRUE	1	0.339928259427729	2		477	707	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0055010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	130	282	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	0.588160440242708	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.604821907182646	1		282	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0055010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	161	713	1	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.604821907182646	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.604821907182646	1		714	337	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934525	9934525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	118	370	0	ENST00000330684.3:c.1630G>A	p.Val544Ile	p.V544I	ENST00000330684	NM_001134407.1	544	Gtc/Atc	7/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.604821907182646	2		370	348	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027229	48027229	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs751867550	NA	P-0055010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	92	357	0	ENST00000234420.5:c.2107A>G	p.Met703Val	p.M703V	ENST00000234420	NM_000179.2	703	Atg/Gtg	4/10	0.604821907182646	3	FACETS	0.913	0.816	1	0.456	0.408	0.508	CLONAL	1	TRUE	1	0.604821907182646	3		357	434	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247289	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0055010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	103	338	0	ENST00000281708.4:c.1513dup	p.Arg505ProfsTer6	p.R505Pfs*6	ENST00000281708	NM_033632.3	505	cgc/cCgc	10/12	1	2	FACETS	0.856	0.772	0.944	0.856	0.772	0.944	CLONAL	1	TRUE	1	0.604821907182646	2		338	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	136	890	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.217617554130765	2		893	1106	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	15	421	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.992	0.731	1	0.992	0.731	1	CLONAL	1	FALSE	1	0.217617554130765	2		423	139	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	52	658	1	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.528	0.448	0.616	0.528	0.448	0.616	SUBCLONAL	1	FALSE	1	0.217617554130765	2		659	905	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	206	811	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.89	0.825	0.957	1	0.993	1	CLONAL	2	FALSE	1	0.217617554130765	2		815	1064	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514495	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	127	669	0	ENST00000269305.4:c.542G>A	p.Arg181His	p.R181H	ENST00000269305	NM_001126112.2	181	cGc/cAc	5/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.217617554130765	2		669	1020	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099312	157099312	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	80	361	0	ENST00000346085.5:c.249G>C	p.Gln83His	p.Q83H	ENST00000346085	NM_020732.3	83	caG/caC	1/20	0.192201632637365	3	FACETS	0.985	0.865	1	0.492	0.432	0.557	CLONAL	1	FALSE	1	0.217617554130765	3		361	828	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298764	15298764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	83	753	2	ENST00000263388.2:c.1534G>A	p.Ala512Thr	p.A512T	ENST00000263388	NM_000435.2	512	Gcc/Acc	10/33	1	2	FACETS	0.642	0.565	0.726	0.642	0.565	0.726	SUBCLONAL	1	FALSE	1	0.217617554130765	2		755	1188	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	83	462	2	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.217617554130765	2		464	600	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061334	38061334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	113	707	0	ENST00000250448.2:c.655C>T	p.Arg219Cys	p.R219C	ENST00000250448	NM_004496.3	219	Cgc/Tgc	2/2	1	2	FACETS	0.955	0.858	1	0.955	0.858	1	CLONAL	1	FALSE	1	0.217617554130765	2		707	1087	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909698	50909698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	148	812	3	ENST00000440232.2:c.1418C>T	p.Thr473Met	p.T473M	ENST00000440232	NM_002691.3	473	aCg/aTg	12/27	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.217617554130765	2		815	1212	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430202	181430202	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	69	366	0	ENST00000325404.1:c.59del	p.Gly20AlafsTer26	p.G20Afs*26	ENST00000325404	NM_003106.3	18	tcG/tc	1/1	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.217617554130765	2		366	552	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139794896	139794896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	182	542	0	ENST00000247668.2:c.290G>A	p.Arg97His	p.R97H	ENST00000247668	NM_021138.3	97	cGc/cAc	4/11	0.179204748801523	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	FALSE	0	0.217617554130765	2		542	822	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274610	198274610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139577219	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	70	616	1	ENST00000335508.6:c.788C>T	p.Ala263Val	p.A263V	ENST00000335508	NM_012433.2	263	gCg/gTg	7/25	1	2	FACETS	0.653	0.568	0.746	0.653	0.568	0.746	SUBCLONAL	1	FALSE	1	0.217617554130765	2		617	985	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857196	9857196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs74935155	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	55	536	1	ENST00000330684.3:c.4205G>A	p.Arg1402Gln	p.R1402Q	ENST00000330684	NM_001134407.1	1402	cGg/cAg	13/13	1	2	FACETS	0.658	0.562	0.764	0.658	0.562	0.764	SUBCLONAL	1	FALSE	1	0.217617554130765	2		537	768	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435342	110435342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	75	553	0	ENST00000375856.3:c.3059G>A	p.Arg1020His	p.R1020H	ENST00000375856	NM_003749.2	1020	cGt/cAt	1/2	0.217617554130765	1	FACETS	0.711	0.622	0.807	0.711	0.622	0.807	SUBCLONAL	1	FALSE	0	0.217617554130765	1		553	864	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138400852	138400852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1455285725	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	15	503	0	ENST00000289153.2:c.2461C>T	p.Arg821Cys	p.R821C	ENST00000289153	NM_006219.2	821	Cgc/Tgc	17/22	1	2	FACETS	0.792	0.582	1	0.792	0.582	1	CLONAL	1	FALSE	1	0.217617554130765	2		503	174	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	rs267608078	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	29	485	0	ENST00000234420.5:c.3260_3261dup	p.Phe1088ProfsTer3	p.F1088Pfs*3	ENST00000234420	NM_000179.2	1085	acc/aCCcc	5/10	0.217617554130765	1	FACETS	0.468	0.375	0.575	0.468	0.375	0.575	SUBCLONAL	1	FALSE	0	0.217617554130765	1		485	507	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944983	31944983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1175067252	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	89	688	1	ENST00000340398.3:c.118C>T	p.Arg40Cys	p.R40C	ENST00000340398	NM_001013699.2	40	Cgc/Tgc	1/1	1	2	FACETS	0.701	0.619	0.789	0.701	0.619	0.789	SUBCLONAL	1	FALSE	1	0.217617554130765	2		689	1167	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256492	16256492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343994383	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	70	599	0	ENST00000375759.3:c.3757G>A	p.Glu1253Lys	p.E1253K	ENST00000375759	NM_015001.2	1253	Gaa/Aaa	11/15	1	2	FACETS	0.809	0.704	0.923	0.809	0.704	0.923	CLONAL	1	FALSE	1	0.217617554130765	2		599	795	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859914	151859914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs546643392	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	25	441	0	ENST00000262189.6:c.10748C>T	p.Pro3583Leu	p.P3583L	ENST00000262189	NM_170606.2	3583	cCg/cTg	43/59	1	2	FACETS	0.601	0.474	0.749	0.601	0.474	0.749	SUBCLONAL	1	FALSE	1	0.217617554130765	2		441	382	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220326	5220326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1034131598	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	73	631	0	ENST00000357368.4:c.3494G>A	p.Arg1165His	p.R1165H	ENST00000357368	NM_002850.3	1165	cGt/cAt	21/38	1	2	FACETS	0.759	0.662	0.864	0.759	0.662	0.864	SUBCLONAL	1	FALSE	1	0.217617554130765	2		631	884	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864492	56864492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771130377	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	64	631	0	ENST00000308159.5:c.980G>A	p.Arg327His	p.R327H	ENST00000308159	NM_014669.4	327	cGc/cAc	10/22	1	2	FACETS	0.795	0.687	0.912	0.795	0.687	0.912	CLONAL	1	FALSE	1	0.217617554130765	2		631	740	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970950	21970951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs749588877	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	124	769	1	ENST00000304494.5:c.407dup	p.Thr137HisfsTer5	p.T137Hfs*5	ENST00000304494	NM_000077.4	136	ggc/ggGc	2/3	0.179204748801523	2	FACETS	1	0.955	1	0.549	0.496	0.606	CLONAL	1	FALSE	0	0.217617554130765	2		770	1037	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524749	187524749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372461501	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	126	744	1	ENST00000441802.2:c.10931C>T	p.Ala3644Val	p.A3644V	ENST00000441802	NM_005245.3	3644	gCg/gTg	19/27	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.217617554130765	2		745	971	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31483681	31483681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	19	342	0	ENST00000344624.3:c.2051G>A	p.Arg684His	p.R684H	ENST00000344624		684	cGt/cAt	13/33	1	2	FACETS	1	0.783	1	1	0.783	1	CLONAL	1	FALSE	1	0.217617554130765	2		342	170	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442757	187442757	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	51	537	0	ENST00000232014.4:c.1949G>A	p.Arg650Gln	p.R650Q	ENST00000232014	NM_001130845.1	650	cGa/cAa	9/10	1	2	FACETS	0.611	0.518	0.714	0.611	0.518	0.714	SUBCLONAL	1	FALSE	1	0.217617554130765	2		537	767	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637034	176637034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137993153	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	42	664	0	ENST00000439151.2:c.1634C>T	p.Thr545Met	p.T545M	ENST00000439151	NM_022455.4	545	aCg/aTg	5/23	1	2	FACETS	0.772	0.644	0.914	0.772	0.644	0.914	CLONAL	1	FALSE	1	0.217617554130765	2		664	500	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226568871	226568871	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	64	603	1	ENST00000366794.5:c.1198A>G	p.Lys400Glu	p.K400E	ENST00000366794	NM_001618.3	400	Aag/Gag	9/23	1	2	FACETS	0.786	0.68	0.902	0.786	0.68	0.902	CLONAL	1	FALSE	1	0.217617554130765	2		604	748	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974763	21974764	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCCGC	novel	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	37	285	0	ENST00000304494.5:c.58_63dup	p.Ala20_Ala21dup	p.A20_A21dup	ENST00000304494	NM_000077.4	20	-/GCGGCC	1/3	0.179204748801523	2	FACETS	0.7	0.576	0.838	0.35	0.288	0.419	SUBCLONAL	1	FALSE	0	0.217617554130765	2		285	486	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145692	11145692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1228120902	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	61	784	2	ENST00000358026.2:c.4054G>A	p.Ala1352Thr	p.A1352T	ENST00000358026	NM_001128849.1	1352	Gcg/Acg	29/36	1	2	FACETS	0.558	0.48	0.644	0.558	0.48	0.644	SUBCLONAL	1	FALSE	1	0.217617554130765	2		786	1005	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087389	27087389	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	66	638	1	ENST00000324856.7:c.1963G>T	p.Gly655Ter	p.G655*	ENST00000324856	NM_006015.4	655	Gga/Tga	5/20	1	2	FACETS	0.789	0.684	0.903	0.789	0.684	0.903	CLONAL	1	FALSE	1	0.217617554130765	2		639	769	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291033	11291033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200143518	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	68	556	0	ENST00000361445.4:c.2728C>T	p.Arg910Trp	p.R910W	ENST00000361445	NM_004958.3	910	Cgg/Tgg	18/58	1	2	FACETS	0.983	0.855	1	0.983	0.855	1	CLONAL	1	FALSE	1	0.217617554130765	2		556	636	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023324	27023324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	90	246	1	ENST00000324856.7:c.430C>T	p.Pro144Ser	p.P144S	ENST00000324856	NM_006015.4	144	Ccg/Tcg	1/20	1	2	FACETS	0.763	0.679	0.853	1	0.98	1	SUBCLONAL	2	FALSE	1	0.217617554130765	2		247	542	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46736402	46736402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1411049111	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	71	550	0	ENST00000371975.4:c.1114G>A	p.Ala372Thr	p.A372T	ENST00000371975	NM_003579.3	372	Gca/Aca	10/18	1	2	FACETS	0.919	0.802	1	0.919	0.802	1	CLONAL	1	FALSE	1	0.217617554130765	2		550	710	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571856	64571856	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1221	151	830	0	ENST00000312049.6:c.1783C>T	p.Pro595Ser	p.P595S	ENST00000312049	NM_130799.2	595	Cct/Tct	10/10	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	FALSE	1	0.217617554130765	2		830	1372	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436980	110436980	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	36	171	0	ENST00000375856.3:c.1421A>G	p.His474Arg	p.H474R	ENST00000375856	NM_003749.2	474	cAc/cGc	1/2	0.217617554130765	1	FACETS	0.806	0.663	0.964	0.806	0.663	0.964	CLONAL	1	FALSE	0	0.217617554130765	1		171	366	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483976	88483976	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	68	485	0	ENST00000360948.2:c.1594C>T	p.His532Tyr	p.H532Y	ENST00000360948	NM_001012338.2	532	Cac/Tac	14/19	1	2	FACETS	0.938	0.816	1	0.938	0.816	1	CLONAL	1	FALSE	1	0.217617554130765	2		485	666	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120483	2120483	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs775195398	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	89	735	0	ENST00000219476.3:c.1743C>A	p.Ser581Arg	p.S581R	ENST00000219476	NM_000548.3	581	agC/agA	17/42	1	2	FACETS	0.807	0.714	0.908	0.807	0.714	0.908	CLONAL	1	FALSE	1	0.217617554130765	2		735	1013	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23640991	23640991	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	38	571	0	ENST00000261584.4:c.2484C>A	p.Cys828Ter	p.C828*	ENST00000261584	NM_024675.3	828	tgC/tgA	5/13	1	2	FACETS	0.674	0.557	0.806	0.674	0.557	0.806	SUBCLONAL	1	FALSE	1	0.217617554130765	2		571	518	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774077	56774077	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587780255	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	34	473	0	ENST00000337432.4:c.428A>G	p.Gln143Arg	p.Q143R	ENST00000337432	NM_058216.2	143	cAg/cGg	3/9	1	2	FACETS	0.927	0.759	1	0.927	0.759	1	CLONAL	1	FALSE	1	0.217617554130765	2		473	337	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231447	5231447	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	87	746	0	ENST00000357368.4:c.2029A>G	p.Thr677Ala	p.T677A	ENST00000357368	NM_002850.3	677	Acc/Gcc	14/38	1	2	FACETS	0.708	0.625	0.798	0.708	0.625	0.798	SUBCLONAL	1	FALSE	1	0.217617554130765	2		746	1129	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797129	42797129	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	133	809	0	ENST00000575354.2:c.3491T>C	p.Leu1164Ser	p.L1164S	ENST00000575354	NM_015125.3	1164	tTa/tCa	15/20	1	2	FACETS	0.941	0.852	1	0.941	0.852	1	CLONAL	1	FALSE	1	0.217617554130765	2		809	1299	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326512	62326512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749331637	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	126	871	2	ENST00000360203.5:c.3437C>T	p.Pro1146Leu	p.P1146L	ENST00000360203	NM_001283009.1	1146	cCg/cTg	33/35	1	2	FACETS	0.986	0.891	1	0.986	0.891	1	CLONAL	1	FALSE	1	0.217617554130765	2		873	1174	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191521	10191521	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	198	530	0	ENST00000256474.2:c.514C>G	p.Pro172Ala	p.P172A	ENST00000256474	NM_000551.3	172	Cct/Gct	3/3	1	2	FACETS	1	0.985	1	1	0.994	1	CLONAL	2	FALSE	1	0.217617554130765	2		530	738	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413015	49413015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	67	568	0	ENST00000418115.1:c.8C>T	p.Ala3Val	p.A3V	ENST00000418115	NM_001664.2	3	gCc/gTc	2/5	1	2	FACETS	0.936	0.813	1	0.936	0.813	1	CLONAL	1	FALSE	1	0.217617554130765	2		568	658	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040032	180040032	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	118	855	2	ENST00000261937.6:c.3410C>T	p.Pro1137Leu	p.P1137L	ENST00000261937	NM_182925.4	1137	cCg/cTg	25/30	1	2	FACETS	0.981	0.883	1	0.981	0.883	1	CLONAL	1	FALSE	1	0.217617554130765	2		857	1105	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946396	2946396	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1197	121	902	0	ENST00000396946.4:c.3341C>T	p.Pro1114Leu	p.P1114L	ENST00000396946	NM_032415.4	1114	cCg/cTg	25/25	1	2	FACETS	0.844	0.76	0.933	0.844	0.76	0.933	CLONAL	1	FALSE	1	0.217617554130765	2		902	1318	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759481	133759481	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755568851	NA	P-0055011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	158	685	1	ENST00000318560.5:c.1804G>A	p.Ala602Thr	p.A602T	ENST00000318560	NM_005157.4	602	Gcc/Acc	11/11	0.179204748801523	2	FACETS	0.885	0.812	0.962	0.885	0.812	0.962	CLONAL	2	FALSE	0	0.217617554130765	2		686	820	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22007916	22008835	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCTATACTATTAACAAGATCCCTTAATATTAGCTTAGTTTTAGAGGGTGATAGTGAGGTGAGTACTGAATATGACCACTAGCCAACGGTAAAGTACAAAAGAGTTGTCCGAGATTGTAAAAGAAATAAAAAATATCAGTACTAATTAAAGCAGGATTCGTACTTAAACATTGAATAAGTGTATTTTAACAATGAAGATAAAGATGCATTATTTATGAAGATCCTTTGCCATTCAAAAAGGACCTAACAGTTGCTGCAGGAATATTTTTGTAATCTGGGCACTGAGTATGATAATTAAAGAATGAGAAACCTATAGAACTATATATTTTTTCTCTTATGCATCACTCATAAGACACTGCTAACATAAAAGGAACTAAGTACTGTGGTTGAGGAATCCCGTCTCATTCTCAATTAACCTCTATGAGAAAACAATACAACAGATTTCATATAGTAGCTTAGAAGTTTACATTGATTTTTTCCATGTACTATGATTTTGTAGAATTCCTTAAATCCAATCTAGAATGCGTAACTTATACTTTACTTATCTTTATCGTTGAAAGCAGACAGACAAGATAATCTTCTTCCCTAAATAAGCTTTCCTTTTCTCCTTTTCTCCCCAATTCAGTCTATTCCTTGCATCTCTGATCATGAGATGGCAGAACAAAAACCACTAAAAAAAGCTTAAACAGTGGGTTTTTCAATGTCTCTCTTTAGGATTTTTGCTGGGTAAAAGCCTGTTTTACGCGTGGAATGCACACCTCCGGCCAACGGAGACTCCTGTACAAATCTACATCGGCGATCTAGGTTCCAGCCCCGATCCGCCGAGGCCGCGCCCCGCGTTCGCGCGCCCCCTGCCGGCGAGGCCCTGGGGCCCCAGCTACCTGGATCGCGCGCCTCCCGAAACGGTTGACTCCGTTGGG	ATCTATACTATTAACAAGATCCCTTAATATTAGCTTAGTTTTAGAGGGTGATAGTGAGGTGAGTACTGAATATGACCACTAGCCAACGGTAAAGTACAAAAGAGTTGTCCGAGATTGTAAAAGAAATAAAAAATATCAGTACTAATTAAAGCAGGATTCGTACTTAAACATTGAATAAGTGTATTTTAACAATGAAGATAAAGATGCATTATTTATGAAGATCCTTTGCCATTCAAAAAGGACCTAACAGTTGCTGCAGGAATATTTTTGTAATCTGGGCACTGAGTATGATAATTAAAGAATGAGAAACCTATAGAACTATATATTTTTTCTCTTATGCATCACTCATAAGACACTGCTAACATAAAAGGAACTAAGTACTGTGGTTGAGGAATCCCGTCTCATTCTCAATTAACCTCTATGAGAAAACAATACAACAGATTTCATATAGTAGCTTAGAAGTTTACATTGATTTTTTCCATGTACTATGATTTTGTAGAATTCCTTAAATCCAATCTAGAATGCGTAACTTATACTTTACTTATCTTTATCGTTGAAAGCAGACAGACAAGATAATCTTCTTCCCTAAATAAGCTTTCCTTTTCTCCTTTTCTCCCCAATTCAGTCTATTCCTTGCATCTCTGATCATGAGATGGCAGAACAAAAACCACTAAAAAAAGCTTAAACAGTGGGTTTTTCAATGTCTCTCTTTAGGATTTTTGCTGGGTAAAAGCCTGTTTTACGCGTGGAATGCACACCTCCGGCCAACGGAGACTCCTGTACAAATCTACATCGGCGATCTAGGTTCCAGCCCCGATCCGCCGAGGCCGCGCCCCGCGTTCGCGCGCCCCCTGCCGGCGAGGCCCTGGGGCCCCAGCTACCTGGATCGCGCGCCTCCCGAAACGGTTGACTCCGTTGGG	-	novel	NA	P-0055012-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	108	10	0	ENST00000276925.6:c.118_156+881del		p.X40_splice	ENST00000276925	NM_004936.3	40		1/2	0.324564023035871	1	FACETS	0.978	0.948	1	1	0.993	1	CLONAL	5	TRUE	0	0.324564023035871	1		10	114	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22008888	22008890	+	inframe_deletion	In_Frame_Del	DEL	GCG	GCG	-	novel	NA	P-0055012-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	128	794	0	ENST00000276925.6:c.63_65del	p.Ala23del	p.A23del	ENST00000276925	NM_004936.3	21	gcCGCg/gcg	1/2	0.324564023035871	1	FACETS	0.781	0.714	0.85	1	0.988	1	SUBCLONAL	2	TRUE	0	0.324564023035871	1		794	423	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194130	94194130	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055012-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	55	469	0	ENST00000323929.3:c.1298T>C	p.Val433Ala	p.V433A	ENST00000323929	NM_005591.3	433	gTa/gCa	12/20	0.272119952961953	4	FACETS	0.818	0.7	0.947	0.273	0.233	0.316	CLONAL	1	TRUE	1	0.324564023035871	4		469	549	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157256625	157256625	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055012-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	45	353	0	ENST00000346085.5:c.1952C>T	p.Thr651Ile	p.T651I	ENST00000346085	NM_020732.3	651	aCt/aTt	5/20	0.267213332705211	2	FACETS	1	0.847	1	0.501	0.423	0.585	CLONAL	1	TRUE	0	0.324564023035871	2		353	277	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0055013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	29	272	0	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	1	2	FACETS	0.9	0.728	1	0.9	0.728	1	CLONAL	1	TRUE	1	0.33923586044479	2		272	190	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600329	10600329	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	105	552	0	ENST00000171111.5:c.1526G>T	p.Gly509Val	p.G509V	ENST00000171111	NM_203500.1	509	gGg/gTg	4/6	0.33923586044479	1	FACETS	0.806	0.723	0.893	0.806	0.723	0.893	CLONAL	1	TRUE	0	0.33923586044479	1		552	638	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027813	152027813	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	65	424	0	ENST00000262189.6:c.262C>T	p.Gln88Ter	p.Q88*	ENST00000262189	NM_170606.2	88	Caa/Taa	3/59	NA	2	FACETS	0.757	0.658	0.865			1	INDETERMINATE	1	TRUE	NA	0.33923586044479	2		424	506	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30103701	30103701	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	67	490	0	ENST00000331968.5:c.1237G>C	p.Val413Leu	p.V413L	ENST00000331968	NM_002742.2	413	Gtc/Ctc	8/18	1	2	FACETS	0.654	0.568	0.747	0.654	0.568	0.747	SUBCLONAL	1	TRUE	1	0.33923586044479	2		490	604	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657441	29657441	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0055013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	66	473	0	ENST00000356175.3:c.5674A>T	p.Lys1892Ter	p.K1892*	ENST00000356175	NM_000267.3	1892	Aag/Tag	38/57	1	2	FACETS	0.916	0.798	1	0.916	0.798	1	CLONAL	1	TRUE	1	0.33923586044479	2		473	425	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876556	35876556	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	53	379	1	ENST00000303115.3:c.1348G>T	p.Val450Phe	p.V450F	ENST00000303115	NM_002185.3	450	Gtc/Ttc	8/8	1	2	FACETS	0.604	0.515	0.702	0.604	0.515	0.702	SUBCLONAL	1	TRUE	1	0.33923586044479	2		380	517	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039580	180039580	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	145	660	0	ENST00000261937.6:c.3463G>T	p.Asp1155Tyr	p.D1155Y	ENST00000261937	NM_182925.4	1155	Gac/Tac	26/30	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.33923586044479	2		660	809	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409438	80409439	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0055013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	37	304	1	ENST00000286548.4:c.675dup	p.Ile226TyrfsTer8	p.I226Yfs*8	ENST00000286548	NM_002072.3	225	-/T	5/7	0.33923586044479	1	FACETS	0.958	0.799	1	0.958	0.799	1	CLONAL	1	TRUE	0	0.33923586044479	1		305	189	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0055014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	111	421	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.812	0.738	0.888	0.812	0.738	0.888	CLONAL	1	TRUE	1	0.794613996547516	2		423	344	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866987936	NA	P-0055014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	90	262	1	ENST00000281708.4:c.1436G>C	p.Arg479Pro	p.R479P	ENST00000281708	NM_033632.3	479	cGa/cCa	10/12	1	2	FACETS	0.865	0.779	0.953	0.865	0.779	0.953	CLONAL	1	TRUE	1	0.794613996547516	2		263	262	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453150	140453150	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913341	NA	P-0055014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	127	405	0	ENST00000288602.6:c.1785T>G	p.Phe595Leu	p.F595L	ENST00000288602	NM_004333.4	595	ttT/ttG	15/18	0.768692338880371	3	FACETS	0.932	0.85	1	0.466	0.425	0.509	CLONAL	1	TRUE	1	0.794613996547516	3		405	479	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186501404	186501404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764605841	NA	P-0055014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	19	339	0	ENST00000323963.5:c.5C>T	p.Ser2Phe	p.S2F	ENST00000323963		2	tCt/tTt	1/11	0.246019073693498	1	FACETS	0.091	0.069	0.118	0.091	0.069	0.118	INDETERMINATE	1	TRUE	0	0.794613996547516	1		339	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0055015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	182	613	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.361288823684813	3	FACETS	1	0.984	1	0.778	0.727	0.828	CLONAL	2	TRUE	0	0.492325718639327	3		614	395	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256074	123256074	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	116	617	0	ENST00000358487.5:c.1835G>C	p.Arg612Thr	p.R612T	ENST00000358487	NM_000141.4	612	aGa/aCa	13/18	0.00828028356629673	3	FACETS	0.887	0.81	0.967			1	INDETERMINATE	2	TRUE	NA	0.492325718639327	3		617	331	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0055015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	67	363	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	0.361288823684813	3	FACETS	1	0.958	1	0.407	0.357	0.46	CLONAL	1	TRUE	0	0.492325718639327	3		363	278	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86658425	86658425	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	40	233	0	ENST00000274376.6:c.1390C>T	p.Arg464Cys	p.R464C	ENST00000274376	NM_002890.2	464	Cgt/Tgt	10/25	0.492325718639327	5	FACETS	1	0.932	1	0.785	0.668	0.907	CLONAL	2	TRUE	2	0.492325718639327	5		233	120	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614571	38614571	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	123	603	0	ENST00000299084.4:c.337G>C	p.Asp113His	p.D113H	ENST00000299084	NM_152594.2	113	Gat/Cat	3/7	0.257493515120512	2	FACETS	1	0.987	1	0.746	0.683	0.81	INDETERMINATE	1	TRUE	0	0.492325718639327	2		603	335	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609760	117609760	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	128	565	0	ENST00000368508.3:c.6939A>T	p.Lys2313Asn	p.K2313N	ENST00000368508	NM_002944.2	2313	aaA/aaT	43/43	0.475101872192965	4	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	2	0.492325718639327	4		565	374	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931792	68931792	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	86	412	0	ENST00000288368.4:c.222C>G	p.Phe74Leu	p.F74L	ENST00000288368	NM_024870.2	74	ttC/ttG	3/40	0.492325718639327	1	FACETS	0.784	0.714	0.854	1	0.985	1	SUBCLONAL	2	TRUE	0	0.492325718639327	1		412	168	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511575	38511575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866375031	NA	P-0055025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	90	778	0	ENST00000254066.5:c.1073C>T	p.Ala358Val	p.A358V	ENST00000254066	NM_000964.3	358	gCg/gTg	8/9	0.0787448896970573	4	FACETS	0.885	0.784	0.994	0.443	0.392	0.497	INDETERMINATE	1	TRUE	2	0.287709033071346	4		778	910	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006373	12006373	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	85	411	0	ENST00000396373.4:c.341A>G	p.Tyr114Cys	p.Y114C	ENST00000396373	NM_001987.4	114	tAt/tGt	4/8	0.287709033071346	7	FACETS	0.914	0.809	1	0.457	0.404	0.513	CLONAL	2	TRUE	3	0.287709033071346	7		411	556	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828131	72828131	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	62	705	0	ENST00000268489.5:c.8450C>T	p.Ser2817Phe	p.S2817F	ENST00000268489	NM_006885.3	2817	tCc/tTc	9/10	1	2	FACETS	0.639	0.552	0.735	0.639	0.552	0.735	SUBCLONAL	1	TRUE	1	0.287709033071346	2		705	674	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325990	30325990	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	65	315	0	ENST00000322652.5:c.2188G>C	p.Val730Leu	p.V730L	ENST00000322652	NM_015355.2	730	Gtt/Ctt	16/16	0.0787448896970573	4	FACETS	1	0.961	1	0.646	0.562	0.738	INDETERMINATE	1	TRUE	2	0.287709033071346	4		315	450	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276777	15276777	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	95	908	1	ENST00000263388.2:c.5488C>T	p.Gln1830Ter	p.Q1830*	ENST00000263388	NM_000435.2	1830	Cag/Tag	30/33	0.214949896579471	2	FACETS	0.863	0.768	0.964	0.432	0.384	0.482	CLONAL	1	TRUE	0	0.287709033071346	2		909	765	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595922	52595922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	67	668	1	ENST00000394830.3:c.3993G>A	p.Met1331Ile	p.M1331I	ENST00000394830	NM_018313.4	1331	atG/atA	26/30	0.217093267725511	3	FACETS	0.602	0.522	0.689	0.301	0.261	0.345	SUBCLONAL	1	TRUE	1	0.287709033071346	3		669	885	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509997	187509997	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	42	548	0	ENST00000441802.2:c.13516A>T	p.Thr4506Ser	p.T4506S	ENST00000441802	NM_005245.3	4506	Act/Tct	27/27	0.259417639166449	4	FACETS	0.649	0.541	0.77	0.216	0.18	0.257	SUBCLONAL	1	TRUE	1	0.287709033071346	4		548	579	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861032	35861032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	48	417	0	ENST00000303115.3:c.161C>T	p.Ser54Leu	p.S54L	ENST00000303115	NM_002185.3	54	tCa/tTa	2/8	0.156491660982544	5	FACETS	0.774	0.654	0.907	0.258	0.218	0.303	INDETERMINATE	1	TRUE	2	0.287709033071346	5		417	617	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246447	53246448	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	123	378	0	ENST00000375401.3:c.534dup	p.Arg179ThrfsTer4	p.R179Tfs*4	ENST00000375401	NM_004187.3	178	-/A	5/26	0.102994123563489	2	FACETS	1	0.975	1			1	INDETERMINATE	2	TRUE	NA	0.287709033071346	2		378	363	SUCCESS
AR	367	MSKCC	GRCh37	X	66766333	66766333	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	22	128	0	ENST00000374690.3:c.1345C>A	p.Pro449Thr	p.P449T	ENST00000374690	NM_000044.3	449	Ccg/Acg	1/8	0.102994123563489	2	FACETS	1	0.924	1			1	INDETERMINATE	1	TRUE	NA	0.287709033071346	2		128	104	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578181	7578207	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCTCATAGGGCACCACCACACTA	GGCGGCTCATAGGGCACCACCACACTA	C	novel	NA	P-0055025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	147	727	0	ENST00000269305.4:c.642_668delinsG	p.His214GlnfsTer2	p.H214Qfs*2	ENST00000269305	NM_001126112.2	214	caTAGTGTGGTGGTGCCCTATGAGCCGCCt/caGt	6/11	0.214949896579471	2	FACETS	1	0.986	1	0.707	0.646	0.77	CLONAL	1	TRUE	0	0.287709033071346	2		727	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0055026-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	180	890	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.292841160973947	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	0	0.292841160973947	2		893	613	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0055026-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	122	421	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.292841160973947	4	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	2	0.292841160973947	4		423	483	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250250	133250250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs483352909	NA	P-0055026-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	165	812	0	ENST00000320574.5:c.1270C>T	p.Leu424Phe	p.L424F	ENST00000320574	NM_006231.2	424	Ctc/Ttc	13/49	0.292841160973947	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	0	0.292841160973947	2		812	552	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051211	13051211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200173883	NA	P-0055026-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	51	644	0	ENST00000316448.5:c.647C>T	p.Pro216Leu	p.P216L	ENST00000316448	NM_004343.3	216	cCg/cTg	5/9	0.239620285935258	3	FACETS	0.731	0.621	0.852	0.366	0.31	0.426	SUBCLONAL	1	TRUE	1	0.292841160973947	3		644	546	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225609	26225609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055026-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	52	706	0	ENST00000360408.1:c.227C>T	p.Ala76Val	p.A76V	ENST00000360408	NM_003532.2	76	gCt/gTt	1/1	1	2	FACETS	0.706	0.601	0.821	0.706	0.601	0.821	SUBCLONAL	1	TRUE	1	0.292841160973947	2		706	503	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194904	29194904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372203752	NA	P-0055026-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	201	852	0	ENST00000240100.2:c.824G>A	p.Arg275His	p.R275H	ENST00000240100	NM_001394.6	275	cGc/cAc	4/4	0.188829720757887	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.292841160973947	4		852	814	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579369	7579369	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555526581	NA	P-0055035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	461	711	0	ENST00000269305.4:c.318C>G	p.Ser106Arg	p.S106R	ENST00000269305	NM_001126112.2	106	agC/agG	4/11	0.769360117675295	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.771825951058892	2		711	597	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435183	18435183	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055038-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	28	401	0	ENST00000266497.5:c.168T>G	p.Ser56Arg	p.S56R	ENST00000266497		56	agT/agG	1/31	0.224228974509971	5	FACETS	1	0.818	1	0.205	0.163	0.252	CLONAL	1	TRUE	0	0.224228974509971	5		401	326	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751110	128751110	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055038-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	62	693	0	ENST00000377970.2:c.647A>T	p.Asp216Val	p.D216V	ENST00000377970	NM_002467.4	216	gAc/gTc	2/3	0.18019195555707	4	FACETS	0.762	0.66	0.873	0.508	0.44	0.582	SUBCLONAL	2	TRUE	1	0.224228974509971	4		693	444	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915993	127915993	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055038-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	74	443	0	ENST00000373547.4:c.488A>C	p.His163Pro	p.H163P	ENST00000373547	NM_002721.4	163	cAt/cCt	6/7	0.224228974509971	1	FACETS	0.904	0.798	1	1	0.982	1	CLONAL	2	TRUE	0	0.224228974509971	1		443	324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0055040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	594	797	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.698619239003201	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.698619239003201	2		798	832	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468391	89468391	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	81	223	0	ENST00000336596.2:c.1925T>G	p.Leu642Arg	p.L642R	ENST00000336596	NM_005233.5	642	cTt/cGt	11/17	1	2	FACETS	0.974	0.872	1	0.974	0.872	1	CLONAL	1	TRUE	1	0.698619239003201	2		223	238	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985840	60985840	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	411	469	0	ENST00000333681.4:c.60T>A	p.His20Gln	p.H20Q	ENST00000333681		20	caT/caA	2/3	0.61840332242489	3	FACETS	0.973	0.944	1	0.973	0.944	1	CLONAL	3	TRUE	0	0.698619239003201	3		469	544	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177000	56177000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs553060905	NA	P-0055040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	173	341	0	ENST00000399503.3:c.2270G>A	p.Arg757His	p.R757H	ENST00000399503	NM_005921.1	757	cGc/cAc	13/20	0.675334086601215	2	FACETS	0.907	0.857	0.956	0.907	0.857	0.956	CLONAL	2	TRUE	0	0.698619239003201	2		341	273	SUCCESS
APC	324	MSKCC	GRCh37	5	112177241	112177244	+	frameshift_variant	Frame_Shift_Del	DEL	AATG	AATG	-	rs1057517544	NA	P-0055040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	144	286	0	ENST00000257430.4:c.5952_5955del	p.Glu1985LeufsTer58	p.E1985Lfs*58	ENST00000257430	NM_000038.5	1984	AATGaa/aa	16/16	0.675334086601215	2	FACETS	0.908	0.853	0.962	0.908	0.853	0.962	CLONAL	2	TRUE	0	0.698619239003201	2		286	227	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720705	89720706	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0055040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	148	139	0	ENST00000371953.3:c.856_857del	p.Thr286LeufsTer11	p.T286Lfs*11	ENST00000371953	NM_000314.4	286	ACc/c	8/9	0.698619239003201	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.698619239003201	2		139	190	SUCCESS
AXL	558	MSKCC	GRCh37	19	41725325	41725325	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1152	76	734	0	ENST00000301178.4:c.28A>T	p.Arg10Trp	p.R10W	ENST00000301178	NM_021913.4	10	Agg/Tgg	1/20	0.572010401836701	4	FACETS	0.301	0.263	0.342	0.15	0.131	0.171	SUBCLONAL	1	TRUE	2	0.698619239003201	4		734	1228	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267433	198267433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	133	417	0	ENST00000335508.6:c.1924C>T	p.Pro642Ser	p.P642S	ENST00000335508	NM_012433.2	642	Cct/Tct	14/25	1	2	FACETS	0.854	0.781	0.928	0.854	0.781	0.928	CLONAL	1	TRUE	1	0.698619239003201	2		417	446	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340460	8340460	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	176	355	0	ENST00000356435.5:c.5136A>T	p.Lys1712Asn	p.K1712N	ENST00000356435		1712	aaA/aaT	31/35	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.698619239003201	2		355	472	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486117	8486117	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	181	530	0	ENST00000356435.5:c.2700A>C	p.Lys900Asn	p.K900N	ENST00000356435		900	aaA/aaC	17/35	1	2	FACETS	0.985	0.916	1	0.985	0.916	1	CLONAL	1	TRUE	1	0.698619239003201	2		530	526	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0055041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	186	327	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.450676662917502	4	FACETS	0.8	0.742	0.86	0.8	0.742	0.86	SUBCLONAL	2	TRUE	2	0.569103032205627	4		327	641	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923739	39923752	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCGGGAGGCTCG	CTGCGGGAGGCTCG	-	novel	NA	P-0055041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	395	391	0	ENST00000378444.4:c.3339_3352del	p.Ser1113ArgfsTer24	p.S1113Rfs*24	ENST00000378444	NM_001123385.1	1113	agCGAGCCTCCCGCAGac/agac	7/15	0.50046334905289	2	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.569103032205627	2		391	605	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0055043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	103	398	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.142064804174163	4	FACETS	0.773	0.693	0.857	0.773	0.693	0.857	INDETERMINATE	2	TRUE	2	0.305184590982691	4		398	570	SUCCESS
APC	324	MSKCC	GRCh37	5	112175524	112175524	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	72	303	0	ENST00000257430.4:c.4233del	p.Ser1411ArgfsTer4	p.S1411Rfs*4	ENST00000257430	NM_000038.5	1411	agT/ag	16/16	NA	2	FACETS	0.84	0.741	0.943			1	INDETERMINATE	2	TRUE	NA	0.305184590982691	2		303	281	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256709	19256709	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	67	576	0	ENST00000162023.5:c.1004A>C	p.Lys335Thr	p.K335T	ENST00000162023		335	aAg/aCg	13/13	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.305184590982691	2		576	404	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391211	139391212	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0055043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	97	932	0	ENST00000277541.6:c.6979dup	p.Arg2327ProfsTer27	p.R2327Pfs*27	ENST00000277541	NM_017617.3	2327	cgg/cCgg	34/34	0.305184590982691	3	FACETS	1	0.959	1	0.578	0.516	0.644	CLONAL	1	TRUE	1	0.305184590982691	3		932	634	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	38	115	0				ENST00000310581	NM_198253.2	-/1132			0.233282671466259	5	FACETS	1	0.852	1	0.677	0.569	0.794	CLONAL	2	TRUE	2	0.370811784568923	5		115	157	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657051	215657051	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs758972589	NA	P-0055046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	118	341	1	ENST00000260947.4:c.334C>T	p.Arg112Ter	p.R112*	ENST00000260947	NM_000465.2	112	Cga/Tga	3/11	0.349790526601928	3	FACETS	1	0.914	1	1	0.914	1	CLONAL	2	TRUE	1	0.370811784568923	3		342	376	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285182	212285182	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	57	408	0	ENST00000342788.4:c.3119G>A	p.Arg1040Lys	p.R1040K	ENST00000342788	NM_005235.2	1040	aGa/aAa	25/28	0.349790526601928	3	FACETS	0.934	0.805	1	0.467	0.402	0.538	CLONAL	1	TRUE	1	0.370811784568923	3		408	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587782272	NA	P-0055046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	262	608	0	ENST00000269305.4:c.994-1G>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.33231137613729	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.370811784568923	3		608	512	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435985	116435985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1443741792	NA	P-0055046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	126	591	0	ENST00000397752.3:c.3980G>A	p.Arg1327His	p.R1327H	ENST00000397752	NM_000245.2	1327	cGc/cAc	21/21	0.260931929800572	3	FACETS	1	0.982	1	0.677	0.615	0.742	CLONAL	1	TRUE	1	0.370811784568923	3		591	595	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874091	151874091	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	100	471	0	ENST00000262189.6:c.8447C>G	p.Ser2816Cys	p.S2816C	ENST00000262189	NM_170606.2	2816	tCc/tGc	38/59	0.260931929800572	3	FACETS	1	0.942	1	0.539	0.482	0.599	CLONAL	1	TRUE	1	0.370811784568923	3		471	593	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224251	98224251	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	39	298	0	ENST00000331920.6:c.2590G>A	p.Glu864Lys	p.E864K	ENST00000331920	NM_000264.3	864	Gaa/Aaa	16/24	0.370811784568923	2	FACETS	0.664	0.552	0.787	0.332	0.276	0.394	SUBCLONAL	1	TRUE	0	0.370811784568923	2		298	317	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622086	43622086	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	46	496	0	ENST00000355710.3:c.3103G>C	p.Glu1035Gln	p.E1035Q	ENST00000355710	NM_020975.4	1035	Gag/Cag	19/20	0.260931929800572	3	FACETS	0.611	0.515	0.718	0.306	0.257	0.359	SUBCLONAL	1	TRUE	1	0.370811784568923	3		496	481	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828878	26828878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	82	219	1	ENST00000381527.3:c.100C>T	p.His34Tyr	p.H34Y	ENST00000381527	NM_001260.1	34	Cac/Tac	1/13	0.260931929800572	3	FACETS	1	0.974	1	0.681	0.604	0.762	CLONAL	1	TRUE	1	0.370811784568923	3		220	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572932	7572932	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	230	458	0	ENST00000269305.4:c.1177G>C	p.Asp393His	p.D393H	ENST00000269305	NM_001126112.2	393	Gac/Cac	11/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.370811784568923	NA		458	487	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193462	99193462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746015383	NA	P-0055046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	72	619	0	ENST00000074304.5:c.2657G>A	p.Arg886His	p.R886H	ENST00000074304	NM_001134224.1	886	cGc/cAc	25/26	0.206261284629938	4	FACETS	0.842	0.736	0.957	0.421	0.368	0.479	INDETERMINATE	1	TRUE	2	0.370811784568923	4		619	632	SUCCESS
APC	324	MSKCC	GRCh37	5	112154831	112154831	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	59	500	0	ENST00000257430.4:c.1102G>C	p.Val368Leu	p.V368L	ENST00000257430	NM_000038.5	368	Gta/Cta	10/16	0.349790526601928	3	FACETS	0.85	0.733	0.976	0.425	0.366	0.488	CLONAL	1	TRUE	1	0.370811784568923	3		500	444	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176671248	176671248	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	58	316	0	ENST00000439151.2:c.4355C>G	p.Ser1452Cys	p.S1452C	ENST00000439151	NM_022455.4	1452	tCt/tGt	9/23	0.349790526601928	3	FACETS	0.966	0.833	1	0.483	0.416	0.555	CLONAL	1	TRUE	1	0.370811784568923	3		316	384	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087952	27087952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	104	545	1	ENST00000324856.7:c.2239G>A	p.Ala747Thr	p.A747T	ENST00000324856	NM_006015.4	747	Gcc/Acc	6/20	0.566032955270539	3	FACETS	1	0.978	1	0.422	0.383	0.462	CLONAL	1	TRUE	0	0.758157320210212	3		546	299	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239883	41239883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	65	262	0	ENST00000379561.5:c.467G>A	p.Arg156His	p.R156H	ENST00000379561	NM_002015.3	156	cGc/cAc	1/3	0.684957653121862	3	FACETS	0.821	0.718	0.93	0.411	0.359	0.465	CLONAL	1	TRUE	1	0.758157320210212	3		262	288	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0055048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	273	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.887503508593978	2		622	582	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0055048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	162	328	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.887503508593978	2		328	361	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0055048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	157	563	2	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.975	0.906	1	0.975	0.906	1	CLONAL	1	TRUE	1	0.887503508593978	2		565	363	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101195	27101195	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	375	641	1	ENST00000324856.7:c.4477C>T	p.Gln1493Ter	p.Q1493*	ENST00000324856	NM_006015.4	1493	Cag/Tag	18/20	0.887503508593978	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.887503508593978	2		642	422	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259397	11259398	+	missense_variant	Missense_Mutation	DNP	GG	GG	CC	novel	NA	P-0055048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	351	580	3	ENST00000361445.4:c.4170_4171inv	p.Cys1390_Arg1391delinsTrpGly	p.C1390_R1391delinsWG	ENST00000361445	NM_004958.3	1390	tgCCga/tgGGga	28/58	0.762112299377039	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.887503508593978	1		583	392	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223484	2223484	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	66	286	0	ENST00000398665.3:c.3595C>T	p.Arg1199Ter	p.R1199*	ENST00000398665	NM_032482.2	1199	Cga/Tga	25/28	1	2	FACETS	0.953	0.849	1	0.953	0.849	1	CLONAL	1	TRUE	1	0.887503508593978	2		286	156	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967226	93967226	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1307419633	NA	P-0055048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	167	305	0	ENST00000369303.4:c.2126T>C	p.Ile709Thr	p.I709T	ENST00000369303	NM_004440.3	709	aTa/aCa	12/17	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.887503508593978	2		305	352	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891136	151891136	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	253	410	1	ENST00000262189.6:c.4618C>T	p.Gln1540Ter	p.Q1540*	ENST00000262189	NM_170606.2	1540	Cag/Tag	31/59	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.887503508593978	2		411	561	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0055057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	63	347	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.828	0.722	0.942	0.828	0.722	0.942	CLONAL	1	TRUE	1	0.482823216409189	2		347	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs17849781	NA	P-0055057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	158	759	0	ENST00000269305.4:c.832C>G	p.Pro278Ala	p.P278A	ENST00000269305	NM_001126112.2	278	Cct/Gct	8/11	0.482823216409189	1	FACETS	0.931	0.859	1	0.931	0.859	1	CLONAL	1	TRUE	0	0.482823216409189	1		759	533	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584560	48584560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	81	450	0	ENST00000342988.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000342988	NM_005359.5	245	Cag/Tag	6/12	0.482823216409189	1	FACETS	0.932	0.832	1	0.932	0.832	1	CLONAL	1	TRUE	0	0.482823216409189	1		450	273	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0055057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	46	328	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.874	0.744	1	0.874	0.744	1	CLONAL	1	TRUE	1	0.482823216409189	2		328	218	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0055057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	37	277	0	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	1	2	FACETS	0.647	0.537	0.768	0.647	0.537	0.768	SUBCLONAL	1	TRUE	1	0.482823216409189	2		277	237	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849848	156849848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374918502	NA	P-0055057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	103	723	1	ENST00000524377.1:c.2104C>T	p.Arg702Cys	p.R702C	ENST00000524377	NM_002529.3	702	Cgt/Tgt	16/17	1	2	FACETS	0.847	0.761	0.937	0.847	0.761	0.937	CLONAL	1	TRUE	1	0.482823216409189	2		724	504	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257780	133257780	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	122	622	0	ENST00000320574.5:c.148T>G	p.Phe50Val	p.F50V	ENST00000320574	NM_006231.2	50	Ttt/Gtt	2/49	1	2	FACETS	0.855	0.775	0.939	0.855	0.775	0.939	CLONAL	1	TRUE	1	0.482823216409189	2		622	591	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119101	70119102	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0055057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	56	415	0	ENST00000245479.2:c.675_676dup	p.Glu226AlafsTer28	p.E226Afs*28	ENST00000245479	NM_000346.3	225	ggc/gGCgc	2/3	1	2	FACETS	0.773	0.667	0.887	0.773	0.667	0.887	SUBCLONAL	1	TRUE	1	0.482823216409189	2		415	300	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	695	115	0				ENST00000310581	NM_198253.2	-/1132			0.329621603252328	19	FACETS	0.988	0.971	1	1	0.997	1	CLONAL	20	FALSE	1	0.329621603252328	19		115	811	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0055058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	327	890	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.18152092483864	4	FACETS	0.899	0.851	0.948	1	0.993	1	INDETERMINATE	3	FALSE	2	0.329621603252328	4		893	978	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089676	27089676	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	477	636	0	ENST00000324856.7:c.2632C>T	p.Gln878Ter	p.Q878*	ENST00000324856	NM_006015.4	878	Cag/Tag	8/20	0.329621603252328	5	FACETS	0.99	0.95	1	1	0.996	1	CLONAL	4	FALSE	2	0.329621603252328	5		636	1092	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256485	115256485	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753954415	NA	P-0055058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	124	518	0	ENST00000369535.4:c.226G>A	p.Glu76Lys	p.E76K	ENST00000369535	NM_002524.4	76	Gaa/Aaa	3/7	0.329621603252328	5	FACETS	1	0.96	1	0.372	0.336	0.411	CLONAL	1	FALSE	2	0.329621603252328	5		518	1007	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800956	18800956	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	86	302	0	ENST00000266497.5:c.4332A>G	p.Ile1444Met	p.I1444M	ENST00000266497		1444	atA/atG	31/31	1	2	FACETS	0.858	0.768	0.953	1	0.984	1	CLONAL	2	FALSE	1	0.329621603252328	2		302	304	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916811	48916811	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	122	383	0	ENST00000267163.4:c.341C>A	p.Ser114Ter	p.S114*	ENST00000267163	NM_000321.2	114	tCg/tAg	3/27	0.329621603252328	1	FACETS	1	0.981	1	1	0.992	1	CLONAL	2	FALSE	0	0.329621603252328	1		383	253	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789667	3789668	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0055058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	239	511	0	ENST00000262367.5:c.4191dup	p.Ala1398CysfsTer3	p.A1398Cfs*3	ENST00000262367	NM_004380.2	1397	-/T	25/31	0.111319079358813	4	FACETS	0.983	0.923	1	1	0.993	1	INDETERMINATE	3	FALSE	2	0.329621603252328	4		511	654	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50827573	50827573	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	69	364	0	ENST00000398568.2:c.2458C>G	p.Gln820Glu	p.Q820E	ENST00000398568	NM_001042412.1	820	Caa/Gaa	16/18	0.111319079358813	4	FACETS	1	0.947	1	0.582	0.508	0.662	INDETERMINATE	1	FALSE	2	0.329621603252328	4		364	478	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585383	29585383	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691072	NA	P-0055058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	107	504	0	ENST00000356175.3:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000356175	NM_000267.3	1378	Cag/Tag	31/57	0.18152092483864	4	FACETS	1	0.959	1	0.569	0.51	0.631	INDETERMINATE	1	FALSE	2	0.329621603252328	4		504	759	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936103	178936103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519699	NA	P-0055058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	312	677	0	ENST00000263967.3:c.1645G>A	p.Asp549Asn	p.D549N	ENST00000263967	NM_006218.2	549	Gat/Aat	10/21	0.243350442047236	5	FACETS	0.92	0.872	0.968	1	0.992	1	CLONAL	4	FALSE	2	0.329621603252328	5		677	769	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187558050	187558050	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs559543285	NA	P-0055058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	40	276	0	ENST00000441802.2:c.3661G>T	p.Gly1221Cys	p.G1221C	ENST00000441802	NM_005245.3	1221	Ggt/Tgt	5/27	0.190996841822718	2	FACETS	0.804	0.671	0.95	0.402	0.335	0.475	INDETERMINATE	1	FALSE	0	0.329621603252328	2		276	302	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652071	36652072	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0055058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	927	948	0	ENST00000244741.5:c.196dup	p.Glu66GlyfsTer23	p.E66Gfs*23	ENST00000244741	NM_000389.4	65	tgg/tGgg	2/3	0.329621603252328	6	FACETS	1	0.993	1	1	0.993	1	CLONAL	5	FALSE	1	0.329621603252328	6		948	1757	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350112	81350112	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	66	370	0	ENST00000222390.5:c.1220G>C	p.Arg407Thr	p.R407T	ENST00000222390	NM_000601.4	407	aGa/aCa	10/18	0.329621603252328	4	FACETS	0.999	0.868	1	0.333	0.289	0.38	CLONAL	1	FALSE	1	0.329621603252328	4		370	533	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039344	47039344	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	374	428	0	ENST00000377604.3:c.967T>A	p.Tyr323Asn	p.Y323N	ENST00000377604	NM_001204468.1	323	Tac/Aac	10/24	0.329621603252328	2	FACETS	1	0.987	1			1	CLONAL	4	FALSE	NA	0.329621603252328	2		428	543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	718	909	0	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.386582190462988	3	FACETS	0.999	0.967	1	0.999	0.967	1	CLONAL	3	TRUE	0	0.386582190462988	3		909	1479	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136806	69136806	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	87	402	0	ENST00000288368.4:c.4720C>G	p.Gln1574Glu	p.Q1574E	ENST00000288368	NM_024870.2	1574	Cag/Gag	39/40	1	2	FACETS	0.852	0.757	0.954	0.852	0.757	0.954	CLONAL	1	TRUE	1	0.386582190462988	2		402	528	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199711	11199711	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	112	484	0	ENST00000361445.4:c.4877G>T	p.Cys1626Phe	p.C1626F	ENST00000361445	NM_004958.3	1626	tGc/tTc	35/58	0.374723825683779	1	FACETS	0.956	0.864	1	0.956	0.864	1	CLONAL	1	TRUE	0	0.386582190462988	1		484	489	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65323389	65323389	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	123	629	0	ENST00000342505.4:c.1408A>T	p.Thr470Ser	p.T470S	ENST00000342505	NM_002227.2	470	Acc/Tcc	10/25	0.222193848652571	1	FACETS	0.817	0.741	0.898	0.817	0.741	0.898	INDETERMINATE	1	TRUE	0	0.386582190462988	1		629	628	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163325182	163325182	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	109	393	0	ENST00000271452.3:c.1318G>C	p.Ala440Pro	p.A440P	ENST00000271452	NM_145697.2	440	Gca/Cca	14/14	0.386582190462988	3	FACETS	0.843	0.763	0.926	0.843	0.763	0.926	CLONAL	2	TRUE	1	0.386582190462988	3		393	399	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625185	69625185	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	100	968	1	ENST00000334134.2:c.608G>T	p.Gly203Val	p.G203V	ENST00000334134	NM_005247.2	203	gGt/gTt	3/3	1	2	FACETS	0.599	0.535	0.668	0.599	0.535	0.668	SUBCLONAL	1	TRUE	1	0.386582190462988	2		969	863	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122590	108122590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878853485	NA	P-0055060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	30	372	0	ENST00000278616.4:c.1634C>T	p.Ala545Val	p.A545V	ENST00000278616	NM_000051.3	545	gCa/gTa	11/63	1	2	FACETS	0.38	0.306	0.465	0.38	0.306	0.465	SUBCLONAL	1	TRUE	1	0.386582190462988	2		372	408	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249290	133249290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	195	839	1	ENST00000320574.5:c.1609G>A	p.Glu537Lys	p.E537K	ENST00000320574	NM_006231.2	537	Gag/Aag	15/49	1	2	FACETS	0.999	0.924	1	0.999	0.924	1	CLONAL	1	TRUE	1	0.386582190462988	2		840	1010	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133857	41133857	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	189	348	0	ENST00000379561.5:c.1771G>T	p.Gly591Cys	p.G591C	ENST00000379561	NM_002015.3	591	Ggc/Tgc	2/3	0.372650967246239	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.386582190462988	2		348	429	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54959330	54959330	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs751452141	NA	P-0055060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	149	381	0	ENST00000312783.6:c.370A>G	p.Lys124Glu	p.K124E	ENST00000312783	NM_198436.1	124	Aaa/Gaa	5/10	0.386582190462988	3	FACETS	0.874	0.804	0.947	0.874	0.804	0.947	CLONAL	2	TRUE	1	0.386582190462988	3		381	526	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177662	56177662	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	97	376	0	ENST00000399503.3:c.2635G>C	p.Gly879Arg	p.G879R	ENST00000399503	NM_005921.1	879	Ggt/Cgt	14/20	0.374723825683779	1	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	0	0.386582190462988	1		376	405	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526706	106526706	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	104	434	0	ENST00000359195.3:c.2999A>G	p.Lys1000Arg	p.K1000R	ENST00000359195	NM_002649.2	1000	aAg/aGg	10/11	1	2	FACETS	0.996	0.895	1	0.996	0.895	1	CLONAL	1	TRUE	1	0.386582190462988	2		434	540	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371994	55371994	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	76	241	0	ENST00000297316.4:c.684C>A	p.Asp228Glu	p.D228E	ENST00000297316	NM_022454.3	228	gaC/gaA	2/2	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.386582190462988	2		241	354	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239988	53239988	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	197	755	0	ENST00000375401.3:c.1453T>C	p.Ser485Pro	p.S485P	ENST00000375401	NM_004187.3	485	Tct/Cct	11/26	0.386582190462988	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.386582190462988	1		755	720	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0055061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	168	314	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.981	0.907	1	0.981	0.907	1	CLONAL	1	TRUE	1	0.610491901262111	2		314	561	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	292	671	2	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	0.610491901262111	1	FACETS	0.931	0.881	0.981	0.931	0.881	0.981	CLONAL	1	TRUE	0	0.610491901262111	1		673	714	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577505	7577505	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs745425759	NA	P-0055061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	275	648	1	ENST00000269305.4:c.776A>T	p.Asp259Val	p.D259V	ENST00000269305	NM_001126112.2	259	gAc/gTc	7/11	0.610491901262111	1	FACETS	0.96	0.908	1	0.96	0.908	1	CLONAL	1	TRUE	0	0.610491901262111	1		649	652	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12043155	12043155	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0055061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	88	185	0	ENST00000353533.5:c.1041-1G>T		p.X347_splice	ENST00000353533	NM_003010.3	347			0.610491901262111	1	FACETS	0.875	0.789	0.962	0.875	0.789	0.962	CLONAL	1	TRUE	0	0.610491901262111	1		185	229	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974782	21974782	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs138677674	NA	P-0055061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	62	107	0	ENST00000304494.5:c.45G>A	p.Trp15Ter	p.W15*	ENST00000304494	NM_000077.4	15	tgG/tgA	1/3	0.610491901262111	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.610491901262111	1		107	116	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713826	30713826	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs193922660	NA	P-0055061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	307	636	0	ENST00000295754.5:c.1151A>G	p.Asn384Ser	p.N384S	ENST00000295754	NM_003242.5	384	aAt/aGt	4/7	0.610491901262111	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.610491901262111	1		636	660	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0055062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	431	785	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.567696089379349	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.567696089379349	2		785	719	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881704	111881704	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1360413239	NA	P-0055062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	134	465	0	ENST00000393256.3:c.382C>T	p.Leu128Phe	p.L128F	ENST00000393256	NM_006538.4	128	Ctc/Ttc	2/4	0.337013872565285	6	FACETS	0.799	0.728	0.873	0.399	0.364	0.437	INDETERMINATE	2	TRUE	2	0.567696089379349	6		465	631	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	61	115	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.904	0.785	1	0.904	0.785	1	CLONAL	1	TRUE	1	0.406399940079023	2		115	332	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725042	89725042	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1085308041	NA	P-0055064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	50	173	0	ENST00000371953.3:c.1027-2A>G		p.X343_splice	ENST00000371953	NM_000314.4	343			0.406399940079023	1	FACETS	0.891	0.765	1	0.891	0.765	1	CLONAL	1	TRUE	0	0.406399940079023	1		173	220	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0055064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	170	740	0	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.406399940079023	3	FACETS	1	0.955	1	0.528	0.485	0.573	CLONAL	1	TRUE	1	0.406399940079023	3		740	953	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958190	2958190	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753952757	NA	P-0055064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	100	617	3	ENST00000396946.4:c.2542C>T	p.Arg848Cys	p.R848C	ENST00000396946	NM_032415.4	848	Cgc/Tgc	19/25	0.221183286373243	2	FACETS	0.743	0.665	0.827	0.372	0.332	0.414	INDETERMINATE	1	TRUE	0	0.406399940079023	2		620	662	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100085	27100086	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0055064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	127	615	0	ENST00000324856.7:c.3882_3883dup	p.Gly1295GlufsTer7	p.G1295Efs*7	ENST00000324856	NM_006015.4	1294	ata/atAGa	16/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.406399940079023	2		615	585	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041963	42041963	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055064-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	108	424	0	ENST00000219905.7:c.6158T>C	p.Ile2053Thr	p.I2053T	ENST00000219905	NM_001164273.1	2053	aTc/aCc	17/24	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.406399940079023	2		424	500	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149894	99149894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368448330	NA	P-0055078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	111	602	0	ENST00000074304.5:c.206C>T	p.Ala69Val	p.A69V	ENST00000074304	NM_001134224.1	69	gCg/gTg	5/26	0.212810456657703	2	FACETS	1	0.976	1	0.641	0.578	0.708	CLONAL	1	FALSE	0	0.293042015738514	2		602	591	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160428	108160428	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1060501658	NA	P-0055078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	29	427	0	ENST00000278616.4:c.4336G>T	p.Val1446Phe	p.V1446F	ENST00000278616	NM_000051.3	1446	Gtt/Ttt	29/63	0.21723239289307	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	2	FALSE	0	0.293042015738514	2		427	93	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003812	45003812	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0055078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	159	662	0	ENST00000558401.1:c.67+1G>C		p.X23_splice	ENST00000558401	NM_004048.2	23			0.293042015738514	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	0	0.293042015738514	1		662	691	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608407	43608407	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	67	1398	0	ENST00000355710.3:c.1755C>A	p.Cys585Ter	p.C585*	ENST00000355710	NM_020975.4	585	tgC/tgA	9/20	0.233062197146468	2	FACETS	0.425	0.368	0.488	0.213	0.184	0.244	SUBCLONAL	1	FALSE	0	0.293042015738514	2		1398	1075	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683144	88683144	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	44	553	0	ENST00000372037.3:c.1354G>T	p.Glu452Ter	p.E452*	ENST00000372037	NM_004329.2	452	Gaa/Taa	12/13	0.233062197146468	2	FACETS	0.751	0.637	0.873	0.751	0.637	0.873	SUBCLONAL	2	FALSE	0	0.293042015738514	2		553	200	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449549	32449549	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	265	1127	0	ENST00000332351.3:c.825C>G	p.Asp275Glu	p.D275E	ENST00000332351	NM_024426.4	275	gaC/gaG	3/10	0.21723239289307	2	FACETS	0.824	0.772	0.877	0.824	0.772	0.877	CLONAL	2	FALSE	0	0.293042015738514	2		1127	1098	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574483	64574483	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	232	1031	0	ENST00000312049.6:c.912G>C	p.Lys304Asn	p.K304N	ENST00000312049	NM_130799.2	304	aaG/aaC	6/10	0.21723239289307	2	FACETS	0.844	0.788	0.902	0.844	0.788	0.902	CLONAL	2	FALSE	0	0.293042015738514	2		1031	938	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254732	46254732	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	31	304	2	ENST00000334344.6:c.4922A>G	p.Lys1641Arg	p.K1641R	ENST00000334344	NM_152641.2	1641	aAg/aGg	16/21	0.293042015738514	5	FACETS	1	0.938	1	0.712	0.58	0.859	CLONAL	1	FALSE	3	0.293042015738514	5		306	214	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427522	49427522	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	143	1018	1	ENST00000301067.7:c.10966C>A	p.Arg3656Ser	p.R3656S	ENST00000301067	NM_003482.3	3656	Cgc/Agc	39/54	0.293042015738514	5	FACETS	0.769	0.7	0.84	0.769	0.7	0.84	SUBCLONAL	2	FALSE	3	0.293042015738514	5		1019	914	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427527	49427527	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	213	1016	1	ENST00000301067.7:c.10961G>T	p.Gly3654Val	p.G3654V	ENST00000301067	NM_003482.3	3654	gGt/gTt	39/54	0.293042015738514	5	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	FALSE	3	0.293042015738514	5		1017	940	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872019	37872019	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	291	1072	0	ENST00000269571.5:c.1340G>T	p.Gly447Val	p.G447V	ENST00000269571		447	gGg/gTg	12/27	0.293042015738514	3	FACETS	0.805	0.756	0.856	0.805	0.756	0.856	CLONAL	2	FALSE	1	0.293042015738514	3		1072	1414	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212029	36212029	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	266	1165	1	ENST00000222270.7:c.1780G>T	p.Val594Phe	p.V594F	ENST00000222270	NM_014727.1	594	Gtt/Ttt	3/37	0.293042015738514	5	FACETS	1	0.981	1	0.741	0.695	0.79	CLONAL	2	FALSE	2	0.293042015738514	5		1166	1175	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22143014	22143014	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	29	513	3	ENST00000215832.6:c.693G>T	p.Lys231Asn	p.K231N	ENST00000215832	NM_002745.4	231	aaG/aaT	5/9	0.293042015738514	1	FACETS	0.866	0.701	1	0.866	0.701	1	CLONAL	1	FALSE	0	0.293042015738514	1		516	195	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1941496	1941496	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	26	439	0	ENST00000382891.5:c.1872del	p.Glu625ArgfsTer38	p.E625Rfs*38	ENST00000382891	NM_133335.3	624	acT/ac	9/22	0.293042015738514	4	FACETS	1	0.893	1	0.601	0.479	0.738	CLONAL	1	FALSE	2	0.293042015738514	4		439	191	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515286	31515286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	52	773	0	ENST00000344624.3:c.1099G>A	p.Glu367Lys	p.E367K	ENST00000344624		367	Gaa/Aaa	5/33	0.293042015738514	3	FACETS	1	0.929	1	0.573	0.49	0.664	CLONAL	1	FALSE	1	0.293042015738514	3		773	355	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876411	35876411	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	122	794	0	ENST00000303115.3:c.1203C>A	p.Tyr401Ter	p.Y401*	ENST00000303115	NM_002185.3	401	taC/taA	8/8	0.293042015738514	3	FACETS	1	0.975	1	0.62	0.56	0.683	CLONAL	1	FALSE	1	0.293042015738514	3		794	770	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287866	33287866	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	94	823	1	ENST00000374542.5:c.1387G>T	p.Glu463Ter	p.E463*	ENST00000374542	NM_001141970.1	463	Gag/Tag	5/8	0.241887826900021	3	FACETS	0.789	0.705	0.878	0.526	0.47	0.585	SUBCLONAL	2	FALSE	0	0.293042015738514	3		824	466	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528528	157528528	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	118	737	0	ENST00000346085.5:c.6253del	p.Thr2085ProfsTer14	p.T2085Pfs*14	ENST00000346085	NM_020732.3	2085	Acc/cc	20/20	0.241887826900021	3	FACETS	0.842	0.763	0.926	0.562	0.508	0.617	CLONAL	2	FALSE	0	0.293042015738514	3		737	548	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508250	106508250	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs761383890	NA	P-0055078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	124	560	0	ENST00000359195.3:c.244A>T	p.Ser82Cys	p.S82C	ENST00000359195	NM_002649.2	82	Agc/Tgc	2/11	0.293042015738514	4	FACETS	0.888	0.806	0.975	0.888	0.806	0.975	CLONAL	2	FALSE	2	0.293042015738514	4		560	616	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760448	133760448	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	192	997	1	ENST00000318560.5:c.2771G>T	p.Gly924Val	p.G924V	ENST00000318560	NM_005157.4	924	gGg/gTg	11/11	0.293042015738514	3	FACETS	1	0.989	1	0.713	0.659	0.769	CLONAL	1	FALSE	1	0.293042015738514	3		998	1054	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786019	135786019	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	148	922	0	ENST00000298552.3:c.1202G>C	p.Cys401Ser	p.C401S	ENST00000298552	NM_001162426.1	401	tGt/tCt	12/23	0.293042015738514	3	FACETS	0.942	0.858	1	0.471	0.429	0.515	CLONAL	1	FALSE	1	0.293042015738514	3		922	1230	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223851	53223851	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1268423491	NA	P-0055078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1235	263	1278	0	ENST00000375401.3:c.3508G>T	p.Ala1170Ser	p.A1170S	ENST00000375401	NM_004187.3	1170	Gcc/Tcc	23/26	0.293042015738514	3	FACETS	1	0.991	1	0.687	0.642	0.733	CLONAL	1	FALSE	1	0.293042015738514	3		1278	1498	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938424	76938424	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	21	667	0	ENST00000373344.5:c.2324A>T	p.Asp775Val	p.D775V	ENST00000373344	NM_000489.3	775	gAt/gTt	9/35	0.293042015738514	3	FACETS	1	0.889	1	0.627	0.489	0.784	CLONAL	1	FALSE	1	0.293042015738514	3		667	131	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0055080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	85	354	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.936	1	1	0.986	1	CLONAL	2	TRUE	1	0.288529626246268	2		355	277	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534285	534285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894226	NA	P-0055080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	141	772	0	ENST00000451590.1:c.38G>T	p.Gly13Val	p.G13V	ENST00000451590	NM_001130442.1	13	gGt/gTt	2/5	1	2	FACETS	0.866	0.793	0.943	1	0.99	1	CLONAL	2	TRUE	1	0.288529626246268	2		772	564	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030813	69030813	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	63	475	0	ENST00000288368.4:c.3355G>C	p.Ala1119Pro	p.A1119P	ENST00000288368	NM_024870.2	1119	Gcc/Ccc	27/40	0.288529626246268	6	FACETS	0.802	0.692	0.922	0.16	0.138	0.185	CLONAL	1	TRUE	1	0.288529626246268	6		475	859	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0055082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	293	689	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.555702886580408	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	0	0.555702886580408	1		690	648	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0055082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	161	327	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.555702886580408	3	FACETS	1	0.934	1	0.509	0.468	0.552	CLONAL	1	FALSE	1	0.555702886580408	3		327	727	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0055082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	167	317	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.290983097123119	0	FACETS	0.482	0.445	0.52			1	INDETERMINATE	1	FALSE	0	0.555702886580408	0		317	554	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0055082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	141	417	1	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	1	0.555702886580408	2		418	488	SUCCESS
APC	324	MSKCC	GRCh37	5	112174264	112174267	+	frameshift_variant	Frame_Shift_Del	DEL	AAGT	AAGT	-	novel	NA	P-0055082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	139	426	0	ENST00000257430.4:c.2977_2980del	p.Lys993PhefsTer11	p.K993Ffs*11	ENST00000257430	NM_000038.5	991	gaAAGT/ga	16/16	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.555702886580408	2		426	428	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95563003	95563003	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	155	464	0	ENST00000393063.1:c.4254G>C	p.Glu1418Asp	p.E1418D	ENST00000393063	NM_030621.3	1418	gaG/gaC	24/28	1	2	FACETS	0.946	0.87	1	0.946	0.87	1	CLONAL	1	FALSE	1	0.555702886580408	2		464	590	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829566	72829566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1445487502	NA	P-0055082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	276	701	2	ENST00000268489.5:c.7015C>T	p.Arg2339Cys	p.R2339C	ENST00000268489	NM_006885.3	2339	Cgc/Tgc	9/10	0.116492024897475	4	FACETS	0.854	0.803	0.905	0.854	0.803	0.905	INDETERMINATE	2	FALSE	2	0.555702886580408	4		703	905	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	70	115	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.438003705370021	2		115	266	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037144	71037144	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0055083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	50	457	0	ENST00000318789.4:c.1146+1G>A		p.X382_splice	ENST00000318789	NM_032682.5	382			0.34020649376506	0	FACETS	0.388	0.33	0.45			1	SUBCLONAL	1	TRUE	0	0.438003705370021	0		457	331	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0055083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	295	443	2	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.438003705370021	2	FACETS	0.887	0.847	0.927	1	0.994	1	CLONAL	3	TRUE	0	0.438003705370021	2		445	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0055083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	136	756	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.373242126441819	1	FACETS	0.915	0.836	0.997	0.915	0.836	0.997	CLONAL	1	TRUE	0	0.438003705370021	1		756	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0055083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	82	.	.	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.373242126441819	1	FACETS	0.453	0.399	0.51	0.453	0.399	0.51	SUBCLONAL	1	TRUE	0	0.438003705370021	1		0	646	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670234	134670234	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764139128	NA	P-0055083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	102	595	1	ENST00000398015.3:c.145G>A	p.Asp49Asn	p.D49N	ENST00000398015	NM_004441.4	49	Gat/Aat	3/16	1	2	FACETS	0.949	0.852	1	0.949	0.852	1	CLONAL	1	TRUE	1	0.438003705370021	2		596	491	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323978	31323978	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	44	66	0	ENST00000412585.2:c.585C>A	p.Tyr195Ter	p.Y195*	ENST00000412585	NM_005514.6	195	taC/taA	3/8	0.438003705370021	2	FACETS	0.848	0.746	0.947	1	0.961	1	CLONAL	3	TRUE	0	0.438003705370021	2		66	79	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78914299	78914299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	131	610	1	ENST00000306801.3:c.2923C>T	p.Pro975Ser	p.P975S	ENST00000306801	NM_020761.2	975	Cca/Tca	25/34	1	2	FACETS	0.858	0.78	0.94	0.858	0.78	0.94	CLONAL	1	TRUE	1	0.438003705370021	2		611	697	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920507	50920507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1315638826	NA	P-0055083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	65	679	1	ENST00000440232.2:c.3199G>A	p.Glu1067Lys	p.E1067K	ENST00000440232	NM_002691.3	1067	Gag/Aag	26/27	0.373242126441819	1	FACETS	0.479	0.416	0.547	0.479	0.416	0.547	SUBCLONAL	1	TRUE	0	0.438003705370021	1		680	484	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979637	55979637	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	55	558	0	ENST00000263923.4:c.810G>T	p.Lys270Asn	p.K270N	ENST00000263923	NM_002253.2	270	aaG/aaT	7/30	0.373242126441819	1	FACETS	0.389	0.333	0.451	0.389	0.333	0.451	SUBCLONAL	1	TRUE	0	0.438003705370021	1		558	504	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911150	29911151	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAAA	novel	NA	P-0055083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	30	483	0	ENST00000376809.5:c.452_453insAGAA	p.Asn151LysfsTer27	p.N151Kfs*27	ENST00000376809	NM_002116.7	150	ctg/ctGAAAg	3/8	0.438003705370021	2	FACETS	0.413	0.333	0.503	0.206	0.166	0.252	SUBCLONAL	1	TRUE	0	0.438003705370021	2		483	332	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141565995	141565995	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	123	541	0	ENST00000220592.5:c.1269G>T	p.Arg423Ser	p.R423S	ENST00000220592	NM_012154.3	423	agG/agT	10/19	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.438003705370021	2		541	381	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439898	52439898	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	118	706	2	ENST00000460680.1:c.814C>T	p.Gln272Ter	p.Q272*	ENST00000460680	NM_004656.3	272	Cag/Tag	10/17	0.373182344813375	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.373182344813375	1		708	489	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007717	45007717	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	57	492	0	ENST00000558401.1:c.164T>G	p.Ile55Ser	p.I55S	ENST00000558401	NM_004048.2	55	aTt/aGt	2/4	1	2	FACETS	0.937	0.809	1	0.937	0.809	1	CLONAL	1	TRUE	1	0.373182344813375	2		492	326	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198260821	198260821	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	48	606	0	ENST00000335508.6:c.3498T>G	p.Ile1166Met	p.I1166M	ENST00000335508	NM_012433.2	1166	atT/atG	23/25	1	2	FACETS	0.768	0.652	0.894	0.768	0.652	0.894	SUBCLONAL	1	TRUE	1	0.373182344813375	2		606	335	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188295	10188296	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0055084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	93	710	0	ENST00000256474.2:c.439_440del	p.Ile147PhefsTer26	p.I147Ffs*26	ENST00000256474	NM_000551.3	146	ccTAtt/cctt	2/3	0.373182344813375	1	FACETS	0.891	0.796	0.991	0.891	0.796	0.991	CLONAL	1	TRUE	0	0.373182344813375	1		710	455	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	58	115	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	FALSE	1	0.242544899480776	2		115	460	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0055085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	50	535	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.0977422979521418	3	FACETS	1	0.868	1	0.511	0.434	0.596	INDETERMINATE	1	FALSE	1	0.242544899480776	3		535	452	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16021276	16021276	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	51	426	0	ENST00000268712.3:c.1981C>T	p.Gln661Ter	p.Q661*	ENST00000268712	NM_006311.3	661	Caa/Taa	18/46	0.242544899480776	1	FACETS	0.745	0.634	0.867	0.745	0.634	0.867	SUBCLONAL	1	FALSE	0	0.242544899480776	1		426	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579855	7579855	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1131691018	NA	P-0055085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	91	771	0	ENST00000269305.4:c.58del	p.Ser20GlnfsTer24	p.S20Qfs*24	ENST00000269305	NM_001126112.2	20	Tca/ca	2/11	0.242544899480776	1	FACETS	0.66	0.585	0.741	0.66	0.585	0.741	SUBCLONAL	1	FALSE	0	0.242544899480776	1		771	999	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217532	142217532	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	41	544	0	ENST00000350721.4:c.5465C>T	p.Ser1822Leu	p.S1822L	ENST00000350721	NM_001184.3	1822	tCa/tTa	32/47	0.0977422979521418	3	FACETS	0.52	0.432	0.619	0.26	0.216	0.31	INDETERMINATE	1	FALSE	1	0.242544899480776	3		544	729	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267264	41267264	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	37	536	1	ENST00000349496.5:c.848T>C	p.Val283Ala	p.V283A	ENST00000349496	NM_001904.3	283	gTt/gCt	6/15	0.233112193691297	1	FACETS	0.437	0.359	0.524	0.437	0.359	0.524	SUBCLONAL	1	FALSE	0	0.242544899480776	1		537	614	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428454	72428454	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	46	689	0	ENST00000477973.2:c.550G>C	p.Asp184His	p.D184H	ENST00000477973	NM_012234.5	184	Gac/Cac	2/4	0.233112193691297	1	FACETS	0.366	0.307	0.432	0.366	0.307	0.432	SUBCLONAL	1	FALSE	0	0.242544899480776	1		689	910	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294924	1294924	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	11	16	0	ENST00000310581.5:c.181G>A	p.Asp61Asn	p.D61N	ENST00000310581	NM_198253.2	61	Gac/Aac	1/16	1	2	FACETS	0.926	0.646	1	0.926	0.646	1	CLONAL	1	FALSE	1	0.242544899480776	2		16	98	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959921	38959921	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	22	358	1	ENST00000357387.3:c.2011C>A	p.His671Asn	p.H671N	ENST00000357387	NM_152756.3	671	Cat/Aat	21/38	1	2	FACETS	0.441	0.341	0.558	0.441	0.341	0.558	SUBCLONAL	1	FALSE	1	0.242544899480776	2		359	411	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039411	47039411	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	88	389	0	ENST00000377604.3:c.1034T>C	p.Phe345Ser	p.F345S	ENST00000377604	NM_001204468.1	345	tTt/tCt	10/24	1	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	FALSE	0	0.242544899480776	1		389	570	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233140	66233140	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs769393148	NA	P-0055086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	104	630	0	ENST00000273854.3:c.1859G>A	p.Arg620Gln	p.R620Q	ENST00000273854	NM_004439.5	620	cGg/cAg	10/18	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.384961261983853	2		630	535	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328368	137328368	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	178	978	0	ENST00000481739.1:c.1297C>G	p.Leu433Val	p.L433V	ENST00000481739	NM_002957.4	433	Ctg/Gtg	10/10	0.384961261983853	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.384961261983853	1		978	715	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522551	176522551	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	122	749	0	ENST00000292408.4:c.1648G>C	p.Val550Leu	p.V550L	ENST00000292408	NM_213647.1	550	Gtg/Ctg	13/18	0.540635007054862	3	FACETS	0.605	0.546	0.667	0.302	0.273	0.334	SUBCLONAL	1	TRUE	1	0.561930164830914	3		749	920	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0055092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	167	285	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.944	0.879	1	1	0.993	1	CLONAL	2	TRUE	1	0.462105993304694	2		285	383	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	735	671	2	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	0.915	0.899	0.931	1	0.999	1	CLONAL	4	TRUE	1	0.462105993304694	2		673	869	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0055092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	187	324	1	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	0.899	0.84	0.959	1	0.993	1	CLONAL	2	TRUE	1	0.462105993304694	2		325	450	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560476	95560476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	243	467	0	ENST00000393063.1:c.5113G>A	p.Glu1705Lys	p.E1705K	ENST00000393063	NM_030621.3	1705	Gaa/Aaa	25/28	0.411526934764902	0	FACETS	0.839	0.805	0.873			1	CLONAL	2	TRUE	0	0.462105993304694	0		467	337	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380338	14380339	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCCCACGCC	novel	NA	P-0055092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	164	261	0	ENST00000256196.4:c.70_78dup	p.Gly24_Gly26dup	p.G24_G26dup	ENST00000256196		24	-/GGCGTGGGC	1/6	0.462105993304694	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.462105993304694	2		261	285	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332916	153332916	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1362274408	NA	P-0055092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	177	397	1	ENST00000281708.4:c.40C>T	p.Arg14Ter	p.R14*	ENST00000281708	NM_033632.3	14	Cga/Tga	2/12	1	2	FACETS	0.81	0.753	0.867	1	0.992	1	CLONAL	2	TRUE	1	0.462105993304694	2		398	473	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49399928	49399928	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0055092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	36	428	0	ENST00000418115.1:c.408+1G>A		p.X136_splice	ENST00000418115	NM_001664.2	136			1	2	FACETS	0.245	0.201	0.295	0.245	0.201	0.295	SUBCLONAL	1	TRUE	1	0.462105993304694	2		428	635	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349140	11349140	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	163	253	0	ENST00000332029.2:c.196C>A	p.Arg66Ser	p.R66S	ENST00000332029	NM_003745.1	66	Cgc/Agc	2/2	1	2	FACETS	0.818	0.759	0.879	1	0.991	1	CLONAL	2	TRUE	1	0.462105993304694	2		253	431	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52709234	52709234	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	301	530	0	ENST00000322088.6:c.188A>C	p.Asp63Ala	p.D63A	ENST00000322088	NM_014225.5	63	gAt/gCt	3/15	1	2	FACETS	0.923	0.875	0.971	1	0.996	1	CLONAL	2	TRUE	1	0.462105993304694	2		530	706	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256759	46256759	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	28	315	0	ENST00000371998.3:c.815A>T	p.Asp272Val	p.D272V	ENST00000371998		272	gAt/gTt	8/23	0.462105993304694	3	FACETS	0.29	0.231	0.358	0.145	0.115	0.179	SUBCLONAL	1	TRUE	1	0.462105993304694	3		315	514	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816558	32816558	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	394	676	0	ENST00000354258.4:c.1617del	p.Phe539LeufsTer16	p.F539Lfs*16	ENST00000354258	NM_000593.5	539	ttT/tt	7/11	0.462105993304694	3	FACETS	0.817	0.777	0.859	0.817	0.777	0.859	CLONAL	2	TRUE	1	0.462105993304694	3		676	1284	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100093	157100123	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCGGCGGCGGCAGCAGCAGGAGGCGGCG	GCGGCGGCGGCGGCAGCAGCAGGAGGCGGCG	-	novel	NA	P-0055092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	13	10	0	ENST00000346085.5:c.1041_1071del	p.Ala348MetfsTer11	p.A348Mfs*11	ENST00000346085	NM_020732.3	344	GCGGCGGCGGCGGCAGCAGCAGGAGGCGGCGgc/gc	1/20	0.436758288236203	2	FACETS	1	0.827	1	0.586	0.433	0.758	CLONAL	1	TRUE	0	0.462105993304694	2		10	48	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0055093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	368	620	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.879662546448397	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.879662546448397	1		620	432	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462038	120462038	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	91	650	0	ENST00000256646.2:c.5678C>G	p.Ala1893Gly	p.A1893G	ENST00000256646	NM_024408.3	1893	gCc/gGc	31/34	0.51758600398115	1	FACETS	0.322	0.288	0.358	0.322	0.288	0.358	INDETERMINATE	1	TRUE	0	0.879662546448397	1		650	360	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450634	70450634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747878740	NA	P-0055093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	94	457	0	ENST00000373644.4:c.5474C>T	p.Ser1825Leu	p.S1825L	ENST00000373644	NM_030625.2	1825	tCa/tTa	12/12	0.392820467174064	1	FACETS	0.384	0.345	0.424	0.384	0.345	0.424	INDETERMINATE	1	TRUE	0	0.879662546448397	1		457	312	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629027	14629027	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	190	546	0	ENST00000254322.2:c.135C>G	p.Phe45Leu	p.F45L	ENST00000254322	NM_006145.1	45	ttC/ttG	1/3	1	2	FACETS	0.919	0.858	0.981	0.919	0.858	0.981	CLONAL	1	TRUE	1	0.879662546448397	2		546	470	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719593	61719593	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	38	406	0	ENST00000401558.2:c.1590G>T	p.Gln530His	p.Q530H	ENST00000401558	NM_003400.3	530	caG/caT	15/25	0.136348871051	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.879662546448397	0		406	184	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125415	47125415	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	48	440	0	ENST00000409792.3:c.5855C>G	p.Ser1952Cys	p.S1952C	ENST00000409792	NM_014159.6	1952	tCt/tGt	12/21	0.20570458775838	1	FACETS	0.229	0.195	0.266	0.229	0.195	0.266	INDETERMINATE	1	TRUE	0	0.879662546448397	1		440	267	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295254	1295254	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0055093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	203	341	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.879662546448397	2		341	422	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31405790	31405790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	52	296	1	ENST00000344624.3:c.3988G>A	p.Glu1330Lys	p.E1330K	ENST00000344624		1330	Gaa/Aaa	32/33	1	2	FACETS	0.411	0.352	0.474	0.411	0.352	0.474	SUBCLONAL	1	TRUE	1	0.879662546448397	2		297	288	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211823	123211823	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	78	326	0	ENST00000218089.9:c.2690G>T	p.Gly897Val	p.G897V	ENST00000218089	NM_001042749.1	897	gGa/gTa	27/35	0.51758600398115	1	FACETS	0.456	0.407	0.506	0.456	0.407	0.506	INDETERMINATE	1	TRUE	0	0.879662546448397	1		326	218	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577571	7577572	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0055094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	638	628	0	ENST00000269305.4:c.708_709dup	p.Met237ThrfsTer11	p.M237Tfs*11	ENST00000269305	NM_001126112.2	237	atg/aCAtg	7/11	NA	2	FACETS	0.968	0.947	0.989			1	INDETERMINATE	2	TRUE	NA	0.820395115889882	2		628	803	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779620	3779620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	502	957	1	ENST00000262367.5:c.5428C>T	p.Arg1810Cys	p.R1810C	ENST00000262367	NM_004380.2	1810	Cgc/Tgc	31/31	1	2	FACETS	1	0.993	1	1	0.998	1	CLONAL	2	TRUE	1	0.341314447885674	2		958	1253	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942745	68942745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781270008	NA	P-0055095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	187	466	1	ENST00000288368.4:c.557G>A	p.Arg186Gln	p.R186Q	ENST00000288368	NM_024870.2	186	cGg/cAg	6/40	1	2	FACETS	0.977	0.908	1	1	0.993	1	CLONAL	2	TRUE	1	0.341314447885674	2		467	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579714	7579753	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGGAAGTCTGAAAGACAAGAGCAGAAAGTCAGTCCCATG	CAGGAAGTCTGAAAGACAAGAGCAGAAAGTCAGTCCCATG	-	novel	NA	P-0055095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	244	662	1	ENST00000269305.4:c.75-32_82del		p.X25_splice	ENST00000269305	NM_001126112.2	25		3/11	0.327553438008465	0	FACETS	0.934	0.883	0.985			1	CLONAL	2	TRUE	0	0.341314447885674	0		663	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0055097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	235	591	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.650172033339637	4	FACETS	0.985	0.928	1			1	CLONAL	2	TRUE	NA	0.813097130287629	4		591	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691022	NA	P-0055097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	282	400	0	ENST00000269305.4:c.1024del	p.Arg342GlufsTer3	p.R342Efs*3	ENST00000269305	NM_001126112.2	342	Cga/ga	10/11	0.650172033339637	4	FACETS	0.984	0.932	1			1	CLONAL	2	TRUE	NA	0.813097130287629	4		400	639	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252155	226252155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553260624	NA	P-0055097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	58	80	0	ENST00000366813.1:c.103G>A	p.Gly35Arg	p.G35R	ENST00000366813		35	Ggg/Agg	1/3	0.813097130287629	3	FACETS	1	0.901	1	1	0.901	1	CLONAL	2	TRUE	1	0.813097130287629	3		80	100	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562887	21562888	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs746424000	NA	P-0055097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	8	343	1	ENST00000382592.4:c.1031dup	p.Gln345AlafsTer17	p.Q345Afs*17	ENST00000382592	NM_014572.2	344	ccg/ccCg	4/8	0.527861956985862	1	FACETS	0.037	0.023	0.054	0.037	0.023	0.054	SUBCLONAL	1	TRUE	0	0.813097130287629	1		344	318	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710947	117710947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767371570	NA	P-0055097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	60	202	0	ENST00000368508.3:c.1325G>A	p.Arg442Gln	p.R442Q	ENST00000368508	NM_002944.2	442	cGg/cAg	12/43	NA	2	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.813097130287629	2		202	109	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131206	55131206	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	103	215	0	ENST00000257290.5:c.749C>A	p.Pro250His	p.P250H	ENST00000257290	NM_006206.4	250	cCt/cAt	5/23	0.813097130287629	4	FACETS	1	0.978	1			1	CLONAL	2	TRUE	NA	0.813097130287629	4		215	193	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040891	42040891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753360563	NA	P-0055097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	77	312	0	ENST00000219905.7:c.5269C>T	p.Arg1757Cys	p.R1757C	ENST00000219905	NM_001164273.1	1757	Cgt/Tgt	16/24	0.154032012342114	2	FACETS	0.928	0.831	1	0.464	0.415	0.514	INDETERMINATE	1	TRUE	0	0.813097130287629	2		312	204	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590694	189590694	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	31	265	0	ENST00000264731.3:c.1259C>A	p.Ser420Tyr	p.S420Y	ENST00000264731	NM_003722.4	420	tCc/tAc	10/14	0.312420323185574	3	FACETS	0.666	0.545	0.799	0.333	0.272	0.4	INDETERMINATE	1	TRUE	1	0.813097130287629	3		265	161	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133559	55133559	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	65	280	0	ENST00000257290.5:c.863A>C	p.Tyr288Ser	p.Y288S	ENST00000257290	NM_006206.4	288	tAc/tCc	6/23	0.813097130287629	4	FACETS	0.765	0.666	0.871			1	SUBCLONAL	1	TRUE	NA	0.813097130287629	4		280	379	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0055102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	1370	635	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.377439853717012	15	FACETS	1	0.995	1	1	0.995	1	CLONAL	13	TRUE	2	0.377439853717012	15		635	1868	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578380	7578384	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CTGAG	CTGAG	-	novel	NA	P-0055102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	170	1073	0	ENST00000269305.4:c.546_550del	p.Cys182Ter	p.C182*	ENST00000269305	NM_001126112.2	182	tgCTCAGat/tgat	5/11	0.307659037656774	2	FACETS	0.782	0.723	0.843	0.782	0.723	0.843	SUBCLONAL	2	TRUE	0	0.377439853717012	2		1073	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0055111-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	630	1050	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.690613555181378	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.690613555181378	1		1050	1131	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983971	2983971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055111-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	368	858	0	ENST00000396946.4:c.559C>T	p.Arg187Trp	p.R187W	ENST00000396946	NM_032415.4	187	Cgg/Tgg	5/25	1	2	FACETS	0.78	0.739	0.821	0.78	0.739	0.821	SUBCLONAL	1	TRUE	1	0.690613555181378	2		858	1367	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0055117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	153	635	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.199929960576887	4	FACETS	0.908	0.833	0.985	0.908	0.833	0.985	CLONAL	3	TRUE	1	0.213839201948118	4		635	638	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933732	39933732	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	44	525	0	ENST00000378444.4:c.867G>A	p.Trp289Ter	p.W289*	ENST00000378444	NM_001123385.1	289	tgG/tgA	4/15	0.213839201948118	1	FACETS	0.629	0.527	0.743	0.629	0.527	0.743	SUBCLONAL	1	TRUE	0	0.213839201948118	1		525	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573996	7574005	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTCTCGGA	AGCTCTCGGA	-	novel	NA	P-0055117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	57	605	0	ENST00000269305.4:c.1022_1031del	p.Phe341Ter	p.F341*	ENST00000269305	NM_001126112.2	341	tTCCGAGAGCTg/tg	10/11	0.213839201948118	1	FACETS	0.75	0.643	0.867	0.75	0.643	0.867	SUBCLONAL	1	TRUE	0	0.213839201948118	1		605	635	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520264	9520264	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs368616079	NA	P-0055117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	55	323	0	ENST00000353224.5:c.2005G>T	p.Val669Phe	p.V669F	ENST00000353224	NM_177990.2	669	Gtt/Ttt	10/10	0.213839201948118	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.213839201948118	1		323	397	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651334	52651334	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	60	412	0	ENST00000394830.3:c.1762G>T	p.Glu588Ter	p.E588*	ENST00000394830	NM_018313.4	588	Gaa/Taa	15/30	0.213839201948118	1	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	0	0.213839201948118	1		412	485	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0055118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	156	354	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.67	2		355	464	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692911	89692911	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121909241	NA	P-0055118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	76	409	0	ENST00000371953.3:c.395G>T	p.Gly132Val	p.G132V	ENST00000371953	NM_000314.4	132	gGt/gTt	5/9	0.620492542836151	1	FACETS	0.32	0.281	0.361	0.32	0.281	0.361	SUBCLONAL	1	TRUE	0	0.67	1		409	472	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410343	63410343	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1404477878	NA	P-0055118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	287	748	0	ENST00000330258.3:c.2824C>T	p.Arg942Ter	p.R942*	ENST00000330258	NM_152424.3	942	Cga/Tga	2/2	1	2	FACETS	0.826	0.777	0.876	0.826	0.777	0.876	CLONAL	1	TRUE	1	0.67	2		748	1037	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240750	55240750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1313	20755	717	2	ENST00000275493.2:c.1994G>A	p.Gly665Asp	p.G665D	ENST00000275493	NM_005228.3	665	gGc/gAc	17/28	0.620492542836151	33	FACETS	0.999	0.996	1			1	CLONAL	32	TRUE	NA	0.67	33		719	22068	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240729	55240729	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20711	1984	740	0	ENST00000275493.2:c.1973T>A	p.Leu658Gln	p.L658Q	ENST00000275493	NM_005228.3	658	cTg/cAg	17/28	0.620492542836151	33	FACETS	0.99	0.965	1			1	CLONAL	3	TRUE	NA	0.67	33		740	22695	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362500	40362500	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219718677	NA	P-0055118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	234	492	2	ENST00000293328.3:c.1696C>T	p.Arg566Trp	p.R566W	ENST00000293328	NM_012448.3	566	Cgg/Tgg	14/19	1	2	FACETS	0.875	0.819	0.933	0.875	0.819	0.933	CLONAL	1	TRUE	1	0.67	2		494	798	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0055119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	8	230	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	1	2	FACETS	0.058	0.036	0.085	0.058	0.036	0.085	SUBCLONAL	1	TRUE	1	0.742295132311796	2		230	374	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424809	49424810	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0055119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	25	206	0	ENST00000301067.7:c.13537_13538del	p.Ala4513SerfsTer61	p.A4513Sfs*61	ENST00000301067	NM_003482.3	4513	GCa/a	40/54	0.686665750464119	3	FACETS	0.257	0.202	0.32	0.129	0.101	0.16	SUBCLONAL	1	TRUE	1	0.742295132311796	3		206	359	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347975	347978	+	frameshift_variant	Frame_Shift_Del	DEL	AGGC	AGGC	-	novel	NA	P-0055119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	140	281	0	ENST00000262320.3:c.1528_1531del	p.Ala510ArgfsTer194	p.A510Rfs*194	ENST00000262320	NM_003502.3	510	GCCTcg/cg	6/11	0.742295132311796	3	FACETS	0.946	0.865	1	0.473	0.432	0.515	CLONAL	1	TRUE	1	0.742295132311796	3		281	547	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40860096	40860096	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs763625751	NA	P-0055119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	144	140	0	ENST00000428826.2:c.1540T>G	p.Ser514Ala	p.S514A	ENST00000428826		514	Tct/Gct	15/21	0.742295132311796	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.742295132311796	3		140	244	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630681	187630681	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0055119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	30	237	0	ENST00000441802.2:c.301A>T	p.Lys101Ter	p.K101*	ENST00000441802	NM_005245.3	101	Aaa/Taa	2/27	0.686665750464119	3	FACETS	0.749	0.612	0.9	0.374	0.306	0.45	SUBCLONAL	1	TRUE	1	0.742295132311796	3		237	148	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750433	133750433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867460090	NA	P-0055119-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	135	602	0	ENST00000318560.5:c.1264G>A	p.Val422Ile	p.V422I	ENST00000318560	NM_005157.4	422	Gtc/Atc	7/11	1	2	FACETS	0.74	0.678	0.805	0.74	0.678	0.805	SUBCLONAL	1	TRUE	1	0.806866281357607	2		602	452	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0055120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	260	492	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.712109328749989	2		492	730	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109873	115109873	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	193	425	0	ENST00000257566.3:c.2005C>T	p.Pro669Ser	p.P669S	ENST00000257566	NM_016569.3	669	Ccc/Tcc	8/8	0.712109328749989	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.712109328749989	1		425	321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578549	7578559	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGAGTACTGTA	GGAGTACTGTA	-	novel	NA	P-0055120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	270	733	0	ENST00000269305.4:c.376-5_381del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	0.712109328749989	1	FACETS	0.916	0.87	0.963	0.916	0.87	0.963	CLONAL	1	TRUE	0	0.712109328749989	1		733	533	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044576	12044576	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0055120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	144	310	0	ENST00000353533.5:c.1199G>C	p.Ter400SerextTer8	p.*400Sext*8	ENST00000353533	NM_003010.3	400	tGa/tCa	11/11	0.712109328749989	1	FACETS	0.972	0.906	1	0.972	0.906	1	CLONAL	1	TRUE	0	0.712109328749989	1		310	268	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813475	32813475	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	82	603	0	ENST00000354258.4:c.2308G>C	p.Asp770His	p.D770H	ENST00000354258	NM_000593.5	770	Gac/Cac	11/11	1	2	FACETS	0.319	0.28	0.359	0.319	0.28	0.359	SUBCLONAL	1	TRUE	1	0.712109328749989	2		603	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0055122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	297	705	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.57364535781261	2		705	738	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223289	36223289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755671444	NA	P-0055122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	333	895	2	ENST00000222270.7:c.5839G>A	p.Val1947Ile	p.V1947I	ENST00000222270	NM_014727.1	1947	Gtc/Atc	28/37	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.57364535781261	2		897	1082	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859425	151859425	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	158	389	0	ENST00000262189.6:c.11237del	p.Gly3746GlufsTer4	p.G3746Efs*4	ENST00000262189	NM_170606.2	3746	gGa/ga	43/59	1	2	FACETS	0.869	0.799	0.941	0.869	0.799	0.941	CLONAL	1	TRUE	1	0.57364535781261	2		389	634	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859440	151859440	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	168	410	0	ENST00000262189.6:c.11222G>C	p.Gly3741Ala	p.G3741A	ENST00000262189	NM_170606.2	3741	gGt/gCt	43/59	1	2	FACETS	0.897	0.827	0.969	0.897	0.827	0.969	CLONAL	1	TRUE	1	0.57364535781261	2		410	653	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609102	43609102	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs77316810	NA	P-0055123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	239	789	0	ENST00000355710.3:c.1858T>C	p.Cys620Arg	p.C620R	ENST00000355710	NM_020975.4	620	Tgc/Cgc	10/20	1	2	FACETS	0.81	0.76	0.862	1	0.994	1	CLONAL	2	TRUE	1	0.406336843765283	2		789	726	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	253	115	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.805840462414292	2		115	584	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0055124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	286	610	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.862	0.814	0.912	0.862	0.814	0.912	CLONAL	1	TRUE	1	0.805840462414292	2		610	823	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0055124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	320	563	2	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.805840462414292	2		565	786	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356179	66356179	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	283	481	0	ENST00000273854.3:c.1318G>A	p.Glu440Lys	p.E440K	ENST00000273854	NM_004439.5	440	Gag/Aag	5/18	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.805840462414292	2		481	687	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873782	151873782	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0055124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	241	444	0	ENST00000262189.6:c.8756C>G	p.Ser2919Ter	p.S2919*	ENST00000262189	NM_170606.2	2919	tCa/tGa	38/59	1	2	FACETS	0.976	0.918	1	0.976	0.918	1	CLONAL	1	TRUE	1	0.805840462414292	2		444	613	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708450	43708450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	343	549	0	ENST00000382044.4:c.4846C>T	p.Leu1616Phe	p.L1616F	ENST00000382044	NM_001141980.1	1616	Ctt/Ttt	22/28	1	2	FACETS	0.978	0.93	1	0.978	0.93	1	CLONAL	1	TRUE	1	0.805840462414292	2		549	870	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432191	121432191	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	389	661	0	ENST00000257555.6:c.938C>A	p.Ser313Tyr	p.S313Y	ENST00000257555		313	tCc/tAc	4/10	1	2	FACETS	0.994	0.948	1	0.994	0.948	1	CLONAL	1	TRUE	1	0.805840462414292	2		661	971	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715995	52715995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	397	619	0	ENST00000322088.6:c.560C>T	p.Ser187Phe	p.S187F	ENST00000322088	NM_014225.5	187	tCc/tTc	5/15	1	2	FACETS	0.967	0.922	1	0.967	0.922	1	CLONAL	1	TRUE	1	0.805840462414292	2		619	1019	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11308044	11308044	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	409	654	0	ENST00000361445.4:c.948C>A	p.Phe316Leu	p.F316L	ENST00000361445	NM_004958.3	316	ttC/ttA	7/58	1	2	FACETS	0.93	0.887	0.973	0.93	0.887	0.973	CLONAL	1	TRUE	1	0.805840462414292	2		654	1092	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028778	42028778	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1461667002	NA	P-0055124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	343	538	0	ENST00000219905.7:c.4316C>T	p.Ser1439Leu	p.S1439L	ENST00000219905	NM_001164273.1	1439	tCa/tTa	13/24	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.805840462414292	2		538	798	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473681	67473681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	382	596	1	ENST00000327367.4:c.761C>T	p.Ser254Phe	p.S254F	ENST00000327367	NM_005902.3	254	tCc/tTc	6/9	1	2	FACETS	0.972	0.926	1	0.972	0.926	1	CLONAL	1	TRUE	1	0.805840462414292	2		597	975	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897468	78897468	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	439	669	0	ENST00000306801.3:c.2803G>A	p.Glu935Lys	p.E935K	ENST00000306801	NM_020761.2	935	Gag/Aag	23/34	0.789062719097146	2	FACETS	1	0.977	1	0.516	0.493	0.539	CLONAL	1	TRUE	0	0.805840462414292	2		669	1056	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856550	45856550	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	462	757	0	ENST00000391945.4:c.1708G>C	p.Glu570Gln	p.E570Q	ENST00000391945	NM_000400.3	570	Gag/Cag	18/23	1	2	FACETS	0.989	0.947	1	0.989	0.947	1	CLONAL	1	TRUE	1	0.805840462414292	2		757	1159	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462411	89462411	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	257	430	0	ENST00000336596.2:c.1883G>C	p.Gly628Ala	p.G628A	ENST00000336596	NM_005233.5	628	gGa/gCa	10/17	1	2	FACETS	0.974	0.918	1	0.974	0.918	1	CLONAL	1	TRUE	1	0.805840462414292	2		430	655	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960137	134960137	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	292	499	0	ENST00000398015.3:c.2494G>C	p.Asp832His	p.D832H	ENST00000398015	NM_004441.4	832	Gat/Cat	13/16	1	2	FACETS	0.986	0.933	1	0.986	0.933	1	CLONAL	1	TRUE	1	0.805840462414292	2		499	735	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176662893	176662893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	169	294	0	ENST00000439151.2:c.3868C>T	p.Gln1290Ter	p.Q1290*	ENST00000439151	NM_022455.4	1290	Cag/Tag	6/23	0.805840462414292	1	FACETS	0.96	0.907	1	0.96	0.907	1	CLONAL	1	TRUE	0	0.805840462414292	1		294	261	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971177	21971177	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913382	NA	P-0055124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	312	399	0	ENST00000304494.5:c.181G>A	p.Glu61Lys	p.E61K	ENST00000304494	NM_000077.4	61	Gag/Aag	2/3	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.805840462414292	2		399	734	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399182	139399182	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381525257	NA	P-0055124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	444	679	0	ENST00000277541.6:c.4961C>T	p.Pro1654Leu	p.P1654L	ENST00000277541	NM_017617.3	1654	cCt/cTt	26/34	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.805840462414292	2		679	1082	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233586	69233589	+	missense_variant	Missense_Mutation	ONP	GTAG	GTAG	ATAA	novel	NA	P-0055124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	151	285	0	ENST00000462284.1:c.1451_1454delinsATAA	p.Cys484_Arg485delinsTyrLys	p.C484_R485delinsYK	ENST00000462284	NM_002392.5	484	tGTAGa/tATAAa	11/11	1	2	FACETS	0.907	0.838	0.978	0.907	0.838	0.978	CLONAL	1	TRUE	1	0.805840462414292	2		285	413	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	105	115	0				ENST00000310581	NM_198253.2	-/1132			0.155969362171081	3	FACETS	1	0.973	1	0.829	0.745	0.916	CLONAL	2	TRUE	0	0.176833516150909	3		115	520	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913273	NA	P-0055125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	25	514	0	ENST00000263967.3:c.1624G>C	p.Glu542Gln	p.E542Q	ENST00000263967	NM_006218.2	542	Gaa/Caa	10/21	1	2	FACETS	0.445	0.349	0.556	0.445	0.349	0.556	SUBCLONAL	1	TRUE	1	0.176833516150909	2		514	635	SUCCESS
FH	2271	MSKCC	GRCh37	1	241683007	241683007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	47	513	1	ENST00000366560.3:c.16C>T	p.Arg6Trp	p.R6W	ENST00000366560	NM_000143.3	6	Cgg/Tgg	1/10	1	2	FACETS	0.76	0.64	0.894	0.76	0.64	0.894	SUBCLONAL	1	TRUE	1	0.176833516150909	2		514	699	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236109	108236109	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	56	535	0	ENST00000278616.4:c.9045G>C	p.Glu3015Asp	p.E3015D	ENST00000278616	NM_000051.3	3015	gaG/gaC	63/63	1	2	FACETS	0.832	0.712	0.965	0.832	0.712	0.965	CLONAL	1	TRUE	1	0.176833516150909	2		535	761	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100754	8100754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749708566	NA	P-0055125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	72	855	0	ENST00000346208.3:c.728C>T	p.Ser243Phe	p.S243F	ENST00000346208		243	tCc/tTc	3/6	1	2	FACETS	0.773	0.673	0.881	0.773	0.673	0.881	SUBCLONAL	1	TRUE	1	0.176833516150909	2		855	1054	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420241	49420241	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	54	794	2	ENST00000301067.7:c.15508C>T	p.Gln5170Ter	p.Q5170*	ENST00000301067	NM_003482.3	5170	Cag/Tag	48/54	1	2	FACETS	0.599	0.509	0.697	0.599	0.509	0.697	SUBCLONAL	1	TRUE	1	0.176833516150909	2		796	1020	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0055125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	212	846	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	1	2	FACETS	1	0.943	1	1	0.994	1	CLONAL	2	TRUE	1	0.176833516150909	2		846	1177	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092799	27092799	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	89	618	0	ENST00000324856.7:c.2820G>C	p.Met940Ile	p.M940I	ENST00000324856	NM_006015.4	940	atG/atC	9/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.176833516150909	2		618	835	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193172964	193172964	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	48	293	1	ENST00000367435.3:c.1012C>T	p.Gln338Ter	p.Q338*	ENST00000367435	NM_024529.4	338	Cag/Tag	11/17	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.176833516150909	2		294	485	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600525	43600525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs562449603	NA	P-0055125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	51	860	0	ENST00000355710.3:c.751G>A	p.Glu251Lys	p.E251K	ENST00000355710	NM_020975.4	251	Gag/Aag	4/20	1	2	FACETS	0.612	0.519	0.716	0.612	0.519	0.716	SUBCLONAL	1	TRUE	1	0.176833516150909	2		860	942	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138867	64138867	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	77	778	0	ENST00000334205.4:c.2234C>A	p.Ser745Tyr	p.S745Y	ENST00000334205	NM_003942.2	745	tCc/tAc	17/17	1	2	FACETS	0.889	0.778	1	0.889	0.778	1	CLONAL	1	TRUE	1	0.176833516150909	2		778	980	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143452	108143452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	29	416	0	ENST00000278616.4:c.3157G>A	p.Asp1053Asn	p.D1053N	ENST00000278616	NM_000051.3	1053	Gat/Aat	22/63	1	2	FACETS	0.63	0.504	0.773	0.63	0.504	0.773	SUBCLONAL	1	TRUE	1	0.176833516150909	2		416	521	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163440	108163440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	64	619	0	ENST00000278616.4:c.4531G>A	p.Asp1511Asn	p.D1511N	ENST00000278616	NM_000051.3	1511	Gat/Aat	30/63	1	2	FACETS	0.869	0.751	0.998	0.869	0.751	0.998	CLONAL	1	TRUE	1	0.176833516150909	2		619	833	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165775	108165775	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	26	314	0	ENST00000278616.4:c.4898G>A	p.Arg1633Lys	p.R1633K	ENST00000278616	NM_000051.3	1633	aGa/aAa	32/63	1	2	FACETS	0.673	0.532	0.835	0.673	0.532	0.835	SUBCLONAL	1	TRUE	1	0.176833516150909	2		314	437	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245303	46245303	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	37	494	0	ENST00000334344.6:c.3397G>A	p.Ala1133Thr	p.A1133T	ENST00000334344	NM_152641.2	1133	Gca/Aca	15/21	1	2	FACETS	0.616	0.507	0.74	0.616	0.507	0.74	SUBCLONAL	1	TRUE	1	0.176833516150909	2		494	679	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488302	56488302	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	50	561	0	ENST00000267101.3:c.1821G>C	p.Gln607His	p.Q607H	ENST00000267101	NM_001982.3	607	caG/caC	15/28	1	2	FACETS	0.718	0.607	0.84	0.718	0.607	0.84	SUBCLONAL	1	TRUE	1	0.176833516150909	2		561	788	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459914	99459914	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1225643101	NA	P-0055125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	31	466	0	ENST00000268035.6:c.2010C>G	p.Ile670Met	p.I670M	ENST00000268035	NM_000875.3	670	atC/atG	10/21	1	2	FACETS	0.617	0.498	0.753	0.617	0.498	0.753	SUBCLONAL	1	TRUE	1	0.176833516150909	2		466	568	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459968	99459968	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	51	568	0	ENST00000268035.6:c.2064G>C	p.Lys688Asn	p.K688N	ENST00000268035	NM_000875.3	688	aaG/aaC	10/21	1	2	FACETS	0.799	0.678	0.933	0.799	0.678	0.933	CLONAL	1	TRUE	1	0.176833516150909	2		568	722	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2206763	2206763	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	63	528	0	ENST00000398665.3:c.823C>G	p.Leu275Val	p.L275V	ENST00000398665	NM_032482.2	275	Ctg/Gtg	10/28	1	2	FACETS	0.991	0.856	1	0.991	0.856	1	CLONAL	1	TRUE	1	0.176833516150909	2		528	719	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213568	2213568	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	56	729	0	ENST00000398665.3:c.1588C>T	p.Gln530Ter	p.Q530*	ENST00000398665	NM_032482.2	530	Cag/Tag	17/28	1	2	FACETS	0.633	0.541	0.735	0.633	0.541	0.735	SUBCLONAL	1	TRUE	1	0.176833516150909	2		729	1000	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4123794	4123794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1414051360	NA	P-0055125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	58	530	1	ENST00000262948.5:c.79G>A	p.Glu27Lys	p.E27K	ENST00000262948	NM_030662.3	27	Gag/Aag	1/11	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.176833516150909	2		531	611	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051430	13051430	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	40	489	0	ENST00000316448.5:c.778G>C	p.Glu260Gln	p.E260Q	ENST00000316448	NM_004343.3	260	Gag/Cag	6/9	1	2	FACETS	0.621	0.515	0.741	0.621	0.515	0.741	SUBCLONAL	1	TRUE	1	0.176833516150909	2		489	728	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902911	1902911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	46	563	0	ENST00000382891.5:c.530C>T	p.Ser177Phe	p.S177F	ENST00000382891	NM_133335.3	177	tCc/tTc	2/22	1	2	FACETS	0.697	0.586	0.821	0.697	0.586	0.821	SUBCLONAL	1	TRUE	1	0.176833516150909	2		563	746	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005102	150005102	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	29	498	0	ENST00000253339.5:c.1123C>G	p.Pro375Ala	p.P375A	ENST00000253339		375	Cca/Gca	3/7	1	2	FACETS	0.589	0.471	0.723	0.589	0.471	0.723	SUBCLONAL	1	TRUE	1	0.176833516150909	2		498	557	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099866	157099866	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	42	543	0	ENST00000346085.5:c.803C>G	p.Ser268Cys	p.S268C	ENST00000346085	NM_020732.3	268	tCc/tGc	1/20	1	2	FACETS	0.637	0.53	0.756	0.637	0.53	0.756	SUBCLONAL	1	TRUE	1	0.176833516150909	2		543	746	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394413	162394413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	29	366	0	ENST00000366898.1:c.655G>A	p.Asp219Asn	p.D219N	ENST00000366898	NM_004562.2	219	Gac/Aac	6/12	1	2	FACETS	0.696	0.558	0.854	0.696	0.558	0.854	SUBCLONAL	1	TRUE	1	0.176833516150909	2		366	471	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92355107	92355107	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	15	185	0	ENST00000265734.4:c.370G>A	p.Asp124Asn	p.D124N	ENST00000265734	NM_001259.6	124	Gat/Aat	4/8	1	2	FACETS	0.757	0.555	1	0.757	0.555	1	CLONAL	1	TRUE	1	0.176833516150909	2		185	224	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759865	133759865	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	150	807	0	ENST00000318560.5:c.2188G>C	p.Glu730Gln	p.E730Q	ENST00000318560	NM_005157.4	730	Gag/Cag	11/11	0.176833516150909	2	FACETS	0.845	0.771	0.922	0.845	0.771	0.922	CLONAL	2	TRUE	0	0.176833516150909	2		807	1004	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615116	43615116	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377767424	NA	P-0055127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	129	831	1	ENST00000355710.3:c.2530C>T	p.Arg844Trp	p.R844W	ENST00000355710	NM_020975.4	844	Cgg/Tgg	14/20	0.620914741722228	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.620914741722228	1		832	207	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577578	7577578	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	163	516	0	ENST00000269305.4:c.703A>G	p.Asn235Asp	p.N235D	ENST00000269305	NM_001126112.2	235	Aac/Gac	7/11	0.620914741722228	2	FACETS	0.991	0.933	1	0.991	0.933	1	CLONAL	2	TRUE	0	0.620914741722228	2		516	265	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929465	81929465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766133588	NA	P-0055127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	47	582	0	ENST00000359376.3:c.1126C>T	p.Arg376Trp	p.R376W	ENST00000359376	NM_002661.3	376	Cgg/Tgg	13/33	0.613641106900591	1	FACETS	0.495	0.422	0.573	0.495	0.422	0.573	SUBCLONAL	1	TRUE	0	0.620914741722228	1		582	211	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039413	49039423	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGGAGGGAA	CCTGGAGGGAA	-	novel	NA	P-0055127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	107	555	1	ENST00000267163.4:c.2399_2409del	p.Pro800HisfsTer11	p.P800Hfs*11	ENST00000267163	NM_000321.2	800	CCTGGAGGGAAc/c	23/27	0.620914741722228	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.620914741722228	1		556	200	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321702	62321702	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs771721817	NA	P-0055127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	108	639	0	ENST00000360203.5:c.2321T>C	p.Val774Ala	p.V774A	ENST00000360203	NM_001283009.1	774	gTc/gCc	26/35	0.613491290216954	2	FACETS	0.985	0.894	1	0.493	0.447	0.541	CLONAL	1	TRUE	0	0.620914741722228	2		639	353	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431050	181431050	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1270775176	NA	P-0055127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	89	727	0	ENST00000325404.1:c.902G>T	p.Gly301Val	p.G301V	ENST00000325404	NM_003106.3	301	gGc/gTc	1/1	0.305609664091022	3	FACETS	0.77	0.694	0.848	0.77	0.694	0.848	INDETERMINATE	2	TRUE	1	0.620914741722228	3		727	244	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553485	29553499	+	frameshift_variant	Frame_Shift_Del	DEL	GATTTGCCGACAAGC	GATTTGCCGACAAGC	AACAAGT	novel	NA	P-0055127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	90	695	0	ENST00000356175.3:c.2034_2048delinsAACAAGT	p.Ile679ThrfsTer18	p.I679Tfs*18	ENST00000356175	NM_000267.3	678	ccGATTTGCCGACAAGCc/ccAACAAGTc	18/57	0.469281382088307	4	FACETS	0.857	0.771	0.947	0.429	0.385	0.474	CLONAL	2	TRUE	0	0.620914741722228	4		695	274	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	175	115	0				ENST00000310581	NM_198253.2	-/1132			0.382255545872741	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.400973116737448	4		115	543	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	152	366	1				ENST00000310581	NM_198253.2	-/1132			0.382255545872741	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.400973116737448	4		367	475	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	199	499	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.382255545872741	4	FACETS	0.954	0.886	1	0.954	0.886	1	CLONAL	2	TRUE	2	0.400973116737448	4		499	729	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584555	187584555	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	294	462	0	ENST00000441802.2:c.3478C>T	p.Gln1160Ter	p.Q1160*	ENST00000441802	NM_005245.3	1160	Cag/Tag	3/27	0.400973116737448	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.400973116737448	3		462	525	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971029	21971029	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519852	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	821	622	1	ENST00000304494.5:c.329G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tGg/tAg	2/3	0.400973116737448	6	FACETS	0.964	0.944	0.984	1	0.997	1	CLONAL	7	TRUE	0	0.400973116737448	6		623	1093	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916193	9916193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	101	649	0	ENST00000330684.3:c.2096C>T	p.Pro699Leu	p.P699L	ENST00000330684	NM_001134407.1	699	cCc/cTc	10/13	0.400973116737448	3	FACETS	0.933	0.835	1	0.467	0.417	0.519	CLONAL	1	TRUE	1	0.400973116737448	3		649	648	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412252	139412252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057523819	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	877	964	0	ENST00000277541.6:c.1393G>A	p.Ala465Thr	p.A465T	ENST00000277541	NM_017617.3	465	Gcc/Acc	8/34	0.400973116737448	7	FACETS	1	0.982	1	1	0.982	1	CLONAL	5	TRUE	2	0.400973116737448	7		964	1726	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468474	89468474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	70	321	2	ENST00000336596.2:c.2008G>A	p.Glu670Lys	p.E670K	ENST00000336596	NM_005233.5	670	Gaa/Aaa	11/17	0.400973116737448	3	FACETS	1	0.935	1	0.553	0.485	0.626	CLONAL	1	TRUE	1	0.400973116737448	3		323	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519985	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	429	931	0	ENST00000269305.4:c.857A>C	p.Glu286Ala	p.E286A	ENST00000269305	NM_001126112.2	286	gAa/gCa	8/11	0.400973116737448	4	FACETS	0.933	0.892	0.975	0.933	0.892	0.975	CLONAL	3	TRUE	1	0.400973116737448	4		931	1071	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672686	47672686	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs267607948	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	66	462	0	ENST00000233146.2:c.1277-1G>A		p.X426_splice	ENST00000233146	NM_000251.2	426			0.400973116737448	3	FACETS	0.844	0.735	0.963	0.422	0.367	0.482	CLONAL	1	TRUE	1	0.400973116737448	3		462	468	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713514	30713514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	111	586	0	ENST00000295754.5:c.839C>T	p.Pro280Leu	p.P280L	ENST00000295754	NM_003242.5	280	cCc/cTc	4/7	0.400973116737448	3	FACETS	1	0.968	1	0.588	0.53	0.649	CLONAL	1	TRUE	1	0.400973116737448	3		586	565	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955096	17955096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201650430	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	344	967	1	ENST00000458235.1:c.131C>T	p.Ser44Phe	p.S44F	ENST00000458235	NM_000215.3	44	tCc/tTc	2/24	0.400973116737448	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.400973116737448	3		968	972	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482926	140482927	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs777474487	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	106	645	1	ENST00000288602.6:c.1208dup	p.Ala404CysfsTer9	p.A404Cfs*9	ENST00000288602	NM_004333.4	403	cct/ccCt	10/18	0.382255545872741	4	FACETS	0.92	0.825	1	0.46	0.412	0.511	CLONAL	1	TRUE	2	0.400973116737448	4		646	805	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777685	9777685	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	91	692	0	ENST00000377346.4:c.1020+1G>A		p.X340_splice	ENST00000377346	NM_005026.3	340			0.400973116737448	4	FACETS	0.728	0.645	0.816	0.243	0.215	0.272	SUBCLONAL	1	TRUE	1	0.400973116737448	4		692	874	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941013	71941013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1241	390	1050	0	ENST00000298229.2:c.889C>T	p.Pro297Ser	p.P297S	ENST00000298229	NM_001567.3	297	Ccg/Tcg	8/28	0.400973116737448	6	FACETS	1	0.982	1	0.537	0.509	0.566	CLONAL	2	TRUE	2	0.400973116737448	6		1050	1631	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401225	139401225	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1272	346	971	0	ENST00000277541.6:c.3844C>T	p.Gln1282Ter	p.Q1282*	ENST00000277541	NM_017617.3	1282	Cag/Tag	23/34	0.400973116737448	7	FACETS	1	0.978	1	0.427	0.403	0.452	CLONAL	2	TRUE	2	0.400973116737448	7		971	1618	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943379	71943379	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1165709765	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	220	615	0	ENST00000298229.2:c.1711C>T	p.Arg571Trp	p.R571W	ENST00000298229	NM_001567.3	571	Cgg/Tgg	14/28	0.400973116737448	6	FACETS	1	0.954	1	0.515	0.48	0.552	CLONAL	2	TRUE	2	0.400973116737448	6		615	959	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367320	50367320	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	173	554	0	ENST00000331340.3:c.127G>A	p.Gly43Arg	p.G43R	ENST00000331340	NM_006060.4	43	Gga/Aga	3/8	0.382255545872741	4	FACETS	0.893	0.825	0.963	0.893	0.825	0.963	CLONAL	2	TRUE	2	0.400973116737448	4		554	677	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739415	46739415	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377020524	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	235	433	0	ENST00000371975.4:c.1606C>T	p.Arg536Ter	p.R536*	ENST00000371975	NM_003579.3	536	Cga/Tga	14/18	0.400973116737448	4	FACETS	0.926	0.871	0.982	0.926	0.871	0.982	CLONAL	3	TRUE	1	0.400973116737448	4		433	591	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342713	118342713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	142	279	0	ENST00000534358.1:c.839C>T	p.Pro280Leu	p.P280L	ENST00000534358	NM_005933.3	280	cCt/cTt	3/36	0.400973116737448	5	FACETS	0.927	0.853	1	0.927	0.853	1	CLONAL	3	TRUE	2	0.400973116737448	5		279	408	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166098	118166098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	272	467	0	ENST00000369448.3:c.608C>T	p.Ser203Phe	p.S203F	ENST00000369448	NM_017709.3	203	tCt/tTt	2/2	0.400973116737448	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	1	0.400973116737448	4		467	580	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020486	69020486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	219	647	0	ENST00000288368.4:c.2858C>T	p.Ser953Phe	p.S953F	ENST00000288368	NM_024870.2	953	tCt/tTt	24/40	0.382255545872741	4	FACETS	0.953	0.889	1	0.953	0.889	1	CLONAL	2	TRUE	2	0.400973116737448	4		647	803	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952444	38952444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	137	342	0	ENST00000357387.3:c.2981G>A	p.Arg994Lys	p.R994K	ENST00000357387	NM_152756.3	994	aGg/aAg	30/38	0.382255545872741	4	FACETS	0.977	0.894	1	0.977	0.894	1	CLONAL	2	TRUE	2	0.400973116737448	4		342	490	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258586	16258586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	123	631	0	ENST00000375759.3:c.5851G>A	p.Gly1951Arg	p.G1951R	ENST00000375759	NM_015001.2	1951	Gga/Aga	11/15	0.400973116737448	4	FACETS	1	0.967	1	0.384	0.347	0.423	CLONAL	1	TRUE	1	0.400973116737448	4		631	746	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120460296	120460296	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	87	509	0	ENST00000256646.2:c.6019G>T	p.Asp2007Tyr	p.D2007Y	ENST00000256646	NM_024408.3	2007	Gac/Tac	33/34	0.400973116737448	4	FACETS	0.963	0.854	1	0.321	0.284	0.361	CLONAL	1	TRUE	1	0.400973116737448	4		509	631	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433827	49433827	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	406	1082	0	ENST00000301067.7:c.7726C>T	p.Gln2576Ter	p.Q2576*	ENST00000301067	NM_003482.3	2576	Caa/Taa	31/54	0.382255545872741	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.400973116737448	4		1082	1323	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504539	103504539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1333614535	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	119	312	0	ENST00000355739.4:c.160C>T	p.His54Tyr	p.H54Y	ENST00000355739	NM_000123.3	54	Cat/Tat	2/15	0.320876286605579	4	FACETS	0.951	0.865	1	0.951	0.865	1	CLONAL	2	TRUE	2	0.400973116737448	4		312	437	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636852	2636852	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	150	874	0	ENST00000342085.4:c.1301A>G	p.Glu434Gly	p.E434G	ENST00000342085	NM_002613.4	434	gAg/gGg	11/14	0.400973116737448	3	FACETS	0.941	0.86	1	0.471	0.43	0.514	CLONAL	1	TRUE	1	0.400973116737448	3		874	954	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273956	10273956	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	179	1059	1	ENST00000330684.3:c.313G>A	p.Asp105Asn	p.D105N	ENST00000330684	NM_001134407.1	105	Gac/Aac	2/13	0.400973116737448	3	FACETS	1	0.954	1	0.525	0.484	0.569	CLONAL	1	TRUE	1	0.400973116737448	3		1060	1020	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849466	89849467	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	252	811	0	ENST00000389301.3:c.1514_1515delinsTT	p.Ser505Phe	p.S505F	ENST00000389301	NM_000135.2	505	tCC/tTT	16/43	0.400973116737448	3	FACETS	0.96	0.901	1	0.96	0.901	1	CLONAL	2	TRUE	1	0.400973116737448	3		811	786	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577576	7577576	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	121	657	0	ENST00000269305.4:c.705del	p.Tyr236ThrfsTer11	p.Y236Tfs*11	ENST00000269305	NM_001126112.2	235	aaC/aa	7/11	0.400973116737448	4	FACETS	1	0.932	1	0.347	0.313	0.382	CLONAL	1	TRUE	1	0.400973116737448	4		657	813	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16005024	16005024	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	128	760	0	ENST00000268712.3:c.2230C>G	p.Arg744Gly	p.R744G	ENST00000268712	NM_006311.3	744	Cga/Gga	20/46	1	2	FACETS	0.982	0.892	1	0.982	0.892	1	CLONAL	1	TRUE	1	0.400973116737448	2		760	650	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368202	31368202	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	301	871	0	ENST00000328111.2:c.73G>T	p.Gly25Trp	p.G25W	ENST00000328111	NM_006892.3	25	Ggg/Tgg	2/23	0.382255545872741	4	FACETS	0.961	0.906	1	0.961	0.906	1	CLONAL	2	TRUE	2	0.400973116737448	4		871	1094	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977955	134977955	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	204	554	0	ENST00000398015.3:c.2948T>C	p.Met983Thr	p.M983T	ENST00000398015	NM_004441.4	983	aTg/aCg	16/16	0.400973116737448	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.400973116737448	3		554	592	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447492	187447492	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1343118986	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	290	794	1	ENST00000232014.4:c.701G>A	p.Ser234Asn	p.S234N	ENST00000232014	NM_001130845.1	234	aGt/aAt	5/10	0.400973116737448	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.400973116737448	3		795	818	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405098	405098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	315	662	0	ENST00000380956.4:c.1180C>T	p.Pro394Ser	p.P394S	ENST00000380956	NM_001195286.1	394	Cct/Tct	8/9	0.400973116737448	5	FACETS	0.987	0.935	1	0.987	0.935	1	CLONAL	3	TRUE	2	0.400973116737448	5		662	850	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056568	26056569	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	104	279	0	ENST00000343677.2:c.88_89delinsAA	p.Gly30Asn	p.G30N	ENST00000343677	NM_005319.3	30	GGt/AAt	1/1	0.400973116737448	5	FACETS	0.873	0.785	0.964	0.582	0.523	0.643	CLONAL	2	TRUE	2	0.400973116737448	5		279	476	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964430	93964430	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	230	596	0	ENST00000369303.4:c.2467G>A	p.Gly823Arg	p.G823R	ENST00000369303	NM_004440.3	823	Gga/Aga	14/17	0.400973116737448	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.400973116737448	3		596	601	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120819	94120820	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	94	600	0	ENST00000369303.4:c.231_232delinsAA	p.Met77_Glu78delinsIleLys	p.M77_E78delinsIK	ENST00000369303	NM_004440.3	77	atGGag/atAAag	3/17	0.400973116737448	3	FACETS	0.893	0.796	0.997	0.447	0.398	0.499	CLONAL	1	TRUE	1	0.400973116737448	3		600	630	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207525	29207525	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775138249	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	205	625	0	ENST00000240100.2:c.271G>A	p.Glu91Lys	p.E91K	ENST00000240100	NM_001394.6	91	Gag/Aag	1/4	0.382255545872741	4	FACETS	0.922	0.857	0.988	0.922	0.857	0.988	CLONAL	2	TRUE	2	0.400973116737448	4		625	777	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772656	135772656	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1033463168	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	531	585	0	ENST00000298552.3:c.2890G>A	p.Asp964Asn	p.D964N	ENST00000298552	NM_001162426.1	964	Gat/Aat	22/23	0.400973116737448	7	FACETS	0.966	0.93	1	0.966	0.93	1	CLONAL	5	TRUE	2	0.400973116737448	7		585	1098	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139794928	139794928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	601	622	0	ENST00000247668.2:c.322C>T	p.Pro108Ser	p.P108S	ENST00000247668	NM_021138.3	108	Ccc/Tcc	4/11	0.400973116737448	7	FACETS	0.976	0.942	1			1	CLONAL	5	TRUE	NA	0.400973116737448	7		622	1230	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939987	76939987	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	439	339	0	ENST00000373344.5:c.761C>T	p.Ser254Phe	p.S254F	ENST00000373344	NM_000489.3	254	tCc/tTc	9/35	0.400973116737448	4	FACETS	1	0.983	1			1	CLONAL	5	TRUE	NA	0.400973116737448	4		339	602	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259207	89259211	+	missense_variant	Missense_Mutation	ONP	GGAGA	GGAGA	AGAGG	novel	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	78	361	0	ENST00000336596.2:c.351_355delinsAGAGG	p.Thr119Ala	p.T119A	ENST00000336596	NM_005233.5	117	aaGGAGAca/aaAGAGGca	3/17	0.400973116737448	3	FACETS	0.975	0.86	1	0.488	0.43	0.549	CLONAL	1	TRUE	1	0.400973116737448	3		361	479	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5239052	5239054	+	missense_variant	Missense_Mutation	TNP	GTC	GTC	TTT	novel	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	166	917	0	ENST00000357368.4:c.1725_1727delinsAAA	p.Thr576Lys	p.T576K	ENST00000357368	NM_002850.3	575	ccGACg/ccAAAg	13/38	0.400973116737448	3	FACETS	1	0.955	1	0.53	0.486	0.575	CLONAL	1	TRUE	1	0.400973116737448	3		917	938	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5258081	5258083	+	missense_variant	Missense_Mutation	TNP	GCC	GCC	CCA	novel	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	229	661	0	ENST00000357368.4:c.651_653delinsTGG	p.Ala218Gly	p.A218G	ENST00000357368	NM_002850.3	217	gtGGCc/gtTGGc	8/38	0.400973116737448	3	FACETS	0.963	0.901	1	0.963	0.901	1	CLONAL	2	TRUE	1	0.400973116737448	3		661	712	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448297	56448301	+	missense_variant	Missense_Mutation	ONP	CGGGG	CGGGG	TGGGA	novel	NA	P-0055129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	124	844	0	ENST00000407977.2:c.346_350delinsTCCCA	p.Pro116_Arg117delinsSerHis	p.P116_R117delinsSH	ENST00000407977		116	CCCCGc/TCCCAc	3/10	0.400973116737448	4	FACETS	0.911	0.823	1	0.304	0.274	0.335	CLONAL	1	TRUE	1	0.400973116737448	4		844	951	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578217	7578217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	546	665	0	ENST00000269305.4:c.632C>T	p.Thr211Ile	p.T211I	ENST00000269305	NM_001126112.2	211	aCt/aTt	6/11	0.671649649927887	2	FACETS	0.859	0.834	0.884	0.859	0.834	0.884	CLONAL	2	TRUE	0	0.780574221420469	2		665	814	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878678	151878678	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	176	418	0	ENST00000262189.6:c.6267G>T	p.Gln2089His	p.Q2089H	ENST00000262189	NM_170606.2	2089	caG/caT	36/59	0.629565079473108	1	FACETS	0.92	0.866	0.972	0.92	0.866	0.972	CLONAL	1	TRUE	0	0.780574221420469	1		418	299	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56338936	56338936	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	62	41	0	ENST00000348428.3:c.61C>G	p.Leu21Val	p.L21V	ENST00000348428	NM_006785.3	21	Ctg/Gtg	1/17	0.778917628843077	3	FACETS	0.92	0.851	0.982			1	CLONAL	3	TRUE	NA	0.780574221420469	3		41	80	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593711	215593711	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	184	320	0	ENST00000260947.4:c.2023T>C	p.Cys675Arg	p.C675R	ENST00000260947	NM_000465.2	675	Tgc/Cgc	11/11	0.671649649927887	2	FACETS	0.788	0.745	0.831	0.788	0.745	0.831	SUBCLONAL	2	TRUE	0	0.780574221420469	2		320	299	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513522	149513522	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	226	664	0	ENST00000261799.4:c.681G>C	p.Gln227His	p.Q227H	ENST00000261799	NM_002609.3	227	caG/caC	5/23	0.701270083032	3	FACETS	0.845	0.787	0.904	0.422	0.393	0.452	CLONAL	1	TRUE	1	0.780574221420469	3		664	953	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056257	26056258	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0055130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	771	544	0	ENST00000343677.2:c.399_400del	p.Ala134SerfsTer18	p.A134Sfs*18	ENST00000343677	NM_005319.3	133	ggGGca/ggca	1/1	0.637082604540731	4	FACETS	0.887	0.869	0.905	0.887	0.869	0.905	CLONAL	4	TRUE	0	0.780574221420469	4		544	991	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2949714	2949714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	266	750	0	ENST00000396946.4:c.3230G>A	p.Arg1077Gln	p.R1077Q	ENST00000396946	NM_032415.4	1077	cGg/cAg	24/25	0.718127883354011	3	FACETS	0.851	0.797	0.905	0.425	0.398	0.453	CLONAL	1	TRUE	1	0.780574221420469	3		750	1114	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6031620	6031620	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	100	294	0	ENST00000265849.7:c.972C>G	p.Asn324Lys	p.N324K	ENST00000265849	NM_000535.5	324	aaC/aaG	9/15	0.718127883354011	3	FACETS	0.768	0.689	0.85	0.384	0.344	0.425	SUBCLONAL	1	TRUE	1	0.780574221420469	3		294	464	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	56	778	2	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.69	0.591	0.798	0.69	0.591	0.798	SUBCLONAL	1	TRUE	1	0.28	2		780	580	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	72	658	1	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.91	0.796	1	0.91	0.796	1	CLONAL	1	TRUE	1	0.28	2		659	565	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	29	392	3	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	1	2	FACETS	0.724	0.583	0.884	0.724	0.583	0.884	SUBCLONAL	1	TRUE	1	0.28	2		395	286	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	40	546	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.674	0.56	0.8	0.674	0.56	0.8	SUBCLONAL	1	TRUE	1	0.28	2		546	424	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003808	45003808	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	72	623	0	ENST00000558401.1:c.64C>T	p.Gln22Ter	p.Q22*	ENST00000558401	NM_004048.2	22	Cag/Tag	1/4	1	2	FACETS	0.987	0.864	1	0.987	0.864	1	CLONAL	1	TRUE	1	0.28	2		623	521	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660544	227660544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1801278	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	57	858	0	ENST00000305123.5:c.2911G>A	p.Gly971Arg	p.G971R	ENST00000305123	NM_005544.2	971	Ggg/Agg	1/2	1	2	FACETS	0.809	0.695	0.934	0.809	0.695	0.934	CLONAL	1	TRUE	1	0.28	2		858	503	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	64	657	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.828	0.718	0.948	0.828	0.718	0.948	CLONAL	1	TRUE	1	0.28	2		657	552	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	41	316	2	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.28	2		318	229	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084146	47084146	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	42	519	0	ENST00000409792.3:c.7143del	p.Ser2382LeufsTer29	p.S2382Lfs*29	ENST00000409792	NM_014159.6	2381	ccC/cc	17/21	1	2	FACETS	0.746	0.624	0.882	0.746	0.624	0.882	SUBCLONAL	1	TRUE	1	0.28	2		519	402	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247411	71247411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756099573	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	80	693	3	ENST00000318789.4:c.122C>T	p.Thr41Met	p.T41M	ENST00000318789	NM_032682.5	41	aCg/aTg	6/21	1	2	FACETS	0.889	0.783	1	0.889	0.783	1	CLONAL	1	TRUE	1	0.28	2		696	643	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619228	23619228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201657283	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	59	506	0	ENST00000261584.4:c.3307G>A	p.Val1103Met	p.V1103M	ENST00000261584	NM_024675.3	1103	Gtg/Atg	12/13	1	2	FACETS	0.81	0.698	0.933	0.81	0.698	0.933	CLONAL	1	TRUE	1	0.28	2		506	520	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421541	32421541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	85	669	1	ENST00000332351.3:c.1051G>A	p.Gly351Arg	p.G351R	ENST00000332351	NM_024426.4	351	Gga/Aga	6/10	1	2	FACETS	0.938	0.83	1	0.938	0.83	1	CLONAL	1	TRUE	1	0.28	2		670	647	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280036	18280036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	31	402	0	ENST00000222254.8:c.2119G>A	p.Ala707Thr	p.A707T	ENST00000222254	NM_005027.3	707	Gcg/Acg	16/16	1	2	FACETS	0.644	0.521	0.782	0.644	0.521	0.782	SUBCLONAL	1	TRUE	1	0.28	2		402	344	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210893	36210893	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	98	1161	3	ENST00000222270.7:c.649del	p.Arg217GlyfsTer22	p.R217Gfs*22	ENST00000222270	NM_014727.1	215	aCc/ac	3/37	1	2	FACETS	0.913	0.814	1	0.913	0.814	1	CLONAL	1	TRUE	1	0.28	2		1164	767	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372259	55372264	+	inframe_deletion	In_Frame_Del	DEL	CACCAG	CACCAG	-	rs564144826	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	26	502	1	ENST00000297316.4:c.972_977del	p.Gln324_His325del	p.Q324_H325del	ENST00000297316	NM_022454.3	317	CACCAG/-	2/2	1	2	FACETS	0.502	0.397	0.622	0.502	0.397	0.622	SUBCLONAL	1	TRUE	1	0.28	2		503	370	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136260	202136262	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs763516126	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	51	439	0	ENST00000358485.4:c.509_511del	p.Glu170del	p.E170del	ENST00000358485	NM_001080125.1	168	tcAGAa/tca	3/9	1	2	FACETS	0.99	0.844	1	0.99	0.844	1	CLONAL	1	TRUE	1	0.28	2		439	368	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79966113	79966114	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	32	409	0	ENST00000265081.6:c.781dup	p.Glu261GlyfsTer43	p.E261Gfs*43	ENST00000265081	NM_002439.4	259	-/G	4/24	1	2	FACETS	0.77	0.627	0.93	0.77	0.627	0.93	CLONAL	1	TRUE	1	0.28	2		409	297	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846165	68846165	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs587782856	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	62	570	0	ENST00000261769.5:c.1136C>T	p.Thr379Met	p.T379M	ENST00000261769	NM_004360.3	379	aCg/aTg	8/16	1	2	FACETS	0.9	0.779	1	0.9	0.779	1	CLONAL	1	TRUE	1	0.28	2		570	492	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222232	2222232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571375214	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	130	1128	0	ENST00000398665.3:c.3064G>A	p.Glu1022Lys	p.E1022K	ENST00000398665	NM_032482.2	1022	Gag/Aag	24/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.28	2		1128	782	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492636	56492636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769811937	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	54	618	0	ENST00000267101.3:c.2786G>A	p.Arg929Gln	p.R929Q	ENST00000267101	NM_001982.3	929	cGg/cAg	23/28	1	2	FACETS	0.735	0.628	0.852	0.735	0.628	0.852	SUBCLONAL	1	TRUE	1	0.28	2		618	525	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007694	62007694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746592632	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	66	588	0	ENST00000392795.3:c.173G>A	p.Arg58Gln	p.R58Q	ENST00000392795	NM_001039933.1	58	cGg/cAg	3/6	1	2	FACETS	0.968	0.842	1	0.968	0.842	1	CLONAL	1	TRUE	1	0.28	2		588	487	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753549	42753549	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754203690	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	110	1189	0	ENST00000222329.4:c.715C>T	p.Arg239Trp	p.R239W	ENST00000222329	NM_006494.2	239	Cgg/Tgg	4/4	1	2	FACETS	0.996	0.895	1	0.996	0.895	1	CLONAL	1	TRUE	1	0.28	2		1189	789	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739863	46739863	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	65	394	0	ENST00000371975.4:c.1664T>C	p.Val555Ala	p.V555A	ENST00000371975	NM_003579.3	555	gTt/gCt	15/18	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.28	2		394	443	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436138	51436138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	43	292	0	ENST00000262662.1:c.98C>T	p.Ala33Val	p.A33V	ENST00000262662		33	gCa/gTa	3/4	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.28	2		292	298	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226573228	226573228	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1179367477	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	64	791	1	ENST00000366794.5:c.988C>T	p.Arg330Trp	p.R330W	ENST00000366794	NM_001618.3	330	Cgg/Tgg	7/23	1	2	FACETS	0.825	0.715	0.944	0.825	0.715	0.944	CLONAL	1	TRUE	1	0.28	2		792	554	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977144	85977144	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	27	301	0	ENST00000263360.6:c.751del	p.Ile251Ter	p.I251*	ENST00000263360	NM_003797.3	249	gAa/ga	8/12	1	2	FACETS	0.897	0.718	1	0.897	0.718	1	CLONAL	1	TRUE	1	0.28	2		301	215	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864588	57864588	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	79	1027	3	ENST00000228682.2:c.2070del	p.Ser691AlafsTer28	p.S691Afs*28	ENST00000228682	NM_005269.2	689	Ccc/cc	12/12	1	2	FACETS	0.813	0.715	0.919	0.813	0.715	0.919	CLONAL	1	TRUE	1	0.28	2		1030	694	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133208911	133208911	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	45	505	0	ENST00000320574.5:c.6320A>G	p.Tyr2107Cys	p.Y2107C	ENST00000320574	NM_006231.2	2107	tAc/tGc	45/49	1	2	FACETS	0.81	0.682	0.95	0.81	0.682	0.95	CLONAL	1	TRUE	1	0.28	2		505	397	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549014	21549014	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777319923	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	23	252	0	ENST00000382592.4:c.3262G>A	p.Val1088Met	p.V1088M	ENST00000382592	NM_014572.2	1088	Gtg/Atg	8/8	1	2	FACETS	0.996	0.783	1	0.996	0.783	1	CLONAL	1	TRUE	1	0.28	2		252	165	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019576	42019576	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	46	483	0	ENST00000219905.7:c.3629G>A	p.Arg1210Gln	p.R1210Q	ENST00000219905	NM_001164273.1	1210	cGg/cAg	10/24	1	2	FACETS	0.987	0.834	1	0.987	0.834	1	CLONAL	1	TRUE	1	0.28	2		483	333	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896522	78896522	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	115	940	0	ENST00000306801.3:c.2521-2A>G		p.X841_splice	ENST00000306801	NM_020761.2	841			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.28	2		940	737	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214145	36214145	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	120	1059	2	ENST00000222270.7:c.2975del	p.Gly992AlafsTer17	p.G992Afs*17	ENST00000222270	NM_014727.1	991	Ggg/gg	6/37	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.28	2		1061	777	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221682	36221682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754543672	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	128	1091	0	ENST00000222270.7:c.5351G>A	p.Arg1784Gln	p.R1784Q	ENST00000222270	NM_014727.1	1784	cGg/cAg	26/37	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.28	2		1091	775	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224110	36224111	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	61	702	1	ENST00000222270.7:c.6666dup	p.Thr2223HisfsTer80	p.T2223Hfs*80	ENST00000222270	NM_014727.1	2220	-/C	28/37	1	2	FACETS	0.721	0.622	0.829	0.721	0.622	0.829	SUBCLONAL	1	TRUE	1	0.28	2		703	604	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978930	25978930	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	51	397	0	ENST00000435504.4:c.993C>G	p.Phe331Leu	p.F331L	ENST00000435504		331	ttC/ttG	10/13	0.27719288814398	2	FACETS	1	0.901	1	0.536	0.457	0.621	CLONAL	1	TRUE	0	0.28	2		397	340	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445436	29445436	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	100	775	2	ENST00000389048.3:c.3397G>T	p.Gly1133Cys	p.G1133C	ENST00000389048	NM_004304.4	1133	Ggc/Tgc	21/29	0.27719288814398	2	FACETS	1	0.949	1	0.551	0.493	0.613	CLONAL	1	TRUE	0	0.28	2		777	648	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272515	142272515	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	57	541	0	ENST00000350721.4:c.2600A>T	p.Asp867Val	p.D867V	ENST00000350721	NM_001184.3	867	gAt/gTt	12/47	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.28	2		541	372	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521308	187521309	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs1395974139	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	86	617	0	ENST00000441802.2:c.11846_11847del	p.Tyr3949CysfsTer22	p.Y3949Cfs*22	ENST00000441802	NM_005245.3	3949	tAT/t	22/27	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.28	2		617	542	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194697	29194697	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	113	1121	2	ENST00000240100.2:c.1031C>T	p.Ala344Val	p.A344V	ENST00000240100	NM_001394.6	344	gCt/gTt	4/4	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.28	2		1123	768	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521337	8521337	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	41	427	0	ENST00000356435.5:c.901A>T	p.Thr301Ser	p.T301S	ENST00000356435		301	Acc/Tcc	9/35	1	2	FACETS	0.893	0.746	1	0.893	0.746	1	CLONAL	1	TRUE	1	0.28	2		427	328	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797351	135797351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777484049	NA	P-0055131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	35	275	0	ENST00000298552.3:c.518C>T	p.Ala173Val	p.A173V	ENST00000298552	NM_001162426.1	173	gCg/gTg	7/23	1	2	FACETS	0.847	0.697	1	0.847	0.697	1	CLONAL	1	TRUE	1	0.28	2		275	295	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841030	15841030	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	207	714	1	ENST00000307771.7:c.1114G>A	p.Asp372Asn	p.D372N	ENST00000307771	NM_005089.3	372	Gac/Aac	11/11	0.681679410715236	1	FACETS	0.979	0.922	1	0.979	0.922	1	CLONAL	1	TRUE	0	0.681679410715236	1		715	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0055134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	545	859	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.681679410715236	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.681679410715236	2		859	781	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553474	29553474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779546178	NA	P-0055134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	245	641	0	ENST00000356175.3:c.2023G>A	p.Gly675Arg	p.G675R	ENST00000356175	NM_000267.3	675	Gga/Aga	18/57	0.681679410715236	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.681679410715236	1		641	466	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849015	156849015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771421920	NA	P-0055134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	420	771	1	ENST00000524377.1:c.1907C>T	p.Ala636Val	p.A636V	ENST00000524377	NM_002529.3	636	gCg/gTg	15/17	0.57134452627264	5	FACETS	1	0.975	1	0.689	0.657	0.722	CLONAL	2	TRUE	2	0.681679410715236	5		772	1206	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	477	559	3	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	0.27680204794029	2	FACETS	1	0.97	1	1	0.998	1	CLONAL	5	TRUE	0	0.27680204794029	2		562	689	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	89	368	0	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.27680204794029	2		368	476	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797331	45797331	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0055136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	95	611	0	ENST00000450313.1:c.1186+2T>C		p.X396_splice	ENST00000450313	NM_012222.2	396			0.27680204794029	2	FACETS	1	0.971	1	0.633	0.565	0.705	CLONAL	1	TRUE	0	0.27680204794029	2		611	542	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307262	65307262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1293957402	NA	P-0055136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	56	421	1	ENST00000342505.4:c.2426G>A	p.Arg809Gln	p.R809Q	ENST00000342505	NM_002227.2	809	cGg/cAg	18/25	0.27680204794029	2	FACETS	0.966	0.83	1	0.483	0.415	0.557	CLONAL	1	TRUE	0	0.27680204794029	2		422	419	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0055136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	79	552	2	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	0.27680204794029	2	FACETS	0.971	0.855	1	0.485	0.427	0.548	CLONAL	1	TRUE	0	0.27680204794029	2		554	588	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624242	89624242	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	65	216	0	ENST00000371953.3:c.18del	p.Glu7ArgfsTer17	p.E7Rfs*17	ENST00000371953	NM_000314.4	6	Aaa/aa	1/9	1	2	FACETS	1	0.934	1	1	0.983	1	CLONAL	2	TRUE	1	0.27680204794029	2		216	215	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653841	89653841	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786204855	NA	P-0055136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	187	378	0	ENST00000371953.3:c.139A>G	p.Arg47Gly	p.R47G	ENST00000371953	NM_000314.4	47	Agg/Ggg	2/9	1	2	FACETS	0.858	0.799	0.918	1	0.994	1	CLONAL	3	TRUE	1	0.27680204794029	2		378	525	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123246935	123246935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113014479	NA	P-0055136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	155	391	0	ENST00000358487.5:c.1990C>T	p.Arg664Trp	p.R664W	ENST00000358487	NM_000141.4	664	Cgg/Tgg	15/18	1	2	FACETS	0.891	0.824	0.959	1	0.993	1	CLONAL	3	TRUE	1	0.27680204794029	2		391	419	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0055136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	269	577	1	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	1	2	FACETS	1	0.975	1	1	0.996	1	CLONAL	3	TRUE	1	0.27680204794029	2		578	616	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0055136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	242	763	17	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.27680204794029	2		780	767	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748607	43748608	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0055136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	83	931	0	ENST00000382044.4:c.2198dup	p.Gln734SerfsTer7	p.Q734Sfs*7	ENST00000382044	NM_001141980.1	733	cct/ccCt	12/28	1	2	FACETS	0.621	0.546	0.701	0.621	0.546	0.701	SUBCLONAL	1	TRUE	1	0.27680204794029	2		931	966	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225905	2225905	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	71	818	0	ENST00000326181.6:c.1697C>T	p.Ala566Val	p.A566V	ENST00000326181	NM_032271.2	566	gCt/gTt	18/21	0.116264334649137	3	FACETS	0.709	0.617	0.808	0.354	0.308	0.404	INDETERMINATE	1	TRUE	1	0.27680204794029	3		818	824	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827459	72827459	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	261	734	0	ENST00000268489.5:c.9122A>C	p.Asp3041Ala	p.D3041A	ENST00000268489	NM_006885.3	3041	gAc/gCc	9/10	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.27680204794029	2		734	767	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871746	37871746	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142783371	NA	P-0055136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	409	813	0	ENST00000269571.5:c.1270G>A	p.Val424Ile	p.V424I	ENST00000269571		424	Gtc/Atc	11/27	0.164765502027318	3	FACETS	1	0.983	1	1	0.996	1	INDETERMINATE	3	TRUE	1	0.27680204794029	3		813	1057	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78811765	78811765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	55	633	2	ENST00000306801.3:c.1180C>T	p.Pro394Ser	p.P394S	ENST00000306801	NM_020761.2	394	Ccg/Tcg	10/34	0.27680204794029	2	FACETS	0.598	0.51	0.693	0.299	0.255	0.347	SUBCLONAL	1	TRUE	0	0.27680204794029	2		635	665	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387696	17387698	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0055136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	219	683	0	ENST00000359435.4:c.772_774del	p.Glu258del	p.E258del	ENST00000359435	NM_001033549.1	255	aAGGag/aag	8/9	1	2	FACETS	1	0.969	1	1	0.994	1	CLONAL	2	TRUE	1	0.27680204794029	2		683	744	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211939	36211939	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519283	NA	P-0055136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	415	1016	0	ENST00000222270.7:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000222270	NM_014727.1	564	Cga/Tga	3/37	1	2	FACETS	0.967	0.923	1	1	0.997	1	CLONAL	3	TRUE	1	0.27680204794029	2		1016	1034	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617532	158617532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	197	537	0	ENST00000263640.3:c.1124G>A	p.Arg375His	p.R375H	ENST00000263640	NM_001105.4	375	cGt/cAt	9/11	1	2	FACETS	0.834	0.777	0.891	1	0.994	1	CLONAL	3	TRUE	1	0.27680204794029	2		537	569	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738280	190738280	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	123	279	0	ENST00000441310.2:c.2532del	p.Tyr845MetfsTer3	p.Y845Mfs*3	ENST00000441310	NM_000534.4	844	ttC/tt	12/13	1	2	FACETS	0.965	0.886	1	1	0.992	1	CLONAL	3	TRUE	1	0.27680204794029	2		279	307	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24134057	24134057	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	174	412	0	ENST00000263121.7:c.214del	p.Thr72GlnfsTer13	p.T72Qfs*13	ENST00000263121	NM_003073.3	70	Aaa/aa	2/9	1	2	FACETS	1	0.981	1	1	0.994	1	CLONAL	2	TRUE	1	0.27680204794029	2		412	537	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231179	142231179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483924843	NA	P-0055136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	38	599	2	ENST00000350721.4:c.4775C>T	p.Ala1592Val	p.A1592V	ENST00000350721	NM_001184.3	1592	gCa/gTa	27/47	1	2	FACETS	0.392	0.323	0.469	0.392	0.323	0.469	SUBCLONAL	1	TRUE	1	0.27680204794029	2		601	701	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589591	67589592	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATAACACTCAGTTGA	novel	NA	P-0055136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	114	243	0	ENST00000274335.5:c.1367_1368insGAATAACACTCAGTT	p.Gln455_Phe456insLeuAsnAsnThrGln	p.Q455_F456insLNNTQ	ENST00000274335		452	tat/tATAACACTCAGTTGAat	10/15	1	2	FACETS	1	0.97	1	1	0.99	1	CLONAL	2	TRUE	1	0.27680204794029	2		243	356	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482927	140482927	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	76	664	3	ENST00000288602.6:c.1208del	p.Pro403LeufsTer8	p.P403Lfs*8	ENST00000288602	NM_004333.4	403	cCt/ct	10/18	1	2	FACETS	0.792	0.695	0.898	0.792	0.695	0.898	SUBCLONAL	1	TRUE	1	0.27680204794029	2		667	693	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748399150	NA	P-0055136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	127	978	9	ENST00000220592.5:c.1806del	p.Ala603ProfsTer92	p.A603Pfs*92	ENST00000220592	NM_012154.3	602	ccC/cc	14/19	1	2	FACETS	0.937	0.848	1	0.937	0.848	1	CLONAL	1	TRUE	1	0.27680204794029	2		987	979	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs730881677	NA	P-0055136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	69	436	0	ENST00000304494.5:c.151-1G>T		p.X51_splice	ENST00000304494	NM_000077.4	51			0.145953851951525	0	FACETS	0.875	0.765	0.993			1	INDETERMINATE	1	TRUE	0	0.27680204794029	0		436	412	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798864	135798864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372215435	NA	P-0055136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	62	237	0	ENST00000298552.3:c.379G>A	p.Val127Ile	p.V127I	ENST00000298552	NM_001162426.1	127	Gtt/Att	6/23	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.27680204794029	2		237	313	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0055137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	38	325	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.997	0.824	1	0.997	0.824	1	CLONAL	1	TRUE	1	0.15	2		326	508	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0055137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	17	327	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.64	0.477	0.835	0.64	0.477	0.835	SUBCLONAL	1	TRUE	1	0.15	2		327	354	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857125	9857125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138415164	NA	P-0055137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	25	385	1	ENST00000330684.3:c.4276G>A	p.Glu1426Lys	p.E1426K	ENST00000330684	NM_001134407.1	1426	Gag/Aag	13/13	1	2	FACETS	0.842	0.663	1	0.842	0.663	1	CLONAL	1	TRUE	1	0.15	2		386	396	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508727	148508727	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	37	421	0	ENST00000320356.2:c.1937A>G	p.Tyr646Cys	p.Y646C	ENST00000320356	NM_004456.4	646	tAc/tGc	16/20	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.15	2		421	409	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0055138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	17	668	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.273	0.203	0.358	0.273	0.203	0.358	SUBCLONAL	1	TRUE	1	0.2	2		668	622	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0055138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	96	406	0	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	1	1	FACETS	0.919	0.823	1	1	0.986	1	CLONAL	2	TRUE	0	0.2	1		406	470	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720726	89720726	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs878853944	NA	P-0055138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	20	186	2	ENST00000371953.3:c.877G>T	p.Gly293Ter	p.G293*	ENST00000371953	NM_000314.4	293	Gga/Tga	8/9	0.21646636692239	1	FACETS	1	0.782	1	1	0.782	1	CLONAL	1	TRUE	0	0.2	1		188	177	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114806	108114814	+	inframe_deletion	In_Frame_Del	DEL	AATTTTTGG	AATTTTTGG	-	novel	NA	P-0055138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	44	575	0	ENST00000278616.4:c.624_632del	p.Lys208_Asp211delinsAsn	p.K208_D211delinsN	ENST00000278616	NM_000051.3	208	aAATTTTTGGac/aac	6/63	1	2	FACETS	0.635	0.531	0.75	0.635	0.531	0.75	SUBCLONAL	1	TRUE	1	0.2	2		575	693	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163480	108163480	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	59	604	0	ENST00000278616.4:c.4571T>G	p.Leu1524Arg	p.L1524R	ENST00000278616	NM_000051.3	1524	cTt/cGt	30/63	1	2	FACETS	0.86	0.739	0.992	0.86	0.739	0.992	CLONAL	1	TRUE	1	0.2	2		604	686	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42381426	42381426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782760214	NA	P-0055138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	46	775	2	ENST00000221972.3:c.52C>T	p.Leu18Phe	p.L18F	ENST00000221972	NM_021601.3	18	Ctc/Ttc	1/5	1	2	FACETS	0.579	0.486	0.682	0.579	0.486	0.682	SUBCLONAL	1	TRUE	1	0.2	2		777	795	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910722	29910722	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs199474425	NA	P-0055138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	92	952	0	ENST00000376809.5:c.262A>T	p.Thr88Ser	p.T88S	ENST00000376809	NM_002116.7	88	Aca/Tca	2/8	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.2	2		952	814	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	95	115	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.2	2		115	713	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804212	43804212	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs867404262	NA	P-0055139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	73	433	0	ENST00000372470.3:c.213-1G>A		p.X71_splice	ENST00000372470	NM_005373.2	71			1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.2	2		433	689	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936149	71936149	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	43	350	0	ENST00000298229.2:c.121G>C	p.Asp41His	p.D41H	ENST00000298229	NM_001567.3	41	Gat/Cat	1/28	1	2	FACETS	0.664	0.554	0.785	0.664	0.554	0.785	SUBCLONAL	1	TRUE	1	0.2	2		350	648	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042214	42042214	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	54	495	0	ENST00000219905.7:c.6409G>C	p.Glu2137Gln	p.E2137Q	ENST00000219905	NM_001164273.1	2137	Gaa/Caa	17/24	1	2	FACETS	0.66	0.562	0.768	0.66	0.562	0.768	SUBCLONAL	1	TRUE	1	0.2	2		495	818	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042721	42042721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	64	464	0	ENST00000219905.7:c.6916G>A	p.Glu2306Lys	p.E2306K	ENST00000219905	NM_001164273.1	2306	Gaa/Aaa	17/24	1	2	FACETS	0.816	0.706	0.937	0.816	0.706	0.937	CLONAL	1	TRUE	1	0.2	2		464	784	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645514	67645514	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	40	210	0	ENST00000264010.4:c.779A>G	p.Lys260Arg	p.K260R	ENST00000264010	NM_006565.3	260	aAa/aGa	3/12	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.2	2		210	389	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89839711	89839711	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1461108636	NA	P-0055139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	105	737	0	ENST00000389301.3:c.1982G>C	p.Arg661Thr	p.R661T	ENST00000389301	NM_000135.2	661	aGa/aCa	22/43	1	2	FACETS	0.848	0.758	0.945	0.848	0.758	0.945	CLONAL	1	TRUE	1	0.2	2		737	1238	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736892	736892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	81	586	1	ENST00000314574.4:c.1207C>T	p.Leu403Phe	p.L403F	ENST00000314574	NM_005433.3	403	Ctt/Ttt	10/12	1	2	FACETS	0.707	0.621	0.8	0.707	0.621	0.8	SUBCLONAL	1	TRUE	1	0.2	2		587	1146	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374350	15374350	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	87	578	1	ENST00000263377.2:c.1222G>T	p.Glu408Ter	p.E408*	ENST00000263377	NM_058243.2	408	Gag/Tag	7/20	1	2	FACETS	0.831	0.734	0.936	0.831	0.734	0.936	CLONAL	1	TRUE	1	0.2	2		579	1047	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926885	112926885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507544	NA	P-0055140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	158	757	0	ENST00000351677.2:c.1505C>T	p.Ser502Leu	p.S502L	ENST00000351677	NM_002834.3	502	tCa/tTa	13/16	0.281123529028941	5	FACETS	0.989	0.907	1	0.494	0.453	0.537	CLONAL	2	FALSE	1	0.281123529028941	5		757	808	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781371	NA	P-0055140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	40	1020	0	ENST00000269305.4:c.328C>T	p.Arg110Cys	p.R110C	ENST00000269305	NM_001126112.2	110	Cgt/Tgt	4/11	1	2	FACETS	0.381	0.315	0.454	0.381	0.315	0.454	SUBCLONAL	1	FALSE	1	0.281123529028941	2		1020	747	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498415	89498415	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	35	362	0	ENST00000336596.2:c.2387T>A	p.Ile796Lys	p.I796K	ENST00000336596	NM_005233.5	796	aTa/aAa	14/17	1	2	FACETS	0.666	0.546	0.8	0.666	0.546	0.8	SUBCLONAL	1	FALSE	1	0.281123529028941	2		362	374	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740467	58740467	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs773389405	NA	P-0055140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	57	662	0	ENST00000305921.3:c.1372C>T	p.Arg458Ter	p.R458*	ENST00000305921	NM_003620.3	458	Cga/Tga	6/6	0.11723708347553	4	FACETS	0.813	0.697	0.94	0.407	0.348	0.47	INDETERMINATE	1	FALSE	2	0.281123529028941	4		662	639	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0055140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	17	272	0	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	0.281123529028941	4	FACETS	0.316	0.235	0.414			1	SUBCLONAL	1	FALSE	NA	0.281123529028941	4		272	490	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968586	55968586	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	57	762	2	ENST00000263923.4:c.2077A>T	p.Asn693Tyr	p.N693Y	ENST00000263923	NM_002253.2	693	Aat/Tat	14/30	1	2	FACETS	0.57	0.488	0.659	0.57	0.488	0.659	SUBCLONAL	1	FALSE	1	0.281123529028941	2		764	712	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872100	76872100	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	195	245	0	ENST00000373344.5:c.5547del	p.Tyr1850ThrfsTer2	p.Y1850Tfs*2	ENST00000373344	NM_000489.3	1849	taC/ta	22/35	1	1	FACETS	1	0.981	1	1	0.996	1	CLONAL	5	FALSE	0	0.281123529028941	1		245	232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0055141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	74	796	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.16	2		796	857	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676174	29676177	+	frameshift_variant	Frame_Shift_Del	DEL	CAGT	CAGT	-	novel	NA	P-0055141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	38	322	0	ENST00000356175.3:c.7166_7169del	p.Val2389GlufsTer7	p.V2389Efs*7	ENST00000356175	NM_000267.3	2388	aCAGTc/ac	48/57	1	2	FACETS	1	0.828	1	1	0.828	1	CLONAL	1	TRUE	1	0.16	2		322	474	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180037003	180037003	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	21	674	0	ENST00000261937.6:c.3709C>T	p.Pro1237Ser	p.P1237S	ENST00000261937	NM_182925.4	1237	Ccc/Tcc	28/30	1	2	FACETS	0.397	0.304	0.506	0.397	0.304	0.506	SUBCLONAL	1	TRUE	1	0.16	2		674	662	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0055141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	76	796	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.225983524668245	1	FACETS	0.921	0.808	1	0.921	0.808	1	CLONAL	1	FALSE	0	0.225983524668245	1		796	648	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676174	29676177	+	frameshift_variant	Frame_Shift_Del	DEL	CAGT	CAGT	-	novel	NA	P-0055141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	36	322	0	ENST00000356175.3:c.7166_7169del	p.Val2389GlufsTer7	p.V2389Efs*7	ENST00000356175	NM_000267.3	2388	aCAGTc/ac	48/57	1	2	FACETS	0.836	0.688	1	0.836	0.688	1	CLONAL	1	FALSE	1	0.225983524668245	2		322	381	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180037003	180037003	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	54	674	0	ENST00000261937.6:c.3709C>T	p.Pro1237Ser	p.P1237S	ENST00000261937	NM_182925.4	1237	Ccc/Tcc	28/30	0.225983524668245	3	FACETS	0.851	0.726	0.988	0.426	0.363	0.494	CLONAL	1	FALSE	1	0.225983524668245	3		674	625	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	118	115	0				ENST00000310581	NM_198253.2	-/1132			0.3	0	FACETS	0.388	0.355	0.422			1	INDETERMINATE	1	TRUE	0	0.66	0		115	313	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58725409	58725409	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	193	563	0	ENST00000305921.3:c.983T>C	p.Met328Thr	p.M328T	ENST00000305921	NM_003620.3	328	aTg/aCg	4/6	1	2	FACETS	0.92	0.855	0.986	0.92	0.855	0.986	CLONAL	1	TRUE	1	0.66	2		563	636	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482437	56482437	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	86	552	0	ENST00000267101.3:c.985A>G	p.Lys329Glu	p.K329E	ENST00000267101	NM_001982.3	329	Aaa/Gaa	8/28	0.336658944753267	3	FACETS	0.863	0.77	0.96	0.863	0.77	0.96	CLONAL	2	FALSE	1	0.336658944753267	3		552	346	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173724	108173724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	27	323	0	ENST00000278616.4:c.5464G>A	p.Glu1822Lys	p.E1822K	ENST00000278616	NM_000051.3	1822	Gaa/Aaa	36/63	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	FALSE	1	0.336658944753267	2		323	128	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983120	201983121	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0055143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	97	574	0	ENST00000359651.3:c.970_971dup	p.Met324IlefsTer2	p.M324Ifs*2	ENST00000359651		323	-/AT	7/8	0.336658944753267	3	FACETS	0.858	0.764	0.957	0.429	0.382	0.479	CLONAL	1	FALSE	1	0.336658944753267	3		574	785	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557462	21557462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	118	546	0	ENST00000382592.4:c.2383G>A	p.Asp795Asn	p.D795N	ENST00000382592	NM_014572.2	795	Gat/Aat	5/8	0.206946211421921	2	FACETS	0.89	0.81	0.972	0.89	0.81	0.972	CLONAL	2	FALSE	0	0.336658944753267	2		546	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577128	7577130	+	missense_variant	Missense_Mutation	TNP	AAA	AAA	TTT	novel	NA	P-0055143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	266	625	0	ENST00000269305.4:c.808_810inv	p.Phe270Lys	p.F270K	ENST00000269305	NM_001126112.2	270	TTT/AAA	8/11	0.336658944753267	3	FACETS	1	0.99	1	0.818	0.771	0.867	CLONAL	2	FALSE	0	0.336658944753267	3		625	752	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285713	87285713	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	172	635	0	ENST00000277120.3:c.50G>T	p.Gly17Val	p.G17V	ENST00000277120		17	gGc/gTc	2/19	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.336658944753267	2		635	716	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525996	41525996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	14	350	1	ENST00000263253.7:c.1271G>A	p.Arg424Lys	p.R424K	ENST00000263253	NM_001429.3	424	aGa/aAa	5/31	0.336658944753267	1	FACETS	0.567	0.413	0.75	0.567	0.413	0.75	SUBCLONAL	1	FALSE	0	0.336658944753267	1		351	122	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482437	56482437	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055143-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	198	552	0	ENST00000267101.3:c.985A>G	p.Lys329Glu	p.K329E	ENST00000267101	NM_001982.3	329	Aaa/Gaa	8/28	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.476129287949062	2		552	791	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173724	108173724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055143-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	91	323	0	ENST00000278616.4:c.5464G>A	p.Glu1822Lys	p.E1822K	ENST00000278616	NM_000051.3	1822	Gaa/Aaa	36/63	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.476129287949062	2		323	329	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983120	201983121	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0055143-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	249	574	0	ENST00000359651.3:c.970_971dup	p.Met324IlefsTer2	p.M324Ifs*2	ENST00000359651		323	-/AT	7/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.476129287949062	2		574	964	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557462	21557462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055143-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	228	546	0	ENST00000382592.4:c.2383G>A	p.Asp795Asn	p.D795N	ENST00000382592	NM_014572.2	795	Gat/Aat	5/8	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.476129287949062	2		546	928	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577128	7577130	+	missense_variant	Missense_Mutation	TNP	AAA	AAA	TTT	novel	NA	P-0055143-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	323	625	0	ENST00000269305.4:c.808_810inv	p.Phe270Lys	p.F270K	ENST00000269305	NM_001126112.2	270	TTT/AAA	8/11	0.436117203643738	2	FACETS	0.774	0.733	0.815	0.774	0.733	0.815	SUBCLONAL	2	TRUE	0	0.476129287949062	2		625	877	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285713	87285713	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055143-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	265	635	0	ENST00000277120.3:c.50G>T	p.Gly17Val	p.G17V	ENST00000277120		17	gGc/gTc	2/19	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.476129287949062	2		635	1015	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136002	64136002	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055143-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	383	781	1	ENST00000334205.4:c.1263C>A	p.Ser421Arg	p.S421R	ENST00000334205	NM_003942.2	421	agC/agA	11/17	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.476129287949062	2		782	1481	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	61	423	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.608	0.527	0.695	0.608	0.527	0.695	SUBCLONAL	1	TRUE	1	0.546773453568861	2		424	367	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	75	496	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.634	0.557	0.715	0.634	0.557	0.715	SUBCLONAL	1	TRUE	1	0.546773453568861	2		496	433	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	64	778	2	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.422	0.365	0.483	0.422	0.365	0.483	SUBCLONAL	1	TRUE	1	0.546773453568861	2		780	555	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	13	633	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	1	2	FACETS	0.076	0.054	0.104	0.076	0.054	0.104	SUBCLONAL	1	TRUE	1	0.546773453568861	2		633	622	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	84	811	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.496	0.438	0.557	0.496	0.438	0.557	SUBCLONAL	1	TRUE	1	0.546773453568861	2		815	620	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296358	15296358	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	82	976	2	ENST00000263388.2:c.2084del	p.Pro695ArgfsTer165	p.P695Rfs*165	ENST00000263388	NM_000435.2	695	cCg/cg	13/33	1	2	FACETS	0.491	0.433	0.553	0.491	0.433	0.553	SUBCLONAL	1	TRUE	1	0.546773453568861	2		978	611	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	13	421	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.128	0.091	0.174	0.128	0.091	0.174	SUBCLONAL	1	TRUE	1	0.546773453568861	2		421	371	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	67	341	4	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	1	2	FACETS	0.759	0.664	0.859	0.759	0.664	0.859	SUBCLONAL	1	TRUE	1	0.546773453568861	2		345	323	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263973	104263974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776579	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	60	336	2	ENST00000369902.3:c.71dup	p.Ala25GlyfsTer23	p.A25Gfs*23	ENST00000369902	NM_016169.3	22	gcc/gCcc	1/12	1	2	FACETS	0.688	0.597	0.786	0.688	0.597	0.786	SUBCLONAL	1	TRUE	1	0.546773453568861	2		338	319	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560500	65560500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs387906651	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	110	556	0	ENST00000358664.4:c.97C>T	p.Arg33Ter	p.R33*	ENST00000358664	NM_002382.4	33	Cga/Tga	3/5	1	2	FACETS	0.774	0.698	0.853	0.774	0.698	0.853	SUBCLONAL	1	TRUE	1	0.546773453568861	2		556	520	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952006	178952006	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	10	394	0	ENST00000263967.3:c.3061T>C	p.Tyr1021His	p.Y1021H	ENST00000263967	NM_006218.2	1021	Tac/Cac	21/21	1	2	FACETS	0.126	0.084	0.178	0.126	0.084	0.178	SUBCLONAL	1	TRUE	1	0.546773453568861	2		394	291	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692922	89692922	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201044	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	108	596	0	ENST00000371953.3:c.406T>C	p.Cys136Arg	p.C136R	ENST00000371953	NM_000314.4	136	Tgt/Cgt	5/9	1	2	FACETS	0.964	0.871	1	0.964	0.871	1	CLONAL	1	TRUE	1	0.546773453568861	2		596	410	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	76	599	2	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.595	0.524	0.672	0.595	0.524	0.672	SUBCLONAL	1	TRUE	1	0.546773453568861	2		601	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	145	901	0	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	1	2	FACETS	0.707	0.646	0.771	0.707	0.646	0.771	SUBCLONAL	1	TRUE	1	0.546773453568861	2		901	750	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560493	65560493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	102	582	0	ENST00000358664.4:c.104G>A	p.Arg35His	p.R35H	ENST00000358664	NM_002382.4	35	cGt/cAt	3/5	1	2	FACETS	0.693	0.622	0.769	0.693	0.622	0.769	SUBCLONAL	1	TRUE	1	0.546773453568861	2		582	538	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951964	178951964	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	97	410	0	ENST00000263967.3:c.3019G>C	p.Gly1007Arg	p.G1007R	ENST00000263967	NM_006218.2	1007	Ggc/Cgc	21/21	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.546773453568861	2		410	330	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390585	139390585	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111627256	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	196	1033	1	ENST00000277541.6:c.7606G>A	p.Val2536Ile	p.V2536I	ENST00000277541	NM_017617.3	2536	Gtc/Atc	34/34	1	2	FACETS	0.785	0.727	0.845	0.785	0.727	0.845	SUBCLONAL	1	TRUE	1	0.546773453568861	2		1034	913	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444659	78444659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs908264837	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	86	573	1	ENST00000370768.2:c.30del	p.Ser11LeufsTer43	p.S11Lfs*43	ENST00000370768	NM_003902.3	10	ccC/cc	1/20	1	2	FACETS	0.534	0.473	0.599	0.534	0.473	0.599	SUBCLONAL	1	TRUE	1	0.546773453568861	2		574	589	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158465	26158467	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs766586530	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	69	758	0	ENST00000289316.2:c.73_75del	p.Lys25del	p.K25del	ENST00000289316	NM_138720.2	23	cAGAag/cag	1/2	1	2	FACETS	0.319	0.277	0.365	0.319	0.277	0.365	SUBCLONAL	1	TRUE	1	0.546773453568861	2		758	791	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579582	7579583	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	200	701	0	ENST00000269305.4:c.104dup	p.Leu35PhefsTer8	p.L35Ffs*8	ENST00000269305	NM_001126112.2	35	ttg/ttTg	4/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.546773453568861	2		701	618	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101125	41101125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756719404	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	142	733	0	ENST00000373198.4:c.1231G>A	p.Gly411Ser	p.G411S	ENST00000373198	NM_133170.3	411	Ggc/Agc	8/32	1	2	FACETS	0.886	0.811	0.965	0.886	0.811	0.965	CLONAL	1	TRUE	1	0.546773453568861	2		733	586	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916929	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	17	470	0	ENST00000263967.3:c.316G>T	p.Gly106Cys	p.G106C	ENST00000263967	NM_006218.2	106	Ggc/Tgc	2/21	1	2	FACETS	0.182	0.136	0.238	0.182	0.136	0.238	SUBCLONAL	1	TRUE	1	0.546773453568861	2		470	341	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621035	1621035	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	88	1045	0	ENST00000344749.5:c.1025del	p.Pro342ArgfsTer52	p.P342Rfs*52	ENST00000344749	NM_001136139.2	342	cCg/cg	13/19	1	2	FACETS	0.389	0.344	0.437	0.389	0.344	0.437	SUBCLONAL	1	TRUE	1	0.546773453568861	2		1045	828	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163356	47163356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	33	413	0	ENST00000409792.3:c.2770G>A	p.Ala924Thr	p.A924T	ENST00000409792	NM_014159.6	924	Gca/Aca	3/21	1	2	FACETS	0.501	0.41	0.602	0.501	0.41	0.602	SUBCLONAL	1	TRUE	1	0.546773453568861	2		413	241	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	123	894	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.778	0.706	0.854	0.778	0.706	0.854	SUBCLONAL	1	TRUE	1	0.546773453568861	2		896	578	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878106	48878106	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1469887040	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	24	85	0	ENST00000267163.4:c.62del	p.Pro21ArgfsTer44	p.P21Rfs*44	ENST00000267163	NM_000321.2	20	Ccc/cc	1/27	1	2	FACETS	0.61	0.483	0.751	0.61	0.483	0.751	SUBCLONAL	1	TRUE	1	0.546773453568861	2		85	144	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860603	3860603	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	30	647	0	ENST00000262367.5:c.975+1G>A		p.X325_splice	ENST00000262367	NM_004380.2	325			1	2	FACETS	0.186	0.149	0.228	0.186	0.149	0.228	SUBCLONAL	1	TRUE	1	0.546773453568861	2		647	590	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300040	137300040	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	66	875	0	ENST00000481739.1:c.331del	p.Leu111TrpfsTer57	p.L111Wfs*57	ENST00000481739	NM_002957.4	109	Ccc/cc	3/10	1	2	FACETS	0.32	0.277	0.366	0.32	0.277	0.366	SUBCLONAL	1	TRUE	1	0.546773453568861	2		875	755	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916840	48916841	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs1566186125	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	52	321	0	ENST00000267163.4:c.371_372del	p.Ile124ArgfsTer6	p.I124Rfs*6	ENST00000267163	NM_000321.2	124	ATa/a	3/27	1	2	FACETS	0.712	0.611	0.821	0.712	0.611	0.821	SUBCLONAL	1	TRUE	1	0.546773453568861	2		321	267	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456887	32456887	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1049509674	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	64	530	0	ENST00000332351.3:c.5A>G	p.Gln2Arg	p.Q2R	ENST00000332351	NM_024426.4	2	cAg/cGg	1/10	1	2	FACETS	0.647	0.563	0.737	0.647	0.563	0.737	SUBCLONAL	1	TRUE	1	0.546773453568861	2		530	362	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936950	48936950	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	47	332	0	ENST00000267163.4:c.719-1G>A		p.X240_splice	ENST00000267163	NM_000321.2	240			1	2	FACETS	0.71	0.605	0.825	0.71	0.605	0.825	SUBCLONAL	1	TRUE	1	0.546773453568861	2		332	242	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572669	141572669	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	132	681	0	ENST00000220592.5:c.401G>T	p.Trp134Leu	p.W134L	ENST00000220592	NM_012154.3	134	tGg/tTg	4/19	1	2	FACETS	0.87	0.793	0.95	0.87	0.793	0.95	CLONAL	1	TRUE	1	0.546773453568861	2		681	555	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741924	17741924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444003943	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	29	293	0	ENST00000250003.3:c.595G>A	p.Ala199Thr	p.A199T	ENST00000250003	NM_002478.4	199	Gcg/Acg	1/3	1	2	FACETS	0.44	0.355	0.536	0.44	0.355	0.536	SUBCLONAL	1	TRUE	1	0.546773453568861	2		293	241	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492686	56492686	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	56	464	0	ENST00000407977.2:c.252+1G>A		p.X84_splice	ENST00000407977		84			1	2	FACETS	0.595	0.513	0.685	0.595	0.513	0.685	SUBCLONAL	1	TRUE	1	0.546773453568861	2		464	344	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181822	56181822	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	81	367	0	ENST00000399503.3:c.4046A>G	p.Tyr1349Cys	p.Y1349C	ENST00000399503	NM_005921.1	1349	tAc/tGc	17/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.546773453568861	2		367	264	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661656	227661656	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777791193	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	70	708	3	ENST00000305123.5:c.1799G>A	p.Arg600His	p.R600H	ENST00000305123	NM_005544.2	600	cGc/cAc	1/2	1	2	FACETS	0.621	0.544	0.704	0.621	0.544	0.704	SUBCLONAL	1	TRUE	1	0.546773453568861	2		711	412	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974254	18974254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149336516	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	26	581	0	ENST00000262803.5:c.2608G>A	p.Val870Ile	p.V870I	ENST00000262803	NM_002911.3	870	Gtc/Atc	19/24	1	2	FACETS	0.183	0.144	0.228	0.183	0.144	0.228	SUBCLONAL	1	TRUE	1	0.546773453568861	2		581	519	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439922	56439923	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCGGCACCGGATGC	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	61	723	0	ENST00000407977.2:c.656_669dup	p.Pro224AlafsTer200	p.P224Afs*200	ENST00000407977		223	-/GCATCCGGTGCCGC	6/10	1	2	FACETS	0.274	0.236	0.316	0.274	0.236	0.316	SUBCLONAL	1	TRUE	1	0.546773453568861	2		723	814	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511684	46511684	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs762065227	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	100	557	0	ENST00000262741.5:c.1093C>T	p.Arg365Ter	p.R365*	ENST00000262741	NM_003629.3	365	Cga/Tga	9/10	1	2	FACETS	0.754	0.677	0.836	0.754	0.677	0.836	SUBCLONAL	1	TRUE	1	0.546773453568861	2		557	485	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443653	49443653	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs773215579	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	111	760	0	ENST00000301067.7:c.3718A>G	p.Met1240Val	p.M1240V	ENST00000301067	NM_003482.3	1240	Atg/Gtg	11/54	1	2	FACETS	0.709	0.639	0.782	0.709	0.639	0.782	SUBCLONAL	1	TRUE	1	0.546773453568861	2		760	573	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166089	118166089	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	81	472	0	ENST00000369448.3:c.599A>T	p.Asn200Ile	p.N200I	ENST00000369448	NM_017709.3	200	aAt/aTt	2/2	1	2	FACETS	0.788	0.699	0.882	0.788	0.699	0.882	SUBCLONAL	1	TRUE	1	0.546773453568861	2		472	376	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956140	175956140	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749431618	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	32	431	0	ENST00000367669.3:c.2072G>A	p.Arg691Gln	p.R691Q	ENST00000367669	NM_022457.5	691	cGa/cAa	18/20	0.546773453568861	3	FACETS	0.316	0.256	0.385	0.158	0.128	0.193	SUBCLONAL	1	TRUE	1	0.546773453568861	3		431	471	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570763	226570763	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	138	546	0	ENST00000366794.5:c.1133C>T	p.Ala378Val	p.A378V	ENST00000366794	NM_001618.3	378	gCt/gTt	8/23	0.546773453568861	3	FACETS	0.857	0.781	0.937	0.429	0.39	0.469	CLONAL	1	TRUE	1	0.546773453568861	3		546	750	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624268	89624269	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	120	397	0	ENST00000371953.3:c.43dup	p.Arg15LysfsTer29	p.R15Kfs*29	ENST00000371953	NM_000314.4	14	-/A	1/9	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.546773453568861	2		397	360	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112764476	112764476	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	67	484	0	ENST00000369452.4:c.1085T>C	p.Met362Thr	p.M362T	ENST00000369452	NM_007373.3	362	aTg/aCg	5/9	1	2	FACETS	0.723	0.632	0.82	0.723	0.632	0.82	SUBCLONAL	1	TRUE	1	0.546773453568861	2		484	339	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943307	71943307	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	103	707	0	ENST00000298229.2:c.1639T>C	p.Ser547Pro	p.S547P	ENST00000298229	NM_001567.3	547	Tcc/Ccc	14/28	1	2	FACETS	0.611	0.547	0.678	0.611	0.547	0.678	SUBCLONAL	1	TRUE	1	0.546773453568861	2		707	617	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076693	102076693	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	84	538	0	ENST00000282441.5:c.872A>G	p.Gln291Arg	p.Q291R	ENST00000282441	NM_001130145.2	291	cAg/cGg	5/9	1	2	FACETS	0.61	0.54	0.684	0.61	0.54	0.684	SUBCLONAL	1	TRUE	1	0.546773453568861	2		538	504	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435130	49435130	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	23	631	0	ENST00000301067.7:c.6423del	p.Phe2142SerfsTer2	p.F2142Sfs*2	ENST00000301067	NM_003482.3	2141	ggG/gg	31/54	1	2	FACETS	0.189	0.146	0.238	0.189	0.146	0.238	SUBCLONAL	1	TRUE	1	0.546773453568861	2		631	446	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879620	123879620	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs945284217	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	88	409	0	ENST00000330479.4:c.316C>T	p.Arg106Trp	p.R106W	ENST00000330479	NM_020382.3	106	Cgg/Tgg	4/9	1	2	FACETS	0.779	0.695	0.869	0.779	0.695	0.869	SUBCLONAL	1	TRUE	1	0.546773453568861	2		409	413	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518655	103518655	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	29	302	0	ENST00000355739.4:c.2243A>T	p.Asn748Ile	p.N748I	ENST00000355739	NM_000123.3	748	aAt/aTt	10/15	1	2	FACETS	0.428	0.345	0.521	0.428	0.345	0.521	SUBCLONAL	1	TRUE	1	0.546773453568861	2		302	248	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524687	103524687	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146344855	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	84	438	0	ENST00000355739.4:c.2818G>A	p.Val940Met	p.V940M	ENST00000355739	NM_000123.3	940	Gtg/Atg	13/15	1	2	FACETS	0.635	0.563	0.712	0.635	0.563	0.712	SUBCLONAL	1	TRUE	1	0.546773453568861	2		438	484	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832070	72832071	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	93	600	0	ENST00000268489.5:c.4510_4511del	p.Ser1504ProfsTer5	p.S1504Pfs*5	ENST00000268489	NM_006885.3	1504	AGc/c	9/10	1	2	FACETS	0.741	0.662	0.825	0.741	0.662	0.825	SUBCLONAL	1	TRUE	1	0.546773453568861	2		600	459	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16041495	16041495	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	16	249	0	ENST00000268712.3:c.1384A>T	p.Ile462Phe	p.I462F	ENST00000268712	NM_006311.3	462	Att/Ttt	13/46	1	2	FACETS	0.217	0.16	0.285	0.217	0.16	0.285	SUBCLONAL	1	TRUE	1	0.546773453568861	2		249	270	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117117	7117117	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	70	791	0	ENST00000302850.5:c.4099G>T	p.Gly1367Cys	p.G1367C	ENST00000302850	NM_000208.2	1367	Ggc/Tgc	22/22	1	2	FACETS	0.417	0.363	0.475	0.417	0.363	0.475	SUBCLONAL	1	TRUE	1	0.546773453568861	2		791	614	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184326	7184326	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	47	555	0	ENST00000302850.5:c.974+1G>A		p.X325_splice	ENST00000302850	NM_000208.2	325			1	2	FACETS	0.297	0.25	0.349	0.297	0.25	0.349	SUBCLONAL	1	TRUE	1	0.546773453568861	2		555	578	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184339	7184339	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	54	606	0	ENST00000302850.5:c.962T>C	p.Met321Thr	p.M321T	ENST00000302850	NM_000208.2	321	aTg/aCg	3/22	1	2	FACETS	0.302	0.257	0.351	0.302	0.257	0.351	SUBCLONAL	1	TRUE	1	0.546773453568861	2		606	655	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383146	42383146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	39	838	0	ENST00000221972.3:c.166C>T	p.His56Tyr	p.H56Y	ENST00000221972	NM_021601.3	56	Cac/Tac	2/5	1	2	FACETS	0.246	0.204	0.294	0.246	0.204	0.294	SUBCLONAL	1	TRUE	1	0.546773453568861	2		838	579	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61722715	61722715	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	57	378	0	ENST00000401558.2:c.922T>C	p.Tyr308His	p.Y308H	ENST00000401558	NM_003400.3	308	Tac/Cac	11/25	1	2	FACETS	0.555	0.478	0.638	0.555	0.478	0.638	SUBCLONAL	1	TRUE	1	0.546773453568861	2		378	376	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750400	39750400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	68	418	0	ENST00000361337.2:c.2015C>T	p.Ala672Val	p.A672V	ENST00000361337	NM_003286.2	672	gCc/gTc	19/21	1	2	FACETS	0.723	0.633	0.819	0.723	0.633	0.819	SUBCLONAL	1	TRUE	1	0.546773453568861	2		418	344	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916642	178916642	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	51	348	1	ENST00000263967.3:c.29T>C	p.Leu10Pro	p.L10P	ENST00000263967	NM_006218.2	10	cTg/cCg	2/21	1	2	FACETS	0.774	0.664	0.892	0.774	0.664	0.892	SUBCLONAL	1	TRUE	1	0.546773453568861	2		349	241	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181813	56181813	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	16	340	0	ENST00000399503.3:c.4037T>G	p.Val1346Gly	p.V1346G	ENST00000399503	NM_005921.1	1346	gTt/gGt	17/20	1	2	FACETS	0.227	0.167	0.298	0.227	0.167	0.298	SUBCLONAL	1	TRUE	1	0.546773453568861	2		340	258	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755595	57755595	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	108	713	1	ENST00000274289.3:c.192C>A	p.His64Gln	p.H64Q	ENST00000274289	NM_006622.3	64	caC/caA	1/14	1	2	FACETS	0.745	0.671	0.823	0.745	0.671	0.823	SUBCLONAL	1	TRUE	1	0.546773453568861	2		714	530	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151833925	151833925	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	58	560	0	ENST00000262189.6:c.14728A>G	p.Met4910Val	p.M4910V	ENST00000262189	NM_170606.2	4910	Atg/Gtg	59/59	1	2	FACETS	0.374	0.321	0.431	0.374	0.321	0.431	SUBCLONAL	1	TRUE	1	0.546773453568861	2		560	568	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801036	135801036	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	89	506	0	ENST00000298552.3:c.301C>A	p.Pro101Thr	p.P101T	ENST00000298552	NM_001162426.1	101	Cca/Aca	5/23	1	2	FACETS	0.647	0.576	0.723	0.647	0.576	0.723	SUBCLONAL	1	TRUE	1	0.546773453568861	2		506	503	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923754	39923754	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	241	901	0	ENST00000378444.4:c.3337A>T	p.Ser1113Cys	p.S1113C	ENST00000378444	NM_001123385.1	1113	Agc/Tgc	7/15	0.286734085034436	1	FACETS	1	0.949	1	1	0.949	1	INDETERMINATE	1	TRUE	0	0.546773453568861	1		901	634	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222515	53222515	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0055144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	100	818	0	ENST00000375401.3:c.4318-1G>A		p.X1440_splice	ENST00000375401	NM_004187.3	1440			0.286734085034436	1	FACETS	0.542	0.486	0.601	0.542	0.486	0.601	INDETERMINATE	1	TRUE	0	0.546773453568861	1		818	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578528	7578528	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	864	954	0	ENST00000269305.4:c.402T>G	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	ttT/ttG	5/11	0.734134134703461	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.734134134703461	2		954	1113	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027158	48027158	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0055145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	212	463	0	ENST00000234420.5:c.2036T>A	p.Leu679Ter	p.L679*	ENST00000234420	NM_000179.2	679	tTg/tAg	4/10	0.734134134703461	2	FACETS	0.999	0.935	1	0.5	0.467	0.533	CLONAL	1	TRUE	0	0.734134134703461	2		463	578	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566788	212566788	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	157	356	0	ENST00000342788.4:c.1393A>C	p.Asn465His	p.N465H	ENST00000342788	NM_005235.2	465	Aac/Cac	12/28	1	2	FACETS	0.886	0.818	0.955	0.886	0.818	0.955	CLONAL	1	TRUE	1	0.734134134703461	2		356	483	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0055146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	43	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.565007900250292	2		622	147	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562482	21562483	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGGCG	rs550642106	NA	P-0055146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	10	132	1	ENST00000382592.4:c.1431_1436dup	p.Pro479_Ala480dup	p.P479_A480dup	ENST00000382592	NM_014572.2	479	ccg/ccCGCCCCg	4/8	1	2	FACETS	0.22	0.149	0.309	0.22	0.149	0.309	SUBCLONAL	1	TRUE	1	0.565007900250292	2		133	161	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792755	33792757	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs746430067	NA	P-0055146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	8	54	0	ENST00000498907.2:c.564_566del	p.Pro189del	p.P189del	ENST00000498907	NM_004364.3	188	ccGCCc/ccc	1/1	0.370407967482691	1	FACETS	0.089	0.057	0.131	0.089	0.057	0.131	SUBCLONAL	1	TRUE	0	0.565007900250292	1		54	228	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716220	243716220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	15	495	0	ENST00000263826.5:c.974G>A	p.Arg325Gln	p.R325Q	ENST00000263826	NM_005465.4	325	cGa/cAa	10/13	0.565007900250292	3	FACETS	0.283	0.206	0.374	0.141	0.103	0.187	SUBCLONAL	1	TRUE	1	0.565007900250292	3		495	241	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405969	49405969	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	77	312	0	ENST00000418115.1:c.169T>G	p.Leu57Val	p.L57V	ENST00000418115	NM_001664.2	57	Ttg/Gtg	3/5	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.2	2		312	747	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983782	15983782	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	48	301	0	ENST00000268712.3:c.3340del	p.Ser1114AlafsTer18	p.S1114Afs*18	ENST00000268712	NM_006311.3	1114	Agc/gc	25/46	0.3	1	FACETS	0.741	0.626	0.868	0.741	0.626	0.868	SUBCLONAL	1	TRUE	0	0.2	1		301	583	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	21	115	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.744	0.572	0.946	0.744	0.572	0.946	CLONAL	1	TRUE	1	0.14	2		115	403	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61197647	61197647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	37	461	0	ENST00000301761.2:c.29C>T	p.Ser10Leu	p.S10L	ENST00000301761	NM_017841.2	10	tCg/tTg	1/4	1	2	FACETS	0.749	0.615	0.899	0.749	0.615	0.899	SUBCLONAL	1	TRUE	1	0.14	2		461	706	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696642	47696642	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519965	NA	P-0055166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	30	396	0	ENST00000347630.2:c.306C>G	p.Phe102Leu	p.F102L	ENST00000347630	NM_001007230.1	102	ttC/ttG	5/11	1	2	FACETS	0.893	0.718	1	0.893	0.718	1	CLONAL	1	TRUE	1	0.14	2		396	480	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0055166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	144	827	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	0.995	0.906	1	1	0.991	1	CLONAL	2	TRUE	1	0.14	2		827	1034	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900158	101900158	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	29	217	0	ENST00000374994.4:c.592C>T	p.Gln198Ter	p.Q198*	ENST00000374994	NM_004612.2	198	Cag/Tag	4/9	1	2	FACETS	1	0.817	1	1	0.957	1	CLONAL	2	TRUE	1	0.14	2		217	205	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971139	21971139	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730881679	NA	P-0055166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	26	410	1	ENST00000579755.1:c.262C>T	p.Arg88Ter	p.R88*	ENST00000579755		88	Cga/Tga	2/3	1	2	FACETS	0.844	0.668	1	0.844	0.668	1	CLONAL	1	TRUE	1	0.14	2		411	440	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974763	21974763	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	9	222	0	ENST00000304494.5:c.64del	p.Arg22GlyfsTer4	p.R22Gfs*4	ENST00000304494	NM_000077.4	22	Cgg/gg	1/3	1	2	FACETS	0.561	0.371	0.805	0.561	0.371	0.805	SUBCLONAL	1	TRUE	1	0.14	2		222	229	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244139	46244139	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	19	388	0	ENST00000334344.6:c.2233C>T	p.Gln745Ter	p.Q745*	ENST00000334344	NM_152641.2	745	Cag/Tag	15/21	1	2	FACETS	0.784	0.595	1	0.784	0.595	1	CLONAL	1	TRUE	1	0.14	2		388	346	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684350	29684350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	29	428	0	ENST00000356175.3:c.7870G>A	p.Glu2624Lys	p.E2624K	ENST00000356175	NM_000267.3	2624	Gag/Aag	53/57	1	2	FACETS	0.961	0.771	1	0.961	0.771	1	CLONAL	1	TRUE	1	0.14	2		428	431	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411027	63411027	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	37	333	0	ENST00000330258.3:c.2140C>T	p.Gln714Ter	p.Q714*	ENST00000330258	NM_152424.3	714	Caa/Taa	2/2	1	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.14	1		333	328	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105536	30105536	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	66	675	0	ENST00000331968.5:c.1150G>A	p.Asp384Asn	p.D384N	ENST00000331968	NM_002742.2	384	Gat/Aat	7/18	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.14	2		675	873	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880997	37880997	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28933369	NA	P-0055166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	45	953	1	ENST00000269571.5:c.2326G>A	p.Gly776Ser	p.G776S	ENST00000269571		776	Ggt/Agt	20/27	1	2	FACETS	0.592	0.495	0.7	0.592	0.495	0.7	SUBCLONAL	1	TRUE	1	0.14	2		954	1086	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204572	128204572	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	44	639	0	ENST00000341105.2:c.869C>T	p.Ser290Leu	p.S290L	ENST00000341105	NM_032638.4	290	tCa/tTa	3/6	1	2	FACETS	0.79	0.66	0.934	0.79	0.66	0.934	CLONAL	1	TRUE	1	0.14	2		639	796	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925407	131925407	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	19	143	0	ENST00000265335.6:c.1330G>A	p.Glu444Lys	p.E444K	ENST00000265335		444	Gag/Aag	9/25	1	2	FACETS	1	0.777	1	1	0.936	1	CLONAL	2	TRUE	1	0.14	2		143	134	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340339	116340339	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0055166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	14	154	0	ENST00000397752.3:c.1200+1G>A		p.X400_splice	ENST00000397752	NM_000245.2	400			1	2	FACETS	1	0.766	1	1	0.766	1	CLONAL	1	TRUE	1	0.14	2		154	188	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81962169	81962169	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	28	489	0	ENST00000359376.3:c.2521G>A	p.Glu841Lys	p.E841K	ENST00000359376	NM_002661.3	841	Gaa/Aaa	24/33	1	2	FACETS	0.808	0.645	0.995	0.808	0.645	0.995	CLONAL	1	TRUE	1	0.14	2		489	495	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075200	16075200	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	21	335	1	ENST00000268712.3:c.352C>T	p.His118Tyr	p.H118Y	ENST00000268712	NM_006311.3	118	Cat/Tat	4/46	1	2	FACETS	0.744	0.572	0.946	0.744	0.572	0.946	CLONAL	1	TRUE	1	0.14	2		336	403	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462320	89462320	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753127242	NA	P-0055166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	24	393	0	ENST00000336596.2:c.1792G>A	p.Asp598Asn	p.D598N	ENST00000336596	NM_005233.5	598	Gac/Aac	10/17	1	2	FACETS	1	0.788	1	1	0.788	1	CLONAL	1	TRUE	1	0.14	2		393	341	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981794	70981794	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1475	92	1391	0	ENST00000276594.2:c.302G>A	p.Trp101Ter	p.W101*	ENST00000276594	NM_024504.3	101	tGg/tAg	2/8	0.0941908083245926	3	FACETS	0.897	0.794	1	0.449	0.397	0.505	CLONAL	1	TRUE	1	0.14	3		1391	1567	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696644	47696644	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519964	NA	P-0055167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	10	407	0	ENST00000347630.2:c.304T>G	p.Phe102Val	p.F102V	ENST00000347630	NM_001007230.1	102	Ttc/Gtc	5/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		407	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782177	NA	P-0055169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	423	795	0	ENST00000269305.4:c.644G>T	p.Ser215Ile	p.S215I	ENST00000269305	NM_001126112.2	215	aGt/aTt	6/11	0.461089550111183	4	FACETS	0.935	0.9	0.97	0.935	0.9	0.97	CLONAL	4	TRUE	0	0.457108673047916	4		795	721	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437307	121437307	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	89	859	0	ENST00000257555.6:c.1645G>C	p.Ala549Pro	p.A549P	ENST00000257555		549	Gcc/Ccc	9/10	0.115543135475277	3	FACETS	0.993	0.883	1			1	INDETERMINATE	1	TRUE	NA	0.457108673047916	3		859	482	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953568	32953568	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs276174913	NA	P-0055169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	117	569	0	ENST00000380152.3:c.8869C>T	p.Gln2957Ter	p.Q2957*	ENST00000380152		2957	Caa/Taa	22/27	NA	2	FACETS	0.762	0.695	0.83			1	INDETERMINATE	2	TRUE	NA	0.457108673047916	2		569	336	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857584	78857584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	70	681	0	ENST00000306801.3:c.1654G>A	p.Ala552Thr	p.A552T	ENST00000306801	NM_020761.2	552	Gcc/Acc	16/34	0.461089550111183	4	FACETS	1	0.877	1	0.251	0.219	0.285	CLONAL	1	TRUE	0	0.457108673047916	4		681	445	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905978	50905978	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	24	818	0	ENST00000440232.2:c.950T>C	p.Ile317Thr	p.I317T	ENST00000440232	NM_002691.3	317	aTc/aCc	8/27	0.461089550111183	1	FACETS	0.196	0.153	0.245	0.196	0.153	0.245	SUBCLONAL	1	TRUE	0	0.457108673047916	1		818	414	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728736	190728736	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	55	380	0	ENST00000441310.2:c.2124A>G	p.Ile708Met	p.I708M	ENST00000441310	NM_000534.4	708	atA/atG	10/13	0.268617051847538	3	FACETS	1	0.958	1	0.432	0.374	0.494	INDETERMINATE	1	TRUE	0	0.457108673047916	3		380	228	SUCCESS
APC	324	MSKCC	GRCh37	5	112090718	112090734	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGAAGGTATCAAGACTG	TGAAGGTATCAAGACTG	-	novel	NA	P-0055169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	31	276	0	ENST00000257430.4:c.134_135+15del		p.X45_splice	ENST00000257430	NM_000038.5	45		2/16	0.461089550111183	4	FACETS	0.827	0.673	1	0.207	0.168	0.25	CLONAL	1	TRUE	0	0.457108673047916	4		276	239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0055170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	797	773	2	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.841569575716429	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.847784904235573	2		775	931	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338671	70338671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	218	675	0	ENST00000374080.3:c.67G>T	p.Asp23Tyr	p.D23Y	ENST00000374080		23	Gat/Tat	1/45	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.847784904235573	2		675	514	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712773	43712773	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267604218	NA	P-0055170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	296	772	2	ENST00000382044.4:c.4411C>T	p.Pro1471Ser	p.P1471S	ENST00000382044	NM_001141980.1	1471	Cct/Tct	21/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.847784904235573	2		774	669	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95599013	95599013	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1060503624	NA	P-0055170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	127	293	0	ENST00000393063.1:c.146T>C	p.Val49Ala	p.V49A	ENST00000393063	NM_030621.3	49	gTt/gCt	4/28	1	2	FACETS	0.945	0.869	1	0.945	0.869	1	CLONAL	1	TRUE	1	0.847784904235573	2		293	317	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396601	396601	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	267	785	0	ENST00000262320.3:c.425G>C	p.Arg142Thr	p.R142T	ENST00000262320	NM_003502.3	142	aGa/aCa	2/11	0.847784904235573	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.847784904235573	1		785	347	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719287	52719287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760606403	NA	P-0055173-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	89	474	0	ENST00000322088.6:c.953G>A	p.Arg318Gln	p.R318Q	ENST00000322088	NM_014225.5	318	cGg/cAg	8/15	1	2	FACETS	0.934	0.827	1	0.934	0.827	1	CLONAL	1	TRUE	1	0.236856611905123	2		474	805	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69458683	69458684	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0055173-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	63	484	0	ENST00000227507.2:c.498_499del	p.Lys167AsnfsTer73	p.K167Nfs*73	ENST00000227507	NM_053056.2	166	tcCAaa/tcaa	3/5	1	2	FACETS	0.591	0.51	0.68	0.591	0.51	0.68	SUBCLONAL	1	TRUE	1	0.236856611905123	2		484	900	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077494	30077494	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055173-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	74	332	0	ENST00000338641.4:c.1642del	p.Ala548ProfsTer2	p.A548Pfs*2	ENST00000338641	NM_000268.3	547	gaG/ga	15/16	0.236856611905123	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.236856611905123	1		332	461	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056484	26056484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs550065694	NA	P-0055173-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	31	214	0	ENST00000343677.2:c.173C>T	p.Ser58Phe	p.S58F	ENST00000343677	NM_005319.3	58	tCt/tTt	1/1	1	2	FACETS	0.748	0.606	0.909	0.748	0.606	0.909	CLONAL	1	TRUE	1	0.236856611905123	2		214	350	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0055175-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	84	285	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.19406628249447	2	FACETS	0.999	0.89	1	0.999	0.89	1	CLONAL	2	TRUE	0	0.244497941656652	2		285	344	SUCCESS
ATM	472	MSKCC	GRCh37	11	108099973	108099973	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0055175-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	22	240	0	ENST00000278616.4:c.254C>G	p.Ser85Ter	p.S85*	ENST00000278616	NM_000051.3	85	tCa/tGa	4/63	0.244497941656652	1	FACETS	0.721	0.561	0.906	0.721	0.561	0.906	CLONAL	1	TRUE	0	0.244497941656652	1		240	219	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597327	10597354	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	CTCAACAGGTACAGTTCTGCTGGTCAAT	CTCAACAGGTACAGTTCTGCTGGTCAAT	-	novel	NA	P-0055175-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	47	680	0	ENST00000171111.5:c.1849_*1del		p.*617*	ENST00000171111	NM_203500.1	617		6/6	0.244497941656652	1	FACETS	0.709	0.598	0.831	0.709	0.598	0.831	SUBCLONAL	1	TRUE	0	0.244497941656652	1		680	476	SUCCESS
APC	324	MSKCC	GRCh37	5	112174404	112174404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1375326078	NA	P-0055175-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	35	226	0	ENST00000257430.4:c.3113C>T	p.Ser1038Phe	p.S1038F	ENST00000257430	NM_000038.5	1038	tCt/tTt	16/16	0.244497941656652	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.244497941656652	1		226	201	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0055176-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	55	411	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	1	0.944	1	1	0.98	1	CLONAL	2	TRUE	1	0.149517826320294	2		411	307	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055176-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	43	1126	1	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.803	0.671	0.951	0.803	0.671	0.951	CLONAL	1	TRUE	1	0.149517826320294	2		1127	716	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296358	15296358	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055176-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	121	976	2	ENST00000263388.2:c.2084del	p.Pro695ArgfsTer165	p.P695Rfs*165	ENST00000263388	NM_000435.2	695	cCg/cg	13/33	1	2	FACETS	1	0.972	1	1	0.99	1	CLONAL	2	TRUE	1	0.149517826320294	2		978	679	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0055176-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	78	456	2	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.937	0.829	1	1	0.987	1	CLONAL	3	TRUE	1	0.149517826320294	2		458	371	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528825	157528825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055176-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	97	721	2	ENST00000346085.5:c.6554del	p.Pro2185ArgfsTer8	p.P2185Rfs*8	ENST00000346085	NM_020732.3	2184	Ccc/cc	20/20	1	2	FACETS	0.905	0.81	1	1	0.989	1	CLONAL	3	TRUE	1	0.149517826320294	2		723	478	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055176-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	88	741	3	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	1	0.954	1	1	0.987	1	CLONAL	2	TRUE	1	0.149517826320294	2		744	515	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0055176-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	42	598	0	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.149517826320294	2		598	430	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226259095	226259095	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055176-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	12	49	0	ENST00000366813.1:c.326A>G	p.Asn109Ser	p.N109S	ENST00000366813		109	aAc/aGc	3/3	1	2	FACETS	0.991	0.716	1	1	0.923	1	CLONAL	3	TRUE	1	0.149517826320294	2		49	54	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903746	41903746	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055176-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	122	911	1	ENST00000372991.4:c.811del	p.Arg271GlyfsTer33	p.R271Gfs*33	ENST00000372991	NM_001760.3	271	Cgg/gg	5/5	1	2	FACETS	1	0.962	1	1	0.99	1	CLONAL	2	TRUE	1	0.149517826320294	2		912	727	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984968	55984968	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0055176-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	63	436	0	ENST00000263923.4:c.162-1G>A		p.X54_splice	ENST00000263923	NM_002253.2	54			1	2	FACETS	0.846	0.737	0.963	1	0.983	1	CLONAL	3	TRUE	1	0.149517826320294	2		436	332	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201565	133201565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765125852	NA	P-0055176-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	62	908	0	ENST00000320574.5:c.6673C>T	p.Arg2225Cys	p.R2225C	ENST00000320574	NM_006231.2	2225	Cgc/Tgc	48/49	0.0314222541000786	3	FACETS	1	0.966	1	0.71	0.613	0.815	INDETERMINATE	1	TRUE	1	0.149517826320294	3		908	628	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775611	9775611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1375117381	NA	P-0055176-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	107	846	2	ENST00000377346.4:c.154C>T	p.Arg52Cys	p.R52C	ENST00000377346	NM_005026.3	52	Cgc/Tgc	4/24	1	2	FACETS	1	0.973	1	1	0.99	1	CLONAL	2	TRUE	1	0.149517826320294	2		848	576	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672551	30672551	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773270002	NA	P-0055176-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	119	747	0	ENST00000376406.3:c.4409C>T	p.Thr1470Met	p.T1470M	ENST00000376406	NM_014641.2	1470	aCg/aTg	10/15	1	2	FACETS	0.886	0.802	0.974	1	0.991	1	CLONAL	3	TRUE	1	0.149517826320294	2		747	599	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776098	9776098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754531708	NA	P-0055176-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	131	866	0	ENST00000377346.4:c.562C>T	p.Arg188Trp	p.R188W	ENST00000377346	NM_005026.3	188	Cgg/Tgg	5/24	1	2	FACETS	0.859	0.781	0.941	1	0.992	1	CLONAL	3	TRUE	1	0.149517826320294	2		866	680	SUCCESS
FH	2271	MSKCC	GRCh37	1	241671991	241671991	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055176-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	86	509	1	ENST00000366560.3:c.650C>T	p.Ala217Val	p.A217V	ENST00000366560	NM_000143.3	217	gCt/gTt	5/10	1	2	FACETS	0.924	0.822	1	1	0.988	1	CLONAL	3	TRUE	1	0.149517826320294	2		510	415	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121661	108121661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1565383172	NA	P-0055176-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	82	589	0	ENST00000278616.4:c.1469T>C	p.Ile490Thr	p.I490T	ENST00000278616	NM_000051.3	490	aTt/aCt	10/63	1	2	FACETS	0.89	0.789	0.997	1	0.987	1	CLONAL	3	TRUE	1	0.149517826320294	2		589	411	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373908	118373908	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055176-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	46	393	0	ENST00000534358.1:c.7301A>G	p.Lys2434Arg	p.K2434R	ENST00000534358	NM_005933.3	2434	aAa/aGa	27/36	1	2	FACETS	0.837	0.711	0.974	1	0.977	1	CLONAL	3	TRUE	1	0.149517826320294	2		393	245	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219306	133219306	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs192908615	NA	P-0055176-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	105	733	1	ENST00000320574.5:c.4738C>T	p.Arg1580Trp	p.R1580W	ENST00000320574	NM_006231.2	1580	Cgg/Tgg	37/49	0.0314222541000786	3	FACETS	0.977	0.879	1	1	0.982	1	INDETERMINATE	3	TRUE	1	0.149517826320294	3		734	515	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748612	43748612	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055176-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	46	979	0	ENST00000382044.4:c.2194T>C	p.Ser732Pro	p.S732P	ENST00000382044	NM_001141980.1	732	Tcc/Ccc	12/28	1	2	FACETS	0.966	0.812	1	0.966	0.812	1	CLONAL	1	TRUE	1	0.149517826320294	2		979	637	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023290	31023290	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055176-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	46	674	0	ENST00000375687.4:c.2775G>T	p.Gln925His	p.Q925H	ENST00000375687	NM_015338.5	925	caG/caT	13/13	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.149517826320294	2		674	488	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911209	29911210	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0055176-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	29	484	0	ENST00000376809.5:c.508_509del	p.Lys170ValfsTer6	p.K170Vfs*6	ENST00000376809	NM_002116.7	170	AAg/g	3/8	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.149517826320294	2		484	284	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020417	69020417	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055176-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	28	671	1	ENST00000288368.4:c.2789G>A	p.Ser930Asn	p.S930N	ENST00000288368	NM_024870.2	930	aGc/aAc	24/40	1	2	FACETS	0.734	0.586	0.905	0.734	0.586	0.905	CLONAL	1	TRUE	1	0.149517826320294	2		672	510	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0055182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	247	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.883	0.828	0.94	0.883	0.828	0.94	CLONAL	1	TRUE	1	0.667527676430557	2		622	838	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	187	557	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	0.871	0.809	0.936	0.871	0.809	0.936	CLONAL	1	TRUE	1	0.667527676430557	2		557	643	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092809	27092809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	222	559	0	ENST00000324856.7:c.2830C>T	p.Gln944Ter	p.Q944*	ENST00000324856	NM_006015.4	944	Cag/Tag	9/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.667527676430557	2		559	661	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012397	176012397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	98	283	0	ENST00000367669.3:c.1537G>A	p.Glu513Lys	p.E513K	ENST00000367669	NM_022457.5	513	Gag/Aag	14/20	1	2	FACETS	0.822	0.74	0.908	0.822	0.74	0.908	CLONAL	1	TRUE	1	0.667527676430557	2		283	357	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176618933	176618933	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	203	429	0	ENST00000439151.2:c.976C>G	p.Leu326Val	p.L326V	ENST00000439151	NM_022455.4	326	Ctc/Gtc	3/23	1	2	FACETS	0.981	0.915	1	0.981	0.915	1	CLONAL	1	TRUE	1	0.667527676430557	2		429	620	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178136	56178137	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0055182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	114	295	0	ENST00000399503.3:c.3110_3111del	p.Lys1037ArgfsTer4	p.K1037Rfs*4	ENST00000399503	NM_005921.1	1037	AAa/a	14/20	0.667527676430557	3	FACETS	1	0.951	1	0.537	0.487	0.589	CLONAL	1	TRUE	1	0.667527676430557	3		295	424	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28601483	28601483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1430082772	NA	P-0055182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	272	680	0	ENST00000253063.3:c.1168C>T	p.Arg390Cys	p.R390C	ENST00000253063	NM_031459.4	390	Cgc/Tgc	8/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.667527676430557	2		680	783	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853327	68853328	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0055182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	179	524	0	ENST00000261769.5:c.1711+1dup		p.-570fs	ENST00000261769	NM_004360.3	570	-/G	11/16	0.667527676430557	1	FACETS	0.95	0.889	1	0.95	0.889	1	CLONAL	1	TRUE	0	0.667527676430557	1		524	376	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496911	29496911	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0055182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	76	174	0	ENST00000356175.3:c.482T>A	p.Leu161Ter	p.L161*	ENST00000356175	NM_000267.3	161	tTa/tAa	5/57	NA	2	FACETS	0.777	0.689	0.87			1	INDETERMINATE	1	TRUE	NA	0.667527676430557	2		174	293	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957519	1957519	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	280	703	0	ENST00000382891.5:c.2618G>T	p.Arg873Met	p.R873M	ENST00000382891	NM_133335.3	873	aGg/aTg	14/22	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.667527676430557	2		703	828	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179439	56179439	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	177	214	0	ENST00000399503.3:c.3752T>C	p.Leu1251Pro	p.L1251P	ENST00000399503	NM_005921.1	1251	cTt/cCt	15/20	0.667527676430557	3	FACETS	0.923	0.863	0.984	0.923	0.863	0.984	CLONAL	2	TRUE	1	0.667527676430557	3		214	383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0055183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	204	937	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.688195877319172	2	FACETS	0.959	0.912	1	0.959	0.912	1	CLONAL	2	TRUE	0	0.688195877319172	2		937	309	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434650	99434650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1297968262	NA	P-0055183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	30	778	1	ENST00000268035.6:c.737C>T	p.Thr246Met	p.T246M	ENST00000268035	NM_000875.3	246	aCg/aTg	3/21	0.688257590947535	3	FACETS	0.287	0.23	0.35	0.143	0.115	0.175	SUBCLONAL	1	TRUE	1	0.688195877319172	3		779	409	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144868	47144868	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	350	429	1	ENST00000409792.3:c.4885C>T	p.His1629Tyr	p.H1629Y	ENST00000409792	NM_014159.6	1629	Cac/Tac	7/21	0.649554495235101	5	FACETS	0.961	0.934	0.987	0.961	0.934	0.987	CLONAL	5	TRUE	0	0.688195877319172	5		430	430	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984370	201984370	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	237	772	1	ENST00000359651.3:c.1036del	p.Asp346MetfsTer101	p.D346Mfs*101	ENST00000359651		345	gtG/gt	8/8	0.688257590947535	4	FACETS	0.942	0.886	1	0.942	0.886	1	CLONAL	2	TRUE	2	0.688195877319172	4		773	617	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104386947	104386947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	68	239	0	ENST00000369902.3:c.1312G>A	p.Glu438Lys	p.E438K	ENST00000369902	NM_016169.3	438	Gag/Aag	11/12	0.688257590947535	4	FACETS	1	0.974	1			1	CLONAL	1	TRUE	NA	0.688195877319172	4		239	232	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599300	28599300	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	147	1047	0	ENST00000253063.3:c.746C>G	p.Ser249Cys	p.S249C	ENST00000253063	NM_031459.4	249	tCt/tGt	5/10	0.688257590947535	3	FACETS	0.955	0.876	1	0.478	0.438	0.519	CLONAL	1	TRUE	1	0.688195877319172	3		1047	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0055183-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	362	937	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.825831738351735	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.825831738351735	1		937	514	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144868	47144868	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055183-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	479	429	1	ENST00000409792.3:c.4885C>T	p.His1629Tyr	p.H1629Y	ENST00000409792	NM_014159.6	1629	Cac/Tac	7/21	0.822312344846599	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.825831738351735	2		430	565	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984370	201984370	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055183-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	294	772	1	ENST00000359651.3:c.1036del	p.Asp346MetfsTer101	p.D346Mfs*101	ENST00000359651		345	gtG/gt	8/8	1	2	FACETS	0.93	0.879	0.98	0.93	0.879	0.98	CLONAL	1	TRUE	1	0.825831738351735	2		773	766	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104386947	104386947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055183-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	114	239	0	ENST00000369902.3:c.1312G>A	p.Glu438Lys	p.E438K	ENST00000369902	NM_016169.3	438	Gag/Aag	11/12	1	2	FACETS	0.923	0.844	1	0.923	0.844	1	CLONAL	1	TRUE	1	0.825831738351735	2		239	299	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430207	181430226	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCGGCGGCAACTCCACC	GCGGCGGCGGCAACTCCACC	-	rs398123693	NA	P-0055183-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	95	137	0	ENST00000325404.1:c.70_89del	p.Asn24ArgfsTer65	p.N24Rfs*65	ENST00000325404	NM_003106.3	20	gGCGGCGGCGGCAACTCCACC/g	1/1	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.825831738351735	2		137	190	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751021	128751026	+	inframe_deletion	In_Frame_Del	DEL	CTCCAC	CTCCAC	-	novel	NA	P-0055183-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1418	164	571	0	ENST00000377970.2:c.563_568del	p.Thr188_Ser189del	p.T188_S189del	ENST00000377970	NM_002467.4	186	tgCTCCACc/tgc	2/3	0.825831738351735	7	FACETS	0.769	0.704	0.839	0.128	0.117	0.14	SUBCLONAL	1	TRUE	1	0.825831738351735	7		571	1582	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0055184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	31	205	1	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.19	2		206	254	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0055184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	67	634	0	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.19	2		634	694	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412297	139412297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	74	1269	2	ENST00000277541.6:c.1348G>A	p.Glu450Lys	p.E450K	ENST00000277541	NM_017617.3	450	Gag/Aag	8/34	1	2	FACETS	0.648	0.565	0.737	0.648	0.565	0.737	SUBCLONAL	1	TRUE	1	0.19	2		1271	1203	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0055189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	18	374	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	0.291604007704839	3	FACETS	0.371	0.278	0.481	0.185	0.139	0.241	SUBCLONAL	1	TRUE	1	0.21	3		374	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs17849781	NA	P-0055189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	149	759	0	ENST00000269305.4:c.832C>G	p.Pro278Ala	p.P278A	ENST00000269305	NM_001126112.2	278	Cct/Gct	8/11	0.3	3	FACETS	0.886	0.809	0.966	0.886	0.809	0.966	CLONAL	2	TRUE	1	0.21	3		759	885	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599939	28599939	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757342510	NA	P-0055189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	48	789	0	ENST00000253063.3:c.821G>A	p.Arg274Gln	p.R274Q	ENST00000253063	NM_031459.4	274	cGg/cAg	6/10	1	2	FACETS	0.594	0.5	0.697	0.594	0.5	0.697	SUBCLONAL	1	TRUE	1	0.21	2		789	770	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586048	29586048	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1555618634	NA	P-0055189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	38	266	0	ENST00000356175.3:c.4270-2A>G		p.X1424_splice	ENST00000356175	NM_000267.3	1424			1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.21	2		266	299	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838399	156838399	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	92	1052	0	ENST00000524377.1:c.677G>T	p.Gly226Val	p.G226V	ENST00000524377	NM_002529.3	226	gGc/gTc	6/17	1	2	FACETS	0.784	0.694	0.88	0.784	0.694	0.88	SUBCLONAL	1	TRUE	1	0.21	2		1052	1118	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748398	162748398	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	45	375	0	ENST00000367921.3:c.2312G>A	p.Trp771Ter	p.W771*	ENST00000367921	NM_006182.2	771	tGg/tAg	17/18	1	2	FACETS	0.85	0.715	1	0.85	0.715	1	CLONAL	1	TRUE	1	0.21	2		375	504	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111004	193111005	+	missense_variant	Missense_Mutation	DNP	GG	GG	TA	novel	NA	P-0055189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	14	164	0	ENST00000367435.3:c.537_538delinsTA	p.Glu180Lys	p.E180K	ENST00000367435	NM_024529.4	179	gtGGaa/gtTAaa	7/17	1	2	FACETS	0.58	0.419	0.774	0.58	0.419	0.774	SUBCLONAL	1	TRUE	1	0.21	2		164	230	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612115	43612115	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	65	522	1	ENST00000355710.3:c.2220G>T	p.Lys740Asn	p.K740N	ENST00000355710	NM_020975.4	740	aaG/aaT	12/20	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.21	2		523	619	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475221	475221	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	63	577	0	ENST00000399788.2:c.416G>T	p.Trp139Leu	p.W139L	ENST00000399788	NM_001042603.1	139	tGg/tTg	4/28	0.3	3	FACETS	0.844	0.728	0.969	0.422	0.364	0.485	CLONAL	1	TRUE	1	0.21	3		577	786	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563033	21563033	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	127	1010	0	ENST00000382592.4:c.886G>T	p.Gly296Ter	p.G296*	ENST00000382592	NM_014572.2	296	Gga/Tga	4/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.21	2		1010	978	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712599	43712599	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	61	777	0	ENST00000382044.4:c.4585G>T	p.Glu1529Ter	p.E1529*	ENST00000382044	NM_001141980.1	1529	Gaa/Taa	21/28	1	2	FACETS	0.607	0.522	0.7	0.607	0.522	0.7	SUBCLONAL	1	TRUE	1	0.21	2		777	957	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716059	52716059	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	97	880	0	ENST00000322088.6:c.624G>T	p.Met208Ile	p.M208I	ENST00000322088	NM_014225.5	208	atG/atT	5/15	1	2	FACETS	0.884	0.786	0.989	0.884	0.786	0.989	CLONAL	1	TRUE	1	0.21	2		880	1045	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127711	47127711	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	40	437	0	ENST00000409792.3:c.5371del	p.Glu1791LysfsTer11	p.E1791Kfs*11	ENST00000409792	NM_014159.6	1791	Gaa/aa	11/21	1	2	FACETS	0.774	0.643	0.92	0.774	0.643	0.92	CLONAL	1	TRUE	1	0.21	2		437	492	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681172	86681173	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0055189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	21	247	0	ENST00000274376.6:c.2814_2815del	p.Asn939LeufsTer10	p.N939Lfs*10	ENST00000274376	NM_002890.2	938	cAG/c	22/25	1	2	FACETS	0.93	0.719	1	0.93	0.719	1	CLONAL	1	TRUE	1	0.21	2		247	215	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869608	117869608	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	81	329	0	ENST00000297338.2:c.586G>T	p.Glu196Ter	p.E196*	ENST00000297338	NM_006265.2	196	Gaa/Taa	6/14	0.3	3	FACETS	0.854	0.755	0.96	0.854	0.755	0.96	CLONAL	2	TRUE	1	0.21	3		329	499	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141567295	141567295	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	153	702	0	ENST00000220592.5:c.919A>T	p.Thr307Ser	p.T307S	ENST00000220592	NM_012154.3	307	Acg/Tcg	8/19	0.3	3	FACETS	0.914	0.836	0.995	0.914	0.836	0.995	CLONAL	2	TRUE	1	0.21	3		702	881	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0055190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	109	644	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.242121143996676	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.242121143996676	1		646	688	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258744	115258744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434596	NA	P-0055190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	63	428	0	ENST00000369535.4:c.38G>A	p.Gly13Asp	p.G13D	ENST00000369535	NM_002524.4	13	gGt/gAt	2/7	0.242121143996676	1	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	0	0.242121143996676	1		428	441	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928065	178928076	+	inframe_deletion	In_Frame_Del	DEL	TACCTCATGGAT	TACCTCATGGAT	-	novel	NA	P-0055190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	53	543	0	ENST00000263967.3:c.1345_1356del	p.Pro449_Leu452del	p.P449_L452del	ENST00000263967	NM_006218.2	448	gTACCTCATGGATta/gta	8/21	1	2	FACETS	0.905	0.772	1	0.905	0.772	1	CLONAL	1	TRUE	1	0.242121143996676	2		543	484	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354371	354371	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	255	1172	0	ENST00000262320.3:c.1187T>C	p.Leu396Pro	p.L396P	ENST00000262320	NM_003502.3	396	cTg/cCg	5/11	0.229640248690669	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.242121143996676	2		1172	1001	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910079	29911085	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	TCAGAGTCTCAGGCCCCGAAGGCGGTGTATGGATTGGGGAGTCCCAGCCTTGGGGATTCCCCAACTCCGCAGTTTCTTTTCTCCCTCTCCCAACCTACGTAGGGTCCTTCATCCTGGATACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGTGTCGGGTTTCCAGAGAAGCCAATCAGTGTCGTCGCGGTCGCTGTTCTAAAGCCCGCACGCACCCACCGGGACTCAGATTCTCCCCAGACGCCGAGGATGGCCGTCATGGCGCCCCGAACCCTCCTCCTGCTACTCTCGGGGGCCCTGGCCCTGACCCAGACCTGGGCGGGTGAGTGCGGGGTCGGGAGGGAAACCGCCTCTGCGGGGAGAAGCAAGGGGCCCTCCTGGCGGGGGCGCAGGACCGGGGGAGCCGCGCCGGGACGAGGGTCGGGCAGGTCTCAGCCACTGCTCGCCCCCAGGCTCCCACTCCATGAGGTATTTCTTCACATCCGTGTCCCGGCCCGGCCGCGGGGAGCCCCGCTTCATCGCCGTGGGCTACGTGGACGACACGCAGTTCGTGCGGTTCGACAGCGACGCCGCGAGCCAGAGGATGGAGCCGCGGGCGCCGTGGATAGAGCAGGAGGGGCCGGAGTATTGGGACCAGGAGACACGGAATGTGAAGGCCCAGTCACAGACTGACCGAGTGGACCTGGGGACCCTGCGCGGCTACTACAACCAGAGCGAGGCCGGTGAGTGACCCCGGCCGGGGGCGCAGGTCAGGACCCCTCATCCCCCACGGACGGGCCAGGTCGCCCACAGTCTCCGGGTCCGAGATCCACCCCGAAGCCGCGGGACCCCGAGACCCTTGCCCCGGGAGAGGCCCAGGCGCCTTTACCCGGTTTCATTTTCAGTTTAGGCCAAAAATCCCCCCGGGTTGGTCGGGGCTGGGCGGGGCTCGGGGGACTGGGCTGACCGCGGGGTCGGGGCCAGGTTCTCACACCATCCAGATAATGTATGGCTGCGACGTGGGG	TCAGAGTCTCAGGCCCCGAAGGCGGTGTATGGATTGGGGAGTCCCAGCCTTGGGGATTCCCCAACTCCGCAGTTTCTTTTCTCCCTCTCCCAACCTACGTAGGGTCCTTCATCCTGGATACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGTGTCGGGTTTCCAGAGAAGCCAATCAGTGTCGTCGCGGTCGCTGTTCTAAAGCCCGCACGCACCCACCGGGACTCAGATTCTCCCCAGACGCCGAGGATGGCCGTCATGGCGCCCCGAACCCTCCTCCTGCTACTCTCGGGGGCCCTGGCCCTGACCCAGACCTGGGCGGGTGAGTGCGGGGTCGGGAGGGAAACCGCCTCTGCGGGGAGAAGCAAGGGGCCCTCCTGGCGGGGGCGCAGGACCGGGGGAGCCGCGCCGGGACGAGGGTCGGGCAGGTCTCAGCCACTGCTCGCCCCCAGGCTCCCACTCCATGAGGTATTTCTTCACATCCGTGTCCCGGCCCGGCCGCGGGGAGCCCCGCTTCATCGCCGTGGGCTACGTGGACGACACGCAGTTCGTGCGGTTCGACAGCGACGCCGCGAGCCAGAGGATGGAGCCGCGGGCGCCGTGGATAGAGCAGGAGGGGCCGGAGTATTGGGACCAGGAGACACGGAATGTGAAGGCCCAGTCACAGACTGACCGAGTGGACCTGGGGACCCTGCGCGGCTACTACAACCAGAGCGAGGCCGGTGAGTGACCCCGGCCGGGGGCGCAGGTCAGGACCCCTCATCCCCCACGGACGGGCCAGGTCGCCCACAGTCTCCGGGTCCGAGATCCACCCCGAAGCCGCGGGACCCCGAGACCCTTGCCCCGGGAGAGGCCCAGGCGCCTTTACCCGGTTTCATTTTCAGTTTAGGCCAAAAATCCCCCCGGGTTGGTCGGGGCTGGGCGGGGCTCGGGGGACTGGGCTGACCGCGGGGTCGGGGCCAGGTTCTCACACCATCCAGATAATGTATGGCTGCGACGTGGGG	-	novel	NA	P-0055190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	67	56	0				ENST00000376809	NM_002116.7	?-128/365		1-3/8	1	2	FACETS	1	0.946	1	1	0.988	1	CLONAL	4	TRUE	1	0.242121143996676	2		56	128	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0055191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	98	314	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.924	0.828	1	1	0.986	1	CLONAL	2	TRUE	1	0.224243910743597	2		314	473	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0055191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	185	563	2	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.222091127757875	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.224243910743597	2		565	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577107	7577107	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1057523347	NA	P-0055191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	81	753	0	ENST00000269305.4:c.831T>A	p.Cys277Ter	p.C277*	ENST00000269305	NM_001126112.2	277	tgT/tgA	8/11	0.224243910743597	1	FACETS	0.719	0.632	0.813	0.719	0.632	0.813	SUBCLONAL	1	TRUE	0	0.224243910743597	1		753	892	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184591	11184591	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	90	601	1	ENST00000361445.4:c.6626T>C	p.Leu2209Pro	p.L2209P	ENST00000361445	NM_004958.3	2209	cTg/cCg	47/58	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.224243910743597	2		602	735	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440719	56440719	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	41	627	0	ENST00000407977.2:c.499A>G	p.Asn167Asp	p.N167D	ENST00000407977		167	Aat/Gat	5/10	0.224243910743597	1	FACETS	0.466	0.387	0.554	0.466	0.387	0.554	SUBCLONAL	1	TRUE	0	0.224243910743597	1		627	697	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	35	115	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.945	0.774	1	0.945	0.774	1	CLONAL	1	TRUE	1	0.14	2		115	529	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412958	49412958	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	88	685	0	ENST00000418115.1:c.65T>C	p.Leu22Pro	p.L22P	ENST00000418115	NM_001664.2	22	cTc/cCc	2/5	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.14	2		685	1215	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	99	325	1				ENST00000310581	NM_198253.2	-/1132			0.172326782415435	3	FACETS	1	0.944	1	1	0.944	1	CLONAL	3	TRUE	0	0.192236168617788	3		326	352	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520219	9520219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867360779	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	75	519	0	ENST00000353224.5:c.2050G>A	p.Glu684Lys	p.E684K	ENST00000353224	NM_177990.2	684	Gag/Aag	10/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.192236168617788	2		519	528	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	237	349	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.192236168617788	4	FACETS	1	0.948	1	1	0.99	1	CLONAL	5	TRUE	0	0.192236168617788	4		349	583	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	166	838	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.192236168617788	3	FACETS	0.985	0.904	1	0.985	0.904	1	CLONAL	2	TRUE	1	0.192236168617788	3		838	961	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	78	979	0	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	0.192236168617788	3	FACETS	0.896	0.785	1	0.448	0.392	0.508	CLONAL	1	TRUE	1	0.192236168617788	3		979	993	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725025	47725025	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199804290	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	108	1325	1	ENST00000449228.1:c.719C>T	p.Ser240Leu	p.S240L	ENST00000449228	NM_001127240.2	240	tCg/tTg	4/4	1	2	FACETS	0.974	0.872	1	0.974	0.872	1	CLONAL	1	TRUE	1	0.192236168617788	2		1326	1154	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728671	190728671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	19	345	0	ENST00000441310.2:c.2059G>A	p.Glu687Lys	p.E687K	ENST00000441310	NM_000534.4	687	Gaa/Aaa	10/13	1	2	FACETS	0.817	0.621	1	0.817	0.621	1	CLONAL	1	TRUE	1	0.192236168617788	2		345	242	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492537	50492537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750026102	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	140	822	1	ENST00000394963.4:c.1433G>A	p.Arg478Gln	p.R478Q	ENST00000394963	NM_003076.4	478	cGa/cAa	12/13	0.0868904115644928	4	FACETS	0.913	0.831	1	0.913	0.831	1	INDETERMINATE	2	TRUE	2	0.192236168617788	4		823	951	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622332	1622332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs551790548	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	280	1253	1	ENST00000344749.5:c.632C>T	p.Pro211Leu	p.P211L	ENST00000344749	NM_001136139.2	211	cCc/cTc	9/19	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.192236168617788	2		1254	1205	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317520	1317520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	60	666	1	ENST00000400841.2:c.545C>T	p.Ser182Phe	p.S182F	ENST00000400841		182	tCt/tTt	5/6	1	1	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	0	0.192236168617788	1		667	558	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945785	17945785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	73	1003	1	ENST00000458235.1:c.2075C>T	p.Ala692Val	p.A692V	ENST00000458235	NM_000215.3	692	gCc/gTc	16/24	0.192236168617788	4	FACETS	0.889	0.775	1	0.296	0.258	0.338	CLONAL	1	TRUE	1	0.192236168617788	4		1004	1019	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965326	25965326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs984403631	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	111	662	0	ENST00000435504.4:c.3880C>T	p.Leu1294Phe	p.L1294F	ENST00000435504		1294	Ctt/Ttt	13/13	1	2	FACETS	0.84	0.756	0.929	1	0.986	1	CLONAL	2	TRUE	1	0.192236168617788	2		662	687	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857673	9857673	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471308483	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	83	537	0	ENST00000330684.3:c.3728G>A	p.Gly1243Glu	p.G1243E	ENST00000330684	NM_001134407.1	1243	gGg/gAg	13/13	0.0868904115644928	4	FACETS	1	0.89	1	1	0.89	1	INDETERMINATE	2	TRUE	2	0.192236168617788	4		537	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579421	7579421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881994	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	124	1000	1	ENST00000269305.4:c.266C>T	p.Pro89Leu	p.P89L	ENST00000269305	NM_001126112.2	89	cCc/cTc	4/11	0.192236168617788	3	FACETS	1	0.978	1	0.649	0.585	0.716	CLONAL	1	TRUE	1	0.192236168617788	3		1001	1090	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194832	30194832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1434470951	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	31	580	1	ENST00000331968.5:c.313C>T	p.Arg105Cys	p.R105C	ENST00000331968	NM_002742.2	105	Cgc/Tgc	2/18	1	2	FACETS	0.64	0.517	0.78	0.64	0.517	0.78	SUBCLONAL	1	TRUE	1	0.192236168617788	2		581	504	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499371	89499371	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	228	515	0	ENST00000336596.2:c.2541G>A	p.Met847Ile	p.M847I	ENST00000336596	NM_005233.5	847	atG/atA	15/17	0.192236168617788	4	FACETS	1	0.951	1	1	0.991	1	CLONAL	4	TRUE	1	0.192236168617788	4		515	694	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093456	30093456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1008608681	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	32	318	0	ENST00000331968.5:c.1807C>T	p.Arg603Cys	p.R603C	ENST00000331968	NM_002742.2	603	Cgt/Tgt	13/18	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.192236168617788	2		318	254	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163772	72163772	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148707586	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	52	529	0	ENST00000357731.5:c.586G>A	p.Asp196Asn	p.D196N	ENST00000357731	NM_173808.2	196	Gac/Aac	4/7	0.192236168617788	3	FACETS	0.799	0.683	0.926	0.799	0.683	0.926	CLONAL	2	TRUE	1	0.192236168617788	3		529	371	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267836	7267836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs52836744	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	44	515	0	ENST00000302850.5:c.172G>A	p.Gly58Arg	p.G58R	ENST00000302850	NM_000208.2	58	Gga/Aga	2/22	0.192236168617788	4	FACETS	0.858	0.718	1	0.286	0.239	0.338	CLONAL	1	TRUE	1	0.192236168617788	4		515	636	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876491	59876491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	57	425	0	ENST00000259008.2:c.1310C>T	p.Pro437Leu	p.P437L	ENST00000259008	NM_032043.2	437	cCc/cTc	9/20	0.192236168617788	3	FACETS	0.893	0.77	1	0.893	0.77	1	CLONAL	2	TRUE	1	0.192236168617788	3		425	364	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88671957	88671957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs574695821	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	31	199	0	ENST00000360948.2:c.1213G>A	p.Asp405Asn	p.D405N	ENST00000360948	NM_001012338.2	405	Gat/Aat	10/19	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.192236168617788	2		199	220	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873878	151873878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	68	503	0	ENST00000262189.6:c.8660C>T	p.Ala2887Val	p.A2887V	ENST00000262189	NM_170606.2	2887	gCt/gTt	38/59	0.0868904115644928	4	FACETS	0.882	0.769	1	0.882	0.769	1	INDETERMINATE	2	TRUE	2	0.192236168617788	4		503	478	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590606	95590606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1222748384	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	38	274	0	ENST00000393063.1:c.1303C>T	p.Pro435Ser	p.P435S	ENST00000393063	NM_030621.3	435	Cct/Tct	9/28	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.192236168617788	2		274	312	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264404	16264405	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	158	986	0	ENST00000375759.3:c.10607_10608delinsAA	p.Arg3536Gln	p.R3536Q	ENST00000375759	NM_015001.2	3536	cGG/cAA	13/15	0.192236168617788	3	FACETS	0.935	0.856	1	0.935	0.856	1	CLONAL	2	TRUE	1	0.192236168617788	3		986	964	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087534	27087534	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	105	977	0	ENST00000324856.7:c.2108C>T	p.Pro703Leu	p.P703L	ENST00000324856	NM_006015.4	703	cCc/cTc	5/20	0.192236168617788	3	FACETS	1	0.967	1	0.6	0.536	0.668	CLONAL	1	TRUE	1	0.192236168617788	3		977	998	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464373	120464373	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	67	717	0	ENST00000256646.2:c.5273G>A	p.Trp1758Ter	p.W1758*	ENST00000256646	NM_024408.3	1758	tGg/tAg	29/34	0.192236168617788	3	FACETS	0.999	0.867	1	0.499	0.433	0.571	CLONAL	1	TRUE	1	0.192236168617788	3		717	765	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218916	193218916	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	17	297	0	ENST00000367435.3:c.1474T>G	p.Trp492Gly	p.W492G	ENST00000367435	NM_024529.4	492	Tgg/Ggg	16/17	0.192236168617788	3	FACETS	0.95	0.711	1	0.475	0.355	0.616	CLONAL	1	TRUE	1	0.192236168617788	3		297	204	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567833	226567834	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	106	760	0	ENST00000366794.5:c.1332_1333delinsAA	p.Glu445Lys	p.E445K	ENST00000366794	NM_001618.3	444	gaGGaa/gaAAaa	10/23	0.192236168617788	3	FACETS	0.759	0.68	0.843	0.759	0.68	0.843	SUBCLONAL	2	TRUE	1	0.192236168617788	3		760	796	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342841	118342841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	14	263	0	ENST00000534358.1:c.967G>A	p.Glu323Lys	p.E323K	ENST00000534358	NM_005933.3	323	Gaa/Aaa	3/36	1	2	FACETS	0.604	0.437	0.807	0.604	0.437	0.807	SUBCLONAL	1	TRUE	1	0.192236168617788	2		263	241	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343318	118343318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	25	359	0	ENST00000534358.1:c.1444C>T	p.Pro482Ser	p.P482S	ENST00000534358	NM_005933.3	482	Ccc/Tcc	3/36	1	2	FACETS	0.885	0.698	1	0.885	0.698	1	CLONAL	1	TRUE	1	0.192236168617788	2		359	294	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343363	118343363	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	23	399	1	ENST00000534358.1:c.1489C>T	p.Gln497Ter	p.Q497*	ENST00000534358	NM_005933.3	497	Cag/Tag	3/36	1	2	FACETS	0.727	0.567	0.913	0.727	0.567	0.913	CLONAL	1	TRUE	1	0.192236168617788	2		400	329	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374359	118374360	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	26	425	0	ENST00000534358.1:c.7752_7753delinsAA	p.Asp2585Asn	p.D2585N	ENST00000534358	NM_005933.3	2584	caGGat/caAAat	27/36	1	2	FACETS	0.796	0.63	0.985	0.796	0.63	0.985	CLONAL	1	TRUE	1	0.192236168617788	2		425	340	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1036429	1036429	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	71	555	0	ENST00000358495.3:c.349G>A	p.Asp117Asn	p.D117N	ENST00000358495	NM_134424.2	117	Gat/Aat	6/12	0.106278528764864	4	FACETS	0.798	0.697	0.906			1	INDETERMINATE	2	TRUE	NA	0.192236168617788	4		555	552	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421801	49421801	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	247	1129	0	ENST00000301067.7:c.14506G>T	p.Glu4836Ter	p.E4836*	ENST00000301067	NM_003482.3	4836	Gag/Tag	46/54	0.0868904115644928	4	FACETS	1	0.98	1	1	0.98	1	INDETERMINATE	2	TRUE	2	0.192236168617788	4		1129	1357	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794703	120794703	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	133	907	0	ENST00000257552.2:c.652+2T>A		p.X218_splice	ENST00000257552	NM_002442.3	218			0.0868904115644928	4	FACETS	1	0.963	1	1	0.963	1	INDETERMINATE	2	TRUE	2	0.192236168617788	4		907	742	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794764	120794765	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	176	1172	1	ENST00000257552.2:c.592_593delinsAA	p.Gly198Lys	p.G198K	ENST00000257552	NM_002442.3	198	GGg/AAg	9/15	0.0868904115644928	4	FACETS	0.893	0.821	0.969	0.893	0.821	0.969	INDETERMINATE	2	TRUE	2	0.192236168617788	4		1173	1222	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562453	95562454	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	58	529	2	ENST00000393063.1:c.4803_4804delinsAA	p.Ala1602Thr	p.A1602T	ENST00000393063	NM_030621.3	1601	aaGGcc/aaAAcc	24/28	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.192236168617788	2		531	515	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43766915	43766915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	19	232	0	ENST00000382044.4:c.1136C>T	p.Pro379Leu	p.P379L	ENST00000382044	NM_001141980.1	379	cCt/cTt	10/28	1	2	FACETS	0.845	0.643	1	0.845	0.643	1	CLONAL	1	TRUE	1	0.192236168617788	2		232	234	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634354	23634354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	96	594	0	ENST00000261584.4:c.2932G>A	p.Val978Ile	p.V978I	ENST00000261584	NM_024675.3	978	Gtt/Att	9/13	0.0868904115644928	4	FACETS	0.912	0.813	1	0.912	0.813	1	INDETERMINATE	2	TRUE	2	0.192236168617788	4		594	653	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868686	56868686	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	39	395	2	ENST00000308159.5:c.1778G>A	p.Arg593Lys	p.R593K	ENST00000308159	NM_014669.4	593	aGa/aAa	16/22	0.0868904115644928	4	FACETS	1	0.948	1	0.703	0.584	0.835	INDETERMINATE	1	TRUE	2	0.192236168617788	4		397	344	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821444	72821445	+	missense_variant	Missense_Mutation	DNP	GC	GC	TA	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	109	686	0	ENST00000268489.5:c.10730_10731delinsTA	p.Cys3577Leu	p.C3577L	ENST00000268489	NM_006885.3	3577	tGC/tTA	10/10	0.0868904115644928	4	FACETS	0.799	0.717	0.886	0.799	0.717	0.886	INDETERMINATE	2	TRUE	2	0.192236168617788	4		686	846	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832035	72832036	+	missense_variant	Missense_Mutation	DNP	CT	CT	TA	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	106	733	0	ENST00000268489.5:c.4545_4546delinsTA	p.Glu1515_Asp1516delinsAspAsn	p.E1515_D1516delinsDN	ENST00000268489	NM_006885.3	1515	gaAGac/gaTAac	9/10	0.0868904115644928	4	FACETS	0.981	0.881	1	0.981	0.881	1	INDETERMINATE	2	TRUE	2	0.192236168617788	4		733	670	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89833568	89833568	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs980582362	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	41	357	0	ENST00000389301.3:c.2582C>T	p.Ser861Phe	p.S861F	ENST00000389301	NM_000135.2	861	tCt/tTt	27/43	0.0868904115644928	4	FACETS	1	0.947	1	0.684	0.571	0.809	INDETERMINATE	1	TRUE	2	0.192236168617788	4		357	372	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223102	1223102	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	255	1028	0	ENST00000326873.7:c.1039G>C	p.Ala347Pro	p.A347P	ENST00000326873	NM_000455.4	347	Gcg/Ccg	8/10	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.192236168617788	2		1028	1143	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097222	11097223	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	69	1084	3	ENST00000358026.2:c.713_714delinsTT	p.Pro238Leu	p.P238L	ENST00000358026	NM_001128849.1	238	cCC/cTT	4/36	0.192236168617788	4	FACETS	0.813	0.706	0.929	0.271	0.235	0.31	CLONAL	1	TRUE	1	0.192236168617788	4		1087	1053	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277954	18277954	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	135	638	0	ENST00000222254.8:c.1574C>T	p.Ser525Phe	p.S525F	ENST00000222254	NM_005027.3	525	tCc/tTc	13/16	0.192236168617788	4	FACETS	1	0.973	1	0.783	0.713	0.856	CLONAL	2	TRUE	1	0.192236168617788	4		638	713	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743891	41743891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	80	1117	0	ENST00000301178.4:c.826C>T	p.Pro276Ser	p.P276S	ENST00000301178	NM_021913.4	276	Cca/Tca	7/20	1	2	FACETS	0.822	0.722	0.931	0.822	0.722	0.931	CLONAL	1	TRUE	1	0.192236168617788	2		1117	1012	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222405	39222405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	100	667	1	ENST00000402219.2:c.3205C>T	p.Pro1069Ser	p.P1069S	ENST00000402219	NM_005633.3	1069	Cct/Tct	20/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.192236168617788	2		668	706	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46588200	46588201	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	52	755	1	ENST00000263734.3:c.750_751delinsAA	p.Met250_Asp251delinsIleAsn	p.M250_D251delinsIN	ENST00000263734	NM_001430.4	250	atGGac/atAAac	6/16	1	2	FACETS	0.757	0.643	0.882	0.757	0.643	0.882	SUBCLONAL	1	TRUE	1	0.192236168617788	2		756	715	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607829	46607829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	69	1027	0	ENST00000263734.3:c.2018C>T	p.Pro673Leu	p.P673L	ENST00000263734	NM_001430.4	673	cCa/cTa	12/16	1	2	FACETS	0.866	0.753	0.989	0.866	0.753	0.989	CLONAL	1	TRUE	1	0.192236168617788	2		1027	829	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574440	41574440	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	56	824	0	ENST00000263253.7:c.6725T>A	p.Ile2242Lys	p.I2242K	ENST00000263253	NM_001429.3	2242	aTa/aAa	31/31	1	2	FACETS	0.858	0.734	0.994	0.858	0.734	0.994	CLONAL	1	TRUE	1	0.192236168617788	2		824	679	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164561	47164561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	29	345	0	ENST00000409792.3:c.1565C>T	p.Ser522Leu	p.S522L	ENST00000409792	NM_014159.6	522	tCa/tTa	3/21	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.192236168617788	2		345	229	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272504	142272504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	118	553	0	ENST00000350721.4:c.2611C>T	p.Leu871Phe	p.L871F	ENST00000350721	NM_001184.3	871	Ctt/Ttt	12/47	0.192236168617788	4	FACETS	1	0.919	1	1	0.919	1	CLONAL	3	TRUE	1	0.192236168617788	4		553	481	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916767	178916767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	95	419	0	ENST00000263967.3:c.154G>A	p.Glu52Lys	p.E52K	ENST00000263967	NM_006218.2	52	Gaa/Aaa	2/21	0.192236168617788	4	FACETS	0.967	0.867	1	0.967	0.867	1	CLONAL	3	TRUE	1	0.192236168617788	4		419	406	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258962	153258963	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	23	192	0	ENST00000281708.4:c.852_853delinsTT	p.Pro285Ser	p.P285S	ENST00000281708	NM_033632.3	284	ctCCct/ctTTct	5/12	0.192236168617788	2	FACETS	1	0.915	1	0.696	0.547	0.865	CLONAL	1	TRUE	0	0.192236168617788	2		192	172	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541222	187541222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	171	473	1	ENST00000441802.2:c.6518C>T	p.Thr2173Ile	p.T2173I	ENST00000441802	NM_005245.3	2173	aCt/aTt	10/27	0.192236168617788	7	FACETS	0.985	0.912	1	0.985	0.912	1	CLONAL	5	TRUE	2	0.192236168617788	7		474	535	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674230	86674230	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	59	322	0	ENST00000274376.6:c.2362T>A	p.Phe788Ile	p.F788I	ENST00000274376	NM_002890.2	788	Ttt/Att	18/25	0.172326782415435	3	FACETS	0.988	0.861	1	0.988	0.861	1	CLONAL	3	TRUE	0	0.192236168617788	3		322	227	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165260	32165260	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	109	1143	1	ENST00000375023.3:c.4868G>A	p.Gly1623Glu	p.G1623E	ENST00000375023	NM_004557.3	1623	gGg/gAg	27/30	0.192236168617788	4	FACETS	1	0.965	1	0.394	0.353	0.438	CLONAL	1	TRUE	1	0.192236168617788	4		1144	1144	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265577	152265577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	57	580	0	ENST00000206249.3:c.1030G>A	p.Gly344Ser	p.G344S	ENST00000206249	NM_000125.3	344	Ggc/Agc	4/8	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.192236168617788	2		580	550	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469968	157469968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	63	688	0	ENST00000346085.5:c.2762C>T	p.Pro921Leu	p.P921L	ENST00000346085	NM_020732.3	921	cCt/cTt	9/20	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.192236168617788	2		688	557	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528042	157528043	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	54	697	0	ENST00000346085.5:c.5767_5768delinsTT	p.Pro1923Phe	p.P1923F	ENST00000346085	NM_020732.3	1923	CCc/TTc	20/20	1	2	FACETS	0.879	0.75	1	0.879	0.75	1	CLONAL	1	TRUE	1	0.192236168617788	2		697	639	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38153434	38153434	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	143	560	0	ENST00000317025.8:c.2795C>T	p.Ser932Phe	p.S932F	ENST00000317025	NM_023034.1	932	tCc/tTc	16/24	0.192236168617788	5	FACETS	0.885	0.808	0.965	0.885	0.808	0.965	CLONAL	3	TRUE	2	0.192236168617788	5		560	722	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139392010	139392011	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	91	781	1	ENST00000277541.6:c.6181-1_6181delinsAA		p.X2061_splice	ENST00000277541	NM_017617.3	2061		34/34	0.192236168617788	2	FACETS	1	0.979	1	0.741	0.658	0.829	CLONAL	1	TRUE	0	0.192236168617788	2		782	639	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357181	70357182	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	113	402	2	ENST00000374080.3:c.5696_5697delinsAA	p.Arg1899Gln	p.R1899Q	ENST00000374080		1899	cGG/cAA	39/45	0.192236168617788	2	FACETS	0.96	0.871	1			1	CLONAL	3	TRUE	NA	0.192236168617788	2		404	408	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629426	187629428	+	frameshift_variant	Frame_Shift_Del	DEL	ACG	ACG	CA	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	129	796	2	ENST00000441802.2:c.1554_1556delinsTG	p.Val519GlyfsTer11	p.V519Gfs*11	ENST00000441802	NM_005245.3	518	gcCGTg/gcTGg	2/27	0.192236168617788	7	FACETS	1	0.916	1	0.405	0.367	0.446	CLONAL	2	TRUE	2	0.192236168617788	7		798	981	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628116	187628126	+	frameshift_variant	Frame_Shift_Del	DEL	AATCAGGATCG	AATCAGGATCG	T	novel	NA	P-0055194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	312	755	0	ENST00000441802.2:c.2856_2866delinsA	p.His952GlnfsTer2	p.H952Qfs*2	ENST00000441802	NM_005245.3	952	caCGATCCTGATTta/caAta	2/27	0.192236168617788	7	FACETS	0.955	0.902	1	0.955	0.902	1	CLONAL	5	TRUE	2	0.192236168617788	7		755	1007	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	134	397	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.97	0.891	1	0.97	0.891	1	CLONAL	1	TRUE	1	0.71	2		397	389	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	58	439	0	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	1	2	FACETS	0.211	0.181	0.245	0.211	0.181	0.245	SUBCLONAL	1	TRUE	1	0.71	2		439	773	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	134	457	2	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	0.993	0.913	1	0.993	0.913	1	CLONAL	1	TRUE	1	0.71	2		459	380	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	160	414	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.71	2		414	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	184	845	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.527	0.486	0.57	0.527	0.486	0.57	SUBCLONAL	1	TRUE	1	0.71	2		845	983	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039374	49039374	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853293	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	37	485	0	ENST00000267163.4:c.2359C>T	p.Arg787Ter	p.R787*	ENST00000267163	NM_000321.2	787	Cga/Tga	23/27	1	2	FACETS	0.178	0.146	0.214	0.178	0.146	0.214	SUBCLONAL	1	TRUE	1	0.71	2		485	586	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226579931	226579931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765535441	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	60	534	1	ENST00000366794.5:c.371C>T	p.Thr124Met	p.T124M	ENST00000366794	NM_001618.3	124	aCg/aTg	3/23	1	2	FACETS	0.194	0.167	0.225	0.194	0.167	0.225	SUBCLONAL	1	TRUE	1	0.71	2		535	869	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513327	44513327	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755118626	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	443	618	1	ENST00000291552.4:c.608G>A	p.Arg203His	p.R203H	ENST00000291552	NM_006758.2	203	cGt/cAt	8/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.71	2		619	1159	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	452	797	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.71	2		798	1074	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175528	108175528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs376603775	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	175	340	0	ENST00000278616.4:c.5623C>T	p.Arg1875Ter	p.R1875*	ENST00000278616	NM_000051.3	1875	Cga/Tga	37/63	1	2	FACETS	0.939	0.871	1	0.939	0.871	1	CLONAL	1	TRUE	1	0.71	2		340	525	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357069	70357069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200279192	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	432	755	1	ENST00000374080.3:c.5584C>T	p.Arg1862Cys	p.R1862C	ENST00000374080		1862	Cgc/Tgc	39/45	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.71	2		756	1070	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	90	257	2	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.851	0.764	0.941	0.851	0.764	0.941	CLONAL	1	TRUE	1	0.71	2		259	298	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546847	9546847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	56	458	0	ENST00000353224.5:c.1175C>T	p.Ser392Leu	p.S392L	ENST00000353224	NM_177990.2	392	tCg/tTg	5/10	1	2	FACETS	0.239	0.204	0.278	0.239	0.204	0.278	SUBCLONAL	1	TRUE	1	0.71	2		458	659	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38954956	38954956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759388560	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	17	163	1	ENST00000357387.3:c.2617C>T	p.Arg873Cys	p.R873C	ENST00000357387	NM_152756.3	873	Cgt/Tgt	27/38	1	2	FACETS	0.297	0.223	0.385	0.297	0.223	0.385	SUBCLONAL	1	TRUE	1	0.71	2		164	161	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026664	6026664	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750534	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	511	823	1	ENST00000265849.7:c.1732C>T	p.Arg578Cys	p.R578C	ENST00000265849	NM_000535.5	578	Cgt/Tgt	11/15	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.71	2		824	1275	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053589	37053589	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs63751615	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	125	358	0	ENST00000231790.2:c.676C>T	p.Arg226Ter	p.R226*	ENST00000231790	NM_000249.3	226	Cga/Tga	8/19	1	2	FACETS	0.885	0.808	0.964	0.885	0.808	0.964	CLONAL	1	TRUE	1	0.71	2		358	398	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553761	106553761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	44	318	0	ENST00000369096.4:c.1726G>A	p.Glu576Lys	p.E576K	ENST00000369096	NM_001198.3	576	Gaa/Aaa	5/7	1	2	FACETS	0.192	0.161	0.228	0.192	0.161	0.228	SUBCLONAL	1	TRUE	1	0.71	2		318	644	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40742171	40742171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1206035617	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	65	759	0	ENST00000392038.2:c.953C>T	p.Ala318Val	p.A318V	ENST00000392038	NM_001626.4	318	gCg/gTg	10/14	1	2	FACETS	0.186	0.161	0.214	0.186	0.161	0.214	SUBCLONAL	1	TRUE	1	0.71	2		759	982	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709523	176709523	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs797045057	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	26	256	1	ENST00000439151.2:c.5950C>T	p.Arg1984Ter	p.R1984*	ENST00000439151	NM_022455.4	1984	Cga/Tga	19/23	1	2	FACETS	0.284	0.225	0.351	0.284	0.225	0.351	SUBCLONAL	1	TRUE	1	0.71	2		257	258	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480621	120480621	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	127	264	0	ENST00000256646.2:c.3196C>A	p.Leu1066Ile	p.L1066I	ENST00000256646	NM_024408.3	1066	Ctc/Atc	20/34	1	2	FACETS	0.778	0.709	0.849	0.778	0.709	0.849	SUBCLONAL	1	TRUE	1	0.71	2		264	460	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941657	48941657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1060503077	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	52	154	0	ENST00000267163.4:c.967G>T	p.Glu323Ter	p.E323*	ENST00000267163	NM_000321.2	323	Gaa/Taa	10/27	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.71	2		154	139	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52693404	52693404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	443	823	1	ENST00000322088.6:c.55G>A	p.Glu19Lys	p.E19K	ENST00000322088	NM_014225.5	19	Gaa/Aaa	1/15	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.71	2		824	1079	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914890	32914890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	78	296	0	ENST00000380152.3:c.6398C>T	p.Ser2133Leu	p.S2133L	ENST00000380152		2133	tCa/tTa	11/27	1	2	FACETS	0.882	0.786	0.982	0.882	0.786	0.982	CLONAL	1	TRUE	1	0.71	2		296	249	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900171	101900171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564161322	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	24	222	0	ENST00000374994.4:c.605C>T	p.Ala202Val	p.A202V	ENST00000374994	NM_004612.2	202	gCg/gTg	4/9	1	2	FACETS	0.264	0.207	0.329	0.264	0.207	0.329	SUBCLONAL	1	TRUE	1	0.71	2		222	256	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067192	37067192	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201673334	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	185	340	1	ENST00000231790.2:c.1103C>T	p.Ser368Leu	p.S368L	ENST00000231790	NM_000249.3	368	tCg/tTg	12/19	1	2	FACETS	0.976	0.908	1	0.976	0.908	1	CLONAL	1	TRUE	1	0.71	2		341	534	SUCCESS
APC	324	MSKCC	GRCh37	5	112176056	112176056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs72541813	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	38	239	0	ENST00000257430.4:c.4765C>T	p.Arg1589Cys	p.R1589C	ENST00000257430	NM_000038.5	1589	Cgt/Tgt	16/16	1	2	FACETS	0.285	0.235	0.339	0.285	0.235	0.339	SUBCLONAL	1	TRUE	1	0.71	2		239	376	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134688	41134688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1034299550	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	158	335	0	ENST00000379561.5:c.940C>T	p.Arg314Cys	p.R314C	ENST00000379561	NM_002015.3	314	Cgc/Tgc	2/3	1	2	FACETS	0.991	0.917	1	0.991	0.917	1	CLONAL	1	TRUE	1	0.71	2		335	449	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70355083	70355083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779481901	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	400	716	0	ENST00000374080.3:c.5005G>A	p.Asp1669Asn	p.D1669N	ENST00000374080		1669	Gat/Aat	36/45	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.71	2		716	1125	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191488	10191488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs5030818	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	48	340	0	ENST00000256474.2:c.481C>T	p.Arg161Ter	p.R161*	ENST00000256474	NM_000551.3	161	Cga/Tga	3/3	1	2	FACETS	0.216	0.182	0.254	0.216	0.182	0.254	SUBCLONAL	1	TRUE	1	0.71	2		340	625	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964125	28964125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377395740	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	87	326	0	ENST00000282397.4:c.1777C>T	p.Arg593Trp	p.R593W	ENST00000282397	NM_002019.4	593	Cgg/Tgg	13/30	1	2	FACETS	0.773	0.691	0.858	0.773	0.691	0.858	SUBCLONAL	1	TRUE	1	0.71	2		326	317	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103513946	103513946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	81	298	0	ENST00000355739.4:c.762G>A	p.Met254Ile	p.M254I	ENST00000355739	NM_000123.3	254	atG/atA	7/15	1	2	FACETS	0.809	0.721	0.901	0.809	0.721	0.901	CLONAL	1	TRUE	1	0.71	2		298	282	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127447	55127447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1333247214	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	289	483	0	ENST00000257290.5:c.235G>A	p.Gly79Ser	p.G79S	ENST00000257290	NM_006206.4	79	Ggc/Agc	3/23	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.71	2		483	795	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012465	29012465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373801409	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	28	348	0	ENST00000282397.4:c.406G>A	p.Val136Ile	p.V136I	ENST00000282397	NM_002019.4	136	Gta/Ata	4/30	1	2	FACETS	0.203	0.162	0.25	0.203	0.162	0.25	SUBCLONAL	1	TRUE	1	0.71	2		348	389	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344760	65344760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768706312	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	50	304	0	ENST00000342505.4:c.277C>T	p.Arg93Cys	p.R93C	ENST00000342505	NM_002227.2	93	Cgc/Tgc	4/25	1	2	FACETS	0.29	0.246	0.338	0.29	0.246	0.338	SUBCLONAL	1	TRUE	1	0.71	2		304	486	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257789	133257789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143626223	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	87	490	1	ENST00000320574.5:c.139C>T	p.Arg47Trp	p.R47W	ENST00000320574	NM_006231.2	47	Cgg/Tgg	2/49	1	2	FACETS	0.286	0.252	0.322	0.286	0.252	0.322	SUBCLONAL	1	TRUE	1	0.71	2		491	858	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730859	40730859	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	377	669	0	ENST00000373198.4:c.3676C>T	p.Arg1226Ter	p.R1226*	ENST00000373198	NM_133170.3	1226	Cga/Tga	27/32	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.71	2		669	1024	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921567	178921567	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553821144	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	62	362	0	ENST00000263967.3:c.1049A>G	p.Asp350Gly	p.D350G	ENST00000263967	NM_006218.2	350	gAc/gGc	5/21	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.71	2		362	147	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39644733	39644733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	20	226	1	ENST00000262039.4:c.2462C>T	p.Ser821Phe	p.S821F	ENST00000262039	NM_002647.2	821	tCc/tTc	23/25	1	2	FACETS	0.235	0.18	0.299	0.235	0.18	0.299	SUBCLONAL	1	TRUE	1	0.71	2		227	240	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65323452	65323452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765489448	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	51	384	0	ENST00000342505.4:c.1345G>A	p.Ala449Thr	p.A449T	ENST00000342505	NM_002227.2	449	Gcc/Acc	10/25	1	2	FACETS	0.256	0.217	0.298	0.256	0.217	0.298	SUBCLONAL	1	TRUE	1	0.71	2		384	562	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851131	63851131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778262915	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	321	511	1	ENST00000279873.7:c.1909G>A	p.Asp637Asn	p.D637N	ENST00000279873	NM_032199.2	637	Gac/Aac	10/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.71	2		512	792	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394896	394896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	54	411	1	ENST00000380956.4:c.292C>T	p.Arg98Trp	p.R98W	ENST00000380956	NM_001195286.1	98	Cgg/Tgg	3/9	1	2	FACETS	0.217	0.185	0.252	0.217	0.185	0.252	SUBCLONAL	1	TRUE	1	0.71	2		412	701	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735422	204735422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	190	365	1	ENST00000302823.3:c.223C>T	p.Arg75Trp	p.R75W	ENST00000302823	NM_005214.4	75	Cgg/Tgg	2/4	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.71	2		366	530	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428511	78428511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408536007	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	88	369	0	ENST00000370768.2:c.1288C>T	p.Arg430Cys	p.R430C	ENST00000370768	NM_003902.3	430	Cgt/Tgt	14/20	1	2	FACETS	0.681	0.608	0.758	0.681	0.608	0.758	SUBCLONAL	1	TRUE	1	0.71	2		369	364	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267600319	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	140	326	0	ENST00000257430.4:c.4199C>T	p.Ser1400Leu	p.S1400L	ENST00000257430	NM_000038.5	1400	tCg/tTg	16/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.71	2		326	368	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219113	133219113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771896231	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	393	691	0	ENST00000320574.5:c.4931C>T	p.Ser1644Leu	p.S1644L	ENST00000320574	NM_006231.2	1644	tCg/tTg	37/49	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.71	2		691	976	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	230	461	1	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.71	2		462	632	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650710	67650710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243010179	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	377	515	0	ENST00000264010.4:c.1015C>T	p.Arg339Trp	p.R339W	ENST00000264010	NM_006565.3	339	Cgg/Tgg	5/12	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.71	2		515	972	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586102	29586102	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370852681	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	25	334	0	ENST00000356175.3:c.4322G>A	p.Arg1441Gln	p.R1441Q	ENST00000356175	NM_000267.3	1441	cGg/cAg	32/57	1	2	FACETS	0.207	0.163	0.258	0.207	0.163	0.258	SUBCLONAL	1	TRUE	1	0.71	2		334	340	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023019	150023019	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	226	489	0	ENST00000253339.5:c.244C>T	p.Arg82Ter	p.R82*	ENST00000253339		82	Cga/Tga	1/7	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.71	2		489	623	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993849	72993849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758323451	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	83	588	0	ENST00000268489.5:c.196G>A	p.Ala66Thr	p.A66T	ENST00000268489	NM_006885.3	66	Gcg/Acg	2/10	1	2	FACETS	0.281	0.248	0.318	0.281	0.248	0.318	SUBCLONAL	1	TRUE	1	0.71	2		588	831	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267389	7267389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767658477	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	269	417	0	ENST00000302850.5:c.619G>A	p.Glu207Lys	p.E207K	ENST00000302850	NM_000208.2	207	Gaa/Aaa	2/22	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.71	2		417	714	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918759	50918759	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555793039	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	102	827	0	ENST00000440232.2:c.2629G>A	p.Asp877Asn	p.D877N	ENST00000440232	NM_002691.3	877	Gat/Aat	21/27	1	2	FACETS	0.235	0.209	0.263	0.235	0.209	0.263	SUBCLONAL	1	TRUE	1	0.71	2		827	1221	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955481	48955481	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237070816	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	17	305	0	ENST00000267163.4:c.1597G>A	p.Glu533Lys	p.E533K	ENST00000267163	NM_000321.2	533	Gaa/Aaa	17/27	1	2	FACETS	0.186	0.138	0.242	0.186	0.138	0.242	SUBCLONAL	1	TRUE	1	0.71	2		305	258	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134992	2134992	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774441486	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	426	859	1	ENST00000219476.3:c.4534G>A	p.Asp1512Asn	p.D1512N	ENST00000219476	NM_000548.3	1512	Gac/Aac	35/42	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.71	2		860	1159	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068387	26068387	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	109	336	0	ENST00000435504.4:c.103C>A	p.Leu35Ile	p.L35I	ENST00000435504		35	Ctt/Att	2/13	1	2	FACETS	0.917	0.833	1	0.917	0.833	1	CLONAL	1	TRUE	1	0.71	2		336	335	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115600	108115600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772821016	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	86	334	0	ENST00000278616.4:c.748C>T	p.Arg250Ter	p.R250*	ENST00000278616	NM_000051.3	250	Cga/Tga	7/63	1	2	FACETS	0.835	0.748	0.927	0.835	0.748	0.927	CLONAL	1	TRUE	1	0.71	2		334	290	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245759	41245759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55650082	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	183	449	0	ENST00000357654.3:c.1789G>A	p.Glu597Lys	p.E597K	ENST00000357654	NM_007294.3	597	Gaa/Aaa	10/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.71	2		449	477	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10267124	10267124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751093624	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	48	437	0	ENST00000340748.4:c.1294G>A	p.Glu432Lys	p.E432K	ENST00000340748		432	Gaa/Aaa	17/40	1	2	FACETS	0.169	0.142	0.199	0.169	0.142	0.199	SUBCLONAL	1	TRUE	1	0.71	2		437	798	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428299	33428299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368914740	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	232	608	0	ENST00000345365.6:c.824G>A	p.Arg275Gln	p.R275Q	ENST00000345365	NM_002878.3	275	cGg/cAg	9/10	1	2	FACETS	0.773	0.723	0.825	0.773	0.723	0.825	SUBCLONAL	1	TRUE	1	0.71	2		608	845	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430402	78430402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372081866	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	27	378	0	ENST00000370768.2:c.766C>T	p.Arg256Cys	p.R256C	ENST00000370768	NM_003902.3	256	Cgt/Tgt	10/20	1	2	FACETS	0.199	0.158	0.245	0.199	0.158	0.245	SUBCLONAL	1	TRUE	1	0.71	2		378	383	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120845	94120845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465346253	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	36	405	0	ENST00000369303.4:c.206G>A	p.Arg69Gln	p.R69Q	ENST00000369303	NM_004440.3	69	cGa/cAa	3/17	1	2	FACETS	0.174	0.142	0.209	0.174	0.142	0.209	SUBCLONAL	1	TRUE	1	0.71	2		405	584	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898755	134898755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs546798910	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	131	321	0	ENST00000398015.3:c.1813G>A	p.Glu605Lys	p.E605K	ENST00000398015	NM_004441.4	605	Gaa/Aaa	10/16	1	2	FACETS	0.898	0.822	0.976	0.898	0.822	0.976	CLONAL	1	TRUE	1	0.71	2		321	411	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400902	72400902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1450443698	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	125	231	0	ENST00000357731.5:c.269G>A	p.Arg90Gln	p.R90Q	ENST00000357731	NM_173808.2	90	cGa/cAa	2/7	1	2	FACETS	0.932	0.852	1	0.932	0.852	1	CLONAL	1	TRUE	1	0.71	2		231	378	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216091	7216091	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1332522267	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	196	369	0	ENST00000380728.2:c.968G>A	p.Arg323Gln	p.R323Q	ENST00000380728		323	cGa/cAa	11/11	1	2	FACETS	0.964	0.898	1	0.964	0.898	1	CLONAL	1	TRUE	1	0.71	2		369	573	SUCCESS
APC	324	MSKCC	GRCh37	5	112173495	112173495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147655929	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	16	209	0	ENST00000257430.4:c.2204C>T	p.Ala735Val	p.A735V	ENST00000257430	NM_000038.5	735	gCg/gTg	16/16	1	2	FACETS	0.168	0.124	0.221	0.168	0.124	0.221	SUBCLONAL	1	TRUE	1	0.71	2		209	268	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053236	180053236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200763913	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	66	843	1	ENST00000261937.6:c.1133G>A	p.Arg378His	p.R378H	ENST00000261937	NM_182925.4	378	cGc/cAc	9/30	1	2	FACETS	0.159	0.137	0.183	0.159	0.137	0.183	SUBCLONAL	1	TRUE	1	0.71	2		844	1166	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201008	108201008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881383	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	136	302	0	ENST00000278616.4:c.7375C>T	p.Arg2459Cys	p.R2459C	ENST00000278616	NM_000051.3	2459	Cgt/Tgt	50/63	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.71	2		302	360	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265175	5265175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147257283	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	411	810	3	ENST00000357368.4:c.412G>A	p.Asp138Asn	p.D138N	ENST00000357368	NM_002850.3	138	Gac/Aac	5/38	1	2	FACETS	0.995	0.948	1	0.995	0.948	1	CLONAL	1	TRUE	1	0.71	2		813	1164	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207816	102207816	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	15	187	0	ENST00000263464.3:c.1798C>T	p.Arg600Cys	p.R600C	ENST00000263464	NM_001165.4	600	Cgt/Tgt	9/9	1	2	FACETS	0.182	0.133	0.241	0.182	0.133	0.241	SUBCLONAL	1	TRUE	1	0.71	2		187	232	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274042	10274042	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184494228	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	139	877	2	ENST00000330684.3:c.227G>A	p.Arg76His	p.R76H	ENST00000330684	NM_001134407.1	76	cGc/cAc	2/13	1	2	FACETS	0.307	0.278	0.337	0.307	0.278	0.337	SUBCLONAL	1	TRUE	1	0.71	2		879	1277	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029332	14029332	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866657450	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	36	236	1	ENST00000311895.7:c.1543C>T	p.Arg515Cys	p.R515C	ENST00000311895	NM_005236.2	515	Cgt/Tgt	8/11	1	2	FACETS	0.291	0.24	0.349	0.291	0.24	0.349	SUBCLONAL	1	TRUE	1	0.71	2		237	348	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117753	115117753	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765693432	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	50	275	0	ENST00000257566.3:c.682G>A	p.Ala228Thr	p.A228T	ENST00000257566	NM_016569.3	228	Gct/Act	3/8	1	2	FACETS	0.317	0.269	0.37	0.317	0.269	0.37	SUBCLONAL	1	TRUE	1	0.71	2		275	444	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	9	378	0	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	0.063	0.041	0.091	0.063	0.041	0.091	SUBCLONAL	1	TRUE	1	0.71	2		378	403	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190656594	190656594	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768047966	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	84	185	0	ENST00000441310.2:c.59C>T	p.Ser20Leu	p.S20L	ENST00000441310	NM_000534.4	20	tCg/tTg	2/13	1	2	FACETS	0.886	0.793	0.983	0.886	0.793	0.983	CLONAL	1	TRUE	1	0.71	2		185	267	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919631	28919631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200840674	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	46	480	0	ENST00000282397.4:c.2306C>T	p.Ala769Val	p.A769V	ENST00000282397	NM_002019.4	769	gCg/gTg	16/30	1	2	FACETS	0.238	0.2	0.28	0.238	0.2	0.28	SUBCLONAL	1	TRUE	1	0.71	2		480	545	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340097	116340097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35776110	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	18	206	0	ENST00000397752.3:c.959C>T	p.Ala320Val	p.A320V	ENST00000397752	NM_000245.2	320	gCg/gTg	2/21	1	2	FACETS	0.228	0.172	0.295	0.228	0.172	0.295	SUBCLONAL	1	TRUE	1	0.71	2		206	222	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412637	63412637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779222316	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	266	649	3	ENST00000330258.3:c.530G>A	p.Arg177His	p.R177H	ENST00000330258	NM_152424.3	177	cGc/cAc	2/2	1	2	FACETS	0.893	0.84	0.947	0.893	0.84	0.947	CLONAL	1	TRUE	1	0.71	2		652	839	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576093	88576093	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	70	627	0	ENST00000360948.2:c.1580A>G	p.Asp527Gly	p.D527G	ENST00000360948	NM_001012338.2	527	gAc/gGc	13/19	1	2	FACETS	0.189	0.164	0.216	0.189	0.164	0.216	SUBCLONAL	1	TRUE	1	0.71	2		627	1045	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430276	47430276	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	198	595	1	ENST00000377045.4:c.1552-1G>T		p.X518_splice	ENST00000377045	NM_001654.4	518			1	2	FACETS	0.67	0.622	0.721	0.67	0.622	0.721	SUBCLONAL	1	TRUE	1	0.71	2		596	832	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467842	66467842	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	116	248	0	ENST00000273854.3:c.427G>T	p.Gly143Ter	p.G143*	ENST00000273854	NM_004439.5	143	Gga/Tga	3/18	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.71	2		248	302	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140900	37140900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773910971	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	320	478	1	ENST00000373509.5:c.736G>A	p.Glu246Lys	p.E246K	ENST00000373509	NM_002648.3	246	Gaa/Aaa	5/6	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.71	2		479	803	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342807	87342807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	116	371	2	ENST00000277120.3:c.1092G>T	p.Lys364Asn	p.K364N	ENST00000277120		364	aaG/aaT	9/19	1	2	FACETS	0.734	0.666	0.805	0.734	0.666	0.805	SUBCLONAL	1	TRUE	1	0.71	2		373	445	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259601	89259601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773846066	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	122	322	0	ENST00000336596.2:c.745G>A	p.Glu249Lys	p.E249K	ENST00000336596	NM_005233.5	249	Gaa/Aaa	3/17	1	2	FACETS	0.921	0.842	1	0.921	0.842	1	CLONAL	1	TRUE	1	0.71	2		322	373	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231773	36231773	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1569061762	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	390	591	0	ENST00000300305.3:c.611G>A	p.Arg204Gln	p.R204Q	ENST00000300305		204	cGa/cAa	5/8	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.71	2		591	1006	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003059	42003059	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	212	524	0	ENST00000219905.7:c.2596C>T	p.Arg866Ter	p.R866*	ENST00000219905	NM_001164273.1	866	Cga/Tga	8/24	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.71	2		524	583	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336294	80336294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	54	304	0	ENST00000286548.4:c.1025C>T	p.Ala342Val	p.A342V	ENST00000286548	NM_002072.3	342	gCt/gTt	7/7	1	2	FACETS	0.263	0.224	0.305	0.263	0.224	0.305	SUBCLONAL	1	TRUE	1	0.71	2		304	579	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226308	2226308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	108	932	4	ENST00000326181.6:c.1921C>T	p.Arg641Cys	p.R641C	ENST00000326181	NM_032271.2	641	Cgt/Tgt	20/21	1	2	FACETS	0.233	0.208	0.259	0.233	0.208	0.259	SUBCLONAL	1	TRUE	1	0.71	2		936	1307	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729394	41729394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	82	550	0	ENST00000242208.4:c.1135C>T	p.Arg379Trp	p.R379W	ENST00000242208	NM_002192.2	379	Cgg/Tgg	3/3	1	2	FACETS	0.271	0.238	0.306	0.271	0.238	0.306	SUBCLONAL	1	TRUE	1	0.71	2		550	852	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750681	128750681	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756091827	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	249	644	0	ENST00000377970.2:c.218C>T	p.Thr73Ile	p.T73I	ENST00000377970	NM_002467.4	73	aCc/aTc	2/3	1	2	FACETS	0.86	0.806	0.914	0.86	0.806	0.914	CLONAL	1	TRUE	1	0.71	2		644	816	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101031	4101031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375843855	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	74	527	1	ENST00000262948.5:c.691C>T	p.Arg231Cys	p.R231C	ENST00000262948	NM_030662.3	231	Cgc/Tgc	6/11	1	2	FACETS	0.279	0.244	0.317	0.279	0.244	0.317	SUBCLONAL	1	TRUE	1	0.71	2		528	747	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70005638	70005638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1366402619	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	35	300	0	ENST00000394351.3:c.667C>T	p.Arg223Cys	p.R223C	ENST00000394351	NM_000248.3	223	Cgc/Tgc	7/9	1	2	FACETS	0.331	0.272	0.397	0.331	0.272	0.397	SUBCLONAL	1	TRUE	1	0.71	2		300	298	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578253	28578253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144397269	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	323	408	0	ENST00000241453.7:c.2918G>A	p.Arg973Gln	p.R973Q	ENST00000241453	NM_004119.2	973	cGa/cAa	24/24	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.71	2		408	811	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15969005	15969005	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200294041	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	41	249	0	ENST00000268712.3:c.4745C>T	p.Ala1582Val	p.A1582V	ENST00000268712	NM_006311.3	1582	gCg/gTg	33/46	1	2	FACETS	0.287	0.239	0.34	0.287	0.239	0.34	SUBCLONAL	1	TRUE	1	0.71	2		249	403	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190326	32190326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781213120	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	87	600	0	ENST00000375023.3:c.413C>T	p.Ser138Leu	p.S138L	ENST00000375023	NM_004557.3	138	tCg/tTg	3/30	1	2	FACETS	0.29	0.256	0.326	0.29	0.256	0.326	SUBCLONAL	1	TRUE	1	0.71	2		600	845	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231558	5231558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868011195	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	77	542	2	ENST00000357368.4:c.1918C>T	p.Arg640Cys	p.R640C	ENST00000357368	NM_002850.3	640	Cgc/Tgc	14/38	1	2	FACETS	0.216	0.189	0.246	0.216	0.189	0.246	SUBCLONAL	1	TRUE	1	0.71	2		544	1003	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488443	20488443	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	106	329	0	ENST00000346618.3:c.1099G>T	p.Asp367Tyr	p.D367Y	ENST00000346618	NM_001949.4	367	Gac/Tac	6/7	1	2	FACETS	0.709	0.64	0.781	0.709	0.64	0.781	SUBCLONAL	1	TRUE	1	0.71	2		329	421	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117746794	117746794	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770579408	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	27	264	0	ENST00000368508.3:c.26C>T	p.Pro9Leu	p.P9L	ENST00000368508	NM_002944.2	9	cCg/cTg	1/43	1	2	FACETS	0.245	0.195	0.301	0.245	0.195	0.301	SUBCLONAL	1	TRUE	1	0.71	2		264	311	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228018	53228018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199422238	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	380	733	0	ENST00000375401.3:c.2296C>T	p.Arg766Trp	p.R766W	ENST00000375401	NM_004187.3	766	Cgg/Tgg	16/26	1	2	FACETS	0.992	0.944	1	0.992	0.944	1	CLONAL	1	TRUE	1	0.71	2		733	1079	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383183	42383183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782507150	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	108	622	0	ENST00000221972.3:c.203G>A	p.Arg68His	p.R68H	ENST00000221972	NM_021601.3	68	cGc/cAc	2/5	1	2	FACETS	0.328	0.294	0.365	0.328	0.294	0.365	SUBCLONAL	1	TRUE	1	0.71	2		622	927	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861149	57861149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774058977	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	302	473	1	ENST00000228682.2:c.946G>A	p.Glu316Lys	p.E316K	ENST00000228682	NM_005269.2	316	Gaa/Aaa	9/12	1	2	FACETS	0.974	0.921	1	0.974	0.921	1	CLONAL	1	TRUE	1	0.71	2		474	873	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306960	65306960	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	15	359	0	ENST00000342505.4:c.2617C>T	p.Arg873Cys	p.R873C	ENST00000342505	NM_002227.2	873	Cgc/Tgc	19/25	1	2	FACETS	0.077	0.056	0.103	0.077	0.056	0.103	SUBCLONAL	1	TRUE	1	0.71	2		359	546	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024649	14024649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202243691	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	103	309	0	ENST00000311895.7:c.875G>A	p.Arg292Gln	p.R292Q	ENST00000311895	NM_005236.2	292	cGa/cAa	5/11	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.71	2		309	284	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212495	133212495	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879254168	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	52	373	1	ENST00000320574.5:c.5794C>T	p.Arg1932Cys	p.R1932C	ENST00000320574	NM_006231.2	1932	Cgt/Tgt	42/49	1	2	FACETS	0.252	0.214	0.294	0.252	0.214	0.294	SUBCLONAL	1	TRUE	1	0.71	2		374	581	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519920	29519920	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1172956542	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	208	389	0	ENST00000389048.3:c.1651C>T	p.Arg551Ter	p.R551*	ENST00000389048	NM_004304.4	551	Cga/Tga	9/29	1	2	FACETS	0.986	0.922	1	0.986	0.922	1	CLONAL	1	TRUE	1	0.71	2		389	594	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521999	157521999	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1258284323	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	290	580	0	ENST00000346085.5:c.4271C>T	p.Pro1424Leu	p.P1424L	ENST00000346085	NM_020732.3	1424	cCg/cTg	18/20	1	2	FACETS	0.983	0.928	1	0.983	0.928	1	CLONAL	1	TRUE	1	0.71	2		580	831	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149873	99149873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770541150	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	240	393	0	ENST00000074304.5:c.185G>A	p.Arg62Gln	p.R62Q	ENST00000074304	NM_001134224.1	62	cGa/cAa	5/26	1	2	FACETS	0.973	0.913	1	0.973	0.913	1	CLONAL	1	TRUE	1	0.71	2		393	695	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629400	187629400	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1018407179	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	323	602	1	ENST00000441802.2:c.1582G>A	p.Glu528Lys	p.E528K	ENST00000441802	NM_005245.3	528	Gaa/Aaa	2/27	1	2	FACETS	0.924	0.874	0.974	0.924	0.874	0.974	CLONAL	1	TRUE	1	0.71	2		603	985	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506185	148506185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747933788	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	42	360	0	ENST00000320356.2:c.2173G>A	p.Glu725Lys	p.E725K	ENST00000320356	NM_004456.4	725	Gaa/Aaa	19/20	1	2	FACETS	0.214	0.178	0.254	0.214	0.178	0.254	SUBCLONAL	1	TRUE	1	0.71	2		360	552	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864002	97864002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369636116	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	246	459	1	ENST00000289081.3:c.1664G>A	p.Arg555Gln	p.R555Q	ENST00000289081	NM_000136.2	555	cGa/cAa	15/15	1	2	FACETS	0.998	0.938	1	0.998	0.938	1	CLONAL	1	TRUE	1	0.71	2		460	694	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274007	10274007	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	500	880	0	ENST00000330684.3:c.262G>A	p.Asp88Asn	p.D88N	ENST00000330684	NM_001134407.1	88	Gac/Aac	2/13	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.71	2		880	1306	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267491	7267491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	309	507	0	ENST00000302850.5:c.517G>A	p.Val173Met	p.V173M	ENST00000302850	NM_000208.2	173	Gtg/Atg	2/22	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.71	2		507	807	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216658	2216658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758184437	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	134	992	3	ENST00000398665.3:c.2302G>A	p.Ala768Thr	p.A768T	ENST00000398665	NM_032482.2	768	Gca/Aca	20/28	1	2	FACETS	0.274	0.248	0.301	0.274	0.248	0.301	SUBCLONAL	1	TRUE	1	0.71	2		995	1379	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466972	18466972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	113	256	0	ENST00000266497.5:c.1111G>A	p.Glu371Lys	p.E371K	ENST00000266497		371	Gaa/Aaa	5/31	1	2	FACETS	0.939	0.855	1	0.939	0.855	1	CLONAL	1	TRUE	1	0.71	2		256	339	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910556	29910556	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	152	265	0	ENST00000376809.5:c.96C>A	p.Phe32Leu	p.F32L	ENST00000376809	NM_002116.7	32	ttC/ttA	2/8	1	2	FACETS	0.964	0.911	1	1	0.993	1	CLONAL	2	TRUE	1	0.71	2		265	222	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692978	89692978	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	117	486	0	ENST00000371953.3:c.462C>A	p.Phe154Leu	p.F154L	ENST00000371953	NM_000314.4	154	ttC/ttA	5/9	1	2	FACETS	0.8	0.727	0.875	0.8	0.727	0.875	SUBCLONAL	1	TRUE	1	0.71	2		486	412	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115392	115115392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	186	422	1	ENST00000257566.3:c.934G>A	p.Glu312Lys	p.E312K	ENST00000257566	NM_016569.3	312	Gaa/Aaa	5/8	1	2	FACETS	0.976	0.908	1	0.976	0.908	1	CLONAL	1	TRUE	1	0.71	2		423	537	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376109	225376109	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	126	424	0	ENST00000264414.4:c.845C>A	p.Ser282Tyr	p.S282Y	ENST00000264414	NM_003590.4	282	tCt/tAt	6/16	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.71	2		424	338	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828033	72828033	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774848265	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	84	728	1	ENST00000268489.5:c.8548G>A	p.Glu2850Lys	p.E2850K	ENST00000268489	NM_006885.3	2850	Gag/Aag	9/10	1	2	FACETS	0.198	0.174	0.224	0.198	0.174	0.224	SUBCLONAL	1	TRUE	1	0.71	2		729	1193	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144724	119144724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253824253	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	38	297	1	ENST00000264033.4:c.737G>A	p.Arg246Gln	p.R246Q	ENST00000264033	NM_005188.3	246	cGa/cAa	4/16	1	2	FACETS	0.274	0.227	0.327	0.274	0.227	0.327	SUBCLONAL	1	TRUE	1	0.71	2		298	390	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921773	111921773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765527733	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	47	363	0	ENST00000393256.3:c.562C>T	p.Arg188Cys	p.R188C	ENST00000393256	NM_006538.4	188	Cgt/Tgt	4/4	1	2	FACETS	0.222	0.187	0.261	0.222	0.187	0.261	SUBCLONAL	1	TRUE	1	0.71	2		363	596	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430936	181430936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	94	917	0	ENST00000325404.1:c.788C>T	p.Ala263Val	p.A263V	ENST00000325404	NM_003106.3	263	gCg/gTg	1/1	1	2	FACETS	0.22	0.195	0.247	0.22	0.195	0.247	SUBCLONAL	1	TRUE	1	0.71	2		917	1204	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393440	139393440	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs932710972	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	488	838	0	ENST00000277541.6:c.6091G>A	p.Ala2031Thr	p.A2031T	ENST00000277541	NM_017617.3	2031	Gcc/Acc	33/34	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.71	2		838	1227	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845883	72845883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756387925	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	59	501	0	ENST00000268489.5:c.3584G>A	p.Arg1195His	p.R1195H	ENST00000268489	NM_006885.3	1195	cGc/cAc	6/10	1	2	FACETS	0.221	0.19	0.256	0.221	0.19	0.256	SUBCLONAL	1	TRUE	1	0.71	2		501	751	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347446	91347446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757088548	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	90	345	0	ENST00000355112.3:c.3608C>T	p.Ala1203Val	p.A1203V	ENST00000355112	NM_000057.2	1203	gCg/gTg	19/22	1	2	FACETS	0.657	0.587	0.73	0.657	0.587	0.73	SUBCLONAL	1	TRUE	1	0.71	2		345	386	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647734	206647734	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782440026	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	335	586	0	ENST00000367120.3:c.148G>A	p.Glu50Lys	p.E50K	ENST00000367120	NM_014002.3	50	Gag/Aag	4/22	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.71	2		586	928	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937657	44937657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	126	316	1	ENST00000377967.4:c.2845C>T	p.Arg949Cys	p.R949C	ENST00000377967	NM_021140.2	949	Cgt/Tgt	19/29	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.71	2		317	353	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411777	63411777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767567473	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	370	794	1	ENST00000330258.3:c.1390G>A	p.Ala464Thr	p.A464T	ENST00000330258	NM_152424.3	464	Gcc/Acc	2/2	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.71	2		795	1000	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044541	47044541	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	56	770	2	ENST00000377604.3:c.2038C>T	p.Arg680Ter	p.R680*	ENST00000377604	NM_001204468.1	680	Cga/Tga	18/24	1	2	FACETS	0.155	0.132	0.181	0.155	0.132	0.181	SUBCLONAL	1	TRUE	1	0.71	2		772	1015	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628329	187628329	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	341	569	0	ENST00000441802.2:c.2653C>T	p.Arg885Ter	p.R885*	ENST00000441802	NM_005245.3	885	Cga/Tga	2/27	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.71	2		569	860	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196143	108196143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564652222	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	31	358	1	ENST00000278616.4:c.6679C>T	p.Arg2227Cys	p.R2227C	ENST00000278616	NM_000051.3	2227	Cgc/Tgc	46/63	1	2	FACETS	0.214	0.172	0.26	0.214	0.172	0.26	SUBCLONAL	1	TRUE	1	0.71	2		359	409	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561474	141561474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772070879	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	246	714	0	ENST00000220592.5:c.1331C>T	p.Thr444Met	p.T444M	ENST00000220592	NM_012154.3	444	aCg/aTg	11/19	1	2	FACETS	0.714	0.668	0.761	0.714	0.668	0.761	SUBCLONAL	1	TRUE	1	0.71	2		714	971	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868072	56868072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771065608	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	347	419	0	ENST00000308159.5:c.1570C>T	p.Arg524Trp	p.R524W	ENST00000308159	NM_014669.4	524	Cgg/Tgg	14/22	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.71	2		419	837	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038147	128038147	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144012336	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	52	369	1	ENST00000285398.2:c.1403C>T	p.Ala468Val	p.A468V	ENST00000285398	NM_000122.1	468	gCg/gTg	9/15	1	2	FACETS	0.24	0.204	0.279	0.24	0.204	0.279	SUBCLONAL	1	TRUE	1	0.71	2		370	611	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210688	36210688	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	345	639	1	ENST00000222270.7:c.439C>T	p.Arg147Ter	p.R147*	ENST00000222270	NM_014727.1	147	Cga/Tga	3/37	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.71	2		640	963	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524306	176524306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201490532	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	81	804	0	ENST00000292408.4:c.2167C>T	p.Arg723Cys	p.R723C	ENST00000292408	NM_213647.1	723	Cgt/Tgt	17/18	1	2	FACETS	0.187	0.164	0.212	0.187	0.164	0.212	SUBCLONAL	1	TRUE	1	0.71	2		804	1218	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940079	49940079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778931500	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	130	891	1	ENST00000296474.3:c.964C>T	p.Arg322Trp	p.R322W	ENST00000296474	NM_002447.2	322	Cgg/Tgg	1/20	1	2	FACETS	0.301	0.272	0.331	0.301	0.272	0.331	SUBCLONAL	1	TRUE	1	0.71	2		892	1218	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300906	137300906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	508	772	0	ENST00000481739.1:c.551G>A	p.Arg184Gln	p.R184Q	ENST00000481739	NM_002957.4	184	cGg/cAg	4/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.71	2		772	1306	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486166	99486166	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1287599859	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	176	415	1	ENST00000268035.6:c.3472C>T	p.Arg1158Ter	p.R1158*	ENST00000268035	NM_000875.3	1158	Cga/Tga	19/21	1	2	FACETS	0.783	0.725	0.844	0.783	0.725	0.844	SUBCLONAL	1	TRUE	1	0.71	2		416	633	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128036890	128036890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	44	422	1	ENST00000285398.2:c.1589G>A	p.Arg530Gln	p.R530Q	ENST00000285398	NM_000122.1	530	cGa/cAa	10/15	1	2	FACETS	0.205	0.171	0.243	0.205	0.171	0.243	SUBCLONAL	1	TRUE	1	0.71	2		423	604	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288474	21288474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749456958	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	79	534	0	ENST00000354336.3:c.719C>T	p.Ala240Val	p.A240V	ENST00000354336	NM_005207.3	240	gCg/gTg	2/3	1	2	FACETS	0.29	0.255	0.328	0.29	0.255	0.328	SUBCLONAL	1	TRUE	1	0.71	2		534	767	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128246746	128246746	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	83	476	0	ENST00000265960.3:c.1183C>T	p.Arg395Ter	p.R395*	ENST00000265960	NM_001006617.1	395	Cga/Tga	9/12	1	2	FACETS	0.271	0.239	0.306	0.271	0.239	0.306	SUBCLONAL	1	TRUE	1	0.71	2		476	862	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093455	30093455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776034417	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	26	311	0	ENST00000331968.5:c.1808G>A	p.Arg603His	p.R603H	ENST00000331968	NM_002742.2	603	cGt/cAt	13/18	1	2	FACETS	0.26	0.206	0.321	0.26	0.206	0.321	SUBCLONAL	1	TRUE	1	0.71	2		311	282	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013719	170013719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388201066	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	139	300	1	ENST00000295797.4:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000295797	NM_002740.5	480	Cgc/Tgc	15/18	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.71	2		301	386	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924618	94924618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1400088899	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	54	483	0	ENST00000536441.1:c.292C>T	p.Arg98Cys	p.R98C	ENST00000536441	NM_144665.3	98	Cgc/Tgc	3/10	1	2	FACETS	0.209	0.178	0.243	0.209	0.178	0.243	SUBCLONAL	1	TRUE	1	0.71	2		483	728	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458537	12458537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140204299	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	289	567	1	ENST00000287820.6:c.1154G>A	p.Arg385Gln	p.R385Q	ENST00000287820	NM_015869.4	385	cGa/cAa	6/7	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.71	2		568	797	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958212	11958212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760186886	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	24	268	0	ENST00000353533.5:c.122G>A	p.Arg41His	p.R41H	ENST00000353533	NM_003010.3	41	cGc/cAc	2/11	1	2	FACETS	0.258	0.202	0.322	0.258	0.202	0.322	SUBCLONAL	1	TRUE	1	0.71	2		268	262	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617503	158617503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1034717563	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	285	406	0	ENST00000263640.3:c.1153G>A	p.Glu385Lys	p.E385K	ENST00000263640	NM_001105.4	385	Gaa/Aaa	9/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.71	2		406	731	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859872	117859872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	82	208	0	ENST00000297338.2:c.1763C>T	p.Thr588Met	p.T588M	ENST00000297338	NM_006265.2	588	aCg/aTg	14/14	1	2	FACETS	0.885	0.791	0.983	0.885	0.791	0.983	CLONAL	1	TRUE	1	0.71	2		208	261	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136030	64136030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1380280944	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	106	747	1	ENST00000334205.4:c.1291C>T	p.Arg431Cys	p.R431C	ENST00000334205	NM_003942.2	431	Cgc/Tgc	11/17	1	2	FACETS	0.244	0.218	0.272	0.244	0.218	0.272	SUBCLONAL	1	TRUE	1	0.71	2		748	1222	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080657	5080657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774709145	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	89	302	0	ENST00000381652.3:c.2408G>A	p.Arg803Gln	p.R803Q	ENST00000381652	NM_004972.3	803	cGa/cAa	18/25	1	2	FACETS	0.85	0.763	0.941	0.85	0.763	0.941	CLONAL	1	TRUE	1	0.71	2		302	295	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1272314	1272314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371413388	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	88	775	0	ENST00000310581.5:c.2368G>A	p.Val790Ile	p.V790I	ENST00000310581	NM_198253.2	790	Gtc/Atc	7/16	1	2	FACETS	0.227	0.2	0.256	0.227	0.2	0.256	SUBCLONAL	1	TRUE	1	0.71	2		775	1091	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206664154	206664154	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1553390134	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	58	461	0	ENST00000367120.3:c.1696C>T	p.Leu566Phe	p.L566F	ENST00000367120	NM_014002.3	566	Ctt/Ttt	17/22	1	2	FACETS	0.228	0.195	0.264	0.228	0.195	0.264	SUBCLONAL	1	TRUE	1	0.71	2		461	716	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138845	64138845	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761843231	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	113	587	0	ENST00000334205.4:c.2212G>A	p.Ala738Thr	p.A738T	ENST00000334205	NM_003942.2	738	Gcc/Acc	17/17	1	2	FACETS	0.337	0.303	0.374	0.337	0.303	0.374	SUBCLONAL	1	TRUE	1	0.71	2		587	944	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356269	70356269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	415	672	2	ENST00000374080.3:c.5164C>T	p.Arg1722Trp	p.R1722W	ENST00000374080		1722	Cgg/Tgg	37/45	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.71	2		674	1061	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248598	10248598	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	107	752	0	ENST00000340748.4:c.4155G>T	p.Glu1385Asp	p.E1385D	ENST00000340748		1385	gaG/gaT	35/40	1	2	FACETS	0.258	0.23	0.287	0.258	0.23	0.287	SUBCLONAL	1	TRUE	1	0.71	2		752	1168	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417910	32417910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	85	455	1	ENST00000332351.3:c.1142C>T	p.Ser381Leu	p.S381L	ENST00000332351	NM_024426.4	381	tCg/tTg	7/10	1	2	FACETS	0.295	0.26	0.332	0.295	0.26	0.332	SUBCLONAL	1	TRUE	1	0.71	2		456	813	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348836	89348836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146474985	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	514	924	0	ENST00000301030.4:c.4114G>A	p.Glu1372Lys	p.E1372K	ENST00000301030	NM_001256183.1	1372	Gag/Aag	9/13	1	2	FACETS	0.969	0.928	1	0.969	0.928	1	CLONAL	1	TRUE	1	0.71	2		924	1494	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350105	89350105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368593056	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	138	787	0	ENST00000301030.4:c.2845C>T	p.Arg949Trp	p.R949W	ENST00000301030	NM_001256183.1	949	Cgg/Tgg	9/13	1	2	FACETS	0.305	0.277	0.336	0.305	0.277	0.336	SUBCLONAL	1	TRUE	1	0.71	2		787	1273	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930273	39930273	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769721734	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	101	580	1	ENST00000378444.4:c.3191C>T	p.Ser1064Leu	p.S1064L	ENST00000378444	NM_001123385.1	1064	tCg/tTg	6/15	1	2	FACETS	0.251	0.223	0.28	0.251	0.223	0.28	SUBCLONAL	1	TRUE	1	0.71	2		581	1134	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720315	43720315	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752274598	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	276	484	1	ENST00000382044.4:c.3727C>T	p.Arg1243Cys	p.R1243C	ENST00000382044	NM_001141980.1	1243	Cgt/Tgt	18/28	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.71	2		485	775	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009359	69009359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755479314	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	195	448	0	ENST00000288368.4:c.2476G>A	p.Asp826Asn	p.D826N	ENST00000288368	NM_024870.2	826	Gac/Aac	22/40	1	2	FACETS	0.774	0.718	0.831	0.774	0.718	0.831	SUBCLONAL	1	TRUE	1	0.71	2		448	710	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171378	123171378	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs777893472	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	80	314	1	ENST00000218089.9:c.290C>T	p.Ser97Leu	p.S97L	ENST00000218089	NM_001042749.1	97	tCg/tTg	6/35	1	2	FACETS	0.935	0.836	1	0.935	0.836	1	CLONAL	1	TRUE	1	0.71	2		315	241	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168992	11168992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	165	728	0	ENST00000358026.2:c.4582G>A	p.Glu1528Lys	p.E1528K	ENST00000358026	NM_001128849.1	1528	Gag/Aag	32/36	1	2	FACETS	0.452	0.415	0.491	0.452	0.415	0.491	SUBCLONAL	1	TRUE	1	0.71	2		728	1028	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53244010	53244010	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs945455521	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	82	608	0	ENST00000375401.3:c.983G>A	p.Arg328Gln	p.R328Q	ENST00000375401	NM_004187.3	328	cGg/cAg	8/26	1	2	FACETS	0.286	0.252	0.323	0.286	0.252	0.323	SUBCLONAL	1	TRUE	1	0.71	2		608	807	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527931	103527931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs4150388	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	121	289	0	ENST00000355739.4:c.3239G>A	p.Gly1080Glu	p.G1080E	ENST00000355739	NM_000123.3	1080	gGa/gAa	15/15	1	2	FACETS	0.968	0.885	1	0.968	0.885	1	CLONAL	1	TRUE	1	0.71	2		289	352	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026606	48026606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1358771617	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	139	294	1	ENST00000234420.5:c.1484G>A	p.Arg495Gln	p.R495Q	ENST00000234420	NM_000179.2	495	cGa/cAa	4/10	1	2	FACETS	0.979	0.9	1	0.979	0.9	1	CLONAL	1	TRUE	1	0.71	2		295	400	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266570	115266570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	202	537	1	ENST00000438362.2:c.1945C>T	p.Arg649Cys	p.R649C	ENST00000438362	NM_001242891.1	649	Cgc/Tgc	16/20	1	2	FACETS	0.892	0.831	0.954	0.892	0.831	0.954	CLONAL	1	TRUE	1	0.71	2		538	638	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518270	8518270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556357771	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	143	272	1	ENST00000356435.5:c.1121C>T	p.Ala374Val	p.A374V	ENST00000356435		374	gCg/gTg	10/35	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.71	2		273	389	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151944998	151944998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs546822107	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	11	33	0	ENST00000262189.6:c.2521C>T	p.Arg841Trp	p.R841W	ENST00000262189	NM_170606.2	841	Cgg/Tgg	14/59	1	2	FACETS	0.646	0.46	0.861	0.646	0.46	0.861	SUBCLONAL	1	TRUE	1	0.71	2		33	48	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451194	70451194	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1202179982	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	76	540	0	ENST00000373644.4:c.6034G>A	p.Ala2012Thr	p.A2012T	ENST00000373644	NM_030625.2	2012	Gca/Aca	12/12	1	2	FACETS	0.228	0.199	0.259	0.228	0.199	0.259	SUBCLONAL	1	TRUE	1	0.71	2		540	940	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758852	41758852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756510536	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	306	640	1	ENST00000301178.4:c.1906C>T	p.Arg636Trp	p.R636W	ENST00000301178	NM_021913.4	636	Cgg/Tgg	16/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.71	2		641	817	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969405	44969405	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	94	429	0	ENST00000377967.4:c.4087C>T	p.Arg1363Ter	p.R1363*	ENST00000377967	NM_021140.2	1363	Cga/Tga	28/29	1	2	FACETS	0.637	0.57	0.707	0.637	0.57	0.707	SUBCLONAL	1	TRUE	1	0.71	2		429	416	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783766	50783766	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1196482079	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	205	439	0	ENST00000398568.2:c.157C>T	p.Arg53Cys	p.R53C	ENST00000398568	NM_001042412.1	53	Cgt/Tgt	3/18	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.71	2		439	567	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339776	116339776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367722737	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	147	331	0	ENST00000397752.3:c.638C>T	p.Ser213Leu	p.S213L	ENST00000397752	NM_000245.2	213	tCg/tTg	2/21	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.71	2		331	414	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860023	151860023	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs78004519	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	119	259	0	ENST00000262189.6:c.10639T>C	p.Ser3547Pro	p.S3547P	ENST00000262189	NM_170606.2	3547	Tcc/Ccc	43/59	1	2	FACETS	0.892	0.813	0.973	0.892	0.813	0.973	CLONAL	1	TRUE	1	0.71	2		259	376	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411576	116411576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759522148	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	20	283	0	ENST00000397752.3:c.2755G>A	p.Val919Ile	p.V919I	ENST00000397752	NM_000245.2	919	Gtc/Atc	13/21	1	2	FACETS	0.186	0.142	0.237	0.186	0.142	0.237	SUBCLONAL	1	TRUE	1	0.71	2		283	303	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100975	41100975	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	98	593	0	ENST00000373198.4:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000373198	NM_133170.3	461	Cga/Tga	8/32	1	2	FACETS	0.318	0.283	0.355	0.318	0.283	0.355	SUBCLONAL	1	TRUE	1	0.71	2		593	868	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945021	151945021	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs756918375	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	17	118	0	ENST00000262189.6:c.2498G>T	p.Arg833Ile	p.R833I	ENST00000262189	NM_170606.2	833	aGa/aTa	14/59	1	2	FACETS	0.283	0.212	0.367	0.283	0.212	0.367	SUBCLONAL	1	TRUE	1	0.71	2		118	169	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980613	1980613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764374372	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	62	563	1	ENST00000382891.5:c.4075C>T	p.Arg1359Trp	p.R1359W	ENST00000382891	NM_133335.3	1359	Cgg/Tgg	22/22	1	2	FACETS	0.216	0.186	0.249	0.216	0.186	0.249	SUBCLONAL	1	TRUE	1	0.71	2		564	807	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322412	31322412	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs756666358	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	55	501	2	ENST00000412585.2:c.1043C>T	p.Ala348Val	p.A348V	ENST00000412585	NM_005514.6	348	gCg/gTg	6/8	1	2	FACETS	0.204	0.174	0.237	0.204	0.174	0.237	SUBCLONAL	1	TRUE	1	0.71	2		503	760	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934222	39934222	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1358504792	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	86	675	0	ENST00000378444.4:c.377C>T	p.Pro126Leu	p.P126L	ENST00000378444	NM_001123385.1	126	cCg/cTg	4/15	1	2	FACETS	0.23	0.203	0.26	0.23	0.203	0.26	SUBCLONAL	1	TRUE	1	0.71	2		675	1053	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276798	15276798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763602970	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	391	796	0	ENST00000263388.2:c.5467G>A	p.Asp1823Asn	p.D1823N	ENST00000263388	NM_000435.2	1823	Gac/Aac	30/33	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.71	2		796	1086	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258977	16258977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751501193	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	285	505	0	ENST00000375759.3:c.6242G>A	p.Arg2081Gln	p.R2081Q	ENST00000375759	NM_015001.2	2081	cGa/cAa	11/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.71	2		505	756	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803117	1803117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1330260382	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	487	872	0	ENST00000260795.2:c.469G>A	p.Glu157Lys	p.E157K	ENST00000260795		157	Gag/Aag	4/17	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.71	2		872	1320	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166467	118166467	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755966473	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	182	330	0	ENST00000369448.3:c.977G>A	p.Arg326His	p.R326H	ENST00000369448	NM_017709.3	326	cGc/cAc	2/2	1	2	FACETS	0.99	0.92	1	0.99	0.92	1	CLONAL	1	TRUE	1	0.71	2		330	518	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56409144	56409144	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	103	299	0	ENST00000348428.3:c.1651C>T	p.Arg551Ter	p.R551*	ENST00000348428	NM_006785.3	551	Cga/Tga	14/17	1	2	FACETS	0.984	0.892	1	0.984	0.892	1	CLONAL	1	TRUE	1	0.71	2		299	295	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366353	15366353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200484332	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	236	521	1	ENST00000263377.2:c.1802C>T	p.Ser601Leu	p.S601L	ENST00000263377	NM_058243.2	601	tCg/tTg	10/20	1	2	FACETS	0.944	0.885	1	0.944	0.885	1	CLONAL	1	TRUE	1	0.71	2		522	704	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377048	118377048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	41	361	0	ENST00000534358.1:c.10441C>T	p.Pro3481Ser	p.P3481S	ENST00000534358	NM_005933.3	3481	Ccc/Tcc	27/36	1	2	FACETS	0.219	0.182	0.26	0.219	0.182	0.26	SUBCLONAL	1	TRUE	1	0.71	2		361	528	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006077	22006077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377723228	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	96	653	0	ENST00000276925.6:c.326G>A	p.Arg109His	p.R109H	ENST00000276925	NM_004936.3	109	cGc/cAc	2/2	1	2	FACETS	0.255	0.226	0.286	0.255	0.226	0.286	SUBCLONAL	1	TRUE	1	0.71	2		653	1061	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508580	106508580	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs796052174	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	62	468	0	ENST00000359195.3:c.574G>A	p.Asp192Asn	p.D192N	ENST00000359195	NM_002649.2	192	Gac/Aac	2/11	1	2	FACETS	0.279	0.24	0.32	0.279	0.24	0.32	SUBCLONAL	1	TRUE	1	0.71	2		468	627	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348415	89348415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780686131	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	118	779	0	ENST00000301030.4:c.4535G>A	p.Arg1512His	p.R1512H	ENST00000301030	NM_001256183.1	1512	cGc/cAc	9/13	1	2	FACETS	0.264	0.237	0.293	0.264	0.237	0.293	SUBCLONAL	1	TRUE	1	0.71	2		779	1257	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106435	108106435	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs148590073	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	41	160	0	ENST00000278616.4:c.370A>G	p.Ile124Val	p.I124V	ENST00000278616	NM_000051.3	124	Atc/Gtc	5/63	1	2	FACETS	0.888	0.757	1	0.888	0.757	1	CLONAL	1	TRUE	1	0.71	2		160	130	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248450	212248450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1480034665	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	216	313	0	ENST00000342788.4:c.3817C>T	p.Arg1273Trp	p.R1273W	ENST00000342788	NM_005235.2	1273	Cgg/Tgg	28/28	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.71	2		313	523	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121541	2121541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334081822	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	485	916	0	ENST00000219476.3:c.1870G>A	p.Asp624Asn	p.D624N	ENST00000219476	NM_000548.3	624	Gac/Aac	18/42	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.71	2		916	1281	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517795	187517795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs539528886	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	45	296	0	ENST00000441802.2:c.12899C>T	p.Ala4300Val	p.A4300V	ENST00000441802	NM_005245.3	4300	gCg/gTg	25/27	1	2	FACETS	0.268	0.225	0.315	0.268	0.225	0.315	SUBCLONAL	1	TRUE	1	0.71	2		296	473	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10279024	10279024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1419372864	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	215	389	0	ENST00000340748.4:c.737G>A	p.Arg246Gln	p.R246Q	ENST00000340748		246	cGa/cAa	9/40	1	2	FACETS	0.971	0.908	1	0.971	0.908	1	CLONAL	1	TRUE	1	0.71	2		389	624	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347223	70347223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	46	582	0	ENST00000374080.3:c.2887G>A	p.Asp963Asn	p.D963N	ENST00000374080		963	Gat/Aat	21/45	1	2	FACETS	0.156	0.13	0.184	0.156	0.13	0.184	SUBCLONAL	1	TRUE	1	0.71	2		582	833	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261337	115261337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772339521	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	45	306	0	ENST00000438362.2:c.2384G>A	p.Arg795Gln	p.R795Q	ENST00000438362	NM_001242891.1	795	cGa/cAa	19/20	1	2	FACETS	0.229	0.192	0.27	0.229	0.192	0.27	SUBCLONAL	1	TRUE	1	0.71	2		306	554	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123721	11123721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	386	547	2	ENST00000358026.2:c.2371G>A	p.Ala791Thr	p.A791T	ENST00000358026	NM_001128849.1	791	Gcg/Acg	16/36	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.71	2		549	939	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213317	39213317	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	329	606	0	ENST00000402219.2:c.3650G>A	p.Arg1217Gln	p.R1217Q	ENST00000402219	NM_005633.3	1217	cGa/cAa	23/23	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.71	2		606	913	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705233	52705233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs949208712	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	296	392	0	ENST00000322088.6:c.115G>A	p.Ala39Thr	p.A39T	ENST00000322088	NM_014225.5	39	Gcc/Acc	2/15	1	2	FACETS	0.965	0.911	1	0.965	0.911	1	CLONAL	1	TRUE	1	0.71	2		392	864	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628551	187628551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765982067	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	73	625	0	ENST00000441802.2:c.2431G>A	p.Val811Met	p.V811M	ENST00000441802	NM_005245.3	811	Gtg/Atg	2/27	1	2	FACETS	0.217	0.189	0.248	0.217	0.189	0.248	SUBCLONAL	1	TRUE	1	0.71	2		625	946	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105688	27105688	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	153	344	0	ENST00000324856.7:c.5299G>T	p.Glu1767Ter	p.E1767*	ENST00000324856	NM_006015.4	1767	Gaa/Taa	20/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.71	2		344	422	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360927	118360927	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	202	377	0	ENST00000534358.1:c.4659C>A	p.Phe1553Leu	p.F1553L	ENST00000534358	NM_005933.3	1553	ttC/ttA	13/36	1	2	FACETS	0.905	0.843	0.968	0.905	0.843	0.968	CLONAL	1	TRUE	1	0.71	2		377	629	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918713	32918713	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	40	137	0	ENST00000380152.3:c.6860G>T	p.Arg2287Ile	p.R2287I	ENST00000380152		2287	aGa/aTa	12/27	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.71	2		137	109	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729635	162729635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	275	495	0	ENST00000367921.3:c.721G>A	p.Asp241Asn	p.D241N	ENST00000367921	NM_006182.2	241	Gat/Aat	8/18	1	2	FACETS	0.942	0.888	0.998	0.942	0.888	0.998	CLONAL	1	TRUE	1	0.71	2		495	822	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041379	47041379	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	73	702	1	ENST00000377604.3:c.1723G>A	p.Asp575Asn	p.D575N	ENST00000377604	NM_001204468.1	575	Gat/Aat	16/24	1	2	FACETS	0.219	0.191	0.25	0.219	0.191	0.25	SUBCLONAL	1	TRUE	1	0.71	2		703	938	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992765	68992765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs900217349	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	164	476	1	ENST00000288368.4:c.1730G>A	p.Arg577Gln	p.R577Q	ENST00000288368	NM_024870.2	577	cGa/cAa	16/40	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.71	2		477	457	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395874	395874	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769115445	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	64	571	0	ENST00000380956.4:c.431C>T	p.Pro144Leu	p.P144L	ENST00000380956	NM_001195286.1	144	cCg/cTg	4/9	1	2	FACETS	0.217	0.187	0.25	0.217	0.187	0.25	SUBCLONAL	1	TRUE	1	0.71	2		571	830	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046937	128046937	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	50	466	0	ENST00000285398.2:c.798G>T	p.Gln266His	p.Q266H	ENST00000285398	NM_000122.1	266	caG/caT	6/15	1	2	FACETS	0.19	0.161	0.223	0.19	0.161	0.223	SUBCLONAL	1	TRUE	1	0.71	2		466	740	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379453	225379453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	18	365	0	ENST00000264414.4:c.415G>A	p.Val139Ile	p.V139I	ENST00000264414	NM_003590.4	139	Gtc/Atc	4/16	1	2	FACETS	0.155	0.116	0.2	0.155	0.116	0.2	SUBCLONAL	1	TRUE	1	0.71	2		365	328	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301842	65301842	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	19	172	0	ENST00000342505.4:c.3197C>A	p.Ser1066Tyr	p.S1066Y	ENST00000342505	NM_002227.2	1066	tCt/tAt	23/25	1	2	FACETS	0.238	0.181	0.305	0.238	0.181	0.305	SUBCLONAL	1	TRUE	1	0.71	2		172	225	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519324	176519324	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs777010660	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	60	680	0	ENST00000292408.4:c.730C>T	p.Arg244Trp	p.R244W	ENST00000292408	NM_213647.1	244	Cgg/Tgg	7/18	1	2	FACETS	0.182	0.156	0.211	0.182	0.156	0.211	SUBCLONAL	1	TRUE	1	0.71	2		680	927	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517474	176517474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200344385	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	103	871	2	ENST00000292408.4:c.175C>T	p.Arg59Trp	p.R59W	ENST00000292408	NM_213647.1	59	Cgg/Tgg	3/18	1	2	FACETS	0.237	0.211	0.265	0.237	0.211	0.265	SUBCLONAL	1	TRUE	1	0.71	2		873	1224	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262478	16262478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	132	233	0	ENST00000375759.3:c.9743C>T	p.Ala3248Val	p.A3248V	ENST00000375759	NM_015001.2	3248	gCc/gTc	11/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.71	2		233	319	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514997	103514997	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137877463	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	48	251	1	ENST00000355739.4:c.1498C>T	p.Arg500Trp	p.R500W	ENST00000355739	NM_000123.3	500	Cgg/Tgg	8/15	1	2	FACETS	0.362	0.307	0.423	0.362	0.307	0.423	SUBCLONAL	1	TRUE	1	0.71	2		252	373	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123880971	123880971	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1433378503	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	42	247	1	ENST00000330479.4:c.589G>A	p.Glu197Lys	p.E197K	ENST00000330479	NM_020382.3	197	Gag/Aag	5/9	1	2	FACETS	0.243	0.203	0.288	0.243	0.203	0.288	SUBCLONAL	1	TRUE	1	0.71	2		248	486	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937258	76937258	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	22	405	0	ENST00000373344.5:c.3490G>A	p.Asp1164Asn	p.D1164N	ENST00000373344	NM_000489.3	1164	Gat/Aat	9/35	1	2	FACETS	0.194	0.15	0.245	0.194	0.15	0.245	SUBCLONAL	1	TRUE	1	0.71	2		405	320	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924952	49924952	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1397526390	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	382	665	1	ENST00000296474.3:c.3991C>T	p.Arg1331Ter	p.R1331*	ENST00000296474	NM_002447.2	1331	Cga/Tga	20/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.71	2		666	984	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710735	117710735	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	135	260	0	ENST00000368508.3:c.1537G>T	p.Asp513Tyr	p.D513Y	ENST00000368508	NM_002944.2	513	Gat/Tat	12/43	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.71	2		260	348	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158131	47158131	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	32	306	1	ENST00000409792.3:c.4568G>A	p.Arg1523His	p.R1523H	ENST00000409792	NM_014159.6	1523	cGt/cAt	4/21	1	2	FACETS	0.246	0.199	0.298	0.246	0.199	0.298	SUBCLONAL	1	TRUE	1	0.71	2		307	367	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176700744	176700744	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886041218	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	31	298	0	ENST00000439151.2:c.5581C>T	p.Arg1861Ter	p.R1861*	ENST00000439151	NM_022455.4	1861	Cga/Tga	17/23	1	2	FACETS	0.196	0.158	0.239	0.196	0.158	0.239	SUBCLONAL	1	TRUE	1	0.71	2		298	446	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152614	99152614	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61757084	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	197	313	0	ENST00000074304.5:c.410C>T	p.Thr137Met	p.T137M	ENST00000074304	NM_001134224.1	137	aCg/aTg	7/26	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.71	2		313	533	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212236	36212236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301144035	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	71	709	2	ENST00000222270.7:c.1987G>A	p.Glu663Lys	p.E663K	ENST00000222270	NM_014727.1	663	Gaa/Aaa	3/37	1	2	FACETS	0.204	0.177	0.233	0.204	0.177	0.233	SUBCLONAL	1	TRUE	1	0.71	2		711	982	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142950056	142950056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568595082	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	18	262	0	ENST00000262992.4:c.2654G>A	p.Arg885His	p.R885H	ENST00000262992	NM_001101669.1	885	cGc/cAc	24/24	1	2	FACETS	0.189	0.142	0.245	0.189	0.142	0.245	SUBCLONAL	1	TRUE	1	0.71	2		262	268	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420784	49420784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369790149	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	94	663	0	ENST00000301067.7:c.14965C>T	p.Arg4989Trp	p.R4989W	ENST00000301067	NM_003482.3	4989	Cgg/Tgg	48/54	1	2	FACETS	0.274	0.243	0.307	0.274	0.243	0.307	SUBCLONAL	1	TRUE	1	0.71	2		663	966	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268089	55268089	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1140476	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	387	648	1	ENST00000275493.2:c.2929C>T	p.Arg977Cys	p.R977C	ENST00000275493	NM_005228.3	977	Cgc/Tgc	24/28	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.71	2		649	990	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945640	151945640	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	62	527	0	ENST00000262189.6:c.1879G>T	p.Asp627Tyr	p.D627Y	ENST00000262189	NM_170606.2	627	Gac/Tac	14/59	1	2	FACETS	0.298	0.257	0.342	0.298	0.257	0.342	SUBCLONAL	1	TRUE	1	0.71	2		527	587	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69788814	69788814	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	164	297	0	ENST00000352241.4:c.66A>C	p.Lys22Asn	p.K22N	ENST00000352241	NM_198159.2	22	aaA/aaC	1/10	1	2	FACETS	0.931	0.862	1	0.931	0.862	1	CLONAL	1	TRUE	1	0.71	2		297	496	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712797	43712797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746329471	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	379	650	2	ENST00000382044.4:c.4387C>T	p.Arg1463Cys	p.R1463C	ENST00000382044	NM_001141980.1	1463	Cgt/Tgt	21/28	1	2	FACETS	0.942	0.896	0.99	0.942	0.896	0.99	CLONAL	1	TRUE	1	0.71	2		652	1133	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129917	55129917	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1449637193	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	224	437	0	ENST00000257290.5:c.451C>T	p.Arg151Cys	p.R151C	ENST00000257290	NM_006206.4	151	Cgc/Tgc	4/23	1	2	FACETS	0.998	0.935	1	0.998	0.935	1	CLONAL	1	TRUE	1	0.71	2		437	632	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598311	28598311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1480732926	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	114	824	2	ENST00000253063.3:c.283C>T	p.Arg95Cys	p.R95C	ENST00000253063	NM_031459.4	95	Cgc/Tgc	3/10	1	2	FACETS	0.243	0.218	0.27	0.243	0.218	0.27	SUBCLONAL	1	TRUE	1	0.71	2		826	1321	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396793	139396793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	105	792	1	ENST00000277541.6:c.5315G>A	p.Gly1772Asp	p.G1772D	ENST00000277541	NM_017617.3	1772	gGc/gAc	28/34	1	2	FACETS	0.25	0.223	0.279	0.25	0.223	0.279	SUBCLONAL	1	TRUE	1	0.71	2		793	1181	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908158	41908158	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	461	809	1	ENST00000372991.4:c.364G>A	p.Glu122Lys	p.E122K	ENST00000372991	NM_001760.3	122	Gaa/Aaa	2/5	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.71	2		810	1224	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373196	118373196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377156559	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	41	364	0	ENST00000534358.1:c.6589C>T	p.Arg2197Cys	p.R2197C	ENST00000534358	NM_005933.3	2197	Cgt/Tgt	27/36	1	2	FACETS	0.2	0.166	0.238	0.2	0.166	0.238	SUBCLONAL	1	TRUE	1	0.71	2		364	578	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272236	142272236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367864862	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	14	218	0	ENST00000350721.4:c.2638G>A	p.Ala880Thr	p.A880T	ENST00000350721	NM_001184.3	880	Gca/Aca	13/47	1	2	FACETS	0.163	0.117	0.218	0.163	0.117	0.218	SUBCLONAL	1	TRUE	1	0.71	2		218	242	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930564	32930564	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	35	198	0	ENST00000380152.3:c.7436-1G>T		p.X2479_splice	ENST00000380152		2479			1	2	FACETS	0.342	0.281	0.41	0.342	0.281	0.41	SUBCLONAL	1	TRUE	1	0.71	2		198	288	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256661	16256661	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs371456542	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	159	392	0	ENST00000375759.3:c.3926T>G	p.Phe1309Cys	p.F1309C	ENST00000375759	NM_015001.2	1309	tTt/tGt	11/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.71	2		392	416	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419841	41419841	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	187	447	1	ENST00000373198.4:c.480C>A	p.Phe160Leu	p.F160L	ENST00000373198	NM_133170.3	160	ttC/ttA	3/32	1	2	FACETS	0.994	0.925	1	0.994	0.925	1	CLONAL	1	TRUE	1	0.71	2		448	530	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724998	162724998	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760839128	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	58	392	0	ENST00000367921.3:c.470C>T	p.Pro157Leu	p.P157L	ENST00000367921	NM_006182.2	157	cCg/cTg	6/18	1	2	FACETS	0.264	0.226	0.305	0.264	0.226	0.305	SUBCLONAL	1	TRUE	1	0.71	2		392	620	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724405	43724405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747342463	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	339	538	0	ENST00000382044.4:c.3662C>T	p.Ser1221Leu	p.S1221L	ENST00000382044	NM_001141980.1	1221	tCg/tTg	17/28	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.71	2		538	854	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347134	347134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200996293	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	485	835	3	ENST00000262320.3:c.1877C>T	p.Ala626Val	p.A626V	ENST00000262320	NM_003502.3	626	gCg/gTg	7/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.71	2		838	1292	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149434859	149434859	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	274	544	2	ENST00000286301.3:c.2595C>A	p.Phe865Leu	p.F865L	ENST00000286301	NM_005211.3	865	ttC/ttA	20/22	1	2	FACETS	0.979	0.923	1	0.979	0.923	1	CLONAL	1	TRUE	1	0.71	2		546	788	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723366	49723366	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	94	610	1	ENST00000449682.2:c.1177C>T	p.Arg393Cys	p.R393C	ENST00000449682	NM_020998.3	393	Cgc/Tgc	10/18	1	2	FACETS	0.288	0.255	0.322	0.288	0.255	0.322	SUBCLONAL	1	TRUE	1	0.71	2		611	921	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509368	149509368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765383598	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	88	605	0	ENST00000261799.4:c.1531C>T	p.Arg511Cys	p.R511C	ENST00000261799	NM_002609.3	511	Cgc/Tgc	10/23	1	2	FACETS	0.237	0.209	0.267	0.237	0.209	0.267	SUBCLONAL	1	TRUE	1	0.71	2		605	1044	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347966	70347966	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770988288	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	43	573	0	ENST00000374080.3:c.3205G>A	p.Asp1069Asn	p.D1069N	ENST00000374080		1069	Gat/Aat	22/45	1	2	FACETS	0.146	0.121	0.174	0.146	0.121	0.174	SUBCLONAL	1	TRUE	1	0.71	2		573	829	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874431	76874431	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	64	246	0	ENST00000373344.5:c.5291T>G	p.Phe1764Cys	p.F1764C	ENST00000373344	NM_000489.3	1764	tTt/tGt	21/35	1	2	FACETS	0.897	0.79	1	0.897	0.79	1	CLONAL	1	TRUE	1	0.71	2		246	201	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394891	394891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	283	402	0	ENST00000380956.4:c.287G>A	p.Arg96His	p.R96H	ENST00000380956	NM_001195286.1	96	cGc/cAc	3/9	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.71	2		402	726	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736915	736915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs910562293	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	145	396	0	ENST00000314574.4:c.1184G>A	p.Arg395Gln	p.R395Q	ENST00000314574	NM_005433.3	395	cGa/cAa	10/12	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.71	2		396	403	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76953080	76953080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	41	396	0	ENST00000373344.5:c.233G>A	p.Arg78Gln	p.R78Q	ENST00000373344	NM_000489.3	78	cGa/cAa	4/35	1	2	FACETS	0.285	0.238	0.338	0.285	0.238	0.338	SUBCLONAL	1	TRUE	1	0.71	2		396	405	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128206814	128206814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	35	387	1	ENST00000265960.3:c.1409C>T	p.Ser470Leu	p.S470L	ENST00000265960	NM_001006617.1	470	tCg/tTg	11/12	1	2	FACETS	0.171	0.139	0.206	0.171	0.139	0.206	SUBCLONAL	1	TRUE	1	0.71	2		388	578	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405240	139405240	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1420968156	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1275	105	814	0	ENST00000277541.6:c.2605G>A	p.Asp869Asn	p.D869N	ENST00000277541	NM_017617.3	869	Gac/Aac	17/34	1	2	FACETS	0.214	0.191	0.239	0.214	0.191	0.239	SUBCLONAL	1	TRUE	1	0.71	2		814	1380	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955551	48955551	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773116120	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	68	233	0	ENST00000267163.4:c.1667G>A	p.Arg556Gln	p.R556Q	ENST00000267163	NM_000321.2	556	cGa/cAa	17/27	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.71	2		233	181	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858679	9858679	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	47	483	1	ENST00000330684.3:c.2722T>C	p.Ser908Pro	p.S908P	ENST00000330684	NM_001134407.1	908	Tcc/Ccc	13/13	1	2	FACETS	0.226	0.19	0.266	0.226	0.19	0.266	SUBCLONAL	1	TRUE	1	0.71	2		484	586	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090523	5090523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370705658	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	13	231	0	ENST00000381652.3:c.2839C>T	p.Arg947Trp	p.R947W	ENST00000381652	NM_004972.3	947	Cgg/Tgg	21/25	1	2	FACETS	0.163	0.116	0.22	0.163	0.116	0.22	SUBCLONAL	1	TRUE	1	0.71	2		231	225	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413151	63413151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	203	584	1	ENST00000330258.3:c.16G>A	p.Asp6Asn	p.D6N	ENST00000330258	NM_152424.3	6	Gat/Aat	2/2	1	2	FACETS	0.702	0.652	0.753	0.702	0.652	0.753	SUBCLONAL	1	TRUE	1	0.71	2		585	815	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224174	36224174	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368273689	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	93	703	0	ENST00000222270.7:c.6724G>A	p.Val2242Met	p.V2242M	ENST00000222270	NM_014727.1	2242	Gtg/Atg	28/37	1	2	FACETS	0.257	0.227	0.288	0.257	0.227	0.288	SUBCLONAL	1	TRUE	1	0.71	2		703	1021	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827367	72827367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368568803	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	112	688	0	ENST00000268489.5:c.9214G>A	p.Val3072Ile	p.V3072I	ENST00000268489	NM_006885.3	3072	Gta/Ata	9/10	1	2	FACETS	0.307	0.275	0.34	0.307	0.275	0.34	SUBCLONAL	1	TRUE	1	0.71	2		688	1029	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661620	227661620	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	66	749	0	ENST00000305123.5:c.1835A>G	p.Tyr612Cys	p.Y612C	ENST00000305123	NM_005544.2	612	tAc/tGc	1/2	1	2	FACETS	0.197	0.17	0.226	0.197	0.17	0.226	SUBCLONAL	1	TRUE	1	0.71	2		749	944	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776149	135776149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1169898186	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	168	351	0	ENST00000298552.3:c.2578G>A	p.Glu860Lys	p.E860K	ENST00000298552	NM_001162426.1	860	Gag/Aag	20/23	1	2	FACETS	0.73	0.674	0.789	0.73	0.674	0.789	SUBCLONAL	1	TRUE	1	0.71	2		351	648	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670543	30670543	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	178	427	0	ENST00000376406.3:c.5977C>T	p.Arg1993Ter	p.R1993*	ENST00000376406	NM_014641.2	1993	Cga/Tga	13/15	1	2	FACETS	0.744	0.688	0.802	0.744	0.688	0.802	SUBCLONAL	1	TRUE	1	0.71	2		427	674	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187135	38187135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356401338	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	439	641	3	ENST00000317025.8:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000317025	NM_023034.1	448	Cgg/Tgg	6/24	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.71	2		644	1139	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556164	29556164	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs137854566	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	9	92	0	ENST00000356175.3:c.2531T>G	p.Leu844Arg	p.L844R	ENST00000356175	NM_000267.3	844	cTt/cGt	21/57	1	2	FACETS	0.22	0.146	0.314	0.22	0.146	0.314	SUBCLONAL	1	TRUE	1	0.71	2		92	115	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262660	16262660	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748733011	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	58	466	0	ENST00000375759.3:c.9925G>A	p.Gly3309Ser	p.G3309S	ENST00000375759	NM_015001.2	3309	Ggc/Agc	11/15	1	2	FACETS	0.224	0.192	0.26	0.224	0.192	0.26	SUBCLONAL	1	TRUE	1	0.71	2		466	728	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390363	56390363	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs902013273	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	90	302	0	ENST00000348428.3:c.1102G>A	p.Glu368Lys	p.E368K	ENST00000348428	NM_006785.3	368	Gaa/Aaa	10/17	1	2	FACETS	0.854	0.766	0.944	0.854	0.766	0.944	CLONAL	1	TRUE	1	0.71	2		302	297	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519045	103519045	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751772171	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	273	467	1	ENST00000355739.4:c.2383G>A	p.Ala795Thr	p.A795T	ENST00000355739	NM_000123.3	795	Gcc/Acc	11/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.71	2		468	725	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874391	76874391	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	30	359	0	ENST00000373344.5:c.5331G>T	p.Arg1777Ser	p.R1777S	ENST00000373344	NM_000489.3	1777	agG/agT	21/35	1	2	FACETS	0.274	0.221	0.334	0.274	0.221	0.334	SUBCLONAL	1	TRUE	1	0.71	2		359	308	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56870541	56870541	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	32	338	0	ENST00000308159.5:c.1811A>G	p.Asp604Gly	p.D604G	ENST00000308159	NM_014669.4	604	gAc/gGc	17/22	1	2	FACETS	0.231	0.187	0.281	0.231	0.187	0.281	SUBCLONAL	1	TRUE	1	0.71	2		338	390	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066846	30066846	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758982696	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	94	453	0	ENST00000331968.5:c.2285G>A	p.Arg762His	p.R762H	ENST00000331968	NM_002742.2	762	cGc/cAc	16/18	1	2	FACETS	0.382	0.339	0.426	0.382	0.339	0.426	SUBCLONAL	1	TRUE	1	0.71	2		453	694	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485083	57485083	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	210	344	1	ENST00000371085.3:c.917C>T	p.Ser306Leu	p.S306L	ENST00000371085	NM_000516.4	306	tCg/tTg	11/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.71	2		345	519	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62325731	62325731	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201560152	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	195	526	1	ENST00000360203.5:c.2999C>T	p.Thr1000Met	p.T1000M	ENST00000360203	NM_001283009.1	1000	aCg/aTg	31/35	1	2	FACETS	0.704	0.653	0.757	0.704	0.653	0.757	SUBCLONAL	1	TRUE	1	0.71	2		527	780	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945082	151945082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	62	672	3	ENST00000262189.6:c.2437C>T	p.Pro813Ser	p.P813S	ENST00000262189	NM_170606.2	813	Cca/Tca	14/59	1	2	FACETS	0.23	0.198	0.265	0.23	0.198	0.265	SUBCLONAL	1	TRUE	1	0.71	2		675	759	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858093	9858093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064796904	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	272	503	0	ENST00000330684.3:c.3308G>A	p.Arg1103His	p.R1103H	ENST00000330684	NM_001134407.1	1103	cGc/cAc	13/13	1	2	FACETS	0.994	0.937	1	0.994	0.937	1	CLONAL	1	TRUE	1	0.71	2		503	771	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857016	9857016	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	69	178	0	ENST00000330684.3:c.4385C>A	p.Ser1462Tyr	p.S1462Y	ENST00000330684	NM_001134407.1	1462	tCt/tAt	13/13	1	2	FACETS	0.827	0.73	0.928	0.827	0.73	0.928	CLONAL	1	TRUE	1	0.71	2		178	235	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112152	115112152	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1444457719	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	70	717	3	ENST00000257566.3:c.1588G>A	p.Ala530Thr	p.A530T	ENST00000257566	NM_016569.3	530	Gcc/Acc	7/8	1	2	FACETS	0.199	0.172	0.227	0.199	0.172	0.227	SUBCLONAL	1	TRUE	1	0.71	2		720	992	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213383	39213383	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	64	543	0	ENST00000402219.2:c.3584G>A	p.Arg1195Gln	p.R1195Q	ENST00000402219	NM_005633.3	1195	cGa/cAa	23/23	1	2	FACETS	0.227	0.196	0.261	0.227	0.196	0.261	SUBCLONAL	1	TRUE	1	0.71	2		543	794	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504063	123504064	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	97	253	0	ENST00000371139.4:c.245dup	p.Asn82LysfsTer22	p.N82Kfs*22	ENST00000371139	NM_001114937.2	80	ata/atAa	3/4	1	2	FACETS	0.942	0.851	1	0.942	0.851	1	CLONAL	1	TRUE	1	0.71	2		253	290	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80071522	80071522	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	17	221	0	ENST00000265081.6:c.2263G>T	p.Glu755Ter	p.E755*	ENST00000265081	NM_002439.4	755	Gaa/Taa	16/24	1	2	FACETS	0.202	0.151	0.263	0.202	0.151	0.263	SUBCLONAL	1	TRUE	1	0.71	2		221	237	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340252	116340252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773200558	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	18	218	0	ENST00000397752.3:c.1114G>A	p.Asp372Asn	p.D372N	ENST00000397752	NM_000245.2	372	Gac/Aac	2/21	1	2	FACETS	0.153	0.114	0.198	0.153	0.114	0.198	SUBCLONAL	1	TRUE	1	0.71	2		218	332	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920601	96920601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746883021	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	221	364	0	ENST00000258439.3:c.379C>T	p.Arg127Cys	p.R127C	ENST00000258439	NM_001193304.2	127	Cgt/Tgt	3/4	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.71	2		364	609	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465555	99465555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753047347	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	72	438	0	ENST00000268035.6:c.2380C>T	p.Arg794Trp	p.R794W	ENST00000268035	NM_000875.3	794	Cgg/Tgg	11/21	1	2	FACETS	0.285	0.249	0.325	0.285	0.249	0.325	SUBCLONAL	1	TRUE	1	0.71	2		438	711	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069382	30069382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	78	674	0	ENST00000338641.4:c.1247C>T	p.Ala416Val	p.A416V	ENST00000338641	NM_000268.3	416	gCg/gTg	12/16	1	2	FACETS	0.215	0.188	0.244	0.215	0.188	0.244	SUBCLONAL	1	TRUE	1	0.71	2		674	1023	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456487	89456487	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	129	311	1	ENST00000336596.2:c.1663C>A	p.Leu555Ile	p.L555I	ENST00000336596	NM_005233.5	555	Ctc/Atc	8/17	1	2	FACETS	0.972	0.891	1	0.972	0.891	1	CLONAL	1	TRUE	1	0.71	2		312	374	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350002	70350002	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	364	658	0	ENST00000374080.3:c.3985C>T	p.Arg1329Ter	p.R1329*	ENST00000374080		1329	Cga/Tga	28/45	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.71	2		658	981	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955099	1955099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	88	636	0	ENST00000382891.5:c.2186G>A	p.Arg729His	p.R729H	ENST00000382891	NM_133335.3	729	cGc/cAc	12/22	1	2	FACETS	0.26	0.229	0.293	0.26	0.229	0.293	SUBCLONAL	1	TRUE	1	0.71	2		636	954	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599975	28599975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1450092599	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	88	704	0	ENST00000253063.3:c.857G>A	p.Arg286His	p.R286H	ENST00000253063	NM_031459.4	286	cGc/cAc	6/10	1	2	FACETS	0.215	0.189	0.242	0.215	0.189	0.242	SUBCLONAL	1	TRUE	1	0.71	2		704	1155	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783870	50783870	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	34	483	0	ENST00000398568.2:c.261G>T	p.Lys87Asn	p.K87N	ENST00000398568	NM_001042412.1	87	aaG/aaT	3/18	1	2	FACETS	0.169	0.137	0.204	0.169	0.137	0.204	SUBCLONAL	1	TRUE	1	0.71	2		483	568	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760723	133760723	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1423362935	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	504	870	1	ENST00000318560.5:c.3046C>T	p.Arg1016Cys	p.R1016C	ENST00000318560	NM_005157.4	1016	Cgc/Tgc	11/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.71	2		871	1324	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682691	86682691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	12	150	0	ENST00000274376.6:c.2896C>T	p.Arg966Cys	p.R966C	ENST00000274376	NM_002890.2	966	Cgt/Tgt	23/25	1	2	FACETS	0.205	0.144	0.279	0.205	0.144	0.279	SUBCLONAL	1	TRUE	1	0.71	2		150	165	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061195	38061195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	264	417	1	ENST00000250448.2:c.794G>A	p.Arg265His	p.R265H	ENST00000250448	NM_004496.3	265	cGc/cAc	2/2	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.71	2		418	685	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332001	81332001	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1351384112	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	86	232	0	ENST00000222390.5:c.2083C>T	p.Arg695Cys	p.R695C	ENST00000222390	NM_000601.4	695	Cgt/Tgt	18/18	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.71	2		232	224	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041358	47041358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	56	651	0	ENST00000377604.3:c.1702G>A	p.Asp568Asn	p.D568N	ENST00000377604	NM_001204468.1	568	Gac/Aac	16/24	1	2	FACETS	0.179	0.153	0.209	0.179	0.153	0.209	SUBCLONAL	1	TRUE	1	0.71	2		651	879	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001092	150001092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755260603	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	27	311	0	ENST00000253339.5:c.2512C>T	p.Arg838Cys	p.R838C	ENST00000253339		838	Cgt/Tgt	4/7	1	2	FACETS	0.247	0.196	0.304	0.247	0.196	0.304	SUBCLONAL	1	TRUE	1	0.71	2		311	308	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141108	55141108	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1060501505	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	24	298	0	ENST00000257290.5:c.1754G>T	p.Arg585Ile	p.R585I	ENST00000257290	NM_006206.4	585	aGa/aTa	12/23	1	2	FACETS	0.184	0.144	0.23	0.184	0.144	0.23	SUBCLONAL	1	TRUE	1	0.71	2		298	368	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813315	102813315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761462868	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	325	530	1	ENST00000307046.8:c.374G>A	p.Arg125His	p.R125H	ENST00000307046	NM_001111285.1	125	cGc/cAc	3/4	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.71	2		531	877	SUCCESS
BLM	641	MSKCC	GRCh37	15	91306240	91306240	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373090621	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	61	267	0	ENST00000355112.3:c.1927C>T	p.Arg643Cys	p.R643C	ENST00000355112	NM_000057.2	643	Cgt/Tgt	8/22	1	2	FACETS	0.481	0.417	0.55	0.481	0.417	0.55	SUBCLONAL	1	TRUE	1	0.71	2		267	357	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55987292	55987292	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758252991	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	30	339	0	ENST00000263923.4:c.133G>A	p.Ala45Thr	p.A45T	ENST00000263923	NM_002253.2	45	Gct/Act	2/30	1	2	FACETS	0.241	0.194	0.294	0.241	0.194	0.294	SUBCLONAL	1	TRUE	1	0.71	2		339	351	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192626	94192626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781378	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	32	414	0	ENST00000323929.3:c.1448G>A	p.Arg483Gln	p.R483Q	ENST00000323929	NM_005591.3	483	cGa/cAa	13/20	1	2	FACETS	0.161	0.13	0.196	0.161	0.13	0.196	SUBCLONAL	1	TRUE	1	0.71	2		414	559	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067204	37067204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	43	359	0	ENST00000231790.2:c.1115C>T	p.Ser372Phe	p.S372F	ENST00000231790	NM_000249.3	372	tCt/tTt	12/19	1	2	FACETS	0.217	0.181	0.257	0.217	0.181	0.257	SUBCLONAL	1	TRUE	1	0.71	2		359	557	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146171	38146171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	448	640	0	ENST00000317025.8:c.3335C>T	p.Ser1112Leu	p.S1112L	ENST00000317025	NM_023034.1	1112	tCg/tTg	19/24	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.71	2		640	1261	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438149	438149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	138	297	0	ENST00000399788.2:c.1820G>A	p.Arg607His	p.R607H	ENST00000399788	NM_001042603.1	607	cGc/cAc	14/28	1	2	FACETS	0.738	0.675	0.803	0.738	0.675	0.803	SUBCLONAL	1	TRUE	1	0.71	2		297	527	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572645	141572645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372742713	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	281	595	0	ENST00000220592.5:c.425C>T	p.Ala142Val	p.A142V	ENST00000220592	NM_012154.3	142	gCg/gTg	4/19	1	2	FACETS	0.82	0.772	0.87	0.82	0.772	0.87	CLONAL	1	TRUE	1	0.71	2		595	965	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661579	227661579	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs993467904	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	71	796	2	ENST00000305123.5:c.1876C>T	p.Arg626Ter	p.R626*	ENST00000305123	NM_005544.2	626	Cga/Tga	1/2	1	2	FACETS	0.213	0.185	0.243	0.213	0.185	0.243	SUBCLONAL	1	TRUE	1	0.71	2		798	941	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843452	156843452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs567093941	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	332	643	0	ENST00000524377.1:c.878C>T	p.Ala293Val	p.A293V	ENST00000524377	NM_002529.3	293	gCg/gTg	8/17	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.71	2		643	934	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777093	9777093	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	83	828	0	ENST00000377346.4:c.857G>A	p.Arg286Gln	p.R286Q	ENST00000377346	NM_005026.3	286	cGg/cAg	7/24	1	2	FACETS	0.214	0.188	0.242	0.214	0.188	0.242	SUBCLONAL	1	TRUE	1	0.71	2		828	1094	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298057	11298057	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	100	606	0	ENST00000361445.4:c.2051A>C	p.Asp684Ala	p.D684A	ENST00000361445	NM_004958.3	684	gAt/gCt	13/58	1	2	FACETS	0.287	0.256	0.321	0.287	0.256	0.321	SUBCLONAL	1	TRUE	1	0.71	2		606	980	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307736	11307736	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	197	453	0	ENST00000361445.4:c.1171A>C	p.Thr391Pro	p.T391P	ENST00000361445	NM_004958.3	391	Aca/Cca	8/58	1	2	FACETS	0.797	0.741	0.855	0.797	0.741	0.855	SUBCLONAL	1	TRUE	1	0.71	2		453	696	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11308093	11308093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	371	653	0	ENST00000361445.4:c.899G>A	p.Cys300Tyr	p.C300Y	ENST00000361445	NM_004958.3	300	tGc/tAc	7/58	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.71	2		653	1005	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237754	16237754	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	201	355	0	ENST00000375759.3:c.1201T>G	p.Phe401Val	p.F401V	ENST00000375759	NM_015001.2	401	Ttc/Gtc	5/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.71	2		355	524	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254609	16254609	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	52	345	0	ENST00000375759.3:c.1874A>C	p.Asp625Ala	p.D625A	ENST00000375759	NM_015001.2	625	gAc/gCc	11/15	1	2	FACETS	0.312	0.265	0.362	0.312	0.265	0.362	SUBCLONAL	1	TRUE	1	0.71	2		345	470	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087425	27087425	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	81	665	0	ENST00000324856.7:c.1999T>A	p.Ser667Thr	p.S667T	ENST00000324856	NM_006015.4	667	Tcc/Acc	5/20	1	2	FACETS	0.217	0.19	0.246	0.217	0.19	0.246	SUBCLONAL	1	TRUE	1	0.71	2		665	1051	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087462	27087462	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1412218679	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	59	690	1	ENST00000324856.7:c.2036C>T	p.Ser679Phe	p.S679F	ENST00000324856	NM_006015.4	679	tCt/tTt	5/20	1	2	FACETS	0.142	0.121	0.165	0.142	0.121	0.165	SUBCLONAL	1	TRUE	1	0.71	2		691	1170	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107044	27107044	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	278	536	0	ENST00000324856.7:c.6655C>T	p.Gln2219Ter	p.Q2219*	ENST00000324856	NM_006015.4	2219	Cag/Tag	20/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.71	2		536	782	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39321524	39321524	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs767798265	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	153	392	0	ENST00000373001.3:c.497A>G	p.Lys166Arg	p.K166R	ENST00000373001	NM_022157.3	166	aAa/aGa	3/7	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.71	2		392	416	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325246	39325246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	58	502	1	ENST00000373001.3:c.73G>A	p.Asp25Asn	p.D25N	ENST00000373001	NM_022157.3	25	Gac/Aac	1/7	1	2	FACETS	0.207	0.177	0.24	0.207	0.177	0.24	SUBCLONAL	1	TRUE	1	0.71	2		503	789	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301893	65301893	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	15	163	1	ENST00000342505.4:c.3146C>A	p.Ala1049Asp	p.A1049D	ENST00000342505	NM_002227.2	1049	gCt/gAt	23/25	1	2	FACETS	0.189	0.138	0.25	0.189	0.138	0.25	SUBCLONAL	1	TRUE	1	0.71	2		164	224	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332574	65332574	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	131	269	0	ENST00000342505.4:c.965G>T	p.Gly322Val	p.G322V	ENST00000342505	NM_002227.2	322	gGa/gTa	7/25	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.71	2		269	349	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339121	65339121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776909862	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	239	441	0	ENST00000342505.4:c.415G>A	p.Glu139Lys	p.E139K	ENST00000342505	NM_002227.2	139	Gag/Aag	5/25	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.71	2		441	645	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339169	65339169	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	45	437	0	ENST00000342505.4:c.367G>T	p.Glu123Ter	p.E123*	ENST00000342505	NM_002227.2	123	Gag/Tag	5/25	1	2	FACETS	0.222	0.186	0.262	0.222	0.186	0.262	SUBCLONAL	1	TRUE	1	0.71	2		437	570	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276373	115276373	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	41	393	0	ENST00000438362.2:c.955A>C	p.Lys319Gln	p.K319Q	ENST00000438362	NM_001242891.1	319	Aaa/Caa	9/20	1	2	FACETS	0.262	0.218	0.311	0.262	0.218	0.311	SUBCLONAL	1	TRUE	1	0.71	2		393	440	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115279461	115279461	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	117	367	0	ENST00000438362.2:c.556A>G	p.Thr186Ala	p.T186A	ENST00000438362	NM_001242891.1	186	Act/Gct	6/20	1	2	FACETS	0.874	0.796	0.955	0.874	0.796	0.955	CLONAL	1	TRUE	1	0.71	2		367	377	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461122	120461122	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	230	357	0	ENST00000256646.2:c.5836A>G	p.Thr1946Ala	p.T1946A	ENST00000256646	NM_024408.3	1946	Aca/Gca	32/34	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.71	2		357	629	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468136	120468136	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777091426	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	73	659	2	ENST00000256646.2:c.4303C>T	p.Arg1435Trp	p.R1435W	ENST00000256646	NM_024408.3	1435	Cgg/Tgg	25/34	1	2	FACETS	0.208	0.181	0.237	0.208	0.181	0.237	SUBCLONAL	1	TRUE	1	0.71	2		661	990	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729623	162729623	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	59	453	0	ENST00000367921.3:c.709T>C	p.Ser237Pro	p.S237P	ENST00000367921	NM_006182.2	237	Tct/Cct	8/18	1	2	FACETS	0.211	0.181	0.244	0.211	0.181	0.244	SUBCLONAL	1	TRUE	1	0.71	2		453	787	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740201	162740201	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	45	425	0	ENST00000367921.3:c.1403A>C	p.Asn468Thr	p.N468T	ENST00000367921	NM_006182.2	468	aAc/aCc	12/18	1	2	FACETS	0.165	0.138	0.195	0.165	0.138	0.195	SUBCLONAL	1	TRUE	1	0.71	2		425	770	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163310211	163310211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536480913	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	36	338	0	ENST00000271452.3:c.664C>T	p.Arg222Cys	p.R222C	ENST00000271452	NM_145697.2	222	Cgt/Tgt	9/14	1	2	FACETS	0.314	0.259	0.376	0.314	0.259	0.376	SUBCLONAL	1	TRUE	1	0.71	2		338	323	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983070	201983070	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	415	630	1	ENST00000359651.3:c.919C>T	p.Arg307Cys	p.R307C	ENST00000359651		307	Cgc/Tgc	7/8	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.71	2		631	1037	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666443	206666443	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	64	580	0	ENST00000367120.3:c.1923T>G	p.Ser641Arg	p.S641R	ENST00000367120	NM_014002.3	641	agT/agG	19/22	1	2	FACETS	0.208	0.179	0.239	0.208	0.179	0.239	SUBCLONAL	1	TRUE	1	0.71	2		580	866	SUCCESS
FH	2271	MSKCC	GRCh37	1	241683019	241683019	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs112335468	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	263	506	0	ENST00000366560.3:c.4T>C	p.Tyr2His	p.Y2H	ENST00000366560	NM_000143.3	2	Tac/Cac	1/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.71	2		506	632	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246490505	246490505	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	42	267	0	ENST00000388985.4:c.529A>C	p.Lys177Gln	p.K177Q	ENST00000388985		177	Aaa/Caa	5/12	1	2	FACETS	0.347	0.29	0.409	0.347	0.29	0.409	SUBCLONAL	1	TRUE	1	0.71	2		267	341	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106068	8106068	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	43	463	0	ENST00000346208.3:c.888G>T	p.Gln296His	p.Q296H	ENST00000346208		296	caG/caT	4/6	1	2	FACETS	0.157	0.131	0.187	0.157	0.131	0.187	SUBCLONAL	1	TRUE	1	0.71	2		463	770	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595928	43595928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs76764689	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	363	780	0	ENST00000355710.3:c.95C>T	p.Ser32Leu	p.S32L	ENST00000355710	NM_020975.4	32	tCg/tTg	2/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.71	2		780	997	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609099	43609099	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	68	778	1	ENST00000355710.3:c.1855T>G	p.Phe619Val	p.F619V	ENST00000355710	NM_020975.4	619	Ttc/Gtc	10/20	1	2	FACETS	0.172	0.148	0.197	0.172	0.148	0.197	SUBCLONAL	1	TRUE	1	0.71	2		779	1116	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450966	70450966	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	56	499	0	ENST00000373644.4:c.5806C>G	p.Pro1936Ala	p.P1936A	ENST00000373644	NM_030625.2	1936	Cct/Gct	12/12	1	2	FACETS	0.207	0.177	0.241	0.207	0.177	0.241	SUBCLONAL	1	TRUE	1	0.71	2		499	761	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690808	89690808	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	23	235	0	ENST00000371953.3:c.215C>A	p.Ala72Asp	p.A72D	ENST00000371953	NM_000314.4	72	gCt/gAt	4/9	1	2	FACETS	0.284	0.222	0.355	0.284	0.222	0.355	SUBCLONAL	1	TRUE	1	0.71	2		235	228	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720732	89720732	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	37	151	0	ENST00000371953.3:c.883C>A	p.Leu295Ile	p.L295I	ENST00000371953	NM_000314.4	295	Cta/Ata	8/9	1	2	FACETS	0.695	0.582	0.816	0.695	0.582	0.816	SUBCLONAL	1	TRUE	1	0.71	2		151	150	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724495	112724495	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	29	407	0	ENST00000369452.4:c.379G>T	p.Glu127Ter	p.E127*	ENST00000369452	NM_007373.3	127	Gaa/Taa	2/9	1	2	FACETS	0.17	0.136	0.209	0.17	0.136	0.209	SUBCLONAL	1	TRUE	1	0.71	2		407	480	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769092	112769092	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	127	385	0	ENST00000369452.4:c.1371G>T	p.Glu457Asp	p.E457D	ENST00000369452	NM_007373.3	457	gaG/gaT	7/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.71	2		385	321	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251956	8251956	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1223	76	820	0	ENST00000335790.3:c.121G>A	p.Asp41Asn	p.D41N	ENST00000335790	NM_002315.2	41	Gac/Aac	2/4	1	2	FACETS	0.165	0.144	0.188	0.165	0.144	0.188	SUBCLONAL	1	TRUE	1	0.71	2		820	1299	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316316	14316316	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	145	405	0	ENST00000256196.4:c.289G>T	p.Asp97Tyr	p.D97Y	ENST00000256196		97	Gat/Tat	3/6	1	2	FACETS	0.996	0.918	1	0.996	0.918	1	CLONAL	1	TRUE	1	0.71	2		405	410	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316400	14316400	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	37	347	0	ENST00000256196.4:c.205A>G	p.Thr69Ala	p.T69A	ENST00000256196		69	Aca/Gca	3/6	1	2	FACETS	0.351	0.29	0.418	0.351	0.29	0.418	SUBCLONAL	1	TRUE	1	0.71	2		347	297	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410635	32410635	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	71	517	0	ENST00000332351.3:c.1523G>T	p.Arg508Ile	p.R508I	ENST00000332351	NM_024426.4	508	aGa/aTa	10/10	1	2	FACETS	0.233	0.202	0.266	0.233	0.202	0.266	SUBCLONAL	1	TRUE	1	0.71	2		517	859	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32438066	32438066	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	69	499	0	ENST00000332351.3:c.971G>T	p.Ser324Ile	p.S324I	ENST00000332351	NM_024426.4	324	aGc/aTc	5/10	1	2	FACETS	0.263	0.228	0.3	0.263	0.228	0.3	SUBCLONAL	1	TRUE	1	0.71	2		499	740	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450099	32450099	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	436	755	0	ENST00000332351.3:c.713A>G	p.Gln238Arg	p.Q238R	ENST00000332351	NM_024426.4	238	cAg/cGg	2/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.71	2		755	1204	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138802	64138802	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	76	652	0	ENST00000334205.4:c.2169G>T	p.Glu723Asp	p.E723D	ENST00000334205	NM_003942.2	723	gaG/gaT	17/17	1	2	FACETS	0.204	0.178	0.233	0.204	0.178	0.233	SUBCLONAL	1	TRUE	1	0.71	2		652	1047	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588811	69588811	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	457	956	0	ENST00000168712.1:c.425A>C	p.Lys142Thr	p.K142T	ENST00000168712	NM_002007.2	142	aAg/aCg	2/3	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.71	2		956	1167	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940546	71940546	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	80	683	0	ENST00000298229.2:c.697T>C	p.Ser233Pro	p.S233P	ENST00000298229	NM_001567.3	233	Tcc/Ccc	6/28	1	2	FACETS	0.195	0.171	0.221	0.195	0.171	0.221	SUBCLONAL	1	TRUE	1	0.71	2		683	1157	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94169022	94169022	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	35	259	0	ENST00000323929.3:c.1970C>A	p.Pro657His	p.P657H	ENST00000323929	NM_005591.3	657	cCt/cAt	18/20	1	2	FACETS	0.318	0.261	0.381	0.318	0.261	0.381	SUBCLONAL	1	TRUE	1	0.71	2		259	310	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94209498	94209498	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	32	249	0	ENST00000323929.3:c.616G>T	p.Asp206Tyr	p.D206Y	ENST00000323929	NM_005591.3	206	Gat/Tat	7/20	1	2	FACETS	0.309	0.251	0.373	0.309	0.251	0.373	SUBCLONAL	1	TRUE	1	0.71	2		249	292	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912830	100912830	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	38	250	0	ENST00000325455.5:c.2492C>A	p.Pro831His	p.P831H	ENST00000325455	NM_001202474.3	831	cCt/cAt	7/8	1	2	FACETS	0.288	0.238	0.343	0.288	0.238	0.343	SUBCLONAL	1	TRUE	1	0.71	2		250	372	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056752	102056752	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	31	253	0	ENST00000282441.5:c.692C>T	p.Pro231Leu	p.P231L	ENST00000282441	NM_001130145.2	231	cCt/cTt	4/9	1	2	FACETS	0.441	0.359	0.532	0.441	0.359	0.532	SUBCLONAL	1	TRUE	1	0.71	2		253	198	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195712	102195712	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs141741107	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	24	270	0	ENST00000263464.3:c.472A>G	p.Met158Val	p.M158V	ENST00000263464	NM_001165.4	158	Atg/Gtg	2/9	1	2	FACETS	0.19	0.148	0.238	0.19	0.148	0.238	SUBCLONAL	1	TRUE	1	0.71	2		270	356	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155016	108155016	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	17	334	0	ENST00000278616.4:c.3809C>A	p.Ser1270Tyr	p.S1270Y	ENST00000278616	NM_000051.3	1270	tCc/tAc	26/63	1	2	FACETS	0.182	0.136	0.237	0.182	0.136	0.237	SUBCLONAL	1	TRUE	1	0.71	2		334	263	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192074	108192074	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	256	445	0	ENST00000278616.4:c.6499T>C	p.Tyr2167His	p.Y2167H	ENST00000278616	NM_000051.3	2167	Tat/Cat	45/63	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.71	2		445	693	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198373	108198373	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	19	262	0	ENST00000278616.4:c.6977A>G	p.Asn2326Ser	p.N2326S	ENST00000278616	NM_000051.3	2326	aAc/aGc	48/63	1	2	FACETS	0.19	0.144	0.244	0.19	0.144	0.244	SUBCLONAL	1	TRUE	1	0.71	2		262	282	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214025	108214025	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	22	264	0	ENST00000278616.4:c.8345A>G	p.Asn2782Ser	p.N2782S	ENST00000278616	NM_000051.3	2782	aAc/aGc	57/63	1	2	FACETS	0.217	0.168	0.274	0.217	0.168	0.274	SUBCLONAL	1	TRUE	1	0.71	2		264	285	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371736	118371736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	153	216	0	ENST00000534358.1:c.6193C>T	p.Arg2065Cys	p.R2065C	ENST00000534358	NM_005933.3	2065	Cgc/Tgc	25/36	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.71	2		216	371	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404940	404940	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	55	415	0	ENST00000399788.2:c.4254A>C	p.Lys1418Asn	p.K1418N	ENST00000399788	NM_001042603.1	1418	aaA/aaC	26/28	1	2	FACETS	0.241	0.206	0.28	0.241	0.206	0.28	SUBCLONAL	1	TRUE	1	0.71	2		415	643	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022362	12022362	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1283269910	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	84	713	0	ENST00000396373.4:c.468C>A	p.Asn156Lys	p.N156K	ENST00000396373	NM_001987.4	156	aaC/aaA	5/8	1	2	FACETS	0.197	0.173	0.223	0.197	0.173	0.223	SUBCLONAL	1	TRUE	1	0.71	2		713	1202	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624400	21624400	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1385224458	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	223	446	0	ENST00000421138.2:c.1629G>T	p.Glu543Asp	p.E543D	ENST00000421138		543	gaG/gaT	14/16	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.71	2		446	618	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123870	46123870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	38	243	0	ENST00000334344.6:c.136G>A	p.Asp46Asn	p.D46N	ENST00000334344	NM_152641.2	46	Gat/Aat	2/21	1	2	FACETS	0.262	0.216	0.312	0.262	0.216	0.312	SUBCLONAL	1	TRUE	1	0.71	2		243	409	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246041	46246041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	17	259	0	ENST00000334344.6:c.4135C>T	p.His1379Tyr	p.H1379Y	ENST00000334344	NM_152641.2	1379	Cat/Tat	15/21	1	2	FACETS	0.167	0.125	0.218	0.167	0.125	0.218	SUBCLONAL	1	TRUE	1	0.71	2		259	286	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287282	46287282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	142	371	0	ENST00000334344.6:c.5227G>A	p.Ala1743Thr	p.A1743T	ENST00000334344	NM_152641.2	1743	Gct/Act	19/21	1	2	FACETS	0.712	0.652	0.774	0.712	0.652	0.774	SUBCLONAL	1	TRUE	1	0.71	2		371	562	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418685	49418685	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	55	479	0	ENST00000301067.7:c.15829G>T	p.Glu5277Ter	p.E5277*	ENST00000301067	NM_003482.3	5277	Gag/Tag	49/54	1	2	FACETS	0.204	0.174	0.237	0.204	0.174	0.237	SUBCLONAL	1	TRUE	1	0.71	2		479	760	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422888	49422888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886049472	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	412	769	0	ENST00000301067.7:c.14207C>T	p.Ala4736Val	p.A4736V	ENST00000301067	NM_003482.3	4736	gCc/gTc	44/54	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.71	2		769	1046	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425775	49425775	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769256800	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	418	830	1	ENST00000301067.7:c.12713G>A	p.Arg4238His	p.R4238H	ENST00000301067	NM_003482.3	4238	cGc/cAc	39/54	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.71	2		831	1007	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426027	49426027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775284012	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	93	831	0	ENST00000301067.7:c.12461G>A	p.Gly4154Asp	p.G4154D	ENST00000301067	NM_003482.3	4154	gGc/gAc	39/54	1	2	FACETS	0.233	0.206	0.261	0.233	0.206	0.261	SUBCLONAL	1	TRUE	1	0.71	2		831	1126	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427525	49427525	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	359	661	0	ENST00000301067.7:c.10963C>A	p.Leu3655Ile	p.L3655I	ENST00000301067	NM_003482.3	3655	Ctt/Att	39/54	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.71	2		661	942	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439878	49439878	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	78	717	0	ENST00000301067.7:c.4663T>G	p.Ser1555Ala	p.S1555A	ENST00000301067	NM_003482.3	1555	Tcc/Gcc	17/54	1	2	FACETS	0.2	0.175	0.228	0.2	0.175	0.228	SUBCLONAL	1	TRUE	1	0.71	2		717	1097	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442897	49442897	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	58	474	0	ENST00000301067.7:c.4011G>T	p.Glu1337Asp	p.E1337D	ENST00000301067	NM_003482.3	1337	gaG/gaT	12/54	1	2	FACETS	0.203	0.174	0.236	0.203	0.174	0.236	SUBCLONAL	1	TRUE	1	0.71	2		474	803	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444724	49444724	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1288	111	912	0	ENST00000301067.7:c.2742G>T	p.Glu914Asp	p.E914D	ENST00000301067	NM_003482.3	914	gaG/gaT	10/54	1	2	FACETS	0.224	0.2	0.249	0.224	0.2	0.249	SUBCLONAL	1	TRUE	1	0.71	2		912	1399	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49449068	49449068	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	215	418	0	ENST00000301067.7:c.40G>T	p.Glu14Ter	p.E14*	ENST00000301067	NM_003482.3	14	Gaa/Taa	1/54	1	2	FACETS	0.935	0.873	0.997	0.935	0.873	0.997	CLONAL	1	TRUE	1	0.71	2		418	648	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859019	57859019	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	345	669	0	ENST00000228682.2:c.515G>T	p.Gly172Val	p.G172V	ENST00000228682	NM_005269.2	172	gGa/gTa	5/12	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.71	2		669	971	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864201	57864201	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	306	585	0	ENST00000228682.2:c.1678T>C	p.Ser560Pro	p.S560P	ENST00000228682	NM_005269.2	560	Tcc/Ccc	12/12	1	2	FACETS	0.949	0.897	1	0.949	0.897	1	CLONAL	1	TRUE	1	0.71	2		585	908	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110038	115110038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1291296572	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	484	729	0	ENST00000257566.3:c.1840G>A	p.Ala614Thr	p.A614T	ENST00000257566	NM_016569.3	614	Gcc/Acc	8/8	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.71	2		729	1193	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112638	115112638	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	99	753	0	ENST00000257566.3:c.1102T>G	p.Leu368Val	p.L368V	ENST00000257566	NM_016569.3	368	Tta/Gta	7/8	1	2	FACETS	0.248	0.221	0.278	0.248	0.221	0.278	SUBCLONAL	1	TRUE	1	0.71	2		753	1123	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549016	21549016	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	111	220	0	ENST00000382592.4:c.3260A>G	p.Tyr1087Cys	p.Y1087C	ENST00000382592	NM_014572.2	1087	tAc/tGc	8/8	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.71	2		220	301	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592644	28592644	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	64	388	0	ENST00000241453.7:c.2501G>A	p.Arg834Gln	p.R834Q	ENST00000241453	NM_004119.2	834	cGa/cAa	20/24	1	2	FACETS	0.301	0.261	0.346	0.301	0.261	0.346	SUBCLONAL	1	TRUE	1	0.71	2		388	598	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622508	28622508	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	36	345	0	ENST00000241453.7:c.1109C>A	p.Ser370Tyr	p.S370Y	ENST00000241453	NM_004119.2	370	tCt/tAt	9/24	1	2	FACETS	0.265	0.218	0.317	0.265	0.218	0.317	SUBCLONAL	1	TRUE	1	0.71	2		345	383	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896497	28896497	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	98	268	0	ENST00000282397.4:c.2954-1G>A		p.X985_splice	ENST00000282397	NM_002019.4	985			1	2	FACETS	0.844	0.761	0.93	0.844	0.761	0.93	CLONAL	1	TRUE	1	0.71	2		268	327	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914792	32914792	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	86	346	0	ENST00000380152.3:c.6300A>C	p.Gln2100His	p.Q2100H	ENST00000380152		2100	caA/caC	11/27	1	2	FACETS	0.958	0.86	1	0.958	0.86	1	CLONAL	1	TRUE	1	0.71	2		346	253	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934246	48934246	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	25	339	0	ENST00000267163.4:c.701T>C	p.Leu234Ser	p.L234S	ENST00000267163	NM_000321.2	234	tTg/tCg	7/27	1	2	FACETS	0.226	0.178	0.281	0.226	0.178	0.281	SUBCLONAL	1	TRUE	1	0.71	2		339	312	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954195	48954195	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	57	169	0	ENST00000267163.4:c.1396G>T	p.Glu466Ter	p.E466*	ENST00000267163	NM_000321.2	466	Gaa/Taa	15/27	1	2	FACETS	0.692	0.601	0.789	0.692	0.601	0.789	SUBCLONAL	1	TRUE	1	0.71	2		169	232	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514006	103514006	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	26	330	0	ENST00000355739.4:c.822G>T	p.Lys274Asn	p.K274N	ENST00000355739	NM_000123.3	274	aaG/aaT	7/15	1	2	FACETS	0.195	0.154	0.242	0.195	0.154	0.242	SUBCLONAL	1	TRUE	1	0.71	2		330	375	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434989	110434989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	100	744	2	ENST00000375856.3:c.3412G>A	p.Ala1138Thr	p.A1138T	ENST00000375856	NM_003749.2	1138	Gca/Aca	1/2	1	2	FACETS	0.243	0.216	0.272	0.243	0.216	0.272	SUBCLONAL	1	TRUE	1	0.71	2		746	1159	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436027	110436027	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1410	98	1009	0	ENST00000375856.3:c.2374G>A	p.Gly792Arg	p.G792R	ENST00000375856	NM_003749.2	792	Ggg/Agg	1/2	1	2	FACETS	0.183	0.162	0.205	0.183	0.162	0.205	SUBCLONAL	1	TRUE	1	0.71	2		1009	1508	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046495	30046495	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	72	452	0	ENST00000331968.5:c.2688G>T	p.Glu896Asp	p.E896D	ENST00000331968	NM_002742.2	896	gaG/gaT	18/18	1	2	FACETS	0.262	0.228	0.299	0.262	0.228	0.299	SUBCLONAL	1	TRUE	1	0.71	2		452	774	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066859	30066859	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	245	460	0	ENST00000331968.5:c.2272A>G	p.Lys758Glu	p.K758E	ENST00000331968	NM_002742.2	758	Aag/Gag	16/18	1	2	FACETS	0.967	0.908	1	0.967	0.908	1	CLONAL	1	TRUE	1	0.71	2		460	714	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105556	30105556	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	72	589	0	ENST00000331968.5:c.1130A>G	p.Asn377Ser	p.N377S	ENST00000331968	NM_002742.2	377	aAc/aGc	7/18	1	2	FACETS	0.212	0.185	0.242	0.212	0.185	0.242	SUBCLONAL	1	TRUE	1	0.71	2		589	955	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554353	81554353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	18	286	0	ENST00000298171.2:c.373C>T	p.Leu125Phe	p.L125F	ENST00000298171	NM_000369.2	125	Ctc/Ttc	4/10	1	2	FACETS	0.148	0.111	0.192	0.148	0.111	0.192	SUBCLONAL	1	TRUE	1	0.71	2		286	343	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557406	95557406	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	153	371	0	ENST00000393063.1:c.5568A>C	p.Glu1856Asp	p.E1856D	ENST00000393063	NM_030621.3	1856	gaA/gaC	27/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.71	2		371	413	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95583999	95583999	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1006363970	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	116	309	0	ENST00000393063.1:c.1469G>A	p.Arg490His	p.R490H	ENST00000393063	NM_030621.3	490	cGc/cAc	10/28	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.71	2		309	326	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591681	38591681	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	56	493	0	ENST00000299084.4:c.140T>C	p.Val47Ala	p.V47A	ENST00000299084	NM_152594.2	47	gTc/gCc	2/7	1	2	FACETS	0.198	0.169	0.23	0.198	0.169	0.23	SUBCLONAL	1	TRUE	1	0.71	2		493	798	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019561	42019561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1230873007	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	152	444	0	ENST00000219905.7:c.3614G>A	p.Gly1205Glu	p.G1205E	ENST00000219905	NM_001164273.1	1205	gGa/gAa	10/24	1	2	FACETS	0.881	0.812	0.952	0.881	0.812	0.952	CLONAL	1	TRUE	1	0.71	2		444	486	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028692	42028692	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	72	481	0	ENST00000219905.7:c.4230G>T	p.Glu1410Asp	p.E1410D	ENST00000219905	NM_001164273.1	1410	gaG/gaT	13/24	1	2	FACETS	0.323	0.282	0.367	0.323	0.282	0.367	SUBCLONAL	1	TRUE	1	0.71	2		481	628	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042126	42042126	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	132	386	0	ENST00000219905.7:c.6321A>C	p.Gln2107His	p.Q2107H	ENST00000219905	NM_001164273.1	2107	caA/caC	17/24	1	2	FACETS	0.875	0.801	0.951	0.875	0.801	0.951	CLONAL	1	TRUE	1	0.71	2		386	425	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782847	66782847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	38	471	0	ENST00000307102.5:c.1076C>T	p.Ala359Val	p.A359V	ENST00000307102	NM_002755.3	359	gCt/gTt	11/11	1	2	FACETS	0.169	0.139	0.202	0.169	0.139	0.202	SUBCLONAL	1	TRUE	1	0.71	2		471	635	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479796	67479796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	364	568	0	ENST00000327367.4:c.1103G>A	p.Arg368Gln	p.R368Q	ENST00000327367	NM_005902.3	368	cGa/cAa	8/9	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.71	2		568	958	SUCCESS
BLM	641	MSKCC	GRCh37	15	91290718	91290718	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	26	221	0	ENST00000355112.3:c.96T>G	p.Phe32Leu	p.F32L	ENST00000355112	NM_000057.2	32	ttT/ttG	2/22	1	2	FACETS	0.268	0.213	0.332	0.268	0.213	0.332	SUBCLONAL	1	TRUE	1	0.71	2		221	273	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478636	99478636	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	239	415	0	ENST00000268035.6:c.3278C>A	p.Ser1093Tyr	p.S1093Y	ENST00000268035	NM_000875.3	1093	tCt/tAt	17/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.71	2		415	622	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112995	2112995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397515261	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	68	648	0	ENST00000219476.3:c.1384C>T	p.Arg462Cys	p.R462C	ENST00000219476	NM_000548.3	462	Cgc/Tgc	14/42	1	2	FACETS	0.169	0.146	0.194	0.169	0.146	0.194	SUBCLONAL	1	TRUE	1	0.71	2		648	1132	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640130	3640130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	107	831	0	ENST00000294008.3:c.3509C>A	p.Ser1170Tyr	p.S1170Y	ENST00000294008	NM_032444.2	1170	tCc/tAc	12/15	1	2	FACETS	0.273	0.244	0.304	0.273	0.244	0.304	SUBCLONAL	1	TRUE	1	0.71	2		831	1104	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3651029	3651029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781393524	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	68	490	1	ENST00000294008.3:c.1114C>T	p.Arg372Trp	p.R372W	ENST00000294008	NM_032444.2	372	Cgg/Tgg	5/15	1	2	FACETS	0.222	0.193	0.255	0.222	0.193	0.255	SUBCLONAL	1	TRUE	1	0.71	2		491	861	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779760	3779760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751360168	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	92	774	0	ENST00000262367.5:c.5288G>A	p.Ser1763Asn	p.S1763N	ENST00000262367	NM_004380.2	1763	aGc/aAc	31/31	1	2	FACETS	0.234	0.207	0.263	0.234	0.207	0.263	SUBCLONAL	1	TRUE	1	0.71	2		774	1107	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900465	3900465	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	97	771	0	ENST00000262367.5:c.631G>T	p.Gly211Ter	p.G211*	ENST00000262367	NM_004380.2	211	Gga/Tga	2/31	1	2	FACETS	0.23	0.204	0.258	0.23	0.204	0.258	SUBCLONAL	1	TRUE	1	0.71	2		771	1189	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14016006	14016006	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767586458	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	29	267	0	ENST00000311895.7:c.326C>T	p.Ala109Val	p.A109V	ENST00000311895	NM_005236.2	109	gCg/gTg	2/11	1	2	FACETS	0.287	0.23	0.35	0.287	0.23	0.35	SUBCLONAL	1	TRUE	1	0.71	2		267	285	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614899	23614899	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	51	397	0	ENST00000261584.4:c.3442A>G	p.Thr1148Ala	p.T1148A	ENST00000261584	NM_024675.3	1148	Act/Gct	13/13	1	2	FACETS	0.213	0.181	0.249	0.213	0.181	0.249	SUBCLONAL	1	TRUE	1	0.71	2		397	673	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133187	30133187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774690695	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	86	489	0	ENST00000263025.4:c.311G>A	p.Arg104Gln	p.R104Q	ENST00000263025	NM_002746.2	104	cGa/cAa	2/9	1	2	FACETS	0.307	0.271	0.346	0.307	0.271	0.346	SUBCLONAL	1	TRUE	1	0.71	2		489	789	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56867216	56867216	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	332	493	0	ENST00000308159.5:c.1435C>A	p.Leu479Ile	p.L479I	ENST00000308159	NM_014669.4	479	Ctt/Att	13/22	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.71	2		493	813	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821341	72821341	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	36	369	1	ENST00000268489.5:c.10834G>T	p.Ala3612Ser	p.A3612S	ENST00000268489	NM_006885.3	3612	Gcc/Tcc	10/10	1	2	FACETS	0.195	0.159	0.234	0.195	0.159	0.234	SUBCLONAL	1	TRUE	1	0.71	2		370	521	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821404	72821404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755852557	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	314	535	1	ENST00000268489.5:c.10771G>A	p.Ala3591Thr	p.A3591T	ENST00000268489	NM_006885.3	3591	Gct/Act	10/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.71	2		536	825	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821425	72821425	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769841511	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	93	591	0	ENST00000268489.5:c.10750G>T	p.Ala3584Ser	p.A3584S	ENST00000268489	NM_006885.3	3584	Gca/Tca	10/10	1	2	FACETS	0.269	0.238	0.302	0.269	0.238	0.302	SUBCLONAL	1	TRUE	1	0.71	2		591	974	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827506	72827506	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	309	568	0	ENST00000268489.5:c.9075G>T	p.Glu3025Asp	p.E3025D	ENST00000268489	NM_006885.3	3025	gaG/gaT	9/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.71	2		568	858	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832013	72832013	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	55	532	0	ENST00000268489.5:c.4568G>T	p.Arg1523Ile	p.R1523I	ENST00000268489	NM_006885.3	1523	aGa/aTa	9/10	1	2	FACETS	0.212	0.18	0.246	0.212	0.18	0.246	SUBCLONAL	1	TRUE	1	0.71	2		532	732	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349123	89349123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762783165	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	369	856	1	ENST00000301030.4:c.3827C>T	p.Ala1276Val	p.A1276V	ENST00000301030	NM_001256183.1	1276	gCg/gTg	9/13	1	2	FACETS	0.699	0.661	0.737	0.699	0.661	0.737	SUBCLONAL	1	TRUE	1	0.71	2		857	1488	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350918	89350918	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	61	750	1	ENST00000301030.4:c.2032C>A	p.Leu678Ile	p.L678I	ENST00000301030	NM_001256183.1	678	Ctt/Att	9/13	1	2	FACETS	0.198	0.17	0.228	0.198	0.17	0.228	SUBCLONAL	1	TRUE	1	0.71	2		751	870	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89869687	89869687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	43	496	0	ENST00000389301.3:c.772G>A	p.Glu258Lys	p.E258K	ENST00000389301	NM_000135.2	258	Gag/Aag	8/43	1	2	FACETS	0.162	0.135	0.193	0.162	0.135	0.193	SUBCLONAL	1	TRUE	1	0.71	2		496	746	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877443	89877443	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	81	530	0	ENST00000389301.3:c.320T>C	p.Val107Ala	p.V107A	ENST00000389301	NM_000135.2	107	gTt/gCt	4/43	1	2	FACETS	0.221	0.194	0.25	0.221	0.194	0.25	SUBCLONAL	1	TRUE	1	0.71	2		530	1033	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7978963	7978963	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	50	513	0	ENST00000319144.4:c.1604C>A	p.Ser535Tyr	p.S535Y	ENST00000319144	NM_001139.2	535	tCt/tAt	12/15	1	2	FACETS	0.182	0.154	0.214	0.182	0.154	0.214	SUBCLONAL	1	TRUE	1	0.71	2		513	773	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984686	11984686	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	24	194	0	ENST00000353533.5:c.232A>G	p.Thr78Ala	p.T78A	ENST00000353533	NM_003010.3	78	Aca/Gca	3/11	1	2	FACETS	0.252	0.198	0.315	0.252	0.198	0.315	SUBCLONAL	1	TRUE	1	0.71	2		194	268	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968900	15968900	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	314	405	0	ENST00000268712.3:c.4850A>G	p.Tyr1617Cys	p.Y1617C	ENST00000268712	NM_006311.3	1617	tAc/tGc	33/46	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.71	2		405	718	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619288	37619288	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	73	524	0	ENST00000447079.4:c.964C>T	p.Arg322Ter	p.R322*	ENST00000447079	NM_015083.1	322	Cga/Tga	1/14	1	2	FACETS	0.251	0.219	0.286	0.251	0.219	0.286	SUBCLONAL	1	TRUE	1	0.71	2		524	820	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40500411	40500411	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	43	304	0	ENST00000264657.5:c.124G>T	p.Asp42Tyr	p.D42Y	ENST00000264657	NM_139276.2	42	Gat/Tat	2/24	1	2	FACETS	0.222	0.185	0.263	0.222	0.185	0.263	SUBCLONAL	1	TRUE	1	0.71	2		304	546	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40854557	40854557	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	112	679	0	ENST00000428826.2:c.2237T>C	p.Val746Ala	p.V746A	ENST00000428826		746	gTc/gCc	21/21	1	2	FACETS	0.292	0.262	0.324	0.292	0.262	0.324	SUBCLONAL	1	TRUE	1	0.71	2		679	1080	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40854928	40854928	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	92	514	0	ENST00000428826.2:c.2150T>C	p.Ile717Thr	p.I717T	ENST00000428826		717	aTt/aCt	20/21	1	2	FACETS	0.279	0.247	0.313	0.279	0.247	0.313	SUBCLONAL	1	TRUE	1	0.71	2		514	930	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40854936	40854936	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	76	504	0	ENST00000428826.2:c.2142G>T	p.Lys714Asn	p.K714N	ENST00000428826		714	aaG/aaT	20/21	1	2	FACETS	0.236	0.206	0.268	0.236	0.206	0.268	SUBCLONAL	1	TRUE	1	0.71	2		504	908	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215933	41215933	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	30	384	0	ENST00000357654.3:c.5110T>G	p.Phe1704Val	p.F1704V	ENST00000357654	NM_007294.3	1704	Ttt/Gtt	17/23	1	2	FACETS	0.197	0.159	0.241	0.197	0.159	0.241	SUBCLONAL	1	TRUE	1	0.71	2		384	428	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245967	41245967	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	46	564	0	ENST00000357654.3:c.1581G>T	p.Lys527Asn	p.K527N	ENST00000357654	NM_007294.3	527	aaG/aaT	10/23	1	2	FACETS	0.228	0.192	0.269	0.228	0.192	0.269	SUBCLONAL	1	TRUE	1	0.71	2		564	568	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740510	58740510	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	37	477	0	ENST00000305921.3:c.1415A>C	p.Glu472Ala	p.E472A	ENST00000305921	NM_003620.3	472	gAa/gCa	6/6	1	2	FACETS	0.184	0.151	0.221	0.184	0.151	0.221	SUBCLONAL	1	TRUE	1	0.71	2		477	565	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740835	58740835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	50	377	0	ENST00000305921.3:c.1740G>A	p.Met580Ile	p.M580I	ENST00000305921	NM_003620.3	580	atG/atA	6/6	1	2	FACETS	0.207	0.175	0.242	0.207	0.175	0.242	SUBCLONAL	1	TRUE	1	0.71	2		377	681	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853779	59853779	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	23	301	1	ENST00000259008.2:c.2080T>A	p.Phe694Ile	p.F694I	ENST00000259008	NM_032043.2	694	Ttc/Atc	14/20	1	2	FACETS	0.17	0.132	0.214	0.17	0.132	0.214	SUBCLONAL	1	TRUE	1	0.71	2		302	381	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853887	59853887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786203170	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	32	361	1	ENST00000259008.2:c.1972C>T	p.Arg658Trp	p.R658W	ENST00000259008	NM_032043.2	658	Cgg/Tgg	14/20	1	2	FACETS	0.198	0.16	0.241	0.198	0.16	0.241	SUBCLONAL	1	TRUE	1	0.71	2		362	455	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533613	63533613	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	81	926	0	ENST00000307078.5:c.1541T>C	p.Val514Ala	p.V514A	ENST00000307078	NM_004655.3	514	gTc/gCc	6/11	1	2	FACETS	0.189	0.165	0.214	0.189	0.165	0.214	SUBCLONAL	1	TRUE	1	0.71	2		926	1209	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511637	66511637	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	44	282	1	ENST00000358598.2:c.97G>T	p.Asp33Tyr	p.D33Y	ENST00000358598	NM_212471.2	33	Gat/Tat	2/11	1	2	FACETS	0.208	0.173	0.245	0.208	0.173	0.245	SUBCLONAL	1	TRUE	1	0.71	2		283	597	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78519578	78519578	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	203	353	0	ENST00000306801.3:c.149G>T	p.Arg50Met	p.R50M	ENST00000306801	NM_020761.2	50	aGg/aTg	1/34	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.71	2		353	532	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39575941	39575941	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	27	249	0	ENST00000262039.4:c.874A>G	p.Thr292Ala	p.T292A	ENST00000262039	NM_002647.2	292	Acg/Gcg	8/25	1	2	FACETS	0.193	0.153	0.239	0.193	0.153	0.239	SUBCLONAL	1	TRUE	1	0.71	2		249	394	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39593531	39593531	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	21	173	0	ENST00000262039.4:c.1296T>A	p.Asn432Lys	p.N432K	ENST00000262039	NM_002647.2	432	aaT/aaA	11/25	1	2	FACETS	0.34	0.263	0.428	0.34	0.263	0.428	SUBCLONAL	1	TRUE	1	0.71	2		173	174	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56411606	56411606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	66	278	0	ENST00000348428.3:c.1790G>A	p.Gly597Asp	p.G597D	ENST00000348428	NM_006785.3	597	gGt/gAt	15/17	1	2	FACETS	0.812	0.715	0.914	0.812	0.715	0.914	CLONAL	1	TRUE	1	0.71	2		278	229	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414783	56414783	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	37	533	0	ENST00000348428.3:c.2184A>C	p.Gln728His	p.Q728H	ENST00000348428	NM_006785.3	728	caA/caC	17/17	1	2	FACETS	0.145	0.118	0.174	0.145	0.118	0.174	SUBCLONAL	1	TRUE	1	0.71	2		533	721	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216690	2216690	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs775061899	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	534	1025	0	ENST00000398665.3:c.2334G>T	p.Lys778Asn	p.K778N	ENST00000398665	NM_032482.2	778	aaG/aaT	20/28	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.71	2		1025	1348	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7120743	7120743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	270	567	0	ENST00000302850.5:c.3547G>A	p.Asp1183Asn	p.D1183N	ENST00000302850	NM_000208.2	1183	Gac/Aac	20/22	1	2	FACETS	0.928	0.873	0.983	0.928	0.873	0.983	CLONAL	1	TRUE	1	0.71	2		567	820	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7128909	7128909	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	166	385	0	ENST00000302850.5:c.2899C>A	p.Leu967Ile	p.L967I	ENST00000302850	NM_000208.2	967	Ctc/Atc	15/22	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.71	2		385	448	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254638	10254638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	289	440	0	ENST00000340748.4:c.2872C>T	p.Arg958Cys	p.R958C	ENST00000340748		958	Cgc/Tgc	28/40	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.71	2		440	762	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030603	11030603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	285	751	1	ENST00000327064.4:c.1157G>A	p.Gly386Asp	p.G386D	ENST00000327064	NM_199141.1	386	gGc/gAc	10/16	1	2	FACETS	0.745	0.7	0.79	0.745	0.7	0.79	SUBCLONAL	1	TRUE	1	0.71	2		752	1078	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17382455	17382455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1365789470	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	78	574	0	ENST00000359435.4:c.335C>T	p.Ser112Leu	p.S112L	ENST00000359435	NM_001033549.1	112	tCg/tTg	3/9	1	2	FACETS	0.212	0.185	0.241	0.212	0.185	0.241	SUBCLONAL	1	TRUE	1	0.71	2		574	1036	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273899	18273899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	59	622	1	ENST00000222254.8:c.1232C>T	p.Ala411Val	p.A411V	ENST00000222254	NM_005027.3	411	gCc/gTc	10/16	1	2	FACETS	0.174	0.149	0.201	0.174	0.149	0.201	SUBCLONAL	1	TRUE	1	0.71	2		623	956	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273920	18273920	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	78	585	0	ENST00000222254.8:c.1253A>G	p.Asp418Gly	p.D418G	ENST00000222254	NM_005027.3	418	gAc/gGc	10/16	1	2	FACETS	0.239	0.209	0.271	0.239	0.209	0.271	SUBCLONAL	1	TRUE	1	0.71	2		585	921	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965806	18965806	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	451	812	0	ENST00000262803.5:c.1384C>T	p.Arg462Cys	p.R462C	ENST00000262803	NM_002911.3	462	Cgc/Tgc	10/24	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.71	2		812	1152	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313383	30313383	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	60	487	0	ENST00000262643.3:c.983T>C	p.Val328Ala	p.V328A	ENST00000262643	NM_001238.2	328	gTc/gCc	11/12	1	2	FACETS	0.215	0.185	0.249	0.215	0.185	0.249	SUBCLONAL	1	TRUE	1	0.71	2		487	785	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792620	33792620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	13	34	0	ENST00000498907.2:c.701G>A	p.Ser234Asn	p.S234N	ENST00000498907	NM_004364.3	234	aGc/aAc	1/1	1	2	FACETS	0.421	0.304	0.558	0.421	0.304	0.558	SUBCLONAL	1	TRUE	1	0.71	2		34	87	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745214	41745214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750029623	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	88	546	1	ENST00000301178.4:c.1280G>A	p.Arg427His	p.R427H	ENST00000301178	NM_021913.4	427	cGc/cAc	9/20	1	2	FACETS	0.288	0.254	0.324	0.288	0.254	0.324	SUBCLONAL	1	TRUE	1	0.71	2		547	861	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765520	41765520	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs781612340	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	61	667	0	ENST00000301178.4:c.2396T>G	p.Leu799Arg	p.L799R	ENST00000301178	NM_021913.4	799	cTg/cGg	20/20	1	2	FACETS	0.175	0.15	0.203	0.175	0.15	0.203	SUBCLONAL	1	TRUE	1	0.71	2		667	980	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867028	45867028	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759145034	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	103	632	1	ENST00000391945.4:c.1091G>A	p.Arg364His	p.R364H	ENST00000391945	NM_000400.3	364	cGc/cAc	11/23	1	2	FACETS	0.29	0.259	0.324	0.29	0.259	0.324	SUBCLONAL	1	TRUE	1	0.71	2		633	1000	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873410	45873410	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs773018804	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	87	673	0	ENST00000391945.4:c.86A>C	p.Lys29Thr	p.K29T	ENST00000391945	NM_000400.3	29	aAa/aCa	2/23	1	2	FACETS	0.266	0.235	0.299	0.266	0.235	0.299	SUBCLONAL	1	TRUE	1	0.71	2		673	922	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139934	50139934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142277653	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	518	907	0	ENST00000246792.3:c.395G>A	p.Arg132His	p.R132H	ENST00000246792	NM_006270.3	132	cGc/cAc	4/6	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.71	2		907	1361	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912440	50912440	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	122	804	0	ENST00000440232.2:c.1954C>T	p.Arg652Trp	p.R652W	ENST00000440232	NM_002691.3	652	Cgg/Tgg	16/27	1	2	FACETS	0.298	0.268	0.329	0.298	0.268	0.329	SUBCLONAL	1	TRUE	1	0.71	2		804	1155	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723071	52723071	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	77	563	0	ENST00000322088.6:c.1256T>C	p.Val419Ala	p.V419A	ENST00000322088	NM_014225.5	419	gTg/gCg	10/15	1	2	FACETS	0.248	0.217	0.281	0.248	0.217	0.281	SUBCLONAL	1	TRUE	1	0.71	2		563	876	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086093	16086094	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	69	454	0	ENST00000281043.3:c.1274dup	p.Ala426GlyfsTer3	p.A426Gfs*3	ENST00000281043	NM_005378.4	423	-/A	3/3	1	2	FACETS	0.247	0.214	0.282	0.247	0.214	0.282	SUBCLONAL	1	TRUE	1	0.71	2		454	787	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462640	29462640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	126	800	0	ENST00000389048.3:c.2261C>T	p.Ser754Phe	p.S754F	ENST00000389048	NM_004304.4	754	tCc/tTc	13/29	1	2	FACETS	0.286	0.257	0.315	0.286	0.257	0.315	SUBCLONAL	1	TRUE	1	0.71	2		800	1243	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47600644	47600644	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	30	349	0	ENST00000263735.4:c.119T>C	p.Val40Ala	p.V40A	ENST00000263735	NM_002354.2	40	gTg/gCg	2/9	1	2	FACETS	0.183	0.147	0.224	0.183	0.147	0.224	SUBCLONAL	1	TRUE	1	0.71	2		349	461	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018264	48018264	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	46	396	0	ENST00000234420.5:c.457+2T>C		p.X153_splice	ENST00000234420	NM_000179.2	153			1	2	FACETS	0.218	0.183	0.257	0.218	0.183	0.257	SUBCLONAL	1	TRUE	1	0.71	2		396	594	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032840	48032840	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	98	224	0	ENST00000234420.5:c.3640G>T	p.Glu1214Ter	p.E1214*	ENST00000234420	NM_000179.2	1214	Gaa/Taa	7/10	1	2	FACETS	0.885	0.799	0.974	0.885	0.799	0.974	CLONAL	1	TRUE	1	0.71	2		224	312	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636924	158636924	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	58	478	0	ENST00000263640.3:c.256T>C	p.Ser86Pro	p.S86P	ENST00000263640	NM_001105.4	86	Tcc/Ccc	4/11	1	2	FACETS	0.199	0.17	0.231	0.199	0.17	0.231	SUBCLONAL	1	TRUE	1	0.71	2		478	821	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095559	178095559	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	117	257	0	ENST00000397062.3:c.1772T>C	p.Val591Ala	p.V591A	ENST00000397062	NM_006164.4	591	gTt/gCt	5/5	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.71	2		257	297	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660638	190660638	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	20	315	0	ENST00000441310.2:c.276T>G	p.Phe92Leu	p.F92L	ENST00000441310	NM_000534.4	92	ttT/ttG	3/13	1	2	FACETS	0.143	0.109	0.183	0.143	0.109	0.183	SUBCLONAL	1	TRUE	1	0.71	2		315	394	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738241	190738241	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	62	184	0	ENST00000441310.2:c.2493T>A	p.Asn831Lys	p.N831K	ENST00000441310	NM_000534.4	831	aaT/aaA	12/13	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.71	2		184	174	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266768	198266768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	185	434	0	ENST00000335508.6:c.2164G>A	p.Glu722Lys	p.E722K	ENST00000335508	NM_012433.2	722	Gaa/Aaa	15/25	1	2	FACETS	0.793	0.735	0.853	0.793	0.735	0.853	SUBCLONAL	1	TRUE	1	0.71	2		434	657	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131267	202131267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	36	371	0	ENST00000358485.4:c.235G>A	p.Ala79Thr	p.A79T	ENST00000358485	NM_001080125.1	79	Gcc/Acc	2/9	1	2	FACETS	0.21	0.172	0.253	0.21	0.172	0.253	SUBCLONAL	1	TRUE	1	0.71	2		371	482	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248773	212248773	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	23	186	0	ENST00000342788.4:c.3494C>A	p.Pro1165Gln	p.P1165Q	ENST00000342788	NM_005235.2	1165	cCa/cAa	28/28	1	2	FACETS	0.211	0.164	0.265	0.211	0.164	0.265	SUBCLONAL	1	TRUE	1	0.71	2		186	307	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657144	215657144	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	72	323	0	ENST00000260947.4:c.241A>G	p.Thr81Ala	p.T81A	ENST00000260947	NM_000465.2	81	Act/Gct	3/11	1	2	FACETS	0.642	0.565	0.723	0.642	0.565	0.723	SUBCLONAL	1	TRUE	1	0.71	2		323	316	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339032	225339032	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	20	314	0	ENST00000264414.4:c.2237A>G	p.Glu746Gly	p.E746G	ENST00000264414	NM_003590.4	746	gAa/gGa	16/16	1	2	FACETS	0.171	0.13	0.218	0.171	0.13	0.218	SUBCLONAL	1	TRUE	1	0.71	2		314	330	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370747	225370747	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	113	307	0	ENST00000264414.4:c.1132C>A	p.Leu378Ile	p.L378I	ENST00000264414	NM_003590.4	378	Ctc/Atc	8/16	1	2	FACETS	0.992	0.904	1	0.992	0.904	1	CLONAL	1	TRUE	1	0.71	2		307	321	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662236	227662236	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	115	801	1	ENST00000305123.5:c.1219C>A	p.Leu407Ile	p.L407I	ENST00000305123	NM_005544.2	407	Ctc/Atc	1/2	1	2	FACETS	0.287	0.257	0.318	0.287	0.257	0.318	SUBCLONAL	1	TRUE	1	0.71	2		802	1129	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561007	9561007	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	47	358	1	ENST00000353224.5:c.775C>A	p.Pro259Thr	p.P259T	ENST00000353224	NM_177990.2	259	Ccc/Acc	4/10	1	2	FACETS	0.268	0.226	0.314	0.268	0.226	0.314	SUBCLONAL	1	TRUE	1	0.71	2		359	494	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023477	31023477	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	225	416	0	ENST00000375687.4:c.2962G>T	p.Asp988Tyr	p.D988Y	ENST00000375687	NM_015338.5	988	Gac/Tac	13/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.71	2		416	588	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022660	36022660	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	73	604	0	ENST00000358208.4:c.533G>A	p.Arg178Gln	p.R178Q	ENST00000358208		178	cGa/cAa	5/12	1	2	FACETS	0.216	0.188	0.246	0.216	0.188	0.246	SUBCLONAL	1	TRUE	1	0.71	2		604	953	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262872	46262872	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	35	352	0	ENST00000371998.3:c.1045A>G	p.Ser349Gly	p.S349G	ENST00000371998		349	Agc/Ggc	10/23	1	2	FACETS	0.202	0.165	0.244	0.202	0.165	0.244	SUBCLONAL	1	TRUE	1	0.71	2		352	488	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268699	46268699	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	77	462	0	ENST00000371998.3:c.2984C>A	p.Ala995Asp	p.A995D	ENST00000371998		995	gCt/gAt	16/23	1	2	FACETS	0.3	0.263	0.34	0.3	0.263	0.34	SUBCLONAL	1	TRUE	1	0.71	2		462	722	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945221	54945221	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs778256805	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	71	498	0	ENST00000312783.6:c.1205A>C	p.Gln402Pro	p.Q402P	ENST00000312783	NM_198436.1	402	cAg/cCg	10/10	1	2	FACETS	0.262	0.228	0.299	0.262	0.228	0.299	SUBCLONAL	1	TRUE	1	0.71	2		498	763	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324281	62324281	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369357121	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	470	907	1	ENST00000360203.5:c.2776G>A	p.Asp926Asn	p.D926N	ENST00000360203	NM_001283009.1	926	Gat/Aat	29/35	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.71	2		908	1238	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42842632	42842632	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	87	636	0	ENST00000398585.3:c.1225A>G	p.Met409Val	p.M409V	ENST00000398585	NM_001135099.1	409	Atg/Gtg	11/14	1	2	FACETS	0.225	0.198	0.254	0.225	0.198	0.254	SUBCLONAL	1	TRUE	1	0.71	2		636	1089	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513728	41513728	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	86	558	0	ENST00000263253.7:c.632G>T	p.Gly211Val	p.G211V	ENST00000263253	NM_001429.3	211	gGc/gTc	2/31	1	2	FACETS	0.275	0.243	0.31	0.275	0.243	0.31	SUBCLONAL	1	TRUE	1	0.71	2		558	881	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566555	41566555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1445337631	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	157	267	0	ENST00000263253.7:c.4432C>T	p.Arg1478Cys	p.R1478C	ENST00000263253	NM_001429.3	1478	Cgt/Tgt	27/31	1	2	FACETS	0.978	0.905	1	0.978	0.905	1	CLONAL	1	TRUE	1	0.71	2		267	452	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569685	41569685	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	91	169	0	ENST00000263253.7:c.4676A>C	p.Asn1559Thr	p.N1559T	ENST00000263253	NM_001429.3	1559	aAt/aCt	29/31	1	2	FACETS	0.967	0.872	1	0.967	0.872	1	CLONAL	1	TRUE	1	0.71	2		169	265	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188233	10188233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893831	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	88	525	4	ENST00000256474.2:c.376G>A	p.Asp126Asn	p.D126N	ENST00000256474	NM_000551.3	126	Gat/Aat	2/3	1	2	FACETS	0.309	0.274	0.348	0.309	0.274	0.348	SUBCLONAL	1	TRUE	1	0.71	2		529	801	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042522	37042522	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	118	374	0	ENST00000231790.2:c.284C>A	p.Ser95Tyr	p.S95Y	ENST00000231790	NM_000249.3	95	tCt/tAt	3/19	1	2	FACETS	0.931	0.849	1	0.931	0.849	1	CLONAL	1	TRUE	1	0.71	2		374	357	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266518	41266518	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	57	302	0	ENST00000349496.5:c.315G>T	p.Glu105Asp	p.E105D	ENST00000349496	NM_001904.3	105	gaG/gaT	4/15	1	2	FACETS	0.295	0.253	0.34	0.295	0.253	0.34	SUBCLONAL	1	TRUE	1	0.71	2		302	545	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723790	49723790	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	12	26	0	ENST00000449682.2:c.972A>C	p.Gln324His	p.Q324H	ENST00000449682	NM_020998.3	324	caA/caC	8/18	1	2	FACETS	0.867	0.636	1	0.867	0.636	1	CLONAL	1	TRUE	1	0.71	2		26	39	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799784	72799784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	324	495	0	ENST00000325599.8:c.1385G>A	p.Ser462Asn	p.S462N	ENST00000325599	NM_018130.2	462	aGc/aAc	11/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.71	2		495	796	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499342	89499342	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	48	317	0	ENST00000336596.2:c.2512G>T	p.Asp838Tyr	p.D838Y	ENST00000336596	NM_005233.5	838	Gat/Tat	15/17	1	2	FACETS	0.254	0.214	0.298	0.254	0.214	0.298	SUBCLONAL	1	TRUE	1	0.71	2		317	532	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880908	134880908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	248	488	0	ENST00000398015.3:c.1471G>A	p.Ala491Thr	p.A491T	ENST00000398015	NM_004441.4	491	Gca/Aca	7/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.71	2		488	678	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977870	134977870	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	31	295	0	ENST00000398015.3:c.2863G>T	p.Gly955Cys	p.G955C	ENST00000398015	NM_004441.4	955	Ggc/Tgc	16/16	1	2	FACETS	0.199	0.161	0.243	0.199	0.161	0.243	SUBCLONAL	1	TRUE	1	0.71	2		295	438	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665308	138665308	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1171	117	776	0	ENST00000330315.3:c.257C>T	p.Ala86Val	p.A86V	ENST00000330315	NM_023067.3	86	gCg/gTg	1/1	1	2	FACETS	0.256	0.23	0.284	0.256	0.23	0.284	SUBCLONAL	1	TRUE	1	0.71	2		776	1288	SUCCESS
ATR	545	MSKCC	GRCh37	3	142185344	142185344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765461897	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	13	253	0	ENST00000350721.4:c.6719G>A	p.Ser2240Asn	p.S2240N	ENST00000350721	NM_001184.3	2240	aGc/aAc	40/47	1	2	FACETS	0.152	0.108	0.206	0.152	0.108	0.206	SUBCLONAL	1	TRUE	1	0.71	2		253	241	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268424	142268424	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	18	268	0	ENST00000350721.4:c.3068T>C	p.Val1023Ala	p.V1023A	ENST00000350721	NM_001184.3	1023	gTc/gCc	15/47	1	2	FACETS	0.196	0.147	0.253	0.196	0.147	0.253	SUBCLONAL	1	TRUE	1	0.71	2		268	259	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922355	178922355	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	96	270	0	ENST00000263967.3:c.1124G>T	p.Arg375Ile	p.R375I	ENST00000263967	NM_006218.2	375	aGa/aTa	6/21	1	2	FACETS	0.956	0.863	1	0.956	0.863	1	CLONAL	1	TRUE	1	0.71	2		270	283	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182681684	182681684	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	169	279	0	ENST00000292782.4:c.374G>A	p.Gly125Asp	p.G125D	ENST00000292782	NM_020640.2	125	gGc/gAc	3/7	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.71	2		279	474	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191532	185191532	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	204	476	0	ENST00000265026.3:c.2413A>G	p.Thr805Ala	p.T805A	ENST00000265026	NM_004721.4	805	Aca/Gca	11/14	1	2	FACETS	0.702	0.652	0.753	0.702	0.652	0.753	SUBCLONAL	1	TRUE	1	0.71	2		476	819	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1905982	1905982	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	72	668	0	ENST00000382891.5:c.637G>T	p.Asp213Tyr	p.D213Y	ENST00000382891	NM_133335.3	213	Gac/Tac	3/22	1	2	FACETS	0.192	0.167	0.22	0.192	0.167	0.22	SUBCLONAL	1	TRUE	1	0.71	2		668	1054	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139810	55139810	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs563016888	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	97	511	0	ENST00000257290.5:c.1471G>A	p.Ala491Thr	p.A491T	ENST00000257290	NM_006206.4	491	Gcc/Acc	10/23	1	2	FACETS	0.332	0.296	0.371	0.332	0.296	0.371	SUBCLONAL	1	TRUE	1	0.71	2		511	822	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152060	55152060	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	283	454	0	ENST00000257290.5:c.2492T>G	p.Ile831Ser	p.I831S	ENST00000257290	NM_006206.4	831	aTt/aGt	18/23	1	2	FACETS	0.951	0.897	1	0.951	0.897	1	CLONAL	1	TRUE	1	0.71	2		454	838	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955950	55955950	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	38	390	0	ENST00000263923.4:c.3212G>T	p.Trp1071Leu	p.W1071L	ENST00000263923	NM_002253.2	1071	tGg/tTg	24/30	1	2	FACETS	0.223	0.184	0.267	0.223	0.184	0.267	SUBCLONAL	1	TRUE	1	0.71	2		390	480	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964333	55964333	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	143	387	1	ENST00000263923.4:c.2480G>T	p.Trp827Leu	p.W827L	ENST00000263923	NM_002253.2	827	tGg/tTg	17/30	1	2	FACETS	0.872	0.801	0.945	0.872	0.801	0.945	CLONAL	1	TRUE	1	0.71	2		388	462	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467577	66467577	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	130	288	0	ENST00000273854.3:c.692A>C	p.Lys231Thr	p.K231T	ENST00000273854	NM_004439.5	231	aAa/aCa	3/18	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.71	2		288	314	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156999	106156999	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	29	336	0	ENST00000380013.4:c.1900T>C	p.Tyr634His	p.Y634H	ENST00000380013	NM_001127208.2	634	Tac/Cac	3/11	1	2	FACETS	0.152	0.121	0.187	0.152	0.121	0.187	SUBCLONAL	1	TRUE	1	0.71	2		336	538	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130135	143130135	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	18	400	0	ENST00000262992.4:c.881A>G	p.Asp294Gly	p.D294G	ENST00000262992	NM_001101669.1	294	gAc/gGc	11/24	1	2	FACETS	0.16	0.12	0.207	0.16	0.12	0.207	SUBCLONAL	1	TRUE	1	0.71	2		400	317	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332585	153332585	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	34	288	0	ENST00000281708.4:c.371A>C	p.Asp124Ala	p.D124A	ENST00000281708	NM_033632.3	124	gAt/gCt	2/12	1	2	FACETS	0.284	0.232	0.342	0.284	0.232	0.342	SUBCLONAL	1	TRUE	1	0.71	2		288	337	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530342	187530342	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	41	277	0	ENST00000441802.2:c.10201G>T	p.Glu3401Ter	p.E3401*	ENST00000441802	NM_005245.3	3401	Gaa/Taa	16/27	1	2	FACETS	0.287	0.239	0.34	0.287	0.239	0.34	SUBCLONAL	1	TRUE	1	0.71	2		277	403	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539200	187539200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	24	365	0	ENST00000441802.2:c.8540G>A	p.Ser2847Asn	p.S2847N	ENST00000441802	NM_005245.3	2847	aGc/aAc	10/27	1	2	FACETS	0.164	0.128	0.205	0.164	0.128	0.205	SUBCLONAL	1	TRUE	1	0.71	2		365	413	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542688	187542688	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	28	339	0	ENST00000441802.2:c.5052T>G	p.Ser1684Arg	p.S1684R	ENST00000441802	NM_005245.3	1684	agT/agG	10/27	1	2	FACETS	0.199	0.158	0.245	0.199	0.158	0.245	SUBCLONAL	1	TRUE	1	0.71	2		339	397	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629941	187629941	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	68	582	0	ENST00000441802.2:c.1041C>A	p.Phe347Leu	p.F347L	ENST00000441802	NM_005245.3	347	ttC/ttA	2/27	1	2	FACETS	0.243	0.211	0.278	0.243	0.211	0.278	SUBCLONAL	1	TRUE	1	0.71	2		582	788	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867454	35867454	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	20	263	0	ENST00000303115.3:c.268G>T	p.Glu90Ter	p.E90*	ENST00000303115	NM_002185.3	90	Gag/Tag	3/8	1	2	FACETS	0.204	0.156	0.26	0.204	0.156	0.26	SUBCLONAL	1	TRUE	1	0.71	2		263	276	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38943039	38943039	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1050183137	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	62	224	0	ENST00000357387.3:c.4948A>G	p.Ile1650Val	p.I1650V	ENST00000357387	NM_152756.3	1650	Ata/Gta	37/38	1	2	FACETS	0.75	0.656	0.849	0.75	0.656	0.849	SUBCLONAL	1	TRUE	1	0.71	2		224	233	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56171010	56171010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	44	326	0	ENST00000399503.3:c.1838G>A	p.Ser613Asn	p.S613N	ENST00000399503	NM_005921.1	613	aGc/aAc	10/20	1	2	FACETS	0.259	0.217	0.305	0.259	0.217	0.305	SUBCLONAL	1	TRUE	1	0.71	2		326	479	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177723	56177723	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	38	282	0	ENST00000399503.3:c.2696A>C	p.Asn899Thr	p.N899T	ENST00000399503	NM_005921.1	899	aAc/aCc	14/20	1	2	FACETS	0.257	0.213	0.307	0.257	0.213	0.307	SUBCLONAL	1	TRUE	1	0.71	2		282	416	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183223	56183223	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	139	350	0	ENST00000399503.3:c.4133A>G	p.Asp1378Gly	p.D1378G	ENST00000399503	NM_005921.1	1378	gAc/gGc	18/20	1	2	FACETS	0.785	0.719	0.853	0.785	0.719	0.853	SUBCLONAL	1	TRUE	1	0.71	2		350	499	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79952258	79952258	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	38	257	0	ENST00000265081.6:c.266G>T	p.Arg89Ile	p.R89I	ENST00000265081	NM_002439.4	89	aGa/aTa	2/24	1	2	FACETS	0.322	0.267	0.384	0.322	0.267	0.384	SUBCLONAL	1	TRUE	1	0.71	2		257	332	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961096	79961096	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	49	417	0	ENST00000265081.6:c.493A>G	p.Lys165Glu	p.K165E	ENST00000265081	NM_002439.4	165	Aaa/Gaa	3/24	1	2	FACETS	0.277	0.235	0.324	0.277	0.235	0.324	SUBCLONAL	1	TRUE	1	0.71	2		417	498	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970805	79970805	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	17	261	0	ENST00000265081.6:c.1031T>C	p.Val344Ala	p.V344A	ENST00000265081	NM_002439.4	344	gTg/gCg	7/24	1	2	FACETS	0.195	0.145	0.253	0.195	0.145	0.253	SUBCLONAL	1	TRUE	1	0.71	2		261	246	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80063867	80063867	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1196357562	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	24	352	1	ENST00000265081.6:c.2012T>C	p.Val671Ala	p.V671A	ENST00000265081	NM_002439.4	671	gTt/gCt	14/24	1	2	FACETS	0.202	0.158	0.252	0.202	0.158	0.252	SUBCLONAL	1	TRUE	1	0.71	2		353	335	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80063916	80063916	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	101	328	0	ENST00000265081.6:c.2061G>T	p.Lys687Asn	p.K687N	ENST00000265081	NM_002439.4	687	aaG/aaT	14/24	1	2	FACETS	0.924	0.836	1	0.924	0.836	1	CLONAL	1	TRUE	1	0.71	2		328	308	SUCCESS
APC	324	MSKCC	GRCh37	5	112177545	112177545	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	33	255	0	ENST00000257430.4:c.6254G>T	p.Arg2085Ile	p.R2085I	ENST00000257430	NM_000038.5	2085	aGa/aTa	16/16	1	2	FACETS	0.386	0.316	0.464	0.386	0.316	0.464	SUBCLONAL	1	TRUE	1	0.71	2		255	241	SUCCESS
APC	324	MSKCC	GRCh37	5	112178053	112178053	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	30	296	0	ENST00000257430.4:c.6762G>T	p.Lys2254Asn	p.K2254N	ENST00000257430	NM_000038.5	2254	aaG/aaT	16/16	1	2	FACETS	0.181	0.145	0.221	0.181	0.145	0.221	SUBCLONAL	1	TRUE	1	0.71	2		296	468	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944890	131944890	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748452537	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	52	148	0	ENST00000265335.6:c.2911G>A	p.Asp971Asn	p.D971N	ENST00000265335		971	Gac/Aac	18/25	1	2	FACETS	0.983	0.856	1	0.983	0.856	1	CLONAL	1	TRUE	1	0.71	2		148	149	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149437143	149437143	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	89	603	0	ENST00000286301.3:c.2145C>A	p.Phe715Leu	p.F715L	ENST00000286301	NM_005211.3	715	ttC/ttA	16/22	1	2	FACETS	0.289	0.256	0.325	0.289	0.256	0.325	SUBCLONAL	1	TRUE	1	0.71	2		603	867	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519689	176519689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1410493748	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	100	854	1	ENST00000292408.4:c.961C>T	p.Arg321Trp	p.R321W	ENST00000292408	NM_213647.1	321	Cgg/Tgg	8/18	1	2	FACETS	0.256	0.228	0.287	0.256	0.228	0.287	SUBCLONAL	1	TRUE	1	0.71	2		855	1099	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636646	176636646	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	67	238	0	ENST00000439151.2:c.1246A>C	p.Lys416Gln	p.K416Q	ENST00000439151	NM_022455.4	416	Aaa/Caa	5/23	1	2	FACETS	0.615	0.539	0.696	0.615	0.539	0.696	SUBCLONAL	1	TRUE	1	0.71	2		238	307	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637325	176637325	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	36	442	0	ENST00000439151.2:c.1925C>A	p.Ser642Tyr	p.S642Y	ENST00000439151	NM_022455.4	642	tCt/tAt	5/23	1	2	FACETS	0.169	0.138	0.204	0.169	0.138	0.204	SUBCLONAL	1	TRUE	1	0.71	2		442	599	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637357	176637357	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	55	407	0	ENST00000439151.2:c.1957G>T	p.Glu653Ter	p.E653*	ENST00000439151	NM_022455.4	653	Gaa/Taa	5/23	1	2	FACETS	0.315	0.269	0.365	0.315	0.269	0.365	SUBCLONAL	1	TRUE	1	0.71	2		407	492	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176662927	176662927	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1225220481	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	18	217	0	ENST00000439151.2:c.3902T>C	p.Val1301Ala	p.V1301A	ENST00000439151	NM_022455.4	1301	gTa/gCa	6/23	1	2	FACETS	0.22	0.166	0.284	0.22	0.166	0.284	SUBCLONAL	1	TRUE	1	0.71	2		217	230	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488352	20488352	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	34	357	0	ENST00000346618.3:c.1008A>C	p.Gln336His	p.Q336H	ENST00000346618	NM_001949.4	336	caA/caC	6/7	1	2	FACETS	0.219	0.178	0.264	0.219	0.178	0.264	SUBCLONAL	1	TRUE	1	0.71	2		357	438	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021106	26021106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759581802	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	135	464	1	ENST00000357647.3:c.389G>A	p.Arg130His	p.R130H	ENST00000357647	NM_003529.2	130	cGc/cAc	1/1	1	2	FACETS	0.546	0.497	0.597	0.546	0.497	0.597	SUBCLONAL	1	TRUE	1	0.71	2		465	697	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056619	26056619	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	146	260	0	ENST00000343677.2:c.38C>A	p.Pro13His	p.P13H	ENST00000343677	NM_005319.3	13	cCt/cAt	1/1	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.71	2		260	350	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166797	32166797	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1241	111	907	0	ENST00000375023.3:c.4441C>A	p.Leu1481Ile	p.L1481I	ENST00000375023	NM_004557.3	1481	Ctc/Atc	24/30	1	2	FACETS	0.231	0.207	0.257	0.231	0.207	0.257	SUBCLONAL	1	TRUE	1	0.71	2		907	1352	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188214	32188214	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	329	746	1	ENST00000375023.3:c.1127C>A	p.Ser376Tyr	p.S376Y	ENST00000375023	NM_004557.3	376	tCt/tAt	6/30	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.71	2		747	919	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190847	32190847	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	93	798	0	ENST00000375023.3:c.90T>G	p.Ser30Arg	p.S30R	ENST00000375023	NM_004557.3	30	agT/agG	2/30	1	2	FACETS	0.208	0.184	0.234	0.208	0.184	0.234	SUBCLONAL	1	TRUE	1	0.71	2		798	1257	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748514	43748514	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	212	333	0	ENST00000523873.1:c.468G>T	p.Lys156Asn	p.K156N	ENST00000523873		156	aaG/aaT	6/8	1	2	FACETS	0.982	0.918	1	0.982	0.918	1	CLONAL	1	TRUE	1	0.71	2		333	608	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555236	106555236	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	142	415	0	ENST00000369096.4:c.2353C>A	p.Leu785Ile	p.L785I	ENST00000369096	NM_001198.3	785	Ctc/Atc	7/7	1	2	FACETS	0.707	0.647	0.769	0.707	0.647	0.769	SUBCLONAL	1	TRUE	1	0.71	2		415	566	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983167	149983167	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	25	504	0	ENST00000253339.5:c.3091A>G	p.Thr1031Ala	p.T1031A	ENST00000253339		1031	Aca/Gca	7/7	1	2	FACETS	0.147	0.115	0.183	0.147	0.115	0.183	SUBCLONAL	1	TRUE	1	0.71	2		504	480	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005290	150005290	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	53	462	0	ENST00000253339.5:c.935C>A	p.Pro312His	p.P312H	ENST00000253339		312	cCt/cAt	3/7	1	2	FACETS	0.249	0.212	0.29	0.249	0.212	0.29	SUBCLONAL	1	TRUE	1	0.71	2		462	600	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522409	157522409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	94	651	0	ENST00000346085.5:c.4681C>T	p.Arg1561Cys	p.R1561C	ENST00000346085	NM_020732.3	1561	Cgc/Tgc	18/20	1	2	FACETS	0.271	0.24	0.304	0.271	0.24	0.304	SUBCLONAL	1	TRUE	1	0.71	2		651	977	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987325	2987325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	329	552	2	ENST00000396946.4:c.104G>A	p.Arg35His	p.R35H	ENST00000396946	NM_032415.4	35	cGc/cAc	3/25	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.71	2		554	903	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6029574	6029574	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1234321567	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	40	406	0	ENST00000265849.7:c.1001T>C	p.Ile334Thr	p.I334T	ENST00000265849	NM_000535.5	334	aTc/aCc	10/15	1	2	FACETS	0.224	0.186	0.267	0.224	0.186	0.267	SUBCLONAL	1	TRUE	1	0.71	2		406	503	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729331	41729331	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	273	507	0	ENST00000242208.4:c.1198T>C	p.Ser400Pro	p.S400P	ENST00000242208	NM_002192.2	400	Tcc/Ccc	3/3	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.71	2		507	665	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455117	50455117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	22	305	0	ENST00000331340.3:c.664C>T	p.Arg222Cys	p.R222C	ENST00000331340	NM_006060.4	222	Cgc/Tgc	6/8	1	2	FACETS	0.15	0.115	0.19	0.15	0.115	0.19	SUBCLONAL	1	TRUE	1	0.71	2		305	414	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467795	50467795	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	44	615	0	ENST00000331340.3:c.1030A>G	p.Ile344Val	p.I344V	ENST00000331340	NM_006060.4	344	Atc/Gtc	8/8	1	2	FACETS	0.153	0.127	0.181	0.153	0.127	0.181	SUBCLONAL	1	TRUE	1	0.71	2		615	812	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214388	55214388	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	79	557	0	ENST00000275493.2:c.514T>G	p.Phe172Val	p.F172V	ENST00000275493	NM_005228.3	172	Ttt/Gtt	4/28	1	2	FACETS	0.269	0.236	0.304	0.269	0.236	0.304	SUBCLONAL	1	TRUE	1	0.71	2		557	828	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273030	55273030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773996588	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	91	557	0	ENST00000275493.2:c.3353C>T	p.Ala1118Val	p.A1118V	ENST00000275493	NM_005228.3	1118	gCg/gTg	28/28	1	2	FACETS	0.25	0.221	0.281	0.25	0.221	0.281	SUBCLONAL	1	TRUE	1	0.71	2		557	1027	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514356	148514356	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	27	328	0	ENST00000320356.2:c.1368C>A	p.Phe456Leu	p.F456L	ENST00000320356	NM_004456.4	456	ttC/ttA	11/20	1	2	FACETS	0.205	0.163	0.253	0.205	0.163	0.253	SUBCLONAL	1	TRUE	1	0.71	2		328	371	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843811	151843811	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	29	231	0	ENST00000262189.6:c.13904A>C	p.Asp4635Ala	p.D4635A	ENST00000262189	NM_170606.2	4635	gAt/gCt	53/59	1	2	FACETS	0.237	0.19	0.29	0.237	0.19	0.29	SUBCLONAL	1	TRUE	1	0.71	2		231	345	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845585	151845585	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	74	504	0	ENST00000262189.6:c.13427G>T	p.Arg4476Ile	p.R4476I	ENST00000262189	NM_170606.2	4476	aGa/aTa	52/59	1	2	FACETS	0.255	0.223	0.291	0.255	0.223	0.291	SUBCLONAL	1	TRUE	1	0.71	2		504	816	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873329	151873329	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	137	241	0	ENST00000262189.6:c.9209G>T	p.Arg3070Ile	p.R3070I	ENST00000262189	NM_170606.2	3070	aGa/aTa	38/59	1	2	FACETS	0.997	0.917	1	0.997	0.917	1	CLONAL	1	TRUE	1	0.71	2		241	387	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878347	151878347	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	250	494	0	ENST00000262189.6:c.6598T>G	p.Ser2200Ala	p.S2200A	ENST00000262189	NM_170606.2	2200	Tct/Gct	36/59	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.71	2		494	651	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900035	151900035	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	25	292	0	ENST00000262189.6:c.4076T>G	p.Phe1359Cys	p.F1359C	ENST00000262189	NM_170606.2	1359	tTc/tGc	26/59	1	2	FACETS	0.208	0.164	0.259	0.208	0.164	0.259	SUBCLONAL	1	TRUE	1	0.71	2		292	338	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945337	151945337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771324714	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	64	186	0	ENST00000262189.6:c.2182G>A	p.Glu728Lys	p.E728K	ENST00000262189	NM_170606.2	728	Gaa/Aaa	14/59	1	2	FACETS	0.92	0.811	1	0.92	0.811	1	CLONAL	1	TRUE	1	0.71	2		186	196	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345926	152345926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762828701	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	279	404	0	ENST00000359321.1:c.644G>A	p.Arg215Gln	p.R215Q	ENST00000359321	NM_005431.1	215	cGa/cAa	3/3	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.71	2		404	709	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538988	23538988	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs892777834	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	327	606	0	ENST00000380871.4:c.451G>A	p.Ala151Thr	p.A151T	ENST00000380871	NM_006167.3	151	Gcc/Acc	2/2	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.71	2		606	775	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207738	29207738	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	41	524	0	ENST00000240100.2:c.58A>C	p.Asn20His	p.N20H	ENST00000240100	NM_001394.6	20	Aac/Cac	1/4	1	2	FACETS	0.148	0.123	0.177	0.148	0.123	0.177	SUBCLONAL	1	TRUE	1	0.71	2		524	780	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38283760	38283760	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	61	500	0	ENST00000425967.3:c.718C>A	p.Arg240Ser	p.R240S	ENST00000425967	NM_001174067.1	240	Cgt/Agt	7/19	1	2	FACETS	0.251	0.216	0.289	0.251	0.216	0.289	SUBCLONAL	1	TRUE	1	0.71	2		500	684	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970885	70970885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199993571	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	56	364	0	ENST00000276594.2:c.1376G>A	p.Arg459Gln	p.R459Q	ENST00000276594	NM_024504.3	459	cGg/cAg	6/8	1	2	FACETS	0.247	0.211	0.286	0.247	0.211	0.286	SUBCLONAL	1	TRUE	1	0.71	2		364	639	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862858	117862858	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	23	327	0	ENST00000297338.2:c.1619A>G	p.Glu540Gly	p.E540G	ENST00000297338	NM_006265.2	540	gAg/gGg	12/14	1	2	FACETS	0.186	0.144	0.233	0.186	0.144	0.233	SUBCLONAL	1	TRUE	1	0.71	2		327	349	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864925	117864925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149171113	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	125	317	0	ENST00000297338.2:c.1184C>T	p.Pro395Leu	p.P395L	ENST00000297338	NM_006265.2	395	cCg/cTg	10/14	1	2	FACETS	0.905	0.827	0.985	0.905	0.827	0.985	CLONAL	1	TRUE	1	0.71	2		317	389	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742502	145742502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1181	107	908	1	ENST00000428558.2:c.286C>T	p.Arg96Trp	p.R96W	ENST00000428558	NM_004260.3	96	Cgg/Tgg	4/22	1	2	FACETS	0.234	0.209	0.261	0.234	0.209	0.261	SUBCLONAL	1	TRUE	1	0.71	2		909	1288	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341899	8341899	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1292093096	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	23	331	0	ENST00000356435.5:c.4741A>G	p.Ile1581Val	p.I1581V	ENST00000356435		1581	Att/Gtt	29/35	1	2	FACETS	0.188	0.146	0.237	0.188	0.146	0.237	SUBCLONAL	1	TRUE	1	0.71	2		331	344	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485890	8485890	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	176	340	0	ENST00000356435.5:c.2927A>G	p.Asp976Gly	p.D976G	ENST00000356435		976	gAc/gGc	17/35	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.71	2		340	430	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971052	21971052	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	68	397	0	ENST00000579755.1:c.349G>A	p.Ala117Thr	p.A117T	ENST00000579755		117	Gcg/Acg	2/3	1	2	FACETS	0.269	0.233	0.308	0.269	0.233	0.308	SUBCLONAL	1	TRUE	1	0.71	2		397	712	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80343546	80343546	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	87	349	0	ENST00000286548.4:c.773T>G	p.Ile258Ser	p.I258S	ENST00000286548	NM_002072.3	258	aTt/aGt	6/7	1	2	FACETS	0.604	0.537	0.673	0.604	0.537	0.673	SUBCLONAL	1	TRUE	1	0.71	2		349	406	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285873	87285873	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	49	474	0	ENST00000277120.3:c.210A>C	p.Glu70Asp	p.E70D	ENST00000277120		70	gaA/gaC	2/19	1	2	FACETS	0.232	0.196	0.271	0.232	0.196	0.271	SUBCLONAL	1	TRUE	1	0.71	2		474	596	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359941	87359941	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	52	308	0	ENST00000277120.3:c.1249A>C	p.Ile417Leu	p.I417L	ENST00000277120		417	Atc/Ctc	11/19	1	2	FACETS	0.275	0.234	0.321	0.275	0.234	0.321	SUBCLONAL	1	TRUE	1	0.71	2		308	532	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87366954	87366954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	266	565	3	ENST00000277120.3:c.1350G>A	p.Met450Ile	p.M450I	ENST00000277120		450	atG/atA	12/19	1	2	FACETS	0.976	0.919	1	0.976	0.919	1	CLONAL	1	TRUE	1	0.71	2		568	768	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864105	97864105	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752855423	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	230	409	0	ENST00000289081.3:c.1561G>A	p.Glu521Lys	p.E521K	ENST00000289081	NM_000136.2	521	Gag/Aag	15/15	1	2	FACETS	0.979	0.917	1	0.979	0.917	1	CLONAL	1	TRUE	1	0.71	2		409	662	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98222002	98222002	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	57	416	0	ENST00000331920.6:c.2767C>A	p.Leu923Met	p.L923M	ENST00000331920	NM_000264.3	923	Ctg/Atg	17/24	1	2	FACETS	0.229	0.196	0.265	0.229	0.196	0.265	SUBCLONAL	1	TRUE	1	0.71	2		416	702	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760160	133760160	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762470102	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	55	672	2	ENST00000318560.5:c.2483C>T	p.Ser828Leu	p.S828L	ENST00000318560	NM_005157.4	828	tCg/tTg	11/11	1	2	FACETS	0.178	0.151	0.207	0.178	0.151	0.207	SUBCLONAL	1	TRUE	1	0.71	2		674	872	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801003	135801003	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	34	327	0	ENST00000298552.3:c.334C>A	p.Leu112Ile	p.L112I	ENST00000298552	NM_001162426.1	112	Ctt/Att	5/23	1	2	FACETS	0.226	0.184	0.273	0.226	0.184	0.273	SUBCLONAL	1	TRUE	1	0.71	2		327	424	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293681	137293681	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	446	900	0	ENST00000481739.1:c.232T>C	p.Ser78Pro	p.S78P	ENST00000481739	NM_002957.4	78	Tcg/Ccg	2/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.71	2		900	1155	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393579	139393579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1181025067	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1375	138	955	1	ENST00000277541.6:c.6067G>A	p.Ala2023Thr	p.A2023T	ENST00000277541	NM_017617.3	2023	Gcc/Acc	32/34	1	2	FACETS	0.257	0.233	0.283	0.257	0.233	0.283	SUBCLONAL	1	TRUE	1	0.71	2		956	1513	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393670	139393670	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1014152881	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	578	1000	1	ENST00000277541.6:c.5976G>A	p.Met1992Ile	p.M1992I	ENST00000277541	NM_017617.3	1992	atG/atA	32/34	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.71	2		1001	1414	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045122	47045122	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	68	616	1	ENST00000377604.3:c.2363T>G	p.Leu788Arg	p.L788R	ENST00000377604	NM_001204468.1	788	cTt/cGt	21/24	1	2	FACETS	0.223	0.193	0.256	0.223	0.193	0.256	SUBCLONAL	1	TRUE	1	0.71	2		617	858	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429015	47429015	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	107	752	0	ENST00000377045.4:c.1378G>T	p.Ala460Ser	p.A460S	ENST00000377045	NM_001654.4	460	Gcc/Tcc	13/16	1	2	FACETS	0.286	0.255	0.318	0.286	0.255	0.318	SUBCLONAL	1	TRUE	1	0.71	2		752	1055	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223821	53223821	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	604	1002	0	ENST00000375401.3:c.3538A>G	p.Thr1180Ala	p.T1180A	ENST00000375401	NM_004187.3	1180	Acg/Gcg	23/26	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.71	2		1002	1458	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243923	53243923	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	460	810	0	ENST00000375401.3:c.1070C>A	p.Pro357His	p.P357H	ENST00000375401	NM_004187.3	357	cCt/cAt	8/26	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.71	2		810	1228	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247487	53247487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146232504	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	59	486	1	ENST00000375401.3:c.322C>T	p.Arg108Trp	p.R108W	ENST00000375401	NM_004187.3	108	Cgg/Tgg	3/26	1	2	FACETS	0.222	0.19	0.257	0.222	0.19	0.257	SUBCLONAL	1	TRUE	1	0.71	2		487	749	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411677	63411677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1259792397	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	387	761	0	ENST00000330258.3:c.1490G>A	p.Arg497Gln	p.R497Q	ENST00000330258	NM_152424.3	497	cGa/cAa	2/2	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.71	2		761	988	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412730	63412730	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	65	580	0	ENST00000330258.3:c.437C>A	p.Ser146Tyr	p.S146Y	ENST00000330258	NM_152424.3	146	tCt/tAt	2/2	1	2	FACETS	0.264	0.229	0.303	0.264	0.229	0.303	SUBCLONAL	1	TRUE	1	0.71	2		580	693	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339666	70339666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	326	626	2	ENST00000374080.3:c.335C>T	p.Ala112Val	p.A112V	ENST00000374080		112	gCc/gTc	3/45	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.71	2		628	900	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611821	100611821	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	255	429	0	ENST00000308731.7:c.1300G>A	p.Glu434Lys	p.E434K	ENST00000308731	NM_000061.2	434	Gaa/Aaa	14/19	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.71	2		429	642	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861628	152861628	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781948889	NA	P-0055195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	76	568	1	ENST00000406277.2:c.124C>T	p.Arg42Trp	p.R42W	ENST00000406277	NM_152274.4	42	Cgg/Tgg	4/7	1		FACETS		0.232	0.301				SUBCLONAL	1	TRUE	1	0.71	2		569	808	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0055196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	467	774	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.515707887523218	2	FACETS	0.966	0.93	1	0.966	0.93	1	CLONAL	2	TRUE	0	0.564048228671139	2		776	857	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070551	67070551	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	40	196	0	ENST00000412916.2:c.175G>A	p.Ala59Thr	p.A59T	ENST00000412916		59	Gcc/Acc	3/6	0.297092503977732	1	FACETS	0.377	0.315	0.445	0.377	0.315	0.445	INDETERMINATE	1	TRUE	0	0.564048228671139	1		196	270	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123234437	123234437	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0055196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	16	330	0	ENST00000218089.9:c.3797C>G	p.Ser1266Ter	p.S1266*	ENST00000218089	NM_001042749.1	1266	tCa/tGa	35/35	0.564048228671139	1	FACETS	0.177	0.131	0.232	0.177	0.131	0.232	SUBCLONAL	1	TRUE	0	0.564048228671139	1		330	230	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0055197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	223	285	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.520277350696634	3	FACETS	0.845	0.799	0.892	1	0.991	1	CLONAL	3	TRUE	1	0.520277350696634	3		285	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0055197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	210	591	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.520277350696634	1	FACETS	0.848	0.791	0.907	0.848	0.791	0.907	CLONAL	1	TRUE	0	0.520277350696634	1		591	704	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952148	178952149	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0055197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	43	169	0	ENST00000263967.3:c.3204dup	p.Ter1069LeufsTer4	p.*1069Lfs*4	ENST00000263967	NM_006218.2	1068	aac/aaCc	21/21	0.520277350696634	3	FACETS	0.692	0.582	0.813	0.346	0.291	0.407	SUBCLONAL	1	TRUE	1	0.520277350696634	3		169	301	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020633	37020633	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	117	314	0	ENST00000358127.4:c.212G>T	p.Arg71Met	p.R71M	ENST00000358127	NM_001280556.1	71	aGg/aTg	2/10	1	2	FACETS	0.922	0.836	1	0.922	0.836	1	CLONAL	1	TRUE	1	0.520277350696634	2		314	488	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413054	63413054	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	241	766	0	ENST00000330258.3:c.113A>G	p.Glu38Gly	p.E38G	ENST00000330258	NM_152424.3	38	gAa/gGa	2/2	0.298983117132011	1	FACETS	0.659	0.615	0.704	0.659	0.615	0.704	INDETERMINATE	1	TRUE	0	0.520277350696634	1		766	1040	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937335	76937335	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	136	399	0	ENST00000373344.5:c.3413G>T	p.Arg1138Ile	p.R1138I	ENST00000373344	NM_000489.3	1138	aGa/aTa	9/35	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.613783215019927	2		399	309	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050416	128050416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1453017999	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	160	361	1	ENST00000285398.2:c.241G>A	p.Asp81Asn	p.D81N	ENST00000285398	NM_000122.1	81	Gat/Aat	3/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.613783215019927	2		362	417	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934302	81934302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780141402	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	301	817	0	ENST00000359376.3:c.1279G>A	p.Asp427Asn	p.D427N	ENST00000359376	NM_002661.3	427	Gac/Aac	14/33	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.613783215019927	2		817	846	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	167	457	2	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.613783215019927	2		459	472	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	50	632	1	ENST00000394830.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000394830	NM_018313.4	710	Cga/Tga	17/30	1	2	FACETS	0.262	0.222	0.306	0.262	0.222	0.306	SUBCLONAL	1	TRUE	1	0.613783215019927	2		633	622	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	27	845	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.098	0.077	0.122	0.098	0.077	0.122	SUBCLONAL	1	TRUE	1	0.613783215019927	2		845	899	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267600319	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	148	326	0	ENST00000257430.4:c.4199C>T	p.Ser1400Leu	p.S1400L	ENST00000257430	NM_000038.5	1400	tCg/tTg	16/16	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.613783215019927	2		326	380	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955481	48955481	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237070816	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	110	305	0	ENST00000267163.4:c.1597G>A	p.Glu533Lys	p.E533K	ENST00000267163	NM_000321.2	533	Gaa/Aaa	17/27	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.613783215019927	2		305	322	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919631	28919631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200840674	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	194	480	0	ENST00000282397.4:c.2306C>T	p.Ala769Val	p.A769V	ENST00000282397	NM_002019.4	769	gCg/gTg	16/30	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.613783215019927	2		480	541	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692978	89692978	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	163	486	0	ENST00000371953.3:c.462C>A	p.Phe154Leu	p.F154L	ENST00000371953	NM_000314.4	154	ttC/ttA	5/9	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.613783215019927	2		486	476	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266570	115266570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	231	537	1	ENST00000438362.2:c.1945C>T	p.Arg649Cys	p.R649C	ENST00000438362	NM_001242891.1	649	Cgc/Tgc	16/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.613783215019927	2		538	657	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073350	8073350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	190	438	0	ENST00000377482.5:c.1309G>A	p.Glu437Lys	p.E437K	ENST00000377482	NM_018948.3	437	Gaa/Aaa	4/4	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.613783215019927	2		438	546	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781281	9781281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	78	835	0	ENST00000377346.4:c.1786G>A	p.Ala596Thr	p.A596T	ENST00000377346	NM_005026.3	596	Gcc/Acc	14/24	1	2	FACETS	0.296	0.259	0.335	0.296	0.259	0.335	SUBCLONAL	1	TRUE	1	0.613783215019927	2		835	860	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237635	16237635	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	177	356	0	ENST00000375759.3:c.1082A>C	p.Lys361Thr	p.K361T	ENST00000375759	NM_015001.2	361	aAa/aCa	5/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.613783215019927	2		356	513	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094432	27094432	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	243	598	0	ENST00000324856.7:c.3140A>C	p.Lys1047Thr	p.K1047T	ENST00000324856	NM_006015.4	1047	aAa/aCa	11/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.613783215019927	2		598	704	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322565	39322565	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1442884461	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	52	440	0	ENST00000373001.3:c.427G>A	p.Val143Ile	p.V143I	ENST00000373001	NM_022157.3	143	Gtc/Atc	2/7	1	2	FACETS	0.326	0.277	0.379	0.326	0.277	0.379	SUBCLONAL	1	TRUE	1	0.613783215019927	2		440	520	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78435631	78435631	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	143	457	0	ENST00000370768.2:c.189A>T	p.Gln63His	p.Q63H	ENST00000370768	NM_003902.3	63	caA/caT	2/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.613783215019927	2		457	407	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115252336	115252336	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	100	333	0	ENST00000369535.4:c.304C>T	p.Arg102Ter	p.R102*	ENST00000369535	NM_002524.4	102	Cga/Tga	4/7	1	2	FACETS	0.928	0.837	1	0.928	0.837	1	CLONAL	1	TRUE	1	0.613783215019927	2		333	351	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276472	115276472	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	170	467	0	ENST00000438362.2:c.856G>T	p.Glu286Ter	p.E286*	ENST00000438362	NM_001242891.1	286	Gaa/Taa	9/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.613783215019927	2		467	484	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834214	156834214	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	404	1046	0	ENST00000524377.1:c.281G>T	p.Arg94Ile	p.R94I	ENST00000524377	NM_002529.3	94	aGa/aTa	2/17	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.613783215019927	2		1046	1092	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132997	176132997	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs746336083	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	116	307	0	ENST00000367669.3:c.596G>T	p.Arg199Ile	p.R199I	ENST00000367669	NM_022457.5	199	aGa/aTa	4/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.613783215019927	2		307	329	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945669	206945669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	226	584	0	ENST00000423557.1:c.112C>T	p.Pro38Ser	p.P38S	ENST00000423557	NM_000572.2	38	Cct/Tct	1/5	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.613783215019927	2		584	607	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800978	243800978	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	120	394	0	ENST00000263826.5:c.496C>T	p.Arg166Ter	p.R166*	ENST00000263826	NM_005465.4	166	Cga/Tga	5/13	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.613783215019927	2		394	371	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097840	8097840	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	303	677	0	ENST00000346208.3:c.222G>T	p.Arg74Ser	p.R74S	ENST00000346208		74	agG/agT	2/6	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.613783215019927	2		677	829	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851561	63851561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567464868	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	208	524	0	ENST00000279873.7:c.2339G>A	p.Arg780Gln	p.R780Q	ENST00000279873	NM_032199.2	780	cGa/cAa	10/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.613783215019927	2		524	593	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724743	112724743	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	31	333	0	ENST00000369452.4:c.627G>T	p.Lys209Asn	p.K209N	ENST00000369452	NM_007373.3	209	aaG/aaT	2/9	1	2	FACETS	0.252	0.203	0.307	0.252	0.203	0.307	SUBCLONAL	1	TRUE	1	0.613783215019927	2		333	401	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258036	123258036	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519045	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	232	465	0	ENST00000358487.5:c.1645A>C	p.Asn549His	p.N549H	ENST00000358487	NM_000141.4	549	Aat/Cat	12/18	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.613783215019927	2		465	608	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518562	69518562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	47	636	1	ENST00000294312.3:c.83C>T	p.Ser28Leu	p.S28L	ENST00000294312	NM_005117.2	28	tCg/tTg	1/3	1	2	FACETS	0.251	0.212	0.296	0.251	0.212	0.296	SUBCLONAL	1	TRUE	1	0.613783215019927	2		637	609	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189459	94189459	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	35	321	0	ENST00000323929.3:c.1546G>A	p.Asp516Asn	p.D516N	ENST00000323929	NM_005591.3	516	Gat/Aat	14/20	1	2	FACETS	0.251	0.205	0.302	0.251	0.205	0.302	SUBCLONAL	1	TRUE	1	0.613783215019927	2		321	455	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918652	94918652	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	119	261	0	ENST00000536441.1:c.530T>C	p.Leu177Pro	p.L177P	ENST00000536441	NM_144665.3	177	cTt/cCt	5/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.613783215019927	2		261	329	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119692	108119692	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	13	166	0	ENST00000278616.4:c.1098T>G	p.Ile366Met	p.I366M	ENST00000278616	NM_000051.3	366	atT/atG	9/63	1	2	FACETS	0.181	0.129	0.245	0.181	0.129	0.245	SUBCLONAL	1	TRUE	1	0.613783215019927	2		166	234	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307432	118307432	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	27	93	0	ENST00000534358.1:c.205A>C	p.Ser69Arg	p.S69R	ENST00000534358	NM_005933.3	69	Agc/Cgc	1/36	1	2	FACETS	0.871	0.709	1	0.871	0.709	1	CLONAL	1	TRUE	1	0.613783215019927	2		93	101	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373248	118373248	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	164	406	0	ENST00000534358.1:c.6641C>A	p.Ser2214Tyr	p.S2214Y	ENST00000534358	NM_005933.3	2214	tCt/tAt	27/36	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.613783215019927	2		406	490	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148494	119148494	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	46	390	0	ENST00000264033.4:c.1035G>T	p.Gln345His	p.Q345H	ENST00000264033	NM_005188.3	345	caG/caT	7/16	1	2	FACETS	0.318	0.268	0.374	0.318	0.268	0.374	SUBCLONAL	1	TRUE	1	0.613783215019927	2		390	471	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156011	119156011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143034856	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	362	781	1	ENST00000264033.4:c.1676G>A	p.Arg559Gln	p.R559Q	ENST00000264033	NM_005188.3	559	cGa/cAa	11/16	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.613783215019927	2		782	937	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1022610	1022610	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	185	428	0	ENST00000358495.3:c.1204G>A	p.Glu402Lys	p.E402K	ENST00000358495	NM_134424.2	402	Gaa/Aaa	12/12	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.613783215019927	2		428	513	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409125	4409125	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	170	538	0	ENST00000261254.3:c.820G>T	p.Glu274Ter	p.E274*	ENST00000261254	NM_001759.3	274	Gaa/Taa	5/5	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.613783215019927	2		538	517	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18762518	18762518	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	112	398	0	ENST00000266497.5:c.4014C>A	p.Tyr1338Ter	p.Y1338*	ENST00000266497		1338	taC/taA	29/31	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.613783215019927	2		398	353	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427369	49427369	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1565779294	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	316	856	0	ENST00000301067.7:c.11119C>T	p.Arg3707Ter	p.R3707*	ENST00000301067	NM_003482.3	3707	Cga/Tga	39/54	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.613783215019927	2		856	861	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427940	49427940	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	310	716	0	ENST00000301067.7:c.10650A>C	p.Lys3550Asn	p.K3550N	ENST00000301067	NM_003482.3	3550	aaA/aaC	38/54	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.613783215019927	2		716	853	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446049	49446049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	421	1195	0	ENST00000301067.7:c.1417G>A	p.Glu473Lys	p.E473K	ENST00000301067	NM_003482.3	473	Gaa/Aaa	10/54	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.613783215019927	2		1195	1220	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480132	50480132	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	148	315	0	ENST00000394963.4:c.365+1G>T		p.X122_splice	ENST00000394963	NM_003076.4	122			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.613783215019927	2		315	414	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112939958	112939958	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	144	319	1	ENST00000351677.2:c.1610G>T	p.Arg537Met	p.R537M	ENST00000351677	NM_002834.3	537	aGg/aTg	14/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.613783215019927	2		320	396	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879600	123879600	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	142	391	0	ENST00000330479.4:c.296G>T	p.Arg99Ile	p.R99I	ENST00000330479	NM_020382.3	99	aGa/aTa	4/9	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.613783215019927	2		391	430	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209337	133209337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs115452769	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	320	924	0	ENST00000320574.5:c.6049C>T	p.Arg2017Cys	p.R2017C	ENST00000320574	NM_006231.2	2017	Cgc/Tgc	44/49	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.613783215019927	2		924	972	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	228	510	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.613783215019927	2		510	582	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557636	21557636	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	279	646	0	ENST00000382592.4:c.2209G>T	p.Asp737Tyr	p.D737Y	ENST00000382592	NM_014572.2	737	Gac/Tac	5/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.613783215019927	2		646	772	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626775	28626775	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	160	397	0	ENST00000241453.7:c.521G>T	p.Arg174Ile	p.R174I	ENST00000241453	NM_004119.2	174	aGa/aTa	5/24	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.613783215019927	2		397	466	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911247	32911247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs431825298	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	166	430	0	ENST00000380152.3:c.2755G>A	p.Glu919Lys	p.E919K	ENST00000380152		919	Gaa/Aaa	11/27	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.613783215019927	2		430	434	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912480	32912480	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	130	384	0	ENST00000380152.3:c.3988A>C	p.Asn1330His	p.N1330H	ENST00000380152		1330	Aat/Cat	11/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.613783215019927	2		384	349	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912511	32912511	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555283506	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	26	393	0	ENST00000380152.3:c.4019A>C	p.Asp1340Ala	p.D1340A	ENST00000380152		1340	gAt/gCt	11/27	1	2	FACETS	0.221	0.175	0.274	0.221	0.175	0.274	SUBCLONAL	1	TRUE	1	0.613783215019927	2		393	383	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913023	32913023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376338226	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	222	498	0	ENST00000380152.3:c.4531G>A	p.Glu1511Lys	p.E1511K	ENST00000380152		1511	Gaa/Aaa	11/27	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.613783215019927	2		498	591	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914515	32914515	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	37	494	0	ENST00000380152.3:c.6023A>C	p.Lys2008Thr	p.K2008T	ENST00000380152		2008	aAg/aCg	11/27	1	2	FACETS	0.316	0.261	0.378	0.316	0.261	0.378	SUBCLONAL	1	TRUE	1	0.613783215019927	2		494	381	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941654	48941654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776534331	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	70	158	1	ENST00000267163.4:c.964G>A	p.Glu322Lys	p.E322K	ENST00000267163	NM_000321.2	322	Gaa/Aaa	10/27	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.613783215019927	2		159	185	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281446	49281446	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	50	638	0	ENST00000282018.3:c.493C>A	p.Leu165Ile	p.L165I	ENST00000282018	NM_020377.2	165	Ctt/Att	1/1	1	2	FACETS	0.231	0.195	0.27	0.231	0.195	0.27	SUBCLONAL	1	TRUE	1	0.613783215019927	2		638	706	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515335	103515335	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	26	288	0	ENST00000355739.4:c.1836G>T	p.Glu612Asp	p.E612D	ENST00000355739	NM_000123.3	612	gaG/gaT	8/15	1	2	FACETS	0.269	0.213	0.333	0.269	0.213	0.333	SUBCLONAL	1	TRUE	1	0.613783215019927	2		288	315	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046638	30046638	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1419328188	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	216	533	0	ENST00000331968.5:c.2545C>T	p.Arg849Ter	p.R849*	ENST00000331968	NM_002742.2	849	Cga/Tga	18/18	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.613783215019927	2		533	576	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95583979	95583979	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	123	319	0	ENST00000393063.1:c.1489G>T	p.Glu497Ter	p.E497*	ENST00000393063	NM_030621.3	497	Gaa/Taa	10/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.613783215019927	2		319	333	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643281	38643281	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1172820756	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	157	370	0	ENST00000299084.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000299084	NM_152594.2	251	Cga/Tga	7/7	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.613783215019927	2		370	402	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989128	41989128	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	226	521	0	ENST00000219905.7:c.1920G>T	p.Lys640Asn	p.K640N	ENST00000219905	NM_001164273.1	640	aaG/aaT	3/24	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.613783215019927	2		521	588	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021365	42021365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs984878518	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	20	280	1	ENST00000219905.7:c.3661C>T	p.Arg1221Trp	p.R1221W	ENST00000219905	NM_001164273.1	1221	Cgg/Tgg	11/24	1	2	FACETS	0.181	0.138	0.232	0.181	0.138	0.232	SUBCLONAL	1	TRUE	1	0.613783215019927	2		281	360	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041388	42041388	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	260	600	0	ENST00000219905.7:c.5583C>A	p.Phe1861Leu	p.F1861L	ENST00000219905	NM_001164273.1	1861	ttC/ttA	17/24	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.613783215019927	2		600	719	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052588	42052588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	166	345	0	ENST00000219905.7:c.7259C>T	p.Ala2420Val	p.A2420V	ENST00000219905	NM_001164273.1	2420	gCg/gTg	20/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.613783215019927	2		345	475	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058775	42058775	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	82	286	0	ENST00000219905.7:c.8495T>G	p.Phe2832Cys	p.F2832C	ENST00000219905	NM_001164273.1	2832	tTt/tGt	24/24	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.613783215019927	2		286	267	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701862	43701862	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	15	228	0	ENST00000382044.4:c.5383G>T	p.Asp1795Tyr	p.D1795Y	ENST00000382044	NM_001141980.1	1795	Gat/Tat	25/28	1	2	FACETS	0.191	0.139	0.253	0.191	0.139	0.253	SUBCLONAL	1	TRUE	1	0.613783215019927	2		228	256	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43771617	43771617	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	238	494	0	ENST00000382044.4:c.766G>T	p.Glu256Ter	p.E256*	ENST00000382044	NM_001141980.1	256	Gag/Tag	7/28	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.613783215019927	2		494	676	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304059	91304059	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	218	550	1	ENST00000355112.3:c.1456C>A	p.Leu486Ile	p.L486I	ENST00000355112	NM_000057.2	486	Ctt/Att	7/22	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.613783215019927	2		551	628	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100401	2100401	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	rs1555495676	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	183	439	1	ENST00000219476.3:c.139G>T	p.Glu47Ter	p.E47*	ENST00000219476	NM_000548.3	47	Gaa/Taa	3/42	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.613783215019927	2		440	530	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789613	3789613	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	178	518	0	ENST00000262367.5:c.4246G>T	p.Glu1416Ter	p.E1416*	ENST00000262367	NM_004380.2	1416	Gaa/Taa	25/31	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.613783215019927	2		518	521	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116192	67116192	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	116	526	0	ENST00000412916.2:c.476C>A	p.Ser159Tyr	p.S159Y	ENST00000412916		159	tCt/tAt	5/6	1	2	FACETS	0.588	0.531	0.648	0.588	0.531	0.648	SUBCLONAL	1	TRUE	1	0.613783215019927	2		526	643	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821475	72821475	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	47	629	0	ENST00000268489.5:c.10700A>C	p.Glu3567Ala	p.E3567A	ENST00000268489	NM_006885.3	3567	gAg/gCg	10/10	1	2	FACETS	0.209	0.175	0.246	0.209	0.175	0.246	SUBCLONAL	1	TRUE	1	0.613783215019927	2		629	734	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832265	72832265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267604632	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	31	527	0	ENST00000268489.5:c.4316G>A	p.Arg1439Gln	p.R1439Q	ENST00000268489	NM_006885.3	1439	cGa/cAa	9/10	1	2	FACETS	0.184	0.148	0.225	0.184	0.148	0.225	SUBCLONAL	1	TRUE	1	0.613783215019927	2		527	549	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72863756	72863756	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	180	411	0	ENST00000268489.5:c.3451G>T	p.Glu1151Ter	p.E1151*	ENST00000268489	NM_006885.3	1151	Gaa/Taa	5/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.613783215019927	2		411	509	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888069	81888069	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	22	357	0	ENST00000359376.3:c.214G>T	p.Glu72Ter	p.E72*	ENST00000359376	NM_002661.3	72	Gaa/Taa	3/33	1	2	FACETS	0.196	0.152	0.248	0.196	0.152	0.248	SUBCLONAL	1	TRUE	1	0.613783215019927	2		357	365	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89809275	89809275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs545742908	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	296	624	0	ENST00000389301.3:c.3698C>T	p.Ala1233Val	p.A1233V	ENST00000389301	NM_000135.2	1233	gCg/gTg	37/43	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.613783215019927	2		624	801	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217651	7217651	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	148	477	0	ENST00000380728.2:c.276del	p.Val93PhefsTer16	p.V93Ffs*16	ENST00000380728		92	aaA/aa	4/11	1	2	FACETS	0.982	0.904	1	0.982	0.904	1	CLONAL	1	TRUE	1	0.613783215019927	2		477	491	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217654	7217654	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	174	476	0	ENST00000380728.2:c.273G>T	p.Lys91Asn	p.K91N	ENST00000380728		91	aaG/aaT	4/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.613783215019927	2		476	494	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984786	11984786	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	180	394	0	ENST00000353533.5:c.332G>A	p.Gly111Glu	p.G111E	ENST00000353533	NM_003010.3	111	gGa/gAa	3/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.613783215019927	2		394	490	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16056687	16056687	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs767188997	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	20	249	0	ENST00000268712.3:c.755A>C	p.Lys252Thr	p.K252T	ENST00000268712	NM_006311.3	252	aAa/aCa	7/46	1	2	FACETS	0.208	0.158	0.265	0.208	0.158	0.265	SUBCLONAL	1	TRUE	1	0.613783215019927	2		249	314	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585494	29585494	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660428	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	95	219	0	ENST00000356175.3:c.4243G>A	p.Glu1415Lys	p.E1415K	ENST00000356175	NM_000267.3	1415	Gaa/Aaa	31/57	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.613783215019927	2		219	279	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592265	29592265	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	17	212	0	ENST00000356175.3:c.4680A>C	p.Lys1560Asn	p.K1560N	ENST00000356175	NM_000267.3	1560	aaA/aaC	35/57	1	2	FACETS	0.273	0.204	0.354	0.273	0.204	0.354	SUBCLONAL	1	TRUE	1	0.613783215019927	2		212	203	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375521	40375521	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	245	668	0	ENST00000293328.3:c.429G>T	p.Gln143His	p.Q143H	ENST00000293328	NM_012448.3	143	caG/caT	5/19	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.613783215019927	2		668	741	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474431	40474431	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs193922721	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	227	538	0	ENST00000264657.5:c.1970A>G	p.Tyr657Cys	p.Y657C	ENST00000264657	NM_139276.2	657	tAt/tGt	21/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.613783215019927	2		538	645	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243505	41243505	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	281	625	0	ENST00000357654.3:c.4043G>T	p.Gly1348Val	p.G1348V	ENST00000357654	NM_007294.3	1348	gGa/gTa	10/23	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.613783215019927	2		625	769	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435483	56435483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746033324	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	341	900	0	ENST00000407977.2:c.1654C>T	p.Arg552Cys	p.R552C	ENST00000407977		552	Cgc/Tgc	9/10	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.613783215019927	2		900	885	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436137	56436137	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	92	718	0	ENST00000407977.2:c.1000G>T	p.Glu334Ter	p.E334*	ENST00000407977		334	Gaa/Taa	9/10	1	2	FACETS	0.381	0.338	0.427	0.381	0.338	0.427	SUBCLONAL	1	TRUE	1	0.613783215019927	2		718	787	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59793376	59793376	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	135	471	0	ENST00000259008.2:c.2428C>A	p.Leu810Ile	p.L810I	ENST00000259008	NM_032043.2	810	Ctt/Att	17/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.613783215019927	2		471	389	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66525085	66525085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs749518806	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	121	317	0	ENST00000358598.2:c.844A>G	p.Ile282Val	p.I282V	ENST00000358598	NM_212471.2	282	Att/Gtt	9/11	1	2	FACETS	0.957	0.872	1	0.957	0.872	1	CLONAL	1	TRUE	1	0.613783215019927	2		317	412	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526499	66526499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	181	414	0	ENST00000358598.2:c.1055G>A	p.Arg352Gln	p.R352Q	ENST00000358598	NM_212471.2	352	cGa/cAa	11/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.613783215019927	2		414	488	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39573243	39573243	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	94	288	0	ENST00000262039.4:c.724G>T	p.Glu242Ter	p.E242*	ENST00000262039	NM_002647.2	242	Gaa/Taa	7/25	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.613783215019927	2		288	278	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371814	45371814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	147	303	0	ENST00000262160.6:c.1177C>T	p.Leu393Phe	p.L393F	ENST00000262160	NM_005901.5	393	Ctt/Ttt	10/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.613783215019927	2		303	401	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575096	48575096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555685159	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	127	344	0	ENST00000342988.3:c.290G>A	p.Arg97His	p.R97H	ENST00000342988	NM_005359.5	97	cGt/cAt	3/12	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.613783215019927	2		344	383	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218443	5218443	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	53	634	0	ENST00000357368.4:c.4036T>G	p.Phe1346Val	p.F1346V	ENST00000357368	NM_002850.3	1346	Ttc/Gtc	25/38	1	2	FACETS	0.268	0.228	0.312	0.268	0.228	0.312	SUBCLONAL	1	TRUE	1	0.613783215019927	2		634	644	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135100	11135100	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555780047	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	371	960	2	ENST00000358026.2:c.3067G>A	p.Glu1023Lys	p.E1023K	ENST00000358026	NM_001128849.1	1023	Gag/Aag	21/36	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.613783215019927	2		962	1030	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223707	36223707	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	443	1284	2	ENST00000222270.7:c.6257C>A	p.Ser2086Ter	p.S2086*	ENST00000222270	NM_014727.1	2086	tCg/tAg	28/37	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.613783215019927	2		1286	1255	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416399	29416399	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs774746810	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	302	820	0	ENST00000389048.3:c.4554G>T	p.Lys1518Asn	p.K1518N	ENST00000389048	NM_004304.4	1518	aaG/aaT	29/29	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.613783215019927	2		820	882	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672756	47672756	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	175	433	0	ENST00000233146.2:c.1346A>C	p.Lys449Thr	p.K449T	ENST00000233146	NM_000251.2	449	aAg/aCg	8/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.613783215019927	2		433	498	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693886	47693886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750029	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	158	277	1	ENST00000233146.2:c.1600C>T	p.Arg534Cys	p.R534C	ENST00000233146	NM_000251.2	534	Cgt/Tgt	10/16	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.613783215019927	2		278	356	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026567	48026567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773226008	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	88	443	1	ENST00000234420.5:c.1445G>A	p.Arg482Gln	p.R482Q	ENST00000234420	NM_000179.2	482	cGa/cAa	4/10	1	2	FACETS	0.584	0.519	0.653	0.584	0.519	0.653	SUBCLONAL	1	TRUE	1	0.613783215019927	2		444	491	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026616	48026616	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	142	411	0	ENST00000234420.5:c.1494G>T	p.Lys498Asn	p.K498N	ENST00000234420	NM_000179.2	498	aaG/aaT	4/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.613783215019927	2		411	421	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027026	48027026	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	150	395	0	ENST00000234420.5:c.1904G>T	p.Arg635Ile	p.R635I	ENST00000234420	NM_000179.2	635	aGa/aTa	4/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.613783215019927	2		395	412	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027661	48027661	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	107	234	0	ENST00000234420.5:c.2539G>T	p.Glu847Ter	p.E847*	ENST00000234420	NM_000179.2	847	Gaa/Taa	4/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.613783215019927	2		234	273	SUCCESS
REL	5966	MSKCC	GRCh37	2	61121582	61121582	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	85	276	0	ENST00000295025.8:c.204G>T	p.Lys68Asn	p.K68N	ENST00000295025	NM_002908.2	68	aaG/aaT	3/11	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.613783215019927	2		276	265	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149348	61149348	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	29	297	0	ENST00000295025.8:c.1538G>T	p.Arg513Ile	p.R513I	ENST00000295025	NM_002908.2	513	aGa/aTa	11/11	1	2	FACETS	0.248	0.199	0.304	0.248	0.199	0.304	SUBCLONAL	1	TRUE	1	0.613783215019927	2		297	381	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155369	99155369	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs954252241	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	150	426	0	ENST00000074304.5:c.595G>A	p.Asp199Asn	p.D199N	ENST00000074304	NM_001134224.1	199	Gat/Aat	9/26	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.613783215019927	2		426	415	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128016873	128016873	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1350655187	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	218	537	0	ENST00000285398.2:c.2216A>G	p.Gln739Arg	p.Q739R	ENST00000285398	NM_000122.1	739	cAg/cGg	14/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.613783215019927	2		537	602	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050314	128050314	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	234	554	1	ENST00000285398.2:c.343G>T	p.Glu115Ter	p.E115*	ENST00000285398	NM_000122.1	115	Gag/Tag	3/15	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.613783215019927	2		555	622	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096619	178096619	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	108	289	0	ENST00000397062.3:c.712G>T	p.Glu238Ter	p.E238*	ENST00000397062	NM_006164.4	238	Gaa/Taa	5/5	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.613783215019927	2		289	341	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732577	190732577	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	124	337	0	ENST00000441310.2:c.2395G>T	p.Asp799Tyr	p.D799Y	ENST00000441310	NM_000534.4	799	Gac/Tac	11/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.613783215019927	2		337	367	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270150	198270150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1421809024	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	156	393	0	ENST00000335508.6:c.1286G>A	p.Arg429Gln	p.R429Q	ENST00000335508	NM_012433.2	429	cGa/cAa	10/25	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.613783215019927	2		393	458	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131412	202131412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339962485	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	22	438	0	ENST00000358485.4:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000358485	NM_001080125.1	127	cGa/cAa	2/9	1	2	FACETS	0.147	0.113	0.186	0.147	0.113	0.186	SUBCLONAL	1	TRUE	1	0.613783215019927	2		438	488	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137409	202137409	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	160	337	0	ENST00000358485.4:c.637G>T	p.Glu213Ter	p.E213*	ENST00000358485	NM_001080125.1	213	Gaa/Taa	4/9	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.613783215019927	2		337	421	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661541	227661541	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	80	940	1	ENST00000305123.5:c.1914G>T	p.Lys638Asn	p.K638N	ENST00000305123	NM_005544.2	638	aaG/aaT	1/2	1	2	FACETS	0.267	0.234	0.302	0.267	0.234	0.302	SUBCLONAL	1	TRUE	1	0.613783215019927	2		941	977	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389107	31389107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749860839	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	198	507	0	ENST00000328111.2:c.2020G>A	p.Glu674Lys	p.E674K	ENST00000328111	NM_006892.3	674	Gaa/Aaa	19/23	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.613783215019927	2		507	550	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143253	24143253	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	319	834	0	ENST00000263121.7:c.485G>T	p.Arg162Ile	p.R162I	ENST00000263121	NM_003073.3	162	aGa/aTa	4/9	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.613783215019927	2		834	1011	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130475	29130475	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	41	675	0	ENST00000328354.6:c.235G>T	p.Glu79Ter	p.E79*	ENST00000328354	NM_007194.3	79	Gaa/Taa	2/15	1	2	FACETS	0.182	0.15	0.216	0.182	0.15	0.216	SUBCLONAL	1	TRUE	1	0.613783215019927	2		675	736	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191526	10191526	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	203	491	0	ENST00000256474.2:c.519G>T	p.Glu173Asp	p.E173D	ENST00000256474	NM_000551.3	173	gaG/gaT	3/3	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.613783215019927	2		491	609	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181477	38181477	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	256	607	1	ENST00000396334.3:c.490G>T	p.Asp164Tyr	p.D164Y	ENST00000396334	NM_002468.4	164	Gat/Tat	2/5	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.613783215019927	2		608	755	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	71	333	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.586	0.514	0.663	0.586	0.514	0.663	SUBCLONAL	1	TRUE	1	0.613783215019927	2		333	395	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47205370	47205370	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	191	524	0	ENST00000409792.3:c.45C>A	p.Phe15Leu	p.F15L	ENST00000409792	NM_014159.6	15	ttC/ttA	1/21	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.613783215019927	2		524	538	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620542	52620542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	222	564	0	ENST00000394830.3:c.3211C>T	p.Arg1071Cys	p.R1071C	ENST00000394830	NM_018313.4	1071	Cgc/Tgc	21/30	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.613783215019927	2		564	699	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637690	52637690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239654517	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	177	380	1	ENST00000394830.3:c.2626C>T	p.Arg876Cys	p.R876C	ENST00000394830	NM_018313.4	876	Cgt/Tgt	18/30	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.613783215019927	2		381	487	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281651	142281651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759878676	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	43	455	0	ENST00000350721.4:c.593G>A	p.Ser198Asn	p.S198N	ENST00000350721	NM_001184.3	198	aGt/aAt	4/47	1	2	FACETS	0.291	0.243	0.344	0.291	0.243	0.344	SUBCLONAL	1	TRUE	1	0.613783215019927	2		455	482	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916808	178916808	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	169	424	0	ENST00000263967.3:c.195A>C	p.Glu65Asp	p.E65D	ENST00000263967	NM_006218.2	65	gaA/gaC	2/21	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.613783215019927	2		424	439	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	70	181	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.613783215019927	2		181	186	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921566	178921566	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	95	232	0	ENST00000263967.3:c.1048G>T	p.Asp350Tyr	p.D350Y	ENST00000263967	NM_006218.2	350	Gac/Tac	5/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.613783215019927	2		232	242	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	114	282	0	ENST00000263967.3:c.3132T>G	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaG	21/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.613783215019927	2		282	335	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587161	189587161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173679499	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	123	341	0	ENST00000264731.3:c.1178G>A	p.Arg393Gln	p.R393Q	ENST00000264731	NM_003722.4	393	cGa/cAa	9/14	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.613783215019927	2		341	395	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131106	55131106	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	197	447	0	ENST00000257290.5:c.649G>T	p.Glu217Ter	p.E217*	ENST00000257290	NM_006206.4	217	Gaa/Taa	5/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.613783215019927	2		447	532	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589813	55589813	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	24	394	0	ENST00000288135.5:c.1295G>A	p.Gly432Glu	p.G432E	ENST00000288135	NM_000222.2	432	gGa/gAa	8/21	1	2	FACETS	0.183	0.143	0.23	0.183	0.143	0.23	SUBCLONAL	1	TRUE	1	0.613783215019927	2		394	427	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972903	55972903	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	190	489	0	ENST00000263923.4:c.1487A>C	p.Lys496Thr	p.K496T	ENST00000263923	NM_002253.2	496	aAa/aCa	11/30	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.613783215019927	2		489	521	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114277	143114277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs76891221	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	19	319	0	ENST00000262992.4:c.1144C>T	p.Arg382Trp	p.R382W	ENST00000262992	NM_001101669.1	382	Cgg/Tgg	13/24	1	2	FACETS	0.173	0.131	0.223	0.173	0.131	0.223	SUBCLONAL	1	TRUE	1	0.613783215019927	2		319	358	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	222	478	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.613783215019927	2		478	601	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	175	421	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.613783215019927	2		421	497	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532590	187532590	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	171	321	0	ENST00000441802.2:c.9803C>A	p.Ser3268Ter	p.S3268*	ENST00000441802	NM_005245.3	3268	tCa/tAa	14/27	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.613783215019927	2		321	376	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630240	187630240	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368175691	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	227	556	1	ENST00000441802.2:c.742G>A	p.Glu248Lys	p.E248K	ENST00000441802	NM_005245.3	248	Gaa/Aaa	2/27	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.613783215019927	2		557	640	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228312	228312	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	75	232	1	ENST00000264932.6:c.634G>T	p.Asp212Tyr	p.D212Y	ENST00000264932	NM_004168.2	212	Gat/Tat	6/15	1	2	FACETS	0.895	0.794	1	0.895	0.794	1	CLONAL	1	TRUE	1	0.613783215019927	2		233	273	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31423030	31423030	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	219	446	0	ENST00000344624.3:c.3283C>T	p.Arg1095Ter	p.R1095*	ENST00000344624		1095	Cga/Tga	26/33	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.613783215019927	2		446	562	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950439	38950439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	174	363	1	ENST00000357387.3:c.3511G>A	p.Asp1171Asn	p.D1171N	ENST00000357387	NM_152756.3	1171	Gac/Aac	31/38	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.613783215019927	2		364	414	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38981988	38981988	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263964007	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	114	315	0	ENST00000357387.3:c.734G>A	p.Arg245Gln	p.R245Q	ENST00000357387	NM_152756.3	245	cGa/cAa	8/38	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.613783215019927	2		315	316	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179491	56179491	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	113	246	0	ENST00000399503.3:c.3804A>C	p.Leu1268Phe	p.L1268F	ENST00000399503	NM_005921.1	1268	ttA/ttC	15/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.613783215019927	2		246	324	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522547	67522547	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	96	197	0	ENST00000274335.5:c.44A>C	p.Lys15Thr	p.K15T	ENST00000274335		15	aAa/aCa	1/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.613783215019927	2		197	278	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79966048	79966048	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	188	431	0	ENST00000265081.6:c.712G>T	p.Glu238Ter	p.E238*	ENST00000265081	NM_002439.4	238	Gaa/Taa	4/24	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.613783215019927	2		431	485	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86668008	86668008	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	68	241	0	ENST00000274376.6:c.1772G>A	p.Arg591His	p.R591H	ENST00000274376	NM_002890.2	591	cGt/cAt	13/25	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.613783215019927	2		241	215	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	19	277	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.18	0.136	0.232	0.18	0.136	0.232	SUBCLONAL	1	TRUE	1	0.613783215019927	2		277	344	SUCCESS
APC	324	MSKCC	GRCh37	5	112176209	112176209	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373440614	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	204	430	0	ENST00000257430.4:c.4918C>T	p.Arg1640Trp	p.R1640W	ENST00000257430	NM_000038.5	1640	Cgg/Tgg	16/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.613783215019927	2		430	567	SUCCESS
APC	324	MSKCC	GRCh37	5	112177368	112177368	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	99	245	1	ENST00000257430.4:c.6077C>A	p.Ser2026Tyr	p.S2026Y	ENST00000257430	NM_000038.5	2026	tCt/tAt	16/16	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.613783215019927	2		246	310	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149450022	149450022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	254	719	0	ENST00000286301.3:c.1195C>T	p.Arg399Ter	p.R399*	ENST00000286301	NM_005211.3	399	Cga/Tga	8/22	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.613783215019927	2		719	752	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514525	149514525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138830253	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	38	564	0	ENST00000261799.4:c.419C>T	p.Thr140Met	p.T140M	ENST00000261799	NM_002609.3	140	aCg/aTg	4/23	1	2	FACETS	0.213	0.176	0.255	0.213	0.176	0.255	SUBCLONAL	1	TRUE	1	0.613783215019927	2		564	581	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172120	32172120	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	67	917	0	ENST00000375023.3:c.2912C>A	p.Ala971Asp	p.A971D	ENST00000375023	NM_004557.3	971	gCt/gAt	19/30	1	2	FACETS	0.21	0.181	0.241	0.21	0.181	0.241	SUBCLONAL	1	TRUE	1	0.613783215019927	2		917	1041	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190522	32190522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770403231	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	44	907	2	ENST00000375023.3:c.217C>T	p.Leu73Phe	p.L73F	ENST00000375023	NM_004557.3	73	Ctc/Ttc	3/30	1	2	FACETS	0.171	0.142	0.202	0.171	0.142	0.202	SUBCLONAL	1	TRUE	1	0.613783215019927	2		909	840	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908197	41908197	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	379	970	0	ENST00000372991.4:c.325C>A	p.Leu109Met	p.L109M	ENST00000372991	NM_001760.3	109	Ctg/Atg	2/5	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.613783215019927	2		970	1036	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642497	117642497	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	310	604	0	ENST00000368508.3:c.5702A>T	p.Asn1901Ile	p.N1901I	ENST00000368508	NM_002944.2	1901	aAc/aTc	35/43	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.613783215019927	2		604	748	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642538	117642538	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	265	591	1	ENST00000368508.3:c.5661G>T	p.Lys1887Asn	p.K1887N	ENST00000368508	NM_002944.2	1887	aaG/aaT	35/43	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.613783215019927	2		592	676	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004321	150004321	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	170	312	0	ENST00000253339.5:c.1904C>A	p.Ser635Tyr	p.S635Y	ENST00000253339		635	tCt/tAt	3/7	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.613783215019927	2		312	442	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92355073	92355073	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	89	238	0	ENST00000265734.4:c.404T>G	p.Phe135Cys	p.F135C	ENST00000265734	NM_001259.6	135	tTt/tGt	4/8	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.613783215019927	2		238	276	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841908	151841908	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	151	291	0	ENST00000262189.6:c.14233G>T	p.Glu4745Ter	p.E4745*	ENST00000262189	NM_170606.2	4745	Gaa/Taa	55/59	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.613783215019927	2		291	397	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848577	151848577	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	140	333	0	ENST00000262189.6:c.12616C>A	p.Leu4206Ile	p.L4206I	ENST00000262189	NM_170606.2	4206	Ctt/Att	50/59	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.613783215019927	2		333	388	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874046	151874046	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	200	432	0	ENST00000262189.6:c.8492C>A	p.Ser2831Tyr	p.S2831Y	ENST00000262189	NM_170606.2	2831	tCt/tAt	38/59	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.613783215019927	2		432	540	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152357831	152357831	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	147	350	0	ENST00000359321.1:c.76G>T	p.Glu26Ter	p.E26*	ENST00000359321	NM_005431.1	26	Gaa/Taa	2/3	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.613783215019927	2		350	460	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869569	117869569	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	113	335	0	ENST00000297338.2:c.625T>G	p.Leu209Val	p.L209V	ENST00000297338	NM_006265.2	209	Tta/Gta	6/14	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.613783215019927	2		335	353	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5029830	5029830	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	139	426	0	ENST00000381652.3:c.274G>T	p.Glu92Ter	p.E92*	ENST00000381652	NM_004972.3	92	Gaa/Taa	4/25	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.613783215019927	2		426	380	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050770	5050770	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	150	361	0	ENST00000381652.3:c.553G>T	p.Asp185Tyr	p.D185Y	ENST00000381652	NM_004972.3	185	Gat/Tat	6/25	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.613783215019927	2		361	429	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317089	87317089	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	142	333	0	ENST00000277120.3:c.228G>T	p.Gln76His	p.Q76H	ENST00000277120		76	caG/caT	3/19	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.613783215019927	2		333	422	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339212	87339212	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	162	488	1	ENST00000277120.3:c.794C>A	p.Ser265Tyr	p.S265Y	ENST00000277120		265	tCt/tAt	8/19	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.613783215019927	2		489	480	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97873833	97873833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200719554	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	303	790	1	ENST00000289081.3:c.1241C>T	p.Ser414Leu	p.S414L	ENST00000289081	NM_000136.2	414	tCg/tTg	13/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.613783215019927	2		791	904	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221936	98221936	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1064794260	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	252	648	0	ENST00000331920.6:c.2833C>T	p.Arg945Ter	p.R945*	ENST00000331920	NM_000264.3	945	Cga/Tga	17/24	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.613783215019927	2		648	752	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920567	127920567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	187	485	1	ENST00000373547.4:c.332G>A	p.Arg111Gln	p.R111Q	ENST00000373547	NM_002721.4	111	cGa/cAa	4/7	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.613783215019927	2		486	513	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15840901	15840901	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	147	331	2	ENST00000307771.7:c.985C>A	p.Leu329Ile	p.L329I	ENST00000307771	NM_005089.3	329	Ctt/Att	11/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.613783215019927	2		333	387	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914671	39914671	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	222	540	1	ENST00000378444.4:c.4691G>T	p.Arg1564Ile	p.R1564I	ENST00000378444	NM_001123385.1	1564	aGa/aTa	12/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.613783215019927	2		541	654	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914752	39914752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	37	406	0	ENST00000378444.4:c.4610C>T	p.Ala1537Val	p.A1537V	ENST00000378444	NM_001123385.1	1537	gCt/gTt	12/15	1	2	FACETS	0.239	0.197	0.287	0.239	0.197	0.287	SUBCLONAL	1	TRUE	1	0.613783215019927	2		406	504	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931652	39931652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	255	669	1	ENST00000378444.4:c.2947G>A	p.Glu983Lys	p.E983K	ENST00000378444	NM_001123385.1	983	Gaa/Aaa	4/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.613783215019927	2		670	708	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933219	39933220	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	274	908	0	ENST00000378444.4:c.1379dup	p.Met461AspfsTer21	p.M461Dfs*21	ENST00000378444	NM_001123385.1	460	aag/aaAg	4/15	1	2	FACETS	0.942	0.885	0.999	0.942	0.885	0.999	CLONAL	1	TRUE	1	0.613783215019927	2		908	948	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041667	47041667	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	50	713	1	ENST00000377604.3:c.1892C>T	p.Ala631Val	p.A631V	ENST00000377604	NM_001204468.1	631	gCa/gTa	17/24	1	2	FACETS	0.208	0.175	0.243	0.208	0.175	0.243	SUBCLONAL	1	TRUE	1	0.613783215019927	2		714	784	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045500	47045500	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	77	743	1	ENST00000377604.3:c.2467G>T	p.Glu823Ter	p.E823*	ENST00000377604	NM_001204468.1	823	Gaa/Taa	22/24	1	2	FACETS	0.307	0.269	0.348	0.307	0.269	0.348	SUBCLONAL	1	TRUE	1	0.613783215019927	2		744	818	SUCCESS
AR	367	MSKCC	GRCh37	X	66765763	66765763	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	445	1227	0	ENST00000374690.3:c.775C>A	p.Pro259Thr	p.P259T	ENST00000374690	NM_000044.3	259	Cca/Aca	1/8	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.613783215019927	2		1227	1258	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356385	70356385	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	40	665	0	ENST00000374080.3:c.5280G>T	p.Glu1760Asp	p.E1760D	ENST00000374080		1760	gaG/gaT	37/45	1	2	FACETS	0.168	0.139	0.201	0.168	0.139	0.201	SUBCLONAL	1	TRUE	1	0.613783215019927	2		665	774	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920197	76920197	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	143	446	0	ENST00000373344.5:c.3880G>T	p.Asp1294Tyr	p.D1294Y	ENST00000373344	NM_000489.3	1294	Gat/Tat	11/35	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.613783215019927	2		446	464	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938202	76938202	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	212	560	0	ENST00000373344.5:c.2546C>A	p.Ser849Tyr	p.S849Y	ENST00000373344	NM_000489.3	849	tCt/tAt	9/35	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.613783215019927	2		560	610	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615086	100615086	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	167	399	0	ENST00000308731.7:c.829G>T	p.Glu277Ter	p.E277*	ENST00000308731	NM_000061.2	277	Gaa/Taa	9/19	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.613783215019927	2		399	494	SUCCESS
BTK	695	MSKCC	GRCh37	X	100629548	100629549	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs886041148	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	194	557	0	ENST00000308731.7:c.215dup	p.Asn72LysfsTer13	p.N72Kfs*13	ENST00000308731	NM_000061.2	72	aat/aaAt	3/19	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.613783215019927	2		557	625	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202419	123202419	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	93	337	0	ENST00000218089.9:c.2271C>A	p.Asp757Glu	p.D757E	ENST00000218089	NM_001042749.1	757	gaC/gaA	24/35	1	2	FACETS	0.924	0.83	1	0.924	0.83	1	CLONAL	1	TRUE	1	0.613783215019927	2		337	328	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913409	NA	P-0055198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	45	333	0	ENST00000349496.5:c.134C>A	p.Ser45Tyr	p.S45Y	ENST00000349496	NM_001904.3	45	tCt/tAt	3/15	1	2	FACETS	0.371	0.312	0.436	0.371	0.312	0.436	SUBCLONAL	1	TRUE	1	0.613783215019927	2		333	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0055201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	722	915	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.60085376311166	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.60085376311166	2		915	1154	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0055201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	135	342	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.60085376311166	1	FACETS	0.909	0.837	0.982	0.909	0.837	0.982	CLONAL	1	TRUE	0	0.60085376311166	1		342	346	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955165	17955165	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752820429	NA	P-0055201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	258	970	1	ENST00000458235.1:c.62C>T	p.Thr21Met	p.T21M	ENST00000458235	NM_000215.3	21	aCg/aTg	2/24	0.378565961132884	1	FACETS	0.464	0.434	0.496	0.464	0.434	0.496	SUBCLONAL	1	TRUE	0	0.60085376311166	1		971	1294	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872169	76872169	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	206	374	0	ENST00000373344.5:c.5478C>G	p.Phe1826Leu	p.F1826L	ENST00000373344	NM_000489.3	1826	ttC/ttG	22/35	0.31903322461075	2	FACETS	0.776	0.729	0.823	0.776	0.729	0.823	INDETERMINATE	2	TRUE	0	0.60085376311166	2		374	442	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939033	48939033	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1131690901	NA	P-0055202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	34	263	0	ENST00000267163.4:c.869del	p.Asn290MetfsTer11	p.N290Mfs*11	ENST00000267163	NM_000321.2	289	Aaa/aa	9/27	0.470663813053507	1	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	0	0.470663813053507	1		263	103	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278162	41278162	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	32	441	0	ENST00000349496.5:c.2038A>G	p.Ser680Gly	p.S680G	ENST00000349496	NM_001904.3	680	Agc/Ggc	13/15	0.459947085361841	1	FACETS	0.642	0.527	0.767	0.642	0.527	0.767	SUBCLONAL	1	TRUE	0	0.470663813053507	1		441	162	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0055203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	180	644	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.349210419973542	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.400980122433348	1		646	691	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0055203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	83	597	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	1	2	FACETS	0.536	0.473	0.605	0.536	0.473	0.605	SUBCLONAL	1	TRUE	1	0.400980122433348	2		597	772	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528710	8528710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768826930	NA	P-0055203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	23	391	0	ENST00000356435.5:c.422G>A	p.Arg141His	p.R141H	ENST00000356435		141	cGc/cAc	4/35	0.400980122433348	1	FACETS	0.212	0.164	0.267	0.212	0.164	0.267	SUBCLONAL	1	TRUE	0	0.400980122433348	1		391	433	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436028	56436028	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	147	645	0	ENST00000407977.2:c.1109del	p.Pro370HisfsTer49	p.P370Hfs*49	ENST00000407977		370	cCa/ca	9/10	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.400980122433348	2		645	655	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464895	120464895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557804884	NA	P-0055203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	58	496	1	ENST00000256646.2:c.5177G>A	p.Arg1726His	p.R1726H	ENST00000256646	NM_024408.3	1726	cGt/cAt	28/34	1	2	FACETS	0.689	0.593	0.792	0.689	0.593	0.792	SUBCLONAL	1	TRUE	1	0.400980122433348	2		497	420	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423598	88423598	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	140	566	0	ENST00000360948.2:c.2237A>G	p.Lys746Arg	p.K746R	ENST00000360948	NM_001012338.2	746	aAg/aGg	18/19	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.400980122433348	2		566	618	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089996	16089996	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	21	263	0	ENST00000268712.3:c.114C>A	p.Phe38Leu	p.F38L	ENST00000268712	NM_006311.3	38	ttC/ttA	3/46	0.349210419973542	1	FACETS	0.358	0.276	0.453	0.358	0.276	0.453	SUBCLONAL	1	TRUE	0	0.400980122433348	1		263	234	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583398	46583398	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	102	570	0	ENST00000263734.3:c.326T>A	p.Ile109Asn	p.I109N	ENST00000263734	NM_001430.4	109	aTc/aAc	3/16	0.120135964956677	3	FACETS	1	0.94	1	0.535	0.479	0.593	INDETERMINATE	1	TRUE	1	0.400980122433348	3		570	571	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971063	21971120	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGCAGCACCACCAGCGTGTCCAGGAAGCCCTCCCGGGCAGCGTCGTGCACGGGTCG	GGTGCAGCACCACCAGCGTGTCCAGGAAGCCCTCCCGGGCAGCGTCGTGCACGGGTCG	-	novel	NA	P-0055203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	56	484	0	ENST00000304494.5:c.238_295del	p.Arg80GlyfsTer47	p.R80Gfs*47	ENST00000304494	NM_000077.4	80	CGACCCGTGCACGACGCTGCCCGGGAGGGCTTCCTGGACACGCTGGTGGTGCTGCACCgg/gg	2/3	0.400980122433348	1	FACETS	0.605	0.521	0.697	0.605	0.521	0.697	SUBCLONAL	1	TRUE	0	0.400980122433348	1		484	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579529	7579529	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658483	NA	P-0055204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	380	934	0	ENST00000269305.4:c.158G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tGg/tAg	4/11	0.741689392485072	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.741689392485072	1		934	602	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339327	70339327	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	166	478	0	ENST00000374080.3:c.204G>T	p.Lys68Asn	p.K68N	ENST00000374080		68	aaG/aaT	2/45	1	2	FACETS	0.946	0.877	1	0.946	0.877	1	CLONAL	1	TRUE	1	0.741689392485072	2		478	473	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790421	3790421	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1567272940	NA	P-0055204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	250	559	1	ENST00000262367.5:c.4112T>A	p.Val1371Asp	p.V1371D	ENST00000262367	NM_004380.2	1371	gTc/gAc	24/31	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.741689392485072	2		560	594	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811648	102811648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1188704136	NA	P-0055204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	270	671	0	ENST00000307046.8:c.536G>A	p.Arg179Lys	p.R179K	ENST00000307046	NM_001111285.1	179	aGg/aAg	4/4	1	2	FACETS	0.98	0.924	1	0.98	0.924	1	CLONAL	1	TRUE	1	0.741689392485072	2		671	743	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935255	36935255	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	320	875	1	ENST00000361632.4:c.1472del	p.Lys491ArgfsTer14	p.K491Rfs*14	ENST00000361632		491	aAg/ag	10/16	1	2	FACETS	0.987	0.935	1	0.987	0.935	1	CLONAL	1	TRUE	1	0.741689392485072	2		876	874	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981885	201981885	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	377	1081	0	ENST00000359651.3:c.596C>A	p.Ala199Glu	p.A199E	ENST00000359651		199	gCa/gAa	4/8	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.741689392485072	2		1081	1005	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156161	119156161	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1031634822	NA	P-0055204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	230	592	0	ENST00000264033.4:c.1826G>T	p.Trp609Leu	p.W609L	ENST00000264033	NM_005188.3	609	tGg/tTg	11/16	1	2	FACETS	0.912	0.855	0.971	0.912	0.855	0.971	CLONAL	1	TRUE	1	0.741689392485072	2		592	680	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231343	46231343	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	98	376	0	ENST00000334344.6:c.1183G>T	p.Val395Leu	p.V395L	ENST00000334344	NM_152641.2	395	Gtg/Ttg	10/21	1	2	FACETS	0.878	0.793	0.966	0.878	0.793	0.966	CLONAL	1	TRUE	1	0.741689392485072	2		376	301	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50821762	50821762	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	76	303	0	ENST00000398568.2:c.2098A>G	p.Arg700Gly	p.R700G	ENST00000398568	NM_001042412.1	700	Aga/Gga	13/18	0.741689392485072	1	FACETS	0.895	0.812	0.979	0.895	0.812	0.979	CLONAL	1	TRUE	0	0.741689392485072	1		303	144	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876633	59876633	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	124	327	0	ENST00000259008.2:c.1168G>T	p.Val390Phe	p.V390F	ENST00000259008	NM_032043.2	390	Gtc/Ttc	9/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.741689392485072	2		327	322	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509080	66509080	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0055204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	58	234	0	ENST00000273854.3:c.246+1G>A		p.X82_splice	ENST00000273854	NM_004439.5	82			1	2	FACETS	0.899	0.787	1	0.899	0.787	1	CLONAL	1	TRUE	1	0.741689392485072	2		234	174	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730473	133730473	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	130	394	0	ENST00000318560.5:c.539C>G	p.Ser180Cys	p.S180C	ENST00000318560	NM_005157.4	180	tCt/tGt	3/11	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.741689392485072	2		394	342	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353764	68353782	+	protein_altering_variant	In_Frame_Del	DEL	TCTCAAAAGGAATTAAACT	TCTCAAAAGGAATTAAACT	A	novel	NA	P-0055204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	63	249	0	ENST00000487270.1:c.599_617delinsA	p.Ile200_Leu206delinsAsn	p.I200_L206delinsN	ENST00000487270	NM_133509.3	200	aTCTCAAAAGGAATTAAACTt/aAt	7/11	1	2	FACETS	0.829	0.728	0.934	0.829	0.728	0.934	CLONAL	1	TRUE	1	0.741689392485072	2		249	205	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579523	7579523	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	TT	novel	NA	P-0055205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	112	941	0	ENST00000269305.4:c.164delinsAA	p.Thr55LysfsTer2	p.T55Kfs*2	ENST00000269305	NM_001126112.2	55	aCt/aAAt	4/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.223411253448138	NA		941	712	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0055206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	429	785	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.406588376463139	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.621695022087004	1		785	863	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0055206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	468	285	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.621695022087004	6	FACETS	0.995	0.964	1			1	CLONAL	5	TRUE	NA	0.621695022087004	6		285	679	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911234	32911234	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs759767392	NA	P-0055206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	30	455	0	ENST00000380152.3:c.2742G>C	p.Leu914Phe	p.L914F	ENST00000380152		914	ttG/ttC	11/27	1	2	FACETS	0.193	0.155	0.236	0.193	0.155	0.236	SUBCLONAL	1	TRUE	1	0.621695022087004	2		455	500	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223463	2223463	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1049846753	NA	P-0055206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	24	511	0	ENST00000398665.3:c.3574G>A	p.Glu1192Lys	p.E1192K	ENST00000398665	NM_032482.2	1192	Gag/Aag	25/28	0.621695022087004	1	FACETS	0.156	0.122	0.195	0.156	0.122	0.195	SUBCLONAL	1	TRUE	0	0.621695022087004	1		511	342	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0055207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	112	354	1				ENST00000310581	NM_198253.2	-/1132			0.655625336125977	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.655625336125977	1		355	180	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0055207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	278	492	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.655625336125977	3	FACETS	0.959	0.91	1	0.959	0.91	1	CLONAL	2	TRUE	1	0.655625336125977	3		492	587	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521711	89521711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	142	432	0	ENST00000336596.2:c.2788G>A	p.Glu930Lys	p.E930K	ENST00000336596	NM_005233.5	930	Gaa/Aaa	16/17	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.655625336125977	2		432	401	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597507	28597507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	102	415	0	ENST00000241453.7:c.2398G>A	p.Glu800Lys	p.E800K	ENST00000241453	NM_004119.2	800	Gaa/Aaa	19/24	1	2	FACETS	0.857	0.774	0.944	0.857	0.774	0.944	CLONAL	1	TRUE	1	0.655625336125977	2		415	363	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858735	9858735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	101	339	0	ENST00000330684.3:c.2666G>A	p.Gly889Glu	p.G889E	ENST00000330684	NM_001134407.1	889	gGa/gAa	13/13	1	2	FACETS	0.942	0.852	1	0.942	0.852	1	CLONAL	1	TRUE	1	0.655625336125977	2		339	327	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355310	81355310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	59	227	0	ENST00000222390.5:c.1064G>A	p.Arg355Gln	p.R355Q	ENST00000222390	NM_000601.4	355	cGa/cAa	9/18	0.655625336125977	3	FACETS	0.773	0.67	0.884	0.387	0.335	0.442	SUBCLONAL	1	TRUE	1	0.655625336125977	3		227	309	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381466	81381466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	88	257	0	ENST00000222390.5:c.595G>A	p.Glu199Lys	p.E199K	ENST00000222390	NM_000601.4	199	Gaa/Aaa	5/18	0.655625336125977	3	FACETS	0.966	0.862	1	0.483	0.431	0.538	CLONAL	1	TRUE	1	0.655625336125977	3		257	369	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958791	55958791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	114	430	0	ENST00000263923.4:c.3062C>T	p.Ser1021Leu	p.S1021L	ENST00000263923	NM_002253.2	1021	tCg/tTg	22/30	1	2	FACETS	0.925	0.841	1	0.925	0.841	1	CLONAL	1	TRUE	1	0.655625336125977	2		430	376	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139459	47139459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	123	355	0	ENST00000409792.3:c.5128C>T	p.Arg1710Cys	p.R1710C	ENST00000409792	NM_014159.6	1710	Cgt/Tgt	9/21	1	2	FACETS	0.993	0.907	1	0.993	0.907	1	CLONAL	1	TRUE	1	0.655625336125977	2		355	378	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971209	21971209	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0055207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	137	352	0	ENST00000304494.5:c.151-2A>T		p.X51_splice	ENST00000304494	NM_000077.4	51			0.655625336125977	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.655625336125977	1		352	252	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458480	12458480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	146	565	0	ENST00000287820.6:c.1097G>A	p.Gly366Glu	p.G366E	ENST00000287820	NM_015869.4	366	gGg/gAg	6/7	1	2	FACETS	0.858	0.788	0.931	0.858	0.788	0.931	CLONAL	1	TRUE	1	0.655625336125977	2		565	519	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514156	125514156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	122	289	0	ENST00000428830.2:c.1094C>T	p.Ser365Phe	p.S365F	ENST00000428830	NM_001114121.2	365	tCc/tTc	10/14	0.637978775612135	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.655625336125977	1		289	224	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051428	13051428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	163	537	0	ENST00000316448.5:c.776G>A	p.Gly259Glu	p.G259E	ENST00000316448	NM_004343.3	259	gGa/gAa	6/9	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.655625336125977	2		537	482	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807557	1807557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	227	1028	0	ENST00000260795.2:c.1726G>A	p.Asp576Asn	p.D576N	ENST00000260795		576	Gac/Aac	12/17	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.655625336125977	2		1028	682	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140449185	140449185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	31	313	0	ENST00000288602.6:c.1894C>T	p.Pro632Ser	p.P632S	ENST00000288602	NM_004333.4	632	Cca/Tca	16/18	0.655625336125977	3	FACETS	0.413	0.335	0.501	0.207	0.167	0.251	SUBCLONAL	1	TRUE	1	0.655625336125977	3		313	304	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623662	28623662	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	57	440	0	ENST00000241453.7:c.895G>T	p.Glu299Ter	p.E299*	ENST00000241453	NM_004119.2	299	Gag/Tag	8/24	1	2	FACETS	0.692	0.596	0.795	0.692	0.596	0.795	SUBCLONAL	1	TRUE	1	0.4640732407479	2		440	355	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031737	36031737	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	201	955	0	ENST00000358208.4:c.1566C>A	p.Tyr522Ter	p.Y522*	ENST00000358208		522	taC/taA	12/12	0.186478632389975	3	FACETS	0.923	0.861	0.986	0.923	0.861	0.986	INDETERMINATE	2	TRUE	1	0.4640732407479	3		955	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577544	7577544	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587780074	NA	P-0055212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	254	774	0	ENST00000269305.4:c.737T>G	p.Met246Arg	p.M246R	ENST00000269305	NM_001126112.2	246	aTg/aGg	7/11	0.665142618995277	1	FACETS	0.932	0.881	0.983	0.932	0.881	0.983	CLONAL	1	TRUE	0	0.665142618995277	1		774	547	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821344	72821344	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs200992486	NA	P-0055212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	183	489	0	ENST00000268489.5:c.10831C>G	p.His3611Asp	p.H3611D	ENST00000268489	NM_006885.3	3611	Cac/Gac	10/10	0.665142618995277	3	FACETS	1	0.979	1	0.574	0.532	0.617	CLONAL	1	TRUE	1	0.665142618995277	3		489	639	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131274	17131274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	401	1243	0	ENST00000285071.4:c.178G>A	p.Ala60Thr	p.A60T	ENST00000285071	NM_144997.5	60	Gcg/Acg	4/14	0.665142618995277	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.665142618995277	1		1243	783	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131313	17131313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	384	1206	0	ENST00000285071.4:c.139G>A	p.Glu47Lys	p.E47K	ENST00000285071	NM_144997.5	47	Gaa/Aaa	4/14	0.665142618995277	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.665142618995277	1		1206	750	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927711	131927711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	133	309	0	ENST00000265335.6:c.1778G>A	p.Arg593Lys	p.R593K	ENST00000265335		593	aGa/aAa	11/25	0.665142618995277	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.665142618995277	1		309	267	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434422	140434422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	22	515	0	ENST00000288602.6:c.2276G>A	p.Gly759Glu	p.G759E	ENST00000288602	NM_004333.4	759	gGa/gAa	18/18	0.125968065144459	4	FACETS	1	0.791	1	0.51	0.396	0.643	CLONAL	1	TRUE	2	0.178230125975305	4		515	285	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578463	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371524413	NA	P-0055214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	855	1320	0	ENST00000269305.4:c.467G>C	p.Arg156Pro	p.R156P	ENST00000269305	NM_001126112.2	156	cGc/cCc	5/11	0.791801465835439	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.791801465835439	2		1320	1059	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0055215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	687	804	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.691987477379555	2	FACETS	0.909	0.887	0.931	0.909	0.887	0.931	CLONAL	2	TRUE	0	0.793507177231358	2		804	952	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910455	32910455	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555282375	NA	P-0055215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	210	362	0	ENST00000380152.3:c.1964del	p.Pro655GlnfsTer5	p.P655Qfs*5	ENST00000380152		655	Cca/ca	11/27	0.691987477379555	2	FACETS	0.873	0.833	0.912	0.873	0.833	0.912	CLONAL	2	TRUE	0	0.793507177231358	2		362	303	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310236	91310408	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TATGTCACTCCAGAAAAGGTTTGTATTTATATCATTATTTTAAAATATATTAAAGACCACTAGAATACATATATTTTTAAGATTTTAACAAAATTTTGTATACGTAGTGCAAAGAATTTTTGTACAACTTTCATCCAGAAACCCCAAATGGTAACATTTTACTATAATTGCTT	TATGTCACTCCAGAAAAGGTTTGTATTTATATCATTATTTTAAAATATATTAAAGACCACTAGAATACATATATTTTTAAGATTTTAACAAAATTTTGTATACGTAGTGCAAAGAATTTTTGTACAACTTTCATCCAGAAACCCCAAATGGTAACATTTTACTATAATTGCTT	-	novel	NA	P-0055215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	44	253	0	ENST00000355112.3:c.2291_2307+156del		p.X764_splice	ENST00000355112	NM_000057.2	764		10/22	1	2	FACETS	0.68	0.58	0.787	0.68	0.58	0.787	SUBCLONAL	1	TRUE	1	0.793507177231358	2		253	163	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652123	3652123	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	75	995	0	ENST00000294008.3:c.946A>C	p.Asn316His	p.N316H	ENST00000294008	NM_032444.2	316	Aac/Cac	4/15	0.748263173465728	3	FACETS	0.24	0.209	0.273	0.12	0.104	0.137	SUBCLONAL	1	TRUE	1	0.793507177231358	3		995	1101	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985862	60985862	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	155	600	0	ENST00000333681.4:c.38A>G	p.Glu13Gly	p.E13G	ENST00000333681		13	gAg/gGg	2/3	0.691987477379555	2	FACETS	0.78	0.719	0.842	0.39	0.359	0.421	SUBCLONAL	1	TRUE	0	0.793507177231358	2		600	501	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022685	31022685	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	234	861	0	ENST00000375687.4:c.2170C>G	p.Leu724Val	p.L724V	ENST00000375687	NM_015338.5	724	Ctg/Gtg	13/13	0.56164830616902	4	FACETS	0.962	0.897	1	0.481	0.448	0.515	CLONAL	1	TRUE	2	0.793507177231358	4		861	1099	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417763	138417763	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	134	423	0	ENST00000289153.2:c.1756G>C	p.Glu586Gln	p.E586Q	ENST00000289153	NM_006219.2	586	Gag/Cag	11/22	0.693958943693417	3	FACETS	0.943	0.862	1	0.314	0.287	0.343	CLONAL	1	TRUE	0	0.793507177231358	3		423	500	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742820	145742820	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	181	517	0	ENST00000428558.2:c.191C>A	p.Ser64Ter	p.S64*	ENST00000428558	NM_004260.3	64	tCg/tAg	3/22	0.625112851271976	4	FACETS	1	0.966	1			1	CLONAL	1	TRUE	NA	0.793507177231358	4		517	759	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939883	76939883	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	151	583	0	ENST00000373344.5:c.865C>T	p.Gln289Ter	p.Q289*	ENST00000373344	NM_000489.3	289	Cag/Tag	9/35	0.748263173465728	3	FACETS	0.869	0.797	0.943	0.434	0.398	0.472	CLONAL	1	TRUE	1	0.793507177231358	3		583	612	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0055216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	205	915	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.457408733677518	1	FACETS	0.878	0.817	0.942	0.878	0.817	0.942	CLONAL	1	TRUE	0	0.457408733677518	1		915	787	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556460	29556485	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	AAGTTTTTTGACTCCCAAGGACAGGT	AAGTTTTTTGACTCCCAAGGACAGGT	-	novel	NA	P-0055216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	112	441	0	ENST00000356175.3:c.2829_2850+4del		p.X943_splice	ENST00000356175	NM_000267.3	943		21/57	0.457408733677518	1	FACETS	0.912	0.827	1	0.912	0.827	1	CLONAL	1	TRUE	0	0.457408733677518	1		441	414	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170016886	170016886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	154	567	0	ENST00000295797.4:c.1691C>T	p.Thr564Ile	p.T564I	ENST00000295797	NM_002740.5	564	aCt/aTt	17/18	0.457408733677518	3	FACETS	0.892	0.816	0.971	0.446	0.408	0.486	CLONAL	1	TRUE	1	0.457408733677518	3		567	928	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	223601	223601	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	91	315	0	ENST00000264932.6:c.68C>A	p.Pro23Gln	p.P23Q	ENST00000264932	NM_004168.2	23	cCa/cAa	2/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.457408733677518	2		315	346	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0055217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	26	282	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	0.593	0.471	0.732	0.593	0.471	0.732	SUBCLONAL	1	TRUE	1	0.32984851631213	2		282	266	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0055217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	83	796	0	ENST00000324856.7:c.3972C>G	p.Tyr1324Ter	p.Y1324*	ENST00000324856	NM_006015.4	1324	taC/taG	16/20	1	2	FACETS	0.808	0.713	0.909	0.808	0.713	0.909	CLONAL	1	TRUE	1	0.32984851631213	2		796	623	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145603	24145603	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	76	901	0	ENST00000263121.7:c.622del	p.Met208Ter	p.M208*	ENST00000263121	NM_003073.3	208	Atg/tg	5/9	1	2	FACETS	0.592	0.518	0.671	0.592	0.518	0.671	SUBCLONAL	1	TRUE	1	0.32984851631213	2		901	779	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24158980	24158980	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	156	898	0	ENST00000263121.7:c.655del	p.Ser219GlnfsTer10	p.S219Qfs*10	ENST00000263121	NM_003073.3	218	Ttt/tt	6/9	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.32984851631213	2		898	728	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0055221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	32	347	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.460661761642445	1	FACETS	0.33	0.272	0.392	0.33	0.272	0.392	INDETERMINATE	1	TRUE	0	0.843989330631212	1		347	133	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782082	NA	P-0055221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	135	357	21	ENST00000269305.4:c.745A>T	p.Arg249Trp	p.R249W	ENST00000269305	NM_001126112.2	249	Agg/Tgg	7/11	0.843989330631212	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.843989330631212	1		378	162	SUCCESS
APC	324	MSKCC	GRCh37	5	112175720	112175720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	78	208	8	ENST00000257430.4:c.4429C>T	p.Gln1477Ter	p.Q1477*	ENST00000257430	NM_000038.5	1477	Cag/Tag	16/16	0.244614238364117	2	FACETS	1	0.97	1	0.596	0.54	0.653	INDETERMINATE	1	TRUE	0	0.843989330631212	2		216	155	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584725	48584725	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	120	235	9	ENST00000342988.3:c.803G>A	p.Trp268Ter	p.W268*	ENST00000342988	NM_005359.5	268	tGg/tAg	7/12	0.843989330631212	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.843989330631212	1		244	146	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653852	89653854	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0055221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	40	242	5	ENST00000371953.3:c.155_157del	p.Asp52del	p.D52del	ENST00000371953	NM_000314.4	50	atTGAt/att	2/9	0.843989330631212	1	FACETS	0.945	0.843	1	0.945	0.843	1	CLONAL	1	TRUE	0	0.843989330631212	1		247	58	SUCCESS
APC	324	MSKCC	GRCh37	5	112173516	112173516	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	32	205	4	ENST00000257430.4:c.2226del	p.Met743CysfsTer18	p.M743Cfs*18	ENST00000257430	NM_000038.5	742	aTt/at	16/16	0.244614238364117	2	FACETS	0.579	0.478	0.688	0.289	0.239	0.344	INDETERMINATE	1	TRUE	0	0.843989330631212	2		209	131	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851575	63851575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376632312	NA	P-0055221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	148	344	16	ENST00000279873.7:c.2353C>T	p.Arg785Cys	p.R785C	ENST00000279873	NM_032199.2	785	Cgc/Tgc	10/10	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.843989330631212	2		360	324	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951052	48951052	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0055221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4	30	117	4	ENST00000267163.4:c.1216-2A>C		p.X406_splice	ENST00000267163	NM_000321.2	406			0.830523105514024	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.843989330631212	1		121	34	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591139	67591145	+	protein_altering_variant	In_Frame_Ins	INS	GACCAAT	GACCAAT	TGTAAGAAAG	novel	NA	P-0055221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	59	200	11	ENST00000274335.5:c.1732_1738delinsTGTAAGAAAG	p.Asp578_Tyr580delinsCysLysLysAsp	p.D578_Y580delinsCKKD	ENST00000274335		578	GACCAATac/TGTAAGAAAGac	12/15	0.244614238364117	2	FACETS	1	0.95	1	0.564	0.501	0.627	INDETERMINATE	1	TRUE	0	0.843989330631212	2		211	124	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732957	30732957	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504421	NA	P-0055222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	25	203	0	ENST00000295754.5:c.1570G>A	p.Asp524Asn	p.D524N	ENST00000295754	NM_003242.5	524	Gac/Aac	7/7	1	2	FACETS	0.899	0.707	1	0.899	0.707	1	CLONAL	1	TRUE	1	0.13	2		203	428	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842752	68842752	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0055222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	26	198	0	ENST00000261769.5:c.687+1G>T		p.X229_splice	ENST00000261769	NM_004360.3	229			1	2	FACETS	0.964	0.763	1	0.964	0.763	1	CLONAL	1	TRUE	1	0.13	2		198	415	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119783	70119823	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGCAGACAGCCCCCTATCGACTTCCGCGACGTGGACATC	GGGGCAGACAGCCCCCTATCGACTTCCGCGACGTGGACATC	-	novel	NA	P-0055222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	41	294	0	ENST00000245479.2:c.787_827del	p.Gly263ArgfsTer19	p.G263Rfs*19	ENST00000245479	NM_000346.3	262	gGGGGCAGACAGCCCCCTATCGACTTCCGCGACGTGGACATC/g	3/3	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.13	2		294	615	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0055223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	38	327	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA	2	FACETS	1	0.919	1			1	INDETERMINATE	1	TRUE	NA	0.284798812937811	2		327	226	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923318	9923318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867335598	NA	P-0055223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	51	288	0	ENST00000330684.3:c.1969G>A	p.Glu657Lys	p.E657K	ENST00000330684	NM_001134407.1	657	Gaa/Aaa	9/13	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.284798812937811	2		288	258	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857538	9857538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778951185	NA	P-0055223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	12	217	0	ENST00000330684.3:c.3863G>A	p.Arg1288His	p.R1288H	ENST00000330684	NM_001134407.1	1288	cGt/cAt	13/13	1	2	FACETS	0.351	0.246	0.48	0.351	0.246	0.48	SUBCLONAL	1	TRUE	1	0.284798812937811	2		217	240	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341583	89341583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1336341769	NA	P-0055223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	23	250	0	ENST00000301030.4:c.7487C>T	p.Ser2496Phe	p.S2496F	ENST00000301030	NM_001256183.1	2496	tCc/tTc	10/13	1	2	FACETS	0.923	0.725	1	0.923	0.725	1	CLONAL	1	TRUE	1	0.284798812937811	2		250	175	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610558	52610567	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GAGAATACAT	GAGAATACAT	-	novel	NA	P-0055223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	33	170	0	ENST00000394830.3:c.3606_3615del	p.Cys1203GlufsTer38	p.C1203Efs*38	ENST00000394830	NM_018313.4	1202	acATGTATTCTC/ac	23/30	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.284798812937811	2		170	176	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357663	70357663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	37	379	1	ENST00000374080.3:c.5914C>T	p.Pro1972Ser	p.P1972S	ENST00000374080		1972	Cct/Tct	41/45	0.107187379372598	0	FACETS	0.648	0.536	0.771			1	INDETERMINATE	1	TRUE	0	0.284798812937811	0		380	287	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577119	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0055224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	105	470	0	ENST00000269305.4:c.819dup	p.Val274CysfsTer32	p.V274Cfs*32	ENST00000269305	NM_001126112.2	273	-/T	8/11	0.556472749462375	1	FACETS	0.973	0.885	1	0.973	0.885	1	CLONAL	1	TRUE	0	0.556472749462375	1		470	280	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779727	3779727	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	100	487	0	ENST00000262367.5:c.5321G>A	p.Arg1774His	p.R1774H	ENST00000262367	NM_004380.2	1774	cGc/cAc	31/31	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.556472749462375	2		487	341	SUCCESS
CBL	867	MSKCC	GRCh37	11	119167665	119167665	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	104	341	0	ENST00000264033.4:c.2074T>C	p.Cys692Arg	p.C692R	ENST00000264033	NM_005188.3	692	Tgt/Cgt	13/16	1	2	FACETS	0.966	0.872	1	0.966	0.872	1	CLONAL	1	TRUE	1	0.556472749462375	2		341	387	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349606	89349606	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	117	492	0	ENST00000301030.4:c.3344T>A	p.Ile1115Asn	p.I1115N	ENST00000301030	NM_001256183.1	1115	aTc/aAc	9/13	1	2	FACETS	0.994	0.903	1	0.994	0.903	1	CLONAL	1	TRUE	1	0.556472749462375	2		492	423	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971000	21971000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	397	518	0	ENST00000304494.5:c.358G>T	p.Glu120Ter	p.E120*	ENST00000304494	NM_000077.4	120	Gag/Tag	2/3	0.748302963676286	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.748302963676286	2		518	498	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0055225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	454	576	0	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	0.748302963676286	2	FACETS	0.975	0.946	1	0.975	0.946	1	CLONAL	2	TRUE	0	0.748302963676286	2		576	622	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43767844	43767844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	459	547	0	ENST00000382044.4:c.1004C>T	p.Ser335Phe	p.S335F	ENST00000382044	NM_001141980.1	335	tCt/tTt	9/28	0.748302963676286	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.748302963676286	3		547	765	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440268	187440268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760088914	NA	P-0055225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	237	388	2	ENST00000232014.4:c.2099C>T	p.Pro700Leu	p.P700L	ENST00000232014	NM_001130845.1	700	cCg/cTg	10/10	0.549172902612209	4	FACETS	0.797	0.747	0.847	0.531	0.498	0.565	SUBCLONAL	2	TRUE	1	0.748302963676286	4		390	695	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43749756	43749757	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGT	novel	NA	P-0055225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	197	460	0	ENST00000523873.1:c.611_613dup	p.Cys204dup	p.C204dup	ENST00000523873		204	-/TGT	7/8	1	2	FACETS	0.876	0.816	0.938	0.876	0.816	0.938	CLONAL	1	TRUE	1	0.748302963676286	2		460	601	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0055226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	109	166	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.601622529374482	2		166	256	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574030	7574030	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	464	339	0	ENST00000269305.4:c.997del	p.Arg333ValfsTer12	p.R333Vfs*12	ENST00000269305	NM_001126112.2	333	Cgt/gt	10/11	0.601622529374482	2	FACETS	0.923	0.901	0.944	1	0.997	1	CLONAL	3	TRUE	0	0.601622529374482	2		339	557	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889133	76889133	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	98	210	0	ENST00000373344.5:c.4877G>T	p.Cys1626Phe	p.C1626F	ENST00000373344	NM_000489.3	1626	tGt/tTt	18/35	0.210798796187659	1	FACETS	0.73	0.659	0.804	0.73	0.659	0.804	INDETERMINATE	1	TRUE	0	0.601622529374482	1		210	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578214	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs864309495	NA	P-0055227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	243	524	0	ENST00000269305.4:c.635_636del	p.Phe212SerfsTer3	p.F212Sfs*3	ENST00000269305	NM_001126112.2	212	tTT/t	6/11	0.652008756692837	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.654655664109902	2		524	349	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460531	149460531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	44	535	0	ENST00000286301.3:c.106G>A	p.Ala36Thr	p.A36T	ENST00000286301	NM_005211.3	36	Gca/Aca	3/22	0.64335452704596	3	FACETS	0.423	0.355	0.498	0.141	0.118	0.166	SUBCLONAL	1	TRUE	0	0.654655664109902	3		535	422	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2089956	2089956	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	59	543	0	ENST00000219066.1:c.908A>G	p.Gln303Arg	p.Q303R	ENST00000219066	NM_002528.5	303	cAa/cGa	6/6	0.300299153536627	3	FACETS	0.595	0.514	0.683	0.298	0.257	0.342	INDETERMINATE	1	TRUE	1	0.654655664109902	3		543	402	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309900	30309900	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	459	485	0	ENST00000307677.4:c.122C>G	p.Thr41Ser	p.T41S	ENST00000307677	NM_138578.1	41	aCt/aGt	2/3	0.654655664109902	5	FACETS	0.962	0.93	0.994	0.77	0.744	0.796	CLONAL	4	TRUE	0	0.654655664109902	5		485	722	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713484	40713484	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	92	455	0	ENST00000373198.4:c.4031C>T	p.Pro1344Leu	p.P1344L	ENST00000373198	NM_133170.3	1344	cCa/cTa	30/32	0.531143630357579	1	FACETS	0.654	0.589	0.722	0.654	0.589	0.722	SUBCLONAL	1	TRUE	0	0.654655664109902	1		455	289	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090260	37090467	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGCAGTCCCATTTACAGTTTTAACGCCTAAAGTATCACATTTCGTTTTTTAGCTTTAAGTAGTCTGTGATCTCCGTTTAGAATGAGAATGTTTAAATTCGTACCTATTTTGAGGTATTGAATTTCTTTGGACCAGGTGAATTGGGACGAAGAAAAGGAATGTTTTGAAAGCCTCAGTAAAGAATGCGCTATGTTCTATTCCATCCGGA	AGCAGTCCCATTTACAGTTTTAACGCCTAAAGTATCACATTTCGTTTTTTAGCTTTAAGTAGTCTGTGATCTCCGTTTAGAATGAGAATGTTTAAATTCGTACCTATTTTGAGGTATTGAATTTCTTTGGACCAGGTGAATTGGGACGAAGAAAAGGAATGTTTTGAAAGCCTCAGTAAAGAATGCGCTATGTTCTATTCCATCCGGA	-	novel	NA	P-0055227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	46	136	0	ENST00000231790.2:c.1990-129_2068del		p.X664_splice	ENST00000231790	NM_000249.3	664		18/19	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.654655664109902	2		136	113	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541417	187541417	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs780389120	NA	P-0055227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	31	232	0	ENST00000441802.2:c.6323G>C	p.Arg2108Thr	p.R2108T	ENST00000441802	NM_005245.3	2108	aGa/aCa	10/27	0.304140453615701	1	FACETS	0.358	0.292	0.431	0.358	0.292	0.431	INDETERMINATE	1	TRUE	0	0.654655664109902	1		232	178	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0055228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	241	394	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.552692628464028	2	FACETS	0.926	0.876	0.975	0.926	0.876	0.975	CLONAL	2	TRUE	0	0.552692628464028	2		394	471	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432383	49432383	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	141	548	0	ENST00000301067.7:c.8756A>C	p.Glu2919Ala	p.E2919A	ENST00000301067	NM_003482.3	2919	gAa/gCa	34/54	0.552692628464028	4	FACETS	0.945	0.861	1	0.473	0.43	0.517	CLONAL	1	TRUE	2	0.552692628464028	4		548	838	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33430309	33430309	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	160	468	0	ENST00000345365.6:c.702del	p.Lys235ArgfsTer13	p.K235Rfs*13	ENST00000345365	NM_002878.3	234	ctG/ct	8/10	0.552692628464028	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.552692628464028	1		468	355	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733131	74733131	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	71	455	0	ENST00000359995.5:c.112G>C	p.Gly38Arg	p.G38R	ENST00000359995	NM_001195427.1	38	Ggg/Cgg	1/3	0.552692628464028	2	FACETS	0.526	0.46	0.597	0.263	0.23	0.299	SUBCLONAL	1	TRUE	0	0.552692628464028	2		455	488	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0055229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	95	341	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.443072806826005	4	FACETS	1	0.946	1			1	CLONAL	3	TRUE	NA	0.454796757294499	4		341	193	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348110	89348110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1170699512	NA	P-0055229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	70	601	0	ENST00000301030.4:c.4840C>T	p.Arg1614Trp	p.R1614W	ENST00000301030	NM_001256183.1	1614	Cgg/Tgg	9/13	0.454796757294499	1	FACETS	0.874	0.788	0.96	1	0.983	1	CLONAL	2	TRUE	0	0.454796757294499	1		601	136	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972448	81972448	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	14	383	0	ENST00000359376.3:c.3241G>T	p.Ala1081Ser	p.A1081S	ENST00000359376	NM_002661.3	1081	Gcc/Tcc	29/33	1	2	FACETS	0.36	0.261	0.479	0.36	0.261	0.479	SUBCLONAL	1	TRUE	1	0.454796757294499	2		383	171	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463549	25463578	+	protein_altering_variant	In_Frame_Del	DEL	ATTGCAGGGACTGCCCCCAATCACCAGATC	ATTGCAGGGACTGCCCCCAATCACCAGATC	CTT	novel	NA	P-0055229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	32	486	1	ENST00000264709.3:c.2104_2133delinsAAG	p.Asp702_Asn711delinsLys	p.D702_N711delinsK	ENST00000264709	NM_175629.2	702	GATCTGGTGATTGGGGGCAGTCCCTGCAAT/AAG	18/23	0.288417993213349	1	FACETS	0.659	0.541	0.788	0.659	0.541	0.788	SUBCLONAL	1	TRUE	0	0.454796757294499	1		487	165	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464516	25464516	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	23	601	0	ENST00000264709.3:c.1997G>T	p.Cys666Phe	p.C666F	ENST00000264709	NM_175629.2	666	tGt/tTt	17/23	0.288417993213349	1	FACETS	0.546	0.431	0.677	0.546	0.431	0.677	SUBCLONAL	1	TRUE	0	0.454796757294499	1		601	143	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371694	225371697	+	frameshift_variant	Frame_Shift_Del	DEL	TAAA	TAAA	-	rs780143678	NA	P-0055229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	38	439	0	ENST00000264414.4:c.907_910del	p.Phe303ValfsTer7	p.F303Vfs*7	ENST00000264414	NM_003590.4	303	TTTAgt/gt	7/16	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.454796757294499	2		439	152	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	61	115	0				ENST00000310581	NM_198253.2	-/1132			0.5595088750696	3	FACETS	1	0.954	1	0.589	0.519	0.662	CLONAL	1	TRUE	1	0.861228596815229	3		115	172	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782289	NA	P-0055230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	375	460	0	ENST00000269305.4:c.706T>C	p.Tyr236His	p.Y236H	ENST00000269305	NM_001126112.2	236	Tac/Cac	7/11	0.861228596815229	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.861228596815229	2		460	407	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426074	49426075	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0055230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	193	542	0	ENST00000301067.7:c.12413_12414del	p.Ser4138CysfsTer29	p.S4138Cfs*29	ENST00000301067	NM_003482.3	4138	tCT/t	39/54	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.861228596815229	2		542	427	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626410	12626410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	34	312	0	ENST00000251849.4:c.1739C>T	p.Ala580Val	p.A580V	ENST00000251849	NM_002880.3	580	gCa/gTa	16/17	0.338767801273947	3	FACETS	0.247	0.201	0.298	0.123	0.1	0.149	INDETERMINATE	1	TRUE	1	0.861228596815229	3		312	458	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509756	187509962	+	inframe_deletion	In_Frame_Del	DEL	GTGTGCTGCTGGGAATCCAGGGGCGGGATCGTCACCTCTTCGAAGTGGCCGTCGTCCCCGCTCTCATAGTCACTCATCATGACCTCGGACTCCACTTCGCAGCAGGCTGACACGTCAGAGCAGGAGGCGGTGGAGGCGTACACAGACATGGGCATGCTCTCGACAGCGGGCGCCTCGAAGTGTCTTTGATACCCTGGCGGGTAAGGG	GTGTGCTGCTGGGAATCCAGGGGCGGGATCGTCACCTCTTCGAAGTGGCCGTCGTCCCCGCTCTCATAGTCACTCATCATGACCTCGGACTCCACTTCGCAGCAGGCTGACACGTCAGAGCAGGAGGCGGTGGAGGCGTACACAGACATGGGCATGCTCTCGACAGCGGGCGCCTCGAAGTGTCTTTGATACCCTGGCGGGTAAGGG	-	novel	NA	P-0055230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	67	213	0	ENST00000441802.2:c.13551_13757del	p.Pro4518_Thr4586del	p.P4518_T4586del	ENST00000441802	NM_005245.3	4517	gcCCCTTACCCGCCAGGGTATCAAAGACACTTCGAGGCGCCCGCTGTCGAGAGCATGCCCATGTCTGTGTACGCCTCCACCGCCTCCTGCTCTGACGTGTCAGCCTGCTGCGAAGTGGAGTCCGAGGTCATGATGAGTGACTATGAGAGCGGGGACGACGGCCACTTCGAAGAGGTGACGATCCCGCCCCTGGATTCCCAGCAGCACACg/gcg	27/27	0.861228596815229	1	FACETS	0.974	0.898	1	0.974	0.898	1	CLONAL	1	TRUE	0	0.861228596815229	1		213	91	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294087	1294087	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	317	731	0	ENST00000310581.5:c.914C>A	p.Ala305Glu	p.A305E	ENST00000310581	NM_198253.2	305	gCg/gAg	2/16	0.5595088750696	3	FACETS	0.87	0.83	0.911	0.87	0.83	0.911	CLONAL	2	TRUE	1	0.861228596815229	3		731	605	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385171	41385171	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	26	588	0	ENST00000373198.4:c.790A>C	p.Lys264Gln	p.K264Q	ENST00000373198	NM_133170.3	264	Aag/Cag	6/32	1	2	FACETS	0.257	0.204	0.319	0.257	0.204	0.319	SUBCLONAL	1	TRUE	1	0.629588633434787	2		588	321	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152096	55152107	+	inframe_deletion	In_Frame_Del	DEL	TCATGCATGATT	TCATGCATGATT	-	rs121913268	NA	P-0055232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	113	486	0	ENST00000257290.5:c.2528_2539del	p.Ile843_Ser847delinsThr	p.I843_S847delinsT	ENST00000257290	NM_006206.4	843	aTCATGCATGATTcg/acg	18/23	1	2	FACETS	0.925	0.84	1	0.925	0.84	1	CLONAL	1	TRUE	1	0.629588633434787	2		486	388	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	21	618	0	ENST00000267101.3:c.310G>C	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ctg	3/28	1	2	FACETS	0.56	0.43	0.712	0.56	0.43	0.712	SUBCLONAL	1	TRUE	1	0.17	2		618	441	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070399	37070399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	23	302	1	ENST00000231790.2:c.1534G>A	p.Glu512Lys	p.E512K	ENST00000231790	NM_000249.3	512	Gaa/Aaa	13/19	1	2	FACETS	0.92	0.718	1	0.92	0.718	1	CLONAL	1	TRUE	1	0.17	2		303	294	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411743	139411743	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs771150144	NA	P-0055239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	19	549	0	ENST00000277541.6:c.1536C>G	p.Phe512Leu	p.F512L	ENST00000277541	NM_017617.3	512	ttC/ttG	9/34	1	2	FACETS	0.601	0.455	0.773	0.601	0.455	0.773	SUBCLONAL	1	TRUE	1	0.17	2		549	372	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929481	44929481	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	15	232	0	ENST00000377967.4:c.2581G>A	p.Glu861Lys	p.E861K	ENST00000377967	NM_021140.2	861	Gaa/Aaa	17/29	1	1	FACETS	0.892	0.655	1	0.892	0.655	1	CLONAL	1	TRUE	0	0.17	1		232	181	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877366	28877366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1392528455	NA	P-0055256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	101	532	0	ENST00000282397.4:c.3955G>A	p.Ala1319Thr	p.A1319T	ENST00000282397	NM_002019.4	1319	Gcg/Acg	30/30	1	2	FACETS	0.373	0.334	0.416	0.373	0.334	0.416	SUBCLONAL	1	TRUE	1	0.796516391349041	2		532	679	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266711	198266711	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	70	621	0	ENST00000335508.6:c.2221A>G	p.Lys741Glu	p.K741E	ENST00000335508	NM_012433.2	741	Aag/Gag	15/25	1	2	FACETS	0.313	0.273	0.357	0.313	0.273	0.357	SUBCLONAL	1	TRUE	1	0.796516391349041	2		621	561	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957441	175957441	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	112	456	0	ENST00000367669.3:c.1955G>T	p.Gly652Val	p.G652V	ENST00000367669	NM_022457.5	652	gGa/gTa	17/20	0.662766493977452	3	FACETS	0.692	0.625	0.764	0.346	0.312	0.382	SUBCLONAL	1	TRUE	1	0.796516391349041	3		456	568	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618961	37618961	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	169	718	0	ENST00000447079.4:c.637G>T	p.Val213Leu	p.V213L	ENST00000447079	NM_015083.1	213	Gtg/Ttg	1/14	1	2	FACETS	0.718	0.663	0.774	0.718	0.663	0.774	SUBCLONAL	1	TRUE	1	0.796516391349041	2		718	591	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37038154	37038154	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	29	283	0	ENST00000231790.2:c.161G>T	p.Gly54Val	p.G54V	ENST00000231790	NM_000249.3	54	gGa/gTa	2/19	1	2	FACETS	0.234	0.188	0.286	0.234	0.188	0.286	SUBCLONAL	1	TRUE	1	0.796516391349041	2		283	311	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0055258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	112	766	0	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	1	2	FACETS	0.956	0.866	1	0.956	0.866	1	CLONAL	1	TRUE	1	0.532342848173308	2		766	440	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789590	3789591	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0055258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	79	571	0	ENST00000262367.5:c.4268dup	p.Pro1424SerfsTer13	p.P1424Sfs*13	ENST00000262367	NM_004380.2	1423	cct/ccCt	25/31	1	2	FACETS	0.87	0.772	0.975	0.87	0.772	0.975	CLONAL	1	TRUE	1	0.532342848173308	2		571	341	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874011	123874019	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs780061449	NA	P-0055258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	20	68	0	ENST00000330479.4:c.56_64del	p.Ala19_Ala21del	p.A19_A21del	ENST00000330479	NM_020382.3	14	gaGGCGGCGGCg/gag	2/9	0.533107815098025	3	FACETS	1	0.867	1	0.58	0.454	0.72	CLONAL	1	TRUE	1	0.532342848173308	3		68	82	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0055259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	47	635	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.323067734641364	3	FACETS	1	0.934	1			1	CLONAL	2	FALSE	NA	0.323067734641364	3		635	147	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041720	47041720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	17	669	0	ENST00000377604.3:c.1945C>T	p.Gln649Ter	p.Q649*	ENST00000377604	NM_001204468.1	649	Caa/Taa	17/24	0.32276634716234	2	FACETS	1	0.893	1	0.683	0.522	0.866	CLONAL	1	FALSE	0	0.323067734641364	2		669	77	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0055259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	47	640	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.32276634716234	2	FACETS	0.887	0.762	1	0.887	0.762	1	CLONAL	2	FALSE	0	0.323067734641364	2		640	164	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40861906	40861906	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	28	714	0	ENST00000428826.2:c.1451A>G	p.Asp484Gly	p.D484G	ENST00000428826		484	gAt/gGt	13/21	0.220259216530377	4	FACETS	0.808	0.654	0.977	0.808	0.654	0.977	CLONAL	2	FALSE	2	0.323067734641364	4		714	142	SUCCESS
APC	324	MSKCC	GRCh37	5	112116524	112116524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	62	439	0	ENST00000257430.4:c.570del	p.Glu190AspfsTer15	p.E190Dfs*15	ENST00000257430	NM_000038.5	190	gAa/ga	6/16	0.323067734641364	4	FACETS	1	0.944	1	1	0.944	1	CLONAL	3	FALSE	1	0.323067734641364	4		439	152	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974701	21974704	+	frameshift_variant	Frame_Shift_Del	DEL	ATTC	ATTC	-	novel	NA	P-0055259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	31	517	0	ENST00000304494.5:c.123_126del	p.Asn42ValfsTer10	p.N42Vfs*10	ENST00000304494	NM_000077.4	41	ccGAAT/cc	1/3	1	2	FACETS	1	0.91	1	1	0.967	1	CLONAL	2	FALSE	1	0.323067734641364	2		517	84	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0055262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	1904	635	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.612139729976853	20	FACETS	1	0.996	1			1	CLONAL	18	TRUE	NA	0.612139729976853	20		635	2213	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0055262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	450	802	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.595762645822795	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	4	TRUE	0	0.612139729976853	4		802	586	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265177	46265177	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	72	387	0	ENST00000371998.3:c.2047C>T	p.Arg683Trp	p.R683W	ENST00000371998		683	Cgg/Tgg	12/23	0.612139729976853	5	FACETS	0.874	0.766	0.992	0.219	0.191	0.248	CLONAL	1	TRUE	1	0.612139729976853	5		387	516	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0055262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	222	443	2	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.612139729976853	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.612139729976853	2		445	360	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388054	31388054	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	44	408	0	ENST00000328111.2:c.1855G>C	p.Glu619Gln	p.E619Q	ENST00000328111	NM_006892.3	619	Gag/Cag	17/23	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.24	2		408	330	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568560	41568560	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	103	564	0	ENST00000263253.7:c.4510T>G	p.Phe1504Val	p.F1504V	ENST00000263253	NM_001429.3	1504	Ttc/Gtc	28/31	0.124324484707212	1	FACETS	0.834	0.75	0.921	1	0.985	1	INDETERMINATE	2	TRUE	0	0.24	1		564	453	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439905	52439918	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTGGCTGTGTTA	CTCTGGCTGTGTTA	-	novel	NA	P-0055264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	54	559	0	ENST00000460680.1:c.794_807del	p.Val265AlafsTer14	p.V265Afs*14	ENST00000460680	NM_004656.3	265	gTAACACAGCCAGAG/g	10/17	0.239129011437764	1	FACETS	0.959	0.821	1	0.959	0.821	1	CLONAL	1	TRUE	0	0.24	1		559	413	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0055267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	150	341	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.218365334114983	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	TRUE	0	0.218365334114983	3		341	463	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263989	16263989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	147	841	0	ENST00000375759.3:c.10358C>T	p.Pro3453Leu	p.P3453L	ENST00000375759	NM_015001.2	3453	cCa/cTa	12/15	0.186016732995165	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.218365334114983	1		841	937	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992188	11992188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	298	490	0	ENST00000396373.4:c.278C>T	p.Ala93Val	p.A93V	ENST00000396373	NM_001987.4	93	gCt/gTt	3/8	0.218365334114983	3	FACETS	0.879	0.83	0.928	1	0.989	1	CLONAL	4	TRUE	0	0.218365334114983	3		490	861	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052632	42052632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779811318	NA	P-0055267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	67	535	1	ENST00000219905.7:c.7303C>T	p.Arg2435Trp	p.R2435W	ENST00000219905	NM_001164273.1	2435	Cgg/Tgg	20/24	1	2	FACETS	0.983	0.855	1	0.983	0.855	1	CLONAL	1	TRUE	1	0.218365334114983	2		536	624	SUCCESS
BLM	641	MSKCC	GRCh37	15	91337522	91337522	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1188753950	NA	P-0055267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	48	392	0	ENST00000355112.3:c.3145G>T	p.Gly1049Ter	p.G1049*	ENST00000355112	NM_000057.2	1049	Gga/Tga	16/22	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.218365334114983	2		392	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579415	7579415	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	260	817	0	ENST00000269305.4:c.272G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tGg/tAg	4/11	0.202869574785061	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.218365334114983	2		817	1007	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs80338963	NA	P-0055267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	58	449	0	ENST00000342988.3:c.1081C>G	p.Arg361Gly	p.R361G	ENST00000342988	NM_005359.5	361	Cgc/Ggc	9/12	0.186016732995165	1	FACETS	0.96	0.826	1	0.96	0.826	1	CLONAL	1	TRUE	0	0.218365334114983	1		449	493	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812317	212812317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143662416	NA	P-0055267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	47	318	0	ENST00000342788.4:c.259G>A	p.Val87Met	p.V87M	ENST00000342788	NM_005235.2	87	Gtg/Atg	3/28	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.218365334114983	2		318	361	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021137	31021137	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	83	575	0	ENST00000375687.4:c.1136A>T	p.Glu379Val	p.E379V	ENST00000375687	NM_015338.5	379	gAg/gTg	12/13	1	2	FACETS	0.956	0.843	1	0.956	0.843	1	CLONAL	1	TRUE	1	0.218365334114983	2		575	795	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056275	26056275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377738358	NA	P-0055267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	102	597	0	ENST00000343677.2:c.382C>T	p.Pro128Ser	p.P128S	ENST00000343677	NM_005319.3	128	Cct/Tct	1/1	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.218365334114983	2		597	780	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056298	26056298	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1454195264	NA	P-0055267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	72	561	0	ENST00000343677.2:c.359T>C	p.Val120Ala	p.V120A	ENST00000343677	NM_005319.3	120	gTt/gCt	1/1	1	2	FACETS	0.945	0.825	1	0.945	0.825	1	CLONAL	1	TRUE	1	0.218365334114983	2		561	698	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	61	115	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.588	0.508	0.674	0.588	0.508	0.674	SUBCLONAL	1	TRUE	1	0.428808401355578	2		115	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912655	NA	P-0055268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	139	619	0	ENST00000269305.4:c.725G>C	p.Cys242Ser	p.C242S	ENST00000269305	NM_001126112.2	242	tGc/tCc	7/11	1	2	FACETS	0.798	0.727	0.873	0.798	0.727	0.873	SUBCLONAL	1	TRUE	1	0.428808401355578	2		619	812	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578281	7578281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	151	742	0	ENST00000269305.4:c.568C>T	p.Pro190Ser	p.P190S	ENST00000269305	NM_001126112.2	190	Cct/Tct	6/11	1	2	FACETS	0.837	0.766	0.912	0.837	0.766	0.912	CLONAL	1	TRUE	1	0.428808401355578	2		742	841	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720809	89720809	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	99	298	0	ENST00000371953.3:c.961del	p.Thr321GlnfsTer23	p.T321Qfs*23	ENST00000371953	NM_000314.4	320	ttA/tt	8/9	0.428808401355578	1	FACETS	0.795	0.725	0.867	1	0.986	1	SUBCLONAL	2	TRUE	0	0.428808401355578	1		298	228	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619309	23619309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555458224	NA	P-0055268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	84	450	1	ENST00000261584.4:c.3226C>T	p.His1076Tyr	p.H1076Y	ENST00000261584	NM_024675.3	1076	Cat/Tat	12/13	1	2	FACETS	0.562	0.496	0.633	0.562	0.496	0.633	SUBCLONAL	1	TRUE	1	0.428808401355578	2		451	697	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0055269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	338	327	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.66070456308549	5	FACETS	0.943	0.899	0.988	0.943	0.899	0.988	CLONAL	3	TRUE	2	0.660494402772476	5		327	720	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540040	187540040	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs116784674	NA	P-0055269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	65	794	2	ENST00000441802.2:c.7700G>A	p.Arg2567His	p.R2567H	ENST00000441802	NM_005245.3	2567	cGt/cAt	10/27	0.628826201529574	1	FACETS	0.415	0.362	0.471	0.415	0.362	0.471	SUBCLONAL	1	TRUE	0	0.660494402772476	1		796	318	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806131	1806131	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs17881656	NA	P-0055269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	391	1398	0	ENST00000260795.2:c.1150T>C	p.Phe384Leu	p.F384L	ENST00000260795		384	Ttc/Ctc	8/17	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.660494402772476	2		1398	820	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026959	6026959	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs63750685	NA	P-0055269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	12	315	0	ENST00000265849.7:c.1437C>G	p.His479Gln	p.H479Q	ENST00000265849	NM_000535.5	479	caC/caG	11/15	0.660494402772476	6	FACETS	0.485	0.341	0.66	0.121	0.085	0.165	SUBCLONAL	1	TRUE	2	0.660494402772476	6		315	174	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584500	189584500	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	205	423	0	ENST00000264731.3:c.796C>T	p.Arg266Ter	p.R266*	ENST00000264731	NM_003722.4	266	Cga/Tga	6/14	0.641316875808451	4	FACETS	0.917	0.857	0.978	0.917	0.857	0.978	CLONAL	2	TRUE	2	0.660494402772476	4		423	562	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965761	25965761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377352572	NA	P-0055269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	220	775	1	ENST00000435504.4:c.3445C>T	p.Arg1149Cys	p.R1149C	ENST00000435504		1149	Cgt/Tgt	13/13	0.658399798588243	3	FACETS	0.978	0.911	1	0.489	0.455	0.524	CLONAL	1	TRUE	1	0.660494402772476	3		776	906	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441265	52441265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	416	663	0	ENST00000460680.1:c.505C>T	p.His169Tyr	p.H169Y	ENST00000460680	NM_004656.3	169	Cac/Tac	7/17	0.645656207851885	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.660494402772476	2		663	628	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950733	79950733	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs2405876	NA	P-0055269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	20	466	0	ENST00000265081.6:c.187C>G	p.Pro63Ala	p.P63A	ENST00000265081	NM_002439.4	63	Ccc/Gcc	1/24	1	2	FACETS	0.195	0.149	0.25	0.195	0.149	0.25	SUBCLONAL	1	TRUE	1	0.660494402772476	2		466	310	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858164	152858164	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	299	526	0	ENST00000406277.2:c.451C>T	p.Gln151Ter	p.Q151*	ENST00000406277	NM_152274.4	151	Cag/Tag	6/7	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.660494402772476	1		526	459	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77048440	77048440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1326439583	NA	P-0055269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	177	508	1	ENST00000356341.3:c.1145C>T	p.Ser382Leu	p.S382L	ENST00000356341	NM_002576.4	382	tCg/tTg	12/15	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.660494402772476	2		509	527	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653831	89653832	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1564814541	NA	P-0055269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	159	398	0	ENST00000371953.3:c.131dup	p.Val45ArgfsTer7	p.V45Rfs*7	ENST00000371953	NM_000314.4	43	-/G	2/9	0.657597801496486	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.660494402772476	2		398	237	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934302	81934302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780141402	NA	P-0055269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	122	817	0	ENST00000359376.3:c.1279G>A	p.Asp427Asn	p.D427N	ENST00000359376	NM_002661.3	427	Gac/Aac	14/33	0.657597801496486	2	FACETS	0.494	0.446	0.544	0.247	0.223	0.272	SUBCLONAL	1	TRUE	0	0.660494402772476	2		817	748	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3634859	3634860	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	185	709	0	ENST00000294008.3:c.4649_4650delinsAA	p.Arg1550Gln	p.R1550Q	ENST00000294008	NM_032444.2	1550	cGG/cAA	13/15	0.658399798588243	3	FACETS	0.918	0.849	0.989	0.459	0.424	0.495	CLONAL	1	TRUE	1	0.660494402772476	3		709	812	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6037039	6037039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	399	299	1	ENST00000265849.7:c.721C>T	p.Pro241Ser	p.P241S	ENST00000265849	NM_000535.5	241	Cct/Tct	7/15	0.660494402772476	6	FACETS	0.982	0.943	1	0.982	0.943	1	CLONAL	4	TRUE	2	0.660494402772476	6		300	714	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248725	59248725	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs751178637	NA	P-0055269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	413	1240	0	ENST00000371222.2:c.18A>C	p.Glu6Asp	p.E6D	ENST00000371222	NM_002228.3	6	gaA/gaC	1/1	1	2	FACETS	0.784	0.752	0.816	1	0.996	1	SUBCLONAL	2	TRUE	1	0.660494402772476	2		1240	798	SUCCESS
TERT	7015		GRCh37	5	1295250	1295253	+	upstream_gene_variant	5'Flank	DEL	GAGG	GAGG	-	novel	NA	P-0055269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA			NA	NA	NA		NA	NA	227	137	426	1				ENST00000310581	NM_198253.2	-/1132			1				0.974	1				CLONAL	1	TRUE	1	0.660494402772476	2		427	364	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0055270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	173	672	1	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		673	539	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435357	110435357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	65	481	0	ENST00000375856.3:c.3044C>T	p.Pro1015Leu	p.P1015L	ENST00000375856	NM_003749.2	1015	cCg/cTg	1/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		481	682	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994392	25994392	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	44	304	0	ENST00000435504.4:c.421del	p.Gln141SerfsTer26	p.Q141Sfs*26	ENST00000435504		141	Cag/ag	6/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		304	317	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0055271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	15	341	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.066	0.048	0.089	0.066	0.048	0.089	SUBCLONAL	1	TRUE	1	0.83	2		341	545	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023212	27023230	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGGGCCCTAGGCCCGCC	CGCGGGCCCTAGGCCCGCC	-	novel	NA	P-0055272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	67	244	0	ENST00000324856.7:c.319_337del	p.Ala107Ter	p.A107*	ENST00000324856	NM_006015.4	106	aaCGCGGGCCCTAGGCCCGCC/aa	1/20	1	2	FACETS	0.81	0.709	0.917	0.81	0.709	0.917	CLONAL	1	TRUE	1	0.5	2		244	331	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0055273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	45	314	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.631	0.531	0.74	0.631	0.531	0.74	SUBCLONAL	1	TRUE	1	0.377591125306504	2		314	378	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0055273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	93	285	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.165580390177958	3	FACETS	1	0.969	1	0.62	0.554	0.691	INDETERMINATE	1	TRUE	1	0.377591125306504	3		285	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0055273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	133	591	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.873	0.793	0.957	0.873	0.793	0.957	CLONAL	1	TRUE	1	0.377591125306504	2		591	807	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626635	100626635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	57	219	0	ENST00000308731.7:c.295C>T	p.Pro99Ser	p.P99S	ENST00000308731	NM_000061.2	99	Cct/Tct	4/19	1	1	FACETS	0.854	0.749	0.963	0.854	0.749	0.963	CLONAL	1	TRUE	0	0.59144053448833	1		219	159	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484303	8484303	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	112	486	0	ENST00000356435.5:c.3229C>A	p.Pro1077Thr	p.P1077T	ENST00000356435		1077	Cct/Act	19/35	1	2	FACETS	0.959	0.87	1	0.959	0.87	1	CLONAL	1	TRUE	1	0.59144053448833	2		486	395	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223745	53223746	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0055275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	91	446	0	ENST00000375401.3:c.3613dup	p.Cys1205LeufsTer95	p.C1205Lfs*95	ENST00000375401	NM_004187.3	1205	tgt/tTgt	23/26	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.59144053448833	1		446	150	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0055276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	147	421	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.163004412280564	2	FACETS	1	0.987	1	0.735	0.673	0.8	INDETERMINATE	1	TRUE	0	0.303359952291412	2		423	659	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514420	103514422	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0055276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	24	327	0	ENST00000355739.4:c.923_925del	p.Leu308del	p.L308del	ENST00000355739	NM_000123.3	307	tcTCTt/tct	8/15	1	2	FACETS	0.388	0.303	0.485	0.388	0.303	0.485	SUBCLONAL	1	TRUE	1	0.303359952291412	2		327	408	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572960	7572960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	145	669	1	ENST00000269305.4:c.1149del	p.Met384CysfsTer38	p.M384Cfs*38	ENST00000269305	NM_001126112.2	383	ctC/ct	11/11	0.302310122478822	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.303359952291412	1		670	765	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0055277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	82	535	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.26613248148644	4	FACETS	1	0.971	1	0.654	0.581	0.731	INDETERMINATE	1	TRUE	2	0.520994447178558	4		535	366	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981903	70981903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747860295	NA	P-0055277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	173	825	0	ENST00000276594.2:c.193G>A	p.Ala65Thr	p.A65T	ENST00000276594	NM_024504.3	65	Gcc/Acc	2/8	1	2	FACETS	0.727	0.669	0.787	0.727	0.669	0.787	SUBCLONAL	1	TRUE	1	0.520994447178558	2		825	914	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556728	41556728	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0055277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	128	301	0	ENST00000263253.7:c.3671+2T>G		p.X1224_splice	ENST00000263253	NM_001429.3	1224			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.520994447178558	2		301	437	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439179	52439179	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs869312757	NA	P-0055277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	293	720	1	ENST00000460680.1:c.1063C>T	p.Gln355Ter	p.Q355*	ENST00000460680	NM_004656.3	355	Cag/Tag	11/17	0.520994447178558	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.520994447178558	1		721	737	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749434	41749434	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	93	482	0	ENST00000226382.2:c.361C>T	p.His121Tyr	p.H121Y	ENST00000226382	NM_003924.3	121	Cac/Tac	2/3	0.520994447178558	1	FACETS	0.527	0.47	0.587	0.527	0.47	0.587	SUBCLONAL	1	TRUE	0	0.520994447178558	1		482	501	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054344	42054344	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	64	387	0	ENST00000219905.7:c.7528G>C	p.Val2510Leu	p.V2510L	ENST00000219905	NM_001164273.1	2510	Gtc/Ctc	22/24	0.340917921437163	1	FACETS	0.776	0.679	0.879	0.776	0.679	0.879	SUBCLONAL	1	TRUE	0	0.473408684111556	1		387	266	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014066	14014089	+	inframe_deletion	In_Frame_Del	DEL	TGCTGGAGTACGAGCGACAGCTGG	TGCTGGAGTACGAGCGACAGCTGG	-	novel	NA	P-0055281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	36	751	0	ENST00000311895.7:c.51_74del	p.Tyr18_Glu25del	p.Y18_E25del	ENST00000311895	NM_005236.2	15	cTGCTGGAGTACGAGCGACAGCTGGtg/ctg	1/11	0.473408684111556	3	FACETS	0.281	0.23	0.338	0.14	0.115	0.169	SUBCLONAL	1	TRUE	1	0.473408684111556	3		751	670	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993105	72993105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771899311	NA	P-0055281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	408	912	0	ENST00000268489.5:c.940C>T	p.Arg314Trp	p.R314W	ENST00000268489	NM_006885.3	314	Cgg/Tgg	2/10	0.410257111258061	4	FACETS	1	0.964	1			1	CLONAL	3	TRUE	NA	0.473408684111556	4		912	841	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37665960	37665960	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	62	366	0	ENST00000447079.4:c.2612G>A	p.Gly871Glu	p.G871E	ENST00000447079	NM_015083.1	871	gGg/gAg	7/14	0.288593698854808	3	FACETS	0.764	0.662	0.874	0.255	0.22	0.292	SUBCLONAL	1	TRUE	0	0.473408684111556	3		366	424	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36024597	36024597	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1458527600	NA	P-0055281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	99	869	1	ENST00000358208.4:c.586A>T	p.Asn196Tyr	p.N196Y	ENST00000358208		196	Aac/Tac	6/12	0.171442489821723	5	FACETS	1	0.959	1	0.382	0.341	0.425	INDETERMINATE	1	TRUE	2	0.473408684111556	5		870	624	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662326	117662326	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	148	654	0	ENST00000368508.3:c.5051T>A	p.Leu1684His	p.L1684H	ENST00000368508	NM_002944.2	1684	cTc/cAc	30/43	0.473408684111556	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.473408684111556	1		654	445	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508502	106508502	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs777578185	NA	P-0055281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	46	443	0	ENST00000359195.3:c.496A>T	p.Ser166Cys	p.S166C	ENST00000359195	NM_002649.2	166	Agc/Tgc	2/11	0.150640971190415	3	FACETS	0.834	0.707	0.973	0.278	0.235	0.325	INDETERMINATE	1	TRUE	0	0.473408684111556	3		443	288	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040642	47040642	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	27	342	0	ENST00000377604.3:c.1277C>G	p.Ala426Gly	p.A426G	ENST00000377604	NM_001204468.1	426	gCc/gGc	13/24	0.410257111258061	2	FACETS	0.375	0.299	0.462			1	SUBCLONAL	1	TRUE	NA	0.473408684111556	2		342	304	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0055282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	35	285	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.467472645592815	3	FACETS	0.635	0.523	0.759	0.317	0.261	0.38	SUBCLONAL	1	TRUE	1	0.515415813187206	3		285	269	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741596	145741596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1489813654	NA	P-0055282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	111	1114	2	ENST00000428558.2:c.907G>A	p.Val303Ile	p.V303I	ENST00000428558	NM_004260.3	303	Gta/Ata	5/22	0.182098279486864	6	FACETS	1	0.926	1	0.346	0.31	0.383	INDETERMINATE	1	TRUE	3	0.515415813187206	6		1116	843	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0055283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	36	523	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.985	0.809	1	0.985	0.809	1	CLONAL	1	TRUE	1	0.13	2		523	562	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0055283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	27	457	2	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	0.671	0.532	0.831	0.671	0.532	0.831	SUBCLONAL	1	TRUE	1	0.13	2		459	619	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589580	67589591	+	inframe_deletion	In_Frame_Del	DEL	AATTACATGAAT	AATTACATGAAT	-	novel	NA	P-0055283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	20	232	0	ENST00000274335.5:c.1344_1355del	p.Lys448_Tyr452delinsAsn	p.K448_Y452delinsN	ENST00000274335		448	aAATTACATGAATat/aat	10/15	1	2	FACETS	0.838	0.64	1	0.838	0.64	1	CLONAL	1	TRUE	1	0.13	2		232	367	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950008	44950009	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0055283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	45	580	0	ENST00000377967.4:c.3780dup	p.Leu1261IlefsTer30	p.L1261Ifs*30	ENST00000377967	NM_021140.2	1259	-/A	26/29	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.13	2		580	633	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	117	115	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.365278152518654	2		115	592	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0055284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	108	328	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.991	0.891	1	0.991	0.891	1	CLONAL	1	TRUE	1	0.365278152518654	2		328	597	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098968	178098968	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	25	342	0	ENST00000397062.3:c.77A>G	p.Gln26Arg	p.Q26R	ENST00000397062	NM_006164.4	26	cAa/cGa	2/5	1	2	FACETS	0.284	0.223	0.354	0.284	0.223	0.354	SUBCLONAL	1	TRUE	1	0.365278152518654	2		342	482	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468504	89468504	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	88	377	0	ENST00000336596.2:c.2038C>A	p.Pro680Thr	p.P680T	ENST00000336596	NM_005233.5	680	Ccc/Acc	11/17	1	2	FACETS	0.939	0.835	1	0.939	0.835	1	CLONAL	1	TRUE	1	0.365278152518654	2		377	513	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888825	76888825	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	123	316	0	ENST00000373344.5:c.5004G>C	p.Met1668Ile	p.M1668I	ENST00000373344	NM_000489.3	1668	atG/atC	19/35	1	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.365278152518654	1		316	397	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651922	36651928	+	frameshift_variant	Frame_Shift_Del	DEL	GCAAGGC	GCAAGGC	TG	novel	NA	P-0055284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	327	871	1	ENST00000244741.5:c.44_50delinsTG	p.Ser15MetfsTer19	p.S15Mfs*19	ENST00000244741	NM_000389.4	15	aGCAAGGCc/aTGc	2/3	0.249520249949873	3	FACETS	0.806	0.76	0.852	0.806	0.76	0.852	CLONAL	2	TRUE	1	0.365278152518654	3		872	1314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	202	552	1	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.439179609987344	2	FACETS	0.944	0.885	1	0.944	0.885	1	CLONAL	2	TRUE	0	0.465407129794465	2		553	460	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974730	21974730	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	133	484	1	ENST00000304494.5:c.97G>T	p.Glu33Ter	p.E33*	ENST00000304494	NM_000077.4	33	Gag/Tag	1/3	0.465407129794465	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.465407129794465	1		485	345	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610360	10610360	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	269	961	1	ENST00000171111.5:c.350A>T	p.Glu117Val	p.E117V	ENST00000171111	NM_203500.1	117	gAg/gTg	2/6	0.425326580757762	2	FACETS	0.885	0.836	0.935	0.885	0.836	0.935	CLONAL	2	TRUE	0	0.465407129794465	2		962	653	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793382	42793382	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	204	863	0	ENST00000575354.2:c.1184A>T	p.Tyr395Phe	p.Y395F	ENST00000575354	NM_015125.3	395	tAt/tTt	8/20	0.12573740461497	6	FACETS	1	0.977	1	0.744	0.692	0.798	INDETERMINATE	2	TRUE	3	0.465407129794465	6		863	758	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732687	204732687	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201778935	NA	P-0055285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	59	453	0	ENST00000302823.3:c.22C>T	p.Arg8Trp	p.R8W	ENST00000302823	NM_005214.4	8	Cgg/Tgg	1/4	1	2	FACETS	0.575	0.496	0.661	0.575	0.496	0.661	SUBCLONAL	1	TRUE	1	0.465407129794465	2		453	441	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518319	187518320	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	89	293	0	ENST00000441802.2:c.12374dup	p.Ser4126GlufsTer2	p.S4126Efs*2	ENST00000441802	NM_005245.3	4125	cag/caAg	25/27	NA	2	FACETS	0.797	0.719	0.877			1	INDETERMINATE	2	TRUE	NA	0.465407129794465	2		293	240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055285-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	280	552	1	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.313124526884547	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.313124526884547	2		553	770	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974730	21974730	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055285-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	200	484	1	ENST00000304494.5:c.97G>T	p.Glu33Ter	p.E33*	ENST00000304494	NM_000077.4	33	Gag/Tag	1/3	0.313124526884547	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.313124526884547	2		485	538	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610360	10610360	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055285-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	342	961	1	ENST00000171111.5:c.350A>T	p.Glu117Val	p.E117V	ENST00000171111	NM_203500.1	117	gAg/gTg	2/6	0.313124526884547	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.313124526884547	2		962	1050	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793382	42793382	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055285-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	234	863	0	ENST00000575354.2:c.1184A>T	p.Tyr395Phe	p.Y395F	ENST00000575354	NM_015125.3	395	tAt/tTt	8/20	0.25024029664511	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.313124526884547	4		863	881	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732687	204732687	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201778935	NA	P-0055285-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	60	453	0	ENST00000302823.3:c.22C>T	p.Arg8Trp	p.R8W	ENST00000302823	NM_005214.4	8	Cgg/Tgg	1/4	0.313124526884547	3	FACETS	0.816	0.704	0.939	0.408	0.352	0.47	CLONAL	1	TRUE	1	0.313124526884547	3		453	543	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518319	187518320	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055285-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	88	293	0	ENST00000441802.2:c.12374dup	p.Ser4126GlufsTer2	p.S4126Efs*2	ENST00000441802	NM_005245.3	4125	cag/caAg	25/27	0.313124526884547	2	FACETS	0.946	0.848	1	0.946	0.848	1	CLONAL	2	TRUE	0	0.313124526884547	2		293	297	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0055286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	333	443	0	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	0.512211380582498	2	FACETS	0.806	0.774	0.836	0.806	0.774	0.836	CLONAL	2	TRUE	0	0.816778284288144	2		443	506	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673717	176673717	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784117	NA	P-0055286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	107	352	0	ENST00000439151.2:c.4417C>T	p.Arg1473Ter	p.R1473*	ENST00000439151	NM_022455.4	1473	Cga/Tga	10/23	0.816778284288144	1	FACETS	0.572	0.521	0.624	0.572	0.521	0.624	SUBCLONAL	1	TRUE	0	0.816778284288144	1		352	271	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665483	138665483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	123	973	1	ENST00000330315.3:c.82G>A	p.Glu28Lys	p.E28K	ENST00000330315	NM_023067.3	28	Gaa/Aaa	1/1	0.816778284288144	4	FACETS	0.502	0.453	0.555	0.167	0.151	0.185	SUBCLONAL	1	TRUE	1	0.816778284288144	4		974	1089	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226574134	226574134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200470832	NA	P-0055286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	128	449	0	ENST00000366794.5:c.727G>A	p.Asp243Asn	p.D243N	ENST00000366794	NM_001618.3	243	Gac/Aac	6/23	0.73956749177132	4	FACETS	0.7	0.635	0.77	0.233	0.211	0.257	SUBCLONAL	1	TRUE	1	0.816778284288144	4		449	813	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669315	241669315	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs201395553	NA	P-0055286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	262	388	0	ENST00000366560.3:c.892G>C	p.Ala298Pro	p.A298P	ENST00000366560	NM_000143.3	298	Gct/Cct	6/10	0.73956749177132	4	FACETS	0.753	0.708	0.798	0.502	0.472	0.532	SUBCLONAL	2	TRUE	1	0.816778284288144	4		388	774	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56873481	56873481	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	167	513	0	ENST00000308159.5:c.2185G>C	p.Glu729Gln	p.E729Q	ENST00000308159	NM_014669.4	729	Gag/Cag	20/22	0.175975615366997	3	FACETS	0.825	0.76	0.892	0.413	0.38	0.446	INDETERMINATE	1	TRUE	1	0.816778284288144	3		513	698	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281076	142281076	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	58	282	0	ENST00000350721.4:c.1168G>A	p.Glu390Lys	p.E390K	ENST00000350721	NM_001184.3	390	Gag/Aag	4/47	0.816778284288144	4	FACETS	0.575	0.495	0.661	0.192	0.165	0.221	SUBCLONAL	1	TRUE	1	0.816778284288144	4		282	449	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589598	67589599	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCAGTTTCAAGAAAAAAGTCGAGAATATGA	novel	NA	P-0055286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	70	232	0	ENST00000274335.5:c.1363_1392dup	p.Gln455_Asp464dup	p.Q455_D464dup	ENST00000274335		455	act/acTCAGTTTCAAGAAAAAAGTCGAGAATATGAt	10/15	0.816778284288144	1	FACETS	0.548	0.488	0.61	0.548	0.488	0.61	SUBCLONAL	1	TRUE	0	0.816778284288144	1		232	185	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962914	2962914	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	554	953	1	ENST00000396946.4:c.1994C>A	p.Ser665Ter	p.S665*	ENST00000396946	NM_032415.4	665	tCg/tAg	16/25	0.692949201772398	3	FACETS	0.817	0.787	0.847	0.817	0.787	0.847	CLONAL	2	TRUE	1	0.816778284288144	3		954	1169	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994255	21994255	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	220	465	0	ENST00000579755.1:c.76C>G	p.His26Asp	p.H26D	ENST00000579755		26	Cac/Gac	1/3	1		FACETS		0.634	0.727				SUBCLONAL	1	TRUE	1	0.816778284288144	2		465	792	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0055286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	279	443	0	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	0.15931473084699	2	FACETS	1	0.991	1	0.599	0.568	0.63	INDETERMINATE	1	TRUE	0	0.781808427064632	2		443	596	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673717	176673717	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784117	NA	P-0055286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	41	352	0	ENST00000439151.2:c.4417C>T	p.Arg1473Ter	p.R1473*	ENST00000439151	NM_022455.4	1473	Cga/Tga	10/23	0.781808427064632	1	FACETS	0.163	0.136	0.194	0.163	0.136	0.194	SUBCLONAL	1	TRUE	0	0.781808427064632	1		352	391	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226574134	226574134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200470832	NA	P-0055286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	53	449	0	ENST00000366794.5:c.727G>A	p.Asp243Asn	p.D243N	ENST00000366794	NM_001618.3	243	Gac/Aac	6/23	0.648286791851208	4	FACETS	0.238	0.202	0.278	0.079	0.067	0.093	SUBCLONAL	1	TRUE	1	0.781808427064632	4		449	1013	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669315	241669315	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs201395553	NA	P-0055286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	307	388	0	ENST00000366560.3:c.892G>C	p.Ala298Pro	p.A298P	ENST00000366560	NM_000143.3	298	Gct/Cct	6/10	0.648286791851208	4	FACETS	0.848	0.803	0.894	0.565	0.535	0.596	CLONAL	2	TRUE	1	0.781808427064632	4		388	825	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56873481	56873481	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	93	513	0	ENST00000308159.5:c.2185G>C	p.Glu729Gln	p.E729Q	ENST00000308159	NM_014669.4	729	Gag/Cag	20/22	0.197949058517976	3	FACETS	0.44	0.391	0.492	0.22	0.195	0.246	INDETERMINATE	1	TRUE	1	0.781808427064632	3		513	752	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281076	142281076	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	45	282	0	ENST00000350721.4:c.1168G>A	p.Glu390Lys	p.E390K	ENST00000350721	NM_001184.3	390	Gag/Aag	4/47	0.781808427064632	4	FACETS	0.348	0.292	0.41	0.116	0.097	0.137	SUBCLONAL	1	TRUE	1	0.781808427064632	4		282	590	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589598	67589599	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCAGTTTCAAGAAAAAAGTCGAGAATATGA	novel	NA	P-0055286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	83	232	0	ENST00000274335.5:c.1363_1392dup	p.Gln455_Asp464dup	p.Q455_D464dup	ENST00000274335		455	act/acTCAGTTTCAAGAAAAAAGTCGAGAATATGAt	10/15	0.781808427064632	1	FACETS	0.543	0.487	0.601	0.543	0.487	0.601	SUBCLONAL	1	TRUE	0	0.781808427064632	1		232	238	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962914	2962914	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	178	953	1	ENST00000396946.4:c.1994C>A	p.Ser665Ter	p.S665*	ENST00000396946	NM_032415.4	665	tCg/tAg	16/25	1	2	FACETS	0.372	0.342	0.404	0.372	0.342	0.404	SUBCLONAL	1	TRUE	1	0.781808427064632	2		954	1223	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994255	21994255	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	78	465	0	ENST00000579755.1:c.76C>G	p.His26Asp	p.H26D	ENST00000579755		26	Cac/Gac	1/3	1		FACETS		0.273	0.352				SUBCLONAL	1	TRUE	1	0.781808427064632	2		465	642	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548880	29548880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	59	692	1	ENST00000356175.3:c.1654C>T	p.Leu552Phe	p.L552F	ENST00000356175	NM_000267.3	552	Ctt/Ttt	15/57	1	2	FACETS	0.2	0.171	0.231	0.2	0.171	0.231	SUBCLONAL	1	TRUE	1	0.781808427064632	2		693	756	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637762	176637762	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520339	NA	P-0055286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	167	609	0	ENST00000439151.2:c.2362C>T	p.Arg788Ter	p.R788*	ENST00000439151	NM_022455.4	788	Cga/Tga	5/23	0.781808427064632	1	FACETS	0.437	0.403	0.471	0.437	0.403	0.471	SUBCLONAL	1	TRUE	0	0.781808427064632	1		609	596	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176678794	176678794	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	92	445	0	ENST00000439151.2:c.4705G>T	p.Glu1569Ter	p.E1569*	ENST00000439151	NM_022455.4	1569	Gag/Tag	12/23	0.781808427064632	1	FACETS	0.292	0.26	0.326	0.292	0.26	0.326	SUBCLONAL	1	TRUE	0	0.781808427064632	1		445	491	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624781	9624781	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs758410451	NA	P-0055286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	46	428	0	ENST00000353224.5:c.196C>G	p.Pro66Ala	p.P66A	ENST00000353224	NM_177990.2	66	Cct/Gct	3/10	1	2	FACETS	0.247	0.208	0.291	0.247	0.208	0.291	SUBCLONAL	1	TRUE	1	0.781808427064632	2		428	476	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710953	117710953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	28	315	0	ENST00000368508.3:c.1319C>T	p.Ser440Phe	p.S440F	ENST00000368508	NM_002944.2	440	tCt/tTt	12/43	1	2	FACETS	0.173	0.138	0.213	0.173	0.138	0.213	SUBCLONAL	1	TRUE	1	0.781808427064632	2		315	414	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0055289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	174	461	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.523279170162144	3	FACETS	0.991	0.925	1	0.991	0.925	1	CLONAL	2	TRUE	1	0.582972576396125	3		461	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0055289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	242	779	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	0.582972576396125	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.582972576396125	1		779	500	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951141	48951141	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	128	438	0	ENST00000267163.4:c.1303G>T	p.Gly435Ter	p.G435*	ENST00000267163	NM_000321.2	435	Gga/Tga	13/27	0.582258939569954	2	FACETS	0.878	0.814	0.942	0.878	0.814	0.942	CLONAL	2	TRUE	0	0.582972576396125	2		438	250	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555250	226555250	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	200	594	0	ENST00000366794.5:c.2337G>T	p.Arg779Ser	p.R779S	ENST00000366794	NM_001618.3	779	agG/agT	17/23	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.582972576396125	2		594	552	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959108	28959108	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	215	464	0	ENST00000282397.4:c.2030C>A	p.Ser677Tyr	p.S677Y	ENST00000282397	NM_002019.4	677	tCc/tAc	14/30	0.582258939569954	2	FACETS	0.991	0.939	1	0.991	0.939	1	CLONAL	2	TRUE	0	0.582972576396125	2		464	372	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828205	50828205	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	104	622	0	ENST00000398568.2:c.2543A>C	p.His848Pro	p.H848P	ENST00000398568	NM_001042412.1	848	cAc/cCc	17/18	1	2	FACETS	0.75	0.674	0.828	0.75	0.674	0.828	SUBCLONAL	1	TRUE	1	0.582972576396125	2		622	476	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650659	67650659	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	165	543	0	ENST00000264010.4:c.964C>A	p.His322Asn	p.H322N	ENST00000264010	NM_006565.3	322	Cac/Aac	5/12	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.582972576396125	2		543	503	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108292	8108292	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	283	864	0	ENST00000585124.1:c.932A>T	p.Asn311Ile	p.N311I	ENST00000585124	NM_004217.3	311	aAc/aTc	9/9	0.582972576396125	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.582972576396125	1		864	583	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871591	37871591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	113	1038	0	ENST00000269571.5:c.1201G>A	p.Glu401Lys	p.E401K	ENST00000269571		401	Gag/Aag	10/27	0.222529315923148	3	FACETS	0.566	0.508	0.626	0.283	0.254	0.313	INDETERMINATE	1	TRUE	1	0.582972576396125	3		1038	885	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858823	78858823	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	295	877	0	ENST00000306801.3:c.1858G>T	p.Val620Phe	p.V620F	ENST00000306801	NM_020761.2	620	Gtc/Ttc	17/34	0.222529315923148	3	FACETS	0.854	0.808	0.901	0.854	0.808	0.901	INDETERMINATE	2	TRUE	1	0.582972576396125	3		877	765	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646212	215646212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	61	372	0	ENST00000260947.4:c.386G>A	p.Arg129Lys	p.R129K	ENST00000260947	NM_000465.2	129	aGg/aAg	4/11	1	2	FACETS	0.83	0.724	0.943	0.83	0.724	0.943	CLONAL	1	TRUE	1	0.582972576396125	2		372	252	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031729	36031729	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	198	994	0	ENST00000358208.4:c.1558G>T	p.Glu520Ter	p.E520*	ENST00000358208		520	Gag/Tag	12/12	1	2	FACETS	0.894	0.83	0.96	0.894	0.83	0.96	CLONAL	1	TRUE	1	0.582972576396125	2		994	760	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790052	40790052	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1303470283	NA	P-0055289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	150	817	0	ENST00000373198.4:c.2679G>C	p.Leu893Phe	p.L893F	ENST00000373198	NM_133170.3	893	ttG/ttC	18/32	NA	2	FACETS	0.819	0.752	0.89			1	INDETERMINATE	1	TRUE	NA	0.582972576396125	2		817	628	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485137	57485137	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0055289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	75	359	0	ENST00000371085.3:c.970+1G>T		p.X324_splice	ENST00000371085	NM_000516.4	324			1	2	FACETS	0.675	0.595	0.761	0.675	0.595	0.761	SUBCLONAL	1	TRUE	1	0.582972576396125	2		359	381	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295238	1295238	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0055289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	101	477	0				ENST00000310581	NM_198253.2	-/1132			0.582972576396125	3	FACETS	0.796	0.714	0.884	0.398	0.357	0.442	SUBCLONAL	1	TRUE	1	0.582972576396125	3		477	562	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858418	27858418	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	354	797	0	ENST00000359303.2:c.153G>T	p.Glu51Asp	p.E51D	ENST00000359303	NM_003535.2	51	gaG/gaT	1/1	0.582972576396125	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.582972576396125	3		797	764	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729515	41729515	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	168	730	0	ENST00000242208.4:c.1014G>T	p.Trp338Cys	p.W338C	ENST00000242208	NM_002192.2	338	tgG/tgT	3/3	NA	2	FACETS	0.925	0.854	0.999			1	INDETERMINATE	1	TRUE	NA	0.582972576396125	2		730	623	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534483	140534483	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	100	537	0	ENST00000288602.6:c.430G>T	p.Val144Leu	p.V144L	ENST00000288602	NM_004333.4	144	Gtg/Ttg	3/18	0.523279170162144	3	FACETS	0.803	0.719	0.891	0.401	0.359	0.446	CLONAL	1	TRUE	1	0.582972576396125	3		537	552	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69039654	69039654	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	40	370	0	ENST00000288368.4:c.3766G>C	p.Asp1256His	p.D1256H	ENST00000288368	NM_024870.2	1256	Gat/Cat	31/40	0.478224709508583	1	FACETS	0.575	0.485	0.673	0.575	0.485	0.673	SUBCLONAL	1	TRUE	0	0.582972576396125	1		370	169	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401240	139401240	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	118	1004	1	ENST00000277541.6:c.3829G>T	p.Asp1277Tyr	p.D1277Y	ENST00000277541	NM_017617.3	1277	Gac/Tac	23/34	0.468133091527387	1	FACETS	0.396	0.357	0.436	0.396	0.357	0.436	SUBCLONAL	1	TRUE	0	0.582972576396125	1		1005	725	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176105667	176105669	+	missense_variant	Missense_Mutation	TNP	TGG	TGG	AGT	novel	NA	P-0055289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	96	509	0	ENST00000367669.3:c.846_848delinsACT	p.Gln283Leu	p.Q283L	ENST00000367669	NM_022457.5	282	atCCAg/atACTg	7/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.582972576396125	2		509	279	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0055290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	265	517	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.898	0.846	0.952	0.898	0.846	0.952	CLONAL	1	TRUE	1	0.775281191660063	2		517	761	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0055290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	31	790	0	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	1	2	FACETS	0.073	0.058	0.09	0.073	0.058	0.09	SUBCLONAL	1	TRUE	1	0.775281191660063	2		790	1095	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662373	227662373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746340033	NA	P-0055290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	380	753	3	ENST00000305123.5:c.1082G>A	p.Gly361Asp	p.G361D	ENST00000305123	NM_005544.2	361	gGc/gAc	1/2	1	2	FACETS	0.897	0.853	0.941	0.897	0.853	0.941	CLONAL	1	TRUE	1	0.775281191660063	2		756	1093	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31424569	31424569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773151368	NA	P-0055290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	324	608	0	ENST00000344624.3:c.3226G>A	p.Glu1076Lys	p.E1076K	ENST00000344624		1076	Gaa/Aaa	25/33	1	2	FACETS	0.922	0.873	0.971	0.922	0.873	0.971	CLONAL	1	TRUE	1	0.775281191660063	2		608	907	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430767	47430767	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	399	746	0	ENST00000377045.4:c.1732G>C	p.Glu578Gln	p.E578Q	ENST00000377045	NM_001654.4	578	Gag/Cag	16/16	1	2	FACETS	0.948	0.903	0.993	0.948	0.903	0.993	CLONAL	1	TRUE	1	0.775281191660063	2		746	1086	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0055292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	16	347	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.411	0.302	0.543	0.411	0.302	0.543	SUBCLONAL	1	TRUE	1	0.11	2		347	707	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0055292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	19	411	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.6	0.453	0.773	0.6	0.453	0.773	SUBCLONAL	1	TRUE	1	0.11	2		411	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0055298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	565	608	0	ENST00000269305.4:c.376-1G>T		p.X126_splice	ENST00000269305	NM_001126112.2	126			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		608	705	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0055306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	41	166	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.816	0.682	0.964	0.816	0.682	0.964	CLONAL	1	TRUE	1	0.306327858773477	2		166	328	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610584	52610584	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	60	335	0	ENST00000394830.3:c.3589del	p.Glu1197LysfsTer5	p.E1197Kfs*5	ENST00000394830	NM_018313.4	1197	Gaa/aa	23/30	0.281175290641795	1	FACETS	0.796	0.688	0.912	0.796	0.688	0.912	CLONAL	1	TRUE	0	0.306327858773477	1		335	417	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525109	187525109	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	64	323	0	ENST00000441802.2:c.10571A>T	p.Gln3524Leu	p.Q3524L	ENST00000441802	NM_005245.3	3524	cAg/cTg	19/27	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.306327858773477	2		323	375	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0055310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	41	396	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.836	1	1	0.836	1	CLONAL	1	TRUE	1	0.18	2		396	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0055310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	68	575	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.18	2		575	732	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500477	99500477	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	53	1038	0	ENST00000268035.6:c.3910C>T	p.Pro1304Ser	p.P1304S	ENST00000268035	NM_000875.3	1304	Ccc/Tcc	21/21	1	2	FACETS	0.775	0.659	0.902	0.775	0.659	0.902	CLONAL	1	TRUE	1	0.18	2		1038	760	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578464	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055313-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	466	1129	0	ENST00000269305.4:c.466C>G	p.Arg156Gly	p.R156G	ENST00000269305	NM_001126112.2	156	Cgc/Ggc	5/11	0.445265810663295	2	FACETS	0.938	0.899	0.976	0.938	0.899	0.976	CLONAL	2	TRUE	0	0.472939981969438	2		1129	1051	SUCCESS
APC	324	MSKCC	GRCh37	5	112175060	112175061	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0055313-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	81	165	0	ENST00000257430.4:c.3772dup	p.Thr1258AsnfsTer18	p.T1258Nfs*18	ENST00000257430	NM_000038.5	1257	gaa/gAaa	16/16	0.472939981969438	2	FACETS	0.869	0.783	0.958	0.869	0.783	0.958	CLONAL	2	TRUE	0	0.472939981969438	2		165	197	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857347	68857347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756092625	NA	P-0055313-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	212	493	0	ENST00000261769.5:c.1982G>A	p.Gly661Asp	p.G661D	ENST00000261769	NM_004360.3	661	gGt/gAt	13/16	0.355983582306926	4	FACETS	0.947	0.884	1	0.947	0.884	1	CLONAL	2	TRUE	2	0.472939981969438	4		493	697	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242482	+	protein_altering_variant	In_Frame_Del	DEL	GGAATTAAGAGAAGCAAC	GGAATTAAGAGAAGCAAC	ATT	novel	NA	P-0055313-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	236	453	1	ENST00000275493.2:c.2235_2252delinsATT	p.Glu746_Thr751delinsLeu	p.E746_T751delinsL	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCAACa/aaATTa	19/28	0.472939981969438	5	FACETS	0.916	0.86	0.972	0.916	0.86	0.972	CLONAL	3	TRUE	2	0.472939981969438	5		454	621	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40483518	40483518	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055313-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	46	437	0	ENST00000264657.5:c.1081C>T	p.Gln361Ter	p.Q361*	ENST00000264657	NM_139276.2	361	Cag/Tag	11/24	0.405255955737924	4	FACETS	0.488	0.41	0.574	0.244	0.205	0.287	SUBCLONAL	1	TRUE	2	0.472939981969438	4		437	587	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713565	30713566	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0055313-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	216	554	0	ENST00000295754.5:c.890_891insA	p.Asn298GlnfsTer5	p.N298Qfs*5	ENST00000295754	NM_003242.5	297	atc/atAc	4/7	0.443384396720431	2	FACETS	0.926	0.871	0.983	0.926	0.871	0.983	CLONAL	2	TRUE	0	0.472939981969438	2		554	493	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240776	55240776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17337079	NA	P-0055313-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	843	1080	1	ENST00000275493.2:c.2020G>A	p.Val674Ile	p.V674I	ENST00000275493	NM_005228.3	674	Gtt/Att	17/28	0.472939981969438	5	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	2	0.472939981969438	5		1081	1744	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0055314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	8	134	0	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	1	FACETS	0.468	0.301	0.682	0.468	0.301	0.682	SUBCLONAL	1	TRUE	0	0.19	1		134	163	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696449	47696449	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	61	447	0	ENST00000347630.2:c.374T>G	p.Phe125Cys	p.F125C	ENST00000347630	NM_001007230.1	125	tTt/tGt	6/11	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.19	2		447	589	SUCCESS
APC	324	MSKCC	GRCh37	5	112173831	112173831	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	38	292	0	ENST00000257430.4:c.2544del	p.Asp849IlefsTer12	p.D849Ifs*12	ENST00000257430	NM_000038.5	847	gAa/ga	16/16	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.19	2		292	333	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777893	NA	P-0055314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	31	391	0	ENST00000361445.4:c.5930C>T	p.Thr1977Ile	p.T1977I	ENST00000361445	NM_004958.3	1977	aCa/aTa	43/58	1	2	FACETS	0.537	0.433	0.655	0.537	0.433	0.655	SUBCLONAL	1	TRUE	1	0.19	2		391	608	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401520	401520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751008894	NA	P-0055314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	45	397	1	ENST00000380956.4:c.842C>T	p.Thr281Met	p.T281M	ENST00000380956	NM_001195286.1	281	aCg/aTg	7/9	1	2	FACETS	0.872	0.733	1	0.872	0.733	1	CLONAL	1	TRUE	1	0.19	2		398	543	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933400	39933400	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	61	299	0	ENST00000378444.4:c.1199del	p.Gly400AlafsTer42	p.G400Afs*42	ENST00000378444	NM_001123385.1	400	gGc/gc	4/15	1	1	FACETS	0.767	0.664	0.877	1	0.971	1	SUBCLONAL	2	TRUE	0	0.19	1		299	379	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224149	98224149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531947455	NA	P-0055314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	21	270	0	ENST00000331920.6:c.2692G>A	p.Asp898Asn	p.D898N	ENST00000331920	NM_000264.3	898	Gac/Aac	16/24	1	2	FACETS	0.564	0.433	0.717	0.564	0.433	0.717	SUBCLONAL	1	TRUE	1	0.19	2		270	392	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821341	72821341	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200494604	NA	P-0055314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	30	320	1	ENST00000268489.5:c.10834G>A	p.Ala3612Thr	p.A3612T	ENST00000268489	NM_006885.3	3612	Gcc/Acc	10/10	1	2	FACETS	0.808	0.651	0.986	0.808	0.651	0.986	CLONAL	1	TRUE	1	0.19	2		321	391	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12043919	12043919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398054657	NA	P-0055314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	50	371	1	ENST00000396373.4:c.1298G>A	p.Arg433His	p.R433H	ENST00000396373	NM_001987.4	433	cGt/cAt	8/8	1	2	FACETS	0.952	0.807	1	0.952	0.807	1	CLONAL	1	TRUE	1	0.19	2		372	553	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128036920	128036920	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1034515602	NA	P-0055314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	49	404	0	ENST00000285398.2:c.1559G>A	p.Arg520Gln	p.R520Q	ENST00000285398	NM_000122.1	520	cGg/cAg	10/15	1	2	FACETS	0.94	0.795	1	0.94	0.795	1	CLONAL	1	TRUE	1	0.19	2		404	549	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395624	31395624	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs756972254	NA	P-0055314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	62	607	0	ENST00000328111.2:c.2477G>T	p.Arg826Leu	p.R826L	ENST00000328111	NM_006892.3	826	cGc/cTc	23/23	1	2	FACETS	0.851	0.734	0.979	0.851	0.734	0.979	CLONAL	1	TRUE	1	0.19	2		607	767	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537092	41537092	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	23	303	0	ENST00000263253.7:c.1919T>C	p.Ile640Thr	p.I640T	ENST00000263253	NM_001429.3	640	aTc/aCc	10/31	1	2	FACETS	0.694	0.541	0.871	0.694	0.541	0.871	SUBCLONAL	1	TRUE	1	0.19	2		303	349	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382184	152382184	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	47	428	0	ENST00000206249.3:c.1294T>C	p.Ser432Pro	p.S432P	ENST00000206249	NM_000125.3	432	Tca/Cca	6/8	1	2	FACETS	0.896	0.756	1	0.896	0.756	1	CLONAL	1	TRUE	1	0.19	2		428	552	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0055315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	86	354	1				ENST00000310581	NM_198253.2	-/1132			0.266761122499477	3	FACETS	1	0.979	1	0.738	0.658	0.821	CLONAL	1	TRUE	1	0.408015760392722	3		355	344	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300426	11300426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	74	605	0	ENST00000361445.4:c.1720C>T	p.Pro574Ser	p.P574S	ENST00000361445	NM_004958.3	574	Cct/Tct	11/58	0.310334377695522	3	FACETS	1	0.896	1	0.51	0.448	0.576	CLONAL	1	TRUE	1	0.408015760392722	3		605	428	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0055315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	148	327	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.187081119398409	5	FACETS	1	0.981	1	0.809	0.744	0.875	INDETERMINATE	2	TRUE	2	0.408015760392722	5		327	482	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858517	9858517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765370528	NA	P-0055315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	108	637	1	ENST00000330684.3:c.2884G>A	p.Glu962Lys	p.E962K	ENST00000330684	NM_001134407.1	962	Gaa/Aaa	13/13	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.408015760392722	2		638	417	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976476	25976476	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	75	510	0	ENST00000435504.4:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000435504		357	Cga/Tga	11/13	0.310334377695522	3	FACETS	0.873	0.767	0.987	0.437	0.383	0.494	CLONAL	1	TRUE	1	0.408015760392722	3		510	507	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944947	31944947	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868835690	NA	P-0055315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	57	466	1	ENST00000340398.3:c.154C>T	p.Arg52Cys	p.R52C	ENST00000340398	NM_001013699.2	52	Cgt/Tgt	1/1	0.18736099150886	4	FACETS	0.93	0.8	1	0.465	0.4	0.536	INDETERMINATE	1	TRUE	2	0.408015760392722	4		467	423	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189349321	189349321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	78	386	1	ENST00000264731.3:c.17C>T	p.Ser6Leu	p.S6L	ENST00000264731	NM_003722.4	6	tCa/tTa	1/14	0.301584425200336	4	FACETS	1	0.962	1	0.612	0.54	0.689	CLONAL	1	TRUE	2	0.408015760392722	4		387	440	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715601	30715601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	83	255	0	ENST00000295754.5:c.1259G>A	p.Gly420Glu	p.G420E	ENST00000295754	NM_003242.5	420	gGa/gAa	5/7	0.301584425200336	4	FACETS	0.823	0.732	0.919	0.823	0.732	0.919	CLONAL	2	TRUE	2	0.408015760392722	4		255	348	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352510	89352510	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs978728438	NA	P-0055315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	100	688	0	ENST00000301030.4:c.829C>T	p.Pro277Ser	p.P277S	ENST00000301030	NM_001256183.1	277	Ccc/Tcc	8/13	0.24053101822187	3	FACETS	1	0.946	1	0.544	0.488	0.604	INDETERMINATE	1	TRUE	1	0.408015760392722	3		688	542	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11297916	11297916	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	37	593	0	ENST00000361445.4:c.2192G>A	p.Arg731His	p.R731H	ENST00000361445	NM_004958.3	731	cGc/cAc	13/58	0.310334377695522	3	FACETS	0.53	0.437	0.634	0.265	0.218	0.317	SUBCLONAL	1	TRUE	1	0.408015760392722	3		593	412	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222961	36222961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	200	893	2	ENST00000222270.7:c.5590C>T	p.Arg1864Ter	p.R1864*	ENST00000222270	NM_014727.1	1864	Cga/Tga	27/37	0.18736099150886	4	FACETS	0.85	0.789	0.913	0.85	0.789	0.913	INDETERMINATE	2	TRUE	2	0.408015760392722	4		895	812	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601290	28601290	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	107	524	0	ENST00000241453.7:c.2142G>A	p.Trp714Ter	p.W714*	ENST00000241453	NM_004119.2	714	tgG/tgA	17/24	0.157095169303242	2	FACETS	1	0.979	1	0.657	0.594	0.723	INDETERMINATE	1	TRUE	0	0.408015760392722	2		524	399	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435592	110435592	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	68	439	0	ENST00000375856.3:c.2809C>T	p.Pro937Ser	p.P937S	ENST00000375856	NM_003749.2	937	Ccc/Tcc	1/2	0.266761122499477	3	FACETS	0.969	0.847	1	0.485	0.423	0.551	CLONAL	1	TRUE	1	0.408015760392722	3		439	414	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282209	38282209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	95	692	1	ENST00000425967.3:c.847C>T	p.Pro283Ser	p.P283S	ENST00000425967	NM_001174067.1	283	Cct/Tct	8/19	0.24053101822187	3	FACETS	1	0.951	1	0.555	0.496	0.618	INDETERMINATE	1	TRUE	1	0.408015760392722	3		693	505	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161293423	161293423	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760986608	NA	P-0055315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	151	504	0	ENST00000367975.2:c.40C>T	p.Leu14Phe	p.L14F	ENST00000367975	NM_003001.3	14	Ctc/Ttc	2/6	0.310334377695522	3	FACETS	0.852	0.784	0.922	0.852	0.784	0.922	CLONAL	2	TRUE	1	0.408015760392722	3		504	523	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692802	89692803	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	135	391	0	ENST00000371953.3:c.286_287delinsTT	p.Pro96Leu	p.P96L	ENST00000371953	NM_000314.4	96	CCa/TTa	5/9	0.408015760392722	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.408015760392722	2		391	309	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287489	46287489	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1175264280	NA	P-0055315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	76	520	0	ENST00000334344.6:c.5348C>T	p.Ser1783Leu	p.S1783L	ENST00000334344	NM_152641.2	1783	tCa/tTa	20/21	0.18736099150886	4	FACETS	1	0.942	1	0.559	0.492	0.631	INDETERMINATE	1	TRUE	2	0.408015760392722	4		520	469	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426637	121426637	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	97	593	0	ENST00000257555.6:c.328G>A	p.Glu110Lys	p.E110K	ENST00000257555		110	Gag/Aag	2/10	0.24053101822187	3	FACETS	1	0.955	1	0.562	0.503	0.625	INDETERMINATE	1	TRUE	1	0.408015760392722	3		593	509	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027146	49027146	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	61	399	0	ENST00000267163.4:c.1713T>G	p.Asp571Glu	p.D571E	ENST00000267163	NM_000321.2	571	gaT/gaG	18/27	0.266761122499477	3	FACETS	0.968	0.839	1	0.484	0.419	0.554	CLONAL	1	TRUE	1	0.408015760392722	3		399	372	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712914	43712914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	94	636	0	ENST00000382044.4:c.4270C>T	p.Pro1424Ser	p.P1424S	ENST00000382044	NM_001141980.1	1424	Ccc/Tcc	21/28	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.408015760392722	2		636	432	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132521	11132521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	164	793	1	ENST00000358026.2:c.2737C>T	p.Pro913Ser	p.P913S	ENST00000358026	NM_001128849.1	913	Ccg/Tcg	19/36	0.18736099150886	4	FACETS	0.966	0.891	1	0.966	0.891	1	INDETERMINATE	2	TRUE	2	0.408015760392722	4		794	586	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47061331	47061331	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0055315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	84	342	0	ENST00000409792.3:c.7351-1G>A		p.X2451_splice	ENST00000409792	NM_014159.6	2451			0.301584425200336	4	FACETS	0.821	0.731	0.916	0.821	0.731	0.916	CLONAL	2	TRUE	2	0.408015760392722	4		342	353	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275236	142275237	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	112	392	0	ENST00000350721.4:c.2066_2067delinsTT	p.Pro689Leu	p.P689L	ENST00000350721	NM_001184.3	689	cCC/cTT	9/47	0.301584425200336	4	FACETS	0.945	0.857	1	0.945	0.857	1	CLONAL	2	TRUE	2	0.408015760392722	4		392	409	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165702	185165702	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	52	429	1	ENST00000265026.3:c.977G>A	p.Arg326Gln	p.R326Q	ENST00000265026	NM_004721.4	326	cGg/cAg	5/14	0.301584425200336	4	FACETS	0.801	0.683	0.93	0.401	0.341	0.465	CLONAL	1	TRUE	2	0.408015760392722	4		430	448	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131972814	131972814	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	73	298	0	ENST00000265335.6:c.3397A>C	p.Met1133Leu	p.M1133L	ENST00000265335		1133	Atg/Ctg	22/25	0.301584425200336	4	FACETS	0.813	0.717	0.914	0.813	0.717	0.914	CLONAL	2	TRUE	2	0.408015760392722	4		298	310	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287478	33287479	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	130	783	0	ENST00000374542.5:c.1618_1619delinsTT	p.Pro540Phe	p.P540F	ENST00000374542	NM_001141970.1	540	CCc/TTc	6/8	0.408015760392722	5	FACETS	0.794	0.722	0.869			1	SUBCLONAL	2	TRUE	NA	0.408015760392722	5		783	647	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561528	141561528	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	109	469	0	ENST00000220592.5:c.1277C>T	p.Ala426Val	p.A426V	ENST00000220592	NM_012154.3	426	gCt/gTt	11/19	0.408175354467137	5	FACETS	0.912	0.824	1	0.608	0.549	0.67	CLONAL	2	TRUE	2	0.408015760392722	5		469	472	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801055	1801057	+	missense_variant	Missense_Mutation	TNP	CCC	CCC	TCT	novel	NA	P-0055315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	120	844	0	ENST00000260795.2:c.184_186delinsTCT	p.Pro62Ser	p.P62S	ENST00000260795		62	CCC/TCT	2/17	0.310334377695522	3	FACETS	1	0.979	1	0.646	0.586	0.709	CLONAL	1	TRUE	1	0.408015760392722	3		844	548	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0055316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	191	723	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.376768162582724	2		723	858	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436843	52436854	+	frameshift_variant	Frame_Shift_Del	DEL	GTTTGCAATCTC	GTTTGCAATCTC	A	novel	NA	P-0055316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	153	642	0	ENST00000460680.1:c.1924_1935delinsT	p.Glu642LeufsTer2	p.E642Lfs*2	ENST00000460680	NM_004656.3	642	GAGATTGCAAAC/T	15/17	0.376768162582724	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.376768162582724	1		642	633	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	64	285	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.885	0.767	1	0.885	0.767	1	CLONAL	1	TRUE	1	0.29	2		285	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	160	774	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.29	2		776	1102	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	115	559	3	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.9	0.81	0.996	0.9	0.81	0.996	CLONAL	1	TRUE	1	0.29	2		562	881	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733513	85733513	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs387906350	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	83	562	4	ENST00000370580.1:c.499del	p.Ser167LeufsTer6	p.S167Lfs*6	ENST00000370580	NM_003921.4	167	Tct/ct	3/3	1	2	FACETS	0.828	0.731	0.933	0.828	0.731	0.933	CLONAL	1	TRUE	1	0.29	2		566	691	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	139	672	1	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.29	2		673	926	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522551	176522551	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	170	749	0	ENST00000292408.4:c.1648G>C	p.Val550Leu	p.V550L	ENST00000292408	NM_213647.1	550	Gtg/Ctg	13/18	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.29	2		749	1002	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	153	811	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.29	2		815	987	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	131	597	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.29	2		597	713	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956220	55956220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190050670	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	58	543	1	ENST00000263923.4:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000263923	NM_002253.2	1032	cGa/cAa	23/30	0.204627409440535	1	FACETS	0.496	0.425	0.573	0.496	0.425	0.573	SUBCLONAL	1	TRUE	0	0.29	1		544	690	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	167	781	1	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.29	2		782	1041	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	158	392	3	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	0.224190568309842	3	FACETS	0.874	0.802	0.948	0.874	0.802	0.948	CLONAL	2	TRUE	1	0.29	3		395	714	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	99	1126	1	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.632	0.563	0.706	0.632	0.563	0.706	SUBCLONAL	1	TRUE	1	0.29	2		1127	1080	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732969	30732969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893810	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	104	502	0	ENST00000295754.5:c.1582C>T	p.Arg528Cys	p.R528C	ENST00000295754	NM_003242.5	528	Cgt/Tgt	7/7	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.29	2		502	652	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475061	40475063	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	130	1006	1	ENST00000264657.5:c.1847_1849del	p.Glu616del	p.E616del	ENST00000264657	NM_139276.2	616	gAAGga/gga	20/24	1	2	FACETS	0.945	0.856	1	0.945	0.856	1	CLONAL	1	TRUE	1	0.29	2		1007	949	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347983	347983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760961378	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	181	854	5	ENST00000262320.3:c.1523del	p.Gly508ValfsTer197	p.G508Vfs*197	ENST00000262320	NM_003502.3	508	gGt/gt	6/11	0.283153515168632	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.29	1		859	975	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273534	5273534	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1397380294	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	67	660	1	ENST00000357368.4:c.298C>T	p.Arg100Trp	p.R100W	ENST00000357368	NM_002850.3	100	Cgg/Tgg	4/38	1	2	FACETS	0.5	0.433	0.573	0.5	0.433	0.573	SUBCLONAL	1	TRUE	1	0.29	2		661	924	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812292	212812292	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778048381	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	90	380	0	ENST00000342788.4:c.284G>A	p.Arg95His	p.R95H	ENST00000342788	NM_005235.2	95	cGt/cAt	3/28	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.29	2		380	537	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740623	58740624	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs763475304	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	109	609	1	ENST00000305921.3:c.1535dup	p.Asn512LysfsTer16	p.N512Kfs*16	ENST00000305921	NM_003620.3	510	caa/cAaa	6/6	1	2	FACETS	0.841	0.754	0.933	0.841	0.754	0.933	CLONAL	1	TRUE	1	0.29	2		610	894	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070577	67070578	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	68	306	0	ENST00000412916.2:c.207dup	p.Pro70SerfsTer13	p.P70Sfs*13	ENST00000412916		67	-/T	3/6	1	2	FACETS	0.897	0.781	1	0.897	0.781	1	CLONAL	1	TRUE	1	0.29	2		306	523	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519378	176519378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148292303	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	158	691	0	ENST00000292408.4:c.784G>A	p.Val262Met	p.V262M	ENST00000292408	NM_213647.1	262	Gtg/Atg	7/18	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.29	2		691	864	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436227	110436227	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1394911868	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	67	430	2	ENST00000375856.3:c.2174del	p.Gly725AlafsTer102	p.G725Afs*102	ENST00000375856	NM_003749.2	725	gGc/gc	1/2	1	2	FACETS	0.821	0.714	0.936	0.821	0.714	0.936	CLONAL	1	TRUE	1	0.29	2		432	563	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989590	212989591	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	30	363	0	ENST00000342788.4:c.119_120dup	p.Asp41LeufsTer26	p.D41Lfs*26	ENST00000342788	NM_005235.2	40	-/CT	2/28	1	2	FACETS	0.39	0.313	0.477	0.39	0.313	0.477	SUBCLONAL	1	TRUE	1	0.29	2		363	531	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294057	1294057	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369958224	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	177	894	2	ENST00000310581.5:c.944G>A	p.Arg315His	p.R315H	ENST00000310581	NM_198253.2	315	cGt/cAt	2/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.29	2		896	1114	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645099	86645099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1305400293	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	31	380	0	ENST00000274376.6:c.1171C>T	p.Arg391Trp	p.R391W	ENST00000274376	NM_002890.2	391	Cgg/Tgg	8/25	1	2	FACETS	0.464	0.374	0.565	0.464	0.374	0.565	SUBCLONAL	1	TRUE	1	0.29	2		380	461	SUCCESS
AR	367	MSKCC	GRCh37	X	66765826	66765826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	130	867	1	ENST00000374690.3:c.838C>T	p.Arg280Cys	p.R280C	ENST00000374690	NM_000044.3	280	Cgt/Tgt	1/8	1	2	FACETS	0.759	0.686	0.835	0.759	0.686	0.835	SUBCLONAL	1	TRUE	1	0.29	2		868	1182	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171666	36171666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758682659	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	106	515	1	ENST00000300305.3:c.899C>T	p.Thr300Met	p.T300M	ENST00000300305		300	aCg/aTg	7/8	0.283153515168632	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.29	1		516	568	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191049	185191049	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	142	725	0	ENST00000265026.3:c.1934del	p.Pro645LeufsTer19	p.P645Lfs*19	ENST00000265026	NM_004721.4	644	Ccc/cc	11/14	1	2	FACETS	0.979	0.891	1	0.979	0.891	1	CLONAL	1	TRUE	1	0.29	2		725	1000	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8113516	8113516	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	151	703	0	ENST00000585124.1:c.27del	p.Trp10GlyfsTer12	p.W10Gfs*12	ENST00000585124	NM_004217.3	9	ccC/cc	2/9	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.29	2		703	1009	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604640	55604640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146374006	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	129	582	0	ENST00000288135.5:c.2848G>A	p.Val950Met	p.V950M	ENST00000288135	NM_000222.2	950	Gtg/Atg	21/21	0.204627409440535	1	FACETS	0.971	0.881	1	0.971	0.881	1	CLONAL	1	TRUE	0	0.29	1		582	783	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748583	40748583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444440253	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	68	481	0	ENST00000373198.4:c.2933C>T	p.Ala978Val	p.A978V	ENST00000373198	NM_133170.3	978	gCg/gTg	21/32	1	2	FACETS	0.658	0.572	0.751	0.658	0.572	0.751	SUBCLONAL	1	TRUE	1	0.29	2		481	713	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794925	42794925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768549918	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	71	809	4	ENST00000575354.2:c.2005G>A	p.Ala669Thr	p.A669T	ENST00000575354	NM_015125.3	669	Gcc/Acc	10/20	1	2	FACETS	0.518	0.451	0.591	0.518	0.451	0.591	SUBCLONAL	1	TRUE	1	0.29	2		813	945	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778917	9778917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774975013	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	143	751	0	ENST00000377346.4:c.1186G>A	p.Ala396Thr	p.A396T	ENST00000377346	NM_005026.3	396	Gcc/Acc	9/24	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.29	2		751	964	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	153	941	7	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.99	0.904	1	0.99	0.904	1	CLONAL	1	TRUE	1	0.29	2		948	1066	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743913	40743913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375441200	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	108	569	0	ENST00000373198.4:c.3082G>A	p.Gly1028Arg	p.G1028R	ENST00000373198	NM_133170.3	1028	Gga/Aga	23/32	1	2	FACETS	0.912	0.818	1	0.912	0.818	1	CLONAL	1	TRUE	1	0.29	2		569	817	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512378	149512378	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	89	755	0	ENST00000261799.4:c.1062C>G	p.Asn354Lys	p.N354K	ENST00000261799	NM_002609.3	354	aaC/aaG	7/23	1	2	FACETS	0.661	0.585	0.742	0.661	0.585	0.742	SUBCLONAL	1	TRUE	1	0.29	2		755	929	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46276031	46276031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146235035	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	135	614	0	ENST00000371998.3:c.3467G>A	p.Arg1156Gln	p.R1156Q	ENST00000371998		1156	cGa/cAa	18/23	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.29	2		614	865	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300039	137300040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755912201	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	114	742	4	ENST00000481739.1:c.331dup	p.Leu111ProfsTer70	p.L111Pfs*70	ENST00000481739	NM_002957.4	108	-/C	3/10	1	2	FACETS	0.77	0.692	0.853	0.77	0.692	0.853	SUBCLONAL	1	TRUE	1	0.29	2		746	1021	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122397	17122398	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	rs1555608515	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	136	707	0	ENST00000285071.4:c.997_998del	p.Ser333ArgfsTer56	p.S333Rfs*56	ENST00000285071	NM_144997.5	333	TCa/a	9/14	1	2	FACETS	0.921	0.837	1	0.921	0.837	1	CLONAL	1	TRUE	1	0.29	2		707	1018	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851576	63851576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369904878	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	122	650	0	ENST00000279873.7:c.2354G>A	p.Arg785His	p.R785H	ENST00000279873	NM_032199.2	785	cGc/cAc	10/10	1	2	FACETS	0.962	0.869	1	0.962	0.869	1	CLONAL	1	TRUE	1	0.29	2		650	875	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864218	57864218	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	145	686	2	ENST00000228682.2:c.1700del	p.Pro567LeufsTer46	p.P567Lfs*46	ENST00000228682	NM_005269.2	565	ttC/tt	12/12	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.29	2		688	869	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231557	5231557	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150939732	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	57	489	0	ENST00000357368.4:c.1919G>A	p.Arg640His	p.R640H	ENST00000357368	NM_002850.3	640	cGc/cAc	14/38	1	2	FACETS	0.642	0.551	0.742	0.642	0.551	0.742	SUBCLONAL	1	TRUE	1	0.29	2		489	612	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220184	36220184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	47	644	3	ENST00000222270.7:c.4904G>A	p.Arg1635Gln	p.R1635Q	ENST00000222270	NM_014727.1	1635	cGa/cAa	22/37	1	2	FACETS	0.425	0.357	0.5	0.425	0.357	0.5	SUBCLONAL	1	TRUE	1	0.29	2		647	763	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474338	40474338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	123	599	1	ENST00000264657.5:c.2063G>A	p.Arg688Gln	p.R688Q	ENST00000264657	NM_139276.2	688	cGg/cAg	21/24	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.29	2		600	824	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185041	99185041	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536365553	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	115	478	0	ENST00000074304.5:c.2443G>A	p.Asp815Asn	p.D815N	ENST00000074304	NM_001134224.1	815	Gat/Aat	23/26	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.29	2		478	690	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968342	18968342	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	70	639	0	ENST00000262803.5:c.2182G>T	p.Ala728Ser	p.A728S	ENST00000262803	NM_002911.3	728	Gcg/Tcg	15/24	1	2	FACETS	0.611	0.532	0.697	0.611	0.532	0.697	SUBCLONAL	1	TRUE	1	0.29	2		639	790	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937710	36937710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369185176	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	147	757	1	ENST00000361632.4:c.1028G>A	p.Arg343Gln	p.R343Q	ENST00000361632		343	cGg/cAg	8/16	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.29	2		758	988	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303919	30303919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879397969	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	101	602	0	ENST00000262643.3:c.155C>T	p.Thr52Met	p.T52M	ENST00000262643	NM_001238.2	52	aCg/aTg	4/12	1	2	FACETS	0.863	0.771	0.961	0.863	0.771	0.961	CLONAL	1	TRUE	1	0.29	2		602	807	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031768	36031768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754707860	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	139	593	0	ENST00000358208.4:c.1597G>A	p.Gly533Arg	p.G533R	ENST00000358208		533	Ggg/Agg	12/12	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.29	2		593	901	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879229	151879229	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763438739	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	109	542	1	ENST00000262189.6:c.5716C>T	p.Arg1906Ter	p.R1906*	ENST00000262189	NM_170606.2	1906	Cga/Tga	36/59	1	2	FACETS	0.963	0.864	1	0.963	0.864	1	CLONAL	1	TRUE	1	0.29	2		543	781	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654671	29654671	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760649828	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	79	423	1	ENST00000356175.3:c.5360C>T	p.Thr1787Met	p.T1787M	ENST00000356175	NM_000267.3	1787	aCg/aTg	37/57	1	2	FACETS	0.922	0.812	1	0.922	0.812	1	CLONAL	1	TRUE	1	0.29	2		424	591	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030635	11030635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	120	556	0	ENST00000327064.4:c.1189G>A	p.Gly397Ser	p.G397S	ENST00000327064	NM_199141.1	397	Ggc/Agc	10/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.29	2		556	725	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797375	42797376	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	146	764	0	ENST00000575354.2:c.3743dup	p.Leu1249ThrfsTer6	p.L1249Tfs*6	ENST00000575354	NM_015125.3	1246	agc/agCc	15/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.29	2		764	975	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11018787	11018787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	87	833	0	ENST00000327064.4:c.419G>A	p.Arg140Gln	p.R140Q	ENST00000327064	NM_199141.1	140	cGg/cAg	3/16	1	2	FACETS	0.596	0.527	0.671	0.596	0.527	0.671	SUBCLONAL	1	TRUE	1	0.29	2		833	1006	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643770	52643771	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	145	712	0	ENST00000394830.3:c.2125dup	p.Ile709AsnfsTer14	p.I709Nfs*14	ENST00000394830	NM_018313.4	709	att/aAtt	17/30	0.283153515168632	1	FACETS	0.956	0.872	1	0.956	0.872	1	CLONAL	1	TRUE	0	0.29	1		712	894	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40743949	40743949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145907048	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	135	691	0	ENST00000392038.2:c.758G>A	p.Arg253Gln	p.R253Q	ENST00000392038	NM_001626.4	253	cGg/cAg	9/14	1	2	FACETS	0.981	0.891	1	0.981	0.891	1	CLONAL	1	TRUE	1	0.29	2		691	949	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294420	1294420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	79	655	1	ENST00000310581.5:c.581G>A	p.Arg194Gln	p.R194Q	ENST00000310581	NM_198253.2	194	cGa/cAa	2/16	1	2	FACETS	0.687	0.603	0.777	0.687	0.603	0.777	SUBCLONAL	1	TRUE	1	0.29	2		656	793	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457247	67457247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1566991387	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	130	673	0	ENST00000327367.4:c.221G>A	p.Arg74Gln	p.R74Q	ENST00000327367	NM_005902.3	74	cGg/cAg	2/9	1	2	FACETS	0.935	0.847	1	0.935	0.847	1	CLONAL	1	TRUE	1	0.29	2		673	959	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63829468	63829468	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1001964542	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	66	346	0	ENST00000279873.7:c.1111C>T	p.Arg371Cys	p.R371C	ENST00000279873	NM_032199.2	371	Cgc/Tgc	8/10	1	2	FACETS	0.937	0.815	1	0.937	0.815	1	CLONAL	1	TRUE	1	0.29	2		346	486	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41022125	41022126	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs34091239	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	141	664	1	ENST00000267868.3:c.855dup	p.Pro286ThrfsTer37	p.P286Tfs*37	ENST00000267868	NM_002875.4	283	-/A	9/10	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.29	2		665	937	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107206	27107207	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	110	519	0	ENST00000324856.7:c.6819dup	p.Val2274SerfsTer4	p.V2274Sfs*4	ENST00000324856	NM_006015.4	2273	caa/cAaa	20/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.29	2		519	692	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807503	36807503	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	185	753	0	ENST00000373129.3:c.1161G>T	p.Glu387Asp	p.E387D	ENST00000373129	NM_032017.1	387	gaG/gaT	12/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.29	2		753	1068	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120460342	120460342	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	106	555	0	ENST00000256646.2:c.5973G>T	p.Glu1991Asp	p.E1991D	ENST00000256646	NM_024408.3	1991	gaG/gaT	33/34	1	2	FACETS	0.914	0.819	1	0.914	0.819	1	CLONAL	1	TRUE	1	0.29	2		555	800	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352412	73352412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1458976377	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	108	551	0	ENST00000377767.4:c.493G>A	p.Ala165Thr	p.A165T	ENST00000377767	NM_014953.3	165	Gca/Aca	3/21	1	2	FACETS	0.993	0.892	1	0.993	0.892	1	CLONAL	1	TRUE	1	0.29	2		551	750	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81534600	81534600	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	79	439	1	ENST00000298171.2:c.245A>G	p.Tyr82Cys	p.Y82C	ENST00000298171	NM_000369.2	82	tAc/tGc	3/10	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.29	2		440	534	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619237	23619237	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	137	620	0	ENST00000261584.4:c.3298A>T	p.Thr1100Ser	p.T1100S	ENST00000261584	NM_024675.3	1100	Act/Tct	12/13	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.29	2		620	926	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976568	7976568	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	161	719	0	ENST00000319144.4:c.1824del	p.Leu609Ter	p.L609*	ENST00000319144	NM_001139.2	608	ggG/gg	14/15	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.29	2		719	1061	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5246053	5246053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867992252	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	84	493	2	ENST00000357368.4:c.722G>A	p.Arg241His	p.R241H	ENST00000357368	NM_002850.3	241	cGc/cAc	10/38	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.29	2		495	572	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267401	7267401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545565240	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	114	573	1	ENST00000302850.5:c.607G>A	p.Gly203Arg	p.G203R	ENST00000302850	NM_000208.2	203	Ggg/Agg	2/22	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.29	2		574	710	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032327	11032327	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139191688	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	55	725	0	ENST00000327064.4:c.1721C>T	p.Thr574Met	p.T574M	ENST00000327064	NM_199141.1	574	aCg/aTg	16/16	1	2	FACETS	0.448	0.382	0.52	0.448	0.382	0.52	SUBCLONAL	1	TRUE	1	0.29	2		725	847	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296202	15296203	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	123	828	1	ENST00000263388.2:c.2160_2161dup	p.Glu721ValfsTer140	p.E721Vfs*140	ENST00000263388	NM_000435.2	721	gag/gTGag	14/33	1	2	FACETS	0.878	0.793	0.968	0.878	0.793	0.968	CLONAL	1	TRUE	1	0.29	2		829	966	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211181	36211181	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1454406244	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	101	894	0	ENST00000222270.7:c.932C>T	p.Ala311Val	p.A311V	ENST00000222270	NM_014727.1	311	gCc/gTc	3/37	1	2	FACETS	0.613	0.546	0.684	0.613	0.546	0.684	SUBCLONAL	1	TRUE	1	0.29	2		894	1137	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156099	99156099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755959497	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	188	629	2	ENST00000074304.5:c.779G>A	p.Arg260Gln	p.R260Q	ENST00000074304	NM_001134224.1	260	cGg/cAg	10/26	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.29	2		631	928	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319918	62319918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768582874	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	164	755	0	ENST00000360203.5:c.1760C>T	p.Pro587Leu	p.P587L	ENST00000360203	NM_001283009.1	587	cCg/cTg	21/35	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.29	2		755	1088	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206852	36206852	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	97	534	0	ENST00000300305.3:c.660del	p.Ser222ProfsTer15	p.S222Pfs*15	ENST00000300305		220	tcC/tc	6/8	0.283153515168632	1	FACETS	0.947	0.846	1	0.947	0.846	1	CLONAL	1	TRUE	0	0.29	1		534	604	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665398	182665398	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	69	308	0	ENST00000292782.4:c.543C>G	p.Tyr181Ter	p.Y181*	ENST00000292782	NM_020640.2	181	taC/taG	5/7	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.29	2		308	442	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911097	29911099	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	145	930	0	ENST00000376809.5:c.397_399del	p.Phe133del	p.F133del	ENST00000376809	NM_002116.7	132	cgCTTc/cgc	3/8	1	2	FACETS	0.876	0.798	0.959	0.876	0.798	0.959	CLONAL	1	TRUE	1	0.29	2		930	1141	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651903	36651903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752557277	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	123	738	1	ENST00000244741.5:c.25C>T	p.Arg9Cys	p.R9C	ENST00000244741	NM_000389.4	9	Cgt/Tgt	2/3	1	2	FACETS	0.899	0.812	0.991	0.899	0.812	0.991	CLONAL	1	TRUE	1	0.29	2		739	944	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933691	39933691	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	124	703	0	ENST00000378444.4:c.908C>A	p.Ala303Asp	p.A303D	ENST00000378444	NM_001123385.1	303	gCc/gAc	4/15	1	2	FACETS	0.938	0.848	1	0.938	0.848	1	CLONAL	1	TRUE	1	0.29	2		703	912	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0055319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	62	644	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.14	2		646	819	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0055319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	51	462	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.975	0.827	1	0.975	0.827	1	CLONAL	1	TRUE	1	0.14	2		462	747	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0055320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	77	585	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	FALSE	1	0.379547882739099	2		585	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577115	7577115	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	138	754	1	ENST00000269305.4:c.823T>A	p.Cys275Ser	p.C275S	ENST00000269305	NM_001126112.2	275	Tgt/Agt	8/11	0.379547882739099	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	FALSE	0	0.379547882739099	1		755	562	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0055330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	211	314	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.658365222485377	3	FACETS	0.881	0.842	0.919	0.881	0.842	0.919	CLONAL	3	TRUE	0	0.74865470419465	3		314	293	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0055330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	95	336	0	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	1	2	FACETS	0.843	0.76	0.929	0.843	0.76	0.929	CLONAL	1	TRUE	1	0.74865470419465	2		336	301	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0055330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	116	668	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.783	0.711	0.856	0.783	0.711	0.856	SUBCLONAL	1	TRUE	1	0.74865470419465	2		668	396	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	194	671	2	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	0.316414838072826	2	FACETS	1	0.953	1	0.513	0.479	0.548	INDETERMINATE	1	TRUE	0	0.74865470419465	2		673	505	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653852	89653853	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0055330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	106	381	0	ENST00000371953.3:c.151dup	p.Asp51GlyfsTer2	p.D51Gfs*2	ENST00000371953	NM_000314.4	50	-/G	2/9	0.652524367999962	3	FACETS	1	0.977	1	0.417	0.379	0.457	CLONAL	1	TRUE	0	0.74865470419465	3		381	311	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94153340	94153340	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	61	282	0	ENST00000323929.3:c.2078A>G	p.Asp693Gly	p.D693G	ENST00000323929	NM_005591.3	693	gAt/gGt	20/20	1	2	FACETS	0.915	0.805	1	0.915	0.805	1	CLONAL	1	TRUE	1	0.74865470419465	2		282	178	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0055332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	78	915	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		915	928	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0055333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	363	774	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.438884015797381	2	FACETS	0.92	0.878	0.962	0.92	0.878	0.962	CLONAL	2	TRUE	0	0.506944050993035	2		776	778	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0055333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	303	341	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.402228499163044	4	FACETS	0.997	0.949	1			1	CLONAL	3	TRUE	NA	0.506944050993035	4		341	602	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857758	78857758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs962629512	NA	P-0055333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	378	764	0	ENST00000306801.3:c.1828G>A	p.Asp610Asn	p.D610N	ENST00000306801	NM_020761.2	610	Gac/Aac	16/34	0.450071433698464	3	FACETS	0.868	0.831	0.904	0.868	0.831	0.904	CLONAL	3	TRUE	0	0.506944050993035	3		764	718	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866606	78866606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	445	688	1	ENST00000306801.3:c.2179C>T	p.Arg727Cys	p.R727C	ENST00000306801	NM_020761.2	727	Cgt/Tgt	19/34	0.450071433698464	3	FACETS	0.926	0.891	0.961	0.926	0.891	0.961	CLONAL	3	TRUE	0	0.506944050993035	3		689	792	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218470	1218471	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0055333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	208	632	0	ENST00000326873.7:c.348_349del	p.Leu117IlefsTer45	p.L117Ifs*45	ENST00000326873	NM_000455.4	115	gaTGtg/gatg	2/10	0.470388113615598	2	FACETS	0.789	0.739	0.84	0.789	0.739	0.84	SUBCLONAL	2	TRUE	0	0.506944050993035	2		632	520	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	176	632	1	ENST00000394830.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000394830	NM_018313.4	710	Cga/Tga	17/30	0.476254127352396	3	FACETS	1	0.971	1	0.552	0.509	0.597	CLONAL	1	TRUE	1	0.506944050993035	3		633	788	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629552	187629552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	175	685	0	ENST00000441802.2:c.1430C>T	p.Pro477Leu	p.P477L	ENST00000441802	NM_005245.3	477	cCc/cTc	2/27	0.478891846364969	3	FACETS	1	0.949	1	0.519	0.479	0.562	CLONAL	1	TRUE	1	0.506944050993035	3		685	833	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680388	30680388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748459364	NA	P-0055333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	126	559	0	ENST00000376406.3:c.1331G>A	p.Arg444Gln	p.R444Q	ENST00000376406	NM_014641.2	444	cGa/cAa	5/15	0.506944050993035	3	FACETS	0.765	0.693	0.842	0.383	0.346	0.421	SUBCLONAL	1	TRUE	1	0.506944050993035	3		559	814	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38186924	38186924	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	114	614	0	ENST00000317025.8:c.1553T>G	p.Phe518Cys	p.F518C	ENST00000317025	NM_023034.1	518	tTt/tGt	6/24	0.402228499163044	4	FACETS	0.843	0.759	0.932			1	CLONAL	1	TRUE	NA	0.506944050993035	4		614	804	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370723	55370723	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	82	302	0	ENST00000297316.4:c.25G>A	p.Ala9Thr	p.A9T	ENST00000297316	NM_022454.3	9	Gcc/Acc	1/2	0.506944050993035	7	FACETS	1	0.898	1	0.17	0.149	0.192	CLONAL	1	TRUE	1	0.506944050993035	7		302	719	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	52	115	0				ENST00000310581	NM_198253.2	-/1132			0.141298245639839	4	FACETS	0.943	0.811	1			1	INDETERMINATE	1	TRUE	NA	0.836595598436608	4		115	242	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652198	36652199	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0055334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	969	761	0	ENST00000244741.5:c.322dup	p.Glu108GlyfsTer21	p.E108Gfs*21	ENST00000244741	NM_000389.4	107	gag/gaGg	2/3	0.274007564355373	5	FACETS	0.972	0.952	0.991			1	INDETERMINATE	4	TRUE	NA	0.836595598436608	5		761	1344	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047495	49047495	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0055334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	214	287	0	ENST00000267163.4:c.2490-1G>C		p.X830_splice	ENST00000267163	NM_000321.2	830			NA	2	FACETS	0.934	0.897	0.968			1	INDETERMINATE	2	TRUE	NA	0.836595598436608	2		287	274	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344360	118344360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	168	352	0	ENST00000534358.1:c.2486C>T	p.Ser829Leu	p.S829L	ENST00000534358	NM_005933.3	829	tCa/tTa	3/36	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.836595598436608	2		352	395	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343925	118343925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782402408	NA	P-0055334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	216	372	0	ENST00000534358.1:c.2051C>T	p.Ser684Phe	p.S684F	ENST00000534358	NM_005933.3	684	tCt/tTt	3/36	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.836595598436608	2		372	502	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047658	180047658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753669084	NA	P-0055334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	182	742	0	ENST00000261937.6:c.2357C>T	p.Ala786Val	p.A786V	ENST00000261937	NM_182925.4	786	gCt/gTt	16/30	0.422531481152671	1	FACETS	0.346	0.32	0.373	0.346	0.32	0.373	INDETERMINATE	1	TRUE	0	0.836595598436608	1		742	732	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343608	118343608	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	210	464	0	ENST00000534358.1:c.1734C>G	p.Ile578Met	p.I578M	ENST00000534358	NM_005933.3	578	atC/atG	3/36	1	2	FACETS	0.908	0.85	0.967	0.908	0.85	0.967	CLONAL	1	TRUE	1	0.836595598436608	2		464	553	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099930	27099931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	331	627	0	ENST00000324856.7:c.3810dup	p.Val1271CysfsTer16	p.V1271Cfs*16	ENST00000324856	NM_006015.4	1270	aat/aaTt	15/20	1	2	FACETS	0.914	0.867	0.961	0.914	0.867	0.961	CLONAL	1	TRUE	1	0.836595598436608	2		627	866	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343555	118343555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	215	479	0	ENST00000534358.1:c.1681C>T	p.Pro561Ser	p.P561S	ENST00000534358	NM_005933.3	561	Cca/Tca	3/36	1	2	FACETS	0.983	0.922	1	0.983	0.922	1	CLONAL	1	TRUE	1	0.836595598436608	2		479	523	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244959	133244959	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	197	868	2	ENST00000320574.5:c.2156A>G	p.Glu719Gly	p.E719G	ENST00000320574	NM_006231.2	719	gAg/gGg	19/49	0.452820931950649	3	FACETS	0.572	0.529	0.618	0.286	0.264	0.309	INDETERMINATE	1	TRUE	1	0.836595598436608	3		870	1167	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478058	99478058	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1369647045	NA	P-0055334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	48	413	0	ENST00000268035.6:c.2962G>A	p.Val988Ile	p.V988I	ENST00000268035	NM_000875.3	988	Gtt/Att	16/21	1	2	FACETS	0.222	0.188	0.261	0.222	0.188	0.261	SUBCLONAL	1	TRUE	1	0.836595598436608	2		413	516	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760091	133760095	+	missense_variant	Missense_Mutation	ONP	GCCCG	GCCCG	ACCCA	novel	NA	P-0055334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	202	853	0	ENST00000318560.5:c.2414_2418delinsACCCA	p.Ser805Asn	p.S805N	ENST00000318560	NM_005157.4	805	aGCCCG/aACCCA	11/11	0.422531481152671	1	FACETS	0.408	0.38	0.438	0.408	0.38	0.438	INDETERMINATE	1	TRUE	0	0.836595598436608	1		853	688	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939835	49939835	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371024286	NA	P-0055335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	84	857	0	ENST00000296474.3:c.1208C>T	p.Ser403Leu	p.S403L	ENST00000296474	NM_002447.2	403	tCg/tTg	1/20	0.455403286648462	2	FACETS	0.417	0.368	0.471	0.209	0.184	0.236	SUBCLONAL	1	TRUE	0	0.455403286648462	2		857	884	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579418	7579419	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0055335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	247	847	0	ENST00000269305.4:c.268_269del	p.Ser90LeufsTer58	p.S90Lfs*58	ENST00000269305	NM_001126112.2	90	TCc/c	4/11	0.327420983904603	2	FACETS	1	0.992	1	0.71	0.666	0.755	CLONAL	1	TRUE	0	0.455403286648462	2		847	764	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028821	47028821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782070362	NA	P-0055335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1598	95	884	0	ENST00000377604.3:c.125G>A	p.Arg42His	p.R42H	ENST00000377604	NM_001204468.1	42	cGt/cAt	3/24	0.379571774545025	5	FACETS	0.415	0.367	0.466			1	SUBCLONAL	1	TRUE	NA	0.455403286648462	5		884	1693	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0055339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	54	347	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.431491061899126	NA		347	398	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0055339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	39	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.142869424758841	4	FACETS	0.504	0.418	0.601	0.252	0.209	0.301	INDETERMINATE	1	FALSE	2	0.431491061899126	4		622	513	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0055339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	127	1205	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.431491061899126	2		1205	523	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0055339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	24	343	0	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	0.142869424758841	4	FACETS	0.781	0.615	0.969	0.39	0.307	0.485	INDETERMINATE	1	FALSE	2	0.431491061899126	4		343	204	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372536	55372536	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	107	1202	0	ENST00000297316.4:c.1226G>T	p.Cys409Phe	p.C409F	ENST00000297316	NM_022454.3	409	tGc/tTc	2/2	0.335910057730273	3	FACETS	0.825	0.74	0.915	0.412	0.37	0.458	CLONAL	1	FALSE	1	0.431491061899126	3		1202	731	SUCCESS
APC	324	MSKCC	GRCh37	5	112116486	112116486	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1554072547	NA	P-0055339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	17	282	0	ENST00000257430.4:c.532-1G>A		p.X178_splice	ENST00000257430	NM_000038.5	178			0.142869424758841	4	FACETS	0.728	0.547	0.94	0.364	0.273	0.47	INDETERMINATE	1	FALSE	2	0.431491061899126	4		282	155	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265195	5265195	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	39	1087	0	ENST00000357368.4:c.392C>T	p.Pro131Leu	p.P131L	ENST00000357368	NM_002850.3	131	cCc/cTc	5/38	1	2	FACETS	0.509	0.423	0.605	0.509	0.423	0.605	SUBCLONAL	1	FALSE	1	0.431491061899126	2		1087	355	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762440	41762440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773403341	NA	P-0055339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	59	871	2	ENST00000301178.4:c.2120G>A	p.Arg707His	p.R707H	ENST00000301178	NM_021913.4	707	cGt/cAt	18/20	1	2	FACETS	0.63	0.543	0.724	0.63	0.543	0.724	SUBCLONAL	1	FALSE	1	0.431491061899126	2		873	434	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	20	115	0				ENST00000310581	NM_198253.2	-/1132			0.197697395350855	3	FACETS	0.85	0.684	1	0.85	0.684	1	INDETERMINATE	2	FALSE	1	0.668261911220415	3		115	47	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0055340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	210	472	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	1	2	FACETS	0.89	0.843	0.936	1	0.995	1	CLONAL	2	FALSE	1	0.668261911220415	2		472	353	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134987	41134987	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	52	361	0	ENST00000379561.5:c.641G>C	p.Arg214Pro	p.R214P	ENST00000379561	NM_002015.3	214	cGt/cCt	2/3	0.32737705165967	3	FACETS	0.781	0.682	0.882	0.781	0.682	0.882	INDETERMINATE	2	FALSE	1	0.668261911220415	3		361	133	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472489	88472489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144852342	NA	P-0055341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	221	828	1	ENST00000360948.2:c.2066C>T	p.Ala689Val	p.A689V	ENST00000360948	NM_001012338.2	689	gCg/gTg	16/19	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.435930496701711	2		829	962	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098954	178098954	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	40	410	0	ENST00000397062.3:c.91G>C	p.Gly31Arg	p.G31R	ENST00000397062	NM_006164.4	31	Gga/Cga	2/5	1	2	FACETS	0.405	0.336	0.481	0.405	0.336	0.481	SUBCLONAL	1	TRUE	1	0.435930496701711	2		410	453	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188287	10188287	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs869025650	NA	P-0055341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	192	776	1	ENST00000256474.2:c.430G>T	p.Gly144Ter	p.G144*	ENST00000256474	NM_000551.3	144	Gga/Tga	2/3	0.435930496701711	1	FACETS	0.976	0.906	1	0.976	0.906	1	CLONAL	1	TRUE	0	0.435930496701711	1		777	706	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125290	47125290	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	47	649	0	ENST00000409792.3:c.5980del	p.Arg1994GlyfsTer12	p.R1994Gfs*12	ENST00000409792	NM_014159.6	1994	Agg/gg	12/21	0.435930496701711	1	FACETS	0.335	0.282	0.392	0.335	0.282	0.392	SUBCLONAL	1	TRUE	0	0.435930496701711	1		649	504	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52661362	52661362	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0055341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	134	470	0	ENST00000394830.3:c.1468A>T	p.Arg490Ter	p.R490*	ENST00000394830	NM_018313.4	490	Aga/Tga	14/30	0.435930496701711	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.435930496701711	1		470	422	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157130	106157145	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCACTAGATTTCAT	TGGCACTAGATTTCAT	-	novel	NA	P-0055341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	124	519	0	ENST00000380013.4:c.2032_2047del	p.Gly678PhefsTer17	p.G678Ffs*17	ENST00000380013	NM_001127208.2	677	tgTGGCACTAGATTTCAT/tg	3/11	1	2	FACETS	0.883	0.801	0.97	0.883	0.801	0.97	CLONAL	1	TRUE	1	0.435930496701711	2		519	644	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0055359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	235	700	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	NA	2	FACETS	0.896	0.836	0.957			1	INDETERMINATE	2	FALSE	NA	0.26059517083527	2		700	1007	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142120	108142120	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	47	387	0	ENST00000278616.4:c.3064A>C	p.Ile1022Leu	p.I1022L	ENST00000278616	NM_000051.3	1022	Att/Ctt	20/63	0.26059517083527	3	FACETS	0.751	0.633	0.881	0.375	0.316	0.441	SUBCLONAL	1	FALSE	1	0.26059517083527	3		387	543	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646339	23646339	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	68	544	0	ENST00000261584.4:c.1528A>G	p.Arg510Gly	p.R510G	ENST00000261584	NM_024675.3	510	Aga/Gga	4/13	0.247033168722199	2	FACETS	0.737	0.641	0.842	0.369	0.32	0.421	SUBCLONAL	1	FALSE	0	0.26059517083527	2		544	708	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78938070	78938071	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0055359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	79	779	1	ENST00000306801.3:c.3948_3949delinsTT	p.Ala1317Ser	p.A1317S	ENST00000306801	NM_020761.2	1316	ctGGcc/ctTTcc	34/34	0.26059517083527	3	FACETS	0.701	0.615	0.794	0.351	0.307	0.397	SUBCLONAL	1	FALSE	1	0.26059517083527	3		780	977	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591799	48591827	+	frameshift_variant	Frame_Shift_Del	DEL	AGTATTGGTGTTCCATTGCTTACTTTGAA	AGTATTGGTGTTCCATTGCTTACTTTGAA	-	novel	NA	P-0055359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	37	374	0	ENST00000342988.3:c.963_991del	p.Glu321AspfsTer10	p.E321Dfs*10	ENST00000342988	NM_005359.5	321	gAGTATTGGTGTTCCATTGCTTACTTTGAA/g	9/12	0.13754529135522	1	FACETS	0.678	0.56	0.81	0.678	0.56	0.81	INDETERMINATE	1	FALSE	0	0.26059517083527	1		374	364	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221992	1221992	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	179	788	0	ENST00000326873.7:c.907A>C	p.Ile303Leu	p.I303L	ENST00000326873	NM_000455.4	303	Atc/Ctc	7/10	0.247033168722199	2	FACETS	0.823	0.759	0.888	0.823	0.759	0.888	CLONAL	2	FALSE	0	0.26059517083527	2		788	835	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610349	10610350	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0055359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	200	857	1	ENST00000171111.5:c.360_361delinsTT	p.Met120_Glu121delinsIleTer	p.M120_E121delinsI*	ENST00000171111	NM_203500.1	120	atGGag/atTTag	2/6	0.247033168722199	2	FACETS	0.811	0.752	0.873	0.811	0.752	0.873	CLONAL	2	FALSE	0	0.26059517083527	2		858	946	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376249	225376249	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	107	416	0	ENST00000264414.4:c.705G>C	p.Lys235Asn	p.K235N	ENST00000264414	NM_003590.4	235	aaG/aaC	6/16	0.26059517083527	3	FACETS	0.977	0.881	1	0.977	0.881	1	CLONAL	2	FALSE	1	0.26059517083527	3		416	475	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655248	45655248	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	207	671	0	ENST00000407780.3:c.604G>T	p.Val202Leu	p.V202L	ENST00000407780	NM_001283052.1	202	Gtg/Ttg	4/7	0.247033168722199	2	FACETS	0.951	0.884	1	0.951	0.884	1	CLONAL	2	FALSE	0	0.26059517083527	2		671	835	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31401616	31401616	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	154	571	0	ENST00000344624.3:c.4048C>G	p.Gln1350Glu	p.Q1350E	ENST00000344624		1350	Caa/Gaa	33/33	0.233465507438934	4	FACETS	0.836	0.765	0.91	0.836	0.765	0.91	CLONAL	2	FALSE	2	0.26059517083527	4		571	891	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971199	21971199	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	119	444	0	ENST00000304494.5:c.159G>T	p.Met53Ile	p.M53I	ENST00000304494	NM_000077.4	53	atG/atT	2/3	0.247033168722199	2	FACETS	0.844	0.765	0.927	0.844	0.765	0.927	CLONAL	2	FALSE	0	0.26059517083527	2		444	541	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0055360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	103	237	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.639259921547419	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.639259921547419	1		237	213	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0055360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	338	1032	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.639259921547419	2		1032	986	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856473	111856473	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1002118377	NA	P-0055360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	104	404	0	ENST00000341259.2:c.524G>A	p.Arg175Gln	p.R175Q	ENST00000341259	NM_005475.2	175	cGg/cAg	2/8	1	2	FACETS	0.655	0.589	0.724	0.655	0.589	0.724	SUBCLONAL	1	TRUE	1	0.639259921547419	2		404	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578410	7578410	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	10	722	0	ENST00000269305.4:c.520A>T	p.Arg174Trp	p.R174W	ENST00000269305	NM_001126112.2	174	Agg/Tgg	5/11	0.187162140794402	3	FACETS	0.257	0.173	0.363	0.086	0.057	0.121	SUBCLONAL	1	TRUE	0	0.253913534385716	3		722	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578277	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs1555525902	NA	P-0055361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	72	649	1	ENST00000269305.4:c.572_574del	p.Pro191del	p.P191del	ENST00000269305	NM_001126112.2	191	cCTCag/cag	6/11	0.187162140794402	3	FACETS	0.951	0.837	1	0.634	0.558	0.715	CLONAL	2	TRUE	0	0.253913534385716	3		650	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578429	7578430	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0055361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	11	760	0	ENST00000269305.4:c.499_500dup	p.Gln167HisfsTer4	p.Q167Hfs*4	ENST00000269305	NM_001126112.2	167	cag/caCAg	5/11	0.187162140794402	3	FACETS	0.254	0.174	0.353	0.085	0.058	0.118	SUBCLONAL	1	TRUE	0	0.253913534385716	3		760	385	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737819	145737819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750261857	NA	P-0055361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	59	827	3	ENST00000428558.2:c.3011G>A	p.Arg1004Gln	p.R1004Q	ENST00000428558	NM_004260.3	1004	cGg/cAg	18/22	0.253913534385716	8	FACETS	1	0.966	1	0.241	0.207	0.278	CLONAL	1	TRUE	2	0.253913534385716	8		830	567	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792335	33792335	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	36	808	0	ENST00000498907.2:c.986A>G	p.Glu329Gly	p.E329G	ENST00000498907	NM_004364.3	329	gAa/gGa	1/1	0.210536883560123	3	FACETS	0.731	0.601	0.877	0.366	0.3	0.439	SUBCLONAL	1	TRUE	1	0.253913534385716	3		808	437	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362639	118362639	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782779521	NA	P-0055361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	29	300	2	ENST00000534358.1:c.5000G>A	p.Arg1667Gln	p.R1667Q	ENST00000534358	NM_005933.3	1667	cGg/cAg	15/36	0.175104988465872	4	FACETS	0.847	0.681	1	0.282	0.227	0.346	CLONAL	1	TRUE	1	0.253913534385716	4		302	338	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098564	108098564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762382111	NA	P-0055361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	24	216	0	ENST00000278616.4:c.134G>A	p.Arg45Gln	p.R45Q	ENST00000278616	NM_000051.3	45	cGg/cAg	3/63	0.175104988465872	4	FACETS	0.812	0.637	1	0.271	0.212	0.338	CLONAL	1	TRUE	1	0.253913534385716	4		216	292	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129195	152129195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140555278	NA	P-0055361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	120	817	1	ENST00000206249.3:c.148G>A	p.Ala50Thr	p.A50T	ENST00000206249	NM_000125.3	50	Gcc/Acc	1/8	0.245769496703641	4	FACETS	1	0.976	1	0.821	0.746	0.9	CLONAL	2	TRUE	1	0.253913534385716	4		818	481	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0055364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	212	689	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.328117858567947	2	FACETS	0.932	0.872	0.994	0.932	0.872	0.994	CLONAL	2	TRUE	0	0.384831130472215	2		690	591	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0055364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	89	378	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.179138221369574	3	FACETS	0.836	0.748	0.927	0.557	0.499	0.618	INDETERMINATE	2	TRUE	0	0.384831130472215	3		378	330	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0055364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	79	196	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.384831130472215	2	FACETS	0.925	0.828	1	0.925	0.828	1	CLONAL	2	TRUE	0	0.384831130472215	2		196	222	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920437	114920437	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	226	445	0	ENST00000543371.1:c.1378T>C	p.Cys460Arg	p.C460R	ENST00000543371	NM_001198531.1	460	Tgc/Cgc	13/14	0.179875163312727	3	FACETS	1	0.986	1	0.782	0.734	0.831	INDETERMINATE	2	TRUE	0	0.384831130472215	3		445	597	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278049	18278049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	122	644	0	ENST00000222254.8:c.1669G>A	p.Asp557Asn	p.D557N	ENST00000222254	NM_005027.3	557	Gac/Aac	13/16	0.380185461597378	3	FACETS	0.843	0.761	0.929	0.421	0.38	0.465	CLONAL	1	TRUE	1	0.384831130472215	3		644	897	SUCCESS
APC	324	MSKCC	GRCh37	5	112175218	112175219	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAGATTGGAACTAGGTCAGCTG	novel	NA	P-0055364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	33	185	0	ENST00000257430.4:c.3933_3954dup	p.Pro1319TrpfsTer3	p.P1319Wfs*3	ENST00000257430	NM_000038.5	1309	-/AAGATTGGAACTAGGTCAGCTG	16/16	0.384831130472215	2	FACETS	0.937	0.771	1	0.469	0.385	0.56	CLONAL	1	TRUE	0	0.384831130472215	2		185	183	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0055365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	54	535	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.998	0.853	1	0.998	0.853	1	CLONAL	1	TRUE	1	0.2	2		535	541	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207021	1207021	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913324	NA	P-0055365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	78	617	0	ENST00000326873.7:c.109C>T	p.Gln37Ter	p.Q37*	ENST00000326873	NM_000455.4	37	Cag/Tag	1/10	1	2	FACETS	0.878	0.77	0.995	0.878	0.77	0.995	CLONAL	1	TRUE	1	0.2	2		617	888	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0055365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	37	590	1	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	1	2	FACETS	0.535	0.439	0.642	0.535	0.439	0.642	SUBCLONAL	1	TRUE	1	0.2	2		591	692	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372320	55372320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	90	664	0	ENST00000297316.4:c.1010C>T	p.Pro337Leu	p.P337L	ENST00000297316	NM_022454.3	337	cCg/cTg	2/2	1	2	FACETS	0.902	0.798	1	0.902	0.798	1	CLONAL	1	TRUE	1	0.2	2		664	998	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0055365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	44	348	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	1	2	FACETS	0.806	0.675	0.951	0.806	0.675	0.951	CLONAL	1	TRUE	1	0.2	2		348	546	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663317	67663317	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	35	292	0	ENST00000264010.4:c.1718A>G	p.His573Arg	p.H573R	ENST00000264010	NM_006565.3	573	cAt/cGt	10/12	1	2	FACETS	0.749	0.614	0.902	0.749	0.614	0.902	CLONAL	1	TRUE	1	0.2	2		292	467	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610501	10610501	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	73	627	0	ENST00000171111.5:c.209T>A	p.Leu70Gln	p.L70Q	ENST00000171111	NM_203500.1	70	cTg/cAg	2/6	1	2	FACETS	0.841	0.734	0.957	0.841	0.734	0.957	CLONAL	1	TRUE	1	0.2	2		627	868	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64126759	64126759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	93	506	1	ENST00000334205.4:c.52G>A	p.Glu18Lys	p.E18K	ENST00000334205	NM_003942.2	18	Gaa/Aaa	1/17	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.2	2		507	747	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779658	3779659	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0055365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	73	628	0	ENST00000262367.5:c.5388_5389dup	p.Lys1797ArgfsTer3	p.K1797Rfs*3	ENST00000262367	NM_004380.2	1797	aag/aGAag	31/31	1	2	FACETS	0.749	0.653	0.852	0.749	0.653	0.852	SUBCLONAL	1	TRUE	1	0.2	2		628	975	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086192	16086192	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	41	374	0	ENST00000281043.3:c.1368G>C	p.Lys456Asn	p.K456N	ENST00000281043	NM_005378.4	456	aaG/aaC	3/3	1	2	FACETS	0.775	0.645	0.92	0.775	0.645	0.92	CLONAL	1	TRUE	1	0.2	2		374	529	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009107	27009116	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCGCAGCC	AGGCGCAGCC	-	novel	NA	P-0055365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	19	157	0	ENST00000335756.4:c.43_52del	p.Arg16AlafsTer15	p.R16Afs*15	ENST00000335756	NM_001809.3	15	AGGCGCAGCCcg/cg	1/5	1	2	FACETS	0.691	0.525	0.886	0.691	0.525	0.886	SUBCLONAL	1	TRUE	1	0.2	2		157	275	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665144	138665144	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	70	505	1	ENST00000330315.3:c.421G>T	p.Gly141Cys	p.G141C	ENST00000330315	NM_023067.3	141	Ggc/Tgc	1/1	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.2	2		506	695	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531150	187531150	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	32	237	0	ENST00000441802.2:c.9873G>C	p.Glu3291Asp	p.E3291D	ENST00000441802	NM_005245.3	3291	gaG/gaC	15/27	1	2	FACETS	0.771	0.626	0.935	0.771	0.626	0.935	CLONAL	1	TRUE	1	0.2	2		237	415	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877043	151877043	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	46	386	0	ENST00000262189.6:c.7318C>G	p.Pro2440Ala	p.P2440A	ENST00000262189	NM_170606.2	2440	Cct/Gct	37/59	1	2	FACETS	0.85	0.716	0.999	0.85	0.716	0.999	CLONAL	1	TRUE	1	0.2	2		386	541	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813110	76813110	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	32	307	0	ENST00000373344.5:c.6511A>G	p.Met2171Val	p.M2171V	ENST00000373344	NM_000489.3	2171	Atg/Gtg	30/35	1	2	FACETS	0.652	0.528	0.792	0.652	0.528	0.792	SUBCLONAL	1	TRUE	1	0.2	2		307	491	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0055366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	113	411	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	0.488928948324341	6	FACETS	0.944	0.869	1	0.944	0.869	1	CLONAL	4	TRUE	2	0.552872742173878	6		411	228	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0055366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	424	716	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.552105708826393	2	FACETS	0.999	0.96	1	0.999	0.96	1	CLONAL	2	TRUE	0	0.552872742173878	2		716	768	SUCCESS
APC	324	MSKCC	GRCh37	5	112157627	112157628	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs1554080698	NA	P-0055366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	59	350	0	ENST00000257430.4:c.1354_1355del	p.Val452SerfsTer7	p.V452Sfs*7	ENST00000257430	NM_000038.5	449	gcTGtg/gctg	11/16	0.175908134315574	4	FACETS	0.804	0.703	0.912	0.804	0.703	0.912	INDETERMINATE	2	TRUE	2	0.552872742173878	4		350	206	SUCCESS
APC	324	MSKCC	GRCh37	5	112170746	112170747	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	122	410	0	ENST00000257430.4:c.1847dup	p.Leu616PhefsTer18	p.L616Ffs*18	ENST00000257430	NM_000038.5	614	-/T	15/16	0.175908134315574	4	FACETS	0.781	0.711	0.853	0.781	0.711	0.853	INDETERMINATE	2	TRUE	2	0.552872742173878	4		410	439	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928346	69928346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	109	347	0	ENST00000352241.4:c.166C>T	p.Arg56Cys	p.R56C	ENST00000352241	NM_198159.2	56	Cgc/Tgc	2/10	0.301585657591551	5	FACETS	0.859	0.777	0.944	0.572	0.518	0.63	INDETERMINATE	2	TRUE	2	0.552872742173878	5		347	420	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100904	27100904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	269	403	0	ENST00000324856.7:c.4188del	p.Gln1397ArgfsTer84	p.Q1397Rfs*84	ENST00000324856	NM_006015.4	1396	Ggg/gg	18/20	0.552105708826393	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.552872742173878	2		403	457	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0055367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	52	285	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.205108992894696	2		285	400	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274097	18274097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751032325	NA	P-0055367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	65	540	0	ENST00000222254.8:c.1315G>A	p.Val439Met	p.V439M	ENST00000222254	NM_005027.3	439	Gtg/Atg	11/16	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.205108992894696	2		540	633	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853329	68853329	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs886041161	NA	P-0055367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	43	456	0	ENST00000261769.5:c.1711+1G>A		p.X571_splice	ENST00000261769	NM_004360.3	571			0.205108992894696	1	FACETS	0.849	0.711	1	0.849	0.711	1	CLONAL	1	TRUE	0	0.205108992894696	1		456	443	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100628	8100628	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	96	720	1	ENST00000346208.3:c.604del	p.Arg202ValfsTer4	p.R202Vfs*4	ENST00000346208		201	tCc/tc	3/6	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.205108992894696	2		721	803	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791825	42791825	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	61	654	0	ENST00000575354.2:c.711G>A	p.Trp237Ter	p.W237*	ENST00000575354	NM_015125.3	237	tgG/tgA	5/20	1	2	FACETS	0.926	0.799	1	0.926	0.799	1	CLONAL	1	TRUE	1	0.205108992894696	2		654	642	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0055368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	101	421	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.295449247042125	3	FACETS	1	0.972	1	0.801	0.726	0.878	CLONAL	2	TRUE	0	0.340603532547527	3		423	289	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058033	27058033	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	147	497	0	ENST00000324856.7:c.1741C>T	p.Gln581Ter	p.Q581*	ENST00000324856	NM_006015.4	581	Cag/Tag	3/20	0.316887863277454	2	FACETS	0.942	0.868	1	0.942	0.868	1	CLONAL	2	TRUE	0	0.340603532547527	2		497	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579317	7579317	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	170	485	0	ENST00000269305.4:c.370T>C	p.Cys124Arg	p.C124R	ENST00000269305	NM_001126112.2	124	Tgc/Cgc	4/11	0.316887863277454	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.340603532547527	2		485	463	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851591	134851591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748976557	NA	P-0055368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	72	518	1	ENST00000398015.3:c.997G>A	p.Val333Ile	p.V333I	ENST00000398015	NM_004441.4	333	Gtc/Atc	5/16	0.340603532547527	3	FACETS	1	0.944	1	0.569	0.499	0.644	CLONAL	1	TRUE	1	0.340603532547527	3		519	435	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183788	10183788	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882034	NA	P-0055373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	167	660	0	ENST00000256474.2:c.257C>G	p.Pro86Arg	p.P86R	ENST00000256474	NM_000551.3	86	cCc/cGc	1/3	0.453762697173885	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.45	1		660	557	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712595	52712595	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	63	279	0	ENST00000394830.3:c.157del	p.Leu53SerfsTer42	p.L53Sfs*42	ENST00000394830	NM_018313.4	53	Ctc/tc	3/30	0.453762697173885	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.45	1		279	207	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342647	70342647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	315	551	3	ENST00000374080.3:c.1408C>T	p.Arg470Cys	p.R470C	ENST00000374080		470	Cgc/Tgc	10/45	1	2	FACETS	0.864	0.82	0.908	1	0.996	1	CLONAL	2	FALSE	1	0.487980763550061	2		554	747	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098963	47098963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	47	394	0	ENST00000409792.3:c.6311C>T	p.Ser2104Phe	p.S2104F	ENST00000409792	NM_014159.6	2104	tCt/tTt	15/21	1	2	FACETS	0.325	0.274	0.382	0.325	0.274	0.382	SUBCLONAL	1	FALSE	1	0.487980763550061	2		394	592	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272502	11272502	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752142242	NA	P-0055375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	126	349	6	ENST00000361445.4:c.3428C>T	p.Thr1143Met	p.T1143M	ENST00000361445	NM_004958.3	1143	aCg/aTg	23/58	0.44359489303865	1	FACETS	0.925	0.845	1	0.925	0.845	1	CLONAL	1	FALSE	0	0.487980763550061	1		355	422	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846144	68846145	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0055375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	340	500	7	ENST00000261769.5:c.1116_1117del	p.Pro373AspfsTer13	p.P373Dfs*13	ENST00000261769	NM_004360.3	372	cCT/c	8/16	0.425843681181766	0	FACETS		NA	1			1	NA	3	FALSE	0	0.487980763550061	0		507	412	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425776	49425776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123714	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	345	571	2	ENST00000301067.7:c.12712C>T	p.Arg4238Cys	p.R4238C	ENST00000301067	NM_003482.3	4238	Cgc/Tgc	39/54	1	2	FACETS	0.943	0.896	0.99	0.943	0.896	0.99	CLONAL	1	TRUE	1	0.86	2		573	851	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	160	259	2	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	0.916	0.85	0.984	0.916	0.85	0.984	CLONAL	1	TRUE	1	0.86	2		261	406	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	270	559	3	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.918	0.867	0.97	0.918	0.867	0.97	CLONAL	1	TRUE	1	0.86	2		562	684	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755128667	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	47	610	2	ENST00000407977.2:c.1976dup	p.Pro660SerfsTer87	p.P660Sfs*87	ENST00000407977		659	ggt/ggGt	9/10	1	2	FACETS	0.13	0.109	0.153	0.13	0.109	0.153	SUBCLONAL	1	TRUE	1	0.86	2		612	841	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806119	1806119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931614	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	497	699	0	ENST00000260795.2:c.1138G>A	p.Gly380Arg	p.G380R	ENST00000260795		380	Ggg/Agg	8/17	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.86	2		699	1083	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437697	52437697	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1553644922	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	50	594	0	ENST00000460680.1:c.1464del	p.Ser489AlafsTer82	p.S489Afs*82	ENST00000460680	NM_004656.3	488	ccC/cc	13/17	1	2	FACETS	0.129	0.108	0.151	0.129	0.108	0.151	SUBCLONAL	1	TRUE	1	0.86	2		594	903	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	249	387	0	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	0.915	0.862	0.969	0.915	0.862	0.969	CLONAL	1	TRUE	1	0.86	2		387	633	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909629	76909629	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs919106518	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	31	421	0	ENST00000373344.5:c.4276C>T	p.Arg1426Ter	p.R1426*	ENST00000373344	NM_000489.3	1426	Cga/Tga	14/35	1	2	FACETS	0.16	0.129	0.195	0.16	0.129	0.195	SUBCLONAL	1	TRUE	1	0.86	2		421	450	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	361	658	1	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.86	2		659	792	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	169	376	0	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	1	2	FACETS	0.797	0.739	0.857	0.797	0.739	0.857	SUBCLONAL	1	TRUE	1	0.86	2		376	493	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	190	602	2	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	0.808	0.752	0.865	0.808	0.752	0.865	CLONAL	1	TRUE	1	0.86	2		604	547	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931452	131931452	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507178	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	185	243	6	ENST00000265335.6:c.2165del	p.Lys722ArgfsTer14	p.K722Rfs*14	ENST00000265335		719	ctA/ct	13/25	1	2	FACETS	0.969	0.905	1	0.969	0.905	1	CLONAL	1	TRUE	1	0.86	2		249	444	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	257	471	2	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.943	0.889	0.997	0.943	0.889	0.997	CLONAL	1	TRUE	1	0.86	2		473	634	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278099	15278099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139983430	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	411	642	0	ENST00000263388.2:c.5323G>A	p.Ala1775Thr	p.A1775T	ENST00000263388	NM_000435.2	1775	Gca/Aca	29/33	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.86	2		642	929	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	173	368	0	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.86	2		368	398	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997826	149997826	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	270	409	0	ENST00000253339.5:c.2641del	p.Asp881IlefsTer11	p.D881Ifs*11	ENST00000253339		881	Gat/at	5/7	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.86	2		409	623	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533535	533535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	289	745	1	ENST00000451590.1:c.368G>A	p.Arg123His	p.R123H	ENST00000451590	NM_001130442.1	123	cGc/cAc	4/5	1	2	FACETS	0.654	0.616	0.694	0.654	0.616	0.694	SUBCLONAL	1	TRUE	1	0.86	2		746	1027	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026204	48026204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750440	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	36	265	0	ENST00000234420.5:c.1082G>A	p.Arg361His	p.R361H	ENST00000234420	NM_000179.2	361	cGc/cAc	4/10	1	2	FACETS	0.197	0.161	0.236	0.197	0.161	0.236	SUBCLONAL	1	TRUE	1	0.86	2		265	426	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119758	70119758	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	246	611	1	ENST00000245479.2:c.760C>T	p.Arg254Ter	p.R254*	ENST00000245479	NM_000346.3	254	Cga/Tga	3/3	1	2	FACETS	0.712	0.667	0.757	0.712	0.667	0.757	SUBCLONAL	1	TRUE	1	0.86	2		612	804	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70412277	70412277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	119	195	0	ENST00000373644.4:c.4387G>A	p.Ala1463Thr	p.A1463T	ENST00000373644	NM_030625.2	1463	Gca/Aca	6/12	1	2	FACETS	0.852	0.779	0.926	0.852	0.779	0.926	CLONAL	1	TRUE	1	0.86	2		195	325	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661663	227661664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761880048	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	408	468	13	ENST00000305123.5:c.1791dup	p.His598AlafsTer13	p.H598Afs*13	ENST00000305123	NM_005544.2	597	-/G	1/2	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.86	2		481	709	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156719	20156719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	226	400	0	ENST00000379607.5:c.38G>A	p.Arg13His	p.R13H	ENST00000379607	NM_001412.3	13	cGc/cAc	2/7	1	2	FACETS	0.954	0.896	1	0.954	0.896	1	CLONAL	1	TRUE	1	0.86	2		400	551	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557725	21557725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs915063122	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	65	598	0	ENST00000382592.4:c.2120G>A	p.Arg707Gln	p.R707Q	ENST00000382592	NM_014572.2	707	cGg/cAg	5/8	1	2	FACETS	0.179	0.155	0.206	0.179	0.155	0.206	SUBCLONAL	1	TRUE	1	0.86	2		598	843	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955112	17955112	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755706305	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	425	718	4	ENST00000458235.1:c.115del	p.Gln39SerfsTer108	p.Q39Sfs*108	ENST00000458235	NM_000215.3	39	Cag/ag	2/24	1	2	FACETS	0.96	0.917	1	0.96	0.917	1	CLONAL	1	TRUE	1	0.86	2		722	1030	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200073	128200073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374457534	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	66	750	0	ENST00000341105.2:c.1232C>T	p.Ala411Val	p.A411V	ENST00000341105	NM_032638.4	411	gCg/gTg	6/6	1	2	FACETS	0.142	0.123	0.163	0.142	0.123	0.163	SUBCLONAL	1	TRUE	1	0.86	2		750	1080	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413105	63413105	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374303948	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	332	650	0	ENST00000330258.3:c.62G>A	p.Arg21His	p.R21H	ENST00000330258	NM_152424.3	21	cGt/cAt	2/2	1	2	FACETS	0.913	0.866	0.959	0.913	0.866	0.959	CLONAL	1	TRUE	1	0.86	2		650	846	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021250	31021250	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs375215583	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	53	426	0	ENST00000375687.4:c.1249C>T	p.Arg417Ter	p.R417*	ENST00000375687	NM_015338.5	417	Cga/Tga	12/13	1	2	FACETS	0.18	0.153	0.209	0.18	0.153	0.209	SUBCLONAL	1	TRUE	1	0.86	2		426	686	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546560	9546560	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771840400	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	163	427	0	ENST00000353224.5:c.1462C>T	p.Arg488Ter	p.R488*	ENST00000353224	NM_177990.2	488	Cga/Tga	5/10	1	2	FACETS	0.732	0.676	0.789	0.732	0.676	0.789	SUBCLONAL	1	TRUE	1	0.86	2		427	518	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469614	25469614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775677376	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	341	584	0	ENST00000264709.3:c.1154C>T	p.Pro385Leu	p.P385L	ENST00000264709	NM_175629.2	385	cCg/cTg	10/23	1	2	FACETS	0.912	0.866	0.958	0.912	0.866	0.958	CLONAL	1	TRUE	1	0.86	2		584	870	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	69061312	69061313	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	72	106	0	ENST00000487270.1:c.1153dup	p.Ter385LeufsTer15	p.*385Lfs*15	ENST00000487270	NM_133509.3	383	att/aTtt	11/11	1	2	FACETS	0.809	0.719	0.901	0.809	0.719	0.901	CLONAL	1	TRUE	1	0.86	2		106	207	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976100	18976100	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs750432625	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	303	531	0	ENST00000262803.5:c.2860C>T	p.Arg954Trp	p.R954W	ENST00000262803	NM_002911.3	954	Cgg/Tgg	21/24	1	2	FACETS	0.969	0.919	1	0.969	0.919	1	CLONAL	1	TRUE	1	0.86	2		531	727	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403116	116403116	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45440991	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	42	304	2	ENST00000397752.3:c.2377C>T	p.Arg793Cys	p.R793C	ENST00000397752	NM_000245.2	793	Cgc/Tgc	11/21	1	2	FACETS	0.222	0.185	0.263	0.222	0.185	0.263	SUBCLONAL	1	TRUE	1	0.86	2		306	440	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	268	468	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	0.829	0.781	0.878	0.829	0.781	0.878	CLONAL	1	TRUE	1	0.86	2		468	752	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	427	699	7	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.905	0.865	0.946	0.905	0.865	0.946	CLONAL	1	TRUE	1	0.86	2		706	1097	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144509	11144509	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778685	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	42	572	0	ENST00000358026.2:c.3841G>A	p.Val1281Ile	p.V1281I	ENST00000358026	NM_001128849.1	1281	Gtc/Atc	27/36	1	2	FACETS	0.122	0.101	0.145	0.122	0.101	0.145	SUBCLONAL	1	TRUE	1	0.86	2		572	802	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037144	71037144	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	133	457	0	ENST00000318789.4:c.1146+1G>A		p.X382_splice	ENST00000318789	NM_032682.5	382			1	2	FACETS	0.684	0.626	0.744	0.684	0.626	0.744	SUBCLONAL	1	TRUE	1	0.86	2		457	452	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424970	49424970	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783691	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	388	759	1	ENST00000301067.7:c.13518del	p.Ser4507AlafsTer12	p.S4507Afs*12	ENST00000301067	NM_003482.3	4506	ccC/cc	39/54	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.86	2		760	894	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478220	99478220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	180	285	1	ENST00000268035.6:c.3124C>T	p.Arg1042Cys	p.R1042C	ENST00000268035	NM_000875.3	1042	Cgt/Tgt	16/21	1	2	FACETS	0.926	0.863	0.99	0.926	0.863	0.99	CLONAL	1	TRUE	1	0.86	2		286	452	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549394	21549394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148935054	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	297	474	2	ENST00000382592.4:c.2882G>A	p.Arg961Gln	p.R961Q	ENST00000382592	NM_014572.2	961	cGg/cAg	8/8	1	2	FACETS	0.971	0.921	1	0.971	0.921	1	CLONAL	1	TRUE	1	0.86	2		476	711	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584478	52584478	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142726131	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	108	379	1	ENST00000394830.3:c.4535C>T	p.Ala1512Val	p.A1512V	ENST00000394830	NM_018313.4	1512	gCg/gTg	29/30	1	2	FACETS	0.408	0.367	0.452	0.408	0.367	0.452	SUBCLONAL	1	TRUE	1	0.86	2		380	615	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50483719	50483719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746898820	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	229	491	0	ENST00000394963.4:c.824C>T	p.Pro275Leu	p.P275L	ENST00000394963	NM_003076.4	275	cCg/cTg	7/13	1	2	FACETS	0.918	0.863	0.975	0.918	0.863	0.975	CLONAL	1	TRUE	1	0.86	2		491	580	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115852	8115853	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs1085307641	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	363	531	0	ENST00000346208.3:c.1198_1199del	p.Met400ValfsTer106	p.M400Vfs*106	ENST00000346208		400	ATg/g	6/6	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.86	2		531	825	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222522	2222523	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs750035555	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	272	677	0	ENST00000326181.6:c.722dup	p.Leu242AlafsTer55	p.L242Afs*55	ENST00000326181	NM_032271.2	239	tgc/tgCc	9/21	1	2	FACETS	0.64	0.601	0.679	0.64	0.601	0.679	SUBCLONAL	1	TRUE	1	0.86	2		677	989	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211685	36211685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1416954696	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	373	562	0	ENST00000222270.7:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000222270	NM_014727.1	479	cGg/cAg	3/37	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.86	2		562	857	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523333	176523333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780720945	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	66	703	0	ENST00000292408.4:c.1990C>T	p.Arg664Trp	p.R664W	ENST00000292408	NM_213647.1	664	Cgg/Tgg	15/18	1	2	FACETS	0.158	0.136	0.181	0.158	0.136	0.181	SUBCLONAL	1	TRUE	1	0.86	2		703	972	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026115	71026115	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs797045584	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	58	271	0	ENST00000318789.4:c.1507C>T	p.Arg503Ter	p.R503*	ENST00000318789	NM_032682.5	503	Cga/Tga	17/21	1	2	FACETS	0.293	0.252	0.337	0.293	0.252	0.337	SUBCLONAL	1	TRUE	1	0.86	2		271	461	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274657	123274657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	258	428	0	ENST00000358487.5:c.1261C>T	p.Arg421Cys	p.R421C	ENST00000358487	NM_000141.4	421	Cgt/Tgt	9/18	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.86	2		428	598	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120469232	120469232	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs371580595	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	185	308	0	ENST00000256646.2:c.3895C>T	p.Arg1299Trp	p.R1299W	ENST00000256646	NM_024408.3	1299	Cgg/Tgg	24/34	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.86	2		308	421	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823928	3823928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768288810	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	48	521	1	ENST00000262367.5:c.2287G>A	p.Ala763Thr	p.A763T	ENST00000262367	NM_004380.2	763	Gcc/Acc	13/31	1	2	FACETS	0.147	0.123	0.173	0.147	0.123	0.173	SUBCLONAL	1	TRUE	1	0.86	2		522	761	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645310	67645310	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	273	507	0	ENST00000264010.4:c.579del	p.Asp194ThrfsTer28	p.D194Tfs*28	ENST00000264010	NM_006565.3	192	cAa/ca	3/12	1	2	FACETS	0.914	0.863	0.965	0.914	0.863	0.965	CLONAL	1	TRUE	1	0.86	2		507	695	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298066	15298066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374767079	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	478	712	1	ENST00000263388.2:c.1690G>A	p.Ala564Thr	p.A564T	ENST00000263388	NM_000435.2	564	Gcc/Acc	11/33	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.86	2		713	1040	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285015	15285015	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1337308187	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	432	693	2	ENST00000263388.2:c.4600C>T	p.Arg1534Trp	p.R1534W	ENST00000263388	NM_000435.2	1534	Cgg/Tgg	25/33	1	2	FACETS	0.976	0.934	1	0.976	0.934	1	CLONAL	1	TRUE	1	0.86	2		695	1029	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813088	76813088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	29	394	0	ENST00000373344.5:c.6533G>A	p.Arg2178Gln	p.R2178Q	ENST00000373344	NM_000489.3	2178	cGg/cAg	30/35	1	2	FACETS	0.125	0.099	0.153	0.125	0.099	0.153	SUBCLONAL	1	TRUE	1	0.86	2		394	541	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46543254	46543254	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	188	376	0	ENST00000262741.5:c.247C>T	p.Pro83Ser	p.P83S	ENST00000262741	NM_003629.3	83	Cca/Tca	3/10	1	2	FACETS	0.804	0.748	0.861	0.804	0.748	0.861	CLONAL	1	TRUE	1	0.86	2		376	544	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249830	133249830	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771526654	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	216	346	0	ENST00000320574.5:c.1393G>A	p.Ala465Thr	p.A465T	ENST00000320574	NM_006231.2	465	Gcc/Acc	14/49	1	2	FACETS	0.922	0.864	0.98	0.922	0.864	0.98	CLONAL	1	TRUE	1	0.86	2		346	545	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396974	396974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1170182478	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	50	563	0	ENST00000262320.3:c.52G>A	p.Glu18Lys	p.E18K	ENST00000262320	NM_003502.3	18	Gaa/Aaa	2/11	1	2	FACETS	0.135	0.114	0.159	0.135	0.114	0.159	SUBCLONAL	1	TRUE	1	0.86	2		563	859	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131201	17131201	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs939223011	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	330	605	0	ENST00000285071.4:c.249+2C>T		p.X83_splice	ENST00000285071	NM_144997.5	83			1	2	FACETS	0.874	0.829	0.92	0.874	0.829	0.92	CLONAL	1	TRUE	1	0.86	2		605	878	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487553	38487554	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	320	558	0	ENST00000254066.5:c.89dup	p.Met31TyrfsTer21	p.M31Yfs*21	ENST00000254066	NM_000964.3	28	ttc/ttCc	2/9	1	2	FACETS	0.874	0.829	0.921	0.874	0.829	0.921	CLONAL	1	TRUE	1	0.86	2		558	851	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290919	15290919	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	431	788	1	ENST00000263388.2:c.3291del	p.Thr1098ProfsTer174	p.T1098Pfs*174	ENST00000263388	NM_000435.2	1097	ggG/gg	20/33	1	2	FACETS	0.89	0.85	0.931	0.89	0.85	0.931	CLONAL	1	TRUE	1	0.86	2		789	1126	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741933	40741933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145305228	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	265	785	0	ENST00000392038.2:c.1039C>T	p.Arg347Cys	p.R347C	ENST00000392038	NM_001626.4	347	Cgc/Tgc	11/14	1	2	FACETS	0.647	0.607	0.687	0.647	0.607	0.687	SUBCLONAL	1	TRUE	1	0.86	2		785	953	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416397	29416399	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	397	643	0	ENST00000389048.3:c.4554_4556del	p.Lys1518del	p.K1518del	ENST00000389048	NM_004304.4	1518	aaGAAt/aat	29/29	1	2	FACETS	0.957	0.913	1	0.957	0.913	1	CLONAL	1	TRUE	1	0.86	2		643	965	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46277813	46277813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758545305	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	156	300	0	ENST00000371998.3:c.3611C>T	p.Ala1204Val	p.A1204V	ENST00000371998		1204	gCg/gTg	19/23	1	2	FACETS	0.797	0.737	0.859	0.797	0.737	0.859	SUBCLONAL	1	TRUE	1	0.86	2		300	455	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573728	41573728	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	354	632	1	ENST00000263253.7:c.6013C>T	p.Gln2005Ter	p.Q2005*	ENST00000263253	NM_001429.3	2005	Caa/Taa	31/31	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.86	2		633	813	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047196	180047196	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	63	585	0	ENST00000261937.6:c.2519T>C	p.Phe840Ser	p.F840S	ENST00000261937	NM_182925.4	840	tTc/tCc	17/30	1	2	FACETS	0.17	0.147	0.196	0.17	0.147	0.196	SUBCLONAL	1	TRUE	1	0.86	2		585	860	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965402	68965405	+	frameshift_variant	Frame_Shift_Del	DEL	GTTT	GTTT	-	novel	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	184	528	0	ENST00000288368.4:c.1020_1023del	p.Cys341TrpfsTer16	p.C341Wfs*16	ENST00000288368	NM_024870.2	338	tgGTTT/tg	9/40	1	2	FACETS	0.611	0.566	0.658	0.611	0.566	0.658	SUBCLONAL	1	TRUE	1	0.86	2		528	700	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507350	8507350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1203991786	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	180	295	0	ENST00000356435.5:c.1628C>T	p.Thr543Ile	p.T543I	ENST00000356435		543	aCc/aTc	11/35	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.86	2		295	391	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93607773	93607773	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763445736	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	107	230	0	ENST00000375746.1:c.475G>A	p.Ala159Thr	p.A159T	ENST00000375746	NM_001174167.1	159	Gct/Act	3/14	1	2	FACETS	0.669	0.605	0.735	0.669	0.605	0.735	SUBCLONAL	1	TRUE	1	0.86	2		230	372	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888802	76888802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	192	418	0	ENST00000373344.5:c.5027G>A	p.Gly1676Asp	p.G1676D	ENST00000373344	NM_000489.3	1676	gGt/gAt	19/35	1	2	FACETS	0.726	0.675	0.778	0.726	0.675	0.778	SUBCLONAL	1	TRUE	1	0.86	2		418	615	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	32	354	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.651	0.528	0.79	0.651	0.528	0.79	SUBCLONAL	1	TRUE	1	0.22866391749427	2		355	430	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088807	27088807	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	45	488	0	ENST00000324856.7:c.2416C>T	p.Gln806Ter	p.Q806*	ENST00000324856	NM_006015.4	806	Caa/Taa	7/20	0.184736819114038	3	FACETS	0.86	0.723	1	0.43	0.361	0.506	CLONAL	1	TRUE	1	0.22866391749427	3		488	510	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	153	671	1	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.188838439822474	2	FACETS	0.938	0.86	1	0.938	0.86	1	CLONAL	2	TRUE	0	0.22866391749427	2		672	713	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027160	49027160	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	115	335	0	ENST00000267163.4:c.1727C>G	p.Ser576Ter	p.S576*	ENST00000267163	NM_000321.2	576	tCa/tGa	18/27	0.22866391749427	3	FACETS	0.907	0.823	0.993	1	0.982	1	CLONAL	3	TRUE	1	0.22866391749427	3		335	412	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56792541	56792541	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	32	375	0	ENST00000308159.5:c.271G>C	p.Glu91Gln	p.E91Q	ENST00000308159	NM_014669.4	91	Gag/Cag	3/22	1	2	FACETS	0.693	0.562	0.84	0.693	0.562	0.84	SUBCLONAL	1	TRUE	1	0.22866391749427	2		375	404	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099098	27099098	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	66	392	0	ENST00000324856.7:c.3514C>T	p.Gln1172Ter	p.Q1172*	ENST00000324856	NM_006015.4	1172	Cag/Tag	13/20	0.184736819114038	3	FACETS	0.777	0.677	0.884	0.777	0.677	0.884	SUBCLONAL	2	TRUE	1	0.22866391749427	3		392	414	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160227	22160227	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs797044892	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	37	251	0	ENST00000215832.6:c.404G>C	p.Arg135Thr	p.R135T	ENST00000215832	NM_002745.4	135	aGa/aCa	3/9	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.22866391749427	2		251	308	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827727	72827727	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	36	484	0	ENST00000268489.5:c.8854C>G	p.Gln2952Glu	p.Q2952E	ENST00000268489	NM_006885.3	2952	Caa/Gaa	9/10	0.22866391749427	3	FACETS	0.586	0.48	0.704			1	SUBCLONAL	1	TRUE	NA	0.22866391749427	3		484	599	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739397	46739397	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	61	386	0	ENST00000371975.4:c.1588G>C	p.Glu530Gln	p.E530Q	ENST00000371975	NM_003579.3	530	Gag/Cag	14/18	0.184736819114038	3	FACETS	1	0.932	1	0.566	0.489	0.65	CLONAL	1	TRUE	1	0.22866391749427	3		386	525	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949125	71949125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745724027	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	103	633	2	ENST00000298229.2:c.3592G>A	p.Glu1198Lys	p.E1198K	ENST00000298229	NM_001567.3	1198	Gag/Aag	27/28	0.118958489857333	4	FACETS	1	0.981	1	0.733	0.656	0.815	INDETERMINATE	1	TRUE	2	0.22866391749427	4		635	755	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779037	135779037	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	88	316	0	ENST00000298552.3:c.2208+1G>A		p.X736_splice	ENST00000298552	NM_001162426.1	736			0.22866391749427	2	FACETS	0.997	0.889	1	0.997	0.889	1	CLONAL	2	TRUE	0	0.22866391749427	2		316	386	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383225	4383225	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	45	367	0	ENST00000261254.3:c.19G>C	p.Glu7Gln	p.E7Q	ENST00000261254	NM_001759.3	7	Gag/Cag	1/5	0.22866391749427	3	FACETS	1	0.895	1	0.541	0.456	0.636	CLONAL	1	TRUE	1	0.22866391749427	3		367	405	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556403	29556403	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	44	407	0	ENST00000356175.3:c.2770G>A	p.Glu924Lys	p.E924K	ENST00000356175	NM_000267.3	924	Gaa/Aaa	21/57	0.118958489857333	4	FACETS	0.731	0.612	0.863	0.365	0.306	0.432	INDETERMINATE	1	TRUE	2	0.22866391749427	4		407	647	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045953	47045953	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	132	340	0	ENST00000377604.3:c.2748G>C	p.Glu916Asp	p.E916D	ENST00000377604	NM_001204468.1	916	gaG/gaC	24/24	0.22866391749427	2	FACETS	0.906	0.829	0.984			1	CLONAL	3	TRUE	NA	0.22866391749427	2		340	425	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972453	32972453	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	50	481	0	ENST00000380152.3:c.9803G>C	p.Arg3268Thr	p.R3268T	ENST00000380152		3268	aGa/aCa	27/27	0.22866391749427	3	FACETS	0.699	0.592	0.817	0.35	0.296	0.409	SUBCLONAL	1	TRUE	1	0.22866391749427	3		481	697	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045656	47045656	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	85	273	0	ENST00000377604.3:c.2538-1G>C		p.X846_splice	ENST00000377604	NM_001204468.1	846			0.22866391749427	2	FACETS	1	0.934	1			1	CLONAL	2	TRUE	NA	0.22866391749427	2		273	348	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522443	157522443	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	61	649	2	ENST00000346085.5:c.4715C>A	p.Ser1572Tyr	p.S1572Y	ENST00000346085	NM_020732.3	1572	tCt/tAt	18/20	1	2	FACETS	0.757	0.652	0.871	0.757	0.652	0.871	SUBCLONAL	1	TRUE	1	0.22866391749427	2		651	705	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100301	27100301	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	50	524	0	ENST00000324856.7:c.4013C>G	p.Ser1338Cys	p.S1338C	ENST00000324856	NM_006015.4	1338	tCc/tGc	17/20	0.184736819114038	3	FACETS	0.721	0.611	0.843	0.36	0.305	0.422	SUBCLONAL	1	TRUE	1	0.22866391749427	3		524	676	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420547	49420547	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	49	525	0	ENST00000301067.7:c.15202G>T	p.Glu5068Ter	p.E5068*	ENST00000301067	NM_003482.3	5068	Gag/Tag	48/54	0.187405667051908	4	FACETS	0.742	0.627	0.869	0.371	0.313	0.435	SUBCLONAL	1	TRUE	2	0.22866391749427	4		525	710	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042608	42042608	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	33	367	0	ENST00000219905.7:c.6803G>C	p.Gly2268Ala	p.G2268A	ENST00000219905	NM_001164273.1	2268	gGa/gCa	17/24	1	2	FACETS	0.656	0.534	0.794	0.656	0.534	0.794	SUBCLONAL	1	TRUE	1	0.22866391749427	2		367	440	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042799	42042799	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	30	285	0	ENST00000219905.7:c.6994G>C	p.Asp2332His	p.D2332H	ENST00000219905	NM_001164273.1	2332	Gat/Cat	17/24	1	2	FACETS	0.793	0.64	0.966	0.793	0.64	0.966	CLONAL	1	TRUE	1	0.22866391749427	2		285	331	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559780	29559780	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	30	238	0	ENST00000356175.3:c.3377A>C	p.Gln1126Pro	p.Q1126P	ENST00000356175	NM_000267.3	1126	cAa/cCa	26/57	0.118958489857333	4	FACETS	0.929	0.75	1	0.465	0.375	0.566	INDETERMINATE	1	TRUE	2	0.22866391749427	4		238	347	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149497	61149497	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	66	256	0	ENST00000295025.8:c.1687G>C	p.Glu563Gln	p.E563Q	ENST00000295025	NM_002908.2	563	Gag/Cag	11/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.22866391749427	NA		256	405	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439709	220439709	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	110	814	0	ENST00000243786.2:c.562C>G	p.Leu188Val	p.L188V	ENST00000243786	NM_002191.3	188	Ctg/Gtg	2/2	0.184736819114038	3	FACETS	1	0.98	1	0.699	0.628	0.774	CLONAL	1	TRUE	1	0.22866391749427	3		814	767	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051598	30051598	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	26	240	0	ENST00000338641.4:c.532C>G	p.Gln178Glu	p.Q178E	ENST00000338641	NM_000268.3	178	Cag/Gag	6/16	1	2	FACETS	0.585	0.463	0.725	0.585	0.463	0.725	SUBCLONAL	1	TRUE	1	0.22866391749427	2		240	389	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573790	41573790	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	126	691	0	ENST00000263253.7:c.6075G>C	p.Leu2025Phe	p.L2025F	ENST00000263253	NM_001429.3	2025	ttG/ttC	31/31	1	2	FACETS	0.752	0.681	0.826	1	0.985	1	SUBCLONAL	2	TRUE	1	0.22866391749427	2		691	733	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114193	73114193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	29	287	0	ENST00000356692.5:c.829G>A	p.Glu277Lys	p.E277K	ENST00000356692		277	Gaa/Aaa	8/9	0.188054710519445	2	FACETS	0.699	0.561	0.855	0.349	0.28	0.428	SUBCLONAL	1	TRUE	0	0.22866391749427	2		287	363	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38968075	38968075	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	31	243	0	ENST00000357387.3:c.1030G>C	p.Glu344Gln	p.E344Q	ENST00000357387	NM_152756.3	344	Gag/Cag	12/38	0.219757992162306	4	FACETS	0.775	0.626	0.943	0.387	0.313	0.472	CLONAL	1	TRUE	2	0.22866391749427	4		243	430	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120311	94120311	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	30	236	0	ENST00000369303.4:c.740G>T	p.Arg247Met	p.R247M	ENST00000369303	NM_004440.3	247	aGg/aTg	3/17	0.219757992162306	4	FACETS	0.871	0.703	1	0.436	0.351	0.532	CLONAL	1	TRUE	2	0.22866391749427	4		236	370	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878911	151878911	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs768932767	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	45	421	0	ENST00000262189.6:c.6034C>G	p.Pro2012Ala	p.P2012A	ENST00000262189	NM_170606.2	2012	Cct/Gct	36/59	0.219757992162306	4	FACETS	0.716	0.601	0.845	0.358	0.3	0.423	SUBCLONAL	1	TRUE	2	0.22866391749427	4		421	675	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275398	38275398	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	56	554	0	ENST00000425967.3:c.1635G>C	p.Lys545Asn	p.K545N	ENST00000425967	NM_001174067.1	545	aaG/aaC	12/19	0.22866391749427	7	FACETS	0.793	0.677	0.92			1	CLONAL	1	TRUE	NA	0.22866391749427	7		554	971	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030877	69030877	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	89	282	0	ENST00000288368.4:c.3419C>T	p.Ser1140Leu	p.S1140L	ENST00000288368	NM_024870.2	1140	tCa/tTa	27/40	0.22866391749427	3	FACETS	0.999	0.891	1	0.999	0.891	1	CLONAL	2	TRUE	1	0.22866391749427	3		282	434	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133729483	133729483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	52	430	0	ENST00000318560.5:c.112G>A	p.Glu38Lys	p.E38K	ENST00000318560	NM_005157.4	38	Gag/Aag	2/11	0.22866391749427	2	FACETS	0.887	0.755	1	0.443	0.377	0.516	CLONAL	1	TRUE	0	0.22866391749427	2		430	513	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564064	139564064	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	56	648	0	ENST00000308874.7:c.204C>G	p.Ile68Met	p.I68M	ENST00000308874		68	atC/atG	5/10	0.22866391749427	2	FACETS	0.69	0.59	0.799	0.345	0.295	0.4	SUBCLONAL	1	TRUE	0	0.22866391749427	2		648	710	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045491	47045491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	100	275	0	ENST00000377604.3:c.2458G>A	p.Glu820Lys	p.E820K	ENST00000377604	NM_001204468.1	820	Gaa/Aaa	22/24	0.22866391749427	2	FACETS	1	0.973	1			1	CLONAL	2	TRUE	NA	0.22866391749427	2		275	353	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937335	76937335	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	24	399	0	ENST00000373344.5:c.3413G>T	p.Arg1138Ile	p.R1138I	ENST00000373344	NM_000489.3	1138	aGa/aTa	9/35	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.12	2		399	335	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78426120	78426120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	33	419	0	ENST00000370768.2:c.1405C>T	p.His469Tyr	p.H469Y	ENST00000370768	NM_003902.3	469	Cat/Tat	15/20	1	2	FACETS	1	0.813	1	1	0.813	1	CLONAL	1	TRUE	1	0.12	2		419	550	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	109	115	0				ENST00000310581	NM_198253.2	-/1132			0.501069185781558	1	FACETS	0.337	0.304	0.373	0.337	0.304	0.373	SUBCLONAL	1	TRUE	0	0.717042071108563	1		115	578	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027227	49027228	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0055394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	63	323	0	ENST00000267163.4:c.1796dup	p.Asn599LysfsTer54	p.N599Kfs*54	ENST00000267163	NM_000321.2	598	-/A	18/27	0.717042071108563	1	FACETS	0.811	0.722	0.901	0.811	0.722	0.901	CLONAL	1	TRUE	0	0.717042071108563	1		323	139	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571547	95571547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	92	344	0	ENST00000393063.1:c.3130C>T	p.Pro1044Ser	p.P1044S	ENST00000393063	NM_030621.3	1044	Cca/Tca	21/28	0.717042071108563	1	FACETS	0.496	0.445	0.549	0.496	0.445	0.549	SUBCLONAL	1	TRUE	0	0.717042071108563	1		344	332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0055394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	407	502	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	0.717042071108563	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.717042071108563	1		502	696	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099256	4099256	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1461890634	NA	P-0055394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	275	643	0	ENST00000262948.5:c.862G>A	p.Glu288Lys	p.E288K	ENST00000262948	NM_030662.3	288	Gaa/Aaa	7/11	0.623292471334859	1	FACETS	0.481	0.451	0.511	0.481	0.451	0.511	SUBCLONAL	1	TRUE	0	0.717042071108563	1		643	1024	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099298	4099298	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	220	675	0	ENST00000262948.5:c.820G>C	p.Glu274Gln	p.E274Q	ENST00000262948	NM_030662.3	274	Gag/Cag	7/11	0.623292471334859	1	FACETS	0.362	0.337	0.389	0.362	0.337	0.389	SUBCLONAL	1	TRUE	0	0.717042071108563	1		675	1086	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050416	128050416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1453017999	NA	P-0055394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	65	361	1	ENST00000285398.2:c.241G>A	p.Asp81Asn	p.D81N	ENST00000285398	NM_000122.1	81	Gat/Aat	3/15	0.717042071108563	1	FACETS	0.32	0.279	0.365	0.32	0.279	0.365	SUBCLONAL	1	TRUE	0	0.717042071108563	1		362	363	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565575	41565575	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	141	343	0	ENST00000263253.7:c.4241A>G	p.Tyr1414Cys	p.Y1414C	ENST00000263253	NM_001429.3	1414	tAt/tGt	26/31	0.717042071108563	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.717042071108563	1		343	251	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641276	12641276	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	239	340	0	ENST00000251849.4:c.1022A>T	p.Tyr341Phe	p.Y341F	ENST00000251849	NM_002880.3	341	tAt/tTt	10/17	0.717042071108563	3	FACETS	0.925	0.864	0.988			1	CLONAL	1	TRUE	NA	0.717042071108563	3		340	979	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967302	134967302	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	314	440	0	ENST00000398015.3:c.2641A>C	p.Met881Leu	p.M881L	ENST00000398015	NM_004441.4	881	Atg/Ctg	14/16	1	2	FACETS	0.975	0.923	1	0.975	0.923	1	CLONAL	1	TRUE	1	0.717042071108563	2		440	898	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225722	26225722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1426924061	NA	P-0055394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	344	504	0	ENST00000360408.1:c.340C>T	p.His114Tyr	p.H114Y	ENST00000360408	NM_003532.2	114	Cat/Tat	1/1	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.717042071108563	2		504	949	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188605	32188605	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	340	549	1	ENST00000375023.3:c.850C>T	p.Gln284Ter	p.Q284*	ENST00000375023	NM_004557.3	284	Cag/Tag	5/30	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.717042071108563	2		550	902	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0055395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	27	613	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		614	723	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0055395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	20	396	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		396	539	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288979	212288979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	137	462	0	ENST00000342788.4:c.2767G>A	p.Gly923Arg	p.G923R	ENST00000342788	NM_005235.2	923	Gga/Aga	23/28	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.375800271170634	2		462	704	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867149	45867149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1322620921	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	207	593	0	ENST00000391945.4:c.970C>T	p.Arg324Cys	p.R324C	ENST00000391945	NM_000400.3	324	Cgc/Tgc	11/23	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.375800271170634	2		593	914	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020582	14020582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	91	398	0	ENST00000311895.7:c.553C>T	p.Leu185Phe	p.L185F	ENST00000311895	NM_005236.2	185	Ctt/Ttt	3/11	1	2	FACETS	0.675	0.6	0.756	0.675	0.6	0.756	SUBCLONAL	1	TRUE	1	0.375800271170634	2		398	717	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748538	40748538	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1203244050	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	191	713	2	ENST00000392038.2:c.344C>T	p.Pro115Leu	p.P115L	ENST00000392038	NM_001626.4	115	cCa/cTa	5/14	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.375800271170634	2		715	930	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667525	241667525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368849989	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	64	190	0	ENST00000366560.3:c.925C>T	p.Pro309Ser	p.P309S	ENST00000366560	NM_000143.3	309	Ccg/Tcg	7/10	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.375800271170634	2		190	295	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602286	10602286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	103	619	1	ENST00000171111.5:c.1292C>T	p.Ser431Phe	p.S431F	ENST00000171111	NM_203500.1	431	tCc/tTc	3/6	1	2	FACETS	0.531	0.474	0.591	0.531	0.474	0.591	SUBCLONAL	1	TRUE	1	0.375800271170634	2		620	1033	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641177	117641177	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773843792	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	208	692	0	ENST00000368508.3:c.5794G>A	p.Glu1932Lys	p.E1932K	ENST00000368508	NM_002944.2	1932	Gag/Aag	36/43	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.375800271170634	2		692	969	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745617	162745617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759124429	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	116	467	0	ENST00000367921.3:c.2032G>A	p.Asp678Asn	p.D678N	ENST00000367921	NM_006182.2	678	Gat/Aat	15/18	0.375800271170634	3	FACETS	0.925	0.833	1	0.462	0.416	0.511	CLONAL	1	TRUE	1	0.375800271170634	3		467	793	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47700145	47700145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752686914	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	133	325	0	ENST00000347630.2:c.28C>T	p.Pro10Ser	p.P10S	ENST00000347630	NM_001007230.1	10	Ccg/Tcg	3/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.375800271170634	2		325	663	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710974	117710974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	76	269	0	ENST00000368508.3:c.1298G>A	p.Arg433Lys	p.R433K	ENST00000368508	NM_002944.2	433	aGa/aAa	12/43	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.375800271170634	2		269	398	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666615	206666615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	155	604	0	ENST00000367120.3:c.1949C>T	p.Ser650Phe	p.S650F	ENST00000367120	NM_014002.3	650	tCt/tTt	20/22	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.375800271170634	2		604	796	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	111	325	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.375800271170634	2		326	403	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644591	3644591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767473953	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	150	574	0	ENST00000294008.3:c.2023G>A	p.Gly675Arg	p.G675R	ENST00000294008	NM_032444.2	675	Ggg/Agg	10/15	1	2	FACETS	0.948	0.867	1	0.948	0.867	1	CLONAL	1	TRUE	1	0.375800271170634	2		574	842	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562501	21562501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	12	24	0	ENST00000382592.4:c.1418C>T	p.Pro473Leu	p.P473L	ENST00000382592	NM_014572.2	473	cCc/cTc	4/8	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.375800271170634	2		24	46	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966462	25966462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	206	638	0	ENST00000435504.4:c.2744C>T	p.Pro915Leu	p.P915L	ENST00000435504		915	cCa/cTa	13/13	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.375800271170634	2		638	958	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	163	558	0	ENST00000269305.4:c.560-2A>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.375800271170634	2		558	788	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107713	30107713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1160777726	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	86	491	1	ENST00000331968.5:c.967G>A	p.Glu323Lys	p.E323K	ENST00000331968	NM_002742.2	323	Gaa/Aaa	6/18	0.375800271170634	2	FACETS	0.646	0.571	0.725	0.323	0.285	0.363	SUBCLONAL	1	TRUE	0	0.375800271170634	2		492	709	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420990	49420990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	147	488	0	ENST00000301067.7:c.14759C>T	p.Pro4920Leu	p.P4920L	ENST00000301067	NM_003482.3	4920	cCc/cTc	48/54	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.375800271170634	2		488	746	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449857	149449857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	174	656	0	ENST00000286301.3:c.1207G>A	p.Glu403Lys	p.E403K	ENST00000286301	NM_005211.3	403	Gag/Aag	9/22	1	2	FACETS	0.999	0.92	1	0.999	0.92	1	CLONAL	1	TRUE	1	0.375800271170634	2		656	927	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205281	38205281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	246	807	0	ENST00000317025.8:c.409C>T	p.Pro137Ser	p.P137S	ENST00000317025	NM_023034.1	137	Cct/Tct	2/24	1	2	FACETS	0.973	0.907	1	0.973	0.907	1	CLONAL	1	TRUE	1	0.375800271170634	2		807	1346	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874374	76874374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	117	227	0	ENST00000373344.5:c.5348C>T	p.Pro1783Leu	p.P1783L	ENST00000373344	NM_000489.3	1783	cCa/cTa	21/35	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.375800271170634	1		227	372	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319047	62319047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369940581	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	189	692	0	ENST00000360203.5:c.1405C>T	p.Arg469Cys	p.R469C	ENST00000360203	NM_001283009.1	469	Cgc/Tgc	17/35	1	2	FACETS	0.996	0.92	1	0.996	0.92	1	CLONAL	1	TRUE	1	0.375800271170634	2		692	1010	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740284	162740284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1291790073	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	171	325	0	ENST00000367921.3:c.1486C>T	p.Pro496Ser	p.P496S	ENST00000367921	NM_006182.2	496	Cca/Tca	12/18	0.375800271170634	3	FACETS	0.977	0.905	1	0.977	0.905	1	CLONAL	2	TRUE	1	0.375800271170634	3		325	553	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405967	157405967	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs534990481	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	154	540	0	ENST00000346085.5:c.2209C>T	p.Pro737Ser	p.P737S	ENST00000346085	NM_020732.3	737	Ccc/Tcc	6/20	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.375800271170634	2		540	809	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223602	53223602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	136	286	1	ENST00000375401.3:c.3757C>T	p.Pro1253Ser	p.P1253S	ENST00000375401	NM_004187.3	1253	Ccg/Tcg	23/26	1	1	FACETS	0.769	0.707	0.833	1	0.988	1	SUBCLONAL	2	TRUE	0	0.375800271170634	1		287	382	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602356	10602356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	105	755	0	ENST00000171111.5:c.1222C>T	p.Pro408Ser	p.P408S	ENST00000171111	NM_203500.1	408	Ccc/Tcc	3/6	1	2	FACETS	0.498	0.445	0.555	0.498	0.445	0.555	SUBCLONAL	1	TRUE	1	0.375800271170634	2		755	1121	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240795	55240795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373336251	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	217	725	0	ENST00000275493.2:c.2039G>A	p.Arg680Gln	p.R680Q	ENST00000275493	NM_005228.3	680	cGg/cAg	17/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.375800271170634	2		725	990	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962324	2962324	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	212	684	0	ENST00000396946.4:c.2213G>A	p.Trp738Ter	p.W738*	ENST00000396946	NM_032415.4	738	tGg/tAg	17/25	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.375800271170634	2		684	933	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463565	25463565	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777898555	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	179	574	0	ENST00000264709.3:c.2117G>A	p.Gly706Glu	p.G706E	ENST00000264709	NM_175629.2	706	gGg/gAg	18/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.375800271170634	2		574	865	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586425	189586425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	123	433	0	ENST00000264731.3:c.1049G>A	p.Arg350Lys	p.R350K	ENST00000264731	NM_003722.4	350	aGa/aAa	8/14	0.358729014179406	3	FACETS	1	0.949	1	0.536	0.485	0.59	CLONAL	1	TRUE	1	0.375800271170634	3		433	725	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117061	193117061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1335804597	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	192	337	1	ENST00000367435.3:c.794C>T	p.Pro265Leu	p.P265L	ENST00000367435	NM_024529.4	265	cCt/cTt	8/17	0.375800271170634	3	FACETS	0.956	0.888	1	0.956	0.888	1	CLONAL	2	TRUE	1	0.375800271170634	3		338	635	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524565	176524565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	180	776	0	ENST00000292408.4:c.2297C>T	p.Pro766Leu	p.P766L	ENST00000292408	NM_213647.1	766	cCc/cTc	18/18	1	2	FACETS	0.881	0.812	0.954	0.881	0.812	0.954	CLONAL	1	TRUE	1	0.375800271170634	2		776	1087	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346569	81346569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	69	341	0	ENST00000222390.5:c.1384G>A	p.Asp462Asn	p.D462N	ENST00000222390	NM_000601.4	462	Gat/Aat	11/18	1	2	FACETS	0.749	0.654	0.852	0.749	0.654	0.852	SUBCLONAL	1	TRUE	1	0.375800271170634	2		341	490	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11313928	11313928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	190	576	0	ENST00000361445.4:c.808G>A	p.Glu270Lys	p.E270K	ENST00000361445	NM_004958.3	270	Gag/Aag	6/58	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.375800271170634	2		576	854	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215617193	215617193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	76	288	0	ENST00000260947.4:c.1655C>T	p.Ser552Phe	p.S552F	ENST00000260947	NM_000465.2	552	tCc/tTc	7/11	1	2	FACETS	0.943	0.831	1	0.943	0.831	1	CLONAL	1	TRUE	1	0.375800271170634	2		288	429	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374583	118374583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1390104203	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	108	365	0	ENST00000534358.1:c.7976G>A	p.Arg2659Gln	p.R2659Q	ENST00000534358	NM_005933.3	2659	cGa/cAa	27/36	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.375800271170634	2		365	561	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46724358	46724358	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	156	405	0	ENST00000371975.4:c.211G>A	p.Glu71Lys	p.E71K	ENST00000371975	NM_003579.3	71	Gaa/Aaa	4/18	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.375800271170634	2		405	736	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313279	65313279	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	152	448	0	ENST00000342505.4:c.1835C>T	p.Ser612Phe	p.S612F	ENST00000342505	NM_002227.2	612	tCt/tTt	13/25	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.375800271170634	2		448	761	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444661	78444661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs527349416	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	83	438	0	ENST00000370768.2:c.28C>T	p.Pro10Ser	p.P10S	ENST00000370768	NM_003902.3	10	Ccc/Tcc	1/20	1	2	FACETS	0.587	0.518	0.662	0.587	0.518	0.662	SUBCLONAL	1	TRUE	1	0.375800271170634	2		438	752	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404863	70404863	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	96	437	0	ENST00000373644.4:c.2377T>G	p.Phe793Val	p.F793V	ENST00000373644	NM_030625.2	793	Ttc/Gtc	4/12	1	2	FACETS	0.849	0.757	0.945	0.849	0.757	0.945	CLONAL	1	TRUE	1	0.375800271170634	2		437	602	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405731	70405731	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	72	473	0	ENST00000373644.4:c.3245C>A	p.Thr1082Lys	p.T1082K	ENST00000373644	NM_030625.2	1082	aCa/aAa	4/12	1	2	FACETS	0.615	0.537	0.699	0.615	0.537	0.699	SUBCLONAL	1	TRUE	1	0.375800271170634	2		473	623	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724148	112724148	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1381863749	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	96	347	0	ENST00000369452.4:c.32C>T	p.Ser11Phe	p.S11F	ENST00000369452	NM_007373.3	11	tCt/tTt	2/9	1	2	FACETS	0.885	0.791	0.986	0.885	0.791	0.986	CLONAL	1	TRUE	1	0.375800271170634	2		347	577	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534271	534271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	160	573	0	ENST00000451590.1:c.52G>A	p.Ala18Thr	p.A18T	ENST00000451590	NM_001130442.1	18	Gcg/Acg	2/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.375800271170634	2		573	714	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742963	17742963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	156	563	0	ENST00000250003.3:c.871G>A	p.Gly291Arg	p.G291R	ENST00000250003	NM_002478.4	291	Gga/Aga	3/3	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.375800271170634	2		563	750	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631168	69631168	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	105	534	0	ENST00000334134.2:c.244G>A	p.Glu82Lys	p.E82K	ENST00000334134	NM_005247.2	82	Gag/Aag	2/3	1	2	FACETS	0.789	0.708	0.876	0.789	0.708	0.876	SUBCLONAL	1	TRUE	1	0.375800271170634	2		534	708	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911073	94911073	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	129	413	0	ENST00000536441.1:c.1057G>A	p.Asp353Asn	p.D353N	ENST00000536441	NM_144665.3	353	Gac/Aac	8/10	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.375800271170634	2		413	675	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374750	118374750	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375049498	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	81	342	0	ENST00000534358.1:c.8143C>T	p.Pro2715Ser	p.P2715S	ENST00000534358	NM_005933.3	2715	Cca/Tca	27/36	1	2	FACETS	0.813	0.718	0.915	0.813	0.718	0.915	CLONAL	1	TRUE	1	0.375800271170634	2		342	530	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038935	12038935	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	83	303	0	ENST00000396373.4:c.1228G>A	p.Glu410Lys	p.E410K	ENST00000396373	NM_001987.4	410	Gag/Aag	7/8	1	2	FACETS	0.913	0.808	1	0.913	0.808	1	CLONAL	1	TRUE	1	0.375800271170634	2		303	484	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420871	49420872	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	148	610	3	ENST00000301067.7:c.14877_14878delinsTT	p.Arg4960Ter	p.R4960*	ENST00000301067	NM_003482.3	4959	gcCCga/gcTTga	48/54	1	2	FACETS	0.963	0.88	1	0.963	0.88	1	CLONAL	1	TRUE	1	0.375800271170634	2		613	818	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443858	49443858	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	210	828	2	ENST00000301067.7:c.3513A>T	p.Glu1171Asp	p.E1171D	ENST00000301067	NM_003482.3	1171	gaA/gaT	11/54	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.375800271170634	2		830	1043	SUCCESS
BLM	641	MSKCC	GRCh37	15	91328184	91328184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748054605	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	149	374	0	ENST00000355112.3:c.2696G>A	p.Arg899Gln	p.R899Q	ENST00000355112	NM_000057.2	899	cGa/cAa	14/22	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.375800271170634	2		374	678	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274099	10274100	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	164	659	1	ENST00000330684.3:c.169_170delinsTT	p.Pro57Phe	p.P57F	ENST00000330684	NM_001134407.1	57	CCc/TTc	2/13	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.375800271170634	2		660	817	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953129	81953130	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	69	338	1	ENST00000359376.3:c.2095_2096delinsAA	p.Gly699Asn	p.G699N	ENST00000359376	NM_002661.3	699	GGc/AAc	20/33	1	2	FACETS	0.679	0.592	0.772	0.679	0.592	0.772	SUBCLONAL	1	TRUE	1	0.375800271170634	2		339	541	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89833556	89833556	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	102	279	0	ENST00000389301.3:c.2594T>A	p.Ile865Asn	p.I865N	ENST00000389301	NM_000135.2	865	aTt/aAt	27/43	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.375800271170634	2		279	538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577082	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	180	711	0	ENST00000269305.4:c.856_857delinsAT	p.Glu286Ile	p.E286I	ENST00000269305	NM_001126112.2	286	GAa/ATa	8/11	1	2	FACETS	0.946	0.871	1	0.946	0.871	1	CLONAL	1	TRUE	1	0.375800271170634	2		711	1013	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16001745	16001746	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	105	518	1	ENST00000268712.3:c.2755_2756delinsTT	p.Pro919Leu	p.P919L	ENST00000268712	NM_006311.3	919	CCg/TTg	21/46	1	2	FACETS	0.754	0.676	0.837	0.754	0.676	0.837	SUBCLONAL	1	TRUE	1	0.375800271170634	2		519	741	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646858	37646858	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	141	507	0	ENST00000447079.4:c.1980G>C	p.Gln660His	p.Q660H	ENST00000447079	NM_015083.1	660	caG/caC	3/14	1	2	FACETS	0.902	0.822	0.986	0.902	0.822	0.986	CLONAL	1	TRUE	1	0.375800271170634	2		507	832	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686932	37686932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	126	494	0	ENST00000447079.4:c.3836C>T	p.Pro1279Leu	p.P1279L	ENST00000447079	NM_015083.1	1279	cCc/cTc	14/14	1	2	FACETS	0.852	0.772	0.937	0.852	0.772	0.937	CLONAL	1	TRUE	1	0.375800271170634	2		494	787	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59878765	59878766	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	76	360	0	ENST00000259008.2:c.988_989delinsAA	p.Gly330Lys	p.G330K	ENST00000259008	NM_032043.2	330	GGg/AAg	8/20	1	2	FACETS	0.782	0.688	0.884	0.782	0.688	0.884	SUBCLONAL	1	TRUE	1	0.375800271170634	2		360	517	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936352	78936352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	82	641	0	ENST00000306801.3:c.3784C>T	p.His1262Tyr	p.H1262Y	ENST00000306801	NM_020761.2	1262	Cac/Tac	32/34	0.375800271170634	2	FACETS	0.541	0.477	0.611	0.271	0.238	0.306	SUBCLONAL	1	TRUE	0	0.375800271170634	2		641	806	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367813	15367814	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	187	686	0	ENST00000263377.2:c.1512_1513delinsAA	p.Glu505Lys	p.E505K	ENST00000263377	NM_058243.2	504	gaGGag/gaAAag	8/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.375800271170634	2		686	897	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216162	36216162	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	173	648	0	ENST00000222270.7:c.3570del	p.Ser1191ValfsTer164	p.S1191Vfs*164	ENST00000222270	NM_014727.1	1190	ctG/ct	11/37	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.375800271170634	2		648	863	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216162	36216164	+	frameshift_variant	Frame_Shift_Del	DEL	GAG	GAG	AA	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	176	657	0	ENST00000222270.7:c.3570_3572delinsAA	p.Ser1191MetfsTer164	p.S1191Mfs*164	ENST00000222270	NM_014727.1	1190	ctGAGt/ctAAt	11/37	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.375800271170634	2		657	874	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917764	29917765	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	146	647	0	ENST00000389048.3:c.903_904delinsAA	p.Met301_Asp302delinsIleAsn	p.M301_D302delinsIN	ENST00000389048	NM_004304.4	301	atGGac/atAAac	3/29	1	2	FACETS	0.86	0.785	0.94	0.86	0.785	0.94	CLONAL	1	TRUE	1	0.375800271170634	2		647	903	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530072	212530073	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	71	265	0	ENST00000342788.4:c.1846_1847delinsTT	p.Pro616Leu	p.P616L	ENST00000342788	NM_005235.2	616	CCa/TTa	15/28	1	2	FACETS	0.926	0.812	1	0.926	0.812	1	CLONAL	1	TRUE	1	0.375800271170634	2		265	408	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024194	31024194	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752436984	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	138	582	0	ENST00000375687.4:c.3679G>A	p.Glu1227Lys	p.E1227K	ENST00000375687	NM_015338.5	1227	Gaa/Aaa	13/13	1	2	FACETS	0.886	0.806	0.969	0.886	0.806	0.969	CLONAL	1	TRUE	1	0.375800271170634	2		582	829	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164785	36164786	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCC	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	177	678	0	ENST00000300305.3:c.1086_1089dup	p.Ile364GlyfsTer237	p.I364Gfs*237	ENST00000300305		363	-/GGGC	8/8	0.375800271170634	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.375800271170634	1		678	700	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755522	39755523	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	119	498	1	ENST00000288319.7:c.1242_1243delinsTT	p.Leu415Phe	p.L415F	ENST00000288319	NM_182918.3	414	gaCCtc/gaTTtc	10/10	0.375800271170634	1	FACETS	0.896	0.811	0.985	0.896	0.811	0.985	CLONAL	1	TRUE	0	0.375800271170634	1		499	574	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119666178	119666178	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	108	285	0	ENST00000316626.5:c.303G>A	p.Met101Ile	p.M101I	ENST00000316626		101	atG/atA	3/12	0.358729014179406	3	FACETS	1	0.942	1	0.534	0.48	0.591	CLONAL	1	TRUE	1	0.375800271170634	3		285	639	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670297	134670297	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	99	445	0	ENST00000398015.3:c.208A>C	p.Asn70His	p.N70H	ENST00000398015	NM_004441.4	70	Aat/Cat	3/16	0.358729014179406	3	FACETS	0.802	0.716	0.894	0.401	0.358	0.447	CLONAL	1	TRUE	1	0.375800271170634	3		445	780	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917591	178917591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201705993	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	107	394	0	ENST00000263967.3:c.466C>T	p.Leu156Phe	p.L156F	ENST00000263967	NM_006218.2	156	Ctc/Ttc	3/21	0.358729014179406	3	FACETS	0.887	0.795	0.983	0.443	0.397	0.492	CLONAL	1	TRUE	1	0.375800271170634	3		394	763	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927983	178927984	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	91	248	0	ENST00000263967.3:c.1261_1262delinsTT	p.Pro421Leu	p.P421L	ENST00000263967	NM_006218.2	421	CCa/TTa	8/21	0.358729014179406	3	FACETS	1	0.966	1	0.606	0.54	0.675	CLONAL	1	TRUE	1	0.375800271170634	3		248	475	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526197	189526197	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	172	652	0	ENST00000264731.3:c.461C>T	p.Ser154Phe	p.S154F	ENST00000264731	NM_003722.4	154	tCc/tTc	4/14	0.358729014179406	3	FACETS	1	0.953	1	0.526	0.483	0.57	CLONAL	1	TRUE	1	0.375800271170634	3		652	1034	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1976711	1976711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	141	610	1	ENST00000382891.5:c.3494C>T	p.Ala1165Val	p.A1165V	ENST00000382891	NM_133335.3	1165	gCc/gTc	19/22	1	2	FACETS	0.835	0.76	0.913	0.835	0.76	0.913	CLONAL	1	TRUE	1	0.375800271170634	2		611	899	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31429583	31429584	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	92	365	1	ENST00000344624.3:c.3214_3215delinsTT	p.Pro1072Leu	p.P1072L	ENST00000344624		1072	CCg/TTg	24/33	1	2	FACETS	0.86	0.766	0.961	0.86	0.766	0.961	CLONAL	1	TRUE	1	0.375800271170634	2		366	569	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526984	31526985	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	179	632	0	ENST00000344624.3:c.55_56delinsTT	p.Pro19Phe	p.P19F	ENST00000344624		19	CCc/TTc	2/33	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.375800271170634	2		632	853	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86658488	86658489	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	38	141	0	ENST00000274376.6:c.1453_1453+1delinsAA		p.X485_splice	ENST00000274376	NM_002890.2	485		10/25	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.375800271170634	2		141	185	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665644	86665644	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	63	236	0	ENST00000274376.6:c.1625A>C	p.Gln542Pro	p.Q542P	ENST00000274376	NM_002890.2	542	cAg/cCg	12/25	1	2	FACETS	0.828	0.719	0.945	0.828	0.719	0.945	CLONAL	1	TRUE	1	0.375800271170634	2		236	405	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149434900	149434900	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	122	421	0	ENST00000286301.3:c.2555-1G>A		p.X852_splice	ENST00000286301	NM_005211.3	852			1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.375800271170634	2		421	605	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149498411	149498411	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	139	492	0	ENST00000261799.4:c.2803G>A	p.Glu935Lys	p.E935K	ENST00000261799	NM_002609.3	935	Gag/Aag	21/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.375800271170634	2		492	680	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287213	33287214	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	154	569	1	ENST00000374542.5:c.1883_1884delinsTT	p.Pro628Leu	p.P628L	ENST00000374542	NM_001141970.1	628	cCC/cTT	6/8	1	2	FACETS	0.995	0.911	1	0.995	0.911	1	CLONAL	1	TRUE	1	0.375800271170634	2		570	824	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120408	94120408	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	82	331	0	ENST00000369303.4:c.643T>C	p.Phe215Leu	p.F215L	ENST00000369303	NM_004440.3	215	Ttt/Ctt	3/17	1	2	FACETS	0.999	0.885	1	0.999	0.885	1	CLONAL	1	TRUE	1	0.375800271170634	2		331	437	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983088	111983088	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756230899	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	165	564	0	ENST00000368678.4:c.1459G>A	p.Asp487Asn	p.D487N	ENST00000368678		487	Gac/Aac	13/13	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.375800271170634	2		564	812	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851530	151851531	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	67	227	0	ENST00000262189.6:c.11961-1_11961delinsAA		p.X3987_splice	ENST00000262189	NM_170606.2	3987		47/59	0.375800271170634	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.375800271170634	1		227	246	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974742	21974887	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	GCACCTCCTCTACCCGACCCCGGGCCGCGGCCGTGGCCAGCCAGTCAGCCGAAGGCTCCATGCTGCTCCCCGCCGCCGGCTCCATGCTGCTCCCCGCCGCCCGCTGCCTGCTCTCCCCCTCTCCGCAGCCGCCGAGCGCACGCGGT	GCACCTCCTCTACCCGACCCCGGGCCGCGGCCGTGGCCAGCCAGTCAGCCGAAGGCTCCATGCTGCTCCCCGCCGCCGGCTCCATGCTGCTCCCCGCCGCCCGCTGCCTGCTCTCCCCCTCTCCGCAGCCGCCGAGCGCACGCGGT	-	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	91	274	0	ENST00000304494.5:c.-61_85del		p.*21*	ENST00000304494	NM_000077.4	?-29/156		1/3	0.375800271170634	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.375800271170634	1		274	369	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738354	133738354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	25	541	1	ENST00000318560.5:c.754C>T	p.Gln252Ter	p.Q252*	ENST00000318560	NM_005157.4	252	Cag/Tag	4/11	1	2	FACETS	0.167	0.131	0.209	0.167	0.131	0.209	SUBCLONAL	1	TRUE	1	0.375800271170634	2		542	797	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930321	39930321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	118	266	0	ENST00000378444.4:c.3143C>T	p.Pro1048Leu	p.P1048L	ENST00000378444	NM_001123385.1	1048	cCa/cTa	6/15	1	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.375800271170634	1		266	481	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411216	63411216	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778026	NA	P-0055397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	181	635	0	ENST00000330258.3:c.1951G>A	p.Val651Ile	p.V651I	ENST00000330258	NM_152424.3	651	Gtc/Atc	2/2	0.266689441246082	4	FACETS	0.932	0.862	1	0.932	0.862	1	CLONAL	2	TRUE	2	0.362710255239528	4		635	730	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435086	49435086	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	100	568	0	ENST00000301067.7:c.6467C>T	p.Pro2156Leu	p.P2156L	ENST00000301067	NM_003482.3	2156	cCt/cTt	31/54	0.362710255239528	4	FACETS	0.97	0.866	1	0.485	0.433	0.54	CLONAL	1	TRUE	2	0.362710255239528	4		568	775	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112516	115112517	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0055397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	222	619	0	ENST00000257566.3:c.1223dup	p.Ser409GlnfsTer12	p.S409Qfs*12	ENST00000257566	NM_016569.3	408	ggc/ggGc	7/8	0.362710255239528	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	2	0.362710255239528	4		619	784	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993464	72993464	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	111	663	0	ENST00000268489.5:c.581T>C	p.Ile194Thr	p.I194T	ENST00000268489	NM_006885.3	194	aTc/aCc	2/10	0.362710255239528	2	FACETS	0.932	0.839	1	0.466	0.419	0.515	CLONAL	1	TRUE	0	0.362710255239528	2		663	657	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577566	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0055397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	403	520	0	ENST00000269305.4:c.715_716del	p.Asn239GlnfsTer24	p.N239Qfs*24	ENST00000269305	NM_001126112.2	239	AAc/c	7/11	0.362710255239528	4	FACETS	0.979	0.939	1	0.979	0.939	1	CLONAL	4	TRUE	0	0.362710255239528	4		520	773	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750369	39750369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs530001363	NA	P-0055397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	57	310	0	ENST00000361337.2:c.1984C>T	p.Arg662Trp	p.R662W	ENST00000361337	NM_003286.2	662	Cgg/Tgg	19/21	0.338091899288073	3	FACETS	0.833	0.716	0.959	0.416	0.358	0.48	CLONAL	1	TRUE	1	0.362710255239528	3		310	446	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620443	52620443	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	73	383	0	ENST00000394830.3:c.3310A>G	p.Lys1104Glu	p.K1104E	ENST00000394830	NM_018313.4	1104	Aag/Gag	21/30	0.266689441246082	4	FACETS	1	0.921	1	0.535	0.468	0.606	CLONAL	1	TRUE	2	0.362710255239528	4		383	513	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0055398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	90	314	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.197992648464618	4	FACETS	1	0.936	1			1	CLONAL	2	TRUE	NA	0.229555806975979	4		314	450	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411783	63411783	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	142	688	1	ENST00000330258.3:c.1384G>T	p.Glu462Ter	p.E462*	ENST00000330258	NM_152424.3	462	Gaa/Taa	2/2	NA	2	FACETS	1	0.945	1			1	INDETERMINATE	2	TRUE	NA	0.229555806975979	2		689	593	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784077	120784077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1210006090	NA	P-0055398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	74	773	1	ENST00000257552.2:c.908G>A	p.Arg303His	p.R303H	ENST00000257552	NM_002442.3	303	cGc/cAc	13/15	0.229555806975979	3	FACETS	1	0.94	1	0.562	0.491	0.637	CLONAL	1	TRUE	1	0.229555806975979	3		774	640	SUCCESS
APC	324	MSKCC	GRCh37	5	112175925	112175925	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs863225356	NA	P-0055398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	70	258	0	ENST00000257430.4:c.4634C>A	p.Ser1545Ter	p.S1545*	ENST00000257430	NM_000038.5	1545	tCa/tAa	16/16	0.229555806975979	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.229555806975979	3		258	287	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740362	58740362	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1057524700	NA	P-0055398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	46	361	0	ENST00000305921.3:c.1267G>T	p.Glu423Ter	p.E423*	ENST00000305921	NM_003620.3	423	Gag/Tag	6/6	0.229555806975979	3	FACETS	1	0.905	1	0.552	0.465	0.646	CLONAL	1	TRUE	1	0.229555806975979	3		361	405	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574203	46574203	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0055398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	104	440	0	ENST00000263734.3:c.217+1G>T		p.X73_splice	ENST00000263734	NM_001430.4	73			0.229555806975979	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.229555806975979	3		440	436	SUCCESS
APC	324	MSKCC	GRCh37	5	112174170	112174170	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	22	308	0	ENST00000257430.4:c.2879del	p.Ser960Ter	p.S960*	ENST00000257430	NM_000038.5	960	tCa/ta	16/16	0.229555806975979	3	FACETS	0.698	0.541	0.88	0.349	0.27	0.44	SUBCLONAL	1	TRUE	1	0.229555806975979	3		308	306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0055400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	236	915	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.266392343077295	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.27	2		915	747	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106662	27106750	+	protein_altering_variant	In_Frame_Del	DEL	GGCAGTTTGCCCTTCAGCTGAAGCCCAGGACCCCTTTTCCACCCTGGGCCCCAATGCCGTCCTTTCCCCGCAGAGACTGGTCTTGGAAA	GGCAGTTTGCCCTTCAGCTGAAGCCCAGGACCCCTTTTCCACCCTGGGCCCCAATGCCGTCCTTTCCCCGCAGAGACTGGTCTTGGAAA	CC	novel	NA	P-0055400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	83	601	4	ENST00000324856.7:c.6273_6361delinsCC	p.Trp2091_Thr2121delinsCysPro	p.W2091_T2121delinsCP	ENST00000324856	NM_006015.4	2091	tgGGCAGTTTGCCCTTCAGCTGAAGCCCAGGACCCCTTTTCCACCCTGGGCCCCAATGCCGTCCTTTCCCCGCAGAGACTGGTCTTGGAAAcc/tgCCcc	20/20	0.3	1	FACETS	0.953	0.843	1	0.953	0.843	1	CLONAL	1	TRUE	0	0.27	1		605	558	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513204	106513204	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	50	275	0	ENST00000359195.3:c.2108T>C	p.Ile703Thr	p.I703T	ENST00000359195	NM_002649.2	703	aTa/aCa	4/11	1	2	FACETS	0.715	0.609	0.83	0.715	0.609	0.83	SUBCLONAL	1	TRUE	1	0.42	2		275	333	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	55	115	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		115	297	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468000	120468000	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	350	515	0	ENST00000256646.2:c.4439G>T	p.Cys1480Phe	p.C1480F	ENST00000256646	NM_024408.3	1480	tGt/tTt	25/34	NA	2	FACETS	0.768	0.731	0.806			1	INDETERMINATE	2	TRUE	NA	0.554766089627972	2		515	821	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524069	187524069	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	128	487	0	ENST00000441802.2:c.11470G>T	p.Gly3824Cys	p.G3824C	ENST00000441802	NM_005245.3	3824	Ggt/Tgt	20/27	0.554766089627972	1	FACETS	0.811	0.742	0.883	0.811	0.742	0.883	CLONAL	1	TRUE	0	0.554766089627972	1		487	411	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0055409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	134	561	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	0.517418947531893	1	FACETS	0.445	0.408	0.484	0.445	0.408	0.484	SUBCLONAL	1	TRUE	0	0.834765946860077	1		562	420	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922294	100922294	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1315135533	NA	P-0055409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	87	255	1	ENST00000325455.5:c.2218C>T	p.Arg740Ter	p.R740*	ENST00000325455	NM_001202474.3	740	Cga/Tga	5/8	0.387497166036063	1	FACETS	0.401	0.359	0.445	0.401	0.359	0.445	INDETERMINATE	1	TRUE	0	0.834765946860077	1		256	303	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052629	42052629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	133	452	0	ENST00000219905.7:c.7300C>T	p.Arg2434Trp	p.R2434W	ENST00000219905	NM_001164273.1	2434	Cgg/Tgg	20/24	1	2	FACETS	0.435	0.395	0.476	0.435	0.395	0.476	SUBCLONAL	1	TRUE	1	0.834765946860077	2		452	733	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515025	148515025	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	178	451	2	ENST00000320356.2:c.1184del	p.Gly395GlufsTer29	p.G395Efs*29	ENST00000320356	NM_004456.4	395	gGa/ga	10/20	1	2	FACETS	0.933	0.862	1	0.933	0.862	1	CLONAL	1	TRUE	1	0.512854892951976	2		453	744	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0055426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	180	400	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.916	0.847	0.988	0.916	0.847	0.988	CLONAL	1	TRUE	1	0.512854892951976	2		400	766	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349940	15349940	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	282	616	0	ENST00000263377.2:c.3712G>A	p.Glu1238Lys	p.E1238K	ENST00000263377	NM_058243.2	1238	Gag/Aag	18/20	1	2	FACETS	0.956	0.898	1	0.956	0.898	1	CLONAL	1	TRUE	1	0.512854892951976	2		616	1150	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917637	151917637	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0055426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	160	456	0	ENST00000262189.6:c.3683C>G	p.Ser1228Ter	p.S1228*	ENST00000262189	NM_170606.2	1228	tCa/tGa	23/59	1	2	FACETS	0.81	0.744	0.879	0.81	0.744	0.879	CLONAL	1	TRUE	1	0.512854892951976	2		456	770	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873209	136873209	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1333957805	NA	P-0055426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	188	334	0	ENST00000241393.3:c.289G>A	p.Asp97Asn	p.D97N	ENST00000241393	NM_003467.2	97	Gat/Aat	2/2	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.512854892951976	2		334	660	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37048493	37048493	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs63749818	NA	P-0055426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	118	300	0	ENST00000231790.2:c.392C>G	p.Ser131Ter	p.S131*	ENST00000231790	NM_000249.3	131	tCa/tGa	5/19	0.500822767437468	1	FACETS	0.937	0.855	1	0.937	0.855	1	CLONAL	1	TRUE	0	0.512854892951976	1		300	365	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130301	2130303	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs1060500937	NA	P-0055426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	322	756	0	ENST00000219476.3:c.3535_3537del	p.Glu1179del	p.E1179del	ENST00000219476	NM_000548.3	1178	cAGGag/cag	30/42	0.512854892951976	1	FACETS	0.918	0.868	0.969	0.918	0.868	0.969	CLONAL	1	TRUE	0	0.512854892951976	1		756	1017	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551334	150551334	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14707	7915	752	0	ENST00000369026.2:c.673G>T	p.Glu225Ter	p.E225*	ENST00000369026	NM_021960.4	225	Gag/Tag	1/3	0.508351031075736	3	FACETS	0.857	0.848	0.867	0.857	0.848	0.867	CLONAL	2	TRUE	1	0.512854892951976	3		752	22622	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961242	15961242	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	141	435	0	ENST00000268712.3:c.6147C>G	p.Ile2049Met	p.I2049M	ENST00000268712	NM_006311.3	2049	atC/atG	39/46	1	2	FACETS	0.851	0.778	0.928	0.851	0.778	0.928	CLONAL	1	TRUE	1	0.512854892951976	2		435	646	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10266538	10266538	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	199	474	0	ENST00000340748.4:c.1435T>G	p.Phe479Val	p.F479V	ENST00000340748		479	Ttc/Gtc	18/40	NA	2	FACETS	0.924	0.857	0.993			1	INDETERMINATE	1	TRUE	NA	0.512854892951976	2		474	840	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439932	220439932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1198885682	NA	P-0055426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	342	864	0	ENST00000243786.2:c.785G>A	p.Cys262Tyr	p.C262Y	ENST00000243786	NM_002191.3	262	tGc/tAc	2/2	1	2	FACETS	0.929	0.878	0.982	0.929	0.878	0.982	CLONAL	1	TRUE	1	0.512854892951976	2		864	1435	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162863	47162863	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	150	357	0	ENST00000409792.3:c.3263C>T	p.Ser1088Phe	p.S1088F	ENST00000409792	NM_014159.6	1088	tCt/tTt	3/21	1	2	FACETS	0.947	0.868	1	0.947	0.868	1	CLONAL	1	TRUE	1	0.512854892951976	2		357	618	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163530	47163530	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1180147063	NA	P-0055426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	126	294	0	ENST00000409792.3:c.2596C>T	p.His866Tyr	p.H866Y	ENST00000409792	NM_014159.6	866	Cat/Tat	3/21	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.512854892951976	2		294	467	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908184	41908184	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	304	723	0	ENST00000372991.4:c.338T>C	p.Leu113Pro	p.L113P	ENST00000372991	NM_001760.3	113	cTg/cCg	2/5	1	2	FACETS	0.939	0.884	0.996	0.939	0.884	0.996	CLONAL	1	TRUE	1	0.512854892951976	2		723	1262	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64286836	64286836	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	117	372	0	ENST00000370651.3:c.51G>C	p.Met17Ile	p.M17I	ENST00000370651	NM_003463.4	17	atG/atC	2/6	1	2	FACETS	0.799	0.723	0.879	0.799	0.723	0.879	SUBCLONAL	1	TRUE	1	0.512854892951976	2		372	571	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395495	116395495	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	162	334	1	ENST00000397752.3:c.1788T>A	p.Phe596Leu	p.F596L	ENST00000397752	NM_000245.2	596	ttT/ttA	6/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.512854892951976	2		335	607	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97933395	97933395	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	133	325	0	ENST00000289081.3:c.487G>C	p.Glu163Gln	p.E163Q	ENST00000289081	NM_000136.2	163	Gag/Cag	6/15	1	2	FACETS	0.89	0.811	0.972	0.89	0.811	0.972	CLONAL	1	TRUE	1	0.512854892951976	2		325	583	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400167	139400167	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	315	721	0	ENST00000277541.6:c.4181del	p.Gly1394AlafsTer51	p.G1394Afs*51	ENST00000277541	NM_017617.3	1394	gGc/gc	25/34	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.512854892951976	2		721	1195	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0055449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	213	785	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.483533503608421	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	0	0.483533503608421	3		785	346	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0055449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	165	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.483533503608421	13	FACETS	0.958	0.908	1			1	CLONAL	11	TRUE	NA	0.483533503608421	13		622	237	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391075	89391075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs995238704	NA	P-0055449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	111	718	0	ENST00000336596.2:c.1141C>T	p.Arg381Cys	p.R381C	ENST00000336596	NM_005233.5	381	Cgc/Tgc	5/17	0.466706472842323	2	FACETS	0.973	0.893	1	0.973	0.893	1	CLONAL	2	TRUE	0	0.483533503608421	2		718	236	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231410	46231410	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0055449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	43	408	0	ENST00000334344.6:c.1250C>G	p.Ser417Ter	p.S417*	ENST00000334344	NM_152641.2	417	tCa/tGa	10/21	0.483533503608421	4	FACETS	1	0.863	1	0.513	0.432	0.602	CLONAL	1	TRUE	2	0.483533503608421	4		408	257	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481793	40481793	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	24	419	0	ENST00000264657.5:c.1111G>A	p.Asp371Asn	p.D371N	ENST00000264657	NM_139276.2	371	Gac/Aac	12/24	0.483533503608421	1	FACETS	0.633	0.504	0.776	0.633	0.504	0.776	SUBCLONAL	1	TRUE	0	0.483533503608421	1		419	119	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1331520	1331520	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	72	699	0	ENST00000400841.2:c.8G>C	p.Arg3Pro	p.R3P	ENST00000400841		3	cGg/cCg	1/6	0.483533503608421	1	FACETS	0.965	0.856	1	0.965	0.856	1	CLONAL	1	TRUE	0	0.483533503608421	1		699	234	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	105	397	1	ENST00000256196.4:c.68G>A	p.Gly23Asp	p.G23D	ENST00000256196		23	gGc/gAc	1/6	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.346248022788395	2		398	421	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410304	63410304	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	157	621	0	ENST00000330258.3:c.2863G>C	p.Ala955Pro	p.A955P	ENST00000330258	NM_152424.3	955	Gcc/Ccc	2/2	0.346248022788395	2	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.346248022788395	2		621	778	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579473	+	frameshift_variant	Frame_Shift_Del	DEL	GGG	GGG	CC	novel	NA	P-0055450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	598	1155	0	ENST00000269305.4:c.214_216delinsGG	p.Pro72GlyfsTer51	p.P72Gfs*51	ENST00000269305	NM_001126112.2	72	CCC/GG	4/11	0.269141739023805	3	FACETS	0.921	0.887	0.956	0.921	0.887	0.956	CLONAL	3	TRUE	0	0.346248022788395	3		1155	1466	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148873	119148874	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	AA	AA	T	novel	NA	P-0055450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	142	267	0	ENST00000264033.4:c.1096-3_1096-2delinsT		p.X366_splice	ENST00000264033	NM_005188.3	366			0.29737398240484	3	FACETS	0.869	0.802	0.938	0.869	0.802	0.938	CLONAL	3	TRUE	0	0.346248022788395	3		267	369	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0055451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	75	496	1	ENST00000288602.6:c.1397G>T	p.Gly466Val	p.G466V	ENST00000288602	NM_004333.4	466	gGa/gTa	11/18	0.332794794005921	3	FACETS	0.51	0.446	0.579	0.17	0.148	0.193	SUBCLONAL	1	TRUE	0	0.497805728359398	3		497	738	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006898	47006898	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1556762493	NA	P-0055451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	328	525	0	ENST00000377604.3:c.17+1G>T		p.X6_splice	ENST00000377604	NM_001204468.1	6			1	1	FACETS	0.765	0.729	0.8	1	0.995	1	SUBCLONAL	2	TRUE	0	0.497805728359398	1		525	647	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347895	89347895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	148	919	0	ENST00000301030.4:c.5055G>A	p.Met1685Ile	p.M1685I	ENST00000301030	NM_001256183.1	1685	atG/atA	9/13	0.479152698392549	2	FACETS	0.602	0.55	0.658	0.301	0.275	0.329	SUBCLONAL	1	TRUE	0	0.497805728359398	2		919	987	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280058	66280058	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	172	367	3	ENST00000273854.3:c.1631C>A	p.Thr544Lys	p.T544K	ENST00000273854	NM_004439.5	544	aCa/aAa	7/18	0.497805728359398	2	FACETS	0.873	0.813	0.932	0.873	0.813	0.932	CLONAL	2	TRUE	0	0.497805728359398	2		370	396	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17350491	17350491	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	89	698	0	ENST00000375499.3:c.619C>G	p.Leu207Val	p.L207V	ENST00000375499	NM_003000.2	207	Ctg/Gtg	6/8	0.237390246299924	1	FACETS	0.328	0.29	0.369	0.328	0.29	0.369	INDETERMINATE	1	TRUE	0	0.497805728359398	1		698	818	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937109	36937109	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	284	978	1	ENST00000361632.4:c.1210C>T	p.Gln404Ter	p.Q404*	ENST00000361632		404	Cag/Tag	9/16	0.237390246299924	1	FACETS	0.853	0.802	0.904	0.853	0.802	0.904	INDETERMINATE	1	TRUE	0	0.497805728359398	1		979	1005	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844416	156844416	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	364	1189	0	ENST00000524377.1:c.1249G>T	p.Gly417Trp	p.G417W	ENST00000524377	NM_002529.3	417	Ggg/Tgg	10/17	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.497805728359398	2		1189	1402	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117708	108117708	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1387448237	NA	P-0055451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	52	257	0	ENST00000278616.4:c.919A>G	p.Lys307Glu	p.K307E	ENST00000278616	NM_000051.3	307	Aaa/Gaa	8/63	1	2	FACETS	0.584	0.499	0.676	0.584	0.499	0.676	SUBCLONAL	1	TRUE	1	0.497805728359398	2		257	358	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12043974	12043974	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	56	322	0	ENST00000396373.4:c.1353A>C	p.Glu451Asp	p.E451D	ENST00000396373	NM_001987.4	451	gaA/gaC	8/8	1	2	FACETS	0.574	0.493	0.661	0.574	0.493	0.661	SUBCLONAL	1	TRUE	1	0.497805728359398	2		322	392	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125098	46125098	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0055451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	69	238	0	ENST00000334344.6:c.284+1G>T		p.X95_splice	ENST00000334344	NM_152641.2	95			1	2	FACETS	0.937	0.823	1	0.937	0.823	1	CLONAL	1	TRUE	1	0.497805728359398	2		238	296	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244618	46244619	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0055451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	193	646	0	ENST00000334344.6:c.2712_2713del	p.Gln905SerfsTer45	p.Q905Sfs*45	ENST00000334344	NM_152641.2	904	caGCaa/caaa	15/21	1	2	FACETS	0.944	0.875	1	0.944	0.875	1	CLONAL	1	TRUE	1	0.497805728359398	2		646	821	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233115	69233115	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	130	358	0	ENST00000462284.1:c.980G>C	p.Arg327Thr	p.R327T	ENST00000462284	NM_002392.5	327	aGa/aCa	11/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.497805728359398	2		358	506	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000302	42000303	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	132	472	0	ENST00000219905.7:c.2322dup	p.Ala775CysfsTer8	p.A775Cfs*8	ENST00000219905	NM_001164273.1	774	gat/gaTt	7/24	0.237390246299924	1	FACETS	0.818	0.747	0.891	0.818	0.747	0.891	INDETERMINATE	1	TRUE	0	0.497805728359398	1		472	487	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041828	42041828	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	92	566	0	ENST00000219905.7:c.6023del	p.Ile2008LysfsTer14	p.I2008Kfs*14	ENST00000219905	NM_001164273.1	2008	aTa/aa	17/24	0.237390246299924	1	FACETS	0.447	0.398	0.5	0.447	0.398	0.5	INDETERMINATE	1	TRUE	0	0.497805728359398	1		566	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578564	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTGTAGGAAG	ACTGTAGGAAG	-	novel	NA	P-0055451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	505	1112	0	ENST00000269305.4:c.376-10_376del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	0.479152698392549	2	FACETS	0.867	0.832	0.902	0.867	0.832	0.902	CLONAL	2	TRUE	0	0.497805728359398	2		1112	1170	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976470	25976470	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	73	481	0	ENST00000435504.4:c.1075G>C	p.Glu359Gln	p.E359Q	ENST00000435504		359	Gag/Cag	11/13	0.337259122237456	3	FACETS	0.504	0.44	0.573	0.252	0.22	0.287	SUBCLONAL	1	TRUE	1	0.497805728359398	3		481	727	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241072	39241072	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	110	655	0	ENST00000402219.2:c.1999G>C	p.Asp667His	p.D667H	ENST00000402219	NM_005633.3	667	Gat/Cat	12/23	0.337259122237456	3	FACETS	0.64	0.574	0.709	0.32	0.287	0.355	SUBCLONAL	1	TRUE	1	0.497805728359398	3		655	863	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022302	31022302	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	195	616	1	ENST00000375687.4:c.1787G>C	p.Arg596Pro	p.R596P	ENST00000375687	NM_015338.5	596	cGg/cCg	13/13	0.337259122237456	3	FACETS	1	0.982	1	0.594	0.551	0.639	CLONAL	1	TRUE	1	0.497805728359398	3		617	823	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542680	187542680	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	325	538	0	ENST00000441802.2:c.5060G>T	p.Gly1687Val	p.G1687V	ENST00000441802	NM_005245.3	1687	gGg/gTg	10/27	0.497805728359398	2	FACETS	0.921	0.876	0.966	0.921	0.876	0.966	CLONAL	2	TRUE	0	0.497805728359398	2		538	709	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638860	176638860	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	250	659	0	ENST00000439151.2:c.3460G>T	p.Val1154Leu	p.V1154L	ENST00000439151	NM_022455.4	1154	Gtg/Ttg	5/23	0.222561362001479	3	FACETS	1	0.984	1	0.579	0.541	0.618	INDETERMINATE	1	TRUE	1	0.497805728359398	3		659	1083	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444460	50444460	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	250	393	0	ENST00000331340.3:c.390T>A	p.Asn130Lys	p.N130K	ENST00000331340	NM_006060.4	130	aaT/aaA	4/8	0.486070739681391	3	FACETS	0.98	0.923	1	0.98	0.923	1	CLONAL	2	TRUE	1	0.497805728359398	3		393	640	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371843	116371843	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1715	344	497	0	ENST00000397752.3:c.1322C>G	p.Ser441Cys	p.S441C	ENST00000397752	NM_000245.2	441	tCt/tGt	3/21	0.497805728359398	10	FACETS	1	0.946	1			1	CLONAL	2	TRUE	NA	0.497805728359398	10		497	2059	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0055452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	173	354	1				ENST00000310581	NM_198253.2	-/1132			0.426175129212628	1	FACETS	0.808	0.763	0.853	0.808	0.763	0.853	INDETERMINATE	1	TRUE	0	0.869961023918943	1		355	278	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0055452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	800	436	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	0.860183742212523	4	FACETS	0.972	0.958	0.984	0.972	0.958	0.984	CLONAL	4	TRUE	0	0.869961023918943	4		436	885	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7978952	7978952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139689690	NA	P-0055452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	294	591	3	ENST00000319144.4:c.1615G>A	p.Glu539Lys	p.E539K	ENST00000319144	NM_001139.2	539	Gaa/Aaa	12/15	1	2	FACETS	0.984	0.932	1	0.984	0.932	1	CLONAL	1	TRUE	1	0.869961023918943	2		594	687	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120557	94120557	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	101	343	0	ENST00000369303.4:c.494T>C	p.Met165Thr	p.M165T	ENST00000369303	NM_004440.3	165	aTg/aCg	3/17	0.864630351057979	1	FACETS	0.49	0.444	0.536	0.49	0.444	0.536	SUBCLONAL	1	TRUE	0	0.869961023918943	1		343	268	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747054	40747054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	310	635	1	ENST00000373198.4:c.3028G>A	p.Glu1010Lys	p.E1010K	ENST00000373198	NM_133170.3	1010	Gaa/Aaa	22/32	1	2	FACETS	0.988	0.938	1	0.988	0.938	1	CLONAL	1	TRUE	1	0.869961023918943	2		636	721	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780598	56780598	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	347	515	0	ENST00000337432.4:c.613C>T	p.Leu205Phe	p.L205F	ENST00000337432	NM_058216.2	205	Ctt/Ttt	4/9	1	2	FACETS	0.967	0.92	1	0.967	0.92	1	CLONAL	1	TRUE	1	0.869961023918943	2		515	825	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112641	115112641	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0055452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	407	934	0	ENST00000257566.3:c.1100-1G>A		p.X367_splice	ENST00000257566	NM_016569.3	367			1	2	FACETS	0.925	0.883	0.968	0.925	0.883	0.968	CLONAL	1	TRUE	1	0.869961023918943	2		934	1011	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518499	204518499	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61754765	NA	P-0055452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	347	306	0	ENST00000367182.3:c.1162C>T	p.Pro388Ser	p.P388S	ENST00000367182	NM_001278516.1	388	Ccc/Tcc	11/11	0.869961023918943	3	FACETS	0.982	0.942	1	0.982	0.942	1	CLONAL	2	TRUE	1	0.869961023918943	3		306	583	SUCCESS
APC	324	MSKCC	GRCh37	5	112173441	112173441	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	155	287	0	ENST00000257430.4:c.2150T>C	p.Met717Thr	p.M717T	ENST00000257430	NM_000038.5	717	aTg/aCg	16/16	0.426175129212628	1	FACETS	0.694	0.649	0.739	0.694	0.649	0.739	INDETERMINATE	1	TRUE	0	0.869961023918943	1		287	290	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866098	37866098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs971655376	NA	P-0055452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	466	903	0	ENST00000269571.5:c.607C>T	p.Arg203Cys	p.R203C	ENST00000269571		203	Cgc/Tgc	5/27	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.869961023918943	2		903	1012	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743883	40743883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	242	616	1	ENST00000373198.4:c.3112G>A	p.Glu1038Lys	p.E1038K	ENST00000373198	NM_133170.3	1038	Gag/Aag	23/32	1	2	FACETS	0.883	0.831	0.936	0.883	0.831	0.936	CLONAL	1	TRUE	1	0.869961023918943	2		617	630	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458429	12458429	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	361	667	0	ENST00000287820.6:c.1046G>A	p.Gly349Glu	p.G349E	ENST00000287820	NM_015869.4	349	gGa/gAa	6/7	1	2	FACETS	0.983	0.937	1	0.983	0.937	1	CLONAL	1	TRUE	1	0.869961023918943	2		667	844	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023961	27023961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	84	98	1	ENST00000324856.7:c.1067G>A	p.Arg356Lys	p.R356K	ENST00000324856	NM_006015.4	356	aGg/aAg	1/20	0.869092796180037	2	FACETS	0.985	0.933	1	0.985	0.933	1	CLONAL	2	TRUE	0	0.869961023918943	2		99	98	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78425894	78425894	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	37	413	0	ENST00000370768.2:c.1551G>C	p.Trp517Cys	p.W517C	ENST00000370768	NM_003902.3	517	tgG/tgC	16/20	0.294937527115147	4	FACETS	0.215	0.177	0.259			1	INDETERMINATE	1	TRUE	NA	0.869961023918943	4		413	739	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564867	226564867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	606	592	0	ENST00000366794.5:c.1883C>T	p.Ser628Phe	p.S628F	ENST00000366794	NM_001618.3	628	tCc/tTc	13/23	0.869961023918943	3	FACETS	0.977	0.947	1	0.977	0.947	1	CLONAL	2	TRUE	1	0.869961023918943	3		592	1023	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922192	100922192	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	227	395	1	ENST00000325455.5:c.2320C>T	p.Gln774Ter	p.Q774*	ENST00000325455	NM_001202474.3	774	Cag/Tag	5/8	0.869961023918943	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.869961023918943	1		396	278	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178696	108178696	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	108	214	0	ENST00000278616.4:c.5747T>A	p.Met1916Lys	p.M1916K	ENST00000278616	NM_000051.3	1916	aTg/aAg	38/63	0.869961023918943	1	FACETS	0.894	0.835	0.949	0.894	0.835	0.949	CLONAL	1	TRUE	0	0.869961023918943	1		214	157	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514153	125514153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	195	356	0	ENST00000428830.2:c.1091G>A	p.Gly364Glu	p.G364E	ENST00000428830	NM_001114121.2	364	gGa/gAa	10/14	0.869961023918943	1	FACETS	0.97	0.928	1	0.97	0.928	1	CLONAL	1	TRUE	0	0.869961023918943	1		356	261	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444115	49444115	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	510	998	0	ENST00000301067.7:c.3256T>A	p.Leu1086Met	p.L1086M	ENST00000301067	NM_003482.3	1086	Ttg/Atg	11/54	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.869961023918943	2		998	1083	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939107	48939107	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	152	228	0	ENST00000267163.4:c.939G>C	p.Glu313Asp	p.E313D	ENST00000267163	NM_000321.2	313	gaG/gaC	9/27	0.39877840239693	3	FACETS	1	0.979	1	0.584	0.54	0.63	INDETERMINATE	1	TRUE	1	0.869961023918943	3		228	429	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988229	36988229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	301	764	1	ENST00000354822.5:c.424G>A	p.Gly142Arg	p.G142R	ENST00000354822	NM_001079668.2	142	Gga/Aga	2/3	1	2	FACETS	0.991	0.94	1	0.991	0.94	1	CLONAL	1	TRUE	1	0.869961023918943	2		765	698	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396257	396257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	384	982	0	ENST00000262320.3:c.769G>A	p.Asp257Asn	p.D257N	ENST00000262320	NM_003502.3	257	Gat/Aat	2/11	1	2	FACETS	0.955	0.911	1	0.955	0.911	1	CLONAL	1	TRUE	1	0.869961023918943	2		982	924	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008444	70008444	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	173	292	0	ENST00000394351.3:c.731G>C	p.Gly244Ala	p.G244A	ENST00000394351	NM_000248.3	244	gGa/gCa	8/9	1	2	FACETS	0.98	0.913	1	0.98	0.913	1	CLONAL	1	TRUE	1	0.869961023918943	2		292	406	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638417	176638417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747103756	NA	P-0055452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	393	708	1	ENST00000439151.2:c.3017C>T	p.Pro1006Leu	p.P1006L	ENST00000439151	NM_022455.4	1006	cCt/cTt	5/23	0.426175129212628	1	FACETS	0.689	0.66	0.717	0.689	0.66	0.717	INDETERMINATE	1	TRUE	0	0.869961023918943	1		709	741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0055453-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	104	620	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.309801187612136	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	0	0.309801187612136	1		620	431	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143984	11143984	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs267607070	NA	P-0055453-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	81	776	0	ENST00000358026.2:c.3565C>T	p.Arg1189Ter	p.R1189*	ENST00000358026	NM_001128849.1	1189	Cga/Tga	26/36	0.309801187612136	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	0	0.309801187612136	1		776	385	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940561	71940561	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055453-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	54	923	0	ENST00000298229.2:c.712C>T	p.Gln238Ter	p.Q238*	ENST00000298229	NM_001567.3	238	Cag/Tag	6/28	1	2	FACETS	0.599	0.511	0.695	0.599	0.511	0.695	SUBCLONAL	1	FALSE	1	0.309801187612136	2		923	582	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988188	36988188	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0055453-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	71	483	0	ENST00000354822.5:c.463+2T>A		p.X155_splice	ENST00000354822	NM_001079668.2	155			0.309801187612136	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	0	0.309801187612136	1		483	307	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570421	87570421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1564499587	NA	P-0055453-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	33	919	0	ENST00000277120.3:c.2161G>A	p.Asp721Asn	p.D721N	ENST00000277120		721	Gac/Aac	17/19	0.309801187612136	1	FACETS	0.403	0.328	0.488	0.403	0.328	0.488	SUBCLONAL	1	FALSE	0	0.309801187612136	1		919	447	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187092	11187092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	42	745	2	ENST00000361445.4:c.6326G>A	p.Arg2109Gln	p.R2109Q	ENST00000361445	NM_004958.3	2109	cGa/cAa	45/58	0.33270563123835	2	FACETS	0.686	0.578	0.804	0.343	0.289	0.402	SUBCLONAL	1	TRUE	0	0.534870035160963	2		747	229	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579432	7579433	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0055458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	253	1152	2	ENST00000269305.4:c.254dup	p.Ala86CysfsTer63	p.A86Cfs*63	ENST00000269305	NM_001126112.2	85	cct/ccCt	4/11	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.534870035160963	2		1154	405	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266830	198266830	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	55	611	0	ENST00000335508.6:c.2102T>G	p.Val701Gly	p.V701G	ENST00000335508	NM_012433.2	701	gTt/gGt	15/25	1	2	FACETS	0.846	0.732	0.969	0.846	0.732	0.969	CLONAL	1	TRUE	1	0.534870035160963	2		611	243	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530183	212530183	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	34	355	1	ENST00000342788.4:c.1736A>T	p.Lys579Met	p.K579M	ENST00000342788	NM_005235.2	579	aAg/aTg	15/28	1	2	FACETS	0.908	0.755	1	0.908	0.755	1	CLONAL	1	TRUE	1	0.534870035160963	2		356	140	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	43	115	0				ENST00000310581	NM_198253.2	-/1132			0.386873341503362	3	FACETS	0.715	0.6	0.842	0.358	0.3	0.421	SUBCLONAL	1	TRUE	1	0.386873341503362	3		115	371	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0055460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	281	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.386873341503362	4	FACETS	0.988	0.934	1	0.988	0.934	1	CLONAL	3	TRUE	1	0.386873341503362	4		622	680	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806092	1806092	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913484	NA	P-0055460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	363	1196	0	ENST00000260795.2:c.1111A>T	p.Ser371Cys	p.S371C	ENST00000260795		371	Agt/Tgt	8/17	0.285165910269518	3	FACETS	0.856	0.815	0.897	1	0.994	1	CLONAL	3	TRUE	1	0.386873341503362	3		1196	872	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0055460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	346	893	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.288214625023162	3	FACETS	0.861	0.82	0.904	0.861	0.82	0.904	CLONAL	3	TRUE	0	0.386873341503362	3		893	826	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173675	108173675	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	30	394	0	ENST00000278616.4:c.5415G>A	p.Trp1805Ter	p.W1805*	ENST00000278616	NM_000051.3	1805	tgG/tgA	36/63	0.386873341503362	3	FACETS	0.472	0.38	0.576	0.236	0.19	0.288	SUBCLONAL	1	TRUE	1	0.386873341503362	3		394	392	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787737	135787737	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0055460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	209	539	0	ENST00000298552.3:c.845C>G	p.Ser282Ter	p.S282*	ENST00000298552	NM_001162426.1	282	tCa/tGa	9/23	0.386873341503362	2	FACETS	0.984	0.921	1	0.984	0.921	1	CLONAL	2	TRUE	0	0.386873341503362	2		539	549	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666615	206666615	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	196	795	0	ENST00000367120.3:c.1949C>G	p.Ser650Cys	p.S650C	ENST00000367120	NM_014002.3	650	tCt/tGt	20/22	0.285165910269518	3	FACETS	0.866	0.805	0.929	0.866	0.805	0.929	CLONAL	2	TRUE	1	0.386873341503362	3		795	698	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025517	1025517	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	231	961	0	ENST00000358495.3:c.858G>C	p.Lys286Asn	p.K286N	ENST00000358495	NM_134424.2	286	aaG/aaC	9/12	0.12857083657156	5	FACETS	1	0.955	1			1	INDETERMINATE	2	TRUE	NA	0.386873341503362	5		961	916	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26927979	26927979	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	77	456	0	ENST00000381527.3:c.418C>G	p.His140Asp	p.H140D	ENST00000381527	NM_001260.1	140	Cac/Gac	4/13	1	2	FACETS	0.998	0.881	1	0.998	0.881	1	CLONAL	1	TRUE	1	0.386873341503362	2		456	399	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772382	56772382	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555593569	NA	P-0055460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	146	450	0	ENST00000337432.4:c.236C>T	p.Ser79Phe	p.S79F	ENST00000337432	NM_058216.2	79	tCt/tTt	2/9	0.386873341503362	3	FACETS	0.804	0.738	0.873	0.804	0.738	0.873	CLONAL	2	TRUE	1	0.386873341503362	3		450	560	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262921	46262921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	54	495	0	ENST00000371998.3:c.1094C>T	p.Ser365Leu	p.S365L	ENST00000371998		365	tCa/tTa	10/23	0.160077849122232	3	FACETS	0.777	0.665	0.898	0.388	0.332	0.449	INDETERMINATE	1	TRUE	1	0.386873341503362	3		495	429	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032785	30032790	+	inframe_deletion	In_Frame_Del	DEL	CTGGGG	CTGGGG	-	novel	NA	P-0055460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	180	411	0	ENST00000338641.4:c.162_167del	p.Gly55_Leu56del	p.G55_L56del	ENST00000338641	NM_000268.3	54	CTGGGG/-	2/16	0.288214625023162	3	FACETS	1	0.984	1	0.793	0.738	0.848	CLONAL	2	TRUE	0	0.386873341503362	3		411	467	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233117	55233117	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	137	627	0	ENST00000275493.2:c.1867A>G	p.Asn623Asp	p.N623D	ENST00000275493	NM_005228.3	623	Aac/Gac	15/28	0.173838118488	4	FACETS	1	0.984	1	0.689	0.627	0.753	INDETERMINATE	1	TRUE	2	0.386873341503362	4		627	713	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650893	93650893	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	192	453	0	ENST00000375746.1:c.1819C>A	p.Leu607Met	p.L607M	ENST00000375746	NM_001174167.1	607	Ctg/Atg	13/14	0.386873341503362	2	FACETS	0.958	0.894	1	0.958	0.894	1	CLONAL	2	TRUE	0	0.386873341503362	2		453	518	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945174	44945175	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0055460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	160	665	0	ENST00000377967.4:c.3500_3501dup	p.Val1168LeufsTer11	p.V1168Lfs*11	ENST00000377967	NM_021140.2	1166	-/TT	24/29	0.20694907703611	5	FACETS	0.91	0.837	0.987	0.607	0.558	0.658	INDETERMINATE	2	TRUE	2	0.386873341503362	5		665	718	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210310	123210310	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	86	324	0	ENST00000218089.9:c.2662C>T	p.Gln888Ter	p.Q888*	ENST00000218089	NM_001042749.1	888	Cag/Tag	26/35	0.20694907703611	5	FACETS	1	0.92	1	0.691	0.616	0.769	INDETERMINATE	2	TRUE	2	0.386873341503362	5		324	339	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	34	115	0				ENST00000310581	NM_198253.2	-/1132			0.192220770050646	1	FACETS	0.971	0.801	1	0.971	0.801	1	CLONAL	1	TRUE	0	0.312723920964053	1		115	189	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0055461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	275	571	0	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	0.312723920964053	9	FACETS	0.939	0.885	0.993			1	CLONAL	5	TRUE	NA	0.312723920964053	9		571	785	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3795330	3795330	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	76	378	0	ENST00000262367.5:c.3862del	p.Arg1288GlyfsTer25	p.R1288Gfs*25	ENST00000262367	NM_004380.2	1288	Cgg/gg	22/31	0.192220770050646	1	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	0	0.312723920964053	1		378	392	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132437	11132437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs281875227	NA	P-0055461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	113	947	0	ENST00000358026.2:c.2653C>T	p.Arg885Cys	p.R885C	ENST00000358026	NM_001128849.1	885	Cgc/Tgc	19/36	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.312723920964053	2		947	646	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29107975	29108052	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAAAGCCAGCTTTACCTCTCCACAGGCACCACTAGAGGGAAAAACAAAGATAGTGATTGTCTGAATGTTTTTAATTAT	GAAAGCCAGCTTTACCTCTCCACAGGCACCACTAGAGGGAAAAACAAAGATAGTGATTGTCTGAATGTTTTTAATTAT	-	novel	NA	P-0055461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	21	469	0	ENST00000328354.6:c.684-47_714del		p.X228_splice	ENST00000328354	NM_007194.3	228		6/15	0.192220770050646	1	FACETS	0.278	0.213	0.353	0.278	0.213	0.353	SUBCLONAL	1	TRUE	0	0.312723920964053	1		469	408	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71050179	71050179	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0055461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	43	282	0	ENST00000318789.4:c.1006A>T	p.Arg336Ter	p.R336*	ENST00000318789	NM_032682.5	336	Aga/Tga	13/21	1	2	FACETS	0.733	0.615	0.864	0.733	0.615	0.864	SUBCLONAL	1	TRUE	1	0.312723920964053	2		282	375	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414395	6414395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	27	243	0	ENST00000356142.4:c.29G>A	p.Gly10Glu	p.G10E	ENST00000356142	NM_018890.3	10	gGa/gAa	1/7	1	2	FACETS	0.468	0.372	0.577	0.468	0.372	0.577	SUBCLONAL	1	TRUE	1	0.312723920964053	2		243	369	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772923	135772924	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	105	555	0	ENST00000298552.3:c.2699dup	p.Arg901GlufsTer3	p.R901Efs*3	ENST00000298552	NM_001162426.1	900	cag/caAg	21/23	0.248573732324318	2	FACETS	1	0.979	1	0.672	0.604	0.742	CLONAL	1	TRUE	0	0.312723920964053	2		555	500	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0055462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	47	396	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.220553097679697	2		396	308	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221243	1221243	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1057520606	NA	P-0055462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	84	1110	0	ENST00000326873.7:c.766G>T	p.Glu256Ter	p.E256*	ENST00000326873	NM_000455.4	256	Gaa/Taa	6/10	0.220553097679697	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	FALSE	0	0.220553097679697	1		1110	629	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271870	15271870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528151296	NA	P-0055462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	54	1446	0	ENST00000263388.2:c.6569C>T	p.Ala2190Val	p.A2190V	ENST00000263388	NM_000435.2	2190	gCg/gTg	33/33	0.220553097679697	1	FACETS	0.652	0.556	0.758	0.652	0.556	0.758	SUBCLONAL	1	FALSE	0	0.220553097679697	1		1446	668	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617189	100617189	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	79	832	0	ENST00000308731.7:c.560C>A	p.Pro187His	p.P187H	ENST00000308731	NM_000061.2	187	cCt/cAt	7/19	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	FALSE	1	0.220553097679697	2		832	628	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411387	63411387	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	101	1179	0	ENST00000330258.3:c.1780C>A	p.His594Asn	p.H594N	ENST00000330258	NM_152424.3	594	Cac/Aac	2/2	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.220553097679697	2		1179	674	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741544	17741544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774115486	NA	P-0055462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	52	566	0	ENST00000250003.3:c.215C>T	p.Ala72Val	p.A72V	ENST00000250003	NM_002478.4	72	gCc/gTc	1/3	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.220553097679697	2		566	369	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923808	39923808	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	80	1109	0	ENST00000378444.4:c.3283C>A	p.Pro1095Thr	p.P1095T	ENST00000378444	NM_001123385.1	1095	Cca/Aca	7/15	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	FALSE	1	0.220553097679697	2		1109	715	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132438	11132438	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	83	1230	1	ENST00000358026.2:c.2654G>T	p.Arg885Leu	p.R885L	ENST00000358026	NM_001128849.1	885	cGc/cTc	19/36	0.220553097679697	1	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	FALSE	0	0.220553097679697	1		1231	658	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456787	32456787	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	83	949	0	ENST00000332351.3:c.105C>A	p.Asp35Glu	p.D35E	ENST00000332351	NM_024426.4	35	gaC/gaA	1/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.220553097679697	2		949	565	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954181	32954181	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs80359171	NA	P-0055462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	48	544	0	ENST00000380152.3:c.9155G>T	p.Arg3052Leu	p.R3052L	ENST00000380152		3052	cGg/cTg	24/27	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	FALSE	1	0.220553097679697	2		544	382	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281455	49281455	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	30	806	0	ENST00000282018.3:c.502G>T	p.Ala168Ser	p.A168S	ENST00000282018	NM_020377.2	168	Gct/Tct	1/1	1	2	FACETS	0.584	0.47	0.714	0.584	0.47	0.714	SUBCLONAL	1	FALSE	1	0.220553097679697	2		806	466	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679765	88679765	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	57	827	1	ENST00000360948.2:c.698G>T	p.Gly233Val	p.G233V	ENST00000360948	NM_001012338.2	233	gGc/gTc	7/19	1	2	FACETS	0.968	0.831	1	0.968	0.831	1	CLONAL	1	FALSE	1	0.220553097679697	2		828	534	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396650	396650	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0055462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	91	933	0	ENST00000262320.3:c.376A>T	p.Lys126Ter	p.K126*	ENST00000262320	NM_003502.3	126	Aag/Tag	2/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.220553097679697	2		933	589	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857551	9857551	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	42	586	0	ENST00000330684.3:c.3850C>A	p.Leu1284Ile	p.L1284I	ENST00000330684	NM_001134407.1	1284	Cta/Ata	13/13	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	FALSE	1	0.220553097679697	2		586	337	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794118	242794118	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	78	1061	0	ENST00000334409.5:c.610C>G	p.Arg204Gly	p.R204G	ENST00000334409	NM_005018.2	204	Cgc/Ggc	4/5	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.220553097679697	2		1061	596	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462342	89462342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1301680905	NA	P-0055462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	48	596	1	ENST00000336596.2:c.1814C>T	p.Pro605Leu	p.P605L	ENST00000336596	NM_005233.5	605	cCt/cTt	10/17	0.220553097679697	1	FACETS	0.993	0.842	1	0.993	0.842	1	CLONAL	1	FALSE	0	0.220553097679697	1		597	390	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582445	119582445	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	18	288	0	ENST00000316626.5:c.956G>C	p.Arg319Pro	p.R319P	ENST00000316626		319	cGa/cCa	10/12	0.220553097679697	1	FACETS	0.629	0.474	0.81	0.629	0.474	0.81	SUBCLONAL	1	FALSE	0	0.220553097679697	1		288	231	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513558	149513558	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	57	683	0	ENST00000261799.4:c.645C>A	p.Asn215Lys	p.N215K	ENST00000261799	NM_002609.3	215	aaC/aaA	5/23	0.220553097679697	0	FACETS	0.872	0.75	1			1	CLONAL	1	FALSE	0	0.220553097679697	0		683	462	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519771	137519772	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0055462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	14	226	0	ENST00000367739.4:c.866_867del	p.Ser289CysfsTer12	p.S289Cfs*12	ENST00000367739	NM_000416.2	289	tCT/t	7/7	0.220553097679697	1	FACETS	0.538	0.389	0.717	0.538	0.389	0.717	SUBCLONAL	1	FALSE	0	0.220553097679697	1		226	210	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8733779	8733779	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0055462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	35	650	0	ENST00000356435.5:c.64+1G>A		p.X22_splice	ENST00000356435		22			0.220553097679697	1	FACETS	0.664	0.545	0.799	0.664	0.545	0.799	SUBCLONAL	1	FALSE	0	0.220553097679697	1		650	425	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801112	135801112	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	23	386	0	ENST00000298552.3:c.225G>T	p.Arg75Ser	p.R75S	ENST00000298552	NM_001162426.1	75	agG/agT	5/23	0.220553097679697	1	FACETS	0.61	0.476	0.765	0.61	0.476	0.765	SUBCLONAL	1	FALSE	0	0.220553097679697	1		386	304	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410240	63410240	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	67	1051	0	ENST00000330258.3:c.2927G>T	p.Ser976Ile	p.S976I	ENST00000330258	NM_152424.3	976	aGc/aTc	2/2	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	FALSE	1	0.220553097679697	2		1051	587	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0055463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	52	753	1	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	1	2	FACETS	0.75	0.636	0.877	0.75	0.636	0.877	SUBCLONAL	1	TRUE	1	0.12	2		754	1155	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520017	NA	P-0055463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1668	79	1294	0	ENST00000326873.7:c.647C>T	p.Ser216Phe	p.S216F	ENST00000326873	NM_000455.4	216	tCc/tTc	5/10	0.3	3	FACETS	0.799	0.699	0.907			1	CLONAL	1	TRUE	NA	0.12	3		1294	1747	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs267605076	NA	P-0055463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	57	932	0	ENST00000269305.4:c.672G>T	p.Glu224Asp	p.E224D	ENST00000269305	NM_001126112.2	224	gaG/gaT	6/11	1	2	FACETS	0.798	0.682	0.925	0.798	0.682	0.925	CLONAL	1	TRUE	1	0.12	2		932	1191	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032136	26032136	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	33	731	0	ENST00000244661.2:c.153G>C	p.Glu51Asp	p.E51D	ENST00000244661	NM_003537.3	51	gaG/gaC	1/1	0.226521989198989	4	FACETS	0.565	0.458	0.687	0.283	0.229	0.344	SUBCLONAL	1	TRUE	2	0.12	4		731	1090	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205313	61205313	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	49	588	0	ENST00000301761.2:c.253C>G	p.Leu85Val	p.L85V	ENST00000301761	NM_017841.2	85	Ctt/Gtt	2/4	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.12	2		588	756	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0055464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	174	890	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.245180433772819	2	FACETS	0.975	0.9	1	0.975	0.9	1	CLONAL	2	TRUE	0	0.245180433772819	2		893	728	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38504676	38504676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	73	917	0	ENST00000254066.5:c.287C>T	p.Ser96Leu	p.S96L	ENST00000254066	NM_000964.3	96	tCa/tTa	3/9	0.23693747277744	3	FACETS	0.89	0.778	1	0.445	0.389	0.506	CLONAL	1	TRUE	1	0.245180433772819	3		917	751	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586058	29586058	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876660206	NA	P-0055464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	29	335	0	ENST00000356175.3:c.4278G>C	p.Gln1426His	p.Q1426H	ENST00000356175	NM_000267.3	1426	caG/caC	32/57	0.23693747277744	3	FACETS	1	0.916	1	0.635	0.513	0.772	CLONAL	1	TRUE	1	0.245180433772819	3		335	209	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44515577	44515577	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	67	829	0	ENST00000291552.4:c.319G>C	p.Asp107His	p.D107H	ENST00000291552	NM_006758.2	107	Gac/Cac	5/8	0.245180433772819	3	FACETS	0.73	0.633	0.835	0.365	0.316	0.418	SUBCLONAL	1	TRUE	1	0.245180433772819	3		829	841	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199475	16199475	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	50	386	0	ENST00000375759.3:c.248C>G	p.Thr83Ser	p.T83S	ENST00000375759	NM_015001.2	83	aCc/aGc	2/15	0.245180433772819	5	FACETS	1	0.93	1			1	CLONAL	1	TRUE	NA	0.245180433772819	5		386	477	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264501	16265211	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTAAGACTCTCAGGCCCAGGTGAGCAACTGCCCCACCTACAGGGAGGAAGACGTAGGTAGTCCCTGCCAGCCCATCTCCCTGGCCTGTCATGGAAGCATTAACTGTATTCTTGTTGTTGTTGAAACAGTCTCTGTCGCCTGGGCTGGAGTGCAGCGGTGCGATCTCTGTTCATTATAGCCTCTGCCTCCCGGGTTCAAGCCATTCTCTTGCCTCAGCCTCCTGAGTAGCTGGGATTATAGGCACGCACCACCATGGCACCACCATGCCCAGCTAATTTTTTGTATTTTTAGTAGAGATGGGGTTTCACCATGTTGGCCAGGCCAGCCTTGAACTCCTGACCTCAAGTGATCTGGCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCCTGAGCCACTGTGCCTGGCCAGTAACGGTATTCTTGAAGTGAGCAATGAAGGGTCCACTATGCTTCTACTTGGTGGGGGGATGTAAAGTACCTCTAGACCCAGAAACAAGGCTTTACAGTTTTTAAAAATTATTATTTTTTAAATCAGCTTTCTCAGGTTGAAAAAAAGCTTTTTTTTTTTTTTTTTTTCATTCAAATATCAGGGTAGCCTTTAAAGTCATCTCAGAGGTGGGGGTTTTTGTGGACCTGATACTGTGGGTTGGATGTGGGCTGCTGTTTGACTAGGAGGCCCCTGCTCACTGGCAGCTGGCCTCTGCCTCA	GGTAAGACTCTCAGGCCCAGGTGAGCAACTGCCCCACCTACAGGGAGGAAGACGTAGGTAGTCCCTGCCAGCCCATCTCCCTGGCCTGTCATGGAAGCATTAACTGTATTCTTGTTGTTGTTGAAACAGTCTCTGTCGCCTGGGCTGGAGTGCAGCGGTGCGATCTCTGTTCATTATAGCCTCTGCCTCCCGGGTTCAAGCCATTCTCTTGCCTCAGCCTCCTGAGTAGCTGGGATTATAGGCACGCACCACCATGGCACCACCATGCCCAGCTAATTTTTTGTATTTTTAGTAGAGATGGGGTTTCACCATGTTGGCCAGGCCAGCCTTGAACTCCTGACCTCAAGTGATCTGGCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCCTGAGCCACTGTGCCTGGCCAGTAACGGTATTCTTGAAGTGAGCAATGAAGGGTCCACTATGCTTCTACTTGGTGGGGGGATGTAAAGTACCTCTAGACCCAGAAACAAGGCTTTACAGTTTTTAAAAATTATTATTTTTTAAATCAGCTTTCTCAGGTTGAAAAAAAGCTTTTTTTTTTTTTTTTTTTCATTCAAATATCAGGGTAGCCTTTAAAGTCATCTCAGAGGTGGGGGTTTTTGTGGACCTGATACTGTGGGTTGGATGTGGGCTGCTGTTTGACTAGGAGGCCCCTGCTCACTGGCAGCTGGCCTCTGCCTCA	-	novel	NA	P-0055464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	68	748	1	ENST00000375759.3:c.10704+3_10706del		p.X3568_splice	ENST00000375759	NM_015001.2	3568		13/15	0.23915869544714	3	FACETS	0.816	0.709	0.932			1	CLONAL	1	TRUE	NA	0.245180433772819	3		749	763	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265369	16265787	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGGTCGGTTGTCCTGTGTCCTTCCTTCACATGTACACCCACAGGTGGGGCTGATCAGGGTAGGTGGGCCTACTCATCTGGTGCCCACTAGATCTGGCCCCAGAGGTGGGCAAAGGGGCATTTTGGACAGAAGTCAGTAGAGCACATGGGGCGGGGCGCCATCACCCATCCTGAAGAGAACCCAGGGAACCGCTGAGAACACAGGTTTTCCATGAGTTTAAAGATAGGGCCCCAGGGGGTTCCTGTTTATAGTTTTCTGACACCTGCTAGGTCTTCCAGTAGACATAGTCCTGGCACATTTGCTGGTTGGGGACTGATTTGGCCTGGCTCTTAGCATTGGGCCTCTTCAGGGCTCCCCAATGGAAGTGGAGTTGTGGGGGTGAAGACAGACGGTCCCACTTTGCTCTCTATCCTGTCTC	CAGGTCGGTTGTCCTGTGTCCTTCCTTCACATGTACACCCACAGGTGGGGCTGATCAGGGTAGGTGGGCCTACTCATCTGGTGCCCACTAGATCTGGCCCCAGAGGTGGGCAAAGGGGCATTTTGGACAGAAGTCAGTAGAGCACATGGGGCGGGGCGCCATCACCCATCCTGAAGAGAACCCAGGGAACCGCTGAGAACACAGGTTTTCCATGAGTTTAAAGATAGGGCCCCAGGGGGTTCCTGTTTATAGTTTTCTGACACCTGCTAGGTCTTCCAGTAGACATAGTCCTGGCACATTTGCTGGTTGGGGACTGATTTGGCCTGGCTCTTAGCATTGGGCCTCTTCAGGGCTCCCCAATGGAAGTGGAGTTGTGGGGGTGAAGACAGACGGTCCCACTTTGCTCTCTATCCTGTCTC	-	novel	NA	P-0055464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	78	808	1	ENST00000375759.3:c.10863+1_10864-1del		p.X3621_splice	ENST00000375759	NM_015001.2	3621		14/15	0.23915869544714	3	FACETS	0.807	0.708	0.914			1	CLONAL	1	TRUE	NA	0.245180433772819	3		809	885	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427058	49427059	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0055464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	59	857	0	ENST00000301067.7:c.11429_11430insA	p.Gln3811AlafsTer201	p.Q3811Afs*201	ENST00000301067	NM_003482.3	3810	ttg/ttAg	39/54	1	2	FACETS	0.888	0.764	1	0.888	0.764	1	CLONAL	1	TRUE	1	0.245180433772819	2		857	542	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435963	49435963	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	86	945	0	ENST00000301067.7:c.6018G>A	p.Trp2006Ter	p.W2006*	ENST00000301067	NM_003482.3	2006	tgG/tgA	28/54	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.245180433772819	2		945	639	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81534611	81534611	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	29	333	0	ENST00000298171.2:c.256G>C	p.Asp86His	p.D86H	ENST00000298171	NM_000369.2	86	Gat/Cat	3/10	0.245180433772819	2	FACETS	0.839	0.675	1	0.419	0.337	0.512	CLONAL	1	TRUE	0	0.245180433772819	2		333	282	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821229	72821229	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1326500716	NA	P-0055464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	103	715	0	ENST00000268489.5:c.10946C>T	p.Ser3649Leu	p.S3649L	ENST00000268489	NM_006885.3	3649	tCa/tTa	10/10	0.245180433772819	6	FACETS	1	0.913	1			1	CLONAL	2	TRUE	NA	0.245180433772819	6		715	614	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526763	31526763	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	70	666	0	ENST00000344624.3:c.277C>G	p.Leu93Val	p.L93V	ENST00000344624		93	Ctt/Gtt	2/33	0.23693747277744	3	FACETS	1	0.952	1	0.597	0.521	0.679	CLONAL	1	TRUE	1	0.245180433772819	3		666	537	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952300	38952300	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs557642842	NA	P-0055464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	52	221	0	ENST00000357387.3:c.3125C>T	p.Ser1042Leu	p.S1042L	ENST00000357387	NM_152756.3	1042	tCg/tTg	30/38	0.212002054780115	4	FACETS	1	0.939	1			1	CLONAL	2	TRUE	NA	0.245180433772819	4		221	225	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056463	26056463	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs79562358	NA	P-0055464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	91	411	0	ENST00000343677.2:c.194C>T	p.Ala65Val	p.A65V	ENST00000343677	NM_005319.3	65	gCg/gTg	1/1	0.22612578460858	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.245180433772819	2		411	336	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005620	150005620	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	20	401	0	ENST00000253339.5:c.605C>G	p.Ser202Cys	p.S202C	ENST00000253339		202	tCt/tGt	3/7	1	2	FACETS	0.474	0.362	0.606	0.474	0.362	0.606	SUBCLONAL	1	TRUE	1	0.245180433772819	2		401	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579437	7579437	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	104	1438	1	ENST00000269305.4:c.250del	p.Ala84ProfsTer39	p.A84Pfs*39	ENST00000269305	NM_001126112.2	84	Gcc/cc	4/11	0.174547099707255	1	FACETS	0.844	0.765	0.925	0.844	0.765	0.925	INDETERMINATE	1	TRUE	0	0.571510134555613	1		1439	308	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538909	23538909	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs373263457	NA	P-0055465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	78	997	0	ENST00000380871.4:c.530A>G	p.Tyr177Cys	p.Y177C	ENST00000380871	NM_006167.3	177	tAt/tGt	2/2	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.571510134555613	2		997	273	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425776	49425776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123714	NA	P-0055465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	58	571	2	ENST00000301067.7:c.12712C>T	p.Arg4238Cys	p.R4238C	ENST00000301067	NM_003482.3	4238	Cgc/Tgc	39/54	0.254673288020224	3	FACETS	0.932	0.808	1	0.466	0.404	0.533	INDETERMINATE	1	TRUE	1	0.571510134555613	3		573	280	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0055466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	115	591	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.585	0.526	0.648	0.585	0.526	0.648	SUBCLONAL	1	TRUE	1	0.37	2		591	1062	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241895	133241895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483635586	NA	P-0055466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	275	656	0	ENST00000320574.5:c.2461C>T	p.Arg821Cys	p.R821C	ENST00000320574	NM_006231.2	821	Cgc/Tgc	21/49	1	2	FACETS	0.858	0.808	0.91	1	0.995	1	CLONAL	2	TRUE	1	0.37	2		656	866	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0055466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	168	341	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.787	0.727	0.848	1	0.99	1	SUBCLONAL	2	TRUE	1	0.37	2		341	577	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0055466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	84	196	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.3	1	FACETS	0.907	0.818	0.998	1	0.985	1	CLONAL	2	TRUE	0	0.37	1		196	204	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120114	70120115	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0055466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	35	191	0	ENST00000245479.2:c.1120_1121dup	p.Gln375ArgfsTer9	p.Q375Rfs*9	ENST00000245479	NM_000346.3	372	-/CC	3/3	1	2	FACETS	0.892	0.738	1	0.892	0.738	1	CLONAL	1	TRUE	1	0.37	2		191	212	SUCCESS
ATM	472	MSKCC	GRCh37	11	108137926	108137926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199875915	NA	P-0055466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	102	348	0	ENST00000278616.4:c.2495G>A	p.Arg832His	p.R832H	ENST00000278616	NM_000051.3	832	cGt/cAt	17/63	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.37	2		348	440	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874011	123874013	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs780061449	NA	P-0055466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	12	26	0	ENST00000330479.4:c.62_64del	p.Ala21del	p.A21del	ENST00000330479	NM_020382.3	14	gaGGCg/gag	2/9	1	2	FACETS	0.737	0.525	0.99	0.737	0.525	0.99	CLONAL	1	TRUE	1	0.37	2		26	88	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710566	40710566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760820896	NA	P-0055466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	172	747	1	ENST00000373198.4:c.4285G>A	p.Val1429Met	p.V1429M	ENST00000373198	NM_133170.3	1429	Gtg/Atg	31/32	0.214538242309146	1	FACETS	0.833	0.766	0.902	0.833	0.766	0.902	INDETERMINATE	1	TRUE	0	0.37	1		748	910	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154841	2154841	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	318	1082	0	ENST00000434045.2:c.380G>A	p.Cys127Tyr	p.C127Y	ENST00000434045	NM_001127598.1	127	tGt/tAt	4/5	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.37	2		1082	1209	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975611	26975611	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	90	314	1	ENST00000381527.3:c.1119G>C	p.Gln373His	p.Q373H	ENST00000381527	NM_001260.1	373	caG/caC	12/13	0.274182828912287	3	FACETS	1	0.974	1	0.663	0.591	0.738	CLONAL	1	TRUE	1	0.37	3		315	435	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231507	5231507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200689431	NA	P-0055466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	360	969	0	ENST00000357368.4:c.1969C>T	p.Arg657Cys	p.R657C	ENST00000357368	NM_002850.3	657	Cgc/Tgc	14/38	1	2	FACETS	0.913	0.867	0.96	1	0.996	1	CLONAL	2	TRUE	1	0.37	2		969	1066	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347942	70347942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1321193444	NA	P-0055466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	211	680	0	ENST00000374080.3:c.3181G>A	p.Val1061Ile	p.V1061I	ENST00000374080		1061	Gtc/Atc	22/45	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.37	2		680	867	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0055468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	341	591	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.639718534820206	2		591	1000	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0055468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	119	368	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.639718534820206	2		368	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0055468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	342	513	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.639718534820206	2		513	966	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814303	76814306	+	frameshift_variant	Frame_Shift_Del	DEL	ATAA	ATAA	-	novel	NA	P-0055468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	140	180	0	ENST00000373344.5:c.6338_6341del	p.Phe2113SerfsTer9	p.F2113Sfs*9	ENST00000373344	NM_000489.3	2113	tTTATc/tc	29/35	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.639718534820206	1		180	211	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350772	89350775	+	frameshift_variant	Frame_Shift_Del	DEL	TTTG	TTTG	-	rs886039734	NA	P-0055468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	368	1028	0	ENST00000301030.4:c.2175_2178del	p.Asn725LysfsTer23	p.N725Kfs*23	ENST00000301030	NM_001256183.1	725	aaCAAA/aa	9/13	1	2	FACETS	0.96	0.911	1	0.96	0.911	1	CLONAL	1	TRUE	1	0.639718534820206	2		1028	1198	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	43	115	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.896	0.759	1	0.896	0.759	1	CLONAL	1	TRUE	1	0.5	2		115	192	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0055471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	71	327	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.983	0.866	1	0.983	0.866	1	CLONAL	1	TRUE	1	0.5	2		327	289	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512600	148512600	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	10	385	1	ENST00000320356.2:c.1544A>G	p.Lys515Arg	p.K515R	ENST00000320356	NM_004456.4	515	aAg/aGg	13/20	0.844163186100587	2	FACETS	0.068	0.045	0.096	0.034	0.022	0.048	SUBCLONAL	1	TRUE	0	0.844163186100587	2		386	350	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0055479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	41	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		622	648	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0055479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	19	446	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		446	475	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0055480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	141	517	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.33	2		517	815	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935508	13935508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536563766	NA	P-0055480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	71	415	0	ENST00000405192.2:c.1348G>A	p.Glu450Lys	p.E450K	ENST00000405192	NM_001163147.1	450	Gaa/Aaa	12/12	1	2	FACETS	0.933	0.817	1	0.933	0.817	1	CLONAL	1	TRUE	1	0.33	2		415	461	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0055481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	294	285	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.740641260135329	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.740641260135329	2		285	370	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913403	NA	P-0055481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	167	362	0	ENST00000349496.5:c.110C>A	p.Ser37Tyr	p.S37Y	ENST00000349496	NM_001904.3	37	tCt/tAt	3/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.740641260135329	2		362	391	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913273	NA	P-0055481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	287	514	0	ENST00000263967.3:c.1624G>C	p.Glu542Gln	p.E542Q	ENST00000263967	NM_006218.2	542	Gaa/Caa	10/21	0.740641260135329	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.740641260135329	2		514	362	SUCCESS
AR	367	MSKCC	GRCh37	X	66765997	66765997	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1363782162	NA	P-0055481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	349	998	1	ENST00000374690.3:c.1009G>A	p.Gly337Arg	p.G337R	ENST00000374690	NM_000044.3	337	Ggg/Agg	1/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.740641260135329	2		999	906	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057985	27057985	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	605	740	0	ENST00000324856.7:c.1694del	p.Pro565LeufsTer54	p.P565Lfs*54	ENST00000324856	NM_006015.4	565	Cct/ct	3/20	0.740641260135329	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.740641260135329	2		740	758	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196886	138196886	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375378882	NA	P-0055481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	120	378	2	ENST00000237289.4:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000237289	NM_001270507.1	183	cGa/cAa	4/9	1	2	FACETS	0.953	0.871	1	0.953	0.871	1	CLONAL	1	TRUE	1	0.740641260135329	2		380	340	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157431653	157431653	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	278	614	0	ENST00000346085.5:c.2329T>A	p.Ser777Thr	p.S777T	ENST00000346085	NM_020732.3	777	Tcc/Acc	7/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.740641260135329	2		614	709	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0055482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	58	535	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.521102897862279	2		535	200	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729968	30729968	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs863223852	NA	P-0055482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	84	435	0	ENST00000295754.5:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000295754	NM_003242.5	497	Cga/Tga	6/7	0.521102897862279	1	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	0	0.521102897862279	1		435	237	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427251	49427265	+	inframe_deletion	In_Frame_Del	DEL	TGCTGCTGCTGCTGT	TGCTGCTGCTGCTGT	-	rs1312656236	NA	P-0055482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	25	864	0	ENST00000301067.7:c.11223_11237del	p.Gln3741_Gln3745del	p.Q3741_Q3745del	ENST00000301067	NM_003482.3	3741	caACAGCAGCAGCAGCAc/cac	39/54	0.331782545224319	4	FACETS	0.789	0.626	0.973	0.394	0.313	0.487	CLONAL	1	TRUE	2	0.521102897862279	4		864	185	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583296	46583296	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	59	361	0	ENST00000263734.3:c.224C>G	p.Ser75Cys	p.S75C	ENST00000263734	NM_001430.4	75	tCt/tGt	3/16	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.521102897862279	2		361	186	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80063929	80063929	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	46	430	1	ENST00000265081.6:c.2074C>T	p.Gln692Ter	p.Q692*	ENST00000265081	NM_002439.4	692	Caa/Taa	14/24	0.521102897862279	3	FACETS	1	0.94	1	0.605	0.517	0.699	CLONAL	1	TRUE	1	0.521102897862279	3		431	184	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0055482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	185	535	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.882435354897863	2		535	417	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729968	30729968	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs863223852	NA	P-0055482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	270	435	0	ENST00000295754.5:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000295754	NM_003242.5	497	Cga/Tga	6/7	0.882435354897863	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.882435354897863	1		435	322	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001566	150001566	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	218	381	0	ENST00000253339.5:c.2038C>G	p.Gln680Glu	p.Q680E	ENST00000253339		680	Caa/Gaa	4/7	0.882435354897863	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.882435354897863	1		381	268	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427251	49427265	+	inframe_deletion	In_Frame_Del	DEL	TGCTGCTGCTGCTGT	TGCTGCTGCTGCTGT	-	rs1312656236	NA	P-0055482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	151	864	0	ENST00000301067.7:c.11223_11237del	p.Gln3741_Gln3745del	p.Q3741_Q3745del	ENST00000301067	NM_003482.3	3741	caACAGCAGCAGCAGCAc/cac	39/54	1	2	FACETS	0.579	0.532	0.628	0.579	0.532	0.628	SUBCLONAL	1	TRUE	1	0.882435354897863	2		864	591	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583296	46583296	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	259	361	0	ENST00000263734.3:c.224C>G	p.Ser75Cys	p.S75C	ENST00000263734	NM_001430.4	75	tCt/tGt	3/16	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.882435354897863	2		361	422	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80063929	80063929	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	178	430	1	ENST00000265081.6:c.2074C>T	p.Gln692Ter	p.Q692*	ENST00000265081	NM_002439.4	692	Caa/Taa	14/24	0.523501478619183	4	FACETS	1	0.982	1	0.397	0.368	0.428	INDETERMINATE	1	TRUE	1	0.882435354897863	4		431	637	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302568	15302568	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778895791	NA	P-0055482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	317	761	0	ENST00000263388.2:c.790C>T	p.Pro264Ser	p.P264S	ENST00000263388	NM_000435.2	264	Cct/Tct	5/33	1	2	FACETS	0.99	0.94	1	0.99	0.94	1	CLONAL	1	TRUE	1	0.882435354897863	2		761	726	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001292	150001292	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0055482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	204	473	0	ENST00000253339.5:c.2312C>G	p.Ser771Ter	p.S771*	ENST00000253339		771	tCa/tGa	4/7	0.882435354897863	1	FACETS	0.99	0.95	1	0.99	0.95	1	CLONAL	1	TRUE	0	0.882435354897863	1		473	261	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930321	39930322	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0055482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	213	627	1	ENST00000378444.4:c.3142_3143delinsAG	p.Pro1048Arg	p.P1048R	ENST00000378444	NM_001123385.1	1048	CCa/AGa	6/15	1	2	FACETS	0.753	0.704	0.804	0.753	0.704	0.804	SUBCLONAL	1	TRUE	1	0.882435354897863	2		628	641	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524669	103524669	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201274165	NA	P-0055483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	135	353	0	ENST00000355739.4:c.2800G>A	p.Glu934Lys	p.E934K	ENST00000355739	NM_000123.3	934	Gag/Aag	13/15	1	2	FACETS	0.891	0.813	0.973	0.891	0.813	0.973	CLONAL	1	TRUE	1	0.492614815985854	2		353	615	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349217	11349245	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGGGCGCGCGGGGGCCGCGGGCGAGGA	CGCGGGCGCGCGGGGGCCGCGGGCGAGGA	-	novel	NA	P-0055483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	193	56	0	ENST00000332029.2:c.91_119del	p.Ser31AlafsTer76	p.S31Afs*76	ENST00000332029	NM_003745.1	31	TCCTCGCCCGCGGCCCCCGCGCGCCCGCGg/g	2/2	1	2	FACETS	0.898	0.852	0.941	1	0.995	1	CLONAL	3	TRUE	1	0.492614815985854	2		56	291	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23640969	23640969	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs536644825	NA	P-0055483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	182	484	0	ENST00000261584.4:c.2506G>C	p.Val836Leu	p.V836L	ENST00000261584	NM_024675.3	836	Gtc/Ctc	5/13	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.492614815985854	2		484	734	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068423	16068423	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	11	101	0	ENST00000268712.3:c.488A>G	p.Gln163Arg	p.Q163R	ENST00000268712	NM_006311.3	163	cAa/cGa	5/46	0.492614815985854	1	FACETS	0.293	0.203	0.402	0.293	0.203	0.402	SUBCLONAL	1	TRUE	0	0.492614815985854	1		101	115	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163386	32163386	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	393	942	1	ENST00000375023.3:c.5840A>T	p.Asp1947Val	p.D1947V	ENST00000375023	NM_004557.3	1947	gAt/gTt	30/30	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.492614815985854	2		943	1554	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0055491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	123	332	0	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	1	2	FACETS	0.844	0.77	0.92	0.844	0.77	0.92	CLONAL	1	TRUE	1	0.734415111992725	2		332	397	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061141	38061149	+	inframe_deletion	In_Frame_Del	DEL	CCGCTTCCG	CCGCTTCCG	-	novel	NA	P-0055491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	91	162	0	ENST00000250448.2:c.840_848del	p.Ser280_Gly283delinsArg	p.S280_G283delinsR	ENST00000250448	NM_004496.3	280	agCGGAAGCGGg/agg	2/2	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.734415111992725	2		162	216	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0055492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	7	421	2	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.269	0.167	0.406	0.269	0.167	0.406	SUBCLONAL	1	TRUE	1	0.13	2		423	400	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578220	7578220	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	17	670	0	ENST00000269305.4:c.629del	p.Asn210ThrfsTer37	p.N210Tfs*37	ENST00000269305	NM_001126112.2	210	aAc/ac	6/11	1	2	FACETS	0.455	0.338	0.595	0.455	0.338	0.595	SUBCLONAL	1	TRUE	1	0.13	2		670	575	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0055494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	25	354	1				ENST00000310581	NM_198253.2	-/1132			0.26174286752287	1	FACETS	0.548	0.432	0.68	0.548	0.432	0.68	SUBCLONAL	1	FALSE	0	0.26174286752287	1		355	303	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0055494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	85	459	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.26174286752287	2		459	470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579346	7579348	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs764486868	NA	P-0055494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	72	771	0	ENST00000269305.4:c.339_341del	p.Phe113del	p.F113del	ENST00000269305	NM_001126112.2	113	ttCTTg/ttg	4/11	0.26174286752287	1	FACETS	0.647	0.565	0.736	0.647	0.565	0.736	SUBCLONAL	1	FALSE	0	0.26174286752287	1		771	739	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937038	76937038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1557136793	NA	P-0055494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	33	277	0	ENST00000373344.5:c.3710C>T	p.Ser1237Leu	p.S1237L	ENST00000373344	NM_000489.3	1237	tCa/tTa	9/35	0.26174286752287	1	FACETS	0.748	0.611	0.901	0.748	0.611	0.901	CLONAL	1	FALSE	0	0.26174286752287	1		277	293	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375065	118375065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375644428	NA	P-0055494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	32	299	2	ENST00000534358.1:c.8458G>A	p.Asp2820Asn	p.D2820N	ENST00000534358	NM_005933.3	2820	Gac/Aac	27/36	1	2	FACETS	0.575	0.467	0.698	0.575	0.467	0.698	SUBCLONAL	1	FALSE	1	0.26174286752287	2		301	425	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193205405	193205405	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	38	322	0	ENST00000367435.3:c.1336T>G	p.Phe446Val	p.F446V	ENST00000367435	NM_024529.4	446	Ttt/Gtt	15/17	1	2	FACETS	0.553	0.457	0.661	0.553	0.457	0.661	SUBCLONAL	1	FALSE	1	0.26174286752287	2		322	525	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860788	151860788	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	47	393	0	ENST00000262189.6:c.9874C>A	p.Pro3292Thr	p.P3292T	ENST00000262189	NM_170606.2	3292	Cca/Aca	43/59	1	2	FACETS	0.742	0.626	0.869	0.742	0.626	0.869	SUBCLONAL	1	FALSE	1	0.26174286752287	2		393	484	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0055495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	39	618	1	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	0.855	0.709	1	0.855	0.709	1	CLONAL	1	TRUE	1	0.19	2		619	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0055495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	115	1188	3	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	1	2	FACETS	0.972	0.873	1	0.972	0.873	1	CLONAL	1	TRUE	1	0.19	2		1191	1245	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001438	29001438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1473309404	NA	P-0055495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	26	316	1	ENST00000282397.4:c.1294G>A	p.Glu432Lys	p.E432K	ENST00000282397	NM_002019.4	432	Gaa/Aaa	10/30	1	2	FACETS	0.658	0.52	0.816	0.658	0.52	0.816	SUBCLONAL	1	TRUE	1	0.19	2		317	416	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412494	80412494	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	50	417	1	ENST00000286548.4:c.547C>T	p.Arg183Ter	p.R183*	ENST00000286548	NM_002072.3	183	Cga/Tga	4/7	1	2	FACETS	0.987	0.838	1	0.987	0.838	1	CLONAL	1	TRUE	1	0.19	2		418	533	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288993	212288993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867944951	NA	P-0055495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	27	491	0	ENST00000342788.4:c.2753G>A	p.Gly918Glu	p.G918E	ENST00000342788	NM_005235.2	918	gGa/gAa	23/28	1	2	FACETS	1	0.812	1	1	0.812	1	CLONAL	1	TRUE	1	0.19	2		491	279	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413566	32413566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121907900	NA	P-0055495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	12	478	0	ENST00000332351.3:c.1384C>T	p.Arg462Trp	p.R462W	ENST00000332351	NM_024426.4	462	Cgg/Tgg	9/10	1	2	FACETS	0.231	0.161	0.318	0.231	0.161	0.318	SUBCLONAL	1	TRUE	1	0.19	2		478	547	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437448	49437448	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	82	931	1	ENST00000301067.7:c.5437G>A	p.Glu1813Lys	p.E1813K	ENST00000301067	NM_003482.3	1813	Gaa/Aaa	23/54	1	2	FACETS	0.84	0.739	0.95	0.84	0.739	0.95	CLONAL	1	TRUE	1	0.19	2		932	1027	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060776	38060776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1205	125	1331	0	ENST00000250448.2:c.1213C>T	p.Leu405Phe	p.L405F	ENST00000250448	NM_004496.3	405	Ctc/Ttc	2/2	1	2	FACETS	0.989	0.893	1	0.989	0.893	1	CLONAL	1	TRUE	1	0.19	2		1331	1330	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681778	78681779	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	64	950	0	ENST00000306801.3:c.486_487delinsAA	p.Glu163Lys	p.E163K	ENST00000306801	NM_020761.2	162	ggGGag/ggAAag	4/34	1	2	FACETS	0.575	0.496	0.661	0.575	0.496	0.661	SUBCLONAL	1	TRUE	1	0.19	2		950	1172	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755510	39755510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	41	724	1	ENST00000288319.7:c.1255G>A	p.Gly419Ser	p.G419S	ENST00000288319	NM_182918.3	419	Ggc/Agc	10/10	1	2	FACETS	0.64	0.532	0.761	0.64	0.532	0.761	SUBCLONAL	1	TRUE	1	0.19	2		725	674	SUCCESS
APC	324	MSKCC	GRCh37	5	112164537	112164554	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTGATTAATTTGCAGGT	ATTGATTAATTTGCAGGT	-	novel	NA	P-0055495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	11	137	0	ENST00000257430.4:c.1627-16_1628del		p.X543_splice	ENST00000257430	NM_000038.5	543		14/16	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.19	2		137	89	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509109	106509109	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	77	834	0	ENST00000359195.3:c.1103T>C	p.Ile368Thr	p.I368T	ENST00000359195	NM_002649.2	368	aTt/aCt	2/11	1	2	FACETS	0.857	0.75	0.972	0.857	0.75	0.972	CLONAL	1	TRUE	1	0.19	2		834	946	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395231	139395231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	127	1372	0	ENST00000277541.6:c.5707G>A	p.Glu1903Lys	p.E1903K	ENST00000277541	NM_017617.3	1903	Gag/Aag	31/34	1	2	FACETS	0.997	0.9	1	0.997	0.9	1	CLONAL	1	TRUE	1	0.19	2		1372	1341	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0055496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	273	585	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.940554996513775	2		585	569	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156719	20156719	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	259	388	3	ENST00000379607.5:c.38G>T	p.Arg13Leu	p.R13L	ENST00000379607	NM_001412.3	13	cGc/cTc	2/7	1	2	FACETS	0.912	0.861	0.963	0.912	0.861	0.963	CLONAL	1	TRUE	1	0.940554996513775	2		391	604	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0055496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	155	275	0	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	0.91	0.845	0.976	0.91	0.845	0.976	CLONAL	1	TRUE	1	0.940554996513775	2		275	362	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653808	89653808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	457	302	0	ENST00000371953.3:c.106G>A	p.Gly36Arg	p.G36R	ENST00000371953	NM_000314.4	36	Gga/Aga	2/9	0.940554996513775	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.940554996513775	2		302	473	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965666	90965666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	179	358	1	ENST00000265433.3:c.1651del	p.Arg551GlyfsTer8	p.R551Gfs*8	ENST00000265433	NM_002485.4	551	Agg/gg	11/16	1	2	FACETS	0.812	0.755	0.869	0.812	0.755	0.869	CLONAL	1	TRUE	1	0.940554996513775	2		359	469	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0055496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	319	578	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.941	0.894	0.988	0.941	0.894	0.988	CLONAL	1	TRUE	1	0.940554996513775	2		579	721	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0055496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	284	536	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.940554996513775	2		536	602	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207153	1207155	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs587782056	NA	P-0055496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	368	908	0	ENST00000326873.7:c.250_252del	p.Lys84del	p.K84del	ENST00000326873	NM_000455.4	81	AAG/-	1/10	1	2	FACETS	0.859	0.818	0.9	0.859	0.818	0.9	CLONAL	1	TRUE	1	0.940554996513775	2		908	911	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0055496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	384	827	2	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.904	0.863	0.946	0.904	0.863	0.946	CLONAL	1	TRUE	1	0.940554996513775	2		829	903	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0055496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	223	444	0	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.940554996513775	2		444	470	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612879	228612879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767647652	NA	P-0055496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	380	786	1	ENST00000366696.1:c.148C>T	p.Arg50Cys	p.R50C	ENST00000366696	NM_003493.2	50	Cgc/Tgc	1/1	0.940554996513775	3	FACETS	0.985	0.936	1	0.493	0.468	0.518	CLONAL	1	TRUE	1	0.940554996513775	3		787	1206	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435468	121435468	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs371807951	NA	P-0055496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	425	964	0	ENST00000257555.6:c.1501G>A	p.Ala501Thr	p.A501T	ENST00000257555		501	Gcc/Acc	7/10	1	2	FACETS	0.94	0.9	0.981	0.94	0.9	0.981	CLONAL	1	TRUE	1	0.940554996513775	2		964	961	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522741	67522741	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	112	200	0	ENST00000274335.5:c.244del	p.Ile82SerfsTer32	p.I82Sfs*32	ENST00000274335		80	Aaa/aa	1/15	1	2	FACETS	0.876	0.801	0.951	0.876	0.801	0.951	CLONAL	1	TRUE	1	0.940554996513775	2		200	272	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262102	10262102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	291	528	1	ENST00000340748.4:c.2189G>A	p.Arg730His	p.R730H	ENST00000340748		730	cGc/cAc	23/40	1	2	FACETS	0.889	0.842	0.937	0.889	0.842	0.937	CLONAL	1	TRUE	1	0.940554996513775	2		529	696	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0055496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	301	778	2	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.926	0.879	0.974	0.926	0.879	0.974	CLONAL	1	TRUE	1	0.940554996513775	2		780	691	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831119	72831120	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0055496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	232	478	0	ENST00000268489.5:c.5461dup	p.Ala1821GlyfsTer108	p.A1821Gfs*108	ENST00000268489	NM_006885.3	1821	gca/gGca	9/10	1	2	FACETS	0.958	0.903	1	0.958	0.903	1	CLONAL	1	TRUE	1	0.940554996513775	2		478	515	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0055496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	559	394	11	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	1	2	FACETS	0.888	0.869	0.906	1	0.998	1	CLONAL	2	TRUE	1	0.940554996513775	2		405	669	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77051785	77051785	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	222	415	1	ENST00000356341.3:c.1022G>A	p.Trp341Ter	p.W341*	ENST00000356341	NM_002576.4	341	tGg/tAg	11/15	1	2	FACETS	0.922	0.867	0.978	0.922	0.867	0.978	CLONAL	1	TRUE	1	0.940554996513775	2		416	512	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466017	69466017	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0055496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	374	917	0	ENST00000227507.2:c.855C>A	p.Cys285Ter	p.C285*	ENST00000227507	NM_053056.2	285	tgC/tgA	5/5	1	2	FACETS	0.926	0.883	0.969	0.926	0.883	0.969	CLONAL	1	TRUE	1	0.940554996513775	2		917	859	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800444	32800444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758423176	NA	P-0055496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	503	875	0	ENST00000374899.4:c.1103G>A	p.Arg368Gln	p.R368Q	ENST00000374899	NM_018833.2	368	cGg/cAg	6/12	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.940554996513775	2		875	1026	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905402	11905402	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	155	341	0	ENST00000396373.4:c.52A>G	p.Thr18Ala	p.T18A	ENST00000396373	NM_001987.4	18	Aca/Gca	2/8	1	2	FACETS	0.921	0.855	0.987	0.921	0.855	0.987	CLONAL	1	TRUE	1	0.940554996513775	2		341	358	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265291	16265291	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	317	599	1	ENST00000375759.3:c.10783C>T	p.Leu3595Phe	p.L3595F	ENST00000375759	NM_015001.2	3595	Ctc/Ttc	14/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.940554996513775	2		600	656	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023128	27023159	+	frameshift_variant	Frame_Shift_Del	DEL	GAGCAATGGGGGTGGCGGCGGCGGCGGAGCCG	GAGCAATGGGGGTGGCGGCGGCGGCGGAGCCG	-	novel	NA	P-0055496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	90	53	0	ENST00000324856.7:c.235_266del	p.Ser79GlnfsTer21	p.S79Qfs*21	ENST00000324856	NM_006015.4	78	gaGAGCAATGGGGGTGGCGGCGGCGGCGGAGCCGgc/gagc	1/20	1	2	FACETS	0.903	0.856	0.943	1	0.99	1	CLONAL	2	TRUE	1	0.940554996513775	2		53	106	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491451	18491451	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	193	350	0	ENST00000266497.5:c.1364A>G	p.Glu455Gly	p.E455G	ENST00000266497		455	gAa/gGa	8/31	1	2	FACETS	0.883	0.825	0.941	0.883	0.825	0.941	CLONAL	1	TRUE	1	0.940554996513775	2		350	465	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50481145	50481145	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0055496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	178	283	0	ENST00000394963.4:c.532-1G>A		p.X178_splice	ENST00000394963	NM_003076.4	178			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.940554996513775	2		283	365	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094769	2094769	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	418	930	0	ENST00000219066.1:c.411G>T	p.Met137Ile	p.M137I	ENST00000219066	NM_002528.5	137	atG/atT	3/6	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.940554996513775	2		930	869	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657099	45657099	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0055496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	146	272	0	ENST00000407780.3:c.57T>A	p.Asp19Glu	p.D19E	ENST00000407780	NM_001283052.1	19	gaT/gaA	3/7	NA	2	FACETS	0.989	0.918	1			1	INDETERMINATE	1	TRUE	NA	0.940554996513775	2		272	314	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545085	41545085	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745785745	NA	P-0055496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	266	535	0	ENST00000263253.7:c.2285G>A	p.Gly762Asp	p.G762D	ENST00000263253	NM_001429.3	762	gGc/gAc	13/31	1	2	FACETS	0.881	0.832	0.93	0.881	0.832	0.93	CLONAL	1	TRUE	1	0.940554996513775	2		535	642	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748188	41748188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	335	660	0	ENST00000226382.2:c.581G>A	p.Ser194Asn	p.S194N	ENST00000226382	NM_003924.3	194	aGc/aAc	3/3	1	2	FACETS	0.974	0.928	1	0.974	0.928	1	CLONAL	1	TRUE	1	0.940554996513775	2		660	731	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628940	187628940	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	256	531	0	ENST00000441802.2:c.2042A>C	p.Lys681Thr	p.K681T	ENST00000441802	NM_005245.3	681	aAa/aCa	2/27	1	2	FACETS	0.894	0.844	0.945	0.894	0.844	0.945	CLONAL	1	TRUE	1	0.940554996513775	2		531	609	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753100	128753100	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755283006	NA	P-0055496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	149	314	0	ENST00000377970.2:c.1261G>A	p.Val421Ile	p.V421I	ENST00000377970	NM_002467.4	421	Gtc/Atc	3/3	1	2	FACETS	0.849	0.786	0.914	0.849	0.786	0.914	CLONAL	1	TRUE	1	0.940554996513775	2		314	373	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559251	141559251	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	358	759	0	ENST00000220592.5:c.1550T>C	p.Leu517Pro	p.L517P	ENST00000220592	NM_012154.3	517	cTg/cCg	12/19	1	2	FACETS	0.978	0.933	1	0.978	0.933	1	CLONAL	1	TRUE	1	0.940554996513775	2		759	778	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665755	29665756	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs876657715	NA	P-0055497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	33	200	0	ENST00000356175.3:c.6791dup	p.Tyr2264Ter	p.Y2264*	ENST00000356175	NM_000267.3	2264	tac/tAac	45/57	0.384642727160685	1	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	0	0.384642727160685	1		200	125	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855028	76855029	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0055497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	37	345	0	ENST00000373344.5:c.5807_5808del	p.Lys1936ArgfsTer5	p.K1936Rfs*5	ENST00000373344	NM_000489.3	1936	aAG/a	25/35	0.384642727160685	1	FACETS	0.959	0.802	1	0.959	0.802	1	CLONAL	1	TRUE	0	0.384642727160685	1		345	162	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280040	66280040	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	20	201	0	ENST00000273854.3:c.1649T>C	p.Val550Ala	p.V550A	ENST00000273854	NM_004439.5	550	gTc/gCc	7/18	1	2	FACETS	0.859	0.666	1	0.859	0.666	1	CLONAL	1	TRUE	1	0.384642727160685	2		201	121	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	106	115	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.812792107972419	2		115	251	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0055498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14685	1032	580	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.812792107972419	39	FACETS	0.864	0.833	0.895			1	CLONAL	3	TRUE	NA	0.812792107972419	39		580	15717	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0055498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	203	397	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.812792107972419	1	FACETS	0.966	0.918	1	0.966	0.918	1	CLONAL	1	TRUE	0	0.812792107972419	1		397	307	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0055498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14206	660	453	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.812792107972419	39	FACETS	0.876	0.837	0.916			1	CLONAL	2	TRUE	NA	0.812792107972419	39		453	14866	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780068	NA	P-0055498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	464	857	0	ENST00000269305.4:c.472C>T	p.Arg158Cys	p.R158C	ENST00000269305	NM_001126112.2	158	Cgc/Tgc	5/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.812792107972419	2		857	1046	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856005	111856005	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778291950	NA	P-0055498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	311	614	2	ENST00000341259.2:c.56C>T	p.Pro19Leu	p.P19L	ENST00000341259	NM_005475.2	19	cCg/cTg	2/8	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.812792107972419	2		616	692	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831350	72831350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs967087904	NA	P-0055498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	141	381	1	ENST00000268489.5:c.5231C>T	p.Thr1744Met	p.T1744M	ENST00000268489	NM_006885.3	1744	aCg/aTg	9/10	1	2	FACETS	0.935	0.862	1	0.935	0.862	1	CLONAL	1	TRUE	1	0.812792107972419	2		382	371	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984771	55984771	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	178	322	0	ENST00000263923.4:c.358G>T	p.Asp120Tyr	p.D120Y	ENST00000263923	NM_002253.2	120	Gat/Tat	3/30	1	2	FACETS	0.991	0.923	1	0.991	0.923	1	CLONAL	1	TRUE	1	0.812792107972419	2		322	442	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412923	63412923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	168	747	0	ENST00000330258.3:c.244G>A	p.Gly82Arg	p.G82R	ENST00000330258	NM_152424.3	82	Ggg/Agg	2/2	NA	2	FACETS	0.49	0.45	0.531			1	INDETERMINATE	1	TRUE	NA	0.812792107972419	2		747	844	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0055502-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	77	635	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.223007854247283	2		635	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0055502-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	55	644	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.199333212078237	4	FACETS	1	0.921	1	0.372	0.318	0.431	CLONAL	1	TRUE	1	0.223007854247283	4		646	540	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259439	55259439	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs397517126	NA	P-0055502-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	49	334	0	ENST00000275493.2:c.2497T>G	p.Leu833Val	p.L833V	ENST00000275493	NM_005228.3	833	Ttg/Gtg	21/28	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.223007854247283	2		334	334	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046749	180046749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121909657	NA	P-0055502-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	47	662	0	ENST00000261937.6:c.2563G>A	p.Ala855Thr	p.A855T	ENST00000261937	NM_182925.4	855	Gcc/Acc	18/30	1	2	FACETS	0.853	0.72	1	0.853	0.72	1	CLONAL	1	TRUE	1	0.223007854247283	2		662	494	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003238	42003238	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055502-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	50	374	0	ENST00000219905.7:c.2777del	p.Lys926SerfsTer7	p.K926Sfs*7	ENST00000219905	NM_001164273.1	925	ccA/cc	8/24	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.223007854247283	2		374	381	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105811	27105818	+	frameshift_variant	Frame_Shift_Del	DEL	AAGTTTGA	AAGTTTGA	-	novel	NA	P-0055519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	212	503	0	ENST00000324856.7:c.5422_5429del	p.Lys1808GlnfsTer11	p.K1808Qfs*11	ENST00000324856	NM_006015.4	1808	AAGTTTGAc/c	20/20	1	2	FACETS	0.971	0.91	1	0.971	0.91	1	CLONAL	1	TRUE	1	0.797998580049569	2		503	547	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579410	7579410	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567556123	NA	P-0055520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	199	763	0	ENST00000269305.4:c.277del	p.Leu93CysfsTer30	p.L93Cfs*30	ENST00000269305	NM_001126112.2	93	Ctg/tg	4/11	0.271655319935997	2	FACETS	0.882	0.818	0.947	0.882	0.818	0.947	CLONAL	2	TRUE	0	0.271655319935997	2		763	831	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624199	89624349	+	splice_donor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	CTTTTTCTTCAGCCACAGGCTCCCAGACATGACAGCCATCATCAAAGAGATCGTTAGCAGAAACAAAAGGAGATATCAAGAGGATGGATTCGACTTAGACTTGACCTGTATCCATTTCTGCGGCTGCTCCTCTTTACCTTTCTGTCACTCT	CTTTTTCTTCAGCCACAGGCTCCCAGACATGACAGCCATCATCAAAGAGATCGTTAGCAGAAACAAAAGGAGATATCAAGAGGATGGATTCGACTTAGACTTGACCTGTATCCATTTCTGCGGCTGCTCCTCTTTACCTTTCTGTCACTCT	-	novel	NA	P-0055520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	11	67	0	ENST00000371953.3:c.-25_79+47del		p.X9_splice	ENST00000371953	NM_000314.4	9		1/9	0.267541059699788	3	FACETS	1	0.835	1	0.667	0.469	0.902	CLONAL	1	TRUE	1	0.271655319935997	3		67	69	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223030	5223030	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	45	410	0	ENST00000357368.4:c.2773G>C	p.Glu925Gln	p.E925Q	ENST00000357368	NM_002850.3	925	Gag/Cag	18/38	0.262095023417185	2	FACETS	0.774	0.651	0.909	0.387	0.325	0.455	CLONAL	1	TRUE	0	0.271655319935997	2		410	428	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413096	139413096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	56	842	0	ENST00000277541.6:c.1046C>G	p.Thr349Ser	p.T349S	ENST00000277541	NM_017617.3	349	aCc/aGc	6/34	0.266628893872792	4	FACETS	0.52	0.444	0.604	0.173	0.148	0.202	SUBCLONAL	1	TRUE	1	0.271655319935997	4		842	1008	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0055521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	70	613	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.964	0.841	1	0.964	0.841	1	CLONAL	1	FALSE	1	0.227567542878134	2		614	638	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023769	27023769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	24	402	0	ENST00000324856.7:c.879del	p.Thr294ProfsTer69	p.T294Pfs*69	ENST00000324856	NM_006015.4	292	aCc/ac	1/20	1	2	FACETS	0.743	0.583	0.926	0.743	0.583	0.926	CLONAL	1	FALSE	1	0.227567542878134	2		402	284	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0055521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	31	347	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.531	0.429	0.647	0.531	0.429	0.647	SUBCLONAL	1	FALSE	1	0.227567542878134	2		347	513	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0055522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	569	890	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.604167268296456	4	FACETS	0.892	0.857	0.928	0.892	0.857	0.928	CLONAL	2	TRUE	2	0.687953128123964	4		893	1565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578410	7578410	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	714	722	0	ENST00000269305.4:c.520A>T	p.Arg174Trp	p.R174W	ENST00000269305	NM_001126112.2	174	Agg/Tgg	5/11	0.604167268296456	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	2	0.687953128123964	4		722	1597	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971032	21971065	+	frameshift_variant	Frame_Shift_Del	DEL	GCATCGCGCACGTCCAGCCGCGCCCCGGCCCGGT	GCATCGCGCACGTCCAGCCGCGCCCCGGCCCGGT	-	novel	NA	P-0055522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	437	203	0	ENST00000304494.5:c.293_326del	p.His98ProfsTer37	p.H98Pfs*37	ENST00000304494	NM_000077.4	98	cACCGGGCCGGGGCGCGGCTGGACGTGCGCGATGCc/cc	2/3	0.660372582470101	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.687953128123964	2		203	533	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519896	NA	P-0055522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	289	288	0	ENST00000281708.4:c.1514G>T	p.Arg505Leu	p.R505L	ENST00000281708	NM_033632.3	505	cGc/cTc	10/12	0.660372582470101	2	FACETS	0.961	0.922	1	0.961	0.922	1	CLONAL	2	TRUE	0	0.687953128123964	2		288	437	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428410	49428411	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1284500089	NA	P-0055522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	926	636	0	ENST00000301067.7:c.10394dup	p.Pro3466ThrfsTer2	p.P3466Tfs*2	ENST00000301067	NM_003482.3	3465	gga/ggGa	36/54	0.663084628729847	3	FACETS	0.908	0.888	0.928	0.908	0.888	0.928	CLONAL	3	TRUE	0	0.687953128123964	3		636	1328	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556688	41556688	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs748106711	NA	P-0055522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	147	352	0	ENST00000263253.7:c.3633G>T	p.Glu1211Asp	p.E1211D	ENST00000263253	NM_001429.3	1211	gaG/gaT	20/31	1	2	FACETS	0.915	0.842	0.99	0.915	0.842	0.99	CLONAL	1	TRUE	1	0.687953128123964	2		352	467	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539695	187539696	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0055522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	303	322	0	ENST00000441802.2:c.8044dup	p.Ser2682PhefsTer11	p.S2682Ffs*11	ENST00000441802	NM_005245.3	2682	tca/tTca	10/27	0.660372582470101	2	FACETS	0.97	0.931	1	0.97	0.931	1	CLONAL	2	TRUE	0	0.687953128123964	2		322	454	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752416	57752416	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	149	186	0	ENST00000274289.3:c.1157A>T	p.Asn386Ile	p.N386I	ENST00000274289	NM_006622.3	386	aAt/aTt	9/14	0.660372582470101	2	FACETS	0.954	0.899	1	0.954	0.899	1	CLONAL	2	TRUE	0	0.687953128123964	2		186	227	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0055523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	211	290	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.433308695388451	3	FACETS	0.92	0.867	0.972	0.92	0.867	0.972	INDETERMINATE	2	TRUE	1	0.756610510940267	3		290	418	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111554	8111554	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	292	553	0	ENST00000346208.3:c.1040T>G	p.Leu347Arg	p.L347R	ENST00000346208		347	cTt/cGt	5/6	0.417291880866828	1	FACETS	0.876	0.834	0.917	0.876	0.834	0.917	INDETERMINATE	1	TRUE	0	0.756610510940267	1		553	548	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144627	119144627	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	103	415	0	ENST00000264033.4:c.640C>A	p.Pro214Thr	p.P214T	ENST00000264033	NM_005188.3	214	Ccc/Acc	4/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.305532141619272	2		415	539	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005482	42005486	+	frameshift_variant	Frame_Shift_Del	DEL	GACCA	GACCA	-	novel	NA	P-0055524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	104	658	0	ENST00000219905.7:c.3221_3225del	p.Pro1074LeufsTer16	p.P1074Lfs*16	ENST00000219905	NM_001164273.1	1073	cGACCA/c	9/24	1	2	FACETS	0.911	0.816	1	0.911	0.816	1	CLONAL	1	TRUE	1	0.305532141619272	2		658	747	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188255	10188255	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	73	537	0	ENST00000256474.2:c.398del	p.Thr133MetfsTer26	p.T133Mfs*26	ENST00000256474	NM_000551.3	133	aCt/at	2/3	0.305532141619272	1	FACETS	0.755	0.662	0.856	0.755	0.662	0.856	SUBCLONAL	1	TRUE	0	0.305532141619272	1		537	536	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478113	138478113	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	27	451	0	ENST00000289153.2:c.73G>C	p.Ala25Pro	p.A25P	ENST00000289153	NM_006219.2	25	Gca/Cca	1/22	1	2	FACETS	0.379	0.301	0.469	0.379	0.301	0.469	SUBCLONAL	1	TRUE	1	0.305532141619272	2		451	466	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37058999	37058999	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs63751194	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	56	388	0	ENST00000231790.2:c.793C>T	p.Arg265Cys	p.R265C	ENST00000231790	NM_000249.3	265	Cgt/Tgt	10/19	0.286935728558403	2	FACETS	1	0.919	1	0.55	0.473	0.633	CLONAL	1	TRUE	0	0.286935728558403	2		388	355	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609673	28609673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	84	564	0	ENST00000241453.7:c.1556C>T	p.Ser519Phe	p.S519F	ENST00000241453	NM_004119.2	519	tCc/tTc	12/24	0.275143715891554	4	FACETS	1	0.945	1	0.559	0.494	0.629	CLONAL	1	TRUE	2	0.286935728558403	4		564	674	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944607	40944607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766880457	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	91	417	0	ENST00000373198.4:c.1895G>A	p.Arg632Gln	p.R632Q	ENST00000373198	NM_133170.3	632	cGa/cAa	12/32	0.138192123323903	4	FACETS	0.943	0.842	1	0.943	0.842	1	INDETERMINATE	2	TRUE	2	0.286935728558403	4		417	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	164	578	2	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.286935728558403	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.286935728558403	2		580	534	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096076	11096076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759594383	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	67	821	0	ENST00000358026.2:c.350C>T	p.Ser117Phe	p.S117F	ENST00000358026	NM_001128849.1	117	tCc/tTc	3/36	0.261956581891461	3	FACETS	0.704	0.61	0.805	0.352	0.305	0.403	SUBCLONAL	1	TRUE	1	0.286935728558403	3		821	759	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845946	156845946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	142	937	0	ENST00000524377.1:c.1576C>T	p.Leu526Phe	p.L526F	ENST00000524377	NM_002529.3	526	Ctt/Ttt	13/17	0.286935728558403	4	FACETS	1	0.979	1	0.626	0.57	0.686	CLONAL	1	TRUE	2	0.286935728558403	4		937	1017	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857529	9857529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1325032512	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	69	472	0	ENST00000330684.3:c.3872C>T	p.Ser1291Phe	p.S1291F	ENST00000330684	NM_001134407.1	1291	tCc/tTc	13/13	0.286935728558403	3	FACETS	1	0.898	1	0.517	0.451	0.588	CLONAL	1	TRUE	1	0.286935728558403	3		472	532	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141084	55141084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778015444	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	56	420	0	ENST00000257290.5:c.1730C>T	p.Pro577Leu	p.P577L	ENST00000257290	NM_006206.4	577	cCg/cTg	12/23	0.275143715891554	4	FACETS	1	0.901	1	0.532	0.456	0.615	CLONAL	1	TRUE	2	0.286935728558403	4		420	472	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805236	43805236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	90	709	0	ENST00000372470.3:c.686G>A	p.Arg229Lys	p.R229K	ENST00000372470	NM_005373.2	229	aGa/aAa	4/12	0.286935728558403	4	FACETS	0.968	0.858	1	0.484	0.429	0.543	CLONAL	1	TRUE	2	0.286935728558403	4		709	834	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873660	35873660	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs201559094	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	48	320	0	ENST00000303115.3:c.616C>T	p.Arg206Ter	p.R206*	ENST00000303115	NM_002185.3	206	Cga/Tga	5/8	0.286935728558403	3	FACETS	0.933	0.791	1	0.467	0.395	0.545	CLONAL	1	TRUE	1	0.286935728558403	3		320	410	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121534	193121534	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	38	291	0	ENST00000367435.3:c.932C>T	p.Thr311Ile	p.T311I	ENST00000367435	NM_024529.4	311	aCt/aTt	10/17	0.286935728558403	4	FACETS	0.949	0.787	1	0.475	0.393	0.566	CLONAL	1	TRUE	2	0.286935728558403	4		291	359	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857784	9857784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145861983	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	137	608	0	ENST00000330684.3:c.3617G>A	p.Arg1206Gln	p.R1206Q	ENST00000330684	NM_001134407.1	1206	cGa/cAa	13/13	0.286935728558403	3	FACETS	0.998	0.912	1	0.998	0.912	1	CLONAL	2	TRUE	1	0.286935728558403	3		608	547	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573894	18573894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759658584	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	39	356	0	ENST00000266497.5:c.2212C>T	p.Arg738Cys	p.R738C	ENST00000266497		738	Cgt/Tgt	15/31	0.286935728558403	3	FACETS	1	0.874	1	0.53	0.441	0.629	CLONAL	1	TRUE	1	0.286935728558403	3		356	293	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980844	40980844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	85	750	0	ENST00000373198.4:c.1642G>A	p.Glu548Lys	p.E548K	ENST00000373198	NM_133170.3	548	Gaa/Aaa	10/32	0.138192123323903	4	FACETS	1	0.909	1	0.517	0.456	0.581	INDETERMINATE	1	TRUE	2	0.286935728558403	4		750	738	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892266	9892266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868291959	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	57	510	0	ENST00000330684.3:c.2224G>A	p.Asp742Asn	p.D742N	ENST00000330684	NM_001134407.1	742	Gat/Aat	11/13	0.286935728558403	3	FACETS	0.956	0.822	1	0.478	0.411	0.552	CLONAL	1	TRUE	1	0.286935728558403	3		510	475	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980402	55980402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1357848255	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	32	314	0	ENST00000263923.4:c.689C>T	p.Pro230Leu	p.P230L	ENST00000263923	NM_002253.2	230	cCg/cTg	6/30	0.275143715891554	4	FACETS	0.784	0.637	0.95	0.392	0.318	0.475	CLONAL	1	TRUE	2	0.286935728558403	4		314	366	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	57	411	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	0.286935728558403	3	FACETS	1	0.916	1	0.546	0.47	0.629	CLONAL	1	TRUE	1	0.286935728558403	3		411	416	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053566	37053566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	68	472	1	ENST00000231790.2:c.653C>T	p.Ser218Phe	p.S218F	ENST00000231790	NM_000249.3	218	tCc/tTc	8/19	0.286935728558403	2	FACETS	0.996	0.868	1	0.498	0.434	0.567	CLONAL	1	TRUE	0	0.286935728558403	2		473	476	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	220	363	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.286935728558403	6	FACETS	0.926	0.87	0.983	0.926	0.87	0.983	CLONAL	5	TRUE	1	0.286935728558403	6		363	521	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306712	41306712	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	83	760	0	ENST00000373198.4:c.947G>A	p.Gly316Glu	p.G316E	ENST00000373198	NM_133170.3	316	gGg/gAg	7/32	0.138192123323903	4	FACETS	0.867	0.764	0.978	0.433	0.382	0.489	INDETERMINATE	1	TRUE	2	0.286935728558403	4		760	859	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625158	69625158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377265856	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	111	952	0	ENST00000334134.2:c.635G>A	p.Arg212Gln	p.R212Q	ENST00000334134	NM_005247.2	212	cGg/cAg	3/3	0.286935728558403	3	FACETS	1	0.924	1	0.517	0.465	0.573	CLONAL	1	TRUE	1	0.286935728558403	3		952	855	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523669	176523669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	89	909	0	ENST00000292408.4:c.2080C>T	p.Pro694Ser	p.P694S	ENST00000292408	NM_213647.1	694	Ccg/Tcg	16/18	0.286935728558403	3	FACETS	0.793	0.702	0.891	0.397	0.351	0.446	SUBCLONAL	1	TRUE	1	0.286935728558403	3		909	894	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905495	50905495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774030917	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	98	728	0	ENST00000440232.2:c.623C>T	p.Pro208Leu	p.P208L	ENST00000440232	NM_002691.3	208	cCg/cTg	6/27	0.261956581891461	3	FACETS	1	0.912	1	0.513	0.457	0.572	CLONAL	1	TRUE	1	0.286935728558403	3		728	762	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444401	50444401	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	65	412	0	ENST00000331340.3:c.331C>T	p.Arg111Ter	p.R111*	ENST00000331340	NM_006060.4	111	Cga/Tga	4/8	0.286935728558403	5	FACETS	1	0.92	1	0.362	0.313	0.414	CLONAL	1	TRUE	2	0.286935728558403	5		412	597	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456556	189456556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	52	410	0	ENST00000264731.3:c.317C>T	p.Pro106Leu	p.P106L	ENST00000264731	NM_003722.4	106	cCc/cTc	3/14	0.286935728558403	3	FACETS	0.982	0.838	1	0.491	0.419	0.57	CLONAL	1	TRUE	1	0.286935728558403	3		410	422	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718277	117718277	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1298952570	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	54	349	0	ENST00000368508.3:c.580C>T	p.Pro194Ser	p.P194S	ENST00000368508	NM_002944.2	194	Cct/Tct	7/43	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.286935728558403	2		349	350	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066579	94066579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	67	529	0	ENST00000369303.4:c.1180G>A	p.Gly394Arg	p.G394R	ENST00000369303	NM_004440.3	394	Gga/Aga	5/17	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.286935728558403	2		529	439	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806185	1806185	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	115	899	0	ENST00000260795.2:c.1204C>T	p.Pro402Ser	p.P402S	ENST00000260795		402	Ccc/Tcc	8/17	0.275143715891554	4	FACETS	1	0.911	1	0.507	0.456	0.562	CLONAL	1	TRUE	2	0.286935728558403	4		899	1017	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504317	8504317	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	66	600	0	ENST00000356435.5:c.1766C>T	p.Ser589Phe	p.S589F	ENST00000356435		589	tCc/tTc	12/35	0.286935728558403	1	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	0	0.286935728558403	1		600	386	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455312	29455312	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	49	575	0	ENST00000389048.3:c.2490G>A	p.Met830Ile	p.M830I	ENST00000389048	NM_004304.4	830	atG/atA	15/29	0.286935728558403	3	FACETS	0.824	0.698	0.962	0.412	0.349	0.481	CLONAL	1	TRUE	1	0.286935728558403	3		575	474	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985561	2985561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	104	469	0	ENST00000396946.4:c.250G>A	p.Gly84Arg	p.G84R	ENST00000396946	NM_032415.4	84	Ggg/Agg	4/25	0.286935728558403	5	FACETS	0.803	0.72	0.89	0.535	0.48	0.594	CLONAL	2	TRUE	2	0.286935728558403	5		469	646	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317921	8317921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150063446	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	54	332	0	ENST00000356435.5:c.5692C>T	p.Arg1898Cys	p.R1898C	ENST00000356435		1898	Cgt/Tgt	35/35	0.286935728558403	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.286935728558403	1		332	295	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193748	106193748	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs974106601	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	42	302	0	ENST00000380013.4:c.4210C>T	p.Arg1404Ter	p.R1404*	ENST00000380013	NM_001127208.2	1404	Cga/Tga	10/11	0.275143715891554	4	FACETS	1	0.878	1	0.529	0.443	0.624	CLONAL	1	TRUE	2	0.286935728558403	4		302	356	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582106	189582106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	65	523	0	ENST00000264731.3:c.665G>A	p.Gly222Glu	p.G222E	ENST00000264731	NM_003722.4	222	gGa/gAa	5/14	0.286935728558403	3	FACETS	0.914	0.793	1	0.457	0.396	0.523	CLONAL	1	TRUE	1	0.286935728558403	3		523	567	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198453	108198453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	63	372	0	ENST00000278616.4:c.7057C>T	p.Pro2353Ser	p.P2353S	ENST00000278616	NM_000051.3	2353	Cct/Tct	48/63	0.286935728558403	3	FACETS	1	0.936	1	0.568	0.492	0.649	CLONAL	1	TRUE	1	0.286935728558403	3		372	442	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439722	220439723	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	104	1090	3	ENST00000243786.2:c.575_576delinsTT	p.Pro192Leu	p.P192L	ENST00000243786	NM_002191.3	192	cCC/cTT	2/2	0.286935728558403	3	FACETS	0.813	0.727	0.906	0.407	0.363	0.453	CLONAL	1	TRUE	1	0.286935728558403	3		1093	1019	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876208	35876208	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777033414	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	68	536	0	ENST00000303115.3:c.1000G>A	p.Glu334Lys	p.E334K	ENST00000303115	NM_002185.3	334	Gaa/Aaa	8/8	0.286935728558403	3	FACETS	0.996	0.868	1	0.498	0.434	0.568	CLONAL	1	TRUE	1	0.286935728558403	3		536	544	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244999	123244999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150015885	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	61	515	0	ENST00000358487.5:c.2105C>T	p.Ser702Leu	p.S702L	ENST00000358487	NM_000141.4	702	tCg/tTg	16/18	0.286935728558403	2	FACETS	0.934	0.808	1	0.467	0.404	0.536	CLONAL	1	TRUE	0	0.286935728558403	2		515	455	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197443	106197443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1452689450	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	40	371	0	ENST00000380013.4:c.5776C>T	p.Arg1926Cys	p.R1926C	ENST00000380013	NM_001127208.2	1926	Cgt/Tgt	11/11	0.275143715891554	4	FACETS	0.886	0.737	1	0.443	0.368	0.526	CLONAL	1	TRUE	2	0.286935728558403	4		371	405	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177933	56177933	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750940532	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	86	434	0	ENST00000399503.3:c.2906C>T	p.Ser969Phe	p.S969F	ENST00000399503	NM_005921.1	969	tCc/tTc	14/20	0.286935728558403	3	FACETS	1	0.971	1	0.653	0.579	0.731	CLONAL	1	TRUE	1	0.286935728558403	3		434	525	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264865	46264865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	53	461	0	ENST00000371998.3:c.1735C>T	p.Pro579Ser	p.P579S	ENST00000371998		579	Cca/Tca	12/23	0.286935728558403	4	FACETS	0.868	0.74	1	0.434	0.37	0.504	CLONAL	1	TRUE	2	0.286935728558403	4		461	548	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867570	45867571	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	82	1017	0	ENST00000391945.4:c.737_738delinsTT	p.Ser246Phe	p.S246F	ENST00000391945	NM_000400.3	246	tCC/tTT	9/23	0.261956581891461	3	FACETS	0.744	0.655	0.84	0.372	0.327	0.42	SUBCLONAL	1	TRUE	1	0.286935728558403	3		1017	878	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476382	88476382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	74	637	0	ENST00000360948.2:c.1750G>A	p.Asp584Asn	p.D584N	ENST00000360948	NM_001012338.2	584	Gat/Aat	15/19	0.275143715891554	4	FACETS	0.994	0.87	1	0.497	0.435	0.564	CLONAL	1	TRUE	2	0.286935728558403	4		637	668	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296139	15296139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780152379	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	115	978	0	ENST00000263388.2:c.2225C>T	p.Pro742Leu	p.P742L	ENST00000263388	NM_000435.2	742	cCg/cTg	14/33	0.261956581891461	3	FACETS	0.997	0.897	1	0.499	0.448	0.552	CLONAL	1	TRUE	1	0.286935728558403	3		978	919	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414232	32414232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	52	427	0	ENST00000332351.3:c.1319G>A	p.Arg440Lys	p.R440K	ENST00000332351	NM_024426.4	440	aGa/aAa	8/10	0.286935728558403	3	FACETS	0.873	0.744	1	0.436	0.372	0.507	CLONAL	1	TRUE	1	0.286935728558403	3		427	475	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181950	32181950	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	115	842	1	ENST00000375023.3:c.2104C>T	p.His702Tyr	p.H702Y	ENST00000375023	NM_004557.3	702	Cat/Tat	13/30	0.286935728558403	5	FACETS	1	0.948	1	0.362	0.325	0.401	CLONAL	1	TRUE	2	0.286935728558403	5		843	1057	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248429	212248429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	49	374	0	ENST00000342788.4:c.3838G>A	p.Glu1280Lys	p.E1280K	ENST00000342788	NM_005235.2	1280	Gag/Aag	28/28	0.286935728558403	3	FACETS	1	0.949	1	0.642	0.547	0.746	CLONAL	1	TRUE	1	0.286935728558403	3		374	304	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124437	94124437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	41	400	0	ENST00000369303.4:c.146C>T	p.Ser49Phe	p.S49F	ENST00000369303	NM_004440.3	49	tCc/tTc	2/17	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.286935728558403	2		400	266	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804359	43804359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749391587	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	85	653	0	ENST00000372470.3:c.359G>A	p.Arg120Gln	p.R120Q	ENST00000372470	NM_005373.2	120	cGg/cAg	3/12	0.286935728558403	4	FACETS	1	0.957	1	0.587	0.519	0.659	CLONAL	1	TRUE	2	0.286935728558403	4		653	650	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81939065	81939065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867345397	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	66	644	0	ENST00000359376.3:c.1420G>A	p.Glu474Lys	p.E474K	ENST00000359376	NM_002661.3	474	Gaa/Aaa	15/33	0.261956581891461	3	FACETS	0.85	0.738	0.971	0.425	0.369	0.486	CLONAL	1	TRUE	1	0.286935728558403	3		644	619	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624580	93624580	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	81	618	0	ENST00000375746.1:c.671G>A	p.Gly224Glu	p.G224E	ENST00000375746	NM_001174167.1	224	gGg/gAg	4/14	0.286935728558403	2	FACETS	1	0.948	1	0.566	0.5	0.636	CLONAL	1	TRUE	0	0.286935728558403	2		618	499	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987418	2987418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	52	500	0	ENST00000396946.4:c.11G>A	p.Gly4Glu	p.G4E	ENST00000396946	NM_032415.4	4	gGa/gAa	3/25	0.286935728558403	5	FACETS	0.842	0.716	0.98	0.281	0.238	0.327	CLONAL	1	TRUE	2	0.286935728558403	5		500	616	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284946	15284946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	88	727	0	ENST00000263388.2:c.4669C>T	p.Pro1557Ser	p.P1557S	ENST00000263388	NM_000435.2	1557	Cct/Tct	25/33	0.261956581891461	3	FACETS	0.989	0.876	1	0.495	0.438	0.555	CLONAL	1	TRUE	1	0.286935728558403	3		727	709	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11168271	11168271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	105	574	0	ENST00000361445.4:c.7601C>T	p.Ser2534Phe	p.S2534F	ENST00000361445	NM_004958.3	2534	tCc/tTc	57/58	0.286935728558403	4	FACETS	1	0.969	1	0.609	0.546	0.677	CLONAL	1	TRUE	2	0.286935728558403	4		574	773	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845288	42845288	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	146	934	0	ENST00000398585.3:c.974C>T	p.Pro325Leu	p.P325L	ENST00000398585	NM_001135099.1	325	cCc/cTc	9/14	0.286935728558403	3	FACETS	1	0.966	1	0.559	0.51	0.612	CLONAL	1	TRUE	1	0.286935728558403	3		934	1040	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202573	67202573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200313021	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	119	932	0	ENST00000312629.5:c.1382C>T	p.Pro461Leu	p.P461L	ENST00000312629	NM_003952.2	461	cCt/cTt	15/15	0.286935728558403	3	FACETS	1	0.914	1	0.507	0.457	0.56	CLONAL	1	TRUE	1	0.286935728558403	3		932	935	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265314	152265314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781741770	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	51	330	0	ENST00000206249.3:c.767G>A	p.Arg256Gln	p.R256Q	ENST00000206249	NM_000125.3	256	cGa/cAa	4/8	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.286935728558403	2		330	304	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164604	36164604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1476276192	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	51	305	1	ENST00000300305.3:c.1271C>T	p.Ser424Leu	p.S424L	ENST00000300305		424	tCg/tTg	8/8	0.286935728558403	3	FACETS	1	0.957	1	0.675	0.577	0.781	CLONAL	1	TRUE	1	0.286935728558403	3		306	301	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339361	116339361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	58	411	0	ENST00000397752.3:c.223G>A	p.Glu75Lys	p.E75K	ENST00000397752	NM_000245.2	75	Gag/Aag	2/21	0.286935728558403	6	FACETS	1	0.873	1	0.204	0.174	0.235	CLONAL	1	TRUE	1	0.286935728558403	6		411	625	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681504	117681504	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1415195324	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	36	261	1	ENST00000368508.3:c.3445+1G>A		p.X1149_splice	ENST00000368508	NM_002944.2	1149			1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.286935728558403	2		262	238	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937348	32937348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80359035	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	49	286	0	ENST00000380152.3:c.8009C>T	p.Ser2670Leu	p.S2670L	ENST00000380152		2670	tCg/tTg	18/27	0.275143715891554	4	FACETS	1	0.894	1	0.533	0.453	0.622	CLONAL	1	TRUE	2	0.286935728558403	4		286	412	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528612	8528612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	48	394	0	ENST00000356435.5:c.520C>T	p.Arg174Cys	p.R174C	ENST00000356435		174	Cgt/Tgt	4/35	0.286935728558403	1	FACETS	0.952	0.81	1	0.952	0.81	1	CLONAL	1	TRUE	0	0.286935728558403	1		394	301	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272410	38272410	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121909628	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	50	501	0	ENST00000425967.3:c.1957C>T	p.Arg653Ter	p.R653*	ENST00000425967	NM_001174067.1	653	Cga/Tga	15/19	1	2	FACETS	0.848	0.721	0.987	0.848	0.721	0.987	CLONAL	1	TRUE	1	0.286935728558403	2		501	411	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858066	9858066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	72	570	0	ENST00000330684.3:c.3335C>T	p.Ser1112Phe	p.S1112F	ENST00000330684	NM_001134407.1	1112	tCc/tTc	13/13	0.286935728558403	3	FACETS	1	0.945	1	0.573	0.501	0.649	CLONAL	1	TRUE	1	0.286935728558403	3		570	501	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974318	93974318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	40	391	0	ENST00000369303.4:c.1736G>A	p.Gly579Glu	p.G579E	ENST00000369303	NM_004440.3	579	gGg/gAg	8/17	1	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	TRUE	1	0.286935728558403	2		391	277	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120269	94120269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	46	343	0	ENST00000369303.4:c.782G>A	p.Gly261Glu	p.G261E	ENST00000369303	NM_004440.3	261	gGa/gAa	3/17	1	2	FACETS	0.993	0.84	1	0.993	0.84	1	CLONAL	1	TRUE	1	0.286935728558403	2		343	323	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	25	366	1				ENST00000310581	NM_198253.2	-/1132			0.286935728558403	3	FACETS	0.755	0.603	0.924	0.755	0.603	0.924	CLONAL	2	TRUE	1	0.286935728558403	3		367	132	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955959	55955959	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	61	445	0	ENST00000263923.4:c.3203C>T	p.Pro1068Leu	p.P1068L	ENST00000263923	NM_002253.2	1068	cCt/cTt	24/30	0.275143715891554	4	FACETS	1	0.907	1	0.532	0.46	0.611	CLONAL	1	TRUE	2	0.286935728558403	4		445	514	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730938	40730938	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	62	583	0	ENST00000373198.4:c.3598-1G>A		p.X1200_splice	ENST00000373198	NM_133170.3	1200			0.138192123323903	4	FACETS	0.936	0.809	1	0.468	0.404	0.538	INDETERMINATE	1	TRUE	2	0.286935728558403	4		583	594	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20486948	20486948	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs773975473	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	43	321	0	ENST00000346618.3:c.913C>T	p.Arg305Ter	p.R305*	ENST00000346618	NM_001949.4	305	Cga/Tga	5/7	0.286935728558403	5	FACETS	0.979	0.82	1	0.326	0.273	0.385	CLONAL	1	TRUE	2	0.286935728558403	5		321	438	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40789994	40789994	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs746391800	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	38	581	0	ENST00000373198.4:c.2737G>A	p.Glu913Lys	p.E913K	ENST00000373198	NM_133170.3	913	Gag/Aag	18/32	0.138192123323903	4	FACETS	0.585	0.482	0.699	0.292	0.241	0.35	INDETERMINATE	1	TRUE	2	0.286935728558403	4		581	583	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436696	110436696	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1297955422	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	235	753	0	ENST00000375856.3:c.1705C>T	p.Arg569Ter	p.R569*	ENST00000375856	NM_003749.2	569	Cga/Tga	1/2	0.275143715891554	4	FACETS	0.848	0.793	0.904	1	0.989	1	CLONAL	3	TRUE	2	0.286935728558403	4		753	829	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242646	16242646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	69	391	0	ENST00000375759.3:c.1267C>T	p.Arg423Cys	p.R423C	ENST00000375759	NM_015001.2	423	Cgc/Tgc	6/15	0.286935728558403	4	FACETS	1	0.928	1	0.548	0.477	0.624	CLONAL	1	TRUE	2	0.286935728558403	4		391	565	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826577	50826577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	39	245	1	ENST00000398568.2:c.2302C>T	p.Pro768Ser	p.P768S	ENST00000398568	NM_001042412.1	768	Cct/Tct	15/18	0.286935728558403	3	FACETS	1	0.857	1	0.516	0.43	0.612	CLONAL	1	TRUE	1	0.286935728558403	3		246	301	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1953895	1953895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	138	1006	0	ENST00000382891.5:c.2074C>T	p.Leu692Phe	p.L692F	ENST00000382891	NM_133335.3	692	Ctc/Ttc	11/22	0.275143715891554	4	FACETS	1	0.961	1	0.554	0.503	0.607	CLONAL	1	TRUE	2	0.286935728558403	4		1006	1118	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031913	26031913	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	59	398	0	ENST00000244661.2:c.376C>T	p.Gln126Ter	p.Q126*	ENST00000244661	NM_003537.3	126	Cag/Tag	1/1	0.286935728558403	5	FACETS	1	0.924	1	0.371	0.319	0.427	CLONAL	1	TRUE	2	0.286935728558403	5		398	529	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108602	8108602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	112	746	0	ENST00000585124.1:c.793G>A	p.Glu265Lys	p.E265K	ENST00000585124	NM_004217.3	265	Gag/Aag	8/9	0.286935728558403	2	FACETS	1	0.91	1	0.506	0.455	0.56	CLONAL	1	TRUE	0	0.286935728558403	2		746	771	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865774	57865774	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	97	747	0	ENST00000228682.2:c.3251C>T	p.Ala1084Val	p.A1084V	ENST00000228682	NM_005269.2	1084	gCt/gTt	12/12	0.286935728558403	3	FACETS	0.93	0.829	1	0.465	0.414	0.52	CLONAL	1	TRUE	1	0.286935728558403	3		747	831	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468282	50468282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	78	676	2	ENST00000331340.3:c.1517C>T	p.Ser506Leu	p.S506L	ENST00000331340	NM_006060.4	506	tCg/tTg	8/8	0.286935728558403	5	FACETS	0.894	0.784	1	0.298	0.261	0.338	CLONAL	1	TRUE	2	0.286935728558403	5		678	870	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412088	63412088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs943717871	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	107	452	0	ENST00000330258.3:c.1079C>T	p.Ser360Phe	p.S360F	ENST00000330258	NM_152424.3	360	tCc/tTc	2/2	0.282733633482954	2	FACETS	0.769	0.693	0.848			1	SUBCLONAL	2	TRUE	NA	0.286935728558403	2		452	485	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224124	36224124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276663757	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	78	568	1	ENST00000222270.7:c.6674C>T	p.Ser2225Phe	p.S2225F	ENST00000222270	NM_014727.1	2225	tCc/tTc	28/37	0.261956581891461	3	FACETS	1	0.914	1	0.524	0.461	0.592	CLONAL	1	TRUE	1	0.286935728558403	3		569	593	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940079	31940079	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	115	644	0	ENST00000375333.2:c.221G>A	p.Gly74Glu	p.G74E	ENST00000375333	NM_032454.1	74	gGa/gAa	2/8	0.286935728558403	5	FACETS	1	0.97	1	0.402	0.361	0.445	CLONAL	1	TRUE	2	0.286935728558403	5		644	951	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939502	68939502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	45	353	1	ENST00000288368.4:c.487G>A	p.Glu163Lys	p.E163K	ENST00000288368	NM_024870.2	163	Gaa/Aaa	5/40	1	2	FACETS	0.968	0.817	1	0.968	0.817	1	CLONAL	1	TRUE	1	0.286935728558403	2		354	324	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281980	49281980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777806801	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	89	563	0	ENST00000282018.3:c.1027G>A	p.Glu343Lys	p.E343K	ENST00000282018	NM_020377.2	343	Gaa/Aaa	1/1	0.275143715891554	4	FACETS	1	0.94	1	0.548	0.485	0.614	CLONAL	1	TRUE	2	0.286935728558403	4		563	729	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149465980	149465980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	129	951	0	ENST00000286301.3:c.11G>A	p.Gly4Glu	p.G4E	ENST00000286301	NM_005211.3	4	gGa/gAa	2/22	0.286935728558403	3	FACETS	1	0.955	1	0.545	0.494	0.6	CLONAL	1	TRUE	1	0.286935728558403	3		951	943	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781129	161781129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	72	612	0	ENST00000366898.1:c.1276G>A	p.Glu426Lys	p.E426K	ENST00000366898	NM_004562.2	426	Gaa/Aaa	11/12	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.286935728558403	2		612	501	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031851	10031851	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	91	756	1	ENST00000330684.3:c.972G>A	p.Met324Ile	p.M324I	ENST00000330684	NM_001134407.1	324	atG/atA	3/13	0.286935728558403	3	FACETS	1	0.9	1	0.507	0.45	0.568	CLONAL	1	TRUE	1	0.286935728558403	3		757	715	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553389	106553389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	52	506	0	ENST00000369096.4:c.1354G>A	p.Gly452Ser	p.G452S	ENST00000369096	NM_001198.3	452	Ggt/Agt	5/7	1	2	FACETS	0.849	0.724	0.985	0.849	0.724	0.985	CLONAL	1	TRUE	1	0.286935728558403	2		506	427	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047347	128047347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	85	488	1	ENST00000285398.2:c.575C>T	p.Pro192Leu	p.P192L	ENST00000285398	NM_000122.1	192	cCc/cTc	5/15	0.286935728558403	3	FACETS	1	0.952	1	0.573	0.507	0.644	CLONAL	1	TRUE	1	0.286935728558403	3		489	591	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442794	187442794	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1176821201	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	55	527	0	ENST00000232014.4:c.1912C>T	p.Arg638Cys	p.R638C	ENST00000232014	NM_001130845.1	638	Cgt/Tgt	9/10	0.286935728558403	3	FACETS	0.786	0.672	0.91	0.393	0.336	0.455	CLONAL	1	TRUE	1	0.286935728558403	3		527	558	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517747	187517747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	24	300	0	ENST00000441802.2:c.12947C>T	p.Ser4316Phe	p.S4316F	ENST00000441802	NM_005245.3	4316	tCc/tTc	25/27	0.275143715891554	4	FACETS	0.648	0.508	0.81	0.324	0.254	0.405	SUBCLONAL	1	TRUE	2	0.286935728558403	4		300	332	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432566	49432566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1439459361	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	110	900	0	ENST00000301067.7:c.8573C>T	p.Ser2858Phe	p.S2858F	ENST00000301067	NM_003482.3	2858	tCc/tTc	34/54	0.286935728558403	3	FACETS	1	0.91	1	0.507	0.455	0.563	CLONAL	1	TRUE	1	0.286935728558403	3		900	864	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526735	106526735	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	115	376	0	ENST00000359195.3:c.3028C>T	p.Gln1010Ter	p.Q1010*	ENST00000359195	NM_002649.2	1010	Cag/Tag	10/11	0.286935728558403	6	FACETS	1	0.971	1	0.477	0.431	0.525	CLONAL	2	TRUE	1	0.286935728558403	6		376	529	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976739	2976739	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	106	814	0	ENST00000396946.4:c.1273G>A	p.Glu425Lys	p.E425K	ENST00000396946	NM_032415.4	425	Gag/Aag	9/25	0.286935728558403	5	FACETS	1	0.939	1	0.357	0.319	0.397	CLONAL	1	TRUE	2	0.286935728558403	5		814	988	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120324	94120324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	43	349	0	ENST00000369303.4:c.727G>A	p.Glu243Lys	p.E243K	ENST00000369303	NM_004440.3	243	Gaa/Aaa	3/17	1	2	FACETS	0.892	0.749	1	0.892	0.749	1	CLONAL	1	TRUE	1	0.286935728558403	2		349	336	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210583	5210583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253335014	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	99	783	0	ENST00000357368.4:c.5384C>T	p.Pro1795Leu	p.P1795L	ENST00000357368	NM_002850.3	1795	cCg/cTg	35/38	0.261956581891461	3	FACETS	1	0.952	1	0.559	0.499	0.622	CLONAL	1	TRUE	1	0.286935728558403	3		783	706	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274178	10274178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199942034	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	98	620	0	ENST00000330684.3:c.91C>T	p.Pro31Ser	p.P31S	ENST00000330684	NM_001134407.1	31	Ccc/Tcc	2/13	0.286935728558403	3	FACETS	1	0.961	1	0.581	0.519	0.647	CLONAL	1	TRUE	1	0.286935728558403	3		620	672	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829270	128829270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	226	680	3	ENST00000249373.3:c.278C>T	p.Ala93Val	p.A93V	ENST00000249373	NM_005631.4	93	gCc/gTc	1/12	0.286935728558403	6	FACETS	0.892	0.831	0.954	0.535	0.499	0.572	CLONAL	3	TRUE	1	0.286935728558403	6		683	927	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880875	28880875	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415091072	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	63	576	0	ENST00000282397.4:c.3755C>T	p.Ser1252Phe	p.S1252F	ENST00000282397	NM_002019.4	1252	tCt/tTt	29/30	0.275143715891554	4	FACETS	0.868	0.75	0.996	0.434	0.375	0.498	CLONAL	1	TRUE	2	0.286935728558403	4		576	651	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561475	9561475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	57	609	0	ENST00000353224.5:c.307G>A	p.Glu103Lys	p.E103K	ENST00000353224	NM_177990.2	103	Gaa/Aaa	4/10	0.275143715891554	4	FACETS	0.77	0.66	0.891	0.385	0.33	0.446	SUBCLONAL	1	TRUE	2	0.286935728558403	4		609	664	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795725	42795725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	108	977	1	ENST00000575354.2:c.2714C>T	p.Pro905Leu	p.P905L	ENST00000575354	NM_015125.3	905	cCc/cTc	11/20	0.261956581891461	3	FACETS	0.887	0.795	0.986	0.444	0.397	0.493	CLONAL	1	TRUE	1	0.286935728558403	3		978	970	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763966	76763966	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	95	351	0	ENST00000373344.5:c.7342C>T	p.Pro2448Ser	p.P2448S	ENST00000373344	NM_000489.3	2448	Cct/Tct	35/35	0.282733633482954	2	FACETS	0.82	0.735	0.909			1	CLONAL	2	TRUE	NA	0.286935728558403	2		351	404	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980726	40980726	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	47	425	0	ENST00000373198.4:c.1760C>T	p.Ser587Leu	p.S587L	ENST00000373198	NM_133170.3	587	tCa/tTa	10/32	0.138192123323903	4	FACETS	0.947	0.8	1	0.474	0.4	0.555	INDETERMINATE	1	TRUE	2	0.286935728558403	4		425	445	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838003	156838003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761633256	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	120	1039	2	ENST00000524377.1:c.536G>A	p.Gly179Glu	p.G179E	ENST00000524377	NM_002529.3	179	gGg/gAg	5/17	0.286935728558403	4	FACETS	0.936	0.843	1	0.468	0.421	0.518	CLONAL	1	TRUE	2	0.286935728558403	4		1041	1150	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857769	9857769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	82	583	2	ENST00000330684.3:c.3632C>T	p.Ser1211Phe	p.S1211F	ENST00000330684	NM_001134407.1	1211	tCc/tTc	13/13	0.286935728558403	3	FACETS	1	0.945	1	0.561	0.495	0.631	CLONAL	1	TRUE	1	0.286935728558403	3		585	583	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467756	50467756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781662160	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	75	747	0	ENST00000331340.3:c.991G>A	p.Val331Met	p.V331M	ENST00000331340	NM_006060.4	331	Gtg/Atg	8/8	0.286935728558403	5	FACETS	0.901	0.788	1	0.3	0.262	0.341	CLONAL	1	TRUE	2	0.286935728558403	5		747	830	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444256	49444256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542933613	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	105	1042	0	ENST00000301067.7:c.3115C>T	p.Pro1039Ser	p.P1039S	ENST00000301067	NM_003482.3	1039	Cct/Tct	11/54	0.286935728558403	3	FACETS	0.856	0.765	0.952	0.428	0.382	0.476	CLONAL	1	TRUE	1	0.286935728558403	3		1042	978	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397714	116397714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376459715	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	79	494	0	ENST00000397752.3:c.1988C>T	p.Ser663Leu	p.S663L	ENST00000397752	NM_000245.2	663	tCg/tTg	8/21	0.286935728558403	6	FACETS	1	0.965	1	0.254	0.223	0.287	CLONAL	1	TRUE	1	0.286935728558403	6		494	683	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672638	30672638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	93	693	1	ENST00000376406.3:c.4322C>T	p.Ser1441Phe	p.S1441F	ENST00000376406	NM_014641.2	1441	tCt/tTt	10/15	0.286935728558403	5	FACETS	1	0.95	1	0.374	0.332	0.419	CLONAL	1	TRUE	2	0.286935728558403	5		694	826	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224566	36224566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	112	948	1	ENST00000222270.7:c.7028C>T	p.Pro2343Leu	p.P2343L	ENST00000222270	NM_014727.1	2343	cCc/cTc	29/37	0.261956581891461	3	FACETS	0.966	0.868	1	0.483	0.434	0.535	CLONAL	1	TRUE	1	0.286935728558403	3		949	924	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751532	57751532	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	46	331	0	ENST00000274289.3:c.1459C>T	p.Pro487Ser	p.P487S	ENST00000274289	NM_006622.3	487	Ccg/Tcg	11/14	0.286935728558403	3	FACETS	0.89	0.751	1	0.445	0.375	0.522	CLONAL	1	TRUE	1	0.286935728558403	3		331	412	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750615	41750615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	40	466	0	ENST00000226382.2:c.13G>A	p.Glu5Lys	p.E5K	ENST00000226382	NM_003924.3	5	Gaa/Aaa	1/3	0.275143715891554	4	FACETS	0.667	0.554	0.793	0.333	0.277	0.397	SUBCLONAL	1	TRUE	2	0.286935728558403	4		466	538	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107086	27107086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	194	565	0	ENST00000324856.7:c.6697C>T	p.Arg2233Trp	p.R2233W	ENST00000324856	NM_006015.4	2233	Cgg/Tgg	20/20	0.286935728558403	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.286935728558403	4		565	755	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	75	354	1				ENST00000310581	NM_198253.2	-/1132			0.286935728558403	3	FACETS	0.884	0.795	0.975	1	0.984	1	CLONAL	4	TRUE	1	0.286935728558403	3		355	169	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988304	41988304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs563448726	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	51	551	0	ENST00000219905.7:c.1096C>T	p.Arg366Cys	p.R366C	ENST00000219905	NM_001164273.1	366	Cgt/Tgt	3/24	0.275143715891554	4	FACETS	0.749	0.636	0.873	0.374	0.318	0.437	SUBCLONAL	1	TRUE	2	0.286935728558403	4		551	611	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81954867	81954867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757834798	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	68	555	0	ENST00000359376.3:c.2300C>T	p.Pro767Leu	p.P767L	ENST00000359376	NM_002661.3	767	cCg/cTg	21/33	0.261956581891461	3	FACETS	0.956	0.832	1	0.478	0.416	0.545	CLONAL	1	TRUE	1	0.286935728558403	3		555	567	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631146	69631146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	172	715	1	ENST00000334134.2:c.266G>A	p.Arg89Lys	p.R89K	ENST00000334134	NM_005247.2	89	aGg/aAg	2/3	0.286935728558403	3	FACETS	0.975	0.9	1	0.975	0.9	1	CLONAL	2	TRUE	1	0.286935728558403	3		716	703	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612422	1612422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1312230157	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	89	778	1	ENST00000344749.5:c.1597G>A	p.Glu533Lys	p.E533K	ENST00000344749	NM_001136139.2	533	Gag/Aag	18/19	0.261956581891461	3	FACETS	0.951	0.843	1	0.475	0.421	0.533	CLONAL	1	TRUE	1	0.286935728558403	3		779	746	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877048	151877048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	57	544	0	ENST00000262189.6:c.7313C>T	p.Pro2438Leu	p.P2438L	ENST00000262189	NM_170606.2	2438	cCc/cTc	37/59	0.286935728558403	6	FACETS	0.952	0.816	1	0.19	0.163	0.22	CLONAL	1	TRUE	1	0.286935728558403	6		544	657	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434123	12434123	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	37	325	0	ENST00000287820.6:c.491G>A	p.Arg164Gln	p.R164Q	ENST00000287820	NM_015869.4	164	cGg/cAg	4/7	0.286935728558403	2	FACETS	0.837	0.693	0.998	0.419	0.346	0.499	CLONAL	1	TRUE	0	0.286935728558403	2		325	308	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515325	31515325	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs369352228	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	101	494	3	ENST00000344624.3:c.1060C>T	p.Arg354Cys	p.R354C	ENST00000344624		354	Cgc/Tgc	5/33	0.286935728558403	3	FACETS	1	0.979	1	0.701	0.628	0.778	CLONAL	1	TRUE	1	0.286935728558403	3		497	574	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570805	226570805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	93	704	0	ENST00000366794.5:c.1091C>T	p.Ser364Phe	p.S364F	ENST00000366794	NM_001618.3	364	tCc/tTc	8/23	0.286935728558403	4	FACETS	0.961	0.853	1	0.481	0.426	0.538	CLONAL	1	TRUE	2	0.286935728558403	4		704	868	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36821031	36821031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356391159	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	80	700	0	ENST00000373129.3:c.346C>T	p.Arg116Cys	p.R116C	ENST00000373129	NM_032017.1	116	Cgc/Tgc	6/12	0.286935728558403	4	FACETS	1	0.904	1	0.516	0.453	0.582	CLONAL	1	TRUE	2	0.286935728558403	4		700	696	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815316	32815316	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	100	825	0	ENST00000354258.4:c.2057C>G	p.Ser686Cys	p.S686C	ENST00000354258	NM_000593.5	686	tCt/tGt	9/11	0.286935728558403	6	FACETS	0.992	0.884	1	0.331	0.294	0.37	CLONAL	1	TRUE	3	0.286935728558403	6		825	1106	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475552	12475552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	157	619	0	ENST00000287820.6:c.1426G>A	p.Glu476Lys	p.E476K	ENST00000287820	NM_015869.4	476	Gaa/Aaa	7/7	0.286935728558403	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	0	0.286935728558403	2		619	542	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552808	106552808	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	83	580	0	ENST00000369096.4:c.773C>T	p.Ser258Phe	p.S258F	ENST00000369096	NM_001198.3	258	tCc/tTc	5/7	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.286935728558403	2		580	570	SUCCESS
APC	324	MSKCC	GRCh37	5	112179156	112179156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267600320	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	49	292	0	ENST00000257430.4:c.7865C>T	p.Pro2622Leu	p.P2622L	ENST00000257430	NM_000038.5	2622	cCc/cTc	16/16	0.286935728558403	3	FACETS	1	0.939	1	0.605	0.514	0.703	CLONAL	1	TRUE	1	0.286935728558403	3		292	323	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041192	29041192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	90	585	1	ENST00000282397.4:c.236C>T	p.Ser79Phe	p.S79F	ENST00000282397	NM_002019.4	79	tCt/tTt	3/30	0.275143715891554	4	FACETS	1	0.942	1	0.55	0.488	0.616	CLONAL	1	TRUE	2	0.286935728558403	4		586	734	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291065	10291065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138841970	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	80	634	0	ENST00000340748.4:c.406C>T	p.Arg136Cys	p.R136C	ENST00000340748		136	Cgc/Tgc	4/40	0.261956581891461	3	FACETS	0.942	0.829	1	0.471	0.414	0.532	CLONAL	1	TRUE	1	0.286935728558403	3		634	677	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253376	226253376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	46	307	0	ENST00000366813.1:c.148C>T	p.Arg50Cys	p.R50C	ENST00000366813		50	Cgt/Tgt	2/3	0.286935728558403	4	FACETS	1	0.863	1	0.512	0.432	0.6	CLONAL	1	TRUE	2	0.286935728558403	4		307	403	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416741	416741	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	46	371	0	ENST00000399788.2:c.3809C>T	p.Ser1270Phe	p.S1270F	ENST00000399788	NM_001042603.1	1270	tCc/tTc	23/28	0.286935728558403	3	FACETS	0.926	0.781	1	0.463	0.39	0.543	CLONAL	1	TRUE	1	0.286935728558403	3		371	396	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367293	50367293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	137	517	0	ENST00000331340.3:c.100C>T	p.Pro34Ser	p.P34S	ENST00000331340	NM_006060.4	34	Ccc/Tcc	3/8	0.286935728558403	5	FACETS	0.909	0.828	0.995	0.606	0.552	0.663	CLONAL	2	TRUE	2	0.286935728558403	5		517	751	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447328	187447328	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	98	678	0	ENST00000232014.4:c.865C>T	p.Arg289Ter	p.R289*	ENST00000232014	NM_001130845.1	289	Cga/Tga	5/10	0.286935728558403	3	FACETS	1	0.961	1	0.581	0.519	0.647	CLONAL	1	TRUE	1	0.286935728558403	3		678	672	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117753470	117753470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1248358199	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	75	612	0	ENST00000369458.3:c.8C>T	p.Ser3Phe	p.S3F	ENST00000369458	NM_024626.3	3	tCc/tTc	1/6	0.286935728558403	4	FACETS	1	0.9	1	0.515	0.451	0.584	CLONAL	1	TRUE	2	0.286935728558403	4		612	653	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28971144	28971144	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	46	427	1	ENST00000282397.4:c.1613C>T	p.Ser538Phe	p.S538F	ENST00000282397	NM_002019.4	538	tCc/tTc	12/30	0.275143715891554	4	FACETS	0.884	0.745	1	0.442	0.372	0.519	CLONAL	1	TRUE	2	0.286935728558403	4		428	467	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849827	156849827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866288494	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	111	631	0	ENST00000524377.1:c.2083C>T	p.Pro695Ser	p.P695S	ENST00000524377	NM_002529.3	695	Ccg/Tcg	16/17	0.286935728558403	4	FACETS	1	0.978	1	0.66	0.594	0.731	CLONAL	1	TRUE	2	0.286935728558403	4		631	754	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805016	43805016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1464244274	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	71	707	0	ENST00000372470.3:c.466G>A	p.Glu156Lys	p.E156K	ENST00000372470	NM_005373.2	156	Gag/Aag	4/12	0.286935728558403	4	FACETS	0.883	0.77	1	0.442	0.385	0.503	CLONAL	1	TRUE	2	0.286935728558403	4		707	721	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117384	115117384	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1312058352	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	49	358	0	ENST00000257566.3:c.790C>T	p.Pro264Ser	p.P264S	ENST00000257566	NM_016569.3	264	Cct/Tct	4/8	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.286935728558403	2		358	300	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455139	50455139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1359632331	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	55	442	1	ENST00000331340.3:c.686G>A	p.Ser229Asn	p.S229N	ENST00000331340	NM_006060.4	229	aGc/aAc	6/8	0.286935728558403	5	FACETS	1	0.859	1	0.335	0.286	0.388	CLONAL	1	TRUE	2	0.286935728558403	5		443	546	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180357	27180357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	61	430	0	ENST00000380036.4:c.1021G>A	p.Glu341Lys	p.E341K	ENST00000380036	NM_000459.3	341	Gag/Aag	7/23	0.286935728558403	1	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	0	0.286935728558403	1		430	352	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666693	206666693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782183853	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	88	743	2	ENST00000367120.3:c.2027G>A	p.Arg676Gln	p.R676Q	ENST00000367120	NM_014002.3	676	cGa/cAa	20/22	0.286935728558403	4	FACETS	0.845	0.747	0.95	0.423	0.373	0.475	CLONAL	1	TRUE	2	0.286935728558403	4		745	934	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891678	28891678	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776861138	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	167	641	1	ENST00000282397.4:c.3343G>A	p.Glu1115Lys	p.E1115K	ENST00000282397	NM_002019.4	1115	Gaa/Aaa	25/30	0.275143715891554	4	FACETS	0.988	0.91	1	0.988	0.91	1	CLONAL	2	TRUE	2	0.286935728558403	4		642	758	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670630	134670630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	93	771	0	ENST00000398015.3:c.541G>A	p.Gly181Arg	p.G181R	ENST00000398015	NM_004441.4	181	Gga/Aga	3/16	0.286935728558403	3	FACETS	1	0.908	1	0.512	0.455	0.573	CLONAL	1	TRUE	1	0.286935728558403	3		771	724	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999618	100999618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762965993	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	128	951	1	ENST00000325455.5:c.184C>T	p.Arg62Trp	p.R62W	ENST00000325455	NM_001202474.3	62	Cgg/Tgg	1/8	0.286935728558403	3	FACETS	1	0.969	1	0.581	0.526	0.639	CLONAL	1	TRUE	1	0.286935728558403	3		952	878	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637867	176637867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	92	554	0	ENST00000439151.2:c.2467C>T	p.Pro823Ser	p.P823S	ENST00000439151	NM_022455.4	823	Cct/Tct	5/23	0.286935728558403	3	FACETS	1	0.947	1	0.555	0.494	0.621	CLONAL	1	TRUE	1	0.286935728558403	3		554	660	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917802	29917802	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs112782816	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	122	838	0	ENST00000389048.3:c.866C>T	p.Ser289Phe	p.S289F	ENST00000389048	NM_004304.4	289	tCc/tTc	3/29	0.286935728558403	3	FACETS	1	0.978	1	0.639	0.578	0.703	CLONAL	1	TRUE	1	0.286935728558403	3		838	761	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319917	8319917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	52	343	0	ENST00000356435.5:c.5584G>A	p.Glu1862Lys	p.E1862K	ENST00000356435		1862	Gaa/Aaa	34/35	0.286935728558403	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.286935728558403	1		343	254	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490546	20490546	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	87	616	0	ENST00000346618.3:c.1283C>T	p.Pro428Leu	p.P428L	ENST00000346618	NM_001949.4	428	cCc/cTc	7/7	0.286935728558403	5	FACETS	1	0.921	1	0.351	0.31	0.395	CLONAL	1	TRUE	2	0.286935728558403	5		616	824	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499604	149499604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	85	617	0	ENST00000261799.4:c.2669G>A	p.Gly890Glu	p.G890E	ENST00000261799	NM_002609.3	890	gGg/gAg	19/23	0.286935728558403	3	FACETS	1	0.929	1	0.535	0.473	0.601	CLONAL	1	TRUE	1	0.286935728558403	3		617	633	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647068	23647068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	108	755	0	ENST00000261584.4:c.799C>T	p.Pro267Ser	p.P267S	ENST00000261584	NM_024675.3	267	Cct/Tct	4/13	0.286935728558403	3	FACETS	1	0.913	1	0.51	0.457	0.566	CLONAL	1	TRUE	1	0.286935728558403	3		755	844	SUCCESS
MET	4233	MSKCC	GRCh37	7	116417467	116417467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	51	360	0	ENST00000397752.3:c.3284G>A	p.Gly1095Glu	p.G1095E	ENST00000397752	NM_000245.2	1095	gGg/gAg	16/21	0.286935728558403	6	FACETS	1	0.887	1	0.21	0.178	0.245	CLONAL	1	TRUE	1	0.286935728558403	6		360	532	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897017	28897017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	70	546	0	ENST00000282397.4:c.2863C>T	p.Pro955Ser	p.P955S	ENST00000282397	NM_002019.4	955	Cca/Tca	21/30	0.275143715891554	4	FACETS	0.953	0.831	1	0.476	0.415	0.543	CLONAL	1	TRUE	2	0.286935728558403	4		546	659	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672242	30672242	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	66	678	1	ENST00000376406.3:c.4718C>T	p.Pro1573Leu	p.P1573L	ENST00000376406	NM_014641.2	1573	cCt/cTt	10/15	0.286935728558403	5	FACETS	0.852	0.739	0.976	0.284	0.246	0.326	CLONAL	1	TRUE	2	0.286935728558403	5		679	772	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462933	120462933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1450649026	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	87	542	0	ENST00000256646.2:c.5398C>T	p.Arg1800Cys	p.R1800C	ENST00000256646	NM_024408.3	1800	Cgt/Tgt	30/34	0.286935728558403	4	FACETS	1	0.958	1	0.589	0.521	0.661	CLONAL	1	TRUE	2	0.286935728558403	4		542	663	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435193	18435193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	92	343	0	ENST00000266497.5:c.178G>A	p.Glu60Lys	p.E60K	ENST00000266497		60	Gaa/Aaa	1/31	0.286935728558403	3	FACETS	1	0.913	1	1	0.913	1	CLONAL	2	TRUE	1	0.286935728558403	3		343	359	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281169	15281169	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	90	969	0	ENST00000263388.2:c.5087C>T	p.Pro1696Leu	p.P1696L	ENST00000263388	NM_000435.2	1696	cCc/cTc	27/33	0.261956581891461	3	FACETS	0.844	0.748	0.947	0.422	0.374	0.474	CLONAL	1	TRUE	1	0.286935728558403	3		969	850	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497908	25497908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1247178186	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	115	762	0	ENST00000264709.3:c.541C>T	p.Arg181Cys	p.R181C	ENST00000264709	NM_175629.2	181	Cgt/Tgt	6/23	0.286935728558403	3	FACETS	1	0.959	1	0.562	0.506	0.621	CLONAL	1	TRUE	1	0.286935728558403	3		762	816	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300426	11300426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	71	605	0	ENST00000361445.4:c.1720C>T	p.Pro574Ser	p.P574S	ENST00000361445	NM_004958.3	574	Cct/Tct	11/58	0.286935728558403	4	FACETS	0.892	0.778	1	0.446	0.389	0.508	CLONAL	1	TRUE	2	0.286935728558403	4		605	714	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950442	17950442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200836500	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	83	840	0	ENST00000458235.1:c.1285C>T	p.Leu429Phe	p.L429F	ENST00000458235	NM_000215.3	429	Ctc/Ttc	10/24	0.261956581891461	3	FACETS	0.852	0.752	0.961	0.426	0.376	0.481	CLONAL	1	TRUE	1	0.286935728558403	3		840	776	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781558	9781558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	115	819	0	ENST00000377346.4:c.1868C>T	p.Ser623Phe	p.S623F	ENST00000377346	NM_005026.3	623	tCc/tTc	15/24	0.286935728558403	4	FACETS	1	0.905	1	0.503	0.452	0.557	CLONAL	1	TRUE	2	0.286935728558403	4		819	1025	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11206745	11206746	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	58	483	0	ENST00000361445.4:c.4673_4674delinsTT	p.Ser1558Phe	p.S1558F	ENST00000361445	NM_004958.3	1558	tCC/tTT	32/58	0.286935728558403	4	FACETS	0.845	0.725	0.975	0.422	0.362	0.488	CLONAL	1	TRUE	2	0.286935728558403	4		483	616	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260821	16260822	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	77	739	1	ENST00000375759.3:c.8086_8087delinsTT	p.Pro2696Phe	p.P2696F	ENST00000375759	NM_015001.2	2696	CCt/TTt	11/15	0.286935728558403	4	FACETS	0.847	0.743	0.96	0.424	0.371	0.48	CLONAL	1	TRUE	2	0.286935728558403	4		740	815	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101354	27101354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	228	759	1	ENST00000324856.7:c.4636C>T	p.Pro1546Ser	p.P1546S	ENST00000324856	NM_006015.4	1546	Cct/Tct	18/20	0.286935728558403	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	2	0.286935728558403	4		760	989	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36808972	36808972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	113	757	0	ENST00000373129.3:c.1082C>T	p.Ser361Phe	p.S361F	ENST00000373129	NM_032017.1	361	tCc/tTc	11/12	0.286935728558403	4	FACETS	1	0.937	1	0.53	0.476	0.587	CLONAL	1	TRUE	2	0.286935728558403	4		757	957	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39317362	39317362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	81	507	1	ENST00000373001.3:c.824C>T	p.Ser275Phe	p.S275F	ENST00000373001	NM_022157.3	275	tCc/tTc	5/7	0.286935728558403	4	FACETS	1	0.929	1	0.539	0.475	0.608	CLONAL	1	TRUE	2	0.286935728558403	4		508	674	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797169	45797169	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	120	997	0	ENST00000450313.1:c.1246C>T	p.Gln416Ter	p.Q416*	ENST00000450313	NM_012222.2	416	Cag/Tag	13/16	0.286935728558403	4	FACETS	0.958	0.863	1	0.479	0.431	0.529	CLONAL	1	TRUE	2	0.286935728558403	4		997	1124	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509496	46509496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	79	496	0	ENST00000262741.5:c.1235G>A	p.Gly412Asp	p.G412D	ENST00000262741	NM_003629.3	412	gGc/gAc	10/10	0.286935728558403	4	FACETS	1	0.934	1	0.546	0.48	0.617	CLONAL	1	TRUE	2	0.286935728558403	4		496	649	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076766	72076766	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	76	462	0	ENST00000357731.5:c.731G>A	p.Arg244Lys	p.R244K	ENST00000357731	NM_173808.2	244	aGa/aAa	5/7	0.286935728558403	4	FACETS	1	0.902	1	0.516	0.453	0.585	CLONAL	1	TRUE	2	0.286935728558403	4		462	660	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78426035	78426035	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1363346270	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	68	566	0	ENST00000370768.2:c.1490C>T	p.Ala497Val	p.A497V	ENST00000370768	NM_003902.3	497	gCt/gTt	15/20	0.286935728558403	4	FACETS	0.859	0.747	0.981	0.43	0.373	0.491	CLONAL	1	TRUE	2	0.286935728558403	4		566	710	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263197	115263197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	88	625	1	ENST00000438362.2:c.2153C>T	p.Pro718Leu	p.P718L	ENST00000438362	NM_001242891.1	718	cCc/cTc	17/20	0.286935728558403	4	FACETS	1	0.907	1	0.514	0.455	0.577	CLONAL	1	TRUE	2	0.286935728558403	4		626	768	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266565	115266566	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	83	593	1	ENST00000438362.2:c.1949_1950delinsTT	p.Pro650Leu	p.P650L	ENST00000438362	NM_001242891.1	650	cCC/cTT	16/20	0.286935728558403	4	FACETS	1	0.887	1	0.503	0.443	0.567	CLONAL	1	TRUE	2	0.286935728558403	4		594	740	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166065	118166065	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	57	489	1	ENST00000369448.3:c.575T>G	p.Leu192Arg	p.L192R	ENST00000369448	NM_017709.3	192	cTt/cGt	2/2	0.286935728558403	4	FACETS	0.916	0.786	1	0.458	0.393	0.529	CLONAL	1	TRUE	2	0.286935728558403	4		490	558	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830887	156830887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1220379017	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	76	518	1	ENST00000524377.1:c.161G>A	p.Gly54Glu	p.G54E	ENST00000524377	NM_002529.3	54	gGg/gAg	1/17	0.286935728558403	4	FACETS	1	0.926	1	0.538	0.472	0.61	CLONAL	1	TRUE	2	0.286935728558403	4		519	633	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981854	201981854	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1324378932	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	133	954	0	ENST00000359651.3:c.565C>T	p.Pro189Ser	p.P189S	ENST00000359651		189	Ccc/Tcc	4/8	0.286935728558403	4	FACETS	1	0.976	1	0.612	0.555	0.673	CLONAL	1	TRUE	2	0.286935728558403	4		954	974	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518493	204518493	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	45	322	0	ENST00000367182.3:c.1156T>A	p.Phe386Ile	p.F386I	ENST00000367182	NM_001278516.1	386	Ttt/Att	11/11	0.286935728558403	4	FACETS	0.909	0.765	1	0.455	0.382	0.534	CLONAL	1	TRUE	2	0.286935728558403	4		322	444	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104268997	104268998	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	83	736	0	ENST00000369902.3:c.254_255delinsTT	p.Pro85Leu	p.P85L	ENST00000369902	NM_016169.3	85	cCC/cTT	2/12	0.286935728558403	2	FACETS	0.838	0.74	0.944	0.419	0.37	0.472	CLONAL	1	TRUE	0	0.286935728558403	2		736	690	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276849	123276849	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	51	351	0	ENST00000358487.5:c.1068G>A	p.Trp356Ter	p.W356*	ENST00000358487	NM_000141.4	356	tgG/tgA	8/18	0.286935728558403	2	FACETS	1	0.945	1	0.615	0.526	0.711	CLONAL	1	TRUE	0	0.286935728558403	2		351	289	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251980	8251981	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	111	901	2	ENST00000335790.3:c.96_97delinsAA	p.Asp33Asn	p.D33N	ENST00000335790	NM_002315.2	32	aaGGac/aaAAac	2/4	0.286935728558403	3	FACETS	0.88	0.79	0.976	0.44	0.395	0.488	CLONAL	1	TRUE	1	0.286935728558403	3		903	1005	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588210	69588211	+	missense_variant	Missense_Mutation	DNP	GG	GG	CA	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	67	588	1	ENST00000168712.1:c.487_488delinsTG	p.Pro163Cys	p.P163C	ENST00000168712	NM_002007.2	163	CCc/TGc	3/3	0.286935728558403	3	FACETS	0.916	0.796	1	0.458	0.398	0.523	CLONAL	1	TRUE	1	0.286935728558403	3		589	583	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192620	94192620	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	86	653	0	ENST00000323929.3:c.1454T>C	p.Leu485Pro	p.L485P	ENST00000323929	NM_005591.3	485	cTt/cCt	13/20	0.286935728558403	3	FACETS	1	0.953	1	0.574	0.508	0.644	CLONAL	1	TRUE	1	0.286935728558403	3		653	597	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909880	100909881	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	26	267	0	ENST00000325455.5:c.2768_2769delinsAA	p.Gly923Glu	p.G923E	ENST00000325455	NM_001202474.3	923	gGG/gAA	8/8	0.286935728558403	3	FACETS	0.702	0.557	0.868	0.351	0.278	0.434	SUBCLONAL	1	TRUE	1	0.286935728558403	3		267	295	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933363	100933363	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1348573263	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	64	569	0	ENST00000325455.5:c.2027C>T	p.Ser676Leu	p.S676L	ENST00000325455	NM_001202474.3	676	tCa/tTa	4/8	0.286935728558403	3	FACETS	0.828	0.717	0.949	0.414	0.358	0.475	CLONAL	1	TRUE	1	0.286935728558403	3		569	616	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102033237	102033238	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	86	625	2	ENST00000282441.5:c.623_624delinsTT	p.Ser208Phe	p.S208F	ENST00000282441	NM_001130145.2	208	tCC/tTT	3/9	0.286935728558403	3	FACETS	1	0.93	1	0.535	0.474	0.601	CLONAL	1	TRUE	1	0.286935728558403	3		627	640	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115726	108115726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	39	221	0	ENST00000278616.4:c.874C>T	p.Pro292Ser	p.P292S	ENST00000278616	NM_000051.3	292	Ccg/Tcg	7/63	0.286935728558403	3	FACETS	1	0.929	1	0.612	0.51	0.723	CLONAL	1	TRUE	1	0.286935728558403	3		221	254	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170444	119170444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	61	490	0	ENST00000264033.4:c.2674C>T	p.Leu892Phe	p.L892F	ENST00000264033	NM_005188.3	892	Ctc/Ttc	16/16	0.286935728558403	3	FACETS	1	0.901	1	0.526	0.455	0.603	CLONAL	1	TRUE	1	0.286935728558403	3		490	462	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499574	18499574	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	45	358	0	ENST00000266497.5:c.1430-1G>A		p.X477_splice	ENST00000266497		477			0.286935728558403	3	FACETS	1	0.897	1	0.542	0.457	0.635	CLONAL	1	TRUE	1	0.286935728558403	3		358	331	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658248	18658248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200039549	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	52	458	0	ENST00000266497.5:c.3053C>T	p.Ser1018Phe	p.S1018F	ENST00000266497		1018	tCc/tTc	22/31	0.286935728558403	3	FACETS	0.834	0.71	0.969	0.417	0.355	0.485	CLONAL	1	TRUE	1	0.286935728558403	3		458	497	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691246	18691247	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	25	240	0	ENST00000266497.5:c.3357_3357+1delinsAA		p.X1119_splice	ENST00000266497		1119		23/31	0.286935728558403	3	FACETS	0.813	0.643	1	0.407	0.321	0.504	CLONAL	1	TRUE	1	0.286935728558403	3		240	245	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230533	46230533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	92	325	0	ENST00000334344.6:c.782C>T	p.Ser261Leu	p.S261L	ENST00000334344	NM_152641.2	261	tCa/tTa	8/21	0.286935728558403	3	FACETS	0.952	0.852	1	0.952	0.852	1	CLONAL	2	TRUE	1	0.286935728558403	3		325	385	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425487	49425487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs183702050	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	124	952	1	ENST00000301067.7:c.13001C>T	p.Ala4334Val	p.A4334V	ENST00000301067	NM_003482.3	4334	gCc/gTc	39/54	0.286935728558403	3	FACETS	1	0.949	1	0.538	0.486	0.593	CLONAL	1	TRUE	1	0.286935728558403	3		953	918	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440199	49440199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	78	630	1	ENST00000301067.7:c.4427C>T	p.Ser1476Phe	p.S1476F	ENST00000301067	NM_003482.3	1476	tCc/tTc	16/54	0.286935728558403	3	FACETS	0.956	0.841	1	0.478	0.42	0.541	CLONAL	1	TRUE	1	0.286935728558403	3		631	650	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865749	57865749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	118	791	0	ENST00000228682.2:c.3226C>T	p.Pro1076Ser	p.P1076S	ENST00000228682	NM_005269.2	1076	Cct/Tct	12/12	0.286935728558403	3	FACETS	1	0.948	1	0.54	0.487	0.596	CLONAL	1	TRUE	1	0.286935728558403	3		791	871	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811768	102811768	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	88	599	0	ENST00000307046.8:c.416C>G	p.Ser139Cys	p.S139C	ENST00000307046	NM_001111285.1	139	tCt/tGt	4/4	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.286935728558403	2		599	514	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784112	120784113	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	112	890	1	ENST00000257552.2:c.872_873delinsAA	p.Trp291Ter	p.W291*	ENST00000257552	NM_002442.3	291	tGG/tAA	13/15	1	2	FACETS	0.989	0.89	1	0.989	0.89	1	CLONAL	1	TRUE	1	0.286935728558403	2		891	789	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431475	121431475	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	81	677	0	ENST00000257555.6:c.679G>A	p.Glu227Lys	p.E227K	ENST00000257555		227	Gag/Aag	3/10	1	2	FACETS	0.943	0.831	1	0.943	0.831	1	CLONAL	1	TRUE	1	0.286935728558403	2		677	599	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241915	133241915	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	80	648	0	ENST00000320574.5:c.2441C>A	p.Ser814Tyr	p.S814Y	ENST00000320574	NM_006231.2	814	tCc/tAc	21/49	0.261956581891461	3	FACETS	0.946	0.833	1	0.473	0.416	0.534	CLONAL	1	TRUE	1	0.286935728558403	3		648	674	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557512	21557512	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	102	687	0	ENST00000382592.4:c.2333C>T	p.Ala778Val	p.A778V	ENST00000382592	NM_014572.2	778	gCc/gTc	5/8	0.275143715891554	4	FACETS	1	0.963	1	0.585	0.523	0.651	CLONAL	1	TRUE	2	0.286935728558403	4		687	782	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623774	28623775	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	67	532	0	ENST00000241453.7:c.879_880delinsTA	p.Glu293_Glu294delinsAspLys	p.E293_E294delinsDK	ENST00000241453	NM_004119.2	293	gaGGag/gaTAag	7/24	0.275143715891554	4	FACETS	0.992	0.862	1	0.496	0.431	0.566	CLONAL	1	TRUE	2	0.286935728558403	4		532	606	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28883033	28883033	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	70	469	0	ENST00000282397.4:c.3667G>A	p.Glu1223Lys	p.E1223K	ENST00000282397	NM_002019.4	1223	Gaa/Aaa	28/30	0.275143715891554	4	FACETS	1	0.936	1	0.56	0.488	0.637	CLONAL	1	TRUE	2	0.286935728558403	4		469	561	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911754	32911754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80358572	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	72	476	0	ENST00000380152.3:c.3262C>T	p.Pro1088Ser	p.P1088S	ENST00000380152		1088	Cct/Tct	11/27	0.275143715891554	4	FACETS	1	0.876	1	0.501	0.438	0.57	CLONAL	1	TRUE	2	0.286935728558403	4		476	644	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913745	32913746	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	51	384	0	ENST00000380152.3:c.5253_5254delinsTT	p.His1752Tyr	p.H1752Y	ENST00000380152		1751	taCCat/taTTat	11/27	0.275143715891554	4	FACETS	0.959	0.816	1	0.48	0.408	0.558	CLONAL	1	TRUE	2	0.286935728558403	4		384	477	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347844	73347845	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	28	222	0	ENST00000377767.4:c.1216_1217delinsTT	p.Pro406Phe	p.P406F	ENST00000377767	NM_014953.3	406	CCc/TTc	8/21	0.275143715891554	4	FACETS	0.805	0.645	0.987	0.403	0.322	0.494	CLONAL	1	TRUE	2	0.286935728558403	4		222	312	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514518	103514518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	45	297	0	ENST00000355739.4:c.1019C>T	p.Pro340Leu	p.P340L	ENST00000355739	NM_000123.3	340	cCt/cTt	8/15	0.275143715891554	4	FACETS	1	0.923	1	0.582	0.49	0.682	CLONAL	1	TRUE	2	0.286935728558403	4		297	347	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066730	30066730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	50	463	0	ENST00000331968.5:c.2401C>T	p.Pro801Ser	p.P801S	ENST00000331968	NM_002742.2	801	Cca/Tca	16/18	0.286935728558403	2	FACETS	0.82	0.697	0.955	0.41	0.348	0.478	CLONAL	1	TRUE	0	0.286935728558403	2		463	425	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061258	38061258	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	87	664	0	ENST00000250448.2:c.731G>A	p.Trp244Ter	p.W244*	ENST00000250448	NM_004496.3	244	tGg/tAg	2/2	0.286935728558403	2	FACETS	0.955	0.846	1	0.477	0.423	0.536	CLONAL	1	TRUE	0	0.286935728558403	2		664	635	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609793	81609793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	115	497	0	ENST00000298171.2:c.1391G>A	p.Gly464Glu	p.G464E	ENST00000298171	NM_000369.2	464	gGg/gAg	10/10	0.286935728558403	2	FACETS	0.915	0.83	1	0.915	0.83	1	CLONAL	2	TRUE	0	0.286935728558403	2		497	438	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610515	81610515	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	63	413	0	ENST00000298171.2:c.2113G>A	p.Ala705Thr	p.A705T	ENST00000298171	NM_000369.2	705	Gca/Aca	10/10	0.286935728558403	2	FACETS	0.985	0.854	1	0.492	0.427	0.563	CLONAL	1	TRUE	0	0.286935728558403	2		413	446	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241543	105241543	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1371607114	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	147	665	0	ENST00000349310.3:c.437C>T	p.Thr146Ile	p.T146I	ENST00000349310	NM_001014432.1	146	aCc/aTc	7/15	0.286935728558403	2	FACETS	0.865	0.793	0.94	0.865	0.793	0.94	CLONAL	2	TRUE	0	0.286935728558403	2		665	592	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988302	41988302	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	55	545	0	ENST00000219905.7:c.1094C>T	p.Ser365Phe	p.S365F	ENST00000219905	NM_001164273.1	365	tCc/tTc	3/24	0.275143715891554	4	FACETS	0.792	0.677	0.918	0.396	0.338	0.459	CLONAL	1	TRUE	2	0.286935728558403	4		545	623	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054040	42054040	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762308325	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	44	271	0	ENST00000219905.7:c.7502C>T	p.Ser2501Phe	p.S2501F	ENST00000219905	NM_001164273.1	2501	tCt/tTt	21/24	0.275143715891554	4	FACETS	1	0.892	1	0.539	0.453	0.634	CLONAL	1	TRUE	2	0.286935728558403	4		271	366	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2588127	2588127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	10	26	0	ENST00000342085.4:c.14C>T	p.Thr5Ile	p.T5I	ENST00000342085	NM_002613.4	5	aCc/aTc	1/14	0.286935728558403	3	FACETS	1	0.832	1	0.687	0.475	0.94	CLONAL	1	TRUE	1	0.286935728558403	3		26	58	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646245	3646246	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	132	774	1	ENST00000294008.3:c.1832_1833delinsTT	p.Ala611Val	p.A611V	ENST00000294008	NM_032444.2	611	gCC/gTT	8/15	0.286935728558403	3	FACETS	1	0.98	1	0.645	0.586	0.708	CLONAL	1	TRUE	1	0.286935728558403	3		775	815	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808934	3808934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	82	606	0	ENST00000262367.5:c.3290C>T	p.Thr1097Ile	p.T1097I	ENST00000262367	NM_004380.2	1097	aCc/aTc	17/31	0.286935728558403	3	FACETS	0.934	0.823	1	0.467	0.411	0.526	CLONAL	1	TRUE	1	0.286935728558403	3		606	700	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828063	3828064	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	87	695	2	ENST00000262367.5:c.2061_2062delinsTT	p.Pro688Ser	p.P688S	ENST00000262367	NM_004380.2	687	gcCCcg/gcTTcg	10/31	0.286935728558403	3	FACETS	0.873	0.772	0.981	0.437	0.386	0.491	CLONAL	1	TRUE	1	0.286935728558403	3		697	794	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857163	9857163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	55	510	0	ENST00000330684.3:c.4238C>T	p.Ser1413Phe	p.S1413F	ENST00000330684	NM_001134407.1	1413	tCc/tTc	13/13	0.286935728558403	3	FACETS	0.898	0.769	1	0.449	0.384	0.52	CLONAL	1	TRUE	1	0.286935728558403	3		510	488	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857864	9857865	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	65	572	0	ENST00000330684.3:c.3536_3537delinsTT	p.Ser1179Phe	p.S1179F	ENST00000330684	NM_001134407.1	1179	tCC/tTT	13/13	0.286935728558403	3	FACETS	0.909	0.788	1	0.454	0.394	0.52	CLONAL	1	TRUE	1	0.286935728558403	3		572	570	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943683	9943683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	120	750	0	ENST00000330684.3:c.1258G>A	p.Glu420Lys	p.E420K	ENST00000330684	NM_001134407.1	420	Gaa/Aaa	5/13	0.286935728558403	3	FACETS	1	0.977	1	0.636	0.574	0.701	CLONAL	1	TRUE	1	0.286935728558403	3		750	752	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041821	14041821	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	57	490	0	ENST00000311895.7:c.2368C>T	p.Leu790Phe	p.L790F	ENST00000311895	NM_005236.2	790	Ctt/Ttt	11/11	0.286935728558403	3	FACETS	0.829	0.711	0.957	0.415	0.355	0.479	CLONAL	1	TRUE	1	0.286935728558403	3		490	548	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619323	23619323	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	52	408	0	ENST00000261584.4:c.3212T>G	p.Phe1071Cys	p.F1071C	ENST00000261584	NM_024675.3	1071	tTt/tGt	12/13	0.286935728558403	3	FACETS	0.849	0.724	0.987	0.425	0.362	0.494	CLONAL	1	TRUE	1	0.286935728558403	3		408	488	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813653	50813653	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543887233	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	105	640	0	ENST00000398568.2:c.1207C>T	p.Pro403Ser	p.P403S	ENST00000398568	NM_001042412.1	403	Cct/Tct	8/18	0.286935728558403	3	FACETS	1	0.96	1	0.573	0.514	0.636	CLONAL	1	TRUE	1	0.286935728558403	3		640	730	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828135	50828135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	65	323	0	ENST00000398568.2:c.2473C>T	p.Pro825Ser	p.P825S	ENST00000398568	NM_001042412.1	825	Ccg/Tcg	17/18	0.286935728558403	3	FACETS	1	0.966	1	0.675	0.587	0.768	CLONAL	1	TRUE	1	0.286935728558403	3		323	384	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670655	67670655	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	55	452	0	ENST00000264010.4:c.1900C>T	p.Pro634Ser	p.P634S	ENST00000264010	NM_006565.3	634	Cct/Tct	11/12	0.286935728558403	3	FACETS	0.861	0.737	0.996	0.431	0.368	0.498	CLONAL	1	TRUE	1	0.286935728558403	3		452	509	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993702	72993702	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886891334	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	65	794	0	ENST00000268489.5:c.343G>A	p.Asp115Asn	p.D115N	ENST00000268489	NM_006885.3	115	Gac/Aac	2/10	0.261956581891461	3	FACETS	0.795	0.689	0.91	0.397	0.344	0.455	CLONAL	1	TRUE	1	0.286935728558403	3		794	652	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350738	89350738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139523271	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	115	747	1	ENST00000301030.4:c.2212C>T	p.Arg738Cys	p.R738C	ENST00000301030	NM_001256183.1	738	Cgt/Tgt	9/13	0.261956581891461	3	FACETS	1	0.955	1	0.553	0.498	0.611	CLONAL	1	TRUE	1	0.286935728558403	3		748	829	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89842210	89842211	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	43	528	0	ENST00000389301.3:c.1839_1840delinsTT	p.Pro614Ser	p.P614S	ENST00000389301	NM_000135.2	613	atCCcc/atTTcc	21/43	0.286935728558403	3	FACETS	0.607	0.507	0.717	0.303	0.253	0.359	SUBCLONAL	1	TRUE	1	0.286935728558403	3		528	565	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8109887	8109887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	98	606	0	ENST00000585124.1:c.608C>T	p.Pro203Leu	p.P203L	ENST00000585124	NM_004217.3	203	cCa/cTa	7/9	0.286935728558403	2	FACETS	1	0.962	1	0.582	0.52	0.647	CLONAL	1	TRUE	0	0.286935728558403	2		606	587	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983923	15983923	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	50	436	0	ENST00000268712.3:c.3296C>T	p.Ser1099Leu	p.S1099L	ENST00000268712	NM_006311.3	1099	tCa/tTa	24/46	0.286935728558403	2	FACETS	0.95	0.809	1	0.475	0.404	0.552	CLONAL	1	TRUE	0	0.286935728558403	2		436	367	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16021324	16021324	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	54	313	0	ENST00000268712.3:c.1933C>T	p.Arg645Cys	p.R645C	ENST00000268712	NM_006311.3	645	Cgt/Tgt	18/46	0.286935728558403	2	FACETS	1	0.948	1	0.615	0.529	0.708	CLONAL	1	TRUE	0	0.286935728558403	2		313	306	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119730	17119730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	94	833	0	ENST00000285071.4:c.1264C>T	p.Pro422Ser	p.P422S	ENST00000285071	NM_144997.5	422	Ccg/Tcg	11/14	0.286935728558403	2	FACETS	0.945	0.842	1	0.473	0.421	0.528	CLONAL	1	TRUE	0	0.286935728558403	2		833	693	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119793	17119793	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143183215	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	95	759	1	ENST00000285071.4:c.1201C>T	p.Arg401Cys	p.R401C	ENST00000285071	NM_144997.5	401	Cgc/Tgc	11/14	0.286935728558403	2	FACETS	1	0.894	1	0.502	0.447	0.56	CLONAL	1	TRUE	0	0.286935728558403	2		760	660	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864631	37864631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	96	786	1	ENST00000269571.5:c.283C>T	p.Pro95Ser	p.P95S	ENST00000269571		95	Cca/Tca	3/27	0.286935728558403	2	FACETS	0.861	0.767	0.962	0.431	0.383	0.481	CLONAL	1	TRUE	0	0.286935728558403	2		787	777	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481447	40481447	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	104	581	0	ENST00000264657.5:c.1262G>T	p.Gly421Val	p.G421V	ENST00000264657	NM_139276.2	421	gGg/gTg	14/24	0.286935728558403	2	FACETS	1	0.974	1	0.634	0.569	0.702	CLONAL	1	TRUE	0	0.286935728558403	2		581	572	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617771	39617771	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	46	305	0	ENST00000262039.4:c.1955C>T	p.Ser652Leu	p.S652L	ENST00000262039	NM_002647.2	652	tCa/tTa	17/25	0.286935728558403	3	FACETS	1	0.93	1	0.591	0.5	0.691	CLONAL	1	TRUE	1	0.286935728558403	3		305	310	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414883	56414883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150624858	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	77	608	0	ENST00000348428.3:c.2284C>T	p.His762Tyr	p.H762Y	ENST00000348428	NM_006785.3	762	Cat/Tat	17/17	0.286935728558403	3	FACETS	0.985	0.865	1	0.493	0.432	0.557	CLONAL	1	TRUE	1	0.286935728558403	3		608	623	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226212	2226213	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	80	1002	1	ENST00000398665.3:c.3692_3693delinsTT	p.Pro1231Leu	p.P1231L	ENST00000398665	NM_032482.2	1231	cCC/cTT	27/28	0.261956581891461	3	FACETS	0.773	0.679	0.874	0.386	0.339	0.437	SUBCLONAL	1	TRUE	1	0.286935728558403	3		1003	825	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170655	7170655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	71	731	0	ENST00000302850.5:c.1376C>T	p.Pro459Leu	p.P459L	ENST00000302850	NM_000208.2	459	cCc/cTc	6/22	0.261956581891461	3	FACETS	0.806	0.703	0.918	0.403	0.351	0.459	CLONAL	1	TRUE	1	0.286935728558403	3		731	702	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267510	7267511	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	61	638	0	ENST00000302850.5:c.497_498delinsTT	p.Ser166Phe	p.S166F	ENST00000302850	NM_000208.2	166	tCC/tTT	2/22	0.261956581891461	3	FACETS	0.777	0.67	0.893	0.388	0.335	0.447	SUBCLONAL	1	TRUE	1	0.286935728558403	3		638	626	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602602	10602603	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	78	826	1	ENST00000171111.5:c.975_976delinsTT	p.Arg326Cys	p.R326C	ENST00000171111	NM_203500.1	325	ggCCgc/ggTTgc	3/6	0.261956581891461	3	FACETS	0.828	0.727	0.937	0.414	0.363	0.469	CLONAL	1	TRUE	1	0.286935728558403	3		827	751	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097239	11097239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	66	630	0	ENST00000358026.2:c.730C>T	p.Pro244Ser	p.P244S	ENST00000358026	NM_001128849.1	244	Ccg/Tcg	4/36	0.261956581891461	3	FACETS	0.912	0.792	1	0.456	0.396	0.521	CLONAL	1	TRUE	1	0.286935728558403	3		630	577	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097661	11097661	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	103	902	0	ENST00000358026.2:c.841C>T	p.Pro281Ser	p.P281S	ENST00000358026	NM_001128849.1	281	Ccc/Tcc	5/36	0.261956581891461	3	FACETS	0.984	0.88	1	0.492	0.44	0.548	CLONAL	1	TRUE	1	0.286935728558403	3		902	834	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105510	11105510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	56	490	1	ENST00000358026.2:c.1426C>T	p.Leu476Phe	p.L476F	ENST00000358026	NM_001128849.1	476	Ctc/Ttc	9/36	0.261956581891461	3	FACETS	0.841	0.72	0.972	0.42	0.36	0.486	CLONAL	1	TRUE	1	0.286935728558403	3		491	531	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295160	15295160	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs566970022	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	95	900	0	ENST00000263388.2:c.2512C>T	p.His838Tyr	p.H838Y	ENST00000263388	NM_000435.2	838	Cat/Tat	16/33	0.261956581891461	3	FACETS	0.893	0.794	0.998	0.446	0.397	0.499	CLONAL	1	TRUE	1	0.286935728558403	3		900	848	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299150	15299150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1221495694	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	78	774	0	ENST00000263388.2:c.1388G>A	p.Gly463Glu	p.G463E	ENST00000263388	NM_000435.2	463	gGa/gAa	9/33	0.261956581891461	3	FACETS	0.793	0.696	0.898	0.396	0.348	0.449	SUBCLONAL	1	TRUE	1	0.286935728558403	3		774	784	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353892	15353893	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	44	506	1	ENST00000263377.2:c.2987_2988delinsTT	p.Pro996Leu	p.P996L	ENST00000263377	NM_058243.2	996	cCC/cTT	14/20	0.261956581891461	3	FACETS	0.689	0.578	0.812	0.344	0.289	0.406	SUBCLONAL	1	TRUE	1	0.286935728558403	3		507	509	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353948	15353949	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	40	232	0	ENST00000263377.2:c.2931_2932delinsTT	p.Pro978Ser	p.P978S	ENST00000263377	NM_058243.2	977	ccCCca/ccTTca	14/20	0.261956581891461	3	FACETS	1	0.95	1	0.696	0.583	0.819	CLONAL	1	TRUE	1	0.286935728558403	3		232	229	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966794	18966795	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	98	1074	1	ENST00000262803.5:c.1605_1606delinsTT	p.Gln536Ter	p.Q536*	ENST00000262803	NM_002911.3	535	caCCag/caTTag	12/24	0.261956581891461	3	FACETS	0.866	0.771	0.967	0.433	0.385	0.484	CLONAL	1	TRUE	1	0.286935728558403	3		1075	902	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257672	19257672	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1464036677	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	104	941	0	ENST00000162023.5:c.554C>T	p.Pro185Leu	p.P185L	ENST00000162023		185	cCt/cTt	10/13	0.261956581891461	3	FACETS	0.972	0.869	1	0.486	0.434	0.541	CLONAL	1	TRUE	1	0.286935728558403	3		941	853	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222991	36222991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs937393842	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	138	1060	0	ENST00000222270.7:c.5620C>T	p.Arg1874Trp	p.R1874W	ENST00000222270	NM_014727.1	1874	Cgg/Tgg	27/37	0.261956581891461	3	FACETS	1	0.965	1	0.562	0.51	0.616	CLONAL	1	TRUE	1	0.286935728558403	3		1060	979	SUCCESS
AXL	558	MSKCC	GRCh37	19	41736890	41736890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755470829	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	92	783	0	ENST00000301178.4:c.605C>T	p.Ser202Phe	p.S202F	ENST00000301178	NM_021913.4	202	tCt/tTt	5/20	0.261956581891461	3	FACETS	0.879	0.78	0.985	0.44	0.39	0.493	CLONAL	1	TRUE	1	0.286935728558403	3		783	834	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744056	41744057	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	57	724	2	ENST00000301178.4:c.991_992delinsAA	p.Gly331Lys	p.G331K	ENST00000301178	NM_021913.4	331	GGa/AAa	7/20	0.261956581891461	3	FACETS	0.709	0.607	0.819	0.354	0.303	0.41	SUBCLONAL	1	TRUE	1	0.286935728558403	3		726	641	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42790947	42790947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	108	804	0	ENST00000575354.2:c.92C>T	p.Ser31Phe	p.S31F	ENST00000575354	NM_015125.3	31	tCt/tTt	2/20	0.261956581891461	3	FACETS	1	0.926	1	0.52	0.466	0.577	CLONAL	1	TRUE	1	0.286935728558403	3		804	828	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905071	50905071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780604625	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	97	832	1	ENST00000440232.2:c.353C>T	p.Ser118Phe	p.S118F	ENST00000440232	NM_002691.3	118	tCc/tTc	4/27	0.261956581891461	3	FACETS	1	0.898	1	0.504	0.449	0.563	CLONAL	1	TRUE	1	0.286935728558403	3		833	767	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918766	50918766	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	106	953	0	ENST00000440232.2:c.2636C>T	p.Ser879Phe	p.S879F	ENST00000440232	NM_002691.3	879	tCc/tTc	21/27	0.261956581891461	3	FACETS	0.885	0.792	0.984	0.442	0.396	0.492	CLONAL	1	TRUE	1	0.286935728558403	3		953	955	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497912	25497912	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	118	757	0	ENST00000264709.3:c.537C>G	p.Ser179Arg	p.S179R	ENST00000264709	NM_175629.2	179	agC/agG	6/23	0.286935728558403	3	FACETS	1	0.958	1	0.556	0.502	0.615	CLONAL	1	TRUE	1	0.286935728558403	3		757	845	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445226	29445227	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	67	716	3	ENST00000389048.3:c.3498_3499delinsAA	p.Met1166_Glu1167delinsIleLys	p.M1166_E1167delinsIK	ENST00000389048	NM_004304.4	1166	atGGaa/atAAaa	22/29	0.286935728558403	3	FACETS	0.752	0.653	0.86	0.376	0.326	0.43	SUBCLONAL	1	TRUE	1	0.286935728558403	3		719	710	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498324	29498324	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	63	662	0	ENST00000389048.3:c.1856C>T	p.Ser619Phe	p.S619F	ENST00000389048	NM_004304.4	619	tCc/tTc	10/29	0.286935728558403	3	FACETS	0.867	0.75	0.994	0.434	0.375	0.497	CLONAL	1	TRUE	1	0.286935728558403	3		662	579	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543721	29543721	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	81	572	0	ENST00000389048.3:c.1442A>G	p.Asn481Ser	p.N481S	ENST00000389048	NM_004304.4	481	aAc/aGc	7/29	0.286935728558403	3	FACETS	1	0.916	1	0.524	0.462	0.591	CLONAL	1	TRUE	1	0.286935728558403	3		572	616	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046317	128046317	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	125	487	0	ENST00000285398.2:c.946C>T	p.Leu316Phe	p.L316F	ENST00000285398	NM_000122.1	316	Ctc/Ttc	7/15	0.286935728558403	3	FACETS	0.871	0.791	0.954	0.871	0.791	0.954	CLONAL	2	TRUE	1	0.286935728558403	3		487	572	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626952	158626952	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750691291	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	50	447	0	ENST00000263640.3:c.718C>T	p.Arg240Cys	p.R240C	ENST00000263640	NM_001105.4	240	Cgt/Tgt	7/11	0.286935728558403	3	FACETS	0.837	0.711	0.976	0.419	0.355	0.488	CLONAL	1	TRUE	1	0.286935728558403	3		447	476	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103886	209103886	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	59	427	0	ENST00000345146.2:c.1063T>G	p.Phe355Val	p.F355V	ENST00000345146	NM_005896.2	355	Ttt/Gtt	9/10	0.286935728558403	3	FACETS	0.98	0.844	1	0.49	0.422	0.564	CLONAL	1	TRUE	1	0.286935728558403	3		427	480	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248653	212248653	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	67	547	0	ENST00000342788.4:c.3614A>C	p.Glu1205Ala	p.E1205A	ENST00000342788	NM_005235.2	1205	gAg/gCg	28/28	0.286935728558403	3	FACETS	0.95	0.826	1	0.475	0.413	0.542	CLONAL	1	TRUE	1	0.286935728558403	3		547	562	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286768	212286769	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	36	345	0	ENST00000342788.4:c.2927_2928delinsAA	p.Arg976Lys	p.R976K	ENST00000342788	NM_005235.2	976	aGG/aAA	24/28	0.286935728558403	3	FACETS	0.738	0.607	0.884	0.369	0.303	0.442	SUBCLONAL	1	TRUE	1	0.286935728558403	3		345	389	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812278	212812279	+	missense_variant	Missense_Mutation	DNP	CC	CC	GT	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	48	326	0	ENST00000342788.4:c.297_298delinsAC	p.Glu100Gln	p.E100Q	ENST00000342788	NM_005235.2	99	ctGGag/ctACag	3/28	0.286935728558403	3	FACETS	1	0.86	1	0.507	0.43	0.592	CLONAL	1	TRUE	1	0.286935728558403	3		326	377	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546689	9546689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	60	449	0	ENST00000353224.5:c.1333C>T	p.Pro445Ser	p.P445S	ENST00000353224	NM_177990.2	445	Ccc/Tcc	5/10	0.275143715891554	4	FACETS	1	0.881	1	0.512	0.441	0.588	CLONAL	1	TRUE	2	0.286935728558403	4		449	526	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022556	31022556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	77	573	0	ENST00000375687.4:c.2041C>T	p.Pro681Ser	p.P681S	ENST00000375687	NM_015338.5	681	Ccg/Tcg	13/13	0.275143715891554	4	FACETS	1	0.886	1	0.505	0.443	0.572	CLONAL	1	TRUE	2	0.286935728558403	4		573	684	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375162	31375162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	130	872	1	ENST00000328111.2:c.559C>T	p.Pro187Ser	p.P187S	ENST00000328111	NM_006892.3	187	Ccc/Tcc	6/23	0.275143715891554	4	FACETS	1	0.962	1	0.56	0.507	0.616	CLONAL	1	TRUE	2	0.286935728558403	4		873	1042	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713377	40713378	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	87	845	1	ENST00000373198.4:c.4137_4138delinsAA	p.Glu1380Lys	p.E1380K	ENST00000373198	NM_133170.3	1379	ctGGag/ctAAag	30/32	0.138192123323903	4	FACETS	0.927	0.819	1	0.463	0.409	0.521	INDETERMINATE	1	TRUE	2	0.286935728558403	4		846	842	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733358	40733359	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	38	430	0	ENST00000373198.4:c.3448-1_3448delinsAA		p.X1150_splice	ENST00000373198	NM_133170.3	1150		26/32	0.138192123323903	4	FACETS	0.698	0.577	0.834	0.349	0.288	0.417	INDETERMINATE	1	TRUE	2	0.286935728558403	4		430	488	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748610	40748611	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	41	451	1	ENST00000373198.4:c.2905_2906delinsAA	p.Gly969Lys	p.G969K	ENST00000373198	NM_133170.3	969	GGa/AAa	21/32	0.138192123323903	4	FACETS	0.761	0.634	0.903	0.381	0.317	0.452	INDETERMINATE	1	TRUE	2	0.286935728558403	4		452	483	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306557	41306558	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	74	660	0	ENST00000373198.4:c.1101_1102delinsAA	p.Gly368Arg	p.G368R	ENST00000373198	NM_133170.3	367	gaGGgg/gaAAgg	7/32	0.138192123323903	4	FACETS	0.93	0.813	1	0.465	0.406	0.528	INDETERMINATE	1	TRUE	2	0.286935728558403	4		660	714	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385247	41385247	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	80	696	1	ENST00000373198.4:c.714G>T	p.Met238Ile	p.M238I	ENST00000373198	NM_133170.3	238	atG/atT	6/32	0.138192123323903	4	FACETS	1	0.881	1	0.5	0.44	0.565	INDETERMINATE	1	TRUE	2	0.286935728558403	4		697	717	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514517	41514518	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	81	556	1	ENST00000373198.4:c.143_144delinsAA	p.Gly48Glu	p.G48E	ENST00000373198	NM_133170.3	48	gGG/gAA	2/32	0.286935728558403	4	FACETS	1	0.93	1	0.54	0.475	0.609	CLONAL	1	TRUE	2	0.286935728558403	4		557	673	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422983	12422983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767853271	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	60	369	0	ENST00000287820.6:c.473G>A	p.Gly158Glu	p.G158E	ENST00000287820	NM_015869.4	158	gGa/gAa	3/7	0.286935728558403	2	FACETS	1	0.927	1	0.555	0.48	0.635	CLONAL	1	TRUE	0	0.286935728558403	2		369	377	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660162	12660162	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1438827623	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	74	521	0	ENST00000251849.4:c.59C>T	p.Ala20Val	p.A20V	ENST00000251849	NM_002880.3	20	gCc/gTc	2/17	0.286935728558403	2	FACETS	0.971	0.852	1	0.486	0.426	0.55	CLONAL	1	TRUE	0	0.286935728558403	2		521	531	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665017	138665017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	13	85	2	ENST00000330315.3:c.548C>T	p.Ala183Val	p.A183V	ENST00000330315	NM_023067.3	183	gCc/gTc	1/1	0.286935728558403	3	FACETS	1	0.859	1	0.673	0.488	0.889	CLONAL	1	TRUE	1	0.286935728558403	3		87	77	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231192	142231192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	67	453	0	ENST00000350721.4:c.4762C>T	p.Leu1588Phe	p.L1588F	ENST00000350721	NM_001184.3	1588	Ctc/Ttc	27/47	0.286935728558403	3	FACETS	0.96	0.835	1	0.48	0.417	0.548	CLONAL	1	TRUE	1	0.286935728558403	3		453	556	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149238612	149238612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239352404	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	70	481	2	ENST00000360632.3:c.1183C>T	p.Pro395Ser	p.P395S	ENST00000360632	NM_015472.4	395	Ccc/Tcc	7/7	0.286935728558403	3	FACETS	1	0.943	1	0.57	0.498	0.648	CLONAL	1	TRUE	1	0.286935728558403	3		483	489	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182681835	182681835	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs374689513	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	41	320	2	ENST00000292782.4:c.223C>T	p.Pro75Ser	p.P75S	ENST00000292782	NM_020640.2	75	Cct/Tct	3/7	0.286935728558403	3	FACETS	0.993	0.83	1	0.497	0.415	0.587	CLONAL	1	TRUE	1	0.286935728558403	3		322	329	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447522	187447522	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	88	757	0	ENST00000232014.4:c.671T>G	p.Phe224Cys	p.F224C	ENST00000232014	NM_001130845.1	224	tTc/tGc	5/10	0.286935728558403	3	FACETS	0.953	0.844	1	0.476	0.422	0.535	CLONAL	1	TRUE	1	0.286935728558403	3		757	736	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801170	1801170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778352	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	117	1068	1	ENST00000260795.2:c.299C>T	p.Ser100Phe	p.S100F	ENST00000260795		100	tCc/tTc	2/17	0.275143715891554	4	FACETS	0.932	0.838	1	0.466	0.419	0.516	CLONAL	1	TRUE	2	0.286935728558403	4		1069	1126	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808338	1808338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	274	1112	1	ENST00000260795.2:c.2096C>T	p.Pro699Leu	p.P699L	ENST00000260795		699	cCt/cTt	15/17	0.275143715891554	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.286935728558403	4		1113	1156	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957793	1957793	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	84	619	0	ENST00000382891.5:c.2759T>G	p.Val920Gly	p.V920G	ENST00000382891	NM_133335.3	920	gTg/gGg	15/22	0.275143715891554	4	FACETS	0.957	0.845	1	0.479	0.422	0.539	CLONAL	1	TRUE	2	0.286935728558403	4		619	787	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133535	55133535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	77	512	0	ENST00000257290.5:c.839C>T	p.Ala280Val	p.A280V	ENST00000257290	NM_006206.4	280	gCc/gTc	6/23	0.275143715891554	4	FACETS	1	0.92	1	0.531	0.466	0.601	CLONAL	1	TRUE	2	0.286935728558403	4		512	650	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139894	55139895	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	52	389	1	ENST00000257290.5:c.1555_1556delinsTT	p.Pro519Phe	p.P519F	ENST00000257290	NM_006206.4	519	CCc/TTc	10/23	0.275143715891554	4	FACETS	1	0.869	1	0.51	0.435	0.593	CLONAL	1	TRUE	2	0.286935728558403	4		390	457	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155226	55155226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	80	646	0	ENST00000257290.5:c.2825C>T	p.Ser942Phe	p.S942F	ENST00000257290	NM_006206.4	942	tCc/tTc	21/23	0.275143715891554	4	FACETS	0.987	0.868	1	0.494	0.434	0.558	CLONAL	1	TRUE	2	0.286935728558403	4		646	727	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953826	55953826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	65	571	1	ENST00000263923.4:c.3610G>A	p.Glu1204Lys	p.E1204K	ENST00000263923	NM_002253.2	1204	Gag/Aag	27/30	0.275143715891554	4	FACETS	0.914	0.792	1	0.457	0.396	0.523	CLONAL	1	TRUE	2	0.286935728558403	4		572	638	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158179	106158180	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	43	357	0	ENST00000380013.4:c.3080_3081delinsTT	p.Thr1027Ile	p.T1027I	ENST00000380013	NM_001127208.2	1027	aCC/aTT	3/11	0.275143715891554	4	FACETS	0.918	0.77	1	0.459	0.385	0.542	CLONAL	1	TRUE	2	0.286935728558403	4		357	420	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197236	106197237	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	39	408	0	ENST00000380013.4:c.5569_5570delinsTT	p.Pro1857Phe	p.P1857F	ENST00000380013	NM_001127208.2	1857	CCt/TTt	11/11	0.275143715891554	4	FACETS	0.766	0.634	0.912	0.383	0.317	0.456	CLONAL	1	TRUE	2	0.286935728558403	4		408	457	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522574	187522574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	93	351	0	ENST00000441802.2:c.11489C>T	p.Ser3830Leu	p.S3830L	ENST00000441802	NM_005245.3	3830	tCa/tTa	21/27	0.275143715891554	4	FACETS	0.946	0.846	1	0.946	0.846	1	CLONAL	2	TRUE	2	0.286935728558403	4		351	441	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629996	187629997	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	83	673	0	ENST00000441802.2:c.985_986delinsTT	p.Pro329Phe	p.P329F	ENST00000441802	NM_005245.3	329	CCt/TTt	2/27	0.275143715891554	4	FACETS	0.899	0.792	1	0.45	0.396	0.507	CLONAL	1	TRUE	2	0.286935728558403	4		673	828	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294679	1294679	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	19	203	0	ENST00000310581.5:c.322C>T	p.Arg108Cys	p.R108C	ENST00000310581	NM_198253.2	108	Cgc/Tgc	2/16	0.286935728558403	3	FACETS	0.543	0.412	0.696	0.271	0.206	0.348	SUBCLONAL	1	TRUE	1	0.286935728558403	3		203	279	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79968093	79968093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs922169592	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	74	519	0	ENST00000265081.6:c.823C>T	p.His275Tyr	p.H275Y	ENST00000265081	NM_002439.4	275	Cat/Tat	5/24	0.286935728558403	3	FACETS	0.986	0.864	1	0.493	0.432	0.559	CLONAL	1	TRUE	1	0.286935728558403	3		519	598	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515166	149515167	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	92	781	2	ENST00000261799.4:c.315_316delinsTT	p.Arg106Cys	p.R106C	ENST00000261799	NM_002609.3	105	tcCCgt/tcTTgt	3/23	0.286935728558403	3	FACETS	0.971	0.863	1	0.486	0.431	0.544	CLONAL	1	TRUE	1	0.286935728558403	3		783	755	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638092	176638092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	91	627	1	ENST00000439151.2:c.2692C>T	p.His898Tyr	p.H898Y	ENST00000439151	NM_022455.4	898	Cac/Tac	5/23	0.286935728558403	3	FACETS	1	0.944	1	0.551	0.49	0.617	CLONAL	1	TRUE	1	0.286935728558403	3		628	658	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045856	180045856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	77	666	0	ENST00000261937.6:c.2915G>A	p.Arg972Lys	p.R972K	ENST00000261937	NM_182925.4	972	aGg/aAg	21/30	0.286935728558403	3	FACETS	0.951	0.836	1	0.476	0.418	0.538	CLONAL	1	TRUE	1	0.286935728558403	3		666	645	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180050945	180050945	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780843533	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	109	796	0	ENST00000261937.6:c.1538G>A	p.Gly513Glu	p.G513E	ENST00000261937	NM_182925.4	513	gGa/gAa	11/30	0.286935728558403	3	FACETS	1	0.954	1	0.555	0.498	0.615	CLONAL	1	TRUE	1	0.286935728558403	3		796	783	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055897	180055898	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	72	705	0	ENST00000261937.6:c.1087_1088delinsTT	p.Pro363Leu	p.P363L	ENST00000261937	NM_182925.4	363	CCg/TTg	8/30	0.286935728558403	3	FACETS	0.868	0.758	0.987	0.434	0.379	0.494	CLONAL	1	TRUE	1	0.286935728558403	3		705	661	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30668267	30668267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	62	532	0	ENST00000376406.3:c.6245C>T	p.Ser2082Phe	p.S2082F	ENST00000376406	NM_014641.2	2082	tCc/tTc	15/15	0.286935728558403	5	FACETS	0.975	0.842	1	0.325	0.28	0.374	CLONAL	1	TRUE	2	0.286935728558403	5		532	634	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671559	30671559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	112	712	1	ENST00000376406.3:c.5401C>T	p.Pro1801Ser	p.P1801S	ENST00000376406	NM_014641.2	1801	Ccg/Tcg	10/15	0.286935728558403	5	FACETS	1	0.976	1	0.429	0.385	0.475	CLONAL	1	TRUE	2	0.286935728558403	5		713	868	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940273	31940273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769305522	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	110	746	0	ENST00000375333.2:c.415C>T	p.Leu139Phe	p.L139F	ENST00000375333	NM_032454.1	139	Ctt/Ttt	2/8	0.286935728558403	5	FACETS	1	0.953	1	0.369	0.331	0.41	CLONAL	1	TRUE	2	0.286935728558403	5		746	990	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169043	32169043	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	103	932	0	ENST00000375023.3:c.3990G>C	p.Arg1330Ser	p.R1330S	ENST00000375023	NM_004557.3	1330	agG/agC	22/30	0.286935728558403	5	FACETS	0.938	0.837	1	0.313	0.279	0.349	CLONAL	1	TRUE	2	0.286935728558403	5		932	1095	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170219	32170219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750821289	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	105	883	0	ENST00000375023.3:c.3389C>T	p.Ala1130Val	p.A1130V	ENST00000375023	NM_004557.3	1130	gCt/gTt	21/30	0.286935728558403	5	FACETS	0.9	0.804	1	0.3	0.268	0.335	CLONAL	1	TRUE	2	0.286935728558403	5		883	1163	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188847	32188847	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	90	866	0	ENST00000375023.3:c.707G>C	p.Gly236Ala	p.G236A	ENST00000375023	NM_004557.3	236	gGa/gCa	4/30	0.286935728558403	5	FACETS	0.822	0.727	0.923	0.274	0.242	0.308	CLONAL	1	TRUE	2	0.286935728558403	5		866	1092	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800524	32800525	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	210	902	2	ENST00000374899.4:c.1022_1023delinsTT	p.Thr341Ile	p.T341I	ENST00000374899	NM_018833.2	341	aCC/aTT	6/12	0.286935728558403	6	FACETS	1	0.944	1	0.68	0.631	0.731	CLONAL	2	TRUE	3	0.286935728558403	6		904	1129	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803083	32803083	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	103	621	0	ENST00000374899.4:c.793C>T	p.Pro265Ser	p.P265S	ENST00000374899	NM_018833.2	265	Cct/Tct	5/12	0.286935728558403	6	FACETS	1	0.979	1	0.466	0.416	0.518	CLONAL	1	TRUE	3	0.286935728558403	6		621	809	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815308	32815308	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	101	815	0	ENST00000354258.4:c.2065C>G	p.Pro689Ala	p.P689A	ENST00000354258	NM_000593.5	689	Cct/Gct	9/11	0.286935728558403	6	FACETS	1	0.898	1	0.336	0.299	0.375	CLONAL	1	TRUE	3	0.286935728558403	6		815	1100	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287200	33287200	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773398360	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	151	667	0	ENST00000374542.5:c.1897C>T	p.Arg633Trp	p.R633W	ENST00000374542	NM_001141970.1	633	Cgg/Tgg	6/8	0.286935728558403	6	FACETS	0.93	0.85	1	0.62	0.566	0.676	CLONAL	2	TRUE	3	0.286935728558403	6		667	891	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36653561	36653561	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs981464191	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	108	601	0	ENST00000244741.5:c.479C>G	p.Ser160Cys	p.S160C	ENST00000244741	NM_000389.4	160	tCc/tGc	3/3	0.286935728558403	6	FACETS	1	0.973	1	0.42	0.376	0.467	CLONAL	1	TRUE	3	0.286935728558403	6		601	940	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967967	93967967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	62	427	0	ENST00000369303.4:c.1960C>T	p.Leu654Phe	p.L654F	ENST00000369303	NM_004440.3	654	Ctt/Ttt	11/17	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.286935728558403	2		427	386	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117629961	117629961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	40	313	0	ENST00000368508.3:c.6565G>A	p.Asp2189Asn	p.D2189N	ENST00000368508	NM_002944.2	2189	Gat/Aat	41/43	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.286935728558403	2		313	273	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665324	117665325	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	54	419	2	ENST00000368508.3:c.4422_4423delinsTT	p.Leu1475Phe	p.L1475F	ENST00000368508	NM_002944.2	1474	aaCCtc/aaTTtc	27/43	1	2	FACETS	0.916	0.784	1	0.916	0.784	1	CLONAL	1	TRUE	1	0.286935728558403	2		421	411	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714441	117714441	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	47	414	0	ENST00000368508.3:c.1208T>C	p.Ile403Thr	p.I403T	ENST00000368508	NM_002944.2	403	aTt/aCt	11/43	1	2	FACETS	0.91	0.77	1	0.91	0.77	1	CLONAL	1	TRUE	1	0.286935728558403	2		414	360	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004871	150004871	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	68	467	0	ENST00000253339.5:c.1354C>T	p.Pro452Ser	p.P452S	ENST00000253339		452	Cct/Tct	3/7	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.286935728558403	2		467	434	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954927	2954927	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	235	892	0	ENST00000396946.4:c.2783G>C	p.Gly928Ala	p.G928A	ENST00000396946	NM_032415.4	928	gGg/gCg	21/25	0.286935728558403	5	FACETS	1	0.972	1	0.719	0.671	0.769	CLONAL	2	TRUE	2	0.286935728558403	5		892	1086	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963978	2963978	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	170	714	0	ENST00000396946.4:c.1829C>G	p.Ser610Cys	p.S610C	ENST00000396946	NM_032415.4	610	tCc/tGc	15/25	0.286935728558403	5	FACETS	0.98	0.902	1	0.653	0.601	0.708	CLONAL	2	TRUE	2	0.286935728558403	5		714	865	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976696	2976696	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760856731	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	164	624	0	ENST00000396946.4:c.1316C>T	p.Ser439Phe	p.S439F	ENST00000396946	NM_032415.4	439	tCc/tTc	9/25	0.286935728558403	5	FACETS	1	0.942	1	0.687	0.632	0.745	CLONAL	2	TRUE	2	0.286935728558403	5		624	793	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971176	13971177	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	67	482	0	ENST00000405192.2:c.752_753delinsTT	p.Pro251Leu	p.P251L	ENST00000405192	NM_001163147.1	251	cCC/cTT	8/12	0.286935728558403	5	FACETS	1	0.934	1	0.374	0.324	0.427	CLONAL	1	TRUE	2	0.286935728558403	5		482	596	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508185	106508186	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	53	404	1	ENST00000359195.3:c.179_180delinsTT	p.His60Leu	p.H60L	ENST00000359195	NM_002649.2	60	cAC/cTT	2/11	0.286935728558403	6	FACETS	1	0.856	1	0.201	0.171	0.234	CLONAL	1	TRUE	1	0.286935728558403	6		405	579	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508952	106508952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	334	643	0	ENST00000359195.3:c.946G>A	p.Asp316Asn	p.D316N	ENST00000359195	NM_002649.2	316	Gac/Aac	2/11	0.286935728558403	6	FACETS	1	0.985	1	0.871	0.828	0.916	CLONAL	4	TRUE	1	0.286935728558403	6		643	841	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509489	106509489	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	299	635	0	ENST00000359195.3:c.1483G>A	p.Gly495Arg	p.G495R	ENST00000359195	NM_002649.2	495	Gga/Aga	2/11	0.286935728558403	6	FACETS	0.893	0.843	0.944	0.715	0.675	0.755	CLONAL	4	TRUE	1	0.286935728558403	6		635	918	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509550	106509550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	91	632	0	ENST00000359195.3:c.1544C>T	p.Ser515Phe	p.S515F	ENST00000359195	NM_002649.2	515	tCc/tTc	2/11	0.286935728558403	6	FACETS	1	0.947	1	0.224	0.198	0.251	CLONAL	1	TRUE	1	0.286935728558403	6		632	893	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397518	116397518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	66	416	0	ENST00000397752.3:c.1890G>A	p.Met630Ile	p.M630I	ENST00000397752	NM_000245.2	630	atG/atA	7/21	0.286935728558403	6	FACETS	1	0.944	1	0.233	0.202	0.267	CLONAL	1	TRUE	1	0.286935728558403	6		416	621	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877051	151877051	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	54	571	0	ENST00000262189.6:c.7310C>G	p.Pro2437Arg	p.P2437R	ENST00000262189	NM_170606.2	2437	cCt/cGt	37/59	0.286935728558403	6	FACETS	0.883	0.753	1	0.177	0.15	0.205	CLONAL	1	TRUE	1	0.286935728558403	6		571	671	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879060	151879060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1252490950	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	193	596	0	ENST00000262189.6:c.5885C>T	p.Pro1962Leu	p.P1962L	ENST00000262189	NM_170606.2	1962	cCc/cTc	36/59	0.286935728558403	6	FACETS	0.836	0.775	0.9	0.502	0.465	0.54	CLONAL	3	TRUE	1	0.286935728558403	6		596	844	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891630	151891630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	134	286	0	ENST00000262189.6:c.4402C>T	p.Pro1468Ser	p.P1468S	ENST00000262189	NM_170606.2	1468	Cct/Tct	29/59	0.286935728558403	6	FACETS	1	0.927	1	0.609	0.557	0.663	CLONAL	3	TRUE	1	0.286935728558403	6		286	483	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917662	151917662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	52	341	0	ENST00000262189.6:c.3658C>T	p.Pro1220Ser	p.P1220S	ENST00000262189	NM_170606.2	1220	Cct/Tct	23/59	0.286935728558403	6	FACETS	1	0.859	1	0.202	0.171	0.235	CLONAL	1	TRUE	1	0.286935728558403	6		341	565	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287418	38287418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747480026	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	76	821	1	ENST00000425967.3:c.239C>T	p.Pro80Leu	p.P80L	ENST00000425967	NM_001174067.1	80	cCc/cTc	4/19	1	2	FACETS	0.803	0.704	0.909	0.803	0.704	0.909	CLONAL	1	TRUE	1	0.286935728558403	2		822	660	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956816	68956816	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11784582	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	60	563	0	ENST00000288368.4:c.934G>A	p.Asp312Asn	p.D312N	ENST00000288368	NM_024870.2	312	Gat/Aat	8/40	1	2	FACETS	0.734	0.632	0.844	0.734	0.632	0.844	SUBCLONAL	1	TRUE	1	0.286935728558403	2		563	570	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050706	69050707	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	38	397	1	ENST00000288368.4:c.4041_4042delinsAA	p.Val1348Ile	p.V1348I	ENST00000288368	NM_024870.2	1347	aaGGtt/aaAAtt	33/40	1	2	FACETS	0.83	0.689	0.987	0.83	0.689	0.987	CLONAL	1	TRUE	1	0.286935728558403	2		398	319	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70967569	70967569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	80	577	0	ENST00000276594.2:c.1454G>A	p.Gly485Glu	p.G485E	ENST00000276594	NM_024504.3	485	gGa/gAa	7/8	1	2	FACETS	0.978	0.862	1	0.978	0.862	1	CLONAL	1	TRUE	1	0.286935728558403	2		577	570	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978487	70978487	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	49	456	0	ENST00000276594.2:c.1166C>T	p.Pro389Leu	p.P389L	ENST00000276594	NM_024504.3	389	cCa/cTa	5/8	1	2	FACETS	0.802	0.68	0.935	0.802	0.68	0.935	CLONAL	1	TRUE	1	0.286935728558403	2		456	426	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542588	141542589	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	100	875	1	ENST00000220592.5:c.2397_2398delinsTT	p.Pro800Ser	p.P800S	ENST00000220592	NM_012154.3	799	atCCca/atTTca	18/19	1	2	FACETS	0.909	0.812	1	0.909	0.812	1	CLONAL	1	TRUE	1	0.286935728558403	2		876	767	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331675	8331675	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	67	566	0	ENST00000356435.5:c.5441C>T	p.Pro1814Leu	p.P1814L	ENST00000356435		1814	cCa/cTa	33/35	0.286935728558403	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.286935728558403	1		566	383	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27190568	27190568	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	82	600	0	ENST00000380036.4:c.1369G>A	p.Gly457Arg	p.G457R	ENST00000380036	NM_000459.3	457	Gga/Aga	10/23	0.286935728558403	1	FACETS	0.971	0.859	1	0.971	0.859	1	CLONAL	1	TRUE	0	0.286935728558403	1		600	504	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563431	87563431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	56	664	0	ENST00000277120.3:c.1819C>T	p.Leu607Phe	p.L607F	ENST00000277120		607	Ctc/Ttc	16/19	0.286935728558403	2	FACETS	0.708	0.607	0.819	0.354	0.303	0.41	SUBCLONAL	1	TRUE	0	0.286935728558403	2		664	551	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563441	87563441	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	146	659	0	ENST00000277120.3:c.1829A>G	p.Asn610Ser	p.N610S	ENST00000277120		610	aAc/aGc	16/19	0.286935728558403	2	FACETS	0.923	0.847	1	0.923	0.847	1	CLONAL	2	TRUE	0	0.286935728558403	2		659	551	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209201	98209201	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	78	626	0	ENST00000331920.6:c.4337C>T	p.Ser1446Phe	p.S1446F	ENST00000331920	NM_000264.3	1446	tCc/tTc	23/24	0.286935728558403	2	FACETS	1	0.913	1	0.523	0.46	0.59	CLONAL	1	TRUE	0	0.286935728558403	2		626	520	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98241392	98241392	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	77	523	1	ENST00000331920.6:c.1105C>T	p.Pro369Ser	p.P369S	ENST00000331920	NM_000264.3	369	Ccc/Tcc	8/24	0.286935728558403	2	FACETS	1	0.922	1	0.531	0.467	0.6	CLONAL	1	TRUE	0	0.286935728558403	2		524	505	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391432	139391433	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	110	871	2	ENST00000277541.6:c.6758_6759delinsTT	p.Pro2253Leu	p.P2253L	ENST00000277541	NM_017617.3	2253	cCC/cTT	34/34	0.286935728558403	2	FACETS	1	0.915	1	0.51	0.458	0.565	CLONAL	1	TRUE	0	0.286935728558403	2		873	752	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395146	139395146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	124	1115	0	ENST00000277541.6:c.5792C>T	p.Ala1931Val	p.A1931V	ENST00000277541	NM_017617.3	1931	gCc/gTc	31/34	0.286935728558403	2	FACETS	1	0.906	1	0.501	0.453	0.552	CLONAL	1	TRUE	0	0.286935728558403	2		1115	863	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396809	139396809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	91	695	0	ENST00000277541.6:c.5299C>T	p.Leu1767Phe	p.L1767F	ENST00000277541	NM_017617.3	1767	Ctc/Ttc	28/34	0.286935728558403	2	FACETS	1	0.929	1	0.529	0.471	0.592	CLONAL	1	TRUE	0	0.286935728558403	2		695	599	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911577	39911577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	102	338	1	ENST00000378444.4:c.5053C>T	p.Pro1685Ser	p.P1685S	ENST00000378444	NM_001123385.1	1685	Cca/Tca	15/15	0.282733633482954	2	FACETS	0.852	0.768	0.941			1	CLONAL	2	TRUE	NA	0.286935728558403	2		339	417	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933599	39933599	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	96	340	0	ENST00000378444.4:c.1000C>G	p.Pro334Ala	p.P334A	ENST00000378444	NM_001123385.1	334	Ccc/Gcc	4/15	0.282733633482954	2	FACETS	0.759	0.68	0.842			1	SUBCLONAL	2	TRUE	NA	0.286935728558403	2		340	441	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239682	53239682	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	95	432	0	ENST00000375401.3:c.1660C>T	p.Pro554Ser	p.P554S	ENST00000375401	NM_004187.3	554	Cct/Tct	12/26	0.282733633482954	2	FACETS	0.772	0.691	0.857			1	SUBCLONAL	2	TRUE	NA	0.286935728558403	2		432	429	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412524	63412524	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756142618	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	87	381	0	ENST00000330258.3:c.643C>T	p.Pro215Ser	p.P215S	ENST00000330258	NM_152424.3	215	Ccc/Tcc	2/2	0.282733633482954	2	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.286935728558403	2		381	407	SUCCESS
AR	367	MSKCC	GRCh37	X	66942692	66942692	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	43	197	0	ENST00000374690.3:c.2473C>T	p.Gln825Ter	p.Q825*	ENST00000374690	NM_000044.3	825	Caa/Taa	7/8	0.282733633482954	2	FACETS	1	0.937	1			1	CLONAL	1	TRUE	NA	0.286935728558403	2		197	243	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341598	70341599	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	107	418	0	ENST00000374080.3:c.1033_1034delinsTT	p.Pro345Phe	p.P345F	ENST00000374080		345	CCc/TTc	7/45	0.282733633482954	2	FACETS	0.777	0.7	0.857			1	SUBCLONAL	2	TRUE	NA	0.286935728558403	2		418	480	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345528	70345528	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	63	233	1	ENST00000374080.3:c.2387T>G	p.Ile796Ser	p.I796S	ENST00000374080		796	aTt/aGt	17/45	0.282733633482954	2	FACETS	0.864	0.756	0.979			1	CLONAL	2	TRUE	NA	0.286935728558403	2		234	254	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	92	115	0				ENST00000310581	NM_198253.2	-/1132			0.452752191685758	1	FACETS	0.741	0.684	0.795	0.741	0.684	0.795	INDETERMINATE	1	TRUE	0	0.919434200733793	1		115	146	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0055529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	360	610	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.594835908196234	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.919434200733793	1		610	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs879253911	NA	P-0055529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	673	746	0	ENST00000269305.4:c.538G>T	p.Glu180Ter	p.E180*	ENST00000269305	NM_001126112.2	180	Gag/Tag	5/11	NA	2	FACETS	0.975	0.959	0.989			1	INDETERMINATE	2	TRUE	NA	0.919434200733793	2		746	751	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518698	204518698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1270135772	NA	P-0055529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	289	286	0	ENST00000367182.3:c.1361C>T	p.Thr454Met	p.T454M	ENST00000367182	NM_001278516.1	454	aCg/aTg	11/11	0.497654384273176	3	FACETS	0.815	0.775	0.855	0.815	0.775	0.855	INDETERMINATE	2	TRUE	1	0.919434200733793	3		286	563	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424126	49424133	+	frameshift_variant	Frame_Shift_Del	DEL	CAGATGGG	CAGATGGG	-	novel	NA	P-0055529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	381	627	0	ENST00000301067.7:c.13929_13936del	p.Pro4644ArgfsTer15	p.P4644Rfs*15	ENST00000301067	NM_003482.3	4643	acCCCATCTGaa/acaa	42/54	1	2	FACETS	0.929	0.886	0.972	0.929	0.886	0.972	CLONAL	1	TRUE	1	0.919434200733793	2		627	892	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445360	49445369	+	frameshift_variant	Frame_Shift_Del	DEL	AGGTGGTGGG	AGGTGGTGGG	-	novel	NA	P-0055529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	475	811	0	ENST00000301067.7:c.2097_2106del	p.Pro700ArgfsTer227	p.P700Rfs*227	ENST00000301067	NM_003482.3	699	tcCCCACCACCT/tc	10/54	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.919434200733793	2		811	1007	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743086	743086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	287	337	0	ENST00000314574.4:c.892G>A	p.Gly298Arg	p.G298R	ENST00000314574	NM_005433.3	298	Gga/Aga	8/12	1	2	FACETS	0.914	0.865	0.963	0.914	0.865	0.963	CLONAL	1	TRUE	1	0.919434200733793	2		337	683	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215248	123215248	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	195	100	1	ENST00000218089.9:c.2794C>T	p.Gln932Ter	p.Q932*	ENST00000218089	NM_001042749.1	932	Caa/Taa	28/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.919434200733793	1		101	206	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519985	NA	P-0055531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	54	828	0	ENST00000269305.4:c.857A>G	p.Glu286Gly	p.E286G	ENST00000269305	NM_001126112.2	286	gAa/gGa	8/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		828	769	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	170	115	0				ENST00000310581	NM_198253.2	-/1132			0.524250866652494	8	FACETS	0.936	0.88	0.992			1	CLONAL	6	TRUE	NA	0.524250866652494	8		115	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0055532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	765	890	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.524250866652494	6	FACETS	0.979	0.953	1	0.979	0.953	1	CLONAL	5	TRUE	1	0.524250866652494	6		893	1221	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	100	466	0	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	0.524250866652494	6	FACETS	0.898	0.801	1	0.18	0.16	0.201	CLONAL	1	TRUE	1	0.524250866652494	6		466	870	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032748	30032748	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	160	348	0	ENST00000338641.4:c.123G>A	p.Trp41Ter	p.W41*	ENST00000338641	NM_000268.3	41	tgG/tgA	2/16	0.50383817715903	2	FACETS	0.939	0.876	1	0.939	0.876	1	CLONAL	2	TRUE	0	0.524250866652494	2		348	325	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444574	78444574	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	102	429	0	ENST00000370768.2:c.115C>G	p.Arg39Gly	p.R39G	ENST00000370768	NM_003902.3	39	Cgg/Ggg	1/20	0.486169608370583	3	FACETS	1	0.945	1	0.539	0.484	0.596	CLONAL	1	TRUE	1	0.524250866652494	3		429	456	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58142342	58142342	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	22	314	0	ENST00000257904.6:c.878C>G	p.Ser293Cys	p.S293C	ENST00000257904	NM_000075.3	293	tCt/tGt	8/8	0.486169608370583	3	FACETS	0.291	0.225	0.368	0.146	0.112	0.184	SUBCLONAL	1	TRUE	1	0.524250866652494	3		314	364	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303678	30303678	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1355673586	NA	P-0055532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	109	476	0	ENST00000262643.3:c.106A>G	p.Thr36Ala	p.T36A	ENST00000262643	NM_001238.2	36	Acc/Gcc	3/12	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.524250866652494	2		476	399	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46525066	46525066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	84	347	1	ENST00000263734.3:c.16G>A	p.Glu6Lys	p.E6K	ENST00000263734	NM_001430.4	6	Gag/Aag	1/16	0.458321815419708	4	FACETS	0.947	0.838	1	0.473	0.419	0.531	CLONAL	1	TRUE	2	0.524250866652494	4		348	516	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014184	70014184	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	120	565	0	ENST00000394351.3:c.1045A>C	p.Thr349Pro	p.T349P	ENST00000394351	NM_000248.3	349	Acc/Ccc	9/9	NA	2	FACETS	0.982	0.893	1			1	INDETERMINATE	1	TRUE	NA	0.524250866652494	2		565	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0055533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	134	797	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.222970047045978	2		797	1083	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0055533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	100	582	0	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.222970047045978	2		582	772	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663346	227663346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024227751	NA	P-0055533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	57	564	0	ENST00000305123.5:c.109G>A	p.Glu37Lys	p.E37K	ENST00000305123	NM_005544.2	37	Gag/Aag	1/2	1	2	FACETS	0.703	0.602	0.814	0.703	0.602	0.814	SUBCLONAL	1	TRUE	1	0.222970047045978	2		564	727	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219381	1219381	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	96	474	0	ENST00000326873.7:c.433G>T	p.Glu145Ter	p.E145*	ENST00000326873	NM_000455.4	145	Gag/Tag	3/10	0.222970047045978	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.222970047045978	1		474	604	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401856	139401856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	130	811	0	ENST00000277541.6:c.3544G>A	p.Glu1182Lys	p.E1182K	ENST00000277541	NM_017617.3	1182	Gag/Aag	22/34	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.222970047045978	2		811	1086	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344036	118344036	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	30	369	0	ENST00000534358.1:c.2162G>C	p.Arg721Pro	p.R721P	ENST00000534358	NM_005933.3	721	cGa/cCa	3/36	0.176928264483664	3	FACETS	0.553	0.444	0.676	0.276	0.222	0.338	SUBCLONAL	1	TRUE	1	0.222970047045978	3		369	541	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95595882	95595882	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	37	353	0	ENST00000393063.1:c.661G>C	p.Glu221Gln	p.E221Q	ENST00000393063	NM_030621.3	221	Gaa/Caa	7/28	1	2	FACETS	0.785	0.647	0.938	0.785	0.647	0.938	CLONAL	1	TRUE	1	0.222970047045978	2		353	423	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43767824	43767824	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	81	548	0	ENST00000382044.4:c.1024A>C	p.Thr342Pro	p.T342P	ENST00000382044	NM_001141980.1	342	Acc/Ccc	9/28	0.222970047045978	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.222970047045978	1		548	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572947	7572947	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	51	485	0	ENST00000269305.4:c.1162G>C	p.Glu388Gln	p.E388Q	ENST00000269305	NM_001126112.2	388	Gaa/Caa	11/11	1	2	FACETS	0.609	0.516	0.711	0.609	0.516	0.711	SUBCLONAL	1	TRUE	1	0.222970047045978	2		485	751	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560161	29560161	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	51	285	0	ENST00000356175.3:c.3638C>G	p.Thr1213Arg	p.T1213R	ENST00000356175	NM_000267.3	1213	aCa/aGa	27/57	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.222970047045978	2		285	397	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885962	59885962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	66	474	0	ENST00000259008.2:c.784G>A	p.Glu262Lys	p.E262K	ENST00000259008	NM_032043.2	262	Gag/Aag	7/20	1	2	FACETS	0.924	0.801	1	0.924	0.801	1	CLONAL	1	TRUE	1	0.222970047045978	2		474	641	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120362	70120362	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	140	723	0	ENST00000245479.2:c.1364del	p.Ala455GlyfsTer15	p.A455Gfs*15	ENST00000245479	NM_000346.3	455	gCg/gg	3/3	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.222970047045978	2		723	1001	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2164242	2164242	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0055533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	65	429	0	ENST00000398665.3:c.59A>C	p.Tyr20Ser	p.Y20S	ENST00000398665	NM_032482.2	20	tAc/tCc	1/28	0.222970047045978	1	FACETS	0.951	0.825	1	0.951	0.825	1	CLONAL	1	TRUE	0	0.222970047045978	1		429	545	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095003	11095004	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0055533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	128	887	0	ENST00000358026.2:c.180dup	p.Pro61AlafsTer21	p.P61Afs*21	ENST00000358026	NM_001128849.1	59	cag/caGg	2/36	0.222970047045978	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	0	0.222970047045978	1		887	1013	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968241	18968241	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	107	802	0	ENST00000262803.5:c.2081G>T	p.Arg694Leu	p.R694L	ENST00000262803	NM_002911.3	694	cGg/cTg	15/24	0.222970047045978	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.222970047045978	1		802	810	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161990423	161990423	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0055533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	38	459	1	ENST00000366898.1:c.897A>T	p.Lys299Asn	p.K299N	ENST00000366898	NM_004562.2	299	aaA/aaT	8/12	1	2	FACETS	0.628	0.518	0.75	0.628	0.518	0.75	SUBCLONAL	1	TRUE	1	0.222970047045978	2		460	543	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956778	68956778	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	53	580	0	ENST00000288368.4:c.896G>C	p.Arg299Pro	p.R299P	ENST00000288368	NM_024870.2	299	cGg/cCg	8/40	0.210214084024174	1	FACETS	0.526	0.447	0.613	0.526	0.447	0.613	SUBCLONAL	1	TRUE	0	0.222970047045978	1		580	803	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	49	423	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.414	0.351	0.483	0.414	0.351	0.483	SUBCLONAL	1	TRUE	1	0.572830097234599	2		424	413	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589586	67589591	+	inframe_deletion	In_Frame_Del	DEL	ATGAAT	ATGAAT	-	novel	NA	P-0055534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	38	197	0	ENST00000274335.5:c.1351_1356del	p.Glu451_Tyr452del	p.E451_Y452del	ENST00000274335		450	cATGAATat/cat	10/15	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.572830097234599	2		197	125	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063359	67063359	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	29	336	0	ENST00000412916.2:c.54del	p.Phe18LeufsTer4	p.F18Lfs*4	ENST00000412916		17	Ttt/tt	1/6	1	2	FACETS	0.228	0.182	0.28	0.228	0.182	0.28	SUBCLONAL	1	TRUE	1	0.572830097234599	2		336	444	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720677	89720678	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0055534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	40	221	0	ENST00000371953.3:c.829dup	p.Thr277AsnfsTer21	p.T277Nfs*21	ENST00000371953	NM_000314.4	276	-/A	8/9	1	2	FACETS	0.735	0.618	0.862	0.735	0.618	0.862	SUBCLONAL	1	TRUE	1	0.572830097234599	2		221	190	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539870	187539870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	131	431	0	ENST00000441802.2:c.7870G>A	p.Asp2624Asn	p.D2624N	ENST00000441802	NM_005245.3	2624	Gat/Aat	10/27	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.572830097234599	2		431	449	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372518	55372519	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0055534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	248	915	2	ENST00000297316.4:c.1208_1209delinsTT	p.Ser403Ile	p.S403I	ENST00000297316	NM_022454.3	403	aGC/aTT	2/2	1	2	FACETS	0.967	0.906	1	0.967	0.906	1	CLONAL	1	TRUE	1	0.572830097234599	2		917	895	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720719	89720723	+	frameshift_variant	Frame_Shift_Del	DEL	AGAAA	AGAAA	-	novel	NA	P-0055534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	24	110	0	ENST00000371953.3:c.871_875del	p.Glu291TrpfsTer5	p.E291Wfs*5	ENST00000371953	NM_000314.4	290	gtAGAAAat/gtat	8/9	1	2	FACETS	0.822	0.657	1	0.822	0.657	1	CLONAL	1	TRUE	1	0.572830097234599	2		110	102	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050904	49050929	+	frameshift_variant	Frame_Shift_Del	DEL	CTGAAGGAAGCAACCCTCCTAAACCA	CTGAAGGAAGCAACCCTCCTAAACCA	-	novel	NA	P-0055534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	48	398	0	ENST00000267163.4:c.2593_2618del	p.Gly865LysfsTer5	p.G865Kfs*5	ENST00000267163	NM_000321.2	863	gCTGAAGGAAGCAACCCTCCTAAACCA/g	25/27	1	2	FACETS	0.522	0.443	0.608	0.522	0.443	0.608	SUBCLONAL	1	TRUE	1	0.572830097234599	2		398	321	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660554	67660554	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	196	502	0	ENST00000264010.4:c.1454A>G	p.His485Arg	p.H485R	ENST00000264010	NM_006565.3	485	cAt/cGt	8/12	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.572830097234599	2		502	616	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533496	63533496	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1453965356	NA	P-0055534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	228	839	1	ENST00000307078.5:c.1658C>T	p.Ser553Leu	p.S553L	ENST00000307078	NM_004655.3	553	tCg/tTg	6/11	1	2	FACETS	0.92	0.859	0.983	0.92	0.859	0.983	CLONAL	1	TRUE	1	0.572830097234599	2		840	865	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47601117	47601117	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	196	530	0	ENST00000263735.4:c.355G>T	p.Val119Leu	p.V119L	ENST00000263735	NM_002354.2	119	Gtg/Ttg	3/9	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.572830097234599	2		530	622	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0055535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	43	354	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.28503010675677	2		355	243	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246137	46246137	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	135	370	0	ENST00000334344.6:c.4231C>T	p.Gln1411Ter	p.Q1411*	ENST00000334344	NM_152641.2	1411	Caa/Taa	15/21	0.187790299430532	5	FACETS	1	0.934	1	1	0.934	1	CLONAL	3	TRUE	2	0.28503010675677	5		370	441	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138645	55138645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1031763557	NA	P-0055535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	35	447	1	ENST00000257290.5:c.1322C>T	p.Pro441Leu	p.P441L	ENST00000257290	NM_006206.4	441	cCg/cTg	9/23	0.159945769838681	4	FACETS	0.493	0.403	0.595	0.247	0.201	0.298	INDETERMINATE	1	TRUE	2	0.28503010675677	4		448	640	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755612	39755612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776452839	NA	P-0055535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1201	86	641	0	ENST00000288319.7:c.1153C>T	p.Arg385Cys	p.R385C	ENST00000288319	NM_182918.3	385	Cgc/Tgc	10/10	0.28503010675677	7	FACETS	0.803	0.708	0.906	0.201	0.177	0.227	CLONAL	1	TRUE	3	0.28503010675677	7		641	1287	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	244	280	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	0.28503010675677	2	FACETS	0.966	0.917	1			1	CLONAL	4	TRUE	NA	0.28503010675677	2		280	443	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669547	88669547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56394626	NA	P-0055535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	49	409	1	ENST00000360948.2:c.1351G>A	p.Val451Ile	p.V451I	ENST00000360948	NM_001012338.2	451	Gtc/Atc	12/19	0.121649468058831	3	FACETS	0.647	0.547	0.757	0.216	0.182	0.253	INDETERMINATE	1	TRUE	0	0.28503010675677	3		410	607	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088756	27088756	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0055535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	231	655	0	ENST00000324856.7:c.2365C>T	p.Gln789Ter	p.Q789*	ENST00000324856	NM_006015.4	789	Cag/Tag	7/20	0.0900755118840348	3	FACETS	1	0.956	1			1	INDETERMINATE	2	TRUE	NA	0.28503010675677	3		655	898	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961321	54961321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs2230743	NA	P-0055535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	49	564	0	ENST00000312783.6:c.311C>T	p.Ser104Leu	p.S104L	ENST00000312783	NM_198436.1	104	tCg/tTg	4/10	0.28503010675677	5	FACETS	0.519	0.438	0.609	0.173	0.146	0.203	SUBCLONAL	1	TRUE	2	0.28503010675677	5		564	946	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223539	53223539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	61	373	0	ENST00000375401.3:c.3820G>A	p.Glu1274Lys	p.E1274K	ENST00000375401	NM_004187.3	1274	Gag/Aag	23/26	0.28503010675677	2	FACETS	0.87	0.752	0.998			1	CLONAL	1	TRUE	NA	0.28503010675677	2		373	492	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846206	128846206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761081288	NA	P-0055535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	73	680	0	ENST00000249373.3:c.1136C>T	p.Ala379Val	p.A379V	ENST00000249373	NM_005631.4	379	gCg/gTg	5/12	0.187790299430532	5	FACETS	0.71	0.619	0.809	0.237	0.206	0.27	SUBCLONAL	1	TRUE	2	0.28503010675677	5		680	1030	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106681	27106681	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0055535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	182	700	0	ENST00000324856.7:c.6292G>T	p.Glu2098Ter	p.E2098*	ENST00000324856	NM_006015.4	2098	Gaa/Taa	20/20	0.0900755118840348	3	FACETS	0.868	0.802	0.937			1	INDETERMINATE	2	TRUE	NA	0.28503010675677	3		700	840	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45794997	45794997	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	109	563	0	ENST00000450313.1:c.1631T>C	p.Leu544Pro	p.L544P	ENST00000450313	NM_012222.2	544	cTc/cCc	16/16	0.28503010675677	6	FACETS	1	0.962	1			1	CLONAL	1	TRUE	NA	0.28503010675677	6		563	1038	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462939	120462939	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	75	545	0	ENST00000256646.2:c.5392G>C	p.Asp1798His	p.D1798H	ENST00000256646	NM_024408.3	1798	Gac/Cac	30/34	0.103583673809542	4	FACETS	0.847	0.742	0.962	0.424	0.371	0.481	INDETERMINATE	1	TRUE	2	0.28503010675677	4		545	798	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094297	193094297	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	32	336	0	ENST00000367435.3:c.187C>G	p.Leu63Val	p.L63V	ENST00000367435	NM_024529.4	63	Cta/Gta	2/17	1	2	FACETS	0.599	0.486	0.726	0.599	0.486	0.726	SUBCLONAL	1	TRUE	1	0.28503010675677	2		336	375	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138376639	138376639	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	39	420	0	ENST00000289153.2:c.2835C>G	p.Phe945Leu	p.F945L	ENST00000289153	NM_006219.2	945	ttC/ttG	20/22	0.187790299430532	5	FACETS	0.76	0.629	0.906	0.253	0.209	0.302	CLONAL	1	TRUE	2	0.28503010675677	5		420	514	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591085	67591085	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519839	NA	P-0055542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	89	288	1	ENST00000274335.5:c.1678G>T	p.Asp560Tyr	p.D560Y	ENST00000274335		560	Gac/Tac	12/15	0.328106339080037	3	FACETS	1	0.971	1	0.816	0.734	0.9	CLONAL	2	TRUE	0	0.328106339080037	3		289	258	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263850	133263850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	48	326	0	ENST00000320574.5:c.52G>A	p.Glu18Lys	p.E18K	ENST00000320574	NM_006231.2	18	Gag/Aag	1/49	0.261920442793065	4	FACETS	1	0.937	1	0.603	0.512	0.703	CLONAL	1	TRUE	2	0.328106339080037	4		326	322	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502264	186502264	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	46	376	0	ENST00000323963.5:c.73G>C	p.Glu25Gln	p.E25Q	ENST00000323963		25	Gag/Cag	2/11	0.261920442793065	4	FACETS	0.746	0.628	0.876	0.373	0.314	0.438	SUBCLONAL	1	TRUE	2	0.328106339080037	4		376	499	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164142	47164142	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0055542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	19	342	0	ENST00000409792.3:c.1984C>T	p.Gln662Ter	p.Q662*	ENST00000409792	NM_014159.6	662	Caa/Taa	3/21	0.285384805291053	2	FACETS	0.698	0.533	0.888	0.349	0.266	0.444	SUBCLONAL	1	TRUE	0	0.328106339080037	2		342	166	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910239	50910239	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0055542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	58	539	0	ENST00000440232.2:c.1495-1G>A		p.X499_splice	ENST00000440232	NM_002691.3	499			0.291631074357955	3	FACETS	0.75	0.644	0.864	0.375	0.322	0.432	SUBCLONAL	1	TRUE	1	0.328106339080037	3		539	549	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670334	134670334	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	78	538	0	ENST00000398015.3:c.245C>G	p.Ala82Gly	p.A82G	ENST00000398015	NM_004441.4	82	gCc/gGc	3/16	0.261920442793065	4	FACETS	0.907	0.797	1	0.454	0.398	0.513	CLONAL	1	TRUE	2	0.328106339080037	4		538	696	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399991	139399991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746144524	NA	P-0055542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	58	972	0	ENST00000277541.6:c.4357G>A	p.Glu1453Lys	p.E1453K	ENST00000277541	NM_017617.3	1453	Gag/Aag	25/34	0.159140863173456	4	FACETS	0.441	0.378	0.511	0.221	0.189	0.256	INDETERMINATE	1	TRUE	2	0.328106339080037	4		972	1064	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16248841	16248841	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	27	405	0	ENST00000375759.3:c.1847G>C	p.Arg616Thr	p.R616T	ENST00000375759	NM_015001.2	616	aGa/aCa	10/15	1	2	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	TRUE	1	0.328106339080037	2		405	157	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870376	155870376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	69	567	0	ENST00000368323.3:c.463G>A	p.Glu155Lys	p.E155K	ENST00000368323	NM_006912.5	155	Gaa/Aaa	6/6	0.328106339080037	4	FACETS	0.843	0.733	0.961	0.421	0.366	0.481	CLONAL	1	TRUE	2	0.328106339080037	4		567	663	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310884	123310884	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200766273	NA	P-0055542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	82	642	1	ENST00000358487.5:c.544G>A	p.Gly182Arg	p.G182R	ENST00000358487	NM_000141.4	182	Ggg/Agg	5/18	0.260435939141367	2	FACETS	0.728	0.641	0.82	0.364	0.32	0.41	SUBCLONAL	1	TRUE	0	0.328106339080037	2		643	687	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444764	49444764	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	111	928	1	ENST00000301067.7:c.2702C>T	p.Ser901Phe	p.S901F	ENST00000301067	NM_003482.3	901	tCt/tTt	10/54	0.261920442793065	4	FACETS	0.882	0.791	0.978	0.441	0.395	0.489	CLONAL	1	TRUE	2	0.328106339080037	4		929	1019	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603114	48603114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	51	531	0	ENST00000342988.3:c.1415C>T	p.Pro472Leu	p.P472L	ENST00000342988	NM_005359.5	472	cCa/cTa	11/12	0.232152550742059	4	FACETS	0.62	0.526	0.723	0.31	0.263	0.362	SUBCLONAL	1	TRUE	2	0.328106339080037	4		531	666	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609717	46609717	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765717751	NA	P-0055542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	59	885	0	ENST00000263734.3:c.2441C>T	p.Ser814Leu	p.S814L	ENST00000263734	NM_001430.4	814	tCg/tTg	15/16	0.102701149946101	5	FACETS	0.601	0.515	0.695	0.15	0.128	0.174	INDETERMINATE	1	TRUE	1	0.328106339080037	5		885	893	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662539	227662539	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	62	799	0	ENST00000305123.5:c.916G>C	p.Glu306Gln	p.E306Q	ENST00000305123	NM_005544.2	306	Gag/Cag	1/2	0.102701149946101	5	FACETS	0.746	0.643	0.858	0.186	0.16	0.215	INDETERMINATE	1	TRUE	1	0.328106339080037	5		799	756	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017163	31017163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	48	377	0	ENST00000375687.4:c.494C>T	p.Thr165Ile	p.T165I	ENST00000375687	NM_015338.5	165	aCt/aTt	7/13	0.328106339080037	6	FACETS	0.773	0.652	0.906			1	CLONAL	1	TRUE	NA	0.328106339080037	6		377	627	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326162	62326162	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs116768542	NA	P-0055542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1332	109	1045	1	ENST00000360203.5:c.3178G>A	p.Val1060Met	p.V1060M	ENST00000360203	NM_001283009.1	1060	Gtg/Atg	32/35	0.328106339080037	6	FACETS	0.764	0.683	0.85			1	SUBCLONAL	1	TRUE	NA	0.328106339080037	6		1046	1441	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650348	12650348	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	48	584	0	ENST00000251849.4:c.498G>C	p.Gln166His	p.Q166H	ENST00000251849	NM_002880.3	166	caG/caC	5/17	0.328106339080037	5	FACETS	0.705	0.595	0.827			1	SUBCLONAL	1	TRUE	NA	0.328106339080037	5		584	619	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38968075	38968075	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	10	368	0	ENST00000357387.3:c.1030G>A	p.Glu344Lys	p.E344K	ENST00000357387	NM_152756.3	344	Gag/Aag	12/38	0.328106339080037	5	FACETS	0.517	0.35	0.725	0.172	0.116	0.242	SUBCLONAL	1	TRUE	2	0.328106339080037	5		368	176	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391547	139391547	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1401419952	NA	P-0055543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	34	787	0	ENST00000277541.6:c.6644C>T	p.Ser2215Leu	p.S2215L	ENST00000277541	NM_017617.3	2215	tCg/tTg	34/34	1	2	FACETS	0.261	0.212	0.315	0.261	0.212	0.315	SUBCLONAL	1	FALSE	1	0.424288624562134	2		787	615	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828301	50828301	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	17	487	0	ENST00000398568.2:c.2639C>G	p.Ser880Cys	p.S880C	ENST00000398568	NM_001042412.1	880	tCt/tGt	17/18	1	2	FACETS	0.307	0.229	0.4	0.307	0.229	0.4	SUBCLONAL	1	FALSE	1	0.424288624562134	2		487	261	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579566	7579566	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	118	799	0	ENST00000269305.4:c.121del	p.Asp41MetfsTer3	p.D41Mfs*3	ENST00000269305	NM_001126112.2	41	Gat/at	4/11	0.361514764175466	2	FACETS	0.795	0.725	0.866	0.795	0.725	0.866	SUBCLONAL	2	FALSE	0	0.424288624562134	2		799	350	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275418	142275418	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0055543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	12	304	0	ENST00000350721.4:c.1886-1G>A		p.X629_splice	ENST00000350721	NM_001184.3	629			0.210324826863725	5	FACETS	0.718	0.507	0.973	0.239	0.169	0.325	INDETERMINATE	1	FALSE	2	0.424288624562134	5		304	129	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502374	186502374	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	16	400	0	ENST00000323963.5:c.97G>C	p.Asp33His	p.D33H	ENST00000323963		33	Gat/Cat	3/11	0.210324826863725	5	FACETS	0.596	0.442	0.78	0.199	0.147	0.26	INDETERMINATE	1	FALSE	2	0.424288624562134	5		400	207	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557927	187557927	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs369805914	NA	P-0055544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	162	485	1	ENST00000441802.2:c.3784C>T	p.Arg1262Ter	p.R1262*	ENST00000441802	NM_005245.3	1262	Cga/Tga	5/27	1	2	FACETS	0.878	0.81	0.947	0.878	0.81	0.947	CLONAL	1	TRUE	1	0.676066349754945	2		486	546	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256530	+	missense_variant	Missense_Mutation	DNP	TG	TG	CT	rs1057519834	NA	P-0055544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	299	531	0	ENST00000369535.4:c.181_182delinsAG	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	CAa/AGa	3/7	0.664218586790772	2	FACETS	0.981	0.941	1	0.981	0.941	1	CLONAL	2	TRUE	0	0.676066349754945	2		531	451	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157868	27157868	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	123	560	0	ENST00000380036.4:c.92C>T	p.Ser31Phe	p.S31F	ENST00000380036	NM_000459.3	31	tCc/tTc	2/23	0.313594107325888	1	FACETS	0.538	0.489	0.588	0.538	0.489	0.588	INDETERMINATE	1	TRUE	0	0.676066349754945	1		560	448	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223123	41223123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794054	NA	P-0055544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	167	616	0	ENST00000357654.3:c.4808C>T	p.Pro1603Leu	p.P1603L	ENST00000357654	NM_007294.3	1603	cCc/cTc	15/23	1	2	FACETS	0.956	0.884	1	0.956	0.884	1	CLONAL	1	TRUE	1	0.676066349754945	2		616	517	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0055547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	13	115	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		115	116	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0055550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	161	523	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.318181755465121	3	FACETS	1	0.981	1	0.784	0.727	0.844	CLONAL	2	TRUE	0	0.367226687333369	3		523	441	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	79	518	0	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	0.727	0.64	0.82	0.727	0.64	0.82	SUBCLONAL	1	TRUE	1	0.367226687333369	2		518	592	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451784	29451784	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs772809305	NA	P-0055550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	48	415	0	ENST00000389048.3:c.2781del	p.Cys928AlafsTer11	p.C928Afs*11	ENST00000389048	NM_004304.4	927	ggG/gg	16/29	1	2	FACETS	0.703	0.596	0.82	0.703	0.596	0.82	SUBCLONAL	1	TRUE	1	0.367226687333369	2		415	372	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0055550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	55	336	0	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	1	2	FACETS	0.657	0.563	0.759	0.657	0.563	0.759	SUBCLONAL	1	TRUE	1	0.367226687333369	2		336	456	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	54	496	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.595	0.509	0.69	0.595	0.509	0.69	SUBCLONAL	1	TRUE	1	0.367226687333369	2		496	494	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007332	143007332	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	63	385	2	ENST00000262992.4:c.2452del	p.Arg818GlufsTer4	p.R818Efs*4	ENST00000262992	NM_001101669.1	818	Aga/ga	22/24	1	2	FACETS	0.805	0.699	0.92	0.805	0.699	0.92	CLONAL	1	TRUE	1	0.367226687333369	2		387	426	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863319	57863319	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	110	746	0	ENST00000228682.2:c.1418del	p.Gly473AlafsTer40	p.G473Afs*40	ENST00000228682	NM_005269.2	472	Ggg/gg	11/12	1	2	FACETS	0.714	0.641	0.791	0.714	0.641	0.791	SUBCLONAL	1	TRUE	1	0.367226687333369	2		746	839	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099103	27099103	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0055550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	68	463	1	ENST00000324856.7:c.3524del	p.Pro1175HisfsTer5	p.P1175Hfs*5	ENST00000324856	NM_006015.4	1173	atC/at	13/20	1	2	FACETS	0.643	0.56	0.733	0.643	0.56	0.733	SUBCLONAL	1	TRUE	1	0.367226687333369	2		464	576	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813023	89813023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142833057	NA	P-0055550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	91	703	1	ENST00000389301.3:c.3482C>T	p.Thr1161Met	p.T1161M	ENST00000389301	NM_000135.2	1161	aCg/aTg	35/43	1	2	FACETS	0.675	0.599	0.756	0.675	0.599	0.756	SUBCLONAL	1	TRUE	1	0.367226687333369	2		704	734	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193850	106193850	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	54	386	0	ENST00000380013.4:c.4317del	p.Lys1439AsnfsTer9	p.K1439Nfs*9	ENST00000380013	NM_001127208.2	1438	Aaa/aa	10/11	1	2	FACETS	0.615	0.526	0.713	0.615	0.526	0.713	SUBCLONAL	1	TRUE	1	0.367226687333369	2		386	478	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0055550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	113	871	0	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	1	2	FACETS	0.727	0.654	0.805	0.727	0.654	0.805	SUBCLONAL	1	TRUE	1	0.367226687333369	2		871	846	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994934	73994934	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs373331287	NA	P-0055550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	38	270	0	ENST00000318443.5:c.418G>A	p.Ala140Thr	p.A140T	ENST00000318443	NM_001024736.1	140	Gct/Act	3/10	1	2	FACETS	0.945	0.788	1	0.945	0.788	1	CLONAL	1	TRUE	1	0.367226687333369	2		270	219	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155399	99155399	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1559033620	NA	P-0055550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	84	470	1	ENST00000074304.5:c.625C>T	p.Arg209Ter	p.R209*	ENST00000074304	NM_001134224.1	209	Cga/Tga	9/26	1	2	FACETS	0.769	0.68	0.864	0.769	0.68	0.864	SUBCLONAL	1	TRUE	1	0.367226687333369	2		471	595	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721713	176721713	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0055550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	62	528	0	ENST00000439151.2:c.7349del	p.Asn2450IlefsTer6	p.N2450Ifs*6	ENST00000439151	NM_022455.4	2448	tcA/tc	23/23	1	2	FACETS	0.689	0.596	0.79	0.689	0.596	0.79	SUBCLONAL	1	TRUE	1	0.367226687333369	2		528	490	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723073	49723073	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs374627079	NA	P-0055550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	22	151	0	ENST00000449682.2:c.1343T>C	p.Met448Thr	p.M448T	ENST00000449682	NM_020998.3	448	aTg/aCg	11/18	1	2	FACETS	0.768	0.601	0.959	0.768	0.601	0.959	CLONAL	1	TRUE	1	0.367226687333369	2		151	156	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522700	67522700	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0055550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	39	274	1	ENST00000274335.5:c.202del	p.Asp68ThrfsTer7	p.D68Tfs*7	ENST00000274335		66	aGg/ag	1/15	1	2	FACETS	0.676	0.563	0.802	0.676	0.563	0.802	SUBCLONAL	1	TRUE	1	0.367226687333369	2		275	314	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261262	115261262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1375202283	NA	P-0055550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	67	541	0	ENST00000438362.2:c.2459G>A	p.Arg820His	p.R820H	ENST00000438362	NM_001242891.1	820	cGt/cAt	19/20	1	2	FACETS	0.638	0.555	0.728	0.638	0.555	0.728	SUBCLONAL	1	TRUE	1	0.367226687333369	2		541	572	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195730	102195731	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0055550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	57	413	0	ENST00000263464.3:c.492_493del	p.Ala165AsnfsTer3	p.A165Nfs*3	ENST00000263464	NM_001165.4	164	TGt/t	2/9	1	2	FACETS	0.786	0.677	0.904	0.786	0.677	0.904	CLONAL	1	TRUE	1	0.367226687333369	2		413	395	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953617	32953617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80359143	NA	P-0055550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	73	501	0	ENST00000380152.3:c.8918G>A	p.Arg2973His	p.R2973H	ENST00000380152		2973	cGt/cAt	22/27	1	2	FACETS	0.947	0.832	1	0.947	0.832	1	CLONAL	1	TRUE	1	0.367226687333369	2		501	420	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041761	42041764	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	novel	NA	P-0055550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	56	430	0	ENST00000219905.7:c.5958_5961del	p.Arg1986SerfsTer15	p.R1986Sfs*15	ENST00000219905	NM_001164273.1	1986	AGAGag/ag	17/24	1	2	FACETS	0.667	0.573	0.77	0.667	0.573	0.77	SUBCLONAL	1	TRUE	1	0.367226687333369	2		430	457	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662321	67662322	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0055550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	89	504	0	ENST00000264010.4:c.1568dup	p.Tyr523Ter	p.Y523*	ENST00000264010	NM_006565.3	523	tac/tAac	9/12	1	2	FACETS	0.776	0.688	0.869	0.776	0.688	0.869	SUBCLONAL	1	TRUE	1	0.367226687333369	2		504	625	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881638	37881638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	70	584	0	ENST00000269571.5:c.2708G>A	p.Ser903Asn	p.S903N	ENST00000269571		903	aGt/aAt	22/27	1	2	FACETS	0.594	0.518	0.676	0.594	0.518	0.676	SUBCLONAL	1	TRUE	1	0.367226687333369	2		584	642	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99181187	99181187	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	74	604	0	ENST00000074304.5:c.2128G>A	p.Gly710Arg	p.G710R	ENST00000074304	NM_001134224.1	710	Ggg/Agg	20/26	1	2	FACETS	0.594	0.52	0.675	0.594	0.52	0.675	SUBCLONAL	1	TRUE	1	0.367226687333369	2		604	678	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182605	99182605	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	83	511	1	ENST00000074304.5:c.2408T>C	p.Ile803Thr	p.I803T	ENST00000074304	NM_001134224.1	803	aTc/aCc	22/26	1	2	FACETS	0.866	0.766	0.972	0.866	0.766	0.972	CLONAL	1	TRUE	1	0.367226687333369	2		512	522	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660714	227660714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	103	764	0	ENST00000305123.5:c.2741C>T	p.Ala914Val	p.A914V	ENST00000305123	NM_005544.2	914	gCt/gTt	1/2	1	2	FACETS	0.704	0.629	0.783	0.704	0.629	0.783	SUBCLONAL	1	TRUE	1	0.367226687333369	2		764	797	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094785	143094785	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	29	299	0	ENST00000262992.4:c.1359del	p.Thr454GlnfsTer18	p.T454Qfs*18	ENST00000262992	NM_001101669.1	453	aaA/aa	14/24	1	2	FACETS	0.624	0.503	0.761	0.624	0.503	0.761	SUBCLONAL	1	TRUE	1	0.367226687333369	2		299	253	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393611	139393611	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0055550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	138	914	0	ENST00000277541.6:c.6035A>G	p.Glu2012Gly	p.E2012G	ENST00000277541	NM_017617.3	2012	gAg/gGg	32/34	1	2	FACETS	0.82	0.745	0.898	0.82	0.745	0.898	CLONAL	1	TRUE	1	0.367226687333369	2		914	917	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246991	53246991	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	91	570	0	ENST00000375401.3:c.509G>T	p.Gly170Val	p.G170V	ENST00000375401	NM_004187.3	170	gGa/gTa	4/26	1	2	FACETS	0.733	0.651	0.821	0.733	0.651	0.821	SUBCLONAL	1	TRUE	1	0.367226687333369	2		570	676	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776282	76776282	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0055550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	96	652	0	ENST00000373344.5:c.7184T>C	p.Leu2395Ser	p.L2395S	ENST00000373344	NM_000489.3	2395	tTg/tCg	34/35	1	2	FACETS	0.885	0.79	0.985	0.885	0.79	0.985	CLONAL	1	TRUE	1	0.367226687333369	2		652	591	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0055551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	10	285	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.13	0.088	0.185	0.13	0.088	0.185	SUBCLONAL	1	TRUE	1	0.482011030584634	2		285	318	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981244	201981290	+	frameshift_variant	Frame_Shift_Del	DEL	AGGAGCTGCGTCTGGTCTTTGGGCCTCTGGGGGACCAACTCCATGCC	AGGAGCTGCGTCTGGTCTTTGGGCCTCTGGGGGACCAACTCCATGCC	-	novel	NA	P-0055551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	404	780	3	ENST00000359651.3:c.323_369del	p.Glu108AlafsTer11	p.E108Afs*11	ENST00000359651		108	gAGGAGCTGCGTCTGGTCTTTGGGCCTCTGGGGGACCAACTCCATGCC/g	2/8	0.174483506505494	2	FACETS	1	0.992	1	0.604	0.574	0.634	INDETERMINATE	1	TRUE	0	0.482011030584634	2		783	1388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579849	7579853	+	frameshift_variant	Frame_Shift_Del	DEL	GGTCT	GGTCT	-	novel	NA	P-0055551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	264	650	0	ENST00000269305.4:c.60_64del	p.Asp21MetfsTer6	p.D21Mfs*6	ENST00000269305	NM_001126112.2	20	tcAGACCta/tcta	2/11	0.482011030584634	1	FACETS	0.948	0.891	1	0.948	0.891	1	CLONAL	1	TRUE	0	0.482011030584634	1		650	877	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27205002	27205002	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0055551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	60	560	0	ENST00000380036.4:c.2303T>G	p.Ile768Ser	p.I768S	ENST00000380036	NM_000459.3	768	aTc/aGc	14/23	0.482011030584634	1	FACETS	0.246	0.211	0.284	0.246	0.211	0.284	SUBCLONAL	1	TRUE	0	0.482011030584634	1		560	769	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922817	44922824	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGCCTG	CCTGCCTG	-	novel	NA	P-0055551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	129	247	0	ENST00000377967.4:c.1680_1687del	p.Ala561TrpfsTer17	p.A561Wfs*17	ENST00000377967	NM_021140.2	560	CCTGCCTGc/c	16/29	1	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.482011030584634	1		247	353	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0055552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	182	623	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.568230771864742	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.568230771864742	1		623	436	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0055552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	63	333	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	1	2	FACETS	0.85	0.743	0.963	0.85	0.743	0.963	CLONAL	1	TRUE	1	0.568230771864742	2		333	261	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0055552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	309	611	1	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.568230771864742	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.568230771864742	2		612	519	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101118	41101118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751886972	NA	P-0055552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	182	666	0	ENST00000373198.4:c.1238C>T	p.Ala413Val	p.A413V	ENST00000373198	NM_133170.3	413	gCg/gTg	8/32	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.568230771864742	2		666	613	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100499	8100499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	152	743	4	ENST00000346208.3:c.473C>T	p.Pro158Leu	p.P158L	ENST00000346208		158	cCg/cTg	3/6	1	2	FACETS	0.902	0.829	0.978	0.902	0.829	0.978	CLONAL	1	TRUE	1	0.568230771864742	2		747	593	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0055553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	64	523	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.748646670292798	1	FACETS	0.787	0.702	0.871	0.787	0.702	0.871	SUBCLONAL	1	TRUE	0	0.748646670292798	1		523	136	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834587	156834587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757031354	NA	P-0055553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	106	965	1	ENST00000524377.1:c.355C>T	p.Arg119Cys	p.R119C	ENST00000524377	NM_002529.3	119	Cgc/Tgc	3/17	0.140389842974081	3	FACETS	0.811	0.742	0.881	0.811	0.742	0.881	INDETERMINATE	2	TRUE	1	0.748646670292798	3		966	240	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554272	29554272	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199474762	NA	P-0055553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	69	501	0	ENST00000356175.3:c.2288T>C	p.Leu763Pro	p.L763P	ENST00000356175	NM_000267.3	763	cTg/cCg	19/57	0.74352437547892	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.748646670292798	1		501	114	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712508	43712508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1052588816	NA	P-0055553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	59	575	0	ENST00000382044.4:c.4676G>A	p.Ser1559Asn	p.S1559N	ENST00000382044	NM_001141980.1	1559	aGt/aAt	21/28	1	2	FACETS	0.916	0.804	1	0.916	0.804	1	CLONAL	1	TRUE	1	0.748646670292798	2		575	172	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52709236	52709256	+	inframe_deletion	In_Frame_Del	DEL	GAGGTCCTCCTGGCCCTGGCA	GAGGTCCTCCTGGCCCTGGCA	-	novel	NA	P-0055553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	30	607	1	ENST00000322088.6:c.192_212del	p.Val65_Glu71del	p.V65_E71del	ENST00000322088	NM_014225.5	64	GAGGTCCTCCTGGCCCTGGCA/-	3/15	1	2	FACETS	0.594	0.486	0.712	0.594	0.486	0.712	SUBCLONAL	1	TRUE	1	0.748646670292798	2		608	135	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294141	1294141	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	19	945	0	ENST00000310581.5:c.860G>A	p.Gly287Asp	p.G287D	ENST00000310581	NM_198253.2	287	gGt/gAt	2/16	0.251524456546276	4	FACETS	0.323	0.245	0.414	0.108	0.081	0.138	INDETERMINATE	1	TRUE	1	0.748646670292798	4		945	275	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680419	30680419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	51	610	0	ENST00000376406.3:c.1300G>A	p.Asp434Asn	p.D434N	ENST00000376406	NM_014641.2	434	Gac/Aac	5/15	0.748646670292798	3	FACETS	1	0.869	1	0.503	0.434	0.576	CLONAL	1	TRUE	1	0.748646670292798	3		610	186	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0055554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	284	622	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.428785534494928	4	FACETS	0.927	0.872	0.982	0.927	0.872	0.982	CLONAL	2	TRUE	2	0.451760510424657	4		622	985	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215818	98215818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566619057	NA	P-0055554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	193	556	1	ENST00000331920.6:c.3391G>A	p.Val1131Met	p.V1131M	ENST00000331920	NM_000264.3	1131	Gtg/Atg	20/24	0.451760510424657	3	FACETS	1	0.945	1	0.513	0.474	0.553	CLONAL	1	TRUE	1	0.451760510424657	3		557	1021	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841030	15841030	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	191	714	1	ENST00000307771.7:c.1114G>A	p.Asp372Asn	p.D372N	ENST00000307771	NM_005089.3	372	Gac/Aac	11/11	0.136963291961183	6	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.451760510424657	6		715	1164	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705404	43705404	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	242	736	0	ENST00000382044.4:c.5218C>G	p.Leu1740Val	p.L1740V	ENST00000382044	NM_001141980.1	1740	Ctc/Gtc	24/28	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.451760510424657	2		736	1039	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272227	21272227	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745921293	NA	P-0055554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	56	444	0	ENST00000354336.3:c.5C>T	p.Ser2Phe	p.S2F	ENST00000354336	NM_005207.3	2	tCc/tTc	1/3	1	2	FACETS	0.419	0.358	0.485	0.419	0.358	0.485	SUBCLONAL	1	TRUE	1	0.451760510424657	2		444	592	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910647	29910647	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs199474387	NA	P-0055554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1625	303	1411	0	ENST00000376809.5:c.187G>C	p.Asp63His	p.D63H	ENST00000376809	NM_002116.7	63	Gac/Cac	2/8	0.277027705669929	2	FACETS	0.696	0.653	0.74	0.348	0.326	0.37	SUBCLONAL	1	TRUE	0	0.451760510424657	2		1411	1928	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162146	38162146	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	163	483	0	ENST00000317025.8:c.2570C>G	p.Ser857Cys	p.S857C	ENST00000317025	NM_023034.1	857	tCt/tGt	14/24	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.451760510424657	2		483	698	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937521	76937521	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0055554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	164	479	0	ENST00000373344.5:c.3227C>G	p.Ser1076Cys	p.S1076C	ENST00000373344	NM_000489.3	1076	tCt/tGt	9/35	0.451760510424657	3	FACETS	1	0.966	1	0.547	0.503	0.594	CLONAL	1	TRUE	1	0.451760510424657	3		479	813	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0055555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	199	354	1				ENST00000310581	NM_198253.2	-/1132			0.530036768015195	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	1	0.530036768015195	4		355	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579405	7579405	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0055555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	343	905	0	ENST00000269305.4:c.282del	p.Ser95LeufsTer28	p.S95Lfs*28	ENST00000269305	NM_001126112.2	94	tcA/tc	4/11	0.399060260096906	3	FACETS	0.842	0.805	0.879	0.842	0.805	0.879	CLONAL	3	TRUE	0	0.530036768015195	3		905	648	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0055556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	98	396	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.167996272638089	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	FALSE	1	0.167996272638089	3		396	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0055556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	123	591	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.167996272638089	2	FACETS	0.996	0.902	1	0.996	0.902	1	CLONAL	2	FALSE	0	0.167996272638089	2		591	735	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303035	15303035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777257132	NA	P-0055556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	152	1168	1	ENST00000263388.2:c.415G>A	p.Asp139Asn	p.D139N	ENST00000263388	NM_000435.2	139	Gat/Aat	4/33	0.167996272638089	3	FACETS	0.962	0.878	1	0.962	0.878	1	CLONAL	2	FALSE	1	0.167996272638089	3		1169	1020	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604685	48604686	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TATCC	novel	NA	P-0055556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	69	452	0	ENST00000342988.3:c.1508_1509insATCCT	p.Met503IlefsTer3	p.M503Ifs*3	ENST00000342988	NM_005359.5	503	atg/aTATCCtg	12/12	0.167996272638089	2	FACETS	0.831	0.726	0.945	0.831	0.726	0.945	CLONAL	2	FALSE	0	0.167996272638089	2		452	494	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0055557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	183	237	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.68243729919881	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.685230264078178	1		237	313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782329	NA	P-0055557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	240	574	0	ENST00000269305.4:c.746G>C	p.Arg249Thr	p.R249T	ENST00000269305	NM_001126112.2	249	aGg/aCg	7/11	0.685230264078178	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.685230264078178	1		574	459	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333982	70333982	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	60	271	0	ENST00000373644.4:c.1887G>T	p.Lys629Asn	p.K629N	ENST00000373644	NM_030625.2	629	aaG/aaT	2/12	0.378347140952324	1	FACETS	0.377	0.327	0.431	0.377	0.327	0.431	INDETERMINATE	1	TRUE	0	0.685230264078178	1		271	305	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042359	16042359	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0055557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	119	454	0	ENST00000268712.3:c.1315G>T	p.Val439Phe	p.V439F	ENST00000268712	NM_006311.3	439	Gtt/Ttt	12/46	0.685230264078178	1	FACETS	0.533	0.485	0.584	0.533	0.485	0.584	SUBCLONAL	1	TRUE	0	0.685230264078178	1		454	428	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18956825	18956825	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0055557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	128	568	0	ENST00000262803.5:c.268G>A	p.Asp90Asn	p.D90N	ENST00000262803	NM_002911.3	90	Gac/Aac	2/24	0.456547903821749	1	FACETS	0.397	0.36	0.435	0.397	0.36	0.435	SUBCLONAL	1	TRUE	0	0.685230264078178	1		568	619	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958060	54958060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0055557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	121	249	0	ENST00000312783.6:c.547G>A	p.Glu183Lys	p.E183K	ENST00000312783	NM_198436.1	183	Gaa/Aaa	6/10	0.375355208467963	5	FACETS	1	0.985	1	0.37	0.336	0.405	INDETERMINATE	1	TRUE	1	0.685230264078178	5		249	484	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428439	72428439	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0055557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	351	562	1	ENST00000477973.2:c.565C>A	p.Pro189Thr	p.P189T	ENST00000477973	NM_012234.5	189	Cct/Act	2/4	0.372871390438272	1	FACETS	0.764	0.727	0.802	0.764	0.727	0.802	INDETERMINATE	1	TRUE	0	0.685230264078178	1		563	881	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117717356	117717356	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0055557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	65	282	0	ENST00000368508.3:c.851C>G	p.Ser284Ter	p.S284*	ENST00000368508	NM_002944.2	284	tCa/tGa	8/43	0.32821017833554	1	FACETS	0.389	0.339	0.441	0.389	0.339	0.441	INDETERMINATE	1	TRUE	0	0.685230264078178	1		282	321	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508399	106508399	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0055557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	67	354	0	ENST00000359195.3:c.393C>G	p.Ser131Arg	p.S131R	ENST00000359195	NM_002649.2	131	agC/agG	2/11	0.657140426449954	2	FACETS	0.619	0.542	0.701	0.309	0.271	0.351	SUBCLONAL	1	TRUE	0	0.685230264078178	2		354	316	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994275	21994275	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748616717	NA	P-0055557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	122	550	0	ENST00000579755.1:c.56G>A	p.Arg19Gln	p.R19Q	ENST00000579755		19	cGa/cAa	1/3	0.332381446273712		FACETS		0.468	0.569				INDETERMINATE	1	TRUE	0	0.685230264078178	2		550	689	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0002110-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	230	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.135329311764737	4	FACETS	1	0.965	1			1	INDETERMINATE	3	FALSE	NA	0.404976321179952	4		457	515	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504383	149504383	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002110-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	48	474	0	ENST00000261799.4:c.1819G>A	p.Gly607Ser	p.G607S	ENST00000261799	NM_002609.3	607	Ggc/Agc	13/23	0.404976321179952	4	FACETS	0.994	0.844	1	0.497	0.422	0.579	CLONAL	1	FALSE	2	0.404976321179952	4		474	335	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0002110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	435	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.712737989853251	5	FACETS	0.937	0.899	0.975	0.937	0.899	0.975	CLONAL	3	TRUE	2	0.746047220455787	5		457	879	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350120	89350120	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	134	565	0	ENST00000301030.4:c.2830T>C	p.Ser944Pro	p.S944P	ENST00000301030	NM_001256183.1	944	Tcc/Ccc	9/13	1	2	FACETS	0.921	0.846	0.998	0.921	0.846	0.998	CLONAL	1	TRUE	1	0.746047220455787	2		565	390	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53244001	53244001	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	134	538	0	ENST00000375401.3:c.992C>A	p.Ser331Tyr	p.S331Y	ENST00000375401	NM_004187.3	331	tCt/tAt	8/26	0.746047220455787	2	FACETS	1	0.937	1	0.51	0.469	0.552	CLONAL	1	TRUE	0	0.746047220455787	2		538	352	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591857	48591857	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002898-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	287	394	0	ENST00000342988.3:c.1020G>C	p.Lys340Asn	p.K340N	ENST00000342988	NM_005359.5	340	aaG/aaC	9/12	0.822585087823371	1	FACETS	0.992	0.953	1	0.992	0.953	1	CLONAL	1	TRUE	0	0.822585087823371	1		394	414	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0002898-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	212	323	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	1	2	FACETS	0.989	0.928	1	0.989	0.928	1	CLONAL	1	TRUE	1	0.822585087823371	2		323	521	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0002898-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	379	213	0	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.822585087823371	1		213	439	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969468	44969471	+	frameshift_variant	Frame_Shift_Del	DEL	ATGC	ATGC	-	novel	NA	P-0002898-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	270	195	0	ENST00000377967.4:c.4151_4154del	p.Met1384LysfsTer8	p.M1384Kfs*8	ENST00000377967	NM_021140.2	1384	ATGCaa/aa	28/29	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.822585087823371	1		195	324	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849801	156849801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754452975	NA	P-0002898-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	802	301	1	ENST00000524377.1:c.2057G>A	p.Arg686His	p.R686H	ENST00000524377	NM_002529.3	686	cGc/cAc	16/17	0.761520028876109	3	FACETS	0.991	0.964	1	0.991	0.964	1	CLONAL	2	TRUE	1	0.822585087823371	3		302	1388	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229572	5229572	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1027605608	NA	P-0002898-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	127	97	0	ENST00000357368.4:c.2279A>T	p.Tyr760Phe	p.Y760F	ENST00000357368	NM_002850.3	760	tAc/tTc	15/38	0.205424193985251	4	FACETS	1	0.95	1	1	0.95	1	INDETERMINATE	2	TRUE	2	0.822585087823371	4		97	271	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721124	39721125	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0002898-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	244	315	0	ENST00000361337.2:c.629_630del	p.Arg210LeufsTer3	p.R210Lfs*3	ENST00000361337	NM_003286.2	209	gaGCgc/gagc	9/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.822585087823371	2		315	564	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643801	38643801	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002898-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	412	719	1	ENST00000299084.4:c.1271G>A	p.Arg424Lys	p.R424K	ENST00000299084	NM_152594.2	424	aGa/aAa	7/7	1	2	FACETS	0.99	0.945	1	0.99	0.945	1	CLONAL	1	TRUE	1	0.822585087823371	2		720	1012	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0003274-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	123	452	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.213914680156584	3	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	1	0.213914680156584	3		452	623	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0003274-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	215	729	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.213914680156584	3	FACETS	1	0.953	1	0.689	0.64	0.74	CLONAL	2	TRUE	0	0.213914680156584	3		730	1076	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0003274-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	201	624	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.213914680156584	3	FACETS	0.979	0.907	1	0.979	0.907	1	CLONAL	2	TRUE	1	0.213914680156584	3		625	1062	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986958	36986958	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003274-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	65	790	0	ENST00000354822.5:c.731A>G	p.Tyr244Cys	p.Y244C	ENST00000354822	NM_001079668.2	244	tAc/tGc	3/3	0.213914680156584	3	FACETS	0.784	0.678	0.899	0.392	0.339	0.45	SUBCLONAL	1	TRUE	1	0.213914680156584	3		790	858	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0005745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	241	835	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.676682544785401	2	FACETS	0.893	0.852	0.933	0.893	0.852	0.933	CLONAL	2	TRUE	0	0.723737979697094	2		835	373	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003746	45003746	+	start_lost	Translation_Start_Site	SNP	T	T	C	rs1057519879	NA	P-0005745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	128	456	0	ENST00000558401.1:c.2T>C	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	aTg/aCg	1/4	0.723737979697094	1	FACETS	0.735	0.677	0.795	0.735	0.677	0.795	SUBCLONAL	1	TRUE	0	0.723737979697094	1		456	307	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149683	202149683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762734568	NA	P-0005745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	123	890	0	ENST00000358485.4:c.1124C>T	p.Ser375Phe	p.S375F	ENST00000358485	NM_001080125.1	375	tCc/tTc	8/9	1	2	FACETS	0.949	0.868	1	0.949	0.868	1	CLONAL	1	TRUE	1	0.723737979697094	2		890	358	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205651	128205651	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1559987952	NA	P-0005745-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	56	751	0	ENST00000341105.2:c.224C>G	p.Ala75Gly	p.A75G	ENST00000341105	NM_032638.4	75	gCg/gGg	2/6	0.723737979697094	5	FACETS	0.823	0.708	0.949	0.274	0.236	0.317	CLONAL	1	TRUE	2	0.723737979697094	5		751	392	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0007216-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	444	571	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.639678343600955	5	FACETS	0.904	0.878	0.929	0.904	0.878	0.929	CLONAL	5	TRUE	0	0.656467419505128	5		571	594	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0007216-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	209	550	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.338649784891692	3	FACETS	1	0.99	1	0.799	0.756	0.84	INDETERMINATE	2	TRUE	0	0.656467419505128	3		552	353	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0007216-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	132	394	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	0.656467419505128	3	FACETS	0.961	0.889	1	0.961	0.889	1	CLONAL	2	TRUE	1	0.656467419505128	3		394	278	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0007216-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	53	413	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.656467419505128	3	FACETS	0.681	0.584	0.786	0.34	0.292	0.393	SUBCLONAL	1	TRUE	1	0.656467419505128	3		413	315	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0007216-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	326	378	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.656467419505128	4	FACETS	0.946	0.904	0.987			1	CLONAL	3	TRUE	NA	0.656467419505128	4		378	580	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106072	8106072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007216-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	134	540	1	ENST00000346208.3:c.892C>T	p.Arg298Trp	p.R298W	ENST00000346208		298	Cgg/Tgg	4/6	0.609985825774132	3	FACETS	0.77	0.709	0.833	0.77	0.709	0.833	SUBCLONAL	2	TRUE	1	0.656467419505128	3		541	352	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47166034	47166034	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007216-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	71	354	0	ENST00000409792.3:c.92A>C	p.Lys31Thr	p.K31T	ENST00000409792	NM_014159.6	31	aAg/aCg	3/21	0.533564923737813	3	FACETS	1	0.967	1	0.424	0.375	0.474	CLONAL	1	TRUE	0	0.656467419505128	3		354	226	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450293	50450293	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007216-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	59	531	0	ENST00000331340.3:c.477C>A	p.Asn159Lys	p.N159K	ENST00000331340	NM_006060.4	159	aaC/aaA	5/8	0.609985825774132	3	FACETS	0.871	0.757	0.994	0.436	0.378	0.497	CLONAL	1	TRUE	1	0.656467419505128	3		531	274	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602575	10602575	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007216-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	79	687	0	ENST00000171111.5:c.1003T>G	p.Phe335Val	p.F335V	ENST00000171111	NM_203500.1	335	Ttc/Gtc	3/6	0.30382428691979	2	FACETS	0.586	0.518	0.658	0.293	0.259	0.329	INDETERMINATE	1	TRUE	0	0.656467419505128	2		687	411	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939455	71939455	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007216-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	106	737	0	ENST00000298229.2:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000298229	NM_001567.3	104	Cag/Tag	3/28	0.588207384978257	4	FACETS	0.881	0.792	0.976	0.441	0.396	0.488	CLONAL	1	TRUE	2	0.656467419505128	4		737	607	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434115	121434115	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007216-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	98	635	0	ENST00000257555.6:c.1006A>C	p.Ser336Arg	p.S336R	ENST00000257555		336	Agc/Cgc	5/10	0.656467419505128	3	FACETS	0.685	0.612	0.762	0.342	0.306	0.381	SUBCLONAL	1	TRUE	1	0.656467419505128	3		635	579	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893406	32893407	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs276174825	NA	P-0007216-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	63	347	0	ENST00000380152.3:c.262_263del	p.Leu88AlafsTer12	p.L88Afs*12	ENST00000380152		87	aCT/a	3/27	0.656467419505128	6	FACETS	0.756	0.654	0.867	0.252	0.218	0.289	SUBCLONAL	1	TRUE	3	0.656467419505128	6		347	587	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78931471	78931471	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs903707218	NA	P-0007216-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	65	654	0	ENST00000306801.3:c.3418A>G	p.Ser1140Gly	p.S1140G	ENST00000306801	NM_020761.2	1140	Agc/Ggc	29/34	0.118243432619933	4	FACETS	0.599	0.519	0.684			1	INDETERMINATE	1	TRUE	NA	0.656467419505128	4		654	548	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0008978-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	59	490	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.692293699352362	5	FACETS	0.881	0.782	0.981	0.881	0.782	0.981	CLONAL	3	TRUE	2	0.731942284517616	5		490	128	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0008978-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	78	729	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.643139722070684	3	FACETS	0.961	0.896	1	0.961	0.896	1	CLONAL	3	TRUE	0	0.731942284517616	3		730	101	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976922	18976922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008978-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	10	525	0	ENST00000262803.5:c.3307G>A	p.Gly1103Arg	p.G1103R	ENST00000262803	NM_002911.3	1103	Gga/Aga	23/24	1	2	FACETS	0.38	0.261	0.523	0.38	0.261	0.523	SUBCLONAL	1	TRUE	1	0.731942284517616	2		525	72	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602340	10602340	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	187	817	2	ENST00000171111.5:c.1238G>A	p.Arg413His	p.R413H	ENST00000171111	NM_203500.1	413	cGt/cAt	3/6	0.239689924986588	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.239689924986588	2		819	701	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660508	227660508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	167	616	0	ENST00000305123.5:c.2947C>T	p.Pro983Ser	p.P983S	ENST00000305123	NM_005544.2	983	Ccc/Tcc	1/2	0.239689924986588	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.239689924986588	2		616	644	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200001	128200001	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	162	721	0	ENST00000341105.2:c.1304G>T	p.Gly435Val	p.G435V	ENST00000341105	NM_032638.4	435	gGa/gTa	6/6	0.220858007964906	5	FACETS	1	0.938	1	0.684	0.628	0.743	CLONAL	2	TRUE	2	0.239689924986588	5		721	895	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542642	187542642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	64	477	1	ENST00000441802.2:c.5098G>A	p.Glu1700Lys	p.E1700K	ENST00000441802	NM_005245.3	1700	Gaa/Aaa	10/27	0.239689924986588	2	FACETS	0.75	0.653	0.854	0.75	0.653	0.854	SUBCLONAL	2	TRUE	0	0.239689924986588	2		478	356	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679544	86679544	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	30	504	0	ENST00000274376.6:c.2705T>C	p.Leu902Pro	p.L902P	ENST00000274376	NM_002890.2	902	cTt/cCt	21/25	0.239689924986588	2	FACETS	1	0.849	1	0.528	0.428	0.641	CLONAL	1	TRUE	0	0.239689924986588	2		504	237	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020734	26020734	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	53	314	0	ENST00000357647.3:c.17A>T	p.Gln6Leu	p.Q6L	ENST00000357647	NM_003529.2	6	cAa/cTa	1/1	0.239689924986588	5	FACETS	1	0.96	1	0.464	0.396	0.538	CLONAL	1	TRUE	2	0.239689924986588	5		314	432	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485234	8485234	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	65	519	0	ENST00000356435.5:c.3146C>A	p.Pro1049His	p.P1049H	ENST00000356435		1049	cCt/cAt	18/35	0.239689924986588	2	FACETS	0.842	0.735	0.956	0.842	0.735	0.956	CLONAL	2	TRUE	0	0.239689924986588	2		519	322	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514499	103514499	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	37	343	0	ENST00000355739.4:c.1000G>T	p.Glu334Ter	p.E334*	ENST00000355739	NM_000123.3	334	Gag/Tag	8/15	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.239689924986588	2		343	291	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103520541	103520541	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs772219063	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	25	392	0	ENST00000355739.4:c.2612G>T	p.Cys871Phe	p.C871F	ENST00000355739	NM_000123.3	871	tGt/tTt	12/15	1	2	FACETS	0.793	0.627	0.983	0.793	0.627	0.983	CLONAL	1	TRUE	1	0.239689924986588	2		392	263	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225398	2225398	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	197	692	0	ENST00000326181.6:c.1483G>T	p.Gly495Cys	p.G495C	ENST00000326181	NM_032271.2	495	Ggc/Tgc	16/21	0.239689924986588	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.239689924986588	2		692	689	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576853	7576853	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs11575996	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	202	609	0	ENST00000269305.4:c.993G>T	p.Gln331His	p.Q331H	ENST00000269305	NM_001126112.2	331	caG/caT	9/11	0.239689924986588	4	FACETS	1	0.979	1	0.843	0.785	0.901	CLONAL	3	TRUE	0	0.239689924986588	4		609	620	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121151	11121151	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	177	836	0	ENST00000358026.2:c.2218G>T	p.Glu740Ter	p.E740*	ENST00000358026	NM_001128849.1	740	Gag/Tag	15/36	0.239689924986588	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.239689924986588	2		836	711	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909559	50909559	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	89	652	0	ENST00000440232.2:c.1363G>T	p.Val455Leu	p.V455L	ENST00000440232	NM_002691.3	455	Gtg/Ttg	11/27	0.239689924986588	4	FACETS	1	0.954	1	0.288	0.255	0.323	CLONAL	1	TRUE	0	0.239689924986588	4		652	800	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739036	40739036	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	147	650	0	ENST00000373198.4:c.3248G>C	p.Gly1083Ala	p.G1083A	ENST00000373198	NM_133170.3	1083	gGc/gCc	24/32	0.239689924986588	5	FACETS	1	0.96	1	0.724	0.661	0.789	CLONAL	2	TRUE	2	0.239689924986588	5		650	768	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295810	212295810	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	51	536	0	ENST00000342788.4:c.2503del	p.Glu835LysfsTer16	p.E835Kfs*16	ENST00000342788	NM_005235.2	835	Gaa/aa	21/28	0.239689924986588	2	FACETS	1	0.955	1	0.663	0.566	0.768	CLONAL	1	TRUE	0	0.239689924986588	2		536	321	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457192	25457192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771922296	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	140	768	1	ENST00000264709.3:c.2695C>T	p.Arg899Cys	p.R899C	ENST00000264709	NM_175629.2	899	Cgc/Tgc	23/23	0.220858007964906	5	FACETS	0.999	0.91	1	0.666	0.607	0.728	CLONAL	2	TRUE	2	0.239689924986588	5		769	795	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971099	21971099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749714198	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	68	545	0	ENST00000304494.5:c.259C>T	p.Arg87Trp	p.R87W	ENST00000304494	NM_000077.4	87	Cgg/Tgg	2/3	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.239689924986588	2		545	462	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223028	41223029	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	241	705	1	ENST00000357654.3:c.4902_4903delinsTT	p.Arg1634_Glu1635delinsSerTer	p.R1634_E1635delinsS*	ENST00000357654	NM_007294.3	1634	agGGag/agTTag	15/23	0.239689924986588	7	FACETS	1	0.982	1	0.681	0.636	0.726	CLONAL	3	TRUE	2	0.239689924986588	7		706	945	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821382	72821382	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs774585182	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	33	535	0	ENST00000268489.5:c.10793del	p.Pro3598LeufsTer96	p.P3598Lfs*96	ENST00000268489	NM_006885.3	3598	cCt/ct	10/10	0.220858007964906	5	FACETS	0.666	0.541	0.807	0.222	0.18	0.269	SUBCLONAL	1	TRUE	2	0.239689924986588	5		535	562	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969933	161969933	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	66	616	0	ENST00000366898.1:c.1036G>T	p.Asp346Tyr	p.D346Y	ENST00000366898	NM_004562.2	346	Gac/Tac	9/12	0.126611495946076	5	FACETS	1	0.962	1	0.438	0.38	0.5	INDETERMINATE	1	TRUE	2	0.239689924986588	5		616	570	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324079	123324079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780458049	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	50	541	0	ENST00000358487.5:c.391G>A	p.Gly131Arg	p.G131R	ENST00000358487	NM_000141.4	131	Gga/Aga	4/18	1	2	FACETS	0.891	0.757	1	0.891	0.757	1	CLONAL	1	TRUE	1	0.239689924986588	2		541	468	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256282	16256282	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	67	620	3	ENST00000375759.3:c.3547G>T	p.Glu1183Ter	p.E1183*	ENST00000375759	NM_015001.2	1183	Gaa/Taa	11/15	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.239689924986588	2		623	501	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456819	32456819	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	100	607	0	ENST00000332351.3:c.73C>A	p.Leu25Ile	p.L25I	ENST00000332351	NM_024426.4	25	Cta/Ata	1/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.239689924986588	2		607	582	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443490	49443490	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	129	612	0	ENST00000301067.7:c.3881C>A	p.Ser1294Tyr	p.S1294Y	ENST00000301067	NM_003482.3	1294	tCc/tAc	11/54	0.239689924986588	5	FACETS	0.996	0.904	1	0.398	0.361	0.437	CLONAL	2	TRUE	0	0.239689924986588	5		612	735	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28624324	28624324	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	31	580	0	ENST00000241453.7:c.650A>C	p.Glu217Ala	p.E217A	ENST00000241453	NM_004119.2	217	gAg/gCg	6/24	1	2	FACETS	0.695	0.563	0.845	0.695	0.563	0.845	SUBCLONAL	1	TRUE	1	0.239689924986588	2		580	372	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270046	198270046	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	36	475	0	ENST00000335508.6:c.1390C>G	p.Leu464Val	p.L464V	ENST00000335508	NM_012433.2	464	Ctt/Gtt	10/25	0.239689924986588	2	FACETS	0.936	0.772	1	0.468	0.386	0.56	CLONAL	1	TRUE	0	0.239689924986588	2		475	321	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101110	41101110	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	164	706	0	ENST00000373198.4:c.1246C>G	p.Arg416Gly	p.R416G	ENST00000373198	NM_133170.3	416	Cgc/Ggc	8/32	0.239689924986588	5	FACETS	1	0.958	1	0.712	0.654	0.773	CLONAL	2	TRUE	2	0.239689924986588	5		706	871	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911285	29911285	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	27	462	0	ENST00000376809.5:c.584A>T	p.Tyr195Phe	p.Y195F	ENST00000376809	NM_002116.7	195	tAc/tTc	3/8	0.126611495946076	5	FACETS	0.659	0.523	0.814	0.22	0.174	0.272	INDETERMINATE	1	TRUE	2	0.239689924986588	5		462	465	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846425	128846425	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	139	509	0	ENST00000249373.3:c.1261C>G	p.Arg421Gly	p.R421G	ENST00000249373	NM_005631.4	421	Cga/Gga	6/12	0.239689924986588	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.239689924986588	3		509	615	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778786	76778786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	35	630	0	ENST00000373344.5:c.6793G>A	p.Glu2265Lys	p.E2265K	ENST00000373344	NM_000489.3	2265	Gag/Aag	31/35	0.239689924986588	3	FACETS	1	0.944	1	0.705	0.582	0.841	CLONAL	1	TRUE	1	0.239689924986588	3		630	232	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855265	76855266	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	18	429	1	ENST00000373344.5:c.5721_5722delinsTA	p.Met1907_Asp1908delinsIleAsn	p.M1907_D1908delinsIN	ENST00000373344	NM_000489.3	1907	atGGat/atTAat	24/35	0.239689924986588	3	FACETS	0.945	0.715	1	0.472	0.357	0.607	CLONAL	1	TRUE	1	0.239689924986588	3		430	178	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938268	76938268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs897147546	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	73	674	0	ENST00000373344.5:c.2480G>A	p.Ser827Asn	p.S827N	ENST00000373344	NM_000489.3	827	aGc/aAc	9/35	0.239689924986588	3	FACETS	0.983	0.866	1	0.983	0.866	1	CLONAL	2	TRUE	1	0.239689924986588	3		674	347	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939457	76939457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	85	678	0	ENST00000373344.5:c.1291G>A	p.Glu431Lys	p.E431K	ENST00000373344	NM_000489.3	431	Gag/Aag	9/35	0.239689924986588	3	FACETS	0.85	0.755	0.952	0.85	0.755	0.952	CLONAL	2	TRUE	1	0.239689924986588	3		678	467	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046409	69046410	+	frameshift_variant	Frame_Shift_Ins	INS	GG	GG	AGA	novel	NA	P-0009110-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	101	720	0	ENST00000288368.4:c.3882_3883delinsAGA	p.Asn1296LysfsTer2	p.N1296Kfs*2	ENST00000288368	NM_024870.2	1294	aaGGaa/aaAGAaa	32/40	0.19223427022714	2	FACETS	1	0.98	1	0.718	0.643	0.797	CLONAL	1	TRUE	0	0.239689924986588	2		720	587	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	174	290	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.857	0.797	0.918	0.857	0.797	0.918	CLONAL	1	TRUE	1	0.894309233361407	2		291	454	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78435700	78435700	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	121	213	0	ENST00000370768.2:c.121-1G>C		p.X41_splice	ENST00000370768	NM_003902.3	41			0.894309233361407	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.894309233361407	1		213	135	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666659	206666659	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	484	658	0	ENST00000367120.3:c.1993C>T	p.Pro665Ser	p.P665S	ENST00000367120	NM_014002.3	665	Ccg/Tcg	20/22	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.894309233361407	2		658	1063	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63662119	63662119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766556983	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	254	462	0	ENST00000279873.7:c.223C>T	p.Leu75Phe	p.L75F	ENST00000279873	NM_032199.2	75	Ctt/Ttt	2/10	1	2	FACETS	0.922	0.87	0.975	0.922	0.87	0.975	CLONAL	1	TRUE	1	0.894309233361407	2		462	616	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446252	70446252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	389	490	0	ENST00000373644.4:c.5192C>T	p.Ser1731Phe	p.S1731F	ENST00000373644	NM_030625.2	1731	tCt/tTt	11/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.894309233361407	2		490	851	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573780	64573780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	493	752	0	ENST00000312049.6:c.973G>A	p.Ala325Thr	p.A325T	ENST00000312049	NM_130799.2	325	Gct/Act	7/10	1	2	FACETS	0.98	0.941	1	0.98	0.941	1	CLONAL	1	TRUE	1	0.894309233361407	2		752	1125	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102196287	102196287	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	112	283	0	ENST00000263464.3:c.944G>A	p.Trp315Ter	p.W315*	ENST00000263464	NM_001165.4	315	tGg/tAg	3/9	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.894309233361407	2		283	249	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156220	119156220	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	300	477	0	ENST00000264033.4:c.1885G>A	p.Glu629Lys	p.E629K	ENST00000264033	NM_005188.3	629	Gag/Aag	11/16	1	2	FACETS	0.876	0.829	0.923	0.876	0.829	0.923	CLONAL	1	TRUE	1	0.894309233361407	2		477	766	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444309	49444309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	447	900	1	ENST00000301067.7:c.3062C>T	p.Pro1021Leu	p.P1021L	ENST00000301067	NM_003482.3	1021	cCt/cTt	11/54	1	2	FACETS	0.865	0.827	0.903	0.865	0.827	0.903	CLONAL	1	TRUE	1	0.894309233361407	2		901	1156	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447898	49447898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	408	575	0	ENST00000301067.7:c.536G>A	p.Gly179Asp	p.G179D	ENST00000301067	NM_003482.3	179	gGt/gAt	5/54	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.894309233361407	2		575	868	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118814	115118814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	348	474	0	ENST00000257566.3:c.527C>T	p.Ala176Val	p.A176V	ENST00000257566	NM_016569.3	176	gCc/gTc	2/8	1	2	FACETS	0.988	0.941	1	0.988	0.941	1	CLONAL	1	TRUE	1	0.894309233361407	2		474	788	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133697	41133697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554193370	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	263	397	0	ENST00000379561.5:c.1931G>A	p.Ser644Asn	p.S644N	ENST00000379561	NM_002015.3	644	aGt/aAt	2/3	1	2	FACETS	0.941	0.889	0.994	0.941	0.889	0.994	CLONAL	1	TRUE	1	0.894309233361407	2		397	625	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134939	41134939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	212	327	0	ENST00000379561.5:c.689G>A	p.Gly230Glu	p.G230E	ENST00000379561	NM_002015.3	230	gGa/gAa	2/3	1	2	FACETS	0.996	0.936	1	0.996	0.936	1	CLONAL	1	TRUE	1	0.894309233361407	2		327	476	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436288	110436288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1006865204	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	156	310	0	ENST00000375856.3:c.2113G>A	p.Ala705Thr	p.A705T	ENST00000375856	NM_003749.2	705	Gcg/Acg	1/2	0.511077109402515	1	FACETS	0.454	0.42	0.489	0.454	0.42	0.489	INDETERMINATE	1	TRUE	0	0.894309233361407	1		310	425	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436923	110436923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	191	515	1	ENST00000375856.3:c.1478G>A	p.Ser493Asn	p.S493N	ENST00000375856	NM_003749.2	493	aGc/aAc	1/2	0.511077109402515	1	FACETS	0.371	0.344	0.398	0.371	0.344	0.398	INDETERMINATE	1	TRUE	0	0.894309233361407	1		516	637	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042050	42042050	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	265	508	1	ENST00000219905.7:c.6245C>T	p.Ala2082Val	p.A2082V	ENST00000219905	NM_001164273.1	2082	gCt/gTt	17/24	0.894309233361407	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.894309233361407	1		509	327	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712548	43712548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	478	646	0	ENST00000382044.4:c.4636G>A	p.Asp1546Asn	p.D1546N	ENST00000382044	NM_001141980.1	1546	Gac/Aac	21/28	0.894309233361407	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.894309233361407	1		646	571	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632686	3632686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776382556	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	441	682	0	ENST00000294008.3:c.5162C>T	p.Ser1721Phe	p.S1721F	ENST00000294008	NM_032444.2	1721	tCc/tTc	15/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.894309233361407	2		682	935	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831220	3831220	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1168098333	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	215	410	0	ENST00000262367.5:c.1661C>T	p.Ser554Phe	p.S554F	ENST00000262367	NM_004380.2	554	tCc/tTc	7/31	1	2	FACETS	0.932	0.875	0.99	0.932	0.875	0.99	CLONAL	1	TRUE	1	0.894309233361407	2		410	516	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830139	72830139	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	413	662	0	ENST00000268489.5:c.6442C>T	p.Pro2148Ser	p.P2148S	ENST00000268489	NM_006885.3	2148	Cct/Tct	9/10	1	2	FACETS	0.967	0.925	1	0.967	0.925	1	CLONAL	1	TRUE	1	0.894309233361407	2		662	955	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	428	1082	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	1	2	FACETS	0.93	0.889	0.971	0.93	0.889	0.971	CLONAL	1	TRUE	1	0.894309233361407	2		1082	1029	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028672	12028672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	197	430	1	ENST00000353533.5:c.875G>A	p.Ser292Asn	p.S292N	ENST00000353533	NM_003010.3	292	aGt/aAt	8/11	1	2	FACETS	0.798	0.744	0.853	0.798	0.744	0.853	SUBCLONAL	1	TRUE	1	0.894309233361407	2		431	552	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681140	37681140	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	183	502	0	ENST00000447079.4:c.3307+2T>A		p.X1103_splice	ENST00000447079	NM_015083.1	1103			1	2	FACETS	0.462	0.427	0.499	0.462	0.427	0.499	SUBCLONAL	1	TRUE	1	0.894309233361407	2		502	885	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40364015	40364015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	490	685	0	ENST00000293328.3:c.1667C>T	p.Ser556Phe	p.S556F	ENST00000293328	NM_012448.3	556	tCc/tTc	13/19	1	2	FACETS	0.917	0.879	0.955	0.917	0.879	0.955	CLONAL	1	TRUE	1	0.894309233361407	2		685	1195	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370301	40370301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	533	820	0	ENST00000293328.3:c.1037C>T	p.Thr346Ile	p.T346I	ENST00000293328	NM_012448.3	346	aCc/aTc	9/19	1	2	FACETS	0.949	0.912	0.986	0.949	0.912	0.986	CLONAL	1	TRUE	1	0.894309233361407	2		820	1256	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59934440	59934440	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	179	401	0	ENST00000259008.2:c.358G>A	p.Gly120Ser	p.G120S	ENST00000259008	NM_032043.2	120	Ggc/Agc	4/20	1	2	FACETS	0.944	0.881	1	0.944	0.881	1	CLONAL	1	TRUE	1	0.894309233361407	2		401	424	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866583	78866583	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	442	632	0	ENST00000306801.3:c.2156C>T	p.Ser719Phe	p.S719F	ENST00000306801	NM_020761.2	719	tCt/tTt	19/34	1	2	FACETS	0.946	0.905	0.987	0.946	0.905	0.987	CLONAL	1	TRUE	1	0.894309233361407	2		632	1045	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619322	1619322	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	478	738	0	ENST00000344749.5:c.1319C>T	p.Ala440Val	p.A440V	ENST00000344749	NM_001136139.2	440	gCa/gTa	15/19	1	2	FACETS	0.963	0.924	1	0.963	0.924	1	CLONAL	1	TRUE	1	0.894309233361407	2		738	1110	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792591	33792591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs957444896	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1	33	7	0	ENST00000498907.2:c.730G>A	p.Ala244Thr	p.A244T	ENST00000498907	NM_004364.3	244	Gcc/Acc	1/1	0.894309233361407	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.894309233361407	1		7	34	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791757	42791757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568504941	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	499	697	3	ENST00000575354.2:c.643C>T	p.Arg215Trp	p.R215W	ENST00000575354	NM_015125.3	215	Cgg/Tgg	5/20	0.894309233361407	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.894309233361407	1		700	579	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086157	16086157	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	407	500	2	ENST00000281043.3:c.1333G>A	p.Glu445Lys	p.E445K	ENST00000281043	NM_005378.4	445	Gaa/Aaa	3/3	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.894309233361407	2		502	900	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505510	25505510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	464	688	1	ENST00000264709.3:c.248G>A	p.Gly83Asp	p.G83D	ENST00000264709	NM_175629.2	83	gGc/gAc	4/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.894309233361407	2		689	1021	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551237	29551237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553411110	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	412	695	0	ENST00000389048.3:c.1393G>A	p.Glu465Lys	p.E465K	ENST00000389048	NM_004304.4	465	Gaa/Aaa	6/29	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.894309233361407	2		695	899	SUCCESS
REL	5966	MSKCC	GRCh37	2	61148948	61148948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	205	353	0	ENST00000295025.8:c.1138G>A	p.Val380Ile	p.V380I	ENST00000295025	NM_002908.2	380	Gtt/Att	11/11	1	2	FACETS	0.892	0.835	0.95	0.892	0.835	0.95	CLONAL	1	TRUE	1	0.894309233361407	2		353	514	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170780	99170780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	312	583	0	ENST00000074304.5:c.1409C>T	p.Ser470Phe	p.S470F	ENST00000074304	NM_001134224.1	470	tCc/tTc	16/26	1	2	FACETS	0.927	0.879	0.975	0.927	0.879	0.975	CLONAL	1	TRUE	1	0.894309233361407	2		583	753	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	151	269	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.933	0.865	1	0.933	0.865	1	CLONAL	1	TRUE	1	0.894309233361407	2		269	362	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285335	212285335	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs757867095	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	94	324	0	ENST00000342788.4:c.2966G>A	p.Gly989Asp	p.G989D	ENST00000342788	NM_005235.2	989	gGt/gAt	25/28	1	2	FACETS	0.88	0.797	0.964	0.88	0.797	0.964	CLONAL	1	TRUE	1	0.894309233361407	2		324	239	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660766	227660766	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1054357901	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	361	778	0	ENST00000305123.5:c.2689G>A	p.Val897Ile	p.V897I	ENST00000305123	NM_005544.2	897	Gtc/Atc	1/2	1	2	FACETS	0.922	0.878	0.966	0.922	0.878	0.966	CLONAL	1	TRUE	1	0.894309233361407	2		778	876	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663270	227663270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	364	652	1	ENST00000305123.5:c.185G>A	p.Arg62His	p.R62H	ENST00000305123	NM_005544.2	62	cGc/cAc	1/2	1	2	FACETS	0.893	0.85	0.936	0.893	0.85	0.936	CLONAL	1	TRUE	1	0.894309233361407	2		653	912	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024432	31024432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769761920	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	419	617	3	ENST00000375687.4:c.3917G>A	p.Gly1306Asp	p.G1306D	ENST00000375687	NM_015338.5	1306	gGc/gAc	13/13	1	2	FACETS	0.962	0.92	1	0.962	0.92	1	CLONAL	1	TRUE	1	0.894309233361407	2		620	974	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394037	31394037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	266	334	1	ENST00000328111.2:c.2324C>T	p.Thr775Ile	p.T775I	ENST00000328111	NM_006892.3	775	aCc/aTc	22/23	1	2	FACETS	0.985	0.931	1	0.985	0.931	1	CLONAL	1	TRUE	1	0.894309233361407	2		335	604	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42870077	42870077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	386	582	3	ENST00000398585.3:c.95C>T	p.Ala32Val	p.A32V	ENST00000398585	NM_001135099.1	32	gCt/gTt	2/14	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.894309233361407	2		585	856	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000087	30000087	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	357	629	0	ENST00000338641.4:c.100G>A	p.Glu34Lys	p.E34K	ENST00000338641	NM_000268.3	34	Gag/Aag	1/16	1	2	FACETS	0.905	0.861	0.949	0.905	0.861	0.949	CLONAL	1	TRUE	1	0.894309233361407	2		629	882	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566478	41566478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	263	425	0	ENST00000263253.7:c.4355C>T	p.Pro1452Leu	p.P1452L	ENST00000263253	NM_001429.3	1452	cCt/cTt	27/31	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.894309233361407	2		425	570	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568665	41568665	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	109	293	0	ENST00000263253.7:c.4615G>A	p.Asp1539Asn	p.D1539N	ENST00000263253	NM_001429.3	1539	Gat/Aat	28/31	1	2	FACETS	0.841	0.766	0.917	0.841	0.766	0.917	CLONAL	1	TRUE	1	0.894309233361407	2		293	290	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573213	41573213	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	535	806	0	ENST00000263253.7:c.5499del	p.Ser1834AlafsTer72	p.S1834Afs*72	ENST00000263253	NM_001429.3	1833	gCc/gc	31/31	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.894309233361407	2		806	1069	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183697	10183697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1421828060	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	392	728	0	ENST00000256474.2:c.166G>A	p.Ala56Thr	p.A56T	ENST00000256474	NM_000551.3	56	Gcc/Acc	1/3	NA	2	FACETS	0.916	0.874	0.959			1	INDETERMINATE	1	TRUE	NA	0.894309233361407	2		728	957	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119666196	119666196	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	15	301	0	ENST00000316626.5:c.285T>A	p.Asn95Lys	p.N95K	ENST00000316626		95	aaT/aaA	3/12	0.511077109402515	1	FACETS	0.083	0.06	0.11	0.083	0.06	0.11	INDETERMINATE	1	TRUE	0	0.894309233361407	1		301	224	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204603	128204603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	275	717	0	ENST00000341105.2:c.838C>T	p.Pro280Ser	p.P280S	ENST00000341105	NM_032638.4	280	Cct/Tct	3/6	0.511077109402515	1	FACETS	0.408	0.384	0.432	0.408	0.384	0.432	INDETERMINATE	1	TRUE	0	0.894309233361407	1		717	834	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920463	134920463	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	406	588	0	ENST00000398015.3:c.2278G>A	p.Val760Met	p.V760M	ENST00000398015	NM_004441.4	760	Gtg/Atg	12/16	0.511077109402515	1	FACETS	0.656	0.629	0.683	0.656	0.629	0.683	INDETERMINATE	1	TRUE	0	0.894309233361407	1		588	765	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967197	134967197	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	188	483	0	ENST00000398015.3:c.2536C>T	p.Pro846Ser	p.P846S	ENST00000398015	NM_004441.4	846	Ccc/Tcc	14/16	0.511077109402515	1	FACETS	0.359	0.333	0.386	0.359	0.333	0.386	INDETERMINATE	1	TRUE	0	0.894309233361407	1		483	648	SUCCESS
ATR	545	MSKCC	GRCh37	3	142218523	142218523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	173	431	0	ENST00000350721.4:c.5326G>A	p.Glu1776Lys	p.E1776K	ENST00000350721	NM_001184.3	1776	Gaa/Aaa	31/47	0.511077109402515	1	FACETS	0.381	0.352	0.41	0.381	0.352	0.41	INDETERMINATE	1	TRUE	0	0.894309233361407	1		431	562	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149290717	149290717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755578307	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	210	517	0	ENST00000360632.3:c.502C>T	p.Leu168Phe	p.L168F	ENST00000360632	NM_015472.4	168	Ctc/Ttc	3/7	0.511077109402515	1	FACETS	0.339	0.316	0.364	0.339	0.316	0.364	INDETERMINATE	1	TRUE	0	0.894309233361407	1		517	765	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	67	380	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	0.511077109402515	1	FACETS	0.345	0.304	0.389	0.345	0.304	0.389	INDETERMINATE	1	TRUE	0	0.894309233361407	1		380	240	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139792	55139792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1354231704	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	362	562	0	ENST00000257290.5:c.1453G>A	p.Glu485Lys	p.E485K	ENST00000257290	NM_006206.4	485	Gag/Aag	10/23	1	2	FACETS	0.9	0.856	0.943	0.9	0.856	0.943	CLONAL	1	TRUE	1	0.894309233361407	2		562	900	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139819	55139819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	375	551	0	ENST00000257290.5:c.1480G>A	p.Glu494Lys	p.E494K	ENST00000257290	NM_006206.4	494	Gag/Aag	10/23	1	2	FACETS	0.926	0.882	0.969	0.926	0.882	0.969	CLONAL	1	TRUE	1	0.894309233361407	2		551	906	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217316	66217316	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	125	235	0	ENST00000273854.3:c.2299A>G	p.Lys767Glu	p.K767E	ENST00000273854	NM_004439.5	767	Aaa/Gaa	14/18	1	2	FACETS	0.951	0.875	1	0.951	0.875	1	CLONAL	1	TRUE	1	0.894309233361407	2		235	294	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247330	153247330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	191	344	0	ENST00000281708.4:c.1472G>A	p.Gly491Asp	p.G491D	ENST00000281708	NM_033632.3	491	gGc/gAc	10/12	1	2	FACETS	0.844	0.787	0.902	0.844	0.787	0.902	CLONAL	1	TRUE	1	0.894309233361407	2		344	506	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554837	187554837	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs780613153	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	214	339	0	ENST00000441802.2:c.4323+1G>A		p.X1441_splice	ENST00000441802	NM_005245.3	1441			1	2	FACETS	0.965	0.906	1	0.965	0.906	1	CLONAL	1	TRUE	1	0.894309233361407	2		339	496	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460534	149460534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1331779557	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	425	707	0	ENST00000286301.3:c.103G>A	p.Gly35Arg	p.G35R	ENST00000286301	NM_005211.3	35	Gga/Aga	3/22	1	2	FACETS	0.933	0.892	0.974	0.933	0.892	0.974	CLONAL	1	TRUE	1	0.894309233361407	2		707	1019	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562763	176562763	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	357	533	1	ENST00000439151.2:c.659G>A	p.Gly220Asp	p.G220D	ENST00000439151	NM_022455.4	220	gGt/gAt	2/23	1	2	FACETS	0.925	0.881	0.97	0.925	0.881	0.97	CLONAL	1	TRUE	1	0.894309233361407	2		534	863	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638491	176638491	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784096	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	182	586	0	ENST00000439151.2:c.3091C>T	p.Arg1031Ter	p.R1031*	ENST00000439151	NM_022455.4	1031	Cga/Tga	5/23	1	2	FACETS	0.396	0.364	0.428	0.396	0.364	0.428	SUBCLONAL	1	TRUE	1	0.894309233361407	2		586	1029	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176671224	176671224	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	180	404	1	ENST00000439151.2:c.4331G>A	p.Gly1444Asp	p.G1444D	ENST00000439151	NM_022455.4	1444	gGc/gAc	9/23	1	2	FACETS	0.877	0.817	0.938	0.877	0.817	0.938	CLONAL	1	TRUE	1	0.894309233361407	2		405	459	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180050962	180050962	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	454	782	0	ENST00000261937.6:c.1521G>A	p.Trp507Ter	p.W507*	ENST00000261937	NM_182925.4	507	tgG/tgA	11/30	1	2	FACETS	0.955	0.915	0.996	0.955	0.915	0.996	CLONAL	1	TRUE	1	0.894309233361407	2		782	1063	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056754	180056754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	536	791	0	ENST00000261937.6:c.758C>T	p.Thr253Ile	p.T253I	ENST00000261937	NM_182925.4	253	aCc/aTc	6/30	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.894309233361407	2		791	1191	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056540	26056541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs35716118	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	85	352	0	ENST00000343677.2:c.116dup	p.Val40GlyfsTer13	p.V40Gfs*13	ENST00000343677	NM_005319.3	39	ccg/ccCg	1/1	1	2	FACETS	0.392	0.347	0.439	0.392	0.347	0.439	SUBCLONAL	1	TRUE	1	0.894309233361407	2		352	485	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839775	27839775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	351	739	0	ENST00000328488.2:c.319G>A	p.Asp107Asn	p.D107N	ENST00000328488	NM_003533.2	107	Gat/Aat	1/1	1	2	FACETS	0.809	0.768	0.851	0.809	0.768	0.851	CLONAL	1	TRUE	1	0.894309233361407	2		739	970	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910738	29910738	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	398	963	1	ENST00000376809.5:c.278C>T	p.Ala93Val	p.A93V	ENST00000376809	NM_002116.7	93	gCc/gTc	2/8	1	2	FACETS	0.761	0.725	0.799	0.761	0.725	0.799	SUBCLONAL	1	TRUE	1	0.894309233361407	2		964	1169	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30676006	30676006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	406	618	0	ENST00000376406.3:c.2350G>A	p.Ala784Thr	p.A784T	ENST00000376406	NM_014641.2	784	Gca/Aca	8/15	1	2	FACETS	0.996	0.952	1	0.996	0.952	1	CLONAL	1	TRUE	1	0.894309233361407	2		618	912	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169200	32169200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	422	861	0	ENST00000375023.3:c.3833G>A	p.Gly1278Asp	p.G1278D	ENST00000375023	NM_004557.3	1278	gGc/gAc	22/30	1	2	FACETS	0.908	0.868	0.949	0.908	0.868	0.949	CLONAL	1	TRUE	1	0.894309233361407	2		861	1039	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715426	117715426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	157	428	0	ENST00000368508.3:c.1063G>A	p.Asp355Asn	p.D355N	ENST00000368508	NM_002944.2	355	Gat/Aat	10/43	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.894309233361407	2		428	351	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997502	149997502	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	171	348	0	ENST00000253339.5:c.2777G>A	p.Gly926Glu	p.G926E	ENST00000253339		926	gGa/gAa	6/7	1	2	FACETS	0.951	0.886	1	0.951	0.886	1	CLONAL	1	TRUE	1	0.894309233361407	2		348	402	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729723	41729723	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779220866	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	369	508	0	ENST00000242208.4:c.806G>A	p.Gly269Glu	p.G269E	ENST00000242208	NM_002192.2	269	gGg/gAg	3/3	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.894309233361407	2		508	797	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346574	81346574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	224	405	0	ENST00000222390.5:c.1379C>T	p.Pro460Leu	p.P460L	ENST00000222390	NM_000601.4	460	cCt/cTt	11/18	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.894309233361407	2		405	472	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508373	106508373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	264	498	0	ENST00000359195.3:c.367C>T	p.Arg123Cys	p.R123C	ENST00000359195	NM_002649.2	123	Cgc/Tgc	2/11	1	2	FACETS	0.984	0.93	1	0.984	0.93	1	CLONAL	1	TRUE	1	0.894309233361407	2		498	600	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403308	116403308	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	203	461	1	ENST00000397752.3:c.2569G>A	p.Val857Ile	p.V857I	ENST00000397752	NM_000245.2	857	Gta/Ata	11/21	1	2	FACETS	0.956	0.896	1	0.956	0.896	1	CLONAL	1	TRUE	1	0.894309233361407	2		462	475	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151164261	151164261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178576070	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	251	317	0	ENST00000262187.5:c.499G>A	p.Ala167Thr	p.A167T	ENST00000262187	NM_005614.3	167	Gca/Aca	8/8	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.894309233361407	2		317	553	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56854494	56854494	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	232	509	0	ENST00000519728.1:c.76A>G	p.Asn26Asp	p.N26D	ENST00000519728	NM_002350.3	26	Aat/Gat	2/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.894309233361407	2		509	502	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972936	68972936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	203	460	0	ENST00000288368.4:c.1261G>A	p.Glu421Lys	p.E421K	ENST00000288368	NM_024870.2	421	Gaa/Aaa	11/40	1	2	FACETS	0.858	0.803	0.915	0.858	0.803	0.915	CLONAL	1	TRUE	1	0.894309233361407	2		460	529	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750621	128750621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	397	626	1	ENST00000377970.2:c.158G>A	p.Ser53Asn	p.S53N	ENST00000377970	NM_002467.4	53	aGc/aAc	2/3	1	2	FACETS	0.977	0.933	1	0.977	0.933	1	CLONAL	1	TRUE	1	0.894309233361407	2		627	909	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127951937	127951937	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1215936071	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	414	690	1	ENST00000373547.4:c.61G>A	p.Glu21Lys	p.E21K	ENST00000373547	NM_002721.4	21	Gag/Aag	1/7	1	2	FACETS	0.999	0.955	1	0.999	0.955	1	CLONAL	1	TRUE	1	0.894309233361407	2		691	927	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409988	139409988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1442661141	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	548	929	0	ENST00000277541.6:c.1850C>T	p.Thr617Ile	p.T617I	ENST00000277541	NM_017617.3	617	aCc/aTc	11/34	1	2	FACETS	0.944	0.908	0.981	0.944	0.908	0.981	CLONAL	1	TRUE	1	0.894309233361407	2		929	1298	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649691	48649691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	541	394	2	ENST00000376670.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000376670	NM_002049.3	59	Gca/Aca	2/6	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.894309233361407	1		396	610	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225950	53225950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	544	444	0	ENST00000375401.3:c.2899G>A	p.Asp967Asn	p.D967N	ENST00000375401	NM_004187.3	967	Gat/Aat	19/26	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.894309233361407	1		444	596	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361214	70361214	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	222	370	0	ENST00000374080.3:c.6402G>T	p.Gln2134His	p.Q2134H	ENST00000374080		2134	caG/caT	43/45	1	1	FACETS	0.511	0.48	0.543	0.511	0.48	0.543	SUBCLONAL	1	TRUE	0	0.894309233361407	1		370	537	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0012428-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	377	718	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.494809500664402	3	FACETS	0.982	0.935	1	0.982	0.935	1	CLONAL	2	TRUE	1	0.494809500664402	3		718	968	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0012428-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	316	726	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.494809500664402	3	FACETS	0.839	0.794	0.886	0.839	0.794	0.886	CLONAL	2	TRUE	1	0.494809500664402	3		726	949	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579315	7579315	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1555526478	NA	P-0012428-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	240	671	0	ENST00000269305.4:c.372C>A	p.Cys124Ter	p.C124*	ENST00000269305	NM_001126112.2	124	tgC/tgA	4/11	0.477293031174377	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.494809500664402	1		671	637	SUCCESS
MET	4233	MSKCC	GRCh37	7	116414961	116414961	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012428-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	297	717	1	ENST00000397752.3:c.3055G>T	p.Gly1019Cys	p.G1019C	ENST00000397752	NM_000245.2	1019	Ggt/Tgt	15/21	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.494809500664402	2		718	1009	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56798136	56798136	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012428-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	188	351	0	ENST00000337432.4:c.867G>C	p.Lys289Asn	p.K289N	ENST00000337432	NM_058216.2	289	aaG/aaC	6/9	0.387174348666532	3	FACETS	0.757	0.703	0.813	0.757	0.703	0.813	SUBCLONAL	2	TRUE	1	0.494809500664402	3		351	626	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176469	123176469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012428-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	22	261	0	ENST00000218089.9:c.436C>T	p.Arg146Ter	p.R146*	ENST00000218089	NM_001042749.1	146	Cga/Tga	7/35	1	2	FACETS	0.22	0.17	0.278	0.22	0.17	0.278	SUBCLONAL	1	TRUE	1	0.494809500664402	2		261	405	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346975	89346975	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	120	663	0	ENST00000301030.4:c.5975A>G	p.Lys1992Arg	p.K1992R	ENST00000301030	NM_001256183.1	1992	aAg/aGg	9/13	1	2	FACETS	0.88	0.794	0.972	0.88	0.794	0.972	CLONAL	1	TRUE	1	0.272313233320895	2		663	1001	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122418	17122418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138031155	NA	P-0013641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	142	704	0	ENST00000285071.4:c.977C>T	p.Pro326Leu	p.P326L	ENST00000285071	NM_144997.5	326	cCg/cTg	9/14	0.24495404503093	2	FACETS	1	0.977	1	0.606	0.552	0.662	CLONAL	1	TRUE	0	0.272313233320895	2		704	861	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274328	5274328	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs115231439	NA	P-0013641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	99	501	0	ENST00000357368.4:c.119A>G	p.Lys40Arg	p.K40R	ENST00000357368	NM_002850.3	40	aAg/aGg	3/38	1	2	FACETS	0.885	0.789	0.986	0.885	0.789	0.986	CLONAL	1	TRUE	1	0.272313233320895	2		501	822	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793236	33793236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	11	116	1	ENST00000498907.2:c.85G>A	p.Ala29Thr	p.A29T	ENST00000498907	NM_004364.3	29	Gcc/Acc	1/1	0.171704340962868	4	FACETS	0.476	0.328	0.659	0.238	0.164	0.33	SUBCLONAL	1	TRUE	2	0.272313233320895	4		117	216	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672012	30672012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767942235	NA	P-0013641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1481	158	856	0	ENST00000376406.3:c.4948C>T	p.Pro1650Ser	p.P1650S	ENST00000376406	NM_014641.2	1650	Ccc/Tcc	10/15	0.272313233320895	3	FACETS	0.804	0.734	0.878	0.268	0.244	0.293	CLONAL	1	TRUE	0	0.272313233320895	3		856	1639	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87322811	87322811	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	58	537	0	ENST00000277120.3:c.412C>A	p.Leu138Ile	p.L138I	ENST00000277120		138	Ctt/Att	5/19	1	2	FACETS	0.426	0.364	0.493	0.426	0.364	0.493	SUBCLONAL	1	TRUE	1	0.272313233320895	2		537	1001	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348291	70348291	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	182	693	0	ENST00000374080.3:c.3354+1G>A		p.X1118_splice	ENST00000374080		1118			0.213530088125329	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.272313233320895	1		693	1002	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0013982-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	371	819	1	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	0.672727743760461	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.685702051484631	1		820	700	SUCCESS
APC	324	MSKCC	GRCh37	5	112175746	112175746	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013982-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	57	343	0	ENST00000257430.4:c.4455del	p.Asp1486IlefsTer21	p.D1486Ifs*21	ENST00000257430	NM_000038.5	1485	gcT/gc	16/16	0.434210118856518	1	FACETS	0.367	0.317	0.42	0.367	0.317	0.42	SUBCLONAL	1	TRUE	0	0.685702051484631	1		343	298	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920422	114920422	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013982-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	297	612	0	ENST00000543371.1:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000543371	NM_001198531.1	455	Cga/Tga	13/14	0.434210118856518	1	FACETS	0.742	0.702	0.783	0.742	0.702	0.783	SUBCLONAL	1	TRUE	0	0.685702051484631	1		612	767	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41962023	41962023	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013982-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	271	514	0	ENST00000219905.7:c.931T>G	p.Ser311Ala	p.S311A	ENST00000219905	NM_001164273.1	311	Tca/Gca	2/24	0.685702051484631	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.685702051484631	1		514	434	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980426	201980427	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0013982-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	334	706	0	ENST00000359651.3:c.162_163insC	p.Glu55ArgfsTer37	p.E55Rfs*37	ENST00000359651		54	-/C	1/8	0.37062957992409	1	FACETS	0.782	0.743	0.821	0.782	0.743	0.821	INDETERMINATE	1	TRUE	0	0.685702051484631	1		706	819	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829545	72829550	+	inframe_deletion	In_Frame_Del	DEL	GCTTGA	GCTTGA	-	novel	NA	P-0013982-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	54	736	0	ENST00000268489.5:c.7031_7036del	p.Ile2344_His2346delinsAsn	p.I2344_H2346delinsN	ENST00000268489	NM_006885.3	2344	aTCAAGCac/aac	9/10	1	2	FACETS	0.181	0.153	0.211	0.181	0.153	0.211	SUBCLONAL	1	TRUE	1	0.685702051484631	2		736	872	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37876075	37876075	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	361	537	0	ENST00000269571.5:c.1934A>G	p.Glu645Gly	p.E645G	ENST00000269571		645	gAg/gGg	16/27	0.246155051380386	10	FACETS	0.97	0.957	0.981	1	0.997	1	CLONAL	16	TRUE	0	0.246155051380386	10		537	375	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554352	106554352	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	30	418	0	ENST00000369096.4:c.1880G>A	p.Gly627Glu	p.G627E	ENST00000369096	NM_001198.3	627	gGa/gAa	6/7	0.246155051380386	1	FACETS	1	0.897	1	1	0.965	1	CLONAL	2	TRUE	0	0.246155051380386	1		418	95	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0014768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	54	501	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.445722131214738	1	FACETS	0.865	0.75	0.986	0.865	0.75	0.986	CLONAL	1	TRUE	0	0.490930489155596	1		502	192	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	45	261	0	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	0.490930489155596	0	FACETS	0.622	0.552	0.69			1	SUBCLONAL	2	TRUE	0	0.490930489155596	0		261	75	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149946	202149946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1280661555	NA	P-0014768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	102	1278	2	ENST00000358485.4:c.1387G>A	p.Ala463Thr	p.A463T	ENST00000358485	NM_001080125.1	463	Gcc/Acc	8/9	0.454126071714836	3	FACETS	0.903	0.81	1	0.301	0.27	0.334	CLONAL	1	TRUE	0	0.490930489155596	3		1280	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	672	660	0	ENST00000269305.4:c.376T>C	p.Tyr126His	p.Y126H	ENST00000269305	NM_001126112.2	126	Tac/Cac	5/11	0.490930489155596	1	FACETS	0.906	0.891	0.92	1	0.998	1	CLONAL	3	TRUE	0	0.490930489155596	1		660	760	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943623	9943623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758815434	NA	P-0014768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	130	1121	0	ENST00000330684.3:c.1318G>A	p.Val440Ile	p.V440I	ENST00000330684	NM_001134407.1	440	Gtc/Atc	5/13	0.490930489155596	3	FACETS	0.777	0.705	0.853	0.388	0.352	0.427	SUBCLONAL	1	TRUE	1	0.490930489155596	3		1121	849	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266502	115266502	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0014768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	49	989	0	ENST00000438362.2:c.2011+2T>G		p.X671_splice	ENST00000438362	NM_001242891.1	671			NA	2	FACETS	0.777	0.663	0.899			1	INDETERMINATE	1	TRUE	NA	0.490930489155596	2		989	257	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462632	29462632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371005946	NA	P-0014768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	937	1637	2	ENST00000389048.3:c.2269G>A	p.Val757Met	p.V757M	ENST00000389048	NM_004304.4	757	Gtg/Atg	13/29	0.443292695272715	3	FACETS	0.924	0.904	0.942	1	0.998	1	CLONAL	4	TRUE	0	0.490930489155596	3		1639	1287	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561756	55561756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376469897	NA	P-0014768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	77	788	0	ENST00000288135.5:c.146G>A	p.Arg49His	p.R49H	ENST00000288135	NM_000222.2	49	cGc/cAc	2/21	0.445722131214738	1	FACETS	0.903	0.803	1	0.903	0.803	1	CLONAL	1	TRUE	0	0.490930489155596	1		788	262	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0014951-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	257	638	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.911	0.867	0.954	1	0.995	1	CLONAL	2	TRUE	1	0.651642265062617	2		638	433	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197716	123197716	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014951-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	76	440	0	ENST00000218089.9:c.1840C>T	p.Arg614Ter	p.R614*	ENST00000218089	NM_001042749.1	614	Cga/Tga	20/35	0.137799431588301	1	FACETS	0.634	0.564	0.707	0.634	0.564	0.707	INDETERMINATE	1	TRUE	0	0.651642265062617	1		440	248	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847332	68847333	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0014951-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	129	714	0	ENST00000261769.5:c.1254_1255del	p.Asp418GlufsTer27	p.D418Efs*27	ENST00000261769	NM_004360.3	418	gaTGat/gaat	9/16	0.63634337207884	1	FACETS	0.981	0.907	1	0.981	0.907	1	CLONAL	1	TRUE	0	0.651642265062617	1		714	272	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0015095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	931	612	0	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	0.594129927307223	5	FACETS	0.986	0.969	1			1	CLONAL	5	TRUE	NA	0.680350842132654	5		612	1122	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876397	35876397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	125	816	0	ENST00000303115.3:c.1189G>A	p.Gly397Arg	p.G397R	ENST00000303115	NM_002185.3	397	Ggg/Agg	8/8	0.680350842132654	3	FACETS	0.677	0.614	0.744	0.339	0.307	0.372	SUBCLONAL	1	TRUE	1	0.680350842132654	3		816	727	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342504	118342504	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	59	511	0	ENST00000534358.1:c.630C>G	p.Ile210Met	p.I210M	ENST00000534358	NM_005933.3	210	atC/atG	3/36	0.491946520340412	5	FACETS	1	0.963	1	0.442	0.384	0.505	CLONAL	1	TRUE	2	0.680350842132654	5		511	264	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807837	3807837	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	98	716	0	ENST00000262367.5:c.3582G>T	p.Gln1194His	p.Q1194H	ENST00000262367	NM_004380.2	1194	caG/caT	18/31	0.680350842132654	3	FACETS	0.864	0.775	0.957	0.432	0.387	0.479	CLONAL	1	TRUE	1	0.680350842132654	3		716	447	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41521969	41521969	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	110	995	0	ENST00000263253.7:c.831A>C	p.Lys277Asn	p.K277N	ENST00000263253	NM_001429.3	277	aaA/aaC	3/31	0.351762389923613	3	FACETS	1	0.965	1	0.379	0.343	0.416	INDETERMINATE	1	TRUE	0	0.680350842132654	3		995	381	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016699-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	165	801	0	ENST00000206249.3:c.1607T>A	p.Leu536His	p.L536H	ENST00000206249	NM_000125.3	536	cTc/cAc	8/8	0.15320091295416	2	FACETS	0.983	0.903	1	0.492	0.451	0.534	INDETERMINATE	1	TRUE	0	0.37618384197984	2		801	892	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104264077	104264077	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016699-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	116	779	0	ENST00000369902.3:c.168del	p.Ile57SerfsTer39	p.I57Sfs*39	ENST00000369902	NM_016169.3	56	gcT/gc	1/12	1	2	FACETS	0.752	0.678	0.831	0.752	0.678	0.831	SUBCLONAL	1	TRUE	1	0.37618384197984	2		779	820	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0017046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	399	1045	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.436170038597413	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.436170038597413	2		1046	876	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132982	30132982	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	153	467	0	ENST00000331968.5:c.619G>T	p.Val207Phe	p.V207F	ENST00000331968	NM_002742.2	207	Gtt/Ttt	4/18	1	2	FACETS	0.808	0.74	0.88	0.808	0.74	0.88	CLONAL	1	TRUE	1	0.436170038597413	2		467	868	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629060	14629274	+	coding_sequence_variant,5_prime_UTR_variant	Frame_Shift_Del	DEL	GTCCGGGTGGTAGCGCAGCGCCTGGCGGCGGTAGGCCCGCTTGATCTCCTCGTCCGACGCGCCGCGGGCCAGGCCCAACGTCTGGTAGTAGTCTTTACCCATGACCCCCTCCTGCGGCCCGCCGACCCGCTGTCGCCGTCCCCCGGCTCCGCCGCCGACCAGTCCCGGACTCTATATACCCGTCCGGCGGAAGCTTCCAGAGCCCGCCAGCCCCC	GTCCGGGTGGTAGCGCAGCGCCTGGCGGCGGTAGGCCCGCTTGATCTCCTCGTCCGACGCGCCGCGGGCCAGGCCCAACGTCTGGTAGTAGTCTTTACCCATGACCCCCTCCTGCGGCCCGCCGACCCGCTGTCGCCGTCCCCCGGCTCCGCCGCCGACCAGTCCCGGACTCTATATACCCGTCCGGCGGAAGCTTCCAGAGCCCGCCAGCCCCC	-	novel	NA	P-0017046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	104	360	0				ENST00000254322	NM_006145.1	?-34/340		1/3	0.432612784057543	3	FACETS	0.767	0.687	0.853	0.384	0.343	0.427	SUBCLONAL	1	TRUE	1	0.436170038597413	3		360	757	SUCCESS
APC	324	MSKCC	GRCh37	5	112173299	112173299	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0017046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	210	164	0	ENST00000257430.4:c.2008A>T	p.Lys670Ter	p.K670*	ENST00000257430	NM_000038.5	670	Aaa/Taa	16/16	0.436170038597413	2	FACETS	0.977	0.916	1	0.977	0.916	1	CLONAL	2	TRUE	0	0.436170038597413	2		164	493	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287398	38287398	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778531708	NA	P-0017046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	496	352	1	ENST00000425967.3:c.259C>T	p.Arg87Cys	p.R87C	ENST00000425967	NM_001174067.1	87	Cgc/Tgc	4/19	0.206101627183078	1	FACETS	0.837	0.805	0.87	1	0.997	1	INDETERMINATE	2	TRUE	0	0.436170038597413	1		353	1062	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287433	38287433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	486	329	0	ENST00000425967.3:c.224C>T	p.Ser75Phe	p.S75F	ENST00000425967	NM_001174067.1	75	tCc/tTc	4/19	0.206101627183078	1	FACETS	0.787	0.755	0.819	1	0.997	1	INDETERMINATE	2	TRUE	0	0.436170038597413	1		329	1107	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863253	56863253	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	773	461	0	ENST00000519728.1:c.397G>T	p.Asp133Tyr	p.D133Y	ENST00000519728	NM_002350.3	133	Gat/Tat	6/13	0.436170038597413	4	FACETS	1	0.994	1	0.823	0.798	0.848	CLONAL	3	TRUE	0	0.436170038597413	4		461	1546	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0017196-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	571	718	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.234021901795218	7	FACETS	0.935	0.899	0.971	0.935	0.899	0.971	CLONAL	6	TRUE	1	0.234021901795218	7		718	1379	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045872	47045872	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0017196-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	245	446	1	ENST00000377604.3:c.2668-1G>T		p.X890_splice	ENST00000377604	NM_001204468.1	890			0.234021901795218	2	FACETS	1	0.97	1			1	CLONAL	3	TRUE	NA	0.234021901795218	2		447	664	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746132	162746132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1374086542	NA	P-0017196-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	34	333	0	ENST00000367921.3:c.2255G>A	p.Arg752His	p.R752H	ENST00000367921	NM_006182.2	752	cGc/cAc	16/18	0.234021901795218	6	FACETS	0.692	0.564	0.837	0.138	0.112	0.168	SUBCLONAL	1	TRUE	1	0.234021901795218	6		333	616	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591892	48591892	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017196-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	90	551	0	ENST00000342988.3:c.1055G>T	p.Gly352Val	p.G352V	ENST00000342988	NM_005359.5	352	gGa/gTa	9/12	0.170410593357468	3	FACETS	1	0.979	1	0.741	0.658	0.828	CLONAL	1	TRUE	1	0.234021901795218	3		551	580	SUCCESS
ALK	238	MSKCC	GRCh37	2	29448339	29448339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375889530	NA	P-0017196-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1262	146	1102	0	ENST00000389048.3:c.3160G>A	p.Gly1054Ser	p.G1054S	ENST00000389048	NM_004304.4	1054	Ggc/Agc	19/29	0.234021901795218	3	FACETS	0.99	0.901	1	0.495	0.45	0.542	CLONAL	1	TRUE	1	0.234021901795218	3		1102	1408	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241704	55241704	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017196-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	496	675	0	ENST00000275493.2:c.2152C>G	p.Leu718Val	p.L718V	ENST00000275493	NM_005228.3	718	Ctg/Gtg	18/28	0.234021901795218	7	FACETS	0.965	0.924	1	0.804	0.77	0.839	CLONAL	5	TRUE	1	0.234021901795218	7		675	1393	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28929495	NA	P-0017319-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	48	603	0	ENST00000275493.2:c.2155G>T	p.Gly719Cys	p.G719C	ENST00000275493	NM_005228.3	719	Ggc/Tgc	18/28	1	2	FACETS	0.39	0.33	0.457	0.39	0.33	0.457	SUBCLONAL	1	TRUE	1	0.470431928473015	2		603	523	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0017319-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	30	726	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	1	2	FACETS	0.286	0.23	0.35	0.286	0.23	0.35	SUBCLONAL	1	TRUE	1	0.470431928473015	2		726	446	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148991	119148991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs192712314	NA	P-0017319-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	10	459	0	ENST00000264033.4:c.1211G>A	p.Cys404Tyr	p.C404Y	ENST00000264033	NM_005188.3	404	tGt/tAt	8/16	1	2	FACETS	0.103	0.069	0.146	0.103	0.069	0.146	SUBCLONAL	1	TRUE	1	0.470431928473015	2		459	412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577521	7577521	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017319-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	22	636	0	ENST00000269305.4:c.760A>T	p.Ile254Phe	p.I254F	ENST00000269305	NM_001126112.2	254	Atc/Ttc	7/11	1	2	FACETS	0.187	0.144	0.237	0.187	0.144	0.237	SUBCLONAL	1	TRUE	1	0.470431928473015	2		636	501	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0017959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	30	469	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.221626203703816	1	FACETS	0.286	0.229	0.351	0.286	0.229	0.351	SUBCLONAL	1	TRUE	0	0.233631035135505	1		469	793	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0017959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	165	620	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.221626203703816	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.233631035135505	1		620	1015	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188280	10188281	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0017959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	159	621	0	ENST00000256474.2:c.424_425del	p.Val142Ter	p.V142*	ENST00000256474	NM_000551.3	141	aaTGtt/aatt	2/3	0.233631035135505	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.233631035135505	1		621	843	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610715	52610715	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0017959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	70	346	0	ENST00000394830.3:c.3459-1G>T		p.X1153_splice	ENST00000394830	NM_018313.4	1153			0.233631035135505	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.233631035135505	1		346	366	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782721	135782721	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0017959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	111	460	0	ENST00000298552.3:c.1300A>T	p.Arg434Ter	p.R434*	ENST00000298552	NM_001162426.1	434	Aga/Tga	13/23	0.233631035135505	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.233631035135505	1		460	640	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0018277-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	40	670	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.220283200782428	4	FACETS	0.82	0.682	0.974	0.41	0.341	0.487	CLONAL	1	TRUE	2	0.286575733426489	4		670	438	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0018277-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	75	519	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.286575733426489	3	FACETS	1	0.97	1	0.678	0.597	0.766	CLONAL	1	TRUE	1	0.286575733426489	3		519	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0018277-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	61	889	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	1	2	FACETS	0.784	0.677	0.9	0.784	0.677	0.9	SUBCLONAL	1	TRUE	1	0.286575733426489	2		889	543	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0018277-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	31	483	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.17550870747815	4	FACETS	0.638	0.516	0.777	0.319	0.258	0.389	SUBCLONAL	1	TRUE	2	0.286575733426489	4		483	436	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0018277-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	13	197	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.515	0.368	0.694	0.515	0.368	0.694	SUBCLONAL	1	TRUE	1	0.286575733426489	2		197	176	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0018277-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	31	459	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.286575733426489	4	FACETS	0.613	0.495	0.747			1	SUBCLONAL	1	TRUE	NA	0.286575733426489	4		459	454	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604789	48604789	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018277-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	25	444	0	ENST00000342988.3:c.1611C>G	p.Asp537Glu	p.D537E	ENST00000342988	NM_005359.5	537	gaC/gaG	12/12	0.17550870747815	4	FACETS	0.597	0.47	0.743	0.299	0.235	0.372	SUBCLONAL	1	TRUE	2	0.286575733426489	4		444	376	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412095	63412095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852217	NA	P-0018277-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	69	438	0	ENST00000330258.3:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000330258	NM_152424.3	358	Cga/Tga	2/2	0.240159678767006	0	FACETS	0.777	0.687	0.871			1	SUBCLONAL	2	TRUE	NA	0.286575733426489	0		438	221	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627250	12627250	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018277-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	28	478	0	ENST00000251849.4:c.1466T>C	p.Leu489Ser	p.L489S	ENST00000251849	NM_002880.3	489	tTg/tCg	14/17	0.111189691757983	4	FACETS	0.669	0.534	0.822	0.334	0.267	0.411	INDETERMINATE	1	TRUE	2	0.286575733426489	4		478	376	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271193	153271193	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0018277-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	39	231	0	ENST00000281708.4:c.584+1G>A		p.X195_splice	ENST00000281708	NM_033632.3	195			0.286575733426489	3	FACETS	1	0.913	1	0.578	0.482	0.685	CLONAL	1	TRUE	1	0.286575733426489	3		231	269	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879673	151879673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018277-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	17	207	0	ENST00000262189.6:c.5272C>T	p.Arg1758Cys	p.R1758C	ENST00000262189	NM_170606.2	1758	Cgt/Tgt	36/59	0.286575733426489	3	FACETS	0.637	0.476	0.826	0.318	0.238	0.413	SUBCLONAL	1	TRUE	1	0.286575733426489	3		207	213	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217705	7217707	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs757139280	NA	P-0019589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	337	565	1	ENST00000380728.2:c.220_222del	p.Glu74del	p.E74del	ENST00000380728		74	GAG/-	4/11	0.668629406364054	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.668629406364054	1		566	670	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881489	48881492	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	novel	NA	P-0019589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	82	430	0	ENST00000267163.4:c.217_220del	p.Arg73LeufsTer3	p.R73Lfs*3	ENST00000267163	NM_000321.2	71	AGAGag/ag	2/27	0.668629406364054	1	FACETS	0.365	0.323	0.41	0.365	0.323	0.41	SUBCLONAL	1	TRUE	0	0.668629406364054	1		430	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578229	7578229	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	537	855	0	ENST00000269305.4:c.620del	p.Asp207ValfsTer40	p.D207Vfs*40	ENST00000269305	NM_001126112.2	207	gAt/gt	6/11	0.668629406364054	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.668629406364054	1		855	950	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629030	14629032	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs759159082	NA	P-0019589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	311	606	0	ENST00000254322.2:c.130_132del	p.Lys44del	p.K44del	ENST00000254322	NM_006145.1	44	AAG/-	1/3	0.668629406364054	1	FACETS	0.903	0.858	0.948	0.903	0.858	0.948	CLONAL	1	TRUE	0	0.668629406364054	1		606	686	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035190	30035192	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs1555987732	NA	P-0019589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	339	530	0	ENST00000338641.4:c.357_359del	p.Phe119del	p.F119del	ENST00000338641	NM_000268.3	118	TTC/-	3/16	0.668629406364054	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.668629406364054	1		530	669	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0021421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	246	483	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.656364182677277	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.656364182677277	1		483	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	595	743	3	ENST00000269305.4:c.569del	p.Pro190LeufsTer57	p.P190Lfs*57	ENST00000269305	NM_001126112.2	190	cCt/ct	6/11	NA	2	FACETS	0.985	0.956	1			1	INDETERMINATE	2	TRUE	NA	0.656364182677277	2		746	920	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435487	110435487	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1420	427	853	6	ENST00000375856.3:c.2914C>T	p.Arg972Trp	p.R972W	ENST00000375856	NM_003749.2	972	Cgg/Tgg	1/2	0.556835769040676	4	FACETS	1	0.991	1	0.389	0.369	0.409	CLONAL	1	TRUE	1	0.656364182677277	4		859	1847	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943760	9943760	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	284	674	0	ENST00000330684.3:c.1181A>T	p.Lys394Met	p.K394M	ENST00000330684	NM_001134407.1	394	aAg/aTg	5/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.656364182677277	2		674	807	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437558	56437558	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	301	804	2	ENST00000407977.2:c.904T>C	p.Trp302Arg	p.W302R	ENST00000407977		302	Tgg/Cgg	8/10	0.656364182677277	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.656364182677277	1		806	596	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633242	12633242	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	128	797	0	ENST00000251849.4:c.1158A>T	p.Gln386His	p.Q386H	ENST00000251849	NM_002880.3	386	caA/caT	11/17	1	2	FACETS	0.375	0.339	0.413	0.375	0.339	0.413	SUBCLONAL	1	TRUE	1	0.656364182677277	2		797	1041	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178500	56178500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778769478	NA	P-0021421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	137	358	3	ENST00000399503.3:c.3473C>T	p.Pro1158Leu	p.P1158L	ENST00000399503	NM_005921.1	1158	cCt/cTt	14/20	1	2	FACETS	0.992	0.91	1	0.992	0.91	1	CLONAL	1	TRUE	1	0.656364182677277	2		361	421	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0022549-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	68	195	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.720417425813983	1	FACETS	0.675	0.6	0.752	0.675	0.6	0.752	SUBCLONAL	1	TRUE	0	0.720417425813983	1		195	179	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022549-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	344	1014	0	ENST00000269305.4:c.455C>G	p.Pro152Arg	p.P152R	ENST00000269305	NM_001126112.2	152	cCg/cGg	5/11	0.720417425813983	1	FACETS	0.842	0.802	0.881	0.842	0.802	0.881	CLONAL	1	TRUE	0	0.720417425813983	1		1014	726	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0023910-T15-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	228	718	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.861998523241258	5	FACETS	0.993	0.972	1	0.993	0.972	1	CLONAL	5	TRUE	0	0.880930033400116	5		718	242	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0023910-T15-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	28	624	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.861998523241258	5	FACETS	0.555	0.445	0.679	0.111	0.089	0.136	SUBCLONAL	1	TRUE	0	0.880930033400116	5		625	266	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241704	55241704	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023910-T15-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	35	675	0	ENST00000275493.2:c.2152C>G	p.Leu718Val	p.L718V	ENST00000275493	NM_005228.3	718	Ctg/Gtg	18/28	0.861998523241258	5	FACETS	0.785	0.648	0.937	0.157	0.129	0.188	CLONAL	1	TRUE	0	0.880930033400116	5		675	235	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445007	89445007	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023910-T15-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	85	341	0	ENST00000336596.2:c.1327A>G	p.Ile443Val	p.I443V	ENST00000336596	NM_005233.5	443	Att/Gtt	6/17	0.713119727191605	4	FACETS	0.881	0.795	0.968	0.587	0.53	0.646	CLONAL	2	TRUE	1	0.880930033400116	4		341	206	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280314	1280314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561203868	NA	P-0023910-T15-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	402	817	0	ENST00000310581.5:c.1909G>A	p.Asp637Asn	p.D637N	ENST00000310581	NM_198253.2	637	Gac/Aac	4/16	0.880930033400116	9	FACETS	1	0.977	1			1	CLONAL	5	TRUE	NA	0.880930033400116	9		817	727	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039380	47039380	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0023910-T15-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	189	627	0	ENST00000377604.3:c.1003A>T	p.Lys335Ter	p.K335*	ENST00000377604	NM_001204468.1	335	Aag/Tag	10/24	0.887660285635516	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.880930033400116	2		627	203	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241705	55241705	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023910-T15-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	19	558	2	ENST00000275493.2:c.2153T>A	p.Leu718Gln	p.L718Q	ENST00000275493	NM_005228.3	718	cTg/cAg	18/28	0.861998523241258	5	FACETS	0.414	0.314	0.53	0.083	0.062	0.106	SUBCLONAL	1	TRUE	0	0.880930033400116	5		560	242	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967252	134967252	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023910-T15-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	21	537	0	ENST00000398015.3:c.2591A>G	p.Asp864Gly	p.D864G	ENST00000398015	NM_004441.4	864	gAc/gGc	14/16	0.713119727191605	4	FACETS	0.303	0.233	0.384	0.101	0.077	0.128	SUBCLONAL	1	TRUE	1	0.880930033400116	4		537	296	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0024292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	100	469	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.280513363346305	1	FACETS	0.982	0.88	1	1	0.987	1	CLONAL	2	TRUE	0	0.17	1		469	548	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	85	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.101758606997207	4	FACETS	0.794	0.701	0.893	0.794	0.701	0.893	INDETERMINATE	2	TRUE	2	0.17	4		487	737	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0024292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	35	638	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.86	0.704	1	0.86	0.704	1	CLONAL	1	TRUE	1	0.17	2		638	479	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0024292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	57	494	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.17	2		494	520	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285116	15285116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	52	623	0	ENST00000263388.2:c.4499G>A	p.Cys1500Tyr	p.C1500Y	ENST00000263388	NM_000435.2	1500	tGt/tAt	25/33	0.280513363346305	1	FACETS	0.928	0.79	1	0.928	0.79	1	CLONAL	1	TRUE	0	0.17	1		623	603	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0024312-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	613	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.822649638085354	5	FACETS	0.977	0.945	1	0.977	0.945	1	CLONAL	3	TRUE	2	0.829718087021693	5		487	1132	SUCCESS
APC	324	MSKCC	GRCh37	5	112175466	112175466	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786204170	NA	P-0024312-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	305	364	0	ENST00000257430.4:c.4175C>A	p.Ser1392Ter	p.S1392*	ENST00000257430	NM_000038.5	1392	tCa/tAa	16/16	0.829718087021693	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.829718087021693	2		364	360	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367512	40367512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1334492695	NA	P-0024312-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	59	12	0	ENST00000397332.2:c.49G>A	p.Gly17Ser	p.G17S	ENST00000397332	NM_001033082.2	17	Ggt/Agt	1/3	0.829718087021693	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.829718087021693	2		12	66	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920446	114920446	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024312-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	470	279	0	ENST00000543371.1:c.1387T>C	p.Cys463Arg	p.C463R	ENST00000543371	NM_001198531.1	463	Tgc/Cgc	13/14	0.829718087021693	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.829718087021693	2		279	542	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682685	86682685	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0024312-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	110	153	0	ENST00000274376.6:c.2890A>T	p.Lys964Ter	p.K964*	ENST00000274376	NM_002890.2	964	Aaa/Taa	23/25	0.829718087021693	2	FACETS	0.921	0.84	1	0.46	0.42	0.502	CLONAL	1	TRUE	0	0.829718087021693	2		153	288	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989672	68989672	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs757775649	NA	P-0024312-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	542	364	0	ENST00000288368.4:c.1610T>C	p.Val537Ala	p.V537A	ENST00000288368	NM_024870.2	537	gTt/gCt	15/40	0.829718087021693	3	FACETS	0.97	0.937	1	0.97	0.937	1	CLONAL	2	TRUE	1	0.829718087021693	3		364	953	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0024333-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	84	339	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.746929733728365	2	FACETS	0.905	0.812	1	0.452	0.406	0.501	CLONAL	1	TRUE	0	0.748583544099058	2		339	248	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241704	55241704	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024333-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	289	675	0	ENST00000275493.2:c.2152C>G	p.Leu718Val	p.L718V	ENST00000275493	NM_005228.3	718	Ctg/Gtg	18/28	0.748583544099058	7	FACETS	1	0.941	1	0.4	0.376	0.425	CLONAL	2	TRUE	2	0.748583544099058	7		675	1108	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0024333-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	339	441	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.748583544099058	7	FACETS	1	0.971	1	0.817	0.78	0.853	CLONAL	4	TRUE	2	0.748583544099058	7		441	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0025449-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	315	1025	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.640335841903788	2	FACETS	0.974	0.937	1	0.974	0.937	1	CLONAL	2	TRUE	0	0.696922886454995	2		1026	464	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913250	NA	P-0025449-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	77	436	0	ENST00000369535.4:c.34G>T	p.Gly12Cys	p.G12C	ENST00000369535	NM_002524.4	12	Ggt/Tgt	2/7	0.215962329758644	3	FACETS	1	0.965	1	0.606	0.539	0.675	INDETERMINATE	1	TRUE	1	0.696922886454995	3		436	246	SUCCESS
AR	367	MSKCC	GRCh37	X	66937403	66937403	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886039558	NA	P-0025449-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	49	341	0	ENST00000374690.3:c.2257C>T	p.Arg753Ter	p.R753*	ENST00000374690	NM_000044.3	753	Cga/Tga	5/8	0.696922886454995	2	FACETS	0.346	0.294	0.404			1	SUBCLONAL	1	TRUE	NA	0.696922886454995	2		341	406	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225573	26225573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343949085	NA	P-0025449-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	153	633	2	ENST00000360408.1:c.191G>A	p.Arg64Gln	p.R64Q	ENST00000360408	NM_003532.2	64	cGg/cAg	1/1	0.696922886454995	3	FACETS	0.946	0.869	1	0.315	0.289	0.342	CLONAL	1	TRUE	0	0.696922886454995	3		635	626	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659614	88659614	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025449-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	17	617	0	ENST00000372037.3:c.397del	p.Tyr133IlefsTer11	p.Y133Ifs*11	ENST00000372037	NM_004329.2	133	Tat/at	6/13	1	2	FACETS	0.243	0.181	0.315	0.243	0.181	0.315	SUBCLONAL	1	TRUE	1	0.696922886454995	2		617	201	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0026070-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	278	415	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.516951132616555	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.516951132616555	3		415	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0026070-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	314	469	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.345301131211478	1	FACETS	0.915	0.865	0.967	0.915	0.865	0.967	CLONAL	1	TRUE	0	0.516951132616555	1		469	984	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977555	2977555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349696922	NA	P-0026070-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	217	737	0	ENST00000396946.4:c.1129C>T	p.Arg377Trp	p.R377W	ENST00000396946	NM_032415.4	377	Cgg/Tgg	8/25	0.516951132616555	3	FACETS	0.773	0.717	0.831	0.386	0.358	0.416	SUBCLONAL	1	TRUE	1	0.516951132616555	3		737	1367	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726618	41726618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026070-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	336	244	0	ENST00000301178.4:c.163C>T	p.Arg55Trp	p.R55W	ENST00000301178	NM_021913.4	55	Cgg/Tgg	2/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.516951132616555	2		244	1204	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492936	56492936	+	start_lost	Translation_Start_Site	SNP	C	C	A	novel	NA	P-0026070-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	88	322	0	ENST00000407977.2:c.3G>T	p.Met1?	p.M1?	ENST00000407977		1	atG/atT	2/10	0.490827856033046	1	FACETS	0.898	0.806	0.994	0.898	0.806	0.994	CLONAL	1	TRUE	0	0.516951132616555	1		322	281	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122637	7122637	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026070-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	270	768	0	ENST00000302850.5:c.3517G>A	p.Val1173Ile	p.V1173I	ENST00000302850	NM_000208.2	1173	Gtc/Atc	19/22	0.490827856033046	1	FACETS	0.963	0.907	1	0.963	0.907	1	CLONAL	1	TRUE	0	0.516951132616555	1		768	804	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0028337-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	220	571	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.966106957208352	3	FACETS	1	0.968	1	0.527	0.493	0.562	CLONAL	1	TRUE	1	0.966106957208352	3		571	641	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0028337-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	286	457	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.966106957208352	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.966106957208352	1		457	292	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0028337-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	211	397	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.874	0.82	0.928	0.874	0.82	0.928	CLONAL	1	TRUE	1	0.966106957208352	2		397	500	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186791	11186791	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028337-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	387	419	0	ENST00000361445.4:c.6414G>T	p.Leu2138Phe	p.L2138F	ENST00000361445	NM_004958.3	2138	ttG/ttT	46/58	0.966106957208352	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.966106957208352	1		419	409	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939856	76939858	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1064795918	NA	P-0028337-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	248	480	0	ENST00000373344.5:c.890_892del	p.Lys297del	p.K297del	ENST00000373344	NM_000489.3	297	aAGAta/ata	9/35	1	2	FACETS	0.86	0.811	0.91	0.86	0.811	0.91	CLONAL	1	TRUE	1	0.966106957208352	2		480	597	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432664	29432664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113994087	NA	P-0028376-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	257	758	1	ENST00000389048.3:c.3824G>A	p.Arg1275Gln	p.R1275Q	ENST00000389048	NM_004304.4	1275	cGa/cAa	25/29	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.73001738327485	2		759	642	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0028376-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	612	638	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.407477522643947	6	FACETS	1	0.995	1			1	INDETERMINATE	5	TRUE	NA	0.73001738327485	6		638	769	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0028376-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	267	729	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.681316320950673	1	FACETS	0.982	0.935	1	0.982	0.935	1	CLONAL	1	TRUE	0	0.73001738327485	1		730	473	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575219	48575219	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028376-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	53	279	0	ENST00000342988.3:c.413C>A	p.Ser138Ter	p.S138*	ENST00000342988	NM_005359.5	138	tCa/tAa	3/12	0.73001738327485	1	FACETS	0.895	0.794	0.996	0.895	0.794	0.996	CLONAL	1	TRUE	0	0.73001738327485	1		279	103	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67646006	67646006	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028376-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	386	537	0	ENST00000264010.4:c.934C>G	p.His312Asp	p.H312D	ENST00000264010	NM_006565.3	312	Cac/Gac	4/12	0.73001738327485	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.73001738327485	2		537	519	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012385	152012386	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028376-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	84	335	0	ENST00000262189.6:c.427dup	p.Ser143LysfsTer27	p.S143Kfs*27	ENST00000262189	NM_170606.2	143	agt/aAgt	4/59	0.73001738327485	1	FACETS	0.994	0.909	1	0.994	0.909	1	CLONAL	1	TRUE	0	0.73001738327485	1		335	147	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260326	10260326	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028376-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	208	641	0	ENST00000340748.4:c.2341G>A	p.Ala781Thr	p.A781T	ENST00000340748		781	Gcg/Acg	25/40	0.701562623511994	3	FACETS	0.882	0.82	0.946			1	CLONAL	1	TRUE	NA	0.73001738327485	3		641	882	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80109489	80109489	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028376-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	128	591	0	ENST00000265081.6:c.2742C>G	p.Ile914Met	p.I914M	ENST00000265081	NM_002439.4	914	atC/atG	20/24	1	2	FACETS	0.901	0.825	0.98	0.901	0.825	0.98	CLONAL	1	TRUE	1	0.73001738327485	2		591	389	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0028913-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	146	466	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.817	0.75	0.888	0.817	0.75	0.888	CLONAL	1	TRUE	1	0.634437930017156	2		466	563	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028913-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	619	803	1	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	0.504817754411006	3	FACETS	1	0.971	1			1	CLONAL	2	TRUE	NA	0.634437930017156	3		804	1278	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481412	140481412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913353	NA	P-0028913-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	170	573	0	ENST00000288602.6:c.1396G>A	p.Gly466Arg	p.G466R	ENST00000288602	NM_004333.4	466	Gga/Aga	11/18	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.634437930017156	2		573	514	SUCCESS
APC	324	MSKCC	GRCh37	5	112174658	112174658	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028913-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	104	402	1	ENST00000257430.4:c.3367C>T	p.Gln1123Ter	p.Q1123*	ENST00000257430	NM_000038.5	1123	Caa/Taa	16/16	0.634437930017156	1	FACETS	0.906	0.827	0.987	0.906	0.827	0.987	CLONAL	1	TRUE	0	0.634437930017156	1		403	247	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577546	7577547	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0028913-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	580	794	0	ENST00000269305.4:c.734dup	p.Met246HisfsTer18	p.M246Hfs*18	ENST00000269305	NM_001126112.2	245	ggc/ggGc	7/11	0.634437930017156	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.634437930017156	2		794	913	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295759	212295759	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028913-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	410	670	0	ENST00000342788.4:c.2554A>C	p.Lys852Gln	p.K852Q	ENST00000342788	NM_005235.2	852	Aaa/Caa	21/28	0.634437930017156	5	FACETS	0.988	0.941	1	0.494	0.47	0.519	CLONAL	2	TRUE	1	0.634437930017156	5		670	1276	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748097	43748097	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028913-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	191	566	1	ENST00000382044.4:c.2709T>G	p.Ser903Arg	p.S903R	ENST00000382044	NM_001141980.1	903	agT/agG	12/28	0.634437930017156	4	FACETS	1	0.945	1			1	CLONAL	1	TRUE	NA	0.634437930017156	4		567	958	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15938110	15938110	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028913-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	146	358	0	ENST00000268712.3:c.7104del	p.Trp2369GlyfsTer20	p.W2369Gfs*20	ENST00000268712	NM_006311.3	2368	ggG/gg	45/46	0.270321113031482	3	FACETS	1	0.987	1	0.471	0.434	0.509	INDETERMINATE	1	TRUE	0	0.634437930017156	3		358	429	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131926938	131926938	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028913-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	61	192	0	ENST00000265335.6:c.1475A>C	p.Glu492Ala	p.E492A	ENST00000265335		492	gAg/gCg	10/25	0.634437930017156	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.634437930017156	1		192	127	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729681	41729681	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028913-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	223	733	0	ENST00000242208.4:c.848A>C	p.Glu283Ala	p.E283A	ENST00000242208	NM_002192.2	283	gAg/gCg	3/3	0.634437930017156	3	FACETS	0.758	0.705	0.814	0.379	0.352	0.407	SUBCLONAL	1	TRUE	1	0.634437930017156	3		733	1221	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248998	55248999	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCAGCG	rs727504263	NA	P-0031010-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	445	547	0	ENST00000275493.2:c.2300_2308dup	p.Ala767_Val769dup	p.A767_V769dup	ENST00000275493	NM_005228.3	767	atg/aTGGCCAGCGtg	20/28	0.248817413051411	6	FACETS	0.993	0.948	1	0.795	0.758	0.832	CLONAL	4	TRUE	1	0.248817413051411	6		547	1348	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126540	2126540	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031010-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	92	577	0	ENST00000219476.3:c.2791G>T	p.Asp931Tyr	p.D931Y	ENST00000219476	NM_000548.3	931	Gac/Tac	25/42	0.248817413051411	4	FACETS	0.923	0.818	1	0.461	0.409	0.518	CLONAL	1	TRUE	2	0.248817413051411	4		577	1001	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0031304-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	193	452	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.698351148289233	6	FACETS	1	0.985	1	0.862	0.81	0.914	CLONAL	3	TRUE	2	0.698351148289233	6		452	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0031304-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	138	606	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.696189871836718	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.698351148289233	2		606	187	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26046026	26046026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031304-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	105	395	0	ENST00000540144.1:c.388C>T	p.Arg130Cys	p.R130C	ENST00000540144	NM_003531.2	130	Cgc/Tgc	1/1	0.329666431974831	5	FACETS	1	0.979	1	0.831	0.759	0.904	INDETERMINATE	2	TRUE	2	0.698351148289233	5		395	247	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939473	71939473	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031304-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	177	896	0	ENST00000298229.2:c.328G>C	p.Val110Leu	p.V110L	ENST00000298229	NM_001567.3	110	Gtg/Ctg	3/28	0.309017204211288	6	FACETS	1	0.942	1	1	0.942	1	INDETERMINATE	3	TRUE	3	0.698351148289233	6		896	401	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800822	18800822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031304-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	94	331	0	ENST00000266497.5:c.4198G>A	p.Glu1400Lys	p.E1400K	ENST00000266497		1400	Gaa/Aaa	31/31	0.59359324759687	5	FACETS	0.91	0.819	1			1	CLONAL	2	TRUE	NA	0.698351148289233	5		331	303	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223138	1223138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060499967	NA	P-0031304-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	226	729	0	ENST00000326873.7:c.1075G>A	p.Asp359Asn	p.D359N	ENST00000326873	NM_000455.4	359	Gac/Aac	8/10	0.696189871836718	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.698351148289233	2		729	295	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395878	395878	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031304-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	27	625	0	ENST00000380956.4:c.435G>C	p.Gln145His	p.Q145H	ENST00000380956	NM_001195286.1	145	caG/caC	4/9	0.329666431974831	5	FACETS	0.353	0.28	0.436	0.118	0.093	0.146	INDETERMINATE	1	TRUE	2	0.698351148289233	5		625	449	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883215	37883215	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	82	978	0	ENST00000269571.5:c.3118G>A	p.Gly1040Arg	p.G1040R	ENST00000269571		1040	Ggg/Agg	25/27	0.446989299351909	1	FACETS	0.389	0.342	0.438	0.389	0.342	0.438	SUBCLONAL	1	TRUE	0	0.446989299351909	1		978	733	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431117	49431117	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	95	879	0	ENST00000301067.7:c.10022A>C	p.Gln3341Pro	p.Q3341P	ENST00000301067	NM_003482.3	3341	cAa/cCa	34/54	0.23562743954648	3	FACETS	0.549	0.487	0.614	0.274	0.243	0.307	INDETERMINATE	1	TRUE	1	0.446989299351909	3		879	948	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803108	1803108	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	94	1037	0	ENST00000260795.2:c.460A>G	p.Thr154Ala	p.T154A	ENST00000260795		154	Aca/Gca	4/17	NA	2	FACETS	0.434	0.385	0.486			1	INDETERMINATE	1	TRUE	NA	0.446989299351909	2		1037	969	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0032269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	285	775	2	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.460573992594723	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.460573992594723	2		777	602	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380346	14380346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1523	1065	214	0	ENST00000256196.4:c.71G>A	p.Gly24Asp	p.G24D	ENST00000256196		24	gGc/gAc	1/6	0.460573992594723	42	FACETS	1	0.982	1			1	CLONAL	18	TRUE	NA	0.460573992594723	42		214	2588	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492920	56492920	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	19	194	0	ENST00000407977.2:c.19C>G	p.Leu7Val	p.L7V	ENST00000407977		7	Ctg/Gtg	2/10	0.442119870373902	4	FACETS	0.406	0.308	0.521	0.203	0.154	0.261	SUBCLONAL	1	TRUE	2	0.460573992594723	4		194	297	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436026	56436026	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771831816	NA	P-0032569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	202	426	0	ENST00000407977.2:c.1111C>T	p.Arg371Ter	p.R371*	ENST00000407977		371	Cga/Tga	9/10	0.468459442456658	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.468459442456658	2		426	386	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0032569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	281	757	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.468459442456658	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.468459442456658	2		757	588	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161398	55161398	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752633017	NA	P-0032569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	174	294	0	ENST00000257290.5:c.3229G>A	p.Gly1077Ser	p.G1077S	ENST00000257290	NM_006206.4	1077	Ggc/Agc	23/23	0.313905280627832	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.468459442456658	1		294	400	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0033313-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	396	490	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.851544090245699	9	FACETS	0.985	0.954	1	0.985	0.954	1	CLONAL	7	TRUE	2	0.851544090245699	9		490	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0033313-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	235	620	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.851544090245699	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.851544090245699	3		620	250	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0033716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	285	449	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.413678356169372	3	FACETS	0.931	0.878	0.986	0.931	0.878	0.986	CLONAL	2	TRUE	1	0.413118051488472	3		449	894	SUCCESS
APC	324	MSKCC	GRCh37	5	112175447	112175447	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0033716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	183	356	0	ENST00000257430.4:c.4156A>T	p.Arg1386Ter	p.R1386*	ENST00000257430	NM_000038.5	1386	Aga/Tga	16/16	0.413118051488472	2	FACETS	0.935	0.871	0.999	0.935	0.871	0.999	CLONAL	2	TRUE	0	0.413118051488472	2		356	474	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356248	66356248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202046693	NA	P-0033716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	163	528	0	ENST00000273854.3:c.1249C>T	p.Arg417Trp	p.R417W	ENST00000273854	NM_004439.5	417	Cgg/Tgg	5/18	1	2	FACETS	0.957	0.879	1	0.957	0.879	1	CLONAL	1	TRUE	1	0.413118051488472	2		528	825	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520141	9520141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560752200	NA	P-0033716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	132	493	1	ENST00000353224.5:c.2128G>A	p.Val710Ile	p.V710I	ENST00000353224	NM_177990.2	710	Gtc/Atc	10/10	NA	2	FACETS	1	0.935	1			1	INDETERMINATE	1	TRUE	NA	0.413118051488472	2		494	619	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099063	27099064	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	159	553	0	ENST00000324856.7:c.3482dup	p.Pro1162AlafsTer31	p.P1162Afs*31	ENST00000324856	NM_006015.4	1160	tta/ttAa	13/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.413118051488472	2		553	692	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831822	72831822	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	203	886	1	ENST00000268489.5:c.4759C>A	p.Pro1587Thr	p.P1587T	ENST00000268489	NM_006885.3	1587	Ccc/Acc	9/10	1	2	FACETS	0.947	0.877	1	0.947	0.877	1	CLONAL	1	TRUE	1	0.413118051488472	2		887	1038	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554422	63554422	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	170	719	0	ENST00000307078.5:c.317A>G	p.Asp106Gly	p.D106G	ENST00000307078	NM_004655.3	106	gAt/gGt	2/11	1	2	FACETS	0.953	0.877	1	0.953	0.877	1	CLONAL	1	TRUE	1	0.413118051488472	2		719	864	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142987	47142987	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	149	542	0	ENST00000409792.3:c.4976G>T	p.Gly1659Val	p.G1659V	ENST00000409792	NM_014159.6	1659	gGc/gTc	8/21	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.413118051488472	2		542	703	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912658	29912852	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCAGGAGGGCTATTGGTCCAGGACCCACACCTGCTTTCTTCATGTTTCCTGATCCCGCCCTGGGTCTGCAGTCACACATTTCTGGAAACTTCTCTGGGGTCCAAGACTAGGAGGTTCCTCTAGGACCTTAAGGCCCTGGCTCCTTTCTGGTATCTCACAGGACATTTTCTTCTCACAGATAGAAAAGGAGGGAGT	TCAGGAGGGCTATTGGTCCAGGACCCACACCTGCTTTCTTCATGTTTCCTGATCCCGCCCTGGGTCTGCAGTCACACATTTCTGGAAACTTCTCTGGGGTCCAAGACTAGGAGGTTCCTCTAGGACCTTAAGGCCCTGGCTCCTTTCTGGTATCTCACAGGACATTTTCTTCTCACAGATAGAAAAGGAGGGAGT	-	novel	NA	P-0033716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	91	142	0	ENST00000376809.5:c.1013-177_1030del		p.X338_splice	ENST00000376809	NM_002116.7	338		6/8	1	2	FACETS	0.798	0.718	0.881	1	0.984	1	SUBCLONAL	2	TRUE	1	0.413118051488472	2		142	276	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900180	101900180	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1554700593	NA	P-0033716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	94	369	0	ENST00000374994.4:c.614T>C	p.Ile205Thr	p.I205T	ENST00000374994	NM_004612.2	205	aTt/aCt	4/9	1	2	FACETS	0.905	0.808	1	0.905	0.808	1	CLONAL	1	TRUE	1	0.413118051488472	2		369	503	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0035716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	73	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.442504248678991	3	FACETS	0.815	0.724	0.909	0.815	0.724	0.909	CLONAL	2	TRUE	1	0.502760539615834	3		457	223	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691872	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs762282124	NA	P-0035716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	103	388	0	ENST00000295754.5:c.374A>G	p.Glu125Gly	p.E125G	ENST00000295754	NM_003242.5	125	gAa/gGa	3/7	0.212797256736695	4	FACETS	0.974	0.883	1	0.974	0.883	1	INDETERMINATE	2	TRUE	2	0.502760539615834	4		388	316	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473616	67473616	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	162	463	0	ENST00000327367.4:c.696G>T	p.Trp232Cys	p.W232C	ENST00000327367	NM_005902.3	232	tgG/tgT	6/9	0.472832415708653	2	FACETS	1	0.984	1	0.626	0.578	0.675	CLONAL	1	TRUE	0	0.502760539615834	2		463	515	SUCCESS
APC	324	MSKCC	GRCh37	5	112175219	112175219	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0035716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	82	160	0	ENST00000257430.4:c.3928A>T	p.Lys1310Ter	p.K1310*	ENST00000257430	NM_000038.5	1310	Aag/Tag	16/16	0.484821629482085	3	FACETS	0.861	0.783	0.939	0.861	0.783	0.939	CLONAL	3	TRUE	0	0.502760539615834	3		160	158	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093411	30093411	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs201154555	NA	P-0035716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	145	528	0	ENST00000331968.5:c.1852C>T	p.Arg618Ter	p.R618*	ENST00000331968	NM_002742.2	618	Cga/Tga	13/18	0.500959072434058	2	FACETS	0.924	0.858	0.991	0.924	0.858	0.991	CLONAL	2	TRUE	0	0.502760539615834	2		528	312	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400830	72400830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	39	333	1	ENST00000357731.5:c.341G>A	p.Gly114Asp	p.G114D	ENST00000357731	NM_173808.2	114	gGc/gAc	2/7	1	2	FACETS	0.702	0.587	0.828	0.702	0.587	0.828	SUBCLONAL	1	TRUE	1	0.502760539615834	2		334	221	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710541	114710550	+	frameshift_variant	Frame_Shift_Del	DEL	GGGATGACCT	GGGATGACCT	-	novel	NA	P-0035716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	74	237	0	ENST00000543371.1:c.26_35del	p.Gly9GlufsTer7	p.G9Efs*7	ENST00000543371	NM_001198531.1	9	gGGGATGACCTa/ga	1/14	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.502760539615834	2		237	290	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137000	64137000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1480788742	NA	P-0035716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	125	392	1	ENST00000334205.4:c.1511C>T	p.Ser504Leu	p.S504L	ENST00000334205	NM_003942.2	504	tCg/tTg	13/17	0.442504248678991	3	FACETS	0.929	0.842	1	0.464	0.421	0.51	CLONAL	1	TRUE	1	0.502760539615834	3		393	670	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024379	16024379	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	130	311	0	ENST00000268712.3:c.1839del	p.Pro614HisfsTer27	p.P614Hfs*27	ENST00000268712	NM_006311.3	613	ccG/cc	16/46	0.238344280883014	2	FACETS	0.856	0.789	0.924	0.856	0.789	0.924	INDETERMINATE	2	TRUE	0	0.502760539615834	2		311	302	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653086	29653086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555533367	NA	P-0035716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	35	305	0	ENST00000356175.3:c.5021G>A	p.Arg1674Gln	p.R1674Q	ENST00000356175	NM_000267.3	1674	cGg/cAg	36/57	0.238344280883014	2	FACETS	0.469	0.385	0.562	0.234	0.192	0.281	INDETERMINATE	1	TRUE	0	0.502760539615834	2		305	297	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483937	212483937	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	47	470	0	ENST00000342788.4:c.2266A>G	p.Thr756Ala	p.T756A	ENST00000342788	NM_005235.2	756	Aca/Gca	19/28	0.274049996019314	4	FACETS	0.859	0.728	1	0.43	0.364	0.501	INDETERMINATE	1	TRUE	2	0.502760539615834	4		470	327	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0035773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	96	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.23198921536098	2		457	687	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0035773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	64	197	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.232496651817689	3	FACETS	0.89	0.775	1	0.89	0.775	1	CLONAL	2	TRUE	1	0.23198921536098	3		197	346	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0035773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	82	260	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	0.232496651817689	3	FACETS	0.899	0.796	1	0.899	0.796	1	CLONAL	2	TRUE	1	0.23198921536098	3		260	439	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411576	63411576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	182	430	0	ENST00000330258.3:c.1591C>T	p.Arg531Ter	p.R531*	ENST00000330258	NM_152424.3	531	Cga/Tga	2/2	0.232496651817689	2	FACETS	0.85	0.789	0.914			1	CLONAL	3	TRUE	NA	0.23198921536098	2		430	615	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579713	7579713	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786202289	NA	P-0035773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	119	635	0	ENST00000269305.4:c.83A>T	p.Glu28Val	p.E28V	ENST00000269305	NM_001126112.2	28	gAa/gTa	3/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.23198921536098	2		635	868	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629102	86629102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	61	291	0	ENST00000274376.6:c.847C>T	p.Arg283Cys	p.R283C	ENST00000274376	NM_002890.2	283	Cgt/Tgt	4/25	0.232496651817689	3	FACETS	0.795	0.689	0.909	0.795	0.689	0.909	CLONAL	2	TRUE	1	0.23198921536098	3		291	369	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2949727	2949727	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	197	880	0	ENST00000396946.4:c.3217G>A	p.Val1073Met	p.V1073M	ENST00000396946	NM_032415.4	1073	Gtg/Atg	24/25	0.187672307035223	3	FACETS	0.788	0.729	0.851	0.788	0.729	0.851	SUBCLONAL	2	TRUE	1	0.23198921536098	3		880	1202	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0035871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	77	415	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.908	0.798	1	0.908	0.798	1	CLONAL	1	TRUE	1	0.27	2		415	628	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0035871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	93	638	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.27	2		638	689	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604790	48604790	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1568211615	NA	P-0035871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	169	428	0	ENST00000342988.3:c.1612G>T	p.Glu538Ter	p.E538*	ENST00000342988	NM_005359.5	538	Gaa/Taa	12/12	1	2	FACETS	1	0.956	1	1	0.993	1	CLONAL	2	TRUE	1	0.27	2		428	597	SUCCESS
APC	324	MSKCC	GRCh37	5	112175749	112175750	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	164	404	0	ENST00000257430.4:c.4459dup	p.Thr1487AsnfsTer27	p.T1487Nfs*27	ENST00000257430	NM_000038.5	1486	-/A	16/16	0.274727936800966	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.27	2		404	587	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920402	114920402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs927089403	NA	P-0035871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	111	478	0	ENST00000543371.1:c.1343G>A	p.Arg448Gln	p.R448Q	ENST00000543371	NM_001198531.1	448	cGg/cAg	13/14	1	2	FACETS	0.967	0.869	1	0.967	0.869	1	CLONAL	1	TRUE	1	0.27	2		478	850	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30326004	30326005	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs769517721	NA	P-0035871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	50	347	0	ENST00000322652.5:c.2208dup	p.Gln737ThrfsTer20	p.Q737Tfs*20	ENST00000322652	NM_015355.2	734	-/A	16/16	1	2	FACETS	0.861	0.732	1	0.861	0.732	1	CLONAL	1	TRUE	1	0.27	2		347	430	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948250	71948250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770973654	NA	P-0035871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	123	980	1	ENST00000298229.2:c.2962G>A	p.Val988Ile	p.V988I	ENST00000298229	NM_001567.3	988	Gtc/Atc	26/28	1	2	FACETS	0.891	0.804	0.982	0.891	0.804	0.982	CLONAL	1	TRUE	1	0.27	2		981	1023	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779551	3779551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	94	1084	0	ENST00000262367.5:c.5497T>C	p.Cys1833Arg	p.C1833R	ENST00000262367	NM_004380.2	1833	Tgc/Cgc	31/31	1	2	FACETS	0.633	0.562	0.71	0.633	0.562	0.71	SUBCLONAL	1	TRUE	1	0.27	2		1084	1100	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119114	70119114	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0035871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	71	359	0	ENST00000245479.2:c.685+1G>T		p.X229_splice	ENST00000245479	NM_000346.3	229			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.27	2		359	385	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119866	70119866	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	100	706	0	ENST00000245479.2:c.868G>T	p.Asp290Tyr	p.D290Y	ENST00000245479	NM_000346.3	290	Gat/Tat	3/3	1	2	FACETS	0.992	0.886	1	0.992	0.886	1	CLONAL	1	TRUE	1	0.27	2		706	747	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55963879	55963879	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	113	654	0	ENST00000263923.4:c.2564G>T	p.Gly855Val	p.G855V	ENST00000263923	NM_002253.2	855	gGa/gTa	18/30	NA	2	FACETS	0.988	0.889	1			1	INDETERMINATE	1	TRUE	NA	0.27	2		654	847	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036163-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	225	846	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.965852204835318	2	FACETS	0.977	0.921	1	0.488	0.46	0.517	CLONAL	1	TRUE	0	0.965852204835318	2		846	477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0036163-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	433	955	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	0.965852204835318	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.965852204835318	2		955	441	SUCCESS
APC	324	MSKCC	GRCh37	5	112179080	112179080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036163-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	101	243	0	ENST00000257430.4:c.7789G>A	p.Gly2597Arg	p.G2597R	ENST00000257430	NM_000038.5	2597	Gga/Aga	16/16	0.491840005043136	4	FACETS	1	0.978	1	0.434	0.392	0.477	INDETERMINATE	1	TRUE	1	0.965852204835318	4		243	316	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550502	29550502	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036163-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	181	150	0	ENST00000356175.3:c.1762C>A	p.His588Asn	p.H588N	ENST00000356175	NM_000267.3	588	Cat/Aat	16/57	0.861268460268036	4	FACETS	0.98	0.906	1			1	CLONAL	1	TRUE	NA	0.965852204835318	4		150	752	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036163-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	540	846	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.985302226972871	1	FACETS	0.54	0.521	0.56	0.54	0.521	0.56	SUBCLONAL	1	TRUE	0	0.985302226972871	1		846	1029	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0036163-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	1080	955	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	0.952229757205117	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.985302226972871	1		955	1092	SUCCESS
APC	324	MSKCC	GRCh37	5	112179080	112179080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036163-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	284	243	0	ENST00000257430.4:c.7789G>A	p.Gly2597Arg	p.G2597R	ENST00000257430	NM_000038.5	2597	Gga/Aga	16/16	0.503392247078925	1	FACETS	0.297	0.279	0.315	0.297	0.279	0.315	INDETERMINATE	1	TRUE	0	0.985302226972871	1		243	986	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550502	29550502	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036163-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	260	150	0	ENST00000356175.3:c.1762C>A	p.His588Asn	p.H588N	ENST00000356175	NM_000267.3	588	Cat/Aat	16/57	NA	2	FACETS	0.415	0.388	0.443			1	INDETERMINATE	1	TRUE	NA	0.985302226972871	2		150	1271	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0036633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	87	661	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.776	0.686	0.873	0.776	0.686	0.873	SUBCLONAL	1	TRUE	1	0.258898199198786	2		662	866	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0036633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	90	835	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.755	0.669	0.847	0.755	0.669	0.847	SUBCLONAL	1	TRUE	1	0.258898199198786	2		835	921	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0036633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	21	257	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.453	0.348	0.575	0.453	0.348	0.575	SUBCLONAL	1	TRUE	1	0.258898199198786	2		258	358	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006897	47006897	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	159	772	1	ENST00000377604.3:c.17G>A	p.Arg6His	p.R6H	ENST00000377604	NM_001204468.1	6	cGt/cAt	2/24	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.258898199198786	2		773	972	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0036834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	365	469	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.101703563005255	1	FACETS	1	0.994	1	1	0.994	1	INDETERMINATE	1	TRUE	0	0.720222506432593	1		469	557	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920402	114920402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs927089403	NA	P-0036834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	298	478	0	ENST00000543371.1:c.1343G>A	p.Arg448Gln	p.R448Q	ENST00000543371	NM_001198531.1	448	cGg/cAg	13/14	0.344135782439674	2	FACETS	1	0.994	1	0.663	0.63	0.696	INDETERMINATE	1	TRUE	0	0.720222506432593	2		478	624	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0036834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	85	275	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.263451863427081	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.720222506432593	0		275	279	SUCCESS
APC	324	MSKCC	GRCh37	5	112175536	112175536	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	56	345	0	ENST00000257430.4:c.4245del	p.Ser1415ArgfsTer4	p.S1415Rfs*4	ENST00000257430	NM_000038.5	1415	agT/ag	16/16	0.263451863427081	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.720222506432593	0		345	274	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562387	21562387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764960515	NA	P-0036834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	370	528	0	ENST00000382592.4:c.1532G>A	p.Arg511Gln	p.R511Q	ENST00000382592	NM_014572.2	511	cGg/cAg	4/8	0.720222506432593	4	FACETS	0.952	0.907	0.998	0.952	0.907	0.998	CLONAL	2	TRUE	2	0.720222506432593	4		528	928	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792755	33792757	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs746430067	NA	P-0036834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	17	73	0	ENST00000498907.2:c.564_566del	p.Pro189del	p.P189del	ENST00000498907	NM_004364.3	188	ccGCCc/ccc	1/1	1	2	FACETS	0.315	0.236	0.406	0.315	0.236	0.406	SUBCLONAL	1	TRUE	1	0.720222506432593	2		73	150	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670843	134670843	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	139	363	1	ENST00000398015.3:c.754C>T	p.Arg252Ter	p.R252*	ENST00000398015	NM_004441.4	252	Cga/Tga	3/16	0.180751033278079	2	FACETS	1	0.971	1	0.555	0.512	0.598	INDETERMINATE	1	TRUE	0	0.720222506432593	2		364	348	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622057	1622057	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763476552	NA	P-0036834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	227	762	0	ENST00000344749.5:c.818G>A	p.Arg273His	p.R273H	ENST00000344749	NM_001136139.2	273	cGt/cAt	10/19	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.720222506432593	2		762	594	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467988	50467988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	225	450	0	ENST00000331340.3:c.1223G>A	p.Arg408His	p.R408H	ENST00000331340	NM_006060.4	408	cGc/cAc	8/8	0.308855384431175	4	FACETS	0.963	0.905	1	0.963	0.905	1	INDETERMINATE	2	TRUE	2	0.720222506432593	4		450	558	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651681	48651681	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	348	320	1	ENST00000376670.3:c.847G>A	p.Gly283Ser	p.G283S	ENST00000376670	NM_002049.3	283	Ggc/Agc	5/6	0.675769803196024	2	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.720222506432593	2		321	432	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0036977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	52	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.203400630690009	3	FACETS	0.981	0.842	1	0.981	0.842	1	CLONAL	2	TRUE	1	0.203400630690009	3		457	287	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480345	89480345	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs774448099	NA	P-0036977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	23	267	0	ENST00000336596.2:c.2182C>T	p.Arg728Ter	p.R728*	ENST00000336596	NM_005233.5	728	Cga/Tga	13/17	0.203400630690009	4	FACETS	1	0.84	1	0.364	0.285	0.456	CLONAL	1	TRUE	1	0.203400630690009	4		267	249	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0036977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	79	654	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			1	2	FACETS	0.901	0.796	1	1	0.982	1	CLONAL	2	TRUE	1	0.203400630690009	2		654	431	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545898	41545898	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774840930	NA	P-0036977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	149	670	0	ENST00000263253.7:c.2513G>A	p.Arg838His	p.R838H	ENST00000263253	NM_001429.3	838	cGt/cAt	14/31	1	2	FACETS	1	0.966	1	1	0.992	1	CLONAL	2	TRUE	1	0.203400630690009	2		670	665	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288765	33288765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761608312	NA	P-0036977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	79	433	1	ENST00000374542.5:c.787C>T	p.Arg263Cys	p.R263C	ENST00000374542	NM_001141970.1	263	Cgc/Tgc	3/8	0.203400630690009	5	FACETS	1	0.944	1	0.744	0.657	0.837	CLONAL	2	TRUE	2	0.203400630690009	5		434	454	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041903	42041903	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	15	442	0	ENST00000219905.7:c.6098A>C	p.Asp2033Ala	p.D2033A	ENST00000219905	NM_001164273.1	2033	gAt/gCt	17/24	1	2	FACETS	0.625	0.457	0.826	0.625	0.457	0.826	SUBCLONAL	1	TRUE	1	0.203400630690009	2		442	236	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143351	30143351	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1553380428	NA	P-0036977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	43	323	0	ENST00000389048.3:c.175G>T	p.Val59Leu	p.V59L	ENST00000389048	NM_004304.4	59	Gtg/Ttg	1/29	1	2	FACETS	0.905	0.758	1	0.905	0.758	1	CLONAL	1	TRUE	1	0.203400630690009	2		323	467	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285296	212285296	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs751857242	NA	P-0036977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	29	366	0	ENST00000342788.4:c.3005A>G	p.Lys1002Arg	p.K1002R	ENST00000342788	NM_005235.2	1002	aAg/aGg	25/28	0.179907484107552	4	FACETS	1	0.846	1	0.531	0.427	0.649	CLONAL	1	TRUE	2	0.203400630690009	4		366	323	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576886	212576886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	15	320	0	ENST00000342788.4:c.1013G>A	p.Gly338Asp	p.G338D	ENST00000342788	NM_005235.2	338	gGc/gAc	9/28	0.179907484107552	4	FACETS	0.716	0.523	0.947	0.358	0.261	0.474	CLONAL	1	TRUE	2	0.203400630690009	4		320	248	SUCCESS
APC	324	MSKCC	GRCh37	5	112175544	112175545	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	23	270	0	ENST00000257430.4:c.4255dup	p.Ser1419LysfsTer4	p.S1419Kfs*4	ENST00000257430	NM_000038.5	1418	ata/atAa	16/16	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.203400630690009	2		270	184	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0037084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	246	1045	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.254850896380357	3	FACETS	0.854	0.8	0.909	0.854	0.8	0.909	CLONAL	3	TRUE	0	0.26	3		1046	835	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920469	134920469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	65	481	0	ENST00000398015.3:c.2284G>A	p.Asp762Asn	p.D762N	ENST00000398015	NM_004441.4	762	Gac/Aac	12/16	1	2	FACETS	0.654	0.566	0.749	0.654	0.566	0.749	SUBCLONAL	1	TRUE	1	0.26	2		481	765	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593532	48593532	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	28	170	0	ENST00000342988.3:c.1283A>T	p.Lys428Met	p.K428M	ENST00000342988	NM_005359.5	428	aAg/aTg	10/12	0.3	1	FACETS	0.822	0.66	1	0.822	0.66	1	CLONAL	1	TRUE	0	0.26	1		170	228	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361108	66361108	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	35	264	0	ENST00000273854.3:c.1064C>A	p.Thr355Lys	p.T355K	ENST00000273854	NM_004439.5	355	aCa/aAa	4/18	1	2	FACETS	0.935	0.769	1	0.935	0.769	1	CLONAL	1	TRUE	1	0.26	2		264	288	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0037415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	56	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.467064809307589	2		326	186	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0037415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	13	1025	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.467064809307589	1	FACETS	0.186	0.132	0.251	0.186	0.132	0.251	SUBCLONAL	1	TRUE	0	0.467064809307589	1		1026	230	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849470	68849470	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	24	475	0	ENST00000261769.5:c.1373A>T	p.Asn458Ile	p.N458I	ENST00000261769	NM_004360.3	458	aAt/aTt	10/16	0.467064809307589	1	FACETS	0.331	0.26	0.412	0.331	0.26	0.412	SUBCLONAL	1	TRUE	0	0.467064809307589	1		475	238	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754656	57754659	+	frameshift_variant	Frame_Shift_Del	DEL	TTTC	TTTC	-	novel	NA	P-0037415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	31	307	0	ENST00000274289.3:c.388_391del	p.Glu130Ter	p.E130*	ENST00000274289	NM_006622.3	130	GAAAta/ta	3/14	1	2	FACETS	0.714	0.583	0.859	0.714	0.583	0.859	SUBCLONAL	1	TRUE	1	0.467064809307589	2		307	186	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037465-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	86	290	1				ENST00000310581	NM_198253.2	-/1132			0.303317222969465	5	FACETS	1	0.93	1	0.705	0.628	0.786	CLONAL	2	TRUE	2	0.32	5		291	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0037465-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	180	695	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.278352312483398	2	FACETS	0.824	0.762	0.887	0.824	0.762	0.887	CLONAL	2	TRUE	0	0.32	2		695	683	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477837	140477851	+	inframe_deletion	In_Frame_Del	DEL	TAGGTGCTGTCACAT	TAGGTGCTGTCACAT	-	novel	NA	P-0037465-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	157	573	0	ENST00000288602.6:c.1457_1471del	p.Asn486_Pro490del	p.N486_P490del	ENST00000288602	NM_004333.4	486	aATGTGACAGCACCTAca/aca	12/18	0.268532388899044	4	FACETS	0.981	0.902	1	0.654	0.601	0.709	CLONAL	2	TRUE	1	0.32	4		573	660	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256243	16256243	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037465-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	52	509	0	ENST00000375759.3:c.3508C>G	p.Arg1170Gly	p.R1170G	ENST00000375759	NM_015001.2	1170	Cga/Gga	11/15	1	2	FACETS	0.612	0.521	0.712	0.612	0.521	0.712	SUBCLONAL	1	TRUE	1	0.32	2		509	531	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982329	201982330	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0037465-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	106	892	0	ENST00000359651.3:c.710dup	p.Asp239GlyfsTer62	p.D239Gfs*62	ENST00000359651		236	-/A	6/8	1	2	FACETS	0.777	0.696	0.863	0.777	0.696	0.863	SUBCLONAL	1	TRUE	1	0.32	2		892	853	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405688	139405688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377353441	NA	P-0037465-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	173	961	0	ENST00000277541.6:c.2503C>T	p.Pro835Ser	p.P835S	ENST00000277541	NM_017617.3	835	Ccc/Tcc	16/34	0.303317222969465	3	FACETS	1	0.941	1	0.343	0.315	0.373	CLONAL	1	TRUE	0	0.32	3		961	1218	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112760256	112760256	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037465-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	24	342	0	ENST00000369452.4:c.925C>T	p.Leu309Phe	p.L309F	ENST00000369452	NM_007373.3	309	Ctt/Ttt	4/9	0.285784971439585	2	FACETS	0.404	0.317	0.506	0.202	0.158	0.253	SUBCLONAL	1	TRUE	0	0.32	2		342	371	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0037486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	219	257	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.548485205272047	3	FACETS	0.947	0.9	0.994	0.947	0.9	0.994	CLONAL	3	TRUE	0	0.548485205272047	3		258	358	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	278	522	1	ENST00000269305.4:c.313G>T	p.Gly105Cys	p.G105C	ENST00000269305	NM_001126112.2	105	Ggc/Tgc	4/11	0.46660836536305	2	FACETS	0.905	0.859	0.951	0.905	0.859	0.951	CLONAL	2	TRUE	0	0.548485205272047	2		523	560	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800921	18800921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201612275	NA	P-0037486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	193	356	1	ENST00000266497.5:c.4297G>A	p.Asp1433Asn	p.D1433N	ENST00000266497		1433	Gat/Aat	31/31	0.29921599048137	4	FACETS	0.958	0.901	1	0.719	0.676	0.762	INDETERMINATE	3	TRUE	0	0.548485205272047	4		357	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0037571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	84	1126	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.178	0.156	0.201	0.178	0.156	0.201	SUBCLONAL	1	TRUE	1	0.99	2		1126	954	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79966025	79966025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763873895	NA	P-0037571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	40	497	0	ENST00000265081.6:c.689C>T	p.Thr230Met	p.T230M	ENST00000265081	NM_002439.4	230	aCg/aTg	4/24	1	2	FACETS	0.127	0.105	0.151	0.127	0.105	0.151	SUBCLONAL	1	TRUE	1	0.99	2		497	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0037673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	355	789	3	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.692754442853626	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.692754442853626	1		792	645	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0037673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	130	364	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.396673774927587	1	FACETS	0.755	0.695	0.816	0.755	0.695	0.816	INDETERMINATE	1	TRUE	0	0.692754442853626	1		365	325	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844776	156844776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1292790967	NA	P-0037673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	232	450	0	ENST00000524377.1:c.1330C>T	p.Arg444Trp	p.R444W	ENST00000524377	NM_002529.3	444	Cgg/Tgg	11/17	0.396673774927587	1	FACETS	0.703	0.66	0.747	0.703	0.66	0.747	INDETERMINATE	1	TRUE	0	0.692754442853626	1		450	623	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0037673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	218	308	0	ENST00000269305.4:c.375+1G>T		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.692754442853626	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.692754442853626	1		308	379	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813553	32813553	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1254925741	NA	P-0037673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	19	270	0	ENST00000354258.4:c.2230C>T	p.Leu744Phe	p.L744F	ENST00000354258	NM_000593.5	744	Ctc/Ttc	11/11	0.396673774927587	1	FACETS	0.111	0.084	0.143	0.111	0.084	0.143	INDETERMINATE	1	TRUE	0	0.692754442853626	1		270	322	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044988	47044988	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	316	292	0	ENST00000377604.3:c.2314G>T	p.Glu772Ter	p.E772*	ENST00000377604	NM_001204468.1	772	Gag/Tag	20/24	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.692754442853626	1		292	461	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743932	41743933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs778012871	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	182	965	3	ENST00000301178.4:c.874dup	p.His292ProfsTer47	p.H292Pfs*47	ENST00000301178	NM_021913.4	289	-/C	7/20	1	2	FACETS	0.836	0.773	0.902	0.836	0.773	0.902	CLONAL	1	TRUE	1	0.54	2		968	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	174	855	2	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	1	2	FACETS	0.845	0.779	0.913	0.845	0.779	0.913	CLONAL	1	TRUE	1	0.54	2		857	763	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	170	120	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	0.3	2	FACETS	0.82	0.764	0.876	0.82	0.764	0.876	INDETERMINATE	2	TRUE	0	0.54	2		120	384	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	185	807	2	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.54	2		809	668	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	236	362	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.3	2	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	2	TRUE	0	0.54	2		362	414	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478786	56478786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324972550	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	163	514	0	ENST00000267101.3:c.242G>A	p.Arg81Gln	p.R81Q	ENST00000267101	NM_001982.3	81	cGa/cAa	3/28	1	2	FACETS	0.985	0.908	1	0.985	0.908	1	CLONAL	1	TRUE	1	0.54	2		514	613	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750762	128750764	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	rs1274246760	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	132	628	0	ENST00000377970.2:c.301_303del	p.Asn101del	p.N101del	ENST00000377970	NM_002467.4	100	gACAac/gac	2/3	1	2	FACETS	0.83	0.756	0.907	0.83	0.756	0.907	CLONAL	1	TRUE	1	0.54	2		628	589	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279443	1279443	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	221	1086	1	ENST00000310581.5:c.2093G>A	p.Arg698Gln	p.R698Q	ENST00000310581	NM_198253.2	698	cGg/cAg	5/16	1	2	FACETS	0.965	0.9	1	0.965	0.9	1	CLONAL	1	TRUE	1	0.54	2		1087	848	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	249	1187	15	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.917	0.868	0.966	1	0.995	1	CLONAL	2	TRUE	1	0.54	2		1202	503	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606304	93606304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	219	907	1	ENST00000375746.1:c.124C>T	p.Arg42Cys	p.R42C	ENST00000375746	NM_001174167.1	42	Cgc/Tgc	2/14	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.54	2		908	774	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445005	89445005	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112239794	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	102	421	0	ENST00000336596.2:c.1325C>T	p.Thr442Met	p.T442M	ENST00000336596	NM_005233.5	442	aCg/aTg	6/17	1	2	FACETS	0.915	0.824	1	0.915	0.824	1	CLONAL	1	TRUE	1	0.54	2		421	413	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639588	47639588	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63749897	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	118	448	0	ENST00000233146.2:c.687del	p.Ala230LeufsTer16	p.A230Lfs*16	ENST00000233146	NM_000251.2	227	agA/ag	4/16	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.54	2		448	393	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012726	36012726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	73	128	1	ENST00000358208.4:c.170C>T	p.Ala57Val	p.A57V	ENST00000358208		57	gCg/gTg	2/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.54	2		129	206	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358367	91358367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779891	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	143	543	1	ENST00000355112.3:c.4112C>T	p.Thr1371Met	p.T1371M	ENST00000355112	NM_000057.2	1371	aCg/aTg	22/22	1	2	FACETS	0.932	0.854	1	0.932	0.854	1	CLONAL	1	TRUE	1	0.54	2		544	568	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339535	81339535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1192583398	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	124	466	0	ENST00000222390.5:c.1469C>T	p.Thr490Met	p.T490M	ENST00000222390	NM_000601.4	490	aCg/aTg	13/18	1	2	FACETS	0.881	0.801	0.965	0.881	0.801	0.965	CLONAL	1	TRUE	1	0.54	2		466	521	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101278	27101278	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	169	768	0	ENST00000324856.7:c.4563del	p.Ala1522ProfsTer5	p.A1522Pfs*5	ENST00000324856	NM_006015.4	1520	ggC/gg	18/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.54	2		768	607	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	201	588	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.942	0.875	1	0.942	0.875	1	CLONAL	1	TRUE	1	0.54	2		592	790	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	209	1590	2	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.891	0.828	0.955	0.891	0.828	0.955	CLONAL	1	TRUE	1	0.54	2		1592	869	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	204	638	2	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.965	0.897	1	0.965	0.897	1	CLONAL	1	TRUE	1	0.54	2		640	783	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910819	114910819	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	236	604	2	ENST00000543371.1:c.938C>T	p.Ala313Val	p.A313V	ENST00000543371	NM_001198531.1	313	gCc/gTc	9/14	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.54	2		606	739	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874149	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	139	460	2	ENST00000262189.6:c.8389_8390del	p.Lys2797GlyfsTer11	p.K2797Gfs*11	ENST00000262189	NM_170606.2	2797	AAg/g	38/59	1	2	FACETS	0.966	0.884	1	0.966	0.884	1	CLONAL	1	TRUE	1	0.54	2		462	533	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007140	152007140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	138	403	1	ENST00000262189.6:c.760C>T	p.Arg254Cys	p.R254C	ENST00000262189	NM_170606.2	254	Cgt/Tgt	6/59	1	2	FACETS	0.898	0.821	0.979	0.898	0.821	0.979	CLONAL	1	TRUE	1	0.54	2		404	569	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299097	15299097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	163	819	4	ENST00000263388.2:c.1441G>A	p.Gly481Ser	p.G481S	ENST00000263388	NM_000435.2	481	Ggt/Agt	9/33	1	2	FACETS	0.886	0.816	0.96	0.886	0.816	0.96	CLONAL	1	TRUE	1	0.54	2		823	681	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744410	41744410	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148886744	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	192	911	0	ENST00000301178.4:c.1030C>T	p.Arg344Trp	p.R344W	ENST00000301178	NM_021913.4	344	Cgg/Tgg	8/20	1	2	FACETS	0.973	0.902	1	0.973	0.902	1	CLONAL	1	TRUE	1	0.54	2		911	731	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631153	176631153	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1172667661	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	162	468	1	ENST00000439151.2:c.1096G>A	p.Val366Met	p.V366M	ENST00000439151	NM_022455.4	366	Gtg/Atg	4/23	1	2	FACETS	0.932	0.858	1	0.932	0.858	1	CLONAL	1	TRUE	1	0.54	2		469	644	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956113	175956113	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	143	438	0	ENST00000367669.3:c.2099T>A	p.Val700Asp	p.V700D	ENST00000367669	NM_022457.5	700	gTt/gAt	18/20	1	2	FACETS	0.944	0.865	1	0.944	0.865	1	CLONAL	1	TRUE	1	0.54	2		438	561	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499743	18499745	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	102	343	0	ENST00000266497.5:c.1601_1603del	p.Asn534del	p.N534del	ENST00000266497		533	cACAac/cac	10/31	1	2	FACETS	0.94	0.847	1	0.94	0.847	1	CLONAL	1	TRUE	1	0.54	2		343	402	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427275	49427275	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs549521409	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	182	672	0	ENST00000301067.7:c.11213A>G	p.Gln3738Arg	p.Q3738R	ENST00000301067	NM_003482.3	3738	cAg/cGg	39/54	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.54	2		672	614	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557551	21557551	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	186	656	0	ENST00000382592.4:c.2294A>C	p.Glu765Ala	p.E765A	ENST00000382592	NM_014572.2	765	gAg/gCg	5/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.54	2		656	655	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467788	99467788	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	118	334	0	ENST00000268035.6:c.2657G>T	p.Arg886Met	p.R886M	ENST00000268035	NM_000875.3	886	aGg/aTg	13/21	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.54	2		334	401	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396308	396308	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	213	885	0	ENST00000262320.3:c.718A>C	p.Thr240Pro	p.T240P	ENST00000262320	NM_003502.3	240	Acc/Ccc	2/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.54	2		885	762	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857587	9857587	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1363459634	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	98	438	0	ENST00000330684.3:c.3814G>C	p.Ala1272Pro	p.A1272P	ENST00000330684	NM_001134407.1	1272	Gca/Cca	13/13	1	2	FACETS	0.898	0.807	0.994	0.898	0.807	0.994	CLONAL	1	TRUE	1	0.54	2		438	404	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989463	7989463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	179	799	2	ENST00000319144.4:c.223G>A	p.Ala75Thr	p.A75T	ENST00000319144	NM_001139.2	75	Gcc/Acc	2/15	1	2	FACETS	0.972	0.899	1	0.972	0.899	1	CLONAL	1	TRUE	1	0.54	2		801	682	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428336	33428336	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	158	671	0	ENST00000345365.6:c.787G>A	p.Ala263Thr	p.A263T	ENST00000345365	NM_002878.3	263	Gcc/Acc	9/10	1	2	FACETS	0.811	0.744	0.879	0.811	0.744	0.879	CLONAL	1	TRUE	1	0.54	2		671	722	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369187	40369187	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	158	512	0	ENST00000293328.3:c.1371del	p.Gln458LysfsTer11	p.Q458Kfs*11	ENST00000293328	NM_012448.3	457	ttT/tt	11/19	1	2	FACETS	0.984	0.905	1	0.984	0.905	1	CLONAL	1	TRUE	1	0.54	2		512	595	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031541	11031541	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	227	1041	0	ENST00000327064.4:c.1456G>T	p.Gly486Cys	p.G486C	ENST00000327064	NM_199141.1	486	Ggc/Tgc	13/16	1	2	FACETS	0.956	0.893	1	0.956	0.893	1	CLONAL	1	TRUE	1	0.54	2		1041	879	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537046	41537047	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	novel	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	70	207	0	ENST00000263253.7:c.1879-2dup		p.X627_splice	ENST00000263253	NM_001429.3	627			1	2	FACETS	0.975	0.86	1	0.975	0.86	1	CLONAL	1	TRUE	1	0.54	2		207	266	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053576	37053576	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63750385	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	288	493	0	ENST00000231790.2:c.665del	p.Asn222MetfsTer7	p.N222Mfs*7	ENST00000231790	NM_000249.3	221	ggA/gg	8/19	0.3	2	FACETS	0.921	0.875	0.967	0.921	0.875	0.967	INDETERMINATE	2	TRUE	0	0.54	2		493	579	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164793	47164793	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1306620044	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	107	342	0	ENST00000409792.3:c.1333C>T	p.Arg445Cys	p.R445C	ENST00000409792	NM_014159.6	445	Cgc/Tgc	3/21	0.3	2	FACETS	1	0.949	1	0.537	0.486	0.59	INDETERMINATE	1	TRUE	0	0.54	2		342	369	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412896	49412896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	128	644	0	ENST00000418115.1:c.127G>A	p.Val43Met	p.V43M	ENST00000418115	NM_001664.2	43	Gtg/Atg	2/5	0.3	2	FACETS	0.625	0.566	0.686	0.312	0.283	0.343	INDETERMINATE	1	TRUE	0	0.54	2		644	759	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665422	182665422	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	73	224	0	ENST00000292782.4:c.521-2A>C		p.X174_splice	ENST00000292782	NM_020640.2	174			1	2	FACETS	0.884	0.78	0.993	0.884	0.78	0.993	CLONAL	1	TRUE	1	0.54	2		224	306	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505033	186505033	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	89	308	0	ENST00000323963.5:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000323963		297	Gac/Tac	8/11	1	2	FACETS	0.777	0.693	0.866	0.777	0.693	0.866	SUBCLONAL	1	TRUE	1	0.54	2		308	424	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180861	106180861	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	118	340	0	ENST00000380013.4:c.3889G>T	p.Gly1297Ter	p.G1297*	ENST00000380013	NM_001127208.2	1297	Gga/Tga	7/11	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.54	2		340	412	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541490	187541490	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	108	342	0	ENST00000441802.2:c.6250C>A	p.Leu2084Ile	p.L2084I	ENST00000441802	NM_005245.3	2084	Ctt/Att	10/27	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.54	2		342	386	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911231	29911231	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199474554	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	45	385	0	ENST00000376809.5:c.530C>T	p.Ala177Val	p.A177V	ENST00000376809	NM_002116.7	177	gCg/gTg	3/8	1	2	FACETS	0.524	0.442	0.614	0.524	0.442	0.614	SUBCLONAL	1	TRUE	1	0.54	2		385	318	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671398	30671398	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	150	644	1	ENST00000376406.3:c.5562G>T	p.Glu1854Asp	p.E1854D	ENST00000376406	NM_014641.2	1854	gaG/gaT	10/15	1	2	FACETS	0.846	0.775	0.919	0.846	0.775	0.919	CLONAL	1	TRUE	1	0.54	2		645	657	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508995	106508995	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	115	559	0	ENST00000359195.3:c.989del	p.Thr330ArgfsTer54	p.T330Rfs*54	ENST00000359195	NM_002649.2	330	aCg/ag	2/11	1	2	FACETS	0.827	0.748	0.909	0.827	0.748	0.909	CLONAL	1	TRUE	1	0.54	2		559	515	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020744	37020744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	144	616	0	ENST00000358127.4:c.101C>T	p.Pro34Leu	p.P34L	ENST00000358127	NM_001280556.1	34	cCg/cTg	2/10	1	2	FACETS	0.931	0.853	1	0.931	0.853	1	CLONAL	1	TRUE	1	0.54	2		616	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0037957-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	465	1045	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.551600462696087	2	FACETS	0.926	0.893	0.958	0.926	0.893	0.958	CLONAL	2	TRUE	0	0.642366013542854	2		1046	782	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0037957-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	158	378	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.352919938468738	6	FACETS	0.951	0.882	1	0.951	0.882	1	INDETERMINATE	3	TRUE	3	0.642366013542854	6		378	394	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0037957-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	77	295	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.546979333607755	4	FACETS	0.81	0.722	0.902	0.81	0.722	0.902	CLONAL	2	TRUE	2	0.642366013542854	4		295	243	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0037957-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	93	240	0	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	0.546979333607755	4	FACETS	0.823	0.741	0.907	0.823	0.741	0.907	CLONAL	2	TRUE	2	0.642366013542854	4		240	289	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199670	11199670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766533620	NA	P-0037957-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	137	557	2	ENST00000361445.4:c.4918C>T	p.Arg1640Trp	p.R1640W	ENST00000361445	NM_004958.3	1640	Cgg/Tgg	35/58	0.521553070009734	3	FACETS	0.766	0.697	0.837	0.383	0.348	0.419	SUBCLONAL	1	TRUE	1	0.642366013542854	3		559	736	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589648	69589648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037957-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	63	163	1	ENST00000168712.1:c.205G>A	p.Val69Ile	p.V69I	ENST00000168712	NM_002007.2	69	Gtc/Atc	1/3	0.608268898736727	3	FACETS	1	0.875	1	0.5	0.437	0.567	CLONAL	1	TRUE	1	0.642366013542854	3		164	259	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435111	110435111	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037957-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1707	393	710	0	ENST00000375856.3:c.3290G>C	p.Arg1097Pro	p.R1097P	ENST00000375856	NM_003749.2	1097	cGc/cCc	1/2	0.642366013542854	6	FACETS	1	0.993	1	0.333	0.315	0.351	CLONAL	1	TRUE	2	0.642366013542854	6		710	2100	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120471	70120472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0037957-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	254	879	0	ENST00000245479.2:c.1474_1475dup	p.His493ProfsTer31	p.H493Pfs*31	ENST00000245479	NM_000346.3	491	-/AC	3/3	0.608268898736727	3	FACETS	0.814	0.76	0.869	0.407	0.38	0.435	CLONAL	1	TRUE	1	0.642366013542854	3		879	1284	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410907	63410907	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037957-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	84	329	0	ENST00000330258.3:c.2260C>A	p.Pro754Thr	p.P754T	ENST00000330258	NM_152424.3	754	Cca/Aca	2/2	0.642366013542854	4	FACETS	0.673	0.595	0.757			1	SUBCLONAL	1	TRUE	NA	0.642366013542854	4		329	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0038599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	190	590	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.565416800053067	1	FACETS	0.795	0.739	0.853	0.795	0.739	0.853	SUBCLONAL	1	TRUE	0	0.565416800053067	1		590	606	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0038599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	120	165	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.477148408201256	2	FACETS	0.859	0.793	0.926	0.859	0.793	0.926	CLONAL	2	TRUE	0	0.565416800053067	2		165	247	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	156	416	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	0.804	0.739	0.873	0.804	0.739	0.873	CLONAL	1	TRUE	1	0.565416800053067	2		416	686	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920419	114920419	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs750925453	NA	P-0038599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	202	533	0	ENST00000543371.1:c.1360G>T	p.Asp454Tyr	p.D454Y	ENST00000543371	NM_001198531.1	454	Gac/Tac	13/14	1	2	FACETS	0.799	0.742	0.859	0.799	0.742	0.859	SUBCLONAL	1	TRUE	1	0.565416800053067	2		533	894	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457408	67457408	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	331	725	0	ENST00000327367.4:c.382C>T	p.Gln128Ter	p.Q128*	ENST00000327367	NM_005902.3	128	Cag/Tag	2/9	0.477148408201256	2	FACETS	0.841	0.801	0.881	0.841	0.801	0.881	CLONAL	2	TRUE	0	0.565416800053067	2		725	696	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0038903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	242	440	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.64863734994635	2	FACETS	0.974	0.928	1	0.974	0.928	1	CLONAL	2	TRUE	0	0.64863734994635	2		440	383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0038903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	438	757	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	1	0.969	1	1	0.997	1	CLONAL	2	TRUE	1	0.64863734994635	2		757	673	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973851	131973851	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747603489	NA	P-0038903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	139	432	0	ENST00000265335.6:c.3554G>A	p.Arg1185Gln	p.R1185Q	ENST00000265335		1185	cGa/cAa	23/25	0.64863734994635	3	FACETS	0.859	0.784	0.937	0.429	0.392	0.469	CLONAL	1	TRUE	1	0.64863734994635	3		432	661	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134423	41134423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148177044	NA	P-0038903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1330	450	540	0	ENST00000379561.5:c.1205C>T	p.Thr402Met	p.T402M	ENST00000379561	NM_002015.3	402	aCg/aTg	2/3	0.64863734994635	7	FACETS	1	0.968	1	0.409	0.389	0.429	CLONAL	2	TRUE	2	0.64863734994635	7		540	1780	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0038903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	495	545	0	ENST00000311936.3:c.180_181delinsAA	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggAAaa	3/5	0.64863734994635	5	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	2	0.64863734994635	5		545	975	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913836	32913837	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359507	NA	P-0038903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	607	484	0	ENST00000380152.3:c.5351dup	p.Asn1784LysfsTer3	p.N1784Kfs*3	ENST00000380152		1782	caa/cAaa	11/27	0.64863734994635	7	FACETS	0.921	0.891	0.95	0.921	0.891	0.95	CLONAL	5	TRUE	2	0.64863734994635	7		484	1066	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031691	69031691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748595305	NA	P-0038903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	216	426	0	ENST00000288368.4:c.3446G>A	p.Arg1149His	p.R1149H	ENST00000288368	NM_024870.2	1149	cGc/cAc	28/40	0.546475094873007	5	FACETS	0.837	0.78	0.895	0.558	0.52	0.597	CLONAL	2	TRUE	2	0.64863734994635	5		426	785	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907618	76907618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	90	530	0	ENST00000373344.5:c.4543G>A	p.Glu1515Lys	p.E1515K	ENST00000373344	NM_000489.3	1515	Gaa/Aaa	15/35	0.504245617617562	4	FACETS	0.475	0.42	0.534	0.119	0.105	0.134	SUBCLONAL	1	TRUE	0	0.64863734994635	4		530	963	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675073	40675073	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs777367353	NA	P-0038903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1350	266	739	0	ENST00000249776.8:c.37T>G	p.Phe13Val	p.F13V	ENST00000249776	NM_033286.3	13	Ttc/Gtc	1/9	0.511345747530925	5	FACETS	1	0.936	1	0.334	0.312	0.357	CLONAL	1	TRUE	2	0.64863734994635	5		739	1616	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448297	56448298	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0038903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	580	666	0	ENST00000407977.2:c.348_349dup	p.Arg117ProfsTer42	p.R117Pfs*42	ENST00000407977		117	cgc/cCCgc	3/10	0.64863734994635	3	FACETS	1	0.996	1	0.816	0.79	0.841	CLONAL	2	TRUE	0	0.64863734994635	3		666	968	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	51	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.726	0.617	0.847	0.726	0.617	0.847	SUBCLONAL	1	TRUE	1	0.24	2		487	585	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	38	394	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	0.591	0.488	0.706	0.591	0.488	0.706	SUBCLONAL	1	TRUE	1	0.24	2		394	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	66	757	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.665	0.576	0.762	0.665	0.576	0.762	SUBCLONAL	1	TRUE	1	0.24	2		757	827	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736457	85736457	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	84	424	0	ENST00000370580.1:c.190A>G	p.Arg64Gly	p.R64G	ENST00000370580	NM_003921.4	64	Agg/Ggg	2/3	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.24	2		424	594	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957464	175957465	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	58	486	0	ENST00000367669.3:c.1931dup	p.Asn644LysfsTer17	p.N644Kfs*17	ENST00000367669	NM_022457.5	644	aac/aaAc	17/20	1	2	FACETS	0.711	0.61	0.821	0.711	0.61	0.821	SUBCLONAL	1	TRUE	1	0.24	2		486	680	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564991	226564991	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	77	495	0	ENST00000366794.5:c.1759A>G	p.Arg587Gly	p.R587G	ENST00000366794	NM_001618.3	587	Agg/Ggg	13/23	1	2	FACETS	0.934	0.82	1	0.934	0.82	1	CLONAL	1	TRUE	1	0.24	2		495	687	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100370	8100371	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	93	838	0	ENST00000346208.3:c.348dup	p.Phe117LeufsTer186	p.F117Lfs*186	ENST00000346208		115	agc/agCc	3/6	1	2	FACETS	0.812	0.72	0.909	0.812	0.72	0.909	CLONAL	1	TRUE	1	0.24	2		838	955	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604533	43604533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs546866208	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	132	733	1	ENST00000355710.3:c.1118C>T	p.Ala373Val	p.A373V	ENST00000355710	NM_020975.4	373	gCg/gTg	6/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.24	2		734	936	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451151	70451151	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	82	698	1	ENST00000373644.4:c.5991T>A	p.Ser1997Arg	p.S1997R	ENST00000373644	NM_030625.2	1997	agT/agA	12/12	1	2	FACETS	0.829	0.73	0.936	0.829	0.73	0.936	CLONAL	1	TRUE	1	0.24	2		699	824	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138041	64138041	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	99	753	0	ENST00000334205.4:c.1964T>C	p.Leu655Pro	p.L655P	ENST00000334205	NM_003942.2	655	cTg/cCg	16/17	1	2	FACETS	0.942	0.84	1	0.942	0.84	1	CLONAL	1	TRUE	1	0.24	2		753	876	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	56	449	1	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	0.783	0.67	0.906	0.783	0.67	0.906	CLONAL	1	TRUE	1	0.24	2		450	596	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123592	108123593	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	61	361	0	ENST00000278616.4:c.1856dup	p.Asn619LysfsTer3	p.N619Kfs*3	ENST00000278616	NM_000051.3	617	-/A	12/63	1	2	FACETS	0.983	0.849	1	0.983	0.849	1	CLONAL	1	TRUE	1	0.24	2		361	517	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025803	1025803	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	38	455	0	ENST00000358495.3:c.725+2T>C		p.X242_splice	ENST00000358495	NM_134424.2	242			1	2	FACETS	0.622	0.514	0.743	0.622	0.514	0.743	SUBCLONAL	1	TRUE	1	0.24	2		455	509	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs770248150	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	56	433	0	ENST00000311936.3:c.351A>T	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaT	4/5	1	2	FACETS	0.855	0.732	0.988	0.855	0.732	0.988	CLONAL	1	TRUE	1	0.24	2		433	546	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495646	56495647	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	69	642	0	ENST00000267101.3:c.3841dup	p.Ala1281GlyfsTer6	p.A1281Gfs*6	ENST00000267101	NM_001982.3	1279	atg/atGg	28/28	1	2	FACETS	0.89	0.775	1	0.89	0.775	1	CLONAL	1	TRUE	1	0.24	2		642	646	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541748	120541748	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	77	592	0	ENST00000229340.5:c.109T>C	p.Tyr37His	p.Y37H	ENST00000229340	NM_006861.6	37	Tac/Cac	3/6	1	2	FACETS	0.809	0.709	0.917	0.809	0.709	0.917	CLONAL	1	TRUE	1	0.24	2		592	793	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879643	123879643	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	45	369	0	ENST00000330479.4:c.339A>C	p.Glu113Asp	p.E113D	ENST00000330479	NM_020382.3	113	gaA/gaC	4/9	1	2	FACETS	0.712	0.598	0.838	0.712	0.598	0.838	SUBCLONAL	1	TRUE	1	0.24	2		369	527	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133208998	133208998	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	92	700	0	ENST00000320574.5:c.6233G>T	p.Arg2078Leu	p.R2078L	ENST00000320574	NM_006231.2	2078	cGg/cTg	45/49	1	2	FACETS	0.829	0.735	0.929	0.829	0.735	0.929	CLONAL	1	TRUE	1	0.24	2		700	925	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32931945	32931945	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs80358995	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	53	401	0	ENST00000380152.3:c.7684T>C	p.Phe2562Leu	p.F2562L	ENST00000380152		2562	Ttt/Ctt	16/27	0.321572701012996	3	FACETS	0.888	0.757	1	0.444	0.378	0.516	CLONAL	1	TRUE	1	0.24	3		401	557	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954272	32954273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359752	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	55	466	0	ENST00000380152.3:c.9253dup	p.Thr3085AsnfsTer26	p.T3085Nfs*26	ENST00000380152		3082	-/A	24/27	0.321572701012996	3	FACETS	0.835	0.713	0.967	0.417	0.356	0.484	CLONAL	1	TRUE	1	0.24	3		466	615	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021441	42021442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	67	564	0	ENST00000219905.7:c.3744dup	p.Glu1249ArgfsTer25	p.E1249Rfs*25	ENST00000219905	NM_001164273.1	1246	cga/cgAa	11/24	1	2	FACETS	0.772	0.67	0.883	0.772	0.67	0.883	SUBCLONAL	1	TRUE	1	0.24	2		564	723	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748660	43748661	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	138	893	0	ENST00000382044.4:c.2145dup	p.Glu716ArgfsTer9	p.E716Rfs*9	ENST00000382044	NM_001141980.1	715	-/A	12/28	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.24	2		893	1109	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994829	73994829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751833994	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	40	262	3	ENST00000318443.5:c.313G>A	p.Ala105Thr	p.A105T	ENST00000318443	NM_001024736.1	105	Gca/Aca	3/10	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.24	2		265	305	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396394	396394	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368975881	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	101	694	0	ENST00000262320.3:c.632C>T	p.Thr211Met	p.T211M	ENST00000262320	NM_003502.3	211	aCg/aTg	2/11	0.162223061623535	3	FACETS	0.921	0.822	1	0.461	0.411	0.514	CLONAL	1	TRUE	1	0.24	3		694	1023	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106646	2106646	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	105	694	0	ENST00000219476.3:c.650T>C	p.Val217Ala	p.V217A	ENST00000219476	NM_000548.3	217	gTc/gCc	8/42	0.162223061623535	3	FACETS	1	0.939	1	0.535	0.478	0.595	CLONAL	1	TRUE	1	0.24	3		694	916	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786733	3786734	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	58	684	0	ENST00000262367.5:c.4477dup	p.Ile1493AsnfsTer26	p.I1493Nfs*26	ENST00000262367	NM_004380.2	1493	ata/aAta	27/31	0.162223061623535	3	FACETS	0.508	0.435	0.588	0.254	0.217	0.294	SUBCLONAL	1	TRUE	1	0.24	3		684	1066	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857961	9857961	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	90	633	0	ENST00000330684.3:c.3440T>C	p.Phe1147Ser	p.F1147S	ENST00000330684	NM_001134407.1	1147	tTc/tCc	13/13	0.162223061623535	3	FACETS	0.887	0.785	0.996	0.444	0.392	0.498	CLONAL	1	TRUE	1	0.24	3		633	947	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	23	780	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	1	2	FACETS	0.199	0.154	0.252	0.199	0.154	0.252	SUBCLONAL	1	TRUE	1	0.24	2		780	963	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110129	8110130	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs745673717	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	78	636	0	ENST00000585124.1:c.475dup	p.Arg159ProfsTer15	p.R159Pfs*15	ENST00000585124	NM_004217.3	159	cgc/cCgc	6/9	1	2	FACETS	0.813	0.713	0.92	0.813	0.713	0.92	CLONAL	1	TRUE	1	0.24	2		636	800	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040682	16040683	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	67	344	0	ENST00000268712.3:c.1451dup	p.Asn484LysfsTer2	p.N484Kfs*2	ENST00000268712	NM_006311.3	484	aat/aaAt	14/46	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.24	2		344	541	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663419	29663421	+	inframe_deletion	In_Frame_Del	DEL	AAT	AAT	-	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	90	579	0	ENST00000356175.3:c.6014_6016del	p.Ile2005del	p.I2005del	ENST00000356175	NM_000267.3	2004	tcAATa/tca	40/57	1	2	FACETS	0.853	0.756	0.958	0.853	0.756	0.958	CLONAL	1	TRUE	1	0.24	2		579	879	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453398	40453399	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs759027671	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	61	909	0	ENST00000345506.4:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000345506	NM_003152.3	365	-/C	10/20	1	2	FACETS	0.48	0.412	0.553	0.48	0.412	0.553	SUBCLONAL	1	TRUE	1	0.24	2		909	1060	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870526	40870526	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	146	702	0	ENST00000428826.2:c.877T>C	p.Ser293Pro	p.S293P	ENST00000428826		293	Tcc/Ccc	9/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.24	2		702	1124	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	95	782	4	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.734	0.652	0.822	0.734	0.652	0.822	SUBCLONAL	1	TRUE	1	0.24	2		786	1079	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118954	70118954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555629169	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	90	799	0	ENST00000245479.2:c.526C>T	p.Pro176Ser	p.P176S	ENST00000245479	NM_000346.3	176	Ccg/Tcg	2/3	1	2	FACETS	0.821	0.727	0.921	0.821	0.727	0.921	CLONAL	1	TRUE	1	0.24	2		799	914	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775203	73775204	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs779064600	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	63	572	2	ENST00000254810.4:c.52dup	p.Arg18ProfsTer80	p.R18Pfs*80	ENST00000254810	NM_005324.3	18	cgc/cCgc	2/4	1	2	FACETS	0.678	0.586	0.779	0.678	0.586	0.779	SUBCLONAL	1	TRUE	1	0.24	2		574	774	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632091	1632091	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	48	730	0	ENST00000344749.5:c.244A>G	p.Thr82Ala	p.T82A	ENST00000344749	NM_001136139.2	82	Act/Gct	5/19	1	2	FACETS	0.434	0.365	0.51	0.434	0.365	0.51	SUBCLONAL	1	TRUE	1	0.24	2		730	922	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226320	2226320	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	121	876	0	ENST00000398665.3:c.3800T>C	p.Leu1267Pro	p.L1267P	ENST00000398665	NM_032482.2	1267	cTc/cCc	27/28	1	2	FACETS	0.967	0.872	1	0.967	0.872	1	CLONAL	1	TRUE	1	0.24	2		876	1043	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184425	7184425	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	135	715	0	ENST00000302850.5:c.876A>T	p.Lys292Asn	p.K292N	ENST00000302850	NM_000208.2	292	aaA/aaT	3/22	1	2	FACETS	0.966	0.876	1	0.966	0.876	1	CLONAL	1	TRUE	1	0.24	2		715	1164	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272512	15272512	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	78	608	1	ENST00000263388.2:c.5927T>C	p.Leu1976Pro	p.L1976P	ENST00000263388	NM_000435.2	1976	cTa/cCa	33/33	1	2	FACETS	0.903	0.793	1	0.903	0.793	1	CLONAL	1	TRUE	1	0.24	2		609	720	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961574	18961574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	109	671	1	ENST00000262803.5:c.707G>A	p.Arg236His	p.R236H	ENST00000262803	NM_002911.3	236	cGc/cAc	5/24	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.24	2		672	829	SUCCESS
AXL	558	MSKCC	GRCh37	19	41759523	41759523	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	97	641	1	ENST00000301178.4:c.1946T>G	p.Leu649Arg	p.L649R	ENST00000301178	NM_021913.4	649	cTa/cGa	17/20	1	2	FACETS	0.95	0.846	1	0.95	0.846	1	CLONAL	1	TRUE	1	0.24	2		642	851	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910289	50910289	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	115	822	0	ENST00000440232.2:c.1544A>G	p.Asp515Gly	p.D515G	ENST00000440232	NM_002691.3	515	gAt/gGt	13/27	1	2	FACETS	0.985	0.886	1	0.985	0.886	1	CLONAL	1	TRUE	1	0.24	2		822	973	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469529	25469530	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755744291	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	84	704	0	ENST00000264709.3:c.1238dup	p.Phe414LeufsTer7	p.F414Lfs*7	ENST00000264709	NM_175629.2	413	ggc/ggGc	10/23	1	2	FACETS	0.848	0.748	0.956	0.848	0.748	0.956	CLONAL	1	TRUE	1	0.24	2		704	825	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47604158	47604158	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	63	381	0	ENST00000263735.4:c.497T>G	p.Leu166Arg	p.L166R	ENST00000263735	NM_002354.2	166	cTt/cGt	5/9	0.162223061623535	3	FACETS	0.906	0.783	1	0.453	0.391	0.52	CLONAL	1	TRUE	1	0.24	3		381	649	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719825	61719825	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	65	576	0	ENST00000401558.2:c.1443C>A	p.His481Gln	p.H481Q	ENST00000401558	NM_003400.3	481	caC/caA	14/25	0.162223061623535	3	FACETS	0.837	0.725	0.959	0.418	0.362	0.48	CLONAL	1	TRUE	1	0.24	3		576	725	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178129258	178129258	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	51	356	0	ENST00000397062.3:c.45+2T>C		p.X15_splice	ENST00000397062	NM_006164.4	15			1	2	FACETS	0.995	0.848	1	0.995	0.848	1	CLONAL	1	TRUE	1	0.24	2		356	427	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379359	225379359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	82	598	0	ENST00000264414.4:c.509C>T	p.Ala170Val	p.A170V	ENST00000264414	NM_003590.4	170	gCa/gTa	4/16	1	2	FACETS	0.973	0.858	1	0.973	0.858	1	CLONAL	1	TRUE	1	0.24	2		598	702	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422554	225422554	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	18	267	0	ENST00000264414.4:c.86A>G	p.Tyr29Cys	p.Y29C	ENST00000264414	NM_003590.4	29	tAt/tGt	2/16	1	2	FACETS	0.519	0.391	0.671	0.519	0.391	0.671	SUBCLONAL	1	TRUE	1	0.24	2		267	289	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	24	402	0	ENST00000375687.4:c.1933_1934dup	p.Gly646ValfsTer58	p.G646Vfs*58	ENST00000375687	NM_015338.5	642	-/GG	13/13	1	2	FACETS	0.548	0.429	0.685	0.548	0.429	0.685	SUBCLONAL	1	TRUE	1	0.24	2		402	365	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735506	40735506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	90	655	0	ENST00000373198.4:c.3367G>A	p.Ala1123Thr	p.A1123T	ENST00000373198	NM_133170.3	1123	Gcc/Acc	25/32	1	2	FACETS	0.872	0.773	0.979	0.872	0.773	0.979	CLONAL	1	TRUE	1	0.24	2		655	860	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790090	40790090	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	99	714	0	ENST00000373198.4:c.2641C>G	p.Arg881Gly	p.R881G	ENST00000373198	NM_133170.3	881	Cgg/Ggg	18/32	1	2	FACETS	0.876	0.78	0.978	0.876	0.78	0.978	CLONAL	1	TRUE	1	0.24	2		714	942	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279958	46279958	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	110	819	0	ENST00000371998.3:c.3884T>G	p.Leu1295Arg	p.L1295R	ENST00000371998		1295	cTt/cGt	20/23	1	2	FACETS	0.804	0.721	0.893	0.804	0.721	0.893	CLONAL	1	TRUE	1	0.24	2		819	1140	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62316928	62316928	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	58	677	1	ENST00000360203.5:c.1244T>C	p.Leu415Pro	p.L415P	ENST00000360203	NM_001283009.1	415	cTg/cCg	15/35	1	2	FACETS	0.563	0.482	0.651	0.563	0.482	0.651	SUBCLONAL	1	TRUE	1	0.24	2		678	859	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183598	10183598	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	59	769	0	ENST00000256474.2:c.67T>C	p.Tyr23His	p.Y23H	ENST00000256474	NM_000551.3	23	Tac/Cac	1/3	1	2	FACETS	0.511	0.438	0.591	0.511	0.438	0.591	SUBCLONAL	1	TRUE	1	0.24	2		769	962	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72881585	72881586	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	68	428	0	ENST00000325599.8:c.533dup	p.Ala179CysfsTer3	p.A179Cfs*3	ENST00000325599	NM_018130.2	178	cct/ccCt	5/11	1	2	FACETS	0.805	0.7	0.919	0.805	0.7	0.919	CLONAL	1	TRUE	1	0.24	2		428	704	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261505	142261505	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	56	330	0	ENST00000350721.4:c.3450+2T>C		p.X1150_splice	ENST00000350721	NM_001184.3	1150			1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.24	2		330	465	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575705	55575705	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	68	350	0	ENST00000288135.5:c.1231A>G	p.Thr411Ala	p.T411A	ENST00000288135	NM_000222.2	411	Aca/Gca	7/21	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.24	2		350	519	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532709	187532710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	90	571	0	ENST00000441802.2:c.9683dup	p.Val3229CysfsTer3	p.V3229Cfs*3	ENST00000441802	NM_005245.3	3228	cct/ccCt	14/27	1	2	FACETS	0.934	0.828	1	0.934	0.828	1	CLONAL	1	TRUE	1	0.24	2		571	803	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542109	187542110	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1560943587	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	41	457	0	ENST00000441802.2:c.5630dup	p.Val1878CysfsTer8	p.V1878Cfs*8	ENST00000441802	NM_005245.3	1877	cct/ccCt	10/27	1	2	FACETS	0.7	0.583	0.83	0.7	0.583	0.83	SUBCLONAL	1	TRUE	1	0.24	2		457	488	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628773	187628773	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	110	749	0	ENST00000441802.2:c.2209A>T	p.Ile737Phe	p.I737F	ENST00000441802	NM_005245.3	737	Att/Ttt	2/27	1	2	FACETS	0.931	0.835	1	0.931	0.835	1	CLONAL	1	TRUE	1	0.24	2		749	985	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295330	1295330	+	upstream_gene_variant	5'Flank	SNP	A	A	G	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	44	399	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.77	0.646	0.908	0.77	0.646	0.908	CLONAL	1	TRUE	1	0.24	2		399	476	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953152	38953152	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	33	277	0	ENST00000357387.3:c.2832G>T	p.Gln944His	p.Q944H	ENST00000357387	NM_152756.3	944	caG/caT	29/38	1	2	FACETS	0.802	0.654	0.967	0.802	0.654	0.967	CLONAL	1	TRUE	1	0.24	2		277	343	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754819	57754819	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	61	316	0	ENST00000274289.3:c.371G>T	p.Arg124Met	p.R124M	ENST00000274289	NM_006622.3	124	aGg/aTg	2/14	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.24	2		316	459	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961020	79961020	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	84	509	0	ENST00000265081.6:c.417A>T	p.Glu139Asp	p.E139D	ENST00000265081	NM_002439.4	139	gaA/gaT	3/24	1	2	FACETS	0.938	0.828	1	0.938	0.828	1	CLONAL	1	TRUE	1	0.24	2		509	746	SUCCESS
APC	324	MSKCC	GRCh37	5	112137078	112137078	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1554076217	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	85	393	0	ENST00000257430.4:c.832C>T	p.Gln278Ter	p.Q278*	ENST00000257430	NM_000038.5	278	Cag/Tag	8/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.24	2		393	529	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	49	395	0	ENST00000257430.4:c.4199del	p.Ser1400Ter	p.S1400*	ENST00000257430	NM_000038.5	1400	tCg/tg	16/16	1	2	FACETS	0.773	0.655	0.904	0.773	0.655	0.904	CLONAL	1	TRUE	1	0.24	2		395	528	SUCCESS
APC	324	MSKCC	GRCh37	5	112175920	112175920	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	39	292	0	ENST00000257430.4:c.4629A>C	p.Lys1543Asn	p.K1543N	ENST00000257430	NM_000038.5	1543	aaA/aaC	16/16	1	2	FACETS	0.874	0.726	1	0.874	0.726	1	CLONAL	1	TRUE	1	0.24	2		292	372	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030341	180030341	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	112	749	0	ENST00000261937.6:c.3943T>A	p.Ser1315Thr	p.S1315T	ENST00000261937	NM_182925.4	1315	Tcc/Acc	30/30	0.3	1	FACETS	0.887	0.797	0.983	0.887	0.797	0.983	CLONAL	1	TRUE	0	0.24	1		749	926	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490538	20490538	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	103	632	0	ENST00000346618.3:c.1275A>T	p.Leu425Phe	p.L425F	ENST00000346618	NM_001949.4	425	ttA/ttT	7/7	0.3	2	FACETS	0.969	0.866	1			1	CLONAL	1	TRUE	NA	0.24	2		632	886	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020719	26020719	+	start_lost	Translation_Start_Site	SNP	T	T	C	rs184531972	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	41	287	0	ENST00000357647.3:c.2T>C	p.Met1?	p.M1?	ENST00000357647	NM_003529.2	1	aTg/aCg	1/1	0.3	2	FACETS	0.954	0.797	1			1	CLONAL	1	TRUE	NA	0.24	2		287	358	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158525	26158525	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1222808686	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	72	551	0	ENST00000289316.2:c.128A>G	p.Tyr43Cys	p.Y43C	ENST00000289316	NM_138720.2	43	tAc/tGc	1/2	0.3	2	FACETS	0.922	0.805	1			1	CLONAL	1	TRUE	NA	0.24	2		551	651	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798163	32798163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	117	752	0	ENST00000374899.4:c.1516G>A	p.Gly506Arg	p.G506R	ENST00000374899	NM_018833.2	506	Ggg/Agg	9/12	1	2	FACETS	0.973	0.876	1	0.973	0.876	1	CLONAL	1	TRUE	1	0.24	2		752	1002	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805715	32805716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	81	757	0	ENST00000374899.4:c.295dup	p.Trp99LeufsTer68	p.W99Lfs*68	ENST00000374899	NM_018833.2	99	tgg/tTgg	2/12	1	2	FACETS	0.785	0.69	0.887	0.785	0.69	0.887	SUBCLONAL	1	TRUE	1	0.24	2		757	860	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813366	32813366	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	98	874	1	ENST00000354258.4:c.2417C>T	p.Ala806Val	p.A806V	ENST00000354258	NM_000593.5	806	gCt/gTt	11/11	1	2	FACETS	0.761	0.677	0.851	0.761	0.677	0.851	SUBCLONAL	1	TRUE	1	0.24	2		875	1073	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554970	106554970	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs751928266	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	80	560	0	ENST00000369096.4:c.2087A>G	p.Tyr696Cys	p.Y696C	ENST00000369096	NM_001198.3	696	tAc/tGc	7/7	1	2	FACETS	0.884	0.778	0.999	0.884	0.778	0.999	CLONAL	1	TRUE	1	0.24	2		560	754	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706869	117706869	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	51	478	0	ENST00000368508.3:c.2281T>G	p.Tyr761Asp	p.Y761D	ENST00000368508	NM_002944.2	761	Tac/Gac	15/43	1	2	FACETS	0.722	0.613	0.841	0.722	0.613	0.841	SUBCLONAL	1	TRUE	1	0.24	2		478	589	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502149	157502149	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	79	562	0	ENST00000346085.5:c.3182A>G	p.Tyr1061Cys	p.Y1061C	ENST00000346085	NM_020732.3	1061	tAc/tGc	12/20	1	2	FACETS	0.801	0.703	0.906	0.801	0.703	0.906	CLONAL	1	TRUE	1	0.24	2		562	822	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453987	140453987	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs180177040	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	43	280	0	ENST00000288602.6:c.1741A>C	p.Asn581His	p.N581H	ENST00000288602	NM_004333.4	581	Aat/Cat	14/18	0.225774214773111	3	FACETS	1	0.922	1	0.585	0.491	0.688	CLONAL	1	TRUE	1	0.24	3		280	343	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38315054	38315054	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs765497063	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	77	557	0	ENST00000425967.3:c.12-2A>G		p.X4_splice	ENST00000425967	NM_001174067.1	4			1	2	FACETS	0.847	0.742	0.959	0.847	0.742	0.959	CLONAL	1	TRUE	1	0.24	2		557	758	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992720	68992721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs764112302	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	89	594	6	ENST00000288368.4:c.1693dup	p.Ser565PhefsTer3	p.S565Ffs*3	ENST00000288368	NM_024870.2	562	cgt/cgTt	16/40	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.24	2		600	732	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866617	117866617	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	88	542	0	ENST00000297338.2:c.1028A>G	p.Asp343Gly	p.D343G	ENST00000297338	NM_006265.2	343	gAt/gGt	9/14	1	2	FACETS	0.912	0.807	1	0.912	0.807	1	CLONAL	1	TRUE	1	0.24	2		542	804	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566375	141566375	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1564084326	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	42	410	0	ENST00000220592.5:c.1037T>C	p.Ile346Thr	p.I346T	ENST00000220592	NM_012154.3	346	aTt/aCt	9/19	1	2	FACETS	0.68	0.567	0.805	0.68	0.567	0.805	SUBCLONAL	1	TRUE	1	0.24	2		410	515	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738396	145738396	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	91	824	0	ENST00000428558.2:c.2589G>T	p.Glu863Asp	p.E863D	ENST00000428558	NM_004260.3	863	gaG/gaT	16/22	1	2	FACETS	0.808	0.716	0.907	0.808	0.716	0.907	CLONAL	1	TRUE	1	0.24	2		824	938	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637119	93637119	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	81	489	0	ENST00000375746.1:c.1169A>G	p.Tyr390Cys	p.Y390C	ENST00000375746	NM_001174167.1	390	tAc/tGc	9/14	1	2	FACETS	0.936	0.824	1	0.936	0.824	1	CLONAL	1	TRUE	1	0.24	2		489	721	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912301	97912301	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	77	583	0	ENST00000289081.3:c.590A>G	p.Asp197Gly	p.D197G	ENST00000289081	NM_000136.2	197	gAc/gGc	7/15	1	2	FACETS	0.84	0.737	0.951	0.84	0.737	0.951	CLONAL	1	TRUE	1	0.24	2		583	764	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15840946	15840946	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	19	211	0	ENST00000307771.7:c.1030A>G	p.Arg344Gly	p.R344G	ENST00000307771	NM_005089.3	344	Aga/Gga	11/11	0.3	2	FACETS	0.498	0.378	0.64	0.249	0.189	0.32	SUBCLONAL	1	TRUE	0	0.24	2		211	318	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932258	39932258	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	165	456	0	ENST00000378444.4:c.2341A>G	p.Thr781Ala	p.T781A	ENST00000378444	NM_001123385.1	781	Acc/Gcc	4/15	0.3	2	FACETS	0.913	0.84	0.989	0.913	0.84	0.989	CLONAL	2	TRUE	0	0.24	2		456	753	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028881	47028881	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	111	314	0	ENST00000377604.3:c.185A>G	p.Glu62Gly	p.E62G	ENST00000377604	NM_001204468.1	62	gAg/gGg	3/24	0.3	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	0	0.24	2		314	444	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034471	47034471	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	114	378	2	ENST00000377604.3:c.556C>T	p.Arg186Ter	p.R186*	ENST00000377604	NM_001204468.1	186	Cga/Tga	6/24	0.3	2	FACETS	0.802	0.724	0.884	0.802	0.724	0.884	CLONAL	2	TRUE	0	0.24	2		380	592	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222354	53222354	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1451567527	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	43	438	0	ENST00000375401.3:c.4478A>G	p.Gln1493Arg	p.Q1493R	ENST00000375401	NM_004187.3	1493	cAg/cGg	26/26	0.3	2	FACETS	0.659	0.551	0.779	0.329	0.275	0.39	SUBCLONAL	1	TRUE	0	0.24	2		438	544	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411014	63411014	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	28	382	1	ENST00000330258.3:c.2153T>C	p.Leu718Pro	p.L718P	ENST00000330258	NM_152424.3	718	cTg/cCg	2/2	0.3	2	FACETS	0.515	0.411	0.634	0.258	0.205	0.317	SUBCLONAL	1	TRUE	0	0.24	2		383	453	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412602	63412602	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	95	349	0	ENST00000330258.3:c.565C>T	p.Gln189Ter	p.Q189*	ENST00000330258	NM_152424.3	189	Caa/Taa	2/2	0.3	2	FACETS	0.904	0.809	1	0.904	0.809	1	CLONAL	2	TRUE	0	0.24	2		349	438	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347765	70347765	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	86	282	0	ENST00000374080.3:c.3004A>G	p.Asn1002Asp	p.N1002D	ENST00000374080		1002	Aac/Gac	22/45	0.3	2	FACETS	0.777	0.69	0.869	0.777	0.69	0.869	SUBCLONAL	2	TRUE	0	0.24	2		282	461	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0039259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	38	571	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.757	0.636	0.887	1	0.957	1	SUBCLONAL	2	TRUE	1	0.328169204823068	2		571	153	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0039259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	29	378	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.166339372250284	2	FACETS	1	0.923	1	0.645	0.525	0.776	INDETERMINATE	1	TRUE	0	0.328169204823068	2		378	137	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0039259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	11	197	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.729	0.509	0.995	0.729	0.509	0.995	CLONAL	1	TRUE	1	0.328169204823068	2		197	92	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0039259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	26	364	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.714	0.568	0.879	0.714	0.568	0.879	SUBCLONAL	1	TRUE	1	0.328169204823068	2		365	222	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220454	133220454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41561818	NA	P-0039259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	41	440	1	ENST00000320574.5:c.4259C>T	p.Ala1420Val	p.A1420V	ENST00000320574	NM_006231.2	1420	gCg/gTg	33/49	0.328169204823068	1	FACETS	0.639	0.534	0.754	0.639	0.534	0.754	SUBCLONAL	1	TRUE	0	0.328169204823068	1		441	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	101	514	0	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	0.318968217299622	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	2	TRUE	0	0.328169204823068	2		514	303	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0039259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	98	533	1	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	0.328169204823068	1	FACETS	1	0.94	1	1	0.989	1	CLONAL	2	TRUE	0	0.328169204823068	1		534	239	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411530	63411530	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	51	728	0	ENST00000330258.3:c.1637del	p.Leu546CysfsTer16	p.L546Cfs*16	ENST00000330258	NM_152424.3	546	tTg/tg	2/2	1	2	FACETS	0.987	0.843	1	0.987	0.843	1	CLONAL	1	TRUE	1	0.328169204823068	2		728	315	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405220	70405220	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	47	345	0	ENST00000373644.4:c.2734A>G	p.Lys912Glu	p.K912E	ENST00000373644	NM_030625.2	912	Aag/Gag	4/12	1	2	FACETS	0.823	0.706	0.948	1	0.969	1	CLONAL	2	TRUE	1	0.328169204823068	2		345	174	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560457	65560457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	37	323	0	ENST00000358664.4:c.140G>A	p.Arg47Gln	p.R47Q	ENST00000358664	NM_002382.4	47	cGg/cAg	3/5	1	2	FACETS	0.943	0.783	1	0.943	0.783	1	CLONAL	1	TRUE	1	0.328169204823068	2		323	239	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277992	41277992	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0039259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	27	423	0	ENST00000349496.5:c.1954+2T>C		p.X652_splice	ENST00000349496	NM_001904.3	652			1	2	FACETS	0.909	0.73	1	0.909	0.73	1	CLONAL	1	TRUE	1	0.328169204823068	2		423	181	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944414	76944414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	20	340	0	ENST00000373344.5:c.491G>A	p.Gly164Glu	p.G164E	ENST00000373344	NM_000489.3	164	gGg/gAg	7/35	1	2	FACETS	0.807	0.623	1	0.807	0.623	1	CLONAL	1	TRUE	1	0.328169204823068	2		340	151	SUCCESS
APC	324	MSKCC	GRCh37	5	112174094	112174095	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs863225332	NA	P-0039323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	254	283	0	ENST00000257430.4:c.2804dup	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	tac/tAac	16/16	0.868713000678549	3	FACETS	0.982	0.935	1	0.982	0.935	1	CLONAL	2	TRUE	1	0.868713000678549	3		283	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	G	rs11575997	NA	P-0039323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	453	500	0	ENST00000269305.4:c.993+1G>C		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.86695535338221	2	FACETS	0.999	0.978	1	0.999	0.978	1	CLONAL	2	TRUE	0	0.868713000678549	2		500	522	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397640	139397640	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	553	565	0	ENST00000277541.6:c.5161G>A	p.Val1721Met	p.V1721M	ENST00000277541	NM_017617.3	1721	Gtg/Atg	27/34	0.785385708778755	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.868713000678549	4		565	1170	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59820468	59820468	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200960251	NA	P-0039323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	241	399	0	ENST00000259008.2:c.2285G>A	p.Arg762His	p.R762H	ENST00000259008	NM_032043.2	762	cGt/cAt	16/20	0.860726897424403	4	FACETS	0.919	0.866	0.973	0.919	0.866	0.973	CLONAL	2	TRUE	2	0.868713000678549	4		399	564	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236074	108236074	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	176	461	0	ENST00000278616.4:c.9012del	p.Val3005Ter	p.V3005*	ENST00000278616	NM_000051.3	3004	Aaa/aa	63/63	0.868713000678549	3	FACETS	1	0.934	1	0.505	0.467	0.543	CLONAL	1	TRUE	1	0.868713000678549	3		461	576	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156038	119156038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762016318	NA	P-0039323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	293	603	0	ENST00000264033.4:c.1703C>T	p.Thr568Ile	p.T568I	ENST00000264033	NM_005188.3	568	aCa/aTa	11/16	0.868713000678549	3	FACETS	1	0.966	1	0.516	0.487	0.547	CLONAL	1	TRUE	1	0.868713000678549	3		603	937	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624959	9624959	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs757331403	NA	P-0039323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	128	236	0	ENST00000353224.5:c.18G>T	p.Lys6Asn	p.K6N	ENST00000353224	NM_177990.2	6	aaG/aaT	3/10	0.868713000678549	5	FACETS	1	0.951	1	0.357	0.324	0.391	CLONAL	1	TRUE	2	0.868713000678549	5		236	634	SUCCESS
APC	324	MSKCC	GRCh37	5	112175745	112175751	+	frameshift_variant	Frame_Shift_Del	DEL	CTGATAC	CTGATAC	-	novel	NA	P-0039323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	91	301	0	ENST00000257430.4:c.4454_4460del	p.Ala1485ValfsTer20	p.A1485Vfs*20	ENST00000257430	NM_000038.5	1485	gCTGATACt/gt	16/16	0.868713000678549	3	FACETS	0.886	0.795	0.983	0.443	0.397	0.492	CLONAL	1	TRUE	1	0.868713000678549	3		301	339	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638368	117638368	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	151	397	0	ENST00000368508.3:c.6073A>G	p.Ile2025Val	p.I2025V	ENST00000368508	NM_002944.2	2025	Atc/Gtc	38/43	0.868713000678549	3	FACETS	0.897	0.824	0.972	0.299	0.274	0.324	CLONAL	1	TRUE	0	0.868713000678549	3		397	556	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317435	1317435	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	254	483	0	ENST00000400841.2:c.630G>T	p.Gln210His	p.Q210H	ENST00000400841		210	caG/caT	5/6	0.860416570884571	2	FACETS	0.995	0.939	1	0.497	0.469	0.526	CLONAL	1	TRUE	0	0.868713000678549	2		483	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0039412-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	198	731	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.551766965859385	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.551766965859385	2		731	355	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252155	226252155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553260624	NA	P-0039412-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	51	100	0	ENST00000366813.1:c.103G>A	p.Gly35Arg	p.G35R	ENST00000366813		35	Ggg/Agg	1/3	0.551766965859385	3	FACETS	1	0.907	1	1	0.977	1	CLONAL	3	TRUE	1	0.551766965859385	3		100	78	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131161	55131161	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039412-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	106	352	0	ENST00000257290.5:c.704G>T	p.Cys235Phe	p.C235F	ENST00000257290	NM_006206.4	235	tGt/tTt	5/23	0.176908337295733	3	FACETS	1	0.983	1	0.719	0.651	0.789	INDETERMINATE	1	TRUE	1	0.551766965859385	3		352	341	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907706	76907707	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0039412-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	61	175	0	ENST00000373344.5:c.4454_4455del	p.Lys1485ArgfsTer2	p.K1485Rfs*2	ENST00000373344	NM_000489.3	1485	aAA/a	15/35	1	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.551766965859385	1		175	121	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0039581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	191	378	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.391871259708517	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	0	0.391871259708517	2		378	482	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0039581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	48	333	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	NA	2	FACETS	0.914	0.779	1			1	INDETERMINATE	1	TRUE	NA	0.391871259708517	2		333	268	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0039581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	286	450	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.372784263418855	3	FACETS	0.968	0.919	1	0.968	0.919	1	CLONAL	3	TRUE	0	0.391871259708517	3		451	601	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374909	45374909	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	241	525	0	ENST00000262160.6:c.934T>G	p.Cys312Gly	p.C312G	ENST00000262160	NM_005901.5	312	Tgc/Ggc	8/11	0.27334746552509	2	FACETS	0.981	0.922	1	0.981	0.922	1	CLONAL	2	TRUE	0	0.391871259708517	2		525	627	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643585	52643585	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190579793	NA	P-0039581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	92	476	0	ENST00000394830.3:c.2311G>A	p.Val771Ile	p.V771I	ENST00000394830	NM_018313.4	771	Gtc/Atc	17/30	1	2	FACETS	0.97	0.866	1	0.97	0.866	1	CLONAL	1	TRUE	1	0.391871259708517	2		476	484	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	30	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.82	1	1	0.82	1	CLONAL	1	FALSE	1	0.375164712424228	2		326	159	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	112	339	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.374147382824926	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	FALSE	0	0.375164712424228	3		339	208	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639588	47639588	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63749897	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	14	448	0	ENST00000233146.2:c.687del	p.Ala230LeufsTer16	p.A230Lfs*16	ENST00000233146	NM_000251.2	227	agA/ag	4/16	1	2	FACETS	0.533	0.388	0.707	0.533	0.388	0.707	SUBCLONAL	1	FALSE	1	0.375164712424228	2		448	140	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	58	1590	2	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.615	0.529	0.708	0.615	0.529	0.708	SUBCLONAL	1	FALSE	1	0.375164712424228	2		1592	503	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491363	2491363	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376398200	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	58	879	0	ENST00000355716.4:c.406G>A	p.Ala136Thr	p.A136T	ENST00000355716	NM_003820.2	136	Gcc/Acc	4/8	1	2	FACETS	0.468	0.401	0.54	0.468	0.401	0.54	SUBCLONAL	1	FALSE	1	0.375164712424228	2		879	661	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	39	118	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	0.932	0.779	1	0.932	0.779	1	CLONAL	1	FALSE	1	0.375164712424228	2		118	223	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736510	85736511	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs387906351	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	29	222	1	ENST00000370580.1:c.136dup	p.Ile46AsnfsTer4	p.I46Nfs*4	ENST00000370580	NM_003921.4	46	ata/aAta	2/3	1	2	FACETS	0.859	0.696	1	0.859	0.696	1	CLONAL	1	FALSE	1	0.375164712424228	2		223	180	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099332	193099332	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	20	348	0	ENST00000367435.3:c.266C>A	p.Pro89His	p.P89H	ENST00000367435	NM_024529.4	89	cCt/cAt	3/17	1	2	FACETS	0.555	0.427	0.704	0.555	0.427	0.704	SUBCLONAL	1	FALSE	1	0.375164712424228	2		348	192	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226568838	226568838	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	69	774	1	ENST00000366794.5:c.1231A>G	p.Met411Val	p.M411V	ENST00000366794	NM_001618.3	411	Atg/Gtg	9/23	1	2	FACETS	0.685	0.597	0.78	0.685	0.597	0.78	SUBCLONAL	1	FALSE	1	0.375164712424228	2		775	537	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597940	43597940	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149403911	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	88	1000	3	ENST00000355710.3:c.488G>A	p.Arg163Gln	p.R163Q	ENST00000355710	NM_020975.4	163	cGg/cAg	3/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.375164712424228	2		1003	394	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724511	112724511	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	27	555	1	ENST00000369452.4:c.395G>C	p.Ser132Thr	p.S132T	ENST00000369452	NM_007373.3	132	aGt/aCt	2/9	1	2	FACETS	0.612	0.49	0.752	0.612	0.49	0.752	SUBCLONAL	1	FALSE	1	0.375164712424228	2		556	235	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	66	498	4	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.375164712424228	2		502	245	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138920	64138920	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770200186	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	86	693	1	ENST00000334205.4:c.2287C>T	p.Arg763Cys	p.R763C	ENST00000334205	NM_003942.2	763	Cgc/Tgc	17/17	1	2	FACETS	0.928	0.824	1	0.928	0.824	1	CLONAL	1	FALSE	1	0.375164712424228	2		694	494	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625143	69625143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	44	859	4	ENST00000334134.2:c.650C>T	p.Pro217Leu	p.P217L	ENST00000334134	NM_005247.2	217	cCg/cTg	3/3	1	2	FACETS	0.503	0.422	0.593	0.503	0.422	0.593	SUBCLONAL	1	FALSE	1	0.375164712424228	2		863	466	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948483	71948484	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	70	1006	1	ENST00000298229.2:c.3201dup	p.Ser1068GlnfsTer17	p.S1068Qfs*17	ENST00000298229	NM_001567.3	1065	-/C	26/28	1	2	FACETS	0.682	0.595	0.776	0.682	0.595	0.776	SUBCLONAL	1	FALSE	1	0.375164712424228	2		1007	547	SUCCESS
EED	8726	MSKCC	GRCh37	11	85967540	85967540	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	18	351	0	ENST00000263360.6:c.538A>G	p.Met180Val	p.M180V	ENST00000263360	NM_003797.3	180	Atg/Gtg	5/12	1	2	FACETS	0.542	0.41	0.696	0.542	0.41	0.696	SUBCLONAL	1	FALSE	1	0.375164712424228	2		351	177	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114817	108114817	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786204543	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	32	537	2	ENST00000278616.4:c.640del	p.Ser214ProfsTer16	p.S214Pfs*16	ENST00000278616	NM_000051.3	212	Ttt/tt	6/63	1	2	FACETS	0.536	0.436	0.649	0.536	0.436	0.649	SUBCLONAL	1	FALSE	1	0.375164712424228	2		539	318	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201067	108201067	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	19	360	0	ENST00000278616.4:c.7434A>C	p.Glu2478Asp	p.E2478D	ENST00000278616	NM_000051.3	2478	gaA/gaC	50/63	1	2	FACETS	0.603	0.46	0.768	0.603	0.46	0.768	SUBCLONAL	1	FALSE	1	0.375164712424228	2		360	168	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352745	118352747	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	23	487	0	ENST00000534358.1:c.3953_3955del	p.Glu1318del	p.E1318del	ENST00000534358	NM_005933.3	1317	aAAGaa/aaa	7/36	1	2	FACETS	0.324	0.252	0.408	0.324	0.252	0.408	SUBCLONAL	1	FALSE	1	0.375164712424228	2		487	378	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497611	125497611	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	14	326	0	ENST00000428830.2:c.175A>G	p.Asn59Asp	p.N59D	ENST00000428830	NM_001114121.2	59	Aat/Gat	3/14	1	2	FACETS	0.406	0.294	0.54	0.406	0.294	0.54	SUBCLONAL	1	FALSE	1	0.375164712424228	2		326	184	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	15	363	1	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.53	0.389	0.696	0.53	0.389	0.696	SUBCLONAL	1	FALSE	1	0.375164712424228	2		364	151	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406360	406360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	18	547	2	ENST00000399788.2:c.4081G>A	p.Ala1361Thr	p.A1361T	ENST00000399788	NM_001042603.1	1361	Gcc/Acc	25/28	0.302153825470104	0	FACETS	0.275	0.207	0.355			1	SUBCLONAL	1	FALSE	0	0.375164712424228	0		549	218	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498235	498235	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	10	298	1	ENST00000399788.2:c.23del	p.Gly8AlafsTer58	p.G8Afs*58	ENST00000399788	NM_001042603.1	8	gGc/gc	1/28	0.302153825470104	0	FACETS	0.18	0.122	0.253			1	SUBCLONAL	1	FALSE	0	0.375164712424228	0		299	185	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245000	46245000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	49	669	1	ENST00000334344.6:c.3094C>T	p.Gln1032Ter	p.Q1032*	ENST00000334344	NM_152641.2	1032	Cag/Tag	15/21	0.375164712424228	4	FACETS	1	0.881	1	0.521	0.443	0.606	CLONAL	1	FALSE	2	0.375164712424228	4		670	345	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287469	46287469	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	16	324	0	ENST00000334344.6:c.5333del	p.Asn1778IlefsTer13	p.N1778Ifs*13	ENST00000334344	NM_152641.2	1776	ttA/tt	20/21	0.375164712424228	4	FACETS	0.631	0.468	0.824	0.315	0.234	0.412	SUBCLONAL	1	FALSE	2	0.375164712424228	4		324	186	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50482355	50482355	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	95	564	1	ENST00000394963.4:c.711del	p.Phe237LeufsTer5	p.F237Lfs*5	ENST00000394963	NM_003076.4	236	Ttt/tt	6/13	0.375164712424228	4	FACETS	1	0.907	1	1	0.907	1	CLONAL	2	FALSE	2	0.375164712424228	4		565	345	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856373	111856373	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	61	213	0	ENST00000341259.2:c.424C>A	p.Leu142Ile	p.L142I	ENST00000341259	NM_005475.2	142	Ctc/Atc	2/8	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	FALSE	1	0.375164712424228	2		213	292	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241002	133241002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	79	656	1	ENST00000320574.5:c.2515G>A	p.Gly839Arg	p.G839R	ENST00000320574	NM_006231.2	839	Ggg/Agg	22/49	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	FALSE	1	0.375164712424228	2		657	413	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563047	21563047	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	132	909	1	ENST00000382592.4:c.872C>T	p.Thr291Met	p.T291M	ENST00000382592	NM_014572.2	291	aCg/aTg	4/8	0.198636264897182	3	FACETS	0.846	0.773	0.922	0.846	0.773	0.922	INDETERMINATE	2	FALSE	1	0.375164712424228	3		910	494	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975441	26975441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	45	505	0	ENST00000381527.3:c.1067G>A	p.Arg356Gln	p.R356Q	ENST00000381527	NM_001260.1	356	cGa/cAa	11/13	0.198636264897182	3	FACETS	1	0.924	1	0.577	0.489	0.672	INDETERMINATE	1	FALSE	1	0.375164712424228	3		505	247	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582875	95582875	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	12	345	0	ENST00000393063.1:c.1667C>A	p.Pro556His	p.P556H	ENST00000393063	NM_030621.3	556	cCc/cAc	11/28	1	2	FACETS	0.464	0.327	0.629	0.464	0.327	0.629	SUBCLONAL	1	FALSE	1	0.375164712424228	2		345	138	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73995370	73995370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199765601	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	25	422	0	ENST00000318443.5:c.676G>A	p.Val226Met	p.V226M	ENST00000318443	NM_001024736.1	226	Gtg/Atg	4/10	1	2	FACETS	0.614	0.486	0.759	0.614	0.486	0.759	SUBCLONAL	1	FALSE	1	0.375164712424228	2		422	217	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478221	99478221	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1313769986	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	23	377	0	ENST00000268035.6:c.3125G>A	p.Arg1042His	p.R1042H	ENST00000268035	NM_000875.3	1042	cGt/cAt	16/21	1	2	FACETS	0.56	0.438	0.699	0.56	0.438	0.699	SUBCLONAL	1	FALSE	1	0.375164712424228	2		377	219	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2224321	2224321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	144	819	0	ENST00000326181.6:c.1333C>T	p.Leu445Phe	p.L445F	ENST00000326181	NM_032271.2	445	Ctc/Ttc	14/21	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.375164712424228	2		819	524	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226049	2226049	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	50	850	0	ENST00000326181.6:c.1747-1G>T		p.X583_splice	ENST00000326181	NM_032271.2	583			1	2	FACETS	0.599	0.509	0.698	0.599	0.509	0.698	SUBCLONAL	1	FALSE	1	0.375164712424228	2		850	445	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646297	3646297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	79	921	0	ENST00000294008.3:c.1781G>A	p.Gly594Asp	p.G594D	ENST00000294008	NM_032444.2	594	gGc/gAc	8/15	1	2	FACETS	0.773	0.681	0.871	0.773	0.681	0.871	SUBCLONAL	1	FALSE	1	0.375164712424228	2		921	545	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781901	3781903	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs751071525	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	23	697	0	ENST00000262367.5:c.4764_4766del	p.Lys1588del	p.K1588del	ENST00000262367	NM_004380.2	1588	aaGAAc/aac	29/31	1	2	FACETS	0.303	0.236	0.382	0.303	0.236	0.382	SUBCLONAL	1	FALSE	1	0.375164712424228	2		697	404	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817766	3817766	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs555109138	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	104	577	1	ENST00000262367.5:c.3205G>A	p.Gly1069Ser	p.G1069S	ENST00000262367	NM_004380.2	1069	Ggc/Agc	16/31	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.375164712424228	2		578	403	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	37	445	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.638	0.528	0.761	0.638	0.528	0.761	SUBCLONAL	1	FALSE	1	0.375164712424228	2		445	309	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923836	72923836	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	24	555	0	ENST00000268489.5:c.3242T>C	p.Val1081Ala	p.V1081A	ENST00000268489	NM_006885.3	1081	gTa/gCa	4/10	1	2	FACETS	0.46	0.361	0.574	0.46	0.361	0.574	SUBCLONAL	1	FALSE	1	0.375164712424228	2		555	278	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991703	72991703	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201821212	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	23	459	3	ENST00000268489.5:c.2342C>T	p.Ala781Val	p.A781V	ENST00000268489	NM_006885.3	781	gCg/gTg	2/10	1	2	FACETS	0.645	0.506	0.804	0.645	0.506	0.804	SUBCLONAL	1	FALSE	1	0.375164712424228	2		462	190	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	75	619	1	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	0.599	0.525	0.68	0.599	0.525	0.68	SUBCLONAL	1	FALSE	1	0.375164712424228	2		620	667	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	95	660	3	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.375164712424228	2		663	408	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865349	40865349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1396223464	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	166	737	0	ENST00000428826.2:c.1082G>A	p.Arg361His	p.R361H	ENST00000428826		361	cGc/cAc	11/21	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.375164712424228	2		737	612	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532644	63532644	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	73	860	0	ENST00000307078.5:c.1935del	p.Leu646TrpfsTer43	p.L646Wfs*43	ENST00000307078	NM_004655.3	645	ccC/cc	8/11	1	2	FACETS	0.576	0.503	0.654	0.576	0.503	0.654	SUBCLONAL	1	FALSE	1	0.375164712424228	2		860	676	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554038	63554038	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	134	574	1	ENST00000307078.5:c.701G>A	p.Trp234Ter	p.W234*	ENST00000307078	NM_004655.3	234	tGg/tAg	2/11	1	2	FACETS	0.766	0.701	0.834	1	0.988	1	SUBCLONAL	2	FALSE	1	0.375164712424228	2		575	466	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78933974	78933974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375708825	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	111	857	0	ENST00000306801.3:c.3574G>A	p.Val1192Ile	p.V1192I	ENST00000306801	NM_020761.2	1192	Gtc/Atc	30/34	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.375164712424228	2		857	491	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395793	45395793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1404495202	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	39	298	0	ENST00000262160.6:c.341G>A	p.Arg114His	p.R114H	ENST00000262160	NM_005901.5	114	cGt/cAt	4/11	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	1	0.375164712424228	2		298	172	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231449	5231449	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	114	762	1	ENST00000357368.4:c.2027del	p.Pro676ArgfsTer134	p.P676Rfs*134	ENST00000357368	NM_002850.3	676	cCg/cg	14/38	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	1	0.375164712424228	2		763	568	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291507	15291507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	59	698	2	ENST00000263388.2:c.3127G>A	p.Ala1043Thr	p.A1043T	ENST00000263388	NM_000435.2	1043	Gcc/Acc	19/33	1	2	FACETS	0.917	0.793	1	0.917	0.793	1	CLONAL	1	FALSE	1	0.375164712424228	2		700	343	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303055	15303055	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	35	1020	1	ENST00000263388.2:c.395C>T	p.Ala132Val	p.A132V	ENST00000263388	NM_000435.2	132	gCc/gTc	4/33	1	2	FACETS	0.344	0.281	0.414	0.344	0.281	0.414	SUBCLONAL	1	FALSE	1	0.375164712424228	2		1021	543	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19261529	19261529	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	44	674	2	ENST00000162023.5:c.16del	p.Ile6SerfsTer14	p.I6Sfs*14	ENST00000162023		6	Atc/tc	6/13	1	2	FACETS	0.557	0.468	0.656	0.557	0.468	0.656	SUBCLONAL	1	FALSE	1	0.375164712424228	2		676	421	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209221	36209221	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs774099554	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	14	343	0	ENST00000222270.7:c.301T>C	p.Trp101Arg	p.W101R	ENST00000222270	NM_014727.1	101	Tgg/Cgg	1/37	1	2	FACETS	0.277	0.2	0.371	0.277	0.2	0.371	SUBCLONAL	1	FALSE	1	0.375164712424228	2		343	269	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	50	886	1	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.48	0.407	0.561	0.48	0.407	0.561	SUBCLONAL	1	FALSE	1	0.375164712424228	2		887	555	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224699	36224699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781596697	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	70	1017	1	ENST00000222270.7:c.7085C>T	p.Pro2362Leu	p.P2362L	ENST00000222270	NM_014727.1	2362	cCg/cTg	30/37	1	2	FACETS	0.65	0.567	0.74	0.65	0.567	0.74	SUBCLONAL	1	FALSE	1	0.375164712424228	2		1018	574	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796784	42796784	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	98	908	0	ENST00000575354.2:c.3242C>A	p.Pro1081Gln	p.P1081Q	ENST00000575354	NM_015125.3	1081	cCg/cAg	14/20	1	2	FACETS	0.84	0.75	0.935	0.84	0.75	0.935	CLONAL	1	FALSE	1	0.375164712424228	2		908	622	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50916702	50916702	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	89	672	0	ENST00000440232.2:c.2174G>A	p.Arg725His	p.R725H	ENST00000440232	NM_002691.3	725	cGt/cAt	18/27	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.375164712424228	2		672	381	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52729053	52729053	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	42	558	0	ENST00000322088.6:c.1745C>A	p.Ala582Asp	p.A582D	ENST00000322088	NM_014225.5	582	gCt/gAt	14/15	1	2	FACETS	0.878	0.738	1	0.878	0.738	1	CLONAL	1	FALSE	1	0.375164712424228	2		558	255	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085971	16085971	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	25	605	0	ENST00000281043.3:c.1147C>T	p.Arg383Cys	p.R383C	ENST00000281043	NM_005378.4	383	Cgc/Tgc	3/3	1	2	FACETS	0.37	0.291	0.461	0.37	0.291	0.461	SUBCLONAL	1	FALSE	1	0.375164712424228	2		605	360	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964953	25964953	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs779368997	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	38	460	0	ENST00000435504.4:c.4253A>G	p.His1418Arg	p.H1418R	ENST00000435504		1418	cAt/cGt	13/13	1	2	FACETS	0.576	0.477	0.685	0.576	0.477	0.685	SUBCLONAL	1	FALSE	1	0.375164712424228	2		460	352	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145358	61145358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1298545694	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	20	381	2	ENST00000295025.8:c.568C>T	p.Arg190Cys	p.R190C	ENST00000295025	NM_002908.2	190	Cgt/Tgt	6/11	1	2	FACETS	0.561	0.431	0.712	0.561	0.431	0.712	SUBCLONAL	1	FALSE	1	0.375164712424228	2		383	190	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339003	225339003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	18	430	0	ENST00000264414.4:c.2266C>T	p.Arg756Ter	p.R756*	ENST00000264414	NM_003590.4	756	Cga/Tga	16/16	1	2	FACETS	0.421	0.317	0.543	0.421	0.317	0.543	SUBCLONAL	1	FALSE	1	0.375164712424228	2		430	228	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574502	41574502	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	60	653	0	ENST00000263253.7:c.6787C>T	p.Arg2263Ter	p.R2263*	ENST00000263253	NM_001429.3	2263	Cga/Tga	31/31	1	2	FACETS	0.661	0.57	0.759	0.661	0.57	0.759	SUBCLONAL	1	FALSE	1	0.375164712424228	2		653	484	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73047264	73047264	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	32	451	0	ENST00000356692.5:c.71T>G	p.Val24Gly	p.V24G	ENST00000356692		24	gTc/gGc	2/9	1	2	FACETS	0.623	0.507	0.752	0.623	0.507	0.752	SUBCLONAL	1	FALSE	1	0.375164712424228	2		451	274	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467573	66467573	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	11	352	1	ENST00000273854.3:c.696del	p.Lys232AsnfsTer36	p.K232Nfs*36	ENST00000273854	NM_004439.5	232	aaA/aa	3/18	0.198636264897182	3	FACETS	0.557	0.387	0.766	0.279	0.193	0.383	INDETERMINATE	1	FALSE	1	0.375164712424228	3		353	125	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540251	187540251	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	37	489	0	ENST00000441802.2:c.7489T>C	p.Tyr2497His	p.Y2497H	ENST00000441802	NM_005245.3	2497	Tat/Cat	10/27	0.198636264897182	3	FACETS	1	0.892	1	0.55	0.457	0.651	INDETERMINATE	1	FALSE	1	0.375164712424228	3		489	213	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31504699	31504699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1032572786	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	34	650	0	ENST00000344624.3:c.1631G>A	p.Arg544His	p.R544H	ENST00000344624		544	cGc/cAc	8/33	0.315127153578581	0	FACETS	0.351	0.287	0.422			1	SUBCLONAL	1	FALSE	0	0.375164712424228	0		650	323	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592099	67592099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	36	342	0	ENST00000274335.5:c.1915C>T	p.Arg639Ter	p.R639*	ENST00000274335		639	Cga/Tga	14/15	1	2	FACETS	0.592	0.488	0.708	0.592	0.488	0.708	SUBCLONAL	1	FALSE	1	0.375164712424228	2		342	324	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675570	86675571	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	16	282	0	ENST00000274376.6:c.2513dup	p.Asn838LysfsTer2	p.N838Kfs*2	ENST00000274376	NM_002890.2	836	gaa/gAaa	19/25	1	2	FACETS	0.82	0.614	1	0.82	0.614	1	CLONAL	1	FALSE	1	0.375164712424228	2		282	104	SUCCESS
APC	324	MSKCC	GRCh37	5	112178879	112178879	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881265	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	13	359	0	ENST00000257430.4:c.7588C>T	p.Arg2530Trp	p.R2530W	ENST00000257430	NM_000038.5	2530	Cgg/Tgg	16/16	1	2	FACETS	0.521	0.374	0.698	0.521	0.374	0.698	SUBCLONAL	1	FALSE	1	0.375164712424228	2		359	133	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524364	176524364	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759042869	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	32	987	0	ENST00000292408.4:c.2225C>T	p.Ala742Val	p.A742V	ENST00000292408	NM_213647.1	742	gCg/gTg	17/18	1	2	FACETS	0.326	0.264	0.397	0.326	0.264	0.397	SUBCLONAL	1	FALSE	1	0.375164712424228	2		987	523	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046050	180046050	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757762772	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	49	419	1	ENST00000261937.6:c.2821G>A	p.Ala941Thr	p.A941T	ENST00000261937	NM_182925.4	941	Gcc/Acc	20/30	0.243494891183657	0	FACETS	0.51	0.434	0.593			1	SUBCLONAL	1	FALSE	0	0.375164712424228	0		420	320	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402683	20402683	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	59	637	0	ENST00000346618.3:c.220C>A	p.Leu74Ile	p.L74I	ENST00000346618	NM_001949.4	74	Ctc/Atc	1/7	0.157457386749768	4	FACETS	0.727	0.625	0.838	0.363	0.312	0.419	INDETERMINATE	1	FALSE	2	0.375164712424228	4		637	595	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912333	29912334	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	60	789	0	ENST00000376809.5:c.954dup	p.Gly319TrpfsTer21	p.G319Wfs*21	ENST00000376809	NM_002116.7	318	ctt/cTtt	5/8	0.157457386749768	4	FACETS	0.812	0.7	0.933	0.406	0.35	0.467	INDETERMINATE	1	FALSE	2	0.375164712424228	4		789	542	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675438	30675438	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780670990	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	77	652	5	ENST00000376406.3:c.2918C>T	p.Ala973Val	p.A973V	ENST00000376406	NM_014641.2	973	gCg/gTg	8/15	0.157457386749768	4	FACETS	1	0.917	1	0.527	0.463	0.595	INDETERMINATE	1	FALSE	2	0.375164712424228	4		657	536	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813522	32813522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566329319	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	80	574	1	ENST00000354258.4:c.2261G>A	p.Arg754His	p.R754H	ENST00000354258	NM_000593.5	754	cGc/cAc	11/11	0.157457386749768	4	FACETS	1	0.946	1	0.563	0.496	0.634	INDETERMINATE	1	FALSE	2	0.375164712424228	4		575	521	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004926	150004926	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	25	413	0	ENST00000253339.5:c.1299G>A	p.Trp433Ter	p.W433*	ENST00000253339		433	tgG/tgA	3/7	0.157457386749768	4	FACETS	0.894	0.709	1	0.447	0.354	0.552	INDETERMINATE	1	FALSE	2	0.375164712424228	4		413	205	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969983	161969983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	57	647	0	ENST00000366898.1:c.986del	p.Gly329AlafsTer106	p.G329Afs*106	ENST00000366898	NM_004562.2	329	gGc/gc	9/12	0.157457386749768	4	FACETS	1	0.902	1	0.53	0.456	0.61	INDETERMINATE	1	FALSE	2	0.375164712424228	4		647	394	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	13	630	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	0.292	0.208	0.395	0.292	0.208	0.395	SUBCLONAL	1	FALSE	1	0.375164712424228	2		630	237	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38134008	38134008	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753149466	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	43	439	1	ENST00000317025.8:c.3878C>T	p.Ala1293Val	p.A1293V	ENST00000317025	NM_023034.1	1293	gCg/gTg	23/24	0.198636264897182	3	FACETS	1	0.918	1	0.572	0.482	0.669	INDETERMINATE	1	FALSE	1	0.375164712424228	3		440	238	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187222	38187222	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	61	765	1	ENST00000317025.8:c.1255del	p.Thr419ProfsTer8	p.T419Pfs*8	ENST00000317025	NM_023034.1	419	Acc/cc	6/24	0.198636264897182	3	FACETS	0.611	0.527	0.703	0.306	0.263	0.352	INDETERMINATE	1	FALSE	1	0.375164712424228	3		766	632	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521528	8521528	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	69	544	0	ENST00000356435.5:c.710G>T	p.Arg237Ile	p.R237I	ENST00000356435		237	aGa/aTa	9/35	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.375164712424228	2		544	285	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636766	8636766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776233840	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	70	538	0	ENST00000356435.5:c.143C>T	p.Thr48Met	p.T48M	ENST00000356435		48	aCg/aTg	2/35	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	FALSE	1	0.375164712424228	2		538	364	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	67	702	3	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.888	0.775	1	0.888	0.775	1	CLONAL	1	FALSE	1	0.375164712424228	2		705	402	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390736	139390736	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	67	907	1	ENST00000277541.6:c.7455del	p.Ser2486ArgfsTer103	p.S2486Rfs*103	ENST00000277541	NM_017617.3	2485	ccC/cc	34/34	1	2	FACETS	0.554	0.481	0.633	0.554	0.481	0.633	SUBCLONAL	1	FALSE	1	0.375164712424228	2		908	645	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652397	48652397	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	23	962	2	ENST00000376670.3:c.1073del	p.Pro358GlnfsTer74	p.P358Qfs*74	ENST00000376670	NM_002049.3	356	ggC/gg	6/6	0.150054206816889	0	FACETS	0.18	0.14	0.227			1	INDETERMINATE	1	FALSE	0	0.375164712424228	0		964	425	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981863	201981863	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774203623	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	103	879	0	ENST00000359651.3:c.574G>A	p.Gly192Ser	p.G192S	ENST00000359651		192	Ggc/Agc	4/8	1	2	FACETS	0.696	0.622	0.774	0.696	0.622	0.774	SUBCLONAL	1	FALSE	1	0.375164712424228	2		879	789	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324892	31324892	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs765875917	NA	P-0039938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	22	180	0	ENST00000412585.2:c.44del	p.Ala15GlyfsTer5	p.A15Gfs*5	ENST00000412585	NM_005514.6	15	gCg/gg	1/8	0.157457386749768	4	FACETS	1	0.868	1	0.58	0.455	0.722	INDETERMINATE	1	FALSE	2	0.375164712424228	4		180	139	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039967-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	68	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.2	2		457	566	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984927	101984927	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039967-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	38	473	0	ENST00000282441.5:c.374C>G	p.Ala125Gly	p.A125G	ENST00000282441	NM_001130145.2	125	gCt/gGt	2/9	1	2	FACETS	0.688	0.568	0.823	0.688	0.568	0.823	SUBCLONAL	1	TRUE	1	0.2	2		473	552	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974696	21974697	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039967-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	46	548	0	ENST00000304494.5:c.130dup	p.Tyr44LeufsTer76	p.Y44Lfs*76	ENST00000304494	NM_000077.4	44	tac/tTac	1/3	0.270405492759367	1	FACETS	0.612	0.514	0.72	0.612	0.514	0.72	SUBCLONAL	1	TRUE	0	0.2	1		548	677	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0040004-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	66	583	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.790873315416878	2		583	149	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040004-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	91	887	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.790873315416878	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.790873315416878	1		887	108	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0040004-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	16	414	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.349	0.26	0.452	0.349	0.26	0.452	SUBCLONAL	1	TRUE	1	0.790873315416878	2		414	116	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519925	NA	P-0040004-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	57	511	0	ENST00000263967.3:c.1357G>C	p.Glu453Gln	p.E453Q	ENST00000263967	NM_006218.2	453	Gaa/Caa	8/21	1	2	FACETS	0.955	0.839	1	0.955	0.839	1	CLONAL	1	TRUE	1	0.790873315416878	2		511	151	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158225	47158225	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040004-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	61	332	1	ENST00000409792.3:c.4474C>T	p.Arg1492Ter	p.R1492*	ENST00000409792	NM_014159.6	1492	Cga/Tga	4/21	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.790873315416878	2		333	149	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828579	72828579	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040004-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	12	762	0	ENST00000268489.5:c.8002C>T	p.Arg2668Ter	p.R2668*	ENST00000268489	NM_006885.3	2668	Cga/Tga	9/10	0.790873315416878	1	FACETS	0.178	0.126	0.241	0.178	0.126	0.241	SUBCLONAL	1	TRUE	0	0.790873315416878	1		762	103	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838350	156838350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745366033	NA	P-0040004-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	48	922	2	ENST00000524377.1:c.628G>A	p.Asp210Asn	p.D210N	ENST00000524377	NM_002529.3	210	Gac/Aac	6/17	0.594032246453501	5	FACETS	1	0.866	1	0.254	0.216	0.295	CLONAL	1	TRUE	1	0.790873315416878	5		924	261	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374999	118374999	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040004-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	42	379	0	ENST00000534358.1:c.8392G>C	p.Asp2798His	p.D2798H	ENST00000534358	NM_005933.3	2798	Gat/Cat	27/36	0.790873315416878	1	FACETS	0.868	0.763	0.97	0.868	0.763	0.97	CLONAL	1	TRUE	0	0.790873315416878	1		379	74	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490518	20490518	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040004-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	45	602	0	ENST00000346618.3:c.1255G>C	p.Glu419Gln	p.E419Q	ENST00000346618	NM_001949.4	419	Gaa/Caa	7/7	0.382831008691142	4	FACETS	1	0.96	1	0.703	0.603	0.808	INDETERMINATE	1	TRUE	2	0.790873315416878	4		602	145	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158109	27158109	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040004-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	43	463	0	ENST00000380036.4:c.333C>G	p.Ile111Met	p.I111M	ENST00000380036	NM_000459.3	111	atC/atG	2/23	1	2	FACETS	0.836	0.716	0.963	0.836	0.716	0.963	CLONAL	1	TRUE	1	0.790873315416878	2		463	130	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827727	72827727	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040004-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	20	582	0	ENST00000268489.5:c.8854C>T	p.Gln2952Ter	p.Q2952*	ENST00000268489	NM_006885.3	2952	Caa/Taa	9/10	0.790873315416878	1	FACETS	0.382	0.299	0.474	0.382	0.299	0.474	SUBCLONAL	1	TRUE	0	0.790873315416878	1		582	80	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0040042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	26	535	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		535	498	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782620	NA	P-0040042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	53	825	1	ENST00000269305.4:c.427G>A	p.Val143Met	p.V143M	ENST00000269305	NM_001126112.2	143	Gtg/Atg	5/11	0.123908809830715	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		826	975	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554668	63554668	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040042-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	30	559	0	ENST00000307078.5:c.71C>A	p.Pro24His	p.P24H	ENST00000307078	NM_004655.3	24	cCc/cAc	2/11	0.123908809830715	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		559	430	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593595	55593657	+	inframe_deletion	In_Frame_Del	DEL	AAGTACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCCAACAC	AAGTACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCCAACAC	-	novel	NA	P-0040351-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	90	560	0	ENST00000288135.5:c.1663_1725del	p.Val555_Gln575del	p.V555_Q575del	ENST00000288135	NM_000222.2	554	gAAGTACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCCAACACaa/gaa	11/21	1	2	FACETS	0.717	0.638	0.801	0.717	0.638	0.801	SUBCLONAL	1	TRUE	1	0.46224342196831	2		560	543	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	108	415	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.55386392322667	2		415	357	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912361	32912361	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41293485	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	49	189	0	ENST00000380152.3:c.3869G>A	p.Cys1290Tyr	p.C1290Y	ENST00000380152		1290	tGc/tAc	11/27	0.504368608620762	3	FACETS	0.801	0.683	0.929	0.401	0.341	0.465	CLONAL	1	TRUE	1	0.55386392322667	3		189	282	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844776	156844776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1292790967	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	152	450	0	ENST00000524377.1:c.1330C>T	p.Arg444Trp	p.R444W	ENST00000524377	NM_002529.3	444	Cgg/Tgg	11/17	1	2	FACETS	0.891	0.818	0.967	0.891	0.818	0.967	CLONAL	1	TRUE	1	0.55386392322667	2		450	616	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	258	588	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.85	0.804	0.896	1	0.995	1	CLONAL	2	TRUE	1	0.55386392322667	2		592	548	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	164	886	1	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.936	0.862	1	0.936	0.862	1	CLONAL	1	TRUE	1	0.55386392322667	2		887	633	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11227537	11227537	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	117	337	0	ENST00000361445.4:c.4291G>A	p.Gly1431Arg	p.G1431R	ENST00000361445	NM_004958.3	1431	Gga/Aga	29/58	1	2	FACETS	0.918	0.833	1	0.918	0.833	1	CLONAL	1	TRUE	1	0.55386392322667	2		337	460	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106488	27106488	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	148	439	0	ENST00000324856.7:c.6099G>T	p.Lys2033Asn	p.K2033N	ENST00000324856	NM_006015.4	2033	aaG/aaT	20/20	1	2	FACETS	0.923	0.847	1	0.923	0.847	1	CLONAL	1	TRUE	1	0.55386392322667	2		439	579	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	183	412	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.839	0.785	0.893	1	0.993	1	CLONAL	2	TRUE	1	0.55386392322667	2		412	394	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466326	120466326	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	119	344	0	ENST00000256646.2:c.4793C>T	p.Ala1598Val	p.A1598V	ENST00000256646	NM_024408.3	1598	gCt/gTt	26/34	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.55386392322667	2		344	396	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	59	191	0	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	1	2	FACETS	0.964	0.841	1	0.964	0.841	1	CLONAL	1	TRUE	1	0.55386392322667	2		191	221	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446283	70446284	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	140	385	0	ENST00000373644.4:c.5230dup	p.Arg1744LysfsTer26	p.R1744Kfs*26	ENST00000373644	NM_030625.2	1741	-/A	11/12	1	2	FACETS	0.919	0.841	1	0.919	0.841	1	CLONAL	1	TRUE	1	0.55386392322667	2		385	550	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	97	259	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	0.937	0.842	1	0.937	0.842	1	CLONAL	1	TRUE	1	0.55386392322667	2		259	374	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717778	89717778	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	72	185	0	ENST00000371953.3:c.801+2T>G		p.X267_splice	ENST00000371953	NM_000314.4	267			1	2	FACETS	0.963	0.851	1	0.963	0.851	1	CLONAL	1	TRUE	1	0.55386392322667	2		185	270	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417809	32417809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	96	262	0	ENST00000332351.3:c.1243C>T	p.His415Tyr	p.H415Y	ENST00000332351	NM_024426.4	415	Cac/Tac	7/10	1	2	FACETS	0.887	0.796	0.982	0.887	0.796	0.982	CLONAL	1	TRUE	1	0.55386392322667	2		262	391	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573764	64573764	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373135175	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	137	412	0	ENST00000312049.6:c.989G>A	p.Arg330His	p.R330H	ENST00000312049	NM_130799.2	330	cGc/cAc	7/10	1	2	FACETS	0.868	0.793	0.946	0.868	0.793	0.946	CLONAL	1	TRUE	1	0.55386392322667	2		412	570	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67197068	67197068	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	105	216	0	ENST00000312629.5:c.309+2T>C		p.X103_splice	ENST00000312629	NM_003952.2	103			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.55386392322667	2		216	347	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589720	69589720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	27	68	2	ENST00000168712.1:c.133C>T	p.Arg45Cys	p.R45C	ENST00000168712	NM_002007.2	45	Cgc/Tgc	1/3	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.55386392322667	2		70	91	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589848	69589848	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	18	28	0	ENST00000168712.1:c.5C>T	p.Ser2Leu	p.S2L	ENST00000168712	NM_002007.2	2	tCg/tTg	1/3	1	2	FACETS	0.97	0.752	1	0.97	0.752	1	CLONAL	1	TRUE	1	0.55386392322667	2		28	67	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431308	49431308	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	97	319	0	ENST00000301067.7:c.9831G>T	p.Gln3277His	p.Q3277H	ENST00000301067	NM_003482.3	3277	caG/caT	34/54	1	2	FACETS	0.97	0.873	1	0.97	0.873	1	CLONAL	1	TRUE	1	0.55386392322667	2		319	361	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856127	111856127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1256080768	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	114	243	0	ENST00000341259.2:c.178G>A	p.Ala60Thr	p.A60T	ENST00000341259	NM_005475.2	60	Gcc/Acc	2/8	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.55386392322667	2		243	392	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112910829	112910829	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	120	247	0	ENST00000351677.2:c.842del	p.Asn281ThrfsTer58	p.N281Tfs*58	ENST00000351677	NM_002834.3	280	Aaa/aa	7/16	1	2	FACETS	0.974	0.886	1	0.974	0.886	1	CLONAL	1	TRUE	1	0.55386392322667	2		247	445	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800902	120800903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748469666	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	161	650	6	ENST00000257552.2:c.345dup	p.Leu116AlafsTer15	p.L116Afs*15	ENST00000257552	NM_002442.3	115	-/G	6/15	1	2	FACETS	0.805	0.74	0.873	0.805	0.74	0.873	CLONAL	1	TRUE	1	0.55386392322667	2		656	722	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28674634	28674634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1428286474	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	15	22	0	ENST00000241453.7:c.14C>T	p.Ala5Val	p.A5V	ENST00000241453	NM_004119.2	5	gCg/gTg	1/24	0.504368608620762	3	FACETS	0.752	0.573	0.947	0.752	0.573	0.947	CLONAL	2	TRUE	1	0.55386392322667	3		22	46	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609759	81609759	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	114	281	0	ENST00000298171.2:c.1357A>G	p.Met453Val	p.M453V	ENST00000298171	NM_000369.2	453	Atg/Gtg	10/10	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.55386392322667	2		281	386	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242076	105242076	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	177	464	0	ENST00000349310.3:c.348G>T	p.Glu116Asp	p.E116D	ENST00000349310	NM_001014432.1	116	gaG/gaT	6/15	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.55386392322667	2		464	625	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41021799	41021799	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	129	298	0	ENST00000267868.3:c.741G>C	p.Arg247Ser	p.R247S	ENST00000267868	NM_002875.4	247	agG/agC	8/10	1	2	FACETS	0.892	0.813	0.975	0.892	0.813	0.975	CLONAL	1	TRUE	1	0.55386392322667	2		298	522	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720257	43720257	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	121	359	0	ENST00000382044.4:c.3785T>C	p.Val1262Ala	p.V1262A	ENST00000382044	NM_001141980.1	1262	gTg/gCg	18/28	1	2	FACETS	0.897	0.815	0.983	0.897	0.815	0.983	CLONAL	1	TRUE	1	0.55386392322667	2		359	487	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003773	45003773	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	221	326	0	ENST00000558401.1:c.29T>G	p.Leu10Arg	p.L10R	ENST00000558401	NM_004048.2	10	cTc/cGc	1/4	1	2	FACETS	0.941	0.889	0.993	1	0.995	1	CLONAL	2	TRUE	1	0.55386392322667	2		326	424	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67459125	67459125	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	334	419	0	ENST00000327367.4:c.545del	p.Pro182LeufsTer4	p.P182Lfs*4	ENST00000327367	NM_005902.3	181	Ccc/cc	4/9	0.55386392322667	2	FACETS	0.945	0.903	0.988	0.945	0.903	0.988	CLONAL	2	TRUE	0	0.55386392322667	2		419	638	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251016	99251016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763743119	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	273	416	0	ENST00000268035.6:c.320G>A	p.Arg107His	p.R107H	ENST00000268035	NM_000875.3	107	cGc/cAc	2/21	0.55386392322667	2	FACETS	0.982	0.934	1	0.982	0.934	1	CLONAL	2	TRUE	0	0.55386392322667	2		416	502	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347983	347983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760961378	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	147	478	0	ENST00000262320.3:c.1523del	p.Gly508ValfsTer197	p.G508Vfs*197	ENST00000262320	NM_003502.3	508	gGt/gt	6/11	1	2	FACETS	0.948	0.87	1	0.948	0.87	1	CLONAL	1	TRUE	1	0.55386392322667	2		478	560	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2111963	2111963	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1567428610	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	42	461	0	ENST00000219476.3:c.1211A>G	p.Gln404Arg	p.Q404R	ENST00000219476	NM_000548.3	404	cAg/cGg	12/42	1	2	FACETS	0.233	0.194	0.277	0.233	0.194	0.277	SUBCLONAL	1	TRUE	1	0.55386392322667	2		461	651	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	93	333	1	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	0.93	0.834	1	0.93	0.834	1	CLONAL	1	TRUE	1	0.55386392322667	2		334	361	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644890	67644890	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs777308398	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	109	346	0	ENST00000264010.4:c.155A>G	p.Gln52Arg	p.Q52R	ENST00000264010	NM_006565.3	52	cAg/cGg	3/12	1	2	FACETS	0.823	0.743	0.907	0.823	0.743	0.907	CLONAL	1	TRUE	1	0.55386392322667	2		346	478	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821889	72821890	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	66	219	0	ENST00000268489.5:c.10285dup	p.Arg3429ProfsTer2	p.R3429Pfs*2	ENST00000268489	NM_006885.3	3429	cgt/cCgt	10/10	1	2	FACETS	0.747	0.653	0.847	0.747	0.653	0.847	SUBCLONAL	1	TRUE	1	0.55386392322667	2		219	319	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993845	72993845	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372931285	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	37	376	1	ENST00000268489.5:c.200C>T	p.Ser67Leu	p.S67L	ENST00000268489	NM_006885.3	67	tCg/tTg	2/10	1	2	FACETS	0.399	0.329	0.476	0.399	0.329	0.476	SUBCLONAL	1	TRUE	1	0.55386392322667	2		377	335	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351197	89351197	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	163	397	0	ENST00000301030.4:c.1753A>G	p.Ser585Gly	p.S585G	ENST00000301030	NM_001256183.1	585	Agt/Ggt	9/13	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.55386392322667	2		397	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	176	1196	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.55386392322667	2		1196	553	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	97	179	1	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	0.905	0.813	1	0.905	0.813	1	CLONAL	1	TRUE	1	0.55386392322667	2		180	387	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38504699	38504699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773619675	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	155	387	0	ENST00000254066.5:c.310G>A	p.Ala104Thr	p.A104T	ENST00000254066	NM_000964.3	104	Gcc/Acc	3/9	1	2	FACETS	0.968	0.891	1	0.968	0.891	1	CLONAL	1	TRUE	1	0.55386392322667	2		387	578	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40364169	40364169	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	149	394	0	ENST00000293328.3:c.1513C>T	p.Pro505Ser	p.P505S	ENST00000293328	NM_012448.3	505	Cca/Tca	13/19	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.55386392322667	2		394	488	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40451808	40451808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766259233	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	128	448	0	ENST00000345506.4:c.590G>A	p.Arg197His	p.R197H	ENST00000345506	NM_003152.3	197	cGt/cAt	7/20	1	2	FACETS	0.967	0.882	1	0.967	0.882	1	CLONAL	1	TRUE	1	0.55386392322667	2		448	478	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	303	1445	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.977	0.932	1	1	0.996	1	CLONAL	2	TRUE	1	0.55386392322667	2		1452	560	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740623	58740624	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs763475304	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	127	318	1	ENST00000305921.3:c.1535dup	p.Asn512LysfsTer16	p.N512Kfs*16	ENST00000305921	NM_003620.3	510	caa/cAaa	6/6	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.55386392322667	2		319	439	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59820469	59820469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778136	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	82	225	1	ENST00000259008.2:c.2284C>T	p.Arg762Cys	p.R762C	ENST00000259008	NM_032043.2	762	Cgt/Tgt	16/20	1	2	FACETS	0.8	0.711	0.895	0.8	0.711	0.895	SUBCLONAL	1	TRUE	1	0.55386392322667	2		226	370	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221222	1221222	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	89	498	0	ENST00000326873.7:c.745A>G	p.Thr249Ala	p.T249A	ENST00000326873	NM_000455.4	249	Acc/Gcc	6/10	1	2	FACETS	0.485	0.43	0.544	0.485	0.43	0.544	SUBCLONAL	1	TRUE	1	0.55386392322667	2		498	662	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350722	15350722	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	198	475	1	ENST00000263377.2:c.3281A>G	p.Gln1094Arg	p.Q1094R	ENST00000263377	NM_058243.2	1094	cAg/cGg	15/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.55386392322667	2		476	688	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946817	17946817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778415	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	172	487	0	ENST00000458235.1:c.1830G>A	p.Met610Ile	p.M610I	ENST00000458235	NM_000215.3	610	atG/atA	14/24	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.55386392322667	2		487	587	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257163	19257163	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	99	335	2	ENST00000162023.5:c.800del	p.Pro267LeufsTer?	p.P267Lfs*?	ENST00000162023		267	cCt/ct	12/13	1	2	FACETS	0.977	0.88	1	0.977	0.88	1	CLONAL	1	TRUE	1	0.55386392322667	2		337	366	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220868	36220868	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	15	149	0	ENST00000222270.7:c.4918C>T	p.Arg1640Cys	p.R1640C	ENST00000222270	NM_014727.1	1640	Cgc/Tgc	23/37	1	2	FACETS	0.426	0.314	0.559	0.426	0.314	0.559	SUBCLONAL	1	TRUE	1	0.55386392322667	2		149	127	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919786	50919786	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1555793361	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	131	400	0	ENST00000440232.2:c.2953+1G>A		p.X985_splice	ENST00000440232	NM_002691.3	985			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.55386392322667	2		400	438	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010482	48010482	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1558644995	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	84	229	0	ENST00000234420.5:c.114del	p.Ala40ProfsTer41	p.A40Pfs*41	ENST00000234420	NM_000179.2	37	gCc/gc	1/10	1	2	FACETS	0.991	0.885	1	0.991	0.885	1	CLONAL	1	TRUE	1	0.55386392322667	2		229	306	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	120	309	7	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.901	0.818	0.987	0.901	0.818	0.987	CLONAL	1	TRUE	1	0.55386392322667	2		316	481	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190742010	190742010	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142159998	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	54	226	0	ENST00000441310.2:c.2647C>T	p.Arg883Cys	p.R883C	ENST00000441310	NM_000534.4	883	Cgt/Tgt	13/13	1	2	FACETS	0.816	0.704	0.935	0.816	0.704	0.935	CLONAL	1	TRUE	1	0.55386392322667	2		226	239	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426722	212426722	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	122	314	0	ENST00000342788.4:c.2393T>G	p.Leu798Arg	p.L798R	ENST00000342788	NM_005235.2	798	cTt/cGt	20/28	1	2	FACETS	0.937	0.853	1	0.937	0.853	1	CLONAL	1	TRUE	1	0.55386392322667	2		314	470	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	120	410	1	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	1	2	FACETS	0.853	0.774	0.935	0.853	0.774	0.935	CLONAL	1	TRUE	1	0.55386392322667	2		411	508	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574678	41574679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs754418509	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	166	545	0	ENST00000263253.7:c.6970dup	p.His2324ProfsTer55	p.H2324Pfs*55	ENST00000263253	NM_001429.3	2321	-/C	31/31	1	2	FACETS	0.929	0.857	1	0.929	0.857	1	CLONAL	1	TRUE	1	0.55386392322667	2		545	645	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042545	37042545	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs267607734	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	73	190	1	ENST00000231790.2:c.306+1G>A		p.X102_splice	ENST00000231790	NM_000249.3	102			1	2	FACETS	0.861	0.76	0.968	0.861	0.76	0.968	CLONAL	1	TRUE	1	0.55386392322667	2		191	306	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050349	37050349	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63749959	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	90	237	0	ENST00000231790.2:c.503del	p.Asn168IlefsTer34	p.N168Ifs*34	ENST00000231790	NM_000249.3	166	ttA/tt	6/19	1	2	FACETS	0.823	0.735	0.915	0.823	0.735	0.915	CLONAL	1	TRUE	1	0.55386392322667	2		237	395	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181390	38181390	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	48	270	0	ENST00000396334.3:c.403C>G	p.Gln135Glu	p.Q135E	ENST00000396334	NM_002468.4	135	Cag/Gag	2/5	1	2	FACETS	0.423	0.358	0.494	0.423	0.358	0.494	SUBCLONAL	1	TRUE	1	0.55386392322667	2		270	410	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158111	47158111	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	114	233	0	ENST00000409792.3:c.4586+2T>C		p.X1529_splice	ENST00000409792	NM_014159.6	1529			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.55386392322667	2		233	368	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651313	52651313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777012889	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	92	278	0	ENST00000394830.3:c.1783C>T	p.Arg595Trp	p.R595W	ENST00000394830	NM_018313.4	595	Cgg/Tgg	15/30	1	2	FACETS	0.91	0.815	1	0.91	0.815	1	CLONAL	1	TRUE	1	0.55386392322667	2		278	365	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447426	187447426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1379487528	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	129	426	1	ENST00000232014.4:c.767G>A	p.Ser256Asn	p.S256N	ENST00000232014	NM_001130845.1	256	aGc/aAc	5/10	1	2	FACETS	0.894	0.815	0.977	0.894	0.815	0.977	CLONAL	1	TRUE	1	0.55386392322667	2		427	521	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980558	1980559	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs752037034	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	123	446	9	ENST00000382891.5:c.4028dup	p.Glu1344ArgfsTer91	p.E1344Rfs*91	ENST00000382891	NM_133335.3	1340	-/C	22/22	1	2	FACETS	0.912	0.83	0.998	0.912	0.83	0.998	CLONAL	1	TRUE	1	0.55386392322667	2		455	487	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	72	233	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.915	0.808	1	0.915	0.808	1	CLONAL	1	TRUE	1	0.55386392322667	2		233	284	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521346	187521346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	120	376	0	ENST00000441802.2:c.11809G>A	p.Ala3937Thr	p.A3937T	ENST00000441802	NM_005245.3	3937	Gcc/Acc	22/27	1	2	FACETS	0.994	0.904	1	0.994	0.904	1	CLONAL	1	TRUE	1	0.55386392322667	2		376	436	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534269	187534269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1401735284	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	91	260	0	ENST00000441802.2:c.9457G>A	p.Asp3153Asn	p.D3153N	ENST00000441802	NM_005245.3	3153	Gac/Aac	13/27	1	2	FACETS	0.915	0.82	1	0.915	0.82	1	CLONAL	1	TRUE	1	0.55386392322667	2		260	359	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675571	86675571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1561325048	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	19	121	0	ENST00000274376.6:c.2513del	p.Asn838MetfsTer4	p.N838Mfs*4	ENST00000274376	NM_002890.2	836	gAa/ga	19/25	1	2	FACETS	0.369	0.281	0.471	0.369	0.281	0.471	SUBCLONAL	1	TRUE	1	0.55386392322667	2		121	186	SUCCESS
APC	324	MSKCC	GRCh37	5	112176210	112176210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529480958	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	102	278	0	ENST00000257430.4:c.4919G>A	p.Arg1640Gln	p.R1640Q	ENST00000257430	NM_000038.5	1640	cGg/cAg	16/16	1	2	FACETS	0.828	0.745	0.915	0.828	0.745	0.915	CLONAL	1	TRUE	1	0.55386392322667	2		278	445	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631305	117631305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355678032	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	24	274	0	ENST00000368508.3:c.6373G>A	p.Val2125Ile	p.V2125I	ENST00000368508	NM_002944.2	2125	Gtt/Att	40/43	1	2	FACETS	0.198	0.154	0.248	0.198	0.154	0.248	SUBCLONAL	1	TRUE	1	0.55386392322667	2		274	438	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146945	38146945	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	150	658	0	ENST00000317025.8:c.3197del	p.Asn1066ThrfsTer16	p.N1066Tfs*16	ENST00000317025	NM_023034.1	1066	aAc/ac	18/24	1	2	FACETS	0.849	0.779	0.922	0.849	0.779	0.922	CLONAL	1	TRUE	1	0.55386392322667	2		658	638	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992721	68992721	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs764112302	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	82	306	2	ENST00000288368.4:c.1693del	p.Ser565ArgfsTer10	p.S565Rfs*10	ENST00000288368	NM_024870.2	562	cgT/cg	16/40	1	2	FACETS	0.634	0.561	0.712	0.634	0.561	0.712	SUBCLONAL	1	TRUE	1	0.55386392322667	2		308	467	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129903	69129903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752113779	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	98	253	1	ENST00000288368.4:c.4657G>A	p.Gly1553Arg	p.G1553R	ENST00000288368	NM_024870.2	1553	Gga/Aga	38/40	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.55386392322667	2		254	344	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229625	98229625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747762028	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	90	236	0	ENST00000331920.6:c.2333C>T	p.Thr778Met	p.T778M	ENST00000331920	NM_000264.3	778	aCg/aTg	15/24	1	2	FACETS	0.853	0.762	0.948	0.853	0.762	0.948	CLONAL	1	TRUE	1	0.55386392322667	2		236	381	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564755	139564755	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	164	737	1	ENST00000308874.7:c.549del	p.Arg184GlyfsTer13	p.R184Gfs*13	ENST00000308874		182	Ccc/cc	7/10	1	2	FACETS	0.994	0.917	1	0.994	0.917	1	CLONAL	1	TRUE	1	0.55386392322667	2		738	596	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918596	44918597	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	104	146	0	ENST00000377967.4:c.1083_1084del	p.Tyr362Ter	p.Y362*	ENST00000377967	NM_021140.2	360	aCT/a	12/29	1	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.55386392322667	1		146	203	SUCCESS
AR	367	MSKCC	GRCh37	X	66937449	66937449	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	141	199	0	ENST00000374690.3:c.2303A>G	p.Asp768Gly	p.D768G	ENST00000374690	NM_000044.3	768	gAt/gGt	5/8	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.55386392322667	1		199	261	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354588	70354588	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	145	162	0	ENST00000374080.3:c.4753A>G	p.Met1585Val	p.M1585V	ENST00000374080		1585	Atg/Gtg	35/45	1	1	FACETS	0.876	0.826	0.925	1	0.993	1	CLONAL	2	TRUE	0	0.55386392322667	1		162	216	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512376	38512377	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	69	443	0	ENST00000254066.5:c.1293dup	p.Arg432AlafsTer14	p.R432Afs*14	ENST00000254066	NM_000964.3	429	-/G	9/9	1	2	FACETS	0.545	0.476	0.619	0.545	0.476	0.619	SUBCLONAL	1	TRUE	1	0.55386392322667	2		443	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0040601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	149	661	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.280172824859704	1	FACETS	0.979	0.894	1	0.979	0.894	1	CLONAL	1	TRUE	0	0.280172824859704	1		662	934	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	212	518	0	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	0.280172824859704	2	FACETS	0.851	0.792	0.913	0.851	0.792	0.913	CLONAL	2	TRUE	0	0.280172824859704	2		518	889	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591825	48591825	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	89	438	0	ENST00000342988.3:c.988G>C	p.Glu330Gln	p.E330Q	ENST00000342988	NM_005359.5	330	Gaa/Caa	9/12	0.280172824859704	1	FACETS	0.843	0.748	0.944	0.843	0.748	0.944	CLONAL	1	TRUE	0	0.280172824859704	1		438	648	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611132	100611132	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	147	593	0	ENST00000308731.7:c.1474C>T	p.Arg492Cys	p.R492C	ENST00000308731	NM_000061.2	492	Cgc/Tgc	15/19	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.280172824859704	2		593	958	SUCCESS
APC	324	MSKCC	GRCh37	5	112174878	112174878	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	69	264	0	ENST00000257430.4:c.3587C>A	p.Ser1196Ter	p.S1196*	ENST00000257430	NM_000038.5	1196	tCa/tAa	16/16	1	2	FACETS	0.935	0.815	1	0.935	0.815	1	CLONAL	1	TRUE	1	0.280172824859704	2		264	527	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237614	16237614	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	96	375	1	ENST00000375759.3:c.1061G>A	p.Gly354Asp	p.G354D	ENST00000375759	NM_015001.2	354	gGc/gAc	5/15	1	2	FACETS	0.922	0.822	1	0.922	0.822	1	CLONAL	1	TRUE	1	0.280172824859704	2		376	743	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793418	18793418	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs527467030	NA	P-0040601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	109	395	0	ENST00000266497.5:c.4115A>G	p.Tyr1372Cys	p.Y1372C	ENST00000266497		1372	tAt/tGt	30/31	1	2	FACETS	0.949	0.852	1	0.949	0.852	1	CLONAL	1	TRUE	1	0.280172824859704	2		395	820	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412907	49412907	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	138	625	0	ENST00000418115.1:c.116T>C	p.Phe39Ser	p.F39S	ENST00000418115	NM_001664.2	39	tTt/tCt	2/5	1	2	FACETS	0.825	0.749	0.905	0.825	0.749	0.905	CLONAL	1	TRUE	1	0.280172824859704	2		625	1194	SUCCESS
APC	324	MSKCC	GRCh37	5	112116595	112116595	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	63	344	0	ENST00000257430.4:c.640del	p.Ala214HisfsTer5	p.A214Hfs*5	ENST00000257430	NM_000038.5	214	Gca/ca	6/16	1	2	FACETS	0.764	0.66	0.875	0.764	0.66	0.875	SUBCLONAL	1	TRUE	1	0.280172824859704	2		344	589	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0040654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	303	550	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.249036683600771	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	TRUE	0	0.263922709043526	3		552	822	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	63	168	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	0.263922709043526	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	2	TRUE	0	0.263922709043526	2		168	224	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250823	153250823	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1159697496	NA	P-0040654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	93	216	1	ENST00000281708.4:c.1236+1G>A		p.X412_splice	ENST00000281708	NM_033632.3	412			0.263922709043526	2	FACETS	0.849	0.76	0.943	0.849	0.76	0.943	CLONAL	2	TRUE	0	0.263922709043526	2		217	415	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939165	36939165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779773667	NA	P-0040654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	215	592	0	ENST00000361632.4:c.544G>A	p.Gly182Arg	p.G182R	ENST00000361632		182	Ggg/Agg	5/16	0.263922709043526	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.263922709043526	3		592	848	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551943	150551943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	78	323	0	ENST00000369026.2:c.64G>A	p.Gly22Arg	p.G22R	ENST00000369026	NM_021960.4	22	Ggg/Agg	1/3	0.263922709043526	3	FACETS	1	0.943	1	0.562	0.494	0.635	CLONAL	1	TRUE	1	0.263922709043526	3		323	595	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573894	18573894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759658584	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	85	345	0	ENST00000266497.5:c.2212C>T	p.Arg738Cys	p.R738C	ENST00000266497		738	Cgt/Tgt	15/31	1	2	FACETS	0.882	0.784	0.987	0.882	0.784	0.987	CLONAL	1	TRUE	1	0.43	2		345	448	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	71	333	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.992	0.872	1	0.992	0.872	1	CLONAL	1	TRUE	1	0.43	2		333	333	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104712	193104712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	91	290	0	ENST00000367435.3:c.416G>A	p.Arg139Gln	p.R139Q	ENST00000367435	NM_024529.4	139	cGa/cAa	5/17	1	2	FACETS	0.996	0.889	1	0.996	0.889	1	CLONAL	1	TRUE	1	0.43	2		290	425	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793710	89793710	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	142	404	0	ENST00000336032.3:c.779A>C	p.Lys260Thr	p.K260T	ENST00000336032	NM_006813.2	260	aAa/aCa	2/2	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.43	2		404	648	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339746	116339746	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	125	389	0	ENST00000397752.3:c.608C>A	p.Ser203Tyr	p.S203Y	ENST00000397752	NM_000245.2	203	tCt/tAt	2/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.43	2		389	510	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416138	416138	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	114	362	0	ENST00000399788.2:c.4048C>T	p.Arg1350Ter	p.R1350*	ENST00000399788	NM_001042603.1	1350	Cga/Tga	24/28	1	2	FACETS	0.908	0.82	1	0.908	0.82	1	CLONAL	1	TRUE	1	0.43	2		362	584	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724120	61724120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781425578	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	96	304	0	ENST00000401558.2:c.782G>A	p.Arg261Gln	p.R261Q	ENST00000401558	NM_003400.3	261	cGa/cAa	10/25	1	2	FACETS	0.921	0.824	1	0.921	0.824	1	CLONAL	1	TRUE	1	0.43	2		304	485	SUCCESS
APC	324	MSKCC	GRCh37	5	112174802	112174802	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201830995	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	72	269	0	ENST00000257430.4:c.3511C>T	p.Arg1171Cys	p.R1171C	ENST00000257430	NM_000038.5	1171	Cgt/Tgt	16/16	1	2	FACETS	0.925	0.813	1	0.925	0.813	1	CLONAL	1	TRUE	1	0.43	2		269	362	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	368	622	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	1	0.991	1	1	0.997	1	CLONAL	2	TRUE	1	0.43	2		622	753	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55597561	55597561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751005114	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	113	446	1	ENST00000288135.5:c.2209G>A	p.Asp737Asn	p.D737N	ENST00000288135	NM_000222.2	737	Gac/Aac	15/21	0.3	1	FACETS	0.69	0.622	0.761	0.69	0.622	0.761	SUBCLONAL	1	TRUE	0	0.43	1		447	598	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	22	337	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.188	0.145	0.239	0.188	0.145	0.239	SUBCLONAL	1	TRUE	1	0.43	2		337	543	SUCCESS
APC	324	MSKCC	GRCh37	5	112175060	112175060	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	52	219	0	ENST00000257430.4:c.3769G>T	p.Glu1257Ter	p.E1257*	ENST00000257430	NM_000038.5	1257	Gaa/Taa	16/16	1	2	FACETS	0.93	0.799	1	0.93	0.799	1	CLONAL	1	TRUE	1	0.43	2		219	260	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586502	189586502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757536818	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	28	339	0	ENST00000264731.3:c.1126C>T	p.Arg376Cys	p.R376C	ENST00000264731	NM_003722.4	376	Cgc/Tgc	8/14	1	2	FACETS	0.239	0.19	0.295	0.239	0.19	0.295	SUBCLONAL	1	TRUE	1	0.43	2		339	545	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426812	121426812	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377110124	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	166	610	1	ENST00000257555.6:c.503G>A	p.Arg168His	p.R168H	ENST00000257555		168	cGc/cAc	2/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.43	2		611	734	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612028	189612028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs900140738	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	37	426	2	ENST00000264731.3:c.1780C>T	p.Arg594Ter	p.R594*	ENST00000264731	NM_003722.4	594	Cga/Tga	14/14	1	2	FACETS	0.277	0.227	0.332	0.277	0.227	0.332	SUBCLONAL	1	TRUE	1	0.43	2		428	622	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576407	67576407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201598843	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	40	301	0	ENST00000274335.5:c.686C>T	p.Ser229Leu	p.S229L	ENST00000274335		229	tCg/tTg	5/15	1	2	FACETS	0.424	0.352	0.504	0.424	0.352	0.504	SUBCLONAL	1	TRUE	1	0.43	2		301	439	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457763	149457763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376495524	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	101	634	0	ENST00000286301.3:c.641G>A	p.Arg214Gln	p.R214Q	ENST00000286301	NM_005211.3	214	cGg/cAg	5/22	1	2	FACETS	0.576	0.514	0.641	0.576	0.514	0.641	SUBCLONAL	1	TRUE	1	0.43	2		634	816	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228613019	228613019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773567566	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	100	416	1	ENST00000366696.1:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000366696	NM_003493.2	3	cGa/cAa	1/1	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.43	2		417	454	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698180	47698180	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63751411	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	122	317	0	ENST00000233146.2:c.1738G>T	p.Glu580Ter	p.E580*	ENST00000233146	NM_000251.2	580	Gaa/Taa	11/16	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.43	2		317	564	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672462	30672462	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148215318	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	246	742	2	ENST00000376406.3:c.4498G>A	p.Ala1500Thr	p.A1500T	ENST00000376406	NM_014641.2	1500	Gcc/Acc	10/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.43	2		744	997	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953624	38953624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199645898	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	33	229	0	ENST00000357387.3:c.2729G>A	p.Arg910His	p.R910H	ENST00000357387	NM_152756.3	910	cGt/cAt	28/38	1	2	FACETS	0.387	0.315	0.468	0.387	0.315	0.468	SUBCLONAL	1	TRUE	1	0.43	2		229	397	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163542	32163542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1187763031	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	120	665	0	ENST00000375023.3:c.5684C>T	p.Ser1895Phe	p.S1895F	ENST00000375023	NM_004557.3	1895	tCt/tTt	30/30	1	2	FACETS	0.882	0.798	0.97	0.882	0.798	0.97	CLONAL	1	TRUE	1	0.43	2		665	633	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349799	89349799	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	293	801	0	ENST00000301030.4:c.3151G>T	p.Glu1051Ter	p.E1051*	ENST00000301030	NM_001256183.1	1051	Gaa/Taa	9/13	1	2	FACETS	0.992	0.932	1	0.992	0.932	1	CLONAL	1	TRUE	1	0.43	2		801	1374	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961059	55961059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530419081	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	187	724	0	ENST00000263923.4:c.2881C>T	p.Arg961Trp	p.R961W	ENST00000263923	NM_002253.2	961	Cgg/Tgg	21/30	0.3	1	FACETS	0.688	0.635	0.743	0.688	0.635	0.743	SUBCLONAL	1	TRUE	0	0.43	1		724	992	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944562	40944562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868189942	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	41	462	0	ENST00000373198.4:c.1940C>T	p.Ser647Leu	p.S647L	ENST00000373198	NM_133170.3	647	tCg/tTg	12/32	1	2	FACETS	0.319	0.265	0.38	0.319	0.265	0.38	SUBCLONAL	1	TRUE	1	0.43	2		462	597	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589618	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519838	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	89	214	0	ENST00000274335.5:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000274335		461	Cga/Tga	10/15	1	2	FACETS	0.902	0.803	1	0.902	0.803	1	CLONAL	1	TRUE	1	0.43	2		214	459	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624245	89624245	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554890335	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	57	211	0	ENST00000371953.3:c.19G>T	p.Glu7Ter	p.E7*	ENST00000371953	NM_000314.4	7	Gag/Tag	1/9	1	2	FACETS	0.828	0.715	0.95	0.828	0.715	0.95	CLONAL	1	TRUE	1	0.43	2		211	320	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456431	99456431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	146	521	0	ENST00000268035.6:c.1748C>T	p.Ala583Val	p.A583V	ENST00000268035	NM_000875.3	583	gCt/gTt	8/21	1	2	FACETS	0.935	0.855	1	0.935	0.855	1	CLONAL	1	TRUE	1	0.43	2		521	726	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534356	187534356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770029391	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	60	696	3	ENST00000441802.2:c.9370G>A	p.Glu3124Lys	p.E3124K	ENST00000441802	NM_005245.3	3124	Gaa/Aaa	13/27	1	2	FACETS	0.302	0.259	0.349	0.302	0.259	0.349	SUBCLONAL	1	TRUE	1	0.43	2		699	924	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539690	187539690	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs748166431	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	127	460	0	ENST00000441802.2:c.8050G>T	p.Glu2684Ter	p.E2684*	ENST00000441802	NM_005245.3	2684	Gaa/Taa	10/27	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.43	2		460	557	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119819	108119819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786203815	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	44	245	0	ENST00000278616.4:c.1225C>T	p.Leu409Phe	p.L409F	ENST00000278616	NM_000051.3	409	Ctt/Ttt	9/63	1	2	FACETS	0.47	0.395	0.554	0.47	0.395	0.554	SUBCLONAL	1	TRUE	1	0.43	2		245	435	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339799	116339799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	129	462	0	ENST00000397752.3:c.661G>A	p.Glu221Lys	p.E221K	ENST00000397752	NM_000245.2	221	Gaa/Aaa	2/21	1	2	FACETS	0.966	0.879	1	0.966	0.879	1	CLONAL	1	TRUE	1	0.43	2		462	621	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027958	48027958	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1558666905	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	107	341	0	ENST00000234420.5:c.2836G>T	p.Glu946Ter	p.E946*	ENST00000234420	NM_000179.2	946	Gaa/Taa	4/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.43	2		341	424	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503099	125503099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140276570	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	123	332	0	ENST00000428830.2:c.466C>T	p.Arg156Trp	p.R156W	ENST00000428830	NM_001114121.2	156	Cgg/Tgg	6/14	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.43	2		332	520	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845518	128845518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748004767	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	81	731	0	ENST00000249373.3:c.815C>T	p.Ala272Val	p.A272V	ENST00000249373	NM_005631.4	272	gCg/gTg	4/12	1	2	FACETS	0.387	0.34	0.438	0.387	0.34	0.438	SUBCLONAL	1	TRUE	1	0.43	2		731	973	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809476	36809476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	88	783	0	ENST00000373129.3:c.989C>T	p.Ala330Val	p.A330V	ENST00000373129	NM_032017.1	330	gCc/gTc	10/12	1	2	FACETS	0.376	0.332	0.423	0.376	0.332	0.423	SUBCLONAL	1	TRUE	1	0.43	2		783	1089	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47684730	47684730	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	93	381	0	ENST00000347630.2:c.719G>A	p.Arg240Gln	p.R240Q	ENST00000347630	NM_001007230.1	240	cGa/cAa	9/11	1	2	FACETS	0.741	0.66	0.827	0.741	0.66	0.827	SUBCLONAL	1	TRUE	1	0.43	2		381	584	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008324	29008324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770377283	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	68	288	0	ENST00000282397.4:c.547C>T	p.Arg183Cys	p.R183C	ENST00000282397	NM_002019.4	183	Cgc/Tgc	5/30	1	2	FACETS	0.797	0.696	0.904	0.797	0.696	0.904	CLONAL	1	TRUE	1	0.43	2		288	397	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817871	3817871	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	158	469	0	ENST00000262367.5:c.3100G>T	p.Glu1034Ter	p.E1034*	ENST00000262367	NM_004380.2	1034	Gaa/Taa	16/31	1	2	FACETS	0.946	0.868	1	0.946	0.868	1	CLONAL	1	TRUE	1	0.43	2		469	777	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50784011	50784011	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	201	634	0	ENST00000398568.2:c.402G>T	p.Gln134His	p.Q134H	ENST00000398568	NM_001042412.1	134	caG/caT	3/18	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.43	2		634	854	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712823	43712823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28903077	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	247	842	2	ENST00000382044.4:c.4361G>A	p.Arg1454Gln	p.R1454Q	ENST00000382044	NM_001141980.1	1454	cGa/cAa	21/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.43	2		844	1020	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931826	68931826	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs759461290	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	52	450	1	ENST00000288368.4:c.256G>T	p.Glu86Ter	p.E86*	ENST00000288368	NM_024870.2	86	Gaa/Taa	3/40	1	2	FACETS	0.308	0.262	0.36	0.308	0.262	0.36	SUBCLONAL	1	TRUE	1	0.43	2		451	784	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884466	151884466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1435892915	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	116	333	0	ENST00000262189.6:c.4889C>T	p.Ser1630Leu	p.S1630L	ENST00000262189	NM_170606.2	1630	tCg/tTg	33/59	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.43	2		333	506	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793198	33793198	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	27	126	1	ENST00000498907.2:c.123G>T	p.Gln41His	p.Q41H	ENST00000498907	NM_004364.3	41	caG/caT	1/1	1	2	FACETS	0.743	0.597	0.906	0.743	0.597	0.906	CLONAL	1	TRUE	1	0.43	2		127	169	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783338	9783338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	141	573	0	ENST00000377346.4:c.2582C>T	p.Ser861Phe	p.S861F	ENST00000377346	NM_005026.3	861	tCc/tTc	20/24	1	2	FACETS	0.877	0.8	0.957	0.877	0.8	0.957	CLONAL	1	TRUE	1	0.43	2		573	748	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556080	29556080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762709897	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	80	260	0	ENST00000356175.3:c.2447G>A	p.Arg816Gln	p.R816Q	ENST00000356175	NM_000267.3	816	cGa/cAa	21/57	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.43	2		260	315	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945780	17945780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1009464631	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	81	861	1	ENST00000458235.1:c.2080G>A	p.Glu694Lys	p.E694K	ENST00000458235	NM_000215.3	694	Gag/Aag	16/24	1	2	FACETS	0.403	0.354	0.456	0.403	0.354	0.456	SUBCLONAL	1	TRUE	1	0.43	2		862	935	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696399	47696399	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	162	577	0	ENST00000347630.2:c.424C>A	p.Leu142Ile	p.L142I	ENST00000347630	NM_001007230.1	142	Ctt/Att	6/11	1	2	FACETS	0.905	0.831	0.982	0.905	0.831	0.982	CLONAL	1	TRUE	1	0.43	2		577	833	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163297332	163297332	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1292835761	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	111	440	1	ENST00000271452.3:c.178C>T	p.Arg60Ter	p.R60*	ENST00000271452	NM_145697.2	60	Cga/Tga	3/14	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.43	2		441	488	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162750028	162750028	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771898787	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	107	341	0	ENST00000367921.3:c.2560G>A	p.Asp854Asn	p.D854N	ENST00000367921	NM_006182.2	854	Gac/Aac	18/18	1	2	FACETS	0.867	0.78	0.959	0.867	0.78	0.959	CLONAL	1	TRUE	1	0.43	2		341	574	SUCCESS
APC	324	MSKCC	GRCh37	5	112178969	112178969	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	82	300	0	ENST00000257430.4:c.7678C>T	p.Arg2560Ter	p.R2560*	ENST00000257430	NM_000038.5	2560	Cga/Tga	16/16	1	2	FACETS	0.893	0.791	1	0.893	0.791	1	CLONAL	1	TRUE	1	0.43	2		300	427	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359017	81359017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	44	492	0	ENST00000222390.5:c.944G>A	p.Gly315Asp	p.G315D	ENST00000222390	NM_000601.4	315	gGc/gAc	8/18	1	2	FACETS	0.282	0.236	0.334	0.282	0.236	0.334	SUBCLONAL	1	TRUE	1	0.43	2		492	725	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117351	115117351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1234535767	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	33	318	0	ENST00000257566.3:c.823G>A	p.Glu275Lys	p.E275K	ENST00000257566	NM_016569.3	275	Gaa/Aaa	4/8	1	2	FACETS	0.321	0.261	0.389	0.321	0.261	0.389	SUBCLONAL	1	TRUE	1	0.43	2		318	478	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902622	1902622	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs771287635	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	92	769	1	ENST00000382891.5:c.241G>T	p.Asp81Tyr	p.D81Y	ENST00000382891	NM_133335.3	81	Gat/Tat	2/22	1	2	FACETS	0.381	0.337	0.428	0.381	0.337	0.428	SUBCLONAL	1	TRUE	1	0.43	2		770	1124	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858351	9858351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	43	403	0	ENST00000330684.3:c.3050C>T	p.Ser1017Phe	p.S1017F	ENST00000330684	NM_001134407.1	1017	tCc/tTc	13/13	1	2	FACETS	0.393	0.328	0.464	0.393	0.328	0.464	SUBCLONAL	1	TRUE	1	0.43	2		403	509	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350164	81350164	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	30	255	0	ENST00000222390.5:c.1169-1G>T		p.X390_splice	ENST00000222390	NM_000601.4	390			1	2	FACETS	0.348	0.28	0.425	0.348	0.28	0.425	SUBCLONAL	1	TRUE	1	0.43	2		255	401	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733524	85733524	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370432633	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	161	436	1	ENST00000370580.1:c.488C>T	p.Thr163Met	p.T163M	ENST00000370580	NM_003921.4	163	aCg/aTg	3/3	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.43	2		437	720	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103322	119103322	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	150	511	0	ENST00000264033.4:c.360G>T	p.Glu120Asp	p.E120D	ENST00000264033	NM_005188.3	120	gaG/gaT	2/16	1	2	FACETS	0.973	0.891	1	0.973	0.891	1	CLONAL	1	TRUE	1	0.43	2		511	717	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911517	39911517	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	58	310	1	ENST00000378444.4:c.5113C>A	p.Leu1705Ile	p.L1705I	ENST00000378444	NM_001123385.1	1705	Ctc/Atc	15/15	1	1	FACETS	0.415	0.357	0.479	0.415	0.357	0.479	SUBCLONAL	1	TRUE	0	0.43	1		311	510	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965800	18965800	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	53	807	0	ENST00000262803.5:c.1378C>T	p.Pro460Ser	p.P460S	ENST00000262803	NM_002911.3	460	Ccc/Tcc	10/24	1	2	FACETS	0.277	0.235	0.323	0.277	0.235	0.323	SUBCLONAL	1	TRUE	1	0.43	2		807	889	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240738	53240738	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	235	350	0	ENST00000375401.3:c.1342G>T	p.Glu448Ter	p.E448*	ENST00000375401	NM_004187.3	448	Gaa/Taa	10/26	1	1	FACETS	0.835	0.787	0.882	1	0.994	1	CLONAL	2	TRUE	0	0.43	1		350	514	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630190	100630190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs128620185	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	163	285	0	ENST00000308731.7:c.83G>A	p.Arg28His	p.R28H	ENST00000308731	NM_000061.2	28	cGc/cAc	2/19	1	1	FACETS	0.773	0.719	0.828	1	0.991	1	SUBCLONAL	2	TRUE	0	0.43	1		285	385	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912733	32912733	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs70953664	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	50	447	0	ENST00000380152.3:c.4241C>T	p.Thr1414Met	p.T1414M	ENST00000380152		1414	aCg/aTg	11/27	1	2	FACETS	0.361	0.306	0.422	0.361	0.306	0.422	SUBCLONAL	1	TRUE	1	0.43	2		447	644	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271691	15271691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	72	1001	0	ENST00000263388.2:c.6748G>A	p.Glu2250Lys	p.E2250K	ENST00000263388	NM_000435.2	2250	Gaa/Aaa	33/33	1	2	FACETS	0.312	0.271	0.356	0.312	0.271	0.356	SUBCLONAL	1	TRUE	1	0.43	2		1001	1074	SUCCESS
APC	324	MSKCC	GRCh37	5	112174590	112174590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224541	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	113	421	1	ENST00000257430.4:c.3299C>T	p.Ser1100Phe	p.S1100F	ENST00000257430	NM_000038.5	1100	tCt/tTt	16/16	1	2	FACETS	0.898	0.811	0.991	0.898	0.811	0.991	CLONAL	1	TRUE	1	0.43	2		422	585	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523280	9523280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769363113	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	180	590	1	ENST00000353224.5:c.1957C>T	p.Arg653Trp	p.R653W	ENST00000353224	NM_177990.2	653	Cgg/Tgg	9/10	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.43	2		591	799	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256431	46256431	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs72645252	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	35	475	1	ENST00000371998.3:c.659G>T	p.Arg220Ile	p.R220I	ENST00000371998		220	aGa/aTa	7/23	1	2	FACETS	0.258	0.21	0.311	0.258	0.21	0.311	SUBCLONAL	1	TRUE	1	0.43	2		476	632	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129839	55129839	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs762935664	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	97	429	0	ENST00000257290.5:c.373G>T	p.Asp125Tyr	p.D125Y	ENST00000257290	NM_006206.4	125	Gat/Tat	4/23	1	2	FACETS	0.778	0.695	0.866	0.778	0.695	0.866	SUBCLONAL	1	TRUE	1	0.43	2		429	580	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39321554	39321554	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs756733917	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	151	457	0	ENST00000373001.3:c.467G>T	p.Arg156Ile	p.R156I	ENST00000373001	NM_022157.3	156	aGa/aTa	3/7	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.43	2		457	564	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321352	65321352	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	124	624	0	ENST00000342505.4:c.1488G>T	p.Lys496Asn	p.K496N	ENST00000342505	NM_002227.2	496	aaG/aaT	11/25	1	2	FACETS	0.66	0.597	0.727	0.66	0.597	0.727	SUBCLONAL	1	TRUE	1	0.43	2		624	874	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028055	69028055	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	42	500	0	ENST00000288368.4:c.3214G>T	p.Asp1072Tyr	p.D1072Y	ENST00000288368	NM_024870.2	1072	Gac/Tac	26/40	1	2	FACETS	0.287	0.239	0.341	0.287	0.239	0.341	SUBCLONAL	1	TRUE	1	0.43	2		500	680	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63661997	63661997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	136	435	0	ENST00000279873.7:c.101G>A	p.Arg34Lys	p.R34K	ENST00000279873	NM_032199.2	34	aGa/aAa	2/10	1	2	FACETS	0.91	0.829	0.995	0.91	0.829	0.995	CLONAL	1	TRUE	1	0.43	2		435	695	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685303	89685303	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	31	253	0	ENST00000371953.3:c.198G>T	p.Lys66Asn	p.K66N	ENST00000371953	NM_000314.4	66	aaG/aaT	3/9	1	2	FACETS	0.376	0.304	0.458	0.376	0.304	0.458	SUBCLONAL	1	TRUE	1	0.43	2		253	383	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719938	18719938	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	117	395	0	ENST00000266497.5:c.3835G>T	p.Asp1279Tyr	p.D1279Y	ENST00000266497		1279	Gat/Tat	27/31	1	2	FACETS	0.794	0.717	0.876	0.794	0.717	0.876	SUBCLONAL	1	TRUE	1	0.43	2		395	685	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332931	70332931	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	195	640	0	ENST00000373644.4:c.836C>A	p.Ser279Tyr	p.S279Y	ENST00000373644	NM_030625.2	279	tCt/tAt	2/12	1	2	FACETS	0.994	0.921	1	0.994	0.921	1	CLONAL	1	TRUE	1	0.43	2		640	912	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266725	198266725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	58	487	0	ENST00000335508.6:c.2207G>A	p.Arg736His	p.R736H	ENST00000335508	NM_012433.2	736	cGc/cAc	15/25	1	2	FACETS	0.339	0.29	0.392	0.339	0.29	0.392	SUBCLONAL	1	TRUE	1	0.43	2		487	796	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858064	9858064	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	151	582	0	ENST00000330684.3:c.3337C>T	p.Pro1113Ser	p.P1113S	ENST00000330684	NM_001134407.1	1113	Cct/Tct	13/13	1	2	FACETS	0.933	0.854	1	0.933	0.854	1	CLONAL	1	TRUE	1	0.43	2		582	753	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250189	133250189	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	175	737	0	ENST00000320574.5:c.1331T>A	p.Met444Lys	p.M444K	ENST00000320574	NM_006231.2	444	aTg/aAg	13/49	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.43	2		737	788	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291858	15291858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	106	956	0	ENST00000263388.2:c.2908C>T	p.Pro970Ser	p.P970S	ENST00000263388	NM_000435.2	970	Ccc/Tcc	18/33	1	2	FACETS	0.51	0.457	0.568	0.51	0.457	0.568	SUBCLONAL	1	TRUE	1	0.43	2		956	966	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266692	142266692	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	123	440	0	ENST00000350721.4:c.3232G>T	p.Glu1078Ter	p.E1078*	ENST00000350721	NM_001184.3	1078	Gaa/Taa	16/47	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.43	2		440	566	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256028	16256028	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	198	600	0	ENST00000375759.3:c.3293A>C	p.Asn1098Thr	p.N1098T	ENST00000375759	NM_015001.2	1098	aAt/aCt	11/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.43	2		600	873	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264457	16264457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	206	791	0	ENST00000375759.3:c.10660C>T	p.Arg3554Trp	p.R3554W	ENST00000375759	NM_015001.2	3554	Cgg/Tgg	13/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.43	2		791	857	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100317	27100317	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	67	664	0	ENST00000324856.7:c.4029C>A	p.Phe1343Leu	p.F1343L	ENST00000324856	NM_006015.4	1343	ttC/ttA	17/20	1	2	FACETS	0.36	0.312	0.413	0.36	0.312	0.413	SUBCLONAL	1	TRUE	1	0.43	2		664	865	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243778403	243778403	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	96	365	0	ENST00000263826.5:c.622T>G	p.Leu208Val	p.L208V	ENST00000263826	NM_005465.4	208	Tta/Gta	6/13	1	2	FACETS	0.971	0.869	1	0.971	0.869	1	CLONAL	1	TRUE	1	0.43	2		365	460	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243859007	243859007	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	60	285	0	ENST00000263826.5:c.58A>C	p.Lys20Gln	p.K20Q	ENST00000263826	NM_005465.4	20	Aaa/Caa	2/13	1	2	FACETS	0.769	0.666	0.88	0.769	0.666	0.88	SUBCLONAL	1	TRUE	1	0.43	2		285	363	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851555	63851555	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	49	572	0	ENST00000279873.7:c.2333T>G	p.Leu778Arg	p.L778R	ENST00000279873	NM_032199.2	778	cTg/cGg	10/10	1	2	FACETS	0.318	0.269	0.373	0.318	0.269	0.373	SUBCLONAL	1	TRUE	1	0.43	2		572	716	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70411688	70411688	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	98	373	0	ENST00000373644.4:c.4362G>T	p.Glu1454Asp	p.E1454D	ENST00000373644	NM_030625.2	1454	gaG/gaT	5/12	1	2	FACETS	0.913	0.818	1	0.913	0.818	1	CLONAL	1	TRUE	1	0.43	2		373	499	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720814	89720814	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	109	376	0	ENST00000371953.3:c.965A>C	p.Lys322Thr	p.K322T	ENST00000371953	NM_000314.4	322	aAa/aCa	8/9	1	2	FACETS	0.818	0.736	0.904	0.818	0.736	0.904	CLONAL	1	TRUE	1	0.43	2		376	620	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771540	112771540	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	38	500	0	ENST00000369452.4:c.1713C>A	p.Phe571Leu	p.F571L	ENST00000369452	NM_007373.3	571	ttC/ttA	9/9	1	2	FACETS	0.26	0.214	0.311	0.26	0.214	0.311	SUBCLONAL	1	TRUE	1	0.43	2		500	680	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711029	114711029	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	32	245	0	ENST00000543371.1:c.253G>T	p.Glu85Ter	p.E85*	ENST00000543371	NM_001198531.1	85	Gaa/Taa	2/14	1	2	FACETS	0.416	0.338	0.504	0.416	0.338	0.504	SUBCLONAL	1	TRUE	1	0.43	2		245	358	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94153304	94153304	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs750057222	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	116	450	1	ENST00000323929.3:c.2114G>T	p.Arg705Ile	p.R705I	ENST00000323929	NM_005591.3	705	aGa/aTa	20/20	1	2	FACETS	0.824	0.744	0.908	0.824	0.744	0.908	CLONAL	1	TRUE	1	0.43	2		451	655	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119694	108119694	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	59	192	0	ENST00000278616.4:c.1100C>A	p.Ser367Tyr	p.S367Y	ENST00000278616	NM_000051.3	367	tCt/tAt	9/63	1	2	FACETS	0.94	0.815	1	0.94	0.815	1	CLONAL	1	TRUE	1	0.43	2		192	292	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235878	108235878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs984616023	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	32	414	2	ENST00000278616.4:c.8920C>T	p.Pro2974Ser	p.P2974S	ENST00000278616	NM_000051.3	2974	Ccg/Tcg	62/63	1	2	FACETS	0.244	0.198	0.298	0.244	0.198	0.298	SUBCLONAL	1	TRUE	1	0.43	2		416	609	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343217	118343217	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs782576050	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	46	389	0	ENST00000534358.1:c.1343A>C	p.Asn448Thr	p.N448T	ENST00000534358	NM_005933.3	448	aAt/aCt	3/36	1	2	FACETS	0.427	0.359	0.502	0.427	0.359	0.502	SUBCLONAL	1	TRUE	1	0.43	2		389	501	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347543	118347543	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs782157422	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	67	442	0	ENST00000534358.1:c.3180G>T	p.Glu1060Asp	p.E1060D	ENST00000534358	NM_005933.3	1060	gaG/gaT	4/36	1	2	FACETS	0.507	0.44	0.579	0.507	0.44	0.579	SUBCLONAL	1	TRUE	1	0.43	2		442	615	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374685	118374685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	80	473	0	ENST00000534358.1:c.8078C>T	p.Ser2693Phe	p.S2693F	ENST00000534358	NM_005933.3	2693	tCt/tTt	27/36	1	2	FACETS	0.644	0.567	0.726	0.644	0.567	0.726	SUBCLONAL	1	TRUE	1	0.43	2		473	578	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417156	417156	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	28	213	0	ENST00000399788.2:c.3394G>T	p.Glu1132Ter	p.E1132*	ENST00000399788	NM_001042603.1	1132	Gaa/Taa	23/28	1	2	FACETS	0.417	0.334	0.512	0.417	0.334	0.512	SUBCLONAL	1	TRUE	1	0.43	2		213	312	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435026	18435026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	29	247	1	ENST00000266497.5:c.11C>A	p.Ser4Tyr	p.S4Y	ENST00000266497		4	tCt/tAt	1/31	1	2	FACETS	0.349	0.279	0.427	0.349	0.279	0.427	SUBCLONAL	1	TRUE	1	0.43	2		248	387	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443811	18443811	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	26	322	0	ENST00000266497.5:c.784G>T	p.Ala262Ser	p.A262S	ENST00000266497		262	Gct/Tct	3/31	1	2	FACETS	0.307	0.243	0.381	0.307	0.243	0.381	SUBCLONAL	1	TRUE	1	0.43	2		322	394	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656299	18656299	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	117	416	0	ENST00000266497.5:c.2978C>A	p.Thr993Lys	p.T993K	ENST00000266497		993	aCa/aAa	21/31	1	2	FACETS	0.958	0.867	1	0.958	0.867	1	CLONAL	1	TRUE	1	0.43	2		416	568	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793372	18793372	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	93	367	1	ENST00000266497.5:c.4069G>T	p.Asp1357Tyr	p.D1357Y	ENST00000266497		1357	Gat/Tat	30/31	1	2	FACETS	0.885	0.79	0.985	0.885	0.79	0.985	CLONAL	1	TRUE	1	0.43	2		368	489	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125011	46125011	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	57	251	1	ENST00000334344.6:c.198G>T	p.Lys66Asn	p.K66N	ENST00000334344	NM_152641.2	66	aaG/aaT	3/21	1	2	FACETS	0.7	0.602	0.804	0.7	0.602	0.804	SUBCLONAL	1	TRUE	1	0.43	2		252	379	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445815	49445815	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1255	93	1100	1	ENST00000301067.7:c.1651G>T	p.Glu551Ter	p.E551*	ENST00000301067	NM_003482.3	551	Gaa/Taa	10/54	1	2	FACETS	0.321	0.284	0.361	0.321	0.284	0.361	SUBCLONAL	1	TRUE	1	0.43	2		1101	1348	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869547	102869547	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	165	535	0	ENST00000307046.8:c.94C>A	p.Leu32Ile	p.L32I	ENST00000307046	NM_001111285.1	32	Ctc/Atc	2/4	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.43	2		535	679	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32899311	32899311	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	65	264	0	ENST00000380152.3:c.415C>A	p.Leu139Ile	p.L139I	ENST00000380152		139	Ctt/Att	4/27	1	2	FACETS	0.73	0.635	0.832	0.73	0.635	0.832	SUBCLONAL	1	TRUE	1	0.43	2		264	414	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881473	48881473	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	72	244	0	ENST00000267163.4:c.195G>T	p.Lys65Asn	p.K65N	ENST00000267163	NM_000321.2	65	aaG/aaT	2/27	1	2	FACETS	0.813	0.713	0.919	0.813	0.713	0.919	CLONAL	1	TRUE	1	0.43	2		244	412	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519172	103519172	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	36	371	0	ENST00000355739.4:c.2510A>G	p.Tyr837Cys	p.Y837C	ENST00000355739	NM_000123.3	837	tAt/tGt	11/15	1	2	FACETS	0.264	0.216	0.318	0.264	0.216	0.318	SUBCLONAL	1	TRUE	1	0.43	2		371	634	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041995	42041995	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1415282137	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	94	565	0	ENST00000219905.7:c.6190G>T	p.Asp2064Tyr	p.D2064Y	ENST00000219905	NM_001164273.1	2064	Gat/Tat	17/24	1	2	FACETS	0.588	0.523	0.658	0.588	0.523	0.658	SUBCLONAL	1	TRUE	1	0.43	2		565	743	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43739581	43739581	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	105	371	0	ENST00000382044.4:c.2819G>T	p.Arg940Ile	p.R940I	ENST00000382044	NM_001141980.1	940	aGa/aTa	13/28	1	2	FACETS	0.981	0.883	1	0.981	0.883	1	CLONAL	1	TRUE	1	0.43	2		371	498	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748837	43748837	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	224	672	1	ENST00000382044.4:c.1969G>T	p.Glu657Ter	p.E657*	ENST00000382044	NM_001141980.1	657	Gaa/Taa	12/28	1	2	FACETS	0.929	0.864	0.996	0.929	0.864	0.996	CLONAL	1	TRUE	1	0.43	2		673	1122	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90633789	90633789	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	120	759	0	ENST00000330062.3:c.295G>T	p.Asp99Tyr	p.D99Y	ENST00000330062	NM_002168.2	99	Gac/Tac	3/11	1	2	FACETS	0.581	0.524	0.641	0.581	0.524	0.641	SUBCLONAL	1	TRUE	1	0.43	2		759	961	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347493	91347493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	66	504	0	ENST00000355112.3:c.3655C>A	p.Leu1219Ile	p.L1219I	ENST00000355112	NM_000057.2	1219	Ctt/Att	19/22	1	2	FACETS	0.369	0.319	0.422	0.369	0.319	0.422	SUBCLONAL	1	TRUE	1	0.43	2		504	833	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645417	67645417	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	51	422	0	ENST00000264010.4:c.682T>G	p.Phe228Val	p.F228V	ENST00000264010	NM_006565.3	228	Ttt/Gtt	3/12	1	2	FACETS	0.368	0.312	0.429	0.368	0.312	0.429	SUBCLONAL	1	TRUE	1	0.43	2		422	645	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828147	72828147	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	86	687	0	ENST00000268489.5:c.8434G>T	p.Asp2812Tyr	p.D2812Y	ENST00000268489	NM_006885.3	2812	Gac/Tac	9/10	1	2	FACETS	0.448	0.395	0.504	0.448	0.395	0.504	SUBCLONAL	1	TRUE	1	0.43	2		687	893	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829632	72829632	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	157	581	0	ENST00000268489.5:c.6949A>C	p.Asn2317His	p.N2317H	ENST00000268489	NM_006885.3	2317	Aat/Cat	9/10	1	2	FACETS	0.856	0.785	0.931	0.856	0.785	0.931	CLONAL	1	TRUE	1	0.43	2		581	853	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830731	72830731	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	55	636	1	ENST00000268489.5:c.5850G>T	p.Glu1950Asp	p.E1950D	ENST00000268489	NM_006885.3	1950	gaG/gaT	9/10	1	2	FACETS	0.317	0.27	0.368	0.317	0.27	0.368	SUBCLONAL	1	TRUE	1	0.43	2		637	807	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830944	72830944	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	31	484	0	ENST00000268489.5:c.5637A>C	p.Lys1879Asn	p.K1879N	ENST00000268489	NM_006885.3	1879	aaA/aaC	9/10	1	2	FACETS	0.25	0.201	0.305	0.25	0.201	0.305	SUBCLONAL	1	TRUE	1	0.43	2		484	577	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993124	72993124	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	245	877	1	ENST00000268489.5:c.921G>T	p.Met307Ile	p.M307I	ENST00000268489	NM_006885.3	307	atG/atT	2/10	1	2	FACETS	0.967	0.902	1	0.967	0.902	1	CLONAL	1	TRUE	1	0.43	2		878	1179	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942121	81942121	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	51	638	0	ENST00000359376.3:c.1658A>G	p.Glu553Gly	p.E553G	ENST00000359376	NM_002661.3	553	gAg/gGg	17/33	1	2	FACETS	0.267	0.226	0.312	0.267	0.226	0.312	SUBCLONAL	1	TRUE	1	0.43	2		638	889	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40874924	40874924	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	170	555	0	ENST00000428826.2:c.376G>T	p.Glu126Ter	p.E126*	ENST00000428826		126	Gag/Tag	6/21	1	2	FACETS	0.936	0.861	1	0.936	0.861	1	CLONAL	1	TRUE	1	0.43	2		555	845	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243658	41243658	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	45	590	0	ENST00000357654.3:c.3890C>A	p.Ser1297Tyr	p.S1297Y	ENST00000357654	NM_007294.3	1297	tCt/tAt	10/23	1	2	FACETS	0.264	0.221	0.312	0.264	0.221	0.312	SUBCLONAL	1	TRUE	1	0.43	2		590	793	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740684	58740684	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	182	603	0	ENST00000305921.3:c.1589C>A	p.Pro530His	p.P530H	ENST00000305921	NM_003620.3	530	cCt/cAt	6/6	1	2	FACETS	0.966	0.892	1	0.966	0.892	1	CLONAL	1	TRUE	1	0.43	2		603	876	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619853	1619853	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	204	740	0	ENST00000344749.5:c.1094-1G>C		p.X365_splice	ENST00000344749	NM_001136139.2	365			1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.43	2		740	946	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223306	2223306	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	209	872	0	ENST00000398665.3:c.3417G>T	p.Glu1139Asp	p.E1139D	ENST00000398665	NM_032482.2	1139	gaG/gaT	25/28	1	2	FACETS	0.933	0.866	1	0.933	0.866	1	CLONAL	1	TRUE	1	0.43	2		872	1042	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254586	10254586	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	191	624	0	ENST00000340748.4:c.2924A>C	p.Lys975Thr	p.K975T	ENST00000340748		975	aAa/aCa	28/40	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.43	2		624	816	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18958592	18958592	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	245	710	0	ENST00000262803.5:c.411T>G	p.Cys137Trp	p.C137W	ENST00000262803	NM_002911.3	137	tgT/tgG	3/24	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.43	2		710	1072	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724238	52724238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	120	411	0	ENST00000322088.6:c.1370C>T	p.Ala457Val	p.A457V	ENST00000322088	NM_014225.5	457	gCc/gTc	12/15	1	2	FACETS	0.944	0.855	1	0.944	0.855	1	CLONAL	1	TRUE	1	0.43	2		411	591	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446218	29446218	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	133	515	0	ENST00000389048.3:c.3349A>G	p.Thr1117Ala	p.T1117A	ENST00000389048	NM_004304.4	1117	Acc/Gcc	20/29	0.0893247318272496	0	FACETS	0.645	0.588	0.703			1	INDETERMINATE	1	TRUE	0	0.43	0		515	547	SUCCESS
REL	5966	MSKCC	GRCh37	2	61128157	61128157	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	64	303	0	ENST00000295025.8:c.333G>T	p.Lys111Asn	p.K111N	ENST00000295025	NM_002908.2	111	aaG/aaT	4/11	1	2	FACETS	0.518	0.448	0.593	0.518	0.448	0.593	SUBCLONAL	1	TRUE	1	0.43	2		303	575	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738322	190738322	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	30	331	0	ENST00000441310.2:c.2574A>C	p.Leu858Phe	p.L858F	ENST00000441310	NM_000534.4	858	ttA/ttC	12/13	1	2	FACETS	0.239	0.192	0.293	0.239	0.192	0.293	SUBCLONAL	1	TRUE	1	0.43	2		331	584	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131209	202131209	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	94	347	0	ENST00000358485.4:c.177G>T	p.Lys59Asn	p.K59N	ENST00000358485	NM_001080125.1	59	aaG/aaT	2/9	1	2	FACETS	0.851	0.759	0.947	0.851	0.759	0.947	CLONAL	1	TRUE	1	0.43	2		347	514	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113162	209113162	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	52	369	0	ENST00000345146.2:c.345A>C	p.Lys115Asn	p.K115N	ENST00000345146	NM_005896.2	115	aaA/aaC	4/10	1	2	FACETS	0.489	0.416	0.568	0.489	0.416	0.568	SUBCLONAL	1	TRUE	1	0.43	2		369	495	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662795	227662795	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	81	873	0	ENST00000305123.5:c.660C>A	p.Phe220Leu	p.F220L	ENST00000305123	NM_005544.2	220	ttC/ttA	1/2	1	2	FACETS	0.372	0.327	0.421	0.372	0.327	0.421	SUBCLONAL	1	TRUE	1	0.43	2		873	1013	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024187	31024187	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	97	607	0	ENST00000375687.4:c.3672G>T	p.Arg1224Ser	p.R1224S	ENST00000375687	NM_015338.5	1224	agG/agT	13/13	1	2	FACETS	0.57	0.507	0.636	0.57	0.507	0.636	SUBCLONAL	1	TRUE	1	0.43	2		607	792	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54956587	54956587	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	79	442	0	ENST00000312783.6:c.607G>A	p.Ala203Thr	p.A203T	ENST00000312783	NM_198436.1	203	Gct/Act	7/10	1	2	FACETS	0.747	0.659	0.841	0.747	0.659	0.841	SUBCLONAL	1	TRUE	1	0.43	2		442	492	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961583	54961583	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	57	374	0	ENST00000312783.6:c.49G>A	p.Ala17Thr	p.A17T	ENST00000312783	NM_198436.1	17	Gct/Act	4/10	1	2	FACETS	0.5	0.429	0.578	0.5	0.429	0.578	SUBCLONAL	1	TRUE	1	0.43	2		374	530	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125218	47125218	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	88	379	0	ENST00000409792.3:c.6052G>T	p.Asp2018Tyr	p.D2018Y	ENST00000409792	NM_014159.6	2018	Gac/Tac	12/21	1	2	FACETS	0.88	0.783	0.983	0.88	0.783	0.983	CLONAL	1	TRUE	1	0.43	2		379	465	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162109	47162109	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs748587569	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	89	371	0	ENST00000409792.3:c.4017G>T	p.Glu1339Asp	p.E1339D	ENST00000409792	NM_014159.6	1339	gaG/gaT	3/21	1	2	FACETS	0.81	0.72	0.905	0.81	0.72	0.905	CLONAL	1	TRUE	1	0.43	2		371	511	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390923	89390923	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1559654048	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	124	447	0	ENST00000336596.2:c.989G>T	p.Arg330Ile	p.R330I	ENST00000336596	NM_005233.5	330	aGa/aTa	5/17	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.43	2		447	534	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521730	89521730	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs961598471	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	39	395	0	ENST00000336596.2:c.2807A>G	p.Glu936Gly	p.E936G	ENST00000336596	NM_005233.5	936	gAg/gGg	16/17	1	2	FACETS	0.287	0.237	0.342	0.287	0.237	0.342	SUBCLONAL	1	TRUE	1	0.43	2		395	633	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938773	178938773	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	161	547	0	ENST00000263967.3:c.2016-1G>T		p.X672_splice	ENST00000263967	NM_006218.2	672			1	2	FACETS	0.963	0.884	1	0.963	0.884	1	CLONAL	1	TRUE	1	0.43	2		547	778	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191002	185191002	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	263	831	0	ENST00000265026.3:c.1883A>G	p.Tyr628Cys	p.Y628C	ENST00000265026	NM_004721.4	628	tAc/tGc	11/14	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.43	2		831	1151	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502367	186502367	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	49	354	0	ENST00000323963.5:c.90G>T	p.Glu30Asp	p.E30D	ENST00000323963		30	gaG/gaT	3/11	1	2	FACETS	0.391	0.331	0.457	0.391	0.331	0.457	SUBCLONAL	1	TRUE	1	0.43	2		354	583	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444684	187444684	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	81	324	0	ENST00000232014.4:c.1543A>G	p.Asn515Asp	p.N515D	ENST00000232014	NM_001130845.1	515	Aac/Gac	7/10	1	2	FACETS	0.959	0.85	1	0.959	0.85	1	CLONAL	1	TRUE	1	0.43	2		324	393	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456541	189456541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755677647	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	105	452	0	ENST00000264731.3:c.302C>T	p.Ser101Leu	p.S101L	ENST00000264731	NM_003722.4	101	tCg/tTg	3/14	1	2	FACETS	0.792	0.711	0.877	0.792	0.711	0.877	SUBCLONAL	1	TRUE	1	0.43	2		452	617	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956188	55956188	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	172	534	0	ENST00000263923.4:c.3127A>C	p.Lys1043Gln	p.K1043Q	ENST00000263923	NM_002253.2	1043	Aaa/Caa	23/30	0.3	1	FACETS	0.773	0.712	0.837	0.773	0.712	0.837	SUBCLONAL	1	TRUE	0	0.43	1		534	812	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970907	55970907	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	154	536	0	ENST00000263923.4:c.1890G>T	p.Lys630Asn	p.K630N	ENST00000263923	NM_002253.2	630	aaG/aaT	13/30	0.3	1	FACETS	0.823	0.755	0.894	0.823	0.755	0.894	CLONAL	1	TRUE	0	0.43	1		536	683	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538311	187538311	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	154	506	0	ENST00000441802.2:c.8923G>T	p.Glu2975Ter	p.E2975*	ENST00000441802	NM_005245.3	2975	Gaa/Taa	11/27	1	2	FACETS	0.965	0.885	1	0.965	0.885	1	CLONAL	1	TRUE	1	0.43	2		506	742	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630410	187630410	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758938184	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	230	627	1	ENST00000441802.2:c.572G>A	p.Arg191Gln	p.R191Q	ENST00000441802	NM_005245.3	191	cGa/cAa	2/27	1	2	FACETS	0.993	0.926	1	0.993	0.926	1	CLONAL	1	TRUE	1	0.43	2		628	1077	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754857	57754857	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	115	277	0	ENST00000274289.3:c.333A>C	p.Lys111Asn	p.K111N	ENST00000274289	NM_006622.3	111	aaA/aaC	2/14	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.43	2		277	484	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575540	67575540	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	103	286	0	ENST00000274335.5:c.613G>T	p.Glu205Ter	p.E205*	ENST00000274335		205	Gaa/Taa	4/15	1	2	FACETS	0.866	0.778	0.96	0.866	0.778	0.96	CLONAL	1	TRUE	1	0.43	2		286	553	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961030	79961030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138381683	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	54	499	0	ENST00000265081.6:c.427G>A	p.Asp143Asn	p.D143N	ENST00000265081	NM_002439.4	143	Gat/Aat	3/24	1	2	FACETS	0.345	0.294	0.402	0.345	0.294	0.402	SUBCLONAL	1	TRUE	1	0.43	2		499	727	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79966033	79966033	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs756632960	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	149	506	0	ENST00000265081.6:c.697G>T	p.Glu233Ter	p.E233*	ENST00000265081	NM_002439.4	233	Gaa/Taa	4/24	1	2	FACETS	0.947	0.867	1	0.947	0.867	1	CLONAL	1	TRUE	1	0.43	2		506	732	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674356	86674356	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	27	210	0	ENST00000274376.6:c.2487+1G>T		p.X829_splice	ENST00000274376	NM_002890.2	829			1	2	FACETS	0.339	0.27	0.419	0.339	0.27	0.419	SUBCLONAL	1	TRUE	1	0.43	2		210	370	SUCCESS
APC	324	MSKCC	GRCh37	5	112174893	112174893	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs730881247	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	89	247	0	ENST00000257430.4:c.3602C>A	p.Ser1201Ter	p.S1201*	ENST00000257430	NM_000038.5	1201	tCa/tAa	16/16	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.43	2		247	377	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323147	31323147	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	55	769	0	ENST00000412585.2:c.842A>G	p.Tyr281Cys	p.Y281C	ENST00000412585	NM_005514.6	281	tAc/tGc	4/8	1	2	FACETS	0.287	0.245	0.334	0.287	0.245	0.334	SUBCLONAL	1	TRUE	1	0.43	2		769	890	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289208	33289208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772405114	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	157	555	1	ENST00000374542.5:c.344G>A	p.Arg115Gln	p.R115Q	ENST00000374542	NM_001141970.1	115	cGg/cAg	3/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.43	2		556	645	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120612	94120612	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	102	376	0	ENST00000369303.4:c.439G>T	p.Asp147Tyr	p.D147Y	ENST00000369303	NM_004440.3	147	Gac/Tac	3/17	1	2	FACETS	0.916	0.822	1	0.916	0.822	1	CLONAL	1	TRUE	1	0.43	2		376	518	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120862	94120862	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	118	450	0	ENST00000369303.4:c.189G>T	p.Glu63Asp	p.E63D	ENST00000369303	NM_004440.3	63	gaG/gaT	3/17	1	2	FACETS	0.943	0.853	1	0.943	0.853	1	CLONAL	1	TRUE	1	0.43	2		450	582	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374383	81374383	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	49	346	0	ENST00000222390.5:c.679G>T	p.Glu227Ter	p.E227*	ENST00000222390	NM_000601.4	227	Gaa/Taa	6/18	1	2	FACETS	0.464	0.393	0.542	0.464	0.393	0.542	SUBCLONAL	1	TRUE	1	0.43	2		346	491	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411869	116411869	+	intron_variant	Intron	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1492	39	1047	0	ENST00000397752.3:c.2888-34C>A		p.*963*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.118	0.097	0.142	0.118	0.097	0.142	SUBCLONAL	1	TRUE	1	0.43	2		1047	1531	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412220	116412220	+	intron_variant	Intron	SNP	C	C	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	24	697	1	ENST00000397752.3:c.3028+177C>T		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.097	0.075	0.122	0.097	0.075	0.122	SUBCLONAL	1	TRUE	1	0.43	2		698	1153	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012226	152012226	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	52	410	0	ENST00000262189.6:c.587G>T	p.Arg196Ile	p.R196I	ENST00000262189	NM_170606.2	196	aGa/aTa	4/59	1	2	FACETS	0.403	0.343	0.469	0.403	0.343	0.469	SUBCLONAL	1	TRUE	1	0.43	2		410	600	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132713	152132713	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	16	170	0	ENST00000262189.6:c.159G>T	p.Lys53Asn	p.K53N	ENST00000262189	NM_170606.2	53	aaG/aaT	1/59	1	2	FACETS	0.271	0.2	0.355	0.271	0.2	0.355	SUBCLONAL	1	TRUE	1	0.43	2		170	275	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146156	38146156	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	248	771	0	ENST00000317025.8:c.3350G>T	p.Arg1117Ile	p.R1117I	ENST00000317025	NM_023034.1	1117	aGa/aTa	19/24	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.43	2		771	1017	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275504	38275504	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	52	573	0	ENST00000425967.3:c.1529T>G	p.Val510Gly	p.V510G	ENST00000425967	NM_001174067.1	510	gTc/gGc	12/19	1	2	FACETS	0.31	0.263	0.362	0.31	0.263	0.362	SUBCLONAL	1	TRUE	1	0.43	2		573	780	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561499	141561499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	166	586	0	ENST00000220592.5:c.1306G>A	p.Asp436Asn	p.D436N	ENST00000220592	NM_012154.3	436	Gac/Aac	11/19	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.43	2		586	771	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022093	5022093	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	72	493	0	ENST00000381652.3:c.106G>T	p.Asp36Tyr	p.D36Y	ENST00000381652	NM_004972.3	36	Gat/Tat	3/25	1	2	FACETS	0.527	0.46	0.598	0.527	0.46	0.598	SUBCLONAL	1	TRUE	1	0.43	2		493	636	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202846	27202846	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1373898272	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	63	424	0	ENST00000380036.4:c.1938G>T	p.Lys646Asn	p.K646N	ENST00000380036	NM_000459.3	646	aaG/aaT	13/23	1	2	FACETS	0.495	0.428	0.568	0.495	0.428	0.568	SUBCLONAL	1	TRUE	1	0.43	2		424	592	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900268	101900268	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	120	418	0	ENST00000374994.4:c.702C>A	p.Phe234Leu	p.F234L	ENST00000374994	NM_004612.2	234	ttC/ttA	4/9	1	2	FACETS	0.887	0.803	0.976	0.887	0.803	0.976	CLONAL	1	TRUE	1	0.43	2		418	629	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941842	44941842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	117	351	0	ENST00000377967.4:c.3166C>A	p.His1056Asn	p.H1056N	ENST00000377967	NM_021140.2	1056	Cat/Aat	21/29	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.43	1		351	321	SUCCESS
AR	367	MSKCC	GRCh37	X	66942713	66942713	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	140	243	0	ENST00000374690.3:c.2494C>T	p.Arg832Ter	p.R832*	ENST00000374690	NM_000044.3	832	Cga/Tga	7/8	1	1	FACETS	0.786	0.727	0.846	1	0.99	1	SUBCLONAL	2	TRUE	0	0.43	1		243	325	SUCCESS
BTK	695	MSKCC	GRCh37	X	100612572	100612572	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0040787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	38	181	0	ENST00000308731.7:c.1103-1G>A		p.X368_splice	ENST00000308731	NM_000061.2	368			1	1	FACETS	0.506	0.421	0.601	0.506	0.421	0.601	SUBCLONAL	1	TRUE	0	0.43	1		181	274	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0040948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	563	835	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.670426043425284	2	FACETS	0.926	0.898	0.953	0.926	0.898	0.953	CLONAL	2	TRUE	0	0.703908497519439	2		835	864	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0040948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	231	378	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.703908497519439	2		378	645	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604778	48604778	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767383	NA	P-0040948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	212	402	1	ENST00000342988.3:c.1600C>T	p.Gln534Ter	p.Q534*	ENST00000342988	NM_005359.5	534	Cag/Tag	12/12	0.703908497519439	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.703908497519439	1		403	380	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877391	40877391	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372713520	NA	P-0040948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	307	740	0	ENST00000373198.4:c.2305G>A	p.Val769Met	p.V769M	ENST00000373198	NM_133170.3	769	Gtg/Atg	15/32	0.126926637703043	5	FACETS	0.78	0.735	0.826			1	INDETERMINATE	2	TRUE	NA	0.703908497519439	5		740	1150	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518246	8518246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	44	421	0	ENST00000356435.5:c.1145G>A	p.Gly382Glu	p.G382E	ENST00000356435		382	gGa/gAa	10/35	1	2	FACETS	0.243	0.203	0.287	0.243	0.203	0.287	SUBCLONAL	1	TRUE	1	0.703908497519439	2		421	515	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622038	43622038	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	169	492	0	ENST00000355710.3:c.3055G>A	p.Ala1019Thr	p.A1019T	ENST00000355710	NM_020975.4	1019	Gcg/Acg	19/20	0.422311245935202	1	FACETS	0.702	0.652	0.753	0.702	0.652	0.753	INDETERMINATE	1	TRUE	0	0.703908497519439	1		492	443	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133685	41133685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1216360372	NA	P-0040948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	52	537	0	ENST00000379561.5:c.1943C>T	p.Thr648Met	p.T648M	ENST00000379561	NM_002015.3	648	aCg/aTg	2/3	1	2	FACETS	0.247	0.209	0.287	0.247	0.209	0.287	SUBCLONAL	1	TRUE	1	0.703908497519439	2		537	599	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0041391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	317	1045	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.456972849049709	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.456972849049709	2		1046	580	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0041391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	138	519	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.456972849049709	2	FACETS	0.921	0.851	0.992	0.921	0.851	0.992	CLONAL	2	TRUE	0	0.456972849049709	2		519	328	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0041391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	101	295	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.456972849049709	2	FACETS	0.957	0.873	1	0.957	0.873	1	CLONAL	2	TRUE	0	0.456972849049709	2		295	231	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433310	78433310	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0041391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	82	368	1	ENST00000370768.2:c.290+1G>A		p.X97_splice	ENST00000370768	NM_003902.3	97			0.456972849049709	2	FACETS	1	0.945	1	0.55	0.49	0.614	CLONAL	1	TRUE	0	0.456972849049709	2		369	326	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982989	201982990	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0041391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	348	790	0	ENST00000359651.3:c.841dup	p.Asp281GlyfsTer20	p.D281Gfs*20	ENST00000359651		280	cgg/cGgg	7/8	0.456972849049709	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.456972849049709	3		790	899	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32905124	32905127	+	frameshift_variant	Frame_Shift_Del	DEL	GACA	GACA	-	rs80359659	NA	P-0041391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	53	391	0	ENST00000380152.3:c.755_758del	p.Asp252ValfsTer24	p.D252Vfs*24	ENST00000380152		250	gtGACA/gt	9/27	0.456972849049709	5	FACETS	0.717	0.612	0.833	0.179	0.153	0.209	SUBCLONAL	1	TRUE	1	0.456972849049709	5		391	545	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023193	33023193	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	258	499	0	ENST00000300177.4:c.302A>C	p.Gln101Pro	p.Q101P	ENST00000300177	NM_001191322.1	101	cAg/cCg	2/2	0.456972849049709	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.456972849049709	2		499	511	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738759	43738759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766450587	NA	P-0041391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	152	462	0	ENST00000382044.4:c.2866G>A	p.Ala956Thr	p.A956T	ENST00000382044	NM_001141980.1	956	Gca/Aca	14/28	0.456972849049709	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.456972849049709	2		462	298	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36024598	36024598	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1152	184	748	0	ENST00000358208.4:c.587A>G	p.Asn196Ser	p.N196S	ENST00000358208		196	aAc/aGc	6/12	0.456972849049709	5	FACETS	1	0.934	1	0.203	0.187	0.22	CLONAL	1	TRUE	0	0.456972849049709	5		748	1336	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72866404	72866404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747683290	NA	P-0041391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	26	320	0	ENST00000325599.8:c.859C>T	p.Arg287Cys	p.R287C	ENST00000325599	NM_018130.2	287	Cgt/Tgt	7/11	0.354652354556256	3	FACETS	0.506	0.402	0.626	0.253	0.201	0.313	SUBCLONAL	1	TRUE	1	0.456972849049709	3		320	276	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425977	49425977	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	259	700	0	ENST00000301067.7:c.12511C>T	p.Gln4171Ter	p.Q4171*	ENST00000301067	NM_003482.3	4171	Caa/Taa	39/54	0.27390805443267	5	FACETS	0.906	0.853	0.959	0.906	0.853	0.959	INDETERMINATE	3	TRUE	2	0.456972849049709	5		700	703	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0041696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	76	415	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.282973656048164	5	FACETS	0.888	0.787	0.995	0.592	0.524	0.663	INDETERMINATE	2	TRUE	2	0.510435942605025	5		415	296	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0041696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	258	564	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.451110504800967	2	FACETS	0.927	0.878	0.977	0.927	0.878	0.977	CLONAL	2	TRUE	0	0.510435942605025	2		564	545	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528489	29528489	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764079291	NA	P-0041696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	66	422	0	ENST00000356175.3:c.1246C>T	p.Arg416Ter	p.R416*	ENST00000356175	NM_000267.3	416	Cga/Tga	11/57	0.451110504800967	2	FACETS	1	0.955	1	0.59	0.52	0.664	CLONAL	1	TRUE	0	0.510435942605025	2		422	219	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437531	56437531	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	199	807	0	ENST00000407977.2:c.931del	p.Leu311SerfsTer108	p.L311Sfs*108	ENST00000407977		311	Ctc/tc	8/10	0.451110504800967	2	FACETS	0.963	0.905	1	0.963	0.905	1	CLONAL	2	TRUE	0	0.510435942605025	2		807	405	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644781	67644781	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	62	515	2	ENST00000264010.4:c.46T>C	p.Phe16Leu	p.F16L	ENST00000264010	NM_006565.3	16	Ttt/Ctt	3/12	0.282973656048164	5	FACETS	0.977	0.846	1	0.326	0.282	0.373	INDETERMINATE	1	TRUE	2	0.510435942605025	5		517	439	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	53	571	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.896	0.765	1	0.896	0.765	1	CLONAL	1	FALSE	1	0.227423089097165	2		571	520	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	92	670	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.899	0.803	1	1	0.985	1	CLONAL	2	FALSE	1	0.227423089097165	2		670	450	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	25	233	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.0898430352540076	3	FACETS	0.69	0.544	0.858	0.345	0.272	0.429	INDETERMINATE	1	FALSE	1	0.227423089097165	3		233	355	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173631	108173631	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	75	418	0	ENST00000278616.4:c.5371G>A	p.Asp1791Asn	p.D1791N	ENST00000278616	NM_000051.3	1791	Gat/Aat	36/63	0.227423089097165	1	FACETS	0.842	0.743	0.947	1	0.98	1	CLONAL	2	FALSE	0	0.227423089097165	1		418	347	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493443	56493443	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	190	523	0	ENST00000267101.3:c.2851G>C	p.Asp951His	p.D951H	ENST00000267101	NM_001982.3	951	Gat/Cat	24/28	0.0876330279409734	3	FACETS	1	0.971	1	1	0.992	1	INDETERMINATE	3	FALSE	1	0.227423089097165	3		523	573	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636169	28636169	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	102	584	0	ENST00000241453.7:c.203G>C	p.Arg68Thr	p.R68T	ENST00000241453	NM_004119.2	68	aGa/aCa	3/24	1	2	FACETS	0.791	0.709	0.877	1	0.983	1	SUBCLONAL	2	FALSE	1	0.227423089097165	2		584	567	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003117	42003117	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	71	616	0	ENST00000219905.7:c.2654C>G	p.Ser885Cys	p.S885C	ENST00000219905	NM_001164273.1	885	tCt/tGt	8/24	0.227423089097165	0	FACETS	1	0.963	1			1	CLONAL	1	FALSE	0	0.227423089097165	0		616	381	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43700226	43700226	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	50	629	0	ENST00000382044.4:c.5661G>C	p.Gln1887His	p.Q1887H	ENST00000382044	NM_001141980.1	1887	caG/caC	27/28	0.227423089097165	0	FACETS	0.867	0.737	1			1	CLONAL	1	FALSE	0	0.227423089097165	0		629	392	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789685	3789685	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	118	522	0	ENST00000262367.5:c.4174C>T	p.Arg1392Ter	p.R1392*	ENST00000262367	NM_004380.2	1392	Cga/Tga	25/31	1	2	FACETS	1	0.937	1	1	0.99	1	CLONAL	2	FALSE	1	0.227423089097165	2		522	498	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526089	66526089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	43	352	0	ENST00000358598.2:c.920C>T	p.Ser307Leu	p.S307L	ENST00000358598	NM_212471.2	307	tCa/tTa	10/11	1	2	FACETS	0.848	0.71	1	0.848	0.71	1	CLONAL	1	FALSE	1	0.227423089097165	2		352	446	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291541	10291541	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1234060339	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	40	464	0	ENST00000340748.4:c.138G>T	p.Leu46Phe	p.L46F	ENST00000340748		46	ttG/ttT	3/40	0.227423089097165	1	FACETS	0.639	0.531	0.759	0.639	0.531	0.759	SUBCLONAL	1	FALSE	0	0.227423089097165	1		464	488	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227600	36227600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367682204	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	181	447	1	ENST00000222270.7:c.7169C>T	p.Ser2390Leu	p.S2390L	ENST00000222270	NM_014727.1	2390	tCg/tTg	31/37	1	2	FACETS	1	0.96	1	1	0.995	1	CLONAL	3	FALSE	1	0.227423089097165	2		448	507	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99137170	99137170	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	23	337	0	ENST00000074304.5:c.127G>A	p.Glu43Lys	p.E43K	ENST00000074304	NM_001134224.1	43	Gag/Aag	4/26	0.227423089097165	1	FACETS	0.542	0.422	0.68	0.542	0.422	0.68	SUBCLONAL	1	FALSE	0	0.227423089097165	1		337	331	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412969	49412969	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	225	761	0	ENST00000418115.1:c.54G>C	p.Lys18Asn	p.K18N	ENST00000418115	NM_001664.2	18	aaG/aaC	2/5	1	2	FACETS	1	0.982	1	1	0.995	1	CLONAL	2	FALSE	1	0.227423089097165	2		761	866	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247353	71247353	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	52	614	0	ENST00000318789.4:c.180G>C	p.Gln60His	p.Q60H	ENST00000318789	NM_032682.5	60	caG/caC	6/21	1	2	FACETS	0.709	0.603	0.826	0.709	0.603	0.826	SUBCLONAL	1	FALSE	1	0.227423089097165	2		614	645	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526187	189526187	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	102	785	1	ENST00000264731.3:c.451C>T	p.Gln151Ter	p.Q151*	ENST00000264731	NM_003722.4	151	Cag/Tag	4/14	1	2	FACETS	0.994	0.888	1	0.994	0.888	1	CLONAL	1	FALSE	1	0.227423089097165	2		786	902	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180912	106180912	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	107	374	0	ENST00000380013.4:c.3940G>C	p.Asp1314His	p.D1314H	ENST00000380013	NM_001127208.2	1314	Gat/Cat	7/11	0.0898430352540076	3	FACETS	1	0.968	1	1	0.968	1	INDETERMINATE	2	FALSE	1	0.227423089097165	3		374	446	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160703	56160703	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	94	444	0	ENST00000399503.3:c.977C>G	p.Ser326Cys	p.S326C	ENST00000399503	NM_005921.1	326	tCt/tGt	4/20	1	2	FACETS	0.803	0.716	0.894	1	0.983	1	CLONAL	2	FALSE	1	0.227423089097165	2		444	515	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158564	26158564	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	136	653	0	ENST00000289316.2:c.167C>T	p.Ser56Phe	p.S56F	ENST00000289316	NM_138720.2	56	tCt/tTt	1/2	0.227423089097165	5	FACETS	1	0.949	1	0.708	0.644	0.775	CLONAL	2	FALSE	2	0.227423089097165	5		653	755	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672483	30672483	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	258	786	1	ENST00000376406.3:c.4477G>T	p.Ala1493Ser	p.A1493S	ENST00000376406	NM_014641.2	1493	Gcc/Tcc	10/15	0.227423089097165	5	FACETS	0.919	0.863	0.976	1	0.989	1	CLONAL	4	FALSE	2	0.227423089097165	5		787	828	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652070	36652071	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	362	1122	0	ENST00000244741.5:c.193dup	p.Trp65LeufsTer24	p.W65Lfs*24	ENST00000244741	NM_000389.4	64	-/T	2/3	1	2	FACETS	1	0.965	1	1	0.997	1	CLONAL	3	FALSE	1	0.227423089097165	2		1122	1040	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652200	36652201	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	251	929	0	ENST00000244741.5:c.324dup	p.Asp109ArgfsTer20	p.D109Rfs*20	ENST00000244741	NM_000389.4	108	gaa/gAaa	2/3	1	2	FACETS	1	0.989	1	1	0.995	1	CLONAL	2	FALSE	1	0.227423089097165	2		929	885	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140929	37140929	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	43	498	0	ENST00000373509.5:c.765C>G	p.Phe255Leu	p.F255L	ENST00000373509	NM_002648.3	255	ttC/ttG	5/6	1	2	FACETS	0.577	0.482	0.683	0.577	0.482	0.683	SUBCLONAL	1	FALSE	1	0.227423089097165	2		498	655	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140946	37140946	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1426492223	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	32	423	0	ENST00000373509.5:c.782C>T	p.Ser261Leu	p.S261L	ENST00000373509	NM_002648.3	261	tCa/tTa	5/6	1	2	FACETS	0.514	0.417	0.625	0.514	0.417	0.625	SUBCLONAL	1	FALSE	1	0.227423089097165	2		423	547	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202309	138202309	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	73	787	0	ENST00000237289.4:c.2226G>T	p.Arg742Ser	p.R742S	ENST00000237289	NM_001270507.1	742	agG/agT	9/9	1	2	FACETS	0.853	0.745	0.969	0.853	0.745	0.969	CLONAL	1	FALSE	1	0.227423089097165	2		787	753	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386620	81386620	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	87	379	0	ENST00000222390.5:c.368-1G>C		p.X123_splice	ENST00000222390	NM_000601.4	123			1	2	FACETS	0.952	0.854	1	1	0.989	1	CLONAL	3	FALSE	1	0.227423089097165	2		379	268	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868444	117868444	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	79	579	0	ENST00000297338.2:c.898G>C	p.Glu300Gln	p.E300Q	ENST00000297338	NM_006265.2	300	Gag/Cag	8/14	0.227423089097165	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	0	0.227423089097165	1		579	533	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8339047	8339047	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	109	431	0	ENST00000356435.5:c.5254G>A	p.Glu1752Lys	p.E1752K	ENST00000356435		1752	Gag/Aag	32/35	1	2	FACETS	0.893	0.81	0.978	1	0.991	1	CLONAL	3	FALSE	1	0.227423089097165	2		431	358	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	271	843	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	0.943	0.888	1	1	0.996	1	CLONAL	3	FALSE	1	0.227423089097165	2		843	842	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44919321	44919321	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	10	0	0	ENST00000377967.4:c.1249C>G	p.Pro417Ala	p.P417A	ENST00000377967	NM_021140.2	417	Cct/Gct	13/29	0.035048038096364	2	FACETS	0.176	0.118	0.25			1	INDETERMINATE	1	FALSE	NA	0.227423089097165	2		0	499	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295235	1295235	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	6	0	0				ENST00000310581	NM_198253.2	-/1132			0.227423089097165	0	FACETS	0.131	0.077	0.203			1	SUBCLONAL	1	FALSE	0	0.227423089097165	0		0	312	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627670	37627670	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	16	0	0	ENST00000447079.4:c.1585C>G	p.Leu529Val	p.L529V	ENST00000447079	NM_015083.1	529	Ctt/Gtt	2/14	1	2	FACETS	0.166	0.121	0.219	0.166	0.121	0.219	SUBCLONAL	1	FALSE	1	0.227423089097165	2		0	849	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342965	118342965	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	5	0	0	ENST00000534358.1:c.1091C>G	p.Ser364Ter	p.S364*	ENST00000534358	NM_005933.3	364	tCa/tGa	3/36	0.227423089097165	1	FACETS	0.145	0.081	0.234	0.145	0.081	0.234	SUBCLONAL	1	FALSE	0	0.227423089097165	1		0	269	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041449	42041449	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	7	0	0	ENST00000219905.7:c.5644C>G	p.Gln1882Glu	p.Q1882E	ENST00000219905	NM_001164273.1	1882	Cag/Gag	17/24	0.227423089097165	0	FACETS	0.12	0.074	0.181			1	SUBCLONAL	1	FALSE	0	0.227423089097165	0		0	396	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851500	128851500	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	12	0	0	ENST00000249373.3:c.1825G>T	p.Glu609Ter	p.E609*	ENST00000249373	NM_005631.4	609	Gag/Tag	11/12	1	2	FACETS	0.133	0.092	0.183	0.133	0.092	0.183	SUBCLONAL	1	FALSE	1	0.227423089097165	2		0	794	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175869	24175869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555881572	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	9	0	0	ENST00000263121.7:c.1097G>A	p.Arg366His	p.R366H	ENST00000263121	NM_003073.3	366	cGc/cAc	8/9	1	2	FACETS	0.118	0.077	0.171	0.118	0.077	0.171	SUBCLONAL	1	FALSE	1	0.227423089097165	2		0	669	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378305	225378305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	4	0	0	ENST00000264414.4:c.590G>A	p.Gly197Glu	p.G197E	ENST00000264414	NM_003590.4	197	gGa/gAa	5/16	0.227423089097165	1	FACETS	0.094	0.048	0.16	0.094	0.048	0.16	SUBCLONAL	1	FALSE	0	0.227423089097165	1		0	333	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121313	29121313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	7	0	0	ENST00000328354.6:c.362G>A	p.Cys121Tyr	p.C121Y	ENST00000328354	NM_007194.3	121	tGt/tAt	3/15	1	2	FACETS	0.1	0.061	0.151	0.1	0.061	0.151	SUBCLONAL	1	FALSE	1	0.227423089097165	2		0	618	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37680952	37680952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	7	0	0	ENST00000447079.4:c.3121G>A	p.Glu1041Lys	p.E1041K	ENST00000447079	NM_015083.1	1041	Gag/Aag	12/14	1	2	FACETS	0.099	0.061	0.15	0.099	0.061	0.15	SUBCLONAL	1	FALSE	1	0.227423089097165	2		0	620	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81528560	81528560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	3	0	0	ENST00000298171.2:c.239G>A	p.Arg80Lys	p.R80K	ENST00000298171	NM_000369.2	80	aGa/aAa	2/10	1	2	FACETS	0.099	0.046	0.182	0.099	0.046	0.182	SUBCLONAL	1	FALSE	1	0.227423089097165	2		0	267	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70432668	70432668	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	4	0	0	ENST00000373644.4:c.4690C>G	p.Gln1564Glu	p.Q1564E	ENST00000373644	NM_030625.2	1564	Caa/Gaa	8/12	1	2	FACETS	0.088	0.046	0.151	0.088	0.046	0.151	SUBCLONAL	1	FALSE	1	0.227423089097165	2		0	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578223	7578223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	7	0	0	ENST00000269305.4:c.626G>A	p.Arg209Lys	p.R209K	ENST00000269305	NM_001126112.2	209	aGa/aAa	6/11	1	2	FACETS	0.081	0.05	0.123	0.081	0.05	0.123	SUBCLONAL	1	FALSE	1	0.227423089097165	2		0	757	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578227	7578227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	6	0	0	ENST00000269305.4:c.622G>A	p.Asp208Asn	p.D208N	ENST00000269305	NM_001126112.2	208	Gac/Aac	6/11	1	2	FACETS	0.071	0.042	0.111	0.071	0.042	0.111	SUBCLONAL	1	FALSE	1	0.227423089097165	2		0	743	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159748	20159748	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	363	275	0	ENST00000379607.5:c.11A>G	p.Asn4Ser	p.N4S	ENST00000379607	NM_001412.3	4	aAt/aGt	1/7	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	FALSE	0	0.850955810762132	1		275	438	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336077	73336077	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	116	179	0	ENST00000377767.4:c.2326A>C	p.Thr776Pro	p.T776P	ENST00000377767	NM_014953.3	776	Act/Cct	17/21	0.850955810762132	1	FACETS	0.973	0.915	1	0.973	0.915	1	CLONAL	1	FALSE	0	0.850955810762132	1		179	161	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005486	42005487	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0042872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	413	589	0	ENST00000219905.7:c.3223_3224del	p.Asp1075LeufsTer16	p.D1075Lfs*16	ENST00000219905	NM_001164273.1	1074	ccAGac/ccac	9/24	1	2	FACETS	0.978	0.934	1	0.978	0.934	1	CLONAL	1	FALSE	1	0.850955810762132	2		589	993	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0042887-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	112	372	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.0130503226755669	3	FACETS	1	0.943	1	1	0.943	1	INDETERMINATE	2	TRUE	1	0.29	3		372	419	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255710	16255710	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs756479101	NA	P-0042887-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	157	401	0	ENST00000375759.3:c.2975A>G	p.Asn992Ser	p.N992S	ENST00000375759	NM_015001.2	992	aAt/aGt	11/15	1	2	FACETS	1	0.972	1	1	0.993	1	CLONAL	2	TRUE	1	0.29	2		401	486	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	108	638	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.973	1	1	0.99	1	CLONAL	2	FALSE	1	0.167339582508046	2		638	525	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	88	831	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.128888928675309	0	FACETS	1	0.97	1			1	CLONAL	1	FALSE	0	0.167339582508046	0		831	679	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	105	635	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	1	0.91	1	1	0.988	1	CLONAL	2	FALSE	1	0.167339582508046	2		636	618	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	61	120	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	0.167339582508046	3	FACETS	0.923	0.808	1	1	0.957	1	CLONAL	4	FALSE	0	0.167339582508046	3		120	214	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	105	362	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.167339582508046	3	FACETS	1	0.941	1	1	0.988	1	CLONAL	5	FALSE	0	0.167339582508046	3		362	261	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	55	588	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.925	0.8	1	1	0.982	1	CLONAL	3	FALSE	1	0.167339582508046	2		592	237	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874149	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	27	460	2	ENST00000262189.6:c.8389_8390del	p.Lys2797GlyfsTer11	p.K2797Gfs*11	ENST00000262189	NM_170606.2	2797	AAg/g	38/59	1	2	FACETS	0.955	0.767	1	1	0.952	1	CLONAL	2	FALSE	1	0.167339582508046	2		462	169	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	60	498	4	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.857	0.745	0.976	1	0.982	1	CLONAL	3	FALSE	1	0.167339582508046	2		502	279	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	18	363	1	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	1	0.834	1	1	0.834	1	CLONAL	1	FALSE	1	0.167339582508046	2		364	189	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	28	360	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.152945188479798	3	FACETS	0.996	0.803	1	0.996	0.803	1	CLONAL	2	FALSE	1	0.167339582508046	3		360	182	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979987	7979987	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746723399	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	112	605	0	ENST00000319144.4:c.1350del	p.Leu451SerfsTer16	p.L451Sfs*16	ENST00000319144	NM_001139.2	450	ggG/gg	10/15	0.167339582508046	1	FACETS	0.876	0.789	0.968	1	0.987	1	CLONAL	2	FALSE	0	0.167339582508046	1		605	700	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	16	729	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.167339582508046	1	FACETS	0.234	0.172	0.309	0.234	0.172	0.309	SUBCLONAL	1	FALSE	0	0.167339582508046	1		730	749	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	24	579	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.167339582508046	1	FACETS	0.544	0.426	0.682	0.544	0.426	0.682	SUBCLONAL	1	FALSE	0	0.167339582508046	1		579	483	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509085	66509085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	18	285	0	ENST00000273854.3:c.242del	p.Asn81MetfsTer24	p.N81Mfs*24	ENST00000273854	NM_004439.5	81	aAt/at	2/18	0.152945188479798	3	FACETS	0.767	0.582	0.982	0.767	0.582	0.982	CLONAL	2	FALSE	1	0.167339582508046	3		285	152	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928347	69928347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	72	532	0	ENST00000352241.4:c.167G>A	p.Arg56His	p.R56H	ENST00000352241	NM_198159.2	56	cGc/cAc	2/10	1	2	FACETS	0.859	0.752	0.973	1	0.979	1	CLONAL	2	FALSE	1	0.167339582508046	2		532	501	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687471	37687472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs760014508	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	61	513	1	ENST00000447079.4:c.4382dup	p.Thr1463AsnfsTer50	p.T1463Nfs*50	ENST00000447079	NM_015083.1	1459	tgg/tGgg	14/14	0.167339582508046	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	0	0.167339582508046	1		514	454	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272337	15272337	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs771517374	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	161	685	4	ENST00000263388.2:c.6102del	p.Gly2035ValfsTer50	p.G2035Vfs*50	ENST00000263388	NM_000435.2	2034	ccC/cc	33/33	1	2	FACETS	1	0.98	1	1	0.993	1	CLONAL	2	FALSE	1	0.167339582508046	2		689	794	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914422	32914422	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	27	536	0	ENST00000380152.3:c.5934del	p.Phe1978LeufsTer26	p.F1978Lfs*26	ENST00000380152		1977	aTt/at	11/27	0.152945188479798	3	FACETS	1	0.825	1	1	0.825	1	CLONAL	2	FALSE	1	0.167339582508046	3		536	170	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150022	202150022	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	80	561	0	ENST00000358485.4:c.1463T>C	p.Leu488Pro	p.L488P	ENST00000358485	NM_001080125.1	488	cTg/cCg	8/9	1	2	FACETS	0.912	0.805	1	1	0.982	1	CLONAL	2	FALSE	1	0.167339582508046	2		561	524	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279860	46279861	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAA	rs753491875	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	35	567	0	ENST00000371998.3:c.3788_3789insACA	p.Gln1276dup	p.Q1276dup	ENST00000371998		1276	-/CAA	20/23	0.167339582508046	1	FACETS	0.654	0.535	0.788	0.654	0.535	0.788	SUBCLONAL	1	FALSE	0	0.167339582508046	1		567	586	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	33	465	0	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	1	0.885	1	1	0.965	1	CLONAL	2	FALSE	1	0.167339582508046	2		465	179	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116262	209116263	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs754375602	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	13	270	0	ENST00000345146.2:c.13dup	p.Ile5AsnfsTer13	p.I5Nfs*13	ENST00000345146	NM_005896.2	5	atc/aAtc	3/10	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	FALSE	1	0.167339582508046	2		270	111	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554492	63554493	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	86	703	0	ENST00000307078.5:c.246dup	p.His83ThrfsTer58	p.H83Tfs*58	ENST00000307078	NM_004655.3	82	-/A	2/11	0.167339582508046	1	FACETS	0.906	0.803	1	1	0.983	1	CLONAL	2	FALSE	0	0.167339582508046	1		703	520	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	128	600	6	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	1	2	FACETS	0.897	0.812	0.986	1	0.988	1	CLONAL	2	FALSE	1	0.167339582508046	2		606	853	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865540	57865540	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1295636010	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	96	715	1	ENST00000228682.2:c.3017G>A	p.Gly1006Asp	p.G1006D	ENST00000228682	NM_005269.2	1006	gGc/gAc	12/12	0.152945188479798	3	FACETS	1	0.915	1	1	0.915	1	CLONAL	2	FALSE	1	0.167339582508046	3		716	604	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347608	89347608	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	123	691	1	ENST00000301030.4:c.5342G>T	p.Arg1781Met	p.R1781M	ENST00000301030	NM_001256183.1	1781	aGg/aTg	9/13	1	2	FACETS	0.977	0.885	1	1	0.989	1	CLONAL	2	FALSE	1	0.167339582508046	2		692	752	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270529	98270530	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs751977093	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	49	179	0	ENST00000331920.6:c.114dup	p.Leu39AlafsTer51	p.L39Afs*51	ENST00000331920	NM_000264.3	38	-/G	1/24	1	2	FACETS	0.777	0.66	0.904	1	0.965	1	CLONAL	2	FALSE	1	0.167339582508046	2		179	377	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190818	106190818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	24	528	0	ENST00000380013.4:c.4096C>T	p.Arg1366Cys	p.R1366C	ENST00000380013	NM_001127208.2	1366	Cgt/Tgt	9/11	0.152945188479798	3	FACETS	0.695	0.544	0.871	0.348	0.272	0.436	SUBCLONAL	1	FALSE	1	0.167339582508046	3		528	447	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628601	90628601	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	190	793	0	ENST00000330062.3:c.986T>C	p.Leu329Pro	p.L329P	ENST00000330062	NM_002168.2	329	cTg/cCg	8/11	0.128888928675309	0	FACETS	1	0.965	1			1	CLONAL	2	FALSE	0	0.167339582508046	0		793	882	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18576934	18576934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765821860	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	58	514	2	ENST00000266497.5:c.2342G>A	p.Arg781His	p.R781H	ENST00000266497		781	cGc/cAc	16/31	0.152945188479798	3	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	FALSE	1	0.167339582508046	3		516	318	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	25	539	3	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	1	2	FACETS	0.905	0.714	1	0.905	0.714	1	CLONAL	1	FALSE	1	0.167339582508046	2		542	330	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523088	25523088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758534627	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	155	693	1	ENST00000264709.3:c.97C>T	p.Arg33Cys	p.R33C	ENST00000264709	NM_175629.2	33	Cgt/Tgt	3/23	1	2	FACETS	0.978	0.895	1	1	0.991	1	CLONAL	2	FALSE	1	0.167339582508046	2		694	947	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998128	169998128	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs753143066	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	24	428	1	ENST00000295797.4:c.826del	p.Thr276GlnfsTer7	p.T276Qfs*7	ENST00000295797	NM_002740.5	273	ttA/tt	9/18	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	1	0.167339582508046	2		429	199	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007752	45007753	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	32	410	0	ENST00000558401.1:c.204dup	p.Val69SerfsTer21	p.V69Sfs*21	ENST00000558401	NM_004048.2	67	gaa/gAaa	2/4	0.128888928675309	0	FACETS	1	0.93	1			1	CLONAL	1	FALSE	0	0.167339582508046	0		410	240	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918992	50918992	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568638496	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	117	522	0	ENST00000440232.2:c.2729G>A	p.Arg910Gln	p.R910Q	ENST00000440232	NM_002691.3	910	cGg/cAg	22/27	1	2	FACETS	1	0.916	1	1	0.989	1	CLONAL	2	FALSE	1	0.167339582508046	2		522	688	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600496	43600496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178140696	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	142	437	1	ENST00000355710.3:c.722C>T	p.Ala241Val	p.A241V	ENST00000355710	NM_020975.4	241	gCc/gTc	4/20	1	2	FACETS	0.837	0.764	0.912	1	0.992	1	CLONAL	3	FALSE	1	0.167339582508046	2		438	676	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	101	670	4	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	1	2	FACETS	0.868	0.777	0.966	1	0.985	1	CLONAL	2	FALSE	1	0.167339582508046	2		674	695	SUCCESS
BLM	641	MSKCC	GRCh37	15	91333930	91333930	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs762354041	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	34	574	1	ENST00000355112.3:c.2875C>T	p.Arg959Ter	p.R959*	ENST00000355112	NM_000057.2	959	Cga/Tga	15/22	0.128888928675309	0	FACETS	1	0.883	1			1	CLONAL	1	FALSE	0	0.167339582508046	0		575	306	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445095	49445095	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	92	624	1	ENST00000301067.7:c.2371del	p.Gln791ArgfsTer139	p.Q791Rfs*139	ENST00000301067	NM_003482.3	791	Cag/ag	10/54	0.152945188479798	3	FACETS	0.866	0.77	0.969	0.866	0.77	0.969	CLONAL	2	FALSE	1	0.167339582508046	3		625	688	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820183	139820183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1353820572	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	109	686	0	ENST00000247668.2:c.1336G>A	p.Ala446Thr	p.A446T	ENST00000247668	NM_021138.3	446	Gcc/Acc	11/11	1	2	FACETS	0.807	0.725	0.895	1	0.984	1	CLONAL	2	FALSE	1	0.167339582508046	2		686	807	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138382755	138382756	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1224981079	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	44	448	1	ENST00000289153.2:c.2788dup	p.Thr930AsnfsTer8	p.T930Nfs*8	ENST00000289153	NM_006219.2	930	act/aAct	19/22	1	2	FACETS	1	0.848	1	1	0.971	1	CLONAL	2	FALSE	1	0.167339582508046	2		449	262	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265554	152265554	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	36	523	0	ENST00000206249.3:c.1007C>A	p.Pro336His	p.P336H	ENST00000206249	NM_000125.3	336	cCc/cAc	4/8	0.160642773754809	4	FACETS	1	0.948	1	0.739	0.609	0.884	CLONAL	1	FALSE	2	0.167339582508046	4		523	340	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80088585	80088585	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	29	386	0	ENST00000265081.6:c.2582del	p.Asn861MetfsTer6	p.N861Mfs*6	ENST00000265081	NM_002439.4	859	atA/at	19/24	1	2	FACETS	0.869	0.708	1	1	0.965	1	CLONAL	3	FALSE	1	0.167339582508046	2		386	133	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486587	56486587	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	94	591	0	ENST00000267101.3:c.1166C>T	p.Thr389Ile	p.T389I	ENST00000267101	NM_001982.3	389	aCa/aTa	10/28	0.152945188479798	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	FALSE	1	0.167339582508046	3		591	543	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029445	16029445	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	30	365	0	ENST00000268712.3:c.1585G>A	p.Glu529Lys	p.E529K	ENST00000268712	NM_006311.3	529	Gaa/Aaa	15/46	0.167339582508046	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	FALSE	0	0.167339582508046	1		365	252	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006228	22006228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	116	543	0	ENST00000276925.6:c.175G>A	p.Ala59Thr	p.A59T	ENST00000276925	NM_004936.3	59	Gcc/Acc	2/2	1	2	FACETS	1	0.961	1	1	0.99	1	CLONAL	2	FALSE	1	0.167339582508046	2		543	617	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447880	49447880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771025627	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	155	593	1	ENST00000301067.7:c.554G>A	p.Arg185His	p.R185H	ENST00000301067	NM_003482.3	185	cGc/cAc	5/54	0.152945188479798	3	FACETS	0.838	0.767	0.911	1	0.982	1	CLONAL	3	FALSE	1	0.167339582508046	3		594	799	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89825093	89825093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1374262828	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	105	550	1	ENST00000389301.3:c.2873C>T	p.Ala958Val	p.A958V	ENST00000389301	NM_000135.2	958	gCg/gTg	30/43	1	2	FACETS	1	0.95	1	1	0.988	1	CLONAL	2	FALSE	1	0.167339582508046	2		551	574	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332646	65332646	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	28	379	0	ENST00000342505.4:c.893A>T	p.Glu298Val	p.E298V	ENST00000342505	NM_002227.2	298	gAg/gTg	7/25	1	2	FACETS	0.956	0.772	1	1	0.954	1	CLONAL	2	FALSE	1	0.167339582508046	2		379	175	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651186	206651186	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	138	818	0	ENST00000367120.3:c.796A>G	p.Thr266Ala	p.T266A	ENST00000367120	NM_014002.3	266	Acc/Gcc	8/22	1	2	FACETS	1	0.945	1	1	0.991	1	CLONAL	2	FALSE	1	0.167339582508046	2		818	784	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104377066	104377066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201326378	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	51	525	1	ENST00000369902.3:c.1177C>T	p.Arg393Trp	p.R393W	ENST00000369902	NM_016169.3	393	Cgg/Tgg	10/12	1	2	FACETS	0.837	0.714	0.971	1	0.97	1	CLONAL	2	FALSE	1	0.167339582508046	2		526	364	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413552	32413553	+	missense_variant	Missense_Mutation	DNP	CA	CA	TG	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	74	540	0	ENST00000332351.3:c.1397_1398inv	p.Leu466Pro	p.L466P	ENST00000332351	NM_024426.4	466	cTG/cCA	9/10	1	2	FACETS	0.838	0.738	0.943	1	0.985	1	CLONAL	3	FALSE	1	0.167339582508046	2		540	352	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344656	118344656	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	36	428	0	ENST00000534358.1:c.2787del	p.Ala930GlnfsTer19	p.A930Qfs*19	ENST00000534358	NM_005933.3	928	Aaa/aa	3/36	1	2	FACETS	1	0.918	1	1	0.97	1	CLONAL	2	FALSE	1	0.167339582508046	2		428	182	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489568	56489568	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	44	511	0	ENST00000267101.3:c.2033G>A	p.Arg678Lys	p.R678K	ENST00000267101	NM_001982.3	678	aGg/aAg	17/28	0.152945188479798	3	FACETS	1	0.93	1	0.604	0.506	0.711	CLONAL	1	FALSE	1	0.167339582508046	3		511	472	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336108	73336109	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	18	271	0	ENST00000377767.4:c.2294_2295del	p.Tyr765TrpfsTer15	p.Y765Wfs*15	ENST00000377767	NM_014953.3	765	tAT/t	17/21	0.152945188479798	3	FACETS	0.925	0.711	1	1	0.901	1	CLONAL	3	FALSE	1	0.167339582508046	3		271	84	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81558886	81558886	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	42	428	0	ENST00000298171.2:c.479A>G	p.Asp160Gly	p.D160G	ENST00000298171	NM_000369.2	160	gAc/gGc	6/10	1	2	FACETS	0.909	0.769	1	1	0.976	1	CLONAL	3	FALSE	1	0.167339582508046	2		428	184	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478269	99478269	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs780382569	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	40	314	0	ENST00000268035.6:c.3173A>G	p.Asn1058Ser	p.N1058S	ENST00000268035	NM_000875.3	1058	aAt/aGt	16/21	0.128888928675309	0	FACETS	1	0.893	1			1	CLONAL	2	FALSE	0	0.167339582508046	0		314	184	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781863	3781863	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	111	773	1	ENST00000262367.5:c.4804C>T	p.Arg1602Cys	p.R1602C	ENST00000262367	NM_004380.2	1602	Cgc/Tgc	29/31	1	2	FACETS	0.986	0.887	1	1	0.988	1	CLONAL	2	FALSE	1	0.167339582508046	2		774	673	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843488	3843488	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	80	506	0	ENST00000262367.5:c.1115A>G	p.Gln372Arg	p.Q372R	ENST00000262367	NM_004380.2	372	cAa/cGa	4/31	1	2	FACETS	0.863	0.761	0.972	1	0.981	1	CLONAL	2	FALSE	1	0.167339582508046	2		506	554	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835621	68835621	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	90	601	0	ENST00000261769.5:c.212T>C	p.Leu71Pro	p.L71P	ENST00000261769	NM_004360.3	71	cTc/cCc	3/16	1	2	FACETS	1	0.963	1	1	0.987	1	CLONAL	2	FALSE	1	0.167339582508046	2		601	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578391	7578391	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	14	756	0	ENST00000269305.4:c.539A>G	p.Glu180Gly	p.E180G	ENST00000269305	NM_001126112.2	180	gAg/gGg	5/11	0.167339582508046	1	FACETS	0.22	0.158	0.296	0.22	0.158	0.296	SUBCLONAL	1	FALSE	0	0.167339582508046	1		756	698	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576121	29576121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	38	468	1	ENST00000356175.3:c.4094G>A	p.Cys1365Tyr	p.C1365Y	ENST00000356175	NM_000267.3	1365	tGc/tAc	30/57	0.167339582508046	1	FACETS	0.897	0.747	1	1	0.963	1	CLONAL	2	FALSE	0	0.167339582508046	1		469	232	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664545	29664545	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	44	516	0	ENST00000356175.3:c.6524C>T	p.Thr2175Ile	p.T2175I	ENST00000356175	NM_000267.3	2175	aCt/aTt	42/57	0.167339582508046	1	FACETS	0.883	0.745	1	1	0.968	1	CLONAL	2	FALSE	0	0.167339582508046	1		516	273	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40368033	40368033	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	87	521	0	ENST00000293328.3:c.1472C>T	p.Pro491Leu	p.P491L	ENST00000293328	NM_012448.3	491	cCt/cTt	12/19	0.167339582508046	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	0	0.167339582508046	1		521	655	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78704480	78704480	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560409938	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	99	550	0	ENST00000306801.3:c.628G>A	p.Ala210Thr	p.A210T	ENST00000306801	NM_020761.2	210	Gca/Aca	5/34	0.167339582508046	1	FACETS	0.866	0.774	0.963	1	0.985	1	CLONAL	2	FALSE	0	0.167339582508046	1		550	626	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288772	15288772	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	30	70	0	ENST00000263388.2:c.3967T>C	p.Ser1323Pro	p.S1323P	ENST00000263388	NM_000435.2	1323	Tcc/Ccc	24/33	1	2	FACETS	0.888	0.721	1	1	0.953	1	CLONAL	2	FALSE	1	0.167339582508046	2		70	202	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376372	15376372	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	170	860	1	ENST00000263377.2:c.642T>A	p.Asn214Lys	p.N214K	ENST00000263377	NM_058243.2	214	aaT/aaA	5/20	1	2	FACETS	1	0.942	1	1	0.992	1	CLONAL	2	FALSE	1	0.167339582508046	2		861	986	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17389777	17389777	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	114	827	1	ENST00000359435.4:c.910C>T	p.Gln304Ter	p.Q304*	ENST00000359435	NM_001033549.1	304	Cag/Tag	9/9	1	2	FACETS	0.773	0.696	0.856	1	0.984	1	SUBCLONAL	2	FALSE	1	0.167339582508046	2		828	881	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273271	18273271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1182625237	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	110	630	0	ENST00000222254.8:c.1064G>A	p.Arg355Gln	p.R355Q	ENST00000222254	NM_005027.3	355	cGa/cAa	9/16	1	2	FACETS	0.871	0.782	0.964	1	0.986	1	CLONAL	2	FALSE	1	0.167339582508046	2		630	755	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212279	36212280	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	110	707	0	ENST00000222270.7:c.2030_2031insA	p.Glu678Ter	p.E678*	ENST00000222270	NM_014727.1	677	cct/ccAt	3/37	1	2	FACETS	1	0.913	1	1	0.988	1	CLONAL	2	FALSE	1	0.167339582508046	2		707	647	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229232	36229232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	81	725	0	ENST00000222270.7:c.7922C>T	p.Ala2641Val	p.A2641V	ENST00000222270	NM_014727.1	2641	gCc/gTc	37/37	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.167339582508046	2		725	660	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082472	16082472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	171	607	0	ENST00000281043.3:c.286G>A	p.Ala96Thr	p.A96T	ENST00000281043	NM_005378.4	96	Gcg/Acg	2/3	1	2	FACETS	0.976	0.901	1	1	0.994	1	CLONAL	3	FALSE	1	0.167339582508046	2		607	698	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439734	220439734	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	150	878	0	ENST00000243786.2:c.587T>C	p.Leu196Pro	p.L196P	ENST00000243786	NM_002191.3	196	cTg/cCg	2/2	1	2	FACETS	1	0.958	1	1	0.992	1	CLONAL	2	FALSE	1	0.167339582508046	2		878	832	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662395	227662395	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	59	601	0	ENST00000305123.5:c.1060A>G	p.Thr354Ala	p.T354A	ENST00000305123	NM_005544.2	354	Acc/Gcc	1/2	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	FALSE	1	0.167339582508046	2		601	702	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713757	30713757	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	128	602	0	ENST00000295754.5:c.1082T>C	p.Leu361Pro	p.L361P	ENST00000295754	NM_003242.5	361	cTc/cCc	4/7	0.167339582508046	3	FACETS	0.933	0.849	1	0.933	0.849	1	CLONAL	3	FALSE	0	0.167339582508046	3		602	592	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37048540	37048540	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	76	445	0	ENST00000231790.2:c.439G>A	p.Gly147Arg	p.G147R	ENST00000231790	NM_000249.3	147	Ggg/Agg	5/19	0.167339582508046	3	FACETS	1	0.94	1	1	0.977	1	CLONAL	4	FALSE	0	0.167339582508046	3		445	227	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933242	49933242	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	145	830	0	ENST00000296474.3:c.2868C>G	p.Ser956Arg	p.S956R	ENST00000296474	NM_002447.2	956	agC/agG	12/20	1	2	FACETS	1	0.946	1	1	0.991	1	CLONAL	2	FALSE	1	0.167339582508046	2		830	825	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356169	66356169	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	34	523	0	ENST00000273854.3:c.1328C>T	p.Ala443Val	p.A443V	ENST00000273854	NM_004439.5	443	gCa/gTa	5/18	0.152945188479798	3	FACETS	1	0.943	1	0.722	0.592	0.867	CLONAL	1	FALSE	1	0.167339582508046	3		523	305	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800568	32800568	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	192	760	0	ENST00000374899.4:c.979A>G	p.Arg327Gly	p.R327G	ENST00000374899	NM_018833.2	327	Agg/Ggg	6/12	0.160642773754809	4	FACETS	0.88	0.813	0.949	1	0.987	1	CLONAL	3	FALSE	2	0.167339582508046	4		760	1015	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681085	117681085	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	21	539	0	ENST00000368508.3:c.3535del	p.Ser1179GlnfsTer64	p.S1179Qfs*64	ENST00000368508	NM_002944.2	1179	Tca/ca	23/43	0.160642773754809	4	FACETS	1	0.902	1	0.678	0.524	0.856	CLONAL	1	FALSE	2	0.167339582508046	4		539	216	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14027735	14027735	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	27	397	0	ENST00000405192.2:c.109A>G	p.Arg37Gly	p.R37G	ENST00000405192	NM_001163147.1	37	Aga/Gga	3/12	1	2	FACETS	0.776	0.621	0.95	1	0.939	1	CLONAL	2	FALSE	1	0.167339582508046	2		397	208	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140508740	140508740	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	40	475	0	ENST00000288602.6:c.560T>C	p.Met187Thr	p.M187T	ENST00000288602	NM_004333.4	187	aTg/aCg	4/18	1	2	FACETS	1	0.92	1	1	0.972	1	CLONAL	2	FALSE	1	0.167339582508046	2		475	205	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842354	151842355	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	26	302	0	ENST00000262189.6:c.14057dup	p.Asn4686LysfsTer19	p.N4686Kfs*19	ENST00000262189	NM_170606.2	4686	aat/aaAt	54/59	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	1	0.167339582508046	2		302	210	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372435	55372435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	125	803	1	ENST00000297316.4:c.1125G>A	p.Met375Ile	p.M375I	ENST00000297316	NM_022454.3	375	atG/atA	2/2	1	2	FACETS	1	0.974	1	1	0.991	1	CLONAL	2	FALSE	1	0.167339582508046	2		804	620	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215904	98215904	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	138	649	0	ENST00000331920.6:c.3307-2A>G		p.X1103_splice	ENST00000331920	NM_000264.3	1103			1	2	FACETS	0.867	0.791	0.946	1	0.992	1	CLONAL	3	FALSE	1	0.167339582508046	2		649	634	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53244011	53244011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377276125	NA	P-0043127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	80	594	1	ENST00000375401.3:c.982C>T	p.Arg328Trp	p.R328W	ENST00000375401	NM_004187.3	328	Cgg/Tgg	8/26	0.128888928675309	0	FACETS	0.98	0.868	1			1	CLONAL	2	FALSE	0	0.167339582508046	0		595	406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0043235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	129	863	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.273542996128446	1	FACETS	0.977	0.886	1	0.977	0.886	1	CLONAL	1	TRUE	0	0.273542996128446	1		864	833	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648230	206648230	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	125	624	0	ENST00000367120.3:c.251T>A	p.Leu84Gln	p.L84Q	ENST00000367120	NM_014002.3	84	cTg/cAg	5/22	0.105396727015718	3	FACETS	1	0.984	1	0.719	0.652	0.791	INDETERMINATE	1	TRUE	1	0.273542996128446	3		624	722	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653862	89653866	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GTAAG	GTAAG	-	novel	NA	P-0043235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	50	438	0	ENST00000371953.3:c.164+1_164+5del		p.VR54fs	ENST00000371953	NM_000314.4	54	GTAAGg/g	2/9	0.118878511930377	3	FACETS	0.917	0.779	1			1	INDETERMINATE	1	TRUE	NA	0.273542996128446	3		438	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0043293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	311	1045	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.602858789999012	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.602858789999012	1		1046	679	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0043293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	78	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.955	0.849	1	0.955	0.849	1	CLONAL	1	TRUE	1	0.602858789999012	2		326	271	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0043293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	178	692	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	0.979	0.907	1	0.979	0.907	1	CLONAL	1	TRUE	1	0.602858789999012	2		692	603	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593426	48593426	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	156	489	0	ENST00000342988.3:c.1178del	p.Gly393ValfsTer22	p.G393Vfs*22	ENST00000342988	NM_005359.5	393	Ggt/gt	10/12	0.602858789999012	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.602858789999012	1		489	351	SUCCESS
APC	324	MSKCC	GRCh37	5	112173306	112173317	+	frameshift_variant	Frame_Shift_Del	DEL	ATAGTTTGACAA	ATAGTTTGACAA	T	novel	NA	P-0043293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	53	247	0	ENST00000257430.4:c.2015_2026delinsT	p.His672LeufsTer4	p.H672Lfs*4	ENST00000257430	NM_000038.5	672	cATAGTTTGACAAta/cTta	16/16	1	2	FACETS	0.966	0.838	1	0.966	0.838	1	CLONAL	1	TRUE	1	0.602858789999012	2		247	182	SUCCESS
APC	324	MSKCC	GRCh37	5	112175595	112175600	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGTA	GAAGTA	AAAGT	novel	NA	P-0043293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	146	444	2	ENST00000257430.4:c.4304_4309delinsAAAGT	p.Arg1435LysfsTer38	p.R1435Kfs*38	ENST00000257430	NM_000038.5	1435	aGAAGTAaa/aAAAGTaa	16/16	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.602858789999012	2		446	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0043555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	408	835	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.604018755835854	2	FACETS	0.762	0.731	0.793	0.762	0.731	0.793	SUBCLONAL	2	TRUE	0	0.697239312605022	2		835	768	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0043555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	131	378	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.174739010983396	4	FACETS	1	0.984	1	0.683	0.624	0.744	INDETERMINATE	1	TRUE	2	0.697239312605022	4		378	467	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310820	123310820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747502397	NA	P-0043555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	138	613	3	ENST00000358487.5:c.608G>A	p.Arg203His	p.R203H	ENST00000358487	NM_000141.4	203	cGc/cAc	5/18	0.697239312605022	1	FACETS	0.402	0.367	0.439	0.402	0.367	0.439	SUBCLONAL	1	TRUE	0	0.697239312605022	1		616	641	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0043555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	63	368	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.188815559757996	2	FACETS	0.657	0.574	0.746	0.329	0.287	0.373	INDETERMINATE	1	TRUE	0	0.697239312605022	2		368	275	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857910	9857910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	211	674	0	ENST00000330684.3:c.3491C>T	p.Thr1164Met	p.T1164M	ENST00000330684	NM_001134407.1	1164	aCg/aTg	13/13	0.348194088729826	1	FACETS	0.675	0.631	0.72	0.675	0.631	0.72	INDETERMINATE	1	TRUE	0	0.697239312605022	1		674	584	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117964	70117965	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0043555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	163	348	0	ENST00000245479.2:c.431+2dup		p.X144_splice	ENST00000245479	NM_000346.3	144			0.639353284503061	2	FACETS	0.889	0.837	0.939	0.889	0.837	0.939	CLONAL	2	TRUE	0	0.697239312605022	2		348	263	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925316	114925317	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs745872748	NA	P-0043555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	250	422	20	ENST00000543371.1:c.1403dup	p.Cys469ValfsTer8	p.C469Vfs*8	ENST00000543371	NM_001198531.1	465	aga/agAa	14/14	0.697239312605022	1	FACETS	0.949	0.899	0.999	0.949	0.899	0.999	CLONAL	1	TRUE	0	0.697239312605022	1		442	492	SUCCESS
APC	324	MSKCC	GRCh37	5	112162945	112162945	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1114167599	NA	P-0043555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	92	364	0	ENST00000257430.4:c.1548+1G>T		p.X516_splice	ENST00000257430	NM_000038.5	516			0.188815559757996	2	FACETS	1	0.954	1	0.548	0.495	0.601	INDETERMINATE	1	TRUE	0	0.697239312605022	2		364	241	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563428	21563428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	351	831	0	ENST00000382592.4:c.491C>T	p.Pro164Leu	p.P164L	ENST00000382592	NM_014572.2	164	cCa/cTa	4/8	0.604097476068631	3	FACETS	1	0.99	1	0.584	0.553	0.615	CLONAL	1	TRUE	1	0.697239312605022	3		831	1163	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894961	101895339	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCAGAGGGTACTACGTTGAAAGACTTAATTTATGATATGACAACGTCAGGTTCTGGCTCAGGTAACATAATTGTTTCTCCTTTTTCCTAAGACATCTTTTTAAAATTAAGCGATACTTATTTTATTAGTTTTCTAATAAGCCAACTTGCTAGAATGTGAGATAGTATAAATAATATTGCAGGTTTGAACCTAATAAAAATCTTTAAGCTTGATGTATATATGACTGTGGCTGGTTTAAAATAGATTGGAACTTAACTTTAACTGTTAAAGCGAATCAATAAGTCAGCTCCATGGTGGTATAAATTTCAAAGCGTTCTCACTTGTATAATCTAATTTGCTTTTCATCACTGTGAGGTAGAAAGGATAAGAACAATTATTC	TCAGAGGGTACTACGTTGAAAGACTTAATTTATGATATGACAACGTCAGGTTCTGGCTCAGGTAACATAATTGTTTCTCCTTTTTCCTAAGACATCTTTTTAAAATTAAGCGATACTTATTTTATTAGTTTTCTAATAAGCCAACTTGCTAGAATGTGAGATAGTATAAATAATATTGCAGGTTTGAACCTAATAAAAATCTTTAAGCTTGATGTATATATGACTGTGGCTGGTTTAAAATAGATTGGAACTTAACTTTAACTGTTAAAGCGAATCAATAAGTCAGCTCCATGGTGGTATAAATTTCAAAGCGTTCTCACTTGTATAATCTAATTTGCTTTTCATCACTGTGAGGTAGAAAGGATAAGAACAATTATTC	-	novel	NA	P-0043555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	50	338	0	ENST00000374994.4:c.517_574+321del		p.X173_splice	ENST00000374994	NM_004612.2	173		3/9	0.63231056989513	1	FACETS	0.415	0.356	0.479	0.415	0.356	0.479	SUBCLONAL	1	TRUE	0	0.697239312605022	1		338	225	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	72	588	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.924	0.809	1	0.924	0.809	1	CLONAL	1	TRUE	1	0.32	2		592	487	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	222	1445	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.872	0.813	0.931	1	0.993	1	CLONAL	2	TRUE	1	0.32	2		1452	796	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650109	93650109	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	40	525	0	ENST00000375746.1:c.1660G>A	p.Asp554Asn	p.D554N	ENST00000375746	NM_001174167.1	554	Gat/Aat	12/14	1	2	FACETS	0.362	0.3	0.432	0.362	0.3	0.432	SUBCLONAL	1	TRUE	1	0.32	2		525	690	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274172	10274173	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1555491538	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	65	558	0	ENST00000330684.3:c.96dup	p.Ala33ArgfsTer105	p.A33Rfs*105	ENST00000330684	NM_001134407.1	32	-/C	2/13	1	2	FACETS	0.758	0.658	0.866	0.758	0.658	0.866	SUBCLONAL	1	TRUE	1	0.32	2		558	536	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100728	8100728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs771019738	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	105	830	3	ENST00000346208.3:c.708del	p.Ser237AlafsTer28	p.S237Afs*28	ENST00000346208		234	ttC/tt	3/6	1	2	FACETS	0.883	0.792	0.981	0.883	0.792	0.981	CLONAL	1	TRUE	1	0.32	2		833	743	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	114	747	5	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.774	0.696	0.857	0.774	0.696	0.857	SUBCLONAL	1	TRUE	1	0.32	2		752	920	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874637	35874637	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	48	398	1	ENST00000303115.3:c.799del	p.Arg267GlyfsTer28	p.R267Gfs*28	ENST00000303115	NM_002185.3	265	Aaa/aa	6/8	1	2	FACETS	0.777	0.659	0.907	0.777	0.659	0.907	CLONAL	1	TRUE	1	0.32	2		399	386	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	81	1056	1	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	1	2	FACETS	0.814	0.718	0.917	0.814	0.718	0.917	CLONAL	1	TRUE	1	0.32	2		1057	622	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142913	7142913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1283504748	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	150	744	2	ENST00000302850.5:c.2456G>A	p.Arg819His	p.R819H	ENST00000302850	NM_000208.2	819	cGc/cAc	12/22	1	2	FACETS	0.966	0.883	1	0.966	0.883	1	CLONAL	1	TRUE	1	0.32	2		746	970	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043349	6043349	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781716	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	24	213	0	ENST00000265849.7:c.325del	p.Glu109LysfsTer3	p.E109Kfs*3	ENST00000265849	NM_000535.5	109	Gaa/aa	4/15	1	2	FACETS	0.628	0.494	0.781	0.628	0.494	0.781	SUBCLONAL	1	TRUE	1	0.32	2		213	239	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363570	40363570	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756565978	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	100	653	0	ENST00000397332.2:c.659C>T	p.Thr220Met	p.T220M	ENST00000397332	NM_001033082.2	220	aCg/aTg	3/3	1	2	FACETS	0.857	0.766	0.954	0.857	0.766	0.954	CLONAL	1	TRUE	1	0.32	2		653	729	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346714	225346714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	74	383	0	ENST00000264414.4:c.1924C>T	p.Arg642Trp	p.R642W	ENST00000264414	NM_003590.4	642	Cgg/Tgg	14/16	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.32	2		383	433	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902143	50902143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1389018181	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	97	709	0	ENST00000440232.2:c.35G>A	p.Gly12Glu	p.G12E	ENST00000440232	NM_002691.3	12	gGg/gAg	2/27	1	2	FACETS	0.973	0.869	1	0.973	0.869	1	CLONAL	1	TRUE	1	0.32	2		709	623	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025857	48025857	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs267608041	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	20	342	1	ENST00000234420.5:c.741del	p.Lys247AsnfsTer32	p.K247Nfs*32	ENST00000234420	NM_000179.2	245	atA/at	4/10	1	2	FACETS	0.335	0.256	0.428	0.335	0.256	0.428	SUBCLONAL	1	TRUE	1	0.32	2		343	373	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324711	31324711	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs2596492	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	10	106	2	ENST00000412585.2:c.97T>C	p.Tyr33His	p.Y33H	ENST00000412585	NM_005514.6	33	Tac/Cac	2/8	1	2	FACETS	0.772	0.529	1	0.772	0.529	1	CLONAL	1	TRUE	1	0.32	2		108	81	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248366	212248366	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	29	281	0	ENST00000342788.4:c.3901T>C	p.Tyr1301His	p.Y1301H	ENST00000342788	NM_005235.2	1301	Tac/Cac	28/28	1	2	FACETS	0.684	0.551	0.834	0.684	0.551	0.834	SUBCLONAL	1	TRUE	1	0.32	2		281	265	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24134057	24134057	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	74	490	0	ENST00000263121.7:c.214del	p.Thr72GlnfsTer13	p.T72Qfs*13	ENST00000263121	NM_003073.3	70	Aaa/aa	2/9	1	2	FACETS	0.799	0.7	0.905	0.799	0.7	0.905	CLONAL	1	TRUE	1	0.32	2		490	579	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883113	37883113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780434636	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	46	822	1	ENST00000269571.5:c.3016C>T	p.Arg1006Cys	p.R1006C	ENST00000269571		1006	Cgc/Tgc	25/27	1	2	FACETS	0.344	0.289	0.406	0.344	0.289	0.406	SUBCLONAL	1	TRUE	1	0.32	2		823	835	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777677	9777677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145191685	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	127	676	0	ENST00000377346.4:c.1013G>A	p.Arg338Gln	p.R338Q	ENST00000377346	NM_005026.3	338	cGg/cAg	8/24	1	2	FACETS	0.906	0.82	0.996	0.906	0.82	0.996	CLONAL	1	TRUE	1	0.32	2		676	876	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464961	120464961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764895571	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	110	516	0	ENST00000256646.2:c.5111G>A	p.Arg1704His	p.R1704H	ENST00000256646	NM_024408.3	1704	cGt/cAt	28/34	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.32	2		516	557	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104356980	104356981	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1477199832	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	74	625	1	ENST00000369902.3:c.846dup	p.Glu283ArgfsTer3	p.E283Rfs*3	ENST00000369902	NM_016169.3	280	-/C	7/12	1	2	FACETS	0.824	0.723	0.934	0.824	0.723	0.934	CLONAL	1	TRUE	1	0.32	2		626	561	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222522	2222523	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs750035555	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	109	778	0	ENST00000326181.6:c.722dup	p.Leu242AlafsTer55	p.L242Afs*55	ENST00000326181	NM_032271.2	239	tgc/tgCc	9/21	1	2	FACETS	0.866	0.777	0.959	0.866	0.777	0.959	CLONAL	1	TRUE	1	0.32	2		778	787	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462033	120462033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753822819	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	128	598	0	ENST00000256646.2:c.5683C>T	p.Arg1895Cys	p.R1895C	ENST00000256646	NM_024408.3	1895	Cgt/Tgt	31/34	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.32	2		598	751	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43817931	43817931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3820551	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	120	674	0	ENST00000372470.3:c.1610G>A	p.Arg537Gln	p.R537Q	ENST00000372470	NM_005373.2	537	cGg/cAg	11/12	1	2	FACETS	0.946	0.854	1	0.946	0.854	1	CLONAL	1	TRUE	1	0.32	2		674	793	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858053	40858053	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	99	696	3	ENST00000428826.2:c.1811del	p.Asn604ThrfsTer26	p.N604Tfs*26	ENST00000428826		604	aAc/ac	16/21	1	2	FACETS	0.743	0.662	0.828	0.743	0.662	0.828	SUBCLONAL	1	TRUE	1	0.32	2		699	833	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425694	49425694	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	66	850	1	ENST00000301067.7:c.12794del	p.Gly4265AlafsTer13	p.G4265Afs*13	ENST00000301067	NM_003482.3	4265	gGc/gc	39/54	1	2	FACETS	0.628	0.545	0.718	0.628	0.545	0.718	SUBCLONAL	1	TRUE	1	0.32	2		851	657	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994595	73994595	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	102	821	1	ENST00000318443.5:c.80-1G>T		p.X27_splice	ENST00000318443	NM_001024736.1	27			1	2	FACETS	0.894	0.8	0.994	0.894	0.8	0.994	CLONAL	1	TRUE	1	0.32	2		822	713	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039341	49039341	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	87	495	0	ENST00000267163.4:c.2330del	p.Pro777LeufsTer33	p.P777Lfs*33	ENST00000267163	NM_000321.2	776	Ccc/cc	23/27	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.32	2		495	524	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16235956	16235956	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	48	479	0	ENST00000375759.3:c.1022A>G	p.Asn341Ser	p.N341S	ENST00000375759	NM_015001.2	341	aAt/aGt	4/15	1	2	FACETS	0.555	0.468	0.649	0.555	0.468	0.649	SUBCLONAL	1	TRUE	1	0.32	2		479	541	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023382	27023382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	75	312	0	ENST00000324856.7:c.488C>T	p.Ala163Val	p.A163V	ENST00000324856	NM_006015.4	163	gCc/gTc	1/20	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.32	2		312	448	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089631	27089631	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	45	688	0	ENST00000324856.7:c.2587A>G	p.Met863Val	p.M863V	ENST00000324856	NM_006015.4	863	Atg/Gtg	8/20	1	2	FACETS	0.446	0.374	0.526	0.446	0.374	0.526	SUBCLONAL	1	TRUE	1	0.32	2		688	631	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36821036	36821036	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	52	552	0	ENST00000373129.3:c.343-2A>G		p.X115_splice	ENST00000373129	NM_032017.1	115			1	2	FACETS	0.578	0.492	0.673	0.578	0.492	0.673	SUBCLONAL	1	TRUE	1	0.32	2		552	562	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981102	201981102	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	140	606	0	ENST00000359651.3:c.181G>T	p.Gly61Trp	p.G61W	ENST00000359651		61	Ggg/Tgg	2/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.32	2		606	756	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226573302	226573302	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	99	598	0	ENST00000366794.5:c.914A>G	p.Lys305Arg	p.K305R	ENST00000366794	NM_001618.3	305	aAg/aGg	7/23	1	2	FACETS	0.992	0.887	1	0.992	0.887	1	CLONAL	1	TRUE	1	0.32	2		598	624	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999555	100999555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	75	951	1	ENST00000325455.5:c.247G>A	p.Val83Met	p.V83M	ENST00000325455	NM_001202474.3	83	Gtg/Atg	1/8	1	2	FACETS	0.538	0.47	0.611	0.538	0.47	0.611	SUBCLONAL	1	TRUE	1	0.32	2		952	871	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100538	102100538	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	105	596	0	ENST00000282441.5:c.1382A>G	p.Asp461Gly	p.D461G	ENST00000282441	NM_001130145.2	461	gAt/gGt	9/9	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.32	2		596	553	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344035	118344035	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	57	349	0	ENST00000534358.1:c.2161C>T	p.Arg721Ter	p.R721*	ENST00000534358	NM_005933.3	721	Cga/Tga	3/36	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.32	2		349	344	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348780	118348780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	61	412	0	ENST00000534358.1:c.3433C>T	p.Pro1145Ser	p.P1145S	ENST00000534358	NM_005933.3	1145	Cca/Tca	5/36	1	2	FACETS	0.783	0.676	0.898	0.783	0.676	0.898	SUBCLONAL	1	TRUE	1	0.32	2		412	487	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870870	12870871	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	53	296	0	ENST00000228872.4:c.97_98del	p.Phe33ArgfsTer91	p.F33Rfs*91	ENST00000228872	NM_004064.3	33	TTc/c	1/3	1	2	FACETS	0.957	0.82	1	0.957	0.82	1	CLONAL	1	TRUE	1	0.32	2		296	346	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641423	18641423	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs374310738	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	45	288	0	ENST00000266497.5:c.2422T>C	p.Trp808Arg	p.W808R	ENST00000266497		808	Tgg/Cgg	17/31	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.32	2		288	280	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628710	21628710	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	75	443	0	ENST00000421138.2:c.998G>C	p.Ser333Thr	p.S333T	ENST00000421138		333	aGt/aCt	10/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.32	2		443	386	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219917	133219917	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	75	686	0	ENST00000320574.5:c.4445-1G>T		p.X1482_splice	ENST00000320574	NM_006231.2	1482			1	2	FACETS	0.777	0.682	0.88	0.777	0.682	0.88	SUBCLONAL	1	TRUE	1	0.32	2		686	603	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562304	21562304	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	46	749	1	ENST00000382592.4:c.1615G>T	p.Gly539Cys	p.G539C	ENST00000382592	NM_014572.2	539	Ggc/Tgc	4/8	1	2	FACETS	0.342	0.287	0.403	0.342	0.287	0.403	SUBCLONAL	1	TRUE	1	0.32	2		750	841	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582025	95582025	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750410087	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	28	315	0	ENST00000393063.1:c.1886C>T	p.Thr629Met	p.T629M	ENST00000393063	NM_030621.3	629	aCg/aTg	12/28	1	2	FACETS	0.378	0.301	0.465	0.378	0.301	0.465	SUBCLONAL	1	TRUE	1	0.32	2		315	463	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857778	9857778	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780055204	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	91	628	1	ENST00000330684.3:c.3623G>A	p.Arg1208Gln	p.R1208Q	ENST00000330684	NM_001134407.1	1208	cGg/cAg	13/13	1	2	FACETS	0.862	0.766	0.964	0.862	0.766	0.964	CLONAL	1	TRUE	1	0.32	2		629	660	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858570	9858570	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064797025	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	57	527	1	ENST00000330684.3:c.2831C>T	p.Ser944Leu	p.S944L	ENST00000330684	NM_001134407.1	944	tCa/tTa	13/13	1	2	FACETS	0.733	0.63	0.845	0.733	0.63	0.845	SUBCLONAL	1	TRUE	1	0.32	2		528	486	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862851	9862851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555483699	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	111	635	0	ENST00000330684.3:c.2452G>A	p.Ala818Thr	p.A818T	ENST00000330684	NM_001134407.1	818	Gcg/Acg	12/13	1	2	FACETS	0.958	0.862	1	0.958	0.862	1	CLONAL	1	TRUE	1	0.32	2		635	724	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875671	56875671	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	96	623	1	ENST00000308159.5:c.2275C>T	p.Gln759Ter	p.Q759*	ENST00000308159	NM_014669.4	759	Cag/Tag	21/22	1	2	FACETS	0.929	0.828	1	0.929	0.828	1	CLONAL	1	TRUE	1	0.32	2		624	646	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350668	89350668	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	99	743	0	ENST00000301030.4:c.2282A>G	p.Tyr761Cys	p.Y761C	ENST00000301030	NM_001256183.1	761	tAc/tGc	9/13	1	2	FACETS	0.938	0.838	1	0.938	0.838	1	CLONAL	1	TRUE	1	0.32	2		743	660	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679292	29679292	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	64	332	0	ENST00000356175.3:c.7412A>G	p.Gln2471Arg	p.Q2471R	ENST00000356175	NM_000267.3	2471	cAg/cGg	50/57	1	2	FACETS	0.917	0.797	1	0.917	0.797	1	CLONAL	1	TRUE	1	0.32	2		332	436	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775028	73775028	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	79	457	0	ENST00000254810.4:c.145C>T	p.Leu49Phe	p.L49F	ENST00000254810	NM_005324.3	49	Ctt/Ttt	3/4	1	2	FACETS	0.955	0.842	1	0.955	0.842	1	CLONAL	1	TRUE	1	0.32	2		457	517	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56401607	56401607	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	48	387	0	ENST00000348428.3:c.1469A>G	p.Tyr490Cys	p.Y490C	ENST00000348428	NM_006785.3	490	tAt/tGt	12/17	1	2	FACETS	0.699	0.592	0.817	0.699	0.592	0.817	SUBCLONAL	1	TRUE	1	0.32	2		387	429	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119267	3119267	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	53	827	0	ENST00000078429.4:c.799T>C	p.Ser267Pro	p.S267P	ENST00000078429	NM_002067.2	267	Tcc/Ccc	6/7	1	2	FACETS	0.401	0.341	0.467	0.401	0.341	0.467	SUBCLONAL	1	TRUE	1	0.32	2		827	826	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278179	15278179	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769483312	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	118	773	0	ENST00000263388.2:c.5243G>A	p.Arg1748His	p.R1748H	ENST00000263388	NM_000435.2	1748	cGt/cAt	29/33	1	2	FACETS	0.921	0.831	1	0.921	0.831	1	CLONAL	1	TRUE	1	0.32	2		773	801	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224536	36224536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	117	927	1	ENST00000222270.7:c.6998G>A	p.Gly2333Glu	p.G2333E	ENST00000222270	NM_014727.1	2333	gGg/gAg	29/37	1	2	FACETS	0.811	0.73	0.896	0.811	0.73	0.896	CLONAL	1	TRUE	1	0.32	2		928	902	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228554	36228554	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	69	738	0	ENST00000222270.7:c.7568T>C	p.Met2523Thr	p.M2523T	ENST00000222270	NM_014727.1	2523	aTg/aCg	34/37	1	2	FACETS	0.502	0.436	0.574	0.502	0.436	0.574	SUBCLONAL	1	TRUE	1	0.32	2		738	859	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727854	41727854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	104	805	0	ENST00000301178.4:c.479G>A	p.Cys160Tyr	p.C160Y	ENST00000301178	NM_021913.4	160	tGc/tAc	4/20	1	2	FACETS	0.867	0.776	0.963	0.867	0.776	0.963	CLONAL	1	TRUE	1	0.32	2		805	750	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026800	48026800	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs863224617	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	51	489	0	ENST00000234420.5:c.1678T>C	p.Phe560Leu	p.F560L	ENST00000234420	NM_000179.2	560	Ttt/Ctt	4/10	1	2	FACETS	0.799	0.681	0.928	0.799	0.681	0.928	CLONAL	1	TRUE	1	0.32	2		489	399	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738360	190738360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760863069	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	16	216	0	ENST00000441310.2:c.2612G>A	p.Arg871His	p.R871H	ENST00000441310	NM_000534.4	871	cGc/cAc	12/13	1	2	FACETS	0.455	0.336	0.595	0.455	0.336	0.595	SUBCLONAL	1	TRUE	1	0.32	2		216	220	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578329	212578329	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1377345647	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	36	412	0	ENST00000342788.4:c.928A>G	p.Ser310Gly	p.S310G	ENST00000342788	NM_005235.2	310	Agt/Ggt	8/28	1	2	FACETS	0.65	0.536	0.778	0.65	0.536	0.778	SUBCLONAL	1	TRUE	1	0.32	2		412	346	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661941	227661941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	111	720	0	ENST00000305123.5:c.1514C>T	p.Ala505Val	p.A505V	ENST00000305123	NM_005544.2	505	gCc/gTc	1/2	1	2	FACETS	0.885	0.795	0.98	0.885	0.795	0.98	CLONAL	1	TRUE	1	0.32	2		720	784	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553272	41553272	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	94	585	0	ENST00000263253.7:c.3361A>G	p.Ile1121Val	p.I1121V	ENST00000263253	NM_001429.3	1121	Att/Gtt	18/31	1	2	FACETS	0.999	0.891	1	0.999	0.891	1	CLONAL	1	TRUE	1	0.32	2		585	588	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574584	41574584	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	75	838	0	ENST00000263253.7:c.6869A>G	p.Gln2290Arg	p.Q2290R	ENST00000263253	NM_001429.3	2290	cAg/cGg	31/31	1	2	FACETS	0.533	0.466	0.606	0.533	0.466	0.606	SUBCLONAL	1	TRUE	1	0.32	2		838	879	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47061293	47061293	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	70	428	0	ENST00000409792.3:c.7388C>T	p.Ser2463Phe	p.S2463F	ENST00000409792	NM_014159.6	2463	tCc/tTc	19/21	1	2	FACETS	0.921	0.805	1	0.921	0.805	1	CLONAL	1	TRUE	1	0.32	2		428	475	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190870	185190870	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	53	696	0	ENST00000265026.3:c.1751A>G	p.Tyr584Cys	p.Y584C	ENST00000265026	NM_004721.4	584	tAt/tGt	11/14	1	2	FACETS	0.353	0.3	0.412	0.353	0.3	0.412	SUBCLONAL	1	TRUE	1	0.32	2		696	938	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233098	66233098	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	55	375	0	ENST00000273854.3:c.1901A>G	p.Lys634Arg	p.K634R	ENST00000273854	NM_004439.5	634	aAg/aGg	10/18	1	2	FACETS	0.872	0.749	1	0.872	0.749	1	CLONAL	1	TRUE	1	0.32	2		375	394	SUCCESS
APC	324	MSKCC	GRCh37	5	112178384	112178384	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	49	371	0	ENST00000257430.4:c.7093T>C	p.Ser2365Pro	p.S2365P	ENST00000257430	NM_000038.5	2365	Tca/Cca	16/16	1	2	FACETS	0.825	0.701	0.961	0.825	0.701	0.961	CLONAL	1	TRUE	1	0.32	2		371	371	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449520	149449520	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs868679766	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	136	729	0	ENST00000286301.3:c.1426A>G	p.Thr476Ala	p.T476A	ENST00000286301	NM_005211.3	476	Acc/Gcc	10/22	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.32	2		729	829	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120825	94120826	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	130	483	0	ENST00000369303.4:c.225dup	p.Val76SerfsTer13	p.V76Sfs*13	ENST00000369303	NM_004440.3	75	-/A	3/17	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.32	2		483	708	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200408	138200408	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	122	671	1	ENST00000237289.4:c.1826A>G	p.Lys609Arg	p.K609R	ENST00000237289	NM_001270507.1	609	aAa/aGa	7/9	1	2	FACETS	0.865	0.781	0.953	0.865	0.781	0.953	CLONAL	1	TRUE	1	0.32	2		672	882	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405929	157405929	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs563771544	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	87	599	0	ENST00000346085.5:c.2171C>T	p.Ala724Val	p.A724V	ENST00000346085	NM_020732.3	724	gCg/gTg	6/20	1	2	FACETS	0.85	0.753	0.953	0.85	0.753	0.953	CLONAL	1	TRUE	1	0.32	2		599	640	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772052	135772052	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	75	572	0	ENST00000298552.3:c.3065G>T	p.Arg1022Met	p.R1022M	ENST00000298552	NM_001162426.1	1022	aGg/aTg	23/23	1	2	FACETS	0.831	0.729	0.941	0.831	0.729	0.941	CLONAL	1	TRUE	1	0.32	2		572	564	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412207	139412207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	39	639	0	ENST00000277541.6:c.1438C>T	p.Pro480Ser	p.P480S	ENST00000277541	NM_017617.3	480	Ccc/Tcc	8/34	1	2	FACETS	0.386	0.319	0.461	0.386	0.319	0.461	SUBCLONAL	1	TRUE	1	0.32	2		639	631	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	41	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.829	0.695	0.977	0.829	0.695	0.977	CLONAL	1	TRUE	1	0.355604953648944	2		326	278	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	59	466	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.937	0.811	1	0.937	0.811	1	CLONAL	1	TRUE	1	0.355604953648944	2		466	354	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003746	45003746	+	start_lost	Translation_Start_Site	SNP	T	T	C	rs1057519879	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	188	456	0	ENST00000558401.1:c.2T>C	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	aTg/aCg	1/4	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.355604953648944	2		456	986	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	65	364	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.7	0.608	0.8	0.7	0.608	0.8	SUBCLONAL	1	TRUE	1	0.355604953648944	2		365	522	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	45	360	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.355604953648944	2		360	219	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007752	45007753	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	73	410	0	ENST00000558401.1:c.204dup	p.Val69SerfsTer21	p.V69Sfs*21	ENST00000558401	NM_004048.2	67	gaa/gAaa	2/4	1	2	FACETS	0.877	0.77	0.993	0.877	0.77	0.993	CLONAL	1	TRUE	1	0.355604953648944	2		410	468	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120232	70120232	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1205	256	639	0	ENST00000245479.2:c.1234C>T	p.Gln412Ter	p.Q412*	ENST00000245479	NM_000346.3	412	Cag/Tag	3/3	1	2	FACETS	0.985	0.92	1	0.985	0.92	1	CLONAL	1	TRUE	1	0.355604953648944	2		639	1461	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	90	383	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.355604953648944	2		383	483	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	171	620	0	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.876	0.805	0.95	0.876	0.805	0.95	CLONAL	1	TRUE	1	0.355604953648944	2		620	1098	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138729528	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	219	695	0	ENST00000269305.4:c.523C>T	p.Arg175Cys	p.R175C	ENST00000269305	NM_001126112.2	175	Cgc/Tgc	5/11	1	2	FACETS	0.952	0.884	1	0.952	0.884	1	CLONAL	1	TRUE	1	0.355604953648944	2		695	1294	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007824	45007825	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	88	379	0	ENST00000558401.1:c.276dup	p.Thr93HisfsTer2	p.T93Hfs*2	ENST00000558401	NM_004048.2	91	acc/aCcc	2/4	1	2	FACETS	0.998	0.887	1	0.998	0.887	1	CLONAL	1	TRUE	1	0.355604953648944	2		379	496	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790455	3790455	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783490	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	208	593	3	ENST00000262367.5:c.4078C>T	p.Arg1360Ter	p.R1360*	ENST00000262367	NM_004380.2	1360	Cga/Tga	24/31	1	2	FACETS	0.97	0.899	1	0.97	0.899	1	CLONAL	1	TRUE	1	0.355604953648944	2		596	1206	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136949	64136949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749917386	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	203	555	0	ENST00000334205.4:c.1460G>A	p.Arg487Gln	p.R487Q	ENST00000334205	NM_003942.2	487	cGg/cAg	13/17	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.355604953648944	2		555	1091	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	156	482	0	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.355604953648944	2		482	854	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411291	63411291	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1408150272	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	255	369	1	ENST00000330258.3:c.1876C>T	p.Arg626Ter	p.R626*	ENST00000330258	NM_152424.3	626	Cga/Tga	2/2	1	1	FACETS	0.875	0.824	0.926	1	0.995	1	CLONAL	2	TRUE	0	0.355604953648944	1		370	674	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004247	150004247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	26	298	0	ENST00000253339.5:c.1978C>T	p.Arg660Cys	p.R660C	ENST00000253339		660	Cgt/Tgt	3/7	1	2	FACETS	0.77	0.614	0.945	0.77	0.614	0.945	CLONAL	1	TRUE	1	0.355604953648944	2		298	190	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119758	70119758	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	192	625	0	ENST00000245479.2:c.760C>T	p.Arg254Ter	p.R254*	ENST00000245479	NM_000346.3	254	Cga/Tga	3/3	1	2	FACETS	0.924	0.853	0.997	0.924	0.853	0.997	CLONAL	1	TRUE	1	0.355604953648944	2		625	1169	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44520566	44520566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	118	351	0	ENST00000291552.4:c.196C>T	p.Arg66Cys	p.R66C	ENST00000291552	NM_006758.2	66	Cgc/Tgc	3/8	1	2	FACETS	0.958	0.865	1	0.958	0.865	1	CLONAL	1	TRUE	1	0.355604953648944	2		351	693	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945048	31945048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764152739	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	236	677	1	ENST00000340398.3:c.53G>A	p.Arg18His	p.R18H	ENST00000340398	NM_001013699.2	18	cGc/cAc	1/1	1	2	FACETS	0.972	0.905	1	0.972	0.905	1	CLONAL	1	TRUE	1	0.355604953648944	2		678	1365	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905324	50905324	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1241	252	840	6	ENST00000440232.2:c.537del	p.Arg180GlyfsTer3	p.R180Gfs*3	ENST00000440232	NM_002691.3	178	Ggg/gg	5/27	1	2	FACETS	0.949	0.886	1	0.949	0.886	1	CLONAL	1	TRUE	1	0.355604953648944	2		846	1493	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99203950	99203950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755469992	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	64	353	0	ENST00000074304.5:c.2813G>A	p.Arg938Gln	p.R938Q	ENST00000074304	NM_001134224.1	938	cGa/cAa	26/26	1	2	FACETS	0.983	0.856	1	0.983	0.856	1	CLONAL	1	TRUE	1	0.355604953648944	2		353	366	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719724	61719724	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	50	546	0	ENST00000401558.2:c.1544G>A	p.Arg515Gln	p.R515Q	ENST00000401558	NM_003400.3	515	cGa/cAa	14/25	0.355604953648944	2	FACETS	0.871	0.742	1	0.435	0.371	0.505	CLONAL	1	TRUE	0	0.355604953648944	2		546	323	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159112	24159112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1341827515	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	150	416	1	ENST00000263121.7:c.784G>A	p.Val262Ile	p.V262I	ENST00000263121	NM_003073.3	262	Gtc/Atc	6/9	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.355604953648944	2		417	836	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856595	111856595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1454335466	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	122	144	0	ENST00000341259.2:c.646C>T	p.Arg216Cys	p.R216C	ENST00000341259	NM_005475.2	216	Cgc/Tgc	2/8	1	2	FACETS	0.866	0.79	0.945	1	0.989	1	CLONAL	2	TRUE	1	0.355604953648944	2		144	396	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637062	93637062	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369986984	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	169	501	0	ENST00000375746.1:c.1112C>T	p.Thr371Met	p.T371M	ENST00000375746	NM_001174167.1	371	aCg/aTg	9/14	1	2	FACETS	0.998	0.918	1	0.998	0.918	1	CLONAL	1	TRUE	1	0.355604953648944	2		501	952	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738315	133738315	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	220	569	1	ENST00000318560.5:c.715C>T	p.Arg239Cys	p.R239C	ENST00000318560	NM_005157.4	239	Cgc/Tgc	4/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.355604953648944	2		570	1148	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210893	36210893	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1206	246	761	4	ENST00000222270.7:c.649del	p.Arg217GlyfsTer22	p.R217Gfs*22	ENST00000222270	NM_014727.1	215	aCc/ac	3/37	1	2	FACETS	0.953	0.888	1	0.953	0.888	1	CLONAL	1	TRUE	1	0.355604953648944	2		765	1452	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759395	133759395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1194832601	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	212	651	0	ENST00000318560.5:c.1718C>T	p.Pro573Leu	p.P573L	ENST00000318560	NM_005157.4	573	cCt/cTt	11/11	1	2	FACETS	0.973	0.903	1	0.973	0.903	1	CLONAL	1	TRUE	1	0.355604953648944	2		651	1225	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140172	50140172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774218911	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	169	541	0	ENST00000246792.3:c.253G>A	p.Ala85Thr	p.A85T	ENST00000246792	NM_006270.3	85	Gcg/Acg	3/6	1	2	FACETS	0.96	0.882	1	0.96	0.882	1	CLONAL	1	TRUE	1	0.355604953648944	2		541	990	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633207	12633207	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs730880382	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	154	502	0	ENST00000251849.4:c.1193G>T	p.Arg398Leu	p.R398L	ENST00000251849	NM_002880.3	398	cGc/cTc	11/17	1	2	FACETS	0.898	0.821	0.978	0.898	0.821	0.978	CLONAL	1	TRUE	1	0.355604953648944	2		502	965	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528952	157528952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263114512	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	143	468	1	ENST00000346085.5:c.6677C>T	p.Ser2226Leu	p.S2226L	ENST00000346085	NM_020732.3	2226	tCg/tTg	20/20	1	2	FACETS	0.911	0.83	0.995	0.911	0.83	0.995	CLONAL	1	TRUE	1	0.355604953648944	2		469	883	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741660	17741660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	166	348	2	ENST00000250003.3:c.331C>T	p.Arg111Cys	p.R111C	ENST00000250003	NM_002478.4	111	Cgc/Tgc	1/3	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.355604953648944	2		350	878	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246518359	246518359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746219350	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	82	418	0	ENST00000388985.4:c.202G>A	p.Ala68Thr	p.A68T	ENST00000388985		68	Gcc/Acc	2/12	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.355604953648944	2		418	453	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745596	162745596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777473405	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	105	490	0	ENST00000367921.3:c.2011C>T	p.Pro671Ser	p.P671S	ENST00000367921	NM_006182.2	671	Ccc/Tcc	15/18	1	2	FACETS	0.673	0.602	0.748	0.673	0.602	0.748	SUBCLONAL	1	TRUE	1	0.355604953648944	2		490	878	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964400	55964400	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149212892	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	113	496	0	ENST00000263923.4:c.2413G>A	p.Val805Ile	p.V805I	ENST00000263923	NM_002253.2	805	Gtc/Atc	17/30	1	2	FACETS	0.84	0.756	0.928	0.84	0.756	0.928	CLONAL	1	TRUE	1	0.355604953648944	2		496	757	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356406	66356406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	57	388	0	ENST00000273854.3:c.1091C>T	p.Ala364Val	p.A364V	ENST00000273854	NM_004439.5	364	gCc/gTc	5/18	1	2	FACETS	0.799	0.688	0.92	0.799	0.688	0.92	CLONAL	1	TRUE	1	0.355604953648944	2		388	401	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729709	41729709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768547360	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	177	580	0	ENST00000242208.4:c.820G>A	p.Gly274Arg	p.G274R	ENST00000242208	NM_002192.2	274	Gga/Aga	3/3	1	2	FACETS	0.991	0.912	1	0.991	0.912	1	CLONAL	1	TRUE	1	0.355604953648944	2		580	1005	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28586359	28586359	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	132	514	0	ENST00000253063.3:c.1A>G	p.Met1?	p.M1?	ENST00000253063	NM_031459.4	1	Atg/Gtg	1/10	1	2	FACETS	0.884	0.802	0.97	0.884	0.802	0.97	CLONAL	1	TRUE	1	0.355604953648944	2		514	840	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430375	78430375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569612114	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	68	425	0	ENST00000370768.2:c.793C>T	p.Arg265Trp	p.R265W	ENST00000370768	NM_003902.3	265	Cgg/Tgg	10/20	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.355604953648944	2		425	330	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600424	43600424	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	177	546	0	ENST00000355710.3:c.650C>T	p.Ala217Val	p.A217V	ENST00000355710	NM_020975.4	217	gCc/gTc	4/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.355604953648944	2		546	970	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333485	70333485	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	111	533	0	ENST00000373644.4:c.1390G>T	p.Gly464Cys	p.G464C	ENST00000373644	NM_030625.2	464	Ggt/Tgt	2/12	1	2	FACETS	0.977	0.88	1	0.977	0.88	1	CLONAL	1	TRUE	1	0.355604953648944	2		533	639	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201718	67201718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199570304	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	160	564	0	ENST00000312629.5:c.1019G>A	p.Arg340His	p.R340H	ENST00000312629	NM_003952.2	340	cGt/cAt	12/15	1	2	FACETS	0.84	0.769	0.915	0.84	0.769	0.915	CLONAL	1	TRUE	1	0.355604953648944	2		564	1071	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879659	123879659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374415100	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	89	237	0	ENST00000330479.4:c.355G>A	p.Ala119Thr	p.A119T	ENST00000330479	NM_020382.3	119	Gcc/Acc	4/9	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.355604953648944	2		237	487	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217287	7217287	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	181	560	0	ENST00000380728.2:c.418C>T	p.Arg140Cys	p.R140C	ENST00000380728		140	Cgc/Tgc	6/11	1	2	FACETS	0.971	0.895	1	0.971	0.895	1	CLONAL	1	TRUE	1	0.355604953648944	2		560	1048	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657548	37657548	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	41	455	1	ENST00000447079.4:c.2465G>T	p.Gly822Val	p.G822V	ENST00000447079	NM_015083.1	822	gGa/gTa	6/14	1	2	FACETS	0.771	0.645	0.91	0.771	0.645	0.91	CLONAL	1	TRUE	1	0.355604953648944	2		456	299	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612394	1612394	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	250	775	0	ENST00000344749.5:c.1625T>C	p.Leu542Pro	p.L542P	ENST00000344749	NM_001136139.2	542	cTg/cCg	18/19	1	2	FACETS	0.949	0.885	1	0.949	0.885	1	CLONAL	1	TRUE	1	0.355604953648944	2		775	1482	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7141771	7141771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766938463	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	181	682	0	ENST00000302850.5:c.2599G>A	p.Val867Ile	p.V867I	ENST00000302850	NM_000208.2	867	Gtc/Atc	13/22	1	2	FACETS	0.838	0.771	0.907	0.838	0.771	0.907	CLONAL	1	TRUE	1	0.355604953648944	2		682	1215	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10277309	10277309	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368960099	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1257	229	765	0	ENST00000340748.4:c.808G>A	p.Val270Met	p.V270M	ENST00000340748		270	Gtg/Atg	10/40	1	2	FACETS	0.867	0.805	0.93	0.867	0.805	0.93	CLONAL	1	TRUE	1	0.355604953648944	2		765	1486	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170754	11170754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1484835507	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	246	697	0	ENST00000358026.2:c.4898G>A	p.Arg1633Gln	p.R1633Q	ENST00000358026	NM_001128849.1	1633	cGg/cAg	35/36	1	2	FACETS	0.985	0.919	1	0.985	0.919	1	CLONAL	1	TRUE	1	0.355604953648944	2		697	1404	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314584	30314584	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	140	642	0	ENST00000262643.3:c.1133C>T	p.Ala378Val	p.A378V	ENST00000262643	NM_001238.2	378	gCc/gTc	12/12	1	2	FACETS	0.861	0.783	0.942	0.861	0.783	0.942	CLONAL	1	TRUE	1	0.355604953648944	2		642	915	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860548	45860548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs562132292	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	258	730	0	ENST00000391945.4:c.1459C>T	p.Arg487Trp	p.R487W	ENST00000391945	NM_000400.3	487	Cgg/Tgg	15/23	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.355604953648944	2		730	1451	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920501	50920501	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	184	602	0	ENST00000440232.2:c.3193C>A	p.Leu1065Met	p.L1065M	ENST00000440232	NM_002691.3	1065	Ctg/Atg	26/27	1	2	FACETS	0.965	0.89	1	0.965	0.89	1	CLONAL	1	TRUE	1	0.355604953648944	2		602	1072	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131394	202131394	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	118	521	0	ENST00000358485.4:c.362T>C	p.Leu121Pro	p.L121P	ENST00000358485	NM_001080125.1	121	cTg/cCg	2/9	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.355604953648944	2		521	606	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167529	24167529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1295909994	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	226	650	1	ENST00000263121.7:c.913G>A	p.Gly305Arg	p.G305R	ENST00000263121	NM_003073.3	305	Ggg/Agg	7/9	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.355604953648944	2		651	1270	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098705	47098705	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	177	617	0	ENST00000409792.3:c.6569C>A	p.Pro2190His	p.P2190H	ENST00000409792	NM_014159.6	2190	cCc/cAc	15/21	1	2	FACETS	0.919	0.846	0.996	0.919	0.846	0.996	CLONAL	1	TRUE	1	0.355604953648944	2		617	1083	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921558	178921558	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs761766361	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	23	347	0	ENST00000263967.3:c.1040A>T	p.Asn347Ile	p.N347I	ENST00000263967	NM_006218.2	347	aAt/aTt	5/21	1	2	FACETS	0.862	0.679	1	0.862	0.679	1	CLONAL	1	TRUE	1	0.355604953648944	2		347	150	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155038	55155038	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	105	460	0	ENST00000257290.5:c.2747C>T	p.Ala916Val	p.A916V	ENST00000257290	NM_006206.4	916	gCc/gTc	20/23	1	2	FACETS	0.835	0.749	0.927	0.835	0.749	0.927	CLONAL	1	TRUE	1	0.355604953648944	2		460	707	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564453	55564453	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	123	384	0	ENST00000288135.5:c.341C>A	p.Pro114His	p.P114H	ENST00000288135	NM_000222.2	114	cCt/cAt	3/21	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.355604953648944	2		384	611	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946307	2946307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370705908	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	285	807	0	ENST00000396946.4:c.3430C>T	p.Arg1144Cys	p.R1144C	ENST00000396946	NM_032415.4	1144	Cgc/Tgc	25/25	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.355604953648944	2		807	1425	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639944	93639944	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	89	295	0	ENST00000375746.1:c.1273C>T	p.Gln425Ter	p.Q425*	ENST00000375746	NM_001174167.1	425	Cag/Tag	10/14	1	2	FACETS	0.886	0.787	0.991	0.886	0.787	0.991	CLONAL	1	TRUE	1	0.355604953648944	2		295	565	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321297	1321297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370445430	NA	P-0043595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	161	532	0	ENST00000400841.2:c.458G>A	p.Arg153Gln	p.R153Q	ENST00000400841		153	cGg/cAg	4/6	1	1	FACETS	0.798	0.732	0.867	0.798	0.732	0.867	SUBCLONAL	1	TRUE	0	0.355604953648944	1		532	933	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0043708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	478	582	7	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	0.773027230407944	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.773027230407944	2		589	581	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260476	16260476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	311	406	8	ENST00000375759.3:c.7741C>T	p.Pro2581Ser	p.P2581S	ENST00000375759	NM_015001.2	2581	Cct/Tct	11/15	0.714041287492015	4	FACETS	0.951	0.902	1	0.951	0.902	1	CLONAL	2	TRUE	2	0.773027230407944	4		414	750	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039462	49039462	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	297	408	3	ENST00000267163.4:c.2447del	p.Ser816Ter	p.S816*	ENST00000267163	NM_000321.2	816	tCa/ta	23/27	0.773027230407944	2	FACETS	0.995	0.961	1	0.995	0.961	1	CLONAL	2	TRUE	0	0.773027230407944	2		411	386	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061675	38061675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	216	207	1	ENST00000250448.2:c.314G>A	p.Gly105Asp	p.G105D	ENST00000250448	NM_004496.3	105	gGt/gAt	2/2	0.714041287492015	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.773027230407944	4		208	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0043737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	365	469	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.623006308544925	2	FACETS	0.867	0.83	0.903	0.867	0.83	0.903	CLONAL	2	TRUE	0	0.625719410962687	2		469	673	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0043737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	256	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.605983270228136	3	FACETS	0.997	0.943	1	0.997	0.943	1	CLONAL	2	TRUE	1	0.625719410962687	3		487	539	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0043737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	343	240	0	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	0.625719410962687	4	FACETS	0.911	0.879	0.943	0.911	0.879	0.943	CLONAL	4	TRUE	0	0.625719410962687	4		240	489	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0043737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	109	243	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.538957017726157	4	FACETS	0.805	0.73	0.882	0.805	0.73	0.882	CLONAL	2	TRUE	2	0.625719410962687	4		243	352	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0043804-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	71	234	3				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.415426802833545	2		237	327	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0043804-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	138	590	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.856	0.78	0.936	0.856	0.78	0.936	CLONAL	1	TRUE	1	0.415426802833545	2		591	776	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118859	115118859	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043804-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	100	478	0	ENST00000257566.3:c.482G>C	p.Cys161Ser	p.C161S	ENST00000257566	NM_016569.3	161	tGt/tCt	2/8	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.415426802833545	2		478	480	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	66	197	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.934	0.825	1	1	0.988	1	CLONAL	7	TRUE	1	0.0999144429763154	2		197	202	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	154	619	1	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	0.0999144429763154	0	FACETS	0.953	0.872	1			1	CLONAL	3	TRUE	0	0.0999144429763154	0		620	970	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	294	886	1	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	0.0999144429763154	0	FACETS	0.886	0.837	0.936			1	CLONAL	7	TRUE	0	0.0999144429763154	0		887	854	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007824	45007825	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	91	379	0	ENST00000558401.1:c.276dup	p.Thr93HisfsTer2	p.T93Hfs*2	ENST00000558401	NM_004048.2	91	acc/aCcc	2/4	0.0999144429763154	0	FACETS	0.865	0.771	0.964			1	CLONAL	4	TRUE	0	0.0999144429763154	0		379	474	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666657	206666657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782804652	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	178	634	1	ENST00000367120.3:c.1991C>T	p.Ser664Leu	p.S664L	ENST00000367120	NM_014002.3	664	tCg/tTg	20/22	0.0999144429763154	0	FACETS	0.997	0.921	1			1	CLONAL	4	TRUE	0	0.0999144429763154	0		635	804	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053022	180053023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750808726	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	54	859	1	ENST00000261937.6:c.1267dup	p.Gln423ProfsTer4	p.Q423Pfs*4	ENST00000261937	NM_182925.4	423	cag/cCag	10/30	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.0999144429763154	2		860	722	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247226	153247226	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	81	300	0	ENST00000281708.4:c.1576T>C	p.Trp526Arg	p.W526R	ENST00000281708	NM_033632.3	526	Tgg/Cgg	10/12	1	2	FACETS	1	0.952	1	1	0.988	1	CLONAL	3	TRUE	1	0.0999144429763154	2		300	471	SUCCESS
APC	324	MSKCC	GRCh37	5	112176063	112176064	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	66	295	0	ENST00000257430.4:c.4778dup	p.Pro1594AlafsTer38	p.P1594Afs*38	ENST00000257430	NM_000038.5	1591	gca/gcAa	16/16	1	2	FACETS	1	0.927	1	1	0.985	1	CLONAL	3	TRUE	1	0.0999144429763154	2		295	403	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100727	8100728	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs771019738	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	140	775	0	ENST00000346208.3:c.708dup	p.Ser237GlnfsTer66	p.S237Qfs*66	ENST00000346208		234	ttc/ttCc	3/6	1	2	FACETS	0.938	0.855	1	1	0.993	1	CLONAL	4	TRUE	1	0.0999144429763154	2		775	747	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116168	67116168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1467426352	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	78	405	0	ENST00000412916.2:c.452G>A	p.Arg151His	p.R151H	ENST00000412916		151	cGc/cAc	5/6	0.0999144429763154	0	FACETS	1	0.95	1			1	CLONAL	2	TRUE	0	0.0999144429763154	0		405	608	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512401	38512402	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs745553450	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	108	692	2	ENST00000254066.5:c.1319dup	p.Pro441AlafsTer5	p.P441Afs*5	ENST00000254066	NM_000964.3	438	gcc/gCcc	9/9	0.0999144429763154	0	FACETS	0.97	0.871	1			1	CLONAL	3	TRUE	0	0.0999144429763154	0		694	669	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436083	51436084	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	85	360	0	ENST00000262662.1:c.49dup	p.Asp17GlyfsTer7	p.D17Gfs*7	ENST00000262662		15	agg/aGgg	3/4	0.0999144429763154	0	FACETS	1	0.924	1			1	CLONAL	3	TRUE	0	0.0999144429763154	0		360	484	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572092	64572093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767319284	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	131	774	4	ENST00000312049.6:c.1546dup	p.Arg516ProfsTer15	p.R516Pfs*15	ENST00000312049	NM_130799.2	516	cgg/cCgg	10/10	1	2	FACETS	0.92	0.834	1	1	0.992	1	CLONAL	3	TRUE	1	0.0999144429763154	2		778	950	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21304066	21304066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444326760	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	151	433	0	ENST00000354336.3:c.845G>A	p.Arg282His	p.R282H	ENST00000354336	NM_005207.3	282	cGc/cAc	3/3	0.0999144429763154	0	FACETS	1	0.921	1			1	CLONAL	4	TRUE	0	0.0999144429763154	0		433	677	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119909	70119910	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	99	577	0	ENST00000245479.2:c.916dup	p.Val306GlyfsTer272	p.V306Gfs*272	ENST00000245479	NM_000346.3	304	ccg/ccGg	3/3	0.0999144429763154	0	FACETS	0.911	0.814	1			1	CLONAL	3	TRUE	0	0.0999144429763154	0		577	653	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372224	55372224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	46	538	1	ENST00000297316.4:c.914C>T	p.Ala305Val	p.A305V	ENST00000297316	NM_022454.3	305	gCg/gTg	2/2	0.0999144429763154	0	FACETS	1	0.952	1			1	CLONAL	1	TRUE	0	0.0999144429763154	0		539	600	SUCCESS
APC	324	MSKCC	GRCh37	5	112174674	112174674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	65	279	0	ENST00000257430.4:c.3383C>T	p.Ser1128Phe	p.S1128F	ENST00000257430	NM_000038.5	1128	tCt/tTt	16/16	1	2	FACETS	0.91	0.796	1	1	0.987	1	CLONAL	5	TRUE	1	0.0999144429763154	2		279	286	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502764	149502764	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1176688330	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	107	459	0	ENST00000261799.4:c.2024G>A	p.Gly675Glu	p.G675E	ENST00000261799	NM_002609.3	675	gGa/gAa	15/23	1	2	FACETS	1	0.954	1	1	0.992	1	CLONAL	4	TRUE	1	0.0999144429763154	2		459	487	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577523	64577523	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	95	570	0	ENST00000312049.6:c.59T>C	p.Val20Ala	p.V20A	ENST00000312049	NM_130799.2	20	gTg/gCg	2/10	1	2	FACETS	1	0.909	1	1	0.99	1	CLONAL	4	TRUE	1	0.0999144429763154	2		570	467	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111965562	111965563	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	54	215	0	ENST00000375549.3:c.352dup	p.Asp118GlyfsTer73	p.D118Gfs*73	ENST00000375549	NM_003002.3	116	-/G	4/4	1	2	FACETS	1	0.875	1	1	0.983	1	CLONAL	4	TRUE	1	0.0999144429763154	2		215	266	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426870	49426870	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	35	597	0	ENST00000301067.7:c.11618T>C	p.Leu3873Pro	p.L3873P	ENST00000301067	NM_003482.3	3873	cTg/cCg	39/54	NA	4	FACETS	0.753	0.616	0.906	0.753	0.616	0.906	INDETERMINATE	2	TRUE	2	0.0999144429763154	4		597	512	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115111968	115111968	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	136	619	0	ENST00000257566.3:c.1770+2T>C		p.X590_splice	ENST00000257566	NM_016569.3	590			0.0999144429763154	0	FACETS	0.991	0.904	1			1	CLONAL	4	TRUE	0	0.0999144429763154	0		619	618	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519184	103519184	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	21	339	0	ENST00000355739.4:c.2522A>G	p.His841Arg	p.H841R	ENST00000355739	NM_000123.3	841	cAc/cGc	11/15	1	2	FACETS	1	0.804	1	1	0.804	1	CLONAL	1	TRUE	1	0.0999144429763154	2		339	400	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778068	3778068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	51	835	1	ENST00000262367.5:c.6980C>T	p.Ala2327Val	p.A2327V	ENST00000262367	NM_004380.2	2327	gCc/gTc	31/31	0.0999144429763154	0	FACETS	1	0.856	1			1	CLONAL	1	TRUE	0	0.0999144429763154	0		836	909	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789648	3789648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	98	417	0	ENST00000262367.5:c.4211G>A	p.Gly1404Asp	p.G1404D	ENST00000262367	NM_004380.2	1404	gGc/gAc	25/31	0.0999144429763154	0	FACETS	1	0.948	1			1	CLONAL	3	TRUE	0	0.0999144429763154	0		417	537	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349002	11349002	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	161	576	1	ENST00000332029.2:c.334T>C	p.Phe112Leu	p.F112L	ENST00000332029	NM_003745.1	112	Ttt/Ctt	2/2	0.0999144429763154	0	FACETS	0.921	0.846	1			1	CLONAL	4	TRUE	0	0.0999144429763154	0		577	787	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821272	72821272	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	149	521	0	ENST00000268489.5:c.10903C>T	p.Leu3635Phe	p.L3635F	ENST00000268489	NM_006885.3	3635	Ctc/Ttc	10/10	0.0999144429763154	0	FACETS	0.931	0.854	1			1	CLONAL	5	TRUE	0	0.0999144429763154	0		521	577	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984468	72984468	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs997093111	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	112	672	0	ENST00000268489.5:c.3116A>G	p.His1039Arg	p.H1039R	ENST00000268489	NM_006885.3	1039	cAc/cGc	3/10	0.0999144429763154	0	FACETS	0.853	0.767	0.943			1	CLONAL	3	TRUE	0	0.0999144429763154	0		672	789	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509681	29509681	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	58	289	0	ENST00000356175.3:c.886A>G	p.Lys296Glu	p.K296E	ENST00000356175	NM_000267.3	296	Aag/Gag	8/57	0.0999144429763154	0	FACETS	1	0.89	1			1	CLONAL	3	TRUE	0	0.0999144429763154	0		289	337	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553535	29553535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199474761	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	97	378	0	ENST00000356175.3:c.2084T>C	p.Leu695Pro	p.L695P	ENST00000356175	NM_000267.3	695	cTg/cCg	18/57	0.0999144429763154	0	FACETS	0.874	0.782	0.971			1	CLONAL	4	TRUE	0	0.0999144429763154	0		378	500	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611770	1611770	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs766945088	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	191	733	0	ENST00000344749.5:c.1892A>G	p.Gln631Arg	p.Q631R	ENST00000344749	NM_001136139.2	631	cAg/cGg	19/19	0.0999144429763154	0	FACETS	1	0.956	1			1	CLONAL	4	TRUE	0	0.0999144429763154	0		733	824	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609585	46609585	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1161977628	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	189	754	0	ENST00000263734.3:c.2309T>C	p.Met770Thr	p.M770T	ENST00000263734	NM_001430.4	770	aTg/aCg	15/16	1	2	FACETS	1	0.962	1	1	0.995	1	CLONAL	4	TRUE	1	0.0999144429763154	2		754	890	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989499	212989499	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	67	266	0	ENST00000342788.4:c.212A>G	p.Asn71Ser	p.N71S	ENST00000342788	NM_005235.2	71	aAc/aGc	2/28	1	2	FACETS	1	0.9	1	1	0.985	1	CLONAL	3	TRUE	1	0.0999144429763154	2		266	431	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067888	30067888	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	130	553	0	ENST00000338641.4:c.1073G>A	p.Arg358Lys	p.R358K	ENST00000338641	NM_000268.3	358	aGg/aAg	11/16	0.0999144429763154	0	FACETS	0.966	0.879	1			1	CLONAL	4	TRUE	0	0.0999144429763154	0		553	606	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165212	47165213	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	26	265	0	ENST00000409792.3:c.912_913dup	p.Thr305LysfsTer36	p.T305Kfs*36	ENST00000409792	NM_014159.6	305	aca/aAAca	3/21	1	2	FACETS	0.867	0.688	1	1	0.943	1	CLONAL	2	TRUE	1	0.0999144429763154	2		265	300	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934287	49934288	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	123	636	1	ENST00000296474.3:c.2219dup	p.Gly741TrpfsTer10	p.G741Wfs*10	ENST00000296474	NM_002447.2	740	cct/ccCt	8/20	1	2	FACETS	0.897	0.813	0.986	1	0.992	1	CLONAL	4	TRUE	1	0.0999144429763154	2		637	686	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197345	106197346	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	73	352	0	ENST00000380013.4:c.5682dup	p.Thr1895HisfsTer11	p.T1895Hfs*11	ENST00000380013	NM_001127208.2	1893	cac/caCc	11/11	1	2	FACETS	0.972	0.855	1	1	0.987	1	CLONAL	4	TRUE	1	0.0999144429763154	2		352	376	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187558019	187558019	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	42	300	0	ENST00000441802.2:c.3692T>C	p.Val1231Ala	p.V1231A	ENST00000441802	NM_005245.3	1231	gTc/gCc	5/27	1	2	FACETS	1	0.9	1	1	0.972	1	CLONAL	2	TRUE	1	0.0999144429763154	2		300	380	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629384	187629384	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	152	536	0	ENST00000441802.2:c.1598T>C	p.Val533Ala	p.V533A	ENST00000441802	NM_005245.3	533	gTt/gCt	2/27	1	2	FACETS	1	0.925	1	1	0.994	1	CLONAL	4	TRUE	1	0.0999144429763154	2		536	753	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515214	31515215	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	182	628	0	ENST00000344624.3:c.1170dup	p.Glu391ArgfsTer8	p.E391Rfs*8	ENST00000344624		390	-/A	5/33	1	2	FACETS	1	0.931	1	1	0.995	1	CLONAL	4	TRUE	1	0.0999144429763154	2		628	902	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250022	110250022	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779073392	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	174	791	0	ENST00000374672.4:c.653C>A	p.Pro218Gln	p.P218Q	ENST00000374672	NM_004235.4	218	cCg/cAg	3/5	0.0999144429763154	0	FACETS	0.859	0.793	0.927			1	CLONAL	5	TRUE	0	0.0999144429763154	0		791	730	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412045	63412046	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	134	282	0	ENST00000330258.3:c.1121dup	p.Leu374PhefsTer4	p.L374Ffs*4	ENST00000330258	NM_152424.3	374	ttg/ttTg	2/2	NA	2	FACETS	1	0.928	1			1	INDETERMINATE	9	TRUE	NA	0.0999144429763154	2		282	297	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935606	13935606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326846768	NA	P-0043939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	142	286	0	ENST00000405192.2:c.1250G>A	p.Arg417His	p.R417H	ENST00000405192	NM_001163147.1	417	cGt/cAt	12/12	0.368005579961136	3	FACETS	1	0.94	1	0.517	0.473	0.563	INDETERMINATE	1	TRUE	1	0.624848213982399	3		286	577	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354667	70354667	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1569482153	NA	P-0043939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	151	323	0	ENST00000374080.3:c.4832G>A	p.Arg1611His	p.R1611H	ENST00000374080		1611	cGt/cAt	35/45	0.561605869088574	3	FACETS	0.714	0.652	0.778	0.357	0.326	0.389	SUBCLONAL	1	TRUE	1	0.624848213982399	3		323	889	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912760	100912760	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	33	278	0	ENST00000325455.5:c.2562G>T	p.Lys854Asn	p.K854N	ENST00000325455	NM_001202474.3	854	aaG/aaT	7/8	0.591060141213628	2	FACETS	0.204	0.166	0.248	0.102	0.083	0.124	SUBCLONAL	1	TRUE	0	0.624848213982399	2		278	517	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941169	36941169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746657668	NA	P-0043939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	46	390	0	ENST00000361632.4:c.170C>T	p.Pro57Leu	p.P57L	ENST00000361632		57	cCg/cTg	3/16	0.531523516421503	2	FACETS	0.217	0.182	0.255	0.108	0.091	0.128	SUBCLONAL	1	TRUE	0	0.624848213982399	2		390	680	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435260	56435260	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	81	375	0	ENST00000407977.2:c.1877del	p.Pro626GlnfsTer74	p.P626Qfs*74	ENST00000407977		626	cCa/ca	9/10	0.541618576746126	3	FACETS	0.441	0.388	0.498	0.147	0.129	0.166	SUBCLONAL	1	TRUE	0	0.624848213982399	3		375	772	SUCCESS
APC	324	MSKCC	GRCh37	5	112175358	112175358	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	95	168	0	ENST00000257430.4:c.4067del	p.Ser1356Ter	p.S1356*	ENST00000257430	NM_000038.5	1356	tCa/ta	16/16	0.624848213982399	1	FACETS	0.921	0.837	1	0.921	0.837	1	CLONAL	1	TRUE	0	0.624848213982399	1		168	227	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	GG	novel	NA	P-0043939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	483	307	0	ENST00000269305.4:c.584delinsCC	p.Ile195ThrfsTer14	p.I195Tfs*14	ENST00000269305	NM_001126112.2	195	aTc/aCCc	6/11	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.624848213982399	2		307	739	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156732	20156732	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	169	235	0	ENST00000379607.5:c.25G>C	p.Gly9Arg	p.G9R	ENST00000379607	NM_001412.3	9	Ggt/Cgt	2/7	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.767628207218199	2		235	408	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105831	27105831	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	245	427	0	ENST00000324856.7:c.5444del	p.Lys1815ArgfsTer68	p.K1815Rfs*68	ENST00000324856	NM_006015.4	1814	gtA/gt	20/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.767628207218199	2		427	628	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65311260	65311260	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	184	360	0	ENST00000342505.4:c.2051A>T	p.Asp684Val	p.D684V	ENST00000342505	NM_002227.2	684	gAt/gTt	15/25	1	2	FACETS	0.917	0.853	0.982	0.917	0.853	0.982	CLONAL	1	TRUE	1	0.767628207218199	2		360	523	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143991	11143991	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	280	451	0	ENST00000358026.2:c.3572A>G	p.His1191Arg	p.H1191R	ENST00000358026	NM_001128849.1	1191	cAc/cGc	26/36	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.767628207218199	2		451	696	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0044143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	314	1025	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.430531471193241	2	FACETS	0.965	0.915	1	0.965	0.915	1	CLONAL	2	TRUE	0	0.430531471193241	2		1026	756	SUCCESS
APC	324	MSKCC	GRCh37	5	112175153	112175153	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	37	208	1	ENST00000257430.4:c.3862G>T	p.Gly1288Ter	p.G1288*	ENST00000257430	NM_000038.5	1288	Gga/Tga	16/16	0.430531471193241	3	FACETS	0.954	0.793	1	0.477	0.396	0.565	CLONAL	1	TRUE	1	0.430531471193241	3		209	219	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303270	15303270	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	297	1008	0	ENST00000263388.2:c.258del	p.Cys87ValfsTer149	p.C87Vfs*149	ENST00000263388	NM_000435.2	86	ccC/cc	3/33	0.180420545989543	2	FACETS	1	0.994	1	0.725	0.683	0.767	INDETERMINATE	1	TRUE	0	0.430531471193241	2		1008	952	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0044302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	335	835	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.389016676234769	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.390371414925434	2		835	782	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053562	37053562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs4986984	NA	P-0044302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	103	493	1	ENST00000231790.2:c.649C>T	p.Arg217Cys	p.R217C	ENST00000231790	NM_000249.3	217	Cgc/Tgc	8/19	1	2	FACETS	0.864	0.774	0.958	0.864	0.774	0.958	CLONAL	1	TRUE	1	0.390371414925434	2		494	611	SUCCESS
APC	324	MSKCC	GRCh37	5	112175452	112175452	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0044302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	131	339	0	ENST00000257430.4:c.4161T>A	p.Cys1387Ter	p.C1387*	ENST00000257430	NM_000038.5	1387	tgT/tgA	16/16	0.389016676234769	2	FACETS	0.935	0.859	1	0.935	0.859	1	CLONAL	2	TRUE	0	0.390371414925434	2		339	359	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30099978	30099978	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	41	461	0	ENST00000331968.5:c.1642T>A	p.Ser548Thr	p.S548T	ENST00000331968	NM_002742.2	548	Tcc/Acc	10/18	0.389016676234769	2	FACETS	0.387	0.322	0.459	0.193	0.161	0.23	SUBCLONAL	1	TRUE	0	0.390371414925434	2		461	543	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473653	67473653	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863223737	NA	P-0044302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	166	548	0	ENST00000327367.4:c.733G>C	p.Gly245Arg	p.G245R	ENST00000327367	NM_005902.3	245	Ggg/Cgg	6/9	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.390371414925434	2		548	766	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509857	106509857	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	131	625	0	ENST00000359195.3:c.1851G>T	p.Trp617Cys	p.W617C	ENST00000359195	NM_002649.2	617	tgG/tgT	2/11	0.390371414925434	3	FACETS	0.904	0.82	0.993	0.452	0.41	0.497	CLONAL	1	TRUE	1	0.390371414925434	3		625	887	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0044364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	25	360	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.775	0.615	0.954	1	0.934	1	CLONAL	2	TRUE	1	0.183397337329226	2		360	176	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473653	67473653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223737	NA	P-0044364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	123	520	0	ENST00000327367.4:c.733G>A	p.Gly245Arg	p.G245R	ENST00000327367	NM_005902.3	245	Ggg/Agg	6/9	0.183397337329226	2	FACETS	0.93	0.842	1	0.93	0.842	1	CLONAL	2	TRUE	0	0.183397337329226	2		520	721	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428562	78428562	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	31	322	1	ENST00000370768.2:c.1237C>T	p.Gln413Ter	p.Q413*	ENST00000370768	NM_003902.3	413	Cag/Tag	14/20	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.183397337329226	2		323	269	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422959	45422959	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	42	292	0	ENST00000262160.6:c.169C>T	p.Arg57Ter	p.R57*	ENST00000262160	NM_005901.5	57	Cga/Tga	2/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.183397337329226	2		292	343	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946337	2946337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759681668	NA	P-0044364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	160	624	0	ENST00000396946.4:c.3400G>A	p.Val1134Ile	p.V1134I	ENST00000396946	NM_032415.4	1134	Gtt/Att	25/25	1	2	FACETS	0.995	0.912	1	1	0.992	1	CLONAL	2	TRUE	1	0.183397337329226	2		624	877	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56339006	56339007	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0044364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	19	62	0	ENST00000348428.3:c.133dup	p.Leu45ProfsTer36	p.L45Pfs*36	ENST00000348428	NM_006785.3	44	ctc/ctCc	1/17	1	2	FACETS	0.964	0.734	1	0.964	0.734	1	CLONAL	1	TRUE	1	0.183397337329226	2		62	215	SUCCESS
APC	324	MSKCC	GRCh37	5	112102895	112102898	+	frameshift_variant	Frame_Shift_Del	DEL	TAGA	TAGA	-	rs1064793020	NA	P-0044364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	18	222	0	ENST00000257430.4:c.233_236del	p.Asp78AlafsTer7	p.D78Afs*7	ENST00000257430	NM_000038.5	77	tTAGAt/tt	4/16	1	2	FACETS	0.939	0.709	1	0.939	0.709	1	CLONAL	1	TRUE	1	0.183397337329226	2		222	209	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	45	290	1				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	0	0.18	1		291	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0044386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	52	1045	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.556	0.471	0.649	0.556	0.471	0.649	SUBCLONAL	1	TRUE	1	0.18	2		1046	1040	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	107	1218	1	ENST00000269305.4:c.166G>T	p.Glu56Ter	p.E56*	ENST00000269305	NM_001126112.2	56	Gaa/Taa	4/11	1	2	FACETS	0.967	0.864	1	0.967	0.864	1	CLONAL	1	TRUE	1	0.18	2		1219	1230	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163720	32163720	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	45	692	0	ENST00000375023.3:c.5506G>C	p.Glu1836Gln	p.E1836Q	ENST00000375023	NM_004557.3	1836	Gag/Cag	30/30	0.0867894851042834	3	FACETS	0.956	0.803	1			1	INDETERMINATE	1	TRUE	NA	0.18	3		692	570	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30061031	30061031	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0044386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	50	557	0	ENST00000338641.4:c.863C>G	p.Ser288Ter	p.S288*	ENST00000338641	NM_000268.3	288	tCa/tGa	9/16	0.3	1	FACETS	0.821	0.696	0.959	0.821	0.696	0.959	CLONAL	1	TRUE	0	0.18	1		557	616	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651879	36651879	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0044386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	33	760	0	ENST00000244741.5:c.1A>G	p.Met1?	p.M1?	ENST00000244741	NM_000389.4	1	Atg/Gtg	2/3	0.112059120579411	3	FACETS	0.44	0.356	0.534	0.22	0.178	0.267	SUBCLONAL	1	TRUE	1	0.18	3		760	909	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652225	36652226	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	79	944	0	ENST00000244741.5:c.349dup	p.Cys117LeufsTer12	p.C117Lfs*12	ENST00000244741	NM_000389.4	116	tct/tcTt	2/3	0.112059120579411	3	FACETS	0.893	0.783	1	0.447	0.391	0.506	CLONAL	1	TRUE	1	0.18	3		944	1071	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940456	29940456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771593278	NA	P-0044386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	26	456	0	ENST00000389048.3:c.775C>T	p.Arg259Cys	p.R259C	ENST00000389048	NM_004304.4	259	Cgc/Tgc	2/29	0.224747818311329	0	FACETS	0.671	0.532	0.831			1	SUBCLONAL	1	TRUE	0	0.18	0		456	353	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032069	26032069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	26	571	0	ENST00000244661.2:c.220G>A	p.Glu74Lys	p.E74K	ENST00000244661	NM_003537.3	74	Gaa/Aaa	1/1	0.246112544886133	4	FACETS	0.414	0.326	0.516	0.207	0.163	0.258	SUBCLONAL	1	TRUE	2	0.18	4		571	823	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437052	110437052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	15	149	0	ENST00000375856.3:c.1349C>T	p.Ser450Phe	p.S450F	ENST00000375856	NM_003749.2	450	tCc/tTc	1/2	1	2	FACETS	0.882	0.647	1	0.882	0.647	1	CLONAL	1	TRUE	1	0.18	2		149	189	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670452	246670452	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	41	671	0	ENST00000388985.4:c.68C>A	p.Pro23Gln	p.P23Q	ENST00000388985		23	cCg/cAg	1/12	1	2	FACETS	0.806	0.671	0.957	0.806	0.671	0.957	CLONAL	1	TRUE	1	0.18	2		671	565	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609084	43609084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769971379	NA	P-0044386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	134	1115	1	ENST00000355710.3:c.1840G>A	p.Glu614Lys	p.E614K	ENST00000355710	NM_020975.4	614	Gag/Aag	10/20	0.3	1	FACETS	0.79	0.717	0.866	1	0.987	1	SUBCLONAL	2	TRUE	0	0.18	1		1116	858	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155165	108155165	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	48	610	0	ENST00000278616.4:c.3958G>C	p.Asp1320His	p.D1320H	ENST00000278616	NM_000051.3	1320	Gat/Cat	26/63	1	2	FACETS	0.915	0.773	1	0.915	0.773	1	CLONAL	1	TRUE	1	0.18	2		610	583	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406210	406210	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	56	374	0	ENST00000399788.2:c.4231C>G	p.Gln1411Glu	p.Q1411E	ENST00000399788	NM_001042603.1	1411	Caa/Gaa	25/28	0.0867894851042834	3	FACETS	0.809	0.695	0.933			1	INDETERMINATE	2	TRUE	NA	0.18	3		374	419	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406233	406233	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	71	460	0	ENST00000399788.2:c.4208C>G	p.Ser1403Cys	p.S1403C	ENST00000399788	NM_001042603.1	1403	tCt/tGt	25/28	0.0867894851042834	3	FACETS	0.808	0.706	0.918			1	INDETERMINATE	2	TRUE	NA	0.18	3		460	532	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457371	67457371	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	155	913	0	ENST00000327367.4:c.345G>A	p.Met115Ile	p.M115I	ENST00000327367	NM_005902.3	115	atG/atA	2/9	1	2	FACETS	0.889	0.813	0.968	1	0.99	1	CLONAL	2	TRUE	1	0.18	2		913	969	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900978	3900978	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	75	754	1	ENST00000262367.5:c.118C>G	p.Leu40Val	p.L40V	ENST00000262367	NM_004380.2	40	Ctt/Gtt	2/31	1	2	FACETS	0.9	0.787	1	0.9	0.787	1	CLONAL	1	TRUE	1	0.18	2		755	926	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760950	59760950	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	76	733	0	ENST00000259008.2:c.3457G>C	p.Asp1153His	p.D1153H	ENST00000259008	NM_032043.2	1153	Gat/Cat	20/20	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.18	2		733	728	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944470	40944470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	44	804	0	ENST00000373198.4:c.2032C>T	p.Pro678Ser	p.P678S	ENST00000373198	NM_133170.3	678	Cca/Tca	12/32	0.3	1	FACETS	0.533	0.445	0.63	0.533	0.445	0.63	SUBCLONAL	1	TRUE	0	0.18	1		804	835	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259775	142259775	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	75	635	0	ENST00000350721.4:c.3552C>G	p.Phe1184Leu	p.F1184L	ENST00000350721	NM_001184.3	1184	ttC/ttG	18/47	0.112059120579411	3	FACETS	1	0.965	1	0.65	0.569	0.737	CLONAL	1	TRUE	1	0.18	3		635	699	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679918	30679918	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	44	671	0	ENST00000376406.3:c.1801C>T	p.Pro601Ser	p.P601S	ENST00000376406	NM_014641.2	601	Cca/Tca	5/15	0.246112544886133	4	FACETS	0.705	0.59	0.834	0.353	0.295	0.417	SUBCLONAL	1	TRUE	2	0.18	4		671	818	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441652	6441652	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1343	100	1350	0	ENST00000356142.4:c.499G>C	p.Glu167Gln	p.E167Q	ENST00000356142	NM_018890.3	167	Gag/Cag	6/7	1	2	FACETS	0.77	0.685	0.861	0.77	0.685	0.861	SUBCLONAL	1	TRUE	1	0.18	2		1350	1443	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3929911	3929911	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	44	547	0	ENST00000262367.5:c.7G>C	p.Glu3Gln	p.E3Q	ENST00000262367	NM_004380.2	3	Gag/Cag	1/31	1	2	FACETS	0.767	0.642	0.906	0.767	0.642	0.906	CLONAL	1	TRUE	1	0.18	2		547	637	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264342	46264342	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	36	534	0	ENST00000371998.3:c.1389G>C	p.Met463Ile	p.M463I	ENST00000371998		463	atG/atC	11/23	1	2	FACETS	0.629	0.516	0.756	0.629	0.516	0.756	SUBCLONAL	1	TRUE	1	0.18	2		534	636	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268395	46268395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376679137	NA	P-0044386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	41	483	0	ENST00000371998.3:c.2782G>A	p.Gly928Ser	p.G928S	ENST00000371998		928	Ggc/Agc	15/23	1	2	FACETS	0.663	0.551	0.788	0.663	0.551	0.788	SUBCLONAL	1	TRUE	1	0.18	2		483	687	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361242	66361242	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	28	442	0	ENST00000273854.3:c.930C>G	p.Phe310Leu	p.F310L	ENST00000273854	NM_004439.5	310	ttC/ttG	4/18	0.195775955538854	0	FACETS	0.493	0.393	0.608			1	SUBCLONAL	1	TRUE	0	0.18	0		442	517	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0044437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	197	364	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.561002850632803	2	FACETS	0.788	0.739	0.836	0.788	0.739	0.836	SUBCLONAL	2	TRUE	0	0.608642274494191	2		365	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0044437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	261	698	0	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	0.582057437346508	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.608642274494191	1		698	587	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426006	138426006	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755672708	NA	P-0044437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	80	352	1	ENST00000289153.2:c.1525G>A	p.Asp509Asn	p.D509N	ENST00000289153	NM_006219.2	509	Gat/Aat	9/22	0.3244141260163	1	FACETS	0.517	0.458	0.579	0.517	0.458	0.579	INDETERMINATE	1	TRUE	0	0.608642274494191	1		353	354	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28605738	28605738	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1006193399	NA	P-0044437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	82	514	0	ENST00000253063.3:c.1342C>T	p.Arg448Cys	p.R448C	ENST00000253063	NM_031459.4	448	Cgc/Tgc	9/10	0.323034870692899	1	FACETS	0.265	0.233	0.299	0.265	0.233	0.299	INDETERMINATE	1	TRUE	0	0.608642274494191	1		514	707	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14027792	14027792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555395802	NA	P-0044437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	97	239	0	ENST00000405192.2:c.52C>T	p.Arg18Cys	p.R18C	ENST00000405192	NM_001163147.1	18	Cgt/Tgt	3/12	1	2	FACETS	0.869	0.781	0.96	0.869	0.781	0.96	CLONAL	1	TRUE	1	0.608642274494191	2		239	367	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	110	1045	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.837	0.753	0.927	0.837	0.753	0.927	CLONAL	1	TRUE	1	0.3541175285411	2		1046	742	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	9	571	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.117	0.077	0.169	0.117	0.077	0.169	SUBCLONAL	1	TRUE	1	0.3541175285411	2		571	434	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	45	670	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.691	0.582	0.81	0.691	0.582	0.81	SUBCLONAL	1	TRUE	1	0.3541175285411	2		670	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555525857	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	70	751	0	ENST00000269305.4:c.596G>A	p.Gly199Glu	p.G199E	ENST00000269305	NM_001126112.2	199	gGa/gAa	6/11	1	2	FACETS	0.564	0.491	0.643	0.564	0.491	0.643	SUBCLONAL	1	TRUE	1	0.3541175285411	2		751	701	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481417	140481417	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913348	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	44	402	0	ENST00000288602.6:c.1391G>T	p.Gly464Val	p.G464V	ENST00000288602	NM_004333.4	464	gGa/gTa	11/18	1	2	FACETS	0.631	0.53	0.742	0.631	0.53	0.742	SUBCLONAL	1	TRUE	1	0.3541175285411	2		402	394	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781509	9781509	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	51	654	0	ENST00000377346.4:c.1819G>A	p.Glu607Lys	p.E607K	ENST00000377346	NM_005026.3	607	Gag/Aag	15/24	1	2	FACETS	0.612	0.52	0.712	0.612	0.52	0.712	SUBCLONAL	1	TRUE	1	0.3541175285411	2		654	471	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339409	116339409	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	52	481	0	ENST00000397752.3:c.271G>A	p.Glu91Lys	p.E91K	ENST00000397752	NM_000245.2	91	Gaa/Aaa	2/21	1	2	FACETS	0.811	0.693	0.939	0.811	0.693	0.939	CLONAL	1	TRUE	1	0.3541175285411	2		481	362	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933480	100933480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766277966	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	33	213	0	ENST00000325455.5:c.1910G>A	p.Arg637Gln	p.R637Q	ENST00000325455	NM_001202474.3	637	cGa/cAa	4/8	1	2	FACETS	0.793	0.65	0.952	0.793	0.65	0.952	CLONAL	1	TRUE	1	0.3541175285411	2		213	235	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597430	10597430	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	125	898	1	ENST00000171111.5:c.1773G>A	p.Trp591Ter	p.W591*	ENST00000171111	NM_203500.1	591	tgG/tgA	6/6	1	2	FACETS	0.777	0.702	0.855	0.777	0.702	0.855	SUBCLONAL	1	TRUE	1	0.3541175285411	2		899	909	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665360	138665360	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906920	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	95	1003	0	ENST00000330315.3:c.205G>A	p.Glu69Lys	p.E69K	ENST00000330315	NM_023067.3	69	Gag/Aag	1/1	1	2	FACETS	0.643	0.571	0.719	0.643	0.571	0.719	SUBCLONAL	1	TRUE	1	0.3541175285411	2		1003	835	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921499	39921499	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	208	438	0	ENST00000378444.4:c.4321C>T	p.Gln1441Ter	p.Q1441*	ENST00000378444	NM_001123385.1	1441	Cag/Tag	10/15	0.219897067938422	2	FACETS	1	0.983	1			1	CLONAL	2	TRUE	NA	0.3541175285411	2		438	516	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574232	95574232	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	31	354	0	ENST00000393063.1:c.2635C>G	p.Leu879Val	p.L879V	ENST00000393063	NM_030621.3	879	Cta/Gta	17/28	1	2	FACETS	0.912	0.744	1	0.912	0.744	1	CLONAL	1	TRUE	1	0.3541175285411	2		354	192	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923102	48923102	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	51	315	0	ENST00000267163.4:c.550G>T	p.Glu184Ter	p.E184*	ENST00000267163	NM_000321.2	184	Gaa/Taa	6/27	0.164476580984138	3	FACETS	1	0.912	1	0.547	0.467	0.633	INDETERMINATE	1	TRUE	1	0.3541175285411	3		315	310	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163848	32163848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1210630301	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	160	480	0	ENST00000375023.3:c.5378G>A	p.Arg1793Gln	p.R1793Q	ENST00000375023	NM_004557.3	1793	cGa/cAa	30/30	0.259948177172106	2	FACETS	1	0.987	1	0.69	0.635	0.747	CLONAL	1	TRUE	0	0.3541175285411	2		480	655	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	73	323	2				ENST00000310581	NM_198253.2	-/1132			0.275883716244246	2	FACETS	0.769	0.681	0.862	0.769	0.681	0.862	SUBCLONAL	2	TRUE	0	0.3541175285411	2		325	268	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023756	27023756	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	61	488	1	ENST00000324856.7:c.862C>T	p.Gln288Ter	p.Q288*	ENST00000324856	NM_006015.4	288	Cag/Tag	1/20	1	2	FACETS	0.84	0.727	0.962	0.84	0.727	0.962	CLONAL	1	TRUE	1	0.3541175285411	2		489	410	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508408	106508408	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	52	448	0	ENST00000359195.3:c.402G>T	p.Gln134His	p.Q134H	ENST00000359195	NM_002649.2	134	caG/caT	2/11	1	2	FACETS	0.718	0.613	0.833	0.718	0.613	0.833	SUBCLONAL	1	TRUE	1	0.3541175285411	2		448	409	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007842	45007842	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	105	436	0	ENST00000558401.1:c.289G>T	p.Glu97Ter	p.E97*	ENST00000558401	NM_004048.2	97	Gag/Tag	2/4	0.267307889659455	2	FACETS	1	0.977	1	0.652	0.587	0.719	CLONAL	1	TRUE	0	0.3541175285411	2		436	455	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55334132	55334132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	52	428	0	ENST00000284073.2:c.29C>T	p.Ser10Leu	p.S10L	ENST00000284073	NM_138962.2	10	tCg/tTg	1/14	1	2	FACETS	0.703	0.599	0.815	0.703	0.599	0.815	SUBCLONAL	1	TRUE	1	0.3541175285411	2		428	418	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513574	41513574	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	159	706	0	ENST00000263253.7:c.478C>T	p.Gln160Ter	p.Q160*	ENST00000263253	NM_001429.3	160	Cag/Tag	2/31	0.3541175285411	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.3541175285411	1		706	588	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186583	108186583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375783941	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	35	330	0	ENST00000278616.4:c.6040G>A	p.Glu2014Lys	p.E2014K	ENST00000278616	NM_000051.3	2014	Gag/Aag	41/63	1	2	FACETS	0.648	0.533	0.777	0.648	0.533	0.777	SUBCLONAL	1	TRUE	1	0.3541175285411	2		330	305	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546420	46546420	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	49	353	0	ENST00000262741.5:c.109C>G	p.Leu37Val	p.L37V	ENST00000262741	NM_003629.3	37	Ctt/Gtt	2/10	1	2	FACETS	0.926	0.789	1	0.926	0.789	1	CLONAL	1	TRUE	1	0.3541175285411	2		353	299	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426637	212426637	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	65	583	0	ENST00000342788.4:c.2478G>C	p.Gln826His	p.Q826H	ENST00000342788	NM_005235.2	826	caG/caC	20/28	1	2	FACETS	0.71	0.616	0.811	0.71	0.616	0.811	SUBCLONAL	1	TRUE	1	0.3541175285411	2		583	517	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983772	15983772	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	76	574	0	ENST00000268712.3:c.3350C>G	p.Ser1117Ter	p.S1117*	ENST00000268712	NM_006311.3	1117	tCa/tGa	25/46	1	2	FACETS	0.707	0.621	0.8	0.707	0.621	0.8	SUBCLONAL	1	TRUE	1	0.3541175285411	2		574	607	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934234	48934234	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	42	523	0	ENST00000267163.4:c.689C>G	p.Ser230Ter	p.S230*	ENST00000267163	NM_000321.2	230	tCa/tGa	7/27	0.164476580984138	3	FACETS	0.611	0.51	0.723	0.305	0.255	0.362	INDETERMINATE	1	TRUE	1	0.3541175285411	3		523	457	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5239023	5239023	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	96	885	0	ENST00000357368.4:c.1756C>G	p.Pro586Ala	p.P586A	ENST00000357368	NM_002850.3	586	Ccc/Gcc	13/38	1	2	FACETS	0.765	0.681	0.853	0.765	0.681	0.853	SUBCLONAL	1	TRUE	1	0.3541175285411	2		885	709	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139028	50139028	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769754956	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	127	1001	0	ENST00000246792.3:c.535G>A	p.Val179Met	p.V179M	ENST00000246792	NM_006270.3	179	Gtg/Atg	5/6	1	2	FACETS	0.799	0.723	0.879	0.799	0.723	0.879	SUBCLONAL	1	TRUE	1	0.3541175285411	2		1001	898	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874008	151874008	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	54	484	0	ENST00000262189.6:c.8530G>A	p.Glu2844Lys	p.E2844K	ENST00000262189	NM_170606.2	2844	Gag/Aag	38/59	1	2	FACETS	0.692	0.592	0.8	0.692	0.592	0.8	SUBCLONAL	1	TRUE	1	0.3541175285411	2		484	441	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101985061	101985061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748877056	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	110	786	0	ENST00000282441.5:c.508G>A	p.Asp170Asn	p.D170N	ENST00000282441	NM_001130145.2	170	Gat/Aat	2/9	1	2	FACETS	0.717	0.644	0.795	0.717	0.644	0.795	SUBCLONAL	1	TRUE	1	0.3541175285411	2		786	866	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665118	138665118	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	56	552	0	ENST00000330315.3:c.447G>A	p.Met149Ile	p.M149I	ENST00000330315	NM_023067.3	149	atG/atA	1/1	1	2	FACETS	0.679	0.582	0.784	0.679	0.582	0.784	SUBCLONAL	1	TRUE	1	0.3541175285411	2		552	466	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017155	31017155	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	178	315	0	ENST00000375687.4:c.486G>C	p.Lys162Asn	p.K162N	ENST00000375687	NM_015338.5	162	aaG/aaC	7/13	0.267669274356885	3	FACETS	0.846	0.788	0.906	0.846	0.788	0.906	CLONAL	3	TRUE	0	0.3541175285411	3		315	466	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057296	30057296	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	155	598	0	ENST00000338641.4:c.778G>T	p.Glu260Ter	p.E260*	ENST00000338641	NM_000268.3	260	Gaa/Taa	8/16	0.3541175285411	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.3541175285411	1		598	528	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780943	9780943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	93	763	0	ENST00000377346.4:c.1665G>A	p.Trp555Ter	p.W555*	ENST00000377346	NM_005026.3	555	tgG/tgA	13/24	1	2	FACETS	0.817	0.727	0.912	0.817	0.727	0.912	CLONAL	1	TRUE	1	0.3541175285411	2		763	643	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259699	11259699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	57	497	0	ENST00000361445.4:c.4006G>A	p.Glu1336Lys	p.E1336K	ENST00000361445	NM_004958.3	1336	Gag/Aag	27/58	1	2	FACETS	0.644	0.553	0.743	0.644	0.553	0.743	SUBCLONAL	1	TRUE	1	0.3541175285411	2		497	500	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023640	27023640	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	52	425	0	ENST00000324856.7:c.746C>G	p.Ser249Cys	p.S249C	ENST00000324856	NM_006015.4	249	tCc/tGc	1/20	1	2	FACETS	0.785	0.671	0.91	0.785	0.671	0.91	CLONAL	1	TRUE	1	0.3541175285411	2		425	374	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023707	27023707	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	87	526	0	ENST00000324856.7:c.813C>A	p.Phe271Leu	p.F271L	ENST00000324856	NM_006015.4	271	ttC/ttA	1/20	1	2	FACETS	0.977	0.868	1	0.977	0.868	1	CLONAL	1	TRUE	1	0.3541175285411	2		526	503	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795082	45795082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	89	635	1	ENST00000450313.1:c.1546C>T	p.Pro516Ser	p.P516S	ENST00000450313	NM_012222.2	516	Ccg/Tcg	16/16	1	2	FACETS	0.785	0.697	0.88	0.785	0.697	0.88	SUBCLONAL	1	TRUE	1	0.3541175285411	2		636	640	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852364	63852364	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1172094709	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	93	751	1	ENST00000279873.7:c.3142G>A	p.Glu1048Lys	p.E1048K	ENST00000279873	NM_032199.2	1048	Gag/Aag	10/10	1	2	FACETS	0.75	0.667	0.839	0.75	0.667	0.839	SUBCLONAL	1	TRUE	1	0.3541175285411	2		752	700	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404926	70404926	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	84	644	0	ENST00000373644.4:c.2440G>C	p.Asp814His	p.D814H	ENST00000373644	NM_030625.2	814	Gat/Cat	4/12	1	2	FACETS	0.864	0.765	0.97	0.864	0.765	0.97	CLONAL	1	TRUE	1	0.3541175285411	2		644	549	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136252	64136252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	107	826	2	ENST00000334205.4:c.1411G>A	p.Glu471Lys	p.E471K	ENST00000334205	NM_003942.2	471	Gag/Aag	12/17	1	2	FACETS	0.983	0.883	1	0.983	0.883	1	CLONAL	1	TRUE	1	0.3541175285411	2		828	615	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	465673	465673	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374194423	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	67	595	0	ENST00000399788.2:c.703G>A	p.Glu235Lys	p.E235K	ENST00000399788	NM_001042603.1	235	Gaa/Aaa	6/28	1	2	FACETS	0.681	0.592	0.776	0.681	0.592	0.776	SUBCLONAL	1	TRUE	1	0.3541175285411	2		595	556	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446798	49446798	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	124	793	0	ENST00000301067.7:c.1012G>C	p.Glu338Gln	p.E338Q	ENST00000301067	NM_003482.3	338	Gag/Cag	8/54	0.164476580984138	3	FACETS	1	0.962	1	0.559	0.506	0.615	INDETERMINATE	1	TRUE	1	0.3541175285411	3		793	737	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912588	32912588	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1566229657	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	97	481	0	ENST00000380152.3:c.4096C>G	p.Leu1366Val	p.L1366V	ENST00000380152		1366	Ctt/Gtt	11/27	0.164476580984138	3	FACETS	0.757	0.679	0.839	0.757	0.679	0.839	INDETERMINATE	2	TRUE	1	0.3541175285411	3		481	426	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953507	32953507	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs80359138	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	71	462	0	ENST00000380152.3:c.8808G>C	p.Leu2936Phe	p.L2936F	ENST00000380152		2936	ttG/ttC	22/27	0.164476580984138	3	FACETS	1	0.965	1	0.641	0.563	0.725	INDETERMINATE	1	TRUE	1	0.3541175285411	3		462	368	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242132	105242132	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	94	832	0	ENST00000349310.3:c.292G>C	p.Glu98Gln	p.E98Q	ENST00000349310	NM_001014432.1	98	Gag/Cag	6/15	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.3541175285411	2		832	504	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007736	45007736	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1370797084	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	105	380	0	ENST00000558401.1:c.183G>C	p.Lys61Asn	p.K61N	ENST00000558401	NM_004048.2	61	aaG/aaC	2/4	0.267307889659455	2	FACETS	1	0.981	1	0.704	0.635	0.776	CLONAL	1	TRUE	0	0.3541175285411	2		380	421	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251119	99251119	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	193	723	0	ENST00000268035.6:c.423C>G	p.Ile141Met	p.I141M	ENST00000268035	NM_000875.3	141	atC/atG	2/21	0.267307889659455	2	FACETS	0.891	0.828	0.954	0.891	0.828	0.954	CLONAL	2	TRUE	0	0.3541175285411	2		723	612	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50784085	50784085	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	82	602	0	ENST00000398568.2:c.476C>G	p.Ser159Cys	p.S159C	ENST00000398568	NM_001042412.1	159	tCc/tGc	3/18	1	2	FACETS	0.746	0.658	0.84	0.746	0.658	0.84	SUBCLONAL	1	TRUE	1	0.3541175285411	2		602	621	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645448	67645448	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	47	395	0	ENST00000264010.4:c.713C>G	p.Ser238Ter	p.S238*	ENST00000264010	NM_006565.3	238	tCa/tGa	3/12	1	2	FACETS	0.721	0.61	0.843	0.721	0.61	0.843	SUBCLONAL	1	TRUE	1	0.3541175285411	2		395	368	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816165	89816165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs924918296	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	110	834	0	ENST00000389301.3:c.3212G>A	p.Arg1071Lys	p.R1071K	ENST00000389301	NM_000135.2	1071	aGa/aAa	32/43	1	2	FACETS	0.94	0.846	1	0.94	0.846	1	CLONAL	1	TRUE	1	0.3541175285411	2		834	661	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15943788	15943788	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	41	314	0	ENST00000268712.3:c.6700G>A	p.Glu2234Lys	p.E2234K	ENST00000268712	NM_006311.3	2234	Gag/Aag	43/46	1	2	FACETS	0.673	0.562	0.796	0.673	0.562	0.796	SUBCLONAL	1	TRUE	1	0.3541175285411	2		314	344	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291073	10291073	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	80	802	0	ENST00000340748.4:c.398C>G	p.Ser133Cys	p.S133C	ENST00000340748		133	tCc/tGc	4/40	1	2	FACETS	0.582	0.512	0.658	0.582	0.512	0.658	SUBCLONAL	1	TRUE	1	0.3541175285411	2		802	776	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471118	25471118	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	79	679	0	ENST00000264709.3:c.643G>C	p.Glu215Gln	p.E215Q	ENST00000264709	NM_175629.2	215	Gag/Cag	7/23	1	2	FACETS	0.773	0.681	0.872	0.773	0.681	0.872	SUBCLONAL	1	TRUE	1	0.3541175285411	2		679	577	SUCCESS
REL	5966	MSKCC	GRCh37	2	61148897	61148897	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	23	262	0	ENST00000295025.8:c.1088-1G>A		p.X363_splice	ENST00000295025	NM_002908.2	363			1	2	FACETS	0.593	0.464	0.741	0.593	0.464	0.741	SUBCLONAL	1	TRUE	1	0.3541175285411	2		262	219	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176341	24176341	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	93	1015	0	ENST00000263121.7:c.1132C>G	p.Leu378Val	p.L378V	ENST00000263121	NM_003073.3	378	Ctt/Gtt	9/9	0.3541175285411	1	FACETS	0.541	0.48	0.606	0.541	0.48	0.606	SUBCLONAL	1	TRUE	0	0.3541175285411	1		1015	799	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960051	134960051	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs928158346	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	74	806	1	ENST00000398015.3:c.2408C>T	p.Ser803Leu	p.S803L	ENST00000398015	NM_004441.4	803	tCa/tTa	13/16	1	2	FACETS	0.629	0.551	0.714	0.629	0.551	0.714	SUBCLONAL	1	TRUE	1	0.3541175285411	2		807	664	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266640	142266640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1051324098	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	46	397	0	ENST00000350721.4:c.3284C>T	p.Ser1095Leu	p.S1095L	ENST00000350721	NM_001184.3	1095	tCa/tTa	16/47	1	2	FACETS	0.708	0.598	0.829	0.708	0.598	0.829	SUBCLONAL	1	TRUE	1	0.3541175285411	2		397	367	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277586	142277586	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	46	394	0	ENST00000350721.4:c.1765G>T	p.Asp589Tyr	p.D589Y	ENST00000350721	NM_001184.3	589	Gat/Tat	8/47	1	2	FACETS	0.802	0.678	0.937	0.802	0.678	0.937	CLONAL	1	TRUE	1	0.3541175285411	2		394	324	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149243812	149243812	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	106	749	0	ENST00000360632.3:c.1006G>C	p.Glu336Gln	p.E336Q	ENST00000360632	NM_015472.4	336	Gag/Cag	6/7	1	2	FACETS	0.687	0.615	0.764	0.687	0.615	0.764	SUBCLONAL	1	TRUE	1	0.3541175285411	2		749	871	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152129	55152129	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	91	736	1	ENST00000257290.5:c.2561G>C	p.Ser854Thr	p.S854T	ENST00000257290	NM_006206.4	854	aGt/aCt	18/23	1	2	FACETS	0.721	0.64	0.807	0.721	0.64	0.807	SUBCLONAL	1	TRUE	1	0.3541175285411	2		737	713	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542113	187542113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1229134544	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	35	465	0	ENST00000441802.2:c.5627C>T	p.Pro1876Leu	p.P1876L	ENST00000441802	NM_005245.3	1876	cCc/cTc	10/27	1	2	FACETS	0.537	0.441	0.645	0.537	0.441	0.645	SUBCLONAL	1	TRUE	1	0.3541175285411	2		465	368	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628071	187628071	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	68	681	0	ENST00000441802.2:c.2911G>C	p.Glu971Gln	p.E971Q	ENST00000441802	NM_005245.3	971	Gaa/Caa	2/27	1	2	FACETS	0.563	0.489	0.643	0.563	0.489	0.643	SUBCLONAL	1	TRUE	1	0.3541175285411	2		681	682	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754259	57754259	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	118	427	0	ENST00000274289.3:c.592G>C	p.Glu198Gln	p.E198Q	ENST00000274289	NM_006622.3	198	Gaa/Caa	4/14	0.259948177172106	2	FACETS	1	0.985	1	0.736	0.668	0.806	CLONAL	1	TRUE	0	0.3541175285411	2		427	453	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959180	2959180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184296576	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	117	1010	2	ENST00000396946.4:c.2336G>A	p.Arg779Gln	p.R779Q	ENST00000396946	NM_032415.4	779	cGg/cAg	18/25	1	2	FACETS	0.886	0.799	0.977	0.886	0.799	0.977	CLONAL	1	TRUE	1	0.3541175285411	2		1012	746	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187391	38187391	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	76	491	0	ENST00000317025.8:c.1086G>C	p.Gln362His	p.Q362H	ENST00000317025	NM_023034.1	362	caG/caC	6/24	1	2	FACETS	0.847	0.744	0.956	0.847	0.744	0.956	CLONAL	1	TRUE	1	0.3541175285411	2		491	507	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249801	110249801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1337270879	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	294	960	0	ENST00000374672.4:c.874C>T	p.Pro292Ser	p.P292S	ENST00000374672	NM_004235.4	292	Ccc/Tcc	3/5	0.3541175285411	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.3541175285411	2		960	795	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179174	123179174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	121	186	0	ENST00000218089.9:c.623C>T	p.Ser208Phe	p.S208F	ENST00000218089	NM_001042749.1	208	tCt/tTt	8/35	0.219897067938422	2	FACETS	0.847	0.78	0.915			1	CLONAL	3	TRUE	NA	0.3541175285411	2		186	269	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0044573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	103	449	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.936	0.847	1	0.936	0.847	1	CLONAL	1	TRUE	1	0.64735959157602	2		449	340	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207021	1207021	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913324	NA	P-0044573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	239	665	1	ENST00000326873.7:c.109C>T	p.Gln37Ter	p.Q37*	ENST00000326873	NM_000455.4	37	Cag/Tag	1/10	0.64735959157602	1	FACETS	0.97	0.915	1	0.97	0.915	1	CLONAL	1	TRUE	0	0.64735959157602	1		666	515	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602581	10602581	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	100	659	0	ENST00000171111.5:c.997G>A	p.Gly333Ser	p.G333S	ENST00000171111	NM_203500.1	333	Ggc/Agc	3/6	0.64735959157602	1	FACETS	0.459	0.412	0.509	0.459	0.412	0.509	SUBCLONAL	1	TRUE	0	0.64735959157602	1		659	455	SUCCESS
ATM	472	MSKCC	GRCh37	11	108138042	108138042	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	127	365	0	ENST00000278616.4:c.2611G>T	p.Glu871Ter	p.E871*	ENST00000278616	NM_000051.3	871	Gaa/Taa	17/63	0.64735959157602	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.64735959157602	1		365	242	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858574	57858574	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1566558833	NA	P-0044573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	258	616	0	ENST00000228682.2:c.312C>G	p.Ser104Arg	p.S104R	ENST00000228682	NM_005269.2	104	agC/agG	4/12	1	2	FACETS	0.957	0.899	1	0.957	0.899	1	CLONAL	1	TRUE	1	0.64735959157602	2		616	833	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644821	67644821	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	186	397	0	ENST00000264010.4:c.86G>T	p.Arg29Leu	p.R29L	ENST00000264010	NM_006565.3	29	cGg/cTg	3/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.64735959157602	2		397	536	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990625	7990625	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	146	418	1	ENST00000319144.4:c.136G>A	p.Ala46Thr	p.A46T	ENST00000319144	NM_001139.2	46	Gca/Aca	1/15	1	2	FACETS	0.895	0.822	0.97	0.895	0.822	0.97	CLONAL	1	TRUE	1	0.64735959157602	2		419	504	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38955718	38955718	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs750704208	NA	P-0044573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	93	304	0	ENST00000357387.3:c.2588A>G	p.Tyr863Cys	p.Y863C	ENST00000357387	NM_152756.3	863	tAt/tGt	26/38	1	2	FACETS	0.863	0.775	0.955	0.863	0.775	0.955	CLONAL	1	TRUE	1	0.64735959157602	2		304	333	SUCCESS
APC	324	MSKCC	GRCh37	5	112162822	112162822	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	91	344	0	ENST00000257430.4:c.1426G>T	p.Ala476Ser	p.A476S	ENST00000257430	NM_000038.5	476	Gca/Tca	12/16	1	2	FACETS	0.96	0.863	1	0.96	0.863	1	CLONAL	1	TRUE	1	0.64735959157602	2		344	293	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376034	8376034	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	14	329	0	ENST00000356435.5:c.4563T>A	p.Asp1521Glu	p.D1521E	ENST00000356435		1521	gaT/gaA	28/35	0.592461650078868	1	FACETS	0.127	0.091	0.169	0.127	0.091	0.169	SUBCLONAL	1	TRUE	0	0.64735959157602	1		329	231	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37006481	37006481	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	90	292	0	ENST00000358127.4:c.464G>T	p.Ser155Ile	p.S155I	ENST00000358127	NM_001280556.1	155	aGt/aTt	4/10	0.485224195385973	1	FACETS	0.936	0.849	1	0.936	0.849	1	CLONAL	1	TRUE	0	0.64735959157602	1		292	201	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0044664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	191	392	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	0.557718495581207	4	FACETS	0.977	0.919	1	0.977	0.919	1	CLONAL	3	TRUE	1	0.557718495581207	4		392	364	SUCCESS
APC	324	MSKCC	GRCh37	5	112175524	112175524	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	150	344	0	ENST00000257430.4:c.4233del	p.Ser1411ArgfsTer4	p.S1411Rfs*4	ENST00000257430	NM_000038.5	1411	agT/ag	16/16	0.33443695913013	4	FACETS	0.954	0.88	1	0.954	0.88	1	INDETERMINATE	2	TRUE	2	0.557718495581207	4		344	439	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421519	32421519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	219	570	0	ENST00000332351.3:c.1073C>T	p.Thr358Met	p.T358M	ENST00000332351	NM_024426.4	358	aCg/aTg	6/10	0.38000172736109	5	FACETS	0.87	0.811	0.931	0.58	0.54	0.621	CLONAL	2	TRUE	2	0.557718495581207	5		570	829	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606700	29606700	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775514690	NA	P-0044664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	80	551	0	ENST00000389048.3:c.1180G>A	p.Gly394Arg	p.G394R	ENST00000389048	NM_004304.4	394	Ggg/Agg	5/29	0.557718495581207	3	FACETS	0.551	0.485	0.622	0.275	0.242	0.311	SUBCLONAL	1	TRUE	1	0.557718495581207	3		551	666	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222867	5222867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1193352037	NA	P-0044664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	188	532	0	ENST00000357368.4:c.2936G>A	p.Arg979Gln	p.R979Q	ENST00000357368	NM_002850.3	979	cGa/cAa	18/38	0.557718495581207	3	FACETS	1	0.981	1	0.588	0.545	0.633	CLONAL	1	TRUE	1	0.557718495581207	3		532	733	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577563	7577571	+	inframe_deletion	In_Frame_Del	DEL	TGTTACACA	TGTTACACA	-	novel	NA	P-0044664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	320	602	1	ENST00000269305.4:c.710_718del	p.Met237_Asn239del	p.M237_N239del	ENST00000269305	NM_001126112.2	237	aTGTGTAACAgt/agt	7/11	0.55629939273691	2	FACETS	0.934	0.891	0.977	0.934	0.891	0.977	CLONAL	2	TRUE	0	0.557718495581207	2		603	614	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633574	69633574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	183	220	0	ENST00000334134.2:c.128C>T	p.Pro43Leu	p.P43L	ENST00000334134	NM_005247.2	43	cCc/cTc	1/3	0.38000172736109	5	FACETS	0.943	0.881	1	0.943	0.881	1	CLONAL	3	TRUE	2	0.557718495581207	5		220	426	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99451936	99451936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1287177223	NA	P-0044664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	93	310	0	ENST00000268035.6:c.1270G>A	p.Asp424Asn	p.D424N	ENST00000268035	NM_000875.3	424	Gac/Aac	6/21	1	2	FACETS	0.926	0.831	1	0.926	0.831	1	CLONAL	1	TRUE	1	0.557718495581207	2		310	360	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259167	89259167	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	121	343	0	ENST00000336596.2:c.311G>T	p.Arg104Leu	p.R104L	ENST00000336596	NM_005233.5	104	cGa/cTa	3/17	0.463583230163086	4	FACETS	0.916	0.836	0.998	0.916	0.836	0.998	CLONAL	2	TRUE	2	0.557718495581207	4		343	369	SUCCESS
APC	324	MSKCC	GRCh37	5	112173348	112173349	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0044664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	84	301	0	ENST00000257430.4:c.2062_2063dup	p.Ala689GlnfsTer30	p.A689Qfs*30	ENST00000257430	NM_000038.5	686	aat/aaTCt	16/16	0.33443695913013	4	FACETS	1	0.976	1	0.688	0.613	0.767	INDETERMINATE	1	TRUE	2	0.557718495581207	4		301	341	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622147	117622147	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	20	260	0	ENST00000368508.3:c.6723A>C	p.Glu2241Asp	p.E2241D	ENST00000368508	NM_002944.2	2241	gaA/gaC	42/43	0.557718495581207	3	FACETS	0.411	0.315	0.523	0.206	0.157	0.262	SUBCLONAL	1	TRUE	1	0.557718495581207	3		260	223	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0045109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	422	469	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.627949134480282	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.635100191784921	2		469	639	SUCCESS
APC	324	MSKCC	GRCh37	5	112175171	112175171	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085373	NA	P-0045109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	149	295	0	ENST00000257430.4:c.3880C>T	p.Gln1294Ter	p.Q1294*	ENST00000257430	NM_000038.5	1294	Cag/Tag	16/16	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	2	TRUE	NA	0.635100191784921	2		295	226	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988037	85988037	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	34	189	0	ENST00000263360.6:c.982A>C	p.Ile328Leu	p.I328L	ENST00000263360	NM_003797.3	328	Att/Ctt	10/12	0.635100191784921	3	FACETS	0.635	0.523	0.76	0.318	0.261	0.38	SUBCLONAL	1	TRUE	1	0.635100191784921	3		189	222	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482898	140482898	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377093637	NA	P-0045109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	382	557	2	ENST00000288602.6:c.1237G>A	p.Val413Met	p.V413M	ENST00000288602	NM_004333.4	413	Gtg/Atg	10/18	0.613827632316447	3	FACETS	0.948	0.905	0.991	0.948	0.905	0.991	CLONAL	2	TRUE	1	0.635100191784921	3		559	836	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	73	415	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.82	0.72	0.928	0.82	0.72	0.928	CLONAL	1	TRUE	1	0.386172120880924	2		415	461	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	291	1445	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.978	1	1	0.996	1	CLONAL	2	TRUE	1	0.386172120880924	2		1452	711	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874637	35874637	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	92	398	1	ENST00000303115.3:c.799del	p.Arg267GlyfsTer28	p.R267Gfs*28	ENST00000303115	NM_002185.3	265	Aaa/aa	6/8	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.386172120880924	2		399	425	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374293	138374293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	146	543	0	ENST00000289153.2:c.3151G>A	p.Glu1051Lys	p.E1051K	ENST00000289153	NM_006219.2	1051	Gaa/Aaa	22/22	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.386172120880924	2		543	682	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563311	21563311	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs77919685	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	185	1026	2	ENST00000382592.4:c.608C>T	p.Ala203Val	p.A203V	ENST00000382592	NM_014572.2	203	gCg/gTg	4/8	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.386172120880924	2		1028	894	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	77	338	3	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.386172120880924	2		341	382	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	143	831	5	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.945	0.862	1	0.945	0.862	1	CLONAL	1	TRUE	1	0.386172120880924	2		836	784	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014077	70014077	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201351378	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	97	525	0	ENST00000394351.3:c.938G>A	p.Arg313Gln	p.R313Q	ENST00000394351	NM_000248.3	313	cGg/cAg	9/9	1	2	FACETS	0.975	0.873	1	0.975	0.873	1	CLONAL	1	TRUE	1	0.386172120880924	2		525	515	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	141	853	5	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.386172120880924	2		858	694	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	87	510	1	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.386172120880924	2		511	424	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646981	23646981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	171	782	8	ENST00000261584.4:c.886del	p.Met296Ter	p.M296*	ENST00000261584	NM_024675.3	296	Atg/tg	4/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.386172120880924	2		790	775	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152198	11152200	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	171	793	0	ENST00000358026.2:c.4487_4489del	p.Lys1496del	p.K1496del	ENST00000358026	NM_001128849.1	1494	atGAAg/atg	31/36	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.386172120880924	2		793	801	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720803	89720804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs786204892	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	39	328	0	ENST00000371953.3:c.955dup	p.Thr319AsnfsTer6	p.T319Nfs*6	ENST00000371953	NM_000314.4	318	-/A	8/9	1	2	FACETS	0.78	0.65	0.922	0.78	0.65	0.922	CLONAL	1	TRUE	1	0.386172120880924	2		328	259	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110203	3110203	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147528229	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	166	838	1	ENST00000078429.4:c.193G>A	p.Ala65Thr	p.A65T	ENST00000078429	NM_002067.2	65	Gcc/Acc	2/7	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.386172120880924	2		839	728	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755426	39755427	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	108	601	2	ENST00000288319.7:c.1338dup	p.Ala447CysfsTer19	p.A447Cfs*19	ENST00000288319	NM_182918.3	446	-/T	10/10	1	2	FACETS	0.871	0.783	0.964	0.871	0.783	0.964	CLONAL	1	TRUE	1	0.386172120880924	2		603	642	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354007	15354008	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	24	310	0	ENST00000263377.2:c.2872dup	p.Leu958ProfsTer135	p.L958Pfs*135	ENST00000263377	NM_058243.2	958	ctg/cCtg	14/20	1	2	FACETS	0.522	0.411	0.65	0.522	0.411	0.65	SUBCLONAL	1	TRUE	1	0.386172120880924	2		310	238	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	133	396	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	0.386172120880924	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.386172120880924	1		396	497	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	65	762	2	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	0.386172120880924	1	FACETS	0.423	0.366	0.485	0.423	0.366	0.485	SUBCLONAL	1	TRUE	0	0.386172120880924	1		764	642	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434182	12434182	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776687	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	119	496	0	ENST00000287820.6:c.556del	p.Ser186ValfsTer47	p.S186Vfs*47	ENST00000287820	NM_015869.4	184	Aaa/aa	4/7	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.386172120880924	2		496	527	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350772	89350775	+	frameshift_variant	Frame_Shift_Del	DEL	TTTG	TTTG	-	rs886039734	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	196	845	0	ENST00000301030.4:c.2175_2178del	p.Asn725LysfsTer23	p.N725Kfs*23	ENST00000301030	NM_001256183.1	725	aaCAAA/aa	9/13	1	2	FACETS	0.978	0.905	1	0.978	0.905	1	CLONAL	1	TRUE	1	0.386172120880924	2		845	1038	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214398	36214398	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs868041281	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	172	691	2	ENST00000222270.7:c.3057del	p.Gly1020AlafsTer4	p.G1020Afs*4	ENST00000222270	NM_014727.1	1018	Aaa/aa	7/37	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.386172120880924	2		693	779	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350105	89350105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368593056	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	220	947	0	ENST00000301030.4:c.2845C>T	p.Arg949Trp	p.R949W	ENST00000301030	NM_001256183.1	949	Cgg/Tgg	9/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.386172120880924	2		947	958	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099427	157099432	+	inframe_deletion	In_Frame_Del	DEL	CAGCAG	CAGCAG	-	rs587779744	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	38	313	0	ENST00000346085.5:c.381_386del	p.Gln130_Gln131del	p.Q130_Q131del	ENST00000346085	NM_020732.3	122	CAGCAG/-	1/20	1	2	FACETS	0.817	0.68	0.967	0.817	0.68	0.967	CLONAL	1	TRUE	1	0.386172120880924	2		313	241	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46587791	46587791	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	101	437	2	ENST00000263734.3:c.475del	p.Ser159AlafsTer12	p.S159Afs*12	ENST00000263734	NM_001430.4	157	Aaa/aa	5/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.386172120880924	2		439	471	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925402	114925402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748822481	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	188	822	0	ENST00000543371.1:c.1485del	p.Ser496ProfsTer5	p.S496Pfs*5	ENST00000543371	NM_001198531.1	494	Ccc/cc	14/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.386172120880924	2		822	834	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220100	133220100	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	158	874	0	ENST00000320574.5:c.4337T>C	p.Val1446Ala	p.V1446A	ENST00000320574	NM_006231.2	1446	gTg/gCg	34/49	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.386172120880924	2		874	796	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192645	138192645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776714084	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	103	414	0	ENST00000237289.4:c.281C>T	p.Ala94Val	p.A94V	ENST00000237289	NM_001270507.1	94	gCg/gTg	2/9	1	2	FACETS	0.941	0.844	1	0.941	0.844	1	CLONAL	1	TRUE	1	0.386172120880924	2		414	567	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092947	29092947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881688	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	126	520	0	ENST00000328354.6:c.1037G>A	p.Arg346His	p.R346H	ENST00000328354	NM_007194.3	346	cGt/cAt	10/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.386172120880924	2		520	568	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808001	3808001	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	134	574	1	ENST00000262367.5:c.3418C>T	p.Arg1140Trp	p.R1140W	ENST00000262367	NM_004380.2	1140	Cgg/Tgg	18/31	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.386172120880924	2		575	642	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1620979	1620979	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1329397192	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	212	1065	2	ENST00000344749.5:c.1081del	p.Gln361ArgfsTer33	p.Q361Rfs*33	ENST00000344749	NM_001136139.2	361	Cag/ag	13/19	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.386172120880924	2		1067	1035	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098009	178098009	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749353894	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	78	357	0	ENST00000397062.3:c.371C>T	p.Ala124Val	p.A124V	ENST00000397062	NM_006164.4	124	gCg/gTg	3/5	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.386172120880924	2		357	382	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11015633	11015634	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	131	496	1	ENST00000327064.4:c.235_236dup	p.Phe80SerfsTer46	p.F80Sfs*46	ENST00000327064	NM_199141.1	76	gat/gaTGt	2/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.386172120880924	2		497	640	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162429	47162429	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	100	448	0	ENST00000409792.3:c.3697del	p.Thr1233GlnfsTer3	p.T1233Qfs*3	ENST00000409792	NM_014159.6	1233	Aca/ca	3/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.386172120880924	2		448	461	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022738	12022738	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772622167	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	117	559	0	ENST00000396373.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000396373	NM_001987.4	282	Cgg/Tgg	5/8	0.118324706619286	4	FACETS	0.866	0.785	0.95	0.866	0.785	0.95	INDETERMINATE	2	TRUE	2	0.386172120880924	4		559	485	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244124	133244124	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794759	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	172	525	2	ENST00000320574.5:c.2284C>T	p.Arg762Trp	p.R762W	ENST00000320574	NM_006231.2	762	Cgg/Tgg	20/49	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.386172120880924	2		527	713	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271507	15271507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771682246	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	245	1205	1	ENST00000263388.2:c.6932C>T	p.Pro2311Leu	p.P2311L	ENST00000263388	NM_000435.2	2311	cCg/cTg	33/33	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.386172120880924	2		1206	1029	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1936885	1936885	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1445291234	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	72	462	1	ENST00000382891.5:c.1576del	p.Arg526GlufsTer72	p.R526Efs*72	ENST00000382891	NM_133335.3	524	Aaa/aa	7/22	1	2	FACETS	0.756	0.662	0.857	0.756	0.662	0.857	SUBCLONAL	1	TRUE	1	0.386172120880924	2		463	493	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258735	16258735	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	116	583	2	ENST00000375759.3:c.6005del	p.Asn2002MetfsTer20	p.N2002Mfs*20	ENST00000375759	NM_015001.2	2000	ggA/gg	11/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.386172120880924	2		585	547	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204515953	204515953	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	63	417	0	ENST00000367182.3:c.851T>G	p.Leu284Arg	p.L284R	ENST00000367182	NM_001278516.1	284	cTg/cGg	10/11	1	2	FACETS	0.81	0.703	0.924	0.81	0.703	0.924	CLONAL	1	TRUE	1	0.386172120880924	2		417	403	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715673	18715673	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	52	304	0	ENST00000266497.5:c.3504A>T	p.Lys1168Asn	p.K1168N	ENST00000266497		1168	aaA/aaT	25/31	1	2	FACETS	0.895	0.767	1	0.895	0.767	1	CLONAL	1	TRUE	1	0.386172120880924	2		304	301	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495604	56495604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142809206	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	96	580	0	ENST00000267101.3:c.3794G>A	p.Arg1265Gln	p.R1265Q	ENST00000267101	NM_001982.3	1265	cGg/cAg	28/28	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.386172120880924	2		580	461	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560386	95560386	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	137	565	0	ENST00000393063.1:c.5203C>A	p.Leu1735Met	p.L1735M	ENST00000393063	NM_030621.3	1735	Ctg/Atg	25/28	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.386172120880924	2		565	575	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482758	67482758	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	98	505	0	ENST00000327367.4:c.1162A>T	p.Thr388Ser	p.T388S	ENST00000327367	NM_005902.3	388	Act/Tct	9/9	1	2	FACETS	0.982	0.879	1	0.982	0.879	1	CLONAL	1	TRUE	1	0.386172120880924	2		505	517	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250839	99250839	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	99	501	0	ENST00000268035.6:c.143G>C	p.Arg48Pro	p.R48P	ENST00000268035	NM_000875.3	48	cGc/cCc	2/21	1	2	FACETS	0.986	0.883	1	0.986	0.883	1	CLONAL	1	TRUE	1	0.386172120880924	2		501	520	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134431	30134431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	164	748	2	ENST00000263025.4:c.100C>T	p.Gln34Ter	p.Q34*	ENST00000263025	NM_002746.2	34	Cag/Tag	1/9	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.386172120880924	2		750	742	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828136	50828136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528100675	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	65	338	0	ENST00000398568.2:c.2474C>T	p.Pro825Leu	p.P825L	ENST00000398568	NM_001042412.1	825	cCg/cTg	17/18	1	2	FACETS	0.962	0.839	1	0.962	0.839	1	CLONAL	1	TRUE	1	0.386172120880924	2		338	350	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618866	37618868	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs955200004	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	150	663	0	ENST00000447079.4:c.544_546del	p.Glu182del	p.E182del	ENST00000447079	NM_015083.1	181	aAGGag/aag	1/14	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.386172120880924	2		663	692	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184535	7184535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781007453	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	180	552	1	ENST00000302850.5:c.766C>T	p.Arg256Cys	p.R256C	ENST00000302850	NM_000208.2	256	Cgc/Tgc	3/22	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.386172120880924	2		553	764	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250885	10250885	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	163	789	1	ENST00000340748.4:c.3595A>G	p.Met1199Val	p.M1199V	ENST00000340748		1199	Atg/Gtg	32/40	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.386172120880924	2		790	697	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213533	36213533	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	244	1193	0	ENST00000222270.7:c.2635C>A	p.Leu879Met	p.L879M	ENST00000222270	NM_014727.1	879	Ctg/Atg	5/37	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.386172120880924	2		1193	1019	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716224	52716224	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	147	670	0	ENST00000322088.6:c.668T>C	p.Leu223Pro	p.L223P	ENST00000322088	NM_014225.5	223	cTg/cCg	6/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.386172120880924	2		670	656	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566886	212566886	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	65	214	0	ENST00000342788.4:c.1295T>C	p.Leu432Pro	p.L432P	ENST00000342788	NM_005235.2	432	cTg/cCg	12/28	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.386172120880924	2		214	286	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023506	31023506	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	116	506	0	ENST00000375687.4:c.2991G>C	p.Glu997Asp	p.E997D	ENST00000375687	NM_015338.5	997	gaG/gaC	13/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.386172120880924	2		506	525	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175836	24175836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	137	781	0	ENST00000263121.7:c.1064C>T	p.Thr355Ile	p.T355I	ENST00000263121	NM_003073.3	355	aCt/aTt	8/9	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.386172120880924	2		781	659	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374672	149374672	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	175	751	0	ENST00000360632.3:c.422A>G	p.Tyr141Cys	p.Y141C	ENST00000360632	NM_015472.4	141	tAc/tGc	2/7	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.386172120880924	2		751	771	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250933	153250933	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	44	245	0	ENST00000281708.4:c.1127T>C	p.Leu376Pro	p.L376P	ENST00000281708	NM_033632.3	376	cTg/cCg	8/12	1	2	FACETS	0.938	0.793	1	0.938	0.793	1	CLONAL	1	TRUE	1	0.386172120880924	2		245	243	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589238	67589238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748784250	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	81	366	0	ENST00000274335.5:c.1226G>A	p.Arg409Gln	p.R409Q	ENST00000274335		409	cGg/cAg	9/15	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.386172120880924	2		366	369	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047918	180047918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770591360	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	173	938	0	ENST00000261937.6:c.2257G>A	p.Ala753Thr	p.A753T	ENST00000261937	NM_182925.4	753	Gcc/Acc	15/30	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.386172120880924	2		938	834	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975415	13975415	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	127	483	0	ENST00000405192.2:c.472A>G	p.Thr158Ala	p.T158A	ENST00000405192	NM_001163147.1	158	Aca/Gca	7/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.386172120880924	2		483	561	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482918	140482918	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	151	724	1	ENST00000288602.6:c.1217T>C	p.Leu406Ser	p.L406S	ENST00000288602	NM_004333.4	406	tTa/tCa	10/18	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.386172120880924	2		725	732	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020741	37020741	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	147	609	0	ENST00000358127.4:c.104A>G	p.Asp35Gly	p.D35G	ENST00000358127	NM_001280556.1	35	gAt/gGt	2/10	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.386172120880924	2		609	738	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309058	137309058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139536056	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	224	1087	0	ENST00000481739.1:c.665C>T	p.Ser222Leu	p.S222L	ENST00000481739	NM_002957.4	222	tCg/tTg	5/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.386172120880924	2		1087	970	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006840	47006840	+	5_prime_UTR_variant	5'UTR	SNP	T	T	C	novel	NA	P-0045253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	197	420	0	ENST00000377604.3:c.-41T>C		p.*14*	ENST00000377604	NM_001204468.1	-/852		2/24	1	1	FACETS	0.99	0.929	1	1	0.994	1	CLONAL	2	TRUE	0	0.386172120880924	1		420	416	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456365	32456365	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	78	922	0	ENST00000332351.3:c.527G>T	p.Arg176Leu	p.R176L	ENST00000332351	NM_024426.4	176	cGc/cTc	1/10	1	2	FACETS	0.84	0.74	0.949	0.84	0.74	0.949	CLONAL	1	TRUE	1	0.328509268663311	2		922	565	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	43	290	1				ENST00000310581	NM_198253.2	-/1132			0.173485177411588	3	FACETS	0.883	0.746	1	0.883	0.746	1	CLONAL	2	TRUE	1	0.23	3		291	236	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0045437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	109	1196	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	1	2	FACETS	0.851	0.762	0.945	0.851	0.762	0.945	CLONAL	1	TRUE	1	0.23	2		1196	1114	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0045437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	106	863	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.921	0.824	1	0.921	0.824	1	CLONAL	1	TRUE	1	0.23	2		864	1001	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923045	44923048	+	frameshift_variant	Frame_Shift_Del	DEL	CTAT	CTAT	-	rs398122969	NA	P-0045437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	82	732	0	ENST00000377967.4:c.1909_1912del	p.Ser637ThrfsTer53	p.S637Tfs*53	ENST00000377967	NM_021140.2	636	CTATct/ct	16/29	1	2	FACETS	0.961	0.847	1	0.961	0.847	1	CLONAL	1	TRUE	1	0.23	2		732	742	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845569	63845569	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	21	263	1	ENST00000279873.7:c.1311del	p.Val438TyrfsTer41	p.V438Yfs*41	ENST00000279873	NM_032199.2	436	acA/ac	9/10	1	2	FACETS	0.853	0.66	1	0.853	0.66	1	CLONAL	1	TRUE	1	0.23	2		264	214	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652206	36652207	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045437-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	95	1083	0	ENST00000244741.5:c.329dup	p.His110GlnfsTer19	p.H110Qfs*19	ENST00000244741	NM_000389.4	110	cat/cAat	2/3	1	2	FACETS	0.803	0.713	0.899	0.803	0.713	0.899	CLONAL	1	TRUE	1	0.23	2		1083	1029	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0045463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	96	605	4	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.377524952990419	1	FACETS	0.467	0.416	0.522	0.467	0.416	0.522	SUBCLONAL	1	TRUE	0	0.410965246041298	1		609	794	SUCCESS
APC	324	MSKCC	GRCh37	5	112175219	112175219	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0045463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	63	160	0	ENST00000257430.4:c.3928A>T	p.Lys1310Ter	p.K1310*	ENST00000257430	NM_000038.5	1310	Aag/Tag	16/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.410965246041298	2		160	242	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0045463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	65	275	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.410965246041298	2		275	289	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776057	9776057	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148638384	NA	P-0045463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	233	786	1	ENST00000377346.4:c.521C>T	p.Ser174Leu	p.S174L	ENST00000377346	NM_005026.3	174	tCg/tTg	5/24	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.410965246041298	2		787	1058	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984430	201984430	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	106	531	1	ENST00000359651.3:c.1095G>T	p.Glu365Asp	p.E365D	ENST00000359651		365	gaG/gaT	8/8	0.304312022454662	3	FACETS	0.647	0.579	0.72	0.324	0.289	0.36	SUBCLONAL	1	TRUE	1	0.410965246041298	3		532	961	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201519	133201519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	184	769	0	ENST00000320574.5:c.6719G>A	p.Gly2240Glu	p.G2240E	ENST00000320574	NM_006231.2	2240	gGa/gAa	48/49	NA	2	FACETS	0.681	0.627	0.738			1	INDETERMINATE	1	TRUE	NA	0.410965246041298	2		769	1314	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209259	133209259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	382	719	1	ENST00000320574.5:c.6127G>A	p.Ala2043Thr	p.A2043T	ENST00000320574	NM_006231.2	2043	Gcc/Acc	44/49	NA	2	FACETS	0.837	0.796	0.878			1	INDETERMINATE	2	TRUE	NA	0.410965246041298	2		720	1111	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0045463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	158	555	0	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.377524952990419	1	FACETS	0.908	0.834	0.984	0.908	0.834	0.984	CLONAL	1	TRUE	0	0.410965246041298	1		555	673	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006635	62006635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1169314441	NA	P-0045463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	151	650	0	ENST00000392795.3:c.644G>A	p.Arg215Gln	p.R215Q	ENST00000392795	NM_001039933.1	215	cGg/cAg	6/6	1	2	FACETS	0.767	0.701	0.837	0.767	0.701	0.837	SUBCLONAL	1	TRUE	1	0.410965246041298	2		650	958	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290984	15290984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1438626607	NA	P-0045463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1228	128	885	1	ENST00000263388.2:c.3226C>T	p.Arg1076Cys	p.R1076C	ENST00000263388	NM_000435.2	1076	Cgt/Tgt	20/33	1	2	FACETS	0.459	0.415	0.507	0.459	0.415	0.507	SUBCLONAL	1	TRUE	1	0.410965246041298	2		886	1356	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937560	17937562	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0045463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	157	746	0	ENST00000458235.1:c.3365_3367del	p.Ser1122del	p.S1122del	ENST00000458235	NM_000215.3	1122	tCCTtt/ttt	24/24	1	2	FACETS	0.642	0.586	0.7	0.642	0.586	0.7	SUBCLONAL	1	TRUE	1	0.410965246041298	2		746	1191	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626736	12626736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149580968	NA	P-0045463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	125	378	0	ENST00000251849.4:c.1553G>A	p.Arg518Gln	p.R518Q	ENST00000251849	NM_002880.3	518	cGa/cAa	15/17	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.410965246041298	2		378	548	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958189	2958189	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	149	696	0	ENST00000396946.4:c.2543G>T	p.Arg848Leu	p.R848L	ENST00000396946	NM_032415.4	848	cGc/cTc	19/25	NA	2	FACETS	0.675	0.616	0.738			1	INDETERMINATE	1	TRUE	NA	0.410965246041298	2		696	1074	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0045514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	42	425	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.258004497560758	1	FACETS	0.75	0.628	0.886	0.75	0.628	0.886	SUBCLONAL	1	TRUE	0	0.258004497560758	1		425	378	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440957	56440957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35219874	NA	P-0045514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	108	497	0	ENST00000407977.2:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000407977		127	cGg/cAg	4/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.258004497560758	2		497	697	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510683	38510683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	99	518	1	ENST00000254066.5:c.937G>A	p.Ala313Thr	p.A313T	ENST00000254066	NM_000964.3	313	Gcc/Acc	7/9	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.258004497560758	2		519	657	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271228	153271228	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs866145254	NA	P-0045514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	20	203	0	ENST00000281708.4:c.550G>T	p.Gly184Ter	p.G184*	ENST00000281708	NM_033632.3	184	Gga/Tga	3/12	1	2	FACETS	0.649	0.497	0.825	0.649	0.497	0.825	SUBCLONAL	1	TRUE	1	0.258004497560758	2		203	239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577562	7577563	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTT	novel	NA	P-0045514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	80	422	0	ENST00000269305.4:c.715_718dup	p.Ser240LysfsTer25	p.S240Kfs*25	ENST00000269305	NM_001126112.2	240	agt/aAACAgt	7/11	0.258004497560758	1	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	0	0.258004497560758	1		422	533	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0045543-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	422	234	3				ENST00000310581	NM_198253.2	-/1132			0.819758846794357	7	FACETS	0.998	0.953	1	0.599	0.572	0.626	CLONAL	3	FALSE	2	0.819758846794357	7		237	1049	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0045543-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	302	813	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.765583443057742	3	FACETS	0.958	0.903	1	0.479	0.451	0.508	CLONAL	1	FALSE	1	0.819758846794357	3		813	1084	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941653	48941653	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0045543-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	89	220	0	ENST00000267163.4:c.963C>G	p.Tyr321Ter	p.Y321*	ENST00000267163	NM_000321.2	321	taC/taG	10/27	0.742425641566583	4	FACETS	1	0.982	1	0.874	0.821	0.922	CLONAL	3	FALSE	0	0.819758846794357	4		220	113	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs121913468	NA	P-0045543-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	261	561	0	ENST00000269571.5:c.2305G>C	p.Asp769His	p.D769H	ENST00000269571		769	Gac/Cac	19/27	0.765583443057742	3	FACETS	0.831	0.787	0.875	0.831	0.787	0.875	CLONAL	2	FALSE	1	0.819758846794357	3		561	540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0045543-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	776	889	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.765583443057742	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	FALSE	1	0.819758846794357	3		889	1320	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910587	29910587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41549014	NA	P-0045543-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	1864	1429	1	ENST00000376809.5:c.127G>A	p.Glu43Lys	p.E43K	ENST00000376809	NM_002116.7	43	Gag/Aag	2/8	0.726539405173577	4	FACETS	0.967	0.957	0.977	0.967	0.957	0.977	CLONAL	4	FALSE	0	0.819758846794357	4		1430	2139	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105892	27105892	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045543-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	874	586	1	ENST00000324856.7:c.5503C>T	p.Gln1835Ter	p.Q1835*	ENST00000324856	NM_006015.4	1835	Cag/Tag	20/20	0.819758846794357	4	FACETS	0.958	0.943	0.972	0.958	0.943	0.972	CLONAL	4	FALSE	0	0.819758846794357	4		587	1013	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10277291	10277291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257025095	NA	P-0045543-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	331	903	0	ENST00000340748.4:c.826G>A	p.Glu276Lys	p.E276K	ENST00000340748		276	Gaa/Aaa	10/40	0.819758846794357	3	FACETS	0.922	0.871	0.974	0.461	0.435	0.487	CLONAL	1	FALSE	1	0.819758846794357	3		903	1235	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456447	32456447	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045543-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	267	731	0	ENST00000332351.3:c.445G>A	p.Ala149Thr	p.A149T	ENST00000332351	NM_024426.4	149	Gcg/Acg	1/10	0.350706381325381	1	FACETS	0.68	0.644	0.717	0.68	0.644	0.717	INDETERMINATE	1	FALSE	0	0.819758846794357	1		731	565	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264627	11264627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045543-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	648	627	0	ENST00000361445.4:c.3935C>T	p.Pro1312Leu	p.P1312L	ENST00000361445	NM_004958.3	1312	cCg/cTg	26/58	0.742425641566583	4	FACETS	0.925	0.898	0.951	0.694	0.673	0.714	CLONAL	3	FALSE	0	0.819758846794357	4		627	1037	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623894	28623894	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045543-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	203	423	0	ENST00000241453.7:c.760C>G	p.Gln254Glu	p.Q254E	ENST00000241453	NM_004119.2	254	Cag/Gag	7/24	0.742425641566583	4	FACETS	1	0.985	1	0.808	0.771	0.842	CLONAL	3	FALSE	0	0.819758846794357	4		423	279	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135286	30135286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1179272987	NA	P-0045543-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	79	415	1	ENST00000331968.5:c.532G>A	p.Glu178Lys	p.E178K	ENST00000331968	NM_002742.2	178	Gaa/Aaa	3/18	0.819758846794357	3	FACETS	0.768	0.68	0.86	0.384	0.34	0.43	SUBCLONAL	1	FALSE	1	0.819758846794357	3		416	354	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014103	70014103	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs756384799	NA	P-0045543-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	137	563	0	ENST00000394351.3:c.964G>C	p.Glu322Gln	p.E322Q	ENST00000394351	NM_000248.3	322	Gag/Cag	9/9	0.819758846794357	3	FACETS	0.954	0.873	1	0.477	0.436	0.519	CLONAL	1	FALSE	1	0.819758846794357	3		563	494	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671985	30671985	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045543-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	627	934	1	ENST00000376406.3:c.4975G>A	p.Asp1659Asn	p.D1659N	ENST00000376406	NM_014641.2	1659	Gat/Aat	10/15	0.726539405173577	4	FACETS	1	0.996	1	0.615	0.595	0.635	CLONAL	2	FALSE	0	0.819758846794357	4		935	1132	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139804433	139804433	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1250915147	NA	P-0045543-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1415	324	862	0	ENST00000247668.2:c.590T>A	p.Ile197Asn	p.I197N	ENST00000247668	NM_021138.3	197	aTc/aAc	6/11	0.819758846794357	4	FACETS	0.827	0.779	0.877	0.276	0.259	0.293	CLONAL	1	FALSE	1	0.819758846794357	4		862	1739	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139804439	139804439	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045543-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1389	314	825	0	ENST00000247668.2:c.596G>C	p.Arg199Pro	p.R199P	ENST00000247668	NM_021138.3	199	cGg/cCg	6/11	0.819758846794357	4	FACETS	0.819	0.77	0.869	0.273	0.256	0.29	CLONAL	1	FALSE	1	0.819758846794357	4		825	1703	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41521897	41521897	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0045543-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	82	607	0	ENST00000263253.7:c.759T>G	p.Tyr253Ter	p.Y253*	ENST00000263253	NM_001429.3	253	taT/taG	3/31	0.623081153190462	6	FACETS	0.886	0.782	0.997	0.295	0.26	0.333	CLONAL	1	FALSE	3	0.819758846794357	6		607	596	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528627	89528627	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0045543-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	54	177	0	ENST00000336596.2:c.2927C>G	p.Ser976Ter	p.S976*	ENST00000336596	NM_005233.5	976	tCa/tGa	17/17	0.819758846794357	4	FACETS	0.838	0.721	0.964	0.419	0.36	0.482	CLONAL	1	FALSE	2	0.819758846794357	4		177	286	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0045582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	32	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.22	2		326	230	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0045582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	19	299	0	ENST00000311936.3:c.34_35delinsTT	p.Gly12Phe	p.G12F	ENST00000311936	NM_004985.3	12	GGt/TTt	2/5	1	2	FACETS	0.819	0.623	1	0.819	0.623	1	CLONAL	1	TRUE	1	0.22	2		299	211	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575194	48575194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555685186	NA	P-0045582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	10	247	0	ENST00000342988.3:c.388C>T	p.Pro130Ser	p.P130S	ENST00000342988	NM_005359.5	130	Cca/Tca	3/12	1	2	FACETS	0.514	0.348	0.721	0.514	0.348	0.721	SUBCLONAL	1	TRUE	1	0.22	2		247	177	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794917	42794917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199751904	NA	P-0045582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	37	593	0	ENST00000575354.2:c.1997G>A	p.Arg666His	p.R666H	ENST00000575354	NM_015125.3	666	cGt/cAt	10/20	1	2	FACETS	0.471	0.387	0.566	0.471	0.387	0.566	SUBCLONAL	1	TRUE	1	0.22	2		593	714	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578369	7578369	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0045582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	54	505	0	ENST00000269305.4:c.559+2T>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			1	2	FACETS	0.846	0.723	0.982	0.846	0.723	0.982	CLONAL	1	TRUE	1	0.22	2		505	580	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0045717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	56	275	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	0.898	0.781	1	0.898	0.781	1	CLONAL	1	TRUE	1	0.627013715832305	2		275	199	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0045717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	274	784	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.542179798542232	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.627013715832305	2		784	423	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448570	89448570	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1472226095	NA	P-0045717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	111	556	0	ENST00000336596.2:c.1534C>T	p.Arg512Ter	p.R512*	ENST00000336596	NM_005233.5	512	Cga/Tga	7/17	1	2	FACETS	0.874	0.792	0.96	0.874	0.792	0.96	CLONAL	1	TRUE	1	0.627013715832305	2		556	405	SUCCESS
APC	324	MSKCC	GRCh37	5	112175246	112175246	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1057517558	NA	P-0045717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	45	246	0	ENST00000257430.4:c.3956del	p.Pro1319LeufsTer2	p.P1319Lfs*2	ENST00000257430	NM_000038.5	1319	Cct/ct	16/16	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.627013715832305	2		246	142	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195475	102195475	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	67	505	0	ENST00000263464.3:c.235G>C	p.Gly79Arg	p.G79R	ENST00000263464	NM_001165.4	79	Gga/Cga	2/9	0.627013715832305	3	FACETS	0.804	0.703	0.912	0.402	0.351	0.456	CLONAL	1	TRUE	1	0.627013715832305	3		505	349	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675215	30675215	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	112	714	0	ENST00000376406.3:c.3030G>C	p.Lys1010Asn	p.K1010N	ENST00000376406	NM_014641.2	1010	aaG/aaC	9/15	0.627013715832305	4	FACETS	0.868	0.781	0.958	0.217	0.195	0.24	CLONAL	1	TRUE	0	0.627013715832305	4		714	670	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956983	2956983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223006535	NA	P-0045717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	98	747	0	ENST00000396946.4:c.2644G>A	p.Asp882Asn	p.D882N	ENST00000396946	NM_032415.4	882	Gac/Aac	20/25	NA	2	FACETS	0.62	0.555	0.689			1	INDETERMINATE	1	TRUE	NA	0.627013715832305	2		747	504	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0045717-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	45	275	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.352214347653778	3	FACETS	0.919	0.776	1	0.46	0.388	0.538	CLONAL	1	TRUE	1	0.352214347653778	3		275	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0045717-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	299	784	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.332243881895174	2	FACETS	0.965	0.911	1	0.965	0.911	1	CLONAL	2	TRUE	0	0.352214347653778	2		784	880	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448570	89448570	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1472226095	NA	P-0045717-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	125	556	0	ENST00000336596.2:c.1534C>T	p.Arg512Ter	p.R512*	ENST00000336596	NM_005233.5	512	Cga/Tga	7/17	1	2	FACETS	0.966	0.875	1	0.966	0.875	1	CLONAL	1	TRUE	1	0.352214347653778	2		556	735	SUCCESS
APC	324	MSKCC	GRCh37	5	112175246	112175246	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1057517558	NA	P-0045717-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	94	246	0	ENST00000257430.4:c.3956del	p.Pro1319LeufsTer2	p.P1319Lfs*2	ENST00000257430	NM_000038.5	1319	Cct/ct	16/16	0.352214347653778	3	FACETS	0.94	0.845	1	0.94	0.845	1	CLONAL	2	TRUE	1	0.352214347653778	3		246	334	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195475	102195475	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045717-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	40	505	0	ENST00000263464.3:c.235G>C	p.Gly79Arg	p.G79R	ENST00000263464	NM_001165.4	79	Gga/Cga	2/9	0.352214347653778	3	FACETS	0.383	0.317	0.456	0.191	0.158	0.228	SUBCLONAL	1	TRUE	1	0.352214347653778	3		505	698	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675215	30675215	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045717-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	179	714	0	ENST00000376406.3:c.3030G>C	p.Lys1010Asn	p.K1010N	ENST00000376406	NM_014641.2	1010	aaG/aaC	9/15	0.352214347653778	3	FACETS	1	0.952	1	0.349	0.321	0.379	CLONAL	1	TRUE	0	0.352214347653778	3		714	1141	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956983	2956983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223006535	NA	P-0045717-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	160	747	0	ENST00000396946.4:c.2644G>A	p.Asp882Asn	p.D882N	ENST00000396946	NM_032415.4	882	Gac/Aac	20/25	0.352214347653778	4	FACETS	1	0.935	1	0.342	0.313	0.373	CLONAL	1	TRUE	1	0.352214347653778	4		747	1197	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751185	57751185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045717-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	73	435	0	ENST00000274289.3:c.1682C>T	p.Ala561Val	p.A561V	ENST00000274289	NM_006622.3	561	gCt/gTt	12/14	0.352214347653778	3	FACETS	0.91	0.797	1	0.455	0.398	0.516	CLONAL	1	TRUE	1	0.352214347653778	3		435	536	SUCCESS
APC	324	MSKCC	GRCh37	5	112175419	112175419	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0045943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	62	240	0	ENST00000257430.4:c.4128T>A	p.Tyr1376Ter	p.Y1376*	ENST00000257430	NM_000038.5	1376	taT/taA	16/16	0.497276616431203	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	FALSE	0	0.497276616431203	2		240	111	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519986	NA	P-0045943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	273	386	0	ENST00000269305.4:c.809T>G	p.Phe270Cys	p.F270C	ENST00000269305	NM_001126112.2	270	tTt/tGt	8/11	0.380458132459569	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	FALSE	0	0.497276616431203	2		386	474	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212230	5212230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367918810	NA	P-0045943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	100	626	0	ENST00000357368.4:c.4801G>A	p.Val1601Ile	p.V1601I	ENST00000357368	NM_002850.3	1601	Gtc/Atc	32/38	0.497276616431203	3	FACETS	1	0.901	1	0.502	0.45	0.557	CLONAL	1	FALSE	1	0.497276616431203	3		626	500	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711275	114711276	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0045943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	182	282	0	ENST00000543371.1:c.290_291insT	p.Pro98AlafsTer47	p.P98Afs*47	ENST00000543371	NM_001198531.1	97	ggg/ggTg	3/14	0.353835164216929	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	FALSE	2	0.497276616431203	4		282	523	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511206	148511206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	42	399	1	ENST00000320356.2:c.1696C>T	p.Arg566Cys	p.R566C	ENST00000320356	NM_004456.4	566	Cgc/Tgc	15/20	0.406427582241675	5	FACETS	0.465	0.387	0.552	0.155	0.129	0.184	SUBCLONAL	1	FALSE	2	0.497276616431203	5		400	634	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0045955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	115	415	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.771809750620529	3	FACETS	0.967	0.878	1	0.484	0.439	0.53	CLONAL	1	TRUE	1	0.771809750620529	3		415	427	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0045955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	157	450	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.929	0.859	1	0.929	0.859	1	CLONAL	1	TRUE	1	0.771809750620529	2		451	438	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156088	119156088	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187952822	NA	P-0045955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	212	521	0	ENST00000264033.4:c.1753C>T	p.Arg585Cys	p.R585C	ENST00000264033	NM_005188.3	585	Cgc/Tgc	11/16	1	2	FACETS	0.913	0.853	0.973	0.913	0.853	0.973	CLONAL	1	TRUE	1	0.771809750620529	2		521	602	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977949	134977949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56186270	NA	P-0045955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	141	361	0	ENST00000398015.3:c.2942C>T	p.Thr981Met	p.T981M	ENST00000398015	NM_004441.4	981	aCg/aTg	16/16	1	2	FACETS	0.834	0.767	0.904	0.834	0.767	0.904	CLONAL	1	TRUE	1	0.771809750620529	2		361	438	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671684	30671684	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	209	544	0	ENST00000376406.3:c.5276G>A	p.Gly1759Glu	p.G1759E	ENST00000376406	NM_014641.2	1759	gGa/gAa	10/15	1	2	FACETS	0.944	0.882	1	0.944	0.882	1	CLONAL	1	TRUE	1	0.771809750620529	2		544	574	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845102	128845102	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759466401	NA	P-0045955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	278	569	0	ENST00000249373.3:c.596G>A	p.Arg199Gln	p.R199Q	ENST00000249373	NM_005631.4	199	cGg/cAg	3/12	NA	2	FACETS	0.991	0.936	1			1	INDETERMINATE	1	TRUE	NA	0.771809750620529	2		569	727	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434644	110434644	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	188	499	0	ENST00000375856.3:c.3757T>C	p.Tyr1253His	p.Y1253H	ENST00000375856	NM_003749.2	1253	Tac/Cac	1/2	1	2	FACETS	0.912	0.849	0.976	0.912	0.849	0.976	CLONAL	1	TRUE	1	0.771809750620529	2		499	534	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831156	72831156	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	24	374	0	ENST00000268489.5:c.5425C>G	p.Leu1809Val	p.L1809V	ENST00000268489	NM_006885.3	1809	Ctt/Gtt	9/10	1	2	FACETS	0.146	0.114	0.183	0.146	0.114	0.183	SUBCLONAL	1	TRUE	1	0.771809750620529	2		374	426	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925343	131925344	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0045955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	30	106	1	ENST00000265335.6:c.1266_1267delinsAT	p.Thr423Ser	p.T423S	ENST00000265335		422	gaGAct/gaATct	9/25	1	2	FACETS	0.74	0.611	0.88	0.74	0.611	0.88	SUBCLONAL	1	TRUE	1	0.771809750620529	2		107	105	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969123	93969123	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs149602525	NA	P-0045955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	104	257	0	ENST00000369303.4:c.1873G>T	p.Ala625Ser	p.A625S	ENST00000369303	NM_004440.3	625	Gcc/Tcc	10/17	1	2	FACETS	0.959	0.872	1	0.959	0.872	1	CLONAL	1	TRUE	1	0.771809750620529	2		257	281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578181	7578181	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138983188	NA	P-0046055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	214	649	1	ENST00000269305.4:c.668C>T	p.Pro223Leu	p.P223L	ENST00000269305	NM_001126112.2	223	cCt/cTt	6/11	0.330499275388544	3	FACETS	0.768	0.716	0.822	0.768	0.716	0.822	SUBCLONAL	2	TRUE	1	0.430154367213309	3		650	787	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0046055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	329	870	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.330499275388544	3	FACETS	0.759	0.717	0.802	0.759	0.717	0.802	SUBCLONAL	2	TRUE	1	0.430154367213309	3		870	1224	SUCCESS
APC	324	MSKCC	GRCh37	5	112175328	112175328	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	127	230	0	ENST00000257430.4:c.4037C>A	p.Ser1346Ter	p.S1346*	ENST00000257430	NM_000038.5	1346	tCa/tAa	16/16	0.430154367213309	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	3	TRUE	0	0.430154367213309	3		230	234	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727513	88727513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374069724	NA	P-0046055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	159	602	0	ENST00000360948.2:c.266G>A	p.Arg89His	p.R89H	ENST00000360948	NM_001012338.2	89	cGc/cAc	3/19	0.172459928630555	3	FACETS	0.805	0.742	0.87	0.805	0.742	0.87	INDETERMINATE	2	TRUE	1	0.430154367213309	3		602	558	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440334	187440334	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	76	573	0	ENST00000232014.4:c.2033G>A	p.Arg678His	p.R678H	ENST00000232014	NM_001130845.1	678	cGc/cAc	10/10	0.330499275388544	3	FACETS	0.675	0.592	0.764	0.338	0.296	0.382	SUBCLONAL	1	TRUE	1	0.430154367213309	3		573	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519986	NA	P-0046103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	286	386	0	ENST00000269305.4:c.809T>G	p.Phe270Cys	p.F270C	ENST00000269305	NM_001126112.2	270	tTt/tGt	8/11	0.551750009625217	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.551750009625217	2		386	455	SUCCESS
APC	324	MSKCC	GRCh37	5	112175346	112175356	+	frameshift_variant	Frame_Shift_Del	DEL	TTGAATTTTCT	TTGAATTTTCT	-	novel	NA	P-0046103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	93	128	0	ENST00000257430.4:c.4056_4066del	p.Glu1353ArgfsTer18	p.E1353Rfs*18	ENST00000257430	NM_000038.5	1352	gTTGAATTTTCT/g	16/16	0.551750009625217	3	FACETS	0.925	0.852	0.996	0.925	0.852	0.996	CLONAL	3	TRUE	0	0.551750009625217	3		128	155	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343060	70343060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	270	283	0	ENST00000374080.3:c.1601C>T	p.Ala534Val	p.A534V	ENST00000374080		534	gCg/gTg	11/45	0.551750009625217	4	FACETS	0.868	0.822	0.915	1	0.992	1	CLONAL	3	TRUE	2	0.551750009625217	4		283	583	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983288	15983288	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1299209343	NA	P-0046103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	143	227	0	ENST00000268712.3:c.3491C>G	p.Ser1164Cys	p.S1164C	ENST00000268712	NM_006311.3	1164	tCt/tGt	26/46	0.551750009625217	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.551750009625217	2		227	216	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117948	70117948	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	172	269	0	ENST00000245479.2:c.416T>A	p.Leu139Gln	p.L139Q	ENST00000245479	NM_000346.3	139	cTg/cAg	1/3	0.551750009625217	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.551750009625217	3		269	350	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157303	106157303	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	26	167	0	ENST00000380013.4:c.2204G>C	p.Ser735Thr	p.S735T	ENST00000380013	NM_001127208.2	735	aGt/aCt	3/11	0.551750009625217	3	FACETS	0.485	0.385	0.598	0.242	0.192	0.299	SUBCLONAL	1	TRUE	1	0.551750009625217	3		167	248	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993026	90993026	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	62	248	0	ENST00000265433.3:c.416C>T	p.Thr139Ile	p.T139I	ENST00000265433	NM_002485.4	139	aCt/aTt	4/16	0.551750009625217	3	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	1	0.551750009625217	3		248	136	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982157	201982157	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	112	697	1	ENST00000359651.3:c.684del	p.Ser229AlafsTer25	p.S229Afs*25	ENST00000359651		227	ttC/tt	5/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.218543047407198	2		698	769	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	80	483	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.218543047407198	1	FACETS	0.762	0.674	0.855	1	0.978	1	SUBCLONAL	2	TRUE	0	0.218543047407198	1		483	428	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	102	757	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.218543047407198	2		757	662	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	147	789	3	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.218543047407198	2		792	924	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	97	383	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.959	1	1	0.988	1	CLONAL	2	TRUE	1	0.218543047407198	2		383	392	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	129	1149	10	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.218543047407198	2		1159	813	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030613	48030613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779617676	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	73	418	0	ENST00000234420.5:c.3227G>A	p.Arg1076His	p.R1076H	ENST00000234420	NM_000179.2	1076	cGc/cAc	5/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.218543047407198	2		418	563	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248030	98248030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772368023	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	51	477	1	ENST00000331920.6:c.521C>T	p.Ala174Val	p.A174V	ENST00000331920	NM_000264.3	174	gCg/gTg	3/24	1	2	FACETS	0.78	0.663	0.91	0.78	0.663	0.91	CLONAL	1	TRUE	1	0.218543047407198	2		478	598	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602667	55602667	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1330182390	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	60	208	0	ENST00000288135.5:c.2488C>T	p.Arg830Ter	p.R830*	ENST00000288135	NM_000222.2	830	Cga/Tga	18/21	1	2	FACETS	0.773	0.67	0.885	1	0.971	1	SUBCLONAL	2	TRUE	1	0.218543047407198	2		208	355	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032029	10032029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747214620	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	203	552	2	ENST00000330684.3:c.794C>T	p.Thr265Met	p.T265M	ENST00000330684	NM_001134407.1	265	aCg/aTg	3/13	0.181350845295393	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	1	0.218543047407198	4		554	703	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572450	41572450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	142	782	0	ENST00000263253.7:c.4979C>T	p.Thr1660Met	p.T1660M	ENST00000263253	NM_001429.3	1660	aCg/aTg	30/31	0.218543047407198	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.218543047407198	1		782	797	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391075	89391075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs995238704	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	87	525	0	ENST00000336596.2:c.1141C>T	p.Arg381Cys	p.R381C	ENST00000336596	NM_005233.5	381	Cgc/Tgc	5/17	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.218543047407198	2		525	617	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867304	45867304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1372639983	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	70	778	0	ENST00000391945.4:c.889G>A	p.Ala297Thr	p.A297T	ENST00000391945	NM_000400.3	297	Gcc/Acc	10/23	1	2	FACETS	0.847	0.738	0.966	0.847	0.738	0.966	CLONAL	1	TRUE	1	0.218543047407198	2		778	756	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158132	27158132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773256013	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	60	333	0	ENST00000380036.4:c.356G>A	p.Arg119His	p.R119H	ENST00000380036	NM_000459.3	119	cGt/cAt	2/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.218543047407198	2		333	422	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706974	117706974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776027945	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	39	411	1	ENST00000368508.3:c.2176G>A	p.Val726Ile	p.V726I	ENST00000368508	NM_002944.2	726	Gtt/Att	15/43	1	2	FACETS	0.529	0.437	0.632	0.529	0.437	0.632	SUBCLONAL	1	TRUE	1	0.218543047407198	2		412	675	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804304	43804304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763568293	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	98	536	0	ENST00000372470.3:c.304C>T	p.Arg102Cys	p.R102C	ENST00000372470	NM_005373.2	102	Cgt/Tgt	3/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.218543047407198	2		536	649	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724632	162724632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767283136	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	50	383	0	ENST00000367921.3:c.404G>A	p.Arg135His	p.R135H	ENST00000367921	NM_006182.2	135	cGt/cAt	5/18	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.218543047407198	2		383	440	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910883	114910883	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1477809102	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	53	480	0	ENST00000543371.1:c.1001+1G>A		p.X334_splice	ENST00000543371	NM_001198531.1	334			1	2	FACETS	0.959	0.818	1	0.959	0.818	1	CLONAL	1	TRUE	1	0.218543047407198	2		480	506	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435253	110435253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771232244	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	70	352	1	ENST00000375856.3:c.3148G>A	p.Val1050Ile	p.V1050I	ENST00000375856	NM_003749.2	1050	Gtt/Att	1/2	1	2	FACETS	0.863	0.757	0.977	1	0.979	1	CLONAL	2	TRUE	1	0.218543047407198	2		353	371	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647400	3647400	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763869769	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	97	652	2	ENST00000294008.3:c.1663G>A	p.Val555Met	p.V555M	ENST00000294008	NM_032444.2	555	Gtg/Atg	7/15	0.181350845295393	4	FACETS	1	0.98	1	0.494	0.44	0.551	CLONAL	1	TRUE	1	0.218543047407198	4		654	730	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592354	29592354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659197	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	60	367	0	ENST00000356175.3:c.4769G>A	p.Arg1590Gln	p.R1590Q	ENST00000356175	NM_000267.3	1590	cGg/cAg	35/57	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.218543047407198	2		367	515	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819345	3819345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	65	480	0	ENST00000262367.5:c.2890G>A	p.Ala964Thr	p.A964T	ENST00000262367	NM_004380.2	964	Gca/Aca	15/31	0.181350845295393	4	FACETS	1	0.905	1	0.352	0.305	0.404	CLONAL	1	TRUE	1	0.218543047407198	4		480	686	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723074	52723074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	100	533	0	ENST00000322088.6:c.1259G>A	p.Arg420Gln	p.R420Q	ENST00000322088	NM_014225.5	420	cGg/cAg	10/15	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.218543047407198	2		533	622	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209366	98209366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773676486	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	92	652	0	ENST00000331920.6:c.4172G>A	p.Arg1391Gln	p.R1391Q	ENST00000331920	NM_000264.3	1391	cGg/cAg	23/24	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.218543047407198	2		652	666	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264751	11264751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1384864432	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	101	590	0	ENST00000361445.4:c.3811G>A	p.Ala1271Thr	p.A1271T	ENST00000361445	NM_004958.3	1271	Gct/Act	26/58	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.218543047407198	2		590	707	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800444	32800444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758423176	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	133	785	0	ENST00000374899.4:c.1103G>A	p.Arg368Gln	p.R368Q	ENST00000374899	NM_018833.2	368	cGg/cAg	6/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.218543047407198	2		785	948	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104264060	104264060	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	119	564	1	ENST00000369902.3:c.151C>A	p.Pro51Thr	p.P51T	ENST00000369902	NM_016169.3	51	Ccg/Acg	1/12	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.218543047407198	2		565	751	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123875183	123875183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751091053	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	55	359	0	ENST00000330479.4:c.139G>A	p.Val47Ile	p.V47I	ENST00000330479	NM_020382.3	47	Gta/Ata	3/9	1	2	FACETS	0.961	0.822	1	0.961	0.822	1	CLONAL	1	TRUE	1	0.218543047407198	2		359	524	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248871	133248871	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	95	578	0	ENST00000320574.5:c.1724A>G	p.Glu575Gly	p.E575G	ENST00000320574	NM_006231.2	575	gAg/gGg	16/49	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.218543047407198	2		578	695	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435697	110435697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745496477	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	52	429	0	ENST00000375856.3:c.2704C>T	p.Pro902Ser	p.P902S	ENST00000375856	NM_003749.2	902	Ccc/Tcc	1/2	1	2	FACETS	0.881	0.75	1	0.881	0.75	1	CLONAL	1	TRUE	1	0.218543047407198	2		429	540	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873741	35873741	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	102	495	0	ENST00000216797.5:c.110T>C	p.Met37Thr	p.M37T	ENST00000216797	NM_020529.2	37	aTg/aCg	1/6	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.218543047407198	2		495	698	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671741	67671741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1247514121	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	38	572	0	ENST00000264010.4:c.2150C>T	p.Thr717Met	p.T717M	ENST00000264010	NM_006565.3	717	aCg/aTg	12/12	0.218543047407198	1	FACETS	0.534	0.441	0.639	0.534	0.441	0.639	SUBCLONAL	1	TRUE	0	0.218543047407198	1		572	580	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368266	45368266	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	88	341	0	ENST00000262160.6:c.1336C>A	p.Leu446Ile	p.L446I	ENST00000262160	NM_005901.5	446	Cta/Ata	11/11	0.218543047407198	1	FACETS	0.881	0.786	0.982	1	0.984	1	CLONAL	2	TRUE	0	0.218543047407198	1		341	407	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661674	227661674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760535759	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	81	671	0	ENST00000305123.5:c.1781G>A	p.Arg594His	p.R594H	ENST00000305123	NM_005544.2	594	cGt/cAt	1/2	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.218543047407198	2		671	627	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478746	57478746	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	64	313	0	ENST00000371085.3:c.332G>T	p.Ser111Ile	p.S111I	ENST00000371085	NM_000516.4	111	aGc/aTc	5/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.218543047407198	2		313	431	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267003	41267003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144087793	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	85	371	0	ENST00000349496.5:c.674G>A	p.Arg225His	p.R225H	ENST00000349496	NM_001904.3	225	cGt/cAt	5/15	1	2	FACETS	0.779	0.691	0.873	1	0.98	1	SUBCLONAL	2	TRUE	1	0.218543047407198	2		371	499	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937482	178937482	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs762727422	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	104	363	0	ENST00000263967.3:c.1870A>G	p.Thr624Ala	p.T624A	ENST00000263967	NM_006218.2	624	Aca/Gca	12/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.218543047407198	2		363	667	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339730	116339730	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	49	305	0	ENST00000397752.3:c.592G>T	p.Gly198Cys	p.G198C	ENST00000397752	NM_000245.2	198	Ggc/Tgc	2/21	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.218543047407198	2		305	387	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117861248	117861249	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	24	298	0	ENST00000297338.2:c.1640dup	p.Asp548ArgfsTer26	p.D548Rfs*26	ENST00000297338	NM_006265.2	547	ggc/ggGc	13/14	1	2	FACETS	0.458	0.358	0.573	0.458	0.358	0.573	SUBCLONAL	1	TRUE	1	0.218543047407198	2		298	480	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002755	37002755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1234226210	NA	P-0046312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	64	511	1	ENST00000358127.4:c.494C>T	p.Thr165Met	p.T165M	ENST00000358127	NM_001280556.1	165	aCg/aTg	5/10	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.218543047407198	2		512	529	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052998	180052998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867280522	NA	P-0046565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	291	1377	0	ENST00000261937.6:c.1292C>T	p.Ser431Phe	p.S431F	ENST00000261937	NM_182925.4	431	tCc/tTc	10/30	0.169558995014239	2	FACETS	0.924	0.868	0.983	0.462	0.434	0.492	INDETERMINATE	1	TRUE	0	0.437246496809638	2		1377	1440	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579378	7579379	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0046565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	607	776	0	ENST00000269305.4:c.308dup	p.Tyr103Ter	p.Y103*	ENST00000269305	NM_001126112.2	103	tac/taAc	4/11	0.395898485995279	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	TRUE	0	0.437246496809638	3		776	1115	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164069	47164069	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	13	338	0	ENST00000409792.3:c.2057T>C	p.Phe686Ser	p.F686S	ENST00000409792	NM_014159.6	686	tTt/tCt	3/21	0.437246496809638	5	FACETS	0.569	0.407	0.766	0.19	0.135	0.256	SUBCLONAL	1	TRUE	2	0.437246496809638	5		338	173	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412986	63412986	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	325	411	0	ENST00000330258.3:c.181G>C	p.Gly61Arg	p.G61R	ENST00000330258	NM_152424.3	61	Ggt/Cgt	2/2	0.437246496809638	2	FACETS	0.86	0.823	0.898			1	CLONAL	3	TRUE	NA	0.437246496809638	2		411	576	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	19	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.18	0.136	0.233	0.18	0.136	0.233	SUBCLONAL	1	TRUE	1	0.35	2		487	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0046672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	44	606	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	1	2	FACETS	0.264	0.22	0.313	0.264	0.22	0.313	SUBCLONAL	1	TRUE	1	0.35	2		606	953	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0046672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	20	249	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	1	2	FACETS	0.358	0.274	0.457	0.358	0.274	0.457	SUBCLONAL	1	TRUE	1	0.35	2		249	319	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0046735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	73	378	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.281156691903869	1	FACETS	0.881	0.773	0.997	0.881	0.773	0.997	CLONAL	1	TRUE	0	0.309801631330063	1		378	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579529	7579529	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658483	NA	P-0046735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	167	862	0	ENST00000269305.4:c.158G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tGg/tAg	4/11	0.309801631330063	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.309801631330063	1		862	822	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273940	10273940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	159	1042	0	ENST00000330684.3:c.329C>T	p.Ala110Val	p.A110V	ENST00000330684	NM_001134407.1	110	gCc/gTc	2/13	0.309801631330063	3	FACETS	1	0.92	1	0.503	0.46	0.548	CLONAL	1	TRUE	1	0.309801631330063	3		1042	1178	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965572	93965572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	32	351	0	ENST00000369303.4:c.2356G>A	p.Asp786Asn	p.D786N	ENST00000369303	NM_004440.3	786	Gat/Aat	13/17	1	2	FACETS	0.566	0.46	0.686	0.566	0.46	0.686	SUBCLONAL	1	TRUE	1	0.309801631330063	2		351	365	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449442	31449442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766022493	NA	P-0046735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	87	426	1	ENST00000344624.3:c.2767C>T	p.Arg923Trp	p.R923W	ENST00000344624		923	Cgg/Tgg	19/33	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.309801631330063	2		427	561	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936077	178936085	+	inframe_deletion	In_Frame_Del	DEL	TCTCTGAAA	TCTCTGAAA	-	novel	NA	P-0046735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	154	447	0	ENST00000263967.3:c.1621_1629del	p.Ser541_Ile543del	p.S541_I543del	ENST00000263967	NM_006218.2	540	cTCTCTGAAAtc/ctc	10/21	0.309801631330063	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.309801631330063	2		447	472	SUCCESS
APC	324	MSKCC	GRCh37	5	112170856	112170883	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCACAGGTATATATAGAGTTTTATATT	ACCACAGGTATATATAGAGTTTTATATT	-	novel	NA	P-0046735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	65	405	0	ENST00000257430.4:c.1954_1958+23del		p.X652_splice	ENST00000257430	NM_000038.5	652		15/16	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.309801631330063	2		405	391	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256219	16256219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	183	717	1	ENST00000375759.3:c.3484G>A	p.Asp1162Asn	p.D1162N	ENST00000375759	NM_015001.2	1162	Gac/Aac	11/15	0.705758324360687	4	FACETS	1	0.988	1	0.452	0.419	0.487	CLONAL	1	FALSE	1	0.705758324360687	4		718	652	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023030	27023030	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	54	68	0	ENST00000324856.7:c.136G>T	p.Glu46Ter	p.E46*	ENST00000324856	NM_006015.4	46	Gag/Tag	1/20	NA	2	FACETS	0.879	0.791	0.965			1	INDETERMINATE	2	FALSE	NA	0.705758324360687	2		68	87	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981276	201981276	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	278	1082	0	ENST00000359651.3:c.355G>T	p.Asp119Tyr	p.D119Y	ENST00000359651		119	Gac/Tac	2/8	0.705758324360687	5	FACETS	1	0.984	1	0.383	0.359	0.408	CLONAL	1	FALSE	2	0.705758324360687	5		1082	1412	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206918	102206918	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	114	415	0	ENST00000263464.3:c.1546G>C	p.Glu516Gln	p.E516Q	ENST00000263464	NM_001165.4	516	Gaa/Caa	7/9	0.535434676360367	4	FACETS	1	0.982	1	0.459	0.417	0.503	CLONAL	1	FALSE	1	0.705758324360687	4		415	400	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871770	12871770	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	104	236	0	ENST00000228872.4:c.487C>G	p.Gln163Glu	p.Q163E	ENST00000228872	NM_004064.3	163	Caa/Gaa	2/3	0.705758324360687	2	FACETS	1	0.976	1	0.604	0.551	0.658	CLONAL	1	FALSE	0	0.705758324360687	2		236	244	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21626529	21626529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	182	623	0	ENST00000421138.2:c.1403C>T	p.Ser468Leu	p.S468L	ENST00000421138		468	tCa/tTa	13/16	0.705758324360687	2	FACETS	1	0.988	1	0.627	0.586	0.669	CLONAL	1	FALSE	0	0.705758324360687	2		623	411	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427912	49427912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	234	880	0	ENST00000301067.7:c.10678G>A	p.Asp3560Asn	p.D3560N	ENST00000301067	NM_003482.3	3560	Gat/Aat	38/54	0.616164445564053	6	FACETS	1	0.991	1	0.468	0.436	0.502	CLONAL	1	FALSE	3	0.705758324360687	6		880	1138	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448094	49448094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	201	697	0	ENST00000301067.7:c.506C>T	p.Ser169Leu	p.S169L	ENST00000301067	NM_003482.3	169	tCa/tTa	4/54	0.616164445564053	6	FACETS	0.787	0.73	0.845	0.524	0.486	0.564	SUBCLONAL	2	FALSE	3	0.705758324360687	6		697	873	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864378	57864378	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	335	1049	0	ENST00000228682.2:c.1855C>A	p.Pro619Thr	p.P619T	ENST00000228682	NM_005269.2	619	Cct/Act	12/12	0.616164445564053	6	FACETS	0.994	0.94	1	0.662	0.626	0.699	CLONAL	2	FALSE	3	0.705758324360687	6		1049	1152	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42002948	42002948	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	183	614	0	ENST00000219905.7:c.2485G>C	p.Glu829Gln	p.E829Q	ENST00000219905	NM_001164273.1	829	Gaa/Caa	8/24	0.530633116918073	5	FACETS	0.754	0.698	0.812			1	SUBCLONAL	2	FALSE	NA	0.705758324360687	5		614	708	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	253	662	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	0.458421528646598	6	FACETS	0.848	0.793	0.903	0.565	0.529	0.602	CLONAL	2	FALSE	3	0.705758324360687	6		662	1020	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865899	56865899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779103749	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	132	428	0	ENST00000308159.5:c.1231G>A	p.Glu411Lys	p.E411K	ENST00000308159	NM_014669.4	411	Gag/Aag	11/22	0.458421528646598	6	FACETS	0.764	0.696	0.835	0.51	0.464	0.557	SUBCLONAL	2	FALSE	3	0.705758324360687	6		428	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	287	834	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.705758324360687	2	FACETS		NA	1	1	0.996	1	NA	3	FALSE	0	0.705758324360687	2		834	314	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040727	16040727	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	126	291	0	ENST00000268712.3:c.1408-1G>C		p.X470_splice	ENST00000268712	NM_006311.3	470			0.705758324360687	2	FACETS	1	0.984	1	0.647	0.597	0.698	CLONAL	1	FALSE	0	0.705758324360687	2		291	276	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761247	59761247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	441	846	1	ENST00000259008.2:c.3160G>A	p.Glu1054Lys	p.E1054K	ENST00000259008	NM_032043.2	1054	Gaa/Aaa	20/20	0.705758324360687	4	FACETS	1	0.991	1	0.562	0.539	0.586	CLONAL	2	FALSE	0	0.705758324360687	4		847	948	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78865595	78865595	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	237	746	0	ENST00000306801.3:c.2059G>C	p.Glu687Gln	p.E687Q	ENST00000306801	NM_020761.2	687	Gaa/Caa	18/34	0.705758324360687	7	FACETS	1	0.991	1	0.204	0.189	0.218	CLONAL	1	FALSE	0	0.705758324360687	7		746	1303	SUCCESS
YES1	7525	MSKCC	GRCh37	18	732848	732848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755971181	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	266	751	0	ENST00000314574.4:c.1409G>A	p.Arg470Gln	p.R470Q	ENST00000314574	NM_005433.3	470	cGa/cAa	11/12	0.278228125599104	5	FACETS	1	0.971	1			1	INDETERMINATE	3	FALSE	NA	0.705758324360687	5		751	501	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291582	15291582	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	111	1163	0	ENST00000263388.2:c.3052A>T	p.Thr1018Ser	p.T1018S	ENST00000263388	NM_000435.2	1018	Act/Tct	19/33	0.705758324360687	4	FACETS	0.483	0.433	0.536			1	SUBCLONAL	1	FALSE	NA	0.705758324360687	4		1163	1111	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189334	99189334	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	244	785	0	ENST00000074304.5:c.2590C>T	p.Gln864Ter	p.Q864*	ENST00000074304	NM_001134224.1	864	Cag/Tag	24/26	0.705758324360687	4	FACETS	0.826	0.775	0.877	0.551	0.517	0.585	CLONAL	2	FALSE	1	0.705758324360687	4		785	714	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096592	178096592	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	132	429	0	ENST00000397062.3:c.739C>T	p.Leu247Phe	p.L247F	ENST00000397062	NM_006164.4	247	Ctt/Ttt	5/5	0.705758324360687	4	FACETS	0.82	0.752	0.89	0.547	0.501	0.593	CLONAL	2	FALSE	1	0.705758324360687	4		429	389	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729866	39729866	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs990347811	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	200	595	0	ENST00000361337.2:c.1181C>T	p.Ser394Phe	p.S394F	ENST00000361337	NM_003286.2	394	tCt/tTt	13/21	0.509614425793387	6	FACETS	0.829	0.77	0.891	0.553	0.513	0.594	CLONAL	2	FALSE	3	0.705758324360687	6		595	824	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755705	39755705	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs547051424	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	205	755	1	ENST00000288319.7:c.1060C>T	p.Arg354Trp	p.R354W	ENST00000288319	NM_182918.3	354	Cgg/Tgg	10/10	0.705758324360687	3	FACETS	0.78	0.73	0.83	0.78	0.73	0.83	SUBCLONAL	2	FALSE	1	0.705758324360687	3		756	504	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42840456	42840456	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	271	613	0	ENST00000398585.3:c.1292C>T	p.Ser431Leu	p.S431L	ENST00000398585	NM_001135099.1	431	tCa/tTa	12/14	0.705758324360687	4	FACETS	1	0.99	1	0.418	0.392	0.444	CLONAL	1	FALSE	1	0.705758324360687	4		613	1045	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051626	30051626	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	168	454	0	ENST00000338641.4:c.560G>C	p.Arg187Thr	p.R187T	ENST00000338641	NM_000268.3	187	aGa/aCa	6/16	0.530633116918073	5	FACETS	0.893	0.826	0.962			1	CLONAL	2	FALSE	NA	0.705758324360687	5		454	549	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077543	30077543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	173	636	0	ENST00000338641.4:c.1690G>A	p.Glu564Lys	p.E564K	ENST00000338641	NM_000268.3	564	Gag/Aag	15/16	0.530633116918073	5	FACETS	0.769	0.711	0.83			1	SUBCLONAL	2	FALSE	NA	0.705758324360687	5		636	656	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	174	928	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	0.289851238517829	3	FACETS	0.999	0.923	1	0.499	0.461	0.539	INDETERMINATE	1	FALSE	1	0.705758324360687	3		928	668	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961237	1961237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	211	706	0	ENST00000382891.5:c.3025G>A	p.Asp1009Asn	p.D1009N	ENST00000382891	NM_133335.3	1009	Gat/Aat	17/22	0.62673533386957	4	FACETS	1	0.977	1	0.373	0.347	0.401	CLONAL	1	FALSE	1	0.705758324360687	4		706	911	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127539	55127539	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	191	483	0	ENST00000257290.5:c.327G>C	p.Glu109Asp	p.E109D	ENST00000257290	NM_006206.4	109	gaG/gaC	3/23	0.62673533386957	4	FACETS	0.903	0.843	0.965	0.602	0.562	0.644	CLONAL	2	FALSE	1	0.705758324360687	4		483	511	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751931	57751931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55768901	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	159	597	1	ENST00000274289.3:c.1306G>A	p.Glu436Lys	p.E436K	ENST00000274289	NM_006622.3	436	Gaa/Aaa	10/14	0.705758324360687	6	FACETS	1	0.983	1			1	CLONAL	1	FALSE	NA	0.705758324360687	6		598	844	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176619009	176619009	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	197	549	0	ENST00000439151.2:c.1052C>T	p.Ser351Leu	p.S351L	ENST00000439151	NM_022455.4	351	tCa/tTa	3/23	0.630876550666329	5	FACETS	0.792	0.735	0.85	0.396	0.367	0.425	SUBCLONAL	2	FALSE	1	0.705758324360687	5		549	726	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839889	27839889	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	328	972	2	ENST00000328488.2:c.205C>T	p.Gln69Ter	p.Q69*	ENST00000328488	NM_003533.2	69	Cag/Tag	1/1	0.705758324360687	6	FACETS	0.817	0.771	0.865	0.545	0.514	0.577	CLONAL	2	FALSE	3	0.705758324360687	6		974	1371	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32191635	32191635	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	265	1026	0	ENST00000375023.3:c.71G>A	p.Arg24Lys	p.R24K	ENST00000375023	NM_004557.3	24	aGa/aAa	1/30	0.705758324360687	4	FACETS	1	0.988	1	0.603	0.565	0.642	CLONAL	1	FALSE	2	0.705758324360687	4		1026	1062	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32191641	32191641	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	255	1008	0	ENST00000375023.3:c.65G>C	p.Arg22Thr	p.R22T	ENST00000375023	NM_004557.3	22	aGa/aCa	1/30	0.705758324360687	4	FACETS	1	0.987	1	0.601	0.562	0.64	CLONAL	1	FALSE	2	0.705758324360687	4		1008	1026	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265569	152265569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	252	721	0	ENST00000206249.3:c.1022C>T	p.Ser341Leu	p.S341L	ENST00000206249	NM_000125.3	341	tCg/tTg	4/8	0.705758324360687	4	FACETS	0.8	0.752	0.85	0.534	0.501	0.567	SUBCLONAL	2	FALSE	1	0.705758324360687	4		721	761	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414370	6414370	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	93	195	0	ENST00000356142.4:c.4C>T	p.Gln2Ter	p.Q2*	ENST00000356142	NM_018890.3	2	Cag/Tag	1/7	0.358598783433757	5	FACETS	0.84	0.755	0.929	0.56	0.503	0.619	INDETERMINATE	2	FALSE	2	0.705758324360687	5		195	323	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729400	41729400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	307	849	0	ENST00000242208.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000242208	NM_002192.2	377	Cgc/Tgc	3/3	0.705758324360687	6	FACETS	1	0.964	1	0.686	0.647	0.725	CLONAL	2	FALSE	3	0.705758324360687	6		849	1020	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949054	151949054	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	199	626	0	ENST00000262189.6:c.1591G>C	p.Glu531Gln	p.E531Q	ENST00000262189	NM_170606.2	531	Gag/Cag	11/59	0.705758324360687	3	FACETS	1	0.985	1	0.602	0.56	0.644	CLONAL	1	FALSE	1	0.705758324360687	3		626	634	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56882350	56882350	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	218	693	0	ENST00000519728.1:c.1048C>T	p.Gln350Ter	p.Q350*	ENST00000519728	NM_002350.3	350	Cag/Tag	10/13	0.705758324360687	8	FACETS	1	0.99	1	0.283	0.262	0.305	CLONAL	1	FALSE	3	0.705758324360687	8		693	1361	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870260	44870260	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	126	586	0	ENST00000377967.4:c.439C>T	p.Gln147Ter	p.Q147*	ENST00000377967	NM_021140.2	147	Cag/Tag	5/29	0.705758324360687	3	FACETS	1	0.938	1			1	CLONAL	1	FALSE	NA	0.705758324360687	3		586	466	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429293	47429293	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	54	876	0	ENST00000377045.4:c.1421C>A	p.Ala474Glu	p.A474E	ENST00000377045	NM_001654.4	474	gCa/gAa	14/16	0.705758324360687	4	FACETS	0.264	0.224	0.308			1	SUBCLONAL	1	FALSE	NA	0.705758324360687	4		876	989	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224729	123224729	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	137	588	0	ENST00000218089.9:c.3493C>T	p.Gln1165Ter	p.Q1165*	ENST00000218089	NM_001042749.1	1165	Caa/Taa	32/35	NA	2	FACETS	0.735	0.672	0.801			1	INDETERMINATE	1	FALSE	NA	0.705758324360687	2		588	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577126	7577126	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	98	524	0	ENST00000269305.4:c.812A>T	p.Glu271Val	p.E271V	ENST00000269305	NM_001126112.2	271	gAg/gTg	8/11	0.212418519597209	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.212418519597209	1		524	656	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	21	275	0	ENST00000257430.4:c.4199C>A	p.Ser1400Ter	p.S1400*	ENST00000257430	NM_000038.5	1400	tCg/tAg	16/16	1	2	FACETS	0.601	0.463	0.762	0.601	0.463	0.762	SUBCLONAL	1	TRUE	1	0.212418519597209	2		275	329	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358979	81358979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754502188	NA	P-0047054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	28	431	0	ENST00000222390.5:c.982C>T	p.Arg328Cys	p.R328C	ENST00000222390	NM_000601.4	328	Cgt/Tgt	8/18	1	2	FACETS	0.571	0.455	0.703	0.571	0.455	0.703	SUBCLONAL	1	TRUE	1	0.212418519597209	2		431	462	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999677	100999677	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	79	823	0	ENST00000325455.5:c.125C>A	p.Ser42Ter	p.S42*	ENST00000325455	NM_001202474.3	42	tCg/tAg	1/8	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.212418519597209	2		823	733	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0047197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	148	1045	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.35958434848458	3	FACETS	0.913	0.834	0.997	0.457	0.417	0.499	CLONAL	1	TRUE	1	0.428710543483388	3		1046	918	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0047197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	256	1025	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.35958434848458	3	FACETS	0.964	0.907	1	0.964	0.907	1	CLONAL	2	TRUE	1	0.428710543483388	3		1026	752	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028835	47028835	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	259	438	0	ENST00000377604.3:c.139G>T	p.Glu47Ter	p.E47*	ENST00000377604	NM_001204468.1	47	Gag/Tag	3/24	0.327120693805628	2	FACETS	1	0.99	1			1	CLONAL	2	TRUE	NA	0.428710543483388	2		438	514	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372447	118372447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782001089	NA	P-0047197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	111	443	0	ENST00000534358.1:c.6380G>A	p.Arg2127Gln	p.R2127Q	ENST00000534358	NM_005933.3	2127	cGa/cAa	26/36	0.428710543483388	2	FACETS	0.935	0.843	1	0.467	0.421	0.516	CLONAL	1	TRUE	0	0.428710543483388	2		443	554	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0047200-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	19	457	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.862	0.654	1	0.862	0.654	1	CLONAL	1	TRUE	1	0.13	2		457	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0047200-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	46	757	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.13	2		757	652	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0047200-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	23	321	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.967	0.753	1	0.967	0.753	1	CLONAL	1	TRUE	1	0.13	2		321	366	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508389	106508389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758375337	NA	P-0047200-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	25	457	1	ENST00000359195.3:c.383C>T	p.Thr128Met	p.T128M	ENST00000359195	NM_002649.2	128	aCg/aTg	2/11	1	2	FACETS	0.966	0.761	1	0.966	0.761	1	CLONAL	1	TRUE	1	0.13	2		458	398	SUCCESS
APC	324	MSKCC	GRCh37	5	112175358	112175358	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047200-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	13	0	0	ENST00000257430.4:c.4067C>A	p.Ser1356Ter	p.S1356*	ENST00000257430	NM_000038.5	1356	tCa/tAa	16/16	1	2	FACETS	0.717	0.511	0.969	0.717	0.511	0.969	CLONAL	1	TRUE	1	0.13	2		0	279	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43773107	43773108	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047200-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	36	661	0	ENST00000382044.4:c.484dup	p.Ser162PhefsTer5	p.S162Ffs*5	ENST00000382044	NM_001141980.1	162	tcc/tTcc	5/28	1	2	FACETS	0.936	0.768	1	0.936	0.768	1	CLONAL	1	TRUE	1	0.13	2		661	592	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858179	40858179	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047200-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	46	780	2	ENST00000428826.2:c.1685G>A	p.Arg562His	p.R562H	ENST00000428826		562	cGc/cAc	16/21	1	2	FACETS	0.931	0.782	1	0.931	0.782	1	CLONAL	1	TRUE	1	0.13	2		782	760	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0047231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	36	583	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.292059379689537	4	FACETS	0.541	0.444	0.65	0.27	0.222	0.325	SUBCLONAL	1	TRUE	2	0.329520936041006	4		583	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781504	NA	P-0047231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	230	1023	2	ENST00000269305.4:c.314G>T	p.Gly105Val	p.G105V	ENST00000269305	NM_001126112.2	105	gGc/gTc	4/11	0.265258943903614	2	FACETS	0.979	0.917	1	0.979	0.917	1	CLONAL	2	TRUE	0	0.329520936041006	2		1025	713	SUCCESS
APC	324	MSKCC	GRCh37	5	112175351	112175352	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0047231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	51	252	0	ENST00000257430.4:c.4062_4063del	p.Ser1355PhefsTer19	p.S1355Ffs*19	ENST00000257430	NM_000038.5	1354	TTt/t	16/16	0.329520936041006	2	FACETS	0.938	0.812	1	0.938	0.812	1	CLONAL	2	TRUE	0	0.329520936041006	2		252	165	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628773	187628773	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	152	721	0	ENST00000441802.2:c.2209A>G	p.Ile737Val	p.I737V	ENST00000441802	NM_005245.3	737	Att/Gtt	2/27	0.292059379689537	4	FACETS	0.949	0.871	1	0.949	0.871	1	CLONAL	2	TRUE	2	0.329520936041006	4		721	646	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519732	176519732	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	113	1055	0	ENST00000292408.4:c.1004C>T	p.Ala335Val	p.A335V	ENST00000292408	NM_213647.1	335	gCa/gTa	8/18	0.329520936041006	2	FACETS	1	0.935	1	0.524	0.472	0.579	CLONAL	1	TRUE	0	0.329520936041006	2		1055	654	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579310	7579310	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1555526469	NA	P-0047234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	198	553	0	ENST00000269305.4:c.375+2T>C		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.3	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	FALSE	0	0.3	2		553	553	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0047234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	126	519	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.3	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	FALSE	1	0.3	3		519	457	SUCCESS
APC	324	MSKCC	GRCh37	5	112174094	112174095	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs863225332	NA	P-0047234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	66	283	0	ENST00000257430.4:c.2804dup	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	tac/tAac	16/16	0.229285371498221	4	FACETS	0.869	0.76	0.986	0.869	0.76	0.986	CLONAL	2	FALSE	2	0.3	4		283	329	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0047234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	35	109	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	0.240364780974049	4	FACETS	0.838	0.688	1	0.419	0.344	0.503	CLONAL	1	FALSE	2	0.3	4		109	362	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851230	63851230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1271514044	NA	P-0047234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	94	595	0	ENST00000279873.7:c.2008C>T	p.His670Tyr	p.H670Y	ENST00000279873	NM_032199.2	670	Cat/Tat	10/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.3	2		595	575	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068121	94068121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149408123	NA	P-0047234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	43	193	0	ENST00000369303.4:c.841C>T	p.Arg281Cys	p.R281C	ENST00000369303	NM_004440.3	281	Cgt/Tgt	4/17	0.229285371498221	4	FACETS	0.875	0.74	1	0.875	0.74	1	CLONAL	2	FALSE	2	0.3	4		193	213	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177877	142177877	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376735982	NA	P-0047234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	77	275	0	ENST00000350721.4:c.7426C>T	p.Arg2476Cys	p.R2476C	ENST00000350721	NM_001184.3	2476	Cgt/Tgt	44/47	0.240364780974049	4	FACETS	0.904	0.799	1	0.904	0.799	1	CLONAL	2	FALSE	2	0.3	4		275	369	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992692	68992692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529924687	NA	P-0047234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	59	446	0	ENST00000288368.4:c.1657G>A	p.Glu553Lys	p.E553K	ENST00000288368	NM_024870.2	553	Gaa/Aaa	16/40	0.3	3	FACETS	1	0.935	1	0.573	0.494	0.657	CLONAL	1	FALSE	1	0.3	3		446	395	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125052	46125052	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	32	239	0	ENST00000334344.6:c.239G>T	p.Arg80Ile	p.R80I	ENST00000334344	NM_152641.2	80	aGa/aTa	3/21	0.3	3	FACETS	1	0.843	1	0.518	0.422	0.624	CLONAL	1	FALSE	1	0.3	3		239	237	SUCCESS
APC	324	MSKCC	GRCh37	5	112175321	112175322	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0047234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	54	186	0	ENST00000257430.4:c.4031dup	p.Glu1345ArgfsTer9	p.E1345Rfs*9	ENST00000257430	NM_000038.5	1344	tca/tCca	16/16	0.229285371498221	4	FACETS	0.94	0.811	1	0.94	0.811	1	CLONAL	2	FALSE	2	0.3	4		186	249	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	236	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.58821239460425	3	FACETS	0.927	0.873	0.982	0.927	0.873	0.982	CLONAL	2	TRUE	1	0.58821239460425	3		457	560	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928065	178928076	+	inframe_deletion	In_Frame_Del	DEL	TACCTCATGGAT	TACCTCATGGAT	-	novel	NA	P-0047322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	103	591	0	ENST00000263967.3:c.1345_1356del	p.Pro449_Leu452del	p.P449_L452del	ENST00000263967	NM_006218.2	448	gTACCTCATGGATta/gta	8/21	1	2	FACETS	0.684	0.614	0.757	0.684	0.614	0.757	SUBCLONAL	1	TRUE	1	0.58821239460425	2		591	512	SUCCESS
APC	324	MSKCC	GRCh37	5	112173975	112173975	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	127	379	0	ENST00000257430.4:c.2684C>A	p.Ser895Ter	p.S895*	ENST00000257430	NM_000038.5	895	tCa/tAa	16/16	1	2	FACETS	0.973	0.888	1	0.973	0.888	1	CLONAL	1	TRUE	1	0.58821239460425	2		379	444	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880998	37880998	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs144434331	NA	P-0047322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	304	842	1	ENST00000269571.5:c.2327G>T	p.Gly776Val	p.G776V	ENST00000269571		776	gGt/gTt	20/27	1	2	FACETS	0.882	0.831	0.934	0.882	0.831	0.934	CLONAL	1	TRUE	1	0.58821239460425	2		843	1172	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941125	36941125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375879178	NA	P-0047322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	285	858	1	ENST00000361632.4:c.214G>A	p.Gly72Arg	p.G72R	ENST00000361632		72	Ggg/Agg	3/16	1	2	FACETS	0.963	0.907	1	0.963	0.907	1	CLONAL	1	TRUE	1	0.58821239460425	2		859	1006	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058228	42058228	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	85	308	0	ENST00000219905.7:c.7948C>T	p.Arg2650Ter	p.R2650*	ENST00000219905	NM_001164273.1	2650	Cga/Tga	24/24	1	2	FACETS	0.923	0.825	1	0.923	0.825	1	CLONAL	1	TRUE	1	0.58821239460425	2		308	313	SUCCESS
APC	324	MSKCC	GRCh37	5	112157658	112157658	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	106	418	0	ENST00000257430.4:c.1378G>T	p.Glu460Ter	p.E460*	ENST00000257430	NM_000038.5	460	Gaa/Taa	11/16	1	2	FACETS	0.936	0.846	1	0.936	0.846	1	CLONAL	1	TRUE	1	0.58821239460425	2		418	385	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176671268	176671268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1562251167	NA	P-0047322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	90	394	0	ENST00000439151.2:c.4375G>A	p.Gly1459Arg	p.G1459R	ENST00000439151	NM_022455.4	1459	Gga/Aga	9/23	1	2	FACETS	0.89	0.796	0.987	0.89	0.796	0.987	CLONAL	1	TRUE	1	0.58821239460425	2		394	344	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989642	68989642	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767992923	NA	P-0047322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	189	519	0	ENST00000288368.4:c.1580G>A	p.Arg527His	p.R527H	ENST00000288368	NM_024870.2	527	cGc/cAc	15/40	1	2	FACETS	0.98	0.909	1	0.98	0.909	1	CLONAL	1	TRUE	1	0.58821239460425	2		519	656	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0047378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	157	635	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.474932521471588	3	FACETS	0.94	0.861	1	0.47	0.43	0.511	CLONAL	1	TRUE	1	0.479976773226845	3		636	863	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0047378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	167	283	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	0.458193742785908	4	FACETS	0.977	0.904	1	0.977	0.904	1	CLONAL	2	TRUE	2	0.479976773226845	4		283	527	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473647	67473647	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886039137	NA	P-0047378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	364	868	4	ENST00000327367.4:c.727C>T	p.Arg243Cys	p.R243C	ENST00000327367	NM_005902.3	243	Cgc/Tgc	6/9	0.479976773226845	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.479976773226845	2		872	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577508	7577508	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060501201	NA	P-0047378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	393	921	2	ENST00000269305.4:c.773A>G	p.Glu258Gly	p.E258G	ENST00000269305	NM_001126112.2	258	gAa/gGa	7/11	0.479976773226845	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.479976773226845	2		923	767	SUCCESS
APC	324	MSKCC	GRCh37	5	112175751	112175751	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	191	356	0	ENST00000257430.4:c.4460del	p.Thr1487IlefsTer20	p.T1487Ifs*20	ENST00000257430	NM_000038.5	1487	aCt/at	16/16	0.458193742785908	4	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	2	0.479976773226845	4		356	572	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247344	153247344	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	162	377	0	ENST00000281708.4:c.1458G>A	p.Trp486Ter	p.W486*	ENST00000281708	NM_033632.3	486	tgG/tgA	10/12	0.289704257154567	4	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	2	0.479976773226845	4		377	486	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860469	151860469	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	67	839	1	ENST00000262189.6:c.10193G>A	p.Arg3398Gln	p.R3398Q	ENST00000262189	NM_170606.2	3398	cGg/cAg	43/59	0.480205421238096	4	FACETS	0.372	0.322	0.427	0.186	0.161	0.214	SUBCLONAL	1	TRUE	2	0.479976773226845	4		840	1111	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207092	1207092	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555735008	NA	P-0047473-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	49	1182	0	ENST00000326873.7:c.180del	p.Tyr60Ter	p.Y60*	ENST00000326873	NM_000455.4	60	taC/ta	1/10	0.267869946684606	1	FACETS	0.36	0.304	0.423	0.36	0.304	0.423	SUBCLONAL	1	TRUE	0	0.267869946684606	1		1182	879	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0047485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	50	449	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.0147709629199606	3	FACETS	0.855	0.727	0.994	0.427	0.363	0.497	INDETERMINATE	1	TRUE	1	0.341676568570266	3		449	401	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250883	153250883	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	31	276	2	ENST00000281708.4:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000281708	NM_033632.3	393	Cga/Tga	8/12	0.0147709629199606	3	FACETS	0.817	0.664	0.989	0.409	0.332	0.495	INDETERMINATE	1	TRUE	1	0.341676568570266	3		278	260	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	46	808	0	ENST00000263121.7:c.1130G>T	p.Arg377Leu	p.R377L	ENST00000263121	NM_003073.3	377	cGt/cTt	9/9	0.341676568570266	1	FACETS	0.44	0.371	0.517	0.44	0.371	0.517	SUBCLONAL	1	TRUE	0	0.341676568570266	1		808	507	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155420	99155420	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	38	431	0	ENST00000074304.5:c.646C>T	p.Arg216Ter	p.R216*	ENST00000074304	NM_001134224.1	216	Cga/Tga	9/26	1	2	FACETS	0.614	0.509	0.732	0.614	0.509	0.732	SUBCLONAL	1	TRUE	1	0.341676568570266	2		431	362	SUCCESS
APC	324	MSKCC	GRCh37	5	112176016	112176016	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	17	226	0	ENST00000257430.4:c.4725del	p.Glu1576LysfsTer74	p.E1576Kfs*74	ENST00000257430	NM_000038.5	1575	ctA/ct	16/16	0.0948890925854859	3	FACETS	0.626	0.469	0.811	0.313	0.234	0.406	INDETERMINATE	1	TRUE	1	0.341676568570266	3		226	186	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551118	41551118	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0047485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	25	434	1	ENST00000263253.7:c.3261+1G>A		p.X1087_splice	ENST00000263253	NM_001429.3	1087			0.341676568570266	1	FACETS	0.286	0.225	0.357	0.286	0.225	0.357	SUBCLONAL	1	TRUE	0	0.341676568570266	1		435	424	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306613	163306613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1368454011	NA	P-0047485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	31	332	0	ENST00000271452.3:c.410C>T	p.Thr137Met	p.T137M	ENST00000271452	NM_145697.2	137	aCg/aTg	6/14	1	2	FACETS	0.67	0.544	0.811	0.67	0.544	0.811	SUBCLONAL	1	TRUE	1	0.341676568570266	2		332	271	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663851	241663851	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	33	290	0	ENST00000366560.3:c.1276G>C	p.Ala426Pro	p.A426P	ENST00000366560	NM_000143.3	426	Gct/Cct	9/10	1	2	FACETS	0.683	0.558	0.822	0.683	0.558	0.822	SUBCLONAL	1	TRUE	1	0.341676568570266	2		290	283	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45391476	45391476	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	45	261	0	ENST00000262160.6:c.684A>C	p.Glu228Asp	p.E228D	ENST00000262160	NM_005901.5	228	gaA/gaC	6/11	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.341676568570266	2		261	254	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264428	46264428	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	31	295	0	ENST00000371998.3:c.1475T>A	p.Ile492Lys	p.I492K	ENST00000371998		492	aTa/aAa	11/23	1	2	FACETS	0.611	0.495	0.741	0.611	0.495	0.741	SUBCLONAL	1	TRUE	1	0.341676568570266	2		295	297	SUCCESS
APC	324	MSKCC	GRCh37	5	112174929	112174935	+	frameshift_variant	Frame_Shift_Del	DEL	CAAGCAG	CAAGCAG	-	novel	NA	P-0047485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	16	156	0	ENST00000257430.4:c.3638_3644del	p.Ser1213LeufsTer50	p.S1213Lfs*50	ENST00000257430	NM_000038.5	1213	tCAAGCAGt/tt	16/16	0.0948890925854859	3	FACETS	0.649	0.482	0.846	0.324	0.241	0.423	INDETERMINATE	1	TRUE	1	0.341676568570266	3		156	169	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	860	1023	0	ENST00000269305.4:c.472C>G	p.Arg158Gly	p.R158G	ENST00000269305	NM_001126112.2	158	Cgc/Ggc	5/11	0.693077433942774	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.699148124248006	2		1023	1215	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0047545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	11964	866	7	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.699148124248006	24	FACETS	1	0.999	1			1	CLONAL	23	TRUE	NA	0.699148124248006	24		873	12863	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867540	35867541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs869312857	NA	P-0047545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	37	207	0	ENST00000303115.3:c.361dup	p.Ile121AsnfsTer8	p.I121Nfs*8	ENST00000303115	NM_002185.3	118	-/A	3/8	0.321423166791799	4	FACETS	0.638	0.528	0.759	0.159	0.132	0.19	INDETERMINATE	1	TRUE	0	0.699148124248006	4		207	282	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321073	137321073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768721235	NA	P-0047545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	274	673	1	ENST00000481739.1:c.1030G>A	p.Ala344Thr	p.A344T	ENST00000481739	NM_002957.4	344	Gcc/Acc	7/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.699148124248006	2		674	713	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106123	27106123	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	205	481	0	ENST00000324856.7:c.5734G>A	p.Asp1912Asn	p.D1912N	ENST00000324856	NM_006015.4	1912	Gat/Aat	20/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.699148124248006	2		481	566	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143063	30143063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	555	1041	1	ENST00000389048.3:c.463G>A	p.Val155Ile	p.V155I	ENST00000389048	NM_004304.4	155	Gtc/Atc	1/29	0.323382957641426	3	FACETS	0.869	0.836	0.902	0.869	0.836	0.902	INDETERMINATE	2	TRUE	1	0.699148124248006	3		1042	1233	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652814	212652814	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	103	274	0	ENST00000342788.4:c.492A>C	p.Gln164His	p.Q164H	ENST00000342788	NM_005235.2	164	caA/caC	4/28	0.639225294262084	3	FACETS	1	0.944	1	0.533	0.481	0.587	CLONAL	1	TRUE	1	0.699148124248006	3		274	373	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860365	151860365	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	141	416	0	ENST00000262189.6:c.10297C>T	p.Gln3433Ter	p.Q3433*	ENST00000262189	NM_170606.2	3433	Cag/Tag	43/59	0.699148124248006	4	FACETS	0.895	0.816	0.977	0.298	0.272	0.326	CLONAL	1	TRUE	1	0.699148124248006	4		416	766	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	277	638	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.345652677435553	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.34	2		638	786	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	76	364	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.887	0.78	1	0.887	0.78	1	CLONAL	1	TRUE	1	0.34	2		365	504	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	90	498	4	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.908	0.807	1	0.908	0.807	1	CLONAL	1	TRUE	1	0.34	2		502	583	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	116	445	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.916	0.826	1	0.916	0.826	1	CLONAL	1	TRUE	1	0.34	2		445	745	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	113	412	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.34	2		412	557	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	76	360	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.844	0.741	0.953	0.844	0.741	0.953	CLONAL	1	TRUE	1	0.34	2		360	530	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317878	8317878	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151311972	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	102	524	0	ENST00000356435.5:c.5735C>T	p.Thr1912Met	p.T1912M	ENST00000356435		1912	aCg/aTg	35/35	1	2	FACETS	0.985	0.883	1	0.985	0.883	1	CLONAL	1	TRUE	1	0.34	2		524	609	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271991	15271991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777802431	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	145	793	0	ENST00000263388.2:c.6448C>T	p.Arg2150Cys	p.R2150C	ENST00000263388	NM_000435.2	2150	Cgc/Tgc	33/33	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.34	2		793	780	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840607	36840607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528158465	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	147	791	2	ENST00000358127.4:c.1126G>A	p.Ala376Thr	p.A376T	ENST00000358127	NM_001280556.1	376	Gcc/Acc	10/10	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.34	2		793	855	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973547	15973547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143125039	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	80	477	0	ENST00000268712.3:c.4445G>A	p.Arg1482Gln	p.R1482Q	ENST00000268712	NM_006311.3	1482	cGg/cAg	31/46	1	2	FACETS	0.871	0.769	0.981	0.871	0.769	0.981	CLONAL	1	TRUE	1	0.34	2		477	540	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844127	68844127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780537	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	152	739	0	ENST00000261769.5:c.715G>A	p.Gly239Arg	p.G239R	ENST00000261769	NM_004360.3	239	Ggg/Agg	6/16	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.34	2		739	875	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216091	7216091	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1332522267	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	134	556	1	ENST00000380728.2:c.968G>A	p.Arg323Gln	p.R323Q	ENST00000380728		323	cGa/cAa	11/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.34	2		557	673	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346077	89346077	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	19	123	0	ENST00000301030.4:c.6873G>T	p.Glu2291Asp	p.E2291D	ENST00000301030	NM_001256183.1	2291	gaG/gaT	9/13	1	2	FACETS	1	0.775	1	1	0.775	1	CLONAL	1	TRUE	1	0.34	2		123	111	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593466	48593466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064796102	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	114	512	0	ENST00000342988.3:c.1217C>T	p.Ala406Val	p.A406V	ENST00000342988	NM_005359.5	406	gCg/gTg	10/12	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.34	2		512	615	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924421	131924421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146370443	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	81	448	0	ENST00000265335.6:c.1094G>A	p.Arg365Gln	p.R365Q	ENST00000265335		365	cGa/cAa	8/25	1	2	FACETS	0.876	0.773	0.986	0.876	0.773	0.986	CLONAL	1	TRUE	1	0.34	2		448	544	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596032	43596032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749390385	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	174	845	1	ENST00000355710.3:c.199C>T	p.Arg67Cys	p.R67C	ENST00000355710	NM_020975.4	67	Cgc/Tgc	2/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.34	2		846	893	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248461	59248461	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	152	635	3	ENST00000371222.2:c.282del	p.Thr95ProfsTer9	p.T95Pfs*9	ENST00000371222	NM_002228.3	94	ccC/cc	1/1	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.34	2		638	856	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903763	114903763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	120	562	0	ENST00000543371.1:c.767C>T	p.Pro256Leu	p.P256L	ENST00000543371	NM_001198531.1	256	cCg/cTg	7/14	1	2	FACETS	0.968	0.875	1	0.968	0.875	1	CLONAL	1	TRUE	1	0.34	2		562	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576899	7576899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555524979	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	154	857	0	ENST00000269305.4:c.947C>T	p.Pro316Leu	p.P316L	ENST00000269305	NM_001126112.2	316	cCc/cTc	9/11	1	2	FACETS	0.84	0.767	0.916	0.84	0.767	0.916	CLONAL	1	TRUE	1	0.34	2		857	1079	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955043	17955043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs199602590	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	151	865	1	ENST00000458235.1:c.184G>A	p.Gly62Ser	p.G62S	ENST00000458235	NM_000215.3	62	Ggc/Agc	2/24	1	2	FACETS	0.919	0.84	1	0.919	0.84	1	CLONAL	1	TRUE	1	0.34	2		866	966	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602340	10602340	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	163	817	2	ENST00000171111.5:c.1238G>A	p.Arg413His	p.R413H	ENST00000171111	NM_203500.1	413	cGt/cAt	3/6	1	2	FACETS	0.978	0.897	1	0.978	0.897	1	CLONAL	1	TRUE	1	0.34	2		819	980	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106879	27106879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	116	753	2	ENST00000324856.7:c.6490C>T	p.Arg2164Trp	p.R2164W	ENST00000324856	NM_006015.4	2164	Cgg/Tgg	20/20	1	2	FACETS	0.809	0.729	0.894	0.809	0.729	0.894	CLONAL	1	TRUE	1	0.34	2		755	843	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150039	202150039	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1368296717	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	152	698	0	ENST00000358485.4:c.1480C>T	p.Arg494Ter	p.R494*	ENST00000358485	NM_001080125.1	494	Cga/Tga	8/9	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.34	2		698	786	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952993	2952993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369115970	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	186	914	3	ENST00000396946.4:c.2947G>A	p.Val983Met	p.V983M	ENST00000396946	NM_032415.4	983	Gtg/Atg	22/25	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.34	2		917	953	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198283258	198283258	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	148	641	0	ENST00000335508.6:c.470G>A	p.Arg157Gln	p.R157Q	ENST00000335508	NM_012433.2	157	cGa/cAa	5/25	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.34	2		641	828	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575065	48575065	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	77	423	0	ENST00000342988.3:c.259C>T	p.Arg87Trp	p.R87W	ENST00000342988	NM_005359.5	87	Cgg/Tgg	3/12	1	2	FACETS	0.863	0.759	0.974	0.863	0.759	0.974	CLONAL	1	TRUE	1	0.34	2		423	525	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710593	117710593	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145765584	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	78	367	1	ENST00000368508.3:c.1679G>A	p.Arg560His	p.R560H	ENST00000368508	NM_002944.2	560	cGc/cAc	12/43	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.34	2		368	445	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133236017	133236017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555225676	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	160	732	2	ENST00000320574.5:c.3139G>A	p.Gly1047Arg	p.G1047R	ENST00000320574	NM_006231.2	1047	Ggg/Agg	26/49	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.34	2		734	833	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641388	23641388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780820	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	200	1043	0	ENST00000261584.4:c.2087C>T	p.Thr696Met	p.T696M	ENST00000261584	NM_024675.3	696	aCg/aTg	5/13	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.34	2		1043	1155	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275420	38275420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369356672	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	172	880	1	ENST00000425967.3:c.1613G>A	p.Arg538His	p.R538H	ENST00000425967	NM_001174067.1	538	cGt/cAt	12/19	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.34	2		881	999	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707624	176707624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1315206249	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	140	637	0	ENST00000439151.2:c.5681G>A	p.Arg1894His	p.R1894H	ENST00000439151	NM_022455.4	1894	cGt/cAt	18/23	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.34	2		637	798	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784478	9784478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1414657892	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	82	451	0	ENST00000377346.4:c.2863C>T	p.Arg955Trp	p.R955W	ENST00000377346	NM_005026.3	955	Cgg/Tgg	22/24	1	2	FACETS	0.877	0.775	0.986	0.877	0.775	0.986	CLONAL	1	TRUE	1	0.34	2		451	550	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18964097	18964097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770535477	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	140	752	0	ENST00000262803.5:c.1094G>A	p.Arg365Gln	p.R365Q	ENST00000262803	NM_002911.3	365	cGg/cAg	8/24	1	2	FACETS	0.941	0.857	1	0.941	0.857	1	CLONAL	1	TRUE	1	0.34	2		752	875	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658481	3658481	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140876043	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	164	836	1	ENST00000294008.3:c.485C>T	p.Thr162Met	p.T162M	ENST00000294008	NM_032444.2	162	aCg/aTg	2/15	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.34	2		837	945	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37665993	37665993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	83	443	0	ENST00000447079.4:c.2645G>A	p.Arg882Gln	p.R882Q	ENST00000447079	NM_015083.1	882	cGg/cAg	7/14	1	2	FACETS	0.848	0.749	0.953	0.848	0.749	0.953	CLONAL	1	TRUE	1	0.34	2		443	576	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603007	48603007	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	70	354	0	ENST00000342988.3:c.1309-1G>T		p.X437_splice	ENST00000342988	NM_005359.5	437			1	2	FACETS	0.917	0.802	1	0.917	0.802	1	CLONAL	1	TRUE	1	0.34	2		354	449	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632669	3632669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	143	907	0	ENST00000294008.3:c.5179G>A	p.Ala1727Thr	p.A1727T	ENST00000294008	NM_032444.2	1727	Gca/Aca	15/15	1	2	FACETS	0.832	0.758	0.91	0.832	0.758	0.91	CLONAL	1	TRUE	1	0.34	2		907	1011	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939140	36939140	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754176065	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	183	893	3	ENST00000361632.4:c.569G>A	p.Arg190His	p.R190H	ENST00000361632		190	cGc/cAc	5/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.34	2		896	1018	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572621	141572621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748022421	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	149	745	0	ENST00000220592.5:c.449G>A	p.Arg150Gln	p.R150Q	ENST00000220592	NM_012154.3	150	cGg/cAg	4/19	1	2	FACETS	0.974	0.89	1	0.974	0.89	1	CLONAL	1	TRUE	1	0.34	2		745	900	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625405	69625405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1442579536	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	170	940	1	ENST00000334134.2:c.388G>A	p.Ala130Thr	p.A130T	ENST00000334134	NM_005247.2	130	Gcc/Acc	3/3	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.34	2		941	962	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169415	99169415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs909251709	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	101	610	0	ENST00000074304.5:c.1345G>A	p.Ala449Thr	p.A449T	ENST00000074304	NM_001134224.1	449	Gcc/Acc	15/26	1	2	FACETS	0.883	0.79	0.981	0.883	0.79	0.981	CLONAL	1	TRUE	1	0.34	2		610	673	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681341	88681341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786202611	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	47	279	2	ENST00000372037.3:c.1231G>A	p.Glu411Lys	p.E411K	ENST00000372037	NM_004329.2	411	Gaa/Aaa	11/13	1	2	FACETS	0.861	0.73	1	0.861	0.73	1	CLONAL	1	TRUE	1	0.34	2		281	321	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7168022	7168022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	115	755	1	ENST00000302850.5:c.1567G>A	p.Asp523Asn	p.D523N	ENST00000302850	NM_000208.2	523	Gac/Aac	7/22	1	2	FACETS	0.731	0.658	0.809	0.731	0.658	0.809	SUBCLONAL	1	TRUE	1	0.34	2		756	925	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104359302	104359302	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776578	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	116	600	1	ENST00000369902.3:c.1022+1G>A		p.X341_splice	ENST00000369902	NM_016169.3	341			1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.34	2		601	676	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981297	201981297	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs756079277	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	209	853	0	ENST00000359651.3:c.376C>T	p.Arg126Ter	p.R126*	ENST00000359651		126	Cga/Tga	2/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.34	2		853	939	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107086	27107086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	112	653	0	ENST00000324856.7:c.6697C>T	p.Arg2233Trp	p.R2233W	ENST00000324856	NM_006015.4	2233	Cgg/Tgg	20/20	1	2	FACETS	0.924	0.832	1	0.924	0.832	1	CLONAL	1	TRUE	1	0.34	2		653	713	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250353	39250353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	110	704	1	ENST00000402219.2:c.1216C>T	p.Arg406Trp	p.R406W	ENST00000402219	NM_005633.3	406	Cgg/Tgg	10/23	1	2	FACETS	0.878	0.789	0.972	0.878	0.789	0.972	CLONAL	1	TRUE	1	0.34	2		705	737	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919881	50919881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1410415830	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	158	803	0	ENST00000440232.2:c.2968C>T	p.Arg990Cys	p.R990C	ENST00000440232	NM_002691.3	990	Cgc/Tgc	24/27	1	2	FACETS	0.999	0.916	1	0.999	0.916	1	CLONAL	1	TRUE	1	0.34	2		803	930	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797891	45797891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199840380	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	185	856	0	ENST00000450313.1:c.880C>T	p.Arg294Cys	p.R294C	ENST00000450313	NM_012222.2	294	Cgc/Tgc	10/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.34	2		856	1013	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227015	53227015	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782562716	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	171	871	1	ENST00000375401.3:c.2560C>T	p.Arg854Trp	p.R854W	ENST00000375401	NM_004187.3	854	Cgg/Tgg	18/26	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.34	2		872	963	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720928	119720928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	119	474	0	ENST00000316626.5:c.247G>A	p.Ala83Thr	p.A83T	ENST00000316626		83	Gcc/Acc	2/12	1	2	FACETS	0.997	0.901	1	0.997	0.901	1	CLONAL	1	TRUE	1	0.34	2		474	702	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956977	2956977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1450077193	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	165	793	0	ENST00000396946.4:c.2650C>T	p.Arg884Trp	p.R884W	ENST00000396946	NM_032415.4	884	Cgg/Tgg	20/25	1	2	FACETS	0.982	0.902	1	0.982	0.902	1	CLONAL	1	TRUE	1	0.34	2		793	988	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829901	72829901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751440593	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	157	870	1	ENST00000268489.5:c.6680G>A	p.Arg2227Gln	p.R2227Q	ENST00000268489	NM_006885.3	2227	cGg/cAg	9/10	1	2	FACETS	0.951	0.871	1	0.951	0.871	1	CLONAL	1	TRUE	1	0.34	2		871	971	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2215893	2215893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370203279	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	177	814	6	ENST00000326181.6:c.95C>T	p.Thr32Met	p.T32M	ENST00000326181	NM_032271.2	32	aCg/aTg	3/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.34	2		820	935	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64286793	64286793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	100	421	0	ENST00000370651.3:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000370651	NM_003463.4	3	cGa/cAa	2/6	1	2	FACETS	0.967	0.866	1	0.967	0.866	1	CLONAL	1	TRUE	1	0.34	2		421	608	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615791	1615791	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs562975911	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	139	824	2	ENST00000344749.5:c.1480G>A	p.Ala494Thr	p.A494T	ENST00000344749	NM_001136139.2	494	Gcc/Acc	17/19	1	2	FACETS	0.91	0.828	0.996	0.91	0.828	0.996	CLONAL	1	TRUE	1	0.34	2		826	899	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288983	33288983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1026215586	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	146	656	0	ENST00000374542.5:c.569G>A	p.Arg190His	p.R190H	ENST00000374542	NM_001141970.1	190	cGt/cAt	3/8	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.34	2		656	797	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028757	47028757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782165166	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	169	853	1	ENST00000377604.3:c.61C>T	p.Arg21Cys	p.R21C	ENST00000377604	NM_001204468.1	21	Cgc/Tgc	3/24	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.34	2		854	909	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246473	10246473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	165	888	2	ENST00000340748.4:c.4664G>A	p.Arg1555His	p.R1555H	ENST00000340748		1555	cGc/cAc	38/40	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.34	2		890	970	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484287	120484287	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	128	609	1	ENST00000256646.2:c.2843C>T	p.Thr948Ile	p.T948I	ENST00000256646	NM_024408.3	948	aCa/aTa	18/34	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.34	2		610	698	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843677	156843677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867144076	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	188	908	1	ENST00000524377.1:c.1103G>A	p.Gly368Asp	p.G368D	ENST00000524377	NM_002529.3	368	gGc/gAc	8/17	1	2	FACETS	0.999	0.922	1	0.999	0.922	1	CLONAL	1	TRUE	1	0.34	2		909	1107	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903744	114903744	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375223335	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	155	641	1	ENST00000543371.1:c.748G>A	p.Val250Ile	p.V250I	ENST00000543371	NM_001198531.1	250	Gta/Ata	7/14	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.34	2		642	851	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090950	77090950	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	104	556	0	ENST00000356341.3:c.280G>T	p.Gly94Trp	p.G94W	ENST00000356341	NM_002576.4	94	Ggg/Tgg	3/15	1	2	FACETS	0.913	0.819	1	0.913	0.819	1	CLONAL	1	TRUE	1	0.34	2		556	670	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409080	4409080	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	111	537	2	ENST00000261254.3:c.775C>T	p.Gln259Ter	p.Q259*	ENST00000261254	NM_001759.3	259	Cag/Tag	5/5	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.34	2		539	644	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120992	115120992	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	136	632	0	ENST00000257566.3:c.14T>C	p.Met5Thr	p.M5T	ENST00000257566	NM_016569.3	5	aTg/aCg	1/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.34	2		632	711	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913358	28913358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374468544	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	145	821	0	ENST00000282397.4:c.2435G>A	p.Arg812Gln	p.R812Q	ENST00000282397	NM_002019.4	812	cGg/cAg	17/30	1	2	FACETS	0.924	0.843	1	0.924	0.843	1	CLONAL	1	TRUE	1	0.34	2		821	923	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48921999	48921999	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs367654488	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	40	441	0	ENST00000267163.4:c.539C>T	p.Ser180Leu	p.S180L	ENST00000267163	NM_000321.2	180	tCg/tTg	5/27	1	2	FACETS	0.663	0.552	0.785	0.663	0.552	0.785	SUBCLONAL	1	TRUE	1	0.34	2		441	355	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562482	95562482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	230	551	0	ENST00000393063.1:c.4775C>T	p.Pro1592Leu	p.P1592L	ENST00000393063	NM_030621.3	1592	cCg/cTg	24/28	0.345652677435553	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.34	2		551	664	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830168	72830168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	148	748	1	ENST00000268489.5:c.6413C>T	p.Pro2138Leu	p.P2138L	ENST00000268489	NM_006885.3	2138	cCa/cTa	9/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.34	2		749	762	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984816	11984816	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	104	600	0	ENST00000353533.5:c.362A>G	p.His121Arg	p.H121R	ENST00000353533	NM_003010.3	121	cAc/cGc	3/11	1	2	FACETS	0.897	0.804	0.996	0.897	0.804	0.996	CLONAL	1	TRUE	1	0.34	2		600	682	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548920	29548920	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	41	492	0	ENST00000356175.3:c.1694C>A	p.Ala565Asp	p.A565D	ENST00000356175	NM_000267.3	565	gCt/gAt	15/57	1	2	FACETS	0.563	0.47	0.668	0.563	0.47	0.668	SUBCLONAL	1	TRUE	1	0.34	2		492	428	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526448	66526448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	120	567	0	ENST00000358598.2:c.1004G>A	p.Arg335His	p.R335H	ENST00000358598	NM_212471.2	335	cGt/cAt	11/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.34	2		567	676	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290282	15290282	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs755229930	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	190	862	1	ENST00000263388.2:c.3353A>G	p.Asn1118Ser	p.N1118S	ENST00000263388	NM_000435.2	1118	aAc/aGc	21/33	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.34	2		863	997	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279603	18279603	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs765153304	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	164	964	0	ENST00000222254.8:c.1876A>G	p.Lys626Glu	p.K626E	ENST00000222254	NM_005027.3	626	Aag/Gag	15/16	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.34	2		964	950	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872232	45872232	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	160	858	0	ENST00000391945.4:c.202A>G	p.Thr68Ala	p.T68A	ENST00000391945	NM_000400.3	68	Acc/Gcc	4/23	1	2	FACETS	0.91	0.834	0.99	0.91	0.834	0.99	CLONAL	1	TRUE	1	0.34	2		858	1034	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912817	50912817	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754913337	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	166	856	1	ENST00000440232.2:c.2048G>A	p.Arg683His	p.R683H	ENST00000440232	NM_002691.3	683	cGc/cAc	17/27	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.34	2		857	873	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCC	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	39	586	0	ENST00000234420.5:c.3259_3261dup	p.Pro1087dup	p.P1087dup	ENST00000234420	NM_000179.2	1087	acc/aCCCcc	5/10	1	2	FACETS	0.327	0.27	0.391	0.327	0.27	0.391	SUBCLONAL	1	TRUE	1	0.34	2		586	702	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661581	227661581	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	171	874	0	ENST00000305123.5:c.1874G>T	p.Gly625Val	p.G625V	ENST00000305123	NM_005544.2	625	gGc/gTc	1/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.34	2		874	892	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564807	41564807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	143	754	0	ENST00000263253.7:c.4108G>A	p.Asp1370Asn	p.D1370N	ENST00000263253	NM_001429.3	1370	Gac/Aac	25/31	1	2	FACETS	0.894	0.814	0.977	0.894	0.814	0.977	CLONAL	1	TRUE	1	0.34	2		754	941	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960002	134960002	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	107	596	0	ENST00000398015.3:c.2359C>A	p.Pro787Thr	p.P787T	ENST00000398015	NM_004441.4	787	Cct/Act	13/16	0.102536659020007	0	FACETS	0.679	0.61	0.751			1	INDETERMINATE	1	TRUE	0	0.34	0		596	612	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268341	142268341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367641692	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	39	389	0	ENST00000350721.4:c.3151C>T	p.Arg1051Cys	p.R1051C	ENST00000350721	NM_001184.3	1051	Cgt/Tgt	15/47	1	2	FACETS	0.811	0.675	0.96	0.811	0.675	0.96	CLONAL	1	TRUE	1	0.34	2		389	283	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468095	31468095	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1265142476	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	170	724	1	ENST00000344624.3:c.2317G>A	p.Val773Ile	p.V773I	ENST00000344624		773	Gtc/Atc	15/33	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.34	2		725	829	SUCCESS
APC	324	MSKCC	GRCh37	5	112128194	112128194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554074772	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	104	484	0	ENST00000257430.4:c.697C>T	p.Gln233Ter	p.Q233*	ENST00000257430	NM_000038.5	233	Cag/Tag	7/16	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.34	2		484	584	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032240	26032240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	71	391	0	ENST00000244661.2:c.49C>T	p.Pro17Ser	p.P17S	ENST00000244661	NM_003537.3	17	Cca/Tca	1/1	1	2	FACETS	0.883	0.773	1	0.883	0.773	1	CLONAL	1	TRUE	1	0.34	2		391	473	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839739	27839739	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	165	718	0	ENST00000328488.2:c.355A>G	p.Thr119Ala	p.T119A	ENST00000328488	NM_003533.2	119	Act/Gct	1/1	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.34	2		718	902	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805554	32805554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	229	910	0	ENST00000374899.4:c.457G>A	p.Val153Ile	p.V153I	ENST00000374899	NM_018833.2	153	Gtt/Att	2/12	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.34	2		910	1141	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969953	161969953	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746620234	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	134	713	1	ENST00000366898.1:c.1016C>T	p.Ala339Val	p.A339V	ENST00000366898	NM_004562.2	339	gCg/gTg	9/12	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.34	2		714	757	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471080	8471080	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	69	381	0	ENST00000356435.5:c.3419A>G	p.Tyr1140Cys	p.Y1140C	ENST00000356435		1140	tAc/tGc	20/35	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.34	2		381	404	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499806	8499807	+	missense_variant	Missense_Mutation	DNP	CT	CT	AC	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	114	611	1	ENST00000356435.5:c.2162_2163delinsGT	p.Glu721Gly	p.E721G	ENST00000356435		721	gAG/gGT	14/35	1	2	FACETS	0.924	0.832	1	0.924	0.832	1	CLONAL	1	TRUE	1	0.34	2		612	726	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218682	98218682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1409913416	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	110	445	0	ENST00000331920.6:c.3182C>T	p.Ala1061Val	p.A1061V	ENST00000331920	NM_000264.3	1061	gCg/gTg	19/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.34	2		445	536	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240363	98240363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	124	550	0	ENST00000331920.6:c.1321C>T	p.Arg441Cys	p.R441C	ENST00000331920	NM_000264.3	441	Cgc/Tgc	9/24	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.34	2		550	703	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128420055	128420055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	147	743	0	ENST00000265960.3:c.373G>A	p.Glu125Lys	p.E125K	ENST00000265960	NM_001006617.1	125	Gaa/Aaa	4/12	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.34	2		743	847	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396517	139396517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	135	840	0	ENST00000277541.6:c.5408G>A	p.Gly1803Asp	p.G1803D	ENST00000277541	NM_017617.3	1803	gGt/gAt	29/34	1	2	FACETS	0.841	0.764	0.923	0.841	0.764	0.923	CLONAL	1	TRUE	1	0.34	2		840	944	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139440184	139440184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	30	98	0	ENST00000277541.6:c.55G>A	p.Ala19Thr	p.A19T	ENST00000277541	NM_017617.3	19	Gca/Aca	1/34	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.34	2		98	127	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182895	123182895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	58	433	0	ENST00000218089.9:c.860C>T	p.Ala287Val	p.A287V	ENST00000218089	NM_001042749.1	287	gCa/gTa	10/35	1	2	FACETS	0.891	0.768	1	0.891	0.768	1	CLONAL	1	TRUE	1	0.34	2		433	383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0047678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1423	451	889	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.607178382106509	3	FACETS	1	0.974	1	0.517	0.492	0.543	CLONAL	1	TRUE	1	0.606803019722991	3		889	1874	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0047678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	593	746	0	ENST00000269305.4:c.97-1G>A		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.607178382106509	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	1	0.606803019722991	3		746	1063	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339251	70339251	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs199469668	NA	P-0047678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	238	634	0	ENST00000374080.3:c.128A>C	p.Gln43Pro	p.Q43P	ENST00000374080		43	cAa/cCa	2/45	0.607178382106509	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.606803019722991	1		634	490	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309841	104309841	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	174	511	0	ENST00000369902.3:c.432G>T	p.Leu144Phe	p.L144F	ENST00000369902	NM_016169.3	144	ttG/ttT	3/12	0.607178382106509	3	FACETS	1	0.969	1			1	CLONAL	1	TRUE	NA	0.606803019722991	3		511	683	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434688	128434688	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1207056791	NA	P-0047678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	127	717	1	ENST00000265960.3:c.166G>A	p.Gly56Arg	p.G56R	ENST00000265960	NM_001006617.1	56	Gga/Aga	2/12	1	2	FACETS	0.552	0.5	0.607	0.552	0.5	0.607	SUBCLONAL	1	TRUE	1	0.606803019722991	2		718	758	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937645	76937645	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	128	472	0	ENST00000373344.5:c.3103del	p.Ile1035LeufsTer15	p.I1035Lfs*15	ENST00000373344	NM_000489.3	1035	Att/tt	9/35	0.607178382106509	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.606803019722991	1		472	292	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0047717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	252	1045	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.557433800197814	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.557433800197814	1		1046	556	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0047717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	123	519	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	NA	2	FACETS	0.951	0.866	1			1	INDETERMINATE	1	TRUE	NA	0.557433800197814	2		519	464	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956958	2956958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1347465052	NA	P-0047717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	222	544	0	ENST00000396946.4:c.2669C>T	p.Ser890Leu	p.S890L	ENST00000396946	NM_032415.4	890	tCg/tTg	20/25	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.557433800197814	2		544	736	SUCCESS
APC	324	MSKCC	GRCh37	5	112170652	112170652	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	68	222	0	ENST00000257430.4:c.1748C>A	p.Ser583Ter	p.S583*	ENST00000257430	NM_000038.5	583	tCa/tAa	15/16	0.557433800197814	1	FACETS	0.772	0.681	0.867	0.772	0.681	0.867	SUBCLONAL	1	TRUE	0	0.557433800197814	1		222	228	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434116	121434116	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	229	605	0	ENST00000257555.6:c.1007G>T	p.Ser336Ile	p.S336I	ENST00000257555		336	aGc/aTc	5/10	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.557433800197814	2		605	820	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654757	29654757	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	98	262	0	ENST00000356175.3:c.5446G>T	p.Asp1816Tyr	p.D1816Y	ENST00000356175	NM_000267.3	1816	Gac/Tac	37/57	0.557433800197814	3	FACETS	0.875	0.783	0.971	0.437	0.391	0.486	CLONAL	1	TRUE	1	0.557433800197814	3		262	514	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266661	41266661	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	117	317	0	ENST00000349496.5:c.458T>G	p.Ile153Ser	p.I153S	ENST00000349496	NM_001904.3	153	aTc/aGc	4/15	1	2	FACETS	0.948	0.86	1	0.948	0.86	1	CLONAL	1	TRUE	1	0.557433800197814	2		317	443	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808303	99808303	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs758100407	NA	P-0047717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	47	260	0	ENST00000280892.6:c.386G>T	p.Arg129Leu	p.R129L	ENST00000280892	NM_001130678.1	129	cGg/cTg	5/7	1	2	FACETS	0.448	0.379	0.524	0.448	0.379	0.524	SUBCLONAL	1	TRUE	1	0.557433800197814	2		260	376	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349256	11349256	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047833-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	78	267	0	ENST00000332029.2:c.80C>G	p.Ser27Cys	p.S27C	ENST00000332029	NM_003745.1	27	tCc/tGc	2/2	0.496390231926724	2	FACETS	0.674	0.595	0.759	0.337	0.297	0.38	SUBCLONAL	1	FALSE	0	0.507319206780378	2		267	456	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0047888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	51	670	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.854	0.735	0.982	0.854	0.735	0.982	CLONAL	1	TRUE	1	0.54271391326369	2		670	220	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0047888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	89	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.843	0.753	0.938	0.843	0.753	0.938	CLONAL	1	TRUE	1	0.54271391326369	2		487	389	SUCCESS
APC	324	MSKCC	GRCh37	5	112175360	112175360	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	126	169	0	ENST00000257430.4:c.4069G>T	p.Gly1357Ter	p.G1357*	ENST00000257430	NM_000038.5	1357	Gga/Tga	16/16	0.535845928129513	2	FACETS	0.854	0.788	0.92	0.854	0.788	0.92	CLONAL	2	TRUE	0	0.54271391326369	2		169	272	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520008	NA	P-0047888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	204	507	0	ENST00000269305.4:c.613T>C	p.Tyr205His	p.Y205H	ENST00000269305	NM_001126112.2	205	Tat/Cat	6/11	0.54271391326369	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.54271391326369	1		507	548	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023853	27023853	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	47	223	0	ENST00000324856.7:c.959C>T	p.Pro320Leu	p.P320L	ENST00000324856	NM_006015.4	320	cCc/cTc	1/20	0.330801366071295	1	FACETS	0.397	0.336	0.463	0.397	0.336	0.463	SUBCLONAL	1	TRUE	0	0.54271391326369	1		223	318	SUCCESS
APC	324	MSKCC	GRCh37	5	112175834	112175834	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	130	218	0	ENST00000257430.4:c.4543T>C	p.Phe1515Leu	p.F1515L	ENST00000257430	NM_000038.5	1515	Ttt/Ctt	16/16	0.535845928129513	2	FACETS	0.907	0.84	0.975	0.907	0.84	0.975	CLONAL	2	TRUE	0	0.54271391326369	2		218	264	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041358	47041358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	207	559	0	ENST00000377604.3:c.1702G>A	p.Asp568Asn	p.D568N	ENST00000377604	NM_001204468.1	568	Gac/Aac	16/24	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.54271391326369	2		559	706	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344949	70344949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs192331892	NA	P-0047888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	194	502	1	ENST00000374080.3:c.2179G>A	p.Asp727Asn	p.D727N	ENST00000374080		727	Gac/Aac	15/45	1	2	FACETS	0.961	0.892	1	0.961	0.892	1	CLONAL	1	TRUE	1	0.54271391326369	2		503	744	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0047950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	66	415	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.889	0.782	1	0.889	0.782	1	CLONAL	1	TRUE	1	0.624128217901293	2		415	238	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0047950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	343	494	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.624128217901293	2	FACETS	0.985	0.945	1	0.985	0.945	1	CLONAL	2	TRUE	0	0.624128217901293	2		494	558	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0047950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	125	482	0	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	1	2	FACETS	0.7	0.636	0.767	0.7	0.636	0.767	SUBCLONAL	1	TRUE	1	0.624128217901293	2		482	572	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56852646	56852646	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756006928	NA	P-0047950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	173	379	0	ENST00000308159.5:c.560G>A	p.Arg187Gln	p.R187Q	ENST00000308159	NM_014669.4	187	cGg/cAg	6/22	1	2	FACETS	0.94	0.869	1	0.94	0.869	1	CLONAL	1	TRUE	1	0.624128217901293	2		379	590	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118890	70118890	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	262	806	0	ENST00000245479.2:c.462C>A	p.Phe154Leu	p.F154L	ENST00000245479	NM_000346.3	154	ttC/ttA	2/3	1	2	FACETS	0.906	0.85	0.963	0.906	0.85	0.963	CLONAL	1	TRUE	1	0.624128217901293	2		806	927	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245533	153245533	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	97	314	0	ENST00000281708.4:c.1658A>C	p.His553Pro	p.H553P	ENST00000281708	NM_033632.3	553	cAt/cCt	11/12	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.624128217901293	2		314	293	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042163	6042163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	214	544	0	ENST00000265849.7:c.458G>A	p.Arg153Lys	p.R153K	ENST00000265849	NM_000535.5	153	aGa/aAa	5/15	1	2	FACETS	0.932	0.869	0.996	0.932	0.869	0.996	CLONAL	1	TRUE	1	0.624128217901293	2		544	736	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428124	47428124	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs756741810	NA	P-0047950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	212	773	2	ENST00000377045.4:c.1084C>T	p.Arg362Ter	p.R362*	ENST00000377045	NM_001654.4	362	Cga/Tga	11/16	1	2	FACETS	0.712	0.662	0.764	0.712	0.662	0.764	SUBCLONAL	1	TRUE	1	0.624128217901293	2		775	954	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039610	180039610	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs202140363	NA	P-0047972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	249	897	0	ENST00000261937.6:c.3433C>T	p.Arg1145Cys	p.R1145C	ENST00000261937	NM_182925.4	1145	Cgc/Tgc	26/30	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.561151838583891	2		897	638	SUCCESS
APC	324	MSKCC	GRCh37	5	112175411	112175411	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	93	200	0	ENST00000257430.4:c.4120G>T	p.Glu1374Ter	p.E1374*	ENST00000257430	NM_000038.5	1374	Gaa/Taa	16/16	0.474983657035222	4	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	2	0.561151838583891	4		200	250	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646980	37646981	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACC	novel	NA	P-0047972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	89	293	0	ENST00000447079.4:c.2104_2106dup	p.Pro702dup	p.P702dup	ENST00000447079	NM_015083.1	702	aga/agACCa	3/14	0.500750290474472	4	FACETS	1	0.929	1	0.529	0.471	0.591	CLONAL	1	TRUE	2	0.561151838583891	4		293	468	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386408	31386408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372550911	NA	P-0047972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1277	177	656	1	ENST00000328111.2:c.1633C>T	p.Arg545Cys	p.R545C	ENST00000328111	NM_006892.3	545	Cgc/Tgc	15/23	0.561151838583891	7	FACETS	1	0.948	1	0.209	0.191	0.227	CLONAL	1	TRUE	2	0.561151838583891	7		657	1454	SUCCESS
APC	324	MSKCC	GRCh37	5	112162896	112162896	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs387906230	NA	P-0047972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	86	272	0	ENST00000257430.4:c.1500T>A	p.Tyr500Ter	p.Y500*	ENST00000257430	NM_000038.5	500	taT/taA	12/16	0.474983657035222	4	FACETS	0.876	0.786	0.971	0.876	0.786	0.971	CLONAL	2	TRUE	2	0.561151838583891	4		272	273	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93607869	93607869	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0047972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	73	284	0	ENST00000375746.1:c.571A>T	p.Lys191Ter	p.K191*	ENST00000375746	NM_001174167.1	191	Aag/Tag	3/14	0.561151838583891	3	FACETS	1	0.948	1	0.567	0.5	0.637	CLONAL	1	TRUE	1	0.561151838583891	3		284	294	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0047979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	68	378	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.119762989233854	4	FACETS	1	0.971	1	0.725	0.632	0.825	INDETERMINATE	1	TRUE	2	0.232542734279854	4		378	497	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0047979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	29	257	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.151613207605257	4	FACETS	1	0.821	1	0.34	0.274	0.416	CLONAL	1	TRUE	1	0.232542734279854	4		258	301	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223093	5223093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269321557	NA	P-0047979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	62	1120	1	ENST00000357368.4:c.2710C>T	p.Arg904Trp	p.R904W	ENST00000357368	NM_002850.3	904	Cgg/Tgg	18/38	1	2	FACETS	0.658	0.567	0.757	0.658	0.567	0.757	SUBCLONAL	1	TRUE	1	0.232542734279854	2		1121	811	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374929	45374929	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	100	509	0	ENST00000262160.6:c.914C>T	p.Pro305Leu	p.P305L	ENST00000262160	NM_005901.5	305	cCa/cTa	8/11	0.145169269937046	4	FACETS	0.955	0.856	1	0.637	0.57	0.707	CLONAL	2	TRUE	1	0.232542734279854	4		509	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs1202793339	NA	P-0047979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	89	730	0	ENST00000269305.4:c.560-1G>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			1	2	FACETS	0.759	0.675	0.848	1	0.98	1	SUBCLONAL	2	TRUE	1	0.232542734279854	2		730	504	SUCCESS
APC	324	MSKCC	GRCh37	5	112175433	112175434	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	33	280	0	ENST00000257430.4:c.4142_4143insT	p.Leu1382ThrfsTer4	p.L1382Tfs*4	ENST00000257430	NM_000038.5	1381	cca/ccTa	16/16	0.151613207605257	4	FACETS	1	0.884	1	0.371	0.303	0.448	CLONAL	1	TRUE	1	0.232542734279854	4		280	314	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929562	44929563	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0047979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	78	446	0	ENST00000377967.4:c.2664dup	p.Ile889HisfsTer17	p.I889Hfs*17	ENST00000377967	NM_021140.2	888	tcc/tCcc	17/29	0.232542734279854	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.232542734279854	1		446	415	SUCCESS
APC	324	MSKCC	GRCh37	5	112175360	112175360	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	37	169	0	ENST00000257430.4:c.4069G>T	p.Gly1357Ter	p.G1357*	ENST00000257430	NM_000038.5	1357	Gga/Tga	16/16	0.334779357821519	3	FACETS	1	0.941	1	0.661	0.551	0.781	CLONAL	1	TRUE	1	0.345636183965432	3		169	190	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411444	63411444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	49	352	0	ENST00000330258.3:c.1723C>T	p.Arg575Trp	p.R575W	ENST00000330258	NM_152424.3	575	Cgg/Tgg	2/2	0.317272380742205	2	FACETS	0.799	0.679	0.929			1	CLONAL	1	TRUE	NA	0.345636183965432	2		352	355	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174395	11174395	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	124	473	0	ENST00000361445.4:c.7280T>G	p.Leu2427Arg	p.L2427R	ENST00000361445	NM_004958.3	2427	cTg/cGg	53/58	0.125961564912191	3	FACETS	0.795	0.723	0.871	0.795	0.723	0.871	INDETERMINATE	2	TRUE	1	0.345636183965432	3		473	529	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206908	162206908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1233588284	NA	P-0048063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	34	299	0	ENST00000366898.1:c.767G>A	p.Arg256His	p.R256H	ENST00000366898	NM_004562.2	256	cGc/cAc	7/12	0.334779357821519	3	FACETS	0.764	0.626	0.918	0.382	0.313	0.459	CLONAL	1	TRUE	1	0.345636183965432	3		299	302	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253381	226253381	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	14	191	0	ENST00000366813.1:c.153A>T	p.Glu51Asp	p.E51D	ENST00000366813		51	gaA/gaT	2/3	0.125961564912191	3	FACETS	0.356	0.257	0.476	0.178	0.128	0.238	INDETERMINATE	1	TRUE	1	0.345636183965432	3		191	267	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118995	70118995	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	97	831	0	ENST00000245479.2:c.567del	p.Glu190ArgfsTer29	p.E190Rfs*29	ENST00000245479	NM_000346.3	189	gcA/gc	2/3	1	2	FACETS	0.942	0.841	1	0.942	0.841	1	CLONAL	1	TRUE	1	0.345636183965432	2		831	596	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256658	19256658	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377453711	NA	P-0048063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	103	840	1	ENST00000162023.5:c.1055G>A	p.Arg352Gln	p.R352Q	ENST00000162023		352	cGg/cAg	13/13	0.334779357821519	3	FACETS	1	0.942	1	0.538	0.482	0.597	CLONAL	1	TRUE	1	0.345636183965432	3		841	650	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905573	50905573	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	154	1153	1	ENST00000440232.2:c.701C>T	p.Ala234Val	p.A234V	ENST00000440232	NM_002691.3	234	gCa/gTa	6/27	0.334779357821519	3	FACETS	1	0.962	1	0.546	0.499	0.595	CLONAL	1	TRUE	1	0.345636183965432	3		1154	957	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	45	413	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.853	0.721	0.997	0.853	0.721	0.997	CLONAL	1	TRUE	1	0.36	2		413	293	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	216	1187	15	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.958	0.896	1	1	0.994	1	CLONAL	2	TRUE	1	0.36	2		1202	626	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	99	588	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.881	0.788	0.98	0.881	0.788	0.98	CLONAL	1	TRUE	1	0.36	2		592	624	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736510	85736511	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs387906351	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	29	222	1	ENST00000370580.1:c.136dup	p.Ile46AsnfsTer4	p.I46Nfs*4	ENST00000370580	NM_003921.4	46	ata/aAta	2/3	1	2	FACETS	0.527	0.423	0.643	0.527	0.423	0.643	SUBCLONAL	1	TRUE	1	0.36	2		223	306	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	82	498	4	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.36	2		502	434	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	92	352	2	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.881	0.793	0.973	1	0.985	1	CLONAL	2	TRUE	1	0.36	2		354	290	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944256	206944256	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374619208	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	75	380	0	ENST00000423557.1:c.374G>A	p.Arg125His	p.R125H	ENST00000423557	NM_000572.2	125	cGc/cAc	3/5	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.36	2		380	401	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	159	638	2	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.36	2		640	730	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101090	26101090	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	29	460	0	ENST00000435504.4:c.2T>C	p.Met1?	p.M1?	ENST00000435504		1	aTg/aCg	1/13	0.0865586335084049	0	FACETS	0.205	0.164	0.252			1	INDETERMINATE	1	TRUE	0	0.36	0		460	503	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436867	110436867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367592112	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	154	814	1	ENST00000375856.3:c.1534G>A	p.Ala512Thr	p.A512T	ENST00000375856	NM_003749.2	512	Gcc/Acc	1/2	1	2	FACETS	0.941	0.861	1	0.941	0.861	1	CLONAL	1	TRUE	1	0.36	2		815	909	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374301	138374301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1170276441	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	32	470	2	ENST00000289153.2:c.3143C>T	p.Ala1048Val	p.A1048V	ENST00000289153	NM_006219.2	1048	gCg/gTg	22/22	0.3	1	FACETS	0.259	0.21	0.316	0.259	0.21	0.316	SUBCLONAL	1	TRUE	0	0.36	1		472	562	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340407	8340407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201651279	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	88	431	0	ENST00000356435.5:c.5189G>A	p.Arg1730Gln	p.R1730Q	ENST00000356435		1730	cGg/cAg	31/35	1	2	FACETS	0.917	0.815	1	0.917	0.815	1	CLONAL	1	TRUE	1	0.36	2		431	533	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387087	31387087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778795266	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	152	687	0	ENST00000328111.2:c.1712G>A	p.Arg571Gln	p.R571Q	ENST00000328111	NM_006892.3	571	cGa/cAa	16/23	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.36	2		687	787	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86668008	86668008	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	37	182	0	ENST00000274376.6:c.1772G>A	p.Arg591His	p.R591H	ENST00000274376	NM_002890.2	591	cGt/cAt	13/25	1	2	FACETS	0.842	0.699	1	0.842	0.699	1	CLONAL	1	TRUE	1	0.36	2		182	244	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937104	39937104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	32	340	0	ENST00000378444.4:c.79G>A	p.Glu27Lys	p.E27K	ENST00000378444	NM_001123385.1	27	Gaa/Aaa	2/15	1	1	FACETS	0.339	0.275	0.412	0.339	0.275	0.412	SUBCLONAL	1	TRUE	0	0.36	1		340	430	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874604	35874604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137868226	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	66	344	0	ENST00000303115.3:c.760G>A	p.Ala254Thr	p.A254T	ENST00000303115	NM_002185.3	254	Gct/Act	6/8	1	2	FACETS	0.792	0.689	0.903	0.792	0.689	0.903	CLONAL	1	TRUE	1	0.36	2		344	463	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527328	157527328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	49	209	0	ENST00000346085.5:c.5053G>A	p.Glu1685Lys	p.E1685K	ENST00000346085	NM_020732.3	1685	Gag/Aag	20/20	1	2	FACETS	0.962	0.82	1	0.962	0.82	1	CLONAL	1	TRUE	1	0.36	2		209	283	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117594	70117594	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	52	716	0	ENST00000245479.2:c.66del	p.Ser23AlafsTer38	p.S23Afs*38	ENST00000245479	NM_000346.3	21	gCc/gc	1/3	1	2	FACETS	0.412	0.35	0.48	0.412	0.35	0.48	SUBCLONAL	1	TRUE	1	0.36	2		716	701	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793677	89793677	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	35	224	0	ENST00000336032.3:c.752del	p.Lys251SerfsTer14	p.K251Sfs*14	ENST00000336032	NM_006813.2	249	gAa/ga	2/2	1	2	FACETS	0.67	0.552	0.803	0.67	0.552	0.803	SUBCLONAL	1	TRUE	1	0.36	2		224	290	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50481153	50481153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	55	285	0	ENST00000394963.4:c.539G>A	p.Arg180Gln	p.R180Q	ENST00000394963	NM_003076.4	180	cGg/cAg	5/13	1	2	FACETS	0.802	0.689	0.925	0.802	0.689	0.925	CLONAL	1	TRUE	1	0.36	2		285	381	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223614	53223614	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	151	365	0	ENST00000375401.3:c.3745C>T	p.Arg1249Cys	p.R1249C	ENST00000375401	NM_004187.3	1249	Cgc/Tgc	23/26	1	1	FACETS	0.877	0.812	0.944	1	0.991	1	CLONAL	2	TRUE	0	0.36	1		365	392	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030050	36030050	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	46	628	1	ENST00000358208.4:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000358208		362	cGg/cAg	9/12	1	2	FACETS	0.376	0.316	0.443	0.376	0.316	0.443	SUBCLONAL	1	TRUE	1	0.36	2		629	679	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857275	9857275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426934537	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	84	605	1	ENST00000330684.3:c.4126C>T	p.Arg1376Cys	p.R1376C	ENST00000330684	NM_001134407.1	1376	Cgc/Tgc	13/13	1	2	FACETS	0.842	0.745	0.946	0.842	0.745	0.946	CLONAL	1	TRUE	1	0.36	2		606	554	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916726	178916726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772110575	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	16	220	0	ENST00000263967.3:c.113G>A	p.Arg38His	p.R38H	ENST00000263967	NM_006218.2	38	cGt/cAt	2/21	1	2	FACETS	0.332	0.245	0.435	0.332	0.245	0.435	SUBCLONAL	1	TRUE	1	0.36	2		220	268	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202351	138202351	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	75	504	1	ENST00000237289.4:c.2274del	p.Lys759SerfsTer57	p.K759Sfs*57	ENST00000237289	NM_001270507.1	756	gaC/ga	9/9	1	2	FACETS	0.709	0.621	0.802	0.709	0.621	0.802	SUBCLONAL	1	TRUE	1	0.36	2		505	588	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141026	55141026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765680542	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	34	253	0	ENST00000257290.5:c.1672C>T	p.Arg558Cys	p.R558C	ENST00000257290	NM_006206.4	558	Cgc/Tgc	12/23	0.3	2	FACETS	0.592	0.485	0.712			1	SUBCLONAL	1	TRUE	NA	0.36	2		253	319	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170312	119170312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141710973	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	60	239	0	ENST00000264033.4:c.2542G>A	p.Ala848Thr	p.A848T	ENST00000264033	NM_005188.3	848	Gcc/Acc	16/16	0.3	2	FACETS	1	0.932	1			1	CLONAL	1	TRUE	NA	0.36	2		239	298	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226091	226091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148246073	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	86	425	0	ENST00000264932.6:c.550G>A	p.Gly184Arg	p.G184R	ENST00000264932	NM_004168.2	184	Ggg/Agg	5/15	1	2	FACETS	0.895	0.793	1	0.895	0.793	1	CLONAL	1	TRUE	1	0.36	2		425	534	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500579	99500579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34102392	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	95	624	0	ENST00000268035.6:c.4012G>A	p.Ala1338Thr	p.A1338T	ENST00000268035	NM_000875.3	1338	Gcc/Acc	21/21	1	2	FACETS	0.854	0.762	0.952	0.854	0.762	0.952	CLONAL	1	TRUE	1	0.36	2		624	618	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435658	18435658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143896492	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	26	222	0	ENST00000266497.5:c.643G>A	p.Gly215Arg	p.G215R	ENST00000266497		215	Gga/Aga	1/31	0.3	1	FACETS	0.592	0.472	0.728	0.592	0.472	0.728	SUBCLONAL	1	TRUE	0	0.36	1		222	200	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156729	106156729	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1440692352	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	84	254	0	ENST00000380013.4:c.1630C>T	p.Arg544Ter	p.R544*	ENST00000380013	NM_001127208.2	544	Cga/Tga	3/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.36	2		254	364	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923711	72923711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs537344910	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	114	588	0	ENST00000268489.5:c.3367C>T	p.Arg1123Trp	p.R1123W	ENST00000268489	NM_006885.3	1123	Cgg/Tgg	4/10	1	2	FACETS	0.985	0.889	1	0.985	0.889	1	CLONAL	1	TRUE	1	0.36	2		588	643	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346220	152346220	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	93	421	6	ENST00000359321.1:c.350del	p.Leu117TrpfsTer17	p.L117Wfs*17	ENST00000359321	NM_005431.1	117	tTg/tg	3/3	0.131712893867963	3	FACETS	1	0.945	1	0.548	0.489	0.612	INDETERMINATE	1	TRUE	1	0.36	3		427	556	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397142	397142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs999945656	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	59	350	0	ENST00000380956.4:c.527G>A	p.Arg176Gln	p.R176Q	ENST00000380956	NM_001195286.1	176	cGa/cAa	5/9	1	2	FACETS	0.73	0.629	0.839	0.73	0.629	0.839	SUBCLONAL	1	TRUE	1	0.36	2		350	449	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs753143066	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	112	481	5	ENST00000295797.4:c.826dup	p.Thr276AsnfsTer16	p.T276Nfs*16	ENST00000295797	NM_002740.5	273	tta/ttAa	9/18	1	2	FACETS	0.87	0.783	0.962	0.87	0.783	0.962	CLONAL	1	TRUE	1	0.36	2		486	715	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821918	72821918	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	88	312	0	ENST00000268489.5:c.10257del	p.Lys3420AsnfsTer65	p.K3420Nfs*65	ENST00000268489	NM_006885.3	3419	ccC/cc	10/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.36	2		312	363	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465301	120465301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758689134	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	28	412	1	ENST00000256646.2:c.4960G>A	p.Ala1654Thr	p.A1654T	ENST00000256646	NM_024408.3	1654	Gcc/Acc	27/34	1	2	FACETS	0.303	0.241	0.373	0.303	0.241	0.373	SUBCLONAL	1	TRUE	1	0.36	2		413	514	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383227	31383227	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148132847	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	63	363	0	ENST00000328111.2:c.1139G>A	p.Arg380Gln	p.R380Q	ENST00000328111	NM_006892.3	380	cGa/cAa	11/23	1	2	FACETS	0.882	0.766	1	0.882	0.766	1	CLONAL	1	TRUE	1	0.36	2		363	397	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924618	94924618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1400088899	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	94	450	1	ENST00000536441.1:c.292C>T	p.Arg98Cys	p.R98C	ENST00000536441	NM_144665.3	98	Cgc/Tgc	3/10	1	2	FACETS	0.915	0.816	1	0.915	0.816	1	CLONAL	1	TRUE	1	0.36	2		451	571	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435079	56435079	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	135	617	0	ENST00000407977.2:c.2058del	p.Ser687ValfsTer13	p.S687Vfs*13	ENST00000407977		686	ccC/cc	9/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.36	2		617	704	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120546244	120546244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	95	431	0	ENST00000229340.5:c.80G>A	p.Arg27His	p.R27H	ENST00000229340	NM_006861.6	27	cGt/cAt	2/6	1	2	FACETS	0.883	0.787	0.984	0.883	0.787	0.984	CLONAL	1	TRUE	1	0.36	2		431	598	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276974	123276974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918504	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	32	177	0	ENST00000358487.5:c.943G>A	p.Ala315Thr	p.A315T	ENST00000358487	NM_000141.4	315	Gcc/Acc	8/18	1	2	FACETS	0.794	0.649	0.955	0.794	0.649	0.955	CLONAL	1	TRUE	1	0.36	2		177	224	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437163	121437163	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1421619915	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	65	917	1	ENST00000257555.6:c.1594G>A	p.Ala532Thr	p.A532T	ENST00000257555		532	Gcc/Acc	8/10	1	2	FACETS	0.359	0.31	0.413	0.359	0.31	0.413	SUBCLONAL	1	TRUE	1	0.36	2		918	1005	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31431707	31431707	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	30	330	0	ENST00000344624.3:c.3121G>A	p.Ala1041Thr	p.A1041T	ENST00000344624		1041	Gcc/Acc	23/33	1	2	FACETS	0.395	0.318	0.482	0.395	0.318	0.482	SUBCLONAL	1	TRUE	1	0.36	2		330	422	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40864422	40864422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374952991	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	207	861	1	ENST00000428826.2:c.1286C>T	p.Ser429Leu	p.S429L	ENST00000428826		429	tCg/tTg	12/21	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.36	2		862	931	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457614	67457614	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253901433	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	130	656	0	ENST00000327367.4:c.424C>T	p.Arg142Cys	p.R142C	ENST00000327367	NM_005902.3	142	Cgc/Tgc	3/9	1	2	FACETS	0.998	0.906	1	0.998	0.906	1	CLONAL	1	TRUE	1	0.36	2		656	724	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354312	354312	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1432410713	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	159	788	2	ENST00000262320.3:c.1246G>A	p.Val416Met	p.V416M	ENST00000262320	NM_003502.3	416	Gtg/Atg	5/11	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.36	2		790	855	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66525038	66525038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329426125	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	21	257	1	ENST00000358598.2:c.797C>T	p.Thr266Met	p.T266M	ENST00000358598	NM_212471.2	266	aCg/aTg	9/11	1	2	FACETS	0.378	0.291	0.479	0.378	0.291	0.479	SUBCLONAL	1	TRUE	1	0.36	2		258	309	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489788	2489788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs527252361	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	136	704	0	ENST00000355716.4:c.185G>A	p.Arg62His	p.R62H	ENST00000355716	NM_003820.2	62	cGt/cAt	3/8	1	2	FACETS	0.967	0.88	1	0.967	0.88	1	CLONAL	1	TRUE	1	0.36	2		704	781	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828771	3828771	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	99	527	1	ENST00000262367.5:c.1871G>A	p.Arg624His	p.R624H	ENST00000262367	NM_004380.2	624	cGc/cAc	9/31	1	2	FACETS	0.835	0.746	0.929	0.835	0.746	0.929	CLONAL	1	TRUE	1	0.36	2		528	659	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191157	185191157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs903937665	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	89	455	0	ENST00000265026.3:c.2038C>T	p.Arg680Trp	p.R680W	ENST00000265026	NM_004721.4	680	Cgg/Tgg	11/14	1	2	FACETS	0.971	0.864	1	0.971	0.864	1	CLONAL	1	TRUE	1	0.36	2		455	509	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111995786	111995786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	93	398	0	ENST00000368678.4:c.1312G>A	p.Gly438Arg	p.G438R	ENST00000368678		438	Ggg/Agg	12/13	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.36	2		398	511	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691095	18691095	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1368705250	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	49	269	0	ENST00000266497.5:c.3206G>A	p.Arg1069Gln	p.R1069Q	ENST00000266497		1069	cGa/cAa	23/31	0.3	1	FACETS	0.695	0.592	0.808	0.695	0.592	0.808	SUBCLONAL	1	TRUE	0	0.36	1		269	321	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244184	133244184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768004570	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	42	510	0	ENST00000320574.5:c.2224C>T	p.Arg742Cys	p.R742C	ENST00000320574	NM_006231.2	742	Cgt/Tgt	20/49	1	2	FACETS	0.371	0.309	0.44	0.371	0.309	0.44	SUBCLONAL	1	TRUE	1	0.36	2		510	629	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209390	98209390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571030658	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	113	688	0	ENST00000331920.6:c.4148C>T	p.Pro1383Leu	p.P1383L	ENST00000331920	NM_000264.3	1383	cCg/cTg	23/24	1	2	FACETS	0.929	0.837	1	0.929	0.837	1	CLONAL	1	TRUE	1	0.36	2		688	676	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793160	42793160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	166	881	2	ENST00000575354.2:c.1052G>A	p.Arg351Gln	p.R351Q	ENST00000575354	NM_015125.3	351	cGg/cAg	7/20	1	2	FACETS	0.879	0.807	0.955	0.879	0.807	0.955	CLONAL	1	TRUE	1	0.36	2		883	1049	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026415	6026415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778531080	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	63	302	1	ENST00000265849.7:c.1981G>A	p.Glu661Lys	p.E661K	ENST00000265849	NM_000535.5	661	Gaa/Aaa	11/15	0.3	3	FACETS	1	0.923	1			1	CLONAL	1	TRUE	NA	0.36	3		303	379	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204623	128204623	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	128	669	1	ENST00000341105.2:c.818del	p.Gly273AspfsTer53	p.G273Dfs*53	ENST00000341105	NM_032638.4	273	gGa/ga	3/6	0.3	1	FACETS	0.749	0.679	0.822	0.749	0.679	0.822	SUBCLONAL	1	TRUE	0	0.36	1		670	779	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517762	187517762	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	46	228	0	ENST00000441802.2:c.12932del	p.Pro4311HisfsTer38	p.P4311Hfs*38	ENST00000441802	NM_005245.3	4311	cCa/ca	25/27	1	2	FACETS	0.819	0.693	0.957	0.819	0.693	0.957	CLONAL	1	TRUE	1	0.36	2		228	312	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591031	67591033	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs1370788402	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	13	136	0	ENST00000274335.5:c.1630_1632del	p.Arg544del	p.R544del	ENST00000274335		542	AGA/-	12/15	1	2	FACETS	0.384	0.274	0.517	0.384	0.274	0.517	SUBCLONAL	1	TRUE	1	0.36	2		136	188	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155657	106155657	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1229417452	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	47	262	0	ENST00000380013.4:c.561del	p.Ser189ValfsTer18	p.S189Vfs*18	ENST00000380013	NM_001127208.2	186	gaG/ga	3/11	1	2	FACETS	0.891	0.756	1	0.891	0.756	1	CLONAL	1	TRUE	1	0.36	2		262	293	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256832	19256832	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	57	570	0	ENST00000162023.5:c.882-1G>A		p.X294_splice	ENST00000162023		294			1	2	FACETS	0.58	0.498	0.67	0.58	0.498	0.67	SUBCLONAL	1	TRUE	1	0.36	2		570	546	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199888	138199888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766691413	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	73	486	0	ENST00000237289.4:c.1306G>A	p.Gly436Arg	p.G436R	ENST00000237289	NM_001270507.1	436	Ggg/Agg	7/9	1	2	FACETS	0.85	0.746	0.962	0.85	0.746	0.962	CLONAL	1	TRUE	1	0.36	2		486	477	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574729	95574729	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	39	205	0	ENST00000393063.1:c.2368C>T	p.Arg790Trp	p.R790W	ENST00000393063	NM_030621.3	790	Cgg/Tgg	16/28	1	2	FACETS	0.706	0.587	0.837	0.706	0.587	0.837	SUBCLONAL	1	TRUE	1	0.36	2		205	307	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778909	9778909	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1048477125	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	157	689	1	ENST00000377346.4:c.1178C>T	p.Ala393Val	p.A393V	ENST00000377346	NM_005026.3	393	gCg/gTg	9/24	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.36	2		690	791	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2493137	2493137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766866458	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	89	480	0	ENST00000355716.4:c.577G>A	p.Gly193Arg	p.G193R	ENST00000355716	NM_003820.2	193	Gga/Aga	6/8	1	2	FACETS	0.936	0.833	1	0.936	0.833	1	CLONAL	1	TRUE	1	0.36	2		480	528	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199705	11199705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777925640	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	62	398	0	ENST00000361445.4:c.4883G>A	p.Arg1628His	p.R1628H	ENST00000361445	NM_004958.3	1628	cGt/cAt	35/58	1	2	FACETS	0.674	0.583	0.773	0.674	0.583	0.773	SUBCLONAL	1	TRUE	1	0.36	2		398	511	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599974	28599974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770593988	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	110	732	0	ENST00000253063.3:c.856C>T	p.Arg286Cys	p.R286C	ENST00000253063	NM_031459.4	286	Cgc/Tgc	6/10	1	2	FACETS	0.795	0.714	0.88	0.795	0.714	0.88	SUBCLONAL	1	TRUE	1	0.36	2		732	769	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464895	120464895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557804884	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	66	339	0	ENST00000256646.2:c.5177G>A	p.Arg1726His	p.R1726H	ENST00000256646	NM_024408.3	1726	cGt/cAt	28/34	1	2	FACETS	0.855	0.744	0.973	0.855	0.744	0.973	CLONAL	1	TRUE	1	0.36	2		339	429	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692820	89692820	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	35	196	0	ENST00000371953.3:c.304A>G	p.Lys102Glu	p.K102E	ENST00000371953	NM_000314.4	102	Aaa/Gaa	5/9	1	2	FACETS	0.864	0.714	1	0.864	0.714	1	CLONAL	1	TRUE	1	0.36	2		196	225	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128020	64128020	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	156	808	0	ENST00000334205.4:c.418G>A	p.Val140Met	p.V140M	ENST00000334205	NM_003942.2	140	Gtg/Atg	4/17	1	2	FACETS	0.976	0.894	1	0.976	0.894	1	CLONAL	1	TRUE	1	0.36	2		808	888	SUCCESS
EED	8726	MSKCC	GRCh37	11	85963206	85963206	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	25	218	0	ENST00000263360.6:c.284C>A	p.Pro95Gln	p.P95Q	ENST00000263360	NM_003797.3	95	cCa/cAa	3/12	1	2	FACETS	0.417	0.329	0.519	0.417	0.329	0.519	SUBCLONAL	1	TRUE	1	0.36	2		218	333	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99460059	99460059	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757536805	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	63	325	0	ENST00000268035.6:c.2155C>T	p.Arg719Cys	p.R719C	ENST00000268035	NM_000875.3	719	Cgc/Tgc	10/21	1	2	FACETS	0.827	0.718	0.945	0.827	0.718	0.945	CLONAL	1	TRUE	1	0.36	2		325	423	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396916	396916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201808684	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	162	804	1	ENST00000262320.3:c.110C>T	p.Pro37Leu	p.P37L	ENST00000262320	NM_003502.3	37	cCg/cTg	2/11	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.36	2		805	872	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805935	89805935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755375493	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	117	590	1	ENST00000389301.3:c.3961C>T	p.Arg1321Cys	p.R1321C	ENST00000389301	NM_000135.2	1321	Cgt/Tgt	40/43	1	2	FACETS	0.921	0.831	1	0.921	0.831	1	CLONAL	1	TRUE	1	0.36	2		591	706	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152157	11152157	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568528491	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	125	520	0	ENST00000358026.2:c.4441G>A	p.Glu1481Lys	p.E1481K	ENST00000358026	NM_001128849.1	1481	Gag/Aag	31/36	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.36	2		520	616	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967753	18967753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	172	710	0	ENST00000262803.5:c.1892G>A	p.Arg631His	p.R631H	ENST00000262803	NM_002911.3	631	cGc/cAc	14/24	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.36	2		710	895	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224262	36224262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753813107	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	118	745	1	ENST00000222270.7:c.6812C>T	p.Pro2271Leu	p.P2271L	ENST00000222270	NM_014727.1	2271	cCg/cTg	28/37	1	2	FACETS	0.899	0.812	0.991	0.899	0.812	0.991	CLONAL	1	TRUE	1	0.36	2		746	729	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707869	47707869	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	48	300	0	ENST00000233146.2:c.2493del	p.Glu832SerfsTer9	p.E832Sfs*9	ENST00000233146	NM_000251.2	831	gcA/gc	15/16	1	2	FACETS	0.813	0.69	0.947	0.813	0.69	0.947	CLONAL	1	TRUE	1	0.36	2		300	328	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99136566	99136566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773945053	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	42	713	1	ENST00000074304.5:c.55C>T	p.Arg19Trp	p.R19W	ENST00000074304	NM_001134224.1	19	Cgg/Tgg	3/26	1	2	FACETS	0.296	0.246	0.352	0.296	0.246	0.352	SUBCLONAL	1	TRUE	1	0.36	2		714	788	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212615400	212615400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769311799	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	64	353	0	ENST00000342788.4:c.586C>T	p.Arg196Cys	p.R196C	ENST00000342788	NM_005235.2	196	Cgt/Tgt	5/28	1	2	FACETS	0.761	0.661	0.87	0.761	0.661	0.87	SUBCLONAL	1	TRUE	1	0.36	2		353	467	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326487	62326487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs6062495	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	163	879	1	ENST00000360203.5:c.3412C>T	p.Arg1138Trp	p.R1138W	ENST00000360203	NM_001283009.1	1138	Cgg/Tgg	33/35	1	2	FACETS	0.861	0.789	0.936	0.861	0.789	0.936	CLONAL	1	TRUE	1	0.36	2		880	1052	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52685792	52685792	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	58	278	0	ENST00000394830.3:c.680C>A	p.Pro227His	p.P227H	ENST00000394830	NM_018313.4	227	cCt/cAt	7/30	1	2	FACETS	0.885	0.764	1	0.885	0.764	1	CLONAL	1	TRUE	1	0.36	2		278	364	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880981	134880981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	94	497	0	ENST00000398015.3:c.1544G>A	p.Gly515Asp	p.G515D	ENST00000398015	NM_004441.4	515	gGc/gAc	7/16	0.3	1	FACETS	0.731	0.651	0.815	0.731	0.651	0.815	SUBCLONAL	1	TRUE	0	0.36	1		497	586	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374865	149374865	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	128	560	0	ENST00000360632.3:c.229C>T	p.Arg77Ter	p.R77*	ENST00000360632	NM_015472.4	77	Cga/Tga	2/7	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.36	2		560	641	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803738	1803738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774047997	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	62	840	1	ENST00000260795.2:c.916G>A	p.Val306Ile	p.V306I	ENST00000260795		306	Gtt/Att	6/17	0.3	2	FACETS	0.393	0.338	0.452			1	SUBCLONAL	1	TRUE	NA	0.36	2		841	877	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565910	55565910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755508624	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	29	324	0	ENST00000288135.5:c.734C>T	p.Thr245Met	p.T245M	ENST00000288135	NM_000222.2	245	aCg/aTg	4/21	0.3	1	FACETS	0.381	0.306	0.466	0.381	0.306	0.466	SUBCLONAL	1	TRUE	0	0.36	1		324	347	SUCCESS
APC	324	MSKCC	GRCh37	5	112164566	112164567	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	35	151	0	ENST00000257430.4:c.1642_1643del	p.Leu548GlufsTer11	p.L548Efs*11	ENST00000257430	NM_000038.5	547	gTT/g	14/16	1	2	FACETS	0.748	0.616	0.894	0.748	0.616	0.894	SUBCLONAL	1	TRUE	1	0.36	2		151	260	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923257	131923257	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs555367432	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	11	90	0	ENST00000265335.6:c.760C>T	p.Arg254Cys	p.R254C	ENST00000265335		254	Cgt/Tgt	6/25	1	2	FACETS	0.571	0.398	0.782	0.571	0.398	0.782	SUBCLONAL	1	TRUE	1	0.36	2		90	107	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878446	151878446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367881455	NA	P-0048063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	155	543	0	ENST00000262189.6:c.6499C>T	p.Arg2167Trp	p.R2167W	ENST00000262189	NM_170606.2	2167	Cgg/Tgg	36/59	0.131712893867963	3	FACETS	0.773	0.71	0.839	0.773	0.71	0.839	INDETERMINATE	2	TRUE	1	0.36	3		543	657	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0048112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	293	1025	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	NA	2	FACETS	0.996	0.944	1			1	INDETERMINATE	2	TRUE	NA	0.420695915337279	2		1026	699	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971292	13971292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772105404	NA	P-0048112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	176	456	1	ENST00000405192.2:c.637C>T	p.Arg213Cys	p.R213C	ENST00000405192	NM_001163147.1	213	Cgc/Tgc	8/12	0.420695915337279	7	FACETS	0.857	0.789	0.929	0.343	0.315	0.372	CLONAL	2	TRUE	2	0.420695915337279	7		457	1001	SUCCESS
APC	324	MSKCC	GRCh37	5	112175349	112175353	+	frameshift_variant	Frame_Shift_Del	DEL	AATTT	AATTT	-	novel	NA	P-0048112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	36	255	0	ENST00000257430.4:c.4058_4062del	p.Glu1353ValfsTer20	p.E1353Vfs*20	ENST00000257430	NM_000038.5	1353	gAATTT/g	16/16	0.420695915337279	1	FACETS	0.8	0.666	0.945	0.8	0.666	0.945	CLONAL	1	TRUE	0	0.420695915337279	1		255	169	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508673	106508673	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs554272230	NA	P-0048112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	204	1057	1	ENST00000359195.3:c.667G>A	p.Val223Ile	p.V223I	ENST00000359195	NM_002649.2	223	Gtc/Atc	2/11	0.420695915337279	3	FACETS	0.872	0.812	0.933	0.872	0.812	0.933	CLONAL	2	TRUE	1	0.420695915337279	3		1058	673	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862766	9862766	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746978701	NA	P-0048112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	348	533	1	ENST00000330684.3:c.2537G>A	p.Arg846His	p.R846H	ENST00000330684	NM_001134407.1	846	cGc/cAc	12/13	0.354249110267131	4	FACETS	0.896	0.852	0.941			1	CLONAL	3	TRUE	NA	0.420695915337279	4		534	874	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56792500	56792500	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755282882	NA	P-0048112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	225	463	0	ENST00000308159.5:c.230G>A	p.Arg77Gln	p.R77Q	ENST00000308159	NM_014669.4	77	cGa/cAa	3/22	0.420695915337279	5	FACETS	0.943	0.879	1	0.629	0.586	0.673	CLONAL	2	TRUE	2	0.420695915337279	5		463	925	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61720122	61720122	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	110	431	0	ENST00000401558.2:c.1312G>A	p.Gly438Arg	p.G438R	ENST00000401558	NM_003400.3	438	Gga/Aga	13/25	0.420695915337279	3	FACETS	1	0.91	1	0.506	0.455	0.559	CLONAL	1	TRUE	1	0.420695915337279	3		431	626	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171570	32171570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424338671	NA	P-0048112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	242	666	0	ENST00000375023.3:c.3208G>A	p.Gly1070Ser	p.G1070S	ENST00000375023	NM_004557.3	1070	Ggt/Agt	20/30	0.343873459544694	4	FACETS	0.821	0.767	0.876	0.821	0.767	0.876	CLONAL	2	TRUE	2	0.420695915337279	4		666	996	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741742	145741742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1260734064	NA	P-0048112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1258	97	771	0	ENST00000428558.2:c.761C>T	p.Pro254Leu	p.P254L	ENST00000428558	NM_004260.3	254	cCc/cTc	5/22	0.225651992119953	6	FACETS	0.627	0.557	0.702	0.104	0.092	0.117	INDETERMINATE	1	TRUE	0	0.420695915337279	6		771	1355	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0048170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	40	165	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.374624877477875	3	FACETS	0.837	0.698	0.989	0.418	0.349	0.495	CLONAL	1	TRUE	1	0.380586852759096	3		165	299	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0048170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	341	863	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.295746956309088	3	FACETS	0.86	0.817	0.902	0.86	0.817	0.902	CLONAL	3	TRUE	0	0.380586852759096	3		864	827	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0048170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	86	225	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	0.374624877477875	3	FACETS	0.825	0.737	0.917	0.825	0.737	0.917	CLONAL	2	TRUE	1	0.380586852759096	3		225	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579400	7579401	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	958	865	3	ENST00000269305.4:c.286dup	p.Ser96PhefsTer53	p.S96Ffs*53	ENST00000269305	NM_001126112.2	96	tct/tTct	4/11	0.87840748005595	4	FACETS	0.993	0.982	1	0.993	0.982	1	CLONAL	4	TRUE	0	0.87840748005595	4		868	1032	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788648	3788648	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	575	472	0	ENST00000262367.5:c.4306A>T	p.Ser1436Cys	p.S1436C	ENST00000262367	NM_004380.2	1436	Agt/Tgt	26/31	0.764761132026847	5	FACETS	0.968	0.942	0.992	0.968	0.942	0.992	CLONAL	4	TRUE	1	0.87840748005595	5		472	784	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	77	261	0	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	0.381092249573512	1	FACETS	0.684	0.607	0.764	0.684	0.607	0.764	SUBCLONAL	1	TRUE	0	0.581056576682503	1		261	275	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925329	114925329	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	166	431	0	ENST00000543371.1:c.1407C>G	p.Cys469Trp	p.C469W	ENST00000543371	NM_001198531.1	469	tgC/tgG	14/14	0.375910841119902	1	FACETS	0.826	0.765	0.888	0.826	0.765	0.888	CLONAL	1	TRUE	0	0.581056576682503	1		431	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0048220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	267	487	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.581056576682503	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.581056576682503	1		487	579	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1962801	1962801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772470710	NA	P-0048220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	204	448	0	ENST00000382891.5:c.3295G>A	p.Glu1099Lys	p.E1099K	ENST00000382891	NM_133335.3	1099	Gag/Aag	18/22	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.581056576682503	2		448	579	SUCCESS
APC	324	MSKCC	GRCh37	5	112116523	112116523	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	60	256	0	ENST00000257430.4:c.568G>T	p.Glu190Ter	p.E190*	ENST00000257430	NM_000038.5	190	Gaa/Taa	6/16	0.381092249573512	1	FACETS	0.44	0.381	0.503	0.44	0.381	0.503	SUBCLONAL	1	TRUE	0	0.581056576682503	1		256	333	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0048230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	110	428	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.231364353051527	3	FACETS	1	0.982	1	0.712	0.642	0.787	CLONAL	1	TRUE	1	0.294772757657032	3		428	601	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056053	26056067	+	inframe_deletion	In_Frame_Del	DEL	CCTTGGGCTTAGCGG	CCTTGGGCTTAGCGG	-	rs756916945	NA	P-0048230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	120	416	0	ENST00000343677.2:c.590_604del	p.Ala197_Lys201del	p.A197_K201del	ENST00000343677	NM_005319.3	197	gCCGCTAAGCCCAAGGtt/gtt	1/1	0.247553616996976	2	FACETS	0.76	0.689	0.833	0.76	0.689	0.833	SUBCLONAL	2	TRUE	0	0.294772757657032	2		416	536	SUCCESS
APC	324	MSKCC	GRCh37	5	112175184	112175194	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCTAATACC	CTGCTAATACC	-	novel	NA	P-0048230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	67	196	0	ENST00000257430.4:c.3897_3907del	p.Thr1301SerfsTer10	p.T1301Sfs*10	ENST00000257430	NM_000038.5	1298	tCTGCTAATACC/t	16/16	0.294772757657032	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	2	TRUE	0	0.294772757657032	2		196	227	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119857	70119857	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	283	843	0	ENST00000245479.2:c.859G>T	p.Glu287Ter	p.E287*	ENST00000245479	NM_000346.3	287	Gag/Tag	3/3	0.294772757657032	2	FACETS	0.931	0.876	0.988	0.931	0.876	0.988	CLONAL	2	TRUE	0	0.294772757657032	2		843	1031	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0048242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	70	415	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.336161868963962	2		415	358	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0048242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	159	383	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.304008380286019	3	FACETS	0.937	0.87	1	0.937	0.87	1	CLONAL	3	TRUE	0	0.336161868963962	3		383	393	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244098	5244098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs73545312	NA	P-0048242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	403	885	0	ENST00000357368.4:c.1384G>A	p.Val462Ile	p.V462I	ENST00000357368	NM_002850.3	462	Gtc/Atc	11/38	1	2	FACETS	0.83	0.789	0.872	1	0.996	1	CLONAL	2	TRUE	1	0.336161868963962	2		885	1444	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725043	89725043	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1057517809	NA	P-0048242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	48	142	0	ENST00000371953.3:c.1027-1G>A		p.X343_splice	ENST00000371953	NM_000314.4	343			0.322707005370797	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.336161868963962	1		142	191	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186757	108186757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs864622251	NA	P-0048242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	67	354	0	ENST00000278616.4:c.6115G>A	p.Glu2039Lys	p.E2039K	ENST00000278616	NM_000051.3	2039	Gaa/Aaa	42/63	1	2	FACETS	0.852	0.742	0.97	0.852	0.742	0.97	CLONAL	1	TRUE	1	0.336161868963962	2		354	468	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976192	7976192	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756877833	NA	P-0048242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	107	691	0	ENST00000319144.4:c.2003G>A	p.Arg668His	p.R668H	ENST00000319144	NM_001139.2	668	cGc/cAc	15/15	1	2	FACETS	0.596	0.533	0.662	0.596	0.533	0.662	SUBCLONAL	1	TRUE	1	0.336161868963962	2		691	1069	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489870	40489871	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0048242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	124	456	0	ENST00000264657.5:c.555dup	p.Gln186AlafsTer35	p.Q186Afs*35	ENST00000264657	NM_139276.2	185	-/G	7/24	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.336161868963962	2		456	663	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141548	202141548	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0048242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	77	296	0	ENST00000358485.4:c.838-2A>G		p.X280_splice	ENST00000358485	NM_001080125.1	280			1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.336161868963962	2		296	457	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180390	38180390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	237	791	0	ENST00000396334.3:c.238C>T	p.Gln80Ter	p.Q80*	ENST00000396334	NM_002468.4	80	Caa/Taa	1/5	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.336161868963962	2		791	1243	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0048483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	110	670	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.663999132330591	2		670	324	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	187	550	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.663999132330591	2		550	519	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945478	151945478	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	268	757	0	ENST00000262189.6:c.2041G>T	p.Glu681Ter	p.E681*	ENST00000262189	NM_170606.2	681	Gaa/Taa	14/59	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.663999132330591	2		757	749	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075631	8075631	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	137	359	0	ENST00000377482.5:c.49A>T	p.Thr17Ser	p.T17S	ENST00000377482	NM_018948.3	17	Act/Tct	2/4	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.663999132330591	2		359	392	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242374	98242374	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0048483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	83	277	0	ENST00000331920.6:c.946-2A>G		p.X316_splice	ENST00000331920	NM_000264.3	316			1	2	FACETS	0.929	0.831	1	0.929	0.831	1	CLONAL	1	TRUE	1	0.663999132330591	2		277	269	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0048626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	122	273	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	1	2	FACETS	0.965	0.88	1	0.965	0.88	1	CLONAL	1	TRUE	1	0.641762819233922	2		273	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578466	7578466	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786202752	NA	P-0048626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	298	605	0	ENST00000269305.4:c.464C>A	p.Thr155Asn	p.T155N	ENST00000269305	NM_001126112.2	155	aCc/aAc	5/11	0.641762819233922	1	FACETS	0.969	0.92	1	0.969	0.92	1	CLONAL	1	TRUE	0	0.641762819233922	1		605	651	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575200	48575200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500743	NA	P-0048626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	113	198	0	ENST00000342988.3:c.394C>T	p.His132Tyr	p.H132Y	ENST00000342988	NM_005359.5	132	Cac/Tac	3/12	0.641762819233922	1	FACETS	0.938	0.86	1	0.938	0.86	1	CLONAL	1	TRUE	0	0.641762819233922	1		198	255	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450267	50450267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	212	439	0	ENST00000331340.3:c.451G>A	p.Gly151Arg	p.G151R	ENST00000331340	NM_006060.4	151	Ggg/Agg	5/8	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.641762819233922	2		439	651	SUCCESS
APC	324	MSKCC	GRCh37	5	112155043	112155043	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1114167579	NA	P-0048626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	192	283	0	ENST00000257430.4:c.1312+2T>C		p.X438_splice	ENST00000257430	NM_000038.5	438			0.221461119715138	2	FACETS	1	0.989	1	0.65	0.608	0.693	INDETERMINATE	1	TRUE	0	0.641762819233922	2		283	460	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718969	190718969	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	22	165	0	ENST00000441310.2:c.971C>G	p.Ser324Cys	p.S324C	ENST00000441310	NM_000534.4	324	tCt/tGt	9/13	1	2	FACETS	0.339	0.264	0.426	0.339	0.264	0.426	SUBCLONAL	1	TRUE	1	0.641762819233922	2		165	202	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0048658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	136	370	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.43937661047436	2		370	583	SUCCESS
AR	367	MSKCC	GRCh37	X	66765655	66765655	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1036966197	NA	P-0048658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	205	761	0	ENST00000374690.3:c.667G>A	p.Asp223Asn	p.D223N	ENST00000374690	NM_000044.3	223	Gac/Aac	1/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.43937661047436	2		761	830	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928108	+	inframe_deletion	In_Frame_Del	DEL	GAAGATTTGCTGAACCCTATTGGTGTTACT	GAAGATTTGCTGAACCCTATTGGTGTTACT	-	novel	NA	P-0048658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	56	435	0	ENST00000263967.3:c.1358_1387del	p.Glu453_Thr462del	p.E453_T462del	ENST00000263967	NM_006218.2	453	GAAGATTTGCTGAACCCTATTGGTGTTACT/-	8/21	1	2	FACETS	0.542	0.465	0.626	0.542	0.465	0.626	SUBCLONAL	1	TRUE	1	0.43937661047436	2		435	470	SUCCESS
APC	324	MSKCC	GRCh37	5	112175235	112175235	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0048658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	60	281	0	ENST00000257430.4:c.3944C>G	p.Ser1315Ter	p.S1315*	ENST00000257430	NM_000038.5	1315	tCa/tGa	16/16	1	2	FACETS	0.982	0.854	1	0.982	0.854	1	CLONAL	1	TRUE	1	0.43937661047436	2		281	278	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000019	42000019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	109	517	0	ENST00000219905.7:c.2282C>T	p.Pro761Leu	p.P761L	ENST00000219905	NM_001164273.1	761	cCt/cTt	6/24	1	2	FACETS	0.87	0.784	0.961	0.87	0.784	0.961	CLONAL	1	TRUE	1	0.43937661047436	2		517	570	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643348	52643348	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	80	408	1	ENST00000394830.3:c.2548C>T	p.Arg850Ter	p.R850*	ENST00000394830	NM_018313.4	850	Cga/Tga	17/30	1	2	FACETS	0.833	0.737	0.936	0.833	0.737	0.936	CLONAL	1	TRUE	1	0.43937661047436	2		409	437	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106194031	106194031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777027345	NA	P-0048658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	66	283	0	ENST00000380013.4:c.4493G>A	p.Arg1498His	p.R1498H	ENST00000380013	NM_001127208.2	1498	cGt/cAt	10/11	1	2	FACETS	0.801	0.699	0.911	0.801	0.699	0.911	CLONAL	1	TRUE	1	0.43937661047436	2		283	375	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061346	38061346	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	187	650	0	ENST00000250448.2:c.643C>T	p.Gln215Ter	p.Q215*	ENST00000250448	NM_004496.3	215	Cag/Tag	2/2	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.43937661047436	2		650	750	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117755	70117756	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	55	752	0	ENST00000245479.2:c.224dup	p.Ala76GlyfsTer176	p.A76Gfs*176	ENST00000245479	NM_000346.3	75	gag/gAag	1/3	1	2	FACETS	0.316	0.269	0.367	0.316	0.269	0.367	SUBCLONAL	1	TRUE	1	0.43937661047436	2		752	792	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120050	70120051	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0048658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	10	16	0	ENST00000245479.2:c.1054dup	p.Ala352GlyfsTer226	p.A352Gfs*226	ENST00000245479	NM_000346.3	351	cag/caGg	3/3	1	2	FACETS	1	0.821	1	1	0.821	1	CLONAL	1	TRUE	1	0.43937661047436	2		16	36	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0048933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	38	449	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.797595785902505	2		449	68	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0048933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	343	749	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.411442943614565	2	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.797595785902505	2		749	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0048933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	256	618	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.735481017066604	2	FACETS	0.912	0.876	0.947	0.912	0.876	0.947	CLONAL	2	TRUE	0	0.797595785902505	2		618	352	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672317	86672317	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	15	349	0	ENST00000274376.6:c.2119C>T	p.Arg707Cys	p.R707C	ENST00000274376	NM_002890.2	707	Cgt/Tgt	16/25	0.797595785902505	1	FACETS	0.983	0.8	1	0.983	0.8	1	CLONAL	1	TRUE	0	0.797595785902505	1		349	23	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678458	88678458	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747624231	NA	P-0048933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	118	647	0	ENST00000360948.2:c.1078G>A	p.Glu360Lys	p.E360K	ENST00000360948	NM_001012338.2	360	Gag/Aag	9/19	0.602361343792367	0	FACETS		NA	1			1	NA	1	TRUE	0	0.797595785902505	0		647	253	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298023	15298023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745672629	NA	P-0048933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	390	856	0	ENST00000263388.2:c.1733G>A	p.Arg578His	p.R578H	ENST00000263388	NM_000435.2	578	cGc/cAc	11/33	0.412364130731524	4	FACETS	0.919	0.877	0.962	0.919	0.877	0.962	INDETERMINATE	2	TRUE	2	0.797595785902505	4		856	956	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233987	133233987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761355093	NA	P-0048933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	240	594	0	ENST00000320574.5:c.3407G>A	p.Arg1136Gln	p.R1136Q	ENST00000320574	NM_006231.2	1136	cGg/cAg	28/49	0.194763408077931	3	FACETS	1	0.991	1	0.655	0.615	0.695	INDETERMINATE	1	TRUE	1	0.797595785902505	3		594	643	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457247	67457247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1566991387	NA	P-0048933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	324	703	2	ENST00000327367.4:c.221G>A	p.Arg74Gln	p.R74Q	ENST00000327367	NM_005902.3	74	cGg/cAg	2/9	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.797595785902505	2		705	764	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575161	48575161	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	16	236	0	ENST00000342988.3:c.357del	p.Phe119LeufsTer3	p.F119Lfs*3	ENST00000342988	NM_005359.5	119	Ttt/tt	3/12	0.723037282279884	1	FACETS	1	0.826	1	1	0.826	1	CLONAL	1	TRUE	0	0.797595785902505	1		236	24	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880972	134880972	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	144	586	0	ENST00000398015.3:c.1535C>A	p.Ala512Asp	p.A512D	ENST00000398015	NM_004441.4	512	gCt/gAt	7/16	0.797595785902505	1	FACETS	0.615	0.568	0.662	0.615	0.568	0.662	SUBCLONAL	1	TRUE	0	0.797595785902505	1		586	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0048971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	194	965	2	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.289424381696918	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.289424381696918	1		967	1040	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820528	44820528	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0048971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	29	230	0	ENST00000377967.4:c.226-1G>A		p.X76_splice	ENST00000377967	NM_021140.2	76			0.289424381696918	1	FACETS	0.587	0.472	0.717	0.587	0.472	0.717	SUBCLONAL	1	TRUE	0	0.289424381696918	1		230	292	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12043876	12043876	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	99	226	0	ENST00000396373.4:c.1255T>A	p.Phe419Ile	p.F419I	ENST00000396373	NM_001987.4	419	Ttt/Att	8/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.289424381696918	2		226	566	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883974	37883974	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	175	489	3	ENST00000269571.5:c.3445C>G	p.Pro1149Ala	p.P1149A	ENST00000269571		1149	Ccc/Gcc	27/27	0.289424381696918	1	FACETS	0.995	0.916	1	0.995	0.916	1	CLONAL	1	TRUE	0	0.289424381696918	1		492	1039	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165983	47165983	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	44	295	0	ENST00000409792.3:c.143G>T	p.Gly48Val	p.G48V	ENST00000409792	NM_014159.6	48	gGt/gTt	3/21	0.273720887200019	2	FACETS	0.429	0.359	0.507	0.214	0.179	0.254	SUBCLONAL	1	TRUE	0	0.289424381696918	2		295	709	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111534	56111534	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	14	50	0	ENST00000399503.3:c.136del	p.Glu46ArgfsTer139	p.E46Rfs*139	ENST00000399503	NM_005921.1	45	cGg/cg	1/20	1	2	FACETS	0.677	0.492	0.897	0.677	0.492	0.897	SUBCLONAL	1	TRUE	1	0.289424381696918	2		50	143	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224317	55224317	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2327	128	319	1	ENST00000275493.2:c.1098T>A	p.Ser366Arg	p.S366R	ENST00000275493	NM_005228.3	366	agT/agA	9/28	0.289424381696918	16	FACETS	1	0.951	1	0.073	0.065	0.081	CLONAL	1	TRUE	1	0.289424381696918	16		320	2455	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393192	139393456	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTGCCCGCATCATGCGGGTGGGGCCCACATGCGGGCCCAGCGACCCTCGAGACCCTGTGGGTCAGGCCCTTGTGTCCCTGCGCCCCGTGGGTTTGGCCCTCACTTCTCTGTGGATTCAGCCCTCACGTCTCCCCTGGCATCCCAGCCTCGCGCTCACCCTGTTGTTCTGCATATCTTTGTTAGCCCCGTTCTTCAGGAGCACAACTGCGGCATCCACATTGTTCACGGCGGCGGCCCAGTGCAGGGCGGACTTGCCTGCGTGA	AGGTGCCCGCATCATGCGGGTGGGGCCCACATGCGGGCCCAGCGACCCTCGAGACCCTGTGGGTCAGGCCCTTGTGTCCCTGCGCCCCGTGGGTTTGGCCCTCACTTCTCTGTGGATTCAGCCCTCACGTCTCCCCTGGCATCCCAGCCTCGCGCTCACCCTGTTGTTCTGCATATCTTTGTTAGCCCCGTTCTTCAGGAGCACAACTGCGGCATCCACATTGTTCACGGCGGCGGCCCAGTGCAGGGCGGACTTGCCTGCGTGA	-	novel	NA	P-0048971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	40	96	0	ENST00000277541.6:c.6083-8_6180+159del		p.X2028_splice	ENST00000277541	NM_017617.3	2028		33/34	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.289424381696918	2		96	200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0049063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	76	1045	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.14	2		1046	982	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953011	2953011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1172378918	NA	P-0049063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	60	771	1	ENST00000396946.4:c.2929G>A	p.Val977Met	p.V977M	ENST00000396946	NM_032415.4	977	Gtg/Atg	22/25	0.3	2	FACETS	0.806	0.692	0.931			1	CLONAL	1	TRUE	NA	0.14	2		772	1064	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559731	29559731	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	23	262	0	ENST00000356175.3:c.3328T>G	p.Phe1110Val	p.F1110V	ENST00000356175	NM_000267.3	1110	Ttt/Gtt	26/57	1	2	FACETS	0.903	0.703	1	0.903	0.703	1	CLONAL	1	TRUE	1	0.14	2		262	364	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559743	29559743	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	29	303	0	ENST00000356175.3:c.3340T>G	p.Leu1114Val	p.L1114V	ENST00000356175	NM_000267.3	1114	Ttg/Gtg	26/57	1	2	FACETS	0.948	0.76	1	0.948	0.76	1	CLONAL	1	TRUE	1	0.14	2		303	437	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368322	45368322	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0049063-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	27	330	0	ENST00000262160.6:c.1281-1G>C		p.X427_splice	ENST00000262160	NM_005901.5	427			1	2	FACETS	0.79	0.628	0.977	0.79	0.628	0.977	CLONAL	1	TRUE	1	0.14	2		330	488	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0049065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	87	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.0832840534805424	4	FACETS	0.797	0.71	0.89	0.797	0.71	0.89	INDETERMINATE	2	TRUE	2	0.359042427298851	4		457	413	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0049065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	50	208	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.321694025220351	4	FACETS	1	0.951	1	0.431	0.367	0.499	CLONAL	1	TRUE	1	0.359042427298851	4		208	293	SUCCESS
APC	324	MSKCC	GRCh37	5	112173299	112173299	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0049065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	66	164	0	ENST00000257430.4:c.2008A>T	p.Lys670Ter	p.K670*	ENST00000257430	NM_000038.5	670	Aaa/Taa	16/16	0.108764783591763	3	FACETS	1	0.937	1	0.73	0.645	0.818	INDETERMINATE	2	TRUE	0	0.359042427298851	3		164	198	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577599	7577600	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1567550002	NA	P-0049065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	173	403	0	ENST00000269305.4:c.681dup	p.Asp228Ter	p.D228*	ENST00000269305	NM_001126112.2	227	-/T	7/11	0.359042427298851	1	FACETS	0.854	0.793	0.915	1	0.992	1	CLONAL	2	TRUE	0	0.359042427298851	1		403	463	SUCCESS
APC	324	MSKCC	GRCh37	5	112175754	112175755	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0049065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	61	234	0	ENST00000257430.4:c.4464_4465del	p.Leu1488PhefsTer25	p.L1488Ffs*25	ENST00000257430	NM_000038.5	1488	tTA/t	16/16	0.108764783591763	3	FACETS	1	0.941	1	0.385	0.334	0.44	INDETERMINATE	1	TRUE	0	0.359042427298851	3		234	347	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719941	18719941	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1234321768	NA	P-0049065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	41	338	0	ENST00000266497.5:c.3838C>A	p.Leu1280Ile	p.L1280I	ENST00000266497		1280	Cta/Ata	27/31	0.0832840534805424	4	FACETS	0.605	0.504	0.718	0.303	0.252	0.359	INDETERMINATE	1	TRUE	2	0.359042427298851	4		338	513	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119692	70119692	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	369	529	0	ENST00000245479.2:c.694C>T	p.Gln232Ter	p.Q232*	ENST00000245479	NM_000346.3	232	Cag/Tag	3/3	0.359042427298851	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	1	0.359042427298851	4		529	834	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026833	71026857	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTGCGTTCTTATAAAATTCTTGG	TTCTGCGTTCTTATAAAATTCTTGG	-	novel	NA	P-0049065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	27	186	0	ENST00000318789.4:c.1365_1389del	p.Asn455LysfsTer11	p.N455Kfs*11	ENST00000318789	NM_032682.5	455	aaCCAAGAATTTTATAAGAACGCAGAA/aa	16/21	1	2	FACETS	0.611	0.488	0.751	0.611	0.488	0.751	SUBCLONAL	1	TRUE	1	0.359042427298851	2		186	246	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27168562	27168563	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	61	376	0	ENST00000380036.4:c.434_435insC	p.Lys145AsnfsTer5	p.K145Nfs*5	ENST00000380036	NM_000459.3	145	aag/aaCg	3/23	1	2	FACETS	0.691	0.597	0.792	0.691	0.597	0.792	SUBCLONAL	1	TRUE	1	0.359042427298851	2		376	492	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0049069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	85	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.137114920964356	3	FACETS	0.916	0.811	1	0.458	0.405	0.514	INDETERMINATE	1	TRUE	1	0.41225055228193	3		457	543	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0049069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	40	501	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.41225055228193	1	FACETS	0.326	0.27	0.387	0.326	0.27	0.387	SUBCLONAL	1	TRUE	0	0.41225055228193	1		502	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0049069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	173	863	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.41225055228193	1	FACETS	0.971	0.897	1	0.971	0.897	1	CLONAL	1	TRUE	0	0.41225055228193	1		864	686	SUCCESS
APC	324	MSKCC	GRCh37	5	112175766	112175766	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	114	315	0	ENST00000257430.4:c.4476del	p.Thr1493ArgfsTer14	p.T1493Rfs*14	ENST00000257430	NM_000038.5	1492	gCc/gc	16/16	0.145915086800309	3	FACETS	0.813	0.738	0.892	0.813	0.738	0.892	INDETERMINATE	2	TRUE	1	0.41225055228193	3		315	410	SUCCESS
APC	324	MSKCC	GRCh37	5	112174092	112174093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	80	283	0	ENST00000257430.4:c.2803dup	p.Tyr935LeufsTer5	p.Y935Lfs*5	ENST00000257430	NM_000038.5	934	act/acTt	16/16	0.145915086800309	3	FACETS	1	0.94	1	0.549	0.486	0.617	INDETERMINATE	1	TRUE	1	0.41225055228193	3		283	426	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121912580	NA	P-0049069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	97	281	0	ENST00000342988.3:c.1157G>T	p.Gly386Val	p.G386V	ENST00000342988	NM_005359.5	386	gGt/gTt	10/12	0.41225055228193	1	FACETS	0.92	0.826	1	0.92	0.826	1	CLONAL	1	TRUE	0	0.41225055228193	1		281	406	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619835	1619835	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	240	867	2	ENST00000344749.5:c.1111C>T	p.Arg371Ter	p.R371*	ENST00000344749	NM_001136139.2	371	Cga/Tga	14/19	0.41225055228193	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.41225055228193	1		869	866	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50827519	50827519	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568978023	NA	P-0049069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	64	449	1	ENST00000398568.2:c.2404G>A	p.Asp802Asn	p.D802N	ENST00000398568	NM_001042412.1	802	Gat/Aat	16/18	1	2	FACETS	0.473	0.409	0.543	0.473	0.409	0.543	SUBCLONAL	1	TRUE	1	0.41225055228193	2		450	656	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435987	110435987	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	228	972	0	ENST00000375856.3:c.2414C>A	p.Ser805Tyr	p.S805Y	ENST00000375856	NM_003749.2	805	tCc/tAc	1/2	0.145915086800309	3	FACETS	1	0.985	1	0.597	0.556	0.64	INDETERMINATE	1	TRUE	1	0.41225055228193	3		972	1117	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003757	45003866	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTGGCCTTAGCTGTGCTCGCGCTACTCTCTCTTTCTGGCCTGGAGGCTATCCAGCGTGAGTCTCTCCTACCCTCCCGCTCTGGTCCTTCCTCTCCCGCTCTGCACCCTCT	GTGGCCTTAGCTGTGCTCGCGCTACTCTCTCTTTCTGGCCTGGAGGCTATCCAGCGTGAGTCTCTCCTACCCTCCCGCTCTGGTCCTTCCTCTCCCGCTCTGCACCCTCT	-	novel	NA	P-0049069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	32	573	0	ENST00000558401.1:c.19_67+61del		p.X7_splice	ENST00000558401	NM_004048.2	7		1/4	0.41225055228193	1	FACETS	0.228	0.184	0.277	0.228	0.184	0.277	SUBCLONAL	1	TRUE	0	0.41225055228193	1		573	541	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0049078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	52	1445	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.16	2		1452	644	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864117	57864117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749783306	NA	P-0049182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	123	737	0	ENST00000228682.2:c.1594C>T	p.Arg532Cys	p.R532C	ENST00000228682	NM_005269.2	532	Cgc/Tgc	12/12	0.555981149619868	4	FACETS	0.816	0.738	0.897	0.408	0.369	0.449	CLONAL	1	TRUE	2	0.715742945482753	4		737	723	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640428	3640428	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	101	933	1	ENST00000294008.3:c.3211C>A	p.Pro1071Thr	p.P1071T	ENST00000294008	NM_032444.2	1071	Cca/Aca	12/15	0.189671975106474	3	FACETS	0.412	0.367	0.459	0.206	0.183	0.23	INDETERMINATE	1	TRUE	1	0.715742945482753	3		934	931	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578448	7578448	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1064795691	NA	P-0049182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	714	898	2	ENST00000269305.4:c.482C>A	p.Ala161Asp	p.A161D	ENST00000269305	NM_001126112.2	161	gCc/gAc	5/11	0.695037170169349	3	FACETS	0.989	0.968	1	0.989	0.968	1	CLONAL	3	TRUE	0	0.715742945482753	3		900	913	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913403	NA	P-0049182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	327	364	1	ENST00000349496.5:c.110C>A	p.Ser37Tyr	p.S37Y	ENST00000349496	NM_001904.3	37	tCt/tAt	3/15	0.55971117820286	4	FACETS	0.992	0.951	1	0.992	0.951	1	CLONAL	3	TRUE	1	0.715742945482753	4		365	527	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275649	41275649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	154	486	0	ENST00000349496.5:c.1544G>A	p.Arg515Gln	p.R515Q	ENST00000349496	NM_001904.3	515	cGa/cAa	10/15	0.55971117820286	4	FACETS	1	0.983	1	0.418	0.384	0.453	CLONAL	1	TRUE	1	0.715742945482753	4		486	589	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277899	41277901	+	inframe_deletion	In_Frame_Del	DEL	TGC	TGC	-	novel	NA	P-0049182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	312	475	0	ENST00000349496.5:c.1864_1866del	p.Ala622del	p.A622del	ENST00000349496	NM_001904.3	621	ctTGCt/ctt	12/15	0.55971117820286	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	TRUE	1	0.715742945482753	4		475	492	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029298	143029298	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779066563	NA	P-0049182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	88	314	0	ENST00000262992.4:c.2322C>A	p.Phe774Leu	p.F774L	ENST00000262992	NM_001101669.1	774	ttC/ttA	21/24	0.189671975106474	3	FACETS	1	0.959	1	0.57	0.511	0.631	INDETERMINATE	1	TRUE	1	0.715742945482753	3		314	293	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523717	148523717	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	84	274	0	ENST00000320356.2:c.736G>C	p.Glu246Gln	p.E246Q	ENST00000320356	NM_004456.4	246	Gaa/Caa	8/20	0.715742945482753	6	FACETS	0.996	0.881	1	0.249	0.22	0.28	CLONAL	1	TRUE	2	0.715742945482753	6		274	573	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932264	39932264	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	54	916	1	ENST00000378444.4:c.2335G>T	p.Val779Phe	p.V779F	ENST00000378444	NM_001123385.1	779	Gtc/Ttc	4/15	1	2	FACETS	0.186	0.158	0.216	0.186	0.158	0.216	SUBCLONAL	1	TRUE	1	0.715742945482753	2		917	813	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	97	466	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.787	0.702	0.876	0.787	0.702	0.876	SUBCLONAL	1	TRUE	1	0.38	2		466	649	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	31	195	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.502	0.407	0.61	0.502	0.407	0.61	SUBCLONAL	1	TRUE	1	0.38	2		195	325	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	47	514	0	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	1	2	FACETS	0.29	0.244	0.342	0.29	0.244	0.342	SUBCLONAL	1	TRUE	1	0.38	2		514	852	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	244	498	4	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.949	1	1	0.995	1	CLONAL	2	TRUE	1	0.38	2		502	636	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979987	7979987	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746723399	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	57	605	0	ENST00000319144.4:c.1350del	p.Leu451SerfsTer16	p.L451Sfs*16	ENST00000319144	NM_001139.2	450	ggG/gg	10/15	1	2	FACETS	0.326	0.279	0.378	0.326	0.279	0.378	SUBCLONAL	1	TRUE	1	0.38	2		605	920	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	178	747	5	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.914	0.842	0.989	0.914	0.842	0.989	CLONAL	1	TRUE	1	0.38	2		752	1025	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	104	383	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.38	2		383	520	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	131	638	2	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.795	0.721	0.873	0.795	0.721	0.873	SUBCLONAL	1	TRUE	1	0.38	2		640	867	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	66	277	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.949	0.828	1	0.949	0.828	1	CLONAL	1	TRUE	1	0.38	2		277	366	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	75	219	1	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.38	2		220	379	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	81	236	1	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	1	2	FACETS	0.985	0.872	1	0.985	0.872	1	CLONAL	1	TRUE	1	0.38	2		237	433	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	110	585	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	0.698	0.626	0.773	0.698	0.626	0.773	SUBCLONAL	1	TRUE	1	0.38	2		585	830	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	40	200	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.804	0.672	0.948	0.804	0.672	0.948	CLONAL	1	TRUE	1	0.38	2		200	262	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	182	720	2	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	0.991	0.914	1	0.991	0.914	1	CLONAL	1	TRUE	1	0.38	2		722	967	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	26	308	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.262	0.207	0.326	0.262	0.207	0.326	SUBCLONAL	1	TRUE	1	0.38	2		308	522	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310208	91310208	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs747341586	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	50	137	0	ENST00000355112.3:c.2268del	p.Asp757ThrfsTer4	p.D757Tfs*4	ENST00000355112	NM_000057.2	754	tcA/tc	10/22	1	2	FACETS	0.748	0.637	0.868	0.748	0.637	0.868	SUBCLONAL	1	TRUE	1	0.38	2		137	352	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	60	465	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.562	0.484	0.647	0.562	0.484	0.647	SUBCLONAL	1	TRUE	1	0.38	2		465	562	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857881	89857881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772567344	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	70	618	4	ENST00000389301.3:c.1289C>T	p.Ala430Val	p.A430V	ENST00000389301	NM_000135.2	430	gCg/gTg	14/43	1	2	FACETS	0.393	0.341	0.449	0.393	0.341	0.449	SUBCLONAL	1	TRUE	1	0.38	2		622	938	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151290	202151290	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	105	313	0	ENST00000358485.4:c.1596del	p.Lys532AsnfsTer73	p.K532Nfs*73	ENST00000358485	NM_001080125.1	530	agA/ag	9/9	1	2	FACETS	0.945	0.849	1	0.945	0.849	1	CLONAL	1	TRUE	1	0.38	2		313	585	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957465	175957465	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	98	354	1	ENST00000367669.3:c.1931del	p.Asn644ThrfsTer3	p.N644Tfs*3	ENST00000367669	NM_022457.5	644	aAc/ac	17/20	1	2	FACETS	0.848	0.758	0.944	0.848	0.758	0.944	CLONAL	1	TRUE	1	0.38	2		355	608	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910405	29910405	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	117	784	0	ENST00000376809.5:c.73+2T>C		p.X25_splice	ENST00000376809	NM_002116.7	25			1	2	FACETS	0.623	0.56	0.689	0.623	0.56	0.689	SUBCLONAL	1	TRUE	1	0.38	2		784	989	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657020	47657020	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63751108	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	87	290	2	ENST00000233146.2:c.1216C>T	p.Arg406Ter	p.R406*	ENST00000233146	NM_000251.2	406	Cga/Tga	7/16	1	2	FACETS	0.876	0.777	0.98	0.876	0.777	0.98	CLONAL	1	TRUE	1	0.38	2		292	523	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306553	41306553	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	112	518	1	ENST00000373198.4:c.1106del	p.Gly369ValfsTer28	p.G369Vfs*28	ENST00000373198	NM_133170.3	369	gGt/gt	7/32	1	2	FACETS	0.814	0.733	0.9	0.814	0.733	0.9	CLONAL	1	TRUE	1	0.38	2		519	724	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446388	29446388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769322016	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	197	769	1	ENST00000389048.3:c.3179G>A	p.Arg1060His	p.R1060H	ENST00000389048	NM_004304.4	1060	cGc/cAc	20/29	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.38	2		770	1021	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	120	800	0	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	1	2	FACETS	0.577	0.52	0.638	0.577	0.52	0.638	SUBCLONAL	1	TRUE	1	0.38	2		800	1094	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913436	32913436	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	93	291	0	ENST00000380152.3:c.4948del	p.Ser1650ValfsTer20	p.S1650Vfs*20	ENST00000380152		1648	gcA/gc	11/27	1	2	FACETS	0.787	0.701	0.879	0.787	0.701	0.879	SUBCLONAL	1	TRUE	1	0.38	2		291	622	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412473	63412473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	131	338	0	ENST00000330258.3:c.694del	p.Gln232LysfsTer50	p.Q232Kfs*50	ENST00000330258	NM_152424.3	232	Caa/aa	2/2	1	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.38	1		338	472	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679577	86679577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	118	414	1	ENST00000274376.6:c.2738G>A	p.Arg913Gln	p.R913Q	ENST00000274376	NM_002890.2	913	cGg/cAg	21/25	1	2	FACETS	0.95	0.858	1	0.95	0.858	1	CLONAL	1	TRUE	1	0.38	2		415	654	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912052	50912052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773180520	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	161	745	0	ENST00000440232.2:c.1786G>A	p.Val596Ile	p.V596I	ENST00000440232	NM_002691.3	596	Gtc/Atc	15/27	1	2	FACETS	0.859	0.788	0.934	0.859	0.788	0.934	CLONAL	1	TRUE	1	0.38	2		745	986	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143204	30143204	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1268240399	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	141	764	1	ENST00000389048.3:c.322del	p.Val108SerfsTer20	p.V108Sfs*20	ENST00000389048	NM_004304.4	108	Gtc/tc	1/29	1	2	FACETS	0.933	0.851	1	0.933	0.851	1	CLONAL	1	TRUE	1	0.38	2		765	795	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43730536	43730536	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	104	454	1	ENST00000382044.4:c.3177del	p.Thr1060ProfsTer36	p.T1060Pfs*36	ENST00000382044	NM_001141980.1	1059	ccC/cc	16/28	1	2	FACETS	0.805	0.721	0.893	0.805	0.721	0.893	CLONAL	1	TRUE	1	0.38	2		455	680	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805884	46805884	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	109	627	2	ENST00000290295.7:c.72del	p.Arg25GlyfsTer9	p.R25Gfs*9	ENST00000290295	NM_006361.5	24	ggG/gg	1/2	1	2	FACETS	0.86	0.773	0.952	0.86	0.773	0.952	CLONAL	1	TRUE	1	0.38	2		629	667	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276929	123276929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200204947	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	66	382	0	ENST00000358487.5:c.988C>T	p.Arg330Trp	p.R330W	ENST00000358487	NM_000141.4	330	Cgg/Tgg	8/18	1	2	FACETS	0.544	0.472	0.623	0.544	0.472	0.623	SUBCLONAL	1	TRUE	1	0.38	2		382	638	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023010	27023010	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	15	76	0	ENST00000324856.7:c.116C>A	p.Ala39Glu	p.A39E	ENST00000324856	NM_006015.4	39	gCg/gAg	1/20	1	2	FACETS	0.774	0.573	1	0.774	0.573	1	CLONAL	1	TRUE	1	0.38	2		76	102	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346437	89346437	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555525603	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	180	1386	4	ENST00000301030.4:c.6513del	p.Val2173SerfsTer2	p.V2173Sfs*2	ENST00000301030	NM_001256183.1	2171	ccC/cc	9/13	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.38	2		1390	909	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81891943	81891943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771121259	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	163	565	1	ENST00000359376.3:c.413C>T	p.Thr138Met	p.T138M	ENST00000359376	NM_002661.3	138	aCg/aTg	4/33	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.38	2		566	819	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778282	3778282	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	151	715	1	ENST00000262367.5:c.6766del	p.Leu2256SerfsTer46	p.L2256Sfs*46	ENST00000262367	NM_004380.2	2256	Ctc/tc	31/31	1	2	FACETS	0.859	0.785	0.937	0.859	0.785	0.937	CLONAL	1	TRUE	1	0.38	2		716	925	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845479	128845479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	204	673	1	ENST00000249373.3:c.776C>T	p.Ser259Leu	p.S259L	ENST00000249373	NM_005631.4	259	tCg/tTg	4/12	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.38	2		674	986	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042169	6042169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35629870	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	113	453	0	ENST00000265849.7:c.452G>A	p.Arg151His	p.R151H	ENST00000265849	NM_000535.5	151	cGc/cAc	5/15	1	2	FACETS	0.861	0.775	0.951	0.861	0.775	0.951	CLONAL	1	TRUE	1	0.38	2		453	691	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500479	149500479	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218819598	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	139	646	2	ENST00000261799.4:c.2558G>A	p.Arg853Gln	p.R853Q	ENST00000261799	NM_002609.3	853	cGg/cAg	18/23	1	2	FACETS	0.839	0.764	0.918	0.839	0.764	0.918	CLONAL	1	TRUE	1	0.38	2		648	872	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443582	29443582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143790259	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	140	669	0	ENST00000389048.3:c.3635G>A	p.Arg1212His	p.R1212H	ENST00000389048	NM_004304.4	1212	cGc/cAc	23/29	1	2	FACETS	0.831	0.756	0.909	0.831	0.756	0.909	CLONAL	1	TRUE	1	0.38	2		669	887	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006101	22006101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1425823622	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	168	698	0	ENST00000276925.6:c.302G>A	p.Arg101Gln	p.R101Q	ENST00000276925	NM_004936.3	101	cGg/cAg	2/2	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.38	2		698	837	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786409	135786409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564488001	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	118	429	1	ENST00000298552.3:c.1121G>A	p.Ser374Asn	p.S374N	ENST00000298552	NM_001162426.1	374	aGt/aAt	11/23	1	2	FACETS	0.897	0.811	0.989	0.897	0.811	0.989	CLONAL	1	TRUE	1	0.38	2		430	692	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347605	118347605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756562807	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	147	493	0	ENST00000534358.1:c.3242G>A	p.Arg1081Gln	p.R1081Q	ENST00000534358	NM_005933.3	1081	cGa/cAa	4/36	1	2	FACETS	0.886	0.809	0.967	0.886	0.809	0.967	CLONAL	1	TRUE	1	0.38	2		493	873	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223188	2223188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373051088	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	162	644	3	ENST00000326181.6:c.800C>T	p.Thr267Met	p.T267M	ENST00000326181	NM_032271.2	267	aCg/aTg	10/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.38	2		647	787	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223355	36223355	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	195	858	0	ENST00000222270.7:c.5909del	p.Pro1970LeufsTer17	p.P1970Lfs*17	ENST00000222270	NM_014727.1	1969	Ccc/cc	28/37	1	2	FACETS	0.956	0.884	1	0.956	0.884	1	CLONAL	1	TRUE	1	0.38	2		858	1073	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246490641	246490641	+	splice_acceptor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	60	198	2	ENST00000388985.4:c.395-2del		p.X132_splice	ENST00000388985		132			1	2	FACETS	0.738	0.637	0.846	0.738	0.637	0.846	SUBCLONAL	1	TRUE	1	0.38	2		200	428	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851678	63851678	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	60	470	0	ENST00000279873.7:c.2456T>C	p.Leu819Pro	p.L819P	ENST00000279873	NM_032199.2	819	cTc/cCc	10/10	1	2	FACETS	0.486	0.418	0.56	0.486	0.418	0.56	SUBCLONAL	1	TRUE	1	0.38	2		470	650	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94922944	94922944	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	91	235	0	ENST00000536441.1:c.524A>G	p.Gln175Arg	p.Q175R	ENST00000536441	NM_144665.3	175	cAg/cGg	4/10	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.38	2		235	477	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203574	108203574	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	59	317	0	ENST00000278616.4:c.7874A>G	p.Asp2625Gly	p.D2625G	ENST00000278616	NM_000051.3	2625	gAt/gGt	53/63	1	2	FACETS	0.569	0.489	0.655	0.569	0.489	0.655	SUBCLONAL	1	TRUE	1	0.38	2		317	546	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373338	118373340	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	89	465	0	ENST00000534358.1:c.6731_6733del	p.Lys2244_Val2245delinsIle	p.K2244_V2245delinsI	ENST00000534358	NM_005933.3	2244	aAAGta/ata	27/36	1	2	FACETS	0.683	0.605	0.765	0.683	0.605	0.765	SUBCLONAL	1	TRUE	1	0.38	2		465	686	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426380	49426380	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	171	733	1	ENST00000301067.7:c.12108G>T	p.Glu4036Asp	p.E4036D	ENST00000301067	NM_003482.3	4036	gaG/gaT	39/54	1	2	FACETS	0.807	0.741	0.876	0.807	0.741	0.876	CLONAL	1	TRUE	1	0.38	2		734	1115	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495713	56495713	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	112	481	0	ENST00000267101.3:c.3903G>T	p.Gln1301His	p.Q1301H	ENST00000267101	NM_001982.3	1301	caG/caT	28/28	1	2	FACETS	0.963	0.868	1	0.963	0.868	1	CLONAL	1	TRUE	1	0.38	2		481	612	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112133	115112133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	164	653	1	ENST00000257566.3:c.1607C>T	p.Ala536Val	p.A536V	ENST00000257566	NM_016569.3	536	gCc/gTc	7/8	1	2	FACETS	0.973	0.894	1	0.973	0.894	1	CLONAL	1	TRUE	1	0.38	2		654	887	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252087	133252087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556789278	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	172	665	1	ENST00000320574.5:c.1123C>T	p.Arg375Trp	p.R375W	ENST00000320574	NM_006231.2	375	Cgg/Tgg	12/49	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.38	2		666	854	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528027	103528027	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	75	347	0	ENST00000355739.4:c.3335A>T	p.Asn1112Ile	p.N1112I	ENST00000355739	NM_000123.3	1112	aAt/aTt	15/15	1	2	FACETS	0.765	0.672	0.865	0.765	0.672	0.865	SUBCLONAL	1	TRUE	1	0.38	2		347	516	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639828	3639828	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	173	731	0	ENST00000294008.3:c.3811T>C	p.Ser1271Pro	p.S1271P	ENST00000294008	NM_032444.2	1271	Tcc/Ccc	12/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.38	2		731	854	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646281	23646281	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	166	539	0	ENST00000261584.4:c.1586C>A	p.Pro529Gln	p.P529Q	ENST00000261584	NM_024675.3	529	cCa/cAa	4/13	1	2	FACETS	0.909	0.835	0.987	0.909	0.835	0.987	CLONAL	1	TRUE	1	0.38	2		539	961	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644873	67644874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	147	508	0	ENST00000264010.4:c.143dup	p.Glu49Ter	p.E49*	ENST00000264010	NM_006565.3	46	-/G	3/12	1	2	FACETS	0.983	0.898	1	0.983	0.898	1	CLONAL	1	TRUE	1	0.38	2		508	787	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271789	15271789	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	88	900	1	ENST00000263388.2:c.6650A>G	p.His2217Arg	p.H2217R	ENST00000263388	NM_000435.2	2217	cAt/cGt	33/33	1	2	FACETS	0.433	0.383	0.488	0.433	0.383	0.488	SUBCLONAL	1	TRUE	1	0.38	2		901	1069	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266758	18266758	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	184	743	1	ENST00000222254.8:c.70del	p.Glu24SerfsTer9	p.E24Sfs*9	ENST00000222254	NM_005027.3	23	ctG/ct	2/16	1	2	FACETS	0.973	0.898	1	0.973	0.898	1	CLONAL	1	TRUE	1	0.38	2		744	995	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218612	36218612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	175	762	0	ENST00000222270.7:c.4316G>A	p.Gly1439Glu	p.G1439E	ENST00000222270	NM_014727.1	1439	gGg/gAg	17/37	1	2	FACETS	0.956	0.881	1	0.956	0.881	1	CLONAL	1	TRUE	1	0.38	2		762	963	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639556	47639557	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	55	145	0	ENST00000233146.2:c.651dup	p.Gln218SerfsTer14	p.Q218Sfs*14	ENST00000233146	NM_000251.2	217	att/aTtt	4/16	1	2	FACETS	0.846	0.728	0.975	0.846	0.728	0.975	CLONAL	1	TRUE	1	0.38	2		145	342	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561123	9561123	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	49	329	2	ENST00000353224.5:c.659A>G	p.Gln220Arg	p.Q220R	ENST00000353224	NM_177990.2	220	cAg/cGg	4/10	1	2	FACETS	0.497	0.421	0.581	0.497	0.421	0.581	SUBCLONAL	1	TRUE	1	0.38	2		331	519	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498420	89498420	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	35	304	0	ENST00000336596.2:c.2392T>C	p.Tyr798His	p.Y798H	ENST00000336596	NM_005233.5	798	Tac/Cac	14/17	1	2	FACETS	0.35	0.286	0.421	0.35	0.286	0.421	SUBCLONAL	1	TRUE	1	0.38	2		304	527	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188982	142188982	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	58	245	1	ENST00000350721.4:c.6265C>T	p.Arg2089Ter	p.R2089*	ENST00000350721	NM_001184.3	2089	Cga/Tga	37/47	1	2	FACETS	0.725	0.625	0.834	0.725	0.625	0.834	SUBCLONAL	1	TRUE	1	0.38	2		246	421	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612241	189612241	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	130	462	0	ENST00000264731.3:c.1993A>G	p.Met665Val	p.M665V	ENST00000264731	NM_003722.4	665	Atg/Gtg	14/14	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.38	2		462	684	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747995	41747996	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCG	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	10	89	0	ENST00000226382.2:c.773_774insCGC	p.Ala260dup	p.A260dup	ENST00000226382	NM_003924.3	260	gcg/gcCGCg	3/3	1	2	FACETS	0.605	0.414	0.838	0.605	0.414	0.838	SUBCLONAL	1	TRUE	1	0.38	2		89	87	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541682	187541682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	75	371	0	ENST00000441802.2:c.6058G>A	p.Asp2020Asn	p.D2020N	ENST00000441802	NM_005245.3	2020	Gat/Aat	10/27	1	2	FACETS	0.91	0.8	1	0.91	0.8	1	CLONAL	1	TRUE	1	0.38	2		371	434	SUCCESS
APC	324	MSKCC	GRCh37	5	112174086	112174089	+	frameshift_variant	Frame_Shift_Del	DEL	CAAA	CAAA	-	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	80	280	0	ENST00000257430.4:c.2797_2800del	p.Asn933LeufsTer21	p.N933Lfs*21	ENST00000257430	NM_000038.5	932	tCAAAc/tc	16/16	1	2	FACETS	0.917	0.811	1	0.917	0.811	1	CLONAL	1	TRUE	1	0.38	2		280	459	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223578	55223578	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	170	616	1	ENST00000275493.2:c.945C>A	p.Ser315Arg	p.S315R	ENST00000275493	NM_005228.3	315	agC/agA	8/28	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.38	2		617	838	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436129	116436129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	108	398	0	ENST00000397752.3:c.4124C>T	p.Ala1375Val	p.A1375V	ENST00000397752	NM_000245.2	1375	gCt/gTt	21/21	1	2	FACETS	0.915	0.823	1	0.915	0.823	1	CLONAL	1	TRUE	1	0.38	2		398	621	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148526902	148526902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	56	171	0	ENST00000320356.2:c.402G>A	p.Met134Ile	p.M134I	ENST00000320356	NM_004456.4	134	atG/atA	5/20	1	2	FACETS	0.71	0.61	0.819	0.71	0.61	0.819	SUBCLONAL	1	TRUE	1	0.38	2		171	415	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194670	29194670	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs772256235	NA	P-0049376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	110	750	1	ENST00000240100.2:c.1058G>T	p.Arg353Leu	p.R353L	ENST00000240100	NM_001394.6	353	cGg/cTg	4/4	1	2	FACETS	0.643	0.577	0.713	0.643	0.577	0.713	SUBCLONAL	1	TRUE	1	0.38	2		751	900	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	49	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.2	2		487	464	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223669	36223669	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	70	796	0	ENST00000222270.7:c.6219G>C	p.Glu2073Asp	p.E2073D	ENST00000222270	NM_014727.1	2073	gaG/gaC	28/37	1	2	FACETS	0.752	0.654	0.858	0.752	0.654	0.858	SUBCLONAL	1	TRUE	1	0.2	2		796	931	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	63	445	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.214302071611114	1	FACETS	0.774	0.669	0.889	0.774	0.669	0.889	SUBCLONAL	1	TRUE	0	0.214302071611114	1		445	678	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0049511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	21	195	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.841	0.65	1	0.841	0.65	1	CLONAL	1	TRUE	1	0.214302071611114	2		195	233	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140449139	140449139	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1562939198	NA	P-0049511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	65	347	0	ENST00000288602.6:c.1940A>G	p.Tyr647Cys	p.Y647C	ENST00000288602	NM_004333.4	647	tAt/tGt	16/18	0.18755313055796	3	FACETS	1	0.953	1	0.613	0.532	0.701	CLONAL	1	TRUE	1	0.214302071611114	3		347	548	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	207	290	1				ENST00000310581	NM_198253.2	-/1132			0.319459411420651	3	FACETS	0.92	0.862	0.978	0.613	0.575	0.652	INDETERMINATE	2	TRUE	0	0.597966335273216	3		291	489	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0049606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	184	804	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.275439796632649	1	FACETS	0.625	0.579	0.673	0.625	0.579	0.673	INDETERMINATE	1	TRUE	0	0.597966335273216	1		804	690	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451474	187451474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145456310	NA	P-0049606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	109	435	0	ENST00000232014.4:c.8C>T	p.Ser3Leu	p.S3L	ENST00000232014	NM_001130845.1	3	tCg/tTg	3/10	1	2	FACETS	0.896	0.811	0.984	0.896	0.811	0.984	CLONAL	1	TRUE	1	0.597966335273216	2		435	407	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	57	455	0	ENST00000371953.3:c.511C>G	p.Gln171Glu	p.Q171E	ENST00000371953	NM_000314.4	171	Cag/Gag	6/9	0.398708108210178	1	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	0	0.597966335273216	1		455	133	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525053	157525053	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554236623	NA	P-0049606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	19	364	0	ENST00000346085.5:c.4948G>T	p.Glu1650Ter	p.E1650*	ENST00000346085	NM_020732.3	1650	Gag/Tag	19/20	0.103112530930403	4	FACETS	0.391	0.297	0.501	0.195	0.148	0.251	INDETERMINATE	1	TRUE	2	0.597966335273216	4		364	260	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338650	70338650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	327	808	1	ENST00000374080.3:c.46C>T	p.Arg16Trp	p.R16W	ENST00000374080		16	Cgg/Tgg	1/45	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.597966335273216	2		809	937	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165914	118165914	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	73	447	0	ENST00000369448.3:c.424C>G	p.Leu142Val	p.L142V	ENST00000369448	NM_017709.3	142	Cta/Gta	2/2	1	2	FACETS	0.885	0.782	0.992	0.885	0.782	0.992	CLONAL	1	TRUE	1	0.597966335273216	2		447	276	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980316	201980317	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0049606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	270	883	0	ENST00000359651.3:c.54_55dup	p.Tyr19CysfsTer25	p.Y19Cfs*25	ENST00000359651		18	atg/aTGtg	1/8	0.275439796632649	1	FACETS	1	0.986	1	1	0.986	1	INDETERMINATE	1	TRUE	0	0.597966335273216	1		883	569	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770075	56770075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	181	715	0	ENST00000337432.4:c.73del	p.Val25Ter	p.V25*	ENST00000337432	NM_058216.2	24	cGg/cg	1/9	1	2	FACETS	0.947	0.878	1	0.947	0.878	1	CLONAL	1	TRUE	1	0.597966335273216	2		715	639	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756691	756691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763332220	NA	P-0049606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	88	633	0	ENST00000314574.4:c.137C>T	p.Ser46Leu	p.S46L	ENST00000314574	NM_005433.3	46	tCa/tTa	2/12	1	2	FACETS	0.94	0.842	1	0.94	0.842	1	CLONAL	1	TRUE	1	0.597966335273216	2		633	313	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44910900	44910970	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTTCCTTAAAGATTATGTTAATTTTTCTCCAAATCTCTTTTTCTGTTCTTTAGAGGAAATATCATTCTGC	AGTTCCTTAAAGATTATGTTAATTTTTCTCCAAATCTCTTTTTCTGTTCTTTAGAGGAAATATCATTCTGC	-	novel	NA	P-0049606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	20	152	0	ENST00000377967.4:c.655-53_672del		p.X219_splice	ENST00000377967	NM_021140.2	219		9/29	1	2	FACETS	0.858	0.7	1	1	0.944	1	CLONAL	2	TRUE	1	0.597966335273216	2		152	39	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0049749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	327	243	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.240095871340812	15	FACETS	1	0.98	1			1	CLONAL	12	TRUE	NA	0.240095871340812	15		243	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577128	7577128	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519987	NA	P-0049749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	154	609	1	ENST00000269305.4:c.810T>G	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	ttT/ttG	8/11	0.240095871340812	4	FACETS	1	0.968	1	0.742	0.68	0.806	CLONAL	2	TRUE	1	0.240095871340812	4		610	715	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404813	70404813	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	29	366	0	ENST00000373644.4:c.2327A>C	p.Lys776Thr	p.K776T	ENST00000373644	NM_030625.2	776	aAa/aCa	4/12	0.112266078238808	5	FACETS	0.661	0.53	0.811	0.165	0.132	0.203	INDETERMINATE	1	TRUE	1	0.240095871340812	5		366	497	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	51	290	1				ENST00000310581	NM_198253.2	-/1132			0.353708722799907	5	FACETS	1	0.959	1			1	CLONAL	1	TRUE	NA	0.443559887619026	5		291	280	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0049866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	80	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.383520969794206	3	FACETS	0.914	0.808	1	0.457	0.404	0.514	CLONAL	1	TRUE	1	0.443559887619026	3		326	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	366	853	0	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	0.358328252580653	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.443559887619026	2		853	796	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182032	38182032	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	155	680	0	ENST00000396334.3:c.656C>G	p.Ser219Cys	p.S219C	ENST00000396334	NM_002468.4	219	tCt/tGt	3/5	0.443559887619026	3	FACETS	1	0.968	1	0.557	0.51	0.605	CLONAL	1	TRUE	1	0.443559887619026	3		680	767	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121909	2121909	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760489473	NA	P-0049866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	346	920	1	ENST00000219476.3:c.2071C>T	p.Arg691Cys	p.R691C	ENST00000219476	NM_000548.3	691	Cgc/Tgc	19/42	0.383520969794206	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	1	0.443559887619026	3		921	952	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942703	44942703	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0049866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	240	496	0	ENST00000377967.4:c.3285-2A>T		p.X1095_splice	ENST00000377967	NM_021140.2	1095			NA	2	FACETS	0.989	0.933	1			1	INDETERMINATE	2	TRUE	NA	0.443559887619026	2		496	547	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982157	201982157	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	340	697	1	ENST00000359651.3:c.684del	p.Ser229AlafsTer25	p.S229Afs*25	ENST00000359651		227	ttC/tt	5/8	0.373743682954578	4	FACETS	0.957	0.906	1	0.957	0.906	1	CLONAL	2	TRUE	2	0.443559887619026	4		698	1156	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524812	187524812	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs184690159	NA	P-0049866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	538	814	2	ENST00000441802.2:c.10868C>T	p.Thr3623Met	p.T3623M	ENST00000441802	NM_005245.3	3623	aCg/aTg	19/27	0.443559887619026	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.443559887619026	3		816	941	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981085	201981086	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0049866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	238	621	0	ENST00000359651.3:c.165_166insGG	p.Lys56GlyfsTer100	p.K56Gfs*100	ENST00000359651		55	gag/gaGGg	2/8	0.373743682954578	4	FACETS	0.942	0.882	1	0.942	0.882	1	CLONAL	2	TRUE	2	0.443559887619026	4		621	822	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545842	41545842	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0049866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	397	945	0	ENST00000263253.7:c.2457T>A	p.Cys819Ter	p.C819*	ENST00000263253	NM_001429.3	819	tgT/tgA	14/31	0.42947273876299	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	2	0.443559887619026	4		945	1279	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286922	33286922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	373	879	0	ENST00000374542.5:c.2015C>T	p.Pro672Leu	p.P672L	ENST00000374542	NM_001141970.1	672	cCc/cTc	7/8	0.443559887619026	3	FACETS	0.984	0.936	1	0.984	0.936	1	CLONAL	2	TRUE	1	0.443559887619026	3		879	1044	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448523	89448523	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	151	593	0	ENST00000336596.2:c.1487T>G	p.Ile496Ser	p.I496S	ENST00000336596	NM_005233.5	496	aTc/aGc	7/17	0.443559887619026	3	FACETS	1	0.941	1	0.518	0.474	0.564	CLONAL	1	TRUE	1	0.443559887619026	3		593	803	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207789	102207789	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	30	484	0	ENST00000263464.3:c.1771T>A	p.Cys591Ser	p.C591S	ENST00000263464	NM_001165.4	591	Tgt/Agt	9/9	0.383520969794206	3	FACETS	0.323	0.26	0.396	0.162	0.13	0.198	SUBCLONAL	1	TRUE	1	0.443559887619026	3		484	511	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049866-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	67	290	1				ENST00000310581	NM_198253.2	-/1132			0.481262689492307	3	FACETS	1	0.971	1			1	CLONAL	1	TRUE	NA	0.481058878167571	3		291	248	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0049866-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	109	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.95	0.858	1	0.95	0.858	1	CLONAL	1	TRUE	1	0.481058878167571	2		326	477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049866-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	250	853	0	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	0.481262689492307	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.481058878167571	1		853	675	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182032	38182032	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049866-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	128	680	0	ENST00000396334.3:c.656C>G	p.Ser219Cys	p.S219C	ENST00000396334	NM_002468.4	219	tCt/tGt	3/5	0.296357825713695	1	FACETS	0.708	0.644	0.775	0.708	0.644	0.775	SUBCLONAL	1	TRUE	0	0.481058878167571	1		680	571	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121909	2121909	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760489473	NA	P-0049866-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	242	920	1	ENST00000219476.3:c.2071C>T	p.Arg691Cys	p.R691C	ENST00000219476	NM_000548.3	691	Cgc/Tgc	19/42	0.296282901386387	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.481058878167571	1		921	755	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942703	44942703	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0049866-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	217	496	0	ENST00000377967.4:c.3285-2A>T		p.X1095_splice	ENST00000377967	NM_021140.2	1095			0.339875935347606	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.481058878167571	1		496	470	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982157	201982157	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049866-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	179	697	1	ENST00000359651.3:c.684del	p.Ser229AlafsTer25	p.S229Afs*25	ENST00000359651		227	ttC/tt	5/8	0.296357825713695	1	FACETS	0.671	0.619	0.725	0.671	0.619	0.725	SUBCLONAL	1	TRUE	0	0.481058878167571	1		698	842	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524812	187524812	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs184690159	NA	P-0049866-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	338	814	2	ENST00000441802.2:c.10868C>T	p.Thr3623Met	p.T3623M	ENST00000441802	NM_005245.3	3623	aCg/aTg	19/27	0.234859866492838	2	FACETS	0.796	0.755	0.836	0.796	0.755	0.836	INDETERMINATE	2	TRUE	0	0.481058878167571	2		816	883	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981085	201981086	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0049866-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	166	621	0	ENST00000359651.3:c.165_166insGG	p.Lys56GlyfsTer100	p.K56Gfs*100	ENST00000359651		55	gag/gaGGg	2/8	0.296357825713695	1	FACETS	0.858	0.792	0.926	0.858	0.792	0.926	CLONAL	1	TRUE	0	0.481058878167571	1		621	611	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545842	41545842	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0049866-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	150	945	0	ENST00000263253.7:c.2457T>A	p.Cys819Ter	p.C819*	ENST00000263253	NM_001429.3	819	tgT/tgA	14/31	1	2	FACETS	0.716	0.654	0.781	0.716	0.654	0.781	SUBCLONAL	1	TRUE	1	0.481058878167571	2		945	871	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286922	33286922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049866-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	258	879	0	ENST00000374542.5:c.2015C>T	p.Pro672Leu	p.P672L	ENST00000374542	NM_001141970.1	672	cCc/cTc	7/8	0.157399743683066	2	FACETS	1	0.991	1	0.647	0.608	0.687	INDETERMINATE	1	TRUE	0	0.481058878167571	2		879	829	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448523	89448523	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049866-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	89	593	0	ENST00000336596.2:c.1487T>G	p.Ile496Ser	p.I496S	ENST00000336596	NM_005233.5	496	aTc/aGc	7/17	0.296357825713695	1	FACETS	0.565	0.503	0.632	0.565	0.503	0.632	SUBCLONAL	1	TRUE	0	0.481058878167571	1		593	497	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515145	103515145	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049866-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	23	389	0	ENST00000355739.4:c.1646T>C	p.Leu549Pro	p.L549P	ENST00000355739	NM_000123.3	549	cTt/cCt	8/15	0.413668068641687	1	FACETS	0.204	0.159	0.257	0.204	0.159	0.257	SUBCLONAL	1	TRUE	0	0.481058878167571	1		389	356	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624296	89624296	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs786201995	NA	P-0049898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	49	548	0	ENST00000371953.3:c.70G>C	p.Asp24His	p.D24H	ENST00000371953	NM_000314.4	24	Gac/Cac	1/9	0.510313889794937	1	FACETS	0.98	0.848	1	0.98	0.848	1	CLONAL	1	TRUE	0	0.510313889794937	1		548	146	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575023	64575023	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs794728652	NA	P-0049898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	94	480	0	ENST00000312049.6:c.783+1G>A		p.X261_splice	ENST00000312049	NM_130799.2	261			0.510313889794937	1	FACETS	0.924	0.832	1	0.924	0.832	1	CLONAL	1	TRUE	0	0.510313889794937	1		480	297	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125479	47125479	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	28	448	0	ENST00000409792.3:c.5791C>T	p.Gln1931Ter	p.Q1931*	ENST00000409792	NM_014159.6	1931	Caa/Taa	12/21	0.510313889794937	1	FACETS	0.929	0.764	1	0.929	0.764	1	CLONAL	1	TRUE	0	0.510313889794937	1		448	88	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286781	33286782	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	50	460	0	ENST00000374542.5:c.2155dup	p.Thr719AsnfsTer22	p.T719Nfs*22	ENST00000374542	NM_001141970.1	719	act/aAct	7/8	0.510313889794937	1	FACETS	0.719	0.618	0.827	0.719	0.618	0.827	SUBCLONAL	1	TRUE	0	0.510313889794937	1		460	203	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579355	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519997	NA	P-0049956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	517	826	1	ENST00000269305.4:c.332T>A	p.Leu111Gln	p.L111Q	ENST00000269305	NM_001126112.2	111	cTg/cAg	4/11	0.458307086370933	2	FACETS	0.967	0.93	1	0.967	0.93	1	CLONAL	2	TRUE	0	0.458307086370933	2		827	1166	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128268652	128268652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145885264	NA	P-0049956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	297	891	0	ENST00000265960.3:c.1003G>A	p.Val335Ile	p.V335I	ENST00000265960	NM_001006617.1	335	Gtt/Att	8/12	0.451187009029007	3	FACETS	1	0.988	1	0.592	0.556	0.628	CLONAL	1	TRUE	1	0.458307086370933	3		891	1346	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969190	93969190	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	191	324	0	ENST00000369303.4:c.1806del	p.Pro603GlnfsTer26	p.P603Qfs*26	ENST00000369303	NM_004440.3	602	ttT/tt	10/17	0.458307086370933	2	FACETS	0.96	0.899	1	0.96	0.899	1	CLONAL	2	TRUE	0	0.458307086370933	2		324	434	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469669	NA	P-0049969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	202	274	1	ENST00000374080.3:c.130G>A	p.Gly44Ser	p.G44S	ENST00000374080		44	Ggt/Agt	2/45	0.308887127552989	2	FACETS	0.942	0.884	1			1	CLONAL	3	TRUE	NA	0.318342683800782	2		275	449	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286205	66286205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777851171	NA	P-0049969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	55	220	2	ENST00000273854.3:c.1481G>A	p.Arg494His	p.R494H	ENST00000273854	NM_004439.5	494	cGt/cAt	6/18	0.287758191109988	1	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	0	0.318342683800782	1		222	268	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	330	731	0	ENST00000269305.4:c.596del	p.Gly199GlufsTer48	p.G199Efs*48	ENST00000269305	NM_001126112.2	199	gGa/ga	6/11	0.252681871537921	3	FACETS	0.979	0.93	1			1	CLONAL	3	TRUE	NA	0.318342683800782	3		731	818	SUCCESS
APC	324	MSKCC	GRCh37	5	112175569	112175569	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	48	317	0	ENST00000257430.4:c.4280del	p.Pro1427LeufsTer46	p.P1427Lfs*46	ENST00000257430	NM_000038.5	1426	agC/ag	16/16	1	2	FACETS	0.906	0.769	1	0.906	0.769	1	CLONAL	1	TRUE	1	0.318342683800782	2		317	333	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998468	100998468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	276	658	0	ENST00000325455.5:c.1334G>A	p.Ser445Asn	p.S445N	ENST00000325455	NM_001202474.3	445	aGt/aAt	1/8	0.315382445512777	3	FACETS	0.932	0.88	0.985	0.932	0.88	0.985	CLONAL	3	TRUE	0	0.318342683800782	3		658	719	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719887	52719887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377119375	NA	P-0049969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	106	742	0	ENST00000322088.6:c.1099C>T	p.Pro367Ser	p.P367S	ENST00000322088	NM_014225.5	367	Ccc/Tcc	9/15	NA	2	FACETS	0.957	0.859	1			1	INDETERMINATE	1	TRUE	NA	0.318342683800782	2		742	696	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0050069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	248	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.429063326252435	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.429063326252435	2		326	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0050069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	421	729	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.429063326252435	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.429063326252435	2		730	946	SUCCESS
APC	324	MSKCC	GRCh37	5	112175171	112175171	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085373	NA	P-0050069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	97	295	0	ENST00000257430.4:c.3880C>T	p.Gln1294Ter	p.Q1294*	ENST00000257430	NM_000038.5	1294	Cag/Tag	16/16	0.429063326252435	2	FACETS	0.834	0.755	0.916	0.834	0.755	0.916	CLONAL	2	TRUE	0	0.429063326252435	2		295	271	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0050069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	321	642	1	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	0.429063326252435	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.429063326252435	2		643	730	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247516	123247516	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519795	NA	P-0050069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	290	555	0	ENST00000358487.5:c.1975A>G	p.Lys659Glu	p.K659E	ENST00000358487	NM_000141.4	659	Aag/Gag	14/18	0.429063326252435	2	FACETS	0.953	0.902	1	0.953	0.902	1	CLONAL	2	TRUE	0	0.429063326252435	2		555	709	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175996801	175996801	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	263	524	0	ENST00000367669.3:c.1636G>T	p.Asp546Tyr	p.D546Y	ENST00000367669	NM_022457.5	546	Gac/Tac	15/20	0.27742380459798	4	FACETS	0.959	0.901	1	0.959	0.901	1	CLONAL	2	TRUE	2	0.429063326252435	4		524	913	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941231	71941231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1166410104	NA	P-0050069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	208	1055	0	ENST00000298229.2:c.1006G>A	p.Val336Met	p.V336M	ENST00000298229	NM_001567.3	336	Gtg/Atg	9/28	0.429063326252435	3	FACETS	0.919	0.851	0.99	0.46	0.425	0.495	CLONAL	1	TRUE	1	0.429063326252435	3		1055	1281	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1039258	1039258	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	145	630	1	ENST00000358495.3:c.239G>T	p.Gly80Val	p.G80V	ENST00000358495	NM_134424.2	80	gGt/gTt	4/12	NA	2	FACETS	0.906	0.828	0.988			1	INDETERMINATE	1	TRUE	NA	0.429063326252435	2		631	746	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268805	41268805	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	424	547	0	ENST00000349496.5:c.1043C>A	p.Ser348Tyr	p.S348Y	ENST00000349496	NM_001904.3	348	tCt/tAt	7/15	0.429063326252435	3	FACETS	0.959	0.92	0.998	0.959	0.92	0.998	CLONAL	3	TRUE	0	0.429063326252435	3		547	834	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288244	33288244	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	335	642	0	ENST00000374542.5:c.1164G>T	p.Glu388Asp	p.E388D	ENST00000374542	NM_001141970.1	388	gaG/gaT	4/8	0.27742380459798	4	FACETS	0.971	0.919	1	0.971	0.919	1	CLONAL	2	TRUE	2	0.429063326252435	4		642	1149	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061221	38061232	+	inframe_deletion	In_Frame_Del	DEL	GTTCTCGAACAT	GTTCTCGAACAT	-	novel	NA	P-0050083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	326	525	0	ENST00000250448.2:c.757_768del	p.Met253_Asn256del	p.M253_N256del	ENST00000250448	NM_004496.3	253	ATGTTCGAGAAC/-	2/2	0.469061800298906	1	FACETS	0.562	0.534	0.591	0.562	0.534	0.591	INDETERMINATE	1	TRUE	0	0.853617201757359	1		525	779	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749305	43749305	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	542	507	1	ENST00000382044.4:c.1501G>T	p.Glu501Ter	p.E501*	ENST00000382044	NM_001141980.1	501	Gaa/Taa	12/28	0.853617201757359	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.853617201757359	2		508	621	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991847	72991848	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	357	554	1	ENST00000268489.5:c.2197dup	p.Tyr733LeufsTer16	p.Y733Lfs*16	ENST00000268489	NM_006885.3	733	tac/tTac	2/10	0.507305887830052	1	FACETS	0.785	0.752	0.817	0.785	0.752	0.817	INDETERMINATE	1	TRUE	0	0.853617201757359	1		555	611	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155907	106155908	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0050083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	261	364	0	ENST00000380013.4:c.808_809insT	p.Thr270IlefsTer12	p.T270Ifs*12	ENST00000380013	NM_001127208.2	270	acc/aTcc	3/11	0.693862542399079	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.853617201757359	1		364	325	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554928	106554928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	54	606	0	ENST00000369096.4:c.2045C>T	p.Thr682Ile	p.T682I	ENST00000369096	NM_001198.3	682	aCc/aTc	7/7	0.220258040158693	4	FACETS	1	0.886	1	0.522	0.445	0.606	CLONAL	1	TRUE	2	0.21	4		606	596	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425476	49425476	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	80	877	1	ENST00000301067.7:c.13012C>G	p.Pro4338Ala	p.P4338A	ENST00000301067	NM_003482.3	4338	Ccc/Gcc	39/54	0.3	5	FACETS	1	0.967	1	0.651	0.573	0.736	CLONAL	1	TRUE	3	0.21	5		878	769	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670401	88670401	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	53	408	0	ENST00000360948.2:c.1285A>T	p.Thr429Ser	p.T429S	ENST00000360948	NM_001012338.2	429	Act/Tct	11/19	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.21	2		408	348	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723017	52723017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	70	735	0	ENST00000322088.6:c.1202C>T	p.Ser401Phe	p.S401F	ENST00000322088	NM_014225.5	401	tCc/tTc	10/15	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.21	2		735	651	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101756	71101756	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0050084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	27	250	0	ENST00000318789.4:c.442A>T	p.Lys148Ter	p.K148*	ENST00000318789	NM_032682.5	148	Aaa/Taa	9/21	0.158869285199134	4	FACETS	0.94	0.749	1	0.47	0.374	0.579	CLONAL	1	TRUE	2	0.21	4		250	331	SUCCESS
APC	324	MSKCC	GRCh37	5	112164661	112164661	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	28	251	0	ENST00000257430.4:c.1735G>T	p.Val579Phe	p.V579F	ENST00000257430	NM_000038.5	579	Gtt/Ttt	14/16	0.158869285199134	4	FACETS	1	0.812	1	0.507	0.406	0.623	CLONAL	1	TRUE	2	0.21	4		251	318	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910547	29910547	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	92	760	0	ENST00000376809.5:c.87G>C	p.Met29Ile	p.M29I	ENST00000376809	NM_002116.7	29	atG/atC	2/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.21	2		760	665	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636611	176636635	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	AATTCTTTTTCTCCTTTAAATTTAA	AATTCTTTTTCTCCTTTAAATTTAA	G	novel	NA	P-0050084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	24	293	0	ENST00000439151.2:c.1237-26_1237-2delinsG		p.X413_splice	ENST00000439151	NM_022455.4	413			0.158869285199134	4	FACETS	0.97	0.762	1	0.485	0.381	0.605	CLONAL	1	TRUE	2	0.21	4		293	285	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	164	660	0	ENST00000269305.4:c.376T>C	p.Tyr126His	p.Y126H	ENST00000269305	NM_001126112.2	126	Tac/Cac	5/11	0.51069229624392	1	FACETS	0.97	0.898	1	0.97	0.898	1	CLONAL	1	TRUE	0	0.51069229624392	1		660	493	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0050137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	44	368	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	1	2	FACETS	0.681	0.575	0.796	0.681	0.575	0.796	SUBCLONAL	1	TRUE	1	0.51069229624392	2		368	253	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462683	29462683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766541301	NA	P-0050137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	196	627	2	ENST00000389048.3:c.2218G>A	p.Gly740Arg	p.G740R	ENST00000389048	NM_004304.4	740	Gga/Aga	13/29	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.51069229624392	2		629	748	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668670	52668671	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0050137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	17	514	0	ENST00000394830.3:c.1248dup	p.Tyr417IlefsTer3	p.Y417Ifs*3	ENST00000394830	NM_018313.4	416	-/A	12/30	1	2	FACETS	0.202	0.15	0.263	0.202	0.15	0.263	SUBCLONAL	1	TRUE	1	0.51069229624392	2		514	330	SUCCESS
APC	324	MSKCC	GRCh37	5	112175118	112175118	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060503299	NA	P-0050137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	30	263	0	ENST00000257430.4:c.3827C>G	p.Ser1276Ter	p.S1276*	ENST00000257430	NM_000038.5	1276	tCa/tGa	16/16	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.51069229624392	2		263	102	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0050143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	84	368	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.160709848732181	4	FACETS	1	0.913	1	1	0.913	1	CLONAL	2	TRUE	2	0.208726430414278	4		368	470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0050143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	188	557	1	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	NA	2	FACETS	1	0.962	1			1	INDETERMINATE	2	TRUE	NA	0.208726430414278	2		558	848	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0050143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	59	422	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.160709848732181	4	FACETS	1	0.95	1	0.62	0.534	0.714	CLONAL	1	TRUE	2	0.208726430414278	4		422	551	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956723	68956723	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs750933833	NA	P-0050143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	86	475	0	ENST00000288368.4:c.841C>T	p.Arg281Trp	p.R281W	ENST00000288368	NM_024870.2	281	Cgg/Tgg	8/40	0.208726430414278	5	FACETS	1	0.966	1	0.315	0.278	0.355	CLONAL	1	TRUE	1	0.208726430414278	5		475	858	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711003	114711004	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0050143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	85	314	0	ENST00000543371.1:c.229_230del	p.Asp77GlnfsTer19	p.D77Qfs*19	ENST00000543371	NM_001198531.1	76	cGA/c	2/14	0.202840176980277	3	FACETS	1	0.921	1	1	0.921	1	CLONAL	2	TRUE	1	0.208726430414278	3		314	430	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358653	67358653	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	44	565	0	ENST00000327367.4:c.161C>A	p.Ala54Asp	p.A54D	ENST00000327367	NM_005902.3	54	gCc/gAc	1/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.208726430414278	NA		565	773	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243947	5243947	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	83	544	1	ENST00000357368.4:c.1535T>C	p.Leu512Pro	p.L512P	ENST00000357368	NM_002850.3	512	cTc/cCc	11/38	0.208726430414278	5	FACETS	1	0.889	1	0.253	0.222	0.286	CLONAL	1	TRUE	1	0.208726430414278	5		545	1033	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	279	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	0.82	0.776	0.864			1	INDETERMINATE	2	TRUE	NA	0.534190542398264	2		487	637	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0050152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	140	165	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.534190542398264	2	FACETS	0.874	0.81	0.938	0.874	0.81	0.938	CLONAL	2	TRUE	0	0.534190542398264	2		165	300	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982331	201982332	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0050152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	334	849	0	ENST00000359651.3:c.715dup	p.Asp239GlyfsTer62	p.D239Gfs*62	ENST00000359651		237	aag/aaGg	6/8	1	2	FACETS	0.949	0.897	1	0.949	0.897	1	CLONAL	1	TRUE	1	0.534190542398264	2		849	1317	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920404	114920404	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	281	467	0	ENST00000543371.1:c.1345G>C	p.Ala449Pro	p.A449P	ENST00000543371	NM_001198531.1	449	Gca/Cca	13/14	0.255922389562553	2	FACETS	1	0.993	1	0.681	0.643	0.72	INDETERMINATE	1	TRUE	0	0.534190542398264	2		467	772	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198851	67198851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373631670	NA	P-0050152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	201	424	0	ENST00000312629.5:c.322C>T	p.Arg108Cys	p.R108C	ENST00000312629	NM_003952.2	108	Cgc/Tgc	5/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.534190542398264	2		424	704	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920411	114920412	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0050152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	298	470	0	ENST00000543371.1:c.1353dup	p.Gly452ArgfsTer3	p.G452Rfs*3	ENST00000543371	NM_001198531.1	451	ttc/ttCc	13/14	0.255922389562553	2	FACETS	1	0.993	1	0.682	0.645	0.72	INDETERMINATE	1	TRUE	0	0.534190542398264	2		470	818	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0050213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	68	295	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.855	0.752	0.964	0.855	0.752	0.964	CLONAL	1	TRUE	1	0.591103797632792	2		295	269	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0050213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	121	233	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.591103797632792	2		233	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876658468	NA	P-0050213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	274	646	0	ENST00000269305.4:c.577C>A	p.His193Asn	p.H193N	ENST00000269305	NM_001126112.2	193	Cat/Aat	6/11	0.591103797632792	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.591103797632792	1		646	642	SUCCESS
APC	324	MSKCC	GRCh37	5	112175162	112175162	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561588104	NA	P-0050213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	80	181	0	ENST00000257430.4:c.3871C>T	p.Gln1291Ter	p.Q1291*	ENST00000257430	NM_000038.5	1291	Cag/Tag	16/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.591103797632792	2		181	225	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030224	180030224	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761089407	NA	P-0050213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	303	762	0	ENST00000261937.6:c.4060C>T	p.Arg1354Cys	p.R1354C	ENST00000261937	NM_182925.4	1354	Cgc/Tgc	30/30	1	2	FACETS	0.963	0.908	1	0.963	0.908	1	CLONAL	1	TRUE	1	0.591103797632792	2		762	1065	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965472	68965472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200682883	NA	P-0050213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	95	523	1	ENST00000288368.4:c.1084C>T	p.Arg362Trp	p.R362W	ENST00000288368	NM_024870.2	362	Cgg/Tgg	9/40	0.591103797632792	4	FACETS	0.659	0.586	0.737	0.22	0.195	0.246	SUBCLONAL	1	TRUE	1	0.591103797632792	4		524	776	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	99	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.849	0.763	0.938	0.849	0.763	0.938	CLONAL	1	TRUE	1	0.581740336181185	2		457	401	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0050238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	351	965	2	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.581740336181185	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.581740336181185	1		967	840	SUCCESS
APC	324	MSKCC	GRCh37	5	112175162	112175162	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561588104	NA	P-0050238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	90	181	0	ENST00000257430.4:c.3871C>T	p.Gln1291Ter	p.Q1291*	ENST00000257430	NM_000038.5	1291	Cag/Tag	16/16	0.581740336181185	2	FACETS	0.938	0.858	1	0.938	0.858	1	CLONAL	2	TRUE	0	0.581740336181185	2		181	165	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456719	138456719	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs773791563	NA	P-0050238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	26	375	0	ENST00000289153.2:c.631A>G	p.Ser211Gly	p.S211G	ENST00000289153	NM_006219.2	211	Agc/Ggc	4/22	1	2	FACETS	0.262	0.207	0.325	0.262	0.207	0.325	SUBCLONAL	1	TRUE	1	0.581740336181185	2		375	341	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0050246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	15	415	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.378	0.275	0.503	0.378	0.275	0.503	SUBCLONAL	1	TRUE	1	0.15	2		415	529	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425694	49425694	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	81	850	1	ENST00000301067.7:c.12794del	p.Gly4265AlafsTer13	p.G4265Afs*13	ENST00000301067	NM_003482.3	4265	gGc/gc	39/54	0.110300458476282	3	FACETS	1	0.971	1	0.678	0.596	0.766	CLONAL	1	TRUE	1	0.15	3		851	856	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587781525	NA	P-0050246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	28	727	0	ENST00000269305.4:c.842A>G	p.Asp281Gly	p.D281G	ENST00000269305	NM_001126112.2	281	gAc/gGc	8/11	1	2	FACETS	0.454	0.361	0.56	0.454	0.361	0.56	SUBCLONAL	1	TRUE	1	0.15	2		727	823	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0050246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	38	458	4	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	0.789	0.651	0.944	0.789	0.651	0.944	CLONAL	1	TRUE	1	0.15	2		462	642	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871053	12871053	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	47	365	0	ENST00000228872.4:c.285del	p.Gly97ValfsTer22	p.G97Vfs*22	ENST00000228872	NM_004064.3	94	Ccc/cc	1/3	0.232317358832528	3	FACETS	1	0.942	1	0.632	0.533	0.741	CLONAL	1	TRUE	1	0.15	3		365	533	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034435	47034435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	37	664	0	ENST00000377604.3:c.520G>A	p.Ala174Thr	p.A174T	ENST00000377604	NM_001204468.1	174	Gcc/Acc	6/24	1	2	FACETS	0.701	0.576	0.841	0.701	0.576	0.841	SUBCLONAL	1	TRUE	1	0.15	2		664	704	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007689	45007690	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0050246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	30	328	0	ENST00000558401.1:c.137_138del	p.Tyr46CysfsTer10	p.Y46Cfs*10	ENST00000558401	NM_004048.2	46	TAt/t	2/4	1	2	FACETS	0.83	0.668	1	0.83	0.668	1	CLONAL	1	TRUE	1	0.15	2		328	482	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27204926	27204926	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	47	471	0	ENST00000380036.4:c.2232del	p.Lys745ArgfsTer5	p.K745Rfs*5	ENST00000380036	NM_000459.3	743	Ggg/gg	14/23	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.15	2		471	541	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972645	32972645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	33	391	0	ENST00000380152.3:c.9995C>T	p.Ser3332Phe	p.S3332F	ENST00000380152		3332	tCt/tTt	27/27	1	2	FACETS	0.782	0.635	0.947	0.782	0.635	0.947	CLONAL	1	TRUE	1	0.15	2		391	563	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	137	536	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.42	2		536	619	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	146	590	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.42	2		591	668	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624245	89624245	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554890335	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	58	211	0	ENST00000371953.3:c.19G>T	p.Glu7Ter	p.E7*	ENST00000371953	NM_000314.4	7	Gag/Tag	1/9	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.42	2		211	244	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931826	68931826	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs759461290	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	106	450	1	ENST00000288368.4:c.256G>T	p.Glu86Ter	p.E86*	ENST00000288368	NM_024870.2	86	Gaa/Taa	3/40	0.202691235086814	0	FACETS	0.591	0.532	0.653			1	INDETERMINATE	1	TRUE	0	0.42	0		451	495	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106094	8106094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	114	487	0	ENST00000346208.3:c.914G>A	p.Arg305Gln	p.R305Q	ENST00000346208		305	cGa/cAa	4/6	1	2	FACETS	0.881	0.795	0.972	0.881	0.795	0.972	CLONAL	1	TRUE	1	0.42	2		487	616	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380223	25380223	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	102	443	0	ENST00000311936.3:c.235C>A	p.Leu79Ile	p.L79I	ENST00000311936	NM_004985.3	79	Ctt/Att	3/5	1	2	FACETS	0.987	0.887	1	0.987	0.887	1	CLONAL	1	TRUE	1	0.42	2		443	492	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604736	48604736	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	107	389	0	ENST00000342988.3:c.1558G>T	p.Glu520Ter	p.E520*	ENST00000342988	NM_005359.5	520	Gaa/Taa	12/12	1	2	FACETS	0.923	0.831	1	0.923	0.831	1	CLONAL	1	TRUE	1	0.42	2		389	552	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210733	5210733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779302415	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	48	837	1	ENST00000357368.4:c.5318C>T	p.Ser1773Leu	p.S1773L	ENST00000357368	NM_002850.3	1773	tCg/tTg	34/38	1	2	FACETS	0.257	0.217	0.303	0.257	0.217	0.303	SUBCLONAL	1	TRUE	1	0.42	2		838	888	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857784	9857784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145861983	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	120	573	0	ENST00000330684.3:c.3617G>A	p.Arg1206Gln	p.R1206Q	ENST00000330684	NM_001134407.1	1206	cGa/cAa	13/13	1	2	FACETS	0.817	0.739	0.9	0.817	0.739	0.9	CLONAL	1	TRUE	1	0.42	2		573	699	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163749	152163749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1207112399	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	80	455	0	ENST00000206249.3:c.470G>A	p.Arg157Gln	p.R157Q	ENST00000206249	NM_000125.3	157	cGa/cAa	2/8	1	2	FACETS	0.843	0.745	0.947	0.843	0.745	0.947	CLONAL	1	TRUE	1	0.42	2		455	452	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125024	46125024	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	57	211	0	ENST00000334344.6:c.211G>T	p.Glu71Ter	p.E71*	ENST00000334344	NM_152641.2	71	Gaa/Taa	3/21	1	2	FACETS	0.926	0.801	1	0.926	0.801	1	CLONAL	1	TRUE	1	0.42	2		211	293	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95577791	95577791	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1555371642	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	67	167	0	ENST00000393063.1:c.2119G>A	p.Glu707Lys	p.E707K	ENST00000393063	NM_030621.3	707	Gaa/Aaa	15/28	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.42	2		167	278	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311662	30311662	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	126	346	0	ENST00000262643.3:c.516C>A	p.Phe172Leu	p.F172L	ENST00000262643	NM_001238.2	172	ttC/ttA	7/12	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.42	2		346	582	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588626	28588626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548609046	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	160	410	0	ENST00000241453.7:c.2822C>T	p.Ser941Leu	p.S941L	ENST00000241453	NM_004119.2	941	tCg/tTg	23/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.42	2		410	602	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405971	49405971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	149	528	0	ENST00000418115.1:c.167C>T	p.Ala56Val	p.A56V	ENST00000418115	NM_001664.2	56	gCt/gTt	3/5	1	2	FACETS	0.983	0.9	1	0.983	0.9	1	CLONAL	1	TRUE	1	0.42	2		528	722	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50481162	50481162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	85	345	0	ENST00000394963.4:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000394963	NM_003076.4	183	cGa/cAa	5/13	1	2	FACETS	0.744	0.659	0.835	0.744	0.659	0.835	SUBCLONAL	1	TRUE	1	0.42	2		345	544	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47710037	47710037	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1553370893	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	59	301	0	ENST00000233146.2:c.2754G>T	p.Lys918Asn	p.K918N	ENST00000233146	NM_000251.2	918	aaG/aaT	16/16	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.42	2		301	273	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325762	30325762	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs771704089	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	74	247	0	ENST00000322652.5:c.1960C>T	p.Arg654Ter	p.R654*	ENST00000322652	NM_015355.2	654	Cga/Tga	16/16	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.42	2		247	308	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418997	116418997	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200754673	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	27	266	0	ENST00000397752.3:c.3508C>T	p.Arg1170Ter	p.R1170*	ENST00000397752	NM_000245.2	1170	Cga/Tga	17/21	1	2	FACETS	0.415	0.33	0.511	0.415	0.33	0.511	SUBCLONAL	1	TRUE	1	0.42	2		266	310	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176662843	176662843	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1362208576	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	86	341	0	ENST00000439151.2:c.3818G>A	p.Arg1273His	p.R1273H	ENST00000439151	NM_022455.4	1273	cGc/cAc	6/23	1	2	FACETS	0.97	0.863	1	0.97	0.863	1	CLONAL	1	TRUE	1	0.42	2		341	422	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812293	212812293	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569995088	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	53	311	1	ENST00000342788.4:c.283C>T	p.Arg95Cys	p.R95C	ENST00000342788	NM_005235.2	95	Cgt/Tgt	3/28	1	2	FACETS	0.756	0.648	0.873	0.756	0.648	0.873	SUBCLONAL	1	TRUE	1	0.42	2		312	334	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468516	89468516	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1453560937	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	77	279	0	ENST00000336596.2:c.2050C>T	p.Arg684Ter	p.R684*	ENST00000336596	NM_005233.5	684	Cga/Tga	11/17	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.42	2		279	337	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043904	180043904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56082504	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	118	719	0	ENST00000261937.6:c.3092G>A	p.Arg1031Gln	p.R1031Q	ENST00000261937	NM_182925.4	1031	cGa/cAa	22/30	1	2	FACETS	0.699	0.63	0.771	0.699	0.63	0.771	SUBCLONAL	1	TRUE	1	0.42	2		719	804	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857127	9857127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs976259560	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	62	304	0	ENST00000330684.3:c.4274C>T	p.Ser1425Leu	p.S1425L	ENST00000330684	NM_001134407.1	1425	tCg/tTg	13/13	1	2	FACETS	0.722	0.626	0.825	0.722	0.626	0.825	SUBCLONAL	1	TRUE	1	0.42	2		304	409	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095836	178095836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1328262363	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	94	494	1	ENST00000397062.3:c.1495C>T	p.Arg499Trp	p.R499W	ENST00000397062	NM_006164.4	499	Cgg/Tgg	5/5	1	2	FACETS	0.856	0.764	0.953	0.856	0.764	0.953	CLONAL	1	TRUE	1	0.42	2		495	523	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267600319	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	66	280	0	ENST00000257430.4:c.4199C>T	p.Ser1400Leu	p.S1400L	ENST00000257430	NM_000038.5	1400	tCg/tTg	16/16	1	2	FACETS	0.816	0.712	0.928	0.816	0.712	0.928	CLONAL	1	TRUE	1	0.42	2		280	385	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915943	127915943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781486938	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	106	443	0	ENST00000373547.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000373547	NM_002721.4	180	Gaa/Aaa	6/7	1	2	FACETS	0.867	0.78	0.96	0.867	0.78	0.96	CLONAL	1	TRUE	1	0.42	2		443	582	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023019	150023019	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	136	592	0	ENST00000253339.5:c.244C>T	p.Arg82Ter	p.R82*	ENST00000253339		82	Cga/Tga	1/7	1	2	FACETS	0.898	0.818	0.982	0.898	0.818	0.982	CLONAL	1	TRUE	1	0.42	2		592	721	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772411	56772411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658197	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	112	512	1	ENST00000337432.4:c.265G>A	p.Glu89Lys	p.E89K	ENST00000337432	NM_058216.2	89	Gaa/Aaa	2/9	1	2	FACETS	0.779	0.701	0.86	0.779	0.701	0.86	SUBCLONAL	1	TRUE	1	0.42	2		513	685	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524675	106524675	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	60	265	0	ENST00000359195.3:c.2836G>A	p.Asp946Asn	p.D946N	ENST00000359195	NM_002649.2	946	Gac/Aac	9/11	1	2	FACETS	0.91	0.789	1	0.91	0.789	1	CLONAL	1	TRUE	1	0.42	2		265	314	SUCCESS
APC	324	MSKCC	GRCh37	5	112178000	112178000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768922431	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	74	333	0	ENST00000257430.4:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000257430	NM_000038.5	2237	Cga/Tga	16/16	1	2	FACETS	0.851	0.749	0.961	0.851	0.749	0.961	CLONAL	1	TRUE	1	0.42	2		333	414	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676141	29676141	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1567623401	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	78	235	0	ENST00000356175.3:c.7130A>G	p.Tyr2377Cys	p.Y2377C	ENST00000356175	NM_000267.3	2377	tAc/tGc	48/57	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.42	2		235	348	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270162	198270162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	82	312	0	ENST00000335508.6:c.1274G>A	p.Arg425Gln	p.R425Q	ENST00000335508	NM_012433.2	425	cGa/cAa	10/25	1	2	FACETS	0.819	0.724	0.919	0.819	0.724	0.919	CLONAL	1	TRUE	1	0.42	2		312	477	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169179	119169179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150811339	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	41	507	1	ENST00000264033.4:c.2363G>A	p.Arg788Gln	p.R788Q	ENST00000264033	NM_005188.3	788	cGa/cAa	15/16	1	2	FACETS	0.294	0.244	0.35	0.294	0.244	0.35	SUBCLONAL	1	TRUE	1	0.42	2		508	664	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209264	98209264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778630	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	170	796	0	ENST00000331920.6:c.4274C>T	p.Ser1425Leu	p.S1425L	ENST00000331920	NM_000264.3	1425	tCg/tTg	23/24	1	2	FACETS	0.899	0.827	0.975	0.899	0.827	0.975	CLONAL	1	TRUE	1	0.42	2		796	900	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729271	41729271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749989847	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	73	404	0	ENST00000242208.4:c.1258G>A	p.Val420Met	p.V420M	ENST00000242208	NM_002192.2	420	Gtg/Atg	3/3	1	2	FACETS	0.774	0.679	0.876	0.774	0.679	0.876	SUBCLONAL	1	TRUE	1	0.42	2		404	449	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92404119	92404119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761377867	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	111	350	0	ENST00000265734.4:c.260G>A	p.Arg87Gln	p.R87Q	ENST00000265734	NM_001259.6	87	cGa/cAa	3/8	1	2	FACETS	0.99	0.893	1	0.99	0.893	1	CLONAL	1	TRUE	1	0.42	2		350	534	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72891539	72891539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755870786	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	35	358	0	ENST00000325599.8:c.223C>T	p.Arg75Cys	p.R75C	ENST00000325599	NM_018130.2	75	Cgc/Tgc	3/11	1	2	FACETS	0.346	0.283	0.416	0.346	0.283	0.416	SUBCLONAL	1	TRUE	1	0.42	2		358	482	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989562	85989562	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs767548896	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	95	337	0	ENST00000263360.6:c.1321C>T	p.Arg441Ter	p.R441*	ENST00000263360	NM_003797.3	441	Cga/Tga	12/12	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.42	2		337	447	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	115	260	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	1	0.937	1	1	0.99	1	CLONAL	2	TRUE	1	0.42	2		260	267	SUCCESS
APC	324	MSKCC	GRCh37	5	112173350	112173350	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	64	292	0	ENST00000257430.4:c.2059C>A	p.Leu687Ile	p.L687I	ENST00000257430	NM_000038.5	687	Ctc/Atc	16/16	1	2	FACETS	0.894	0.779	1	0.894	0.779	1	CLONAL	1	TRUE	1	0.42	2		292	341	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162055	22162055	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	33	458	0	ENST00000215832.6:c.200G>T	p.Arg67Ile	p.R67I	ENST00000215832	NM_002745.4	67	aGa/aTa	2/9	1	2	FACETS	0.265	0.215	0.321	0.265	0.215	0.321	SUBCLONAL	1	TRUE	1	0.42	2		458	594	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347916	73347916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139907646	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	72	224	0	ENST00000377767.4:c.1145G>A	p.Arg382Gln	p.R382Q	ENST00000377767	NM_014953.3	382	cGa/cAa	8/21	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.42	2		224	301	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971370	13971370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748346103	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	82	333	0	ENST00000405192.2:c.559C>T	p.Arg187Cys	p.R187C	ENST00000405192	NM_001163147.1	187	Cgc/Tgc	8/12	1	2	FACETS	0.894	0.792	1	0.894	0.792	1	CLONAL	1	TRUE	1	0.42	2		333	437	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419956	152419956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775806382	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	40	693	0	ENST00000206249.3:c.1643G>A	p.Arg548His	p.R548H	ENST00000206249	NM_000125.3	548	cGc/cAc	8/8	1	2	FACETS	0.268	0.222	0.32	0.268	0.222	0.32	SUBCLONAL	1	TRUE	1	0.42	2		693	710	SUCCESS
APC	324	MSKCC	GRCh37	5	112174119	112174119	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1554084512	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	78	285	0	ENST00000257430.4:c.2828C>A	p.Ser943Ter	p.S943*	ENST00000257430	NM_000038.5	943	tCa/tAa	16/16	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.42	2		285	348	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066675	94066675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	110	495	2	ENST00000369303.4:c.1084G>A	p.Asp362Asn	p.D362N	ENST00000369303	NM_004440.3	362	Gat/Aat	5/17	1	2	FACETS	0.914	0.824	1	0.914	0.824	1	CLONAL	1	TRUE	1	0.42	2		497	573	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444384	50444384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761574077	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	90	410	0	ENST00000331340.3:c.314C>T	p.Ser105Leu	p.S105L	ENST00000331340	NM_006060.4	105	tCg/tTg	4/8	1	2	FACETS	0.824	0.733	0.92	0.824	0.733	0.92	CLONAL	1	TRUE	1	0.42	2		410	520	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008201	29008201	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	59	278	0	ENST00000282397.4:c.670C>T	p.Arg224Ter	p.R224*	ENST00000282397	NM_002019.4	224	Cga/Tga	5/30	1	2	FACETS	0.81	0.7	0.927	0.81	0.7	0.927	CLONAL	1	TRUE	1	0.42	2		278	347	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347294	70347294	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	108	522	0	ENST00000374080.3:c.2958G>T	p.Lys986Asn	p.K986N	ENST00000374080		986	aaG/aaT	21/45	1	2	FACETS	0.893	0.804	0.987	0.893	0.804	0.987	CLONAL	1	TRUE	1	0.42	2		522	576	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88677032	88677032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782400	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	82	257	2	ENST00000372037.3:c.817C>T	p.Arg273Ter	p.R273*	ENST00000372037	NM_004329.2	273	Cga/Tga	9/13	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.42	2		259	359	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274877	41274877	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	120	398	0	ENST00000349496.5:c.1127G>A	p.Arg376His	p.R376H	ENST00000349496	NM_001904.3	376	cGt/cAt	8/15	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.42	2		398	571	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73333960	73333960	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	92	348	0	ENST00000377767.4:c.2850G>T	p.Lys950Asn	p.K950N	ENST00000377767	NM_014953.3	950	aaG/aaT	21/21	1	2	FACETS	0.987	0.881	1	0.987	0.881	1	CLONAL	1	TRUE	1	0.42	2		348	444	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56862974	56862974	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	103	419	1	ENST00000308159.5:c.880C>T	p.Arg294Ter	p.R294*	ENST00000308159	NM_014669.4	294	Cga/Tga	9/22	1	2	FACETS	0.879	0.789	0.974	0.879	0.789	0.974	CLONAL	1	TRUE	1	0.42	2		420	558	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938406	76938406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	113	483	0	ENST00000373344.5:c.2342G>A	p.Arg781Gln	p.R781Q	ENST00000373344	NM_000489.3	781	cGa/cAa	9/35	1	2	FACETS	0.827	0.745	0.912	0.827	0.745	0.912	CLONAL	1	TRUE	1	0.42	2		483	651	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247418	71247418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752297898	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	159	652	0	ENST00000318789.4:c.115G>A	p.Gly39Arg	p.G39R	ENST00000318789	NM_032682.5	39	Gga/Aga	6/21	1	2	FACETS	0.894	0.82	0.971	0.894	0.82	0.971	CLONAL	1	TRUE	1	0.42	2		652	847	SUCCESS
EED	8726	MSKCC	GRCh37	11	85963241	85963241	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	46	258	0	ENST00000263360.6:c.319G>A	p.Glu107Lys	p.E107K	ENST00000263360	NM_003797.3	107	Gaa/Aaa	3/12	1	2	FACETS	0.61	0.515	0.714	0.61	0.515	0.714	SUBCLONAL	1	TRUE	1	0.42	2		258	359	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414232	32414232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	91	332	0	ENST00000332351.3:c.1319G>A	p.Arg440Lys	p.R440K	ENST00000332351	NM_024426.4	440	aGa/aAa	8/10	1	2	FACETS	0.867	0.772	0.967	0.867	0.772	0.967	CLONAL	1	TRUE	1	0.42	2		332	500	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867256	45867256	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780129241	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	158	942	0	ENST00000391945.4:c.937G>A	p.Glu313Lys	p.E313K	ENST00000391945	NM_000400.3	313	Gaa/Aaa	10/23	1	2	FACETS	0.759	0.695	0.826	0.759	0.695	0.826	SUBCLONAL	1	TRUE	1	0.42	2		942	991	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140704	55140704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765271720	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	43	515	0	ENST00000257290.5:c.1565G>A	p.Arg522His	p.R522H	ENST00000257290	NM_006206.4	522	cGt/cAt	11/23	1	2	FACETS	0.295	0.246	0.349	0.295	0.246	0.349	SUBCLONAL	1	TRUE	1	0.42	2		515	695	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428244	47428244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	177	774	0	ENST00000377045.4:c.1204G>A	p.Asp402Asn	p.D402N	ENST00000377045	NM_001654.4	402	Gac/Aac	11/16	1	2	FACETS	0.883	0.813	0.955	0.883	0.813	0.955	CLONAL	1	TRUE	1	0.42	2		774	955	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024169	112024169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465963577	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	75	381	0	ENST00000368678.4:c.616C>T	p.Arg206Cys	p.R206C	ENST00000368678		206	Cgc/Tgc	7/13	1	2	FACETS	0.788	0.693	0.89	0.788	0.693	0.89	SUBCLONAL	1	TRUE	1	0.42	2		381	453	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038082	128038082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367552856	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	119	413	0	ENST00000285398.2:c.1468G>A	p.Glu490Lys	p.E490K	ENST00000285398	NM_000122.1	490	Gaa/Aaa	9/15	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.42	2		413	563	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181425	185181425	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1435276633	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	96	371	0	ENST00000265026.3:c.1366C>T	p.Arg456Ter	p.R456*	ENST00000265026	NM_004721.4	456	Cga/Tga	8/14	1	2	FACETS	0.92	0.823	1	0.92	0.823	1	CLONAL	1	TRUE	1	0.42	2		371	497	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793716	89793716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754149624	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	99	321	0	ENST00000336032.3:c.785C>T	p.Ser262Leu	p.S262L	ENST00000336032	NM_006813.2	262	tCg/tTg	2/2	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.42	2		321	431	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984773	11984773	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	78	316	0	ENST00000353533.5:c.319G>T	p.Glu107Ter	p.E107*	ENST00000353533	NM_003010.3	107	Gaa/Taa	3/11	1	2	FACETS	0.904	0.798	1	0.904	0.798	1	CLONAL	1	TRUE	1	0.42	2		316	411	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626461	12626461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs727504827	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	99	480	0	ENST00000251849.4:c.1688G>A	p.Arg563Gln	p.R563Q	ENST00000251849	NM_002880.3	563	cGa/cAa	16/17	1	2	FACETS	0.958	0.859	1	0.958	0.859	1	CLONAL	1	TRUE	1	0.42	2		480	492	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918695	44918695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746746824	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	84	454	2	ENST00000377967.4:c.1178G>A	p.Arg393Gln	p.R393Q	ENST00000377967	NM_021140.2	393	cGa/cAa	12/29	1	2	FACETS	0.798	0.707	0.895	0.798	0.707	0.895	SUBCLONAL	1	TRUE	1	0.42	2		456	501	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871797	12871797	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	78	179	0	ENST00000228872.4:c.514G>T	p.Glu172Ter	p.E172*	ENST00000228872	NM_004064.3	172	Gaa/Taa	2/3	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.42	2		179	341	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827580	72827580	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	136	540	0	ENST00000268489.5:c.9001G>T	p.Glu3001Ter	p.E3001*	ENST00000268489	NM_006885.3	3001	Gaa/Taa	9/10	1	2	FACETS	0.804	0.732	0.881	0.804	0.732	0.881	CLONAL	1	TRUE	1	0.42	2		540	805	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570469	39570469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1380208670	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	14	138	0	ENST00000262039.4:c.665G>A	p.Arg222Gln	p.R222Q	ENST00000262039	NM_002647.2	222	cGa/cAa	6/25	1	2	FACETS	0.312	0.225	0.416	0.312	0.225	0.416	SUBCLONAL	1	TRUE	1	0.42	2		138	214	SUCCESS
REL	5966	MSKCC	GRCh37	2	61128173	61128173	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	71	194	0	ENST00000295025.8:c.349G>T	p.Glu117Ter	p.E117*	ENST00000295025	NM_002908.2	117	Gaa/Taa	4/11	1	2	FACETS	0.869	0.762	0.983	0.869	0.762	0.983	CLONAL	1	TRUE	1	0.42	2		194	389	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435088	18435088	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs777959749	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	81	371	0	ENST00000266497.5:c.73C>A	p.Leu25Ile	p.L25I	ENST00000266497		25	Ctc/Atc	1/31	1	2	FACETS	0.936	0.829	1	0.936	0.829	1	CLONAL	1	TRUE	1	0.42	2		371	412	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95596408	95596408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775207591	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	81	257	0	ENST00000393063.1:c.560G>A	p.Arg187Gln	p.R187Q	ENST00000393063	NM_030621.3	187	cGa/cAa	6/28	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.42	2		257	378	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650601	48650601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140561920	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	119	743	1	ENST00000376670.3:c.571C>T	p.Arg191Cys	p.R191C	ENST00000376670	NM_002049.3	191	Cgt/Tgt	3/6	1	2	FACETS	0.726	0.655	0.8	0.726	0.655	0.8	SUBCLONAL	1	TRUE	1	0.42	2		744	781	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58701094	58701094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	105	499	0	ENST00000305921.3:c.685G>A	p.Glu229Lys	p.E229K	ENST00000305921	NM_003620.3	229	Gaa/Aaa	2/6	1	2	FACETS	0.809	0.726	0.897	0.809	0.726	0.897	CLONAL	1	TRUE	1	0.42	2		499	618	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957133	81957133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1476399695	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	148	607	2	ENST00000359376.3:c.2351G>A	p.Arg784Gln	p.R784Q	ENST00000359376	NM_002661.3	784	cGa/cAa	22/33	1	2	FACETS	0.955	0.874	1	0.955	0.874	1	CLONAL	1	TRUE	1	0.42	2		609	738	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748583	40748583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444440253	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	85	435	0	ENST00000373198.4:c.2933C>T	p.Ala978Val	p.A978V	ENST00000373198	NM_133170.3	978	gCg/gTg	21/32	1	2	FACETS	0.892	0.791	0.998	0.892	0.791	0.998	CLONAL	1	TRUE	1	0.42	2		435	454	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56409145	56409145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1308397244	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	75	367	0	ENST00000348428.3:c.1652G>A	p.Arg551Gln	p.R551Q	ENST00000348428	NM_006785.3	551	cGa/cAa	14/17	1	2	FACETS	0.882	0.777	0.994	0.882	0.777	0.994	CLONAL	1	TRUE	1	0.42	2		367	405	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100016	11100016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749059769	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	171	670	2	ENST00000358026.2:c.1142G>A	p.Arg381Gln	p.R381Q	ENST00000358026	NM_001128849.1	381	cGa/cAa	7/36	1	2	FACETS	0.917	0.844	0.993	0.917	0.844	0.993	CLONAL	1	TRUE	1	0.42	2		672	888	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670400	88670400	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs140016144	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	67	299	1	ENST00000360948.2:c.1286C>A	p.Thr429Asn	p.T429N	ENST00000360948	NM_001012338.2	429	aCt/aAt	11/19	1	2	FACETS	0.84	0.733	0.953	0.84	0.733	0.953	CLONAL	1	TRUE	1	0.42	2		300	380	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525525	137525525	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146687518	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	32	466	0	ENST00000367739.4:c.490G>A	p.Glu164Lys	p.E164K	ENST00000367739	NM_000416.2	164	Gaa/Aaa	4/7	1	2	FACETS	0.276	0.223	0.336	0.276	0.223	0.336	SUBCLONAL	1	TRUE	1	0.42	2		466	552	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638900	176638900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763399938	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	138	535	0	ENST00000439151.2:c.3500G>A	p.Arg1167His	p.R1167H	ENST00000439151	NM_022455.4	1167	cGc/cAc	5/23	1	2	FACETS	0.88	0.801	0.962	0.88	0.801	0.962	CLONAL	1	TRUE	1	0.42	2		535	747	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158095	27158095	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	35	444	1	ENST00000380036.4:c.319C>T	p.Arg107Ter	p.R107*	ENST00000380036	NM_000459.3	107	Cga/Tga	2/23	1	2	FACETS	0.269	0.22	0.325	0.269	0.22	0.325	SUBCLONAL	1	TRUE	1	0.42	2		445	619	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662700	117662700	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	111	373	1	ENST00000368508.3:c.4765G>T	p.Glu1589Ter	p.E1589*	ENST00000368508	NM_002944.2	1589	Gaa/Taa	29/43	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.42	2		374	496	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513314	106513314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559655430	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	85	323	0	ENST00000359195.3:c.2218G>A	p.Glu740Lys	p.E740K	ENST00000359195	NM_002649.2	740	Gag/Aag	4/11	1	2	FACETS	0.91	0.808	1	0.91	0.808	1	CLONAL	1	TRUE	1	0.42	2		323	445	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246518379	246518379	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773483378	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	109	394	0	ENST00000388985.4:c.182G>A	p.Arg61Gln	p.R61Q	ENST00000388985		61	cGa/cAa	2/12	1	2	FACETS	0.925	0.833	1	0.925	0.833	1	CLONAL	1	TRUE	1	0.42	2		394	561	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532732	187532732	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	122	494	0	ENST00000441802.2:c.9661C>A	p.Leu3221Ile	p.L3221I	ENST00000441802	NM_005245.3	3221	Ctt/Att	14/27	1	2	FACETS	0.936	0.848	1	0.936	0.848	1	CLONAL	1	TRUE	1	0.42	2		494	621	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955524	90955524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753270166	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	35	386	1	ENST00000265433.3:c.2141G>A	p.Arg714Gln	p.R714Q	ENST00000265433	NM_002485.4	714	cGa/cAa	14/16	0.0822528338184849	3	FACETS	0.378	0.309	0.456	0.189	0.154	0.228	INDETERMINATE	1	TRUE	1	0.42	3		387	533	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223853	53223853	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	199	966	3	ENST00000375401.3:c.3506C>T	p.Ser1169Leu	p.S1169L	ENST00000375401	NM_004187.3	1169	tCg/tTg	23/26	1	2	FACETS	0.889	0.823	0.958	0.889	0.823	0.958	CLONAL	1	TRUE	1	0.42	2		969	1066	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001395	150001395	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	30	524	1	ENST00000253339.5:c.2209C>T	p.Arg737Ter	p.R737*	ENST00000253339		737	Cga/Tga	4/7	1	2	FACETS	0.275	0.221	0.336	0.275	0.221	0.336	SUBCLONAL	1	TRUE	1	0.42	2		525	520	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180252	38180252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	170	806	0	ENST00000396334.3:c.100C>T	p.Pro34Ser	p.P34S	ENST00000396334	NM_002468.4	34	Ccc/Tcc	1/5	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.42	2		806	806	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992930	72992930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1398839726	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	180	790	1	ENST00000268489.5:c.1115G>A	p.Arg372Gln	p.R372Q	ENST00000268489	NM_006885.3	372	cGa/cAa	2/10	1	2	FACETS	0.883	0.814	0.955	0.883	0.814	0.955	CLONAL	1	TRUE	1	0.42	2		791	971	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193116996	193116996	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	72	237	0	ENST00000367435.3:c.730-1G>T		p.X244_splice	ENST00000367435	NM_024529.4	244			1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.42	2		237	335	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937553	76937553	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	72	326	0	ENST00000373344.5:c.3195G>T	p.Glu1065Asp	p.E1065D	ENST00000373344	NM_000489.3	1065	gaG/gaT	9/35	1	2	FACETS	0.884	0.776	0.998	0.884	0.776	0.998	CLONAL	1	TRUE	1	0.42	2		326	388	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439945	56439945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775028128	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	197	703	0	ENST00000407977.2:c.647C>T	p.Ser216Leu	p.S216L	ENST00000407977		216	tCg/tTg	6/10	1	2	FACETS	0.869	0.804	0.937	0.869	0.804	0.937	CLONAL	1	TRUE	1	0.42	2		703	1079	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932000	39932000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	51	725	2	ENST00000378444.4:c.2599G>A	p.Glu867Lys	p.E867K	ENST00000378444	NM_001123385.1	867	Gaa/Aaa	4/15	1	2	FACETS	0.281	0.238	0.329	0.281	0.238	0.329	SUBCLONAL	1	TRUE	1	0.42	2		727	863	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413077	63413077	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	166	808	1	ENST00000330258.3:c.90G>T	p.Lys30Asn	p.K30N	ENST00000330258	NM_152424.3	30	aaG/aaT	2/2	1	2	FACETS	0.877	0.806	0.952	0.877	0.806	0.952	CLONAL	1	TRUE	1	0.42	2		809	901	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417946	32417946	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772590420	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	117	455	0	ENST00000332351.3:c.1106G>A	p.Arg369Gln	p.R369Q	ENST00000332351	NM_024426.4	369	cGa/cAa	7/10	1	2	FACETS	0.879	0.794	0.968	0.879	0.794	0.968	CLONAL	1	TRUE	1	0.42	2		455	634	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117503	4117503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187018595	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	23	397	0	ENST00000262948.5:c.217G>A	p.Glu73Lys	p.E73K	ENST00000262948	NM_030662.3	73	Gaa/Aaa	2/11	1	2	FACETS	0.245	0.19	0.309	0.245	0.19	0.309	SUBCLONAL	1	TRUE	1	0.42	2		397	447	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582249	52582249	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	22	199	1	ENST00000394830.3:c.4579C>T	p.Arg1527Ter	p.R1527*	ENST00000394830	NM_018313.4	1527	Cga/Tga	30/30	1	2	FACETS	0.33	0.256	0.417	0.33	0.256	0.417	SUBCLONAL	1	TRUE	1	0.42	2		200	317	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961137	79961137	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs569679162	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	128	434	0	ENST00000265081.6:c.534G>T	p.Lys178Asn	p.K178N	ENST00000265081	NM_002439.4	178	aaG/aaT	3/24	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.42	2		434	567	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924402	131924402	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	87	262	0	ENST00000265335.6:c.1075C>T	p.Arg359Cys	p.R359C	ENST00000265335		359	Cgc/Tgc	8/25	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.42	2		262	392	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797788	32797788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370090254	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	48	615	0	ENST00000374899.4:c.1714G>A	p.Glu572Lys	p.E572K	ENST00000374899	NM_018833.2	572	Gaa/Aaa	10/12	1	2	FACETS	0.295	0.248	0.346	0.295	0.248	0.346	SUBCLONAL	1	TRUE	1	0.42	2		615	775	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339776	116339776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367722737	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	101	381	0	ENST00000397752.3:c.638C>T	p.Ser213Leu	p.S213L	ENST00000397752	NM_000245.2	213	tCg/tTg	2/21	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.42	2		381	465	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650169	93650169	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	74	428	0	ENST00000375746.1:c.1720C>T	p.Arg574Ter	p.R574*	ENST00000375746	NM_001174167.1	574	Cga/Tga	12/14	1	2	FACETS	0.734	0.644	0.83	0.734	0.644	0.83	SUBCLONAL	1	TRUE	1	0.42	2		428	480	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547973	41547973	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1232641756	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	146	593	0	ENST00000263253.7:c.2954A>G	p.Asp985Gly	p.D985G	ENST00000263253	NM_001429.3	985	gAt/gGt	15/31	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.42	2		593	695	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211219	36211219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765836382	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	250	913	1	ENST00000222270.7:c.970G>A	p.Glu324Lys	p.E324K	ENST00000222270	NM_014727.1	324	Gaa/Aaa	3/37	1	2	FACETS	0.954	0.891	1	0.954	0.891	1	CLONAL	1	TRUE	1	0.42	2		914	1248	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136820	69136820	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	88	422	2	ENST00000288368.4:c.4734G>T	p.Lys1578Asn	p.K1578N	ENST00000288368	NM_024870.2	1578	aaG/aaT	39/40	0.202691235086814	0	FACETS	0.449	0.399	0.503			1	INDETERMINATE	1	TRUE	0	0.42	0		424	541	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557804	187557804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1321370436	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	111	404	0	ENST00000441802.2:c.3907G>A	p.Glu1303Lys	p.E1303K	ENST00000441802	NM_005245.3	1303	Gaa/Aaa	5/27	1	2	FACETS	0.97	0.875	1	0.97	0.875	1	CLONAL	1	TRUE	1	0.42	2		404	545	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125473	7125473	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913144	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	64	749	1	ENST00000302850.5:c.3079C>T	p.Arg1027Ter	p.R1027*	ENST00000302850	NM_000208.2	1027	Cga/Tga	17/22	1	2	FACETS	0.331	0.285	0.38	0.331	0.285	0.38	SUBCLONAL	1	TRUE	1	0.42	2		750	921	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48921968	48921968	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs587778826	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	77	186	0	ENST00000267163.4:c.508G>T	p.Glu170Ter	p.E170*	ENST00000267163	NM_000321.2	170	Gaa/Taa	5/27	1	2	FACETS	0.943	0.832	1	0.943	0.832	1	CLONAL	1	TRUE	1	0.42	2		186	389	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436148	56436148	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760556127	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	47	602	0	ENST00000407977.2:c.989G>A	p.Arg330Gln	p.R330Q	ENST00000407977		330	cGa/cAa	9/10	1	2	FACETS	0.32	0.269	0.376	0.32	0.269	0.376	SUBCLONAL	1	TRUE	1	0.42	2		602	700	SUCCESS
APC	324	MSKCC	GRCh37	5	112179582	112179582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520223	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	65	314	0	ENST00000257430.4:c.8291C>T	p.Ser2764Phe	p.S2764F	ENST00000257430	NM_000038.5	2764	tCt/tTt	16/16	1	2	FACETS	0.839	0.731	0.954	0.839	0.731	0.954	CLONAL	1	TRUE	1	0.42	2		314	369	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750417	133750417	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	148	524	0	ENST00000318560.5:c.1248C>A	p.Phe416Leu	p.F416L	ENST00000318560	NM_005157.4	416	ttC/ttA	7/11	1	2	FACETS	0.976	0.893	1	0.976	0.893	1	CLONAL	1	TRUE	1	0.42	2		524	722	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273218	115273218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	89	430	0	ENST00000438362.2:c.1240C>T	p.Arg414Cys	p.R414C	ENST00000438362	NM_001242891.1	414	Cgt/Tgt	11/20	1	2	FACETS	0.778	0.691	0.87	0.778	0.691	0.87	SUBCLONAL	1	TRUE	1	0.42	2		430	545	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031690	69031690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371787029	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	99	389	0	ENST00000288368.4:c.3445C>T	p.Arg1149Cys	p.R1149C	ENST00000288368	NM_024870.2	1149	Cgc/Tgc	28/40	0.202691235086814	0	FACETS	0.582	0.522	0.645			1	INDETERMINATE	1	TRUE	0	0.42	0		389	470	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95599661	95599661	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	79	310	0	ENST00000393063.1:c.135A>C	p.Arg45Ser	p.R45S	ENST00000393063	NM_030621.3	45	agA/agC	3/28	1	2	FACETS	0.809	0.714	0.91	0.809	0.714	0.91	CLONAL	1	TRUE	1	0.42	2		310	465	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443676	29443676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56315533	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	133	635	1	ENST00000389048.3:c.3541C>T	p.Arg1181Cys	p.R1181C	ENST00000389048	NM_004304.4	1181	Cgc/Tgc	23/29	1	2	FACETS	0.819	0.745	0.898	0.819	0.745	0.898	CLONAL	1	TRUE	1	0.42	2		636	773	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350734	89350734	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146294483	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	199	648	1	ENST00000301030.4:c.2216C>T	p.Ser739Leu	p.S739L	ENST00000301030	NM_001256183.1	739	tCg/tTg	9/13	1	2	FACETS	0.934	0.865	1	0.934	0.865	1	CLONAL	1	TRUE	1	0.42	2		649	1015	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243238	123243238	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs868056281	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	159	697	1	ENST00000358487.5:c.2275C>T	p.Arg759Ter	p.R759*	ENST00000358487	NM_000141.4	759	Cga/Tga	17/18	1	2	FACETS	0.945	0.867	1	0.945	0.867	1	CLONAL	1	TRUE	1	0.42	2		698	801	SUCCESS
APC	324	MSKCC	GRCh37	5	112176209	112176209	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373440614	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	94	422	0	ENST00000257430.4:c.4918C>T	p.Arg1640Trp	p.R1640W	ENST00000257430	NM_000038.5	1640	Cgg/Tgg	16/16	1	2	FACETS	0.886	0.792	0.987	0.886	0.792	0.987	CLONAL	1	TRUE	1	0.42	2		422	505	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816896	32816896	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1159721335	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	102	409	0	ENST00000354258.4:c.1429-1G>T		p.X477_splice	ENST00000354258	NM_000593.5	477			1	2	FACETS	0.969	0.871	1	0.969	0.871	1	CLONAL	1	TRUE	1	0.42	2		409	501	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729635	162729635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	51	529	0	ENST00000367921.3:c.721G>A	p.Asp241Asn	p.D241N	ENST00000367921	NM_006182.2	241	Gat/Aat	8/18	1	2	FACETS	0.394	0.334	0.46	0.394	0.334	0.46	SUBCLONAL	1	TRUE	1	0.42	2		529	616	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902934	1902934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	156	562	1	ENST00000382891.5:c.553G>A	p.Glu185Lys	p.E185K	ENST00000382891	NM_133335.3	185	Gaa/Aaa	2/22	1	2	FACETS	0.99	0.909	1	0.99	0.909	1	CLONAL	1	TRUE	1	0.42	2		563	750	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818213	32818213	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs143800384	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	187	725	1	ENST00000354258.4:c.1312C>T	p.Arg438Ter	p.R438*	ENST00000354258	NM_000593.5	438	Cga/Tga	5/11	1	2	FACETS	0.952	0.88	1	0.952	0.88	1	CLONAL	1	TRUE	1	0.42	2		726	935	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114169	115114169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773465537	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	128	584	0	ENST00000257566.3:c.1048G>A	p.Ala350Thr	p.A350T	ENST00000257566	NM_016569.3	350	Gcc/Acc	6/8	1	2	FACETS	0.771	0.699	0.846	0.771	0.699	0.846	SUBCLONAL	1	TRUE	1	0.42	2		584	791	SUCCESS
APC	324	MSKCC	GRCh37	5	112175925	112175925	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs863225356	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	49	212	0	ENST00000257430.4:c.4634C>A	p.Ser1545Ter	p.S1545*	ENST00000257430	NM_000038.5	1545	tCa/tAa	16/16	1	2	FACETS	0.937	0.801	1	0.937	0.801	1	CLONAL	1	TRUE	1	0.42	2		212	249	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176490	123176490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	81	107	0	ENST00000218089.9:c.457G>A	p.Asp153Asn	p.D153N	ENST00000218089	NM_001042749.1	153	Gat/Aat	7/35	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.42	2		107	356	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880126	151880126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146495785	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	89	378	0	ENST00000262189.6:c.5198C>T	p.Ser1733Leu	p.S1733L	ENST00000262189	NM_170606.2	1733	tCg/tTg	35/59	1	2	FACETS	0.776	0.69	0.868	0.776	0.69	0.868	SUBCLONAL	1	TRUE	1	0.42	2		378	546	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597612	28597612	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	91	346	1	ENST00000241453.7:c.2293G>T	p.Glu765Ter	p.E765*	ENST00000241453	NM_004119.2	765	Gaa/Taa	19/24	1	2	FACETS	0.833	0.742	0.93	0.833	0.742	0.93	CLONAL	1	TRUE	1	0.42	2		347	520	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55963886	55963886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	106	413	0	ENST00000263923.4:c.2557G>A	p.Ala853Thr	p.A853T	ENST00000263923	NM_002253.2	853	Gcc/Acc	18/30	1	2	FACETS	0.908	0.816	1	0.908	0.816	1	CLONAL	1	TRUE	1	0.42	2		413	556	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76953086	76953086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782664370	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	89	396	0	ENST00000373344.5:c.227C>T	p.Ser76Leu	p.S76L	ENST00000373344	NM_000489.3	76	tCg/tTg	4/35	1	2	FACETS	0.804	0.715	0.899	0.804	0.715	0.899	CLONAL	1	TRUE	1	0.42	2		396	527	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740444	58740444	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs1163049039	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	81	503	0	ENST00000305921.3:c.1349T>G	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	450	tTa/tGa	6/6	1	2	FACETS	0.65	0.574	0.733	0.65	0.574	0.733	SUBCLONAL	1	TRUE	1	0.42	2		503	593	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279297	142279297	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	78	258	0	ENST00000350721.4:c.1350-1G>T		p.X450_splice	ENST00000350721	NM_001184.3	450			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.42	2		258	298	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017155	31017155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	24	275	0	ENST00000375687.4:c.486G>T	p.Lys162Asn	p.K162N	ENST00000375687	NM_015338.5	162	aaG/aaT	7/13	1	2	FACETS	0.249	0.194	0.312	0.249	0.194	0.312	SUBCLONAL	1	TRUE	1	0.42	2		275	459	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020096	123020096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	191	688	1	ENST00000355640.3:c.584G>A	p.Gly195Asp	p.G195D	ENST00000355640		195	gGt/gAt	2/7	1	2	FACETS	0.911	0.842	0.983	0.911	0.842	0.983	CLONAL	1	TRUE	1	0.42	2		689	998	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752361	57752361	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	85	295	0	ENST00000274289.3:c.1212G>T	p.Lys404Asn	p.K404N	ENST00000274289	NM_006622.3	404	aaG/aaT	9/14	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.42	2		295	368	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176719015	176719015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1321310131	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	71	275	1	ENST00000439151.2:c.6319C>T	p.Arg2107Cys	p.R2107C	ENST00000439151	NM_022455.4	2107	Cgc/Tgc	22/23	1	2	FACETS	0.74	0.648	0.839	0.74	0.648	0.839	SUBCLONAL	1	TRUE	1	0.42	2		276	457	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523334	9523334	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	63	504	0	ENST00000353224.5:c.1903G>T	p.Glu635Ter	p.E635*	ENST00000353224	NM_177990.2	635	Gaa/Taa	9/10	1	2	FACETS	0.596	0.516	0.683	0.596	0.516	0.683	SUBCLONAL	1	TRUE	1	0.42	2		504	503	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131364	202131364	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	86	410	0	ENST00000358485.4:c.332G>T	p.Arg111Ile	p.R111I	ENST00000358485	NM_001080125.1	111	aGa/aTa	2/9	1	2	FACETS	0.822	0.73	0.921	0.822	0.73	0.921	CLONAL	1	TRUE	1	0.42	2		410	498	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104673	193104673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	82	300	0	ENST00000367435.3:c.377G>A	p.Arg126Gln	p.R126Q	ENST00000367435	NM_024529.4	126	cGa/cAa	5/17	1	2	FACETS	0.917	0.812	1	0.917	0.812	1	CLONAL	1	TRUE	1	0.42	2		300	426	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471054	25471054	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	58	870	1	ENST00000264709.3:c.707C>A	p.Ser236Tyr	p.S236Y	ENST00000264709	NM_175629.2	236	tCt/tAt	7/23	1	2	FACETS	0.284	0.243	0.329	0.284	0.243	0.329	SUBCLONAL	1	TRUE	1	0.42	2		871	973	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819291	3819291	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	146	488	0	ENST00000262367.5:c.2944G>T	p.Glu982Ter	p.E982*	ENST00000262367	NM_004380.2	982	Gaa/Taa	15/31	1	2	FACETS	0.864	0.789	0.942	0.864	0.789	0.942	CLONAL	1	TRUE	1	0.42	2		488	805	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940449	29940449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375097381	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	74	294	0	ENST00000389048.3:c.782G>A	p.Arg261Gln	p.R261Q	ENST00000389048	NM_004304.4	261	cGa/cAa	2/29	1	2	FACETS	0.979	0.863	1	0.979	0.863	1	CLONAL	1	TRUE	1	0.42	2		294	360	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56832433	56832433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367699010	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	62	383	0	ENST00000308159.5:c.343G>A	p.Glu115Lys	p.E115K	ENST00000308159	NM_014669.4	115	Gaa/Aaa	4/22	1	2	FACETS	0.696	0.603	0.797	0.696	0.603	0.797	SUBCLONAL	1	TRUE	1	0.42	2		383	424	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739335	46739335	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748191191	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	87	499	0	ENST00000371975.4:c.1526G>A	p.Arg509Gln	p.R509Q	ENST00000371975	NM_003579.3	509	cGa/cAa	14/18	1	2	FACETS	0.642	0.569	0.721	0.642	0.569	0.721	SUBCLONAL	1	TRUE	1	0.42	2		499	645	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852036	128852036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761586263	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	68	929	0	ENST00000249373.3:c.2108G>A	p.Arg703Gln	p.R703Q	ENST00000249373	NM_005631.4	703	cGa/cAa	12/12	1	2	FACETS	0.352	0.305	0.403	0.352	0.305	0.403	SUBCLONAL	1	TRUE	1	0.42	2		929	919	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911048	29911048	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs765200653	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	196	1142	2	ENST00000376809.5:c.347C>A	p.Ser116Tyr	p.S116Y	ENST00000376809	NM_002116.7	116	tCt/tAt	3/8	1	2	FACETS	0.904	0.837	0.975	0.904	0.837	0.975	CLONAL	1	TRUE	1	0.42	2		1144	1032	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112152	115112152	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1444457719	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	147	783	3	ENST00000257566.3:c.1588G>A	p.Ala530Thr	p.A530T	ENST00000257566	NM_016569.3	530	Gcc/Acc	7/8	1	2	FACETS	0.846	0.773	0.923	0.846	0.773	0.923	CLONAL	1	TRUE	1	0.42	2		786	827	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924292	112924292	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	44	686	0	ENST00000351677.2:c.1238G>T	p.Arg413Ile	p.R413I	ENST00000351677	NM_002834.3	413	aGa/aTa	11/16	1	2	FACETS	0.245	0.204	0.29	0.245	0.204	0.29	SUBCLONAL	1	TRUE	1	0.42	2		686	855	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808233	99808233	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	45	476	0	ENST00000280892.6:c.456G>T	p.Glu152Asp	p.E152D	ENST00000280892	NM_001130678.1	152	gaG/gaT	5/7	1	2	FACETS	0.289	0.242	0.341	0.289	0.242	0.341	SUBCLONAL	1	TRUE	1	0.42	2		476	741	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911648	39911648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752359195	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	112	483	0	ENST00000378444.4:c.4982G>A	p.Arg1661Gln	p.R1661Q	ENST00000378444	NM_001123385.1	1661	cGa/cAa	15/15	1	2	FACETS	0.818	0.737	0.904	0.818	0.737	0.904	CLONAL	1	TRUE	1	0.42	2		483	652	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960059	134960059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	134	628	0	ENST00000398015.3:c.2416G>A	p.Asp806Asn	p.D806N	ENST00000398015	NM_004441.4	806	Gac/Aac	13/16	1	2	FACETS	0.811	0.737	0.888	0.811	0.737	0.888	CLONAL	1	TRUE	1	0.42	2		628	787	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701940	43701940	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	31	124	0	ENST00000382044.4:c.5306-1G>T		p.X1769_splice	ENST00000382044	NM_001141980.1	1769			1	2	FACETS	1	0.83	1	1	0.83	1	CLONAL	1	TRUE	1	0.42	2		124	146	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484375	8484375	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	61	258	0	ENST00000356435.5:c.3157C>A	p.Leu1053Ile	p.L1053I	ENST00000356435		1053	Ctt/Att	19/35	1	2	FACETS	0.847	0.735	0.967	0.847	0.735	0.967	CLONAL	1	TRUE	1	0.42	2		258	343	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938149	76938149	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	142	544	0	ENST00000373344.5:c.2599A>C	p.Asn867His	p.N867H	ENST00000373344	NM_000489.3	867	Aat/Cat	9/35	1	2	FACETS	0.917	0.837	1	0.917	0.837	1	CLONAL	1	TRUE	1	0.42	2		544	737	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644588	21644588	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	122	404	0	ENST00000421138.2:c.79G>T	p.Glu27Ter	p.E27*	ENST00000421138		27	Gaa/Taa	4/16	1	2	FACETS	0.951	0.862	1	0.951	0.862	1	CLONAL	1	TRUE	1	0.42	2		404	611	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074259	8074259	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	97	455	0	ENST00000377482.5:c.400A>C	p.Lys134Gln	p.K134Q	ENST00000377482	NM_018948.3	134	Aaa/Caa	4/4	1	2	FACETS	0.933	0.835	1	0.933	0.835	1	CLONAL	1	TRUE	1	0.42	2		455	495	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254836	16254836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	145	497	0	ENST00000375759.3:c.2101G>A	p.Glu701Lys	p.E701K	ENST00000375759	NM_015001.2	701	Gaa/Aaa	11/15	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.42	2		497	683	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255539	16255539	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	105	440	0	ENST00000375759.3:c.2804T>G	p.Val935Gly	p.V935G	ENST00000375759	NM_015001.2	935	gTt/gGt	11/15	1	2	FACETS	0.846	0.76	0.937	0.846	0.76	0.937	CLONAL	1	TRUE	1	0.42	2		440	591	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256657	16256657	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	103	423	0	ENST00000375759.3:c.3922A>C	p.Lys1308Gln	p.K1308Q	ENST00000375759	NM_015001.2	1308	Aaa/Caa	11/15	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.42	2		423	489	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097812	27097812	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	65	348	0	ENST00000324856.7:c.3401C>A	p.Ser1134Tyr	p.S1134Y	ENST00000324856	NM_006015.4	1134	tCt/tAt	12/20	1	2	FACETS	0.78	0.679	0.888	0.78	0.679	0.888	SUBCLONAL	1	TRUE	1	0.42	2		348	397	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39311614	39311614	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	102	324	0	ENST00000373001.3:c.1045A>C	p.Lys349Gln	p.K349Q	ENST00000373001	NM_022157.3	349	Aaa/Caa	6/7	1	2	FACETS	0.962	0.864	1	0.962	0.864	1	CLONAL	1	TRUE	1	0.42	2		324	505	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163771	72163771	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	93	491	0	ENST00000357731.5:c.587A>G	p.Asp196Gly	p.D196G	ENST00000357731	NM_173808.2	196	gAc/gGc	4/7	1	2	FACETS	0.836	0.745	0.931	0.836	0.745	0.931	CLONAL	1	TRUE	1	0.42	2		491	530	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690341	117690341	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	121	447	0	ENST00000369458.3:c.788C>A	p.Ser263Tyr	p.S263Y	ENST00000369458	NM_024626.3	263	tCt/tAt	5/6	1	2	FACETS	0.857	0.776	0.943	0.857	0.776	0.943	CLONAL	1	TRUE	1	0.42	2		447	672	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849121	156849121	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	151	821	1	ENST00000524377.1:c.2013G>T	p.Met671Ile	p.M671I	ENST00000524377	NM_002529.3	671	atG/atT	15/17	1	2	FACETS	0.763	0.697	0.832	0.763	0.697	0.832	SUBCLONAL	1	TRUE	1	0.42	2		822	943	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054974	176054974	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	137	498	0	ENST00000367669.3:c.1079T>G	p.Leu360Arg	p.L360R	ENST00000367669	NM_022457.5	360	cTt/cGt	10/20	1	2	FACETS	0.941	0.858	1	0.941	0.858	1	CLONAL	1	TRUE	1	0.42	2		498	693	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204513681	204513681	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs776150230	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	65	214	1	ENST00000367182.3:c.691G>T	p.Val231Phe	p.V231F	ENST00000367182	NM_001278516.1	231	Gtt/Ttt	9/11	1	2	FACETS	0.938	0.819	1	0.938	0.819	1	CLONAL	1	TRUE	1	0.42	2		215	330	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333293	70333293	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	163	616	1	ENST00000373644.4:c.1198G>A	p.Gly400Ser	p.G400S	ENST00000373644	NM_030625.2	400	Ggt/Agt	2/12	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.42	2		617	739	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333858	70333858	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	91	369	0	ENST00000373644.4:c.1763G>T	p.Arg588Ile	p.R588I	ENST00000373644	NM_030625.2	588	aGa/aTa	2/12	1	2	FACETS	0.94	0.838	1	0.94	0.838	1	CLONAL	1	TRUE	1	0.42	2		369	461	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405613	70405613	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	67	406	0	ENST00000373644.4:c.3127A>C	p.Asn1043His	p.N1043H	ENST00000373644	NM_030625.2	1043	Aat/Cat	4/12	1	2	FACETS	0.645	0.561	0.734	0.645	0.561	0.734	SUBCLONAL	1	TRUE	1	0.42	2		406	495	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405743	70405743	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	79	424	1	ENST00000373644.4:c.3257C>A	p.Ser1086Ter	p.S1086*	ENST00000373644	NM_030625.2	1086	tCg/tAg	4/12	1	2	FACETS	0.922	0.815	1	0.922	0.815	1	CLONAL	1	TRUE	1	0.42	2		425	408	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112745388	112745388	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	24	327	0	ENST00000369452.4:c.706G>T	p.Glu236Ter	p.E236*	ENST00000369452	NM_007373.3	236	Gaa/Taa	3/9	1	2	FACETS	0.273	0.213	0.342	0.273	0.213	0.342	SUBCLONAL	1	TRUE	1	0.42	2		327	419	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243247	123243247	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	162	727	0	ENST00000358487.5:c.2266G>T	p.Asp756Tyr	p.D756Y	ENST00000358487	NM_000141.4	756	Gac/Tac	17/18	1	2	FACETS	0.959	0.881	1	0.959	0.881	1	CLONAL	1	TRUE	1	0.42	2		727	804	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14300952	14300952	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	106	326	0	ENST00000256196.4:c.546A>C	p.Glu182Asp	p.E182D	ENST00000256196		182	gaA/gaC	6/6	1	2	FACETS	0.951	0.855	1	0.951	0.855	1	CLONAL	1	TRUE	1	0.42	2		326	531	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205149	61205149	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	147	563	0	ENST00000301761.2:c.89C>A	p.Ser30Ter	p.S30*	ENST00000301761	NM_017841.2	30	tCa/tAa	2/4	1	2	FACETS	0.936	0.856	1	0.936	0.856	1	CLONAL	1	TRUE	1	0.42	2		563	748	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189489	94189489	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587781384	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	124	270	0	ENST00000323929.3:c.1516G>T	p.Glu506Ter	p.E506*	ENST00000323929	NM_005591.3	506	Gaa/Taa	14/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.42	2		270	495	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918473	94918473	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	89	398	0	ENST00000536441.1:c.709C>A	p.Leu237Ile	p.L237I	ENST00000536441	NM_144665.3	237	Ctt/Att	5/10	1	2	FACETS	0.82	0.729	0.916	0.82	0.729	0.916	CLONAL	1	TRUE	1	0.42	2		398	517	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373947	118373947	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	88	285	0	ENST00000534358.1:c.7340A>C	p.Lys2447Thr	p.K2447T	ENST00000534358	NM_005933.3	2447	aAa/aCa	27/36	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.42	2		285	414	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144672	119144672	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	126	418	0	ENST00000264033.4:c.685G>T	p.Asp229Tyr	p.D229Y	ENST00000264033	NM_005188.3	229	Gat/Tat	4/16	1	2	FACETS	0.974	0.885	1	0.974	0.885	1	CLONAL	1	TRUE	1	0.42	2		418	616	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514453	125514453	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	87	311	0	ENST00000428830.2:c.1148A>C	p.Lys383Thr	p.K383T	ENST00000428830	NM_001114121.2	383	aAa/aCa	11/14	1	2	FACETS	0.889	0.79	0.994	0.889	0.79	0.994	CLONAL	1	TRUE	1	0.42	2		311	466	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871034	12871034	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	105	375	0	ENST00000228872.4:c.261C>A	p.Phe87Leu	p.F87L	ENST00000228872	NM_004064.3	87	ttC/ttA	1/3	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.42	2		375	487	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21643189	21643189	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs759043067	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	155	524	1	ENST00000421138.2:c.338T>C	p.Met113Thr	p.M113T	ENST00000421138		113	aTg/aCg	5/16	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.42	2		525	737	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233214	46233214	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	96	339	0	ENST00000334344.6:c.1433T>G	p.Leu478Ter	p.L478*	ENST00000334344	NM_152641.2	478	tTa/tGa	11/21	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.42	2		339	434	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243524	46243524	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	64	286	0	ENST00000334344.6:c.1877C>A	p.Ser626Tyr	p.S626Y	ENST00000334344	NM_152641.2	626	tCt/tAt	14/21	1	2	FACETS	0.983	0.858	1	0.983	0.858	1	CLONAL	1	TRUE	1	0.42	2		286	310	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438734	49438734	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759873461	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	173	646	0	ENST00000301067.7:c.4756C>T	p.Arg1586Cys	p.R1586C	ENST00000301067	NM_003482.3	1586	Cgc/Tgc	19/54	1	2	FACETS	0.903	0.832	0.978	0.903	0.832	0.978	CLONAL	1	TRUE	1	0.42	2		646	912	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58142358	58142358	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587779897	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	106	407	0	ENST00000257904.6:c.862C>T	p.Arg288Ter	p.R288*	ENST00000257904	NM_000075.3	288	Cga/Tga	8/8	1	2	FACETS	0.791	0.71	0.877	0.791	0.71	0.877	SUBCLONAL	1	TRUE	1	0.42	2		407	638	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120789165	120789165	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	40	512	0	ENST00000257552.2:c.772G>A	p.Val258Ile	p.V258I	ENST00000257552	NM_002442.3	258	Gtc/Atc	11/15	1	2	FACETS	0.284	0.235	0.339	0.284	0.235	0.339	SUBCLONAL	1	TRUE	1	0.42	2		512	671	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911551	32911551	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	24	297	1	ENST00000380152.3:c.3059C>A	p.Ser1020Tyr	p.S1020Y	ENST00000380152		1020	tCt/tAt	11/27	1	2	FACETS	0.32	0.251	0.4	0.32	0.251	0.4	SUBCLONAL	1	TRUE	1	0.42	2		298	357	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103508433	103508433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	42	144	0	ENST00000355739.4:c.499G>A	p.Glu167Lys	p.E167K	ENST00000355739	NM_000123.3	167	Gaa/Aaa	5/15	1	2	FACETS	0.837	0.704	0.981	0.837	0.704	0.981	CLONAL	1	TRUE	1	0.42	2		144	239	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519130	103519130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	38	454	0	ENST00000355739.4:c.2468G>T	p.Arg823Ile	p.R823I	ENST00000355739	NM_000123.3	823	aGa/aTa	11/15	1	2	FACETS	0.303	0.249	0.362	0.303	0.249	0.362	SUBCLONAL	1	TRUE	1	0.42	2		454	598	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81534632	81534632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	77	372	0	ENST00000298171.2:c.277G>A	p.Glu93Lys	p.E93K	ENST00000298171	NM_000369.2	93	Gaa/Aaa	3/10	1	2	FACETS	0.68	0.598	0.768	0.68	0.598	0.768	SUBCLONAL	1	TRUE	1	0.42	2		372	539	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643393	38643393	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	109	381	2	ENST00000299084.4:c.863A>C	p.Lys288Thr	p.K288T	ENST00000299084	NM_152594.2	288	aAa/aCa	7/7	1	2	FACETS	0.961	0.866	1	0.961	0.866	1	CLONAL	1	TRUE	1	0.42	2		383	540	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003367	42003367	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	146	455	0	ENST00000219905.7:c.2904T>G	p.Ile968Met	p.I968M	ENST00000219905	NM_001164273.1	968	atT/atG	8/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.42	2		455	613	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720305	43720305	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	171	544	0	ENST00000382044.4:c.3737G>T	p.Arg1246Ile	p.R1246I	ENST00000382044	NM_001141980.1	1246	aGa/aTa	18/28	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.42	2		544	796	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738660	43738660	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1566938581	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	127	528	0	ENST00000382044.4:c.2965A>C	p.Lys989Gln	p.K989Q	ENST00000382044	NM_001141980.1	989	Aaa/Caa	14/28	1	2	FACETS	0.889	0.807	0.976	0.889	0.807	0.976	CLONAL	1	TRUE	1	0.42	2		528	680	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630482	90630482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	151	507	0	ENST00000330062.3:c.829G>A	p.Asp277Asn	p.D277N	ENST00000330062	NM_002168.2	277	Gac/Aac	7/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.42	2		507	643	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396898	396898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	170	749	1	ENST00000262320.3:c.128G>A	p.Ser43Asn	p.S43N	ENST00000262320	NM_003502.3	43	aGt/aAt	2/11	1	2	FACETS	0.859	0.79	0.932	0.859	0.79	0.932	CLONAL	1	TRUE	1	0.42	2		750	942	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778302	3778909	+	frameshift_variant	Frame_Shift_Del	DEL	CGCTGCTGCTGCTGCATGGCCGGTGGGTAGCCTCCGGGTCCTTGAGGCTGCTGGAACTGGCCGTGCCCCGCCATGCCCCCAGCCATGCCGGCACTCCCTTGCTGCTGCTGCTGTTGCTGCTGTTGTTGCTGCTGCTGTTGCTGCTGCTGCTGCAGCAGCTGCCTCCGTAACATTTCTCGGTACTGTGGATTCATACTCGCCATGTTGGGGTTGTGTCCTGGGTTCATGATGTTCAAGGCCTGGCCCTGGGGGTTCAGGCCTCCCATCGCCTGCTGCTGTGGAGGCACACCGGGCCGCGGCACGCCAGCCTGCATGGCATTCAGGTTCTGCAGGCTGGGCTGCTGGTGCATGCCAGGCTGGGGTTGCATGCCGGGCTGGGACTGGAGGCCAGGCTGGGGCTGCATGCCGGGCTGATTGGCCACGTACTTGGCTGTGCGCTGTTTGATGAAAGCTGCCATTAGCTGCGGGTTTGATTTGAGAATGTTCAGCACCTGCTGTTGCTGCTGAGGGGAGCTGGGCGACTTCAGGGTCCGCAGCAGGTCTTGCAGAGCGCTGGGTGAGATGCTCCTGGGTGGCTGCACGCTGGGCATCCGGGGCCCAGCCACGGC	CGCTGCTGCTGCTGCATGGCCGGTGGGTAGCCTCCGGGTCCTTGAGGCTGCTGGAACTGGCCGTGCCCCGCCATGCCCCCAGCCATGCCGGCACTCCCTTGCTGCTGCTGCTGTTGCTGCTGTTGTTGCTGCTGCTGTTGCTGCTGCTGCTGCAGCAGCTGCCTCCGTAACATTTCTCGGTACTGTGGATTCATACTCGCCATGTTGGGGTTGTGTCCTGGGTTCATGATGTTCAAGGCCTGGCCCTGGGGGTTCAGGCCTCCCATCGCCTGCTGCTGTGGAGGCACACCGGGCCGCGGCACGCCAGCCTGCATGGCATTCAGGTTCTGCAGGCTGGGCTGCTGGTGCATGCCAGGCTGGGGTTGCATGCCGGGCTGGGACTGGAGGCCAGGCTGGGGCTGCATGCCGGGCTGATTGGCCACGTACTTGGCTGTGCGCTGTTTGATGAAAGCTGCCATTAGCTGCGGGTTTGATTTGAGAATGTTCAGCACCTGCTGTTGCTGCTGAGGGGAGCTGGGCGACTTCAGGGTCCGCAGCAGGTCTTGCAGAGCGCTGGGTGAGATGCTCCTGGGTGGCTGCACGCTGGGCATCCGGGGCCCAGCCACGGC	-	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	39	919	0	ENST00000262367.5:c.6139_6746del	p.Ala2047HisfsTer91	p.A2047Hfs*91	ENST00000262367	NM_004380.2	2047	GCCGTGGCTGGGCCCCGGATGCCCAGCGTGCAGCCACCCAGGAGCATCTCACCCAGCGCTCTGCAAGACCTGCTGCGGACCCTGAAGTCGCCCAGCTCCCCTCAGCAGCAACAGCAGGTGCTGAACATTCTCAAATCAAACCCGCAGCTAATGGCAGCTTTCATCAAACAGCGCACAGCCAAGTACGTGGCCAATCAGCCCGGCATGCAGCCCCAGCCTGGCCTCCAGTCCCAGCCCGGCATGCAACCCCAGCCTGGCATGCACCAGCAGCCCAGCCTGCAGAACCTGAATGCCATGCAGGCTGGCGTGCCGCGGCCCGGTGTGCCTCCACAGCAGCAGGCGATGGGAGGCCTGAACCCCCAGGGCCAGGCCTTGAACATCATGAACCCAGGACACAACCCCAACATGGCGAGTATGAATCCACAGTACCGAGAAATGTTACGGAGGCAGCTGCTGCAGCAGCAGCAGCAACAGCAGCAGCAACAACAGCAGCAACAGCAGCAGCAGCAAGGGAGTGCCGGCATGGCTGGGGGCATGGCGGGGCACGGCCAGTTCCAGCAGCCTCAAGGACCCGGAGGCTACCCACCGGCCATGCAGCAGCAGCAGCGc/c	31/31	1	2	FACETS	0.245	0.202	0.293	0.245	0.202	0.293	SUBCLONAL	1	TRUE	1	0.42	2		919	758	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029165	14029165	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201179693	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	63	224	0	ENST00000311895.7:c.1376C>A	p.Ser459Ter	p.S459*	ENST00000311895	NM_005236.2	459	tCa/tAa	8/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.42	2		224	256	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813676	50813676	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	163	647	0	ENST00000398568.2:c.1230G>T	p.Glu410Asp	p.E410D	ENST00000398568	NM_001042412.1	410	gaG/gaT	8/18	1	2	FACETS	0.912	0.838	0.99	0.912	0.838	0.99	CLONAL	1	TRUE	1	0.42	2		647	851	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645247	67645247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	155	545	0	ENST00000264010.4:c.512C>T	p.Ala171Val	p.A171V	ENST00000264010	NM_006565.3	171	gCc/gTc	3/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.42	2		545	670	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845920	72845920	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	115	411	0	ENST00000268489.5:c.3547G>A	p.Glu1183Lys	p.E1183K	ENST00000268489	NM_006885.3	1183	Gag/Aag	6/10	1	2	FACETS	0.962	0.87	1	0.962	0.87	1	CLONAL	1	TRUE	1	0.42	2		411	569	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925192	81925192	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	87	412	0	ENST00000359376.3:c.983A>C	p.Asn328Thr	p.N328T	ENST00000359376	NM_002661.3	328	aAc/aCc	11/33	1	2	FACETS	0.749	0.665	0.839	0.749	0.665	0.839	SUBCLONAL	1	TRUE	1	0.42	2		412	553	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348898	89348898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	193	776	0	ENST00000301030.4:c.4052G>A	p.Arg1351Lys	p.R1351K	ENST00000301030	NM_001256183.1	1351	aGa/aAa	9/13	1	2	FACETS	0.996	0.922	1	0.996	0.922	1	CLONAL	1	TRUE	1	0.42	2		776	923	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877208	89877208	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	38	368	0	ENST00000389301.3:c.429G>T	p.Lys143Asn	p.K143N	ENST00000389301	NM_000135.2	143	aaG/aaT	5/43	1	2	FACETS	0.339	0.28	0.405	0.339	0.28	0.405	SUBCLONAL	1	TRUE	1	0.42	2		368	534	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968319	15968319	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	69	236	0	ENST00000268712.3:c.4966A>G	p.Thr1656Ala	p.T1656A	ENST00000268712	NM_006311.3	1656	Acc/Gcc	34/46	1	2	FACETS	0.872	0.763	0.987	0.872	0.763	0.987	CLONAL	1	TRUE	1	0.42	2		236	377	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618341	37618341	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	67	376	0	ENST00000447079.4:c.17G>T	p.Arg6Ile	p.R6I	ENST00000447079	NM_015083.1	6	aGa/aTa	1/14	1	2	FACETS	0.849	0.741	0.963	0.849	0.741	0.963	CLONAL	1	TRUE	1	0.42	2		376	376	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37672043	37672043	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	134	426	0	ENST00000447079.4:c.2828C>T	p.Ala943Val	p.A943V	ENST00000447079	NM_015083.1	943	gCt/gTt	9/14	1	2	FACETS	0.962	0.877	1	0.962	0.877	1	CLONAL	1	TRUE	1	0.42	2		426	663	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681036	37681036	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	119	474	0	ENST00000447079.4:c.3205G>T	p.Glu1069Ter	p.E1069*	ENST00000447079	NM_015083.1	1069	Gaa/Taa	12/14	1	2	FACETS	0.817	0.738	0.899	0.817	0.738	0.899	CLONAL	1	TRUE	1	0.42	2		474	694	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40476739	40476739	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	151	519	0	ENST00000264657.5:c.1590G>T	p.Glu530Asp	p.E530D	ENST00000264657	NM_139276.2	530	gaG/gaT	17/24	1	2	FACETS	0.93	0.852	1	0.93	0.852	1	CLONAL	1	TRUE	1	0.42	2		519	773	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40872368	40872368	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1465203821	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	173	659	0	ENST00000428826.2:c.587A>G	p.Asp196Gly	p.D196G	ENST00000428826		196	gAc/gGc	7/21	1	2	FACETS	0.862	0.793	0.933	0.862	0.793	0.933	CLONAL	1	TRUE	1	0.42	2		659	956	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770859	59770859	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1060501736	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	85	271	0	ENST00000259008.2:c.2507G>T	p.Arg836Ile	p.R836I	ENST00000259008	NM_032043.2	836	aGa/aTa	18/20	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.42	2		271	403	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66521910	66521910	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	67	301	1	ENST00000358598.2:c.565G>T	p.Glu189Ter	p.E189*	ENST00000358598	NM_212471.2	189	Gaa/Taa	7/11	1	2	FACETS	0.867	0.758	0.984	0.867	0.758	0.984	CLONAL	1	TRUE	1	0.42	2		302	368	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39595519	39595519	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749282868	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	18	231	0	ENST00000262039.4:c.1405G>A	p.Glu469Lys	p.E469K	ENST00000262039	NM_002647.2	469	Gaa/Aaa	12/25	1	2	FACETS	0.271	0.204	0.351	0.271	0.204	0.351	SUBCLONAL	1	TRUE	1	0.42	2		231	316	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604755	48604755	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	117	398	0	ENST00000342988.3:c.1577A>T	p.Glu526Val	p.E526V	ENST00000342988	NM_005359.5	526	gAa/gTa	12/12	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.42	2		398	552	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390314	56390314	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	59	231	1	ENST00000348428.3:c.1053G>T	p.Met351Ile	p.M351I	ENST00000348428	NM_006785.3	351	atG/atT	10/17	1	2	FACETS	0.796	0.688	0.912	0.796	0.688	0.912	CLONAL	1	TRUE	1	0.42	2		232	353	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219336	5219336	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	153	728	0	ENST00000357368.4:c.3908T>C	p.Ile1303Thr	p.I1303T	ENST00000357368	NM_002850.3	1303	aTc/aCc	23/38	1	2	FACETS	0.941	0.862	1	0.941	0.862	1	CLONAL	1	TRUE	1	0.42	2		728	774	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5260819	5260819	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs530233682	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	127	677	1	ENST00000357368.4:c.592C>T	p.Arg198Ter	p.R198*	ENST00000357368	NM_002850.3	198	Cga/Tga	7/38	1	2	FACETS	0.87	0.79	0.955	0.87	0.79	0.955	CLONAL	1	TRUE	1	0.42	2		678	695	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302370	15302370	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775584737	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	220	996	0	ENST00000263388.2:c.901G>A	p.Val301Met	p.V301M	ENST00000263388	NM_000435.2	301	Gtg/Atg	6/33	1	2	FACETS	0.938	0.872	1	0.938	0.872	1	CLONAL	1	TRUE	1	0.42	2		996	1117	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744394	41744394	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	164	818	0	ENST00000301178.4:c.1014G>T	p.Glu338Asp	p.E338D	ENST00000301178	NM_021913.4	338	gaG/gaT	8/20	1	2	FACETS	0.916	0.841	0.993	0.916	0.841	0.993	CLONAL	1	TRUE	1	0.42	2		818	853	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46597047	46597047	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	41	506	0	ENST00000263734.3:c.861G>T	p.Glu287Asp	p.E287D	ENST00000263734	NM_001430.4	287	gaG/gaT	7/16	1	2	FACETS	0.31	0.257	0.369	0.31	0.257	0.369	SUBCLONAL	1	TRUE	1	0.42	2		506	630	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693916	47693916	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	82	282	0	ENST00000233146.2:c.1630A>C	p.Ile544Leu	p.I544L	ENST00000233146	NM_000251.2	544	Atc/Ctc	10/16	1	2	FACETS	0.967	0.857	1	0.967	0.857	1	CLONAL	1	TRUE	1	0.42	2		282	404	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873082	136873082	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	99	461	0	ENST00000241393.3:c.416T>C	p.Val139Ala	p.V139A	ENST00000241393	NM_003467.2	139	gTc/gCc	2/2	1	2	FACETS	0.997	0.894	1	0.997	0.894	1	CLONAL	1	TRUE	1	0.42	2		461	473	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198263244	198263244	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	83	355	0	ENST00000335508.6:c.3075G>T	p.Lys1025Asn	p.K1025N	ENST00000335508	NM_012433.2	1025	aaG/aaT	21/25	1	2	FACETS	0.743	0.657	0.834	0.743	0.657	0.834	SUBCLONAL	1	TRUE	1	0.42	2		355	532	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248708	212248708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144842611	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	67	353	0	ENST00000342788.4:c.3559G>A	p.Glu1187Lys	p.E1187K	ENST00000342788	NM_005235.2	1187	Gaa/Aaa	28/28	1	2	FACETS	0.814	0.711	0.925	0.814	0.711	0.925	CLONAL	1	TRUE	1	0.42	2		353	392	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578311	212578311	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	80	412	1	ENST00000342788.4:c.946G>T	p.Glu316Ter	p.E316*	ENST00000342788	NM_005235.2	316	Gaa/Taa	8/28	1	2	FACETS	0.715	0.63	0.805	0.715	0.63	0.805	SUBCLONAL	1	TRUE	1	0.42	2		413	533	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520188	9520188	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	77	447	0	ENST00000353224.5:c.2081T>A	p.Leu694His	p.L694H	ENST00000353224	NM_177990.2	694	cTc/cAc	10/10	1	2	FACETS	0.657	0.578	0.742	0.657	0.578	0.742	SUBCLONAL	1	TRUE	1	0.42	2		447	558	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770580	40770580	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	30	419	0	ENST00000373198.4:c.2802G>T	p.Lys934Asn	p.K934N	ENST00000373198	NM_133170.3	934	aaG/aaT	19/32	1	2	FACETS	0.273	0.219	0.334	0.273	0.219	0.334	SUBCLONAL	1	TRUE	1	0.42	2		419	524	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626703	12626703	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756160717	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	121	490	0	ENST00000251849.4:c.1586C>T	p.Ser529Leu	p.S529L	ENST00000251849	NM_002880.3	529	tCg/tTg	15/17	1	2	FACETS	0.957	0.867	1	0.957	0.867	1	CLONAL	1	TRUE	1	0.42	2		490	602	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084172	47084172	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	86	332	0	ENST00000409792.3:c.7117A>G	p.Asn2373Asp	p.N2373D	ENST00000409792	NM_014159.6	2373	Aat/Gat	17/21	1	2	FACETS	0.862	0.766	0.965	0.862	0.766	0.965	CLONAL	1	TRUE	1	0.42	2		332	475	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163605	47163605	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	34	288	0	ENST00000409792.3:c.2521T>G	p.Leu841Val	p.L841V	ENST00000409792	NM_014159.6	841	Ttg/Gtg	3/21	1	2	FACETS	0.527	0.432	0.634	0.527	0.432	0.634	SUBCLONAL	1	TRUE	1	0.42	2		288	307	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026810	71026810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	43	178	0	ENST00000318789.4:c.1412C>T	p.Ala471Val	p.A471V	ENST00000318789	NM_032682.5	471	gCa/gTa	16/21	1	2	FACETS	0.753	0.634	0.883	0.753	0.634	0.883	SUBCLONAL	1	TRUE	1	0.42	2		178	272	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212068	142212068	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	135	421	0	ENST00000350721.4:c.5984A>C	p.Asn1995Thr	p.N1995T	ENST00000350721	NM_001184.3	1995	aAc/aCc	35/47	1	2	FACETS	0.987	0.9	1	0.987	0.9	1	CLONAL	1	TRUE	1	0.42	2		421	651	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133463	55133463	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	82	370	0	ENST00000257290.5:c.767A>C	p.Lys256Thr	p.K256T	ENST00000257290	NM_006206.4	256	aAa/aCa	6/23	1	2	FACETS	0.843	0.747	0.946	0.843	0.747	0.946	CLONAL	1	TRUE	1	0.42	2		370	463	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133609	55133609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1396396699	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	94	434	0	ENST00000257290.5:c.913G>A	p.Val305Ile	p.V305I	ENST00000257290	NM_006206.4	305	Gtc/Atc	6/23	1	2	FACETS	0.874	0.781	0.973	0.874	0.781	0.973	CLONAL	1	TRUE	1	0.42	2		434	512	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955584	55955584	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	123	474	0	ENST00000263923.4:c.3361G>T	p.Glu1121Ter	p.E1121*	ENST00000263923	NM_002253.2	1121	Gaa/Taa	25/30	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.42	2		474	551	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180899	106180899	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	20	310	0	ENST00000380013.4:c.3927T>G	p.Phe1309Leu	p.F1309L	ENST00000380013	NM_001127208.2	1309	ttT/ttG	7/11	1	2	FACETS	0.267	0.203	0.341	0.267	0.203	0.341	SUBCLONAL	1	TRUE	1	0.42	2		310	357	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521256	187521256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	152	631	0	ENST00000441802.2:c.11899C>T	p.Pro3967Ser	p.P3967S	ENST00000441802	NM_005245.3	3967	Cct/Tct	22/27	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.42	2		631	722	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293721	1293721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	188	1041	1	ENST00000310581.5:c.1280C>T	p.Ala427Val	p.A427V	ENST00000310581	NM_198253.2	427	gCc/gTc	2/16	1	2	FACETS	0.858	0.792	0.927	0.858	0.792	0.927	CLONAL	1	TRUE	1	0.42	2		1042	1043	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177679	56177679	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	74	334	1	ENST00000399503.3:c.2652C>A	p.Phe884Leu	p.F884L	ENST00000399503	NM_005921.1	884	ttC/ttA	14/20	1	2	FACETS	0.74	0.65	0.837	0.74	0.65	0.837	SUBCLONAL	1	TRUE	1	0.42	2		335	476	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591276	67591276	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	98	313	0	ENST00000274335.5:c.1774A>C	p.Lys592Gln	p.K592Q	ENST00000274335		592	Aag/Cag	13/15	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.42	2		313	455	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064706	80064706	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	105	311	0	ENST00000265081.6:c.2137A>C	p.Lys713Gln	p.K713Q	ENST00000265081	NM_002439.4	713	Aaa/Caa	15/24	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.42	2		311	475	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685247	86685247	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	79	260	0	ENST00000274376.6:c.2963G>T	p.Arg988Ile	p.R988I	ENST00000274376	NM_002890.2	988	aGa/aTa	24/25	1	2	FACETS	0.929	0.821	1	0.929	0.821	1	CLONAL	1	TRUE	1	0.42	2		260	405	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925413	131925413	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	67	179	0	ENST00000265335.6:c.1336A>C	p.Lys446Gln	p.K446Q	ENST00000265335		446	Aaa/Caa	9/25	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.42	2		179	244	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523065	176523065	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	139	734	0	ENST00000292408.4:c.1829A>G	p.His610Arg	p.H610R	ENST00000292408	NM_213647.1	610	cAc/cGc	14/18	1	2	FACETS	0.849	0.773	0.928	0.849	0.773	0.928	CLONAL	1	TRUE	1	0.42	2		734	780	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562704	176562704	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	103	546	0	ENST00000439151.2:c.600G>T	p.Glu200Asp	p.E200D	ENST00000439151	NM_022455.4	200	gaG/gaT	2/23	1	2	FACETS	0.718	0.643	0.798	0.718	0.643	0.798	SUBCLONAL	1	TRUE	1	0.42	2		546	683	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056376	180056376	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	131	835	0	ENST00000261937.6:c.868G>C	p.Glu290Gln	p.E290Q	ENST00000261937	NM_182925.4	290	Gaa/Caa	7/30	1	2	FACETS	0.755	0.685	0.829	0.755	0.685	0.829	SUBCLONAL	1	TRUE	1	0.42	2		835	826	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816553	32816553	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	153	792	0	ENST00000354258.4:c.1622A>G	p.Tyr541Cys	p.Y541C	ENST00000354258	NM_000593.5	541	tAc/tGc	7/11	1	2	FACETS	0.723	0.66	0.788	0.723	0.66	0.788	SUBCLONAL	1	TRUE	1	0.42	2		792	1008	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120630	94120630	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	75	378	0	ENST00000369303.4:c.421A>C	p.Asn141His	p.N141H	ENST00000369303	NM_004440.3	141	Aac/Cac	3/17	1	2	FACETS	0.904	0.797	1	0.904	0.797	1	CLONAL	1	TRUE	1	0.42	2		378	395	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120878	94120878	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	75	341	0	ENST00000369303.4:c.173T>G	p.Ile58Ser	p.I58S	ENST00000369303	NM_004440.3	58	aTt/aGt	3/17	1	2	FACETS	0.88	0.775	0.991	0.88	0.775	0.991	CLONAL	1	TRUE	1	0.42	2		341	406	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117650561	117650561	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	110	562	0	ENST00000368508.3:c.5297A>C	p.Lys1766Thr	p.K1766T	ENST00000368508	NM_002944.2	1766	aAa/aCa	32/43	1	2	FACETS	0.862	0.776	0.952	0.862	0.776	0.952	CLONAL	1	TRUE	1	0.42	2		562	608	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718144	117718144	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	133	446	0	ENST00000368508.3:c.713A>C	p.Lys238Thr	p.K238T	ENST00000368508	NM_002944.2	238	aAa/aCa	7/43	1	2	FACETS	0.982	0.894	1	0.982	0.894	1	CLONAL	1	TRUE	1	0.42	2		446	645	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001211	150001211	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	103	477	0	ENST00000253339.5:c.2393G>A	p.Gly798Asp	p.G798D	ENST00000253339		798	gGc/gAc	4/7	1	2	FACETS	0.917	0.823	1	0.917	0.823	1	CLONAL	1	TRUE	1	0.42	2		477	535	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622195	162622195	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	96	419	0	ENST00000366898.1:c.502A>G	p.Thr168Ala	p.T168A	ENST00000366898	NM_004562.2	168	Acc/Gcc	4/12	1	2	FACETS	0.783	0.699	0.872	0.783	0.699	0.872	SUBCLONAL	1	TRUE	1	0.42	2		419	584	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268891	55268891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	149	685	0	ENST00000275493.2:c.2957G>T	p.Arg986Ile	p.R986I	ENST00000275493	NM_005228.3	986	aGa/aTa	25/28	1	2	FACETS	0.972	0.89	1	0.972	0.89	1	CLONAL	1	TRUE	1	0.42	2		685	730	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509510	106509510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	117	530	0	ENST00000359195.3:c.1504C>T	p.Leu502Phe	p.L502F	ENST00000359195	NM_002649.2	502	Ctc/Ttc	2/11	1	2	FACETS	0.842	0.76	0.927	0.842	0.76	0.927	CLONAL	1	TRUE	1	0.42	2		530	662	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509810	106509810	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	120	580	1	ENST00000359195.3:c.1804G>T	p.Glu602Ter	p.E602*	ENST00000359195	NM_002649.2	602	Gaa/Taa	2/11	1	2	FACETS	0.862	0.78	0.948	0.862	0.78	0.948	CLONAL	1	TRUE	1	0.42	2		581	663	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106519967	106519967	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	35	182	1	ENST00000359195.3:c.2395G>T	p.Glu799Ter	p.E799*	ENST00000359195	NM_002649.2	799	Gaa/Taa	6/11	1	2	FACETS	0.952	0.79	1	0.952	0.79	1	CLONAL	1	TRUE	1	0.42	2		183	175	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106519993	106519993	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	41	217	0	ENST00000359195.3:c.2421G>T	p.Lys807Asn	p.K807N	ENST00000359195	NM_002649.2	807	aaG/aaT	6/11	1	2	FACETS	0.827	0.695	0.972	0.827	0.695	0.972	CLONAL	1	TRUE	1	0.42	2		217	236	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545706	106545706	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	136	463	0	ENST00000359195.3:c.3183G>T	p.Glu1061Asp	p.E1061D	ENST00000359195	NM_002649.2	1061	gaG/gaT	11/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.42	2		463	606	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860073	151860073	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	89	318	0	ENST00000262189.6:c.10589C>A	p.Ser3530Tyr	p.S3530Y	ENST00000262189	NM_170606.2	3530	tCt/tAt	43/59	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.42	2		318	402	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960154	151960154	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	111	359	0	ENST00000262189.6:c.1246T>G	p.Phe416Val	p.F416V	ENST00000262189	NM_170606.2	416	Ttt/Gtt	9/59	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.42	2		359	517	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133164	38133164	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1043561773	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	116	408	0	ENST00000317025.8:c.4309G>T	p.Glu1437Ter	p.E1437*	ENST00000317025	NM_023034.1	1437	Gaa/Taa	24/24	1	2	FACETS	0.959	0.867	1	0.959	0.867	1	CLONAL	1	TRUE	1	0.42	2		408	576	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205105	38205105	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	169	503	0	ENST00000317025.8:c.585A>C	p.Glu195Asp	p.E195D	ENST00000317025	NM_023034.1	195	gaA/gaC	2/24	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.42	2		503	803	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972919	68972919	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	78	355	0	ENST00000288368.4:c.1244T>G	p.Phe415Cys	p.F415C	ENST00000288368	NM_024870.2	415	tTt/tGt	11/40	0.202691235086814	0	FACETS	0.495	0.437	0.557			1	INDETERMINATE	1	TRUE	0	0.42	0		355	435	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375954	8375954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	23	297	0	ENST00000356435.5:c.4643C>T	p.Pro1548Leu	p.P1548L	ENST00000356435		1548	cCg/cTg	28/35	1	2	FACETS	0.251	0.195	0.316	0.251	0.195	0.316	SUBCLONAL	1	TRUE	1	0.42	2		297	437	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158028	27158028	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	121	607	0	ENST00000380036.4:c.252A>C	p.Lys84Asn	p.K84N	ENST00000380036	NM_000459.3	84	aaA/aaC	2/23	1	2	FACETS	0.764	0.691	0.842	0.764	0.691	0.842	SUBCLONAL	1	TRUE	1	0.42	2		607	754	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197366	27197366	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	125	539	0	ENST00000380036.4:c.1678A>C	p.Asn560His	p.N560H	ENST00000380036	NM_000459.3	560	Aat/Cat	12/23	1	2	FACETS	0.875	0.794	0.961	0.875	0.794	0.961	CLONAL	1	TRUE	1	0.42	2		539	680	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966709	36966709	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	88	421	0	ENST00000358127.4:c.617C>T	p.Ser206Phe	p.S206F	ENST00000358127	NM_001280556.1	206	tCt/tTt	6/10	1	2	FACETS	0.901	0.802	1	0.901	0.802	1	CLONAL	1	TRUE	1	0.42	2		421	465	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97897632	97897632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749230615	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	101	326	0	ENST00000289081.3:c.839C>T	p.Ser280Leu	p.S280L	ENST00000289081	NM_000136.2	280	tCg/tTg	8/15	1	2	FACETS	0.98	0.879	1	0.98	0.879	1	CLONAL	1	TRUE	1	0.42	2		326	491	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248047	110248047	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	37	407	0	ENST00000374672.4:c.1425G>T	p.Met475Ile	p.M475I	ENST00000374672	NM_004235.4	475	atG/atT	5/5	1	2	FACETS	0.283	0.232	0.34	0.283	0.232	0.34	SUBCLONAL	1	TRUE	1	0.42	2		407	623	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250023	110250023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	46	819	1	ENST00000374672.4:c.652C>T	p.Pro218Ser	p.P218S	ENST00000374672	NM_004235.4	218	Ccg/Tcg	3/5	1	2	FACETS	0.286	0.24	0.338	0.286	0.24	0.338	SUBCLONAL	1	TRUE	1	0.42	2		820	765	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127933424	127933424	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	129	487	0	ENST00000373547.4:c.111A>C	p.Glu37Asp	p.E37D	ENST00000373547	NM_002721.4	37	gaA/gaC	2/7	1	2	FACETS	0.955	0.868	1	0.955	0.868	1	CLONAL	1	TRUE	1	0.42	2		487	643	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222803	53222803	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556833050	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	176	853	0	ENST00000375401.3:c.4133C>T	p.Ser1378Phe	p.S1378F	ENST00000375401	NM_004187.3	1378	tCc/tTc	25/26	1	2	FACETS	0.831	0.765	0.9	0.831	0.765	0.9	CLONAL	1	TRUE	1	0.42	2		853	1009	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225220	53225220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	150	604	0	ENST00000375401.3:c.2998G>A	p.Ala1000Thr	p.A1000T	ENST00000375401	NM_004187.3	1000	Gcc/Acc	20/26	1	2	FACETS	0.965	0.884	1	0.965	0.884	1	CLONAL	1	TRUE	1	0.42	2		604	740	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243918	53243918	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	181	832	0	ENST00000375401.3:c.1075C>T	p.Pro359Ser	p.P359S	ENST00000375401	NM_004187.3	359	Cct/Tct	8/26	1	2	FACETS	0.891	0.822	0.964	0.891	0.822	0.964	CLONAL	1	TRUE	1	0.42	2		832	967	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410735	63410735	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	127	617	0	ENST00000330258.3:c.2432T>C	p.Ile811Thr	p.I811T	ENST00000330258	NM_152424.3	811	aTc/aCc	2/2	1	2	FACETS	0.87	0.79	0.955	0.87	0.79	0.955	CLONAL	1	TRUE	1	0.42	2		617	695	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345318	70345318	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	50	680	0	ENST00000374080.3:c.2344C>A	p.Leu782Met	p.L782M	ENST00000374080		782	Ctg/Atg	16/45	1	2	FACETS	0.318	0.269	0.372	0.318	0.269	0.372	SUBCLONAL	1	TRUE	1	0.42	2		680	749	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890140	76890140	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	81	470	0	ENST00000373344.5:c.4754C>A	p.Ser1585Tyr	p.S1585Y	ENST00000373344	NM_000489.3	1585	tCt/tAt	17/35	1	2	FACETS	0.604	0.532	0.68	0.604	0.532	0.68	SUBCLONAL	1	TRUE	1	0.42	2		470	639	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034418	123034418	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	32	292	0	ENST00000355640.3:c.1175T>G	p.Ile392Arg	p.I392R	ENST00000355640		392	aTa/aGa	6/7	1	2	FACETS	0.302	0.245	0.368	0.302	0.245	0.368	SUBCLONAL	1	TRUE	1	0.42	2		292	504	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0050437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	131	165	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.703927946687259	1	FACETS	0.976	0.916	1	0.976	0.916	1	CLONAL	1	TRUE	0	0.80571554559449	1		165	199	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519966	NA	P-0050437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	216	687	0	ENST00000347630.2:c.397T>A	p.Phe133Ile	p.F133I	ENST00000347630	NM_001007230.1	133	Ttc/Atc	6/11	1	2	FACETS	0.928	0.869	0.987	0.928	0.869	0.987	CLONAL	1	TRUE	1	0.80571554559449	2		687	578	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183797	10183797	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs5030807	NA	P-0050510-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	273	928	0	ENST00000256474.2:c.266T>C	p.Leu89Pro	p.L89P	ENST00000256474	NM_000551.3	89	cTc/cCc	1/3	0.471772291812828	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.471970353760104	1		928	794	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103900	209103902	+	inframe_deletion	In_Frame_Del	DEL	TTA	TTA	-	novel	NA	P-0050510-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	113	386	0	ENST00000345146.2:c.1047_1049del	p.Asn349del	p.N349del	ENST00000345146	NM_005896.2	349	aaTAAa/aaa	9/10	1	2	FACETS	0.946	0.856	1	0.946	0.856	1	CLONAL	1	TRUE	1	0.471970353760104	2		386	506	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582105	52582106	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0050510-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	93	263	0	ENST00000394830.3:c.4722_4723del	p.Gln1575SerfsTer20	p.Q1575Sfs*20	ENST00000394830	NM_018313.4	1574	cgCCaa/cgaa	30/30	0.471772291812828	1	FACETS	0.938	0.843	1	0.938	0.843	1	CLONAL	1	TRUE	0	0.471970353760104	1		263	321	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183797	10183797	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs5030807	NA	P-0050510-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	283	928	0	ENST00000256474.2:c.266T>C	p.Leu89Pro	p.L89P	ENST00000256474	NM_000551.3	89	cTc/cCc	1/3	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.258822799638925	2		928	893	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073431	8073432	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0050510-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	29	563	0	ENST00000377482.5:c.1227dup	p.Phe410IlefsTer3	p.F410Ifs*3	ENST00000377482	NM_018948.3	409	-/A	4/4	1	2	FACETS	0.4	0.32	0.492	0.4	0.32	0.492	SUBCLONAL	1	TRUE	1	0.258822799638925	2		563	560	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165007	47165010	+	frameshift_variant	Frame_Shift_Del	DEL	TCTG	TCTG	-	rs752743762	NA	P-0050510-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	59	357	0	ENST00000409792.3:c.1116_1119del	p.Asp372GlufsTer111	p.D372Efs*111	ENST00000409792	NM_014159.6	372	gaCAGA/ga	3/21	0.169232454065631	2	FACETS	1	0.938	1	0.577	0.498	0.662	CLONAL	1	TRUE	0	0.258822799638925	2		357	395	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41020910	41020910	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050510-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	38	509	0	ENST00000267868.3:c.532T>C	p.Tyr178His	p.Y178H	ENST00000267868	NM_002875.4	178	Tat/Cat	7/10	1	2	FACETS	0.533	0.44	0.637	0.533	0.44	0.637	SUBCLONAL	1	TRUE	1	0.258822799638925	2		509	551	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103900	209103902	+	inframe_deletion	In_Frame_Del	DEL	TTA	TTA	-	novel	NA	P-0050510-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	80	386	0	ENST00000345146.2:c.1047_1049del	p.Asn349del	p.N349del	ENST00000345146	NM_005896.2	349	aaTAAa/aaa	9/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.258822799638925	2		386	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577152	7577171	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCACTACTCAGGATAGGAA	ACCACTACTCAGGATAGGAA	-	novel	NA	P-0050510-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	120	639	0	ENST00000269305.4:c.783-16_786del		p.X261_splice	ENST00000269305	NM_001126112.2	261		8/11	0.169232454065631	2	FACETS	0.806	0.731	0.886	0.806	0.731	0.886	CLONAL	2	TRUE	0	0.258822799638925	2		639	575	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441221	52441231	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCTCAAAGA	CAGCTCAAAGA	-	novel	NA	P-0050510-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	73	562	0	ENST00000460680.1:c.539_549del	p.Leu180ArgfsTer9	p.L180Rfs*9	ENST00000460680	NM_004656.3	180	cTCTTTGAGCTG/c	7/17	0.169232454065631	2	FACETS	1	0.953	1	0.591	0.518	0.669	CLONAL	1	TRUE	0	0.258822799638925	2		562	477	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0050516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	133	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.415741364088546	2		326	589	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	125	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.925	0.839	1	0.925	0.839	1	CLONAL	1	TRUE	1	0.415741364088546	2		457	650	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0050516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	107	275	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	0.881	0.793	0.975	0.881	0.793	0.975	CLONAL	1	TRUE	1	0.415741364088546	2		275	584	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40468838	40468839	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCACCATTA	novel	NA	P-0050516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	153	407	0	ENST00000264657.5:c.2217_2225dup	p.Gly741_Glu742insAspAsnGly	p.G741_E742insDNG	ENST00000264657	NM_139276.2	742	gaa/gaTAATGGTGAa	23/24	1	2	FACETS	0.81	0.741	0.882	0.81	0.741	0.882	CLONAL	1	TRUE	1	0.415741364088546	2		407	909	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218392	36218392	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371758121	NA	P-0050516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	279	751	1	ENST00000222270.7:c.4171G>A	p.Gly1391Arg	p.G1391R	ENST00000222270	NM_014727.1	1391	Gga/Aga	16/37	1	2	FACETS	0.999	0.936	1	0.999	0.936	1	CLONAL	1	TRUE	1	0.415741364088546	2		752	1344	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251643	212251643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377737065	NA	P-0050516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	109	408	1	ENST00000342788.4:c.3416G>A	p.Arg1139Gln	p.R1139Q	ENST00000342788	NM_005235.2	1139	cGg/cAg	27/28	1	2	FACETS	0.763	0.686	0.845	0.763	0.686	0.845	SUBCLONAL	1	TRUE	1	0.415741364088546	2		409	687	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541661	187541661	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	60	297	0	ENST00000441802.2:c.6079C>A	p.Arg2027Ser	p.R2027S	ENST00000441802	NM_005245.3	2027	Cgc/Agc	10/27	0.415741364088546	1	FACETS	0.504	0.435	0.578	0.504	0.435	0.578	SUBCLONAL	1	TRUE	0	0.415741364088546	1		297	454	SUCCESS
APC	324	MSKCC	GRCh37	5	112175647	112175647	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	98	289	0	ENST00000257430.4:c.4356del	p.Pro1453LeufsTer20	p.P1453Lfs*20	ENST00000257430	NM_000038.5	1452	gtA/gt	16/16	1	2	FACETS	0.837	0.749	0.931	0.837	0.749	0.931	CLONAL	1	TRUE	1	0.415741364088546	2		289	563	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050545-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	24	290	1				ENST00000310581	NM_198253.2	-/1132			0.2514725248372	3	FACETS	0.682	0.535	0.851	0.341	0.267	0.426	SUBCLONAL	1	TRUE	1	0.2514725248372	3		291	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0050545-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	159	1136	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.2514725248372	2		1137	1127	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8497247	8497247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050545-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	26	302	0	ENST00000356435.5:c.2344G>A	p.Glu782Lys	p.E782K	ENST00000356435		782	Gaa/Aaa	15/35	1	2	FACETS	0.783	0.622	0.967	0.783	0.622	0.967	CLONAL	1	TRUE	1	0.2514725248372	2		302	264	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050980	49050980	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0050545-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	30	344	0	ENST00000267163.4:c.2663+1G>A		p.X888_splice	ENST00000267163	NM_000321.2	888			0.2514725248372	1	FACETS	0.745	0.602	0.906	0.745	0.602	0.906	CLONAL	1	TRUE	0	0.2514725248372	1		344	280	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17359601	17359601	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050545-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	57	523	0	ENST00000375499.3:c.240G>C	p.Lys80Asn	p.K80N	ENST00000375499	NM_003000.2	80	aaG/aaC	3/8	1	2	FACETS	0.865	0.743	0.998	0.865	0.743	0.998	CLONAL	1	TRUE	1	0.2514725248372	2		523	524	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793095	33793095	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050545-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	23	0	0	ENST00000498907.2:c.226G>T	p.Glu76Ter	p.E76*	ENST00000498907	NM_004364.3	76	Gag/Tag	1/1	1	2	FACETS	0.27	0.209	0.341	0.27	0.209	0.341	SUBCLONAL	1	TRUE	1	0.2514725248372	2		0	677	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738308	190738308	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1238956903	NA	P-0050545-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	39	387	0	ENST00000441310.2:c.2560C>G	p.Leu854Val	p.L854V	ENST00000441310	NM_000534.4	854	Ctt/Gtt	12/13	0.2514725248372	1	FACETS	0.91	0.758	1	0.91	0.758	1	CLONAL	1	TRUE	0	0.2514725248372	1		387	298	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400125	41400125	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050545-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	57	735	0	ENST00000373198.4:c.634C>T	p.Gln212Ter	p.Q212*	ENST00000373198	NM_133170.3	212	Cag/Tag	5/32	1	2	FACETS	0.596	0.511	0.691	0.596	0.511	0.691	SUBCLONAL	1	TRUE	1	0.2514725248372	2		735	760	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433707	49433707	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050545-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	70	1714	0	ENST00000301067.7:c.7846C>G	p.Leu2616Val	p.L2616V	ENST00000301067	NM_003482.3	2616	Ctg/Gtg	31/54	1	2	FACETS	0.493	0.428	0.564	0.493	0.428	0.564	SUBCLONAL	1	TRUE	1	0.2514725248372	2		1714	1129	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95599689	95599689	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050545-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	27	0	0	ENST00000393063.1:c.107C>G	p.Ala36Gly	p.A36G	ENST00000393063	NM_030621.3	36	gCa/gGa	3/28	1	2	FACETS	0.333	0.264	0.413	0.333	0.264	0.413	SUBCLONAL	1	TRUE	1	0.2514725248372	2		0	645	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960951	15960951	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050545-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	49	513	0	ENST00000268712.3:c.6269C>G	p.Ser2090Cys	p.S2090C	ENST00000268712	NM_006311.3	2090	tCt/tGt	40/46	1	2	FACETS	0.641	0.542	0.75	0.641	0.542	0.75	SUBCLONAL	1	TRUE	1	0.2514725248372	2		513	608	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855828	45855828	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050545-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1301	51	0	0	ENST00000391945.4:c.1982C>A	p.Ala661Asp	p.A661D	ENST00000391945	NM_000400.3	661	gCc/gAc	21/23	1	2	FACETS	0.3	0.253	0.352	0.3	0.253	0.352	SUBCLONAL	1	TRUE	1	0.2514725248372	2		0	1352	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617491	158617491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050545-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	45	712	0	ENST00000263640.3:c.1165G>A	p.Glu389Lys	p.E389K	ENST00000263640	NM_001105.4	389	Gaa/Aaa	9/11	0.2514725248372	1	FACETS	0.448	0.375	0.528	0.448	0.375	0.528	SUBCLONAL	1	TRUE	0	0.2514725248372	1		712	699	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80646089	80646089	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050545-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	20	0	0	ENST00000286548.4:c.63C>G	p.Ile21Met	p.I21M	ENST00000286548	NM_002072.3	21	atC/atG	1/7	1	2	FACETS	0.486	0.372	0.621	0.486	0.372	0.621	SUBCLONAL	1	TRUE	1	0.2514725248372	2		0	327	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988655	41988655	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1444000023	NA	P-0050545-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	28	576	0	ENST00000219905.7:c.1447A>G	p.Ile483Val	p.I483V	ENST00000219905	NM_001164273.1	483	Att/Gtt	3/24	0.2514725248372	1	FACETS	0.395	0.315	0.487	0.395	0.315	0.487	SUBCLONAL	1	TRUE	0	0.2514725248372	1		576	493	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057833	27057835	+	stop_gained	Nonsense_Mutation	TNP	CTC	CTC	TTT	novel	NA	P-0050545-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	118	1137	0	ENST00000324856.7:c.1541_1543delinsTTT	p.Ser514_Gln515delinsPheTer	p.S514_Q515delinsF*	ENST00000324856	NM_006015.4	514	tCTCag/tTTTag	3/20	1	2	FACETS	0.88	0.793	0.974	0.88	0.793	0.974	CLONAL	1	TRUE	1	0.2514725248372	2		1137	1066	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0050567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	198	378	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.937	0.869	1	0.937	0.869	1	CLONAL	1	TRUE	1	0.511735513080148	2		378	826	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0050567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	141	422	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	1	2	FACETS	0.883	0.807	0.962	0.883	0.807	0.962	CLONAL	1	TRUE	1	0.511735513080148	2		422	624	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013691	12013691	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0050567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	145	449	0	ENST00000353533.5:c.634-1G>C		p.X212_splice	ENST00000353533	NM_003010.3	212			0.498648002375644	1	FACETS	0.897	0.825	0.972	0.897	0.825	0.972	CLONAL	1	TRUE	0	0.511735513080148	1		449	470	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0050567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	98	241	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.511735513080148	2		241	374	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735470	40735470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761910971	NA	P-0050567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	309	498	0	ENST00000373198.4:c.3403G>A	p.Val1135Met	p.V1135M	ENST00000373198	NM_133170.3	1135	Gtg/Atg	25/32	0.12498623566039	6	FACETS	0.892	0.84	0.946			1	INDETERMINATE	2	TRUE	NA	0.511735513080148	6		498	1370	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101574	27101574	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763947592	NA	P-0050567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	289	780	1	ENST00000324856.7:c.4856C>T	p.Pro1619Leu	p.P1619L	ENST00000324856	NM_006015.4	1619	cCa/cTa	18/20	0.498648002375644	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.511735513080148	1		781	831	SUCCESS
ATM	472	MSKCC	GRCh37	11	108154991	108154991	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	171	491	0	ENST00000278616.4:c.3784del	p.Arg1262GlufsTer7	p.R1262Efs*7	ENST00000278616	NM_000051.3	1262	Aga/ga	26/63	1	2	FACETS	0.94	0.867	1	0.94	0.867	1	CLONAL	1	TRUE	1	0.511735513080148	2		491	711	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970928	70970928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774392514	NA	P-0050567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	214	749	0	ENST00000276594.2:c.1333G>A	p.Asp445Asn	p.D445N	ENST00000276594	NM_024504.3	445	Gac/Aac	6/8	0.511735513080148	3	FACETS	0.851	0.789	0.914	0.425	0.394	0.457	CLONAL	1	TRUE	1	0.511735513080148	3		749	1235	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	333	588	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.772	0.736	0.809	1	0.995	1	SUBCLONAL	2	TRUE	1	0.636737884787795	2		592	677	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	46	782	4	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.167	0.14	0.197	0.167	0.14	0.197	SUBCLONAL	1	TRUE	1	0.636737884787795	2		786	864	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	196	1445	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.944	0.878	1	0.944	0.878	1	CLONAL	1	TRUE	1	0.636737884787795	2		1452	652	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564755	139564755	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	112	737	1	ENST00000308874.7:c.549del	p.Arg184GlyfsTer13	p.R184Gfs*13	ENST00000308874		182	Ccc/cc	7/10	0.274560674568175	3	FACETS	0.602	0.541	0.666	0.201	0.18	0.222	INDETERMINATE	1	TRUE	0	0.636737884787795	3		738	771	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247967	59247967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	233	592	3	ENST00000371222.2:c.776G>A	p.Arg259His	p.R259H	ENST00000371222	NM_002228.3	259	cGc/cAc	1/1	1	2	FACETS	0.986	0.924	1	0.986	0.924	1	CLONAL	1	TRUE	1	0.636737884787795	2		595	742	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306942	65306942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776082057	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	121	345	0	ENST00000342505.4:c.2635C>T	p.Arg879Cys	p.R879C	ENST00000342505	NM_002227.2	879	Cgt/Tgt	19/25	1	2	FACETS	0.8	0.727	0.876	0.8	0.727	0.876	SUBCLONAL	1	TRUE	1	0.636737884787795	2		345	475	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958589	175958589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	117	336	0	ENST00000367669.3:c.1756C>T	p.Arg586Cys	p.R586C	ENST00000367669	NM_022457.5	586	Cgt/Tgt	16/20	1	2	FACETS	0.802	0.728	0.88	0.802	0.728	0.88	CLONAL	1	TRUE	1	0.636737884787795	2		336	458	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63829525	63829525	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	153	325	1	ENST00000279873.7:c.1168G>A	p.Ala390Thr	p.A390T	ENST00000279873	NM_032199.2	390	Gct/Act	8/10	1	2	FACETS	0.975	0.898	1	0.975	0.898	1	CLONAL	1	TRUE	1	0.636737884787795	2		326	493	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205266	61205266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753474292	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	172	548	0	ENST00000301761.2:c.206G>A	p.Arg69His	p.R69H	ENST00000301761	NM_017841.2	69	cGc/cAc	2/4	1	2	FACETS	0.906	0.838	0.977	0.906	0.838	0.977	CLONAL	1	TRUE	1	0.636737884787795	2		548	596	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885939	111885939	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	156	644	1	ENST00000341259.2:c.1566del	p.Glu523SerfsTer25	p.E523Sfs*25	ENST00000341259	NM_005475.2	521	Ccc/cc	8/8	1	2	FACETS	0.763	0.701	0.827	0.763	0.701	0.827	SUBCLONAL	1	TRUE	1	0.636737884787795	2		645	642	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701236	43701236	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	192	480	0	ENST00000382044.4:c.5459A>G	p.Tyr1820Cys	p.Y1820C	ENST00000382044	NM_001141980.1	1820	tAc/tGc	26/28	1	2	FACETS	0.914	0.849	0.981	0.914	0.849	0.981	CLONAL	1	TRUE	1	0.636737884787795	2		480	660	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	188	506	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	0.581819553812285	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.636737884787795	1		506	402	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90645619	90645619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	103	255	0	ENST00000330062.3:c.4G>A	p.Ala2Thr	p.A2T	ENST00000330062	NM_002168.2	2	Gcc/Acc	1/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.636737884787795	2		255	261	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096285	2096285	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	276	704	0	ENST00000219066.1:c.222G>T	p.Glu74Asp	p.E74D	ENST00000219066	NM_002528.5	74	gaG/gaT	2/6	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.636737884787795	2		704	788	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821959	72821960	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762108866	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	111	360	1	ENST00000268489.5:c.10215dup	p.Gly3406ArgfsTer25	p.G3406Rfs*25	ENST00000268489	NM_006885.3	3405	-/C	10/10	1	2	FACETS	0.874	0.792	0.959	0.874	0.792	0.959	CLONAL	1	TRUE	1	0.636737884787795	2		361	399	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822741	72822741	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368861672	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	142	436	0	ENST00000268489.5:c.9434C>T	p.Thr3145Met	p.T3145M	ENST00000268489	NM_006885.3	3145	aCg/aTg	10/10	1	2	FACETS	0.859	0.788	0.933	0.859	0.788	0.933	CLONAL	1	TRUE	1	0.636737884787795	2		436	519	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	107	547	7	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	1	2	FACETS	0.66	0.595	0.729	0.66	0.595	0.729	SUBCLONAL	1	TRUE	1	0.636737884787795	2		554	509	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440750	56440750	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	160	159	0	ENST00000407977.2:c.468del	p.Leu157Ter	p.L157*	ENST00000407977		156	ggG/gg	5/10	1	2	FACETS	0.945	0.872	1	0.945	0.872	1	CLONAL	1	TRUE	1	0.636737884787795	2		159	532	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256768	19256769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1202792889	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	115	775	0	ENST00000162023.5:c.944dup	p.Val316SerfsTer6	p.V316Sfs*6	ENST00000162023		315	cca/ccCa	13/13	1	2	FACETS	0.545	0.491	0.601	0.545	0.491	0.601	SUBCLONAL	1	TRUE	1	0.636737884787795	2		775	663	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795060	42795060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	252	751	0	ENST00000575354.2:c.2140G>A	p.Gly714Arg	p.G714R	ENST00000575354	NM_015125.3	714	Ggg/Agg	10/20	1	2	FACETS	0.9	0.844	0.958	0.9	0.844	0.958	CLONAL	1	TRUE	1	0.636737884787795	2		751	879	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	200	745	2	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.855	0.794	0.917	0.855	0.794	0.917	CLONAL	1	TRUE	1	0.636737884787795	2		747	735	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727155	40727155	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	151	594	0	ENST00000373198.4:c.3809A>G	p.His1270Arg	p.H1270R	ENST00000373198	NM_133170.3	1270	cAc/cGc	28/32	1	2	FACETS	0.823	0.756	0.893	0.823	0.756	0.893	CLONAL	1	TRUE	1	0.636737884787795	2		594	576	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573820	41573820	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	252	710	0	ENST00000263253.7:c.6105G>T	p.Gln2035His	p.Q2035H	ENST00000263253	NM_001429.3	2035	caG/caT	31/31	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.636737884787795	2		710	784	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713609	30713609	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	30	511	0	ENST00000295754.5:c.934G>T	p.Glu312Ter	p.E312*	ENST00000295754	NM_003242.5	312	Gag/Tag	4/7	1	2	FACETS	0.178	0.143	0.218	0.178	0.143	0.218	SUBCLONAL	1	TRUE	1	0.636737884787795	2		511	530	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268762	41268762	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1245266458	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	161	377	2	ENST00000349496.5:c.1000G>A	p.Glu334Lys	p.E334K	ENST00000349496	NM_001904.3	334	Gaa/Aaa	7/15	1	2	FACETS	0.942	0.869	1	0.942	0.869	1	CLONAL	1	TRUE	1	0.636737884787795	2		379	537	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936518	49936518	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	251	667	0	ENST00000296474.3:c.1409del	p.Arg470LeufsTer11	p.R470Lfs*11	ENST00000296474	NM_002447.2	470	cGt/ct	2/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.636737884787795	2		667	781	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928518	69928518	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	156	573	0	ENST00000352241.4:c.338C>A	p.Pro113Gln	p.P113Q	ENST00000352241	NM_198159.2	113	cCg/cAg	2/10	1	2	FACETS	0.793	0.729	0.859	0.793	0.729	0.859	SUBCLONAL	1	TRUE	1	0.636737884787795	2		573	618	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027015	71027015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	177	468	2	ENST00000318789.4:c.1312C>T	p.Arg438Trp	p.R438W	ENST00000318789	NM_032682.5	438	Cgg/Tgg	15/21	1	2	FACETS	0.962	0.891	1	0.962	0.891	1	CLONAL	1	TRUE	1	0.636737884787795	2		470	578	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665122	138665122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1559922423	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	186	437	1	ENST00000330315.3:c.443G>A	p.Arg148His	p.R148H	ENST00000330315	NM_023067.3	148	cGc/cAc	1/1	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.636737884787795	2		438	488	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261555	142261555	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	127	320	0	ENST00000350721.4:c.3402del	p.Phe1134LeufsTer6	p.F1134Lfs*6	ENST00000350721	NM_001184.3	1134	ttT/tt	17/47	1	2	FACETS	0.816	0.743	0.891	0.816	0.743	0.891	CLONAL	1	TRUE	1	0.636737884787795	2		320	489	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	20	359	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.131	0.1	0.169	0.131	0.1	0.169	SUBCLONAL	1	TRUE	1	0.636737884787795	2		359	478	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805552	1805552	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	158	583	0	ENST00000260795.2:c.1064T>C	p.Val355Ala	p.V355A	ENST00000260795		355	gTg/gCg	7/17	1	2	FACETS	0.856	0.788	0.926	0.856	0.788	0.926	CLONAL	1	TRUE	1	0.636737884787795	2		583	580	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280428	1280428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767166646	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	198	594	3	ENST00000310581.5:c.1795C>T	p.Arg599Trp	p.R599W	ENST00000310581	NM_198253.2	599	Cgg/Tgg	4/16	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.636737884787795	2		597	622	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31464432	31464432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771607570	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	194	537	0	ENST00000344624.3:c.2485C>T	p.Arg829Trp	p.R829W	ENST00000344624		829	Cgg/Tgg	17/33	1	2	FACETS	0.852	0.791	0.915	0.852	0.791	0.915	CLONAL	1	TRUE	1	0.636737884787795	2		537	715	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526755	31526755	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	40	454	2	ENST00000344624.3:c.285del	p.Cys96AlafsTer12	p.C96Afs*12	ENST00000344624		95	ccC/cc	2/33	1	2	FACETS	0.26	0.216	0.31	0.26	0.216	0.31	SUBCLONAL	1	TRUE	1	0.636737884787795	2		456	483	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174824	56174824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	145	351	0	ENST00000399503.3:c.1983G>A	p.Met661Ile	p.M661I	ENST00000399503	NM_005921.1	661	atG/atA	11/20	1	2	FACETS	0.999	0.919	1	0.999	0.919	1	CLONAL	1	TRUE	1	0.636737884787795	2		351	456	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177763	56177763	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	107	327	0	ENST00000399503.3:c.2739del	p.Gly914AspfsTer7	p.G914Dfs*7	ENST00000399503	NM_005921.1	912	ggA/gg	14/20	1	2	FACETS	0.878	0.794	0.964	0.878	0.794	0.964	CLONAL	1	TRUE	1	0.636737884787795	2		327	383	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629108	86629108	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853218	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	112	249	0	ENST00000274376.6:c.853C>T	p.Arg285Ter	p.R285*	ENST00000274376	NM_002890.2	285	Cga/Tga	4/25	1	2	FACETS	0.936	0.85	1	0.936	0.85	1	CLONAL	1	TRUE	1	0.636737884787795	2		249	376	SUCCESS
APC	324	MSKCC	GRCh37	5	112179494	112179494	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	143	292	0	ENST00000257430.4:c.8203G>T	p.Gly2735Ter	p.G2735*	ENST00000257430	NM_000038.5	2735	Gga/Tga	16/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.636737884787795	2		292	406	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367244	50367244	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	115	345	0	ENST00000331340.3:c.56del	p.Pro19LeufsTer2	p.P19Lfs*2	ENST00000331340	NM_006060.4	17	agC/ag	3/8	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.636737884787795	2		345	351	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194671	29194671	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370779406	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	236	705	1	ENST00000240100.2:c.1057C>T	p.Arg353Trp	p.R353W	ENST00000240100	NM_001394.6	353	Cgg/Tgg	4/4	1	2	FACETS	0.975	0.914	1	0.975	0.914	1	CLONAL	1	TRUE	1	0.636737884787795	2		706	760	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732942	44732942	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	153	469	0	ENST00000377967.4:c.145C>T	p.Leu49Phe	p.L49F	ENST00000377967	NM_021140.2	49	Ctc/Ttc	1/29	1	2	FACETS	0.999	0.921	1	0.999	0.921	1	CLONAL	1	TRUE	1	0.636737884787795	2		469	481	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228160	53228160	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050574-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	165	550	0	ENST00000375401.3:c.2242C>T	p.Arg748Trp	p.R748W	ENST00000375401	NM_004187.3	748	Cgg/Tgg	15/26	1	2	FACETS	0.972	0.899	1	0.972	0.899	1	CLONAL	1	TRUE	1	0.636737884787795	2		550	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	206	263	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.395755677497765	4	FACETS	1	0.975	1	0.8	0.753	0.848	CLONAL	3	TRUE	0	0.430051063323071	4		263	428	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114139	115114139	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	136	226	0	ENST00000257566.3:c.1078G>C	p.Val360Leu	p.V360L	ENST00000257566	NM_016569.3	360	Gta/Cta	6/8	0.324957323900271	4	FACETS	0.864	0.796	0.933	0.648	0.597	0.7	CLONAL	3	TRUE	0	0.430051063323071	4		226	349	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044484	12044484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	36	121	0	ENST00000353533.5:c.1107G>A	p.Met369Ile	p.M369I	ENST00000353533	NM_003010.3	369	atG/atA	11/11	0.395755677497765	4	FACETS	1	0.935	1	0.322	0.267	0.381	CLONAL	1	TRUE	0	0.430051063323071	4		121	186	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100264	157100264	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	59	39	0	ENST00000346085.5:c.1201G>T	p.Gly401Cys	p.G401C	ENST00000346085	NM_020732.3	401	Ggc/Tgc	1/20	0.400749942833998	4	FACETS	1	0.954	1			1	CLONAL	3	TRUE	NA	0.430051063323071	4		39	115	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444453	50444454	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0050631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	60	119	0	ENST00000331340.3:c.383_384delinsTT	p.Gly128Val	p.G128V	ENST00000331340	NM_006060.4	128	gGG/gTT	4/8	0.334168918139241	2	FACETS	1	0.967	1	0.677	0.592	0.766	CLONAL	1	TRUE	0	0.430051063323071	2		119	206	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0050641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	50	580	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.3	2	FACETS	1	0.935	1			1	CLONAL	1	TRUE	NA	0.23	2		580	366	SUCCESS
CALR	811	MSKCC	GRCh37	19	13049954	13049954	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	50	502	0	ENST00000316448.5:c.98G>A	p.Trp33Ter	p.W33*	ENST00000316448	NM_004343.3	33	tGg/tAg	2/9	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.23	2		502	417	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795024	42795024	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs748419463	NA	P-0050641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	33	1019	1	ENST00000575354.2:c.2104A>G	p.Asn702Asp	p.N702D	ENST00000575354	NM_015125.3	702	Aat/Gat	10/20	1	2	FACETS	0.607	0.494	0.734	0.607	0.494	0.734	SUBCLONAL	1	TRUE	1	0.23	2		1020	473	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62317181	62317181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	57	919	0	ENST00000360203.5:c.1304C>T	p.Ala435Val	p.A435V	ENST00000360203	NM_001283009.1	435	gCt/gTt	16/35	0.215996258316573	3	FACETS	0.976	0.838	1	0.488	0.419	0.564	CLONAL	1	TRUE	1	0.23	3		919	566	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	156	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.264668154076003	3	FACETS	1	0.989	1	0.734	0.677	0.792	INDETERMINATE	1	TRUE	1	0.558473535453314	3		457	487	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686326	30686326	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	131	335	0	ENST00000295754.5:c.182G>A	p.Cys61Tyr	p.C61Y	ENST00000295754	NM_003242.5	61	tGt/tAt	2/7	0.558473535453314	1	FACETS	0.829	0.759	0.901	0.829	0.759	0.901	CLONAL	1	TRUE	0	0.558473535453314	1		335	408	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539002	187539003	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGTTGAC	novel	NA	P-0050650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	148	395	0	ENST00000441802.2:c.8731_8737dup	p.Asp2913GlyfsTer4	p.D2913Gfs*4	ENST00000441802	NM_005245.3	2913	gat/gGTCAACGat	10/27	0.264668154076003	3	FACETS	1	0.98	1	0.606	0.557	0.658	INDETERMINATE	1	TRUE	1	0.558473535453314	3		395	559	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	46	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.142321234787371	4	FACETS	1	0.932	1	1	0.932	1	INDETERMINATE	2	TRUE	2	0.316758135571365	4		326	165	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	152	831	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.316758135571365	4	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	2	0.316758135571365	4		831	614	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	17	197	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.142321234787371	4	FACETS	0.777	0.59	0.99	0.777	0.59	0.99	INDETERMINATE	2	TRUE	2	0.316758135571365	4		197	91	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	50	275	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.142321234787371	4	FACETS	0.969	0.841	1	1	0.967	1	INDETERMINATE	3	TRUE	2	0.316758135571365	4		275	143	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	27	1590	2	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	0.175100253515481	3	FACETS	0.5	0.397	0.617	0.25	0.198	0.309	INDETERMINATE	1	TRUE	1	0.316758135571365	3		1592	395	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411530	63411530	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	80	728	0	ENST00000330258.3:c.1637del	p.Leu546CysfsTer16	p.L546Cfs*16	ENST00000330258	NM_152424.3	546	tTg/tg	2/2	0.262172575152279	0	FACETS	0.826	0.741	0.913			1	CLONAL	2	TRUE	0	0.316758135571365	0		728	209	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	59	498	4	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.847	0.738	0.961	1	0.976	1	CLONAL	2	TRUE	1	0.316758135571365	2		502	220	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390736	139390736	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	162	907	1	ENST00000277541.6:c.7455del	p.Ser2486ArgfsTer103	p.S2486Rfs*103	ENST00000277541	NM_017617.3	2485	ccC/cc	34/34	1	2	FACETS	0.882	0.813	0.953	1	0.991	1	CLONAL	2	TRUE	1	0.316758135571365	2		908	580	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	76	1445	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.268897668693842	4	FACETS	0.759	0.669	0.856	0.759	0.669	0.856	SUBCLONAL	2	TRUE	2	0.316758135571365	4		1452	416	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	56	277	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	0.316758135571365	4	FACETS	0.779	0.672	0.893	0.779	0.672	0.893	SUBCLONAL	2	TRUE	2	0.316758135571365	4		277	299	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778282	3778282	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	84	715	1	ENST00000262367.5:c.6766del	p.Leu2256SerfsTer46	p.L2256Sfs*46	ENST00000262367	NM_004380.2	2256	Ctc/tc	31/31	0.316758135571365	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	2	0.316758135571365	4		716	309	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	109	364	1	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	0.316758135571365	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.316758135571365	4		365	392	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294665	1294665	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	73	392	4	ENST00000310581.5:c.336del	p.Glu113ArgfsTer15	p.E113Rfs*15	ENST00000310581	NM_198253.2	112	ccC/cc	2/16	0.222697646833025	0	FACETS	0.795	0.709	0.884			1	SUBCLONAL	2	TRUE	0	0.316758135571365	0		396	198	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504401	8504401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757922864	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	74	424	0	ENST00000356435.5:c.1682G>A	p.Arg561Gln	p.R561Q	ENST00000356435		561	cGa/cAa	12/35	1	2	FACETS	1	0.951	1	1	0.985	1	CLONAL	2	TRUE	1	0.316758135571365	2		424	208	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070349	37070349	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs63750855	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	37	423	0	ENST00000231790.2:c.1489del	p.Arg497GlyfsTer11	p.R497Gfs*11	ENST00000231790	NM_000249.3	495	aCc/ac	13/19	0.175100253515481	3	FACETS	1	0.947	1	0.694	0.578	0.82	INDETERMINATE	1	TRUE	1	0.316758135571365	3		423	195	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438316	110438317	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	rs532810290	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	23	187	0	ENST00000375856.3:c.82_84dup	p.Asn28dup	p.N28dup	ENST00000375856	NM_003749.2	28	-/AAC	1/2	1	2	FACETS	0.839	0.66	1	0.839	0.66	1	CLONAL	1	TRUE	1	0.316758135571365	2		187	173	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834552	156834552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540521894	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	84	728	1	ENST00000524377.1:c.320C>T	p.Ala107Val	p.A107V	ENST00000524377	NM_002529.3	107	gCg/gTg	3/17	1	2	FACETS	0.944	0.844	1	1	0.985	1	CLONAL	2	TRUE	1	0.316758135571365	2		729	281	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395560	116395560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753407699	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	96	373	0	ENST00000397752.3:c.1853C>T	p.Thr618Met	p.T618M	ENST00000397752	NM_000245.2	618	aCg/aTg	6/21	0.142321234787371	4	FACETS	1	0.951	1	1	0.985	1	INDETERMINATE	3	TRUE	2	0.316758135571365	4		373	247	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852118	63852118	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	87	562	1	ENST00000279873.7:c.2901del	p.Lys967AsnfsTer15	p.K967Nfs*15	ENST00000279873	NM_032199.2	966	Aaa/aa	10/10	0.316758135571365	4	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	2	0.316758135571365	4		563	345	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900984	114900984	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778855667	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	108	545	2	ENST00000543371.1:c.598del	p.Leu200SerfsTer25	p.L200Sfs*25	ENST00000543371	NM_001198531.1	198	caC/ca	6/14	1	2	FACETS	0.952	0.863	1	1	0.988	1	CLONAL	2	TRUE	1	0.316758135571365	2		547	358	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	97	595	4	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	0.316758135571365	5	FACETS	1	0.963	1	0.77	0.692	0.852	CLONAL	2	TRUE	2	0.316758135571365	5		599	391	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619428	1619428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757623802	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	192	712	0	ENST00000344749.5:c.1213C>T	p.Arg405Cys	p.R405C	ENST00000344749	NM_001136139.2	405	Cgc/Tgc	15/19	0.175100253515481	3	FACETS	1	0.987	1	1	0.987	1	INDETERMINATE	2	TRUE	1	0.316758135571365	3		712	564	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252940	36252940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	114	382	0	ENST00000300305.3:c.422C>T	p.Ser141Leu	p.S141L	ENST00000300305		141	tCg/tTg	4/8	0.121360509207024	0	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	0	0.316758135571365	0		382	427	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916957	178916957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	46	300	0	ENST00000263967.3:c.344G>A	p.Arg115Gln	p.R115Q	ENST00000263967	NM_006218.2	115	cGa/cAa	2/21	0.142321234787371	4	FACETS	1	0.868	1	1	0.868	1	INDETERMINATE	2	TRUE	2	0.316758135571365	4		300	188	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622192	1622193	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	185	791	0	ENST00000344749.5:c.682_683del	p.Trp228GlufsTer25	p.W228Efs*25	ENST00000344749	NM_001136139.2	228	TGg/g	10/19	0.175100253515481	3	FACETS	0.928	0.865	0.992	1	0.99	1	INDETERMINATE	3	TRUE	1	0.316758135571365	3		791	486	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562259	21562259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148138215	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	115	816	0	ENST00000382592.4:c.1660G>A	p.Gly554Ser	p.G554S	ENST00000382592	NM_014572.2	554	Ggc/Agc	4/8	1	2	FACETS	1	0.95	1	1	0.99	1	CLONAL	2	TRUE	1	0.316758135571365	2		816	342	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	134	633	4	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	0.316758135571365	5	FACETS	0.908	0.831	0.988	0.908	0.831	0.988	CLONAL	3	TRUE	2	0.316758135571365	5		637	458	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223858	36223858	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	106	851	3	ENST00000222270.7:c.6413del	p.Pro2138ArgfsTer15	p.P2138Rfs*15	ENST00000222270	NM_014727.1	2136	ctC/ct	28/37	0.175100253515481	3	FACETS	1	0.973	1	1	0.973	1	INDETERMINATE	2	TRUE	1	0.316758135571365	3		854	322	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720648	89720649	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TA	TA	-	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	19	404	0	ENST00000371953.3:c.802-3_802-2del		p.X268_splice	ENST00000371953	NM_000314.4	268			0.316758135571365	4	FACETS	0.494	0.374	0.634	0.247	0.187	0.317	SUBCLONAL	1	TRUE	2	0.316758135571365	4		404	320	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610164	43610164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137855422	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	55	752	3	ENST00000355710.3:c.2116G>A	p.Val706Met	p.V706M	ENST00000355710	NM_020975.4	706	Gtg/Atg	11/20	0.222697646833025	0	FACETS	1	0.896	1			1	CLONAL	1	TRUE	0	0.316758135571365	0		755	228	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31429602	31429602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370990538	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	33	362	0	ENST00000344624.3:c.3196C>T	p.Arg1066Cys	p.R1066C	ENST00000344624		1066	Cgc/Tgc	24/33	0.222697646833025	0	FACETS	0.753	0.619	0.901			1	CLONAL	1	TRUE	0	0.316758135571365	0		362	189	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55974007	55974007	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	81	515	0	ENST00000263923.4:c.1309T>C	p.Tyr437His	p.Y437H	ENST00000263923	NM_002253.2	437	Tac/Cac	10/30	1	2	FACETS	0.947	0.845	1	1	0.984	1	CLONAL	2	TRUE	1	0.316758135571365	2		515	270	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438650	49438650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375118713	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	148	665	0	ENST00000301067.7:c.4840C>T	p.Arg1614Trp	p.R1614W	ENST00000301067	NM_003482.3	1614	Cgg/Tgg	19/54	0.316758135571365	5	FACETS	1	0.94	1	1	0.94	1	CLONAL	3	TRUE	2	0.316758135571365	5		665	449	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291546	15291546	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1179899018	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	87	734	1	ENST00000263388.2:c.3088G>A	p.Gly1030Arg	p.G1030R	ENST00000263388	NM_000435.2	1030	Gga/Aga	19/33	0.175100253515481	3	FACETS	1	0.895	1	1	0.895	1	INDETERMINATE	2	TRUE	1	0.316758135571365	3		735	318	SUCCESS
AR	367	MSKCC	GRCh37	X	66765446	66765446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765142941	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	47	672	0	ENST00000374690.3:c.458C>T	p.Pro153Leu	p.P153L	ENST00000374690	NM_000044.3	153	cCg/cTg	1/8	0.262172575152279	0	FACETS	0.622	0.534	0.715			1	SUBCLONAL	2	TRUE	0	0.316758135571365	0		672	163	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048797	180048797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	102	856	0	ENST00000261937.6:c.1765C>T	p.Arg589Cys	p.R589C	ENST00000261937	NM_182925.4	589	Cgc/Tgc	13/30	0.262172575152279	0	FACETS	0.675	0.61	0.742			1	SUBCLONAL	2	TRUE	0	0.316758135571365	0		856	326	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931700	39931700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	78	604	0	ENST00000378444.4:c.2899G>A	p.Ala967Thr	p.A967T	ENST00000378444	NM_001123385.1	967	Gcc/Acc	4/15	0.262172575152279	0	FACETS	1	0.942	1			1	CLONAL	1	TRUE	0	0.316758135571365	0		604	306	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11018786	11018786	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762459878	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	177	776	1	ENST00000327064.4:c.418C>T	p.Arg140Trp	p.R140W	ENST00000327064	NM_199141.1	140	Cgg/Tgg	3/16	0.175100253515481	3	FACETS	1	0.976	1	1	0.976	1	INDETERMINATE	2	TRUE	1	0.316758135571365	3		777	578	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324156	62324158	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGG	AGG	-	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	108	510	0	ENST00000360203.5:c.2656_2658del		p.X886_splice	ENST00000360203	NM_001283009.1	886		29/35	0.121360509207024	0	FACETS	0.7	0.635	0.766			1	INDETERMINATE	2	TRUE	0	0.316758135571365	0		510	333	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631962	90631964	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	47	511	1	ENST00000330062.3:c.389_391del	p.Lys130del	p.K130del	ENST00000330062	NM_002168.2	130	aAGAtg/atg	4/11	0.316758135571365	5	FACETS	0.995	0.841	1			1	CLONAL	1	TRUE	NA	0.316758135571365	5		512	440	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977548	2977548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751008087	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	54	544	0	ENST00000396946.4:c.1136G>A	p.Arg379Gln	p.R379Q	ENST00000396946	NM_032415.4	379	cGg/cAg	8/25	0.160624131521191	0	FACETS	0.939	0.81	1			1	INDETERMINATE	1	TRUE	0	0.316758135571365	0		544	248	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506308	120506308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140311741	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	64	421	1	ENST00000256646.2:c.1804G>A	p.Ala602Thr	p.A602T	ENST00000256646	NM_024408.3	602	Gcc/Acc	11/34	1	2	FACETS	0.825	0.723	0.932	1	0.977	1	CLONAL	2	TRUE	1	0.316758135571365	2		422	245	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176104164	176104164	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	62	320	0	ENST00000367669.3:c.950C>T	p.Ala317Val	p.A317V	ENST00000367669	NM_022457.5	317	gCt/gTt	8/20	1	2	FACETS	1	0.882	1	1	0.981	1	CLONAL	2	TRUE	1	0.316758135571365	2		320	195	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742826	17742826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	92	874	0	ENST00000250003.3:c.734C>T	p.Ala245Val	p.A245V	ENST00000250003	NM_002478.4	245	gCg/gTg	3/3	0.175100253515481	3	FACETS	1	0.969	1	1	0.969	1	INDETERMINATE	2	TRUE	1	0.316758135571365	3		874	280	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94211931	94211932	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	31	449	0	ENST00000323929.3:c.513dup	p.Gly172ArgfsTer16	p.G172Rfs*16	ENST00000323929	NM_005591.3	171	-/A	6/20	0.175100253515481	3	FACETS	0.846	0.687	1	0.423	0.343	0.512	INDETERMINATE	1	TRUE	1	0.316758135571365	3		449	268	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001889	29001889	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	57	356	0	ENST00000282397.4:c.1276G>A	p.Val426Met	p.V426M	ENST00000282397	NM_002019.4	426	Gtg/Atg	9/30	1	2	FACETS	0.811	0.704	0.923	1	0.974	1	CLONAL	2	TRUE	1	0.316758135571365	2		356	222	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830904	72830904	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1465596056	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	62	564	1	ENST00000268489.5:c.5677A>G	p.Arg1893Gly	p.R1893G	ENST00000268489	NM_006885.3	1893	Agg/Ggg	9/10	1	2	FACETS	1	0.913	1	1	0.982	1	CLONAL	2	TRUE	1	0.316758135571365	2		565	187	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984847	72984847	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	80	519	0	ENST00000268489.5:c.2737del	p.Leu913Ter	p.L913*	ENST00000268489	NM_006885.3	913	Cta/ta	3/10	0.315817548535895	0	FACETS	0.674	0.602	0.749			1	SUBCLONAL	2	TRUE	0	0.316758135571365	0		519	256	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348824	89348825	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	242	868	1	ENST00000301030.4:c.4125_4126del	p.Lys1376GlyfsTer9	p.K1376Gfs*9	ENST00000301030	NM_001256183.1	1375	gaGAag/gaag	9/13	0.316758135571365	4	FACETS	0.87	0.815	0.925	1	0.99	1	CLONAL	3	TRUE	2	0.316758135571365	4		869	771	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145753	11145753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	156	1253	4	ENST00000358026.2:c.4115G>A	p.Arg1372His	p.R1372H	ENST00000358026	NM_001128849.1	1372	cGc/cAc	29/36	0.175100253515481	3	FACETS	1	0.963	1	1	0.963	1	INDETERMINATE	2	TRUE	1	0.316758135571365	3		1257	531	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367975	15367975	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	105	641	0	ENST00000263377.2:c.1351G>A	p.Glu451Lys	p.E451K	ENST00000263377	NM_058243.2	451	Gaa/Aaa	8/20	0.175100253515481	3	FACETS	1	0.96	1	1	0.96	1	INDETERMINATE	2	TRUE	1	0.316758135571365	3		641	345	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791338	42791339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1384930527	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	118	748	1	ENST00000575354.2:c.404dup	p.Gly136ArgfsTer8	p.G136Rfs*8	ENST00000575354	NM_015125.3	133	ggc/ggCc	3/20	0.175100253515481	3	FACETS	0.968	0.879	1	0.968	0.879	1	INDETERMINATE	2	TRUE	1	0.316758135571365	3		749	446	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593536	215593536	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	59	334	0	ENST00000260947.4:c.2198G>A	p.Cys733Tyr	p.C733Y	ENST00000260947	NM_000465.2	733	tGc/tAc	11/11	1	2	FACETS	0.806	0.702	0.916	1	0.974	1	CLONAL	2	TRUE	1	0.316758135571365	2		334	231	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661454	227661454	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	60	668	0	ENST00000305123.5:c.2001del	p.Ser668AlafsTer36	p.S668Afs*36	ENST00000305123	NM_005544.2	667	ccC/cc	1/2	1	2	FACETS	0.803	0.7	0.911	1	0.974	1	CLONAL	2	TRUE	1	0.316758135571365	2		668	236	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37038120	37038120	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	34	196	0	ENST00000231790.2:c.127A>T	p.Lys43Ter	p.K43*	ENST00000231790	NM_000249.3	43	Aaa/Taa	2/19	0.175100253515481	3	FACETS	0.942	0.784	1	0.942	0.784	1	INDETERMINATE	2	TRUE	1	0.316758135571365	3		196	132	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807820	1807820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200849753	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	169	894	1	ENST00000260795.2:c.1879G>A	p.Glu627Lys	p.E627K	ENST00000260795		627	Gag/Aag	13/17	1	2	FACETS	1	0.983	1	1	0.994	1	CLONAL	2	TRUE	1	0.316758135571365	2		895	448	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106162531	106162531	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	44	287	0	ENST00000380013.4:c.3445A>G	p.Thr1149Ala	p.T1149A	ENST00000380013	NM_001127208.2	1149	Acc/Gcc	4/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.316758135571365	2		287	193	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044956	47044956	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	140	812	0	ENST00000377604.3:c.2282G>A	p.Cys761Tyr	p.C761Y	ENST00000377604	NM_001204468.1	761	tGt/tAt	20/24	0.262172575152279	0	FACETS	0.837	0.772	0.903			1	CLONAL	2	TRUE	0	0.316758135571365	0		812	361	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245115	53245115	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	27	658	0	ENST00000375401.3:c.825G>T	p.Glu275Asp	p.E275D	ENST00000375401	NM_004187.3	275	gaG/gaT	7/26	0.262172575152279	0	FACETS	0.448	0.357	0.551			1	SUBCLONAL	1	TRUE	0	0.316758135571365	0		658	260	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720647	89720649	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TTA	TTA	-	novel	NA	P-0050653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	50	403	0	ENST00000371953.3:c.802-4_802-2del		p.X268_splice	ENST00000371953	NM_000314.4	268			0.316758135571365	4	FACETS	1	0.948	1	0.636	0.542	0.738	CLONAL	1	TRUE	2	0.316758135571365	4		403	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0050702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	223	550	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.598035728229171	1	FACETS	0.975	0.916	1	0.975	0.916	1	CLONAL	1	TRUE	0	0.598035728229171	1		552	536	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870897	12870898	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0050702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	118	312	1	ENST00000228872.4:c.127dup	p.Arg43ProfsTer82	p.R43Pfs*82	ENST00000228872	NM_004064.3	42	acc/aCcc	1/3	1	2	FACETS	0.879	0.798	0.963	0.879	0.798	0.963	CLONAL	1	TRUE	1	0.598035728229171	2		313	449	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998989	11999012	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TTTATGGTGCACTCTTCAGAGAGG	TTTATGGTGCACTCTTCAGAGAGG	-	novel	NA	P-0050702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	105	308	0	ENST00000353533.5:c.492_513+2del		p.X164_splice	ENST00000353533	NM_003010.3	164		4/11	0.598035728229171	1	FACETS	0.918	0.837	1	0.918	0.837	1	CLONAL	1	TRUE	0	0.598035728229171	1		308	268	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0050763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	252	835	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.297048894662982	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.317941295053181	2		835	779	SUCCESS
APC	324	MSKCC	GRCh37	5	112175246	112175246	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1057517558	NA	P-0050763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	45	246	0	ENST00000257430.4:c.3956del	p.Pro1319LeufsTer2	p.P1319Lfs*2	ENST00000257430	NM_000038.5	1319	Cct/ct	16/16	0.317941295053181	1	FACETS	0.841	0.711	0.983	0.841	0.711	0.983	CLONAL	1	TRUE	0	0.317941295053181	1		246	283	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288785	33288785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765273333	NA	P-0050763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	102	468	1	ENST00000374542.5:c.767G>A	p.Arg256His	p.R256H	ENST00000374542	NM_001141970.1	256	cGc/cAc	3/8	0.317941295053181	3	FACETS	1	0.907	1	0.338	0.302	0.376	CLONAL	1	TRUE	0	0.317941295053181	3		469	733	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937591	76937591	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	63	410	0	ENST00000373344.5:c.3157A>T	p.Thr1053Ser	p.T1053S	ENST00000373344	NM_000489.3	1053	Act/Tct	9/35	0.2965766011978	3	FACETS	0.844	0.731	0.967	0.422	0.365	0.484	CLONAL	1	TRUE	1	0.317941295053181	3		410	544	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0050790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	76	571	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.358712628958331	2		571	423	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0050790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	186	428	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.206118731381447	3	FACETS	1	0.942	1	0.677	0.629	0.727	INDETERMINATE	2	TRUE	0	0.358712628958331	3		428	602	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0050790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	110	306	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.358712628958331	3	FACETS	0.996	0.904	1	0.996	0.904	1	CLONAL	2	TRUE	1	0.358712628958331	3		306	363	SUCCESS
APC	324	MSKCC	GRCh37	5	112111325	112111325	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs397514031	NA	P-0050790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	30	199	0	ENST00000257430.4:c.423-1G>A		p.X141_splice	ENST00000257430	NM_000038.5	141			0.358712628958331	3	FACETS	0.765	0.619	0.929	0.382	0.309	0.465	CLONAL	1	TRUE	1	0.358712628958331	3		199	258	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334992	81334992	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	101	518	0	ENST00000222390.5:c.1835G>T	p.Cys612Phe	p.C612F	ENST00000222390	NM_000601.4	612	tGc/tTc	16/18	0.358712628958331	4	FACETS	0.93	0.83	1	0.465	0.415	0.518	CLONAL	1	TRUE	2	0.358712628958331	4		518	823	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0050837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	138	707	1	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	0.315076416011746	1	FACETS	0.975	0.888	1	0.975	0.888	1	CLONAL	1	TRUE	0	0.315076416011746	1		708	757	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0050837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	15	447	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	1	2	FACETS	0.159	0.116	0.213	0.159	0.116	0.213	SUBCLONAL	1	TRUE	1	0.315076416011746	2		447	597	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398917	398917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356308443	NA	P-0050837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	76	624	0	ENST00000380956.4:c.727G>A	p.Glu243Lys	p.E243K	ENST00000380956	NM_001195286.1	243	Gaa/Aaa	6/9	1	2	FACETS	0.656	0.575	0.744	0.656	0.575	0.744	SUBCLONAL	1	TRUE	1	0.315076416011746	2		624	735	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862107	68862107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501244	NA	P-0050837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	181	493	0	ENST00000261769.5:c.2195G>A	p.Arg732Gln	p.R732Q	ENST00000261769	NM_004360.3	732	cGg/cAg	14/16	0.315076416011746	3	FACETS	0.823	0.76	0.888	0.823	0.76	0.888	CLONAL	2	TRUE	1	0.315076416011746	3		493	808	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508490	106508490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	61	387	0	ENST00000359195.3:c.484G>A	p.Val162Ile	p.V162I	ENST00000359195	NM_002649.2	162	Gtc/Atc	2/11	0.181022604057199	3	FACETS	0.884	0.764	1	0.442	0.382	0.508	INDETERMINATE	1	TRUE	1	0.315076416011746	3		387	507	SUCCESS
APC	324	MSKCC	GRCh37	5	112175350	112175351	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0050837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	87	277	0	ENST00000257430.4:c.4063dup	p.Ser1355PhefsTer20	p.S1355Ffs*20	ENST00000257430	NM_000038.5	1353	-/T	16/16	0.315076416011746	2	FACETS	0.827	0.739	0.919	0.827	0.739	0.919	CLONAL	2	TRUE	0	0.315076416011746	2		277	334	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291617	15291617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150941674	NA	P-0050837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	371	1086	5	ENST00000263388.2:c.3017G>A	p.Arg1006His	p.R1006H	ENST00000263388	NM_000435.2	1006	cGc/cAc	19/33	0.315076416011746	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.315076416011746	2		1091	1178	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522119	157522119	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	123	737	0	ENST00000346085.5:c.4391del	p.Met1464SerfsTer30	p.M1464Sfs*30	ENST00000346085	NM_020732.3	1464	aTg/ag	18/20	1	2	FACETS	0.923	0.834	1	0.923	0.834	1	CLONAL	1	TRUE	1	0.315076416011746	2		737	846	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0050932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	23	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.665	0.517	0.838	0.665	0.517	0.838	SUBCLONAL	1	TRUE	1	0.13	2		326	532	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0050932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	29	590	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.548	0.438	0.674	0.548	0.438	0.674	SUBCLONAL	1	TRUE	1	0.13	2		591	814	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0050932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	75	1445	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.13	2		1452	1113	SUCCESS
EED	8726	MSKCC	GRCh37	11	85961344	85961344	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138343311	NA	P-0050932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	15	198	0	ENST00000263360.6:c.121G>A	p.Ala41Thr	p.A41T	ENST00000263360	NM_003797.3	41	Gct/Act	2/12	1	2	FACETS	0.931	0.681	1	0.931	0.681	1	CLONAL	1	TRUE	1	0.13	2		198	248	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380283	25380283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913528	NA	P-0050932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	21	430	0	ENST00000311936.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000311936	NM_004985.3	59	Gca/Aca	3/5	1	2	FACETS	0.45	0.345	0.574	0.45	0.345	0.574	SUBCLONAL	1	TRUE	1	0.13	2		430	718	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7218293	7218293	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	41	802	0	ENST00000380728.2:c.79G>T	p.Glu27Ter	p.E27*	ENST00000380728		27	Gag/Tag	2/11	1	2	FACETS	0.913	0.759	1	0.913	0.759	1	CLONAL	1	TRUE	1	0.13	2		802	691	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798867	135798867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514843	NA	P-0050932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	18	272	0	ENST00000298552.3:c.376G>A	p.Val126Ile	p.V126I	ENST00000298552	NM_001162426.1	126	Gtc/Atc	6/23	1	2	FACETS	0.896	0.674	1	0.896	0.674	1	CLONAL	1	TRUE	1	0.13	2		272	309	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0051002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	92	449	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.373982853804914	2		449	437	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0051002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	81	394	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.373982853804914	2		394	396	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0051002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	169	382	2	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	0.373982853804914	4	FACETS	0.883	0.819	0.948	0.883	0.819	0.948	CLONAL	3	TRUE	1	0.373982853804914	4		384	469	SUCCESS
APC	324	MSKCC	GRCh37	5	112174310	112174310	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0051002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	76	344	0	ENST00000257430.4:c.3019A>T	p.Lys1007Ter	p.K1007*	ENST00000257430	NM_000038.5	1007	Aaa/Taa	16/16	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.373982853804914	2		344	355	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578537	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs879254214	NA	P-0051002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	163	677	0	ENST00000269305.4:c.393_395del	p.Asn131del	p.N131del	ENST00000269305	NM_001126112.2	131	aaCAAg/aag	5/11	0.373982853804914	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.373982853804914	1		677	702	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168969	32168969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs567483221	NA	P-0051002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	156	658	0	ENST00000375023.3:c.4064G>A	p.Arg1355Gln	p.R1355Q	ENST00000375023	NM_004557.3	1355	cGg/cAg	22/30	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.373982853804914	2		658	776	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927439	49927439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761180266	NA	P-0051002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	175	632	0	ENST00000296474.3:c.3865C>T	p.Arg1289Cys	p.R1289C	ENST00000296474	NM_002447.2	1289	Cgc/Tgc	19/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.373982853804914	2		632	823	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333660	70333660	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	27	497	0	ENST00000373644.4:c.1565G>T	p.Gly522Val	p.G522V	ENST00000373644	NM_030625.2	522	gGa/gTa	2/12	1	2	FACETS	0.288	0.228	0.356	0.288	0.228	0.356	SUBCLONAL	1	TRUE	1	0.373982853804914	2		497	502	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0051029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	31	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.16	2		326	311	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199670	11199670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766533620	NA	P-0051029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	41	557	2	ENST00000361445.4:c.4918C>T	p.Arg1640Trp	p.R1640W	ENST00000361445	NM_004958.3	1640	Cgg/Tgg	35/58	1	2	FACETS	0.775	0.644	0.922	0.775	0.644	0.922	CLONAL	1	TRUE	1	0.16	2		559	661	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0051029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	56	1445	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.864	0.739	1	0.864	0.739	1	CLONAL	1	TRUE	1	0.16	2		1452	810	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0051029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	46	720	2	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	0.725	0.609	0.854	0.725	0.609	0.854	SUBCLONAL	1	TRUE	1	0.16	2		722	793	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199450	16199450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200367310	NA	P-0051029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	31	344	0	ENST00000375759.3:c.223C>T	p.Arg75Cys	p.R75C	ENST00000375759	NM_015001.2	75	Cgc/Tgc	2/15	1	2	FACETS	0.685	0.552	0.835	0.685	0.552	0.835	SUBCLONAL	1	TRUE	1	0.16	2		344	566	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404575	70404575	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	31	498	0	ENST00000373644.4:c.2093del	p.Asn698MetfsTer5	p.N698Mfs*5	ENST00000373644	NM_030625.2	697	Aaa/aa	4/12	1	2	FACETS	0.871	0.704	1	0.871	0.704	1	CLONAL	1	TRUE	1	0.16	2		498	445	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438533	49438533	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	46	581	0	ENST00000301067.7:c.4957G>T	p.Gly1653Cys	p.G1653C	ENST00000301067	NM_003482.3	1653	Ggt/Tgt	19/54	1	2	FACETS	0.841	0.706	0.989	0.841	0.706	0.989	CLONAL	1	TRUE	1	0.16	2		581	684	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281836	49281836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	43	606	1	ENST00000282018.3:c.883G>A	p.Ala295Thr	p.A295T	ENST00000282018	NM_020377.2	295	Gca/Aca	1/1	1	2	FACETS	0.735	0.614	0.871	0.735	0.614	0.871	SUBCLONAL	1	TRUE	1	0.16	2		607	731	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105236744	105236745	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0051029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	49	657	0	ENST00000349310.3:c.1376_1377del	p.Glu459ValfsTer43	p.E459Vfs*43	ENST00000349310	NM_001014432.1	459	gAG/g	15/15	1	2	FACETS	0.853	0.721	0.999	0.853	0.721	0.999	CLONAL	1	TRUE	1	0.16	2		657	718	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028454	42028454	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	36	397	0	ENST00000219905.7:c.3992G>A	p.Gly1331Asp	p.G1331D	ENST00000219905	NM_001164273.1	1331	gGt/gAt	13/24	1	2	FACETS	0.974	0.801	1	0.974	0.801	1	CLONAL	1	TRUE	1	0.16	2		397	462	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705449	43705450	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0051029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	50	719	0	ENST00000382044.4:c.5172_5173del	p.Gly1725AlafsTer23	p.G1725Afs*23	ENST00000382044	NM_001141980.1	1724	agAGgg/aggg	24/28	1	2	FACETS	0.819	0.693	0.958	0.819	0.693	0.958	CLONAL	1	TRUE	1	0.16	2		719	763	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825519	50825519	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	14	451	1	ENST00000398568.2:c.2156del	p.Asn719MetfsTer13	p.N719Mfs*13	ENST00000398568	NM_001042412.1	717	gAa/ga	14/18	1	2	FACETS	0.625	0.451	0.836	0.625	0.451	0.836	SUBCLONAL	1	TRUE	1	0.16	2		452	280	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56862933	56862933	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	31	465	0	ENST00000308159.5:c.839A>G	p.Gln280Arg	p.Q280R	ENST00000308159	NM_014669.4	280	cAg/cGg	9/22	1	2	FACETS	0.707	0.571	0.862	0.707	0.571	0.862	SUBCLONAL	1	TRUE	1	0.16	2		465	548	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17125878	17125878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753948488	NA	P-0051029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	56	722	0	ENST00000285071.4:c.716G>A	p.Arg239His	p.R239H	ENST00000285071	NM_144997.5	239	cGc/cAc	7/14	1	2	FACETS	0.83	0.71	0.963	0.83	0.71	0.963	CLONAL	1	TRUE	1	0.16	2		722	843	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439919	56439919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	54	633	2	ENST00000407977.2:c.673del	p.Arg225AlafsTer194	p.R225Afs*194	ENST00000407977		225	Cgc/gc	6/10	1	2	FACETS	0.916	0.781	1	0.916	0.781	1	CLONAL	1	TRUE	1	0.16	2		635	737	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753887	42753887	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	54	759	0	ENST00000222329.4:c.377del	p.Gly126ValfsTer145	p.G126Vfs*145	ENST00000222329	NM_006494.2	126	gGt/gt	4/4	1	2	FACETS	0.764	0.65	0.888	0.764	0.65	0.888	SUBCLONAL	1	TRUE	1	0.16	2		759	884	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0051029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	21	268	0	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	1	2	FACETS	0.905	0.698	1	0.905	0.698	1	CLONAL	1	TRUE	1	0.16	2		268	290	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682400	52682400	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	17	422	0	ENST00000394830.3:c.773del	p.Asn258MetfsTer25	p.N258Mfs*25	ENST00000394830	NM_018313.4	258	aAt/at	8/30	1	2	FACETS	0.662	0.493	0.863	0.662	0.493	0.863	SUBCLONAL	1	TRUE	1	0.16	2		422	321	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665096	138665096	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs758370933	NA	P-0051029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	23	327	0	ENST00000330315.3:c.469C>G	p.Pro157Ala	p.P157A	ENST00000330315	NM_023067.3	157	Ccc/Gcc	1/1	1	2	FACETS	0.887	0.692	1	0.887	0.692	1	CLONAL	1	TRUE	1	0.16	2		327	324	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156202	106156202	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	34	405	0	ENST00000380013.4:c.1103A>T	p.Glu368Val	p.E368V	ENST00000380013	NM_001127208.2	368	gAa/gTa	3/11	1	2	FACETS	0.936	0.765	1	0.936	0.765	1	CLONAL	1	TRUE	1	0.16	2		405	454	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372731	81372731	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	36	453	0	ENST00000222390.5:c.803G>T	p.Arg268Met	p.R268M	ENST00000222390	NM_000601.4	268	aGg/aTg	7/18	1	2	FACETS	0.789	0.648	0.949	0.789	0.648	0.949	CLONAL	1	TRUE	1	0.16	2		453	570	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608237	100608237	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	41	299	1	ENST00000308731.7:c.1853G>T	p.Arg618Met	p.R618M	ENST00000308731	NM_000061.2	618	aGg/aTg	18/19	1	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.16	1		300	350	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0051038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	339	378	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.453070045155041	4	FACETS	1	0.978	1	0.782	0.746	0.818	CLONAL	3	TRUE	0	0.453070045155041	4		378	695	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604778	48604778	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767383	NA	P-0051038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	215	402	1	ENST00000342988.3:c.1600C>T	p.Gln534Ter	p.Q534*	ENST00000342988	NM_005359.5	534	Cag/Tag	12/12	0.453070045155041	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.453070045155041	2		403	463	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231707	66231707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1211795184	NA	P-0051038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	142	499	0	ENST00000273854.3:c.1993G>A	p.Glu665Lys	p.E665K	ENST00000273854	NM_004439.5	665	Gaa/Aaa	11/18	0.453070045155041	3	FACETS	1	0.975	1	0.587	0.536	0.64	CLONAL	1	TRUE	1	0.453070045155041	3		499	655	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937219	36937219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140159756	NA	P-0051038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	168	769	1	ENST00000361632.4:c.1100G>A	p.Arg367Gln	p.R367Q	ENST00000361632		367	cGg/cAg	9/16	0.453070045155041	3	FACETS	0.893	0.82	0.969	0.446	0.41	0.485	CLONAL	1	TRUE	1	0.453070045155041	3		770	1019	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620674	52620674	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	249	350	2	ENST00000394830.3:c.3079C>T	p.Arg1027Ter	p.R1027*	ENST00000394830	NM_018313.4	1027	Cga/Tga	21/30	0.398038336704447	3	FACETS	1	0.977	1			1	CLONAL	3	TRUE	NA	0.453070045155041	3		352	430	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652237	3652237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141597706	NA	P-0051038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	195	766	0	ENST00000294008.3:c.832C>T	p.Arg278Trp	p.R278W	ENST00000294008	NM_032444.2	278	Cgg/Tgg	4/15	0.453070045155041	3	FACETS	1	0.964	1	0.534	0.494	0.575	CLONAL	1	TRUE	1	0.453070045155041	3		766	989	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343635	343635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375187798	NA	P-0051038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	196	753	1	ENST00000262320.3:c.2039G>A	p.Arg680Gln	p.R680Q	ENST00000262320	NM_003502.3	680	cGg/cAg	8/11	NA	2	FACETS	1	0.956	1			1	INDETERMINATE	1	TRUE	NA	0.453070045155041	2		754	830	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778867	9778867	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	195	849	0	ENST00000377346.4:c.1136T>C	p.Ile379Thr	p.I379T	ENST00000377346	NM_005026.3	379	aTc/aCc	9/24	0.453070045155041	3	FACETS	0.962	0.89	1	0.481	0.445	0.519	CLONAL	1	TRUE	1	0.453070045155041	3		849	1097	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206667324	206667324	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs781809827	NA	P-0051038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	636	674	0	ENST00000367120.3:c.2117G>A	p.Arg706Gln	p.R706Q	ENST00000367120	NM_014002.3	706	cGg/cAg	21/22	0.453070045155041	5	FACETS	0.977	0.945	1	0.977	0.945	1	CLONAL	4	TRUE	1	0.453070045155041	5		674	1207	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576835	7576871	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTCCCAAGACTTAGTACCTGAAGGGTGAAATATTCT	GGTCCCAAGACTTAGTACCTGAAGGGTGAAATATTCT	-	novel	NA	P-0051038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	208	513	0	ENST00000269305.4:c.975_993+18del		p.X325_splice	ENST00000269305	NM_001126112.2	325		9/11	0.453070045155041	2	FACETS	0.803	0.75	0.856	0.803	0.75	0.856	CLONAL	2	TRUE	0	0.453070045155041	2		513	572	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492803	56492803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	297	570	0	ENST00000407977.2:c.136G>A	p.Ala46Thr	p.A46T	ENST00000407977		46	Gct/Act	2/10	0.453070045155041	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.453070045155041	2		570	621	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213476	36213476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368744106	NA	P-0051038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	617	830	0	ENST00000222270.7:c.2578G>A	p.Glu860Lys	p.E860K	ENST00000222270	NM_014727.1	860	Gag/Aag	5/37	0.453070045155041	4	FACETS	0.936	0.903	0.97	0.936	0.903	0.97	CLONAL	3	TRUE	1	0.453070045155041	4		830	1409	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749580	41749580	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	165	682	0	ENST00000301178.4:c.1505A>G	p.Lys502Arg	p.K502R	ENST00000301178	NM_021913.4	502	aAg/aGg	12/20	0.453070045155041	4	FACETS	0.973	0.892	1	0.324	0.297	0.353	CLONAL	1	TRUE	1	0.453070045155041	4		682	1088	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0051053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	83	424	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.423506114047317	2		424	363	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469086	25469086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1420356837	NA	P-0051053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	165	764	0	ENST00000264709.3:c.1372C>T	p.Arg458Trp	p.R458W	ENST00000264709	NM_175629.2	458	Cgg/Tgg	11/23	0.423506114047317	3	FACETS	1	0.971	1	0.561	0.515	0.608	CLONAL	1	TRUE	1	0.423506114047317	3		764	842	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577061	7577062	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0051053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	273	703	0	ENST00000269305.4:c.876_877del	p.Glu294AlafsTer11	p.E294Afs*11	ENST00000269305	NM_001126112.2	292	aaAGgg/aagg	8/11	0.375483004458721	2	FACETS	0.996	0.942	1	0.996	0.942	1	CLONAL	2	TRUE	0	0.423506114047317	2		703	647	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446227	187446227	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	315	732	0	ENST00000232014.4:c.1461G>C	p.Glu487Asp	p.E487D	ENST00000232014	NM_001130845.1	487	gaG/gaC	6/10	0.350616614657638	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.423506114047317	4		732	918	SUCCESS
APC	324	MSKCC	GRCh37	5	112175068	112175392	+	frameshift_variant	Frame_Shift_Del	DEL	ACAGACTTATTGTGTAGAAGATACTCCAATATGTTTTTCAAGATGTAGTTCATTATCATCTTTGTCATCAGCTGAAGATGAAATAGGATGTAATCAGACGACACAGGAAGCAGATTCTGCTAATACCCTGCAAATAGCAGAAATAAAAGAAAAGATTGGAACTAGGTCAGCTGAAGATCCTGTGAGCGAAGTTCCAGCAGTGTCACAGCACCCTAGAACCAAATCCAGCAGACTGCAGGGTTCTAGTTTATCTTCAGAATCAGCCAGGCACAAAGCTGTTGAATTTTCTTCAGGAGCGAAATCTCCCTCCAAAAGTGGTGCTCAG	ACAGACTTATTGTGTAGAAGATACTCCAATATGTTTTTCAAGATGTAGTTCATTATCATCTTTGTCATCAGCTGAAGATGAAATAGGATGTAATCAGACGACACAGGAAGCAGATTCTGCTAATACCCTGCAAATAGCAGAAATAAAAGAAAAGATTGGAACTAGGTCAGCTGAAGATCCTGTGAGCGAAGTTCCAGCAGTGTCACAGCACCCTAGAACCAAATCCAGCAGACTGCAGGGTTCTAGTTTATCTTCAGAATCAGCCAGGCACAAAGCTGTTGAATTTTCTTCAGGAGCGAAATCTCCCTCCAAAAGTGGTGCTCAG	-	novel	NA	P-0051053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	42	237	0	ENST00000257430.4:c.3780_4104del	p.Gln1260HisfsTer47	p.Q1260Hfs*47	ENST00000257430	NM_000038.5	1259	atACAGACTTATTGTGTAGAAGATACTCCAATATGTTTTTCAAGATGTAGTTCATTATCATCTTTGTCATCAGCTGAAGATGAAATAGGATGTAATCAGACGACACAGGAAGCAGATTCTGCTAATACCCTGCAAATAGCAGAAATAAAAGAAAAGATTGGAACTAGGTCAGCTGAAGATCCTGTGAGCGAAGTTCCAGCAGTGTCACAGCACCCTAGAACCAAATCCAGCAGACTGCAGGGTTCTAGTTTATCTTCAGAATCAGCCAGGCACAAAGCTGTTGAATTTTCTTCAGGAGCGAAATCTCCCTCCAAAAGTGGTGCTCAG/at	16/16	1	2	FACETS	0.82	0.69	0.961	0.82	0.69	0.961	CLONAL	1	TRUE	1	0.423506114047317	2		237	242	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131893113	131893113	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	79	359	0	ENST00000265335.6:c.97A>T	p.Ile33Phe	p.I33F	ENST00000265335		33	Att/Ttt	1/25	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.423506114047317	2		359	359	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	155	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.180325070349767	5	FACETS	0.901	0.826	0.978	0.6	0.55	0.652	INDETERMINATE	2	TRUE	2	0.354275093845765	5		487	744	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0051087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	173	661	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.267385897787498	2	FACETS	0.878	0.813	0.945	0.878	0.813	0.945	CLONAL	2	TRUE	0	0.354275093845765	2		662	556	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0051087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	112	165	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.301279224129309	2	FACETS	0.985	0.897	1	0.985	0.897	1	CLONAL	2	TRUE	0	0.354275093845765	2		165	321	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268144	153268144	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs920052554	NA	P-0051087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	69	448	0	ENST00000281708.4:c.664C>T	p.Arg222Ter	p.R222*	ENST00000281708	NM_033632.3	222	Cga/Tga	4/12	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.354275093845765	2		448	360	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457639	67457640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0051087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	264	700	1	ENST00000327367.4:c.455dup	p.Leu153ThrfsTer13	p.L153Tfs*13	ENST00000327367	NM_005902.3	150	ttc/ttCc	3/9	0.354275093845765	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.354275093845765	2		701	728	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78599490	78599490	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0051087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	41	370	0	ENST00000306801.3:c.163-1G>C		p.X55_splice	ENST00000306801	NM_020761.2	55			0.122416199240098	4	FACETS	0.532	0.442	0.632	0.266	0.221	0.316	INDETERMINATE	1	TRUE	2	0.354275093845765	4		370	589	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163848	32163848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1210630301	NA	P-0051135-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	38	480	0	ENST00000375023.3:c.5378G>A	p.Arg1793Gln	p.R1793Q	ENST00000375023	NM_004557.3	1793	cGa/cAa	30/30	0.202086836709289	3	FACETS	0.823	0.68	0.983	0.411	0.34	0.492	CLONAL	1	TRUE	1	0.2	3		480	508	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0051135-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	62	449	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.3	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.2	1		449	418	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0051135-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	30	194	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.938	0.757	1	0.938	0.757	1	CLONAL	1	TRUE	1	0.2	2		194	320	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220626	1220626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057520038	NA	P-0051135-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	82	554	0	ENST00000326873.7:c.644G>A	p.Gly215Asp	p.G215D	ENST00000326873	NM_000455.4	215	gGc/gAc	5/10	0.3	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.2	1		554	590	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980777	40980777	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051135-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	38	420	0	ENST00000373198.4:c.1709C>G	p.Thr570Arg	p.T570R	ENST00000373198	NM_133170.3	570	aCa/aGa	10/32	1	2	FACETS	0.795	0.657	0.949	0.795	0.657	0.949	CLONAL	1	TRUE	1	0.2	2		420	478	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867414	35867415	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0051135-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	16	0	0	ENST00000303115.3:c.228_229delinsAG	p.Leu77Val	p.L77V	ENST00000303115	NM_002185.3	76	gcCCtc/gcAGtc	3/8	1	2	FACETS	0.468	0.345	0.615	0.468	0.345	0.615	SUBCLONAL	1	TRUE	1	0.2	2		0	342	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633115	3633116	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTGTCA	novel	NA	P-0051135-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	34	512	0	ENST00000294008.3:c.5135_5136insTGACAA	p.Ser1712_Ser1713insAspAsn	p.S1712_S1713insDN	ENST00000294008	NM_032444.2	1712	agc/agTGACAAc	14/15	1	2	FACETS	0.66	0.539	0.797	0.66	0.539	0.797	SUBCLONAL	1	TRUE	1	0.2	2		512	515	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0051225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	97	457	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.263278354840091	5	FACETS	1	0.955	1			1	CLONAL	3	TRUE	NA	0.310060749342834	5		457	279	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0051225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	22	364	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.198741431007185	4	FACETS	0.819	0.637	1	0.409	0.318	0.515	CLONAL	1	TRUE	2	0.310060749342834	4		365	227	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0051225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	53	383	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.198741431007185	4	FACETS	0.995	0.859	1	0.995	0.859	1	CLONAL	2	TRUE	2	0.310060749342834	4		383	225	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0051225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	84	499	0	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	0.226820845913766	2	FACETS	0.944	0.844	1	0.944	0.844	1	CLONAL	2	TRUE	0	0.310060749342834	2		499	287	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575666	48575667	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TC	TC	-	rs377767328	NA	P-0051225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	60	400	0	ENST00000342988.3:c.430_431del	p.Ser144ArgfsTer7	p.S144Rfs*7	ENST00000342988	NM_005359.5	142	gaTCtc/gatc	4/12	0.310060749342834	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	0	0.310060749342834	2		400	176	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216575	7216575	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	111	571	0	ENST00000380728.2:c.760A>C	p.Lys254Gln	p.K254Q	ENST00000380728		254	Aag/Cag	9/11	0.226820845913766	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.310060749342834	2		571	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0051227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	166	469	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.399483773705808	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.399483773705808	1		469	595	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0051227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	38	413	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.556	0.461	0.662	0.556	0.461	0.662	SUBCLONAL	1	TRUE	1	0.399483773705808	2		413	342	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0051227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	43	165	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.861	0.726	1	0.861	0.726	1	CLONAL	1	TRUE	1	0.399483773705808	2		165	250	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267306	41267306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759085197	NA	P-0051227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	55	293	0	ENST00000349496.5:c.890C>T	p.Thr297Met	p.T297M	ENST00000349496	NM_001904.3	297	aCg/aTg	6/15	1	2	FACETS	0.685	0.588	0.791	0.685	0.588	0.791	SUBCLONAL	1	TRUE	1	0.399483773705808	2		293	402	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873713	35873714	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0051227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	146	460	1	ENST00000216797.5:c.137_138delinsAT	p.Val46Asp	p.V46D	ENST00000216797	NM_020529.2	46	gTC/gAT	1/6	1	2	FACETS	0.996	0.91	1	0.996	0.91	1	CLONAL	1	TRUE	1	0.399483773705808	2		461	734	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188363	32188363	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1388018947	NA	P-0051227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	120	647	0	ENST00000375023.3:c.978C>A	p.Cys326Ter	p.C326*	ENST00000375023	NM_004557.3	326	tgC/tgA	6/30	1	2	FACETS	0.924	0.836	1	0.924	0.836	1	CLONAL	1	TRUE	1	0.399483773705808	2		647	650	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0051314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	26	670	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.183078413696627	1	FACETS	0.492	0.389	0.612	0.492	0.389	0.612	SUBCLONAL	1	TRUE	0	0.183078413696627	1		670	524	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	73	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.113284899960205	3	FACETS	1	0.949	1	0.587	0.512	0.667	CLONAL	1	TRUE	1	0.183078413696627	3		487	742	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480028	50480028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs759976916	NA	P-0051314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	86	592	0	ENST00000394963.4:c.262C>T	p.Arg88Ter	p.R88*	ENST00000394963	NM_003076.4	88	Cga/Tga	2/13	0.113284899960205	3	FACETS	1	0.938	1	0.549	0.484	0.618	CLONAL	1	TRUE	1	0.183078413696627	3		592	934	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390656	139390656	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	69	748	0	ENST00000277541.6:c.7535del	p.Pro2512ArgfsTer77	p.P2512Rfs*77	ENST00000277541	NM_017617.3	2512	cCg/cg	34/34	1	2	FACETS	0.774	0.672	0.885	0.774	0.672	0.885	SUBCLONAL	1	TRUE	1	0.183078413696627	2		748	974	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643395	38643395	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	75	435	0	ENST00000299084.4:c.865A>G	p.Lys289Glu	p.K289E	ENST00000299084	NM_152594.2	289	Aaa/Gaa	7/7	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.183078413696627	2		435	686	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390734	139390734	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1183279486	NA	P-0051314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	56	836	0	ENST00000277541.6:c.7457C>T	p.Ser2486Leu	p.S2486L	ENST00000277541	NM_017617.3	2486	tCg/tTg	34/34	1	2	FACETS	0.611	0.521	0.709	0.611	0.521	0.709	SUBCLONAL	1	TRUE	1	0.183078413696627	2		836	1002	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0051328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	89	729	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.259419516769008	1	FACETS	0.927	0.823	1	0.927	0.823	1	CLONAL	1	TRUE	0	0.259419516769008	1		730	644	SUCCESS
APC	324	MSKCC	GRCh37	5	112175235	112175235	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	96	249	0	ENST00000257430.4:c.3944C>A	p.Ser1315Ter	p.S1315*	ENST00000257430	NM_000038.5	1315	tCa/tAa	16/16	0.258699059243696	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	2	TRUE	0	0.259419516769008	2		249	366	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0051329-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	38	1045	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.87	0.721	1	0.87	0.721	1	CLONAL	1	TRUE	1	0.244719809217078	2		1046	357	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119949	70119950	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGCT	novel	NA	P-0051329-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	20	464	0	ENST00000245479.2:c.953_956dup	p.Tyr319Ter	p.Y319*	ENST00000245479	NM_000346.3	317	-/AGCT	3/3	1	2	FACETS	0.58	0.443	0.739	0.58	0.443	0.739	SUBCLONAL	1	TRUE	1	0.244719809217078	2		464	282	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220150	36220150	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051329-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	28	713	0	ENST00000222270.7:c.4870G>A	p.Gly1624Ser	p.G1624S	ENST00000222270	NM_014727.1	1624	Ggc/Agc	22/37	1	2	FACETS	0.565	0.451	0.695	0.565	0.451	0.695	SUBCLONAL	1	TRUE	1	0.244719809217078	2		713	405	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423497	116423497	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051329-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	36	281	0	ENST00000397752.3:c.3772C>A	p.Gln1258Lys	p.Q1258K	ENST00000397752	NM_000245.2	1258	Caa/Aaa	19/21	0.12671437294771	3	FACETS	0.796	0.654	0.954	0.398	0.327	0.477	INDETERMINATE	1	TRUE	1	0.244719809217078	3		281	415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0051330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	74	863	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.184689052755864	1	FACETS	0.882	0.772	1	0.882	0.772	1	CLONAL	1	FALSE	0	0.22529729452987	1		864	661	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735470	40735470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761910971	NA	P-0051330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	171	498	0	ENST00000373198.4:c.3403G>A	p.Val1135Met	p.V1135M	ENST00000373198	NM_133170.3	1135	Gtg/Atg	25/32	0.22529729452987	3	FACETS	0.954	0.878	1	0.954	0.878	1	CLONAL	2	FALSE	1	0.22529729452987	3		498	885	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346961	89346961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775491352	NA	P-0051330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	35	483	0	ENST00000301030.4:c.5989G>A	p.Ala1997Thr	p.A1997T	ENST00000301030	NM_001256183.1	1997	Gcg/Acg	9/13	1	2	FACETS	0.595	0.487	0.717	0.595	0.487	0.717	SUBCLONAL	1	FALSE	1	0.22529729452987	2		483	522	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982393	201982394	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0051330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	84	699	0	ENST00000359651.3:c.775dup	p.Asp259GlyfsTer42	p.D259Gfs*42	ENST00000359651		258	tgg/tGgg	6/8	1	2	FACETS	0.886	0.781	0.998	0.886	0.781	0.998	CLONAL	1	FALSE	1	0.22529729452987	2		699	842	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993622	90993622	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202139	NA	P-0051330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	20	223	0	ENST00000265433.3:c.301G>A	p.Val101Met	p.V101M	ENST00000265433	NM_002485.4	101	Gtg/Atg	3/16	1	2	FACETS	0.471	0.359	0.602	0.471	0.359	0.602	SUBCLONAL	1	FALSE	1	0.22529729452987	2		223	377	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	142	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.985	0.903	1	0.985	0.903	1	CLONAL	1	TRUE	1	0.542881750979579	2		487	531	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0051331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	100	283	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.98	0.883	1	0.98	0.883	1	CLONAL	1	TRUE	1	0.542881750979579	2		283	376	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856623	111856623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	87	156	0	ENST00000341259.2:c.674G>A	p.Arg225His	p.R225H	ENST00000341259	NM_005475.2	225	cGc/cAc	2/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.542881750979579	2		156	252	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911541	134911541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	296	403	1	ENST00000398015.3:c.2006C>T	p.Ala669Val	p.A669V	ENST00000398015	NM_004441.4	669	gCg/gTg	11/16	0.542881750979579	3	FACETS	0.988	0.936	1	0.988	0.936	1	CLONAL	2	TRUE	1	0.542881750979579	3		404	702	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759967	133759967	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773883545	NA	P-0051331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	215	604	0	ENST00000318560.5:c.2290C>T	p.Arg764Trp	p.R764W	ENST00000318560	NM_005157.4	764	Cgg/Tgg	11/11	0.514517134200328	3	FACETS	0.968	0.9	1	0.484	0.45	0.52	CLONAL	1	TRUE	1	0.542881750979579	3		604	1040	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066740	5066740	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777015472	NA	P-0051331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	193	303	0	ENST00000381652.3:c.1277G>A	p.Arg426Gln	p.R426Q	ENST00000381652	NM_004972.3	426	cGa/cAa	10/25	0.514517134200328	3	FACETS	0.922	0.862	0.984	0.922	0.862	0.984	CLONAL	2	TRUE	1	0.542881750979579	3		303	490	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542456	187542456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371394820	NA	P-0051331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	163	412	0	ENST00000441802.2:c.5284G>A	p.Ala1762Thr	p.A1762T	ENST00000441802	NM_005245.3	1762	Gcg/Acg	10/27	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.542881750979579	2		412	600	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482802	67482803	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCTTTGCAGTGGCTTGACAAGGT	novel	NA	P-0051331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	229	457	0	ENST00000327367.4:c.1210_1232dup	p.Thr412CysfsTer72	p.T412Cfs*72	ENST00000327367	NM_005902.3	402	-/CCTTTGCAGTGGCTTGACAAGGT	9/9	0.542881750979579	2	FACETS	1	0.983	1	0.572	0.535	0.609	CLONAL	1	TRUE	0	0.542881750979579	2		457	738	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119697	70119700	+	frameshift_variant	Frame_Shift_Del	DEL	CCCA	CCCA	-	novel	NA	P-0051331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	102	474	0	ENST00000245479.2:c.701_704del	p.Pro234ArgfsTer18	p.P234Rfs*18	ENST00000245479	NM_000346.3	233	ggCCCA/gg	3/3	1	2	FACETS	0.603	0.54	0.67	0.603	0.54	0.67	SUBCLONAL	1	TRUE	1	0.542881750979579	2		474	623	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368171	45368228	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	TTTTCATGGGACTTGATTGGTGAAGCTTTATGACATGCTTGAGCAACGCACTGAAGGG	TTTTCATGGGACTTGATTGGTGAAGCTTTATGACATGCTTGAGCAACGCACTGAAGGG	-	novel	NA	P-0051331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	151	176	0	ENST00000262160.6:c.1374_*27del		p.*458*	ENST00000262160	NM_005901.5	458		11/11	0.542881750979579	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.542881750979579	2		176	272	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022569	31022569	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	142	389	0	ENST00000375687.4:c.2054G>T	p.Gly685Val	p.G685V	ENST00000375687	NM_015338.5	685	gGa/gTa	13/13	1	2	FACETS	0.995	0.912	1	0.995	0.912	1	CLONAL	1	TRUE	1	0.542881750979579	2		389	526	SUCCESS
APC	324	MSKCC	GRCh37	5	112175782	112175783	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0051331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	96	271	0	ENST00000257430.4:c.4492_4493del	p.Asp1498TrpfsTer15	p.D1498Wfs*15	ENST00000257430	NM_000038.5	1497	ccAGat/ccat	16/16	1	2	FACETS	0.916	0.823	1	0.916	0.823	1	CLONAL	1	TRUE	1	0.542881750979579	2		271	386	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	183	831	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.991	0.92	1	1	0.993	1	CLONAL	2	TRUE	1	0.316094697531726	2		831	584	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	106	378	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.316094697531726	2		378	667	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	138	120	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.889	0.814	0.966	1	0.99	1	CLONAL	2	TRUE	1	0.316094697531726	2		120	491	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	223	588	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.954	1	1	0.994	1	CLONAL	2	TRUE	1	0.316094697531726	2		592	689	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	71	498	4	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.972	0.851	1	0.972	0.851	1	CLONAL	1	TRUE	1	0.316094697531726	2		502	462	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	91	518	0	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	1	2	FACETS	0.921	0.819	1	0.921	0.819	1	CLONAL	1	TRUE	1	0.316094697531726	2		518	625	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	120	670	4	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	1	2	FACETS	0.977	0.883	1	0.977	0.883	1	CLONAL	1	TRUE	1	0.316094697531726	2		674	777	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	82	425	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.942	0.832	1	0.942	0.832	1	CLONAL	1	TRUE	1	0.316094697531726	2		425	551	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	235	745	2	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.957	0.896	1	1	0.994	1	CLONAL	2	TRUE	1	0.316094697531726	2		747	777	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	144	644	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.316094697531726	2		644	751	SUCCESS
APC	324	MSKCC	GRCh37	5	112174490	112174493	+	frameshift_variant	Frame_Shift_Del	DEL	CAAT	CAAT	-	rs587779353	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	64	297	0	ENST00000257430.4:c.3202_3205del	p.Ser1068GlyfsTer57	p.S1068Gfs*57	ENST00000257430	NM_000038.5	1067	CAATca/ca	16/16	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.316094697531726	2		297	380	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486049	29486050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	73	289	0	ENST00000356175.3:c.233dup	p.Asn78LysfsTer29	p.N78Kfs*29	ENST00000356175	NM_000267.3	76	gaa/gAaa	3/57	1	2	FACETS	0.952	0.835	1	0.952	0.835	1	CLONAL	1	TRUE	1	0.316094697531726	2		289	485	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209616	98209617	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761353734	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	96	624	0	ENST00000331920.6:c.3921dup	p.Arg1308GlnfsTer17	p.R1308Qfs*17	ENST00000331920	NM_000264.3	1307	-/C	23/24	1	2	FACETS	0.978	0.873	1	0.978	0.873	1	CLONAL	1	TRUE	1	0.316094697531726	2		624	621	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106421	27106421	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	135	557	0	ENST00000324856.7:c.6032T>G	p.Leu2011Arg	p.L2011R	ENST00000324856	NM_006015.4	2011	cTg/cGg	20/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.316094697531726	2		557	623	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	74	494	10	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.316094697531726	2		504	457	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523313	176523313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	145	749	2	ENST00000292408.4:c.1970C>T	p.Ala657Val	p.A657V	ENST00000292408	NM_213647.1	657	gCg/gTg	15/18	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.316094697531726	2		751	831	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913274	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	15	384	0	ENST00000263967.3:c.1634A>C	p.Glu545Ala	p.E545A	ENST00000263967	NM_006218.2	545	gAg/gCg	10/21	0.316094697531726	3	FACETS	0.243	0.177	0.323	0.122	0.088	0.162	SUBCLONAL	1	TRUE	1	0.316094697531726	3		384	452	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135246	2135246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1051502900	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	140	717	3	ENST00000219476.3:c.4585C>T	p.Arg1529Trp	p.R1529W	ENST00000219476	NM_000548.3	1529	Cgg/Tgg	36/42	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.316094697531726	2		720	751	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656969	47656969	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779075	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	80	288	1	ENST00000233146.2:c.1165C>T	p.Arg389Ter	p.R389*	ENST00000233146	NM_000251.2	389	Cga/Tga	7/16	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.316094697531726	2		289	470	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819261	3819261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61731383	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	105	526	0	ENST00000262367.5:c.2974G>A	p.Val992Ile	p.V992I	ENST00000262367	NM_004380.2	992	Gta/Ata	15/31	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.316094697531726	2		526	622	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098417	11098417	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	78	304	0	ENST00000358026.2:c.939del	p.Ala314ArgfsTer12	p.A314Rfs*12	ENST00000358026	NM_001128849.1	312	tCc/tc	6/36	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.316094697531726	2		304	403	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	145	618	2	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.316094697531726	2		620	844	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164508	47164508	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs201756643	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	62	350	0	ENST00000409792.3:c.1618C>T	p.Arg540Ter	p.R540*	ENST00000409792	NM_014159.6	540	Cga/Tga	3/21	1	2	FACETS	0.833	0.721	0.954	0.833	0.721	0.954	CLONAL	1	TRUE	1	0.316094697531726	2		350	471	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752695	42752695	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1366176199	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	114	594	3	ENST00000222329.4:c.1569del	p.Leu525SerfsTer6	p.L525Sfs*6	ENST00000222329	NM_006494.2	523	ggG/gg	4/4	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.316094697531726	2		597	616	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435889	149435889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768825118	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	101	560	0	ENST00000286301.3:c.2335G>A	p.Val779Met	p.V779M	ENST00000286301	NM_005211.3	779	Gtg/Atg	18/22	1	2	FACETS	0.971	0.869	1	0.971	0.869	1	CLONAL	1	TRUE	1	0.316094697531726	2		560	658	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097688	27097688	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	118	524	0	ENST00000324856.7:c.3281del	p.Lys1094SerfsTer67	p.K1094Sfs*67	ENST00000324856	NM_006015.4	1093	Aaa/aa	12/20	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.316094697531726	2		524	727	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775779	9775779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1205317546	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	134	701	3	ENST00000377346.4:c.322C>T	p.Arg108Cys	p.R108C	ENST00000377346	NM_005026.3	108	Cgc/Tgc	4/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.316094697531726	2		704	731	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096314	2096314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767591879	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	140	678	3	ENST00000219066.1:c.193C>T	p.Arg65Cys	p.R65C	ENST00000219066	NM_002528.5	65	Cgt/Tgt	2/6	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.316094697531726	2		681	816	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67646012	67646013	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	88	413	1	ENST00000264010.4:c.950_951dup	p.Gly318GlnfsTer16	p.G318Qfs*16	ENST00000264010	NM_006565.3	314	aac/aACac	4/12	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.316094697531726	2		414	537	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803663	1803663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	124	694	2	ENST00000260795.2:c.841G>A	p.Ala281Thr	p.A281T	ENST00000260795		281	Gca/Aca	6/17	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.316094697531726	2		696	704	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471799	120471799	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1366907623	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	69	444	2	ENST00000256646.2:c.3692G>A	p.Arg1231Gln	p.R1231Q	ENST00000256646	NM_024408.3	1231	cGg/cAg	23/34	1	2	FACETS	0.949	0.829	1	0.949	0.829	1	CLONAL	1	TRUE	1	0.316094697531726	2		446	460	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92300846	92300846	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766767871	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	97	434	1	ENST00000265734.4:c.541G>A	p.Val181Ile	p.V181I	ENST00000265734	NM_001259.6	181	Gtc/Atc	5/8	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.316094697531726	2		435	541	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849299	89849299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374490484	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	123	520	0	ENST00000389301.3:c.1594G>A	p.Glu532Lys	p.E532K	ENST00000389301	NM_000135.2	532	Gag/Aag	17/43	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.316094697531726	2		520	633	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120491	2120491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751147419	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	128	711	0	ENST00000219476.3:c.1751C>T	p.Thr584Met	p.T584M	ENST00000219476	NM_000548.3	584	aCg/aTg	17/42	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.316094697531726	2		711	804	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72873689	72873690	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	81	320	0	ENST00000325599.8:c.612dup	p.Glu205Ter	p.E205*	ENST00000325599	NM_018130.2	204	-/T	6/11	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.316094697531726	2		320	505	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110050	115110050	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751628989	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	124	599	0	ENST00000257566.3:c.1828G>A	p.Ala610Thr	p.A610T	ENST00000257566	NM_016569.3	610	Gca/Aca	8/8	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.316094697531726	2		599	740	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49054155	49054155	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	67	308	0	ENST00000267163.4:c.2738del	p.Lys913SerfsTer4	p.K913Sfs*4	ENST00000267163	NM_000321.2	912	cAa/ca	27/27	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.316094697531726	2		308	392	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456424	99456424	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774280289	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	80	515	1	ENST00000268035.6:c.1741G>A	p.Val581Ile	p.V581I	ENST00000268035	NM_000875.3	581	Gtc/Atc	8/21	1	2	FACETS	0.871	0.768	0.982	0.871	0.768	0.982	CLONAL	1	TRUE	1	0.316094697531726	2		516	581	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222368	2222368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768623972	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	116	627	1	ENST00000326181.6:c.652G>A	p.Ala218Thr	p.A218T	ENST00000326181	NM_032271.2	218	Gcc/Acc	8/21	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.316094697531726	2		628	706	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59878830	59878830	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	58	211	0	ENST00000259008.2:c.924del	p.Lys308AsnfsTer30	p.K308Nfs*30	ENST00000259008	NM_032043.2	308	aaA/aa	8/20	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.316094697531726	2		211	323	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11015681	11015681	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	112	620	0	ENST00000327064.4:c.275G>A	p.Arg92His	p.R92H	ENST00000327064	NM_199141.1	92	cGt/cAt	2/16	1	2	FACETS	0.998	0.899	1	0.998	0.899	1	CLONAL	1	TRUE	1	0.316094697531726	2		620	710	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272324	15272324	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	125	604	0	ENST00000263388.2:c.6115C>A	p.Leu2039Met	p.L2039M	ENST00000263388	NM_000435.2	2039	Ctg/Atg	33/33	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.316094697531726	2		604	732	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221615	36221615	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	152	714	0	ENST00000222270.7:c.5284C>A	p.Arg1762Ser	p.R1762S	ENST00000222270	NM_014727.1	1762	Cgt/Agt	26/37	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.316094697531726	2		714	810	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762911	40762911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	139	646	3	ENST00000392038.2:c.97G>A	p.Gly33Ser	p.G33S	ENST00000392038	NM_001626.4	33	Ggc/Agc	3/14	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.316094697531726	2		649	757	SUCCESS
APC	324	MSKCC	GRCh37	5	112179479	112179479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060503348	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	75	355	0	ENST00000257430.4:c.8188G>A	p.Ala2730Thr	p.A2730T	ENST00000257430	NM_000038.5	2730	Gcc/Acc	16/16	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.316094697531726	2		355	452	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522560	176522560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201831200	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	144	598	0	ENST00000292408.4:c.1657G>A	p.Ala553Thr	p.A553T	ENST00000292408	NM_213647.1	553	Gcc/Acc	13/18	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.316094697531726	2		598	709	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178681	32178681	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	143	694	0	ENST00000375023.3:c.2713G>T	p.Gly905Cys	p.G905C	ENST00000375023	NM_004557.3	905	Ggc/Tgc	18/30	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.316094697531726	2		694	799	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94128975	94128975	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	87	378	0	ENST00000369303.4:c.85G>A	p.Ala29Thr	p.A29T	ENST00000369303	NM_004440.3	29	Gct/Act	1/17	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.316094697531726	2		378	490	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192410	138192410	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1414718116	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	63	238	0	ENST00000237289.4:c.46C>T	p.Arg16Trp	p.R16W	ENST00000237289	NM_001270507.1	16	Cgg/Tgg	2/9	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.316094697531726	2		238	363	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38137196	38137196	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs531093378	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	85	386	1	ENST00000317025.8:c.3622C>T	p.Arg1208Cys	p.R1208C	ENST00000317025	NM_023034.1	1208	Cgt/Tgt	21/24	1	2	FACETS	0.976	0.865	1	0.976	0.865	1	CLONAL	1	TRUE	1	0.316094697531726	2		387	551	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922596	56922596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	119	528	2	ENST00000519728.1:c.1466C>T	p.Thr489Met	p.T489M	ENST00000519728	NM_002350.3	489	aCg/aTg	13/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.316094697531726	2		530	662	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750320	133750320	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	89	472	0	ENST00000318560.5:c.1151T>C	p.Leu384Pro	p.L384P	ENST00000318560	NM_005157.4	384	cTg/cCg	7/11	1	2	FACETS	0.884	0.785	0.99	0.884	0.785	0.99	CLONAL	1	TRUE	1	0.316094697531726	2		472	637	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0051349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	108	378	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	FALSE	1	0.319099040420361	2		378	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0051349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	137	1025	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.300423680079904	1	FACETS	0.948	0.864	1	0.948	0.864	1	CLONAL	1	FALSE	0	0.319099040420361	1		1026	761	SUCCESS
APC	324	MSKCC	GRCh37	5	112174658	112174658	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	71	402	1	ENST00000257430.4:c.3367C>T	p.Gln1123Ter	p.Q1123*	ENST00000257430	NM_000038.5	1123	Caa/Taa	16/16	0.29670194122723	1	FACETS	0.935	0.82	1	0.935	0.82	1	CLONAL	1	FALSE	0	0.319099040420361	1		403	400	SUCCESS
APC	324	MSKCC	GRCh37	5	112175755	112175759	+	frameshift_variant	Frame_Shift_Del	DEL	ATTAC	ATTAC	-	novel	NA	P-0051349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	27	414	0	ENST00000257430.4:c.4467_4471del	p.Leu1489PhefsTer23	p.L1489Ffs*23	ENST00000257430	NM_000038.5	1488	ttATTACat/ttat	16/16	0.29670194122723	1	FACETS	0.304	0.241	0.376	0.304	0.241	0.376	SUBCLONAL	1	FALSE	0	0.319099040420361	1		414	468	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491000	56491000	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	58	697	0	ENST00000267101.3:c.2446G>A	p.Val816Ile	p.V816I	ENST00000267101	NM_001982.3	816	Gta/Ata	20/28	1	2	FACETS	0.403	0.345	0.467	0.403	0.345	0.467	SUBCLONAL	1	FALSE	1	0.319099040420361	2		697	901	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716068	52716068	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	96	721	0	ENST00000322088.6:c.633C>A	p.Asn211Lys	p.N211K	ENST00000322088	NM_014225.5	211	aaC/aaA	5/15	0.319099040420361	1	FACETS	0.548	0.487	0.613	0.548	0.487	0.613	SUBCLONAL	1	FALSE	0	0.319099040420361	1		721	923	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249496	153249496	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	107	560	0	ENST00000281708.4:c.1282C>T	p.Gln428Ter	p.Q428*	ENST00000281708	NM_033632.3	428	Caa/Taa	9/12	1	2	FACETS	0.968	0.869	1	0.968	0.869	1	CLONAL	1	FALSE	1	0.319099040420361	2		560	693	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	126	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.234327449328962	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	1	0.273840776531368	3		487	479	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356248	66356248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202046693	NA	P-0051439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	74	528	0	ENST00000273854.3:c.1249C>T	p.Arg417Trp	p.R417W	ENST00000273854	NM_004439.5	417	Cgg/Tgg	5/18	1	2	FACETS	0.729	0.638	0.828	0.729	0.638	0.828	SUBCLONAL	1	TRUE	1	0.273840776531368	2		528	741	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953228	81953228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369760877	NA	P-0051439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	66	271	0	ENST00000359376.3:c.2194C>T	p.Arg732Cys	p.R732C	ENST00000359376	NM_002661.3	732	Cgc/Tgc	20/33	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.273840776531368	2		271	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579365	7579365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782461	NA	P-0051439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	105	1232	2	ENST00000269305.4:c.322G>A	p.Gly108Ser	p.G108S	ENST00000269305	NM_001126112.2	108	Ggt/Agt	4/11	1	2	FACETS	0.893	0.799	0.992	0.893	0.799	0.992	CLONAL	1	TRUE	1	0.273840776531368	2		1234	859	SUCCESS
APC	324	MSKCC	GRCh37	5	112174205	112174205	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	100	366	0	ENST00000257430.4:c.2915del	p.Gly972ValfsTer8	p.G972Vfs*8	ENST00000257430	NM_000038.5	972	Ggt/gt	16/16	0.273840776531368	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.273840776531368	2		366	329	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928067	178928067	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	73	510	0	ENST00000263967.3:c.1345C>A	p.Pro449Thr	p.P449T	ENST00000263967	NM_006218.2	449	Cct/Act	8/21	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.273840776531368	2		510	480	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26927935	26927935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775029551	NA	P-0051439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	44	343	0	ENST00000381527.3:c.374G>A	p.Arg125Gln	p.R125Q	ENST00000381527	NM_001260.1	125	cGg/cAg	4/13	0.273840776531368	4	FACETS	0.916	0.769	1	0.305	0.256	0.36	CLONAL	1	TRUE	1	0.273840776531368	4		343	447	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477111	67477111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	104	538	1	ENST00000327367.4:c.918G>T	p.Glu306Asp	p.E306D	ENST00000327367	NM_005902.3	306	gaG/gaT	7/9	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.273840776531368	2		539	721	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	218	917	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.345941017060783	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.346767537007691	2		917	609	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0051446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	60	252	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.299048995006023	2	FACETS	0.897	0.786	1	0.897	0.786	1	CLONAL	2	TRUE	0	0.346767537007691	2		252	193	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482169	87482169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201028496	NA	P-0051446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	56	733	0	ENST00000277120.3:c.1456G>A	p.Val486Ile	p.V486I	ENST00000277120		486	Gtt/Att	14/19	0.25881922498477	3	FACETS	0.972	0.836	1	0.486	0.418	0.56	CLONAL	1	TRUE	1	0.346767537007691	3		733	390	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130168	2130168	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	32	967	0	ENST00000219476.3:c.3400G>A	p.Gly1134Ser	p.G1134S	ENST00000219476	NM_000548.3	1134	Ggc/Agc	30/42	1	2	FACETS	0.293	0.237	0.357	0.293	0.237	0.357	SUBCLONAL	1	TRUE	1	0.346767537007691	2		967	630	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622181	1622181	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778016789	NA	P-0051446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	250	934	0	ENST00000344749.5:c.694G>T	p.Gly232Cys	p.G232C	ENST00000344749	NM_001136139.2	232	Ggc/Tgc	10/19	0.247614033860213	1	FACETS	0.758	0.712	0.806	1	0.993	1	SUBCLONAL	2	TRUE	0	0.346767537007691	1		934	786	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719248	190719248	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	58	370	0	ENST00000441310.2:c.1250G>C	p.Gly417Ala	p.G417A	ENST00000441310	NM_000534.4	417	gGt/gCt	9/13	0.346767537007691	3	FACETS	1	0.909	1	1	0.909	1	CLONAL	2	TRUE	1	0.346767537007691	3		370	187	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182681729	182681729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778511513	NA	P-0051446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	64	558	0	ENST00000292782.4:c.329G>A	p.Arg110Lys	p.R110K	ENST00000292782	NM_020640.2	110	aGa/aAa	3/7	0.25881922498477	3	FACETS	1	0.911	1	0.531	0.461	0.606	CLONAL	1	TRUE	1	0.346767537007691	3		558	408	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0051482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	232	415	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.427800086912587	3	FACETS	0.976	0.917	1	0.976	0.917	1	CLONAL	2	TRUE	1	0.510047146881995	3		415	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0051482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	231	469	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.510047146881995	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.510047146881995	1		469	558	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0051482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	187	466	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.193971129271181	5	FACETS	0.918	0.851	0.987			1	INDETERMINATE	2	TRUE	NA	0.510047146881995	5		466	705	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968266	2968266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773909937	NA	P-0051482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	181	956	0	ENST00000396946.4:c.1720G>A	p.Val574Ile	p.V574I	ENST00000396946	NM_032415.4	574	Gtc/Atc	13/25	0.427800086912587	3	FACETS	0.875	0.807	0.946	0.437	0.403	0.473	CLONAL	1	TRUE	1	0.510047146881995	3		956	1018	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604785	48604785	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	116	416	0	ENST00000342988.3:c.1607T>C	p.Leu536Pro	p.L536P	ENST00000342988	NM_005359.5	536	cTa/cCa	12/12	0.510047146881995	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.510047146881995	1		416	303	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288888	15288888	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	63	256	0	ENST00000263388.2:c.3851C>T	p.Pro1284Leu	p.P1284L	ENST00000263388	NM_000435.2	1284	cCg/cTg	24/33	1	2	FACETS	0.992	0.868	1	0.992	0.868	1	CLONAL	1	TRUE	1	0.510047146881995	2		256	249	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410438	139410438	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746796894	NA	P-0051482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	228	919	0	ENST00000277541.6:c.1664C>T	p.Thr555Met	p.T555M	ENST00000277541	NM_017617.3	555	aCg/aTg	10/34	1	2	FACETS	0.99	0.924	1	0.99	0.924	1	CLONAL	1	TRUE	1	0.510047146881995	2		919	903	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933535	39933535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747038834	NA	P-0051482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	207	766	0	ENST00000378444.4:c.1064C>T	p.Ser355Leu	p.S355L	ENST00000378444	NM_001123385.1	355	tCg/tTg	4/15	0.510047146881995	3	FACETS	0.997	0.925	1	0.498	0.462	0.536	CLONAL	1	TRUE	1	0.510047146881995	3		766	1022	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912394	29912395	+	splice_donor_variant,intron_variant	Splice_Site	INS	GT	GT	AAGG	novel	NA	P-0051482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	37	540	0	ENST00000376809.5:c.1012+1_1012+2delinsAAGG		p.X338_splice	ENST00000376809	NM_002116.7	338			0.510047146881995	1	FACETS	0.217	0.178	0.26	0.217	0.178	0.26	SUBCLONAL	1	TRUE	0	0.510047146881995	1		540	498	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0051489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	341	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	0.886	0.849	0.923			1	INDETERMINATE	2	TRUE	NA	0.650938874748386	2		457	591	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0051489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	88	243	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.650938874748386	2		243	265	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	151	300	4	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.650938874748386	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.650938874748386	1		304	300	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101342	27101342	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	409	841	1	ENST00000324856.7:c.4624G>T	p.Glu1542Ter	p.E1542*	ENST00000324856	NM_006015.4	1542	Gaa/Taa	18/20	1	2	FACETS	0.986	0.938	1	0.986	0.938	1	CLONAL	1	TRUE	1	0.650938874748386	2		842	1275	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0051489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	335	612	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.650938874748386	1	FACETS	0.917	0.873	0.962	0.917	0.873	0.962	CLONAL	1	TRUE	0	0.650938874748386	1		612	757	SUCCESS
APC	324	MSKCC	GRCh37	5	112175788	112175789	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0051489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	133	263	0	ENST00000257430.4:c.4500_4501dup	p.Ser1501PhefsTer7	p.S1501Ffs*7	ENST00000257430	NM_000038.5	1499	-/TT	16/16	1	2	FACETS	0.948	0.868	1	0.948	0.868	1	CLONAL	1	TRUE	1	0.650938874748386	2		263	431	SUCCESS
APC	324	MSKCC	GRCh37	5	112174106	112174106	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0051489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	116	218	0	ENST00000257430.4:c.2815A>T	p.Lys939Ter	p.K939*	ENST00000257430	NM_000038.5	939	Aag/Tag	16/16	1	2	FACETS	0.859	0.78	0.94	0.859	0.78	0.94	CLONAL	1	TRUE	1	0.650938874748386	2		218	415	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741951	17741951	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	159	333	0	ENST00000250003.3:c.622G>A	p.Asp208Asn	p.D208N	ENST00000250003	NM_002478.4	208	Gac/Aac	1/3	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.650938874748386	2		333	479	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249419	153249419	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0051489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	456	329	1	ENST00000281708.4:c.1359T>A	p.Cys453Ter	p.C453*	ENST00000281708	NM_033632.3	453	tgT/tgA	9/12	0.650938874748386	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.650938874748386	2		330	693	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739659	145739659	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	481	1200	0	ENST00000428558.2:c.1792C>A	p.Pro598Thr	p.P598T	ENST00000428558	NM_004260.3	598	Cca/Aca	11/22	1	2	FACETS	0.988	0.944	1	0.988	0.944	1	CLONAL	1	TRUE	1	0.650938874748386	2		1200	1496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0051490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	183	1045	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.386588553575397	1	FACETS	0.839	0.775	0.906	0.839	0.775	0.906	CLONAL	1	TRUE	0	0.400061726223005	1		1046	872	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0051490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	33	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.249	0.202	0.302	0.249	0.202	0.302	SUBCLONAL	1	TRUE	1	0.400061726223005	2		457	663	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0051490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	175	756	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.889	0.818	0.963	0.889	0.818	0.963	CLONAL	1	TRUE	1	0.400061726223005	2		756	984	SUCCESS
APC	324	MSKCC	GRCh37	5	112175271	112175271	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	128	264	0	ENST00000257430.4:c.3980C>A	p.Ser1327Ter	p.S1327*	ENST00000257430	NM_000038.5	1327	tCa/tAa	16/16	0.400061726223005	2	FACETS	0.936	0.859	1	0.936	0.859	1	CLONAL	2	TRUE	0	0.400061726223005	2		264	342	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701282	43701283	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0051490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	100	412	0	ENST00000382044.4:c.5411_5412dup	p.Tyr1805LeufsTer6	p.Y1805Lfs*6	ENST00000382044	NM_001141980.1	1804	-/CT	26/28	1	2	FACETS	0.846	0.757	0.94	0.846	0.757	0.94	CLONAL	1	TRUE	1	0.400061726223005	2		412	591	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6438308	6438308	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	299	467	0	ENST00000356142.4:c.241G>A	p.Gly81Ser	p.G81S	ENST00000356142	NM_018890.3	81	Ggt/Agt	4/7	0.287022722655038	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	2	0.400061726223005	4		467	1031	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	129	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.454035651953704	3	FACETS	0.787	0.72	0.856	0.787	0.72	0.856	SUBCLONAL	2	TRUE	1	0.502491604460331	3		487	408	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519818	29519818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772496459	NA	P-0051580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	340	525	0	ENST00000389048.3:c.1753G>A	p.Ala585Thr	p.A585T	ENST00000389048	NM_004304.4	585	Gcc/Acc	9/29	0.227277146677565	3	FACETS	1	0.989	1	0.75	0.714	0.786	INDETERMINATE	2	TRUE	0	0.502491604460331	3		525	753	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589151	67589152	+	inframe_insertion	In_Frame_Ins	INS	-	-	AATCAA	novel	NA	P-0051580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	70	347	0	ENST00000274335.5:c.1143_1148dup	p.Lys382_Ile383dup	p.K382_I383dup	ENST00000274335		382	tta/ttAATCAAa	9/15	0.137636722947192	3	FACETS	0.958	0.853	1	0.638	0.569	0.71	INDETERMINATE	2	TRUE	0	0.502491604460331	3		347	182	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523712	41523712	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	132	573	0	ENST00000263253.7:c.1130del	p.Asn377ThrfsTer3	p.N377Tfs*3	ENST00000263253	NM_001429.3	376	ctA/ct	4/31	1	2	FACETS	0.884	0.806	0.967	0.884	0.806	0.967	CLONAL	1	TRUE	1	0.502491604460331	2		573	594	SUCCESS
APC	324	MSKCC	GRCh37	5	112175748	112175748	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	151	342	0	ENST00000257430.4:c.4457del	p.Asp1486ValfsTer21	p.D1486Vfs*21	ENST00000257430	NM_000038.5	1486	gAt/gt	16/16	0.502491604460331	2	FACETS	0.942	0.876	1	0.942	0.876	1	CLONAL	2	TRUE	0	0.502491604460331	2		342	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	189	1082	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	1	2	FACETS	0.949	0.879	1	0.949	0.879	1	CLONAL	1	TRUE	1	0.51	2		1082	781	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	154	445	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.933	0.857	1	0.933	0.857	1	CLONAL	1	TRUE	1	0.51	2		445	647	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	114	383	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.978	0.886	1	0.978	0.886	1	CLONAL	1	TRUE	1	0.51	2		383	457	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205266	61205266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753474292	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	181	548	0	ENST00000301761.2:c.206G>A	p.Arg69His	p.R69H	ENST00000301761	NM_017841.2	69	cGc/cAc	2/4	1	2	FACETS	0.881	0.814	0.95	0.881	0.814	0.95	CLONAL	1	TRUE	1	0.51	2		548	806	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	132	447	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	1	2	FACETS	0.946	0.863	1	0.946	0.863	1	CLONAL	1	TRUE	1	0.51	2		447	547	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	178	514	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	0.942	0.87	1	0.942	0.87	1	CLONAL	1	TRUE	1	0.51	2		514	741	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023544	31023544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs116112525	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	153	490	0	ENST00000375687.4:c.3029C>T	p.Thr1010Met	p.T1010M	ENST00000375687	NM_015338.5	1010	aCg/aTg	13/13	1	2	FACETS	0.881	0.808	0.957	0.881	0.808	0.957	CLONAL	1	TRUE	1	0.51	2		490	681	SUCCESS
APC	324	MSKCC	GRCh37	5	112173656	112173656	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123117	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	102	393	0	ENST00000257430.4:c.2365C>T	p.Gln789Ter	p.Q789*	ENST00000257430	NM_000038.5	789	Cag/Tag	16/16	1	2	FACETS	0.873	0.785	0.966	0.873	0.785	0.966	CLONAL	1	TRUE	1	0.51	2		393	458	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085728	16085728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144939456	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	209	534	1	ENST00000281043.3:c.904C>T	p.Arg302Cys	p.R302C	ENST00000281043	NM_005378.4	302	Cgt/Tgt	3/3	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.51	2		535	820	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	196	694	3	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.932	0.864	1	0.932	0.864	1	CLONAL	1	TRUE	1	0.51	2		697	825	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	58	226	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	0.763	0.661	0.873	0.763	0.661	0.873	SUBCLONAL	1	TRUE	1	0.51	2		226	298	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395736	45395736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	143	379	0	ENST00000262160.6:c.398G>A	p.Arg133His	p.R133H	ENST00000262160	NM_005901.5	133	cGc/cAc	4/11	1	2	FACETS	0.959	0.878	1	0.959	0.878	1	CLONAL	1	TRUE	1	0.51	2		379	585	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851754	134851754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56396912	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	152	498	2	ENST00000398015.3:c.1160C>T	p.Thr387Met	p.T387M	ENST00000398015	NM_004441.4	387	aCg/aTg	5/16	1	2	FACETS	0.928	0.852	1	0.928	0.852	1	CLONAL	1	TRUE	1	0.51	2		500	642	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99460005	99460005	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201631492	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	177	462	0	ENST00000268035.6:c.2101G>A	p.Ala701Thr	p.A701T	ENST00000268035	NM_000875.3	701	Gcc/Acc	10/21	1	2	FACETS	0.9	0.831	0.972	0.9	0.831	0.972	CLONAL	1	TRUE	1	0.51	2		462	771	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428511	78428511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408536007	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	158	472	0	ENST00000370768.2:c.1288C>T	p.Arg430Cys	p.R430C	ENST00000370768	NM_003902.3	430	Cgt/Tgt	14/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.51	2		472	540	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007619	45007619	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs111482205	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	56	288	0	ENST00000558401.1:c.68-2A>G		p.X23_splice	ENST00000558401	NM_004048.2	23			1	2	FACETS	0.583	0.501	0.671	0.583	0.501	0.671	SUBCLONAL	1	TRUE	1	0.51	2		288	377	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120178	70120178	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057518216	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	150	296	1	ENST00000245479.2:c.1180C>T	p.Arg394Ter	p.R394*	ENST00000245479	NM_000346.3	394	Cga/Tga	3/3	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.51	2		297	554	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182709	38182709	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370623345	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	234	496	0	ENST00000396334.3:c.862G>A	p.Asp288Asn	p.D288N	ENST00000396334	NM_002468.4	288	Gac/Aac	5/5	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.51	2		496	871	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141587	202141587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771150445	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	148	387	0	ENST00000358485.4:c.875G>A	p.Arg292Gln	p.R292Q	ENST00000358485	NM_001080125.1	292	cGg/cAg	7/9	1	2	FACETS	0.975	0.895	1	0.975	0.895	1	CLONAL	1	TRUE	1	0.51	2		387	595	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685313	86685313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886060844	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	98	209	0	ENST00000274376.6:c.3029G>A	p.Arg1010Gln	p.R1010Q	ENST00000274376	NM_002890.2	1010	cGa/cAa	24/25	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.51	2		209	366	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646084	215646085	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs746325928	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	132	499	0	ENST00000260947.4:c.513dup	p.Asp172ArgfsTer10	p.D172Rfs*10	ENST00000260947	NM_000465.2	171	-/A	4/11	1	2	FACETS	0.766	0.697	0.838	0.766	0.697	0.838	SUBCLONAL	1	TRUE	1	0.51	2		499	676	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928318	178928318	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	119	442	1	ENST00000263967.3:c.1504C>T	p.Arg502Ter	p.R502*	ENST00000263967	NM_006218.2	502	Cga/Tga	9/21	1	2	FACETS	0.832	0.754	0.914	0.832	0.754	0.914	CLONAL	1	TRUE	1	0.51	2		443	561	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715678	30715678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039551	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	125	284	0	ENST00000295754.5:c.1336G>A	p.Asp446Asn	p.D446N	ENST00000295754	NM_003242.5	446	Gat/Aat	5/7	1	2	FACETS	0.878	0.798	0.962	0.878	0.798	0.962	CLONAL	1	TRUE	1	0.51	2		284	558	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11269467	11269467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	162	470	1	ENST00000361445.4:c.3703C>T	p.Arg1235Trp	p.R1235W	ENST00000361445	NM_004958.3	1235	Cgg/Tgg	25/58	1	2	FACETS	0.91	0.837	0.986	0.91	0.837	0.986	CLONAL	1	TRUE	1	0.51	2		471	698	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007901	45007901	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	105	390	0	ENST00000558401.1:c.346+2T>C		p.X116_splice	ENST00000558401	NM_004048.2	116			1	2	FACETS	0.897	0.808	0.99	0.897	0.808	0.99	CLONAL	1	TRUE	1	0.51	2		390	459	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119666150	119666150	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	104	409	0	ENST00000316626.5:c.331C>T	p.Arg111Ter	p.R111*	ENST00000316626		111	Cga/Tga	3/12	1	2	FACETS	0.978	0.882	1	0.978	0.882	1	CLONAL	1	TRUE	1	0.51	2		409	417	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218348	133218348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1171272614	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	207	576	2	ENST00000320574.5:c.5263G>A	p.Gly1755Arg	p.G1755R	ENST00000320574	NM_006231.2	1755	Ggg/Agg	39/49	1	2	FACETS	0.975	0.906	1	0.975	0.906	1	CLONAL	1	TRUE	1	0.51	2		578	833	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180793	106180793	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1197941414	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	122	304	0	ENST00000380013.4:c.3821A>G	p.Gln1274Arg	p.Q1274R	ENST00000380013	NM_001127208.2	1274	cAg/cGg	7/11	1	2	FACETS	0.972	0.884	1	0.972	0.884	1	CLONAL	1	TRUE	1	0.51	2		304	492	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56855485	56855485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs79070284	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	122	385	0	ENST00000308159.5:c.634G>A	p.Val212Ile	p.V212I	ENST00000308159	NM_014669.4	212	Gtc/Atc	7/22	1	2	FACETS	0.787	0.713	0.864	0.787	0.713	0.864	SUBCLONAL	1	TRUE	1	0.51	2		385	608	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030877	36030877	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751005087	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	160	533	0	ENST00000358208.4:c.1156G>A	p.Val386Ile	p.V386I	ENST00000358208		386	Gtc/Atc	10/12	1	2	FACETS	0.927	0.852	1	0.927	0.852	1	CLONAL	1	TRUE	1	0.51	2		533	677	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357185	89357185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777070083	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	248	579	0	ENST00000301030.4:c.449C>T	p.Thr150Met	p.T150M	ENST00000301030	NM_001256183.1	150	aCg/aTg	6/13	1	2	FACETS	0.97	0.907	1	0.97	0.907	1	CLONAL	1	TRUE	1	0.51	2		579	1003	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612250	189612250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749906547	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	140	442	0	ENST00000264731.3:c.2002C>T	p.Arg668Cys	p.R668C	ENST00000264731	NM_003722.4	668	Cgc/Tgc	14/14	1	2	FACETS	0.955	0.873	1	0.955	0.873	1	CLONAL	1	TRUE	1	0.51	2		442	575	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20486948	20486948	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs773975473	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	100	344	0	ENST00000346618.3:c.913C>T	p.Arg305Ter	p.R305*	ENST00000346618	NM_001949.4	305	Cga/Tga	5/7	1	2	FACETS	0.858	0.771	0.95	0.858	0.771	0.95	CLONAL	1	TRUE	1	0.51	2		344	457	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437266	220437266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753111199	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	192	661	0	ENST00000243786.2:c.170G>A	p.Arg57Gln	p.R57Q	ENST00000243786	NM_002191.3	57	cGg/cAg	1/2	1	2	FACETS	0.869	0.805	0.936	0.869	0.805	0.936	CLONAL	1	TRUE	1	0.51	2		661	866	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982057	38982057	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	107	469	0	ENST00000357387.3:c.665G>A	p.Arg222Gln	p.R222Q	ENST00000357387	NM_152756.3	222	cGa/cAa	8/38	1	2	FACETS	0.773	0.695	0.854	0.773	0.695	0.854	SUBCLONAL	1	TRUE	1	0.51	2		469	543	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346811	89346811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748373867	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	106	394	0	ENST00000301030.4:c.6139G>A	p.Ala2047Thr	p.A2047T	ENST00000301030	NM_001256183.1	2047	Gcc/Acc	9/13	1	2	FACETS	0.906	0.816	0.999	0.906	0.816	0.999	CLONAL	1	TRUE	1	0.51	2		394	459	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589782	55589782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1560414398	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	137	403	0	ENST00000288135.5:c.1264G>A	p.Val422Met	p.V422M	ENST00000288135	NM_000222.2	422	Gtg/Atg	8/21	0.129159195088479	1	FACETS	0.655	0.598	0.715	0.655	0.598	0.715	INDETERMINATE	1	TRUE	0	0.51	1		403	611	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25368467	25368467	+	intron_variant	Intron	SNP	C	C	T	rs755877953	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	129	393	0	ENST00000311936.3:c.451-5622G>A		p.*151*	ENST00000311936	NM_004985.3	160/189			1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.51	2		393	498	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422929	12422929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773089349	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	213	514	1	ENST00000287820.6:c.419G>A	p.Arg140His	p.R140H	ENST00000287820	NM_015869.4	140	cGt/cAt	3/7	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.51	2		515	801	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012245	152012245	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	105	411	1	ENST00000262189.6:c.568C>T	p.Arg190Ter	p.R190*	ENST00000262189	NM_170606.2	190	Cga/Tga	4/59	1	2	FACETS	0.822	0.74	0.908	0.822	0.74	0.908	CLONAL	1	TRUE	1	0.51	2		412	501	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445178	49445178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771291128	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	195	677	0	ENST00000301067.7:c.2288C>T	p.Pro763Leu	p.P763L	ENST00000301067	NM_003482.3	763	cCg/cTg	10/54	1	2	FACETS	0.942	0.873	1	0.942	0.873	1	CLONAL	1	TRUE	1	0.51	2		677	812	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469632	25469632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1036696061	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	189	515	0	ENST00000264709.3:c.1136G>A	p.Arg379His	p.R379H	ENST00000264709	NM_175629.2	379	cGc/cAc	10/23	1	2	FACETS	0.921	0.852	0.991	0.921	0.852	0.991	CLONAL	1	TRUE	1	0.51	2		515	805	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220637	2220637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750885564	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	208	427	0	ENST00000326181.6:c.254G>A	p.Arg85His	p.R85H	ENST00000326181	NM_032271.2	85	cGc/cAc	5/21	1	2	FACETS	0.964	0.896	1	0.964	0.896	1	CLONAL	1	TRUE	1	0.51	2		427	846	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022455	31022455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745371501	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	61	333	0	ENST00000375687.4:c.1940C>T	p.Pro647Leu	p.P647L	ENST00000375687	NM_015338.5	647	cCg/cTg	13/13	1	2	FACETS	0.75	0.651	0.855	0.75	0.651	0.855	SUBCLONAL	1	TRUE	1	0.51	2		333	319	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723323	49723323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	29	94	0	ENST00000449682.2:c.1220G>A	p.Arg407His	p.R407H	ENST00000449682	NM_020998.3	407	cGc/cAc	10/18	1	2	FACETS	1	0.824	1	1	0.824	1	CLONAL	1	TRUE	1	0.51	2		94	113	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101923	11101923	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502063	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	205	664	0	ENST00000358026.2:c.1343G>A	p.Arg448His	p.R448H	ENST00000358026	NM_001128849.1	448	cGc/cAc	8/36	1	2	FACETS	0.942	0.876	1	0.942	0.876	1	CLONAL	1	TRUE	1	0.51	2		664	853	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434646	99434646	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1361565953	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	214	581	0	ENST00000268035.6:c.733G>A	p.Asp245Asn	p.D245N	ENST00000268035	NM_000875.3	245	Gac/Aac	3/21	1	2	FACETS	0.914	0.85	0.98	0.914	0.85	0.98	CLONAL	1	TRUE	1	0.51	2		581	918	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218848	36218848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774736378	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	209	674	0	ENST00000222270.7:c.4459C>T	p.Arg1487Cys	p.R1487C	ENST00000222270	NM_014727.1	1487	Cgc/Tgc	18/37	1	2	FACETS	0.922	0.857	0.989	0.922	0.857	0.989	CLONAL	1	TRUE	1	0.51	2		674	889	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900330	101900330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	107	415	0	ENST00000374994.4:c.764G>A	p.Arg255His	p.R255H	ENST00000374994	NM_004612.2	255	cGt/cAt	4/9	1	2	FACETS	0.801	0.721	0.885	0.801	0.721	0.885	CLONAL	1	TRUE	1	0.51	2		415	524	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245109	46245109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754489425	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	191	543	0	ENST00000334344.6:c.3203G>A	p.Arg1068His	p.R1068H	ENST00000334344	NM_152641.2	1068	cGt/cAt	15/21	1	2	FACETS	0.947	0.877	1	0.947	0.877	1	CLONAL	1	TRUE	1	0.51	2		543	791	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300061	137300061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754761323	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	72	597	0	ENST00000481739.1:c.346G>A	p.Val116Ile	p.V116I	ENST00000481739	NM_002957.4	116	Gtc/Atc	3/10	1	2	FACETS	0.318	0.277	0.362	0.318	0.277	0.362	SUBCLONAL	1	TRUE	1	0.51	2		597	888	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866483	56866483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1387477088	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	223	551	1	ENST00000519728.1:c.730C>T	p.Arg244Trp	p.R244W	ENST00000519728	NM_002350.3	244	Cgg/Tgg	8/13	1	2	FACETS	0.896	0.834	0.96	0.896	0.834	0.96	CLONAL	1	TRUE	1	0.51	2		552	976	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343465	70343465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370812643	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	202	566	0	ENST00000374080.3:c.1639G>A	p.Ala547Thr	p.A547T	ENST00000374080		547	Gca/Aca	12/45	1	2	FACETS	0.915	0.849	0.983	0.915	0.849	0.983	CLONAL	1	TRUE	1	0.51	2		566	866	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244269	5244269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568465790	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	199	614	1	ENST00000357368.4:c.1213G>A	p.Val405Ile	p.V405I	ENST00000357368	NM_002850.3	405	Gtc/Atc	11/38	1	2	FACETS	0.927	0.86	0.996	0.927	0.86	0.996	CLONAL	1	TRUE	1	0.51	2		615	842	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947872	178947872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	87	364	0	ENST00000263967.3:c.2747G>A	p.Arg916His	p.R916H	ENST00000263967	NM_006218.2	916	cGt/cAt	19/21	1	2	FACETS	0.964	0.86	1	0.964	0.86	1	CLONAL	1	TRUE	1	0.51	2		364	354	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40468878	40468878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	182	406	0	ENST00000264657.5:c.2186G>A	p.Arg729His	p.R729H	ENST00000264657	NM_139276.2	729	cGc/cAc	23/24	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.51	2		406	643	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598910	28598910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758133085	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	228	598	1	ENST00000253063.3:c.470G>A	p.Arg157His	p.R157H	ENST00000253063	NM_031459.4	157	cGc/cAc	4/10	1	2	FACETS	0.996	0.929	1	0.996	0.929	1	CLONAL	1	TRUE	1	0.51	2		599	898	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248057	110248057	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	184	412	2	ENST00000374672.4:c.1415C>T	p.Ala472Val	p.A472V	ENST00000374672	NM_004235.4	472	gCc/gTc	5/5	1	2	FACETS	0.892	0.825	0.962	0.892	0.825	0.962	CLONAL	1	TRUE	1	0.51	2		414	809	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448461	49448461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748173147	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	224	583	0	ENST00000301067.7:c.250C>T	p.Arg84Cys	p.R84C	ENST00000301067	NM_003482.3	84	Cgc/Tgc	3/54	1	2	FACETS	0.99	0.924	1	0.99	0.924	1	CLONAL	1	TRUE	1	0.51	2		583	887	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264549	1264549	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199741493	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	129	513	0	ENST00000310581.5:c.2813G>A	p.Arg938Gln	p.R938Q	ENST00000310581	NM_198253.2	938	cGg/cAg	11/16	1	2	FACETS	0.862	0.784	0.943	0.862	0.784	0.943	CLONAL	1	TRUE	1	0.51	2		513	587	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967285	25967285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	154	433	0	ENST00000435504.4:c.1921C>T	p.Arg641Cys	p.R641C	ENST00000435504		641	Cgt/Tgt	13/13	1	2	FACETS	0.896	0.822	0.973	0.896	0.822	0.973	CLONAL	1	TRUE	1	0.51	2		433	674	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993161	72993161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754613484	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	122	683	1	ENST00000268489.5:c.884G>A	p.Arg295His	p.R295H	ENST00000268489	NM_006885.3	295	cGt/cAt	2/10	1	2	FACETS	0.436	0.393	0.481	0.436	0.393	0.481	SUBCLONAL	1	TRUE	1	0.51	2		684	1098	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554277	29554277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1383770460	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	171	446	0	ENST00000356175.3:c.2293C>T	p.Arg765Cys	p.R765C	ENST00000356175	NM_000267.3	765	Cgc/Tgc	19/57	1	2	FACETS	0.944	0.871	1	0.944	0.871	1	CLONAL	1	TRUE	1	0.51	2		446	710	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17371377	17371377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs74315369	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	153	375	0	ENST00000375499.3:c.79C>T	p.Arg27Ter	p.R27*	ENST00000375499	NM_003000.2	27	Cga/Tga	2/8	1	2	FACETS	0.916	0.841	0.994	0.916	0.841	0.994	CLONAL	1	TRUE	1	0.51	2		375	655	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106787	27106787	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	193	581	0	ENST00000324856.7:c.6398A>G	p.Asp2133Gly	p.D2133G	ENST00000324856	NM_006015.4	2133	gAc/gGc	20/20	1	2	FACETS	0.945	0.876	1	0.945	0.876	1	CLONAL	1	TRUE	1	0.51	2		581	801	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799231	45799231	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	173	508	0	ENST00000450313.1:c.202C>A	p.Leu68Met	p.L68M	ENST00000450313	NM_012222.2	68	Ctg/Atg	3/16	1	2	FACETS	0.971	0.896	1	0.971	0.896	1	CLONAL	1	TRUE	1	0.51	2		508	699	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176145082	176145082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138668228	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	122	400	0	ENST00000367669.3:c.529G>A	p.Val177Met	p.V177M	ENST00000367669	NM_022457.5	177	Gtg/Atg	3/20	1	2	FACETS	0.864	0.784	0.947	0.864	0.784	0.947	CLONAL	1	TRUE	1	0.51	2		400	554	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243668553	243668553	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	novel	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	105	351	0	ENST00000263826.5:c.1438T>C	p.Ter480GlnextTer116	p.*480Qext*116	ENST00000263826	NM_005465.4	480	Taa/Caa	13/13	1	2	FACETS	0.792	0.712	0.876	0.792	0.712	0.876	SUBCLONAL	1	TRUE	1	0.51	2		351	520	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998828	100998828	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	152	490	0	ENST00000325455.5:c.974A>G	p.Glu325Gly	p.E325G	ENST00000325455	NM_001202474.3	325	gAa/gGa	1/8	1	2	FACETS	0.869	0.797	0.944	0.869	0.797	0.944	CLONAL	1	TRUE	1	0.51	2		490	686	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348891	118348891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	145	321	0	ENST00000534358.1:c.3544C>T	p.Arg1182Cys	p.R1182C	ENST00000534358	NM_005933.3	1182	Cgc/Tgc	5/36	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.51	2		321	470	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362632	118362632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782721568	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	146	397	1	ENST00000534358.1:c.4993C>T	p.Arg1665Cys	p.R1665C	ENST00000534358	NM_005933.3	1665	Cgc/Tgc	15/36	1	2	FACETS	0.953	0.873	1	0.953	0.873	1	CLONAL	1	TRUE	1	0.51	2		398	601	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245031	133245031	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	212	624	1	ENST00000320574.5:c.2084T>C	p.Phe695Ser	p.F695S	ENST00000320574	NM_006231.2	695	tTc/tCc	19/49	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.51	2		625	805	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438192	110438192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1165891062	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	60	129	0	ENST00000375856.3:c.209C>T	p.Pro70Leu	p.P70L	ENST00000375856	NM_003749.2	70	cCg/cTg	1/2	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.51	2		129	217	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244481	41244481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	137	536	0	ENST00000357654.3:c.3067G>A	p.Val1023Met	p.V1023M	ENST00000357654	NM_007294.3	1023	Gtg/Atg	10/23	1	2	FACETS	0.966	0.883	1	0.966	0.883	1	CLONAL	1	TRUE	1	0.51	2		536	556	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191024	2191024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1449424439	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	134	349	0	ENST00000398665.3:c.278C>T	p.Thr93Met	p.T93M	ENST00000398665	NM_032482.2	93	aCg/aTg	5/28	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.51	2		349	492	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222508	2222508	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771710239	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	179	452	0	ENST00000398665.3:c.3340G>A	p.Ala1114Thr	p.A1114T	ENST00000398665	NM_032482.2	1114	Gct/Act	24/28	1	2	FACETS	0.927	0.857	1	0.927	0.857	1	CLONAL	1	TRUE	1	0.51	2		452	757	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218451	5218451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201934952	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	197	533	2	ENST00000357368.4:c.4028G>A	p.Arg1343His	p.R1343H	ENST00000357368	NM_002850.3	1343	cGc/cAc	25/38	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.51	2		535	745	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212590	36212590	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	226	691	0	ENST00000222270.7:c.2341G>A	p.Gly781Ser	p.G781S	ENST00000222270	NM_014727.1	781	Ggt/Agt	3/37	1	2	FACETS	0.872	0.813	0.934	0.872	0.813	0.934	CLONAL	1	TRUE	1	0.51	2		691	1016	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033468	48033468	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750554	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	155	522	0	ENST00000234420.5:c.3772C>T	p.Gln1258Ter	p.Q1258*	ENST00000234420	NM_000179.2	1258	Caa/Taa	8/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.51	2		522	532	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267344	198267344	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	163	524	0	ENST00000335508.6:c.2013A>G	p.Ile671Met	p.I671M	ENST00000335508	NM_012433.2	671	atA/atG	14/25	1	2	FACETS	0.856	0.787	0.927	0.856	0.787	0.927	CLONAL	1	TRUE	1	0.51	2		524	747	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215609826	215609826	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782252	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	121	423	0	ENST00000260947.4:c.1868G>A	p.Gly623Glu	p.G623E	ENST00000260947	NM_000465.2	623	gGg/gAg	9/11	1	2	FACETS	0.88	0.799	0.966	0.88	0.799	0.966	CLONAL	1	TRUE	1	0.51	2		423	539	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023540	31023540	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	148	485	0	ENST00000375687.4:c.3025C>A	p.Leu1009Ile	p.L1009I	ENST00000375687	NM_015338.5	1009	Ctc/Atc	13/13	1	2	FACETS	0.854	0.781	0.929	0.854	0.781	0.929	CLONAL	1	TRUE	1	0.51	2		485	680	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920292	1920292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528156709	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	228	573	0	ENST00000382891.5:c.1352G>A	p.Ser451Asn	p.S451N	ENST00000382891	NM_133335.3	451	aGc/aAc	5/22	0.3	2	FACETS	0.997	0.93	1			1	INDETERMINATE	1	TRUE	NA	0.51	2		573	897	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131972860	131972860	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782637	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	146	371	0	ENST00000265335.6:c.3443G>A	p.Arg1148His	p.R1148H	ENST00000265335		1148	cGt/cAt	22/25	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.51	2		371	572	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505091	149505091	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	192	578	0	ENST00000261799.4:c.1724A>G	p.Asp575Gly	p.D575G	ENST00000261799	NM_002609.3	575	gAc/gGc	12/23	1	2	FACETS	0.934	0.866	1	0.934	0.866	1	CLONAL	1	TRUE	1	0.51	2		578	806	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057579	180057579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760182219	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	201	619	0	ENST00000261937.6:c.376G>A	p.Ala126Thr	p.A126T	ENST00000261937	NM_182925.4	126	Gcc/Acc	3/30	1	2	FACETS	0.952	0.884	1	0.952	0.884	1	CLONAL	1	TRUE	1	0.51	2		619	828	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020720	26020720	+	start_lost	Translation_Start_Site	SNP	G	G	T	rs768998955	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	81	294	0	ENST00000357647.3:c.3G>T	p.Met1?	p.M1?	ENST00000357647	NM_003529.2	1	atG/atT	1/1	1	2	FACETS	0.744	0.658	0.835	0.744	0.658	0.835	SUBCLONAL	1	TRUE	1	0.51	2		294	427	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372418	55372418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	223	527	0	ENST00000297316.4:c.1108G>A	p.Val370Met	p.V370M	ENST00000297316	NM_022454.3	370	Gtg/Atg	2/2	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.51	2		527	854	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212762	27212762	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906745	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	217	637	0	ENST00000380036.4:c.2744G>A	p.Arg915His	p.R915H	ENST00000380036	NM_000459.3	915	cGc/cAc	17/23	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.51	2		637	845	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639866	93639866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	89	250	0	ENST00000375746.1:c.1195G>A	p.Val399Met	p.V399M	ENST00000375746	NM_001174167.1	399	Gtg/Atg	10/14	1	2	FACETS	0.801	0.713	0.893	0.801	0.713	0.893	CLONAL	1	TRUE	1	0.51	2		250	436	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0051626-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	88	571	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.859	0.768	0.954	0.859	0.768	0.954	CLONAL	1	TRUE	1	0.619185982121758	2		571	331	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533661	41533661	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs142823793	NA	P-0051626-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	100	534	0	ENST00000263253.7:c.1627A>G	p.Met543Val	p.M543V	ENST00000263253	NM_001429.3	543	Atg/Gtg	8/31	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.619185982121758	2		534	313	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3929881	3929881	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587783484	NA	P-0051626-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	162	798	0	ENST00000262367.5:c.37A>G	p.Lys13Glu	p.K13E	ENST00000262367	NM_004380.2	13	Aaa/Gaa	1/31	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.619185982121758	2		798	421	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533656	41533656	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0051626-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	94	506	0	ENST00000263253.7:c.1623-1G>T		p.X541_splice	ENST00000263253	NM_001429.3	541			1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.619185982121758	2		506	291	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69027999	69027999	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051626-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	60	351	0	ENST00000288368.4:c.3158C>A	p.Ser1053Ter	p.S1053*	ENST00000288368	NM_024870.2	1053	tCa/tAa	26/40	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.619185982121758	2		351	170	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390628	139390628	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051626-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	202	1282	0	ENST00000277541.6:c.7563del	p.Ser2522AlafsTer67	p.S2522Afs*67	ENST00000277541	NM_017617.3	2521	tcC/tc	34/34	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.619185982121758	2		1282	586	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397632	139397633	+	splice_donor_variant	Splice_Site	INS	-	-	CTCTGCACGGCCTCGATCTTGTAGGGGATGTTGAGGCTG	novel	NA	P-0051626-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	113	1161	0	ENST00000277541.6:c.5130_5167+1dup		p.X1710_splice	ENST00000277541	NM_017617.3	1710			1	2	FACETS	0.55	0.495	0.607	0.55	0.495	0.607	SUBCLONAL	1	TRUE	1	0.619185982121758	2		1161	664	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	160	536	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	0.923	0.846	1	0.923	0.846	1	CLONAL	1	TRUE	1	0.412950475476611	2		536	840	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	207	1025	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.412950475476611	2		1026	936	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	229	803	1	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.412950475476611	2		804	1099	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612028	189612028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs900140738	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	158	426	2	ENST00000264731.3:c.1780C>T	p.Arg594Ter	p.R594*	ENST00000264731	NM_003722.4	594	Cga/Tga	14/14	0.402019098989049	3	FACETS	1	0.948	1	0.523	0.479	0.569	CLONAL	1	TRUE	1	0.412950475476611	3		428	882	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163297332	163297332	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1292835761	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	153	440	1	ENST00000271452.3:c.178C>T	p.Arg60Ter	p.R60*	ENST00000271452	NM_145697.2	60	Cga/Tga	3/14	1	2	FACETS	0.989	0.907	1	0.989	0.907	1	CLONAL	1	TRUE	1	0.412950475476611	2		441	749	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685303	89685303	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	86	253	0	ENST00000371953.3:c.198G>T	p.Lys66Asn	p.K66N	ENST00000371953	NM_000314.4	66	aaG/aaT	3/9	1	2	FACETS	0.848	0.753	0.95	0.848	0.753	0.95	CLONAL	1	TRUE	1	0.412950475476611	2		253	491	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630410	187630410	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758938184	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	221	627	1	ENST00000441802.2:c.572G>A	p.Arg191Gln	p.R191Q	ENST00000441802	NM_005245.3	191	cGa/cAa	2/27	1	2	FACETS	0.983	0.914	1	0.983	0.914	1	CLONAL	1	TRUE	1	0.412950475476611	2		628	1089	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941842	44941842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	171	351	0	ENST00000377967.4:c.3166C>A	p.His1056Asn	p.H1056N	ENST00000377967	NM_021140.2	1056	Cat/Aat	21/29	0.41295152558514	3	FACETS	1	0.961	1	0.537	0.494	0.582	CLONAL	1	TRUE	1	0.412950475476611	3		351	930	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	107	422	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	1	2	FACETS	0.939	0.845	1	0.939	0.845	1	CLONAL	1	TRUE	1	0.412950475476611	2		422	552	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915943	127915943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781486938	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	79	443	0	ENST00000373547.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000373547	NM_002721.4	180	Gaa/Aaa	6/7	1	2	FACETS	0.419	0.368	0.475	0.419	0.368	0.475	SUBCLONAL	1	TRUE	1	0.412950475476611	2		443	913	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92404119	92404119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761377867	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	149	350	0	ENST00000265734.4:c.260G>A	p.Arg87Gln	p.R87Q	ENST00000265734	NM_001259.6	87	cGa/cAa	3/8	1	2	FACETS	0.966	0.884	1	0.966	0.884	1	CLONAL	1	TRUE	1	0.412950475476611	2		350	747	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989562	85989562	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs767548896	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	55	337	0	ENST00000263360.6:c.1321C>T	p.Arg441Ter	p.R441*	ENST00000263360	NM_003797.3	441	Cga/Tga	12/12	1	2	FACETS	0.418	0.357	0.484	0.418	0.357	0.484	SUBCLONAL	1	TRUE	1	0.412950475476611	2		337	638	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56409145	56409145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1308397244	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	59	367	0	ENST00000348428.3:c.1652G>A	p.Arg551Gln	p.R551Q	ENST00000348428	NM_006785.3	551	cGa/cAa	14/17	0.412950475476611	2	FACETS	0.43	0.369	0.496	0.215	0.184	0.248	SUBCLONAL	1	TRUE	0	0.412950475476611	2		367	665	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001395	150001395	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	162	524	1	ENST00000253339.5:c.2209C>T	p.Arg737Ter	p.R737*	ENST00000253339		737	Cga/Tga	4/7	1	2	FACETS	0.949	0.871	1	0.949	0.871	1	CLONAL	1	TRUE	1	0.412950475476611	2		525	827	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871034	12871034	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	141	375	0	ENST00000228872.4:c.261C>A	p.Phe87Leu	p.F87L	ENST00000228872	NM_004064.3	87	ttC/ttA	1/3	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.412950475476611	2		375	624	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	91	241	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.412950475476611	2		241	400	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440855	52440855	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553645702	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	195	564	1	ENST00000460680.1:c.649G>A	p.Ala217Thr	p.A217T	ENST00000460680	NM_004656.3	217	Gcc/Acc	8/17	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.412950475476611	2		565	927	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891035	112891035	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs755619262	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	152	318	0	ENST00000351677.2:c.369G>T	p.Glu123Asp	p.E123D	ENST00000351677	NM_002834.3	123	gaG/gaT	4/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.412950475476611	2		318	666	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913371	28913371	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	69	588	0	ENST00000282397.4:c.2422G>T	p.Glu808Ter	p.E808*	ENST00000282397	NM_002019.4	808	Gag/Tag	17/30	1	2	FACETS	0.328	0.284	0.375	0.328	0.284	0.375	SUBCLONAL	1	TRUE	1	0.412950475476611	2		588	1020	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97897674	97897674	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	186	427	0	ENST00000289081.3:c.797G>T	p.Arg266Ile	p.R266I	ENST00000289081	NM_000136.2	266	aGa/aTa	8/15	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.412950475476611	2		427	869	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727483	66727483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504317	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	166	472	0	ENST00000307102.5:c.199G>A	p.Asp67Asn	p.D67N	ENST00000307102	NM_002755.3	67	Gac/Aac	2/11	1	2	FACETS	0.972	0.894	1	0.972	0.894	1	CLONAL	1	TRUE	1	0.412950475476611	2		472	827	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579395	7579395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	153	684	1	ENST00000269305.4:c.292C>T	p.Pro98Ser	p.P98S	ENST00000269305	NM_001126112.2	98	Cct/Tct	4/11	1	2	FACETS	0.745	0.681	0.812	0.745	0.681	0.812	SUBCLONAL	1	TRUE	1	0.412950475476611	2		685	995	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254906	16254906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	195	457	0	ENST00000375759.3:c.2171G>A	p.Arg724Gln	p.R724Q	ENST00000375759	NM_015001.2	724	cGa/cAa	11/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.412950475476611	2		457	854	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172385	108172385	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764389018	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	124	352	0	ENST00000278616.4:c.5188C>T	p.Arg1730Ter	p.R1730*	ENST00000278616	NM_000051.3	1730	Cga/Tga	35/63	1	2	FACETS	0.972	0.882	1	0.972	0.882	1	CLONAL	1	TRUE	1	0.412950475476611	2		352	618	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430873	181430873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	218	754	0	ENST00000325404.1:c.725C>T	p.Ser242Leu	p.S242L	ENST00000325404	NM_003106.3	242	tCg/tTg	1/1	0.402019098989049	3	FACETS	0.964	0.894	1	0.482	0.447	0.518	CLONAL	1	TRUE	1	0.412950475476611	3		754	1322	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712580	52712580	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	117	440	1	ENST00000394830.3:c.172C>T	p.Arg58Ter	p.R58*	ENST00000394830	NM_018313.4	58	Cga/Tga	3/30	1	2	FACETS	0.715	0.644	0.789	0.715	0.644	0.789	SUBCLONAL	1	TRUE	1	0.412950475476611	2		441	793	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374881	45374881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	395	467	1	ENST00000262160.6:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000262160	NM_005901.5	321	cGa/cAa	8/11	0.412950475476611	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.412950475476611	2		468	898	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588981	67588981	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	36	251	1	ENST00000274335.5:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000274335		358	Cga/Tga	8/15	1	2	FACETS	0.373	0.306	0.447	0.373	0.306	0.447	SUBCLONAL	1	TRUE	1	0.412950475476611	2		252	468	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270180	66270180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763063348	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	109	273	0	ENST00000273854.3:c.1702G>A	p.Asp568Asn	p.D568N	ENST00000273854	NM_004439.5	568	Gat/Aat	8/18	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.412950475476611	2		273	512	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582108	52582108	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775162970	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	33	291	1	ENST00000394830.3:c.4720C>T	p.Arg1574Cys	p.R1574C	ENST00000394830	NM_018313.4	1574	Cgc/Tgc	30/30	1	2	FACETS	0.284	0.23	0.344	0.284	0.23	0.344	SUBCLONAL	1	TRUE	1	0.412950475476611	2		292	563	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593519	48593519	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	89	233	0	ENST00000342988.3:c.1270G>T	p.Asp424Tyr	p.D424Y	ENST00000342988	NM_005359.5	424	Gat/Tat	10/12	0.412950475476611	2	FACETS	0.919	0.818	1	0.46	0.409	0.513	CLONAL	1	TRUE	0	0.412950475476611	2		233	469	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	134	312	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.412950475476611	2		312	610	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115600	108115600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772821016	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	164	450	0	ENST00000278616.4:c.748C>T	p.Arg250Ter	p.R250*	ENST00000278616	NM_000051.3	250	Cga/Tga	7/63	1	2	FACETS	0.976	0.897	1	0.976	0.897	1	CLONAL	1	TRUE	1	0.412950475476611	2		450	814	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	461474	461474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770858476	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	202	425	1	ENST00000399788.2:c.1046G>A	p.Arg349Gln	p.R349Q	ENST00000399788	NM_001042603.1	349	cGa/cAa	9/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.412950475476611	2		426	887	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61720166	61720166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1194061733	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	162	363	0	ENST00000401558.2:c.1268G>A	p.Arg423Gln	p.R423Q	ENST00000401558	NM_003400.3	423	cGa/cAa	13/25	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.412950475476611	2		363	775	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245825	41245825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397508902	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	218	555	1	ENST00000357654.3:c.1723G>A	p.Glu575Lys	p.E575K	ENST00000357654	NM_007294.3	575	Gaa/Aaa	10/23	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.412950475476611	2		556	963	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884908	134884908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202034365	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	113	477	1	ENST00000398015.3:c.1684G>A	p.Val562Ile	p.V562I	ENST00000398015	NM_004441.4	562	Gtc/Atc	8/16	1	2	FACETS	0.733	0.659	0.81	0.733	0.659	0.81	SUBCLONAL	1	TRUE	1	0.412950475476611	2		478	747	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357745	70357745	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	48	700	0	ENST00000374080.3:c.5996T>C	p.Val1999Ala	p.V1999A	ENST00000374080		1999	gTg/gCg	41/45	0.41295152558514	1	FACETS	0.201	0.169	0.236	0.201	0.169	0.236	SUBCLONAL	1	TRUE	0	0.412950475476611	1		700	918	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637690	52637690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239654517	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	202	503	0	ENST00000394830.3:c.2626C>T	p.Arg876Cys	p.R876C	ENST00000394830	NM_018313.4	876	Cgt/Tgt	18/30	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.412950475476611	2		503	976	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610695	52610695	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	137	338	0	ENST00000394830.3:c.3478C>T	p.Arg1160Ter	p.R1160*	ENST00000394830	NM_018313.4	1160	Cga/Tga	23/30	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.412950475476611	2		338	640	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482242	87482242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	213	564	0	ENST00000277120.3:c.1529C>T	p.Ser510Leu	p.S510L	ENST00000277120		510	tCg/tTg	14/19	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.412950475476611	2		564	1006	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148513849	148513849	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	154	412	0	ENST00000320356.2:c.1432G>T	p.Glu478Ter	p.E478*	ENST00000320356	NM_004456.4	478	Gaa/Taa	12/20	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.412950475476611	2		412	746	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480495	57480495	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1422801076	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	108	316	0	ENST00000371085.3:c.490G>A	p.Glu164Lys	p.E164K	ENST00000371085	NM_000516.4	164	Gaa/Aaa	6/13	1	2	FACETS	0.873	0.786	0.966	0.873	0.786	0.966	CLONAL	1	TRUE	1	0.412950475476611	2		316	599	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212008	5212008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753640223	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	180	549	1	ENST00000357368.4:c.5023G>A	p.Glu1675Lys	p.E1675K	ENST00000357368	NM_002850.3	1675	Gaa/Aaa	32/38	1	2	FACETS	0.994	0.917	1	0.994	0.917	1	CLONAL	1	TRUE	1	0.412950475476611	2		550	877	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685268	89685268	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	87	198	0	ENST00000371953.3:c.165-2A>C		p.X55_splice	ENST00000371953	NM_000314.4	55			1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.412950475476611	2		198	417	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718123	117718123	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	154	589	1	ENST00000368508.3:c.734G>T	p.Arg245Ile	p.R245I	ENST00000368508	NM_002944.2	245	aGa/aTa	7/43	1	2	FACETS	0.84	0.769	0.915	0.84	0.769	0.915	CLONAL	1	TRUE	1	0.412950475476611	2		590	888	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710666	114710666	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	141	447	0	ENST00000543371.1:c.151G>T	p.Glu51Ter	p.E51*	ENST00000543371	NM_001198531.1	51	Gaa/Taa	1/14	1	2	FACETS	0.955	0.872	1	0.955	0.872	1	CLONAL	1	TRUE	1	0.412950475476611	2		447	715	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961109	55961109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374755237	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	167	440	0	ENST00000263923.4:c.2831G>A	p.Arg944Gln	p.R944Q	ENST00000263923	NM_002253.2	944	cGa/cAa	21/30	1	2	FACETS	0.92	0.846	0.998	0.92	0.846	0.998	CLONAL	1	TRUE	1	0.412950475476611	2		440	879	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857436	9857436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	52	464	0	ENST00000330684.3:c.3965G>A	p.Gly1322Glu	p.G1322E	ENST00000330684	NM_001134407.1	1322	gGa/gAa	13/13	1	2	FACETS	0.36	0.306	0.42	0.36	0.306	0.42	SUBCLONAL	1	TRUE	1	0.412950475476611	2		464	699	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201885	152201885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778449608	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	120	296	1	ENST00000206249.3:c.739G>A	p.Glu247Lys	p.E247K	ENST00000206249	NM_000125.3	247	Gaa/Aaa	3/8	1	2	FACETS	0.959	0.869	1	0.959	0.869	1	CLONAL	1	TRUE	1	0.412950475476611	2		297	606	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021441	42021441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	180	496	1	ENST00000219905.7:c.3737G>A	p.Arg1246Gln	p.R1246Q	ENST00000219905	NM_001164273.1	1246	cGa/cAa	11/24	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.412950475476611	2		497	860	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030396	49030396	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	143	365	0	ENST00000267163.4:c.1871C>A	p.Ser624Tyr	p.S624Y	ENST00000267163	NM_000321.2	624	tCt/tAt	19/27	1	2	FACETS	0.977	0.892	1	0.977	0.892	1	CLONAL	1	TRUE	1	0.412950475476611	2		365	709	SUCCESS
APC	324	MSKCC	GRCh37	5	112154954	112154954	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	56	531	1	ENST00000257430.4:c.1225C>A	p.Leu409Ile	p.L409I	ENST00000257430	NM_000038.5	409	Ctt/Att	10/16	1	2	FACETS	0.282	0.24	0.328	0.282	0.24	0.328	SUBCLONAL	1	TRUE	1	0.412950475476611	2		532	962	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136805	55136805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41279521	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	140	331	0	ENST00000257290.5:c.1127G>A	p.Arg376Gln	p.R376Q	ENST00000257290	NM_006206.4	376	cGa/cAa	8/23	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.412950475476611	2		331	636	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197747	66197747	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	165	357	0	ENST00000273854.3:c.2952G>T	p.Glu984Asp	p.E984D	ENST00000273854	NM_004439.5	984	gaG/gaT	17/18	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.412950475476611	2		357	715	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618727	37618727	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	172	499	0	ENST00000447079.4:c.403G>T	p.Glu135Ter	p.E135*	ENST00000447079	NM_015083.1	135	Gaa/Taa	1/14	1	2	FACETS	0.981	0.904	1	0.981	0.904	1	CLONAL	1	TRUE	1	0.412950475476611	2		499	849	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397767	49397767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	234	493	1	ENST00000418115.1:c.457G>A	p.Ala153Thr	p.A153T	ENST00000418115	NM_001664.2	153	Gct/Act	5/5	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.412950475476611	2		494	1065	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116173	209116173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781398075	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	116	353	0	ENST00000345146.2:c.103G>A	p.Val35Met	p.V35M	ENST00000345146	NM_005896.2	35	Gtg/Atg	3/10	1	2	FACETS	0.905	0.817	0.997	0.905	0.817	0.997	CLONAL	1	TRUE	1	0.412950475476611	2		353	621	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005327	29005327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759189221	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	143	462	0	ENST00000282397.4:c.934C>T	p.Arg312Cys	p.R312C	ENST00000282397	NM_002019.4	312	Cgt/Tgt	7/30	1	2	FACETS	0.855	0.78	0.934	0.855	0.78	0.934	CLONAL	1	TRUE	1	0.412950475476611	2		462	810	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267784	46267784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753240956	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	231	523	0	ENST00000371998.3:c.2545C>T	p.Arg849Cys	p.R849C	ENST00000371998		849	Cgt/Tgt	14/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.412950475476611	2		523	1012	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210506	5210506	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	191	563	0	ENST00000357368.4:c.5461C>T	p.Arg1821Ter	p.R1821*	ENST00000357368	NM_002850.3	1821	Cga/Tga	35/38	1	2	FACETS	0.965	0.892	1	0.965	0.892	1	CLONAL	1	TRUE	1	0.412950475476611	2		563	959	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952013	178952013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	49	392	0	ENST00000263967.3:c.3068G>A	p.Arg1023Gln	p.R1023Q	ENST00000263967	NM_006218.2	1023	cGa/cAa	21/21	0.402019098989049	3	FACETS	0.359	0.303	0.421	0.18	0.151	0.211	SUBCLONAL	1	TRUE	1	0.412950475476611	3		392	797	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672787	86672787	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	138	300	1	ENST00000274376.6:c.2274G>T	p.Arg758Ser	p.R758S	ENST00000274376	NM_002890.2	758	agG/agT	17/25	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.412950475476611	2		301	594	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864328	57864328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201538749	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	216	559	1	ENST00000228682.2:c.1805C>T	p.Ser602Leu	p.S602L	ENST00000228682	NM_005269.2	602	tCg/tTg	12/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.412950475476611	2		560	907	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046638	30046638	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1419328188	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	150	490	0	ENST00000331968.5:c.2545C>T	p.Arg849Ter	p.R849*	ENST00000331968	NM_002742.2	849	Cga/Tga	18/18	1	2	FACETS	0.941	0.861	1	0.941	0.861	1	CLONAL	1	TRUE	1	0.412950475476611	2		490	772	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724723	112724723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	133	429	0	ENST00000369452.4:c.607C>T	p.Arg203Cys	p.R203C	ENST00000369452	NM_007373.3	203	Cgt/Tgt	2/9	1	2	FACETS	0.816	0.742	0.895	0.816	0.742	0.895	CLONAL	1	TRUE	1	0.412950475476611	2		429	789	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260151	149260151	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1307297959	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	149	458	0	ENST00000360632.3:c.742C>T	p.Arg248Ter	p.R248*	ENST00000360632	NM_015472.4	248	Cga/Tga	4/7	1	2	FACETS	0.95	0.869	1	0.95	0.869	1	CLONAL	1	TRUE	1	0.412950475476611	2		458	760	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723053	49723053	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	56	161	2	ENST00000449682.2:c.1363G>A	p.Asp455Asn	p.D455N	ENST00000449682	NM_020998.3	455	Gac/Aac	11/18	1	2	FACETS	0.923	0.796	1	0.923	0.796	1	CLONAL	1	TRUE	1	0.412950475476611	2		163	294	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251901	153251901	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	166	365	0	ENST00000281708.4:c.1105G>T	p.Glu369Ter	p.E369*	ENST00000281708	NM_033632.3	369	Gaa/Taa	7/12	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.412950475476611	2		365	757	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028136	48028136	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782324	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	124	352	0	ENST00000234420.5:c.3014G>A	p.Arg1005Gln	p.R1005Q	ENST00000234420	NM_000179.2	1005	cGa/cAa	4/10	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.412950475476611	2		352	578	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161750	56161750	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	182	507	0	ENST00000399503.3:c.1247C>A	p.Ser416Ter	p.S416*	ENST00000399503	NM_005921.1	416	tCa/tAa	6/20	1	2	FACETS	0.96	0.886	1	0.96	0.886	1	CLONAL	1	TRUE	1	0.412950475476611	2		507	918	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727811	41727811	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779440422	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	236	721	1	ENST00000301178.4:c.436G>A	p.Glu146Lys	p.E146K	ENST00000301178	NM_021913.4	146	Gaa/Aaa	4/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.412950475476611	2		722	1138	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999588	100999588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868064003	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	254	817	1	ENST00000325455.5:c.214G>A	p.Glu72Lys	p.E72K	ENST00000325455	NM_001202474.3	72	Gaa/Aaa	1/8	1	2	FACETS	0.989	0.924	1	0.989	0.924	1	CLONAL	1	TRUE	1	0.412950475476611	2		818	1244	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772345	56772345	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1567785872	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	163	440	1	ENST00000337432.4:c.199G>T	p.Glu67Ter	p.E67*	ENST00000337432	NM_058216.2	67	Gaa/Taa	2/9	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.412950475476611	2		441	781	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851828	63851828	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs201944744	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	222	612	0	ENST00000279873.7:c.2606C>A	p.Ser869Tyr	p.S869Y	ENST00000279873	NM_032199.2	869	tCt/tAt	10/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.412950475476611	2		612	956	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720822	89720822	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	100	290	0	ENST00000371953.3:c.973C>A	p.Leu325Ile	p.L325I	ENST00000371953	NM_000314.4	325	Ctt/Att	8/9	1	2	FACETS	0.959	0.86	1	0.959	0.86	1	CLONAL	1	TRUE	1	0.412950475476611	2		290	505	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528631	89528631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	81	235	0	ENST00000336596.2:c.2931G>T	p.Lys977Asn	p.K977N	ENST00000336596	NM_005233.5	977	aaG/aaT	17/17	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.412950475476611	2		235	367	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513165	106513165	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs778461029	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	32	266	0	ENST00000359195.3:c.2069G>T	p.Arg690Ile	p.R690I	ENST00000359195	NM_002649.2	690	aGa/aTa	4/11	1	2	FACETS	0.333	0.27	0.405	0.333	0.27	0.405	SUBCLONAL	1	TRUE	1	0.412950475476611	2		266	465	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47004894	47004894	+	intron_variant	Intron	SNP	G	G	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	203	499	1	ENST00000377604.3:c.-126+10G>A		p.*42*	ENST00000377604	NM_001204468.1	-/163			0.41295152558514	3	FACETS	1	0.98	1	0.58	0.538	0.625	CLONAL	1	TRUE	1	0.412950475476611	3		500	1022	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242692	16242692	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	191	528	0	ENST00000375759.3:c.1313G>T	p.Arg438Ile	p.R438I	ENST00000375759	NM_015001.2	438	aGa/aTa	6/15	1	2	FACETS	0.938	0.867	1	0.938	0.867	1	CLONAL	1	TRUE	1	0.412950475476611	2		528	986	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288236	33288236	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	203	498	0	ENST00000374542.5:c.1172G>T	p.Arg391Ile	p.R391I	ENST00000374542	NM_001141970.1	391	aGa/aTa	4/8	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.412950475476611	2		498	814	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673442	30673442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758105701	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	217	633	0	ENST00000376406.3:c.3518C>T	p.Ser1173Phe	p.S1173F	ENST00000376406	NM_014641.2	1173	tCc/tTc	10/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.412950475476611	2		633	998	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522657	67522657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	114	286	0	ENST00000274335.5:c.154G>T	p.Glu52Ter	p.E52*	ENST00000274335		52	Gaa/Taa	1/15	1	2	FACETS	0.944	0.852	1	0.944	0.852	1	CLONAL	1	TRUE	1	0.412950475476611	2		286	585	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356241	66356241	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	72	479	1	ENST00000273854.3:c.1256G>T	p.Ser419Ile	p.S419I	ENST00000273854	NM_004439.5	419	aGc/aTc	5/18	1	2	FACETS	0.381	0.332	0.434	0.381	0.332	0.434	SUBCLONAL	1	TRUE	1	0.412950475476611	2		480	916	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31020765	31020765	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	57	251	0	ENST00000375687.4:c.1062C>A	p.Phe354Leu	p.F354L	ENST00000375687	NM_015338.5	354	ttC/ttA	11/13	1	2	FACETS	0.524	0.45	0.605	0.524	0.45	0.605	SUBCLONAL	1	TRUE	1	0.412950475476611	2		251	527	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219468	133219468	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768741587	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	234	706	0	ENST00000320574.5:c.4666C>T	p.Arg1556Trp	p.R1556W	ENST00000320574	NM_006231.2	1556	Cgg/Tgg	36/49	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.412950475476611	2		706	1089	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910721	29910721	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1389	143	1011	0	ENST00000376809.5:c.261G>T	p.Glu87Asp	p.E87D	ENST00000376809	NM_002116.7	87	gaG/gaT	2/8	1	2	FACETS	0.452	0.41	0.496	0.452	0.41	0.496	SUBCLONAL	1	TRUE	1	0.412950475476611	2		1011	1532	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025841	48025841	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542848931	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	119	277	0	ENST00000234420.5:c.719G>A	p.Arg240Gln	p.R240Q	ENST00000234420	NM_000179.2	240	cGa/cAa	4/10	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.412950475476611	2		277	530	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038531	47038531	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	428	638	0	ENST00000377604.3:c.693G>T	p.Glu231Asp	p.E231D	ENST00000377604	NM_001204468.1	231	gaG/gaT	8/24	0.41295152558514	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.412950475476611	3		638	1197	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285495	38285495	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223331	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	206	563	0	ENST00000425967.3:c.658C>T	p.Arg220Cys	p.R220C	ENST00000425967	NM_001174067.1	220	Cgc/Tgc	6/19	1	2	FACETS	0.984	0.913	1	0.984	0.913	1	CLONAL	1	TRUE	1	0.412950475476611	2		563	1014	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952012	178952012	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	141	398	0	ENST00000263967.3:c.3067C>T	p.Arg1023Ter	p.R1023*	ENST00000263967	NM_006218.2	1023	Cga/Tga	21/21	0.402019098989049	3	FACETS	1	0.939	1	0.519	0.473	0.567	CLONAL	1	TRUE	1	0.412950475476611	3		398	794	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510782	157510782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1321954955	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	161	426	0	ENST00000346085.5:c.3557C>T	p.Ser1186Leu	p.S1186L	ENST00000346085	NM_020732.3	1186	tCg/tTg	14/20	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.412950475476611	2		426	778	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59871053	59871053	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	143	347	0	ENST00000259008.2:c.1378G>T	p.Asp460Tyr	p.D460Y	ENST00000259008	NM_032043.2	460	Gat/Tat	10/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.412950475476611	2		347	656	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166202	118166202	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	150	343	0	ENST00000369448.3:c.712G>T	p.Glu238Ter	p.E238*	ENST00000369448	NM_017709.3	238	Gaa/Taa	2/2	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.412950475476611	2		343	624	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128849185	128849185	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	90	584	0	ENST00000249373.3:c.1413C>A	p.Phe471Leu	p.F471L	ENST00000249373	NM_005631.4	471	ttC/ttA	8/12	1	2	FACETS	0.425	0.376	0.478	0.425	0.376	0.478	SUBCLONAL	1	TRUE	1	0.412950475476611	2		584	1025	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066846	30066846	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758982696	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	66	501	1	ENST00000331968.5:c.2285G>A	p.Arg762His	p.R762H	ENST00000331968	NM_002742.2	762	cGc/cAc	16/18	1	2	FACETS	0.403	0.349	0.462	0.403	0.349	0.462	SUBCLONAL	1	TRUE	1	0.412950475476611	2		502	793	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131972851	131972851	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	166	362	0	ENST00000265335.6:c.3434A>C	p.Lys1145Thr	p.K1145T	ENST00000265335		1145	aAa/aCa	22/25	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.412950475476611	2		362	708	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657596	37657596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748453656	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	251	551	2	ENST00000447079.4:c.2513C>T	p.Ser838Leu	p.S838L	ENST00000447079	NM_015083.1	838	tCg/tTg	6/14	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.412950475476611	2		553	1037	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827733	72827733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1362078452	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	194	508	0	ENST00000268489.5:c.8848C>T	p.Arg2950Cys	p.R2950C	ENST00000268489	NM_006885.3	2950	Cgc/Tgc	9/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.412950475476611	2		508	831	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919074	50919074	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	187	519	0	ENST00000440232.2:c.2811G>T	p.Met937Ile	p.M937I	ENST00000440232	NM_002691.3	937	atG/atT	22/27	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.412950475476611	2		519	901	SUCCESS
APC	324	MSKCC	GRCh37	5	112176882	112176882	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	133	406	0	ENST00000257430.4:c.5591C>A	p.Ser1864Tyr	p.S1864Y	ENST00000257430	NM_000038.5	1864	tCt/tAt	16/16	1	2	FACETS	0.951	0.866	1	0.951	0.866	1	CLONAL	1	TRUE	1	0.412950475476611	2		406	677	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229562	98229562	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	74	411	0	ENST00000331920.6:c.2396C>A	p.Ser799Tyr	p.S799Y	ENST00000331920	NM_000264.3	799	tCt/tAt	15/24	1	2	FACETS	0.502	0.439	0.57	0.502	0.439	0.57	SUBCLONAL	1	TRUE	1	0.412950475476611	2		411	714	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143240	30143240	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057065255	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	101	572	0	ENST00000389048.3:c.286G>A	p.Ala96Thr	p.A96T	ENST00000389048	NM_004304.4	96	Gcc/Acc	1/29	1	2	FACETS	0.548	0.489	0.611	0.548	0.489	0.611	SUBCLONAL	1	TRUE	1	0.412950475476611	2		572	892	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258874	16258874	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	257	575	2	ENST00000375759.3:c.6139G>T	p.Asp2047Tyr	p.D2047Y	ENST00000375759	NM_015001.2	2047	Gat/Tat	11/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.412950475476611	2		577	1062	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088693	27088693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767536659	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	231	661	1	ENST00000324856.7:c.2302G>A	p.Gly768Ser	p.G768S	ENST00000324856	NM_006015.4	768	Ggc/Agc	7/20	1	2	FACETS	0.977	0.91	1	0.977	0.91	1	CLONAL	1	TRUE	1	0.412950475476611	2		662	1145	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937177	36937177	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	69	661	0	ENST00000361632.4:c.1142C>A	p.Ala381Asp	p.A381D	ENST00000361632		381	gCt/gAt	9/16	1	2	FACETS	0.307	0.266	0.351	0.307	0.266	0.351	SUBCLONAL	1	TRUE	1	0.412950475476611	2		661	1089	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363096	40363096	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775863077	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	176	510	0	ENST00000397332.2:c.1133G>A	p.Arg378Gln	p.R378Q	ENST00000397332	NM_001033082.2	378	cGa/cAa	3/3	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.412950475476611	2		510	798	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339132	65339132	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	168	410	0	ENST00000342505.4:c.404A>C	p.Lys135Thr	p.K135T	ENST00000342505	NM_002227.2	135	aAa/aCa	5/25	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.412950475476611	2		410	747	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226551698	226551698	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	82	491	0	ENST00000366794.5:c.2732C>A	p.Ser911Tyr	p.S911Y	ENST00000366794	NM_001618.3	911	tCt/tAt	20/23	1	2	FACETS	0.471	0.414	0.531	0.471	0.414	0.531	SUBCLONAL	1	TRUE	1	0.412950475476611	2		491	844	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226576406	226576406	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs756906729	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	206	439	0	ENST00000366794.5:c.668A>C	p.Lys223Thr	p.K223T	ENST00000366794	NM_001618.3	223	aAa/aCa	5/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.412950475476611	2		439	860	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100271	8100271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	192	561	0	ENST00000346208.3:c.245G>A	p.Ser82Asn	p.S82N	ENST00000346208		82	aGc/aAc	3/6	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.412950475476611	2		561	825	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601837	43601837	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	64	485	0	ENST00000355710.3:c.881C>A	p.Ala294Asp	p.A294D	ENST00000355710	NM_020975.4	294	gCc/gAc	5/20	1	2	FACETS	0.422	0.364	0.484	0.422	0.364	0.484	SUBCLONAL	1	TRUE	1	0.412950475476611	2		485	735	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405313	70405313	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	178	501	1	ENST00000373644.4:c.2827G>T	p.Asp943Tyr	p.D943Y	ENST00000373644	NM_030625.2	943	Gac/Tac	4/12	1	2	FACETS	0.973	0.897	1	0.973	0.897	1	CLONAL	1	TRUE	1	0.412950475476611	2		502	886	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446144	70446144	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	145	428	0	ENST00000373644.4:c.5084C>A	p.Ser1695Tyr	p.S1695Y	ENST00000373644	NM_030625.2	1695	tCt/tAt	11/12	1	2	FACETS	0.982	0.898	1	0.982	0.898	1	CLONAL	1	TRUE	1	0.412950475476611	2		428	715	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274702	123274702	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	95	557	0	ENST00000358487.5:c.1216A>G	p.Lys406Glu	p.K406E	ENST00000358487	NM_000141.4	406	Aag/Gag	9/18	1	2	FACETS	0.498	0.443	0.558	0.498	0.443	0.558	SUBCLONAL	1	TRUE	1	0.412950475476611	2		557	923	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8246251	8246251	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	129	386	0	ENST00000335790.3:c.383A>C	p.Lys128Thr	p.K128T	ENST00000335790	NM_002315.2	128	aAa/aCa	4/4	1	2	FACETS	0.891	0.809	0.977	0.891	0.809	0.977	CLONAL	1	TRUE	1	0.412950475476611	2		386	701	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103453	77103453	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	165	351	1	ENST00000356341.3:c.113C>A	p.Ser38Tyr	p.S38Y	ENST00000356341	NM_002576.4	38	tCt/tAt	2/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.412950475476611	2		352	740	SUCCESS
EED	8726	MSKCC	GRCh37	11	85961454	85961454	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	69	212	0	ENST00000263360.6:c.231A>C	p.Lys77Asn	p.K77N	ENST00000263360	NM_003797.3	77	aaA/aaC	2/12	1	2	FACETS	0.805	0.704	0.914	0.805	0.704	0.914	CLONAL	1	TRUE	1	0.412950475476611	2		212	415	SUCCESS
EED	8726	MSKCC	GRCh37	11	85963278	85963278	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	99	331	0	ENST00000263360.6:c.356A>G	p.Asn119Ser	p.N119S	ENST00000263360	NM_003797.3	119	aAc/aGc	3/12	1	2	FACETS	0.809	0.723	0.899	0.809	0.723	0.899	CLONAL	1	TRUE	1	0.412950475476611	2		331	593	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	459805	459805	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	225	580	1	ENST00000399788.2:c.1290G>T	p.Lys430Asn	p.K430N	ENST00000399788	NM_001042603.1	430	aaG/aaT	10/28	1	2	FACETS	0.959	0.893	1	0.959	0.893	1	CLONAL	1	TRUE	1	0.412950475476611	2		581	1136	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1039050	1039050	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	134	464	0	ENST00000358495.3:c.283T>G	p.Phe95Val	p.F95V	ENST00000358495	NM_134424.2	95	Ttt/Gtt	5/12	1	2	FACETS	0.845	0.768	0.926	0.845	0.768	0.926	CLONAL	1	TRUE	1	0.412950475476611	2		464	768	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435426	18435426	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	91	321	0	ENST00000266497.5:c.411T>A	p.Asp137Glu	p.D137E	ENST00000266497		137	gaT/gaA	1/31	1	2	FACETS	0.885	0.789	0.987	0.885	0.789	0.987	CLONAL	1	TRUE	1	0.412950475476611	2		321	498	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490288	56490288	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	94	255	0	ENST00000267101.3:c.2057G>A	p.Ser686Asn	p.S686N	ENST00000267101	NM_001982.3	686	aGc/aAc	18/28	1	2	FACETS	0.981	0.877	1	0.981	0.877	1	CLONAL	1	TRUE	1	0.412950475476611	2		255	464	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114276	115114276	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	159	430	0	ENST00000257566.3:c.942-1G>T		p.X314_splice	ENST00000257566	NM_016569.3	314			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.412950475476611	2		430	727	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794806	120794806	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	267	748	1	ENST00000257552.2:c.551C>T	p.Ala184Val	p.A184V	ENST00000257552	NM_002442.3	184	gCt/gTt	9/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.412950475476611	2		749	1192	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123875203	123875203	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	109	308	0	ENST00000330479.4:c.159G>T	p.Lys53Asn	p.K53N	ENST00000330479	NM_020382.3	53	aaG/aaT	3/9	1	2	FACETS	0.898	0.808	0.992	0.898	0.808	0.992	CLONAL	1	TRUE	1	0.412950475476611	2		308	588	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619920	21619920	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	144	529	0	ENST00000382592.4:c.246T>G	p.Tyr82Ter	p.Y82*	ENST00000382592	NM_014572.2	82	taT/taG	2/8	1	2	FACETS	0.82	0.747	0.895	0.82	0.747	0.895	CLONAL	1	TRUE	1	0.412950475476611	2		529	851	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959474	26959474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	115	308	0	ENST00000381527.3:c.641C>T	p.Ala214Val	p.A214V	ENST00000381527	NM_001260.1	214	gCt/gTt	6/13	1	2	FACETS	0.912	0.823	1	0.912	0.823	1	CLONAL	1	TRUE	1	0.412950475476611	2		308	611	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588623	28588623	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	84	467	0	ENST00000241453.7:c.2825T>G	p.Phe942Cys	p.F942C	ENST00000241453	NM_004119.2	942	tTt/tGt	23/24	1	2	FACETS	0.474	0.418	0.535	0.474	0.418	0.535	SUBCLONAL	1	TRUE	1	0.412950475476611	2		467	858	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893435	32893435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	110	269	0	ENST00000380152.3:c.289G>A	p.Glu97Lys	p.E97K	ENST00000380152		97	Gaa/Aaa	3/27	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.412950475476611	2		269	512	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900278	32900278	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	46	333	0	ENST00000380152.3:c.466G>T	p.Asp156Tyr	p.D156Y	ENST00000380152		156	Gat/Tat	5/27	1	2	FACETS	0.318	0.267	0.375	0.318	0.267	0.375	SUBCLONAL	1	TRUE	1	0.412950475476611	2		333	700	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912436	32912436	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	125	362	0	ENST00000380152.3:c.3944G>T	p.Arg1315Ile	p.R1315I	ENST00000380152		1315	aGa/aTa	11/27	1	2	FACETS	0.828	0.75	0.91	0.828	0.75	0.91	CLONAL	1	TRUE	1	0.412950475476611	2		362	731	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281068	49281068	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	201	623	2	ENST00000282018.3:c.115G>T	p.Glu39Ter	p.E39*	ENST00000282018	NM_020377.2	39	Gaa/Taa	1/1	1	2	FACETS	0.94	0.87	1	0.94	0.87	1	CLONAL	1	TRUE	1	0.412950475476611	2		625	1036	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007773	45007773	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	158	415	0	ENST00000558401.1:c.220T>G	p.Leu74Val	p.L74V	ENST00000558401	NM_004048.2	74	Ttg/Gtg	2/4	1	2	FACETS	0.933	0.856	1	0.933	0.856	1	CLONAL	1	TRUE	1	0.412950475476611	2		415	820	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304322	91304322	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	85	388	0	ENST00000355112.3:c.1719T>G	p.Asn573Lys	p.N573K	ENST00000355112	NM_000057.2	573	aaT/aaG	7/22	1	2	FACETS	0.526	0.465	0.593	0.526	0.465	0.593	SUBCLONAL	1	TRUE	1	0.412950475476611	2		388	782	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652228	3652228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	239	636	0	ENST00000294008.3:c.841G>A	p.Ala281Thr	p.A281T	ENST00000294008	NM_032444.2	281	Gca/Aca	4/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.412950475476611	2		636	1050	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658572	3658572	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	242	685	0	ENST00000294008.3:c.394G>T	p.Glu132Ter	p.E132*	ENST00000294008	NM_032444.2	132	Gaa/Taa	2/15	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.412950475476611	2		685	1164	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828036	72828036	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	117	792	1	ENST00000268489.5:c.8545G>T	p.Asp2849Tyr	p.D2849Y	ENST00000268489	NM_006885.3	2849	Gac/Tac	9/10	1	2	FACETS	0.46	0.413	0.51	0.46	0.413	0.51	SUBCLONAL	1	TRUE	1	0.412950475476611	2		793	1232	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81939061	81939061	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	179	561	0	ENST00000359376.3:c.1416G>T	p.Lys472Asn	p.K472N	ENST00000359376	NM_002661.3	472	aaG/aaT	15/33	1	2	FACETS	0.984	0.908	1	0.984	0.908	1	CLONAL	1	TRUE	1	0.412950475476611	2		561	881	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974968	15974968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	135	344	0	ENST00000268712.3:c.3907G>A	p.Ala1303Thr	p.A1303T	ENST00000268712	NM_006311.3	1303	Gca/Aca	30/46	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.412950475476611	2		344	564	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004702	16004702	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	185	575	0	ENST00000268712.3:c.2552A>G	p.Glu851Gly	p.E851G	ENST00000268712	NM_006311.3	851	gAg/gGg	20/46	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.412950475476611	2		575	850	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245371	41245371	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	249	584	0	ENST00000357654.3:c.2177T>A	p.Leu726His	p.L726H	ENST00000357654	NM_007294.3	726	cTt/cAt	10/23	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.412950475476611	2		584	1142	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59886011	59886011	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	73	540	0	ENST00000259008.2:c.735A>C	p.Lys245Asn	p.K245N	ENST00000259008	NM_032043.2	245	aaA/aaC	7/20	1	2	FACETS	0.377	0.329	0.43	0.377	0.329	0.43	SUBCLONAL	1	TRUE	1	0.412950475476611	2		540	937	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604723	48604723	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	270	402	0	ENST00000342988.3:c.1545A>C	p.Arg515Ser	p.R515S	ENST00000342988	NM_005359.5	515	agA/agC	12/12	0.412950475476611	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.412950475476611	2		402	629	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288721	15288721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1167835026	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	30	61	0	ENST00000263388.2:c.4018G>A	p.Ala1340Thr	p.A1340T	ENST00000263388	NM_000435.2	1340	Gcg/Acg	24/33	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.412950475476611	2		61	113	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292584	15292584	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	106	668	0	ENST00000263388.2:c.2595A>T	p.Gln865His	p.Q865H	ENST00000263388	NM_000435.2	865	caA/caT	17/33	1	2	FACETS	0.458	0.409	0.51	0.458	0.409	0.51	SUBCLONAL	1	TRUE	1	0.412950475476611	2		668	1121	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257167	19257167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	240	555	0	ENST00000162023.5:c.796C>T	p.Pro266Ser	p.P266S	ENST00000162023		266	Ccc/Tcc	12/13	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.412950475476611	2		555	910	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140095	50140095	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	95	619	0	ENST00000246792.3:c.330T>G	p.Ile110Met	p.I110M	ENST00000246792	NM_006270.3	110	atT/atG	3/6	1	2	FACETS	0.446	0.396	0.499	0.446	0.396	0.499	SUBCLONAL	1	TRUE	1	0.412950475476611	2		619	1032	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416271	29416271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1209157216	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	163	546	0	ENST00000389048.3:c.4682C>T	p.Ser1561Leu	p.S1561L	ENST00000389048	NM_004304.4	1561	tCg/tTg	29/29	1	2	FACETS	0.882	0.81	0.958	0.882	0.81	0.958	CLONAL	1	TRUE	1	0.412950475476611	2		546	895	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416371	29416371	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	226	689	1	ENST00000389048.3:c.4582C>T	p.His1528Tyr	p.H1528Y	ENST00000389048	NM_004304.4	1528	Cac/Tac	29/29	1	2	FACETS	0.994	0.925	1	0.994	0.925	1	CLONAL	1	TRUE	1	0.412950475476611	2		690	1101	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606129	47606129	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	147	408	1	ENST00000263735.4:c.593A>C	p.Asn198Thr	p.N198T	ENST00000263735	NM_002354.2	198	aAt/aCt	6/9	1	2	FACETS	0.832	0.759	0.907	0.832	0.759	0.907	CLONAL	1	TRUE	1	0.412950475476611	2		409	856	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672773	47672773	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	183	489	0	ENST00000233146.2:c.1363G>T	p.Glu455Ter	p.E455*	ENST00000233146	NM_000251.2	455	Gaa/Taa	8/16	1	2	FACETS	0.976	0.901	1	0.976	0.901	1	CLONAL	1	TRUE	1	0.412950475476611	2		489	908	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030689	48030689	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs370353868	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	60	359	0	ENST00000234420.5:c.3303G>T	p.Lys1101Asn	p.K1101N	ENST00000234420	NM_000179.2	1101	aaG/aaT	5/10	1	2	FACETS	0.414	0.356	0.477	0.414	0.356	0.477	SUBCLONAL	1	TRUE	1	0.412950475476611	2		359	702	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715794	61715794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	125	354	0	ENST00000401558.2:c.2135G>A	p.Arg712Lys	p.R712K	ENST00000401558	NM_003400.3	712	aGa/aAa	18/25	1	2	FACETS	0.917	0.832	1	0.917	0.832	1	CLONAL	1	TRUE	1	0.412950475476611	2		354	660	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719091	190719091	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	110	288	0	ENST00000441310.2:c.1093G>T	p.Glu365Ter	p.E365*	ENST00000441310	NM_000534.4	365	Gaa/Taa	9/13	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.412950475476611	2		288	522	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719668	190719668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	82	234	0	ENST00000441310.2:c.1670C>T	p.Ser557Phe	p.S557F	ENST00000441310	NM_000534.4	557	tCt/tTt	9/13	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.412950475476611	2		234	382	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131426	202131426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	164	493	0	ENST00000358485.4:c.394G>A	p.Asp132Asn	p.D132N	ENST00000358485	NM_001080125.1	132	Gat/Aat	2/9	1	2	FACETS	0.979	0.9	1	0.979	0.9	1	CLONAL	1	TRUE	1	0.412950475476611	2		493	811	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537887	212537887	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	151	402	0	ENST00000342788.4:c.1716+2T>C		p.X572_splice	ENST00000342788	NM_005235.2	572			1	2	FACETS	0.969	0.887	1	0.969	0.887	1	CLONAL	1	TRUE	1	0.412950475476611	2		402	755	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568839	212568839	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	110	399	2	ENST00000342788.4:c.1279G>T	p.Val427Leu	p.V427L	ENST00000342788	NM_005235.2	427	Gta/Tta	11/28	1	2	FACETS	0.692	0.622	0.766	0.692	0.622	0.766	SUBCLONAL	1	TRUE	1	0.412950475476611	2		401	770	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570093	212570093	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	35	365	1	ENST00000342788.4:c.1148C>T	p.Ala383Val	p.A383V	ENST00000342788	NM_005235.2	383	gCc/gTc	10/28	1	2	FACETS	0.263	0.215	0.317	0.263	0.215	0.317	SUBCLONAL	1	TRUE	1	0.412950475476611	2		366	645	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422429	225422429	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	158	460	1	ENST00000264414.4:c.211G>T	p.Glu71Ter	p.E71*	ENST00000264414	NM_003590.4	71	Gaa/Taa	2/16	1	2	FACETS	0.933	0.856	1	0.933	0.856	1	CLONAL	1	TRUE	1	0.412950475476611	2		461	820	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387110	31387110	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	95	548	0	ENST00000328111.2:c.1735T>C	p.Ser579Pro	p.S579P	ENST00000328111	NM_006892.3	579	Tca/Cca	16/23	1	2	FACETS	0.481	0.427	0.539	0.481	0.427	0.539	SUBCLONAL	1	TRUE	1	0.412950475476611	2		548	956	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533736	41533736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1046073854	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	180	514	3	ENST00000263253.7:c.1702C>T	p.Arg568Trp	p.R568W	ENST00000263253	NM_001429.3	568	Cgg/Tgg	8/31	1	2	FACETS	0.977	0.902	1	0.977	0.902	1	CLONAL	1	TRUE	1	0.412950475476611	2		517	892	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545125	41545125	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	224	532	1	ENST00000263253.7:c.2325G>T	p.Met775Ile	p.M775I	ENST00000263253	NM_001429.3	775	atG/atT	13/31	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.412950475476611	2		533	1077	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660157	12660157	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	203	485	0	ENST00000251849.4:c.64T>C	p.Phe22Leu	p.F22L	ENST00000251849	NM_002880.3	22	Ttt/Ctt	2/17	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.412950475476611	2		485	897	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089156	37089156	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs63751214	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	139	393	0	ENST00000231790.2:c.1878C>A	p.Phe626Leu	p.F626L	ENST00000231790	NM_000249.3	626	ttC/ttA	16/19	1	2	FACETS	0.942	0.859	1	0.942	0.859	1	CLONAL	1	TRUE	1	0.412950475476611	2		393	715	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181368	38181368	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	99	287	0	ENST00000396334.3:c.381A>C	p.Gln127His	p.Q127H	ENST00000396334	NM_002468.4	127	caA/caC	2/5	1	2	FACETS	0.917	0.821	1	0.917	0.821	1	CLONAL	1	TRUE	1	0.412950475476611	2		287	523	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637656	52637656	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	87	478	1	ENST00000394830.3:c.2660T>G	p.Leu887Arg	p.L887R	ENST00000394830	NM_018313.4	887	cTt/cGt	18/30	1	2	FACETS	0.408	0.36	0.459	0.408	0.36	0.459	SUBCLONAL	1	TRUE	1	0.412950475476611	2		479	1034	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662993	52662993	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	138	347	0	ENST00000394830.3:c.1360T>G	p.Leu454Val	p.L454V	ENST00000394830	NM_018313.4	454	Tta/Gta	13/30	1	2	FACETS	0.992	0.904	1	0.992	0.904	1	CLONAL	1	TRUE	1	0.412950475476611	2		347	674	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72891527	72891527	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	175	369	0	ENST00000325599.8:c.235G>T	p.Glu79Ter	p.E79*	ENST00000325599	NM_018130.2	79	Gaa/Taa	3/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.412950475476611	2		369	817	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114268	73114268	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	85	270	0	ENST00000356692.5:c.904G>T	p.Glu302Ter	p.E302*	ENST00000356692		302	Gaa/Taa	8/9	1	2	FACETS	0.913	0.81	1	0.913	0.81	1	CLONAL	1	TRUE	1	0.412950475476611	2		270	451	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977952	134977952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1324574213	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	187	518	0	ENST00000398015.3:c.2945C>T	p.Ala982Val	p.A982V	ENST00000398015	NM_004441.4	982	gCa/gTa	16/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.412950475476611	2		518	840	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916806	178916806	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	170	490	0	ENST00000263967.3:c.193G>T	p.Glu65Ter	p.E65*	ENST00000263967	NM_006218.2	65	Gaa/Taa	2/21	0.402019098989049	3	FACETS	0.88	0.808	0.955	0.44	0.404	0.478	CLONAL	1	TRUE	1	0.412950475476611	3		490	1129	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182681707	182681707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1405994082	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	188	414	1	ENST00000292782.4:c.351C>A	p.Phe117Leu	p.F117L	ENST00000292782	NM_020640.2	117	ttC/ttA	3/7	0.402019098989049	3	FACETS	1	0.969	1	0.547	0.505	0.591	CLONAL	1	TRUE	1	0.412950475476611	3		415	1004	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750396	41750396	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	67	386	0	ENST00000226382.2:c.232T>C	p.Tyr78His	p.Y78H	ENST00000226382	NM_003924.3	78	Tac/Cac	1/3	1	2	FACETS	0.502	0.435	0.573	0.502	0.435	0.573	SUBCLONAL	1	TRUE	1	0.412950475476611	2		386	647	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133874	55133874	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs750157633	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	149	362	0	ENST00000257290.5:c.1087A>C	p.Ile363Leu	p.I363L	ENST00000257290	NM_006206.4	363	Atc/Ctc	7/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.412950475476611	2		362	613	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589787	55589787	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	165	397	0	ENST00000288135.5:c.1269T>G	p.Asn423Lys	p.N423K	ENST00000288135	NM_000222.2	423	aaT/aaG	8/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.412950475476611	2		397	725	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955939	55955939	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	148	458	0	ENST00000263923.4:c.3223G>T	p.Glu1075Ter	p.E1075*	ENST00000263923	NM_002253.2	1075	Gaa/Taa	24/30	1	2	FACETS	0.958	0.877	1	0.958	0.877	1	CLONAL	1	TRUE	1	0.412950475476611	2		458	748	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970853	55970853	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	138	414	0	ENST00000263923.4:c.1944G>T	p.Lys648Asn	p.K648N	ENST00000263923	NM_002253.2	648	aaG/aaT	13/30	1	2	FACETS	0.918	0.837	1	0.918	0.837	1	CLONAL	1	TRUE	1	0.412950475476611	2		414	728	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467554	66467554	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	41	342	0	ENST00000273854.3:c.715C>A	p.His239Asn	p.H239N	ENST00000273854	NM_004439.5	239	Cac/Aac	3/18	1	2	FACETS	0.386	0.321	0.459	0.386	0.321	0.459	SUBCLONAL	1	TRUE	1	0.412950475476611	2		342	514	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557993	187557993	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	150	342	0	ENST00000441802.2:c.3718G>T	p.Asp1240Tyr	p.D1240Y	ENST00000441802	NM_005245.3	1240	Gac/Tac	5/27	1	2	FACETS	0.976	0.894	1	0.976	0.894	1	CLONAL	1	TRUE	1	0.412950475476611	2		342	744	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168544	56168544	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	114	274	0	ENST00000399503.3:c.1500C>A	p.Phe500Leu	p.F500L	ENST00000399503	NM_005921.1	500	ttC/ttA	8/20	1	2	FACETS	0.941	0.849	1	0.941	0.849	1	CLONAL	1	TRUE	1	0.412950475476611	2		274	587	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178602	56178602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	116	257	0	ENST00000399503.3:c.3575C>T	p.Ala1192Val	p.A1192V	ENST00000399503	NM_005921.1	1192	gCc/gTc	14/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.412950475476611	2		257	493	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179454	56179454	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	102	235	0	ENST00000399503.3:c.3767C>A	p.Ser1256Tyr	p.S1256Y	ENST00000399503	NM_005921.1	1256	tCt/tAt	15/20	1	2	FACETS	0.898	0.806	0.996	0.898	0.806	0.996	CLONAL	1	TRUE	1	0.412950475476611	2		235	550	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670674	86670674	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	79	266	0	ENST00000274376.6:c.1952T>C	p.Ile651Thr	p.I651T	ENST00000274376	NM_002890.2	651	aTc/aCc	15/25	1	2	FACETS	0.743	0.655	0.837	0.743	0.655	0.837	SUBCLONAL	1	TRUE	1	0.412950475476611	2		266	515	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715384	117715384	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	34	383	0	ENST00000368508.3:c.1105A>C	p.Ile369Leu	p.I369L	ENST00000368508	NM_002944.2	369	Att/Ctt	10/43	1	2	FACETS	0.243	0.198	0.294	0.243	0.198	0.294	SUBCLONAL	1	TRUE	1	0.412950475476611	2		383	678	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729969	41729969	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	54	565	0	ENST00000242208.4:c.560A>T	p.Asp187Val	p.D187V	ENST00000242208	NM_002192.2	187	gAc/gTc	3/3	1	2	FACETS	0.26	0.221	0.303	0.26	0.221	0.303	SUBCLONAL	1	TRUE	1	0.412950475476611	2		565	1005	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334801	81334801	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	130	408	0	ENST00000222390.5:c.1915A>G	p.Asn639Asp	p.N639D	ENST00000222390	NM_000601.4	639	Aat/Gat	17/18	1	2	FACETS	0.83	0.753	0.91	0.83	0.753	0.91	CLONAL	1	TRUE	1	0.412950475476611	2		408	759	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523588	106523588	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	95	260	0	ENST00000359195.3:c.2740A>T	p.Lys914Ter	p.K914*	ENST00000359195	NM_002649.2	914	Aaa/Taa	8/11	1	2	FACETS	0.875	0.781	0.974	0.875	0.781	0.974	CLONAL	1	TRUE	1	0.412950475476611	2		260	526	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850882	128850882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	81	651	0	ENST00000249373.3:c.1729C>T	p.His577Tyr	p.H577Y	ENST00000249373	NM_005631.4	577	Cac/Tac	10/12	1	2	FACETS	0.373	0.327	0.422	0.373	0.327	0.422	SUBCLONAL	1	TRUE	1	0.412950475476611	2		651	1053	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851602	128851602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764646280	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	169	597	1	ENST00000249373.3:c.1927G>A	p.Ala643Thr	p.A643T	ENST00000249373	NM_005631.4	643	Gca/Aca	11/12	1	2	FACETS	0.883	0.812	0.957	0.883	0.812	0.957	CLONAL	1	TRUE	1	0.412950475476611	2		598	927	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38173052	38173052	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	117	391	0	ENST00000317025.8:c.1997G>A	p.Gly666Glu	p.G666E	ENST00000317025	NM_023034.1	666	gGa/gAa	11/24	1	2	FACETS	0.798	0.72	0.88	0.798	0.72	0.88	SUBCLONAL	1	TRUE	1	0.412950475476611	2		391	710	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70967620	70967620	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	136	454	0	ENST00000276594.2:c.1403A>C	p.Lys468Thr	p.K468T	ENST00000276594	NM_024504.3	468	aAa/aCa	7/8	1	2	FACETS	0.839	0.763	0.918	0.839	0.763	0.918	CLONAL	1	TRUE	1	0.412950475476611	2		454	785	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5463112	5463112	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	83	255	0	ENST00000381577.3:c.673G>T	p.Val225Phe	p.V225F	ENST00000381577	NM_014143.3	225	Gtc/Ttc	4/7	1	2	FACETS	0.889	0.788	0.997	0.889	0.788	0.997	CLONAL	1	TRUE	1	0.412950475476611	2		255	452	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732866	44732866	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	88	456	0	ENST00000377967.4:c.69G>T	p.Lys23Asn	p.K23N	ENST00000377967	NM_021140.2	23	aaG/aaT	1/29	0.41295152558514	3	FACETS	0.492	0.434	0.553	0.246	0.217	0.277	SUBCLONAL	1	TRUE	1	0.412950475476611	3		456	1046	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44921910	44921910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1322780338	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	287	395	0	ENST00000377967.4:c.1444G>A	p.Ala482Thr	p.A482T	ENST00000377967	NM_021140.2	482	Gca/Aca	15/29	0.41295152558514	3	FACETS	0.929	0.875	0.983	0.929	0.875	0.983	CLONAL	2	TRUE	1	0.412950475476611	3		395	903	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928966	44928966	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	196	451	0	ENST00000377967.4:c.2066C>A	p.Ser689Ter	p.S689*	ENST00000377967	NM_021140.2	689	tCa/tAa	17/29	0.41295152558514	3	FACETS	1	0.951	1	0.519	0.479	0.56	CLONAL	1	TRUE	1	0.412950475476611	3		451	1104	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147520	61147520	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	16	33	0	ENST00000295025.8:c.925G>T	p.Glu309Ter	p.E309*	ENST00000295025	NM_002908.2	309	Gaa/Taa	9/11	1	2	FACETS	1	0.835	1	1	0.835	1	CLONAL	1	TRUE	1	0.412950475476611	2		33	68	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	208	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.945	0.881	1	0.945	0.881	1	CLONAL	1	TRUE	1	0.658859204203393	2		487	668	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021817	71021817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs797045586	NA	P-0051647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	130	250	1	ENST00000318789.4:c.1541G>A	p.Arg514His	p.R514H	ENST00000318789	NM_032682.5	514	cGt/cAt	18/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.658859204203393	2		251	314	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575132	48575132	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	67	368	1	ENST00000342988.3:c.326T>C	p.Leu109Pro	p.L109P	ENST00000342988	NM_005359.5	109	cTa/cCa	3/12	0.658859204203393	1	FACETS	0.339	0.296	0.386	0.339	0.296	0.386	SUBCLONAL	1	TRUE	0	0.658859204203393	1		369	402	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105727	27105727	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	183	413	2	ENST00000324856.7:c.5338G>T	p.Glu1780Ter	p.E1780*	ENST00000324856	NM_006015.4	1780	Gaa/Taa	20/20	0.658859204203393	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.658859204203393	1		415	330	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266088	41266111	+	inframe_deletion	In_Frame_Del	DEL	TCTTACCTGGACTCTGGAATCCAT	TCTTACCTGGACTCTGGAATCCAT	-	novel	NA	P-0051647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	133	337	1	ENST00000349496.5:c.88_111del	p.Tyr30_Ser37del	p.Y30_S37del	ENST00000349496	NM_001904.3	29	TCTTACCTGGACTCTGGAATCCAT/-	3/15	1	2	FACETS	0.889	0.814	0.967	0.889	0.814	0.967	CLONAL	1	TRUE	1	0.658859204203393	2		338	454	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857307	68857307	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs971882211	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	22	323	0	ENST00000261769.5:c.1942G>T	p.Glu648Ter	p.E648*	ENST00000261769	NM_004360.3	648	Gaa/Taa	13/16	1	2	FACETS	0.231	0.179	0.292	0.231	0.179	0.292	SUBCLONAL	1	FALSE	1	0.628459867302617	2		323	303	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	89	364	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.963	0.865	1	0.963	0.865	1	CLONAL	1	FALSE	1	0.628459867302617	2		365	294	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228613019	228613019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773567566	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	21	416	1	ENST00000366696.1:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000366696	NM_003493.2	3	cGa/cAa	1/1	1	2	FACETS	0.189	0.145	0.241	0.189	0.145	0.241	SUBCLONAL	1	FALSE	1	0.628459867302617	2		417	353	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748837	43748837	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	48	672	1	ENST00000382044.4:c.1969G>T	p.Glu657Ter	p.E657*	ENST00000382044	NM_001141980.1	657	Gaa/Taa	12/28	1	2	FACETS	0.244	0.206	0.286	0.244	0.206	0.286	SUBCLONAL	1	FALSE	1	0.628459867302617	2		673	626	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132713	152132713	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	92	170	0	ENST00000262189.6:c.159G>T	p.Lys53Asn	p.K53N	ENST00000262189	NM_170606.2	53	aaG/aaT	1/59	0.628459867302617	3	FACETS	1	0.971	1	0.613	0.55	0.678	CLONAL	1	FALSE	1	0.628459867302617	3		170	314	SUCCESS
BLM	641	MSKCC	GRCh37	15	91333930	91333930	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs762354041	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	155	574	1	ENST00000355112.3:c.2875C>T	p.Arg959Ter	p.R959*	ENST00000355112	NM_000057.2	959	Cga/Tga	15/22	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	1	0.628459867302617	2		575	480	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343060	70343060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	184	283	0	ENST00000374080.3:c.1601C>T	p.Ala534Val	p.A534V	ENST00000374080		534	gCg/gTg	11/45	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	FALSE	0	0.628459867302617	1		283	271	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720928	119720928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	101	474	0	ENST00000316626.5:c.247G>A	p.Ala83Thr	p.A83T	ENST00000316626		83	Gcc/Acc	2/12	1	2	FACETS	0.763	0.687	0.844	0.763	0.687	0.844	SUBCLONAL	1	FALSE	1	0.628459867302617	2		474	421	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47710037	47710037	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1553370893	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	54	301	0	ENST00000233146.2:c.2754G>T	p.Lys918Asn	p.K918N	ENST00000233146	NM_000251.2	918	aaG/aaT	16/16	1	2	FACETS	0.976	0.849	1	0.976	0.849	1	CLONAL	1	FALSE	1	0.628459867302617	2		301	176	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418997	116418997	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200754673	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	75	266	0	ENST00000397752.3:c.3508C>T	p.Arg1170Ter	p.R1170*	ENST00000397752	NM_000245.2	1170	Cga/Tga	17/21	0.628459867302617	3	FACETS	1	0.961	1	0.596	0.529	0.667	CLONAL	1	FALSE	1	0.628459867302617	3		266	263	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095836	178095836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1328262363	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	131	494	1	ENST00000397062.3:c.1495C>T	p.Arg499Trp	p.R499W	ENST00000397062	NM_006164.4	499	Cgg/Tgg	5/5	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.628459867302617	2		495	371	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023019	150023019	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	148	592	0	ENST00000253339.5:c.244C>T	p.Arg82Ter	p.R82*	ENST00000253339		82	Cga/Tga	1/7	1	2	FACETS	0.967	0.89	1	0.967	0.89	1	CLONAL	1	FALSE	1	0.628459867302617	2		592	487	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	62	260	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	FALSE	1	0.628459867302617	2		260	186	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435088	18435088	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs777959749	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	96	371	0	ENST00000266497.5:c.73C>A	p.Leu25Ile	p.L25I	ENST00000266497		25	Ctc/Atc	1/31	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	1	0.628459867302617	2		371	289	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748583	40748583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444440253	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	113	435	0	ENST00000373198.4:c.2933C>T	p.Ala978Val	p.A978V	ENST00000373198	NM_133170.3	978	gCg/gTg	21/32	0.628459867302617	3	FACETS	0.947	0.857	1	0.474	0.428	0.521	CLONAL	1	FALSE	1	0.628459867302617	3		435	499	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729635	162729635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	148	529	0	ENST00000367921.3:c.721G>A	p.Asp241Asn	p.D241N	ENST00000367921	NM_006182.2	241	Gat/Aat	8/18	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	1	0.628459867302617	2		529	459	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117650561	117650561	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	116	562	0	ENST00000368508.3:c.5297A>C	p.Lys1766Thr	p.K1766T	ENST00000368508	NM_002944.2	1766	aAa/aCa	32/43	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	1	0.628459867302617	2		562	352	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891035	112891035	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs755619262	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	115	318	0	ENST00000351677.2:c.369G>T	p.Glu123Asp	p.E123D	ENST00000351677	NM_002834.3	123	gaG/gaT	4/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.628459867302617	2		318	329	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637690	52637690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239654517	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	147	503	0	ENST00000394830.3:c.2626C>T	p.Arg876Cys	p.R876C	ENST00000394830	NM_018313.4	876	Cgt/Tgt	18/30	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.628459867302617	2		503	397	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221123	5221123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769925793	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	230	731	0	ENST00000357368.4:c.3343G>A	p.Ala1115Thr	p.A1115T	ENST00000357368	NM_002850.3	1115	Gcc/Acc	20/38	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.628459867302617	2		731	676	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	80	393	1	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	0.972	0.867	1	0.972	0.867	1	CLONAL	1	FALSE	1	0.628459867302617	2		394	262	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509637	106509637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766453335	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	151	514	0	ENST00000359195.3:c.1631G>A	p.Arg544Gln	p.R544Q	ENST00000359195	NM_002649.2	544	cGa/cAa	2/11	0.628459867302617	3	FACETS	1	0.954	1	0.529	0.485	0.574	CLONAL	1	FALSE	1	0.628459867302617	3		514	597	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911534	101911534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111426349	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	18	431	0	ENST00000374994.4:c.1459C>T	p.Arg487Trp	p.R487W	ENST00000374994	NM_004612.2	487	Cgg/Tgg	9/9	1	2	FACETS	0.174	0.131	0.226	0.174	0.131	0.226	SUBCLONAL	1	FALSE	1	0.628459867302617	2		431	329	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726669	88726669	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	121	470	0	ENST00000360948.2:c.375G>T	p.Lys125Asn	p.K125N	ENST00000360948	NM_001012338.2	125	aaG/aaT	4/19	1	2	FACETS	0.921	0.839	1	0.921	0.839	1	CLONAL	1	FALSE	1	0.628459867302617	2		470	418	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171607	36171607	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1569008655	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	20	298	0	ENST00000300305.3:c.958C>T	p.Arg320Ter	p.R320*	ENST00000300305		320	Cga/Tga	7/8	1	2	FACETS	0.185	0.141	0.237	0.185	0.141	0.237	SUBCLONAL	1	FALSE	1	0.628459867302617	2		298	344	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508805	106508805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762805000	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	123	533	0	ENST00000359195.3:c.799G>A	p.Glu267Lys	p.E267K	ENST00000359195	NM_002649.2	267	Gaa/Aaa	2/11	0.628459867302617	3	FACETS	0.738	0.668	0.811	0.369	0.334	0.406	SUBCLONAL	1	FALSE	1	0.628459867302617	3		533	697	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589874	212589874	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	169	517	0	ENST00000342788.4:c.668G>A	p.Gly223Glu	p.G223E	ENST00000342788	NM_005235.2	223	gGa/gAa	6/28	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	FALSE	1	0.628459867302617	2		517	527	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259071	153259071	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	67	203	0	ENST00000281708.4:c.744G>T	p.Glu248Asp	p.E248D	ENST00000281708	NM_033632.3	248	gaG/gaT	5/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.628459867302617	2		203	169	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673064	30673064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144657716	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	190	628	3	ENST00000376406.3:c.3896G>A	p.Arg1299Gln	p.R1299Q	ENST00000376406	NM_014641.2	1299	cGa/cAa	10/15	1	2	FACETS	0.946	0.879	1	0.946	0.879	1	CLONAL	1	FALSE	1	0.628459867302617	2		631	639	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561352	9561352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773981325	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	44	438	1	ENST00000353224.5:c.430G>A	p.Glu144Lys	p.E144K	ENST00000353224	NM_177990.2	144	Gaa/Aaa	4/10	0.628459867302617	3	FACETS	0.389	0.326	0.459	0.195	0.163	0.23	SUBCLONAL	1	FALSE	1	0.628459867302617	3		439	473	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495034	56495034	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150312718	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	181	654	1	ENST00000267101.3:c.3391G>A	p.Ala1131Thr	p.A1131T	ENST00000267101	NM_001982.3	1131	Gcc/Acc	27/28	1	2	FACETS	0.837	0.775	0.902	0.837	0.775	0.902	CLONAL	1	FALSE	1	0.628459867302617	2		655	688	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858261	27858261	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	170	729	0	ENST00000359303.2:c.310C>A	p.Leu104Ile	p.L104I	ENST00000359303	NM_003535.2	104	Ctc/Atc	1/1	1	2	FACETS	0.856	0.791	0.924	0.856	0.791	0.924	CLONAL	1	FALSE	1	0.628459867302617	2		729	632	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746018	162746018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	86	387	0	ENST00000367921.3:c.2141G>A	p.Arg714Gln	p.R714Q	ENST00000367921	NM_006182.2	714	cGa/cAa	16/18	1	2	FACETS	0.891	0.797	0.99	0.891	0.797	0.99	CLONAL	1	FALSE	1	0.628459867302617	2		387	307	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521666	89521666	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs748629890	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	96	494	0	ENST00000336596.2:c.2743A>G	p.Thr915Ala	p.T915A	ENST00000336596	NM_005233.5	915	Aca/Gca	16/17	1	2	FACETS	0.727	0.652	0.807	0.727	0.652	0.807	SUBCLONAL	1	FALSE	1	0.628459867302617	2		494	420	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968610	55968610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374980446	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	132	575	1	ENST00000263923.4:c.2053G>A	p.Glu685Lys	p.E685K	ENST00000263923	NM_002253.2	685	Gaa/Aaa	14/30	1	2	FACETS	0.741	0.675	0.809	0.741	0.675	0.809	SUBCLONAL	1	FALSE	1	0.628459867302617	2		576	567	SUCCESS
MET	4233	MSKCC	GRCh37	7	116422057	116422057	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	195	354	0	ENST00000397752.3:c.3538G>T	p.Asp1180Tyr	p.D1180Y	ENST00000397752	NM_000245.2	1180	Gat/Tat	18/21	0.628459867302617	3	FACETS	0.946	0.887	1	0.946	0.887	1	CLONAL	2	FALSE	1	0.628459867302617	3		354	431	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103510743	103510743	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	24	443	0	ENST00000355739.4:c.647G>T	p.Arg216Ile	p.R216I	ENST00000355739	NM_000123.3	216	aGa/aTa	6/15	1	2	FACETS	0.284	0.223	0.354	0.284	0.223	0.354	SUBCLONAL	1	FALSE	1	0.628459867302617	2		443	269	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727098	40727098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	137	642	1	ENST00000373198.4:c.3866C>T	p.Ser1289Phe	p.S1289F	ENST00000373198	NM_133170.3	1289	tCc/tTc	28/32	0.628459867302617	3	FACETS	0.905	0.826	0.988	0.453	0.413	0.494	CLONAL	1	FALSE	1	0.628459867302617	3		643	633	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560913	9560913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559720359	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	47	380	2	ENST00000353224.5:c.869C>T	p.Ser290Leu	p.S290L	ENST00000353224	NM_177990.2	290	tCg/tTg	4/10	0.628459867302617	3	FACETS	0.357	0.301	0.419	0.178	0.15	0.21	SUBCLONAL	1	FALSE	1	0.628459867302617	3		382	551	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508955	106508955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759136884	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	129	563	0	ENST00000359195.3:c.949G>A	p.Glu317Lys	p.E317K	ENST00000359195	NM_002649.2	317	Gag/Aag	2/11	0.628459867302617	3	FACETS	0.976	0.888	1	0.488	0.444	0.534	CLONAL	1	FALSE	1	0.628459867302617	3		563	553	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243675668	243675668	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	74	317	0	ENST00000263826.5:c.1312G>T	p.Glu438Ter	p.E438*	ENST00000263826	NM_005465.4	438	Gaa/Taa	12/13	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	FALSE	1	0.628459867302617	2		317	228	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198263220	198263220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	87	345	0	ENST00000335508.6:c.3099G>T	p.Glu1033Asp	p.E1033D	ENST00000335508	NM_012433.2	1033	gaG/gaT	21/25	1	2	FACETS	0.942	0.844	1	0.942	0.844	1	CLONAL	1	FALSE	1	0.628459867302617	2		345	294	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197845	66197845	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	53	241	1	ENST00000273854.3:c.2854G>T	p.Val952Leu	p.V952L	ENST00000273854	NM_004439.5	952	Gta/Tta	17/18	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	FALSE	1	0.628459867302617	2		242	151	SUCCESS
APC	324	MSKCC	GRCh37	5	112176008	112176008	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	78	260	0	ENST00000257430.4:c.4717G>T	p.Glu1573Ter	p.E1573*	ENST00000257430	NM_000038.5	1573	Gaa/Taa	16/16	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	1	0.628459867302617	2		260	227	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972440	81972440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs891516801	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	147	506	0	ENST00000359376.3:c.3233G>A	p.Arg1078Gln	p.R1078Q	ENST00000359376	NM_002661.3	1078	cGa/cAa	29/33	1	2	FACETS	0.957	0.88	1	0.957	0.88	1	CLONAL	1	FALSE	1	0.628459867302617	2		506	489	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096009	11096009	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	211	777	0	ENST00000358026.2:c.283G>T	p.Gly95Ter	p.G95*	ENST00000358026	NM_001128849.1	95	Gga/Tga	3/36	1	2	FACETS	0.947	0.883	1	0.947	0.883	1	CLONAL	1	FALSE	1	0.628459867302617	2		777	709	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948135	55948135	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1001071878	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	112	467	0	ENST00000263923.4:c.3836C>A	p.Ser1279Tyr	p.S1279Y	ENST00000263923	NM_002253.2	1279	tCt/tAt	29/30	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.628459867302617	2		467	334	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215609807	215609807	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs878854003	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	40	351	0	ENST00000260947.4:c.1887G>A	p.Trp629Ter	p.W629*	ENST00000260947	NM_000465.2	629	tgG/tgA	9/11	1	2	FACETS	0.458	0.382	0.541	0.458	0.382	0.541	SUBCLONAL	1	FALSE	1	0.628459867302617	2		351	278	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003767	45003767	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	141	614	2	ENST00000558401.1:c.23C>A	p.Ala8Asp	p.A8D	ENST00000558401	NM_004048.2	8	gCt/gAt	1/4	1	2	FACETS	0.984	0.904	1	0.984	0.904	1	CLONAL	1	FALSE	1	0.628459867302617	2		616	456	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537975	212537975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267599192	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	104	354	1	ENST00000342788.4:c.1630C>T	p.Arg544Trp	p.R544W	ENST00000342788	NM_005235.2	544	Cgg/Tgg	14/28	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	FALSE	1	0.628459867302617	2		355	329	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501350	140501350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906660	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	74	275	0	ENST00000288602.6:c.722C>T	p.Thr241Met	p.T241M	ENST00000288602	NM_004333.4	241	aCg/aTg	6/18	0.628459867302617	3	FACETS	0.929	0.82	1	0.465	0.41	0.523	CLONAL	1	FALSE	1	0.628459867302617	3		275	333	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989557	85989557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	84	365	1	ENST00000263360.6:c.1316G>A	p.Arg439Gln	p.R439Q	ENST00000263360	NM_003797.3	439	cGa/cAa	12/12	1	2	FACETS	0.906	0.809	1	0.906	0.809	1	CLONAL	1	FALSE	1	0.628459867302617	2		366	295	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508517	106508517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs549157001	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	67	357	0	ENST00000359195.3:c.511G>A	p.Asp171Asn	p.D171N	ENST00000359195	NM_002649.2	171	Gat/Aat	2/11	0.628459867302617	3	FACETS	0.99	0.869	1	0.495	0.434	0.56	CLONAL	1	FALSE	1	0.628459867302617	3		357	283	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740668	58740668	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs759850701	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	151	508	0	ENST00000305921.3:c.1573G>T	p.Glu525Ter	p.E525*	ENST00000305921	NM_003620.3	525	Gaa/Taa	6/6	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.628459867302617	2		508	452	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2105507	2105507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45517113	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	192	520	1	ENST00000219476.3:c.586G>A	p.Ala196Thr	p.A196T	ENST00000219476	NM_000548.3	196	Gca/Aca	6/42	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.628459867302617	2		521	548	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151289	202151289	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	94	382	0	ENST00000358485.4:c.1589G>T	p.Arg530Ile	p.R530I	ENST00000358485	NM_001080125.1	530	aGa/aTa	9/9	1	2	FACETS	0.918	0.825	1	0.918	0.825	1	CLONAL	1	FALSE	1	0.628459867302617	2		382	326	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659246	86659246	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	65	243	0	ENST00000274376.6:c.1535G>A	p.Arg512Gln	p.R512Q	ENST00000274376	NM_002890.2	512	cGa/cAa	11/25	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	1	0.628459867302617	2		243	195	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133894	55133894	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	95	341	0	ENST00000257290.5:c.1107G>T	p.Lys369Asn	p.K369N	ENST00000257290	NM_006206.4	369	aaG/aaT	7/23	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	1	0.628459867302617	2		341	277	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249857	133249857	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1565972665	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	112	432	0	ENST00000320574.5:c.1366G>C	p.Ala456Pro	p.A456P	ENST00000320574	NM_006231.2	456	Gcc/Ccc	14/49	1	2	FACETS	0.859	0.778	0.943	0.859	0.778	0.943	CLONAL	1	FALSE	1	0.628459867302617	2		432	415	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582935	95582935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs965350808	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	60	389	0	ENST00000393063.1:c.1607G>A	p.Arg536His	p.R536H	ENST00000393063	NM_030621.3	536	cGt/cAt	11/28	1	2	FACETS	0.864	0.755	0.979	0.864	0.755	0.979	CLONAL	1	FALSE	1	0.628459867302617	2		389	221	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965631	25965631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	117	608	0	ENST00000435504.4:c.3575C>A	p.Ser1192Tyr	p.S1192Y	ENST00000435504		1192	tCt/tAt	13/13	1	2	FACETS	0.666	0.603	0.733	0.666	0.603	0.733	SUBCLONAL	1	FALSE	1	0.628459867302617	2		608	559	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749490	41749490	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	133	583	1	ENST00000226382.2:c.305G>A	p.Arg102His	p.R102H	ENST00000226382	NM_003924.3	102	cGc/cAc	2/3	1	2	FACETS	0.793	0.723	0.865	0.793	0.723	0.865	SUBCLONAL	1	FALSE	1	0.628459867302617	2		584	534	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907420	32907421	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359306	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	21	309	2	ENST00000380152.3:c.1813dup	p.Ile605AsnfsTer11	p.I605Nfs*11	ENST00000380152		602	gga/ggAa	10/27	1	2	FACETS	0.338	0.261	0.426	0.338	0.261	0.426	SUBCLONAL	1	FALSE	1	0.628459867302617	2		311	198	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839719	42839719	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs368268847	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	218	698	1	ENST00000398585.3:c.1520G>T	p.Arg507Ile	p.R507I	ENST00000398585	NM_001135099.1	507	aGa/aTa	13/14	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.628459867302617	2		699	665	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484270	8484270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867884876	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	177	497	0	ENST00000356435.5:c.3262C>T	p.Arg1088Cys	p.R1088C	ENST00000356435		1088	Cgt/Tgt	19/35	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.628459867302617	2		497	542	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933424	100933424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	22	401	0	ENST00000325455.5:c.1966C>A	p.Leu656Ile	p.L656I	ENST00000325455	NM_001202474.3	656	Ctc/Atc	4/8	1	2	FACETS	0.212	0.164	0.267	0.212	0.164	0.267	SUBCLONAL	1	FALSE	1	0.628459867302617	2		401	331	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472592	88472592	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	24	473	0	ENST00000360948.2:c.1963C>A	p.Gln655Lys	p.Q655K	ENST00000360948	NM_001012338.2	655	Caa/Aaa	16/19	1	2	FACETS	0.209	0.164	0.262	0.209	0.164	0.262	SUBCLONAL	1	FALSE	1	0.628459867302617	2		473	365	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967900	93967900	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	147	543	0	ENST00000369303.4:c.2027G>T	p.Arg676Met	p.R676M	ENST00000369303	NM_004440.3	676	aGg/aTg	11/17	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.628459867302617	2		543	437	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912131	114912131	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	152	528	0	ENST00000543371.1:c.1201G>A	p.Glu401Lys	p.E401K	ENST00000543371	NM_001198531.1	401	Gag/Aag	11/14	1	2	FACETS	0.969	0.893	1	0.969	0.893	1	CLONAL	1	FALSE	1	0.628459867302617	2		528	499	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271369	26271369	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	29	692	0	ENST00000305910.3:c.244G>T	p.Asp82Tyr	p.D82Y	ENST00000305910	NM_003534.2	82	Gat/Tat	1/1	1	2	FACETS	0.169	0.135	0.208	0.169	0.135	0.208	SUBCLONAL	1	FALSE	1	0.628459867302617	2		692	547	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612398	1612398	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	245	786	0	ENST00000344749.5:c.1621G>T	p.Asp541Tyr	p.D541Y	ENST00000344749	NM_001136139.2	541	Gac/Tac	18/19	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	1	0.628459867302617	2		786	779	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221756	36221756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377420237	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	260	817	1	ENST00000222270.7:c.5425G>A	p.Ala1809Thr	p.A1809T	ENST00000222270	NM_014727.1	1809	Gcc/Acc	26/37	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	1	0.628459867302617	2		818	827	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129934	55129934	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	151	607	0	ENST00000257290.5:c.468G>T	p.Glu156Asp	p.E156D	ENST00000257290	NM_006206.4	156	gaG/gaT	4/23	1	2	FACETS	0.937	0.862	1	0.937	0.862	1	CLONAL	1	FALSE	1	0.628459867302617	2		607	513	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992764	68992764	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs769067107	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	63	566	0	ENST00000288368.4:c.1729C>T	p.Arg577Ter	p.R577*	ENST00000288368	NM_024870.2	577	Cga/Tga	16/40	1	2	FACETS	0.502	0.436	0.574	0.502	0.436	0.574	SUBCLONAL	1	FALSE	1	0.628459867302617	2		566	399	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832852	3832852	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	131	507	0	ENST00000262367.5:c.1406C>A	p.Ser469Tyr	p.S469Y	ENST00000262367	NM_004380.2	469	tCt/tAt	6/31	1	2	FACETS	0.952	0.871	1	0.952	0.871	1	CLONAL	1	FALSE	1	0.628459867302617	2		507	438	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659851	227659851	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	97	313	0	ENST00000305123.5:c.3604C>T	p.Pro1202Ser	p.P1202S	ENST00000305123	NM_005544.2	1202	Ccc/Tcc	1/2	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.628459867302617	2		313	269	SUCCESS
APC	324	MSKCC	GRCh37	5	112175825	112175825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778699501	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	71	278	0	ENST00000257430.4:c.4534G>A	p.Asp1512Asn	p.D1512N	ENST00000257430	NM_000038.5	1512	Gat/Aat	16/16	1	2	FACETS	0.97	0.859	1	0.97	0.859	1	CLONAL	1	FALSE	1	0.628459867302617	2		278	233	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28885788	28885788	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1256173877	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	38	507	0	ENST00000282397.4:c.3574G>T	p.Asp1192Tyr	p.D1192Y	ENST00000282397	NM_002019.4	1192	Gac/Tac	27/30	1	2	FACETS	0.33	0.273	0.393	0.33	0.273	0.393	SUBCLONAL	1	FALSE	1	0.628459867302617	2		507	367	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482577	56482577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762035321	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	209	630	0	ENST00000267101.3:c.1034C>T	p.Ser345Leu	p.S345L	ENST00000267101	NM_001982.3	345	tCg/tTg	9/28	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.628459867302617	2		630	646	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262906	46262906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	136	444	0	ENST00000371998.3:c.1079G>A	p.Arg360Gln	p.R360Q	ENST00000371998		360	cGa/cAa	10/23	0.628459867302617	3	FACETS	1	0.984	1	0.661	0.607	0.718	CLONAL	1	FALSE	1	0.628459867302617	3		444	430	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134681	41134681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	105	407	0	ENST00000379561.5:c.947G>A	p.Arg316Gln	p.R316Q	ENST00000379561	NM_002015.3	316	cGa/cAa	2/3	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	FALSE	1	0.628459867302617	2		407	321	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859879	117859879	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	32	295	0	ENST00000297338.2:c.1756C>T	p.Arg586Ter	p.R586*	ENST00000297338	NM_006265.2	586	Cga/Tga	14/14	1	2	FACETS	0.463	0.378	0.557	0.463	0.378	0.557	SUBCLONAL	1	FALSE	1	0.628459867302617	2		295	220	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467869	66467869	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	60	327	1	ENST00000273854.3:c.400C>A	p.Leu134Met	p.L134M	ENST00000273854	NM_004439.5	134	Ctg/Atg	3/18	1	2	FACETS	0.779	0.679	0.886	0.779	0.679	0.886	SUBCLONAL	1	FALSE	1	0.628459867302617	2		328	245	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864365	162864365	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	86	420	0	ENST00000366898.1:c.148C>A	p.Leu50Met	p.L50M	ENST00000366898	NM_004562.2	50	Ctg/Atg	2/12	1	2	FACETS	0.704	0.626	0.785	0.704	0.626	0.785	SUBCLONAL	1	FALSE	1	0.628459867302617	2		420	389	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934278	68934278	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	106	429	0	ENST00000288368.4:c.344A>C	p.Lys115Thr	p.K115T	ENST00000288368	NM_024870.2	115	aAg/aCg	4/40	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.628459867302617	2		429	279	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434141	49434141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770491652	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	203	767	1	ENST00000301067.7:c.7412G>A	p.Arg2471Gln	p.R2471Q	ENST00000301067	NM_003482.3	2471	cGa/cAa	31/54	1	2	FACETS	0.983	0.916	1	0.983	0.916	1	CLONAL	1	FALSE	1	0.628459867302617	2		768	657	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042482	16042482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	77	398	3	ENST00000268712.3:c.1192C>T	p.Arg398Trp	p.R398W	ENST00000268712	NM_006311.3	398	Cgg/Tgg	12/46	1	2	FACETS	0.888	0.789	0.992	0.888	0.789	0.992	CLONAL	1	FALSE	1	0.628459867302617	2		401	276	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39237759	39237759	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	102	348	0	ENST00000402219.2:c.2476C>T	p.Arg826Ter	p.R826*	ENST00000402219	NM_005633.3	826	Cga/Tga	15/23	1	2	FACETS	0.981	0.887	1	0.981	0.887	1	CLONAL	1	FALSE	1	0.628459867302617	2		348	331	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622278	162622278	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	17	397	0	ENST00000366898.1:c.419G>T	p.Arg140Ile	p.R140I	ENST00000366898	NM_004562.2	140	aGa/aTa	4/12	1	2	FACETS	0.17	0.126	0.222	0.17	0.126	0.222	SUBCLONAL	1	FALSE	1	0.628459867302617	2		397	318	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244163	5244163	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373884789	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	193	728	0	ENST00000357368.4:c.1319C>T	p.Ala440Val	p.A440V	ENST00000357368	NM_002850.3	440	gCg/gTg	11/38	1	2	FACETS	0.978	0.909	1	0.978	0.909	1	CLONAL	1	FALSE	1	0.628459867302617	2		728	628	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322511	109322511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769935193	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	146	505	0	ENST00000436639.2:c.526C>T	p.Arg176Cys	p.R176C	ENST00000436639	NM_014454.2	176	Cgt/Tgt	3/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.628459867302617	2		505	442	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122412	17122412	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	136	686	0	ENST00000285071.4:c.983A>C	p.Glu328Ala	p.E328A	ENST00000285071	NM_144997.5	328	gAg/gCg	9/14	1	2	FACETS	0.668	0.609	0.73	0.668	0.609	0.73	SUBCLONAL	1	FALSE	1	0.628459867302617	2		686	648	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860908	151860908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	65	324	1	ENST00000262189.6:c.9754C>T	p.Arg3252Cys	p.R3252C	ENST00000262189	NM_170606.2	3252	Cgt/Tgt	43/59	0.628459867302617	3	FACETS	0.931	0.814	1	0.466	0.407	0.528	CLONAL	1	FALSE	1	0.628459867302617	3		325	292	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953931	17953931	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	165	881	0	ENST00000458235.1:c.471G>T	p.Lys157Asn	p.K157N	ENST00000458235	NM_000215.3	157	aaG/aaT	5/24	1	2	FACETS	0.709	0.652	0.767	0.709	0.652	0.767	SUBCLONAL	1	FALSE	1	0.628459867302617	2		881	741	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719961	18719961	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	106	459	0	ENST00000266497.5:c.3858G>T	p.Gln1286His	p.Q1286H	ENST00000266497		1286	caG/caT	27/31	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.628459867302617	2		459	270	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250398	10250398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1010743136	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	174	592	0	ENST00000340748.4:c.3854G>A	p.Arg1285His	p.R1285H	ENST00000340748		1285	cGc/cAc	33/40	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.628459867302617	2		592	523	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435082	18435082	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	93	350	0	ENST00000266497.5:c.67G>T	p.Glu23Ter	p.E23*	ENST00000266497		23	Gaa/Taa	1/31	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	1	0.628459867302617	2		350	277	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445029	89445029	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	58	394	0	ENST00000336596.2:c.1349G>T	p.Arg450Ile	p.R450I	ENST00000336596	NM_005233.5	450	aGa/aTa	6/17	1	2	FACETS	0.516	0.445	0.592	0.516	0.445	0.592	SUBCLONAL	1	FALSE	1	0.628459867302617	2		394	358	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491459	18491459	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs200273120	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	19	357	0	ENST00000266497.5:c.1372C>A	p.Leu458Ile	p.L458I	ENST00000266497		458	Cta/Ata	8/31	1	2	FACETS	0.232	0.176	0.297	0.232	0.176	0.297	SUBCLONAL	1	FALSE	1	0.628459867302617	2		357	261	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027887	48027887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752839086	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	103	311	0	ENST00000234420.5:c.2765G>A	p.Arg922Gln	p.R922Q	ENST00000234420	NM_000179.2	922	cGa/cAa	4/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.628459867302617	2		311	288	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162701	47162701	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	80	490	0	ENST00000409792.3:c.3425A>G	p.Glu1142Gly	p.E1142G	ENST00000409792	NM_014159.6	1142	gAa/gGa	3/21	1	2	FACETS	0.705	0.625	0.79	0.705	0.625	0.79	SUBCLONAL	1	FALSE	1	0.628459867302617	2		490	361	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298125	15298125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751284168	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	227	794	1	ENST00000263388.2:c.1631G>A	p.Arg544His	p.R544H	ENST00000263388	NM_000435.2	544	cGc/cAc	11/33	1	2	FACETS	0.999	0.935	1	0.999	0.935	1	CLONAL	1	FALSE	1	0.628459867302617	2		795	723	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162742010	162742010	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	118	422	0	ENST00000367921.3:c.1701G>T	p.Glu567Asp	p.E567D	ENST00000367921	NM_006182.2	567	gaG/gaT	13/18	1	2	FACETS	0.986	0.898	1	0.986	0.898	1	CLONAL	1	FALSE	1	0.628459867302617	2		422	381	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510219	187510219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276553545	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	173	498	0	ENST00000441802.2:c.13294G>A	p.Glu4432Lys	p.E4432K	ENST00000441802	NM_005245.3	4432	Gaa/Aaa	27/27	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.628459867302617	2		498	481	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019136	31019136	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139716375	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	46	448	0	ENST00000375687.4:c.731G>A	p.Arg244His	p.R244H	ENST00000375687	NM_015338.5	244	cGc/cAc	9/13	0.628459867302617	3	FACETS	0.358	0.301	0.42	0.179	0.15	0.21	SUBCLONAL	1	FALSE	1	0.628459867302617	3		448	538	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814756	139814756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376884527	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	221	811	0	ENST00000247668.2:c.749C>T	p.Ser250Leu	p.S250L	ENST00000247668	NM_021138.3	250	tCg/tTg	8/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.628459867302617	2		811	664	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271769	15271769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	261	908	0	ENST00000263388.2:c.6670G>A	p.Ala2224Thr	p.A2224T	ENST00000263388	NM_000435.2	2224	Gct/Act	33/33	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	1	0.628459867302617	2		908	822	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811747	102811747	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	180	597	0	ENST00000307046.8:c.437C>A	p.Ser146Tyr	p.S146Y	ENST00000307046	NM_001111285.1	146	tCt/tAt	4/4	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.628459867302617	2		597	545	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26928012	26928012	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	20	404	0	ENST00000381527.3:c.451G>T	p.Asp151Tyr	p.D151Y	ENST00000381527	NM_001260.1	151	Gat/Tat	4/13	1	2	FACETS	0.218	0.166	0.278	0.218	0.166	0.278	SUBCLONAL	1	FALSE	1	0.628459867302617	2		404	292	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185039	32185039	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	161	583	0	ENST00000375023.3:c.1629C>A	p.Phe543Leu	p.F543L	ENST00000375023	NM_004557.3	543	ttC/ttA	10/30	1	2	FACETS	0.908	0.838	0.981	0.908	0.838	0.981	CLONAL	1	FALSE	1	0.628459867302617	2		583	564	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711913	89711913	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs878853012	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	71	543	0	ENST00000371953.3:c.531T>G	p.Tyr177Ter	p.Y177*	ENST00000371953	NM_000314.4	177	taT/taG	6/9	1	2	FACETS	0.691	0.608	0.779	0.691	0.608	0.779	SUBCLONAL	1	FALSE	1	0.628459867302617	2		543	327	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997696	149997696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749907686	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	65	324	0	ENST00000253339.5:c.2771G>A	p.Arg924Gln	p.R924Q	ENST00000253339		924	cGa/cAa	5/7	1	2	FACETS	0.708	0.62	0.803	0.708	0.62	0.803	SUBCLONAL	1	FALSE	1	0.628459867302617	2		324	292	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222973	5222973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1014796224	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	151	424	1	ENST00000357368.4:c.2830G>A	p.Gly944Arg	p.G944R	ENST00000357368	NM_002850.3	944	Ggg/Agg	18/38	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.628459867302617	2		425	451	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216486	108216486	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	14	256	0	ENST00000278616.4:c.8435C>A	p.Ser2812Tyr	p.S2812Y	ENST00000278616	NM_000051.3	2812	tCt/tAt	58/63	1	2	FACETS	0.301	0.218	0.4	0.301	0.218	0.4	SUBCLONAL	1	FALSE	1	0.628459867302617	2		256	148	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410597	63410597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758807218	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	178	406	1	ENST00000330258.3:c.2570G>A	p.Arg857Gln	p.R857Q	ENST00000330258	NM_152424.3	857	cGa/cAa	2/2	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	FALSE	0	0.628459867302617	1		407	269	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607663	43607663	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	52	956	0	ENST00000355710.3:c.1639G>T	p.Asp547Tyr	p.D547Y	ENST00000355710	NM_020975.4	547	Gat/Tat	8/20	1	2	FACETS	0.209	0.178	0.245	0.209	0.178	0.245	SUBCLONAL	1	FALSE	1	0.628459867302617	2		956	790	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736915	736915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs910562293	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	143	531	0	ENST00000314574.4:c.1184G>A	p.Arg395Gln	p.R395Q	ENST00000314574	NM_005433.3	395	cGa/cAa	10/12	0.628459867302617	3	FACETS	1	0.944	1	0.52	0.476	0.566	CLONAL	1	FALSE	1	0.628459867302617	3		531	575	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326261	62326261	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767674666	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	261	999	0	ENST00000360203.5:c.3277G>A	p.Asp1093Asn	p.D1093N	ENST00000360203	NM_001283009.1	1093	Gac/Aac	32/35	0.628459867302617	3	FACETS	0.935	0.875	0.996	0.467	0.437	0.498	CLONAL	1	FALSE	1	0.628459867302617	3		999	1168	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670256	134670256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	124	465	0	ENST00000398015.3:c.167G>A	p.Arg56His	p.R56H	ENST00000398015	NM_004441.4	56	cGc/cAc	3/16	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	FALSE	1	0.628459867302617	2		465	385	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739368	46739368	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759993383	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	172	515	3	ENST00000371975.4:c.1559C>T	p.Ser520Leu	p.S520L	ENST00000371975	NM_003579.3	520	tCg/tTg	14/18	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.628459867302617	2		518	519	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182681676	182681676	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	89	388	0	ENST00000292782.4:c.382G>T	p.Glu128Ter	p.E128*	ENST00000292782	NM_020640.2	128	Gaa/Taa	3/7	1	2	FACETS	0.88	0.788	0.975	0.88	0.788	0.975	CLONAL	1	FALSE	1	0.628459867302617	2		388	322	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198283248	198283248	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	122	462	0	ENST00000335508.6:c.480C>A	p.His160Gln	p.H160Q	ENST00000335508	NM_012433.2	160	caC/caA	5/25	1	2	FACETS	0.954	0.87	1	0.954	0.87	1	CLONAL	1	FALSE	1	0.628459867302617	2		462	407	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597540	28597540	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	140	570	0	ENST00000241453.7:c.2365C>A	p.Leu789Ile	p.L789I	ENST00000241453	NM_004119.2	789	Ctt/Att	19/24	1	2	FACETS	0.954	0.875	1	0.954	0.875	1	CLONAL	1	FALSE	1	0.628459867302617	2		570	467	SUCCESS
AR	367	MSKCC	GRCh37	X	66765620	66765620	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370893700	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	28	463	0	ENST00000374690.3:c.632C>T	p.Ala211Val	p.A211V	ENST00000374690	NM_000044.3	211	gCg/gTg	1/8	1	1	FACETS	0.164	0.131	0.202	0.164	0.131	0.202	SUBCLONAL	1	FALSE	0	0.628459867302617	1		463	373	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589609	67589609	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	50	311	0	ENST00000274335.5:c.1372G>T	p.Glu458Ter	p.E458*	ENST00000274335		458	Gaa/Taa	10/15	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	FALSE	1	0.628459867302617	2		311	148	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163909	152163909	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	24	481	0	ENST00000206249.3:c.630G>T	p.Lys210Asn	p.K210N	ENST00000206249	NM_000125.3	210	aaG/aaT	2/8	1	2	FACETS	0.205	0.161	0.257	0.205	0.161	0.257	SUBCLONAL	1	FALSE	1	0.628459867302617	2		481	372	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206852	102206852	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	97	399	1	ENST00000263464.3:c.1480G>T	p.Glu494Ter	p.E494*	ENST00000263464	NM_001165.4	494	Gaa/Taa	7/9	1	2	FACETS	0.897	0.808	0.991	0.897	0.808	0.991	CLONAL	1	FALSE	1	0.628459867302617	2		400	344	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906894	32906894	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	90	469	0	ENST00000380152.3:c.1279G>T	p.Asp427Tyr	p.D427Y	ENST00000380152		427	Gac/Tac	10/27	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	FALSE	1	0.628459867302617	2		469	264	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740632	58740632	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs202221678	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	137	538	0	ENST00000305921.3:c.1537T>G	p.Leu513Val	p.L513V	ENST00000305921	NM_003620.3	513	Ttg/Gtg	6/6	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	1	0.628459867302617	2		538	424	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726601	41726601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775741490	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	213	701	0	ENST00000301178.4:c.146G>A	p.Gly49Glu	p.G49E	ENST00000301178	NM_021913.4	49	gGa/gAa	2/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.628459867302617	2		701	609	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49280961	49280961	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	107	411	0	ENST00000282018.3:c.8G>T	p.Arg3Ile	p.R3I	ENST00000282018	NM_020377.2	3	aGa/aTa	1/1	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.628459867302617	2		411	295	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142949972	142949972	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	18	506	1	ENST00000262992.4:c.2738G>T	p.Arg913Ile	p.R913I	ENST00000262992	NM_001101669.1	913	aGa/aTa	24/24	1	2	FACETS	0.205	0.154	0.266	0.205	0.154	0.266	SUBCLONAL	1	FALSE	1	0.628459867302617	2		507	279	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374942	149374942	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	429	649	1	ENST00000360632.3:c.152C>A	p.Ser51Tyr	p.S51Y	ENST00000360632	NM_015472.4	51	tCt/tAt	2/7	0.442284616665144	3	FACETS	1	0.982	1			1	CLONAL	2	FALSE	NA	0.628459867302617	3		650	861	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578239	28578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	138	580	0	ENST00000241453.7:c.2932G>T	p.Glu978Ter	p.E978*	ENST00000241453	NM_004119.2	978	Gag/Tag	24/24	1	2	FACETS	0.858	0.785	0.933	0.858	0.785	0.933	CLONAL	1	FALSE	1	0.628459867302617	2		580	512	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609667	28609667	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	153	562	0	ENST00000241453.7:c.1562G>A	p.Gly521Asp	p.G521D	ENST00000241453	NM_004119.2	521	gGc/gAc	12/24	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	1	0.628459867302617	2		562	466	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866112	37866112	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	183	688	0	ENST00000269571.5:c.621G>T	p.Glu207Asp	p.E207D	ENST00000269571		207	gaG/gaT	5/27	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.628459867302617	2		688	565	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032475	12032475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194360851	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	61	340	0	ENST00000353533.5:c.911G>A	p.Arg304Gln	p.R304Q	ENST00000353533	NM_003010.3	304	cGa/cAa	9/11	1	2	FACETS	0.871	0.761	0.986	0.871	0.761	0.986	CLONAL	1	FALSE	1	0.628459867302617	2		340	223	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509768	106509768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146487441	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	100	555	0	ENST00000359195.3:c.1762G>A	p.Ala588Thr	p.A588T	ENST00000359195	NM_002649.2	588	Gca/Aca	2/11	0.628459867302617	3	FACETS	0.773	0.693	0.858	0.387	0.346	0.429	SUBCLONAL	1	FALSE	1	0.628459867302617	3		555	541	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52663052	52663052	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	12	221	0	ENST00000394830.3:c.1302-1G>T		p.X434_splice	ENST00000394830	NM_018313.4	434			1	2	FACETS	0.253	0.178	0.344	0.253	0.178	0.344	SUBCLONAL	1	FALSE	1	0.628459867302617	2		221	151	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028161	48028161	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1060502920	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	92	331	0	ENST00000234420.5:c.3039G>T	p.Lys1013Asn	p.K1013N	ENST00000234420	NM_000179.2	1013	aaG/aaT	4/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.628459867302617	2		331	251	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641559	18641559	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	55	334	0	ENST00000266497.5:c.2558G>T	p.Arg853Ile	p.R853I	ENST00000266497		853	aGa/aTa	17/31	1	2	FACETS	0.826	0.716	0.942	0.826	0.716	0.942	CLONAL	1	FALSE	1	0.628459867302617	2		334	212	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069589	69069589	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	78	518	0	ENST00000288368.4:c.4264G>T	p.Asp1422Tyr	p.D1422Y	ENST00000288368	NM_024870.2	1422	Gac/Tac	35/40	1	2	FACETS	0.88	0.782	0.983	0.88	0.782	0.983	CLONAL	1	FALSE	1	0.628459867302617	2		518	282	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028074	69028074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	126	552	1	ENST00000288368.4:c.3233G>A	p.Gly1078Glu	p.G1078E	ENST00000288368	NM_024870.2	1078	gGa/gAa	26/40	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.628459867302617	2		553	362	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37141769	37141769	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761967890	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	149	584	0	ENST00000373509.5:c.844G>A	p.Glu282Lys	p.E282K	ENST00000373509	NM_002648.3	282	Gaa/Aaa	6/6	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	1	0.628459867302617	2		584	473	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075442	8075442	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	77	324	0	ENST00000377482.5:c.128A>C	p.Asn43Thr	p.N43T	ENST00000377482	NM_018948.3	43	aAc/aCc	3/4	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.628459867302617	2		324	216	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781609	9781609	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	86	727	0	ENST00000377346.4:c.1919A>G	p.Asn640Ser	p.N640S	ENST00000377346	NM_005026.3	640	aAc/aGc	15/24	1	2	FACETS	0.418	0.37	0.47	0.418	0.37	0.47	SUBCLONAL	1	FALSE	1	0.628459867302617	2		727	654	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237749	16237749	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	140	561	0	ENST00000375759.3:c.1196A>C	p.Lys399Thr	p.K399T	ENST00000375759	NM_015001.2	399	aAa/aCa	5/15	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	FALSE	1	0.628459867302617	2		561	438	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255154	16255154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766167369	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	23	423	0	ENST00000375759.3:c.2419C>T	p.Arg807Cys	p.R807C	ENST00000375759	NM_015001.2	807	Cgc/Tgc	11/15	1	2	FACETS	0.189	0.147	0.238	0.189	0.147	0.238	SUBCLONAL	1	FALSE	1	0.628459867302617	2		423	387	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255394	16255394	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	143	531	0	ENST00000375759.3:c.2659G>T	p.Glu887Ter	p.E887*	ENST00000375759	NM_015001.2	887	Gag/Tag	11/15	1	2	FACETS	0.896	0.822	0.972	0.896	0.822	0.972	CLONAL	1	FALSE	1	0.628459867302617	2		531	508	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257170	16257170	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	120	489	0	ENST00000375759.3:c.4435G>T	p.Asp1479Tyr	p.D1479Y	ENST00000375759	NM_015001.2	1479	Gat/Tat	11/15	1	2	FACETS	0.903	0.822	0.987	0.903	0.822	0.987	CLONAL	1	FALSE	1	0.628459867302617	2		489	423	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257226	16257226	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	123	547	0	ENST00000375759.3:c.4491G>T	p.Lys1497Asn	p.K1497N	ENST00000375759	NM_015001.2	1497	aaG/aaT	11/15	1	2	FACETS	0.952	0.869	1	0.952	0.869	1	CLONAL	1	FALSE	1	0.628459867302617	2		547	411	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257309	16257309	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1423904427	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	138	589	0	ENST00000375759.3:c.4574T>G	p.Leu1525Trp	p.L1525W	ENST00000375759	NM_015001.2	1525	tTg/tGg	11/15	1	2	FACETS	0.854	0.782	0.929	0.854	0.782	0.929	CLONAL	1	FALSE	1	0.628459867302617	2		589	514	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258210	16258210	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	191	593	0	ENST00000375759.3:c.5475G>T	p.Lys1825Asn	p.K1825N	ENST00000375759	NM_015001.2	1825	aaG/aaT	11/15	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	1	0.628459867302617	2		593	596	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106487	27106487	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	175	690	0	ENST00000324856.7:c.6098A>C	p.Lys2033Thr	p.K2033T	ENST00000324856	NM_006015.4	2033	aAg/aCg	20/20	1	2	FACETS	0.954	0.883	1	0.954	0.883	1	CLONAL	1	FALSE	1	0.628459867302617	2		690	584	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428466	78428466	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	100	387	0	ENST00000370768.2:c.1333G>T	p.Glu445Ter	p.E445*	ENST00000370768	NM_003902.3	445	Gaa/Taa	14/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.628459867302617	2		387	284	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736317	85736317	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	79	253	0	ENST00000370580.1:c.330A>C	p.Lys110Asn	p.K110N	ENST00000370580	NM_003921.4	110	aaA/aaC	2/3	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	1	0.628459867302617	2		253	231	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462132	120462132	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs745390221	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	187	696	0	ENST00000256646.2:c.5584T>G	p.Leu1862Val	p.L1862V	ENST00000256646	NM_024408.3	1862	Ttg/Gtg	31/34	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.628459867302617	2		696	559	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551467	150551467	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	60	851	1	ENST00000369026.2:c.540G>T	p.Glu180Asp	p.E180D	ENST00000369026	NM_021960.4	180	gaG/gaT	1/3	1	2	FACETS	0.229	0.197	0.265	0.229	0.197	0.265	SUBCLONAL	1	FALSE	1	0.628459867302617	2		852	833	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163297346	163297346	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	72	395	0	ENST00000271452.3:c.192T>G	p.Phe64Leu	p.F64L	ENST00000271452	NM_145697.2	64	ttT/ttG	3/14	1	2	FACETS	0.836	0.739	0.939	0.836	0.739	0.939	CLONAL	1	FALSE	1	0.628459867302617	2		395	274	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193110982	193110982	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	32	175	0	ENST00000367435.3:c.515C>A	p.Ser172Tyr	p.S172Y	ENST00000367435	NM_024529.4	172	tCt/tAt	7/17	1	2	FACETS	0.878	0.728	1	0.878	0.728	1	CLONAL	1	FALSE	1	0.628459867302617	2		175	116	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653258	206653258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782747957	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	238	758	0	ENST00000367120.3:c.1229C>T	p.Ala410Val	p.A410V	ENST00000367120	NM_014002.3	410	gCg/gTg	11/22	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.628459867302617	2		758	692	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809248	243809248	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	66	492	0	ENST00000263826.5:c.376G>A	p.Asp126Asn	p.D126N	ENST00000263826	NM_005465.4	126	Gat/Aat	4/13	1	2	FACETS	0.717	0.628	0.811	0.717	0.628	0.811	SUBCLONAL	1	FALSE	1	0.628459867302617	2		492	293	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858997	243858997	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	47	363	0	ENST00000263826.5:c.68G>T	p.Arg23Met	p.R23M	ENST00000263826	NM_005465.4	23	aGg/aTg	2/13	1	2	FACETS	0.631	0.537	0.732	0.631	0.537	0.732	SUBCLONAL	1	FALSE	1	0.628459867302617	2		363	237	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604509	43604509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763670106	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	179	658	0	ENST00000355710.3:c.1094C>T	p.Ser365Leu	p.S365L	ENST00000355710	NM_020975.4	365	tCg/tTg	6/20	1	2	FACETS	0.987	0.916	1	0.987	0.916	1	CLONAL	1	FALSE	1	0.628459867302617	2		658	577	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332343	70332343	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	144	508	0	ENST00000373644.4:c.248A>C	p.Asn83Thr	p.N83T	ENST00000373644	NM_030625.2	83	aAt/aCt	2/12	1	2	FACETS	0.99	0.91	1	0.99	0.91	1	CLONAL	1	FALSE	1	0.628459867302617	2		508	463	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406692	70406692	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	104	533	0	ENST00000373644.4:c.4206C>A	p.Phe1402Leu	p.F1402L	ENST00000373644	NM_030625.2	1402	ttC/ttA	4/12	1	2	FACETS	0.935	0.846	1	0.935	0.846	1	CLONAL	1	FALSE	1	0.628459867302617	2		533	354	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450594	70450594	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	116	399	0	ENST00000373644.4:c.5434G>T	p.Val1812Leu	p.V1812L	ENST00000373644	NM_030625.2	1812	Gta/Tta	12/12	1	2	FACETS	0.873	0.793	0.956	0.873	0.793	0.956	CLONAL	1	FALSE	1	0.628459867302617	2		399	423	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451510	70451510	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	172	610	0	ENST00000373644.4:c.6350T>G	p.Val2117Gly	p.V2117G	ENST00000373644	NM_030625.2	2117	gTt/gGt	12/12	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	1	0.628459867302617	2		610	531	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659850	88659850	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	82	366	0	ENST00000372037.3:c.497C>A	p.Ala166Asp	p.A166D	ENST00000372037	NM_004329.2	166	gCt/gAt	7/13	1	2	FACETS	0.974	0.87	1	0.974	0.87	1	CLONAL	1	FALSE	1	0.628459867302617	2		366	268	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912113	114912113	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	146	460	0	ENST00000543371.1:c.1183G>T	p.Glu395Ter	p.E395*	ENST00000543371	NM_001198531.1	395	Gag/Tag	11/14	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	FALSE	1	0.628459867302617	2		460	456	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239531	123239531	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	69	841	0	ENST00000358487.5:c.2306A>G	p.Tyr769Cys	p.Y769C	ENST00000358487	NM_000141.4	769	tAc/tGc	18/18	1	2	FACETS	0.284	0.246	0.324	0.284	0.246	0.324	SUBCLONAL	1	FALSE	1	0.628459867302617	2		841	774	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514286	69514286	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1487423822	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	192	687	0	ENST00000294312.3:c.395A>C	p.Asn132Thr	p.N132T	ENST00000294312	NM_005117.2	132	aAt/aCt	3/3	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.628459867302617	2		687	602	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631092	69631092	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	43	546	1	ENST00000334134.2:c.320C>A	p.Ala107Asp	p.A107D	ENST00000334134	NM_005247.2	107	gCt/gAt	2/3	1	2	FACETS	0.312	0.261	0.369	0.312	0.261	0.369	SUBCLONAL	1	FALSE	1	0.628459867302617	2		547	438	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194137	94194137	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	116	455	0	ENST00000323929.3:c.1291G>T	p.Asp431Tyr	p.D431Y	ENST00000323929	NM_005591.3	431	Gat/Tat	12/20	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	FALSE	1	0.628459867302617	2		455	369	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204870	94204870	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	98	415	0	ENST00000323929.3:c.715G>T	p.Asp239Tyr	p.D239Y	ENST00000323929	NM_005591.3	239	Gat/Tat	8/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.628459867302617	2		415	273	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999583	100999583	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1355191904	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	53	952	0	ENST00000325455.5:c.219G>T	p.Lys73Asn	p.K73N	ENST00000325455	NM_001202474.3	73	aaG/aaT	1/8	1	2	FACETS	0.206	0.175	0.241	0.206	0.175	0.241	SUBCLONAL	1	FALSE	1	0.628459867302617	2		952	817	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417097	417097	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	115	386	1	ENST00000399788.2:c.3453G>T	p.Lys1151Asn	p.K1151N	ENST00000399788	NM_001042603.1	1151	aaG/aaT	23/28	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	FALSE	NA	0.628459867302617	2		387	329	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905393	11905393	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	94	334	0	ENST00000396373.4:c.43A>C	p.Ile15Leu	p.I15L	ENST00000396373	NM_001987.4	15	Att/Ctt	2/8	NA	2	FACETS	0.87	0.781	0.962			1	INDETERMINATE	1	FALSE	NA	0.628459867302617	2		334	344	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534809	18534809	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	28	447	0	ENST00000266497.5:c.1867C>A	p.Leu623Met	p.L623M	ENST00000266497		623	Ctg/Atg	12/31	1	2	FACETS	0.244	0.195	0.3	0.244	0.195	0.3	SUBCLONAL	1	FALSE	1	0.628459867302617	2		447	365	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552742	18552742	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	105	526	0	ENST00000266497.5:c.2153T>C	p.Phe718Ser	p.F718S	ENST00000266497		718	tTt/tCt	14/31	1	2	FACETS	0.974	0.882	1	0.974	0.882	1	CLONAL	1	FALSE	1	0.628459867302617	2		526	343	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650661	18650661	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	12	368	0	ENST00000266497.5:c.2872C>A	p.Leu958Ile	p.L958I	ENST00000266497		958	Cta/Ata	20/31	1	2	FACETS	0.174	0.122	0.239	0.174	0.122	0.239	SUBCLONAL	1	FALSE	1	0.628459867302617	2		368	219	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656347	18656347	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	80	354	0	ENST00000266497.5:c.3026A>T	p.Glu1009Val	p.E1009V	ENST00000266497		1009	gAa/gTa	21/31	1	2	FACETS	0.987	0.881	1	0.987	0.881	1	CLONAL	1	FALSE	1	0.628459867302617	2		354	258	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18762475	18762475	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	72	406	0	ENST00000266497.5:c.3971A>C	p.Lys1324Thr	p.K1324T	ENST00000266497		1324	aAg/aCg	29/31	1	2	FACETS	0.849	0.75	0.952	0.849	0.75	0.952	CLONAL	1	FALSE	1	0.628459867302617	2		406	270	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437688	49437688	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	318	839	0	ENST00000301067.7:c.5282A>C	p.Lys1761Thr	p.K1761T	ENST00000301067	NM_003482.3	1761	aAg/aCg	22/54	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.628459867302617	2		839	867	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448497	49448497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770192344	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	202	665	0	ENST00000301067.7:c.214G>A	p.Gly72Arg	p.G72R	ENST00000301067	NM_003482.3	72	Ggg/Agg	3/54	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	FALSE	1	0.628459867302617	2		665	643	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487947	56487947	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	118	647	0	ENST00000267101.3:c.1678G>T	p.Glu560Ter	p.E560*	ENST00000267101	NM_001982.3	560	Gag/Tag	14/28	1	2	FACETS	0.683	0.618	0.75	0.683	0.618	0.75	SUBCLONAL	1	FALSE	1	0.628459867302617	2		647	550	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495384	56495384	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	181	660	0	ENST00000267101.3:c.3574G>T	p.Asp1192Tyr	p.D1192Y	ENST00000267101	NM_001982.3	1192	Gat/Tat	28/28	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.628459867302617	2		660	538	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102874128	102874128	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	83	387	0	ENST00000307046.8:c.32T>G	p.Leu11Ter	p.L11*	ENST00000307046	NM_001111285.1	11	tTa/tGa	1/4	1	2	FACETS	0.957	0.855	1	0.957	0.855	1	CLONAL	1	FALSE	1	0.628459867302617	2		387	276	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120785284	120785284	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775588129	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	217	667	1	ENST00000257552.2:c.824C>T	p.Ala275Val	p.A275V	ENST00000257552	NM_002442.3	275	gCg/gTg	12/15	1	2	FACETS	0.997	0.931	1	0.997	0.931	1	CLONAL	1	FALSE	1	0.628459867302617	2		668	693	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123880981	123880981	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	91	277	1	ENST00000330479.4:c.597+2T>C		p.X199_splice	ENST00000330479	NM_020382.3	199			1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	FALSE	1	0.628459867302617	2		278	286	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123888162	123888162	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	76	282	0	ENST00000330479.4:c.640A>G	p.Lys214Glu	p.K214E	ENST00000330479	NM_020382.3	214	Aag/Gag	6/9	1	2	FACETS	0.899	0.798	1	0.899	0.798	1	CLONAL	1	FALSE	1	0.628459867302617	2		282	269	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563384	21563384	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	290	962	0	ENST00000382592.4:c.535T>C	p.Ser179Pro	p.S179P	ENST00000382592	NM_014572.2	179	Tcg/Ccg	4/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.628459867302617	2		962	913	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589394	28589394	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	16	323	0	ENST00000241453.7:c.2654-1G>T		p.X885_splice	ENST00000241453	NM_004119.2	885			1	2	FACETS	0.201	0.148	0.264	0.201	0.148	0.264	SUBCLONAL	1	FALSE	1	0.628459867302617	2		323	253	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28883039	28883039	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	118	395	0	ENST00000282397.4:c.3661A>C	p.Ser1221Arg	p.S1221R	ENST00000282397	NM_002019.4	1221	Agc/Cgc	28/30	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	FALSE	1	0.628459867302617	2		395	373	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28901669	28901669	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1262900671	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	28	366	0	ENST00000282397.4:c.2726T>C	p.Val909Ala	p.V909A	ENST00000282397	NM_002019.4	909	gTt/gCt	20/30	1	2	FACETS	0.247	0.197	0.304	0.247	0.197	0.304	SUBCLONAL	1	FALSE	1	0.628459867302617	2		366	361	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001898	29001898	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	121	447	0	ENST00000282397.4:c.1267A>G	p.Ile423Val	p.I423V	ENST00000282397	NM_002019.4	423	Att/Gtt	9/30	1	2	FACETS	0.98	0.894	1	0.98	0.894	1	CLONAL	1	FALSE	1	0.628459867302617	2		447	393	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004305	29004305	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	63	301	0	ENST00000282397.4:c.989-1G>T		p.X330_splice	ENST00000282397	NM_002019.4	330			1	2	FACETS	0.969	0.851	1	0.969	0.851	1	CLONAL	1	FALSE	1	0.628459867302617	2		301	207	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907281	32907281	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	56	455	0	ENST00000380152.3:c.1666A>C	p.Asn556His	p.N556H	ENST00000380152		556	Aat/Cat	10/27	1	2	FACETS	0.588	0.507	0.675	0.588	0.507	0.675	SUBCLONAL	1	FALSE	1	0.628459867302617	2		455	303	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907381	32907381	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	54	360	0	ENST00000380152.3:c.1766A>C	p.Lys589Thr	p.K589T	ENST00000380152		589	aAg/aCg	10/27	1	2	FACETS	0.859	0.745	0.981	0.859	0.745	0.981	CLONAL	1	FALSE	1	0.628459867302617	2		360	200	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907425	32907425	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	50	302	0	ENST00000380152.3:c.1810A>C	p.Lys604Gln	p.K604Q	ENST00000380152		604	Aaa/Caa	10/27	1	2	FACETS	0.812	0.699	0.932	0.812	0.699	0.932	CLONAL	1	FALSE	1	0.628459867302617	2		302	196	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913631	32913631	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	13	383	0	ENST00000380152.3:c.5139T>G	p.Asn1713Lys	p.N1713K	ENST00000380152		1713	aaT/aaG	11/27	1	2	FACETS	0.204	0.145	0.275	0.204	0.145	0.275	SUBCLONAL	1	FALSE	1	0.628459867302617	2		383	203	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913644	32913644	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	66	387	0	ENST00000380152.3:c.5152A>C	p.Asn1718His	p.N1718H	ENST00000380152		1718	Aat/Cat	11/27	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	FALSE	1	0.628459867302617	2		387	201	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914295	32914295	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	79	527	0	ENST00000380152.3:c.5803A>C	p.Asn1935His	p.N1935H	ENST00000380152		1935	Aat/Cat	11/27	1	2	FACETS	0.935	0.832	1	0.935	0.832	1	CLONAL	1	FALSE	1	0.628459867302617	2		527	269	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915039	32915039	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs397507866	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	125	508	0	ENST00000380152.3:c.6547G>T	p.Glu2183Ter	p.E2183*	ENST00000380152		2183	Gaa/Taa	11/27	1	2	FACETS	0.992	0.906	1	0.992	0.906	1	CLONAL	1	FALSE	1	0.628459867302617	2		508	401	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972303	32972303	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	61	369	0	ENST00000380152.3:c.9653C>A	p.Ser3218Tyr	p.S3218Y	ENST00000380152		3218	tCt/tAt	27/27	1	2	FACETS	0.792	0.691	0.899	0.792	0.691	0.899	SUBCLONAL	1	FALSE	1	0.628459867302617	2		369	245	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955449	48955449	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	86	340	0	ENST00000267163.4:c.1565A>C	p.Asn522Thr	p.N522T	ENST00000267163	NM_000321.2	522	aAt/aCt	17/27	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	FALSE	1	0.628459867302617	2		340	273	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355039	73355039	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	60	414	0	ENST00000377767.4:c.331G>T	p.Asp111Tyr	p.D111Y	ENST00000377767	NM_014953.3	111	Gat/Tat	2/21	1	2	FACETS	0.589	0.511	0.673	0.589	0.511	0.673	SUBCLONAL	1	FALSE	1	0.628459867302617	2		414	324	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527667	103527667	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377390651	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	58	219	0	ENST00000355739.4:c.2975G>A	p.Arg992Gln	p.R992Q	ENST00000355739	NM_000123.3	992	cGa/cAa	15/15	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	FALSE	1	0.628459867302617	2		219	174	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438324	110438324	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	69	130	0	ENST00000375856.3:c.77A>G	p.Asn26Ser	p.N26S	ENST00000375856	NM_003749.2	26	aAc/aGc	1/2	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.628459867302617	2		130	182	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100070	30100070	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	75	653	0	ENST00000331968.5:c.1550A>G	p.Asn517Ser	p.N517S	ENST00000331968	NM_002742.2	517	aAc/aGc	10/18	1	2	FACETS	0.485	0.426	0.548	0.485	0.426	0.548	SUBCLONAL	1	FALSE	1	0.628459867302617	2		653	492	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135341	30135341	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	117	435	0	ENST00000331968.5:c.477C>A	p.Phe159Leu	p.F159L	ENST00000331968	NM_002742.2	159	ttC/ttA	3/18	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	FALSE	1	0.628459867302617	2		435	369	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81534662	81534662	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs755428708	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	91	407	0	ENST00000298171.2:c.307G>T	p.Val103Leu	p.V103L	ENST00000298171	NM_000369.2	103	Gtg/Ttg	3/10	1	2	FACETS	0.894	0.802	0.99	0.894	0.802	0.99	CLONAL	1	FALSE	1	0.628459867302617	2		407	324	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554299	81554299	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	40	382	0	ENST00000298171.2:c.319G>T	p.Glu107Ter	p.E107*	ENST00000298171	NM_000369.2	107	Gaa/Taa	4/10	1	2	FACETS	0.42	0.35	0.497	0.42	0.35	0.497	SUBCLONAL	1	FALSE	1	0.628459867302617	2		382	303	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560312	95560312	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	165	393	0	ENST00000393063.1:c.5277A>C	p.Lys1759Asn	p.K1759N	ENST00000393063	NM_030621.3	1759	aaA/aaC	25/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.628459867302617	2		393	452	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570011	95570011	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	17	513	0	ENST00000393063.1:c.3722A>C	p.Lys1241Thr	p.K1241T	ENST00000393063	NM_030621.3	1241	aAa/aCa	22/28	1	2	FACETS	0.169	0.125	0.22	0.169	0.125	0.22	SUBCLONAL	1	FALSE	1	0.628459867302617	2		513	321	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40993395	40993395	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	23	299	0	ENST00000267868.3:c.221T>G	p.Ile74Ser	p.I74S	ENST00000267868	NM_002875.4	74	aTt/aGt	3/10	1	2	FACETS	0.265	0.207	0.332	0.265	0.207	0.332	SUBCLONAL	1	FALSE	1	0.628459867302617	2		299	276	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035338	42035338	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	82	394	0	ENST00000219905.7:c.5180T>G	p.Ile1727Ser	p.I1727S	ENST00000219905	NM_001164273.1	1727	aTt/aGt	15/24	1	2	FACETS	0.761	0.676	0.85	0.761	0.676	0.85	SUBCLONAL	1	FALSE	1	0.628459867302617	2		394	343	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701254	43701254	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	98	548	0	ENST00000382044.4:c.5441A>G	p.His1814Arg	p.H1814R	ENST00000382044	NM_001141980.1	1814	cAt/cGt	26/28	1	2	FACETS	0.576	0.516	0.641	0.576	0.516	0.641	SUBCLONAL	1	FALSE	1	0.628459867302617	2		548	541	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43771625	43771625	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	162	565	0	ENST00000382044.4:c.758T>C	p.Val253Ala	p.V253A	ENST00000382044	NM_001141980.1	253	gTt/gCt	7/28	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	FALSE	1	0.628459867302617	2		565	515	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43783912	43783912	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	148	579	0	ENST00000382044.4:c.326T>C	p.Ile109Thr	p.I109T	ENST00000382044	NM_001141980.1	109	aTc/aCc	4/28	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	1	0.628459867302617	2		579	459	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292763	91292763	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	120	485	0	ENST00000355112.3:c.265T>C	p.Phe89Leu	p.F89L	ENST00000355112	NM_000057.2	89	Ttc/Ctc	3/22	1	2	FACETS	0.828	0.753	0.907	0.828	0.753	0.907	CLONAL	1	FALSE	1	0.628459867302617	2		485	461	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292973	91292973	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	106	570	0	ENST00000355112.3:c.475G>T	p.Asp159Tyr	p.D159Y	ENST00000355112	NM_000057.2	159	Gac/Tac	3/22	1	2	FACETS	0.767	0.692	0.845	0.767	0.692	0.845	SUBCLONAL	1	FALSE	1	0.628459867302617	2		570	440	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304059	91304059	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	39	559	1	ENST00000355112.3:c.1456C>A	p.Leu486Ile	p.L486I	ENST00000355112	NM_000057.2	486	Ctt/Att	7/22	1	2	FACETS	0.261	0.216	0.312	0.261	0.216	0.312	SUBCLONAL	1	FALSE	1	0.628459867302617	2		560	475	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639087	3639087	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	212	720	0	ENST00000294008.3:c.4552G>T	p.Glu1518Ter	p.E1518*	ENST00000294008	NM_032444.2	1518	Gag/Tag	12/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.628459867302617	2		720	640	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778780	3778780	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	233	962	0	ENST00000262367.5:c.6268C>A	p.Leu2090Ile	p.L2090I	ENST00000262367	NM_004380.2	2090	Ctc/Atc	31/31	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.628459867302617	2		962	729	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820972	3820972	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	37	584	0	ENST00000262367.5:c.2479G>T	p.Ala827Ser	p.A827S	ENST00000262367	NM_004380.2	827	Gct/Tct	14/31	1	2	FACETS	0.222	0.183	0.267	0.222	0.183	0.267	SUBCLONAL	1	FALSE	1	0.628459867302617	2		584	530	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828769	3828769	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	178	599	0	ENST00000262367.5:c.1873C>A	p.Arg625Ser	p.R625S	ENST00000262367	NM_004380.2	625	Cgc/Agc	9/31	1	2	FACETS	0.96	0.89	1	0.96	0.89	1	CLONAL	1	FALSE	1	0.628459867302617	2		599	590	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858122	9858122	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	140	588	0	ENST00000330684.3:c.3279A>C	p.Lys1093Asn	p.K1093N	ENST00000330684	NM_001134407.1	1093	aaA/aaC	13/13	1	2	FACETS	0.94	0.862	1	0.94	0.862	1	CLONAL	1	FALSE	1	0.628459867302617	2		588	474	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916195	9916195	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	64	528	0	ENST00000330684.3:c.2094T>G	p.Tyr698Ter	p.Y698*	ENST00000330684	NM_001134407.1	698	taT/taG	10/13	1	2	FACETS	0.458	0.397	0.523	0.458	0.397	0.523	SUBCLONAL	1	FALSE	1	0.628459867302617	2		528	445	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923472	9923472	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs986690961	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	128	552	0	ENST00000330684.3:c.1815A>G	p.Ile605Met	p.I605M	ENST00000330684	NM_001134407.1	605	atA/atG	9/13	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	FALSE	1	0.628459867302617	2		552	407	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934828	9934828	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	30	529	0	ENST00000330684.3:c.1462A>G	p.Lys488Glu	p.K488E	ENST00000330684	NM_001134407.1	488	Aaa/Gaa	6/13	1	2	FACETS	0.245	0.197	0.299	0.245	0.197	0.299	SUBCLONAL	1	FALSE	1	0.628459867302617	2		529	390	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031990	10031990	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	167	645	2	ENST00000330684.3:c.833C>A	p.Ser278Tyr	p.S278Y	ENST00000330684	NM_001134407.1	278	tCt/tAt	3/13	1	2	FACETS	0.981	0.907	1	0.981	0.907	1	CLONAL	1	FALSE	1	0.628459867302617	2		647	542	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026055	14026055	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	17	303	0	ENST00000311895.7:c.1015G>A	p.Ala339Thr	p.A339T	ENST00000311895	NM_005236.2	339	Gct/Act	6/11	1	2	FACETS	0.189	0.14	0.246	0.189	0.14	0.246	SUBCLONAL	1	FALSE	1	0.628459867302617	2		303	287	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042164	14042164	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	72	258	1	ENST00000311895.7:c.2711C>A	p.Ser904Tyr	p.S904Y	ENST00000311895	NM_005236.2	904	tCt/tAt	11/11	1	2	FACETS	0.821	0.725	0.922	0.821	0.725	0.922	CLONAL	1	FALSE	1	0.628459867302617	2		259	279	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56855438	56855438	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	102	344	0	ENST00000308159.5:c.587T>G	p.Ile196Ser	p.I196S	ENST00000308159	NM_014669.4	196	aTt/aGt	7/22	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	FALSE	1	0.628459867302617	2		344	322	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828369	72828369	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	165	567	0	ENST00000268489.5:c.8212G>T	p.Ala2738Ser	p.A2738S	ENST00000268489	NM_006885.3	2738	Gcc/Tcc	9/10	1	2	FACETS	0.991	0.916	1	0.991	0.916	1	CLONAL	1	FALSE	1	0.628459867302617	2		567	530	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934265	81934265	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	226	695	0	ENST00000359376.3:c.1242G>T	p.Gln414His	p.Q414H	ENST00000359376	NM_002661.3	414	caG/caT	14/33	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.628459867302617	2		695	684	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81960768	81960768	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	29	457	1	ENST00000359376.3:c.2499G>T	p.Glu833Asp	p.E833D	ENST00000359376	NM_002661.3	833	gaG/gaT	23/33	1	2	FACETS	0.216	0.173	0.265	0.216	0.173	0.265	SUBCLONAL	1	FALSE	1	0.628459867302617	2		458	428	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216889	7216889	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	108	534	0	ENST00000380728.2:c.632G>T	p.Arg211Ile	p.R211I	ENST00000380728		211	aGa/aTa	7/11	1	2	FACETS	0.797	0.72	0.878	0.797	0.72	0.878	SUBCLONAL	1	FALSE	1	0.628459867302617	2		534	431	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653074	29653074	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	107	385	0	ENST00000356175.3:c.5009A>C	p.Lys1670Thr	p.K1670T	ENST00000356175	NM_000267.3	1670	aAg/aCg	36/57	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	FALSE	1	0.628459867302617	2		385	338	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858105	40858105	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	67	812	0	ENST00000428826.2:c.1759C>A	p.Leu587Ile	p.L587I	ENST00000428826		587	Ctc/Atc	16/21	1	2	FACETS	0.276	0.239	0.316	0.276	0.239	0.316	SUBCLONAL	1	FALSE	1	0.628459867302617	2		812	773	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245219	41245219	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	173	674	0	ENST00000357654.3:c.2329T>C	p.Tyr777His	p.Y777H	ENST00000357654	NM_007294.3	777	Tat/Cat	10/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.628459867302617	2		674	483	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55478750	55478750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	130	398	0	ENST00000284073.2:c.323G>T	p.Arg108Ile	p.R108I	ENST00000284073	NM_138962.2	108	aGa/aTa	6/14	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	FALSE	1	0.628459867302617	2		398	408	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55674265	55674265	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	105	418	0	ENST00000284073.2:c.491T>G	p.Val164Gly	p.V164G	ENST00000284073	NM_138962.2	164	gTg/gGg	8/14	1	2	FACETS	0.974	0.882	1	0.974	0.882	1	CLONAL	1	FALSE	1	0.628459867302617	2		418	343	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760708	59760708	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1060501734	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	115	603	1	ENST00000259008.2:c.3699C>A	p.Asn1233Lys	p.N1233K	ENST00000259008	NM_032043.2	1233	aaC/aaA	20/20	1	2	FACETS	0.971	0.883	1	0.971	0.883	1	CLONAL	1	FALSE	1	0.628459867302617	2		604	377	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59878831	59878831	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	43	289	0	ENST00000259008.2:c.923A>C	p.Lys308Thr	p.K308T	ENST00000259008	NM_032043.2	308	aAa/aCa	8/20	1	2	FACETS	0.861	0.733	0.997	0.861	0.733	0.997	CLONAL	1	FALSE	1	0.628459867302617	2		289	159	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554607	63554607	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	37	614	0	ENST00000307078.5:c.132G>T	p.Gln44His	p.Q44H	ENST00000307078	NM_004655.3	44	caG/caT	2/11	1	2	FACETS	0.209	0.172	0.251	0.209	0.172	0.251	SUBCLONAL	1	FALSE	1	0.628459867302617	2		614	563	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39573273	39573273	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	22	402	0	ENST00000262039.4:c.754T>G	p.Leu252Val	p.L252V	ENST00000262039	NM_002647.2	252	Tta/Gta	7/25	1	2	FACETS	0.208	0.161	0.263	0.208	0.161	0.263	SUBCLONAL	1	FALSE	1	0.628459867302617	2		402	336	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39613817	39613817	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	76	417	0	ENST00000262039.4:c.1735G>T	p.Asp579Tyr	p.D579Y	ENST00000262039	NM_002647.2	579	Gat/Tat	16/25	1	2	FACETS	0.964	0.857	1	0.964	0.857	1	CLONAL	1	FALSE	1	0.628459867302617	2		417	251	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617746	39617746	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	91	379	1	ENST00000262039.4:c.1930G>T	p.Asp644Tyr	p.D644Y	ENST00000262039	NM_002647.2	644	Gat/Tat	17/25	1	2	FACETS	0.925	0.831	1	0.925	0.831	1	CLONAL	1	FALSE	1	0.628459867302617	2		380	313	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985834	60985834	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	116	412	0	ENST00000333681.4:c.66G>T	p.Lys22Asn	p.K22N	ENST00000333681		22	aaG/aaT	2/3	1	2	FACETS	0.869	0.789	0.952	0.869	0.789	0.952	CLONAL	1	FALSE	1	0.628459867302617	2		412	425	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5225797	5225797	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	55	810	0	ENST00000357368.4:c.2435A>G	p.Tyr812Cys	p.Y812C	ENST00000357368	NM_002850.3	812	tAc/tGc	17/38	1	2	FACETS	0.247	0.21	0.286	0.247	0.21	0.286	SUBCLONAL	1	FALSE	1	0.628459867302617	2		810	710	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117359	7117359	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	52	732	0	ENST00000302850.5:c.3857T>G	p.Ile1286Ser	p.I1286S	ENST00000302850	NM_000208.2	1286	aTt/aGt	22/22	1	2	FACETS	0.262	0.223	0.306	0.262	0.223	0.306	SUBCLONAL	1	FALSE	1	0.628459867302617	2		732	631	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265043	10265043	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1228041705	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	186	621	1	ENST00000340748.4:c.1897G>A	p.Ala633Thr	p.A633T	ENST00000340748		633	Gca/Aca	21/40	1	2	FACETS	0.998	0.927	1	0.998	0.927	1	CLONAL	1	FALSE	1	0.628459867302617	2		622	593	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144044	11144044	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	46	760	0	ENST00000358026.2:c.3625A>T	p.Ser1209Cys	p.S1209C	ENST00000358026	NM_001128849.1	1209	Agc/Tgc	26/36	1	2	FACETS	0.197	0.165	0.232	0.197	0.165	0.232	SUBCLONAL	1	FALSE	1	0.628459867302617	2		760	743	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169479	11169479	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	203	636	0	ENST00000358026.2:c.4645C>A	p.His1549Asn	p.H1549N	ENST00000358026	NM_001128849.1	1549	Cac/Aac	33/36	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.628459867302617	2		636	625	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350059	15350059	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	192	790	0	ENST00000263377.2:c.3593A>C	p.Asn1198Thr	p.N1198T	ENST00000263377	NM_058243.2	1198	aAc/aCc	18/20	1	2	FACETS	0.924	0.859	0.992	0.924	0.859	0.992	CLONAL	1	FALSE	1	0.628459867302617	2		790	661	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943352	17943352	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	55	642	0	ENST00000458235.1:c.2656T>G	p.Tyr886Asp	p.Y886D	ENST00000458235	NM_000215.3	886	Tat/Gat	19/24	1	2	FACETS	0.281	0.24	0.326	0.281	0.24	0.326	SUBCLONAL	1	FALSE	1	0.628459867302617	2		642	623	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271373	18271373	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	34	606	0	ENST00000222254.8:c.415G>T	p.Gly139Trp	p.G139W	ENST00000222254	NM_005027.3	139	Ggg/Tgg	3/16	1	2	FACETS	0.197	0.16	0.238	0.197	0.16	0.238	SUBCLONAL	1	FALSE	1	0.628459867302617	2		606	550	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18963845	18963845	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	28	506	0	ENST00000262803.5:c.1022G>T	p.Arg341Ile	p.R341I	ENST00000262803	NM_002911.3	341	aGa/aTa	7/24	1	2	FACETS	0.18	0.143	0.222	0.18	0.143	0.222	SUBCLONAL	1	FALSE	1	0.628459867302617	2		506	496	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749594	41749594	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1366012932	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	238	727	1	ENST00000301178.4:c.1519C>T	p.Arg507Trp	p.R507W	ENST00000301178	NM_021913.4	507	Cgg/Tgg	12/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	FALSE	1	0.628459867302617	2		728	749	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716076	52716076	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	42	826	0	ENST00000322088.6:c.641C>A	p.Ser214Tyr	p.S214Y	ENST00000322088	NM_014225.5	214	tCt/tAt	5/15	1	2	FACETS	0.201	0.167	0.238	0.201	0.167	0.238	SUBCLONAL	1	FALSE	1	0.628459867302617	2		826	666	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086005	16086005	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893648	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	161	511	0	ENST00000281043.3:c.1181G>A	p.Arg394His	p.R394H	ENST00000281043	NM_005378.4	394	cGc/cAc	3/3	1	2	FACETS	0.917	0.845	0.99	0.917	0.845	0.99	CLONAL	1	FALSE	1	0.628459867302617	2		511	559	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25536782	25536782	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	209	677	1	ENST00000264709.3:c.72G>T	p.Lys24Asn	p.K24N	ENST00000264709	NM_175629.2	24	aaG/aaT	2/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.628459867302617	2		678	617	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101068	26101068	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	186	569	0	ENST00000435504.4:c.24G>T	p.Lys8Asn	p.K8N	ENST00000435504		8	aaG/aaT	1/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.628459867302617	2		569	551	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142947	30142947	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	228	822	1	ENST00000389048.3:c.579G>T	p.Lys193Asn	p.K193N	ENST00000389048	NM_004304.4	193	aaG/aaT	1/29	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.628459867302617	2		823	677	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47600993	47600993	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	32	607	0	ENST00000263735.4:c.231A>C	p.Lys77Asn	p.K77N	ENST00000263735	NM_002354.2	77	aaA/aaC	3/9	1	2	FACETS	0.175	0.141	0.213	0.175	0.141	0.213	SUBCLONAL	1	FALSE	1	0.628459867302617	2		607	583	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635670	47635670	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	122	453	0	ENST00000233146.2:c.342G>T	p.Glu114Asp	p.E114D	ENST00000233146	NM_000251.2	114	gaG/gaT	2/16	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	1	0.628459867302617	2		453	374	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657077	47657077	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1064795063	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	85	229	0	ENST00000233146.2:c.1273G>T	p.Glu425Ter	p.E425*	ENST00000233146	NM_000251.2	425	Gaa/Taa	7/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.628459867302617	2		229	233	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026424	48026424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	119	480	0	ENST00000234420.5:c.1302G>T	p.Glu434Asp	p.E434D	ENST00000234420	NM_000179.2	434	gaG/gaT	4/10	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	FALSE	1	0.628459867302617	2		480	371	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033717	48033717	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	75	428	0	ENST00000234420.5:c.3928G>T	p.Glu1310Ter	p.E1310*	ENST00000234420	NM_000179.2	1310	Gag/Tag	9/10	1	2	FACETS	0.82	0.726	0.919	0.82	0.726	0.919	CLONAL	1	FALSE	1	0.628459867302617	2		428	291	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61749804	61749804	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	31	340	0	ENST00000401558.2:c.243A>C	p.Gln81His	p.Q81H	ENST00000401558	NM_003400.3	81	caA/caC	4/25	1	2	FACETS	0.363	0.294	0.44	0.363	0.294	0.44	SUBCLONAL	1	FALSE	1	0.628459867302617	2		340	272	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128036860	128036860	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	67	579	0	ENST00000285398.2:c.1619A>C	p.Lys540Thr	p.K540T	ENST00000285398	NM_000122.1	540	aAa/aCa	10/15	1	2	FACETS	0.413	0.359	0.471	0.413	0.359	0.471	SUBCLONAL	1	FALSE	1	0.628459867302617	2		579	516	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594961	158594961	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	119	411	0	ENST00000263640.3:c.1386C>A	p.Phe462Leu	p.F462L	ENST00000263640	NM_001105.4	462	ttC/ttA	10/11	1	2	FACETS	0.969	0.882	1	0.969	0.882	1	CLONAL	1	FALSE	1	0.628459867302617	2		411	391	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617449	158617449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1314502834	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	87	533	0	ENST00000263640.3:c.1207G>A	p.Asp403Asn	p.D403N	ENST00000263640	NM_001105.4	403	Gat/Aat	9/11	1	2	FACETS	0.602	0.535	0.673	0.602	0.535	0.673	SUBCLONAL	1	FALSE	1	0.628459867302617	2		533	460	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095716	178095716	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	94	438	1	ENST00000397062.3:c.1615T>G	p.Leu539Val	p.L539V	ENST00000397062	NM_006164.4	539	Ttg/Gtg	5/5	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.628459867302617	2		439	258	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728592	190728592	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	116	501	0	ENST00000441310.2:c.1980G>T	p.Trp660Cys	p.W660C	ENST00000441310	NM_000534.4	660	tgG/tgT	10/13	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.628459867302617	2		501	347	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732568	190732568	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	23	489	0	ENST00000441310.2:c.2386A>G	p.Thr796Ala	p.T796A	ENST00000441310	NM_000534.4	796	Aca/Gca	11/13	1	2	FACETS	0.229	0.178	0.287	0.229	0.178	0.287	SUBCLONAL	1	FALSE	1	0.628459867302617	2		489	320	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738329	190738329	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	91	364	0	ENST00000441310.2:c.2581A>G	p.Asn861Asp	p.N861D	ENST00000441310	NM_000534.4	861	Aat/Gat	12/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.628459867302617	2		364	250	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267282	198267282	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	73	338	0	ENST00000335508.6:c.2075A>C	p.His692Pro	p.H692P	ENST00000335508	NM_012433.2	692	cAt/cCt	14/25	1	2	FACETS	0.818	0.723	0.918	0.818	0.723	0.918	CLONAL	1	FALSE	1	0.628459867302617	2		338	284	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273134	198273134	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	129	598	2	ENST00000335508.6:c.1076C>A	p.Pro359Gln	p.P359Q	ENST00000335508	NM_012433.2	359	cCa/cAa	8/25	1	2	FACETS	0.757	0.69	0.828	0.757	0.69	0.828	SUBCLONAL	1	FALSE	1	0.628459867302617	2		600	542	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285850	198285850	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	27	426	0	ENST00000335508.6:c.203A>G	p.Asp68Gly	p.D68G	ENST00000335508	NM_012433.2	68	gAt/gGt	3/25	1	2	FACETS	0.253	0.201	0.312	0.253	0.201	0.312	SUBCLONAL	1	FALSE	1	0.628459867302617	2		426	340	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568841	212568841	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	93	469	0	ENST00000342788.4:c.1277G>T	p.Arg426Ile	p.R426I	ENST00000342788	NM_005235.2	426	aGa/aTa	11/28	1	2	FACETS	0.937	0.842	1	0.937	0.842	1	CLONAL	1	FALSE	1	0.628459867302617	2		469	316	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570080	212570080	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	92	396	0	ENST00000342788.4:c.1161G>T	p.Glu387Asp	p.E387D	ENST00000342788	NM_005235.2	387	gaG/gaT	10/28	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	FALSE	1	0.628459867302617	2		396	280	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812179	212812179	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	40	255	0	ENST00000342788.4:c.397G>T	p.Glu133Ter	p.E133*	ENST00000342788	NM_005235.2	133	Gaa/Taa	3/28	1	2	FACETS	0.571	0.478	0.672	0.571	0.478	0.672	SUBCLONAL	1	FALSE	1	0.628459867302617	2		255	223	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593502	215593502	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	85	325	0	ENST00000260947.4:c.2232T>G	p.Asn744Lys	p.N744K	ENST00000260947	NM_000465.2	744	aaT/aaG	11/11	1	2	FACETS	0.977	0.874	1	0.977	0.874	1	CLONAL	1	FALSE	1	0.628459867302617	2		325	277	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439733	220439733	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	271	903	0	ENST00000243786.2:c.586C>G	p.Leu196Val	p.L196V	ENST00000243786	NM_002191.3	196	Ctg/Gtg	2/2	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.628459867302617	2		903	795	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225343002	225343002	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	80	526	0	ENST00000264414.4:c.2090A>G	p.Asp697Gly	p.D697G	ENST00000264414	NM_003590.4	697	gAc/gGc	15/16	1	2	FACETS	0.613	0.543	0.689	0.613	0.543	0.689	SUBCLONAL	1	FALSE	1	0.628459867302617	2		526	415	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376097	225376097	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	19	478	0	ENST00000264414.4:c.857A>C	p.His286Pro	p.H286P	ENST00000264414	NM_003590.4	286	cAt/cCt	6/16	1	2	FACETS	0.209	0.158	0.268	0.209	0.158	0.268	SUBCLONAL	1	FALSE	1	0.628459867302617	2		478	290	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378285	225378285	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	71	356	0	ENST00000264414.4:c.610G>T	p.Asp204Tyr	p.D204Y	ENST00000264414	NM_003590.4	204	Gat/Tat	5/16	1	2	FACETS	0.911	0.806	1	0.911	0.806	1	CLONAL	1	FALSE	1	0.628459867302617	2		356	248	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661538	227661538	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	159	754	0	ENST00000305123.5:c.1917C>A	p.Ser639Arg	p.S639R	ENST00000305123	NM_005544.2	639	agC/agA	1/2	1	2	FACETS	0.902	0.831	0.975	0.902	0.831	0.975	CLONAL	1	FALSE	1	0.628459867302617	2		754	561	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793237	242793237	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	57	815	0	ENST00000334409.5:c.840G>T	p.Glu280Asp	p.E280D	ENST00000334409	NM_005018.2	280	gaG/gaT	5/5	1	2	FACETS	0.274	0.234	0.317	0.274	0.234	0.317	SUBCLONAL	1	FALSE	1	0.628459867302617	2		815	663	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546815	9546815	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	111	464	0	ENST00000353224.5:c.1207T>C	p.Ser403Pro	p.S403P	ENST00000353224	NM_177990.2	403	Tcc/Ccc	5/10	0.628459867302617	3	FACETS	0.963	0.87	1	0.482	0.435	0.53	CLONAL	1	FALSE	1	0.628459867302617	3		464	482	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561480	9561480	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	176	531	0	ENST00000353224.5:c.302G>T	p.Arg101Met	p.R101M	ENST00000353224	NM_177990.2	101	aGg/aTg	4/10	0.628459867302617	3	FACETS	1	0.97	1	0.549	0.507	0.591	CLONAL	1	FALSE	1	0.628459867302617	3		531	671	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30955529	30955529	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	84	365	0	ENST00000375687.4:c.141-1G>T		p.X47_splice	ENST00000375687	NM_015338.5	47			0.628459867302617	3	FACETS	1	0.925	1	0.524	0.467	0.585	CLONAL	1	FALSE	1	0.628459867302617	3		365	335	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023526	31023526	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	162	538	0	ENST00000375687.4:c.3011A>C	p.Asp1004Ala	p.D1004A	ENST00000375687	NM_015338.5	1004	gAc/gCc	13/13	0.628459867302617	3	FACETS	1	0.976	1	0.571	0.526	0.618	CLONAL	1	FALSE	1	0.628459867302617	3		538	593	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388649	31388649	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	113	499	0	ENST00000328111.2:c.1914A>T	p.Glu638Asp	p.E638D	ENST00000328111	NM_006892.3	638	gaA/gaT	18/23	0.628459867302617	3	FACETS	0.71	0.639	0.784	0.355	0.319	0.392	SUBCLONAL	1	FALSE	1	0.628459867302617	3		499	666	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742656	39742656	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	107	366	0	ENST00000361337.2:c.1499A>G	p.Asp500Gly	p.D500G	ENST00000361337	NM_003286.2	500	gAc/gGc	15/21	0.628459867302617	3	FACETS	1	0.931	1	0.519	0.469	0.572	CLONAL	1	FALSE	1	0.628459867302617	3		366	431	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757398	40757398	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	158	619	0	ENST00000373198.4:c.2900T>A	p.Ile967Asn	p.I967N	ENST00000373198	NM_133170.3	967	aTt/aAt	20/32	0.628459867302617	3	FACETS	0.958	0.88	1	0.479	0.44	0.519	CLONAL	1	FALSE	1	0.628459867302617	3		619	690	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264067	46264067	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	57	264	1	ENST00000371998.3:c.1114G>T	p.Glu372Ter	p.E372*	ENST00000371998		372	Gaa/Taa	11/23	0.628459867302617	3	FACETS	0.883	0.764	1	0.441	0.382	0.505	CLONAL	1	FALSE	1	0.628459867302617	3		265	270	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267889	46267889	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs753055086	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	111	535	0	ENST00000371998.3:c.2650A>G	p.Met884Val	p.M884V	ENST00000371998		884	Atg/Gtg	14/23	0.628459867302617	3	FACETS	0.786	0.708	0.867	0.393	0.354	0.434	SUBCLONAL	1	FALSE	1	0.628459867302617	3		535	591	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945564	54945564	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	228	780	1	ENST00000312783.6:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000312783	NM_198436.1	336	Gag/Tag	9/10	0.628459867302617	3	FACETS	1	0.977	1	0.551	0.514	0.589	CLONAL	1	FALSE	1	0.628459867302617	3		781	865	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948498	54948498	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	100	444	0	ENST00000312783.6:c.820G>T	p.Asp274Tyr	p.D274Y	ENST00000312783	NM_198436.1	274	Gat/Tat	8/10	0.628459867302617	3	FACETS	0.898	0.806	0.994	0.449	0.403	0.497	CLONAL	1	FALSE	1	0.628459867302617	3		444	466	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62293225	62293225	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	428	644	0	ENST00000360203.5:c.324G>T	p.Lys108Asn	p.K108N	ENST00000360203	NM_001283009.1	108	aaG/aaT	4/35	0.628459867302617	3	FACETS	0.989	0.948	1	0.989	0.948	1	CLONAL	2	FALSE	1	0.628459867302617	3		644	905	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62293826	62293826	+	intron_variant	Intron	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	184	503	0	ENST00000360203.5:c.396-73G>T		p.*132*	ENST00000360203	NM_001283009.1	132/1243			0.628459867302617	3	FACETS	1	0.983	1	0.597	0.553	0.641	CLONAL	1	FALSE	1	0.628459867302617	3		503	645	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866480	42866480	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	259	875	0	ENST00000398585.3:c.152A>G	p.Tyr51Cys	p.Y51C	ENST00000398585	NM_001135099.1	51	tAc/tGc	3/14	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.628459867302617	2		875	750	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22142630	22142630	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	60	377	0	ENST00000215832.6:c.772T>G	p.Leu258Val	p.L258V	ENST00000215832	NM_002745.4	258	Tta/Gta	6/9	1	2	FACETS	0.758	0.66	0.862	0.758	0.66	0.862	SUBCLONAL	1	FALSE	1	0.628459867302617	2		377	252	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537224	41537224	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	126	441	0	ENST00000263253.7:c.2051C>A	p.Ser684Tyr	p.S684Y	ENST00000263253	NM_001429.3	684	tCt/tAt	10/31	1	2	FACETS	0.99	0.905	1	0.99	0.905	1	CLONAL	1	FALSE	1	0.628459867302617	2		441	405	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573990	41573990	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	151	567	0	ENST00000263253.7:c.6275A>G	p.Tyr2092Cys	p.Y2092C	ENST00000263253	NM_001429.3	2092	tAt/tGt	31/31	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	1	0.628459867302617	2		567	463	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12632314	12632314	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	43	542	0	ENST00000251849.4:c.1353G>T	p.Gln451His	p.Q451H	ENST00000251849	NM_002880.3	451	caG/caT	12/17	1	2	FACETS	0.274	0.229	0.324	0.274	0.229	0.324	SUBCLONAL	1	FALSE	1	0.628459867302617	2		542	500	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162572	47162572	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	16	380	0	ENST00000409792.3:c.3554A>C	p.Asn1185Thr	p.N1185T	ENST00000409792	NM_014159.6	1185	aAt/aCt	3/21	1	2	FACETS	0.187	0.138	0.246	0.187	0.138	0.246	SUBCLONAL	1	FALSE	1	0.628459867302617	2		380	272	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163460	47163460	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	38	342	0	ENST00000409792.3:c.2666G>T	p.Gly889Val	p.G889V	ENST00000409792	NM_014159.6	889	gGa/gTa	3/21	1	2	FACETS	0.517	0.43	0.612	0.517	0.43	0.612	SUBCLONAL	1	FALSE	1	0.628459867302617	2		342	234	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164540	47164540	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	49	380	0	ENST00000409792.3:c.1586G>T	p.Arg529Ile	p.R529I	ENST00000409792	NM_014159.6	529	aGa/aTa	3/21	1	2	FACETS	0.591	0.504	0.684	0.591	0.504	0.684	SUBCLONAL	1	FALSE	1	0.628459867302617	2		380	264	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165206	47165206	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1303561180	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	51	328	0	ENST00000409792.3:c.920C>A	p.Ser307Tyr	p.S307Y	ENST00000409792	NM_014159.6	307	tCt/tAt	3/21	1	2	FACETS	0.592	0.507	0.684	0.592	0.507	0.684	SUBCLONAL	1	FALSE	1	0.628459867302617	2		328	274	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437667	52437667	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	40	713	0	ENST00000460680.1:c.1494G>T	p.Glu498Asp	p.E498D	ENST00000460680	NM_004656.3	498	gaG/gaT	13/17	1	2	FACETS	0.206	0.171	0.246	0.206	0.171	0.246	SUBCLONAL	1	FALSE	1	0.628459867302617	2		713	617	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620700	52620700	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	91	251	0	ENST00000394830.3:c.3053A>G	p.Tyr1018Cys	p.Y1018C	ENST00000394830	NM_018313.4	1018	tAc/tGc	21/30	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.628459867302617	2		251	260	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52676053	52676053	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	72	393	1	ENST00000394830.3:c.1004G>T	p.Arg335Ile	p.R335I	ENST00000394830	NM_018313.4	335	aGa/aTa	11/30	1	2	FACETS	0.865	0.764	0.97	0.865	0.764	0.97	CLONAL	1	FALSE	1	0.628459867302617	2		394	265	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096185	71096185	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	31	386	0	ENST00000318789.4:c.572T>C	p.Leu191Ser	p.L191S	ENST00000318789	NM_032682.5	191	tTa/tCa	10/21	1	2	FACETS	0.266	0.215	0.324	0.266	0.215	0.324	SUBCLONAL	1	FALSE	1	0.628459867302617	2		386	371	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890297	72890297	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	29	473	0	ENST00000325599.8:c.385A>C	p.Ile129Leu	p.I129L	ENST00000325599	NM_018130.2	129	Att/Ctt	4/11	1	2	FACETS	0.241	0.193	0.295	0.241	0.193	0.295	SUBCLONAL	1	FALSE	1	0.628459867302617	2		473	383	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114215	73114215	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	95	402	0	ENST00000356692.5:c.851A>C	p.Asp284Ala	p.D284A	ENST00000356692		284	gAt/gCt	8/9	1	2	FACETS	0.963	0.867	1	0.963	0.867	1	CLONAL	1	FALSE	1	0.628459867302617	2		402	314	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448547	89448547	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	26	487	0	ENST00000336596.2:c.1511T>C	p.Ile504Thr	p.I504T	ENST00000336596	NM_005233.5	504	aTa/aCa	7/17	1	2	FACETS	0.188	0.148	0.234	0.188	0.148	0.234	SUBCLONAL	1	FALSE	1	0.628459867302617	2		487	440	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89478290	89478290	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	17	354	0	ENST00000336596.2:c.2109G>T	p.Glu703Asp	p.E703D	ENST00000336596	NM_005233.5	703	gaG/gaT	12/17	1	2	FACETS	0.236	0.176	0.307	0.236	0.176	0.307	SUBCLONAL	1	FALSE	1	0.628459867302617	2		354	229	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480463	89480463	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	84	301	0	ENST00000336596.2:c.2300T>C	p.Leu767Pro	p.L767P	ENST00000336596	NM_005233.5	767	cTt/cCt	13/17	1	2	FACETS	0.779	0.694	0.869	0.779	0.694	0.869	SUBCLONAL	1	FALSE	1	0.628459867302617	2		301	343	SUCCESS
ATR	545	MSKCC	GRCh37	3	142254991	142254991	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	37	315	0	ENST00000350721.4:c.3778G>T	p.Glu1260Ter	p.E1260*	ENST00000350721	NM_001184.3	1260	Gaa/Taa	20/47	0.442284616665144	3	FACETS	0.723	0.601	0.857			1	SUBCLONAL	1	FALSE	NA	0.628459867302617	3		315	214	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266590	142266590	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	125	367	0	ENST00000350721.4:c.3334G>T	p.Asp1112Tyr	p.D1112Y	ENST00000350721	NM_001184.3	1112	Gat/Tat	16/47	0.442284616665144	3	FACETS	0.99	0.914	1			1	CLONAL	2	FALSE	NA	0.628459867302617	3		367	264	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268353	142268353	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	44	396	0	ENST00000350721.4:c.3139G>T	p.Asp1047Tyr	p.D1047Y	ENST00000350721	NM_001184.3	1047	Gat/Tat	15/47	0.442284616665144	3	FACETS	0.664	0.561	0.778			1	SUBCLONAL	1	FALSE	NA	0.628459867302617	3		396	277	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268411	142268411	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	81	437	0	ENST00000350721.4:c.3081G>T	p.Glu1027Asp	p.E1027D	ENST00000350721	NM_001184.3	1027	gaG/gaT	15/47	0.442284616665144	3	FACETS	0.96	0.852	1			1	CLONAL	1	FALSE	NA	0.628459867302617	3		437	353	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281573	142281573	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	230	531	0	ENST00000350721.4:c.671G>T	p.Arg224Met	p.R224M	ENST00000350721	NM_001184.3	224	aGg/aTg	4/47	0.442284616665144	3	FACETS	1	0.953	1			1	CLONAL	2	FALSE	NA	0.628459867302617	3		531	476	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149375028	149375028	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	311	883	0	ENST00000360632.3:c.66G>T	p.Gln22His	p.Q22H	ENST00000360632	NM_015472.4	22	caG/caT	2/7	0.442284616665144	3	FACETS	1	0.948	1			1	CLONAL	1	FALSE	NA	0.628459867302617	3		883	1292	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917651	178917651	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	41	306	0	ENST00000263967.3:c.526G>T	p.Glu176Ter	p.E176*	ENST00000263967	NM_006218.2	176	Gaa/Taa	3/21	1	2	FACETS	0.68	0.573	0.795	0.68	0.573	0.795	SUBCLONAL	1	FALSE	1	0.628459867302617	2		306	192	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936076	178936076	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	88	409	0	ENST00000263967.3:c.1618C>A	p.Leu540Ile	p.L540I	ENST00000263967	NM_006218.2	540	Ctc/Atc	10/21	1	2	FACETS	0.949	0.851	1	0.949	0.851	1	CLONAL	1	FALSE	1	0.628459867302617	2		409	295	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447407	187447407	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	190	699	0	ENST00000232014.4:c.786G>T	p.Lys262Asn	p.K262N	ENST00000232014	NM_001130845.1	262	aaG/aaT	5/10	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.628459867302617	2		699	589	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526125	189526125	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1278311377	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	198	631	0	ENST00000264731.3:c.389C>A	p.Ser130Tyr	p.S130Y	ENST00000264731	NM_003722.4	130	tCc/tAc	4/14	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.628459867302617	2		631	598	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1918703	1918703	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	98	426	0	ENST00000382891.5:c.866A>T	p.Gln289Leu	p.Q289L	ENST00000382891	NM_133335.3	289	cAg/cTg	4/22	1	2	FACETS	0.748	0.672	0.828	0.748	0.672	0.828	SUBCLONAL	1	FALSE	1	0.628459867302617	2		426	417	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1953893	1953893	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	62	895	0	ENST00000382891.5:c.2072A>G	p.His691Arg	p.H691R	ENST00000382891	NM_133335.3	691	cAc/cGc	11/22	1	2	FACETS	0.252	0.217	0.291	0.252	0.217	0.291	SUBCLONAL	1	FALSE	1	0.628459867302617	2		895	782	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127539	55127539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	104	372	0	ENST00000257290.5:c.327G>T	p.Glu109Asp	p.E109D	ENST00000257290	NM_006206.4	109	gaG/gaT	3/23	1	2	FACETS	0.957	0.865	1	0.957	0.865	1	CLONAL	1	FALSE	1	0.628459867302617	2		372	346	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129990	55129990	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	166	599	0	ENST00000257290.5:c.524G>T	p.Arg175Ile	p.R175I	ENST00000257290	NM_006206.4	175	aGa/aTa	4/23	1	2	FACETS	0.909	0.84	0.981	0.909	0.84	0.981	CLONAL	1	FALSE	1	0.628459867302617	2		599	581	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129996	55129996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	72	609	0	ENST00000257290.5:c.530G>A	p.Gly177Asp	p.G177D	ENST00000257290	NM_006206.4	177	gGc/gAc	4/23	1	2	FACETS	0.404	0.353	0.459	0.404	0.353	0.459	SUBCLONAL	1	FALSE	1	0.628459867302617	2		609	567	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144115	55144115	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	152	552	0	ENST00000257290.5:c.1944G>T	p.Met648Ile	p.M648I	ENST00000257290	NM_006206.4	648	atG/atT	14/23	1	2	FACETS	0.937	0.863	1	0.937	0.863	1	CLONAL	1	FALSE	1	0.628459867302617	2		552	516	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217217	66217217	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	90	451	0	ENST00000273854.3:c.2398G>T	p.Asp800Tyr	p.D800Y	ENST00000273854	NM_004439.5	800	Gat/Tat	14/18	1	2	FACETS	0.876	0.785	0.971	0.876	0.785	0.971	CLONAL	1	FALSE	1	0.628459867302617	2		451	327	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270182	66270182	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	79	260	0	ENST00000273854.3:c.1700G>T	p.Ser567Ile	p.S567I	ENST00000273854	NM_004439.5	567	aGc/aTc	8/18	1	2	FACETS	0.971	0.865	1	0.971	0.865	1	CLONAL	1	FALSE	1	0.628459867302617	2		260	259	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155626	106155626	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	59	396	0	ENST00000380013.4:c.527A>C	p.Asn176Thr	p.N176T	ENST00000380013	NM_001127208.2	176	aAt/aCt	3/11	1	2	FACETS	0.61	0.528	0.697	0.61	0.528	0.697	SUBCLONAL	1	FALSE	1	0.628459867302617	2		396	308	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157419	106157419	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	21	325	0	ENST00000380013.4:c.2320T>G	p.Ser774Ala	p.S774A	ENST00000380013	NM_001127208.2	774	Tca/Gca	3/11	1	2	FACETS	0.23	0.177	0.291	0.23	0.177	0.291	SUBCLONAL	1	FALSE	1	0.628459867302617	2		325	291	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143350334	143350334	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	53	243	0	ENST00000262992.4:c.128T>C	p.Phe43Ser	p.F43S	ENST00000262992	NM_001101669.1	43	tTc/tCc	3/24	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	FALSE	1	0.628459867302617	2		243	147	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250858	153250858	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	58	411	0	ENST00000281708.4:c.1202A>C	p.Asn401Thr	p.N401T	ENST00000281708	NM_033632.3	401	aAc/aCc	8/12	1	2	FACETS	0.659	0.571	0.753	0.659	0.571	0.753	SUBCLONAL	1	FALSE	1	0.628459867302617	2		411	280	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510034	187510034	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	26	454	0	ENST00000441802.2:c.13479T>G	p.Phe4493Leu	p.F4493L	ENST00000441802	NM_005245.3	4493	ttT/ttG	27/27	1	2	FACETS	0.222	0.175	0.275	0.222	0.175	0.275	SUBCLONAL	1	FALSE	1	0.628459867302617	2		454	373	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510294	187510294	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1315498369	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	25	423	0	ENST00000441802.2:c.13219G>T	p.Asp4407Tyr	p.D4407Y	ENST00000441802	NM_005245.3	4407	Gat/Tat	27/27	1	2	FACETS	0.242	0.19	0.301	0.242	0.19	0.301	SUBCLONAL	1	FALSE	1	0.628459867302617	2		423	329	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629136	187629136	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	146	514	0	ENST00000441802.2:c.1846A>G	p.Ser616Gly	p.S616G	ENST00000441802	NM_005245.3	616	Agt/Ggt	2/27	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	1	0.628459867302617	2		514	459	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228301	228301	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	65	203	0	ENST00000264932.6:c.623C>A	p.Ser208Tyr	p.S208Y	ENST00000264932	NM_004168.2	208	tCt/tAt	6/15	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.628459867302617	2		203	174	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282588	1282588	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	188	623	1	ENST00000310581.5:c.1725C>A	p.Phe575Leu	p.F575L	ENST00000310581	NM_198253.2	575	ttC/ttA	3/16	1	2	FACETS	0.963	0.895	1	0.963	0.895	1	CLONAL	1	FALSE	1	0.628459867302617	2		624	621	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871261	35871261	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	25	362	0	ENST00000303115.3:c.483A>C	p.Lys161Asn	p.K161N	ENST00000303115	NM_002185.3	161	aaA/aaC	4/8	1	2	FACETS	0.266	0.21	0.331	0.266	0.21	0.331	SUBCLONAL	1	FALSE	1	0.628459867302617	2		362	299	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876418	35876418	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs761882064	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	171	622	0	ENST00000303115.3:c.1210C>A	p.Leu404Ile	p.L404I	ENST00000303115	NM_002185.3	404	Ctc/Atc	8/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.628459867302617	2		622	525	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38943074	38943074	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	45	210	0	ENST00000357387.3:c.4914-1G>T		p.X1638_splice	ENST00000357387	NM_152756.3	1638			1	2	FACETS	0.837	0.715	0.968	0.837	0.715	0.968	CLONAL	1	FALSE	1	0.628459867302617	2		210	171	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944616	38944616	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	76	442	0	ENST00000357387.3:c.4845A>C	p.Glu1615Asp	p.E1615D	ENST00000357387	NM_152756.3	1615	gaA/gaC	36/38	1	2	FACETS	0.87	0.772	0.973	0.87	0.772	0.973	CLONAL	1	FALSE	1	0.628459867302617	2		442	278	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950665	38950665	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1249602445	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	80	362	0	ENST00000357387.3:c.3285G>T	p.Lys1095Asn	p.K1095N	ENST00000357387	NM_152756.3	1095	aaG/aaT	31/38	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	FALSE	1	0.628459867302617	2		362	242	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179451	56179451	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	57	293	0	ENST00000399503.3:c.3764C>A	p.Ser1255Tyr	p.S1255Y	ENST00000399503	NM_005921.1	1255	tCt/tAt	15/20	1	2	FACETS	0.907	0.79	1	0.907	0.79	1	CLONAL	1	FALSE	1	0.628459867302617	2		293	200	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753372	57753372	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	93	481	0	ENST00000274289.3:c.752T>C	p.Val251Ala	p.V251A	ENST00000274289	NM_006622.3	251	gTc/gCc	6/14	1	2	FACETS	0.891	0.801	0.986	0.891	0.801	0.986	CLONAL	1	FALSE	1	0.628459867302617	2		481	332	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80021328	80021328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	110	485	0	ENST00000265081.6:c.1397G>A	p.Ser466Asn	p.S466N	ENST00000265081	NM_002439.4	466	aGc/aAc	9/24	1	2	FACETS	0.852	0.771	0.936	0.852	0.771	0.936	CLONAL	1	FALSE	1	0.628459867302617	2		485	411	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659212	86659212	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	16	213	0	ENST00000274376.6:c.1501G>T	p.Asp501Tyr	p.D501Y	ENST00000274376	NM_002890.2	501	Gat/Tat	11/25	1	2	FACETS	0.3	0.222	0.391	0.3	0.222	0.391	SUBCLONAL	1	FALSE	1	0.628459867302617	2		213	170	SUCCESS
APC	324	MSKCC	GRCh37	5	112173366	112173366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	74	291	0	ENST00000257430.4:c.2075C>A	p.Pro692His	p.P692H	ENST00000257430	NM_000038.5	692	cCt/cAt	16/16	1	2	FACETS	0.961	0.853	1	0.961	0.853	1	CLONAL	1	FALSE	1	0.628459867302617	2		291	245	SUCCESS
APC	324	MSKCC	GRCh37	5	112174376	112174376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	65	277	0	ENST00000257430.4:c.3085C>T	p.Leu1029Phe	p.L1029F	ENST00000257430	NM_000038.5	1029	Ctt/Ttt	16/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.628459867302617	2		277	168	SUCCESS
APC	324	MSKCC	GRCh37	5	112175370	112175370	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	63	245	0	ENST00000257430.4:c.4079C>A	p.Ser1360Tyr	p.S1360Y	ENST00000257430	NM_000038.5	1360	tCt/tAt	16/16	1	2	FACETS	0.842	0.738	0.953	0.842	0.738	0.953	CLONAL	1	FALSE	1	0.628459867302617	2		245	238	SUCCESS
APC	324	MSKCC	GRCh37	5	112175778	112175778	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	14	298	0	ENST00000257430.4:c.4487C>A	p.Thr1496Asn	p.T1496N	ENST00000257430	NM_000038.5	1496	aCt/aAt	16/16	1	2	FACETS	0.179	0.129	0.239	0.179	0.129	0.239	SUBCLONAL	1	FALSE	1	0.628459867302617	2		298	249	SUCCESS
APC	324	MSKCC	GRCh37	5	112175844	112175844	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1554085963	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	64	250	0	ENST00000257430.4:c.4553A>C	p.Lys1518Thr	p.K1518T	ENST00000257430	NM_000038.5	1518	aAa/aCa	16/16	1	2	FACETS	0.934	0.821	1	0.934	0.821	1	CLONAL	1	FALSE	1	0.628459867302617	2		250	218	SUCCESS
APC	324	MSKCC	GRCh37	5	112176650	112176650	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1312187161	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	58	267	0	ENST00000257430.4:c.5359A>G	p.Thr1787Ala	p.T1787A	ENST00000257430	NM_000038.5	1787	Aca/Gca	16/16	1	2	FACETS	0.835	0.727	0.95	0.835	0.727	0.95	CLONAL	1	FALSE	1	0.628459867302617	2		267	221	SUCCESS
APC	324	MSKCC	GRCh37	5	112178497	112178497	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1561613624	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	66	299	0	ENST00000257430.4:c.7206T>G	p.Asn2402Lys	p.N2402K	ENST00000257430	NM_000038.5	2402	aaT/aaG	16/16	1	2	FACETS	0.917	0.807	1	0.917	0.807	1	CLONAL	1	FALSE	1	0.628459867302617	2		299	229	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915128	131915128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	155	520	0	ENST00000265335.6:c.485C>T	p.Ser162Phe	p.S162F	ENST00000265335		162	tCt/tTt	4/25	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.628459867302617	2		520	430	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924445	131924445	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	16	443	0	ENST00000265335.6:c.1118C>A	p.Ser373Tyr	p.S373Y	ENST00000265335		373	tCt/tAt	8/25	1	2	FACETS	0.16	0.117	0.21	0.16	0.117	0.21	SUBCLONAL	1	FALSE	1	0.628459867302617	2		443	319	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953887	131953887	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	71	398	0	ENST00000265335.6:c.3290T>G	p.Phe1097Cys	p.F1097C	ENST00000265335		1097	tTt/tGt	21/25	1	2	FACETS	0.813	0.717	0.914	0.813	0.717	0.914	CLONAL	1	FALSE	1	0.628459867302617	2		398	278	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131978000	131978000	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	24	443	0	ENST00000265335.6:c.3883C>A	p.Gln1295Lys	p.Q1295K	ENST00000265335		1295	Cag/Aag	25/25	1	2	FACETS	0.194	0.152	0.243	0.194	0.152	0.243	SUBCLONAL	1	FALSE	1	0.628459867302617	2		443	393	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519734	176519734	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	190	806	0	ENST00000292408.4:c.1006G>T	p.Gly336Cys	p.G336C	ENST00000292408	NM_213647.1	336	Ggc/Tgc	8/18	1	2	FACETS	0.985	0.915	1	0.985	0.915	1	CLONAL	1	FALSE	1	0.628459867302617	2		806	614	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562854	176562854	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	37	574	0	ENST00000439151.2:c.750A>T	p.Lys250Asn	p.K250N	ENST00000439151	NM_022455.4	250	aaA/aaT	2/23	1	2	FACETS	0.229	0.188	0.274	0.229	0.188	0.274	SUBCLONAL	1	FALSE	1	0.628459867302617	2		574	515	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636770	176636770	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	122	517	0	ENST00000439151.2:c.1370T>G	p.Phe457Cys	p.F457C	ENST00000439151	NM_022455.4	457	tTt/tGt	5/23	1	2	FACETS	0.966	0.881	1	0.966	0.881	1	CLONAL	1	FALSE	1	0.628459867302617	2		517	402	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176678743	176678743	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	23	423	0	ENST00000439151.2:c.4654T>G	p.Leu1552Val	p.L1552V	ENST00000439151	NM_022455.4	1552	Ttg/Gtg	12/23	1	2	FACETS	0.18	0.14	0.226	0.18	0.14	0.226	SUBCLONAL	1	FALSE	1	0.628459867302617	2		423	407	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672961	30672961	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs371569455	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	39	825	0	ENST00000376406.3:c.3999G>T	p.Gln1333His	p.Q1333H	ENST00000376406	NM_014641.2	1333	caG/caT	10/15	1	2	FACETS	0.163	0.134	0.195	0.163	0.134	0.195	SUBCLONAL	1	FALSE	1	0.628459867302617	2		825	763	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680145	30680145	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	211	673	0	ENST00000376406.3:c.1574T>C	p.Val525Ala	p.V525A	ENST00000376406	NM_014641.2	525	gTg/gCg	5/15	1	2	FACETS	0.985	0.919	1	0.985	0.919	1	CLONAL	1	FALSE	1	0.628459867302617	2		673	682	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681615	30681615	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	150	446	0	ENST00000376406.3:c.482G>T	p.Arg161Met	p.R161M	ENST00000376406	NM_014641.2	161	aGg/aTg	3/15	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	1	0.628459867302617	2		446	467	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681866	30681866	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	179	583	0	ENST00000376406.3:c.231G>T	p.Glu77Asp	p.E77D	ENST00000376406	NM_014641.2	77	gaG/gaT	3/15	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.628459867302617	2		583	544	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165292	32165292	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1179648729	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	254	962	0	ENST00000375023.3:c.4836T>A	p.Cys1612Ter	p.C1612*	ENST00000375023	NM_004557.3	1612	tgT/tgA	27/30	1	2	FACETS	0.997	0.936	1	0.997	0.936	1	CLONAL	1	FALSE	1	0.628459867302617	2		962	811	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172039	32172039	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	191	699	0	ENST00000375023.3:c.2993T>G	p.Phe998Cys	p.F998C	ENST00000375023	NM_004557.3	998	tTt/tGt	19/30	1	2	FACETS	0.985	0.916	1	0.985	0.916	1	CLONAL	1	FALSE	1	0.628459867302617	2		699	617	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748575	43748575	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	114	379	0	ENST00000523873.1:c.529A>G	p.Ser177Gly	p.S177G	ENST00000523873		177	Agc/Ggc	6/8	1	2	FACETS	0.989	0.899	1	0.989	0.899	1	CLONAL	1	FALSE	1	0.628459867302617	2		379	367	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974369	93974369	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	85	421	0	ENST00000369303.4:c.1685C>A	p.Ala562Asp	p.A562D	ENST00000369303	NM_004440.3	562	gCt/gAt	8/17	1	2	FACETS	0.848	0.757	0.943	0.848	0.757	0.943	CLONAL	1	FALSE	1	0.628459867302617	2		421	319	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536237	106536237	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	33	508	0	ENST00000369096.4:c.204T>G	p.Asp68Glu	p.D68E	ENST00000369096	NM_001198.3	68	gaT/gaG	2/7	1	2	FACETS	0.217	0.176	0.263	0.217	0.176	0.263	SUBCLONAL	1	FALSE	1	0.628459867302617	2		508	485	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609861	117609861	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1319948197	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	150	541	0	ENST00000368508.3:c.6838G>T	p.Glu2280Ter	p.E2280*	ENST00000368508	NM_002944.2	2280	Gaa/Taa	43/43	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	1	0.628459867302617	2		541	467	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630067	117630067	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	12	322	0	ENST00000368508.3:c.6459G>T	p.Glu2153Asp	p.E2153D	ENST00000368508	NM_002944.2	2153	gaG/gaT	41/43	1	2	FACETS	0.167	0.117	0.229	0.167	0.117	0.229	SUBCLONAL	1	FALSE	1	0.628459867302617	2		322	228	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198307	138198307	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	76	280	0	ENST00000237289.4:c.900G>T	p.Glu300Asp	p.E300D	ENST00000237289	NM_001270507.1	300	gaG/gaT	6/9	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	FALSE	1	0.628459867302617	2		280	240	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382206	152382206	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	24	424	0	ENST00000206249.3:c.1316A>C	p.Asn439Thr	p.N439T	ENST00000206249	NM_000125.3	439	aAt/aCt	6/8	1	2	FACETS	0.171	0.134	0.215	0.171	0.134	0.215	SUBCLONAL	1	FALSE	1	0.628459867302617	2		424	446	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956929	2956929	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	161	611	0	ENST00000396946.4:c.2698C>A	p.Leu900Ile	p.L900I	ENST00000396946	NM_032415.4	900	Ctt/Att	20/25	0.628459867302617	3	FACETS	0.955	0.878	1	0.478	0.439	0.518	CLONAL	1	FALSE	1	0.628459867302617	3		611	705	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441557	6441557	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	17	169	0	ENST00000356142.4:c.404A>C	p.Lys135Thr	p.K135T	ENST00000356142	NM_018890.3	135	aAa/aCa	6/7	0.628459867302617	3	FACETS	0.402	0.301	0.52	0.201	0.15	0.26	SUBCLONAL	1	FALSE	1	0.628459867302617	3		169	177	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14027770	14027770	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	97	365	0	ENST00000405192.2:c.74A>C	p.Lys25Thr	p.K25T	ENST00000405192	NM_001163147.1	25	aAa/aCa	3/12	0.628459867302617	3	FACETS	1	0.902	1	0.502	0.451	0.556	CLONAL	1	FALSE	1	0.628459867302617	3		365	404	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346567	81346567	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	77	345	0	ENST00000222390.5:c.1386T>G	p.Asp462Glu	p.D462E	ENST00000222390	NM_000601.4	462	gaT/gaG	11/18	0.628459867302617	3	FACETS	0.933	0.826	1	0.467	0.413	0.524	CLONAL	1	FALSE	1	0.628459867302617	3		345	345	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350074	81350074	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	21	397	0	ENST00000222390.5:c.1258G>T	p.Glu420Ter	p.E420*	ENST00000222390	NM_000601.4	420	Gaa/Taa	10/18	0.628459867302617	3	FACETS	0.246	0.189	0.313	0.123	0.094	0.157	SUBCLONAL	1	FALSE	1	0.628459867302617	3		397	357	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392155	81392155	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	48	319	0	ENST00000222390.5:c.122A>T	p.Glu41Val	p.E41V	ENST00000222390	NM_000601.4	41	gAa/gTa	2/18	0.628459867302617	3	FACETS	0.784	0.668	0.909	0.392	0.334	0.455	CLONAL	1	FALSE	1	0.628459867302617	3		319	256	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508964	106508964	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	115	551	0	ENST00000359195.3:c.958A>G	p.Lys320Glu	p.K320E	ENST00000359195	NM_002649.2	320	Aag/Gag	2/11	0.628459867302617	3	FACETS	0.87	0.786	0.957	0.435	0.393	0.479	CLONAL	1	FALSE	1	0.628459867302617	3		551	553	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398529	116398529	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	98	458	0	ENST00000397752.3:c.2119C>A	p.Leu707Ile	p.L707I	ENST00000397752	NM_000245.2	707	Ctt/Att	9/21	0.628459867302617	3	FACETS	0.995	0.894	1	0.497	0.447	0.551	CLONAL	1	FALSE	1	0.628459867302617	3		458	412	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434465	140434465	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	116	389	0	ENST00000288602.6:c.2233C>A	p.Leu745Ile	p.L745I	ENST00000288602	NM_004333.4	745	Cta/Ata	18/18	0.628459867302617	3	FACETS	0.959	0.868	1	0.479	0.434	0.527	CLONAL	1	FALSE	1	0.628459867302617	3		389	506	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140449184	140449184	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	33	423	0	ENST00000288602.6:c.1895C>A	p.Pro632Gln	p.P632Q	ENST00000288602	NM_004333.4	632	cCa/cAa	16/18	0.628459867302617	3	FACETS	0.346	0.282	0.418	0.173	0.141	0.209	SUBCLONAL	1	FALSE	1	0.628459867302617	3		423	399	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512029	148512029	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	47	356	0	ENST00000320356.2:c.1649A>G	p.Lys550Arg	p.K550R	ENST00000320356	NM_004456.4	550	aAg/aGg	14/20	0.628459867302617	3	FACETS	0.453	0.382	0.53	0.226	0.191	0.265	SUBCLONAL	1	FALSE	1	0.628459867302617	3		356	434	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524269	148524269	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	79	363	0	ENST00000320356.2:c.715G>T	p.Glu239Ter	p.E239*	ENST00000320356	NM_004456.4	239	Gaa/Taa	7/20	0.628459867302617	3	FACETS	0.989	0.877	1	0.495	0.438	0.554	CLONAL	1	FALSE	1	0.628459867302617	3		363	334	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148529792	148529792	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	98	355	0	ENST00000320356.2:c.297G>T	p.Lys99Asn	p.K99N	ENST00000320356	NM_004456.4	99	aaG/aaT	4/20	0.628459867302617	3	FACETS	1	0.947	1	0.541	0.486	0.598	CLONAL	1	FALSE	1	0.628459867302617	3		355	379	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841880	151841880	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	100	370	0	ENST00000262189.6:c.14261T>C	p.Phe4754Ser	p.F4754S	ENST00000262189	NM_170606.2	4754	tTt/tCt	55/59	0.628459867302617	3	FACETS	0.884	0.794	0.979	0.442	0.397	0.49	CLONAL	1	FALSE	1	0.628459867302617	3		370	473	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853397	151853397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	32	388	0	ENST00000262189.6:c.11705C>T	p.Ala3902Val	p.A3902V	ENST00000262189	NM_170606.2	3902	gCc/gTc	45/59	0.628459867302617	3	FACETS	0.262	0.212	0.319	0.131	0.106	0.16	SUBCLONAL	1	FALSE	1	0.628459867302617	3		388	510	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860422	151860422	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	191	578	0	ENST00000262189.6:c.10240C>A	p.Gln3414Lys	p.Q3414K	ENST00000262189	NM_170606.2	3414	Caa/Aaa	43/59	0.628459867302617	3	FACETS	1	0.952	1	0.517	0.479	0.557	CLONAL	1	FALSE	1	0.628459867302617	3		578	772	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877898	151877898	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	124	405	0	ENST00000262189.6:c.7047C>A	p.Phe2349Leu	p.F2349L	ENST00000262189	NM_170606.2	2349	ttC/ttA	36/59	0.628459867302617	3	FACETS	1	0.939	1	0.521	0.473	0.57	CLONAL	1	FALSE	1	0.628459867302617	3		405	498	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945079	151945079	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753360496	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	43	600	0	ENST00000262189.6:c.2440A>G	p.Thr814Ala	p.T814A	ENST00000262189	NM_170606.2	814	Aca/Gca	14/59	0.628459867302617	3	FACETS	0.361	0.302	0.427	0.181	0.151	0.214	SUBCLONAL	1	FALSE	1	0.628459867302617	3		600	498	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945356	151945356	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	24	181	0	ENST00000262189.6:c.2163A>C	p.Gln721His	p.Q721H	ENST00000262189	NM_170606.2	721	caA/caC	14/59	0.628459867302617	3	FACETS	0.555	0.438	0.687	0.277	0.219	0.344	SUBCLONAL	1	FALSE	1	0.628459867302617	3		181	181	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29197718	29197718	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	247	796	0	ENST00000240100.2:c.476C>A	p.Ser159Tyr	p.S159Y	ENST00000240100	NM_001394.6	159	tCt/tAt	2/4	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	1	0.628459867302617	2		796	785	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38156975	38156975	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	105	537	0	ENST00000317025.8:c.2745G>T	p.Lys915Asn	p.K915N	ENST00000317025	NM_023034.1	915	aaG/aaT	15/24	1	2	FACETS	0.98	0.887	1	0.98	0.887	1	CLONAL	1	FALSE	1	0.628459867302617	2		537	341	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370987	55370987	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	98	652	0	ENST00000297316.4:c.289G>A	p.Glu97Lys	p.E97K	ENST00000297316	NM_022454.3	97	Gag/Aag	1/2	1	2	FACETS	0.542	0.485	0.603	0.542	0.485	0.603	SUBCLONAL	1	FALSE	1	0.628459867302617	2		652	575	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931838	68931838	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	83	578	0	ENST00000288368.4:c.268G>T	p.Val90Phe	p.V90F	ENST00000288368	NM_024870.2	90	Gtc/Ttc	3/40	1	2	FACETS	0.716	0.636	0.8	0.716	0.636	0.8	SUBCLONAL	1	FALSE	1	0.628459867302617	2		578	369	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934376	68934376	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	83	410	0	ENST00000288368.4:c.441+1G>T		p.X147_splice	ENST00000288368	NM_024870.2	147			1	2	FACETS	0.947	0.846	1	0.947	0.846	1	CLONAL	1	FALSE	1	0.628459867302617	2		410	279	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995590	68995590	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	125	603	1	ENST00000288368.4:c.1994C>A	p.Pro665His	p.P665H	ENST00000288368	NM_024870.2	665	cCt/cAt	18/40	1	2	FACETS	0.97	0.886	1	0.97	0.886	1	CLONAL	1	FALSE	1	0.628459867302617	2		604	410	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970887	70970887	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	81	483	0	ENST00000276594.2:c.1374C>A	p.His458Gln	p.H458Q	ENST00000276594	NM_024504.3	458	caC/caA	6/8	1	2	FACETS	0.591	0.523	0.664	0.591	0.523	0.664	SUBCLONAL	1	FALSE	1	0.628459867302617	2		483	436	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864854	117864854	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	133	510	0	ENST00000297338.2:c.1255G>T	p.Glu419Ter	p.E419*	ENST00000297338	NM_006265.2	419	Gaa/Taa	10/14	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	FALSE	1	0.628459867302617	2		510	418	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868428	117868428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	25	536	0	ENST00000297338.2:c.914C>T	p.Ala305Val	p.A305V	ENST00000297338	NM_006265.2	305	gCa/gTa	8/14	1	2	FACETS	0.179	0.141	0.224	0.179	0.141	0.224	SUBCLONAL	1	FALSE	1	0.628459867302617	2		536	444	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141570575	141570575	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	121	619	0	ENST00000220592.5:c.553T>C	p.Ser185Pro	p.S185P	ENST00000220592	NM_012154.3	185	Tcc/Ccc	5/19	1	2	FACETS	0.797	0.724	0.873	0.797	0.724	0.873	SUBCLONAL	1	FALSE	1	0.628459867302617	2		619	483	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5081859	5081859	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	11	198	0	ENST00000381652.3:c.2569A>G	p.Lys857Glu	p.K857E	ENST00000381652	NM_004972.3	857	Aag/Gag	19/25	1	2	FACETS	0.235	0.163	0.324	0.235	0.163	0.324	SUBCLONAL	1	FALSE	1	0.628459867302617	2		198	149	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158059	27158059	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	159	554	0	ENST00000380036.4:c.283A>C	p.Lys95Gln	p.K95Q	ENST00000380036	NM_000459.3	95	Aag/Cag	2/23	1	2	FACETS	0.975	0.9	1	0.975	0.9	1	CLONAL	1	FALSE	1	0.628459867302617	2		554	519	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180291	27180291	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs944559197	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	43	566	0	ENST00000380036.4:c.955A>G	p.Asn319Asp	p.N319D	ENST00000380036	NM_000459.3	319	Aat/Gat	7/23	1	2	FACETS	0.228	0.191	0.271	0.228	0.191	0.271	SUBCLONAL	1	FALSE	1	0.628459867302617	2		566	599	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27205025	27205025	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	179	548	0	ENST00000380036.4:c.2326A>C	p.Asn776His	p.N776H	ENST00000380036	NM_000459.3	776	Aat/Cat	14/23	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.628459867302617	2		548	547	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98011424	98011424	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	121	408	0	ENST00000289081.3:c.150A>C	p.Glu50Asp	p.E50D	ENST00000289081	NM_000136.2	50	gaA/gaC	2/15	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	FALSE	1	0.628459867302617	2		408	384	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750288	133750288	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	32	551	0	ENST00000318560.5:c.1119G>T	p.Glu373Asp	p.E373D	ENST00000318560	NM_005157.4	373	gaG/gaT	7/11	1	2	FACETS	0.189	0.152	0.23	0.189	0.152	0.23	SUBCLONAL	1	FALSE	1	0.628459867302617	2		551	540	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760681	133760681	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	277	879	0	ENST00000318560.5:c.3004T>C	p.Phe1002Leu	p.F1002L	ENST00000318560	NM_005157.4	1002	Ttc/Ctc	11/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.628459867302617	2		879	850	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15840923	15840923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	84	180	0	ENST00000307771.7:c.1007A>C	p.Asn336Thr	p.N336T	ENST00000307771	NM_005089.3	336	aAc/aCc	11/11	1	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	0	0.628459867302617	1		180	137	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922983	39922983	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs768062133	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	60	335	0	ENST00000378444.4:c.3725A>G	p.Gln1242Arg	p.Q1242R	ENST00000378444	NM_001123385.1	1242	cAg/cGg	8/15	1	1	FACETS	0.364	0.315	0.417	0.364	0.315	0.417	SUBCLONAL	1	FALSE	0	0.628459867302617	1		335	360	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038527	47038527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556777479	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	198	356	1	ENST00000377604.3:c.689G>A	p.Arg230Gln	p.R230Q	ENST00000377604	NM_001204468.1	230	cGa/cAa	8/24	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	0	0.628459867302617	1		357	320	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410567	63410567	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	162	414	0	ENST00000330258.3:c.2600G>T	p.Ser867Ile	p.S867I	ENST00000330258	NM_152424.3	867	aGc/aTc	2/2	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	0	0.628459867302617	1		414	274	SUCCESS
BTK	695	MSKCC	GRCh37	X	100629534	100629534	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	55	300	0	ENST00000308731.7:c.230G>T	p.Arg77Ile	p.R77I	ENST00000308731	NM_000061.2	77	aGa/aTa	3/19	1	1	FACETS	0.616	0.535	0.701	0.616	0.535	0.701	SUBCLONAL	1	FALSE	0	0.628459867302617	1		300	195	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	101	413	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.818	0.734	0.907	0.818	0.734	0.907	CLONAL	1	TRUE	1	0.464015052727711	2		413	532	SUCCESS
APC	324	MSKCC	GRCh37	5	112175466	112175466	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786204170	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	97	364	0	ENST00000257430.4:c.4175C>A	p.Ser1392Ter	p.S1392*	ENST00000257430	NM_000038.5	1392	tCa/tAa	16/16	1	2	FACETS	0.979	0.878	1	0.979	0.878	1	CLONAL	1	TRUE	1	0.464015052727711	2		364	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	211	1025	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.905	0.84	0.972	0.905	0.84	0.972	CLONAL	1	TRUE	1	0.464015052727711	2		1026	1005	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	483	803	1	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	0.441801639013302	3	FACETS	0.916	0.876	0.956	0.916	0.876	0.956	CLONAL	2	TRUE	1	0.464015052727711	3		804	1400	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277992	41277992	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	98	423	0	ENST00000349496.5:c.1954+2T>C		p.X652_splice	ENST00000349496	NM_001904.3	652			1	2	FACETS	0.761	0.681	0.846	0.761	0.681	0.846	SUBCLONAL	1	TRUE	1	0.464015052727711	2		423	555	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	92	233	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.885	0.79	0.985	0.885	0.79	0.985	CLONAL	1	TRUE	1	0.464015052727711	2		233	448	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	368	622	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	0.388490233440222	2	FACETS	0.887	0.845	0.93	0.887	0.845	0.93	CLONAL	2	TRUE	0	0.464015052727711	2		622	894	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40864422	40864422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374952991	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	240	861	1	ENST00000428826.2:c.1286C>T	p.Ser429Leu	p.S429L	ENST00000428826		429	tCg/tTg	12/21	1	2	FACETS	0.842	0.785	0.901	0.842	0.785	0.901	CLONAL	1	TRUE	1	0.464015052727711	2		862	1229	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812293	212812293	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569995088	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	35	311	1	ENST00000342788.4:c.283C>T	p.Arg95Cys	p.R95C	ENST00000342788	NM_005235.2	95	Cgt/Tgt	3/28	1	2	FACETS	0.322	0.264	0.388	0.322	0.264	0.388	SUBCLONAL	1	TRUE	1	0.464015052727711	2		312	468	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	141	260	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	0.858	0.792	0.925	1	0.991	1	CLONAL	2	TRUE	1	0.464015052727711	2		260	354	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710666	114710666	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	143	447	0	ENST00000543371.1:c.151G>T	p.Glu51Ter	p.E51*	ENST00000543371	NM_001198531.1	51	Gaa/Taa	1/14	1	2	FACETS	0.909	0.831	0.991	0.909	0.831	0.991	CLONAL	1	TRUE	1	0.464015052727711	2		447	678	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	112	393	1	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	0.87	0.785	0.959	0.87	0.785	0.959	CLONAL	1	TRUE	1	0.464015052727711	2		394	555	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736915	736915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs910562293	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	124	531	0	ENST00000314574.4:c.1184G>A	p.Arg395Gln	p.R395Q	ENST00000314574	NM_005433.3	395	cGa/cAa	10/12	1	2	FACETS	0.852	0.773	0.936	0.852	0.773	0.936	CLONAL	1	TRUE	1	0.464015052727711	2		531	627	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	157	408	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.985	0.905	1	0.985	0.905	1	CLONAL	1	TRUE	1	0.464015052727711	2		408	687	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068357	26068357	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	61	308	0	ENST00000435504.4:c.133G>T	p.Glu45Ter	p.E45*	ENST00000435504		45	Gaa/Taa	2/13	1	2	FACETS	0.799	0.694	0.912	0.799	0.694	0.912	CLONAL	1	TRUE	1	0.464015052727711	2		308	329	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741858	17741858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	38	155	0	ENST00000250003.3:c.529G>A	p.Ala177Thr	p.A177T	ENST00000250003	NM_002478.4	177	Gcc/Acc	1/3	1	2	FACETS	0.91	0.762	1	0.91	0.762	1	CLONAL	1	TRUE	1	0.464015052727711	2		155	180	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242662	46242662	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	182	383	0	ENST00000334344.6:c.1624C>T	p.Arg542Ter	p.R542*	ENST00000334344	NM_152641.2	542	Cga/Tga	13/21	0.441801639013302	3	FACETS	0.91	0.846	0.976	0.91	0.846	0.976	CLONAL	2	TRUE	1	0.464015052727711	3		383	531	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	167	521	1	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	0.374512614167352	3	FACETS	1	0.955	1	0.528	0.485	0.572	CLONAL	1	TRUE	1	0.464015052727711	3		522	840	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905391	11905391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781494988	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	94	340	0	ENST00000396373.4:c.41G>A	p.Arg14Gln	p.R14Q	ENST00000396373	NM_001987.4	14	cGa/cAa	2/8	0.441801639013302	3	FACETS	0.84	0.749	0.937	0.42	0.374	0.469	CLONAL	1	TRUE	1	0.464015052727711	3		340	594	SUCCESS
APC	324	MSKCC	GRCh37	5	112177901	112177901	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs752654519	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	83	335	0	ENST00000257430.4:c.6610C>T	p.Arg2204Ter	p.R2204*	ENST00000257430	NM_000038.5	2204	Cga/Tga	16/16	1	2	FACETS	0.786	0.697	0.881	0.786	0.697	0.881	SUBCLONAL	1	TRUE	1	0.464015052727711	2		335	455	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094337	193094337	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	98	393	0	ENST00000367435.3:c.227G>A	p.Arg76Gln	p.R76Q	ENST00000367435	NM_024529.4	76	cGa/cAa	2/17	1	2	FACETS	0.774	0.692	0.86	0.774	0.692	0.86	SUBCLONAL	1	TRUE	1	0.464015052727711	2		393	546	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178199	142178199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746049210	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	64	290	0	ENST00000350721.4:c.7219C>T	p.Arg2407Cys	p.R2407C	ENST00000350721	NM_001184.3	2407	Cgc/Tgc	43/47	1	2	FACETS	0.684	0.595	0.781	0.684	0.595	0.781	SUBCLONAL	1	TRUE	1	0.464015052727711	2		290	403	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068393	26068393	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	87	411	0	ENST00000435504.4:c.97G>T	p.Glu33Ter	p.E33*	ENST00000435504		33	Gaa/Taa	2/13	1	2	FACETS	0.957	0.852	1	0.957	0.852	1	CLONAL	1	TRUE	1	0.464015052727711	2		411	392	SUCCESS
APC	324	MSKCC	GRCh37	5	112177203	112177203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs754691867	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	102	327	0	ENST00000257430.4:c.5912C>A	p.Ser1971Tyr	p.S1971Y	ENST00000257430	NM_000038.5	1971	tCt/tAt	16/16	1	2	FACETS	0.962	0.865	1	0.962	0.865	1	CLONAL	1	TRUE	1	0.464015052727711	2		327	457	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486794	56486794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370847503	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	140	660	0	ENST00000267101.3:c.1208C>T	p.Pro403Leu	p.P403L	ENST00000267101	NM_001982.3	403	cCg/cTg	11/28	0.441801639013302	3	FACETS	0.624	0.566	0.684	0.312	0.283	0.342	SUBCLONAL	1	TRUE	1	0.464015052727711	3		660	1192	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6031648	6031648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs116314131	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	167	464	0	ENST00000265849.7:c.944G>A	p.Arg315Gln	p.R315Q	ENST00000265849	NM_000535.5	315	cGa/cAa	9/15	1	2	FACETS	0.952	0.877	1	0.952	0.877	1	CLONAL	1	TRUE	1	0.464015052727711	2		464	756	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215595214	215595214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752870879	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	73	316	0	ENST00000260947.4:c.1922G>A	p.Arg641Gln	p.R641Q	ENST00000260947	NM_000465.2	641	cGa/cAa	10/11	1	2	FACETS	0.668	0.586	0.756	0.668	0.586	0.756	SUBCLONAL	1	TRUE	1	0.464015052727711	2		316	471	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620099	21620099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	186	658	1	ENST00000382592.4:c.67C>T	p.Arg23Cys	p.R23C	ENST00000382592	NM_014572.2	23	Cgt/Tgt	2/8	1	2	FACETS	0.891	0.823	0.961	0.891	0.823	0.961	CLONAL	1	TRUE	1	0.464015052727711	2		659	900	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285871	87285871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408094711	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	155	486	0	ENST00000277120.3:c.208G>A	p.Glu70Lys	p.E70K	ENST00000277120		70	Gaa/Aaa	2/19	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.464015052727711	2		486	667	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934931	9934931	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	90	404	0	ENST00000330684.3:c.1359G>T	p.Lys453Asn	p.K453N	ENST00000330684	NM_001134407.1	453	aaG/aaT	6/13	1	2	FACETS	0.764	0.68	0.853	0.764	0.68	0.853	SUBCLONAL	1	TRUE	1	0.464015052727711	2		404	508	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931964	39931964	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	238	411	0	ENST00000378444.4:c.2635A>C	p.Ser879Arg	p.S879R	ENST00000378444	NM_001123385.1	879	Agc/Cgc	4/15	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.464015052727711	1		411	588	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32903612	32903612	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507873	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	45	308	0	ENST00000380152.3:c.664C>T	p.Pro222Ser	p.P222S	ENST00000380152		222	Cct/Tct	8/27	1	2	FACETS	0.669	0.565	0.782	0.669	0.565	0.782	SUBCLONAL	1	TRUE	1	0.464015052727711	2		308	290	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74000721	74000721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150498569	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	264	869	1	ENST00000318443.5:c.1411G>A	p.Val471Met	p.V471M	ENST00000318443	NM_001024736.1	471	Gtg/Atg	7/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.464015052727711	2		870	1102	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876188	35876188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536561203	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	161	552	3	ENST00000303115.3:c.980C>T	p.Thr327Met	p.T327M	ENST00000303115	NM_002185.3	327	aCg/aTg	8/8	1	2	FACETS	0.902	0.829	0.979	0.902	0.829	0.979	CLONAL	1	TRUE	1	0.464015052727711	2		555	769	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647140	2647140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	123	518	0	ENST00000342085.4:c.1418G>A	p.Arg473Gln	p.R473Q	ENST00000342085	NM_002613.4	473	cGa/cAa	13/14	1	2	FACETS	0.787	0.712	0.864	0.787	0.712	0.864	SUBCLONAL	1	TRUE	1	0.464015052727711	2		518	674	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641221	3641221	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	264	905	1	ENST00000294008.3:c.2418G>T	p.Glu806Asp	p.E806D	ENST00000294008	NM_032444.2	806	gaG/gaT	12/15	1	2	FACETS	0.906	0.848	0.966	0.906	0.848	0.966	CLONAL	1	TRUE	1	0.464015052727711	2		906	1256	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820827	36820827	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	276	519	0	ENST00000373129.3:c.550G>C	p.Val184Leu	p.V184L	ENST00000373129	NM_032017.1	184	Gtg/Ctg	6/12	0.388490233440222	2	FACETS	0.897	0.848	0.946	0.897	0.848	0.946	CLONAL	2	TRUE	0	0.464015052727711	2		519	663	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267291	41267291	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	118	437	0	ENST00000349496.5:c.875A>C	p.Lys292Thr	p.K292T	ENST00000349496	NM_001904.3	292	aAa/aCa	6/15	1	2	FACETS	0.874	0.791	0.961	0.874	0.791	0.961	CLONAL	1	TRUE	1	0.464015052727711	2		437	582	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229233	123229233	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	93	171	0	ENST00000218089.9:c.3717G>T	p.Lys1239Asn	p.K1239N	ENST00000218089	NM_001042749.1	1239	aaG/aaT	34/35	1	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.464015052727711	1		171	221	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553117	106553117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750485966	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	153	630	0	ENST00000369096.4:c.1082C>T	p.Ser361Phe	p.S361F	ENST00000369096	NM_001198.3	361	tCc/tTc	5/7	1	2	FACETS	0.823	0.754	0.896	0.823	0.754	0.896	CLONAL	1	TRUE	1	0.464015052727711	2		630	801	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624301	89624301	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786201506	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	207	640	0	ENST00000371953.3:c.75G>T	p.Leu25Phe	p.L25F	ENST00000371953	NM_000314.4	25	ttG/ttT	1/9	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.464015052727711	2		640	891	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394827	394827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	100	411	1	ENST00000380956.4:c.223G>T	p.Ala75Ser	p.A75S	ENST00000380956	NM_001195286.1	75	Gca/Tca	3/9	1	2	FACETS	0.789	0.707	0.876	0.789	0.707	0.876	SUBCLONAL	1	TRUE	1	0.464015052727711	2		412	546	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333589	70333589	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	149	521	0	ENST00000373644.4:c.1494A>C	p.Glu498Asp	p.E498D	ENST00000373644	NM_030625.2	498	gaA/gaC	2/12	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.464015052727711	2		521	634	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417850	32417850	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	165	597	0	ENST00000332351.3:c.1202G>T	p.Arg401Ile	p.R401I	ENST00000332351	NM_024426.4	401	aGa/aTa	7/10	1	2	FACETS	0.913	0.84	0.989	0.913	0.84	0.989	CLONAL	1	TRUE	1	0.464015052727711	2		597	779	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192672	94192672	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	161	620	1	ENST00000323929.3:c.1402G>T	p.Asp468Tyr	p.D468Y	ENST00000323929	NM_005591.3	468	Gat/Tat	13/20	1	2	FACETS	0.905	0.831	0.981	0.905	0.831	0.981	CLONAL	1	TRUE	1	0.464015052727711	2		621	767	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	459846	459846	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	215	753	0	ENST00000399788.2:c.1249G>T	p.Asp417Tyr	p.D417Y	ENST00000399788	NM_001042603.1	417	Gac/Tac	10/28	0.441801639013302	3	FACETS	0.908	0.843	0.976	0.454	0.421	0.488	CLONAL	1	TRUE	1	0.464015052727711	3		753	1257	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1034620	1034620	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372461582	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	145	523	1	ENST00000358495.3:c.539G>A	p.Arg180His	p.R180H	ENST00000358495	NM_134424.2	180	cGc/cAc	7/12	0.441801639013302	3	FACETS	0.921	0.841	1	0.461	0.42	0.503	CLONAL	1	TRUE	1	0.464015052727711	3		524	836	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21630751	21630751	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	98	392	0	ENST00000421138.2:c.853A>C	p.Asn285His	p.N285H	ENST00000421138		285	Aat/Cat	8/16	0.441801639013302	3	FACETS	0.885	0.791	0.984	0.443	0.395	0.492	CLONAL	1	TRUE	1	0.464015052727711	3		392	588	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230764	46230764	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	67	306	0	ENST00000334344.6:c.1013T>G	p.Ile338Ser	p.I338S	ENST00000334344	NM_152641.2	338	aTt/aGt	8/21	0.441801639013302	3	FACETS	0.835	0.728	0.95	0.418	0.364	0.475	CLONAL	1	TRUE	1	0.464015052727711	3		306	426	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490286	56490286	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	69	342	0	ENST00000267101.3:c.2056-1G>T		p.X686_splice	ENST00000267101	NM_001982.3	686			0.441801639013302	3	FACETS	0.765	0.668	0.869	0.382	0.334	0.435	SUBCLONAL	1	TRUE	1	0.464015052727711	3		342	479	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28979931	28979931	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	139	495	0	ENST00000282397.4:c.1537G>T	p.Glu513Ter	p.E513*	ENST00000282397	NM_002019.4	513	Gaa/Taa	11/30	1	2	FACETS	0.871	0.794	0.951	0.871	0.794	0.951	CLONAL	1	TRUE	1	0.464015052727711	2		495	688	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007665	45007665	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	106	363	0	ENST00000558401.1:c.112G>T	p.Gly38Ter	p.G38*	ENST00000558401	NM_004048.2	38	Gga/Tga	2/4	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.464015052727711	2		363	371	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992895	72992895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs553932870	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	214	735	0	ENST00000268489.5:c.1150G>A	p.Ala384Thr	p.A384T	ENST00000268489	NM_006885.3	384	Gcc/Acc	2/10	1	2	FACETS	0.973	0.905	1	0.973	0.905	1	CLONAL	1	TRUE	1	0.464015052727711	2		735	948	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882996	89882996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs965036018	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	76	157	1	ENST00000389301.3:c.28G>A	p.Ala10Thr	p.A10T	ENST00000389301	NM_000135.2	10	Gcc/Acc	1/43	1	2	FACETS	0.978	0.865	1	0.978	0.865	1	CLONAL	1	TRUE	1	0.464015052727711	2		158	335	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968182	15968182	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	70	229	0	ENST00000268712.3:c.5101+2T>C		p.X1701_splice	ENST00000268712	NM_006311.3	1701			1	2	FACETS	0.845	0.741	0.956	0.845	0.741	0.956	CLONAL	1	TRUE	1	0.464015052727711	2		229	357	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646817	37646817	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	37	359	0	ENST00000447079.4:c.1939G>T	p.Glu647Ter	p.E647*	ENST00000447079	NM_015083.1	647	Gaa/Taa	3/14	1	2	FACETS	0.271	0.223	0.326	0.271	0.223	0.326	SUBCLONAL	1	TRUE	1	0.464015052727711	2		359	588	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40854581	40854581	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	231	763	0	ENST00000428826.2:c.2213T>C	p.Val738Ala	p.V738A	ENST00000428826		738	gTg/gCg	21/21	1	2	FACETS	0.904	0.843	0.968	0.904	0.843	0.968	CLONAL	1	TRUE	1	0.464015052727711	2		763	1101	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66518930	66518930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	123	367	0	ENST00000358598.2:c.211G>A	p.Ala71Thr	p.A71T	ENST00000358598	NM_212471.2	71	Gca/Aca	3/11	1	2	FACETS	0.943	0.856	1	0.943	0.856	1	CLONAL	1	TRUE	1	0.464015052727711	2		367	562	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606619	29606619	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	153	497	0	ENST00000389048.3:c.1261G>T	p.Ala421Ser	p.A421S	ENST00000389048	NM_004304.4	421	Gcc/Tcc	5/29	NA	2	FACETS	0.964	0.884	1			1	INDETERMINATE	1	TRUE	NA	0.464015052727711	2		497	684	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488646	212488646	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	106	390	0	ENST00000342788.4:c.2202+1G>A		p.X734_splice	ENST00000342788	NM_005235.2	734			1	2	FACETS	0.857	0.771	0.948	0.857	0.771	0.948	CLONAL	1	TRUE	1	0.464015052727711	2		390	533	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439577	220439577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	208	847	0	ENST00000243786.2:c.430G>A	p.Ala144Thr	p.A144T	ENST00000243786	NM_002191.3	144	Gcc/Acc	2/2	1	2	FACETS	0.853	0.791	0.917	0.853	0.791	0.917	CLONAL	1	TRUE	1	0.464015052727711	2		847	1051	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368448	225368448	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	128	487	0	ENST00000264414.4:c.1298A>C	p.Lys433Thr	p.K433T	ENST00000264414	NM_003590.4	433	aAa/aCa	9/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.464015052727711	2		487	503	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750614	41750614	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	129	471	0	ENST00000226382.2:c.14A>C	p.Glu5Ala	p.E5A	ENST00000226382	NM_003924.3	5	gAa/gCa	1/3	1	2	FACETS	0.867	0.788	0.95	0.867	0.788	0.95	CLONAL	1	TRUE	1	0.464015052727711	2		471	641	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590501	67590501	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	72	229	2	ENST00000274335.5:c.1563A>G	p.Ile521Met	p.I521M	ENST00000274335		521	atA/atG	11/15	1	2	FACETS	0.976	0.86	1	0.976	0.86	1	CLONAL	1	TRUE	1	0.464015052727711	2		231	318	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633810	86633810	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	53	255	0	ENST00000274376.6:c.919T>C	p.Phe307Leu	p.F307L	ENST00000274376	NM_002890.2	307	Ttc/Ctc	5/25	1	2	FACETS	0.96	0.827	1	0.96	0.827	1	CLONAL	1	TRUE	1	0.464015052727711	2		255	238	SUCCESS
APC	324	MSKCC	GRCh37	5	112090610	112090610	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	90	281	0	ENST00000257430.4:c.23A>G	p.Gln8Arg	p.Q8R	ENST00000257430	NM_000038.5	8	cAg/cGg	2/16	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.464015052727711	2		281	387	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170832333	170832333	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	113	457	0	ENST00000296930.5:c.697A>C	p.Lys233Gln	p.K233Q	ENST00000296930	NM_002520.6	233	Aaa/Caa	9/11	1	2	FACETS	0.968	0.876	1	0.968	0.876	1	CLONAL	1	TRUE	1	0.464015052727711	2		457	503	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793850	89793850	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	143	431	0	ENST00000336032.3:c.919A>C	p.Asn307His	p.N307H	ENST00000336032	NM_006813.2	307	Aat/Cat	2/2	1	2	FACETS	0.98	0.896	1	0.98	0.896	1	CLONAL	1	TRUE	1	0.464015052727711	2		431	629	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956562	93956562	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	99	385	0	ENST00000369303.4:c.2674A>C	p.Lys892Gln	p.K892Q	ENST00000369303	NM_004440.3	892	Aaa/Caa	15/17	1	2	FACETS	0.883	0.792	0.98	0.883	0.792	0.98	CLONAL	1	TRUE	1	0.464015052727711	2		385	483	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033273	69033273	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	118	411	0	ENST00000288368.4:c.3713A>G	p.Lys1238Arg	p.K1238R	ENST00000288368	NM_024870.2	1238	aAa/aGa	30/40	1	2	FACETS	0.862	0.78	0.948	0.862	0.78	0.948	CLONAL	1	TRUE	1	0.464015052727711	2		411	590	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90994993	90994993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759146120	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	116	410	1	ENST00000265433.3:c.128G>A	p.Arg43Gln	p.R43Q	ENST00000265433	NM_002485.4	43	cGa/cAa	2/16	1	2	FACETS	0.787	0.711	0.868	0.787	0.711	0.868	SUBCLONAL	1	TRUE	1	0.464015052727711	2		411	635	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969399	44969399	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	177	276	0	ENST00000377967.4:c.4081T>G	p.Cys1361Gly	p.C1361G	ENST00000377967	NM_021140.2	1361	Tgt/Ggt	28/29	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.464015052727711	1		276	406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0051778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	320	662	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.498167924803232	2	FACETS	0.93	0.885	0.975	0.93	0.885	0.975	CLONAL	2	TRUE	0	0.508381890281286	2		662	677	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683228	88683228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876658515	NA	P-0051778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	88	450	1	ENST00000372037.3:c.1438C>T	p.Arg480Trp	p.R480W	ENST00000372037	NM_004329.2	480	Cgg/Tgg	12/13	1	2	FACETS	0.807	0.719	0.9	0.807	0.719	0.9	CLONAL	1	TRUE	1	0.508381890281286	2		451	429	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829787	76829787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057517948	NA	P-0051778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	66	537	2	ENST00000373344.5:c.6254G>A	p.Arg2085His	p.R2085H	ENST00000373344	NM_000489.3	2085	cGt/cAt	28/35	0.142216857594323	0	FACETS	0.44	0.385	0.498			1	INDETERMINATE	1	TRUE	0	0.508381890281286	0		539	290	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12043158	12043158	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	43	233	0	ENST00000353533.5:c.1043T>G	p.Leu348Arg	p.L348R	ENST00000353533	NM_003010.3	348	cTt/cGt	10/11	0.508381890281286	1	FACETS	0.908	0.776	1	0.908	0.776	1	CLONAL	1	TRUE	0	0.508381890281286	1		233	139	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600459	10600460	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0051778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	191	719	0	ENST00000171111.5:c.1394_1395dup	p.Ala466TrpfsTer35	p.A466Wfs*35	ENST00000171111	NM_203500.1	465	-/TG	4/6	0.508381890281286	3	FACETS	0.93	0.86	1	0.465	0.43	0.502	CLONAL	1	TRUE	1	0.508381890281286	3		719	1013	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0051779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	65	449	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.973	0.846	1	0.973	0.846	1	CLONAL	1	TRUE	1	0.315193357984495	2		449	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0051779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	160	505	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.315193357984495	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.315193357984495	1		505	642	SUCCESS
APC	324	MSKCC	GRCh37	5	112175606	112175606	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	114	277	0	ENST00000257430.4:c.4316del	p.Pro1439LeufsTer34	p.P1439Lfs*34	ENST00000257430	NM_000038.5	1439	Cct/ct	16/16	0.287434655366141	2	FACETS	0.859	0.779	0.942	0.859	0.779	0.942	CLONAL	2	TRUE	0	0.315193357984495	2		277	421	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11019832	11019832	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	206	430	0	ENST00000327064.4:c.507del	p.Gly170AlafsTer57	p.G170Afs*57	ENST00000327064	NM_199141.1	169	acA/ac	4/16	0.137090985909296	3	FACETS	1	0.96	1	0.697	0.649	0.746	INDETERMINATE	2	TRUE	0	0.315193357984495	3		430	724	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0051780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	116	378	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.281138957345087	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.281138957345087	2		378	383	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0051780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	120	290	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	0.230541931821383	3	FACETS	1	0.975	1	0.801	0.73	0.875	CLONAL	2	TRUE	0	0.281138957345087	3		290	405	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0051780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	111	552	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.281138957345087	2	FACETS	0.933	0.845	1	0.933	0.845	1	CLONAL	2	TRUE	0	0.281138957345087	2		554	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934874	NA	P-0051780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	258	710	0	ENST00000269305.4:c.451C>G	p.Pro151Ala	p.P151A	ENST00000269305	NM_001126112.2	151	Ccc/Gcc	5/11	0.281138957345087	2	FACETS	0.907	0.85	0.965	0.907	0.85	0.965	CLONAL	2	TRUE	0	0.281138957345087	2		710	1012	SUCCESS
APC	324	MSKCC	GRCh37	5	112175750	112175750	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	111	285	0	ENST00000257430.4:c.4459del	p.Thr1487LeufsTer20	p.T1487Lfs*20	ENST00000257430	NM_000038.5	1487	Act/ct	16/16	0.281138957345087	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	2	TRUE	0	0.281138957345087	2		285	393	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098521	11098521	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	79	493	0	ENST00000358026.2:c.1039C>T	p.Gln347Ter	p.Q347*	ENST00000358026	NM_001128849.1	347	Cag/Tag	6/36	0.281138957345087	2	FACETS	0.849	0.747	0.959	0.424	0.373	0.48	CLONAL	1	TRUE	0	0.281138957345087	2		493	662	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920401	114920401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1422891742	NA	P-0051780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	60	318	3	ENST00000543371.1:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000543371	NM_001198531.1	448	Cgg/Tgg	13/14	0.281138957345087	2	FACETS	0.801	0.69	0.921	0.4	0.345	0.461	CLONAL	1	TRUE	0	0.281138957345087	2		321	533	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288989	212288989	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	79	355	0	ENST00000342788.4:c.2757A>C	p.Lys919Asn	p.K919N	ENST00000342788	NM_005235.2	919	aaA/aaC	23/28	0.281138957345087	3	FACETS	0.793	0.701	0.891	0.793	0.701	0.891	SUBCLONAL	2	TRUE	1	0.281138957345087	3		355	404	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534407	63534407	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	130	571	0	ENST00000307078.5:c.1114G>A	p.Ala372Thr	p.A372T	ENST00000307078	NM_004655.3	372	Gct/Act	5/11	0.281138957345087	2	FACETS	0.925	0.838	1	0.462	0.419	0.509	CLONAL	1	TRUE	0	0.281138957345087	2		571	1000	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593435	215593435	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	62	238	0	ENST00000260947.4:c.2299G>A	p.Val767Met	p.V767M	ENST00000260947	NM_000465.2	767	Gtg/Atg	11/11	0.281138957345087	3	FACETS	0.811	0.706	0.924	0.811	0.706	0.924	CLONAL	2	TRUE	1	0.281138957345087	3		238	310	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21304042	21304051	+	frameshift_variant	Frame_Shift_Del	DEL	AGTGGGAAGG	AGTGGGAAGG	TT	novel	NA	P-0051780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	62	358	0	ENST00000354336.3:c.821_830delinsTT	p.Gln274LeufsTer19	p.Q274Lfs*19	ENST00000354336	NM_005207.3	274	cAGTGGGAAGGc/cTTc	3/3	0.281138957345087	2	FACETS	0.814	0.703	0.933	0.407	0.351	0.467	CLONAL	1	TRUE	0	0.281138957345087	2		358	542	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	130	415	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.864	0.788	0.944	0.864	0.788	0.944	CLONAL	1	TRUE	1	0.576311217196318	2		415	522	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	226	588	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.576311217196318	2		592	778	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	112	333	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.576311217196318	2		333	344	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	139	498	4	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.995	0.912	1	0.995	0.912	1	CLONAL	1	TRUE	1	0.576311217196318	2		502	485	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800902	120800903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748469666	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	123	650	6	ENST00000257552.2:c.345dup	p.Leu116AlafsTer15	p.L116Afs*15	ENST00000257552	NM_002442.3	115	-/G	6/15	1	2	FACETS	0.552	0.499	0.608	0.552	0.499	0.608	SUBCLONAL	1	TRUE	1	0.576311217196318	2		656	773	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	384	1445	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.925	0.887	0.964	1	0.997	1	CLONAL	2	TRUE	1	0.576311217196318	2		1452	720	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992721	68992721	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs764112302	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	176	306	2	ENST00000288368.4:c.1693del	p.Ser565ArgfsTer10	p.S565Rfs*10	ENST00000288368	NM_024870.2	562	cgT/cg	16/40	1	2	FACETS	0.916	0.847	0.987	0.916	0.847	0.987	CLONAL	1	TRUE	1	0.576311217196318	2		308	667	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821959	72821960	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762108866	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	140	360	1	ENST00000268489.5:c.10215dup	p.Gly3406ArgfsTer25	p.G3406Rfs*25	ENST00000268489	NM_006885.3	3405	-/C	10/10	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.576311217196318	2		361	469	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256768	19256769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1202792889	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	95	775	0	ENST00000162023.5:c.944dup	p.Val316SerfsTer6	p.V316Sfs*6	ENST00000162023		315	cca/ccCa	13/13	1	2	FACETS	0.486	0.433	0.543	0.486	0.433	0.543	SUBCLONAL	1	TRUE	1	0.576311217196318	2		775	678	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199450	16199450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200367310	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	139	344	0	ENST00000375759.3:c.223C>T	p.Arg75Cys	p.R75C	ENST00000375759	NM_015001.2	75	Cgc/Tgc	2/15	1	2	FACETS	0.971	0.889	1	0.971	0.889	1	CLONAL	1	TRUE	1	0.576311217196318	2		344	497	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	130	494	10	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.946	0.864	1	0.946	0.864	1	CLONAL	1	TRUE	1	0.576311217196318	2		504	477	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	169	552	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.576311217196318	2		554	580	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023909	27023923	+	inframe_deletion	In_Frame_Del	DEL	GCTGCGGCGGCGGCA	GCTGCGGCGGCGGCA	-	rs751352361	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	41	99	0	ENST00000324856.7:c.1029_1043del	p.Ala345_Ala349del	p.A345_A349del	ENST00000324856	NM_006015.4	339	GCTGCGGCGGCGGCA/-	1/20	1	2	FACETS	0.842	0.712	0.982	0.842	0.712	0.982	CLONAL	1	TRUE	1	0.576311217196318	2		99	169	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467646	66467646	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	73	359	0	ENST00000273854.3:c.623del	p.Lys208ArgfsTer60	p.K208Rfs*60	ENST00000273854	NM_004439.5	208	aAg/ag	3/18	NA	2	FACETS	0.67	0.589	0.756			1	INDETERMINATE	1	TRUE	NA	0.576311217196318	2		359	378	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449800	29449800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs76742576	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	270	885	2	ENST00000389048.3:c.3055G>A	p.Val1019Ile	p.V1019I	ENST00000389048	NM_004304.4	1019	Gtc/Atc	18/29	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.576311217196318	2		887	862	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661664	227661664	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs761880048	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	169	625	12	ENST00000305123.5:c.1791del	p.His598ThrfsTer38	p.H598Tfs*38	ENST00000305123	NM_005544.2	597	ggG/gg	1/2	NA	2	FACETS	0.921	0.85	0.994			1	INDETERMINATE	1	TRUE	NA	0.576311217196318	2		637	637	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984782	11984782	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1164096095	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	48	388	0	ENST00000353533.5:c.328C>T	p.Arg110Ter	p.R110*	ENST00000353533	NM_003010.3	110	Cga/Tga	3/11	0.576311217196318	1	FACETS	0.525	0.448	0.607	0.525	0.448	0.607	SUBCLONAL	1	TRUE	0	0.576311217196318	1		388	226	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882050	36882050	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs780753361	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	203	769	3	ENST00000358127.4:c.963del	p.Ala322LeufsTer11	p.A322Lfs*11	ENST00000358127	NM_001280556.1	321	ccC/cc	8/10	1	2	FACETS	0.862	0.801	0.926	0.862	0.801	0.926	CLONAL	1	TRUE	1	0.576311217196318	2		772	817	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370236	40370236	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs761761205	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	128	780	12	ENST00000293328.3:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000293328	NM_012448.3	368	Cag/ag	9/19	1	2	FACETS	0.596	0.541	0.655	0.596	0.541	0.655	SUBCLONAL	1	TRUE	1	0.576311217196318	2		792	745	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371684	55371684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	210	795	1	ENST00000297316.4:c.374G>A	p.Arg125His	p.R125H	ENST00000297316	NM_022454.3	125	cGc/cAc	2/2	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.576311217196318	2		796	631	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099579	157099579	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1562376341	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	28	106	2	ENST00000346085.5:c.521del	p.Pro174ArgfsTer6	p.P174Rfs*6	ENST00000346085	NM_020732.3	172	gaC/ga	1/20	1	2	FACETS	0.731	0.593	0.882	0.731	0.593	0.882	SUBCLONAL	1	TRUE	1	0.576311217196318	2		108	133	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375194	31375194	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	229	800	1	ENST00000328111.2:c.596del	p.Gly199AlafsTer27	p.G199Afs*27	ENST00000328111	NM_006892.3	197	caG/ca	6/23	1	2	FACETS	0.956	0.893	1	0.956	0.893	1	CLONAL	1	TRUE	1	0.576311217196318	2		801	831	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188309	10188309	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	195	477	0	ENST00000256474.2:c.452T>A	p.Ile151Asn	p.I151N	ENST00000256474	NM_000551.3	151	aTc/aAc	2/3	0.165939042955152	2	FACETS	1	0.968	1	0.535	0.497	0.573	INDETERMINATE	1	TRUE	0	0.576311217196318	2		477	633	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563349	21563349	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	207	961	0	ENST00000382592.4:c.570del	p.Tyr191ThrfsTer49	p.Y191Tfs*49	ENST00000382592	NM_014572.2	190	ccC/cc	4/8	1	2	FACETS	0.915	0.851	0.981	0.915	0.851	0.981	CLONAL	1	TRUE	1	0.576311217196318	2		961	785	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384650	31384651	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs756395138	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	190	606	0	ENST00000328111.2:c.1359dup	p.Leu454AlafsTer11	p.L454Afs*11	ENST00000328111	NM_006892.3	451	gag/gaGg	13/23	1	2	FACETS	0.953	0.884	1	0.953	0.884	1	CLONAL	1	TRUE	1	0.576311217196318	2		606	692	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778917	9778917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774975013	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	186	664	0	ENST00000377346.4:c.1186G>A	p.Ala396Thr	p.A396T	ENST00000377346	NM_005026.3	396	Gcc/Acc	9/24	NA	2	FACETS	0.963	0.893	1			1	INDETERMINATE	1	TRUE	NA	0.576311217196318	2		664	670	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953258	81953258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776768909	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	89	243	0	ENST00000359376.3:c.2224C>T	p.Arg742Cys	p.R742C	ENST00000359376	NM_002661.3	742	Cgc/Tgc	20/33	1	2	FACETS	0.936	0.838	1	0.936	0.838	1	CLONAL	1	TRUE	1	0.576311217196318	2		243	330	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646980	23646981	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	233	555	0	ENST00000261584.4:c.886dup	p.Met296AsnfsTer7	p.M296Nfs*7	ENST00000261584	NM_024675.3	296	atg/aAtg	4/13	1	2	FACETS	0.985	0.921	1	0.985	0.921	1	CLONAL	1	TRUE	1	0.576311217196318	2		555	821	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983091	111983091	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	199	632	0	ENST00000368678.4:c.1456C>T	p.Gln486Ter	p.Q486*	ENST00000368678		486	Cag/Tag	13/13	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.576311217196318	2		632	688	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806605	1806605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17884368	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	219	806	0	ENST00000260795.2:c.1321G>A	p.Ala441Thr	p.A441T	ENST00000260795		441	Gca/Aca	9/17	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.576311217196318	2		806	749	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994302	21994302	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	183	619	2	ENST00000579755.1:c.29G>A	p.Arg10Gln	p.R10Q	ENST00000579755		10	cGg/cAg	1/3	1		FACETS		0.896	1				CLONAL	1	TRUE	1	0.576311217196318	2		621	657	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859859	151859859	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	38	359	0	ENST00000262189.6:c.10803del	p.Lys3604ArgfsTer26	p.K3604Rfs*26	ENST00000262189	NM_170606.2	3601	aaA/aa	43/59	1	2	FACETS	0.292	0.241	0.349	0.292	0.241	0.349	SUBCLONAL	1	TRUE	1	0.576311217196318	2		359	452	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710607	40710607	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	227	568	2	ENST00000373198.4:c.4244A>T	p.Glu1415Val	p.E1415V	ENST00000373198	NM_133170.3	1415	gAg/gTg	31/32	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.576311217196318	2		570	671	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526792	31526792	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	171	557	0	ENST00000344624.3:c.248del	p.Pro83HisfsTer25	p.P83Hfs*25	ENST00000344624		83	cCa/ca	2/33	1	2	FACETS	0.974	0.901	1	0.974	0.901	1	CLONAL	1	TRUE	1	0.576311217196318	2		557	609	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128305365	128305365	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	430	504	0	ENST00000265960.3:c.931C>T	p.Arg311Ter	p.R311*	ENST00000265960	NM_001006617.1	311	Cga/Tga	7/12	0.576306038519423	2	FACETS	0.98	0.943	1	0.98	0.943	1	CLONAL	2	TRUE	0	0.576311217196318	2		504	761	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599885	28599885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371066600	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	170	521	0	ENST00000253063.3:c.767G>A	p.Arg256His	p.R256H	ENST00000253063	NM_031459.4	256	cGc/cAc	6/10	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.576311217196318	2		521	577	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223820	53223820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781841978	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	225	891	1	ENST00000375401.3:c.3539C>T	p.Thr1180Met	p.T1180M	ENST00000375401	NM_004187.3	1180	aCg/aTg	23/26	1	2	FACETS	0.966	0.902	1	0.966	0.902	1	CLONAL	1	TRUE	1	0.576311217196318	2		892	808	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450351	50450351	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	101	559	0	ENST00000331340.3:c.535A>G	p.Asn179Asp	p.N179D	ENST00000331340	NM_006060.4	179	Aac/Gac	5/8	1	2	FACETS	0.665	0.596	0.737	0.665	0.596	0.737	SUBCLONAL	1	TRUE	1	0.576311217196318	2		559	527	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259877	16259878	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	173	558	0	ENST00000375759.3:c.7143dup	p.Gln2382ThrfsTer7	p.Q2382Tfs*7	ENST00000375759	NM_015001.2	2381	cca/ccAa	11/15	1	2	FACETS	0.953	0.881	1	0.953	0.881	1	CLONAL	1	TRUE	1	0.576311217196318	2		558	630	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46724401	46724401	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	172	354	0	ENST00000371975.4:c.254C>A	p.Pro85His	p.P85H	ENST00000371975	NM_003579.3	85	cCc/cAc	4/18	1	2	FACETS	0.878	0.81	0.948	0.878	0.81	0.948	CLONAL	1	TRUE	1	0.576311217196318	2		354	680	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740337	46740337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374574941	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	170	483	1	ENST00000371975.4:c.1817G>A	p.Arg606Gln	p.R606Q	ENST00000371975	NM_003579.3	606	cGg/cAg	16/18	1	2	FACETS	0.956	0.883	1	0.956	0.883	1	CLONAL	1	TRUE	1	0.576311217196318	2		484	617	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619193	43619193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745650861	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	175	580	2	ENST00000355710.3:c.2876G>A	p.Arg959Gln	p.R959Q	ENST00000355710	NM_020975.4	959	cGg/cAg	17/20	1	2	FACETS	0.967	0.895	1	0.967	0.895	1	CLONAL	1	TRUE	1	0.576311217196318	2		582	628	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998943	100998943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775608193	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	204	813	2	ENST00000325455.5:c.859G>A	p.Ala287Thr	p.A287T	ENST00000325455	NM_001202474.3	287	Gcg/Acg	1/8	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.576311217196318	2		815	676	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396657	30396657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1401121972	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	18	48	0	ENST00000331968.5:c.62C>T	p.Ala21Val	p.A21V	ENST00000331968	NM_002742.2	21	gCc/gTc	1/18	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.576311217196318	2		48	45	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831201	72831201	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	142	509	0	ENST00000268489.5:c.5380C>G	p.Gln1794Glu	p.Q1794E	ENST00000268489	NM_006885.3	1794	Cag/Gag	9/10	1	2	FACETS	0.948	0.869	1	0.948	0.869	1	CLONAL	1	TRUE	1	0.576311217196318	2		509	520	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991824	72991824	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	250	586	0	ENST00000268489.5:c.2221C>A	p.Leu741Ile	p.L741I	ENST00000268489	NM_006885.3	741	Ctc/Atc	2/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.576311217196318	2		586	763	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663381	29663381	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876658710	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	173	349	0	ENST00000356175.3:c.5974A>G	p.Ser1992Gly	p.S1992G	ENST00000356175	NM_000267.3	1992	Agt/Ggt	40/57	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.576311217196318	2		349	594	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619169	37619169	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	187	529	0	ENST00000447079.4:c.845C>A	p.Pro282His	p.P282H	ENST00000447079	NM_015083.1	282	cCt/cAt	1/14	1	2	FACETS	0.956	0.886	1	0.956	0.886	1	CLONAL	1	TRUE	1	0.576311217196318	2		529	679	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78921042	78921042	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	159	589	0	ENST00000306801.3:c.3156G>T	p.Glu1052Asp	p.E1052D	ENST00000306801	NM_020761.2	1052	gaG/gaT	27/34	1	2	FACETS	0.923	0.85	0.998	0.923	0.85	0.998	CLONAL	1	TRUE	1	0.576311217196318	2		589	598	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246525	10246525	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	184	688	0	ENST00000340748.4:c.4612C>T	p.Arg1538Cys	p.R1538C	ENST00000340748		1538	Cgc/Tgc	38/40	1	2	FACETS	0.981	0.909	1	0.981	0.909	1	CLONAL	1	TRUE	1	0.576311217196318	2		688	651	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617508	158617508	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750147467	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	134	415	1	ENST00000263640.3:c.1148C>T	p.Ala383Val	p.A383V	ENST00000263640	NM_001105.4	383	gCc/gTc	9/11	1	2	FACETS	0.817	0.746	0.892	0.817	0.746	0.892	CLONAL	1	TRUE	1	0.576311217196318	2		416	569	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573497	41573497	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	228	703	0	ENST00000263253.7:c.5782A>G	p.Met1928Val	p.M1928V	ENST00000263253	NM_001429.3	1928	Atg/Gtg	31/31	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.576311217196318	2		703	728	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183583	10183583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1332272921	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	221	810	2	ENST00000256474.2:c.52G>A	p.Ala18Thr	p.A18T	ENST00000256474	NM_000551.3	18	Gca/Aca	1/3	0.165939042955152	2	FACETS	0.947	0.883	1	0.473	0.441	0.506	INDETERMINATE	1	TRUE	0	0.576311217196318	2		812	810	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165695	185165695	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	143	321	0	ENST00000265026.3:c.970G>A	p.Val324Met	p.V324M	ENST00000265026	NM_004721.4	324	Gtg/Atg	5/14	1	2	FACETS	0.965	0.886	1	0.965	0.886	1	CLONAL	1	TRUE	1	0.576311217196318	2		321	514	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144610	55144610	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	144	351	0	ENST00000257290.5:c.2084G>T	p.Ser695Ile	p.S695I	ENST00000257290	NM_006206.4	695	aGc/aTc	15/23	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.576311217196318	2		351	499	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800228	32800228	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	123	397	0	ENST00000374899.4:c.1154T>C	p.Leu385Ser	p.L385S	ENST00000374899	NM_018833.2	385	tTg/tCg	7/12	1	2	FACETS	0.977	0.89	1	0.977	0.89	1	CLONAL	1	TRUE	1	0.576311217196318	2		397	437	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001412	150001412	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1406955871	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	197	440	0	ENST00000253339.5:c.2192A>G	p.Tyr731Cys	p.Y731C	ENST00000253339		731	tAt/tGt	4/7	1	2	FACETS	0.963	0.895	1	0.963	0.895	1	CLONAL	1	TRUE	1	0.576311217196318	2		440	710	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396484	139396484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768161812	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	213	748	0	ENST00000277541.6:c.5441G>A	p.Gly1814Glu	p.G1814E	ENST00000277541	NM_017617.3	1814	gGg/gAg	29/34	0.576306038519423	2	FACETS	1	0.967	1	0.529	0.493	0.565	CLONAL	1	TRUE	0	0.576311217196318	2		748	699	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041625	47041625	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	184	674	0	ENST00000377604.3:c.1850C>T	p.Pro617Leu	p.P617L	ENST00000377604	NM_001204468.1	617	cCc/cTc	17/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.576311217196318	2		674	594	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344848	70344848	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	163	557	0	ENST00000374080.3:c.2078G>A	p.Cys693Tyr	p.C693Y	ENST00000374080		693	tGt/tAt	15/45	1	2	FACETS	0.926	0.853	1	0.926	0.853	1	CLONAL	1	TRUE	1	0.576311217196318	2		557	611	SUCCESS
BTK	695	MSKCC	GRCh37	X	100629548	100629549	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs886041148	NA	P-0051805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	190	550	0	ENST00000308731.7:c.215dup	p.Asn72LysfsTer13	p.N72Kfs*13	ENST00000308731	NM_000061.2	72	aat/aaAt	3/19	1	2	FACETS	0.922	0.855	0.991	0.922	0.855	0.991	CLONAL	1	TRUE	1	0.576311217196318	2		550	715	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0051809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	263	1045	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.497505670520687	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.497505670520687	2		1046	504	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0051809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	119	583	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.469498204631182	4	FACETS	1	0.954	1	0.546	0.494	0.601	CLONAL	1	TRUE	2	0.497505670520687	4		583	656	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0051809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	100	241	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	0.497505670520687	3	FACETS	1	0.979	1	0.833	0.763	0.902	CLONAL	2	TRUE	0	0.497505670520687	3		241	201	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570325	87570325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	99	663	0	ENST00000277120.3:c.2065G>A	p.Val689Met	p.V689M	ENST00000277120		689	Gtg/Atg	17/19	0.480690142660146	3	FACETS	0.826	0.738	0.918	0.413	0.369	0.459	CLONAL	1	TRUE	1	0.497505670520687	3		663	602	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041026	112041026	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746134687	NA	P-0051809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	151	368	0	ENST00000368678.4:c.229C>T	p.Arg77Cys	p.R77C	ENST00000368678		77	Cgt/Tgt	3/13	0.448568676228457	4	FACETS	0.959	0.884	1	0.959	0.884	1	CLONAL	2	TRUE	2	0.497505670520687	4		368	474	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711248	114711251	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	GA	novel	NA	P-0051809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	125	322	1	ENST00000543371.1:c.263_266delinsGA	p.Lys88ArgfsTer8	p.K88Rfs*8	ENST00000543371	NM_001198531.1	88	aAGAGg/aGAg	3/14	0.4393080414204	3	FACETS	0.937	0.859	1	0.937	0.859	1	CLONAL	2	TRUE	1	0.497505670520687	3		323	335	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432664	29432664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113994087	NA	P-0121449-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	549	758	1	ENST00000389048.3:c.3824G>A	p.Arg1275Gln	p.R1275Q	ENST00000389048	NM_004304.4	1275	cGa/cAa	25/29	0.578852997339069	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	NA	1	0.584346342177364	3		759	1097	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0051970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	86	197	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.87	0.774	0.972	0.87	0.774	0.972	CLONAL	1	TRUE	1	0.458603222642083	2		197	431	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0051970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	118	233	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.458603222642083	2		233	451	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0051970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	211	370	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.458603222642083	2		370	877	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411276	63411276	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	415	860	0	ENST00000330258.3:c.1891C>T	p.Arg631Ter	p.R631*	ENST00000330258	NM_152424.3	631	Cga/Tga	2/2	0.337984220602894	3	FACETS	0.911	0.868	0.955	0.911	0.868	0.955	CLONAL	2	TRUE	1	0.458603222642083	3		860	1221	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604721	48604721	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	171	534	0	ENST00000342988.3:c.1543A>G	p.Arg515Gly	p.R515G	ENST00000342988	NM_005359.5	515	Aga/Gga	12/12	0.458603222642083	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.458603222642083	1		534	545	SUCCESS
APC	324	MSKCC	GRCh37	5	112174025	112174025	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	144	400	0	ENST00000257430.4:c.2735del	p.Leu912TyrfsTer4	p.L912Yfs*4	ENST00000257430	NM_000038.5	912	Tta/ta	16/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.458603222642083	2		400	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0051973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	269	1025	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.318810245062251	2	FACETS	0.903	0.849	0.958	0.903	0.849	0.958	CLONAL	2	TRUE	0	0.343912395138918	2		1026	866	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31025023	31025023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	246	512	0	ENST00000375687.4:c.4508C>T	p.Ser1503Leu	p.S1503L	ENST00000375687	NM_015338.5	1503	tCg/tTg	13/13	0.266825682825181	5	FACETS	0.863	0.808	0.918	0.863	0.808	0.918	CLONAL	3	TRUE	2	0.343912395138918	5		512	838	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527811	103527811	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	127	460	1	ENST00000355739.4:c.3119C>A	p.Ala1040Asp	p.A1040D	ENST00000355739	NM_000123.3	1040	gCc/gAc	15/15	0.343912395138918	4	FACETS	1	0.98	1	0.656	0.594	0.72	CLONAL	1	TRUE	2	0.343912395138918	4		461	757	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350666	89350666	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0051973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1276	101	987	1	ENST00000301030.4:c.2284A>T	p.Lys762Ter	p.K762*	ENST00000301030	NM_001256183.1	762	Aaa/Taa	9/13	1	2	FACETS	0.427	0.38	0.477	0.427	0.38	0.477	SUBCLONAL	1	TRUE	1	0.343912395138918	2		988	1377	SUCCESS
APC	324	MSKCC	GRCh37	5	112175222	112175223	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0051973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	124	245	1	ENST00000257430.4:c.3933dup	p.Gly1312TrpfsTer3	p.G1312Wfs*3	ENST00000257430	NM_000038.5	1311	att/aTtt	16/16	0.318810245062251	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	0	0.343912395138918	2		246	350	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0052130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	62	571	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.995	0.871	1	0.995	0.871	1	CLONAL	1	TRUE	1	0.539664240061419	2		571	231	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0052130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	20	440	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.539664240061419	1	FACETS	0.376	0.29	0.474	0.376	0.29	0.474	SUBCLONAL	1	TRUE	0	0.539664240061419	1		440	144	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0052130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	54	378	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.539664240061419	2		378	200	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728678	190728678	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	33	349	0	ENST00000441310.2:c.2066G>C	p.Arg689Thr	p.R689T	ENST00000441310	NM_000534.4	689	aGa/aCa	10/13	1	2	FACETS	0.64	0.526	0.766	0.64	0.526	0.766	SUBCLONAL	1	TRUE	1	0.539664240061419	2		349	191	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467942	66467942	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	21	326	0	ENST00000273854.3:c.327G>C	p.Gln109His	p.Q109H	ENST00000273854	NM_004439.5	109	caG/caC	3/18	0.225902366811707	1	FACETS	0.427	0.333	0.535	0.427	0.333	0.535	INDETERMINATE	1	TRUE	0	0.539664240061419	1		326	133	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986896	36986896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	222	341	0	ENST00000354822.5:c.793G>A	p.Gly265Ser	p.G265S	ENST00000354822	NM_001079668.2	265	Ggc/Agc	3/3	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.539664240061419	2		341	555	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250934	153250934	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	23	211	0	ENST00000281708.4:c.1126del	p.Leu376Ter	p.L376*	ENST00000281708	NM_033632.3	376	Ctg/tg	8/12	0.225902366811707	1	FACETS	0.622	0.495	0.763	0.622	0.495	0.763	INDETERMINATE	1	TRUE	0	0.539664240061419	1		211	100	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864751	68864751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	172	451	0	ENST00000288368.4:c.122C>T	p.Thr41Met	p.T41M	ENST00000288368	NM_024870.2	41	aCg/aTg	1/40	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.539664240061419	2		451	608	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741736	145741736	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	195	780	0	ENST00000428558.2:c.767G>T	p.Ser256Ile	p.S256I	ENST00000428558	NM_004260.3	256	aGc/aTc	5/22	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.539664240061419	2		780	707	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932728	39932728	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756608150	NA	P-0052130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	171	718	1	ENST00000378444.4:c.1871C>T	p.Pro624Leu	p.P624L	ENST00000378444	NM_001123385.1	624	cCg/cTg	4/15	0.539664240061419	1	FACETS	0.9	0.834	0.968	0.9	0.834	0.968	CLONAL	1	TRUE	0	0.539664240061419	1		719	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0052134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	294	1045	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.497660207359291	2		1046	1040	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0052134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	177	661	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.797	0.734	0.861	0.797	0.734	0.861	SUBCLONAL	1	TRUE	1	0.497660207359291	2		662	893	SUCCESS
APC	324	MSKCC	GRCh37	5	112173668	112173668	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	61	403	0	ENST00000257430.4:c.2377C>T	p.Gln793Ter	p.Q793*	ENST00000257430	NM_000038.5	793	Caa/Taa	16/16	0.251267740988224	1	FACETS	0.439	0.38	0.504	0.439	0.38	0.504	INDETERMINATE	1	TRUE	0	0.497660207359291	1		403	419	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604784	48604784	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	199	431	0	ENST00000342988.3:c.1606C>A	p.Leu536Ile	p.L536I	ENST00000342988	NM_005359.5	536	Cta/Ata	12/12	0.497660207359291	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.497660207359291	1		431	489	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187845	11187845	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	193	520	0	ENST00000361445.4:c.6052C>T	p.Arg2018Ter	p.R2018*	ENST00000361445	NM_004958.3	2018	Cga/Tga	44/58	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.497660207359291	2		520	759	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925318	114925318	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	173	517	0	ENST00000543371.1:c.1396A>G	p.Lys466Glu	p.K466E	ENST00000543371	NM_001198531.1	466	Aaa/Gaa	14/14	0.311621666610401	1	FACETS	0.876	0.811	0.944	0.876	0.811	0.944	CLONAL	1	TRUE	0	0.497660207359291	1		517	596	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0052197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	92	378	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.42384623998955	2		378	422	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	64	226	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	0.974	0.85	1	0.974	0.85	1	CLONAL	1	TRUE	1	0.42384623998955	2		226	310	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912181	114912181	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	140	632	0	ENST00000543371.1:c.1251G>T	p.Trp417Cys	p.W417C	ENST00000543371	NM_001198531.1	417	tgG/tgT	11/14	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.42384623998955	2		632	605	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244214	153244214	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	131	462	0	ENST00000281708.4:c.1943T>G	p.Leu648Arg	p.L648R	ENST00000281708	NM_033632.3	648	cTa/cGa	12/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.42384623998955	2		462	481	SUCCESS
APC	324	MSKCC	GRCh37	5	112175057	112175057	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs77056664	NA	P-0052197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	38	228	0	ENST00000257430.4:c.3766C>T	p.Gln1256Ter	p.Q1256*	ENST00000257430	NM_000038.5	1256	Caa/Taa	16/16	1	2	FACETS	0.846	0.706	0.999	0.846	0.706	0.999	CLONAL	1	TRUE	1	0.42384623998955	2		228	212	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101135	27101135	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	132	854	0	ENST00000324856.7:c.4417C>T	p.Gln1473Ter	p.Q1473*	ENST00000324856	NM_006015.4	1473	Cag/Tag	18/20	1	2	FACETS	0.998	0.909	1	0.998	0.909	1	CLONAL	1	TRUE	1	0.42384623998955	2		854	624	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375090	118375090	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	90	449	0	ENST00000534358.1:c.8483A>T	p.Asn2828Ile	p.N2828I	ENST00000534358	NM_005933.3	2828	aAt/aTt	27/36	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.42384623998955	2		449	392	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120381	70120382	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0052197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	365	942	0	ENST00000245479.2:c.1386_1387dup	p.Tyr463SerfsTer8	p.Y463Sfs*8	ENST00000245479	NM_000346.3	461	-/CT	3/3	0.42384623998955	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.42384623998955	2		942	795	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250293	39250293	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	159	743	0	ENST00000402219.2:c.1276C>G	p.Gln426Glu	p.Q426E	ENST00000402219	NM_005633.3	426	Cag/Gag	10/23	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.42384623998955	2		743	670	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670443	134670444	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0052197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	99	632	0	ENST00000398015.3:c.356_357del	p.Ser119CysfsTer12	p.S119Cfs*12	ENST00000398015	NM_004441.4	118	gaCTct/gact	3/16	1	2	FACETS	0.931	0.834	1	0.931	0.834	1	CLONAL	1	TRUE	1	0.42384623998955	2		632	502	SUCCESS
APC	324	MSKCC	GRCh37	5	112175337	112176043	+	frameshift_variant	Frame_Shift_Del	DEL	ACAAAGCTGTTGAATTTTCTTCAGGAGCGAAATCTCCCTCCAAAAGTGGTGCTCAGACACCCAAAAGTCCACCTGAACACTATGTTCAGGAGACCCCACTCATGTTTAGCAGATGTACTTCTGTCAGTTCACTTGATAGTTTTGAGAGTCGTTCGATTGCCAGCTCCGTTCAGAGTGAACCATGCAGTGGAATGGTAAGTGGCATTATAAGCCCCAGTGATCTTCCAGATAGCCCTGGACAAACCATGCCACCAAGCAGAAGTAAAACACCTCCACCACCTCCTCAAACAGCTCAAACCAAGCGAGAAGTACCTAAAAATAAAGCACCTACTGCTGAAAAGAGAGAGAGTGGACCTAAGCAAGCTGCAGTAAATGCTGCAGTTCAGAGGGTCCAGGTTCTTCCAGATGCTGATACTTTATTACATTTTGCCACGGAAAGTACTCCAGATGGATTTTCTTGTTCATCCAGCCTGAGTGCTCTGAGCCTCGATGAGCCATTTATACAGAAAGATGTGGAATTAAGAATAATGCCTCCAGTTCAGGAAAATGACAATGGGAATGAAACAGAATCAGAGCAGCCTAAAGAATCAAATGAAAACCAAGAGAAAGAGGCAGAAAAAACTATTGATTCTGAAAAGGACCTATTAGATGATTCAGATGATGATGATATTGAAATACTAGAAGAATGTATTATTTCTGCCATGCCA	ACAAAGCTGTTGAATTTTCTTCAGGAGCGAAATCTCCCTCCAAAAGTGGTGCTCAGACACCCAAAAGTCCACCTGAACACTATGTTCAGGAGACCCCACTCATGTTTAGCAGATGTACTTCTGTCAGTTCACTTGATAGTTTTGAGAGTCGTTCGATTGCCAGCTCCGTTCAGAGTGAACCATGCAGTGGAATGGTAAGTGGCATTATAAGCCCCAGTGATCTTCCAGATAGCCCTGGACAAACCATGCCACCAAGCAGAAGTAAAACACCTCCACCACCTCCTCAAACAGCTCAAACCAAGCGAGAAGTACCTAAAAATAAAGCACCTACTGCTGAAAAGAGAGAGAGTGGACCTAAGCAAGCTGCAGTAAATGCTGCAGTTCAGAGGGTCCAGGTTCTTCCAGATGCTGATACTTTATTACATTTTGCCACGGAAAGTACTCCAGATGGATTTTCTTGTTCATCCAGCCTGAGTGCTCTGAGCCTCGATGAGCCATTTATACAGAAAGATGTGGAATTAAGAATAATGCCTCCAGTTCAGGAAAATGACAATGGGAATGAAACAGAATCAGAGCAGCCTAAAGAATCAAATGAAAACCAAGAGAAAGAGGCAGAAAAAACTATTGATTCTGAAAAGGACCTATTAGATGATTCAGATGATGATGATATTGAAATACTAGAAGAATGTATTATTTCTGCCATGCCA	-	novel	NA	P-0052197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	65	273	0	ENST00000257430.4:c.4052_4758del	p.Ala1351ValfsTer4	p.A1351Vfs*4	ENST00000257430	NM_000038.5	1349	cACAAAGCTGTTGAATTTTCTTCAGGAGCGAAATCTCCCTCCAAAAGTGGTGCTCAGACACCCAAAAGTCCACCTGAACACTATGTTCAGGAGACCCCACTCATGTTTAGCAGATGTACTTCTGTCAGTTCACTTGATAGTTTTGAGAGTCGTTCGATTGCCAGCTCCGTTCAGAGTGAACCATGCAGTGGAATGGTAAGTGGCATTATAAGCCCCAGTGATCTTCCAGATAGCCCTGGACAAACCATGCCACCAAGCAGAAGTAAAACACCTCCACCACCTCCTCAAACAGCTCAAACCAAGCGAGAAGTACCTAAAAATAAAGCACCTACTGCTGAAAAGAGAGAGAGTGGACCTAAGCAAGCTGCAGTAAATGCTGCAGTTCAGAGGGTCCAGGTTCTTCCAGATGCTGATACTTTATTACATTTTGCCACGGAAAGTACTCCAGATGGATTTTCTTGTTCATCCAGCCTGAGTGCTCTGAGCCTCGATGAGCCATTTATACAGAAAGATGTGGAATTAAGAATAATGCCTCCAGTTCAGGAAAATGACAATGGGAATGAAACAGAATCAGAGCAGCCTAAAGAATCAAATGAAAACCAAGAGAAAGAGGCAGAAAAAACTATTGATTCTGAAAAGGACCTATTAGATGATTCAGATGATGATGATATTGAAATACTAGAAGAATGTATTATTTCTGCCATGCCA/c	16/16	1	2	FACETS	0.965	0.843	1	0.965	0.843	1	CLONAL	1	TRUE	1	0.42384623998955	2		273	318	SUCCESS
APC	324	MSKCC	GRCh37	5	112176087	112176098	+	inframe_deletion	In_Frame_Del	DEL	CAAAATTACCTC	CAAAATTACCTC	-	novel	NA	P-0052197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	92	440	0	ENST00000257430.4:c.4798_4809del	p.Lys1600_Pro1603del	p.K1600_P1603del	ENST00000257430	NM_000038.5	1599	tCAAAATTACCTCca/tca	16/16	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.42384623998955	2		440	411	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324907	31324908	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0052197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	175	1124	0	ENST00000412585.2:c.28dup	p.Leu10ProfsTer89	p.L10Pfs*89	ENST00000412585	NM_005514.6	10	ctc/cCtc	1/8	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.42384623998955	2		1124	815	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859801	151859801	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	64	438	0	ENST00000262189.6:c.10861del	p.Ala3621LeufsTer9	p.A3621Lfs*9	ENST00000262189	NM_170606.2	3621	Gct/ct	43/59	1	2	FACETS	0.858	0.747	0.977	0.858	0.747	0.977	CLONAL	1	TRUE	1	0.42384623998955	2		438	352	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76812944	76812944	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557059590	NA	P-0052197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	107	311	0	ENST00000373344.5:c.6677G>A	p.Arg2226Lys	p.R2226K	ENST00000373344	NM_000489.3	2226	aGg/aAg	30/35	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.42384623998955	1		311	266	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	104	415	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.858	0.772	0.949	0.858	0.772	0.949	CLONAL	1	TRUE	1	0.489698784272587	2		415	495	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	189	831	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.981	0.908	1	0.981	0.908	1	CLONAL	1	TRUE	1	0.489698784272587	2		831	787	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	164	588	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.489698784272587	2		592	614	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	222	1445	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.489698784272587	2		1452	907	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992721	68992721	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs764112302	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	121	306	2	ENST00000288368.4:c.1693del	p.Ser565ArgfsTer10	p.S565Rfs*10	ENST00000288368	NM_024870.2	562	cgT/cg	16/40	1	2	FACETS	0.99	0.9	1	0.99	0.9	1	CLONAL	1	TRUE	1	0.489698784272587	2		308	499	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426812	121426812	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377110124	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	208	610	1	ENST00000257555.6:c.503G>A	p.Arg168His	p.R168H	ENST00000257555		168	cGc/cAc	2/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.489698784272587	2		611	796	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998128	169998128	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs753143066	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	167	428	1	ENST00000295797.4:c.826del	p.Thr276GlnfsTer7	p.T276Qfs*7	ENST00000295797	NM_002740.5	273	ttA/tt	9/18	1	2	FACETS	0.947	0.873	1	0.947	0.873	1	CLONAL	1	TRUE	1	0.489698784272587	2		429	720	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	150	482	0	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.489698784272587	2		482	609	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	92	494	10	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.921	0.824	1	0.921	0.824	1	CLONAL	1	TRUE	1	0.489698784272587	2		504	408	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	210	756	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.949	0.882	1	0.949	0.882	1	CLONAL	1	TRUE	1	0.489698784272587	2		756	904	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	58	226	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	0.951	0.826	1	0.951	0.826	1	CLONAL	1	TRUE	1	0.489698784272587	2		226	249	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	229	937	14	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.489698784272587	2		951	915	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422384	47422384	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	148	554	1	ENST00000377045.4:c.23del	p.Pro8LeufsTer26	p.P8Lfs*26	ENST00000377045	NM_001654.4	6	ggC/gg	2/16	1	2	FACETS	0.973	0.892	1	0.973	0.892	1	CLONAL	1	TRUE	1	0.489698784272587	2		555	621	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528525	157528525	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	173	579	0	ENST00000346085.5:c.6250G>A	p.Glu2084Lys	p.E2084K	ENST00000346085	NM_020732.3	2084	Gag/Aag	20/20	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.489698784272587	2		579	693	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158633	26158633	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	75	264	0	ENST00000289316.2:c.236C>T	p.Ser79Phe	p.S79F	ENST00000289316	NM_138720.2	79	tCc/tTc	1/2	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.489698784272587	2		264	281	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448297	56448298	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1567880599	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	201	776	1	ENST00000407977.2:c.349dup	p.Arg117ProfsTer8	p.R117Pfs*8	ENST00000407977		117	cgc/cCgc	3/10	1	2	FACETS	0.922	0.856	0.991	0.922	0.856	0.991	CLONAL	1	TRUE	1	0.489698784272587	2		777	890	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222796	5222796	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756049037	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	186	803	2	ENST00000357368.4:c.3007G>A	p.Asp1003Asn	p.D1003N	ENST00000357368	NM_002850.3	1003	Gac/Aac	18/38	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.489698784272587	2		805	728	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574391	41574391	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752587236	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	117	707	0	ENST00000263253.7:c.6676C>T	p.Arg2226Trp	p.R2226W	ENST00000263253	NM_001429.3	2226	Cgg/Tgg	31/31	1	2	FACETS	0.688	0.621	0.758	0.688	0.621	0.758	SUBCLONAL	1	TRUE	1	0.489698784272587	2		707	695	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512370	38512370	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567767560	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	120	584	2	ENST00000254066.5:c.1286del	p.Gly429ValfsTer214	p.G429Vfs*214	ENST00000254066	NM_000964.3	427	ccG/cc	9/9	1	2	FACETS	0.88	0.798	0.966	0.88	0.798	0.966	CLONAL	1	TRUE	1	0.489698784272587	2		586	557	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135100	11135100	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555780047	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	226	952	0	ENST00000358026.2:c.3067G>A	p.Glu1023Lys	p.E1023K	ENST00000358026	NM_001128849.1	1023	Gag/Aag	21/36	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.489698784272587	2		952	874	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102918	71102918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148369068	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	106	310	0	ENST00000318789.4:c.289G>A	p.Val97Met	p.V97M	ENST00000318789	NM_032682.5	97	Gtg/Atg	8/21	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.489698784272587	2		310	403	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976484	18976484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140671518	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	286	1048	2	ENST00000262803.5:c.3134C>T	p.Ala1045Val	p.A1045V	ENST00000262803	NM_002911.3	1045	gCg/gTg	22/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.489698784272587	2		1050	1040	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948747	71948748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760925109	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	200	1061	12	ENST00000298229.2:c.3466dup	p.Arg1156ProfsTer59	p.R1156Pfs*59	ENST00000298229	NM_001567.3	1153	-/C	26/28	1	2	FACETS	0.863	0.799	0.928	0.863	0.799	0.928	CLONAL	1	TRUE	1	0.489698784272587	2		1073	947	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581330	48581330	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863224732	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	139	482	0	ENST00000342988.3:c.634G>A	p.Ala212Thr	p.A212T	ENST00000342988	NM_005359.5	212	Gcc/Acc	5/12	1	2	FACETS	0.831	0.758	0.907	0.831	0.758	0.907	CLONAL	1	TRUE	1	0.489698784272587	2		482	683	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128246731	128246731	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754789924	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	166	522	0	ENST00000265960.3:c.1198G>A	p.Val400Ile	p.V400I	ENST00000265960	NM_001006617.1	400	Gta/Ata	9/12	1	2	FACETS	0.935	0.861	1	0.935	0.861	1	CLONAL	1	TRUE	1	0.489698784272587	2		522	725	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107184	11107186	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs1484395538	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	177	702	0	ENST00000358026.2:c.1778_1780del	p.Glu593del	p.E593del	ENST00000358026	NM_001128849.1	592	gcAGAa/gca	11/36	1	2	FACETS	0.905	0.835	0.977	0.905	0.835	0.977	CLONAL	1	TRUE	1	0.489698784272587	2		702	799	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003773	45003773	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	177	687	0	ENST00000558401.1:c.29T>C	p.Leu10Pro	p.L10P	ENST00000558401	NM_004048.2	10	cTc/cCc	1/4	1	2	FACETS	0.928	0.857	1	0.928	0.857	1	CLONAL	1	TRUE	1	0.489698784272587	2		687	779	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041092	112041092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376211530	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	154	553	0	ENST00000368678.4:c.163G>A	p.Ala55Thr	p.A55T	ENST00000368678		55	Gca/Aca	3/13	1	2	FACETS	0.859	0.788	0.934	0.859	0.788	0.934	CLONAL	1	TRUE	1	0.489698784272587	2		553	732	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911487	131911487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658808	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	75	297	0	ENST00000265335.6:c.232G>A	p.Val78Met	p.V78M	ENST00000265335		78	Gtg/Atg	3/25	1	2	FACETS	0.729	0.642	0.823	0.729	0.642	0.823	SUBCLONAL	1	TRUE	1	0.489698784272587	2		297	420	SUCCESS
ATM	472	MSKCC	GRCh37	11	108159797	108159797	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	34	124	1	ENST00000278616.4:c.4207del	p.Ser1403AlafsTer3	p.S1403Afs*3	ENST00000278616	NM_000051.3	1401	ttA/tt	28/63	1	2	FACETS	0.798	0.66	0.949	0.798	0.66	0.949	CLONAL	1	TRUE	1	0.489698784272587	2		125	174	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089462	27089462	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	160	741	1	ENST00000324856.7:c.2420-2A>G		p.X807_splice	ENST00000324856	NM_006015.4	807			1	2	FACETS	0.905	0.832	0.981	0.905	0.832	0.981	CLONAL	1	TRUE	1	0.489698784272587	2		742	722	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019779	123019779	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	167	560	0	ENST00000355640.3:c.267T>A	p.Asn89Lys	p.N89K	ENST00000355640		89	aaT/aaA	2/7	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.489698784272587	2		560	638	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261656	16261656	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	169	605	0	ENST00000375759.3:c.8921A>G	p.Gln2974Arg	p.Q2974R	ENST00000375759	NM_015001.2	2974	cAg/cGg	11/15	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.489698784272587	2		605	675	SUCCESS
FH	2271	MSKCC	GRCh37	1	241676979	241676979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs75086406	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	140	434	0	ENST00000366560.3:c.302G>A	p.Arg101Gln	p.R101Q	ENST00000366560	NM_000143.3	101	cGa/cAa	3/10	1	2	FACETS	0.959	0.877	1	0.959	0.877	1	CLONAL	1	TRUE	1	0.489698784272587	2		434	596	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70360784	70360784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	68	177	0	ENST00000373644.4:c.1964del	p.Leu655Ter	p.L655*	ENST00000373644	NM_030625.2	654	gTt/gt	3/12	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.489698784272587	2		177	267	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574555	64574555	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	212	805	1	ENST00000312049.6:c.840A>T	p.Leu280Phe	p.L280F	ENST00000312049	NM_130799.2	280	ttA/ttT	6/10	1	2	FACETS	0.961	0.894	1	0.961	0.894	1	CLONAL	1	TRUE	1	0.489698784272587	2		806	901	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419071	419071	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	97	404	1	ENST00000399788.2:c.3276del	p.Val1093Ter	p.V1093*	ENST00000399788	NM_001042603.1	1092	aaA/aa	22/28	NA	2	FACETS	0.745	0.666	0.828			1	INDETERMINATE	1	TRUE	NA	0.489698784272587	2		405	532	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335586	73335586	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760027235	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	64	215	0	ENST00000377767.4:c.2585T>C	p.Val862Ala	p.V862A	ENST00000377767	NM_014953.3	862	gTa/gCa	19/21	1	2	FACETS	0.809	0.706	0.92	0.809	0.706	0.92	CLONAL	1	TRUE	1	0.489698784272587	2		215	323	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527811	103527811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	94	301	0	ENST00000355739.4:c.3119C>T	p.Ala1040Val	p.A1040V	ENST00000355739	NM_000123.3	1040	gCc/gTc	15/15	1	2	FACETS	0.851	0.761	0.946	0.851	0.761	0.946	CLONAL	1	TRUE	1	0.489698784272587	2		301	451	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422181	81422181	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs886050853	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	168	576	0	ENST00000298171.2:c.157A>C	p.Ser53Arg	p.S53R	ENST00000298171	NM_000369.2	53	Agt/Cgt	1/10	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.489698784272587	2		576	683	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454654	99454654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201778894	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	156	551	2	ENST00000268035.6:c.1573G>A	p.Val525Ile	p.V525I	ENST00000268035	NM_000875.3	525	Gtt/Att	7/21	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.489698784272587	2		553	626	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274201	10274201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs969233060	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	148	563	0	ENST00000330684.3:c.68C>T	p.Pro23Leu	p.P23L	ENST00000330684	NM_001134407.1	23	cCg/cTg	2/13	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.489698784272587	2		563	576	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56871584	56871584	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	173	547	0	ENST00000308159.5:c.1964C>T	p.Ala655Val	p.A655V	ENST00000308159	NM_014669.4	655	gCc/gTc	18/22	1	2	FACETS	0.992	0.916	1	0.992	0.916	1	CLONAL	1	TRUE	1	0.489698784272587	2		547	712	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650677	67650677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	173	548	0	ENST00000264010.4:c.982G>A	p.Asp328Asn	p.D328N	ENST00000264010	NM_006565.3	328	Gac/Aac	5/12	1	2	FACETS	0.976	0.901	1	0.976	0.901	1	CLONAL	1	TRUE	1	0.489698784272587	2		548	724	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829124	72829124	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	177	582	0	ENST00000268489.5:c.7457A>G	p.Gln2486Arg	p.Q2486R	ENST00000268489	NM_006885.3	2486	cAa/cGa	9/10	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.489698784272587	2		582	714	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993944	72993944	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	217	901	0	ENST00000268489.5:c.101A>G	p.Asp34Gly	p.D34G	ENST00000268489	NM_006885.3	34	gAc/gGc	2/10	1	2	FACETS	0.955	0.889	1	0.955	0.889	1	CLONAL	1	TRUE	1	0.489698784272587	2		901	928	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351929	89351929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	266	868	4	ENST00000301030.4:c.1021G>A	p.Ala341Thr	p.A341T	ENST00000301030	NM_001256183.1	341	Gcc/Acc	9/13	1	2	FACETS	0.982	0.921	1	0.982	0.921	1	CLONAL	1	TRUE	1	0.489698784272587	2		872	1106	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870011	40870011	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	97	505	0	ENST00000428826.2:c.1006G>A	p.Asp336Asn	p.D336N	ENST00000428826		336	Gac/Aac	10/21	1	2	FACETS	0.7	0.625	0.779	0.7	0.625	0.779	SUBCLONAL	1	TRUE	1	0.489698784272587	2		505	566	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295221	15295221	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	256	997	0	ENST00000263388.2:c.2451del	p.Ala818HisfsTer42	p.A818Hfs*42	ENST00000263388	NM_000435.2	817	ccC/cc	16/33	1	2	FACETS	0.998	0.934	1	0.998	0.934	1	CLONAL	1	TRUE	1	0.489698784272587	2		997	1048	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641556	47641556	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	37	148	0	ENST00000233146.2:c.941A>T	p.Gln314Leu	p.Q314L	ENST00000233146	NM_000251.2	314	cAg/cTg	5/16	1	2	FACETS	0.494	0.408	0.589	0.494	0.408	0.589	SUBCLONAL	1	TRUE	1	0.489698784272587	2		148	306	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872794	136872794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377287446	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	138	499	0	ENST00000241393.3:c.704G>A	p.Arg235His	p.R235H	ENST00000241393	NM_003467.2	235	cGc/cAc	2/2	1	2	FACETS	0.944	0.862	1	0.944	0.862	1	CLONAL	1	TRUE	1	0.489698784272587	2		499	597	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645496	215645496	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	157	552	0	ENST00000260947.4:c.1102T>C	p.Cys368Arg	p.C368R	ENST00000260947	NM_000465.2	368	Tgc/Cgc	4/11	1	2	FACETS	0.954	0.877	1	0.954	0.877	1	CLONAL	1	TRUE	1	0.489698784272587	2		552	672	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012681	36012681	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	57	189	0	ENST00000358208.4:c.125C>A	p.Ala42Asp	p.A42D	ENST00000358208		42	gCc/gAc	2/12	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.489698784272587	2		189	225	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161847	47161850	+	frameshift_variant	Frame_Shift_Del	DEL	CTTT	CTTT	-	novel	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	39	360	0	ENST00000409792.3:c.4276_4279del	p.Lys1426LeufsTer5	p.K1426Lfs*5	ENST00000409792	NM_014159.6	1426	AAAGtt/tt	3/21	1	2	FACETS	0.291	0.24	0.347	0.291	0.24	0.347	SUBCLONAL	1	TRUE	1	0.489698784272587	2		360	548	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183549	185183549	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	125	434	1	ENST00000265026.3:c.1403T>A	p.Ile468Asn	p.I468N	ENST00000265026	NM_004721.4	468	aTt/aAt	9/14	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.489698784272587	2		435	503	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680934	30680934	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	179	636	1	ENST00000376406.3:c.785A>G	p.Gln262Arg	p.Q262R	ENST00000376406	NM_014641.2	262	cAg/cGg	5/15	1	2	FACETS	0.964	0.891	1	0.964	0.891	1	CLONAL	1	TRUE	1	0.489698784272587	2		637	758	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112025211	112025211	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	158	422	0	ENST00000368678.4:c.538A>G	p.Thr180Ala	p.T180A	ENST00000368678		180	Acc/Gcc	6/13	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.489698784272587	2		422	629	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753038	128753038	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	158	480	0	ENST00000377970.2:c.1199A>T	p.Glu400Val	p.E400V	ENST00000377970	NM_002467.4	400	gAa/gTa	3/3	1	2	FACETS	0.987	0.907	1	0.987	0.907	1	CLONAL	1	TRUE	1	0.489698784272587	2		480	654	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27209169	27209169	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	135	437	0	ENST00000380036.4:c.2626C>T	p.Leu876Phe	p.L876F	ENST00000380036	NM_000459.3	876	Ctt/Ttt	16/23	1	2	FACETS	0.925	0.844	1	0.925	0.844	1	CLONAL	1	TRUE	1	0.489698784272587	2		437	596	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152864433	152864433	+	synonymous_variant	Silent	SNP	G	G	A	novel	NA	P-0052250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	45	161	0	ENST00000406277.2:c.93C>T	p.Phe31=	p.F31=	ENST00000406277	NM_152274.4	31	ttC/ttT	3/7	1		FACETS		0.723	0.989				CLONAL	1	TRUE	1	0.489698784272587	2		161	216	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0052269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	249	1045	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.32742937269033	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.371873272290065	2		1046	575	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0052269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	122	364	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.35877633360593	3	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	1	0.371873272290065	3		365	370	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986751	36986751	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	21	75	0	ENST00000354822.5:c.938A>G	p.Gln313Arg	p.Q313R	ENST00000354822	NM_001079668.2	313	cAa/cGa	3/3	0.35877633360593	3	FACETS	1	0.868	1	0.582	0.455	0.726	CLONAL	1	TRUE	1	0.371873272290065	3		75	115	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356177	66356177	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	66	581	1	ENST00000273854.3:c.1320G>T	p.Glu440Asp	p.E440D	ENST00000273854	NM_004439.5	440	gaG/gaT	5/18	1	2	FACETS	0.613	0.532	0.7	0.613	0.532	0.7	SUBCLONAL	1	TRUE	1	0.371873272290065	2		582	579	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920402	114920402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs927089403	NA	P-0052270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	173	478	0	ENST00000543371.1:c.1343G>A	p.Arg448Gln	p.R448Q	ENST00000543371	NM_001198531.1	448	cGg/cAg	13/14	0.140708385432704	3	FACETS	1	0.988	1	0.712	0.656	0.77	INDETERMINATE	1	TRUE	1	0.356427261355912	3		478	803	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0052270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	182	608	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.356427261355912	3	FACETS	1	0.972	1	0.557	0.513	0.602	CLONAL	1	TRUE	1	0.356427261355912	3		608	1081	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0052270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	271	653	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.356427261355912	3	FACETS	0.807	0.757	0.858	0.807	0.757	0.858	CLONAL	2	TRUE	1	0.356427261355912	3		654	1110	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259485	55259485	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148934350	NA	P-0052270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	334	566	0	ENST00000275493.2:c.2543C>T	p.Pro848Leu	p.P848L	ENST00000275493	NM_005228.3	848	cCg/cTg	21/28	0.356427261355912	5	FACETS	0.879	0.832	0.927	0.879	0.832	0.927	CLONAL	3	TRUE	2	0.356427261355912	5		566	1091	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0052275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	104	415	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.952	0.862	1	0.952	0.862	1	CLONAL	1	TRUE	1	0.65028605735396	2		415	336	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0052275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	72	197	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.95	0.843	1	0.95	0.843	1	CLONAL	1	TRUE	1	0.65028605735396	2		197	233	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0052275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	127	588	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.851	0.776	0.928	0.851	0.776	0.928	CLONAL	1	TRUE	1	0.65028605735396	2		592	459	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	143	396	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	0.851	0.78	0.924	0.851	0.78	0.924	CLONAL	1	TRUE	1	0.65028605735396	2		396	517	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0052275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	261	1149	10	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.888	0.834	0.944	0.888	0.834	0.944	CLONAL	1	TRUE	1	0.65028605735396	2		1159	904	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0052275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	241	633	4	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.894	0.837	0.952	0.894	0.837	0.952	CLONAL	1	TRUE	1	0.65028605735396	2		637	829	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099406	157099426	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAA	CAGCAGCAGCAGCAGCAGCAA	-	rs762617219	NA	P-0052275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	66	266	0	ENST00000346085.5:c.363_383del	p.Gln125_Gln131del	p.Q125_Q131del	ENST00000346085	NM_020732.3	115	CAGCAGCAGCAGCAGCAGCAA/-	1/20	1	2	FACETS	0.58	0.506	0.659	0.58	0.506	0.659	SUBCLONAL	1	TRUE	1	0.65028605735396	2		266	350	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0052275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	78	283	0	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	1	2	FACETS	0.787	0.698	0.88	0.787	0.698	0.88	SUBCLONAL	1	TRUE	1	0.65028605735396	2		283	305	SUCCESS
APC	324	MSKCC	GRCh37	5	112175000	112175000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	70	297	0	ENST00000257430.4:c.3709C>T	p.Gln1237Ter	p.Q1237*	ENST00000257430	NM_000038.5	1237	Cag/Tag	16/16	1	2	FACETS	0.872	0.77	0.978	0.872	0.77	0.978	CLONAL	1	TRUE	1	0.65028605735396	2		297	247	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0052275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	35	459	1	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	1	2	FACETS	0.165	0.135	0.2	0.165	0.135	0.2	SUBCLONAL	1	TRUE	1	0.65028605735396	2		460	651	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291083	10291084	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755889652	NA	P-0052275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	253	527	5	ENST00000340748.4:c.387dup	p.Lys130GlnfsTer19	p.K130Qfs*19	ENST00000340748		129	-/C	4/40	1	2	FACETS	0.882	0.827	0.939	0.882	0.827	0.939	CLONAL	1	TRUE	1	0.65028605735396	2		532	882	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969884	81969884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199840870	NA	P-0052275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	89	594	1	ENST00000359376.3:c.2953G>A	p.Val985Ile	p.V985I	ENST00000359376	NM_002661.3	985	Gtc/Atc	27/33	1	2	FACETS	0.372	0.329	0.417	0.372	0.329	0.417	SUBCLONAL	1	TRUE	1	0.65028605735396	2		595	736	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286237	66286238	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	86	302	0	ENST00000273854.3:c.1448dup	p.Asn483LysfsTer21	p.N483Kfs*21	ENST00000273854	NM_004439.5	483	aac/aaAc	6/18	1	2	FACETS	0.845	0.755	0.939	0.845	0.755	0.939	CLONAL	1	TRUE	1	0.65028605735396	2		302	313	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264985	46264985	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	169	376	0	ENST00000371998.3:c.1860del	p.Lys620AsnfsTer18	p.K620Nfs*18	ENST00000371998		619	Aaa/aa	12/23	1	2	FACETS	0.928	0.858	1	0.928	0.858	1	CLONAL	1	TRUE	1	0.65028605735396	2		376	560	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003782	45003782	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	203	442	0	ENST00000558401.1:c.38T>G	p.Leu13Arg	p.L13R	ENST00000558401	NM_004048.2	13	cTc/cGc	1/4	1	2	FACETS	0.952	0.887	1	0.952	0.887	1	CLONAL	1	TRUE	1	0.65028605735396	2		442	656	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527264	187527264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754008095	NA	P-0052275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	212	372	0	ENST00000441802.2:c.10310C>T	p.Ala3437Val	p.A3437V	ENST00000441802	NM_005245.3	3437	gCg/gTg	17/27	1	2	FACETS	0.965	0.9	1	0.965	0.9	1	CLONAL	1	TRUE	1	0.65028605735396	2		372	676	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733512	85733513	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs387906350	NA	P-0052275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	134	372	1	ENST00000370580.1:c.499dup	p.Ser167PhefsTer3	p.S167Ffs*3	ENST00000370580	NM_003921.4	167	tct/tTct	3/3	1	2	FACETS	0.89	0.815	0.968	0.89	0.815	0.968	CLONAL	1	TRUE	1	0.65028605735396	2		373	463	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592336	29592336	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs876658492	NA	P-0052275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	119	322	0	ENST00000356175.3:c.4756del	p.Tyr1586IlefsTer17	p.Y1586Ifs*17	ENST00000356175	NM_000267.3	1584	aTt/at	35/57	1	2	FACETS	0.984	0.897	1	0.984	0.897	1	CLONAL	1	TRUE	1	0.65028605735396	2		322	372	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348031	348031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765982081	NA	P-0052275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	256	856	2	ENST00000262320.3:c.1475G>A	p.Arg492His	p.R492H	ENST00000262320	NM_003502.3	492	cGc/cAc	6/11	1	2	FACETS	0.781	0.732	0.832	0.781	0.732	0.832	SUBCLONAL	1	TRUE	1	0.65028605735396	2		858	1008	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056331	26056333	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs762045774	NA	P-0052275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	167	382	0	ENST00000343677.2:c.324_326del	p.Asn108del	p.N108del	ENST00000343677	NM_005319.3	108	aaCAAg/aag	1/1	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.65028605735396	2		382	506	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199600	16199600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	158	419	0	ENST00000375759.3:c.373C>T	p.Arg125Ter	p.R125*	ENST00000375759	NM_015001.2	125	Cga/Tga	2/15	1	2	FACETS	0.822	0.757	0.89	0.822	0.757	0.89	CLONAL	1	TRUE	1	0.65028605735396	2		419	591	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273187	115273187	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	170	392	0	ENST00000438362.2:c.1271A>T	p.Glu424Val	p.E424V	ENST00000438362	NM_001242891.1	424	gAa/gTa	11/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.65028605735396	2		392	486	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870946	12870947	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0052275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	120	298	0	ENST00000228872.4:c.174dup	p.Lys59GlnfsTer66	p.K59Qfs*66	ENST00000228872	NM_004064.3	58	cgc/cgCc	1/3	1	2	FACETS	0.916	0.834	1	0.916	0.834	1	CLONAL	1	TRUE	1	0.65028605735396	2		298	403	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967647	26967647	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	99	271	0	ENST00000381527.3:c.790G>T	p.Asp264Tyr	p.D264Y	ENST00000381527	NM_001260.1	264	Gat/Tat	7/13	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.65028605735396	2		271	290	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845521	72845521	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	241	510	0	ENST00000268489.5:c.3819C>A	p.His1273Gln	p.H1273Q	ENST00000268489	NM_006885.3	1273	caC/caA	7/10	1	2	FACETS	0.968	0.907	1	0.968	0.907	1	CLONAL	1	TRUE	1	0.65028605735396	2		510	766	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240310	5240310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	301	721	0	ENST00000357368.4:c.1604C>T	p.Ala535Val	p.A535V	ENST00000357368	NM_002850.3	535	gCc/gTc	12/38	1	2	FACETS	0.932	0.88	0.986	0.932	0.88	0.986	CLONAL	1	TRUE	1	0.65028605735396	2		721	993	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99180101	99180101	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0052275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	227	433	0	ENST00000074304.5:c.2043+1G>A		p.X681_splice	ENST00000074304	NM_001134224.1	681			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.65028605735396	2		433	630	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595852	52595852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276256973	NA	P-0052275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	260	445	0	ENST00000394830.3:c.4063G>A	p.Gly1355Arg	p.G1355R	ENST00000394830	NM_018313.4	1355	Ggg/Agg	26/30	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.65028605735396	2		445	769	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643352	52643353	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	94	278	0	ENST00000394830.3:c.2543dup	p.Leu848PhefsTer16	p.L848Ffs*16	ENST00000394830	NM_018313.4	848	ttg/ttTg	17/30	1	2	FACETS	0.831	0.746	0.919	0.831	0.746	0.919	CLONAL	1	TRUE	1	0.65028605735396	2		278	348	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549512	187549512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	133	312	0	ENST00000441802.2:c.4606G>A	p.Asp1536Asn	p.D1536N	ENST00000441802	NM_005245.3	1536	Gat/Aat	9/27	1	2	FACETS	0.915	0.838	0.995	0.915	0.838	0.995	CLONAL	1	TRUE	1	0.65028605735396	2		312	447	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226044	226044	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1553997748	NA	P-0052275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	30	70	0	ENST00000264932.6:c.503T>C	p.Ile168Thr	p.I168T	ENST00000264932	NM_004168.2	168	aTt/aCt	5/15	1	2	FACETS	0.914	0.755	1	0.914	0.755	1	CLONAL	1	TRUE	1	0.65028605735396	2		70	101	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527296	137527297	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0052275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	161	468	0	ENST00000367739.4:c.349_350del	p.Glu117ArgfsTer14	p.E117Rfs*14	ENST00000367739	NM_000416.2	117	GAa/a	3/7	1	2	FACETS	0.996	0.921	1	0.996	0.921	1	CLONAL	1	TRUE	1	0.65028605735396	2		468	497	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759511	133759511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	165	644	0	ENST00000318560.5:c.1834C>T	p.Pro612Ser	p.P612S	ENST00000318560	NM_005157.4	612	Cca/Tca	11/11	1	2	FACETS	0.631	0.58	0.684	0.631	0.58	0.684	SUBCLONAL	1	TRUE	1	0.65028605735396	2		644	804	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0052340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	69	670	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	FALSE	1	0.571316166037381	2		670	229	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691039	NA	P-0052340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	617	779	0	ENST00000269305.4:c.919+1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.571316166037381	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	FALSE	0	0.571316166037381	2		779	964	SUCCESS
APC	324	MSKCC	GRCh37	5	112170863	112170863	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1114167569	NA	P-0052340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	69	419	1	ENST00000257430.4:c.1958+1G>A		p.X653_splice	ENST00000257430	NM_000038.5	653			0.536496925580161	3	FACETS	0.853	0.759	0.95	0.853	0.759	0.95	CLONAL	2	FALSE	1	0.571316166037381	3		420	182	SUCCESS
APC	324	MSKCC	GRCh37	5	112175338	112175339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	38	305	0	ENST00000257430.4:c.4050dup	p.Ala1351SerfsTer3	p.A1351Sfs*3	ENST00000257430	NM_000038.5	1349	-/A	16/16	0.536496925580161	3	FACETS	0.994	0.833	1	0.497	0.416	0.585	CLONAL	1	FALSE	1	0.571316166037381	3		305	172	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970942	70970942	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	122	731	0	ENST00000276594.2:c.1319C>A	p.Ser440Tyr	p.S440Y	ENST00000276594	NM_024504.3	440	tCc/tAc	6/8	0.435221759167205	3	FACETS	0.837	0.758	0.92	0.419	0.379	0.46	CLONAL	1	FALSE	1	0.571316166037381	3		731	656	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27190688	27190688	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	42	460	0	ENST00000380036.4:c.1489G>A	p.Val497Met	p.V497M	ENST00000380036	NM_000459.3	497	Gtg/Atg	10/23	0.26339960852419	3	FACETS	0.887	0.749	1	0.296	0.249	0.346	INDETERMINATE	1	FALSE	0	0.571316166037381	3		460	213	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0052364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	296	680	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	NA	2	FACETS	0.879	0.831	0.928			1	INDETERMINATE	1	TRUE	NA	0.828174137976166	2		680	813	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0052364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	257	275	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.828174137976166	2		275	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0052364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	343	519	4	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.828174137976166	1	FACETS	0.982	0.947	1	0.982	0.947	1	CLONAL	1	TRUE	0	0.828174137976166	1		523	494	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038526	47038526	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	431	961	1	ENST00000377604.3:c.688C>T	p.Arg230Ter	p.R230*	ENST00000377604	NM_001204468.1	230	Cga/Tga	8/24	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.828174137976166	2		962	1040	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187188	11187188	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	396	764	0	ENST00000361445.4:c.6230A>T	p.Asp2077Val	p.D2077V	ENST00000361445	NM_004958.3	2077	gAt/gTt	45/58	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.828174137976166	2		764	882	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247169	153247169	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	431	414	0	ENST00000281708.4:c.1633T>G	p.Tyr545Asp	p.Y545D	ENST00000281708	NM_033632.3	545	Tat/Gat	10/12	0.820480728809863	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.828174137976166	2		414	514	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867431	35867431	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs757797163	NA	P-0052364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	207	551	0	ENST00000303115.3:c.245G>T	p.Cys82Phe	p.C82F	ENST00000303115	NM_002185.3	82	tGc/tTc	3/8	1	2	FACETS	0.784	0.731	0.837	0.784	0.731	0.837	SUBCLONAL	1	TRUE	1	0.828174137976166	2		551	638	SUCCESS
APC	324	MSKCC	GRCh37	5	112175556	112175556	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	220	508	0	ENST00000257430.4:c.4265del	p.Asp1422ValfsTer51	p.D1422Vfs*51	ENST00000257430	NM_000038.5	1422	gAt/gt	16/16	1	2	FACETS	0.908	0.851	0.966	0.908	0.851	0.966	CLONAL	1	TRUE	1	0.828174137976166	2		508	585	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0052424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	135	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.126229681609173	4	FACETS	0.823	0.754	0.894	0.823	0.754	0.894	INDETERMINATE	2	TRUE	2	0.585883492901414	4		457	444	SUCCESS
APC	324	MSKCC	GRCh37	5	112175324	112175324	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1211642532	NA	P-0052424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	115	263	0	ENST00000257430.4:c.4033G>T	p.Glu1345Ter	p.E1345*	ENST00000257430	NM_000038.5	1345	Gaa/Taa	16/16	0.520805232964318	2	FACETS	0.814	0.75	0.88	0.814	0.75	0.88	CLONAL	2	TRUE	0	0.585883492901414	2		263	241	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008017	29008017	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs767050810	NA	P-0052424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	178	419	0	ENST00000282397.4:c.752A>G	p.Asn251Ser	p.N251S	ENST00000282397	NM_002019.4	251	aAt/aGt	6/30	0.564239351276307	2	FACETS	0.944	0.887	0.999	0.944	0.887	0.999	CLONAL	2	TRUE	0	0.585883492901414	2		419	322	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844722	156844722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs986498490	NA	P-0052424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	206	924	1	ENST00000524377.1:c.1276G>A	p.Val426Ile	p.V426I	ENST00000524377	NM_002529.3	426	Gtc/Atc	11/17	0.255785614258485	4	FACETS	1	0.979	1	0.736	0.689	0.783	INDETERMINATE	2	TRUE	1	0.585883492901414	4		925	505	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923411	9923411	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	36	688	0	ENST00000330684.3:c.1876A>G	p.Thr626Ala	p.T626A	ENST00000330684	NM_001134407.1	626	Acc/Gcc	9/13	1	2	FACETS	0.374	0.308	0.447	0.374	0.308	0.447	SUBCLONAL	1	TRUE	1	0.585883492901414	2		688	329	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204669	108204669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	91	238	0	ENST00000278616.4:c.7984G>T	p.Val2662Phe	p.V2662F	ENST00000278616	NM_000051.3	2662	Gtt/Ttt	54/63	0.578055817539457	1	FACETS	0.927	0.838	1	0.927	0.838	1	CLONAL	1	TRUE	0	0.585883492901414	1		238	237	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637623	23637657	+	frameshift_variant	Frame_Shift_Del	DEL	TACATCTTCGCAAGCAGTTATGATACATGGCTCTT	TACATCTTCGCAAGCAGTTATGATACATGGCTCTT	-	novel	NA	P-0052424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	123	574	0	ENST00000261584.4:c.2648_2682del	p.Lys883SerfsTer33	p.K883Sfs*33	ENST00000261584	NM_024675.3	883	aAAGAGCCATGTATCATAACTGCTTGCGAAGATGTA/a	7/13	1	2	FACETS	0.95	0.865	1	0.95	0.865	1	CLONAL	1	TRUE	1	0.585883492901414	2		574	442	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276215	15276215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748889237	NA	P-0052424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	85	683	2	ENST00000263388.2:c.5779G>A	p.Ala1927Thr	p.A1927T	ENST00000263388	NM_000435.2	1927	Gcc/Acc	31/33	1	2	FACETS	0.942	0.842	1	0.942	0.842	1	CLONAL	1	TRUE	1	0.585883492901414	2		685	308	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361136	66361136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	97	431	0	ENST00000273854.3:c.1036G>A	p.Glu346Lys	p.E346K	ENST00000273854	NM_004439.5	346	Gag/Aag	4/18	0.585883492901414	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.585883492901414	1		431	214	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204515933	204515933	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	30	424	0	ENST00000367182.3:c.831A>C	p.Glu277Asp	p.E277D	ENST00000367182	NM_001278516.1	277	gaA/gaC	10/11	0.585883492901414	3	FACETS	0.288	0.232	0.353	0.144	0.116	0.177	SUBCLONAL	1	TRUE	1	0.585883492901414	3		424	459	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0052431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	55	670	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.372731543926574	2	FACETS	1	0.908	1	0.535	0.461	0.614	CLONAL	1	TRUE	0	0.372731543926574	2		670	276	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0052431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	135	449	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.974	0.895	1	1	0.991	1	CLONAL	2	TRUE	1	0.372731543926574	2		449	372	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0052431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	175	835	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.372731543926574	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.372731543926574	1		835	691	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	151	518	0	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	0.372731543926574	2	FACETS	0.938	0.866	1	0.938	0.866	1	CLONAL	2	TRUE	0	0.372731543926574	2		518	432	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818383	43818383	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	192	636	0	ENST00000372470.3:c.1848C>A	p.Cys616Ter	p.C616*	ENST00000372470	NM_005373.2	616	tgC/tgA	12/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.372731543926574	2		636	770	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472471	88472471	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs779320655	NA	P-0052431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	241	616	0	ENST00000360948.2:c.2084T>C	p.Ile695Thr	p.I695T	ENST00000360948	NM_001012338.2	695	aTt/aCt	16/19	1	2	FACETS	0.88	0.825	0.935	1	0.994	1	CLONAL	2	TRUE	1	0.372731543926574	2		616	735	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	137	418	0	ENST00000257430.4:c.4285del	p.Gln1429LysfsTer44	p.Q1429Kfs*44	ENST00000257430	NM_000038.5	1429	Caa/aa	16/16	1	2	FACETS	0.881	0.809	0.956	1	0.99	1	CLONAL	2	TRUE	1	0.372731543926574	2		418	417	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006641	62006641	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149266494	NA	P-0052431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	153	662	1	ENST00000392795.3:c.638C>T	p.Thr213Met	p.T213M	ENST00000392795	NM_001039933.1	213	aCg/aTg	6/6	0.372731543926574	3	FACETS	1	0.948	1	0.35	0.32	0.382	CLONAL	1	TRUE	0	0.372731543926574	3		663	927	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857196	9857196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs74935155	NA	P-0052431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	31	555	0	ENST00000330684.3:c.4205G>A	p.Arg1402Gln	p.R1402Q	ENST00000330684	NM_001134407.1	1402	cGg/cAg	13/13	1	2	FACETS	0.278	0.224	0.339	0.278	0.224	0.339	SUBCLONAL	1	TRUE	1	0.372731543926574	2		555	599	SUCCESS
APC	324	MSKCC	GRCh37	5	112174973	112174973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085227	NA	P-0052431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	48	276	0	ENST00000257430.4:c.3682C>T	p.Gln1228Ter	p.Q1228*	ENST00000257430	NM_000038.5	1228	Cag/Tag	16/16	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.372731543926574	2		276	212	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934900	9934900	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	85	484	0	ENST00000330684.3:c.1390C>A	p.Leu464Met	p.L464M	ENST00000330684	NM_001134407.1	464	Ctg/Atg	6/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.372731543926574	2		484	375	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941260	36941260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759364352	NA	P-0052431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	218	706	1	ENST00000361632.4:c.79G>A	p.Gly27Arg	p.G27R	ENST00000361632		27	Ggg/Agg	3/16	1	2	FACETS	0.782	0.73	0.836	1	0.992	1	SUBCLONAL	2	TRUE	1	0.372731543926574	2		707	748	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279600	123279600	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	242	717	0	ENST00000358487.5:c.832T>C	p.Cys278Arg	p.C278R	ENST00000358487	NM_000141.4	278	Tgc/Cgc	7/18	1	2	FACETS	0.785	0.735	0.836	1	0.993	1	SUBCLONAL	2	TRUE	1	0.372731543926574	2		717	827	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59886090	59886090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782238	NA	P-0052431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	26	508	0	ENST00000259008.2:c.656G>A	p.Cys219Tyr	p.C219Y	ENST00000259008	NM_032043.2	219	tGt/tAt	7/20	0.372731543926574	3	FACETS	0.406	0.321	0.503	0.135	0.107	0.168	SUBCLONAL	1	TRUE	0	0.372731543926574	3		508	408	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395709	45395709	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	57	476	0	ENST00000262160.6:c.425A>G	p.Glu142Gly	p.E142G	ENST00000262160	NM_005901.5	142	gAa/gGa	4/11	0.349982831870108	0	FACETS	0.553	0.477	0.635			1	SUBCLONAL	1	TRUE	0	0.372731543926574	0		476	347	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56367743	56367743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	59	457	1	ENST00000348428.3:c.569G>A	p.Cys190Tyr	p.C190Y	ENST00000348428	NM_006785.3	190	tGt/tAt	4/17	0.349982831870108	0	FACETS	0.634	0.549	0.726			1	SUBCLONAL	1	TRUE	0	0.372731543926574	0		458	313	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295779	212295779	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	140	515	0	ENST00000342788.4:c.2534C>A	p.Ala845Glu	p.A845E	ENST00000342788	NM_005235.2	845	gCa/gAa	21/28	1	2	FACETS	0.789	0.724	0.857	1	0.989	1	SUBCLONAL	2	TRUE	1	0.372731543926574	2		515	476	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40738986	40738986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	151	517	0	ENST00000373198.4:c.3298G>A	p.Val1100Met	p.V1100M	ENST00000373198	NM_133170.3	1100	Gtg/Atg	24/32	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.372731543926574	2		517	594	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612022	189612022	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	287	555	0	ENST00000264731.3:c.1774C>A	p.Gln592Lys	p.Q592K	ENST00000264731	NM_003722.4	592	Caa/Aaa	14/14	0.372731543926574	2	FACETS	0.93	0.885	0.975	1	0.994	1	CLONAL	3	TRUE	0	0.372731543926574	2		555	552	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0052469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	368	378	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.35402123513532	3	FACETS	1	0.993	1	0.828	0.788	0.869	CLONAL	2	TRUE	0	0.35402123513532	3		378	985	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0052469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	227	863	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.253725082830074	2	FACETS	0.798	0.745	0.852	0.798	0.745	0.852	SUBCLONAL	2	TRUE	0	0.35402123513532	2		864	804	SUCCESS
APC	324	MSKCC	GRCh37	5	112175000	112175000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	53	297	0	ENST00000257430.4:c.3709C>T	p.Gln1237Ter	p.Q1237*	ENST00000257430	NM_000038.5	1237	Cag/Tag	16/16	1	2	FACETS	0.673	0.575	0.78	0.673	0.575	0.78	SUBCLONAL	1	TRUE	1	0.35402123513532	2		297	445	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0052469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	255	758	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	0.286778057619427	3	FACETS	0.788	0.737	0.84	0.788	0.737	0.84	SUBCLONAL	2	TRUE	1	0.35402123513532	3		758	1076	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021623	31021623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	96	570	0	ENST00000375687.4:c.1622G>A	p.Arg541Gln	p.R541Q	ENST00000375687	NM_015338.5	541	cGg/cAg	12/13	0.35402123513532	4	FACETS	0.735	0.653	0.822	0.184	0.163	0.206	SUBCLONAL	1	TRUE	0	0.35402123513532	4		570	999	SUCCESS
APC	324	MSKCC	GRCh37	5	112175487	112175487	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	76	436	0	ENST00000257430.4:c.4196del	p.Arg1399LeufsTer16	p.R1399Lfs*16	ENST00000257430	NM_000038.5	1399	cGt/ct	16/16	1	2	FACETS	0.775	0.681	0.876	0.775	0.681	0.876	SUBCLONAL	1	TRUE	1	0.35402123513532	2		436	554	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109315795	109315798	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	rs779935597	NA	P-0052469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	92	612	0	ENST00000436639.2:c.987_990del	p.Phe329LeufsTer10	p.F329Lfs*10	ENST00000436639	NM_014454.2	329	ttCTTT/tt	6/10	1	2	FACETS	0.547	0.484	0.613	0.547	0.484	0.613	SUBCLONAL	1	TRUE	1	0.35402123513532	2		612	951	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982389	201982390	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	141	744	0	ENST00000359651.3:c.769dup	p.Tyr257LeufsTer44	p.Y257Lfs*44	ENST00000359651		256	-/T	6/8	1	2	FACETS	0.921	0.839	1	0.921	0.839	1	CLONAL	1	TRUE	1	0.35402123513532	2		744	865	SUCCESS
BLM	641	MSKCC	GRCh37	15	91333955	91333955	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	80	636	0	ENST00000355112.3:c.2900C>T	p.Pro967Leu	p.P967L	ENST00000355112	NM_000057.2	967	cCt/cTt	15/22	1	2	FACETS	0.461	0.405	0.522	0.461	0.405	0.522	SUBCLONAL	1	TRUE	1	0.35402123513532	2		636	980	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302456	15302456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749561286	NA	P-0052513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	257	683	1	ENST00000263388.2:c.815C>T	p.Thr272Met	p.T272M	ENST00000263388	NM_000435.2	272	aCg/aTg	6/33	0.177244504223464	4	FACETS	1	0.989	1	0.634	0.594	0.675	INDETERMINATE	1	TRUE	2	0.641791525060117	4		684	1037	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215356	5215356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1420232605	NA	P-0052513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	187	710	0	ENST00000357368.4:c.4262G>A	p.Arg1421His	p.R1421H	ENST00000357368	NM_002850.3	1421	cGc/cAc	28/38	0.177244504223464	4	FACETS	1	0.982	1	0.597	0.552	0.644	INDETERMINATE	1	TRUE	2	0.641791525060117	4		710	801	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624296	89624296	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786201995	NA	P-0052513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	179	520	0	ENST00000371953.3:c.70G>T	p.Asp24Tyr	p.D24Y	ENST00000371953	NM_000314.4	24	Gac/Tac	1/9	0.547620248245365	2	FACETS	1	0.992	1	0.746	0.698	0.794	CLONAL	1	TRUE	0	0.641791525060117	2		520	374	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352351	143352351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	97	645	0	ENST00000262992.4:c.62C>T	p.Ala21Val	p.A21V	ENST00000262992	NM_001101669.1	21	gCc/gTc	2/24	1	2	FACETS	0.81	0.728	0.896	0.81	0.728	0.896	CLONAL	1	TRUE	1	0.641791525060117	2		645	373	SUCCESS
APC	324	MSKCC	GRCh37	5	112155026	112155026	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs863225309	NA	P-0052513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	230	496	0	ENST00000257430.4:c.1297C>T	p.Gln433Ter	p.Q433*	ENST00000257430	NM_000038.5	433	Cag/Tag	10/16	0.547620248245365	2	FACETS	0.881	0.835	0.926	0.881	0.835	0.926	CLONAL	2	TRUE	0	0.641791525060117	2		496	407	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324584	31324584	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	325	379	0	ENST00000412585.2:c.224G>T	p.Trp75Leu	p.W75L	ENST00000412585	NM_005514.6	75	tGg/tTg	2/8	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.641791525060117	2		379	730	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0052524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	57	422	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	1	2	FACETS	0.888	0.764	1	0.888	0.764	1	CLONAL	1	TRUE	1	0.31	2		422	414	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0052524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	128	377	0	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.31	2		377	605	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528086	29528086	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs864622107	NA	P-0052524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	23	202	0	ENST00000356175.3:c.1094C>G	p.Ser365Ter	p.S365*	ENST00000356175	NM_000267.3	365	tCa/tGa	10/57	1	2	FACETS	0.552	0.431	0.691	0.552	0.431	0.691	SUBCLONAL	1	TRUE	1	0.31	2		202	269	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248566	8248568	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	novel	NA	P-0052524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	101	760	0	ENST00000335790.3:c.319_321del	p.Asn107del	p.N107del	ENST00000335790	NM_002315.2	107	AAC/-	3/4	1	2	FACETS	0.77	0.688	0.858	0.77	0.688	0.858	SUBCLONAL	1	TRUE	1	0.31	2		760	846	SUCCESS
APC	324	MSKCC	GRCh37	5	112175531	112175532	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0052524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	37	294	0	ENST00000257430.4:c.4240_4241del	p.Val1414LysfsTer8	p.V1414Kfs*8	ENST00000257430	NM_000038.5	1414	GTa/a	16/16	1	2	FACETS	0.739	0.611	0.881	0.739	0.611	0.881	SUBCLONAL	1	TRUE	1	0.31	2		294	323	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878413	151878413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	109	559	0	ENST00000262189.6:c.6532C>T	p.Pro2178Ser	p.P2178S	ENST00000262189	NM_170606.2	2178	Ccc/Tcc	36/59	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.31	2		559	656	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0052529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	48	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.533	0.451	0.625	0.533	0.451	0.625	SUBCLONAL	1	TRUE	1	0.324254060128066	2		326	555	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0052529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	84	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.851	0.752	0.956	0.851	0.752	0.956	CLONAL	1	TRUE	1	0.324254060128066	2		487	609	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0052529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	128	612	0	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	0.324254060128066	1	FACETS	0.938	0.852	1	0.938	0.852	1	CLONAL	1	TRUE	0	0.324254060128066	1		612	705	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0052529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	142	622	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.324254060128066	2		622	787	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0052529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	93	425	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.958	0.853	1	0.958	0.853	1	CLONAL	1	TRUE	1	0.324254060128066	2		425	599	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0052529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	116	749	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	1	FACETS	0.761	0.692	0.832	1	0.986	1	SUBCLONAL	2	TRUE	0	0.324254060128066	1		749	394	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026058	14026058	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	71	284	0	ENST00000311895.7:c.1018C>G	p.Arg340Gly	p.R340G	ENST00000311895	NM_005236.2	340	Cga/Gga	6/11	1	2	FACETS	0.958	0.839	1	0.958	0.839	1	CLONAL	1	TRUE	1	0.324254060128066	2		284	457	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120194	70120195	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0052529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	140	532	0	ENST00000245479.2:c.1197_1198dup	p.Glu400GlyfsTer4	p.E400Gfs*4	ENST00000245479	NM_000346.3	399	acg/acGGg	3/3	0.324254060128066	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.324254060128066	1		532	613	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521640	89521640	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	90	383	0	ENST00000336596.2:c.2717G>C	p.Ser906Thr	p.S906T	ENST00000336596	NM_005233.5	906	aGc/aCc	16/17	1	2	FACETS	0.96	0.854	1	0.96	0.854	1	CLONAL	1	TRUE	1	0.324254060128066	2		383	578	SUCCESS
APC	324	MSKCC	GRCh37	5	112175419	112175419	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	62	269	0	ENST00000257430.4:c.4128del	p.Tyr1376Ter	p.Y1376*	ENST00000257430	NM_000038.5	1376	taT/ta	16/16	1	2	FACETS	0.94	0.815	1	0.94	0.815	1	CLONAL	1	TRUE	1	0.324254060128066	2		269	407	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	162	378	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.864	0.796	0.934	1	0.991	1	CLONAL	2	TRUE	1	0.308839419540546	2		378	607	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	125	498	4	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.809	0.737	0.885	1	0.987	1	CLONAL	2	TRUE	1	0.308839419540546	2		502	500	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	405	1445	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.988	1	1	0.997	1	CLONAL	3	TRUE	1	0.308839419540546	2		1452	807	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	144	1056	1	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.308839419540546	2		1057	677	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	64	277	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.308839419540546	2		277	359	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	252	694	3	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.913	0.856	0.971	1	0.994	1	CLONAL	2	TRUE	1	0.308839419540546	2		697	894	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715678	30715678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039551	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	117	284	0	ENST00000295754.5:c.1336G>A	p.Asp446Asn	p.D446N	ENST00000295754	NM_003242.5	446	Gat/Aat	5/7	1	2	FACETS	0.913	0.83	0.999	1	0.989	1	CLONAL	2	TRUE	1	0.308839419540546	2		284	415	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	464	844	1	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	1	0.994	1	1	0.998	1	CLONAL	3	TRUE	1	0.308839419540546	2		845	870	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	179	343	2	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	0.941	0.872	1	1	0.993	1	CLONAL	2	TRUE	1	0.308839419540546	2		345	616	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	177	702	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.85	0.786	0.916	1	0.992	1	CLONAL	2	TRUE	1	0.308839419540546	2		703	674	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	87	293	1	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.308839419540546	2		294	412	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	91	352	4	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	0.801	0.717	0.889	1	0.983	1	CLONAL	2	TRUE	1	0.308839419540546	2		356	368	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303028	15303028	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773630799	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	60	931	0	ENST00000263388.2:c.422G>A	p.Arg141His	p.R141H	ENST00000263388	NM_000435.2	141	cGc/cAc	4/33	1	2	FACETS	0.409	0.351	0.472	0.409	0.351	0.472	SUBCLONAL	1	TRUE	1	0.308839419540546	2		931	951	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	249	679	0	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	1	2	FACETS	0.875	0.82	0.932	1	0.994	1	CLONAL	2	TRUE	1	0.308839419540546	2		679	921	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216546	108216546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529296539	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	124	213	0	ENST00000278616.4:c.8495G>A	p.Arg2832His	p.R2832H	ENST00000278616	NM_000051.3	2832	cGt/cAt	58/63	1	2	FACETS	0.972	0.887	1	1	0.99	1	CLONAL	2	TRUE	1	0.308839419540546	2		213	413	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226949	2226949	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	224	576	1	ENST00000398665.3:c.4429G>A	p.Gly1477Ser	p.G1477S	ENST00000398665	NM_032482.2	1477	Ggc/Agc	27/28	1	2	FACETS	0.918	0.857	0.981	1	0.994	1	CLONAL	2	TRUE	1	0.308839419540546	2		577	790	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417944	32417944	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1172760612	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	158	499	1	ENST00000332351.3:c.1108C>T	p.Arg370Cys	p.R370C	ENST00000332351	NM_024426.4	370	Cgt/Tgt	7/10	1	2	FACETS	0.92	0.848	0.995	1	0.991	1	CLONAL	2	TRUE	1	0.308839419540546	2		500	556	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332915	153332915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200698994	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	100	286	0	ENST00000281708.4:c.41G>A	p.Arg14Gln	p.R14Q	ENST00000281708	NM_033632.3	14	cGa/cAa	2/12	1	2	FACETS	0.882	0.795	0.973	1	0.986	1	CLONAL	2	TRUE	1	0.308839419540546	2		286	367	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181765	56181765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1287268127	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	108	222	0	ENST00000399503.3:c.3989C>T	p.Ser1330Leu	p.S1330L	ENST00000399503	NM_005921.1	1330	tCg/tTg	17/20	1	2	FACETS	0.897	0.812	0.985	1	0.987	1	CLONAL	2	TRUE	1	0.308839419540546	2		222	390	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707683	176707683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587784154	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	185	456	1	ENST00000439151.2:c.5740C>T	p.Arg1914Cys	p.R1914C	ENST00000439151	NM_022455.4	1914	Cgc/Tgc	18/23	1	2	FACETS	0.987	0.916	1	1	0.993	1	CLONAL	2	TRUE	1	0.308839419540546	2		457	607	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	142	383	1	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.847	0.776	0.92	1	0.99	1	CLONAL	2	TRUE	1	0.308839419540546	2		384	543	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372092	55372093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	170	323	2	ENST00000297316.4:c.788dup	p.Glu264GlyfsTer101	p.E264Gfs*101	ENST00000297316	NM_022454.3	261	ggc/ggCc	2/2	1	2	FACETS	0.917	0.848	0.989	1	0.992	1	CLONAL	2	TRUE	1	0.308839419540546	2		325	600	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444276	50444276	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144637662	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	84	242	0	ENST00000331340.3:c.206G>A	p.Arg69His	p.R69H	ENST00000331340	NM_006060.4	69	cGt/cAt	4/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.308839419540546	2		242	377	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892293	9892293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs796052550	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	99	389	0	ENST00000330684.3:c.2197G>A	p.Ala733Thr	p.A733T	ENST00000330684	NM_001134407.1	733	Gca/Aca	11/13	1	2	FACETS	0.771	0.692	0.852	1	0.983	1	SUBCLONAL	2	TRUE	1	0.308839419540546	2		389	416	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288969	212288969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148791072	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	198	402	0	ENST00000342788.4:c.2777C>T	p.Thr926Met	p.T926M	ENST00000342788	NM_005235.2	926	aCg/aTg	23/28	0.298629441286088	3	FACETS	0.855	0.797	0.914	1	0.988	1	CLONAL	3	TRUE	1	0.308839419540546	3		402	577	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469037	25469037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457323351	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	299	668	2	ENST00000264709.3:c.1421G>A	p.Arg474His	p.R474H	ENST00000264709	NM_175629.2	474	cGc/cAc	11/23	0.298629441286088	3	FACETS	0.906	0.857	0.957	1	0.993	1	CLONAL	3	TRUE	1	0.308839419540546	3		670	822	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340357	8340357	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324340491	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	191	468	3	ENST00000356435.5:c.5239C>T	p.Arg1747Cys	p.R1747C	ENST00000356435		1747	Cgt/Tgt	31/35	1	2	FACETS	0.895	0.831	0.961	1	0.993	1	CLONAL	2	TRUE	1	0.308839419540546	2		471	691	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863054	56863054	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1266824391	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	161	387	1	ENST00000519728.1:c.327del	p.Glu110LysfsTer15	p.E110Kfs*15	ENST00000519728	NM_002350.3	107	acA/ac	5/13	1	2	FACETS	0.831	0.766	0.9	1	0.99	1	CLONAL	2	TRUE	1	0.308839419540546	2		388	627	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785984	135785984	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	217	667	0	ENST00000298552.3:c.1237del	p.Gln413ArgfsTer27	p.Q413Rfs*27	ENST00000298552	NM_001162426.1	413	Cag/ag	12/23	1	2	FACETS	0.85	0.792	0.909	1	0.993	1	CLONAL	2	TRUE	1	0.308839419540546	2		667	827	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030278	180030278	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201796032	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	312	829	1	ENST00000261937.6:c.4006G>A	p.Glu1336Lys	p.E1336K	ENST00000261937	NM_182925.4	1336	Gag/Aag	30/30	1	2	FACETS	0.979	0.924	1	1	0.996	1	CLONAL	2	TRUE	1	0.308839419540546	2		830	1032	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111145	193111146	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	rs760591174	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	59	263	0	ENST00000367435.3:c.687_688dup	p.Val230GlufsTer28	p.V230Efs*28	ENST00000367435	NM_024529.4	226	-/AG	7/17	1	2	FACETS	0.769	0.662	0.884	0.769	0.662	0.884	SUBCLONAL	1	TRUE	1	0.308839419540546	2		263	497	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356412	66356412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763166233	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	109	344	0	ENST00000273854.3:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000273854	NM_004439.5	362	cGg/cAg	5/18	0.308839419540546	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.308839419540546	1		344	419	SUCCESS
APC	324	MSKCC	GRCh37	5	112174213	112174214	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554084587	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	101	261	0	ENST00000257430.4:c.2926dup	p.Arg976LysfsTer9	p.R976Kfs*9	ENST00000257430	NM_000038.5	974	-/A	16/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.308839419540546	2		261	457	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523641	41523641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	240	685	0	ENST00000263253.7:c.1057C>T	p.Arg353Cys	p.R353C	ENST00000263253	NM_001429.3	353	Cgc/Tgc	4/31	1	2	FACETS	0.89	0.833	0.949	1	0.994	1	CLONAL	2	TRUE	1	0.308839419540546	2		685	873	SUCCESS
AXL	558	MSKCC	GRCh37	19	41737106	41737106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771116052	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	107	776	1	ENST00000301178.4:c.686G>A	p.Arg229His	p.R229H	ENST00000301178	NM_021913.4	229	cGt/cAt	6/20	1	2	FACETS	0.708	0.634	0.787	0.708	0.634	0.787	SUBCLONAL	1	TRUE	1	0.308839419540546	2		777	979	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615023	43615023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779996040	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	212	1538	0	ENST00000355710.3:c.2437C>T	p.Arg813Trp	p.R813W	ENST00000355710	NM_020975.4	813	Cgg/Tgg	14/20	1	2	FACETS	0.839	0.781	0.899	1	0.993	1	CLONAL	2	TRUE	1	0.308839419540546	2		1538	818	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115043	3115043	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	276	808	0	ENST00000078429.4:c.578C>A	p.Pro193His	p.P193H	ENST00000078429	NM_002067.2	193	cCt/cAt	4/7	1	2	FACETS	0.928	0.873	0.985	1	0.995	1	CLONAL	2	TRUE	1	0.308839419540546	2		808	963	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680731	30680731	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761210355	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	138	488	0	ENST00000376406.3:c.988G>A	p.Asp330Asn	p.D330N	ENST00000376406	NM_014641.2	330	Gac/Aac	5/15	1	2	FACETS	0.764	0.698	0.833	1	0.987	1	SUBCLONAL	2	TRUE	1	0.308839419540546	2		488	585	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120571	2120571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45469298	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	266	863	1	ENST00000219476.3:c.1831C>T	p.Arg611Trp	p.R611W	ENST00000219476	NM_000548.3	611	Cgg/Tgg	17/42	1	2	FACETS	0.863	0.81	0.918	1	0.994	1	CLONAL	2	TRUE	1	0.308839419540546	2		864	998	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953369	17953369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	257	862	0	ENST00000458235.1:c.617G>A	p.Ser206Asn	p.S206N	ENST00000458235	NM_000215.3	206	aGc/aAc	6/24	1	2	FACETS	0.862	0.808	0.918	1	0.994	1	CLONAL	2	TRUE	1	0.308839419540546	2		862	965	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138563	37138563	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs34095970	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	186	581	0	ENST00000373509.5:c.100del	p.Leu34TrpfsTer60	p.L34Wfs*60	ENST00000373509	NM_002648.3	33	Ccc/cc	2/6	1	2	FACETS	0.887	0.822	0.954	1	0.992	1	CLONAL	2	TRUE	1	0.308839419540546	2		581	679	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223613	36223614	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs765758919	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	257	896	1	ENST00000222270.7:c.6169dup	p.Arg2057ProfsTer3	p.R2057Pfs*3	ENST00000222270	NM_014727.1	2055	gcc/gCcc	28/37	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.308839419540546	2		897	1112	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725046	47725046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755414185	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	275	961	1	ENST00000449228.1:c.698G>A	p.Arg233His	p.R233H	ENST00000449228	NM_001127240.2	233	cGc/cAc	4/4	1	2	FACETS	0.862	0.81	0.916	1	0.994	1	CLONAL	2	TRUE	1	0.308839419540546	2		962	1033	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254677	16254677	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	169	407	0	ENST00000375759.3:c.1942C>T	p.Arg648Trp	p.R648W	ENST00000375759	NM_015001.2	648	Cgg/Tgg	11/15	1	2	FACETS	0.869	0.802	0.937	1	0.991	1	CLONAL	2	TRUE	1	0.308839419540546	2		407	630	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142993	47142993	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	72	389	0	ENST00000409792.3:c.4970C>A	p.Pro1657His	p.P1657H	ENST00000409792	NM_014159.6	1657	cCt/cAt	8/21	1	2	FACETS	0.571	0.498	0.65	0.571	0.498	0.65	SUBCLONAL	1	TRUE	1	0.308839419540546	2		389	817	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753096	57753096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	132	345	0	ENST00000274289.3:c.920C>T	p.Ala307Val	p.A307V	ENST00000274289	NM_006622.3	307	gCc/gTc	7/14	1	2	FACETS	0.845	0.771	0.921	1	0.989	1	CLONAL	2	TRUE	1	0.308839419540546	2		345	506	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101051	27101051	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471914196	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	225	696	2	ENST00000324856.7:c.4333C>T	p.Arg1445Cys	p.R1445C	ENST00000324856	NM_006015.4	1445	Cgc/Tgc	18/20	1	2	FACETS	0.87	0.812	0.93	1	0.993	1	CLONAL	2	TRUE	1	0.308839419540546	2		698	837	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344476	118344476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782640926	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	95	230	1	ENST00000534358.1:c.2602G>A	p.Val868Met	p.V868M	ENST00000534358	NM_005933.3	868	Gtg/Atg	3/36	1	2	FACETS	1	0.919	1	1	0.988	1	CLONAL	2	TRUE	1	0.308839419540546	2		231	301	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261752	16261752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	198	494	2	ENST00000375759.3:c.9017G>A	p.Ser3006Asn	p.S3006N	ENST00000375759	NM_015001.2	3006	aGc/aAc	11/15	1	2	FACETS	1	0.958	1	1	0.994	1	CLONAL	2	TRUE	1	0.308839419540546	2		496	617	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310493	65310493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	193	643	0	ENST00000342505.4:c.2195G>A	p.Gly732Asp	p.G732D	ENST00000342505	NM_002227.2	732	gGc/gAc	16/25	1	2	FACETS	0.823	0.764	0.885	1	0.992	1	CLONAL	2	TRUE	1	0.308839419540546	2		643	759	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241906	72241906	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	113	324	0	ENST00000357731.5:c.484G>A	p.Ala162Thr	p.A162T	ENST00000357731	NM_173808.2	162	Gcc/Acc	3/7	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.308839419540546	2		324	493	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874223	155874223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	124	492	0	ENST00000368323.3:c.308C>T	p.Thr103Met	p.T103M	ENST00000368323	NM_006912.5	103	aCg/aTg	5/6	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.308839419540546	2		492	750	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439868	49439868	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	109	666	1	ENST00000301067.7:c.4673C>A	p.Pro1558His	p.P1558H	ENST00000301067	NM_003482.3	1558	cCc/cAc	17/54	1	2	FACETS	0.82	0.736	0.909	0.82	0.736	0.909	CLONAL	1	TRUE	1	0.308839419540546	2		667	861	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134033	41134033	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	188	531	0	ENST00000379561.5:c.1595C>A	p.Ser532Tyr	p.S532Y	ENST00000379561	NM_002015.3	532	tCt/tAt	2/3	1	2	FACETS	0.899	0.834	0.966	1	0.993	1	CLONAL	2	TRUE	1	0.308839419540546	2		531	677	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132967	30132967	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	187	507	0	ENST00000331968.5:c.634del	p.Val212SerfsTer52	p.V212Sfs*52	ENST00000331968	NM_002742.2	212	Gtc/tc	4/18	1	2	FACETS	0.837	0.776	0.901	1	0.992	1	CLONAL	2	TRUE	1	0.308839419540546	2		507	723	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609700	81609700	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	78	522	0	ENST00000298171.2:c.1298T>C	p.Val433Ala	p.V433A	ENST00000298171	NM_000369.2	433	gTc/gCc	10/10	1	2	FACETS	0.812	0.714	0.917	0.812	0.714	0.917	CLONAL	1	TRUE	1	0.308839419540546	2		522	622	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610570	81610570	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	126	272	0	ENST00000298171.2:c.2168A>G	p.Lys723Arg	p.K723R	ENST00000298171	NM_000369.2	723	aAg/aGg	10/10	1	2	FACETS	0.988	0.902	1	1	0.99	1	CLONAL	2	TRUE	1	0.308839419540546	2		272	413	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442775	99442775	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	165	548	1	ENST00000268035.6:c.1172G>A	p.Arg391His	p.R391H	ENST00000268035	NM_000875.3	391	cGc/cAc	5/21	1	2	FACETS	0.788	0.726	0.852	1	0.99	1	SUBCLONAL	2	TRUE	1	0.308839419540546	2		549	678	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658895	3658895	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	189	454	0	ENST00000294008.3:c.71C>A	p.Pro24His	p.P24H	ENST00000294008	NM_032444.2	24	cCt/cAt	2/15	1	2	FACETS	0.851	0.789	0.915	1	0.992	1	CLONAL	2	TRUE	1	0.308839419540546	2		454	719	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89851261	89851261	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555556175	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	144	468	0	ENST00000389301.3:c.1470+1G>A		p.X490_splice	ENST00000389301	NM_000135.2	490			1	2	FACETS	0.784	0.718	0.852	1	0.988	1	SUBCLONAL	2	TRUE	1	0.308839419540546	2		468	595	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58711239	58711239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	189	343	0	ENST00000305921.3:c.727C>T	p.Arg243Cys	p.R243C	ENST00000305921	NM_003620.3	243	Cgt/Tgt	3/6	1	2	FACETS	0.837	0.776	0.9	1	0.992	1	CLONAL	2	TRUE	1	0.308839419540546	2		343	731	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39623744	39623744	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	151	267	0	ENST00000262039.4:c.2151T>G	p.Ile717Met	p.I717M	ENST00000262039	NM_002647.2	717	atT/atG	20/25	1	2	FACETS	0.949	0.874	1	1	0.991	1	CLONAL	2	TRUE	1	0.308839419540546	2		267	515	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245914	5245914	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs764335621	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	120	890	0	ENST00000357368.4:c.861del	p.Glu288ArgfsTer41	p.E288Rfs*41	ENST00000357368	NM_002850.3	287	ccC/cc	10/38	1	2	FACETS	0.815	0.735	0.899	0.815	0.735	0.899	CLONAL	1	TRUE	1	0.308839419540546	2		890	954	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285864	39285864	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	148	308	1	ENST00000402219.2:c.295C>T	p.Arg99Ter	p.R99*	ENST00000402219	NM_005633.3	99	Cga/Tga	3/23	0.298629441286088	3	FACETS	0.858	0.786	0.932	0.858	0.786	0.932	CLONAL	2	TRUE	1	0.308839419540546	3		309	645	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47643552	47643552	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	152	322	0	ENST00000233146.2:c.1061del	p.Asn354ThrfsTer3	p.N354Tfs*3	ENST00000233146	NM_000251.2	354	Aac/ac	6/16	0.298629441286088	3	FACETS	0.823	0.755	0.895	0.823	0.755	0.895	CLONAL	2	TRUE	1	0.308839419540546	3		322	690	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693933	47693934	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	144	262	0	ENST00000233146.2:c.1650dup	p.Phe551IlefsTer11	p.F551Ifs*11	ENST00000233146	NM_000251.2	549	-/A	10/16	0.298629441286088	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.308839419540546	3		262	466	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225338987	225338987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766471279	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	231	273	1	ENST00000264414.4:c.2282G>A	p.Arg761His	p.R761H	ENST00000264414	NM_003590.4	761	cGc/cAc	16/16	0.298629441286088	3	FACETS	0.981	0.921	1	1	0.993	1	CLONAL	3	TRUE	1	0.308839419540546	3		274	587	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225343039	225343039	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	216	366	0	ENST00000264414.4:c.2053G>A	p.Asp685Asn	p.D685N	ENST00000264414	NM_003590.4	685	Gac/Aac	15/16	0.298629441286088	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.308839419540546	3		366	774	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803247	1803247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778353	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	237	810	0	ENST00000260795.2:c.599G>A	p.Arg200His	p.R200H	ENST00000260795		200	cGc/cAc	4/17	1	2	FACETS	0.927	0.867	0.988	1	0.994	1	CLONAL	2	TRUE	1	0.308839419540546	2		810	828	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807295	1807295	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	219	758	0	ENST00000260795.2:c.1544C>A	p.Thr515Asn	p.T515N	ENST00000260795		515	aCt/aAt	11/17	1	2	FACETS	0.939	0.877	1	1	0.994	1	CLONAL	2	TRUE	1	0.308839419540546	2		758	755	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247307	153247307	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	77	295	0	ENST00000281708.4:c.1495G>T	p.Gly499Cys	p.G499C	ENST00000281708	NM_033632.3	499	Ggt/Tgt	10/12	1	2	FACETS	0.991	0.873	1	0.991	0.873	1	CLONAL	1	TRUE	1	0.308839419540546	2		295	503	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024189	112024189	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	120	296	0	ENST00000368678.4:c.596A>G	p.His199Arg	p.H199R	ENST00000368678		199	cAt/cGt	7/13	1	2	FACETS	0.825	0.75	0.904	1	0.987	1	CLONAL	2	TRUE	1	0.308839419540546	2		296	471	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848085	151848085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781715925	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	100	263	0	ENST00000262189.6:c.12674G>A	p.Arg4225Gln	p.R4225Q	ENST00000262189	NM_170606.2	4225	cGa/cAa	51/59	1	2	FACETS	0.784	0.705	0.867	1	0.984	1	SUBCLONAL	2	TRUE	1	0.308839419540546	2		263	413	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97873777	97873777	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	208	698	1	ENST00000289081.3:c.1297del	p.Arg433ValfsTer14	p.R433Vfs*14	ENST00000289081	NM_000136.2	433	Cgt/gt	13/15	1	2	FACETS	0.906	0.844	0.971	1	0.993	1	CLONAL	2	TRUE	1	0.308839419540546	2		699	743	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0052532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	125	257	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.344153484766504	3	FACETS	0.872	0.796	0.951	0.872	0.796	0.951	CLONAL	2	TRUE	1	0.40688194221985	3		258	424	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001366	29001366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779189056	NA	P-0052532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	181	324	0	ENST00000282397.4:c.1366G>A	p.Ala456Thr	p.A456T	ENST00000282397	NM_002019.4	456	Gca/Aca	10/30	0.40688194221985	10	FACETS	0.986	0.908	1	0.329	0.302	0.356	CLONAL	2	TRUE	4	0.40688194221985	10		324	1185	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367798	15367798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144627512	NA	P-0052532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	299	705	4	ENST00000263377.2:c.1528C>T	p.Arg510Trp	p.R510W	ENST00000263377	NM_058243.2	510	Cgg/Tgg	8/20	0.377883908209087	3	FACETS	0.961	0.908	1			1	CLONAL	2	TRUE	NA	0.40688194221985	3		709	920	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs11575997	NA	P-0052532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	399	515	0	ENST00000269305.4:c.993+1G>T		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.377883908209087	3	FACETS	0.992	0.95	1			1	CLONAL	3	TRUE	NA	0.40688194221985	3		515	793	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125076	46125076	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	158	159	0	ENST00000334344.6:c.263C>A	p.Ala88Asp	p.A88D	ENST00000334344	NM_152641.2	88	gCt/gAt	3/21	0.40688194221985	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	1	0.40688194221985	4		159	340	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853346	151853347	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0052532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	181	380	0	ENST00000262189.6:c.11755_11756del	p.Gly3919PhefsTer5	p.G3919Ffs*5	ENST00000262189	NM_170606.2	3919	GGt/t	45/59	0.40688194221985	2	FACETS	0.89	0.828	0.953	0.89	0.828	0.953	CLONAL	2	TRUE	0	0.40688194221985	2		380	500	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371684	55371684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	81	795	1	ENST00000297316.4:c.374G>A	p.Arg125His	p.R125H	ENST00000297316	NM_022454.3	125	cGc/cAc	2/2	0.338363868557558	4	FACETS	0.989	0.872	1	0.33	0.29	0.372	CLONAL	1	TRUE	1	0.338363868557558	4		796	648	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466809	57466809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	26	282	0	ENST00000371085.3:c.28G>A	p.Glu10Lys	p.E10K	ENST00000371085	NM_000516.4	10	Gag/Aag	1/13	0.277618239438085	5	FACETS	0.807	0.641	0.997	0.269	0.213	0.333	CLONAL	1	TRUE	2	0.338363868557558	5		282	287	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852659	63852659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1349220963	NA	P-0052623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	55	718	1	ENST00000279873.7:c.3437C>T	p.Ala1146Val	p.A1146V	ENST00000279873	NM_032199.2	1146	gCg/gTg	10/10	0.297283174097052	3	FACETS	0.69	0.59	0.799	0.345	0.295	0.4	SUBCLONAL	1	TRUE	1	0.338363868557558	3		719	551	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65349101	65349101	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	55	676	0	ENST00000342505.4:c.64T>A	p.Ser22Thr	p.S22T	ENST00000342505	NM_002227.2	22	Tcc/Acc	3/25	0.297283174097052	3	FACETS	0.655	0.56	0.759	0.328	0.28	0.38	SUBCLONAL	1	TRUE	1	0.338363868557558	3		676	580	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915755	112915755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs535800148	NA	P-0052623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	67	478	0	ENST00000351677.2:c.1028G>A	p.Arg343Gln	p.R343Q	ENST00000351677	NM_002834.3	343	cGg/cAg	9/16	0.338363868557558	8	FACETS	0.78	0.676	0.894	0.13	0.112	0.149	SUBCLONAL	1	TRUE	2	0.338363868557558	8		478	1023	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669502	88669502	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	46	443	0	ENST00000360948.2:c.1396G>T	p.Gly466Cys	p.G466C	ENST00000360948	NM_001012338.2	466	Ggt/Tgt	12/19	0.28152160270003	3	FACETS	0.764	0.645	0.896	0.382	0.322	0.448	SUBCLONAL	1	TRUE	1	0.338363868557558	3		443	416	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323141	31323141	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	53	1235	0	ENST00000412585.2:c.848G>A	p.Cys283Tyr	p.C283Y	ENST00000412585	NM_005514.6	283	tGc/tAc	4/8	0.158718174424267	2	FACETS	0.414	0.352	0.483	0.207	0.176	0.242	INDETERMINATE	1	TRUE	0	0.338363868557558	2		1235	756	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0052734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	144	729	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.352514805025854	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.352514805025854	1		730	464	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012465	29012465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373801409	NA	P-0052734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	44	377	0	ENST00000282397.4:c.406G>A	p.Val136Ile	p.V136I	ENST00000282397	NM_002019.4	136	Gta/Ata	4/30	0.303860849404167	4	FACETS	0.622	0.521	0.734	0.207	0.173	0.245	SUBCLONAL	1	TRUE	1	0.352514805025854	4		377	543	SUCCESS
APC	324	MSKCC	GRCh37	5	112175225	112175225	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	27	211	0	ENST00000257430.4:c.3935del	p.Gly1312GlufsTer9	p.G1312Efs*9	ENST00000257430	NM_000038.5	1312	Gga/ga	16/16	1	2	FACETS	0.641	0.512	0.787	0.641	0.512	0.787	SUBCLONAL	1	TRUE	1	0.352514805025854	2		211	239	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968251	134968251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373797543	NA	P-0052734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	92	492	2	ENST00000398015.3:c.2764G>A	p.Ala922Thr	p.A922T	ENST00000398015	NM_004441.4	922	Gcc/Acc	15/16	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.352514805025854	2		494	389	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342776	118342776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781978595	NA	P-0052734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	25	284	0	ENST00000534358.1:c.902G>A	p.Arg301Gln	p.R301Q	ENST00000534358	NM_005933.3	301	cGa/cAa	3/36	1	2	FACETS	0.456	0.36	0.567	0.456	0.36	0.567	SUBCLONAL	1	TRUE	1	0.352514805025854	2		284	311	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14317388	14317388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782670869	NA	P-0052734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	86	316	2	ENST00000256196.4:c.122C>T	p.Thr41Met	p.T41M	ENST00000256196		41	aCg/aTg	2/6	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.352514805025854	2		318	425	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346256	89346256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760007187	NA	P-0052734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	33	298	0	ENST00000301030.4:c.6694C>T	p.Arg2232Cys	p.R2232C	ENST00000301030	NM_001256183.1	2232	Cgt/Tgt	9/13	1	2	FACETS	0.777	0.636	0.933	0.777	0.636	0.933	CLONAL	1	TRUE	1	0.352514805025854	2		298	241	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155682	119155682	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	46	323	0	ENST00000264033.4:c.1435G>T	p.Glu479Ter	p.E479*	ENST00000264033	NM_005188.3	479	Gaa/Taa	10/16	1	2	FACETS	0.731	0.618	0.855	0.731	0.618	0.855	SUBCLONAL	1	TRUE	1	0.352514805025854	2		323	357	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112893839	112893839	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	25	312	0	ENST00000351677.2:c.728T>C	p.Val243Ala	p.V243A	ENST00000351677	NM_002834.3	243	gTc/gCc	6/16	0.258204489342568	1	FACETS	0.321	0.253	0.4	0.321	0.253	0.4	SUBCLONAL	1	TRUE	0	0.352514805025854	1		312	364	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81927346	81927346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	40	515	0	ENST00000359376.3:c.1019C>T	p.Ser340Leu	p.S340L	ENST00000359376	NM_002661.3	340	tCg/tTg	12/33	1	2	FACETS	0.456	0.378	0.542	0.456	0.378	0.542	SUBCLONAL	1	TRUE	1	0.352514805025854	2		515	498	SUCCESS
APC	324	MSKCC	GRCh37	5	112175038	112175045	+	frameshift_variant	Frame_Shift_Del	DEL	CAAAGTTT	CAAAGTTT	-	novel	NA	P-0052734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	44	217	0	ENST00000257430.4:c.3748_3755del	p.Lys1250PhefsTer3	p.K1250Ffs*3	ENST00000257430	NM_000038.5	1249	tgCAAAGTTTct/tgct	16/16	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.352514805025854	2		217	217	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0052825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	76	428	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.286603089458082	2		428	521	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43739647	43739647	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	45	202	0	ENST00000382044.4:c.2753A>C	p.Asp918Ala	p.D918A	ENST00000382044	NM_001141980.1	918	gAt/gCt	13/28	0.286603089458082	1	FACETS	0.982	0.831	1	0.982	0.831	1	CLONAL	1	TRUE	0	0.286603089458082	1		202	274	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374881	45374881	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	72	380	0	ENST00000262160.6:c.962G>C	p.Arg321Pro	p.R321P	ENST00000262160	NM_005901.5	321	cGa/cCa	8/11	0.286603089458082	1	FACETS	0.806	0.705	0.914	0.806	0.705	0.914	CLONAL	1	TRUE	0	0.286603089458082	1		380	534	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861461	152861461	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0052825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	38	165	0	ENST00000406277.2:c.290+1G>C		p.X97_splice	ENST00000406277	NM_152274.4	97			1		FACETS		0.869	1				CLONAL	1	TRUE	1	0.286603089458082	2		165	252	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221161	5221161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs575201235	NA	P-0052843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	157	704	1	ENST00000357368.4:c.3305G>A	p.Arg1102His	p.R1102H	ENST00000357368	NM_002850.3	1102	cGc/cAc	20/38	0.120535523396621	5	FACETS	1	0.979	1	0.781	0.721	0.843	INDETERMINATE	2	TRUE	2	0.457087171062987	5		705	494	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347930	347930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141148118	NA	P-0052843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	224	780	0	ENST00000262320.3:c.1576G>A	p.Ala526Thr	p.A526T	ENST00000262320	NM_003502.3	526	Gcg/Acg	6/11	0.120535523396621	5	FACETS	1	0.983	1	0.765	0.715	0.816	INDETERMINATE	2	TRUE	2	0.457087171062987	5		780	720	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741837	17741837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199584989	NA	P-0052843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	50	188	1	ENST00000250003.3:c.508G>A	p.Ala170Thr	p.A170T	ENST00000250003	NM_002478.4	170	Gcg/Acg	1/3	0.160324247499042	3	FACETS	0.786	0.679	0.899	0.786	0.679	0.899	INDETERMINATE	2	TRUE	1	0.457087171062987	3		189	171	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979552	55979552	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368062574	NA	P-0052843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	186	593	0	ENST00000263923.4:c.895C>T	p.Arg299Trp	p.R299W	ENST00000263923	NM_002253.2	299	Cgg/Tgg	7/30	0.359853360927849	2	FACETS	1	0.99	1	0.728	0.677	0.78	CLONAL	1	TRUE	0	0.457087171062987	2		593	559	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535412	66535412	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	129	283	0	ENST00000273854.3:c.49G>A	p.Gly17Ser	p.G17S	ENST00000273854	NM_004439.5	17	Ggc/Agc	1/18	0.359853360927849	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.457087171062987	2		283	256	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609330	81609330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121908882	NA	P-0052843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	66	338	4	ENST00000298171.2:c.928C>T	p.Arg310Cys	p.R310C	ENST00000298171	NM_000369.2	310	Cgc/Tgc	10/10	0.331776236479385	3	FACETS	1	0.94	1	0.565	0.494	0.64	CLONAL	1	TRUE	1	0.457087171062987	3		342	314	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450120	32450120	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1372808262	NA	P-0052843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	79	669	0	ENST00000332351.3:c.692C>T	p.Thr231Met	p.T231M	ENST00000332351	NM_024426.4	231	aCg/aTg	2/10	0.160324247499042	3	FACETS	0.851	0.751	0.958	0.426	0.375	0.479	INDETERMINATE	1	TRUE	1	0.457087171062987	3		669	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577552	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0052843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	275	668	0	ENST00000269305.4:c.729_730delinsTT	p.Met243_Gly244delinsIleCys	p.M243_G244delinsIC	ENST00000269305	NM_001126112.2	243	atGGgc/atTTgc	7/11	0.41598328265999	3	FACETS	0.875	0.83	0.92	0.875	0.83	0.92	CLONAL	3	TRUE	0	0.457087171062987	3		668	563	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574424	95574424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	51	274	0	ENST00000393063.1:c.2443C>A	p.His815Asn	p.H815N	ENST00000393063	NM_030621.3	815	Cac/Aac	17/28	0.331776236479385	3	FACETS	1	0.933	1	0.576	0.494	0.664	CLONAL	1	TRUE	1	0.457087171062987	3		274	238	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55693389	55693389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374064960	NA	P-0052843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	72	726	1	ENST00000284073.2:c.596G>A	p.Arg199Gln	p.R199Q	ENST00000284073	NM_138962.2	199	cGg/cAg	9/14	0.41598328265999	3	FACETS	0.564	0.492	0.642	0.188	0.164	0.214	SUBCLONAL	1	TRUE	0	0.457087171062987	3		727	686	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946245	55946245	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243160272	NA	P-0052843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	58	382	0	ENST00000263923.4:c.3934G>A	p.Asp1312Asn	p.D1312N	ENST00000263923	NM_002253.2	1312	Gat/Aat	30/30	0.359853360927849	2	FACETS	0.793	0.686	0.908	0.397	0.343	0.454	CLONAL	1	TRUE	0	0.457087171062987	2		382	320	SUCCESS
APC	324	MSKCC	GRCh37	5	112162899	112162900	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0052843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	139	445	0	ENST00000257430.4:c.1504_1505dup	p.Met503GlufsTer4	p.M503Efs*4	ENST00000257430	NM_000038.5	501	-/GG	12/16	0.384912025065314	2	FACETS	1	0.987	1	0.714	0.656	0.774	CLONAL	1	TRUE	0	0.457087171062987	2		445	426	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056547	26056547	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	154	271	0	ENST00000343677.2:c.110G>T	p.Gly37Val	p.G37V	ENST00000343677	NM_005319.3	37	gGt/gTt	1/1	0.457087171062987	5	FACETS	1	0.974	1	0.825	0.767	0.884	CLONAL	3	TRUE	1	0.457087171062987	5		271	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0052847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	42	1045	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.483842784544057	5	FACETS	1	0.885	1	0.803	0.708	0.896	CLONAL	4	TRUE	0	0.514571079489443	5		1046	72	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81914540	81914540	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770601419	NA	P-0052847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	22	552	0	ENST00000359376.3:c.674C>T	p.Ser225Leu	p.S225L	ENST00000359376	NM_002661.3	225	tCg/tTg	8/33	1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	1	0.514571079489443	2		552	79	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0052848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	350	1045	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.368655824607117	2	FACETS	0.807	0.766	0.848	0.807	0.766	0.848	CLONAL	2	FALSE	0	0.452003493045444	2		1046	960	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0052848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	45	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.16019360214408	5	FACETS	0.491	0.412	0.58	0.164	0.137	0.194	INDETERMINATE	1	FALSE	2	0.452003493045444	5		326	680	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0052848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	258	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.295840138093176	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	FALSE	1	0.452003493045444	3		487	689	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	65	570	0	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	0.243847028300483	3	FACETS	0.422	0.365	0.485	0.141	0.121	0.162	INDETERMINATE	1	FALSE	0	0.452003493045444	3		570	835	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178641	108178641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775036118	NA	P-0052848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	33	0	0	ENST00000278616.4:c.5692C>T	p.Arg1898Ter	p.R1898*	ENST00000278616	NM_000051.3	1898	Cga/Tga	38/63	0.235018463854581	2	FACETS	0.416	0.339	0.502	0.208	0.169	0.251	INDETERMINATE	1	FALSE	0	0.452003493045444	2		0	351	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827886	40827886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201911869	NA	P-0052848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	69	0	0	ENST00000373198.4:c.2542G>A	p.Gly848Arg	p.G848R	ENST00000373198	NM_133170.3	848	Gga/Aga	17/32	0.452003493045444	4	FACETS	0.381	0.33	0.436			1	SUBCLONAL	1	FALSE	NA	0.452003493045444	4		0	1165	SUCCESS
APC	324	MSKCC	GRCh37	5	112175784	112175799	+	frameshift_variant	Frame_Shift_Del	DEL	ATGGATTTTCTTGTTC	ATGGATTTTCTTGTTC	-	novel	NA	P-0052848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	277	348	0	ENST00000257430.4:c.4495_4510del	p.Gly1499ProfsTer3	p.G1499Pfs*3	ENST00000257430	NM_000038.5	1498	gATGGATTTTCTTGTTCa/ga	16/16	0.452003493045444	4	FACETS	0.98	0.936	1	0.98	0.936	1	CLONAL	4	FALSE	0	0.452003493045444	4		348	454	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114917781	114917781	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	56	323	1	ENST00000543371.1:c.1271G>A	p.Gly424Glu	p.G424E	ENST00000543371	NM_001198531.1	424	gGa/gAa	12/14	0.31548871634784	3	FACETS	0.56	0.48	0.648	0.28	0.24	0.324	SUBCLONAL	1	FALSE	1	0.452003493045444	3		324	542	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0052848-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	242	1045	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.308629275951272	2	FACETS	0.923	0.867	0.98	0.923	0.867	0.98	CLONAL	2	TRUE	0	0.383967399415481	2		1046	683	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0052848-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	58	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.331983851021126	3	FACETS	0.744	0.64	0.857	0.372	0.32	0.429	SUBCLONAL	1	TRUE	1	0.383967399415481	3		326	484	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0052848-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	172	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.360340649831995	3	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	1	0.383967399415481	3		487	534	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052848-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	27	570	0	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	0.337160282696426	2	FACETS	0.282	0.223	0.349	0.141	0.111	0.175	SUBCLONAL	1	TRUE	0	0.383967399415481	2		570	499	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178641	108178641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775036118	NA	P-0052848-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	11	0	0	ENST00000278616.4:c.5692C>T	p.Arg1898Ter	p.R1898*	ENST00000278616	NM_000051.3	1898	Cga/Tga	38/63	0.331983851021126	3	FACETS	0.196	0.134	0.272	0.098	0.067	0.136	SUBCLONAL	1	TRUE	1	0.383967399415481	3		0	349	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827886	40827886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201911869	NA	P-0052848-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	27	0	0	ENST00000373198.4:c.2542G>A	p.Gly848Arg	p.G848R	ENST00000373198	NM_133170.3	848	Gga/Aga	17/32	0.383967399415481	5	FACETS	0.269	0.213	0.334			1	SUBCLONAL	1	TRUE	NA	0.383967399415481	5		0	823	SUCCESS
APC	324	MSKCC	GRCh37	5	112175784	112175799	+	frameshift_variant	Frame_Shift_Del	DEL	ATGGATTTTCTTGTTC	ATGGATTTTCTTGTTC	-	novel	NA	P-0052848-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	163	348	0	ENST00000257430.4:c.4495_4510del	p.Gly1499ProfsTer3	p.G1499Pfs*3	ENST00000257430	NM_000038.5	1498	gATGGATTTTCTTGTTCa/ga	16/16	0.383967399415481	3	FACETS	0.917	0.853	0.981	0.917	0.853	0.981	CLONAL	3	TRUE	0	0.383967399415481	3		348	368	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114917781	114917781	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052848-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	19	323	1	ENST00000543371.1:c.1271G>A	p.Gly424Glu	p.G424E	ENST00000543371	NM_001198531.1	424	gGa/gAa	12/14	1	2	FACETS	0.306	0.232	0.394	0.306	0.232	0.394	SUBCLONAL	1	TRUE	1	0.383967399415481	2		324	323	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196502	106196502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052848-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	35	375	0	ENST00000380013.4:c.4835C>T	p.Ser1612Phe	p.S1612F	ENST00000380013	NM_001127208.2	1612	tCt/tTt	11/11	0.337160282696426	2	FACETS	0.472	0.387	0.568	0.236	0.193	0.284	SUBCLONAL	1	TRUE	0	0.383967399415481	2		375	386	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0052851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	246	863	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.446461221113827	2	FACETS	0.952	0.897	1	0.952	0.897	1	CLONAL	2	TRUE	0	0.446461221113827	2		864	579	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0052851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	165	428	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.446461221113827	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	3	TRUE	0	0.446461221113827	3		428	294	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0052851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	24	168	0	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	0.446461221113827	3	FACETS	0.629	0.496	0.781			1	SUBCLONAL	1	TRUE	NA	0.446461221113827	3		168	209	SUCCESS
APC	324	MSKCC	GRCh37	5	112175561	112175561	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	81	364	0	ENST00000257430.4:c.4271del	p.Pro1424GlnfsTer49	p.P1424Qfs*49	ENST00000257430	NM_000038.5	1424	Cca/ca	16/16	0.20204023601777	5	FACETS	1	0.964	1	0.795	0.71	0.883	INDETERMINATE	2	TRUE	2	0.446461221113827	5		364	254	SUCCESS
APC	324	MSKCC	GRCh37	5	112173817	112173820	+	frameshift_variant	Frame_Shift_Del	DEL	TAGT	TAGT	-	rs879254091	NA	P-0052851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	63	371	0	ENST00000257430.4:c.2527_2530del	p.Ser843LeufsTer17	p.S843Lfs*17	ENST00000257430	NM_000038.5	842	gaTAGT/ga	16/16	0.20204023601777	5	FACETS	0.954	0.835	1	0.636	0.556	0.72	INDETERMINATE	2	TRUE	2	0.446461221113827	5		371	247	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046466	30046467	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0052851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	50	633	1	ENST00000331968.5:c.2716_2717delinsTT	p.Gly906Phe	p.G906F	ENST00000331968	NM_002742.2	906	GGt/TTt	18/18	0.441391158065171	3	FACETS	0.67	0.57	0.78	0.335	0.285	0.39	SUBCLONAL	1	TRUE	1	0.446461221113827	3		634	409	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250874	153250875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	142	331	0	ENST00000281708.4:c.1185dup	p.Ser396Ter	p.S396*	ENST00000281708	NM_033632.3	395	-/T	8/12	0.441391158065171	3	FACETS	1	0.963	1	1	0.991	1	CLONAL	3	TRUE	1	0.446461221113827	3		331	248	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0052883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	67	378	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.695	0.604	0.794	0.695	0.604	0.794	SUBCLONAL	1	FALSE	1	0.285979332996352	2		378	674	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0052883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	138	498	4	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.904	0.827	0.984	1	0.99	1	CLONAL	2	FALSE	1	0.285979332996352	2		502	534	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574502	41574502	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	83	653	0	ENST00000263253.7:c.6787C>T	p.Arg2263Ter	p.R2263*	ENST00000263253	NM_001429.3	2263	Cga/Tga	31/31	1	2	FACETS	0.862	0.761	0.971	0.862	0.761	0.971	CLONAL	1	FALSE	1	0.285979332996352	2		653	673	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924618	94924618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1400088899	NA	P-0052883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	104	450	1	ENST00000536441.1:c.292C>T	p.Arg98Cys	p.R98C	ENST00000536441	NM_144665.3	98	Cgc/Tgc	3/10	1	2	FACETS	0.841	0.752	0.935	0.841	0.752	0.935	CLONAL	1	FALSE	1	0.285979332996352	2		451	865	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885939	111885939	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	61	644	1	ENST00000341259.2:c.1566del	p.Glu523SerfsTer25	p.E523Sfs*25	ENST00000341259	NM_005475.2	521	Ccc/cc	8/8	1	2	FACETS	0.636	0.548	0.732	0.636	0.548	0.732	SUBCLONAL	1	FALSE	1	0.285979332996352	2		645	671	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821959	72821960	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762108866	NA	P-0052883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	46	360	1	ENST00000268489.5:c.10215dup	p.Gly3406ArgfsTer25	p.G3406Rfs*25	ENST00000268489	NM_006885.3	3405	-/C	10/10	1	2	FACETS	0.707	0.596	0.83	0.707	0.596	0.83	SUBCLONAL	1	FALSE	1	0.285979332996352	2		361	455	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427579	72427579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1424267110	NA	P-0052883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	44	269	1	ENST00000477973.2:c.911C>T	p.Thr304Met	p.T304M	ENST00000477973	NM_012234.5	304	aCg/aTg	4/4	1	2	FACETS	0.841	0.707	0.988	0.841	0.707	0.988	CLONAL	1	FALSE	1	0.285979332996352	2		270	366	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0052883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	44	269	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.649	0.544	0.765	0.649	0.544	0.765	SUBCLONAL	1	FALSE	1	0.285979332996352	2		269	474	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0052883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	77	783	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	1	2	FACETS	0.673	0.59	0.763	0.673	0.59	0.763	SUBCLONAL	1	FALSE	1	0.285979332996352	2		783	800	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659550	88659550	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0052883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	92	388	0	ENST00000372037.3:c.334-1G>T		p.X112_splice	ENST00000372037	NM_004329.2	112			1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	FALSE	1	0.285979332996352	2		388	637	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402537	20402537	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	48	386	0	ENST00000346618.3:c.74T>C	p.Val25Ala	p.V25A	ENST00000346618	NM_001949.4	25	gTc/gCc	1/7	1	2	FACETS	0.713	0.603	0.833	0.713	0.603	0.833	SUBCLONAL	1	FALSE	1	0.285979332996352	2		386	471	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795103	242795104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768249210	NA	P-0052883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	49	759	2	ENST00000334409.5:c.105dup	p.Thr36HisfsTer70	p.T36Hfs*70	ENST00000334409	NM_005018.2	35	-/C	2/5	0.285979332996352	1	FACETS	0.387	0.327	0.454	0.387	0.327	0.454	SUBCLONAL	1	FALSE	0	0.285979332996352	1		761	759	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0052883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	113	651	10	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.285979332996352	2		661	703	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647028	23647028	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1555461597	NA	P-0052883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	104	502	0	ENST00000261584.4:c.839del	p.Asn280ThrfsTer8	p.N280Tfs*8	ENST00000261584	NM_024675.3	280	aAc/ac	4/13	1	2	FACETS	0.798	0.713	0.887	0.798	0.713	0.887	SUBCLONAL	1	FALSE	1	0.285979332996352	2		502	912	SUCCESS
APC	324	MSKCC	GRCh37	5	112170768	112170769	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0052883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	107	500	0	ENST00000257430.4:c.1865dup	p.Tyr622Ter	p.Y622*	ENST00000257430	NM_000038.5	622	tac/tAac	15/16	1	2	FACETS	0.868	0.778	0.964	0.868	0.778	0.964	CLONAL	1	FALSE	1	0.285979332996352	2		500	862	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290271	15290271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140147764	NA	P-0052883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	96	658	0	ENST00000263388.2:c.3364G>A	p.Asp1122Asn	p.D1122N	ENST00000263388	NM_000435.2	1122	Gac/Aac	21/33	1	2	FACETS	0.787	0.7	0.88	0.787	0.7	0.88	SUBCLONAL	1	FALSE	1	0.285979332996352	2		658	853	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	75	800	2	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.618	0.54	0.702	0.618	0.54	0.702	SUBCLONAL	1	FALSE	1	0.285979332996352	2		802	849	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066695	94066695	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	78	412	1	ENST00000369303.4:c.1064C>T	p.Ala355Val	p.A355V	ENST00000369303	NM_004440.3	355	gCa/gTa	5/17	1	2	FACETS	0.785	0.689	0.888	0.785	0.689	0.888	SUBCLONAL	1	FALSE	1	0.285979332996352	2		413	695	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797749	32797749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753393321	NA	P-0052883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	44	553	0	ENST00000374899.4:c.1753G>A	p.Ala585Thr	p.A585T	ENST00000374899	NM_018833.2	585	Gca/Aca	10/12	1	2	FACETS	0.357	0.298	0.422	0.357	0.298	0.422	SUBCLONAL	1	FALSE	1	0.285979332996352	2		553	863	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872936	136872936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	63	323	0	ENST00000241393.3:c.562C>T	p.Arg188Cys	p.R188C	ENST00000241393	NM_003467.2	188	Cgc/Tgc	2/2	1	2	FACETS	0.874	0.757	1	0.874	0.757	1	CLONAL	1	FALSE	1	0.285979332996352	2		323	504	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805787	32805788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1174402903	NA	P-0052883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	104	773	1	ENST00000374899.4:c.223dup	p.Leu75ProfsTer92	p.L75Pfs*92	ENST00000374899	NM_018833.2	75	ctg/cCtg	2/12	1	2	FACETS	0.815	0.729	0.907	0.815	0.729	0.907	CLONAL	1	FALSE	1	0.285979332996352	2		774	892	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797191	42797191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778202	NA	P-0052883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	116	948	1	ENST00000575354.2:c.3553G>A	p.Ala1185Thr	p.A1185T	ENST00000575354	NM_015125.3	1185	Gcc/Acc	15/20	1	2	FACETS	0.86	0.774	0.951	0.86	0.774	0.951	CLONAL	1	FALSE	1	0.285979332996352	2		949	943	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342917	118342917	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	44	241	0	ENST00000534358.1:c.1043T>C	p.Val348Ala	p.V348A	ENST00000534358	NM_005933.3	348	gTc/gCc	3/36	1	2	FACETS	0.731	0.614	0.86	0.731	0.614	0.86	SUBCLONAL	1	FALSE	1	0.285979332996352	2		241	421	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656567	3656567	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762475814	NA	P-0052883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	110	713	0	ENST00000294008.3:c.668G>A	p.Arg223His	p.R223H	ENST00000294008	NM_032444.2	223	cGt/cAt	3/15	1	2	FACETS	0.76	0.682	0.844	0.76	0.682	0.844	SUBCLONAL	1	FALSE	1	0.285979332996352	2		713	1012	SUCCESS
APC	324	MSKCC	GRCh37	5	112111328	112111328	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	35	143	0	ENST00000257430.4:c.425C>A	p.Ser142Ter	p.S142*	ENST00000257430	NM_000038.5	142	tCa/tAa	5/16	1	2	FACETS	0.96	0.791	1	0.96	0.791	1	CLONAL	1	FALSE	1	0.285979332996352	2		143	255	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274124	10274124	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	83	619	0	ENST00000330684.3:c.145C>T	p.Arg49Cys	p.R49C	ENST00000330684	NM_001134407.1	49	Cgc/Tgc	2/13	1	2	FACETS	0.9	0.795	1	0.9	0.795	1	CLONAL	1	FALSE	1	0.285979332996352	2		619	645	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980340	7980340	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	71	573	0	ENST00000319144.4:c.1243A>G	p.Arg415Gly	p.R415G	ENST00000319144	NM_001139.2	415	Agg/Ggg	9/15	1	2	FACETS	0.782	0.682	0.889	0.782	0.682	0.889	SUBCLONAL	1	FALSE	1	0.285979332996352	2		573	635	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223425	36223425	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	112	975	2	ENST00000222270.7:c.5975A>T	p.Asp1992Val	p.D1992V	ENST00000222270	NM_014727.1	1992	gAc/gTc	28/37	1	2	FACETS	0.824	0.74	0.913	0.824	0.74	0.913	CLONAL	1	FALSE	1	0.285979332996352	2		977	951	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797776	42797776	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	93	715	0	ENST00000575354.2:c.3828G>A	p.Trp1276Ter	p.W1276*	ENST00000575354	NM_015125.3	1276	tgG/tgA	16/20	1	2	FACETS	0.769	0.683	0.861	0.769	0.683	0.861	SUBCLONAL	1	FALSE	1	0.285979332996352	2		715	846	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160431	99160431	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	99	438	0	ENST00000074304.5:c.910A>G	p.Thr304Ala	p.T304A	ENST00000074304	NM_001134224.1	304	Aca/Gca	11/26	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	FALSE	1	0.285979332996352	2		438	649	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940022	49940022	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	110	737	0	ENST00000296474.3:c.1021G>T	p.Glu341Ter	p.E341*	ENST00000296474	NM_002447.2	341	Gag/Tag	1/20	0.234722820464834	2	FACETS	0.831	0.745	0.921	0.415	0.372	0.461	CLONAL	1	FALSE	0	0.285979332996352	2		737	926	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31495403	31495403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780163067	NA	P-0052883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	71	384	0	ENST00000344624.3:c.1745C>T	p.Thr582Met	p.T582M	ENST00000344624		582	aCg/aTg	9/33	1	2	FACETS	0.711	0.62	0.81	0.711	0.62	0.81	SUBCLONAL	1	FALSE	1	0.285979332996352	2		384	698	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058537	69058537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372345316	NA	P-0052883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	99	486	0	ENST00000288368.4:c.4181G>A	p.Arg1394Gln	p.R1394Q	ENST00000288368	NM_024870.2	1394	cGg/cAg	34/40	1	2	FACETS	0.756	0.674	0.844	0.756	0.674	0.844	SUBCLONAL	1	FALSE	1	0.285979332996352	2		486	916	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	92	466	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.943	0.839	1	0.943	0.839	1	CLONAL	1	TRUE	1	0.32	2		466	610	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	77	459	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	0.903	0.794	1	0.903	0.794	1	CLONAL	1	TRUE	1	0.32	2		459	533	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589618	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519838	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	38	214	0	ENST00000274335.5:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000274335		461	Cga/Tga	10/15	1	2	FACETS	0.578	0.478	0.689	0.578	0.478	0.689	SUBCLONAL	1	TRUE	1	0.32	2		214	411	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	62	383	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.859	0.744	0.984	0.859	0.744	0.984	CLONAL	1	TRUE	1	0.32	2		383	451	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	59	364	1	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	0.736	0.634	0.847	0.736	0.634	0.847	SUBCLONAL	1	TRUE	1	0.32	2		365	501	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742826	17742826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	64	874	0	ENST00000250003.3:c.734C>T	p.Ala245Val	p.A245V	ENST00000250003	NM_002478.4	245	gCg/gTg	3/3	1	2	FACETS	0.424	0.366	0.488	0.424	0.366	0.488	SUBCLONAL	1	TRUE	1	0.32	2		874	943	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380283	25380283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913528	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	73	430	0	ENST00000311936.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000311936	NM_004985.3	59	Gca/Aca	3/5	1	2	FACETS	0.666	0.582	0.757	0.666	0.582	0.757	SUBCLONAL	1	TRUE	1	0.32	2		430	685	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	119	756	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.832	0.75	0.918	0.832	0.75	0.918	CLONAL	1	TRUE	1	0.32	2		756	894	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003767	45003767	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	68	614	2	ENST00000558401.1:c.23C>A	p.Ala8Asp	p.A8D	ENST00000558401	NM_004048.2	8	gCt/gAt	1/4	1	2	FACETS	0.556	0.482	0.635	0.556	0.482	0.635	SUBCLONAL	1	TRUE	1	0.32	2		616	765	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	35	468	2	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	1	2	FACETS	0.508	0.416	0.61	0.508	0.416	0.61	SUBCLONAL	1	TRUE	1	0.32	2		470	431	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	100	483	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	1	2	FACETS	0.826	0.737	0.919	0.826	0.737	0.919	CLONAL	1	TRUE	1	0.32	2		483	757	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412110	63412110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852216	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	153	437	0	ENST00000330258.3:c.1057C>T	p.Arg353Ter	p.R353*	ENST00000330258	NM_152424.3	353	Cga/Tga	2/2	1	1	FACETS	0.86	0.793	0.928	1	0.991	1	CLONAL	2	TRUE	0	0.32	1		437	467	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720661	89720661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs142420551	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	92	352	0	ENST00000371953.3:c.812T>C	p.Phe271Ser	p.F271S	ENST00000371953	NM_000314.4	271	tTt/tCt	8/9	1	2	FACETS	0.893	0.794	0.998	0.893	0.794	0.998	CLONAL	1	TRUE	1	0.32	2		352	644	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543650	148543650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768812143	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	81	339	0	ENST00000320356.2:c.158C>T	p.Thr53Met	p.T53M	ENST00000320356	NM_004456.4	53	aCg/aTg	3/20	1	2	FACETS	0.786	0.693	0.886	0.786	0.693	0.886	SUBCLONAL	1	TRUE	1	0.32	2		339	644	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250089	53250089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	88	264	0	ENST00000375401.3:c.160C>T	p.Pro54Ser	p.P54S	ENST00000375401	NM_004187.3	54	Cca/Tca	2/26	1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.32	1		264	315	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828772	3828772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	50	566	0	ENST00000262367.5:c.1870C>T	p.Arg624Cys	p.R624C	ENST00000262367	NM_004380.2	624	Cgc/Tgc	9/31	1	2	FACETS	0.375	0.317	0.439	0.375	0.317	0.439	SUBCLONAL	1	TRUE	1	0.32	2		566	834	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222982	5222982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201435229	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	95	596	1	ENST00000357368.4:c.2821G>A	p.Ala941Thr	p.A941T	ENST00000357368	NM_002850.3	941	Gcc/Acc	18/38	1	2	FACETS	0.793	0.706	0.886	0.793	0.706	0.886	SUBCLONAL	1	TRUE	1	0.32	2		597	749	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720711	89720712	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	45	189	0	ENST00000371953.3:c.867dup	p.Val290SerfsTer8	p.V290Sfs*8	ENST00000371953	NM_000314.4	288	gaa/gAaa	8/9	1	2	FACETS	0.822	0.694	0.964	0.822	0.694	0.964	CLONAL	1	TRUE	1	0.32	2		189	342	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244875	46244875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758368727	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	107	501	0	ENST00000334344.6:c.2969C>T	p.Ser990Leu	p.S990L	ENST00000334344	NM_152641.2	990	tCg/tTg	15/21	1	2	FACETS	0.893	0.801	0.99	0.893	0.801	0.99	CLONAL	1	TRUE	1	0.32	2		501	749	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254872	16254872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761290842	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	99	468	0	ENST00000375759.3:c.2137C>T	p.Arg713Trp	p.R713W	ENST00000375759	NM_015001.2	713	Cgg/Tgg	11/15	1	2	FACETS	0.901	0.805	1	0.901	0.805	1	CLONAL	1	TRUE	1	0.32	2		468	687	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202283	133202283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764457707	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	167	826	0	ENST00000320574.5:c.6605C>T	p.Thr2202Met	p.T2202M	ENST00000320574	NM_006231.2	2202	aCg/aTg	47/49	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.32	2		826	1037	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235926	133235926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768950975	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	129	726	1	ENST00000320574.5:c.3230G>A	p.Arg1077His	p.R1077H	ENST00000320574	NM_006231.2	1077	cGc/cAc	26/49	1	2	FACETS	0.952	0.863	1	0.952	0.863	1	CLONAL	1	TRUE	1	0.32	2		727	847	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534270	534270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	51	741	3	ENST00000451590.1:c.53C>T	p.Ala18Val	p.A18V	ENST00000451590	NM_001130442.1	18	gCg/gTg	2/5	1	2	FACETS	0.342	0.289	0.4	0.342	0.289	0.4	SUBCLONAL	1	TRUE	1	0.32	2		744	932	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877349	40877349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747289224	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	83	499	0	ENST00000373198.4:c.2347G>A	p.Val783Met	p.V783M	ENST00000373198	NM_133170.3	783	Gtg/Atg	15/32	0.3	1	FACETS	0.678	0.598	0.763	0.678	0.598	0.763	SUBCLONAL	1	TRUE	0	0.32	1		499	643	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953156	81953156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381167403	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	63	334	0	ENST00000359376.3:c.2122G>A	p.Ala708Thr	p.A708T	ENST00000359376	NM_002661.3	708	Gcc/Acc	20/33	1	2	FACETS	0.769	0.666	0.881	0.769	0.666	0.881	SUBCLONAL	1	TRUE	1	0.32	2		334	512	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190746	11190746	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs563143860	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	132	805	0	ENST00000361445.4:c.5453G>A	p.Arg1818His	p.R1818H	ENST00000361445	NM_004958.3	1818	cGt/cAt	39/58	1	2	FACETS	0.849	0.77	0.932	0.849	0.77	0.932	CLONAL	1	TRUE	1	0.32	2		805	972	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40476777	40476777	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	69	614	2	ENST00000264657.5:c.1552C>T	p.Arg518Ter	p.R518*	ENST00000264657	NM_139276.2	518	Cga/Tga	17/24	1	2	FACETS	0.517	0.449	0.591	0.517	0.449	0.591	SUBCLONAL	1	TRUE	1	0.32	2		616	834	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95563044	95563044	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	62	256	0	ENST00000393063.1:c.4213G>T	p.Asp1405Tyr	p.D1405Y	ENST00000393063	NM_030621.3	1405	Gac/Tac	24/28	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.32	2		256	371	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859766	151859767	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	81	428	0	ENST00000262189.6:c.10895dup	p.Pro3633ThrfsTer19	p.P3633Tfs*19	ENST00000262189	NM_170606.2	3632	cca/ccCa	43/59	1	2	FACETS	0.936	0.826	1	0.936	0.826	1	CLONAL	1	TRUE	1	0.32	2		428	541	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793208	139793208	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561210418	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	155	682	0	ENST00000247668.2:c.16G>A	p.Val6Met	p.V6M	ENST00000247668	NM_021138.3	6	Gtg/Atg	2/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.32	2		682	912	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676267	37676267	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	141	539	1	ENST00000447079.4:c.3022C>T	p.Arg1008Trp	p.R1008W	ENST00000447079	NM_015083.1	1008	Cgg/Tgg	11/14	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.32	2		540	783	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753452	42753452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	192	963	0	ENST00000222329.4:c.812C>T	p.Thr271Met	p.T271M	ENST00000222329	NM_006494.2	271	aCg/aTg	4/4	1	2	FACETS	0.964	0.89	1	0.964	0.89	1	CLONAL	1	TRUE	1	0.32	2		963	1245	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905891	50905891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755550936	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	191	1059	2	ENST00000440232.2:c.863C>T	p.Ala288Val	p.A288V	ENST00000440232	NM_002691.3	288	gCg/gTg	8/27	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.32	2		1061	1172	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456504	32456504	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	24	156	0	ENST00000332351.3:c.388C>A	p.Pro130Thr	p.P130T	ENST00000332351	NM_024426.4	130	Cca/Aca	1/10	1	2	FACETS	0.664	0.523	0.825	0.664	0.523	0.825	SUBCLONAL	1	TRUE	1	0.32	2		156	226	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323214	31323214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	105	691	0	ENST00000412585.2:c.775C>T	p.Pro259Ser	p.P259S	ENST00000412585	NM_005514.6	259	Cca/Tca	4/8	1	2	FACETS	0.705	0.631	0.784	0.705	0.631	0.784	SUBCLONAL	1	TRUE	1	0.32	2		691	931	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120805842	120805842	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	101	921	3	ENST00000257552.2:c.236C>T	p.Ala79Val	p.A79V	ENST00000257552	NM_002442.3	79	gCg/gTg	4/15	1	2	FACETS	0.615	0.549	0.686	0.615	0.549	0.686	SUBCLONAL	1	TRUE	1	0.32	2		924	1026	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422892	49422892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751383638	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	158	779	1	ENST00000301067.7:c.14203C>T	p.Arg4735Trp	p.R4735W	ENST00000301067	NM_003482.3	4735	Cgg/Tgg	44/54	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.32	2		780	960	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428251	33428251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150134822	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	63	619	0	ENST00000345365.6:c.872G>A	p.Arg291His	p.R291H	ENST00000345365	NM_002878.3	291	cGc/cAc	9/10	1	2	FACETS	0.565	0.488	0.649	0.565	0.488	0.649	SUBCLONAL	1	TRUE	1	0.32	2		619	697	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396760	139396760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	157	850	0	ENST00000277541.6:c.5348G>A	p.Arg1783Gln	p.R1783Q	ENST00000277541	NM_017617.3	1783	cGg/cAg	28/34	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.32	2		850	969	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045569	47045569	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1396222722	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	147	364	0	ENST00000377604.3:c.2536G>A	p.Val846Ile	p.V846I	ENST00000377604	NM_001204468.1	846	Gta/Ata	22/24	1	1	FACETS	0.846	0.779	0.915	1	0.99	1	CLONAL	2	TRUE	0	0.32	1		364	456	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748014	72748014	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1364690756	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	67	688	0	ENST00000357731.5:c.164C>T	p.Thr55Met	p.T55M	ENST00000357731	NM_173808.2	55	aCg/aTg	1/7	1	2	FACETS	0.523	0.453	0.598	0.523	0.453	0.598	SUBCLONAL	1	TRUE	1	0.32	2		688	801	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765164	+	missense_variant	Missense_Mutation	ONP	AGCA	AGCA	TGCT	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	41	177	1	ENST00000374690.3:c.173_176inv	p.Gln58_Gln59delinsLeuLeu	p.Q58_Q59delinsLL	ENST00000374690	NM_000044.3	58	cAGCAg/cTGCTg	1/8	1	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.32	1		178	184	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255013	16255013	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	76	409	0	ENST00000375759.3:c.2278T>G	p.Ser760Ala	p.S760A	ENST00000375759	NM_015001.2	760	Tca/Gca	11/15	1	2	FACETS	0.872	0.766	0.985	0.872	0.766	0.985	CLONAL	1	TRUE	1	0.32	2		409	545	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70412337	70412337	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	38	272	0	ENST00000373644.4:c.4447C>A	p.Pro1483Thr	p.P1483T	ENST00000373644	NM_030625.2	1483	Cca/Aca	6/12	1	2	FACETS	0.513	0.424	0.613	0.513	0.424	0.613	SUBCLONAL	1	TRUE	1	0.32	2		272	463	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481880	56481880	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	133	687	0	ENST00000267101.3:c.808T>C	p.Phe270Leu	p.F270L	ENST00000267101	NM_001982.3	270	Ttc/Ctc	7/28	1	2	FACETS	0.988	0.898	1	0.988	0.898	1	CLONAL	1	TRUE	1	0.32	2		687	841	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123892068	123892068	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	79	348	1	ENST00000330479.4:c.877C>A	p.Leu293Ile	p.L293I	ENST00000330479	NM_020382.3	293	Cta/Ata	8/9	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.32	2		349	484	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249215	133249215	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs990959129	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	127	526	0	ENST00000320574.5:c.1684A>G	p.Met562Val	p.M562V	ENST00000320574	NM_006231.2	562	Atg/Gtg	15/49	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.32	2		526	682	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249750	133249750	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	60	417	0	ENST00000320574.5:c.1473G>T	p.Glu491Asp	p.E491D	ENST00000320574	NM_006231.2	491	gaG/gaT	14/49	1	2	FACETS	0.668	0.576	0.769	0.668	0.576	0.769	SUBCLONAL	1	TRUE	1	0.32	2		417	561	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38641680	38641680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376699107	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	87	409	0	ENST00000299084.4:c.640C>T	p.Arg214Trp	p.R214W	ENST00000299084	NM_152594.2	214	Cgg/Tgg	6/7	1	2	FACETS	0.859	0.761	0.963	0.859	0.761	0.963	CLONAL	1	TRUE	1	0.32	2		409	633	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640823	3640823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768474876	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	161	854	3	ENST00000294008.3:c.2816G>A	p.Arg939Gln	p.R939Q	ENST00000294008	NM_032444.2	939	cGg/cAg	12/15	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.32	2		857	955	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655402	67655402	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	114	535	1	ENST00000264010.4:c.1265T>C	p.Met422Thr	p.M422T	ENST00000264010	NM_006565.3	422	aTg/aCg	7/12	1	2	FACETS	0.995	0.897	1	0.995	0.897	1	CLONAL	1	TRUE	1	0.32	2		536	716	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842382	68842382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	76	539	0	ENST00000261769.5:c.443G>A	p.Gly148Asp	p.G148D	ENST00000261769	NM_004360.3	148	gGc/gAc	4/16	1	2	FACETS	0.714	0.626	0.809	0.714	0.626	0.809	SUBCLONAL	1	TRUE	1	0.32	2		539	665	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883790	37883790	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	122	883	0	ENST00000269571.5:c.3406del	p.Gln1136SerfsTer5	p.Q1136Sfs*5	ENST00000269571		1134	agC/ag	26/27	1	2	FACETS	0.72	0.649	0.795	0.72	0.649	0.795	SUBCLONAL	1	TRUE	1	0.32	2		883	1059	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475069	40475069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	151	632	1	ENST00000264657.5:c.1841G>A	p.Ser614Asn	p.S614N	ENST00000264657	NM_139276.2	614	aGc/aAc	20/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.32	2		633	843	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250965	10250965	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	142	740	0	ENST00000340748.4:c.3515C>A	p.Pro1172His	p.P1172H	ENST00000340748		1172	cCt/cAt	32/40	1	2	FACETS	0.974	0.887	1	0.974	0.887	1	CLONAL	1	TRUE	1	0.32	2		740	911	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967066	18967066	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	166	823	0	ENST00000262803.5:c.1781G>T	p.Arg594Leu	p.R594L	ENST00000262803	NM_002911.3	594	cGg/cTg	13/24	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.32	2		823	1024	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139037	50139037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775719606	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	96	861	1	ENST00000246792.3:c.526C>T	p.Arg176Cys	p.R176C	ENST00000246792	NM_006270.3	176	Cgt/Tgt	5/6	1	2	FACETS	0.576	0.512	0.645	0.576	0.512	0.645	SUBCLONAL	1	TRUE	1	0.32	2		862	1041	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909557	50909557	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1004124075	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	126	848	4	ENST00000440232.2:c.1361G>A	p.Arg454His	p.R454H	ENST00000440232	NM_002691.3	454	cGc/cAc	11/27	1	2	FACETS	0.845	0.764	0.93	0.845	0.764	0.93	CLONAL	1	TRUE	1	0.32	2		852	932	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027202	48027202	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587779228	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	81	461	0	ENST00000234420.5:c.2080T>C	p.Cys694Arg	p.C694R	ENST00000234420	NM_000179.2	694	Tgc/Cgc	4/10	1	2	FACETS	0.919	0.811	1	0.919	0.811	1	CLONAL	1	TRUE	1	0.32	2		461	551	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660915	227660915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	181	817	0	ENST00000305123.5:c.2540C>T	p.Thr847Ile	p.T847I	ENST00000305123	NM_005544.2	847	aCa/aTa	1/2	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.32	2		817	1015	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62293946	62293946	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	73	830	0	ENST00000360203.5:c.443C>A	p.Pro148His	p.P148H	ENST00000360203	NM_001283009.1	148	cCt/cAt	5/35	1	2	FACETS	0.452	0.394	0.515	0.452	0.394	0.515	SUBCLONAL	1	TRUE	1	0.32	2		830	1010	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275306	142275306	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	38	484	0	ENST00000350721.4:c.1997T>C	p.Val666Ala	p.V666A	ENST00000350721	NM_001184.3	666	gTa/gCa	9/47	1	2	FACETS	0.331	0.272	0.396	0.331	0.272	0.396	SUBCLONAL	1	TRUE	1	0.32	2		484	718	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541108	187541108	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	84	339	0	ENST00000441802.2:c.6632G>A	p.Gly2211Asp	p.G2211D	ENST00000441802	NM_005245.3	2211	gGc/gAc	10/27	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.32	2		339	525	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522772	67522772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1402146204	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	31	257	0	ENST00000274335.5:c.269G>A	p.Arg90Gln	p.R90Q	ENST00000274335		90	cGg/cAg	1/15	1	2	FACETS	0.511	0.413	0.622	0.511	0.413	0.622	SUBCLONAL	1	TRUE	1	0.32	2		257	379	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188559	32188559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1363046520	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	124	802	0	ENST00000375023.3:c.896C>T	p.Thr299Ile	p.T299I	ENST00000375023	NM_004557.3	299	aCc/aTc	5/30	1	2	FACETS	0.837	0.756	0.922	0.837	0.756	0.922	CLONAL	1	TRUE	1	0.32	2		802	926	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984050	2984050	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	75	579	0	ENST00000396946.4:c.480G>T	p.Glu160Asp	p.E160D	ENST00000396946	NM_032415.4	160	gaG/gaT	5/25	0.3	1	FACETS	0.553	0.484	0.627	0.553	0.484	0.627	SUBCLONAL	1	TRUE	0	0.32	1		579	712	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389293	8389293	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	84	516	0	ENST00000356435.5:c.4325T>A	p.Met1442Lys	p.M1442K	ENST00000356435		1442	aTg/aAg	26/35	1	2	FACETS	0.751	0.663	0.845	0.751	0.663	0.845	SUBCLONAL	1	TRUE	1	0.32	2		516	699	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606239	93606239	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	76	821	0	ENST00000375746.1:c.59T>A	p.Ile20Asn	p.I20N	ENST00000375746	NM_001174167.1	20	aTc/aAc	2/14	1	2	FACETS	0.479	0.419	0.544	0.479	0.419	0.544	SUBCLONAL	1	TRUE	1	0.32	2		821	991	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738422	133738422	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	46	413	0	ENST00000318560.5:c.822G>T	p.Lys274Asn	p.K274N	ENST00000318560	NM_005157.4	274	aaG/aaT	4/11	1	2	FACETS	0.545	0.458	0.64	0.545	0.458	0.64	SUBCLONAL	1	TRUE	1	0.32	2		413	528	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759589	133759589	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs151335502	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	96	896	1	ENST00000318560.5:c.1912G>T	p.Gly638Cys	p.G638C	ENST00000318560	NM_005157.4	638	Ggc/Tgc	11/11	1	2	FACETS	0.559	0.496	0.625	0.559	0.496	0.625	SUBCLONAL	1	TRUE	1	0.32	2		897	1074	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401769	139401769	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766644919	NA	P-0052886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	113	893	0	ENST00000277541.6:c.3631C>T	p.Arg1211Trp	p.R1211W	ENST00000277541	NM_017617.3	1211	Cgg/Tgg	22/34	1	2	FACETS	0.613	0.55	0.68	0.613	0.55	0.68	SUBCLONAL	1	TRUE	1	0.32	2		893	1152	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0052887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	61	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.182092780043092	2		487	597	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0052887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	56	483	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.16019249560365	2	FACETS	1	0.931	1	0.575	0.493	0.665	CLONAL	1	TRUE	0	0.182092780043092	2		483	535	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0052887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	53	165	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.182092780043092	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	2	TRUE	0	0.182092780043092	2		165	272	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250883	153250883	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	27	276	2	ENST00000281708.4:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000281708	NM_033632.3	393	Cga/Tga	8/12	1	2	FACETS	0.615	0.489	0.761	0.615	0.489	0.761	SUBCLONAL	1	TRUE	1	0.182092780043092	2		278	482	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	32	226	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.182092780043092	2		226	334	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047135	77047135	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	53	385	1	ENST00000356341.3:c.1409T>A	p.Leu470Gln	p.L470Q	ENST00000356341	NM_002576.4	470	cTg/cAg	13/15	1	2	FACETS	0.961	0.819	1	0.961	0.819	1	CLONAL	1	TRUE	1	0.182092780043092	2		386	606	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912188	114912188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	69	456	0	ENST00000543371.1:c.1258C>T	p.Arg420Trp	p.R420W	ENST00000543371	NM_001198531.1	420	Cgg/Tgg	11/14	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.182092780043092	2		456	635	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2137898	2137898	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	187	761	0	ENST00000219476.3:c.5024C>G	p.Pro1675Arg	p.P1675R	ENST00000219476	NM_000548.3	1675	cCg/cGg	39/42	0.182092780043092	2	FACETS	0.955	0.882	1	0.955	0.882	1	CLONAL	2	TRUE	0	0.182092780043092	2		761	1075	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578207	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0052887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	97	562	0	ENST00000269305.4:c.642_643del	p.His214GlnfsTer7	p.H214Qfs*7	ENST00000269305	NM_001126112.2	214	caTAgt/cagt	6/11	0.16019249560365	2	FACETS	1	0.978	1	0.713	0.636	0.796	CLONAL	1	TRUE	0	0.182092780043092	2		562	747	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164805	106164805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	66	407	0	ENST00000380013.4:c.3673G>A	p.Val1225Met	p.V1225M	ENST00000380013	NM_001127208.2	1225	Gtg/Atg	6/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.182092780043092	2		407	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0052888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	294	835	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.327154542514178	2	FACETS	0.937	0.888	0.986	0.937	0.888	0.986	CLONAL	2	TRUE	0	0.456090517991063	2		835	688	SUCCESS
APC	324	MSKCC	GRCh37	5	112173847	112173848	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0052888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	96	214	0	ENST00000257430.4:c.2563_2564dup	p.Arg856AsnfsTer6	p.R856Nfs*6	ENST00000257430	NM_000038.5	852	-/GA	16/16	0.456090517991063	3	FACETS	1	0.981	1	0.722	0.649	0.798	CLONAL	1	TRUE	1	0.456090517991063	3		214	358	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114901003	114901004	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGAC	novel	NA	P-0052888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	201	491	0	ENST00000543371.1:c.615_616insACCG	p.Tyr206ThrfsTer5	p.Y206Tfs*5	ENST00000543371	NM_001198531.1	205	acg/aCGACcg	6/14	0.456090517991063	3	FACETS	0.81	0.754	0.868	0.81	0.754	0.868	CLONAL	2	TRUE	1	0.456090517991063	3		491	668	SUCCESS
APC	324	MSKCC	GRCh37	5	112175422	112175423	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0052888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	46	222	0	ENST00000257430.4:c.4131_4132del	p.Gln1378GlyfsTer7	p.Q1378Gfs*7	ENST00000257430	NM_000038.5	1377	gtTCag/gtag	16/16	0.456090517991063	3	FACETS	0.767	0.649	0.896	0.383	0.324	0.448	SUBCLONAL	1	TRUE	1	0.456090517991063	3		222	323	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624434	140624434	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	25	83	0	ENST00000288602.6:c.70G>C	p.Glu24Gln	p.E24Q	ENST00000288602	NM_004333.4	24	Gag/Cag	1/18	0.43337407936591	5	FACETS	1	0.818	1	0.344	0.273	0.424	CLONAL	1	TRUE	2	0.456090517991063	5		83	179	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0052889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	43	252	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.214494777141491	3	FACETS	0.847	0.71	0.997	0.423	0.355	0.499	CLONAL	1	FALSE	1	0.303082916911795	3		252	386	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863224499	NA	P-0052889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	195	597	0	ENST00000269305.4:c.672+1G>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.215632589376618	2	FACETS	0.753	0.698	0.811	0.753	0.698	0.811	SUBCLONAL	2	FALSE	0	0.303082916911795	2		597	854	SUCCESS
APC	324	MSKCC	GRCh37	5	112173387	112173387	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1060503336	NA	P-0052889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	92	221	0	ENST00000257430.4:c.2096G>A	p.Trp699Ter	p.W699*	ENST00000257430	NM_000038.5	699	tGg/tAg	16/16	0.214494777141491	3	FACETS	0.789	0.705	0.878	0.789	0.705	0.878	SUBCLONAL	2	FALSE	1	0.303082916911795	3		221	443	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740765	58740765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201236946	NA	P-0052889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	168	426	1	ENST00000305921.3:c.1670G>A	p.Arg557Gln	p.R557Q	ENST00000305921	NM_003620.3	557	cGa/cAa	6/6	0.216786356530367	4	FACETS	0.833	0.766	0.903	0.833	0.766	0.903	CLONAL	2	FALSE	2	0.303082916911795	4		427	867	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449787	29449787	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0052889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	102	769	0	ENST00000389048.3:c.3067+1G>T		p.X1023_splice	ENST00000389048	NM_004304.4	1023			0.214494777141491	3	FACETS	0.635	0.566	0.709	0.317	0.283	0.355	SUBCLONAL	1	FALSE	1	0.303082916911795	3		769	1221	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522636	67522636	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	43	271	0	ENST00000274335.5:c.133G>T	p.Gly45Ter	p.G45*	ENST00000274335		45	Gga/Tga	1/15	0.214494777141491	3	FACETS	0.647	0.541	0.764	0.324	0.27	0.382	SUBCLONAL	1	FALSE	1	0.303082916911795	3		271	505	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061334	38061334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3463	539	823	0	ENST00000250448.2:c.655C>A	p.Arg219Ser	p.R219S	ENST00000250448	NM_004496.3	219	Cgc/Agc	2/2	0.689142467151358	12	FACETS	0.869	0.828	0.911	0.193	0.184	0.203	CLONAL	2	TRUE	3	0.689142467151358	12		823	4002	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576883	7576883	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	846	885	0	ENST00000269305.4:c.963del	p.Lys321AsnfsTer24	p.K321Nfs*24	ENST00000269305	NM_001126112.2	321	aaA/aa	9/11	0.689142467151358	4	FACETS	0.951	0.932	0.97	0.951	0.932	0.97	CLONAL	4	TRUE	0	0.689142467151358	4		885	1090	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780684	9780684	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	500	807	2	ENST00000377346.4:c.1486C>T	p.Arg496Ter	p.R496*	ENST00000377346	NM_005026.3	496	Cga/Tga	12/24	0.608610901400834	5	FACETS	0.888	0.853	0.923	0.888	0.853	0.923	CLONAL	3	TRUE	2	0.689142467151358	5		809	1108	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713343	40713343	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	400	829	0	ENST00000373198.4:c.4172G>T	p.Gly1391Val	p.G1391V	ENST00000373198	NM_133170.3	1391	gGa/gTa	30/32	0.608610901400834	5	FACETS	0.989	0.942	1	0.66	0.628	0.692	CLONAL	2	TRUE	2	0.689142467151358	5		829	1193	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324521	62324521	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs373996455	NA	P-0052917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1710	210	1108	0	ENST00000360203.5:c.2877C>A	p.His959Gln	p.H959Q	ENST00000360203	NM_001283009.1	959	caC/caA	30/35	0.689142467151358	6	FACETS	0.755	0.698	0.815	0.252	0.232	0.272	SUBCLONAL	1	TRUE	3	0.689142467151358	6		1108	1920	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707576	176707576	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	392	563	0	ENST00000439151.2:c.5633C>G	p.Pro1878Arg	p.P1878R	ENST00000439151	NM_022455.4	1878	cCt/cGt	18/23	0.679439887101176	4	FACETS	0.956	0.919	0.993			1	CLONAL	3	TRUE	NA	0.689142467151358	4		563	670	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0052918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	158	469	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.350190662763322	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.350190662763322	1		469	686	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0052918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	80	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.896	0.791	1	0.896	0.791	1	CLONAL	1	TRUE	1	0.350190662763322	2		457	510	SUCCESS
APC	324	MSKCC	GRCh37	5	112175147	112175147	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	36	238	0	ENST00000257430.4:c.3856G>T	p.Glu1286Ter	p.E1286*	ENST00000257430	NM_000038.5	1286	Gaa/Taa	16/16	1	2	FACETS	0.882	0.731	1	0.882	0.731	1	CLONAL	1	TRUE	1	0.350190662763322	2		238	233	SUCCESS
APC	324	MSKCC	GRCh37	5	112175351	112175351	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	60	229	0	ENST00000257430.4:c.4063del	p.Ser1355LeufsTer60	p.S1355Lfs*60	ENST00000257430	NM_000038.5	1354	Ttt/tt	16/16	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.350190662763322	2		229	327	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	34	415	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.582	0.474	0.705	0.582	0.474	0.705	SUBCLONAL	1	TRUE	1	0.17	2		415	687	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	28	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.612	0.488	0.755	0.612	0.488	0.755	SUBCLONAL	1	TRUE	1	0.17	2		326	538	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	32	635	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.651	0.527	0.792	0.651	0.527	0.792	SUBCLONAL	1	TRUE	1	0.17	2		636	578	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	53	1445	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.856	0.729	0.997	0.856	0.729	0.997	CLONAL	1	TRUE	1	0.17	2		1452	728	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	28	396	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	0.682	0.544	0.84	0.682	0.544	0.84	SUBCLONAL	1	TRUE	1	0.17	2		396	483	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	42	762	2	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	0.673	0.56	0.799	0.673	0.56	0.799	SUBCLONAL	1	TRUE	1	0.17	2		764	734	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27204926	27204926	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	28	471	0	ENST00000380036.4:c.2232del	p.Lys745ArgfsTer5	p.K745Rfs*5	ENST00000380036	NM_000459.3	743	Ggg/gg	14/23	1	2	FACETS	0.638	0.509	0.786	0.638	0.509	0.786	SUBCLONAL	1	TRUE	1	0.17	2		471	516	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	53	805	3	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	2	FACETS	0.867	0.738	1	0.867	0.738	1	CLONAL	1	TRUE	1	0.17	2		808	719	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796883	42796883	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	60	964	1	ENST00000575354.2:c.3347del	p.Pro1116GlnfsTer45	p.P1116Qfs*45	ENST00000575354	NM_015125.3	1114	gCc/gc	14/20	1	2	FACETS	0.892	0.767	1	0.892	0.767	1	CLONAL	1	TRUE	1	0.17	2		965	791	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740810	58740810	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1179832290	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	37	550	0	ENST00000305921.3:c.1715G>A	p.Arg572Gln	p.R572Q	ENST00000305921	NM_003620.3	572	cGa/cAa	6/6	1	2	FACETS	0.649	0.533	0.779	0.649	0.533	0.779	SUBCLONAL	1	TRUE	1	0.17	2		550	671	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845549	72845551	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs763986819	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	48	720	1	ENST00000268489.5:c.3789_3791del	p.Asn1263del	p.N1263del	ENST00000268489	NM_006885.3	1263	aaCAAg/aag	7/10	1	2	FACETS	0.87	0.734	1	0.87	0.734	1	CLONAL	1	TRUE	1	0.17	2		721	649	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730254	133730254	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	44	559	2	ENST00000318560.5:c.320G>A	p.Gly107Asp	p.G107D	ENST00000318560	NM_005157.4	107	gGc/gAc	3/11	1	2	FACETS	0.826	0.691	0.975	0.826	0.691	0.975	CLONAL	1	TRUE	1	0.17	2		561	627	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933456	49933456	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	44	745	5	ENST00000296474.3:c.2734del	p.Asp912ThrfsTer24	p.D912Tfs*24	ENST00000296474	NM_002447.2	912	Gac/ac	11/20	1	2	FACETS	0.813	0.68	0.96	0.813	0.68	0.96	CLONAL	1	TRUE	1	0.17	2		750	637	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134248	2134250	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs878854100	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	41	823	0	ENST00000219476.3:c.4030_4032del	p.Glu1344del	p.E1344del	ENST00000219476	NM_000548.3	1342	cAGGag/cag	34/42	1	2	FACETS	0.73	0.606	0.867	0.73	0.606	0.867	SUBCLONAL	1	TRUE	1	0.17	2		823	661	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026838	71026838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138415721	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	36	323	0	ENST00000318789.4:c.1384G>A	p.Ala462Thr	p.A462T	ENST00000318789	NM_032682.5	462	Gca/Aca	16/21	1	2	FACETS	0.795	0.652	0.955	0.795	0.652	0.955	CLONAL	1	TRUE	1	0.17	2		323	533	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911141	29911141	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	43	849	0	ENST00000376809.5:c.440A>G	p.Tyr147Cys	p.Y147C	ENST00000376809	NM_002116.7	147	tAc/tGc	3/8	1	2	FACETS	0.74	0.617	0.876	0.74	0.617	0.876	SUBCLONAL	1	TRUE	1	0.17	2		849	684	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020769	37020769	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	51	539	0	ENST00000358127.4:c.76G>T	p.Val26Phe	p.V26F	ENST00000358127	NM_001280556.1	26	Gtt/Ttt	2/10	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.17	2		539	594	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418618	49418618	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	36	675	0	ENST00000301067.7:c.15896A>G	p.His5299Arg	p.H5299R	ENST00000301067	NM_003482.3	5299	cAt/cGt	49/54	1	2	FACETS	0.605	0.496	0.728	0.605	0.496	0.728	SUBCLONAL	1	TRUE	1	0.17	2		675	700	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500476	99500476	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	37	814	2	ENST00000268035.6:c.3913del	p.Leu1305TrpfsTer45	p.L1305Wfs*45	ENST00000268035	NM_000875.3	1303	gtC/gt	21/21	1	2	FACETS	0.597	0.491	0.717	0.597	0.491	0.717	SUBCLONAL	1	TRUE	1	0.17	2		816	729	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191621	10191621	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777130107	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	46	548	0	ENST00000256474.2:c.614G>A	p.Arg205His	p.R205H	ENST00000256474	NM_000551.3	205	cGc/cAc	3/3	1	2	FACETS	0.714	0.6	0.841	0.714	0.6	0.841	SUBCLONAL	1	TRUE	1	0.17	2		548	758	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435827	56435827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140873038	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	53	698	1	ENST00000407977.2:c.1310G>A	p.Arg437Gln	p.R437Q	ENST00000407977		437	cGg/cAg	9/10	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.17	2		699	597	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163309259	163309260	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	31	327	0	ENST00000271452.3:c.604dup	p.Thr202AsnfsTer24	p.T202Nfs*24	ENST00000271452	NM_145697.2	200	caa/cAaa	8/14	1	2	FACETS	0.669	0.54	0.816	0.669	0.54	0.816	SUBCLONAL	1	TRUE	1	0.17	2		327	545	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs758286312	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	56	641	1	ENST00000407977.2:c.349C>A	p.Arg117Ser	p.R117S	ENST00000407977		117	Cgc/Agc	3/10	1	2	FACETS	0.931	0.796	1	0.931	0.796	1	CLONAL	1	TRUE	1	0.17	2		642	708	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261263	115261263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	46	572	0	ENST00000438362.2:c.2458C>T	p.Arg820Cys	p.R820C	ENST00000438362	NM_001242891.1	820	Cgt/Tgt	19/20	1	2	FACETS	0.785	0.66	0.925	0.785	0.66	0.925	CLONAL	1	TRUE	1	0.17	2		572	689	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041116	42041116	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780889520	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	46	557	0	ENST00000219905.7:c.5494C>T	p.Arg1832Trp	p.R1832W	ENST00000219905	NM_001164273.1	1832	Cgg/Tgg	16/24	1	2	FACETS	0.746	0.627	0.879	0.746	0.627	0.879	SUBCLONAL	1	TRUE	1	0.17	2		557	725	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112578	115112578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	35	753	0	ENST00000257566.3:c.1162G>A	p.Glu388Lys	p.E388K	ENST00000257566	NM_016569.3	388	Gag/Aag	7/8	1	2	FACETS	0.613	0.501	0.739	0.613	0.501	0.739	SUBCLONAL	1	TRUE	1	0.17	2		753	672	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194902	29194902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750523072	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	115	809	3	ENST00000240100.2:c.826G>A	p.Val276Met	p.V276M	ENST00000240100	NM_001394.6	276	Gtg/Atg	4/4	1	2	FACETS	0.808	0.728	0.893	1	0.985	1	CLONAL	2	TRUE	1	0.17	2		812	837	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26970440	26970441	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	36	231	0	ENST00000381527.3:c.815dup	p.Met273AspfsTer3	p.M273Dfs*3	ENST00000381527	NM_001260.1	270	ata/atAa	8/13	1	2	FACETS	0.905	0.744	1	0.905	0.744	1	CLONAL	1	TRUE	1	0.17	2		231	468	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485311	8485312	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	36	423	0	ENST00000356435.5:c.3068dup	p.Asn1023LysfsTer23	p.N1023Kfs*23	ENST00000356435		1023	aat/aaAt	18/35	1	2	FACETS	0.744	0.611	0.895	0.744	0.611	0.895	SUBCLONAL	1	TRUE	1	0.17	2		423	569	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130433	29130434	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs876661156	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	41	635	0	ENST00000328354.6:c.276dup	p.Trp93LeufsTer15	p.W93Lfs*15	ENST00000328354	NM_007194.3	92	-/C	2/15	1	2	FACETS	0.705	0.586	0.838	0.705	0.586	0.838	SUBCLONAL	1	TRUE	1	0.17	2		635	684	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11269395	11269395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	38	653	0	ENST00000361445.4:c.3775C>T	p.His1259Tyr	p.H1259Y	ENST00000361445	NM_004958.3	1259	Cac/Tac	25/58	1	2	FACETS	0.624	0.515	0.748	0.624	0.515	0.748	SUBCLONAL	1	TRUE	1	0.17	2		653	716	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518431	69518431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	16	255	0	ENST00000294312.3:c.214C>T	p.Arg72Trp	p.R72W	ENST00000294312	NM_005117.2	72	Cgg/Tgg	1/3	1	2	FACETS	0.852	0.631	1	0.852	0.631	1	CLONAL	1	TRUE	1	0.17	2		255	221	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369170	118369170	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	42	482	0	ENST00000534358.1:c.5888G>A	p.Arg1963Gln	p.R1963Q	ENST00000534358	NM_005933.3	1963	cGa/cAa	22/36	1	2	FACETS	0.814	0.679	0.965	0.814	0.679	0.965	CLONAL	1	TRUE	1	0.17	2		482	607	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424212	49424212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	13	217	0	ENST00000301067.7:c.13850G>A	p.Ser4617Asn	p.S4617N	ENST00000301067	NM_003482.3	4617	aGt/aAt	42/54	1	2	FACETS	0.677	0.483	0.913	0.677	0.483	0.913	SUBCLONAL	1	TRUE	1	0.17	2		217	226	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864120	57864120	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779612265	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	49	626	0	ENST00000228682.2:c.1597G>A	p.Val533Met	p.V533M	ENST00000228682	NM_005269.2	533	Gtg/Atg	12/12	1	2	FACETS	0.869	0.735	1	0.869	0.735	1	CLONAL	1	TRUE	1	0.17	2		626	663	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986989	36986989	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	27	494	0	ENST00000354822.5:c.700C>G	p.Gln234Glu	p.Q234E	ENST00000354822	NM_001079668.2	234	Cag/Gag	3/3	1	2	FACETS	0.635	0.504	0.786	0.635	0.504	0.786	SUBCLONAL	1	TRUE	1	0.17	2		494	500	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060763	38060765	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	41	854	0	ENST00000250448.2:c.1224_1226del	p.Ser409del	p.S409del	ENST00000250448	NM_004496.3	408	tcCTCg/tcg	2/2	1	2	FACETS	0.594	0.493	0.707	0.594	0.493	0.707	SUBCLONAL	1	TRUE	1	0.17	2		854	812	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830099	72830099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264343788	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	41	629	1	ENST00000268489.5:c.6482G>A	p.Arg2161Gln	p.R2161Q	ENST00000268489	NM_006885.3	2161	cGg/cAg	9/10	1	2	FACETS	0.631	0.524	0.751	0.631	0.524	0.751	SUBCLONAL	1	TRUE	1	0.17	2		630	764	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40491333	40491333	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	33	545	0	ENST00000264657.5:c.467A>G	p.Gln156Arg	p.Q156R	ENST00000264657	NM_139276.2	156	cAg/cGg	5/24	1	2	FACETS	0.611	0.496	0.742	0.611	0.496	0.742	SUBCLONAL	1	TRUE	1	0.17	2		545	635	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214023	36214023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1013479394	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	45	841	0	ENST00000222270.7:c.2849G>A	p.Arg950Gln	p.R950Q	ENST00000222270	NM_014727.1	950	cGg/cAg	6/37	1	2	FACETS	0.784	0.658	0.925	0.784	0.658	0.925	CLONAL	1	TRUE	1	0.17	2		841	675	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218446	36218446	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	32	758	0	ENST00000222270.7:c.4225C>A	p.Leu1409Ile	p.L1409I	ENST00000222270	NM_014727.1	1409	Ctc/Atc	16/37	1	2	FACETS	0.648	0.525	0.788	0.648	0.525	0.788	SUBCLONAL	1	TRUE	1	0.17	2		758	581	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868386	45868386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752794877	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	62	768	1	ENST00000391945.4:c.391G>A	p.Asp131Asn	p.D131N	ENST00000391945	NM_000400.3	131	Gat/Aat	6/23	1	2	FACETS	0.983	0.848	1	0.983	0.848	1	CLONAL	1	TRUE	1	0.17	2		769	742	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249918	39249918	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	41	637	0	ENST00000402219.2:c.1651G>A	p.Glu551Lys	p.E551K	ENST00000402219	NM_005633.3	551	Gaa/Aaa	10/23	1	2	FACETS	0.617	0.512	0.734	0.617	0.512	0.734	SUBCLONAL	1	TRUE	1	0.17	2		637	782	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682901	190682901	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	41	417	0	ENST00000441310.2:c.577A>G	p.Asn193Asp	p.N193D	ENST00000441310	NM_000534.4	193	Aac/Gac	5/13	1	2	FACETS	0.738	0.613	0.877	0.738	0.613	0.877	SUBCLONAL	1	TRUE	1	0.17	2		417	654	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31495470	31495470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	67	502	2	ENST00000344624.3:c.1678C>T	p.Pro560Ser	p.P560S	ENST00000344624		560	Ccc/Tcc	9/33	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.17	2		504	724	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323095	31323095	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	47	870	0	ENST00000412585.2:c.894G>A	p.Trp298Ter	p.W298*	ENST00000412585	NM_005514.6	298	tgG/tgA	4/8	1	2	FACETS	0.69	0.581	0.812	0.69	0.581	0.812	SUBCLONAL	1	TRUE	1	0.17	2		870	801	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805858	32805858	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	40	809	0	ENST00000374899.4:c.153del	p.Leu52CysfsTer2	p.L52Cfs*2	ENST00000374899	NM_018833.2	51	ggG/gg	2/12	1	2	FACETS	0.61	0.505	0.727	0.61	0.505	0.727	SUBCLONAL	1	TRUE	1	0.17	2		809	772	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469817	157469817	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	58	740	0	ENST00000346085.5:c.2611G>T	p.Gly871Trp	p.G871W	ENST00000346085	NM_020732.3	871	Ggg/Tgg	9/20	1	2	FACETS	0.86	0.738	0.995	0.86	0.738	0.995	CLONAL	1	TRUE	1	0.17	2		740	793	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	181	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.233772435851692	1	FACETS	1	0.965	1	1	0.995	1	CLONAL	3	FALSE	0	0.233772435851692	1		487	433	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0053063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	85	394	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	0.218215777803993	1	FACETS	0.925	0.825	1	1	0.984	1	CLONAL	2	FALSE	0	0.233772435851692	1		394	347	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0053063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	106	364	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.218215777803993	1	FACETS	1	0.963	1	1	0.989	1	CLONAL	2	FALSE	0	0.233772435851692	1		365	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520008	NA	P-0053063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	28	507	0	ENST00000269305.4:c.613T>C	p.Tyr205His	p.Y205H	ENST00000269305	NM_001126112.2	205	Tat/Cat	6/11	0.233772435851692	0	FACETS	0.376	0.3	0.463			1	SUBCLONAL	1	FALSE	0	0.233772435851692	0		507	488	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755666	39755666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	75	456	1	ENST00000288319.7:c.1099C>T	p.Arg367Cys	p.R367C	ENST00000288319	NM_182918.3	367	Cgc/Tgc	10/10	0.193801156523672	4	FACETS	1	0.937	1	0.556	0.487	0.631	CLONAL	1	FALSE	2	0.233772435851692	4		457	712	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983053	201983053	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	243	539	0	ENST00000359651.3:c.902G>C	p.Gly301Ala	p.G301A	ENST00000359651		301	gGc/gCc	7/8	1	2	FACETS	1	0.983	1	1	0.995	1	CLONAL	2	FALSE	1	0.233772435851692	2		539	906	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499592	149499592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	174	418	1	ENST00000261799.4:c.2681G>A	p.Trp894Ter	p.W894*	ENST00000261799	NM_002609.3	894	tGg/tAg	19/23	0.218215777803993	1	FACETS	1	0.955	1	1	0.993	1	CLONAL	2	FALSE	0	0.233772435851692	1		419	629	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405999	157405999	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	153	431	0	ENST00000346085.5:c.2241C>G	p.Asn747Lys	p.N747K	ENST00000346085	NM_020732.3	747	aaC/aaG	6/20	1	2	FACETS	1	0.981	1	1	0.993	1	CLONAL	2	FALSE	1	0.233772435851692	2		431	539	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	146	275	0	ENST00000257430.4:c.4199C>A	p.Ser1400Ter	p.S1400*	ENST00000257430	NM_000038.5	1400	tCg/tAg	16/16	0.377905321528751	2	FACETS	0.973	0.899	1	0.973	0.899	1	CLONAL	2	TRUE	0	0.400133548462493	2		275	375	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560913	9560913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559720359	NA	P-0053072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	100	380	2	ENST00000353224.5:c.869C>T	p.Ser290Leu	p.S290L	ENST00000353224	NM_177990.2	290	tCg/tTg	4/10	0.282615104466929	3	FACETS	1	0.918	1	0.514	0.46	0.572	CLONAL	1	TRUE	1	0.400133548462493	3		382	583	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943641	9943641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	60	567	1	ENST00000330684.3:c.1300G>A	p.Val434Met	p.V434M	ENST00000330684	NM_001134407.1	434	Gtg/Atg	5/13	0.390083804316706	4	FACETS	0.468	0.402	0.54	0.234	0.201	0.27	SUBCLONAL	1	TRUE	2	0.400133548462493	4		568	898	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0053072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	163	346	0	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	0.400133548462493	4	FACETS	0.834	0.768	0.903	0.834	0.768	0.903	CLONAL	2	TRUE	2	0.400133548462493	4		346	684	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780677	56780677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502588	NA	P-0053072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	44	412	0	ENST00000337432.4:c.692C>T	p.Ser231Leu	p.S231L	ENST00000337432	NM_058216.2	231	tCa/tTa	4/9	0.400133548462493	4	FACETS	0.36	0.301	0.426	0.18	0.15	0.213	SUBCLONAL	1	TRUE	2	0.400133548462493	4		412	855	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778874	9778874	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	75	665	0	ENST00000377346.4:c.1143C>G	p.Ile381Met	p.I381M	ENST00000377346	NM_005026.3	381	atC/atG	9/24	0.400133548462493	3	FACETS	0.441	0.386	0.502	0.221	0.193	0.251	SUBCLONAL	1	TRUE	1	0.400133548462493	3		665	1019	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175838	24175838	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	81	523	0	ENST00000263121.7:c.1066C>A	p.Leu356Met	p.L356M	ENST00000263121	NM_003073.3	356	Ctg/Atg	8/9	0.400133548462493	3	FACETS	0.593	0.522	0.67	0.297	0.261	0.335	SUBCLONAL	1	TRUE	1	0.400133548462493	3		523	819	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	117	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.480789982018921	2		487	483	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959241	2959241	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369433934	NA	P-0053078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	84	532	0	ENST00000396946.4:c.2275C>T	p.Arg759Trp	p.R759W	ENST00000396946	NM_032415.4	759	Cgg/Tgg	18/25	0.476461634961787	3	FACETS	0.78	0.69	0.875	0.39	0.345	0.438	SUBCLONAL	1	TRUE	1	0.480789982018921	3		532	556	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175217	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	104	261	0	ENST00000257430.4:c.3929dup	p.Ile1311AspfsTer4	p.I1311Dfs*4	ENST00000257430	NM_000038.5	1309	gaa/gAaa	16/16	0.449377051027215	2	FACETS	0.879	0.802	0.957	0.879	0.802	0.957	CLONAL	2	TRUE	0	0.480789982018921	2		261	246	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596150	43596150	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	113	602	0	ENST00000355710.3:c.317G>T	p.Trp106Leu	p.W106L	ENST00000355710	NM_020975.4	106	tGg/tTg	2/20	1	2	FACETS	0.885	0.8	0.975	0.885	0.8	0.975	CLONAL	1	TRUE	1	0.480789982018921	2		602	531	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347687	89347687	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752613308	NA	P-0053078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	156	700	1	ENST00000301030.4:c.5263G>A	p.Ala1755Thr	p.A1755T	ENST00000301030	NM_001256183.1	1755	Gcc/Acc	9/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.480789982018921	2		701	573	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564853	41564853	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	119	496	1	ENST00000263253.7:c.4154G>T	p.Cys1385Phe	p.C1385F	ENST00000263253	NM_001429.3	1385	tGc/tTc	25/31	1	2	FACETS	0.992	0.9	1	0.992	0.9	1	CLONAL	1	TRUE	1	0.480789982018921	2		497	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0053117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	198	863	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.53077405589045	1	FACETS	0.937	0.873	1	0.937	0.873	1	CLONAL	1	TRUE	0	0.53077405589045	1		864	585	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	142	426	0	ENST00000263967.3:c.3129G>C	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atC	21/21	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.53077405589045	2		426	518	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575209	48575209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767326	NA	P-0053117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	124	342	0	ENST00000342988.3:c.403C>T	p.Arg135Ter	p.R135*	ENST00000342988	NM_005359.5	135	Cga/Tga	3/12	0.53077405589045	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.53077405589045	1		342	334	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097020	11097020	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	223	664	0	ENST00000358026.2:c.511C>T	p.Pro171Ser	p.P171S	ENST00000358026	NM_001128849.1	171	Cca/Tca	4/36	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.53077405589045	2		664	780	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060985	38060985	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	51	184	0	ENST00000250448.2:c.1004T>C	p.Leu335Pro	p.L335P	ENST00000250448	NM_004496.3	335	cTg/cCg	2/2	1	2	FACETS	0.801	0.687	0.922	0.801	0.687	0.922	CLONAL	1	TRUE	1	0.53077405589045	2		184	240	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211645	36211645	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs920487561	NA	P-0053117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	172	524	0	ENST00000222270.7:c.1396T>C	p.Ser466Pro	p.S466P	ENST00000222270	NM_014727.1	466	Tcc/Ccc	3/37	1	2	FACETS	0.962	0.888	1	0.962	0.888	1	CLONAL	1	TRUE	1	0.53077405589045	2		524	674	SUCCESS
ATR	545	MSKCC	GRCh37	3	142257447	142257447	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1173633134	NA	P-0053117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	104	435	0	ENST00000350721.4:c.3602G>A	p.Arg1201His	p.R1201H	ENST00000350721	NM_001184.3	1201	cGc/cAc	19/47	1	2	FACETS	0.714	0.641	0.79	0.714	0.641	0.79	SUBCLONAL	1	TRUE	1	0.53077405589045	2		435	549	SUCCESS
APC	324	MSKCC	GRCh37	5	112175253	112175254	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0053117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	196	286	1	ENST00000257430.4:c.3963_3964del	p.Ser1321ArgfsTer10	p.S1321Rfs*10	ENST00000257430	NM_000038.5	1321	aGC/a	16/16	0.520142047472892	2	FACETS	0.969	0.912	1	0.969	0.912	1	CLONAL	2	TRUE	0	0.53077405589045	2		287	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0053123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	330	863	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.299176244948344	3	FACETS	1	0.993	1	0.812	0.777	0.846	INDETERMINATE	2	TRUE	0	0.63554917523787	3		864	562	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0053123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	85	422	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	1	2	FACETS	0.841	0.751	0.936	0.841	0.751	0.936	CLONAL	1	TRUE	1	0.63554917523787	2		422	318	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38942414	38942414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	109	342	0	ENST00000357387.3:c.5119G>A	p.Glu1707Lys	p.E1707K	ENST00000357387	NM_152756.3	1707	Gaa/Aaa	38/38	0.60440079235753	3	FACETS	1	0.947	1	0.536	0.484	0.589	CLONAL	1	TRUE	1	0.63554917523787	3		342	422	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111965554	111965554	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	119	217	0	ENST00000375549.3:c.340T>G	p.Tyr114Asp	p.Y114D	ENST00000375549	NM_003002.3	114	Tat/Gat	4/4	0.635551319534524	3	FACETS	0.875	0.803	0.948	0.583	0.535	0.632	CLONAL	2	TRUE	0	0.63554917523787	3		217	282	SUCCESS
APC	324	MSKCC	GRCh37	5	112151256	112151260	+	frameshift_variant	Frame_Shift_Del	DEL	CACCT	CACCT	-	novel	NA	P-0053123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	95	365	0	ENST00000257430.4:c.900_904del	p.Pro301LysfsTer24	p.P301Kfs*24	ENST00000257430	NM_000038.5	300	gCACCT/g	9/16	1	2	FACETS	0.89	0.8	0.983	0.89	0.8	0.983	CLONAL	1	TRUE	1	0.63554917523787	2		365	336	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0053129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	9	670	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.305153232862014	3	FACETS	0.131	0.086	0.189	0.066	0.043	0.095	SUBCLONAL	1	TRUE	1	0.420335842407484	3		670	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0053129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	174	605	4	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.319814146647548	2	FACETS	1	0.987	1	0.667	0.616	0.718	CLONAL	1	TRUE	0	0.420335842407484	2		609	621	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0053129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	67	165	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.305153232862014	3	FACETS	1	0.973	1	0.722	0.635	0.815	CLONAL	1	TRUE	1	0.420335842407484	3		165	267	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0053129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	57	422	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.305153232862014	3	FACETS	0.758	0.652	0.873	0.379	0.326	0.437	SUBCLONAL	1	TRUE	1	0.420335842407484	3		422	433	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5078361	5078361	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	8	388	0	ENST00000381652.3:c.2048G>T	p.Arg683Ile	p.R683I	ENST00000381652	NM_004972.3	683	aGa/aTa	16/25	0.397168293712115	3	FACETS	0.116	0.074	0.171	0.058	0.037	0.086	SUBCLONAL	1	TRUE	1	0.420335842407484	3		388	397	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676309	37676309	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	66	517	2	ENST00000447079.4:c.3064G>T	p.Asp1022Tyr	p.D1022Y	ENST00000447079	NM_015083.1	1022	Gat/Tat	11/14	0.305153232862014	3	FACETS	0.561	0.487	0.642	0.281	0.243	0.321	SUBCLONAL	1	TRUE	1	0.420335842407484	3		519	677	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412680	63412680	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	85	545	2	ENST00000330258.3:c.487C>A	p.Pro163Thr	p.P163T	ENST00000330258	NM_152424.3	163	Ccc/Acc	2/2	0.178735511545787	3	FACETS	0.938	0.831	1	0.469	0.415	0.526	INDETERMINATE	1	TRUE	1	0.420335842407484	3		547	522	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0053132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	33	415	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.38	0.309	0.461	0.38	0.309	0.461	SUBCLONAL	1	FALSE	1	0.321014135093325	2		415	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0053132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	33	1045	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.285	0.231	0.346	0.285	0.231	0.346	SUBCLONAL	1	FALSE	1	0.321014135093325	2		1046	721	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0053132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	15	197	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.315	0.23	0.417	0.315	0.23	0.417	SUBCLONAL	1	FALSE	1	0.321014135093325	2		197	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577059	7577068	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTTTCTTG	CCCTTTCTTG	-	novel	NA	P-0053132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	46	707	2	ENST00000269305.4:c.870_879del	p.Lys291SerfsTer51	p.K291Sfs*51	ENST00000269305	NM_001126112.2	290	cgCAAGAAAGGG/cg	8/11	1	2	FACETS	0.345	0.29	0.407	0.345	0.29	0.407	SUBCLONAL	1	FALSE	1	0.321014135093325	2		709	830	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066846	30066846	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758982696	NA	P-0053138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	226	501	1	ENST00000331968.5:c.2285G>A	p.Arg762His	p.R762H	ENST00000331968	NM_002742.2	762	cGc/cAc	16/18	0.49084725607414	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.49084725607414	2		502	451	SUCCESS
APC	324	MSKCC	GRCh37	5	112155042	112155042	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs863225310	NA	P-0053138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	156	404	0	ENST00000257430.4:c.1312+1G>A		p.X438_splice	ENST00000257430	NM_000038.5	438			0.456810328971472	3	FACETS	0.938	0.868	1	0.938	0.868	1	CLONAL	2	TRUE	1	0.49084725607414	3		404	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912657	NA	P-0053138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	292	624	0	ENST00000269305.4:c.814G>C	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ctg	8/11	0.49084725607414	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.49084725607414	2		624	595	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982021	93982021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867625037	NA	P-0053138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	176	262	1	ENST00000369303.4:c.1444G>A	p.Glu482Lys	p.E482K	ENST00000369303	NM_004440.3	482	Gag/Aag	6/17	0.49084725607414	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.49084725607414	3		263	359	SUCCESS
APC	324	MSKCC	GRCh37	5	112175346	112175350	+	frameshift_variant	Frame_Shift_Del	DEL	TTGAA	TTGAA	-	novel	NA	P-0053138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	41	258	0	ENST00000257430.4:c.4057_4061del	p.Glu1353PhefsTer20	p.E1353Ffs*20	ENST00000257430	NM_000038.5	1352	gTTGAA/g	16/16	0.456810328971472	3	FACETS	0.782	0.656	0.921	0.391	0.328	0.461	CLONAL	1	TRUE	1	0.49084725607414	3		258	266	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056265	27056265	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	127	541	2	ENST00000324856.7:c.1261C>T	p.Pro421Ser	p.P421S	ENST00000324856	NM_006015.4	421	Cca/Tca	2/20	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.49084725607414	2		543	503	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420735	49420735	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	39	640	0	ENST00000301067.7:c.15014A>G	p.Asp5005Gly	p.D5005G	ENST00000301067	NM_003482.3	5005	gAt/gGt	48/54	0.49084725607414	3	FACETS	0.264	0.218	0.316	0.132	0.109	0.158	SUBCLONAL	1	TRUE	1	0.49084725607414	3		640	750	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16021264	16021264	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	127	294	0	ENST00000268712.3:c.1993T>C	p.Phe665Leu	p.F665L	ENST00000268712	NM_006311.3	665	Ttc/Ctc	18/46	0.49084725607414	2	FACETS	0.965	0.892	1	0.965	0.892	1	CLONAL	2	TRUE	0	0.49084725607414	2		294	268	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619471	1619471	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	45	525	0	ENST00000344749.5:c.1170G>C	p.Gln390His	p.Q390H	ENST00000344749	NM_001136139.2	390	caG/caC	15/19	0.456810328971472	3	FACETS	0.412	0.346	0.486	0.206	0.173	0.243	SUBCLONAL	1	TRUE	1	0.49084725607414	3		525	554	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0053139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	20	275	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.265497865748285	2	FACETS	0.948	0.757	1	1	0.923	1	CLONAL	3	TRUE	0	0.265497865748285	2		275	53	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0053139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	132	1126	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.167608555272529	3	FACETS	0.816	0.742	0.894	0.544	0.495	0.596	CLONAL	2	TRUE	0	0.265497865748285	3		1126	690	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0053139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	25	370	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.265497865748285	1	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	0	0.265497865748285	1		370	152	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357164	89357164	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	144	660	1	ENST00000301030.4:c.470C>A	p.Thr157Asn	p.T157N	ENST00000301030	NM_001256183.1	157	aCc/aAc	6/13	0.225315227720319	4	FACETS	1	0.917	1	0.669	0.611	0.729	CLONAL	2	TRUE	1	0.265497865748285	4		661	684	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0053147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	47	459	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	0.795	0.672	0.93	0.795	0.672	0.93	CLONAL	1	TRUE	1	0.27	2		459	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0053147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	70	1025	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.85	0.741	0.967	0.85	0.741	0.967	CLONAL	1	TRUE	1	0.27	2		1026	610	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0053147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	80	571	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.922	0.812	1	0.922	0.812	1	CLONAL	1	TRUE	1	0.27	2		571	643	SUCCESS
APC	324	MSKCC	GRCh37	5	112175198	112175198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	25	220	0	ENST00000257430.4:c.3907C>T	p.Gln1303Ter	p.Q1303*	ENST00000257430	NM_000038.5	1303	Caa/Taa	16/16	1	2	FACETS	0.874	0.692	1	0.874	0.692	1	CLONAL	1	TRUE	1	0.27	2		220	212	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259177	36259177	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	49	520	0	ENST00000300305.3:c.314A>T	p.His105Leu	p.H105L	ENST00000300305		105	cAc/cTc	3/8	1	2	FACETS	0.628	0.531	0.734	0.628	0.531	0.734	SUBCLONAL	1	TRUE	1	0.27	2		520	578	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0053195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	89	684	2	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	1	2	FACETS	0.895	0.795	1	0.895	0.795	1	CLONAL	1	TRUE	1	0.358474596957771	2		686	555	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120002	70120002	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	76	94	0	ENST00000245479.2:c.1004G>A	p.Trp335Ter	p.W335*	ENST00000245479	NM_000346.3	335	tGg/tAg	3/3	0.358474596957771	2	FACETS	0.918	0.829	1	1	0.979	1	CLONAL	3	TRUE	0	0.358474596957771	2		94	154	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692908	89692908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514560	NA	P-0053195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	83	422	0	ENST00000371953.3:c.392C>T	p.Thr131Ile	p.T131I	ENST00000371953	NM_000314.4	131	aCt/aTt	5/9	0.358474596957771	1	FACETS	0.943	0.837	1	0.943	0.837	1	CLONAL	1	TRUE	0	0.358474596957771	1		422	403	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118365419	118365419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555043444	NA	P-0053195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	48	275	0	ENST00000534358.1:c.5300G>A	p.Arg1767His	p.R1767H	ENST00000534358	NM_005933.3	1767	cGt/cAt	18/36	1	2	FACETS	0.712	0.604	0.831	0.712	0.604	0.831	SUBCLONAL	1	TRUE	1	0.358474596957771	2		275	376	SUCCESS
APC	324	MSKCC	GRCh37	5	112162881	112162882	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	74	371	0	ENST00000257430.4:c.1486dup	p.Thr496AsnfsTer41	p.T496Nfs*41	ENST00000257430	NM_000038.5	495	-/A	12/16	1	2	FACETS	0.903	0.794	1	0.903	0.794	1	CLONAL	1	TRUE	1	0.358474596957771	2		371	457	SUCCESS
APC	324	MSKCC	GRCh37	5	112175330	112175865	+	frameshift_variant	Frame_Shift_Del	DEL	GCCAGGCACAAAGCTGTTGAATTTTCTTCAGGAGCGAAATCTCCCTCCAAAAGTGGTGCTCAGACACCCAAAAGTCCACCTGAACACTATGTTCAGGAGACCCCACTCATGTTTAGCAGATGTACTTCTGTCAGTTCACTTGATAGTTTTGAGAGTCGTTCGATTGCCAGCTCCGTTCAGAGTGAACCATGCAGTGGAATGGTAAGTGGCATTATAAGCCCCAGTGATCTTCCAGATAGCCCTGGACAAACCATGCCACCAAGCAGAAGTAAAACACCTCCACCACCTCCTCAAACAGCTCAAACCAAGCGAGAAGTACCTAAAAATAAAGCACCTACTGCTGAAAAGAGAGAGAGTGGACCTAAGCAAGCTGCAGTAAATGCTGCAGTTCAGAGGGTCCAGGTTCTTCCAGATGCTGATACTTTATTACATTTTGCCACGGAAAGTACTCCAGATGGATTTTCTTGTTCATCCAGCCTGAGTGCTCTGAGCCTCGATGAGCCATTTATACAGAAAGATGTGGAATTAAGAATAAT	GCCAGGCACAAAGCTGTTGAATTTTCTTCAGGAGCGAAATCTCCCTCCAAAAGTGGTGCTCAGACACCCAAAAGTCCACCTGAACACTATGTTCAGGAGACCCCACTCATGTTTAGCAGATGTACTTCTGTCAGTTCACTTGATAGTTTTGAGAGTCGTTCGATTGCCAGCTCCGTTCAGAGTGAACCATGCAGTGGAATGGTAAGTGGCATTATAAGCCCCAGTGATCTTCCAGATAGCCCTGGACAAACCATGCCACCAAGCAGAAGTAAAACACCTCCACCACCTCCTCAAACAGCTCAAACCAAGCGAGAAGTACCTAAAAATAAAGCACCTACTGCTGAAAAGAGAGAGAGTGGACCTAAGCAAGCTGCAGTAAATGCTGCAGTTCAGAGGGTCCAGGTTCTTCCAGATGCTGATACTTTATTACATTTTGCCACGGAAAGTACTCCAGATGGATTTTCTTGTTCATCCAGCCTGAGTGCTCTGAGCCTCGATGAGCCATTTATACAGAAAGATGTGGAATTAAGAATAAT	-	novel	NA	P-0053195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	37	244	0	ENST00000257430.4:c.4042_4577del	p.Arg1348SerfsTer6	p.R1348Sfs*6	ENST00000257430	NM_000038.5	1347	GCCAGGCACAAAGCTGTTGAATTTTCTTCAGGAGCGAAATCTCCCTCCAAAAGTGGTGCTCAGACACCCAAAAGTCCACCTGAACACTATGTTCAGGAGACCCCACTCATGTTTAGCAGATGTACTTCTGTCAGTTCACTTGATAGTTTTGAGAGTCGTTCGATTGCCAGCTCCGTTCAGAGTGAACCATGCAGTGGAATGGTAAGTGGCATTATAAGCCCCAGTGATCTTCCAGATAGCCCTGGACAAACCATGCCACCAAGCAGAAGTAAAACACCTCCACCACCTCCTCAAACAGCTCAAACCAAGCGAGAAGTACCTAAAAATAAAGCACCTACTGCTGAAAAGAGAGAGAGTGGACCTAAGCAAGCTGCAGTAAATGCTGCAGTTCAGAGGGTCCAGGTTCTTCCAGATGCTGATACTTTATTACATTTTGCCACGGAAAGTACTCCAGATGGATTTTCTTGTTCATCCAGCCTGAGTGCTCTGAGCCTCGATGAGCCATTTATACAGAAAGATGTGGAATTAAGAATAATg/g	16/16	1	2	FACETS	0.712	0.589	0.848	0.712	0.589	0.848	SUBCLONAL	1	TRUE	1	0.358474596957771	2		244	290	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053217-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	106	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.418117290918137	2		487	348	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573894	18573894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759658584	NA	P-0053217-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	51	345	0	ENST00000266497.5:c.2212C>T	p.Arg738Cys	p.R738C	ENST00000266497		738	Cgt/Tgt	15/31	0.418117290918137	8	FACETS	0.87	0.739	1			1	CLONAL	1	TRUE	NA	0.418117290918137	8		345	632	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213375	36213375	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0053217-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	162	987	1	ENST00000222270.7:c.2571+1G>A		p.X857_splice	ENST00000222270	NM_014727.1	857			1	2	FACETS	0.991	0.91	1	0.991	0.91	1	CLONAL	1	TRUE	1	0.418117290918137	2		988	782	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974696	21974699	+	frameshift_variant	Frame_Shift_Del	DEL	TAAC	TAAC	-	novel	NA	P-0053217-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	85	561	0	ENST00000304494.5:c.128_131del	p.Ser43ThrfsTer9	p.S43Tfs*9	ENST00000304494	NM_000077.4	43	aGTTAc/ac	1/3	0.418117290918137	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.418117290918137	1		561	294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	CA	novel	NA	P-0053217-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	150	989	0	ENST00000269305.4:c.528delinsTG	p.Pro177AlafsTer4	p.P177Afs*4	ENST00000269305	NM_001126112.2	176	tgC/tgTG	5/11	0.418117290918137	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.418117290918137	1		989	534	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146945	38146945	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	187	658	0	ENST00000317025.8:c.3197del	p.Asn1066ThrfsTer16	p.N1066Tfs*16	ENST00000317025	NM_023034.1	1066	aAc/ac	18/24	1	2	FACETS	0.896	0.826	0.969	0.896	0.826	0.969	CLONAL	1	TRUE	1	0.340892231475406	2		658	1224	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0053250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	194	653	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.17540418929944	2	FACETS	1	0.946	1	0.514	0.475	0.555	INDETERMINATE	1	TRUE	0	0.340892231475406	2		654	1107	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032207	10032207	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	112	685	1	ENST00000330684.3:c.616C>A	p.Leu206Met	p.L206M	ENST00000330684	NM_001134407.1	206	Ctg/Atg	3/13	1	2	FACETS	0.614	0.551	0.681	0.614	0.551	0.681	SUBCLONAL	1	TRUE	1	0.340892231475406	2		686	1070	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146062	38146062	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	205	711	0	ENST00000317025.8:c.3444G>C	p.Glu1148Asp	p.E1148D	ENST00000317025	NM_023034.1	1148	gaG/gaC	19/24	1	2	FACETS	0.966	0.894	1	0.966	0.894	1	CLONAL	1	TRUE	1	0.340892231475406	2		711	1245	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146248	38146248	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	184	526	0	ENST00000317025.8:c.3258G>C	p.Gln1086His	p.Q1086H	ENST00000317025	NM_023034.1	1086	caG/caC	19/24	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.340892231475406	2		526	1018	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146976	38146976	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	187	635	0	ENST00000317025.8:c.3166G>C	p.Glu1056Gln	p.E1056Q	ENST00000317025	NM_023034.1	1056	Gaa/Caa	18/24	1	2	FACETS	0.966	0.891	1	0.966	0.891	1	CLONAL	1	TRUE	1	0.340892231475406	2		635	1136	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0053268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	74	466	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.218834947575281	1	FACETS	0.792	0.696	0.894	0.792	0.696	0.894	SUBCLONAL	1	TRUE	0	0.35773447436066	1		466	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0053268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	278	564	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.304292969316564	2	FACETS	0.964	0.909	1	0.964	0.909	1	CLONAL	2	TRUE	0	0.35773447436066	2		564	806	SUCCESS
APC	324	MSKCC	GRCh37	5	112175039	112175040	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs1114167583	NA	P-0053268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	38	164	0	ENST00000257430.4:c.3749_3750del	p.Lys1250SerfsTer5	p.K1250Sfs*5	ENST00000257430	NM_000038.5	1250	AAa/a	16/16	0.35773447436066	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	0	0.35773447436066	1		164	155	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89811386	89811386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752561405	NA	P-0053268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	146	546	0	ENST00000389301.3:c.3607G>A	p.Gly1203Ser	p.G1203S	ENST00000389301	NM_000135.2	1203	Ggc/Agc	36/43	1	2	FACETS	0.967	0.883	1	0.967	0.883	1	CLONAL	1	TRUE	1	0.35773447436066	2		546	844	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554518	63554518	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	151	458	0	ENST00000307078.5:c.221del	p.Pro74LeufsTer2	p.P74Lfs*2	ENST00000307078	NM_004655.3	74	cCt/ct	2/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.35773447436066	2		458	601	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0053385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	109	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.948	0.86	1	1	0.988	1	CLONAL	2	TRUE	1	0.316633864003337	2		457	363	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0053385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	31	197	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.837	0.691	0.994	1	0.955	1	CLONAL	2	TRUE	1	0.316633864003337	2		197	117	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912813	50912813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758260006	NA	P-0053385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	33	1117	0	ENST00000440232.2:c.2044C>T	p.Arg682Trp	p.R682W	ENST00000440232	NM_002691.3	682	Cgg/Tgg	17/27	1	2	FACETS	0.432	0.352	0.524	0.432	0.352	0.524	SUBCLONAL	1	TRUE	1	0.316633864003337	2		1117	482	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245344	153245344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	110	505	0	ENST00000281708.4:c.1847C>T	p.Thr616Ile	p.T616I	ENST00000281708	NM_033632.3	616	aCa/aTa	11/12	0.316633864003337	3	FACETS	1	0.925	1	1	0.925	1	CLONAL	3	TRUE	0	0.316633864003337	3		505	265	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11177077	11177077	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	53	459	0	ENST00000361445.4:c.7000T>G	p.Leu2334Val	p.L2334V	ENST00000361445	NM_004958.3	2334	Tta/Gta	50/58	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.316633864003337	2		459	253	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405334	70405334	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	54	684	0	ENST00000373644.4:c.2848C>A	p.Pro950Thr	p.P950T	ENST00000373644	NM_030625.2	950	Cca/Aca	4/12	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.316633864003337	2		684	321	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883761	37883761	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	44	1079	1	ENST00000269571.5:c.3373G>T	p.Asp1125Tyr	p.D1125Y	ENST00000269571		1125	Gat/Tat	26/27	1	2	FACETS	0.495	0.415	0.585	0.495	0.415	0.585	SUBCLONAL	1	TRUE	1	0.316633864003337	2		1080	561	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730112	41730112	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	45	448	0	ENST00000242208.4:c.417G>T	p.Glu139Asp	p.E139D	ENST00000242208	NM_002192.2	139	gaG/gaT	3/3	1	2	FACETS	0.824	0.695	0.965	0.824	0.695	0.965	CLONAL	1	TRUE	1	0.316633864003337	2		448	345	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053385-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	75	290	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.844	0.744	0.951	0.844	0.744	0.951	CLONAL	1	TRUE	1	0.472438745159779	2		291	376	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0053385-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	133	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.977	0.891	1	0.977	0.891	1	CLONAL	1	TRUE	1	0.472438745159779	2		457	576	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480335	56480335	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053385-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	184	657	0	ENST00000267101.3:c.442T>C	p.Tyr148His	p.Y148H	ENST00000267101	NM_001982.3	148	Tat/Cat	4/28	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.472438745159779	2		657	646	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94129030	94129030	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053385-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	147	486	0	ENST00000369303.4:c.30G>C	p.Trp10Cys	p.W10C	ENST00000369303	NM_004440.3	10	tgG/tgC	1/17	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.472438745159779	2		486	570	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188361	32188361	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053385-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	172	985	0	ENST00000375023.3:c.980G>A	p.Arg327Lys	p.R327K	ENST00000375023	NM_004557.3	327	aGa/aAa	6/30	1	2	FACETS	0.896	0.825	0.969	0.896	0.825	0.969	CLONAL	1	TRUE	1	0.472438745159779	2		985	813	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106417	27106418	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0053385-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	175	899	0	ENST00000324856.7:c.6028_6029del	p.Ile2010ProfsTer22	p.I2010Pfs*22	ENST00000324856	NM_006015.4	2010	ATc/c	20/20	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.472438745159779	2		899	732	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781900	3781900	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053385-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	224	942	0	ENST00000262367.5:c.4767del	p.Asn1589LysfsTer46	p.N1589Kfs*46	ENST00000262367	NM_004380.2	1589	aaC/aa	29/31	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.472438745159779	2		942	945	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881636	37881636	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193920750	NA	P-0053385-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	167	833	0	ENST00000269571.5:c.2706G>C	p.Gln902His	p.Q902H	ENST00000269571		902	caG/caC	22/27	0.472438745159779	3	FACETS	0.875	0.803	0.95	0.437	0.401	0.475	CLONAL	1	TRUE	1	0.472438745159779	3		833	999	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40856620	40856620	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053385-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	250	626	0	ENST00000428826.2:c.2017G>T	p.Asp673Tyr	p.D673Y	ENST00000428826		673	Gat/Tat	18/21	0.472438745159779	3	FACETS	0.941	0.885	0.998	0.941	0.885	0.998	CLONAL	2	TRUE	1	0.472438745159779	3		626	695	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752920	57752920	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0053385-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	62	594	0	ENST00000274289.3:c.1009-1G>C		p.X337_splice	ENST00000274289	NM_006622.3	337			1	2	FACETS	0.428	0.37	0.492	0.428	0.37	0.492	SUBCLONAL	1	TRUE	1	0.472438745159779	2		594	613	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188346	32188346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053385-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	206	1057	0	ENST00000375023.3:c.995G>A	p.Cys332Tyr	p.C332Y	ENST00000375023	NM_004557.3	332	tGc/tAc	6/30	1	2	FACETS	0.956	0.888	1	0.956	0.888	1	CLONAL	1	TRUE	1	0.472438745159779	2		1057	912	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15818036	15818036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555899273	NA	P-0053385-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	127	447	0	ENST00000307771.7:c.163G>A	p.Glu55Lys	p.E55K	ENST00000307771	NM_005089.3	55	Gaa/Aaa	3/11	NA	2	FACETS	1	0.918	1			1	INDETERMINATE	1	TRUE	NA	0.472438745159779	2		447	533	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053447-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	50	290	1				ENST00000310581	NM_198253.2	-/1132			0.161068729370488	0	FACETS	0.904	0.777	1			1	INDETERMINATE	1	FALSE	0	0.348346241026338	0		291	207	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0053447-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	50	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.9	0.768	1	0.9	0.768	1	CLONAL	1	FALSE	1	0.348346241026338	2		326	319	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0053447-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	247	519	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.327306933700661	3	FACETS	0.988	0.932	1			1	CLONAL	3	FALSE	NA	0.348346241026338	3		519	562	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952138	178952138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053447-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	30	300	0	ENST00000263967.3:c.3193C>T	p.His1065Tyr	p.H1065Y	ENST00000263967	NM_006218.2	1065	Cat/Tat	21/21	1	2	FACETS	0.709	0.574	0.86	0.709	0.574	0.86	SUBCLONAL	1	FALSE	1	0.348346241026338	2		300	243	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161751	47161751	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053447-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	49	364	0	ENST00000409792.3:c.4375C>T	p.Arg1459Ter	p.R1459*	ENST00000409792	NM_014159.6	1459	Cga/Tga	3/21	1	2	FACETS	0.825	0.702	0.959	0.825	0.702	0.959	CLONAL	1	FALSE	1	0.348346241026338	2		364	341	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609462	81609462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200523471	NA	P-0053447-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	9	0	0	ENST00000298171.2:c.1060G>A	p.Val354Ile	p.V354I	ENST00000298171	NM_000369.2	354	Gtc/Atc	10/10	1	2	FACETS	0.119	0.078	0.172	0.119	0.078	0.172	SUBCLONAL	1	FALSE	1	0.348346241026338	2		0	433	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0053491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	74	440	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.393992715299227	1	FACETS	0.794	0.699	0.895	0.794	0.699	0.895	SUBCLONAL	1	TRUE	0	0.393992715299227	1		440	380	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986803	36986803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	12	135	0	ENST00000354822.5:c.886G>A	p.Asp296Asn	p.D296N	ENST00000354822	NM_001079668.2	296	Gac/Aac	3/3	1	2	FACETS	0.322	0.227	0.44	0.322	0.227	0.44	SUBCLONAL	1	TRUE	1	0.393992715299227	2		135	189	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0053491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	281	649	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.349070380809829	2	FACETS	0.921	0.87	0.974	0.921	0.87	0.974	CLONAL	2	TRUE	0	0.393992715299227	2		649	774	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218520	5218520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs936142250	NA	P-0053491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	39	686	1	ENST00000357368.4:c.3959G>A	p.Arg1320His	p.R1320H	ENST00000357368	NM_002850.3	1320	cGc/cAc	25/38	0.393992715299227	1	FACETS	0.223	0.184	0.266	0.223	0.184	0.266	SUBCLONAL	1	TRUE	0	0.393992715299227	1		687	714	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622595	158622595	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	75	472	0	ENST00000263640.3:c.904A>G	p.Thr302Ala	p.T302A	ENST00000263640	NM_001105.4	302	Aca/Gca	8/11	1	2	FACETS	0.602	0.528	0.683	0.602	0.528	0.683	SUBCLONAL	1	TRUE	1	0.393992715299227	2		472	632	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635236	87635236	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	90	535	0	ENST00000277120.3:c.2288T>G	p.Phe763Cys	p.F763C	ENST00000277120		763	tTc/tGc	18/19	0.172396481120854	2	FACETS	0.81	0.72	0.905	0.405	0.36	0.453	INDETERMINATE	1	TRUE	0	0.393992715299227	2		535	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0053663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	82	550	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.19	2		552	821	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0053663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	45	680	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	1	2	FACETS	0.621	0.52	0.733	0.621	0.52	0.733	SUBCLONAL	1	TRUE	1	0.19	2		680	763	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793008	33793010	+	inframe_deletion	In_Frame_Del	DEL	CGC	CGC	-	rs780345232	NA	P-0053663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	8	78	1	ENST00000498907.2:c.311_313del	p.Gly104del	p.G104del	ENST00000498907	NM_004364.3	104	gGCGac/gac	1/1	0.175333346807498	3	FACETS	0.802	0.519	1	0.401	0.259	0.582	CLONAL	1	TRUE	1	0.19	3		79	115	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0053674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	169	857	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.298165833324866	1	FACETS	0.905	0.831	0.981	0.905	0.831	0.981	CLONAL	1	TRUE	0	0.318341098559392	1		857	987	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390878	139390915	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTCTCCACTCAGGAAGCTCCGGCCCAGGTGGCCGCT	GGCTCTCCACTCAGGAAGCTCCGGCCCAGGTGGCCGCT	-	novel	NA	P-0053674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	69	1047	0	ENST00000277541.6:c.7276_7313del	p.Ser2426GlufsTer68	p.S2426Efs*68	ENST00000277541	NM_017617.3	2426	AGCGGCCACCTGGGCCGGAGCTTCCTGAGTGGAGAGCCg/g	34/34	1	2	FACETS	0.347	0.301	0.397	0.347	0.301	0.397	SUBCLONAL	1	TRUE	1	0.318341098559392	2		1047	1249	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0053746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	89	422	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	1	2	FACETS	0.857	0.762	0.958	0.857	0.762	0.958	CLONAL	1	FALSE	1	0.392704175562837	2		422	529	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0053746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	80	398	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.858	0.758	0.964	0.858	0.758	0.964	CLONAL	1	FALSE	1	0.392704175562837	2		398	475	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451861	29451861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774488715	NA	P-0053746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	148	488	0	ENST00000389048.3:c.2704G>A	p.Gly902Arg	p.G902R	ENST00000389048	NM_004304.4	902	Gga/Aga	16/29	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.392704175562837	2		488	714	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101179	41101179	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770753852	NA	P-0053746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	170	562	1	ENST00000373198.4:c.1177G>A	p.Val393Met	p.V393M	ENST00000373198	NM_133170.3	393	Gtg/Atg	8/32	0.375238966120688	3	FACETS	1	0.943	1	0.516	0.474	0.56	CLONAL	1	FALSE	1	0.392704175562837	3		563	1004	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435894	149435894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs690016548	NA	P-0053746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	124	496	2	ENST00000286301.3:c.2330G>A	p.Arg777Gln	p.R777Q	ENST00000286301	NM_005211.3	777	cGg/cAg	18/22	1	2	FACETS	0.893	0.809	0.982	0.893	0.809	0.982	CLONAL	1	FALSE	1	0.392704175562837	2		498	707	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974420	18974420	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs189120195	NA	P-0053746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	107	384	0	ENST00000262803.5:c.2774C>T	p.Pro925Leu	p.P925L	ENST00000262803	NM_002911.3	925	cCg/cTg	19/24	1	2	FACETS	0.949	0.854	1	0.949	0.854	1	CLONAL	1	FALSE	1	0.392704175562837	2		384	574	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398297	25398297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	72	366	0	ENST00000311936.3:c.22G>A	p.Val8Ile	p.V8I	ENST00000311936	NM_004985.3	8	Gta/Ata	2/5	1	2	FACETS	0.855	0.75	0.967	0.855	0.75	0.967	CLONAL	1	FALSE	1	0.392704175562837	2		366	429	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911553	134911553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	130	494	1	ENST00000398015.3:c.2018G>A	p.Gly673Asp	p.G673D	ENST00000398015	NM_004441.4	673	gGc/gAc	11/16	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.392704175562837	2		495	631	SUCCESS
APC	324	MSKCC	GRCh37	5	112175524	112175545	+	frameshift_variant	Frame_Shift_Del	DEL	TGGAATGGTAAGTGGCATTATA	TGGAATGGTAAGTGGCATTATA	-	novel	NA	P-0053746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	79	322	0	ENST00000257430.4:c.4233_4254del	p.Ser1411ArgfsTer55	p.S1411Rfs*55	ENST00000257430	NM_000038.5	1411	agTGGAATGGTAAGTGGCATTATA/ag	16/16	1	2	FACETS	0.856	0.755	0.963	0.856	0.755	0.963	CLONAL	1	FALSE	1	0.392704175562837	2		322	470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0053749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	393	469	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.426041905161432	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.430018337254418	2		469	909	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	234	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.393962728533226	2	FACETS	0.927	0.872	0.983	0.927	0.872	0.983	CLONAL	2	TRUE	0	0.430018337254418	2		487	587	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0053749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	43	383	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.430018337254418	1	FACETS	0.412	0.345	0.486	0.412	0.345	0.486	SUBCLONAL	1	TRUE	0	0.430018337254418	1		383	381	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888168	81888168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754914807	NA	P-0053749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	75	451	0	ENST00000359376.3:c.313G>A	p.Val105Ile	p.V105I	ENST00000359376	NM_002661.3	105	Gtc/Atc	3/33	0.18359968428221	5	FACETS	0.493	0.431	0.561	0.164	0.143	0.187	INDETERMINATE	1	TRUE	2	0.430018337254418	5		451	1163	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724358	117724358	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772261492	NA	P-0053749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	327	572	0	ENST00000368508.3:c.521C>T	p.Ala174Val	p.A174V	ENST00000368508	NM_002944.2	174	gCg/gTg	6/43	0.187737075391853	4	FACETS	0.858	0.81	0.907	0.858	0.81	0.907	INDETERMINATE	2	TRUE	2	0.430018337254418	4		572	1267	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435113	49435113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764604229	NA	P-0053749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	50	621	0	ENST00000301067.7:c.6440C>T	p.Ala2147Val	p.A2147V	ENST00000301067	NM_003482.3	2147	gCg/gTg	31/54	0.351879650678776	3	FACETS	0.289	0.244	0.339	0.096	0.081	0.113	SUBCLONAL	1	TRUE	0	0.430018337254418	3		621	976	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212112	5212112	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1262	1360	748	1	ENST00000357368.4:c.4919T>C	p.Phe1640Ser	p.F1640S	ENST00000357368	NM_002850.3	1640	tTc/tCc	32/38	0.430018337254418	6	FACETS	1	0.997	1	0.897	0.877	0.918	CLONAL	4	TRUE	1	0.430018337254418	6		749	2622	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356303	66356303	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	116	444	0	ENST00000273854.3:c.1194C>A	p.Cys398Ter	p.C398*	ENST00000273854	NM_004439.5	398	tgC/tgA	5/18	1	2	FACETS	0.716	0.646	0.791	0.716	0.646	0.791	SUBCLONAL	1	TRUE	1	0.430018337254418	2		444	753	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0053758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	71	394	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	0.271816992926379	1	FACETS	1	0.925	1	1	0.984	1	CLONAL	2	TRUE	0	0.271816992926379	1		394	214	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0053758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	242	378	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.0595604584696026	4	FACETS	0.908	0.858	0.957			1	INDETERMINATE	5	TRUE	NA	0.271816992926379	4		378	499	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398279	25398279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894365	NA	P-0053758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	25	505	0	ENST00000311936.3:c.40G>A	p.Val14Ile	p.V14I	ENST00000311936	NM_004985.3	14	Gta/Ata	2/5	0.0595604584696026	4	FACETS	0.463	0.364	0.578			1	INDETERMINATE	1	TRUE	NA	0.271816992926379	4		505	505	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120013	70120013	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	70	161	0	ENST00000245479.2:c.1015C>T	p.Gln339Ter	p.Q339*	ENST00000245479	NM_000346.3	339	Cag/Tag	3/3	0.271816992926379	2	FACETS	1	0.958	1	1	0.986	1	CLONAL	4	TRUE	0	0.271816992926379	2		161	117	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323288	31323288	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs74428022	NA	P-0053758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	20	419	0	ENST00000412585.2:c.701C>T	p.Pro234Leu	p.P234L	ENST00000412585	NM_005514.6	234	cCt/cTt	4/8	0.167372230379797	2	FACETS	0.416	0.317	0.531	0.208	0.158	0.266	SUBCLONAL	1	TRUE	0	0.271816992926379	2		419	354	SUCCESS
APC	324	MSKCC	GRCh37	5	112170814	112170814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	20	643	0	ENST00000257430.4:c.1910G>A	p.Gly637Glu	p.G637E	ENST00000257430	NM_000038.5	637	gGg/gAg	15/16	0.271816992926379	1	FACETS	0.385	0.294	0.492	0.385	0.294	0.492	SUBCLONAL	1	TRUE	0	0.271816992926379	1		643	330	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941861	44941938	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATAGTGAATCTACATCGTCAGATAAGTAAGTCATTTTTAATGTCCACTTAGTATTTCTTTTTAAAAGGCATGTTTCTA	ATAGTGAATCTACATCGTCAGATAAGTAAGTCATTTTTAATGTCCACTTAGTATTTCTTTTTAAAAGGCATGTTTCTA	-	novel	NA	P-0053758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	182	510	0	ENST00000377967.4:c.3188_3210-19del		p.X1063_splice	ENST00000377967	NM_021140.2	1063		21/29	0.20182860354081	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	TRUE	0	0.271816992926379	3		510	468	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0053791-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	29	457	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.971	0.778	1	0.971	0.778	1	CLONAL	1	TRUE	1	0.11	2		457	543	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220370	1220370	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0053791-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	20	609	0	ENST00000326873.7:c.465-2A>T		p.X155_splice	ENST00000326873	NM_000455.4	155			1	2	FACETS	0.675	0.514	0.864	0.675	0.514	0.864	SUBCLONAL	1	TRUE	1	0.11	2		609	539	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190848	106190848	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053791-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	31	505	0	ENST00000380013.4:c.4126G>C	p.Asp1376His	p.D1376H	ENST00000380013	NM_001127208.2	1376	Gac/Cac	9/11	1	2	FACETS	0.962	0.776	1	0.962	0.776	1	CLONAL	1	TRUE	1	0.11	2		505	586	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348012	89348012	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053791-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	50	882	0	ENST00000301030.4:c.4938C>G	p.Asp1646Glu	p.D1646E	ENST00000301030	NM_001256183.1	1646	gaC/gaG	9/13	1	2	FACETS	0.975	0.825	1	0.975	0.825	1	CLONAL	1	TRUE	1	0.11	2		882	932	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0053817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	145	670	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.432905114229357	2	FACETS	1	0.932	1	0.51	0.467	0.555	CLONAL	1	TRUE	0	0.469666476103767	2		670	605	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	200	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.401332109690122	3	FACETS	0.894	0.834	0.956	0.894	0.834	0.956	CLONAL	2	TRUE	1	0.469666476103767	3		487	588	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323133	31323133	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	223	938	0	ENST00000412585.2:c.856C>T	p.Gln286Ter	p.Q286*	ENST00000412585	NM_005514.6	286	Cag/Tag	4/8	0.469328567907585	2	FACETS	0.894	0.832	0.958	0.447	0.416	0.479	CLONAL	1	TRUE	0	0.469666476103767	2		938	1062	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117423	115117423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	192	352	0	ENST00000257566.3:c.751C>T	p.Arg251Trp	p.R251W	ENST00000257566	NM_016569.3	251	Cgg/Tgg	4/8	0.401332109690122	3	FACETS	0.803	0.746	0.861	0.803	0.746	0.861	CLONAL	2	TRUE	1	0.469666476103767	3		352	629	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981121	201981121	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	256	765	3	ENST00000359651.3:c.200G>A	p.Trp67Ter	p.W67*	ENST00000359651		67	tGg/tAg	2/8	1	2	FACETS	0.979	0.917	1	0.979	0.917	1	CLONAL	1	TRUE	1	0.469666476103767	2		768	1113	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175508	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0053817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	215	335	0	ENST00000257430.4:c.4216_4217del	p.Gln1406GlufsTer2	p.Q1406Efs*2	ENST00000257430	NM_000038.5	1406	CAg/g	16/16	0.469666476103767	2	FACETS	0.962	0.904	1	0.962	0.904	1	CLONAL	2	TRUE	0	0.469666476103767	2		335	476	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900299	101900299	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	208	398	0	ENST00000374994.4:c.733G>C	p.Glu245Gln	p.E245Q	ENST00000374994	NM_004612.2	245	Gag/Cag	4/9	0.469328567907585	2	FACETS	0.946	0.888	1	0.946	0.888	1	CLONAL	2	TRUE	0	0.469666476103767	2		398	468	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0053824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	45	257	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.715	0.605	0.835	0.715	0.605	0.835	SUBCLONAL	1	TRUE	1	0.476527624704322	2		258	264	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578281	7578281	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660254	NA	P-0053824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	146	753	0	ENST00000269305.4:c.568C>A	p.Pro190Thr	p.P190T	ENST00000269305	NM_001126112.2	190	Cct/Act	6/11	0.476527624704322	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.476527624704322	1		753	410	SUCCESS
APC	324	MSKCC	GRCh37	5	112174998	112174999	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs1554085246	NA	P-0053824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	32	214	0	ENST00000257430.4:c.3709_3710del	p.Gln1237GlufsTer2	p.Q1237Efs*2	ENST00000257430	NM_000038.5	1236	gCA/g	16/16	1	2	FACETS	0.98	0.809	1	0.98	0.809	1	CLONAL	1	TRUE	1	0.476527624704322	2		214	137	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831350	72831350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs967087904	NA	P-0053824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	20	452	0	ENST00000268489.5:c.5231C>T	p.Thr1744Met	p.T1744M	ENST00000268489	NM_006885.3	1744	aCg/aTg	9/10	0.476527624704322	2	FACETS	0.272	0.207	0.347	0.136	0.103	0.174	SUBCLONAL	1	TRUE	0	0.476527624704322	2		452	309	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729709	41729709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768547360	NA	P-0053834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	64	580	0	ENST00000242208.4:c.820G>A	p.Gly274Arg	p.G274R	ENST00000242208	NM_002192.2	274	Gga/Aga	3/3	0.234523750442513	4	FACETS	0.372	0.321	0.428	0.093	0.08	0.107	INDETERMINATE	1	TRUE	0	0.664775785795622	4		580	861	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520006	NA	P-0053834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	389	901	0	ENST00000269305.4:c.821T>G	p.Val274Gly	p.V274G	ENST00000269305	NM_001126112.2	274	gTt/gGt	8/11	0.664775785795622	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.664775785795622	1		901	713	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395738	45395738	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	163	336	1	ENST00000262160.6:c.396G>A	p.Trp132Ter	p.W132*	ENST00000262160	NM_005901.5	132	tgG/tgA	4/11	0.664775785795622	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.664775785795622	1		337	294	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582446	119582446	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs768552900	NA	P-0053834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	123	197	1	ENST00000316626.5:c.955C>T	p.Arg319Ter	p.R319*	ENST00000316626		319	Cga/Tga	10/12	0.341399594625744	3	FACETS	0.752	0.689	0.816	0.752	0.689	0.816	INDETERMINATE	2	TRUE	1	0.664775785795622	3		198	328	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969947	81969947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	224	516	0	ENST00000359376.3:c.3016G>A	p.Gly1006Ser	p.G1006S	ENST00000359376	NM_002661.3	1006	Ggt/Agt	27/33	0.220697586372638	2	FACETS	1	0.99	1	0.636	0.597	0.674	INDETERMINATE	1	TRUE	0	0.664775785795622	2		516	530	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457308	67457308	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	584	706	0	ENST00000327367.4:c.282G>A	p.Trp94Ter	p.W94*	ENST00000327367	NM_005902.3	94	tgG/tgA	2/9	0.664775785795622	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.664775785795622	2		706	823	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384653	31384653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	336	760	0	ENST00000328111.2:c.1355G>A	p.Gly452Glu	p.G452E	ENST00000328111	NM_006892.3	452	gGg/gAg	13/23	0.664775785795622	5	FACETS	0.786	0.743	0.831	0.524	0.495	0.554	SUBCLONAL	2	TRUE	2	0.664775785795622	5		760	1284	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265717	41266209	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATGGCTTGGTGAAATAGCAAACAAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGG	ATGGCTTGGTGAAATAGCAAACAAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGG	-	novel	NA	P-0053834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	50	89	0	ENST00000349496.5:c.13+147_208del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.627639698296506	3	FACETS	1	0.893	1	0.348	0.299	0.4	CLONAL	1	TRUE	0	0.664775785795622	3		89	192	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807107	1807107	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	550	888	1	ENST00000260795.2:c.1438G>A	p.Glu480Lys	p.E480K	ENST00000260795		480	Gag/Aag	10/17	0.269237290825355	2	FACETS	0.965	0.936	0.995	0.965	0.936	0.995	INDETERMINATE	2	TRUE	0	0.664775785795622	2		889	857	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857646	59857657	+	frameshift_variant	Frame_Shift_Del	DEL	AGCCTCCAGCTG	AGCCTCCAGCTG	T	novel	NA	P-0053834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	27	260	0	ENST00000259008.2:c.1900_1911delinsA	p.Gln634LysfsTer5	p.Q634Kfs*5	ENST00000259008	NM_032043.2	634	CAGCTGGAGGCT/A	13/20	0.220697586372638	2	FACETS	0.282	0.225	0.347	0.141	0.112	0.174	INDETERMINATE	1	TRUE	0	0.664775785795622	2		260	288	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	30	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		487	501	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0053843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	15	197	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.145123782264751	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		197	250	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	41	822	0	ENST00000267101.3:c.310G>C	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ctg	3/28	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		822	840	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916575	39916575	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0053843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	25	282	0	ENST00000378444.4:c.4429-1G>A		p.X1477_splice	ENST00000378444	NM_001123385.1	1477			0.3	2	FACETS		NA	1			1	NA	NA	FALSE	0	NA	2		282	291	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053877-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	24	290	1				ENST00000310581	NM_198253.2	-/1132			0.535958160027315	1	FACETS	0.937	0.76	1	0.937	0.76	1	CLONAL	1	TRUE	0	0.535958160027315	1		291	70	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122374	17122374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770396757	NA	P-0053877-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	38	835	0	ENST00000285071.4:c.1021C>T	p.Arg341Trp	p.R341W	ENST00000285071	NM_144997.5	341	Cgg/Tgg	9/14	0.35575538466515	1	FACETS	0.468	0.39	0.553	0.468	0.39	0.553	SUBCLONAL	1	TRUE	0	0.535958160027315	1		835	222	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782169	135782187	+	frameshift_variant	Frame_Shift_Del	DEL	AAAACCCTGGAAGATCACT	AAAACCCTGGAAGATCACT	-	novel	NA	P-0053877-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	49	545	0	ENST00000298552.3:c.1369_1387del	p.Ser457Ter	p.S457*	ENST00000298552	NM_001162426.1	457	AGTGATCTTCCAGGGTTTTta/ta	14/23	0.533122162746092	1	FACETS	0.574	0.491	0.664	0.574	0.491	0.664	SUBCLONAL	1	TRUE	0	0.535958160027315	1		545	233	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024888	31024888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053877-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	36	855	0	ENST00000375687.4:c.4373C>T	p.Ser1458Phe	p.S1458F	ENST00000375687	NM_015338.5	1458	tCt/tTt	13/13	0.360952475285832	2	FACETS	0.278	0.228	0.333	0.139	0.114	0.167	SUBCLONAL	1	TRUE	0	0.535958160027315	2		855	484	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317123	87317123	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053877-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	29	485	0	ENST00000277120.3:c.262G>C	p.Glu88Gln	p.E88Q	ENST00000277120		88	Gaa/Caa	3/19	0.533122162746092	1	FACETS	0.39	0.315	0.474	0.39	0.315	0.474	SUBCLONAL	1	TRUE	0	0.535958160027315	1		485	203	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0053895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	62	321	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.209274921750281	5	FACETS	0.778	0.678	0.884	0.519	0.452	0.589	INDETERMINATE	2	FALSE	2	0.509509287778947	5		321	276	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236153	108236153	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876658529	NA	P-0053895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	183	599	0	ENST00000278616.4:c.9089G>T	p.Gly3030Val	p.G3030V	ENST00000278616	NM_000051.3	3030	gGa/gTa	63/63	0.470217654065433	4	FACETS	0.93	0.863	0.998	0.93	0.863	0.998	CLONAL	2	FALSE	2	0.509509287778947	4		599	583	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577126	7577127	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAAAG	novel	NA	P-0053895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	299	721	0	ENST00000269305.4:c.807_811dup	p.Glu271AlafsTer76	p.E271Afs*76	ENST00000269305	NM_001126112.2	271	gag/gCTTTGag	8/11	0.509509287778947	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	FALSE	0	0.509509287778947	2		721	567	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022757	31022757	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1202551247	NA	P-0053895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	944	736	0	ENST00000375687.4:c.2242C>T	p.Gln748Ter	p.Q748*	ENST00000375687	NM_015338.5	748	Caa/Taa	13/13	0.509509287778947	9	FACETS	1	0.993	1	1	0.993	1	CLONAL	7	FALSE	2	0.509509287778947	9		736	1417	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29099492	29099492	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs587781699	NA	P-0053895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	78	182	0	ENST00000328354.6:c.908+1G>T		p.X303_splice	ENST00000328354	NM_007194.3	303			0.509509287778947	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	3	FALSE	0	0.509509287778947	3		182	118	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0053895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	98	321	0	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	0.209274921750281	5	FACETS	0.854	0.774	0.936	0.854	0.774	0.936	INDETERMINATE	3	FALSE	2	0.509509287778947	5		321	265	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0053896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	263	844	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.614842119614216	2		845	780	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0053896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	55	378	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.836	0.725	0.954	0.836	0.725	0.954	CLONAL	1	TRUE	1	0.614842119614216	2		378	214	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0053896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	357	870	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.614842119614216	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.614842119614216	1		870	756	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068423	26068423	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0053896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	92	301	0	ENST00000435504.4:c.67A>T	p.Lys23Ter	p.K23*	ENST00000435504		23	Aaa/Taa	2/13	0.614842119614216	2	FACETS	0.947	0.871	1	0.947	0.871	1	CLONAL	2	TRUE	0	0.614842119614216	2		301	158	SUCCESS
APC	324	MSKCC	GRCh37	5	112175162	112175162	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561588104	NA	P-0053919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	26	181	0	ENST00000257430.4:c.3871C>T	p.Gln1291Ter	p.Q1291*	ENST00000257430	NM_000038.5	1291	Cag/Tag	16/16	1	2	FACETS	0.912	0.723	1	0.912	0.723	1	CLONAL	1	TRUE	1	0.188213440894531	2		181	303	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	31	226	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	0.933	0.756	1	0.933	0.756	1	CLONAL	1	TRUE	1	0.188213440894531	2		226	353	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0053919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	51	552	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.772	0.655	0.901	0.772	0.655	0.901	CLONAL	1	TRUE	1	0.188213440894531	2		554	702	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0053919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	124	483	0	ENST00000269305.4:c.673-1G>C		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.188213440894531	1	FACETS	0.841	0.761	0.924	1	0.987	1	CLONAL	2	TRUE	0	0.188213440894531	1		483	710	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119881	70119881	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	271	634	0	ENST00000245479.2:c.883G>C	p.Asp295His	p.D295H	ENST00000245479	NM_000346.3	295	Gac/Cac	3/3	0.184253283183864	3	FACETS	1	0.945	1	1	0.945	1	CLONAL	3	TRUE	0	0.188213440894531	3		634	1043	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374497	118374498	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	47	357	2	ENST00000534358.1:c.7896dup	p.Gly2633TrpfsTer13	p.G2633Wfs*13	ENST00000534358	NM_005933.3	2630	-/T	27/36	1	2	FACETS	0.779	0.656	0.915	0.779	0.656	0.915	CLONAL	1	TRUE	1	0.188213440894531	2		359	641	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998959	11998959	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1208900089	NA	P-0053919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	64	303	0	ENST00000353533.5:c.461G>A	p.Arg154Gln	p.R154Q	ENST00000353533	NM_003010.3	154	cGg/cAg	4/11	0.188213440894531	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.188213440894531	1		303	463	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712655	43712655	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	70	639	0	ENST00000382044.4:c.4529A>T	p.Lys1510Ile	p.K1510I	ENST00000382044	NM_001141980.1	1510	aAa/aTa	21/28	1	2	FACETS	0.745	0.647	0.85	0.745	0.647	0.85	SUBCLONAL	1	TRUE	1	0.188213440894531	2		639	999	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240352	98240352	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs373930674	NA	P-0053919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	44	398	0	ENST00000331920.6:c.1332C>A	p.Ser444Arg	p.S444R	ENST00000331920	NM_000264.3	444	agC/agA	9/24	1	2	FACETS	0.783	0.656	0.924	0.783	0.656	0.924	CLONAL	1	TRUE	1	0.188213440894531	2		398	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0053922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	255	835	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.358010301945634	2	FACETS	0.963	0.906	1	0.963	0.906	1	CLONAL	2	TRUE	0	0.370826217733552	2		835	714	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0053922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	71	270	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	0.337508409943493	3	FACETS	0.863	0.762	0.969	0.863	0.762	0.969	CLONAL	2	TRUE	1	0.370826217733552	3		270	263	SUCCESS
APC	324	MSKCC	GRCh37	5	112174920	112174921	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs1554085190	NA	P-0053922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	24	154	0	ENST00000257430.4:c.3631_3632del	p.Met1211ValfsTer5	p.M1211Vfs*5	ENST00000257430	NM_000038.5	1210	cAT/c	16/16	0.337508409943493	3	FACETS	0.808	0.637	1	0.404	0.318	0.501	CLONAL	1	TRUE	1	0.370826217733552	3		154	190	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196695	67196701	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGGGG	AGGGGGG	-	novel	NA	P-0053922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	125	702	0	ENST00000312629.5:c.224_230del	p.Lys75ThrfsTer22	p.K75Tfs*22	ENST00000312629	NM_003952.2	75	aAGGGGGGc/ac	3/15	0.337508409943493	3	FACETS	1	0.979	1	0.642	0.583	0.705	CLONAL	1	TRUE	1	0.370826217733552	3		702	622	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533925	63533926	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	103	714	0	ENST00000307078.5:c.1228dup	p.Thr410AsnfsTer52	p.T410Nfs*52	ENST00000307078	NM_004655.3	410	aca/aAca	6/11	0.310399695657442	4	FACETS	1	0.938	1	0.356	0.318	0.396	CLONAL	1	TRUE	1	0.370826217733552	4		714	713	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0053923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	75	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.883	0.781	0.992	0.883	0.781	0.992	CLONAL	1	TRUE	1	0.53235801392111	2		457	319	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0053923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	111	494	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.939	0.85	1	0.939	0.85	1	CLONAL	1	TRUE	1	0.53235801392111	2		494	444	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044850	47044850	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	232	1210	1	ENST00000377604.3:c.2176C>T	p.Arg726Ter	p.R726*	ENST00000377604	NM_001204468.1	726	Cga/Tga	20/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.53235801392111	2		1211	817	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2185874	2185874	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1378442482	NA	P-0053923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	140	512	0	ENST00000398665.3:c.146C>T	p.Pro49Leu	p.P49L	ENST00000398665	NM_032482.2	49	cCg/cTg	3/28	1	2	FACETS	0.974	0.892	1	0.974	0.892	1	CLONAL	1	TRUE	1	0.53235801392111	2		512	540	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941064	71941064	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0053923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	205	981	0	ENST00000298229.2:c.939+1G>A		p.X313_splice	ENST00000298229	NM_001567.3	313			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.53235801392111	2		981	731	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775012	73775012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	100	466	1	ENST00000254810.4:c.161G>A	p.Arg54His	p.R54H	ENST00000254810	NM_005324.3	54	cGt/cAt	3/4	1	2	FACETS	0.949	0.854	1	0.949	0.854	1	CLONAL	1	TRUE	1	0.53235801392111	2		467	396	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713856	30713856	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553630289	NA	P-0053923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	302	704	0	ENST00000295754.5:c.1181G>A	p.Cys394Tyr	p.C394Y	ENST00000295754	NM_003242.5	394	tGc/tAc	4/7	0.53235801392111	2	FACETS	0.889	0.845	0.933	0.889	0.845	0.933	CLONAL	2	TRUE	0	0.53235801392111	2		704	638	SUCCESS
APC	324	MSKCC	GRCh37	5	112179035	112179036	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	57	151	0	ENST00000257430.4:c.7749dup	p.Ala2584SerfsTer4	p.A2584Sfs*4	ENST00000257430	NM_000038.5	2582	gaa/gAaa	16/16	1	2	FACETS	0.84	0.728	0.959	0.84	0.728	0.959	CLONAL	1	TRUE	1	0.53235801392111	2		151	255	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877198	151877198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	179	342	0	ENST00000262189.6:c.7163G>A	p.Arg2388His	p.R2388H	ENST00000262189	NM_170606.2	2388	cGt/cAt	37/59	0.53235801392111	3	FACETS	0.904	0.841	0.968	0.904	0.841	0.968	CLONAL	2	TRUE	1	0.53235801392111	3		342	471	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38139000	38139000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	74	134	0	ENST00000317025.8:c.3603G>A	p.Met1201Ile	p.M1201I	ENST00000317025	NM_023034.1	1201	atG/atA	20/24	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.53235801392111	2		134	265	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0053924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	188	501	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.247522909960582	1	FACETS	0.947	0.878	1	1	0.993	1	CLONAL	2	TRUE	0	0.247522909960582	1		502	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0053924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	192	550	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.247522909960582	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.247522909960582	1		552	1117	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0053924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	239	252	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.240486439678011	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.247522909960582	3		252	642	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519893	NA	P-0053924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	206	691	0	ENST00000267101.3:c.310G>T	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ttg	3/28	0.119429156468028	4	FACETS	0.75	0.694	0.809	0.75	0.694	0.809	INDETERMINATE	2	TRUE	2	0.247522909960582	4		691	1384	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244196	5244196	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs919253826	NA	P-0053924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	112	900	1	ENST00000357368.4:c.1286C>T	p.Ala429Val	p.A429V	ENST00000357368	NM_002850.3	429	gCg/gTg	11/38	0.247522909960582	1	FACETS	0.649	0.582	0.72	0.649	0.582	0.72	SUBCLONAL	1	TRUE	0	0.247522909960582	1		901	1222	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468492	89468492	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	33	187	0	ENST00000336596.2:c.2026C>G	p.Gln676Glu	p.Q676E	ENST00000336596	NM_005233.5	676	Cag/Gag	11/17	0.147088245145117	1	FACETS	0.429	0.348	0.52	0.429	0.348	0.52	INDETERMINATE	1	TRUE	0	0.247522909960582	1		187	545	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0053930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	61	364	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.26407302170644	3	FACETS	0.972	0.839	1	0.486	0.419	0.558	CLONAL	1	TRUE	1	0.26407302170644	3		365	538	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039610	180039610	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs202140363	NA	P-0053930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	118	897	0	ENST00000261937.6:c.3433C>T	p.Arg1145Cys	p.R1145C	ENST00000261937	NM_182925.4	1145	Cgc/Tgc	26/30	0.26407302170644	3	FACETS	1	0.949	1	0.542	0.488	0.599	CLONAL	1	TRUE	1	0.26407302170644	3		897	934	SUCCESS
APC	324	MSKCC	GRCh37	5	112175419	112175419	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0053930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	104	207	2	ENST00000257430.4:c.4128T>G	p.Tyr1376Ter	p.Y1376*	ENST00000257430	NM_000038.5	1376	taT/taG	16/16	0.26407302170644	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	1	0.26407302170644	3		209	413	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120040	70120040	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	11	24	0	ENST00000245479.2:c.1042C>T	p.Gln348Ter	p.Q348*	ENST00000245479	NM_000346.3	348	Cag/Tag	3/3	0.26407302170644	4	FACETS	1	0.758	1	1	0.758	1	CLONAL	2	TRUE	2	0.26407302170644	4		24	49	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120247	70120247	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	266	847	2	ENST00000245479.2:c.1249del	p.Gln417ArgfsTer53	p.Q417Rfs*53	ENST00000245479	NM_000346.3	417	Cag/ag	3/3	0.26407302170644	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.26407302170644	4		849	1112	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517955	176517955	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	249	787	2	ENST00000292408.4:c.453C>A	p.His151Gln	p.H151Q	ENST00000292408	NM_213647.1	151	caC/caA	5/18	0.26407302170644	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.26407302170644	3		789	1002	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959366	26959366	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1418353379	NA	P-0053945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	43	386	0	ENST00000381527.3:c.533G>A	p.Arg178Gln	p.R178Q	ENST00000381527	NM_001260.1	178	cGa/cAa	6/13	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.14	2		386	544	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715685	30715688	+	frameshift_variant	Frame_Shift_Del	DEL	ACTC	ACTC	-	novel	NA	P-0053945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	73	361	0	ENST00000295754.5:c.1343_1346del	p.Tyr448SerfsTer9	p.Y448Sfs*9	ENST00000295754	NM_003242.5	448	tACTCc/tc	5/7	1	2	FACETS	0.826	0.723	0.938	1	0.978	1	CLONAL	2	TRUE	1	0.14	2		361	631	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259500	89259500	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	40	538	0	ENST00000336596.2:c.644C>G	p.Thr215Arg	p.T215R	ENST00000336596	NM_005233.5	215	aCg/aGg	3/17	1	2	FACETS	0.716	0.593	0.854	0.716	0.593	0.854	SUBCLONAL	1	TRUE	1	0.14	2		538	798	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0053958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	309	1045	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.791	0.747	0.836	1	0.995	1	SUBCLONAL	2	TRUE	1	0.391253227544994	2		1046	999	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0053958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	175	571	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.391253227544994	2		571	665	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	184	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.307789653336368	4	FACETS	1	0.933	1	0.671	0.622	0.722	CLONAL	2	TRUE	1	0.391253227544994	4		487	650	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791758	42791758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1380826096	NA	P-0053958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	178	899	0	ENST00000575354.2:c.644G>A	p.Arg215Gln	p.R215Q	ENST00000575354	NM_015125.3	215	cGg/cAg	5/20	1	2	FACETS	0.941	0.867	1	0.941	0.867	1	CLONAL	1	TRUE	1	0.391253227544994	2		899	967	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386409	31386409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572676072	NA	P-0053958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	117	879	0	ENST00000328111.2:c.1634G>A	p.Arg545His	p.R545H	ENST00000328111	NM_006892.3	545	cGc/cAc	15/23	0.250332761082243	1	FACETS	0.493	0.444	0.546	0.493	0.444	0.546	SUBCLONAL	1	TRUE	0	0.391253227544994	1		879	975	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281344	49281344	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202077345	NA	P-0053958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	119	803	0	ENST00000282018.3:c.391G>A	p.Val131Met	p.V131M	ENST00000282018	NM_020377.2	131	Gtg/Atg	1/1	1	2	FACETS	0.632	0.569	0.698	0.632	0.569	0.698	SUBCLONAL	1	TRUE	1	0.391253227544994	2		803	963	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125496706	125496706	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	30	416	0	ENST00000428830.2:c.43C>G	p.Leu15Val	p.L15V	ENST00000428830	NM_001114121.2	15	Ctg/Gtg	2/14	1	2	FACETS	0.275	0.221	0.337	0.275	0.221	0.337	SUBCLONAL	1	TRUE	1	0.391253227544994	2		416	557	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557828	187557832	+	frameshift_variant	Frame_Shift_Del	DEL	TCCCG	TCCCG	-	novel	NA	P-0053958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	51	509	0	ENST00000441802.2:c.3879_3883del	p.Asp1293GlufsTer2	p.D1293Efs*2	ENST00000441802	NM_005245.3	1293	gaCGGGAat/gaat	5/27	0.357737493664203	2	FACETS	0.385	0.326	0.45	0.193	0.163	0.225	SUBCLONAL	1	TRUE	0	0.391253227544994	2		509	677	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987214	2987214	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	34	465	0	ENST00000396946.4:c.215G>C	p.Arg72Pro	p.R72P	ENST00000396946	NM_032415.4	72	cGa/cCa	3/25	1	2	FACETS	0.279	0.227	0.338	0.279	0.227	0.338	SUBCLONAL	1	TRUE	1	0.391253227544994	2		465	623	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0053975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	113	775	2	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.32622751944516	1	FACETS	0.642	0.578	0.71	0.642	0.578	0.71	SUBCLONAL	1	TRUE	0	0.39237200273202	1		777	721	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0053975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	73	165	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.276294929526855	2	FACETS	1	0.952	1	0.58	0.511	0.652	CLONAL	1	TRUE	0	0.39237200273202	2		165	321	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169376	11169376	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	36	620	0	ENST00000361445.4:c.7499T>A	p.Ile2500Asn	p.I2500N	ENST00000361445	NM_004958.3	2500	aTt/aAt	56/58	1	2	FACETS	0.252	0.206	0.304	0.252	0.206	0.304	SUBCLONAL	1	TRUE	1	0.39237200273202	2		620	728	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118924	70118926	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0053975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	231	924	0	ENST00000245479.2:c.499_501del	p.Lys167del	p.K167del	ENST00000245479	NM_000346.3	166	AAG/-	2/3	1	2	FACETS	0.971	0.905	1	0.971	0.905	1	CLONAL	1	TRUE	1	0.39237200273202	2		924	1212	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956143	55956143	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	96	570	0	ENST00000263923.4:c.3172G>T	p.Asp1058Tyr	p.D1058Y	ENST00000263923	NM_002253.2	1058	Gat/Tat	23/30	1	2	FACETS	0.736	0.656	0.821	0.736	0.656	0.821	SUBCLONAL	1	TRUE	1	0.39237200273202	2		570	665	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0053984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	610	457	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.978	1	1	0.998	1	CLONAL	2	TRUE	1	0.623686678906216	2		457	969	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0053984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	275	654	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.610949408814063	1	FACETS	0.937	0.886	0.988	0.937	0.886	0.988	CLONAL	1	TRUE	0	0.623686678906216	1		654	648	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594221	55594221	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913512	NA	P-0053988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	1403	181	0	ENST00000288135.5:c.1924A>G	p.Lys642Glu	p.K642E	ENST00000288135	NM_000222.2	642	Aaa/Gaa	13/21	0.848687769356672	6	FACETS	0.968	0.952	0.983	0.968	0.952	0.983	CLONAL	5	TRUE	1	0.848687769356672	6		181	1843	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0054018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	191	382	2	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	0.641024195676213	5	FACETS	1	0.986	1	0.81	0.756	0.865	CLONAL	2	TRUE	2	0.641024195676213	5		384	481	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0054018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	322	519	4	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.641024195676213	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.641024195676213	2		523	502	SUCCESS
APC	324	MSKCC	GRCh37	5	112175199	112175199	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	70	260	0	ENST00000257430.4:c.3910del	p.Ile1304Ter	p.I1304*	ENST00000257430	NM_000038.5	1303	cAa/ca	16/16	0.641024195676213	2	FACETS	0.925	0.841	1	0.925	0.841	1	CLONAL	2	TRUE	0	0.641024195676213	2		260	118	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5258067	5258067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	173	598	9	ENST00000357368.4:c.667G>A	p.Gly223Ser	p.G223S	ENST00000357368	NM_002850.3	223	Ggc/Agc	8/38	0.403715851681732	1	FACETS	0.762	0.708	0.818	0.762	0.708	0.818	SUBCLONAL	1	TRUE	0	0.641024195676213	1		607	481	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214705	133214705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1445288473	NA	P-0054018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	32	519	0	ENST00000320574.5:c.5573G>A	p.Arg1858His	p.R1858H	ENST00000320574	NM_006231.2	1858	cGc/cAc	41/49	0.641024195676213	3	FACETS	0.238	0.192	0.289	0.119	0.096	0.145	SUBCLONAL	1	TRUE	1	0.641024195676213	3		519	555	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278092	15278092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	79	824	1	ENST00000263388.2:c.5330C>T	p.Ala1777Val	p.A1777V	ENST00000263388	NM_000435.2	1777	gCt/gTt	29/33	0.641024195676213	4	FACETS	0.405	0.355	0.459	0.135	0.118	0.153	SUBCLONAL	1	TRUE	1	0.641024195676213	4		825	998	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419959	152419959	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	158	602	2	ENST00000206249.3:c.1646T>A	p.Leu549Gln	p.L549Q	ENST00000206249	NM_000125.3	549	cTa/cAa	8/8	0.641024195676213	3	FACETS	1	0.936	1	0.51	0.469	0.553	CLONAL	1	TRUE	1	0.641024195676213	3		604	638	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0054058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	71	378	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.271496002972872	4	FACETS	0.998	0.882	1			1	CLONAL	2	TRUE	NA	0.383019699571659	4		378	257	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0054058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	123	252	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.383019699571659	3	FACETS	0.959	0.884	1	0.959	0.884	1	CLONAL	3	TRUE	0	0.383019699571659	3		252	266	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578476	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTGCCGGGCGG	GGGTGCCGGGCGG	-	rs876659215	NA	P-0054058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	341	929	0	ENST00000269305.4:c.454_466del	p.Pro152AlafsTer14	p.P152Afs*14	ENST00000269305	NM_001126112.2	152	CCGCCCGGCACCCgc/gc	5/11	0.278310507048457	3	FACETS	1	0.99	1	0.775	0.736	0.815	CLONAL	2	TRUE	0	0.383019699571659	3		929	912	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158476	26158476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776467875	NA	P-0054058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	106	655	0	ENST00000289316.2:c.79G>A	p.Gly27Arg	p.G27R	ENST00000289316	NM_138720.2	27	Ggg/Agg	1/2	0.383019699571659	3	FACETS	1	0.911	1	0.508	0.456	0.563	CLONAL	1	TRUE	1	0.383019699571659	3		655	649	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170753	11170753	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766797299	NA	P-0054058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	235	816	0	ENST00000358026.2:c.4897C>T	p.Arg1633Trp	p.R1633W	ENST00000358026	NM_001128849.1	1633	Cgg/Tgg	35/36	0.383019699571659	3	FACETS	0.914	0.855	0.974	0.914	0.855	0.974	CLONAL	2	TRUE	1	0.383019699571659	3		816	800	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742444	145742444	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	109	932	0	ENST00000428558.2:c.344G>C	p.Gly115Ala	p.G115A	ENST00000428558	NM_004260.3	115	gGc/gCc	4/22	0.383019699571659	7	FACETS	0.852	0.762	0.947	0.213	0.19	0.237	CLONAL	1	TRUE	3	0.383019699571659	7		932	1308	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0054065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	350	729	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.437432201356207	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.437432201356207	2		730	782	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	85	351	0	ENST00000342988.3:c.1067C>G	p.Pro356Arg	p.P356R	ENST00000342988	NM_005359.5	356	cCt/cGt	9/12	0.437432201356207	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.437432201356207	1		351	260	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031954	10031954	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199528312	NA	P-0054065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	105	577	1	ENST00000330684.3:c.869C>T	p.Ala290Val	p.A290V	ENST00000330684	NM_001134407.1	290	gCg/gTg	3/13	1	2	FACETS	0.767	0.688	0.85	0.767	0.688	0.85	SUBCLONAL	1	TRUE	1	0.437432201356207	2		578	626	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750528	57750528	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs768613514	NA	P-0054065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	27	368	0	ENST00000274289.3:c.1940A>G	p.Asn647Ser	p.N647S	ENST00000274289	NM_006622.3	647	aAt/aGt	14/14	1	2	FACETS	0.398	0.317	0.491	0.398	0.317	0.491	SUBCLONAL	1	TRUE	1	0.437432201356207	2		368	310	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266070	41266287	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGC	AGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGC	-	novel	NA	P-0054065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	87	291	0	ENST00000349496.5:c.70_241+46del		p.X24_splice	ENST00000349496	NM_001904.3	24		3/15	0.437432201356207	4	FACETS	0.805	0.719	0.896	0.537	0.479	0.598	CLONAL	2	TRUE	1	0.437432201356207	4		291	355	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0054093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	222	757	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.200972933377423	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.236782557829967	2		757	766	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0054093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	149	360	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.22495627386969	3	FACETS	0.99	0.911	1	0.99	0.911	1	CLONAL	3	TRUE	0	0.236782557829967	3		360	474	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395736	45395736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	24	379	0	ENST00000262160.6:c.398G>A	p.Arg133His	p.R133H	ENST00000262160	NM_005901.5	133	cGc/cAc	4/11	0.20259543469508	2	FACETS	0.457	0.357	0.572	0.228	0.178	0.286	SUBCLONAL	1	TRUE	0	0.236782557829967	2		379	444	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981551	201981551	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	102	835	0	ENST00000359651.3:c.467del	p.Pro156GlnfsTer98	p.P156Qfs*98	ENST00000359651		155	gaC/ga	3/8	1	2	FACETS	0.932	0.833	1	0.932	0.833	1	CLONAL	1	TRUE	1	0.236782557829967	2		835	924	SUCCESS
APC	324	MSKCC	GRCh37	5	112174658	112174659	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	40	283	0	ENST00000257430.4:c.3371dup	p.Asn1124LysfsTer11	p.N1124Kfs*11	ENST00000257430	NM_000038.5	1123	caa/cAaa	16/16	0.236782557829967	2	FACETS	1	0.843	1	0.506	0.421	0.599	CLONAL	1	TRUE	0	0.236782557829967	2		283	334	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69103988	69103988	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	76	440	0	ENST00000288368.4:c.4378C>G	p.Pro1460Ala	p.P1460A	ENST00000288368	NM_024870.2	1460	Cca/Gca	36/40	0.00376788181055199	3	FACETS	1	0.924	1	0.537	0.47	0.608	INDETERMINATE	1	TRUE	1	0.236782557829967	3		440	669	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0054116-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	9	670	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.537	0.355	0.769	0.537	0.355	0.769	SUBCLONAL	1	TRUE	1	0.17	2		670	197	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959180	2959180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184296576	NA	P-0054116-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	39	1010	2	ENST00000396946.4:c.2336G>A	p.Arg779Gln	p.R779Q	ENST00000396946	NM_032415.4	779	cGg/cAg	18/25	1	2	FACETS	0.681	0.563	0.813	0.681	0.563	0.813	SUBCLONAL	1	TRUE	1	0.17	2		1012	674	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054116-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	9	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.375	0.248	0.539	0.375	0.248	0.539	SUBCLONAL	1	TRUE	1	0.17	2		457	282	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473723	67473723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223740	NA	P-0054116-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	68	797	0	ENST00000327367.4:c.803G>A	p.Arg268His	p.R268H	ENST00000327367	NM_005902.3	268	cGc/cAc	6/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.17	2		797	566	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436026	56436026	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771831816	NA	P-0054116-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	58	426	0	ENST00000407977.2:c.1111C>T	p.Arg371Ter	p.R371*	ENST00000407977		371	Cga/Tga	9/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.17	2		426	482	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045136	47045136	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054116-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	31	837	1	ENST00000377604.3:c.2377C>T	p.Arg793Ter	p.R793*	ENST00000377604	NM_001204468.1	793	Cga/Tga	21/24	1	2	FACETS	0.743	0.6	0.905	0.743	0.6	0.905	CLONAL	1	TRUE	1	0.17	2		838	491	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981851	201981852	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0054116-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	56	1243	0	ENST00000359651.3:c.566_567dup	p.Ser190ProfsTer65	p.S190Pfs*65	ENST00000359651		188	gcc/gCCcc	4/8	1	2	FACETS	0.881	0.753	1	0.881	0.753	1	CLONAL	1	TRUE	1	0.17	2		1243	748	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0054135-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	524	490	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.244072879735326	9	FACETS	0.951	0.916	0.987	0.951	0.916	0.987	CLONAL	8	TRUE	1	0.244072879735326	9		490	1046	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126343	5126343	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41316003	NA	P-0054135-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	15	295	0	ENST00000381652.3:c.3188G>A	p.Arg1063His	p.R1063H	ENST00000381652	NM_004972.3	1063	cGt/cAt	24/25	0.244072879735326	1	FACETS	0.624	0.458	0.821	0.624	0.458	0.821	SUBCLONAL	1	TRUE	0	0.244072879735326	1		295	173	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934576	NA	P-0054135-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	201	835	0	ENST00000269305.4:c.818G>C	p.Arg273Pro	p.R273P	ENST00000269305	NM_001126112.2	273	cGt/cCt	8/11	0.200443601788094	2	FACETS	0.844	0.782	0.908	0.844	0.782	0.908	CLONAL	2	TRUE	0	0.244072879735326	2		835	976	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0054137-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	27	449	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.17	2		449	306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0054137-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	44	947	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	1	2	FACETS	0.827	0.692	0.976	0.827	0.692	0.976	CLONAL	1	TRUE	1	0.17	2		947	626	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589743	28589743	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054137-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	18	455	1	ENST00000241453.7:c.2637G>A	p.Trp879Ter	p.W879*	ENST00000241453	NM_004119.2	879	tgG/tgA	21/24	0.134228990402112	1	FACETS	0.633	0.476	0.819	0.633	0.476	0.819	SUBCLONAL	1	TRUE	0	0.17	1		456	306	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914056	32914056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054137-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	11	530	0	ENST00000380152.3:c.5564C>T	p.Ser1855Leu	p.S1855L	ENST00000380152		1855	tCa/tTa	11/27	0.134228990402112	1	FACETS	0.592	0.409	0.819	0.592	0.409	0.819	SUBCLONAL	1	TRUE	0	0.17	1		530	200	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945672	54945672	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054137-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	19	384	1	ENST00000312783.6:c.898A>G	p.Met300Val	p.M300V	ENST00000312783	NM_198436.1	300	Atg/Gtg	9/10	1	2	FACETS	0.891	0.677	1	0.891	0.677	1	CLONAL	1	TRUE	1	0.17	2		385	251	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518024	8518024	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054137-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	28	517	0	ENST00000356435.5:c.1367C>A	p.Thr456Lys	p.T456K	ENST00000356435		456	aCa/aAa	10/35	1	2	FACETS	0.89	0.712	1	0.89	0.712	1	CLONAL	1	TRUE	1	0.17	2		517	370	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0054173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	18	197	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.517	0.39	0.665	0.517	0.39	0.665	SUBCLONAL	1	TRUE	1	0.324096818348808	2		197	215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0054173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	199	590	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.322938394413033	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.324096818348808	1		590	838	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0054173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	26	165	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.827	0.66	1	0.827	0.66	1	CLONAL	1	TRUE	1	0.324096818348808	2		165	194	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120049	70120049	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	17	23	0	ENST00000245479.2:c.1051C>T	p.Gln351Ter	p.Q351*	ENST00000245479	NM_000346.3	351	Cag/Tag	3/3	0.31431722886633	3	FACETS	1	0.847	1	1	0.847	1	CLONAL	2	TRUE	1	0.324096818348808	3		23	54	SUCCESS
APC	324	MSKCC	GRCh37	5	112174424	112174424	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	30	187	0	ENST00000257430.4:c.3133C>T	p.Gln1045Ter	p.Q1045*	ENST00000257430	NM_000038.5	1045	Cag/Tag	16/16	1	2	FACETS	0.723	0.585	0.878	0.723	0.585	0.878	SUBCLONAL	1	TRUE	1	0.324096818348808	2		187	256	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517946	187517946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	72	429	0	ENST00000441802.2:c.12748C>T	p.Pro4250Ser	p.P4250S	ENST00000441802	NM_005245.3	4250	Cct/Tct	25/27	0.31431722886633	3	FACETS	0.764	0.667	0.868	0.382	0.333	0.434	SUBCLONAL	1	TRUE	1	0.324096818348808	3		429	676	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401739	139401756	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CCGTGCAGCGGCCCTTAC	CCGTGCAGCGGCCCTTAC	-	novel	NA	P-0054173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	71	739	0	ENST00000277541.6:c.3643+1_3643+18del		p.X1215_splice	ENST00000277541	NM_017617.3	1215			1	2	FACETS	0.437	0.38	0.499	0.437	0.38	0.499	SUBCLONAL	1	TRUE	1	0.324096818348808	2		739	1002	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054212-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	31	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.19003895502711	1	FACETS	0.421	0.34	0.512	0.421	0.34	0.512	INDETERMINATE	1	TRUE	0	0.329744951048332	1		457	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0054212-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	76	731	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.302560699101631	1	FACETS	0.691	0.607	0.781	0.691	0.607	0.781	SUBCLONAL	1	TRUE	0	0.329744951048332	1		731	557	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969884	81969884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199840870	NA	P-0054212-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	93	594	1	ENST00000359376.3:c.2953G>A	p.Val985Ile	p.V985I	ENST00000359376	NM_002661.3	985	Gtc/Atc	27/33	1	2	FACETS	0.948	0.844	1	0.948	0.844	1	CLONAL	1	TRUE	1	0.329744951048332	2		595	595	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	34	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.788	0.644	0.948	0.788	0.644	0.948	CLONAL	1	TRUE	1	0.23395276180105	2		487	369	SUCCESS
APC	324	MSKCC	GRCh37	5	112175199	112175199	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	26	260	0	ENST00000257430.4:c.3910del	p.Ile1304Ter	p.I1304*	ENST00000257430	NM_000038.5	1303	cAa/ca	16/16	1	2	FACETS	0.907	0.721	1	0.907	0.721	1	CLONAL	1	TRUE	1	0.23395276180105	2		260	245	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433673	149433673	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1467770819	NA	P-0054231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	111	1046	3	ENST00000286301.3:c.2878G>A	p.Ala960Thr	p.A960T	ENST00000286301	NM_005211.3	960	Gcc/Acc	22/22	1	2	FACETS	0.783	0.702	0.869	0.783	0.702	0.869	SUBCLONAL	1	TRUE	1	0.23395276180105	2		1049	1212	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202313	133202313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756301031	NA	P-0054231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	142	1082	0	ENST00000320574.5:c.6575C>T	p.Ala2192Val	p.A2192V	ENST00000320574	NM_006231.2	2192	gCg/gTg	47/49	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.23395276180105	2		1082	1162	SUCCESS
APC	324	MSKCC	GRCh37	5	112175273	112175273	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123121	NA	P-0054231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	27	308	0	ENST00000257430.4:c.3982C>T	p.Gln1328Ter	p.Q1328*	ENST00000257430	NM_000038.5	1328	Cag/Tag	16/16	1	2	FACETS	0.762	0.607	0.938	0.762	0.607	0.938	CLONAL	1	TRUE	1	0.23395276180105	2		308	303	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579871	7579871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	170	1045	2	ENST00000269305.4:c.42del	p.Ser15ValfsTer29	p.S15Vfs*29	ENST00000269305	NM_001126112.2	14	ctG/ct	2/11	0.23395276180105	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.23395276180105	1		1047	1064	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223239	5223239	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1325	208	1345	1	ENST00000357368.4:c.2564C>A	p.Pro855Gln	p.P855Q	ENST00000357368	NM_002850.3	855	cCg/cAg	18/38	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.23395276180105	2		1346	1533	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604789	48604789	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	101	444	0	ENST00000342988.3:c.1611C>G	p.Asp537Glu	p.D537E	ENST00000342988	NM_005359.5	537	gaC/gaG	12/12	0.398009961575331	1	FACETS	0.818	0.734	0.906	0.818	0.734	0.906	CLONAL	1	TRUE	0	0.398009961575331	1		444	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0054239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	227	487	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.398009961575331	1	FACETS	0.921	0.858	0.986	0.921	0.858	0.986	CLONAL	1	TRUE	0	0.398009961575331	1		487	992	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0054239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	89	428	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.398009961575331	NA		428	521	SUCCESS
APC	324	MSKCC	GRCh37	5	112175350	112175351	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0054239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	99	231	0	ENST00000257430.4:c.4059_4060del	p.Glu1353AspfsTer21	p.E1353Dfs*21	ENST00000257430	NM_000038.5	1353	gaATtt/gatt	16/16	0.319882299058024	2	FACETS	0.824	0.745	0.905	0.824	0.745	0.905	CLONAL	2	TRUE	0	0.398009961575331	2		231	302	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372019	55372019	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	119	511	0	ENST00000297316.4:c.709T>G	p.Phe237Val	p.F237V	ENST00000297316	NM_022454.3	237	Ttc/Gtc	2/2	0.398009961575331	1	FACETS	0.692	0.625	0.762	0.692	0.625	0.762	SUBCLONAL	1	TRUE	0	0.398009961575331	1		511	692	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	106	466	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.811	0.729	0.898	0.811	0.729	0.898	CLONAL	1	TRUE	1	0.44	2		466	594	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	214	588	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.956	0.888	1	0.956	0.888	1	CLONAL	1	TRUE	1	0.44	2		592	1018	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	116	498	4	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.964	0.872	1	0.964	0.872	1	CLONAL	1	TRUE	1	0.44	2		502	547	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	107	412	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.967	0.871	1	0.967	0.871	1	CLONAL	1	TRUE	1	0.44	2		412	503	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	343	1445	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.858	0.814	0.901	1	0.996	1	CLONAL	2	TRUE	1	0.44	2		1452	909	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	58	382	2	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.819	0.708	0.938	0.819	0.708	0.938	CLONAL	1	TRUE	1	0.44	2		384	322	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70441195	70441195	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	152	482	0	ENST00000373644.4:c.4864C>T	p.Arg1622Ter	p.R1622*	ENST00000373644	NM_030625.2	1622	Cga/Tga	9/12	1	2	FACETS	0.833	0.763	0.907	0.833	0.763	0.907	CLONAL	1	TRUE	1	0.44	2		482	829	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112154	115112154	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	201	977	0	ENST00000257566.3:c.1586del	p.Gly529AlafsTer103	p.G529Afs*103	ENST00000257566	NM_016569.3	529	gGc/gc	7/8	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.44	2		977	875	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198936	67198936	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs747230226	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	65	638	1	ENST00000312629.5:c.407A>G	p.Tyr136Cys	p.Y136C	ENST00000312629	NM_003952.2	136	tAt/tGt	5/15	1	2	FACETS	0.387	0.335	0.444	0.387	0.335	0.444	SUBCLONAL	1	TRUE	1	0.44	2		639	763	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950396	15950396	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201721277	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	138	468	0	ENST00000268712.3:c.6548G>A	p.Arg2183His	p.R2183H	ENST00000268712	NM_006311.3	2183	cGc/cAc	42/46	1	2	FACETS	0.948	0.864	1	0.948	0.864	1	CLONAL	1	TRUE	1	0.44	2		468	662	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132428	11132428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	275	1102	1	ENST00000358026.2:c.2644G>A	p.Glu882Lys	p.E882K	ENST00000358026	NM_001128849.1	882	Gaa/Aaa	19/36	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.44	2		1103	1060	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274794	123274794	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913478	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	160	555	0	ENST00000358487.5:c.1124A>G	p.Tyr375Cys	p.Y375C	ENST00000358487	NM_000141.4	375	tAc/tGc	9/18	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.44	2		555	726	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141492	11141492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	181	936	1	ENST00000358026.2:c.3469C>T	p.Arg1157Trp	p.R1157W	ENST00000358026	NM_001128849.1	1157	Cgg/Tgg	25/36	1	2	FACETS	0.899	0.83	0.972	0.899	0.83	0.972	CLONAL	1	TRUE	1	0.44	2		937	915	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638555	176638555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210270412	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	187	601	0	ENST00000439151.2:c.3155G>A	p.Arg1052His	p.R1052H	ENST00000439151	NM_022455.4	1052	cGc/cAc	5/23	1	2	FACETS	0.97	0.897	1	0.97	0.897	1	CLONAL	1	TRUE	1	0.44	2		601	876	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276256	15276256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759704420	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	188	840	0	ENST00000263388.2:c.5738C>T	p.Ala1913Val	p.A1913V	ENST00000263388	NM_000435.2	1913	gCg/gTg	31/33	1	2	FACETS	0.902	0.834	0.974	0.902	0.834	0.974	CLONAL	1	TRUE	1	0.44	2		840	947	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149355	119149356	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATG	rs397507494	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	86	419	0	ENST00000264033.4:c.1380_1382dup	p.Asp460dup	p.D460dup	ENST00000264033	NM_005188.3	460	tat/tATGat	9/16	1	2	FACETS	0.686	0.608	0.769	0.686	0.608	0.769	SUBCLONAL	1	TRUE	1	0.44	2		419	570	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900329	101900329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	110	286	0	ENST00000374994.4:c.763C>T	p.Arg255Cys	p.R255C	ENST00000374994	NM_004612.2	255	Cgt/Tgt	4/9	1	2	FACETS	0.936	0.845	1	0.936	0.845	1	CLONAL	1	TRUE	1	0.44	2		286	534	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155325	185155325	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746379057	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	116	422	0	ENST00000265026.3:c.566C>T	p.Ala189Val	p.A189V	ENST00000265026	NM_004721.4	189	gCg/gTg	3/14	1	2	FACETS	0.84	0.758	0.925	0.84	0.758	0.925	CLONAL	1	TRUE	1	0.44	2		422	628	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596110	43596110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1477699803	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	172	803	1	ENST00000355710.3:c.277G>A	p.Gly93Ser	p.G93S	ENST00000355710	NM_020975.4	93	Ggc/Agc	2/20	1	2	FACETS	0.976	0.899	1	0.976	0.899	1	CLONAL	1	TRUE	1	0.44	2		804	801	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484772	57484772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	138	614	0	ENST00000371085.3:c.752G>A	p.Ser251Asn	p.S251N	ENST00000371085	NM_000516.4	251	aGc/aAc	10/13	1	2	FACETS	0.815	0.742	0.891	0.815	0.742	0.891	CLONAL	1	TRUE	1	0.44	2		614	770	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432609	78432609	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1233786882	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	158	416	0	ENST00000370768.2:c.374G>A	p.Arg125His	p.R125H	ENST00000370768	NM_003902.3	125	cGc/cAc	6/20	1	2	FACETS	0.995	0.914	1	0.995	0.914	1	CLONAL	1	TRUE	1	0.44	2		416	722	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347446	91347446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757088548	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	123	324	2	ENST00000355112.3:c.3608C>T	p.Ala1203Val	p.A1203V	ENST00000355112	NM_000057.2	1203	gCg/gTg	19/22	1	2	FACETS	0.969	0.879	1	0.969	0.879	1	CLONAL	1	TRUE	1	0.44	2		326	577	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396234	396234	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	178	814	1	ENST00000262320.3:c.792del	p.Gly265GlufsTer149	p.G265Efs*149	ENST00000262320	NM_003502.3	264	ccC/cc	2/11	1	2	FACETS	0.857	0.79	0.927	0.857	0.79	0.927	CLONAL	1	TRUE	1	0.44	2		815	944	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	128	565	0	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.754	0.683	0.828	0.754	0.683	0.828	SUBCLONAL	1	TRUE	1	0.44	2		565	772	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701231	43701231	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	163	580	1	ENST00000382044.4:c.5464C>A	p.Leu1822Met	p.L1822M	ENST00000382044	NM_001141980.1	1822	Ctg/Atg	26/28	1	2	FACETS	0.931	0.855	1	0.931	0.855	1	CLONAL	1	TRUE	1	0.44	2		581	796	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480484	57480484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11554274	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	121	339	0	ENST00000371085.3:c.479G>A	p.Arg160His	p.R160H	ENST00000371085	NM_000516.4	160	cGt/cAt	6/13	1	2	FACETS	0.987	0.896	1	0.987	0.896	1	CLONAL	1	TRUE	1	0.44	2		339	557	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737644	145737644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370867731	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	224	1204	0	ENST00000428558.2:c.3119C>T	p.Pro1040Leu	p.P1040L	ENST00000428558	NM_004260.3	1040	cCg/cTg	19/22	1	2	FACETS	0.991	0.923	1	0.991	0.923	1	CLONAL	1	TRUE	1	0.44	2		1204	1027	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967091	18967092	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1384543747	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	64	1001	0	ENST00000262803.5:c.1814_1815del	p.Glu605AlafsTer17	p.E605Afs*17	ENST00000262803	NM_002911.3	602	gcAGag/gcag	13/24	1	2	FACETS	0.297	0.256	0.341	0.297	0.256	0.341	SUBCLONAL	1	TRUE	1	0.44	2		1001	981	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146583	185146583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142468620	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	139	561	0	ENST00000265026.3:c.214G>A	p.Val72Ile	p.V72I	ENST00000265026	NM_004721.4	72	Gta/Ata	2/14	1	2	FACETS	0.935	0.853	1	0.935	0.853	1	CLONAL	1	TRUE	1	0.44	2		561	676	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309069	137309069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756234164	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	249	1234	4	ENST00000481739.1:c.676G>A	p.Ala226Thr	p.A226T	ENST00000481739	NM_002957.4	226	Gcc/Acc	5/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.44	2		1238	1121	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453399	40453399	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs759027671	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	221	995	16	ENST00000345506.4:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000345506	NM_003152.3	366	Ccc/cc	10/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.44	2		1011	974	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098831	178098831	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1135118	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	193	653	2	ENST00000397062.3:c.214G>A	p.Ala72Thr	p.A72T	ENST00000397062	NM_006164.4	72	Gct/Act	2/5	1	2	FACETS	0.985	0.912	1	0.985	0.912	1	CLONAL	1	TRUE	1	0.44	2		655	891	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534600	140534601	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	128	399	0	ENST00000288602.6:c.312dup	p.Asn105GlufsTer4	p.N105Efs*4	ENST00000288602	NM_004333.4	104	-/G	3/18	1	2	FACETS	0.968	0.88	1	0.968	0.88	1	CLONAL	1	TRUE	1	0.44	2		399	601	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348798	118348798	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs868985556	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	95	285	0	ENST00000534358.1:c.3451C>T	p.Arg1151Ter	p.R1151*	ENST00000534358	NM_005933.3	1151	Cga/Tga	5/36	1	2	FACETS	0.913	0.817	1	0.913	0.817	1	CLONAL	1	TRUE	1	0.44	2		285	473	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702367	47702367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs549467183	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	85	319	0	ENST00000233146.2:c.1963G>A	p.Val655Ile	p.V655I	ENST00000233146	NM_000251.2	655	Gta/Ata	12/16	1	2	FACETS	0.777	0.689	0.871	0.777	0.689	0.871	SUBCLONAL	1	TRUE	1	0.44	2		319	497	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127615	2127615	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	195	828	0	ENST00000219476.3:c.2859del	p.Lys954AsnfsTer4	p.K954Nfs*4	ENST00000219476	NM_000548.3	952	Ccc/cc	26/42	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.44	2		828	882	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017790	31017790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564841799	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	215	980	3	ENST00000375687.4:c.652C>T	p.Arg218Cys	p.R218C	ENST00000375687	NM_015338.5	218	Cgt/Tgt	8/13	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.44	2		983	941	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346225	89346225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372632879	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	111	659	0	ENST00000301030.4:c.6725C>T	p.Ala2242Val	p.A2242V	ENST00000301030	NM_001256183.1	2242	gCg/gTg	9/13	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.44	2		659	502	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678767	52678767	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	57	316	0	ENST00000394830.3:c.852G>T	p.Lys284Asn	p.K284N	ENST00000394830	NM_018313.4	284	aaG/aaT	9/30	1	2	FACETS	0.459	0.393	0.53	0.459	0.393	0.53	SUBCLONAL	1	TRUE	1	0.44	2		316	565	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660772	227660772	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	175	908	1	ENST00000305123.5:c.2683del	p.Glu895AsnfsTer48	p.E895Nfs*48	ENST00000305123	NM_005544.2	895	Gaa/aa	1/2	1	2	FACETS	0.956	0.881	1	0.956	0.881	1	CLONAL	1	TRUE	1	0.44	2		909	832	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86658452	86658452	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	55	165	0	ENST00000274376.6:c.1421del	p.Asn474ThrfsTer9	p.N474Tfs*9	ENST00000274376	NM_002890.2	473	Aaa/aa	10/25	1	2	FACETS	0.883	0.762	1	0.883	0.762	1	CLONAL	1	TRUE	1	0.44	2		165	283	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38955713	38955713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	76	344	1	ENST00000357387.3:c.2593C>T	p.Arg865Cys	p.R865C	ENST00000357387	NM_152756.3	865	Cgt/Tgt	26/38	1	2	FACETS	0.756	0.665	0.853	0.756	0.665	0.853	SUBCLONAL	1	TRUE	1	0.44	2		345	457	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934378	39934378	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1434826738	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	198	341	0	ENST00000378444.4:c.221G>A	p.Arg74His	p.R74H	ENST00000378444	NM_001123385.1	74	cGc/cAc	4/15	1	1	FACETS	0.787	0.738	0.837	1	0.993	1	SUBCLONAL	2	TRUE	0	0.44	1		341	446	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181423	38181423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	136	527	0	ENST00000396334.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000396334	NM_002468.4	146	Gct/Act	2/5	1	2	FACETS	0.988	0.901	1	0.988	0.901	1	CLONAL	1	TRUE	1	0.44	2		527	626	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795373	39795373	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	208	805	0	ENST00000288319.7:c.347del	p.Pro116GlnfsTer3	p.P116Qfs*3	ENST00000288319	NM_182918.3	116	cCa/ca	3/10	1	2	FACETS	0.972	0.902	1	0.972	0.902	1	CLONAL	1	TRUE	1	0.44	2		805	973	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335642	81335642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	99	378	0	ENST00000222390.5:c.1718G>A	p.Gly573Asp	p.G573D	ENST00000222390	NM_000601.4	573	gGc/gAc	15/18	1	2	FACETS	0.756	0.676	0.841	0.756	0.676	0.841	SUBCLONAL	1	TRUE	1	0.44	2		378	595	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219827	133219827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147354120	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	162	796	0	ENST00000320574.5:c.4534G>A	p.Val1512Ile	p.V1512I	ENST00000320574	NM_006231.2	1512	Gtc/Atc	35/49	1	2	FACETS	0.954	0.877	1	0.954	0.877	1	CLONAL	1	TRUE	1	0.44	2		796	772	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601986	43601986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749883001	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	268	1093	1	ENST00000355710.3:c.1030G>A	p.Gly344Ser	p.G344S	ENST00000355710	NM_020975.4	344	Ggc/Agc	5/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.44	2		1094	1131	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200902	67200902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755385727	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	175	762	1	ENST00000312629.5:c.890G>A	p.Arg297Gln	p.R297Q	ENST00000312629	NM_003952.2	297	cGg/cAg	10/15	1	2	FACETS	0.947	0.873	1	0.947	0.873	1	CLONAL	1	TRUE	1	0.44	2		763	840	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440044	49440044	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1234276911	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	208	830	0	ENST00000301067.7:c.4582C>T	p.Arg1528Trp	p.R1528W	ENST00000301067	NM_003482.3	1528	Cgg/Tgg	16/54	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.44	2		830	925	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318775	163318775	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	29	367	0	ENST00000271452.3:c.1165G>A	p.Glu389Lys	p.E389K	ENST00000271452	NM_145697.2	389	Gaa/Aaa	13/14	1	2	FACETS	0.232	0.185	0.285	0.232	0.185	0.285	SUBCLONAL	1	TRUE	1	0.44	2		367	568	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8252003	8252003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775620259	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	202	997	0	ENST00000335790.3:c.74C>T	p.Ala25Val	p.A25V	ENST00000335790	NM_002315.2	25	gCg/gTg	2/4	1	2	FACETS	0.916	0.849	0.986	0.916	0.849	0.986	CLONAL	1	TRUE	1	0.44	2		997	1002	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137045	64137045	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	52	961	1	ENST00000334205.4:c.1556T>C	p.Phe519Ser	p.F519S	ENST00000334205	NM_003942.2	519	tTc/tCc	13/17	1	2	FACETS	0.23	0.194	0.269	0.23	0.194	0.269	SUBCLONAL	1	TRUE	1	0.44	2		962	1029	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426600	49426602	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	rs780886030	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	230	924	0	ENST00000301067.7:c.11886_11888del	p.Gln3965del	p.Q3965del	ENST00000301067	NM_003482.3	3962	caACAg/cag	39/54	1	2	FACETS	0.872	0.812	0.934	0.872	0.812	0.934	CLONAL	1	TRUE	1	0.44	2		924	1199	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481917	56481917	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	62	763	0	ENST00000267101.3:c.845A>G	p.Tyr282Cys	p.Y282C	ENST00000267101	NM_001982.3	282	tAt/tGt	7/28	1	2	FACETS	0.314	0.27	0.362	0.314	0.27	0.362	SUBCLONAL	1	TRUE	1	0.44	2		763	897	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784000	120784000	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	229	1320	0	ENST00000257552.2:c.985del	p.Val329SerfsTer24	p.V329Sfs*24	ENST00000257552	NM_002442.3	329	Gtc/tc	13/15	1	2	FACETS	0.908	0.846	0.973	0.908	0.846	0.973	CLONAL	1	TRUE	1	0.44	2		1320	1146	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913080	32913080	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507731	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	168	524	0	ENST00000380152.3:c.4593del	p.Val1532LeufsTer11	p.V1532Lfs*11	ENST00000380152		1530	Aaa/aa	11/27	1	2	FACETS	0.962	0.885	1	0.962	0.885	1	CLONAL	1	TRUE	1	0.44	2		524	794	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194847	30194847	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	144	520	1	ENST00000331968.5:c.298A>G	p.Lys100Glu	p.K100E	ENST00000331968	NM_002742.2	100	Aag/Gag	2/18	1	2	FACETS	0.926	0.846	1	0.926	0.846	1	CLONAL	1	TRUE	1	0.44	2		521	707	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727469	88727469	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751831141	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	173	706	0	ENST00000360948.2:c.310G>A	p.Gly104Arg	p.G104R	ENST00000360948	NM_001012338.2	104	Gga/Aga	3/19	1	2	FACETS	0.973	0.897	1	0.973	0.897	1	CLONAL	1	TRUE	1	0.44	2		706	808	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434763	99434763	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	190	907	0	ENST00000268035.6:c.850A>G	p.Asn284Asp	p.N284D	ENST00000268035	NM_000875.3	284	Aac/Gac	3/21	1	2	FACETS	0.948	0.877	1	0.948	0.877	1	CLONAL	1	TRUE	1	0.44	2		907	911	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99472871	99472871	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	135	511	0	ENST00000268035.6:c.2867A>G	p.Tyr956Cys	p.Y956C	ENST00000268035	NM_000875.3	956	tAc/tGc	14/21	1	2	FACETS	0.874	0.796	0.956	0.874	0.796	0.956	CLONAL	1	TRUE	1	0.44	2		511	702	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396962	396962	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1238203898	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	245	1039	2	ENST00000262320.3:c.64C>T	p.Arg22Ter	p.R22*	ENST00000262320	NM_003502.3	22	Cga/Tga	2/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.44	2		1041	1082	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993654	72993654	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1270904589	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	173	1030	0	ENST00000268489.5:c.391G>A	p.Gly131Arg	p.G131R	ENST00000268489	NM_006885.3	131	Ggg/Agg	2/10	1	2	FACETS	0.874	0.804	0.946	0.874	0.804	0.946	CLONAL	1	TRUE	1	0.44	2		1030	900	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81939078	81939079	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	184	679	0	ENST00000359376.3:c.1438dup	p.Glu480GlyfsTer9	p.E480Gfs*9	ENST00000359376	NM_002661.3	478	cag/caGg	15/33	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.44	2		679	814	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990396	81990396	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	125	608	0	ENST00000359376.3:c.3667T>G	p.Leu1223Val	p.L1223V	ENST00000359376	NM_002661.3	1223	Ttg/Gtg	32/33	1	2	FACETS	0.755	0.683	0.829	0.755	0.683	0.829	SUBCLONAL	1	TRUE	1	0.44	2		608	753	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243483	41243485	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs80358341	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	187	652	0	ENST00000357654.3:c.4063_4065del	p.Asn1355del	p.N1355del	ENST00000357654	NM_007294.3	1355	AAT/-	10/23	1	2	FACETS	0.955	0.883	1	0.955	0.883	1	CLONAL	1	TRUE	1	0.44	2		652	890	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853911	59853911	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	120	400	0	ENST00000259008.2:c.1948A>G	p.Thr650Ala	p.T650A	ENST00000259008	NM_032043.2	650	Acc/Gcc	14/20	1	2	FACETS	0.937	0.849	1	0.937	0.849	1	CLONAL	1	TRUE	1	0.44	2		400	582	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39644732	39644732	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	91	270	0	ENST00000262039.4:c.2461T>C	p.Ser821Pro	p.S821P	ENST00000262039	NM_002647.2	821	Tcc/Ccc	23/25	1	2	FACETS	0.803	0.715	0.896	0.803	0.715	0.896	CLONAL	1	TRUE	1	0.44	2		270	515	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366161	15366161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1183026299	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	187	739	1	ENST00000263377.2:c.1994G>A	p.Arg665His	p.R665H	ENST00000263377	NM_058243.2	665	cGt/cAt	10/20	1	2	FACETS	0.969	0.896	1	0.969	0.896	1	CLONAL	1	TRUE	1	0.44	2		740	877	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214894	36214894	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555729827	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	185	1041	7	ENST00000222270.7:c.3325del	p.Arg1109GlufsTer73	p.R1109Efs*73	ENST00000222270	NM_014727.1	1107	aCc/ac	8/37	1	2	FACETS	0.831	0.767	0.898	0.831	0.767	0.898	CLONAL	1	TRUE	1	0.44	2		1048	1012	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753111	42753111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	192	1050	0	ENST00000222329.4:c.1153G>A	p.Gly385Arg	p.G385R	ENST00000222329	NM_006494.2	385	Gga/Aga	4/4	1	2	FACETS	0.899	0.831	0.969	0.899	0.831	0.969	CLONAL	1	TRUE	1	0.44	2		1050	971	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909562	50909562	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs878854520	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	228	1022	0	ENST00000440232.2:c.1366C>T	p.Gln456Ter	p.Q456*	ENST00000440232	NM_002691.3	456	Cag/Tag	11/27	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.44	2		1022	996	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657081	47657081	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs267607950	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	81	196	0	ENST00000233146.2:c.1276+1G>T		p.X426_splice	ENST00000233146	NM_000251.2	426			1	2	FACETS	0.927	0.822	1	0.927	0.822	1	CLONAL	1	TRUE	1	0.44	2		196	397	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961465	54961465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749883403	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	159	464	0	ENST00000312783.6:c.167G>A	p.Arg56His	p.R56H	ENST00000312783	NM_198436.1	56	cGc/cAc	4/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.44	2		464	671	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326274	62326274	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	271	1346	0	ENST00000360203.5:c.3290C>A	p.Ala1097Asp	p.A1097D	ENST00000360203	NM_001283009.1	1097	gCt/gAt	32/35	1	2	FACETS	0.909	0.851	0.969	0.909	0.851	0.969	CLONAL	1	TRUE	1	0.44	2		1346	1355	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866331	42866331	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs574582815	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	237	982	1	ENST00000398585.3:c.301G>A	p.Val101Ile	p.V101I	ENST00000398585	NM_001135099.1	101	Gtc/Atc	3/14	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.44	2		983	1055	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566494	41566494	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	118	375	0	ENST00000263253.7:c.4371A>G	p.Ile1457Met	p.I1457M	ENST00000263253	NM_001429.3	1457	atA/atG	27/31	1	2	FACETS	0.906	0.82	0.996	0.906	0.82	0.996	CLONAL	1	TRUE	1	0.44	2		375	592	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940075	49940075	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	218	1117	0	ENST00000296474.3:c.968T>C	p.Val323Ala	p.V323A	ENST00000296474	NM_002447.2	323	gTg/gCg	1/20	1	2	FACETS	0.934	0.868	1	0.934	0.868	1	CLONAL	1	TRUE	1	0.44	2		1117	1061	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390986	89390986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	137	436	0	ENST00000336596.2:c.1052C>T	p.Thr351Ile	p.T351I	ENST00000336596	NM_005233.5	351	aCa/aTa	5/17	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.44	2		436	605	SUCCESS
ATR	545	MSKCC	GRCh37	3	142257371	142257371	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	124	376	0	ENST00000350721.4:c.3678G>T	p.Gln1226His	p.Q1226H	ENST00000350721	NM_001184.3	1226	caG/caT	19/47	1	2	FACETS	0.9	0.817	0.988	0.9	0.817	0.988	CLONAL	1	TRUE	1	0.44	2		376	626	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157987	106157987	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	89	298	1	ENST00000380013.4:c.2888A>T	p.Gln963Leu	p.Q963L	ENST00000380013	NM_001127208.2	963	cAg/cTg	3/11	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.44	2		299	391	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249402	153249402	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	116	435	0	ENST00000281708.4:c.1376G>A	p.Gly459Glu	p.G459E	ENST00000281708	NM_033632.3	459	gGg/gAg	9/12	1	2	FACETS	0.824	0.744	0.908	0.824	0.744	0.908	CLONAL	1	TRUE	1	0.44	2		435	640	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026886	6026886	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	48	525	0	ENST00000265849.7:c.1510G>T	p.Glu504Ter	p.E504*	ENST00000265849	NM_000535.5	504	Gag/Tag	11/15	1	2	FACETS	0.429	0.362	0.502	0.429	0.362	0.502	SUBCLONAL	1	TRUE	1	0.44	2		525	509	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233014	55233014	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	126	528	0	ENST00000275493.2:c.1768del	p.His590ThrfsTer115	p.H590Tfs*115	ENST00000275493	NM_005228.3	588	ggC/gg	15/28	1	2	FACETS	0.865	0.785	0.949	0.865	0.785	0.949	CLONAL	1	TRUE	1	0.44	2		528	662	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033240	69033240	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	146	469	0	ENST00000288368.4:c.3680G>T	p.Ser1227Ile	p.S1227I	ENST00000288368	NM_024870.2	1227	aGc/aTc	30/40	1	2	FACETS	0.962	0.88	1	0.962	0.88	1	CLONAL	1	TRUE	1	0.44	2		469	690	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209400	98209400	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111481152	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	181	965	1	ENST00000331920.6:c.4138G>A	p.Ala1380Thr	p.A1380T	ENST00000331920	NM_000264.3	1380	Gcc/Acc	23/24	1	2	FACETS	0.926	0.855	1	0.926	0.855	1	CLONAL	1	TRUE	1	0.44	2		966	888	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211548	98211549	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0054300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	151	781	2	ENST00000331920.6:c.3606dup	p.Ser1203GlnfsTer17	p.S1203Qfs*17	ENST00000331920	NM_000264.3	1202	-/C	22/24	1	2	FACETS	0.783	0.715	0.853	0.783	0.715	0.853	SUBCLONAL	1	TRUE	1	0.44	2		783	877	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0054322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	133	415	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.435057423741034	3	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	1	0.435057423741034	3		415	370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0054322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	285	778	3	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.435057423741034	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.435057423741034	1		781	828	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0054322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	75	483	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.435057423741034	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.435057423741034	1		483	256	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374949	45374952	+	frameshift_variant	Frame_Shift_Del	DEL	AGTG	AGTG	-	novel	NA	P-0054322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	35	560	0	ENST00000262160.6:c.891_894del	p.Thr298Ter	p.T298*	ENST00000262160	NM_005901.5	297	ctCACT/ct	8/11	0.435057423741034	1	FACETS	0.386	0.317	0.463	0.386	0.317	0.463	SUBCLONAL	1	TRUE	0	0.435057423741034	1		560	326	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164782	36164782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752616540	NA	P-0054322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	252	1512	1	ENST00000300305.3:c.1093G>A	p.Gly365Ser	p.G365S	ENST00000300305		365	Ggc/Agc	8/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.435057423741034	2		1513	1030	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780812	9780812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765797019	NA	P-0054322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	175	1066	1	ENST00000377346.4:c.1534C>T	p.Arg512Trp	p.R512W	ENST00000377346	NM_005026.3	512	Cgg/Tgg	13/24	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.435057423741034	2		1067	783	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344719	118344719	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	119	398	0	ENST00000534358.1:c.2845A>G	p.Thr949Ala	p.T949A	ENST00000534358	NM_005933.3	949	Act/Gct	3/36	0.316104232300909	2	FACETS	0.934	0.856	1	0.934	0.856	1	CLONAL	2	TRUE	0	0.435057423741034	2		398	293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0054328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	193	487	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.303644680854028	2	FACETS	0.89	0.826	0.955	0.89	0.826	0.955	CLONAL	2	TRUE	0	0.32	2		487	678	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0054328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	154	370	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.298115448115251	3	FACETS	0.958	0.881	1	0.958	0.881	1	CLONAL	2	TRUE	1	0.32	3		370	583	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101402	27101402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	90	370	0	ENST00000324856.7:c.4689del	p.Met1564Ter	p.M1564*	ENST00000324856	NM_006015.4	1562	Ccc/cc	18/20	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.32	2		370	531	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	93	276	0	ENST00000342988.3:c.1610A>T	p.Asp537Val	p.D537V	ENST00000342988	NM_005359.5	537	gAc/gTc	12/12	0.303644680854028	2	FACETS	0.821	0.736	0.909	0.821	0.736	0.909	CLONAL	2	TRUE	0	0.32	2		276	354	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814729	139814729	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs557861295	NA	P-0054328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	262	638	0	ENST00000247668.2:c.722G>A	p.Arg241Gln	p.R241Q	ENST00000247668	NM_021138.3	241	cGg/cAg	8/11	0.296231444949862	3	FACETS	0.963	0.904	1	0.963	0.904	1	CLONAL	2	TRUE	1	0.32	3		638	986	SUCCESS
APC	324	MSKCC	GRCh37	5	112155002	112155002	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	87	433	0	ENST00000257430.4:c.1273G>T	p.Glu425Ter	p.E425*	ENST00000257430	NM_000038.5	425	Gaa/Taa	10/16	1	2	FACETS	0.966	0.857	1	0.966	0.857	1	CLONAL	1	TRUE	1	0.32	2		433	563	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096108	71096108	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	51	198	0	ENST00000318789.4:c.649C>T	p.Gln217Ter	p.Q217*	ENST00000318789	NM_032682.5	217	Caa/Taa	10/21	1	2	FACETS	0.99	0.846	1	0.99	0.846	1	CLONAL	1	TRUE	1	0.32	2		198	322	SUCCESS
APC	324	MSKCC	GRCh37	5	112175755	112175760	+	frameshift_variant	Frame_Shift_Del	DEL	ATTACA	ATTACA	T	novel	NA	P-0054328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	36	182	0	ENST00000257430.4:c.4464_4469delinsT	p.Leu1488PhefsTer24	p.L1488Ffs*24	ENST00000257430	NM_000038.5	1488	ttATTACAt/ttTt	16/16	1	2	FACETS	0.773	0.638	0.923	0.773	0.638	0.923	CLONAL	1	TRUE	1	0.32	2		182	291	SUCCESS
APC	324	MSKCC	GRCh37	5	112136980	112136980	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1554076133	NA	P-0054330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	84	211	0	ENST00000257430.4:c.734C>A	p.Ser245Ter	p.S245*	ENST00000257430	NM_000038.5	245	tCa/tAa	8/16	1	2	FACETS	0.972	0.864	1	0.972	0.864	1	CLONAL	1	TRUE	1	0.437585352521552	2		211	395	SUCCESS
APC	324	MSKCC	GRCh37	5	112174835	112174835	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0054330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	49	163	0	ENST00000257430.4:c.3544A>T	p.Lys1182Ter	p.K1182*	ENST00000257430	NM_000038.5	1182	Aaa/Taa	16/16	1	2	FACETS	0.97	0.83	1	0.97	0.83	1	CLONAL	1	TRUE	1	0.437585352521552	2		163	231	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577151	+	frameshift_variant	Frame_Shift_Del	DEL	GTCCCAGTAGATT	GTCCCAGTAGATT	-	novel	NA	P-0054330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	159	520	0	ENST00000269305.4:c.787_799del	p.Asn263GlyfsTer78	p.N263Gfs*78	ENST00000269305	NM_001126112.2	263	AATCTACTGGGACgg/gg	8/11	0.437585352521552	1	FACETS	0.891	0.82	0.965	0.891	0.82	0.965	CLONAL	1	TRUE	0	0.437585352521552	1		520	637	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60795985	60795986	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGGCATCCTGCAGTTGGGGGAGAGG	novel	NA	P-0054330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	50	356	0	ENST00000333681.4:c.586-18_592dup	p.Phe198SerfsTer22	p.F198Sfs*22	ENST00000333681		198	ttt/tCCTCTCCCCCAACTGCAGGATGCCTtt	3/3	0.437585352521552	1	FACETS	0.367	0.312	0.428	0.367	0.312	0.428	SUBCLONAL	1	TRUE	0	0.437585352521552	1		356	486	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225701	26225701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777435873	NA	P-0054330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	332	679	0	ENST00000360408.1:c.319G>A	p.Asp107Asn	p.D107N	ENST00000360408	NM_003532.2	107	Gac/Aac	1/1	0.414964772025833	2	FACETS	0.841	0.798	0.885	0.841	0.798	0.885	CLONAL	2	TRUE	0	0.437585352521552	2		679	902	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0054412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	264	835	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.623556693028088	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.623556693028088	1		835	540	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0054412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	123	459	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	0.928	0.846	1	0.928	0.846	1	CLONAL	1	TRUE	1	0.623556693028088	2		459	425	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910883	114910883	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1477809102	NA	P-0054412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	166	480	0	ENST00000543371.1:c.1001+1G>A		p.X334_splice	ENST00000543371	NM_001198531.1	334			1	2	FACETS	0.91	0.84	0.982	0.91	0.84	0.982	CLONAL	1	TRUE	1	0.623556693028088	2		480	585	SUCCESS
APC	324	MSKCC	GRCh37	5	112175235	112175235	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	88	249	0	ENST00000257430.4:c.3944C>A	p.Ser1315Ter	p.S1315*	ENST00000257430	NM_000038.5	1315	tCa/tAa	16/16	1	2	FACETS	0.994	0.892	1	0.994	0.892	1	CLONAL	1	TRUE	1	0.623556693028088	2		249	284	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0054413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	58	241	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	0.561085616867661	3	FACETS	0.977	0.847	1	0.488	0.423	0.558	CLONAL	1	TRUE	1	0.561085616867661	3		241	271	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268144	153268144	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs920052554	NA	P-0054413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	136	448	0	ENST00000281708.4:c.664C>T	p.Arg222Ter	p.R222*	ENST00000281708	NM_033632.3	222	Cga/Tga	4/12	1	2	FACETS	0.923	0.844	1	0.923	0.844	1	CLONAL	1	TRUE	1	0.561085616867661	2		448	525	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0054413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	565	682	1	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	0.109932214166152	5	FACETS	0.956	0.93	0.981			1	INDETERMINATE	5	TRUE	NA	0.561085616867661	5		683	776	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245431	153245439	+	inframe_deletion	In_Frame_Del	DEL	ATTCCACTT	ATTCCACTT	-	novel	NA	P-0054413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	120	634	0	ENST00000281708.4:c.1752_1760del	p.Ser585_Met587del	p.S585_M587del	ENST00000281708	NM_033632.3	584	acAAGTGGAATg/acg	11/12	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.561085616867661	2		634	413	SUCCESS
APC	324	MSKCC	GRCh37	5	112174521	112174521	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	141	401	0	ENST00000257430.4:c.3232del	p.Tyr1078IlefsTer48	p.Y1078Ifs*48	ENST00000257430	NM_000038.5	1077	gTt/gt	16/16	0.561085616867661	3	FACETS	0.969	0.896	1	0.969	0.896	1	CLONAL	2	TRUE	1	0.561085616867661	3		401	332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0054455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	253	469	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.666724496599306	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.666724496599306	1		469	499	SUCCESS
APC	324	MSKCC	GRCh37	5	112175175	112175175	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	176	222	0	ENST00000257430.4:c.3885del	p.Ala1296GlnfsTer9	p.A1296Qfs*9	ENST00000257430	NM_000038.5	1295	gAa/ga	16/16	0.653510130191269	2	FACETS	0.946	0.894	0.997	0.946	0.894	0.997	CLONAL	2	TRUE	0	0.666724496599306	2		222	279	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852605	63852605	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	155	527	0	ENST00000279873.7:c.3383G>C	p.Arg1128Thr	p.R1128T	ENST00000279873	NM_032199.2	1128	aGa/aCa	10/10	1	2	FACETS	0.839	0.773	0.908	0.839	0.773	0.908	CLONAL	1	TRUE	1	0.666724496599306	2		527	554	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435301	110435303	+	missense_variant	Missense_Mutation	TNP	GTG	GTG	AGC	novel	NA	P-0054455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	59	120	0	ENST00000375856.3:c.3098_3100delinsGCT	p.Pro1033_Pro1034delinsArgSer	p.P1033_P1034delinsRS	ENST00000375856	NM_003749.2	1033	cCACcg/cGCTcg	1/2	0.666724496599306	4	FACETS	0.939	0.814	1	0.313	0.271	0.358	CLONAL	1	TRUE	1	0.666724496599306	4		120	314	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	28	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.101609301819416	0	FACETS	0.728	0.583	0.891			1	INDETERMINATE	1	FALSE	0	0.218670336074815	0		487	275	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0054456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	99	863	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.181473126489179	0	FACETS	0.636	0.566	0.711			1	SUBCLONAL	1	FALSE	0	0.218670336074815	0		864	1112	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857275	9857275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426934537	NA	P-0054456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	33	605	1	ENST00000330684.3:c.4126C>T	p.Arg1376Cys	p.R1376C	ENST00000330684	NM_001134407.1	1376	Cgc/Tgc	13/13	1	2	FACETS	0.506	0.411	0.614	0.506	0.411	0.614	SUBCLONAL	1	FALSE	1	0.218670336074815	2		606	596	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974703	21974728	+	frameshift_variant	Frame_Shift_Del	DEL	TCGGTGCGTTGGGCAGCGCCCCCGCC	TCGGTGCGTTGGGCAGCGCCCCCGCC	-	novel	NA	P-0054456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1473	219	430	0	ENST00000304494.5:c.99_124del	p.Ala34Ter	p.A34*	ENST00000304494	NM_000077.4	33	gaGGCGGGGGCGCTGCCCAACGCACCGAat/gaat	1/3	0.218670336074815	3	FACETS	1	0.988	1			1	CLONAL	1	FALSE	NA	0.218670336074815	3		430	1692	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782159	135782160	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0054456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	41	460	0	ENST00000298552.3:c.1396_1397del	p.Leu466GlyfsTer3	p.L466Gfs*3	ENST00000298552	NM_001162426.1	466	CTg/g	14/23	1	2	FACETS	0.987	0.824	1	0.987	0.824	1	CLONAL	1	FALSE	1	0.218670336074815	2		460	380	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	37	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.268	0.221	0.321	0.268	0.221	0.321	SUBCLONAL	1	TRUE	1	0.761544928477554	2		326	362	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	302	588	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.761544928477554	2		592	726	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	213	450	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.913	0.853	0.973	0.913	0.853	0.973	CLONAL	1	TRUE	1	0.761544928477554	2		451	613	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	279	660	3	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	0.986	0.931	1	0.986	0.931	1	CLONAL	1	TRUE	1	0.761544928477554	2		663	743	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	998	1149	10	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	0.761544928477554	4	FACETS	0.875	0.853	0.897	0.875	0.853	0.897	CLONAL	3	TRUE	1	0.761544928477554	4		1159	1758	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145753	11145753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	379	1253	4	ENST00000358026.2:c.4115G>A	p.Arg1372His	p.R1372H	ENST00000358026	NM_001128849.1	1372	cGc/cAc	29/36	1	2	FACETS	0.974	0.927	1	0.974	0.927	1	CLONAL	1	TRUE	1	0.761544928477554	2		1257	1022	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	47	702	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.202	0.17	0.237	0.202	0.17	0.237	SUBCLONAL	1	TRUE	1	0.761544928477554	2		703	612	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420204	49420204	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	311	971	0	ENST00000301067.7:c.15545del	p.Gly5182AlafsTer61	p.G5182Afs*61	ENST00000301067	NM_003482.3	5182	gGc/gc	48/54	0.761544928477554	4	FACETS	0.947	0.891	1	0.316	0.297	0.335	CLONAL	1	TRUE	1	0.761544928477554	4		971	1519	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043377	180043377	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771345898	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	364	979	2	ENST00000261937.6:c.3209G>A	p.Arg1070His	p.R1070H	ENST00000261937	NM_182925.4	1070	cGc/cAc	23/30	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.761544928477554	2		981	884	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	140	469	11	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.761544928477554	2		480	367	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	239	600	12	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	0.958	0.9	1	0.958	0.9	1	CLONAL	1	TRUE	1	0.761544928477554	2		612	655	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179386	56179386	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	90	246	0	ENST00000399503.3:c.3702del	p.Lys1234AsnfsTer11	p.K1234Nfs*11	ENST00000399503	NM_005921.1	1233	gcA/gc	15/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.761544928477554	2		246	209	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483185	120483185	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	173	431	0	ENST00000256646.2:c.3176del	p.Asn1059ThrfsTer6	p.N1059Tfs*6	ENST00000256646	NM_024408.3	1059	aAc/ac	19/34	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.761544928477554	2		431	432	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691872	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs79375991	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	267	488	18	ENST00000295754.5:c.383del	p.Lys128SerfsTer35	p.K128Sfs*35	ENST00000295754	NM_003242.5	125	gAa/ga	3/7	0.749299918695088	2	FACETS	0.823	0.786	0.859	0.823	0.786	0.859	CLONAL	2	TRUE	0	0.761544928477554	2		506	426	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533467	533467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894231	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	402	1213	0	ENST00000451590.1:c.436G>A	p.Ala146Thr	p.A146T	ENST00000451590	NM_001130442.1	146	Gcc/Acc	4/5	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.761544928477554	2		1213	966	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491682	120491683	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	130	395	1	ENST00000256646.2:c.2546_2547del	p.Lys849ArgfsTer6	p.K849Rfs*6	ENST00000256646	NM_024408.3	849	aAA/a	16/34	1	2	FACETS	0.821	0.751	0.893	0.821	0.751	0.893	CLONAL	1	TRUE	1	0.761544928477554	2		396	416	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832811	3832811	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555484797	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	258	790	2	ENST00000262367.5:c.1447C>T	p.Arg483Ter	p.R483*	ENST00000262367	NM_004380.2	483	Cga/Tga	6/31	1	2	FACETS	0.922	0.867	0.977	0.922	0.867	0.977	CLONAL	1	TRUE	1	0.761544928477554	2		792	735	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012647	36012647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1437496392	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	106	236	0	ENST00000358208.4:c.91G>A	p.Ala31Thr	p.A31T	ENST00000358208		31	Gct/Act	2/12	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.761544928477554	2		236	240	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438262	49438262	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	967	913	0	ENST00000301067.7:c.5007del	p.Val1670SerfsTer52	p.V1670Sfs*52	ENST00000301067	NM_003482.3	1669	ccC/cc	20/54	0.761544928477554	4	FACETS	0.99	0.967	1	0.99	0.967	1	CLONAL	3	TRUE	1	0.761544928477554	4		913	1506	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438206	110438206	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	51	168	0	ENST00000375856.3:c.195del	p.Ser66ArgfsTer27	p.S66Rfs*27	ENST00000375856	NM_003749.2	65	ggG/gg	1/2	1	2	FACETS	0.827	0.716	0.943	0.827	0.716	0.943	CLONAL	1	TRUE	1	0.761544928477554	2		168	162	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132285	7132285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750954241	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	359	987	2	ENST00000302850.5:c.2726G>A	p.Arg909Gln	p.R909Q	ENST00000302850	NM_000208.2	909	cGg/cAg	14/22	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.761544928477554	2		989	847	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845190	151845190	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764910946	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	258	749	0	ENST00000262189.6:c.13822C>T	p.Arg4608Cys	p.R4608C	ENST00000262189	NM_170606.2	4608	Cgc/Tgc	52/59	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.761544928477554	2		749	672	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391748	139391748	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	372	1157	2	ENST00000277541.6:c.6443G>A	p.Ser2148Asn	p.S2148N	ENST00000277541	NM_017617.3	2148	aGc/aAc	34/34	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.761544928477554	2		1159	868	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459187	120459187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	271	817	2	ENST00000256646.2:c.6158G>A	p.Arg2053His	p.R2053H	ENST00000256646	NM_024408.3	2053	cGc/cAc	34/34	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.761544928477554	2		819	677	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623611	43623611	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	223	558	0	ENST00000355710.3:c.3239C>A	p.Ala1080Asp	p.A1080D	ENST00000355710	NM_020975.4	1080	gCt/gAt	20/20	1	2	FACETS	0.994	0.933	1	0.994	0.933	1	CLONAL	1	TRUE	1	0.761544928477554	2		558	589	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417836	32417836	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	47	613	0	ENST00000332351.3:c.1216T>A	p.Ser406Thr	p.S406T	ENST00000332351	NM_024426.4	406	Tcc/Acc	7/10	1	2	FACETS	0.195	0.164	0.229	0.195	0.164	0.229	SUBCLONAL	1	TRUE	1	0.761544928477554	2		613	634	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135650	64135650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	424	1289	0	ENST00000334205.4:c.1118C>T	p.Ala373Val	p.A373V	ENST00000334205	NM_003942.2	373	gCg/gTg	10/17	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.761544928477554	2		1289	1111	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466919	18466919	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs377284533	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	142	429	0	ENST00000266497.5:c.1058A>G	p.Lys353Arg	p.K353R	ENST00000266497		353	aAa/aGa	5/31	0.761544928477554	4	FACETS	0.937	0.856	1	0.312	0.285	0.341	CLONAL	1	TRUE	1	0.761544928477554	4		429	701	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644555	21644556	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	171	615	0	ENST00000421138.2:c.111dup	p.Lys38GlufsTer17	p.K38Efs*17	ENST00000421138		37	-/G	4/16	0.761544928477554	4	FACETS	0.761	0.699	0.825	0.254	0.233	0.275	SUBCLONAL	1	TRUE	1	0.761544928477554	4		615	1040	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433805	49433805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1829	448	1585	1	ENST00000301067.7:c.7748C>T	p.Ala2583Val	p.A2583V	ENST00000301067	NM_003482.3	2583	gCc/gTc	31/54	0.761544928477554	4	FACETS	0.91	0.865	0.957	0.303	0.288	0.319	CLONAL	1	TRUE	1	0.761544928477554	4		1586	2277	SUCCESS
YES1	7525	MSKCC	GRCh37	18	732942	732942	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	180	632	2	ENST00000314574.4:c.1315A>G	p.Thr439Ala	p.T439A	ENST00000314574	NM_005433.3	439	Aca/Gca	11/12	1	2	FACETS	0.855	0.794	0.918	0.855	0.794	0.918	CLONAL	1	TRUE	1	0.761544928477554	2		634	553	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265352	10265352	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	409	1016	1	ENST00000340748.4:c.1694A>T	p.Asp565Val	p.D565V	ENST00000340748		565	gAc/gTc	20/40	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.761544928477554	2		1017	962	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326786	62326786	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	516	1392	0	ENST00000360203.5:c.3605C>A	p.Pro1202His	p.P1202H	ENST00000360203	NM_001283009.1	1202	cCc/cAc	34/35	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.761544928477554	2		1392	1182	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38954943	38954943	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1192682059	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	16	307	0	ENST00000357387.3:c.2630A>G	p.Tyr877Cys	p.Y877C	ENST00000357387	NM_152756.3	877	tAc/tGc	27/38	1	2	FACETS	0.159	0.117	0.208	0.159	0.117	0.208	SUBCLONAL	1	TRUE	1	0.761544928477554	2		307	265	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851576	128851576	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	312	952	0	ENST00000249373.3:c.1901C>A	p.Pro634His	p.P634H	ENST00000249373	NM_005631.4	634	cCc/cAc	11/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.761544928477554	2		952	811	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397637	139397637	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	366	1178	1	ENST00000277541.6:c.5164C>T	p.Gln1722Ter	p.Q1722*	ENST00000277541	NM_017617.3	1722	Cag/Tag	27/34	1	2	FACETS	0.953	0.906	1	0.953	0.906	1	CLONAL	1	TRUE	1	0.761544928477554	2		1179	1009	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405168	139405168	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	433	1522	0	ENST00000277541.6:c.2677T>G	p.Cys893Gly	p.C893G	ENST00000277541	NM_017617.3	893	Tgc/Ggc	17/34	1	2	FACETS	0.921	0.879	0.964	0.921	0.879	0.964	CLONAL	1	TRUE	1	0.761544928477554	2		1522	1235	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413072	139413072	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054478-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	336	1033	0	ENST00000277541.6:c.1070T>G	p.Phe357Cys	p.F357C	ENST00000277541	NM_017617.3	357	tTc/tGc	6/34	1	2	FACETS	0.957	0.908	1	0.957	0.908	1	CLONAL	1	TRUE	1	0.761544928477554	2		1033	922	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911143	40911143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370795038	NA	P-0054486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	37	346	1	ENST00000373198.4:c.2162G>A	p.Arg721His	p.R721H	ENST00000373198	NM_133170.3	721	cGt/cAt	13/32	NA	2	FACETS	0.553	0.455	0.663			1	INDETERMINATE	1	TRUE	NA	0.233180943850918	2		347	574	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0054486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	161	859	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.233180943850918	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.233180943850918	1		859	859	SUCCESS
APC	324	MSKCC	GRCh37	5	112175476	112175476	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	62	343	0	ENST00000257430.4:c.4188del	p.Phe1396LeufsTer19	p.F1396Lfs*19	ENST00000257430	NM_000038.5	1395	agT/ag	16/16	0.233180943850918	2	FACETS	0.798	0.694	0.91	0.798	0.694	0.91	CLONAL	2	TRUE	0	0.233180943850918	2		343	333	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047151	77047151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	78	610	0	ENST00000356341.3:c.1393C>T	p.Leu465Phe	p.L465F	ENST00000356341	NM_002576.4	465	Ctc/Ttc	13/15	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.233180943850918	2		610	656	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954019	32954019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80359162	NA	P-0054486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	85	377	0	ENST00000380152.3:c.9086C>T	p.Ala3029Val	p.A3029V	ENST00000380152		3029	gCg/gTg	23/27	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.233180943850918	2		377	574	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114917819	114917819	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	96	505	0	ENST00000543371.1:c.1309G>T	p.Glu437Ter	p.E437*	ENST00000543371	NM_001198531.1	437	Gag/Tag	12/14	0.20072139578758	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.233180943850918	1		505	614	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119043	70119043	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	173	769	0	ENST00000245479.2:c.616del	p.Ala206ArgfsTer13	p.A206Rfs*13	ENST00000245479	NM_000346.3	205	aaG/aa	2/3	1	2	FACETS	0.865	0.796	0.936	1	0.991	1	CLONAL	2	TRUE	1	0.233180943850918	2		769	858	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	44	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.127606778970926	3	FACETS	1	0.959	1	0.748	0.629	0.878	CLONAL	1	TRUE	1	0.192583636164113	3		487	335	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0054526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	53	483	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.192583636164113	1	FACETS	0.953	0.813	1	0.953	0.813	1	CLONAL	1	TRUE	0	0.192583636164113	1		483	522	SUCCESS
APC	324	MSKCC	GRCh37	5	112175524	112175524	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	30	344	0	ENST00000257430.4:c.4233del	p.Ser1411ArgfsTer4	p.S1411Rfs*4	ENST00000257430	NM_000038.5	1411	agT/ag	16/16	1	2	FACETS	0.705	0.567	0.861	0.705	0.567	0.861	SUBCLONAL	1	TRUE	1	0.192583636164113	2		344	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750600586	NA	P-0054526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1345	275	1177	1	ENST00000269305.4:c.413C>T	p.Ala138Val	p.A138V	ENST00000269305	NM_001126112.2	138	gCc/gTc	5/11	0.153075645744851	2	FACETS	0.881	0.825	0.94	0.881	0.825	0.94	CLONAL	2	TRUE	0	0.192583636164113	2		1178	1620	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266503	55266503	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	59	716	0	ENST00000275493.2:c.2795G>A	p.Arg932His	p.R932H	ENST00000275493	NM_005228.3	932	cGc/cAc	23/28	0.127606778970926	3	FACETS	0.726	0.623	0.839	0.363	0.311	0.42	SUBCLONAL	1	TRUE	1	0.192583636164113	3		716	925	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180891	106180891	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	51	391	0	ENST00000380013.4:c.3919A>G	p.Arg1307Gly	p.R1307G	ENST00000380013	NM_001127208.2	1307	Agg/Ggg	7/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.192583636164113	2		391	427	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488250	56488250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs865824076	NA	P-0054526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	124	716	0	ENST00000267101.3:c.1769C>T	p.Pro590Leu	p.P590L	ENST00000267101	NM_001982.3	590	cCc/cTc	15/28	0.127606778970926	3	FACETS	1	0.984	1	0.731	0.661	0.806	CLONAL	1	TRUE	1	0.192583636164113	3		716	965	SUCCESS
APC	324	MSKCC	GRCh37	5	112174295	112174296	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCGA	novel	NA	P-0054526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	22	351	0	ENST00000257430.4:c.3007_3010dup	p.Leu1004ArgfsTer5	p.L1004Rfs*5	ENST00000257430	NM_000038.5	1002	gcc/gCCGAcc	16/16	1	2	FACETS	0.849	0.659	1	0.849	0.659	1	CLONAL	1	TRUE	1	0.192583636164113	2		351	269	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0054576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	123	1045	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.287641884960532	1	FACETS	0.745	0.672	0.822	0.745	0.672	0.822	SUBCLONAL	1	TRUE	0	0.25	1		1046	1156	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	39	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.197090712465521	0	FACETS	0.572	0.475	0.681			1	SUBCLONAL	1	TRUE	0	0.25	0		457	409	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0054576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	47	364	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.647	0.545	0.76	0.647	0.545	0.76	SUBCLONAL	1	TRUE	1	0.25	2		365	581	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0054576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	66	383	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.25	2		383	438	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	14	300	4	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.287641884960532	1	FACETS	0.314	0.226	0.421	0.314	0.226	0.421	SUBCLONAL	1	TRUE	0	0.25	1		304	312	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043355	6043355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188006077	NA	P-0054576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	23	170	3	ENST00000265849.7:c.319C>T	p.Arg107Trp	p.R107W	ENST00000265849	NM_000535.5	107	Cgg/Tgg	4/15	1	2	FACETS	0.719	0.562	0.899	0.719	0.562	0.899	SUBCLONAL	1	TRUE	1	0.25	2		173	256	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0054576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	52	653	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.287641884960532	1	FACETS	0.404	0.343	0.472	0.404	0.343	0.472	SUBCLONAL	1	TRUE	0	0.25	1		653	901	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058045	27058045	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	91	540	3	ENST00000324856.7:c.1753C>T	p.Gln585Ter	p.Q585*	ENST00000324856	NM_006015.4	585	Cag/Tag	3/20	1	2	FACETS	0.891	0.79	0.999	0.891	0.79	0.999	CLONAL	1	TRUE	1	0.25	2		543	817	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910504	32910504	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	53	330	2	ENST00000380152.3:c.2012C>T	p.Ser671Phe	p.S671F	ENST00000380152		671	tCt/tTt	11/27	1	2	FACETS	0.972	0.831	1	0.972	0.831	1	CLONAL	1	TRUE	1	0.25	2		332	436	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40498654	40498655	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0054576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	90	495	0	ENST00000264657.5:c.204_205dup	p.Ser69IlefsTer70	p.S69Ifs*70	ENST00000264657	NM_139276.2	69	agc/aTAgc	3/24	1	2	FACETS	0.863	0.765	0.968	0.863	0.765	0.968	CLONAL	1	TRUE	1	0.25	2		495	834	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222366	53222367	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCTCTGGCCCTGAGCTCCGTAC	novel	NA	P-0054576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	41	451	1	ENST00000375401.3:c.4444_4465dup	p.Ala1489GlyfsTer9	p.A1489Gfs*9	ENST00000375401	NM_004187.3	1489	gct/gGTACGGAGCTCAGGGCCAGAGGct	26/26	0.22078478026749	2	FACETS	0.422	0.35	0.502			1	SUBCLONAL	1	TRUE	NA	0.25	2		452	777	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560464	95560464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054619-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	255	523	0	ENST00000393063.1:c.5125G>A	p.Asp1709Asn	p.D1709N	ENST00000393063	NM_030621.3	1709	Gat/Aat	25/28	1	2	FACETS	0.95	0.895	1	0.95	0.895	1	CLONAL	1	TRUE	1	0.821974062404377	2		523	653	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954037	32954037	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs80359165	NA	P-0054619-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	50	383	0	ENST00000380152.3:c.9104A>G	p.Tyr3035Cys	p.Y3035C	ENST00000380152		3035	tAt/tGt	23/27	1	2	FACETS	0.213	0.18	0.249	0.213	0.18	0.249	SUBCLONAL	1	TRUE	1	0.821974062404377	2		383	572	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574789	95574789	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054619-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	175	364	0	ENST00000393063.1:c.2308del	p.Leu770CysfsTer3	p.L770Cfs*3	ENST00000393063	NM_030621.3	770	Ctg/tg	16/28	1	2	FACETS	0.889	0.826	0.953	0.889	0.826	0.953	CLONAL	1	TRUE	1	0.821974062404377	2		364	479	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0054623-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	113	415	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.67	2		415	332	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054623-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	60	290	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.67	2		291	178	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0054623-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	27	115	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	1	2	FACETS	0.983	0.806	1	0.983	0.806	1	CLONAL	1	TRUE	1	0.67	2		115	82	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	48	670	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.59	0.5	0.69	0.59	0.5	0.69	SUBCLONAL	1	TRUE	1	0.39	2		670	417	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849266	76849266	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	79	209	1	ENST00000373344.5:c.6010G>T	p.Asp2004Tyr	p.D2004Y	ENST00000373344	NM_000489.3	2004	Gat/Tat	26/35	1	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.39	1		210	287	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	79	275	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.39	2		275	391	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	238	533	1	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	1	2	FACETS	0.958	0.9	1	1	0.995	1	CLONAL	2	TRUE	1	0.39	2		534	637	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	94	465	0	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	0.923	0.824	1	0.923	0.824	1	CLONAL	1	TRUE	1	0.39	2		465	522	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	59	383	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.845	0.731	0.968	0.845	0.731	0.968	CLONAL	1	TRUE	1	0.39	2		383	358	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944256	206944256	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374619208	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	114	380	0	ENST00000423557.1:c.374G>A	p.Arg125His	p.R125H	ENST00000423557	NM_000572.2	125	cGc/cAc	3/5	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.39	2		380	520	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679577	86679577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	87	414	1	ENST00000274376.6:c.2738G>A	p.Arg913Gln	p.R913Q	ENST00000274376	NM_002890.2	913	cGg/cAg	21/25	1	2	FACETS	0.983	0.874	1	0.983	0.874	1	CLONAL	1	TRUE	1	0.39	2		415	454	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915943	127915943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781486938	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	104	443	0	ENST00000373547.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000373547	NM_002721.4	180	Gaa/Aaa	6/7	1	2	FACETS	0.997	0.896	1	0.997	0.896	1	CLONAL	1	TRUE	1	0.39	2		443	535	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176490	123176490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	57	107	0	ENST00000218089.9:c.457G>A	p.Asp153Asn	p.D153N	ENST00000218089	NM_001042749.1	153	Gat/Aat	7/35	1	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.39	1		107	167	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374881	45374881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	140	467	1	ENST00000262160.6:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000262160	NM_005901.5	321	cGa/cAa	8/11	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.39	2		468	718	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	132	312	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.967	0.889	1	1	0.991	1	CLONAL	2	TRUE	1	0.39	2		312	350	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	88	393	1	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	0.895	0.796	1	0.895	0.796	1	CLONAL	1	TRUE	1	0.39	2		394	504	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510219	187510219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276553545	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	137	498	0	ENST00000441802.2:c.13294G>A	p.Glu4432Lys	p.E4432K	ENST00000441802	NM_005245.3	4432	Gaa/Aaa	27/27	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.39	2		498	680	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042164	14042164	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	66	258	1	ENST00000311895.7:c.2711C>A	p.Ser904Tyr	p.S904Y	ENST00000311895	NM_005236.2	904	tCt/tAt	11/11	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.39	2		259	328	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	99	521	1	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	1	2	FACETS	0.942	0.844	1	0.942	0.844	1	CLONAL	1	TRUE	1	0.39	2		522	539	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068393	26068393	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	226	411	0	ENST00000435504.4:c.97G>T	p.Glu33Ter	p.E33*	ENST00000435504		33	Gaa/Taa	2/13	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.39	2		411	503	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638555	176638555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210270412	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	146	601	0	ENST00000439151.2:c.3155G>A	p.Arg1052His	p.R1052H	ENST00000439151	NM_022455.4	1052	cGc/cAc	5/23	1	2	FACETS	0.936	0.855	1	0.936	0.855	1	CLONAL	1	TRUE	1	0.39	2		601	800	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870953	12870953	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	96	381	1	ENST00000228872.4:c.180G>T	p.Trp60Cys	p.W60C	ENST00000228872	NM_004064.3	60	tgG/tgT	1/3	1	2	FACETS	0.985	0.881	1	0.985	0.881	1	CLONAL	1	TRUE	1	0.39	2		382	500	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220274	55220274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	163	738	1	ENST00000275493.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000275493	NM_005228.3	222	Cgc/Tgc	6/28	1	2	FACETS	0.911	0.836	0.989	0.911	0.836	0.989	CLONAL	1	TRUE	1	0.39	2		739	918	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099338	193099338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	83	98	0	ENST00000367435.3:c.272G>A	p.Arg91Gln	p.R91Q	ENST00000367435	NM_024529.4	91	cGa/cAa	3/17	1	2	FACETS	0.961	0.852	1	0.961	0.852	1	CLONAL	1	TRUE	1	0.39	2		98	443	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	75	453	1	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	1	2	FACETS	0.724	0.636	0.819	0.724	0.636	0.819	SUBCLONAL	1	TRUE	1	0.39	2		454	531	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126756	5126756	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	75	400	0	ENST00000381652.3:c.3364C>T	p.Arg1122Ter	p.R1122*	ENST00000381652	NM_004972.3	1122	Cga/Tga	25/25	1	2	FACETS	0.94	0.828	1	0.94	0.828	1	CLONAL	1	TRUE	1	0.39	2		400	409	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844193	68844193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121964873	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	140	614	2	ENST00000261769.5:c.781G>A	p.Glu261Lys	p.E261K	ENST00000261769	NM_004360.3	261	Gaa/Aaa	6/16	1	2	FACETS	0.836	0.761	0.914	0.836	0.761	0.914	CLONAL	1	TRUE	1	0.39	2		616	859	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411783	63411783	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	141	384	0	ENST00000330258.3:c.1384G>T	p.Glu462Ter	p.E462*	ENST00000330258	NM_152424.3	462	Gaa/Taa	2/2	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.39	1		384	431	SUCCESS
APC	324	MSKCC	GRCh37	5	112178211	112178211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs901983934	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	70	389	1	ENST00000257430.4:c.6920C>T	p.Ser2307Leu	p.S2307L	ENST00000257430	NM_000038.5	2307	tCg/tTg	16/16	1	2	FACETS	0.717	0.626	0.814	0.717	0.626	0.814	SUBCLONAL	1	TRUE	1	0.39	2		390	501	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564477	55564477	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	70	451	1	ENST00000288135.5:c.365G>A	p.Arg122His	p.R122H	ENST00000288135	NM_000222.2	122	cGc/cAc	3/21	1	2	FACETS	0.739	0.645	0.839	0.739	0.645	0.839	SUBCLONAL	1	TRUE	1	0.39	2		452	486	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307902	11307902	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	46	620	0	ENST00000361445.4:c.1090G>T	p.Asp364Tyr	p.D364Y	ENST00000361445	NM_004958.3	364	Gac/Tac	7/58	1	2	FACETS	0.322	0.27	0.38	0.322	0.27	0.38	SUBCLONAL	1	TRUE	1	0.39	2		620	732	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278247	142278247	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	129	498	0	ENST00000350721.4:c.1578G>T	p.Lys526Asn	p.K526N	ENST00000350721	NM_001184.3	526	aaG/aaT	7/47	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.39	2		498	623	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485115	57485115	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754097818	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	70	358	0	ENST00000371085.3:c.949C>T	p.Arg317Cys	p.R317C	ENST00000371085	NM_000516.4	317	Cgc/Tgc	11/13	1	2	FACETS	0.721	0.63	0.819	0.721	0.63	0.819	SUBCLONAL	1	TRUE	1	0.39	2		358	498	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862850	9862850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751455326	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	149	678	0	ENST00000330684.3:c.2453C>T	p.Ala818Val	p.A818V	ENST00000330684	NM_001134407.1	818	gCg/gTg	12/13	1	2	FACETS	0.939	0.858	1	0.939	0.858	1	CLONAL	1	TRUE	1	0.39	2		678	814	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109744	115109744	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	47	740	0	ENST00000257566.3:c.2134G>A	p.Ala712Thr	p.A712T	ENST00000257566	NM_016569.3	712	Gcg/Acg	8/8	1	2	FACETS	0.268	0.225	0.316	0.268	0.225	0.316	SUBCLONAL	1	TRUE	1	0.39	2		740	899	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562982	29562982	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1306237220	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	99	459	0	ENST00000356175.3:c.3917G>A	p.Arg1306Gln	p.R1306Q	ENST00000356175	NM_000267.3	1306	cGa/cAa	29/57	1	2	FACETS	0.892	0.799	0.991	0.892	0.799	0.991	CLONAL	1	TRUE	1	0.39	2		459	569	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166818	32166818	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1441415979	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	226	896	1	ENST00000375023.3:c.4420C>T	p.Arg1474Ter	p.R1474*	ENST00000375023	NM_004557.3	1474	Cga/Tga	24/30	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.39	2		897	1044	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033753	48033753	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1553333707	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	76	308	0	ENST00000234420.5:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000234420	NM_000179.2	1322	Gaa/Taa	9/10	1	2	FACETS	0.989	0.872	1	0.989	0.872	1	CLONAL	1	TRUE	1	0.39	2		308	394	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604665	48604665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660045	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	100	352	0	ENST00000342988.3:c.1487G>A	p.Arg496His	p.R496H	ENST00000342988	NM_005359.5	496	cGt/cAt	12/12	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.39	2		352	491	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736176	204736176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	99	376	0	ENST00000302823.3:c.533G>A	p.Ser178Asn	p.S178N	ENST00000302823	NM_005214.4	178	aGc/aAc	3/4	1	2	FACETS	0.962	0.861	1	0.962	0.861	1	CLONAL	1	TRUE	1	0.39	2		376	528	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914859	32914860	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359577	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	74	378	0	ENST00000380152.3:c.6373dup	p.Thr2125AsnfsTer4	p.T2125Nfs*4	ENST00000380152		2123	gaa/gAaa	11/27	1	2	FACETS	0.855	0.751	0.965	0.855	0.751	0.965	CLONAL	1	TRUE	1	0.39	2		378	444	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685312	86685312	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	36	163	0	ENST00000274376.6:c.3028C>T	p.Arg1010Ter	p.R1010*	ENST00000274376	NM_002890.2	1010	Cga/Tga	24/25	1	2	FACETS	0.806	0.668	0.959	0.806	0.668	0.959	CLONAL	1	TRUE	1	0.39	2		163	229	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012219	16012219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	30	371	0	ENST00000268712.3:c.2063G>A	p.Arg688Gln	p.R688Q	ENST00000268712	NM_006311.3	688	cGa/cAa	19/46	1	2	FACETS	0.315	0.253	0.385	0.315	0.253	0.385	SUBCLONAL	1	TRUE	1	0.39	2		371	489	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291528	10291528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755995375	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	27	506	0	ENST00000340748.4:c.151G>A	p.Glu51Lys	p.E51K	ENST00000340748		51	Gaa/Aaa	3/40	1	2	FACETS	0.23	0.182	0.285	0.23	0.182	0.285	SUBCLONAL	1	TRUE	1	0.39	2		506	602	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950376	17950376	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs267605358	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	204	785	1	ENST00000458235.1:c.1351C>T	p.Arg451Ter	p.R451*	ENST00000458235	NM_000215.3	451	Cga/Tga	10/24	1	2	FACETS	0.994	0.922	1	0.994	0.922	1	CLONAL	1	TRUE	1	0.39	2		786	1052	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622451	28622451	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	92	496	0	ENST00000241453.7:c.1166C>A	p.Ser389Ter	p.S389*	ENST00000241453	NM_004119.2	389	tCa/tAa	9/24	1	2	FACETS	0.812	0.723	0.907	0.812	0.723	0.907	CLONAL	1	TRUE	1	0.39	2		496	581	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175871	24175871	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	134	559	2	ENST00000263121.7:c.1099G>A	p.Asp367Asn	p.D367N	ENST00000263121	NM_003073.3	367	Gac/Aac	8/9	1	2	FACETS	0.917	0.834	1	0.917	0.834	1	CLONAL	1	TRUE	1	0.39	2		561	749	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880270	155880270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	82	419	0	ENST00000368323.3:c.134G>A	p.Arg45Gln	p.R45Q	ENST00000368323	NM_006912.5	45	cGa/cAa	3/6	1	2	FACETS	0.763	0.674	0.858	0.763	0.674	0.858	SUBCLONAL	1	TRUE	1	0.39	2		419	551	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62309650	62309650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753838163	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	137	667	1	ENST00000360203.5:c.988G>A	p.Asp330Asn	p.D330N	ENST00000360203	NM_001283009.1	330	Gat/Aat	12/35	1	2	FACETS	0.951	0.866	1	0.951	0.866	1	CLONAL	1	TRUE	1	0.39	2		668	739	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763489	41763489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201238916	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	118	624	1	ENST00000301178.4:c.2288G>A	p.Arg763His	p.R763H	ENST00000301178	NM_021913.4	763	cGc/cAc	19/20	1	2	FACETS	0.894	0.808	0.985	0.894	0.808	0.985	CLONAL	1	TRUE	1	0.39	2		625	677	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641280	3641280	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140600202	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	133	723	0	ENST00000294008.3:c.2359G>A	p.Glu787Lys	p.E787K	ENST00000294008	NM_032444.2	787	Gaa/Aaa	12/15	1	2	FACETS	0.772	0.701	0.847	0.772	0.701	0.847	SUBCLONAL	1	TRUE	1	0.39	2		723	883	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795032	45795032	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768671057	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	151	572	0	ENST00000450313.1:c.1596C>A	p.Phe532Leu	p.F532L	ENST00000450313	NM_012222.2	532	ttC/ttA	16/16	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.39	2		572	772	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431650	6431650	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	127	477	0	ENST00000356142.4:c.203G>A	p.Arg68His	p.R68H	ENST00000356142	NM_018890.3	68	cGc/cAc	3/7	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.39	2		477	635	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745593	162745593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769532262	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	126	456	0	ENST00000367921.3:c.2008G>A	p.Glu670Lys	p.E670K	ENST00000367921	NM_006182.2	670	Gag/Aag	15/18	1	2	FACETS	0.92	0.835	1	0.92	0.835	1	CLONAL	1	TRUE	1	0.39	2		456	702	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519117	103519117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770975661	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	103	557	0	ENST00000355739.4:c.2455C>T	p.Arg819Trp	p.R819W	ENST00000355739	NM_000123.3	819	Cgg/Tgg	11/15	1	2	FACETS	0.792	0.709	0.879	0.792	0.709	0.879	SUBCLONAL	1	TRUE	1	0.39	2		557	667	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40872305	40872305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773742282	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	102	607	0	ENST00000428826.2:c.650G>A	p.Arg217Gln	p.R217Q	ENST00000428826		217	cGa/cAa	7/21	1	2	FACETS	0.64	0.572	0.713	0.64	0.572	0.713	SUBCLONAL	1	TRUE	1	0.39	2		607	817	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770575	40770575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1294592345	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	125	479	0	ENST00000373198.4:c.2807G>A	p.Arg936Gln	p.R936Q	ENST00000373198	NM_133170.3	936	cGa/cAa	19/32	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.39	2		479	595	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090886	5090886	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	23	166	0	ENST00000381652.3:c.3034G>T	p.Glu1012Ter	p.E1012*	ENST00000381652	NM_004972.3	1012	Gaa/Taa	22/25	1	2	FACETS	0.813	0.641	1	0.813	0.641	1	CLONAL	1	TRUE	1	0.39	2		166	145	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963878	2963878	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	127	622	3	ENST00000396946.4:c.1929C>A	p.Phe643Leu	p.F643L	ENST00000396946	NM_032415.4	643	ttC/ttA	15/25	1	2	FACETS	0.856	0.776	0.94	0.856	0.776	0.94	CLONAL	1	TRUE	1	0.39	2		625	761	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16248837	16248837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767352538	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	75	366	0	ENST00000375759.3:c.1843G>A	p.Glu615Lys	p.E615K	ENST00000375759	NM_015001.2	615	Gaa/Aaa	10/15	1	2	FACETS	0.959	0.845	1	0.959	0.845	1	CLONAL	1	TRUE	1	0.39	2		366	401	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69986988	69986988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs994568417	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	96	523	0	ENST00000394351.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000394351	NM_000248.3	17	Gaa/Aaa	2/9	1	2	FACETS	0.79	0.705	0.881	0.79	0.705	0.881	SUBCLONAL	1	TRUE	1	0.39	2		523	623	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932040	36932040	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs952518863	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	146	732	0	ENST00000361632.4:c.2429A>G	p.Asp810Gly	p.D810G	ENST00000361632		810	gAc/gGc	16/16	1	2	FACETS	0.853	0.778	0.931	0.853	0.778	0.931	CLONAL	1	TRUE	1	0.39	2		732	878	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39317430	39317430	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	106	411	0	ENST00000373001.3:c.757-1G>T		p.X253_splice	ENST00000373001	NM_022157.3	253			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.39	2		411	492	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749297	43749297	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs748115671	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	54	525	1	ENST00000382044.4:c.1509G>T	p.Lys503Asn	p.K503N	ENST00000382044	NM_001141980.1	503	aaG/aaT	12/28	1	2	FACETS	0.404	0.344	0.469	0.404	0.344	0.469	SUBCLONAL	1	TRUE	1	0.39	2		526	686	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206668	108206668	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	74	344	0	ENST00000278616.4:c.8248T>G	p.Leu2750Val	p.L2750V	ENST00000278616	NM_000051.3	2750	Tta/Gta	56/63	1	2	FACETS	0.807	0.709	0.913	0.807	0.709	0.913	CLONAL	1	TRUE	1	0.39	2		344	470	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480168	20480168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765868574	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	74	297	1	ENST00000346618.3:c.485G>A	p.Arg162Gln	p.R162Q	ENST00000346618	NM_001949.4	162	cGa/cAa	2/7	1	2	FACETS	0.895	0.787	1	0.895	0.787	1	CLONAL	1	TRUE	1	0.39	2		298	424	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643536	38643536	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373477920	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	67	451	0	ENST00000299084.4:c.1006G>A	p.Val336Ile	p.V336I	ENST00000299084	NM_152594.2	336	Gta/Ata	7/7	1	2	FACETS	0.535	0.465	0.611	0.535	0.465	0.611	SUBCLONAL	1	TRUE	1	0.39	2		451	642	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477161	67477161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758586312	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	146	694	0	ENST00000327367.4:c.968G>A	p.Arg323His	p.R323H	ENST00000327367	NM_005902.3	323	cGc/cAc	7/9	1	2	FACETS	0.994	0.909	1	0.994	0.909	1	CLONAL	1	TRUE	1	0.39	2		694	753	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348079	89348079	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	208	939	0	ENST00000301030.4:c.4871C>T	p.Ala1624Val	p.A1624V	ENST00000301030	NM_001256183.1	1624	gCg/gTg	9/13	1	2	FACETS	0.999	0.926	1	0.999	0.926	1	CLONAL	1	TRUE	1	0.39	2		939	1068	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11022897	11022897	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	200	780	0	ENST00000327064.4:c.596C>T	p.Ser199Leu	p.S199L	ENST00000327064	NM_199141.1	199	tCg/tTg	5/16	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.39	2		780	1013	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662769	227662769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	170	703	4	ENST00000305123.5:c.686C>T	p.Ala229Val	p.A229V	ENST00000305123	NM_005544.2	229	gCc/gTc	1/2	1	2	FACETS	0.925	0.851	1	0.925	0.851	1	CLONAL	1	TRUE	1	0.39	2		707	942	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041067	29041067	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	99	467	0	ENST00000282397.4:c.361G>T	p.Glu121Ter	p.E121*	ENST00000282397	NM_002019.4	121	Gaa/Taa	3/30	1	2	FACETS	0.988	0.885	1	0.988	0.885	1	CLONAL	1	TRUE	1	0.39	2		467	514	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261767	16261767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759881159	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	129	576	1	ENST00000375759.3:c.9032G>A	p.Arg3011Gln	p.R3011Q	ENST00000375759	NM_015001.2	3011	cGa/cAa	11/15	1	2	FACETS	0.948	0.861	1	0.948	0.861	1	CLONAL	1	TRUE	1	0.39	2		577	698	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212459	5212459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs182037655	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	180	765	0	ENST00000357368.4:c.4658C>T	p.Thr1553Met	p.T1553M	ENST00000357368	NM_002850.3	1553	aCg/aTg	31/38	1	2	FACETS	0.947	0.873	1	0.947	0.873	1	CLONAL	1	TRUE	1	0.39	2		765	975	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176484	123176484	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	60	114	0	ENST00000218089.9:c.451G>T	p.Glu151Ter	p.E151*	ENST00000218089	NM_001042749.1	151	Gaa/Taa	7/35	1	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.39	1		114	183	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719947	18719947	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	98	396	0	ENST00000266497.5:c.3844C>A	p.His1282Asn	p.H1282N	ENST00000266497		1282	Cat/Aat	27/31	1	2	FACETS	0.945	0.846	1	0.945	0.846	1	CLONAL	1	TRUE	1	0.39	2		396	532	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131978051	131978051	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	87	346	0	ENST00000265335.6:c.3934C>A	p.His1312Asn	p.H1312N	ENST00000265335		1312	Cat/Aat	25/25	1	2	FACETS	0.941	0.837	1	0.941	0.837	1	CLONAL	1	TRUE	1	0.39	2		346	474	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487185	56487185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777498890	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	76	502	1	ENST00000267101.3:c.1331G>A	p.Arg444Gln	p.R444Q	ENST00000267101	NM_001982.3	444	cGa/cAa	12/28	1	2	FACETS	0.586	0.514	0.664	0.586	0.514	0.664	SUBCLONAL	1	TRUE	1	0.39	2		503	665	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152009026	152009026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369725088	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	64	261	0	ENST00000262189.6:c.596G>A	p.Arg199Gln	p.R199Q	ENST00000262189	NM_170606.2	199	cGa/cAa	5/59	1	2	FACETS	0.96	0.836	1	0.96	0.836	1	CLONAL	1	TRUE	1	0.39	2		261	342	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339499	81339499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	88	450	0	ENST00000222390.5:c.1505G>A	p.Arg502Gln	p.R502Q	ENST00000222390	NM_000601.4	502	cGa/cAa	13/18	1	2	FACETS	0.802	0.712	0.897	0.802	0.712	0.897	CLONAL	1	TRUE	1	0.39	2		450	563	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937017	48937017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752342013	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	100	364	1	ENST00000267163.4:c.785G>A	p.Arg262Gln	p.R262Q	ENST00000267163	NM_000321.2	262	cGg/cAg	8/27	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.39	2		365	484	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805081	43805081	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	149	668	0	ENST00000372470.3:c.531G>T	p.Lys177Asn	p.K177N	ENST00000372470	NM_005373.2	177	aaG/aaT	4/12	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.39	2		668	738	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968288	18968288	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776533487	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	62	907	0	ENST00000262803.5:c.2128G>A	p.Ala710Thr	p.A710T	ENST00000262803	NM_002911.3	710	Gcc/Acc	15/24	1	2	FACETS	0.311	0.268	0.359	0.311	0.268	0.359	SUBCLONAL	1	TRUE	1	0.39	2		907	1021	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575128	48575128	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	71	345	0	ENST00000342988.3:c.322G>T	p.Glu108Ter	p.E108*	ENST00000342988	NM_005359.5	108	Gaa/Taa	3/12	1	2	FACETS	0.829	0.726	0.94	0.829	0.726	0.94	CLONAL	1	TRUE	1	0.39	2		345	439	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698123	47698123	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63750328	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	39	254	0	ENST00000233146.2:c.1681G>T	p.Glu561Ter	p.E561*	ENST00000233146	NM_000251.2	561	Gaa/Taa	11/16	1	2	FACETS	0.697	0.58	0.825	0.697	0.58	0.825	SUBCLONAL	1	TRUE	1	0.39	2		254	287	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266735	18266735	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80233027	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	170	771	0	ENST00000222254.8:c.46C>T	p.Arg16Cys	p.R16C	ENST00000222254	NM_005027.3	16	Cgc/Tgc	2/16	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.39	2		771	865	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190800	11190800	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	103	553	0	ENST00000361445.4:c.5399C>T	p.Ala1800Val	p.A1800V	ENST00000361445	NM_004958.3	1800	gCt/gTt	39/58	1	2	FACETS	0.77	0.69	0.855	0.77	0.69	0.855	SUBCLONAL	1	TRUE	1	0.39	2		553	686	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193141	11193141	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	148	526	0	ENST00000361445.4:c.5360A>G	p.Tyr1787Cys	p.Y1787C	ENST00000361445	NM_004958.3	1787	tAc/tGc	38/58	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.39	2		526	686	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166434	118166434	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	80	362	1	ENST00000369448.3:c.944A>G	p.Asn315Ser	p.N315S	ENST00000369448	NM_017709.3	315	aAc/aGc	2/2	1	2	FACETS	0.902	0.797	1	0.902	0.797	1	CLONAL	1	TRUE	1	0.39	2		363	455	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838032	156838032	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200167354	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	190	1009	1	ENST00000524377.1:c.565G>A	p.Ala189Thr	p.A189T	ENST00000524377	NM_002529.3	189	Gcc/Acc	5/17	1	2	FACETS	0.932	0.861	1	0.932	0.861	1	CLONAL	1	TRUE	1	0.39	2		1010	1045	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161298208	161298208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	127	405	0	ENST00000367975.2:c.100G>A	p.Ala34Thr	p.A34T	ENST00000367975	NM_003001.3	34	Gcc/Acc	3/6	1	2	FACETS	0.941	0.854	1	0.941	0.854	1	CLONAL	1	TRUE	1	0.39	2		405	692	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175916336	175916336	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	83	290	0	ENST00000367669.3:c.2173A>C	p.Ile725Leu	p.I725L	ENST00000367669	NM_022457.5	725	Att/Ctt	19/20	1	2	FACETS	0.985	0.874	1	0.985	0.874	1	CLONAL	1	TRUE	1	0.39	2		290	432	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104542	193104542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	86	357	0	ENST00000367435.3:c.329G>A	p.Arg110Lys	p.R110K	ENST00000367435	NM_024529.4	110	aGa/aAa	4/17	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.39	2		357	372	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549240	226549240	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	79	296	0	ENST00000366794.5:c.2966A>G	p.Tyr989Cys	p.Y989C	ENST00000366794	NM_001618.3	989	tAc/tGc	23/23	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.39	2		296	394	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555188	226555188	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	85	484	0	ENST00000366794.5:c.2399A>G	p.Asp800Gly	p.D800G	ENST00000366794	NM_001618.3	800	gAc/gGc	17/23	1	2	FACETS	0.824	0.73	0.924	0.824	0.73	0.924	CLONAL	1	TRUE	1	0.39	2		484	529	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663803	241663803	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs771503401	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	45	248	0	ENST00000366560.3:c.1324A>G	p.Thr442Ala	p.T442A	ENST00000366560	NM_000143.3	442	Aca/Gca	9/10	1	2	FACETS	0.836	0.707	0.977	0.836	0.707	0.977	CLONAL	1	TRUE	1	0.39	2		248	276	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716133	243716133	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	93	502	0	ENST00000263826.5:c.1061T>G	p.Leu354Arg	p.L354R	ENST00000263826	NM_005465.4	354	cTt/cGt	10/13	0.3	1	FACETS	0.782	0.698	0.871	0.782	0.698	0.871	SUBCLONAL	1	TRUE	0	0.39	1		502	491	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927345	245927345	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	44	390	0	ENST00000388985.4:c.1183C>A	p.Leu395Met	p.L395M	ENST00000388985		395	Ctg/Atg	11/12	0.3	1	FACETS	0.375	0.315	0.443	0.375	0.315	0.443	SUBCLONAL	1	TRUE	0	0.39	1		390	484	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100330	8100330	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs772010450	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	134	884	0	ENST00000346208.3:c.304G>T	p.Ala102Ser	p.A102S	ENST00000346208		102	Gcc/Tcc	3/6	1	2	FACETS	0.694	0.63	0.762	0.694	0.63	0.762	SUBCLONAL	1	TRUE	1	0.39	2		884	990	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724234	112724234	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	90	406	1	ENST00000369452.4:c.118G>T	p.Glu40Ter	p.E40*	ENST00000369452	NM_007373.3	40	Gaa/Taa	2/9	1	2	FACETS	0.844	0.75	0.943	0.844	0.75	0.943	CLONAL	1	TRUE	1	0.39	2		407	547	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457955	69457956	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	111	442	0	ENST00000227507.2:c.355_356insA	p.Leu119HisfsTer44	p.L119Hfs*44	ENST00000227507	NM_053056.2	119	ctg/cAtg	2/5	1	2	FACETS	0.946	0.852	1	0.946	0.852	1	CLONAL	1	TRUE	1	0.39	2		442	602	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047207	77047207	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	119	565	0	ENST00000356341.3:c.1337A>G	p.Asp446Gly	p.D446G	ENST00000356341	NM_002576.4	446	gAc/gGc	13/15	1	2	FACETS	0.861	0.778	0.948	0.861	0.778	0.948	CLONAL	1	TRUE	1	0.39	2		565	709	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100655	102100655	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	70	285	0	ENST00000282441.5:c.1499T>C	p.Phe500Ser	p.F500S	ENST00000282441	NM_001130145.2	500	tTt/tCt	9/9	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.39	2		285	348	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121628	108121628	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555070958	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	126	449	0	ENST00000278616.4:c.1436A>G	p.Asp479Gly	p.D479G	ENST00000278616	NM_000051.3	479	gAt/gGt	10/63	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.39	2		449	582	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373316	118373316	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	112	444	0	ENST00000534358.1:c.6709A>G	p.Thr2237Ala	p.T2237A	ENST00000534358	NM_005933.3	2237	Act/Gct	27/36	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.39	2		444	571	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390750	118390750	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	110	388	0	ENST00000534358.1:c.11400A>C	p.Glu3800Asp	p.E3800D	ENST00000534358	NM_005933.3	3800	gaA/gaC	33/36	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.39	2		388	540	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644550	21644550	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	109	527	0	ENST00000421138.2:c.117A>C	p.Lys39Asn	p.K39N	ENST00000421138		39	aaA/aaC	4/16	1	2	FACETS	0.827	0.743	0.915	0.827	0.743	0.915	CLONAL	1	TRUE	1	0.39	2		527	676	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231412	46231412	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	67	367	0	ENST00000334344.6:c.1252A>C	p.Thr418Pro	p.T418P	ENST00000334344	NM_152641.2	418	Aca/Cca	10/21	1	2	FACETS	0.853	0.744	0.969	0.853	0.744	0.969	CLONAL	1	TRUE	1	0.39	2		367	403	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478928	56478928	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	187	710	2	ENST00000267101.3:c.384C>A	p.Ser128Arg	p.S128R	ENST00000267101	NM_001982.3	128	agC/agA	3/28	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.39	2		712	955	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863223	57863223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	125	551	0	ENST00000228682.2:c.1318C>T	p.Pro440Ser	p.P440S	ENST00000228682	NM_005269.2	440	Cca/Tca	11/12	1	2	FACETS	0.9	0.816	0.989	0.9	0.816	0.989	CLONAL	1	TRUE	1	0.39	2		551	712	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233425	69233425	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	88	372	0	ENST00000462284.1:c.1290G>T	p.Glu430Asp	p.E430D	ENST00000462284	NM_002392.5	430	gaG/gaT	11/11	1	2	FACETS	0.948	0.843	1	0.948	0.843	1	CLONAL	1	TRUE	1	0.39	2		372	476	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112047	115112047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767500073	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	211	862	1	ENST00000257566.3:c.1693G>A	p.Ala565Thr	p.A565T	ENST00000257566	NM_016569.3	565	Gct/Act	7/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.39	2		863	1000	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235942	133235942	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	146	699	0	ENST00000320574.5:c.3214G>T	p.Ala1072Ser	p.A1072S	ENST00000320574	NM_006231.2	1072	Gca/Tca	26/49	1	2	FACETS	0.941	0.859	1	0.941	0.859	1	CLONAL	1	TRUE	1	0.39	2		699	796	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28979925	28979925	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	109	406	0	ENST00000282397.4:c.1543A>C	p.Lys515Gln	p.K515Q	ENST00000282397	NM_002019.4	515	Aag/Cag	11/30	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.39	2		406	513	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437887	110437887	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	34	99	0	ENST00000375856.3:c.514G>T	p.Gly172Cys	p.G172C	ENST00000375856	NM_003749.2	172	Ggc/Tgc	1/2	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.39	2		99	138	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986718	36986718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1268490942	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	16	40	0	ENST00000354822.5:c.971C>T	p.Ala324Val	p.A324V	ENST00000354822	NM_001079668.2	324	gCg/gTg	3/3	1	2	FACETS	1	0.821	1	1	0.821	1	CLONAL	1	TRUE	1	0.39	2		40	74	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986977	36986977	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	133	511	0	ENST00000354822.5:c.712T>C	p.Trp238Arg	p.W238R	ENST00000354822	NM_001079668.2	238	Tgg/Cgg	3/3	1	2	FACETS	0.98	0.892	1	0.98	0.892	1	CLONAL	1	TRUE	1	0.39	2		511	696	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68290271	68290271	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	92	388	0	ENST00000487270.1:c.11A>C	p.Lys4Thr	p.K4T	ENST00000487270	NM_133509.3	4	aAg/aCg	2/11	1	2	FACETS	0.932	0.831	1	0.932	0.831	1	CLONAL	1	TRUE	1	0.39	2		388	506	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675053	40675053	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	142	714	2	ENST00000249776.8:c.17C>T	p.Ala6Val	p.A6V	ENST00000249776	NM_033286.3	6	gCc/gTc	1/9	1	2	FACETS	0.851	0.775	0.93	0.851	0.775	0.93	CLONAL	1	TRUE	1	0.39	2		716	856	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058743	42058743	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	42	208	0	ENST00000219905.7:c.8463G>T	p.Glu2821Asp	p.E2821D	ENST00000219905	NM_001164273.1	2821	gaG/gaT	24/24	1	2	FACETS	0.816	0.686	0.958	0.816	0.686	0.958	CLONAL	1	TRUE	1	0.39	2		208	264	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748966	43748966	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	182	737	0	ENST00000382044.4:c.1840G>T	p.Glu614Ter	p.E614*	ENST00000382044	NM_001141980.1	614	Gaa/Taa	12/28	1	2	FACETS	0.935	0.862	1	0.935	0.862	1	CLONAL	1	TRUE	1	0.39	2		737	998	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99192813	99192813	+	start_lost	Translation_Start_Site	SNP	G	G	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	126	462	2	ENST00000268035.6:c.3G>T	p.Met1?	p.M1?	ENST00000268035	NM_000875.3	1	atG/atT	1/21	1	2	FACETS	0.943	0.856	1	0.943	0.856	1	CLONAL	1	TRUE	1	0.39	2		464	685	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121578	2121578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	219	862	0	ENST00000219476.3:c.1907G>A	p.Gly636Glu	p.G636E	ENST00000219476	NM_000548.3	636	gGa/gAa	18/42	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.39	2		862	1031	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50784074	50784074	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	78	581	0	ENST00000398568.2:c.465G>T	p.Glu155Asp	p.E155D	ENST00000398568	NM_001042412.1	155	gaG/gaT	3/18	1	2	FACETS	0.554	0.486	0.627	0.554	0.486	0.627	SUBCLONAL	1	TRUE	1	0.39	2		581	722	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50784076	50784076	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	123	577	0	ENST00000398568.2:c.467G>T	p.Arg156Met	p.R156M	ENST00000398568	NM_001042412.1	156	aGg/aTg	3/18	1	2	FACETS	0.865	0.783	0.952	0.865	0.783	0.952	CLONAL	1	TRUE	1	0.39	2		577	729	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969903	81969903	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	157	563	1	ENST00000359376.3:c.2972G>T	p.Arg991Ile	p.R991I	ENST00000359376	NM_002661.3	991	aGa/aTa	27/33	1	2	FACETS	0.983	0.901	1	0.983	0.901	1	CLONAL	1	TRUE	1	0.39	2		564	819	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845218	89845218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	137	502	0	ENST00000389301.3:c.1817C>T	p.Ser606Phe	p.S606F	ENST00000389301	NM_000135.2	606	tCt/tTt	20/43	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.39	2		502	694	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577073	7577073	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	186	745	0	ENST00000269305.4:c.865C>A	p.Leu289Ile	p.L289I	ENST00000269305	NM_001126112.2	289	Ctc/Atc	8/11	1	2	FACETS	0.986	0.911	1	0.986	0.911	1	CLONAL	1	TRUE	1	0.39	2		745	967	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215370	41215370	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs80357291	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	105	435	0	ENST00000357654.3:c.5173G>T	p.Glu1725Ter	p.E1725*	ENST00000357654	NM_007294.3	1725	Gaa/Taa	18/23	1	2	FACETS	0.983	0.883	1	0.983	0.883	1	CLONAL	1	TRUE	1	0.39	2		435	548	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876524	59876524	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	111	416	0	ENST00000259008.2:c.1277T>C	p.Val426Ala	p.V426A	ENST00000259008	NM_032043.2	426	gTc/gCc	9/20	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.39	2		416	534	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372033	45372033	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	85	385	0	ENST00000262160.6:c.1135+1G>A		p.X379_splice	ENST00000262160	NM_005901.5	379			1	2	FACETS	0.927	0.823	1	0.927	0.823	1	CLONAL	1	TRUE	1	0.39	2		385	470	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117466	4117466	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	102	590	0	ENST00000262948.5:c.254T>C	p.Val85Ala	p.V85A	ENST00000262948	NM_030662.3	85	gTg/gCg	2/11	1	2	FACETS	0.894	0.802	0.992	0.894	0.802	0.992	CLONAL	1	TRUE	1	0.39	2		590	585	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610363	10610363	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290253160	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	184	862	0	ENST00000171111.5:c.347G>A	p.Arg116Gln	p.R116Q	ENST00000171111	NM_203500.1	116	cGg/cAg	2/6	1	2	FACETS	0.882	0.813	0.953	0.882	0.813	0.953	CLONAL	1	TRUE	1	0.39	2		862	1070	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464543	25464543	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	145	827	0	ENST00000264709.3:c.1970T>C	p.Val657Ala	p.V657A	ENST00000264709	NM_175629.2	657	gTg/gCg	17/23	1	2	FACETS	0.857	0.782	0.935	0.857	0.782	0.935	CLONAL	1	TRUE	1	0.39	2		827	868	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635680	47635680	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	102	379	0	ENST00000233146.2:c.352T>C	p.Tyr118His	p.Y118H	ENST00000233146	NM_000251.2	118	Tat/Cat	2/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.39	2		379	484	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286822	212286822	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	73	327	0	ENST00000342788.4:c.2874G>T	p.Met958Ile	p.M958I	ENST00000342788	NM_005235.2	958	atG/atT	24/28	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.39	2		327	372	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339074	225339074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745316138	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	70	299	0	ENST00000264414.4:c.2195C>T	p.Ala732Val	p.A732V	ENST00000264414	NM_003590.4	732	gCg/gTg	16/16	1	2	FACETS	0.916	0.802	1	0.916	0.802	1	CLONAL	1	TRUE	1	0.39	2		299	392	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46271030	46271030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747049477	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	98	506	1	ENST00000371998.3:c.3154G>A	p.Ala1052Thr	p.A1052T	ENST00000371998		1052	Gca/Aca	17/23	1	2	FACETS	0.861	0.769	0.957	0.861	0.769	0.957	CLONAL	1	TRUE	1	0.39	2		507	584	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171721	36171721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762953695	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	111	406	0	ENST00000300305.3:c.844G>A	p.Asp282Asn	p.D282N	ENST00000300305		282	Gat/Aat	7/8	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.39	2		406	560	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057206	30057206	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	100	477	0	ENST00000338641.4:c.688A>G	p.Thr230Ala	p.T230A	ENST00000338641	NM_000268.3	230	Aca/Gca	8/16	1	2	FACETS	0.924	0.828	1	0.924	0.828	1	CLONAL	1	TRUE	1	0.39	2		477	555	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574751	41574751	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	182	757	1	ENST00000263253.7:c.7036T>C	p.Ser2346Pro	p.S2346P	ENST00000263253	NM_001429.3	2346	Tcc/Ccc	31/31	1	2	FACETS	0.957	0.883	1	0.957	0.883	1	CLONAL	1	TRUE	1	0.39	2		758	975	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626036	12626036	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	113	470	0	ENST00000251849.4:c.1924T>C	p.Ser642Pro	p.S642P	ENST00000251849	NM_002880.3	642	Tcc/Ccc	17/17	1	2	FACETS	0.984	0.888	1	0.984	0.888	1	CLONAL	1	TRUE	1	0.39	2		470	589	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162116	47162116	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	89	386	0	ENST00000409792.3:c.4010A>T	p.Glu1337Val	p.E1337V	ENST00000409792	NM_014159.6	1337	gAa/gTa	3/21	1	2	FACETS	0.918	0.817	1	0.918	0.817	1	CLONAL	1	TRUE	1	0.39	2		386	497	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162781	47162781	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	52	364	0	ENST00000409792.3:c.3345A>C	p.Glu1115Asp	p.E1115D	ENST00000409792	NM_014159.6	1115	gaA/gaC	3/21	1	2	FACETS	0.548	0.466	0.636	0.548	0.466	0.636	SUBCLONAL	1	TRUE	1	0.39	2		364	487	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164969	47164969	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1315789205	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	75	269	0	ENST00000409792.3:c.1157A>G	p.Asp386Gly	p.D386G	ENST00000409792	NM_014159.6	386	gAt/gGt	3/21	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.39	2		269	375	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204753	128204753	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769473824	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	108	900	1	ENST00000341105.2:c.688C>T	p.Arg230Cys	p.R230C	ENST00000341105	NM_032638.4	230	Cgc/Tgc	3/6	1	2	FACETS	0.56	0.502	0.622	0.56	0.502	0.622	SUBCLONAL	1	TRUE	1	0.39	2		901	989	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272146	142272146	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	107	428	0	ENST00000350721.4:c.2728G>T	p.Glu910Ter	p.E910*	ENST00000350721	NM_001184.3	910	Gaa/Taa	13/47	1	2	FACETS	0.946	0.851	1	0.946	0.851	1	CLONAL	1	TRUE	1	0.39	2		428	580	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917543	178917543	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	26	394	0	ENST00000263967.3:c.418C>T	p.Arg140Ter	p.R140*	ENST00000263967	NM_006218.2	140	Cga/Tga	3/21	1	2	FACETS	0.302	0.238	0.374	0.302	0.238	0.374	SUBCLONAL	1	TRUE	1	0.39	2		394	442	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182679131	182679131	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	78	404	1	ENST00000292782.4:c.403G>T	p.Glu135Ter	p.E135*	ENST00000292782	NM_020640.2	135	Gaa/Taa	4/7	1	2	FACETS	0.998	0.881	1	0.998	0.881	1	CLONAL	1	TRUE	1	0.39	2		405	401	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467818	66467818	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	61	334	0	ENST00000273854.3:c.451T>G	p.Phe151Val	p.F151V	ENST00000273854	NM_004439.5	151	Ttt/Gtt	3/18	1	2	FACETS	0.81	0.702	0.927	0.81	0.702	0.927	CLONAL	1	TRUE	1	0.39	2		334	386	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158448	106158448	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	63	210	0	ENST00000380013.4:c.3349A>C	p.Lys1117Gln	p.K1117Q	ENST00000380013	NM_001127208.2	1117	Aaa/Caa	3/11	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.39	2		210	310	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521076	187521076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376826855	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	118	463	0	ENST00000441802.2:c.12079G>A	p.Val4027Ile	p.V4027I	ENST00000441802	NM_005245.3	4027	Gtt/Att	22/27	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.39	2		463	520	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183285	56183285	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	100	510	0	ENST00000399503.3:c.4195G>T	p.Gly1399Ter	p.G1399*	ENST00000399503	NM_005921.1	1399	Gga/Tga	18/20	1	2	FACETS	0.751	0.671	0.835	0.751	0.671	0.835	SUBCLONAL	1	TRUE	1	0.39	2		510	683	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645182	86645182	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	50	260	0	ENST00000274376.6:c.1253+1G>A		p.X418_splice	ENST00000274376	NM_002890.2	418			1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.39	2		260	254	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043959	180043959	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	127	766	1	ENST00000261937.6:c.3037G>T	p.Asp1013Tyr	p.D1013Y	ENST00000261937	NM_182925.4	1013	Gat/Tat	22/30	1	2	FACETS	0.852	0.773	0.936	0.852	0.773	0.936	CLONAL	1	TRUE	1	0.39	2		767	764	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323289	31323289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs281864640	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	15	167	0	ENST00000412585.2:c.700C>T	p.Pro234Ser	p.P234S	ENST00000412585	NM_005514.6	234	Cct/Tct	4/8	1	2	FACETS	0.347	0.253	0.458	0.347	0.253	0.458	SUBCLONAL	1	TRUE	1	0.39	2		167	222	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940496	31940496	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	190	789	0	ENST00000375333.2:c.529A>C	p.Ser177Arg	p.S177R	ENST00000375333	NM_032454.1	177	Agc/Cgc	3/8	1	2	FACETS	0.946	0.874	1	0.946	0.874	1	CLONAL	1	TRUE	1	0.39	2		789	1030	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956621	93956621	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	80	421	0	ENST00000369303.4:c.2615G>T	p.Cys872Phe	p.C872F	ENST00000369303	NM_004440.3	872	tGt/tTt	15/17	1	2	FACETS	0.821	0.724	0.923	0.821	0.724	0.923	CLONAL	1	TRUE	1	0.39	2		421	500	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965620	93965620	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs964339668	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	94	436	0	ENST00000369303.4:c.2308C>T	p.Leu770Phe	p.L770F	ENST00000369303	NM_004440.3	770	Ctc/Ttc	13/17	1	2	FACETS	0.92	0.821	1	0.92	0.821	1	CLONAL	1	TRUE	1	0.39	2		436	524	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066560	94066560	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	91	399	0	ENST00000369303.4:c.1199T>C	p.Val400Ala	p.V400A	ENST00000369303	NM_004440.3	400	gTc/gCc	5/17	1	2	FACETS	0.91	0.81	1	0.91	0.81	1	CLONAL	1	TRUE	1	0.39	2		399	513	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199724	138199724	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	131	538	0	ENST00000237289.4:c.1142C>A	p.Ser381Tyr	p.S381Y	ENST00000237289	NM_001270507.1	381	tCt/tAt	7/9	1	2	FACETS	0.914	0.83	1	0.914	0.83	1	CLONAL	1	TRUE	1	0.39	2		538	735	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459495	50459495	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	82	299	0	ENST00000331340.3:c.784C>A	p.Leu262Ile	p.L262I	ENST00000331340	NM_006060.4	262	Ctc/Atc	7/8	1	2	FACETS	0.947	0.839	1	0.947	0.839	1	CLONAL	1	TRUE	1	0.39	2		299	444	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334831	81334831	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	86	415	0	ENST00000222390.5:c.1885T>G	p.Leu629Val	p.L629V	ENST00000222390	NM_000601.4	629	Tta/Gta	17/18	1	2	FACETS	0.963	0.856	1	0.963	0.856	1	CLONAL	1	TRUE	1	0.39	2		415	458	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273511	38273511	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	171	966	0	ENST00000425967.3:c.1824G>C	p.Arg608Ser	p.R608S	ENST00000425967	NM_001174067.1	608	agG/agC	14/19	1	2	FACETS	0.967	0.89	1	0.967	0.89	1	CLONAL	1	TRUE	1	0.39	2		966	907	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70971050	70971050	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	115	626	1	ENST00000276594.2:c.1211G>T	p.Arg404Ile	p.R404I	ENST00000276594	NM_024504.3	404	aGa/aTa	6/8	0.3	1	FACETS	0.621	0.56	0.687	0.621	0.56	0.687	SUBCLONAL	1	TRUE	0	0.39	1		627	764	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5077573	5077573	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	56	374	0	ENST00000381652.3:c.1985A>C	p.His662Pro	p.H662P	ENST00000381652	NM_004972.3	662	cAt/cCt	15/25	1	2	FACETS	0.756	0.65	0.87	0.756	0.65	0.87	SUBCLONAL	1	TRUE	1	0.39	2		374	380	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089753	5089753	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	57	277	0	ENST00000381652.3:c.2651T>G	p.Leu884Arg	p.L884R	ENST00000381652	NM_004972.3	884	cTt/cGt	20/25	1	2	FACETS	0.916	0.791	1	0.916	0.791	1	CLONAL	1	TRUE	1	0.39	2		277	319	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486206	8486206	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	60	407	0	ENST00000356435.5:c.2611C>A	p.Leu871Ile	p.L871I	ENST00000356435		871	Ctt/Att	17/35	1	2	FACETS	0.646	0.558	0.742	0.646	0.558	0.742	SUBCLONAL	1	TRUE	1	0.39	2		407	476	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006024	22006024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	214	843	0	ENST00000276925.6:c.379G>A	p.Asp127Asn	p.D127N	ENST00000276925	NM_004936.3	127	Gac/Aac	2/2	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.39	2		843	951	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27173286	27173286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	48	655	0	ENST00000380036.4:c.827C>T	p.Ser276Phe	p.S276F	ENST00000380036	NM_000459.3	276	tCt/tTt	6/23	1	2	FACETS	0.317	0.267	0.372	0.317	0.267	0.372	SUBCLONAL	1	TRUE	1	0.39	2		655	777	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197349	27197349	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	123	520	0	ENST00000380036.4:c.1661A>C	p.Lys554Thr	p.K554T	ENST00000380036	NM_000459.3	554	aAa/aCa	12/23	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.39	2		520	614	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966709	36966709	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	74	480	0	ENST00000358127.4:c.617C>A	p.Ser206Tyr	p.S206Y	ENST00000358127	NM_001280556.1	206	tCt/tAt	6/10	1	2	FACETS	0.802	0.704	0.907	0.802	0.704	0.907	CLONAL	1	TRUE	1	0.39	2		480	473	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781512	135781512	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1564482622	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	84	410	0	ENST00000298552.3:c.1453G>T	p.Glu485Ter	p.E485*	ENST00000298552	NM_001162426.1	485	Gaa/Taa	15/23	1	2	FACETS	0.856	0.759	0.96	0.856	0.759	0.96	CLONAL	1	TRUE	1	0.39	2		410	503	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921564	39921564	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	166	354	0	ENST00000378444.4:c.4256T>C	p.Phe1419Ser	p.F1419S	ENST00000378444	NM_001123385.1	1419	tTc/tCc	10/15	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.39	1		354	462	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410193	63410193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	133	385	0	ENST00000330258.3:c.2974G>A	p.Ala992Thr	p.A992T	ENST00000330258	NM_152424.3	992	Gca/Aca	2/2	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.39	1		385	378	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347202	70347202	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	125	298	0	ENST00000374080.3:c.2866A>G	p.Lys956Glu	p.K956E	ENST00000374080		956	Aag/Gag	21/45	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.39	1		298	359	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	144	290	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.265774497675357	2		291	733	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1406	527	928	1	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.259805234841855	4	FACETS	0.866	0.828	0.904	0.866	0.828	0.904	CLONAL	3	TRUE	1	0.265774497675357	4		929	1933	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0054665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1459	209	776	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	0.259805234841855	4	FACETS	1	0.982	1	0.398	0.368	0.429	CLONAL	1	TRUE	1	0.265774497675357	4		776	1668	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434943	56434943	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775335997	NA	P-0054665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1445	295	741	1	ENST00000407977.2:c.2194C>T	p.Arg732Cys	p.R732C	ENST00000407977		732	Cgc/Tgc	9/10	0.265774497675357	3	FACETS	1	0.993	1	0.723	0.678	0.769	CLONAL	1	TRUE	1	0.265774497675357	3		742	1740	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872213	45872213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1647	166	752	0	ENST00000391945.4:c.221C>T	p.Ser74Leu	p.S74L	ENST00000391945	NM_000400.3	74	tCa/tTa	4/23	0.265774497675357	5	FACETS	0.964	0.881	1	0.241	0.22	0.263	CLONAL	1	TRUE	1	0.265774497675357	5		752	1813	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796451	42796451	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0054665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1840	258	981	0	ENST00000575354.2:c.3009-1G>A		p.X1003_splice	ENST00000575354	NM_015125.3	1003			0.265774497675357	5	FACETS	1	0.989	1	0.324	0.301	0.347	CLONAL	1	TRUE	1	0.265774497675357	5		981	2098	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023471	27023471	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1541	258	520	0	ENST00000324856.7:c.577G>T	p.Glu193Ter	p.E193*	ENST00000324856	NM_006015.4	193	Gag/Tag	1/20	0.265774497675357	5	FACETS	0.755	0.704	0.807	0.503	0.469	0.538	SUBCLONAL	2	TRUE	2	0.265774497675357	5		520	1799	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400019	49400019	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	100	541	0	ENST00000418115.1:c.318C>G	p.Phe106Leu	p.F106L	ENST00000418115	NM_001664.2	106	ttC/ttG	4/5	0.248065600365094	5	FACETS	0.765	0.684	0.851	0.51	0.456	0.568	SUBCLONAL	2	TRUE	2	0.265774497675357	5		541	688	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241974	72241974	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	12	218	0	ENST00000357731.5:c.416C>T	p.Pro139Leu	p.P139L	ENST00000357731	NM_173808.2	139	cCt/cTt	3/7	0.265774497675357	5	FACETS	0.848	0.598	1	0.283	0.199	0.384	CLONAL	1	TRUE	2	0.265774497675357	5		218	149	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923043	44923046	+	frameshift_variant	Frame_Shift_Del	DEL	AACT	AACT	-	novel	NA	P-0054665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	65	284	0	ENST00000377967.4:c.1905_1908del	p.Gln635HisfsTer55	p.Q635Hfs*55	ENST00000377967	NM_021140.2	635	cAACTa/ca	16/29	0.265774497675357	3	FACETS	1	0.966	1			1	CLONAL	1	TRUE	NA	0.265774497675357	3		284	410	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098808	178098808	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	48	568	0	ENST00000397062.3:c.237G>C	p.Glu79Asp	p.E79D	ENST00000397062	NM_006164.4	79	gaG/gaC	2/5	0.265774497675357	3	FACETS	0.658	0.555	0.771	0.329	0.277	0.386	SUBCLONAL	1	TRUE	1	0.265774497675357	3		568	622	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098966	178098966	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	10	305	0	ENST00000397062.3:c.79G>C	p.Asp27His	p.D27H	ENST00000397062	NM_006164.4	27	Gat/Cat	2/5	0.265774497675357	3	FACETS	0.627	0.426	0.877	0.313	0.213	0.439	SUBCLONAL	1	TRUE	1	0.265774497675357	3		305	136	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596158	43596160	+	missense_variant	Missense_Mutation	TNP	CTC	CTC	GCT	novel	NA	P-0054665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	96	559	1	ENST00000355710.3:c.325_327delinsGCT	p.Leu109Ala	p.L109A	ENST00000355710	NM_020975.4	109	CTC/GCT	2/20	0.265774497675357	3	FACETS	0.733	0.651	0.82	0.366	0.325	0.41	SUBCLONAL	1	TRUE	1	0.265774497675357	3		560	1117	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118353151	118353151	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0054665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	43	372	0	ENST00000534358.1:c.4027A>T	p.Lys1343Ter	p.K1343*	ENST00000534358	NM_005933.3	1343	Aaa/Taa	8/36	0.101741701520634	5	FACETS	1	0.928	1	0.586	0.497	0.683	INDETERMINATE	2	TRUE	1	0.265774497675357	5		372	193	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025570	1025570	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1449954844	NA	P-0054665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1584	178	832	0	ENST00000358495.3:c.805C>T	p.Arg269Trp	p.R269W	ENST00000358495	NM_134424.2	269	Cgg/Tgg	9/12	0.191652987821149	5	FACETS	1	0.956	1	0.354	0.325	0.385	CLONAL	1	TRUE	2	0.265774497675357	5		832	1762	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112608	115112608	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1854	126	793	1	ENST00000257566.3:c.1132G>C	p.Glu378Gln	p.E378Q	ENST00000257566	NM_016569.3	378	Gag/Cag	7/8	0.248065600365094	5	FACETS	0.67	0.603	0.74	0.223	0.201	0.247	SUBCLONAL	1	TRUE	2	0.265774497675357	5		794	1980	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434572	110434572	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1554	89	591	0	ENST00000375856.3:c.3829C>A	p.Gln1277Lys	p.Q1277K	ENST00000375856	NM_003749.2	1277	Cag/Aag	1/2	0.265774497675357	5	FACETS	0.57	0.503	0.642	0.285	0.251	0.321	SUBCLONAL	1	TRUE	3	0.265774497675357	5		591	1643	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749191	43749191	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	25	641	0	ENST00000382044.4:c.1615C>A	p.His539Asn	p.H539N	ENST00000382044	NM_001141980.1	539	Cac/Aac	12/28	0.122509871512225	4	FACETS	0.98	0.775	1	0.49	0.387	0.607	INDETERMINATE	1	TRUE	2	0.265774497675357	4		641	243	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217415	7217416	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0054665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	317	496	0	ENST00000380728.2:c.380_381insAA	p.His127GlnfsTer219	p.H127Qfs*219	ENST00000380728		127	cat/caAAt	5/11	0.259805234841855	4	FACETS	0.857	0.808	0.906	0.857	0.808	0.906	CLONAL	3	TRUE	1	0.265774497675357	4		496	1175	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627970	37627970	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146621695	NA	P-0054665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1668	99	504	0	ENST00000447079.4:c.1885C>T	p.Pro629Ser	p.P629S	ENST00000447079	NM_015083.1	629	Cct/Tct	2/14	0.265774497675357	27	FACETS	0.911	0.81	1			1	CLONAL	2	TRUE	NA	0.265774497675357	27		504	1767	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184544	7184544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1233	174	704	1	ENST00000302850.5:c.757G>A	p.Val253Met	p.V253M	ENST00000302850	NM_000208.2	253	Gtg/Atg	3/22	0.265774497675357	5	FACETS	1	0.984	1	0.325	0.298	0.354	CLONAL	1	TRUE	1	0.265774497675357	5		705	1407	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291891	15291891	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2036	245	1088	0	ENST00000263388.2:c.2875T>G	p.Cys959Gly	p.C959G	ENST00000263388	NM_000435.2	959	Tgc/Ggc	18/33	0.265774497675357	5	FACETS	1	0.979	1	0.283	0.262	0.304	CLONAL	1	TRUE	1	0.265774497675357	5		1088	2281	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40709562	40709562	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	40	424	0	ENST00000373198.4:c.4340A>C	p.Lys1447Thr	p.K1447T	ENST00000373198	NM_133170.3	1447	aAa/aCa	32/32	0.191652987821149	5	FACETS	0.849	0.705	1	0.283	0.235	0.337	CLONAL	1	TRUE	2	0.265774497675357	5		424	496	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49724615	49724615	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	93	589	0	ENST00000449682.2:c.574T>C	p.Phe192Leu	p.F192L	ENST00000449682	NM_020998.3	192	Ttc/Ctc	5/18	0.248065600365094	5	FACETS	0.772	0.684	0.866	0.257	0.228	0.289	SUBCLONAL	1	TRUE	2	0.265774497675357	5		589	1268	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955154	1955155	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0054665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	95	627	2	ENST00000382891.5:c.2241_2242delinsTA	p.Pro748Thr	p.P748T	ENST00000382891	NM_133335.3	747	taCCct/taTAct	12/22	0.191652987821149	5	FACETS	1	0.912	1	0.344	0.305	0.385	CLONAL	1	TRUE	2	0.265774497675357	5		629	970	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55603372	55603372	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	24	286	0	ENST00000288135.5:c.2728G>C	p.Asp910His	p.D910H	ENST00000288135	NM_000222.2	910	Gat/Cat	20/21	0.191652987821149	5	FACETS	1	0.815	1	0.347	0.272	0.431	CLONAL	1	TRUE	2	0.265774497675357	5		286	243	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527363	187527364	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	71	423	0	ENST00000441802.2:c.10210dup	p.Ser3404PhefsTer11	p.S3404Ffs*11	ENST00000441802	NM_005245.3	3404	tca/tTca	17/27	0.191652987821149	5	FACETS	1	0.92	1	0.358	0.312	0.408	CLONAL	1	TRUE	2	0.265774497675357	5		423	695	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978581	70978581	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	63	599	1	ENST00000276594.2:c.1072C>A	p.Gln358Lys	p.Q358K	ENST00000276594	NM_024504.3	358	Cag/Aag	5/8	0.265774497675357	3	FACETS	0.653	0.564	0.751	0.327	0.282	0.376	SUBCLONAL	1	TRUE	1	0.265774497675357	3		600	822	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922810	44922811	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTCC	novel	NA	P-0054665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	109	254	0	ENST00000377967.4:c.1676_1679dup	p.Ala561SerfsTer21	p.A561Sfs*21	ENST00000377967	NM_021140.2	557	-/GTCC	16/29	0.265774497675357	3	FACETS	0.836	0.753	0.923			1	CLONAL	2	TRUE	NA	0.265774497675357	3		254	556	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0054667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	348	622	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	0.554248731846205	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.554248731846205	1		622	826	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40368072	40368072	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555548678	NA	P-0054667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	142	646	2	ENST00000293328.3:c.1433C>T	p.Ala478Val	p.A478V	ENST00000293328	NM_012448.3	478	gCg/gTg	12/19	1	2	FACETS	0.438	0.398	0.48	0.438	0.398	0.48	SUBCLONAL	1	TRUE	1	0.554248731846205	2		648	1171	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244511	41244511	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555588500	NA	P-0054667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	49	596	0	ENST00000357654.3:c.3037G>A	p.Glu1013Lys	p.E1013K	ENST00000357654	NM_007294.3	1013	Gaa/Aaa	10/23	1	2	FACETS	0.231	0.195	0.271	0.231	0.195	0.271	SUBCLONAL	1	TRUE	1	0.554248731846205	2		596	766	SUCCESS
APC	324	MSKCC	GRCh37	5	112175111	112175112	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0054667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	84	191	0	ENST00000257430.4:c.3821_3822del	p.Cys1274Ter	p.C1274*	ENST00000257430	NM_000038.5	1274	TGt/t	16/16	0.491319027458072	1	FACETS	0.818	0.732	0.907	0.818	0.732	0.907	CLONAL	1	TRUE	0	0.554248731846205	1		191	268	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0054678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	64	372	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.317057494661961	2		372	352	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0054678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	49	233	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.317057494661961	2		233	289	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374293	138374293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	95	543	0	ENST00000289153.2:c.3151G>A	p.Glu1051Lys	p.E1051K	ENST00000289153	NM_006219.2	1051	Gaa/Aaa	22/22	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.317057494661961	2		543	566	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0054678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	23	277	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.669	0.524	0.835	0.669	0.524	0.835	SUBCLONAL	1	TRUE	1	0.317057494661961	2		277	217	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0054678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	63	408	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.317057494661961	2		408	356	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	12	620	1	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	1	2	FACETS	0.134	0.093	0.185	0.134	0.093	0.185	SUBCLONAL	1	TRUE	1	0.317057494661961	2		621	565	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791797	42791797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	126	777	0	ENST00000575354.2:c.683G>A	p.Arg228Gln	p.R228Q	ENST00000575354	NM_015125.3	228	cGg/cAg	5/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.317057494661961	2		777	679	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101410	27101410	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	47	474	0	ENST00000324856.7:c.4692del	p.Met1564IlefsTer48	p.M1564Ifs*48	ENST00000324856	NM_006015.4	1564	atG/at	18/20	1	2	FACETS	0.791	0.669	0.924	0.791	0.669	0.924	CLONAL	1	TRUE	1	0.317057494661961	2		474	375	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415613	49415613	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	57	432	0	ENST00000301067.7:c.16564A>G	p.Lys5522Glu	p.K5522E	ENST00000301067	NM_003482.3	5522	Aag/Gag	54/54	1	2	FACETS	0.903	0.778	1	0.903	0.778	1	CLONAL	1	TRUE	1	0.317057494661961	2		432	398	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831641	72831641	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0054678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	71	652	0	ENST00000268489.5:c.4940T>A	p.Leu1647Ter	p.L1647*	ENST00000268489	NM_006885.3	1647	tTg/tAg	9/10	1	2	FACETS	0.843	0.737	0.958	0.843	0.737	0.958	CLONAL	1	TRUE	1	0.317057494661961	2		652	531	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371739	55371740	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	63	563	0	ENST00000297316.4:c.430dup	p.Gln144ProfsTer18	p.Q144Pfs*18	ENST00000297316	NM_022454.3	143	-/C	2/2	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.317057494661961	2		563	387	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345949	70345952	+	protein_altering_variant	In_Frame_Del	DEL	TCTT	TCTT	G	novel	NA	P-0054678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	75	578	0	ENST00000374080.3:c.2486_2489delinsG	p.Ile829_Phe830delinsSer	p.I829_F830delinsS	ENST00000374080		829	aTCTTt/aGt	18/45	1	2	FACETS	0.848	0.744	0.959	0.848	0.744	0.959	CLONAL	1	TRUE	1	0.317057494661961	2		578	558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577567	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1567549651	NA	P-0054679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	71	626	0	ENST00000269305.4:c.714dup	p.Asn239Ter	p.N239*	ENST00000269305	NM_001126112.2	238	-/T	7/11	0.273221603830522	1	FACETS	0.505	0.439	0.576	0.505	0.439	0.576	SUBCLONAL	1	TRUE	0	0.273221603830522	1		626	889	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0054680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	117	243	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.373234015772151	5	FACETS	1	0.929	1	1	0.929	1	CLONAL	3	FALSE	2	0.373234015772151	5		243	320	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0054680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	166	726	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.373234015772151	2		726	635	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579314	7579314	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	187	642	0	ENST00000269305.4:c.373del	p.Thr125ArgfsTer45	p.T125Rfs*45	ENST00000269305	NM_001126112.2	125	Acg/cg	4/11	0.373234015772151	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	FALSE	0	0.373234015772151	2		642	485	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950473	17950473	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0054680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	119	626	2	ENST00000458235.1:c.1255-1G>T		p.X419_splice	ENST00000458235	NM_000215.3	419			0.373234015772151	7	FACETS	1	0.949	1			1	CLONAL	1	FALSE	NA	0.373234015772151	7		628	1136	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49929247	49929247	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780525228	NA	P-0054680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	113	664	0	ENST00000296474.3:c.3296G>A	p.Gly1099Glu	p.G1099E	ENST00000296474	NM_002447.2	1099	gGa/gAa	15/20	0.171064083254204	5	FACETS	1	0.981	1	0.462	0.416	0.51	INDETERMINATE	1	FALSE	2	0.373234015772151	5		664	682	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914644	32914644	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs398122549	NA	P-0054681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	80	642	0	ENST00000380152.3:c.6152A>G	p.Asn2051Ser	p.N2051S	ENST00000380152		2051	aAt/aGt	11/27	0.485445023949448	6	FACETS	0.921	0.811	1	0.23	0.202	0.26	CLONAL	1	TRUE	2	0.485445023949448	6		642	705	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639255	3639255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138484365	NA	P-0054681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	207	996	2	ENST00000294008.3:c.4384G>A	p.Ala1462Thr	p.A1462T	ENST00000294008	NM_032444.2	1462	Gcc/Acc	12/15	0.485445023949448	3	FACETS	1	0.95	1	0.515	0.478	0.554	CLONAL	1	TRUE	1	0.485445023949448	3		998	1029	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577495	7577501	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGACCTG	TGACCTG	-	novel	NA	P-0054681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	293	738	0	ENST00000269305.4:c.780_782+4del		p.X260_splice	ENST00000269305	NM_001126112.2	260		7/11	0.485445023949448	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.485445023949448	2		738	600	SUCCESS
APC	324	MSKCC	GRCh37	5	112170770	112170770	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs876658355	NA	P-0054681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	121	693	0	ENST00000257430.4:c.1866C>A	p.Tyr622Ter	p.Y622*	ENST00000257430	NM_000038.5	622	taC/taA	15/16	0.485445023949448	3	FACETS	0.866	0.784	0.954	0.433	0.392	0.477	CLONAL	1	TRUE	1	0.485445023949448	3		693	715	SUCCESS
APC	324	MSKCC	GRCh37	5	112175291	112175292	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0054681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	131	272	0	ENST00000257430.4:c.4000_4001del	p.Ser1334GlnfsTer7	p.S1334Qfs*7	ENST00000257430	NM_000038.5	1334	TCc/c	16/16	0.485445023949448	3	FACETS	0.876	0.803	0.95	0.876	0.803	0.95	CLONAL	2	TRUE	1	0.485445023949448	3		272	383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579867	7579879	+	frameshift_variant	Frame_Shift_Del	DEL	GACTCAGAGGGGG	GACTCAGAGGGGG	-	novel	NA	P-0054682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	297	803	2	ENST00000269305.4:c.34_46del	p.Pro12ArgfsTer28	p.P12Rfs*28	ENST00000269305	NM_001126112.2	12	CCCCCTCTGAGTCag/ag	2/11	0.475790510866762	2	FACETS	0.916	0.869	0.963	0.916	0.869	0.963	CLONAL	2	TRUE	0	0.492217511588921	2		805	659	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067852	30067852	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	76	525	0	ENST00000338641.4:c.1037G>C	p.Arg346Thr	p.R346T	ENST00000338641	NM_000268.3	346	aGg/aCg	11/16	0.493411727036493	3	FACETS	0.461	0.404	0.524	0.154	0.134	0.175	SUBCLONAL	1	TRUE	0	0.492217511588921	3		525	834	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	274	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.371789919973321	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	TRUE	1	0.371789919973321	4		487	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0054683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	332	778	3	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.371789919973321	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.371789919973321	2		781	782	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775512	39775512	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	118	700	1	ENST00000288319.7:c.508A>G	p.Lys170Glu	p.K170E	ENST00000288319	NM_182918.3	170	Aag/Gag	4/10	0.343518800495701	3	FACETS	1	0.902	1	0.5	0.451	0.551	CLONAL	1	TRUE	1	0.371789919973321	3		701	753	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971150	21971164	+	frameshift_variant	Frame_Shift_Del	DEL	GCTCCGCGCCGTGGA	GCTCCGCGCCGTGGA	T	novel	NA	P-0054683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	289	548	5	ENST00000304494.5:c.194_208delinsA	p.Leu65HisfsTer50	p.L65Hfs*50	ENST00000304494	NM_000077.4	65	cTCCACGGCGCGGAGCcc/cAcc	2/3	0.371789919973321	3	FACETS	0.98	0.93	1	0.98	0.93	1	CLONAL	3	TRUE	0	0.371789919973321	3		553	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0054684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	828	928	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.909028489898994	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.909028489898994	1		928	952	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692841	89692845	+	protein_altering_variant	In_Frame_Del	DEL	GACCA	GACCA	AG	novel	NA	P-0054684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	155	204	2	ENST00000371953.3:c.325_329delinsAG	p.Asp109_Gln110delinsArg	p.D109_Q110delinsR	ENST00000371953	NM_000314.4	109	GACCAa/AGa	5/9	0.909028489898994	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.909028489898994	1		206	185	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427423	49427423	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	738	939	0	ENST00000301067.7:c.11065del	p.Ala3689LeufsTer60	p.A3689Lfs*60	ENST00000301067	NM_003482.3	3689	Gct/ct	39/54	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.909028489898994	2		939	1624	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955493	48955493	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0054684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	187	372	0	ENST00000267163.4:c.1609A>T	p.Lys537Ter	p.K537*	ENST00000267163	NM_000321.2	537	Aaa/Taa	17/27	0.909028489898994	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.909028489898994	1		372	221	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422181	81422181	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	500	606	0	ENST00000298171.2:c.157A>T	p.Ser53Cys	p.S53C	ENST00000298171	NM_000369.2	53	Agt/Tgt	1/10	0.478583930330755	1	FACETS	0.716	0.692	0.74	0.716	0.692	0.74	INDETERMINATE	1	TRUE	0	0.909028489898994	1		606	838	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099199	4099199	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	563	782	0	ENST00000262948.5:c.919G>C	p.Gly307Arg	p.G307R	ENST00000262948	NM_030662.3	307	Ggt/Cgt	7/11	1	2	FACETS	0.977	0.94	1	0.977	0.94	1	CLONAL	1	TRUE	1	0.909028489898994	2		782	1268	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288501	15288501	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs535965132	NA	P-0054684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	158	262	0	ENST00000263388.2:c.4238A>G	p.Asp1413Gly	p.D1413G	ENST00000263388	NM_000435.2	1413	gAc/gGc	24/33	1	2	FACETS	0.834	0.772	0.896	0.834	0.772	0.896	CLONAL	1	TRUE	1	0.909028489898994	2		262	417	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157531	106157531	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	245	345	0	ENST00000380013.4:c.2432A>G	p.Asn811Ser	p.N811S	ENST00000380013	NM_001127208.2	811	aAt/aGt	3/11	0.45830611947543	1	FACETS	0.724	0.689	0.759	0.724	0.689	0.759	INDETERMINATE	1	TRUE	0	0.909028489898994	1		345	406	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	157	290	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.787	0.729	0.845	1	0.991	1	SUBCLONAL	2	FALSE	1	0.509134481200367	2		291	392	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0054685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	205	571	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.786	0.736	0.837	1	0.993	1	SUBCLONAL	2	FALSE	1	0.509134481200367	2		571	512	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034471	47034471	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	458	378	2	ENST00000377604.3:c.556C>T	p.Arg186Ter	p.R186*	ENST00000377604	NM_001204468.1	186	Cga/Tga	6/24	1	1	FACETS	1	0.996	1	1	0.998	1	CLONAL	2	FALSE	0	0.509134481200367	1		380	567	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0054685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	255	804	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	1	0.509134481200367	2		804	717	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136180	64136180	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	400	842	0	ENST00000334205.4:c.1339G>C	p.Glu447Gln	p.E447Q	ENST00000334205	NM_003942.2	447	Gag/Cag	12/17	1	2	FACETS	0.842	0.804	0.88	1	0.996	1	CLONAL	2	FALSE	1	0.509134481200367	2		842	933	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786786	3786796	+	frameshift_variant	Frame_Shift_Del	DEL	AGGACAGGCCC	AGGACAGGCCC	-	novel	NA	P-0054685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	98	506	0	ENST00000262367.5:c.4415_4425del	p.Trp1472SerfsTer3	p.W1472Sfs*3	ENST00000262367	NM_004380.2	1472	tGGGCCTGTCCT/t	27/31	0.180412020375116	2	FACETS	0.673	0.602	0.748	0.337	0.301	0.374	INDETERMINATE	1	FALSE	0	0.509134481200367	2		506	572	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041872	14041872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	246	418	0	ENST00000311895.7:c.2419C>T	p.His807Tyr	p.H807Y	ENST00000311895	NM_005236.2	807	Cat/Tat	11/11	0.180412020375116	2	FACETS	0.944	0.892	0.995	0.944	0.892	0.995	INDETERMINATE	2	FALSE	0	0.509134481200367	2		418	512	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174806	56174806	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0054685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	89	264	0	ENST00000399503.3:c.1966-1G>A		p.X656_splice	ENST00000399503	NM_005921.1	656			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.509134481200367	2		264	273	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177752	56177752	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs765395275	NA	P-0054685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	145	339	0	ENST00000399503.3:c.2725G>C	p.Glu909Gln	p.E909Q	ENST00000399503	NM_005921.1	909	Gag/Cag	14/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.509134481200367	2		339	388	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872107	76872107	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	159	254	0	ENST00000373344.5:c.5540A>G	p.Tyr1847Cys	p.Y1847C	ENST00000373344	NM_000489.3	1847	tAt/tGt	22/35	1	1	FACETS	1	0.975	1	1	0.994	1	CLONAL	2	FALSE	0	0.509134481200367	1		254	222	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179206	123179216	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AGCACCCTGGC	AGCACCCTGGC	-	novel	NA	P-0054685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	74	195	0	ENST00000218089.9:c.657_667del	p.Thr220TyrfsTer15	p.T220Yfs*15	ENST00000218089	NM_001042749.1	219	AGCACCCTGGCa/a	8/35	1	1	FACETS	0.809	0.734	0.882	1	0.984	1	CLONAL	2	FALSE	0	0.509134481200367	1		195	134	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	37	290	1				ENST00000310581	NM_198253.2	-/1132			0.334589611728321	1	FACETS	0.403	0.336	0.475	0.403	0.336	0.475	INDETERMINATE	1	TRUE	0	0.690890840814624	1		291	174	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	268	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.690890840814624	2		457	524	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0054686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	472	638	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.669391531611581	3	FACETS	1	0.98	1			1	CLONAL	3	TRUE	NA	0.690890840814624	3		638	608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0054686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	223	675	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.690890840814624	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.690890840814624	1		675	408	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970969	21970969	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	217	710	0	ENST00000304494.5:c.389T>A	p.Leu130Gln	p.L130Q	ENST00000304494	NM_000077.4	130	cTg/cAg	2/3	0.690890840814624	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.690890840814624	1		710	392	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745588	162745588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754868982	NA	P-0054686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	219	515	0	ENST00000367921.3:c.2003G>A	p.Arg668His	p.R668H	ENST00000367921	NM_006182.2	668	cGc/cAc	15/18	0.144740972292174	1	FACETS	0.694	0.65	0.739	0.694	0.65	0.739	INDETERMINATE	1	TRUE	0	0.690890840814624	1		515	598	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295186	1295187	+	upstream_gene_variant	5'Flank	INS	-	-	GGGGCCGCGGAAAGGAAGGGGA	novel	NA	P-0054687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	51	265	0				ENST00000310581	NM_198253.2	-/1132			0.578378545211941	3	FACETS	1	0.92	1	0.368	0.316	0.422	CLONAL	1	TRUE	0	0.579073190716592	3		265	206	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097754	8097754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	79	775	0	ENST00000346208.3:c.136G>A	p.Glu46Lys	p.E46K	ENST00000346208		46	Gag/Aag	2/6	0.579073190716592	7	FACETS	0.7	0.614	0.793	0.175	0.153	0.199	SUBCLONAL	1	TRUE	3	0.579073190716592	7		775	954	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41199702	41199702	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28897698	NA	P-0054687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	154	730	0	ENST00000357654.3:c.5425G>T	p.Val1809Phe	p.V1809F	ENST00000357654	NM_007294.3	1809	Gtt/Ttt	22/23	0.519037325964524	4	FACETS	0.959	0.886	1	0.959	0.886	1	CLONAL	2	TRUE	2	0.579073190716592	4		730	438	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770612	40770613	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0054687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	70	533	2	ENST00000373198.4:c.2769_2770delinsTT	p.Trp923_Asp924delinsCysTyr	p.W923_D924delinsCY	ENST00000373198	NM_133170.3	923	tgGGac/tgTTac	19/32	0.280114223683006	5	FACETS	0.859	0.758	0.965	0.573	0.505	0.644	INDETERMINATE	2	TRUE	2	0.579073190716592	5		535	263	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182681750	182681750	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	203	565	0	ENST00000292782.4:c.308T>C	p.Leu103Ser	p.L103S	ENST00000292782	NM_020640.2	103	tTg/tCg	3/7	0.306155758171769	5	FACETS	0.845	0.79	0.9	0.845	0.79	0.9	INDETERMINATE	3	TRUE	2	0.579073190716592	5		565	517	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637081	176637081	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	115	702	0	ENST00000439151.2:c.1681T>A	p.Ser561Thr	p.S561T	ENST00000439151	NM_022455.4	561	Tcc/Acc	5/23	0.469744155757935	2	FACETS	0.993	0.921	1	0.993	0.921	1	CLONAL	2	TRUE	0	0.579073190716592	2		702	200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0054688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	179	1045	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.221002077285709	2		1046	1223	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	41	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.918	0.766	1	0.918	0.766	1	CLONAL	1	TRUE	1	0.221002077285709	2		487	404	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790512	3790512	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	107	587	0	ENST00000262367.5:c.4021C>T	p.Arg1341Ter	p.R1341*	ENST00000262367	NM_004380.2	1341	Cga/Tga	24/31	1	2	FACETS	0.853	0.763	0.949	0.853	0.763	0.949	CLONAL	1	TRUE	1	0.221002077285709	2		587	1135	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857767	9857767	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	109	537	0	ENST00000330684.3:c.3634del	p.Thr1212ArgfsTer19	p.T1212Rfs*19	ENST00000330684	NM_001134407.1	1212	Acg/cg	13/13	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.221002077285709	2		537	908	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	115	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.867	0.783	0.954	1	0.987	1	CLONAL	2	TRUE	1	0.22955991236323	2		457	578	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	141	590	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.835	0.761	0.911	1	0.989	1	CLONAL	2	TRUE	1	0.22955991236323	2		591	736	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	84	588	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.87	0.767	0.981	0.87	0.767	0.981	CLONAL	1	TRUE	1	0.22955991236323	2		592	841	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	121	449	1	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	0.818	0.741	0.9	1	0.987	1	CLONAL	2	TRUE	1	0.22955991236323	2		450	644	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	64	412	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.22955991236323	2		412	539	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	171	1173	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.766	0.704	0.83	1	0.989	1	SUBCLONAL	2	TRUE	1	0.22955991236323	2		1174	973	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	74	481	2	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.22955991236323	2		483	642	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	122	508	3	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	1	2	FACETS	0.78	0.706	0.858	1	0.986	1	SUBCLONAL	2	TRUE	1	0.22955991236323	2		511	681	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100117	157100119	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs797045268	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	18	43	0	ENST00000346085.5:c.1069_1071del	p.Gly357del	p.G357del	ENST00000346085	NM_020732.3	352	GGC/-	1/20	1	2	FACETS	0.98	0.755	1	1	0.934	1	CLONAL	2	TRUE	1	0.22955991236323	2		43	80	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084146	47084146	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	40	545	0	ENST00000409792.3:c.7143del	p.Ser2382LeufsTer29	p.S2382Lfs*29	ENST00000409792	NM_014159.6	2381	ccC/cc	17/21	1	2	FACETS	0.5	0.414	0.596	0.5	0.414	0.596	SUBCLONAL	1	TRUE	1	0.22955991236323	2		545	697	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785964	135785964	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs118203506	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	325	732	1	ENST00000298552.3:c.1257del	p.Arg420GlyfsTer20	p.R420Gfs*20	ENST00000298552	NM_001162426.1	419	ccC/cc	12/23	1	2	FACETS	1	0.99	1	1	0.997	1	CLONAL	3	TRUE	1	0.22955991236323	2		733	815	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106364	27106364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	145	676	0	ENST00000324856.7:c.5975C>T	p.Ser1992Leu	p.S1992L	ENST00000324856	NM_006015.4	1992	tCa/tTa	20/20	1	2	FACETS	0.891	0.814	0.971	1	0.99	1	CLONAL	2	TRUE	1	0.22955991236323	2		676	709	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052636	42052636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1054243525	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	141	523	0	ENST00000219905.7:c.7307G>A	p.Arg2436His	p.R2436H	ENST00000219905	NM_001164273.1	2436	cGt/cAt	20/24	1	2	FACETS	1	0.922	1	1	0.991	1	CLONAL	2	TRUE	1	0.22955991236323	2		523	609	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829404	72829404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200268844	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	50	780	0	ENST00000268489.5:c.7177G>A	p.Ala2393Thr	p.A2393T	ENST00000268489	NM_006885.3	2393	Gcc/Acc	9/10	1	2	FACETS	0.584	0.494	0.683	0.584	0.494	0.683	SUBCLONAL	1	TRUE	1	0.22955991236323	2		780	746	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508557	106508557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	103	511	0	ENST00000359195.3:c.551G>A	p.Arg184His	p.R184H	ENST00000359195	NM_002649.2	184	cGc/cAc	2/11	1	2	FACETS	0.834	0.749	0.924	1	0.985	1	CLONAL	2	TRUE	1	0.22955991236323	2		511	538	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	168	946	9	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	1	2	FACETS	0.848	0.78	0.919	1	0.991	1	CLONAL	2	TRUE	1	0.22955991236323	2		955	863	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	57	699	0	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	1	2	FACETS	0.722	0.618	0.835	0.722	0.618	0.835	SUBCLONAL	1	TRUE	1	0.22955991236323	2		699	688	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939797	71939797	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	190	1010	0	ENST00000298229.2:c.428del	p.Pro143ArgfsTer36	p.P143Rfs*36	ENST00000298229	NM_001567.3	142	Ccc/cc	4/28	1	2	FACETS	0.842	0.778	0.908	1	0.992	1	CLONAL	2	TRUE	1	0.22955991236323	2		1010	983	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912079	127912079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	51	342	0	ENST00000373547.4:c.791G>A	p.Arg264His	p.R264H	ENST00000373547	NM_002721.4	264	cGt/cAt	7/7	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.22955991236323	2		342	424	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434005	49434005	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	224	1040	1	ENST00000301067.7:c.7548del	p.Asn2517IlefsTer26	p.N2517Ifs*26	ENST00000301067	NM_003482.3	2516	ccC/cc	31/54	1	2	FACETS	0.99	0.922	1	1	0.994	1	CLONAL	2	TRUE	1	0.22955991236323	2		1041	986	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350537	89350538	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	30	622	0	ENST00000301030.4:c.2412dup	p.Glu805ArgfsTer5	p.E805Rfs*5	ENST00000301030	NM_001256183.1	804	-/A	9/13	1	2	FACETS	0.299	0.24	0.367	0.299	0.24	0.367	SUBCLONAL	1	TRUE	1	0.22955991236323	2		622	873	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524267	148524269	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	28	360	0	ENST00000320356.2:c.715_717del	p.Glu239del	p.E239del	ENST00000320356	NM_004456.4	239	GAA/-	7/20	1	2	FACETS	0.558	0.446	0.687	0.558	0.446	0.687	SUBCLONAL	1	TRUE	1	0.22955991236323	2		360	437	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245405	133245405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565966539	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	168	804	0	ENST00000320574.5:c.1915C>T	p.Arg639Cys	p.R639C	ENST00000320574	NM_006231.2	639	Cgc/Tgc	17/49	1	2	FACETS	0.842	0.774	0.913	1	0.991	1	CLONAL	2	TRUE	1	0.22955991236323	2		804	869	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468038	50468038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1459868445	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	33	767	1	ENST00000331340.3:c.1273G>A	p.Gly425Arg	p.G425R	ENST00000331340	NM_006060.4	425	Ggg/Agg	8/8	1	2	FACETS	0.44	0.357	0.534	0.44	0.357	0.534	SUBCLONAL	1	TRUE	1	0.22955991236323	2		768	653	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549476	5549476	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	179	885	0	ENST00000397747.3:c.503G>T	p.Arg168Met	p.R168M	ENST00000397747	NM_025239.3	168	aGg/aTg	4/7	1	2	FACETS	0.864	0.796	0.933	1	0.991	1	CLONAL	2	TRUE	1	0.22955991236323	2		885	903	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023322	27023323	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	40	169	0	ENST00000324856.7:c.429dup	p.Pro144AlafsTer256	p.P144Afs*256	ENST00000324856	NM_006015.4	143	ttg/ttGg	1/20	1	2	FACETS	1	0.896	1	1	0.972	1	CLONAL	2	TRUE	1	0.22955991236323	2		169	161	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456498	32456498	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	66	252	0	ENST00000332351.3:c.394C>A	p.Pro132Thr	p.P132T	ENST00000332351	NM_024426.4	132	Ccg/Acg	1/10	1	2	FACETS	0.844	0.743	0.95	1	0.984	1	CLONAL	3	TRUE	1	0.22955991236323	2		252	227	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433511	49433511	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	115	1068	0	ENST00000301067.7:c.8042G>T	p.Arg2681Leu	p.R2681L	ENST00000301067	NM_003482.3	2681	cGg/cTg	31/54	1	2	FACETS	0.998	0.897	1	0.998	0.897	1	CLONAL	1	TRUE	1	0.22955991236323	2		1068	1004	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857542	57857542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1429409127	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	44	841	0	ENST00000228682.2:c.68C>T	p.Pro23Leu	p.P23L	ENST00000228682	NM_005269.2	23	cCc/cTc	2/12	1	2	FACETS	0.469	0.392	0.555	0.469	0.392	0.555	SUBCLONAL	1	TRUE	1	0.22955991236323	2		841	817	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779464	3779464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	242	1104	0	ENST00000262367.5:c.5584G>A	p.Ala1862Thr	p.A1862T	ENST00000262367	NM_004380.2	1862	Gcc/Acc	31/31	1	2	FACETS	0.994	0.928	1	1	0.994	1	CLONAL	2	TRUE	1	0.22955991236323	2		1104	1061	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349241	11349243	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs1489186405	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	18	219	0	ENST00000332029.2:c.93_95del	p.Ser32del	p.S32del	ENST00000332029	NM_003745.1	31	tcCTCg/tcg	2/2	1	2	FACETS	0.98	0.743	1	0.98	0.743	1	CLONAL	1	TRUE	1	0.22955991236323	2		219	160	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829503	72829503	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	111	641	0	ENST00000268489.5:c.7078C>T	p.Gln2360Ter	p.Q2360*	ENST00000268489	NM_006885.3	2360	Cag/Tag	9/10	1	2	FACETS	0.758	0.682	0.837	1	0.984	1	SUBCLONAL	2	TRUE	1	0.22955991236323	2		641	638	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81904497	81904497	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	69	379	0	ENST00000359376.3:c.605T>C	p.Phe202Ser	p.F202S	ENST00000359376	NM_002661.3	202	tTc/tCc	7/33	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.22955991236323	2		379	432	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47607008	47607008	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	78	511	0	ENST00000263735.4:c.758A>T	p.Asp253Val	p.D253V	ENST00000263735	NM_002354.2	253	gAt/gTt	7/9	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.22955991236323	2		511	671	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881486	111881487	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	38	640	0	ENST00000393256.3:c.169dup	p.His57ProfsTer44	p.H57Pfs*44	ENST00000393256	NM_006538.4	55	tgc/tgCc	2/4	1	2	FACETS	0.531	0.438	0.636	0.531	0.438	0.636	SUBCLONAL	1	TRUE	1	0.22955991236323	2		640	623	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794991	242794991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	93	1147	0	ENST00000334409.5:c.218G>A	p.Ser73Asn	p.S73N	ENST00000334409	NM_005018.2	73	aGc/aAc	2/5	1	2	FACETS	0.817	0.725	0.916	0.817	0.725	0.916	CLONAL	1	TRUE	1	0.22955991236323	2		1147	992	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586421	189586421	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	118	459	0	ENST00000264731.3:c.1045G>T	p.Gly349Ter	p.G349*	ENST00000264731	NM_003722.4	349	Gga/Tga	8/14	1	2	FACETS	0.928	0.84	1	1	0.988	1	CLONAL	2	TRUE	1	0.22955991236323	2		459	554	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371788	55371807	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGAGCCGCAGGCGGCCGC	GCTGAGCCGCAGGCGGCCGC	-	novel	NA	P-0054695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	77	266	0	ENST00000297316.4:c.482_501del	p.Glu161GlyfsTer197	p.E161Gfs*197	ENST00000297316	NM_022454.3	160	GCTGAGCCGCAGGCGGCCGCg/g	2/2	1	2	FACETS	1	0.961	1	1	0.986	1	CLONAL	2	TRUE	1	0.22955991236323	2		266	282	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	131	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.47784733891242	2		457	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0054696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	311	993	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.453890905063792	1	FACETS	0.896	0.845	0.947	0.896	0.845	0.947	CLONAL	1	TRUE	0	0.47784733891242	1		993	1106	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591902	48591902	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	162	510	0	ENST00000342988.3:c.1065C>G	p.Asp355Glu	p.D355E	ENST00000342988	NM_005359.5	355	gaC/gaG	9/12	0.450527031292235	1	FACETS	0.94	0.868	1	0.94	0.868	1	CLONAL	1	TRUE	0	0.47784733891242	1		510	549	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106880	11106923	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTTTGTAGGCTGAAGATGAGGAGGGGTACCGCAAGCTCATCGA	CTTTTGTAGGCTGAAGATGAGGAGGGGTACCGCAAGCTCATCGA	-	novel	NA	P-0054696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	37	692	0	ENST00000358026.2:c.1594-8_1629del		p.X532_splice	ENST00000358026	NM_001128849.1	532		10/36	1	2	FACETS	0.155	0.127	0.187	0.155	0.127	0.187	SUBCLONAL	1	TRUE	1	0.47784733891242	2		692	1000	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032847	30032847	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	112	365	0	ENST00000338641.4:c.222G>A	p.Trp74Ter	p.W74*	ENST00000338641	NM_000268.3	74	tgG/tgA	2/16	0.47784733891242	1	FACETS	0.689	0.622	0.759	0.689	0.622	0.759	SUBCLONAL	1	TRUE	0	0.47784733891242	1		365	518	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572005	64572005	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	187	979	0	ENST00000312049.6:c.1634del	p.Pro545ArgfsTer14	p.P545Rfs*14	ENST00000312049	NM_130799.2	545	cCg/cg	10/10	0.405855997079482	1	FACETS	0.981	0.908	1	0.981	0.908	1	CLONAL	1	TRUE	0	0.405855997079482	1		979	749	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183724	10183724	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs869025616	NA	P-0054697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	134	1041	0	ENST00000256474.2:c.193T>G	p.Ser65Ala	p.S65A	ENST00000256474	NM_000551.3	65	Tcg/Gcg	1/3	0.405855997079482	1	FACETS	0.88	0.803	0.961	0.88	0.803	0.961	CLONAL	1	TRUE	0	0.405855997079482	1		1041	598	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47088021	47088021	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	46	632	0	ENST00000409792.3:c.7054del	p.Val2352Ter	p.V2352*	ENST00000409792	NM_014159.6	2352	Gtg/tg	16/21	0.405855997079482	1	FACETS	0.296	0.249	0.349	0.296	0.249	0.349	SUBCLONAL	1	TRUE	0	0.405855997079482	1		632	610	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0054698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	22	450	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.856	0.661	1	0.856	0.661	1	CLONAL	1	TRUE	1	0.09	2		450	571	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692794	89692794	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121909238	NA	P-0054698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	15	377	0	ENST00000371953.3:c.278A>G	p.His93Arg	p.H93R	ENST00000371953	NM_000314.4	93	cAt/cGt	5/9	1	2	FACETS	0.921	0.672	1	0.921	0.672	1	CLONAL	1	TRUE	1	0.09	2		377	362	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249457	153249457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	15	511	0	ENST00000281708.4:c.1321C>T	p.Arg441Trp	p.R441W	ENST00000281708	NM_033632.3	441	Cgg/Tgg	9/12	1	2	FACETS	0.577	0.42	0.767	0.577	0.42	0.767	SUBCLONAL	1	TRUE	1	0.09	2		511	578	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912702	100912702	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	29	429	0	ENST00000325455.5:c.2620A>T	p.Thr874Ser	p.T874S	ENST00000325455	NM_001202474.3	874	Aca/Tca	7/8	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.09	2		429	544	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0054699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	54	457	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.449	0.385	0.518	0.449	0.385	0.518	SUBCLONAL	1	TRUE	1	0.722342730621804	2		457	333	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0054699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	143	749	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.598	0.547	0.652	0.598	0.547	0.652	SUBCLONAL	1	TRUE	1	0.722342730621804	2		749	662	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589151	67589152	+	inframe_insertion	In_Frame_Ins	INS	-	-	AATCAA	novel	NA	P-0054699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	42	347	0	ENST00000274335.5:c.1143_1148dup	p.Lys382_Ile383dup	p.K382_I383dup	ENST00000274335		382	tta/ttAATCAAa	9/15	1	2	FACETS	0.497	0.418	0.583	0.497	0.418	0.583	SUBCLONAL	1	TRUE	1	0.722342730621804	2		347	234	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	56	702	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.246	0.21	0.285	0.246	0.21	0.285	SUBCLONAL	1	TRUE	1	0.722342730621804	2		703	631	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204864	NA	P-0054699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	73	494	0	ENST00000371953.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000371953	NM_000314.4	171	Cag/Tag	6/9	1	2	FACETS	0.551	0.484	0.621	0.551	0.484	0.621	SUBCLONAL	1	TRUE	1	0.722342730621804	2		494	367	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0054699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	39	359	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	0.347	0.289	0.412	0.347	0.289	0.412	SUBCLONAL	1	TRUE	1	0.722342730621804	2		359	311	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195974	102195975	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0054699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	57	352	0	ENST00000263464.3:c.737_738del	p.Thr246SerfsTer3	p.T246Sfs*3	ENST00000263464	NM_001165.4	245	tAC/t	2/9	1	2	FACETS	0.464	0.4	0.533	0.464	0.4	0.533	SUBCLONAL	1	TRUE	1	0.722342730621804	2		352	340	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515070	103515070	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201684551	NA	P-0054699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	31	332	0	ENST00000355739.4:c.1571C>T	p.Pro524Leu	p.P524L	ENST00000355739	NM_000123.3	524	cCg/cTg	8/15	1	2	FACETS	0.215	0.173	0.261	0.215	0.173	0.261	SUBCLONAL	1	TRUE	1	0.722342730621804	2		332	400	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934644	9934644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1331671132	NA	P-0054699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	45	454	0	ENST00000330684.3:c.1511G>A	p.Arg504Gln	p.R504Q	ENST00000330684	NM_001134407.1	504	cGg/cAg	7/13	1	2	FACETS	0.255	0.214	0.3	0.255	0.214	0.3	SUBCLONAL	1	TRUE	1	0.722342730621804	2		454	489	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274063	10274063	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	62	1014	0	ENST00000330684.3:c.206T>C	p.Val69Ala	p.V69A	ENST00000330684	NM_001134407.1	69	gTg/gCg	2/13	1	2	FACETS	0.195	0.167	0.224	0.195	0.167	0.224	SUBCLONAL	1	TRUE	1	0.722342730621804	2		1014	882	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923642	72923643	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	139	896	0	ENST00000268489.5:c.3435_3436insA	p.Ser1146IlefsTer9	p.S1146Ifs*9	ENST00000268489	NM_006885.3	1145	-/A	4/10	1	2	FACETS	0.519	0.473	0.567	0.519	0.473	0.567	SUBCLONAL	1	TRUE	1	0.722342730621804	2		896	742	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291942	15291942	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	160	1318	0	ENST00000263388.2:c.2824G>A	p.Gly942Ser	p.G942S	ENST00000263388	NM_000435.2	942	Ggc/Agc	18/33	1	2	FACETS	0.435	0.398	0.473	0.435	0.398	0.473	SUBCLONAL	1	TRUE	1	0.722342730621804	2		1318	1019	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374299	15374299	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	59	759	0	ENST00000263377.2:c.1273A>T	p.Met425Leu	p.M425L	ENST00000263377	NM_058243.2	425	Atg/Ttg	7/20	1	2	FACETS	0.206	0.176	0.238	0.206	0.176	0.238	SUBCLONAL	1	TRUE	1	0.722342730621804	2		759	794	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967048	18967048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762952797	NA	P-0054699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	153	852	1	ENST00000262803.5:c.1763C>T	p.Ser588Leu	p.S588L	ENST00000262803	NM_002911.3	588	tCg/tTg	13/24	1	2	FACETS	0.497	0.455	0.542	0.497	0.455	0.542	SUBCLONAL	1	TRUE	1	0.722342730621804	2		853	852	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792249	33792249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	44	905	0	ENST00000498907.2:c.1072G>A	p.Ala358Thr	p.A358T	ENST00000498907	NM_004364.3	358	Gcg/Acg	1/1	1	2	FACETS	0.165	0.138	0.196	0.165	0.138	0.196	SUBCLONAL	1	TRUE	1	0.722342730621804	2		905	738	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519886	NA	P-0054699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	20	442	0	ENST00000349496.5:c.97T>C	p.Ser33Pro	p.S33P	ENST00000349496	NM_001904.3	33	Tct/Cct	3/15	1	2	FACETS	0.132	0.101	0.17	0.132	0.101	0.17	SUBCLONAL	1	TRUE	1	0.722342730621804	2		442	418	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664984	138664984	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	46	305	0	ENST00000330315.3:c.581A>G	p.Tyr194Cys	p.Y194C	ENST00000330315	NM_023067.3	194	tAc/tGc	1/1	1	2	FACETS	0.36	0.304	0.421	0.36	0.304	0.421	SUBCLONAL	1	TRUE	1	0.722342730621804	2		305	354	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155821	106155821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771996203	NA	P-0054699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	38	496	1	ENST00000380013.4:c.722C>T	p.Ala241Val	p.A241V	ENST00000380013	NM_001127208.2	241	gCg/gTg	3/11	1	2	FACETS	0.217	0.179	0.259	0.217	0.179	0.259	SUBCLONAL	1	TRUE	1	0.722342730621804	2		497	485	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056588	26056590	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs751086925	NA	P-0054699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	31	429	0	ENST00000343677.2:c.67_69del	p.Lys23del	p.K23del	ENST00000343677	NM_005319.3	23	AAG/-	1/1	1	2	FACETS	0.216	0.175	0.263	0.216	0.175	0.263	SUBCLONAL	1	TRUE	1	0.722342730621804	2		429	397	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680778	30680778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767988940	NA	P-0054699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	99	692	0	ENST00000376406.3:c.941C>T	p.Ala314Val	p.A314V	ENST00000376406	NM_014641.2	314	gCt/gTt	5/15	1	2	FACETS	0.458	0.41	0.51	0.458	0.41	0.51	SUBCLONAL	1	TRUE	1	0.722342730621804	2		692	598	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166764	32166764	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771787319	NA	P-0054699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	179	1084	0	ENST00000375023.3:c.4474C>T	p.Arg1492Trp	p.R1492W	ENST00000375023	NM_004557.3	1492	Cgg/Tgg	24/30	1	2	FACETS	0.497	0.457	0.538	0.497	0.457	0.538	SUBCLONAL	1	TRUE	1	0.722342730621804	2		1084	998	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880452	155880452	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	51	611	0	ENST00000368323.3:c.101A>T	p.Lys34Met	p.K34M	ENST00000368323	NM_006912.5	34	aAg/aTg	2/6	1	2	FACETS	0.225	0.191	0.264	0.225	0.191	0.264	SUBCLONAL	1	TRUE	1	0.5	2		611	905	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11022942	11022942	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	311	860	0	ENST00000327064.4:c.641A>G	p.Glu214Gly	p.E214G	ENST00000327064	NM_199141.1	214	gAg/gGg	5/16	0.266259835603047	4	FACETS	1	0.992	1	0.433	0.408	0.46	INDETERMINATE	1	TRUE	1	0.5	4		860	1435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0054701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	114	757	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.23	2		757	953	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118924	70118926	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0054701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	148	924	0	ENST00000245479.2:c.499_501del	p.Lys167del	p.K167del	ENST00000245479	NM_000346.3	166	AAG/-	2/3	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.23	2		924	1269	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0054720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	146	535	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.619939355489703	2		535	468	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0054720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	154	450	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.976	0.899	1	0.976	0.899	1	CLONAL	1	TRUE	1	0.619939355489703	2		451	509	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492689	56492689	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	162	479	0	ENST00000407977.2:c.250C>T	p.Gln84Ter	p.Q84*	ENST00000407977		84	Cag/Tag	2/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.619939355489703	2		479	465	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435814	56435815	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0054720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	160	912	0	ENST00000407977.2:c.1322dup	p.Asp442Ter	p.D442*	ENST00000407977		441	cct/ccCt	9/10	1	2	FACETS	0.89	0.82	0.962	0.89	0.82	0.962	CLONAL	1	TRUE	1	0.619939355489703	2		912	580	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782620	NA	P-0054723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	373	825	1	ENST00000269305.4:c.427G>A	p.Val143Met	p.V143M	ENST00000269305	NM_001126112.2	143	Gtg/Atg	5/11	0.208667361304105	2	FACETS	1	0.956	1	1	0.956	1	INDETERMINATE	2	TRUE	0	0.348121768980074	2		826	1065	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742931	17742931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	125	526	0	ENST00000250003.3:c.839C>T	p.Pro280Leu	p.P280L	ENST00000250003	NM_002478.4	280	cCg/cTg	3/3	0.330272393667806	3	FACETS	1	0.975	1	0.608	0.551	0.668	CLONAL	1	TRUE	1	0.348121768980074	3		526	693	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873464	136873464	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	85	346	0	ENST00000241393.3:c.34T>C	p.Tyr12His	p.Y12H	ENST00000241393	NM_003467.2	12	Tac/Cac	2/2	0.150577497757813	5	FACETS	0.852	0.757	0.953	0.568	0.505	0.636	INDETERMINATE	2	TRUE	2	0.348121768980074	5		346	436	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027093	71027093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200629338	NA	P-0054723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	44	496	1	ENST00000318789.4:c.1234G>A	p.Ala412Thr	p.A412T	ENST00000318789	NM_032682.5	412	Gcc/Acc	15/21	0.208667361304105	2	FACETS	0.395	0.33	0.467	0.197	0.165	0.234	INDETERMINATE	1	TRUE	0	0.348121768980074	2		497	640	SUCCESS
APC	324	MSKCC	GRCh37	5	112175353	112175358	+	stop_gained	Nonsense_Mutation	ONP	TTCTTC	TTCTTC	ATCTTA	novel	NA	P-0054723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	90	207	0	ENST00000257430.4:c.4062_4067delinsATCTTA	p.Phe1354_Ser1356delinsLeuSerTer	p.F1354_S1356delinsLS*	ENST00000257430	NM_000038.5	1354	ttTTCTTCa/ttATCTTAa	16/16	0.348121768980074	2	FACETS	0.947	0.852	1	0.947	0.852	1	CLONAL	2	TRUE	0	0.348121768980074	2		207	273	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971000	21971000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	111	438	0	ENST00000304494.5:c.358G>T	p.Glu120Ter	p.E120*	ENST00000304494	NM_000077.4	120	Gag/Tag	2/3	0.132939491746738	0	FACETS	0.65	0.587	0.716			1	INDETERMINATE	1	TRUE	0	0.410143730774078	0		438	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057519990	NA	P-0054725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	131	654	0	ENST00000269305.4:c.796G>T	p.Gly266Ter	p.G266*	ENST00000269305	NM_001126112.2	266	Gga/Tga	8/11	0.40100228126325	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.410143730774078	1		654	496	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981167	201981168	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	266	847	0	ENST00000359651.3:c.248dup	p.Asn83LysfsTer9	p.N83Kfs*9	ENST00000359651		82	-/A	2/8	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.410143730774078	2		847	866	SUCCESS
APC	324	MSKCC	GRCh37	5	112175235	112175235	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	21	249	0	ENST00000257430.4:c.3944C>A	p.Ser1315Ter	p.S1315*	ENST00000257430	NM_000038.5	1315	tCa/tAa	16/16	1	2	FACETS	0.583	0.449	0.739	0.583	0.449	0.739	SUBCLONAL	1	TRUE	1	0.239367430315598	2		249	301	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577042	7577043	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0054726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	66	896	0	ENST00000269305.4:c.895_896del	p.Leu299AlafsTer6	p.L299Afs*6	ENST00000269305	NM_001126112.2	299	CTg/g	8/11	1	2	FACETS	0.5	0.432	0.574	0.5	0.432	0.574	SUBCLONAL	1	TRUE	1	0.239367430315598	2		896	1103	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0054727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	369	449	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.84	0.8	0.88	1	0.997	1	CLONAL	3	TRUE	1	0.322978677447777	2		449	907	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0054727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	166	752	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.322978677447777	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.322978677447777	1		752	766	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285250	212285250	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	77	547	0	ENST00000342788.4:c.3051G>T	p.Met1017Ile	p.M1017I	ENST00000342788	NM_005235.2	1017	atG/atT	25/28	1	2	FACETS	0.721	0.633	0.816	0.721	0.633	0.816	SUBCLONAL	1	TRUE	1	0.322978677447777	2		547	661	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182662914	182662914	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1403059883	NA	P-0054727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	61	621	0	ENST00000292782.4:c.748C>G	p.Gln250Glu	p.Q250E	ENST00000292782	NM_020640.2	250	Caa/Gaa	7/7	1	2	FACETS	0.522	0.449	0.601	0.522	0.449	0.601	SUBCLONAL	1	TRUE	1	0.322978677447777	2		621	724	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355084	73355084	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	56	521	0	ENST00000377767.4:c.286C>T	p.Gln96Ter	p.Q96*	ENST00000377767	NM_014953.3	96	Caa/Taa	2/21	0.320687078752791	1	FACETS	0.474	0.406	0.549	0.474	0.406	0.549	SUBCLONAL	1	TRUE	0	0.322978677447777	1		521	613	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552613	18552613	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1371859788	NA	P-0054727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	111	435	1	ENST00000266497.5:c.2024G>T	p.Arg675Ile	p.R675I	ENST00000266497		675	aGa/aTa	14/31	0.322978677447777	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.322978677447777	1		436	515	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059180	27059192	+	frameshift_variant	Frame_Shift_Del	DEL	ATTCATTTGGGTC	ATTCATTTGGGTC	-	novel	NA	P-0054727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	52	455	0	ENST00000324856.7:c.1817_1829del	p.Asp606ValfsTer9	p.D606Vfs*9	ENST00000324856	NM_006015.4	606	gATTCATTTGGGTCt/gt	4/20	1	2	FACETS	0.595	0.507	0.692	0.595	0.507	0.692	SUBCLONAL	1	TRUE	1	0.322978677447777	2		455	541	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67197035	67197035	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	71	469	1	ENST00000312629.5:c.278G>T	p.Gly93Val	p.G93V	ENST00000312629	NM_003952.2	93	gGc/gTc	4/15	1	2	FACETS	0.805	0.704	0.915	0.805	0.704	0.915	CLONAL	1	TRUE	1	0.322978677447777	2		470	546	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433968	49433968	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	118	1055	0	ENST00000301067.7:c.7585G>T	p.Gly2529Cys	p.G2529C	ENST00000301067	NM_003482.3	2529	Ggc/Tgc	31/54	1	2	FACETS	0.585	0.526	0.648	0.585	0.526	0.648	SUBCLONAL	1	TRUE	1	0.322978677447777	2		1055	1248	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12647776	12647776	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	30	390	0	ENST00000251849.4:c.604G>T	p.Gly202Cys	p.G202C	ENST00000251849	NM_002880.3	202	Ggt/Tgt	6/17	NA	2	FACETS	0.423	0.34	0.517			1	INDETERMINATE	1	TRUE	NA	0.322978677447777	2		390	439	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129951	55129951	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	75	710	0	ENST00000257290.5:c.485A>T	p.His162Leu	p.H162L	ENST00000257290	NM_006206.4	162	cAc/cTc	4/23	1	2	FACETS	0.565	0.494	0.642	0.565	0.494	0.642	SUBCLONAL	1	TRUE	1	0.322978677447777	2		710	822	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155544	106155544	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	36	415	0	ENST00000380013.4:c.445G>C	p.Glu149Gln	p.E149Q	ENST00000380013	NM_001127208.2	149	Gaa/Caa	3/11	1	2	FACETS	0.495	0.407	0.594	0.495	0.407	0.594	SUBCLONAL	1	TRUE	1	0.322978677447777	2		415	450	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671877	30671877	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1249782545	NA	P-0054727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	190	996	2	ENST00000376406.3:c.5083C>T	p.Pro1695Ser	p.P1695S	ENST00000376406	NM_014641.2	1695	Cct/Tct	10/15	0.187808802314153	3	FACETS	1	0.981	1	0.598	0.552	0.646	INDETERMINATE	1	TRUE	1	0.322978677447777	3		998	1142	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527733	157527733	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	255	642	0	ENST00000346085.5:c.5458C>A	p.Gln1820Lys	p.Q1820K	ENST00000346085	NM_020732.3	1820	Cag/Aag	20/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	NA	1	0.919366016432945	2		642	535	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	255	823	1	ENST00000397752.3:c.3028G>A	p.Asp1010Asn	p.D1010N	ENST00000397752	NM_000245.2	1010	Gat/Aat	14/21	0.157623531316911	4	FACETS	1	0.986	1	0.795	0.743	0.848	CLONAL	2	TRUE	1	0.215705263500803	4		824	1205	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035973	47035973	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	90	856	1	ENST00000377604.3:c.651G>A	p.Trp217Ter	p.W217*	ENST00000377604	NM_001204468.1	217	tgG/tgA	7/24	0.215705263500803	1	FACETS	0.82	0.726	0.92	0.82	0.726	0.92	CLONAL	1	TRUE	0	0.215705263500803	1		857	908	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643353	38643353	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	39	449	0	ENST00000299084.4:c.823G>C	p.Asp275His	p.D275H	ENST00000299084	NM_152594.2	275	Gat/Cat	7/7	1	2	FACETS	0.659	0.545	0.786	0.659	0.545	0.786	SUBCLONAL	1	TRUE	1	0.215705263500803	2		449	549	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164303	47164328	+	frameshift_variant	Frame_Shift_Del	DEL	TCAGGATTTTTATTAATCATTCTTAA	TCAGGATTTTTATTAATCATTCTTAA	-	novel	NA	P-0054730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	24	322	0	ENST00000409792.3:c.1798_1823del	p.Leu600LysfsTer15	p.L600Kfs*15	ENST00000409792	NM_014159.6	600	TTAAGAATGATTAATAAAAATCCTGAa/a	3/21	1	2	FACETS	0.496	0.388	0.621	0.496	0.388	0.621	SUBCLONAL	1	TRUE	1	0.215705263500803	2		322	449	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933416	49933416	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	195	695	0	ENST00000296474.3:c.2774G>A	p.Gly925Asp	p.G925D	ENST00000296474	NM_002447.2	925	gGc/gAc	11/20	1	2	FACETS	0.911	0.846	0.978	0.911	0.846	0.978	CLONAL	1	TRUE	1	0.58979444470409	2		695	726	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	89	571	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.294023213826289	3	FACETS	0.954	0.846	1	0.477	0.423	0.535	CLONAL	1	TRUE	1	0.294023213826289	3		571	728	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923060	44923060	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	328	273	0	ENST00000377967.4:c.1921C>T	p.Gln641Ter	p.Q641*	ENST00000377967	NM_021140.2	641	Cag/Tag	16/29	0.294023213826289	5	FACETS	1	0.971	1			1	CLONAL	6	TRUE	NA	0.294023213826289	5		273	528	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	126	234	3				ENST00000310581	NM_198253.2	-/1132			0.294023213826289	5	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	2	0.294023213826289	5		237	357	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429276	78429276	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	63	413	0	ENST00000370768.2:c.1166G>C	p.Gly389Ala	p.G389A	ENST00000370768	NM_003902.3	389	gGa/gCa	13/20	0.230337620777691	5	FACETS	0.979	0.846	1			1	CLONAL	1	TRUE	NA	0.294023213826289	5		413	631	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549202	226549202	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	105	403	0	ENST00000366794.5:c.3004C>G	p.Leu1002Val	p.L1002V	ENST00000366794	NM_001618.3	1002	Ctg/Gtg	23/23	0.14436129987883	4	FACETS	0.906	0.815	1	0.906	0.815	1	INDETERMINATE	2	TRUE	2	0.294023213826289	4		403	510	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615190	43615190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	53	701	0	ENST00000355710.3:c.2604G>A	p.Met868Ile	p.M868I	ENST00000355710	NM_020975.4	868	atG/atA	14/20	0.13483894527787	3	FACETS	0.695	0.592	0.808			1	INDETERMINATE	1	TRUE	NA	0.294023213826289	3		701	595	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851833	63851833	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	99	594	0	ENST00000279873.7:c.2611C>T	p.Pro871Ser	p.P871S	ENST00000279873	NM_032199.2	871	Cct/Tct	10/10	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.294023213826289	2		594	618	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852397	63852397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	95	585	0	ENST00000279873.7:c.3175G>A	p.Gly1059Ser	p.G1059S	ENST00000279873	NM_032199.2	1059	Ggt/Agt	10/10	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.294023213826289	2		585	615	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999749	100999749	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	187	806	0	ENST00000325455.5:c.53C>A	p.Pro18Gln	p.P18Q	ENST00000325455	NM_001202474.3	18	cCg/cAg	1/8	0.294023213826289	3	FACETS	0.93	0.861	1	0.93	0.861	1	CLONAL	2	TRUE	1	0.294023213826289	3		806	784	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037473	12037473	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	62	384	0	ENST00000396373.4:c.1104C>A	p.Phe368Leu	p.F368L	ENST00000396373	NM_001987.4	368	ttC/ttA	6/8	0.294023213826289	3	FACETS	1	0.88	1	0.509	0.441	0.583	CLONAL	1	TRUE	1	0.294023213826289	3		384	475	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245027	46245027	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	82	620	0	ENST00000334344.6:c.3121C>T	p.Gln1041Ter	p.Q1041*	ENST00000334344	NM_152641.2	1041	Caa/Taa	15/21	0.21618629587079	3	FACETS	0.964	0.85	1			1	CLONAL	1	TRUE	NA	0.294023213826289	3		620	664	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245832	46245832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	94	356	0	ENST00000334344.6:c.3926C>T	p.Ser1309Leu	p.S1309L	ENST00000334344	NM_152641.2	1309	tCa/tTa	15/21	0.21618629587079	3	FACETS	0.861	0.77	0.956			1	CLONAL	2	TRUE	NA	0.294023213826289	3		356	426	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431423	49431423	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	63	666	0	ENST00000301067.7:c.9716C>G	p.Ser3239Ter	p.S3239*	ENST00000301067	NM_003482.3	3239	tCa/tGa	34/54	0.21618629587079	3	FACETS	0.713	0.616	0.819			1	SUBCLONAL	1	TRUE	NA	0.294023213826289	3		666	689	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431618	49431618	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	174	693	0	ENST00000301067.7:c.9521C>G	p.Ser3174Cys	p.S3174C	ENST00000301067	NM_003482.3	3174	tCt/tGt	34/54	0.21618629587079	3	FACETS	1	0.954	1			1	CLONAL	2	TRUE	NA	0.294023213826289	3		693	650	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434397	49434397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs967482995	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	103	803	1	ENST00000301067.7:c.7156C>T	p.Arg2386Trp	p.R2386W	ENST00000301067	NM_003482.3	2386	Cgg/Tgg	31/54	0.21618629587079	3	FACETS	1	0.914	1			1	CLONAL	1	TRUE	NA	0.294023213826289	3		804	784	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864883	57864883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	202	743	1	ENST00000228682.2:c.2360C>T	p.Ser787Phe	p.S787F	ENST00000228682	NM_005269.2	787	tCt/tTt	12/12	0.294023213826289	5	FACETS	1	0.97	1			1	CLONAL	2	TRUE	NA	0.294023213826289	5		744	913	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112939991	112939991	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs759551230	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	193	527	0	ENST00000351677.2:c.1643C>G	p.Ser548Cys	p.S548C	ENST00000351677	NM_002834.3	548	tCt/tGt	14/16	0.14436129987883	4	FACETS	0.886	0.824	0.95	1	0.989	1	INDETERMINATE	3	TRUE	2	0.294023213826289	4		527	639	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120806003	120806003	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	413	725	0	ENST00000257552.2:c.174G>C	p.Lys58Asn	p.K58N	ENST00000257552	NM_002442.3	58	aaG/aaC	3/15	0.294023213826289	5	FACETS	1	0.987	1	1	0.987	1	CLONAL	4	TRUE	1	0.294023213826289	5		725	940	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435384	121435384	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	106	851	0	ENST00000257555.6:c.1417C>T	p.Gln473Ter	p.Q473*	ENST00000257555		473	Cag/Tag	7/10	0.294023213826289	5	FACETS	0.978	0.875	1	0.245	0.218	0.272	CLONAL	1	TRUE	1	0.294023213826289	5		851	1062	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906699	32906699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	62	467	0	ENST00000380152.3:c.1084G>A	p.Asp362Asn	p.D362N	ENST00000380152		362	Gat/Aat	10/27	0.280980666941043	4	FACETS	0.808	0.698	0.929	0.269	0.232	0.31	CLONAL	1	TRUE	1	0.294023213826289	4		467	675	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911679	32911679	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	231	392	0	ENST00000380152.3:c.3187C>G	p.Gln1063Glu	p.Q1063E	ENST00000380152		1063	Cag/Gag	11/27	0.280980666941043	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	1	0.294023213826289	4		392	625	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679705	88679705	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	64	427	0	ENST00000360948.2:c.758C>A	p.Thr253Asn	p.T253N	ENST00000360948	NM_001012338.2	253	aCt/aAt	7/19	0.280980666941043	4	FACETS	0.956	0.828	1	0.319	0.276	0.365	CLONAL	1	TRUE	1	0.294023213826289	4		427	589	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778106	3778106	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	259	1035	0	ENST00000262367.5:c.6942G>A	p.Met2314Ile	p.M2314I	ENST00000262367	NM_004380.2	2314	atG/atA	31/31	0.14436129987883	4	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	2	TRUE	2	0.294023213826289	4		1035	1044	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14015915	14015915	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	87	191	0	ENST00000311895.7:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000311895	NM_005236.2	79	Gaa/Caa	2/11	0.14436129987883	4	FACETS	1	0.954	1	1	0.954	1	INDETERMINATE	2	TRUE	2	0.294023213826289	4		191	340	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984811	72984811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	322	626	0	ENST00000268489.5:c.2773G>A	p.Glu925Lys	p.E925K	ENST00000268489	NM_006885.3	925	Gag/Aag	3/10	0.294023213826289	6	FACETS	0.992	0.94	1			1	CLONAL	4	TRUE	NA	0.294023213826289	6		626	877	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944279	81944279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747373917	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	61	724	2	ENST00000359376.3:c.1888C>T	p.Arg630Trp	p.R630W	ENST00000359376	NM_002661.3	630	Cgg/Tgg	18/33	0.294023213826289	5	FACETS	0.62	0.533	0.715	0.207	0.177	0.239	SUBCLONAL	1	TRUE	2	0.294023213826289	5		726	964	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	351	1136	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.294023213826289	3	FACETS	0.989	0.94	1	0.989	0.94	1	CLONAL	3	TRUE	0	0.294023213826289	3		1137	923	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16022773	16022773	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	61	379	0	ENST00000268712.3:c.1879C>G	p.Arg627Gly	p.R627G	ENST00000268712	NM_006311.3	627	Cga/Gga	17/46	0.294023213826289	6	FACETS	1	0.863	1			1	CLONAL	1	TRUE	NA	0.294023213826289	6		379	658	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40364046	40364046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768821055	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	238	448	0	ENST00000293328.3:c.1636G>A	p.Glu546Lys	p.E546K	ENST00000293328	NM_012448.3	546	Gag/Aag	13/19	0.294023213826289	4	FACETS	1	0.963	1	1	0.963	1	CLONAL	4	TRUE	0	0.294023213826289	4		448	510	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40468840	40468840	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	297	505	0	ENST00000264657.5:c.2224G>T	p.Glu742Ter	p.E742*	ENST00000264657	NM_139276.2	742	Gaa/Taa	23/24	0.294023213826289	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	4	TRUE	0	0.294023213826289	4		505	648	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256936	41256936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398122661	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	364	542	0	ENST00000357654.3:c.250G>A	p.Glu84Lys	p.E84K	ENST00000357654	NM_007294.3	84	Gaa/Aaa	5/23	0.294023213826289	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	4	TRUE	0	0.294023213826289	4		542	741	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677914	58677914	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	258	268	0	ENST00000305921.3:c.139C>T	p.Gln47Ter	p.Q47*	ENST00000305921	NM_003620.3	47	Cag/Tag	1/6	0.294023213826289	6	FACETS	1	0.978	1	1	0.978	1	CLONAL	6	TRUE	0	0.294023213826289	6		268	443	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78519589	78519589	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	54	349	0	ENST00000306801.3:c.160C>T	p.Arg54Trp	p.R54W	ENST00000306801	NM_020761.2	54	Cgg/Tgg	1/34	0.294023213826289	6	FACETS	0.903	0.77	1	0.15	0.128	0.175	CLONAL	1	TRUE	0	0.294023213826289	6		349	646	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270389	10270389	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	106	682	0	ENST00000340748.4:c.1177G>A	p.Glu393Lys	p.E393K	ENST00000340748		393	Gag/Aag	16/40	0.294023213826289	3	FACETS	0.982	0.88	1	0.491	0.44	0.546	CLONAL	1	TRUE	1	0.294023213826289	3		682	842	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597444	10597444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866539542	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	282	761	1	ENST00000171111.5:c.1759G>A	p.Asp587Asn	p.D587N	ENST00000171111	NM_203500.1	587	Gat/Aat	6/6	0.294023213826289	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.294023213826289	3		762	922	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278032	18278032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756172410	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	101	656	0	ENST00000222254.8:c.1652C>T	p.Ser551Leu	p.S551L	ENST00000222254	NM_005027.3	551	tCg/tTg	13/16	0.294023213826289	3	FACETS	0.994	0.888	1	0.497	0.444	0.553	CLONAL	1	TRUE	1	0.294023213826289	3		656	793	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726555	41726555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	85	577	0	ENST00000301178.4:c.100G>A	p.Glu34Lys	p.E34K	ENST00000301178	NM_021913.4	34	Gaa/Aaa	2/20	0.294023213826289	4	FACETS	1	0.914	1	0.347	0.307	0.391	CLONAL	1	TRUE	1	0.294023213826289	4		577	718	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743981	41743981	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs768277936	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	418	882	0	ENST00000301178.4:c.916C>A	p.His306Asn	p.H306N	ENST00000301178	NM_021913.4	306	Cac/Aac	7/20	0.294023213826289	4	FACETS	0.891	0.851	0.932	1	0.993	1	CLONAL	4	TRUE	1	0.294023213826289	4		882	1032	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775583	39775583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369318352	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	51	478	2	ENST00000288319.7:c.437C>T	p.Ala146Val	p.A146V	ENST00000288319	NM_182918.3	146	gCg/gTg	4/10	0.294023213826289	3	FACETS	0.832	0.708	0.969	0.416	0.354	0.485	CLONAL	1	TRUE	1	0.294023213826289	3		480	478	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24129392	24129392	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	41	354	0	ENST00000263121.7:c.36G>C	p.Gln12His	p.Q12H	ENST00000263121	NM_003073.3	12	caG/caC	1/9	0.294023213826289	3	FACETS	0.73	0.609	0.865	0.365	0.304	0.433	SUBCLONAL	1	TRUE	1	0.294023213826289	3		354	438	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447412	12447412	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	659	536	0	ENST00000287820.6:c.651G>C	p.Glu217Asp	p.E217D	ENST00000287820	NM_015869.4	217	gaG/gaC	5/7	0.294023213826289	11	FACETS	0.955	0.925	0.985			1	CLONAL	9	TRUE	NA	0.294023213826289	11		536	1212	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405914	49405914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	142	621	2	ENST00000418115.1:c.224C>T	p.Pro75Leu	p.P75L	ENST00000418115	NM_001664.2	75	cCa/cTa	3/5	0.203328429590801	5	FACETS	0.881	0.803	0.962	0.587	0.535	0.642	CLONAL	2	TRUE	2	0.294023213826289	5		623	790	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55524221	55524221	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1297912833	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	85	547	0	ENST00000288135.5:c.40C>G	p.Leu14Val	p.L14V	ENST00000288135	NM_000222.2	14	Ctg/Gtg	1/21	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.294023213826289	2		547	578	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230909	66230909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	62	291	0	ENST00000273854.3:c.2062G>A	p.Glu688Lys	p.E688K	ENST00000273854	NM_004439.5	688	Gaa/Aaa	12/18	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.294023213826289	2		291	350	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170834776	170834776	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	42	367	0	ENST00000296930.5:c.844G>C	p.Glu282Gln	p.E282Q	ENST00000296930	NM_002520.6	282	Gag/Cag	10/11	1	2	FACETS	0.646	0.54	0.764	0.646	0.54	0.764	SUBCLONAL	1	TRUE	1	0.294023213826289	2		367	442	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671922	30671922	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	476	770	0	ENST00000376406.3:c.5038C>T	p.Gln1680Ter	p.Q1680*	ENST00000376406	NM_014641.2	1680	Cag/Tag	10/15	0.288725979670804	4	FACETS	0.903	0.868	0.937	1	0.993	1	CLONAL	5	TRUE	0	0.294023213826289	4		770	928	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149982966	149982966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	145	395	2	ENST00000253339.5:c.3292G>A	p.Glu1098Lys	p.E1098K	ENST00000253339		1098	Gaa/Aaa	7/7	0.294023213826289	3	FACETS	1	0.961	1	0.718	0.659	0.78	CLONAL	2	TRUE	0	0.294023213826289	3		397	525	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92244601	92244601	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	141	246	0	ENST00000265734.4:c.835-1G>C		p.X279_splice	ENST00000265734	NM_001259.6	279			0.294023213826289	6	FACETS	0.911	0.838	0.986	0.911	0.838	0.986	CLONAL	4	TRUE	2	0.294023213826289	6		246	418	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526710	106526710	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	45	374	0	ENST00000359195.3:c.3003G>T	p.Lys1001Asn	p.K1001N	ENST00000359195	NM_002649.2	1001	aaG/aaT	10/11	0.294023213826289	6	FACETS	0.802	0.673	0.945	0.201	0.168	0.237	CLONAL	1	TRUE	2	0.294023213826289	6		374	606	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891600	151891600	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	88	301	0	ENST00000262189.6:c.4432C>T	p.Gln1478Ter	p.Q1478*	ENST00000262189	NM_170606.2	1478	Cag/Tag	29/59	0.294023213826289	6	FACETS	0.775	0.688	0.869	0.388	0.344	0.435	SUBCLONAL	2	TRUE	2	0.294023213826289	6		301	613	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945649	151945649	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	214	707	0	ENST00000262189.6:c.1870G>C	p.Asp624His	p.D624H	ENST00000262189	NM_170606.2	624	Gat/Cat	14/59	0.294023213826289	6	FACETS	0.843	0.781	0.907	0.422	0.39	0.454	CLONAL	2	TRUE	2	0.294023213826289	6		707	1371	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	316	293	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	0.294023213826289	6	FACETS	0.943	0.903	0.982			1	CLONAL	7	TRUE	NA	0.294023213826289	6		293	517	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038856	47038856	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	403	416	0	ENST00000377604.3:c.863C>A	p.Ser288Ter	p.S288*	ENST00000377604	NM_001204468.1	288	tCa/tAa	9/24	0.294023213826289	4	FACETS	1	0.983	1			1	CLONAL	5	TRUE	NA	0.294023213826289	4		416	684	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039395	47039395	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	363	358	0	ENST00000377604.3:c.1018C>T	p.Gln340Ter	p.Q340*	ENST00000377604	NM_001204468.1	340	Caa/Taa	10/24	0.294023213826289	4	FACETS	1	0.99	1			1	CLONAL	5	TRUE	NA	0.294023213826289	4		358	587	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410150	63410150	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	87	342	0	ENST00000330258.3:c.3017C>G	p.Ser1006Ter	p.S1006*	ENST00000330258	NM_152424.3	1006	tCa/tGa	2/2	1	1	FACETS	0.828	0.741	0.918	1	0.983	1	CLONAL	2	TRUE	0	0.294023213826289	1		342	305	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338683	70338683	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	91	326	0	ENST00000374080.3:c.79C>G	p.Gln27Glu	p.Q27E	ENST00000374080		27	Cag/Gag	1/45	1	1	FACETS	0.807	0.724	0.894	1	0.983	1	CLONAL	2	TRUE	0	0.294023213826289	1		326	327	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0054733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	105	326	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.597477179899583	2		326	313	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	190	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.75	0.702	0.798	1	0.992	1	SUBCLONAL	2	TRUE	1	0.597477179899583	2		487	424	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239419	105239419	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	231	660	0	ENST00000349310.3:c.968A>G	p.Asp323Gly	p.D323G	ENST00000349310	NM_001014432.1	323	gAc/gGc	12/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.597477179899583	2		660	689	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	192	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.42503628343649	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.42503628343649	2		457	416	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885939	111885939	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	258	644	1	ENST00000341259.2:c.1566del	p.Glu523SerfsTer25	p.E523Sfs*25	ENST00000341259	NM_005475.2	521	Ccc/cc	8/8	0.42503628343649	2	FACETS	0.891	0.84	0.944	0.891	0.84	0.944	CLONAL	2	TRUE	0	0.42503628343649	2		645	681	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372092	55372093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	79	323	2	ENST00000297316.4:c.788dup	p.Glu264GlyfsTer101	p.E264Gfs*101	ENST00000297316	NM_022454.3	261	ggc/ggCc	2/2	1	2	FACETS	0.859	0.758	0.965	0.859	0.758	0.965	CLONAL	1	TRUE	1	0.42503628343649	2		325	433	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0054734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	198	471	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.42503628343649	2	FACETS	0.989	0.926	1	0.989	0.926	1	CLONAL	2	TRUE	0	0.42503628343649	2		471	471	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936338	78936338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1212387005	NA	P-0054734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	165	718	0	ENST00000306801.3:c.3770C>T	p.Thr1257Met	p.T1257M	ENST00000306801	NM_020761.2	1257	aCg/aTg	32/34	1	2	FACETS	0.988	0.908	1	0.988	0.908	1	CLONAL	1	TRUE	1	0.42503628343649	2		718	786	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0054734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	129	631	1	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	1	2	FACETS	0.982	0.893	1	0.982	0.893	1	CLONAL	1	TRUE	1	0.42503628343649	2		632	618	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276860	15276861	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs753725730	NA	P-0054734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	165	800	2	ENST00000263388.2:c.5404dup	p.Ala1802GlyfsTer8	p.A1802Gfs*8	ENST00000263388	NM_000435.2	1802	gct/gGct	30/33	1	2	FACETS	0.904	0.83	0.98	0.904	0.83	0.98	CLONAL	1	TRUE	1	0.42503628343649	2		802	859	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0054734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	89	317	0	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.42503628343649	2		317	418	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106497	27106498	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	168	681	0	ENST00000324856.7:c.6109dup	p.Gln2037ProfsTer62	p.Q2037Pfs*62	ENST00000324856	NM_006015.4	2036	-/C	20/20	1	2	FACETS	0.957	0.881	1	0.957	0.881	1	CLONAL	1	TRUE	1	0.42503628343649	2		681	826	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218428	36218451	+	inframe_deletion	In_Frame_Del	DEL	GAGGCCCTGAGCGGGGCCCTCCAG	GAGGCCCTGAGCGGGGCCCTCCAG	-	novel	NA	P-0054734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	179	761	0	ENST00000222270.7:c.4208_4231del	p.Glu1403_Gln1410del	p.E1403_Q1410del	ENST00000222270	NM_014727.1	1403	GAGGCCCTGAGCGGGGCCCTCCAG/-	16/37	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.42503628343649	2		761	794	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229294	36229294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	168	764	1	ENST00000222270.7:c.7984C>T	p.Arg2662Trp	p.R2662W	ENST00000222270	NM_014727.1	2662	Cgg/Tgg	37/37	1	2	FACETS	0.951	0.875	1	0.951	0.875	1	CLONAL	1	TRUE	1	0.42503628343649	2		765	831	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578220	28578222	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0054734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	129	522	0	ENST00000241453.7:c.2949_2951del	p.Leu984del	p.L984del	ENST00000241453	NM_004119.2	983	ctACTc/ctc	24/24	1	2	FACETS	0.844	0.766	0.926	0.844	0.766	0.926	CLONAL	1	TRUE	1	0.42503628343649	2		522	719	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81563017	81563017	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	101	361	0	ENST00000298171.2:c.580G>T	p.Gly194Ter	p.G194*	ENST00000298171	NM_000369.2	194	Gga/Tga	7/10	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.42503628343649	2		361	469	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0054735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	63	457	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.545664325997207	3	FACETS	0.96	0.852	1	0.96	0.852	1	CLONAL	2	TRUE	1	0.545664325997207	3		457	153	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0054735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	61	450	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.545664325997207	3	FACETS	0.663	0.574	0.76	0.332	0.287	0.38	SUBCLONAL	1	TRUE	1	0.545664325997207	3		451	429	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28929495	NA	P-0054735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	130	603	0	ENST00000275493.2:c.2155G>T	p.Gly719Cys	p.G719C	ENST00000275493	NM_005228.3	719	Ggc/Tgc	18/28	0.545664325997207	3	FACETS	1	0.939	1	0.52	0.473	0.569	CLONAL	1	TRUE	1	0.545664325997207	3		603	583	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491657	120491657	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	161	259	0	ENST00000256646.2:c.2572A>G	p.Thr858Ala	p.T858A	ENST00000256646	NM_024408.3	858	Act/Gct	16/34	0.545664325997207	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.545664325997207	3		259	344	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939078	48939078	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	54	268	0	ENST00000267163.4:c.910G>T	p.Gly304Ter	p.G304*	ENST00000267163	NM_000321.2	304	Gga/Tga	9/27	0.545664325997207	2	FACETS	0.925	0.82	1	0.925	0.82	1	CLONAL	2	TRUE	0	0.545664325997207	2		268	107	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577543	7577543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	331	589	0	ENST00000269305.4:c.738G>T	p.Met246Ile	p.M246I	ENST00000269305	NM_001126112.2	246	atG/atT	7/11	0.545664325997207	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.545664325997207	2		589	547	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120525	94120525	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	60	316	0	ENST00000369303.4:c.526C>A	p.Pro176Thr	p.P176T	ENST00000369303	NM_004440.3	176	Cct/Act	3/17	0.545664325997207	3	FACETS	1	0.936	1	0.562	0.489	0.639	CLONAL	1	TRUE	1	0.545664325997207	3		316	249	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047254	180047254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1314469826	NA	P-0054735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	183	798	0	ENST00000261937.6:c.2461G>A	p.Glu821Lys	p.E821K	ENST00000261937	NM_182925.4	821	Gag/Aag	17/30	0.275760288306852	0	FACETS	0.502	0.466	0.54			1	INDETERMINATE	1	TRUE	0	0.545664325997207	0		798	607	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514352	149514352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1330417953	NA	P-0054735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	102	437	0	ENST00000261799.4:c.592G>A	p.Glu198Lys	p.E198K	ENST00000261799	NM_002609.3	198	Gag/Aag	4/23	1	2	FACETS	0.994	0.897	1	0.994	0.897	1	CLONAL	1	TRUE	1	0.545664325997207	2		437	376	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743285	162743285	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	132	224	0	ENST00000367921.3:c.1755G>C	p.Met585Ile	p.M585I	ENST00000367921	NM_006182.2	585	atG/atC	14/18	0.545664325997207	5	FACETS	0.974	0.9	1	0.974	0.9	1	CLONAL	3	TRUE	2	0.545664325997207	5		224	301	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347459	89347459	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs909732848	NA	P-0054735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	151	633	0	ENST00000301030.4:c.5491G>A	p.Asp1831Asn	p.D1831N	ENST00000301030	NM_001256183.1	1831	Gac/Aac	9/13	0.545664325997207	3	FACETS	1	0.963	1	0.544	0.498	0.591	CLONAL	1	TRUE	1	0.545664325997207	3		633	648	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024417	16024417	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs771531803	NA	P-0054735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	124	339	0	ENST00000268712.3:c.1801G>T	p.Ala601Ser	p.A601S	ENST00000268712	NM_006311.3	601	Gca/Tca	16/46	0.545664325997207	2	FACETS	1	0.978	1	0.609	0.557	0.663	CLONAL	1	TRUE	0	0.545664325997207	2		339	373	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653066	29653066	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587781693	NA	P-0054735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	73	340	0	ENST00000356175.3:c.5001G>T	p.Glu1667Asp	p.E1667D	ENST00000356175	NM_000267.3	1667	gaG/gaT	36/57	0.545664325997207	3	FACETS	0.931	0.819	1	0.465	0.409	0.525	CLONAL	1	TRUE	1	0.545664325997207	3		340	366	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238957	5238957	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	236	357	0	ENST00000357368.4:c.1822G>T	p.Val608Leu	p.V608L	ENST00000357368	NM_002850.3	608	Gtg/Ttg	13/38	0.455670988571058	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.545664325997207	4		357	578	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953982	17953982	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0054735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	330	646	0	ENST00000458235.1:c.421-1G>A		p.X141_splice	ENST00000458235	NM_000215.3	141			0.455670988571058	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	2	0.545664325997207	4		646	913	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743903	41743903	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	404	796	1	ENST00000301178.4:c.838G>T	p.Glu280Ter	p.E280*	ENST00000301178	NM_021913.4	280	Gag/Tag	7/20	0.455670988571058	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.545664325997207	4		797	1048	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872535	136872541	+	frameshift_variant	Frame_Shift_Del	DEL	GCTCACA	GCTCACA	-	novel	NA	P-0054735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	163	251	0	ENST00000241393.3:c.957_963del	p.Val320GlufsTer44	p.V320Efs*44	ENST00000241393	NM_003467.2	319	tcTGTGAGC/tc	2/2	0.545664325997207	3	FACETS	0.91	0.844	0.976	0.91	0.844	0.976	CLONAL	2	TRUE	1	0.545664325997207	3		251	418	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967304	134967304	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	118	558	0	ENST00000398015.3:c.2643G>T	p.Met881Ile	p.M881I	ENST00000398015	NM_004441.4	881	atG/atT	14/16	0.545664325997207	3	FACETS	1	0.907	1	0.5	0.453	0.55	CLONAL	1	TRUE	1	0.545664325997207	3		558	550	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630405	187630405	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	123	571	0	ENST00000441802.2:c.577G>C	p.Asp193His	p.D193H	ENST00000441802	NM_005245.3	193	Gat/Cat	2/27	0.545664325997207	3	FACETS	0.996	0.904	1	0.498	0.452	0.547	CLONAL	1	TRUE	1	0.545664325997207	3		571	576	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501461	149501461	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	192	725	0	ENST00000261799.4:c.2326G>T	p.Asp776Tyr	p.D776Y	ENST00000261799	NM_002609.3	776	Gat/Tat	16/23	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.545664325997207	2		725	517	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681117	30681118	+	missense_variant	Missense_Mutation	DNP	TG	TG	AA	novel	NA	P-0054735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	126	327	0	ENST00000376406.3:c.601_602delinsTT	p.His201Phe	p.H201F	ENST00000376406	NM_014641.2	201	CAt/TTt	5/15	0.545664325997207	5	FACETS	0.859	0.782	0.938	0.572	0.521	0.626	CLONAL	2	TRUE	2	0.545664325997207	5		327	489	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526585	106526585	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	53	292	0	ENST00000359195.3:c.2878C>A	p.Leu960Ile	p.L960I	ENST00000359195	NM_002649.2	960	Cta/Ata	10/11	0.545664325997207	3	FACETS	1	0.911	1	0.538	0.463	0.617	CLONAL	1	TRUE	1	0.545664325997207	3		292	230	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636839	8636839	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	98	332	0	ENST00000356435.5:c.70C>A	p.Pro24Thr	p.P24T	ENST00000356435		24	Cca/Aca	2/35	0.545664325997207	3	FACETS	1	0.969	1	0.602	0.541	0.665	CLONAL	1	TRUE	1	0.545664325997207	3		332	380	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928915	44928915	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	197	472	0	ENST00000377967.4:c.2015C>T	p.Ala672Val	p.A672V	ENST00000377967	NM_021140.2	672	gCt/gTt	17/29	0.16765913284038	6	FACETS	0.91	0.849	0.973	0.91	0.849	0.973	INDETERMINATE	3	TRUE	3	0.545664325997207	6		472	553	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624435	21624435	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775756153	NA	P-0054744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	100	461	0	ENST00000421138.2:c.1594G>A	p.Val532Ile	p.V532I	ENST00000421138		532	Gtt/Att	14/16	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.28	2		461	679	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218498	1218499	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	59	454	0	ENST00000326873.7:c.374dup	p.Met125IlefsTer38	p.M125Ifs*38	ENST00000326873	NM_000455.4	125	atg/aTtg	2/10	0.298976378486677	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.28	1		454	274	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0054746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	86	834	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			1	2	FACETS	0.9	0.794	1	0.9	0.794	1	CLONAL	1	TRUE	1	0.2	2		834	956	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120479946	120479946	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782313621	NA	P-0054746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	51	680	0	ENST00000256646.2:c.3481G>A	p.Gly1161Arg	p.G1161R	ENST00000256646	NM_024408.3	1161	Ggg/Agg	21/34	1	2	FACETS	0.592	0.501	0.692	0.592	0.501	0.692	SUBCLONAL	1	TRUE	1	0.2	2		680	862	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578493	7578493	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1206165503	NA	P-0054747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	2094	1189	11	ENST00000269305.4:c.437G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tGg/tAg	5/11	0.942285122541508	2	FACETS	1	0.999	1	1	0.999	1	CLONAL	2	FALSE	0	0.942285122541508	2		1200	2170	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937034	48937034	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	298	313	0	ENST00000267163.4:c.802G>T	p.Glu268Ter	p.E268*	ENST00000267163	NM_000321.2	268	Gaa/Taa	8/27	0.942285122541508	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	FALSE	0	0.942285122541508	2		313	312	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985314	60985314	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0054747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1462	281	756	1	ENST00000333681.4:c.585+1G>T		p.X195_splice	ENST00000333681		195			NA	2	FACETS	0.342	0.32	0.365			1	INDETERMINATE	1	FALSE	NA	0.942285122541508	2		757	1743	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627816	187627816	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	197	651	1	ENST00000441802.2:c.3166G>T	p.Val1056Leu	p.V1056L	ENST00000441802	NM_005245.3	1056	Gtg/Ttg	2/27	0.39905377016345	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.942285122541508	0		652	586	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151866292	151866292	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	77	373	1	ENST00000262189.6:c.9496A>G	p.Asn3166Asp	p.N3166D	ENST00000262189	NM_170606.2	3166	Aat/Gat	41/59	0.578756463260171	1	FACETS	0.271	0.24	0.304	0.271	0.24	0.304	SUBCLONAL	1	FALSE	0	0.942285122541508	1		374	319	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331612	8331612	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	254	482	0	ENST00000356435.5:c.5504del	p.Gly1835AlafsTer21	p.G1835Afs*21	ENST00000356435		1835	gGc/gc	33/35	0.593494280820078	3	FACETS	0.889	0.834	0.946			1	CLONAL	1	FALSE	NA	0.942285122541508	3		482	892	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412359	139412359	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1506	751	963	2	ENST00000277541.6:c.1286G>A	p.Cys429Tyr	p.C429Y	ENST00000277541	NM_017617.3	429	tGc/tAc	8/34	0.291498590633386	2	FACETS	0.706	0.681	0.732	0.353	0.34	0.366	INDETERMINATE	1	FALSE	0	0.942285122541508	2		965	2257	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0054748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	150	583	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.2612602118377	2	FACETS	0.834	0.766	0.904	1	0.982	1	CLONAL	3	TRUE	0	0.22	2		583	545	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0054748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	101	749	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.22	2		749	681	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024648	14024648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs759268826	NA	P-0054748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	29	345	0	ENST00000311895.7:c.874C>T	p.Arg292Ter	p.R292*	ENST00000311895	NM_005236.2	292	Cga/Tga	5/11	1	2	FACETS	0.796	0.64	0.974	0.796	0.64	0.974	CLONAL	1	TRUE	1	0.22	2		345	331	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692896	89692896	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs398123322	NA	P-0054748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	55	395	0	ENST00000371953.3:c.380G>T	p.Gly127Val	p.G127V	ENST00000371953	NM_000314.4	127	gGa/gTa	5/9	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.22	2		395	387	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720650	89720650	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1257124719	NA	P-0054748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	54	419	0	ENST00000371953.3:c.802-1G>A		p.X268_splice	ENST00000371953	NM_000314.4	268			1	2	FACETS	0.875	0.747	1	0.875	0.747	1	CLONAL	1	TRUE	1	0.22	2		419	561	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331980	81331980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1383506132	NA	P-0054748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	31	244	0	ENST00000222390.5:c.2104C>T	p.Arg702Cys	p.R702C	ENST00000222390	NM_000601.4	702	Cgt/Tgt	18/18	1	2	FACETS	0.959	0.778	1	0.959	0.778	1	CLONAL	1	TRUE	1	0.22	2		244	294	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0054748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	27	264	0	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	1	2	FACETS	0.787	0.627	0.969	0.787	0.627	0.969	CLONAL	1	TRUE	1	0.22	2		264	312	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1255456	1255456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374968697	NA	P-0054748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	100	762	1	ENST00000310581.5:c.3103G>A	p.Val1035Ile	p.V1035I	ENST00000310581	NM_198253.2	1035	Gtc/Atc	14/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.22	2		763	715	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554937	106554937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs565965311	NA	P-0054748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	89	495	0	ENST00000369096.4:c.2054G>A	p.Arg685Gln	p.R685Q	ENST00000369096	NM_001198.3	685	cGg/cAg	7/7	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.22	2		495	620	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864471	56864471	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1015912856	NA	P-0054748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	93	560	1	ENST00000308159.5:c.959C>T	p.Ala320Val	p.A320V	ENST00000308159	NM_014669.4	320	gCg/gTg	10/22	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.22	2		561	721	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528657	157528657	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554238072	NA	P-0054748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	109	698	1	ENST00000346085.5:c.6382C>T	p.Arg2128Ter	p.R2128*	ENST00000346085	NM_020732.3	2128	Cga/Tga	20/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.22	2		699	739	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0054749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	229	234	3				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.893024747533576	2		237	441	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056584	26056584	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770343058	NA	P-0054749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	155	346	0	ENST00000343677.2:c.73G>A	p.Ala25Thr	p.A25T	ENST00000343677	NM_005319.3	25	Gcc/Acc	1/1	1	2	FACETS	0.956	0.888	1	0.956	0.888	1	CLONAL	1	TRUE	1	0.893024747533576	2		346	363	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753146	128753146	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761932135	NA	P-0054749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	171	338	0	ENST00000377970.2:c.1307G>A	p.Arg436Gln	p.R436Q	ENST00000377970	NM_002467.4	436	cGg/cAg	3/3	0.260769352661819	1	FACETS	0.542	0.505	0.579	0.542	0.505	0.579	INDETERMINATE	1	TRUE	0	0.893024747533576	1		338	391	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	86	290	1				ENST00000310581	NM_198253.2	-/1132			0.212250404132309	0	FACETS	0.357	0.319	0.396			1	INDETERMINATE	1	TRUE	0	0.619555896160739	0		291	296	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0054750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	348	1199	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.619555896160739	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.619555896160739	1		1199	732	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994138	21994138	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	200	863	0	ENST00000579755.1:c.193G>C	p.Gly65Arg	p.G65R	ENST00000579755		65	Ggt/Cgt	1/3	1		FACETS		0.835	0.963				CLONAL	1	TRUE	1	0.619555896160739	2		863	719	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431079	181431079	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	250	926	0	ENST00000325404.1:c.931A>G	p.Thr311Ala	p.T311A	ENST00000325404	NM_003106.3	311	Aca/Gca	1/1	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.619555896160739	2		926	761	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692836	89692836	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	72	184	0	ENST00000371953.3:c.320A>C	p.Asp107Ala	p.D107A	ENST00000371953	NM_000314.4	107	gAt/gCt	5/9	0.619555896160739	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	0	0.619555896160739	1		184	158	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050850	49050851	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	135	288	0	ENST00000267163.4:c.2536dup	p.Gln846ProfsTer9	p.Q846Pfs*9	ENST00000267163	NM_000321.2	845	ttc/ttCc	25/27	0.369869691595759	1	FACETS	0.958	0.885	1	0.958	0.885	1	INDETERMINATE	1	TRUE	0	0.619555896160739	1		288	314	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663775	29663775	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	211	649	1	ENST00000356175.3:c.6207del	p.Phe2069LeufsTer21	p.F2069Lfs*21	ENST00000356175	NM_000267.3	2069	ttC/tt	41/57	0.619555896160739	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.619555896160739	1		650	450	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959143	2959143	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	209	1082	0	ENST00000396946.4:c.2373C>G	p.Cys791Trp	p.C791W	ENST00000396946	NM_032415.4	791	tgC/tgG	18/25	0.275309881828727	0	FACETS	0.386	0.36	0.413			1	INDETERMINATE	1	TRUE	0	0.619555896160739	0		1082	665	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508112	106508112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142342118	NA	P-0054750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	77	413	0	ENST00000359195.3:c.106G>A	p.Glu36Lys	p.E36K	ENST00000359195	NM_002649.2	36	Gag/Aag	2/11	0.619555896160739	4	FACETS	0.965	0.852	1	0.322	0.284	0.362	CLONAL	1	TRUE	1	0.619555896160739	4		413	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0054751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	69	858	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.148538149405266	2		858	710	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528707	8528707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs545049137	NA	P-0054752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	126	445	0	ENST00000356435.5:c.425C>T	p.Thr142Met	p.T142M	ENST00000356435		142	aCg/aTg	4/35	1	2	FACETS	0.984	0.893	1	0.984	0.893	1	CLONAL	1	TRUE	1	0.391626526509793	2		445	654	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155793	106155793	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs748785984	NA	P-0054752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	98	401	0	ENST00000380013.4:c.694C>T	p.Gln232Ter	p.Q232*	ENST00000380013	NM_001127208.2	232	Caa/Taa	3/11	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.391626526509793	2		401	494	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	218493	218493	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs878854631	NA	P-0054752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	85	243	0	ENST00000264932.6:c.23C>G	p.Ser8Trp	p.S8W	ENST00000264932	NM_004168.2	8	tCg/tGg	1/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.391626526509793	2		243	352	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074183	30074183	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0054752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	110	414	0	ENST00000338641.4:c.1447-2A>G		p.X483_splice	ENST00000338641	NM_000268.3	483			0.391626526509793	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.391626526509793	1		414	427	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913407	NA	P-0054753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	117	314	0	ENST00000349496.5:c.133T>G	p.Ser45Ala	p.S45A	ENST00000349496	NM_001904.3	45	Tct/Gct	3/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.365985157319792	2		314	486	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045688	26045688	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1350355423	NA	P-0054753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	64	371	0	ENST00000540144.1:c.50C>T	p.Pro17Leu	p.P17L	ENST00000540144	NM_003531.2	17	cCg/cTg	1/1	1	2	FACETS	0.721	0.626	0.824	0.721	0.626	0.824	SUBCLONAL	1	TRUE	1	0.365985157319792	2		371	485	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303029	15303029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1174625611	NA	P-0054753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1443	283	1062	0	ENST00000263388.2:c.421C>T	p.Arg141Cys	p.R141C	ENST00000263388	NM_000435.2	141	Cgc/Tgc	4/33	0.295042919560438	3	FACETS	1	0.97	1	0.53	0.496	0.565	CLONAL	1	TRUE	1	0.365985157319792	3		1062	1726	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101713	27101713	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0054753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	160	717	0	ENST00000324856.7:c.4993+2T>C		p.X1665_splice	ENST00000324856	NM_006015.4	1665			NA	2	FACETS	0.854	0.782	0.929			1	INDETERMINATE	1	TRUE	NA	0.365985157319792	2		717	1024	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577057	7577058	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCCTTTCTTGCGGAGA	novel	NA	P-0054753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	310	784	0	ENST00000269305.4:c.864_880dup	p.Glu294ValfsTer57	p.E294Vfs*57	ENST00000269305	NM_001126112.2	294	gag/gTCTCCGCAAGAAAGGGGag	8/11	0.365985157319792	2	FACETS	1	0.993	1	0.714	0.673	0.756	CLONAL	1	TRUE	0	0.365985157319792	2		784	1186	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0054754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	11	378	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.155	0.107	0.215	0.155	0.107	0.215	SUBCLONAL	1	TRUE	1	0.687377581430932	2		378	206	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0054754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	73	321	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.687377581430932	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.687377581430932	1		321	133	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	190	290	1				ENST00000310581	NM_198253.2	-/1132			0.253334050016174	6	FACETS	1	0.959	1			1	CLONAL	4	TRUE	NA	0.253334050016174	6		291	543	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092809	27092809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	71	490	0	ENST00000324856.7:c.2830C>T	p.Gln944Ter	p.Q944*	ENST00000324856	NM_006015.4	944	Cag/Tag	9/20	0.212891176847085	4	FACETS	0.917	0.799	1	0.459	0.399	0.523	CLONAL	1	TRUE	2	0.253334050016174	4		490	766	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0054755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	195	614	1	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.148033799698996	3	FACETS	1	0.967	1	0.715	0.663	0.769	INDETERMINATE	2	TRUE	0	0.253334050016174	3		615	809	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230774	66230774	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	29	254	0	ENST00000273854.3:c.2197C>T	p.His733Tyr	p.H733Y	ENST00000273854	NM_004439.5	733	Cat/Tat	12/18	0.253334050016174	2	FACETS	0.704	0.566	0.861	0.352	0.283	0.431	SUBCLONAL	1	TRUE	0	0.253334050016174	2		254	325	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916825	48916825	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	103	268	0	ENST00000267163.4:c.355G>T	p.Glu119Ter	p.E119*	ENST00000267163	NM_000321.2	119	Gag/Tag	3/27	0.240108270244313	3	FACETS	1	0.956	1	0.739	0.666	0.816	CLONAL	2	TRUE	0	0.253334050016174	3		268	413	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754240	57754240	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	92	293	0	ENST00000274289.3:c.611G>C	p.Arg204Thr	p.R204T	ENST00000274289	NM_006622.3	204	aGa/aCa	4/14	0.253334050016174	3	FACETS	0.97	0.867	1	0.97	0.867	1	CLONAL	2	TRUE	1	0.253334050016174	3		293	422	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500455	149500455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	72	534	0	ENST00000261799.4:c.2582G>A	p.Gly861Asp	p.G861D	ENST00000261799	NM_002609.3	861	gGc/gAc	18/23	0.2424880346249	2	FACETS	0.831	0.726	0.945	0.416	0.363	0.473	CLONAL	1	TRUE	0	0.253334050016174	2		534	684	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196827	123196828	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	A	novel	NA	P-0054755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	108	341	0	ENST00000218089.9:c.1714_1715delinsA	p.Pro572IlefsTer4	p.P572Ifs*4	ENST00000218089	NM_001042749.1	572	CCt/At	18/35	0.253334050016174	2	FACETS	0.931	0.84	1	0.931	0.84	1	CLONAL	2	TRUE	0	0.253334050016174	2		341	458	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655488	67655488	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	28	393	0	ENST00000264010.4:c.1351G>C	p.Asp451His	p.D451H	ENST00000264010	NM_006565.3	451	Gat/Cat	7/12	1	2	FACETS	0.461	0.368	0.568	0.461	0.368	0.568	SUBCLONAL	1	TRUE	1	0.290346879225734	2		393	418	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843471	3843471	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	43	529	0	ENST00000262367.5:c.1132C>G	p.Arg378Gly	p.R378G	ENST00000262367	NM_004380.2	378	Cgg/Ggg	4/31	1	2	FACETS	0.422	0.352	0.5	0.422	0.352	0.5	SUBCLONAL	1	TRUE	1	0.290346879225734	2		529	702	SUCCESS
CBL	867	MSKCC	GRCh37	11	119168129	119168129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376848406	NA	P-0054757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	18	397	1	ENST00000264033.4:c.2189C>T	p.Thr730Met	p.T730M	ENST00000264033	NM_005188.3	730	aCg/aTg	14/16	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		398	282	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0054758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	95	415	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.257742945954823	3	FACETS	0.863	0.772	0.96	0.863	0.772	0.96	CLONAL	2	TRUE	1	0.257742945954823	3		415	482	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	35	290	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.93	0.765	1	0.93	0.765	1	CLONAL	1	TRUE	1	0.257742945954823	2		291	292	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243859016	243859016	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs397514606	NA	P-0054758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	33	299	0	ENST00000263826.5:c.49G>A	p.Glu17Lys	p.E17K	ENST00000263826	NM_005465.4	17	Gaa/Aaa	2/13	0.257742945954823	4	FACETS	1	0.852	1	0.35	0.285	0.422	CLONAL	1	TRUE	1	0.257742945954823	4		299	307	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	44	290	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.410491121071852	2		291	178	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	CT	rs121913227	NA	P-0054759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	129	326	2	ENST00000288602.6:c.1798_1799delinsAG	p.Val600Arg	p.V600R	ENST00000288602	NM_004333.4	600	GTg/AGg	15/18	0.410491121071852	3	FACETS	0.964	0.883	1	0.964	0.883	1	CLONAL	2	TRUE	1	0.410491121071852	3		328	393	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9779982	9779982	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587777390	NA	P-0054759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	147	782	0	ENST00000377346.4:c.1246T>C	p.Cys416Arg	p.C416R	ENST00000377346	NM_005026.3	416	Tgc/Cgc	10/24	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.410491121071852	2		782	683	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715645	18715645	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	45	247	0	ENST00000266497.5:c.3476A>T	p.Lys1159Met	p.K1159M	ENST00000266497		1159	aAg/aTg	25/31	1	2	FACETS	0.794	0.672	0.928	0.794	0.672	0.928	CLONAL	1	TRUE	1	0.410491121071852	2		247	276	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244893	46244893	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	114	613	0	ENST00000334344.6:c.2987C>T	p.Ser996Leu	p.S996L	ENST00000334344	NM_152641.2	996	tCa/tTa	15/21	1	2	FACETS	0.953	0.86	1	0.953	0.86	1	CLONAL	1	TRUE	1	0.410491121071852	2		613	583	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972476	81972476	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	127	526	0	ENST00000359376.3:c.3269G>T	p.Cys1090Phe	p.C1090F	ENST00000359376	NM_002661.3	1090	tGt/tTt	29/33	0.31718725438788	3	FACETS	1	0.985	1	0.724	0.659	0.792	CLONAL	1	TRUE	1	0.410491121071852	3		526	515	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508727	29508727	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0054759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	67	429	0	ENST00000356175.3:c.655-1G>C		p.X219_splice	ENST00000356175	NM_000267.3	219			1	2	FACETS	0.702	0.612	0.799	0.702	0.612	0.799	SUBCLONAL	1	TRUE	1	0.410491121071852	2		429	465	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5246050	5246050	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1448131962	NA	P-0054759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	81	522	0	ENST00000357368.4:c.725G>A	p.Arg242His	p.R242H	ENST00000357368	NM_002850.3	242	cGc/cAc	10/38	1	2	FACETS	0.987	0.874	1	0.987	0.874	1	CLONAL	1	TRUE	1	0.410491121071852	2		522	400	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505035	149505035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	118	602	0	ENST00000261799.4:c.1780G>A	p.Glu594Lys	p.E594K	ENST00000261799	NM_002609.3	594	Gag/Aag	12/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.410491121071852	2		602	485	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681904	30681904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765160093	NA	P-0054759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	211	589	0	ENST00000376406.3:c.193G>A	p.Ala65Thr	p.A65T	ENST00000376406	NM_014641.2	65	Gcc/Acc	3/15	0.410491121071852	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.410491121071852	3		589	596	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287286	33287286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755054221	NA	P-0054759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	129	624	0	ENST00000374542.5:c.1811G>A	p.Gly604Glu	p.G604E	ENST00000374542	NM_001141970.1	604	gGa/gAa	6/8	0.410491121071852	3	FACETS	1	0.91	1	0.502	0.455	0.551	CLONAL	1	TRUE	1	0.410491121071852	3		624	755	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332007	81332007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	137	357	0	ENST00000222390.5:c.2077C>T	p.Pro693Ser	p.P693S	ENST00000222390	NM_000601.4	693	Cct/Tct	18/18	0.410491121071852	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	1	0.410491121071852	3		357	383	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0054760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	309	466	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.834776092434171	2		466	726	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0054760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	461	863	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.834776092434171	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.834776092434171	1		864	632	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427455	49427455	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	626	1121	0	ENST00000301067.7:c.11033C>G	p.Ala3678Gly	p.A3678G	ENST00000301067	NM_003482.3	3678	gCc/gGc	39/54	1	2	FACETS	0.997	0.961	1	0.997	0.961	1	CLONAL	1	TRUE	1	0.834776092434171	2		1121	1504	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	296	448	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	0.834776092434171	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.834776092434171	1		448	406	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0054761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	189	234	3				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		237	754	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610099	43610099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760088950	NA	P-0054762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	18	898	1	ENST00000355710.3:c.2051C>T	p.Pro684Leu	p.P684L	ENST00000355710	NM_020975.4	684	cCg/cTg	11/20	0.265204926580165	1	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	0	0.265204926580165	1		899	85	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606122	47606122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	29	314	0	ENST00000263735.4:c.586G>A	p.Val196Ile	p.V196I	ENST00000263735	NM_002354.2	196	Gtt/Att	6/9	1	2	FACETS	1	0.889	1	1	0.963	1	CLONAL	2	TRUE	1	0.265204926580165	2		314	98	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0054763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	183	991	1	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	0.169449542596364	1	FACETS	1	0.979	1	1	0.979	1	INDETERMINATE	1	TRUE	0	0.304967941817163	1		992	870	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579365	7579365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782461	NA	P-0054763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	252	1232	2	ENST00000269305.4:c.322G>A	p.Gly108Ser	p.G108S	ENST00000269305	NM_001126112.2	108	Ggt/Agt	4/11	0.169449542596364	1	FACETS	1	0.989	1	1	0.989	1	INDETERMINATE	1	TRUE	0	0.304967941817163	1		1234	1106	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677955	58677956	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCGAAGTCTCGGGGAAA	novel	NA	P-0054763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	55	381	0	ENST00000305921.3:c.184_201dup	p.Glu62_Gly67dup	p.E62_G67dup	ENST00000305921	NM_003620.3	62	-/GGCGAAGTCTCGGGGAAA	1/6	0.169449542596364	1	FACETS	0.687	0.589	0.794	0.687	0.589	0.794	INDETERMINATE	1	TRUE	0	0.304967941817163	1		381	445	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577358	64577361	+	protein_altering_variant	In_Frame_Del	DEL	AGGC	AGGC	G	novel	NA	P-0054763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	70	762	0	ENST00000312049.6:c.221_224delinsC	p.Gly74_Leu75delinsAla	p.G74_L75delinsA	ENST00000312049	NM_130799.2	74	gGCCTc/gCc	2/10	1	2	FACETS	0.595	0.518	0.678	0.595	0.518	0.678	SUBCLONAL	1	TRUE	1	0.304967941817163	2		762	772	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	110	670	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.408808414488528	2		670	520	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	246	831	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.408808414488528	2	FACETS	0.943	0.888	1	0.943	0.888	1	CLONAL	2	TRUE	0	0.408808414488528	2		831	638	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	92	501	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.408808414488528	2		502	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	168	1082	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	1	2	FACETS	0.93	0.855	1	0.93	0.855	1	CLONAL	1	TRUE	1	0.408808414488528	2		1082	884	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	430	1590	2	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	0.122589627725741	3	FACETS	0.88	0.838	0.923	0.587	0.559	0.616	INDETERMINATE	2	TRUE	0	0.408808414488528	3		1592	1439	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	154	853	5	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	0.122589627725741	3	FACETS	0.978	0.895	1	0.326	0.298	0.355	INDETERMINATE	1	TRUE	0	0.408808414488528	3		858	928	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	191	1149	10	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.961	0.889	1	0.961	0.889	1	CLONAL	1	TRUE	1	0.408808414488528	2		1159	972	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	85	468	2	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	1	2	FACETS	0.918	0.815	1	0.918	0.815	1	CLONAL	1	TRUE	1	0.408808414488528	2		470	453	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	204	605	4	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	0.95	0.889	1	1	0.994	1	CLONAL	2	TRUE	1	0.408808414488528	2		609	525	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779211	3779211	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783507	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	76	751	0	ENST00000262367.5:c.5837del	p.Pro1946HisfsTer30	p.P1946Hfs*30	ENST00000262367	NM_004380.2	1946	cCa/ca	31/31	1	2	FACETS	0.745	0.655	0.841	0.745	0.655	0.841	SUBCLONAL	1	TRUE	1	0.408808414488528	2		751	499	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134982	2134984	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs137854239	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	197	1360	0	ENST00000219476.3:c.4527_4529del	p.Phe1510del	p.F1510del	ENST00000219476	NM_000548.3	1508	ccCTTc/ccc	35/42	0.408808414488528	1	FACETS	0.8	0.741	0.862	0.8	0.741	0.862	SUBCLONAL	1	TRUE	0	0.408808414488528	1		1360	958	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306996	65306996	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs375979659	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	100	499	0	ENST00000342505.4:c.2581C>A	p.Pro861Thr	p.P861T	ENST00000342505	NM_002227.2	861	Cca/Aca	19/25	1	2	FACETS	0.956	0.857	1	0.956	0.857	1	CLONAL	1	TRUE	1	0.408808414488528	2		499	512	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222585	157222585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	163	905	2	ENST00000346085.5:c.1852C>T	p.Pro618Ser	p.P618S	ENST00000346085	NM_020732.3	618	Ccg/Tcg	4/20	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.408808414488528	2		907	788	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349641	89349641	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs772267579	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	174	1024	12	ENST00000301030.4:c.3309del	p.Asp1104MetfsTer214	p.D1104Mfs*214	ENST00000301030	NM_001256183.1	1103	aaA/aa	9/13	1	2	FACETS	0.968	0.892	1	0.968	0.892	1	CLONAL	1	TRUE	1	0.408808414488528	2		1036	879	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266651	142266651	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	30	480	0	ENST00000350721.4:c.3273del	p.Phe1091LeufsTer28	p.F1091Lfs*28	ENST00000350721	NM_001184.3	1091	ttT/tt	16/47	1	2	FACETS	0.441	0.355	0.537	0.441	0.355	0.537	SUBCLONAL	1	TRUE	1	0.408808414488528	2		480	333	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411246	63411246	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	179	1167	1	ENST00000330258.3:c.1921C>T	p.Arg641Ter	p.R641*	ENST00000330258	NM_152424.3	641	Cga/Tga	2/2	1	2	FACETS	0.947	0.873	1	0.947	0.873	1	CLONAL	1	TRUE	1	0.408808414488528	2		1168	925	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806180	1806181	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760502257	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	179	1332	3	ENST00000260795.2:c.1206dup	p.Lys403GlnfsTer93	p.K403Qfs*93	ENST00000260795		400	agc/agCc	8/17	1	2	FACETS	0.849	0.782	0.919	0.849	0.782	0.919	CLONAL	1	TRUE	1	0.408808414488528	2		1335	1031	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519505	137519506	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs780346130	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	165	429	4	ENST00000367739.4:c.1132_1133del	p.Ser378PhefsTer6	p.S378Ffs*6	ENST00000367739	NM_000416.2	378	AGt/t	7/7	1	2	FACETS	0.975	0.906	1	1	0.993	1	CLONAL	2	TRUE	1	0.408808414488528	2		433	414	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857075	9857075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	59	420	0	ENST00000330684.3:c.4326del	p.Arg1443GlyfsTer3	p.R1443Gfs*3	ENST00000330684	NM_001134407.1	1442	ccC/cc	13/13	1	2	FACETS	0.902	0.781	1	0.902	0.781	1	CLONAL	1	TRUE	1	0.408808414488528	2		420	320	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344748	65344748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781744573	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	73	418	1	ENST00000342505.4:c.289G>A	p.Val97Ile	p.V97I	ENST00000342505	NM_002227.2	97	Gtt/Att	4/25	1	2	FACETS	0.893	0.785	1	0.893	0.785	1	CLONAL	1	TRUE	1	0.408808414488528	2		419	400	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217705	7217707	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs757139280	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	100	565	1	ENST00000380728.2:c.220_222del	p.Glu74del	p.E74del	ENST00000380728		74	GAG/-	4/11	1	2	FACETS	0.825	0.738	0.917	0.825	0.738	0.917	CLONAL	1	TRUE	1	0.408808414488528	2		566	593	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937163	39937164	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	158	1224	2	ENST00000378444.4:c.19dup	p.Leu7ProfsTer29	p.L7Pfs*29	ENST00000378444	NM_001123385.1	7	ctg/cCtg	2/15	1	2	FACETS	0.778	0.712	0.846	0.778	0.712	0.846	SUBCLONAL	1	TRUE	1	0.408808414488528	2		1226	994	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783245	9783245	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756497515	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	181	907	2	ENST00000377346.4:c.2489G>A	p.Arg830His	p.R830H	ENST00000377346	NM_005026.3	830	cGt/cAt	20/24	1	2	FACETS	0.989	0.913	1	0.989	0.913	1	CLONAL	1	TRUE	1	0.408808414488528	2		909	895	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259480	16259480	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	119	685	0	ENST00000375759.3:c.6750del	p.Ala2251GlnfsTer102	p.A2251Qfs*102	ENST00000375759	NM_015001.2	2249	Ccc/cc	11/15	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.408808414488528	2		685	579	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	232	1173	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.408808414488528	2		1174	989	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572272	64572272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372468697	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	154	860	2	ENST00000312049.6:c.1367G>A	p.Arg456His	p.R456H	ENST00000312049	NM_130799.2	456	cGc/cAc	10/10	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.408808414488528	2		862	745	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391361	139391361	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	259	1460	0	ENST00000277541.6:c.6830C>A	p.Pro2277His	p.P2277H	ENST00000277541	NM_017617.3	2277	cCt/cAt	34/34	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.408808414488528	2		1460	1073	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210725	36210725	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	233	1304	0	ENST00000222270.7:c.481del	p.Leu161PhefsTer6	p.L161Ffs*6	ENST00000222270	NM_014727.1	159	aCc/ac	3/37	0.122589627725741	3	FACETS	1	0.966	1	0.353	0.328	0.379	INDETERMINATE	1	TRUE	0	0.408808414488528	3		1304	1296	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525977	41525977	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	90	525	0	ENST00000263253.7:c.1256del	p.Asn419MetfsTer12	p.N419Mfs*12	ENST00000263253	NM_001429.3	418	Aaa/aa	5/31	1	2	FACETS	0.897	0.799	1	0.897	0.799	1	CLONAL	1	TRUE	1	0.408808414488528	2		525	491	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170487	11170489	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs1375203306	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	186	1203	0	ENST00000358026.2:c.4792_4794del	p.Lys1598del	p.K1598del	ENST00000358026	NM_001128849.1	1597	gAGAag/gag	34/36	0.122589627725741	3	FACETS	0.994	0.917	1	0.331	0.305	0.358	INDETERMINATE	1	TRUE	0	0.408808414488528	3		1203	1103	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132405	11132405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1378511462	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	219	1264	1	ENST00000358026.2:c.2621G>A	p.Arg874His	p.R874H	ENST00000358026	NM_001128849.1	874	cGt/cAt	19/36	0.122589627725741	3	FACETS	1	0.982	1	0.386	0.359	0.415	INDETERMINATE	1	TRUE	0	0.408808414488528	3		1265	1113	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170928	99170928	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	183	930	0	ENST00000074304.5:c.1557G>T	p.Gln519His	p.Q519H	ENST00000074304	NM_001134224.1	519	caG/caT	16/26	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.408808414488528	2		930	822	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425051	49425051	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	209	1289	0	ENST00000301067.7:c.13437del	p.Ser4480ProfsTer39	p.S4480Pfs*39	ENST00000301067	NM_003482.3	4479	ggG/gg	39/54	1	2	FACETS	0.99	0.919	1	0.99	0.919	1	CLONAL	1	TRUE	1	0.408808414488528	2		1289	1033	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135804196	135804196	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749030456	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	143	674	1	ENST00000298552.3:c.64C>T	p.Arg22Trp	p.R22W	ENST00000298552	NM_001162426.1	22	Cgg/Tgg	3/23	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.408808414488528	2		675	635	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853188	68853188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761180883	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	105	632	0	ENST00000261769.5:c.1571G>A	p.Arg524Gln	p.R524Q	ENST00000261769	NM_004360.3	524	cGg/cAg	11/16	1	2	FACETS	0.903	0.811	0.999	0.903	0.811	0.999	CLONAL	1	TRUE	1	0.408808414488528	2		632	569	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610247	10610247	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780079329	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	411	1266	2	ENST00000171111.5:c.463G>A	p.Val155Ile	p.V155I	ENST00000171111	NM_203500.1	155	Gtc/Atc	2/6	0.122589627725741	3	FACETS	0.967	0.921	1	0.645	0.614	0.676	INDETERMINATE	2	TRUE	0	0.408808414488528	3		1268	1252	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259088	16259088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	134	758	2	ENST00000375759.3:c.6353C>T	p.Ala2118Val	p.A2118V	ENST00000375759	NM_015001.2	2118	gCa/gTa	11/15	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.408808414488528	2		760	648	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649589	206649589	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs782543224	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	162	960	0	ENST00000367120.3:c.424A>G	p.Met142Val	p.M142V	ENST00000367120	NM_014002.3	142	Atg/Gtg	6/22	1	2	FACETS	0.985	0.904	1	0.985	0.904	1	CLONAL	1	TRUE	1	0.408808414488528	2		960	805	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609058	43609058	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	172	1124	0	ENST00000355710.3:c.1814G>A	p.Gly605Asp	p.G605D	ENST00000355710	NM_020975.4	605	gGc/gAc	10/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.408808414488528	2		1124	822	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256124	123256124	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	167	810	0	ENST00000358487.5:c.1785G>T	p.Glu595Asp	p.E595D	ENST00000358487	NM_000141.4	595	gaG/gaT	13/18	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.408808414488528	2		810	783	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50482400	50482400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	70	632	0	ENST00000394963.4:c.751C>T	p.Pro251Ser	p.P251S	ENST00000394963	NM_003076.4	251	Cca/Tca	6/13	1	2	FACETS	0.61	0.533	0.694	0.61	0.533	0.694	SUBCLONAL	1	TRUE	1	0.408808414488528	2		632	561	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473650	67473650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773543026	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	165	903	1	ENST00000327367.4:c.730G>A	p.Val244Ile	p.V244I	ENST00000327367	NM_005902.3	244	Gtc/Atc	6/9	0.408808414488528	2	FACETS	0.947	0.871	1	0.474	0.435	0.514	CLONAL	1	TRUE	0	0.408808414488528	2		904	852	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858392	89858392	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	163	775	0	ENST00000389301.3:c.1168C>T	p.Leu390Phe	p.L390F	ENST00000389301	NM_000135.2	390	Ctc/Ttc	13/43	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.408808414488528	2		775	776	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110285	3110285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs941191833	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	192	1090	1	ENST00000078429.4:c.275G>A	p.Arg92Gln	p.R92Q	ENST00000078429	NM_002067.2	92	cGg/cAg	2/7	0.122589627725741	3	FACETS	0.993	0.917	1	0.331	0.305	0.358	INDETERMINATE	1	TRUE	0	0.408808414488528	3		1091	1139	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272237	15272237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs189252435	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	187	899	0	ENST00000263388.2:c.6202G>A	p.Gly2068Arg	p.G2068R	ENST00000263388	NM_000435.2	2068	Ggg/Agg	33/33	0.122589627725741	3	FACETS	1	0.987	1	0.434	0.401	0.468	INDETERMINATE	1	TRUE	0	0.408808414488528	3		899	846	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860955	45860955	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	336	1024	0	ENST00000391945.4:c.1240T>A	p.Phe414Ile	p.F414I	ENST00000391945	NM_000400.3	414	Ttc/Atc	13/23	0.122589627725741	3	FACETS	1	0.986	1	0.737	0.699	0.775	INDETERMINATE	2	TRUE	0	0.408808414488528	3		1024	896	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513310	44513310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs930924689	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	207	791	0	ENST00000291552.4:c.625C>T	p.Arg209Cys	p.R209C	ENST00000291552	NM_006758.2	209	Cgt/Tgt	8/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.408808414488528	2		791	878	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204998	128204998	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	72	1205	0	ENST00000341105.2:c.443G>A	p.Ser148Asn	p.S148N	ENST00000341105	NM_032638.4	148	aGc/aAc	3/6	1	2	FACETS	0.44	0.383	0.501	0.44	0.383	0.501	SUBCLONAL	1	TRUE	1	0.408808414488528	2		1205	801	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295062	1295062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	19	58	0	ENST00000310581.5:c.43C>T	p.Arg15Cys	p.R15C	ENST00000310581	NM_198253.2	15	Cgc/Tgc	1/16	NA	2	FACETS	1	0.921	1			1	INDETERMINATE	1	TRUE	NA	0.408808414488528	2		58	62	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80021373	80021373	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	48	529	0	ENST00000265081.6:c.1442T>C	p.Val481Ala	p.V481A	ENST00000265081	NM_002439.4	481	gTt/gCt	9/24	1	2	FACETS	0.483	0.408	0.565	0.483	0.408	0.565	SUBCLONAL	1	TRUE	1	0.408808414488528	2		529	486	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971237	13971237	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	118	697	0	ENST00000405192.2:c.692A>G	p.Tyr231Cys	p.Y231C	ENST00000405192	NM_001163147.1	231	tAc/tGc	8/12	1	2	FACETS	0.869	0.786	0.958	0.869	0.786	0.958	CLONAL	1	TRUE	1	0.408808414488528	2		697	664	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172167	38172167	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	72	376	0	ENST00000317025.8:c.2240C>T	p.Thr747Ile	p.T747I	ENST00000317025	NM_023034.1	747	aCt/aTt	12/24	1	2	FACETS	0.87	0.763	0.983	0.87	0.763	0.983	CLONAL	1	TRUE	1	0.408808414488528	2		376	405	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752998	128752998	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	147	651	0	ENST00000377970.2:c.1159C>T	p.Arg387Trp	p.R387W	ENST00000377970	NM_002467.4	387	Cgg/Tgg	3/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.408808414488528	2		651	631	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090513	5090513	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	61	317	0	ENST00000381652.3:c.2829A>C	p.Lys943Asn	p.K943N	ENST00000381652	NM_004972.3	943	aaA/aaC	21/25	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.408808414488528	2		317	285	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779828	135779828	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	86	520	0	ENST00000298552.3:c.2011A>C	p.Ser671Arg	p.S671R	ENST00000298552	NM_001162426.1	671	Agc/Cgc	16/23	1	2	FACETS	0.89	0.79	0.995	0.89	0.79	0.995	CLONAL	1	TRUE	1	0.408808414488528	2		520	473	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923148	48923148	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs121913298	NA	P-0054765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	60	295	0	ENST00000267163.4:c.596T>A	p.Leu199Ter	p.L199*	ENST00000267163	NM_000321.2	199	tTa/tAa	6/27	0.772016431495271	2	FACETS	0.762	0.686	0.835	0.762	0.686	0.835	SUBCLONAL	2	FALSE	0	0.772076469008519	2		295	102	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223241	2223241	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765441523	NA	P-0054765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	48	916	1	ENST00000326181.6:c.853G>A	p.Glu285Lys	p.E285K	ENST00000326181	NM_032271.2	285	Gag/Aag	10/21	0.671284186292861	3	FACETS	0.42	0.356	0.491	0.14	0.118	0.164	SUBCLONAL	1	FALSE	0	0.772076469008519	3		917	410	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939220	36939220	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	161	1113	1	ENST00000361632.4:c.489C>A	p.Ser163Arg	p.S163R	ENST00000361632		163	agC/agA	5/16	0.759818064128379	4	FACETS	0.928	0.862	0.996	0.928	0.862	0.996	CLONAL	2	FALSE	2	0.772076469008519	4		1114	398	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120991	115121020	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	CATGGAGAGGCTCATCCACTCCAGGCGGGG	CATGGAGAGGCTCATCCACTCCAGGCGGGG	-	novel	NA	P-0054765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	30	548	0	ENST00000257566.3:c.-15_15del		p.*5*	ENST00000257566	NM_016569.3	?-5/743		1/8	0.737089209497052	3	FACETS	0.36	0.291	0.439	0.18	0.145	0.22	SUBCLONAL	1	FALSE	1	0.772076469008519	3		548	299	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577103	7577160	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGGACAGGCACAAACACGCACCTCAAAGCTGTTCCGTCCCAGTAGATTACCACTACT	CAGGACAGGCACAAACACGCACCTCAAAGCTGTTCCGTCCCAGTAGATTACCACTACT	-	novel	NA	P-0054765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	246	742	0	ENST00000269305.4:c.783-5_835del		p.X261_splice	ENST00000269305	NM_001126112.2	261		8/11	0.603710576352483	3	FACETS	1	0.99	1	0.767	0.731	0.801	CLONAL	2	FALSE	0	0.772076469008519	3		742	384	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546081	29546081	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	181	422	1	ENST00000356175.3:c.1586T>A	p.Leu529His	p.L529H	ENST00000356175	NM_000267.3	529	cTc/cAc	14/57	0.658790994672597	4	FACETS	0.923	0.871	0.974	0.692	0.653	0.731	CLONAL	3	FALSE	0	0.772076469008519	4		423	300	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119624655	119624655	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	106	511	0	ENST00000316626.5:c.760C>T	p.Gln254Ter	p.Q254*	ENST00000316626		254	Caa/Taa	7/12	0.772076469008519	4	FACETS	1	0.982	1	0.703	0.637	0.772	CLONAL	1	FALSE	2	0.772076469008519	4		511	346	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004276	150004276	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	90	438	0	ENST00000253339.5:c.1949T>A	p.Val650Glu	p.V650E	ENST00000253339		650	gTa/gAa	3/7	0.767029889177813	2	FACETS	0.971	0.908	1	0.971	0.908	1	CLONAL	2	FALSE	0	0.772076469008519	2		438	120	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953008	2953008	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	133	1122	0	ENST00000396946.4:c.2932C>G	p.Leu978Val	p.L978V	ENST00000396946	NM_032415.4	978	Ctc/Gtc	22/25	0.190914520695746	1	FACETS	0.551	0.506	0.597	0.551	0.506	0.597	INDETERMINATE	1	FALSE	0	0.772076469008519	1		1122	384	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449755	8449755	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	38	594	0	ENST00000356435.5:c.3958G>A	p.Glu1320Lys	p.E1320K	ENST00000356435		1320	Gaa/Aaa	23/35	0.533395745399933	3	FACETS	0.505	0.42	0.6	0.168	0.14	0.2	SUBCLONAL	1	FALSE	0	0.772076469008519	3		594	270	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0054766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	29	552	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.794	0.636	0.974	0.794	0.636	0.974	CLONAL	1	TRUE	1	0.15	2		554	487	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913283	NA	P-0054766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	13	411	0	ENST00000263967.3:c.3129G>T	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atT	21/21	1	2	FACETS	0.519	0.369	0.703	0.519	0.369	0.703	SUBCLONAL	1	TRUE	1	0.15	2		411	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0054766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	80	1292	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.15	2		1292	1018	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222989	1223001	+	frameshift_variant	Frame_Shift_Del	DEL	TCCGGAAGAAACA	TCCGGAAGAAACA	-	novel	NA	P-0054766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	49	934	1	ENST00000326873.7:c.929_941del	p.Arg310LeufsTer22	p.R310Lfs*22	ENST00000326873	NM_000455.4	309	tTCCGGAAGAAACAt/tt	8/10	1	2	FACETS	0.795	0.671	0.932	0.795	0.671	0.932	CLONAL	1	TRUE	1	0.15	2		935	822	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220560	123220560	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	54	634	0	ENST00000218089.9:c.3217A>C	p.Lys1073Gln	p.K1073Q	ENST00000218089	NM_001042749.1	1073	Aaa/Caa	30/35	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.15	2		634	677	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	64	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.859	0.747	0.98	0.859	0.747	0.98	CLONAL	1	TRUE	1	0.370520073881467	2		487	402	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	56	501	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.689	0.591	0.794	0.689	0.591	0.794	SUBCLONAL	1	TRUE	1	0.370520073881467	2		502	439	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	121	1187	15	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.816	0.738	0.9	0.816	0.738	0.9	CLONAL	1	TRUE	1	0.370520073881467	2		1202	800	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	287	1445	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.849	0.8	0.899	1	0.995	1	CLONAL	2	TRUE	1	0.370520073881467	2		1452	912	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	113	1056	1	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	0.370520073881467	1	FACETS	0.702	0.632	0.776	0.702	0.632	0.776	SUBCLONAL	1	TRUE	0	0.370520073881467	1		1057	708	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	57	352	2	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.944	0.815	1	0.944	0.815	1	CLONAL	1	TRUE	1	0.370520073881467	2		354	326	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508673	106508673	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs554272230	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	112	1057	1	ENST00000359195.3:c.667G>A	p.Val223Ile	p.V223I	ENST00000359195	NM_002649.2	223	Gtc/Atc	2/11	1	2	FACETS	0.844	0.76	0.933	0.844	0.76	0.933	CLONAL	1	TRUE	1	0.370520073881467	2		1058	716	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	159	749	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.370520073881467	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.370520073881467	1		749	595	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346437	89346437	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555525603	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	152	1386	4	ENST00000301030.4:c.6513del	p.Val2173SerfsTer2	p.V2173Sfs*2	ENST00000301030	NM_001256183.1	2171	ccC/cc	9/13	1	2	FACETS	0.962	0.88	1	0.962	0.88	1	CLONAL	1	TRUE	1	0.370520073881467	2		1390	853	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	68	494	10	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.936	0.819	1	0.936	0.819	1	CLONAL	1	TRUE	1	0.370520073881467	2		504	392	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615023	43615023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779996040	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	149	1538	0	ENST00000355710.3:c.2437C>T	p.Arg813Trp	p.R813W	ENST00000355710	NM_020975.4	813	Cgg/Tgg	14/20	1	2	FACETS	0.857	0.783	0.936	0.857	0.783	0.936	CLONAL	1	TRUE	1	0.370520073881467	2		1538	938	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1232964733	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	10	86	2	ENST00000324856.7:c.1015del	p.Ala339LeufsTer24	p.A339Lfs*24	ENST00000324856	NM_006015.4	337	tGg/tg	1/20	1	2	FACETS	0.818	0.564	1	0.818	0.564	1	CLONAL	1	TRUE	1	0.370520073881467	2		88	66	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510160	149510160	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772355478	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	170	1351	2	ENST00000261799.4:c.1309C>T	p.Arg437Cys	p.R437C	ENST00000261799	NM_002609.3	437	Cgt/Tgt	9/23	1	2	FACETS	0.914	0.84	0.991	0.914	0.84	0.991	CLONAL	1	TRUE	1	0.370520073881467	2		1353	1004	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	55	544	2	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.697	0.598	0.805	0.697	0.598	0.805	SUBCLONAL	1	TRUE	1	0.370520073881467	2		546	426	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216477	108216477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587782558	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	35	277	2	ENST00000278616.4:c.8432del	p.Lys2811SerfsTer46	p.K2811Sfs*46	ENST00000278616	NM_000051.3	2809	cAa/ca	58/63	1	2	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	TRUE	1	0.370520073881467	2		279	185	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019198	31019198	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767144159	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	131	872	1	ENST00000375687.4:c.793C>T	p.Arg265Cys	p.R265C	ENST00000375687	NM_015338.5	265	Cgt/Tgt	9/13	1	2	FACETS	0.969	0.88	1	0.969	0.88	1	CLONAL	1	TRUE	1	0.370520073881467	2		873	730	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	91	790	1	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.847	0.753	0.946	0.847	0.753	0.946	CLONAL	1	TRUE	1	0.370520073881467	2		791	580	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436028	56436028	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	110	954	0	ENST00000407977.2:c.1109del	p.Pro370HisfsTer49	p.P370Hfs*49	ENST00000407977		370	cCa/ca	9/10	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.370520073881467	2		954	589	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132897	64132897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs951024884	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	165	1510	0	ENST00000334205.4:c.1031C>T	p.Pro344Leu	p.P344L	ENST00000334205	NM_003942.2	344	cCc/cTc	9/17	1	2	FACETS	0.856	0.786	0.931	0.856	0.786	0.931	CLONAL	1	TRUE	1	0.370520073881467	2		1510	1040	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200087	138200087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150513567	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	119	834	0	ENST00000237289.4:c.1505G>A	p.Arg502Gln	p.R502Q	ENST00000237289	NM_001270507.1	502	cGg/cAg	7/9	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.370520073881467	2		834	629	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	45	378	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	0.906	0.767	1	0.906	0.767	1	CLONAL	1	TRUE	1	0.370520073881467	2		378	268	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851765	134851765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	141	1269	2	ENST00000398015.3:c.1171G>A	p.Val391Ile	p.V391I	ENST00000398015	NM_004441.4	391	Gtc/Atc	5/16	1	2	FACETS	0.909	0.829	0.994	0.909	0.829	0.994	CLONAL	1	TRUE	1	0.370520073881467	2		1271	837	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302390	15302390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146578114	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	234	1740	2	ENST00000263388.2:c.881C>T	p.Thr294Met	p.T294M	ENST00000263388	NM_000435.2	294	aCg/aTg	6/33	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.370520073881467	2		1742	1258	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030631	48030631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs191109849	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	101	674	0	ENST00000234420.5:c.3245C>T	p.Pro1082Leu	p.P1082L	ENST00000234420	NM_000179.2	1082	cCg/cTg	5/10	0.370520073881467	2	FACETS	0.921	0.825	1	0.46	0.412	0.511	CLONAL	1	TRUE	0	0.370520073881467	2		674	592	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665280	176665280	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784107	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	60	559	0	ENST00000439151.2:c.3964C>T	p.Arg1322Ter	p.R1322*	ENST00000439151	NM_022455.4	1322	Cga/Tga	7/23	1	2	FACETS	0.644	0.555	0.74	0.644	0.555	0.74	SUBCLONAL	1	TRUE	1	0.370520073881467	2		559	503	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211145	2211145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775729505	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	235	1881	6	ENST00000398665.3:c.1399G>A	p.Val467Met	p.V467M	ENST00000398665	NM_032482.2	467	Gtg/Atg	15/28	1	2	FACETS	0.985	0.917	1	0.985	0.917	1	CLONAL	1	TRUE	1	0.370520073881467	2		1887	1288	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793340	242793340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201540918	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	189	1773	5	ENST00000334409.5:c.737C>T	p.Thr246Met	p.T246M	ENST00000334409	NM_005018.2	246	aCg/aTg	5/5	1	2	FACETS	0.945	0.872	1	0.945	0.872	1	CLONAL	1	TRUE	1	0.370520073881467	2		1778	1080	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944121	71944123	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	130	1288	1	ENST00000298229.2:c.1960_1962del	p.Glu654del	p.E654del	ENST00000298229	NM_001567.3	652	GAG/-	17/28	1	2	FACETS	0.781	0.707	0.858	0.781	0.707	0.858	SUBCLONAL	1	TRUE	1	0.370520073881467	2		1289	899	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748399150	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	247	1664	7	ENST00000220592.5:c.1806del	p.Ala603ProfsTer92	p.A603Pfs*92	ENST00000220592	NM_012154.3	602	ccC/cc	14/19	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.370520073881467	2		1671	1214	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214866	36214866	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568372429	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	193	1472	6	ENST00000222270.7:c.3296del	p.Gly1099AlafsTer83	p.G1099Afs*83	ENST00000222270	NM_014727.1	1098	Ggg/gg	8/37	1	2	FACETS	0.933	0.862	1	0.933	0.862	1	CLONAL	1	TRUE	1	0.370520073881467	2		1478	1117	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942085	81942085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767040629	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	114	1058	2	ENST00000359376.3:c.1622C>T	p.Thr541Met	p.T541M	ENST00000359376	NM_002661.3	541	aCg/aTg	17/33	1	2	FACETS	0.805	0.725	0.89	0.805	0.725	0.89	CLONAL	1	TRUE	1	0.370520073881467	2		1060	764	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655479	67655479	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs769948988	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	92	641	2	ENST00000264010.4:c.1342C>T	p.Arg448Ter	p.R448*	ENST00000264010	NM_006565.3	448	Cga/Tga	7/12	1	2	FACETS	0.974	0.868	1	0.974	0.868	1	CLONAL	1	TRUE	1	0.370520073881467	2		643	510	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81962229	81962229	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs559219743	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	76	681	2	ENST00000359376.3:c.2581G>A	p.Val861Met	p.V861M	ENST00000359376	NM_002661.3	861	Gtg/Atg	24/33	1	2	FACETS	0.88	0.775	0.993	0.88	0.775	0.993	CLONAL	1	TRUE	1	0.370520073881467	2		683	466	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917736	29917736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150966028	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	160	1336	1	ENST00000389048.3:c.932G>A	p.Arg311His	p.R311H	ENST00000389048	NM_004304.4	311	cGt/cAt	3/29	0.370520073881467	2	FACETS	0.975	0.894	1	0.487	0.447	0.53	CLONAL	1	TRUE	0	0.370520073881467	2		1337	886	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595382	141595382	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	109	1271	1	ENST00000220592.5:c.51del	p.Ile18SerfsTer121	p.I18Sfs*121	ENST00000220592	NM_012154.3	17	ccC/cc	2/19	1	2	FACETS	0.64	0.573	0.71	0.64	0.573	0.71	SUBCLONAL	1	TRUE	1	0.370520073881467	2		1272	920	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450798	70450798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	99	776	0	ENST00000373644.4:c.5638C>T	p.His1880Tyr	p.H1880Y	ENST00000373644	NM_030625.2	1880	Cac/Tac	12/12	1	2	FACETS	0.915	0.819	1	0.915	0.819	1	CLONAL	1	TRUE	1	0.370520073881467	2		776	584	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570245	87570245	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	44	822	0	ENST00000277120.3:c.1985C>T	p.Thr662Met	p.T662M	ENST00000277120		662	aCg/aTg	17/19	1	2	FACETS	0.392	0.328	0.463	0.392	0.328	0.463	SUBCLONAL	1	TRUE	1	0.370520073881467	2		822	606	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350513	15350513	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	173	1480	2	ENST00000263377.2:c.3402del	p.Lys1135SerfsTer18	p.K1135Sfs*18	ENST00000263377	NM_058243.2	1134	ccC/cc	16/20	1	2	FACETS	0.923	0.849	1	0.923	0.849	1	CLONAL	1	TRUE	1	0.370520073881467	2		1482	1012	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642778	3642778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145353518	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	234	1404	1	ENST00000294008.3:c.2249C>T	p.Thr750Met	p.T750M	ENST00000294008	NM_032444.2	750	aCg/aTg	11/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.370520073881467	2		1405	1179	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712701	43712701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483739038	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	137	1286	2	ENST00000382044.4:c.4483C>T	p.Arg1495Cys	p.R1495C	ENST00000382044	NM_001141980.1	1495	Cgt/Tgt	21/28	1	2	FACETS	0.817	0.743	0.895	0.817	0.743	0.895	CLONAL	1	TRUE	1	0.370520073881467	2		1288	905	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797283	32797283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs74770812	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	160	1381	3	ENST00000374899.4:c.1826C>T	p.Ala609Val	p.A609V	ENST00000374899	NM_018833.2	609	gCg/gTg	11/12	1	2	FACETS	0.835	0.765	0.909	0.835	0.765	0.909	CLONAL	1	TRUE	1	0.370520073881467	2		1384	1034	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258680	16258680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	130	992	1	ENST00000375759.3:c.5945G>A	p.Arg1982Gln	p.R1982Q	ENST00000375759	NM_015001.2	1982	cGg/cAg	11/15	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.370520073881467	2		993	697	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468188	50468188	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	126	1164	1	ENST00000331340.3:c.1423G>A	p.Val475Ile	p.V475I	ENST00000331340	NM_006060.4	475	Gtc/Atc	8/8	1	2	FACETS	0.858	0.777	0.943	0.858	0.777	0.943	CLONAL	1	TRUE	1	0.370520073881467	2		1165	793	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62320920	62320920	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	175	1938	4	ENST00000360203.5:c.1949del	p.Pro650HisfsTer17	p.P650Hfs*17	ENST00000360203	NM_001283009.1	648	taC/ta	23/35	1	2	FACETS	0.756	0.695	0.821	0.756	0.695	0.821	SUBCLONAL	1	TRUE	1	0.370520073881467	2		1942	1249	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798340	45798340	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	54	1423	0	ENST00000450313.1:c.596del	p.Gly199AlafsTer41	p.G199Afs*41	ENST00000450313	NM_012222.2	199	gGc/gc	8/16	1	2	FACETS	0.294	0.25	0.342	0.294	0.25	0.342	SUBCLONAL	1	TRUE	1	0.370520073881467	2		1423	993	SUCCESS
EED	8726	MSKCC	GRCh37	11	85966324	85966324	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	30	395	0	ENST00000263360.6:c.421G>A	p.Ala141Thr	p.A141T	ENST00000263360	NM_003797.3	141	Gct/Act	4/12	1	2	FACETS	0.598	0.483	0.726	0.598	0.483	0.726	SUBCLONAL	1	TRUE	1	0.370520073881467	2		395	271	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206672	108206675	+	frameshift_variant	Frame_Shift_Del	DEL	CTAT	CTAT	-	novel	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	44	412	0	ENST00000278616.4:c.8254_8257del	p.Ile2752ValfsTer53	p.I2752Vfs*53	ENST00000278616	NM_000051.3	2751	aCTATc/ac	56/63	1	2	FACETS	0.735	0.619	0.863	0.735	0.619	0.863	SUBCLONAL	1	TRUE	1	0.370520073881467	2		412	323	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477107	67477107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	157	1122	1	ENST00000327367.4:c.914C>T	p.Ala305Val	p.A305V	ENST00000327367	NM_005902.3	305	gCa/gTa	7/9	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.370520073881467	2		1123	814	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312735	91312735	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749632465	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	93	634	0	ENST00000355112.3:c.2474C>T	p.Pro825Leu	p.P825L	ENST00000355112	NM_000057.2	825	cCg/cTg	12/22	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.370520073881467	2		634	491	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354440	354440	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs138744096	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	86	1335	2	ENST00000262320.3:c.1118G>A	p.Arg373His	p.R373H	ENST00000262320	NM_003502.3	373	cGc/cAc	5/11	1	2	FACETS	0.445	0.392	0.502	0.445	0.392	0.502	SUBCLONAL	1	TRUE	1	0.370520073881467	2		1337	1043	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128081	30128081	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs762951234	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	164	1459	0	ENST00000263025.4:c.1048A>G	p.Met350Val	p.M350V	ENST00000263025	NM_002746.2	350	Atg/Gtg	8/9	1	2	FACETS	0.939	0.862	1	0.939	0.862	1	CLONAL	1	TRUE	1	0.370520073881467	2		1459	943	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81968052	81968052	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	88	617	0	ENST00000359376.3:c.2758T>C	p.Trp920Arg	p.W920R	ENST00000359376	NM_002661.3	920	Tgg/Cgg	26/33	1	2	FACETS	0.867	0.77	0.97	0.867	0.77	0.97	CLONAL	1	TRUE	1	0.370520073881467	2		617	548	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346209	89346209	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	57	591	0	ENST00000301030.4:c.6741A>T	p.Glu2247Asp	p.E2247D	ENST00000301030	NM_001256183.1	2247	gaA/gaT	9/13	1	2	FACETS	0.889	0.767	1	0.889	0.767	1	CLONAL	1	TRUE	1	0.370520073881467	2		591	346	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664494	29664494	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772639479	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	98	767	3	ENST00000356175.3:c.6473G>A	p.Arg2158His	p.R2158H	ENST00000356175	NM_000267.3	2158	cGt/cAt	42/57	1	2	FACETS	0.781	0.698	0.87	0.781	0.698	0.87	SUBCLONAL	1	TRUE	1	0.370520073881467	2		770	677	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533649	63533649	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	156	1236	0	ENST00000307078.5:c.1505del	p.Gly502AlafsTer5	p.G502Afs*5	ENST00000307078	NM_004655.3	502	gGc/gc	6/11	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.370520073881467	2		1236	835	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603134	48603134	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	92	643	0	ENST00000342988.3:c.1435G>A	p.Ala479Thr	p.A479T	ENST00000342988	NM_005359.5	479	Gct/Act	11/12	1	2	FACETS	0.856	0.762	0.956	0.856	0.762	0.956	CLONAL	1	TRUE	1	0.370520073881467	2		643	580	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132195	7132195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1156477251	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	148	1381	0	ENST00000302850.5:c.2816C>T	p.Pro939Leu	p.P939L	ENST00000302850	NM_000208.2	939	cCc/cTc	14/22	1	2	FACETS	0.752	0.685	0.821	0.752	0.685	0.821	SUBCLONAL	1	TRUE	1	0.370520073881467	2		1381	1063	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607403	46607403	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	423	1490	0	ENST00000263734.3:c.1592C>G	p.Pro531Arg	p.P531R	ENST00000263734	NM_001430.4	531	cCc/cGc	12/16	0.370520073881467	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.370520073881467	2		1490	1086	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637431	47637461	+	frameshift_variant	Frame_Shift_Del	DEL	GCTCTCCTCATCCAGATTGGACCAAAGGAAT	GCTCTCCTCATCCAGATTGGACCAAAGGAAT	-	novel	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	185	833	0	ENST00000233146.2:c.566_596del	p.Ala189ValfsTer15	p.A189Vfs*15	ENST00000233146	NM_000251.2	189	GCTCTCCTCATCCAGATTGGACCAAAGGAATgt/gt	3/16	0.370520073881467	2	FACETS	0.885	0.823	0.949	0.885	0.823	0.949	CLONAL	2	TRUE	0	0.370520073881467	2		833	564	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96930981	96930981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	43	1123	1	ENST00000258439.3:c.139G>A	p.Ala47Thr	p.A47T	ENST00000258439	NM_001193304.2	47	Gcc/Acc	2/4	1	2	FACETS	0.312	0.26	0.369	0.312	0.26	0.369	SUBCLONAL	1	TRUE	1	0.370520073881467	2		1124	745	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725022	49725022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs575861028	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	166	1331	0	ENST00000449682.2:c.322C>T	p.Arg108Cys	p.R108C	ENST00000449682	NM_020998.3	108	Cgt/Tgt	3/18	1	2	FACETS	0.948	0.871	1	0.948	0.871	1	CLONAL	1	TRUE	1	0.370520073881467	2		1331	945	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090563	71090565	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs751098424	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	85	718	0	ENST00000318789.4:c.783_785del	p.Ser262del	p.S262del	ENST00000318789	NM_032682.5	261	tcCTCt/tct	11/21	1	2	FACETS	0.964	0.855	1	0.964	0.855	1	CLONAL	1	TRUE	1	0.370520073881467	2		718	476	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522328	157522328	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	123	1224	0	ENST00000346085.5:c.4600del	p.Arg1534AlafsTer45	p.R1534Afs*45	ENST00000346085	NM_020732.3	1534	Cgc/gc	18/20	1	2	FACETS	0.715	0.646	0.789	0.715	0.646	0.789	SUBCLONAL	1	TRUE	1	0.370520073881467	2		1224	928	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730467	133730467	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	64	619	0	ENST00000318560.5:c.533C>T	p.Thr178Ile	p.T178I	ENST00000318560	NM_005157.4	178	aCt/aTt	3/11	1	2	FACETS	0.763	0.662	0.871	0.763	0.662	0.871	SUBCLONAL	1	TRUE	1	0.370520073881467	2		619	453	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	20	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.266117047367521	3	FACETS	0.127	0.096	0.163	0.063	0.048	0.082	INDETERMINATE	1	TRUE	1	0.712634625022455	3		457	600	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0054768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	242	535	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.266117047367521	3	FACETS	0.775	0.73	0.821	0.775	0.73	0.821	INDETERMINATE	2	TRUE	1	0.712634625022455	3		535	594	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0054768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	496	1126	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.712634625022455	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.712634625022455	1		1126	858	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133685	41133685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1216360372	NA	P-0054768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	177	537	0	ENST00000379561.5:c.1943C>T	p.Thr648Met	p.T648M	ENST00000379561	NM_002015.3	648	aCg/aTg	2/3	1	2	FACETS	0.941	0.873	1	0.941	0.873	1	CLONAL	1	TRUE	1	0.712634625022455	2		537	528	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911534	101911534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111426349	NA	P-0054768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	9	431	0	ENST00000374994.4:c.1459C>T	p.Arg487Trp	p.R487W	ENST00000374994	NM_004612.2	487	Cgg/Tgg	9/9	0.712634625022455	1	FACETS	0.059	0.039	0.085	0.059	0.039	0.085	SUBCLONAL	1	TRUE	0	0.712634625022455	1		431	275	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0054769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	43	234	3				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.239053102006731	2		237	253	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0054769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	37	269	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.213361767966971	1	FACETS	0.725	0.598	0.866	0.725	0.598	0.866	SUBCLONAL	1	TRUE	0	0.239053102006731	1		269	376	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599321	55599321	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913507	NA	P-0054769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	75	522	0	ENST00000288135.5:c.2447A>T	p.Asp816Val	p.D816V	ENST00000288135	NM_000222.2	816	gAc/gTc	17/21	1	2	FACETS	0.893	0.782	1	0.893	0.782	1	CLONAL	1	TRUE	1	0.239053102006731	2		522	703	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63817050	63817050	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	36	230	0	ENST00000279873.7:c.1021C>T	p.Arg341Ter	p.R341*	ENST00000279873	NM_032199.2	341	Cga/Tga	6/10	1	2	FACETS	0.91	0.75	1	0.91	0.75	1	CLONAL	1	TRUE	1	0.239053102006731	2		230	331	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77054863	77054863	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0054769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	50	406	0	ENST00000356341.3:c.998+1G>A		p.X333_splice	ENST00000356341	NM_002576.4	333			1	2	FACETS	0.875	0.743	1	0.875	0.743	1	CLONAL	1	TRUE	1	0.239053102006731	2		406	478	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042134	42042134	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	50	524	0	ENST00000219905.7:c.6329G>A	p.Gly2110Asp	p.G2110D	ENST00000219905	NM_001164273.1	2110	gGt/gAt	17/24	1	2	FACETS	0.628	0.532	0.734	0.628	0.532	0.734	SUBCLONAL	1	TRUE	1	0.239053102006731	2		524	666	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573566	41573566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	97	1017	0	ENST00000263253.7:c.5851C>T	p.Pro1951Ser	p.P1951S	ENST00000263253	NM_001429.3	1951	Cca/Tca	31/31	1	2	FACETS	0.845	0.752	0.945	0.845	0.752	0.945	CLONAL	1	TRUE	1	0.239053102006731	2		1017	960	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0054770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	224	863	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.395708157193122	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.395708157193122	1		864	849	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0054770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	115	422	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.395708157193122	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.395708157193122	1		422	443	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280094	115280094	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	171	573	0	ENST00000438362.2:c.538G>C	p.Gly180Arg	p.G180R	ENST00000438362	NM_001242891.1	180	Ggg/Cgg	5/20	1	2	FACETS	0.959	0.883	1	0.959	0.883	1	CLONAL	1	TRUE	1	0.395708157193122	2		573	901	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943335	71943335	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	175	956	0	ENST00000298229.2:c.1667G>T	p.Gly556Val	p.G556V	ENST00000298229	NM_001567.3	556	gGc/gTc	14/28	1	2	FACETS	0.842	0.774	0.912	0.842	0.774	0.912	CLONAL	1	TRUE	1	0.395708157193122	2		956	1051	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362642	118362642	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	89	406	0	ENST00000534358.1:c.5003A>T	p.Gln1668Leu	p.Q1668L	ENST00000534358	NM_005933.3	1668	cAg/cTg	15/36	1	2	FACETS	0.865	0.769	0.967	0.865	0.769	0.967	CLONAL	1	TRUE	1	0.395708157193122	2		406	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	672	1219	0	ENST00000269305.4:c.380C>A	p.Ser127Tyr	p.S127Y	ENST00000269305	NM_001126112.2	127	tCc/tAc	5/11	0.912929543830791	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.912929543830791	1		1219	788	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0054772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	19	415	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.963	0.738	1	0.963	0.738	1	CLONAL	1	TRUE	1	0.28	2		415	141	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710652	114710652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1177321517	NA	P-0054772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	39	536	0	ENST00000543371.1:c.137C>T	p.Ser46Leu	p.S46L	ENST00000543371	NM_001198531.1	46	tCg/tTg	1/14	0.3	1	FACETS	0.644	0.535	0.765	0.644	0.535	0.765	SUBCLONAL	1	TRUE	0	0.28	1		536	372	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218538	5218538	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	57	977	0	ENST00000357368.4:c.3941G>T	p.Arg1314Leu	p.R1314L	ENST00000357368	NM_002850.3	1314	cGc/cTc	25/38	1	2	FACETS	0.784	0.674	0.905	0.784	0.674	0.905	CLONAL	1	TRUE	1	0.28	2		977	519	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132573	11132573	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	68	1144	1	ENST00000358026.2:c.2789C>T	p.Pro930Leu	p.P930L	ENST00000358026	NM_001128849.1	930	cCc/cTc	19/36	1	2	FACETS	0.676	0.587	0.772	0.676	0.587	0.772	SUBCLONAL	1	TRUE	1	0.28	2		1145	719	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164877	36164878	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	81	1056	0	ENST00000300305.3:c.997_998insT	p.Pro333LeufsTer267	p.P333Lfs*267	ENST00000300305		333	ccg/cTcg	8/8	1	2	FACETS	0.84	0.74	0.947	0.84	0.74	0.947	CLONAL	1	TRUE	1	0.28	2		1056	689	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098957	47098957	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	36	604	0	ENST00000409792.3:c.6317del	p.Lys2106ArgfsTer41	p.K2106Rfs*41	ENST00000409792	NM_014159.6	2106	aAg/ag	15/21	0.0642600035538563	3	FACETS	0.952	0.785	1	0.476	0.392	0.569	INDETERMINATE	1	TRUE	1	0.28	3		604	308	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162273	47162273	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0054772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	50	503	0	ENST00000409792.3:c.3853A>T	p.Lys1285Ter	p.K1285*	ENST00000409792	NM_014159.6	1285	Aag/Tag	3/21	0.0642600035538563	3	FACETS	1	0.942	1	0.611	0.521	0.71	INDETERMINATE	1	TRUE	1	0.28	3		503	333	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169992	32169992	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	76	1263	0	ENST00000375023.3:c.3616G>T	p.Gly1206Ter	p.G1206*	ENST00000375023	NM_004557.3	1206	Gga/Tga	21/30	0.121505084647423	5	FACETS	1	0.95	1	0.388	0.34	0.44	INDETERMINATE	1	TRUE	2	0.28	5		1263	662	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117861238	117861238	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	21	468	0	ENST00000297338.2:c.1651C>G	p.Gln551Glu	p.Q551E	ENST00000297338	NM_006265.2	551	Cag/Gag	13/14	1	2	FACETS	0.636	0.491	0.803	0.636	0.491	0.803	SUBCLONAL	1	TRUE	1	0.28	2		468	236	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231343	98231343	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	50	903	1	ENST00000331920.6:c.1940G>T	p.Ser647Ile	p.S647I	ENST00000331920	NM_000264.3	647	aGc/aTc	14/24	0.3	1	FACETS	0.557	0.473	0.651	0.557	0.473	0.651	SUBCLONAL	1	TRUE	0	0.28	1		904	551	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045724	47045724	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1556782610	NA	P-0054772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	86	1444	0	ENST00000377604.3:c.2605A>G	p.Met869Val	p.M869V	ENST00000377604	NM_001204468.1	869	Atg/Gtg	23/24	0.3	1	FACETS	0.813	0.719	0.913	0.813	0.719	0.913	CLONAL	1	TRUE	0	0.28	1		1444	650	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252155	226252155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	91	184	0	ENST00000366813.1:c.103G>T	p.Gly35Trp	p.G35W	ENST00000366813		35	Ggg/Tgg	1/3	0.219534178216649	4	FACETS	1	0.936	1	1	0.985	1	INDETERMINATE	3	TRUE	2	0.398122209193197	4		184	205	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028785	47028785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2697	157	1410	4	ENST00000377604.3:c.89G>A	p.Arg30His	p.R30H	ENST00000377604	NM_001204468.1	30	cGc/cAc	3/24	0.543122889989203	9	FACETS	0.588	0.535	0.643			1	SUBCLONAL	1	TRUE	NA	0.543122889989203	9		1414	2854	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778877	76778878	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0054775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	156	485	0	ENST00000373344.5:c.6701_6702insGG	p.Asp2234GlufsTer17	p.D2234Efs*17	ENST00000373344	NM_000489.3	2234	gat/gaGGt	31/35	0.466842096726447	3	FACETS	0.84	0.776	0.904			1	CLONAL	2	TRUE	NA	0.543122889989203	3		485	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572984	7572984	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs730882017	NA	P-0054777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	321	660	0	ENST00000269305.4:c.1125del	p.Gln375HisfsTer47	p.Q375Hfs*47	ENST00000269305	NM_001126112.2	375	caG/ca	11/11	0.701276954217634	2	FACETS	0.96	0.923	0.996	0.96	0.923	0.996	CLONAL	2	TRUE	0	0.704129493450493	2		660	475	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877880	151877880	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	216	474	0	ENST00000262189.6:c.7065del	p.Pro2356LeufsTer9	p.P2356Lfs*9	ENST00000262189	NM_170606.2	2355	ctT/ct	36/59	0.704129493450493	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.704129493450493	4		474	479	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0054778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	166	802	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	0.994	0.923	1	0.994	0.923	1	CLONAL	1	TRUE	1	0.799274220737903	2		802	418	SUCCESS
APC	324	MSKCC	GRCh37	5	112155032	112155032	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554080162	NA	P-0054778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	120	707	0	ENST00000257430.4:c.1307del	p.Asn436IlefsTer18	p.N436Ifs*18	ENST00000257430	NM_000038.5	435	Aaa/aa	10/16	0.752101398108844	1	FACETS	0.777	0.718	0.835	0.777	0.718	0.835	SUBCLONAL	1	TRUE	0	0.799274220737903	1		707	232	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29115459	29115460	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886039609	NA	P-0054778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	79	398	0	ENST00000328354.6:c.606dup	p.Asp203Ter	p.D203*	ENST00000328354	NM_007194.3	202	-/T	5/15	1	2	FACETS	0.903	0.808	1	0.903	0.808	1	CLONAL	1	TRUE	1	0.799274220737903	2		398	219	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396166	396166	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	156	960	0	ENST00000262320.3:c.860G>T	p.Ser287Ile	p.S287I	ENST00000262320	NM_003502.3	287	aGc/aTc	2/11	0.403850432347613	1	FACETS	0.522	0.482	0.563	0.522	0.482	0.563	INDETERMINATE	1	TRUE	0	0.799274220737903	1		960	449	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0054779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	125	234	3				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.954	0.874	1	1	0.993	1	CLONAL	5	TRUE	1	0.15420494260144	2		237	340	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099403	157099429	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAGCAACAG	CAGCAGCAGCAGCAGCAGCAGCAACAG	-	rs910569810	NA	P-0054779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	32	475	0	ENST00000346085.5:c.360_386del	p.Gln123_Gln131del	p.Q123_Q131del	ENST00000346085	NM_020732.3	114	CAGCAGCAGCAGCAGCAGCAGCAACAG/-	1/20	1	2	FACETS	0.751	0.608	0.912	0.751	0.608	0.912	CLONAL	1	TRUE	1	0.15420494260144	2		475	553	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089487	27089488	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0054779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	246	1067	0	ENST00000324856.7:c.2445_2446del	p.Tyr815Ter	p.Y815*	ENST00000324856	NM_006015.4	815	TAt/t	8/20	1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	1	0.15420494260144	2		1067	1301	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156149	119156149	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	265	884	0	ENST00000264033.4:c.1814C>G	p.Ser605Cys	p.S605C	ENST00000264033	NM_005188.3	605	tCc/tGc	11/16	0.151288918153832	1	FACETS	0.984	0.923	1	1	0.996	1	CLONAL	3	TRUE	0	0.15420494260144	1		884	1074	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245811	46245811	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0054779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	171	572	0	ENST00000334344.6:c.3905C>G	p.Ser1302Ter	p.S1302*	ENST00000334344	NM_152641.2	1302	tCa/tGa	15/21	0.15420494260144	1	FACETS	0.893	0.826	0.962	1	0.994	1	CLONAL	4	TRUE	0	0.15420494260144	1		572	573	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929140	32929140	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	220	625	0	ENST00000380152.3:c.7150C>T	p.Gln2384Ter	p.Q2384*	ENST00000380152		2384	Caa/Taa	14/27	1	2	FACETS	1	0.957	1	1	0.995	1	CLONAL	3	TRUE	1	0.15420494260144	2		625	917	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50816365	50816365	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0054779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	106	379	0	ENST00000398568.2:c.1805C>G	p.Ser602Ter	p.S602*	ENST00000398568	NM_001042412.1	602	tCa/tGa	10/18	1	2	FACETS	0.842	0.758	0.932	1	0.99	1	CLONAL	3	TRUE	1	0.15420494260144	2		379	544	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615780	1615780	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	364	1227	0	ENST00000344749.5:c.1491C>G	p.Ile497Met	p.I497M	ENST00000344749	NM_001136139.2	497	atC/atG	17/19	0.151288918153832	1	FACETS	1	0.976	1	1	0.997	1	CLONAL	3	TRUE	0	0.15420494260144	1		1227	1383	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15379772	15379772	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	140	646	0	ENST00000263377.2:c.367C>T	p.Gln123Ter	p.Q123*	ENST00000263377	NM_058243.2	123	Cag/Tag	3/20	0.151288918153832	1	FACETS	1	0.934	1	1	0.991	1	CLONAL	2	TRUE	0	0.15420494260144	1		646	813	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257130	198257130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	131	550	0	ENST00000335508.6:c.3812C>A	p.Ser1271Tyr	p.S1271Y	ENST00000335508	NM_012433.2	1271	tCc/tAc	25/25	0.15420494260144	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.15420494260144	2		550	761	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652072	36652072	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1539	323	1568	0	ENST00000244741.5:c.194G>T	p.Trp65Leu	p.W65L	ENST00000244741	NM_000389.4	65	tGg/tTg	2/3	1	2	FACETS	1	0.984	1	1	0.996	1	CLONAL	2	TRUE	1	0.15420494260144	2		1568	1862	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942750	68942750	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	126	577	0	ENST00000288368.4:c.562C>T	p.Pro188Ser	p.P188S	ENST00000288368	NM_024870.2	188	Cca/Tca	6/40	0.15420494260144	2	FACETS	0.973	0.881	1	0.973	0.881	1	CLONAL	2	TRUE	0	0.15420494260144	2		577	840	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396239	139396239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1370	379	1483	0	ENST00000277541.6:c.5599G>A	p.Val1867Ile	p.V1867I	ENST00000277541	NM_017617.3	1867	Gtt/Att	30/34	1	2	FACETS	0.937	0.887	0.988	1	0.997	1	CLONAL	3	TRUE	1	0.15420494260144	2		1483	1749	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	52	290	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.849	0.727	0.98	0.849	0.727	0.98	CLONAL	1	FALSE	1	0.415453342508737	2		291	295	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0054781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	46	333	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.852	0.723	0.992	0.852	0.723	0.992	CLONAL	1	FALSE	1	0.415453342508737	2		333	260	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549725	187549725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199516712	NA	P-0054781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	97	536	2	ENST00000441802.2:c.4516C>T	p.Arg1506Cys	p.R1506C	ENST00000441802	NM_005245.3	1506	Cgt/Tgt	8/27	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	FALSE	1	0.415453342508737	2		538	446	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0054781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	181	424	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.415453342508737	4	FACETS	1	0.982	1	0.78	0.725	0.837	CLONAL	2	FALSE	1	0.415453342508737	4		424	527	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494149	140494149	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	421	885	0	ENST00000288602.6:c.1099C>T	p.Pro367Ser	p.P367S	ENST00000288602	NM_004333.4	367	Ccc/Tcc	8/18	0.415453342508737	4	FACETS	0.937	0.896	0.979	0.937	0.896	0.979	CLONAL	3	FALSE	1	0.415453342508737	4		885	1020	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432753	78432753	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755383241	NA	P-0054781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	53	474	0	ENST00000370768.2:c.323C>T	p.Pro108Leu	p.P108L	ENST00000370768	NM_003902.3	108	cCa/cTa	5/20	1	2	FACETS	0.675	0.578	0.781	0.675	0.578	0.781	SUBCLONAL	1	FALSE	1	0.415453342508737	2		474	378	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425632	49425632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	187	1202	1	ENST00000301067.7:c.12856C>T	p.Pro4286Ser	p.P4286S	ENST00000301067	NM_003482.3	4286	Cca/Tca	39/54	1	2	FACETS	0.946	0.874	1	0.946	0.874	1	CLONAL	1	FALSE	1	0.415453342508737	2		1203	952	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640259	3640259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	225	1378	0	ENST00000294008.3:c.3380C>T	p.Thr1127Ile	p.T1127I	ENST00000294008	NM_032444.2	1127	aCc/aTc	12/15	1	2	FACETS	0.953	0.887	1	0.953	0.887	1	CLONAL	1	FALSE	1	0.415453342508737	2		1378	1136	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936331	49936331	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	191	976	0	ENST00000296474.3:c.1517G>A	p.Gly506Glu	p.G506E	ENST00000296474	NM_002447.2	506	gGg/gAg	3/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.415453342508737	2		976	853	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111417	56111417	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	106	421	0	ENST00000399503.3:c.17G>A	p.Gly6Glu	p.G6E	ENST00000399503	NM_005921.1	6	gGg/gAg	1/20	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	FALSE	1	0.415453342508737	2		421	508	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048108	180048108	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	188	1272	0	ENST00000261937.6:c.2165C>T	p.Ser722Phe	p.S722F	ENST00000261937	NM_182925.4	722	tCt/tTt	14/30	1	2	FACETS	0.903	0.834	0.975	0.903	0.834	0.975	CLONAL	1	FALSE	1	0.415453342508737	2		1272	1002	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163898	152163898	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	96	619	0	ENST00000206249.3:c.619G>C	p.Ala207Pro	p.A207P	ENST00000206249	NM_000125.3	207	Gcc/Ccc	2/8	1	2	FACETS	0.93	0.832	1	0.93	0.832	1	CLONAL	1	FALSE	1	0.415453342508737	2		619	497	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779798	135779798	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs118203624	NA	P-0054781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	35	537	0	ENST00000298552.3:c.2041G>A	p.Gly681Ser	p.G681S	ENST00000298552	NM_001162426.1	681	Ggc/Agc	16/23	0.415453342508737	0	FACETS	0.221	0.181	0.266			1	SUBCLONAL	1	FALSE	0	0.415453342508737	0		537	446	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	121	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.144225804703423	3	FACETS	0.827	0.756	0.9	0.551	0.504	0.6	INDETERMINATE	2	TRUE	0	0.546157788589087	3		487	341	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0054782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	389	1025	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.546157788589087	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.546157788589087	1		1026	807	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0054782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	79	383	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.546157788589087	1	FACETS	0.773	0.688	0.862	0.773	0.688	0.862	SUBCLONAL	1	TRUE	0	0.546157788589087	1		383	272	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0054782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	113	511	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.546157788589087	2		511	381	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243866	46243866	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	65	400	0	ENST00000334344.6:c.1960C>T	p.Pro654Ser	p.P654S	ENST00000334344	NM_152641.2	654	Cct/Tct	15/21	0.144225804703423	3	FACETS	0.894	0.78	1	0.298	0.26	0.339	INDETERMINATE	1	TRUE	0	0.546157788589087	3		400	339	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523501	106523501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373006568	NA	P-0054782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	30	280	0	ENST00000359195.3:c.2653G>A	p.Ala885Thr	p.A885T	ENST00000359195	NM_002649.2	885	Gcc/Acc	8/11	1	2	FACETS	0.327	0.264	0.399	0.327	0.264	0.399	SUBCLONAL	1	TRUE	1	0.546157788589087	2		280	336	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667607	29667607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781428	NA	P-0054782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	63	762	1	ENST00000356175.3:c.6943G>A	p.Ala2315Thr	p.A2315T	ENST00000356175	NM_000267.3	2315	Gca/Aca	46/57	0.186991014741209	2	FACETS	0.284	0.245	0.327	0.142	0.122	0.164	INDETERMINATE	1	TRUE	0	0.546157788589087	2		763	812	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186835	11186835	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	40	560	0	ENST00000361445.4:c.6370C>T	p.Gln2124Ter	p.Q2124*	ENST00000361445	NM_004958.3	2124	Caa/Taa	46/58	0.479660903021194	1	FACETS	0.228	0.189	0.271	0.228	0.189	0.271	SUBCLONAL	1	TRUE	0	0.546157788589087	1		560	467	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73343028	73343028	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	45	267	0	ENST00000377767.4:c.1778C>T	p.Ala593Val	p.A593V	ENST00000377767	NM_014953.3	593	gCt/gTt	14/21	0.271715585675083	4	FACETS	0.894	0.756	1	0.223	0.189	0.262	INDETERMINATE	1	TRUE	0	0.546157788589087	4		267	285	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537956	212537956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771898021	NA	P-0054782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	172	594	1	ENST00000342788.4:c.1649C>T	p.Ser550Phe	p.S550F	ENST00000342788	NM_005235.2	550	tCc/tTc	14/28	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.546157788589087	2		595	615	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944604	40944604	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	137	470	0	ENST00000373198.4:c.1898T>C	p.Leu633Pro	p.L633P	ENST00000373198	NM_133170.3	633	cTt/cCt	12/32	0.546157788589087	3	FACETS	0.923	0.841	1	0.461	0.42	0.504	CLONAL	1	TRUE	1	0.546157788589087	3		470	692	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907091	101907091	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	229	416	0	ENST00000374994.4:c.1051G>C	p.Asp351His	p.D351H	ENST00000374994	NM_004612.2	351	Gac/Cac	6/9	0.546157788589087	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	0	0.546157788589087	3		416	341	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923059	39923059	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	375	978	2	ENST00000378444.4:c.3649del	p.Arg1217AspfsTer21	p.R1217Dfs*21	ENST00000378444	NM_001123385.1	1217	Cga/ga	8/15	0.186991014741209	2	FACETS	0.761	0.726	0.797	0.761	0.726	0.797	INDETERMINATE	2	TRUE	0	0.546157788589087	2		980	902	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0054783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	161	1045	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.140313636311437	2	FACETS	0.825	0.756	0.898	0.825	0.756	0.898	CLONAL	2	TRUE	0	0.18367525435488	2		1046	1062	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	26	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.140313636311437	2	FACETS	0.642	0.508	0.796	0.321	0.254	0.398	SUBCLONAL	1	TRUE	0	0.18367525435488	2		487	441	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0054783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	23	424	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	1	2	FACETS	0.596	0.464	0.75	0.596	0.464	0.75	SUBCLONAL	1	TRUE	1	0.18367525435488	2		424	420	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344285	118344285	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	37	467	0	ENST00000534358.1:c.2411C>G	p.Thr804Ser	p.T804S	ENST00000534358	NM_005933.3	804	aCt/aGt	3/36	1	2	FACETS	0.785	0.647	0.941	0.785	0.647	0.941	CLONAL	1	TRUE	1	0.18367525435488	2		467	513	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	271	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.719931857076126	2	FACETS	0.959	0.925	0.992	0.959	0.925	0.992	CLONAL	2	TRUE	0	0.800418211695972	2		457	353	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221318	1221319	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	T	novel	NA	P-0054784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	1233	1261	1	ENST00000326873.7:c.841_842delinsT	p.Pro281CysfsTer6	p.P281Cfs*6	ENST00000326873	NM_000455.4	281	CCg/Tg	6/10	0.800418211695972	3	FACETS	0.868	0.852	0.883	0.868	0.852	0.883	CLONAL	3	TRUE	0	0.800418211695972	3		1262	1657	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066583	94066583	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	444	625	0	ENST00000369303.4:c.1176G>T	p.Gln392His	p.Q392H	ENST00000369303	NM_004440.3	392	caG/caT	5/17	0.800418211695972	3	FACETS	0.987	0.95	1	0.987	0.95	1	CLONAL	2	TRUE	1	0.800418211695972	3		625	787	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11297977	11297977	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	395	944	0	ENST00000361445.4:c.2131G>A	p.Ala711Thr	p.A711T	ENST00000361445	NM_004958.3	711	Gcc/Acc	13/58	0.800418211695972	3	FACETS	0.88	0.835	0.926	0.44	0.417	0.463	CLONAL	1	TRUE	1	0.800418211695972	3		944	1570	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949347	71949347	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	940	1242	0	ENST00000298229.2:c.3727G>C	p.Asp1243His	p.D1243H	ENST00000298229	NM_001567.3	1243	Gac/Cac	28/28	0.800418211695972	3	FACETS	0.967	0.941	0.992	0.967	0.941	0.992	CLONAL	2	TRUE	1	0.800418211695972	3		1242	1701	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118758	115118758	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	622	776	0	ENST00000257566.3:c.583G>T	p.Glu195Ter	p.E195*	ENST00000257566	NM_016569.3	195	Gaa/Taa	2/8	0.719931857076126	2	FACETS	0.932	0.909	0.954	0.932	0.909	0.954	CLONAL	2	TRUE	0	0.800418211695972	2		776	834	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95596476	95596476	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	159	400	0	ENST00000393063.1:c.492A>T	p.Leu164Phe	p.L164F	ENST00000393063	NM_030621.3	164	ttA/ttT	6/28	0.800418211695972	4	FACETS	0.866	0.803	0.93	0.866	0.803	0.93	CLONAL	2	TRUE	2	0.800418211695972	4		400	413	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95597923	95597923	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	217	502	0	ENST00000393063.1:c.361G>T	p.Val121Phe	p.V121F	ENST00000393063	NM_030621.3	121	Gtt/Ttt	5/28	0.800418211695972	4	FACETS	1	0.991	1	0.718	0.671	0.766	CLONAL	1	TRUE	2	0.800418211695972	4		502	680	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274012	10274012	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2279	631	1468	0	ENST00000330684.3:c.257T>C	p.Val86Ala	p.V86A	ENST00000330684	NM_001134407.1	86	gTg/gCg	2/13	0.519281312250819	6	FACETS	1	0.996	1	0.47	0.45	0.49	CLONAL	1	TRUE	3	0.800418211695972	6		1468	2910	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	708	828	0	ENST00000269305.4:c.706del	p.Tyr236ThrfsTer11	p.Y236Tfs*11	ENST00000269305	NM_001126112.2	236	Tac/ac	7/11	0.669935163567146	3	FACETS	1	0.997	1	0.802	0.782	0.823	CLONAL	2	TRUE	0	0.800418211695972	3		828	1029	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957426	1957426	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs893318704	NA	P-0054784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	201	813	0	ENST00000382891.5:c.2525G>A	p.Ser842Asn	p.S842N	ENST00000382891	NM_133335.3	842	aGc/aAc	14/22	NA	2	FACETS	0.544	0.504	0.585			1	INDETERMINATE	1	TRUE	NA	0.800418211695972	2		813	923	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120437	94120437	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	90	449	0	ENST00000369303.4:c.614G>T	p.Cys205Phe	p.C205F	ENST00000369303	NM_004440.3	205	tGc/tTc	3/17	0.800418211695972	3	FACETS	0.68	0.606	0.758	0.34	0.303	0.379	SUBCLONAL	1	TRUE	1	0.800418211695972	3		449	463	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135777992	135777992	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	963	666	0	ENST00000298552.3:c.2391G>C	p.Gln797His	p.Q797H	ENST00000298552	NM_001162426.1	797	caG/caC	18/23	0.708996306796038	4	FACETS	0.966	0.952	0.98	0.966	0.952	0.98	CLONAL	4	TRUE	0	0.800418211695972	4		666	1121	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396309	139396309	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2029	254	1496	0	ENST00000277541.6:c.5529G>A	p.Trp1843Ter	p.W1843*	ENST00000277541	NM_017617.3	1843	tgG/tgA	30/34	0.708996306796038	4	FACETS	0.501	0.466	0.537	0.125	0.116	0.135	SUBCLONAL	1	TRUE	0	0.800418211695972	4		1496	2283	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0054785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	16	213	0	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	1	1	FACETS	1	0.781	1	1	0.781	1	CLONAL	1	TRUE	0	0.12	1		213	236	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949116	71949116	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	66	1202	0	ENST00000298229.2:c.3585del	p.Leu1196TrpfsTer6	p.L1196Wfs*6	ENST00000298229	NM_001567.3	1195	Ggg/gg	27/28	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.12	2		1202	1097	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724445	724445	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054793-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	162	800	0	ENST00000314574.4:c.1611C>A	p.Tyr537Ter	p.Y537*	ENST00000314574	NM_005433.3	537	taC/taA	12/12	1	2	FACETS	0.904	0.83	0.981	0.904	0.83	0.981	CLONAL	1	TRUE	1	0.421696253874096	2		800	850	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0054804-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	274	115	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	0.895505861180869	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.895505861180869	3		115	415	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740537	58740537	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs770558142	NA	P-0054804-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	1098	727	0	ENST00000305921.3:c.1444del	p.Leu482Ter	p.L482*	ENST00000305921	NM_003620.3	481	gCc/gc	6/6	0.895505861180869	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.895505861180869	3		727	1712	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	30	290	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.713	0.576	0.867	0.713	0.576	0.867	SUBCLONAL	1	TRUE	1	0.291323424385364	2		291	289	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0054808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	95	670	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.291323424385364	2		670	613	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356359	66356359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199650353	NA	P-0054808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	41	554	0	ENST00000273854.3:c.1138C>T	p.Pro380Ser	p.P380S	ENST00000273854	NM_004439.5	380	Cct/Tct	5/18	0.291323424385364	1	FACETS	0.397	0.33	0.472	0.397	0.33	0.472	SUBCLONAL	1	TRUE	0	0.291323424385364	1		554	606	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087907	27087907	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	175	867	0	ENST00000324856.7:c.2194C>T	p.Gln732Ter	p.Q732*	ENST00000324856	NM_006015.4	732	Cag/Tag	6/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.291323424385364	2		867	910	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752888	42752888	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	117	1283	0	ENST00000222329.4:c.1376C>G	p.Ala459Gly	p.A459G	ENST00000222329	NM_006494.2	459	gCc/gGc	4/4	1	2	FACETS	0.775	0.697	0.857	0.775	0.697	0.857	SUBCLONAL	1	TRUE	1	0.291323424385364	2		1283	1037	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456701	32456701	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	40	790	0	ENST00000332351.3:c.191C>G	p.Ser64Cys	p.S64C	ENST00000332351	NM_024426.4	64	tCt/tGt	1/10	1	2	FACETS	0.5	0.415	0.595	0.5	0.415	0.595	SUBCLONAL	1	TRUE	1	0.291323424385364	2		790	549	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74000697	74000697	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	59	935	0	ENST00000318443.5:c.1387C>A	p.Pro463Thr	p.P463T	ENST00000318443	NM_001024736.1	463	Ccc/Acc	7/10	1	2	FACETS	0.45	0.385	0.52	0.45	0.385	0.52	SUBCLONAL	1	TRUE	1	0.291323424385364	2		935	901	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733358	40733358	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	33	536	0	ENST00000373198.4:c.3448G>A	p.Glu1150Lys	p.E1150K	ENST00000373198	NM_133170.3	1150	Gag/Aag	26/32	0.244632411013991	1	FACETS	0.391	0.318	0.474	0.391	0.318	0.474	SUBCLONAL	1	TRUE	0	0.291323424385364	1		536	495	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061097	38061228	+	inframe_deletion	In_Frame_Del	DEL	AGGGGTCCTTGCGGCTCTCAGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTGGCGGCGCAAGTAGCAGCCGTTCTCGA	AGGGGTCCTTGCGGCTCTCAGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTGGCGGCGCAAGTAGCAGCCGTTCTCGA	-	novel	NA	P-0054809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	10	343	0	ENST00000250448.2:c.761_892del	p.Phe254_Pro297del	p.F254_P297del	ENST00000250448	NM_004496.3	254	tTCGAGAACGGCTGCTACTTGCGCCGCCAGAAGCGCTTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGGCGCCAAGGGCGGCCCTGAGAGCCGCAAGGACCCCTct/tct	2/2	1	2	FACETS	0.585	0.395	0.825	0.585	0.395	0.825	SUBCLONAL	1	TRUE	1	0.11	2		343	311	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984350	201984351	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0054811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	329	839	0	ENST00000359651.3:c.1018dup	p.Glu340GlyfsTer131	p.E340Gfs*131	ENST00000359651		339	cgg/cGgg	8/8	0.294479332695829	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.351030223086974	3		839	1013	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849587	68849587	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	163	1002	0	ENST00000261769.5:c.1490A>G	p.Glu497Gly	p.E497G	ENST00000261769	NM_004360.3	497	gAg/gGg	10/16	0.294479332695829	3	FACETS	1	0.936	1	0.513	0.47	0.558	CLONAL	1	TRUE	1	0.351030223086974	3		1002	1065	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578228	7578228	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	300	944	0	ENST00000269305.4:c.621del	p.Asp207GlufsTer40	p.D207Efs*40	ENST00000269305	NM_001126112.2	207	gaT/ga	6/11	0.345311453702842	2	FACETS	0.996	0.941	1	0.996	0.941	1	CLONAL	2	TRUE	0	0.351030223086974	2		944	858	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514647	44514647	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	145	769	0	ENST00000291552.4:c.509A>G	p.Asn170Ser	p.N170S	ENST00000291552	NM_006758.2	170	aAc/aGc	7/8	0.294479332695829	3	FACETS	1	0.955	1	0.537	0.489	0.586	CLONAL	1	TRUE	1	0.351030223086974	3		769	905	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843420	128843420	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	220	687	0	ENST00000249373.3:c.528del	p.Gly177AlafsTer125	p.G177Afs*125	ENST00000249373	NM_005631.4	176	gAa/ga	2/12	0.351030223086974	5	FACETS	0.808	0.751	0.867	0.539	0.5	0.578	CLONAL	2	TRUE	2	0.351030223086974	5		687	1184	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44911033	44911034	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	117	240	0	ENST00000377967.4:c.735dup	p.Gln247ThrfsTer16	p.Q247Tfs*16	ENST00000377967	NM_021140.2	245	gtc/gtCc	9/29	0.316995137796042	2	FACETS	0.848	0.779	0.918			1	CLONAL	3	TRUE	NA	0.351030223086974	2		240	262	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149798	202149799	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	65	582	0	ENST00000358485.4:c.1245dup	p.Ile416TyrfsTer8	p.I416Yfs*8	ENST00000358485	NM_001080125.1	413	-/T	8/9	1	2	FACETS	0.709	0.613	0.814	0.709	0.613	0.814	SUBCLONAL	1	TRUE	1	0.206637623013831	2		582	887	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932018	39932018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367736022	NA	P-0054812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	95	743	0	ENST00000378444.4:c.2581C>T	p.Arg861Cys	p.R861C	ENST00000378444	NM_001123385.1	861	Cgc/Tgc	4/15	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.206637623013831	2		743	897	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512270	38512270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866777491	NA	P-0054812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	73	747	0	ENST00000254066.5:c.1181G>A	p.Arg394Gln	p.R394Q	ENST00000254066	NM_000964.3	394	cGg/cAg	9/9	1	2	FACETS	0.789	0.689	0.898	0.789	0.689	0.898	SUBCLONAL	1	TRUE	1	0.206637623013831	2		747	895	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434444	49434444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373234419	NA	P-0054812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	84	834	1	ENST00000301067.7:c.7109G>A	p.Arg2370His	p.R2370H	ENST00000301067	NM_003482.3	2370	cGc/cAc	31/54	1	2	FACETS	0.801	0.706	0.904	0.801	0.706	0.904	CLONAL	1	TRUE	1	0.206637623013831	2		835	1015	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847243	68847257	+	inframe_deletion	In_Frame_Del	DEL	GCTAACGTCGTAATC	GCTAACGTCGTAATC	-	novel	NA	P-0054812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	59	510	0	ENST00000261769.5:c.1165_1179del	p.Ala389_Ile393del	p.A389_I393del	ENST00000261769	NM_004360.3	389	GCTAACGTCGTAATC/-	9/16	1	2	FACETS	0.941	0.809	1	0.941	0.809	1	CLONAL	1	TRUE	1	0.206637623013831	2		510	607	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0054813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	254	449	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.615418165701171	3	FACETS	0.9	0.858	0.94	0.9	0.858	0.94	CLONAL	3	TRUE	0	0.615418165701171	3		449	400	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0054813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	257	563	0	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	NA	2	FACETS	0.922	0.877	0.967			1	INDETERMINATE	2	TRUE	NA	0.615418165701171	2		563	453	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446458	49446458	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	471	522	1	ENST00000301067.7:c.1147G>T	p.Asp383Tyr	p.D383Y	ENST00000301067	NM_003482.3	383	Gac/Tac	9/54	0.615418165701171	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	0	0.615418165701171	3		523	661	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220701	1220701	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730881976	NA	P-0054813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	341	782	0	ENST00000326873.7:c.719C>G	p.Ser240Trp	p.S240W	ENST00000326873	NM_000455.4	240	tCg/tGg	5/10	0.615418165701171	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.615418165701171	2		782	543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577546	7577548	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	novel	NA	P-0054814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	487	620	0	ENST00000269305.4:c.733_735del	p.Gly245del	p.G245del	ENST00000269305	NM_001126112.2	245	GGC/-	7/11	0.597712159169042	2	FACETS	0.817	0.789	0.844	0.817	0.789	0.844	CLONAL	2	TRUE	0	0.758471351503239	2		620	786	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639921	3639921	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758413469	NA	P-0054814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	150	810	1	ENST00000294008.3:c.3718G>A	p.Asp1240Asn	p.D1240N	ENST00000294008	NM_032444.2	1240	Gac/Aac	12/15	0.352969169586283	1	FACETS	0.295	0.27	0.322	0.295	0.27	0.322	INDETERMINATE	1	TRUE	0	0.758471351503239	1		811	832	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197235	26197235	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	336	551	0	ENST00000356476.2:c.244G>C	p.Asp82His	p.D82H	ENST00000356476		82	Gat/Cat	1/1	0.296114577227955	4	FACETS	1	0.994	1	0.456	0.431	0.481	INDETERMINATE	1	TRUE	1	0.758471351503239	4		551	1139	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671663	30671663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	203	679	0	ENST00000376406.3:c.5297C>T	p.Ser1766Phe	p.S1766F	ENST00000376406	NM_014641.2	1766	tCc/tTc	10/15	NA	2	FACETS	0.71	0.66	0.761			1	INDETERMINATE	1	TRUE	NA	0.758471351503239	2		679	754	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6439793	6439793	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	116	410	0	ENST00000356142.4:c.319G>C	p.Ala107Pro	p.A107P	ENST00000356142	NM_018890.3	107	Gca/Cca	5/7	0.294011694940863	1	FACETS	0.244	0.22	0.27	0.244	0.22	0.27	INDETERMINATE	1	TRUE	0	0.758471351503239	1		410	778	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0054815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	443	664	2	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.462081030422437	2	FACETS	0.962	0.923	1	0.962	0.923	1	CLONAL	2	TRUE	0	0.508275006575016	2		666	906	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422955	45422955	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	53	460	0	ENST00000262160.6:c.173del	p.Leu58Ter	p.L58*	ENST00000262160	NM_005901.5	58	tTa/ta	2/11	1	2	FACETS	0.332	0.282	0.386	0.332	0.282	0.386	SUBCLONAL	1	TRUE	1	0.508275006575016	2		460	629	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0054816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	69	670	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.261156115582047	2		670	436	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0054816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	66	457	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.261156115582047	2		457	483	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0054816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	60	397	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.823	0.71	0.947	0.823	0.71	0.947	CLONAL	1	TRUE	1	0.261156115582047	2		397	558	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047151	77047151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	88	610	0	ENST00000356341.3:c.1393C>T	p.Leu465Phe	p.L465F	ENST00000356341	NM_002576.4	465	Ctc/Ttc	13/15	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.261156115582047	2		610	634	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650367	48650367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782263736	NA	P-0054816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	156	1007	2	ENST00000376670.3:c.337C>T	p.Arg113Cys	p.R113C	ENST00000376670	NM_002049.3	113	Cgc/Tgc	3/6	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.261156115582047	2		1009	1041	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717714	89717714	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167662	NA	P-0054816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	143	480	0	ENST00000371953.3:c.740del	p.Leu247TyrfsTer9	p.L247Yfs*9	ENST00000371953	NM_000314.4	247	Tta/ta	7/9	0.24866368592666	2	FACETS	0.942	0.863	1	0.942	0.863	1	CLONAL	2	TRUE	0	0.261156115582047	2		480	581	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351830	89351830	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	144	843	0	ENST00000301030.4:c.1120G>C	p.Glu374Gln	p.E374Q	ENST00000301030	NM_001256183.1	374	Gaa/Caa	9/13	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.261156115582047	2		843	1049	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0054817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	301	780	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.780353391000974	1	FACETS	0.993	0.951	1	0.993	0.951	1	CLONAL	1	TRUE	0	0.780353391000974	1		780	474	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1206936	1206936	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1379630288	NA	P-0054817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	457	678	0	ENST00000326873.7:c.24G>C	p.Gln8His	p.Q8H	ENST00000326873	NM_000455.4	8	caG/caC	1/10	0.780353391000974	1	FACETS	0.965	0.932	0.998	0.965	0.932	0.998	CLONAL	1	TRUE	0	0.780353391000974	1		678	740	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	77	415	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA	2	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.360246662849027	2		415	307	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726618	41726618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	250	244	0	ENST00000301178.4:c.163C>T	p.Arg55Trp	p.R55W	ENST00000301178	NM_021913.4	55	Cgg/Tgg	2/20	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.360246662849027	2		244	926	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	241	237	0	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.360246662849027	2		237	1029	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	183	120	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.901	0.844	0.957	1	0.995	1	CLONAL	3	TRUE	1	0.360246662849027	2		120	376	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	103	109	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	0.769	0.694	0.846	1	0.984	1	SUBCLONAL	2	TRUE	1	0.360246662849027	2		109	372	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440750	56440750	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	174	159	0	ENST00000407977.2:c.468del	p.Leu157Ter	p.L157*	ENST00000407977		156	ggG/gg	5/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.360246662849027	2		159	668	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099338	193099338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	52	98	0	ENST00000367435.3:c.272G>A	p.Arg91Gln	p.R91Q	ENST00000367435	NM_024529.4	91	cGa/cAa	3/17	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.360246662849027	2		98	288	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882019	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	291	307	0	ENST00000269305.4:c.455del	p.Pro152ArgfsTer18	p.P152Rfs*18	ENST00000269305	NM_001126112.2	152	cCg/cg	5/11	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.360246662849027	2		307	1167	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	167	605	4	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	0.78	0.721	0.842	1	0.99	1	SUBCLONAL	2	TRUE	1	0.360246662849027	2		609	594	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	216	227	0	ENST00000324856.7:c.4555del	p.Gln1519ArgfsTer8	p.Q1519Rfs*8	ENST00000324856	NM_006015.4	1517	gCc/gc	18/20	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.360246662849027	2		227	816	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	313	276	0	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.819	0.773	0.866	1	0.995	1	CLONAL	2	TRUE	1	0.360246662849027	2		276	1061	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711960	89711960	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1554900620	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	84	121	0	ENST00000371953.3:c.578T>C	p.Leu193Pro	p.L193P	ENST00000371953	NM_000314.4	193	cTg/cCg	6/9	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.360246662849027	2		121	331	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351056	89351057	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	21	238	0	ENST00000301030.4:c.1893dup	p.His632ThrfsTer2	p.H632Tfs*2	ENST00000301030	NM_001256183.1	631	-/A	9/13	1	2	FACETS	0.121	0.093	0.155	0.121	0.093	0.155	SUBCLONAL	1	TRUE	1	0.360246662849027	2		238	960	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859665	57859665	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	93	156	0	ENST00000228682.2:c.719A>G	p.Asp240Gly	p.D240G	ENST00000228682	NM_005269.2	240	gAt/gGt	7/12	1	2	FACETS	0.742	0.66	0.829	0.742	0.66	0.829	SUBCLONAL	1	TRUE	1	0.360246662849027	2		156	696	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851848	134851848	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	214	186	0	ENST00000398015.3:c.1259del	p.Pro420HisfsTer28	p.P420Hfs*28	ENST00000398015	NM_004441.4	418	ttC/tt	5/16	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.360246662849027	2		186	854	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933013	39933013	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	284	221	0	ENST00000378444.4:c.1586del	p.Asn529ThrfsTer60	p.N529Tfs*60	ENST00000378444	NM_001123385.1	529	aAc/ac	4/15	0.240080233913393	4	FACETS	0.903	0.848	0.959			1	CLONAL	2	TRUE	NA	0.360246662849027	4		221	1188	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356423	66356423	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	46	73	0	ENST00000273854.3:c.1074del	p.Ser359LeufsTer63	p.S359Lfs*63	ENST00000273854	NM_004439.5	358	ccC/cc	5/18	1	2	FACETS	0.811	0.686	0.947	0.811	0.686	0.947	CLONAL	1	TRUE	1	0.360246662849027	2		73	315	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440643	56440643	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	240	233	0	ENST00000407977.2:c.575del	p.Pro192ArgfsTer11	p.P192Rfs*11	ENST00000407977		192	cCg/cg	5/10	1	2	FACETS	0.773	0.723	0.824	1	0.993	1	SUBCLONAL	2	TRUE	1	0.360246662849027	2		233	862	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15821896	15821896	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	43	93	0	ENST00000307771.7:c.294del	p.Lys98AsnfsTer10	p.K98Nfs*10	ENST00000307771	NM_005089.3	97	Aaa/aa	4/11	0.261483402662399	3	FACETS	0.875	0.735	1			1	CLONAL	1	TRUE	NA	0.360246662849027	3		93	322	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366987	40366987	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	203	239	0	ENST00000397332.2:c.210del	p.Thr71ArgfsTer69	p.T71Rfs*69	ENST00000397332	NM_001033082.2	70	ccC/cc	2/3	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.360246662849027	2		239	795	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63829504	63829504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529464997	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	97	129	0	ENST00000279873.7:c.1147G>A	p.Gly383Ser	p.G383S	ENST00000279873	NM_032199.2	383	Ggt/Agt	8/10	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.360246662849027	2		129	526	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459891	149459891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143025739	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	138	251	1	ENST00000286301.3:c.316C>T	p.Arg106Trp	p.R106W	ENST00000286301	NM_005211.3	106	Cgg/Tgg	4/22	1	2	FACETS	0.848	0.772	0.929	0.848	0.772	0.929	CLONAL	1	TRUE	1	0.360246662849027	2		252	903	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645168	86645168	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	62	69	0	ENST00000274376.6:c.1240C>T	p.Arg414Trp	p.R414W	ENST00000274376	NM_002890.2	414	Cgg/Tgg	8/25	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.360246662849027	2		69	257	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420204	49420204	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	91	971	0	ENST00000301067.7:c.15545del	p.Gly5182AlafsTer61	p.G5182Afs*61	ENST00000301067	NM_003482.3	5182	gGc/gc	48/54	1	2	FACETS	0.589	0.522	0.66	0.589	0.522	0.66	SUBCLONAL	1	TRUE	1	0.360246662849027	2		971	858	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133981	38133981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	144	161	0	ENST00000317025.8:c.3905del	p.Asn1302MetfsTer4	p.N1302Mfs*4	ENST00000317025	NM_023034.1	1302	aAt/at	23/24	0.360246662849027	3	FACETS	1	0.979	1	0.617	0.564	0.674	CLONAL	1	TRUE	1	0.360246662849027	3		161	764	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294345	1294345	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1340593866	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	178	178	0	ENST00000310581.5:c.656C>T	p.Pro219Leu	p.P219L	ENST00000310581	NM_198253.2	219	cCg/cTg	2/16	1	2	FACETS	0.761	0.705	0.82	1	0.99	1	SUBCLONAL	2	TRUE	1	0.360246662849027	2		178	649	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599939	28599939	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757342510	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	199	246	0	ENST00000253063.3:c.821G>A	p.Arg274Gln	p.R274Q	ENST00000253063	NM_031459.4	274	cGg/cAg	6/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.360246662849027	2		246	777	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007896	45007897	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	92	97	0	ENST00000558401.1:c.346+1dup		p.W115fs	ENST00000558401	NM_004048.2	115	tgg/tGgg	2/4	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.360246662849027	2		97	380	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222382	2222382	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769094667	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	236	196	0	ENST00000398665.3:c.3214C>T	p.Arg1072Cys	p.R1072C	ENST00000398665	NM_032482.2	1072	Cgt/Tgt	24/28	1	2	FACETS	0.791	0.74	0.844	1	0.993	1	SUBCLONAL	2	TRUE	1	0.360246662849027	2		196	828	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653852	89653854	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	39	84	0	ENST00000371953.3:c.155_157del	p.Asp52del	p.D52del	ENST00000371953	NM_000314.4	50	atTGAt/att	2/9	1	2	FACETS	0.802	0.668	0.949	0.802	0.668	0.949	CLONAL	1	TRUE	1	0.360246662849027	2		84	270	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518658	103518658	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	85	111	0	ENST00000355739.4:c.2246C>T	p.Ser749Leu	p.S749L	ENST00000355739	NM_000123.3	749	tCa/tTa	10/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.360246662849027	2		111	390	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416449	49416449	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	80	213	0	ENST00000301067.7:c.16262C>T	p.Thr5421Ile	p.T5421I	ENST00000301067	NM_003482.3	5421	aCa/aTa	51/54	1	2	FACETS	0.592	0.521	0.669	0.592	0.521	0.669	SUBCLONAL	1	TRUE	1	0.360246662849027	2		213	750	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004246	150004246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	54	84	0	ENST00000253339.5:c.1979G>A	p.Arg660His	p.R660H	ENST00000253339		660	cGt/cAt	3/7	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.360246662849027	2		84	243	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188944	11188944	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	170	184	0	ENST00000361445.4:c.5779del	p.Val1927Ter	p.V1927*	ENST00000361445	NM_004958.3	1927	Gtg/tg	41/58	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.360246662849027	2		184	682	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933497	36933497	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	228	253	0	ENST00000361632.4:c.1790A>G	p.His597Arg	p.H597R	ENST00000361632		597	cAc/cGc	13/16	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.360246662849027	2		253	935	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46733283	46733283	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	116	140	0	ENST00000371975.4:c.1042+2T>C		p.X348_splice	ENST00000371975	NM_003579.3	348			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.360246662849027	2		140	481	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46738346	46738346	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	179	135	0	ENST00000371975.4:c.1247T>G	p.Leu416Arg	p.L416R	ENST00000371975	NM_003579.3	416	cTg/cGg	12/18	1	2	FACETS	0.752	0.696	0.81	1	0.99	1	SUBCLONAL	2	TRUE	1	0.360246662849027	2		135	661	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268856	115268856	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	140	150	0	ENST00000438362.2:c.1754A>G	p.Asp585Gly	p.D585G	ENST00000438362	NM_001242891.1	585	gAt/gGt	14/20	1	2	FACETS	0.779	0.714	0.846	1	0.988	1	SUBCLONAL	2	TRUE	1	0.360246662849027	2		150	499	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477076	67477076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1399970718	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	164	170	0	ENST00000327367.4:c.883C>T	p.Arg295Trp	p.R295W	ENST00000327367	NM_005902.3	295	Cgg/Tgg	7/9	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.360246662849027	2		170	637	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343584	343584	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	252	243	0	ENST00000262320.3:c.2090C>A	p.Pro697His	p.P697H	ENST00000262320	NM_003502.3	697	cCc/cAc	8/11	1	2	FACETS	0.767	0.719	0.817	1	0.993	1	SUBCLONAL	2	TRUE	1	0.360246662849027	2		243	912	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888105	81888105	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	164	150	0	ENST00000359376.3:c.250C>T	p.Arg84Ter	p.R84*	ENST00000359376	NM_002661.3	84	Cga/Tga	3/33	1	2	FACETS	0.768	0.708	0.829	1	0.99	1	SUBCLONAL	2	TRUE	1	0.360246662849027	2		150	593	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715370	61715370	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	34	140	0	ENST00000401558.2:c.2243T>C	p.Met748Thr	p.M748T	ENST00000401558	NM_003400.3	748	aTg/aCg	19/25	1	2	FACETS	0.49	0.401	0.591	0.49	0.401	0.591	SUBCLONAL	1	TRUE	1	0.360246662849027	2		140	385	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046262	128046262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1463378560	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	161	154	0	ENST00000285398.2:c.1001G>A	p.Arg334His	p.R334H	ENST00000285398	NM_000122.1	334	cGt/cAt	7/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.360246662849027	2		154	672	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572527	41572528	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	88	225	0	ENST00000263253.7:c.5058_5059del	p.Cys1686Ter	p.C1686*	ENST00000263253	NM_001429.3	1686	TGt/t	30/31	0.188400054376348	2	FACETS	0.594	0.526	0.668	0.297	0.263	0.334	INDETERMINATE	1	TRUE	0	0.360246662849027	2		225	822	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502617	149502617	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	148	163	0	ENST00000261799.4:c.2171T>C	p.Leu724Pro	p.L724P	ENST00000261799	NM_002609.3	724	cTc/cCc	15/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.360246662849027	2		163	594	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679941	30679941	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759438586	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	174	207	0	ENST00000376406.3:c.1778C>T	p.Ala593Val	p.A593V	ENST00000376406	NM_014641.2	593	gCa/gTa	5/15	0.360246662849027	2	FACETS	1	0.989	1	0.729	0.673	0.786	CLONAL	1	TRUE	0	0.360246662849027	2		207	663	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982048	93982048	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1431588483	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	122	112	0	ENST00000369303.4:c.1417A>G	p.Ile473Val	p.I473V	ENST00000369303	NM_004440.3	473	Atc/Gtc	6/17	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.360246662849027	2		112	544	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868917	117868917	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs201565607	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	108	81	0	ENST00000297338.2:c.782A>G	p.His261Arg	p.H261R	ENST00000297338	NM_006265.2	261	cAt/cGt	7/14	0.360246662849027	3	FACETS	1	0.98	1	0.691	0.623	0.763	CLONAL	1	TRUE	1	0.360246662849027	3		81	512	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401237	139401237	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	376	325	0	ENST00000277541.6:c.3832G>T	p.Ala1278Ser	p.A1278S	ENST00000277541	NM_017617.3	1278	Gcc/Tcc	23/34	0.146435891057069	3	FACETS	1	0.983	1	1	0.983	1	INDETERMINATE	2	TRUE	1	0.360246662849027	3		325	1147	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0054820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	51	234	3				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.344938092662301	2		237	288	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0054820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	161	571	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.344938092662301	2		571	825	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971116	21971116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552823	NA	P-0054820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	76	503	0	ENST00000304494.5:c.242C>T	p.Pro81Leu	p.P81L	ENST00000304494	NM_000077.4	81	cCc/cTc	2/3	0.344938092662301	1	FACETS	0.665	0.584	0.752	0.665	0.584	0.752	SUBCLONAL	1	TRUE	0	0.344938092662301	1		503	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	190	928	1	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.316455392802272	1	FACETS	0.938	0.867	1	0.938	0.867	1	CLONAL	1	TRUE	0	0.344938092662301	1		929	972	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956552	93956552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754119070	NA	P-0054820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	41	344	1	ENST00000369303.4:c.2684G>A	p.Arg895Gln	p.R895Q	ENST00000369303	NM_004440.3	895	cGa/cAa	15/17	1	2	FACETS	0.51	0.425	0.605	0.51	0.425	0.605	SUBCLONAL	1	TRUE	1	0.344938092662301	2		345	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578502	7578502	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555526241	NA	P-0054820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	36	936	0	ENST00000269305.4:c.428T>G	p.Val143Gly	p.V143G	ENST00000269305	NM_001126112.2	143	gTg/gGg	5/11	0.316455392802272	1	FACETS	0.173	0.141	0.208	0.173	0.141	0.208	SUBCLONAL	1	TRUE	0	0.344938092662301	1		936	1001	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968231	134968231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	143	752	1	ENST00000398015.3:c.2744C>T	p.Thr915Ile	p.T915I	ENST00000398015	NM_004441.4	915	aCc/aTc	15/16	1	2	FACETS	0.954	0.87	1	0.954	0.87	1	CLONAL	1	TRUE	1	0.344938092662301	2		753	869	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984888	55984888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201719457	NA	P-0054820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	150	531	0	ENST00000263923.4:c.241G>A	p.Asp81Asn	p.D81N	ENST00000263923	NM_002253.2	81	Gat/Aat	3/30	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.344938092662301	2		531	718	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28631597	28631597	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	71	367	0	ENST00000241453.7:c.371G>A	p.Gly124Glu	p.G124E	ENST00000241453	NM_004119.2	124	gGa/gAa	4/24	1	2	FACETS	0.978	0.857	1	0.978	0.857	1	CLONAL	1	TRUE	1	0.344938092662301	2		367	421	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224583	36224583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1462118687	NA	P-0054820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	138	974	0	ENST00000222270.7:c.7045C>T	p.Pro2349Ser	p.P2349S	ENST00000222270	NM_014727.1	2349	Cct/Tct	29/37	1	2	FACETS	0.76	0.69	0.833	0.76	0.69	0.833	SUBCLONAL	1	TRUE	1	0.344938092662301	2		974	1053	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212269	36212269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767783057	NA	P-0054820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	73	775	0	ENST00000222270.7:c.2020C>T	p.Pro674Ser	p.P674S	ENST00000222270	NM_014727.1	674	Cct/Tct	3/37	1	2	FACETS	0.521	0.454	0.592	0.521	0.454	0.592	SUBCLONAL	1	TRUE	1	0.344938092662301	2		775	813	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748390	162748390	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs267598140	NA	P-0054820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	86	436	0	ENST00000367921.3:c.2304T>G	p.Ser768Arg	p.S768R	ENST00000367921	NM_006182.2	768	agT/agG	17/18	1	2	FACETS	0.845	0.749	0.948	0.845	0.749	0.948	CLONAL	1	TRUE	1	0.344938092662301	2		436	590	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63661978	63661978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	54	523	0	ENST00000279873.7:c.82C>T	p.His28Tyr	p.H28Y	ENST00000279873	NM_032199.2	28	Cac/Tac	2/10	1	2	FACETS	0.513	0.438	0.596	0.513	0.438	0.596	SUBCLONAL	1	TRUE	1	0.344938092662301	2		523	610	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742886	17742886	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1370470173	NA	P-0054820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	60	874	0	ENST00000250003.3:c.794C>A	p.Ala265Glu	p.A265E	ENST00000250003	NM_002478.4	265	gCg/gAg	3/3	0.316455392802272	1	FACETS	0.374	0.322	0.432	0.374	0.322	0.432	SUBCLONAL	1	TRUE	0	0.344938092662301	1		874	769	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614544	38614544	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	139	536	0	ENST00000299084.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000299084	NM_152594.2	104	Caa/Taa	3/7	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.344938092662301	2		536	715	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035361	42035361	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	73	380	0	ENST00000219905.7:c.5203C>T	p.Gln1735Ter	p.Q1735*	ENST00000219905	NM_001164273.1	1735	Cag/Tag	15/24	1	2	FACETS	0.803	0.704	0.91	0.803	0.704	0.91	CLONAL	1	TRUE	1	0.344938092662301	2		380	527	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726662	88726662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	143	532	0	ENST00000360948.2:c.382C>T	p.His128Tyr	p.H128Y	ENST00000360948	NM_001012338.2	128	Cat/Tat	4/19	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.344938092662301	2		532	720	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244247	5244247	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	192	965	1	ENST00000357368.4:c.1235C>A	p.Pro412His	p.P412H	ENST00000357368	NM_002850.3	412	cCc/cAc	11/38	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.344938092662301	2		966	992	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795090	42795090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1159134882	NA	P-0054820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	206	960	0	ENST00000575354.2:c.2170G>A	p.Gly724Ser	p.G724S	ENST00000575354	NM_015125.3	724	Ggt/Agt	10/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.344938092662301	2		960	1097	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024857	31024857	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	125	628	0	ENST00000375687.4:c.4342C>T	p.Gln1448Ter	p.Q1448*	ENST00000375687	NM_015338.5	1448	Caa/Taa	13/13	1	2	FACETS	0.93	0.842	1	0.93	0.842	1	CLONAL	1	TRUE	1	0.344938092662301	2		628	779	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167437	24167437	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	201	775	0	ENST00000263121.7:c.821C>T	p.Ser274Phe	p.S274F	ENST00000263121	NM_003073.3	274	tCc/tTc	7/9	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.344938092662301	2		775	956	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644657	134644657	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0054820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	56	422	0	ENST00000398015.3:c.59-1G>A		p.X20_splice	ENST00000398015	NM_004441.4	20			1	2	FACETS	0.638	0.547	0.737	0.638	0.547	0.737	SUBCLONAL	1	TRUE	1	0.344938092662301	2		422	509	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964437	93964437	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	137	609	0	ENST00000369303.4:c.2460G>A	p.Trp820Ter	p.W820*	ENST00000369303	NM_004440.3	820	tgG/tgA	14/17	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.344938092662301	2		609	734	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974179	2974179	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1312943176	NA	P-0054820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	112	768	1	ENST00000396946.4:c.1426G>A	p.Asp476Asn	p.D476N	ENST00000396946	NM_032415.4	476	Gat/Aat	10/25	1	2	FACETS	0.686	0.616	0.761	0.686	0.616	0.761	SUBCLONAL	1	TRUE	1	0.344938092662301	2		769	946	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233093	55233093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	69	587	0	ENST00000275493.2:c.1843C>T	p.His615Tyr	p.H615Y	ENST00000275493	NM_005228.3	615	Cat/Tat	15/28	1	2	FACETS	0.473	0.411	0.54	0.473	0.411	0.54	SUBCLONAL	1	TRUE	1	0.344938092662301	2		587	846	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034364	123034364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	61	141	0	ENST00000355640.3:c.1121C>T	p.Pro374Leu	p.P374L	ENST00000355640		374	cCt/cTt	6/7	1	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.344938092662301	1		141	248	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934234	39934235	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	23	401	0	ENST00000378444.4:c.364dup	p.Met122AsnfsTer64	p.M122Nfs*64	ENST00000378444	NM_001123385.1	122	atg/aAtg	4/15	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		401	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0054834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	660	620	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.448092887628807	3	FACETS	0.948	0.918	0.978	0.948	0.918	0.978	CLONAL	3	TRUE	0	0.482475148422855	3		620	1194	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600446	10600446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	569	911	1	ENST00000171111.5:c.1409G>A	p.Arg470His	p.R470H	ENST00000171111	NM_203500.1	470	cGt/cAt	4/6	0.464160188183397	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.482475148422855	2		912	1139	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913185	32913185	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	152	547	0	ENST00000380152.3:c.4693A>G	p.Lys1565Glu	p.K1565E	ENST00000380152		1565	Aag/Gag	11/27	0.418628453536812	2	FACETS	0.999	0.917	1	0.499	0.458	0.542	CLONAL	1	TRUE	0	0.482475148422855	2		547	631	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772296	68772307	+	inframe_deletion	In_Frame_Del	DEL	GGCCGCGTCCTG	GGCCGCGTCCTG	-	novel	NA	P-0054834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	181	943	0	ENST00000261769.5:c.148_159del	p.Leu52_Val55del	p.L52_V55del	ENST00000261769	NM_004360.3	49	GGCCGCGTCCTG/-	2/16	0.483132249105529	3	FACETS	0.67	0.617	0.727	0.335	0.308	0.364	SUBCLONAL	1	TRUE	1	0.482475148422855	3		943	1389	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743931	40743931	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	143	565	0	ENST00000373198.4:c.3064G>C	p.Asp1022His	p.D1022H	ENST00000373198	NM_133170.3	1022	Gat/Cat	23/32	0.260375472013772	3	FACETS	0.914	0.834	0.998	0.457	0.417	0.499	INDETERMINATE	1	TRUE	1	0.482475148422855	3		565	805	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0054835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	43	670	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.2	2		670	337	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226573309	226573309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	53	727	0	ENST00000366794.5:c.907G>A	p.Val303Ile	p.V303I	ENST00000366794	NM_001618.3	303	Gtc/Atc	7/23	0.245825778760268	4	FACETS	1	0.882	1	0.347	0.295	0.404	CLONAL	1	TRUE	1	0.2	4		727	611	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624397	21624397	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	25	577	0	ENST00000421138.2:c.1632G>T	p.Lys544Asn	p.K544N	ENST00000421138		544	aaG/aaT	14/16	0.155709859763505	0	FACETS	0.473	0.372	0.589			1	SUBCLONAL	1	TRUE	0	0.2	0		577	423	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988953	41988969	+	frameshift_variant	Frame_Shift_Del	DEL	ACTTGGGCAGAAAGAGA	ACTTGGGCAGAAAGAGA	-	novel	NA	P-0054835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	22	592	0	ENST00000219905.7:c.1747_1763del	p.Leu583AsnfsTer4	p.L583Nfs*4	ENST00000219905	NM_001164273.1	582	gACTTGGGCAGAAAGAGA/g	3/24	1	2	FACETS	0.649	0.503	0.819	0.649	0.503	0.819	SUBCLONAL	1	TRUE	1	0.2	2		592	339	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250518	26250518	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	39	944	0	ENST00000446824.2:c.316G>C	p.Glu106Gln	p.E106Q	ENST00000446824	NM_021018.2	106	Gag/Cag	1/1	0.141675607504719	4	FACETS	0.756	0.625	0.902	0.378	0.312	0.451	CLONAL	1	TRUE	2	0.2	4		944	619	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0054836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	189	571	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.334077027726466	3	FACETS	1	0.988	1	0.688	0.635	0.742	CLONAL	1	TRUE	1	0.334077027726466	3		571	960	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073943	8073943	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs116791613	NA	P-0054836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	127	533	0	ENST00000377482.5:c.716C>T	p.Pro239Leu	p.P239L	ENST00000377482	NM_018948.3	239	cCa/cTa	4/4	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.334077027726466	2		533	695	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245204	46245204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	175	502	0	ENST00000334344.6:c.3298C>T	p.Gln1100Ter	p.Q1100*	ENST00000334344	NM_152641.2	1100	Cag/Tag	15/21	0.26447038977914	2	FACETS	1	0.989	1	0.739	0.682	0.797	CLONAL	1	TRUE	0	0.334077027726466	2		502	709	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709099	117709099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	132	532	0	ENST00000368508.3:c.1858C>T	p.Pro620Ser	p.P620S	ENST00000368508	NM_002944.2	620	Cct/Tct	13/43	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.334077027726466	2		532	653	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294984	1294984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	39	62	0	ENST00000310581.5:c.121C>T	p.Arg41Cys	p.R41C	ENST00000310581	NM_198253.2	41	Cgc/Tgc	1/16	NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.334077027726466	2		62	167	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626721	28626721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1224965356	NA	P-0054836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	132	500	0	ENST00000241453.7:c.575C>T	p.Pro192Leu	p.P192L	ENST00000241453	NM_004119.2	192	cCg/cTg	5/24	0.334077027726466	1	FACETS	0.872	0.792	0.955	0.872	0.792	0.955	CLONAL	1	TRUE	0	0.334077027726466	1		500	755	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548944	29548944	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	21	271	0	ENST00000356175.3:c.1718T>G	p.Ile573Ser	p.I573S	ENST00000356175	NM_000267.3	573	aTt/aGt	15/57	1	2	FACETS	0.526	0.406	0.665	0.526	0.406	0.665	SUBCLONAL	1	TRUE	1	0.334077027726466	2		271	239	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216545	2216545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750873331	NA	P-0054836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1191	125	924	0	ENST00000398665.3:c.2189C>T	p.Ser730Leu	p.S730L	ENST00000398665	NM_032482.2	730	tCg/tTg	20/28	1	2	FACETS	0.569	0.513	0.628	0.569	0.513	0.628	SUBCLONAL	1	TRUE	1	0.334077027726466	2		924	1316	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101135	41101135	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	164	757	0	ENST00000373198.4:c.1221G>A	p.Trp407Ter	p.W407*	ENST00000373198	NM_133170.3	407	tgG/tgA	8/32	1	2	FACETS	0.898	0.823	0.977	0.898	0.823	0.977	CLONAL	1	TRUE	1	0.334077027726466	2		757	1093	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39763622	39763622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753741115	NA	P-0054836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	53	346	0	ENST00000288319.7:c.830C>T	p.Pro277Leu	p.P277L	ENST00000288319	NM_182918.3	277	cCt/cTt	8/10	0.270100226290973	1	FACETS	0.512	0.437	0.595	0.512	0.437	0.595	SUBCLONAL	1	TRUE	0	0.334077027726466	1		346	516	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528561	89528561	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	42	198	0	ENST00000336596.2:c.2861T>C	p.Val954Ala	p.V954A	ENST00000336596	NM_005233.5	954	gTt/gCt	17/17	1	2	FACETS	0.723	0.605	0.852	0.723	0.605	0.852	SUBCLONAL	1	TRUE	1	0.334077027726466	2		198	348	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0054837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	119	378	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.654565095187217	2		378	353	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121909229	NA	P-0054837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	124	486	0	ENST00000371953.3:c.389G>T	p.Arg130Leu	p.R130L	ENST00000371953	NM_000314.4	130	cGa/cTa	5/9	0.622320043546671	3	FACETS	0.975	0.886	1	0.487	0.443	0.534	CLONAL	1	TRUE	1	0.654565095187217	3		486	516	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589599	67589604	+	inframe_deletion	In_Frame_Del	DEL	TCAGTT	TCAGTT	-	novel	NA	P-0054837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	33	227	0	ENST00000274335.5:c.1365_1370del	p.Phe456_Gln457del	p.F456_Q457del	ENST00000274335		454	acTCAGTTt/act	10/15	1	2	FACETS	0.579	0.477	0.692	0.579	0.477	0.692	SUBCLONAL	1	TRUE	1	0.654565095187217	2		227	174	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380350	14380350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	160	377	0	ENST00000256196.4:c.67G>A	p.Gly23Ser	p.G23S	ENST00000256196		23	Ggc/Agc	1/6	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.654565095187217	2		377	480	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089727	27089727	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	294	946	2	ENST00000324856.7:c.2683C>T	p.Gln895Ter	p.Q895*	ENST00000324856	NM_006015.4	895	Caa/Taa	8/20	1	2	FACETS	0.874	0.823	0.926	0.874	0.823	0.926	CLONAL	1	TRUE	1	0.654565095187217	2		948	1028	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440415	49440415	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	350	986	0	ENST00000301067.7:c.4395del	p.Lys1466ArgfsTer40	p.K1466Rfs*40	ENST00000301067	NM_003482.3	1465	ccC/cc	15/54	1	2	FACETS	0.947	0.898	0.998	0.947	0.898	0.998	CLONAL	1	TRUE	1	0.654565095187217	2		986	1129	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039416	49039416	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	123	676	1	ENST00000267163.4:c.2401G>T	p.Gly801Ter	p.G801*	ENST00000267163	NM_000321.2	801	Gga/Tga	23/27	1	2	FACETS	0.686	0.623	0.752	0.686	0.623	0.752	SUBCLONAL	1	TRUE	1	0.654565095187217	2		677	548	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0054838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	903	684	2	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	0.645314885939968	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	1	0.646830467872582	4		686	1451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057520007	NA	P-0054838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	313	1047	0	ENST00000269305.4:c.614A>T	p.Tyr205Phe	p.Y205F	ENST00000269305	NM_001126112.2	205	tAt/tTt	6/11	0.646830467872582	1	FACETS	0.989	0.941	1	0.989	0.941	1	CLONAL	1	TRUE	0	0.646830467872582	1		1047	662	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317936	8317936	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	154	471	0	ENST00000356435.5:c.5677T>A	p.Tyr1893Asn	p.Y1893N	ENST00000356435		1893	Tat/Aat	35/35	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.646830467872582	2		471	437	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692826	89692826	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	92	244	0	ENST00000371953.3:c.310T>G	p.Phe104Val	p.F104V	ENST00000371953	NM_000314.4	104	Ttt/Gtt	5/9	1	2	FACETS	0.942	0.847	1	0.942	0.847	1	CLONAL	1	TRUE	1	0.646830467872582	2		244	302	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249387	110249387	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	467	1541	0	ENST00000374672.4:c.1186del	p.His396ThrfsTer48	p.H396Tfs*48	ENST00000374672	NM_004235.4	396	Cac/ac	4/5	1	2	FACETS	0.973	0.929	1	0.973	0.929	1	CLONAL	1	TRUE	1	0.646830467872582	2		1541	1484	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092711	27092711	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0054838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	161	495	0	ENST00000324856.7:c.2733-1G>T		p.X911_splice	ENST00000324856	NM_006015.4	911			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.646830467872582	2		495	466	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625129	69625129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	319	1338	1	ENST00000334134.2:c.664C>T	p.Pro222Ser	p.P222S	ENST00000334134	NM_005247.2	222	Ccc/Tcc	3/3	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.646830467872582	2		1339	974	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941722	48941722	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	97	325	1	ENST00000267163.4:c.1032G>T	p.Gln344His	p.Q344H	ENST00000267163	NM_000321.2	344	caG/caT	10/27	0.646830467872582	1	FACETS	0.818	0.742	0.896	0.818	0.742	0.896	CLONAL	1	TRUE	0	0.646830467872582	1		326	248	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646254	3646254	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1028896815	NA	P-0054838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	351	1456	1	ENST00000294008.3:c.1824G>T	p.Glu608Asp	p.E608D	ENST00000294008	NM_032444.2	608	gaG/gaT	8/15	1	2	FACETS	0.972	0.921	1	0.972	0.921	1	CLONAL	1	TRUE	1	0.646830467872582	2		1457	1117	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968869	15968869	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	64	823	0	ENST00000268712.3:c.4881G>C	p.Leu1627Phe	p.L1627F	ENST00000268712	NM_006311.3	1627	ttG/ttC	33/46	0.646830467872582	1	FACETS	0.225	0.195	0.259	0.225	0.195	0.259	SUBCLONAL	1	TRUE	0	0.646830467872582	1		823	594	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138382840	138382840	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	198	623	0	ENST00000289153.2:c.2704A>G	p.Thr902Ala	p.T902A	ENST00000289153	NM_006219.2	902	Aca/Gca	19/22	NA	2	FACETS	1	0.942	1			1	INDETERMINATE	1	TRUE	NA	0.646830467872582	2		623	605	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968633	55968633	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	285	813	0	ENST00000263923.4:c.2030C>A	p.Thr677Lys	p.T677K	ENST00000263923	NM_002253.2	677	aCg/aAg	14/30	1	2	FACETS	0.984	0.927	1	0.984	0.927	1	CLONAL	1	TRUE	1	0.646830467872582	2		813	896	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518686	176518686	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	300	1046	0	ENST00000292408.4:c.604C>G	p.Leu202Val	p.L202V	ENST00000292408	NM_213647.1	202	Ctg/Gtg	6/18	0.646830467872582	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.646830467872582	1		1046	590	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969953	161969953	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	287	1010	1	ENST00000366898.1:c.1016C>A	p.Ala339Glu	p.A339E	ENST00000366898	NM_004562.2	339	gCg/gAg	9/12	0.646830467872582	1	FACETS	0.902	0.854	0.949	0.902	0.854	0.949	CLONAL	1	TRUE	0	0.646830467872582	1		1011	666	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508725	106508725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	265	928	0	ENST00000359195.3:c.719C>T	p.Thr240Ile	p.T240I	ENST00000359195	NM_002649.2	240	aCc/aTc	2/11	1	2	FACETS	0.932	0.876	0.99	0.932	0.876	0.99	CLONAL	1	TRUE	1	0.646830467872582	2		928	879	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44970649	44970649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	190	646	0	ENST00000377967.4:c.4199C>T	p.Ser1400Leu	p.S1400L	ENST00000377967	NM_021140.2	1400	tCa/tTa	29/29	0.646830467872582	1	FACETS	0.927	0.867	0.986	0.927	0.867	0.986	CLONAL	1	TRUE	0	0.646830467872582	1		646	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0054839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	355	1045	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.61419699727733	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.61419699727733	1		1046	720	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0054839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	112	425	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.590304168638691	1	FACETS	0.865	0.79	0.942	0.865	0.79	0.942	CLONAL	1	TRUE	0	0.61419699727733	1		425	292	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874011	123874013	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs780061449	NA	P-0054839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	10	53	0	ENST00000330479.4:c.62_64del	p.Ala21del	p.A21del	ENST00000330479	NM_020382.3	14	gaGGCg/gag	2/9	0.61419699727733	2	FACETS	0.354	0.242	0.491	0.177	0.121	0.246	SUBCLONAL	1	TRUE	0	0.61419699727733	2		53	92	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106882	27106882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	453	807	0	ENST00000324856.7:c.6493G>A	p.Glu2165Lys	p.E2165K	ENST00000324856	NM_006015.4	2165	Gag/Aag	20/20	0.546682784125397	2	FACETS	0.949	0.915	0.983	0.949	0.915	0.983	CLONAL	2	TRUE	0	0.61419699727733	2		807	777	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572507	141572567	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTGCAGGGGAGTCCCCCGCCCTTGGTCCCGTGTGGCGCCCTCACCTCATGGATGGCAAGT	GCTGCAGGGGAGTCCCCCGCCCTTGGTCCCGTGTGGCGCCCTCACCTCATGGATGGCAAGT	-	novel	NA	P-0054839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	98	417	0	ENST00000220592.5:c.503_518+45del		p.X168_splice	ENST00000220592	NM_012154.3	168		4/19	0.61419699727733	3	FACETS	0.606	0.541	0.676	0.303	0.27	0.338	SUBCLONAL	1	TRUE	1	0.61419699727733	3		417	688	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959462	26959462	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	157	461	0	ENST00000381527.3:c.629A>G	p.His210Arg	p.H210R	ENST00000381527	NM_001260.1	210	cAt/cGt	6/13	0.654460584243574	1	FACETS	0.652	0.602	0.704	0.652	0.602	0.704	SUBCLONAL	1	TRUE	0	0.654460584243574	1		461	495	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557891	187557891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200242253	NA	P-0054840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	283	625	0	ENST00000441802.2:c.3820G>A	p.Val1274Ile	p.V1274I	ENST00000441802	NM_005245.3	1274	Gtc/Atc	5/27	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.654460584243574	2		625	854	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159754	20159754	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	288	608	0	ENST00000379607.5:c.5C>A	p.Pro2His	p.P2H	ENST00000379607	NM_001412.3	2	cCc/cAc	1/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.654460584243574	2		608	825	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0054842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	162	257	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.487399115919253	2	FACETS	0.846	0.786	0.907	0.846	0.786	0.907	CLONAL	2	TRUE	0	0.487399115919253	2		258	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0054842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	345	771	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.487232416360555	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.487399115919253	1		771	1025	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371626	89371626	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	120	682	0	ENST00000301030.4:c.214G>C	p.Asp72His	p.D72H	ENST00000301030	NM_001256183.1	72	Gac/Cac	4/13	0.197491009649485	1	FACETS	0.282	0.254	0.313	0.282	0.254	0.313	INDETERMINATE	1	TRUE	0	0.487399115919253	1		682	1319	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097737	27097737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	251	538	0	ENST00000324856.7:c.3326G>A	p.Arg1109Gln	p.R1109Q	ENST00000324856	NM_006015.4	1109	cGg/cAg	12/20	0.487232416360555	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.487399115919253	1		538	728	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485425	57485425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	110	377	0	ENST00000371085.3:c.1007G>A	p.Arg336Gln	p.R336Q	ENST00000371085	NM_000516.4	336	cGg/cAg	12/13	0.270156829649169	4	FACETS	0.665	0.596	0.738	0.332	0.298	0.369	INDETERMINATE	1	TRUE	2	0.487399115919253	4		377	1010	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151927342	151927342	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	16	45	0	ENST00000262189.6:c.2834T>C	p.Val945Ala	p.V945A	ENST00000262189	NM_170606.2	945	gTg/gCg	17/59	1	2	FACETS	1	0.8	1	1	0.8	1	CLONAL	1	TRUE	1	0.487399115919253	2		45	62	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740546	58740546	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0054844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	141	704	0	ENST00000305921.3:c.1451T>A	p.Leu484Ter	p.L484*	ENST00000305921	NM_003620.3	484	tTa/tAa	6/6	0.59822927237606	3	FACETS	0.999	0.913	1	0.5	0.456	0.544	CLONAL	1	TRUE	1	0.59822927237606	3		704	613	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115981	8115982	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0054844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	113	560	0	ENST00000346208.3:c.1328_1329dup	p.Ter444ValfsTer32	p.*444Vfs*32	ENST00000346208		443	ggt/gGTgt	6/6	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.59822927237606	2		560	319	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	48	290	1				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.825	0.699	0.964			1	INDETERMINATE	1	TRUE	NA	0.276378137942413	2		291	421	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971124	21971125	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0054846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	135	892	0	ENST00000304494.5:c.233_234del	p.Leu78HisfsTer41	p.L78Hfs*41	ENST00000304494	NM_000077.4	78	cTC/c	2/3	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.276378137942413	2		892	839	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720679	89720679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123329	NA	P-0054846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	63	412	0	ENST00000371953.3:c.830C>T	p.Thr277Ile	p.T277I	ENST00000371953	NM_000314.4	277	aCa/aTa	8/9	0.276378137942413	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.276378137942413	1		412	358	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41222950	41222950	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80357401	NA	P-0054846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	116	738	0	ENST00000357654.3:c.4981G>A	p.Glu1661Lys	p.E1661K	ENST00000357654	NM_007294.3	1661	Gaa/Aaa	15/23	1	2	FACETS	0.943	0.849	1	0.943	0.849	1	CLONAL	1	TRUE	1	0.276378137942413	2		738	890	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149437093	149437093	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	60	1196	0	ENST00000286301.3:c.2195C>T	p.Ser732Phe	p.S732F	ENST00000286301	NM_005211.3	732	tCt/tTt	16/22	1	2	FACETS	0.37	0.317	0.427	0.37	0.317	0.427	SUBCLONAL	1	TRUE	1	0.276378137942413	2		1196	1175	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942748	68942748	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	96	552	0	ENST00000288368.4:c.560C>A	p.Thr187Asn	p.T187N	ENST00000288368	NM_024870.2	187	aCt/aAt	6/40	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.276378137942413	2		552	664	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0054847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	34	234	3				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.937	0.766	1	0.937	0.766	1	CLONAL	1	TRUE	1	0.175739850991637	2		237	413	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0054847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9364	380	1036	1	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.175739850991637	75	FACETS	1	0.981	1	0.044	0.041	0.048	CLONAL	3	TRUE	1	0.175739850991637	75		1037	9744	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0054847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3745	2776	604	1	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.175739850991637	75	FACETS	0.998	0.98	1	0.485	0.477	0.494	CLONAL	36	TRUE	1	0.175739850991637	75		605	6521	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0054847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9506	240	1042	0	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.175739850991637	75	FACETS	1	0.953	1	0.028	0.026	0.031	CLONAL	2	TRUE	1	0.175739850991637	75		1042	9746	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs149840192	NA	P-0054847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9439	305	1037	0	ENST00000275493.2:c.866C>A	p.Ala289Asp	p.A289D	ENST00000275493	NM_005228.3	289	gCc/gAc	7/28	0.175739850991637	75	FACETS	0.88	0.823	0.941	0.036	0.033	0.039	CLONAL	3	TRUE	1	0.175739850991637	75		1037	9744	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0054851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	235	729	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.586948292866048	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.600480260771591	1		730	540	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419038	419038	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	145	640	1	ENST00000399788.2:c.3309G>T	p.Lys1103Asn	p.K1103N	ENST00000399788	NM_001042603.1	1103	aaG/aaT	22/28	1	2	FACETS	0.826	0.756	0.897	0.826	0.756	0.897	CLONAL	1	TRUE	1	0.600480260771591	2		641	585	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374431	31374432	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0054851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	161	832	0	ENST00000328111.2:c.432+1dup		p.R144fs	ENST00000328111	NM_006892.3	144	agg/aGgg	5/23	1	2	FACETS	0.954	0.88	1	0.954	0.88	1	CLONAL	1	TRUE	1	0.600480260771591	2		832	562	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909228	41909228	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	229	1283	1	ENST00000372991.4:c.160C>T	p.Pro54Ser	p.P54S	ENST00000372991	NM_001760.3	54	Ccg/Tcg	1/5	0.600480260771591	4	FACETS	0.902	0.839	0.968	0.301	0.279	0.323	CLONAL	1	TRUE	1	0.600480260771591	4		1284	1353	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0054852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	191	234	3				ENST00000310581	NM_198253.2	-/1132			0.239084426734974	4	FACETS	0.956	0.889	1	0.956	0.889	1	INDETERMINATE	2	TRUE	2	0.494025669937787	4		237	604	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0054852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	364	692	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.390033773938173	3	FACETS	1	0.993	1	0.813	0.777	0.85	CLONAL	2	TRUE	0	0.494025669937787	3		692	753	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913355	NA	P-0054852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	158	422	0	ENST00000288602.6:c.1406G>A	p.Gly469Glu	p.G469E	ENST00000288602	NM_004333.4	469	gGa/gAa	11/18	0.239084426734974	4	FACETS	0.922	0.851	0.996	0.922	0.851	0.996	INDETERMINATE	2	TRUE	2	0.494025669937787	4		422	518	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405968	157405968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	156	795	1	ENST00000346085.5:c.2210C>T	p.Pro737Leu	p.P737L	ENST00000346085	NM_020732.3	737	cCc/cTc	6/20	1	2	FACETS	0.715	0.655	0.778	0.715	0.655	0.778	SUBCLONAL	1	TRUE	1	0.494025669937787	2		796	883	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426788	121426788	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	327	1045	0	ENST00000257555.6:c.479C>T	p.Ala160Val	p.A160V	ENST00000257555		160	gCc/gTc	2/10	0.239084426734974	4	FACETS	0.911	0.861	0.961	0.911	0.861	0.961	INDETERMINATE	2	TRUE	2	0.494025669937787	4		1045	1086	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7174592	7174592	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0054852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	243	762	0	ENST00000302850.5:c.1123+2T>G		p.X375_splice	ENST00000302850	NM_000208.2	375			0.126536688240256	3	FACETS	0.764	0.716	0.813	0.509	0.477	0.542	INDETERMINATE	2	TRUE	0	0.494025669937787	3		762	803	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376070	225376070	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0054852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	118	559	0	ENST00000264414.4:c.883+1G>T		p.X295_splice	ENST00000264414	NM_003590.4	295			0.181478535255089	4	FACETS	0.776	0.704	0.85	0.776	0.704	0.85	INDETERMINATE	2	TRUE	2	0.494025669937787	4		559	460	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542026	187542033	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGTAGC	TCTGTAGC	-	novel	NA	P-0054852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	169	511	0	ENST00000441802.2:c.5707_5714del	p.Ala1903CysfsTer2	p.A1903Cfs*2	ENST00000441802	NM_005245.3	1903	GCTACAGAt/t	10/27	0.239084426734974	4	FACETS	1	0.989	1	0.729	0.672	0.788	INDETERMINATE	1	TRUE	2	0.494025669937787	4		511	701	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967853	93967853	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs778876357	NA	P-0054852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	202	540	0	ENST00000369303.4:c.2074C>G	p.Pro692Ala	p.P692A	ENST00000369303	NM_004440.3	692	Ccg/Gcg	11/17	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.494025669937787	2		540	699	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0054853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	973	858	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.582800235535046	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.582800235535046	2		858	1622	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039356	47039358	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0054853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	430	349	0	ENST00000377604.3:c.985_987del	p.Ser329del	p.S329del	ENST00000377604	NM_001204468.1	327	TCC/-	10/24	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.582800235535046	1		349	767	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431405	49431405	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0054853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	249	585	0	ENST00000301067.7:c.9734T>G	p.Leu3245Ter	p.L3245*	ENST00000301067	NM_003482.3	3245	tTa/tGa	34/54	1	2	FACETS	0.863	0.808	0.92	0.863	0.808	0.92	CLONAL	1	TRUE	1	0.582800235535046	2		585	990	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638155	176638156	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0054853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	258	581	0	ENST00000439151.2:c.2757_2758dup	p.Ser920IlefsTer9	p.S920Ifs*9	ENST00000439151	NM_022455.4	919	gat/gATat	5/23	0.582800235535046	1	FACETS	0.915	0.862	0.968	0.915	0.862	0.968	CLONAL	1	TRUE	0	0.582800235535046	1		581	686	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829749	76829750	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTT	novel	NA	P-0054853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	169	259	0	ENST00000373344.5:c.6289_6291dup	p.Lys2097dup	p.K2097dup	ENST00000373344	NM_000489.3	2097	-/AAG	28/35	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.582800235535046	1		259	314	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829757	76829757	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	189	265	0	ENST00000373344.5:c.6284G>C	p.Arg2095Thr	p.R2095T	ENST00000373344	NM_000489.3	2095	aGg/aCg	28/35	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.582800235535046	1		265	322	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0054854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	107	321	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.87	0.786	0.958	0.87	0.786	0.958	CLONAL	1	TRUE	1	0.574632584370672	2		321	428	SUCCESS
APC	324	MSKCC	GRCh37	5	112175147	112175147	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	50	238	0	ENST00000257430.4:c.3856G>T	p.Glu1286Ter	p.E1286*	ENST00000257430	NM_000038.5	1286	Gaa/Taa	16/16	1	2	FACETS	0.866	0.745	0.995	0.866	0.745	0.995	CLONAL	1	TRUE	1	0.574632584370672	2		238	201	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432374	49432374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757791539	NA	P-0054854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	343	1139	1	ENST00000301067.7:c.8765G>A	p.Arg2922Gln	p.R2922Q	ENST00000301067	NM_003482.3	2922	cGg/cAg	34/54	1	2	FACETS	0.967	0.915	1	0.967	0.915	1	CLONAL	1	TRUE	1	0.574632584370672	2		1140	1235	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797152	45797152	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	363	1301	1	ENST00000450313.1:c.1263del	p.Gln422ArgfsTer30	p.Q422Rfs*30	ENST00000450313	NM_012222.2	421	ctG/ct	13/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.574632584370672	2		1302	1220	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964466	93964466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1295357534	NA	P-0054854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	127	682	0	ENST00000369303.4:c.2431C>T	p.Arg811Trp	p.R811W	ENST00000369303	NM_004440.3	811	Cgg/Tgg	14/17	1	2	FACETS	0.886	0.807	0.968	0.886	0.807	0.968	CLONAL	1	TRUE	1	0.574632584370672	2		682	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0054855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	362	709	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.851512024064032	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.851512024064032	1		709	458	SUCCESS
APC	324	MSKCC	GRCh37	5	112173600	112173600	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060503310	NA	P-0054855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	311	309	0	ENST00000257430.4:c.2309C>G	p.Ser770Ter	p.S770*	ENST00000257430	NM_000038.5	770	tCa/tGa	16/16	0.851512024064032	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.851512024064032	2		309	365	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11297986	11297986	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	419	802	2	ENST00000361445.4:c.2122C>T	p.Arg708Trp	p.R708W	ENST00000361445	NM_004958.3	708	Cgg/Tgg	13/58	0.851512024064032	2	FACETS	0.887	0.846	0.928	0.443	0.423	0.464	CLONAL	1	TRUE	0	0.851512024064032	2		804	1110	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977602	2977602	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	769	1021	0	ENST00000396946.4:c.1082A>C	p.Tyr361Ser	p.Y361S	ENST00000396946	NM_032415.4	361	tAc/tCc	8/25	0.15141075368637	2	FACETS	1	0.997	1	0.631	0.612	0.65	INDETERMINATE	1	TRUE	0	0.851512024064032	2		1021	1431	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749935	162749936	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0054855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	310	448	0	ENST00000367921.3:c.2467_2468delinsAT	p.Ser823Ile	p.S823I	ENST00000367921	NM_006182.2	823	TCt/ATt	18/18	0.418892130007949	3	FACETS	1	0.994	1	0.723	0.686	0.76	INDETERMINATE	1	TRUE	1	0.851512024064032	3		448	718	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115894	8115894	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	183	666	0	ENST00000346208.3:c.1240C>T	p.His414Tyr	p.H414Y	ENST00000346208		414	Cac/Tac	6/6	0.407409885309566	1	FACETS	0.307	0.283	0.331	0.307	0.283	0.331	INDETERMINATE	1	TRUE	0	0.851512024064032	1		666	805	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942196	71942196	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	688	936	0	ENST00000298229.2:c.1460G>T	p.Gly487Val	p.G487V	ENST00000298229	NM_001567.3	487	gGg/gTg	12/28	0.621077595889563	1	FACETS	0.874	0.85	0.897	0.874	0.85	0.897	CLONAL	1	TRUE	0	0.851512024064032	1		936	1062	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943965	71943965	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	742	970	1	ENST00000298229.2:c.1898G>T	p.Arg633Met	p.R633M	ENST00000298229	NM_001567.3	633	aGg/aTg	16/28	0.621077595889563	1	FACETS	0.888	0.865	0.911	0.888	0.865	0.911	CLONAL	1	TRUE	0	0.851512024064032	1		971	1127	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656309	18656309	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	242	457	0	ENST00000266497.5:c.2988G>T	p.Lys996Asn	p.K996N	ENST00000266497		996	aaG/aaT	21/31	0.488518419886167	1	FACETS	0.666	0.63	0.702	0.666	0.63	0.702	INDETERMINATE	1	TRUE	0	0.851512024064032	1		457	490	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420966	49420966	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	322	539	0	ENST00000301067.7:c.14783C>G	p.Pro4928Arg	p.P4928R	ENST00000301067	NM_003482.3	4928	cCc/cGc	48/54	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.851512024064032	2		539	661	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865119	57865119	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	624	1091	0	ENST00000228682.2:c.2596A>T	p.Thr866Ser	p.T866S	ENST00000228682	NM_005269.2	866	Acc/Tcc	12/12	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.851512024064032	2		1091	1397	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42050037	42050037	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	152	274	0	ENST00000219905.7:c.7191G>C	p.Lys2397Asn	p.K2397N	ENST00000219905	NM_001164273.1	2397	aaG/aaC	19/24	0.851512024064032	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.851512024064032	1		274	198	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014116	14014117	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	421	866	0	ENST00000311895.7:c.95dup	p.Val33SerfsTer50	p.V33Sfs*50	ENST00000311895	NM_005236.2	32	cta/cTta	1/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.851512024064032	2		866	966	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244765	41244765	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	206	765	0	ENST00000357654.3:c.2783G>T	p.Gly928Val	p.G928V	ENST00000357654	NM_007294.3	928	gGc/gTc	10/23	0.137594537021911	1	FACETS	0.288	0.267	0.309	0.288	0.267	0.309	INDETERMINATE	1	TRUE	0	0.851512024064032	1		765	966	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56809888	56809888	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	439	504	0	ENST00000337432.4:c.1009G>T	p.Val337Leu	p.V337L	ENST00000337432	NM_058216.2	337	Gta/Tta	8/9	0.418892130007949	3	FACETS	0.906	0.871	0.941	0.906	0.871	0.941	INDETERMINATE	2	TRUE	1	0.851512024064032	3		504	811	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52709239	52709239	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	567	760	0	ENST00000322088.6:c.193G>T	p.Val65Phe	p.V65F	ENST00000322088	NM_014225.5	65	Gtc/Ttc	3/15	NA	2	FACETS	0.949	0.927	0.969			1	INDETERMINATE	2	TRUE	NA	0.851512024064032	2		760	702	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980869	40980869	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	299	640	1	ENST00000373198.4:c.1617G>T	p.Arg539Ser	p.R539S	ENST00000373198	NM_133170.3	539	agG/agT	10/32	NA	2	FACETS	0.95	0.9	1			1	INDETERMINATE	1	TRUE	NA	0.851512024064032	2		641	739	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958197	54958197	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	489	451	0	ENST00000312783.6:c.410G>C	p.Arg137Pro	p.R137P	ENST00000312783	NM_198436.1	137	cGc/cCc	6/10	0.851512024064032	3	FACETS	0.978	0.944	1			1	CLONAL	2	TRUE	NA	0.851512024064032	3		451	837	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090410	37090410	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	131	461	1	ENST00000231790.2:c.2005G>T	p.Glu669Ter	p.E669*	ENST00000231790	NM_000249.3	669	Gaa/Taa	18/19	0.851512024064032	2	FACETS	0.463	0.421	0.507	0.231	0.21	0.254	SUBCLONAL	1	TRUE	0	0.851512024064032	2		462	665	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851775	134851775	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	434	839	0	ENST00000398015.3:c.1181G>T	p.Ser394Ile	p.S394I	ENST00000398015	NM_004441.4	394	aGc/aTc	5/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.851512024064032	2		839	972	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170020908	170020908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	29	91	1	ENST00000295797.4:c.1784G>A	p.Cys595Tyr	p.C595Y	ENST00000295797	NM_002740.5	595	tGt/tAt	18/18	0.198904051594112	5	FACETS	1	0.909	1			1	INDETERMINATE	1	TRUE	NA	0.851512024064032	5		92	129	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149434888	149434888	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	454	706	0	ENST00000286301.3:c.2566T>G	p.Tyr856Asp	p.Y856D	ENST00000286301	NM_005211.3	856	Tac/Gac	20/22	0.851512024064032	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.851512024064032	1		706	560	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681090	117681090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370524859	NA	P-0054855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	225	560	0	ENST00000368508.3:c.3530C>T	p.Thr1177Met	p.T1177M	ENST00000368508	NM_002944.2	1177	aCg/aTg	23/43	0.15141075368637	2	FACETS	0.753	0.704	0.803	0.376	0.352	0.402	INDETERMINATE	1	TRUE	0	0.851512024064032	2		560	702	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953038	2953038	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	734	1103	0	ENST00000396946.4:c.2902G>T	p.Ala968Ser	p.A968S	ENST00000396946	NM_032415.4	968	Gcc/Tcc	22/25	0.15141075368637	2	FACETS	1	0.996	1	0.594	0.576	0.613	INDETERMINATE	1	TRUE	0	0.851512024064032	2		1103	1450	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453140	140453148	+	inframe_deletion	In_Frame_Del	DEL	TAGCTAGAC	TAGCTAGAC	-	novel	NA	P-0054855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	222	380	0	ENST00000288602.6:c.1787_1795del	p.Gly596_Thr599delinsAla	p.G596_T599delinsA	ENST00000288602	NM_004333.4	596	gGTCTAGCTAca/gca	15/18	NA	2	FACETS	1	0.944	1			1	INDETERMINATE	1	TRUE	NA	0.851512024064032	2		380	519	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8338927	8338927	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	304	438	0	ENST00000356435.5:c.5374G>T	p.Ala1792Ser	p.A1792S	ENST00000356435		1792	Gcc/Tcc	32/35	0.851512024064032	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.851512024064032	1		438	379	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528590	8528590	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0054855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	311	366	0	ENST00000356435.5:c.541+1G>T		p.X181_splice	ENST00000356435		181			0.851512024064032	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.851512024064032	1		366	382	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137326016	137326016	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	225	1018	0	ENST00000481739.1:c.1204G>C	p.Ala402Pro	p.A402P	ENST00000481739	NM_002957.4	402	Gcc/Ccc	9/10	0.851512024064032	2	FACETS	0.472	0.439	0.506	0.236	0.219	0.253	SUBCLONAL	1	TRUE	0	0.851512024064032	2		1018	1119	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405649	139405649	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	1211	1251	3	ENST00000277541.6:c.2542G>T	p.Glu848Ter	p.E848*	ENST00000277541	NM_017617.3	848	Gag/Tag	16/34	0.851512024064032	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.851512024064032	2		1254	1372	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1331463	1331463	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	374	686	0	ENST00000400841.2:c.65G>T	p.Gly22Val	p.G22V	ENST00000400841		22	gGg/gTg	1/6	0.512885484905254	2	FACETS	0.867	0.825	0.91			1	CLONAL	1	TRUE	NA	0.851512024064032	2		686	1013	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236087	108236087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781894	NA	P-0054856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	532	562	0	ENST00000278616.4:c.9023G>A	p.Arg3008His	p.R3008H	ENST00000278616	NM_000051.3	3008	cGt/cAt	63/63	0.845779336709823	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.845779336709823	2		562	625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519996	NA	P-0054856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	973	1050	0	ENST00000269305.4:c.395A>C	p.Lys132Thr	p.K132T	ENST00000269305	NM_001126112.2	132	aAg/aCg	5/11	0.845779336709823	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.845779336709823	2		1050	1139	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40857139	40857139	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	532	473	1	ENST00000428826.2:c.1902G>T	p.Gln634His	p.Q634H	ENST00000428826		634	caG/caT	17/21	0.845779336709823	3	FACETS	0.981	0.963	0.999	0.981	0.963	0.999	CLONAL	3	TRUE	0	0.845779336709823	3		474	608	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436149	56436149	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	1571	785	0	ENST00000407977.2:c.988C>T	p.Arg330Ter	p.R330*	ENST00000407977		330	Cga/Tga	9/10	0.837377495786142	5	FACETS	1	0.993	1	1	0.993	1	CLONAL	5	TRUE	0	0.845779336709823	5		785	1682	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0054856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	384	440	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.845779336709823	2	FACETS	0.974	0.948	0.999	0.974	0.948	0.999	CLONAL	2	TRUE	0	0.845779336709823	2		440	466	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390914	89390914	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	299	363	0	ENST00000336596.2:c.980C>G	p.Ser327Cys	p.S327C	ENST00000336596	NM_005233.5	327	tCt/tGt	5/17	0.715176270482285	4	FACETS	1	0.952	1			1	CLONAL	2	TRUE	NA	0.845779336709823	4		363	651	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513202	149513202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374864774	NA	P-0054856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	695	853	2	ENST00000261799.4:c.881C>T	p.Thr294Met	p.T294M	ENST00000261799	NM_002609.3	294	aCg/aTg	6/23	0.845779336709823	3	FACETS	0.981	0.952	1	0.981	0.952	1	CLONAL	2	TRUE	1	0.845779336709823	3		855	1192	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180076529	180076529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	35	101	0	ENST00000261937.6:c.17C>T	p.Ala6Val	p.A6V	ENST00000261937	NM_182925.4	6	gCg/gTg	1/30	1	2	FACETS	0.836	0.705	0.973	0.836	0.705	0.973	CLONAL	1	TRUE	1	0.845779336709823	2		101	99	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236087	108236087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781894	NA	P-0054856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	271	562	0	ENST00000278616.4:c.9023G>A	p.Arg3008His	p.R3008H	ENST00000278616	NM_000051.3	3008	cGt/cAt	63/63	0.39575641763947	2	FACETS	0.973	0.918	1	0.973	0.918	1	CLONAL	2	TRUE	0	0.39575641763947	2		562	704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519996	NA	P-0054856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	502	1050	0	ENST00000269305.4:c.395A>C	p.Lys132Thr	p.K132T	ENST00000269305	NM_001126112.2	132	aAg/aCg	5/11	0.139880279192598	3	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.39575641763947	3		1050	1226	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40857139	40857139	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	266	473	1	ENST00000428826.2:c.1902G>T	p.Gln634His	p.Q634H	ENST00000428826		634	caG/caT	17/21	0.366529562962499	3	FACETS	0.89	0.842	0.939	0.89	0.842	0.939	CLONAL	3	TRUE	0	0.39575641763947	3		474	603	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436149	56436149	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	675	785	0	ENST00000407977.2:c.988C>T	p.Arg330Ter	p.R330*	ENST00000407977		330	Cga/Tga	9/10	0.36731047368504	5	FACETS	0.924	0.896	0.951	0.924	0.896	0.951	CLONAL	5	TRUE	0	0.39575641763947	5		785	1177	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0054856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	180	440	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.39575641763947	2	FACETS	0.87	0.808	0.933	0.87	0.808	0.933	CLONAL	2	TRUE	0	0.39575641763947	2		440	523	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390914	89390914	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	159	363	0	ENST00000336596.2:c.980C>G	p.Ser327Cys	p.S327C	ENST00000336596	NM_005233.5	327	tCt/tGt	5/17	0.297773482398282	4	FACETS	0.886	0.815	0.959	0.886	0.815	0.959	CLONAL	2	TRUE	2	0.39575641763947	4		363	633	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513202	149513202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374864774	NA	P-0054856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	314	853	2	ENST00000261799.4:c.881C>T	p.Thr294Met	p.T294M	ENST00000261799	NM_002609.3	294	aCg/aTg	6/23	0.39575641763947	3	FACETS	0.924	0.873	0.976	0.924	0.873	0.976	CLONAL	2	TRUE	1	0.39575641763947	3		855	1029	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180076529	180076529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	36	101	0	ENST00000261937.6:c.17C>T	p.Ala6Val	p.A6V	ENST00000261937	NM_182925.4	6	gCg/gTg	1/30	0.39575641763947	3	FACETS	0.964	0.813	1	0.964	0.813	1	CLONAL	2	TRUE	1	0.39575641763947	3		101	113	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0054859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	273	705	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.429600916114103	2	FACETS	0.803	0.759	0.848	0.803	0.759	0.848	CLONAL	2	TRUE	0	0.516461591318381	2		705	658	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218659	36218659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555731093	NA	P-0054859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	143	807	2	ENST00000222270.7:c.4363C>T	p.Arg1455Cys	p.R1455C	ENST00000222270	NM_014727.1	1455	Cgc/Tgc	17/37	0.28749304732343	5	FACETS	0.923	0.84	1	0.308	0.28	0.337	INDETERMINATE	1	TRUE	2	0.516461591318381	5		809	1065	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551418	150551418	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	426	799	0	ENST00000369026.2:c.589A>G	p.Lys197Glu	p.K197E	ENST00000369026	NM_021960.4	197	Aag/Gag	1/3	0.516461591318381	3	FACETS	0.879	0.838	0.92	0.879	0.838	0.92	CLONAL	2	TRUE	1	0.516461591318381	3		799	1181	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575476	64575476	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	250	826	0	ENST00000312049.6:c.541C>G	p.His181Asp	p.H181D	ENST00000312049	NM_130799.2	181	Cat/Gat	3/10	0.656890876527774	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.656890876527774	1		826	475	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374245	138374245	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054860-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	19	460	0	ENST00000289153.2:c.3199G>C	p.Asp1067His	p.D1067H	ENST00000289153	NM_006219.2	1067	Gac/Cac	22/22	1	2	FACETS	0.064	0.048	0.083	0.064	0.048	0.083	SUBCLONAL	1	TRUE	1	0.890654157078731	2		460	664	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593603	55593603	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913235	NA	P-0054860-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	245	402	0	ENST00000288135.5:c.1669T>A	p.Trp557Arg	p.W557R	ENST00000288135	NM_000222.2	557	Tgg/Agg	11/21	1	2	FACETS	0.989	0.934	1	0.989	0.934	1	CLONAL	1	TRUE	1	0.890654157078731	2		402	556	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359919	87359919	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	31	196	1	ENST00000277120.3:c.1227C>A	p.Asp409Glu	p.D409E	ENST00000277120		409	gaC/gaA	11/19	0.270313429935005	1	FACETS	0.513	0.42	0.614	0.513	0.42	0.614	INDETERMINATE	1	TRUE	0	0.57465221340015	1		197	150	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359919	87359919	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	47	196	1	ENST00000277120.3:c.1227C>A	p.Asp409Glu	p.D409E	ENST00000277120		409	gaC/gaA	11/19	1	2	FACETS	0.884	0.76	1	0.884	0.76	1	CLONAL	1	TRUE	1	0.69524328763554	2		197	153	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431629	6431629	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	18	83	0	ENST00000356142.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000356142	NM_018890.3	61	cAa/cGa	3/7	1	2	FACETS	0.432	0.329	0.55	0.432	0.329	0.55	SUBCLONAL	1	TRUE	1	0.69524328763554	2		83	120	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510627	38510627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	186	600	0	ENST00000254066.5:c.881G>A	p.Arg294Gln	p.R294Q	ENST00000254066	NM_000964.3	294	cGg/cAg	7/9	1	2	FACETS	0.415	0.382	0.45	0.415	0.382	0.45	SUBCLONAL	1	TRUE	1	0.69524328763554	2		600	1288	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390785	139390785	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	73	731	0	ENST00000277541.6:c.7406del	p.Pro2469HisfsTer8	p.P2469Hfs*8	ENST00000277541	NM_017617.3	2469	cCa/ca	34/34	1	2	FACETS	0.166	0.144	0.189	0.166	0.144	0.189	SUBCLONAL	1	TRUE	1	0.69524328763554	2		731	1266	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453095	140453095	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	83	434	0	ENST00000288602.6:c.1840T>C	p.Ser614Pro	p.S614P	ENST00000288602	NM_004333.4	614	Tct/Cct	15/18	0.125877301733728	3	FACETS	1	0.944	1	0.547	0.487	0.609	INDETERMINATE	1	TRUE	1	0.637736781572603	3		434	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573984	7573984	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0054865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	391	938	0	ENST00000269305.4:c.1043T>A	p.Leu348Ter	p.L348*	ENST00000269305	NM_001126112.2	348	tTg/tAg	10/11	0.571712902116072	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.637736781572603	1		938	757	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376175	118376175	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	91	622	1	ENST00000534358.1:c.9568G>A	p.Gly3190Arg	p.G3190R	ENST00000534358	NM_005933.3	3190	Ggg/Agg	27/36	NA	2	FACETS	0.564	0.502	0.629			1	INDETERMINATE	1	TRUE	NA	0.637736781572603	2		623	506	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037868	49037872	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TTATG	TTATG	-	novel	NA	P-0054865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	33	283	0	ENST00000267163.4:c.2108_2112del	p.Ile703AsnfsTer16	p.I703Nfs*16	ENST00000267163	NM_000321.2	703	aTTATG/a	21/27	0.637736781572603	1	FACETS	0.75	0.629	0.877	0.75	0.629	0.877	SUBCLONAL	1	TRUE	0	0.637736781572603	1		283	94	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118682	11118688	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGCGG	CGCGCGG	-	novel	NA	P-0054865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	293	830	0	ENST00000358026.2:c.2107_2113del	p.Ala703ThrfsTer69	p.A703Tfs*69	ENST00000358026	NM_001128849.1	702	gaCGCGCGG/ga	14/36	0.637736781572603	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.637736781572603	1		830	592	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294085	1294085	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	308	1206	0	ENST00000310581.5:c.916G>T	p.Gly306Cys	p.G306C	ENST00000310581	NM_198253.2	306	Ggc/Tgc	2/16	0.302950292991454	1	FACETS	0.774	0.732	0.816	0.774	0.732	0.816	INDETERMINATE	1	TRUE	0	0.637736781572603	1		1206	850	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839858	27839858	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	271	910	0	ENST00000328488.2:c.236T>A	p.Phe79Tyr	p.F79Y	ENST00000328488	NM_003533.2	79	tTt/tAt	1/1	0.287967629748609	1	FACETS	0.79	0.745	0.835	0.79	0.745	0.835	INDETERMINATE	1	TRUE	0	0.637736781572603	1		910	733	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009257	69009257	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	65	433	0	ENST00000288368.4:c.2374A>T	p.Ile792Phe	p.I792F	ENST00000288368	NM_024870.2	792	Att/Ttt	22/40	0.302950292991454	1	FACETS	0.484	0.423	0.548	0.484	0.423	0.548	INDETERMINATE	1	TRUE	0	0.637736781572603	1		433	287	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0054867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	376	928	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.361632045916904	2	FACETS	0.928	0.883	0.975	0.928	0.883	0.975	CLONAL	2	TRUE	0	0.378136774084153	2		928	1071	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346977	73346977	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	172	247	0	ENST00000377767.4:c.1240G>C	p.Gly414Arg	p.G414R	ENST00000377767	NM_014953.3	414	Gga/Cga	9/21	0.307855309392959	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	3	TRUE	0	0.378136774084153	3		247	345	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424405	49424405	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555187117	NA	P-0054867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	132	781	0	ENST00000301067.7:c.13818C>G	p.Tyr4606Ter	p.Y4606*	ENST00000301067	NM_003482.3	4606	taC/taG	41/54	0.149715217207571	5	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.378136774084153	5		781	961	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444308	50444308	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	67	384	0	ENST00000331340.3:c.238G>A	p.Glu80Lys	p.E80K	ENST00000331340	NM_006060.4	80	Gag/Aag	4/8	1	2	FACETS	0.795	0.693	0.904	0.795	0.693	0.904	CLONAL	1	TRUE	1	0.378136774084153	2		384	446	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142576	119142576	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	142	358	0	ENST00000264033.4:c.575A>G	p.Lys192Arg	p.K192R	ENST00000264033	NM_005188.3	192	aAa/aGa	3/16	0.361632045916904	2	FACETS	0.918	0.845	0.993	0.918	0.845	0.993	CLONAL	2	TRUE	0	0.378136774084153	2		358	409	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448380	49448380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	165	869	1	ENST00000301067.7:c.331C>T	p.Pro111Ser	p.P111S	ENST00000301067	NM_003482.3	111	Ccc/Tcc	3/54	0.149715217207571	5	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.378136774084153	5		870	1107	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528188	103528188	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0054867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	245	419	0	ENST00000355739.4:c.3496A>T	p.Arg1166Ter	p.R1166*	ENST00000355739	NM_000123.3	1166	Aga/Tga	15/15	0.307855309392959	3	FACETS	0.917	0.865	0.97	0.917	0.865	0.97	CLONAL	3	TRUE	0	0.378136774084153	3		419	560	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060755	38060756	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	AT	novel	NA	P-0054867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1152	206	1040	2	ENST00000250448.2:c.1233_1234delinsAT	p.Gln412Ter	p.Q412*	ENST00000250448	NM_004496.3	411	caGCag/caATag	2/2	0.37718841383244	3	FACETS	0.954	0.883	1	0.477	0.441	0.514	CLONAL	1	TRUE	1	0.378136774084153	3		1042	1358	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440000	56440000	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	150	737	0	ENST00000407977.2:c.592G>C	p.Asp198His	p.D198H	ENST00000407977		198	Gat/Cat	6/10	0.37718841383244	3	FACETS	1	0.933	1	0.512	0.468	0.559	CLONAL	1	TRUE	1	0.378136774084153	3		737	921	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469956	25469956	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	184	764	0	ENST00000264709.3:c.1086G>C	p.Gln362His	p.Q362H	ENST00000264709	NM_175629.2	362	caG/caC	9/23	0.37718841383244	3	FACETS	1	0.972	1	0.556	0.513	0.602	CLONAL	1	TRUE	1	0.378136774084153	3		764	1040	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295795	212295795	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	203	588	0	ENST00000342788.4:c.2518G>C	p.Val840Leu	p.V840L	ENST00000342788	NM_005235.2	840	Gtt/Ctt	21/28	0.361632045916904	2	FACETS	0.769	0.716	0.824	0.769	0.716	0.824	SUBCLONAL	2	TRUE	0	0.378136774084153	2		588	698	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447145	187447145	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	321	793	1	ENST00000232014.4:c.1048A>G	p.Ser350Gly	p.S350G	ENST00000232014	NM_001130845.1	350	Agt/Ggt	5/10	0.370657786781253	4	FACETS	0.928	0.876	0.982	0.928	0.876	0.982	CLONAL	2	TRUE	2	0.378136774084153	4		794	1260	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047211	180047211	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	342	965	0	ENST00000261937.6:c.2504C>A	p.Ala835Asp	p.A835D	ENST00000261937	NM_182925.4	835	gCc/gAc	17/30	0.163917374881518	3	FACETS	0.983	0.931	1			1	INDETERMINATE	2	TRUE	NA	0.378136774084153	3		965	1094	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048671	180048671	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	160	988	0	ENST00000261937.6:c.1891del	p.Ala631ArgfsTer8	p.A631Rfs*8	ENST00000261937	NM_182925.4	631	Gcg/cg	13/30	0.163917374881518	3	FACETS	0.87	0.796	0.947			1	INDETERMINATE	1	TRUE	NA	0.378136774084153	3		988	1157	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968283	2968283	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	313	848	3	ENST00000396946.4:c.1703C>G	p.Pro568Arg	p.P568R	ENST00000396946	NM_032415.4	568	cCg/cGg	13/25	0.378136774084153	5	FACETS	0.927	0.873	0.982	0.618	0.582	0.655	CLONAL	2	TRUE	2	0.378136774084153	5		851	1400	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434716	128434716	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	278	723	0	ENST00000265960.3:c.138G>T	p.Met46Ile	p.M46I	ENST00000265960	NM_001006617.1	46	atG/atT	2/12	0.316390747358566	5	FACETS	1	0.949	1	0.675	0.634	0.717	CLONAL	2	TRUE	2	0.378136774084153	5		723	1138	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	50	290	1				ENST00000310581	NM_198253.2	-/1132			0.0564152220565952	4	FACETS	1	0.867	1	1	0.867	1	INDETERMINATE	2	TRUE	2	0.190661241997953	4		291	307	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0054868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	671	844	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.190661241997953	12	FACETS	0.991	0.956	1			1	CLONAL	9	TRUE	NA	0.190661241997953	12		845	1542	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793483	18793483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603405	NA	P-0054868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	22	300	1	ENST00000266497.5:c.4180G>A	p.Glu1394Lys	p.E1394K	ENST00000266497		1394	Gaa/Aaa	30/31	1	2	FACETS	0.663	0.514	0.837	0.663	0.514	0.837	SUBCLONAL	1	TRUE	1	0.190661241997953	2		301	348	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303035	15303035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777257132	NA	P-0054868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	52	1025	0	ENST00000263388.2:c.415G>A	p.Asp139Asn	p.D139N	ENST00000263388	NM_000435.2	139	Gat/Aat	4/33	1	2	FACETS	0.519	0.44	0.606	0.519	0.44	0.606	SUBCLONAL	1	TRUE	1	0.190661241997953	2		1025	1051	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134479	30134479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	21	366	0	ENST00000263025.4:c.52G>A	p.Glu18Lys	p.E18K	ENST00000263025	NM_002746.2	18	Gag/Aag	1/9	1	2	FACETS	0.492	0.378	0.625	0.492	0.378	0.625	SUBCLONAL	1	TRUE	1	0.190661241997953	2		366	448	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222759	53222759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	27	528	0	ENST00000375401.3:c.4177G>A	p.Glu1393Lys	p.E1393K	ENST00000375401	NM_004187.3	1393	Gag/Aag	25/26	1	1	FACETS	0.581	0.462	0.718	0.581	0.462	0.718	SUBCLONAL	1	TRUE	0	0.190661241997953	1		528	441	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258781	16258781	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	32	582	0	ENST00000375759.3:c.6046G>T	p.Glu2016Ter	p.E2016*	ENST00000375759	NM_015001.2	2016	Gag/Tag	11/15	1	2	FACETS	0.562	0.455	0.684	0.562	0.455	0.684	SUBCLONAL	1	TRUE	1	0.190661241997953	2		582	597	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61709516	61709516	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	39	347	0	ENST00000401558.2:c.2971G>A	p.Asp991Asn	p.D991N	ENST00000401558	NM_003400.3	991	Gat/Aat	23/25	0.190661241997953	3	FACETS	1	0.915	1	0.587	0.487	0.697	CLONAL	1	TRUE	1	0.190661241997953	3		347	382	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480099	20480099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	24	425	0	ENST00000346618.3:c.416G>A	p.Gly139Glu	p.G139E	ENST00000346618	NM_001949.4	139	gGa/gAa	2/7	1	2	FACETS	0.567	0.444	0.71	0.567	0.444	0.71	SUBCLONAL	1	TRUE	1	0.190661241997953	2		425	444	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962804	2962804	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	84	882	1	ENST00000396946.4:c.2104G>T	p.Glu702Ter	p.E702*	ENST00000396946	NM_032415.4	702	Gag/Tag	16/25	1	2	FACETS	0.902	0.795	1	0.902	0.795	1	CLONAL	1	TRUE	1	0.190661241997953	2		883	977	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088731	27088731	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	32	832	0	ENST00000324856.7:c.2340G>C	p.Gln780His	p.Q780H	ENST00000324856	NM_006015.4	780	caG/caC	7/20	1	2	FACETS	0.42	0.339	0.511	0.42	0.339	0.511	SUBCLONAL	1	TRUE	1	0.190661241997953	2		832	800	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590602	95590602	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	10	0	0	ENST00000393063.1:c.1307C>A	p.Ser436Tyr	p.S436Y	ENST00000393063	NM_030621.3	436	tCt/tAt	9/28	1	2	FACETS	0.313	0.211	0.442	0.313	0.211	0.442	SUBCLONAL	1	TRUE	1	0.190661241997953	2		0	335	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590606	95590606	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	10	0	0	ENST00000393063.1:c.1303C>A	p.Pro435Thr	p.P435T	ENST00000393063	NM_030621.3	435	Cct/Act	9/28	1	2	FACETS	0.31	0.209	0.438	0.31	0.209	0.438	SUBCLONAL	1	TRUE	1	0.190661241997953	2		0	338	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14028120	14028120	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	16	454	0	ENST00000311895.7:c.1174G>T	p.Glu392Ter	p.E392*	ENST00000311895	NM_005236.2	392	Gag/Tag	7/11	1	2	FACETS	0.418	0.308	0.55	0.418	0.308	0.55	SUBCLONAL	1	TRUE	1	0.190661241997953	2		454	402	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39726971	39726971	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	7	275	0	ENST00000361337.2:c.969G>C	p.Glu323Asp	p.E323D	ENST00000361337	NM_003286.2	323	gaG/gaC	11/21	1	2	FACETS	0.288	0.179	0.433	0.288	0.179	0.433	SUBCLONAL	1	TRUE	1	0.190661241997953	2		275	255	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	37	290	1				ENST00000310581	NM_198253.2	-/1132			0.178182826297395	5	FACETS	1	0.899	1	0.742	0.619	0.877	CLONAL	2	TRUE	2	0.237170915660959	5		291	190	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0054868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	702	844	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.237170915660959	10	FACETS	1	0.987	1			1	CLONAL	7	TRUE	NA	0.237170915660959	10		845	1582	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303035	15303035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777257132	NA	P-0054868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	38	1025	0	ENST00000263388.2:c.415G>A	p.Asp139Asn	p.D139N	ENST00000263388	NM_000435.2	139	Gat/Aat	4/33	1	2	FACETS	0.432	0.356	0.518	0.432	0.356	0.518	SUBCLONAL	1	TRUE	1	0.237170915660959	2		1025	741	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134479	30134479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	20	366	0	ENST00000263025.4:c.52G>A	p.Glu18Lys	p.E18K	ENST00000263025	NM_002746.2	18	Gag/Aag	1/9	1	2	FACETS	0.539	0.412	0.687	0.539	0.412	0.687	SUBCLONAL	1	TRUE	1	0.237170915660959	2		366	313	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222759	53222759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	49	528	0	ENST00000375401.3:c.4177G>A	p.Glu1393Lys	p.E1393K	ENST00000375401	NM_004187.3	1393	Gag/Aag	25/26	1	1	FACETS	0.946	0.804	1	0.946	0.804	1	CLONAL	1	TRUE	0	0.237170915660959	1		528	385	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61709516	61709516	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	75	347	0	ENST00000401558.2:c.2971G>A	p.Asp991Asn	p.D991N	ENST00000401558	NM_003400.3	991	Gat/Aat	23/25	0.237170915660959	3	FACETS	0.797	0.701	0.899	0.797	0.701	0.899	SUBCLONAL	2	TRUE	1	0.237170915660959	3		347	444	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962804	2962804	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	58	882	1	ENST00000396946.4:c.2104G>T	p.Glu702Ter	p.E702*	ENST00000396946	NM_032415.4	702	Gag/Tag	16/25	1	2	FACETS	0.682	0.585	0.788	0.682	0.585	0.788	SUBCLONAL	1	TRUE	1	0.237170915660959	2		883	717	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088731	27088731	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	53	832	0	ENST00000324856.7:c.2340G>C	p.Gln780His	p.Q780H	ENST00000324856	NM_006015.4	780	caG/caC	7/20	1	2	FACETS	0.523	0.444	0.609	0.523	0.444	0.609	SUBCLONAL	1	TRUE	1	0.237170915660959	2		832	855	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14028120	14028120	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	22	454	0	ENST00000311895.7:c.1174G>T	p.Glu392Ter	p.E392*	ENST00000311895	NM_005236.2	392	Gag/Tag	7/11	1	2	FACETS	0.507	0.392	0.64	0.507	0.392	0.64	SUBCLONAL	1	TRUE	1	0.237170915660959	2		454	366	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39726971	39726971	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	14	275	0	ENST00000361337.2:c.969G>C	p.Glu323Asp	p.E323D	ENST00000361337	NM_003286.2	323	gaG/gaC	11/21	1	2	FACETS	0.446	0.322	0.596	0.446	0.322	0.596	SUBCLONAL	1	TRUE	1	0.237170915660959	2		275	265	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0054870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	440	778	3	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.452321557187215	2	FACETS	0.907	0.867	0.946	0.907	0.867	0.946	CLONAL	2	TRUE	0	0.452321557187215	2		781	1073	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0054870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	185	831	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.447197896635868	1	FACETS	0.746	0.69	0.805	0.746	0.69	0.805	SUBCLONAL	1	TRUE	0	0.452321557187215	1		831	848	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604750	48604750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	251	504	0	ENST00000342988.3:c.1572G>T	p.Trp524Cys	p.W524C	ENST00000342988	NM_005359.5	524	tgG/tgT	12/12	0.302818040995633	2	FACETS	0.958	0.905	1	0.958	0.905	1	CLONAL	2	TRUE	0	0.452321557187215	2		504	579	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519767	29519767	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	70	578	0	ENST00000389048.3:c.1804G>C	p.Asp602His	p.D602H	ENST00000389048	NM_004304.4	602	Gat/Cat	9/29	0.305192720221751	3	FACETS	0.457	0.398	0.522	0.152	0.132	0.174	SUBCLONAL	1	TRUE	0	0.452321557187215	3		578	830	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865164	57865164	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	239	992	1	ENST00000228682.2:c.2641C>A	p.Leu881Met	p.L881M	ENST00000228682	NM_005269.2	881	Ctg/Atg	12/12	NA	2	FACETS	0.907	0.846	0.97			1	INDETERMINATE	1	TRUE	NA	0.452321557187215	2		993	1165	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101450	27101450	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1323547914	NA	P-0054870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	148	772	0	ENST00000324856.7:c.4732A>T	p.Met1578Leu	p.M1578L	ENST00000324856	NM_006015.4	1578	Atg/Ttg	18/20	1	2	FACETS	0.834	0.762	0.908	0.834	0.762	0.908	CLONAL	1	TRUE	1	0.452321557187215	2		772	785	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922168	100922168	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	97	391	0	ENST00000325455.5:c.2344C>A	p.Leu782Ile	p.L782I	ENST00000325455	NM_001202474.3	782	Cta/Ata	5/8	0.437130562956337	4	FACETS	1	0.939	1	0.358	0.32	0.399	CLONAL	1	TRUE	1	0.452321557187215	4		391	580	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29002038	29002038	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs757020625	NA	P-0054870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	93	420	0	ENST00000282397.4:c.1127C>A	p.Ala376Glu	p.A376E	ENST00000282397	NM_002019.4	376	gCg/gAg	9/30	0.446754184407938	2	FACETS	0.832	0.743	0.927	0.416	0.371	0.464	CLONAL	1	TRUE	0	0.452321557187215	2		420	494	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40678649	40678649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	147	591	0	ENST00000249776.8:c.391C>T	p.Pro131Ser	p.P131S	ENST00000249776	NM_033286.3	131	Cca/Tca	3/9	0.447197896635868	1	FACETS	0.837	0.767	0.909	0.837	0.767	0.909	CLONAL	1	TRUE	0	0.452321557187215	1		591	601	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912798	50912798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1233422134	NA	P-0054870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	298	1139	1	ENST00000440232.2:c.2029G>A	p.Glu677Lys	p.E677K	ENST00000440232	NM_002691.3	677	Gag/Aag	17/27	0.452321557187215	2	FACETS	0.944	0.887	1	0.472	0.443	0.501	CLONAL	1	TRUE	0	0.452321557187215	2		1140	1396	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738237	190738237	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	48	251	0	ENST00000441310.2:c.2489A>C	p.Glu830Ala	p.E830A	ENST00000441310	NM_000534.4	830	gAa/gCa	12/13	0.305192720221751	3	FACETS	0.678	0.574	0.791	0.226	0.191	0.264	SUBCLONAL	1	TRUE	0	0.452321557187215	3		251	384	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660337	227660337	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	460	716	0	ENST00000305123.5:c.3118G>T	p.Ala1040Ser	p.A1040S	ENST00000305123	NM_005544.2	1040	Gcc/Tcc	1/2	0.305192720221751	3	FACETS	1	0.995	1	0.831	0.797	0.865	CLONAL	2	TRUE	0	0.452321557187215	3		716	1000	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294246	1294246	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	470	870	0	ENST00000310581.5:c.755G>T	p.Gly252Val	p.G252V	ENST00000310581	NM_198253.2	252	gGg/gTg	2/16	0.367208867541296	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.452321557187215	4		870	1479	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450324	50450324	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	563	816	1	ENST00000331340.3:c.508G>T	p.Glu170Ter	p.E170*	ENST00000331340	NM_006060.4	170	Gag/Tag	5/8	0.358611317036342	5	FACETS	0.955	0.917	0.992	0.955	0.917	0.992	CLONAL	3	TRUE	2	0.452321557187215	5		817	1459	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335705	81335705	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	109	418	0	ENST00000222390.5:c.1655A>C	p.Asp552Ala	p.D552A	ENST00000222390	NM_000601.4	552	gAt/gCt	15/18	0.437130562956337	4	FACETS	0.961	0.864	1	0.32	0.288	0.355	CLONAL	1	TRUE	1	0.452321557187215	4		418	728	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371797	55371797	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	156	199	0	ENST00000297316.4:c.487C>A	p.Gln163Lys	p.Q163K	ENST00000297316	NM_022454.3	163	Cag/Aag	2/2	0.358611317036342	5	FACETS	0.972	0.901	1	0.972	0.901	1	CLONAL	3	TRUE	2	0.452321557187215	5		199	397	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050670	69050670	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	67	477	0	ENST00000288368.4:c.4005A>T	p.Leu1335Phe	p.L1335F	ENST00000288368	NM_024870.2	1335	ttA/ttT	33/40	0.358611317036342	5	FACETS	0.661	0.574	0.756	0.22	0.191	0.252	SUBCLONAL	1	TRUE	2	0.452321557187215	5		477	752	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562701	29562702	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	G	novel	NA	P-0054870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	421	563	0	ENST00000356175.3:c.3781_3782delinsG	p.Phe1261ValfsTer5	p.F1261Vfs*5	ENST00000356175	NM_000267.3	1261	TTt/Gt	28/57	0.445227333536903	3	FACETS	0.997	0.958	1			1	CLONAL	3	TRUE	NA	0.452321557187215	3		563	763	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	247	323	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.866000778983323	2		325	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691022	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	481	1170	0	ENST00000269305.4:c.1024del	p.Arg342GlufsTer3	p.R342Efs*3	ENST00000269305	NM_001126112.2	342	Cga/ga	10/11	1	2	FACETS	0.935	0.896	0.974	0.935	0.896	0.974	CLONAL	1	TRUE	1	0.866000778983323	2		1170	1188	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005449	150005449	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	299	684	1	ENST00000253339.5:c.776G>A	p.Arg259Lys	p.R259K	ENST00000253339		259	aGa/aAa	3/7	1	2	FACETS	0.986	0.935	1	0.986	0.935	1	CLONAL	1	TRUE	1	0.866000778983323	2		685	700	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647465	117647465	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs867760368	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	120	481	0	ENST00000368508.3:c.5479C>T	p.Gln1827Ter	p.Q1827*	ENST00000368508	NM_002944.2	1827	Cag/Tag	33/43	1	2	FACETS	0.949	0.871	1	0.949	0.871	1	CLONAL	1	TRUE	1	0.866000778983323	2		481	292	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468522	89468522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	126	420	0	ENST00000336596.2:c.2056G>A	p.Glu686Lys	p.E686K	ENST00000336596	NM_005233.5	686	Gaa/Aaa	11/17	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.866000778983323	2		420	289	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857334	9857334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	319	729	0	ENST00000330684.3:c.4067C>T	p.Ser1356Phe	p.S1356F	ENST00000330684	NM_001134407.1	1356	tCt/tTt	13/13	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.866000778983323	2		729	694	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881511	48881511	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	132	357	0	ENST00000267163.4:c.233G>A	p.Trp78Ter	p.W78*	ENST00000267163	NM_000321.2	78	tGg/tAg	2/27	0.866000778983323	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.866000778983323	1		357	163	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874197	155874197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375724784	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	615	798	0	ENST00000368323.3:c.334C>T	p.Arg112Cys	p.R112C	ENST00000368323	NM_006912.5	112	Cgt/Tgt	5/6	0.866000778983323	3	FACETS	0.956	0.925	0.985	0.956	0.925	0.985	CLONAL	2	TRUE	1	0.866000778983323	3		798	1065	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826577	50826577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	79	300	1	ENST00000398568.2:c.2302C>T	p.Pro768Ser	p.P768S	ENST00000398568	NM_001042412.1	768	Cct/Tct	15/18	1	2	FACETS	0.96	0.864	1	0.96	0.864	1	CLONAL	1	TRUE	1	0.866000778983323	2		301	190	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526688	31526688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	504	1049	0	ENST00000344624.3:c.352C>T	p.Pro118Ser	p.P118S	ENST00000344624		118	Cct/Tct	2/33	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.866000778983323	2		1049	1154	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517785	176517785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	463	1126	1	ENST00000292408.4:c.395C>T	p.Ser132Phe	p.S132F	ENST00000292408	NM_213647.1	132	tCc/tTc	4/18	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.866000778983323	2		1127	1043	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022772	12022772	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	276	757	0	ENST00000396373.4:c.878C>T	p.Ser293Phe	p.S293F	ENST00000396373	NM_001987.4	293	tCc/tTc	5/8	1	2	FACETS	0.981	0.928	1	0.981	0.928	1	CLONAL	1	TRUE	1	0.866000778983323	2		757	650	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602738	55602738	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	167	616	0	ENST00000288135.5:c.2559G>A	p.Trp853Ter	p.W853*	ENST00000288135	NM_000222.2	853	tgG/tgA	18/21	1	2	FACETS	0.797	0.738	0.857	0.797	0.738	0.857	SUBCLONAL	1	TRUE	1	0.866000778983323	2		616	484	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440062	49440062	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	444	1049	2	ENST00000301067.7:c.4564C>T	p.Gln1522Ter	p.Q1522*	ENST00000301067	NM_003482.3	1522	Cag/Tag	16/54	1	2	FACETS	0.949	0.908	0.99	0.949	0.908	0.99	CLONAL	1	TRUE	1	0.866000778983323	2		1051	1081	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711992	89711993	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	56	383	0	ENST00000371953.3:c.610_611delinsAT	p.Pro204Ile	p.P204I	ENST00000371953	NM_000314.4	204	CCa/ATa	6/9	0.866000778983323	1	FACETS	0.905	0.823	0.982	0.905	0.823	0.982	CLONAL	1	TRUE	0	0.866000778983323	1		383	81	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488250	56488251	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	350	925	0	ENST00000267101.3:c.1769_1770delinsTT	p.Pro590Leu	p.P590L	ENST00000267101	NM_001982.3	590	cCC/cTT	15/28	1	2	FACETS	0.83	0.788	0.872	0.83	0.788	0.872	CLONAL	1	TRUE	1	0.866000778983323	2		925	974	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226332	133226333	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	527	1394	2	ENST00000320574.5:c.3725_3726delinsTT	p.Ser1242Phe	p.S1242F	ENST00000320574	NM_006231.2	1242	tCC/tTT	30/49	1	2	FACETS	0.875	0.839	0.911	0.875	0.839	0.911	CLONAL	1	TRUE	1	0.866000778983323	2		1396	1391	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937090	48937090	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	69	258	0	ENST00000267163.4:c.858T>G	p.Asp286Glu	p.D286E	ENST00000267163	NM_000321.2	286	gaT/gaG	8/27	0.866000778983323	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.866000778983323	1		258	89	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17129507	17129507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1274919531	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	396	1105	2	ENST00000285071.4:c.379C>T	p.Arg127Trp	p.R127W	ENST00000285071	NM_144997.5	127	Cgg/Tgg	5/14	1	2	FACETS	0.874	0.833	0.916	0.874	0.833	0.916	CLONAL	1	TRUE	1	0.866000778983323	2		1107	1046	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223244	36223244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	694	1564	2	ENST00000222270.7:c.5794C>T	p.Pro1932Ser	p.P1932S	ENST00000222270	NM_014727.1	1932	Cct/Tct	28/37	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.866000778983323	2		1566	1568	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753402	42753403	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	509	1405	0	ENST00000222329.4:c.861_862delinsTT	p.Pro288Ser	p.P288S	ENST00000222329	NM_006494.2	287	taCCcc/taTTcc	4/4	1	2	FACETS	0.844	0.809	0.88	0.844	0.809	0.88	CLONAL	1	TRUE	1	0.866000778983323	2		1405	1393	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321488	62321489	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	584	1400	2	ENST00000360203.5:c.2190_2191delinsTT	p.His731Tyr	p.H731Y	ENST00000360203	NM_001283009.1	730	ccCCac/ccTTac	25/35	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.866000778983323	2		1402	1343	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447449	12447449	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763647203	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	439	912	2	ENST00000287820.6:c.688G>A	p.Asp230Asn	p.D230N	ENST00000287820	NM_015869.4	230	Gac/Aac	5/7	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.866000778983323	2		914	990	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458270	12458270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	295	782	0	ENST00000287820.6:c.887C>T	p.Thr296Ile	p.T296I	ENST00000287820	NM_015869.4	296	aCc/aTc	6/7	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.866000778983323	2		782	665	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119642286	119642286	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	221	612	0	ENST00000316626.5:c.411A>T	p.Glu137Asp	p.E137D	ENST00000316626		137	gaA/gaT	4/12	1	2	FACETS	0.976	0.917	1	0.976	0.917	1	CLONAL	1	TRUE	1	0.866000778983323	2		612	523	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202728	128202728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	575	1178	0	ENST00000341105.2:c.992C>T	p.Pro331Leu	p.P331L	ENST00000341105	NM_032638.4	331	cCa/cTa	4/6	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.866000778983323	2		1178	1250	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131978034	131978035	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	136	496	0	ENST00000265335.6:c.3917_3918delinsTT	p.Ser1306Phe	p.S1306F	ENST00000265335		1306	tCC/tTT	25/25	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.866000778983323	2		496	292	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163663	32163663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	349	667	1	ENST00000375023.3:c.5563G>A	p.Gly1855Ser	p.G1855S	ENST00000375023	NM_004557.3	1855	Ggc/Agc	30/30	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.866000778983323	2		668	725	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467857	50467858	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	295	940	3	ENST00000331340.3:c.1092_1093delinsAA	p.Ala365Thr	p.A365T	ENST00000331340	NM_006060.4	364	tcGGcc/tcAAcc	8/8	1	2	FACETS	0.894	0.846	0.943	0.894	0.846	0.943	CLONAL	1	TRUE	1	0.866000778983323	2		943	762	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848093	151848093	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	94	351	0	ENST00000262189.6:c.12667-1G>A		p.X4223_splice	ENST00000262189	NM_170606.2	4223			1	2	FACETS	0.916	0.83	1	0.916	0.83	1	CLONAL	1	TRUE	1	0.866000778983323	2		351	237	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891154	151891154	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	259	695	0	ENST00000262189.6:c.4600C>T	p.Gln1534Ter	p.Q1534*	ENST00000262189	NM_170606.2	1534	Cag/Tag	31/59	1	2	FACETS	0.935	0.882	0.988	0.935	0.882	0.988	CLONAL	1	TRUE	1	0.866000778983323	2		695	640	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141569565	141569565	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	248	700	0	ENST00000220592.5:c.719T>A	p.Phe240Tyr	p.F240Y	ENST00000220592	NM_012154.3	240	tTt/tAt	6/19	1	2	FACETS	0.964	0.909	1	0.964	0.909	1	CLONAL	1	TRUE	1	0.866000778983323	2		700	594	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882068	36882068	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1487	621	1269	0	ENST00000358127.4:c.945C>A	p.Tyr315Ter	p.Y315*	ENST00000358127	NM_001280556.1	315	taC/taA	8/10	0.866000778983323	3	FACETS	0.975	0.936	1	0.487	0.468	0.507	CLONAL	1	TRUE	1	0.866000778983323	3		1269	2108	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412217	139412217	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	1501	1257	0	ENST00000277541.6:c.1428C>A	p.Cys476Ter	p.C476*	ENST00000277541	NM_017617.3	476	tgC/tgA	8/34	0.866000778983323	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.866000778983323	3		1257	1630	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786775	3786787	+	protein_altering_variant	In_Frame_Del	DEL	CCTTCACTTGGAG	CCTTCACTTGGAG	T	novel	NA	P-0054871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	223	699	0	ENST00000262367.5:c.4424_4436delinsA	p.Pro1475_Gly1479delinsGln	p.P1475_G1479delinsQ	ENST00000262367	NM_004380.2	1475	cCTCCAAGTGAAGGa/cAa	27/31	1	2	FACETS	0.879	0.824	0.934	0.879	0.824	0.934	CLONAL	1	TRUE	1	0.866000778983323	2		699	586	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0054873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	206	1080	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.237149336354135	2	FACETS	0.969	0.9	1	0.969	0.9	1	CLONAL	2	TRUE	0	0.251317921985093	2		1080	846	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0054873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	44	397	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	0.237149336354135	2	FACETS	0.959	0.807	1	0.48	0.403	0.564	CLONAL	1	TRUE	0	0.251317921985093	2		397	365	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207064	1207065	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1131690917	NA	P-0054873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	185	1060	0	ENST00000326873.7:c.157dup	p.Asp53GlyfsTer110	p.D53Gfs*110	ENST00000326873	NM_000455.4	51	atg/atGg	1/10	0.237149336354135	2	FACETS	0.897	0.829	0.967	0.897	0.829	0.967	CLONAL	2	TRUE	0	0.251317921985093	2		1060	821	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485136	57485387	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTGTGTATGGCTTCCACTCTTGCTGGCTGTTCATTGCGGTGGTTCTTTTTCAAACGGTCAGGCTGAAAACCCCCATCCCCCTCCCACCACCAAACCATAAAGGATCTATAAGAGAAGCAAGAAAAACGCACTCCCACTAATTCTCATATGGAAAAATCAGGGTTTTGAAGACTTCAGGAGCTACAGAGATGCTAGCACCCCAGCTCTGCTTGAATTTTAAATTACATTAATATGTATTCCCTTTTTATATA	GGTGTGTATGGCTTCCACTCTTGCTGGCTGTTCATTGCGGTGGTTCTTTTTCAAACGGTCAGGCTGAAAACCCCCATCCCCCTCCCACCACCAAACCATAAAGGATCTATAAGAGAAGCAAGAAAAACGCACTCCCACTAATTCTCATATGGAAAAATCAGGGTTTTGAAGACTTCAGGAGCTACAGAGATGCTAGCACCCCAGCTCTGCTTGAATTTTAAATTACATTAATATGTATTCCCTTTTTATATA	-	novel	NA	P-0054873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	46	466	2	ENST00000371085.3:c.970+1_971-1del		p.X324_splice	ENST00000371085	NM_000516.4	324		11/13	0.251317921985093	11	FACETS	0.922	0.774	1			1	CLONAL	1	TRUE	NA	0.251317921985093	11		468	846	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168785	56168785	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	44	488	0	ENST00000399503.3:c.1639C>T	p.Gln547Ter	p.Q547*	ENST00000399503	NM_005921.1	547	Cag/Tag	9/20	1	2	FACETS	0.886	0.745	1	0.886	0.745	1	CLONAL	1	TRUE	1	0.251317921985093	2		488	395	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11313898	11313898	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	46	625	0	ENST00000361445.4:c.838G>T	p.Glu280Ter	p.E280*	ENST00000361445	NM_004958.3	280	Gag/Tag	6/58	0.190927286309325	3	FACETS	0.974	0.822	1	0.487	0.411	0.571	CLONAL	1	TRUE	1	0.251317921985093	3		625	423	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998726	100998726	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	76	1020	0	ENST00000325455.5:c.1076C>T	p.Pro359Leu	p.P359L	ENST00000325455	NM_001202474.3	359	cCc/cTc	1/8	0.237149336354135	2	FACETS	0.916	0.804	1	0.458	0.402	0.519	CLONAL	1	TRUE	0	0.251317921985093	2		1020	660	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942199	17942199	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	67	798	0	ENST00000458235.1:c.2816A>G	p.Tyr939Cys	p.Y939C	ENST00000458235	NM_000215.3	939	tAc/tGc	21/24	0.237149336354135	2	FACETS	0.824	0.716	0.941	0.412	0.358	0.471	CLONAL	1	TRUE	0	0.251317921985093	2		798	647	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190656608	190656608	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	57	348	1	ENST00000441310.2:c.73G>T	p.Val25Leu	p.V25L	ENST00000441310	NM_000534.4	25	Gta/Tta	2/13	NA	2	FACETS	0.843	0.73	0.964			1	INDETERMINATE	2	TRUE	NA	0.251317921985093	2		349	269	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265325	46265325	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	129	411	0	ENST00000371998.3:c.2195A>T	p.Lys732Met	p.K732M	ENST00000371998		732	aAg/aTg	12/23	0.251317921985093	7	FACETS	1	0.958	1			1	CLONAL	3	TRUE	NA	0.251317921985093	7		411	514	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374369	138374369	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0054873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	40	398	0	ENST00000289153.2:c.3076-1G>A		p.X1026_splice	ENST00000289153	NM_006219.2	1026			0.251317921985093	5	FACETS	1	0.91	1	0.382	0.318	0.454	CLONAL	1	TRUE	2	0.251317921985093	5		398	382	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956594	93956594	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	41	494	0	ENST00000369303.4:c.2642C>A	p.Pro881Gln	p.P881Q	ENST00000369303	NM_004440.3	881	cCa/cAa	15/17	0.251317921985093	1	FACETS	0.875	0.732	1	0.875	0.732	1	CLONAL	1	TRUE	0	0.251317921985093	1		494	326	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455080	50455080	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	240	519	0	ENST00000331340.3:c.627C>A	p.Ser209Arg	p.S209R	ENST00000331340	NM_006060.4	209	agC/agA	6/8	0.251317921985093	5	FACETS	1	0.98	1	1	0.98	1	CLONAL	5	TRUE	0	0.251317921985093	5		519	489	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449788	8449789	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0054873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	47	721	1	ENST00000356435.5:c.3924_3925delinsTT	p.Lys1308_Glu1309delinsAsnTer	p.K1308_E1309delinsN*	ENST00000356435		1308	aaGGag/aaTTag	23/35	0.251317921985093	2	FACETS	0.735	0.62	0.861	0.367	0.31	0.431	SUBCLONAL	1	TRUE	0	0.251317921985093	2		722	509	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652483	48652483	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	101	1155	0	ENST00000376670.3:c.1154C>G	p.Pro385Arg	p.P385R	ENST00000376670	NM_002049.3	385	cCc/cGc	6/6	0.251317921985093	2	FACETS	1	0.898	1	0.502	0.449	0.56	CLONAL	1	TRUE	0	0.251317921985093	2		1155	800	SUCCESS
AR	367	MSKCC	GRCh37	X	66931375	66931375	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	72	774	0	ENST00000374690.3:c.2017A>T	p.Ile673Phe	p.I673F	ENST00000374690	NM_000044.3	673	Atc/Ttc	4/8	0.251317921985093	2	FACETS	1	0.882	1	0.504	0.441	0.573	CLONAL	1	TRUE	0	0.251317921985093	2		774	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0054873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	53	1045	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.742	0.63	0.865	0.742	0.63	0.865	SUBCLONAL	1	TRUE	1	0.14	2		1046	1021	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0054873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	28	457	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.795	0.634	0.979	0.795	0.634	0.979	CLONAL	1	TRUE	1	0.14	2		457	503	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928065	178928076	+	inframe_deletion	In_Frame_Del	DEL	TACCTCATGGAT	TACCTCATGGAT	-	novel	NA	P-0054874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	23	591	0	ENST00000263967.3:c.1345_1356del	p.Pro449_Leu452del	p.P449_L452del	ENST00000263967	NM_006218.2	448	gTACCTCATGGATta/gta	8/21	0.131546001458518	3	FACETS	0.491	0.381	0.62	0.246	0.19	0.31	SUBCLONAL	1	TRUE	1	0.13	3		591	767	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734163	58734163	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs189669693	NA	P-0054874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	75	622	1	ENST00000305921.3:c.1221T>A	p.Cys407Ter	p.C407*	ENST00000305921	NM_003620.3	407	tgT/tgA	5/6	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.13	2		623	867	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0054875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	24	449	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.616	0.482	0.772	0.616	0.482	0.772	SUBCLONAL	1	TRUE	1	0.17	2		449	458	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156734	20156734	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	21	391	0	ENST00000379607.5:c.23G>C	p.Gly8Ala	p.G8A	ENST00000379607	NM_001412.3	8	gGa/gCa	2/7	1	2	FACETS	0.509	0.391	0.648	0.509	0.391	0.648	SUBCLONAL	1	TRUE	1	0.17	2		391	485	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	430262	430262	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	20	314	0	ENST00000399788.2:c.2440A>C	p.Ser814Arg	p.S814R	ENST00000399788	NM_001042603.1	814	Agt/Cgt	18/28	0.3	2	FACETS	0.667	0.509	0.851			1	SUBCLONAL	1	TRUE	NA	0.17	2		314	353	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805506	46805506	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	64	924	0	ENST00000290295.7:c.450G>T	p.Gln150His	p.Q150H	ENST00000290295	NM_006361.5	150	caG/caT	1/2	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.17	2		924	701	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221339	1221339	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	54	678	0	ENST00000326873.7:c.862+1del		p.G288fs	ENST00000326873	NM_000455.4	288	Ggg/gg	6/10	0.3	2	FACETS	1	0.909	1			1	CLONAL	1	TRUE	NA	0.17	2		678	583	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573569	41573569	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs775556373	NA	P-0054875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	43	845	0	ENST00000263253.7:c.5854A>G	p.Ile1952Val	p.I1952V	ENST00000263253	NM_001429.3	1952	Atc/Gtc	31/31	1	2	FACETS	0.802	0.67	0.949	0.802	0.67	0.949	CLONAL	1	TRUE	1	0.17	2		845	631	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428213	47428213	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	63	853	0	ENST00000377045.4:c.1173C>A	p.Tyr391Ter	p.Y391*	ENST00000377045	NM_001654.4	391	taC/taA	11/16	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.17	2		853	734	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	144	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.534475258635014	2		457	499	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1023835002	NA	P-0054879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	10	591	0	ENST00000558401.1:c.1A>G	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Gtg	1/4	0.534475258635014	1	FACETS	0.072	0.048	0.103	0.072	0.048	0.103	SUBCLONAL	1	TRUE	0	0.534475258635014	1		591	379	SUCCESS
APC	324	MSKCC	GRCh37	5	112175015	112175015	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1460397656	NA	P-0054879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	59	196	0	ENST00000257430.4:c.3724C>T	p.Gln1242Ter	p.Q1242*	ENST00000257430	NM_000038.5	1242	Cag/Tag	16/16	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.534475258635014	2		196	210	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180886	108180886	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0054879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	74	255	0	ENST00000278616.4:c.5763-1G>T		p.X1921_splice	ENST00000278616	NM_000051.3	1921			0.534475258635014	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.534475258635014	1		255	183	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930742	32930742	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	96	454	0	ENST00000380152.3:c.7613A>T	p.Lys2538Ile	p.K2538I	ENST00000380152		2538	aAa/aTa	15/27	0.301990252113624	1	FACETS	0.5	0.447	0.557	0.5	0.447	0.557	INDETERMINATE	1	TRUE	0	0.534475258635014	1		454	526	SUCCESS
APC	324	MSKCC	GRCh37	5	112175528	112175529	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGGTAAG	novel	NA	P-0054879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	101	342	0	ENST00000257430.4:c.4241_4247dup	p.Ile1417LysfsTer8	p.I1417Kfs*8	ENST00000257430	NM_000038.5	1413	atg/aTGGTAAGtg	16/16	1	2	FACETS	0.9	0.81	0.994	0.9	0.81	0.994	CLONAL	1	TRUE	1	0.534475258635014	2		342	420	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	41	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.654	0.544	0.775	0.654	0.544	0.775	SUBCLONAL	1	TRUE	1	0.266378414932087	2		487	471	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248736	212248737	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	31	354	0	ENST00000342788.4:c.3530dup	p.Asn1177LysfsTer9	p.N1177Kfs*9	ENST00000342788	NM_005235.2	1177	aat/aaAt	28/28	1	2	FACETS	0.657	0.532	0.799	0.657	0.532	0.799	SUBCLONAL	1	TRUE	1	0.266378414932087	2		354	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577084	7577151	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGTGCGCCGGTCTCTCCCAGGACAGGCACAAACACGCACCTCAAAGCTGTTCCGTCCCAGTAGATT	TCTGTGCGCCGGTCTCTCCCAGGACAGGCACAAACACGCACCTCAAAGCTGTTCCGTCCCAGTAGATT	-	novel	NA	P-0054882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	70	711	2	ENST00000269305.4:c.787_854del	p.Asn263GlyfsTer20	p.N263Gfs*20	ENST00000269305	NM_001126112.2	263	AATCTACTGGGACGGAACAGCTTTGAGGTGCGTGTTTGTGCCTGTCCTGGGAGAGACCGGCGCACAGAg/g	8/11	1	2	FACETS	0.708	0.617	0.807	0.708	0.617	0.807	SUBCLONAL	1	TRUE	1	0.266378414932087	2		713	742	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741666	17741666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	35	494	0	ENST00000250003.3:c.337G>A	p.Ala113Thr	p.A113T	ENST00000250003	NM_002478.4	113	Gcc/Acc	1/3	1	2	FACETS	0.749	0.613	0.902	0.749	0.613	0.902	CLONAL	1	TRUE	1	0.18	2		494	519	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061218	38061235	+	inframe_deletion	In_Frame_Del	DEL	GCCGTTCTCGAACATGTT	GCCGTTCTCGAACATGTT	-	novel	NA	P-0054883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	26	660	0	ENST00000250448.2:c.754_771del	p.Asn252_Gly257del	p.N252_G257del	ENST00000250448	NM_004496.3	252	AACATGTTCGAGAACGGC/-	2/2	1	2	FACETS	0.532	0.42	0.661	0.532	0.42	0.661	SUBCLONAL	1	TRUE	1	0.18	2		660	543	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696688	47696688	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519971	NA	P-0054883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	30	581	0	ENST00000347630.2:c.260A>C	p.Tyr87Ser	p.Y87S	ENST00000347630	NM_001007230.1	87	tAc/tCc	5/11	1	2	FACETS	0.934	0.753	1	0.934	0.753	1	CLONAL	1	TRUE	1	0.18	2		581	357	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1936921	1936931	+	protein_altering_variant	In_Frame_Del	DEL	ACAGAAGATGC	ACAGAAGATGC	GG	novel	NA	P-0054883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	22	602	2	ENST00000382891.5:c.1606_1616delinsGG	p.Thr536_Ala539delinsGly	p.T536_A539delinsG	ENST00000382891	NM_133335.3	536	ACAGAAGATGCt/GGt	7/22	1	2	FACETS	0.711	0.55	0.897	0.711	0.55	0.897	SUBCLONAL	1	TRUE	1	0.18	2		604	344	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673703	30673703	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	59	736	0	ENST00000376406.3:c.3257G>C	p.Ser1086Thr	p.S1086T	ENST00000376406	NM_014641.2	1086	aGt/aCt	10/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.18	2		736	485	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533853	63533853	+	frameshift_variant	Frame_Shift_Ins	INS	T	T	GC	novel	NA	P-0054883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	91	918	0	ENST00000307078.5:c.1301delinsGC	p.Asp434GlyfsTer28	p.D434Gfs*28	ENST00000307078	NM_004655.3	434	gAc/gGCc	6/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.18	2		918	689	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696450	47696450	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	225	482	0	ENST00000347630.2:c.373T>A	p.Phe125Ile	p.F125I	ENST00000347630	NM_001007230.1	125	Ttt/Att	6/11	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.637495536351156	2		482	702	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870863	12870864	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	109	301	0	ENST00000228872.4:c.92dup	p.Asn31LysfsTer94	p.N31Kfs*94	ENST00000228872	NM_004064.3	30	-/A	1/3	1	2	FACETS	0.838	0.758	0.921	0.838	0.758	0.921	CLONAL	1	TRUE	1	0.637495536351156	2		301	408	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831749	72831750	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0054888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	157	832	0	ENST00000268489.5:c.4831_4832del	p.Leu1611GlyfsTer50	p.L1611Gfs*50	ENST00000268489	NM_006885.3	1611	CTg/g	9/10	0.390910959762012	1	FACETS	0.393	0.36	0.428	0.393	0.36	0.428	SUBCLONAL	1	TRUE	0	0.637495536351156	1		832	853	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110621	8110621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754558313	NA	P-0054888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	144	756	1	ENST00000585124.1:c.271G>A	p.Val91Met	p.V91M	ENST00000585124	NM_004217.3	91	Gtg/Atg	5/9	1	2	FACETS	0.492	0.448	0.538	0.492	0.448	0.538	SUBCLONAL	1	TRUE	1	0.637495536351156	2		757	918	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480499	89480499	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs773980261	NA	P-0054888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	62	257	0	ENST00000336596.2:c.2336A>G	p.Tyr779Cys	p.Y779C	ENST00000336596	NM_005233.5	779	tAt/tGt	13/17	1	2	FACETS	0.473	0.41	0.541	0.473	0.41	0.541	SUBCLONAL	1	TRUE	1	0.637495536351156	2		257	411	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	225	831	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.448507561431556	1	FACETS	0.931	0.869	0.995	0.931	0.869	0.995	CLONAL	1	TRUE	0	0.448507561431556	1		831	836	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378648	25378648	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	95	391	0	ENST00000311936.3:c.350A>G	p.Lys117Arg	p.K117R	ENST00000311936	NM_004985.3	117	aAa/aGa	4/5	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.448507561431556	2		391	364	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	322	494	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.26462644447981	2	FACETS	0.82	0.778	0.864	0.82	0.778	0.864	INDETERMINATE	2	TRUE	0	0.448507561431556	2		494	875	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	54	273	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	1	2	FACETS	0.734	0.63	0.846	0.734	0.63	0.846	SUBCLONAL	1	TRUE	1	0.448507561431556	2		273	328	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245843	46245843	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	95	362	0	ENST00000334344.6:c.3937C>T	p.Gln1313Ter	p.Q1313*	ENST00000334344	NM_152641.2	1313	Caa/Taa	15/21	1	2	FACETS	0.844	0.754	0.939	0.844	0.754	0.939	CLONAL	1	TRUE	1	0.448507561431556	2		362	502	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504377	8504377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	182	509	0	ENST00000356435.5:c.1706C>T	p.Ser569Leu	p.S569L	ENST00000356435		569	tCa/tTa	12/35	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.448507561431556	2		509	782	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141502	11141502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	316	799	1	ENST00000358026.2:c.3479G>A	p.Gly1160Glu	p.G1160E	ENST00000358026	NM_001128849.1	1160	gGg/gAg	25/36	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.448507561431556	2		800	1264	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650044	93650044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	165	489	0	ENST00000375746.1:c.1595G>A	p.Gly532Glu	p.G532E	ENST00000375746	NM_001174167.1	532	gGa/gAa	12/14	1	2	FACETS	0.912	0.838	0.988	0.912	0.838	0.988	CLONAL	1	TRUE	1	0.448507561431556	2		489	807	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634746	158634746	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373187352	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	148	358	0	ENST00000263640.3:c.440G>A	p.Arg147Gln	p.R147Q	ENST00000263640	NM_001105.4	147	cGa/cAa	5/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.448507561431556	2		358	573	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36421162	36421162	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750755857	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	103	287	2	ENST00000300305.3:c.35C>T	p.Ser12Leu	p.S12L	ENST00000300305		12	tCg/tTg	1/8	0.448507561431556	1	FACETS	0.935	0.844	1	0.935	0.844	1	CLONAL	1	TRUE	0	0.448507561431556	1		289	381	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031973	26031973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	151	523	0	ENST00000244661.2:c.316G>A	p.Glu106Lys	p.E106K	ENST00000244661	NM_003537.3	106	Gag/Aag	1/1	0.448507561431556	3	FACETS	0.916	0.837	0.998	0.458	0.418	0.499	CLONAL	1	TRUE	1	0.448507561431556	3		523	900	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134379	41134379	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	161	452	0	ENST00000379561.5:c.1249C>T	p.Pro417Ser	p.P417S	ENST00000379561	NM_002015.3	417	Ccc/Tcc	2/3	1	2	FACETS	0.925	0.85	1	0.925	0.85	1	CLONAL	1	TRUE	1	0.448507561431556	2		452	776	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759416	133759416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774635743	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	262	675	4	ENST00000318560.5:c.1739C>T	p.Pro580Leu	p.P580L	ENST00000318560	NM_005157.4	580	cCg/cTg	11/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.448507561431556	2		679	1138	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340201	116340201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561295443	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	110	258	0	ENST00000397752.3:c.1063G>A	p.Glu355Lys	p.E355K	ENST00000397752	NM_000245.2	355	Gaa/Aaa	2/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.448507561431556	2		258	416	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376109	225376109	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	86	519	0	ENST00000264414.4:c.845C>A	p.Ser282Tyr	p.S282Y	ENST00000264414	NM_003590.4	282	tCt/tAt	6/16	1	2	FACETS	0.856	0.761	0.957	0.856	0.761	0.957	CLONAL	1	TRUE	1	0.448507561431556	2		519	448	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486027	29486027	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	49	262	0	ENST00000356175.3:c.205-1G>A		p.X69_splice	ENST00000356175	NM_000267.3	69			0.249153601374159	1	FACETS	0.902	0.775	1	0.902	0.775	1	INDETERMINATE	1	TRUE	0	0.448507561431556	1		262	188	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8497265	8497265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1270795879	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	78	219	1	ENST00000356435.5:c.2326G>A	p.Glu776Lys	p.E776K	ENST00000356435		776	Gaa/Aaa	15/35	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.448507561431556	2		220	294	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2964000	2964000	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	210	621	0	ENST00000396946.4:c.1808-1G>A		p.X603_splice	ENST00000396946	NM_032415.4	603			1	2	FACETS	0.99	0.92	1	0.99	0.92	1	CLONAL	1	TRUE	1	0.448507561431556	2		621	946	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39216420	39216420	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762576997	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	123	383	0	ENST00000402219.2:c.3382C>T	p.His1128Tyr	p.H1128Y	ENST00000402219	NM_005633.3	1128	Cat/Tat	21/23	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.448507561431556	2		383	445	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573794	64573794	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1114167469	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	240	809	0	ENST00000312049.6:c.959C>T	p.Pro320Leu	p.P320L	ENST00000312049	NM_130799.2	320	cCc/cTc	7/10	0.427473326893524	1	FACETS	0.872	0.815	0.931	0.872	0.815	0.931	CLONAL	1	TRUE	0	0.448507561431556	1		809	952	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076903	41076903	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	351	551	0	ENST00000373198.4:c.1517G>A	p.Trp506Ter	p.W506*	ENST00000373198	NM_133170.3	506	tGg/tAg	9/32	0.26462644447981	2	FACETS	0.825	0.783	0.867	0.825	0.783	0.867	INDETERMINATE	2	TRUE	0	0.448507561431556	2		551	949	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524125	18524125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1391898033	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	53	322	0	ENST00000266497.5:c.1637C>T	p.Pro546Leu	p.P546L	ENST00000266497		546	cCc/cTc	11/31	1	2	FACETS	0.835	0.718	0.962	0.835	0.718	0.962	CLONAL	1	TRUE	1	0.448507561431556	2		322	283	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	222	234	3				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.448507561431556	2		237	737	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759720	133759721	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	185	798	0	ENST00000318560.5:c.2043_2044delinsTT	p.Arg682Trp	p.R682W	ENST00000318560	NM_005157.4	681	ttCCgg/ttTTgg	11/11	1	2	FACETS	0.737	0.679	0.797	0.737	0.679	0.797	SUBCLONAL	1	TRUE	1	0.448507561431556	2		798	1120	SUCCESS
MET	4233	MSKCC	GRCh37	7	116409810	116409810	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753911898	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	77	237	0	ENST00000397752.3:c.2695G>A	p.Asp899Asn	p.D899N	ENST00000397752	NM_000245.2	899	Gac/Aac	12/21	1	2	FACETS	0.992	0.878	1	0.992	0.878	1	CLONAL	1	TRUE	1	0.448507561431556	2		237	346	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986956	36986956	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	254	823	1	ENST00000354822.5:c.733A>T	p.Lys245Ter	p.K245*	ENST00000354822	NM_001079668.2	245	Aaa/Taa	3/3	1	2	FACETS	0.942	0.881	1	0.942	0.881	1	CLONAL	1	TRUE	1	0.448507561431556	2		824	1202	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202869	16202869	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757023093	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	191	541	0	ENST00000375759.3:c.577C>T	p.Arg193Cys	p.R193C	ENST00000375759	NM_015001.2	193	Cgc/Tgc	3/15	1	2	FACETS	0.959	0.888	1	0.959	0.888	1	CLONAL	1	TRUE	1	0.448507561431556	2		541	888	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256754	16256754	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	177	527	1	ENST00000375759.3:c.4019G>A	p.Trp1340Ter	p.W1340*	ENST00000375759	NM_015001.2	1340	tGg/tAg	11/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.448507561431556	2		528	750	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46543233	46543234	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	130	488	1	ENST00000262741.5:c.267_268delinsTT	p.Arg90Ter	p.R90*	ENST00000262741	NM_003629.3	89	gtCCga/gtTTga	3/10	1	2	FACETS	0.815	0.741	0.894	0.815	0.741	0.894	CLONAL	1	TRUE	1	0.448507561431556	2		489	711	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204511962	204511962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	32	329	2	ENST00000367182.3:c.562C>T	p.Leu188Phe	p.L188F	ENST00000367182	NM_001278516.1	188	Ctt/Ttt	8/11	0.202800211431737	3	FACETS	0.411	0.333	0.499	0.137	0.111	0.167	INDETERMINATE	1	TRUE	0	0.448507561431556	3		331	425	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652415	206652416	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1236	171	767	2	ENST00000367120.3:c.1122_1123delinsAA	p.Ala375Thr	p.A375T	ENST00000367120	NM_014002.3	374	acGGca/acAAca	10/22	0.202800211431737	3	FACETS	0.663	0.608	0.721	0.221	0.202	0.241	INDETERMINATE	1	TRUE	0	0.448507561431556	3		769	1407	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310962	123310962	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	87	408	0	ENST00000358487.5:c.466T>C	p.Trp156Arg	p.W156R	ENST00000358487	NM_000141.4	156	Tgg/Cgg	5/18	0.204588791814543	0	FACETS	0.351	0.311	0.394			1	INDETERMINATE	1	TRUE	0	0.448507561431556	0		408	610	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137262	64137262	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1266	353	1062	1	ENST00000334205.4:c.1694C>T	p.Pro565Leu	p.P565L	ENST00000334205	NM_003942.2	565	cCc/cTc	14/17	1	2	FACETS	0.972	0.919	1	0.972	0.919	1	CLONAL	1	TRUE	1	0.448507561431556	2		1063	1619	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999693	100999693	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1274	358	1066	2	ENST00000325455.5:c.109C>T	p.Pro37Ser	p.P37S	ENST00000325455	NM_001202474.3	37	Ccg/Tcg	1/8	1	2	FACETS	0.978	0.925	1	0.978	0.925	1	CLONAL	1	TRUE	1	0.448507561431556	2		1068	1632	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195358	102195358	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	136	368	0	ENST00000263464.3:c.118C>T	p.Pro40Ser	p.P40S	ENST00000263464	NM_001165.4	40	Cct/Tct	2/9	1	2	FACETS	0.999	0.912	1	0.999	0.912	1	CLONAL	1	TRUE	1	0.448507561431556	2		368	607	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246321	46246321	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	107	352	0	ENST00000334344.6:c.4415del	p.His1472LeufsTer13	p.H1472Lfs*13	ENST00000334344	NM_152641.2	1472	cAt/ct	15/21	1	2	FACETS	0.871	0.784	0.962	0.871	0.784	0.962	CLONAL	1	TRUE	1	0.448507561431556	2		352	548	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608239	28608239	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	134	501	0	ENST00000241453.7:c.1817C>T	p.Pro606Leu	p.P606L	ENST00000241453	NM_004119.2	606	cCa/cTa	14/24	1	2	FACETS	0.876	0.798	0.958	0.876	0.798	0.958	CLONAL	1	TRUE	1	0.448507561431556	2		501	682	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100154	30100154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	146	603	0	ENST00000331968.5:c.1466C>T	p.Pro489Leu	p.P489L	ENST00000331968	NM_002742.2	489	cCt/cTt	10/18	1	2	FACETS	0.783	0.714	0.854	0.783	0.714	0.854	SUBCLONAL	1	TRUE	1	0.448507561431556	2		603	832	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849462	89849462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1175914862	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	235	778	0	ENST00000389301.3:c.1519C>T	p.Leu507Phe	p.L507F	ENST00000389301	NM_000135.2	507	Ctc/Ttc	16/43	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.448507561431556	2		778	1015	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560031	29560031	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	43	268	1	ENST00000356175.3:c.3508C>T	p.His1170Tyr	p.H1170Y	ENST00000356175	NM_000267.3	1170	Cac/Tac	27/57	0.249153601374159	1	FACETS	0.424	0.355	0.499	0.424	0.355	0.499	INDETERMINATE	1	TRUE	0	0.448507561431556	1		269	351	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271555	15271555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1306777765	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1358	439	1102	0	ENST00000263388.2:c.6884C>T	p.Ser2295Phe	p.S2295F	ENST00000263388	NM_000435.2	2295	tCt/tTt	33/33	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.448507561431556	2		1102	1797	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299821	15299821	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1278	374	1005	2	ENST00000263388.2:c.1357T>C	p.Phe453Leu	p.F453L	ENST00000263388	NM_000435.2	453	Ttc/Ctc	8/33	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.448507561431556	2		1007	1652	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18958551	18958551	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	198	612	0	ENST00000262803.5:c.372-2A>T		p.X124_splice	ENST00000262803	NM_002911.3	124			1	2	FACETS	0.969	0.898	1	0.969	0.898	1	CLONAL	1	TRUE	1	0.448507561431556	2		612	911	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967278	25967278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	131	457	1	ENST00000435504.4:c.1928C>T	p.Pro643Leu	p.P643L	ENST00000435504		643	cCa/cTa	13/13	1	2	FACETS	0.823	0.748	0.901	0.823	0.748	0.901	CLONAL	1	TRUE	1	0.448507561431556	2		458	710	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982484	25982484	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	89	241	0	ENST00000435504.4:c.806T>A	p.Ile269Asn	p.I269N	ENST00000435504		269	aTt/aAt	9/13	1	2	FACETS	0.973	0.868	1	0.973	0.868	1	CLONAL	1	TRUE	1	0.448507561431556	2		241	408	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023292	31023292	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	309	552	2	ENST00000375687.4:c.2777T>C	p.Val926Ala	p.V926A	ENST00000375687	NM_015338.5	926	gTt/gCt	13/13	0.26462644447981	2	FACETS	0.811	0.768	0.856	0.811	0.768	0.856	INDETERMINATE	2	TRUE	0	0.448507561431556	2		554	849	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739050	40739051	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	120	682	0	ENST00000373198.4:c.3233_3234delinsTT	p.Ala1078Val	p.A1078V	ENST00000373198	NM_133170.3	1078	gCC/gTT	24/32	0.26462644447981	2	FACETS	0.452	0.407	0.5	0.226	0.203	0.25	INDETERMINATE	1	TRUE	0	0.448507561431556	2		682	1184	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400143	41400143	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	120	561	0	ENST00000373198.4:c.616G>A	p.Gly206Arg	p.G206R	ENST00000373198	NM_133170.3	206	Ggg/Agg	5/32	0.26462644447981	2	FACETS	0.565	0.509	0.624	0.283	0.254	0.312	INDETERMINATE	1	TRUE	0	0.448507561431556	2		561	947	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41560058	41560058	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs778760907	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	202	292	0	ENST00000263253.7:c.3730T>C	p.Phe1244Leu	p.F1244L	ENST00000263253	NM_001429.3	1244	Ttt/Ctt	22/31	0.448507561431556	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.448507561431556	3		292	488	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573278	41573278	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	774	941	0	ENST00000263253.7:c.5563C>G	p.Pro1855Ala	p.P1855A	ENST00000263253	NM_001429.3	1855	Cca/Gca	31/31	0.448507561431556	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	1	0.448507561431556	3		941	1882	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584566	189584566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1341337563	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	117	281	0	ENST00000264731.3:c.862G>A	p.Val288Ile	p.V288I	ENST00000264731	NM_003722.4	288	Gta/Ata	6/14	0.176893276068739	3	FACETS	1	0.977	1	0.629	0.57	0.691	INDETERMINATE	1	TRUE	1	0.448507561431556	3		281	508	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981178	55981178	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1371982221	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	95	411	0	ENST00000263923.4:c.521G>A	p.Gly174Asp	p.G174D	ENST00000263923	NM_002253.2	174	gGt/gAt	5/30	1	2	FACETS	0.99	0.887	1	0.99	0.887	1	CLONAL	1	TRUE	1	0.448507561431556	2		411	428	SUCCESS
APC	324	MSKCC	GRCh37	5	112179237	112179237	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	72	324	0	ENST00000257430.4:c.7946C>T	p.Pro2649Leu	p.P2649L	ENST00000257430	NM_000038.5	2649	cCt/cTt	16/16	1	2	FACETS	0.84	0.738	0.949	0.84	0.738	0.949	CLONAL	1	TRUE	1	0.448507561431556	2		324	382	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441324	149441324	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	297	628	1	ENST00000286301.3:c.1715A>T	p.Asn572Ile	p.N572I	ENST00000286301	NM_005211.3	572	aAc/aTc	12/22	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.448507561431556	2		629	1112	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512368	149512369	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	335	924	0	ENST00000261799.4:c.1071_1072delinsAA	p.Gly358Ser	p.G358S	ENST00000261799	NM_002609.3	357	ctGGgc/ctAAgc	7/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.448507561431556	2		924	1433	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519360	176519360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	363	861	3	ENST00000292408.4:c.766C>T	p.Pro256Ser	p.P256S	ENST00000292408	NM_213647.1	256	Ccg/Tcg	7/18	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.448507561431556	2		864	1325	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935517	13935517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	156	386	0	ENST00000405192.2:c.1339C>T	p.Pro447Ser	p.P447S	ENST00000405192	NM_001163147.1	447	Ccc/Tcc	12/12	1	2	FACETS	0.958	0.879	1	0.958	0.879	1	CLONAL	1	TRUE	1	0.448507561431556	2		386	726	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266532	55266532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs967910623	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	245	558	1	ENST00000275493.2:c.2824G>A	p.Asp942Asn	p.D942N	ENST00000275493	NM_005228.3	942	Gat/Aat	23/28	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.448507561431556	2		559	1041	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273252	55273252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1480173156	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	236	585	1	ENST00000275493.2:c.3575C>T	p.Ala1192Val	p.A1192V	ENST00000275493	NM_005228.3	1192	gCt/gTt	28/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.448507561431556	2		586	958	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332064	81332064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	40	217	0	ENST00000222390.5:c.2020G>A	p.Gly674Ser	p.G674S	ENST00000222390	NM_000601.4	674	Ggt/Agt	18/18	1	2	FACETS	0.691	0.578	0.816	0.691	0.578	0.816	SUBCLONAL	1	TRUE	1	0.448507561431556	2		217	258	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853005	151853005	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	94	275	0	ENST00000262189.6:c.11950G>T	p.Glu3984Ter	p.E3984*	ENST00000262189	NM_170606.2	3984	Gaa/Taa	46/59	1	2	FACETS	0.989	0.885	1	0.989	0.885	1	CLONAL	1	TRUE	1	0.448507561431556	2		275	424	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760027	133760027	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	257	853	1	ENST00000318560.5:c.2350C>T	p.Pro784Ser	p.P784S	ENST00000318560	NM_005157.4	784	Ccc/Tcc	11/11	1	2	FACETS	0.905	0.846	0.966	0.905	0.846	0.966	CLONAL	1	TRUE	1	0.448507561431556	2		854	1266	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787726	135787726	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	157	508	0	ENST00000298552.3:c.856C>T	p.Pro286Ser	p.P286S	ENST00000298552	NM_001162426.1	286	Cct/Tct	9/23	1	2	FACETS	0.92	0.844	0.999	0.92	0.844	0.999	CLONAL	1	TRUE	1	0.448507561431556	2		508	761	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20152086	20152087	+	missense_variant	Missense_Mutation	DNP	GG	GG	CA	novel	NA	P-0054889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	67	138	0	ENST00000379607.5:c.243_244delinsTG	p.Arg82Gly	p.R82G	ENST00000379607	NM_001412.3	81	ctCCga/ctTGga	4/7	1	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.448507561431556	1		138	182	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0054890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	39	494	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.849	0.702	1	0.849	0.702	1	CLONAL	1	TRUE	1	0.14	2		494	656	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0054890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	21	535	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.661	0.508	0.84	0.661	0.508	0.84	SUBCLONAL	1	TRUE	1	0.14	2		535	454	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0054891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	28	571	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.223100949986307	3	FACETS	0.317	0.252	0.391	0.106	0.084	0.131	SUBCLONAL	1	TRUE	0	0.223100949986307	3		571	881	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0054891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	271	858	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.221561557357607	2	FACETS	0.978	0.917	1	0.978	0.917	1	CLONAL	2	TRUE	0	0.223100949986307	2		858	1242	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752787	42752787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1397259156	NA	P-0054891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1394	83	1285	2	ENST00000222329.4:c.1477C>T	p.Arg493Cys	p.R493C	ENST00000222329	NM_006494.2	493	Cgc/Tgc	4/4	0.223100949986307	3	FACETS	0.56	0.492	0.634	0.28	0.246	0.317	SUBCLONAL	1	TRUE	1	0.223100949986307	3		1287	1477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574027	7574027	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882028	NA	P-0054891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	27	761	0	ENST00000269305.4:c.1000G>C	p.Gly334Arg	p.G334R	ENST00000269305	NM_001126112.2	334	Ggg/Cgg	10/11	0.221561557357607	2	FACETS	0.248	0.196	0.308	0.124	0.098	0.154	SUBCLONAL	1	TRUE	0	0.223100949986307	2		761	977	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52693362	52693362	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	161	929	0	ENST00000322088.6:c.13G>T	p.Asp5Tyr	p.D5Y	ENST00000322088	NM_014225.5	5	Gac/Tac	1/15	0.223100949986307	3	FACETS	1	0.983	1	0.647	0.592	0.705	CLONAL	1	TRUE	1	0.223100949986307	3		929	1240	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669344	241669344	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	181	538	0	ENST00000366560.3:c.863G>C	p.Gly288Ala	p.G288A	ENST00000366560	NM_000143.3	288	gGc/gCc	6/10	1	2	FACETS	0.955	0.885	1	0.955	0.885	1	CLONAL	1	TRUE	1	0.642766195319985	2		538	590	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333267	70333267	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	113	1290	2	ENST00000373644.4:c.1172A>T	p.Glu391Val	p.E391V	ENST00000373644	NM_030625.2	391	gAg/gTg	2/12	0.389620186699498	2	FACETS	0.659	0.594	0.727	0.33	0.297	0.364	SUBCLONAL	1	TRUE	0	0.548597755762806	2		1292	625	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662401	117662401	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	70	730	0	ENST00000368508.3:c.4976del	p.Pro1659GlnfsTer22	p.P1659Qfs*22	ENST00000368508	NM_002944.2	1659	cCa/ca	30/43	0.528650723430779	4	FACETS	0.834	0.729	0.946	0.278	0.243	0.316	CLONAL	1	TRUE	1	0.548597755762806	4		730	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0054894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	363	991	1	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	0.60593096531744	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.60593096531744	1		992	776	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410733	63410733	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374879781	NA	P-0054894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	313	734	2	ENST00000330258.3:c.2434G>A	p.Ala812Thr	p.A812T	ENST00000330258	NM_152424.3	812	Gct/Act	2/2	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.60593096531744	2		736	980	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111498	8111499	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	297	682	1	ENST00000346208.3:c.985dup	p.Arg329LysfsTer23	p.R329Kfs*23	ENST00000346208		328	-/A	5/6	1	2	FACETS	0.984	0.928	1	0.984	0.928	1	CLONAL	1	TRUE	1	0.60593096531744	2		683	996	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802531	139802531	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1193747361	NA	P-0054894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	413	890	0	ENST00000247668.2:c.376G>A	p.Glu126Lys	p.E126K	ENST00000247668	NM_021138.3	126	Gaa/Aaa	5/11	1	2	FACETS	0.986	0.938	1	0.986	0.938	1	CLONAL	1	TRUE	1	0.60593096531744	2		890	1383	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117715	108117715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	91	214	0	ENST00000278616.4:c.926G>A	p.Arg309Lys	p.R309K	ENST00000278616	NM_000051.3	309	aGa/aAa	8/63	0.60593096531744	1	FACETS	0.988	0.896	1	0.988	0.896	1	CLONAL	1	TRUE	0	0.60593096531744	1		214	212	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654724	29654724	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1135402871	NA	P-0054894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	188	344	0	ENST00000356175.3:c.5413C>G	p.His1805Asp	p.H1805D	ENST00000356175	NM_000267.3	1805	Cat/Gat	37/57	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.60593096531744	2		344	617	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435625	56435625	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2100	332	816	0	ENST00000407977.2:c.1512C>G	p.Asp504Glu	p.D504E	ENST00000407977		504	gaC/gaG	9/10	0.60593096531744	6	FACETS	0.997	0.937	1			1	CLONAL	1	TRUE	NA	0.60593096531744	6		816	2432	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740642	58740642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2006	227	541	0	ENST00000305921.3:c.1547C>T	p.Ser516Leu	p.S516L	ENST00000305921	NM_003620.3	516	tCa/tTa	6/6	0.60593096531744	7	FACETS	0.844	0.782	0.908			1	CLONAL	1	TRUE	NA	0.60593096531744	7		541	2233	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597412	52597412	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	222	537	0	ENST00000394830.3:c.3898G>A	p.Asp1300Asn	p.D1300N	ENST00000394830	NM_018313.4	1300	Gat/Aat	25/30	1	2	FACETS	0.99	0.925	1	0.99	0.925	1	CLONAL	1	TRUE	1	0.60593096531744	2		537	740	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0054895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	101	414	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.28895068975691	2		414	686	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685313	89685313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	28	243	0	ENST00000371953.3:c.208C>A	p.Leu70Ile	p.L70I	ENST00000371953	NM_000314.4	70	Ctt/Att	3/9	1	2	FACETS	0.705	0.565	0.863	0.705	0.565	0.863	SUBCLONAL	1	TRUE	1	0.28895068975691	2		243	275	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248666	212248666	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770116535	NA	P-0054895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	100	606	0	ENST00000342788.4:c.3601G>A	p.Glu1201Lys	p.E1201K	ENST00000342788	NM_005235.2	1201	Gag/Aag	28/28	1	2	FACETS	0.761	0.678	0.848	0.761	0.678	0.848	SUBCLONAL	1	TRUE	1	0.28895068975691	2		606	910	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248420	212248420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868458258	NA	P-0054895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	65	353	0	ENST00000342788.4:c.3847G>A	p.Glu1283Lys	p.E1283K	ENST00000342788	NM_005235.2	1283	Gaa/Aaa	28/28	1	2	FACETS	0.814	0.706	0.93	0.814	0.706	0.93	CLONAL	1	TRUE	1	0.28895068975691	2		353	553	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170492	11170492	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	204	980	0	ENST00000358026.2:c.4795G>T	p.Glu1599Ter	p.E1599*	ENST00000358026	NM_001128849.1	1599	Gag/Tag	34/36	0.28895068975691	1	FACETS	0.854	0.789	0.921	0.854	0.789	0.921	CLONAL	1	TRUE	0	0.28895068975691	1		980	1415	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593478	48593479	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs730881952	NA	P-0054895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	76	373	0	ENST00000342988.3:c.1231_1232del	p.Ser411LeufsTer17	p.S411Lfs*17	ENST00000342988	NM_005359.5	410	cAG/c	10/12	0.28895068975691	1	FACETS	0.998	0.879	1	0.998	0.879	1	CLONAL	1	TRUE	0	0.28895068975691	1		373	451	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965421	18965421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	104	613	0	ENST00000262803.5:c.1168G>A	p.Glu390Lys	p.E390K	ENST00000262803	NM_002911.3	390	Gag/Aag	9/24	0.28895068975691	1	FACETS	0.929	0.833	1	0.929	0.833	1	CLONAL	1	TRUE	0	0.28895068975691	1		613	663	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020724	26020724	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1426138687	NA	P-0054895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	64	367	0	ENST00000357647.3:c.7C>T	p.Arg3Cys	p.R3C	ENST00000357647	NM_003529.2	3	Cgc/Tgc	1/1	1	2	FACETS	0.839	0.727	0.96	0.839	0.727	0.96	CLONAL	1	TRUE	1	0.28895068975691	2		367	528	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528180	157528180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	157	719	0	ENST00000346085.5:c.5905C>T	p.Pro1969Ser	p.P1969S	ENST00000346085	NM_020732.3	1969	Cca/Tca	20/20	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.28895068975691	2		719	1065	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659584	88659584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	90	607	1	ENST00000372037.3:c.367G>A	p.Glu123Lys	p.E123K	ENST00000372037	NM_004329.2	123	Gaa/Aaa	6/13	1	2	FACETS	0.84	0.745	0.941	0.84	0.745	0.941	CLONAL	1	TRUE	1	0.28895068975691	2		608	742	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001384	29001384	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	83	425	1	ENST00000282397.4:c.1348C>T	p.Gln450Ter	p.Q450*	ENST00000282397	NM_002019.4	450	Caa/Taa	10/30	1	2	FACETS	0.885	0.782	0.996	0.885	0.782	0.996	CLONAL	1	TRUE	1	0.28895068975691	2		426	649	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436542	110436542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1874	294	1293	0	ENST00000375856.3:c.1859C>T	p.Ser620Phe	p.S620F	ENST00000375856	NM_003749.2	620	tCt/tTt	1/2	0.0823047020820937	3	FACETS	1	0.974	1	0.537	0.503	0.573	INDETERMINATE	1	TRUE	1	0.28895068975691	3		1293	2168	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679316	29679316	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	92	449	0	ENST00000356175.3:c.7436del	p.Ser2479LeufsTer23	p.S2479Lfs*23	ENST00000356175	NM_000267.3	2479	tCt/tt	50/57	1	2	FACETS	0.935	0.831	1	0.935	0.831	1	CLONAL	1	TRUE	1	0.28895068975691	2		449	681	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219405	1219405	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	213	830	0	ENST00000326873.7:c.457G>C	p.Ala153Pro	p.A153P	ENST00000326873	NM_000455.4	153	Gcc/Ccc	3/10	0.28895068975691	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.28895068975691	1		830	1154	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2193708	2193708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	178	955	0	ENST00000398665.3:c.514C>T	p.Gln172Ter	p.Q172*	ENST00000398665	NM_032482.2	172	Cag/Tag	6/28	0.28895068975691	1	FACETS	0.853	0.784	0.924	0.853	0.784	0.924	CLONAL	1	TRUE	0	0.28895068975691	1		955	1236	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610561	10610562	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGTT	novel	NA	P-0054895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1278	211	1109	0	ENST00000171111.5:c.145_148dup	p.Arg50GlnfsTer30	p.R50Qfs*30	ENST00000171111	NM_203500.1	50	cgc/cAACCgc	2/6	0.28895068975691	1	FACETS	0.839	0.777	0.904	0.839	0.777	0.904	CLONAL	1	TRUE	0	0.28895068975691	1		1109	1489	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158201	47158201	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	65	483	1	ENST00000409792.3:c.4498G>T	p.Glu1500Ter	p.E1500*	ENST00000409792	NM_014159.6	1500	Gag/Tag	4/21	1	2	FACETS	0.887	0.771	1	0.887	0.771	1	CLONAL	1	TRUE	1	0.28895068975691	2		484	507	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1936901	1936901	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	90	516	0	ENST00000382891.5:c.1586C>G	p.Thr529Arg	p.T529R	ENST00000382891	NM_133335.3	529	aCa/aGa	7/22	NA	2	FACETS	0.85	0.754	0.952			1	INDETERMINATE	1	TRUE	NA	0.28895068975691	2		516	733	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518761	176518761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1357379967	NA	P-0054895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1451	187	1081	0	ENST00000292408.4:c.679G>A	p.Glu227Lys	p.E227K	ENST00000292408	NM_213647.1	227	Gag/Aag	6/18	1	2	FACETS	0.79	0.727	0.856	0.79	0.727	0.856	SUBCLONAL	1	TRUE	1	0.28895068975691	2		1081	1638	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64290057	64290057	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	73	516	0	ENST00000370651.3:c.500G>A	p.Arg167Lys	p.R167K	ENST00000370651	NM_003463.4	167	aGa/aAa	6/6	1	2	FACETS	0.675	0.589	0.767	0.675	0.589	0.767	SUBCLONAL	1	TRUE	1	0.28895068975691	2		516	749	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864889	117864889	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	85	534	0	ENST00000297338.2:c.1220G>C	p.Gly407Ala	p.G407A	ENST00000297338	NM_006265.2	407	gGa/gCa	10/14	1	2	FACETS	0.784	0.693	0.883	0.784	0.693	0.883	SUBCLONAL	1	TRUE	1	0.28895068975691	2		534	750	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776115	135776115	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0054895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	111	484	0	ENST00000298552.3:c.2612C>G	p.Ser871Ter	p.S871*	ENST00000298552	NM_001162426.1	871	tCa/tGa	20/23	0.28895068975691	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.28895068975691	1		484	631	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663727	29663729	+	frameshift_variant	Frame_Shift_Del	DEL	GTG	GTG	T	novel	NA	P-0054895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	81	566	0	ENST00000356175.3:c.6159_6161delinsT	p.Met2053IlefsTer3	p.M2053Ifs*3	ENST00000356175	NM_000267.3	2053	atGTGg/atTg	41/57	1	2	FACETS	0.754	0.663	0.85	0.754	0.663	0.85	SUBCLONAL	1	TRUE	1	0.28895068975691	2		566	744	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0054897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	14	712	1	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		713	350	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054902-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	261	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.63596253328251	4	FACETS	0.95	0.895	1	0.95	0.895	1	CLONAL	2	TRUE	2	0.63596253328251	4		487	707	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054431	42054431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054902-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	138	436	0	ENST00000219905.7:c.7615G>A	p.Asp2539Asn	p.D2539N	ENST00000219905	NM_001164273.1	2539	Gac/Aac	22/24	0.63596253328251	2	FACETS	1	0.962	1	0.54	0.496	0.585	CLONAL	1	TRUE	0	0.63596253328251	2		436	402	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207009	1207009	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054902-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	383	921	1	ENST00000326873.7:c.97G>T	p.Glu33Ter	p.E33*	ENST00000326873	NM_000455.4	33	Gag/Tag	1/10	0.63596253328251	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.63596253328251	2		922	590	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0054902-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	180	194	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.63596253328251	4	FACETS	0.922	0.858	0.988	0.922	0.858	0.988	CLONAL	2	TRUE	2	0.63596253328251	4		194	502	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119666144	119666144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775155403	NA	P-0054902-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	146	473	0	ENST00000316626.5:c.337C>T	p.Arg113Cys	p.R113C	ENST00000316626		113	Cgt/Tgt	3/12	0.63596253328251	3	FACETS	0.951	0.871	1	0.476	0.435	0.518	CLONAL	1	TRUE	1	0.63596253328251	3		473	636	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272400	38272400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054902-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	115	557	2	ENST00000425967.3:c.1967C>T	p.Ala656Val	p.A656V	ENST00000425967	NM_001174067.1	656	gCa/gTa	15/19	0.63596253328251	3	FACETS	0.971	0.879	1	0.485	0.439	0.534	CLONAL	1	TRUE	1	0.63596253328251	3		559	491	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521283	8521283	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054902-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	165	0	0	ENST00000356435.5:c.955G>T	p.Val319Phe	p.V319F	ENST00000356435		319	Gtc/Ttc	9/35	0.479630562845352	4	FACETS	0.967	0.897	1	0.967	0.897	1	CLONAL	2	TRUE	2	0.63596253328251	4		0	439	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98003014	98003014	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054902-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	120	419	0	ENST00000289081.3:c.262A>G	p.Lys88Glu	p.K88E	ENST00000289081	NM_000136.2	88	Aaa/Gaa	4/15	0.593154973296358	4	FACETS	0.971	0.879	1	0.485	0.439	0.534	CLONAL	1	TRUE	2	0.63596253328251	4		419	636	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424198	47424198	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1410667957	NA	P-0054902-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	131	657	1	ENST00000377045.4:c.203G>A	p.Arg68Gln	p.R68Q	ENST00000377045	NM_001654.4	68	cGa/cAa	4/16	0.471167669797992	6	FACETS	0.97	0.879	1			1	CLONAL	1	TRUE	NA	0.63596253328251	6		658	965	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426794	47426794	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054902-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	436	663	0	ENST00000377045.4:c.1039C>A	p.Gln347Lys	p.Q347K	ENST00000377045	NM_001654.4	347	Cag/Aag	10/16	0.471167669797992	6	FACETS	1	0.988	1			1	CLONAL	3	TRUE	NA	0.63596253328251	6		663	961	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054902-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	27	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.833	1	1	0.965	1	CLONAL	3	TRUE	1	0.142979161752719	2		487	122	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207009	1207009	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054902-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	26	921	1	ENST00000326873.7:c.97G>T	p.Glu33Ter	p.E33*	ENST00000326873	NM_000455.4	33	Gag/Tag	1/10	0.142979161752719	1	FACETS	0.979	0.789	1	1	0.963	1	CLONAL	3	TRUE	0	0.142979161752719	1		922	115	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0054902-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	20	194	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.777	1	1	0.939	1	CLONAL	2	TRUE	1	0.142979161752719	2		194	139	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521283	8521283	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054902-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	9	0	0	ENST00000356435.5:c.955G>T	p.Val319Phe	p.V319F	ENST00000356435		319	Gtc/Ttc	9/35	1	2	FACETS	1	0.821	1	1	0.821	1	CLONAL	1	TRUE	1	0.142979161752719	2		0	88	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426794	47426794	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054902-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	18	663	0	ENST00000377045.4:c.1039C>A	p.Gln347Lys	p.Q347K	ENST00000377045	NM_001654.4	347	Cag/Aag	10/16	0.142979161752719	0	FACETS	0.788	0.598	1			1	CLONAL	2	TRUE	0	0.142979161752719	0		663	137	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0054903-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	255	452	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.490019178982574	3	FACETS	0.799	0.75	0.849	0.799	0.75	0.849	SUBCLONAL	2	TRUE	1	0.490019178982574	3		452	811	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0054903-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	622	605	4	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	NA	2	FACETS	0.986	0.952	1			1	INDETERMINATE	2	TRUE	NA	0.490019178982574	2		609	1288	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68982089	68982089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376775544	NA	P-0054903-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	131	709	0	ENST00000288368.4:c.1463G>A	p.Arg488His	p.R488H	ENST00000288368	NM_024870.2	488	cGt/cAt	13/40	0.490019178982574	1	FACETS	0.52	0.472	0.571	0.52	0.472	0.571	SUBCLONAL	1	TRUE	0	0.490019178982574	1		709	776	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508892	106508892	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054903-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	197	510	0	ENST00000359195.3:c.886T>A	p.Cys296Ser	p.C296S	ENST00000359195	NM_002649.2	296	Tgc/Agc	2/11	0.490019178982574	3	FACETS	0.998	0.924	1	0.499	0.462	0.538	CLONAL	1	TRUE	1	0.490019178982574	3		510	1003	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	767	445	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.485746615403469	4	FACETS	1	0.99	1			1	CLONAL	4	TRUE	NA	0.49069462479676	4		445	1131	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442054	52442054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	386	773	0	ENST00000460680.1:c.295G>A	p.Val99Met	p.V99M	ENST00000460680	NM_004656.3	99	Gtg/Atg	5/17	0.493874852481539	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.49069462479676	2		773	686	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448310	56448310	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567880628	NA	P-0054909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	260	1049	1	ENST00000407977.2:c.337C>T	p.Arg113Ter	p.R113*	ENST00000407977		113	Cga/Tga	3/10	0.245954936266721	3	FACETS	1	0.991	1	0.656	0.615	0.698	INDETERMINATE	1	TRUE	1	0.49069462479676	3		1050	1006	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863323	56863323	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	158	597	0	ENST00000519728.1:c.467G>C	p.Arg156Thr	p.R156T	ENST00000519728	NM_002350.3	156	aGa/aCa	6/13	0.391343250841375	5	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.49069462479676	5		597	919	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577052	7577052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs672601296	NA	P-0054909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	1025	1015	1	ENST00000269305.4:c.886C>T	p.His296Tyr	p.H296Y	ENST00000269305	NM_001126112.2	296	Cac/Tac	8/11	0.485746615403469	4	FACETS	1	0.993	1			1	CLONAL	4	TRUE	NA	0.49069462479676	4		1016	1509	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711918	89711918	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	148	715	0	ENST00000371953.3:c.536G>C	p.Ser179Thr	p.S179T	ENST00000371953	NM_000314.4	179	aGc/aCc	6/9	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.49069462479676	2		715	588	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38064156	38064156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	116	445	0	ENST00000250448.2:c.22del	p.Glu8LysfsTer27	p.E8Kfs*27	ENST00000250448	NM_004496.3	8	Gaa/aa	1/2	1	2	FACETS	0.825	0.746	0.908	0.825	0.746	0.908	CLONAL	1	TRUE	1	0.49069462479676	2		445	573	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858348	89858348	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	172	663	0	ENST00000389301.3:c.1212G>C	p.Gln404His	p.Q404H	ENST00000389301	NM_000135.2	404	caG/caC	13/43	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.49069462479676	2		663	627	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303606	30303606	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	70	531	0	ENST00000262643.3:c.34G>C	p.Glu12Gln	p.E12Q	ENST00000262643	NM_001238.2	12	Gag/Cag	3/12	0.171684059324309	5	FACETS	0.761	0.663	0.866			1	INDETERMINATE	1	TRUE	NA	0.49069462479676	5		531	651	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944361	131944361	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	42	236	0	ENST00000265335.6:c.2773G>T	p.Glu925Ter	p.E925*	ENST00000265335		925	Gaa/Taa	17/25	1	2	FACETS	0.827	0.698	0.967	0.827	0.698	0.967	CLONAL	1	TRUE	1	0.49069462479676	2		236	207	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940526	31940526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1380	436	852	0	ENST00000375333.2:c.559C>T	p.Arg187Trp	p.R187W	ENST00000375333	NM_032454.1	187	Cgg/Tgg	3/8	0.49069462479676	7	FACETS	1	0.986	1	0.436	0.414	0.458	CLONAL	2	TRUE	2	0.49069462479676	7		852	1816	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851527	151851527	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	72	389	0	ENST00000262189.6:c.11964A>G	p.Ile3988Met	p.I3988M	ENST00000262189	NM_170606.2	3988	atA/atG	47/59	0.49069462479676	5	FACETS	0.785	0.686	0.892	0.196	0.171	0.223	SUBCLONAL	1	TRUE	1	0.49069462479676	5		389	649	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	85	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.154793201392607	4	FACETS	0.931	0.832	1	0.931	0.832	1	INDETERMINATE	2	TRUE	2	0.421441521107364	4		457	308	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579310	7579310	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1555526469	NA	P-0054910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	191	553	0	ENST00000269305.4:c.375+2T>C		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.254601452735778	3	FACETS	1	0.981	1	0.756	0.706	0.807	CLONAL	2	TRUE	0	0.421441521107364	3		553	484	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624408	21624408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	87	577	0	ENST00000421138.2:c.1621G>A	p.Asp541Asn	p.D541N	ENST00000421138		541	Gat/Aat	14/16	NA	2	FACETS	1	0.919	1			1	INDETERMINATE	1	TRUE	NA	0.421441521107364	2		577	398	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998940	11998940	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	113	365	0	ENST00000353533.5:c.442G>C	p.Asp148His	p.D148H	ENST00000353533	NM_003010.3	148	Gat/Cat	4/11	0.254601452735778	3	FACETS	1	0.978	1	0.808	0.74	0.876	CLONAL	2	TRUE	0	0.421441521107364	3		365	268	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939052	76939052	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	114	689	0	ENST00000373344.5:c.1696T>C	p.Ser566Pro	p.S566P	ENST00000373344	NM_000489.3	566	Tct/Cct	9/35	NA	2	FACETS	1	0.907	1			1	INDETERMINATE	1	TRUE	NA	0.421441521107364	2		689	539	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2193747	2193747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767206745	NA	P-0054913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	92	800	0	ENST00000398665.3:c.553G>A	p.Val185Ile	p.V185I	ENST00000398665	NM_032482.2	185	Gtc/Atc	6/28	1	2	FACETS	0.306	0.271	0.343	0.306	0.271	0.343	SUBCLONAL	1	TRUE	1	0.727489561389041	2		800	826	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139220	108139221	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	217	819	0	ENST00000278616.4:c.2723dup	p.Thr909AsnfsTer11	p.T909Nfs*11	ENST00000278616	NM_000051.3	908	gta/gTta	18/63	1	2	FACETS	0.932	0.872	0.994	0.932	0.872	0.994	CLONAL	1	TRUE	1	0.727489561389041	2		819	640	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593589	55593594	+	inframe_deletion	In_Frame_Del	DEL	TGTATG	TGTATG	-	novel	NA	P-0054913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	139	417	0	ENST00000288135.5:c.1655_1660del	p.Met552_Glu554delinsLys	p.M552_E554delinsK	ENST00000288135	NM_000222.2	552	aTGTATGaa/aaa	11/21	1	2	FACETS	0.901	0.828	0.977	0.901	0.828	0.977	CLONAL	1	TRUE	1	0.727489561389041	2		417	424	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	165	290	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.929	0.863	0.995	0.929	0.863	0.995	CLONAL	1	TRUE	1	0.877510103410675	2		291	405	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519938	NA	P-0054914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	114	355	1	ENST00000263967.3:c.1034A>T	p.Asn345Ile	p.N345I	ENST00000263967	NM_006218.2	345	aAt/aTt	5/21	0.416440901468342	1	FACETS	0.353	0.32	0.387	0.353	0.32	0.387	INDETERMINATE	1	TRUE	0	0.877510103410675	1		356	413	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958549	175958549	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1271141729	NA	P-0054914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	174	440	0	ENST00000367669.3:c.1796G>A	p.Arg599His	p.R599H	ENST00000367669	NM_022457.5	599	cGt/cAt	16/20	0.463247267160833	1	FACETS	0.334	0.308	0.361	0.334	0.308	0.361	INDETERMINATE	1	TRUE	0	0.877510103410675	1		440	666	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147552	47147552	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057518410	NA	P-0054914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	337	448	0	ENST00000409792.3:c.4774C>T	p.Arg1592Ter	p.R1592*	ENST00000409792	NM_014159.6	1592	Cga/Tga	6/21	0.416440901468342	1	FACETS	0.707	0.676	0.737	0.707	0.676	0.737	INDETERMINATE	1	TRUE	0	0.877510103410675	1		448	610	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435412	121435412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1479408304	NA	P-0054914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	493	820	0	ENST00000257555.6:c.1445G>A	p.Ser482Asn	p.S482N	ENST00000257555		482	aGc/aAc	7/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.877510103410675	2		820	1091	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0054916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	69	635	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.15	2		636	847	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844172	68844172	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1555515445	NA	P-0054916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	47	709	0	ENST00000261769.5:c.760G>T	p.Asp254Tyr	p.D254Y	ENST00000261769	NM_004360.3	254	Gat/Tat	6/16	1	2	FACETS	0.643	0.54	0.757	0.643	0.54	0.757	SUBCLONAL	1	TRUE	1	0.15	2		709	975	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480372	89480372	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	23	311	0	ENST00000336596.2:c.2209C>A	p.Leu737Met	p.L737M	ENST00000336596	NM_005233.5	737	Ctg/Atg	13/17	1	2	FACETS	0.671	0.522	0.844	0.671	0.522	0.844	SUBCLONAL	1	TRUE	1	0.15	2		311	457	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0054918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	73	449	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.931	0.818	1	0.931	0.818	1	CLONAL	1	TRUE	1	0.385432614807861	2		449	407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0054918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	168	778	3	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.385432614807861	1	FACETS	0.956	0.881	1	0.956	0.881	1	CLONAL	1	TRUE	0	0.385432614807861	1		781	736	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544630	65544630	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs786203385	NA	P-0054918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	125	611	0	ENST00000358664.4:c.295+1G>A		p.X99_splice	ENST00000358664	NM_002382.4	99			0.385432614807861	1	FACETS	0.975	0.887	1	0.975	0.887	1	CLONAL	1	TRUE	0	0.385432614807861	1		611	537	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214699	133214699	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	127	537	0	ENST00000320574.5:c.5579G>C	p.Gly1860Ala	p.G1860A	ENST00000320574	NM_006231.2	1860	gGg/gCg	41/49	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.385432614807861	2		537	631	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335784	73335784	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	85	313	0	ENST00000377767.4:c.2511G>T	p.Gln837His	p.Q837H	ENST00000377767	NM_014953.3	837	caG/caT	18/21	0.333570980564243	1	FACETS	0.944	0.841	1	0.944	0.841	1	CLONAL	1	TRUE	0	0.385432614807861	1		313	377	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249782	110249782	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	290	766	0	ENST00000374672.4:c.893A>G	p.His298Arg	p.H298R	ENST00000374672	NM_004235.4	298	cAc/cGc	3/5	0.362432004495719	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.385432614807861	2		766	712	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123159739	123159739	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	73	349	0	ENST00000218089.9:c.94G>C	p.Gly32Arg	p.G32R	ENST00000218089	NM_001042749.1	32	Gga/Cga	4/35	1	2	FACETS	0.9	0.79	1	0.9	0.79	1	CLONAL	1	TRUE	1	0.385432614807861	2		349	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0054921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	206	550	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.326251365959721	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.326251365959721	1		552	907	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347721	347721	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0054921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	186	692	0	ENST00000262320.3:c.1784+1G>T		p.X595_splice	ENST00000262320	NM_003502.3	595			0.326251365959721	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.326251365959721	1		692	842	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633856	86633857	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	85	399	0	ENST00000274376.6:c.968dup	p.Leu323PhefsTer5	p.L323Ffs*5	ENST00000274376	NM_002890.2	322	aat/aaTt	5/25	0.326251365959721	1	FACETS	0.991	0.88	1	0.991	0.88	1	CLONAL	1	TRUE	0	0.326251365959721	1		399	440	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912361	32912361	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41293485	NA	P-0054922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	62	189	0	ENST00000380152.3:c.3869G>A	p.Cys1290Tyr	p.C1290Y	ENST00000380152		1290	tGc/tAc	11/27	0.263572558417649	2	FACETS	1	0.935	1	0.563	0.49	0.642	CLONAL	1	FALSE	0	0.33856353788521	2		189	325	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351014	89351014	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	427	953	0	ENST00000301030.4:c.1936T>C	p.Cys646Arg	p.C646R	ENST00000301030	NM_001256183.1	646	Tgt/Cgt	9/13	0.223471875613329	3	FACETS	1	0.993	1	0.82	0.782	0.858	CLONAL	2	FALSE	0	0.33856353788521	3		953	1199	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054650	13054658	+	inframe_deletion	In_Frame_Del	DEL	GAGGATGAG	GAGGATGAG	-	rs550353351	NA	P-0054922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	99	654	0	ENST00000316448.5:c.1191_1199del	p.Glu398_Asp400del	p.E398_D400del	ENST00000316448	NM_004343.3	393	GAGGATGAG/-	9/9	0.263601899320974	2	FACETS	0.742	0.662	0.827	0.371	0.331	0.414	SUBCLONAL	1	FALSE	0	0.33856353788521	2		654	788	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	227	290	1				ENST00000310581	NM_198253.2	-/1132			0.385731087303592	7	FACETS	0.956	0.906	1	0.82	0.777	0.862	CLONAL	6	TRUE	0	0.385731087303592	7		291	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0054923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	128	991	1	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	1	2	FACETS	0.663	0.6	0.73	0.663	0.6	0.73	SUBCLONAL	1	TRUE	1	0.385731087303592	2		992	1001	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925546	114925546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1260952895	NA	P-0054923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	233	858	0	ENST00000543371.1:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000543371	NM_001198531.1	542	Gag/Aag	14/14	0.297245682444614	2	FACETS	1	0.992	1	0.717	0.67	0.765	CLONAL	1	TRUE	0	0.385731087303592	2		858	843	SUCCESS
ATM	472	MSKCC	GRCh37	11	108099957	108099957	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	122	286	0	ENST00000278616.4:c.238C>A	p.Pro80Thr	p.P80T	ENST00000278616	NM_000051.3	80	Cca/Aca	4/63	0.20019187064292	3	FACETS	1	0.949	1	0.703	0.642	0.765	INDETERMINATE	2	TRUE	0	0.385731087303592	3		286	358	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030434	49030450	+	frameshift_variant	Frame_Shift_Del	DEL	CAGACCCAGAAGCCATT	CAGACCCAGAAGCCATT	-	novel	NA	P-0054923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	214	496	0	ENST00000267163.4:c.1909_1925del	p.Gln637GlufsTer10	p.Q637Efs*10	ENST00000267163	NM_000321.2	637	CAGACCCAGAAGCCATTg/g	19/27	0.385731087303592	3	FACETS	1	0.974	1	0.72	0.673	0.767	CLONAL	2	TRUE	0	0.385731087303592	3		496	613	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437466	110437466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1231147434	NA	P-0054923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	349	612	0	ENST00000375856.3:c.935C>T	p.Ser312Leu	p.S312L	ENST00000375856	NM_003749.2	312	tCg/tTg	1/2	0.385731087303592	3	FACETS	0.99	0.944	1	0.99	0.944	1	CLONAL	3	TRUE	0	0.385731087303592	3		612	727	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786117	3786117	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	402	925	0	ENST00000262367.5:c.4648G>C	p.Glu1550Gln	p.E1550Q	ENST00000262367	NM_004380.2	1550	Gaa/Caa	28/31	0.385731087303592	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.385731087303592	3		925	1183	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0054923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	125	774	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	1	2	FACETS	0.873	0.791	0.96	0.873	0.791	0.96	CLONAL	1	TRUE	1	0.385731087303592	2		774	742	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880257	37880257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	94	652	0	ENST00000269571.5:c.2301C>G	p.Ile767Met	p.I767M	ENST00000269571		767	atC/atG	19/27	1	2	FACETS	0.714	0.635	0.797	0.714	0.635	0.797	SUBCLONAL	1	TRUE	1	0.385731087303592	2		652	683	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466824	57466826	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0054923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	25	282	1	ENST00000371085.3:c.46_48del	p.Glu16del	p.E16del	ENST00000371085	NM_000516.4	15	GAG/-	1/13	0.28859639846138	4	FACETS	0.408	0.321	0.509	0.136	0.107	0.17	SUBCLONAL	1	TRUE	1	0.385731087303592	4		283	440	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126692	5126692	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	114	444	0	ENST00000381652.3:c.3300G>A	p.Met1100Ile	p.M1100I	ENST00000381652	NM_004972.3	1100	atG/atA	25/25	0.219525389561858	4	FACETS	0.751	0.679	0.827	0.751	0.679	0.827	INDETERMINATE	2	TRUE	2	0.385731087303592	4		444	545	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531906	41531908	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CAA	CAA	T	novel	NA	P-0054923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	188	542	0	ENST00000263253.7:c.1618_1620delinsT	p.Gln540Ter	p.Q540*	ENST00000263253	NM_001429.3	540	CAA/T	7/31	0.319152447422507	2	FACETS	0.873	0.813	0.936	0.873	0.813	0.936	CLONAL	2	TRUE	0	0.385731087303592	2		542	558	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436296	110436297	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGG	rs34412495	NA	P-0054923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	22	107	2	ENST00000375856.3:c.2102_2104dup	p.Ala701dup	p.A701dup	ENST00000375856	NM_003749.2	701	gtg/gCCGtg	1/2	0.385731087303592	3	FACETS	0.972	0.762	1	0.324	0.254	0.404	CLONAL	1	TRUE	0	0.385731087303592	3		109	140	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	47	290	1				ENST00000310581	NM_198253.2	-/1132			0.400763409188944	5	FACETS	0.978	0.837	1	0.652	0.558	0.753	CLONAL	2	TRUE	2	0.400763409188944	5		291	192	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163020	47163020	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	120	420	0	ENST00000409792.3:c.3106G>A	p.Glu1036Lys	p.E1036K	ENST00000409792	NM_014159.6	1036	Gaa/Aaa	3/21	0.400763409188944	3	FACETS	0.969	0.876	1	0.484	0.438	0.534	CLONAL	1	TRUE	1	0.400763409188944	3		420	742	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	222	339	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.400763409188944	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.400763409188944	3		339	645	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240762	55240762	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768336804	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	180	792	1	ENST00000275493.2:c.2006G>A	p.Arg669Gln	p.R669Q	ENST00000275493	NM_005228.3	669	cGa/cAa	17/28	0.400763409188944	4	FACETS	0.985	0.907	1	0.493	0.453	0.534	CLONAL	1	TRUE	2	0.400763409188944	4		793	1277	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338671	70338671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	237	330	0	ENST00000374080.3:c.67G>T	p.Asp23Tyr	p.D23Y	ENST00000374080		23	Gat/Tat	1/45	0.34081055925862	2	FACETS	0.878	0.831	0.925			1	CLONAL	3	TRUE	NA	0.400763409188944	2		330	449	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522635	106522635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	153	386	0	ENST00000359195.3:c.2612C>T	p.Ser871Leu	p.S871L	ENST00000359195	NM_002649.2	871	tCa/tTa	7/11	0.400763409188944	4	FACETS	0.814	0.747	0.884	0.814	0.747	0.884	CLONAL	2	TRUE	2	0.400763409188944	4		386	657	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224249	55224249	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	94	504	0	ENST00000275493.2:c.1030G>A	p.Glu344Lys	p.E344K	ENST00000275493	NM_005228.3	344	Gaa/Aaa	9/28	0.400763409188944	4	FACETS	0.769	0.684	0.861	0.385	0.342	0.431	SUBCLONAL	1	TRUE	2	0.400763409188944	4		504	854	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292979	91292979	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	112	539	0	ENST00000355112.3:c.481G>C	p.Asp161His	p.D161H	ENST00000355112	NM_000057.2	161	Gat/Cat	3/22	0.400763409188944	3	FACETS	0.754	0.677	0.835	0.377	0.338	0.418	SUBCLONAL	1	TRUE	1	0.400763409188944	3		539	890	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120833	115120833	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	230	344	0	ENST00000257566.3:c.173G>A	p.Gly58Asp	p.G58D	ENST00000257566	NM_016569.3	58	gGc/gAc	1/8	0.400763409188944	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.400763409188944	3		344	573	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188534	11188534	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	115	504	0	ENST00000361445.4:c.5887G>A	p.Asp1963Asn	p.D1963N	ENST00000361445	NM_004958.3	1963	Gac/Aac	42/58	0.400763409188944	3	FACETS	0.841	0.757	0.93	0.421	0.378	0.465	CLONAL	1	TRUE	1	0.400763409188944	3		504	819	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196062	67196062	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	73	398	0	ENST00000312629.5:c.46G>C	p.Glu16Gln	p.E16Q	ENST00000312629	NM_003952.2	16	Gag/Cag	1/15	0.400763409188944	4	FACETS	0.915	0.801	1	0.457	0.4	0.519	CLONAL	1	TRUE	2	0.400763409188944	4		398	558	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120789	115120789	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266535166	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	268	491	0	ENST00000257566.3:c.217G>A	p.Glu73Lys	p.E73K	ENST00000257566	NM_016569.3	73	Gag/Aag	1/8	0.400763409188944	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.400763409188944	3		491	722	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292806	91292806	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	121	569	0	ENST00000355112.3:c.308G>C	p.Gly103Ala	p.G103A	ENST00000355112	NM_000057.2	103	gGa/gCa	3/22	0.400763409188944	3	FACETS	0.884	0.799	0.974	0.442	0.399	0.487	CLONAL	1	TRUE	1	0.400763409188944	3		569	820	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292964	91292964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	108	533	0	ENST00000355112.3:c.466G>A	p.Asp156Asn	p.D156N	ENST00000355112	NM_000057.2	156	Gat/Aat	3/22	0.400763409188944	3	FACETS	0.744	0.667	0.825	0.372	0.333	0.413	SUBCLONAL	1	TRUE	1	0.400763409188944	3		533	870	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293183	91293183	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	104	413	0	ENST00000355112.3:c.685G>T	p.Glu229Ter	p.E229*	ENST00000355112	NM_000057.2	229	Gaa/Taa	3/22	0.400763409188944	3	FACETS	0.937	0.84	1	0.468	0.42	0.52	CLONAL	1	TRUE	1	0.400763409188944	3		413	665	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645261	67645261	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	160	752	0	ENST00000264010.4:c.526G>C	p.Glu176Gln	p.E176Q	ENST00000264010	NM_006565.3	176	Gag/Cag	3/12	0.400763409188944	4	FACETS	0.818	0.747	0.891	0.273	0.249	0.297	CLONAL	1	TRUE	1	0.400763409188944	4		752	1368	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645435	67645435	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	105	478	0	ENST00000264010.4:c.700G>T	p.Glu234Ter	p.E234*	ENST00000264010	NM_006565.3	234	Gag/Tag	3/12	0.400763409188944	4	FACETS	0.86	0.77	0.956	0.287	0.256	0.319	CLONAL	1	TRUE	1	0.400763409188944	4		478	853	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663414	67663414	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	239	366	0	ENST00000264010.4:c.1815G>C	p.Lys605Asn	p.K605N	ENST00000264010	NM_006565.3	605	aaG/aaC	10/12	0.400763409188944	4	FACETS	0.97	0.914	1	0.97	0.914	1	CLONAL	3	TRUE	1	0.400763409188944	4		366	574	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831442	72831442	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	582	558	0	ENST00000268489.5:c.5139G>C	p.Lys1713Asn	p.K1713N	ENST00000268489	NM_006885.3	1713	aaG/aaC	9/10	0.400763409188944	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	1	0.400763409188944	4		558	1193	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347467	89347467	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs755632399	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	158	655	0	ENST00000301030.4:c.5483C>G	p.Ser1828Trp	p.S1828W	ENST00000301030	NM_001256183.1	1828	tCg/tGg	9/13	0.400763409188944	4	FACETS	0.864	0.79	0.942	0.288	0.263	0.314	CLONAL	1	TRUE	1	0.400763409188944	4		655	1278	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89842160	89842160	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs748122887	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	130	606	0	ENST00000389301.3:c.1890G>C	p.Glu630Asp	p.E630D	ENST00000389301	NM_000135.2	630	gaG/gaC	21/43	0.400763409188944	4	FACETS	0.816	0.738	0.898	0.272	0.246	0.3	CLONAL	1	TRUE	1	0.400763409188944	4		606	1114	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696369	47696369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	258	474	0	ENST00000347630.2:c.454G>A	p.Asp152Asn	p.D152N	ENST00000347630	NM_001007230.1	152	Gat/Aat	6/11	0.400763409188944	5	FACETS	1	0.957	1	0.513	0.481	0.547	CLONAL	2	TRUE	1	0.400763409188944	5		474	1004	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59934499	59934499	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782427	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	75	452	0	ENST00000259008.2:c.299T>C	p.Met100Thr	p.M100T	ENST00000259008	NM_032043.2	100	aTg/aCg	4/20	0.400763409188944	5	FACETS	0.74	0.647	0.84	0.185	0.161	0.21	SUBCLONAL	1	TRUE	1	0.400763409188944	5		452	810	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39575936	39575936	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	146	378	0	ENST00000262039.4:c.869C>G	p.Ala290Gly	p.A290G	ENST00000262039	NM_002647.2	290	gCt/gGt	8/25	0.400763409188944	3	FACETS	0.814	0.747	0.884	0.814	0.747	0.884	CLONAL	2	TRUE	1	0.400763409188944	3		378	537	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099377	4099377	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	288	699	0	ENST00000262948.5:c.741G>T	p.Gln247His	p.Q247H	ENST00000262948	NM_030662.3	247	caG/caT	7/11	0.400763409188944	3	FACETS	0.979	0.923	1	0.979	0.923	1	CLONAL	2	TRUE	1	0.400763409188944	3		699	881	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39216426	39216426	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	65	407	0	ENST00000402219.2:c.3376C>G	p.Leu1126Val	p.L1126V	ENST00000402219	NM_005633.3	1126	Ctg/Gtg	21/23	0.400763409188944	4	FACETS	0.678	0.587	0.777	0.339	0.293	0.389	SUBCLONAL	1	TRUE	2	0.400763409188944	4		407	670	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721090	61721090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	274	482	0	ENST00000401558.2:c.1184C>T	p.Ser395Phe	p.S395F	ENST00000401558	NM_003400.3	395	tCt/tTt	12/25	0.400763409188944	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	2	0.400763409188944	4		482	916	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162255	47162255	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	108	503	1	ENST00000409792.3:c.3871G>A	p.Glu1291Lys	p.E1291K	ENST00000409792	NM_014159.6	1291	Gaa/Aaa	3/21	0.400763409188944	3	FACETS	0.845	0.758	0.936	0.422	0.379	0.468	CLONAL	1	TRUE	1	0.400763409188944	3		504	766	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162814	47162814	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	103	458	0	ENST00000409792.3:c.3312G>C	p.Glu1104Asp	p.E1104D	ENST00000409792	NM_014159.6	1104	gaG/gaC	3/21	0.400763409188944	3	FACETS	0.829	0.742	0.922	0.415	0.371	0.461	CLONAL	1	TRUE	1	0.400763409188944	3		458	744	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520766	176520766	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	95	470	0	ENST00000292408.4:c.1509G>C	p.Lys503Asn	p.K503N	ENST00000292408	NM_213647.1	503	aaG/aaC	11/18	0.400763409188944	2	FACETS	0.875	0.781	0.974	0.437	0.39	0.487	CLONAL	1	TRUE	0	0.400763409188944	2		470	542	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250430	26250430	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	88	546	0	ENST00000446824.2:c.404G>C	p.Arg135Thr	p.R135T	ENST00000446824	NM_021018.2	135	aGg/aCg	1/1	0.348924820370534	4	FACETS	0.71	0.628	0.797	0.355	0.314	0.399	SUBCLONAL	1	TRUE	2	0.400763409188944	4		546	867	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250542	26250542	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	126	664	0	ENST00000446824.2:c.292G>T	p.Glu98Ter	p.E98*	ENST00000446824	NM_021018.2	98	Gag/Tag	1/1	0.348924820370534	4	FACETS	0.841	0.76	0.927	0.421	0.38	0.464	CLONAL	1	TRUE	2	0.400763409188944	4		664	1047	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505480	157505480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	198	459	1	ENST00000346085.5:c.3461G>A	p.Cys1154Tyr	p.C1154Y	ENST00000346085	NM_020732.3	1154	tGc/tAc	13/20	0.358847770038966	2	FACETS	0.889	0.829	0.949	0.889	0.829	0.949	CLONAL	2	TRUE	0	0.400763409188944	2		460	556	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072491	5072491	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs10974945	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	73	244	0	ENST00000381652.3:c.1642-1G>A		p.X548_splice	ENST00000381652	NM_004972.3	548			0.358847770038966	2	FACETS	1	0.975	1	0.712	0.63	0.797	CLONAL	1	TRUE	0	0.400763409188944	2		244	256	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200218	123200218	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	93	281	0	ENST00000218089.9:c.2197G>C	p.Ala733Pro	p.A733P	ENST00000218089	NM_001042749.1	733	Gca/Cca	23/35	0.34081055925862	2	FACETS	1	0.974	1			1	CLONAL	1	TRUE	NA	0.400763409188944	2		281	362	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0054925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	121	571	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.456309248979583	3	FACETS	1	0.961	1	0.558	0.505	0.613	CLONAL	1	TRUE	1	0.456309248979583	3		571	584	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	324	484	3	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.435679095610136	4	FACETS	1	0.986	1	1	0.996	1	CLONAL	3	TRUE	2	0.456309248979583	4		487	635	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056425	26056427	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	rs774779034	NA	P-0054925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	78	383	0	ENST00000343677.2:c.230_232del	p.Asn77del	p.N77del	ENST00000343677	NM_005319.3	77	aACAgc/agc	1/1	0.377801739474873	4	FACETS	0.86	0.756	0.971	0.43	0.378	0.486	CLONAL	1	TRUE	2	0.456309248979583	4		383	579	SUCCESS
APC	324	MSKCC	GRCh37	5	112175530	112175530	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	211	405	0	ENST00000257430.4:c.4240del	p.Val1414Ter	p.V1414*	ENST00000257430	NM_000038.5	1413	atG/at	16/16	NA	2	FACETS	1	0.974	1			1	INDETERMINATE	2	TRUE	NA	0.456309248979583	2		405	435	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514872	44514873	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	121	514	0	ENST00000291552.4:c.374dup	p.Ala126GlyfsTer4	p.A126Gfs*4	ENST00000291552	NM_006758.2	125	aag/aaAg	6/8	0.456309248979583	3	FACETS	0.945	0.855	1	0.473	0.427	0.52	CLONAL	1	TRUE	1	0.456309248979583	3		514	689	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682399	52682400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	69	433	0	ENST00000394830.3:c.773dup	p.Asn258LysfsTer6	p.N258Kfs*6	ENST00000394830	NM_018313.4	258	aat/aaAt	8/30	0.161591150168939	2	FACETS	0.781	0.684	0.885	0.781	0.684	0.885	SUBCLONAL	2	TRUE	0	0.229404979694685	2		433	385	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721028	61721028	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0054926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	60	542	0	ENST00000401558.2:c.1245+1G>C		p.X415_splice	ENST00000401558	NM_003400.3	415			1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.229404979694685	2		542	521	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443623	52443667	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCTGCGATGAGGAAAGGAAAGCAGTAGGGAAGGACAGCCCCTGA	ACCTGCGATGAGGAAAGGAAAGCAGTAGGGAAGGACAGCCCCTGA	-	novel	NA	P-0054926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	130	673	0	ENST00000460680.1:c.68-43_69del		p.X23_splice	ENST00000460680	NM_004656.3	23		3/17	0.161591150168939	2	FACETS	0.887	0.806	0.971	0.887	0.806	0.971	CLONAL	2	TRUE	0	0.229404979694685	2		673	639	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0054930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	90	415	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		415	527	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778168	135778168	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554815054	NA	P-0054931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	97	627	0	ENST00000298552.3:c.2215C>T	p.Gln739Ter	p.Q739*	ENST00000298552	NM_001162426.1	739	Cag/Tag	18/23	0.402801995732098	0	FACETS	0.773	0.697	0.853			1	SUBCLONAL	1	TRUE	0	0.428878744240334	0		627	334	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15938198	15938198	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1237104643	NA	P-0054931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	189	651	0	ENST00000268712.3:c.7016T>C	p.Ile2339Thr	p.I2339T	ENST00000268712	NM_006311.3	2339	aTa/aCa	45/46	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.428878744240334	2		651	737	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120479932	120479932	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	126	668	0	ENST00000256646.2:c.3495T>A	p.Ser1165Arg	p.S1165R	ENST00000256646	NM_024408.3	1165	agT/agA	21/34	1	2	FACETS	0.912	0.828	1	0.912	0.828	1	CLONAL	1	TRUE	1	0.428878744240334	2		668	644	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663082	227663086	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCT	CAGCT	-	novel	NA	P-0054931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	102	681	0	ENST00000305123.5:c.369_373del	p.Ala124GlyfsTer19	p.A124Gfs*19	ENST00000305123	NM_005544.2	123	ggAGCTGcg/ggcg	1/2	NA	2	FACETS	0.894	0.802	0.991			1	INDETERMINATE	1	TRUE	NA	0.428878744240334	2		681	532	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610607	52610608	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	97	623	0	ENST00000394830.3:c.3565dup	p.Glu1189GlyfsTer6	p.E1189Gfs*6	ENST00000394830	NM_018313.4	1189	gaa/gGaa	23/30	0.428878744240334	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.428878744240334	1		623	337	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183745	10183749	+	missense_variant	Missense_Mutation	ONP	TCCCA	TCCCA	CCCCT	novel	NA	P-0054931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	99	775	0	ENST00000256474.2:c.214_218delinsCCCCT	p.Ser72_Gln73delinsProLeu	p.S72_Q73delinsPL	ENST00000256474	NM_000551.3	72	TCCCAg/CCCCTg	1/3	0.428878744240334	1	FACETS	0.78	0.7	0.864	0.78	0.7	0.864	SUBCLONAL	1	TRUE	0	0.428878744240334	1		775	465	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	86	290	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.784	0.697	0.876	0.784	0.697	0.876	SUBCLONAL	1	TRUE	1	0.516326712554113	2		291	425	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904831	101904831	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	232	496	0	ENST00000374994.4:c.819G>A	p.Trp273Ter	p.W273*	ENST00000374994	NM_004612.2	273	tgG/tgA	5/9	0.516326712554113	2	FACETS	0.923	0.871	0.975	0.923	0.871	0.975	CLONAL	2	TRUE	0	0.516326712554113	2		496	487	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	90	464	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	1	2	FACETS	0.84	0.75	0.935	0.84	0.75	0.935	CLONAL	1	TRUE	1	0.516326712554113	2		464	415	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923060	44923060	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	205	273	0	ENST00000377967.4:c.1921C>T	p.Gln641Ter	p.Q641*	ENST00000377967	NM_021140.2	641	Cag/Tag	16/29	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.516326712554113	1		273	437	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134251	11134251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218643327	NA	P-0054932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	230	969	0	ENST00000358026.2:c.2917C>T	p.Arg973Trp	p.R973W	ENST00000358026	NM_001128849.1	973	Cgg/Tgg	20/36	1	2	FACETS	0.943	0.88	1	0.943	0.88	1	CLONAL	1	TRUE	1	0.516326712554113	2		969	945	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137320982	137320982	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	552	1233	0	ENST00000481739.1:c.939C>G	p.Phe313Leu	p.F313L	ENST00000481739	NM_002957.4	313	ttC/ttG	7/10	0.516326712554113	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.516326712554113	2		1233	1065	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739887	46739887	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1420879628	NA	P-0054932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	124	619	0	ENST00000371975.4:c.1688C>T	p.Ser563Leu	p.S563L	ENST00000371975	NM_003579.3	563	tCg/tTg	15/18	1	2	FACETS	0.762	0.691	0.837	0.762	0.691	0.837	SUBCLONAL	1	TRUE	1	0.516326712554113	2		619	630	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728939	190728939	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	110	391	0	ENST00000441310.2:c.2327T>G	p.Ile776Ser	p.I776S	ENST00000441310	NM_000534.4	776	aTt/aGt	10/13	1	2	FACETS	0.971	0.878	1	0.971	0.878	1	CLONAL	1	TRUE	1	0.516326712554113	2		391	439	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0054933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	143	466	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.265888887649243	2	FACETS	0.885	0.809	0.963	0.885	0.809	0.963	CLONAL	2	TRUE	0	0.265888887649243	2		466	608	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	1825	324	0	ENST00000256196.4:c.68G>A	p.Gly23Asp	p.G23D	ENST00000256196		23	gGc/gAc	1/6	0.265888887649243	25	FACETS	1	0.995	1			1	CLONAL	25	TRUE	NA	0.265888887649243	25		324	2195	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563285	21563285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1207863433	NA	P-0054933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	119	1053	0	ENST00000382592.4:c.634G>A	p.Val212Met	p.V212M	ENST00000382592	NM_014572.2	212	Gtg/Atg	4/8	0.265888887649243	2	FACETS	0.97	0.874	1	0.485	0.437	0.536	CLONAL	1	TRUE	0	0.265888887649243	2		1053	923	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521549	46521549	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	50	642	0	ENST00000262741.5:c.859G>A	p.Asp287Asn	p.D287N	ENST00000262741	NM_003629.3	287	Gac/Aac	7/10	0.265888887649243	3	FACETS	0.486	0.411	0.57	0.243	0.205	0.285	SUBCLONAL	1	TRUE	1	0.265888887649243	3		642	876	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457269	67457269	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	214	807	0	ENST00000327367.4:c.243G>C	p.Lys81Asn	p.K81N	ENST00000327367	NM_005902.3	81	aaG/aaC	2/9	0.265888887649243	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.265888887649243	2		807	705	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495426	149495426	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	121	1205	0	ENST00000261799.4:c.3221C>A	p.Pro1074His	p.P1074H	ENST00000261799	NM_002609.3	1074	cCc/cAc	23/23	0.192329504045615	3	FACETS	0.918	0.828	1	0.459	0.414	0.507	CLONAL	1	TRUE	1	0.265888887649243	3		1205	1123	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578491	+	frameshift_variant	Frame_Shift_Del	DEL	CGGACGCGGGTGCCGGGCGGGGGTGTGGAATCAAC	CGGACGCGGGTGCCGGGCGGGGGTGTGGAATCAAC	T	novel	NA	P-0054933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	264	1021	0	ENST00000269305.4:c.439_473delinsA	p.Val147ThrfsTer12	p.V147Tfs*12	ENST00000269305	NM_001126112.2	147	GTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGc/Ac	5/11	0.265888887649243	2	FACETS	0.989	0.928	1	0.989	0.928	1	CLONAL	2	TRUE	0	0.265888887649243	2		1021	1004	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0054938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	187	661	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.480558391868388	1	FACETS	0.882	0.818	0.948	0.882	0.818	0.948	CLONAL	1	TRUE	0	0.480558391868388	1		662	670	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0054938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	91	545	1	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	0.838	0.748	0.933	0.838	0.748	0.933	CLONAL	1	TRUE	1	0.480558391868388	2		546	452	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36989307	36989307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	126	882	0	ENST00000354822.5:c.28C>T	p.Arg10Trp	p.R10W	ENST00000354822	NM_001079668.2	10	Cgg/Tgg	1/3	1	2	FACETS	0.844	0.767	0.926	0.844	0.767	0.926	CLONAL	1	TRUE	1	0.480558391868388	2		882	621	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277892	41277892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	96	585	1	ENST00000349496.5:c.1856G>A	p.Cys619Tyr	p.C619Y	ENST00000349496	NM_001904.3	619	tGt/tAt	12/15	1	2	FACETS	0.954	0.855	1	0.954	0.855	1	CLONAL	1	TRUE	1	0.480558391868388	2		586	419	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797254	32797254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772061173	NA	P-0054938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	223	1054	2	ENST00000374899.4:c.1855C>T	p.Arg619Trp	p.R619W	ENST00000374899	NM_018833.2	619	Cgg/Tgg	11/12	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.480558391868388	2		1056	900	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456506	32456506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748974419	NA	P-0054938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	26	132	0	ENST00000332351.3:c.386C>T	p.Pro129Leu	p.P129L	ENST00000332351	NM_024426.4	129	cCg/cTg	1/10	0.439151107187734	2	FACETS	1	0.93	1	0.676	0.552	0.809	CLONAL	1	TRUE	0	0.480558391868388	2		132	80	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488237	56488237	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1330988114	NA	P-0054938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	166	800	0	ENST00000267101.3:c.1756G>T	p.Val586Leu	p.V586L	ENST00000267101	NM_001982.3	586	Gtg/Ttg	15/28	1	2	FACETS	0.897	0.826	0.972	0.897	0.826	0.972	CLONAL	1	TRUE	1	0.480558391868388	2		800	770	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351496	89351496	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	181	1033	0	ENST00000301030.4:c.1454C>A	p.Ser485Tyr	p.S485Y	ENST00000301030	NM_001256183.1	485	tCc/tAc	9/13	1	2	FACETS	0.897	0.828	0.968	0.897	0.828	0.968	CLONAL	1	TRUE	1	0.480558391868388	2		1033	840	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0054940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	55	670	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.350950394454926	2		670	272	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0054940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	201	519	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.304168663988123	2	FACETS	1	0.99	1	0.715	0.664	0.768	CLONAL	1	TRUE	0	0.350950394454926	2		519	801	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578530	7578530	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs267605077	NA	P-0054940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	238	803	3	ENST00000269305.4:c.400T>C	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	Ttt/Ctt	5/11	0.350950394454926	1	FACETS	0.984	0.917	1	0.984	0.917	1	CLONAL	1	TRUE	0	0.350950394454926	1		806	1137	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120225	70120226	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	411	650	9	ENST00000245479.2:c.1228dup	p.Gln410ProfsTer168	p.Q410Pfs*168	ENST00000245479	NM_000346.3	409	-/C	3/3	0.350950394454926	2	FACETS	0.984	0.938	1	0.984	0.938	1	CLONAL	2	TRUE	0	0.350950394454926	2		659	1190	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981815	101981815	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs965501205	NA	P-0054940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	155	585	1	ENST00000282441.5:c.236A>G	p.Asn79Ser	p.N79S	ENST00000282441	NM_001130145.2	79	aAc/aGc	1/9	1	2	FACETS	0.978	0.895	1	0.978	0.895	1	CLONAL	1	TRUE	1	0.350950394454926	2		586	903	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266026	41266238	+	inframe_deletion	In_Frame_Del	DEL	TGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAG	TGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAG	-	novel	NA	P-0054940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	17	357	0	ENST00000349496.5:c.24_236del	p.Met8_Val79delinsIle	p.M8_V79delinsI	ENST00000349496	NM_001904.3	8	aTGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGta/ata	3/15	0.304168663988123	2	FACETS	0.272	0.202	0.355	0.136	0.101	0.178	SUBCLONAL	1	TRUE	0	0.350950394454926	2		357	356	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	36	457	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.786	0.646	0.944	0.786	0.646	0.944	CLONAL	1	TRUE	1	0.19	2		457	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0054942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	72	739	0	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	0.827	0.721	0.943	0.827	0.721	0.943	CLONAL	1	TRUE	1	0.19	2		739	916	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732948	30732948	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	47	522	0	ENST00000295754.5:c.1561T>C	p.Trp521Arg	p.W521R	ENST00000295754	NM_003242.5	521	Tgg/Cgg	7/7	1	2	FACETS	0.763	0.643	0.897	0.763	0.643	0.897	SUBCLONAL	1	TRUE	1	0.19	2		522	648	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662921	52662921	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	56	430	0	ENST00000394830.3:c.1432C>T	p.Gln478Ter	p.Q478*	ENST00000394830	NM_018313.4	478	Caa/Taa	13/30	1	2	FACETS	0.986	0.844	1	0.986	0.844	1	CLONAL	1	TRUE	1	0.19	2		430	598	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0054943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	9	638	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.133	0.087	0.191	0.133	0.087	0.191	SUBCLONAL	1	TRUE	1	0.409858704902157	2		638	331	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0054943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	56	208	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.409858704902157	2		208	188	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0054943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	150	372	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.282078068528054	4	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.409858704902157	4		372	425	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630626	158630626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912678	NA	P-0054943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	40	339	0	ENST00000263640.3:c.617G>A	p.Arg206His	p.R206H	ENST00000263640	NM_001105.4	206	cGc/cAc	6/11	1	2	FACETS	0.827	0.693	0.974	0.827	0.693	0.974	CLONAL	1	TRUE	1	0.409858704902157	2		339	236	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435007	110435007	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	56	356	0	ENST00000375856.3:c.3394G>A	p.Gly1132Ser	p.G1132S	ENST00000375856	NM_003749.2	1132	Ggc/Agc	1/2	1	2	FACETS	0.625	0.537	0.721	0.625	0.537	0.721	SUBCLONAL	1	TRUE	1	0.409858704902157	2		356	437	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415935	49415935	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0054943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	155	571	0	ENST00000301067.7:c.16413-1G>A		p.X5471_splice	ENST00000301067	NM_003482.3	5471			0.164332928260661	4	FACETS	1	0.981	1	1	0.981	1	INDETERMINATE	2	TRUE	2	0.409858704902157	4		571	447	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523576	148523576	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	30	291	0	ENST00000320356.2:c.877G>T	p.Asp293Tyr	p.D293Y	ENST00000320356	NM_004456.4	293	Gac/Tac	8/20	1	2	FACETS	0.645	0.523	0.782	0.645	0.523	0.782	SUBCLONAL	1	TRUE	1	0.409858704902157	2		291	227	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436674	52436674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	162	710	0	ENST00000460680.1:c.2000G>A	p.Arg667Lys	p.R667K	ENST00000460680	NM_004656.3	667	aGg/aAg	16/17	0.104658775248448	3	FACETS	0.878	0.809	0.95	0.878	0.809	0.95	INDETERMINATE	2	TRUE	1	0.354824597294125	3		710	612	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599336	55599336	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	54	436	0	ENST00000288135.5:c.2462C>G	p.Ser821Cys	p.S821C	ENST00000288135	NM_000222.2	821	tCt/tGt	17/21	0.354824597294125	8	FACETS	0.845	0.72	0.982			1	CLONAL	1	TRUE	NA	0.354824597294125	8		436	744	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996858	100996858	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	111	597	0	ENST00000325455.5:c.1669T>C	p.Tyr557His	p.Y557H	ENST00000325455	NM_001202474.3	557	Tac/Cac	2/8	0.354824597294125	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.354824597294125	1		597	420	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46608745	46608745	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	378	710	0	ENST00000263734.3:c.2056G>C	p.Gly686Arg	p.G686R	ENST00000263734	NM_001430.4	686	Ggt/Cgt	13/16	0.248500816501978	4	FACETS	0.977	0.93	1	0.977	0.93	1	CLONAL	3	TRUE	1	0.354824597294125	4		710	985	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599325	55599325	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	53	439	0	ENST00000288135.5:c.2451C>G	p.Ile817Met	p.I817M	ENST00000288135	NM_000222.2	817	atC/atG	17/21	0.354824597294125	8	FACETS	0.78	0.663	0.908			1	CLONAL	1	TRUE	NA	0.354824597294125	8		439	791	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	269	290	1				ENST00000310581	NM_198253.2	-/1132			0.226510386495367	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	FALSE	0	0.305549753537173	3		291	638	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955432	48955432	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	64	463	0	ENST00000267163.4:c.1548G>A	p.Trp516Ter	p.W516*	ENST00000267163	NM_000321.2	516	tgG/tgA	17/27	0.305549753537173	0	FACETS	0.929	0.811	1			1	CLONAL	1	FALSE	0	0.305549753537173	0		463	313	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576158	88576158	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	143	1079	1	ENST00000360948.2:c.1515G>T	p.Met505Ile	p.M505I	ENST00000360948	NM_001012338.2	505	atG/atT	13/19	0.131883635384249	0	FACETS	0.484	0.44	0.531			1	INDETERMINATE	1	FALSE	0	0.305549753537173	0		1080	1343	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196849	106196849	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	32	528	0	ENST00000380013.4:c.5182G>A	p.Glu1728Lys	p.E1728K	ENST00000380013	NM_001127208.2	1728	Gag/Aag	11/11	0.298268686030798	1	FACETS	0.309	0.25	0.376	0.309	0.25	0.376	SUBCLONAL	1	FALSE	0	0.305549753537173	1		528	574	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678170	58678170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1480	83	1043	1	ENST00000305921.3:c.395C>T	p.Ser132Leu	p.S132L	ENST00000305921	NM_003620.3	132	tCg/tTg	1/6	1	2	FACETS	0.348	0.305	0.394	0.348	0.305	0.394	SUBCLONAL	1	FALSE	1	0.305549753537173	2		1044	1563	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482606	56482606	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1329	38	1073	0	ENST00000267101.3:c.1063A>G	p.Thr355Ala	p.T355A	ENST00000267101	NM_001982.3	355	Acc/Gcc	9/28	0.217056929069205	1	FACETS	0.154	0.126	0.185	0.154	0.126	0.185	SUBCLONAL	1	FALSE	0	0.305549753537173	1		1073	1367	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983049	201983049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1618	160	1107	0	ENST00000359651.3:c.898G>A	p.Glu300Lys	p.E300K	ENST00000359651		300	Gaa/Aaa	7/8	0.12262456716901	4	FACETS	0.769	0.702	0.84	0.385	0.351	0.42	INDETERMINATE	1	FALSE	2	0.305549753537173	4		1107	1778	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415897	49415897	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	66	741	1	ENST00000301067.7:c.16450G>A	p.Glu5484Lys	p.E5484K	ENST00000301067	NM_003482.3	5484	Gaa/Aaa	53/54	0.217056929069205	1	FACETS	0.361	0.312	0.415	0.361	0.312	0.415	SUBCLONAL	1	FALSE	0	0.305549753537173	1		742	1013	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258977	16258978	+	missense_variant	Missense_Mutation	DNP	GA	GA	CT	novel	NA	P-0054945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	246	943	0	ENST00000375759.3:c.6242_6243delinsCT	p.Arg2081Pro	p.R2081P	ENST00000375759	NM_015001.2	2081	cGA/cCT	11/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.305549753537173	2		943	1356	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597792	43597792	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs747483905	NA	P-0054945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	69	958	0	ENST00000355710.3:c.340C>T	p.Arg114Cys	p.R114C	ENST00000355710	NM_020975.4	114	Cgc/Tgc	3/20	0.183118848566435	0	FACETS	0.279	0.242	0.319			1	INDETERMINATE	1	FALSE	0	0.305549753537173	0		958	1125	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893419	32893419	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs145988146	NA	P-0054945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	28	492	0	ENST00000380152.3:c.273C>G	p.Tyr91Ter	p.Y91*	ENST00000380152		91	taC/taG	3/27	1	2	FACETS	0.358	0.285	0.441	0.358	0.285	0.441	SUBCLONAL	1	FALSE	1	0.305549753537173	2		492	512	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061133	38061133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751299919	NA	P-0054945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	24	253	0	ENST00000250448.2:c.856G>A	p.Gly286Ser	p.G286S	ENST00000250448	NM_004496.3	286	Ggc/Agc	2/2	1	2	FACETS	0.417	0.326	0.521	0.417	0.326	0.521	SUBCLONAL	1	FALSE	1	0.305549753537173	2		253	377	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349094	89349094	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779425691	NA	P-0054945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1724	94	1375	0	ENST00000301030.4:c.3856G>A	p.Glu1286Lys	p.E1286K	ENST00000301030	NM_001256183.1	1286	Gaa/Aaa	9/13	0.305549753537173	1	FACETS	0.287	0.254	0.322	0.287	0.254	0.322	SUBCLONAL	1	FALSE	0	0.305549753537173	1		1375	1818	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012109	16012109	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	35	554	0	ENST00000268712.3:c.2173G>T	p.Asp725Tyr	p.D725Y	ENST00000268712	NM_006311.3	725	Gac/Tac	19/46	1	2	FACETS	0.368	0.301	0.444	0.368	0.301	0.444	SUBCLONAL	1	FALSE	1	0.305549753537173	2		554	622	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649101	37649101	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	51	599	0	ENST00000447079.4:c.2207del	p.Gly736GlufsTer17	p.G736Efs*17	ENST00000447079	NM_015083.1	736	Gga/ga	4/14	1	2	FACETS	0.337	0.285	0.395	0.337	0.285	0.395	SUBCLONAL	1	FALSE	1	0.305549753537173	2		599	990	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811477	56811477	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0054945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	37	554	1	ENST00000337432.4:c.1027-2A>T		p.X343_splice	ENST00000337432	NM_058216.2	343			1	2	FACETS	0.335	0.275	0.403	0.335	0.275	0.403	SUBCLONAL	1	FALSE	1	0.305549753537173	2		555	722	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732292	74732292	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	46	619	0	ENST00000359995.5:c.617C>T	p.Ser206Leu	p.S206L	ENST00000359995	NM_001195427.1	206	tCg/tTg	2/3	1	2	FACETS	0.328	0.275	0.387	0.328	0.275	0.387	SUBCLONAL	1	FALSE	1	0.305549753537173	2		619	917	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303229	15303229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1782	131	1438	2	ENST00000263388.2:c.299G>A	p.Gly100Asp	p.G100D	ENST00000263388	NM_000435.2	100	gGc/gAc	3/33	1	2	FACETS	0.448	0.405	0.495	0.448	0.405	0.495	SUBCLONAL	1	FALSE	1	0.305549753537173	2		1440	1913	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354100	15354100	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1289	95	1114	1	ENST00000263377.2:c.2780A>G	p.Gln927Arg	p.Q927R	ENST00000263377	NM_058243.2	927	cAg/cGg	14/20	1	2	FACETS	0.449	0.398	0.504	0.449	0.398	0.504	SUBCLONAL	1	FALSE	1	0.305549753537173	2		1115	1384	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097260	178097260	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	52	704	0	ENST00000397062.3:c.454G>C	p.Glu152Gln	p.E152Q	ENST00000397062	NM_006164.4	152	Gag/Cag	4/5	0.305549753537173	1	FACETS	0.335	0.284	0.391	0.335	0.284	0.391	SUBCLONAL	1	FALSE	0	0.305549753537173	1		704	861	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164235	47164235	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	40	507	0	ENST00000409792.3:c.1891G>C	p.Asp631His	p.D631H	ENST00000409792	NM_014159.6	631	Gat/Cat	3/21	0.152973057532231	4	FACETS	0.519	0.43	0.618	0.259	0.215	0.309	INDETERMINATE	1	FALSE	2	0.305549753537173	4		507	659	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410283	63410283	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	48	599	0	ENST00000330258.3:c.2884G>T	p.Ala962Ser	p.A962S	ENST00000330258	NM_152424.3	962	Gct/Tct	2/2	0.24279787946477	2	FACETS	0.378	0.318	0.444			1	SUBCLONAL	1	FALSE	NA	0.305549753537173	2		599	832	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	120	501	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.390801325590925	2		502	608	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	24	550	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.129	0.1	0.163	0.129	0.1	0.163	SUBCLONAL	1	TRUE	1	0.390801325590925	2		550	952	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	143	846	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	0.784	0.714	0.857	0.784	0.714	0.857	SUBCLONAL	1	TRUE	1	0.390801325590925	2		846	934	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546931	9546931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs562732119	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	42	782	1	ENST00000353224.5:c.1091C>T	p.Ser364Leu	p.S364L	ENST00000353224	NM_177990.2	364	tCg/tTg	5/10	1	2	FACETS	0.261	0.216	0.31	0.261	0.216	0.31	SUBCLONAL	1	TRUE	1	0.390801325590925	2		783	825	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546847	9546847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	193	781	0	ENST00000353224.5:c.1175C>T	p.Ser392Leu	p.S392L	ENST00000353224	NM_177990.2	392	tCg/tTg	5/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.390801325590925	2		781	767	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654642	67654642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	60	736	1	ENST00000264010.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000264010	NM_006565.3	377	Cgt/Tgt	6/12	1	2	FACETS	0.32	0.274	0.369	0.32	0.274	0.369	SUBCLONAL	1	TRUE	1	0.390801325590925	2		737	961	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	220	536	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.390801325590925	2		536	890	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376626	8376626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772303653	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	38	672	0	ENST00000356435.5:c.4487G>A	p.Arg1496Gln	p.R1496Q	ENST00000356435		1496	cGa/cAa	27/35	1	2	FACETS	0.266	0.219	0.319	0.266	0.219	0.319	SUBCLONAL	1	TRUE	1	0.390801325590925	2		672	731	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416809	121416809	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs76845985	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1234	77	1454	0	ENST00000257555.6:c.238G>T	p.Asp80Tyr	p.D80Y	ENST00000257555		80	Gac/Tac	1/10	1	2	FACETS	0.301	0.263	0.342	0.301	0.263	0.342	SUBCLONAL	1	TRUE	1	0.390801325590925	2		1454	1311	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	207	590	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.390801325590925	2		591	891	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	154	554	0	ENST00000349496.5:c.101G>A	p.Gly34Glu	p.G34E	ENST00000349496	NM_001904.3	34	gGa/gAa	3/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.390801325590925	2		554	672	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857307	68857307	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs971882211	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	55	323	0	ENST00000261769.5:c.1942G>T	p.Glu648Ter	p.E648*	ENST00000261769	NM_004360.3	648	Gaa/Taa	13/16	1	2	FACETS	0.557	0.477	0.645	0.557	0.477	0.645	SUBCLONAL	1	TRUE	1	0.390801325590925	2		323	505	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587777894	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	50	882	0	ENST00000361445.4:c.6644C>A	p.Ser2215Tyr	p.S2215Y	ENST00000361445	NM_004958.3	2215	tCt/tAt	47/58	1	2	FACETS	0.244	0.206	0.286	0.244	0.206	0.286	SUBCLONAL	1	TRUE	1	0.390801325590925	2		882	1048	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519920	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	13	442	0	ENST00000397062.3:c.85G>T	p.Asp29Tyr	p.D29Y	ENST00000397062	NM_006164.4	29	Gat/Tat	2/5	1	2	FACETS	0.143	0.101	0.195	0.143	0.101	0.195	SUBCLONAL	1	TRUE	1	0.390801325590925	2		442	464	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447384	187447384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780987785	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	273	1150	0	ENST00000232014.4:c.809G>A	p.Arg270Gln	p.R270Q	ENST00000232014	NM_001130845.1	270	cGa/cAa	5/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.390801325590925	2		1150	1063	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506448	148506448	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	130	526	0	ENST00000320356.2:c.2064A>C	p.Lys688Asn	p.K688N	ENST00000320356	NM_004456.4	688	aaA/aaC	18/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.390801325590925	2		526	538	SUCCESS
APC	324	MSKCC	GRCh37	5	112177368	112177368	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	90	444	0	ENST00000257430.4:c.6077C>A	p.Ser2026Tyr	p.S2026Y	ENST00000257430	NM_000038.5	2026	tCt/tAt	16/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.390801325590925	2		444	397	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832265	72832265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267604632	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	195	833	1	ENST00000268489.5:c.4316G>A	p.Arg1439Gln	p.R1439Q	ENST00000268489	NM_006885.3	1439	cGa/cAa	9/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.390801325590925	2		834	813	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426835	70426835	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	41	591	1	ENST00000373644.4:c.4495C>A	p.Leu1499Ile	p.L1499I	ENST00000373644	NM_030625.2	1499	Ctt/Att	7/12	1	2	FACETS	0.284	0.235	0.338	0.284	0.235	0.338	SUBCLONAL	1	TRUE	1	0.390801325590925	2		592	740	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178943780	178943780	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	86	486	0	ENST00000263967.3:c.2447T>G	p.Ile816Ser	p.I816S	ENST00000263967	NM_006218.2	816	aTt/aGt	17/21	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.390801325590925	2		486	397	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885550	111885550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775891572	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	335	1275	1	ENST00000341259.2:c.1327C>T	p.Arg443Cys	p.R443C	ENST00000341259	NM_005475.2	443	Cgc/Tgc	7/8	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.390801325590925	2		1276	1271	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857912	89857912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760352719	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	55	878	1	ENST00000389301.3:c.1258G>A	p.Glu420Lys	p.E420K	ENST00000389301	NM_000135.2	420	Gag/Aag	14/43	1	2	FACETS	0.302	0.257	0.351	0.302	0.257	0.351	SUBCLONAL	1	TRUE	1	0.390801325590925	2		879	933	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849266	76849266	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	160	209	1	ENST00000373344.5:c.6010G>T	p.Asp2004Tyr	p.D2004Y	ENST00000373344	NM_000489.3	2004	Gat/Tat	26/35	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.390801325590925	2		210	643	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913037	32913037	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1555283835	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	47	862	0	ENST00000380152.3:c.4545G>T	p.Lys1515Asn	p.K1515N	ENST00000380152		1515	aaG/aaT	11/27	1	2	FACETS	0.311	0.262	0.366	0.311	0.262	0.366	SUBCLONAL	1	TRUE	1	0.390801325590925	2		862	773	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651531	52651531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	174	664	0	ENST00000394830.3:c.1565G>A	p.Arg522Gln	p.R522Q	ENST00000394830	NM_018313.4	522	cGa/cAa	15/30	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.390801325590925	2		664	667	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725043	89725043	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	134	319	0	ENST00000371953.3:c.1027-1G>T		p.X343_splice	ENST00000371953	NM_000314.4	343			0.390801325590925	2	FACETS	0.847	0.785	0.908	1	0.985	1	CLONAL	3	TRUE	0	0.390801325590925	2		319	270	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411975	116411975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910937816	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	73	1195	0	ENST00000397752.3:c.2960G>A	p.Arg987Gln	p.R987Q	ENST00000397752	NM_000245.2	987	cGa/cAa	14/21	1	2	FACETS	0.335	0.292	0.382	0.335	0.292	0.382	SUBCLONAL	1	TRUE	1	0.390801325590925	2		1195	1115	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737436	204737436	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	125	513	1	ENST00000302823.3:c.573G>T	p.Lys191Asn	p.K191N	ENST00000302823	NM_005214.4	191	aaG/aaT	4/4	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.390801325590925	2		514	498	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273024	115273024	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	184	916	0	ENST00000438362.2:c.1349G>T	p.Arg450Ile	p.R450I	ENST00000438362	NM_001242891.1	450	aGa/aTa	12/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.390801325590925	2		916	737	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419841	41419841	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	118	683	0	ENST00000373198.4:c.480C>A	p.Phe160Leu	p.F160L	ENST00000373198	NM_133170.3	160	ttC/ttA	3/32	1	2	FACETS	0.889	0.804	0.98	0.889	0.804	0.98	CLONAL	1	TRUE	1	0.390801325590925	2		683	679	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29106017	29106017	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs749963436	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	98	511	0	ENST00000328354.6:c.823G>T	p.Glu275Ter	p.E275*	ENST00000328354	NM_007194.3	275	Gaa/Taa	7/15	1	2	FACETS	0.897	0.803	0.997	0.897	0.803	0.997	CLONAL	1	TRUE	1	0.390801325590925	2		511	559	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223356	2223356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1376643409	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	231	1019	0	ENST00000326181.6:c.968C>T	p.Ser323Leu	p.S323L	ENST00000326181	NM_032271.2	323	tCg/tTg	10/21	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.390801325590925	2		1019	973	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73340168	73340168	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs770832001	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	37	425	1	ENST00000377767.4:c.1912C>T	p.Arg638Ter	p.R638*	ENST00000377767	NM_014953.3	638	Cga/Tga	15/21	1	2	FACETS	0.452	0.373	0.541	0.452	0.373	0.541	SUBCLONAL	1	TRUE	1	0.390801325590925	2		426	419	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917655	94917655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746291519	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	147	818	0	ENST00000536441.1:c.866G>A	p.Arg289His	p.R289H	ENST00000536441	NM_144665.3	289	cGt/cAt	6/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.390801325590925	2		818	719	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931652	39931652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	253	1017	1	ENST00000378444.4:c.2947G>A	p.Glu983Lys	p.E983K	ENST00000378444	NM_001123385.1	983	Gaa/Aaa	4/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.390801325590925	2		1018	1075	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845609	63845609	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	74	339	0	ENST00000279873.7:c.1351del	p.Ser451AlafsTer28	p.S451Afs*28	ENST00000279873	NM_032199.2	450	Aaa/aa	9/10	1	2	FACETS	0.979	0.861	1	0.979	0.861	1	CLONAL	1	TRUE	1	0.390801325590925	2		339	387	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699288	117699288	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	176	744	0	ENST00000369458.3:c.353A>T	p.Lys118Ile	p.K118I	ENST00000369458	NM_024626.3	118	aAa/aTa	3/6	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.390801325590925	2		744	763	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748498	162748498	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs767183927	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	130	603	0	ENST00000367921.3:c.2412C>A	p.Phe804Leu	p.F804L	ENST00000367921	NM_006182.2	804	ttC/ttA	17/18	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.390801325590925	2		603	648	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924626	94924626	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	233	982	0	ENST00000536441.1:c.284A>G	p.Tyr95Cys	p.Y95C	ENST00000536441	NM_144665.3	95	tAc/tGc	3/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.390801325590925	2		982	1033	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254639	46254639	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	182	696	0	ENST00000334344.6:c.4829C>A	p.Ser1610Tyr	p.S1610Y	ENST00000334344	NM_152641.2	1610	tCt/tAt	16/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.390801325590925	2		696	788	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443905	49443905	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1333730892	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	297	1359	0	ENST00000301067.7:c.3466G>A	p.Asp1156Asn	p.D1156N	ENST00000301067	NM_003482.3	1156	Gac/Aac	11/54	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.390801325590925	2		1359	1229	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037919	49037919	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	29	544	0	ENST00000267163.4:c.2159A>C	p.Lys720Thr	p.K720T	ENST00000267163	NM_000321.2	720	aAa/aCa	21/27	1	2	FACETS	0.314	0.252	0.386	0.314	0.252	0.386	SUBCLONAL	1	TRUE	1	0.390801325590925	2		544	472	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749230	43749230	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	51	1064	0	ENST00000382044.4:c.1576G>T	p.Glu526Ter	p.E526*	ENST00000382044	NM_001141980.1	526	Gaa/Taa	12/28	1	2	FACETS	0.282	0.239	0.331	0.282	0.239	0.331	SUBCLONAL	1	TRUE	1	0.390801325590925	2		1064	924	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992226	72992226	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	322	1309	0	ENST00000268489.5:c.1819G>T	p.Glu607Ter	p.E607*	ENST00000268489	NM_006885.3	607	Gaa/Taa	2/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.390801325590925	2		1309	1372	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763380	59763380	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	214	1198	0	ENST00000259008.2:c.2722A>G	p.Thr908Ala	p.T908A	ENST00000259008	NM_032043.2	908	Aca/Gca	19/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.390801325590925	2		1198	903	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639592	47639592	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	160	536	0	ENST00000233146.2:c.685A>C	p.Lys229Gln	p.K229Q	ENST00000233146	NM_000251.2	229	Aaa/Caa	4/16	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.390801325590925	2		536	581	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705423	47705423	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	103	409	0	ENST00000233146.2:c.2223A>C	p.Lys741Asn	p.K741N	ENST00000233146	NM_000251.2	741	aaA/aaC	14/16	1	2	FACETS	0.755	0.683	0.831	1	0.984	1	SUBCLONAL	2	TRUE	1	0.390801325590925	2		409	349	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185089	99185089	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	180	805	0	ENST00000074304.5:c.2491A>C	p.Asn831His	p.N831H	ENST00000074304	NM_001134224.1	831	Aat/Cat	23/26	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.390801325590925	2		805	839	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610478	215610478	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	131	654	0	ENST00000260947.4:c.1778del	p.Lys593ArgfsTer12	p.K593Rfs*12	ENST00000260947	NM_000465.2	593	aAg/ag	8/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.390801325590925	2		654	565	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572948	41572948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	135	1195	0	ENST00000263253.7:c.5233G>A	p.Ala1745Thr	p.A1745T	ENST00000263253	NM_001429.3	1745	Gct/Act	31/31	1	2	FACETS	0.657	0.596	0.721	0.657	0.596	0.721	SUBCLONAL	1	TRUE	1	0.390801325590925	2		1195	1052	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428443	72428443	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	284	1069	0	ENST00000477973.2:c.561T>G	p.Ile187Met	p.I187M	ENST00000477973	NM_012234.5	187	atT/atG	2/4	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.390801325590925	2		1069	1200	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374299	138374299	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	220	803	0	ENST00000289153.2:c.3145C>T	p.Leu1049Phe	p.L1049F	ENST00000289153	NM_006219.2	1049	Ctc/Ttc	22/22	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.390801325590925	2		803	936	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136864	55136864	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1327567130	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	34	599	0	ENST00000257290.5:c.1186G>T	p.Ala396Ser	p.A396S	ENST00000257290	NM_006206.4	396	Gct/Tct	8/23	1	2	FACETS	0.264	0.215	0.32	0.264	0.215	0.32	SUBCLONAL	1	TRUE	1	0.390801325590925	2		599	659	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968556	55968556	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	48	872	0	ENST00000263923.4:c.2107G>T	p.Asp703Tyr	p.D703Y	ENST00000263923	NM_002253.2	703	Gat/Tat	14/30	1	2	FACETS	0.275	0.231	0.323	0.275	0.231	0.323	SUBCLONAL	1	TRUE	1	0.390801325590925	2		872	894	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383804	84383804	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	184	874	1	ENST00000321945.7:c.1048G>T	p.Asp350Tyr	p.D350Y	ENST00000321945	NM_139076.2	350	Gac/Tac	9/9	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.390801325590925	2		875	732	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441308	149441308	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	62	1017	0	ENST00000286301.3:c.1731C>A	p.Phe577Leu	p.F577L	ENST00000286301	NM_005211.3	577	ttC/ttA	12/22	1	2	FACETS	0.328	0.283	0.379	0.328	0.283	0.379	SUBCLONAL	1	TRUE	1	0.390801325590925	2		1017	966	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562418	176562418	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	235	931	0	ENST00000439151.2:c.314C>A	p.Ser105Ter	p.S105*	ENST00000439151	NM_022455.4	105	tCa/tAa	2/23	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.390801325590925	2		931	1022	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045648	26045648	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	80	430	0	ENST00000540144.1:c.10A>G	p.Thr4Ala	p.T4A	ENST00000540144	NM_003531.2	4	Acg/Gcg	1/1	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.390801325590925	2		430	405	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185849	32185849	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	302	1115	0	ENST00000375023.3:c.1547A>C	p.Glu516Ala	p.E516A	ENST00000375023	NM_004557.3	516	gAg/gCg	9/30	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.390801325590925	2		1115	1166	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983119	149983119	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	185	816	0	ENST00000253339.5:c.3139T>G	p.Leu1047Val	p.L1047V	ENST00000253339		1047	Tta/Gta	7/7	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.390801325590925	2		816	754	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450350	50450350	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	222	820	0	ENST00000331340.3:c.534C>A	p.Cys178Ter	p.C178*	ENST00000331340	NM_006060.4	178	tgC/tgA	5/8	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.390801325590925	2		820	855	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846200	128846200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	247	1124	1	ENST00000249373.3:c.1130C>T	p.Ala377Val	p.A377V	ENST00000249373	NM_005631.4	377	gCt/gTt	5/12	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.390801325590925	2		1125	1062	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38156991	38156991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766760275	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	47	874	0	ENST00000317025.8:c.2729C>T	p.Ser910Leu	p.S910L	ENST00000317025	NM_023034.1	910	tCg/tTg	15/24	1	2	FACETS	0.322	0.271	0.379	0.322	0.271	0.379	SUBCLONAL	1	TRUE	1	0.390801325590925	2		874	746	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172266	38172267	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	155	641	0	ENST00000317025.8:c.2140_2141del	p.Leu714AspfsTer4	p.L714Dfs*4	ENST00000317025	NM_023034.1	714	CTg/g	12/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.390801325590925	2		641	671	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028092	69028092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1316821029	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	168	834	0	ENST00000288368.4:c.3251G>A	p.Arg1084Gln	p.R1084Q	ENST00000288368	NM_024870.2	1084	cGg/cAg	26/40	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.390801325590925	2		834	643	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983484	90983484	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	89	467	0	ENST00000265433.3:c.619A>C	p.Ser207Arg	p.S207R	ENST00000265433	NM_002485.4	207	Agt/Cgt	6/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.390801325590925	2		467	396	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123054	5123054	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	134	732	0	ENST00000381652.3:c.3110T>C	p.Val1037Ala	p.V1037A	ENST00000381652	NM_004972.3	1037	gTt/gCt	23/25	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.390801325590925	2		732	624	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912146	127912146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564144380	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	91	427	0	ENST00000373547.4:c.724G>A	p.Glu242Lys	p.E242K	ENST00000373547	NM_002721.4	242	Gaa/Aaa	7/7	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.390801325590925	2		427	388	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802629	135802629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	36	547	0	ENST00000298552.3:c.169G>A	p.Ala57Thr	p.A57T	ENST00000298552	NM_001162426.1	57	Gca/Aca	4/23	1	2	FACETS	0.287	0.235	0.345	0.287	0.235	0.345	SUBCLONAL	1	TRUE	1	0.390801325590925	2		547	642	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351399	70351399	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	227	1051	1	ENST00000374080.3:c.4048-1G>T		p.X1350_splice	ENST00000374080		1350			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.390801325590925	2		1052	1065	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829805	76829805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	133	811	0	ENST00000373344.5:c.6236G>A	p.Arg2079Gln	p.R2079Q	ENST00000373344	NM_000489.3	2079	cGa/cAa	28/35	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.390801325590925	2		811	605	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937683	76937683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781811015	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	38	796	0	ENST00000373344.5:c.3065G>A	p.Arg1022Gln	p.R1022Q	ENST00000373344	NM_000489.3	1022	cGa/cAa	9/35	1	2	FACETS	0.262	0.216	0.315	0.262	0.216	0.315	SUBCLONAL	1	TRUE	1	0.390801325590925	2		796	741	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019658	123019658	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	216	943	0	ENST00000355640.3:c.146G>T	p.Arg49Leu	p.R49L	ENST00000355640		49	cGa/cTa	2/7	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.390801325590925	2		943	975	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	192	290	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.880935605265009	2		291	436	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225060	NA	P-0054947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	353	672	0	ENST00000263967.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000263967	NM_006218.2	104	cCa/cTa	2/21	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.880935605265009	2		672	799	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18747435	18747435	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	161	391	1	ENST00000266497.5:c.3896G>T	p.Cys1299Phe	p.C1299F	ENST00000266497		1299	tGt/tTt	28/31	1	2	FACETS	0.907	0.842	0.973	0.907	0.842	0.973	CLONAL	1	TRUE	1	0.880935605265009	2		392	403	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054947-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	152	290	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.899501900556279	2		291	318	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225060	NA	P-0054947-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	281	672	0	ENST00000263967.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000263967	NM_006218.2	104	cCa/cTa	2/21	1	2	FACETS	0.976	0.925	1	0.976	0.925	1	CLONAL	1	TRUE	1	0.899501900556279	2		672	640	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18747435	18747435	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054947-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	166	391	1	ENST00000266497.5:c.3896G>T	p.Cys1299Phe	p.C1299F	ENST00000266497		1299	tGt/tTt	28/31	1	2	FACETS	0.932	0.867	0.998	0.932	0.867	0.998	CLONAL	1	TRUE	1	0.899501900556279	2		392	396	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602345	28602345	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054947-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	312	740	0	ENST00000241453.7:c.2023G>T	p.Val675Leu	p.V675L	ENST00000241453	NM_004119.2	675	Gtg/Ttg	16/24	1	2	FACETS	0.945	0.897	0.994	0.945	0.897	0.994	CLONAL	1	TRUE	1	0.899501900556279	2		740	734	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560181	29560181	+	stop_gained	Nonsense_Mutation	INS	G	G	TGAT	novel	NA	P-0054988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	138	232	0	ENST00000356175.3:c.3658delinsTGAT	p.Glu1220delinsTer	p.E1220delins*	ENST00000356175	NM_000267.3	1220	Gaa/TGATaa	27/57	1	2	FACETS	0.895	0.823	0.97	0.895	0.823	0.97	CLONAL	1	TRUE	1	0.750153058634867	2		232	411	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154350	2154350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1268163024	NA	P-0000092-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	595	467	0	ENST00000434045.2:c.578G>A	p.Arg193His	p.R193H	ENST00000434045	NM_001127598.1	193	cGc/cAc	5/5	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.626783544071952	2		467	1510	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514866	103514866	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000092-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	265	66	0	ENST00000355739.4:c.1367A>G	p.Glu456Gly	p.E456G	ENST00000355739	NM_000123.3	456	gAg/gGg	8/15	NA	2	FACETS	0.906	0.851	0.963			1	INDETERMINATE	1	TRUE	NA	0.626783544071952	2		66	933	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472510	88472510	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000092-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	545	431	1	ENST00000360948.2:c.2045C>A	p.Thr682Asn	p.T682N	ENST00000360948	NM_001012338.2	682	aCc/aAc	16/19	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.626783544071952	2		432	1331	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554266	63554266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000092-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	459	515	0	ENST00000307078.5:c.473G>A	p.Arg158Lys	p.R158K	ENST00000307078	NM_004655.3	158	aGa/aAa	2/11	1	2	FACETS	0.988	0.942	1	0.988	0.942	1	CLONAL	1	TRUE	1	0.626783544071952	2		515	1483	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs199469672	NA	P-0000092-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	526	504	0	ENST00000374080.3:c.131G>C	p.Gly44Ala	p.G44A	ENST00000374080		44	gGt/gCt	2/45	0.108893554771085	0	FACETS	0.368	0.352	0.385			1	INDETERMINATE	1	TRUE	0	0.626783544071952	0		504	1701	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609948	43609948	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs75076352	NA	P-0000662-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	546	1204	0	ENST00000355710.3:c.1900T>C	p.Cys634Arg	p.C634R	ENST00000355710	NM_020975.4	634	Tgc/Cgc	11/20	0.698895587213943	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.698895587213943	1		1204	949	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615014	43615014	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000662-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	432	1119	0	ENST00000355710.3:c.2428G>C	p.Gly810Arg	p.G810R	ENST00000355710	NM_020975.4	810	Ggc/Cgc	14/20	0.698895587213943	1	FACETS	0.99	0.952	1	0.99	0.952	1	CLONAL	1	TRUE	0	0.698895587213943	1		1119	812	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715806	18715806	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000662-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	166	368	0	ENST00000266497.5:c.3637T>C	p.Phe1213Leu	p.F1213L	ENST00000266497		1213	Ttc/Ctc	25/31	1	2	FACETS	0.962	0.89	1	0.962	0.89	1	CLONAL	1	TRUE	1	0.698895587213943	2		368	494	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021625	31021659	+	frameshift_variant	Frame_Shift_Del	DEL	CTTGAAGATCGTCAGTCCTTTCGTAACACAATTGA	CTTGAAGATCGTCAGTCCTTTCGTAACACAATTGA	-	novel	NA	P-0000662-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	249	650	0	ENST00000375687.4:c.1624_1658del	p.Leu542LysfsTer11	p.L542Kfs*11	ENST00000375687	NM_015338.5	542	CTTGAAGATCGTCAGTCCTTTCGTAACACAATTGAa/a	12/13	1	2	FACETS	0.868	0.814	0.923	0.868	0.814	0.923	CLONAL	1	TRUE	1	0.698895587213943	2		650	821	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053183	180053183	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000662-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	475	1241	1	ENST00000261937.6:c.1186A>T	p.Thr396Ser	p.T396S	ENST00000261937	NM_182925.4	396	Acc/Tcc	9/30	0.698895587213943	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.698895587213943	1		1242	820	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0000978-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	347	26	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.922	0.897	0.946	1	0.997	1	CLONAL	5	TRUE	1	0.36	2		26	418	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0001243-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	17	253	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.26137306826651	1	FACETS	0.064	0.047	0.084	0.064	0.047	0.084	INDETERMINATE	1	FALSE	0	0.530075067770372	1		253	739	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90996767	90996767	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001243-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	557	488	0	ENST00000265433.3:c.23C>A	p.Ala8Glu	p.A8E	ENST00000265433	NM_002485.4	8	gCg/gAg	1/16	0.530075067770372	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	FALSE	1	0.530075067770372	3		488	1210	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63816919	63816919	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001243-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	211	144	0	ENST00000279873.7:c.890A>G	p.Asn297Ser	p.N297S	ENST00000279873	NM_032199.2	297	aAc/aGc	6/10	0.191782855086487	2	FACETS	0.763	0.715	0.811	0.763	0.715	0.811	INDETERMINATE	2	FALSE	0	0.530075067770372	2		144	522	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119912	70119912	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001243-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	56	345	0	ENST00000245479.2:c.914G>T	p.Gly305Val	p.G305V	ENST00000245479	NM_000346.3	305	gGg/gTg	3/3	0.237315794801272	2	FACETS	0.253	0.216	0.294	0.127	0.108	0.147	INDETERMINATE	1	FALSE	0	0.530075067770372	2		345	835	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222741	53222741	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001243-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1301	176	429	0	ENST00000375401.3:c.4195T>A	p.Leu1399Met	p.L1399M	ENST00000375401	NM_004187.3	1399	Ttg/Atg	25/26	0.341712035440374	3	FACETS	0.569	0.522	0.618	0.284	0.261	0.309	SUBCLONAL	1	FALSE	1	0.530075067770372	3		429	1477	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0001243-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	224	285	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.349546406482679	4	FACETS	1	0.991	1	0.724	0.675	0.775	CLONAL	1	FALSE	2	0.530075067770372	4		285	893	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983141	201983141	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004593-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	402	619	0	ENST00000359651.3:c.990C>G	p.Ser330Arg	p.S330R	ENST00000359651		330	agC/agG	7/8	0.847740472062043	6	FACETS	0.858	0.815	0.902	0.429	0.407	0.451	CLONAL	2	TRUE	2	0.847740472062043	6		619	1489	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913867	32913867	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004593-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	27	468	1	ENST00000380152.3:c.5376del	p.Asn1793MetfsTer2	p.N1793Mfs*2	ENST00000380152		1792	tCc/tc	11/27	0.848620343495741	1	FACETS	0.644	0.539	0.75	0.644	0.539	0.75	SUBCLONAL	1	TRUE	0	0.847740472062043	1		469	57	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106216	2106216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139929314	NA	P-0004593-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	168	889	1	ENST00000219476.3:c.619G>A	p.Val207Ile	p.V207I	ENST00000219476	NM_000548.3	207	Gtc/Atc	7/42	0.735758242336754	6	FACETS	0.907	0.832	0.985			1	CLONAL	1	TRUE	NA	0.847740472062043	6		890	1178	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41267759	41267759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879255290	NA	P-0004593-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	267	563	0	ENST00000357654.3:c.118G>A	p.Asp40Asn	p.D40N	ENST00000357654	NM_007294.3	40	Gac/Aac	3/23	0.748762632445626	6	FACETS	0.882	0.833	0.931	0.882	0.833	0.931	CLONAL	3	TRUE	3	0.847740472062043	6		563	642	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965227	25965227	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004593-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	236	759	0	ENST00000435504.4:c.3979T>C	p.Tyr1327His	p.Y1327H	ENST00000435504		1327	Tat/Cat	13/13	0.848620343495741	3	FACETS	1	0.946	1	0.506	0.473	0.539	CLONAL	1	TRUE	1	0.847740472062043	3		759	784	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707900	47707900	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004593-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	135	540	0	ENST00000233146.2:c.2524G>C	p.Glu842Gln	p.E842Q	ENST00000233146	NM_000251.2	842	Gag/Cag	15/16	0.685858017986035	4	FACETS	0.874	0.797	0.956	0.437	0.398	0.478	CLONAL	1	TRUE	2	0.847740472062043	4		540	673	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149453024	149453024	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004593-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	184	489	0	ENST00000286301.3:c.922A>G	p.Asn308Asp	p.N308D	ENST00000286301	NM_005211.3	308	Aac/Gac	7/22	0.333908765644075	3	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.847740472062043	3		489	565	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514349	149514349	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004593-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	122	640	0	ENST00000261799.4:c.595G>C	p.Val199Leu	p.V199L	ENST00000261799	NM_002609.3	199	Gtg/Ctg	4/23	0.848620343495741	3	FACETS	0.6	0.543	0.66	0.3	0.271	0.33	SUBCLONAL	1	TRUE	1	0.847740472062043	3		640	683	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334966	81334966	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004593-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	112	511	0	ENST00000222390.5:c.1861G>T	p.Gly621Ter	p.G621*	ENST00000222390	NM_000601.4	621	Gga/Tga	16/18	NA	2	FACETS	0.71	0.645	0.778			1	INDETERMINATE	1	TRUE	NA	0.847740472062043	2		511	372	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97897771	97897771	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004593-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	162	417	0	ENST00000289081.3:c.700C>A	p.Leu234Ile	p.L234I	ENST00000289081	NM_000136.2	234	Ctc/Atc	8/15	0.841811728300727	5	FACETS	1	0.951	1			1	CLONAL	1	TRUE	NA	0.847740472062043	5		417	828	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922195	39922329	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTTTAATTTTCTGCTGTTTGGCAGGCGGCCTGGAGGCTGGTGCGCAGCTTGGCTGAGCCTGCTTTTTGCCGCCTGCACTGGTGGATGAAAGACTCTTCATGGGCGGAGAGCCGGAGAACACAGGCAAGCCTAAA	TCTTTAATTTTCTGCTGTTTGGCAGGCGGCCTGGAGGCTGGTGCGCAGCTTGGCTGAGCCTGCTTTTTGCCGCCTGCACTGGTGGATGAAAGACTCTTCATGGGCGGAGAGCCGGAGAACACAGGCAAGCCTAAA	-	novel	NA	P-0004593-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	150	399	0	ENST00000378444.4:c.3848-5_3977del		p.X1283_splice	ENST00000378444	NM_001123385.1	1283		9/15	0.695750583650346	2	FACETS	0.81	0.747	0.874			1	CLONAL	1	TRUE	NA	0.847740472062043	2		399	437	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913830	32913854	+	protein_altering_variant	In_Frame_Del	DEL	GAAGATCAAAAAAACACTAGTTTTT	GAAGATCAAAAAAACACTAGTTTTT	TTTC	novel	NA	P-0004593-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	13	457	0	ENST00000380152.3:c.5338_5362delinsTTTC	p.Glu1780_Ser1788delinsPhePro	p.E1780_S1788delinsFP	ENST00000380152		1780	GAAGATCAAAAAAACACTAGTTTTTcc/TTTCcc	11/27	0.848620343495741	1	FACETS	0.393	0.291	0.506	0.393	0.291	0.506	SUBCLONAL	1	TRUE	0	0.847740472062043	1		457	45	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573996	7573996	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006645-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	787	335	0	ENST00000269305.4:c.1031T>A	p.Leu344Gln	p.L344Q	ENST00000269305	NM_001126112.2	344	cTg/cAg	10/11	0.641785287761752	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.666568323079915	2		335	1025	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0008099-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	35	304	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.11	2		304	561	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875627	35875627	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369971728	NA	P-0008099-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	9	0	0	ENST00000303115.3:c.814G>A	p.Val272Ile	p.V272I	ENST00000303115	NM_002185.3	272	Gta/Ata	7/8	1	2	FACETS	0.426	0.281	0.613	0.426	0.281	0.613	SUBCLONAL	1	TRUE	1	0.11	2		0	384	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020377	123020377	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008099-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	10	0	0	ENST00000355640.3:c.865T>C	p.Phe289Leu	p.F289L	ENST00000355640		289	Ttt/Ctt	2/7	1	2	FACETS	0.457	0.308	0.646	0.457	0.308	0.646	SUBCLONAL	1	TRUE	1	0.11	2		0	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576916	7576917	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0008099-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	36	0	0	ENST00000269305.4:c.929_930insG	p.Asn310LysfsTer27	p.N310Kfs*27	ENST00000269305	NM_001126112.2	310	aac/aaGc	9/11	1	2	FACETS	0.802	0.657	0.966	0.802	0.657	0.966	CLONAL	1	TRUE	1	0.11	2		0	816	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009960-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	201	304	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.135465632318573	7	FACETS	0.962	0.9	1			1	CLONAL	8	TRUE	NA	0.135465632318573	7		304	516	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051624	30051624	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1325902176	NA	P-0009960-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	184	78	0	ENST00000338641.4:c.558G>C	p.Glu186Asp	p.E186D	ENST00000338641	NM_000268.3	186	gaG/gaC	6/16	0.149739539116119	1	FACETS	1	0.948	1	1	0.995	1	CLONAL	5	TRUE	0	0.135465632318573	1		78	496	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145701	11145701	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009960-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	508	193	1	ENST00000358026.2:c.4063G>T	p.Glu1355Ter	p.E1355*	ENST00000358026	NM_001128849.1	1355	Gag/Tag	29/36	0.149739539116119	1	FACETS	1	0.985	1	1	0.998	1	CLONAL	5	TRUE	0	0.135465632318573	1		194	1326	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112884198	112884198	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009960-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	268	106	0	ENST00000351677.2:c.133G>T	p.Val45Phe	p.V45F	ENST00000351677	NM_002834.3	45	Gtt/Ttt	2/16	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.135465632318573	NA		106	1003	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589841	212589841	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009960-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	264	102	0	ENST00000342788.4:c.701G>C	p.Cys234Ser	p.C234S	ENST00000342788	NM_005235.2	234	tGt/tCt	6/28	1	2	FACETS	1	0.978	1	1	0.996	1	CLONAL	5	TRUE	1	0.135465632318573	2		102	725	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514452	41514452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009960-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	264	94	0	ENST00000373198.4:c.209C>T	p.Pro70Leu	p.P70L	ENST00000373198	NM_133170.3	70	cCc/cTc	2/32	0.149739539116119	0	FACETS	0.933	0.88	0.988			1	CLONAL	5	TRUE	0	0.135465632318573	0		94	722	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057296	30057296	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009960-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	255	105	0	ENST00000338641.4:c.778G>T	p.Glu260Ter	p.E260*	ENST00000338641	NM_000268.3	260	Gaa/Taa	8/16	0.149739539116119	1	FACETS	1	0.942	1	1	0.996	1	CLONAL	5	TRUE	0	0.135465632318573	1		105	701	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434201	12434201	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009960-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	243	69	0	ENST00000287820.6:c.569G>A	p.Cys190Tyr	p.C190Y	ENST00000287820	NM_015869.4	190	tGt/tAt	4/7	1	2	FACETS	1	0.971	1	1	0.996	1	CLONAL	5	TRUE	1	0.135465632318573	2		69	680	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912169	29912170	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0009960-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	119	46	0	ENST00000376809.5:c.891_892dup	p.Trp298TyrfsTer25	p.W298Yfs*25	ENST00000376809	NM_002116.7	297	aga/agATa	4/8	0.0409370867973566	4	FACETS	0.976	0.888	1	1	0.991	1	INDETERMINATE	5	TRUE	2	0.135465632318573	4		46	409	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426776	121426776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150513055	NA	P-0009991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	52	362	1	ENST00000257555.6:c.467C>T	p.Thr156Met	p.T156M	ENST00000257555		156	aCg/aTg	2/10	0.231499871064893	1	FACETS	0.456	0.387	0.532	0.456	0.387	0.532	SUBCLONAL	1	TRUE	0	0.231499871064893	1		363	871	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752383	57752383	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	22	108	0	ENST00000274289.3:c.1190A>C	p.Lys397Thr	p.K397T	ENST00000274289	NM_006622.3	397	aAg/aCg	9/14	0.0986982205581994	3	FACETS	0.552	0.427	0.698			1	INDETERMINATE	1	TRUE	NA	0.231499871064893	3		108	384	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063628	67063628	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0009991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	86	223	0	ENST00000412916.2:c.79-2A>G		p.X27_splice	ENST00000412916		27			0.231499871064893	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.231499871064893	1		223	488	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983097	201983151	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GGCCAAAAGAAAAAGAACAGCAACATGACCTACGAGAAGCTGAGCCGGGCCATGA	GGCCAAAAGAAAAAGAACAGCAACATGACCTACGAGAAGCTGAGCCGGGCCATGA	-	novel	NA	P-0009991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	75	374	0	ENST00000359651.3:c.948_1001+1del		p.GQKKKNSNMTYEKLSRAMR316fs	ENST00000359651		316	GGCCAAAAGAAAAAGAACAGCAACATGACCTACGAGAAGCTGAGCCGGGCCATGAgg/gg	7/8	0.0613707956606555	4	FACETS	0.934	0.817	1	0.467	0.408	0.531	INDETERMINATE	1	TRUE	2	0.231499871064893	4		374	854	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436482	110436482	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1181	92	511	1	ENST00000375856.3:c.1919A>T	p.His640Leu	p.H640L	ENST00000375856	NM_003749.2	640	cAc/cTc	1/2	0.231499871064893	1	FACETS	0.552	0.489	0.62	0.552	0.489	0.62	SUBCLONAL	1	TRUE	0	0.231499871064893	1		512	1273	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732529	74733516	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	CGGCGACGCCGCCTAGGGCTGCGGGCGGGACGAGCAAGCACAGCGGGGTTAATTCCAGGCAGCGGGGCCGGCCCCGCCCGCGCGCTCCCGCCCAGGCCGCCATTATCTCGCCGCCAGACGCCATTTCCCCAGTCGCGAGGCGGGGTCCTCCGCCCCGCGCCGCCCACACCCCGGCCACTCCCGGGTCGCAGACGGCGGAAGCTCGCGGGGTGGCCGGAGGGTCGCGAGACGCGGCGTGCACCCCCGCCCCGTCCGGGCCCGCACCACGTGCTTCGCCGCGGACCTTTGTGAGGTCGCCCGGGCCTCCCGCGCGCCCCGCCCCGCCTCCCGCGGTCCCCTCAGCCCCGTTTACCTGCGGCTCCGGCGTCCGTAGCCACCGCCCCCGTACCTGCGGGGTGGCGGTCCCCGGCGGCTGTGGTGTGAGTCCGGGGGGCGGCCGTAGCGCGCCATTTGCACCCGCAGCTCGCGGCCGTCCAGCACGGCCCCGTCCATGGCATCCATAGCGTCCTCAGCGTCGCGCTTGTCGTGAAAGCGAACGAAGGCGAAGCCGCGGGACTCCTTGGTGTAGCGGTCCCGCGGGATGTACACGTCGCCGACGCGCCCGTACTTCTCGAAGACGCGCCTCAGCGTGTCGGGCGAGGTGCGGTAGGTCAGGTTGTCCACCTTGAGGGAGGTCATACCCTCCACATCGGGAGGGGGGCGGCCGTAGCTCATAGCTCTGAGTGGCGGCCCGGAGCCCCGCGAACTGGCGCCGGCTTCCTCAGCTCTGGGCGGTGCGACGCCGCGCCTCTCAGGCAGTTGCCTTCCGCGTGGGGACACTGGGAAAGGCCTTGCCGCAGAACAGCACGGACGGGCTCCGCAGGCTAGCGCACCTGAGTAACAACTGGGCGGGCAGCCGGCCTCTGCGCCCGTTTATATCGCTCCTCACAAAATGGCGCCCGCGCCACCCGGAAATGAAACCTTCTGATTGGCCCACCGCGCCCCGCTT	CGGCGACGCCGCCTAGGGCTGCGGGCGGGACGAGCAAGCACAGCGGGGTTAATTCCAGGCAGCGGGGCCGGCCCCGCCCGCGCGCTCCCGCCCAGGCCGCCATTATCTCGCCGCCAGACGCCATTTCCCCAGTCGCGAGGCGGGGTCCTCCGCCCCGCGCCGCCCACACCCCGGCCACTCCCGGGTCGCAGACGGCGGAAGCTCGCGGGGTGGCCGGAGGGTCGCGAGACGCGGCGTGCACCCCCGCCCCGTCCGGGCCCGCACCACGTGCTTCGCCGCGGACCTTTGTGAGGTCGCCCGGGCCTCCCGCGCGCCCCGCCCCGCCTCCCGCGGTCCCCTCAGCCCCGTTTACCTGCGGCTCCGGCGTCCGTAGCCACCGCCCCCGTACCTGCGGGGTGGCGGTCCCCGGCGGCTGTGGTGTGAGTCCGGGGGGCGGCCGTAGCGCGCCATTTGCACCCGCAGCTCGCGGCCGTCCAGCACGGCCCCGTCCATGGCATCCATAGCGTCCTCAGCGTCGCGCTTGTCGTGAAAGCGAACGAAGGCGAAGCCGCGGGACTCCTTGGTGTAGCGGTCCCGCGGGATGTACACGTCGCCGACGCGCCCGTACTTCTCGAAGACGCGCCTCAGCGTGTCGGGCGAGGTGCGGTAGGTCAGGTTGTCCACCTTGAGGGAGGTCATACCCTCCACATCGGGAGGGGGGCGGCCGTAGCTCATAGCTCTGAGTGGCGGCCCGGAGCCCCGCGAACTGGCGCCGGCTTCCTCAGCTCTGGGCGGTGCGACGCCGCGCCTCTCAGGCAGTTGCCTTCCGCGTGGGGACACTGGGAAAGGCCTTGCCGCAGAACAGCACGGACGGGCTCCGCAGGCTAGCGCACCTGAGTAACAACTGGGCGGGCAGCCGGCCTCTGCGCCCGTTTATATCGCTCCTCACAAAATGGCGCCCGCGCCACCCGGAAATGAAACCTTCTGATTGGCCCACCGCGCCCCGCTT	-	novel	NA	P-0009991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	15	128	0				ENST00000359995	NM_001195427.1	-/449		1-2/3	0.220760333675156		FACETS		0.352	0.638				SUBCLONAL	1	TRUE	0	0.231499871064893	2		128	269	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12653501	12653501	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	26	229	0	ENST00000251849.4:c.268G>T	p.Gly90Cys	p.G90C	ENST00000251849	NM_002880.3	90	Ggc/Tgc	3/17	0.231499871064893	1	FACETS	0.388	0.306	0.482	0.388	0.306	0.482	SUBCLONAL	1	TRUE	0	0.231499871064893	1		229	512	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92247519	92247519	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1163572894	NA	P-0009991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	20	124	0	ENST00000265734.4:c.701T>C	p.Val234Ala	p.V234A	ENST00000265734	NM_001259.6	234	gTg/gCg	7/8	1	2	FACETS	0.559	0.427	0.713	0.559	0.427	0.713	SUBCLONAL	1	TRUE	1	0.231499871064893	2		124	309	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	103	455	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.460644921478005	2		456	442	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003191	42003191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs761227360	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	70	489	0	ENST00000219905.7:c.2728C>T	p.Arg910Ter	p.R910*	ENST00000219905	NM_001164273.1	910	Cga/Tga	8/24	0.221047364575162	1	FACETS	0.465	0.406	0.528	0.465	0.406	0.528	INDETERMINATE	1	TRUE	0	0.460644921478005	1		489	503	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	78	584	2	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	0.221047364575162	1	FACETS	0.42	0.369	0.474	0.42	0.369	0.474	INDETERMINATE	1	TRUE	0	0.460644921478005	1		586	621	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	305	1294	6	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.968	0.911	1	0.968	0.911	1	CLONAL	1	TRUE	1	0.460644921478005	2		1300	1368	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007332	143007332	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	69	274	0	ENST00000262992.4:c.2452del	p.Arg818GlufsTer4	p.R818Efs*4	ENST00000262992	NM_001101669.1	818	Aga/ga	22/24	1	2	FACETS	0.823	0.721	0.932	0.823	0.721	0.932	CLONAL	1	TRUE	1	0.460644921478005	2		274	364	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879925	44879925	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs189751539	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	120	469	0	ENST00000377967.4:c.514C>T	p.Arg172Ter	p.R172*	ENST00000377967	NM_021140.2	172	Cga/Tga	6/29	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.460644921478005	2		469	473	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224210	36224210	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	137	678	0	ENST00000222270.7:c.6764del	p.Pro2255ArgfsTer6	p.P2255Rfs*6	ENST00000222270	NM_014727.1	2254	Ccc/cc	28/37	1	2	FACETS	0.806	0.734	0.881	0.806	0.734	0.881	CLONAL	1	TRUE	1	0.460644921478005	2		678	738	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437266	220437266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753111199	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	315	1280	1	ENST00000243786.2:c.170G>A	p.Arg57Gln	p.R57Q	ENST00000243786	NM_002191.3	57	cGg/cAg	1/2	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.460644921478005	2		1281	1281	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	212	981	2	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.865	0.803	0.929	0.865	0.803	0.929	CLONAL	1	TRUE	1	0.460644921478005	2		983	1064	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539564	187539564	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	87	351	0	ENST00000441802.2:c.8176C>T	p.Arg2726Ter	p.R2726*	ENST00000441802	NM_005245.3	2726	Cga/Tga	10/27	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.460644921478005	2		351	340	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	179	1026	15	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.774	0.713	0.838	0.774	0.713	0.838	SUBCLONAL	1	TRUE	1	0.460644921478005	2		1041	1004	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144146	11144146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	203	49	1	ENST00000358026.2:c.3727C>T	p.Arg1243Trp	p.R1243W	ENST00000358026	NM_001128849.1	1243	Cgg/Tgg	26/36	1	2	FACETS	0.917	0.851	0.986	0.917	0.851	0.986	CLONAL	1	TRUE	1	0.460644921478005	2		50	961	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	189	879	2	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.460644921478005	2		881	791	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294078	1294078	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	262	1289	0	ENST00000310581.5:c.923del	p.Pro308HisfsTer43	p.P308Hfs*43	ENST00000310581	NM_198253.2	308	cCa/ca	2/16	1	2	FACETS	0.808	0.755	0.862	0.808	0.755	0.862	CLONAL	1	TRUE	1	0.460644921478005	2		1289	1408	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665274	176665274	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121908070	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	34	307	0	ENST00000439151.2:c.3958C>T	p.Arg1320Ter	p.R1320*	ENST00000439151	NM_022455.4	1320	Cga/Tga	7/23	0.255913949672266	1	FACETS	0.342	0.28	0.412	0.342	0.28	0.412	INDETERMINATE	1	TRUE	0	0.460644921478005	1		307	332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793881	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	121	749	0	ENST00000269305.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGg/gAg	8/11	0.221047364575162	1	FACETS	0.462	0.417	0.509	0.462	0.417	0.509	INDETERMINATE	1	TRUE	0	0.460644921478005	1		749	876	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156535	55156535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778598	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	126	532	0	ENST00000257290.5:c.2936G>A	p.Arg979His	p.R979H	ENST00000257290	NM_006206.4	979	cGc/cAc	22/23	1	2	FACETS	0.916	0.832	1	0.916	0.832	1	CLONAL	1	TRUE	1	0.460644921478005	2		532	597	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344159	70344159	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199582086	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	173	634	1	ENST00000374080.3:c.1895G>A	p.Arg632Gln	p.R632Q	ENST00000374080		632	cGg/cAg	13/45	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.460644921478005	2		635	721	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098533	108098533	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs55861249	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	51	219	0	ENST00000278616.4:c.103C>T	p.Arg35Ter	p.R35*	ENST00000278616	NM_000051.3	35	Cga/Tga	3/63	1	2	FACETS	0.975	0.838	1	0.975	0.838	1	CLONAL	1	TRUE	1	0.460644921478005	2		219	227	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962933	2962933	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs78443994	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	251	1081	0	ENST00000396946.4:c.1975G>A	p.Val659Met	p.V659M	ENST00000396946	NM_032415.4	659	Gtg/Atg	16/25	0.424771187736285	3	FACETS	1	0.954	1	0.513	0.479	0.549	CLONAL	1	TRUE	1	0.460644921478005	3		1081	1306	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988348	36988348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs546402304	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	68	504	3	ENST00000354822.5:c.305C>T	p.Ala102Val	p.A102V	ENST00000354822	NM_001079668.2	102	gCg/gTg	2/3	1	2	FACETS	0.599	0.522	0.682	0.599	0.522	0.682	SUBCLONAL	1	TRUE	1	0.460644921478005	2		507	493	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643942	52643943	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	75	337	0	ENST00000394830.3:c.1953dup	p.Ser652IlefsTer13	p.S652Ifs*13	ENST00000394830	NM_018313.4	651	-/A	17/30	1	2	FACETS	0.757	0.666	0.854	0.757	0.666	0.854	SUBCLONAL	1	TRUE	1	0.460644921478005	2		337	430	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100302	157100302	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1417035592	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	81	358	0	ENST00000346085.5:c.1243del	p.Ala415ProfsTer15	p.A415Pfs*15	ENST00000346085	NM_020732.3	413	tcG/tc	1/20	1	2	FACETS	0.862	0.764	0.966	0.862	0.764	0.966	CLONAL	1	TRUE	1	0.460644921478005	2		358	408	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786734	3786734	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	126	537	2	ENST00000262367.5:c.4477del	p.Ile1493TyrfsTer57	p.I1493Yfs*57	ENST00000262367	NM_004380.2	1493	Ata/ta	27/31	1	2	FACETS	0.828	0.751	0.908	0.828	0.751	0.908	CLONAL	1	TRUE	1	0.460644921478005	2		539	661	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816139	89816139	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs760392231	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	144	624	0	ENST00000389301.3:c.3238C>T	p.Arg1080Trp	p.R1080W	ENST00000389301	NM_000135.2	1080	Cgg/Tgg	32/43	1	2	FACETS	0.843	0.77	0.919	0.843	0.77	0.919	CLONAL	1	TRUE	1	0.460644921478005	2		624	742	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808308	1808308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1455074121	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	297	1254	1	ENST00000260795.2:c.2066C>T	p.Thr689Met	p.T689M	ENST00000260795		689	aCg/aTg	15/17	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.460644921478005	2		1255	1241	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120794	94120794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs570778929	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	105	484	0	ENST00000369303.4:c.257G>A	p.Arg86Gln	p.R86Q	ENST00000369303	NM_004440.3	86	cGg/cAg	3/17	1	2	FACETS	0.826	0.742	0.914	0.826	0.742	0.914	CLONAL	1	TRUE	1	0.460644921478005	2		484	552	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656840	45656840	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	89	654	3	ENST00000407780.3:c.316del	p.Gln106ArgfsTer11	p.Q106Rfs*11	ENST00000407780	NM_001283052.1	106	Cag/ag	3/7	0.255913949672266	1	FACETS	0.392	0.347	0.44	0.392	0.347	0.44	INDETERMINATE	1	TRUE	0	0.460644921478005	1		657	759	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002849	69002849	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	61	284	0	ENST00000288368.4:c.2149C>T	p.Gln717Ter	p.Q717*	ENST00000288368	NM_024870.2	717	Cag/Tag	20/40	0.231781541231944	3	FACETS	0.958	0.832	1	0.479	0.416	0.547	INDETERMINATE	1	TRUE	1	0.460644921478005	3		284	340	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030223	180030223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200835339	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	92	828	3	ENST00000261937.6:c.4061G>A	p.Arg1354His	p.R1354H	ENST00000261937	NM_182925.4	1354	cGc/cAc	30/30	0.255913949672266	1	FACETS	0.385	0.341	0.431	0.385	0.341	0.431	INDETERMINATE	1	TRUE	0	0.460644921478005	1		831	799	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649272	23649272	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs202194596	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	99	250	0	ENST00000261584.4:c.110G>A	p.Arg37His	p.R37H	ENST00000261584	NM_024675.3	37	cGt/cAt	3/13	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.460644921478005	2		250	380	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619391	1619391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779358744	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	221	1083	0	ENST00000344749.5:c.1250C>T	p.Thr417Met	p.T417M	ENST00000344749	NM_001136139.2	417	aCg/aTg	15/19	1	2	FACETS	0.785	0.729	0.843	0.785	0.729	0.843	SUBCLONAL	1	TRUE	1	0.460644921478005	2		1083	1222	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442570	52442570	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1404823823	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	108	411	1	ENST00000460680.1:c.175C>T	p.Arg59Trp	p.R59W	ENST00000460680	NM_004656.3	59	Cgg/Tgg	4/17	1	2	FACETS	0.823	0.74	0.909	0.823	0.74	0.909	CLONAL	1	TRUE	1	0.460644921478005	2		412	570	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223120	5223120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764560600	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	281	1129	1	ENST00000357368.4:c.2683G>A	p.Val895Met	p.V895M	ENST00000357368	NM_002850.3	895	Gtg/Atg	18/38	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.460644921478005	2		1130	1216	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	137	572	0	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.85	0.774	0.929	0.85	0.774	0.929	CLONAL	1	TRUE	1	0.460644921478005	2		572	700	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037144	71037144	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	98	310	2	ENST00000318789.4:c.1146+1G>A		p.X382_splice	ENST00000318789	NM_032682.5	382			1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.460644921478005	2		312	424	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15838385	15838385	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775221448	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	80	397	1	ENST00000307771.7:c.883C>T	p.Arg295Ter	p.R295*	ENST00000307771	NM_005089.3	295	Cga/Tga	10/11	1	2	FACETS	0.755	0.667	0.849	0.755	0.667	0.849	SUBCLONAL	1	TRUE	1	0.460644921478005	2		398	460	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	284	348	17	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	0.424771187736285	3	FACETS	0.924	0.879	0.97	1	0.994	1	CLONAL	3	TRUE	1	0.460644921478005	3		365	547	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165557	47165557	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs563907746	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	126	506	0	ENST00000409792.3:c.569C>T	p.Pro190Leu	p.P190L	ENST00000409792	NM_014159.6	190	cCg/cTg	3/21	1	2	FACETS	0.84	0.763	0.922	0.84	0.763	0.922	CLONAL	1	TRUE	1	0.460644921478005	2		506	651	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778302	3778302	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs794727551	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	238	959	2	ENST00000262367.5:c.6746G>A	p.Arg2249His	p.R2249H	ENST00000262367	NM_004380.2	2249	cGc/cAc	31/31	1	2	FACETS	0.997	0.931	1	0.997	0.931	1	CLONAL	1	TRUE	1	0.460644921478005	2		961	1036	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420109	49420109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123728	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	142	643	0	ENST00000301067.7:c.15640C>T	p.Arg5214Cys	p.R5214C	ENST00000301067	NM_003482.3	5214	Cgc/Tgc	48/54	1	2	FACETS	0.764	0.697	0.835	0.764	0.697	0.835	SUBCLONAL	1	TRUE	1	0.460644921478005	2		643	807	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378265	225378266	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	64	200	0	ENST00000264414.4:c.629dup	p.Leu210PhefsTer20	p.L210Ffs*20	ENST00000264414	NM_003590.4	210	ttg/ttTg	5/16	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.460644921478005	2		200	257	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90971011	90971011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777259845	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	135	339	0	ENST00000265433.3:c.1066G>A	p.Ala356Thr	p.A356T	ENST00000265433	NM_002485.4	356	Gcc/Acc	9/16	0.231781541231944	3	FACETS	0.77	0.705	0.838	0.77	0.705	0.838	INDETERMINATE	2	TRUE	1	0.460644921478005	3		339	468	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345760	152345760	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	60	196	0	ENST00000359321.1:c.810del	p.Phe270LeufsTer27	p.F270Lfs*27	ENST00000359321	NM_005431.1	270	ttT/tt	3/3	0.424771187736285	3	FACETS	0.924	0.8	1	0.462	0.4	0.528	CLONAL	1	TRUE	1	0.460644921478005	3		196	347	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434142	49434142	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057518571	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	196	925	1	ENST00000301067.7:c.7411C>T	p.Arg2471Ter	p.R2471*	ENST00000301067	NM_003482.3	2471	Cga/Tga	31/54	1	2	FACETS	0.87	0.805	0.937	0.87	0.805	0.937	CLONAL	1	TRUE	1	0.460644921478005	2		926	978	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541970	187541970	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs189271562	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	96	409	0	ENST00000441802.2:c.5770G>A	p.Gly1924Arg	p.G1924R	ENST00000441802	NM_005245.3	1924	Ggg/Agg	10/27	1	2	FACETS	0.898	0.804	0.997	0.898	0.804	0.997	CLONAL	1	TRUE	1	0.460644921478005	2		409	464	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207627	2207627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	237	915	0	ENST00000398665.3:c.911C>T	p.Ser304Leu	p.S304L	ENST00000398665	NM_032482.2	304	tCg/tTg	11/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.460644921478005	2		915	1002	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434440	110434440	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754818980	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	105	964	2	ENST00000375856.3:c.3961G>A	p.Ala1321Thr	p.A1321T	ENST00000375856	NM_003749.2	1321	Gcc/Acc	1/2	0.221211587506343	0	FACETS	0.312	0.28	0.347			1	INDETERMINATE	1	TRUE	0	0.460644921478005	0		966	787	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500304	99500304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45512296	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	93	743	0	ENST00000268035.6:c.3737G>A	p.Arg1246His	p.R1246H	ENST00000268035	NM_000875.3	1246	cGc/cAc	21/21	1	2	FACETS	0.554	0.492	0.62	0.554	0.492	0.62	SUBCLONAL	1	TRUE	1	0.460644921478005	2		743	729	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127598	2127598	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	169	682	0	ENST00000219476.3:c.2838-1G>T		p.X946_splice	ENST00000219476	NM_000548.3	946			1	2	FACETS	0.998	0.92	1	0.998	0.92	1	CLONAL	1	TRUE	1	0.460644921478005	2		682	735	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435239	49435239	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772506992	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	193	883	4	ENST00000301067.7:c.6314G>A	p.Arg2105His	p.R2105H	ENST00000301067	NM_003482.3	2105	cGc/cAc	31/54	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.460644921478005	2		887	836	SUCCESS
APC	324	MSKCC	GRCh37	5	112102098	112102098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767741687	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	33	182	0	ENST00000257430.4:c.211C>T	p.Arg71Cys	p.R71C	ENST00000257430	NM_000038.5	71	Cgt/Tgt	3/16	1	2	FACETS	0.868	0.716	1	0.868	0.716	1	CLONAL	1	TRUE	1	0.460644921478005	2		182	165	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2199922	2199922	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	241	934	2	ENST00000398665.3:c.691C>T	p.Arg231Ter	p.R231*	ENST00000398665	NM_032482.2	231	Cga/Tga	8/28	1	2	FACETS	0.959	0.895	1	0.959	0.895	1	CLONAL	1	TRUE	1	0.460644921478005	2		936	1091	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376700	118376700	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375852658	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	44	486	0	ENST00000534358.1:c.10093G>A	p.Val3365Ile	p.V3365I	ENST00000534358	NM_005933.3	3365	Gtc/Atc	27/36	1	2	FACETS	0.394	0.33	0.464	0.394	0.33	0.464	SUBCLONAL	1	TRUE	1	0.460644921478005	2		486	485	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197365	94197365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781646	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	116	452	0	ENST00000323929.3:c.1139G>A	p.Arg380His	p.R380H	ENST00000323929	NM_005591.3	380	cGc/cAc	11/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.460644921478005	2		452	454	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805543	1805543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886043604	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	166	708	0	ENST00000260795.2:c.1055C>T	p.Ala352Val	p.A352V	ENST00000260795		352	gCg/gTg	7/17	1	2	FACETS	0.853	0.784	0.925	0.853	0.784	0.925	CLONAL	1	TRUE	1	0.460644921478005	2		708	845	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272239	142272239	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	42	265	0	ENST00000350721.4:c.2635G>A	p.Ala879Thr	p.A879T	ENST00000350721	NM_001184.3	879	Gcc/Acc	13/47	1	2	FACETS	0.633	0.531	0.745	0.633	0.531	0.745	SUBCLONAL	1	TRUE	1	0.460644921478005	2		265	288	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234211	39234211	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	106	439	1	ENST00000402219.2:c.2634G>A	p.Met878Ile	p.M878I	ENST00000402219	NM_005633.3	878	atG/atA	16/23	0.434046166685621	2	FACETS	0.99	0.892	1	0.495	0.446	0.546	CLONAL	1	TRUE	0	0.460644921478005	2		440	465	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354058	15354058	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	77	645	0	ENST00000263377.2:c.2822del	p.Pro941LeufsTer8	p.P941Lfs*8	ENST00000263377	NM_058243.2	941	cCt/ct	14/20	1	2	FACETS	0.46	0.403	0.521	0.46	0.403	0.521	SUBCLONAL	1	TRUE	1	0.460644921478005	2		645	727	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144045	11144045	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145476154	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	219	757	0	ENST00000358026.2:c.3626G>A	p.Ser1209Asn	p.S1209N	ENST00000358026	NM_001128849.1	1209	aGc/aAc	26/36	1	2	FACETS	0.927	0.862	0.994	0.927	0.862	0.994	CLONAL	1	TRUE	1	0.460644921478005	2		757	1026	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781227	9781227	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	106	868	0	ENST00000377346.4:c.1732A>C	p.Ser578Arg	p.S578R	ENST00000377346	NM_005026.3	578	Agc/Cgc	14/24	0.221047364575162	1	FACETS	0.409	0.366	0.454	0.409	0.366	0.454	INDETERMINATE	1	TRUE	0	0.460644921478005	1		868	867	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256259	16256260	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	79	463	0	ENST00000375759.3:c.3526_3527del	p.Arg1177Ter	p.R1177*	ENST00000375759	NM_015001.2	1175	cAG/c	11/15	0.221047364575162	1	FACETS	0.544	0.48	0.613	0.544	0.48	0.613	INDETERMINATE	1	TRUE	0	0.460644921478005	1		463	485	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115260816	115260819	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	131	475	0	ENST00000438362.2:c.2506_2509del	p.Lys836SerfsTer17	p.K836Sfs*17	ENST00000438362	NM_001242891.1	836	AAGAtc/tc	20/20	0.221047364575162	1	FACETS	0.869	0.793	0.947	0.869	0.793	0.947	INDETERMINATE	1	TRUE	0	0.460644921478005	1		475	504	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015447	176015447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1222131072	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	98	259	1	ENST00000367669.3:c.1291C>T	p.Arg431Trp	p.R431W	ENST00000367669	NM_022457.5	431	Cgg/Tgg	12/20	0.21754943772888	3	FACETS	1	0.913	1	0.671	0.608	0.735	INDETERMINATE	2	TRUE	0	0.460644921478005	3		260	260	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572224	64572224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	205	680	0	ENST00000312049.6:c.1415G>A	p.Gly472Asp	p.G472D	ENST00000312049	NM_130799.2	472	gGc/gAc	10/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.460644921478005	2		680	833	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347539	118347539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555037616	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	84	363	0	ENST00000534358.1:c.3176C>T	p.Ser1059Leu	p.S1059L	ENST00000534358	NM_005933.3	1059	tCa/tTa	4/36	1	2	FACETS	0.796	0.706	0.892	0.796	0.706	0.892	SUBCLONAL	1	TRUE	1	0.460644921478005	2		363	458	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133038	30133038	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	46	391	0	ENST00000331968.5:c.563G>A	p.Cys188Tyr	p.C188Y	ENST00000331968	NM_002742.2	188	tGt/tAt	4/18	1	2	FACETS	0.447	0.376	0.524	0.447	0.376	0.524	SUBCLONAL	1	TRUE	1	0.460644921478005	2		391	447	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042661	42042663	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	97	432	0	ENST00000219905.7:c.6856_6858del	p.Glu2286del	p.E2286del	ENST00000219905	NM_001164273.1	2286	GAG/-	17/24	0.221047364575162	1	FACETS	0.75	0.673	0.832	0.75	0.673	0.832	INDETERMINATE	1	TRUE	0	0.460644921478005	1		432	432	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396164	396164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753904293	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	141	558	0	ENST00000262320.3:c.862G>A	p.Glu288Lys	p.E288K	ENST00000262320	NM_003502.3	288	Gaa/Aaa	2/11	1	2	FACETS	0.885	0.808	0.965	0.885	0.808	0.965	CLONAL	1	TRUE	1	0.460644921478005	2		558	692	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619207	23619207	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	123	447	0	ENST00000261584.4:c.3328C>A	p.Leu1110Ile	p.L1110I	ENST00000261584	NM_024675.3	1110	Ctt/Att	12/13	1	2	FACETS	0.849	0.77	0.932	0.849	0.77	0.932	CLONAL	1	TRUE	1	0.460644921478005	2		447	629	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56870577	56870577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	89	327	0	ENST00000308159.5:c.1847C>T	p.Ala616Val	p.A616V	ENST00000308159	NM_014669.4	616	gCa/gTa	17/22	1	2	FACETS	0.798	0.711	0.891	0.798	0.711	0.891	SUBCLONAL	1	TRUE	1	0.460644921478005	2		327	484	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829704	72829704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	174	652	1	ENST00000268489.5:c.6877G>A	p.Ala2293Thr	p.A2293T	ENST00000268489	NM_006885.3	2293	Gcc/Acc	9/10	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.460644921478005	2		653	751	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349945	89349945	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757870881	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	216	848	1	ENST00000301030.4:c.3005G>A	p.Arg1002Gln	p.R1002Q	ENST00000301030	NM_001256183.1	1002	cGg/cAg	9/13	1	2	FACETS	0.889	0.826	0.954	0.889	0.826	0.954	CLONAL	1	TRUE	1	0.460644921478005	2		849	1055	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276605	15276605	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	194	780	0	ENST00000263388.2:c.5660T>C	p.Val1887Ala	p.V1887A	ENST00000263388	NM_000435.2	1887	gTc/gCc	30/33	1	2	FACETS	0.919	0.85	0.989	0.919	0.85	0.989	CLONAL	1	TRUE	1	0.460644921478005	2		780	917	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965995	18965995	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	190	829	0	ENST00000262803.5:c.1491del	p.Lys498ArgfsTer3	p.K498Rfs*3	ENST00000262803	NM_002911.3	496	acG/ac	11/24	1	2	FACETS	0.815	0.753	0.88	0.815	0.753	0.88	CLONAL	1	TRUE	1	0.460644921478005	2		829	1012	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794362	242794362	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs979390849	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	227	1107	0	ENST00000334409.5:c.580C>T	p.Arg194Trp	p.R194W	ENST00000334409	NM_005018.2	194	Cgg/Tgg	3/5	1	2	FACETS	0.868	0.808	0.93	0.868	0.808	0.93	CLONAL	1	TRUE	1	0.460644921478005	2		1107	1136	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306754	41306754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	132	553	0	ENST00000373198.4:c.905C>T	p.Ala302Val	p.A302V	ENST00000373198	NM_133170.3	302	gCc/gTc	7/32	NA	2	FACETS	0.963	0.878	1			1	INDETERMINATE	1	TRUE	NA	0.460644921478005	2		553	595	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573248	41573248	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	182	960	1	ENST00000263253.7:c.5533C>T	p.Gln1845Ter	p.Q1845*	ENST00000263253	NM_001429.3	1845	Cag/Tag	31/31	1	2	FACETS	0.744	0.686	0.805	0.744	0.686	0.805	SUBCLONAL	1	TRUE	1	0.460644921478005	2		961	1062	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098594	47098594	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	148	579	0	ENST00000409792.3:c.6680C>A	p.Pro2227Gln	p.P2227Q	ENST00000409792	NM_014159.6	2227	cCa/cAa	15/21	1	2	FACETS	0.874	0.8	0.952	0.874	0.8	0.952	CLONAL	1	TRUE	1	0.460644921478005	2		579	735	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924808	49924808	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs780724186	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	231	1077	2	ENST00000296474.3:c.4135C>T	p.Gln1379Ter	p.Q1379*	ENST00000296474	NM_002447.2	1379	Cag/Tag	20/20	1	2	FACETS	0.911	0.849	0.975	0.911	0.849	0.975	CLONAL	1	TRUE	1	0.460644921478005	2		1079	1101	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968082	55968082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	83	321	0	ENST00000263923.4:c.2248G>A	p.Ala750Thr	p.A750T	ENST00000263923	NM_002253.2	750	Gca/Aca	15/30	1	2	FACETS	0.977	0.868	1	0.977	0.868	1	CLONAL	1	TRUE	1	0.460644921478005	2		321	369	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294414	1294414	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779999492	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	195	924	3	ENST00000310581.5:c.587G>A	p.Arg196His	p.R196H	ENST00000310581	NM_198253.2	196	cGt/cAt	2/16	1	2	FACETS	0.906	0.839	0.976	0.906	0.839	0.976	CLONAL	1	TRUE	1	0.460644921478005	2		927	934	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910584	29910584	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	354	1501	0	ENST00000376809.5:c.124G>T	p.Gly42Trp	p.G42W	ENST00000376809	NM_002116.7	42	Ggg/Tgg	2/8	0.221047364575162	1	FACETS	0.806	0.762	0.851	0.806	0.762	0.851	INDETERMINATE	1	TRUE	0	0.460644921478005	1		1501	1468	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553183	106553183	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs548489075	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	161	648	3	ENST00000369096.4:c.1148C>T	p.Thr383Met	p.T383M	ENST00000369096	NM_001198.3	383	aCg/aTg	5/7	1	2	FACETS	0.914	0.839	0.991	0.914	0.839	0.991	CLONAL	1	TRUE	1	0.460644921478005	2		651	765	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879075	151879075	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372410972	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	121	434	0	ENST00000262189.6:c.5870C>T	p.Thr1957Met	p.T1957M	ENST00000262189	NM_170606.2	1957	aCg/aTg	36/59	0.424771187736285	3	FACETS	0.882	0.797	0.971	0.441	0.398	0.486	CLONAL	1	TRUE	1	0.460644921478005	3		434	733	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636728	8636729	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	61	271	0	ENST00000356435.5:c.180dup	p.Gly61ArgfsTer10	p.G61Rfs*10	ENST00000356435		60	-/A	2/35	1	2	FACETS	0.798	0.692	0.911	0.798	0.692	0.911	CLONAL	1	TRUE	1	0.460644921478005	2		271	332	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399918	139399918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1346928665	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	256	1160	0	ENST00000277541.6:c.4430G>A	p.Gly1477Asp	p.G1477D	ENST00000277541	NM_017617.3	1477	gGt/gAt	25/34	1	2	FACETS	0.894	0.836	0.954	0.894	0.836	0.954	CLONAL	1	TRUE	1	0.460644921478005	2		1160	1243	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114004	73114004	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	23	63	0	ENST00000356692.5:c.640G>A	p.Asp214Asn	p.D214N	ENST00000356692		214	Gac/Aac	8/9	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.460644921478005	2		63	90	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055886	180055886	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	86	708	0	ENST00000261937.6:c.1099C>T	p.Gln367Ter	p.Q367*	ENST00000261937	NM_182925.4	367	Cag/Tag	8/30	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.22	2		708	749	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350110	89350110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	112	941	0	ENST00000301030.4:c.2840C>T	p.Ala947Val	p.A947V	ENST00000301030	NM_001256183.1	947	gCc/gTc	9/13	1	2	FACETS	0.867	0.778	0.962	0.867	0.778	0.962	CLONAL	1	TRUE	1	0.22	2		941	1174	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948788	71948788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1259635458	NA	P-0012913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	129	1299	0	ENST00000298229.2:c.3500G>A	p.Ser1167Asn	p.S1167N	ENST00000298229	NM_001567.3	1167	aGc/aAc	26/28	1	2	FACETS	0.928	0.839	1	0.928	0.839	1	CLONAL	1	TRUE	1	0.22	2		1299	1264	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440037	220440037	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	143	1198	0	ENST00000243786.2:c.890T>A	p.Leu297Gln	p.L297Q	ENST00000243786	NM_002191.3	297	cTg/cAg	2/2	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.22	2		1198	1245	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368334	225368476	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAGGTGCACTCTATTTCATCTAAAACACACCTTACCTTTAACTTAGATATCATGTTTTTTTCAGAGTCATCAGAAACACTTTTATTTGTGAGAAGTCTCCTTGCCAAGTGTTGTTTATAATAACGTTCAAATACATCTTTTTC	TAGGTGCACTCTATTTCATCTAAAACACACCTTACCTTTAACTTAGATATCATGTTTTTTTCAGAGTCATCAGAAACACTTTTATTTGTGAGAAGTCTCCTTGCCAAGTGTTGTTTATAATAACGTTCAAATACATCTTTTTC	-	novel	NA	P-0012913-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	15	173	0	ENST00000264414.4:c.1270_1377+35del		p.X424_splice	ENST00000264414	NM_003590.4	424		9/16	1	2	FACETS	0.498	0.364	0.659	0.498	0.364	0.659	SUBCLONAL	1	TRUE	1	0.22	2		173	274	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0014094-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	16	457	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		457	828	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0014769-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	112	866	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.245333406495937	1	FACETS	0.95	0.854	1	0.95	0.854	1	CLONAL	1	TRUE	0	0.245333406495937	1		867	843	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933593	39933594	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0014769-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	67	663	0	ENST00000378444.4:c.1005dup	p.Ser336LeufsTer45	p.S336Lfs*45	ENST00000378444	NM_001123385.1	335	-/C	4/15	0.245333406495937	1	FACETS	0.833	0.725	0.951	0.833	0.725	0.951	CLONAL	1	TRUE	0	0.245333406495937	1		663	575	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	frameshift_variant	Frame_Shift_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	-	novel	NA	P-0014769-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	53	472	0	ENST00000275493.2:c.2239_2248del	p.Leu747GlnfsTer16	p.L747Qfs*16	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/ca	19/28	0.196539787477417				0.685	0.935				CLONAL	1	TRUE	1	0.245333406495937	3		472	603	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015881-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	205	375	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.754175884628579	2		375	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0015881-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	526	367	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.749680978494242	2	FACETS	0.992	0.966	1	0.992	0.966	1	CLONAL	2	TRUE	0	0.754175884628579	2		368	703	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800928	120800928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1337094477	NA	P-0015881-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	519	1112	0	ENST00000257552.2:c.320G>A	p.Arg107Gln	p.R107Q	ENST00000257552	NM_002442.3	107	cGa/cAa	6/15	0.754175884628579	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.754175884628579	1		1112	719	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220448	133220448	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015881-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	89	782	0	ENST00000320574.5:c.4265A>G	p.Asp1422Gly	p.D1422G	ENST00000320574	NM_006231.2	1422	gAc/gGc	33/49	0.754175884628579	1	FACETS	0.292	0.26	0.327	0.292	0.26	0.327	SUBCLONAL	1	TRUE	0	0.754175884628579	1		782	503	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95556921	95556921	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015881-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	165	759	0	ENST00000393063.1:c.5683C>T	p.Arg1895Ter	p.R1895*	ENST00000393063	NM_030621.3	1895	Cga/Tga	28/28	0.304342407602811	1	FACETS	0.455	0.42	0.492	0.455	0.42	0.492	INDETERMINATE	1	TRUE	0	0.754175884628579	1		759	599	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562791	29562791	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1131691075	NA	P-0015881-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	294	463	0	ENST00000356175.3:c.3870+1G>A		p.X1290_splice	ENST00000356175	NM_000267.3	1290			0.749680978494242	2	FACETS	0.982	0.946	1	0.982	0.946	1	CLONAL	2	TRUE	0	0.754175884628579	2		463	397	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881009	37881009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1419499014	NA	P-0015881-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	668	1259	1	ENST00000269571.5:c.2338C>T	p.Pro780Ser	p.P780S	ENST00000269571		780	Cca/Tca	20/27	0.749680978494242	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.754175884628579	2		1260	867	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400679	56400679	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015881-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	210	550	0	ENST00000348428.3:c.1273A>G	p.Met425Val	p.M425V	ENST00000348428	NM_006785.3	425	Atg/Gtg	11/17	0.280460275043281	1	FACETS	0.769	0.723	0.815	0.769	0.723	0.815	INDETERMINATE	1	TRUE	0	0.754175884628579	1		550	451	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221981	1221981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015881-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	468	1103	1	ENST00000326873.7:c.896C>T	p.Ser299Phe	p.S299F	ENST00000326873	NM_000455.4	299	tCc/tTc	7/10	0.224349616769391	2	FACETS	1	0.995	1	0.628	0.603	0.653	INDETERMINATE	1	TRUE	0	0.754175884628579	2		1104	988	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906474	50906474	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1064794926	NA	P-0015881-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	281	1286	0	ENST00000440232.2:c.1135C>T	p.Gln379Ter	p.Q379*	ENST00000440232	NM_002691.3	379	Cag/Tag	9/27	0.224349616769391	2	FACETS	0.725	0.682	0.769	0.362	0.341	0.385	INDETERMINATE	1	TRUE	0	0.754175884628579	2		1286	1028	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966462	25966462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015881-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	323	1042	0	ENST00000435504.4:c.2744C>T	p.Pro915Leu	p.P915L	ENST00000435504		915	cCa/cTa	13/13	1	2	FACETS	0.918	0.869	0.968	0.918	0.869	0.968	CLONAL	1	TRUE	1	0.754175884628579	2		1042	933	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525024	9525024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015881-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	267	689	1	ENST00000353224.5:c.1861G>A	p.Gly621Arg	p.G621R	ENST00000353224	NM_177990.2	621	Ggg/Agg	8/10	0.293381400859482	5	FACETS	0.97	0.913	1	0.647	0.609	0.685	INDETERMINATE	2	TRUE	2	0.754175884628579	5		690	778	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561234	9561234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015881-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	288	602	0	ENST00000353224.5:c.548C>T	p.Ser183Phe	p.S183F	ENST00000353224	NM_177990.2	183	tCt/tTt	4/10	0.293381400859482	5	FACETS	0.974	0.919	1	0.649	0.612	0.686	INDETERMINATE	2	TRUE	2	0.754175884628579	5		602	836	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624897	9624897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015881-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	440	799	0	ENST00000353224.5:c.80C>T	p.Pro27Leu	p.P27L	ENST00000353224	NM_177990.2	27	cCa/cTa	3/10	0.293381400859482	5	FACETS	0.847	0.811	0.883	0.847	0.811	0.883	INDETERMINATE	3	TRUE	2	0.754175884628579	5		799	979	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62320915	62320915	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015881-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1357	751	1657	1	ENST00000360203.5:c.1939C>T	p.Pro647Ser	p.P647S	ENST00000360203	NM_001283009.1	647	Ccg/Tcg	23/35	0.293381400859482	5	FACETS	1	0.971	1	0.671	0.648	0.695	INDETERMINATE	2	TRUE	2	0.754175884628579	5		1658	2108	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656786	45656786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015881-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	341	866	0	ENST00000407780.3:c.370G>A	p.Glu124Lys	p.E124K	ENST00000407780	NM_001283052.1	124	Gag/Aag	3/7	0.405989642759059	3	FACETS	1	0.994	1	0.68	0.645	0.715	INDETERMINATE	1	TRUE	1	0.754175884628579	3		866	916	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546089	41546089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015881-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	566	699	2	ENST00000263253.7:c.2704C>T	p.Pro902Ser	p.P902S	ENST00000263253	NM_001429.3	902	Cct/Tct	14/31	0.634559930357634	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.754175884628579	4		701	1245	SUCCESS
APC	324	MSKCC	GRCh37	5	112128185	112128185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779805	NA	P-0015881-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	299	862	1	ENST00000257430.4:c.688C>T	p.Arg230Cys	p.R230C	ENST00000257430	NM_000038.5	230	Cgt/Tgt	7/16	1	2	FACETS	0.992	0.939	1	0.992	0.939	1	CLONAL	1	TRUE	1	0.754175884628579	2		863	799	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953835	131953835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015881-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	241	818	0	ENST00000265335.6:c.3238G>A	p.Gly1080Ser	p.G1080S	ENST00000265335		1080	Ggt/Agt	21/25	1	2	FACETS	0.986	0.927	1	0.986	0.927	1	CLONAL	1	TRUE	1	0.754175884628579	2		818	648	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974312	93974312	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015881-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	263	673	0	ENST00000369303.4:c.1742G>A	p.Arg581Lys	p.R581K	ENST00000369303	NM_004440.3	581	aGg/aAg	8/17	0.199134758876174	4	FACETS	0.934	0.881	0.987	0.934	0.881	0.987	INDETERMINATE	2	TRUE	2	0.754175884628579	4		673	655	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124437	94124437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015881-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	207	630	0	ENST00000369303.4:c.146C>T	p.Ser49Phe	p.S49F	ENST00000369303	NM_004440.3	49	tCc/tTc	2/17	0.199134758876174	4	FACETS	0.846	0.791	0.902	0.846	0.791	0.902	INDETERMINATE	2	TRUE	2	0.754175884628579	4		630	569	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622184	117622188	+	stop_gained	Nonsense_Mutation	ONP	GACTT	GACTT	CACTA	novel	NA	P-0015881-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	264	544	0	ENST00000368508.3:c.6682_6686delinsTAGTG	p.Lys2228_Ser2229delinsTer	p.K2228_S2229delins*	ENST00000368508	NM_002944.2	2228	AAGTCc/TAGTGc	42/43	0.199134758876174	4	FACETS	0.877	0.827	0.928	0.877	0.827	0.928	INDETERMINATE	2	TRUE	2	0.754175884628579	4		544	700	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265590	152265590	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1462204859	NA	P-0015881-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	338	645	1	ENST00000206249.3:c.1043A>G	p.Asn348Ser	p.N348S	ENST00000206249	NM_000125.3	348	aAc/aGc	4/8	0.199134758876174	4	FACETS	1	0.961	1	1	0.961	1	INDETERMINATE	2	TRUE	2	0.754175884628579	4		646	777	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528477	157528477	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015881-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	333	703	0	ENST00000346085.5:c.6202C>T	p.Pro2068Ser	p.P2068S	ENST00000346085	NM_020732.3	2068	Cca/Tca	20/20	0.199134758876174	4	FACETS	0.954	0.906	1	0.954	0.906	1	INDETERMINATE	2	TRUE	2	0.754175884628579	4		703	812	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485307	8485307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015881-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	357	790	0	ENST00000356435.5:c.3073C>T	p.His1025Tyr	p.H1025Y	ENST00000356435		1025	Cat/Tat	18/35	0.273389307902154	3	FACETS	0.889	0.849	0.93	0.889	0.849	0.93	INDETERMINATE	2	TRUE	1	0.754175884628579	3		790	733	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248125	98248125	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0015881-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	216	726	0	ENST00000331920.6:c.426T>A	p.Tyr142Ter	p.Y142*	ENST00000331920	NM_000264.3	142	taT/taA	3/24	0.273389307902154	3	FACETS	1	0.981	1	0.566	0.528	0.604	INDETERMINATE	1	TRUE	1	0.754175884628579	3		726	697	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317520	1317520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015881-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	439	1116	0	ENST00000400841.2:c.545C>T	p.Ser182Phe	p.S182F	ENST00000400841		182	tCt/tTt	5/6	0.509236619995609	2	FACETS	0.931	0.889	0.974			1	CLONAL	1	TRUE	NA	0.754175884628579	2		1116	1250	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907743	76907743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015881-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	344	380	1	ENST00000373344.5:c.4418C>T	p.Pro1473Leu	p.P1473L	ENST00000373344	NM_000489.3	1473	cCt/cTt	15/35	0.509236619995609	2	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.754175884628579	2		381	447	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272308	38272308	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs869320694	NA	P-0015914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	57	595	0	ENST00000425967.3:c.2059A>G	p.Lys687Glu	p.K687E	ENST00000425967	NM_001174067.1	687	Aag/Gag	15/19	1	2	FACETS	0.233	0.2	0.27	0.233	0.2	0.27	SUBCLONAL	1	TRUE	1	0.832668681344451	2		595	587	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075398	8075398	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	16	227	0	ENST00000377482.5:c.172T>C	p.Ser58Pro	p.S58P	ENST00000377482	NM_018948.3	58	Tct/Cct	3/4	1	2	FACETS	0.164	0.121	0.215	0.164	0.121	0.215	SUBCLONAL	1	TRUE	1	0.832668681344451	2		227	235	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858974	57858974	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1039477087	NA	P-0015914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	152	606	1	ENST00000228682.2:c.470A>G	p.His157Arg	p.H157R	ENST00000228682	NM_005269.2	157	cAt/cGt	5/12	1	2	FACETS	0.522	0.479	0.568	0.522	0.479	0.568	SUBCLONAL	1	TRUE	1	0.832668681344451	2		607	699	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14021962	14021962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	118	552	2	ENST00000311895.7:c.662C>T	p.Thr221Ile	p.T221I	ENST00000311895	NM_005236.2	221	aCc/aTc	4/11	1	2	FACETS	0.712	0.648	0.778	0.712	0.648	0.778	SUBCLONAL	1	TRUE	1	0.832668681344451	2		554	398	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794641	42794641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	49	581	0	ENST00000575354.2:c.1721C>T	p.Pro574Leu	p.P574L	ENST00000575354	NM_015125.3	574	cCa/cTa	10/20	1	2	FACETS	0.185	0.156	0.217	0.185	0.156	0.217	SUBCLONAL	1	TRUE	1	0.832668681344451	2		581	637	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125811	47125811	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	94	293	0	ENST00000409792.3:c.5459T>C	p.Val1820Ala	p.V1820A	ENST00000409792	NM_014159.6	1820	gTa/gCa	12/21	1	2	FACETS	0.763	0.687	0.841	0.763	0.687	0.841	SUBCLONAL	1	TRUE	1	0.832668681344451	2		293	296	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557833	187557833	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	117	460	0	ENST00000441802.2:c.3878A>G	p.Asp1293Gly	p.D1293G	ENST00000441802	NM_005245.3	1293	gAc/gGc	5/27	1	2	FACETS	0.589	0.534	0.647	0.589	0.534	0.647	SUBCLONAL	1	TRUE	1	0.832668681344451	2		460	477	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001182	150001182	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	109	542	0	ENST00000253339.5:c.2422T>C	p.Tyr808His	p.Y808H	ENST00000253339		808	Tac/Cac	4/7	1	2	FACETS	0.721	0.654	0.791	0.721	0.654	0.791	SUBCLONAL	1	TRUE	1	0.832668681344451	2		542	363	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750686	128750686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	41	543	1	ENST00000377970.2:c.223C>T	p.Pro75Ser	p.P75S	ENST00000377970	NM_002467.4	75	Ccc/Tcc	2/3	1	2	FACETS	0.183	0.152	0.217	0.183	0.152	0.217	SUBCLONAL	1	TRUE	1	0.832668681344451	2		544	539	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249830	110249830	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1197622765	NA	P-0015914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	196	610	0	ENST00000374672.4:c.845T>C	p.Val282Ala	p.V282A	ENST00000374672	NM_004235.4	282	gTc/gCc	3/5	1	2	FACETS	0.719	0.668	0.77	0.719	0.668	0.77	SUBCLONAL	1	TRUE	1	0.832668681344451	2		610	655	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410435	139410435	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	145	562	0	ENST00000277541.6:c.1667A>G	p.Glu556Gly	p.E556G	ENST00000277541	NM_017617.3	556	gAa/gGa	10/34	1	2	FACETS	0.567	0.519	0.617	0.567	0.519	0.617	SUBCLONAL	1	TRUE	1	0.832668681344451	2		562	614	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0015985-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	91	169	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.447934248208752	3	FACETS	1	0.957	1	0.561	0.505	0.62	INDETERMINATE	1	TRUE	1	0.764732744401937	3		169	293	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419926	41419926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015985-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	139	860	1	ENST00000373198.4:c.395G>A	p.Gly132Glu	p.G132E	ENST00000373198	NM_133170.3	132	gGg/gAg	3/32	NA	2	FACETS	0.49	0.446	0.536			1	INDETERMINATE	1	TRUE	NA	0.764732744401937	2		861	742	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628055	187628055	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015985-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	388	725	0	ENST00000441802.2:c.2927T>C	p.Val976Ala	p.V976A	ENST00000441802	NM_005245.3	976	gTg/gCg	2/27	0.764732744401937	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.764732744401937	2		725	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572931	7572932	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0015985-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	393	713	0	ENST00000269305.4:c.1177dup	p.Asp393GlyfsTer78	p.D393Gfs*78	ENST00000269305	NM_001126112.2	393	gac/gGac	11/11	0.764732744401937	3	FACETS	0.989	0.963	1	0.989	0.963	1	CLONAL	3	TRUE	0	0.764732744401937	3		713	479	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295100	91295100	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146096923	NA	P-0015985-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	96	305	0	ENST00000355112.3:c.883G>A	p.Asp295Asn	p.D295N	ENST00000355112	NM_000057.2	295	Gat/Aat	4/22	0.363517426498544	5	FACETS	0.934	0.834	1	0.311	0.278	0.347	INDETERMINATE	1	TRUE	2	0.764732744401937	5		305	577	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217918	2217918	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015985-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	148	979	1	ENST00000398665.3:c.2691+1G>A		p.X897_splice	ENST00000398665	NM_032482.2	897			0.523281986496614	4	FACETS	1	0.938	1	0.343	0.314	0.373	CLONAL	1	TRUE	1	0.764732744401937	4		980	664	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117737471	117737471	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015985-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	161	456	0	ENST00000368508.3:c.178G>A	p.Gly60Arg	p.G60R	ENST00000368508	NM_002944.2	60	Gga/Aga	3/43	0.363517426498544	5	FACETS	1	0.986	1	0.445	0.409	0.482	INDETERMINATE	1	TRUE	2	0.764732744401937	5		456	677	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778938	3778938	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1481703137	NA	P-0015985-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	123	879	0	ENST00000262367.5:c.6110G>A	p.Arg2037Lys	p.R2037K	ENST00000262367	NM_004380.2	2037	aGg/aAg	31/31	0.637162267279943	3	FACETS	1	0.956	1	0.54	0.492	0.589	CLONAL	1	TRUE	1	0.764732744401937	3		879	412	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347096	347096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015985-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	172	1055	0	ENST00000262320.3:c.1915G>A	p.Gly639Arg	p.G639R	ENST00000262320	NM_003502.3	639	Ggg/Agg	7/11	0.637162267279943	3	FACETS	1	0.931	1	0.504	0.466	0.543	CLONAL	1	TRUE	1	0.764732744401937	3		1055	617	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818360	43818360	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745606938	NA	P-0015985-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	155	883	1	ENST00000372470.3:c.1825C>T	p.Pro609Ser	p.P609S	ENST00000372470	NM_005373.2	609	Ccc/Tcc	12/12	0.764732744401937	3	FACETS	0.943	0.868	1	0.472	0.434	0.511	CLONAL	1	TRUE	1	0.764732744401937	3		884	594	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149220	119149220	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015985-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	126	582	0	ENST00000264033.4:c.1228G>A	p.Glu410Lys	p.E410K	ENST00000264033	NM_005188.3	410	Gaa/Aaa	9/16	0.689844437818116	4	FACETS	0.814	0.738	0.894	0.271	0.246	0.298	CLONAL	1	TRUE	1	0.764732744401937	4		582	714	SUCCESS
BLM	641	MSKCC	GRCh37	15	91341502	91341502	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs912777535	NA	P-0015985-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	165	430	0	ENST00000355112.3:c.3293G>A	p.Arg1098Lys	p.R1098K	ENST00000355112	NM_000057.2	1098	aGa/aAa	17/22	0.363517426498544	5	FACETS	1	0.986	1	0.447	0.411	0.484	INDETERMINATE	1	TRUE	2	0.764732744401937	5		430	691	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486199	99486199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015985-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	139	751	0	ENST00000268035.6:c.3505G>A	p.Gly1169Arg	p.G1169R	ENST00000268035	NM_000875.3	1169	Gga/Aga	19/21	0.363517426498544	5	FACETS	1	0.968	1	0.377	0.343	0.411	INDETERMINATE	1	TRUE	2	0.764732744401937	5		751	691	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641751	23641751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730881876	NA	P-0015985-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	112	446	0	ENST00000261584.4:c.1724G>A	p.Trp575Ter	p.W575*	ENST00000261584	NM_024675.3	575	tGg/tAg	5/13	0.637162267279943	3	FACETS	1	0.945	1	0.529	0.48	0.579	CLONAL	1	TRUE	1	0.764732744401937	3		446	383	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414838	56414838	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015985-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	162	746	1	ENST00000348428.3:c.2239G>A	p.Ala747Thr	p.A747T	ENST00000348428	NM_006785.3	747	Gca/Aca	17/17	0.62072372058476	5	FACETS	1	0.95	1	0.349	0.32	0.38	CLONAL	1	TRUE	2	0.764732744401937	5		747	868	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218633	36218633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1161161079	NA	P-0015985-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	166	1120	0	ENST00000222270.7:c.4337C>T	p.Pro1446Leu	p.P1446L	ENST00000222270	NM_014727.1	1446	cCc/cTc	17/37	0.743557418687372	4	FACETS	0.911	0.837	0.988	0.304	0.279	0.33	CLONAL	1	TRUE	1	0.764732744401937	4		1120	841	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856035	45856035	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1274611330	NA	P-0015985-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	115	961	0	ENST00000391945.4:c.1871C>T	p.Pro624Leu	p.P624L	ENST00000391945	NM_000400.3	624	cCc/cTc	20/23	0.722836314696988	4	FACETS	0.753	0.679	0.831			1	SUBCLONAL	1	TRUE	NA	0.764732744401937	4		961	705	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867557	45867557	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196791397	NA	P-0015985-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	219	1209	0	ENST00000391945.4:c.751C>T	p.Leu251Phe	p.L251F	ENST00000391945	NM_000400.3	251	Ctc/Ttc	9/23	0.722836314696988	4	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.764732744401937	4		1209	910	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151183	202151183	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015985-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	42	294	0	ENST00000358485.4:c.1483G>A	p.Gly495Ser	p.G495S	ENST00000358485	NM_001080125.1	495	Ggc/Agc	9/9	0.438569643042029	4	FACETS	1	0.877	1			1	INDETERMINATE	1	TRUE	NA	0.764732744401937	4		294	186	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727060	40727060	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0015985-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	75	601	0	ENST00000373198.4:c.3903+1G>A		p.X1301_splice	ENST00000373198	NM_133170.3	1301			0.617793695067616	4	FACETS	0.721	0.634	0.815	0.361	0.317	0.408	SUBCLONAL	1	TRUE	2	0.764732744401937	4		601	480	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41554505	41554505	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015985-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	142	570	0	ENST00000263253.7:c.3590+1G>A		p.X1197_splice	ENST00000263253	NM_001429.3	1197			0.764732744401937	3	FACETS	0.985	0.903	1	0.493	0.451	0.535	CLONAL	1	TRUE	1	0.764732744401937	3		570	521	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612005	189612005	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015985-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	114	574	0	ENST00000264731.3:c.1757G>A	p.Ser586Asn	p.S586N	ENST00000264731	NM_003722.4	586	aGt/aAt	14/14	NA	2	FACETS	1	0.942	1			1	INDETERMINATE	1	TRUE	NA	0.764732744401937	2		574	287	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500799	149500799	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs781051087	NA	P-0015985-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	31	761	1	ENST00000261799.4:c.2431G>T	p.Ala811Ser	p.A811S	ENST00000261799	NM_002609.3	811	Gcc/Tcc	17/23	1	2	FACETS	0.219	0.176	0.266	0.219	0.176	0.266	SUBCLONAL	1	TRUE	1	0.764732744401937	2		762	371	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287611	33287611	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015985-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	112	688	0	ENST00000374542.5:c.1486C>T	p.Pro496Ser	p.P496S	ENST00000374542	NM_001141970.1	496	Ccc/Tcc	6/8	0.363517426498544	5	FACETS	1	0.949	1	0.36	0.325	0.398	INDETERMINATE	1	TRUE	2	0.764732744401937	5		688	582	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151882702	151882702	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015985-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	113	456	0	ENST00000262189.6:c.5023G>A	p.Val1675Met	p.V1675M	ENST00000262189	NM_170606.2	1675	Gtg/Atg	34/59	0.464252488168768	4	FACETS	0.746	0.672	0.824			1	SUBCLONAL	1	TRUE	NA	0.764732744401937	4		456	699	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146103	38146103	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015985-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	219	816	0	ENST00000317025.8:c.3403C>T	p.Gln1135Ter	p.Q1135*	ENST00000317025	NM_023034.1	1135	Cag/Tag	19/24	0.617793695067616	4	FACETS	1	0.984	1	0.589	0.549	0.631	CLONAL	1	TRUE	2	0.764732744401937	4		816	858	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738971	145738971	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1466549456	NA	P-0015985-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	119	884	0	ENST00000428558.2:c.2184G>A	p.Trp728Ter	p.W728*	ENST00000428558	NM_004260.3	728	tgG/tgA	13/22	0.617793695067616	4	FACETS	0.884	0.8	0.973	0.442	0.4	0.487	CLONAL	1	TRUE	2	0.764732744401937	4		884	621	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797352	135797352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015985-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	72	376	0	ENST00000298552.3:c.517G>A	p.Ala173Thr	p.A173T	ENST00000298552	NM_001162426.1	173	Gcg/Acg	7/23	0.746323003088524	3	FACETS	0.75	0.66	0.846	0.375	0.33	0.423	SUBCLONAL	1	TRUE	1	0.764732744401937	3		376	347	SUCCESS
AR	367	MSKCC	GRCh37	X	66766520	66766520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015985-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	21	764	0	ENST00000374690.3:c.1532G>A	p.Arg511Lys	p.R511K	ENST00000374690	NM_000044.3	511	aGa/aAa	1/8	NA	2	FACETS	0.179	0.137	0.227			1	INDETERMINATE	1	TRUE	NA	0.764732744401937	2		764	307	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814192	76814202	+	frameshift_variant	Frame_Shift_Del	DEL	ACTCTGAATAT	ACTCTGAATAT	-	novel	NA	P-0015985-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	108	384	0	ENST00000373344.5:c.6442_6452del	p.Ile2148LeufsTer7	p.I2148Lfs*7	ENST00000373344	NM_000489.3	2148	ATATTCAGAGTt/t	29/35	0.764732744401937	1	FACETS	0.904	0.835	0.972	0.904	0.835	0.972	CLONAL	1	TRUE	0	0.764732744401937	1		384	193	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599320	55599320	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913506	NA	P-0016894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	501	95	0	ENST00000288135.5:c.2446G>C	p.Asp816His	p.D816H	ENST00000288135	NM_000222.2	816	Gac/Cac	17/21	1	2	FACETS	1	0.995	1	1	0.998	1	CLONAL	2	TRUE	1	0.613017956789471	2		95	721	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913517	NA	P-0016894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	411	105	0	ENST00000288135.5:c.1676T>A	p.Val559Asp	p.V559D	ENST00000288135	NM_000222.2	559	gTt/gAt	11/21	1	2	FACETS	0.943	0.907	0.979	1	0.997	1	CLONAL	2	TRUE	1	0.613017956789471	2		105	711	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0016894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	963	242	0	ENST00000269305.4:c.559+1G>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.557844032544384	1	FACETS	0.761	0.744	0.778	1	0.998	1	SUBCLONAL	2	TRUE	0	0.613017956789471	1		242	1432	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916829	48916829	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs983885759	NA	P-0016894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	292	61	1	ENST00000267163.4:c.359T>A	p.Leu120Gln	p.L120Q	ENST00000267163	NM_000321.2	120	cTa/cAa	3/27	0.613017956789471	1	FACETS	0.818	0.787	0.847	1	0.996	1	CLONAL	2	TRUE	0	0.613017956789471	1		62	404	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544649	65544649	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555340540	NA	P-0016894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	884	272	0	ENST00000358664.4:c.277G>C	p.Ala93Pro	p.A93P	ENST00000358664	NM_002382.4	93	Gct/Cct	4/5	0.579926470549555	1	FACETS	0.783	0.765	0.8	1	0.998	1	SUBCLONAL	2	TRUE	0	0.613017956789471	1		272	1278	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019537	42019537	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	635	175	0	ENST00000219905.7:c.3590del	p.Thr1197MetfsTer2	p.T1197Mfs*2	ENST00000219905	NM_001164273.1	1197	aCt/at	10/24	0.579926470549555	1	FACETS	0.851	0.831	0.871	1	0.998	1	CLONAL	2	TRUE	0	0.613017956789471	1		175	844	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692902	89692902	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016894-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	470	111	0	ENST00000371953.3:c.386G>T	p.Gly129Val	p.G129V	ENST00000371953	NM_000314.4	129	gGa/gTa	5/9	0.613017956789471	1	FACETS	0.877	0.854	0.9	1	0.998	1	CLONAL	2	TRUE	0	0.613017956789471	1		111	606	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176176092	176176092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	563	940	1	ENST00000367669.3:c.23G>A	p.Gly8Glu	p.G8E	ENST00000367669	NM_022457.5	8	gGg/gAg	1/20	1	2	FACETS	0.917	0.881	0.953	0.917	0.881	0.953	CLONAL	1	TRUE	1	0.841644262270054	2		941	1459	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988471	41988472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	276	538	0	ENST00000219905.7:c.1264dup	p.Ile422AsnfsTer11	p.I422Nfs*11	ENST00000219905	NM_001164273.1	421	-/A	3/24	1	2	FACETS	0.907	0.856	0.959	0.907	0.856	0.959	CLONAL	1	TRUE	1	0.841644262270054	2		538	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578470	7578471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0016930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	698	1412	0	ENST00000269305.4:c.459dup	p.Gly154ArgfsTer27	p.G154Rfs*27	ENST00000269305	NM_001126112.2	153	-/C	5/11	0.811467501336448	1	FACETS	0.946	0.922	0.97	0.946	0.922	0.97	CLONAL	1	TRUE	0	0.841644262270054	1		1412	1015	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143043329	143043329	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	217	415	0	ENST00000262992.4:c.2087T>C	p.Ile696Thr	p.I696T	ENST00000262992	NM_001101669.1	696	aTa/aCa	19/24	0.449801760087024	1	FACETS	0.698	0.658	0.737	0.698	0.658	0.737	INDETERMINATE	1	TRUE	0	0.841644262270054	1		415	428	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224273	98224273	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	220	314	0	ENST00000331920.6:c.2568G>T	p.Gln856His	p.Q856H	ENST00000331920	NM_000264.3	856	caG/caT	16/24	0.449801760087024	1	FACETS	0.799	0.757	0.84	0.799	0.757	0.84	INDETERMINATE	1	TRUE	0	0.841644262270054	1		314	379	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0018269-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	233	76	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.810351256549704	3	FACETS	0.894	0.846	0.942	0.894	0.846	0.942	CLONAL	2	TRUE	1	0.835676033226272	3		76	442	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097751	27097751	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018269-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	216	148	0	ENST00000324856.7:c.3344del	p.Pro1115GlnfsTer46	p.P1115Qfs*46	ENST00000324856	NM_006015.4	1114	Ccc/cc	12/20	1	2	FACETS	0.822	0.769	0.876	0.822	0.769	0.876	CLONAL	1	TRUE	1	0.835676033226272	2		148	629	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148516749	148516749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018269-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	153	100	0	ENST00000320356.2:c.938G>A	p.Arg313Gln	p.R313Q	ENST00000320356	NM_004456.4	313	cGg/cAg	9/20	0.774446043417211	3	FACETS	1	0.943	1	0.514	0.473	0.556	CLONAL	1	TRUE	1	0.835676033226272	3		100	505	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870985	12870986	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0018269-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	560	164	0	ENST00000228872.4:c.214_215dup	p.Lys73AlafsTer47	p.K73Afs*47	ENST00000228872	NM_004064.3	71	gag/gaGGg	1/3	0.799808333136999	3	FACETS	0.887	0.866	0.908	0.887	0.866	0.908	CLONAL	3	TRUE	0	0.835676033226272	3		164	714	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591925	48591925	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	51	451	0	ENST00000342988.3:c.1088G>T	p.Cys363Phe	p.C363F	ENST00000342988	NM_005359.5	363	tGt/tTt	9/12	0.835477773081513	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.835477773081513	1		451	68	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0018379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	307	639	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.77713282100347	2	FACETS	0.964	0.935	0.993	0.964	0.935	0.993	CLONAL	2	TRUE	0	0.835477773081513	2		639	381	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106696	2106696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	542	738	0	ENST00000219476.3:c.700G>A	p.Glu234Lys	p.E234K	ENST00000219476	NM_000548.3	234	Gag/Aag	8/42	0.835477773081513	3	FACETS	0.952	0.92	0.984			1	CLONAL	2	TRUE	NA	0.835477773081513	3		738	966	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821594	72821596	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs374416547	NA	P-0018379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	12	112	1	ENST00000268489.5:c.10579_10581del	p.Gly3527del	p.G3527del	ENST00000268489	NM_006885.3	3527	GGC/-	10/10	0.763361942426887	3	FACETS	0.173	0.121	0.236	0.086	0.06	0.118	SUBCLONAL	1	TRUE	1	0.835477773081513	3		113	236	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419049	419049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	48	816	0	ENST00000399788.2:c.3298G>A	p.Glu1100Lys	p.E1100K	ENST00000399788	NM_001042603.1	1100	Gaa/Aaa	22/28	0.835477773081513	3	FACETS	0.2	0.168	0.235			1	SUBCLONAL	1	TRUE	NA	0.835477773081513	3		816	815	SUCCESS
AR	367	MSKCC	GRCh37	X	66765261	66765261	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	391	287	1	ENST00000374690.3:c.273G>T	p.Gln91His	p.Q91H	ENST00000374690	NM_000044.3	91	caG/caT	1/8	0.835477773081513	2	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.835477773081513	2		288	444	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783181	9783181	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0018379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	113	496	0	ENST00000377346.4:c.2427-2A>G		p.X809_splice	ENST00000377346	NM_005026.3	809			0.763361942426887	3	FACETS	0.913	0.828	1	0.457	0.414	0.501	CLONAL	1	TRUE	1	0.835477773081513	3		496	420	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246395	46246395	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	14	499	0	ENST00000334344.6:c.4489C>G	p.Pro1497Ala	p.P1497A	ENST00000334344	NM_152641.2	1497	Cct/Gct	15/21	0.543640813652523	1	FACETS	0.3	0.222	0.39	0.3	0.222	0.39	SUBCLONAL	1	TRUE	0	0.835477773081513	1		499	65	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912555	32912555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	64	627	0	ENST00000380152.3:c.4063G>A	p.Asp1355Asn	p.D1355N	ENST00000380152		1355	Gac/Aac	11/27	0.199747762239067	2	FACETS	1	0.946	1	0.551	0.491	0.611	INDETERMINATE	1	TRUE	0	0.835477773081513	2		627	139	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90645522	90645522	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	142	72	0	ENST00000330062.3:c.101A>T	p.Gln34Leu	p.Q34L	ENST00000330062	NM_002168.2	34	cAg/cTg	1/11	0.649380656459816	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.835477773081513	3		72	232	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442747	99442747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	52	778	0	ENST00000268035.6:c.1144G>A	p.Glu382Lys	p.E382K	ENST00000268035	NM_000875.3	382	Gag/Aag	5/21	0.649380656459816	3	FACETS	0.949	0.821	1	0.474	0.41	0.542	CLONAL	1	TRUE	1	0.835477773081513	3		778	186	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599955	10599955	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	406	891	0	ENST00000171111.5:c.1621del	p.Thr541GlnfsTer7	p.T541Qfs*7	ENST00000171111	NM_203500.1	541	Aca/ca	5/6	0.825634826702975	2	FACETS	0.947	0.921	0.972	0.947	0.921	0.972	CLONAL	2	TRUE	0	0.835477773081513	2		891	513	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538294	9538294	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	20	575	0	ENST00000353224.5:c.1704C>A	p.Asp568Glu	p.D568E	ENST00000353224	NM_177990.2	568	gaC/gaA	7/10	NA	2	FACETS	0.577	0.451	0.716			1	INDETERMINATE	1	TRUE	NA	0.835477773081513	2		575	83	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026197	36026197	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1610	966	852	2	ENST00000358208.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000358208		267	Cgg/Tgg	7/12	0.766480684445613	5	FACETS	1	0.979	1	0.674	0.654	0.695	CLONAL	2	TRUE	2	0.835477773081513	5		854	2576	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574155	41574155	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	329	572	0	ENST00000263253.7:c.6440A>T	p.Gln2147Leu	p.Q2147L	ENST00000263253	NM_001429.3	2147	cAg/cTg	31/31	1	2	FACETS	0.944	0.915	0.972	1	0.997	1	CLONAL	2	TRUE	1	0.835477773081513	2		572	417	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176566	142176566	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	80	697	0	ENST00000350721.4:c.7535C>A	p.Pro2512Gln	p.P2512Q	ENST00000350721	NM_001184.3	2512	cCa/cAa	45/47	0.315122941555032	5	FACETS	0.999	0.896	1	0.666	0.597	0.737	INDETERMINATE	2	TRUE	2	0.835477773081513	5		697	216	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156189	106156189	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	24	503	2	ENST00000380013.4:c.1090G>T	p.Gly364Cys	p.G364C	ENST00000380013	NM_001127208.2	364	Ggt/Tgt	3/11	0.835477773081513	1	FACETS	0.904	0.771	1	0.904	0.771	1	CLONAL	1	TRUE	0	0.835477773081513	1		505	37	SUCCESS
APC	324	MSKCC	GRCh37	5	112137040	112137040	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs755437577	NA	P-0018379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	61	617	0	ENST00000257430.4:c.794G>C	p.Gly265Ala	p.G265A	ENST00000257430	NM_000038.5	265	gGa/gCa	8/16	0.835477773081513	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.835477773081513	2		617	66	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511131	148511131	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs761834990	NA	P-0018379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	31	402	0	ENST00000320356.2:c.1771C>G	p.Leu591Val	p.L591V	ENST00000320356	NM_004456.4	591	Ctt/Gtt	15/20	NA	2	FACETS	0.928	0.777	1			1	INDETERMINATE	1	TRUE	NA	0.835477773081513	2		402	80	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129953	69129953	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	38	284	0	ENST00000288368.4:c.4707G>T	p.Gln1569His	p.Q1569H	ENST00000288368	NM_024870.2	1569	caG/caT	38/40	0.835477773081513	3	FACETS	1	0.914	1	0.561	0.475	0.651	CLONAL	1	TRUE	1	0.835477773081513	3		284	115	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411263	63411263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768862604	NA	P-0018379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	154	412	2	ENST00000330258.3:c.1904G>A	p.Cys635Tyr	p.C635Y	ENST00000330258	NM_152424.3	635	tGt/tAt	2/2	0.835477773081513	2	FACETS	0.884	0.818	0.952			1	CLONAL	1	TRUE	NA	0.835477773081513	2		414	417	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435852	110435853	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCTGGCTGGGC	novel	NA	P-0018588-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1350	183	590	0	ENST00000375856.3:c.2538_2548dup	p.Ala850GlyfsTer20	p.A850Gfs*20	ENST00000375856	NM_003749.2	850	gcg/gGCCCAGCCAGGcg	1/2	0.545966869801282	5	FACETS	0.71	0.653	0.77			1	SUBCLONAL	1	TRUE	NA	0.678484934841778	5		590	1533	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646930	37646931	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0018588-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	365	658	0	ENST00000447079.4:c.2055_2056del	p.Pro686ArgfsTer13	p.P686Rfs*13	ENST00000447079	NM_015083.1	684	gaCTct/gact	3/14	1	2	FACETS	0.866	0.821	0.911	0.866	0.821	0.911	CLONAL	1	TRUE	1	0.678484934841778	2		658	1243	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676216	37676217	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0018588-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	529	561	0	ENST00000447079.4:c.2972_2973del	p.Ser991CysfsTer4	p.S991Cfs*4	ENST00000447079	NM_015083.1	991	TCt/t	11/14	0.545966869801282	5	FACETS	1	0.995	1			1	CLONAL	3	TRUE	NA	0.678484934841778	5		561	912	SUCCESS
AR	367	MSKCC	GRCh37	X	66943549	66943549	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519864	NA	P-0018588-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	655	251	0	ENST00000374690.3:c.2629T>C	p.Phe877Leu	p.F877L	ENST00000374690	NM_000044.3	877	Ttc/Ctc	8/8	0.678484934841778	4	FACETS	1	0.992	1			1	CLONAL	3	TRUE	NA	0.678484934841778	4		251	1021	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057712	27057712	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018986-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	145	699	0	ENST00000324856.7:c.1420C>T	p.Gln474Ter	p.Q474*	ENST00000324856	NM_006015.4	474	Caa/Taa	3/20	0.315360922941095	3	FACETS	1	0.947	1	0.528	0.481	0.577	CLONAL	1	TRUE	1	0.315360922941095	3		699	1009	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088681	27088682	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0018986-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	254	685	1	ENST00000324856.7:c.2296dup	p.Gln766ProfsTer51	p.Q766Pfs*51	ENST00000324856	NM_006015.4	764	tcc/tCcc	7/20	0.315360922941095	3	FACETS	0.92	0.861	0.98	0.92	0.861	0.98	CLONAL	2	TRUE	1	0.315360922941095	3		686	1014	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741585	17741585	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018986-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	27	321	0	ENST00000250003.3:c.256G>A	p.Gly86Arg	p.G86R	ENST00000250003	NM_002478.4	86	Ggg/Agg	1/3	0.315360922941095	3	FACETS	0.421	0.334	0.52	0.21	0.167	0.26	SUBCLONAL	1	TRUE	1	0.315360922941095	3		321	471	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359423	118359425	+	inframe_deletion	In_Frame_Del	DEL	GTC	GTC	-	novel	NA	P-0018986-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	74	393	0	ENST00000534358.1:c.4432_4434del	p.Arg1478del	p.R1478del	ENST00000534358	NM_005933.3	1476	tGTCgt/tgt	11/36	0.315360922941095	3	FACETS	0.894	0.783	1	0.447	0.391	0.507	CLONAL	1	TRUE	1	0.315360922941095	3		393	608	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489571	56489571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018986-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	212	459	0	ENST00000267101.3:c.2036G>A	p.Arg679Gln	p.R679Q	ENST00000267101	NM_001982.3	679	cGa/cAa	17/28	0.315360922941095	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	2	0.315360922941095	4		459	838	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819650	81819650	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018986-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	116	574	0	ENST00000359376.3:c.56A>C	p.Lys19Thr	p.K19T	ENST00000359376	NM_002661.3	19	aAg/aCg	2/33	0.315360922941095	3	FACETS	1	0.94	1	0.53	0.478	0.586	CLONAL	1	TRUE	1	0.315360922941095	3		574	803	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0018986-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	292	963	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.310054619972243	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.315360922941095	2		966	802	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621879	1621879	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018986-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	142	631	0	ENST00000344749.5:c.913T>A	p.Ser305Thr	p.S305T	ENST00000344749	NM_001136139.2	305	Tcc/Acc	11/19	0.315360922941095	3	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.315360922941095	3		631	825	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459891	149459891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143025739	NA	P-0018986-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	217	633	0	ENST00000286301.3:c.316C>T	p.Arg106Trp	p.R106W	ENST00000286301	NM_005211.3	106	Cgg/Tgg	4/22	0.315360922941095	4	FACETS	0.894	0.832	0.959	0.894	0.832	0.959	CLONAL	2	TRUE	2	0.315360922941095	4		633	1012	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150520	157150520	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765362265	NA	P-0018986-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	46	541	0	ENST00000346085.5:c.1702G>A	p.Gly568Arg	p.G568R	ENST00000346085	NM_020732.3	568	Ggg/Agg	2/20	0.315360922941095	3	FACETS	0.456	0.383	0.538	0.228	0.191	0.269	SUBCLONAL	1	TRUE	1	0.315360922941095	3		541	740	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405953	157405954	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1554294674	NA	P-0018986-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	177	44	0	ENST00000346085.5:c.2201dup	p.Ser736IlefsTer27	p.S736Ifs*27	ENST00000346085	NM_020732.3	732	ccg/ccGg	6/20	0.315360922941095	3	FACETS	0.763	0.703	0.824	0.763	0.703	0.824	SUBCLONAL	2	TRUE	1	0.315360922941095	3		44	852	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021826	69021826	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018986-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	110	558	0	ENST00000288368.4:c.3114A>C	p.Lys1038Asn	p.K1038N	ENST00000288368	NM_024870.2	1038	aaA/aaC	25/40	0.315360922941095	3	FACETS	0.986	0.886	1	0.493	0.443	0.547	CLONAL	1	TRUE	1	0.315360922941095	3		558	819	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801803	3801803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	51	578	0	ENST00000262367.5:c.3703C>T	p.His1235Tyr	p.H1235Y	ENST00000262367	NM_004380.2	1235	Cat/Tat	20/31	1	2	FACETS	0.891	0.758	1	0.891	0.758	1	CLONAL	1	TRUE	1	0.233978392464199	2		578	489	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988560	41988560	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0019560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	120	712	0	ENST00000219905.7:c.1352C>G	p.Ser451Ter	p.S451*	ENST00000219905	NM_001164273.1	451	tCa/tGa	3/24	0.116081127904644	4	FACETS	1	0.956	1	1	0.956	1	INDETERMINATE	2	TRUE	2	0.233978392464199	4		712	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	78	1089	2	ENST00000269305.4:c.383del	p.Pro128LeufsTer42	p.P128Lfs*42	ENST00000269305	NM_001126112.2	128	cCt/ct	5/11	0.275792937435608	1	FACETS	0.613	0.538	0.694	0.613	0.538	0.694	SUBCLONAL	1	TRUE	0	0.27	1		1091	815	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024682	11024682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	79	558	0	ENST00000327064.4:c.799C>T	p.Arg267Cys	p.R267C	ENST00000327064	NM_199141.1	267	Cgc/Tgc	6/16	0.3	3	FACETS	1	0.966	1	0.639	0.563	0.72	CLONAL	1	TRUE	1	0.27	3		558	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0021076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	48	901	1	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	1	2	FACETS	0.096	0.08	0.113	0.096	0.08	0.113	SUBCLONAL	1	TRUE	1	1.03	2		902	972	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291801	15291801	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021124-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	374	1069	0	ENST00000263388.2:c.2965C>A	p.Leu989Ile	p.L989I	ENST00000263388	NM_000435.2	989	Ctc/Atc	18/33	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.709192030761561	2		1069	1027	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059136	47059136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021124-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	103	527	0	ENST00000409792.3:c.7525G>A	p.Ala2509Thr	p.A2509T	ENST00000409792	NM_014159.6	2509	Gct/Act	20/21	0.709192030761561	1	FACETS	0.478	0.431	0.527	0.478	0.431	0.527	SUBCLONAL	1	TRUE	0	0.709192030761561	1		527	392	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563527	87563528	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0021124-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	112	478	1	ENST00000277120.3:c.1915_1916delinsTT	p.Gly639Leu	p.G639L	ENST00000277120		639	GGg/TTg	16/19	0.409671431414664	1	FACETS	0.361	0.325	0.398	0.361	0.325	0.398	INDETERMINATE	1	TRUE	0	0.709192030761561	1		479	565	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291801	15291801	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021124-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	660	1069	0	ENST00000263388.2:c.2965C>A	p.Leu989Ile	p.L989I	ENST00000263388	NM_000435.2	989	Ctc/Atc	18/33	0.52081299360147	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.664076807809778	4		1069	1622	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059136	47059136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021124-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	164	527	0	ENST00000409792.3:c.7525G>A	p.Ala2509Thr	p.A2509T	ENST00000409792	NM_014159.6	2509	Gct/Act	20/21	0.663233950598114	2	FACETS	0.965	0.892	1	0.482	0.446	0.52	CLONAL	1	TRUE	0	0.664076807809778	2		527	512	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563527	87563528	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0021124-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	154	478	1	ENST00000277120.3:c.1915_1916delinsTT	p.Gly639Leu	p.G639L	ENST00000277120		639	GGg/TTg	16/19	0.664076807809778	3	FACETS	0.808	0.74	0.878	0.404	0.37	0.439	CLONAL	1	TRUE	1	0.664076807809778	3		479	765	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021436-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	78	737	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.378920178621114	2	FACETS	0.897	0.791	1	0.448	0.395	0.505	CLONAL	1	TRUE	0	0.378920178621114	2		737	459	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857896	9857896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369878342	NA	P-0021436-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	325	684	1	ENST00000330684.3:c.3505C>T	p.Arg1169Trp	p.R1169W	ENST00000330684	NM_001134407.1	1169	Cgg/Tgg	13/13	0.378920178621114	5	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	2	0.378920178621114	5		685	819	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098601	108098601	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1555054249	NA	P-0021436-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	76	193	0	ENST00000278616.4:c.171G>T	p.Trp57Cys	p.W57C	ENST00000278616	NM_000051.3	57	tgG/tgT	3/63	0.378920178621114	3	FACETS	0.914	0.822	1	0.914	0.822	1	CLONAL	3	TRUE	0	0.378920178621114	3		193	174	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	93	76	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.913	0.814	1	0.913	0.814	1	CLONAL	1	FALSE	1	0.344023814679963	2		76	592	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0022650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	18	457	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.419206538288509	5	FACETS	0.11	0.082	0.143	0.037	0.027	0.048	INDETERMINATE	1	TRUE	2	0.861122226783494	5		457	874	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864616	57864616	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	362	870	0	ENST00000228682.2:c.2093T>A	p.Met698Lys	p.M698K	ENST00000228682	NM_005269.2	698	aTg/aAg	12/12	0.861122226783494	3	FACETS	1	0.955	1	0.504	0.477	0.53	CLONAL	1	TRUE	1	0.861122226783494	3		870	1194	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023307	27023307	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023768-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	109	113	1	ENST00000324856.7:c.413C>A	p.Ser138Ter	p.S138*	ENST00000324856	NM_006015.4	138	tCa/tAa	1/20	1	2	FACETS	0.906	0.829	0.985	0.906	0.829	0.985	CLONAL	1	FALSE	1	0.946897275367588	2		114	254	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295774	212295774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754127388	NA	P-0023768-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	244	501	0	ENST00000342788.4:c.2539C>T	p.Arg847Cys	p.R847C	ENST00000342788	NM_005235.2	847	Cgt/Tgt	21/28	1	2	FACETS	0.789	0.742	0.837	0.789	0.742	0.837	SUBCLONAL	1	FALSE	1	0.946897275367588	2		501	653	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727096	243727096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023768-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	236	473	0	ENST00000263826.5:c.874C>G	p.Leu292Val	p.L292V	ENST00000263826	NM_005465.4	292	Ctt/Gtt	9/13	1	2	FACETS	0.773	0.726	0.821	0.773	0.726	0.821	SUBCLONAL	1	FALSE	1	0.946897275367588	2		473	645	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0024043-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	290	568	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.896	0.847	0.945	0.896	0.847	0.945	CLONAL	1	TRUE	1	0.864193660202438	2		568	749	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024043-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	369	568	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.982	0.936	1	0.982	0.936	1	CLONAL	1	TRUE	1	0.864193660202438	2		568	870	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022913	27022938	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGCCGCCGCCAGCAGCCTGGGCAA	CCCGCCGCCGCCAGCAGCCTGGGCAA	-	rs797045262	NA	P-0024043-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	33	29	0	ENST00000324856.7:c.31_56del	p.Ser11AlafsTer91	p.S11Afs*91	ENST00000324856	NM_006015.4	7	CCCGCCGCCGCCAGCAGCCTGGGCAAc/c	1/20	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.864193660202438	2		29	75	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106536	27106536	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024043-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	441	769	0	ENST00000324856.7:c.6147G>A	p.Trp2049Ter	p.W2049*	ENST00000324856	NM_006015.4	2049	tgG/tgA	20/20	1	2	FACETS	0.979	0.937	1	0.979	0.937	1	CLONAL	1	TRUE	1	0.864193660202438	2		769	1042	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577157	64577160	+	frameshift_variant	Frame_Shift_Del	DEL	GACT	GACT	-	novel	NA	P-0024043-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	386	798	0	ENST00000312049.6:c.422_425del	p.Gln141ProfsTer43	p.Q141Pfs*43	ENST00000312049	NM_130799.2	141	cAGTCc/cc	2/10	0.802343168515626	1	FACETS	0.908	0.876	0.938	0.908	0.876	0.938	CLONAL	1	TRUE	0	0.864193660202438	1		798	559	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610591	10610591	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024043-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	477	769	0	ENST00000171111.5:c.119C>A	p.Ala40Glu	p.A40E	ENST00000171111	NM_203500.1	40	gCg/gAg	2/6	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.864193660202438	2		769	1082	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015053	27015053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151098324	NA	P-0024043-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	279	563	0	ENST00000335756.4:c.155G>A	p.Arg52Gln	p.R52Q	ENST00000335756	NM_001809.3	52	cGa/cAa	2/5	NA	2	FACETS	0.945	0.894	0.997			1	INDETERMINATE	1	TRUE	NA	0.864193660202438	2		563	683	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513455	41513458	+	frameshift_variant	Frame_Shift_Del	DEL	GCAT	GCAT	-	novel	NA	P-0024043-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	364	656	0	ENST00000263253.7:c.360_363del	p.Ser120ArgfsTer6	p.S120Rfs*6	ENST00000263253	NM_001429.3	120	aGCATg/ag	2/31	1	2	FACETS	0.992	0.946	1	0.992	0.946	1	CLONAL	1	TRUE	1	0.864193660202438	2		656	849	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0024670-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	213	866	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.245425469699507	2	FACETS	0.734	0.681	0.788	0.367	0.34	0.394	INDETERMINATE	1	TRUE	0	0.554659833446954	2		867	1047	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0024670-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	181	645	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.554659833446954	3	FACETS	0.644	0.592	0.698	0.322	0.296	0.349	SUBCLONAL	1	TRUE	1	0.554659833446954	3		645	1295	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533904	63533904	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201460658	NA	P-0024670-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	89	712	1	ENST00000307078.5:c.1250C>T	p.Ala417Val	p.A417V	ENST00000307078	NM_004655.3	417	gCg/gTg	6/11	0.34597822823858	3	FACETS	0.416	0.368	0.468	0.208	0.184	0.234	SUBCLONAL	1	TRUE	1	0.554659833446954	3		713	985	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786440	135786440	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024670-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	68	603	0	ENST00000298552.3:c.1090A>G	p.Asn364Asp	p.N364D	ENST00000298552	NM_001162426.1	364	Aat/Gat	11/23	0.26497529158096	3	FACETS	0.338	0.293	0.387	0.169	0.146	0.194	INDETERMINATE	1	TRUE	1	0.554659833446954	3		603	927	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508932	106508932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025097-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	127	533	2	ENST00000359195.3:c.926C>T	p.Thr309Met	p.T309M	ENST00000359195	NM_002649.2	309	aCg/aTg	2/11	1	2	FACETS	0.885	0.806	0.966	0.885	0.806	0.966	CLONAL	1	TRUE	1	0.588337815492539	2		535	488	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21565432	21565432	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025097-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	232	792	0	ENST00000382592.4:c.454G>A	p.Val152Ile	p.V152I	ENST00000382592	NM_014572.2	152	Gtc/Atc	3/8	1	2	FACETS	0.95	0.888	1	0.95	0.888	1	CLONAL	1	TRUE	1	0.588337815492539	2		792	830	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912172	32912173	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs80359395	NA	P-0025097-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	235	643	0	ENST00000380152.3:c.3680_3681del	p.Leu1227GlnfsTer5	p.L1227Qfs*5	ENST00000380152		1227	cTG/c	11/27	1	2	FACETS	0.958	0.896	1	0.958	0.896	1	CLONAL	1	TRUE	1	0.588337815492539	2		643	834	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813918	50813918	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025097-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	150	503	0	ENST00000398568.2:c.1472C>G	p.Pro491Arg	p.P491R	ENST00000398568	NM_001042412.1	491	cCa/cGa	8/18	NA	2	FACETS	0.844	0.775	0.916			1	INDETERMINATE	1	TRUE	NA	0.588337815492539	2		503	604	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024662	11024662	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025097-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	139	507	0	ENST00000327064.4:c.779G>C	p.Gly260Ala	p.G260A	ENST00000327064	NM_199141.1	260	gGc/gCc	6/16	1	2	FACETS	0.925	0.847	1	0.925	0.847	1	CLONAL	1	TRUE	1	0.588337815492539	2		507	511	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495713	72495713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778318924	NA	P-0025097-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	126	504	0	ENST00000477973.2:c.359C>T	p.Thr120Ile	p.T120I	ENST00000477973	NM_012234.5	120	aCc/aTc	1/4	1	2	FACETS	0.764	0.694	0.836	0.764	0.694	0.836	SUBCLONAL	1	TRUE	1	0.588337815492539	2		504	561	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779215	3779215	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025097-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	144	517	0	ENST00000262367.5:c.5833C>A	p.Pro1945Thr	p.P1945T	ENST00000262367	NM_004380.2	1945	Ccc/Acc	31/31	0.563794347626809	3	FACETS	1	0.964	1	0.548	0.502	0.596	CLONAL	1	TRUE	1	0.588337815492539	3		517	578	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753105	42753122	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGTCCGAGTGGGGGCG	GGCGTCCGAGTGGGGGCG	AGCTGCCC	novel	NA	P-0025097-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	181	876	2	ENST00000222329.4:c.1142_1159delinsGGGCAGCT	p.Pro381ArgfsTer13	p.P381Rfs*13	ENST00000222329	NM_006494.2	381	cCGCCCCCACTCGGACGCCgg/cGGGCAGCTgg	4/4	1	2	FACETS	0.864	0.799	0.931	0.864	0.799	0.931	CLONAL	1	TRUE	1	0.588337815492539	2		878	712	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0026080-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	77	392	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.904	0.796	1	0.904	0.796	1	CLONAL	1	TRUE	1	0.339929618452407	2		392	501	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576036	29576036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146306756	NA	P-0026080-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	68	394	1	ENST00000356175.3:c.4009C>T	p.Arg1337Trp	p.R1337W	ENST00000356175	NM_000267.3	1337	Cgg/Tgg	30/57	0.339929618452407	3	FACETS	0.754	0.656	0.86			1	SUBCLONAL	1	TRUE	NA	0.339929618452407	3		395	621	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073770	8073771	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TGGCTTTACTGGTCTAGGAGGT	novel	NA	P-0026080-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	29	320	0	ENST00000377482.5:c.867_888dup	p.Asp297ThrfsTer3	p.D297Tfs*3	ENST00000377482	NM_018948.3	296	-/ACCTCCTAGACCAGTAAAGCCA	4/4	1	2	FACETS	0.402	0.322	0.493	0.402	0.322	0.493	SUBCLONAL	1	TRUE	1	0.339929618452407	2		320	424	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073866	8073867	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TATCCTTATG	novel	NA	P-0026080-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	52	352	0	ENST00000377482.5:c.783_792dup	p.Ser265HisfsTer14	p.S265Hfs*14	ENST00000377482	NM_018948.3	264	-/CATAAGGATA	4/4	1	2	FACETS	0.652	0.556	0.758	0.652	0.556	0.758	SUBCLONAL	1	TRUE	1	0.339929618452407	2		352	469	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162736	47162737	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0026080-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	82	349	0	ENST00000409792.3:c.3389dup	p.Phe1131ValfsTer5	p.F1131Vfs*5	ENST00000409792	NM_014159.6	1130	aag/aaAg	3/21	0.339929618452407	1	FACETS	0.942	0.835	1	0.942	0.835	1	CLONAL	1	TRUE	0	0.339929618452407	1		349	425	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552837	106552837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1399614609	NA	P-0026369-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	778	157	0	ENST00000369096.4:c.802C>T	p.Arg268Cys	p.R268C	ENST00000369096	NM_001198.3	268	Cgt/Tgt	5/7	1	2	FACETS	1	0.995	1	1	0.998	1	CLONAL	2	TRUE	1	0.53430308357095	2		157	1323	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878136	48878136	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026369-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	192	72	0	ENST00000267163.4:c.88G>T	p.Glu30Ter	p.E30*	ENST00000267163	NM_000321.2	30	Gag/Tag	1/27	0.53430308357095	1	FACETS	0.927	0.881	0.972	1	0.995	1	CLONAL	2	TRUE	0	0.53430308357095	1		72	284	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888254	112888254	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026369-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	516	68	0	ENST00000351677.2:c.270G>T	p.Glu90Asp	p.E90D	ENST00000351677	NM_002834.3	90	gaG/gaT	3/16	1	2	FACETS	0.998	0.962	1	1	0.998	1	CLONAL	2	TRUE	1	0.53430308357095	2		68	968	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0027256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	191	456	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.789910873920182	2		456	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0027256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	23	810	2	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.789910873920182	1	FACETS	0.064	0.049	0.081	0.064	0.049	0.081	SUBCLONAL	1	TRUE	0	0.789910873920182	1		812	551	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986535	36986535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301600327	NA	P-0027256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	318	826	1	ENST00000354822.5:c.1154C>T	p.Ser385Leu	p.S385L	ENST00000354822	NM_001079668.2	385	tCg/tTg	3/3	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.789910873920182	2		827	760	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519990	NA	P-0027256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	101	699	0	ENST00000269305.4:c.796G>C	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Cga	8/11	0.789910873920182	1	FACETS	0.343	0.308	0.38	0.343	0.308	0.38	SUBCLONAL	1	TRUE	0	0.789910873920182	1		699	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519989	NA	P-0027256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	32	719	0	ENST00000269305.4:c.730G>C	p.Gly244Arg	p.G244R	ENST00000269305	NM_001126112.2	244	Ggc/Cgc	7/11	0.789910873920182	1	FACETS	0.123	0.099	0.149	0.123	0.099	0.149	SUBCLONAL	1	TRUE	0	0.789910873920182	1		719	400	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061194	38061555	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCTTCTGGCGGCGCAAGTAGCAGCCGTTCTCGAACATGTTGCCGGAGTCCGGGTGCAGCGTCCAGTAGGAGCCCTTGCCCGGCTTGTCCGGGGAGCGTGCCACCTTGACGAAGCAGTCATTGAAGGACAGCGAGTGGCGGATGGAGTTCTGCCAGCGCTGCTGGTTCTGCCGGTAATAGGGGAAGAGGTCCATGATCCACTGGTAGATCTCGCTCAGCGTGAGCATCTTGCTGGGCGCCTGCTGGATGGCCATGGTGATGAGCGAGATGTACGAGTAGGGCGGCTTGGCGTGCGGGTAGCTGCGCTTGAACGTCTTGGCGTCGCCGCCGCCGCCCGCGCGGCTGCGGCCCAGGTTGGACG	GCGCTTCTGGCGGCGCAAGTAGCAGCCGTTCTCGAACATGTTGCCGGAGTCCGGGTGCAGCGTCCAGTAGGAGCCCTTGCCCGGCTTGTCCGGGGAGCGTGCCACCTTGACGAAGCAGTCATTGAAGGACAGCGAGTGGCGGATGGAGTTCTGCCAGCGCTGCTGGTTCTGCCGGTAATAGGGGAAGAGGTCCATGATCCACTGGTAGATCTCGCTCAGCGTGAGCATCTTGCTGGGCGCCTGCTGGATGGCCATGGTGATGAGCGAGATGTACGAGTAGGGCGGCTTGGCGTGCGGGTAGCTGCGCTTGAACGTCTTGGCGTCGCCGCCGCCGCCCGCGCGGCTGCGGCCCAGGTTGGACG	-	novel	NA	P-0027256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	100	575	0	ENST00000250448.2:c.434_795del	p.Pro145LeufsTer27	p.P145Lfs*27	ENST00000250448	NM_004496.3	145	cCGTCCAACCTGGGCCGCAGCCGCGCGGGCGGCGGCGGCGACGCCAAGACGTTCAAGCGCAGCTACCCGCACGCCAAGCCGCCCTACTCGTACATCTCGCTCATCACCATGGCCATCCAGCAGGCGCCCAGCAAGATGCTCACGCTGAGCGAGATCTACCAGTGGATCATGGACCTCTTCCCCTATTACCGGCAGAACCAGCAGCGCTGGCAGAACTCCATCCGCCACTCGCTGTCCTTCAATGACTGCTTCGTCAAGGTGGCACGCTCCCCGGACAAGCCGGGCAAGGGCTCCTACTGGACGCTGCACCCGGACTCCGGCAACATGTTCGAGAACGGCTGCTACTTGCGCCGCCAGAAGCGC/c	2/2	1	2	FACETS	0.604	0.543	0.668	0.604	0.543	0.668	SUBCLONAL	1	TRUE	1	0.789910873920182	2		575	419	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780690	56780690	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs755849719	NA	P-0027256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	218	458	0	ENST00000337432.4:c.705G>T	p.Lys235Asn	p.K235N	ENST00000337432	NM_058216.2	235	aaG/aaT	4/9	1	2	FACETS	0.952	0.892	1	0.952	0.892	1	CLONAL	1	TRUE	1	0.789910873920182	2		458	580	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128305355	128305355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1204536063	NA	P-0027256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	285	605	0	ENST00000265960.3:c.941G>A	p.Gly314Glu	p.G314E	ENST00000265960	NM_001006617.1	314	gGa/gAa	7/12	1	2	FACETS	0.94	0.888	0.992	0.94	0.888	0.992	CLONAL	1	TRUE	1	0.789910873920182	2		605	768	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579328	7579328	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	13	776	0	ENST00000269305.4:c.359A>G	p.Lys120Arg	p.K120R	ENST00000269305	NM_001126112.2	120	aAg/aGg	4/11	0.789910873920182	1	FACETS	0.044	0.031	0.06	0.044	0.031	0.06	SUBCLONAL	1	TRUE	0	0.789910873920182	1		776	455	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575131	48575131	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	171	366	0	ENST00000342988.3:c.325C>A	p.Leu109Ile	p.L109I	ENST00000342988	NM_005359.5	109	Cta/Ata	3/12	0.622330189083187	3	FACETS	1	0.99	1			1	CLONAL	1	TRUE	NA	0.789910873920182	3		366	429	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435788	116435788	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	57	709	1	ENST00000397752.3:c.3878C>T	p.Thr1293Ile	p.T1293I	ENST00000397752	NM_000245.2	1293	aCt/aTt	20/21	1	2	FACETS	0.189	0.161	0.219	0.189	0.161	0.219	SUBCLONAL	1	TRUE	1	0.789910873920182	2		710	765	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717769	89717770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029409-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	188	370	0	ENST00000371953.3:c.800dup	p.Asp268GlyfsTer30	p.D268Gfs*30	ENST00000371953	NM_000314.4	265	cta/ctAa	7/9	0.81067248532945	1	FACETS	0.893	0.844	0.941	0.893	0.844	0.941	CLONAL	1	TRUE	0	0.81067248532945	1		370	309	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118855	115118856	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0029409-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	218	514	0	ENST00000257566.3:c.485_486del	p.Arg162LeufsTer2	p.R162Lfs*2	ENST00000257566	NM_016569.3	162	cGT/c	2/8	0.358276821540721	1	FACETS	0.381	0.355	0.408	0.381	0.355	0.408	INDETERMINATE	1	TRUE	0	0.81067248532945	1		514	840	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048735	180048735	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029409-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	474	716	0	ENST00000261937.6:c.1827C>G	p.Asp609Glu	p.D609E	ENST00000261937	NM_182925.4	609	gaC/gaG	13/30	0.78060698247704	1	FACETS	0.793	0.763	0.822	0.793	0.763	0.822	SUBCLONAL	1	TRUE	0	0.81067248532945	1		716	877	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194741	30194741	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0029409-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	152	524	0	ENST00000331968.5:c.403+1G>A		p.X135_splice	ENST00000331968	NM_002742.2	135			0.580501676247317	1	FACETS	0.383	0.352	0.416	0.383	0.352	0.416	SUBCLONAL	1	TRUE	0	0.81067248532945	1		524	582	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868417	45868417	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0029409-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1752	287	659	1	ENST00000391945.4:c.361-1G>T		p.X121_splice	ENST00000391945	NM_000400.3	121			0.81067248532945	3	FACETS	0.488	0.457	0.521			1	SUBCLONAL	1	TRUE	NA	0.81067248532945	3		660	2039	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121098	29121098	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029409-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	122	705	0	ENST00000328354.6:c.459A>T	p.Lys153Asn	p.K153N	ENST00000328354	NM_007194.3	153	aaA/aaT	4/15	0.81067248532945	1	FACETS	0.283	0.256	0.311	0.283	0.256	0.311	SUBCLONAL	1	TRUE	0	0.81067248532945	1		705	632	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5064921	5064921	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029409-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	24	432	0	ENST00000381652.3:c.1095C>G	p.Phe365Leu	p.F365L	ENST00000381652	NM_004972.3	365	ttC/ttG	9/25	0.81067248532945	1	FACETS	0.092	0.072	0.116	0.092	0.072	0.116	SUBCLONAL	1	TRUE	0	0.81067248532945	1		432	381	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288972	11288972	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	104	482	0	ENST00000361445.4:c.2783A>T	p.Asp928Val	p.D928V	ENST00000361445	NM_004958.3	928	gAc/gTc	19/58	0.392609133237232	4	FACETS	1	0.978	1	0.658	0.593	0.726	CLONAL	1	TRUE	2	0.591480845351697	4		482	425	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430151	181430151	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs1340243791	NA	P-0029450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	94	58	0	ENST00000325404.1:c.3G>A	p.Met1?	p.M1?	ENST00000325404	NM_003106.3	1	atG/atA	1/1	0.591480845351697	3	FACETS	0.873	0.791	0.956	0.873	0.791	0.956	CLONAL	2	TRUE	1	0.591480845351697	3		58	236	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31521253	31521263	+	frameshift_variant	Frame_Shift_Del	DEL	TTTGTAGGACC	TTTGTAGGACC	-	novel	NA	P-0029450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	26	609	0	ENST00000344624.3:c.914_924del	p.Arg305LysfsTer4	p.R305Kfs*4	ENST00000344624		305	aGGTCCTACAAA/a	3/33	0.571857876639885	2	FACETS	0.323	0.256	0.399	0.162	0.128	0.2	SUBCLONAL	1	TRUE	0	0.591480845351697	2		609	272	SUCCESS
APC	324	MSKCC	GRCh37	5	112174669	112174669	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029450-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	15	433	0	ENST00000257430.4:c.3378C>A	p.Ser1126Arg	p.S1126R	ENST00000257430	NM_000038.5	1126	agC/agA	16/16	0.591480845351697	2	FACETS	0.419	0.309	0.548	0.21	0.154	0.274	SUBCLONAL	1	TRUE	0	0.591480845351697	2		433	121	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	6	375	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.376	0.224	0.584	0.376	0.224	0.584	SUBCLONAL	1	TRUE	1	0.11	2		375	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0029791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	35	681	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.97	0.793	1	0.97	0.793	1	CLONAL	1	TRUE	1	0.11	2		682	656	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0029791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	16	0	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	1	2	FACETS	0.36	0.264	0.475	0.36	0.264	0.475	SUBCLONAL	1	TRUE	1	0.11	2		0	809	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677876	47677876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	12	0	0	ENST00000347630.2:c.989C>T	p.Ser330Leu	p.S330L	ENST00000347630	NM_001007230.1	330	tCg/tTg	11/11	1	2	FACETS	0.526	0.368	0.722	0.526	0.368	0.722	SUBCLONAL	1	TRUE	1	0.11	2		0	415	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435971	49435971	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	31	0	0	ENST00000301067.7:c.6010C>T	p.Gln2004Ter	p.Q2004*	ENST00000301067	NM_003482.3	2004	Cag/Tag	28/54	1	2	FACETS	0.764	0.615	0.933	0.764	0.615	0.933	CLONAL	1	TRUE	1	0.11	2		0	738	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929171	32929171	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	12	0	0	ENST00000380152.3:c.7181G>C	p.Arg2394Thr	p.R2394T	ENST00000380152		2394	aGa/aCa	14/27	1	2	FACETS	0.392	0.274	0.54	0.392	0.274	0.54	SUBCLONAL	1	TRUE	1	0.11	2		0	556	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56376765	56376765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1489009237	NA	P-0029791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	9	0	0	ENST00000348428.3:c.805C>T	p.His269Tyr	p.H269Y	ENST00000348428	NM_006785.3	269	Cat/Tat	5/17	1	2	FACETS	0.395	0.26	0.569	0.395	0.26	0.569	SUBCLONAL	1	TRUE	1	0.11	2		0	414	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467472	25467472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	18	0	0	ENST00000264709.3:c.1604C>T	p.Ser535Phe	p.S535F	ENST00000264709	NM_175629.2	535	tCc/tTc	14/23	1	2	FACETS	0.431	0.322	0.56	0.431	0.322	0.56	SUBCLONAL	1	TRUE	1	0.11	2		0	760	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851865	134851865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	9	0	0	ENST00000398015.3:c.1271C>T	p.Ser424Phe	p.S424F	ENST00000398015	NM_004441.4	424	tCt/tTt	5/16	0.10331725012282	0	FACETS	0.249	0.163	0.358			1	SUBCLONAL	1	TRUE	0	0.11	0		0	586	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0029791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	22	619	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.467	0.36	0.592	0.467	0.36	0.592	SUBCLONAL	1	TRUE	1	0.11	2		620	857	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0029791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	18	0	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	1	2	FACETS	0.57	0.427	0.74	0.57	0.427	0.74	SUBCLONAL	1	TRUE	1	0.11	2		0	574	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253817	153253817	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	7	0	0	ENST00000281708.4:c.916C>T	p.Gln306Ter	p.Q306*	ENST00000281708	NM_033632.3	306	Cag/Tag	6/12	1	2	FACETS	0.381	0.236	0.574	0.381	0.236	0.574	SUBCLONAL	1	TRUE	1	0.11	2		0	334	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056349	27056349	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	21	435	0	ENST00000324856.7:c.1345C>T	p.Gln449Ter	p.Q449*	ENST00000324856	NM_006015.4	449	Cag/Tag	2/20	1	2	FACETS	1	0.822	1	1	0.822	1	CLONAL	1	TRUE	1	0.11	2		435	353	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78914317	78914317	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	20	0	0	ENST00000306801.3:c.2941G>C	p.Glu981Gln	p.E981Q	ENST00000306801	NM_020761.2	981	Gag/Cag	25/34	1	2	FACETS	0.506	0.385	0.649	0.506	0.385	0.649	SUBCLONAL	1	TRUE	1	0.11	2		0	719	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724140	61724140	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	10	0	0	ENST00000401558.2:c.762C>G	p.Phe254Leu	p.F254L	ENST00000401558	NM_003400.3	254	ttC/ttG	10/25	1	2	FACETS	0.656	0.443	0.925	0.656	0.443	0.925	SUBCLONAL	1	TRUE	1	0.11	2		0	277	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626364	12626364	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	10	0	0	ENST00000251849.4:c.1785G>C	p.Glu595Asp	p.E595D	ENST00000251849	NM_002880.3	595	gaG/gaC	16/17	1	2	FACETS	0.37	0.249	0.523	0.37	0.249	0.523	SUBCLONAL	1	TRUE	1	0.11	2		0	492	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170011194	170011194	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	13	0	0	ENST00000295797.4:c.1315C>G	p.Leu439Val	p.L439V	ENST00000295797	NM_002740.5	439	Ctt/Gtt	14/18	1	2	FACETS	0.411	0.291	0.558	0.411	0.291	0.558	SUBCLONAL	1	TRUE	1	0.11	2		0	575	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170011231	170011231	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	20	0	0	ENST00000295797.4:c.1352C>A	p.Ser451Tyr	p.S451Y	ENST00000295797	NM_002740.5	451	tCt/tAt	14/18	1	2	FACETS	0.545	0.415	0.699	0.545	0.415	0.699	SUBCLONAL	1	TRUE	1	0.11	2		0	667	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389336	8389336	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1285563381	NA	P-0029791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	10	0	0	ENST00000356435.5:c.4282A>G	p.Thr1428Ala	p.T1428A	ENST00000356435		1428	Aca/Gca	26/35	1	2	FACETS	0.36	0.242	0.51	0.36	0.242	0.51	SUBCLONAL	1	TRUE	1	0.11	2		0	505	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123199738	123199738	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	18	165	0	ENST00000218089.9:c.2038G>A	p.Asp680Asn	p.D680N	ENST00000218089	NM_001042749.1	680	Gat/Aat	21/35	1	1	FACETS	0.805	0.609	1	1	0.914	1	CLONAL	2	TRUE	0	0.11	1		165	192	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030136-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	549	375	0				ENST00000310581	NM_198253.2	-/1132			0.153042277392404	3	FACETS	0.958	0.933	0.983	1	0.998	1	CLONAL	7	TRUE	1	0.247215004122463	3		375	744	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0030136-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	1246	137	1	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	0.218982604508894	2	FACETS	0.984	0.966	1			1	CLONAL	6	TRUE	0	0.247215004122463	2		138	1707	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0030136-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	943	120	0	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	1	2	FACETS	0.988	0.968	1			1	CLONAL	6	TRUE	1	0.247215004122463	2		120	1287	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151316	202151316	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0030136-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	362	81	0	ENST00000358485.4:c.1616G>C	p.Ter539SerextTer88	p.*539Sext*88	ENST00000358485	NM_001080125.1	539	tGa/tCa	9/9	0.247215004122463	3	FACETS	0.979	0.942	1	1	0.997	1	CLONAL	6	TRUE	0	0.247215004122463	3		81	560	SUCCESS
ATM	472	MSKCC	GRCh37	11	108183205	108183205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030136-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	0	2	0	ENST00000278616.4:c.5986G>A	p.Glu1996Lys	p.E1996K	ENST00000278616	NM_000051.3	1996	Gaa/Aaa	40/63	1	2	FACETS	0.001	0.001	0.032	0.001	0.001	0.032	SUBCLONAL	1	TRUE	1	0.247215004122463	2		2	184	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593508	48593508	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793725	NA	P-0030136-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	292	42	0	ENST00000342988.3:c.1259G>A	p.Arg420His	p.R420H	ENST00000342988	NM_005359.5	420	cGt/cAt	10/12	1	2	FACETS	0.916	0.873	0.957	1	0.997	1	CLONAL	5	TRUE	1	0.247215004122463	2		42	516	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857517	57857517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs890327478	NA	P-0030136-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	1225	90	2	ENST00000228682.2:c.43G>A	p.Glu15Lys	p.E15K	ENST00000228682	NM_005269.2	15	Gag/Aag	2/12	1	2	FACETS	0.935	0.917	0.953			1	CLONAL	6	TRUE	1	0.247215004122463	2		92	1766	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143318	30143345	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGGGCGTAGACACGGAAGAGCGAGGG	CCCGGGCGTAGACACGGAAGAGCGAGGG	-	novel	NA	P-0030136-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	1218	48	0	ENST00000389048.3:c.181_208del	p.Pro61ThrfsTer11	p.P61Tfs*11	ENST00000389048	NM_004304.4	61	CCCTCGCTCTTCCGTGTCTACGCCCGGGac/ac	1/29	0.153042277392404	3	FACETS	1	0.997	1			1	CLONAL	6	TRUE	1	0.247215004122463	3		48	1718	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1427441061	NA	P-0031005-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	154	716	0	ENST00000269305.4:c.560-2A>G		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.32538358245748	2	FACETS	0.932	0.859	1	0.932	0.859	1	CLONAL	2	TRUE	0	0.32653710388635	2		716	506	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242481	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAGCAA	TTAAGAGAAGCAA	C	rs397509368	NA	P-0031005-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	148	383	0	ENST00000275493.2:c.2239_2251delinsC	p.Leu747_Thr751delinsPro	p.L747_T751delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGCAAca/Cca	19/28	0.32653710388635	6	FACETS	1	0.975	1	0.686	0.632	0.741	CLONAL	3	TRUE	1	0.32653710388635	6		383	437	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219336	1219336	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031393-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	179	567	1	ENST00000326873.7:c.388G>T	p.Glu130Ter	p.E130*	ENST00000326873	NM_000455.4	130	Gag/Tag	3/10	0.514051217115838	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.514051217115838	1		568	460	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0031393-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	174	329	0	ENST00000311936.3:c.34_35delinsTT	p.Gly12Phe	p.G12F	ENST00000311936	NM_004985.3	12	GGt/TTt	2/5	0.257959681576283	2	FACETS	1	0.987	1	0.645	0.598	0.693	INDETERMINATE	1	TRUE	0	0.514051217115838	2		329	525	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610285	10610285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031393-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	230	946	1	ENST00000171111.5:c.425C>T	p.Thr142Met	p.T142M	ENST00000171111	NM_203500.1	142	aCg/aTg	2/6	0.514051217115838	1	FACETS	0.962	0.901	1	0.962	0.901	1	CLONAL	1	TRUE	0	0.514051217115838	1		947	691	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026115	71026115	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs797045584	NA	P-0031393-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	173	422	0	ENST00000318789.4:c.1507C>T	p.Arg503Ter	p.R503*	ENST00000318789	NM_032682.5	503	Cga/Tga	17/21	0.514051217115838	1	FACETS	0.975	0.904	1	0.975	0.904	1	CLONAL	1	TRUE	0	0.514051217115838	1		422	513	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105508	30105508	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031393-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	205	606	0	ENST00000331968.5:c.1178A>T	p.Asn393Ile	p.N393I	ENST00000331968	NM_002742.2	393	aAc/aTc	7/18	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.514051217115838	2		606	787	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312944	30312944	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031393-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	151	570	1	ENST00000262643.3:c.747G>T	p.Trp249Cys	p.W249C	ENST00000262643	NM_001238.2	249	tgG/tgT	9/12	1	2	FACETS	0.85	0.779	0.924	0.85	0.779	0.924	CLONAL	1	TRUE	1	0.514051217115838	2		571	691	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685307	86685307	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031393-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	36	157	0	ENST00000274376.6:c.3023A>G	p.Glu1008Gly	p.E1008G	ENST00000274376	NM_002890.2	1008	gAa/gGa	24/25	0.416492789740564	1	FACETS	0.368	0.303	0.439	0.368	0.303	0.439	SUBCLONAL	1	TRUE	0	0.514051217115838	1		157	283	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039686	47039686	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031393-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	205	457	0	ENST00000377604.3:c.1138G>T	p.Glu380Ter	p.E380*	ENST00000377604	NM_001204468.1	380	Gag/Tag	11/24	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.514051217115838	1		457	414	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720290	43720290	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031393-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	78	562	0	ENST00000382044.4:c.3752T>G	p.Val1251Gly	p.V1251G	ENST00000382044	NM_001141980.1	1251	gTa/gGa	18/28	1	2	FACETS	0.343	0.301	0.389	0.343	0.301	0.389	SUBCLONAL	1	TRUE	1	0.514051217115838	2		562	884	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236087	108236087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781894	NA	P-0032059-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	63	604	0	ENST00000278616.4:c.9023G>A	p.Arg3008His	p.R3008H	ENST00000278616	NM_000051.3	3008	cGt/cAt	63/63	1	2	FACETS	0.944	0.816	1	0.944	0.816	1	CLONAL	1	TRUE	1	0.203561085215265	2		604	656	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0032535-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	186	963	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.582304497525519	1	FACETS	0.951	0.887	1	0.951	0.887	1	CLONAL	1	TRUE	0	0.582304497525519	1		966	476	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032535-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	123	304	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.582304497525519	2		304	324	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015434	176015434	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032535-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	48	396	0	ENST00000367669.3:c.1304A>G	p.Tyr435Cys	p.Y435C	ENST00000367669	NM_022457.5	435	tAt/tGt	12/20	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.582304497525519	2		396	158	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713361	30713382	+	frameshift_variant	Frame_Shift_Del	DEL	CCACGTGTGCCAACAACATCAA	CCACGTGTGCCAACAACATCAA	-	novel	NA	P-0032535-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	49	691	0	ENST00000295754.5:c.690_711del	p.Cys231ThrfsTer26	p.C231Tfs*26	ENST00000295754	NM_003242.5	229	tCCACGTGTGCCAACAACATCAAc/tc	4/7	0.582304497525519	1	FACETS	0.352	0.299	0.409	0.352	0.299	0.409	SUBCLONAL	1	TRUE	0	0.582304497525519	1		691	339	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971178	21971184	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCACT	CGCCACT	-	novel	NA	P-0032535-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	108	598	0	ENST00000304494.5:c.174_180del	p.Val59SerfsTer85	p.V59Sfs*85	ENST00000304494	NM_000077.4	58	cgAGTGGCG/cg	2/3	0.582304497525519	1	FACETS	0.919	0.838	1	0.919	0.838	1	CLONAL	1	TRUE	0	0.582304497525519	1		598	286	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0032790-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	391	378	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.971	0.948	0.992	1	0.997	1	CLONAL	2	FALSE	1	0.890964944955408	2		378	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28934577	NA	P-0032790-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	686	311	1	ENST00000269305.4:c.770T>C	p.Leu257Pro	p.L257P	ENST00000269305	NM_001126112.2	257	cTg/cCg	7/11	0.890964944955408	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	FALSE	0	0.890964944955408	1		312	729	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152357845	152357845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032790-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	376	67	0	ENST00000359321.1:c.62G>A	p.Arg21Lys	p.R21K	ENST00000359321	NM_005431.1	21	aGa/aAa	2/3	0.885438283774582	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	FALSE	0	0.890964944955408	1		67	384	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467644	66467644	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032790-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	343	55	0	ENST00000273854.3:c.625G>T	p.Gly209Ter	p.G209*	ENST00000273854	NM_004439.5	209	Gga/Tga	3/18	0.890964944955408	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	FALSE	0	0.890964944955408	1		55	356	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026256	36026256	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032790-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	1334	347	1	ENST00000358208.4:c.858G>T	p.Met286Ile	p.M286I	ENST00000358208		286	atG/atT	7/12	0.110969499754997	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.890964944955408	0		348	1726	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519998	NA	P-0033223-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	756	353	0	ENST00000269305.4:c.581T>A	p.Leu194His	p.L194H	ENST00000269305	NM_001126112.2	194	cTt/cAt	6/11	0.775418106686096	3	FACETS	1	0.998	1	1	0.998	1	CLONAL	3	TRUE	0	0.774056113594641	3		353	813	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837949	156837949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150271893	NA	P-0033223-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	1278	262	4	ENST00000524377.1:c.482G>A	p.Arg161His	p.R161H	ENST00000524377	NM_002529.3	161	cGc/cAc	5/17	0.433096524376707	6	FACETS	0.908	0.89	0.925			1	INDETERMINATE	5	TRUE	NA	0.774056113594641	6		266	1854	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435744	56435744	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033223-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	772	185	0	ENST00000407977.2:c.1393G>T	p.Asp465Tyr	p.D465Y	ENST00000407977		465	Gac/Tac	9/10	0.775418106686096	3	FACETS	0.893	0.873	0.912	0.893	0.873	0.912	CLONAL	3	TRUE	0	0.774056113594641	3		185	1033	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728704	190728704	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033223-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	345	146	0	ENST00000441310.2:c.2092C>A	p.Gln698Lys	p.Q698K	ENST00000441310	NM_000534.4	698	Cag/Aag	10/13	0.71206212359416	5	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	2	0.774056113594641	5		146	554	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665474	138665474	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033223-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	1003	107	1	ENST00000330315.3:c.91C>A	p.Pro31Thr	p.P31T	ENST00000330315	NM_023067.3	31	Ccg/Acg	1/1	0.285736803730954	6	FACETS	1	0.987	1	1	0.998	1	INDETERMINATE	5	TRUE	2	0.774056113594641	6		108	1311	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016359	150016359	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0033223-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	336	77	1	ENST00000253339.5:c.349-2A>T		p.X117_splice	ENST00000253339		117			0.775418106686096	4	FACETS	1	0.992	1	0.59	0.563	0.616	CLONAL	2	TRUE	0	0.774056113594641	4		78	653	SUCCESS
BTK	695	MSKCC	GRCh37	X	100625042	100625042	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033223-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	289	24	0	ENST00000308731.7:c.335A>C	p.Tyr112Ser	p.Y112S	ENST00000308731	NM_000061.2	112	tAc/tCc	5/19	0.774056113594641	3	FACETS	0.807	0.765	0.849			1	CLONAL	2	TRUE	NA	0.774056113594641	3		24	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0033367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	315	817	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.741802448855709	1	FACETS	0.978	0.936	1	0.978	0.936	1	CLONAL	1	TRUE	0	0.758562342203516	1		817	527	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0033367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	186	696	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.989	0.921	1	0.989	0.921	1	CLONAL	1	TRUE	1	0.758562342203516	2		696	496	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0033367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	198	316	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.733477505475071	2	FACETS	0.913	0.869	0.955	0.913	0.869	0.955	CLONAL	2	TRUE	0	0.758562342203516	2		316	286	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509109	66509109	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	113	669	3	ENST00000273854.3:c.218T>A	p.Leu73Gln	p.L73Q	ENST00000273854	NM_004439.5	73	cTg/cAg	2/18	0.758562342203516	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.758562342203516	1		672	180	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658544	3658544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	189	1406	0	ENST00000294008.3:c.422G>A	p.Gly141Glu	p.G141E	ENST00000294008	NM_032444.2	141	gGg/gAg	2/15	1	2	FACETS	0.522	0.483	0.564	0.522	0.483	0.564	SUBCLONAL	1	TRUE	1	0.758562342203516	2		1406	954	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557345	29557345	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	163	652	3	ENST00000356175.3:c.3058G>T	p.Glu1020Ter	p.E1020*	ENST00000356175	NM_000267.3	1020	Gaa/Taa	23/57	1	2	FACETS	0.926	0.858	0.996	0.926	0.858	0.996	CLONAL	1	TRUE	1	0.758562342203516	2		655	464	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096990	11096990	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1295034696	NA	P-0033367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	367	1698	1	ENST00000358026.2:c.481G>T	p.Ala161Ser	p.A161S	ENST00000358026	NM_001128849.1	161	Gcc/Tcc	4/36	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.758562342203516	2		1699	948	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0033485-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	916	963	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.25266003254436	2	FACETS	0.94	0.916	0.964	1	0.998	1	CLONAL	4	TRUE	0	0.309165067148769	2		966	1576	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0033485-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	336	108	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	0.309165067148769	5	FACETS	0.93	0.887	0.973	1	0.996	1	CLONAL	5	TRUE	2	0.309165067148769	5		108	684	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913315	NA	P-0033485-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	1127	204	0	ENST00000326873.7:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000326873	NM_000455.4	194	Gac/Tac	4/10	0.25266003254436	2	FACETS	0.979	0.957	1	1	0.999	1	CLONAL	4	TRUE	0	0.309165067148769	2		204	1861	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729154	66729154	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519731	NA	P-0033485-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	726	179	0	ENST00000307102.5:c.362G>C	p.Cys121Ser	p.C121S	ENST00000307102	NM_002755.3	121	tGc/tCc	3/11	0.290177102554394	3	FACETS	1	0.979	1	1	0.998	1	CLONAL	4	TRUE	1	0.309165067148769	3		179	1340	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038881	12038881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033485-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	329	81	0	ENST00000396373.4:c.1174G>A	p.Glu392Lys	p.E392K	ENST00000396373	NM_001987.4	392	Gag/Aag	7/8	0.29783966348287	4	FACETS	1	0.99	1			1	CLONAL	4	TRUE	NA	0.309165067148769	4		81	621	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064391	30064391	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033485-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	470	118	0	ENST00000338641.4:c.955C>T	p.Gln319Ter	p.Q319*	ENST00000338641	NM_000268.3	319	Cag/Tag	10/16	0.25266003254436	2	FACETS	0.884	0.851	0.917	1	0.997	1	CLONAL	4	TRUE	0	0.309165067148769	2		118	860	SUCCESS
APC	324	MSKCC	GRCh37	5	112111435	112111435	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0033485-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	170	23	0	ENST00000257430.4:c.531+1G>A		p.X177_splice	ENST00000257430	NM_000038.5	177			0.266263630558206	1	FACETS	0.954	0.894	1	1	0.994	1	CLONAL	3	TRUE	0	0.309165067148769	1		23	325	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416690	121416690	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033485-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	1181	78	0	ENST00000257555.6:c.119G>C	p.Gly40Ala	p.G40A	ENST00000257555		40	gGa/gCa	1/10	0.140548275831113	4	FACETS	1	0.996	1	1	0.999	1	INDETERMINATE	4	TRUE	2	0.309165067148769	4		78	2253	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38631936	38631936	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0033485-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	437	88	0	ENST00000299084.4:c.424-2A>G		p.X142_splice	ENST00000299084	NM_152594.2	142			0.290177102554394	3	FACETS	0.947	0.909	0.985	1	0.997	1	CLONAL	4	TRUE	1	0.309165067148769	3		88	862	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994808	73994808	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033485-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	735	81	0	ENST00000318443.5:c.292G>T	p.Asp98Tyr	p.D98Y	ENST00000318443	NM_001024736.1	98	Gac/Tac	3/10	0.290177102554394	3	FACETS	0.978	0.948	1	1	0.998	1	CLONAL	4	TRUE	1	0.309165067148769	3		81	1403	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395722	45395722	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033485-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	346	37	0	ENST00000262160.6:c.412C>T	p.His138Tyr	p.H138Y	ENST00000262160	NM_005901.5	138	Cac/Tac	4/11	0.25266003254436	2	FACETS	1	0.973	1	1	0.996	1	CLONAL	3	TRUE	0	0.309165067148769	2		37	726	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602412	10602412	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033485-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	1382	339	0	ENST00000171111.5:c.1166A>T	p.Asp389Val	p.D389V	ENST00000171111	NM_203500.1	389	gAc/gTc	3/6	0.25266003254436	2	FACETS	0.963	0.943	0.983	1	0.999	1	CLONAL	4	TRUE	0	0.309165067148769	2		339	2321	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149896	99149896	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033485-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	605	149	0	ENST00000074304.5:c.208G>C	p.Val70Leu	p.V70L	ENST00000074304	NM_001134224.1	70	Gtg/Ctg	5/26	0.246871074630315	4	FACETS	1	0.985	1	1	0.998	1	CLONAL	4	TRUE	2	0.309165067148769	4		149	1235	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027171	71027172	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0033485-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	400	96	1	ENST00000318789.4:c.1155_1156delinsTT	p.Val386Leu	p.V386L	ENST00000318789	NM_032682.5	385	ctGGta/ctTTta	15/21	0.25266003254436	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	3	TRUE	0	0.309165067148769	2		97	751	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185840	32185840	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033485-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	1049	81	0	ENST00000375023.3:c.1556C>T	p.Ser519Leu	p.S519L	ENST00000375023	NM_004557.3	519	tCa/tTa	9/30	0.309165067148769	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	4	TRUE	0	0.309165067148769	4		81	2138	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507402	8507402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033485-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	360	35	1	ENST00000356435.5:c.1576C>T	p.Pro526Ser	p.P526S	ENST00000356435		526	Cct/Tct	11/35	0.25266003254436	2	FACETS	1	0.991	1	1	0.996	1	CLONAL	3	TRUE	0	0.309165067148769	2		36	680	SUCCESS
AR	367	MSKCC	GRCh37	X	66942721	66942721	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033485-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	214	113	0	ENST00000374690.3:c.2502C>A	p.Asn834Lys	p.N834K	ENST00000374690	NM_000044.3	834	aaC/aaA	7/8	0.29783966348287	2	FACETS	1	0.988	1			1	CLONAL	3	TRUE	NA	0.309165067148769	2		113	396	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0034775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	258	568	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	2	TRUE	1	0.291663556691588	2		568	771	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0034775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	274	772	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.291663556691588	2		777	793	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653808	89653808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	140	468	0	ENST00000371953.3:c.106G>A	p.Gly36Arg	p.G36R	ENST00000371953	NM_000314.4	36	Gga/Aga	2/9	1	2	FACETS	0.982	0.9	1	1	0.991	1	CLONAL	2	TRUE	1	0.291663556691588	2		468	489	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560514	65560514	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	251	508	0	ENST00000358664.4:c.83A>G	p.His28Arg	p.H28R	ENST00000358664	NM_002382.4	28	cAt/cGt	3/5	1	2	FACETS	1	0.98	1	1	0.995	1	CLONAL	2	TRUE	1	0.291663556691588	2		508	782	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913286	NA	P-0034775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	239	635	0	ENST00000263967.3:c.1636C>G	p.Gln546Glu	p.Q546E	ENST00000263967	NM_006218.2	546	Cag/Gag	10/21	1	2	FACETS	1	0.989	1	1	0.995	1	CLONAL	2	TRUE	1	0.291663556691588	2		635	663	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821890	72821890	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	192	406	1	ENST00000268489.5:c.10285del	p.Arg3429ValfsTer56	p.R3429Vfs*56	ENST00000268489	NM_006885.3	3429	Cgt/gt	10/10	1	2	FACETS	1	0.977	1	1	0.994	1	CLONAL	2	TRUE	1	0.291663556691588	2		407	589	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439919	56439919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	264	540	0	ENST00000407977.2:c.673del	p.Arg225AlafsTer194	p.R225Afs*194	ENST00000407977		225	Cgc/gc	6/10	1	2	FACETS	1	0.975	1	1	0.995	1	CLONAL	2	TRUE	1	0.291663556691588	2		540	847	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861245	57861245	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1460787785	NA	P-0034775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	244	569	0	ENST00000228682.2:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000228682	NM_005269.2	348	Cga/Tga	9/12	1	2	FACETS	1	0.963	1	1	0.995	1	CLONAL	2	TRUE	1	0.291663556691588	2		569	806	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380346	14380346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	351	342	0	ENST00000256196.4:c.71G>A	p.Gly24Asp	p.G24D	ENST00000256196		24	gGc/gAc	1/6	0.291663556691588	1	FACETS	1	0.975	1	1	0.997	1	CLONAL	4	TRUE	0	0.291663556691588	1		342	507	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0034775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	246	593	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.982	1	1	0.995	1	CLONAL	2	TRUE	1	0.291663556691588	2		598	752	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95599668	95599668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367797765	NA	P-0034775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	184	570	2	ENST00000393063.1:c.128C>T	p.Thr43Met	p.T43M	ENST00000393063	NM_030621.3	43	aCg/aTg	3/28	1	2	FACETS	1	0.958	1	1	0.993	1	CLONAL	2	TRUE	1	0.291663556691588	2		572	603	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115446	115115446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	224	650	0	ENST00000257566.3:c.880del	p.Ile294Ter	p.I294*	ENST00000257566	NM_016569.3	294	Ata/ta	5/8	1	2	FACETS	1	0.945	1	1	0.994	1	CLONAL	2	TRUE	1	0.291663556691588	2		650	758	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692949	89692949	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167627	NA	P-0034775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	168	607	1	ENST00000371953.3:c.437del	p.Leu146Ter	p.L146*	ENST00000371953	NM_000314.4	145	Ttt/tt	5/9	1	2	FACETS	1	0.927	1	1	0.993	1	CLONAL	2	TRUE	1	0.291663556691588	2		608	574	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099578	157099579	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	48	106	0	ENST00000346085.5:c.521dup	p.Pro177AlafsTer55	p.P177Afs*55	ENST00000346085	NM_020732.3	172	gac/gaCc	1/20	1	2	FACETS	0.899	0.772	1	1	0.972	1	CLONAL	2	TRUE	1	0.291663556691588	2		106	183	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459318	120459318	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0034775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	137	408	0	ENST00000256646.2:c.6028-1G>T		p.X2010_splice	ENST00000256646	NM_024408.3	2010			1	2	FACETS	1	0.963	1	1	0.992	1	CLONAL	2	TRUE	1	0.291663556691588	2		408	432	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434388	110434388	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0034775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	279	676	0	ENST00000375856.3:c.4012+1G>A		p.X1338_splice	ENST00000375856	NM_003749.2	1338			1	2	FACETS	1	0.985	1	1	0.996	1	CLONAL	2	TRUE	1	0.291663556691588	2		676	848	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78617539	78617539	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	181	425	2	ENST00000306801.3:c.277A>T	p.Met93Leu	p.M93L	ENST00000306801	NM_020761.2	93	Atg/Ttg	3/34	1	2	FACETS	1	0.975	1	1	0.994	1	CLONAL	2	TRUE	1	0.291663556691588	2		427	559	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214824	36214824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	233	709	1	ENST00000222270.7:c.3250C>T	p.Pro1084Ser	p.P1084S	ENST00000222270	NM_014727.1	1084	Ccc/Tcc	8/37	1	2	FACETS	0.953	0.891	1	1	0.994	1	CLONAL	2	TRUE	1	0.291663556691588	2		710	838	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936073	178936073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	153	430	1	ENST00000263967.3:c.1615C>T	p.Pro539Ser	p.P539S	ENST00000263967	NM_006218.2	539	Cct/Tct	10/21	1	2	FACETS	1	0.978	1	1	0.993	1	CLONAL	2	TRUE	1	0.291663556691588	2		431	453	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542230	187542230	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs375087017	NA	P-0034775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	126	504	1	ENST00000441802.2:c.5510A>G	p.Tyr1837Cys	p.Y1837C	ENST00000441802	NM_005245.3	1837	tAt/tGt	10/27	1	2	FACETS	0.956	0.872	1	1	0.99	1	CLONAL	2	TRUE	1	0.291663556691588	2		505	452	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087893	27087920	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCACCCAGTGGCCAGTCGGACAGCAT	GGCCACCCAGTGGCCAGTCGGACAGCAT	AA	novel	NA	P-0034775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	216	748	2	ENST00000324856.7:c.2180_2207delinsAA	p.Arg727GlnfsTer81	p.R727Qfs*81	ENST00000324856	NM_006015.4	727	cGGCCACCCAGTGGCCAGTCGGACAGCATc/cAAc	6/20	1	2	FACETS	0.872	0.812	0.934	1	0.993	1	CLONAL	2	TRUE	1	0.291663556691588	2		750	849	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0034775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	102	693	4	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.849	0.759	0.945	0.849	0.759	0.945	CLONAL	1	TRUE	1	0.291663556691588	2		697	824	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0034775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	211	802	2	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.291663556691588	2		804	1065	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0034775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	41	644	4	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.369	0.307	0.44	0.369	0.307	0.44	SUBCLONAL	1	TRUE	1	0.291663556691588	2		648	761	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1232964733	NA	P-0034775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	42	100	0	ENST00000324856.7:c.1015del	p.Ala339LeufsTer24	p.A339Lfs*24	ENST00000324856	NM_006015.4	337	tGg/tg	1/20	1	2	FACETS	0.986	0.839	1	1	0.972	1	CLONAL	2	TRUE	1	0.291663556691588	2		100	146	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353819	15353819	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	34	490	1	ENST00000263377.2:c.3061del	p.His1021IlefsTer47	p.H1021Ifs*47	ENST00000263377	NM_058243.2	1021	Cat/at	14/20	1	2	FACETS	0.378	0.308	0.457	0.378	0.308	0.457	SUBCLONAL	1	TRUE	1	0.291663556691588	2		491	617	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272337	15272337	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs771517374	NA	P-0034775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	61	811	7	ENST00000263388.2:c.6102del	p.Gly2035ValfsTer50	p.G2035Vfs*50	ENST00000263388	NM_000435.2	2034	ccC/cc	33/33	1	2	FACETS	0.411	0.353	0.474	0.411	0.353	0.474	SUBCLONAL	1	TRUE	1	0.291663556691588	2		818	1018	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435128	110435129	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs772322568	NA	P-0034775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	192	660	4	ENST00000375856.3:c.3272dup	p.Lys1092GlufsTer233	p.K1092Efs*233	ENST00000375856	NM_003749.2	1091	ccg/ccCg	1/2	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.291663556691588	2		664	894	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920173	76920173	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	117	626	6	ENST00000373344.5:c.3904del	p.Arg1302GlufsTer44	p.R1302Efs*44	ENST00000373344	NM_000489.3	1302	Aga/ga	11/35	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.291663556691588	2		632	792	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112526	115112526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358091442	NA	P-0034775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	258	790	0	ENST00000257566.3:c.1214G>A	p.Arg405His	p.R405H	ENST00000257566	NM_016569.3	405	cGt/cAt	7/8	1	2	FACETS	0.865	0.81	0.921	1	0.994	1	CLONAL	2	TRUE	1	0.291663556691588	2		790	1023	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978948	25978949	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0034775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	219	527	0	ENST00000435504.4:c.974dup	p.Ala326SerfsTer3	p.A326Sfs*3	ENST00000435504		325	tca/tcCa	10/13	1	2	FACETS	1	0.977	1	1	0.995	1	CLONAL	2	TRUE	1	0.291663556691588	2		527	684	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683472	182683472	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	103	620	0	ENST00000292782.4:c.73A>C	p.Thr25Pro	p.T25P	ENST00000292782	NM_020640.2	25	Aca/Cca	2/7	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.291663556691588	2		620	662	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	221	568	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.43	2		568	747	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	245	800	7	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.43	2		807	979	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	294	772	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.43	2		777	1061	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	391	90	0	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	1	0.987	1	1	0.997	1	CLONAL	2	TRUE	1	0.43	2		90	838	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	153	292	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.43	2		292	604	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653808	89653808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	147	468	0	ENST00000371953.3:c.106G>A	p.Gly36Arg	p.G36R	ENST00000371953	NM_000314.4	36	Gga/Aga	2/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.43	2		468	611	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560514	65560514	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	195	508	0	ENST00000358664.4:c.83A>G	p.His28Arg	p.H28R	ENST00000358664	NM_002382.4	28	cAt/cGt	3/5	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.43	2		508	757	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	138	379	2	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.43	2		381	550	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913286	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	165	635	0	ENST00000263967.3:c.1636C>G	p.Gln546Glu	p.Q546E	ENST00000263967	NM_006218.2	546	Cag/Gag	10/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.43	2		635	615	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	313	75	0	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.43	2		75	1173	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	175	470	0	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.43	2		470	647	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	161	591	2	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.43	2		593	657	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	243	977	8	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.43	2		985	895	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821890	72821890	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	165	406	1	ENST00000268489.5:c.10285del	p.Arg3429ValfsTer56	p.R3429Vfs*56	ENST00000268489	NM_006885.3	3429	Cgt/gt	10/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.43	2		407	713	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375459	40375459	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	186	799	3	ENST00000293328.3:c.491del	p.Lys164SerfsTer17	p.K164Sfs*17	ENST00000293328	NM_012448.3	164	aAg/ag	5/19	1	2	FACETS	0.8	0.738	0.865	0.8	0.738	0.865	SUBCLONAL	1	TRUE	1	0.43	2		802	1081	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	111	449	0	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	0.863	0.778	0.953	0.863	0.778	0.953	CLONAL	1	TRUE	1	0.43	2		449	598	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405954	157405954	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	223	640	6	ENST00000346085.5:c.2201del	p.Gly734AlafsTer11	p.G734Afs*11	ENST00000346085	NM_020732.3	732	ccG/cc	6/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.43	2		646	917	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439919	56439919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	265	540	0	ENST00000407977.2:c.673del	p.Arg225AlafsTer194	p.R225Afs*194	ENST00000407977		225	Cgc/gc	6/10	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.43	2		540	914	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861245	57861245	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1460787785	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	214	569	0	ENST00000228682.2:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000228682	NM_005269.2	348	Cga/Tga	9/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.43	2		569	917	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248394	59248394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329490786	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	60	423	2	ENST00000371222.2:c.349G>A	p.Ala117Thr	p.A117T	ENST00000371222	NM_002228.3	117	Gcc/Acc	1/1	1	2	FACETS	0.455	0.391	0.523	0.455	0.391	0.523	SUBCLONAL	1	TRUE	1	0.43	2		425	614	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380346	14380346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	227	342	0	ENST00000256196.4:c.71G>A	p.Gly24Asp	p.G24D	ENST00000256196		24	gGc/gAc	1/6	0.3	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.43	2		342	426	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	178	593	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.945	0.872	1	0.945	0.872	1	CLONAL	1	TRUE	1	0.43	2		598	876	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95599668	95599668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367797765	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	140	570	2	ENST00000393063.1:c.128C>T	p.Thr43Met	p.T43M	ENST00000393063	NM_030621.3	43	aCg/aTg	3/28	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.43	2		572	596	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246078851	246078851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61762672	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	230	712	1	ENST00000388985.4:c.794G>A	p.Arg265His	p.R265H	ENST00000388985		265	cGt/cAt	8/12	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.43	2		713	892	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115446	115115446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	186	650	0	ENST00000257566.3:c.880del	p.Ile294Ter	p.I294*	ENST00000257566	NM_016569.3	294	Ata/ta	5/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.43	2		650	744	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692949	89692949	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167627	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	197	607	1	ENST00000371953.3:c.437del	p.Leu146Ter	p.L146*	ENST00000371953	NM_000314.4	145	Ttt/tt	5/9	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.43	2		608	719	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62294236	62294236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs184051277	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	165	641	0	ENST00000360203.5:c.532G>A	p.Val178Ile	p.V178I	ENST00000360203	NM_001283009.1	178	Gta/Ata	6/35	1	2	FACETS	0.859	0.789	0.933	0.859	0.789	0.933	CLONAL	1	TRUE	1	0.43	2		641	893	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099578	157099579	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	31	106	0	ENST00000346085.5:c.521dup	p.Pro177AlafsTer55	p.P177Afs*55	ENST00000346085	NM_020732.3	172	gac/gaCc	1/20	1	2	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	TRUE	1	0.43	2		106	141	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459318	120459318	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	121	408	0	ENST00000256646.2:c.6028-1G>T		p.X2010_splice	ENST00000256646	NM_024408.3	2010			1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.43	2		408	510	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434388	110434388	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	249	676	0	ENST00000375856.3:c.4012+1G>A		p.X1338_splice	ENST00000375856	NM_003749.2	1338			0.281470325853427	3	FACETS	1	0.989	1	0.641	0.599	0.685	CLONAL	1	TRUE	1	0.43	3		676	1097	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78617539	78617539	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	162	425	2	ENST00000306801.3:c.277A>T	p.Met93Leu	p.M93L	ENST00000306801	NM_020761.2	93	Atg/Ttg	3/34	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.43	2		427	606	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214824	36214824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	253	709	1	ENST00000222270.7:c.3250C>T	p.Pro1084Ser	p.P1084S	ENST00000222270	NM_014727.1	1084	Ccc/Tcc	8/37	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.43	2		710	1041	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936073	178936073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	110	430	1	ENST00000263967.3:c.1615C>T	p.Pro539Ser	p.P539S	ENST00000263967	NM_006218.2	539	Cct/Tct	10/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.43	2		431	429	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542230	187542230	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs375087017	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	34	504	1	ENST00000441802.2:c.5510A>G	p.Tyr1837Cys	p.Y1837C	ENST00000441802	NM_005245.3	1837	tAt/tGt	10/27	0.3	1	FACETS	0.261	0.213	0.316	0.261	0.213	0.316	SUBCLONAL	1	TRUE	0	0.43	1		505	475	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184561	11184561	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	169	676	0	ENST00000361445.4:c.6656A>C	p.Asn2219Thr	p.N2219T	ENST00000361445	NM_004958.3	2219	aAc/aCc	47/58	1	2	FACETS	0.872	0.802	0.946	0.872	0.802	0.946	CLONAL	1	TRUE	1	0.43	2		676	901	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088755	27088755	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	290	725	0	ENST00000324856.7:c.2364C>G	p.Tyr788Ter	p.Y788*	ENST00000324856	NM_006015.4	788	taC/taG	7/20	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.43	2		725	1003	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957550	175957550	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	135	423	0	ENST00000367669.3:c.1848-2A>G		p.X616_splice	ENST00000367669	NM_022457.5	616			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.43	2		423	545	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170528	108170528	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	44	466	0	ENST00000278616.4:c.5093A>C	p.Lys1698Thr	p.K1698T	ENST00000278616	NM_000051.3	1698	aAg/aCg	34/63	1	2	FACETS	0.318	0.266	0.376	0.318	0.266	0.376	SUBCLONAL	1	TRUE	1	0.43	2		466	643	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21626546	21626546	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	151	475	0	ENST00000421138.2:c.1386del	p.Phe462LeufsTer28	p.F462Lfs*28	ENST00000421138		462	ttT/tt	13/16	1	2	FACETS	0.992	0.909	1	0.992	0.909	1	CLONAL	1	TRUE	1	0.43	2		475	708	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444810	49444810	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199946966	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	203	960	0	ENST00000301067.7:c.2656C>A	p.Pro886Thr	p.P886T	ENST00000301067	NM_003482.3	886	Cct/Act	10/54	1	2	FACETS	0.802	0.743	0.864	0.802	0.743	0.864	CLONAL	1	TRUE	1	0.43	2		960	1177	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112172	115112172	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	63	572	1	ENST00000257566.3:c.1568G>A	p.Ser523Asn	p.S523N	ENST00000257566	NM_016569.3	523	aGc/aAc	7/8	1	2	FACETS	0.451	0.39	0.518	0.451	0.39	0.518	SUBCLONAL	1	TRUE	1	0.43	2		573	649	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647421	3647421	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	267	753	1	ENST00000294008.3:c.1642G>A	p.Ala548Thr	p.A548T	ENST00000294008	NM_032444.2	548	Gcc/Acc	7/15	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.43	2		754	953	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276776	15276776	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	204	791	0	ENST00000263388.2:c.5489A>G	p.Gln1830Arg	p.Q1830R	ENST00000263388	NM_000435.2	1830	cAg/cGg	30/33	1	2	FACETS	0.909	0.842	0.978	0.909	0.842	0.978	CLONAL	1	TRUE	1	0.43	2		791	1044	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764360	39764360	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	51	543	0	ENST00000288319.7:c.752C>T	p.Pro251Leu	p.P251L	ENST00000288319	NM_182918.3	251	cCa/cTa	7/10	1	2	FACETS	0.288	0.244	0.337	0.288	0.244	0.337	SUBCLONAL	1	TRUE	1	0.43	2		543	823	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12632310	12632310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	179	581	2	ENST00000251849.4:c.1357G>A	p.Ala453Thr	p.A453T	ENST00000251849	NM_002880.3	453	Gct/Act	12/17	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.43	2		583	751	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045840	26045840	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	198	674	0	ENST00000540144.1:c.202T>C	p.Phe68Leu	p.F68L	ENST00000540144	NM_003531.2	68	Ttc/Ctc	1/1	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.43	2		674	880	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271318	26271318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	254	595	0	ENST00000305910.3:c.295G>A	p.Ala99Thr	p.A99T	ENST00000305910	NM_003534.2	99	Gcc/Acc	1/1	0.25236147035609	5	FACETS	1	0.947	1	0.674	0.631	0.718	INDETERMINATE	2	TRUE	2	0.43	5		595	961	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903829	41903829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	216	645	1	ENST00000372991.4:c.728G>A	p.Cys243Tyr	p.C243Y	ENST00000372991	NM_001760.3	243	tGt/tAt	5/5	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.43	2		646	864	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952091	76952091	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	123	454	0	ENST00000373344.5:c.344A>G	p.Asp115Gly	p.D115G	ENST00000373344	NM_000489.3	115	gAt/gGt	5/35	1	2	FACETS	0.971	0.881	1	0.971	0.881	1	CLONAL	1	TRUE	1	0.43	2		454	589	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087893	27087920	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCACCCAGTGGCCAGTCGGACAGCAT	GGCCACCCAGTGGCCAGTCGGACAGCAT	AA	novel	NA	P-0034775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	182	748	2	ENST00000324856.7:c.2180_2207delinsAA	p.Arg727GlnfsTer81	p.R727Qfs*81	ENST00000324856	NM_006015.4	727	cGGCCACCCAGTGGCCAGTCGGACAGCATc/cAAc	6/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.43	2		750	821	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0035162-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	162	532	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	0.316285981519545	2	FACETS	1	0.986	1	0.669	0.615	0.726	CLONAL	1	TRUE	0	0.322268951729947	2		532	751	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295801	212295801	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1423325504	NA	P-0035162-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	86	584	1	ENST00000342788.4:c.2512C>T	p.Arg838Ter	p.R838*	ENST00000342788	NM_005235.2	838	Cga/Tga	21/28	0.322268951729947	3	FACETS	0.943	0.835	1	0.472	0.417	0.53	CLONAL	1	TRUE	1	0.322268951729947	3		585	657	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443936	18443936	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1195125518	NA	P-0035162-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	62	354	0	ENST00000266497.5:c.909T>G	p.Phe303Leu	p.F303L	ENST00000266497		303	ttT/ttG	3/31	0.322268951729947	3	FACETS	1	0.93	1	0.557	0.483	0.637	CLONAL	1	TRUE	1	0.322268951729947	3		354	401	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783871	50783871	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035162-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	105	725	0	ENST00000398568.2:c.262G>A	p.Asp88Asn	p.D88N	ENST00000398568	NM_001042412.1	88	Gat/Aat	3/18	0.322268951729947	3	FACETS	0.859	0.769	0.955	0.429	0.384	0.478	CLONAL	1	TRUE	1	0.322268951729947	3		725	881	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191029	2191029	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035162-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	85	558	0	ENST00000398665.3:c.283C>A	p.Pro95Thr	p.P95T	ENST00000398665	NM_032482.2	95	Ccc/Acc	5/28	1	2	FACETS	0.849	0.752	0.954	0.849	0.752	0.954	CLONAL	1	TRUE	1	0.322268951729947	2		558	621	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120363	94120363	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035162-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	68	392	0	ENST00000369303.4:c.688G>T	p.Val230Phe	p.V230F	ENST00000369303	NM_004440.3	230	Gtt/Ttt	3/17	1	2	FACETS	0.887	0.773	1	0.887	0.773	1	CLONAL	1	TRUE	1	0.322268951729947	2		392	476	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411856	116411880	+	intron_variant	Intron	DEL	CCATGATAGCCGTCTTTAACAAGCT	CCATGATAGCCGTCTTTAACAAGCT	-	novel	NA	P-0035162-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	14859	1020	1	ENST00000397752.3:c.2888-46_2888-22del		p.*963*	ENST00000397752	NM_000245.2	-/1390			0.322268951729947	27	FACETS	0.987	0.985	0.99			1	CLONAL	30	TRUE	NA	0.322268951729947	27		1021	15655	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465595	8465595	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035162-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	49	549	0	ENST00000356435.5:c.3585C>A	p.His1195Gln	p.H1195Q	ENST00000356435		1195	caC/caA	21/35	0.276428054793122	1	FACETS	0.54	0.458	0.631	0.54	0.458	0.631	SUBCLONAL	1	TRUE	0	0.322268951729947	1		549	472	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741603	17741603	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749172312	NA	P-0035162-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	109	462	0	ENST00000250003.3:c.274C>T	p.Arg92Cys	p.R92C	ENST00000250003	NM_002478.4	92	Cgc/Tgc	1/3	0.322268951729947	11	FACETS	1	0.972	1			1	CLONAL	1	TRUE	NA	0.322268951729947	11		462	1320	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470574	25470575	+	missense_variant	Missense_Mutation	DNP	CA	CA	AC	novel	NA	P-0035665-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	10	1201	1	ENST00000264709.3:c.899_900delinsGT	p.Leu300Arg	p.L300R	ENST00000264709	NM_175629.2	300	cTG/cGT	8/23	1	2	FACETS	0.404	0.276	0.562	0.404	0.276	0.562	SUBCLONAL	1	TRUE	1	0.51	2		1202	97	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476265	88476265	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035767-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	150	698	2	ENST00000360948.2:c.1867G>A	p.Gly623Arg	p.G623R	ENST00000360948	NM_001012338.2	623	Gga/Aga	15/19	0.409533774510685	6	FACETS	1	0.958	1			1	CLONAL	1	TRUE	NA	0.561371920750564	6		700	1048	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724805	43724805	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs975712435	NA	P-0035767-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	189	769	0	ENST00000382044.4:c.3262A>G	p.Ile1088Val	p.I1088V	ENST00000382044	NM_001141980.1	1088	Atc/Gtc	17/28	0.561084213530928	3	FACETS	0.954	0.882	1	0.318	0.294	0.343	CLONAL	1	TRUE	0	0.561371920750564	3		769	904	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	172	367	8	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.59713346127393	2		375	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	383	51	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.59713346127393	2		51	957	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	450	392	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.865	0.841	0.888	1	0.998	1	CLONAL	3	TRUE	1	0.59713346127393	2		392	581	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775955	9775955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	402	795	0	ENST00000377346.4:c.419G>A	p.Arg140His	p.R140H	ENST00000377346	NM_005026.3	140	cGc/cAc	5/24	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.59713346127393	2		795	953	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780920	9780920	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780269932	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	416	843	0	ENST00000377346.4:c.1642C>T	p.Arg548Trp	p.R548W	ENST00000377346	NM_005026.3	548	Cgg/Tgg	13/24	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.59713346127393	2		843	1032	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303646	65303646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	332	640	0	ENST00000342505.4:c.3109G>A	p.Val1037Ile	p.V1037I	ENST00000342505	NM_002227.2	1037	Gtc/Atc	22/25	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.59713346127393	2		640	830	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468127	120468127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745861610	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	433	765	0	ENST00000256646.2:c.4312G>A	p.Val1438Ile	p.V1438I	ENST00000256646	NM_024408.3	1438	Gtc/Atc	25/34	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.59713346127393	2		765	975	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710595	114710597	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs754968616	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	262	531	0	ENST00000543371.1:c.85_87del	p.Glu29del	p.E29del	ENST00000543371	NM_001198531.1	27	cAGGag/cag	1/14	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.59713346127393	2		531	660	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533467	533467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894231	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	871	884	3	ENST00000451590.1:c.436G>A	p.Ala146Thr	p.A146T	ENST00000451590	NM_001130442.1	146	Gcc/Acc	4/5	1	2	FACETS	0.968	0.942	0.993	1	0.998	1	CLONAL	2	TRUE	1	0.59713346127393	2		887	1507	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572230	64572230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750112288	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	384	669	0	ENST00000312049.6:c.1409C>T	p.Pro470Leu	p.P470L	ENST00000312049	NM_130799.2	470	cCg/cTg	10/10	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.59713346127393	2		669	859	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198852	67198852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs185889430	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	291	436	0	ENST00000312629.5:c.323G>A	p.Arg108His	p.R108H	ENST00000312629	NM_003952.2	108	cGc/cAc	5/15	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.59713346127393	2		436	652	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342866	118342866	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148514018	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	186	293	0	ENST00000534358.1:c.992G>A	p.Arg331Gln	p.R331Q	ENST00000534358	NM_005933.3	331	cGg/cAg	3/36	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.59713346127393	2		293	491	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392858	118392858	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781866935	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	283	484	1	ENST00000534358.1:c.11890G>A	p.Ala3964Thr	p.A3964T	ENST00000534358	NM_005933.3	3964	Gcc/Acc	36/36	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.59713346127393	2		485	660	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514032	125514032	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	306	495	0	ENST00000428830.2:c.970G>T	p.Gly324Cys	p.G324C	ENST00000428830	NM_001114121.2	324	Ggt/Tgt	10/14	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.59713346127393	2		495	795	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644468	21644468	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754016839	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	262	411	1	ENST00000421138.2:c.199G>A	p.Ala67Thr	p.A67T	ENST00000421138		67	Gct/Act	4/16	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.59713346127393	2		412	613	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418462	49418463	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	372	696	1	ENST00000301067.7:c.15950_15951del	p.Tyr5317PhefsTer27	p.Y5317Ffs*27	ENST00000301067	NM_003482.3	5317	tAT/t	50/54	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.59713346127393	2		697	948	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424087	49424087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs558561472	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	430	807	0	ENST00000301067.7:c.13975C>T	p.Arg4659Trp	p.R4659W	ENST00000301067	NM_003482.3	4659	Cgg/Tgg	42/54	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.59713346127393	2		807	1034	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447773	49447773	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	283	94	0	ENST00000301067.7:c.661del	p.Ala221LeufsTer40	p.A221Lfs*40	ENST00000301067	NM_003482.3	221	Gct/ct	5/54	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.59713346127393	2		94	738	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218787	133218787	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	386	678	0	ENST00000320574.5:c.5149A>G	p.Asn1717Asp	p.N1717D	ENST00000320574	NM_006231.2	1717	Aac/Gac	38/49	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.59713346127393	2		678	891	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610281	81610281	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	296	471	1	ENST00000298171.2:c.1879G>T	p.Ala627Ser	p.A627S	ENST00000298171	NM_000369.2	627	Gct/Tct	10/10	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.59713346127393	2		472	726	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041774	42041774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773653972	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	261	436	0	ENST00000219905.7:c.5969C>T	p.Thr1990Met	p.T1990M	ENST00000219905	NM_001164273.1	1990	aCg/aTg	17/24	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.59713346127393	2		436	620	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724658	43724658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755481776	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	350	805	1	ENST00000382044.4:c.3409C>T	p.Arg1137Trp	p.R1137W	ENST00000382044	NM_001141980.1	1137	Cgg/Tgg	17/28	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.59713346127393	2		806	919	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	280	449	8	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.59713346127393	2		457	747	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346157	89346158	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs878855327	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	172	530	1	ENST00000301030.4:c.6792dup	p.Ala2265ArgfsTer8	p.A2265Rfs*8	ENST00000301030	NM_001256183.1	2264	-/C	9/13	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.59713346127393	2		531	571	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347744	89347744	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	406	832	0	ENST00000301030.4:c.5206G>A	p.Val1736Met	p.V1736M	ENST00000301030	NM_001256183.1	1736	Gtg/Atg	9/13	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.59713346127393	2		832	959	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348439	89348439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	471	901	0	ENST00000301030.4:c.4511C>T	p.Thr1504Ile	p.T1504I	ENST00000301030	NM_001256183.1	1504	aCc/aTc	9/13	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.59713346127393	2		901	1179	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351632	89351632	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	407	735	0	ENST00000301030.4:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000301030	NM_001256183.1	440	Cga/Tga	9/13	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.59713346127393	2		735	1020	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805603	89805603	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201225325	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	440	806	1	ENST00000389301.3:c.4105G>A	p.Val1369Met	p.V1369M	ENST00000389301	NM_000135.2	1369	Gtg/Atg	41/43	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.59713346127393	2		807	1051	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	422	847	0	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.59713346127393	2		847	1098	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979987	7979987	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746723399	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	378	774	0	ENST00000319144.4:c.1350del	p.Leu451SerfsTer16	p.L451Sfs*16	ENST00000319144	NM_001139.2	450	ggG/gg	10/15	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.59713346127393	2		774	946	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968825	15968825	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	305	491	0	ENST00000268712.3:c.4925T>C	p.Leu1642Pro	p.L1642P	ENST00000268712	NM_006311.3	1642	cTg/cCg	33/46	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.59713346127393	2		491	756	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896536	78896536	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770010373	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	427	922	2	ENST00000306801.3:c.2533G>A	p.Ala845Thr	p.A845T	ENST00000306801	NM_020761.2	845	Gcc/Acc	22/34	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.59713346127393	2		924	1049	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400688	56400688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140664950	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	207	399	1	ENST00000348428.3:c.1282G>A	p.Val428Ile	p.V428I	ENST00000348428	NM_006785.3	428	Gtt/Att	11/17	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.59713346127393	2		400	547	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172389	7172389	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	325	539	0	ENST00000302850.5:c.1180T>C	p.Tyr394His	p.Y394H	ENST00000302850	NM_000208.2	394	Tat/Cat	5/22	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.59713346127393	2		539	810	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145662	11145662	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770839933	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	495	877	0	ENST00000358026.2:c.4024G>A	p.Glu1342Lys	p.E1342K	ENST00000358026	NM_001128849.1	1342	Gag/Aag	29/36	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.59713346127393	2		877	1122	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	486	1294	6	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.59713346127393	2		1300	1288	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791591	42791592	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	372	725	0	ENST00000575354.2:c.576dup	p.Asn193GlnfsTer122	p.N193Qfs*122	ENST00000575354	NM_015125.3	191	agc/agCc	4/20	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.59713346127393	2		725	946	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793484	42793484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780297917	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	411	775	1	ENST00000575354.2:c.1286C>T	p.Ala429Val	p.A429V	ENST00000575354	NM_015125.3	429	gCg/gTg	8/20	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.59713346127393	2		776	1073	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856370	45856370	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140522180	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	448	870	0	ENST00000391945.4:c.1802G>A	p.Arg601Gln	p.R601Q	ENST00000391945	NM_000400.3	601	cGg/cAg	19/23	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.59713346127393	2		870	1032	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543746	29543747	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	217	423	0	ENST00000389048.3:c.1416dup	p.Lys473GlufsTer11	p.K473Efs*11	ENST00000389048	NM_004304.4	472	-/G	7/29	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.59713346127393	2		423	591	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607645	46607645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142445582	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	443	921	0	ENST00000263734.3:c.1834G>A	p.Gly612Arg	p.G612R	ENST00000263734	NM_001430.4	612	Gga/Aga	12/16	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.59713346127393	2		921	1080	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635617	47635617	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750970	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	323	475	0	ENST00000233146.2:c.289C>T	p.Gln97Ter	p.Q97*	ENST00000233146	NM_000251.2	97	Cag/Tag	2/16	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.59713346127393	2		475	807	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023544	31023544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs116112525	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	300	599	0	ENST00000375687.4:c.3029C>T	p.Thr1010Met	p.T1010M	ENST00000375687	NM_015338.5	1010	aCg/aTg	13/13	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.59713346127393	2		599	724	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62320928	62320928	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773159241	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	546	985	1	ENST00000360203.5:c.1952G>A	p.Arg651His	p.R651H	ENST00000360203	NM_001283009.1	651	cGc/cAc	23/35	1	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	1	0.59713346127393	2		986	1230	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164475	36164475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1442794209	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	233	444	0	ENST00000300305.3:c.1400C>T	p.Ala467Val	p.A467V	ENST00000300305		467	gCg/gTg	8/8	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.59713346127393	2		444	563	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691872	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs79375991	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	345	397	15	ENST00000295754.5:c.383del	p.Lys128SerfsTer35	p.K128Sfs*35	ENST00000295754	NM_003242.5	125	gAa/ga	3/7	1	2	FACETS	1	0.987	1	1	0.997	1	CLONAL	2	TRUE	1	0.59713346127393	2		412	545	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928509	69928509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs190215588	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	418	782	0	ENST00000352241.4:c.329C>T	p.Thr110Met	p.T110M	ENST00000352241	NM_198159.2	110	aCg/aTg	2/10	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.59713346127393	2		782	1082	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890203	72890203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758931723	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	217	409	1	ENST00000325599.8:c.479G>A	p.Arg160Gln	p.R160Q	ENST00000325599	NM_018130.2	160	cGg/cAg	4/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.59713346127393	2		410	601	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911508	134911508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201816783	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	325	576	3	ENST00000398015.3:c.1973C>T	p.Ser658Leu	p.S658L	ENST00000398015	NM_004441.4	658	tCg/tTg	11/16	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.59713346127393	2		579	804	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161379	185161379	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	243	535	0	ENST00000265026.3:c.806A>G	p.Tyr269Cys	p.Y269C	ENST00000265026	NM_004721.4	269	tAt/tGt	4/14	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.59713346127393	2		535	733	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106182996	106182996	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	125	249	0	ENST00000380013.4:c.4035T>A	p.Tyr1345Ter	p.Y1345*	ENST00000380013	NM_001127208.2	1345	taT/taA	8/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.59713346127393	2		249	298	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007332	143007332	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	209	274	0	ENST00000262992.4:c.2452del	p.Arg818GlufsTer4	p.R818Efs*4	ENST00000262992	NM_001101669.1	818	Aga/ga	22/24	0.59713346127393	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.59713346127393	1		274	378	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244137	153244137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140856583	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	373	529	0	ENST00000281708.4:c.2020C>T	p.Arg674Trp	p.R674W	ENST00000281708	NM_033632.3	674	Cgg/Tgg	12/12	0.59713346127393	1	FACETS	0.81	0.782	0.838	1	0.997	1	CLONAL	2	TRUE	0	0.59713346127393	1		529	541	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628542	187628542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157383372	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	36	739	0	ENST00000441802.2:c.2440G>A	p.Asp814Asn	p.D814N	ENST00000441802	NM_005245.3	814	Gat/Aat	2/27	0.59713346127393	1	FACETS	0.133	0.108	0.16	0.133	0.108	0.16	SUBCLONAL	1	TRUE	0	0.59713346127393	1		739	638	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189412	56189412	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	338	600	0	ENST00000399503.3:c.4444C>T	p.Arg1482Ter	p.R1482*	ENST00000399503	NM_005921.1	1482	Cga/Tga	20/20	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.59713346127393	2		600	814	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939040	131939040	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	188	327	0	ENST00000265335.6:c.2256C>A	p.Asn752Lys	p.N752K	ENST00000265335		752	aaC/aaA	14/25	0.144517148904516	4	FACETS	0.853	0.8	0.906	1	0.989	1	INDETERMINATE	3	TRUE	2	0.59713346127393	4		327	393	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394902	394902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767879003	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	330	559	0	ENST00000380956.4:c.298G>A	p.Ala100Thr	p.A100T	ENST00000380956	NM_001195286.1	100	Gct/Act	3/9	0.176204492573632	3	FACETS	0.968	0.921	1	0.968	0.921	1	INDETERMINATE	2	TRUE	1	0.59713346127393	3		559	741	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202351	138202351	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	50	596	1	ENST00000237289.4:c.2274del	p.Lys759SerfsTer57	p.K759Sfs*57	ENST00000237289	NM_001270507.1	756	gaC/ga	9/9	1	2	FACETS	0.196	0.166	0.23	0.196	0.166	0.23	SUBCLONAL	1	TRUE	1	0.59713346127393	2		597	853	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502280	157502280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775526039	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	328	645	2	ENST00000346085.5:c.3313G>A	p.Val1105Ile	p.V1105I	ENST00000346085	NM_020732.3	1105	Gtc/Atc	12/20	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.59713346127393	2		647	851	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528397	157528397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375017809	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	386	704	0	ENST00000346085.5:c.6122C>T	p.Thr2041Met	p.T2041M	ENST00000346085	NM_020732.3	2041	aCg/aTg	20/20	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.59713346127393	2		704	972	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953011	2953011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1172378918	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	457	794	1	ENST00000396946.4:c.2929G>A	p.Val977Met	p.V977M	ENST00000396946	NM_032415.4	977	Gtg/Atg	22/25	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.59713346127393	2		795	1103	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738648	145738648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767102398	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	417	938	2	ENST00000428558.2:c.2416G>A	p.Gly806Arg	p.G806R	ENST00000428558	NM_004260.3	806	Ggg/Agg	15/22	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.59713346127393	2		940	1127	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341730	8341730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41281783	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	310	561	2	ENST00000356435.5:c.4910C>T	p.Thr1637Met	p.T1637M	ENST00000356435		1637	aCg/aTg	29/35	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.59713346127393	2		563	738	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020764	37020764	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	314	621	5	ENST00000358127.4:c.81del	p.Phe27LeufsTer2	p.F27Lfs*2	ENST00000358127	NM_001280556.1	27	ttT/tt	2/10	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.59713346127393	2		626	833	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336379	80336379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	198	495	0	ENST00000286548.4:c.940G>A	p.Val314Met	p.V314M	ENST00000286548	NM_002072.3	314	Gtg/Atg	7/7	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.59713346127393	2		495	542	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209616	98209617	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761353734	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	166	737	1	ENST00000331920.6:c.3921dup	p.Arg1308GlnfsTer17	p.R1308Qfs*17	ENST00000331920	NM_000264.3	1307	-/C	23/24	1	2	FACETS	0.656	0.603	0.711	0.656	0.603	0.711	SUBCLONAL	1	TRUE	1	0.59713346127393	2		738	848	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399471	139399471	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751810380	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	556	940	0	ENST00000277541.6:c.4672G>A	p.Gly1558Arg	p.G1558R	ENST00000277541	NM_017617.3	1558	Ggg/Agg	26/34	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.59713346127393	2		940	1332	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913577	39913577	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	244	396	0	ENST00000378444.4:c.4751A>G	p.Asn1584Ser	p.N1584S	ENST00000378444	NM_001123385.1	1584	aAt/aGt	13/15	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.59713346127393	2		396	571	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969405	44969405	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	286	567	0	ENST00000377967.4:c.4087C>T	p.Arg1363Ter	p.R1363*	ENST00000377967	NM_021140.2	1363	Cga/Tga	28/29	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.59713346127393	2		567	755	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028805	47028805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	415	818	0	ENST00000377604.3:c.109C>T	p.Arg37Trp	p.R37W	ENST00000377604	NM_001204468.1	37	Cgg/Tgg	3/24	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.59713346127393	2		818	1028	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426043	47426043	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777037087	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	406	770	0	ENST00000377045.4:c.563G>A	p.Arg188His	p.R188H	ENST00000377045	NM_001654.4	188	cGc/cAc	7/16	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.59713346127393	2		770	928	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020768	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs926053251	NA	P-0036564-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	27	600	1	ENST00000358127.4:c.77T>G	p.Val26Gly	p.V26G	ENST00000358127	NM_001280556.1	26	gTt/gGt	2/10	1	2	FACETS	0.114	0.09	0.142	0.114	0.09	0.142	SUBCLONAL	1	TRUE	1	0.59713346127393	2		601	793	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0037701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	381	963	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.965198577641225	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.965198577641225	1		966	396	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521487	8521487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758577045	NA	P-0037701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	352	594	1	ENST00000356435.5:c.751G>A	p.Gly251Arg	p.G251R	ENST00000356435		251	Gga/Aga	9/35	1	2	FACETS	0.986	0.94	1	0.986	0.94	1	CLONAL	1	TRUE	1	0.965198577641225	2		595	740	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40371842	40371842	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	375	776	0	ENST00000293328.3:c.569C>T	p.Ala190Val	p.A190V	ENST00000293328	NM_012448.3	190	gCc/gTc	6/19	1	2	FACETS	0.973	0.929	1	0.973	0.929	1	CLONAL	1	TRUE	1	0.965198577641225	2		776	799	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39317430	39317430	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0037701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	242	472	0	ENST00000373001.3:c.757-1G>T		p.X253_splice	ENST00000373001	NM_022157.3	253			1	2	FACETS	0.936	0.883	0.989	0.936	0.883	0.989	CLONAL	1	TRUE	1	0.965198577641225	2		472	536	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688815	47688815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	236	368	0	ENST00000347630.2:c.485G>A	p.Ser162Asn	p.S162N	ENST00000347630	NM_001007230.1	162	aGt/aAt	7/11	1	2	FACETS	0.963	0.908	1	0.963	0.908	1	CLONAL	1	TRUE	1	0.965198577641225	2		368	508	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025621	1025621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763842232	NA	P-0037834-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	121	655	0	ENST00000358495.3:c.754G>A	p.Glu252Lys	p.E252K	ENST00000358495	NM_134424.2	252	Gag/Aag	9/12	NA	2	FACETS	1	0.921	1			1	INDETERMINATE	1	TRUE	NA	0.404274674737951	2		655	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577148	7577148	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1060501194	NA	P-0037834-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	201	648	0	ENST00000269305.4:c.790del	p.Leu264TyrfsTer81	p.L264Yfs*81	ENST00000269305	NM_001126112.2	264	Cta/ta	8/11	0.402398589578484	2	FACETS	0.888	0.829	0.948	0.888	0.829	0.948	CLONAL	2	TRUE	0	0.404274674737951	2		648	560	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346246	89346246	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1394383095	NA	P-0037834-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	179	432	0	ENST00000301030.4:c.6704C>T	p.Pro2235Leu	p.P2235L	ENST00000301030	NM_001256183.1	2235	cCg/cTg	9/13	0.402398589578484	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.404274674737951	2		432	396	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799518	72799518	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037834-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	157	689	0	ENST00000325599.8:c.1651C>A	p.Gln551Lys	p.Q551K	ENST00000325599	NM_018130.2	551	Cag/Aag	11/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.404274674737951	2		689	667	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265469	152265469	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038005-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	212	677	0	ENST00000206249.3:c.922T>G	p.Leu308Val	p.L308V	ENST00000206249	NM_000125.3	308	Ttg/Gtg	4/8	1	2	FACETS	0.967	0.903	1	0.967	0.903	1	CLONAL	1	TRUE	1	0.637022684719565	2		677	688	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874521	151874521	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	320	110	0	ENST00000262189.6:c.8017G>C	p.Asp2673His	p.D2673H	ENST00000262189	NM_170606.2	2673	Gat/Cat	38/59	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	2	TRUE	NA	0.492311941530961	2		110	639	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95579502	95579502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766707302	NA	P-0038853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	312	86	0	ENST00000393063.1:c.1967G>A	p.Arg656Gln	p.R656Q	ENST00000393063	NM_030621.3	656	cGa/cAa	13/28	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.492311941530961	2		86	577	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040533-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	102	375	0				ENST00000310581	NM_198253.2	-/1132			0.312652935361125	1	FACETS	0.805	0.726	0.888	0.805	0.726	0.888	CLONAL	1	TRUE	0	0.489517935898003	1		375	391	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398917	398917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356308443	NA	P-0040533-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	153	597	0	ENST00000380956.4:c.727G>A	p.Glu243Lys	p.E243K	ENST00000380956	NM_001195286.1	243	Gaa/Aaa	6/9	1	2	FACETS	0.95	0.872	1	0.95	0.872	1	CLONAL	1	TRUE	1	0.489517935898003	2		597	658	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682991	241682991	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1226883651	NA	P-0040533-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	155	678	0	ENST00000366560.3:c.32C>G	p.Ser11Trp	p.S11W	ENST00000366560	NM_000143.3	11	tCg/tGg	1/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.489517935898003	2		678	603	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224531	108224531	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040533-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	68	296	0	ENST00000278616.4:c.8710G>C	p.Glu2904Gln	p.E2904Q	ENST00000278616	NM_000051.3	2904	Gag/Cag	60/63	0.483140271144042	1	FACETS	0.916	0.809	1	0.916	0.809	1	CLONAL	1	TRUE	0	0.489517935898003	1		296	229	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871196	35871196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773491081	NA	P-0040533-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	29	332	0	ENST00000303115.3:c.418C>T	p.Arg140Trp	p.R140W	ENST00000303115	NM_002185.3	140	Cgg/Tgg	4/8	0.312652935361125	1	FACETS	0.358	0.288	0.436	0.358	0.288	0.436	SUBCLONAL	1	TRUE	0	0.489517935898003	1		332	250	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511637	46511637	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040533-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	36	434	0	ENST00000262741.5:c.1140C>G	p.Phe380Leu	p.F380L	ENST00000262741	NM_003629.3	380	ttC/ttG	9/10	0.206833707975529	1	FACETS	0.273	0.224	0.327	0.273	0.224	0.327	INDETERMINATE	1	TRUE	0	0.489517935898003	1		434	407	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106271	27106302	+	frameshift_variant	Frame_Shift_Del	DEL	GTAAGGATGAGACCCCACTGTGTACCCTTCTG	GTAAGGATGAGACCCCACTGTGTACCCTTCTG	-	novel	NA	P-0040533-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	135	651	0	ENST00000324856.7:c.5883_5914del	p.Ser1961ArgfsTer27	p.S1961Rfs*27	ENST00000324856	NM_006015.4	1961	aGTAAGGATGAGACCCCACTGTGTACCCTTCTG/a	20/20	0.483140271144042	1	FACETS	0.84	0.768	0.914	0.84	0.768	0.914	CLONAL	1	TRUE	0	0.489517935898003	1		651	496	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983018	201983019	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040533-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	495	924	0	ENST00000359651.3:c.868dup	p.Glu290GlyfsTer11	p.E290Gfs*11	ENST00000359651		289	-/G	7/8	0.455820997579186	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.489517935898003	3		924	1259	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432341	432341	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040533-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	64	376	0	ENST00000399788.2:c.2182C>G	p.Leu728Val	p.L728V	ENST00000399788	NM_001042603.1	728	Ctg/Gtg	16/28	NA	2	FACETS	0.83	0.724	0.943			1	INDETERMINATE	1	TRUE	NA	0.489517935898003	2		376	315	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864474	57864474	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040533-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	168	884	0	ENST00000228682.2:c.1951C>G	p.Pro651Ala	p.P651A	ENST00000228682	NM_005269.2	651	Cca/Gca	12/12	1	2	FACETS	0.835	0.768	0.905	0.835	0.768	0.905	CLONAL	1	TRUE	1	0.489517935898003	2		884	822	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355171	15355171	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040533-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	249	1084	0	ENST00000263377.2:c.2452G>C	p.Asp818His	p.D818H	ENST00000263377	NM_058243.2	818	Gac/Cac	13/20	1	2	FACETS	0.906	0.847	0.967	0.906	0.847	0.967	CLONAL	1	TRUE	1	0.489517935898003	2		1084	1123	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582062	189582062	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040533-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	136	420	0	ENST00000264731.3:c.621G>C	p.Lys207Asn	p.K207N	ENST00000264731	NM_003722.4	207	aaG/aaC	5/14	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.489517935898003	2		420	545	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280127	66280127	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040533-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	78	256	0	ENST00000273854.3:c.1562A>C	p.Lys521Thr	p.K521T	ENST00000273854	NM_004439.5	521	aAa/aCa	7/18	0.483140271144042	1	FACETS	0.999	0.891	1	0.999	0.891	1	CLONAL	1	TRUE	0	0.489517935898003	1		256	241	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29913230	29913230	+	stop_lost,splice_region_variant	Nonstop_Mutation	SNP	T	T	G	novel	NA	P-0040533-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	134	478	0	ENST00000376809.5:c.1096T>G	p.Ter366GlyextTer8	p.*366Gext*8	ENST00000376809	NM_002116.7	366	Tga/Gga	8/8	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.489517935898003	2		478	502	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040540-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	63	375	0				ENST00000310581	NM_198253.2	-/1132			0.281427150020751	3	FACETS	0.757	0.665	0.855	0.757	0.665	0.855	INDETERMINATE	2	TRUE	1	0.471539793523782	3		375	218	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235329	235329	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749309213	NA	P-0040540-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	206	673	0	ENST00000264932.6:c.1135C>T	p.Arg379Cys	p.R379C	ENST00000264932	NM_004168.2	379	Cgc/Tgc	9/15	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.471539793523782	2		673	645	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999059	100999059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040540-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	120	481	0	ENST00000325455.5:c.743C>T	p.Ala248Val	p.A248V	ENST00000325455	NM_001202474.3	248	gCg/gTg	1/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.471539793523782	2		481	436	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720807	89720822	+	frameshift_variant	Frame_Shift_Del	DEL	TTAACAAAAAATGATC	TTAACAAAAAATGATC	-	novel	NA	P-0040540-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	126	285	0	ENST00000371953.3:c.960_975del	p.Asn323GlnfsTer16	p.N323Qfs*16	ENST00000371953	NM_000314.4	320	TTAACAAAAAATGATCtt/tt	8/9	0.459580734279777	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.471539793523782	1		285	310	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012904	176012904	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040540-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	82	476	0	ENST00000367669.3:c.1472A>G	p.Tyr491Cys	p.Y491C	ENST00000367669	NM_022457.5	491	tAt/tGt	13/20	0.395135652133922	2	FACETS	0.528	0.465	0.595	0.264	0.232	0.298	SUBCLONAL	1	TRUE	0	0.471539793523782	2		476	659	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157422	106157422	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1027662002	NA	P-0040540-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	34	334	0	ENST00000380013.4:c.2323T>C	p.Phe775Leu	p.F775L	ENST00000380013	NM_001127208.2	775	Ttc/Ctc	3/11	1	2	FACETS	0.3	0.244	0.362	0.3	0.244	0.362	SUBCLONAL	1	TRUE	1	0.471539793523782	2		334	481	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040976-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	156	375	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.996	0.925	1	0.996	0.925	1	CLONAL	1	TRUE	1	0.857990860921986	2		375	365	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0040976-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25934	2953	800	1	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.857990860921986	24	FACETS	1	0.998	1	0.104	0.101	0.106	CLONAL	2	TRUE	0	0.857990860921986	24		801	28887	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0040976-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17419	3437	463	1	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.857990860921986	24	FACETS	1	0.983	1	0.167	0.164	0.171	CLONAL	4	TRUE	0	0.857990860921986	24		464	20856	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772950	135772951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs118203724	NA	P-0040976-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	168	365	0	ENST00000298552.3:c.2672dup	p.Asn891LysfsTer13	p.N891Kfs*13	ENST00000298552	NM_001162426.1	891	aac/aaAc	21/23	1	2	FACETS	0.72	0.666	0.775	0.72	0.666	0.775	SUBCLONAL	1	TRUE	1	0.857990860921986	2		365	544	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0041169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	280	603	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.515870856916487	3	FACETS	0.959	0.906	1	0.959	0.906	1	CLONAL	2	TRUE	1	0.515870856916487	3		603	712	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0041169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	495	963	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.515870856916487	2	FACETS	0.985	0.948	1	0.985	0.948	1	CLONAL	2	TRUE	0	0.515870856916487	2		966	974	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0041169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	253	434	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.515870856916487	2	FACETS	0.915	0.865	0.965	0.915	0.865	0.965	CLONAL	2	TRUE	0	0.515870856916487	2		434	536	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0041169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	204	380	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.515870856916487	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.515870856916487	2		380	374	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	125	507	0	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	1	2	FACETS	0.936	0.851	1	0.936	0.851	1	CLONAL	1	TRUE	1	0.515870856916487	2		507	518	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44894229	44894232	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	AAGT	AAGT	-	novel	NA	P-0041169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	127	242	0	ENST00000377967.4:c.619+4_619+7del		p.X207_splice	ENST00000377967	NM_021140.2	207		7/29	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.515870856916487	1		242	256	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024130	112024130	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	116	568	0	ENST00000368678.4:c.655G>T	p.Ala219Ser	p.A219S	ENST00000368678		219	Gcc/Tcc	7/13	1	2	FACETS	0.805	0.728	0.885	0.805	0.728	0.885	CLONAL	1	TRUE	1	0.515870856916487	2		568	559	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52649459	52649459	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	145	506	0	ENST00000394830.3:c.1832C>A	p.Ala611Glu	p.A611E	ENST00000394830	NM_018313.4	611	gCa/gAa	16/30	0.515870856916487	1	FACETS	0.88	0.809	0.953	0.88	0.809	0.953	CLONAL	1	TRUE	0	0.515870856916487	1		506	474	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041988-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	62	375	0				ENST00000310581	NM_198253.2	-/1132			0.161683622672129	4	FACETS	0.792	0.686	0.907	0.792	0.686	0.907	CLONAL	2	FALSE	2	0.206640894685685	4		375	457	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0041988-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	137	791	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.161683622672129	4	FACETS	1	0.985	1	0.729	0.662	0.8	CLONAL	1	FALSE	2	0.206640894685685	4		791	1097	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048638	6048638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041988-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	116	889	0	ENST00000265849.7:c.13G>A	p.Glu5Lys	p.E5K	ENST00000265849	NM_000535.5	5	Gag/Aag	1/15	0.206640894685685	4	FACETS	1	0.978	1	0.658	0.591	0.728	CLONAL	1	FALSE	2	0.206640894685685	4		889	1030	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041988-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	47	340	0	ENST00000335508.6:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000335508	NM_012433.2	902	Gaa/Aaa	18/25	0.206640894685685	3	FACETS	0.804	0.682	0.938	0.804	0.682	0.938	CLONAL	2	FALSE	1	0.206640894685685	3		340	312	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879925	44879925	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs189751539	NA	P-0041988-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	69	469	0	ENST00000377967.4:c.514C>T	p.Arg172Ter	p.R172*	ENST00000377967	NM_021140.2	172	Cga/Tga	6/29	0.206640894685685	2	FACETS	1	0.918	1			1	CLONAL	2	FALSE	NA	0.206640894685685	2		469	315	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109887	115109887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762342872	NA	P-0041988-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	45	787	0	ENST00000257566.3:c.1991C>T	p.Ala664Val	p.A664V	ENST00000257566	NM_016569.3	664	gCg/gTg	8/8	1	2	FACETS	0.607	0.509	0.717	0.607	0.509	0.717	SUBCLONAL	1	FALSE	1	0.206640894685685	2		787	717	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158439	108158439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041988-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	33	374	0	ENST00000278616.4:c.4106C>T	p.Ser1369Leu	p.S1369L	ENST00000278616	NM_000051.3	1369	tCa/tTa	27/63	0.206640894685685	3	FACETS	0.995	0.812	1	0.498	0.406	0.601	CLONAL	1	FALSE	1	0.206640894685685	3		374	354	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435180	18435180	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041988-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	19	322	0	ENST00000266497.5:c.165G>C	p.Glu55Asp	p.E55D	ENST00000266497		55	gaG/gaC	1/31	0.206640894685685	4	FACETS	0.874	0.664	1	0.437	0.332	0.56	CLONAL	1	FALSE	2	0.206640894685685	4		322	254	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032225	26032225	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041988-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	72	439	2	ENST00000244661.2:c.64G>T	p.Ala22Ser	p.A22S	ENST00000244661	NM_003537.3	22	Gct/Tct	1/1	0.206640894685685	9	FACETS	1	0.931	1	0.439	0.384	0.498	CLONAL	2	FALSE	4	0.206640894685685	9		441	547	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042591-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	54	375	0				ENST00000310581	NM_198253.2	-/1132			0.160100259003956	4	FACETS	1	0.943	1	0.599	0.515	0.69	INDETERMINATE	1	TRUE	2	0.40456373204236	4		375	313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057520000	NA	P-0042591-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	233	1078	0	ENST00000269305.4:c.452C>G	p.Pro151Arg	p.P151R	ENST00000269305	NM_001126112.2	151	cCc/cGc	5/11	0.40456373204236	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.40456373204236	1		1078	796	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033206	69033206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1344491711	NA	P-0042591-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	59	635	1	ENST00000288368.4:c.3646C>T	p.Leu1216Phe	p.L1216F	ENST00000288368	NM_024870.2	1216	Ctt/Ttt	30/40	0.40456373204236	1	FACETS	0.471	0.406	0.542	0.471	0.406	0.542	SUBCLONAL	1	TRUE	0	0.40456373204236	1		636	494	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121082	11121082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042591-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	146	913	0	ENST00000358026.2:c.2149G>A	p.Glu717Lys	p.E717K	ENST00000358026	NM_001128849.1	717	Gaa/Aaa	15/36	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.40456373204236	2		913	614	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209101872	209101872	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042591-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	50	444	0	ENST00000345146.2:c.1176G>C	p.Leu392Phe	p.L392F	ENST00000345146	NM_005896.2	392	ttG/ttC	10/10	NA	2	FACETS	0.564	0.479	0.657			1	INDETERMINATE	1	TRUE	NA	0.40456373204236	2		444	438	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586432	189586432	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042591-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	135	541	0	ENST00000264731.3:c.1056G>C	p.Arg352Ser	p.R352S	ENST00000264731	NM_003722.4	352	agG/agC	8/14	0.160100259003956	4	FACETS	0.851	0.777	0.927	0.851	0.777	0.927	INDETERMINATE	2	TRUE	2	0.40456373204236	4		541	551	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295171	1295171	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0042591-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	63	267	0				ENST00000310581	NM_198253.2	-/1132			0.160100259003956	4	FACETS	1	0.97	1	0.724	0.631	0.823	INDETERMINATE	1	TRUE	2	0.40456373204236	4		267	302	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754642	42754642	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042591-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	60	923	0	ENST00000222329.4:c.98T>C	p.Ile33Thr	p.I33T	ENST00000222329	NM_006494.2	33	aTc/aCc	2/4	0.40456373204236	1	FACETS	0.414	0.356	0.476	0.414	0.356	0.476	SUBCLONAL	1	TRUE	0	0.40456373204236	1		923	572	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376297	225376297	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042591-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	28	342	0	ENST00000264414.4:c.657G>A	p.Met219Ile	p.M219I	ENST00000264414	NM_003590.4	219	atG/atA	6/16	0.40456373204236	1	FACETS	0.491	0.394	0.599	0.491	0.394	0.599	SUBCLONAL	1	TRUE	0	0.40456373204236	1		342	225	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0042642-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	11	108	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	1	2	FACETS	0.13	0.089	0.181	0.13	0.089	0.181	SUBCLONAL	1	TRUE	1	0.48	2		108	353	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092809	27092809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042642-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	145	557	1	ENST00000324856.7:c.2830C>T	p.Gln944Ter	p.Q944*	ENST00000324856	NM_006015.4	944	Cag/Tag	9/20	1	2	FACETS	0.909	0.831	0.989	0.909	0.831	0.989	CLONAL	1	TRUE	1	0.48	2		558	665	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922321	178922321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042642-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	16	423	0	ENST00000263967.3:c.1090G>A	p.Gly364Arg	p.G364R	ENST00000263967	NM_006218.2	364	Gga/Aga	6/21	1	2	FACETS	0.129	0.095	0.171	0.129	0.095	0.171	SUBCLONAL	1	TRUE	1	0.48	2		423	516	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788618	3788618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398124146	NA	P-0042642-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	8	493	0	ENST00000262367.5:c.4336C>T	p.Arg1446Cys	p.R1446C	ENST00000262367	NM_004380.2	1446	Cgc/Tgc	26/31	1	2	FACETS	0.085	0.054	0.126	0.085	0.054	0.126	SUBCLONAL	1	TRUE	1	0.48	2		493	390	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0042642-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	157	16	1	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.48	2		17	606	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433005	49433005	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1208681909	NA	P-0042642-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	43	709	0	ENST00000301067.7:c.8366G>A	p.Arg2789Gln	p.R2789Q	ENST00000301067	NM_003482.3	2789	cGg/cAg	33/54	0.134305246890273	4	FACETS	0.52	0.435	0.614	0.26	0.217	0.307	INDETERMINATE	1	TRUE	2	0.48	4		709	510	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300836	137300836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042642-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	152	896	3	ENST00000481739.1:c.481C>T	p.Arg161Trp	p.R161W	ENST00000481739	NM_002957.4	161	Cgg/Tgg	4/10	1	2	FACETS	0.89	0.815	0.967	0.89	0.815	0.967	CLONAL	1	TRUE	1	0.48	2		899	712	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100129	27100129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042642-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	155	692	0	ENST00000324856.7:c.3925C>T	p.Leu1309Phe	p.L1309F	ENST00000324856	NM_006015.4	1309	Ctc/Ttc	16/20	1	2	FACETS	0.931	0.854	1	0.931	0.854	1	CLONAL	1	TRUE	1	0.48	2		692	694	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0042642-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	78	455	1				ENST00000310581	NM_198253.2	-/1132			0.3	0	FACETS	0.707	0.631	0.786			1	SUBCLONAL	1	TRUE	0	0.48	0		456	239	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061812	38061812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1165110401	NA	P-0042642-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	102	768	0	ENST00000250448.2:c.177G>A	p.Met59Ile	p.M59I	ENST00000250448	NM_004496.3	59	atG/atA	2/2	1	2	FACETS	0.513	0.458	0.571	0.513	0.458	0.571	SUBCLONAL	1	TRUE	1	0.48	2		768	829	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051247	128051247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042642-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	162	635	0	ENST00000285398.2:c.76G>A	p.Glu26Lys	p.E26K	ENST00000285398	NM_000122.1	26	Gaa/Aaa	2/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.48	2		635	622	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462791	69462791	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042642-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	31	691	0	ENST00000227507.2:c.604A>G	p.Met202Val	p.M202V	ENST00000227507	NM_053056.2	202	Atg/Gtg	4/5	1	2	FACETS	0.212	0.17	0.259	0.212	0.17	0.259	SUBCLONAL	1	TRUE	1	0.48	2		691	610	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416517	49416519	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	novel	NA	P-0042642-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	38	637	0	ENST00000301067.7:c.16192_16194del	p.Asn5398del	p.N5398del	ENST00000301067	NM_003482.3	5398	AAC/-	51/54	0.134305246890273	4	FACETS	0.319	0.262	0.382	0.159	0.131	0.191	INDETERMINATE	1	TRUE	2	0.48	4		637	735	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061710	38061710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042642-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	60	449	0	ENST00000250448.2:c.279G>A	p.Met93Ile	p.M93I	ENST00000250448	NM_004496.3	93	atG/atA	2/2	1	2	FACETS	0.569	0.492	0.654	0.569	0.492	0.654	SUBCLONAL	1	TRUE	1	0.48	2		449	439	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922689	44922690	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0042642-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	33	207	0	ENST00000377967.4:c.1551_1552dup	p.Val518GlyfsTer31	p.V518Gfs*31	ENST00000377967	NM_021140.2	517	cag/caGGg	16/29	NA	2	FACETS	0.481	0.393	0.579			1	INDETERMINATE	1	TRUE	NA	0.48	2		207	286	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942821	44942821	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042642-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	22	314	0	ENST00000377967.4:c.3401T>C	p.Leu1134Pro	p.L1134P	ENST00000377967	NM_021140.2	1134	cTa/cCa	23/29	NA	2	FACETS	0.302	0.234	0.38			1	INDETERMINATE	1	TRUE	NA	0.48	2		314	304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0042972-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	153	660	2	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.163073248945895	4	FACETS	1	0.979	1	0.604	0.553	0.656	INDETERMINATE	1	TRUE	2	0.52	4		662	741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0042972-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	142	607	1	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.163073248945895	4	FACETS	1	0.973	1	0.581	0.531	0.634	INDETERMINATE	1	TRUE	2	0.52	4		608	714	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861149	57861149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774058977	NA	P-0042972-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	44	515	0	ENST00000228682.2:c.946G>A	p.Glu316Lys	p.E316K	ENST00000228682	NM_005269.2	316	Gaa/Aaa	9/12	0.3	4	FACETS	0.39	0.326	0.461	0.13	0.108	0.154	INDETERMINATE	1	TRUE	1	0.52	4		515	660	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280153	115280153	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1272124838	NA	P-0042972-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	74	319	0	ENST00000438362.2:c.479G>A	p.Ser160Asn	p.S160N	ENST00000438362	NM_001242891.1	160	aGt/aAt	5/20	0.120514791306984	4	FACETS	1	0.888	1	0.505	0.444	0.571	INDETERMINATE	1	TRUE	2	0.52	4		319	428	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18496288	18496288	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042972-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	23	173	0	ENST00000266497.5:c.1423G>T	p.Ala475Ser	p.A475S	ENST00000266497		475	Gca/Tca	9/31	1	2	FACETS	0.53	0.416	0.659	0.53	0.416	0.659	SUBCLONAL	1	TRUE	1	0.52	2		173	167	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829678	72829678	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0042972-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	88	613	0	ENST00000268489.5:c.6903T>A	p.Tyr2301Ter	p.Y2301*	ENST00000268489	NM_006885.3	2301	taT/taA	9/10	0.286163224851264	1	FACETS	0.474	0.421	0.531	0.474	0.421	0.531	INDETERMINATE	1	TRUE	0	0.52	1		613	528	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470583	25470584	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0042972-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	122	831	2	ENST00000264709.3:c.890_891delinsTT	p.Trp297Phe	p.W297F	ENST00000264709	NM_175629.2	297	tGG/tTT	8/23	1	2	FACETS	0.637	0.576	0.701	0.637	0.576	0.701	SUBCLONAL	1	TRUE	1	0.52	2		833	737	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267480	198267480	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042972-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	32	263	0	ENST00000335508.6:c.1877A>T	p.Asn626Ile	p.N626I	ENST00000335508	NM_012433.2	626	aAc/aTc	14/25	1	2	FACETS	0.349	0.283	0.422	0.349	0.283	0.422	SUBCLONAL	1	TRUE	1	0.52	2		263	353	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0043226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	53	603	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.555384737047698	5	FACETS	0.81	0.692	0.938	0.405	0.346	0.469	CLONAL	1	TRUE	3	0.555384737047698	5		603	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0043226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	351	849	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.55019343348195	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	3	TRUE	0	0.555384737047698	3		849	536	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175942	176175942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs964768927	NA	P-0043226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	13	85	0	ENST00000367669.3:c.173C>T	p.Ser58Leu	p.S58L	ENST00000367669	NM_022457.5	58	tCg/tTg	1/20	0.534662706166688	4	FACETS	1	0.856	1	0.433	0.318	0.566	CLONAL	1	TRUE	1	0.555384737047698	4		85	56	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056443	26056443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1252419231	NA	P-0043226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	125	434	0	ENST00000343677.2:c.214G>A	p.Asp72Asn	p.D72N	ENST00000343677	NM_005319.3	72	Gat/Aat	1/1	0.555384737047698	7	FACETS	1	0.978	1	0.618	0.563	0.674	CLONAL	2	TRUE	3	0.555384737047698	7		434	435	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797215	42797215	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	114	1189	1	ENST00000575354.2:c.3577G>C	p.Glu1193Gln	p.E1193Q	ENST00000575354	NM_015125.3	1193	Gag/Cag	15/20	0.402544994379679	5	FACETS	0.881	0.793	0.975			1	CLONAL	1	TRUE	NA	0.555384737047698	5		1190	854	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509128	66509128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1439062174	NA	P-0043226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	88	356	0	ENST00000273854.3:c.199C>T	p.Arg67Cys	p.R67C	ENST00000273854	NM_004439.5	67	Cgc/Tgc	2/18	0.425306213286864	3	FACETS	0.873	0.787	0.96	0.873	0.787	0.96	CLONAL	2	TRUE	1	0.555384737047698	3		356	232	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376135	225376135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	95	554	0	ENST00000264414.4:c.819G>A	p.Met273Ile	p.M273I	ENST00000264414	NM_003590.4	273	atG/atA	6/16	0.555384737047698	3	FACETS	1	0.918	1	0.514	0.46	0.571	CLONAL	1	TRUE	1	0.555384737047698	3		554	425	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193202250	193202250	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	69	418	0	ENST00000367435.3:c.1282G>C	p.Val428Leu	p.V428L	ENST00000367435	NM_024529.4	428	Gta/Cta	14/17	0.555384737047698	5	FACETS	0.821	0.715	0.934	0.205	0.178	0.234	CLONAL	1	TRUE	1	0.555384737047698	5		418	555	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346444	89346444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573380956	NA	P-0043226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	106	1016	0	ENST00000301030.4:c.6506G>A	p.Gly2169Glu	p.G2169E	ENST00000301030	NM_001256183.1	2169	gGg/gAg	9/13	0.551202770440375	2	FACETS	0.9	0.813	0.992	0.45	0.406	0.496	CLONAL	1	TRUE	0	0.555384737047698	2		1016	424	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56378156	56378156	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	59	386	0	ENST00000348428.3:c.929G>A	p.Arg310Lys	p.R310K	ENST00000348428	NM_006785.3	310	aGa/aAa	7/17	0.555384737047698	2	FACETS	0.916	0.798	1	0.458	0.399	0.521	CLONAL	1	TRUE	0	0.555384737047698	2		386	232	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187081	38187081	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	116	838	0	ENST00000317025.8:c.1396G>A	p.Val466Ile	p.V466I	ENST00000317025	NM_023034.1	466	Gtt/Att	6/24	0.551202770440375	2	FACETS	1	0.928	1	0.512	0.465	0.561	CLONAL	1	TRUE	0	0.555384737047698	2		838	408	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189044	38189044	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	121	668	0	ENST00000317025.8:c.970G>C	p.Glu324Gln	p.E324Q	ENST00000317025	NM_023034.1	324	Gaa/Caa	5/24	0.551202770440375	2	FACETS	1	0.968	1	0.566	0.516	0.617	CLONAL	1	TRUE	0	0.555384737047698	2		668	385	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518087	8518087	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	154	598	0	ENST00000356435.5:c.1304del	p.Leu435TrpfsTer33	p.L435Wfs*33	ENST00000356435		435	tTg/tg	10/35	0.551202770440375	2	FACETS	0.963	0.9	1	0.963	0.9	1	CLONAL	2	TRUE	0	0.555384737047698	2		598	288	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271563	26271563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	65	563	1	ENST00000305910.3:c.50C>T	p.Pro17Leu	p.P17L	ENST00000305910	NM_003534.2	17	cCg/cTg	1/1	0.555384737047698	7	FACETS	1	0.94	1	0.286	0.248	0.327	CLONAL	1	TRUE	3	0.555384737047698	7		564	488	SUCCESS
ATM	472	MSKCC	GRCh37	11	108137934	108137934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	55	406	0	ENST00000278616.4:c.2503G>A	p.Val835Ile	p.V835I	ENST00000278616	NM_000051.3	835	Gta/Ata	17/63	0.555384737047698	1	FACETS	0.813	0.708	0.923	0.813	0.708	0.923	CLONAL	1	TRUE	0	0.555384737047698	1		406	176	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028703	42028703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	106	620	0	ENST00000219905.7:c.4241C>T	p.Ser1414Leu	p.S1414L	ENST00000219905	NM_001164273.1	1414	tCa/tTa	13/24	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.555384737047698	2		620	347	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2097730	2097730	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	93	803	0	ENST00000219066.1:c.119G>C	p.Arg40Pro	p.R40P	ENST00000219066	NM_002528.5	40	cGg/cCg	1/6	0.437808557884898	4	FACETS	1	0.894	1			1	CLONAL	1	TRUE	NA	0.555384737047698	4		803	520	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487549	38487549	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	81	888	0	ENST00000254066.5:c.79T>G	p.Phe27Val	p.F27V	ENST00000254066	NM_000964.3	27	Ttc/Gtc	2/9	0.529412804613627	4	FACETS	0.78	0.688	0.878	0.195	0.172	0.22	SUBCLONAL	1	TRUE	0	0.555384737047698	4		888	582	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271475	15271475	+	stop_lost	Nonstop_Mutation	SNP	A	A	T	novel	NA	P-0043226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	49	1148	0	ENST00000263388.2:c.6964T>A	p.Ter2322ArgextTer106	p.*2322Rext*106	ENST00000263388	NM_000435.2	2322	Tga/Aga	33/33	0.555384737047698	5	FACETS	0.336	0.283	0.394			1	SUBCLONAL	1	TRUE	NA	0.555384737047698	5		1148	963	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383230	31383230	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	89	530	1	ENST00000328111.2:c.1142G>A	p.Arg381Lys	p.R381K	ENST00000328111	NM_006892.3	381	aGa/aAa	11/23	0.497733604294483	3	FACETS	1	0.933	1	0.53	0.473	0.59	CLONAL	1	TRUE	1	0.555384737047698	3		531	386	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40789994	40789994	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	55	608	0	ENST00000373198.4:c.2737G>C	p.Glu913Gln	p.E913Q	ENST00000373198	NM_133170.3	913	Gag/Cag	18/32	0.497733604294483	3	FACETS	0.736	0.632	0.847	0.368	0.316	0.424	SUBCLONAL	1	TRUE	1	0.555384737047698	3		608	344	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910756	29910756	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	145	957	0	ENST00000376809.5:c.296G>A	p.Arg99Gln	p.R99Q	ENST00000376809	NM_002116.7	99	cGa/cAa	2/8	0.555384737047698	7	FACETS	0.888	0.812	0.968	0.444	0.406	0.484	CLONAL	2	TRUE	3	0.555384737047698	7		957	702	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399474	139399474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	1625	1083	2	ENST00000277541.6:c.4669G>A	p.Asp1557Asn	p.D1557N	ENST00000277541	NM_017617.3	1557	Gac/Aac	26/34	0.555384737047698	12	FACETS	0.995	0.982	1	0.912	0.9	0.924	CLONAL	11	TRUE	0	0.555384737047698	12		1085	2019	SUCCESS
AR	367	MSKCC	GRCh37	X	66937348	66937348	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	81	709	0	ENST00000374690.3:c.2202G>C	p.Gln734His	p.Q734H	ENST00000374690	NM_000044.3	734	caG/caC	5/8	1	2	FACETS	0.892	0.793	0.996	0.892	0.793	0.996	CLONAL	1	TRUE	1	0.555384737047698	2		709	327	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0043745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	611	603	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.979	0.954	1			1	CLONAL	7	TRUE	1	0.217522812866839	2		603	820	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628235	187628235	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	655	54	0	ENST00000441802.2:c.2747C>T	p.Ser916Leu	p.S916L	ENST00000441802	NM_005245.3	916	tCa/tTa	2/27	1	2	FACETS	1	0.987	1	1	0.998	1	CLONAL	5	TRUE	1	0.217522812866839	2		54	1166	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577537	7577538	+	missense_variant	Missense_Mutation	DNP	CC	CC	GT	novel	NA	P-0043745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	673	64	2	ENST00000269305.4:c.743_744delinsAC	p.Arg248His	p.R248H	ENST00000269305	NM_001126112.2	248	cGG/cAC	7/11	0.188722997317376	1	FACETS	0.907	0.879	0.935	1	0.998	1	CLONAL	5	TRUE	0	0.217522812866839	1		66	1216	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857779	9857779	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs78544202	NA	P-0043745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	530	49	0	ENST00000330684.3:c.3622C>T	p.Arg1208Trp	p.R1208W	ENST00000330684	NM_001134407.1	1208	Cgg/Tgg	13/13	1	2	FACETS	0.967	0.932	1	1	0.998	1	CLONAL	5	TRUE	1	0.217522812866839	2		49	1008	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17129540	17129540	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	946	87	2	ENST00000285071.4:c.346del	p.Gln116SerfsTer14	p.Q116Sfs*14	ENST00000285071	NM_144997.5	116	Cag/ag	5/14	0.188722997317376	1	FACETS	1	0.99	1			1	CLONAL	5	TRUE	0	0.217522812866839	1		89	1509	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211109	36211109	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	1141	84	0	ENST00000222270.7:c.860G>T	p.Arg287Leu	p.R287L	ENST00000222270	NM_014727.1	287	cGt/cTt	3/37	1	2	FACETS	1	0.994	1			1	CLONAL	5	TRUE	1	0.217522812866839	2		84	1993	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412022	116412049	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TACCGAGCTACTTTTCCAGAAGGTATAT	TACCGAGCTACTTTTCCAGAAGGTATAT	-	novel	NA	P-0043745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	672	154	0	ENST00000397752.3:c.3008_3028+7del		p.X1003_splice	ENST00000397752	NM_000245.2	1003		14/21	0.207199547096598	2	FACETS	1	0.993	1	1	0.998	1	CLONAL	5	TRUE	0	0.217522812866839	2		154	1156	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740300	46740300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	503	59	0	ENST00000371975.4:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000371975	NM_003579.3	594	Gac/Aac	16/18	1	2	FACETS	0.954	0.918	0.989	1	0.998	1	CLONAL	5	TRUE	1	0.217522812866839	2		59	970	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118391576	118391576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	285	37	0	ENST00000534358.1:c.11489C>T	p.Ser3830Phe	p.S3830F	ENST00000534358	NM_005933.3	3830	tCt/tTt	34/36	1	2	FACETS	0.969	0.922	1	1	0.997	1	CLONAL	5	TRUE	1	0.217522812866839	2		37	541	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514532	125514532	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	236	39	0	ENST00000428830.2:c.1227G>C	p.Met409Ile	p.M409I	ENST00000428830	NM_001114121.2	409	atG/atC	11/14	1	2	FACETS	0.904	0.854	0.954	1	0.996	1	CLONAL	5	TRUE	1	0.217522812866839	2		39	480	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878053	48878053	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	278	21	0	ENST00000267163.4:c.5C>T	p.Pro2Leu	p.P2L	ENST00000267163	NM_000321.2	2	cCg/cTg	1/27	1	2	FACETS	1	0.986	1	1	0.997	1	CLONAL	4	TRUE	1	0.217522812866839	2		21	576	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919767	50919767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	1057	90	0	ENST00000440232.2:c.2935G>A	p.Ala979Thr	p.A979T	ENST00000440232	NM_002691.3	979	Gcc/Acc	23/27	1	2	FACETS	1	0.995	1			1	CLONAL	5	TRUE	1	0.217522812866839	2		90	1829	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663450	227663450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	403	31	0	ENST00000305123.5:c.5C>T	p.Ala2Val	p.A2V	ENST00000305123	NM_005544.2	2	gCg/gTg	1/2	1	2	FACETS	0.98	0.94	1	1	0.998	1	CLONAL	5	TRUE	1	0.217522812866839	2		31	756	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665398	176665398	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	409	30	0	ENST00000439151.2:c.4082T>C	p.Leu1361Pro	p.L1361P	ENST00000439151	NM_022455.4	1361	cTt/cCt	7/23	0.217522812866839	4	FACETS	0.992	0.949	1	1	0.996	1	CLONAL	5	TRUE	1	0.217522812866839	4		30	923	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795392	39795392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044193-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	985	10	0	ENST00000288319.7:c.328G>A	p.Glu110Lys	p.E110K	ENST00000288319	NM_182918.3	110	Gag/Aag	3/10	0.279846630439236	3	FACETS	0.952	0.942	0.961			1	CLONAL	8	TRUE	1	0.279846630439236	3		10	1054	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149511584	149511584	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044193-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	839	13	0	ENST00000261799.4:c.1201G>A	p.Glu401Lys	p.E401K	ENST00000261799	NM_002609.3	401	Gag/Aag	8/23	0.18358318200712	3	FACETS	1	0.997	1			1	CLONAL	7	TRUE	1	0.279846630439236	3		13	929	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274071	18274088	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGGACCAGATTGTCAAGG	AGGACCAGATTGTCAAGG	-	novel	NA	P-0044193-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	669	12	0	ENST00000222254.8:c.1294_1311del		p.X432_splice	ENST00000222254	NM_005027.3	432		11/16	0.218650399896764	0	FACETS		NA	1			1	NA	6	TRUE	0	0.279846630439236	0		12	711	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0044681-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	159	375	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	1	2	FACETS	0.848	0.784	0.915	0.848	0.784	0.915	CLONAL	1	TRUE	1	0.75873318238517	2		375	494	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625358	69625358	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044681-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	319	856	0	ENST00000334134.2:c.435del	p.Gln146SerfsTer12	p.Q146Sfs*12	ENST00000334134	NM_005247.2	145	cgG/cg	3/3	1	2	FACETS	0.999	0.947	1	0.999	0.947	1	CLONAL	1	TRUE	1	0.75873318238517	2		856	842	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	305	864	2	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	2	TRUE	NA	0.270137812387669	2		866	1064	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033905	49033905	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	71	452	0	ENST00000267163.4:c.2042G>A	p.Trp681Ter	p.W681*	ENST00000267163	NM_000321.2	681	tGg/tAg	20/27	0.263998423558044	1	FACETS	0.922	0.807	1	0.922	0.807	1	CLONAL	1	TRUE	0	0.270137812387669	1		452	493	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827993	40827993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1328809133	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	91	643	0	ENST00000373198.4:c.2435G>A	p.Gly812Glu	p.G812E	ENST00000373198	NM_133170.3	812	gGa/gAa	17/32	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.270137812387669	2		643	657	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914236	32914236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs4987117	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	53	504	0	ENST00000380152.3:c.5744C>T	p.Thr1915Met	p.T1915M	ENST00000380152		1915	aCg/aTg	11/27	0.263998423558044	1	FACETS	0.797	0.681	0.923	0.797	0.681	0.923	CLONAL	1	TRUE	0	0.270137812387669	1		504	426	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641144	117641144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866970127	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	110	663	0	ENST00000368508.3:c.5827G>A	p.Glu1943Lys	p.E1943K	ENST00000368508	NM_002944.2	1943	Gaa/Aaa	36/43	0.263998423558044	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.270137812387669	1		663	645	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428227	33428227	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1379526157	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	85	634	0	ENST00000345365.6:c.896C>T	p.Ser299Phe	p.S299F	ENST00000345365	NM_002878.3	299	tCc/tTc	9/10	0.263998423558044	1	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	0	0.270137812387669	1		634	544	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162107	22162107	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	77	423	1	ENST00000215832.6:c.148C>T	p.Arg50Ter	p.R50*	ENST00000215832	NM_002745.4	50	Cga/Tga	2/9	0.263998423558044	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.270137812387669	1		424	439	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912075	56912075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	90	626	0	ENST00000519728.1:c.1303G>A	p.Glu435Lys	p.E435K	ENST00000519728	NM_002350.3	435	Gaa/Aaa	12/13	1	2	FACETS	0.923	0.819	1	0.923	0.819	1	CLONAL	1	TRUE	1	0.270137812387669	2		626	722	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604769	48604769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766833269	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	86	463	0	ENST00000342988.3:c.1591C>T	p.Arg531Trp	p.R531W	ENST00000342988	NM_005359.5	531	Cgg/Tgg	12/12	0.215022182298585	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.270137812387669	1		463	503	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244595	41244595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555588649	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	119	663	0	ENST00000357654.3:c.2953C>T	p.Pro985Ser	p.P985S	ENST00000357654	NM_007294.3	985	Ccc/Tcc	10/23	0.263998423558044	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.270137812387669	1		663	679	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117074	7117074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	87	595	0	ENST00000302850.5:c.4142C>T	p.Pro1381Leu	p.P1381L	ENST00000302850	NM_000208.2	1381	cCt/cTt	22/22	1	2	FACETS	0.944	0.836	1	0.944	0.836	1	CLONAL	1	TRUE	1	0.270137812387669	2		595	682	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261251	16261251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1188801107	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	97	656	1	ENST00000375759.3:c.8516C>T	p.Pro2839Leu	p.P2839L	ENST00000375759	NM_015001.2	2839	cCg/cTg	11/15	0.270137812387669	3	FACETS	0.898	0.799	1	0.449	0.399	0.502	CLONAL	1	TRUE	1	0.270137812387669	3		657	908	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439622	51439622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	74	416	0	ENST00000262662.1:c.187C>T	p.Pro63Ser	p.P63S	ENST00000262662		63	Ccc/Tcc	4/4	1	2	FACETS	0.968	0.848	1	0.968	0.848	1	CLONAL	1	TRUE	1	0.270137812387669	2		416	566	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074394	8074394	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	67	461	0	ENST00000377482.5:c.265A>C	p.Lys89Gln	p.K89Q	ENST00000377482	NM_018948.3	89	Aag/Cag	4/4	0.270137812387669	3	FACETS	0.91	0.79	1	0.455	0.395	0.52	CLONAL	1	TRUE	1	0.270137812387669	3		461	619	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326502	161326502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	59	389	0	ENST00000367975.2:c.277C>T	p.Pro93Ser	p.P93S	ENST00000367975	NM_003001.3	93	Cct/Tct	5/6	1	2	FACETS	0.979	0.845	1	0.979	0.845	1	CLONAL	1	TRUE	1	0.270137812387669	2		389	446	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716113	243716113	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	63	548	0	ENST00000263826.5:c.1081G>A	p.Glu361Lys	p.E361K	ENST00000263826	NM_005465.4	361	Gaa/Aaa	10/13	1	2	FACETS	0.777	0.672	0.891	0.777	0.672	0.891	SUBCLONAL	1	TRUE	1	0.270137812387669	2		548	600	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860059	57860059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	122	843	0	ENST00000228682.2:c.799G>A	p.Glu267Lys	p.E267K	ENST00000228682	NM_005269.2	267	Gag/Aag	8/12	1	2	FACETS	0.912	0.823	1	0.912	0.823	1	CLONAL	1	TRUE	1	0.270137812387669	2		843	990	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784046	120784047	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	153	976	1	ENST00000257552.2:c.938_939delinsTT	p.Pro313Leu	p.P313L	ENST00000257552	NM_002442.3	313	cCC/cTT	13/15	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.270137812387669	2		977	1131	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066945	30066945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	58	433	0	ENST00000331968.5:c.2186G>A	p.Gly729Asp	p.G729D	ENST00000331968	NM_002742.2	729	gGt/gAt	16/18	1	2	FACETS	0.812	0.698	0.936	0.812	0.698	0.936	CLONAL	1	TRUE	1	0.270137812387669	2		433	529	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68878231	68878231	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	70	364	0	ENST00000487270.1:c.944C>G	p.Ser315Ter	p.S315*	ENST00000487270	NM_133509.3	315	tCa/tGa	9/11	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.270137812387669	2		364	456	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822400	72822400	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	154	974	1	ENST00000268489.5:c.9775A>C	p.Lys3259Gln	p.K3259Q	ENST00000268489	NM_006885.3	3259	Aag/Cag	10/10	1	2	FACETS	0.972	0.888	1	0.972	0.888	1	CLONAL	1	TRUE	1	0.270137812387669	2		975	1173	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991733	72991733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	92	332	0	ENST00000268489.5:c.2312G>A	p.Gly771Glu	p.G771E	ENST00000268489	NM_006885.3	771	gGg/gAg	2/10	1	2	FACETS	0.769	0.687	0.855	1	0.981	1	SUBCLONAL	2	TRUE	1	0.270137812387669	2		332	443	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602385	10602385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	312	1032	0	ENST00000171111.5:c.1193C>T	p.Pro398Leu	p.P398L	ENST00000171111	NM_203500.1	398	cCc/cTc	3/6	0.270137812387669	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	1	0.270137812387669	3		1032	1295	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182122	99182123	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	69	480	0	ENST00000074304.5:c.2187_2188delinsAA	p.Glu730Lys	p.E730K	ENST00000074304	NM_001134224.1	729	ctGGag/ctAAag	21/26	1	2	FACETS	0.861	0.751	0.981	0.861	0.751	0.981	CLONAL	1	TRUE	1	0.270137812387669	2		480	593	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570061	212570063	+	missense_variant	Missense_Mutation	TNP	TCC	TCC	ATT	novel	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	42	482	1	ENST00000342788.4:c.1178_1180delinsAAT	p.Arg393_Thr394delinsGlnSer	p.R393_T394delinsQS	ENST00000342788	NM_005235.2	393	cGGAca/cAATca	10/28	0.26957951100706	2	FACETS	0.632	0.527	0.748	0.316	0.263	0.374	SUBCLONAL	1	TRUE	0	0.270137812387669	2		483	492	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750686	39750686	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	49	280	0	ENST00000361337.2:c.2086G>A	p.Glu696Lys	p.E696K	ENST00000361337	NM_003286.2	696	Gaa/Aaa	20/21	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.270137812387669	2		280	339	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527605	41527605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777025732	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	74	458	0	ENST00000263253.7:c.1496C>T	p.Ser499Phe	p.S499F	ENST00000263253	NM_001429.3	499	tCt/tTt	6/31	0.263998423558044	1	FACETS	0.901	0.79	1	0.901	0.79	1	CLONAL	1	TRUE	0	0.270137812387669	1		458	526	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390904	89390904	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	57	353	0	ENST00000336596.2:c.971-1G>A		p.X324_splice	ENST00000336596	NM_005233.5	324			0.270137812387669	3	FACETS	1	0.889	1	0.52	0.446	0.599	CLONAL	1	TRUE	1	0.270137812387669	3		353	461	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528569	89528569	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	40	302	0	ENST00000336596.2:c.2869A>T	p.Thr957Ser	p.T957S	ENST00000336596	NM_005233.5	957	Acc/Tcc	17/17	0.270137812387669	3	FACETS	1	0.872	1	0.527	0.439	0.624	CLONAL	1	TRUE	1	0.270137812387669	3		302	319	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131181	55131181	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324568225	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	66	486	0	ENST00000257290.5:c.724G>A	p.Val242Met	p.V242M	ENST00000257290	NM_006206.4	242	Gtg/Atg	5/23	0.270137812387669	1	FACETS	0.755	0.656	0.862	0.755	0.656	0.862	SUBCLONAL	1	TRUE	0	0.270137812387669	1		486	560	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526432	31526432	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	127	941	0	ENST00000344624.3:c.608A>T	p.His203Leu	p.H203L	ENST00000344624		203	cAt/cTt	2/33	1	2	FACETS	0.95	0.859	1	0.95	0.859	1	CLONAL	1	TRUE	1	0.270137812387669	2		941	990	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514352	149514352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1330417953	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	107	620	1	ENST00000261799.4:c.592G>A	p.Glu198Lys	p.E198K	ENST00000261799	NM_002609.3	198	Gag/Aag	4/23	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.270137812387669	2		621	771	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721562	176721562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	113	637	0	ENST00000439151.2:c.7193C>T	p.Pro2398Leu	p.P2398L	ENST00000439151	NM_022455.4	2398	cCc/cTc	23/23	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.270137812387669	2		637	806	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725505	117725505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	80	491	0	ENST00000368508.3:c.376G>A	p.Gly126Arg	p.G126R	ENST00000368508	NM_002944.2	126	Gga/Aga	5/43	0.263998423558044	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.270137812387669	1		491	456	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162475202	162475202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	52	365	0	ENST00000366898.1:c.539C>T	p.Pro180Leu	p.P180L	ENST00000366898	NM_004562.2	180	cCa/cTa	5/12	0.263998423558044	1	FACETS	0.849	0.725	0.985	0.849	0.725	0.985	CLONAL	1	TRUE	0	0.270137812387669	1		365	392	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468038	50468038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1459868445	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	78	704	0	ENST00000331340.3:c.1273G>A	p.Gly425Arg	p.G425R	ENST00000331340	NM_006060.4	425	Ggg/Agg	8/8	0.270137812387669	1	FACETS	0.794	0.698	0.897	0.794	0.698	0.897	SUBCLONAL	1	TRUE	0	0.270137812387669	1		704	629	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964515	70964516	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	75	699	0	ENST00000276594.2:c.1512_1513delinsTT	p.Arg505Cys	p.R505C	ENST00000276594	NM_024504.3	504	ctCCgc/ctTTgc	8/8	1	2	FACETS	0.701	0.613	0.796	0.701	0.613	0.796	SUBCLONAL	1	TRUE	1	0.270137812387669	2		699	792	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981501	70981501	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200062567	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	160	946	0	ENST00000276594.2:c.595G>A	p.Glu199Lys	p.E199K	ENST00000276594	NM_024504.3	199	Gag/Aag	2/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.270137812387669	2		946	1064	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741476	145741476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1379758021	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	140	1070	0	ENST00000428558.2:c.1027C>T	p.Pro343Ser	p.P343S	ENST00000428558	NM_004260.3	343	Cct/Tct	5/22	0.270137812387669	3	FACETS	0.923	0.839	1	0.462	0.419	0.507	CLONAL	1	TRUE	1	0.270137812387669	3		1070	1274	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050658	30050673	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	GACCCCAGTGTTCACA	GACCCCAGTGTTCACA	TG	novel	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	41	504	2	ENST00000338641.4:c.460_475delinsTG	p.Asp154Ter	p.D154*	ENST00000338641	NM_000268.3	154	GACCCCAGTGTTCACAag/TGag	5/16	0.263998423558044	1	FACETS	0.485	0.404	0.576	0.485	0.404	0.576	SUBCLONAL	1	TRUE	0	0.270137812387669	1		506	541	SUCCESS
ATR	545	MSKCC	GRCh37	3	142222283	142222284	+	missense_variant	Missense_Mutation	DNP	GA	GA	AG	novel	NA	P-0045878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	118	345	1	ENST00000350721.4:c.5208_5209delinsCT	p.His1737Tyr	p.H1737Y	ENST00000350721	NM_001184.3	1736	taTCat/taCTat	30/47	0.270137812387669	3	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	1	0.270137812387669	3		346	484	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598097	52598097	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0046100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	63	465	0	ENST00000394830.3:c.3769A>T	p.Lys1257Ter	p.K1257*	ENST00000394830	NM_018313.4	1257	Aaa/Taa	24/30	0.410500244005418	1	FACETS	0.942	0.824	1	0.942	0.824	1	CLONAL	1	TRUE	0	0.410500244005418	1		465	259	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939401	36939401	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	145	800	0	ENST00000361632.4:c.449C>A	p.Thr150Asn	p.T150N	ENST00000361632		150	aCc/aAc	4/16	1	2	FACETS	0.762	0.695	0.833	0.762	0.695	0.833	SUBCLONAL	1	TRUE	1	0.410500244005418	2		800	927	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597359	10597359	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	221	812	0	ENST00000171111.5:c.1844A>C	p.Lys615Thr	p.K615T	ENST00000171111	NM_203500.1	615	aAg/aCg	6/6	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.410500244005418	2		812	1058	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188262	10188262	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	149	638	0	ENST00000256474.2:c.405del	p.Leu135PhefsTer24	p.L135Ffs*24	ENST00000256474	NM_000551.3	135	ttA/tt	2/3	0.410500244005418	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.410500244005418	1		638	541	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046925-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	44	375	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.914	0.772	1			1	INDETERMINATE	1	TRUE	NA	0.379179374726216	2		375	254	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0046925-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	159	378	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.350803773590459	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.379179374726216	3		378	420	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121913370	NA	P-0046925-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	43	237	1	ENST00000288602.6:c.1742A>G	p.Asn581Ser	p.N581S	ENST00000288602	NM_004333.4	581	aAt/aGt	15/18	0.379179374726216	3	FACETS	0.978	0.823	1	0.489	0.411	0.573	CLONAL	1	TRUE	1	0.379179374726216	3		238	276	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692979	89692979	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123325	NA	P-0046925-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	67	457	0	ENST00000371953.3:c.463T>C	p.Tyr155His	p.Y155H	ENST00000371953	NM_000314.4	155	Tat/Cat	5/9	0.379179374726216	1	FACETS	0.764	0.667	0.867	0.764	0.667	0.867	SUBCLONAL	1	TRUE	0	0.379179374726216	1		457	375	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	84	375	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.498829207383457	2		375	321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	192	276	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	1	2	FACETS	0.859	0.795	0.926	0.859	0.795	0.926	CLONAL	1	TRUE	1	0.498829207383457	2		276	896	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780071	NA	P-0047232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	204	833	0	ENST00000269305.4:c.580C>T	p.Leu194Phe	p.L194F	ENST00000269305	NM_001126112.2	194	Ctt/Ttt	6/11	1	2	FACETS	0.963	0.895	1	0.963	0.895	1	CLONAL	1	TRUE	1	0.498829207383457	2		833	849	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287229	46287229	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0047232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	154	409	0	ENST00000334344.6:c.5174C>G	p.Ser1725Ter	p.S1725*	ENST00000334344	NM_152641.2	1725	tCa/tGa	19/21	1	2	FACETS	0.974	0.895	1	0.974	0.895	1	CLONAL	1	TRUE	1	0.498829207383457	2		409	634	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135385	30135385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	105	440	0	ENST00000331968.5:c.433C>T	p.Arg145Cys	p.R145C	ENST00000331968	NM_002742.2	145	Cgt/Tgt	3/18	1	2	FACETS	0.824	0.741	0.911	0.824	0.741	0.911	CLONAL	1	TRUE	1	0.498829207383457	2		440	511	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524687	187524687	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs928653182	NA	P-0047232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	275	798	0	ENST00000441802.2:c.10993C>T	p.Arg3665Ter	p.R3665*	ENST00000441802	NM_005245.3	3665	Cga/Tga	19/27	0.498829207383457	1	FACETS	0.991	0.934	1	0.991	0.934	1	CLONAL	1	TRUE	0	0.498829207383457	1		798	835	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748128	43748128	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	217	576	0	ENST00000382044.4:c.2678C>G	p.Ser893Cys	p.S893C	ENST00000382044	NM_001141980.1	893	tCt/tGt	12/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.498829207383457	2		576	782	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348650	89348650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	216	902	1	ENST00000301030.4:c.4300G>A	p.Glu1434Lys	p.E1434K	ENST00000301030	NM_001256183.1	1434	Gag/Aag	9/13	1	2	FACETS	0.895	0.832	0.959	0.895	0.832	0.959	CLONAL	1	TRUE	1	0.498829207383457	2		903	968	SUCCESS
AR	367	MSKCC	GRCh37	X	66765400	66765400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	213	912	4	ENST00000374690.3:c.412G>A	p.Ala138Thr	p.A138T	ENST00000374690	NM_000044.3	138	Gcc/Acc	1/8	0.494439494630808	2	FACETS	0.949	0.883	1	0.474	0.441	0.509	CLONAL	1	TRUE	0	0.498829207383457	2		916	900	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189097	38189097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775871355	NA	P-0047232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	278	465	1	ENST00000317025.8:c.917G>A	p.Arg306Gln	p.R306Q	ENST00000317025	NM_023034.1	306	cGa/cAa	5/24	0.498829207383457	3	FACETS	0.966	0.912	1	0.966	0.912	1	CLONAL	2	TRUE	1	0.498829207383457	3		466	721	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245486	46245486	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	93	393	0	ENST00000334344.6:c.3580C>T	p.Gln1194Ter	p.Q1194*	ENST00000334344	NM_152641.2	1194	Cag/Tag	15/21	1	2	FACETS	0.725	0.647	0.808	0.725	0.647	0.808	SUBCLONAL	1	TRUE	1	0.498829207383457	2		393	514	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347462	89347462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	267	955	0	ENST00000301030.4:c.5488G>A	p.Glu1830Lys	p.E1830K	ENST00000301030	NM_001256183.1	1830	Gaa/Aaa	9/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.498829207383457	2		955	1006	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348125	89348125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	307	979	0	ENST00000301030.4:c.4825G>A	p.Glu1609Lys	p.E1609K	ENST00000301030	NM_001256183.1	1609	Gag/Aag	9/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.498829207383457	2		979	1098	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348541	89348541	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	276	999	0	ENST00000301030.4:c.4409G>C	p.Arg1470Thr	p.R1470T	ENST00000301030	NM_001256183.1	1470	aGa/aCa	9/13	1	2	FACETS	0.952	0.894	1	0.952	0.894	1	CLONAL	1	TRUE	1	0.498829207383457	2		999	1162	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349048	89349048	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	291	964	0	ENST00000301030.4:c.3902G>C	p.Ser1301Thr	p.S1301T	ENST00000301030	NM_001256183.1	1301	aGc/aCc	9/13	1	2	FACETS	0.997	0.938	1	0.997	0.938	1	CLONAL	1	TRUE	1	0.498829207383457	2		964	1170	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349232	89349232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	317	1036	2	ENST00000301030.4:c.3718G>A	p.Glu1240Lys	p.E1240K	ENST00000301030	NM_001256183.1	1240	Gag/Aag	9/13	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.498829207383457	2		1038	1253	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383714	84383714	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	156	631	0	ENST00000321945.7:c.1138G>C	p.Asp380His	p.D380H	ENST00000321945	NM_139076.2	380	Gat/Cat	9/9	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.498829207383457	2		631	616	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249486	153249487	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0047232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	126	500	0	ENST00000281708.4:c.1291_1292del	p.Asp431GlnfsTer5	p.D431Qfs*5	ENST00000281708	NM_033632.3	431	GAc/c	9/12	0.498829207383457	1	FACETS	0.856	0.781	0.934	0.856	0.781	0.934	CLONAL	1	TRUE	0	0.498829207383457	1		500	443	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449389	31449389	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	126	395	0	ENST00000344624.3:c.2820A>T	p.Lys940Asn	p.K940N	ENST00000344624		940	aaA/aaT	19/33	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.498829207383457	2		395	479	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680431	30680431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	166	706	0	ENST00000376406.3:c.1288G>A	p.Asp430Asn	p.D430N	ENST00000376406	NM_014641.2	430	Gat/Aat	5/15	0.498829207383457	3	FACETS	0.908	0.834	0.985	0.454	0.417	0.493	CLONAL	1	TRUE	1	0.498829207383457	3		706	916	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866562	117866562	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	100	541	0	ENST00000297338.2:c.1083G>C	p.Met361Ile	p.M361I	ENST00000297338	NM_006265.2	361	atG/atC	9/14	0.498829207383457	3	FACETS	0.781	0.699	0.869	0.391	0.349	0.435	SUBCLONAL	1	TRUE	1	0.498829207383457	3		541	641	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0047288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	219	15	0	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	1	2	FACETS	1	0.964	1	1	0.996	1	CLONAL	4	FALSE	1	0.247495883083923	2		15	430	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926270	112926270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918457	NA	P-0047288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	596	22	0	ENST00000351677.2:c.1403C>T	p.Thr468Met	p.T468M	ENST00000351677	NM_002834.3	468	aCg/aTg	12/16	1	2	FACETS	0.991	0.961	1	1	0.998	1	CLONAL	5	FALSE	1	0.247495883083923	2		22	972	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988309	36988309	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776709	NA	P-0047288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	1222	37	0	ENST00000354822.5:c.344del	p.Gly115AlafsTer10	p.G115Afs*10	ENST00000354822	NM_001079668.2	115	gGc/gc	2/3	0.247495883083923	1	FACETS	1	0.997	1			1	CLONAL	5	FALSE	0	0.247495883083923	1		37	1629	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623771	28623771	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0047288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	443	32	0	ENST00000241453.7:c.882+1G>T		p.X294_splice	ENST00000241453	NM_004119.2	294			1	2	FACETS	0.917	0.882	0.951	1	0.998	1	CLONAL	5	FALSE	1	0.247495883083923	2		32	781	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967030	18967030	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	1203	30	0	ENST00000262803.5:c.1745A>G	p.Asp582Gly	p.D582G	ENST00000262803	NM_002911.3	582	gAc/gGc	13/24	1	2	FACETS	0.919	0.901	0.937			1	CLONAL	6	FALSE	1	0.247495883083923	2		30	1763	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082321	16082328	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGGAGG	GGGGGAGG	-	novel	NA	P-0047288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	2123	57	0	ENST00000281043.3:c.135_142del	p.Gly46HisfsTer6	p.G46Hfs*6	ENST00000281043	NM_005378.4	45	ccGGGGGAGGac/ccac	2/3	1	2	FACETS	0.987	0.974	1			1	CLONAL	6	FALSE	1	0.247495883083923	2		57	2896	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729699	41729699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	1001	35	0	ENST00000242208.4:c.830G>A	p.Gly277Asp	p.G277D	ENST00000242208	NM_002192.2	277	gGt/gAt	3/3	1	2	FACETS	1	0.994	1			1	CLONAL	5	FALSE	1	0.247495883083923	2		35	1547	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220115	133220115	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047288-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1253	1462	72	0	ENST00000320574.5:c.4322T>A	p.Leu1441Gln	p.L1441Q	ENST00000320574	NM_006231.2	1441	cTg/cAg	34/49	1	2	FACETS	0.97	0.949	0.991	0.97	0.949	0.991	CLONAL	1	TRUE	1	1.11	2		72	2715	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988331	36988331	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047288-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	1112	59	0	ENST00000354822.5:c.322del	p.Leu108SerfsTer17	p.L108Sfs*17	ENST00000354822	NM_001079668.2	108	Ctc/tc	2/3	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	1.11	2		59	1958	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	337	375	0				ENST00000310581	NM_198253.2	-/1132			0.837275507839188	5	FACETS	1	0.993	1	0.86	0.826	0.893	CLONAL	3	TRUE	1	0.83682376158341	5		375	528	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0048286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	455	477	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.837275507839188	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	1	0.83682376158341	3		477	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0048286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	699	619	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.163288613632903	3	FACETS	1	0.997	1			1	INDETERMINATE	3	TRUE	NA	0.83682376158341	3		620	748	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259328	11259328	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	584	282	0	ENST00000361445.4:c.4240G>T	p.Glu1414Ter	p.E1414*	ENST00000361445	NM_004958.3	1414	Gaa/Taa	28/58	1	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	1	0.83682376158341	2		282	964	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101557	27101563	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGAAG	GCAGAAG	-	novel	NA	P-0048286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	741	362	0	ENST00000324856.7:c.4843_4849del	p.Lys1615ValfsTer9	p.K1615Vfs*9	ENST00000324856	NM_006015.4	1613	atGCAGAAG/at	18/20	1	2	FACETS	0.766	0.746	0.786	1	0.998	1	SUBCLONAL	2	TRUE	1	0.83682376158341	2		362	1156	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509539	46509539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755888231	NA	P-0048286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	325	218	0	ENST00000262741.5:c.1192G>A	p.Asp398Asn	p.D398N	ENST00000262741	NM_003629.3	398	Gat/Aat	10/10	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.83682376158341	2		218	568	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880537	155880537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	712	685	0	ENST00000368323.3:c.16C>T	p.Arg6Cys	p.R6C	ENST00000368323	NM_006912.5	6	Cgc/Tgc	2/6	0.837275507839188	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	1	0.83682376158341	3		685	1100	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983105	201983105	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	727	354	0	ENST00000359651.3:c.954G>C	p.Lys318Asn	p.K318N	ENST00000359651		318	aaG/aaC	7/8	0.837275507839188	3	FACETS	0.831	0.805	0.857	0.831	0.805	0.857	CLONAL	2	TRUE	1	0.83682376158341	3		354	1483	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63816987	63816987	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	316	126	0	ENST00000279873.7:c.958G>C	p.Asp320His	p.D320H	ENST00000279873	NM_032199.2	320	Gat/Cat	6/10	0.83682376158341	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.83682376158341	1		126	357	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981807	101981807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	590	322	0	ENST00000282441.5:c.228G>T	p.Lys76Asn	p.K76N	ENST00000282441	NM_001130145.2	76	aaG/aaT	1/9	1	2	FACETS	0.758	0.735	0.781	1	0.997	1	SUBCLONAL	2	TRUE	1	0.83682376158341	2		322	930	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914329	32914329	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	490	169	0	ENST00000380152.3:c.5837C>A	p.Ser1946Ter	p.S1946*	ENST00000380152		1946	tCa/tAa	11/27	1	2	FACETS	0.877	0.852	0.901	1	0.998	1	CLONAL	2	TRUE	1	0.83682376158341	2		169	668	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914766	32914766	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779365	NA	P-0048286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	471	211	0	ENST00000380152.3:c.6274C>T	p.Leu2092Phe	p.L2092F	ENST00000380152		2092	Ctt/Ttt	11/27	1	2	FACETS	0.829	0.803	0.854	1	0.997	1	CLONAL	2	TRUE	1	0.83682376158341	2		211	679	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914851	32914851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507845	NA	P-0048286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	485	162	0	ENST00000380152.3:c.6359C>T	p.Ser2120Leu	p.S2120L	ENST00000380152		2120	tCa/tTa	11/27	1	2	FACETS	0.822	0.797	0.847	1	0.997	1	CLONAL	2	TRUE	1	0.83682376158341	2		162	705	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914961	32914961	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs397507859	NA	P-0048286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	492	161	0	ENST00000380152.3:c.6469C>G	p.Gln2157Glu	p.Q2157E	ENST00000380152		2157	Caa/Gaa	11/27	1	2	FACETS	0.887	0.862	0.911	1	0.998	1	CLONAL	2	TRUE	1	0.83682376158341	2		161	663	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918751	32918751	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	238	85	0	ENST00000380152.3:c.6898C>G	p.Gln2300Glu	p.Q2300E	ENST00000380152		2300	Caa/Gaa	12/27	1	2	FACETS	0.844	0.808	0.879	1	0.995	1	CLONAL	2	TRUE	1	0.83682376158341	2		85	337	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953785	48953785	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0048286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	223	108	0	ENST00000267163.4:c.1388C>G	p.Ser463Ter	p.S463*	ENST00000267163	NM_000321.2	463	tCa/tGa	14/27	0.837275507839188	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.83682376158341	1		108	243	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052623	42052623	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	491	344	2	ENST00000219905.7:c.7294G>T	p.Glu2432Ter	p.E2432*	ENST00000219905	NM_001164273.1	2432	Gag/Tag	20/24	1	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	1	0.83682376158341	2		346	852	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346805	91346805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	434	200	0	ENST00000355112.3:c.3413C>T	p.Ser1138Leu	p.S1138L	ENST00000355112	NM_000057.2	1138	tCa/tTa	18/22	1	2	FACETS	0.768	0.742	0.795	1	0.997	1	SUBCLONAL	2	TRUE	1	0.83682376158341	2		200	675	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0048286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	644	639	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.837275507839188	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.83682376158341	2		639	679	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805601	46805601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	1001	848	0	ENST00000290295.7:c.355G>A	p.Glu119Lys	p.E119K	ENST00000290295	NM_006361.5	119	Gag/Aag	1/2	0.837275507839188	2	FACETS	1	0.999	1	1	0.999	1	CLONAL	2	TRUE	0	0.83682376158341	2		848	1049	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223896	36223896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	834	343	0	ENST00000222270.7:c.6446C>T	p.Ser2149Phe	p.S2149F	ENST00000222270	NM_014727.1	2149	tCc/tTc	28/37	1	2	FACETS	0.79	0.771	0.809	1	0.998	1	SUBCLONAL	2	TRUE	1	0.83682376158341	2		343	1261	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52693371	52693371	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	663	298	0	ENST00000322088.6:c.22G>A	p.Asp8Asn	p.D8N	ENST00000322088	NM_014225.5	8	Gac/Aac	1/15	1	2	FACETS	0.813	0.792	0.835	1	0.998	1	CLONAL	2	TRUE	1	0.83682376158341	2		298	974	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519758	29519758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	516	248	0	ENST00000389048.3:c.1813G>A	p.Asp605Asn	p.D605N	ENST00000389048	NM_004304.4	605	Gac/Aac	9/29	1	2	FACETS	0.766	0.742	0.79	1	0.997	1	SUBCLONAL	2	TRUE	1	0.83682376158341	2		248	805	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719208	190719208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	344	81	0	ENST00000441310.2:c.1210G>A	p.Asp404Asn	p.D404N	ENST00000441310	NM_000534.4	404	Gat/Aat	9/13	1	2	FACETS	0.888	0.858	0.916	1	0.997	1	CLONAL	2	TRUE	1	0.83682376158341	2		81	463	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090407	37090407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750292	NA	P-0048286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	490	211	0	ENST00000231790.2:c.2002G>A	p.Glu668Lys	p.E668K	ENST00000231790	NM_000249.3	668	Gaa/Aaa	18/19	0.83682376158341	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.83682376158341	1		211	555	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090482	37090482	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	409	236	0	ENST00000231790.2:c.2077G>T	p.Glu693Ter	p.E693*	ENST00000231790	NM_000249.3	693	Gag/Tag	18/19	0.83682376158341	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.83682376158341	1		236	479	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526228	31526228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372705339	NA	P-0048286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1772	786	175	1	ENST00000344624.3:c.812G>A	p.Arg271Gln	p.R271Q	ENST00000344624		271	cGa/cAa	2/33	0.837275507839188	5	FACETS	0.828	0.799	0.858	0.414	0.399	0.429	CLONAL	2	TRUE	1	0.83682376158341	5		176	2558	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977958	131977958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781413356	NA	P-0048286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	513	195	0	ENST00000265335.6:c.3841G>A	p.Glu1281Lys	p.E1281K	ENST00000265335		1281	Gaa/Aaa	25/25	1	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	1	0.83682376158341	2		195	818	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636848	176636848	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	454	177	0	ENST00000439151.2:c.1448C>A	p.Ser483Tyr	p.S483Y	ENST00000439151	NM_022455.4	483	tCt/tAt	5/23	1	2	FACETS	0.786	0.76	0.812	1	0.997	1	SUBCLONAL	2	TRUE	1	0.83682376158341	2		177	690	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721675	176721675	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	547	212	0	ENST00000439151.2:c.7306G>C	p.Glu2436Gln	p.E2436Q	ENST00000439151	NM_022455.4	2436	Gaa/Caa	23/23	1	2	FACETS	0.805	0.781	0.828	1	0.998	1	CLONAL	2	TRUE	1	0.83682376158341	2		212	812	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287547	33287547	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	701	470	0	ENST00000374542.5:c.1550C>G	p.Ser517Cys	p.S517C	ENST00000374542	NM_001141970.1	517	tCt/tGt	6/8	1	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	1	0.83682376158341	2		470	1172	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045656	47045656	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0048286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	380	620	1	ENST00000377604.3:c.2538-1G>C		p.X846_splice	ENST00000377604	NM_001204468.1	846			0.767326459506451	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.83682376158341	2		621	400	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0048564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	75	253	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		253	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578260	7578260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204041	NA	P-0048564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	317	584	1	ENST00000269305.4:c.589G>A	p.Val197Met	p.V197M	ENST00000269305	NM_001126112.2	197	Gtg/Atg	6/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		585	521	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504584	103504584	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	109	330	1	ENST00000355739.4:c.205C>T	p.Arg69Ter	p.R69*	ENST00000355739	NM_000123.3	69	Cga/Tga	2/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		331	458	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027380	48027380	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs876660934	NA	P-0048564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	80	340	0	ENST00000234420.5:c.2258C>G	p.Ser753Cys	p.S753C	ENST00000234420	NM_000179.2	753	tCt/tGt	4/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		340	468	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48921999	48921999	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs367654488	NA	P-0048564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	220	288	0	ENST00000267163.4:c.539C>T	p.Ser180Leu	p.S180L	ENST00000267163	NM_000321.2	180	tCg/tTg	5/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		288	588	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242477	+	frameshift_variant	Frame_Shift_Del	DEL	TTAAGAGAA	TTAAGAGAA	C	novel	NA	P-0048564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	170	439	0	ENST00000275493.2:c.2239_2247delinsC	p.Leu747ArgfsTer13	p.L747Rfs*13	ENST00000275493	NM_005228.3	747	TTAAGAGAA/C	19/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		439	552	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70412286	70412286	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	182	276	0	ENST00000373644.4:c.4396A>T	p.Ile1466Leu	p.I1466L	ENST00000373644	NM_030625.2	1466	Ata/Tta	6/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		276	461	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361751	70361751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	329	698	2	ENST00000374080.3:c.6427C>T	p.Gln2143Ter	p.Q2143*	ENST00000374080		2143	Cag/Tag	44/45	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		700	849	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048716-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	254	375	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.837	0.794	0.879	1	0.996	1	CLONAL	3	FALSE	1	0.428749337972772	2		375	472	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0048716-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	1079	201	1	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.428749337972772	3	FACETS	1	0.996	1	1	0.998	1	CLONAL	3	FALSE	1	0.428749337972772	3		202	1852	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151863	108151863	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs377349886	NA	P-0048716-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	469	62	0	ENST00000278616.4:c.3544G>C	p.Glu1182Gln	p.E1182Q	ENST00000278616	NM_000051.3	1182	Gag/Cag	24/63	1	2	FACETS	1	0.992	1	1	0.998	1	CLONAL	3	FALSE	1	0.428749337972772	2		62	679	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830754	3830754	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048716-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	575	84	0	ENST00000262367.5:c.1802G>C	p.Arg601Pro	p.R601P	ENST00000262367	NM_004380.2	601	cGg/cCg	8/31	1	2	FACETS	1	0.994	1	1	0.998	1	CLONAL	3	FALSE	1	0.428749337972772	2		84	829	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971091	21971100	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCTCCCGG	GCCCTCCCGG	-	novel	NA	P-0048716-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	447	81	0	ENST00000304494.5:c.258_267del	p.Arg87SerfsTer56	p.R87Sfs*56	ENST00000304494	NM_000077.4	86	gcCCGGGAGGGC/gc	2/3	0.428749337972772	1	FACETS	1	0.995	1	1	0.998	1	CLONAL	2	FALSE	0	0.428749337972772	1		81	699	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807891	1807894	+	missense_variant	Missense_Mutation	ONP	GACG	GACG	CACA	novel	NA	P-0048716-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	1415	1263	0	ENST00000260795.2:c.1950_1953delinsCACA	p.Lys650Asn	p.K650N	ENST00000260795		650	aaGACG/aaCACA	13/17	0.428749337972772	10	FACETS	1	0.988	1			1	CLONAL	9	FALSE	NA	0.428749337972772	10		1263	1978	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0049350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	684	443	1	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.330826381280101	2	FACETS	1	0.996	1	1	0.998	1	CLONAL	4	TRUE	0	0.343843320150708	2		444	893	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0049350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	477	645	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.343843320150708	64	FACETS	0.999	0.964	1			1	CLONAL	39	TRUE	NA	0.343843320150708	64		645	830	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679366	29679366	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs866445127	NA	P-0049350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	396	118	0	ENST00000356175.3:c.7486C>T	p.Arg2496Ter	p.R2496*	ENST00000356175	NM_000267.3	2496	Cga/Tga	50/57	0.330826381280101	2	FACETS	0.971	0.937	1	1	0.997	1	CLONAL	4	TRUE	0	0.343843320150708	2		118	593	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138639	37138639	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	593	47	0	ENST00000373509.5:c.173T>C	p.Val58Ala	p.V58A	ENST00000373509	NM_002648.3	58	gTc/gCc	2/6	0.343843320150708	4	FACETS	0.914	0.885	0.943	1	0.997	1	CLONAL	5	TRUE	1	0.343843320150708	4		47	1014	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039638	47039638	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1556778349	NA	P-0049350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	535	111	4	ENST00000377604.3:c.1090C>T	p.Gln364Ter	p.Q364*	ENST00000377604	NM_001204468.1	364	Cag/Tag	11/24	0.343843320150708	3	FACETS	1	0.989	1	1	0.998	1	CLONAL	4	TRUE	1	0.343843320150708	3		115	870	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837960	156837960	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	749	80	0	ENST00000524377.1:c.493G>T	p.Glu165Ter	p.E165*	ENST00000524377	NM_002529.3	165	Gag/Tag	5/17	0.343843320150708	4	FACETS	0.962	0.936	0.988	1	0.998	1	CLONAL	5	TRUE	1	0.343843320150708	4		80	1217	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380712	118380712	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	346	53	0	ENST00000534358.1:c.10950G>T	p.Met3650Ile	p.M3650I	ENST00000534358	NM_005933.3	3650	atG/atT	30/36	0.343843320150708	3	FACETS	1	0.963	1	1	0.997	1	CLONAL	4	TRUE	1	0.343843320150708	3		53	587	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920347	50920350	+	frameshift_variant	Frame_Shift_Del	DEL	AGAA	AGAA	-	novel	NA	P-0049350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	713	72	0	ENST00000440232.2:c.3113_3116del	p.Gln1038ArgfsTer6	p.Q1038Rfs*6	ENST00000440232	NM_002691.3	1038	cAGAAg/cg	25/27	0.343843320150708	3	FACETS	1	0.995	1	1	0.998	1	CLONAL	4	TRUE	1	0.343843320150708	3		72	1120	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498443	89498443	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	262	63	0	ENST00000336596.2:c.2415C>G	p.Ser805Arg	p.S805R	ENST00000336596	NM_005233.5	805	agC/agG	14/17	0.343843320150708	8	FACETS	1	0.951	1			1	CLONAL	5	TRUE	NA	0.343843320150708	8		63	615	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38966781	38966781	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	237	27	0	ENST00000357387.3:c.1261G>C	p.Val421Leu	p.V421L	ENST00000357387	NM_152756.3	421	Gtt/Ctt	15/38	0.343843320150708	5	FACETS	1	0.969	1	1	0.969	1	CLONAL	4	TRUE	1	0.343843320150708	5		27	503	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912308	97912308	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	372	104	0	ENST00000289081.3:c.583G>T	p.Asp195Tyr	p.D195Y	ENST00000289081	NM_000136.2	195	Gat/Tat	7/15	0.343843320150708	3	FACETS	1	0.992	1	1	0.997	1	CLONAL	4	TRUE	1	0.343843320150708	3		104	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0049350-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	384	776	0	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	NA	2	FACETS	0.907	0.865	0.949			1	INDETERMINATE	2	TRUE	NA	0.46943685707309	2		776	902	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412046	116412046	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	T	novel	NA	P-0049350-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	532	692	0	ENST00000397752.3:c.3028+3A>T		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.441671053888013	3	FACETS	0.991	0.957	1	0.991	0.957	1	CLONAL	3	TRUE	0	0.46943685707309	3		692	941	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343223	118343223	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049350-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	85	270	0	ENST00000534358.1:c.1349G>T	p.Arg450Ile	p.R450I	ENST00000534358	NM_005933.3	450	aGa/aTa	3/36	0.420302810835948	5	FACETS	1	0.944	1			1	CLONAL	1	TRUE	NA	0.46943685707309	5		270	557	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685998	29685998	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049350-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	81	304	0	ENST00000356175.3:c.8062A>C	p.Asn2688His	p.N2688H	ENST00000356175	NM_000267.3	2688	Aat/Cat	55/57	0.159966405667317	3	FACETS	1	0.912	1	0.517	0.458	0.58	INDETERMINATE	1	TRUE	1	0.46943685707309	3		304	412	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294214	1294214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757340699	NA	P-0049350-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1407	165	996	2	ENST00000310581.5:c.787C>T	p.Arg263Cys	p.R263C	ENST00000310581	NM_198253.2	263	Cgt/Tgt	2/16	0.447318145377091	4	FACETS	0.657	0.601	0.716	0.219	0.2	0.239	SUBCLONAL	1	TRUE	1	0.46943685707309	4		998	1572	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	62	502	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.292240123425704	3	FACETS	0.992	0.868	1	0.992	0.868	1	CLONAL	2	TRUE	1	0.292240123425704	3		502	245	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0049535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	218	747	1	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.267244444980287	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.292240123425704	2		748	630	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023626	27023650	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCTGCCGGCTCCAAGCCGCCT	GGCGGCTGCCGGCTCCAAGCCGCCT	-	novel	NA	P-0049535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	89	463	0	ENST00000324856.7:c.732_756del	p.Ala245ProfsTer110	p.A245Pfs*110	ENST00000324856	NM_006015.4	244	gcGGCGGCTGCCGGCTCCAAGCCGCCT/gc	1/20	0.201736340611613	3	FACETS	1	0.975	1	0.676	0.601	0.756	CLONAL	1	TRUE	1	0.292240123425704	3		463	516	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105578	27105578	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	66	479	0	ENST00000324856.7:c.5192del	p.Leu1731Ter	p.L1731*	ENST00000324856	NM_006015.4	1730	aTt/at	20/20	0.201736340611613	3	FACETS	1	0.95	1	0.595	0.518	0.678	CLONAL	1	TRUE	1	0.292240123425704	3		479	435	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405961	70405961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752034407	NA	P-0049535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	36	471	0	ENST00000373644.4:c.3475C>T	p.Arg1159Trp	p.R1159W	ENST00000373644	NM_030625.2	1159	Cgg/Tgg	4/12	1	2	FACETS	0.858	0.709	1	0.858	0.709	1	CLONAL	1	TRUE	1	0.292240123425704	2		471	287	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577110	7577110	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	225	789	0	ENST00000269305.4:c.828del	p.Cys277ValfsTer68	p.C277Vfs*68	ENST00000269305	NM_001126112.2	276	gcC/gc	8/11	0.250802447795311	3	FACETS	1	0.985	1	0.784	0.733	0.837	CLONAL	2	TRUE	0	0.292240123425704	3		789	750	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575231	48575231	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0049535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	33	214	0	ENST00000342988.3:c.424+1G>C		p.X142_splice	ENST00000342988	NM_005359.5	142			0.278971515450154	3	FACETS	0.966	0.801	1	0.644	0.534	0.763	CLONAL	2	TRUE	0	0.292240123425704	3		214	134	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156731	20156731	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049830-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	188	219	0	ENST00000379607.5:c.26G>C	p.Gly9Ala	p.G9A	ENST00000379607	NM_001412.3	9	gGt/gCt	2/7	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.78	1		219	254	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10277314	10277314	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049830-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	97	876	0	ENST00000340748.4:c.803C>T	p.Ala268Val	p.A268V	ENST00000340748		268	gCa/gTa	10/40	1	2	FACETS	0.224	0.199	0.251	0.224	0.199	0.251	SUBCLONAL	1	TRUE	1	0.78	2		876	1109	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136127	11136127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049830-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	81	866	0	ENST00000358026.2:c.3111C>G	p.Asn1037Lys	p.N1037K	ENST00000358026	NM_001128849.1	1037	aaC/aaG	22/36	1	2	FACETS	0.185	0.162	0.21	0.185	0.162	0.21	SUBCLONAL	1	TRUE	1	0.78	2		866	1122	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	764	502	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.696490965147515	2	FACETS	0.874	0.851	0.897	0.874	0.851	0.897	CLONAL	2	TRUE	0	0.725887847257238	2		502	1204	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0050221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	431	758	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.725887847257238	1	FACETS	0.895	0.859	0.931	0.895	0.859	0.931	CLONAL	1	TRUE	0	0.725887847257238	1		758	845	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499667	149499667	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	316	626	1	ENST00000261799.4:c.2606G>A	p.Trp869Ter	p.W869*	ENST00000261799	NM_002609.3	869	tGg/tAg	19/23	1	2	FACETS	0.942	0.892	0.994	0.942	0.892	0.994	CLONAL	1	TRUE	1	0.725887847257238	2		627	924	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581246	48581267	+	frameshift_variant	Frame_Shift_Del	DEL	CATCCACCAAGTAATCGTGCAT	CATCCACCAAGTAATCGTGCAT	-	novel	NA	P-0050221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	283	504	0	ENST00000342988.3:c.551_572del	p.His184ArgfsTer11	p.H184Rfs*11	ENST00000342988	NM_005359.5	184	CATCCACCAAGTAATCGTGCATcg/cg	5/12	0.725887847257238	1	FACETS	0.952	0.906	0.997	0.952	0.906	0.997	CLONAL	1	TRUE	0	0.725887847257238	1		504	522	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97869457	97869457	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	533	857	0	ENST00000289081.3:c.1424C>G	p.Thr475Arg	p.T475R	ENST00000289081	NM_000136.2	475	aCa/aGa	14/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.725887847257238	2		857	1448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578509	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0050393-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	399	1339	1	ENST00000269305.4:c.421_422insA	p.Cys141Ter	p.C141*	ENST00000269305	NM_001126112.2	141	tgc/tAgc	5/11	1	2	FACETS	1	0.955	1	1	0.997	1	CLONAL	2	TRUE	1	0.377705549566974	2		1340	1054	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	81	375	0				ENST00000310581	NM_198253.2	-/1132			0.389903268090039	1	FACETS	0.74	0.656	0.829	0.74	0.656	0.829	SUBCLONAL	1	TRUE	0	0.440048853263935	1		375	388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0050495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	802	619	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.144547081185857	3	FACETS	0.911	0.888	0.934			1	INDETERMINATE	4	TRUE	NA	0.440048853263935	3		620	1220	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259651	11259651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	397	566	1	ENST00000361445.4:c.4054G>A	p.Glu1352Lys	p.E1352K	ENST00000361445	NM_004958.3	1352	Gaa/Aaa	27/58	0.386395007963018	1	FACETS	0.914	0.876	0.952	1	0.997	1	CLONAL	2	TRUE	0	0.440048853263935	1		567	770	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885731	23885731	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	641	782	0	ENST00000374561.5:c.187C>T	p.Gln63Ter	p.Q63*	ENST00000374561	NM_002167.4	63	Cag/Tag	1/3	0.440048853263935	3	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.440048853263935	3		782	1583	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944947	31944947	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	198	444	0	ENST00000340398.3:c.154C>G	p.Arg52Gly	p.R52G	ENST00000340398	NM_001013699.2	52	Cgt/Ggt	1/1	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.440048853263935	2		444	828	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420670	49420670	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs797045659	NA	P-0050495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	131	715	1	ENST00000301067.7:c.15079C>T	p.Arg5027Ter	p.R5027*	ENST00000301067	NM_003482.3	5027	Cga/Tga	48/54	0.440048853263935	1	FACETS	0.48	0.435	0.527	0.48	0.435	0.527	SUBCLONAL	1	TRUE	0	0.440048853263935	1		716	968	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911836	32911836	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs879255448	NA	P-0050495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	97	590	0	ENST00000380152.3:c.3344C>G	p.Ser1115Cys	p.S1115C	ENST00000380152		1115	tCt/tGt	11/27	0.144547081185857	3	FACETS	0.578	0.514	0.646			1	INDETERMINATE	1	TRUE	NA	0.440048853263935	3		590	931	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43783936	43783936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1027436739	NA	P-0050495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	79	555	0	ENST00000382044.4:c.302C>T	p.Ser101Phe	p.S101F	ENST00000382044	NM_001141980.1	101	tCt/tTt	4/28	0.440048853263935	1	FACETS	0.434	0.381	0.49	0.434	0.381	0.49	SUBCLONAL	1	TRUE	0	0.440048853263935	1		555	646	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223367	2223367	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	47	828	0	ENST00000326181.6:c.979G>C	p.Asp327His	p.D327H	ENST00000326181	NM_032271.2	327	Gac/Cac	10/21	0.328977829091693	0	FACETS	0.143	0.12	0.169			1	SUBCLONAL	1	TRUE	0	0.440048853263935	0		828	834	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81902822	81902822	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	291	511	0	ENST00000359376.3:c.483C>G	p.Ile161Met	p.I161M	ENST00000359376	NM_002661.3	161	atC/atG	6/33	1	2	FACETS	0.854	0.808	0.902	1	0.995	1	CLONAL	2	TRUE	1	0.440048853263935	2		511	774	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673799	37673799	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2564	207	564	0	ENST00000447079.4:c.2953G>C	p.Glu985Gln	p.E985Q	ENST00000447079	NM_015083.1	985	Gaa/Caa	10/14	0.440048853263935	11	FACETS	1	0.933	1			1	CLONAL	1	TRUE	NA	0.440048853263935	11		564	2771	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56409177	56409177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258933374	NA	P-0050495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	65	441	0	ENST00000348428.3:c.1684G>A	p.Asp562Asn	p.D562N	ENST00000348428	NM_006785.3	562	Gat/Aat	14/17	0.231973115044875	1	FACETS	0.394	0.341	0.451	0.394	0.341	0.451	INDETERMINATE	1	TRUE	0	0.440048853263935	1		441	585	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626892	158626892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	222	515	0	ENST00000263640.3:c.778G>A	p.Glu260Lys	p.E260K	ENST00000263640	NM_001105.4	260	Gaa/Aaa	7/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.440048853263935	2		515	836	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934238	49934238	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	120	733	0	ENST00000296474.3:c.2269C>A	p.Gln757Lys	p.Q757K	ENST00000296474	NM_002447.2	757	Cag/Aag	8/20	0.362677167700481	2	FACETS	0.562	0.506	0.62	0.281	0.253	0.31	SUBCLONAL	1	TRUE	0	0.440048853263935	2		733	971	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928351	69928351	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	74	522	0	ENST00000352241.4:c.171C>G	p.Ile57Met	p.I57M	ENST00000352241	NM_198159.2	57	atC/atG	2/10	0.362677167700481	2	FACETS	0.421	0.368	0.478	0.21	0.184	0.239	SUBCLONAL	1	TRUE	0	0.440048853263935	2		522	799	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498505	89498505	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	44	364	0	ENST00000336596.2:c.2477G>T	p.Trp826Leu	p.W826L	ENST00000336596	NM_005233.5	826	tGg/tTg	14/17	0.231002451795861	2	FACETS	0.337	0.282	0.398	0.168	0.141	0.199	INDETERMINATE	1	TRUE	0	0.440048853263935	2		364	594	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278274	142278274	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	212	511	0	ENST00000350721.4:c.1551C>G	p.Phe517Leu	p.F517L	ENST00000350721	NM_001184.3	517	ttC/ttG	7/47	0.241855761659815	3	FACETS	1	0.991	1	0.497	0.462	0.532	INDETERMINATE	1	TRUE	0	0.440048853263935	3		511	789	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808320	1808320	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	283	1142	0	ENST00000260795.2:c.2078C>G	p.Ser693Cys	p.S693C	ENST00000260795		693	tCc/tGc	15/17	0.440048853263935	1	FACETS	0.927	0.872	0.984	0.927	0.872	0.984	CLONAL	1	TRUE	0	0.440048853263935	1		1142	1082	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233715	233715	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	69	450	0	ENST00000264932.6:c.1019G>C	p.Arg340Thr	p.R340T	ENST00000264932	NM_004168.2	340	aGa/aCa	8/15	0.389903268090039	1	FACETS	0.366	0.318	0.417	0.366	0.318	0.417	SUBCLONAL	1	TRUE	0	0.440048853263935	1		450	669	SUCCESS
APC	324	MSKCC	GRCh37	5	112137036	112137036	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1434813233	NA	P-0050495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	56	476	0	ENST00000257430.4:c.790C>G	p.Gln264Glu	p.Q264E	ENST00000257430	NM_000038.5	264	Caa/Gaa	8/16	0.389903268090039	1	FACETS	0.301	0.257	0.349	0.301	0.257	0.349	SUBCLONAL	1	TRUE	0	0.440048853263935	1		476	659	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827887	170827887	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1431020185	NA	P-0050495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	67	372	0	ENST00000296930.5:c.627G>C	p.Gln209His	p.Q209H	ENST00000296930	NM_002520.6	209	caG/caC	8/11	0.440048853263935	1	FACETS	0.536	0.467	0.61	0.536	0.467	0.61	SUBCLONAL	1	TRUE	0	0.440048853263935	1		372	443	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225593	26225593	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1771	104	846	0	ENST00000360408.1:c.211C>G	p.Leu71Val	p.L71V	ENST00000360408	NM_003532.2	71	Ctg/Gtg	1/1	0.440048853263935	6	FACETS	0.474	0.422	0.53	0.079	0.07	0.089	SUBCLONAL	1	TRUE	0	0.440048853263935	6		846	1875	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431634	6431634	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	120	344	0	ENST00000356142.4:c.187G>C	p.Asp63His	p.D63H	ENST00000356142	NM_018890.3	63	Gat/Cat	3/7	0.231002451795861	2	FACETS	0.89	0.806	0.978	0.445	0.403	0.489	INDETERMINATE	1	TRUE	0	0.440048853263935	2		344	613	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902311	151902311	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0050495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	63	203	0	ENST00000262189.6:c.3842-1G>A		p.X1281_splice	ENST00000262189	NM_170606.2	1281			1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.440048853263935	2		203	266	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74868251	74868251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750853574	NA	P-0050495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	78	440	1	ENST00000284811.8:c.43G>A	p.Asp15Asn	p.D15N	ENST00000284811		15	Gat/Aat	3/4	0.25087403133495	4	FACETS	0.538	0.471	0.61	0.269	0.235	0.305	INDETERMINATE	1	TRUE	2	0.440048853263935	4		441	949	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626644	100626644	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	65	255	1	ENST00000308731.7:c.286G>A	p.Glu96Lys	p.E96K	ENST00000308731	NM_000061.2	96	Gaa/Aaa	4/19	0.401062078358449	0	FACETS	0.485	0.423	0.551			1	SUBCLONAL	1	TRUE	NA	0.440048853263935	0		256	341	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164949	47164949	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050510-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	39	320	0	ENST00000409792.3:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000409792	NM_014159.6	393	Cga/Tga	3/21	0.533339354623941	1	FACETS	0.71	0.599	0.83	0.71	0.599	0.83	SUBCLONAL	1	FALSE	0	0.533339354623941	1		320	151	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941252	36941252	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050510-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	280	899	0	ENST00000361632.4:c.87C>G	p.Ile29Met	p.I29M	ENST00000361632		29	atC/atG	3/16	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.533339354623941	2		899	1038	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188248	10188248	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050510-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	265	697	0	ENST00000256474.2:c.391A>T	p.Asn131Tyr	p.N131Y	ENST00000256474	NM_000551.3	131	Aac/Tac	2/3	0.533339354623941	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	0	0.533339354623941	1		697	626	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023009	150023010	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0050522-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	258	615	0	ENST00000253339.5:c.253_254del	p.Leu85AlafsTer6	p.L85Afs*6	ENST00000253339		85	CTg/g	1/7	0.436550919814191	2	FACETS	0.938	0.885	0.992	0.938	0.885	0.992	CLONAL	2	TRUE	0	0.436550919814191	2		615	630	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279542	123279577	+	inframe_deletion	In_Frame_Del	DEL	TTCTTTTCCACGTGCTTGATCCACTGGATGTGGGGC	TTCTTTTCCACGTGCTTGATCCACTGGATGTGGGGC	-	novel	NA	P-0050522-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	507	817	0	ENST00000358487.5:c.855_890del	p.Gln285_Asn297delinsHis	p.Q285_N297delinsH	ENST00000358487	NM_000141.4	285	caGCCCCACATCCAGTGGATCAAGCACGTGGAAAAGAAc/cac	7/18	0.309414003250349	5	FACETS	0.955	0.92	0.991			1	CLONAL	4	TRUE	NA	0.436550919814191	5		817	1006	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128600	30128600	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050522-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	232	515	0	ENST00000263025.4:c.782T>G	p.Leu261Arg	p.L261R	ENST00000263025	NM_002746.2	261	cTg/cGg	6/9	0.402334510217805	4	FACETS	0.933	0.873	0.996	0.933	0.873	0.996	CLONAL	2	TRUE	2	0.436550919814191	4		515	818	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	39	375	0				ENST00000310581	NM_198253.2	-/1132			0.245307107550435	5	FACETS	1	0.947	1	0.465	0.386	0.551	CLONAL	1	TRUE	2	0.245307107550435	5		375	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0050545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	178	619	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.245307107550435	2	FACETS	0.922	0.851	0.995	0.922	0.851	0.995	CLONAL	2	TRUE	0	0.245307107550435	2		620	787	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8497247	8497247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	41	265	1	ENST00000356435.5:c.2344G>A	p.Glu782Lys	p.E782K	ENST00000356435		782	Gaa/Aaa	15/35	0.170714379922608	3	FACETS	0.792	0.665	0.93	0.528	0.443	0.62	CLONAL	2	TRUE	0	0.245307107550435	3		266	237	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25990544	25990544	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0050545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	35	670	0	ENST00000435504.4:c.683C>G	p.Ser228Ter	p.S228*	ENST00000435504		228	tCa/tGa	8/13	0.180812001278319	3	FACETS	0.637	0.521	0.767	0.318	0.26	0.384	SUBCLONAL	1	TRUE	1	0.245307107550435	3		670	503	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050980	49050980	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0050545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	60	308	0	ENST00000267163.4:c.2663+1G>A		p.X888_splice	ENST00000267163	NM_000321.2	888			0.170714379922608	3	FACETS	0.868	0.759	0.982	0.868	0.759	0.982	CLONAL	3	TRUE	0	0.245307107550435	3		308	211	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17359601	17359601	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	107	515	0	ENST00000375499.3:c.240G>C	p.Lys80Asn	p.K80N	ENST00000375499	NM_003000.2	80	aaG/aaC	3/8	0.0831854400278249	4	FACETS	1	0.948	1	1	0.948	1	INDETERMINATE	2	TRUE	2	0.245307107550435	4		515	503	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793095	33793095	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	56	453	0	ENST00000498907.2:c.226G>T	p.Glu76Ter	p.E76*	ENST00000498907	NM_004364.3	76	Gag/Tag	1/1	0.196744258777539	4	FACETS	1	0.901	1	0.355	0.304	0.411	CLONAL	1	TRUE	1	0.245307107550435	4		453	534	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738308	190738308	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1238956903	NA	P-0050545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	66	357	0	ENST00000441310.2:c.2560C>G	p.Leu854Val	p.L854V	ENST00000441310	NM_000534.4	854	Ctt/Gtt	12/13	0.245307107550435	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	2	TRUE	0	0.245307107550435	2		357	267	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400125	41400125	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	81	725	0	ENST00000373198.4:c.634C>T	p.Gln212Ter	p.Q212*	ENST00000373198	NM_133170.3	212	Cag/Tag	5/32	0.180812001278319	3	FACETS	1	0.929	1	0.538	0.474	0.607	CLONAL	1	TRUE	1	0.245307107550435	3		725	689	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260723	16260724	+	missense_variant	Missense_Mutation	DNP	TC	TC	GA	novel	NA	P-0050545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	77	921	1	ENST00000375759.3:c.7988_7989inv	p.Val2663Gly	p.V2663G	ENST00000375759	NM_015001.2	2663	gTC/gGA	11/15	0.0831854400278249	4	FACETS	0.943	0.827	1	0.472	0.413	0.535	INDETERMINATE	1	TRUE	2	0.245307107550435	4		922	829	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433707	49433707	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	99	1390	0	ENST00000301067.7:c.7846C>G	p.Leu2616Val	p.L2616V	ENST00000301067	NM_003482.3	2616	Ctg/Gtg	31/54	0.181660366395449	3	FACETS	1	0.904	1	0.507	0.452	0.566	CLONAL	1	TRUE	1	0.245307107550435	3		1390	893	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95599689	95599689	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	41	484	0	ENST00000393063.1:c.107C>G	p.Ala36Gly	p.A36G	ENST00000393063	NM_030621.3	36	gCa/gGa	3/28	0.180812001278319	3	FACETS	0.711	0.591	0.844	0.355	0.295	0.422	SUBCLONAL	1	TRUE	1	0.245307107550435	3		484	528	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960951	15960951	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	102	526	0	ENST00000268712.3:c.6269C>G	p.Ser2090Cys	p.S2090C	ENST00000268712	NM_006311.3	2090	tCt/tGt	40/46	0.180812001278319	3	FACETS	0.973	0.874	1	0.973	0.874	1	CLONAL	2	TRUE	1	0.245307107550435	3		526	480	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855828	45855828	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	82	1216	2	ENST00000391945.4:c.1982C>A	p.Ala661Asp	p.A661D	ENST00000391945	NM_000400.3	661	gCc/gAc	21/23	0.196744258777539	4	FACETS	0.893	0.786	1	0.298	0.262	0.337	CLONAL	1	TRUE	1	0.245307107550435	4		1218	932	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617491	158617491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	57	694	0	ENST00000263640.3:c.1165G>A	p.Glu389Lys	p.E389K	ENST00000263640	NM_001105.4	389	Gaa/Aaa	9/11	0.245307107550435	2	FACETS	0.796	0.683	0.919	0.398	0.341	0.46	CLONAL	1	TRUE	0	0.245307107550435	2		694	584	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80646089	80646089	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	12	155	0	ENST00000286548.4:c.63C>G	p.Ile21Met	p.I21M	ENST00000286548	NM_002072.3	21	atC/atG	1/7	0.170714379922608	3	FACETS	1	0.789	1	0.381	0.271	0.514	CLONAL	1	TRUE	0	0.245307107550435	3		155	96	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057833	27057835	+	stop_gained	Nonsense_Mutation	TNP	CTC	CTC	TTT	novel	NA	P-0050545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	187	967	1	ENST00000324856.7:c.1541_1543delinsTTT	p.Ser514_Gln515delinsPheTer	p.S514_Q515delinsF*	ENST00000324856	NM_006015.4	514	tCTCag/tTTTag	3/20	0.0831854400278249	4	FACETS	1	0.982	1	1	0.982	1	INDETERMINATE	2	TRUE	2	0.245307107550435	4		968	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0050760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	530	178	0	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	NA	2	FACETS	0.94	0.908	0.972			1	INDETERMINATE	3	TRUE	NA	0.397734885862687	2		178	945	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28882987	28882987	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1459098012	NA	P-0050760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	388	57	0	ENST00000282397.4:c.3713T>C	p.Met1238Thr	p.M1238T	ENST00000282397	NM_002019.4	1238	aTg/aCg	28/30	0.365955546553875	2	FACETS	0.997	0.951	1	0.997	0.951	1	CLONAL	2	TRUE	0	0.397734885862687	2		57	978	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	94	375	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.874	0.791	0.959	0.874	0.791	0.959	CLONAL	1	TRUE	1	0.860573478871891	2		375	250	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0051298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	308	248	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.943	0.894	0.993	0.943	0.894	0.993	CLONAL	1	TRUE	1	0.860573478871891	2		248	759	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0051298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	413	547	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			1	2	FACETS	0.998	0.954	1	0.998	0.954	1	CLONAL	1	TRUE	1	0.860573478871891	2		547	962	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624266	89624268	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0051298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	166	422	0	ENST00000371953.3:c.42_44del	p.Arg15del	p.R15del	ENST00000371953	NM_000314.4	14	AGG/-	1/9	0.860573478871891	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.860573478871891	1		422	213	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941718	48941719	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0051298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	165	308	0	ENST00000267163.4:c.1028_1029del	p.Leu343ProfsTer3	p.L343Pfs*3	ENST00000267163	NM_000321.2	343	cTT/c	10/27	0.860573478871891	1	FACETS	0.993	0.946	1	0.993	0.946	1	CLONAL	1	TRUE	0	0.860573478871891	1		308	220	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933534	39933546	+	frameshift_variant	Frame_Shift_Del	DEL	CGAGTAGGTGTCT	CGAGTAGGTGTCT	-	novel	NA	P-0051298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	317	570	0	ENST00000378444.4:c.1053_1065del	p.Asp352SerfsTer22	p.D352Sfs*22	ENST00000378444	NM_001123385.1	351	gcAGACACCTACTCG/gc	4/15	1	1	FACETS	0.978	0.944	1	0.978	0.944	1	CLONAL	1	TRUE	0	0.860573478871891	1		570	429	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	381	375	0				ENST00000310581	NM_198253.2	-/1132			0.693600825899544	7	FACETS	1	0.987	1	0.856	0.82	0.891	CLONAL	4	TRUE	2	0.693600825899544	7		375	702	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	827	16	1	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	0.772	0.75	0.794	1	0.998	1	SUBCLONAL	2	TRUE	1	0.693600825899544	2		17	1545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	712	619	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.693600825899544	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	1	0.693600825899544	3		620	1171	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	590	335	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.693600825899544	3	FACETS	0.964	0.93	0.997	0.964	0.93	0.997	CLONAL	2	TRUE	1	0.693600825899544	3		335	1189	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817754	3817754	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	442	456	0	ENST00000262367.5:c.3217C>T	p.Gln1073Ter	p.Q1073*	ENST00000262367	NM_004380.2	1073	Cag/Tag	16/31	0.693600825899544	3	FACETS	1	0.993	1	0.761	0.733	0.789	CLONAL	2	TRUE	0	0.693600825899544	3		456	752	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	491	650	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	0.693600825899544	4	FACETS	1	0.986	1	0.705	0.676	0.734	CLONAL	2	TRUE	1	0.693600825899544	4		650	1134	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402595	20402595	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	389	218	0	ENST00000346618.3:c.132C>A	p.Phe44Leu	p.F44L	ENST00000346618	NM_001949.4	44	ttC/ttA	1/7	0.255558572814305	6	FACETS	0.868	0.827	0.91	0.868	0.827	0.91	INDETERMINATE	3	TRUE	3	0.693600825899544	6		218	1028	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742108	145742108	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	703	283	0	ENST00000428558.2:c.395G>C	p.Arg132Thr	p.R132T	ENST00000428558	NM_004260.3	132	aGa/aCa	5/22	0.0919285993720185	6	FACETS	0.881	0.853	0.909			1	INDETERMINATE	4	TRUE	NA	0.693600825899544	6		283	1373	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122397	17122397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	717	288	0	ENST00000285071.4:c.998C>T	p.Ser333Leu	p.S333L	ENST00000285071	NM_144997.5	333	tCa/tTa	9/14	0.693600825899544	3	FACETS	0.969	0.938	0.999	0.969	0.938	0.999	CLONAL	2	TRUE	1	0.693600825899544	3		288	1437	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923119	48923119	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	219	206	1	ENST00000267163.4:c.568del	p.Val190CysfsTer2	p.V190Cfs*2	ENST00000267163	NM_000321.2	189	ttG/tt	6/27	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.693600825899544	2		207	254	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663734	29663734	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	417	192	0	ENST00000356175.3:c.6166G>A	p.Asp2056Asn	p.D2056N	ENST00000356175	NM_000267.3	2056	Gat/Aat	41/57	0.466238429470133	5	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.693600825899544	5		192	1026	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533950	63533950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	457	143	0	ENST00000307078.5:c.1204G>A	p.Glu402Lys	p.E402K	ENST00000307078	NM_004655.3	402	Gaa/Aaa	6/11	0.693600825899544	6	FACETS	0.892	0.853	0.931	0.669	0.64	0.698	CLONAL	3	TRUE	2	0.693600825899544	6		143	1176	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371641	225371641	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	415	137	0	ENST00000264414.4:c.963G>C	p.Leu321Phe	p.L321F	ENST00000264414	NM_003590.4	321	ttG/ttC	7/16	1	2	FACETS	0.897	0.864	0.929	1	0.997	1	CLONAL	2	TRUE	1	0.693600825899544	2		137	667	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120460379	120460379	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	321	508	0	ENST00000256646.2:c.5936C>G	p.Ser1979Cys	p.S1979C	ENST00000256646	NM_024408.3	1979	tCt/tGt	33/34	0.693600825899544	3	FACETS	0.996	0.964	1	0.996	0.964	1	CLONAL	3	TRUE	0	0.693600825899544	3		508	417	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733140	74733140	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1546	675	334	0	ENST00000359995.5:c.103G>C	p.Glu35Gln	p.E35Q	ENST00000359995	NM_001195427.1	35	Gag/Cag	1/3	0.693600825899544	6	FACETS	1	0.985	1	0.523	0.503	0.543	CLONAL	2	TRUE	2	0.693600825899544	6		334	2221	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972753	25972753	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs369128452	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	397	339	0	ENST00000435504.4:c.1672C>G	p.Leu558Val	p.L558V	ENST00000435504		558	Ctt/Gtt	12/13	0.693600825899544	3	FACETS	0.924	0.894	0.954	0.924	0.894	0.954	CLONAL	3	TRUE	0	0.693600825899544	3		339	556	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663366	29663366	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	351	139	0	ENST00000356175.3:c.5959G>C	p.Asp1987His	p.D1987H	ENST00000356175	NM_000267.3	1987	Gat/Cat	40/57	0.466238429470133	5	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.693600825899544	5		139	839	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476785	140476785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	336	175	0	ENST00000288602.6:c.1621C>T	p.Leu541Phe	p.L541F	ENST00000288602	NM_004333.4	541	Ctc/Ttc	13/18	0.693600825899544	3	FACETS	0.927	0.883	0.97	0.927	0.883	0.97	CLONAL	2	TRUE	1	0.693600825899544	3		175	704	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055755	152055755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1403418496	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	332	140	0	ENST00000262189.6:c.167G>A	p.Arg56Gln	p.R56Q	ENST00000262189	NM_170606.2	56	cGa/cAa	2/59	0.693600825899544	3	FACETS	0.917	0.874	0.961	0.917	0.874	0.961	CLONAL	2	TRUE	1	0.693600825899544	3		140	703	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868298	37868298	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs532077147	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	568	199	0	ENST00000269571.5:c.1019G>A	p.Arg340Gln	p.R340Q	ENST00000269571		340	cGa/cAa	8/27	0.693600825899544	3	FACETS	0.97	0.936	1	0.97	0.936	1	CLONAL	2	TRUE	1	0.693600825899544	3		199	1137	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564566	41564566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	457	212	1	ENST00000263253.7:c.3988G>A	p.Asp1330Asn	p.D1330N	ENST00000263253	NM_001429.3	1330	Gac/Aac	24/31	0.693600825899544	1	FACETS		NA	1	1	0.998	1	NA	2	TRUE	0	0.693600825899544	1		213	539	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	618	279	0	ENST00000267101.3:c.273G>C	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atC	3/28	0.693600825899544	4	FACETS	0.985	0.949	1	0.657	0.632	0.681	CLONAL	2	TRUE	1	0.693600825899544	4		279	1532	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201074	108201074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	343	144	0	ENST00000278616.4:c.7441G>A	p.Asp2481Asn	p.D2481N	ENST00000278616	NM_000051.3	2481	Gat/Aat	50/63	0.300713233962596	5	FACETS	1	0.976	1	1	0.976	1	INDETERMINATE	3	TRUE	2	0.693600825899544	5		144	652	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775007	73775007	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	358	125	0	ENST00000254810.4:c.166C>T	p.Gln56Ter	p.Q56*	ENST00000254810	NM_005324.3	56	Cag/Tag	3/4	0.693600825899544	6	FACETS	1	0.992	1	0.607	0.576	0.638	CLONAL	2	TRUE	2	0.693600825899544	6		125	1015	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215282	123215282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	174	132	0	ENST00000218089.9:c.2828C>T	p.Ser943Phe	p.S943F	ENST00000218089	NM_001042749.1	943	tCt/tTt	28/35	0.693600825899544	2	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.693600825899544	2		132	402	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105238746	105238746	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749544983	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	788	293	1	ENST00000349310.3:c.1216C>T	p.Arg406Cys	p.R406C	ENST00000349310	NM_001014432.1	406	Cgc/Tgc	13/15	0.693600825899544	3	FACETS	0.959	0.93	0.988	0.959	0.93	0.988	CLONAL	2	TRUE	1	0.693600825899544	3		294	1595	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11308144	11308144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751686958	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	414	161	0	ENST00000361445.4:c.848G>A	p.Arg283Lys	p.R283K	ENST00000361445	NM_004958.3	283	aGa/aAa	7/58	0.692228389198014	2	FACETS	0.868	0.835	0.9	0.868	0.835	0.9	CLONAL	2	TRUE	0	0.693600825899544	2		161	688	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510724	120510724	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	529	238	0	ENST00000256646.2:c.1240G>A	p.Glu414Lys	p.E414K	ENST00000256646	NM_024408.3	414	Gaa/Aaa	7/34	0.693600825899544	3	FACETS	0.868	0.835	0.902	0.579	0.556	0.601	CLONAL	2	TRUE	0	0.693600825899544	3		238	1183	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226574074	226574074	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	454	206	0	ENST00000366794.5:c.787G>C	p.Glu263Gln	p.E263Q	ENST00000366794	NM_001618.3	263	Gag/Cag	6/23	0.688310414371735	3	FACETS	0.879	0.843	0.915	0.586	0.562	0.61	CLONAL	2	TRUE	0	0.693600825899544	3		206	1003	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402005	402005	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	425	270	0	ENST00000399788.2:c.4786G>C	p.Asp1596His	p.D1596H	ENST00000399788	NM_001042603.1	1596	Gac/Cac	27/28	0.693600825899544	7	FACETS	1	0.993	1	0.615	0.586	0.645	CLONAL	2	TRUE	3	0.693600825899544	7		270	1362	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402286	402286	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1285922080	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1523	568	205	1	ENST00000399788.2:c.4505C>T	p.Ser1502Leu	p.S1502L	ENST00000399788	NM_001042603.1	1502	tCa/tTa	27/28	0.693600825899544	7	FACETS	1	0.987	1	0.535	0.512	0.559	CLONAL	2	TRUE	3	0.693600825899544	7		206	2091	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231349	46231349	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	296	138	0	ENST00000334344.6:c.1189C>T	p.Gln397Ter	p.Q397*	ENST00000334344	NM_152641.2	397	Cag/Tag	10/21	0.693600825899544	4	FACETS	1	0.973	1	0.693	0.657	0.73	CLONAL	2	TRUE	1	0.693600825899544	4		138	695	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222689	69222689	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	406	391	0	ENST00000462284.1:c.662C>G	p.Ser221Cys	p.S221C	ENST00000462284	NM_002392.5	221	tCt/tGt	8/11	0.693600825899544	4	FACETS	1	0.989	1	0.73	0.698	0.763	CLONAL	2	TRUE	1	0.693600825899544	4		391	905	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597565	28597565	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	471	177	0	ENST00000241453.7:c.2340G>C	p.Leu780Phe	p.L780F	ENST00000241453	NM_004119.2	780	ttG/ttC	19/24	0.693600825899544	4	FACETS	0.852	0.814	0.89	0.852	0.814	0.89	CLONAL	2	TRUE	2	0.693600825899544	4		177	1350	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915148	32915148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	376	159	0	ENST00000380152.3:c.6656C>T	p.Ser2219Leu	p.S2219L	ENST00000380152		2219	tCa/tTa	11/27	0.693600825899544	4	FACETS	0.958	0.913	1	0.958	0.913	1	CLONAL	2	TRUE	2	0.693600825899544	4		159	958	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337651	73337651	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	177	85	0	ENST00000377767.4:c.2065C>G	p.Arg689Gly	p.R689G	ENST00000377767	NM_014953.3	689	Cga/Gga	16/21	0.670176477712377	4	FACETS	0.886	0.823	0.949	0.886	0.823	0.949	CLONAL	2	TRUE	2	0.693600825899544	4		85	488	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023294	33023294	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1354011335	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	680	275	1	ENST00000300177.4:c.403G>A	p.Glu135Lys	p.E135K	ENST00000300177	NM_001191322.1	135	Gaa/Aaa	2/2	1	2	FACETS	0.884	0.859	0.909	1	0.998	1	CLONAL	2	TRUE	1	0.693600825899544	2		276	1109	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423587	88423587	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	497	224	0	ENST00000360948.2:c.2248G>C	p.Glu750Gln	p.E750Q	ENST00000360948	NM_001012338.2	750	Gag/Cag	18/19	1	2	FACETS	0.904	0.874	0.933	1	0.997	1	CLONAL	2	TRUE	1	0.693600825899544	2		224	793	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799337	88799337	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	441	170	1	ENST00000360948.2:c.48C>G	p.Phe16Leu	p.F16L	ENST00000360948	NM_001012338.2	16	ttC/ttG	2/19	1	2	FACETS	0.878	0.847	0.909	1	0.997	1	CLONAL	2	TRUE	1	0.693600825899544	2		171	724	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646305	23646305	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	557	198	0	ENST00000261584.4:c.1562C>G	p.Thr521Ser	p.T521S	ENST00000261584	NM_024675.3	521	aCc/aGc	4/13	0.693600825899544	3	FACETS	0.885	0.852	0.918	0.59	0.568	0.612	CLONAL	2	TRUE	0	0.693600825899544	3		198	1222	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663861	29663861	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	420	190	0	ENST00000356175.3:c.6293G>C	p.Arg2098Thr	p.R2098T	ENST00000356175	NM_000267.3	2098	aGa/aCa	41/57	0.466238429470133	5	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.693600825899544	5		190	1060	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664388	29664388	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	319	138	0	ENST00000356175.3:c.6367G>C	p.Glu2123Gln	p.E2123Q	ENST00000356175	NM_000267.3	2123	Gag/Cag	42/57	0.466238429470133	5	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.693600825899544	5		138	761	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325985	30325985	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	226	73	0	ENST00000322652.5:c.2183C>G	p.Ser728Ter	p.S728*	ENST00000322652	NM_015355.2	728	tCa/tGa	16/16	0.466238429470133	5	FACETS	0.866	0.815	0.917			1	CLONAL	3	TRUE	NA	0.693600825899544	5		73	512	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775215	73775215	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1353	664	251	0	ENST00000254810.4:c.41G>T	p.Gly14Val	p.G14V	ENST00000254810	NM_005324.3	14	gGg/gTg	2/4	0.693600825899544	6	FACETS	1	0.993	1	0.567	0.545	0.588	CLONAL	2	TRUE	2	0.693600825899544	6		251	2017	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394784	45394784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	330	145	0	ENST00000262160.6:c.565G>A	p.Glu189Lys	p.E189K	ENST00000262160	NM_005901.5	189	Gaa/Aaa	5/11	0.247354525954313	5	FACETS	0.923	0.879	0.967	0.554	0.527	0.581	INDETERMINATE	3	TRUE	0	0.693600825899544	5		145	701	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943694	17943694	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs201241352	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	808	255	0	ENST00000458235.1:c.2395C>G	p.Arg799Gly	p.R799G	ENST00000458235	NM_000215.3	799	Cgt/Ggt	18/24	0.693600825899544	3	FACETS	0.984	0.955	1	0.984	0.955	1	CLONAL	2	TRUE	1	0.693600825899544	3		255	1595	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630400	47630400	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	830	346	0	ENST00000233146.2:c.70C>A	p.Gln24Lys	p.Q24K	ENST00000233146	NM_000251.2	24	Cag/Aag	1/16	0.693600825899544	3	FACETS	1	0.995	1	0.726	0.706	0.746	CLONAL	2	TRUE	0	0.693600825899544	3		346	1480	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371586	225371586	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	345	100	0	ENST00000264414.4:c.1018G>C	p.Asp340His	p.D340H	ENST00000264414	NM_003590.4	340	Gac/Cac	7/16	1	2	FACETS	0.921	0.885	0.956	1	0.997	1	CLONAL	2	TRUE	1	0.693600825899544	2		100	540	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852507	42852507	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	635	195	1	ENST00000398585.3:c.579C>A	p.Phe193Leu	p.F193L	ENST00000398585	NM_001135099.1	193	ttC/ttA	6/14	0.693600825899544	5	FACETS	1	0.991	1	0.726	0.698	0.753	CLONAL	2	TRUE	2	0.693600825899544	5		196	1716	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165816	47165816	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs539506462	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	390	298	0	ENST00000409792.3:c.310C>A	p.Pro104Thr	p.P104T	ENST00000409792	NM_014159.6	104	Cca/Aca	3/21	0.693600825899544	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.693600825899544	3		298	689	SUCCESS
ATR	545	MSKCC	GRCh37	3	142254021	142254021	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	291	211	0	ENST00000350721.4:c.3846G>C	p.Gln1282His	p.Q1282H	ENST00000350721	NM_001184.3	1282	caG/caC	21/47	0.693600825899544	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	1	0.693600825899544	3		211	456	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149245641	149245641	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	557	225	0	ENST00000360632.3:c.887C>T	p.Ser296Leu	p.S296L	ENST00000360632	NM_015472.4	296	tCa/tTa	5/7	0.693600825899544	3	FACETS	0.876	0.844	0.909	0.876	0.844	0.909	CLONAL	2	TRUE	1	0.693600825899544	3		225	1234	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280088	66280088	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	258	92	0	ENST00000273854.3:c.1601C>T	p.Ser534Leu	p.S534L	ENST00000273854	NM_004439.5	534	tCa/tTa	7/18	0.693600825899544	3	FACETS	0.825	0.779	0.872	0.825	0.779	0.872	CLONAL	2	TRUE	1	0.693600825899544	3		92	607	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158129	106158129	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	246	115	0	ENST00000380013.4:c.3030G>C	p.Glu1010Asp	p.E1010D	ENST00000380013	NM_001127208.2	1010	gaG/gaC	3/11	1	2	FACETS	0.851	0.809	0.892	1	0.995	1	CLONAL	2	TRUE	1	0.693600825899544	2		115	417	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233625	233625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760542965	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	369	100	0	ENST00000264932.6:c.929G>A	p.Gly310Glu	p.G310E	ENST00000264932	NM_004168.2	310	gGa/gAa	8/15	0.693600825899544	7	FACETS	1	0.988	1	0.455	0.431	0.479	CLONAL	2	TRUE	2	0.693600825899544	7		100	1279	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38991158	38991158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	328	136	0	ENST00000357387.3:c.476C>T	p.Ser159Phe	p.S159F	ENST00000357387	NM_152756.3	159	tCc/tTc	7/38	0.693600825899544	7	FACETS	1	0.989	1	0.469	0.443	0.496	CLONAL	2	TRUE	2	0.693600825899544	7		136	1102	SUCCESS
APC	324	MSKCC	GRCh37	5	112173556	112173556	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	232	116	0	ENST00000257430.4:c.2265G>C	p.Arg755Ser	p.R755S	ENST00000257430	NM_000038.5	755	agG/agC	16/16	0.190194491485682	1	FACETS	1	0.988	1	1	0.988	1	INDETERMINATE	1	TRUE	0	0.693600825899544	1		116	385	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927011	131927011	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	206	84	0	ENST00000265335.6:c.1548G>C	p.Arg516Ser	p.R516S	ENST00000265335		516	agG/agC	10/25	0.456815540409315	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.693600825899544	3		84	375	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680137	30680137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	613	296	0	ENST00000376406.3:c.1582G>A	p.Glu528Lys	p.E528K	ENST00000376406	NM_014641.2	528	Gaa/Aaa	5/15	0.670176477712377	4	FACETS	0.938	0.903	0.973	0.938	0.903	0.973	CLONAL	2	TRUE	2	0.693600825899544	4		296	1596	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137540382	137540382	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	604	258	0	ENST00000367739.4:c.83C>T	p.Ser28Leu	p.S28L	ENST00000367739	NM_000416.2	28	tCa/tTa	1/7	0.670176477712377	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.693600825899544	4		258	1398	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527386	157527386	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	314	159	0	ENST00000346085.5:c.5111G>T	p.Gly1704Val	p.G1704V	ENST00000346085	NM_020732.3	1704	gGa/gTa	20/20	0.670176477712377	4	FACETS	0.928	0.88	0.978	0.928	0.88	0.978	CLONAL	2	TRUE	2	0.693600825899544	4		159	826	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527871	157527871	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	413	180	0	ENST00000346085.5:c.5596G>C	p.Glu1866Gln	p.E1866Q	ENST00000346085	NM_020732.3	1866	Gaa/Caa	20/20	0.670176477712377	4	FACETS	0.981	0.937	1	0.981	0.937	1	CLONAL	2	TRUE	2	0.693600825899544	4		180	1028	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92354990	92354990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	261	125	0	ENST00000265734.4:c.487G>A	p.Asp163Asn	p.D163N	ENST00000265734	NM_001259.6	163	Gac/Aac	4/8	0.693600825899544	3	FACETS	0.832	0.786	0.879	0.832	0.786	0.879	CLONAL	2	TRUE	1	0.693600825899544	3		125	609	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506471	148506471	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	248	108	0	ENST00000320356.2:c.2041G>C	p.Asp681His	p.D681H	ENST00000320356	NM_004456.4	681	Gat/Cat	18/20	0.693600825899544	3	FACETS	0.923	0.872	0.973	0.923	0.872	0.973	CLONAL	2	TRUE	1	0.693600825899544	3		108	522	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860534	151860534	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	522	253	0	ENST00000262189.6:c.10128G>C	p.Gln3376His	p.Q3376H	ENST00000262189	NM_170606.2	3376	caG/caC	43/59	0.693600825899544	3	FACETS	0.912	0.878	0.947	0.912	0.878	0.947	CLONAL	2	TRUE	1	0.693600825899544	3		253	1111	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878254	151878254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	594	213	0	ENST00000262189.6:c.6691G>A	p.Glu2231Lys	p.E2231K	ENST00000262189	NM_170606.2	2231	Gag/Aag	36/59	0.693600825899544	3	FACETS	0.971	0.937	1	0.971	0.937	1	CLONAL	2	TRUE	1	0.693600825899544	3		213	1188	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486257	8486257	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs778093636	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	317	114	0	ENST00000356435.5:c.2560C>G	p.Gln854Glu	p.Q854E	ENST00000356435		854	Cag/Gag	17/35	0.593348846794491	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	2	0.693600825899544	4		114	764	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507412	8507412	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	240	94	0	ENST00000356435.5:c.1566C>G	p.Phe522Leu	p.F522L	ENST00000356435		522	ttC/ttG	11/35	0.593348846794491	4	FACETS	0.92	0.865	0.976	0.92	0.865	0.976	CLONAL	2	TRUE	2	0.693600825899544	4		94	637	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342644	70342644	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	309	298	0	ENST00000374080.3:c.1405G>C	p.Glu469Gln	p.E469Q	ENST00000374080		469	Gaa/Caa	10/45	0.693600825899544	2	FACETS	1	0.992	1			1	CLONAL	1	TRUE	NA	0.693600825899544	2		298	717	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344305	118344305	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	302	114	0	ENST00000534358.1:c.2431G>C	p.Glu811Gln	p.E811Q	ENST00000534358	NM_005933.3	811	Gag/Cag	3/36	0.300713233962596	5	FACETS	0.858	0.814	0.903	0.858	0.814	0.903	INDETERMINATE	3	TRUE	2	0.693600825899544	5		114	690	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562797	95562797	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	289	86	0	ENST00000393063.1:c.4460C>G	p.Ser1487Cys	p.S1487C	ENST00000393063	NM_030621.3	1487	tCc/tGc	24/28	0.693600825899544	3	FACETS	0.971	0.923	1	0.971	0.923	1	CLONAL	2	TRUE	1	0.693600825899544	3		86	578	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679696	30679696	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs746649941	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	632	252	0	ENST00000376406.3:c.2023G>C	p.Glu675Gln	p.E675Q	ENST00000376406	NM_014641.2	675	Gaa/Caa	5/15	0.670176477712377	4	FACETS	0.97	0.934	1	0.97	0.934	1	CLONAL	2	TRUE	2	0.693600825899544	4		252	1591	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790830	89790830	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052290-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1446	905	337	1	ENST00000336032.3:c.217C>A	p.Arg73Ser	p.R73S	ENST00000336032	NM_006813.2	73	Cgc/Agc	1/2	0.670176477712377	4	FACETS	0.94	0.911	0.969	0.94	0.911	0.969	CLONAL	2	TRUE	2	0.693600825899544	4		338	2351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0052291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	905	547	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.748109126647283	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.748109126647283	1		547	1176	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225525	133225525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762090058	NA	P-0052291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	735	197	2	ENST00000320574.5:c.4139C>T	p.Ser1380Leu	p.S1380L	ENST00000320574	NM_006231.2	1380	tCg/tTg	32/49	0.455353666253249	1	FACETS	0.916	0.889	0.943	0.916	0.889	0.943	CLONAL	1	TRUE	0	0.748109126647283	1		199	1343	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426124	49426124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326879451	NA	P-0052291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	880	419	0	ENST00000301067.7:c.12364G>A	p.Gly4122Arg	p.G4122R	ENST00000301067	NM_003482.3	4122	Gga/Aga	39/54	0.422449887634585	1	FACETS	1	0.996	1	1	0.996	1	INDETERMINATE	1	TRUE	0	0.748109126647283	1		419	1353	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115413	115115413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	663	112	1	ENST00000257566.3:c.913G>A	p.Asp305Asn	p.D305N	ENST00000257566	NM_016569.3	305	Gac/Aac	5/8	0.455353666253249	1	FACETS	0.992	0.963	1	0.992	0.963	1	CLONAL	1	TRUE	0	0.748109126647283	1		113	1118	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247817	59247817	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1637	907	207	1	ENST00000371222.2:c.926A>T	p.Lys309Ile	p.K309I	ENST00000371222	NM_002228.3	309	aAa/aTa	1/1	0.748109126647283	3	FACETS	1	0.997	1	0.655	0.634	0.676	CLONAL	1	TRUE	1	0.748109126647283	3		208	2544	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508651	38508659	+	inframe_deletion	In_Frame_Del	DEL	CAAGTGCAT	CAAGTGCAT	-	novel	NA	P-0052291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	780	133	1	ENST00000254066.5:c.701_709del	p.Lys234_Ile236del	p.K234_I236del	ENST00000254066	NM_000964.3	233	acCAAGTGCATc/acc	6/9	0.722132664237847	2	FACETS	1	0.998	1	0.742	0.72	0.763	CLONAL	1	TRUE	0	0.748109126647283	2		134	1406	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	114	375	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.874	0.8	0.95	0.874	0.8	0.95	CLONAL	1	TRUE	1	0.918460037734442	2		375	284	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505595	186505595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	136	251	0	ENST00000323963.5:c.1003C>T	p.Arg335Cys	p.R335C	ENST00000323963		335	Cgc/Tgc	10/11	1	2	FACETS	0.849	0.782	0.917	0.849	0.782	0.917	CLONAL	1	TRUE	1	0.918460037734442	2		251	349	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097665	27097665	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0052352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	235	482	0	ENST00000324856.7:c.3254C>G	p.Ser1085Ter	p.S1085*	ENST00000324856	NM_006015.4	1085	tCa/tGa	12/20	0.918460037734442	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.918460037734442	1		482	273	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983123	201983123	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	735	610	1	ENST00000359651.3:c.972G>A	p.Met324Ile	p.M324I	ENST00000359651		324	atG/atA	7/8	0.918460037734442	3	FACETS	0.998	0.987	1	0.998	0.987	1	CLONAL	3	TRUE	0	0.918460037734442	3		611	780	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46725695	46725695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1322473345	NA	P-0052352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	210	464	0	ENST00000371975.4:c.331G>A	p.Asp111Asn	p.D111N	ENST00000371975	NM_003579.3	111	Gac/Aac	5/18	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.918460037734442	2		464	429	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998928	100998928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773960696	NA	P-0052352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	323	855	2	ENST00000325455.5:c.874G>A	p.Gly292Arg	p.G292R	ENST00000325455	NM_001202474.3	292	Ggg/Agg	1/8	0.847349144718294	3	FACETS	1	0.983	1	0.546	0.517	0.576	CLONAL	1	TRUE	1	0.918460037734442	3		857	940	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214009	108214009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	340	293	0	ENST00000278616.4:c.8329G>A	p.Gly2777Ser	p.G2777S	ENST00000278616	NM_000051.3	2777	Ggt/Agt	57/63	0.847349144718294	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.918460037734442	3		293	531	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210913	133210913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755805420	NA	P-0052352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	447	643	0	ENST00000320574.5:c.5863G>A	p.Asp1955Asn	p.D1955N	ENST00000320574	NM_006231.2	1955	Gat/Aat	43/49	0.558709458219325	3	FACETS	0.943	0.909	0.977	0.943	0.909	0.977	CLONAL	2	TRUE	1	0.918460037734442	3		643	753	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675211	40675211	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	256	752	0	ENST00000249776.8:c.175G>C	p.Glu59Gln	p.E59Q	ENST00000249776	NM_033286.3	59	Gag/Cag	1/9	1	2	FACETS	0.938	0.886	0.991	0.938	0.886	0.991	CLONAL	1	TRUE	1	0.918460037734442	2		752	594	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478099	99478099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1163550820	NA	P-0052352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	132	376	0	ENST00000268035.6:c.3003G>A	p.Met1001Ile	p.M1001I	ENST00000268035	NM_000875.3	1001	atG/atA	16/21	1	2	FACETS	0.758	0.696	0.822	0.758	0.696	0.822	SUBCLONAL	1	TRUE	1	0.918460037734442	2		376	379	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640197	3640197	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	313	905	0	ENST00000294008.3:c.3442G>C	p.Glu1148Gln	p.E1148Q	ENST00000294008	NM_032444.2	1148	Gaa/Caa	12/15	1	2	FACETS	0.955	0.907	1	0.955	0.907	1	CLONAL	1	TRUE	1	0.918460037734442	2		905	714	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367942	15367942	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	278	904	0	ENST00000263377.2:c.1384G>C	p.Glu462Gln	p.E462Q	ENST00000263377	NM_058243.2	462	Gag/Cag	8/20	1	2	FACETS	0.94	0.89	0.991	0.94	0.89	0.991	CLONAL	1	TRUE	1	0.918460037734442	2		904	644	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443377	187443377	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	189	393	0	ENST00000232014.4:c.1749C>A	p.Phe583Leu	p.F583L	ENST00000232014	NM_001130845.1	583	ttC/ttA	8/10	1	2	FACETS	0.975	0.913	1	0.975	0.913	1	CLONAL	1	TRUE	1	0.918460037734442	2		393	422	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196295	106196295	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	141	277	0	ENST00000380013.4:c.4628G>C	p.Arg1543Thr	p.R1543T	ENST00000380013	NM_001127208.2	1543	aGa/aCa	11/11	1	2	FACETS	0.978	0.906	1	0.978	0.906	1	CLONAL	1	TRUE	1	0.918460037734442	2		277	314	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531018	187531018	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	199	379	0	ENST00000441802.2:c.10005C>G	p.Phe3335Leu	p.F3335L	ENST00000441802	NM_005245.3	3335	ttC/ttG	15/27	1	2	FACETS	0.938	0.879	0.998	0.938	0.879	0.998	CLONAL	1	TRUE	1	0.918460037734442	2		379	462	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665486	176665487	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0052352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	199	391	0	ENST00000439151.2:c.4171_4172dup	p.Leu1392AsnfsTer3	p.L1392Nfs*3	ENST00000439151	NM_022455.4	1390	-/GA	7/23	0.918460037734442	1	FACETS	0.949	0.912	0.983	0.949	0.912	0.983	CLONAL	1	TRUE	0	0.918460037734442	1		391	247	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120534	94120534	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	177	327	0	ENST00000369303.4:c.517G>C	p.Glu173Gln	p.E173Q	ENST00000369303	NM_004440.3	173	Gag/Cag	3/17	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.918460037734442	2		327	377	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324481	31324481	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs151341201	NA	P-0052352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	364	1013	0	ENST00000412585.2:c.327C>A	p.Tyr109Ter	p.Y109*	ENST00000412585	NM_005514.6	109	taC/taA	2/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.918460037734442	2		1013	728	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241722	55241722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1051753269	NA	P-0052366-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	98	553	0	ENST00000275493.2:c.2170G>A	p.Gly724Ser	p.G724S	ENST00000275493	NM_005228.3	724	Ggc/Agc	18/28	0.363355825516539	5	FACETS	1	0.959	1	0.385	0.343	0.429	CLONAL	1	TRUE	2	0.363355825516539	5		553	722	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0052366-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	111	378	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	0.363355825516539	5	FACETS	1	0.91	1	0.671	0.606	0.738	CLONAL	2	TRUE	2	0.363355825516539	5		378	469	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573094	41573095	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052366-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	100	972	0	ENST00000263253.7:c.5381dup	p.His1795AlafsTer88	p.H1795Afs*88	ENST00000263253	NM_001429.3	1793	-/A	31/31	1	2	FACETS	0.889	0.796	0.988	0.889	0.796	0.988	CLONAL	1	TRUE	1	0.363355825516539	2		972	619	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449782	8449782	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052366-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	83	560	2	ENST00000356435.5:c.3931C>A	p.Pro1311Thr	p.P1311T	ENST00000356435		1311	Cct/Act	23/35	0.363355825516539	5	FACETS	0.926	0.817	1	0.309	0.272	0.348	CLONAL	1	TRUE	2	0.363355825516539	5		562	762	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782144	NA	P-0052560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	471	1030	0	ENST00000269305.4:c.473G>C	p.Arg158Pro	p.R158P	ENST00000269305	NM_001126112.2	158	cGc/cCc	5/11	0.557340438468235	1	FACETS	0.974	0.933	1	0.974	0.933	1	CLONAL	1	TRUE	0	0.615567599441537	1		1030	1088	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272336	15272337	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs771517374	NA	P-0052560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1233	1450	1004	2	ENST00000263388.2:c.6102dup	p.Gly2035ArgfsTer60	p.G2035Rfs*60	ENST00000263388	NM_000435.2	2034	-/C	33/33	0.615567599441537	5	FACETS	1	0.997	1	0.844	0.826	0.862	CLONAL	3	TRUE	1	0.615567599441537	5		1006	2683	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022412	12022412	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	343	926	0	ENST00000396373.4:c.518C>G	p.Pro173Arg	p.P173R	ENST00000396373	NM_001987.4	173	cCt/cGt	5/8	0.311036567115718	6	FACETS	0.815	0.769	0.861			1	INDETERMINATE	2	TRUE	NA	0.615567599441537	6		926	1526	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	98	375	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.974	1			1	INDETERMINATE	2	TRUE	NA	0.311285741474793	2		375	259	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560476	95560476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	237	464	0	ENST00000393063.1:c.5113G>A	p.Glu1705Lys	p.E1705K	ENST00000393063	NM_030621.3	1705	Gaa/Aaa	25/28	1	2	FACETS	0.905	0.852	0.958	1	0.996	1	CLONAL	3	TRUE	1	0.311285741474793	2		464	561	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0052698-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	11	26	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.443	0.304	0.616	0.443	0.304	0.616	SUBCLONAL	1	TRUE	1	0.12	2		26	414	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314572	30314572	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052698-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	19	0	0	ENST00000262643.3:c.1121G>T	p.Arg374Leu	p.R374L	ENST00000262643	NM_001238.2	374	cGa/cTa	12/12	1	2	FACETS	0.372	0.28	0.48	0.372	0.28	0.48	SUBCLONAL	1	TRUE	1	0.12	2		0	852	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578254	7578254	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551821	NA	P-0052698-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	39	770	1	ENST00000269305.4:c.595G>T	p.Gly199Ter	p.G199*	ENST00000269305	NM_001126112.2	199	Gga/Tga	6/11	1	2	FACETS	0.826	0.682	0.987	0.826	0.682	0.987	CLONAL	1	TRUE	1	0.12	2		771	787	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587386	29587386	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0052698-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	18	375	0	ENST00000356175.3:c.4368-1G>T		p.X1456_splice	ENST00000356175	NM_000267.3	1456			1	2	FACETS	0.88	0.662	1	0.88	0.662	1	CLONAL	1	TRUE	1	0.12	2		375	341	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946445	2946445	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052698-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	50	926	0	ENST00000396946.4:c.3292G>T	p.Glu1098Ter	p.E1098*	ENST00000396946	NM_032415.4	1098	Gag/Tag	25/25	1	2	FACETS	0.985	0.833	1	0.985	0.833	1	CLONAL	1	TRUE	1	0.12	2		926	846	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161310	185161310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764242255	NA	P-0052753-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	701	166	0	ENST00000265026.3:c.737G>A	p.Arg246Gln	p.R246Q	ENST00000265026	NM_004721.4	246	cGa/cAa	4/14	1	2	FACETS	0.989	0.959	1	1	0.998	1	CLONAL	3	TRUE	1	0.373432607277697	2		166	1265	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236690	236690	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052753-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	631	122	0	ENST00000264932.6:c.1408A>C	p.Ser470Arg	p.S470R	ENST00000264932	NM_004168.2	470	Agc/Cgc	10/15	1	2	FACETS	1	0.987	1	1	0.998	1	CLONAL	3	TRUE	1	0.373432607277697	2		122	1089	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0052766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	41	271	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.131939556456183	4	FACETS	0.921	0.77	1	0.46	0.385	0.544	INDETERMINATE	1	TRUE	2	0.368124905651158	4		271	331	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121438948	121438948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146855738	NA	P-0052766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	256	712	1	ENST00000257555.6:c.1849G>A	p.Val617Ile	p.V617I	ENST00000257555		617	Gtc/Atc	10/10	0.25567825858222	3	FACETS	1	0.989	1	0.419	0.391	0.448	CLONAL	1	TRUE	0	0.368124905651158	3		713	1310	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0052766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	401	517	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.368124905651158	5	FACETS	0.939	0.894	0.985	0.939	0.894	0.985	CLONAL	3	TRUE	2	0.368124905651158	5		517	1200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0052766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	241	653	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.365050430086413	2	FACETS	1	0.991	1	0.679	0.635	0.725	CLONAL	1	TRUE	0	0.368124905651158	2		653	964	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226551684	226551684	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1393725994	NA	P-0052766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	236	464	0	ENST00000366794.5:c.2746A>G	p.Ile916Val	p.I916V	ENST00000366794	NM_001618.3	916	Ata/Gta	20/23	0.368124905651158	4	FACETS	0.802	0.748	0.858	0.802	0.748	0.858	CLONAL	2	TRUE	2	0.368124905651158	4		464	1094	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288425	15288426	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0052766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	124	440	0	ENST00000263388.2:c.4312_4313dup	p.Asn1438LysfsTer141	p.N1438Kfs*141	ENST00000263388	NM_000435.2	1438	aac/aaAAc	24/33	0.25567825858222	3	FACETS	0.955	0.864	1	0.318	0.288	0.351	CLONAL	1	TRUE	0	0.368124905651158	3		440	835	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052810-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	104	375	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.87	0.789	0.953	0.87	0.789	0.953	CLONAL	1	TRUE	1	0.766593200313546	2		375	312	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806089	1806089	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913479	NA	P-0052810-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	367	874	2	ENST00000260795.2:c.1108G>T	p.Gly370Cys	p.G370C	ENST00000260795		370	Ggc/Tgc	8/17	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.766593200313546	2		876	874	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158132	27158132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773256013	NA	P-0052810-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	173	382	1	ENST00000380036.4:c.356G>A	p.Arg119His	p.R119H	ENST00000380036	NM_000459.3	119	cGt/cAt	2/23	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.766593200313546	2		383	441	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828056	3828057	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0052810-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	588	636	0	ENST00000262367.5:c.2068dup	p.Ala690GlyfsTer36	p.A690Gfs*36	ENST00000262367	NM_004380.2	690	gct/gGct	10/31	0.766593200313546	2	FACETS	0.958	0.933	0.982	0.958	0.933	0.982	CLONAL	2	TRUE	0	0.766593200313546	2		636	801	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250903	153250912	+	frameshift_variant	Frame_Shift_Del	DEL	CATGTGATCA	CATGTGATCA	-	novel	NA	P-0052810-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	24	299	0	ENST00000281708.4:c.1148_1157del	p.Val383AlafsTer9	p.V383Afs*9	ENST00000281708	NM_033632.3	383	gTGATCACATGc/gc	8/12	1	2	FACETS	0.179	0.14	0.224	0.179	0.14	0.224	SUBCLONAL	1	TRUE	1	0.766593200313546	2		299	350	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937713	44937714	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACA	novel	NA	P-0052810-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	205	263	0	ENST00000377967.4:c.2902_2904dup	p.Thr968dup	p.T968dup	ENST00000377967	NM_021140.2	968	-/ACA	19/29	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.766593200313546	1		263	291	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412492	63412492	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052810-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	46	442	0	ENST00000330258.3:c.675A>T	p.Arg225Ser	p.R225S	ENST00000330258	NM_152424.3	225	agA/agT	2/2	1	1	FACETS	0.191	0.161	0.224	0.191	0.161	0.224	SUBCLONAL	1	TRUE	0	0.766593200313546	1		442	387	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123189990	123189991	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0052810-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	240	260	0	ENST00000218089.9:c.1210_1211dup	p.Leu405PhefsTer21	p.L405Ffs*21	ENST00000218089	NM_001042749.1	403	-/GT	14/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.766593200313546	1		260	314	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0052863-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	218	439	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	0.972	0.912	1	0.972	0.912	1	CLONAL	1	TRUE	1	0.832117338930376	2		439	539	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156731	20156731	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052863-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	228	260	0	ENST00000379607.5:c.26G>T	p.Gly9Val	p.G9V	ENST00000379607	NM_001412.3	9	gGt/gTt	2/7	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.832117338930376	1		260	257	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0052865-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	78	568	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.799	0.702	0.904	1	0.978	1	CLONAL	2	TRUE	1	0.14	2		568	697	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0052865-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	25	392	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.873	0.688	1	0.873	0.688	1	CLONAL	1	TRUE	1	0.14	2		392	409	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584825	48584825	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	rs746084369	NA	P-0052865-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	23	309	0	ENST00000342988.3:c.903C>G	p.Tyr301Ter	p.Y301*	ENST00000342988	NM_005359.5	301	taC/taG	7/12	1	2	FACETS	0.799	0.622	1	0.799	0.622	1	CLONAL	1	TRUE	1	0.14	2		309	411	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155395	47155395	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052865-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	33	428	0	ENST00000409792.3:c.4686G>T	p.Trp1562Cys	p.W1562C	ENST00000409792	NM_014159.6	1562	tgG/tgT	5/21	1	2	FACETS	1	0.815	1	1	0.815	1	CLONAL	1	TRUE	1	0.14	2		428	471	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0052866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	85	439	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.812732589703424	2		439	184	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442006	52442056	+	inframe_deletion	In_Frame_Del	DEL	TGCGACTCAGGGTGGGTCCCAGGTCCACGCTGCTGCAGTTCAGGAGCACGC	TGCGACTCAGGGTGGGTCCCAGGTCCACGCTGCTGCAGTTCAGGAGCACGC	-	novel	NA	P-0052866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	221	450	0	ENST00000460680.1:c.293_343del	p.Ser98_Arg114del	p.S98_R114del	ENST00000460680	NM_004656.3	98	aGCGTGCTCCTGAACTGCAGCAGCGTGGACCTGGGACCCACCCTGAGTCGCAtg/atg	5/17	0.812732589703424	1	FACETS	0.939	0.893	0.983	0.939	0.893	0.983	CLONAL	1	TRUE	0	0.812732589703424	1		450	344	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724632	162724632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767283136	NA	P-0052868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	47	479	0	ENST00000367921.3:c.404G>A	p.Arg135His	p.R135H	ENST00000367921	NM_006182.2	135	cGt/cAt	5/18	0.390745120631253	4	FACETS	0.86	0.728	1	0.287	0.242	0.335	CLONAL	1	TRUE	1	0.390745120631253	4		479	389	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374837	149374837	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	135	488	0	ENST00000360632.3:c.257G>C	p.Arg86Pro	p.R86P	ENST00000360632	NM_015472.4	86	cGc/cCc	2/7	0.390745120631253	1	FACETS	0.803	0.74	0.868	1	0.989	1	CLONAL	2	TRUE	0	0.390745120631253	1		488	346	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052926-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	13	375	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		375	96	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052982-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	114	375	0				ENST00000310581	NM_198253.2	-/1132			0.407001180126247	6	FACETS	0.769	0.693	0.848	0.307	0.277	0.34	SUBCLONAL	2	FALSE	1	0.407001180126247	6		375	661	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263850	133263850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052982-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	26	218	1	ENST00000320574.5:c.52G>A	p.Glu18Lys	p.E18K	ENST00000320574	NM_006231.2	18	Gag/Aag	1/49	0.343656734761314	3	FACETS	0.499	0.396	0.617	0.166	0.132	0.206	SUBCLONAL	1	FALSE	0	0.407001180126247	3		219	308	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495511	56495511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052982-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	263	720	0	ENST00000267101.3:c.3701C>T	p.Ser1234Phe	p.S1234F	ENST00000267101	NM_001982.3	1234	tCt/tTt	28/28	0.343656734761314	3	FACETS	1	0.991	1	0.83	0.783	0.876	CLONAL	2	FALSE	0	0.407001180126247	3		720	625	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487277	56487277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035001455	NA	P-0052982-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	227	487	0	ENST00000267101.3:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000267101	NM_001982.3	475	Cgg/Tgg	12/28	0.343656734761314	3	FACETS	1	0.984	1	0.757	0.711	0.804	CLONAL	2	FALSE	0	0.407001180126247	3		487	591	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473647	67473647	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886039137	NA	P-0052982-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	238	662	0	ENST00000327367.4:c.727C>T	p.Arg243Cys	p.R243C	ENST00000327367	NM_005902.3	243	Cgc/Tgc	6/9	1	2	FACETS	0.827	0.776	0.88	1	0.994	1	CLONAL	2	FALSE	1	0.407001180126247	2		662	707	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143293	30143293	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748978993	NA	P-0052982-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	41	548	1	ENST00000389048.3:c.233C>T	p.Ser78Leu	p.S78L	ENST00000389048	NM_004304.4	78	tCg/tTg	1/29	0.165811236176198	3	FACETS	0.445	0.37	0.528	0.222	0.185	0.264	INDETERMINATE	1	FALSE	1	0.407001180126247	3		549	545	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856356	45856356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052982-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	118	735	0	ENST00000391945.4:c.1816G>A	p.Glu606Lys	p.E606K	ENST00000391945	NM_000400.3	606	Gag/Aag	19/23	0.245159024479989	3	FACETS	0.858	0.774	0.947	0.429	0.387	0.474	CLONAL	1	FALSE	1	0.407001180126247	3		735	813	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351238	89351238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1266962947	NA	P-0052982-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	43	796	0	ENST00000301030.4:c.1712C>T	p.Thr571Met	p.T571M	ENST00000301030	NM_001256183.1	571	aCg/aTg	9/13	1	2	FACETS	0.294	0.245	0.349	0.294	0.245	0.349	SUBCLONAL	1	FALSE	1	0.407001180126247	2		796	718	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805038	89805038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1203903110	NA	P-0052982-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	136	740	0	ENST00000389301.3:c.4339G>A	p.Asp1447Asn	p.D1447N	ENST00000389301	NM_000135.2	1447	Gac/Aac	43/43	1	2	FACETS	0.923	0.841	1	0.923	0.841	1	CLONAL	1	FALSE	1	0.407001180126247	2		740	724	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087944	27087944	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052982-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	173	618	0	ENST00000324856.7:c.2231C>A	p.Ser744Ter	p.S744*	ENST00000324856	NM_006015.4	744	tCa/tAa	6/20	0.0396777553963255	4	FACETS	0.787	0.726	0.85	0.787	0.726	0.85	INDETERMINATE	2	FALSE	2	0.407001180126247	4		618	760	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955446	48955446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052982-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	136	510	0	ENST00000267163.4:c.1563del	p.Asn522IlefsTer2	p.N522Ifs*2	ENST00000267163	NM_000321.2	521	cTt/ct	17/27	0.359728131586169	2	FACETS	0.868	0.798	0.94	0.868	0.798	0.94	CLONAL	2	FALSE	0	0.407001180126247	2		510	385	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587123	212587123	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052982-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	123	409	0	ENST00000342788.4:c.878G>A	p.Cys293Tyr	p.C293Y	ENST00000342788	NM_005235.2	293	tGt/tAt	7/28	0.165811236176198	3	FACETS	0.834	0.76	0.911	0.834	0.76	0.911	INDETERMINATE	2	FALSE	1	0.407001180126247	3		409	436	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342761	87342761	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052982-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	161	569	0	ENST00000277120.3:c.1046A>G	p.Asp349Gly	p.D349G	ENST00000277120		349	gAt/gGt	9/19	0.0396777553963255	4	FACETS	0.86	0.792	0.931	0.86	0.792	0.931	INDETERMINATE	2	FALSE	2	0.407001180126247	4		569	647	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	493203	493203	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1329499293	NA	P-0052982-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	33	496	0	ENST00000399788.2:c.360G>C	p.Leu120Phe	p.L120F	ENST00000399788	NM_001042603.1	120	ttG/ttC	3/28	0.0396777553963255	4	FACETS	0.349	0.283	0.424	0.175	0.141	0.212	INDETERMINATE	1	FALSE	2	0.407001180126247	4		496	653	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805234	89805336	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCAGCTGTCAATTCTCATGTCCCCCACATGGCCCAAGGTGGGCATCTTGACGTTACCTCTGCCACGTGTGAGAAGCTCTTTTTCGGGCACCGAGGTATTAACT	GCAGCTGTCAATTCTCATGTCCCCCACATGGCCCAAGGTGGGCATCTTGACGTTACCTCTGCCACGTGTGAGAAGCTCTTTTTCGGGCACCGAGGTATTAACT	-	novel	NA	P-0052982-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	43	372	0	ENST00000389301.3:c.4214_4260+56del		p.X1405_splice	ENST00000389301	NM_000135.2	1405		42/43	1	2	FACETS	0.734	0.617	0.861	0.734	0.617	0.861	SUBCLONAL	1	FALSE	1	0.407001180126247	2		372	288	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89807249	89807249	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052982-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	103	532	0	ENST00000389301.3:c.3791C>T	p.Ser1264Phe	p.S1264F	ENST00000389301	NM_000135.2	1264	tCc/tTc	38/43	1	2	FACETS	0.837	0.75	0.928	0.837	0.75	0.928	CLONAL	1	FALSE	1	0.407001180126247	2		532	605	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89809295	89809296	+	missense_variant	Missense_Mutation	DNP	TG	TG	AA	novel	NA	P-0052982-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	95	621	0	ENST00000389301.3:c.3677_3678delinsTT	p.Ser1226Phe	p.S1226F	ENST00000389301	NM_000135.2	1226	tCA/tTT	37/43	1	2	FACETS	0.722	0.643	0.805	0.722	0.643	0.805	SUBCLONAL	1	FALSE	1	0.407001180126247	2		621	647	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646907	37646907	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052982-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	123	712	0	ENST00000447079.4:c.2029G>A	p.Gly677Ser	p.G677S	ENST00000447079	NM_015083.1	677	Ggt/Agt	3/14	0.0396777553963255	4	FACETS	0.867	0.783	0.956	0.433	0.391	0.478	INDETERMINATE	1	FALSE	2	0.407001180126247	4		712	981	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937619	17937619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757920411	NA	P-0052982-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	50	691	0	ENST00000458235.1:c.3308G>A	p.Arg1103Gln	p.R1103Q	ENST00000458235	NM_000215.3	1103	cGg/cAg	24/24	0.407001180126247	3	FACETS	0.351	0.297	0.411	0.176	0.148	0.206	SUBCLONAL	1	FALSE	1	0.407001180126247	3		691	842	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035121	30035121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1351169677	NA	P-0052982-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	68	556	0	ENST00000338641.4:c.283C>T	p.His95Tyr	p.H95Y	ENST00000338641	NM_000268.3	95	Cac/Tac	3/16	0.407001180126247	6	FACETS	0.679	0.589	0.776			1	SUBCLONAL	1	FALSE	NA	0.407001180126247	6		556	893	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566456	41566456	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052982-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	137	623	1	ENST00000263253.7:c.4333G>A	p.Asp1445Asn	p.D1445N	ENST00000263253	NM_001429.3	1445	Gat/Aat	27/31	0.407001180126247	3	FACETS	1	0.97	1	0.573	0.522	0.626	CLONAL	1	FALSE	1	0.407001180126247	3		624	707	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598048	55598048	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052982-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	140	380	0	ENST00000288135.5:c.2245G>C	p.Glu749Gln	p.E749Q	ENST00000288135	NM_000222.2	749	Gaa/Caa	16/21	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	FALSE	NA	0.407001180126247	2		380	506	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628101	187628101	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052982-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	238	768	0	ENST00000441802.2:c.2881C>T	p.Gln961Ter	p.Q961*	ENST00000441802	NM_005245.3	961	Cag/Tag	2/27	0.346230752833774	5	FACETS	1	0.986	1	0.788	0.738	0.839	CLONAL	2	FALSE	2	0.407001180126247	5		768	797	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191819	123191819	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052982-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	25	227	0	ENST00000218089.9:c.1408G>C	p.Glu470Gln	p.E470Q	ENST00000218089	NM_001042749.1	470	Gaa/Caa	15/35	0.407001180126247	2	FACETS	0.344	0.271	0.428			1	SUBCLONAL	1	FALSE	NA	0.407001180126247	2		227	357	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0053218-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	65	455	1				ENST00000310581	NM_198253.2	-/1132			0.232029723514179	0	FACETS	0.359	0.317	0.402			1	INDETERMINATE	1	TRUE	0	0.665546522989697	0		456	182	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0053218-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	140	913	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.335437259292767	4	FACETS	0.92	0.847	0.994			1	INDETERMINATE	2	TRUE	NA	0.665546522989697	4		913	381	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095917	29095917	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780192	NA	P-0053218-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	513	493	1	ENST00000328354.6:c.917G>A	p.Gly306Glu	p.G306E	ENST00000328354	NM_007194.3	306	gGg/gAg	9/15	0.505054206990473	3	FACETS	1	0.992	1	1	0.998	1	CLONAL	3	TRUE	1	0.665546522989697	3		494	657	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165924	47165924	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053218-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	119	446	0	ENST00000409792.3:c.202C>T	p.Gln68Ter	p.Q68*	ENST00000409792	NM_014159.6	68	Cag/Tag	3/21	0.172477173037816	3	FACETS	1	0.977	1	0.613	0.558	0.669	INDETERMINATE	1	TRUE	1	0.665546522989697	3		446	389	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538244	187538244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746286358	NA	P-0053218-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	163	575	0	ENST00000441802.2:c.8990C>T	p.Thr2997Met	p.T2997M	ENST00000441802	NM_005245.3	2997	aCg/aTg	11/27	0.172477173037816	3	FACETS	1	0.988	1	0.699	0.647	0.752	INDETERMINATE	1	TRUE	1	0.665546522989697	3		575	467	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683487	29683487	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053218-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	89	236	0	ENST00000356175.3:c.7562A>G	p.Lys2521Arg	p.K2521R	ENST00000356175	NM_000267.3	2521	aAa/aGa	51/57	0.272936657587956	3	FACETS	0.755	0.681	0.831	0.755	0.681	0.831	INDETERMINATE	2	TRUE	1	0.665546522989697	3		236	236	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0053222-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1948	136	304	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.612563155305165	18	FACETS	1	0.977	1	0.074	0.066	0.082	CLONAL	1	TRUE	1	0.612563155305165	18		304	2084	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	64	652	0	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.239492529627036	3	FACETS	1	0.952	1	0.603	0.525	0.686	CLONAL	1	TRUE	1	0.370246410101946	3		652	340	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5070046	5070046	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	11	86	0	ENST00000381652.3:c.1635G>C	p.Leu545Phe	p.L545F	ENST00000381652	NM_004972.3	545	ttG/ttC	12/25	0.286641657251839	3	FACETS	0.711	0.496	0.973			1	CLONAL	1	TRUE	NA	0.370246410101946	3		86	99	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044719	47044719	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	50	1187	0	ENST00000377604.3:c.2119C>T	p.Gln707Ter	p.Q707*	ENST00000377604	NM_001204468.1	707	Cag/Tag	19/24	1	2	FACETS	0.538	0.457	0.628	0.538	0.457	0.628	SUBCLONAL	1	TRUE	1	0.370246410101946	2		1187	502	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510806	157510806	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	31	665	0	ENST00000346085.5:c.3586del	p.Gln1196SerfsTer15	p.Q1196Sfs*15	ENST00000346085	NM_020732.3	1194	aCc/ac	14/20	0.239492529627036	3	FACETS	0.434	0.351	0.529	0.217	0.175	0.265	SUBCLONAL	1	TRUE	1	0.370246410101946	3		665	457	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106159	27106159	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	31	658	0	ENST00000324856.7:c.5770G>T	p.Glu1924Ter	p.E1924*	ENST00000324856	NM_006015.4	1924	Gag/Tag	20/20	0.239492529627036	3	FACETS	0.494	0.399	0.601	0.247	0.199	0.301	SUBCLONAL	1	TRUE	1	0.370246410101946	3		658	402	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636758	8636758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	29	480	0	ENST00000356435.5:c.151C>T	p.Pro51Ser	p.P51S	ENST00000356435		51	Cca/Tca	2/35	0.370246410101946	1	FACETS	0.478	0.385	0.583	0.478	0.385	0.583	SUBCLONAL	1	TRUE	0	0.370246410101946	1		480	267	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602869	10602869	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	65	1138	0	ENST00000171111.5:c.709C>G	p.Leu237Val	p.L237V	ENST00000171111	NM_203500.1	237	Ctg/Gtg	3/6	1	2	FACETS	0.699	0.607	0.799	0.699	0.607	0.799	SUBCLONAL	1	TRUE	1	0.370246410101946	2		1138	502	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411197	63411197	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	47	843	0	ENST00000330258.3:c.1970G>T	p.Arg657Met	p.R657M	ENST00000330258	NM_152424.3	657	aGg/aTg	2/2	1	2	FACETS	0.619	0.523	0.724	0.619	0.523	0.724	SUBCLONAL	1	TRUE	1	0.370246410101946	2		843	410	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949089	71949089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	32	1100	0	ENST00000298229.2:c.3556C>T	p.Pro1186Ser	p.P1186S	ENST00000298229	NM_001567.3	1186	Ccg/Tcg	27/28	0.370246410101946	3	FACETS	0.382	0.309	0.465	0.191	0.154	0.233	SUBCLONAL	1	TRUE	1	0.370246410101946	3		1100	536	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151932996	151932996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372408170	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	18	130	0	ENST00000262189.6:c.2675G>A	p.Gly892Glu	p.G892E	ENST00000262189	NM_170606.2	892	gGa/gAa	16/59	0.276077102867192	4	FACETS	1	0.883	1	0.647	0.494	0.821	CLONAL	1	TRUE	2	0.370246410101946	4		130	103	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094325	27094325	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1553152590	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	23	490	1	ENST00000324856.7:c.3033G>T	p.Leu1011Phe	p.L1011F	ENST00000324856	NM_006015.4	1011	ttG/ttT	11/20	0.239492529627036	3	FACETS	0.37	0.288	0.465	0.185	0.144	0.233	SUBCLONAL	1	TRUE	1	0.370246410101946	3		491	398	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36824360	36824360	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	26	744	0	ENST00000373129.3:c.176C>A	p.Thr59Lys	p.T59K	ENST00000373129	NM_032017.1	59	aCg/aAg	4/12	0.239492529627036	3	FACETS	0.35	0.276	0.434	0.175	0.138	0.217	SUBCLONAL	1	TRUE	1	0.370246410101946	3		744	476	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937141	36937141	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	33	1011	0	ENST00000361632.4:c.1178T>A	p.Leu393His	p.L393H	ENST00000361632		393	cTc/cAc	9/16	0.239492529627036	3	FACETS	0.46	0.374	0.557	0.23	0.187	0.279	SUBCLONAL	1	TRUE	1	0.370246410101946	3		1011	459	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332886	65332886	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	13	174	0	ENST00000342505.4:c.653A>T	p.Lys218Met	p.K218M	ENST00000342505	NM_002227.2	218	aAg/aTg	7/25	0.239492529627036	3	FACETS	0.578	0.414	0.775	0.289	0.207	0.388	SUBCLONAL	1	TRUE	1	0.370246410101946	3		174	144	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166191	118166191	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	22	464	0	ENST00000369448.3:c.701A>T	p.Lys234Met	p.K234M	ENST00000369448	NM_017709.3	234	aAg/aTg	2/2	0.239492529627036	3	FACETS	0.435	0.337	0.548	0.217	0.168	0.274	SUBCLONAL	1	TRUE	1	0.370246410101946	3		464	324	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841548	156841548	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	39	986	0	ENST00000524377.1:c.850+1G>T		p.X284_splice	ENST00000524377	NM_002529.3	284			0.370246410101946	3	FACETS	0.493	0.408	0.588	0.247	0.204	0.294	SUBCLONAL	1	TRUE	1	0.370246410101946	3		986	506	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845892	156845892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200575096	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	52	1145	0	ENST00000524377.1:c.1522C>T	p.Arg508Trp	p.R508W	ENST00000524377	NM_002529.3	508	Cgg/Tgg	13/17	0.370246410101946	3	FACETS	0.56	0.477	0.652	0.28	0.238	0.326	SUBCLONAL	1	TRUE	1	0.370246410101946	3		1145	594	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156620	2156620	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	47	923	0	ENST00000434045.2:c.302G>T	p.Cys101Phe	p.C101F	ENST00000434045	NM_001127598.1	101	tGt/tTt	3/5	1	2	FACETS	0.585	0.494	0.685	0.585	0.494	0.685	SUBCLONAL	1	TRUE	1	0.370246410101946	2		923	434	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21630864	21630864	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	28	534	0	ENST00000421138.2:c.740A>C	p.Asn247Thr	p.N247T	ENST00000421138		247	aAc/aCc	8/16	0.370246410101946	3	FACETS	0.545	0.436	0.669	0.272	0.218	0.335	SUBCLONAL	1	TRUE	1	0.370246410101946	3		534	329	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913071	32913071	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	15	355	0	ENST00000380152.3:c.4579G>C	p.Ala1527Pro	p.A1527P	ENST00000380152		1527	Gct/Cct	11/27	0.370246410101946	3	FACETS	0.407	0.298	0.538	0.203	0.149	0.269	SUBCLONAL	1	TRUE	1	0.370246410101946	3		355	236	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435657	110435657	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	36	413	0	ENST00000375856.3:c.2744G>C	p.Ser915Thr	p.S915T	ENST00000375856	NM_003749.2	915	aGc/aCc	1/2	0.370246410101946	3	FACETS	0.771	0.636	0.921	0.385	0.318	0.461	CLONAL	1	TRUE	1	0.370246410101946	3		413	299	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560357	95560357	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	61	549	0	ENST00000393063.1:c.5232C>G	p.Ile1744Met	p.I1744M	ENST00000393063	NM_030621.3	1744	atC/atG	25/28	0.276077102867192	4	FACETS	0.975	0.843	1	0.488	0.421	0.559	CLONAL	1	TRUE	2	0.370246410101946	4		549	463	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40678686	40678686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1032278660	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	34	362	0	ENST00000249776.8:c.428G>A	p.Arg143Gln	p.R143Q	ENST00000249776	NM_033286.3	143	cGa/cAa	3/9	1	2	FACETS	0.572	0.469	0.688	0.572	0.469	0.688	SUBCLONAL	1	TRUE	1	0.370246410101946	2		362	321	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40678690	40678690	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	35	348	0	ENST00000249776.8:c.432G>C	p.Glu144Asp	p.E144D	ENST00000249776	NM_033286.3	144	gaG/gaC	3/9	1	2	FACETS	0.622	0.511	0.745	0.622	0.511	0.745	SUBCLONAL	1	TRUE	1	0.370246410101946	2		348	304	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669568	88669568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	22	461	0	ENST00000360948.2:c.1330G>A	p.Val444Ile	p.V444I	ENST00000360948	NM_001012338.2	444	Gtc/Atc	12/19	1	2	FACETS	0.42	0.326	0.529	0.42	0.326	0.529	SUBCLONAL	1	TRUE	1	0.370246410101946	2		461	283	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633447	3633447	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	56	1155	1	ENST00000294008.3:c.4804A>T	p.Thr1602Ser	p.T1602S	ENST00000294008	NM_032444.2	1602	Act/Tct	14/15	1	2	FACETS	0.54	0.463	0.625	0.54	0.463	0.625	SUBCLONAL	1	TRUE	1	0.370246410101946	2		1156	560	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614908	23614908	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs180177137	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	21	599	0	ENST00000261584.4:c.3433G>T	p.Gly1145Cys	p.G1145C	ENST00000261584	NM_024675.3	1145	Ggt/Tgt	13/13	0.370246410101946	3	FACETS	0.39	0.3	0.495			1	SUBCLONAL	1	TRUE	NA	0.370246410101946	3		599	345	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993569	72993569	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	33	1028	0	ENST00000268489.5:c.476G>T	p.Ser159Ile	p.S159I	ENST00000268489	NM_006885.3	159	aGt/aTt	2/10	1	2	FACETS	0.397	0.323	0.481	0.397	0.323	0.481	SUBCLONAL	1	TRUE	1	0.370246410101946	2		1028	449	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870637	40870637	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	38	543	0	ENST00000428826.2:c.768-2A>G		p.X256_splice	ENST00000428826		256			0.370246410101946	3	FACETS	0.737	0.611	0.877	0.369	0.305	0.439	SUBCLONAL	1	TRUE	1	0.370246410101946	3		543	330	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857639	59857639	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	40	117	0	ENST00000259008.2:c.1918A>T	p.Ile640Phe	p.I640F	ENST00000259008	NM_032043.2	640	Atc/Ttc	13/20	0.370246410101946	3	FACETS	1	0.947	1	0.67	0.564	0.786	CLONAL	1	TRUE	1	0.370246410101946	3		117	191	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39535261	39535261	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	34	340	0	ENST00000262039.4:c.5G>T	p.Gly2Val	p.G2V	ENST00000262039	NM_002647.2	2	gGg/gTg	1/25	1	2	FACETS	0.647	0.53	0.776	0.647	0.53	0.776	SUBCLONAL	1	TRUE	1	0.370246410101946	2		340	284	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273588	5273588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	37	587	0	ENST00000357368.4:c.244G>A	p.Glu82Lys	p.E82K	ENST00000357368	NM_002850.3	82	Gag/Aag	4/38	1	2	FACETS	0.651	0.539	0.776	0.651	0.539	0.776	SUBCLONAL	1	TRUE	1	0.370246410101946	2		587	307	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31393148	31393148	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139777286	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	30	466	1	ENST00000328111.2:c.2236G>A	p.Val746Met	p.V746M	ENST00000328111	NM_006892.3	746	Gtg/Atg	21/23	1	2	FACETS	0.535	0.432	0.651	0.535	0.432	0.651	SUBCLONAL	1	TRUE	1	0.370246410101946	2		467	303	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275028	41275028	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	39	316	0	ENST00000349496.5:c.1194G>T	p.Met398Ile	p.M398I	ENST00000349496	NM_001904.3	398	atG/atT	9/15	0.359157782149006	3	FACETS	0.892	0.743	1	0.446	0.371	0.528	CLONAL	1	TRUE	1	0.370246410101946	3		316	280	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436323	52436323	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	77	980	0	ENST00000460680.1:c.2171A>T	p.Tyr724Phe	p.Y724F	ENST00000460680	NM_004656.3	724	tAc/tTc	17/17	0.359157782149006	3	FACETS	1	0.882	1	0.501	0.441	0.565	CLONAL	1	TRUE	1	0.370246410101946	3		980	492	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799628	72799628	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	63	648	2	ENST00000325599.8:c.1541C>A	p.Ala514Asp	p.A514D	ENST00000325599	NM_018130.2	514	gCc/gAc	11/11	0.359157782149006	3	FACETS	1	0.943	1	0.578	0.502	0.659	CLONAL	1	TRUE	1	0.370246410101946	3		650	349	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430462	181430462	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	42	678	0	ENST00000325404.1:c.314A>T	p.His105Leu	p.H105L	ENST00000325404	NM_003106.3	105	cAc/cTc	1/1	0.221448754989569	5	FACETS	0.854	0.714	1	0.285	0.238	0.337	INDETERMINATE	1	TRUE	2	0.370246410101946	5		678	413	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1932356	1932356	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	24	572	0	ENST00000382891.5:c.1414G>T	p.Val472Leu	p.V472L	ENST00000382891	NM_133335.3	472	Gta/Tta	6/22	1	2	FACETS	0.393	0.308	0.491	0.393	0.308	0.491	SUBCLONAL	1	TRUE	1	0.370246410101946	2		572	330	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152036	55152036	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	45	690	0	ENST00000257290.5:c.2468A>T	p.Asn823Ile	p.N823I	ENST00000257290	NM_006206.4	823	aAc/aTc	18/23	1	2	FACETS	0.605	0.509	0.71	0.605	0.509	0.71	SUBCLONAL	1	TRUE	1	0.370246410101946	2		690	402	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753402	57753402	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	21	255	0	ENST00000274289.3:c.722G>C	p.Cys241Ser	p.C241S	ENST00000274289	NM_006622.3	241	tGt/tCt	6/14	0.369277325236474	4	FACETS	0.713	0.551	0.9	0.357	0.275	0.45	SUBCLONAL	1	TRUE	2	0.370246410101946	4		255	218	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149452864	149452864	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	32	651	0	ENST00000286301.3:c.1082G>T	p.Arg361Met	p.R361M	ENST00000286301	NM_005211.3	361	aGg/aTg	7/22	0.11151886076735	3	FACETS	0.523	0.424	0.634			1	INDETERMINATE	1	TRUE	NA	0.370246410101946	3		651	392	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520462	176520462	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	54	1148	0	ENST00000292408.4:c.1307T>A	p.Val436Glu	p.V436E	ENST00000292408	NM_213647.1	436	gTg/gAg	10/18	0.370246410101946	3	FACETS	0.662	0.566	0.768	0.331	0.283	0.384	SUBCLONAL	1	TRUE	1	0.370246410101946	3		1148	522	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170124	32170124	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	29	1146	1	ENST00000375023.3:c.3484C>A	p.Pro1162Thr	p.P1162T	ENST00000375023	NM_004557.3	1162	Cct/Act	21/30	0.370246410101946	3	FACETS	0.326	0.26	0.4	0.163	0.13	0.2	SUBCLONAL	1	TRUE	1	0.370246410101946	3		1147	570	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171991	32171991	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	26	807	0	ENST00000375023.3:c.3041C>A	p.Pro1014His	p.P1014H	ENST00000375023	NM_004557.3	1014	cCc/cAc	19/30	0.370246410101946	3	FACETS	0.351	0.277	0.436	0.176	0.138	0.218	SUBCLONAL	1	TRUE	1	0.370246410101946	3		807	474	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066636	94066636	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	43	656	0	ENST00000369303.4:c.1123G>C	p.Glu375Gln	p.E375Q	ENST00000369303	NM_004440.3	375	Gag/Cag	5/17	0.239492529627036	3	FACETS	0.817	0.686	0.961	0.408	0.343	0.481	CLONAL	1	TRUE	1	0.370246410101946	3		656	337	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394450	162394450	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	25	311	0	ENST00000366898.1:c.619-1G>T		p.X207_splice	ENST00000366898	NM_004562.2	207			0.239492529627036	3	FACETS	0.744	0.59	0.92	0.372	0.295	0.46	CLONAL	1	TRUE	1	0.370246410101946	3		311	215	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846404	128846404	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	72	814	0	ENST00000249373.3:c.1240G>C	p.Val414Leu	p.V414L	ENST00000249373	NM_005631.4	414	Gtg/Ctg	6/12	0.276077102867192	4	FACETS	1	0.928	1	0.543	0.475	0.615	CLONAL	1	TRUE	2	0.370246410101946	4		814	491	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875079	151875079	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	17	156	0	ENST00000262189.6:c.7459G>T	p.Gly2487Cys	p.G2487C	ENST00000262189	NM_170606.2	2487	Ggt/Tgt	38/59	0.276077102867192	4	FACETS	0.886	0.667	1	0.443	0.333	0.571	CLONAL	1	TRUE	2	0.370246410101946	4		156	142	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270511	98270511	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	36	403	0	ENST00000331920.6:c.133C>G	p.Pro45Ala	p.P45A	ENST00000331920	NM_000264.3	45	Ccg/Gcg	1/24	1	2	FACETS	0.659	0.544	0.787	0.659	0.544	0.787	SUBCLONAL	1	TRUE	1	0.370246410101946	2		403	295	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933706	39933706	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	41	858	0	ENST00000378444.4:c.893C>T	p.Pro298Leu	p.P298L	ENST00000378444	NM_001123385.1	298	cCt/cTt	4/15	1	2	FACETS	0.519	0.432	0.615	0.519	0.432	0.615	SUBCLONAL	1	TRUE	1	0.370246410101946	2		858	427	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045472	47045472	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	50	798	0	ENST00000377604.3:c.2439G>T	p.Lys813Asn	p.K813N	ENST00000377604	NM_001204468.1	813	aaG/aaT	22/24	1	2	FACETS	0.611	0.519	0.712	0.611	0.519	0.712	SUBCLONAL	1	TRUE	1	0.370246410101946	2		798	442	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411079	63411079	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	41	864	0	ENST00000330258.3:c.2088G>T	p.Arg696Ser	p.R696S	ENST00000330258	NM_152424.3	696	agG/agT	2/2	1	2	FACETS	0.559	0.466	0.662	0.559	0.466	0.662	SUBCLONAL	1	TRUE	1	0.370246410101946	2		864	396	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860053	152860053	+	synonymous_variant	Silent	SNP	G	G	T	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	42	783	2	ENST00000406277.2:c.375C>A	p.Leu125=	p.L125=	ENST00000406277	NM_152274.4	125	ctC/ctA	5/7	1		FACETS		0.49	0.692				SUBCLONAL	1	TRUE	1	0.370246410101946	2		785	387	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915696	131915696	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	17	124	0	ENST00000265335.6:c.694G>T	p.Ala232Ser	p.A232S	ENST00000265335		232	Gcc/Tcc	5/25	0.369277325236474	4	FACETS	0.758	0.569	0.98	0.379	0.284	0.49	CLONAL	1	TRUE	2	0.370246410101946	4		124	166	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915694	131915694	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	17	125	0	ENST00000265335.6:c.693del	p.Ala232ProfsTer3	p.A232Pfs*3	ENST00000265335		231	gAa/ga	5/25	0.369277325236474	4	FACETS	0.758	0.569	0.98	0.379	0.284	0.49	CLONAL	1	TRUE	2	0.370246410101946	4		125	166	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105512	27105512	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0053287-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	65	411	0	ENST00000324856.7:c.5125-2A>C		p.X1709_splice	ENST00000324856	NM_006015.4	1709			1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.338090796426921	2		411	365	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94926644	94926644	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053287-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	51	506	0	ENST00000536441.1:c.121A>G	p.Ser41Gly	p.S41G	ENST00000536441	NM_144665.3	41	Agt/Ggt	2/10	1	2	FACETS	0.42	0.356	0.49	0.42	0.356	0.49	SUBCLONAL	1	TRUE	1	0.338090796426921	2		506	719	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0053294-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	164	307	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.96	0.887	1	0.96	0.887	1	CLONAL	1	TRUE	1	0.600229129535257	2		307	569	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224210	36224210	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053294-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	350	678	0	ENST00000222270.7:c.6764del	p.Pro2255ArgfsTer6	p.P2255Rfs*6	ENST00000222270	NM_014727.1	2254	Ccc/cc	28/37	1	2	FACETS	0.817	0.773	0.863	0.817	0.773	0.863	CLONAL	1	TRUE	1	0.600229129535257	2		678	1427	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842677	68842681	+	frameshift_variant	Frame_Shift_Del	DEL	TTTAT	TTTAT	-	novel	NA	P-0053294-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	361	719	1	ENST00000261769.5:c.614_618del	p.Phe205TyrfsTer2	p.F205Yfs*2	ENST00000261769	NM_004360.3	205	TTTATt/t	5/16	0.600229129535257	1	FACETS	0.967	0.92	1	0.967	0.92	1	CLONAL	1	TRUE	0	0.600229129535257	1		720	871	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0053330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	113	455	1				ENST00000310581	NM_198253.2	-/1132			0.391351499964146	3	FACETS	1	0.971	1	1	0.992	1	CLONAL	4	FALSE	1	0.391351499964146	3		456	162	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983123	201983123	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	338	610	1	ENST00000359651.3:c.972G>A	p.Met324Ile	p.M324I	ENST00000359651		324	atG/atA	7/8	0.240686390260497	4	FACETS	0.917	0.881	0.952	1	0.993	1	CLONAL	5	FALSE	0	0.391351499964146	4		611	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	416	276	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.391351499964146	6	FACETS	0.951	0.936	0.964	1	0.998	1	CLONAL	9	FALSE	0	0.391351499964146	6		276	443	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245197	41245197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55914168	NA	P-0053330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	320	646	0	ENST00000357654.3:c.2351C>T	p.Ser784Leu	p.S784L	ENST00000357654	NM_007294.3	784	tCg/tTg	10/23	0.391351499964146	4	FACETS	0.944	0.907	0.98	1	0.996	1	CLONAL	5	FALSE	1	0.391351499964146	4		646	482	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522635	106522635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	143	414	0	ENST00000359195.3:c.2612C>T	p.Ser871Leu	p.S871L	ENST00000359195	NM_002649.2	871	tCa/tTa	7/11	0.391351499964146	10	FACETS	1	0.964	1			1	CLONAL	4	FALSE	NA	0.391351499964146	10		414	432	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821485	32821485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757941717	NA	P-0053330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	136	788	0	ENST00000354258.4:c.109C>T	p.Arg37Trp	p.R37W	ENST00000354258	NM_000593.5	37	Cgg/Tgg	1/11	0.3123101513035	4	FACETS	1	0.936	1	0.684	0.627	0.744	CLONAL	2	FALSE	1	0.391351499964146	4		788	471	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109947	115109947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	205	575	0	ENST00000257566.3:c.1931C>T	p.Ser644Phe	p.S644F	ENST00000257566	NM_016569.3	644	tCc/tTc	8/8	0.391351499964146	5	FACETS	1	0.98	1	1	0.993	1	CLONAL	4	FALSE	2	0.391351499964146	5		575	383	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872189	45872189	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	337	703	0	ENST00000391945.4:c.245A>G	p.Lys82Arg	p.K82R	ENST00000391945	NM_000400.3	82	aAg/aGg	4/23	0.391351499964146	7	FACETS	1	0.984	1	1	0.984	1	CLONAL	4	FALSE	3	0.391351499964146	7		703	790	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472573	88472573	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	105	659	0	ENST00000360948.2:c.1982G>A	p.Ser661Asn	p.S661N	ENST00000360948	NM_001012338.2	661	aGt/aAt	16/19	0.391351499964146	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	0	0.391351499964146	1		659	310	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293183	91293183	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	156	511	2	ENST00000355112.3:c.685G>A	p.Glu229Lys	p.E229K	ENST00000355112	NM_000057.2	229	Gaa/Aaa	3/22	0.3123101513035	4	FACETS	0.936	0.868	1	0.936	0.868	1	CLONAL	3	FALSE	1	0.391351499964146	4		513	395	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729589	162729589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	79	464	0	ENST00000367921.3:c.675G>A	p.Met225Ile	p.M225I	ENST00000367921	NM_006182.2	225	atG/atA	8/18	0.240686390260497	4	FACETS	0.912	0.81	1	0.456	0.405	0.51	CLONAL	2	FALSE	0	0.391351499964146	4		464	308	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88678970	88678970	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1404557708	NA	P-0053330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	57	236	0	ENST00000372037.3:c.910C>T	p.Gln304Ter	p.Q304*	ENST00000372037	NM_004329.2	304	Cag/Tag	10/13	1	2	FACETS	1	0.952	1	1	0.982	1	CLONAL	2	FALSE	1	0.391351499964146	2		236	126	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380755	118380755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	231	460	0	ENST00000534358.1:c.10993G>A	p.Glu3665Lys	p.E3665K	ENST00000534358	NM_005933.3	3665	Gag/Aag	30/36	0.391351499964146	7	FACETS	1	0.968	1	1	0.992	1	CLONAL	5	FALSE	3	0.391351499964146	7		460	452	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471020	25471043	+	inframe_deletion	In_Frame_Del	DEL	CACAGCAGGAGGGCTGGCCTCCTC	CACAGCAGGAGGGCTGGCCTCCTC	-	rs770712092	NA	P-0053330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	266	843	0	ENST00000264709.3:c.718_741del	p.Glu240_Val247del	p.E240_V247del	ENST00000264709	NM_175629.2	240	GAGGAGGCCAGCCCTCCTGCTGTG/-	7/23	0.249834974245823	4	FACETS	0.924	0.877	0.97	1	0.992	1	CLONAL	4	FALSE	1	0.391351499964146	4		843	512	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026080	71026098	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGAAAGCTTACCTTCCAC	GAGAAAGCTTACCTTCCAC	-	novel	NA	P-0053330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	72	329	0	ENST00000318789.4:c.1524_1530+12del		p.X508_splice	ENST00000318789	NM_032682.5	508		17/21	0.183302374265138	3	FACETS	1	0.948	1	0.741	0.66	0.824	INDETERMINATE	2	FALSE	0	0.391351499964146	3		329	198	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612076	189612076	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	209	599	0	ENST00000264731.3:c.1828T>A	p.Phe610Ile	p.F610I	ENST00000264731	NM_003722.4	610	Ttc/Atc	14/14	0.249834974245823	4	FACETS	1	0.952	1	1	0.952	1	CLONAL	3	FALSE	1	0.391351499964146	4		599	487	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929004	44929004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	245	350	0	ENST00000377967.4:c.2104C>T	p.His702Tyr	p.H702Y	ENST00000377967	NM_021140.2	702	Cac/Tac	17/29	0.391351499964146	2	FACETS	0.945	0.923	0.963			1	CLONAL	5	FALSE	NA	0.391351499964146	2		350	265	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023728	27023736	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCTCCGC	CCCCTCCGC	AG	novel	NA	P-0053330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	165	378	1	ENST00000324856.7:c.834_842delinsAG	p.Pro279GlyfsTer82	p.P279Gfs*82	ENST00000324856	NM_006015.4	278	ggCCCCTCCGCg/ggAGg	1/20	0.391351499964146	5	FACETS	1	0.976	1	1	0.991	1	CLONAL	4	FALSE	2	0.391351499964146	5		379	308	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053434-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	34	502	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.913	0.752	1	0.913	0.752	1	CLONAL	1	TRUE	1	0.341469762775931	2		502	218	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053434-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	75	769	3	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.272068958512209	1	FACETS	0.949	0.836	1	0.949	0.836	1	CLONAL	1	TRUE	0	0.341469762775931	1		772	384	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106261	27106261	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053434-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	71	624	0	ENST00000324856.7:c.5872G>A	p.Glu1958Lys	p.E1958K	ENST00000324856	NM_006015.4	1958	Gaa/Aaa	20/20	1	2	FACETS	0.956	0.838	1	0.956	0.838	1	CLONAL	1	TRUE	1	0.341469762775931	2		624	435	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185169080	185169080	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053434-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	42	481	0	ENST00000265026.3:c.1175G>C	p.Ser392Thr	p.S392T	ENST00000265026	NM_004721.4	392	aGt/aCt	7/14	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.341469762775931	2		481	230	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971025	21971026	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0053434-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	63	530	0	ENST00000304494.5:c.331_332dup	p.Arg112AlafsTer35	p.R112Afs*35	ENST00000304494	NM_000077.4	111	ggc/ggGGc	2/3	0.341469762775931	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.341469762775931	1		530	274	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934154	48934155	+	stop_gained,splice_region_variant	Nonsense_Mutation	DNP	GG	GG	CT	novel	NA	P-0053550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	39	269	0	ENST00000267163.4:c.609_610delinsCT	p.Glu204Ter	p.E204*	ENST00000267163	NM_000321.2	203	ggGGaa/ggCTaa	7/27	0.245478857985455	1	FACETS	0.965	0.803	1	0.965	0.803	1	CLONAL	1	FALSE	0	0.245478857985455	1		269	289	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829533	72829543	+	frameshift_variant	Frame_Shift_Del	DEL	GCTTCTTCTGG	GCTTCTTCTGG	-	novel	NA	P-0053550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	90	623	1	ENST00000268489.5:c.7038_7048del	p.Gln2347ValfsTer5	p.Q2347Vfs*5	ENST00000268489	NM_006885.3	2346	caCCAGAAGAAGCtg/catg	9/10	0.245478857985455	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	0	0.245478857985455	1		624	528	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347224	89347224	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780224924	NA	P-0053550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	113	889	1	ENST00000301030.4:c.5726C>T	p.Pro1909Leu	p.P1909L	ENST00000301030	NM_001256183.1	1909	cCg/cTg	9/13	0.245478857985455	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	0	0.245478857985455	1		890	546	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752927	128752927	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	61	360	0	ENST00000377970.2:c.1088C>A	p.Ser363Ter	p.S363*	ENST00000377970	NM_002467.4	363	tCg/tAg	3/3	0.245478857985455	3	FACETS	1	0.936	1	0.572	0.494	0.656	CLONAL	1	FALSE	1	0.245478857985455	3		360	488	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593504	48593504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053607-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	46	361	0	ENST00000342988.3:c.1255G>A	p.Gly419Arg	p.G419R	ENST00000342988	NM_005359.5	419	Ggg/Agg	10/12	0.381437485331873	1	FACETS	0.748	0.634	0.871	0.748	0.634	0.871	SUBCLONAL	1	TRUE	0	0.381437485331873	1		361	261	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515246	149515246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053607-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	131	722	0	ENST00000261799.4:c.236G>A	p.Gly79Asp	p.G79D	ENST00000261799	NM_002609.3	79	gGc/gAc	3/23	1	2	FACETS	0.937	0.851	1	0.937	0.851	1	CLONAL	1	TRUE	1	0.381437485331873	2		722	733	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714111	43714111	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053607-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	109	927	1	ENST00000382044.4:c.4042G>T	p.Gly1348Trp	p.G1348W	ENST00000382044	NM_001141980.1	1348	Ggg/Tgg	19/28	1	2	FACETS	0.883	0.795	0.977	0.883	0.795	0.977	CLONAL	1	TRUE	1	0.381437485331873	2		928	647	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213920	66213920	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053607-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	37	381	0	ENST00000273854.3:c.2510del	p.Gly837GlufsTer14	p.G837Efs*14	ENST00000273854	NM_004439.5	837	gGa/ga	15/18	1	2	FACETS	0.767	0.636	0.911	0.767	0.636	0.911	CLONAL	1	TRUE	1	0.381437485331873	2		381	253	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163836	152163836	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053607-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	65	594	0	ENST00000206249.3:c.557C>A	p.Ala186Glu	p.A186E	ENST00000206249	NM_000125.3	186	gCa/gAa	2/8	0.351705249020636	2	FACETS	0.766	0.666	0.874	0.383	0.333	0.437	SUBCLONAL	1	TRUE	0	0.381437485331873	2		594	445	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611120	100611120	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053607-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	87	730	0	ENST00000308731.7:c.1486C>A	p.Gln496Lys	p.Q496K	ENST00000308731	NM_000061.2	496	Cag/Aag	15/19	0.368167544272895	3	FACETS	0.748	0.662	0.84	0.374	0.331	0.42	SUBCLONAL	1	TRUE	1	0.381437485331873	3		730	726	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0053608-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	162	434	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.296344082045972	4	FACETS	0.9	0.835	0.967	1	0.983	1	CLONAL	4	TRUE	1	0.26	4		434	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0053608-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	90	1002	1	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.19613766338072	2	FACETS	1	0.926	1	0.528	0.469	0.592	CLONAL	1	TRUE	0	0.26	2		1003	655	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724121	61724121	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053608-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	48	352	0	ENST00000401558.2:c.781C>T	p.Arg261Ter	p.R261*	ENST00000401558	NM_003400.3	261	Cga/Tga	10/25	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.26	2		352	330	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599944	10599944	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053608-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	118	993	1	ENST00000171111.5:c.1632del	p.Trp544Ter	p.W544*	ENST00000171111	NM_203500.1	544	tgG/tg	5/6	0.275563715580926	1	FACETS	0.9	0.812	0.994	0.9	0.812	0.994	CLONAL	1	TRUE	0	0.26	1		994	877	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431403	121431403	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053608-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	42	876	1	ENST00000257555.6:c.607C>A	p.Arg203Ser	p.R203S	ENST00000257555		203	Cgt/Agt	3/10	1	2	FACETS	0.49	0.408	0.582	0.49	0.408	0.582	SUBCLONAL	1	TRUE	1	0.26	2		877	659	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059150	42059150	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053608-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	87	534	0	ENST00000219905.7:c.8870A>T	p.Glu2957Val	p.E2957V	ENST00000219905	NM_001164273.1	2957	gAg/gTg	24/24	0.275563715580926	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.26	1		534	446	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374402	31374402	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053608-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	56	1019	0	ENST00000328111.2:c.401A>C	p.Asp134Ala	p.D134A	ENST00000328111	NM_006892.3	134	gAc/gCc	5/23	1	2	FACETS	0.562	0.48	0.651	0.562	0.48	0.651	SUBCLONAL	1	TRUE	1	0.26	2		1019	767	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513026	106513026	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053608-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	52	368	1	ENST00000359195.3:c.2040T>G	p.Phe680Leu	p.F680L	ENST00000359195	NM_002649.2	680	ttT/ttG	3/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.26	2		369	319	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0053622-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	11	76	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.127	0.087	0.177	0.127	0.087	0.177	SUBCLONAL	1	TRUE	1	0.438829119824904	2		76	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0053622-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	234	1025	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.438829119824904	1	FACETS	0.966	0.903	1	0.966	0.903	1	CLONAL	1	TRUE	0	0.438829119824904	1		1026	862	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936995	48936995	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778842	NA	P-0053622-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	82	388	0	ENST00000267163.4:c.763C>T	p.Arg255Ter	p.R255*	ENST00000267163	NM_000321.2	255	Cga/Tga	8/27	0.438829119824904	1	FACETS	0.813	0.722	0.908	0.813	0.722	0.908	CLONAL	1	TRUE	0	0.438829119824904	1		388	359	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805537	32805539	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0053622-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	201	897	0	ENST00000374899.4:c.472_474del	p.Phe158del	p.F158del	ENST00000374899	NM_018833.2	158	TTC/-	2/12	1	2	FACETS	0.87	0.806	0.937	0.87	0.806	0.937	CLONAL	1	TRUE	1	0.438829119824904	2		897	1053	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156169	106156169	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053622-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	38	359	0	ENST00000380013.4:c.1070G>A	p.Ser357Asn	p.S357N	ENST00000380013	NM_001127208.2	357	aGc/aAc	3/11	1	2	FACETS	0.478	0.396	0.57	0.478	0.396	0.57	SUBCLONAL	1	TRUE	1	0.438829119824904	2		359	362	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44919337	44919337	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053622-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	75	448	1	ENST00000377967.4:c.1265C>T	p.Ala422Val	p.A422V	ENST00000377967	NM_021140.2	422	gCg/gTg	13/29	0.411188593940904	1	FACETS	0.684	0.603	0.771	0.684	0.603	0.771	SUBCLONAL	1	TRUE	0	0.438829119824904	1		449	390	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794439	42794439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370252719	NA	P-0053622-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	59	1264	0	ENST00000575354.2:c.1519C>T	p.Arg507Cys	p.R507C	ENST00000575354	NM_015125.3	507	Cgc/Tgc	10/20	1	2	FACETS	0.274	0.234	0.317	0.274	0.234	0.317	SUBCLONAL	1	TRUE	1	0.438829119824904	2		1264	983	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204501345	204501345	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053622-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	107	443	0	ENST00000367182.3:c.314A>G	p.Asn105Ser	p.N105S	ENST00000367182	NM_001278516.1	105	aAt/aGt	5/11	1	2	FACETS	0.97	0.874	1	0.97	0.874	1	CLONAL	1	TRUE	1	0.438829119824904	2		443	503	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643561	38643561	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs376679136	NA	P-0053622-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	88	561	0	ENST00000299084.4:c.1031A>G	p.His344Arg	p.H344R	ENST00000299084	NM_152594.2	344	cAt/cGt	7/7	1	2	FACETS	0.705	0.626	0.789	0.705	0.626	0.789	SUBCLONAL	1	TRUE	1	0.438829119824904	2		561	569	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027021	71027021	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1278430300	NA	P-0053622-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	175	658	0	ENST00000318789.4:c.1306C>T	p.Arg436Cys	p.R436C	ENST00000318789	NM_032682.5	436	Cgc/Tgc	15/21	1	2	FACETS	0.905	0.834	0.979	0.905	0.834	0.979	CLONAL	1	TRUE	1	0.438829119824904	2		658	881	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0053629-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	83	365	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	FALSE	1	0.448471276067688	2		365	354	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933118	39933118	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053629-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	213	591	0	ENST00000378444.4:c.1481G>T	p.Cys494Phe	p.C494F	ENST00000378444	NM_001123385.1	494	tGt/tTt	4/15	0.45049032504146	3	FACETS	0.972	0.901	1	0.486	0.45	0.522	CLONAL	1	FALSE	1	0.448471276067688	3		591	1197	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061053	38061054	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0053629-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	103	314	0	ENST00000250448.2:c.934_935dup	p.His314CysfsTer8	p.H314Cfs*8	ENST00000250448	NM_004496.3	312	ggt/ggGGt	2/2	0.195376592267271	3	FACETS	0.922	0.827	1	0.307	0.275	0.341	INDETERMINATE	1	FALSE	0	0.448471276067688	3		314	610	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742821	145742824	+	frameshift_variant	Frame_Shift_Del	DEL	ACTC	ACTC	-	novel	NA	P-0053629-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	118	271	0	ENST00000428558.2:c.187_190del	p.Glu63ArgfsTer19	p.E63Rfs*19	ENST00000428558	NM_004260.3	63	GAGTcg/cg	3/22	0.268879403175124	4	FACETS	1	0.971	1			1	INDETERMINATE	1	FALSE	NA	0.448471276067688	4		271	641	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053694-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	38	375	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		375	435	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061087	38061190	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGCGCCAGAGGGGTCCTTGCGGCTCTCAGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTT	GAGGCGCCAGAGGGGTCCTTGCGGCTCTCAGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTT	-	novel	NA	P-0053795-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	229	214	0	ENST00000250448.2:c.799_902del	p.Lys267Ter	p.K267*	ENST00000250448	NM_004496.3	267	AAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGGCGCCAAGGGCGGCCCTGAGAGCCGCAAGGACCCCTCTGGCGCCTCt/t	2/2	1	2	FACETS	0.996	0.947	1	1	0.995	1	CLONAL	2	TRUE	1	0.604828680483073	2		214	380	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061111	38061124	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTCAGGGCCGCC	CTCTCAGGGCCGCC	-	novel	NA	P-0053795-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	87	172	0	ENST00000250448.2:c.865_878del	p.Gly289ProfsTer9	p.G289Pfs*9	ENST00000250448	NM_004496.3	289	GGCGGCCCTGAGAGc/c	2/2	1	2	FACETS	0.751	0.67	0.837	0.751	0.67	0.837	SUBCLONAL	1	TRUE	1	0.604828680483073	2		172	383	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491411	18491411	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053795-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	46	407	0	ENST00000266497.5:c.1324G>C	p.Gly442Arg	p.G442R	ENST00000266497		442	Ggg/Cgg	8/31	1	2	FACETS	0.334	0.281	0.392	0.334	0.281	0.392	SUBCLONAL	1	TRUE	1	0.604828680483073	2		407	456	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061202	38061202	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053795-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	241	476	0	ENST00000250448.2:c.787del	p.Gln263ArgfsTer58	p.Q263Rfs*58	ENST00000250448	NM_004496.3	263	Cag/ag	2/2	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.604828680483073	2		476	663	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0053799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	212	603	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.969	0.906	1	0.969	0.906	1	CLONAL	1	TRUE	1	0.723336506311002	2		603	605	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	431	375	0				ENST00000310581	NM_198253.2	-/1132			0.723336506311002	4	FACETS	0.957	0.923	0.992	0.957	0.923	0.992	CLONAL	3	TRUE	1	0.723336506311002	4		375	715	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413010	49413010	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519952	NA	P-0053799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	187	577	0	ENST00000418115.1:c.13C>T	p.Arg5Trp	p.R5W	ENST00000418115	NM_001664.2	5	Cgg/Tgg	2/5	0.723336506311002	3	FACETS	0.763	0.705	0.823	0.381	0.352	0.412	SUBCLONAL	1	TRUE	1	0.723336506311002	3		577	923	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405476	70405476	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0053799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	223	560	0	ENST00000373644.4:c.2990C>G	p.Ser997Ter	p.S997*	ENST00000373644	NM_030625.2	997	tCa/tGa	4/12	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.723336506311002	2		560	603	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440094	49440095	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GACA	novel	NA	P-0053799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	268	679	0	ENST00000301067.7:c.4528_4531dup	p.His1511LeufsTer18	p.H1511Lfs*18	ENST00000301067	NM_003482.3	1511	cat/cTGTCat	16/54	1	2	FACETS	0.893	0.84	0.947	0.893	0.84	0.947	CLONAL	1	TRUE	1	0.723336506311002	2		679	830	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445937	49445937	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	408	1022	2	ENST00000301067.7:c.1529C>T	p.Ser510Leu	p.S510L	ENST00000301067	NM_003482.3	510	tCa/tTa	10/54	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.723336506311002	2		1024	1100	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915295	32915295	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	234	605	0	ENST00000380152.3:c.6803G>C	p.Arg2268Thr	p.R2268T	ENST00000380152		2268	aGa/aCa	11/27	1	2	FACETS	0.931	0.873	0.99	0.931	0.873	0.99	CLONAL	1	TRUE	1	0.723336506311002	2		605	695	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610378	81610378	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	131	405	0	ENST00000298171.2:c.1976C>T	p.Ser659Phe	p.S659F	ENST00000298171	NM_000369.2	659	tCc/tTc	10/10	1	2	FACETS	0.789	0.721	0.859	0.789	0.721	0.859	SUBCLONAL	1	TRUE	1	0.723336506311002	2		405	459	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856012	68856013	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	257	547	0	ENST00000261769.5:c.1823dup	p.Pro609AlafsTer8	p.P609Afs*8	ENST00000261769	NM_004360.3	607	cca/ccAa	12/16	0.723336506311002	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.723336506311002	1		547	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0053799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	270	660	0	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	0.723336506311002	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.723336506311002	1		660	453	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728831	190728831	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778613	NA	P-0053799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	118	375	0	ENST00000441310.2:c.2219C>T	p.Ser740Phe	p.S740F	ENST00000441310	NM_000534.4	740	tCc/tTc	10/13	1	2	FACETS	0.782	0.711	0.856	0.782	0.711	0.856	SUBCLONAL	1	TRUE	1	0.723336506311002	2		375	417	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466824	57466824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	118	296	0	ENST00000371085.3:c.43G>A	p.Glu15Lys	p.E15K	ENST00000371085	NM_000516.4	15	Gag/Aag	1/13	1	2	FACETS	0.909	0.829	0.991	0.909	0.829	0.991	CLONAL	1	TRUE	1	0.723336506311002	2		296	359	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480355	89480355	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	18	289	0	ENST00000336596.2:c.2192C>A	p.Ala731Glu	p.A731E	ENST00000336596	NM_005233.5	731	gCa/gAa	13/17	1	2	FACETS	0.154	0.115	0.199	0.154	0.115	0.199	SUBCLONAL	1	TRUE	1	0.723336506311002	2		289	324	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155363	185155363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	180	425	0	ENST00000265026.3:c.604G>A	p.Glu202Lys	p.E202K	ENST00000265026	NM_004721.4	202	Gag/Aag	3/14	1	2	FACETS	0.907	0.842	0.973	0.907	0.842	0.973	CLONAL	1	TRUE	1	0.723336506311002	2		425	549	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158771	26158771	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1378116292	NA	P-0053799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	310	689	0	ENST00000289316.2:c.374C>A	p.Ser125Tyr	p.S125Y	ENST00000289316	NM_138720.2	125	tCc/tAc	1/2	1	2	FACETS	0.932	0.881	0.983	0.932	0.881	0.983	CLONAL	1	TRUE	1	0.723336506311002	2		689	920	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878176	151878176	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	43	589	1	ENST00000262189.6:c.6769C>T	p.Arg2257Ter	p.R2257*	ENST00000262189	NM_170606.2	2257	Cga/Tga	36/59	1	2	FACETS	0.189	0.158	0.224	0.189	0.158	0.224	SUBCLONAL	1	TRUE	1	0.723336506311002	2		590	628	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391581	139391581	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	353	1001	1	ENST00000277541.6:c.6610G>A	p.Glu2204Lys	p.E2204K	ENST00000277541	NM_017617.3	2204	Gag/Aag	34/34	1	2	FACETS	0.978	0.929	1	0.978	0.929	1	CLONAL	1	TRUE	1	0.723336506311002	2		1002	998	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861584	152861584	+	synonymous_variant	Silent	SNP	G	G	A	novel	NA	P-0053799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	305	354	0	ENST00000406277.2:c.168C>T	p.Phe56=	p.F56=	ENST00000406277	NM_152274.4	56	ttC/ttT	4/7	1		FACETS		0.995	1				CLONAL	1	TRUE	0	0.723336506311002	1		354	412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0053807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	1197	249	0	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	0.794611381221148	1	FACETS	1	0.999	1	1	0.999	1	CLONAL	1	TRUE	0	0.794611381221148	1		249	1324	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876541	35876541	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	642	83	0	ENST00000303115.3:c.1333C>T	p.Gln445Ter	p.Q445*	ENST00000303115	NM_002185.3	445	Caa/Taa	8/8	0.794611381221148	4	FACETS	1	0.995	1	0.756	0.731	0.782	CLONAL	2	TRUE	1	0.794611381221148	4		83	1278	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736927	736927	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	495	14	0	ENST00000314574.4:c.1172A>T	p.Asn391Ile	p.N391I	ENST00000314574	NM_005433.3	391	aAc/aTc	10/12	0.613567043371766	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.794611381221148	1		14	680	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92244504	92244504	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	479	340	0	ENST00000265734.4:c.931G>C	p.Asp311His	p.D311H	ENST00000265734	NM_001259.6	311	Gat/Cat	8/8	0.266178867163588	5	FACETS	1	0.986	1	0.818	0.795	0.841	INDETERMINATE	4	TRUE	0	0.794611381221148	5		340	646	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981360	68981360	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	308	55	0	ENST00000288368.4:c.1432G>C	p.Val478Leu	p.V478L	ENST00000288368	NM_024870.2	478	Gtg/Ctg	12/40	0.22297504190545	3	FACETS	0.876	0.834	0.919	0.876	0.834	0.919	INDETERMINATE	2	TRUE	1	0.794611381221148	3		55	618	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410835	63410835	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	435	163	0	ENST00000330258.3:c.2332A>G	p.Ser778Gly	p.S778G	ENST00000330258	NM_152424.3	778	Agc/Ggc	2/2	0.313750639226284	2	FACETS	1	0.997	1			1	INDETERMINATE	2	TRUE	NA	0.794611381221148	2		163	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0053868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	341	1025	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.34380632713231	2	FACETS	0.863	0.819	0.907	0.863	0.819	0.907	CLONAL	2	TRUE	0	0.424199891691799	2		1026	932	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0053868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	255	627	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.312364259529765	3	FACETS	1	0.95	1	0.674	0.634	0.714	CLONAL	2	TRUE	0	0.424199891691799	3		627	721	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591825	48591825	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	79	612	0	ENST00000342988.3:c.988G>C	p.Glu330Gln	p.E330Q	ENST00000342988	NM_005359.5	330	Gaa/Caa	9/12	0.424199891691799	1	FACETS	0.892	0.791	0.998	0.892	0.791	0.998	CLONAL	1	TRUE	0	0.424199891691799	1		612	329	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831458	72831458	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	84	729	0	ENST00000268489.5:c.5123A>C	p.Lys1708Thr	p.K1708T	ENST00000268489	NM_006885.3	1708	aAa/aCa	9/10	0.424199891691799	4	FACETS	0.615	0.542	0.694	0.205	0.18	0.232	SUBCLONAL	1	TRUE	1	0.424199891691799	4		729	917	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338625	70338625	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1156491049	NA	P-0053868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	104	935	0	ENST00000374080.3:c.21G>C	p.Leu7Phe	p.L7F	ENST00000374080		7	ttG/ttC	1/45	1	2	FACETS	0.575	0.514	0.639	0.575	0.514	0.639	SUBCLONAL	1	TRUE	1	0.424199891691799	2		935	853	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0053870-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	596	866	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.938653098635181	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.938653098635181	1		867	649	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954189	48954189	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053870-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	136	172	0	ENST00000267163.4:c.1390G>T	p.Glu464Ter	p.E464*	ENST00000267163	NM_000321.2	464	Gaa/Taa	15/27	0.938653098635181	2	FACETS	0.972	0.94	0.999	0.972	0.94	0.999	CLONAL	2	TRUE	0	0.938653098635181	2		172	149	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281237	49281237	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053870-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	237	666	0	ENST00000282018.3:c.284C>A	p.Ala95Asp	p.A95D	ENST00000282018	NM_020377.2	95	gCt/gAt	1/1	0.938653098635181	2	FACETS	0.61	0.57	0.65	0.305	0.285	0.325	SUBCLONAL	1	TRUE	0	0.938653098635181	2		666	828	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245033	41245033	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053870-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	922	698	0	ENST00000357654.3:c.2515C>A	p.His839Asn	p.H839N	ENST00000357654	NM_007294.3	839	Cac/Aac	10/23	0.405061935058848	3	FACETS	1	0.997	1	0.756	0.74	0.772	INDETERMINATE	2	TRUE	0	0.938653098635181	3		698	1272	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120479909	120479909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053870-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	186	397	0	ENST00000256646.2:c.3518G>A	p.Cys1173Tyr	p.C1173Y	ENST00000256646	NM_024408.3	1173	tGc/tAc	21/34	0.52819298606309	1	FACETS	0.315	0.292	0.339	0.315	0.292	0.339	INDETERMINATE	1	TRUE	0	0.938653098635181	1		397	668	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864898	57864898	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053870-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	499	817	0	ENST00000228682.2:c.2375G>T	p.Gly792Val	p.G792V	ENST00000228682	NM_005269.2	792	gGc/gTc	12/12	1	2	FACETS	0.951	0.913	0.989	0.951	0.913	0.989	CLONAL	1	TRUE	1	0.938653098635181	2		817	1118	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964017	28964017	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053870-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	410	365	0	ENST00000282397.4:c.1885C>A	p.Gln629Lys	p.Q629K	ENST00000282397	NM_002019.4	629	Caa/Aaa	13/30	0.938653098635181	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.938653098635181	2		365	434	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748595	40748595	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs750813623	NA	P-0053870-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	313	384	0	ENST00000373198.4:c.2921G>C	p.Arg974Pro	p.R974P	ENST00000373198	NM_133170.3	974	cGg/cCg	21/32	1	2	FACETS	0.985	0.937	1	0.985	0.937	1	CLONAL	1	TRUE	1	0.938653098635181	2		384	677	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	19	375	0				ENST00000310581	NM_198253.2	-/1132			0.298543410854305	0	FACETS	0.989	0.755	1			1	CLONAL	1	TRUE	0	0.18	0		375	175	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122374	17122374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770396757	NA	P-0053877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	27	666	0	ENST00000285071.4:c.1021C>T	p.Arg341Trp	p.R341W	ENST00000285071	NM_144997.5	341	Cgg/Tgg	9/14	1	2	FACETS	0.644	0.511	0.796	0.644	0.511	0.796	SUBCLONAL	1	TRUE	1	0.18	2		666	466	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716328	52716328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1343613316	NA	P-0053877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	11	728	0	ENST00000322088.6:c.772C>T	p.Arg258Cys	p.R258C	ENST00000322088	NM_014225.5	258	Cgc/Tgc	6/15	1	2	FACETS	0.237	0.162	0.33	0.237	0.162	0.33	SUBCLONAL	1	TRUE	1	0.18	2		728	516	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782169	135782187	+	frameshift_variant	Frame_Shift_Del	DEL	AAAACCCTGGAAGATCACT	AAAACCCTGGAAGATCACT	-	novel	NA	P-0053877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	36	540	0	ENST00000298552.3:c.1369_1387del	p.Ser457Ter	p.S457*	ENST00000298552	NM_001162426.1	457	AGTGATCTTCCAGGGTTTTta/ta	14/23	0.3	1	FACETS	0.899	0.739	1	0.899	0.739	1	CLONAL	1	TRUE	0	0.18	1		540	405	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053946-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	23	375	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.806	1	1	0.806	1	CLONAL	1	TRUE	1	0.16	2		375	278	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340057	116340057	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0053946-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	20	287	0	ENST00000397752.3:c.919A>T	p.Arg307Ter	p.R307*	ENST00000397752	NM_000245.2	307	Aga/Tga	2/21	1	2	FACETS	0.735	0.562	0.939	0.735	0.562	0.939	CLONAL	1	TRUE	1	0.16	2		287	340	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114724366	114724366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1453320798	NA	P-0053963-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	111	563	0	ENST00000543371.1:c.433C>T	p.His145Tyr	p.H145Y	ENST00000543371	NM_001198531.1	145	Cac/Tac	4/14	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.31	2		563	690	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0053969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	504	568	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.379315754742541	5	FACETS	0.94	0.903	0.977			1	CLONAL	4	TRUE	NA	0.379315754742541	5		568	1109	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0053969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	143	112	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.358321238024385	1	FACETS	0.967	0.884	1	0.967	0.884	1	CLONAL	1	TRUE	0	0.379315754742541	1		113	632	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031885	26031885	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	68	300	0	ENST00000244661.2:c.404G>C	p.Arg135Thr	p.R135T	ENST00000244661	NM_003537.3	135	aGa/aCa	1/1	1	2	FACETS	0.903	0.789	1	0.903	0.789	1	CLONAL	1	TRUE	1	0.379315754742541	2		300	397	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111502	8111503	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0053969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	169	721	0	ENST00000346208.3:c.990dup	p.Asn331GlufsTer21	p.N331Efs*21	ENST00000346208		330	agg/aGgg	5/6	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.379315754742541	2		721	864	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7977075	7977075	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs200687206	NA	P-0053969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	127	468	2	ENST00000319144.4:c.1655G>A	p.Gly552Asp	p.G552D	ENST00000319144	NM_001139.2	552	gGc/gAc	13/15	1	2	FACETS	0.98	0.89	1	0.98	0.89	1	CLONAL	1	TRUE	1	0.379315754742541	2		470	683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579415	7579415	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054011-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	729	857	8	ENST00000269305.4:c.272G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tGg/tAg	4/11	0.54212585150294	3	FACETS	0.965	0.938	0.991	0.965	0.938	0.991	CLONAL	3	TRUE	0	0.541958108939126	3		865	1181	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36208923	36208925	+	start_lost,inframe_deletion	Translation_Start_Site	DEL	GGC	GGC	-	rs898578503	NA	P-0054011-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	16	33	0	ENST00000222270.7:c.14_16del	p.Ala5?	p.A5?	ENST00000222270	NM_014727.1	1	atGGCg/atg	1/37	0.54212585150294	4	FACETS	0.813	0.608	1	0.271	0.202	0.351	CLONAL	1	TRUE	1	0.541958108939126	4		33	112	SUCCESS
AR	367	MSKCC	GRCh37	X	66765159	66765206	+	inframe_deletion	In_Frame_Del	DEL	GCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA	GCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA	-	rs3032358	NA	P-0054011-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	62	195	0	ENST00000374690.3:c.192_239del	p.Gln65_Gln80del	p.Q65_Q80del	ENST00000374690	NM_000044.3	57	ctGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAg/ctg	1/8	0.141426564035491	2	FACETS	0.953	0.834	1			1	INDETERMINATE	1	TRUE	NA	0.541958108939126	2		195	240	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491732	120491735	+	frameshift_variant	Frame_Shift_Del	DEL	CTGT	CTGT	-	novel	NA	P-0054011-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	94	286	1	ENST00000256646.2:c.2494_2497del	p.Thr832TyrfsTer51	p.T832Yfs*51	ENST00000256646	NM_024408.3	832	ACAGta/ta	16/34	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.541958108939126	2		287	333	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138947	64138947	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054011-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	61	278	0	ENST00000334205.4:c.2314del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	772	Tcc/cc	17/17	0.54212585150294	4	FACETS	0.926	0.802	1	0.231	0.2	0.265	CLONAL	1	TRUE	0	0.541958108939126	4		278	375	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241967	39241967	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054011-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	48	244	0	ENST00000402219.2:c.1879T>A	p.Phe627Ile	p.F627I	ENST00000402219	NM_005633.3	627	Ttt/Att	11/23	0.54212585150294	3	FACETS	0.831	0.707	0.964	0.415	0.353	0.482	CLONAL	1	TRUE	1	0.541958108939126	3		244	271	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80071513	80071513	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054011-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	105	215	1	ENST00000265081.6:c.2256del	p.Phe752LeufsTer2	p.F752Lfs*2	ENST00000265081	NM_002439.4	752	Ttt/tt	16/24	0.512545559287761	2	FACETS	0.839	0.767	0.911	0.839	0.767	0.911	CLONAL	2	TRUE	0	0.541958108939126	2		216	231	SUCCESS
APC	324	MSKCC	GRCh37	5	112176879	112176879	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054011-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	52	306	0	ENST00000257430.4:c.5588G>T	p.Ser1863Ile	p.S1863I	ENST00000257430	NM_000038.5	1863	aGt/aTt	16/16	0.512545559287761	2	FACETS	0.711	0.61	0.819	0.355	0.305	0.41	SUBCLONAL	1	TRUE	0	0.541958108939126	2		306	270	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175857	24175859	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs875989800	NA	P-0054017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	304	15	0	ENST00000263121.7:c.1091_1093del	p.Lys364del	p.K364del	ENST00000263121	NM_003073.3	362	gAGAag/gag	8/9	0.649963387281676	2	FACETS	0.896	0.856	0.935	0.896	0.856	0.935	CLONAL	2	TRUE	0	0.649963387281676	2		15	522	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183725	10183725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs5030826	NA	P-0054017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	463	926	0	ENST00000256474.2:c.194C>T	p.Ser65Leu	p.S65L	ENST00000256474	NM_000551.3	65	tCg/tTg	1/3	0.649963387281676	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.649963387281676	2		926	686	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417868	138417868	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	222	472	0	ENST00000289153.2:c.1651T>C	p.Cys551Arg	p.C551R	ENST00000289153	NM_006219.2	551	Tgt/Cgt	11/22	0.608484241965868	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.649963387281676	4		472	507	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141631	202141631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs17860424	NA	P-0054017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	69	404	0	ENST00000358485.4:c.919C>T	p.Arg307Trp	p.R307W	ENST00000358485	NM_001080125.1	307	Cgg/Tgg	7/9	0.522721270257909	4	FACETS	0.739	0.645	0.84	0.37	0.322	0.42	SUBCLONAL	1	TRUE	2	0.649963387281676	4		404	474	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666428	206666428	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	370	695	0	ENST00000367120.3:c.1912del	p.Val638SerfsTer31	p.V638Sfs*31	ENST00000367120	NM_014002.3	636	caG/ca	19/22	0.649963387281676	6	FACETS	0.889	0.842	0.937	0.444	0.421	0.469	CLONAL	2	TRUE	2	0.649963387281676	6		695	1473	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671654	67671655	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	252	507	1	ENST00000264010.4:c.2070dup	p.Glu691ArgfsTer5	p.E691Rfs*5	ENST00000264010	NM_006565.3	688	gta/gtAa	12/12	0.608484241965868	4	FACETS	0.919	0.865	0.975	0.919	0.865	0.975	CLONAL	2	TRUE	2	0.649963387281676	4		508	696	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246116	46246116	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	94	356	0	ENST00000334344.6:c.4210C>T	p.Gln1404Ter	p.Q1404*	ENST00000334344	NM_152641.2	1404	Caa/Taa	15/21	0.649963387281676	3	FACETS	0.99	0.888	1	0.495	0.444	0.549	CLONAL	1	TRUE	1	0.649963387281676	3		356	387	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376326	15376326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1221320388	NA	P-0054017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	273	988	0	ENST00000263377.2:c.688C>T	p.Pro230Ser	p.P230S	ENST00000263377	NM_058243.2	230	Ccg/Tcg	5/20	0.522721270257909	4	FACETS	0.972	0.91	1	0.486	0.455	0.518	CLONAL	1	TRUE	2	0.649963387281676	4		988	1426	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665096	138665096	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs758370933	NA	P-0054017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	242	395	0	ENST00000330315.3:c.469C>G	p.Pro157Ala	p.P157A	ENST00000330315	NM_023067.3	157	Ccc/Gcc	1/1	0.608484241965868	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.649963387281676	4		395	574	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204622	128204623	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1559986946	NA	P-0054017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	420	900	0	ENST00000341105.2:c.818dup	p.Pro274ThrfsTer8	p.P274Tfs*8	ENST00000341105	NM_032638.4	273	gga/ggGa	3/6	0.608484241965868	4	FACETS	0.901	0.859	0.944	0.901	0.859	0.944	CLONAL	2	TRUE	2	0.649963387281676	4		900	1183	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517474	176517474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200344385	NA	P-0054017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	523	1058	3	ENST00000292408.4:c.175C>T	p.Arg59Trp	p.R59W	ENST00000292408	NM_213647.1	59	Cgg/Tgg	3/18	0.608484241965868	4	FACETS	0.966	0.926	1	0.966	0.926	1	CLONAL	2	TRUE	2	0.649963387281676	4		1061	1375	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111006	193111006	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	30	179	0	ENST00000367435.3:c.544del	p.Ile182LeufsTer20	p.I182Lfs*20	ENST00000367435	NM_024529.4	180	gAa/ga	7/17	0.649963387281676	6	FACETS	1	0.82	1	0.253	0.205	0.306	CLONAL	1	TRUE	2	0.649963387281676	6		179	210	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391409	139391409	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	570	1075	0	ENST00000277541.6:c.6782del	p.Gly2261AlafsTer34	p.G2261Afs*34	ENST00000277541	NM_017617.3	2261	gGc/gc	34/34	0.649963387281676	2	FACETS	0.957	0.928	0.987	0.957	0.928	0.987	CLONAL	2	TRUE	0	0.649963387281676	2		1075	916	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830885	72830885	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	330	700	2	ENST00000268489.5:c.5696del	p.Gly1899GlufsTer15	p.G1899Efs*15	ENST00000268489	NM_006885.3	1899	gGa/ga	9/10	0.608484241965868	4	FACETS	0.931	0.883	0.98	0.931	0.883	0.98	CLONAL	2	TRUE	2	0.649963387281676	4		702	900	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228322	53228322	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs199422236	NA	P-0054017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	304	319	0	ENST00000375401.3:c.2080C>T	p.Arg694Ter	p.R694*	ENST00000375401	NM_004187.3	694	Cga/Tga	15/26	0.531146125709047	2	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.649963387281676	2		319	406	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351529	89351529	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	437	768	0	ENST00000301030.4:c.1421A>G	p.Asp474Gly	p.D474G	ENST00000301030	NM_001256183.1	474	gAc/gGc	9/13	0.608484241965868	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	2	0.649963387281676	4		768	1105	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322777	30322777	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	142	296	0	ENST00000322652.5:c.1790T>A	p.Ile597Asn	p.I597N	ENST00000322652	NM_015355.2	597	aTt/aAt	14/16	0.649963387281676	3	FACETS	0.988	0.918	1	0.988	0.918	1	CLONAL	2	TRUE	1	0.649963387281676	3		296	293	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366377	15366377	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766399636	NA	P-0054017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	132	483	0	ENST00000263377.2:c.1778G>A	p.Ser593Asn	p.S593N	ENST00000263377	NM_058243.2	593	aGc/aAc	10/20	0.522721270257909	4	FACETS	0.968	0.881	1	0.484	0.44	0.53	CLONAL	1	TRUE	2	0.649963387281676	4		483	692	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905351	50905351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775620863	NA	P-0054017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	578	1152	1	ENST00000440232.2:c.559G>A	p.Val187Met	p.V187M	ENST00000440232	NM_002691.3	187	Gtg/Atg	5/27	0.522721270257909	4	FACETS	0.976	0.938	1	0.976	0.938	1	CLONAL	2	TRUE	2	0.649963387281676	4		1153	1504	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655408	45655408	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs745559924	NA	P-0054017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	267	866	0	ENST00000407780.3:c.444C>A	p.Ser148Arg	p.S148R	ENST00000407780	NM_001283052.1	148	agC/agA	4/7	0.649963387281676	3	FACETS	1	0.949	1	0.507	0.475	0.539	CLONAL	1	TRUE	1	0.649963387281676	3		866	1074	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053313	37053314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	159	323	0	ENST00000231790.2:c.550dup	p.Ser184PhefsTer8	p.S184Ffs*8	ENST00000231790	NM_000249.3	183	tat/taTt	7/19	0.649963387281676	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.649963387281676	2		323	233	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457252	89457252	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	85	379	0	ENST00000336596.2:c.1738del	p.Arg580AspfsTer9	p.R580Dfs*9	ENST00000336596	NM_005233.5	578	gAa/ga	9/17	0.649963387281676	2	FACETS	0.927	0.83	1	0.464	0.415	0.515	CLONAL	1	TRUE	0	0.649963387281676	2		379	282	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324053	31324054	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	440	816	0	ENST00000412585.2:c.509dup	p.Trp171ValfsTer6	p.W171Vfs*6	ENST00000412585	NM_005514.6	170	aag/aaAg	3/8	0.649963387281676	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.649963387281676	2		816	614	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813502	32813502	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	353	712	0	ENST00000354258.4:c.2281del	p.Gln761SerfsTer98	p.Q761Sfs*98	ENST00000354258	NM_000593.5	761	Cag/ag	11/11	0.649963387281676	2	FACETS	0.943	0.905	0.98	0.943	0.905	0.98	CLONAL	2	TRUE	0	0.649963387281676	2		712	576	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172978	38172978	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	287	493	0	ENST00000317025.8:c.2071T>C	p.Ser691Pro	p.S691P	ENST00000317025	NM_023034.1	691	Tcg/Ccg	11/24	0.188000688160996	5	FACETS	1	0.957	1			1	INDETERMINATE	3	TRUE	NA	0.649963387281676	5		493	577	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0054028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	150	573	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	0.130909689889142	4	FACETS	0.921	0.853	0.989	0.921	0.853	0.989	INDETERMINATE	2	TRUE	2	0.834717647603117	4		573	358	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607436	46607436	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	1019	405	2	ENST00000263734.3:c.1625T>C	p.Leu542Pro	p.L542P	ENST00000263734	NM_001430.4	542	cTa/cCa	12/16	0.121929327672171	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		407	1621	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488381	20488381	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1291546222	NA	P-0054029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	514	72	0	ENST00000346618.3:c.1037T>C	p.Ile346Thr	p.I346T	ENST00000346618	NM_001949.4	346	aTt/aCt	6/7	0.184946587655752	4	FACETS		NA	1			1	NA	NA	FALSE	2	NA	4		72	695	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0054052-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	358	455	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	1	0.446793808973354	2		456	695	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0054052-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	515	543	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.994	1	1	0.998	1	CLONAL	2	TRUE	1	0.446793808973354	2		543	1004	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159747	20159747	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054052-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	655	122	0	ENST00000379607.5:c.12T>G	p.Asn4Lys	p.N4K	ENST00000379607	NM_001412.3	4	aaT/aaG	1/7	1	2	FACETS	0.907	0.881	0.934	1	0.998	1	CLONAL	3	TRUE	1	0.446793808973354	2		122	1077	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0054059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	345	392	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.658141797601063	4	FACETS	0.887	0.849	0.925	1	0.995	1	CLONAL	3	TRUE	2	0.711096962679696	4		392	624	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748451	40748451	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	749	474	0	ENST00000392038.2:c.431G>C	p.Arg144Pro	p.R144P	ENST00000392038	NM_001626.4	144	cGg/cCg	5/14	0.670152734029433	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.711096962679696	2		474	1029	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0054060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	545	112	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.338831780416628	0	FACETS	0.761	0.74	0.781			1	INDETERMINATE	1	TRUE	0	0.659143705908697	0		113	741	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434325	49434325	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	1007	289	2	ENST00000301067.7:c.7228C>T	p.Arg2410Ter	p.R2410*	ENST00000301067	NM_003482.3	2410	Cga/Tga	31/54	0.469980274026373	3	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.659143705908697	3		291	1850	SUCCESS
ATR	545	MSKCC	GRCh37	3	142180875	142180900	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCATATGTTCGAATATGAAGTTCT	CTGCATATGTTCGAATATGAAGTTCT	-	novel	NA	P-0054060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	313	73	0	ENST00000350721.4:c.7074_7099del	p.Arg2358SerfsTer6	p.R2358Sfs*6	ENST00000350721	NM_001184.3	2358	agAGAACTTCATATTCGAACATATGCAGtt/agtt	42/47	0.636759663776596	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.659143705908697	4		73	738	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815515	139815515	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	706	451	0	ENST00000247668.2:c.986G>C	p.Gly329Ala	p.G329A	ENST00000247668	NM_021138.3	329	gGc/gCc	9/11	0.5491203268478	4	FACETS	0.865	0.838	0.893	1	0.997	1	CLONAL	3	TRUE	2	0.659143705908697	4		451	1369	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932717	39932718	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	444	125	0	ENST00000378444.4:c.1881dup	p.Ala628SerfsTer17	p.A628Sfs*17	ENST00000378444	NM_001123385.1	627	-/A	4/15	0.614586439903841	2	FACETS	1	0.996	1			1	CLONAL	1	TRUE	NA	0.659143705908697	2		125	931	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0054061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	539	173	1	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	1	2	FACETS	0.937	0.903	0.97	1	0.998	1	CLONAL	4	TRUE	1	0.278038975002652	2		174	1035	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922363	178922363	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	251	72	0	ENST00000263967.3:c.1132T>C	p.Cys378Arg	p.C378R	ENST00000263967	NM_006218.2	378	Tgt/Cgt	6/21	0.278038975002652	3	FACETS	0.931	0.88	0.983	1	0.995	1	CLONAL	4	TRUE	1	0.278038975002652	3		72	552	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443552	49443552	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	649	75	0	ENST00000301067.7:c.3819C>G	p.Cys1273Trp	p.C1273W	ENST00000301067	NM_003482.3	1273	tgC/tgG	11/54	0.278038975002652	3	FACETS	1	0.968	1	1	0.998	1	CLONAL	4	TRUE	1	0.278038975002652	3		75	1327	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914728	32914728	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622757	NA	P-0054061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	378	40	0	ENST00000380152.3:c.6236T>A	p.Val2079Glu	p.V2079E	ENST00000380152		2079	gTg/gAg	11/27	1	2	FACETS	1	0.972	1	1	0.997	1	CLONAL	4	TRUE	1	0.278038975002652	2		40	669	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396293	396293	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	729	82	1	ENST00000262320.3:c.733G>T	p.Glu245Ter	p.E245*	ENST00000262320	NM_003502.3	245	Gag/Tag	2/11	1	2	FACETS	0.921	0.892	0.949	1	0.998	1	CLONAL	4	TRUE	1	0.278038975002652	2		83	1424	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713843	30713843	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	585	82	1	ENST00000295754.5:c.1168G>T	p.Asp390Tyr	p.D390Y	ENST00000295754	NM_003242.5	390	Gac/Tac	4/7	1	2	FACETS	0.9	0.868	0.931	1	0.998	1	CLONAL	4	TRUE	1	0.278038975002652	2		83	1169	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280116	66280116	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	240	35	0	ENST00000273854.3:c.1573A>T	p.Ile525Phe	p.I525F	ENST00000273854	NM_004439.5	525	Att/Ttt	7/18	1	2	FACETS	1	0.986	1	1	0.996	1	CLONAL	3	TRUE	1	0.278038975002652	2		35	506	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163313	32163314	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0054061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	876	95	1	ENST00000375023.3:c.5912_5913delinsTT	p.Cys1971Phe	p.C1971F	ENST00000375023	NM_004557.3	1971	tGC/tTT	30/30	1	2	FACETS	0.991	0.964	1			1	CLONAL	4	TRUE	1	0.278038975002652	2		96	1589	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0054062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	350	434	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.379506351694677	4	FACETS	0.9	0.862	0.938	1	0.996	1	CLONAL	4	TRUE	2	0.452425597950154	4		434	624	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0054062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	722	817	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.452425597950154	2	FACETS	1	0.994	1	1	0.998	1	CLONAL	3	TRUE	0	0.452425597950154	2		817	1003	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0054062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	273	74	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.440525356920034	4	FACETS	0.99	0.955	1	1	0.995	1	CLONAL	5	TRUE	0	0.452425597950154	4		74	354	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770564	40770564	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1164669135	NA	P-0054062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	470	55	0	ENST00000373198.4:c.2818A>G	p.Ile940Val	p.I940V	ENST00000373198	NM_133170.3	940	Atc/Gtc	19/32	0.452425597950154	6	FACETS	1	0.99	1	1	0.99	1	CLONAL	4	TRUE	2	0.452425597950154	6		55	911	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0054063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	622	817	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.831	0.801	0.86	1	0.997	1	CLONAL	2	TRUE	1	0.53	2		817	1413	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302830	15302830	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs570703724	NA	P-0054063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	926	60	0	ENST00000263388.2:c.620G>A	p.Arg207His	p.R207H	ENST00000263388	NM_000435.2	207	cGt/cAt	4/33	1	2	FACETS	0.968	0.942	0.995	1	0.998	1	CLONAL	2	TRUE	1	0.53	2		60	1804	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0054105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	60	477	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.869	0.751	0.997	0.869	0.751	0.997	CLONAL	1	TRUE	1	0.324198872454671	2		477	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0054105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	192	681	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.284145120416407	2	FACETS	0.925	0.86	0.993	0.925	0.86	0.993	CLONAL	2	TRUE	0	0.324198872454671	2		682	640	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0054105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	34	222	2	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.324198872454671	2		224	192	SUCCESS
APC	324	MSKCC	GRCh37	5	112154723	112154723	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775126020	NA	P-0054105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	51	411	1	ENST00000257430.4:c.994C>T	p.Arg332Ter	p.R332*	ENST00000257430	NM_000038.5	332	Cga/Tga	10/16	1	2	FACETS	0.996	0.851	1	0.996	0.851	1	CLONAL	1	TRUE	1	0.324198872454671	2		412	316	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196261	106196261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	42	294	0	ENST00000380013.4:c.4594C>T	p.Gln1532Ter	p.Q1532*	ENST00000380013	NM_001127208.2	1532	Cag/Tag	11/11	1	2	FACETS	0.867	0.727	1	0.867	0.727	1	CLONAL	1	TRUE	1	0.324198872454671	2		294	299	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046548	30046548	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	111	618	3	ENST00000331968.5:c.2635C>A	p.Gln879Lys	p.Q879K	ENST00000331968	NM_002742.2	879	Cag/Aag	18/18	0.284145120416407	2	FACETS	1	0.981	1	0.685	0.618	0.754	CLONAL	1	TRUE	0	0.324198872454671	2		621	500	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843470	3843470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781492264	NA	P-0054105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	73	555	1	ENST00000262367.5:c.1133G>A	p.Arg378Gln	p.R378Q	ENST00000262367	NM_004380.2	378	cGg/cAg	4/31	1	2	FACETS	0.895	0.785	1	0.895	0.785	1	CLONAL	1	TRUE	1	0.324198872454671	2		556	503	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120168	70120168	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	112	440	0	ENST00000245479.2:c.1171del	p.Gln391SerfsTer12	p.Q391Sfs*12	ENST00000245479	NM_000346.3	390	ggC/gg	3/3	0.284145120416407	2	FACETS	0.946	0.86	1	0.946	0.86	1	CLONAL	2	TRUE	0	0.324198872454671	2		440	365	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604648	48604681	+	frameshift_variant	Frame_Shift_Del	DEL	TGGTGTTGATGACCTTCGTCGCTTATGCATACTC	TGGTGTTGATGACCTTCGTCGCTTATGCATACTC	-	novel	NA	P-0054105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	42	329	0	ENST00000342988.3:c.1470_1503del	p.Val492Ter	p.V492*	ENST00000342988	NM_005359.5	490	atTGGTGTTGATGACCTTCGTCGCTTATGCATACTC/at	12/12	0.324198872454671	1	FACETS	0.845	0.71	0.992	0.845	0.71	0.992	CLONAL	1	TRUE	0	0.324198872454671	1		329	257	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023253	27023271	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCCGGCGGCGGCGGTGG	CGCCCGGCGGCGGCGGTGG	-	novel	NA	P-0054113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	91	59	0	ENST00000324856.7:c.361_379del	p.Pro121AlafsTer105	p.P121Afs*105	ENST00000324856	NM_006015.4	120	cCGCCCGGCGGCGGCGGTGGc/cc	1/20	1	2	FACETS	0.774	0.693	0.859	1	0.982	1	SUBCLONAL	2	TRUE	1	0.320345056794955	2		59	367	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115929	8115930	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	100	543	0	ENST00000346208.3:c.1276dup	p.Ser426PhefsTer81	p.S426Ffs*81	ENST00000346208		425	-/T	6/6	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.320345056794955	2		543	612	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38954938	38954938	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	46	55	0	ENST00000357387.3:c.2635C>T	p.Pro879Ser	p.P879S	ENST00000357387	NM_152756.3	879	Cct/Tct	27/38	0.270985169980652	4	FACETS	0.936	0.79	1	0.312	0.263	0.366	CLONAL	1	TRUE	1	0.320345056794955	4		55	405	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177012	56177022	+	frameshift_variant	Frame_Shift_Del	DEL	TAGATAGACTG	TAGATAGACTG	-	novel	NA	P-0054113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	82	37	0	ENST00000399503.3:c.2283_2293del	p.Asp762ValfsTer6	p.D762Vfs*6	ENST00000399503	NM_005921.1	761	aTAGATAGACTG/a	13/20	0.320345056794955	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.320345056794955	1		37	343	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023253	27023271	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCCGGCGGCGGCGGTGG	CGCCCGGCGGCGGCGGTGG	-	novel	NA	P-0054113-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	382	59	0	ENST00000324856.7:c.361_379del	p.Pro121AlafsTer105	p.P121Afs*105	ENST00000324856	NM_006015.4	120	cCGCCCGGCGGCGGCGGTGGc/cc	1/20	1	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	3	TRUE	1	0.40656999029676	2		59	585	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38954938	38954938	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054113-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	317	55	0	ENST00000357387.3:c.2635C>T	p.Pro879Ser	p.P879S	ENST00000357387	NM_152756.3	879	Cct/Tct	27/38	0.40656999029676	3	FACETS	1	0.991	1	1	0.996	1	CLONAL	3	TRUE	1	0.40656999029676	3		55	548	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177012	56177022	+	frameshift_variant	Frame_Shift_Del	DEL	TAGATAGACTG	TAGATAGACTG	-	novel	NA	P-0054113-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	438	37	0	ENST00000399503.3:c.2283_2293del	p.Asp762ValfsTer6	p.D762Vfs*6	ENST00000399503	NM_005921.1	761	aTAGATAGACTG/a	13/20	0.351775409723543	1	FACETS	0.878	0.849	0.906	1	0.998	1	CLONAL	3	TRUE	0	0.40656999029676	1		37	652	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0054113-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	1010	100	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	1	2	FACETS	1	0.998	1			1	CLONAL	3	TRUE	1	0.40656999029676	2		100	1433	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940146	71940147	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTGAGCACCGTCTCGCACGACTACCT	novel	NA	P-0054113-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	1023	81	0	ENST00000298229.2:c.532_557dup	p.Lys187Ter	p.K187*	ENST00000298229	NM_001567.3	177	-/CTGAGCACCGTCTCGCACGACTACCT	5/28	0.40656999029676	1	FACETS	0.915	0.896	0.934	1	0.999	1	CLONAL	3	TRUE	0	0.40656999029676	1		81	1460	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745117	41745117	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054113-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	1030	102	0	ENST00000301178.4:c.1183G>C	p.Gly395Arg	p.G395R	ENST00000301178	NM_021913.4	395	Ggg/Cgg	9/20	1	2	FACETS	1	0.997	1			1	CLONAL	3	TRUE	1	0.40656999029676	2		102	1503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0054114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	837	98	28	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	0.376575002519786	1	FACETS	1	0.997	1	1	0.999	1	CLONAL	3	TRUE	0	0.376575002519786	1		126	1072	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936093	178936093	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913275	NA	P-0054114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	755	51	36	ENST00000263967.3:c.1635G>T	p.Glu545Asp	p.E545D	ENST00000263967	NM_006218.2	545	gaG/gaT	10/21	0.33525509133854	3	FACETS	1	0.997	1	1	0.999	1	CLONAL	5	TRUE	1	0.376575002519786	3		87	871	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648309	206648316	+	frameshift_variant	Frame_Shift_Del	DEL	TGAGTTCC	TGAGTTCC	-	novel	NA	P-0054114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	929	90	22	ENST00000367120.3:c.332_339del	p.Glu111GlyfsTer53	p.E111Gfs*53	ENST00000367120	NM_014002.3	110	gaTGAGTTCCtg/gatg	5/22	1	2	FACETS	0.912	0.891	0.932			1	CLONAL	4	TRUE	1	0.376575002519786	2		112	1353	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30102151	30102151	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	539	46	18	ENST00000331968.5:c.1316G>T	p.Arg439Leu	p.R439L	ENST00000331968	NM_002742.2	439	cGg/cTg	9/18	1	2	FACETS	0.988	0.962	1	1	0.998	1	CLONAL	4	TRUE	1	0.376575002519786	2		64	724	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78882694	78882694	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	921	100	20	ENST00000306801.3:c.2485G>T	p.Val829Leu	p.V829L	ENST00000306801	NM_020761.2	829	Gtg/Ttg	21/34	1	2	FACETS	0.952	0.932	0.972			1	CLONAL	4	TRUE	1	0.376575002519786	2		120	1284	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518279	187518279	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	435	10	0	ENST00000441802.2:c.12415G>T	p.Gly4139Trp	p.G4139W	ENST00000441802	NM_005245.3	4139	Ggg/Tgg	25/27	0.172415815594271	0	FACETS	0.776	0.751	0.8			1	INDETERMINATE	3	TRUE	0	0.376575002519786	0		10	619	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933853	39933853	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	1182	91	22	ENST00000378444.4:c.746C>A	p.Pro249Gln	p.P249Q	ENST00000378444	NM_001123385.1	249	cCa/cAa	4/15	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	4	TRUE	NA	0.376575002519786	2		113	1569	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349592	70349592	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	972	83	21	ENST00000374080.3:c.3754G>T	p.Glu1252Ter	p.E1252*	ENST00000374080		1252	Gag/Tag	27/45	0.376575002519786	1	FACETS	1	0.996	1			1	CLONAL	3	TRUE	0	0.376575002519786	1		104	1309	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0054115-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	1582	901	1	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.498072412763175	3	FACETS	1	0.998	1	1	0.998	1	CLONAL	3	TRUE	0	0.522391979512556	3		902	2191	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969370	44969371	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054115-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	664	324	2	ENST00000377967.4:c.4055dup	p.Thr1353AspfsTer36	p.T1353Dfs*36	ENST00000377967	NM_021140.2	1351	cga/cgAa	28/29	0.525223735884734	2	FACETS	0.901	0.878	0.924	1	0.998	1	CLONAL	3	TRUE	0	0.522391979512556	2		326	940	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710582	114710596	+	inframe_deletion	In_Frame_Del	DEL	GACGAGGGCGAACAG	GACGAGGGCGAACAG	-	novel	NA	P-0054115-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	715	144	0	ENST00000543371.1:c.69_83del	p.Asp23_Gln27del	p.D23_Q27del	ENST00000543371	NM_001198531.1	23	GACGAGGGCGAACAG/-	1/14	0.219765184613977	3	FACETS	0.94	0.913	0.967	0.94	0.913	0.967	INDETERMINATE	3	TRUE	0	0.522391979512556	3		144	1224	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445979	49445979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774098338	NA	P-0054115-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1703	1752	189	0	ENST00000301067.7:c.1487C>T	p.Pro496Leu	p.P496L	ENST00000301067	NM_003482.3	496	cCg/cTg	10/54	0.459533140919655	4	FACETS	0.985	0.965	1			1	CLONAL	3	TRUE	NA	0.522391979512556	4		189	3455	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197353	26197353	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054115-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	1005	79	0	ENST00000356476.2:c.126C>A	p.Tyr42Ter	p.Y42*	ENST00000356476		42	taC/taA	1/1	0.525223735884734	4	FACETS	0.874	0.849	0.898	1	0.998	1	CLONAL	3	TRUE	2	0.522391979512556	4		79	2235	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828172	3828173	+	missense_variant	Missense_Mutation	DNP	AT	AT	GA	novel	NA	P-0054115-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	465	58	0	ENST00000262367.5:c.1952_1953delinsTC	p.Tyr651Phe	p.Y651F	ENST00000262367	NM_004380.2	651	tAT/tTC	10/31	0.522391979512556	5	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	TRUE	2	0.522391979512556	5		58	1047	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0054121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	128	76	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.460631705902964	3	FACETS	0.96	0.881	1	0.96	0.881	1	CLONAL	2	TRUE	1	0.460556271868705	3		76	356	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0054121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	103	271	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.460631705902964	3	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	1	0.460556271868705	3		271	268	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056500	26056500	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs372319415	NA	P-0054121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	50	299	0	ENST00000343677.2:c.157G>C	p.Glu53Gln	p.E53Q	ENST00000343677	NM_005319.3	53	Gag/Cag	1/1	0.460631705902964	3	FACETS	0.909	0.776	1	0.454	0.388	0.526	CLONAL	1	TRUE	1	0.460556271868705	3		299	294	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430770	47430770	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	119	620	1	ENST00000377045.4:c.1735C>T	p.Arg579Trp	p.R579W	ENST00000377045	NM_001654.4	579	Cgg/Tgg	16/16	0.452132952281154	3	FACETS	1	0.913	1	0.505	0.456	0.555	CLONAL	1	TRUE	1	0.460556271868705	3		621	630	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355242	15355242	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	59	541	0	ENST00000263377.2:c.2381A>G	p.Lys794Arg	p.K794R	ENST00000263377	NM_058243.2	794	aAg/aGg	13/20	1	2	FACETS	0.728	0.629	0.834	0.728	0.629	0.834	SUBCLONAL	1	TRUE	1	0.460556271868705	2		541	352	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938879	178938879	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054121-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	38	115	0	ENST00000263967.3:c.2121G>C	p.Glu707Asp	p.E707D	ENST00000263967	NM_006218.2	707	gaG/gaC	14/21	0.460631705902964	3	FACETS	0.949	0.806	1	0.949	0.806	1	CLONAL	2	TRUE	1	0.460556271868705	3		115	107	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	150	304	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.304868900577127	5	FACETS	1	0.967	1	0.856	0.795	0.918	CLONAL	4	TRUE	0	0.311549409228504	5		304	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913343	NA	P-0054122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	92	717	0	ENST00000269305.4:c.817C>A	p.Arg273Ser	p.R273S	ENST00000269305	NM_001126112.2	273	Cgt/Agt	8/11	0.10282805234048	5	FACETS	0.932	0.837	1	0.699	0.628	0.773	INDETERMINATE	3	TRUE	1	0.311549409228504	5		717	310	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759924	63759924	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	25	360	1	ENST00000279873.7:c.577C>T	p.Arg193Cys	p.R193C	ENST00000279873	NM_032199.2	193	Cgc/Tgc	4/10	0.272159554871584	2	FACETS	0.729	0.578	0.902	0.365	0.289	0.451	CLONAL	1	TRUE	0	0.311549409228504	2		361	220	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955596	90955596	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0054122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	56	286	0	ENST00000265433.3:c.2071-2A>G		p.X691_splice	ENST00000265433	NM_002485.4	691			0.10282805234048	5	FACETS	1	0.945	1	0.589	0.511	0.672	INDETERMINATE	2	TRUE	1	0.311549409228504	5		286	224	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602901	10602901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	50	854	1	ENST00000171111.5:c.677G>A	p.Cys226Tyr	p.C226Y	ENST00000171111	NM_203500.1	226	tGc/tAc	3/6	0.10282805234048	5	FACETS	1	0.926	1	0.288	0.244	0.335	INDETERMINATE	1	TRUE	1	0.311549409228504	5		855	409	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528764	8528764	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	255	408	0	ENST00000356435.5:c.368G>T	p.Arg123Met	p.R123M	ENST00000356435		123	aGg/aTg	4/35	0.311549409228504	7	FACETS	0.995	0.949	1			1	CLONAL	7	TRUE	NA	0.311549409228504	7		408	418	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042235	42042235	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	72	392	0	ENST00000219905.7:c.6430G>T	p.Gly2144Ter	p.G2144*	ENST00000219905	NM_001164273.1	2144	Gga/Tga	17/24	0.272159554871584	2	FACETS	0.996	0.883	1	0.996	0.883	1	CLONAL	2	TRUE	0	0.311549409228504	2		392	232	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420340	88420340	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	61	406	0	ENST00000360948.2:c.2346C>G	p.Cys782Trp	p.C782W	ENST00000360948	NM_001012338.2	782	tgC/tgG	19/19	0.311549409228504	3	FACETS	0.874	0.762	0.993	0.874	0.762	0.993	CLONAL	2	TRUE	1	0.311549409228504	3		406	259	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917516	178917516	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	44	346	0	ENST00000263967.3:c.391G>C	p.Val131Leu	p.V131L	ENST00000263967	NM_006218.2	131	Gtt/Ctt	3/21	0.311549409228504	3	FACETS	0.887	0.754	1	0.887	0.754	1	CLONAL	2	TRUE	1	0.311549409228504	3		346	184	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944571	32944571	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397507981	NA	P-0054122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	29	499	0	ENST00000380152.3:c.8364G>C	p.Trp2788Cys	p.W2788C	ENST00000380152		2788	tgG/tgC	19/27	1	2	FACETS	0.672	0.541	0.82	0.672	0.541	0.82	SUBCLONAL	1	TRUE	1	0.311549409228504	2		499	277	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347893	73347893	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	31	276	0	ENST00000377767.4:c.1168G>T	p.Ala390Ser	p.A390S	ENST00000377767	NM_014953.3	390	Gct/Tct	8/21	0.10282805234048	5	FACETS	1	0.932	1	0.338	0.275	0.408	INDETERMINATE	1	TRUE	1	0.311549409228504	5		276	216	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857919	9857919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	96	597	0	ENST00000330684.3:c.3482G>A	p.Gly1161Glu	p.G1161E	ENST00000330684	NM_001134407.1	1161	gGg/gAg	13/13	0.311549409228504	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	1	0.311549409228504	3		597	326	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804396	46804396	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	65	558	1	ENST00000290295.7:c.611G>T	p.Gly204Val	p.G204V	ENST00000290295	NM_006361.5	204	gGg/gTg	2/2	0.200126050222418	5	FACETS	0.945	0.825	1	0.63	0.55	0.715	CLONAL	2	TRUE	2	0.311549409228504	5		559	324	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795096	42795096	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	92	947	0	ENST00000575354.2:c.2176A>G	p.Ser726Gly	p.S726G	ENST00000575354	NM_015125.3	726	Agc/Ggc	10/20	0.269040594613888	2	FACETS	0.818	0.733	0.907	0.818	0.733	0.907	CLONAL	2	TRUE	0	0.311549409228504	2		947	361	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866376	42866376	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs777667088	NA	P-0054122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	51	810	0	ENST00000398585.3:c.256G>T	p.Val86Leu	p.V86L	ENST00000398585	NM_001135099.1	86	Gtg/Ttg	3/14	0.116229015176023	1	FACETS	0.811	0.692	0.939	0.811	0.692	0.939	INDETERMINATE	1	TRUE	0	0.311549409228504	1		810	341	SUCCESS
APC	324	MSKCC	GRCh37	5	112111323	112111325	+	splice_acceptor_variant,intron_variant	Splice_Site	TNP	TAG	TAG	ATA	novel	NA	P-0054122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	25	142	1	ENST00000257430.4:c.423-3_423-1delinsATA		p.X141_splice	ENST00000257430	NM_000038.5	141			0.272159554871584	2	FACETS	0.863	0.697	1	0.863	0.697	1	CLONAL	2	TRUE	0	0.311549409228504	2		143	93	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956988	2956988	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	63	621	0	ENST00000396946.4:c.2639C>A	p.Thr880Lys	p.T880K	ENST00000396946	NM_032415.4	880	aCa/aAa	20/25	0.311549409228504	5	FACETS	0.779	0.677	0.889	0.519	0.451	0.593	SUBCLONAL	2	TRUE	2	0.311549409228504	5		621	381	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513284	106513284	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	38	296	0	ENST00000359195.3:c.2188C>A	p.His730Asn	p.H730N	ENST00000359195	NM_002649.2	730	Cac/Aac	4/11	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.311549409228504	2		296	214	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981773	70981773	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	86	883	0	ENST00000276594.2:c.323C>A	p.Pro108His	p.P108H	ENST00000276594	NM_024504.3	108	cCc/cAc	2/8	0.10282805234048	5	FACETS	1	0.959	1	0.579	0.516	0.644	INDETERMINATE	2	TRUE	1	0.311549409228504	5		883	350	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404588	8404588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	116	339	0	ENST00000356435.5:c.4159G>A	p.Ala1387Thr	p.A1387T	ENST00000356435		1387	Gcg/Acg	25/35	0.311549409228504	5	FACETS	1	0.971	1	0.896	0.824	0.967	CLONAL	4	TRUE	0	0.311549409228504	5		339	244	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413025	63413025	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	130	826	0	ENST00000330258.3:c.142G>T	p.Gly48Cys	p.G48C	ENST00000330258	NM_152424.3	48	Ggc/Tgc	2/2	0.311549409228504	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	1	0.311549409228504	3		826	453	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344179	70344179	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	61	575	0	ENST00000374080.3:c.1915G>T	p.Asp639Tyr	p.D639Y	ENST00000374080		639	Gat/Tat	13/45	0.311549409228504	3	FACETS	1	0.964	1	0.676	0.586	0.771	CLONAL	1	TRUE	1	0.311549409228504	3		575	335	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855969	76855969	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	75	520	0	ENST00000373344.5:c.5631G>T	p.Gln1877His	p.Q1877H	ENST00000373344	NM_000489.3	1877	caG/caT	23/35	0.311549409228504	3	FACETS	0.823	0.727	0.925	0.823	0.727	0.925	CLONAL	2	TRUE	1	0.311549409228504	3		520	338	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197715	123197715	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054122-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	50	366	0	ENST00000218089.9:c.1839G>C	p.Leu613Phe	p.L613F	ENST00000218089	NM_001042749.1	613	ttG/ttC	20/35	0.311549409228504	3	FACETS	0.766	0.657	0.885	0.766	0.657	0.885	SUBCLONAL	2	TRUE	1	0.311549409228504	3		366	242	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0054123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	743	681	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.617005801634344	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.633989807959242	1		682	1099	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314638	30314638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	771	127	1	ENST00000262643.3:c.1187C>T	p.Pro396Leu	p.P396L	ENST00000262643	NM_001238.2	396	cCg/cTg	12/12	0.633989807959242	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.633989807959242	1		128	1198	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100321	27100321	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	742	165	0	ENST00000324856.7:c.4033A>T	p.Thr1345Ser	p.T1345S	ENST00000324856	NM_006015.4	1345	Acc/Tcc	17/20	0.300792081914644	1	FACETS	1	0.995	1	1	0.995	1	INDETERMINATE	1	TRUE	0	0.633989807959242	1		165	1406	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040958	42040959	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0054123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	721	246	0	ENST00000219905.7:c.5341_5342del	p.Gln1781ThrfsTer12	p.Q1781Tfs*12	ENST00000219905	NM_001164273.1	1779	aAC/a	16/24	0.628963561536752	1	FACETS	0.771	0.752	0.789	1	0.998	1	SUBCLONAL	2	TRUE	0	0.633989807959242	1		246	1008	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210855	2210855	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0054123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	497	199	0	ENST00000398665.3:c.1351+1G>T		p.X451_splice	ENST00000398665	NM_032482.2	451			0.633989807959242	1	FACETS	0.756	0.734	0.778	1	0.997	1	SUBCLONAL	2	TRUE	0	0.633989807959242	1		199	708	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352322	143352322	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1291150478	NA	P-0054123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	459	164	0	ENST00000262992.4:c.91A>G	p.Ser31Gly	p.S31G	ENST00000262992	NM_001101669.1	31	Agt/Ggt	2/24	0.617005801634344	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.633989807959242	1		164	697	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963904	2963904	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	928	301	0	ENST00000396946.4:c.1903C>A	p.Gln635Lys	p.Q635K	ENST00000396946	NM_032415.4	635	Cag/Aag	15/25	1	2	FACETS	0.95	0.926	0.973	1	0.998	1	CLONAL	2	TRUE	1	0.633989807959242	2		301	1541	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410688	63410688	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054123-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	819	240	0	ENST00000330258.3:c.2479G>T	p.Glu827Ter	p.E827*	ENST00000330258	NM_152424.3	827	Gag/Tag	2/2	0.633989807959242	1	FACETS	0.787	0.77	0.804	1	0.998	1	SUBCLONAL	2	TRUE	0	0.633989807959242	1		240	1121	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0054130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	232	390	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.276924202954683	5	FACETS	0.959	0.897	1	0.72	0.673	0.768	CLONAL	3	TRUE	1	0.276924202954683	5		390	824	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913343	NA	P-0054130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	100	745	0	ENST00000269305.4:c.817C>G	p.Arg273Gly	p.R273G	ENST00000269305	NM_001126112.2	273	Cgt/Ggt	8/11	0.276924202954683	1	FACETS	0.786	0.701	0.875	0.786	0.701	0.875	SUBCLONAL	1	TRUE	0	0.276924202954683	1		745	792	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462971	120462971	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1317975644	NA	P-0054130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	67	532	1	ENST00000256646.2:c.5360G>A	p.Arg1787Gln	p.R1787Q	ENST00000256646	NM_024408.3	1787	cGg/cAg	30/34	1	2	FACETS	0.747	0.649	0.853	0.747	0.649	0.853	SUBCLONAL	1	TRUE	1	0.276924202954683	2		533	648	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028627	12028627	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	37	446	0	ENST00000353533.5:c.830C>G	p.Pro277Arg	p.P277R	ENST00000353533	NM_003010.3	277	cCa/cGa	8/11	0.276924202954683	1	FACETS	0.459	0.378	0.549	0.459	0.378	0.549	SUBCLONAL	1	TRUE	0	0.276924202954683	1		446	502	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149511577	149511577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	72	666	0	ENST00000261799.4:c.1208C>T	p.Ala403Val	p.A403V	ENST00000261799	NM_002609.3	403	gCt/gTt	8/23	0.276924202954683	1	FACETS	0.591	0.516	0.673	0.591	0.516	0.673	SUBCLONAL	1	TRUE	0	0.276924202954683	1		666	758	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578491	7578499	+	inframe_deletion	In_Frame_Del	DEL	CCCACAGCT	CCCACAGCT	-	novel	NA	P-0054131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	304	1081	0	ENST00000269305.4:c.431_439del	p.Gln144_Val147delinsLeu	p.Q144_V147delinsL	ENST00000269305	NM_001126112.2	144	cAGCTGTGGGtt/ctt	5/11	0.228844408384135	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	FALSE	0	0.228844408384135	2		1081	1220	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62323167	62323167	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	70	587	0	ENST00000360203.5:c.2629A>G	p.Lys877Glu	p.K877E	ENST00000360203	NM_001283009.1	877	Aag/Gag	28/35	0.107002060419464	5	FACETS	0.976	0.849	1	0.325	0.283	0.371	INDETERMINATE	1	FALSE	2	0.228844408384135	5		587	842	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0054140-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	794	51	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.171973304341718	2	FACETS	0.962	0.931	0.994	1	0.998	1	CLONAL	5	FALSE	0	0.171973304341718	2		51	1919	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659675	NA	P-0054140-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	815	286	0	ENST00000269305.4:c.764T>C	p.Ile255Thr	p.I255T	ENST00000269305	NM_001126112.2	255	aTc/aCc	7/11	0.171973304341718	2	FACETS	1	0.994	1	1	0.998	1	CLONAL	5	FALSE	0	0.171973304341718	2		286	1725	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913499	NA	P-0054140-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	276	14	0	ENST00000345146.2:c.394C>A	p.Arg132Ser	p.R132S	ENST00000345146	NM_005896.2	132	Cgt/Agt	4/10	1	2	FACETS	1	0.969	1	1	0.997	1	CLONAL	5	FALSE	1	0.171973304341718	2		14	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0054142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	192	137	1	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	0.477580053396288	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.475467163028579	1		138	499	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433557	49433578	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGGGTACCTGGGAGTTCAGC	CCTGGGTACCTGGGAGTTCAGC	-	novel	NA	P-0054142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	229	720	0	ENST00000301067.7:c.7975_7996del	p.Ala2659ThrfsTer25	p.A2659Tfs*25	ENST00000301067	NM_003482.3	2659	GCTGAACTCCCAGGTACCCAGGac/ac	31/54	0.477580053396288	3	FACETS	1	0.989	1	0.652	0.608	0.697	CLONAL	1	TRUE	1	0.475467163028579	3		720	914	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134570	41134571	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0054142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	231	490	1	ENST00000379561.5:c.1057_1058delinsTT	p.Ala353Leu	p.A353L	ENST00000379561	NM_002015.3	353	GCa/TTa	2/3	0.477580053396288	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.475467163028579	2		491	466	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619420	1619420	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	46	600	0	ENST00000344749.5:c.1221C>G	p.His407Gln	p.H407Q	ENST00000344749	NM_001136139.2	407	caC/caG	15/19	0.477580053396288	2	FACETS	0.333	0.28	0.392	0.167	0.14	0.196	SUBCLONAL	1	TRUE	0	0.475467163028579	2		600	581	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023013	31023013	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	171	575	0	ENST00000375687.4:c.2498G>C	p.Ser833Thr	p.S833T	ENST00000375687	NM_015338.5	833	aGt/aCt	13/13	0.286294886192844	5	FACETS	0.76	0.7	0.822	0.506	0.466	0.548	SUBCLONAL	2	TRUE	2	0.475467163028579	5		575	811	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801088	1801088	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs753541863	NA	P-0054142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	116	736	0	ENST00000260795.2:c.217G>C	p.Val73Leu	p.V73L	ENST00000260795		73	Gtc/Ctc	2/17	0.477580053396288	3	FACETS	0.676	0.608	0.747			1	SUBCLONAL	1	TRUE	NA	0.475467163028579	3		736	894	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321064	137321100	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGGTGGGCGCCATCTTTGACAGGTGGGGGTGGTCCC	GGGGTGGGCGCCATCTTTGACAGGTGGGGGTGGTCCC	-	novel	NA	P-0054142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	211	554	0	ENST00000481739.1:c.1024_1043+17del		p.X342_splice	ENST00000481739	NM_002957.4	342		7/10	0.477580053396288	2	FACETS	1	0.991	1	0.712	0.665	0.76	CLONAL	1	TRUE	0	0.475467163028579	2		554	623	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	141	375	0				ENST00000310581	NM_198253.2	-/1132			0.508175512241903	3	FACETS	0.95	0.879	1	0.95	0.879	1	CLONAL	2	TRUE	1	0.596554821150529	3		375	323	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799812	72799812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	161	565	0	ENST00000325599.8:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000325599	NM_018130.2	453	Gag/Aag	11/11	1	2	FACETS	0.949	0.875	1	0.949	0.875	1	CLONAL	1	TRUE	1	0.596554821150529	2		565	569	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	356	1150	1	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	0.596554821150529	3	FACETS	0.783	0.743	0.822	0.783	0.743	0.822	SUBCLONAL	2	TRUE	1	0.596554821150529	3		1151	990	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	549	801	1	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.596554821150529	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.596554821150529	2		802	888	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	312	650	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	0.562584907394025	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.596554821150529	4		650	773	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866987936	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	113	230	0	ENST00000281708.4:c.1436G>C	p.Arg479Pro	p.R479P	ENST00000281708	NM_033632.3	479	cGa/cCa	10/12	0.596554821150529	2	FACETS	0.933	0.863	1	0.933	0.863	1	CLONAL	2	TRUE	0	0.596554821150529	2		230	203	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25536796	25536796	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781254365	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	270	866	1	ENST00000264709.3:c.58G>A	p.Glu20Lys	p.E20K	ENST00000264709	NM_175629.2	20	Gag/Aag	2/23	0.582766799283762	3	FACETS	0.997	0.934	1	0.498	0.467	0.531	CLONAL	1	TRUE	1	0.596554821150529	3		867	1179	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26927961	26927961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	60	396	0	ENST00000381527.3:c.400C>T	p.Gln134Ter	p.Q134*	ENST00000381527	NM_001260.1	134	Cag/Tag	4/13	1	2	FACETS	0.919	0.802	1	0.919	0.802	1	CLONAL	1	TRUE	1	0.596554821150529	2		396	219	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793008	33793010	+	inframe_deletion	In_Frame_Del	DEL	CGC	CGC	-	rs780345232	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	9	87	0	ENST00000498907.2:c.311_313del	p.Gly104del	p.G104del	ENST00000498907	NM_004364.3	104	gGCGac/gac	1/1	0.596554821150529	3	FACETS	0.276	0.183	0.394	0.138	0.091	0.197	SUBCLONAL	1	TRUE	1	0.596554821150529	3		87	142	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309857	65309857	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	119	530	0	ENST00000342505.4:c.2293G>C	p.Glu765Gln	p.E765Q	ENST00000342505	NM_002227.2	765	Gag/Cag	17/25	0.508175512241903	3	FACETS	0.906	0.82	0.995	0.453	0.41	0.498	CLONAL	1	TRUE	1	0.596554821150529	3		530	572	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933307	49933307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749037053	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	206	1056	0	ENST00000296474.3:c.2803G>A	p.Val935Ile	p.V935I	ENST00000296474	NM_002447.2	935	Gta/Ata	12/20	1	2	FACETS	0.852	0.792	0.913	0.852	0.792	0.913	CLONAL	1	TRUE	1	0.596554821150529	2		1056	811	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100532	157100532	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	51	199	0	ENST00000346085.5:c.1469G>A	p.Trp490Ter	p.W490*	ENST00000346085	NM_020732.3	490	tGg/tAg	1/20	0.582766799283762	3	FACETS	0.655	0.559	0.759	0.327	0.279	0.38	SUBCLONAL	1	TRUE	1	0.596554821150529	3		199	339	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618629	37618629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1597	154	638	0	ENST00000447079.4:c.305C>T	p.Ser102Leu	p.S102L	ENST00000447079	NM_015083.1	102	tCa/tTa	1/14	0.596554821150529	10	FACETS	0.998	0.91	1			1	CLONAL	1	TRUE	NA	0.596554821150529	10		638	1751	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281550	198281550	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	150	573	0	ENST00000335508.6:c.581C>G	p.Ser194Ter	p.S194*	ENST00000335508	NM_012433.2	194	tCa/tGa	6/25	0.54779165910244	2	FACETS	0.893	0.821	0.969	0.447	0.41	0.485	CLONAL	1	TRUE	0	0.596554821150529	2		573	563	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023163	33023163	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1216397987	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	307	753	0	ENST00000300177.4:c.272G>A	p.Arg91Gln	p.R91Q	ENST00000300177	NM_001191322.1	91	cGa/cAa	2/2	0.582766799283762	3	FACETS	0.934	0.887	0.983	0.934	0.887	0.983	CLONAL	2	TRUE	1	0.596554821150529	3		753	715	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556722	41556722	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	67	368	0	ENST00000263253.7:c.3667C>T	p.Gln1223Ter	p.Q1223*	ENST00000263253	NM_001429.3	1223	Caa/Taa	20/31	1	2	FACETS	0.861	0.756	0.971	0.861	0.756	0.971	CLONAL	1	TRUE	1	0.596554821150529	2		368	261	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830764	3830764	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	207	492	0	ENST00000262367.5:c.1792C>T	p.Gln598Ter	p.Q598*	ENST00000262367	NM_004380.2	598	Cag/Tag	8/31	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.596554821150529	2		492	464	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619091	37619091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	1284	671	0	ENST00000447079.4:c.767C>T	p.Ser256Leu	p.S256L	ENST00000447079	NM_015083.1	256	tCg/tTg	1/14	0.596554821150529	10	FACETS	1	0.987	1			1	CLONAL	9	TRUE	NA	0.596554821150529	10		671	1615	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211616	36211616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	147	591	0	ENST00000222270.7:c.1367C>T	p.Ser456Phe	p.S456F	ENST00000222270	NM_014727.1	456	tCc/tTc	3/37	0.596554821150529	3	FACETS	1	0.965	1	0.548	0.502	0.595	CLONAL	1	TRUE	1	0.596554821150529	3		591	584	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90995054	90995054	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	202	369	0	ENST00000265433.3:c.67G>C	p.Glu23Gln	p.E23Q	ENST00000265433	NM_002485.4	23	Gag/Cag	2/16	0.596554821150529	5	FACETS	0.969	0.918	1	0.969	0.918	1	CLONAL	4	TRUE	1	0.596554821150529	5		369	331	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885791	23885791	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764719782	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	328	956	1	ENST00000374561.5:c.127G>A	p.Asp43Asn	p.D43N	ENST00000374561	NM_002167.4	43	Gac/Aac	1/3	0.158444247187869	6	FACETS	1	0.989	1	0.777	0.736	0.82	INDETERMINATE	2	TRUE	3	0.596554821150529	6		957	1034	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087412	27087416	+	frameshift_variant	Frame_Shift_Del	DEL	CACAT	CACAT	-	novel	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	275	747	0	ENST00000324856.7:c.1988_1992del	p.Thr663ArgfsTer11	p.T663Rfs*11	ENST00000324856	NM_006015.4	662	agCACATca/agca	5/20	0.158444247187869	6	FACETS	1	0.962	1	0.687	0.646	0.729	INDETERMINATE	2	TRUE	3	0.596554821150529	6		747	981	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165569	118165569	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	130	484	0	ENST00000369448.3:c.79G>A	p.Glu27Lys	p.E27K	ENST00000369448	NM_017709.3	27	Gag/Aag	2/2	0.508175512241903	3	FACETS	1	0.966	1	0.559	0.51	0.61	CLONAL	1	TRUE	1	0.596554821150529	3		484	506	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924699	94924699	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	410	729	0	ENST00000536441.1:c.211C>G	p.Arg71Gly	p.R71G	ENST00000536441	NM_144665.3	71	Cgt/Ggt	3/10	0.596554821150529	3	FACETS	1	0.99	1	0.736	0.706	0.767	CLONAL	2	TRUE	0	0.596554821150529	3		729	808	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416673	416673	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	170	362	0	ENST00000399788.2:c.3877G>A	p.Glu1293Lys	p.E1293K	ENST00000399788	NM_001042603.1	1293	Gaa/Aaa	23/28	0.508175512241903	3	FACETS	0.923	0.859	0.987	0.923	0.859	0.987	CLONAL	2	TRUE	1	0.596554821150529	3		362	401	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490868	56490868	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	275	556	0	ENST00000267101.3:c.2314G>A	p.Val772Ile	p.V772I	ENST00000267101	NM_001982.3	772	Gta/Ata	20/28	0.562584907394025	4	FACETS	0.93	0.877	0.985	0.93	0.877	0.985	CLONAL	2	TRUE	2	0.596554821150529	4		556	791	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114136	115114136	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	164	684	0	ENST00000257566.3:c.1081G>T	p.Gly361Trp	p.G361W	ENST00000257566	NM_016569.3	361	Ggg/Tgg	6/8	0.582766799283762	3	FACETS	0.928	0.854	1	0.464	0.427	0.503	CLONAL	1	TRUE	1	0.596554821150529	3		684	769	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033829	49033829	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	70	343	0	ENST00000267163.4:c.1966C>G	p.Arg656Gly	p.R656G	ENST00000267163	NM_000321.2	656	Cgg/Ggg	20/27	1	2	FACETS	0.801	0.705	0.902	0.801	0.705	0.902	CLONAL	1	TRUE	1	0.596554821150529	2		343	293	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614907	23614907	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	108	513	0	ENST00000261584.4:c.3434G>T	p.Gly1145Val	p.G1145V	ENST00000261584	NM_024675.3	1145	gGt/gTt	13/13	NA	2	FACETS	0.621	0.559	0.687			1	INDETERMINATE	1	TRUE	NA	0.596554821150529	2		513	583	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56866225	56866225	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	104	371	0	ENST00000308159.5:c.1270G>C	p.Asp424His	p.D424H	ENST00000308159	NM_014669.4	424	Gac/Cac	12/22	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.596554821150529	2		371	335	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679318	29679318	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	234	414	0	ENST00000356175.3:c.7438G>A	p.Glu2480Lys	p.E2480K	ENST00000356175	NM_000267.3	2480	Gaa/Aaa	50/57	0.596554821150529	3	FACETS	0.786	0.737	0.835	0.786	0.737	0.835	SUBCLONAL	2	TRUE	1	0.596554821150529	3		414	648	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677794	58677794	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	490	732	0	ENST00000305921.3:c.19C>A	p.Leu7Met	p.L7M	ENST00000305921	NM_003620.3	7	Ctg/Atg	1/6	0.596554821150529	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.596554821150529	3		732	987	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729934	47729934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	223	302	2	ENST00000449228.1:c.455G>A	p.Arg152Gln	p.R152Q	ENST00000449228	NM_001127240.2	152	cGg/cAg	3/4	0.596554821150529	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.596554821150529	3		304	477	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224404	39224404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	76	458	0	ENST00000402219.2:c.2954C>T	p.Ser985Leu	p.S985L	ENST00000402219	NM_005633.3	985	tCa/tTa	18/23	0.582766799283762	3	FACETS	1	0.953	1	0.574	0.509	0.643	CLONAL	1	TRUE	1	0.596554821150529	3		458	288	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835949	151835949	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	202	406	0	ENST00000262189.6:c.14575G>A	p.Val4859Met	p.V4859M	ENST00000262189	NM_170606.2	4859	Gtg/Atg	58/59	0.562584907394025	4	FACETS	0.812	0.756	0.869	0.812	0.756	0.869	CLONAL	2	TRUE	2	0.596554821150529	4		406	666	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965504	90965504	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	173	318	0	ENST00000265433.3:c.1813G>A	p.Asp605Asn	p.D605N	ENST00000265433	NM_002485.4	605	Gat/Aat	11/16	0.596554821150529	5	FACETS	0.988	0.933	1	0.988	0.933	1	CLONAL	4	TRUE	1	0.596554821150529	5		318	278	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579415	7579416	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	219	1254	1	ENST00000269305.4:c.271dup	p.Trp91LeufsTer58	p.W91Lfs*58	ENST00000269305	NM_001126112.2	91	tgg/tTgg	4/11	NA	2	FACETS	0.97	0.902	1			1	INDETERMINATE	2	TRUE	NA	0.214995382693603	2		1255	1050	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752386	55752386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1395	135	1569	0	ENST00000284073.2:c.844G>A	p.Val282Ile	p.V282I	ENST00000284073	NM_138962.2	282	Gtc/Atc	12/14	0.214995382693603	4	FACETS	0.997	0.903	1	0.499	0.451	0.549	CLONAL	1	TRUE	2	0.214995382693603	4		1569	1530	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160646	56160656	+	frameshift_variant	Frame_Shift_Del	DEL	GTGTTAACAAA	GTGTTAACAAA	-	novel	NA	P-0054215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	412	80	0	ENST00000399503.3:c.923_933del	p.Val308AspfsTer14	p.V308Dfs*14	ENST00000399503	NM_005921.1	307	cGTGTTAACAAA/c	4/20	0.323640089458107	3	FACETS	1	0.993	1	1	0.997	1	CLONAL	3	TRUE	1	0.435608746000659	3		80	671	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402227	402227	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	699	87	0	ENST00000399788.2:c.4564C>G	p.Gln1522Glu	p.Q1522E	ENST00000399788	NM_001042603.1	1522	Cag/Gag	27/28	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	3	TRUE	NA	0.435608746000659	2		87	995	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358566	67358566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	493	47	0	ENST00000327367.4:c.74G>A	p.Gly25Glu	p.G25E	ENST00000327367	NM_005902.3	25	gGg/gAg	1/9	0.294187191900976	1	FACETS	1	0.976	1	1	0.998	1	CLONAL	2	TRUE	0	0.435608746000659	1		47	872	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218569	98218569	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	436	37	0	ENST00000331920.6:c.3295C>A	p.His1099Asn	p.H1099N	ENST00000331920	NM_000264.3	1099	Cac/Aac	19/24	0.294187191900976	1	FACETS	0.882	0.855	0.907	1	0.998	1	CLONAL	3	TRUE	0	0.435608746000659	1		37	592	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	94	375	0				ENST00000310581	NM_198253.2	-/1132			0.609690330024143	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	TRUE	1	0.609690330024143	4		375	148	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288387	15288387	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	133	540	0	ENST00000263388.2:c.4352G>A	p.Cys1451Tyr	p.C1451Y	ENST00000263388	NM_000435.2	1451	tGc/tAc	24/33	0.609690330024143	3	FACETS	1	0.981	1	0.631	0.577	0.687	CLONAL	1	TRUE	1	0.609690330024143	3		540	451	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257634	19257634	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs759897677	NA	P-0054216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	143	760	0	ENST00000162023.5:c.592C>A	p.Pro198Thr	p.P198T	ENST00000162023		198	Ccc/Acc	10/13	0.609690330024143	3	FACETS	1	0.948	1	0.524	0.48	0.57	CLONAL	1	TRUE	1	0.609690330024143	3		760	584	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220308	55220308	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	265	647	0	ENST00000275493.2:c.698A>T	p.His233Leu	p.H233L	ENST00000275493	NM_005228.3	233	cAc/cTc	6/28	0.545415077207665	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.609690330024143	4		647	634	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246445	105246445	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	221	962	0	ENST00000349310.3:c.155T>G	p.Leu52Arg	p.L52R	ENST00000349310	NM_001014432.1	52	cTc/cGc	4/15	1	2	FACETS	0.763	0.712	0.816	0.763	0.712	0.816	SUBCLONAL	1	FALSE	1	0.723002817605357	2		962	801	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061189	38061205	+	frameshift_variant	Frame_Shift_Del	DEL	TTGAAGCGCTTCTGGCG	TTGAAGCGCTTCTGGCG	AGAA	novel	NA	P-0054217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	151	724	2	ENST00000250448.2:c.784_800delinsTTCT	p.Arg262PhefsTer55	p.R262Ffs*55	ENST00000250448	NM_004496.3	262	CGCCAGAAGCGCTTCAAg/TTCTg	2/2	1	2	FACETS	0.816	0.751	0.883	0.816	0.751	0.883	CLONAL	1	FALSE	1	0.723002817605357	2		726	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579329	7579329	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912658	NA	P-0054218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	161	926	0	ENST00000269305.4:c.358A>G	p.Lys120Glu	p.K120E	ENST00000269305	NM_001126112.2	120	Aag/Gag	4/11	0.356149487814746	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.356149487814746	1		926	742	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845580	151845580	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1287135873	NA	P-0054218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	46	789	0	ENST00000262189.6:c.13432C>T	p.Arg4478Ter	p.R4478*	ENST00000262189	NM_170606.2	4478	Cga/Tga	52/59	1	2	FACETS	0.307	0.258	0.362	0.307	0.258	0.362	SUBCLONAL	1	TRUE	1	0.356149487814746	2		789	841	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060679	38060680	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCT	novel	NA	P-0054218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1463	123	1312	0	ENST00000250448.2:c.1306_1309dup	p.Leu437GlnfsTer122	p.L437Qfs*122	ENST00000250448	NM_004496.3	437	ctg/cAGCCtg	2/2	1	2	FACETS	0.436	0.392	0.482	0.436	0.392	0.482	SUBCLONAL	1	TRUE	1	0.356149487814746	2		1312	1586	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	280	375	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.979	0.934	1	1	0.996	1	CLONAL	2	TRUE	1	0.611434166268858	2		375	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0054219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	1214	963	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.936	0.915	0.957	1	0.999	1	CLONAL	2	TRUE	1	0.611434166268858	2		966	2121	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0054219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	914	302	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	1	2	FACETS	0.961	0.936	0.985	1	0.998	1	CLONAL	2	TRUE	1	0.611434166268858	2		302	1556	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845627	63845627	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	255	74	0	ENST00000279873.7:c.1366G>T	p.Glu456Ter	p.E456*	ENST00000279873	NM_032199.2	456	Gaa/Taa	9/10	1	2	FACETS	0.884	0.839	0.928	1	0.995	1	CLONAL	2	TRUE	1	0.611434166268858	2		74	472	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556727	41556727	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0054219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	443	157	0	ENST00000263253.7:c.3671+1G>A		p.X1224_splice	ENST00000263253	NM_001429.3	1224			1	2	FACETS	0.91	0.876	0.944	1	0.997	1	CLONAL	2	TRUE	1	0.611434166268858	2		157	796	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917682	94917682	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	713	186	0	ENST00000536441.1:c.839A>T	p.Glu280Val	p.E280V	ENST00000536441	NM_144665.3	280	gAg/gTg	6/10	1	2	FACETS	0.977	0.95	1	1	0.998	1	CLONAL	2	TRUE	1	0.611434166268858	2		186	1193	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030271	11030271	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	767	228	0	ENST00000327064.4:c.1021G>A	p.Asp341Asn	p.D341N	ENST00000327064	NM_199141.1	341	Gac/Aac	9/16	0.603411236531423	1	FACETS	0.781	0.762	0.8	1	0.998	1	SUBCLONAL	2	TRUE	0	0.611434166268858	1		228	1115	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613168	52613168	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	796	255	0	ENST00000394830.3:c.3360C>G	p.Cys1120Trp	p.C1120W	ENST00000394830	NM_018313.4	1120	tgC/tgG	22/30	1	2	FACETS	0.916	0.89	0.942	1	0.998	1	CLONAL	2	TRUE	1	0.611434166268858	2		255	1421	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628004	187628013	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTCAAAGT	TTCTCAAAGT	-	novel	NA	P-0054219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	821	266	0	ENST00000441802.2:c.2969_2978del	p.Asp990GlyfsTer9	p.D990Gfs*9	ENST00000441802	NM_005245.3	990	gACTTTGAGAAg/gg	2/27	1	2	FACETS	0.923	0.898	0.949	1	0.998	1	CLONAL	2	TRUE	1	0.611434166268858	2		266	1454	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564440	86564441	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTGGAACT	novel	NA	P-0054219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	977	220	0	ENST00000274376.6:c.177_184dup	p.Gly62GlufsTer14	p.G62Efs*14	ENST00000274376	NM_002890.2	58	gct/gCTGGAACTct	1/25	1	2	FACETS	0.926	0.902	0.949	1	0.998	1	CLONAL	2	TRUE	1	0.611434166268858	2		220	1726	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945737	17945737	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	1040	155	0	ENST00000458235.1:c.2123A>G	p.Lys708Arg	p.K708R	ENST00000458235	NM_000215.3	708	aAg/aGg	16/24	1	2	FACETS	1	0.996	1	1	0.999	1	CLONAL	3	TRUE	1	0.333983964756295	2		155	1878	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627349	37627349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	1435	175	0	ENST00000249071.6:c.370G>A	p.Asp124Asn	p.D124N	ENST00000249071	NM_002872.4	124	Gac/Aac	5/7	1	2	FACETS	1	0.998	1			1	CLONAL	3	TRUE	1	0.333983964756295	2		175	2497	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52692243	52692244	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	426	67	0	ENST00000394830.3:c.616dup	p.Glu206GlyfsTer9	p.E206Gfs*9	ENST00000394830	NM_018313.4	206	gaa/gGaa	6/30	0.333983964756295	1	FACETS	0.984	0.947	1	1	0.998	1	CLONAL	3	TRUE	0	0.333983964756295	1		67	720	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041701	47041701	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	656	156	0	ENST00000377604.3:c.1926G>T	p.Lys642Asn	p.K642N	ENST00000377604	NM_001204468.1	642	aaG/aaT	17/24	0.333983964756295	3	FACETS	1	0.985	1	1	0.998	1	CLONAL	4	TRUE	1	0.333983964756295	3		156	1118	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	467	304	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.864	0.835	0.891	1	0.998	1	CLONAL	3	TRUE	1	0.508484414157608	2		304	709	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782620	NA	P-0054224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	1242	92	1	ENST00000269305.4:c.427G>A	p.Val143Met	p.V143M	ENST00000269305	NM_001126112.2	143	Gtg/Atg	5/11	0.40249344742967	3	FACETS	1	0.996	1	1	0.999	1	CLONAL	4	TRUE	1	0.508484414157608	3		93	1487	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147567	47147567	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	427	13	0	ENST00000409792.3:c.4759A>G	p.Lys1587Glu	p.K1587E	ENST00000409792	NM_014159.6	1587	Aaa/Gaa	6/21	0.204466416549708	5	FACETS	0.901	0.87	0.932	1	0.997	1	INDETERMINATE	5	TRUE	2	0.508484414157608	5		13	657	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064376	30064376	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1365006505	NA	P-0054225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	205	462	0	ENST00000338641.4:c.940G>A	p.Asp314Asn	p.D314N	ENST00000338641	NM_000268.3	314	Gat/Aat	10/16	0.501084825933186	3	FACETS	0.772	0.717	0.83	0.257	0.239	0.277	SUBCLONAL	1	TRUE	0	0.79766577300012	3		462	931	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435717	49435717	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	308	810	0	ENST00000301067.7:c.6166G>C	p.Asp2056His	p.D2056H	ENST00000301067	NM_003482.3	2056	Gac/Cac	29/54	0.79766577300012	1	FACETS	0.506	0.478	0.534	0.506	0.478	0.534	SUBCLONAL	1	TRUE	0	0.79766577300012	1		810	918	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965146	81965146	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	163	664	0	ENST00000359376.3:c.2626C>G	p.Leu876Val	p.L876V	ENST00000359376	NM_002661.3	876	Ctg/Gtg	25/33	NA	2	FACETS	0.394	0.361	0.429			1	INDETERMINATE	1	TRUE	NA	0.79766577300012	2		664	1037	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579445	7579473	+	frameshift_variant	Frame_Shift_Del	DEL	GTAGGAGCTGCTGGTGCAGGGGCCACGGG	GTAGGAGCTGCTGGTGCAGGGGCCACGGG	ACCAGC	novel	NA	P-0054225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	940	995	0	ENST00000269305.4:c.214_242delinsGCTGGT	p.Pro72AlafsTer69	p.P72Afs*69	ENST00000269305	NM_001126112.2	72	CCCGTGGCCCCTGCACCAGCAGCTCCTACa/GCTGGTa	4/11	0.762231208118517	2	FACETS	0.921	0.902	0.94	0.921	0.902	0.94	CLONAL	2	TRUE	0	0.79766577300012	2		995	1279	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	1100	772	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.99	1			1	CLONAL	6	TRUE	1	0.207528696822746	2		777	1731	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223858	36223858	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	1575	116	2	ENST00000222270.7:c.6413del	p.Pro2138ArgfsTer15	p.P2138Rfs*15	ENST00000222270	NM_014727.1	2136	ctC/ct	28/37	1	2	FACETS	1	0.982	1			1	CLONAL	6	TRUE	1	0.207528696822746	2		118	2529	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436171	110436171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs558236298	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	1216	102	0	ENST00000375856.3:c.2230C>T	p.Arg744Cys	p.R744C	ENST00000375856	NM_003749.2	744	Cgc/Tgc	1/2	1	2	FACETS	0.961	0.94	0.982			1	CLONAL	6	TRUE	1	0.207528696822746	2		102	2032	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599251	28599251	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1416314446	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	1451	102	0	ENST00000253063.3:c.701del	p.Pro234LeufsTer13	p.P234Lfs*13	ENST00000253063	NM_031459.4	233	Ccc/cc	5/10	1	2	FACETS	0.99	0.971	1			1	CLONAL	6	TRUE	1	0.207528696822746	2		102	2353	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468105	120468105	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	993	70	0	ENST00000256646.2:c.4334G>T	p.Ser1445Ile	p.S1445I	ENST00000256646	NM_024408.3	1445	aGc/aTc	25/34	1	2	FACETS	0.934	0.911	0.957			1	CLONAL	6	TRUE	1	0.207528696822746	2		70	1707	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	1415	112	11	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.989	0.97	1			1	CLONAL	6	TRUE	1	0.207528696822746	2		123	2297	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924698	94924698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542136270	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	944	64	1	ENST00000536441.1:c.212G>A	p.Arg71His	p.R71H	ENST00000536441	NM_144665.3	71	cGt/cAt	3/10	1	2	FACETS	1	0.995	1			1	CLONAL	5	TRUE	1	0.207528696822746	2		65	1665	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098609	108098609	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	211	23	0	ENST00000278616.4:c.183del	p.Phe61LeufsTer15	p.F61Lfs*15	ENST00000278616	NM_000051.3	60	gTt/gt	3/63	1	2	FACETS	0.968	0.912	1	1	0.996	1	CLONAL	5	TRUE	1	0.207528696822746	2		23	420	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	498	93	2	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.213605660891086	3	FACETS	1	0.982	1	1	0.998	1	CLONAL	6	TRUE	1	0.207528696822746	3		95	859	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427664	49427665	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	rs747016071	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	932	45	0	ENST00000301067.7:c.10821_10823dup	p.Gln3612dup	p.Q3612dup	ENST00000301067	NM_003482.3	3612	caa/caGCAa	39/54	0.213605660891086	3	FACETS	1	0.989	1	1	0.999	1	CLONAL	6	TRUE	1	0.207528696822746	3		45	1612	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	1060	644	4	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	0.213605660891086	3	FACETS	1	0.993	1	1	0.999	1	CLONAL	6	TRUE	1	0.207528696822746	3		648	1797	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	1072	95	1	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	0.213605660891086	3	FACETS	0.94	0.917	0.964	1	0.999	1	CLONAL	6	TRUE	1	0.207528696822746	3		96	2021	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121536	2121536	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	1332	101	0	ENST00000219476.3:c.1865G>T	p.Arg622Leu	p.R622L	ENST00000219476	NM_000548.3	622	cGg/cTg	18/42	1	2	FACETS	0.97	0.95	0.99			1	CLONAL	6	TRUE	1	0.207528696822746	2		101	2206	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822585	72822585	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs141461385	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	779	61	0	ENST00000268489.5:c.9590A>C	p.Gln3197Pro	p.Q3197P	ENST00000268489	NM_006885.3	3197	cAg/cCg	10/10	1	2	FACETS	0.955	0.929	0.981			1	CLONAL	6	TRUE	1	0.207528696822746	2		61	1310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	783	58	2	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	1	2	FACETS	1	0.995	1			1	CLONAL	5	TRUE	1	0.207528696822746	2		60	1379	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044539	12044539	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	563	42	0	ENST00000353533.5:c.1162A>G	p.Met388Val	p.M388V	ENST00000353533	NM_003010.3	388	Atg/Gtg	11/11	1	2	FACETS	0.936	0.906	0.966	1	0.998	1	CLONAL	6	TRUE	1	0.207528696822746	2		42	966	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687471	37687472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs760014508	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	571	38	0	ENST00000447079.4:c.4382dup	p.Thr1463AsnfsTer50	p.T1463Nfs*50	ENST00000447079	NM_015083.1	1459	tgg/tGgg	14/14	1	2	FACETS	0.938	0.907	0.968	1	0.998	1	CLONAL	6	TRUE	1	0.207528696822746	2		38	978	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274304	5274304	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	1260	90	8	ENST00000357368.4:c.143del	p.Gly48ValfsTer17	p.G48Vfs*17	ENST00000357368	NM_002850.3	48	gGt/gt	3/38	1	2	FACETS	0.935	0.915	0.956			1	CLONAL	6	TRUE	1	0.207528696822746	2		98	2164	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132465	11132465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	1374	106	2	ENST00000358026.2:c.2681C>T	p.Thr894Met	p.T894M	ENST00000358026	NM_001128849.1	894	aCg/aTg	19/36	1	2	FACETS	0.955	0.935	0.975			1	CLONAL	6	TRUE	1	0.207528696822746	2		108	2311	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134252	11134252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	950	56	0	ENST00000358026.2:c.2918G>A	p.Arg973Gln	p.R973Q	ENST00000358026	NM_001128849.1	973	cGg/cAg	20/36	1	2	FACETS	0.927	0.903	0.95			1	CLONAL	6	TRUE	1	0.207528696822746	2		56	1646	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626793	14626793	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	821	70	0	ENST00000254322.2:c.982del	p.Gln328ArgfsTer78	p.Q328Rfs*78	ENST00000254322	NM_006145.1	328	Cag/ag	3/3	1	2	FACETS	0.925	0.9	0.951			1	CLONAL	6	TRUE	1	0.207528696822746	2		70	1425	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027289	48027289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	414	38	0	ENST00000234420.5:c.2167G>A	p.Gly723Ser	p.G723S	ENST00000234420	NM_000179.2	723	Ggt/Agt	4/10	0.213605660891086	3	FACETS	0.975	0.936	1	1	0.997	1	CLONAL	6	TRUE	1	0.207528696822746	3		38	753	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747108	40747108	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	736	55	0	ENST00000373198.4:c.2974A>G	p.Arg992Gly	p.R992G	ENST00000373198	NM_133170.3	992	Aga/Gga	22/32	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	5	TRUE	NA	0.207528696822746	2		55	1359	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306553	41306553	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	852	48	0	ENST00000373198.4:c.1106del	p.Gly369ValfsTer28	p.G369Vfs*28	ENST00000373198	NM_133170.3	369	gGt/gt	7/32	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	5	TRUE	NA	0.207528696822746	2		48	1502	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385257	41385257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293875597	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	829	68	2	ENST00000373198.4:c.704C>T	p.Thr235Met	p.T235M	ENST00000373198	NM_133170.3	235	aCg/aTg	6/32	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	5	TRUE	NA	0.207528696822746	2		70	1473	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54963222	54963222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	450	37	0	ENST00000312783.6:c.32G>A	p.Gly11Glu	p.G11E	ENST00000312783	NM_198436.1	11	gGa/gAa	3/10	0.3	3	FACETS	1	0.985	1	1	0.997	1	CLONAL	5	TRUE	1	0.207528696822746	3		37	911	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	647	99	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.3	3	FACETS	0.953	0.922	0.983	1	0.998	1	CLONAL	6	TRUE	1	0.207528696822746	3		99	1204	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656849	45656849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199766847	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	927	74	2	ENST00000407780.3:c.307G>A	p.Val103Ile	p.V103I	ENST00000407780	NM_001283052.1	103	Gtc/Atc	3/7	1	2	FACETS	0.947	0.923	0.971			1	CLONAL	6	TRUE	1	0.207528696822746	2		76	1572	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808311	1808312	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	1716	98	2	ENST00000260795.2:c.2075dup	p.Ser693LeufsTer124	p.S693Lfs*124	ENST00000260795		690	ctg/ctGg	15/17	1	2	FACETS	1	0.996	1			1	CLONAL	6	TRUE	1	0.207528696822746	2		100	2622	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007331	143007332	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs772784869	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	416	33	1	ENST00000262992.4:c.2452dup	p.Arg818LysfsTer26	p.R818Kfs*26	ENST00000262992	NM_001101669.1	818	aga/aAga	22/24	1	2	FACETS	0.984	0.944	1	1	0.998	1	CLONAL	5	TRUE	1	0.207528696822746	2		34	815	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525027	187525028	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	698	42	0	ENST00000441802.2:c.10652dup	p.Ile3552HisfsTer25	p.I3552Hfs*25	ENST00000441802	NM_005245.3	3551	ttc/ttTc	19/27	1	2	FACETS	1	0.994	1			1	CLONAL	5	TRUE	1	0.207528696822746	2		42	1234	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293847	1293847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	1626	165	2	ENST00000310581.5:c.1154G>A	p.Arg385His	p.R385H	ENST00000310581	NM_198253.2	385	cGc/cAc	2/16	1	2	FACETS	0.995	0.976	1			1	CLONAL	6	TRUE	1	0.207528696822746	2		167	2626	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294143	1294143	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	1454	103	2	ENST00000310581.5:c.858G>T	p.Glu286Asp	p.E286D	ENST00000310581	NM_198253.2	286	gaG/gaT	2/16	1	2	FACETS	0.949	0.93	0.969			1	CLONAL	6	TRUE	1	0.207528696822746	2		105	2460	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31511162	31511162	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754562615	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	897	80	0	ENST00000344624.3:c.1412C>T	p.Thr471Met	p.T471M	ENST00000344624		471	aCg/aTg	6/33	1	2	FACETS	1	0.992	1			1	CLONAL	5	TRUE	1	0.207528696822746	2		80	1646	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526291	31526291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750540831	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	1281	80	2	ENST00000344624.3:c.749G>A	p.Arg250Gln	p.R250Q	ENST00000344624		250	cGg/cAg	2/33	1	2	FACETS	1	0.996	1			1	CLONAL	5	TRUE	1	0.207528696822746	2		82	2301	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177821	56177821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	473	38	0	ENST00000399503.3:c.2794G>A	p.Ala932Thr	p.A932T	ENST00000399503	NM_005921.1	932	Gcc/Acc	14/20	1	2	FACETS	0.941	0.908	0.975	1	0.998	1	CLONAL	6	TRUE	1	0.207528696822746	2		38	807	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977876	131977878	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	novel	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	361	27	0	ENST00000265335.6:c.3761_3763del	p.Lys1254del	p.K1254del	ENST00000265335		1253	atAAAa/ata	25/25	1	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	5	TRUE	1	0.207528696822746	2		27	640	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816566	32816567	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	1158	77	0	ENST00000354258.4:c.1608_1609del	p.Lys537AsnfsTer3	p.K537Nfs*3	ENST00000354258	NM_000593.5	536	gaGAaa/gaaa	7/11	0.207528696822746	2	FACETS	0.919	0.898	0.94	1	0.999	1	CLONAL	6	TRUE	0	0.207528696822746	2		77	2024	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32819930	32819931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	1012	101	0	ENST00000354258.4:c.979dup	p.Ala327GlyfsTer17	p.A327Gfs*17	ENST00000354258	NM_000593.5	327	gct/gGct	3/11	0.207528696822746	2	FACETS	0.918	0.896	0.941	1	0.999	1	CLONAL	6	TRUE	0	0.207528696822746	2		101	1770	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332886	152332886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	523	78	1	ENST00000206249.3:c.1192C>T	p.His398Tyr	p.H398Y	ENST00000206249	NM_000125.3	398	Cac/Tac	5/8	0.207528696822746	2	FACETS	0.932	0.901	0.964	1	0.998	1	CLONAL	6	TRUE	0	0.207528696822746	2		79	901	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36846914	36846914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	784	61	0	ENST00000358127.4:c.1025C>T	p.Ser342Phe	p.S342F	ENST00000358127	NM_001280556.1	342	tCc/tTc	9/10	1	2	FACETS	0.988	0.962	1			1	CLONAL	6	TRUE	1	0.207528696822746	2		61	1274	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	1167	83	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	1	0.988	1			1	CLONAL	6	TRUE	1	0.207528696822746	2		83	1848	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732910	44732910	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	391	64	0	ENST00000377967.4:c.117del	p.Ser40AlafsTer2	p.S40Afs*2	ENST00000377967	NM_021140.2	38	tCc/tc	1/29	1	1	FACETS	1	0.99	1	1	0.998	1	CLONAL	5	TRUE	0	0.207528696822746	1		64	628	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	491	46	1	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	1	1	FACETS	0.918	0.888	0.948	1	0.998	1	CLONAL	6	TRUE	0	0.207528696822746	1		47	770	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727443	66727457	+	inframe_deletion	In_Frame_Del	DEL	TCTTACCCAGAAGCA	TCTTACCCAGAAGCA	-	novel	NA	P-0054227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	466	15	0	ENST00000307102.5:c.159_173del	p.Phe53_Gln58delinsLeu	p.F53_Q58delinsL	ENST00000307102	NM_002755.3	53	ttTCTTACCCAGAAGCAg/ttg	2/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		15	1089	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	399	375	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.994	1	1	0.997	1	CLONAL	2	TRUE	1	0.454844058654747	2		375	731	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744443	41744443	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs745425946	NA	P-0054228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	1317	202	0	ENST00000301178.4:c.1063G>C	p.Glu355Gln	p.E355Q	ENST00000301178	NM_021913.4	355	Gag/Cag	8/20	1	2	FACETS	0.863	0.844	0.881	1	0.999	1	CLONAL	3	TRUE	1	0.454844058654747	2		202	2237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0054228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	877	367	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.392030796692949	2	FACETS	0.908	0.885	0.93	1	0.998	1	CLONAL	3	TRUE	0	0.454844058654747	2		368	1416	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056201	26056201	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs766517381	NA	P-0054228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	662	127	0	ENST00000343677.2:c.456G>C	p.Lys152Asn	p.K152N	ENST00000343677	NM_005319.3	152	aaG/aaC	1/1	1	2	FACETS	1	0.996	1	1	0.998	1	CLONAL	2	TRUE	1	0.454844058654747	2		127	1246	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499814	8499814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750362550	NA	P-0054228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	694	142	0	ENST00000356435.5:c.2155G>A	p.Glu719Lys	p.E719K	ENST00000356435		719	Gag/Aag	14/35	1	2	FACETS	1	0.997	1	1	0.998	1	CLONAL	2	TRUE	1	0.454844058654747	2		142	1230	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133178	38133178	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	747	100	0	ENST00000317025.8:c.4295G>T	p.Gly1432Val	p.G1432V	ENST00000317025	NM_023034.1	1432	gGa/gTa	24/24	0.454844058654747	1	FACETS	1	0.995	1	1	0.998	1	CLONAL	2	TRUE	0	0.454844058654747	1		100	1154	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843604	156843604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1044149705	NA	P-0054228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1854	1198	126	2	ENST00000524377.1:c.1030G>A	p.Gly344Arg	p.G344R	ENST00000524377	NM_002529.3	344	Ggg/Agg	8/17	0.454844058654747	5	FACETS	0.968	0.942	0.994	0.968	0.942	0.994	CLONAL	3	TRUE	2	0.454844058654747	5		128	3052	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982391	201982392	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTGGGACTGTCT	novel	NA	P-0054228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	1310	212	0	ENST00000359651.3:c.772_783dup	p.Trp258_Leu261dup	p.W258_L261dup	ENST00000359651		258	tac/taCTGGGACTGTCTc	6/8	0.392030796692949	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.454844058654747	2		212	2465	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917671	94917671	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	641	36	1	ENST00000536441.1:c.850G>T	p.Glu284Ter	p.E284*	ENST00000536441	NM_144665.3	284	Gaa/Taa	6/10	1	2	FACETS	1	0.995	1	1	0.998	1	CLONAL	2	TRUE	1	0.454844058654747	2		37	1239	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680715	88680715	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	1068	188	0	ENST00000360948.2:c.542A>C	p.Lys181Thr	p.K181T	ENST00000360948	NM_001012338.2	181	aAg/aCg	6/19	1	2	FACETS	0.856	0.836	0.877	1	0.999	1	CLONAL	3	TRUE	1	0.454844058654747	2		188	1828	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629037	187629037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	668	110	0	ENST00000441802.2:c.1945G>A	p.Asp649Asn	p.D649N	ENST00000441802	NM_005245.3	649	Gat/Aat	2/27	1	2	FACETS	1	0.996	1	1	0.998	1	CLONAL	2	TRUE	1	0.454844058654747	2		110	1215	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133164	38133164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1043561773	NA	P-0054228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	696	76	0	ENST00000317025.8:c.4309G>A	p.Glu1437Lys	p.E1437K	ENST00000317025	NM_023034.1	1437	Gaa/Aaa	24/24	0.454844058654747	1	FACETS	1	0.995	1	1	0.998	1	CLONAL	2	TRUE	0	0.454844058654747	1		76	1068	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222303	53222303	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	672	53	0	ENST00000375401.3:c.4529C>G	p.Pro1510Arg	p.P1510R	ENST00000375401	NM_004187.3	1510	cCc/cGc	26/26	1	1	FACETS	0.896	0.867	0.924	1	0.998	1	CLONAL	2	TRUE	0	0.454844058654747	1		53	1274	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0054229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	173	392	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.222872785595899	5	FACETS	1	0.965	1	0.71	0.659	0.762	INDETERMINATE	2	TRUE	2	0.696273962089928	5		392	477	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923631	39923631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1282	178	1039	0	ENST00000378444.4:c.3460G>A	p.Glu1154Lys	p.E1154K	ENST00000378444	NM_001123385.1	1154	Gag/Aag	7/15	0.328671934498563	3	FACETS	0.472	0.434	0.513	0.236	0.217	0.257	INDETERMINATE	1	TRUE	1	0.696273962089928	3		1039	1460	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0054230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	305	76	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.94	0.897	0.984	1	0.997	1	CLONAL	6	TRUE	1	0.190695025451242	2		76	567	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0054230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	524	235	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.138393222028838	2	FACETS	1	0.992	1	1	0.998	1	CLONAL	6	TRUE	0	0.190695025451242	2		235	851	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262581	39262581	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs397517180	NA	P-0054230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	458	38	0	ENST00000402219.2:c.925G>T	p.Asp309Tyr	p.D309Y	ENST00000402219	NM_005633.3	309	Gat/Tat	7/23	1	2	FACETS	0.986	0.95	1	1	0.998	1	CLONAL	6	TRUE	1	0.190695025451242	2		38	812	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914223	32914223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	76	345	0	ENST00000380152.3:c.5731G>A	p.Asp1911Asn	p.D1911N	ENST00000380152		1911	Gat/Aat	11/27	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.234731299638773	2		345	602	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032254	26032254	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	56	373	0	ENST00000244661.2:c.35C>G	p.Thr12Ser	p.T12S	ENST00000244661	NM_003537.3	12	aCc/aGc	1/1	1	2	FACETS	0.843	0.722	0.975	0.843	0.722	0.975	CLONAL	1	TRUE	1	0.234731299638773	2		373	566	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750789	128750789	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1314120778	NA	P-0054232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	127	754	1	ENST00000377970.2:c.326C>T	p.Ser109Phe	p.S109F	ENST00000377970	NM_002467.4	109	tCc/tTc	2/3	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.234731299638773	2		755	1024	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241008	39241008	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	35	374	0	ENST00000402219.2:c.2063G>A	p.Arg688Gln	p.R688Q	ENST00000402219	NM_005633.3	688	cGa/cAa	12/23	1	2	FACETS	0.612	0.501	0.737	0.612	0.501	0.737	SUBCLONAL	1	TRUE	1	0.234731299638773	2		374	487	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864356	151864357	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	36	531	0	ENST00000262189.6:c.9624dup	p.Lys3209Ter	p.K3209*	ENST00000262189	NM_170606.2	3208	-/T	42/59	1	2	FACETS	0.481	0.394	0.578	0.481	0.394	0.578	SUBCLONAL	1	TRUE	1	0.234731299638773	2		531	638	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914223	32914223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	36	345	0	ENST00000380152.3:c.5731G>A	p.Asp1911Asn	p.D1911N	ENST00000380152		1911	Gat/Aat	11/27	0.838672379527285	4	FACETS	0.968	0.808	1	0.484	0.404	0.571	CLONAL	1	TRUE	2	0.923518466650911	4		345	155	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032254	26032254	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	101	373	0	ENST00000244661.2:c.35C>G	p.Thr12Ser	p.T12S	ENST00000244661	NM_003537.3	12	aCc/aGc	1/1	0.923518466650911	7	FACETS	1	0.938	1			1	CLONAL	2	TRUE	NA	0.923518466650911	7		373	344	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750789	128750789	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1314120778	NA	P-0054232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	113	754	1	ENST00000377970.2:c.326C>T	p.Ser109Phe	p.S109F	ENST00000377970	NM_002467.4	109	tCc/tTc	2/3	0.923518466650911	5	FACETS	1	0.983	1	0.476	0.431	0.522	CLONAL	1	TRUE	2	0.923518466650911	5		755	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0054233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	884	866	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.963	0.942	0.985	1	0.999	1	CLONAL	3	FALSE	1	0.483981141570257	2		867	1264	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913499	NA	P-0054233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	287	14	0	ENST00000345146.2:c.394C>A	p.Arg132Ser	p.R132S	ENST00000345146	NM_005896.2	132	Cgt/Agt	4/10	1	2	FACETS	0.877	0.852	0.9	1	0.997	1	CLONAL	4	FALSE	1	0.483981141570257	2		14	338	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938407	76938407	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	324	43	0	ENST00000373344.5:c.2341C>T	p.Arg781Ter	p.R781*	ENST00000373344	NM_000489.3	781	Cga/Tga	9/35	0.344913347650559	2	FACETS	1	0.995	1			1	CLONAL	3	FALSE	NA	0.483981141570257	2		43	386	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578281	7578281	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	678	98	0	ENST00000269305.4:c.568C>G	p.Pro190Ala	p.P190A	ENST00000269305	NM_001126112.2	190	Cct/Gct	6/11	1	2	FACETS	1	0.993	1	1	0.998	1	CLONAL	3	FALSE	1	0.483981141570257	2		98	896	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0054234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	403	390	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.461021656329333	5	FACETS	1	0.991	1			1	CLONAL	3	TRUE	NA	0.543020986744819	5		390	796	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132426	11132426	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	1061	304	0	ENST00000358026.2:c.2642A>G	p.Asp881Gly	p.D881G	ENST00000358026	NM_001128849.1	881	gAc/gGc	19/36	1	2	FACETS	1	0.989	1	1	0.999	1	CLONAL	2	TRUE	1	0.543020986744819	2		304	1908	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356285	70356285	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	865	562	0	ENST00000374080.3:c.5180A>T	p.His1727Leu	p.H1727L	ENST00000374080		1727	cAc/cTc	37/45	0.543020986744819	3	FACETS	0.857	0.834	0.881	1	0.997	1	CLONAL	3	TRUE	1	0.543020986744819	3		562	1575	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302456	15302456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749561286	NA	P-0054235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	44	738	1	ENST00000263388.2:c.815C>T	p.Thr272Met	p.T272M	ENST00000263388	NM_000435.2	272	aCg/aTg	6/33	1	2	FACETS	0.198	0.165	0.234	0.198	0.165	0.234	SUBCLONAL	1	TRUE	1	0.523851946990397	2		739	850	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260135	16260135	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	220	649	0	ENST00000375759.3:c.7400del	p.Ile2467ThrfsTer9	p.I2467Tfs*9	ENST00000375759	NM_015001.2	2467	aTc/ac	11/15	0.518632622883525	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.523851946990397	1		649	613	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087368	27087389	+	frameshift_variant	Frame_Shift_Del	DEL	GACCTCCCCATGGGGACAGAAG	GACCTCCCCATGGGGACAGAAG	-	novel	NA	P-0054235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	169	522	0	ENST00000324856.7:c.1944_1965del	p.Asp648GlufsTer3	p.D648Efs*3	ENST00000324856	NM_006015.4	648	GACCTCCCCATGGGGACAGAAGga/ga	5/20	1	2	FACETS	0.899	0.828	0.972	0.899	0.828	0.972	CLONAL	1	TRUE	1	0.523851946990397	2		522	718	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504290	8504290	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	141	500	1	ENST00000356435.5:c.1793C>A	p.Ala598Glu	p.A598E	ENST00000356435		598	gCa/gAa	12/35	0.523851946990397	1	FACETS	0.889	0.817	0.963	0.889	0.817	0.963	CLONAL	1	TRUE	0	0.523851946990397	1		501	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0054236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	380	681	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.417509307667725	2	FACETS	0.937	0.894	0.981	0.937	0.894	0.981	CLONAL	2	TRUE	0	0.452002482609653	2		682	897	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954378	48954378	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0054236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	59	272	0	ENST00000267163.4:c.1498+1G>T		p.X500_splice	ENST00000267163	NM_000321.2	500			0.452002482609653	1	FACETS	0.86	0.749	0.978	0.86	0.749	0.978	CLONAL	1	TRUE	0	0.452002482609653	1		272	235	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0054238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	1002	470	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.717872928353771	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.717872928353771	2		470	1158	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044905	47044905	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	1405	405	0	ENST00000377604.3:c.2231G>A	p.Arg744His	p.R744H	ENST00000377604	NM_001204468.1	744	cGt/cAt	20/24	0.481110697594966	1	FACETS	1	0.999	1	1	0.999	1	CLONAL	1	TRUE	0	0.717872928353771	1		405	1792	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268766	41268766	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	532	175	0	ENST00000349496.5:c.1004A>T	p.Lys335Ile	p.K335I	ENST00000349496	NM_001904.3	335	aAa/aTa	7/15	0.718379364092293	3	FACETS	0.931	0.897	0.966	0.931	0.897	0.966	CLONAL	2	TRUE	1	0.718379364092293	3		175	1081	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30946592	30946594	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs752094508	NA	P-0054240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	289	117	0	ENST00000375687.4:c.25_27del	p.Lys9del	p.K9del	ENST00000375687	NM_015338.5	5	cAGAag/cag	1/13	0.718379364092293	3	FACETS	0.896	0.851	0.942	0.896	0.851	0.942	CLONAL	2	TRUE	1	0.718379364092293	3		117	610	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25368420	25368422	+	intron_variant	Intron	DEL	TTC	TTC	-	novel	NA	P-0054240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	414	129	0	ENST00000311936.3:c.451-5577_451-5575del		p.*151*	ENST00000311936	NM_004985.3	175/189			0.60382591363999	4	FACETS	0.982	0.939	1	0.982	0.939	1	CLONAL	2	TRUE	2	0.718379364092293	4		129	1008	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933497	39933498	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0054240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	1176	377	0	ENST00000378444.4:c.1101_1102del	p.Pro368PhefsTer12	p.P368Ffs*12	ENST00000378444	NM_001123385.1	367	tcTCct/tcct	4/15	1	2	FACETS	0.9	0.881	0.919	1	0.999	1	CLONAL	2	TRUE	1	0.718379364092293	2		377	1819	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578476	7578476	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	597	1220	2	ENST00000269305.4:c.454C>A	p.Pro152Thr	p.P152T	ENST00000269305	NM_001126112.2	152	Ccg/Acg	5/11	NA	2	FACETS	0.986	0.95	1			1	INDETERMINATE	2	TRUE	NA	0.424247852212815	2		1222	1427	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573772	64573772	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	409	929	0	ENST00000312049.6:c.981C>A	p.Tyr327Ter	p.Y327*	ENST00000312049	NM_130799.2	327	taC/taA	7/10	0.292082926054525	4	FACETS	0.986	0.937	1	0.986	0.937	1	CLONAL	2	TRUE	2	0.424247852212815	4		929	1393	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553365	41553365	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	41	482	0	ENST00000263253.7:c.3454G>T	p.Glu1152Ter	p.E1152*	ENST00000263253	NM_001429.3	1152	Gaa/Taa	18/31	1	2	FACETS	0.277	0.23	0.33	0.277	0.23	0.33	SUBCLONAL	1	TRUE	1	0.424247852212815	2		482	698	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	282	375	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.892	0.858	0.925	1	0.996	1	CLONAL	2	TRUE	1	0.80216203967048	2		375	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0054245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	1076	389	1	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	1	2	FACETS	0.792	0.774	0.809	1	0.998	1	SUBCLONAL	2	TRUE	1	0.80216203967048	2		390	1694	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0054245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	742	248	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.823	0.802	0.844	1	0.998	1	CLONAL	2	TRUE	1	0.80216203967048	2		248	1124	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339803	116339803	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200776610	NA	P-0054245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	354	178	0	ENST00000397752.3:c.665C>T	p.Thr222Met	p.T222M	ENST00000397752	NM_000245.2	222	aCg/aTg	2/21	0.80216203967048	3	FACETS	1	0.995	1	0.734	0.699	0.77	CLONAL	1	TRUE	1	0.80216203967048	3		178	842	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0054247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	204	378	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.245528201144614	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	3	TRUE	0	0.245528201144614	3		378	595	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353904	68353904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	33	379	0	ENST00000487270.1:c.739G>A	p.Glu247Lys	p.E247K	ENST00000487270	NM_133509.3	247	Gag/Aag	7/11	0.19348922630473	4	FACETS	0.535	0.434	0.649	0.267	0.217	0.325	SUBCLONAL	1	TRUE	2	0.245528201144614	4		379	626	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031699	69031699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	36	500	0	ENST00000288368.4:c.3454C>T	p.His1152Tyr	p.H1152Y	ENST00000288368	NM_024870.2	1152	Cat/Tat	28/40	0.245528201144614	3	FACETS	0.462	0.378	0.556	0.231	0.189	0.278	SUBCLONAL	1	TRUE	1	0.245528201144614	3		500	713	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211431	98211431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779417284	NA	P-0054247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1291	71	907	0	ENST00000331920.6:c.3724G>A	p.Glu1242Lys	p.E1242K	ENST00000331920	NM_000264.3	1242	Gag/Aag	22/24	0.245528201144614	5	FACETS	0.581	0.505	0.664	0.194	0.168	0.222	SUBCLONAL	1	TRUE	2	0.245528201144614	5		907	1362	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180978	108180978	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	95	295	0	ENST00000278616.4:c.5856del	p.Phe1952LeufsTer38	p.F1952Lfs*38	ENST00000278616	NM_000051.3	1952	Ttt/tt	39/63	0.245528201144614	2	FACETS	0.915	0.819	1	0.915	0.819	1	CLONAL	2	TRUE	0	0.245528201144614	2		295	423	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385255	4385255	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	71	618	0	ENST00000261254.3:c.280C>T	p.Pro94Ser	p.P94S	ENST00000261254	NM_001759.3	94	Ccg/Tcg	2/5	0.245528201144614	3	FACETS	0.733	0.638	0.836	0.244	0.212	0.279	SUBCLONAL	1	TRUE	0	0.245528201144614	3		618	886	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858660	9858660	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	45	559	0	ENST00000330684.3:c.2741G>C	p.Arg914Thr	p.R914T	ENST00000330684	NM_001134407.1	914	aGa/aCa	13/13	0.23233178030323	4	FACETS	0.53	0.443	0.626	0.265	0.221	0.313	SUBCLONAL	1	TRUE	2	0.245528201144614	4		559	862	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031509	11031509	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0054247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1605	87	1096	0	ENST00000327064.4:c.1425-1G>C		p.X475_splice	ENST00000327064	NM_199141.1	475			0.245528201144614	4	FACETS	0.522	0.46	0.589	0.13	0.114	0.148	SUBCLONAL	1	TRUE	0	0.245528201144614	4		1096	1692	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277989	18277989	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1263	110	734	0	ENST00000222254.8:c.1609G>A	p.Glu537Lys	p.E537K	ENST00000222254	NM_005027.3	537	Gag/Aag	13/16	0.245528201144614	7	FACETS	1	0.932	1	0.211	0.188	0.235	CLONAL	1	TRUE	2	0.245528201144614	7		734	1373	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797843	42797843	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1364	137	1159	0	ENST00000575354.2:c.3895C>G	p.Pro1299Ala	p.P1299A	ENST00000575354	NM_015125.3	1299	Cca/Gca	16/20	0.23233178030323	4	FACETS	0.926	0.839	1	0.463	0.419	0.509	CLONAL	1	TRUE	2	0.245528201144614	4		1159	1501	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456452	89456452	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	28	346	0	ENST00000336596.2:c.1628T>C	p.Val543Ala	p.V543A	ENST00000336596	NM_005233.5	543	gTc/gCc	8/17	0.245528201144614	3	FACETS	0.465	0.37	0.573	0.232	0.185	0.287	SUBCLONAL	1	TRUE	1	0.245528201144614	3		346	551	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638177	176638177	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	184	679	0	ENST00000439151.2:c.2777G>C	p.Arg926Pro	p.R926P	ENST00000439151	NM_022455.4	926	cGg/cCg	5/23	0.245528201144614	3	FACETS	0.909	0.839	0.981	0.909	0.839	0.981	CLONAL	2	TRUE	1	0.245528201144614	3		679	926	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205638	38205638	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	54	736	0	ENST00000317025.8:c.52C>T	p.Gln18Ter	p.Q18*	ENST00000317025	NM_023034.1	18	Caa/Taa	2/24	0.245528201144614	2	FACETS	0.495	0.421	0.576	0.247	0.21	0.288	SUBCLONAL	1	TRUE	0	0.245528201144614	2		736	889	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0054248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	14	348	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.554	0.4	0.739	0.554	0.4	0.739	SUBCLONAL	1	TRUE	1	0.225784208397645	2		348	224	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	G	rs11575997	NA	P-0054248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	21	602	0	ENST00000269305.4:c.993+1G>C		p.X331_splice	ENST00000269305	NM_001126112.2	331			1	2	FACETS	0.503	0.387	0.639	0.503	0.387	0.639	SUBCLONAL	1	TRUE	1	0.225784208397645	2		602	370	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151947968	151947968	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	21	511	0	ENST00000262189.6:c.1705C>T	p.Gln569Ter	p.Q569*	ENST00000262189	NM_170606.2	569	Cag/Tag	12/59	0.129347718608431	4	FACETS	0.667	0.513	0.846	0.333	0.256	0.423	INDETERMINATE	1	TRUE	2	0.225784208397645	4		511	342	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023423	27023423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	36	399	0	ENST00000324856.7:c.529C>T	p.Gln177Ter	p.Q177*	ENST00000324856	NM_006015.4	177	Caa/Taa	1/20	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.225784208397645	2		399	289	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934251	48934251	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0054248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	19	406	0	ENST00000267163.4:c.706A>T	p.Lys236Ter	p.K236*	ENST00000267163	NM_000321.2	236	Aaa/Taa	7/27	1	2	FACETS	0.693	0.527	0.887	0.693	0.527	0.887	SUBCLONAL	1	TRUE	1	0.225784208397645	2		406	243	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0054249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1397	123	970	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	0.228	0.205	0.252	0.228	0.205	0.252	SUBCLONAL	1	TRUE	1	0.709864720160871	2		970	1520	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0054250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	295	543	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.284451063029062	4	FACETS	0.92	0.868	0.972	0.92	0.868	0.972	CLONAL	3	TRUE	1	0.311241284212754	4		543	901	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0054250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	122	419	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.311241284212754	1	FACETS	0.968	0.876	1	0.968	0.876	1	CLONAL	1	TRUE	0	0.311241284212754	1		419	684	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102198832	102198832	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	15	330	0	ENST00000263464.3:c.1003C>A	p.Gln335Lys	p.Q335K	ENST00000263464	NM_001165.4	335	Caa/Aaa	4/9	0.311241284212754	1	FACETS	0.484	0.356	0.638	0.484	0.356	0.638	SUBCLONAL	1	TRUE	0	0.311241284212754	1		330	168	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	78	375	0				ENST00000310581	NM_198253.2	-/1132			0.454037910040708	4	FACETS	0.882	0.786	0.982	0.882	0.786	0.982	CLONAL	2	TRUE	2	0.550379351162051	4		375	249	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0054251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	156	378	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.54374516722066	2	FACETS	0.981	0.917	1	0.981	0.917	1	CLONAL	2	TRUE	0	0.550379351162051	2		378	289	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265627	152265627	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	173	382	0	ENST00000206249.3:c.1080G>T	p.Trp360Cys	p.W360C	ENST00000206249	NM_000125.3	360	tgG/tgT	4/8	0.510431226560159	2	FACETS	0.859	0.803	0.915	0.859	0.803	0.915	CLONAL	2	TRUE	0	0.550379351162051	2		382	366	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579406	7579406	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	473	928	1	ENST00000269305.4:c.281C>A	p.Ser94Ter	p.S94*	ENST00000269305	NM_001126112.2	94	tCa/tAa	4/11	0.550379351162051	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.550379351162051	2		929	801	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911435	134911435	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	162	473	0	ENST00000398015.3:c.1900T>C	p.Tyr634His	p.Y634H	ENST00000398015	NM_004441.4	634	Tac/Cac	11/16	0.270267814052664	4	FACETS	0.837	0.773	0.904	0.837	0.773	0.904	INDETERMINATE	2	TRUE	2	0.550379351162051	4		473	545	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958511	175958511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	64	382	0	ENST00000367669.3:c.1834G>A	p.Glu612Lys	p.E612K	ENST00000367669	NM_022457.5	612	Gaa/Aaa	16/20	0.25504176885212	3	FACETS	0.915	0.798	1	0.458	0.399	0.52	INDETERMINATE	1	TRUE	1	0.550379351162051	3		382	324	SUCCESS
FH	2271	MSKCC	GRCh37	1	241661271	241661271	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs863223978	NA	P-0054251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	102	386	0	ENST00000366560.3:c.1391-1G>C		p.X464_splice	ENST00000366560	NM_000143.3	464			0.25504176885212	3	FACETS	1	0.966	1	0.584	0.526	0.644	INDETERMINATE	1	TRUE	1	0.550379351162051	3		386	405	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984803	72984803	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	147	696	0	ENST00000268489.5:c.2781del	p.Met928Ter	p.M928*	ENST00000268489	NM_006885.3	927	ctG/ct	3/10	1	2	FACETS	0.798	0.731	0.869	0.798	0.731	0.869	SUBCLONAL	1	TRUE	1	0.550379351162051	2		696	669	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656836	45656836	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	166	705	0	ENST00000407780.3:c.320A>T	p.Asp107Val	p.D107V	ENST00000407780	NM_001283052.1	107	gAc/gTc	3/7	1	2	FACETS	0.921	0.849	0.995	0.921	0.849	0.995	CLONAL	1	TRUE	1	0.550379351162051	2		705	655	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665361	182665361	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	73	248	1	ENST00000292782.4:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000292782	NM_020640.2	194	Gac/Tac	5/7	0.270267814052664	4	FACETS	0.871	0.773	0.974	0.871	0.773	0.974	INDETERMINATE	2	TRUE	2	0.550379351162051	4		249	236	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156554	55156554	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	171	609	0	ENST00000257290.5:c.2955C>A	p.Asp985Glu	p.D985E	ENST00000257290	NM_006206.4	985	gaC/gaA	22/23	0.484812736616671	3	FACETS	1	0.971	1	0.553	0.51	0.598	CLONAL	1	TRUE	1	0.550379351162051	3		609	716	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066647	94066647	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	184	527	0	ENST00000369303.4:c.1112G>T	p.Arg371Leu	p.R371L	ENST00000369303	NM_004440.3	371	cGg/cTg	5/17	0.510431226560159	2	FACETS	0.817	0.765	0.871	0.817	0.765	0.871	CLONAL	2	TRUE	0	0.550379351162051	2		527	409	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38545413	38545416	+	missense_variant,splice_region_variant	Missense_Mutation	ONP	CAAC	CAAC	AAAA	novel	NA	P-0054251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	181	607	1	ENST00000299084.4:c.27_30delinsAAAA	p.Asp9_Asn10delinsGluLys	p.D9_N10delinsEK	ENST00000299084	NM_152594.2	9	gaCAAC/gaAAAA	1/7	0.35197259755898	1	FACETS	0.769	0.713	0.827	0.769	0.713	0.827	SUBCLONAL	1	TRUE	0	0.550379351162051	1		608	620	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249007	+	missense_variant	Missense_Mutation	TNP	GCG	GCG	TCT	novel	NA	P-0054252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	43	684	0	ENST00000275493.2:c.2303_2305delinsTCT	p.Ser768_Val769delinsIleLeu	p.S768_V769delinsIL	ENST00000275493	NM_005228.3	768	aGCGtg/aTCTtg	20/28	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		684	821	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387983	31387983	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	25	265	0	ENST00000328111.2:c.1784G>T	p.Gly595Val	p.G595V	ENST00000328111	NM_006892.3	595	gGc/gTc	17/23	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		265	442	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0054252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	90	645	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.935	0.831	1	0.935	0.831	1	CLONAL	1	TRUE	1	0.323151579254839	2		645	596	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242511	55242511	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913418	NA	P-0054252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	35	302	0	ENST00000275493.2:c.2281G>T	p.Asp761Tyr	p.D761Y	ENST00000275493	NM_005228.3	761	Gat/Tat	19/28	1	2	FACETS	0.692	0.569	0.829	0.692	0.569	0.829	SUBCLONAL	1	TRUE	1	0.323151579254839	2		302	313	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299145	15299145	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	104	830	0	ENST00000263388.2:c.1393T>C	p.Tyr465His	p.Y465H	ENST00000263388	NM_000435.2	465	Tat/Cat	9/33	1	2	FACETS	0.901	0.808	1	0.901	0.808	1	CLONAL	1	TRUE	1	0.323151579254839	2		830	714	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55963904	55963904	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	69	340	0	ENST00000263923.4:c.2539C>G	p.Gln847Glu	p.Q847E	ENST00000263923	NM_002253.2	847	Caa/Gaa	18/30	1	2	FACETS	0.984	0.86	1	0.984	0.86	1	CLONAL	1	TRUE	1	0.323151579254839	2		340	434	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857891	9857891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	142	707	0	ENST00000330684.3:c.3510C>A	p.Asn1170Lys	p.N1170K	ENST00000330684	NM_001134407.1	1170	aaC/aaA	13/13	0.205121319051661	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.205121319051661	3		707	671	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139440186	139440186	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	15	63	0	ENST00000277541.6:c.53C>T	p.Ala18Val	p.A18V	ENST00000277541	NM_017617.3	18	gCc/gTc	1/34	0.205121319051661	1	FACETS	0.754	0.561	0.978	1	0.895	1	CLONAL	2	TRUE	0	0.205121319051661	1		63	87	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	71	304	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.110975488002369	4	FACETS	0.997	0.872	1	0.997	0.872	1	CLONAL	2	FALSE	2	0.171762091256315	4		304	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0054254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	135	599	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.171762091256315	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	FALSE	0	0.171762091256315	2		599	761	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7119463	7119463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	109	600	0	ENST00000302850.5:c.3791G>A	p.Arg1264Lys	p.R1264K	ENST00000302850	NM_000208.2	1264	aGa/aAa	21/22	0.171762091256315	2	FACETS	0.859	0.771	0.951	0.859	0.771	0.951	CLONAL	2	FALSE	0	0.171762091256315	2		600	739	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0054255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	124	963	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.341387850121262	3	FACETS	0.763	0.699	0.828	0.508	0.466	0.552	INDETERMINATE	2	TRUE	0	0.625975672948628	3		966	341	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112344	115112344	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0054255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	47	109	0	ENST00000257566.3:c.1396A>T	p.Lys466Ter	p.K466*	ENST00000257566	NM_016569.3	466	Aag/Tag	7/8	0.625975672948628	3	FACETS	0.822	0.713	0.934	0.822	0.713	0.934	CLONAL	2	TRUE	1	0.625975672948628	3		109	120	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713925	30713925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	90	490	0	ENST00000295754.5:c.1250G>A	p.Gly417Glu	p.G417E	ENST00000295754	NM_003242.5	417	gGg/gAg	4/7	0.377371275414989	3	FACETS	1	0.919	1	0.673	0.613	0.734	CLONAL	2	TRUE	0	0.625975672948628	3		490	187	SUCCESS
APC	324	MSKCC	GRCh37	5	112175757	112175758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	26	274	0	ENST00000257430.4:c.4467dup	p.His1490ThrfsTer24	p.H1490Tfs*24	ENST00000257430	NM_000038.5	1489	tta/ttAa	16/16	0.625975672948628	3	FACETS	0.866	0.715	1	0.866	0.715	1	CLONAL	2	TRUE	1	0.625975672948628	3		274	63	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932251	39932251	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	78	1110	0	ENST00000378444.4:c.2348A>T	p.Lys783Met	p.K783M	ENST00000378444	NM_001123385.1	783	aAg/aTg	4/15	0.298726411003543	3	FACETS	1	0.928	1	0.531	0.471	0.594	INDETERMINATE	1	TRUE	1	0.625975672948628	3		1110	308	SUCCESS
AR	367	MSKCC	GRCh37	X	66765255	66765255	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	27	620	0	ENST00000374690.3:c.267G>T	p.Gln89His	p.Q89H	ENST00000374690	NM_000044.3	89	caG/caT	1/8	0.298726411003543	3	FACETS	0.506	0.404	0.62	0.253	0.202	0.31	INDETERMINATE	1	TRUE	1	0.625975672948628	3		620	224	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579389	+	frameshift_variant	Frame_Shift_Del	DEL	GGAAACCGTAGCTGCCCTGGTAGGTTTTCTG	GGAAACCGTAGCTGCCCTGGTAGGTTTTCTG	-	novel	NA	P-0054261-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	280	806	0	ENST00000269305.4:c.298_328del	p.Gln100ValfsTer13	p.Q100Vfs*13	ENST00000269305	NM_001126112.2	100	CAGAAAACCTACCAGGGCAGCTACGGTTTCCgt/gt	4/11	0.830787342174814	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.830787342174814	1		806	371	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652973	29652974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054261-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	235	478	1	ENST00000356175.3:c.4911dup	p.Leu1638SerfsTer3	p.L1638Sfs*3	ENST00000356175	NM_000267.3	1636	-/T	36/57	0.830787342174814	3	FACETS	0.956	0.894	1	0.478	0.447	0.51	CLONAL	1	TRUE	1	0.830787342174814	3		479	838	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0054263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1217	63	322	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.3	2	FACETS	0.703	0.606	0.81			1	SUBCLONAL	1	TRUE	NA	0.14	2		322	1280	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052641	42052641	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	41	198	0	ENST00000219905.7:c.7312G>T	p.Glu2438Ter	p.E2438*	ENST00000219905	NM_001164273.1	2438	Gaa/Taa	20/24	0.3	3	FACETS	0.785	0.652	0.934			1	CLONAL	1	TRUE	NA	0.14	3		198	798	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627877	37627877	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	57	232	0	ENST00000447079.4:c.1792C>G	p.Gln598Glu	p.Q598E	ENST00000447079	NM_015083.1	598	Cag/Gag	2/14	1	2	FACETS	0.827	0.707	0.958	0.827	0.707	0.958	CLONAL	1	TRUE	1	0.14	2		232	985	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209242	36209242	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	63	188	0	ENST00000222270.7:c.322G>A	p.Val108Met	p.V108M	ENST00000222270	NM_014727.1	108	Gtg/Atg	1/37	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.14	2		188	836	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584584	189584584	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	23	133	0	ENST00000264731.3:c.880C>T	p.Gln294Ter	p.Q294*	ENST00000264731	NM_003722.4	294	Cag/Tag	6/14	1	2	FACETS	0.819	0.638	1	0.819	0.638	1	CLONAL	1	TRUE	1	0.14	2		133	401	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446318	29446357	+	protein_altering_variant	In_Frame_Del	DEL	GAGCTTGCTCAGCTTGTACTCAGGGCTCTGCAGCTCCATC	GAGCTTGCTCAGCTTGTACTCAGGGCTCTGCAGCTCCATC	T	novel	NA	P-0054264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	280	863	0	ENST00000389048.3:c.3210_3249delinsA	p.Met1071_Leu1083del	p.M1071_L1083del	ENST00000389048	NM_004304.4	1070	caGATGGAGCTGCAGAGCCCTGAGTACAAGCTGAGCAAGCTC/caA	20/29	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.475924163664086	2		863	1127	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166184	118166184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371434677	NA	P-0054268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	149	380	0	ENST00000369448.3:c.694G>A	p.Ala232Thr	p.A232T	ENST00000369448	NM_017709.3	232	Gcc/Acc	2/2	0.331277403837841	4	FACETS	0.998	0.92	1	0.998	0.92	1	CLONAL	2	TRUE	2	0.506719789183407	4		380	444	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725026	47725026	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	180	1248	0	ENST00000449228.1:c.718T>A	p.Ser240Thr	p.S240T	ENST00000449228	NM_001127240.2	240	Tcg/Acg	4/4	0.341167280312242	3	FACETS	0.985	0.909	1	0.493	0.454	0.532	CLONAL	1	TRUE	1	0.506719789183407	3		1248	904	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	17	502	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.645	0.48	0.843	0.645	0.48	0.843	SUBCLONAL	1	TRUE	1	0.12	2		502	439	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0054269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	14	347	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	1	2	FACETS	0.467	0.336	0.627	0.467	0.336	0.627	SUBCLONAL	1	TRUE	1	0.12	2		347	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578196	7578196	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	28	687	0	ENST00000269305.4:c.653T>A	p.Val218Glu	p.V218E	ENST00000269305	NM_001126112.2	218	gTg/gAg	6/11	1	2	FACETS	0.547	0.435	0.676	0.547	0.435	0.676	SUBCLONAL	1	TRUE	1	0.12	2		687	853	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038194	30038194	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0054270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	44	403	0	ENST00000338641.4:c.367A>T	p.Lys123Ter	p.K123*	ENST00000338641	NM_000268.3	123	Aag/Tag	4/16	0.3	1	FACETS	0.752	0.632	0.884	0.752	0.632	0.884	SUBCLONAL	1	TRUE	0	0.27	1		403	375	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482864	67482864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555414503	NA	P-0054270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	65	512	1	ENST00000327367.4:c.1268G>A	p.Ser423Asn	p.S423N	ENST00000327367	NM_005902.3	423	aGt/aAt	9/9	1	2	FACETS	0.888	0.771	1	0.888	0.771	1	CLONAL	1	TRUE	1	0.27	2		513	542	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976255	7976255	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1348985335	NA	P-0054270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	50	697	0	ENST00000319144.4:c.1940A>G	p.His647Arg	p.H647R	ENST00000319144	NM_001139.2	647	cAc/cGc	15/15	1	2	FACETS	0.735	0.624	0.857	0.735	0.624	0.857	SUBCLONAL	1	TRUE	1	0.27	2		697	504	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	225	375	0				ENST00000310581	NM_198253.2	-/1132			0.405772388829474	3	FACETS	0.968	0.906	1	0.968	0.906	1	CLONAL	2	TRUE	1	0.405772388829474	3		375	689	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0054271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	145	392	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.324340677280385	5	FACETS	1	0.966	1	0.731	0.671	0.794	CLONAL	2	TRUE	2	0.405772388829474	5		392	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0054271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	217	694	1	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	1	2	FACETS	0.965	0.897	1	0.965	0.897	1	CLONAL	1	TRUE	1	0.405772388829474	2		695	1108	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352697	NA	P-0054271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	238	700	0	ENST00000269305.4:c.587G>A	p.Arg196Gln	p.R196Q	ENST00000269305	NM_001126112.2	196	cGa/cAa	6/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.405772388829474	2		700	1144	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101103	4101103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs727504382	NA	P-0054271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	59	443	0	ENST00000262948.5:c.619G>A	p.Glu207Lys	p.E207K	ENST00000262948	NM_030662.3	207	Gag/Aag	6/11	1	2	FACETS	0.359	0.308	0.415	0.359	0.308	0.415	SUBCLONAL	1	TRUE	1	0.405772388829474	2		443	809	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945702	151945702	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0054271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	291	511	0	ENST00000262189.6:c.1817C>G	p.Ser606Ter	p.S606*	ENST00000262189	NM_170606.2	606	tCa/tGa	14/59	0.324340677280385	5	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	2	0.405772388829474	5		511	726	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910414	32910414	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	71	228	0	ENST00000380152.3:c.1922C>G	p.Ser641Cys	p.S641C	ENST00000380152		641	tCt/tGt	11/27	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.405772388829474	2		228	258	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346893	73346893	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	38	186	0	ENST00000377767.4:c.1324C>T	p.Gln442Ter	p.Q442*	ENST00000377767	NM_014953.3	442	Cag/Tag	9/21	1	2	FACETS	0.879	0.734	1	0.879	0.734	1	CLONAL	1	TRUE	1	0.405772388829474	2		186	213	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42381387	42381387	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	238	598	0	ENST00000221972.3:c.13C>G	p.Pro5Ala	p.P5A	ENST00000221972	NM_021601.3	5	Cca/Gca	1/5	1	2	FACETS	0.935	0.871	1	0.935	0.871	1	CLONAL	1	TRUE	1	0.405772388829474	2		598	1255	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719668	190719668	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	39	270	0	ENST00000441310.2:c.1670C>G	p.Ser557Cys	p.S557C	ENST00000441310	NM_000534.4	557	tCt/tGt	9/13	1	2	FACETS	0.775	0.657	0.9	1	0.961	1	SUBCLONAL	2	TRUE	1	0.405772388829474	2		270	124	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217479	142217479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	165	297	0	ENST00000350721.4:c.5518G>A	p.Glu1840Lys	p.E1840K	ENST00000350721	NM_001184.3	1840	Gaa/Aaa	32/47	0.277372318254639	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.405772388829474	3		297	448	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054271-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	104	375	0				ENST00000310581	NM_198253.2	-/1132			0.175098072954281	4	FACETS	0.902	0.82	0.986	1	0.99	1	CLONAL	5	FALSE	2	0.199700519079922	4		375	277	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0054271-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	62	392	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.875	0.76	0.998	1	0.977	1	CLONAL	2	FALSE	1	0.199700519079922	2		392	355	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0054271-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	118	694	1	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	1	2	FACETS	1	0.938	1	1	0.989	1	CLONAL	2	FALSE	1	0.199700519079922	2		695	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352697	NA	P-0054271-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	57	700	0	ENST00000269305.4:c.587G>A	p.Arg196Gln	p.R196Q	ENST00000269305	NM_001126112.2	196	cGa/cAa	6/11	1	2	FACETS	0.979	0.84	1	0.979	0.84	1	CLONAL	1	FALSE	1	0.199700519079922	2		700	583	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945702	151945702	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0054271-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	30	511	0	ENST00000262189.6:c.1817C>G	p.Ser606Ter	p.S606*	ENST00000262189	NM_170606.2	606	tCa/tGa	14/59	1	2	FACETS	0.905	0.73	1	0.905	0.73	1	CLONAL	1	FALSE	1	0.199700519079922	2		511	332	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42381387	42381387	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054271-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	48	598	0	ENST00000221972.3:c.13C>G	p.Pro5Ala	p.P5A	ENST00000221972	NM_021601.3	5	Cca/Gca	1/5	0.199700519079922	1	FACETS	0.77	0.65	0.902	0.77	0.65	0.902	CLONAL	1	FALSE	0	0.199700519079922	1		598	562	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719668	190719668	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054271-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	29	270	0	ENST00000441310.2:c.1670C>G	p.Ser557Cys	p.S557C	ENST00000441310	NM_000534.4	557	tCt/tGt	9/13	1	2	FACETS	0.794	0.643	0.962	1	0.945	1	CLONAL	2	FALSE	1	0.199700519079922	2		270	183	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577543	7577543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1019340046	NA	P-0054271-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	56	654	2	ENST00000269305.4:c.738G>A	p.Met246Ile	p.M246I	ENST00000269305	NM_001126112.2	246	atG/atA	7/11	1	2	FACETS	0.962	0.824	1	0.962	0.824	1	CLONAL	1	FALSE	1	0.199700519079922	2		656	583	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	213	375	0				ENST00000310581	NM_198253.2	-/1132			0.587997847242092	4	FACETS	0.94	0.887	0.993	0.94	0.887	0.993	CLONAL	3	TRUE	1	0.587997847242092	4		375	408	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0054272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	104	643	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.985	0.891	1	0.985	0.891	1	CLONAL	1	TRUE	1	0.587997847242092	2		643	359	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631837	90631837	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519736	NA	P-0054272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	120	872	0	ENST00000330062.3:c.516G>C	p.Arg172Ser	p.R172S	ENST00000330062	NM_002168.2	172	agG/agC	4/11	1	2	FACETS	0.872	0.792	0.955	0.872	0.792	0.955	CLONAL	1	TRUE	1	0.587997847242092	2		872	468	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437166	110437167	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0054272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	19	35	0	ENST00000375856.3:c.1234dup	p.Arg412ProfsTer127	p.R412Pfs*127	ENST00000375856	NM_003749.2	412	cgc/cCgc	1/2	1	2	FACETS	0.751	0.603	0.905	1	0.929	1	CLONAL	2	TRUE	1	0.587997847242092	2		35	43	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0054273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	45	603	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.360535790259798	13	FACETS	1	0.894	1	0.602	0.524	0.683	CLONAL	7	FALSE	1	0.360535790259798	13		603	103	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	14	329	0	ENST00000397062.3:c.101G>C	p.Arg34Pro	p.R34P	ENST00000397062	NM_006164.4	34	cGa/cCa	2/5	0.360535790259798	6	FACETS	0.786	0.578	1	0.524	0.385	0.687	CLONAL	2	FALSE	3	0.360535790259798	6		329	85	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782082	NA	P-0054273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	67	764	0	ENST00000269305.4:c.745A>T	p.Arg249Trp	p.R249W	ENST00000269305	NM_001126112.2	249	Agg/Tgg	7/11	0.360535790259798	5	FACETS	0.996	0.902	1	0.996	0.902	1	CLONAL	5	FALSE	0	0.360535790259798	5		764	115	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786705	3786705	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	21	796	0	ENST00000262367.5:c.4506G>C	p.Trp1502Cys	p.W1502C	ENST00000262367	NM_004380.2	1502	tgG/tgC	27/31	0.360535790259798	4	FACETS	0.834	0.655	1	0.834	0.655	1	CLONAL	2	FALSE	2	0.360535790259798	4		796	95	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201737	66201737	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	60	469	0	ENST00000273854.3:c.2765G>T	p.Arg922Met	p.R922M	ENST00000273854	NM_004439.5	922	aGg/aTg	16/18	0.360535790259798	5	FACETS	0.919	0.834	1	1	0.957	1	CLONAL	6	FALSE	0	0.360535790259798	5		469	93	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462059	120462059	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	25	806	0	ENST00000256646.2:c.5657G>C	p.Arg1886Pro	p.R1886P	ENST00000256646	NM_024408.3	1886	cGc/cCc	31/34	0.26212804577586	3	FACETS	1	0.839	1	0.691	0.561	0.83	CLONAL	2	FALSE	0	0.360535790259798	3		806	79	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976489	7976489	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	82	736	0	ENST00000319144.4:c.1903del	p.Leu635SerfsTer28	p.L635Sfs*28	ENST00000319144	NM_001139.2	635	Ctc/tc	14/15	0.360535790259798	5	FACETS	0.904	0.823	0.985	0.904	0.823	0.985	CLONAL	5	FALSE	0	0.360535790259798	5		736	155	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679558	86679558	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561328441	NA	P-0054273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	19	408	0	ENST00000274376.6:c.2719C>T	p.Pro907Ser	p.P907S	ENST00000274376	NM_002890.2	907	Cct/Tct	21/25	0.360535790259798	5	FACETS	1	0.807	1	1	0.807	1	CLONAL	2	FALSE	3	0.360535790259798	5		408	78	SUCCESS
APC	324	MSKCC	GRCh37	5	112178834	112178834	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs554356011	NA	P-0054273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	13	349	0	ENST00000257430.4:c.7543A>G	p.Ile2515Val	p.I2515V	ENST00000257430	NM_000038.5	2515	Ata/Gta	16/16	0.360535790259798	5	FACETS	1	0.85	1	0.654	0.473	0.866	CLONAL	1	FALSE	3	0.360535790259798	5		349	85	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354253	70354253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1436223575	NA	P-0054273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	43	969	1	ENST00000374080.3:c.4664C>A	p.Thr1555Lys	p.T1555K	ENST00000374080		1555	aCg/aAg	34/45	0.360535790259798	3	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	FALSE	1	0.360535790259798	3		970	124	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874392	76874392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	17	504	0	ENST00000373344.5:c.5330G>A	p.Arg1777Lys	p.R1777K	ENST00000373344	NM_000489.3	1777	aGg/aAg	21/35	0.360535790259798	3	FACETS	0.976	0.754	1	0.976	0.754	1	CLONAL	2	FALSE	1	0.360535790259798	3		504	57	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76949316	76949316	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	13	353	0	ENST00000373344.5:c.481G>C	p.Gly161Arg	p.G161R	ENST00000373344	NM_000489.3	161	Gga/Cga	6/35	0.360535790259798	3	FACETS	1	0.883	1	0.747	0.547	0.975	CLONAL	1	FALSE	1	0.360535790259798	3		353	57	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	121	375	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.967	0.878	1	0.967	0.878	1	CLONAL	1	TRUE	1	0.500651149250122	2		375	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0054274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	576	681	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.500651149250122	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.500651149250122	2		682	1055	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487277	56487277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035001455	NA	P-0054274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	263	487	0	ENST00000267101.3:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000267101	NM_001982.3	475	Cgg/Tgg	12/28	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.500651149250122	2		487	845	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041025	112041025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779126684	NA	P-0054274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	303	508	0	ENST00000368678.4:c.230G>A	p.Arg77His	p.R77H	ENST00000368678		77	cGt/cAt	3/13	0.500651149250122	3	FACETS	0.926	0.876	0.977	0.926	0.876	0.977	CLONAL	2	TRUE	1	0.500651149250122	3		508	817	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652057	36652058	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0054274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1716	310	1124	0	ENST00000244741.5:c.182dup	p.Asp62Ter	p.D62*	ENST00000244741	NM_000389.4	60	gag/gaGg	2/3	0.500651149250122	3	FACETS	0.764	0.718	0.813	0.382	0.359	0.407	SUBCLONAL	1	TRUE	1	0.500651149250122	3		1124	2026	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105854	27105855	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	345	476	0	ENST00000324856.7:c.5466dup	p.Phe1823IlefsTer8	p.F1823Ifs*8	ENST00000324856	NM_006015.4	1822	cca/ccAa	20/20	0.451212574281464	3	FACETS	0.899	0.854	0.946	0.899	0.854	0.946	CLONAL	2	TRUE	1	0.500651149250122	3		476	958	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640253	3640253	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1182	389	1061	0	ENST00000294008.3:c.3386C>T	p.Ser1129Leu	p.S1129L	ENST00000294008	NM_032444.2	1129	tCa/tTa	12/15	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.500651149250122	NA		1061	1571	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78914347	78914347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1238	501	844	1	ENST00000306801.3:c.2971C>T	p.Arg991Trp	p.R991W	ENST00000306801	NM_020761.2	991	Cgg/Tgg	25/34	0.500651149250122	4	FACETS	0.864	0.825	0.903	0.864	0.825	0.903	CLONAL	2	TRUE	2	0.500651149250122	4		845	1739	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652125	36652131	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCGAG	CGGCGAG	TC	novel	NA	P-0054274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	656	1002	2	ENST00000244741.5:c.247_253delinsTC	p.Arg83SerfsTer4	p.R83Sfs*4	ENST00000244741	NM_000389.4	83	CGGCGAGgc/TCgc	2/3	0.500651149250122	3	FACETS	0.944	0.91	0.979	0.944	0.91	0.979	CLONAL	2	TRUE	1	0.500651149250122	3		1004	1735	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	55	375	0				ENST00000310581	NM_198253.2	-/1132			0.220054398525733	7	FACETS	1	0.892	1	0.176	0.15	0.204	CLONAL	1	TRUE	1	0.220054398525733	7		375	735	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383225	4383225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	47	533	0	ENST00000261254.3:c.19G>A	p.Glu7Lys	p.E7K	ENST00000261254	NM_001759.3	7	Gag/Aag	1/5	1	2	FACETS	0.621	0.523	0.73	0.621	0.523	0.73	SUBCLONAL	1	TRUE	1	0.220054398525733	2		533	688	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578207	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0054275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	147	839	0	ENST00000269305.4:c.642_643del	p.His214GlnfsTer7	p.H214Qfs*7	ENST00000269305	NM_001126112.2	214	caTAgt/cagt	6/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.220054398525733	2		839	985	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15976757	15976757	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0054275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	93	546	0	ENST00000268712.3:c.3797C>G	p.Ser1266Ter	p.S1266*	ENST00000268712	NM_006311.3	1266	tCa/tGa	28/46	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.220054398525733	2		546	599	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106898	11106900	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0054275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	141	803	0	ENST00000358026.2:c.1607_1609del	p.Glu536del	p.E536del	ENST00000358026	NM_001128849.1	535	GAG/-	10/36	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.220054398525733	2		803	1019	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211286	36211286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	182	1021	0	ENST00000222270.7:c.1037C>T	p.Ser346Phe	p.S346F	ENST00000222270	NM_014727.1	346	tCt/tTt	3/37	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.220054398525733	2		1021	1341	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737489	204737489	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	33	321	0	ENST00000302823.3:c.626C>A	p.Pro209Gln	p.P209Q	ENST00000302823	NM_005214.4	209	cCa/cAa	4/4	1	2	FACETS	0.732	0.596	0.884	0.732	0.596	0.884	SUBCLONAL	1	TRUE	1	0.220054398525733	2		321	410	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56910950	56910950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	93	532	0	ENST00000519728.1:c.1096C>T	p.Arg366Trp	p.R366W	ENST00000519728	NM_002350.3	366	Cgg/Tgg	11/13	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.220054398525733	2		532	773	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	67	344	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.997	0.871	1	0.997	0.871	1	CLONAL	1	TRUE	1	0.35	2		344	384	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	72	90	0	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.707	0.618	0.803	0.707	0.618	0.803	SUBCLONAL	1	TRUE	1	0.35	2		90	582	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560514	65560514	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	108	508	0	ENST00000358664.4:c.83A>G	p.His28Arg	p.H28R	ENST00000358664	NM_002382.4	28	cAt/cGt	3/5	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.35	2		508	519	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	96	593	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.947	0.846	1	0.947	0.846	1	CLONAL	1	TRUE	1	0.35	2		598	579	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	51	392	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.755	0.644	0.876	0.755	0.644	0.876	SUBCLONAL	1	TRUE	1	0.35	2		392	386	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	74	415	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.35	2		415	354	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	58	449	8	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.928	0.802	1	0.928	0.802	1	CLONAL	1	TRUE	1	0.35	2		457	357	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	129	1294	6	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.734	0.665	0.808	0.734	0.665	0.808	SUBCLONAL	1	TRUE	1	0.35	2		1300	1004	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989562	212989562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755026855	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	47	340	0	ENST00000342788.4:c.149G>A	p.Arg50His	p.R50H	ENST00000342788	NM_005235.2	50	cGc/cAc	2/28	1	2	FACETS	0.712	0.603	0.833	0.712	0.603	0.833	SUBCLONAL	1	TRUE	1	0.35	2		340	377	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	57	449	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.744	0.639	0.857	0.744	0.639	0.857	SUBCLONAL	1	TRUE	1	0.35	2		450	438	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097621	27097622	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	65	427	2	ENST00000324856.7:c.3216dup	p.Trp1073MetfsTer32	p.W1073Mfs*32	ENST00000324856	NM_006015.4	1070	-/A	12/20	1	2	FACETS	0.747	0.649	0.853	0.747	0.649	0.853	SUBCLONAL	1	TRUE	1	0.35	2		429	497	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	90	696	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.947	0.843	1	0.947	0.843	1	CLONAL	1	TRUE	1	0.35	2		696	543	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948747	71948748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760925109	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	110	1125	14	ENST00000298229.2:c.3466dup	p.Arg1156ProfsTer59	p.R1156Pfs*59	ENST00000298229	NM_001567.3	1153	-/C	26/28	1	2	FACETS	0.799	0.717	0.885	0.799	0.717	0.885	SUBCLONAL	1	TRUE	1	0.35	2		1139	787	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106562	27106562	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	85	816	0	ENST00000324856.7:c.6176del	p.Asn2059ThrfsTer76	p.N2059Tfs*76	ENST00000324856	NM_006015.4	2058	gAa/ga	20/20	1	2	FACETS	0.603	0.532	0.678	0.603	0.532	0.678	SUBCLONAL	1	TRUE	1	0.35	2		816	806	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870356	155870356	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	73	469	0	ENST00000368323.3:c.483del	p.Phe161LeufsTer47	p.F161Lfs*47	ENST00000368323	NM_006912.5	161	ttT/tt	6/6	1	2	FACETS	0.846	0.742	0.958	0.846	0.742	0.958	CLONAL	1	TRUE	1	0.35	2		469	493	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845585	63845585	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	43	192	0	ENST00000279873.7:c.1326del	p.Lys442AsnfsTer37	p.K442Nfs*37	ENST00000279873	NM_032199.2	442	Aaa/aa	9/10	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.35	2		192	223	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852409	63852409	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	53	757	1	ENST00000279873.7:c.3191del	p.Gly1064AlafsTer43	p.G1064Afs*43	ENST00000279873	NM_032199.2	1063	Ggg/gg	10/10	1	2	FACETS	0.464	0.395	0.54	0.464	0.395	0.54	SUBCLONAL	1	TRUE	1	0.35	2		758	653	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653782	89653782	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs886041877	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	49	233	0	ENST00000371953.3:c.80A>G	p.Tyr27Cys	p.Y27C	ENST00000371953	NM_000314.4	27	tAt/tGt	2/9	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.35	2		233	234	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977143	85977144	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	33	301	0	ENST00000263360.6:c.751dup	p.Ile251AsnfsTer11	p.I251Nfs*11	ENST00000263360	NM_003797.3	249	gaa/gAaa	8/12	1	2	FACETS	0.873	0.716	1	0.873	0.716	1	CLONAL	1	TRUE	1	0.35	2		301	216	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173696	108173696	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	54	372	0	ENST00000278616.4:c.5441del	p.Leu1814TrpfsTer14	p.L1814Wfs*14	ENST00000278616	NM_000051.3	1812	gcT/gc	36/63	1	2	FACETS	0.986	0.847	1	0.986	0.847	1	CLONAL	1	TRUE	1	0.35	2		372	313	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498235	498235	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	34	341	0	ENST00000399788.2:c.23del	p.Gly8AlafsTer58	p.G8Afs*58	ENST00000399788	NM_001042603.1	8	gGc/gc	1/28	1	2	FACETS	0.679	0.557	0.816	0.679	0.557	0.816	SUBCLONAL	1	TRUE	1	0.35	2		341	286	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431702	49431702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1296588434	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	126	1041	0	ENST00000301067.7:c.9437C>T	p.Ala3146Val	p.A3146V	ENST00000301067	NM_003482.3	3146	gCt/gTt	34/54	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.35	2		1041	695	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431874	49431874	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	115	875	2	ENST00000301067.7:c.9265del	p.Val3089TrpfsTer30	p.V3089Wfs*30	ENST00000301067	NM_003482.3	3089	Gtg/tg	34/54	1	2	FACETS	0.917	0.826	1	0.917	0.826	1	CLONAL	1	TRUE	1	0.35	2		877	717	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562171	21562171	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	24	1238	2	ENST00000382592.4:c.1748del	p.Asn583ThrfsTer76	p.N583Tfs*76	ENST00000382592	NM_014572.2	583	aAc/ac	4/8	1	2	FACETS	0.118	0.092	0.149	0.118	0.092	0.149	SUBCLONAL	1	TRUE	1	0.35	2		1240	1162	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519093	103519093	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	89	563	0	ENST00000355739.4:c.2431A>G	p.Ser811Gly	p.S811G	ENST00000355739	NM_000123.3	811	Agt/Ggt	11/15	1	2	FACETS	0.886	0.787	0.991	0.886	0.787	0.991	CLONAL	1	TRUE	1	0.35	2		563	574	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991949	72991949	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs753977275	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	35	670	3	ENST00000268489.5:c.2096del	p.Gly699AlafsTer125	p.G699Afs*125	ENST00000268489	NM_006885.3	699	gGc/gc	2/10	1	2	FACETS	0.348	0.284	0.419	0.348	0.284	0.419	SUBCLONAL	1	TRUE	1	0.35	2		673	575	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349640	89349641	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs772267579	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	138	734	12	ENST00000301030.4:c.3309dup	p.Asp1104ArgfsTer2	p.D1104Rfs*2	ENST00000301030	NM_001256183.1	1103	-/A	9/13	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.35	2		746	760	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960915	15960915	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	54	363	0	ENST00000268712.3:c.6305G>A	p.Ser2102Asn	p.S2102N	ENST00000268712	NM_006311.3	2102	aGc/aAc	40/46	1	2	FACETS	0.754	0.646	0.872	0.754	0.646	0.872	SUBCLONAL	1	TRUE	1	0.35	2		363	409	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532568	63532568	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	205	1213	0	ENST00000307078.5:c.2011del	p.Arg671AlafsTer18	p.R671Afs*18	ENST00000307078	NM_004655.3	671	Cgc/gc	8/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.35	2		1213	1034	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226268	2226268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs927525441	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	63	1311	3	ENST00000398665.3:c.3748G>A	p.Asp1250Asn	p.D1250N	ENST00000398665	NM_032482.2	1250	Gac/Aac	27/28	1	2	FACETS	0.345	0.298	0.398	0.345	0.298	0.398	SUBCLONAL	1	TRUE	1	0.35	2		1314	1042	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291064	10291064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775139340	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	88	715	1	ENST00000340748.4:c.407G>A	p.Arg136His	p.R136H	ENST00000340748		136	cGc/cAc	4/40	1	2	FACETS	0.699	0.619	0.785	0.699	0.619	0.785	SUBCLONAL	1	TRUE	1	0.35	2		716	719	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602890	10602890	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	98	1088	0	ENST00000171111.5:c.688A>G	p.Thr230Ala	p.T230A	ENST00000171111	NM_203500.1	230	Acc/Gcc	3/6	1	2	FACETS	0.51	0.454	0.571	0.51	0.454	0.571	SUBCLONAL	1	TRUE	1	0.35	2		1088	1097	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610475	10610475	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759406594	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	123	908	0	ENST00000171111.5:c.235G>A	p.Val79Ile	p.V79I	ENST00000171111	NM_203500.1	79	Gtc/Atc	2/6	1	2	FACETS	0.918	0.83	1	0.918	0.83	1	CLONAL	1	TRUE	1	0.35	2		908	766	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966873	25966873	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1271466699	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	55	588	7	ENST00000435504.4:c.2333del	p.Pro778GlnfsTer21	p.P778Qfs*21	ENST00000435504		778	cCa/ca	13/13	1	2	FACETS	0.62	0.531	0.717	0.62	0.531	0.717	SUBCLONAL	1	TRUE	1	0.35	2		595	507	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655272	45655272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764295138	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	136	841	1	ENST00000407780.3:c.580C>T	p.Arg194Trp	p.R194W	ENST00000407780	NM_001283052.1	194	Cgg/Tgg	4/7	1	2	FACETS	0.898	0.817	0.984	0.898	0.817	0.984	CLONAL	1	TRUE	1	0.35	2		842	865	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245393	153245393	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	84	473	0	ENST00000281708.4:c.1798G>C	p.Asp600His	p.D600H	ENST00000281708	NM_033632.3	600	Gat/Cat	11/12	1	2	FACETS	0.941	0.834	1	0.941	0.834	1	CLONAL	1	TRUE	1	0.35	2		473	510	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521299	187521299	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1166479124	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	120	594	0	ENST00000441802.2:c.11856del	p.Phe3952LeufsTer31	p.F3952Lfs*31	ENST00000441802	NM_005245.3	3952	ttT/tt	22/27	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.35	2		594	596	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526768	31526768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	71	590	0	ENST00000344624.3:c.272G>A	p.Gly91Asp	p.G91D	ENST00000344624		91	gGc/gAc	2/33	1	2	FACETS	0.961	0.843	1	0.961	0.843	1	CLONAL	1	TRUE	1	0.35	2		590	422	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168716	56168716	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	61	379	0	ENST00000399503.3:c.1570C>T	p.Gln524Ter	p.Q524*	ENST00000399503	NM_005921.1	524	Cag/Tag	9/20	1	2	FACETS	0.764	0.661	0.876	0.764	0.661	0.876	SUBCLONAL	1	TRUE	1	0.35	2		379	456	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589554	67589562	+	inframe_deletion	In_Frame_Del	DEL	AGATAATAT	AGATAATAT	-	novel	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	23	164	0	ENST00000274335.5:c.1317_1325del	p.Glu439_Ile442delinsAsp	p.E439_I442delinsD	ENST00000274335		439	gaAGATAATATt/gat	10/15	1	2	FACETS	0.764	0.6	0.95	0.764	0.6	0.95	CLONAL	1	TRUE	1	0.35	2		164	172	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055896	180055897	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	79	788	2	ENST00000261937.6:c.1088dup	p.Pro364AlafsTer63	p.P364Afs*63	ENST00000261937	NM_182925.4	363	ccg/ccCg	8/30	1	2	FACETS	0.653	0.574	0.738	0.653	0.574	0.738	SUBCLONAL	1	TRUE	1	0.35	2		790	691	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681120	117681120	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs748436511	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	90	420	0	ENST00000368508.3:c.3500del	p.Leu1167Ter	p.L1167*	ENST00000368508	NM_002944.2	1167	tTa/ta	23/43	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.35	2		420	392	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200287	138200287	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769014911	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	87	579	2	ENST00000237289.4:c.1705C>T	p.Arg569Trp	p.R569W	ENST00000237289	NM_001270507.1	569	Cgg/Tgg	7/9	1	2	FACETS	0.909	0.806	1	0.909	0.806	1	CLONAL	1	TRUE	1	0.35	2		581	547	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411880	116411883	+	intron_variant	Intron	DEL	TCTT	TCTT	-	rs747887276	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	17	793	0	ENST00000397752.3:c.2888-16_2888-13del		p.*963*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.132	0.098	0.173	0.132	0.098	0.173	SUBCLONAL	1	TRUE	1	0.35	2		793	735	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205218	38205218	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	93	720	0	ENST00000317025.8:c.472A>G	p.Thr158Ala	p.T158A	ENST00000317025	NM_023034.1	158	Acc/Gcc	2/24	1	2	FACETS	0.75	0.667	0.838	0.75	0.667	0.838	SUBCLONAL	1	TRUE	1	0.35	2		720	709	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181311	123181311	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs774761933	NA	P-0054278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	36	219	0	ENST00000218089.9:c.775C>T	p.Arg259Ter	p.R259*	ENST00000218089	NM_001042749.1	259	Cga/Tga	9/35	1	2	FACETS	0.939	0.779	1	0.939	0.779	1	CLONAL	1	TRUE	1	0.35	2		219	219	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727453	66727453	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397516790	NA	P-0054279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	56	473	0	ENST00000307102.5:c.169A>G	p.Lys57Glu	p.K57E	ENST00000307102	NM_002755.3	57	Aag/Gag	2/11	1	2	FACETS	0.943	0.808	1	0.943	0.808	1	CLONAL	1	TRUE	1	0.22	2		473	540	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183794	10183794	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs119103277	NA	P-0054279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	87	1123	3	ENST00000256474.2:c.263G>A	p.Trp88Ter	p.W88*	ENST00000256474	NM_000551.3	88	tGg/tAg	1/3	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.22	2		1126	788	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103730	47103734	+	frameshift_variant	Frame_Shift_Del	DEL	TTTAT	TTTAT	-	novel	NA	P-0054279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	49	501	0	ENST00000409792.3:c.6212_6216del	p.Asn2071ArgfsTer17	p.N2071Rfs*17	ENST00000409792	NM_014159.6	2071	aATAAA/a	14/21	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.22	2		501	442	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0054280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	172	169	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.988	0.919	1	0.988	0.919	1	CLONAL	1	TRUE	1	0.803889582603525	2		169	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs530941076	NA	P-0054280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	1091	799	0	ENST00000269305.4:c.658T>G	p.Tyr220Asp	p.Y220D	ENST00000269305	NM_001126112.2	220	Tat/Gat	6/11	0.797583882341621	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.803889582603525	2		799	1317	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257729	16257729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199930614	NA	P-0054280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	301	557	0	ENST00000375759.3:c.4994C>T	p.Ala1665Val	p.A1665V	ENST00000375759	NM_015001.2	1665	gCg/gTg	11/15	1	2	FACETS	0.769	0.725	0.813	0.769	0.725	0.813	SUBCLONAL	1	TRUE	1	0.803889582603525	2		557	974	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670064	29670065	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0054280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	106	395	0	ENST00000356175.3:c.7037_7038del	p.Leu2346ArgfsTer18	p.L2346Rfs*18	ENST00000356175	NM_000267.3	2346	cTG/c	47/57	0.803889582603525	1	FACETS	0.414	0.374	0.455	0.414	0.374	0.455	SUBCLONAL	1	TRUE	0	0.803889582603525	1		395	381	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379793	17379793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1963	155	1268	0	ENST00000359435.4:c.178G>A	p.Asp60Asn	p.D60N	ENST00000359435	NM_001033549.1	60	Gat/Aat	2/9	1	2	FACETS	0.182	0.165	0.2	0.182	0.165	0.2	SUBCLONAL	1	TRUE	1	0.803889582603525	2		1268	2118	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813001	76813001	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	191	262	0	ENST00000373344.5:c.6620T>C	p.Leu2207Pro	p.L2207P	ENST00000373344	NM_000489.3	2207	cTt/cCt	30/35	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.803889582603525	1		262	249	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0054281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	581	834	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.466224021810983	2	FACETS	0.872	0.84	0.904	0.872	0.84	0.904	CLONAL	2	TRUE	0	0.527186386728369	2		836	1264	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814665	43814665	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1645	128	581	0	ENST00000372470.3:c.1460C>A	p.Thr487Asn	p.T487N	ENST00000372470	NM_005373.2	487	aCc/aAc	9/12	0.435591103335251	5	FACETS	0.49	0.442	0.542			1	SUBCLONAL	1	TRUE	NA	0.527186386728369	5		581	1773	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005944	69005944	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	175	390	0	ENST00000288368.4:c.2355C>G	p.Asp785Glu	p.D785E	ENST00000288368	NM_024870.2	785	gaC/gaG	21/40	0.271272083864147	1	FACETS	0.756	0.699	0.814	0.756	0.699	0.814	INDETERMINATE	1	TRUE	0	0.527186386728369	1		390	647	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396849	139397063	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCGCAGCCCACGAAGAACAGAAGCACAAAGGCGGCCGCCGCCACGTACATGAAGTGCAGCTGCGCCGGCGGGGGCGGCTCCACGGTCTCACCTGCGGGCACGGGGGCCAGGGGCAGGTGCCCGGACATCAGGCAGCGGCTACGCAGCAGGCTGGTGGCCGGGGGGCGGCGGACTGGCTCCGCGTCCGGGCGCCTCCTCACCCACTCTCCTCCAT	CCCGCAGCCCACGAAGAACAGAAGCACAAAGGCGGCCGCCGCCACGTACATGAAGTGCAGCTGCGCCGGCGGGGGCGGCTCCACGGTCTCACCTGCGGGCACGGGGGCCAGGGGCAGGTGCCCGGACATCAGGCAGCGGCTACGCAGCAGGCTGGTGGCCGGGGGGCGGCGGACTGGCTCCGCGTCCGGGCGCCTCCTCACCCACTCTCCTCCAT	-	novel	NA	P-0054281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3407	200	859	0	ENST00000277541.6:c.5168-123_5259del		p.X1723_splice	ENST00000277541	NM_017617.3	1723		28/34	0.527186386728369	7	FACETS	0.488	0.449	0.529			1	SUBCLONAL	1	TRUE	NA	0.527186386728369	7		859	3607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0054284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	53	868	2	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		870	463	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	130	502	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.129816236165952	0	FACETS	0.74	0.678	0.805			1	INDETERMINATE	3	TRUE	0	0.22	0		502	415	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	111	502	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.108101388271146	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		502	388	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0054288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	74	434	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.19494489666142	2	FACETS	0.968	0.857	1	0.968	0.857	1	CLONAL	2	TRUE	0	0.27	2		434	283	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0054288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	82	457	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.27	2		457	418	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911760	26911760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	20	311	0	ENST00000381527.3:c.185C>T	p.Ser62Leu	p.S62L	ENST00000381527	NM_001260.1	62	tCg/tTg	2/13	1	2	FACETS	0.615	0.471	0.782	0.615	0.471	0.782	SUBCLONAL	1	TRUE	1	0.27	2		311	241	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118949	70118949	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	30	970	0	ENST00000245479.2:c.521A>G	p.Tyr174Cys	p.Y174C	ENST00000245479	NM_000346.3	174	tAc/tGc	2/3	1	2	FACETS	0.464	0.373	0.567	0.464	0.373	0.567	SUBCLONAL	1	TRUE	1	0.27	2		970	479	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137038	64137038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1372636808	NA	P-0054288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	29	773	2	ENST00000334205.4:c.1549G>A	p.Val517Met	p.V517M	ENST00000334205	NM_003942.2	517	Gtg/Atg	13/17	1	2	FACETS	0.61	0.49	0.747	0.61	0.49	0.747	SUBCLONAL	1	TRUE	1	0.27	2		775	352	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117663	70117664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0054288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	86	991	0	ENST00000245479.2:c.132dup	p.Asn45GlufsTer207	p.N45Efs*207	ENST00000245479	NM_000346.3	44	gag/gaGg	1/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.27	2		991	464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0054289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	392	758	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.513480247909736	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.518410541272775	2		758	723	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347783	70347783	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	139	543	0	ENST00000374080.3:c.3022G>T	p.Val1008Leu	p.V1008L	ENST00000374080		1008	Gtg/Ttg	22/45	0.472745660715581	3	FACETS	0.913	0.832	0.997	0.456	0.416	0.499	CLONAL	1	TRUE	1	0.518410541272775	3		543	740	SUCCESS
CBL	867	MSKCC	GRCh37	11	119167698	119167698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1229733932	NA	P-0054289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	136	549	0	ENST00000264033.4:c.2107C>T	p.Pro703Ser	p.P703S	ENST00000264033	NM_005188.3	703	Ccc/Tcc	13/16	0.518410541272775	3	FACETS	0.857	0.78	0.938	0.428	0.39	0.469	CLONAL	1	TRUE	1	0.518410541272775	3		549	771	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524645	106524645	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	170	268	0	ENST00000359195.3:c.2806T>A	p.Cys936Ser	p.C936S	ENST00000359195	NM_002649.2	936	Tgt/Agt	9/11	0.518410541272775	6	FACETS	1	0.977	1	0.833	0.776	0.891	CLONAL	3	TRUE	2	0.518410541272775	6		268	401	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648245	206648256	+	inframe_deletion	In_Frame_Del	DEL	GCTCCAGTGGGA	GCTCCAGTGGGA	-	novel	NA	P-0054289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	709	605	0	ENST00000367120.3:c.268_279del	p.Ser90_Ser93del	p.S90_S93del	ENST00000367120	NM_014002.3	89	tGCTCCAGTGGGAgc/tgc	5/22	0.496921102145423	5	FACETS	0.907	0.879	0.935	0.907	0.879	0.935	CLONAL	4	TRUE	1	0.518410541272775	5		605	1340	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332507	70332507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	247	565	0	ENST00000373644.4:c.412C>T	p.His138Tyr	p.H138Y	ENST00000373644	NM_030625.2	138	Cat/Tat	2/12	0.442053202683783	4	FACETS	1	0.988	1	0.792	0.746	0.838	CLONAL	2	TRUE	1	0.518410541272775	4		565	609	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588819	69588819	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	312	1133	0	ENST00000168712.1:c.417G>A	p.Met139Ile	p.M139I	ENST00000168712	NM_002007.2	139	atG/atA	2/3	0.518410541272775	3	FACETS	1	0.98	1	0.545	0.513	0.578	CLONAL	1	TRUE	1	0.518410541272775	3		1133	1390	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94963975	94963975	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1157993331	NA	P-0054289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	152	424	0	ENST00000536441.1:c.50G>T	p.Cys17Phe	p.C17F	ENST00000536441	NM_144665.3	17	tGt/tTt	1/10	0.518410541272775	3	FACETS	1	0.965	1	0.549	0.503	0.596	CLONAL	1	TRUE	1	0.518410541272775	3		424	673	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023366	31023366	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	122	485	0	ENST00000375687.4:c.2851G>T	p.Asp951Tyr	p.D951Y	ENST00000375687	NM_015338.5	951	Gat/Tat	13/13	0.518410541272775	3	FACETS	0.935	0.847	1			1	CLONAL	1	TRUE	NA	0.518410541272775	3		485	634	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829095	128829095	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	63	56	0	ENST00000249373.3:c.103A>T	p.Asn35Tyr	p.N35Y	ENST00000249373	NM_005631.4	35	Aac/Tac	1/12	0.518410541272775	6	FACETS	0.982	0.879	1	0.982	0.879	1	CLONAL	4	TRUE	2	0.518410541272775	6		56	126	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117861241	117861241	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	119	460	0	ENST00000297338.2:c.1648G>T	p.Asp550Tyr	p.D550Y	ENST00000297338	NM_006265.2	550	Gat/Tat	13/14	0.518410541272775	5	FACETS	1	0.964	1	0.285	0.257	0.314	CLONAL	1	TRUE	1	0.518410541272775	5		460	716	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	81	502	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.993	0.877	1	0.993	0.877	1	CLONAL	1	TRUE	1	0.31	2		502	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0054290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	130	51	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.948	0.859	1	0.948	0.859	1	CLONAL	1	TRUE	1	0.31	2		51	885	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0054290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	92	235	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.31	2		235	496	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752960	128752960	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	77	392	0	ENST00000377970.2:c.1121A>G	p.His374Arg	p.H374R	ENST00000377970	NM_002467.4	374	cAc/cGc	3/3	1	2	FACETS	0.843	0.741	0.953	0.843	0.741	0.953	CLONAL	1	TRUE	1	0.31	2		392	589	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0054290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	64	352	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	0.857	0.743	0.979	0.857	0.743	0.979	CLONAL	1	TRUE	1	0.31	2		352	482	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087911	27087911	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs757025491	NA	P-0054290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	143	658	0	ENST00000324856.7:c.2198C>A	p.Ser733Ter	p.S733*	ENST00000324856	NM_006015.4	733	tCg/tAg	6/20	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.31	2		658	920	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589168	67589168	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	50	273	0	ENST00000274335.5:c.1156C>G	p.Arg386Gly	p.R386G	ENST00000274335		386	Cga/Gga	9/15	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.31	2		273	300	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056341	27056342	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	80	421	0	ENST00000324856.7:c.1339dup	p.Tyr447LeufsTer176	p.Y447Lfs*176	ENST00000324856	NM_006015.4	446	tct/tcTt	2/20	1	2	FACETS	0.985	0.869	1	0.985	0.869	1	CLONAL	1	TRUE	1	0.31	2		421	524	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720679	89720679	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs398123329	NA	P-0054290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	49	323	0	ENST00000371953.3:c.830C>G	p.Thr277Arg	p.T277R	ENST00000371953	NM_000314.4	277	aCa/aGa	8/9	1	2	FACETS	0.823	0.699	0.959	0.823	0.699	0.959	CLONAL	1	TRUE	1	0.31	2		323	384	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645361	67645362	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0054290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	82	425	0	ENST00000264010.4:c.628_629del	p.Ser210GlnfsTer19	p.S210Qfs*19	ENST00000264010	NM_006565.3	209	aAG/a	3/12	1	2	FACETS	0.922	0.814	1	0.922	0.814	1	CLONAL	1	TRUE	1	0.31	2		425	574	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591272	67591328	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCAAAAGAAGTTGAACGAGTGGTTGGGCAATGAAAACACTGAAGAGTAAGTAGTTAC	GCAAAAGAAGTTGAACGAGTGGTTGGGCAATGAAAACACTGAAGAGTAAGTAGTTAC	CCA	novel	NA	P-0054290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	34	376	2	ENST00000274335.5:c.1770_1814+12delinsCCA		p.X590_splice	ENST00000274335		590		13/15	1	2	FACETS	0.496	0.405	0.599	0.496	0.405	0.599	SUBCLONAL	1	TRUE	1	0.31	2		378	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0054291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	289	834	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.310103243638882	2	FACETS	0.913	0.862	0.964	0.913	0.862	0.964	CLONAL	2	FALSE	0	0.384782115908286	2		836	823	SUCCESS
APC	324	MSKCC	GRCh37	5	112174113	112174113	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554084511	NA	P-0054291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	146	285	0	ENST00000257430.4:c.2825del	p.Asn942IlefsTer13	p.N942Ifs*13	ENST00000257430	NM_000038.5	941	gAa/ga	16/16	0.384782115908286	3	FACETS	1	0.974	1	0.752	0.694	0.812	CLONAL	2	FALSE	0	0.384782115908286	3		285	401	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253365	226253365	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	159	336	0	ENST00000366813.1:c.137C>G	p.Thr46Ser	p.T46S	ENST00000366813		46	aCt/aGt	2/3	0.384782115908286	3	FACETS	1	0.964	1	0.713	0.659	0.767	CLONAL	2	FALSE	0	0.384782115908286	3		336	461	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945439	17945439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149982493	NA	P-0054291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	279	816	0	ENST00000458235.1:c.2291C>T	p.Pro764Leu	p.P764L	ENST00000458235	NM_000215.3	764	cCg/cTg	17/24	0.369578950409714	4	FACETS	0.919	0.863	0.976	0.919	0.863	0.976	CLONAL	2	FALSE	2	0.384782115908286	4		816	1093	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418871	116418871	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	313	67	0	ENST00000397752.3:c.3382G>A	p.Gly1128Arg	p.G1128R	ENST00000397752	NM_000245.2	1128	Gga/Aga	17/21	NA	2	FACETS	0.845	0.803	0.889			1	INDETERMINATE	2	FALSE	NA	0.507189917390769	2		67	730	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5206850	5206850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	707	168	0	ENST00000357368.4:c.5782G>A	p.Glu1928Lys	p.E1928K	ENST00000357368	NM_002850.3	1928	Gag/Aag	38/38	0.222245369813918	0	FACETS		NA	1			1	INDETERMINATE	2	FALSE	0	0.507189917390769	0		168	1379	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58711223	58711223	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	440	122	0	ENST00000305921.3:c.711C>G	p.Asn237Lys	p.N237K	ENST00000305921	NM_003620.3	237	aaC/aaG	3/6	1	2	FACETS	0.976	0.936	1	1	0.997	1	CLONAL	2	FALSE	1	0.507189917390769	2		122	889	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939085	131939297	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CATAGAAGAACAAGAAACACTCTTGGGTACAATAATGCCTGAAGAAGAAAGTGCCAAAGTATGCCTGACAGATGTTACAATTATGGAGAGGTTCCAGGTAAGTTTATTGTAGTTTAAGGCAGAATAAAACTTGTTCCATGGTGGCTTGAATTTGAAGTGTGAGAGTTAAAAATAGTAGCTAGTATTCAGGTACAGGTTGTGTTTAGAATTCCC	CATAGAAGAACAAGAAACACTCTTGGGTACAATAATGCCTGAAGAAGAAAGTGCCAAAGTATGCCTGACAGATGTTACAATTATGGAGAGGTTCCAGGTAAGTTTATTGTAGTTTAAGGCAGAATAAAACTTGTTCCATGGTGGCTTGAATTTGAAGTGTGAGAGTTAAAAATAGTAGCTAGTATTCAGGTACAGGTTGTGTTTAGAATTCCC	-	novel	NA	P-0054292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	375	40	0	ENST00000265335.6:c.2304_2397+119del		p.X768_splice	ENST00000265335		768		14/25	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.507189917390769	NA		40	843	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0054294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	743	91	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.196825993183554	1	FACETS	0.876	0.848	0.903	1	0.998	1	CLONAL	4	TRUE	0	0.243136330254982	1		91	1533	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842614	68842655	+	inframe_deletion	In_Frame_Del	DEL	AAAGAAGGCAAGGTTTTCTACAGCATCACTGGCCAAGGAGCT	AAAGAAGGCAAGGTTTTCTACAGCATCACTGGCCAAGGAGCT	-	novel	NA	P-0054294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	601	110	0	ENST00000261769.5:c.550_591del	p.Lys184_Ala197del	p.K184_A197del	ENST00000261769	NM_004360.3	184	AAAGAAGGCAAGGTTTTCTACAGCATCACTGGCCAAGGAGCT/-	5/16	0.198309076115625	2	FACETS	1	0.977	1	1	0.998	1	CLONAL	4	TRUE	0	0.243136330254982	2		110	1218	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0054296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	421	603	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.985	1	1	0.997	1	CLONAL	2	TRUE	1	0.468410422709274	2		603	850	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0054296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	354	235	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.468410422709274	2	FACETS	0.909	0.874	0.944	1	0.996	1	CLONAL	3	TRUE	0	0.468410422709274	2		235	554	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339329	70339329	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0054296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	365	114	0	ENST00000374080.3:c.204+2T>A		p.X68_splice	ENST00000374080		68			1	2	FACETS	1	0.993	1	1	0.997	1	CLONAL	2	TRUE	1	0.468410422709274	2		114	668	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099425	27099426	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0054296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	391	113	0	ENST00000324856.7:c.3666dup	p.Arg1223AlafsTer5	p.R1223Afs*5	ENST00000324856	NM_006015.4	1221	atg/atGg	14/20	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	1	0.468410422709274	2		113	734	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779531	3779531	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	897	189	0	ENST00000262367.5:c.5517del	p.Val1840CysfsTer33	p.V1840Cfs*33	ENST00000262367	NM_004380.2	1839	ccC/cc	31/31	1	2	FACETS	1	0.995	1	1	0.998	1	CLONAL	2	TRUE	1	0.468410422709274	2		189	1746	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255266	16255266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776660027	NA	P-0054297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1501	434	186	0	ENST00000375759.3:c.2531G>A	p.Arg844Gln	p.R844Q	ENST00000375759	NM_015001.2	844	cGa/cAa	11/15	0.759499570182015	9	FACETS	1	0.984	1			1	CLONAL	2	FALSE	NA	0.759499570182015	9		186	1935	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564633	86564633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1187087405	NA	P-0054297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	1006	323	0	ENST00000274376.6:c.365C>T	p.Ser122Leu	p.S122L	ENST00000274376	NM_002890.2	122	tCg/tTg	1/25	1	2	FACETS	0.857	0.838	0.876	1	0.998	1	CLONAL	2	FALSE	1	0.759499570182015	2		323	1545	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719415	190719415	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	259	107	0	ENST00000441310.2:c.1417G>C	p.Asp473His	p.D473H	ENST00000441310	NM_000534.4	473	Gac/Cac	9/13	0.758683558049449	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	FALSE	1	0.759499570182015	3		107	442	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114850	73114850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369142295	NA	P-0054297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	48	40	0	ENST00000356692.5:c.1231G>A	p.Asp411Asn	p.D411N	ENST00000356692		411	Gat/Aat	9/9	0.585163740306502	3	FACETS	0.872	0.765	0.979	0.872	0.765	0.979	CLONAL	2	FALSE	1	0.759499570182015	3		40	100	SUCCESS
ATR	545	MSKCC	GRCh37	3	142286971	142286971	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	349	157	1	ENST00000350721.4:c.85G>C	p.Val29Leu	p.V29L	ENST00000350721	NM_001184.3	29	Gtt/Ctt	2/47	0.758683558049449	5	FACETS	0.96	0.911	1	0.64	0.607	0.673	CLONAL	2	FALSE	2	0.759499570182015	5		158	1024	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803107	1803107	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2289	1068	380	2	ENST00000260795.2:c.459G>A	p.Trp153Ter	p.W153*	ENST00000260795		153	tgG/tgA	4/17	0.759499570182015	6	FACETS	1	0.991	1			1	CLONAL	2	FALSE	NA	0.759499570182015	6		382	3357	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858393	27858393	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	720	264	1	ENST00000359303.2:c.178G>T	p.Glu60Ter	p.E60*	ENST00000359303	NM_003535.2	60	Gag/Tag	1/1	0.758683558049449	5	FACETS	1	0.993	1	0.441	0.426	0.457	CLONAL	2	FALSE	0	0.759499570182015	5		265	1839	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0054298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	555	568	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.892	0.865	0.919	1	0.998	1	CLONAL	3	FALSE	1	0.485200710530533	2		568	855	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225060	NA	P-0054298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	360	17	0	ENST00000263967.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000263967	NM_006218.2	104	cCa/cTa	2/21	1	2	FACETS	0.956	0.912	1	1	0.996	1	CLONAL	2	FALSE	1	0.485200710530533	2		17	776	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211753	36211753	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	816	191	0	ENST00000222270.7:c.1504G>T	p.Ala502Ser	p.A502S	ENST00000222270	NM_014727.1	502	Gcc/Tcc	3/37	0.126940838958367	0	FACETS	0.847	0.831	0.863			1	INDETERMINATE	2	FALSE	0	0.485200710530533	0		191	1022	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390958	139390958	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	1039	802	0	ENST00000277541.6:c.7233del	p.Pro2412HisfsTer10	p.P2412Hfs*10	ENST00000277541	NM_017617.3	2411	ccA/cc	34/34	0.485200710530533	7	FACETS	0.963	0.944	0.981			1	CLONAL	7	FALSE	NA	0.485200710530533	7		802	1406	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922894	39922894	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	625	229	0	ENST00000378444.4:c.3814G>T	p.Glu1272Ter	p.E1272*	ENST00000378444	NM_001123385.1	1272	Gaa/Taa	8/15	0.485200710530533	1	FACETS	0.851	0.833	0.869	1	0.998	1	CLONAL	3	FALSE	0	0.485200710530533	1		229	764	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	493	375	0				ENST00000310581	NM_198253.2	-/1132			0.550601194297385	5	FACETS	1	0.972	1	1	0.972	1	CLONAL	4	TRUE	1	0.595454767170307	5		375	779	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0054299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	882	817	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.595454767170307	4	FACETS	0.982	0.961	1	0.982	0.961	1	CLONAL	4	TRUE	0	0.595454767170307	4		817	1203	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087458	27087458	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	903	541	0	ENST00000324856.7:c.2032C>T	p.Gln678Ter	p.Q678*	ENST00000324856	NM_006015.4	678	Cag/Tag	5/20	0.595454767170307	4	FACETS	0.892	0.866	0.917	1	0.998	1	CLONAL	3	TRUE	2	0.595454767170307	4		541	1809	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	224	90	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	0.595454767170307	2	FACETS	0.961	0.931	0.988	1	0.995	1	CLONAL	3	TRUE	0	0.595454767170307	2		90	261	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164458	36164458	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	547	143	0	ENST00000300305.3:c.1417G>C	p.Glu473Gln	p.E473Q	ENST00000300305		473	Gag/Cag	8/8	0.595454767170307	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	1	0.595454767170307	3		143	1005	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273184	55273184	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	798	394	0	ENST00000275493.2:c.3507C>A	p.Asn1169Lys	p.N1169K	ENST00000275493	NM_005228.3	1169	aaC/aaA	28/28	0.567201420755939	4	FACETS	0.991	0.963	1	0.991	0.963	1	CLONAL	3	TRUE	1	0.595454767170307	4		394	1438	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524927	8524927	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	307	144	0	ENST00000356435.5:c.677G>C	p.Arg226Thr	p.R226T	ENST00000356435		226	aGa/aCa	7/35	0.595454767170307	4	FACETS	0.9	0.857	0.944	1	0.994	1	CLONAL	3	TRUE	2	0.595454767170307	4		144	609	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937927	76937927	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	531	411	0	ENST00000373344.5:c.2821G>T	p.Glu941Ter	p.E941*	ENST00000373344	NM_000489.3	941	Gaa/Taa	9/35	0.595454767170307	5	FACETS	0.902	0.867	0.937	0.902	0.867	0.937	CLONAL	3	TRUE	2	0.595454767170307	5		411	1248	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	528	375	0				ENST00000310581	NM_198253.2	-/1132			0.680521031967708	4	FACETS	0.89	0.86	0.921	1	0.997	1	CLONAL	3	TRUE	2	0.750468719921156	4		375	922	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0054302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	337	76	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.87	0.837	0.903	1	0.996	1	CLONAL	2	TRUE	1	0.750468719921156	2		76	516	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007635	45007635	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	188	31	0	ENST00000558401.1:c.82C>T	p.Gln28Ter	p.Q28*	ENST00000558401	NM_004048.2	28	Cag/Tag	2/4	0.370087130538769	1	FACETS	0.976	0.913	1	1	0.994	1	CLONAL	2	TRUE	0	0.378347001779641	1		31	413	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	314	285	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.265888175363577	3	FACETS	0.951	0.904	0.998	0.951	0.904	0.998	CLONAL	3	TRUE	0	0.378347001779641	3		285	692	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220640	1220640	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690940	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	816	23	0	ENST00000326873.7:c.658C>T	p.Gln220Ter	p.Q220*	ENST00000326873	NM_000455.4	220	Cag/Tag	5/10	0.378347001779641	1	FACETS	1	0.993	1	1	0.998	1	CLONAL	2	TRUE	0	0.378347001779641	1		23	1623	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451792	29451792	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	331	43	0	ENST00000389048.3:c.2773G>T	p.Gly925Ter	p.G925*	ENST00000389048	NM_004304.4	925	Gga/Tga	16/29	0.364222155475403	1	FACETS	1	0.993	1	1	0.997	1	CLONAL	2	TRUE	0	0.378347001779641	1		43	585	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602332	10602332	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	969	184	0	ENST00000171111.5:c.1246A>T	p.Ile416Phe	p.I416F	ENST00000171111	NM_203500.1	416	Atc/Ttc	3/6	0.378347001779641	1	FACETS	0.844	0.823	0.864	1	0.999	1	CLONAL	3	TRUE	0	0.378347001779641	1		184	1641	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604745	48604745	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	334	108	0	ENST00000342988.3:c.1567T>C	p.Cys523Arg	p.C523R	ENST00000342988	NM_005359.5	523	Tgc/Cgc	12/12	0.344997071472993	1	FACETS	1	0.983	1	1	0.997	1	CLONAL	2	TRUE	0	0.378347001779641	1		108	673	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818336	170818336	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	397	80	0	ENST00000296930.5:c.166G>C	p.Glu56Gln	p.E56Q	ENST00000296930	NM_002520.6	56	Gag/Cag	3/11	0.344997071472993	1	FACETS	0.993	0.949	1	1	0.997	1	CLONAL	2	TRUE	0	0.378347001779641	1		80	857	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779313	3779313	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	642	68	0	ENST00000262367.5:c.5735C>T	p.Ser1912Leu	p.S1912L	ENST00000262367	NM_004380.2	1912	tCa/tTa	31/31	1	2	FACETS	0.855	0.826	0.884	1	0.998	1	CLONAL	3	TRUE	1	0.378347001779641	2		68	1323	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459846	149459846	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	793	167	1	ENST00000286301.3:c.361C>A	p.Gln121Lys	p.Q121K	ENST00000286301	NM_005211.3	121	Cag/Aag	4/22	0.378347001779641	1	FACETS	1	0.997	1	1	0.998	1	CLONAL	2	TRUE	0	0.378347001779641	1		168	1400	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670777	134670777	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	457	79	0	ENST00000398015.3:c.688G>T	p.Glu230Ter	p.E230*	ENST00000398015	NM_004441.4	230	Gag/Tag	3/16	1	2	FACETS	0.879	0.844	0.914	1	0.998	1	CLONAL	3	TRUE	1	0.378347001779641	2		79	916	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261682	16261682	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	480	77	0	ENST00000375759.3:c.8947A>G	p.Thr2983Ala	p.T2983A	ENST00000375759	NM_015001.2	2983	Acg/Gcg	11/15	1	2	FACETS	0.878	0.844	0.912	1	0.998	1	CLONAL	3	TRUE	1	0.378347001779641	2		77	963	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510115	120510115	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	334	80	0	ENST00000256646.2:c.1394G>T	p.Cys465Phe	p.C465F	ENST00000256646	NM_024408.3	465	tGc/tTc	8/34	1	2	FACETS	1	0.991	1	1	0.997	1	CLONAL	2	TRUE	1	0.378347001779641	2		80	758	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518074	69518074	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	741	143	0	ENST00000294312.3:c.291C>A	p.Ser97Arg	p.S97R	ENST00000294312	NM_005117.2	97	agC/agA	2/3	1	2	FACETS	0.912	0.884	0.94	1	0.998	1	CLONAL	3	TRUE	1	0.378347001779641	2		143	1432	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641540	18641540	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	265	161	1	ENST00000266497.5:c.2539T>A	p.Ser847Thr	p.S847T	ENST00000266497		847	Tct/Act	17/31	0.265888175363577	3	FACETS	0.995	0.943	1	0.995	0.943	1	CLONAL	3	TRUE	0	0.378347001779641	3		162	558	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225988	133225988	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1233392878	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	763	311	0	ENST00000320574.5:c.3909G>T	p.Arg1303Ser	p.R1303S	ENST00000320574	NM_006231.2	1303	agG/agT	31/49	0.378347001779641	2	FACETS	1	0.993	1	1	0.998	1	CLONAL	3	TRUE	0	0.378347001779641	2		311	1267	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954239	32954239	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs80359184	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	375	135	0	ENST00000380152.3:c.9213G>T	p.Glu3071Asp	p.E3071D	ENST00000380152		3071	gaG/gaT	24/27	0.344997071472993	1	FACETS	0.962	0.919	1	1	0.997	1	CLONAL	2	TRUE	0	0.378347001779641	1		135	835	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641053	23641053	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	576	165	0	ENST00000261584.4:c.2422G>T	p.Gly808Ter	p.G808*	ENST00000261584	NM_024675.3	808	Gga/Tga	5/13	1	2	FACETS	1	0.995	1	1	0.998	1	CLONAL	2	TRUE	1	0.378347001779641	2		165	1271	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645319	67645319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	468	61	0	ENST00000264010.4:c.584C>T	p.Pro195Leu	p.P195L	ENST00000264010	NM_006565.3	195	cCa/cTa	3/12	1	2	FACETS	1	0.994	1	1	0.997	1	CLONAL	2	TRUE	1	0.378347001779641	2		61	1040	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350272	89350272	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1298734986	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	739	152	2	ENST00000301030.4:c.2678G>T	p.Arg893Leu	p.R893L	ENST00000301030	NM_001256183.1	893	cGg/cTg	9/13	1	2	FACETS	0.892	0.864	0.92	1	0.998	1	CLONAL	3	TRUE	1	0.378347001779641	2		154	1460	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16056694	16056694	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	211	78	0	ENST00000268712.3:c.748G>T	p.Ala250Ser	p.A250S	ENST00000268712	NM_006311.3	250	Gct/Tct	7/46	1	2	FACETS	0.962	0.899	1	1	0.994	1	CLONAL	2	TRUE	1	0.378347001779641	2		78	580	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627478	37627478	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	346	109	0	ENST00000447079.4:c.1393G>A	p.Val465Ile	p.V465I	ENST00000447079	NM_015083.1	465	Gta/Ata	2/14	1	2	FACETS	1	0.985	1	1	0.996	1	CLONAL	2	TRUE	1	0.378347001779641	2		109	845	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441440	40441440	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	476	109	1	ENST00000345506.4:c.11G>T	p.Trp4Leu	p.W4L	ENST00000345506	NM_003152.3	4	tGg/tTg	3/20	1	2	FACETS	0.854	0.821	0.888	1	0.998	1	CLONAL	3	TRUE	1	0.378347001779641	2		110	982	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740896	58740896	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	297	74	0	ENST00000305921.3:c.1801A>G	p.Thr601Ala	p.T601A	ENST00000305921	NM_003620.3	601	Act/Gct	6/6	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.378347001779641	2		74	670	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212442	5212442	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	783	143	0	ENST00000357368.4:c.4675G>T	p.Gly1559Cys	p.G1559C	ENST00000357368	NM_002850.3	1559	Ggc/Tgc	31/38	0.378347001779641	1	FACETS	0.866	0.842	0.889	1	0.998	1	CLONAL	3	TRUE	0	0.378347001779641	1		143	1292	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218497	5218497	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	670	168	1	ENST00000357368.4:c.3982G>T	p.Ala1328Ser	p.A1328S	ENST00000357368	NM_002850.3	1328	Gcc/Tcc	25/38	0.378347001779641	1	FACETS	1	0.996	1	1	0.998	1	CLONAL	2	TRUE	0	0.378347001779641	1		169	1192	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469612	25469612	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	675	158	0	ENST00000264709.3:c.1156G>T	p.Val386Leu	p.V386L	ENST00000264709	NM_175629.2	386	Gtg/Ttg	10/23	0.364222155475403	1	FACETS	1	0.996	1	1	0.998	1	CLONAL	2	TRUE	0	0.378347001779641	1		158	1209	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455169	29455169	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	518	118	0	ENST00000389048.3:c.2632+1G>A		p.X878_splice	ENST00000389048	NM_004304.4	878			0.364222155475403	1	FACETS	1	0.996	1	1	0.998	1	CLONAL	2	TRUE	0	0.378347001779641	1		118	891	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278331	39278331	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	486	169	1	ENST00000402219.2:c.818G>T	p.Gly273Val	p.G273V	ENST00000402219	NM_005633.3	273	gGc/gTc	6/23	0.364222155475403	1	FACETS	1	0.99	1	1	0.997	1	CLONAL	2	TRUE	0	0.378347001779641	1		170	964	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172137	99172137	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	578	129	0	ENST00000074304.5:c.1703G>T	p.Ser568Ile	p.S568I	ENST00000074304	NM_001134224.1	568	aGc/aTc	17/26	1	2	FACETS	0.936	0.904	0.968	1	0.998	1	CLONAL	3	TRUE	1	0.378347001779641	2		129	1088	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158595032	158595032	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	343	92	0	ENST00000263640.3:c.1315C>T	p.Pro439Ser	p.P439S	ENST00000263640	NM_001105.4	439	Cca/Tca	10/11	1	2	FACETS	1	0.993	1	1	0.997	1	CLONAL	2	TRUE	1	0.378347001779641	2		92	745	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736104	204736104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	260	42	0	ENST00000302823.3:c.461C>T	p.Pro154Leu	p.P154L	ENST00000302823	NM_005214.4	154	cCa/cTa	3/4	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.378347001779641	2		42	574	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342916	225342916	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	277	76	0	ENST00000264414.4:c.2175+1G>T		p.X725_splice	ENST00000264414	NM_003590.4	725			1	2	FACETS	1	0.957	1	1	0.996	1	CLONAL	2	TRUE	1	0.378347001779641	2		76	721	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660310	227660310	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	505	104	0	ENST00000305123.5:c.3145G>T	p.Gly1049Trp	p.G1049W	ENST00000305123	NM_005544.2	1049	Ggg/Tgg	1/2	1	2	FACETS	0.941	0.906	0.975	1	0.998	1	CLONAL	3	TRUE	1	0.378347001779641	2		104	946	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147506	47147506	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1303122737	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	335	85	0	ENST00000409792.3:c.4820T>C	p.Met1607Thr	p.M1607T	ENST00000409792	NM_014159.6	1607	aTg/aCg	6/21	0.344997071472993	1	FACETS	1	0.985	1	1	0.997	1	CLONAL	2	TRUE	0	0.378347001779641	1		85	668	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162423	47162423	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs747580174	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	347	91	0	ENST00000409792.3:c.3703T>A	p.Leu1235Met	p.L1235M	ENST00000409792	NM_014159.6	1235	Ttg/Atg	3/21	0.344997071472993	1	FACETS	1	0.989	1	1	0.997	1	CLONAL	2	TRUE	0	0.378347001779641	1		91	671	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990420	69990420	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	201	85	0	ENST00000394351.3:c.379G>T	p.Glu127Ter	p.E127*	ENST00000394351	NM_000248.3	127	Gaa/Taa	4/9	0.344997071472993	1	FACETS	0.945	0.886	1	1	0.994	1	CLONAL	2	TRUE	0	0.378347001779641	1		85	456	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391120	89391120	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	481	128	2	ENST00000336596.2:c.1186G>T	p.Val396Leu	p.V396L	ENST00000336596	NM_005233.5	396	Gtg/Ttg	5/17	1	2	FACETS	0.842	0.809	0.875	1	0.998	1	CLONAL	3	TRUE	1	0.378347001779641	2		130	1007	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170002371	170002371	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	191	66	0	ENST00000295797.4:c.1190A>T	p.Tyr397Phe	p.Y397F	ENST00000295797	NM_002740.5	397	tAc/tTc	12/18	1	2	FACETS	1	0.952	1	1	0.994	1	CLONAL	2	TRUE	1	0.378347001779641	2		66	493	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295333	1295333	+	upstream_gene_variant	5'Flank	SNP	C	C	A	rs1290958599	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	357	78	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.993	1	1	0.997	1	CLONAL	2	TRUE	1	0.378347001779641	2		78	765	SUCCESS
APC	324	MSKCC	GRCh37	5	112137003	112137003	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs772806807	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	273	94	0	ENST00000257430.4:c.757G>T	p.Gly253Cys	p.G253C	ENST00000257430	NM_000038.5	253	Ggc/Tgc	8/16	0.35006993380596	1	FACETS	0.995	0.943	1	1	0.996	1	CLONAL	2	TRUE	0	0.378347001779641	1		94	588	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020757	26020757	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	253	139	0	ENST00000357647.3:c.41del	p.Gly14AlafsTer23	p.G14Afs*23	ENST00000357647	NM_003529.2	14	Ggc/gc	1/1	0.378347001779641	3	FACETS	1	0.966	1	1	0.994	1	CLONAL	3	TRUE	1	0.378347001779641	3		139	516	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190381	32190381	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	682	280	0	ENST00000375023.3:c.358G>T	p.Asp120Tyr	p.D120Y	ENST00000375023	NM_004557.3	120	Gac/Tac	3/30	0.378347001779641	3	FACETS	0.998	0.965	1	1	0.997	1	CLONAL	3	TRUE	1	0.378347001779641	3		280	1432	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372731	81372731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	242	58	0	ENST00000222390.5:c.803G>A	p.Arg268Lys	p.R268K	ENST00000222390	NM_000601.4	268	aGg/aAg	7/18	1	2	FACETS	1	0.971	1	1	0.995	1	CLONAL	2	TRUE	1	0.378347001779641	2		58	609	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128848659	128848659	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	529	92	0	ENST00000249373.3:c.1324G>C	p.Ala442Pro	p.A442P	ENST00000249373	NM_005631.4	442	Gcc/Ccc	7/12	1	2	FACETS	1	0.993	1	1	0.998	1	CLONAL	2	TRUE	1	0.378347001779641	2		92	1219	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891527	151891527	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	264	93	0	ENST00000262189.6:c.4505A>T	p.Asp1502Val	p.D1502V	ENST00000262189	NM_170606.2	1502	gAt/gTt	29/59	1	2	FACETS	1	0.979	1	1	0.996	1	CLONAL	2	TRUE	1	0.378347001779641	2		93	648	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345752	152345752	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	150	49	0	ENST00000359321.1:c.818G>C	p.Gly273Ala	p.G273A	ENST00000359321	NM_005431.1	273	gGa/gCa	3/3	1	2	FACETS	0.937	0.865	1	1	0.992	1	CLONAL	2	TRUE	1	0.378347001779641	2		49	423	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021661	69021661	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	303	96	0	ENST00000288368.4:c.2949C>G	p.Ser983Arg	p.S983R	ENST00000288368	NM_024870.2	983	agC/agG	25/40	1	2	FACETS	1	0.992	1	1	0.996	1	CLONAL	2	TRUE	1	0.378347001779641	2		96	653	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028026	69028026	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	315	51	0	ENST00000288368.4:c.3185G>C	p.Arg1062Pro	p.R1062P	ENST00000288368	NM_024870.2	1062	cGt/cCt	26/40	1	2	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	TRUE	1	0.378347001779641	2		51	704	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485872	8485872	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	320	79	2	ENST00000356435.5:c.2945C>A	p.Thr982Asn	p.T982N	ENST00000356435		982	aCt/aAt	17/35	0.378347001779641	1	FACETS	1	0.991	1	1	0.997	1	CLONAL	2	TRUE	0	0.378347001779641	1		81	599	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966704	36966704	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	352	84	0	ENST00000358127.4:c.622G>T	p.Val208Leu	p.V208L	ENST00000358127	NM_001280556.1	208	Gtg/Ttg	6/10	0.205738107783287	2	FACETS	1	0.991	1	1	0.991	1	INDETERMINATE	2	TRUE	0	0.378347001779641	2		84	798	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020669	37020669	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	348	190	0	ENST00000358127.4:c.176G>T	p.Arg59Leu	p.R59L	ENST00000358127	NM_001280556.1	59	cGg/cTg	2/10	0.205738107783287	2	FACETS	1	0.993	1	1	0.993	1	INDETERMINATE	2	TRUE	0	0.378347001779641	2		190	749	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760537	133760537	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	803	169	3	ENST00000318560.5:c.2860G>T	p.Gly954Cys	p.G954C	ENST00000318560	NM_005157.4	954	Ggc/Tgc	11/11	0.212783359783512	1	FACETS	1	0.996	1	1	0.998	1	INDETERMINATE	2	TRUE	0	0.378347001779641	1		172	1469	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044700	47044700	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	798	97	1	ENST00000377604.3:c.2101-1G>T		p.X701_splice	ENST00000377604	NM_001204468.1	701			0.212783359783512	1	FACETS	1	0.996	1	1	0.998	1	INDETERMINATE	2	TRUE	0	0.378347001779641	1		98	1493	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045494	47045494	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	550	90	0	ENST00000377604.3:c.2461C>A	p.Arg821Ser	p.R821S	ENST00000377604	NM_001204468.1	821	Cgc/Agc	22/24	0.212783359783512	1	FACETS	1	0.968	1	1	0.998	1	INDETERMINATE	2	TRUE	0	0.378347001779641	1		90	1172	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426428	47426428	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	660	107	0	ENST00000377045.4:c.771C>A	p.Ser257Arg	p.S257R	ENST00000377045	NM_001654.4	257	agC/agA	9/16	0.212783359783512	1	FACETS	1	0.986	1	1	0.998	1	INDETERMINATE	2	TRUE	0	0.378347001779641	1		107	1365	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239946	53239946	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	544	97	0	ENST00000375401.3:c.1495G>T	p.Val499Leu	p.V499L	ENST00000375401	NM_004187.3	499	Gtg/Ttg	11/26	0.212783359783512	1	FACETS	0.994	0.957	1	1	0.998	1	INDETERMINATE	2	TRUE	0	0.378347001779641	1		97	1173	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357755	70357755	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	656	115	0	ENST00000374080.3:c.6006G>T	p.Gln2002His	p.Q2002H	ENST00000374080		2002	caG/caT	41/45	0.212783359783512	1	FACETS	1	0.988	1	1	0.998	1	INDETERMINATE	2	TRUE	0	0.378347001779641	1		115	1342	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575491	64575492	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	A	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	593	79	0	ENST00000312049.6:c.525_526delinsT	p.Ala176ProfsTer9	p.A176Pfs*9	ENST00000312049	NM_130799.2	175	ctCGcc/ctTcc	3/10	1	2	FACETS	1	0.995	1	1	0.998	1	CLONAL	2	TRUE	1	0.378347001779641	2		79	1293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578465	7578466	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	A	novel	NA	P-0054303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	848	189	0	ENST00000269305.4:c.464_465delinsT	p.Thr155IlefsTer15	p.T155Ifs*15	ENST00000269305	NM_001126112.2	155	aCC/aT	5/11	0.288372350045197	1	FACETS	1	0.996	1	1	0.998	1	CLONAL	2	TRUE	0	0.378347001779641	1		189	1583	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	421	375	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	1.1	2		375	679	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0054304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	277	76	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.999	0.951	1	0.999	0.951	1	CLONAL	1	TRUE	1	1.1	2		76	504	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599938	28599938	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148305939	NA	P-0054305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	888	63	1	ENST00000253063.3:c.820C>T	p.Arg274Trp	p.R274W	ENST00000253063	NM_031459.4	274	Cgg/Tgg	6/10	1	2	FACETS	0.978	0.954	1	0.978	0.954	1	CLONAL	1	TRUE	1	1.29	2		64	1408	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184665	11184665	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	457	28	0	ENST00000361445.4:c.6552C>A	p.Phe2184Leu	p.F2184L	ENST00000361445	NM_004958.3	2184	ttC/ttA	47/58	1	2	FACETS	0.868	0.836	0.9	0.868	0.836	0.9	CLONAL	1	TRUE	1	1.29	2		28	816	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435461	49435461	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	910	65	1	ENST00000301067.7:c.6211C>A	p.His2071Asn	p.H2071N	ENST00000301067	NM_003482.3	2071	Cac/Aac	30/54	0.280909399656404	3	FACETS	0.775	0.756	0.795	0.775	0.756	0.795	INDETERMINATE	2	TRUE	1	1.29	3		66	1497	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137459	202137459	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	455	18	0	ENST00000358485.4:c.688del	p.Leu230CysfsTer2	p.L230Cfs*2	ENST00000358485	NM_001080125.1	229	agC/ag	4/9	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	1.29	2		18	679	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188218	10188219	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0054305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	682	31	1	ENST00000256474.2:c.361_362delinsTT	p.Asp121Phe	p.D121F	ENST00000256474	NM_000551.3	121	GAt/TTt	2/3	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	1.29	2		32	1036	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247171	153247171	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	305	19	0	ENST00000281708.4:c.1631T>C	p.Val544Ala	p.V544A	ENST00000281708	NM_033632.3	544	gTc/gCc	10/12	0.121496816164456	3	FACETS	0.864	0.83	0.897	0.864	0.83	0.897	INDETERMINATE	2	TRUE	1	1.29	3		19	450	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101501	27101501	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1463725053	NA	P-0054306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	1002	492	0	ENST00000324856.7:c.4783A>G	p.Met1595Val	p.M1595V	ENST00000324856	NM_006015.4	1595	Atg/Gtg	18/20	1	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	1	0.835620192815893	2		492	1649	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0054307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	1267	443	1	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.565240715772476	2	FACETS	0.873	0.86	0.887	1	0.999	1	CLONAL	3	TRUE	0	0.611332605273749	2		444	1582	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109992	115109992	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	977	135	0	ENST00000257566.3:c.1886T>A	p.Leu629His	p.L629H	ENST00000257566	NM_016569.3	629	cTc/cAc	8/8	1	2	FACETS	1	0.998	1	1	0.999	1	CLONAL	2	TRUE	1	0.611332605273749	2		135	1379	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0054308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	627	568	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.704794705959539	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.722286182222339	2		568	703	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627281	86627281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	297	176	1	ENST00000274376.6:c.656C>T	p.Ser219Leu	p.S219L	ENST00000274376	NM_002890.2	219	tCa/tTa	2/25	0.635923781280353	4	FACETS	0.913	0.881	0.943	0.913	0.881	0.943	CLONAL	4	TRUE	0	0.722286182222339	4		177	388	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388054	31388054	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs576798456	NA	P-0054309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	402	14	0	ENST00000328111.2:c.1855G>A	p.Glu619Lys	p.E619K	ENST00000328111	NM_006892.3	619	Gag/Aag	17/23	0.332970917541765	4	FACETS	1	0.974	1	1	0.997	1	INDETERMINATE	3	TRUE	2	0.79113239339124	4		14	600	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061851	38061851	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	1292	716	0	ENST00000250448.2:c.138del	p.Tyr47ThrfsTer2	p.Y47Tfs*2	ENST00000250448	NM_004496.3	46	acC/ac	2/2	0.236816208987481	6	FACETS	0.969	0.948	0.989	1	0.998	1	INDETERMINATE	4	TRUE	3	0.79113239339124	6		716	2177	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376154	225376162	+	inframe_deletion	In_Frame_Del	DEL	TCCCTTTCA	TCCCTTTCA	-	novel	NA	P-0054309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	667	253	0	ENST00000264414.4:c.792_800del	p.Glu265_Glu267del	p.E265_E267del	ENST00000264414	NM_003590.4	264	gtTGAAAGGGAa/gta	6/16	0.79113239339124	3	FACETS	0.962	0.943	0.981	1	0.998	1	CLONAL	3	TRUE	1	0.79113239339124	3		253	815	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	726	455	1				ENST00000310581	NM_198253.2	-/1132			0.137980977167589	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.797858857067332	0		456	878	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	322	169	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.798	0.765	0.829	1	0.996	1	SUBCLONAL	2	TRUE	1	0.797858857067332	2		169	506	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541507	187541507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758885671	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	493	47	0	ENST00000441802.2:c.6233C>T	p.Ala2078Val	p.A2078V	ENST00000441802	NM_005245.3	2078	gCg/gTg	10/27	1	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	1	0.797858857067332	2		47	831	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376260	15376260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	921	44	0	ENST00000263377.2:c.754C>T	p.Pro252Ser	p.P252S	ENST00000263377	NM_058243.2	252	Cca/Tca	5/20	0.140014076122612	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.797858857067332	0		44	1284	SUCCESS
AR	367	MSKCC	GRCh37	X	66942785	66942785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886041132	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	623	62	1	ENST00000374690.3:c.2566C>T	p.Arg856Cys	p.R856C	ENST00000374690	NM_000044.3	856	Cgc/Tgc	7/8	0.389178718430707	1	FACETS	0.979	0.951	1	0.979	0.951	1	INDETERMINATE	1	TRUE	0	0.797858857067332	1		63	959	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	426	57	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.797858857067332	2		57	912	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	834	8	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	0.797858857067332	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.797858857067332	1		8	1220	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566418	139566418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374930413	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	1560	108	0	ENST00000308874.7:c.677C>T	p.Ser226Leu	p.S226L	ENST00000308874		226	tCg/tTg	9/10	1	2	FACETS	0.957	0.942	0.971	1	0.999	1	CLONAL	2	TRUE	1	0.797858857067332	2		108	2044	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794714	42794714	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	1587	286	1	ENST00000575354.2:c.1795del	p.Arg599GlyfsTer129	p.R599Gfs*129	ENST00000575354	NM_015125.3	598	ttC/tt	10/20	0.797858857067332	1	FACETS	1	0.999	1	1	0.999	1	CLONAL	1	TRUE	0	0.797858857067332	1		287	1757	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58725388	58725388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	598	76	1	ENST00000305921.3:c.962C>T	p.Pro321Leu	p.P321L	ENST00000305921	NM_003620.3	321	cCa/cTa	4/6	0.302651022260767	2	FACETS	1	0.997	1	0.712	0.689	0.735	INDETERMINATE	1	TRUE	0	0.797858857067332	2		77	1053	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488763	212488763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	533	178	0	ENST00000342788.4:c.2086G>A	p.Glu696Lys	p.E696K	ENST00000342788	NM_005235.2	696	Gaa/Aaa	18/28	1	2	FACETS	0.759	0.734	0.784	1	0.997	1	SUBCLONAL	2	TRUE	1	0.797858857067332	2		178	880	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056703	180056703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	1313	71	0	ENST00000261937.6:c.809G>A	p.Gly270Glu	p.G270E	ENST00000261937	NM_182925.4	270	gGg/gAg	6/30	NA	2	FACETS	0.887	0.87	0.903			1	INDETERMINATE	2	TRUE	NA	0.797858857067332	2		71	1856	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873836	151873836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	546	69	0	ENST00000262189.6:c.8702C>T	p.Pro2901Leu	p.P2901L	ENST00000262189	NM_170606.2	2901	cCt/cTt	38/59	0.349448091106213	3	FACETS	0.965	0.932	0.998	0.965	0.932	0.998	INDETERMINATE	2	TRUE	1	0.797858857067332	3		69	992	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633417	3633417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	1707	139	1	ENST00000294008.3:c.4834G>A	p.Asp1612Asn	p.D1612N	ENST00000294008	NM_032444.2	1612	Gac/Aac	14/15	0.105656029194977	3	FACETS	1	0.998	1	0.772	0.759	0.786	INDETERMINATE	2	TRUE	0	0.797858857067332	3		140	2583	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106852	27106852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	1101	333	1	ENST00000324856.7:c.6463C>T	p.Leu2155Phe	p.L2155F	ENST00000324856	NM_006015.4	2155	Ctc/Ttc	20/20	0.797858857067332	1	FACETS	1	0.999	1	1	0.999	1	CLONAL	1	TRUE	0	0.797858857067332	1		334	1223	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725037	162725037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1386838528	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	607	79	1	ENST00000367921.3:c.509C>T	p.Thr170Ile	p.T170I	ENST00000367921	NM_006182.2	170	aCc/aTc	6/18	0.348033060653763	3	FACETS	0.976	0.945	1	0.976	0.945	1	INDETERMINATE	2	TRUE	1	0.797858857067332	3		80	1090	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104377076	104377076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	812	88	0	ENST00000369902.3:c.1187C>T	p.Thr396Ile	p.T396I	ENST00000369902	NM_016169.3	396	aCa/aTa	10/12	1	2	FACETS	0.836	0.816	0.857	1	0.998	1	CLONAL	2	TRUE	1	0.797858857067332	2		88	1217	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944561	71944561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	959	143	0	ENST00000298229.2:c.2117C>T	p.Ser706Phe	p.S706F	ENST00000298229	NM_001567.3	706	tCt/tTt	18/28	0.105656029194977	3	FACETS	1	0.998	1	0.802	0.784	0.819	INDETERMINATE	2	TRUE	0	0.797858857067332	3		143	1398	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347698	118347698	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1135401764	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	412	85	0	ENST00000534358.1:c.3334+1G>A		p.X1112_splice	ENST00000534358	NM_005933.3	1112			0.349448091106213	3	FACETS	1	0.974	1	1	0.974	1	INDETERMINATE	2	TRUE	1	0.797858857067332	3		85	711	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373685	118373685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	588	72	0	ENST00000534358.1:c.7078G>A	p.Val2360Met	p.V2360M	ENST00000534358	NM_005933.3	2360	Gtg/Atg	27/36	0.349448091106213	3	FACETS	1	0.969	1	1	0.969	1	INDETERMINATE	2	TRUE	1	0.797858857067332	3		72	1029	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125525200	125525200	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	452	128	0	ENST00000428830.2:c.1416G>A	p.Trp472Ter	p.W472*	ENST00000428830	NM_001114121.2	472	tgG/tgA	13/14	0.349448091106213	3	FACETS	0.906	0.87	0.941	0.906	0.87	0.941	INDETERMINATE	2	TRUE	1	0.797858857067332	3		128	875	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402000	402000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	547	74	0	ENST00000399788.2:c.4791G>A	p.Trp1597Ter	p.W1597*	ENST00000399788	NM_001042603.1	1597	tgG/tgA	27/28	1	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	1	0.797858857067332	2		74	1000	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427527	427527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369093435	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	607	89	0	ENST00000399788.2:c.2642G>A	p.Gly881Asp	p.G881D	ENST00000399788	NM_001042603.1	881	gGc/gAc	19/28	1	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	1	0.797858857067332	2		89	1098	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111855993	111855993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758110085	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	1173	122	0	ENST00000341259.2:c.44C>T	p.Pro15Leu	p.P15L	ENST00000341259	NM_005475.2	15	cCc/cTc	2/8	1	2	FACETS	0.84	0.823	0.857	1	0.999	1	CLONAL	2	TRUE	1	0.797858857067332	2		122	1750	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536833	120536833	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	774	80	0	ENST00000229340.5:c.352+1G>A		p.X118_splice	ENST00000229340	NM_006861.6	118			1	2	FACETS	0.841	0.82	0.862	1	0.998	1	CLONAL	2	TRUE	1	0.797858857067332	2		80	1153	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599052	28599052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	481	73	0	ENST00000241453.7:c.2236C>T	p.His746Tyr	p.H746Y	ENST00000241453	NM_004119.2	746	Cac/Tac	18/24	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.797858857067332	2		73	1056	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972618	32972618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	401	65	0	ENST00000380152.3:c.9968C>T	p.Thr3323Ile	p.T3323I	ENST00000380152		3323	aCt/aTt	27/27	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.797858857067332	2		65	816	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881531	48881531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	273	59	0	ENST00000267163.4:c.253G>A	p.Asp85Asn	p.D85N	ENST00000267163	NM_000321.2	85	Gat/Aat	2/27	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.797858857067332	2		59	591	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103513941	103513941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	367	63	0	ENST00000355739.4:c.757G>A	p.Glu253Lys	p.E253K	ENST00000355739	NM_000123.3	253	Gaa/Aaa	7/15	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.797858857067332	2		63	751	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518017	103518017	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	239	18	0	ENST00000355739.4:c.1955G>A	p.Gly652Glu	p.G652E	ENST00000355739	NM_000123.3	652	gGa/gAa	9/15	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.797858857067332	2		18	433	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358373	91358373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	641	88	0	ENST00000355112.3:c.4118C>T	p.Ser1373Phe	p.S1373F	ENST00000355112	NM_000057.2	1373	tCc/tTc	22/22	1	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	1	0.797858857067332	2		88	1119	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127627	2127627	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769199118	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	1173	100	0	ENST00000219476.3:c.2866G>A	p.Gly956Ser	p.G956S	ENST00000219476	NM_000548.3	956	Ggc/Agc	26/42	0.105656029194977	3	FACETS	1	0.998	1	0.787	0.771	0.803	INDETERMINATE	2	TRUE	0	0.797858857067332	3		100	1742	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129315	2129315	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	1400	194	1	ENST00000219476.3:c.3170C>T	p.Thr1057Ile	p.T1057I	ENST00000219476	NM_000548.3	1057	aCc/aTc	28/42	0.105656029194977	3	FACETS	1	0.998	1	0.795	0.78	0.81	INDETERMINATE	2	TRUE	0	0.797858857067332	3		195	2058	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649092	37649153	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTGGAGAAGGAACCTATGGCCAAGTATATAAAGCCAAGGACAAAGACACAGGTAAATATTG	ATTGGAGAAGGAACCTATGGCCAAGTATATAAAGCCAAGGACAAAGACACAGGTAAATATTG	-	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	477	122	0	ENST00000447079.4:c.2197_2248+10del		p.X733_splice	ENST00000447079	NM_015083.1	733		4/14	0.302651022260767	2	FACETS	0.882	0.855	0.908	0.882	0.855	0.908	INDETERMINATE	2	TRUE	0	0.797858857067332	2		122	678	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453349	40453349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778505142	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	1414	79	2	ENST00000345506.4:c.1046C>T	p.Ala349Val	p.A349V	ENST00000345506	NM_003152.3	349	gCa/gTa	10/20	0.302651022260767	2	FACETS	0.849	0.833	0.864	0.849	0.833	0.864	INDETERMINATE	2	TRUE	0	0.797858857067332	2		81	2088	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41197769	41197769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567756588	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	1116	102	0	ENST00000357654.3:c.5518G>A	p.Asp1840Asn	p.D1840N	ENST00000357654	NM_007294.3	1840	Gac/Aac	23/23	0.302651022260767	2	FACETS	0.82	0.803	0.838	0.82	0.803	0.838	INDETERMINATE	2	TRUE	0	0.797858857067332	2		102	1705	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619331	1619331	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756593901	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	1789	125	0	ENST00000344749.5:c.1310G>A	p.Gly437Glu	p.G437E	ENST00000344749	NM_001136139.2	437	gGg/gAg	15/19	0.140014076122612	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.797858857067332	0		125	2395	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7128926	7128926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	477	61	0	ENST00000302850.5:c.2882C>T	p.Pro961Leu	p.P961L	ENST00000302850	NM_000208.2	961	cCc/cTc	15/22	0.140014076122612	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.797858857067332	0		61	910	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855520	45855520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	1588	103	0	ENST00000391945.4:c.2137G>A	p.Gly713Ser	p.G713S	ENST00000391945	NM_000400.3	713	Ggt/Agt	22/23	0.797858857067332	1	FACETS	1	0.999	1	1	0.999	1	CLONAL	1	TRUE	0	0.797858857067332	1		103	1947	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609115	46609115	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1370480723	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	807	75	0	ENST00000263734.3:c.2174G>A	p.Gly725Glu	p.G725E	ENST00000263734	NM_001430.4	725	gGg/gAg	14/16	1	2	FACETS	0.849	0.828	0.869	1	0.998	1	CLONAL	2	TRUE	1	0.797858857067332	2		75	1192	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033950	48033950	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	394	73	0	ENST00000234420.5:c.4034T>C	p.Val1345Ala	p.V1345A	ENST00000234420	NM_000179.2	1345	gTa/gCa	10/10	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.797858857067332	2		73	830	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149053	61149053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	552	57	0	ENST00000295025.8:c.1243G>A	p.Val415Met	p.V415M	ENST00000295025	NM_002908.2	415	Gtg/Atg	11/11	1	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	1	0.797858857067332	2		57	930	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657049	45657049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	592	58	0	ENST00000407780.3:c.107G>A	p.Ser36Asn	p.S36N	ENST00000407780	NM_001283052.1	36	aGc/aAc	3/7	1	2	FACETS	0.833	0.809	0.856	1	0.998	1	CLONAL	2	TRUE	1	0.797858857067332	2		58	891	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103762	47103762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	719	79	1	ENST00000409792.3:c.6184G>A	p.Glu2062Lys	p.E2062K	ENST00000409792	NM_014159.6	2062	Gag/Aag	14/21	1	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	1	0.797858857067332	2		80	1222	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162705	47162705	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	429	77	0	ENST00000409792.3:c.3421C>T	p.Pro1141Ser	p.P1141S	ENST00000409792	NM_014159.6	1141	Ccg/Tcg	3/21	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.797858857067332	2		77	830	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928460	69928460	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	993	142	1	ENST00000352241.4:c.280C>T	p.Gln94Ter	p.Q94*	ENST00000352241	NM_198159.2	94	Cag/Tag	2/10	1	2	FACETS	0.774	0.756	0.793	1	0.998	1	SUBCLONAL	2	TRUE	1	0.797858857067332	2		143	1607	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1952805	1952805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	703	77	0	ENST00000382891.5:c.1888G>A	p.Asp630Asn	p.D630N	ENST00000382891	NM_133335.3	630	Gac/Aac	10/22	1	2	FACETS	0.802	0.78	0.823	1	0.998	1	CLONAL	2	TRUE	1	0.797858857067332	2		77	1099	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950199	38950199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	518	96	0	ENST00000357387.3:c.3751G>A	p.Asp1251Asn	p.D1251N	ENST00000357387	NM_152756.3	1251	Gac/Aac	31/38	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.797858857067332	2		96	1002	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645165	86645165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	295	38	0	ENST00000274376.6:c.1237G>A	p.Gly413Ser	p.G413S	ENST00000274376	NM_002890.2	413	Ggc/Agc	8/25	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.797858857067332	2		38	583	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522537	176522537	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	1502	94	1	ENST00000292408.4:c.1634C>T	p.Pro545Leu	p.P545L	ENST00000292408	NM_213647.1	545	cCc/cTc	13/18	1	2	FACETS	0.925	0.91	0.939	1	0.999	1	CLONAL	2	TRUE	1	0.797858857067332	2		95	2036	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675912	30675912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	1104	125	0	ENST00000376406.3:c.2444G>A	p.Gly815Asp	p.G815D	ENST00000376406	NM_014641.2	815	gGt/gAt	8/15	1	2	FACETS	0.791	0.774	0.809	1	0.998	1	SUBCLONAL	2	TRUE	1	0.797858857067332	2		125	1749	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140915	37140915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1480836301	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	758	49	0	ENST00000373509.5:c.751G>A	p.Gly251Ser	p.G251S	ENST00000373509	NM_002648.3	251	Ggc/Agc	5/6	1	2	FACETS	0.791	0.77	0.812	1	0.998	1	SUBCLONAL	2	TRUE	1	0.797858857067332	2		49	1201	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679132	117679132	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	355	65	1	ENST00000368508.3:c.3689C>T	p.Thr1230Ile	p.T1230I	ENST00000368508	NM_002944.2	1230	aCa/aTa	24/43	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.797858857067332	2		66	700	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519205	137519205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	316	43	0	ENST00000367739.4:c.1433G>A	p.Gly478Asp	p.G478D	ENST00000367739	NM_000416.2	478	gGt/gAt	7/7	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.797858857067332	2		43	585	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509886	106509886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	737	89	0	ENST00000359195.3:c.1880C>T	p.Thr627Ile	p.T627I	ENST00000359195	NM_002649.2	627	aCa/aTa	2/11	0.349448091106213	3	FACETS	1	0.972	1	1	0.972	1	INDETERMINATE	2	TRUE	1	0.797858857067332	3		89	1291	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188100	151188100	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	366	74	0	ENST00000262187.5:c.53G>A	p.Gly18Glu	p.G18E	ENST00000262187	NM_005614.3	18	gGg/gAg	2/8	0.349448091106213	3	FACETS	0.763	0.727	0.799	0.763	0.727	0.799	INDETERMINATE	2	TRUE	1	0.797858857067332	3		74	841	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104001	69104001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	465	97	0	ENST00000288368.4:c.4391C>T	p.Ser1464Phe	p.S1464F	ENST00000288368	NM_024870.2	1464	tCc/tTc	36/40	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.797858857067332	2		97	1028	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753178	128753178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	373	52	0	ENST00000377970.2:c.1339G>A	p.Glu447Lys	p.E447K	ENST00000377970	NM_002467.4	447	Gaa/Aaa	3/3	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.797858857067332	2		52	682	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637019	93637019	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	611	75	0	ENST00000375746.1:c.1069G>A	p.Glu357Lys	p.E357K	ENST00000375746	NM_001174167.1	357	Gag/Aag	9/14	1	2	FACETS	0.774	0.751	0.797	1	0.998	1	SUBCLONAL	2	TRUE	1	0.797858857067332	2		75	989	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787735	135787735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	571	80	0	ENST00000298552.3:c.847G>A	p.Ala283Thr	p.A283T	ENST00000298552	NM_001162426.1	283	Gcc/Acc	9/23	1	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	1	0.797858857067332	2		80	1038	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911519	39911519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775669177	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	861	86	0	ENST00000378444.4:c.5111G>A	p.Ser1704Asn	p.S1704N	ENST00000378444	NM_001123385.1	1704	aGt/aAt	15/15	0.389178718430707	1	FACETS	0.954	0.93	0.977	0.954	0.93	0.977	INDETERMINATE	1	TRUE	0	0.797858857067332	1		86	1360	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422637	47422637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	912	89	0	ENST00000377045.4:c.109G>A	p.Asp37Asn	p.D37N	ENST00000377045	NM_001654.4	37	Gat/Aat	3/16	0.389178718430707	1	FACETS	1	0.995	1	1	0.995	1	INDETERMINATE	1	TRUE	0	0.797858857067332	1		89	1295	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691039	NA	P-0054311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	736	496	0	ENST00000269305.4:c.919+1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.494553126866787	3	FACETS	0.884	0.862	0.906	1	0.997	1	CLONAL	4	TRUE	0	0.491367909462356	3		496	1055	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648328	206648328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782549877	NA	P-0054311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	693	227	0	ENST00000367120.3:c.349C>T	p.Arg117Cys	p.R117C	ENST00000367120	NM_014002.3	117	Cgc/Tgc	5/22	0.326550624049823	1	FACETS	0.967	0.94	0.994	1	0.998	1	CLONAL	2	TRUE	0	0.491367909462356	1		227	1100	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631671	90631671	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1241	741	103	0	ENST00000330062.3:c.598G>C	p.Asp200His	p.D200H	ENST00000330062	NM_002168.2	200	Gat/Cat	5/11	0.491367909462356	5	FACETS	0.881	0.851	0.912	0.881	0.851	0.912	CLONAL	3	TRUE	2	0.491367909462356	5		103	1982	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440125	99440125	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	314	265	0	ENST00000268035.6:c.1093C>G	p.Arg365Gly	p.R365G	ENST00000268035	NM_000875.3	365	Cga/Gga	4/21	0.491367909462356	5	FACETS	0.964	0.914	1	0.964	0.914	1	CLONAL	3	TRUE	2	0.491367909462356	5		265	768	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670505	246670505	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	544	446	0	ENST00000388985.4:c.15G>T	p.Lys5Asn	p.K5N	ENST00000388985		5	aaG/aaT	1/12	0.148512640297274	5	FACETS	1	0.991	1			1	INDETERMINATE	4	TRUE	NA	0.491367909462356	5		446	902	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279608	123279613	+	inframe_deletion	In_Frame_Del	DEL	TCTACG	TCTACG	-	novel	NA	P-0054311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	616	179	0	ENST00000358487.5:c.819_824del	p.Asp273_Val274del	p.D273_V274del	ENST00000358487	NM_000141.4	273	gaCGTAGAg/gag	7/18	1	2	FACETS	1	0.995	1	1	0.998	1	CLONAL	2	TRUE	1	0.491367909462356	2		179	1083	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362476	118362476	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	287	163	0	ENST00000534358.1:c.4837C>G	p.Leu1613Val	p.L1613V	ENST00000534358	NM_005933.3	1613	Cta/Gta	15/36	0.381166287904252	5	FACETS	1	0.967	1			1	CLONAL	3	TRUE	NA	0.491367909462356	5		163	658	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434429	121434429	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	961	143	0	ENST00000257555.6:c.1193A>G	p.Gln398Arg	p.Q398R	ENST00000257555		398	cAg/cGg	6/10	0.37921451014025	3	FACETS	0.855	0.832	0.879	1	0.998	1	CLONAL	3	TRUE	1	0.491367909462356	3		143	1899	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639506	3639506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371580654	NA	P-0054311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	972	425	0	ENST00000294008.3:c.4133C>T	p.Pro1378Leu	p.P1378L	ENST00000294008	NM_032444.2	1378	cCg/cTg	12/15	0.494553126866787	2	FACETS	0.96	0.94	0.98	1	0.998	1	CLONAL	3	TRUE	0	0.491367909462356	2		425	1374	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781778	3781778	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	501	216	0	ENST00000262367.5:c.4889A>T	p.Glu1630Val	p.E1630V	ENST00000262367	NM_004380.2	1630	gAg/gTg	29/31	0.494553126866787	2	FACETS	0.935	0.907	0.963	1	0.997	1	CLONAL	3	TRUE	0	0.491367909462356	2		216	727	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42384788	42384788	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	340	91	0	ENST00000221972.3:c.550G>T	p.Asp184Tyr	p.D184Y	ENST00000221972	NM_021601.3	184	Gat/Tat	4/5	0.494553126866787	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.491367909462356	3		91	704	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637391	47637392	+	missense_variant	Missense_Mutation	DNP	GT	GT	TA	novel	NA	P-0054311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	581	312	1	ENST00000233146.2:c.525_526delinsTA	p.Cys176Ser	p.C176S	ENST00000233146	NM_000251.2	175	ctGTgt/ctTAgt	3/16	0.340146478978787	4	FACETS	1	0.994	1	1	0.998	1	CLONAL	3	TRUE	2	0.491367909462356	4		313	1038	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933472	49933472	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	996	379	0	ENST00000296474.3:c.2718G>T	p.Gln906His	p.Q906H	ENST00000296474	NM_002447.2	906	caG/caT	11/20	0.470662526325294	2	FACETS	0.973	0.953	0.992	1	0.998	1	CLONAL	3	TRUE	0	0.491367909462356	2		379	1389	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921568	178921568	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	237	19	0	ENST00000263967.3:c.1050C>G	p.Asp350Glu	p.D350E	ENST00000263967	NM_006218.2	350	gaC/gaG	5/21	0.491367909462356	5	FACETS	0.858	0.806	0.911	0.858	0.806	0.911	CLONAL	3	TRUE	2	0.491367909462356	5		19	651	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772949	135772949	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	394	137	0	ENST00000298552.3:c.2674A>G	p.Arg892Gly	p.R892G	ENST00000298552	NM_001162426.1	892	Aga/Gga	21/23	0.49449778471311	2	FACETS	0.912	0.88	0.943	1	0.996	1	CLONAL	3	TRUE	0	0.491367909462356	2		137	586	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357603	70357603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	774	1024	0	ENST00000374080.3:c.5854G>A	p.Gly1952Arg	p.G1952R	ENST00000374080		1952	Gga/Aga	41/45	0.491367909462356	6	FACETS	0.934	0.908	0.96			1	CLONAL	5	TRUE	NA	0.491367909462356	6		1024	1337	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0054313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	646	603	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.565744598966754	4	FACETS	1	0.991	1	1	0.998	1	CLONAL	3	FALSE	2	0.565744598966754	4		603	1126	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0054313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	322	25	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	0.565744598966754	4	FACETS	1	0.987	1	1	0.996	1	CLONAL	3	FALSE	2	0.565744598966754	4		25	552	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916758	48916758	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	357	41	0	ENST00000267163.4:c.289del	p.Glu97AsnfsTer14	p.E97Nfs*14	ENST00000267163	NM_000321.2	96	aaG/aa	3/27	0.169456331329838	5	FACETS	0.955	0.916	0.993	1	0.995	1	INDETERMINATE	4	FALSE	2	0.565744598966754	5		41	611	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577529	7577529	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs730882027	NA	P-0054313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	791	69	0	ENST00000269305.4:c.752T>C	p.Ile251Thr	p.I251T	ENST00000269305	NM_001126112.2	251	aTc/aCc	7/11	1	2	FACETS	1	0.997	1	1	0.998	1	CLONAL	2	FALSE	1	0.565744598966754	2		69	1148	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845321	76845322	+	missense_variant	Missense_Mutation	DNP	TT	TT	GG	novel	NA	P-0054313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	346	15	0	ENST00000373344.5:c.6199_6200delinsCC	p.Lys2067Pro	p.K2067P	ENST00000373344	NM_000489.3	2067	AAa/CCa	27/35	1	2	FACETS	1	0.986	1	1	0.997	1	CLONAL	2	FALSE	1	0.565744598966754	2		15	575	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259975	16259975	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	765	61	0	ENST00000375759.3:c.7240G>T	p.Glu2414Ter	p.E2414*	ENST00000375759	NM_015001.2	2414	Gaa/Taa	11/15	0.373287829917983	3	FACETS	1	0.994	1	1	0.998	1	CLONAL	3	FALSE	1	0.565744598966754	3		61	1094	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953918	32953918	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	351	18	0	ENST00000380152.3:c.8985T>G	p.Asp2995Glu	p.D2995E	ENST00000380152		2995	gaT/gaG	23/27	0.169456331329838	5	FACETS	1	0.973	1	1	0.995	1	INDETERMINATE	4	FALSE	2	0.565744598966754	5		18	564	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953925	32953925	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1442009294	NA	P-0054313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	372	17	0	ENST00000380152.3:c.8992T>A	p.Ser2998Thr	p.S2998T	ENST00000380152		2998	Tct/Act	23/27	0.169456331329838	5	FACETS	1	0.978	1	1	0.996	1	INDETERMINATE	4	FALSE	2	0.565744598966754	5		17	594	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575209	48575209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767326	NA	P-0054314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	267	13	0	ENST00000342988.3:c.403C>T	p.Arg135Ter	p.R135*	ENST00000342988	NM_005359.5	135	Cga/Tga	3/12	0.775915156553775	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.775915156553775	1		13	421	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0054314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	418	69	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.519454441569456	3	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.775915156553775	3		69	704	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913399	NA	P-0054314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	385	82	0	ENST00000349496.5:c.100G>C	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Cga	3/15	0.775915156553775	3	FACETS	0.85	0.813	0.888	0.85	0.813	0.888	CLONAL	2	TRUE	1	0.775915156553775	3		82	810	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0054314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	771	305	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	1	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	1	0.775915156553775	2		305	1334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577109	7577109	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1064795369	NA	P-0054314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	909	349	0	ENST00000269305.4:c.829T>G	p.Cys277Gly	p.C277G	ENST00000269305	NM_001126112.2	277	Tgt/Ggt	8/11	1	2	FACETS	0.787	0.767	0.806	1	0.998	1	SUBCLONAL	2	TRUE	1	0.775915156553775	2		349	1489	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434507	140434507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1562931107	NA	P-0054314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	449	179	0	ENST00000288602.6:c.2191C>T	p.Pro731Ser	p.P731S	ENST00000288602	NM_004333.4	731	Ccc/Tcc	18/18	0.519454441569456	3	FACETS	0.949	0.913	0.986			1	CLONAL	2	TRUE	NA	0.775915156553775	3		179	846	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675305	241675305	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1558400504	NA	P-0054314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	466	53	0	ENST00000366560.3:c.517A>T	p.Ile173Leu	p.I173L	ENST00000366560	NM_000143.3	173	Ata/Tta	4/10	0.263211222178243	2	FACETS	1	0.996	1	0.715	0.688	0.741	INDETERMINATE	1	TRUE	0	0.775915156553775	2		53	840	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524731	103524731	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	301	63	0	ENST00000355739.4:c.2862T>G	p.Asp954Glu	p.D954E	ENST00000355739	NM_000123.3	954	gaT/gaG	13/15	0.149727083571386	4	FACETS	0.983	0.932	1	0.983	0.932	1	INDETERMINATE	2	TRUE	2	0.775915156553775	4		63	701	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670118	29670118	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	417	210	0	ENST00000356175.3:c.7091A>C	p.Asn2364Thr	p.N2364T	ENST00000356175	NM_000267.3	2364	aAc/aCc	47/57	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.775915156553775	2		210	724	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267895	46267895	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	597	254	0	ENST00000371998.3:c.2656G>T	p.Gly886Cys	p.G886C	ENST00000371998		886	Ggt/Tgt	14/23	0.498797645566055	3	FACETS	0.938	0.907	0.97	0.938	0.907	0.97	CLONAL	2	TRUE	1	0.775915156553775	3		254	1138	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186813	142186813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	281	108	0	ENST00000350721.4:c.6650G>A	p.Arg2217His	p.R2217H	ENST00000350721	NM_001184.3	2217	cGc/cAc	39/47	1	2	FACETS	0.801	0.766	0.836	1	0.996	1	CLONAL	2	TRUE	1	0.775915156553775	2		108	452	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162475124	162475124	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1554264900	NA	P-0054314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	407	145	0	ENST00000366898.1:c.617C>T	p.Ala206Val	p.A206V	ENST00000366898	NM_004562.2	206	gCa/gTa	5/12	1	2	FACETS	0.756	0.727	0.785	1	0.996	1	SUBCLONAL	2	TRUE	1	0.775915156553775	2		145	694	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872105	76872105	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	367	20	1	ENST00000373344.5:c.5542C>A	p.Gln1848Lys	p.Q1848K	ENST00000373344	NM_000489.3	1848	Cag/Aag	22/35	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.899079305145547	2		21	624	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577411	64577443	+	inframe_deletion	In_Frame_Del	DEL	GTTGGTAGGGATGACGCGGTTGACAGCCAGAAA	GTTGGTAGGGATGACGCGGTTGACAGCCAGAAA	-	novel	NA	P-0054316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	889	225	1	ENST00000312049.6:c.139_171del	p.Phe47_Asn57del	p.F47_N57del	ENST00000312049	NM_130799.2	47	TTTCTGGCTGTCAACCGCGTCATCCCTACCAAC/-	2/10	0.899079305145547	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.899079305145547	1		226	962	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0054317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	590	603	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.603879074716945	7	FACETS	1	0.995	1	1	0.995	1	CLONAL	6	TRUE	1	0.603879074716945	7		603	757	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578490	7578490	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1453167097	NA	P-0054317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	1209	179	0	ENST00000269305.4:c.440T>G	p.Val147Gly	p.V147G	ENST00000269305	NM_001126112.2	147	gTt/gGt	5/11	0.131493418670526	5	FACETS	0.969	0.959	0.979			1	INDETERMINATE	6	TRUE	NA	0.603879074716945	5		179	1312	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983926	2983926	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	946	62	0	ENST00000396946.4:c.604T>G	p.Tyr202Asp	p.Y202D	ENST00000396946	NM_032415.4	202	Tac/Gac	5/25	0.354546686090095	4	FACETS	0.954	0.934	0.974	1	0.999	1	INDETERMINATE	4	TRUE	2	0.603879074716945	4		62	1317	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889110	76889110	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	199	85	0	ENST00000373344.5:c.4900T>A	p.Trp1634Arg	p.W1634R	ENST00000373344	NM_000489.3	1634	Tgg/Agg	18/35	0.389107556682442	2	FACETS	0.981	0.951	1			1	CLONAL	3	TRUE	NA	0.603879074716945	2		85	224	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0054318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	879	289	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.483622733756375	2	FACETS	0.871	0.852	0.889	1	0.998	1	CLONAL	3	TRUE	0	0.557676914023357	2		289	1207	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132841	152132841	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	1102	314	1	ENST00000262189.6:c.31C>T	p.Gln11Ter	p.Q11*	ENST00000262189	NM_170606.2	11	Cag/Tag	1/59	1	2	FACETS	1	0.996	1	1	0.999	1	CLONAL	2	TRUE	1	0.557676914023357	2		315	1809	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568902	212568902	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	443	52	0	ENST00000342788.4:c.1216T>C	p.Ser406Pro	p.S406P	ENST00000342788	NM_005235.2	406	Tca/Cca	11/28	0.285740959886545	1	FACETS	0.885	0.857	0.913	1	0.997	1	INDETERMINATE	2	TRUE	0	0.557676914023357	1		52	647	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97869498	97869500	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	novel	NA	P-0054318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	1002	328	0	ENST00000289081.3:c.1381_1383del	p.Ser461del	p.S461del	ENST00000289081	NM_000136.2	461	AGC/-	14/15	0.557676914023357	3	FACETS	0.86	0.838	0.881	0.86	0.838	0.881	CLONAL	3	TRUE	0	0.557676914023357	3		328	1782	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0054319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	732	306	0	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	0.62734731370161	1	FACETS	0.758	0.739	0.777	1	0.998	1	SUBCLONAL	2	TRUE	0	0.62734731370161	1		306	1056	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0054319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	316	107	1	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	0.62734731370161	1	FACETS	0.758	0.729	0.786	1	0.996	1	SUBCLONAL	2	TRUE	0	0.62734731370161	1		108	456	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0054320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	617	568	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	1.13	2		568	1077	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061240	38061240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	847	266	0	ENST00000250448.2:c.749C>T	p.Ser250Phe	p.S250F	ENST00000250448	NM_004496.3	250	tCc/tTc	2/2	1	2	FACETS	0.977	0.95	1	0.977	0.95	1	CLONAL	1	TRUE	1	1.13	2		266	1534	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0054321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	947	183	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.412499381962787	1	FACETS	0.842	0.823	0.862	1	0.999	1	CLONAL	3	TRUE	0	0.412499381962787	1		183	1442	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370709	55370709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	918	347	0	ENST00000297316.4:c.11C>T	p.Pro4Leu	p.P4L	ENST00000297316	NM_022454.3	4	cCg/cTg	1/2	0.387562668252361	2	FACETS	1	0.995	1	1	0.998	1	CLONAL	3	TRUE	0	0.412499381962787	2		347	1390	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606709	29606709	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	601	110	0	ENST00000389048.3:c.1171G>T	p.Gly391Ter	p.G391*	ENST00000389048	NM_004304.4	391	Gga/Tga	5/29	1	2	FACETS	0.944	0.914	0.974	1	0.998	1	CLONAL	3	TRUE	1	0.412499381962787	2		110	1029	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79968633	79968633	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201336852	NA	P-0054321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	517	98	1	ENST00000265081.6:c.983G>A	p.Arg328Gln	p.R328Q	ENST00000265081	NM_002439.4	328	cGg/cAg	6/24	1	2	FACETS	0.898	0.867	0.93	1	0.998	1	CLONAL	3	TRUE	1	0.412499381962787	2		99	930	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786760	3786760	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	664	148	0	ENST00000262367.5:c.4451T>C	p.Phe1484Ser	p.F1484S	ENST00000262367	NM_004380.2	1484	tTc/tCc	27/31	1	2	FACETS	0.888	0.861	0.916	1	0.998	1	CLONAL	3	TRUE	1	0.412499381962787	2		148	1208	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600426	43600426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1009392744	NA	P-0054321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	991	152	0	ENST00000355710.3:c.652C>T	p.Pro218Ser	p.P218S	ENST00000355710	NM_020975.4	218	Ccg/Tcg	4/20	1	2	FACETS	0.967	0.944	0.99	1	0.999	1	CLONAL	3	TRUE	1	0.412499381962787	2		152	1656	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446425	70446425	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	435	85	0	ENST00000373644.4:c.5365A>G	p.Thr1789Ala	p.T1789A	ENST00000373644	NM_030625.2	1789	Aca/Gca	11/12	0.412499381962787	1	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	0	0.412499381962787	1		85	755	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344534	118344534	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	373	72	0	ENST00000534358.1:c.2660A>T	p.Glu887Val	p.E887V	ENST00000534358	NM_005933.3	887	gAg/gTg	3/36	1	2	FACETS	0.9	0.863	0.937	1	0.997	1	CLONAL	3	TRUE	1	0.412499381962787	2		72	670	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224131	36224132	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0054321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	1125	166	2	ENST00000222270.7:c.6681_6682delinsTT	p.Ala2228Ser	p.A2228S	ENST00000222270	NM_014727.1	2227	acGGct/acTTct	28/37	1	2	FACETS	0.934	0.912	0.956	1	0.999	1	CLONAL	3	TRUE	1	0.412499381962787	2		168	1946	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629755	187629755	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	676	113	0	ENST00000441802.2:c.1227del	p.Lys410AsnfsTer4	p.K410Nfs*4	ENST00000441802	NM_005245.3	409	gcT/gc	2/27	1	2	FACETS	0.895	0.867	0.922	1	0.998	1	CLONAL	3	TRUE	1	0.412499381962787	2		113	1221	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553157	106553157	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	737	130	0	ENST00000369096.4:c.1122C>A	p.Tyr374Ter	p.Y374*	ENST00000369096	NM_001198.3	374	taC/taA	5/7	1	2	FACETS	0.935	0.908	0.962	1	0.998	1	CLONAL	3	TRUE	1	0.412499381962787	2		130	1274	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482941	140482941	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	743	147	0	ENST00000288602.6:c.1194G>T	p.Leu398Phe	p.L398F	ENST00000288602	NM_004333.4	398	ttG/ttT	10/18	1	2	FACETS	0.894	0.868	0.92	1	0.998	1	CLONAL	3	TRUE	1	0.412499381962787	2		147	1343	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938520	76938520	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	516	184	0	ENST00000373344.5:c.2228G>C	p.Arg743Thr	p.R743T	ENST00000373344	NM_000489.3	743	aGg/aCg	9/35	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	3	TRUE	NA	0.412499381962787	2		184	792	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559115	29559116	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	T	novel	NA	P-0054321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	303	58	0	ENST00000356175.3:c.3222_3223delinsT	p.Glu1074AspfsTer3	p.E1074Dfs*3	ENST00000356175	NM_000267.3	1074	gaAGca/gaTca	25/57	0.412499381962787	1	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	0	0.412499381962787	1		58	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0054323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	709	681	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.487803001805522	1	FACETS	1	0.99	1	1	0.998	1	CLONAL	2	TRUE	0	0.487319082735391	1		682	1066	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241872	72241872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752419911	NA	P-0054323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	287	103	0	ENST00000357731.5:c.518G>A	p.Arg173Gln	p.R173Q	ENST00000357731	NM_173808.2	173	cGa/cAa	3/7	0.220499092833583	4	FACETS	0.973	0.924	1	1	0.994	1	INDETERMINATE	3	TRUE	2	0.487319082735391	4		103	600	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70432782	70432782	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	460	56	0	ENST00000373644.4:c.4804G>C	p.Asp1602His	p.D1602H	ENST00000373644	NM_030625.2	1602	Gat/Cat	8/12	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	2	TRUE	NA	0.487319082735391	2		56	917	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679133	88679133	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	356	115	0	ENST00000360948.2:c.904T>A	p.Tyr302Asn	p.Y302N	ENST00000360948	NM_001012338.2	302	Tac/Aac	8/19	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.487319082735391	2		115	597	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132432	11132432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	1020	116	0	ENST00000358026.2:c.2648G>A	p.Gly883Asp	p.G883D	ENST00000358026	NM_001128849.1	883	gGt/gAt	19/36	0.442215144208674	2	FACETS	0.854	0.834	0.874	1	0.998	1	CLONAL	3	TRUE	0	0.487319082735391	2		116	1634	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533859	533860	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGCTGTACTCCTCCTGGC	novel	NA	P-0054324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	874	166	0	ENST00000451590.1:c.179_196dup	p.Gly60_Ser65dup	p.G60_S65dup	ENST00000451590	NM_001130442.1	60	gcc/gGCCAGGAGGAGTACAGCGcc	3/5	1	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	1	0.67	2		166	1791	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752641	128752835	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GAGGAGGAACAAGAAGATGAGGAAGAAATCGATGTTGTTTCTGTGGAAAAGAGGCAGGCTCCTGGCAAAAGGTCAGAGTCTGGATCACCTTCTGCTGGAGGCCACAGCAAACCTCCTCACAGCCCACTGGTCCTCAAGAGGTGCCACGTCTCCACACATCAGCACAACTACGCAGCGCCTCCCTCCACTCGGAAG	GAGGAGGAACAAGAAGATGAGGAAGAAATCGATGTTGTTTCTGTGGAAAAGAGGCAGGCTCCTGGCAAAAGGTCAGAGTCTGGATCACCTTCTGCTGGAGGCCACAGCAAACCTCCTCACAGCCCACTGGTCCTCAAGAGGTGCCACGTCTCCACACATCAGCACAACTACGCAGCGCCTCCCTCCACTCGGAAG	-	novel	NA	P-0054324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2225	195	1529	0	ENST00000377970.2:c.804_998del		p.X268_splice	ENST00000377970	NM_002467.4	268		3/3	0.3	63	FACETS	1	0.944	1			1	INDETERMINATE	5	TRUE	NA	0.67	63		1529	2420	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0054325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	278	76	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.277117347263274	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	1	0.310084784405144	4		76	704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs786201838	NA	P-0054325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	650	172	0	ENST00000269305.4:c.578A>C	p.His193Pro	p.H193P	ENST00000269305	NM_001126112.2	193	cAt/cCt	6/11	0.310084784405144	1	FACETS	1	0.995	1	1	0.998	1	CLONAL	3	TRUE	0	0.310084784405144	1		172	1051	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817493	39817493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755303168	NA	P-0054325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	576	545	0	ENST00000288319.7:c.70G>A	p.Gly24Arg	p.G24R	ENST00000288319	NM_182918.3	24	Gga/Aga	2/10	0.310084784405144	6	FACETS	1	0.989	1	1	0.989	1	CLONAL	5	TRUE	1	0.310084784405144	6		545	1138	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134614	2134614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	1073	286	0	ENST00000219476.3:c.4391C>T	p.Ser1464Phe	p.S1464F	ENST00000219476	NM_000548.3	1464	tCc/tTc	34/42	1	2	FACETS	1	0.997	1			1	CLONAL	3	TRUE	1	0.310084784405144	2		286	2024	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058506	72058506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1308808256	NA	P-0054325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	346	40	0	ENST00000357731.5:c.934C>T	p.Leu312Phe	p.L312F	ENST00000357731	NM_173808.2	312	Ctt/Ttt	6/7	0.305623997327919	3	FACETS	0.892	0.847	0.938	0.892	0.847	0.938	CLONAL	3	TRUE	0	0.310084784405144	3		40	963	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134918	41134918	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	331	70	0	ENST00000379561.5:c.710G>A	p.Trp237Ter	p.W237*	ENST00000379561	NM_002015.3	237	tGg/tAg	2/3	0.177310452266258	4	FACETS	0.999	0.952	1	1	0.996	1	INDETERMINATE	4	TRUE	2	0.310084784405144	4		70	700	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56854546	56854546	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	352	119	0	ENST00000519728.1:c.128G>T	p.Arg43Met	p.R43M	ENST00000519728	NM_002350.3	43	aGg/aTg	2/13	1	2	FACETS	0.98	0.935	1	1	0.997	1	CLONAL	3	TRUE	1	0.310084784405144	2		119	772	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0054326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	420	378	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.991	1	1	0.998	1	CLONAL	4	TRUE	1	0.275090185723151	2		378	698	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045784	143045784	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	590	50	0	ENST00000262992.4:c.1850G>T	p.Cys617Phe	p.C617F	ENST00000262992	NM_001101669.1	617	tGt/tTt	17/24	1	2	FACETS	1	0.992	1	1	0.998	1	CLONAL	4	TRUE	1	0.275090185723151	2		50	1002	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18276969	18276969	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0054326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	370	36	0	ENST00000222254.8:c.1417-1G>A		p.X473_splice	ENST00000222254	NM_005027.3	473			1	2	FACETS	0.969	0.934	1	1	0.997	1	CLONAL	5	TRUE	1	0.275090185723151	2		36	555	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374315	81374315	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0054326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	272	24	0	ENST00000222390.5:c.746+1G>T		p.X249_splice	ENST00000222390	NM_000601.4	249			1	2	FACETS	1	0.982	1	1	0.997	1	CLONAL	4	TRUE	1	0.275090185723151	2		24	465	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040923	47040923	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	1419	113	0	ENST00000377604.3:c.1453G>T	p.Glu485Ter	p.E485*	ENST00000377604	NM_001204468.1	485	Gag/Tag	14/24	1	2	FACETS	0.939	0.921	0.957			1	CLONAL	5	TRUE	1	0.275090185723151	2		113	2197	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749921	162749921	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	515	56	0	ENST00000367921.3:c.2453C>A	p.Ala818Asp	p.A818D	ENST00000367921	NM_006182.2	818	gCc/gAc	18/18	0.275090185723151	4	FACETS	0.959	0.924	0.994	1	0.997	1	CLONAL	5	TRUE	1	0.275090185723151	4		56	996	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220377	1220377	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	944	91	0	ENST00000326873.7:c.470T>G	p.Phe157Cys	p.F157C	ENST00000326873	NM_000455.4	157	tTc/tGc	4/10	0.275090185723151	1	FACETS	1	0.996	1			1	CLONAL	4	TRUE	0	0.275090185723151	1		91	1383	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366957	15366957	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	839	86	1	ENST00000263377.2:c.1669G>T	p.Val557Leu	p.V557L	ENST00000263377	NM_058243.2	557	Gtg/Ttg	9/20	0.275090185723151	1	FACETS	0.967	0.942	0.992	1	0.999	1	CLONAL	4	TRUE	0	0.275090185723151	1		87	1360	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215889	36215889	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0054326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	1146	70	0	ENST00000222270.7:c.3430-1G>T		p.X1144_splice	ENST00000222270	NM_014727.1	1144			1	2	FACETS	0.921	0.901	0.941			1	CLONAL	5	TRUE	1	0.275090185723151	2		70	1809	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268383	198268383	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	440	64	0	ENST00000335508.6:c.1645C>G	p.Arg549Gly	p.R549G	ENST00000335508	NM_012433.2	549	Cgt/Ggt	12/25	0.23108297103564	3	FACETS	1	0.988	1	1	0.998	1	CLONAL	5	TRUE	1	0.275090185723151	3		64	692	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259169	89259169	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	403	30	0	ENST00000336596.2:c.313G>T	p.Asp105Tyr	p.D105Y	ENST00000336596	NM_005233.5	105	Gac/Tac	3/17	1	2	FACETS	0.935	0.901	0.968	1	0.998	1	CLONAL	5	TRUE	1	0.275090185723151	2		30	627	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163736	152163736	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	518	23	0	ENST00000206249.3:c.457A>T	p.Asn153Tyr	p.N153Y	ENST00000206249	NM_000125.3	153	Aat/Tat	2/8	1	2	FACETS	0.922	0.892	0.951	1	0.998	1	CLONAL	5	TRUE	1	0.275090185723151	2		23	817	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166802	32166805	+	missense_variant	Missense_Mutation	ONP	CCAT	CCAT	TTAC	novel	NA	P-0054326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	1228	82	2	ENST00000375023.3:c.4433_4436delinsGTAA	p.His1478_Gly1479delinsArgLys	p.H1478_G1479delinsRK	ENST00000375023	NM_004557.3	1478	cATGGa/cGTAAa	24/30	1	2	FACETS	0.936	0.917	0.956			1	CLONAL	5	TRUE	1	0.275090185723151	2		84	1907	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0054327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	361	69	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	0.829	0.791	0.868	1	0.996	1	CLONAL	2	TRUE	1	0.54	2		69	806	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544756	65544756	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0054327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	488	47	0	ENST00000358664.4:c.172-2A>G		p.X58_splice	ENST00000358664	NM_002382.4	58			0.106960254176083	0	FACETS		NA	1			1	INDETERMINATE	2	TRUE	0	0.54	0		47	862	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202427	123202427	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754256233	NA	P-0054327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	385	79	0	ENST00000218089.9:c.2279G>A	p.Arg760His	p.R760H	ENST00000218089	NM_001042749.1	760	cGt/cAt	24/35	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.54	2		79	1094	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858376	9858376	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	490	87	0	ENST00000330684.3:c.3025A>G	p.Arg1009Gly	p.R1009G	ENST00000330684	NM_001134407.1	1009	Aga/Gga	13/13	1	2	FACETS	0.994	0.957	1	1	0.997	1	CLONAL	2	TRUE	1	0.54	2		87	913	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1064795203	NA	P-0054329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	298	784	0	ENST00000269305.4:c.532C>G	p.His178Asp	p.H178D	ENST00000269305	NM_001126112.2	178	Cac/Gac	5/11	0.731289427931955	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.75339625243378	1		784	485	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962271	2962271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867239716	NA	P-0054329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	236	774	0	ENST00000396946.4:c.2266G>A	p.Glu756Lys	p.E756K	ENST00000396946	NM_032415.4	756	Gaa/Aaa	17/25	0.748826419035065	2	FACETS	0.941	0.883	1	0.47	0.441	0.5	CLONAL	1	TRUE	0	0.75339625243378	2		774	666	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864526	57864526	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	323	859	0	ENST00000228682.2:c.2003C>G	p.Thr668Ser	p.T668S	ENST00000228682	NM_005269.2	668	aCt/aGt	12/12	0.75339625243378	3	FACETS	1	0.981	1	0.54	0.51	0.57	CLONAL	1	TRUE	1	0.75339625243378	3		859	1094	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829228	72829228	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	545	778	0	ENST00000268489.5:c.7353del	p.Lys2451AsnfsTer77	p.K2451Nfs*77	ENST00000268489	NM_006885.3	2451	aaG/aa	9/10	0.75339625243378	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.75339625243378	3		778	990	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210650	2210650	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	228	796	0	ENST00000398665.3:c.1147G>C	p.Ala383Pro	p.A383P	ENST00000398665	NM_032482.2	383	Gca/Cca	14/28	0.75339625243378	2	FACETS	0.897	0.84	0.955	0.448	0.42	0.478	CLONAL	1	TRUE	0	0.75339625243378	2		796	675	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050336	37050336	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	114	282	0	ENST00000231790.2:c.485G>A	p.Arg162Lys	p.R162K	ENST00000231790	NM_000249.3	162	aGg/aAg	6/19	0.413337826507613	6	FACETS	1	0.984	1	0.494	0.447	0.544	INDETERMINATE	1	TRUE	3	0.75339625243378	6		282	512	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575639	55575639	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	100	393	0	ENST00000288135.5:c.1165A>T	p.Thr389Ser	p.T389S	ENST00000288135	NM_000222.2	389	Act/Tct	7/21	0.75339625243378	2	FACETS	0.827	0.747	0.91	0.413	0.373	0.455	CLONAL	1	TRUE	0	0.75339625243378	2		393	321	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891170	101891170	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	101	263	0	ENST00000374994.4:c.131A>G	p.Asp44Gly	p.D44G	ENST00000374994	NM_004612.2	44	gAc/gGc	2/9	1	2	FACETS	0.997	0.905	1	0.997	0.905	1	CLONAL	1	TRUE	1	0.75339625243378	2		263	269	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0054331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	283	963	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.285301998829477	2	FACETS	0.787	0.741	0.835	0.787	0.741	0.835	SUBCLONAL	2	TRUE	0	0.362288231481226	2		966	992	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508068	106508068	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755613711	NA	P-0054331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	21	161	0	ENST00000359195.3:c.62G>A	p.Arg21Gln	p.R21Q	ENST00000359195	NM_002649.2	21	cGg/cAg	2/11	1	2	FACETS	0.439	0.338	0.556	0.439	0.338	0.556	SUBCLONAL	1	TRUE	1	0.362288231481226	2		161	264	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0054333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	139	455	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.901	0.827	0.977	0.901	0.827	0.977	CLONAL	1	TRUE	1	0.704462724699098	2		456	438	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223543	55223543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	29	684	0	ENST00000275493.2:c.910C>T	p.His304Tyr	p.H304Y	ENST00000275493	NM_005228.3	304	Cac/Tac	8/28	0.704462724699098	4	FACETS	0.112	0.089	0.139	0.037	0.029	0.047	SUBCLONAL	1	TRUE	1	0.704462724699098	4		684	1248	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0054333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	157	363	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.704462724699098	1	FACETS	0.944	0.881	1	0.944	0.881	1	CLONAL	1	TRUE	0	0.704462724699098	1		363	306	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242469	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	15	365	0	ENST00000275493.2:c.2239T>G	p.Leu747Val	p.L747V	ENST00000275493	NM_005228.3	747	Tta/Gta	19/28	0.704462724699098	4	FACETS	0.1	0.073	0.134	0.033	0.024	0.045	SUBCLONAL	1	TRUE	1	0.704462724699098	4		365	723	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210077	55210077	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	637	473	0	ENST00000275493.2:c.187G>C	p.Gly63Arg	p.G63R	ENST00000275493	NM_005228.3	63	Ggg/Cgg	2/28	1	2	FACETS	0.912	0.885	0.937	1	0.998	1	CLONAL	2	TRUE	1	0.704462724699098	2		473	992	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911867	32911867	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	177	526	0	ENST00000380152.3:c.3375T>G	p.Phe1125Leu	p.F1125L	ENST00000380152		1125	ttT/ttG	11/27	0.704462724699098	1	FACETS	0.835	0.78	0.89	0.835	0.78	0.89	CLONAL	1	TRUE	0	0.704462724699098	1		526	390	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0054334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	59	455	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.896	0.776	1	0.896	0.776	1	CLONAL	1	TRUE	1	0.411544831066969	2		456	320	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560493	65560493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	86	467	0	ENST00000358664.4:c.104G>A	p.Arg35His	p.R35H	ENST00000358664	NM_002382.4	35	cGt/cAt	3/5	1	2	FACETS	0.862	0.765	0.964	0.862	0.765	0.964	CLONAL	1	TRUE	1	0.411544831066969	2		467	485	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657361	29657361	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1555533853	NA	P-0054334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	80	537	0	ENST00000356175.3:c.5594T>A	p.Leu1865Ter	p.L1865*	ENST00000356175	NM_000267.3	1865	tTa/tAa	38/57	1	2	FACETS	0.896	0.792	1	0.896	0.792	1	CLONAL	1	TRUE	1	0.411544831066969	2		537	434	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439792	51439794	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0054334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	95	341	0	ENST00000262662.1:c.358_360del	p.Glu120del	p.E120del	ENST00000262662		119	gtGGAg/gtg	4/4	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.411544831066969	2		341	378	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711905	89711905	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	84	423	1	ENST00000371953.3:c.523G>A	p.Val175Met	p.V175M	ENST00000371953	NM_000314.4	175	Gtg/Atg	6/9	0.411544831066969	1	FACETS	0.888	0.79	0.991	0.888	0.79	0.991	CLONAL	1	TRUE	0	0.411544831066969	1		424	365	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375045	104375045	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	81	542	0	ENST00000369902.3:c.1045del	p.Ser349ValfsTer12	p.S349Vfs*12	ENST00000369902	NM_016169.3	348	gAa/ga	9/12	0.411544831066969	1	FACETS	0.845	0.75	0.946	0.845	0.75	0.946	CLONAL	1	TRUE	0	0.411544831066969	1		542	370	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554265	29554266	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	105	673	0	ENST00000356175.3:c.2282dup	p.Leu762ThrfsTer6	p.L762Tfs*6	ENST00000356175	NM_000267.3	761	gca/gCca	19/57	1	2	FACETS	0.919	0.826	1	0.919	0.826	1	CLONAL	1	TRUE	1	0.411544831066969	2		673	555	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0054335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	495	645	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.30796628575055	2	FACETS	1	0.997	1	0.743	0.713	0.772	INDETERMINATE	1	TRUE	0	0.604389531480704	2		645	1103	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955550	48955550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913304	NA	P-0054335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	58	294	0	ENST00000267163.4:c.1666C>T	p.Arg556Ter	p.R556*	ENST00000267163	NM_000321.2	556	Cga/Tga	17/27	0.604389531480704	1	FACETS	0.832	0.731	0.937	0.832	0.731	0.937	CLONAL	1	TRUE	0	0.604389531480704	1		294	161	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041720	47041720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	288	544	0	ENST00000377604.3:c.1945C>T	p.Gln649Ter	p.Q649*	ENST00000377604	NM_001204468.1	649	Caa/Taa	17/24	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.604389531480704	2		544	924	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720808	89720808	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs1114167667	NA	P-0054335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	70	358	0	ENST00000371953.3:c.959T>G	p.Leu320Ter	p.L320*	ENST00000371953	NM_000314.4	320	tTa/tGa	8/9	0.604389531480704	1	FACETS	0.821	0.729	0.915	0.821	0.729	0.915	CLONAL	1	TRUE	0	0.604389531480704	1		358	197	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781326	3781326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1445723787	NA	P-0054335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1553	627	1307	1	ENST00000262367.5:c.5039C>T	p.Ser1680Phe	p.S1680F	ENST00000262367	NM_004380.2	1680	tCc/tTc	30/31	1	2	FACETS	0.952	0.914	0.99	0.952	0.914	0.99	CLONAL	1	TRUE	1	0.604389531480704	2		1308	2180	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412575	63412575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774927630	NA	P-0054335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	189	747	1	ENST00000330258.3:c.592G>A	p.Glu198Lys	p.E198K	ENST00000330258	NM_152424.3	198	Gag/Aag	2/2	1	2	FACETS	0.537	0.495	0.58	0.537	0.495	0.58	SUBCLONAL	1	TRUE	1	0.604389531480704	2		748	1165	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578554	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AGTA	AGTA	-	novel	NA	P-0054335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	542	973	0	ENST00000269305.4:c.376_379del	p.Tyr126ProfsTer43	p.Y126Pfs*43	ENST00000269305	NM_001126112.2	126	TACTcc/cc	5/11	0.604389531480704	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.604389531480704	1		973	1180	SUCCESS
MET	4233	MSKCC	GRCh37	7	116409797	116409797	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	46	245	0	ENST00000397752.3:c.2682C>A	p.Cys894Ter	p.C894*	ENST00000397752	NM_000245.2	894	tgC/tgA	12/21	0.30796628575055	2	FACETS	0.502	0.425	0.587	0.251	0.212	0.294	INDETERMINATE	1	TRUE	0	0.604389531480704	2		245	303	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242752	66242752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	20	248	0	ENST00000273854.3:c.1820C>T	p.Ser607Phe	p.S607F	ENST00000273854	NM_004439.5	607	tCt/tTt	9/18	1	2	FACETS	0.59	0.451	0.753	0.59	0.451	0.753	SUBCLONAL	1	TRUE	1	0.211784548724645	2		248	320	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936683	49936684	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0054336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	124	615	2	ENST00000296474.3:c.1243_1244delinsAT	p.Ala415Ile	p.A415I	ENST00000296474	NM_002447.2	415	GCc/ATc	2/20	0.165554811893452	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	1	0.211784548724645	3		617	614	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190532	32190532	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	170	803	0	ENST00000375023.3:c.207G>C	p.Gln69His	p.Q69H	ENST00000375023	NM_004557.3	69	caG/caC	3/30	0.187426044888595	3	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	1	0.211784548724645	3		803	865	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0054337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	143	378	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.958	0.883	1	0.958	0.883	1	CLONAL	1	TRUE	1	0.749893450701186	2		378	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0054337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	332	817	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.689305033010209	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.749893450701186	1		817	536	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250323	39250323	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	137	503	0	ENST00000402219.2:c.1246C>A	p.Gln416Lys	p.Q416K	ENST00000402219	NM_005633.3	416	Caa/Aaa	10/23	0.432114053795738	1	FACETS	0.404	0.369	0.441	0.404	0.369	0.441	INDETERMINATE	1	TRUE	0	0.749893450701186	1		503	565	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526648	31526648	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	239	580	0	ENST00000344624.3:c.392del	p.Pro131GlnfsTer15	p.P131Qfs*15	ENST00000344624		131	cCa/ca	2/33	1	2	FACETS	0.811	0.76	0.864	0.811	0.76	0.864	CLONAL	1	TRUE	1	0.749893450701186	2		580	786	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0054338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	210	477	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.870138648927891	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.870138648927891	1		477	245	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099479	27099479	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0054338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	88	248	2	ENST00000324856.7:c.3715+1G>A		p.X1239_splice	ENST00000324856	NM_006015.4	1239			0.463275536634829	1	FACETS	0.423	0.38	0.468	0.423	0.38	0.468	INDETERMINATE	1	TRUE	0	0.870138648927891	1		250	270	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412109	63412109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157288902	NA	P-0054338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	211	641	0	ENST00000330258.3:c.1058G>A	p.Arg353Gln	p.R353Q	ENST00000330258	NM_152424.3	353	cGa/cAa	2/2	0.453412589196263	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.870138648927891	0		641	533	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11227528	11227528	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	38	376	0	ENST00000361445.4:c.4300G>C	p.Glu1434Gln	p.E1434Q	ENST00000361445	NM_004958.3	1434	Gaa/Caa	29/58	0.463275536634829	1	FACETS	0.091	0.075	0.109	0.091	0.075	0.109	INDETERMINATE	1	TRUE	0	0.870138648927891	1		376	543	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864646	37864646	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749886389	NA	P-0054338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1430	76	593	0	ENST00000269571.5:c.298C>T	p.Arg100Trp	p.R100W	ENST00000269571		100	Cgg/Tgg	3/27	0.457200113059628	4	FACETS	0.217	0.189	0.247	0.072	0.063	0.083	INDETERMINATE	1	TRUE	1	0.870138648927891	4		593	1506	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871771	37871771	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1029745309	NA	P-0054338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	376	545	0	ENST00000269571.5:c.1295G>A	p.Arg432Gln	p.R432Q	ENST00000269571		432	cGg/cAg	11/27	0.457200113059628	4	FACETS	1	0.994	1	0.435	0.413	0.458	INDETERMINATE	1	TRUE	1	0.870138648927891	4		545	1238	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180307	38180307	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	224	707	0	ENST00000396334.3:c.155T>C	p.Val52Ala	p.V52A	ENST00000396334	NM_002468.4	52	gTg/gCg	1/5	0.870138648927891	1	FACETS	0.503	0.472	0.535	0.503	0.472	0.535	SUBCLONAL	1	TRUE	0	0.870138648927891	1		707	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578206	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs886039484	NA	P-0054339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	475	624	0	ENST00000269305.4:c.643A>C	p.Ser215Arg	p.S215R	ENST00000269305	NM_001126112.2	215	Agt/Cgt	6/11	NA	2	FACETS	0.888	0.855	0.921			1	INDETERMINATE	2	TRUE	NA	0.600991971557113	2		624	890	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987024	69987024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200583343	NA	P-0054339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	164	471	1	ENST00000394351.3:c.85C>T	p.Arg29Trp	p.R29W	ENST00000394351	NM_000248.3	29	Cgg/Tgg	2/9	0.600991971557113	1	FACETS	0.784	0.725	0.844	0.784	0.725	0.844	SUBCLONAL	1	TRUE	0	0.600991971557113	1		472	487	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043387	6043387	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	12	78	0	ENST00000265849.7:c.287C>G	p.Ala96Gly	p.A96G	ENST00000265849	NM_000535.5	96	gCc/gGc	4/15	1	2	FACETS	0.344	0.244	0.466	0.344	0.244	0.466	SUBCLONAL	1	TRUE	1	0.600991971557113	2		78	116	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268766	98268767	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCC	novel	NA	P-0054339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	285	489	0	ENST00000331920.6:c.313_316dup	p.Leu106ArgfsTer35	p.L106Rfs*35	ENST00000331920	NM_000264.3	106	ctc/cGGCCtc	2/24	0.600991971557113	1	FACETS	0.944	0.893	0.995	0.944	0.893	0.995	CLONAL	1	TRUE	0	0.600991971557113	1		489	703	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222411	53222411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781803231	NA	P-0054339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	357	499	0	ENST00000375401.3:c.4421G>A	p.Arg1474Gln	p.R1474Q	ENST00000375401	NM_004187.3	1474	cGa/cAa	26/26	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.600991971557113	1		499	682	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	202	393	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.994	0.932	1	1	0.994	1	CLONAL	2	TRUE	1	0.447694612411973	2		396	454	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	92	593	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.751	0.669	0.838	0.751	0.669	0.838	SUBCLONAL	1	TRUE	1	0.447694612411973	2		598	547	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	111	378	1	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.447694612411973	2		379	472	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101117	27101117	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	172	735	0	ENST00000324856.7:c.4403del	p.Pro1468LeufsTer13	p.P1468Lfs*13	ENST00000324856	NM_006015.4	1467	Ccc/cc	18/20	1	2	FACETS	0.942	0.868	1	0.942	0.868	1	CLONAL	1	TRUE	1	0.447694612411973	2		735	816	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796882	45796882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553124891	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	146	507	0	ENST00000450313.1:c.1448C>T	p.Thr483Ile	p.T483I	ENST00000450313	NM_012222.2	483	aCc/aTc	14/16	1	2	FACETS	0.99	0.906	1	0.99	0.906	1	CLONAL	1	TRUE	1	0.447694612411973	2		507	659	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430780	78430780	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	79	330	0	ENST00000370768.2:c.609del	p.Gly205GlufsTer17	p.G205Efs*17	ENST00000370768	NM_003902.3	203	aaA/aa	8/20	1	2	FACETS	0.781	0.689	0.878	0.781	0.689	0.878	SUBCLONAL	1	TRUE	1	0.447694612411973	2		330	452	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745476	162745476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471671366	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	61	222	0	ENST00000367921.3:c.1891C>T	p.Arg631Trp	p.R631W	ENST00000367921	NM_006182.2	631	Cgg/Tgg	15/18	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.447694612411973	2		222	271	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651514	206651514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	91	489	0	ENST00000367120.3:c.824G>A	p.Ser275Asn	p.S275N	ENST00000367120	NM_014002.3	275	aGc/aAc	9/22	1	2	FACETS	0.959	0.856	1	0.959	0.856	1	CLONAL	1	TRUE	1	0.447694612411973	2		489	424	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567646	226567647	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1159330096	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	152	517	1	ENST00000366794.5:c.1519dup	p.Ser507LysfsTer14	p.S507Kfs*14	ENST00000366794	NM_001618.3	507	agc/aAgc	10/23	1	2	FACETS	0.994	0.912	1	0.994	0.912	1	CLONAL	1	TRUE	1	0.447694612411973	2		518	683	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612759	228612759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	218	766	0	ENST00000366696.1:c.268G>A	p.Val90Met	p.V90M	ENST00000366696	NM_003493.2	90	Gtg/Atg	1/1	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.447694612411973	2		766	923	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100728	8100728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs771019738	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	146	734	2	ENST00000346208.3:c.708del	p.Ser237AlafsTer28	p.S237Afs*28	ENST00000346208		234	ttC/tt	3/6	1	2	FACETS	0.83	0.758	0.905	0.83	0.758	0.905	CLONAL	1	TRUE	1	0.447694612411973	2		736	786	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446252	70446252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	137	396	1	ENST00000373644.4:c.5192C>T	p.Ser1731Phe	p.S1731F	ENST00000373644	NM_030625.2	1731	tCt/tTt	11/12	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.447694612411973	2		397	520	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104353408	104353408	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	161	635	0	ENST00000369902.3:c.613A>G	p.Thr205Ala	p.T205A	ENST00000369902	NM_016169.3	205	Act/Gct	5/12	1	2	FACETS	0.967	0.888	1	0.967	0.888	1	CLONAL	1	TRUE	1	0.447694612411973	2		635	744	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711244	114711244	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	88	297	0	ENST00000543371.1:c.259G>A	p.Ala87Thr	p.A87T	ENST00000543371	NM_001198531.1	87	Gcc/Acc	3/14	1	2	FACETS	0.921	0.82	1	0.921	0.82	1	CLONAL	1	TRUE	1	0.447694612411973	2		297	427	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741954	17741954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	77	254	0	ENST00000250003.3:c.625G>A	p.Gly209Ser	p.G209S	ENST00000250003	NM_002478.4	209	Ggc/Agc	1/3	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.447694612411973	2		254	315	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981721	101981721	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555075353	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	86	286	0	ENST00000282441.5:c.147del	p.Ala50ProfsTer24	p.A50Pfs*24	ENST00000282441	NM_001130145.2	48	Ccc/cc	1/9	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.447694612411973	2		286	342	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628681	21628681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	63	403	0	ENST00000421138.2:c.1027G>A	p.Ala343Thr	p.A343T	ENST00000421138		343	Gct/Act	10/16	0.447694612411973	3	FACETS	0.834	0.724	0.953	0.417	0.362	0.477	CLONAL	1	TRUE	1	0.447694612411973	3		403	413	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440519	49440519	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	227	685	0	ENST00000301067.7:c.4291G>T	p.Glu1431Ter	p.E1431*	ENST00000301067	NM_003482.3	1431	Gag/Tag	15/54	0.447694612411973	3	FACETS	1	0.969	1	0.535	0.498	0.574	CLONAL	1	TRUE	1	0.447694612411973	3		685	1159	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443641	49443641	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1064794007	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	154	659	0	ENST00000301067.7:c.3730del	p.Val1244SerfsTer86	p.V1244Sfs*86	ENST00000301067	NM_003482.3	1244	Gtc/tc	11/54	0.447694612411973	3	FACETS	1	0.92	1	0.502	0.46	0.547	CLONAL	1	TRUE	1	0.447694612411973	3		659	838	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856052	111856052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758024019	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	384	633	2	ENST00000341259.2:c.103G>A	p.Val35Ile	p.V35I	ENST00000341259	NM_005475.2	35	Gta/Ata	2/8	0.447694612411973	3	FACETS	0.994	0.946	1	0.994	0.946	1	CLONAL	2	TRUE	1	0.447694612411973	3		635	1056	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856377	111856377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	138	133	0	ENST00000341259.2:c.428G>A	p.Arg143His	p.R143H	ENST00000341259	NM_005475.2	143	cGc/cAc	2/8	0.447694612411973	3	FACETS	0.938	0.872	1	1	0.989	1	CLONAL	3	TRUE	1	0.447694612411973	3		133	268	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245228	133245229	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	197	720	0	ENST00000320574.5:c.2018dup	p.Glu674ArgfsTer36	p.E674Rfs*36	ENST00000320574	NM_006231.2	673	ggc/ggGc	18/49	0.447694612411973	3	FACETS	0.931	0.861	1	0.465	0.43	0.502	CLONAL	1	TRUE	1	0.447694612411973	3		720	1157	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968840	32968840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80359194	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	32	185	0	ENST00000380152.3:c.9271G>A	p.Val3091Ile	p.V3091I	ENST00000380152		3091	Gtc/Atc	25/27	1	2	FACETS	0.773	0.633	0.927	0.773	0.633	0.927	CLONAL	1	TRUE	1	0.447694612411973	2		185	185	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878127	48878127	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1276653645	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	33	96	0	ENST00000267163.4:c.83del	p.Pro28LeufsTer37	p.P28Lfs*37	ENST00000267163	NM_000321.2	27	Ccc/cc	1/27	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.447694612411973	2		96	132	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68292242	68292242	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	71	266	0	ENST00000487270.1:c.146T>C	p.Val49Ala	p.V49A	ENST00000487270	NM_133509.3	49	gTc/gCc	3/11	1	2	FACETS	0.886	0.778	1	0.886	0.778	1	CLONAL	1	TRUE	1	0.447694612411973	2		266	358	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007825	45007825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	63	363	1	ENST00000558401.1:c.276del	p.Thr93LeufsTer10	p.T93Lfs*10	ENST00000558401	NM_004048.2	91	aCc/ac	2/4	1	2	FACETS	0.869	0.756	0.989	0.869	0.756	0.989	CLONAL	1	TRUE	1	0.447694612411973	2		364	324	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007833	45007834	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	68	260	0	ENST00000558401.1:c.285dup	p.Asp96ArgfsTer2	p.D96Rfs*2	ENST00000558401	NM_004048.2	94	gaa/gAaa	2/4	1	2	FACETS	0.91	0.797	1	0.91	0.797	1	CLONAL	1	TRUE	1	0.447694612411973	2		260	334	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66777511	66777511	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs918690546	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	155	589	0	ENST00000307102.5:c.877C>T	p.Pro293Ser	p.P293S	ENST00000307102	NM_002755.3	293	Ccc/Tcc	7/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.447694612411973	2		589	658	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	187	724	0	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	1	2	FACETS	0.965	0.892	1	0.965	0.892	1	CLONAL	1	TRUE	1	0.447694612411973	2		724	866	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222522	2222523	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs750035555	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	250	916	1	ENST00000326181.6:c.722dup	p.Leu242AlafsTer55	p.L242Afs*55	ENST00000326181	NM_032271.2	239	tgc/tgCc	9/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.447694612411973	2		917	1058	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993008	72993008	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	182	674	0	ENST00000268489.5:c.1037del	p.Asn346ThrfsTer6	p.N346Tfs*6	ENST00000268489	NM_006885.3	346	aAc/ac	2/10	1	2	FACETS	0.938	0.866	1	0.938	0.866	1	CLONAL	1	TRUE	1	0.447694612411973	2		674	867	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349914	89349916	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs761762028	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	221	740	0	ENST00000301030.4:c.3034_3036del	p.Lys1012del	p.K1012del	ENST00000301030	NM_001256183.1	1012	AAG/-	9/13	1	2	FACETS	0.975	0.907	1	0.975	0.907	1	CLONAL	1	TRUE	1	0.447694612411973	2		740	1013	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577069	7577069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55819519	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	196	703	0	ENST00000269305.4:c.869G>A	p.Arg290His	p.R290H	ENST00000269305	NM_001126112.2	290	cGc/cAc	8/11	1	2	FACETS	0.986	0.914	1	0.986	0.914	1	CLONAL	1	TRUE	1	0.447694612411973	2		703	888	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028656	12028656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	63	279	0	ENST00000353533.5:c.859C>T	p.Arg287Cys	p.R287C	ENST00000353533	NM_003010.3	287	Cgc/Tgc	8/11	1	2	FACETS	0.806	0.701	0.919	0.806	0.701	0.919	CLONAL	1	TRUE	1	0.447694612411973	2		279	349	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667646	29667646	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56013763	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	83	308	0	ENST00000356175.3:c.6982C>T	p.Arg2328Cys	p.R2328C	ENST00000356175	NM_000267.3	2328	Cgt/Tgt	46/57	1	2	FACETS	0.953	0.847	1	0.953	0.847	1	CLONAL	1	TRUE	1	0.447694612411973	2		308	389	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884268	37884268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	189	581	0	ENST00000269571.5:c.3739G>A	p.Glu1247Lys	p.E1247K	ENST00000269571		1247	Gag/Aag	27/27	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.447694612411973	2		581	685	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740618	58740618	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	104	426	0	ENST00000305921.3:c.1523T>C	p.Met508Thr	p.M508T	ENST00000305921	NM_003620.3	508	aTg/aCg	6/6	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.447694612411973	2		426	429	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	76	38	3	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	0.768	0.676	0.866	0.768	0.676	0.866	SUBCLONAL	1	TRUE	1	0.447694612411973	2		41	442	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207576	2207576	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	162	580	0	ENST00000398665.3:c.860T>C	p.Ile287Thr	p.I287T	ENST00000398665	NM_032482.2	287	aTc/aCc	11/28	1	2	FACETS	0.989	0.909	1	0.989	0.909	1	CLONAL	1	TRUE	1	0.447694612411973	2		580	732	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101829	11101829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	200	668	1	ENST00000358026.2:c.1249C>T	p.Arg417Cys	p.R417C	ENST00000358026	NM_001128849.1	417	Cgc/Tgc	8/36	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.447694612411973	2		669	815	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353815	15353815	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780028668	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	106	373	0	ENST00000263377.2:c.3065C>T	p.Pro1022Leu	p.P1022L	ENST00000263377	NM_058243.2	1022	cCg/cTg	14/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.447694612411973	2		373	419	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223858	36223858	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	228	116	2	ENST00000222270.7:c.6413del	p.Pro2138ArgfsTer15	p.P2138Rfs*15	ENST00000222270	NM_014727.1	2136	ctC/ct	28/37	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.447694612411973	2		118	1004	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605204	46605204	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1459319402	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	105	391	1	ENST00000263734.3:c.1421G>C	p.Ser474Thr	p.S474T	ENST00000263734	NM_001430.4	474	aGc/aCc	10/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.447694612411973	2		392	383	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	49	465	1	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.463	0.392	0.54	0.463	0.392	0.54	SUBCLONAL	1	TRUE	1	0.447694612411973	2		466	473	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578271	212578271	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	78	313	0	ENST00000342788.4:c.986T>C	p.Ile329Thr	p.I329T	ENST00000342788	NM_005235.2	329	aTt/aCt	8/28	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.447694612411973	2		313	339	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379453	225379453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	58	339	0	ENST00000264414.4:c.415G>A	p.Val139Ile	p.V139I	ENST00000264414	NM_003590.4	139	Gtc/Atc	4/16	1	2	FACETS	0.712	0.614	0.817	0.712	0.614	0.817	SUBCLONAL	1	TRUE	1	0.447694612411973	2		339	364	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264985	46264985	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	86	348	0	ENST00000371998.3:c.1860del	p.Lys620AsnfsTer18	p.K620Nfs*18	ENST00000371998		619	Aaa/aa	12/23	1	2	FACETS	0.965	0.859	1	0.965	0.859	1	CLONAL	1	TRUE	1	0.447694612411973	2		348	398	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272450	21272450	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	221	828	0	ENST00000354336.3:c.228G>T	p.Gln76His	p.Q76H	ENST00000354336	NM_005207.3	76	caG/caT	1/3	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.447694612411973	2		828	971	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226898	142226898	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	95	366	0	ENST00000350721.4:c.4906A>G	p.Ile1636Val	p.I1636V	ENST00000350721	NM_001184.3	1636	Ata/Gta	28/47	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.447694612411973	2		366	387	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	111	416	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.447694612411973	2		416	482	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938935	178938935	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519928	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	55	338	0	ENST00000263967.3:c.2177A>C	p.Glu726Ala	p.E726A	ENST00000263967	NM_006218.2	726	gAa/gCa	14/21	1	2	FACETS	0.635	0.545	0.733	0.635	0.545	0.733	SUBCLONAL	1	TRUE	1	0.447694612411973	2		338	387	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806195	1806195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201813356	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	139	769	0	ENST00000260795.2:c.1214G>A	p.Gly405Asp	p.G405D	ENST00000260795		405	gGc/gAc	8/17	1	2	FACETS	0.661	0.601	0.724	0.661	0.601	0.724	SUBCLONAL	1	TRUE	1	0.447694612411973	2		769	939	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	167	418	1	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.447694612411973	2		419	642	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953142	38953142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs569163921	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	17	138	0	ENST00000357387.3:c.2842G>A	p.Val948Met	p.V948M	ENST00000357387	NM_152756.3	948	Gtg/Atg	29/38	1	2	FACETS	0.567	0.427	0.73	0.567	0.427	0.73	SUBCLONAL	1	TRUE	1	0.447694612411973	2		138	134	SUCCESS
APC	324	MSKCC	GRCh37	5	112174214	112174214	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	32	250	0	ENST00000257430.4:c.2926del	p.Arg976GlufsTer4	p.R976Efs*4	ENST00000257430	NM_000038.5	975	Aaa/aa	16/16	1	2	FACETS	0.548	0.446	0.661	0.548	0.446	0.661	SUBCLONAL	1	TRUE	1	0.447694612411973	2		250	261	SUCCESS
APC	324	MSKCC	GRCh37	5	112175631	112175631	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	62	271	0	ENST00000257430.4:c.4342del	p.Thr1448ProfsTer25	p.T1448Pfs*25	ENST00000257430	NM_000038.5	1447	cAa/ca	16/16	1	2	FACETS	0.989	0.862	1	0.989	0.862	1	CLONAL	1	TRUE	1	0.447694612411973	2		271	280	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858357	27858357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	130	583	0	ENST00000359303.2:c.214G>A	p.Val72Met	p.V72M	ENST00000359303	NM_003535.2	72	Gtg/Atg	1/1	0.447694612411973	2	FACETS	0.868	0.789	0.951	0.434	0.394	0.476	CLONAL	1	TRUE	0	0.447694612411973	2		583	669	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099468	157099470	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	rs1429292576	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	71	308	0	ENST00000346085.5:c.413_415del	p.Asn138del	p.N138del	ENST00000346085	NM_020732.3	135	tcCAAc/tcc	1/20	1	2	FACETS	0.789	0.692	0.893	0.789	0.692	0.893	SUBCLONAL	1	TRUE	1	0.447694612411973	2		308	402	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502298	157502298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	116	421	0	ENST00000346085.5:c.3335del	p.Gly1112ValfsTer18	p.G1112Vfs*18	ENST00000346085	NM_020732.3	1111	Ggg/gg	12/20	1	2	FACETS	0.944	0.854	1	0.944	0.854	1	CLONAL	1	TRUE	1	0.447694612411973	2		421	549	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331901	81331901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	30	142	0	ENST00000222390.5:c.2183C>T	p.Ser728Leu	p.S728L	ENST00000222390	NM_000601.4	728	tCa/tTa	18/18	1	2	FACETS	0.918	0.75	1	0.918	0.75	1	CLONAL	1	TRUE	1	0.447694612411973	2		142	146	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829075	128829075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1247591045	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	13	21	0	ENST00000249373.3:c.88del	p.Ala30ArgfsTer25	p.A30Rfs*25	ENST00000249373	NM_005631.4	28	cGg/cg	1/12	1	2	FACETS	0.764	0.571	0.974	1	0.895	1	CLONAL	2	TRUE	1	0.447694612411973	2		21	38	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845707	151845707	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	127	471	0	ENST00000262189.6:c.13305G>A	p.Trp4435Ter	p.W4435*	ENST00000262189	NM_170606.2	4435	tgG/tgA	52/59	1	2	FACETS	0.957	0.87	1	0.957	0.87	1	CLONAL	1	TRUE	1	0.447694612411973	2		471	593	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345930	152345930	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1200646566	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	94	426	0	ENST00000359321.1:c.640C>T	p.Arg214Ter	p.R214*	ENST00000359321	NM_005431.1	214	Cga/Tga	3/3	1	2	FACETS	0.882	0.788	0.981	0.882	0.788	0.981	CLONAL	1	TRUE	1	0.447694612411973	2		426	476	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958376	90958376	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs746135009	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	49	269	0	ENST00000265433.3:c.2062T>A	p.Phe688Ile	p.F688I	ENST00000265433	NM_002485.4	688	Ttc/Atc	13/16	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.447694612411973	2		269	217	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180273	27180273	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	171	451	0	ENST00000380036.4:c.937C>T	p.Leu313Phe	p.L313F	ENST00000380036	NM_000459.3	313	Ctt/Ttt	7/23	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.447694612411973	2		451	628	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570293	87570293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202111708	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	152	602	0	ENST00000277120.3:c.2033C>T	p.Ala678Val	p.A678V	ENST00000277120		678	gCg/gTg	17/19	1	2	FACETS	0.987	0.905	1	0.987	0.905	1	CLONAL	1	TRUE	1	0.447694612411973	2		602	688	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231239	98231239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs570441437	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	218	646	1	ENST00000331920.6:c.2044C>T	p.Arg682Cys	p.R682C	ENST00000331920	NM_000264.3	682	Cgc/Tgc	14/24	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.447694612411973	2		647	956	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759623	133759623	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	136	892	0	ENST00000318560.5:c.1950del	p.Leu651TrpfsTer43	p.L651Wfs*43	ENST00000318560	NM_005157.4	649	aCc/ac	11/11	1	2	FACETS	0.698	0.635	0.765	0.698	0.635	0.765	SUBCLONAL	1	TRUE	1	0.447694612411973	2		892	870	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223899	53223899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	371	420	0	ENST00000375401.3:c.3460del	p.Glu1154AsnfsTer110	p.E1154Nfs*110	ENST00000375401	NM_004187.3	1154	Gaa/aa	23/26	0.413534950837286	2	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.447694612411973	2		420	665	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410252	63410252	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	276	326	0	ENST00000330258.3:c.2915C>A	p.Pro972His	p.P972H	ENST00000330258	NM_152424.3	972	cCt/cAt	2/2	0.413534950837286	2	FACETS	0.867	0.827	0.907			1	CLONAL	3	TRUE	NA	0.447694612411973	2		326	474	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405953	157405954	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1554294674	NA	P-0054342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	704	44	0	ENST00000346085.5:c.2201dup	p.Ser736IlefsTer27	p.S736Ifs*27	ENST00000346085	NM_020732.3	732	ccg/ccGg	6/20	0.204005986998829	1	FACETS	1	0.995	1	1	0.998	1	INDETERMINATE	2	TRUE	0	0.34482634075024	1		44	1454	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0054342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	402	378	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.993	1	1	0.997	1	CLONAL	2	TRUE	1	0.34482634075024	2		378	950	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144146	11144146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	942	49	1	ENST00000358026.2:c.3727C>T	p.Arg1243Trp	p.R1243W	ENST00000358026	NM_001128849.1	1243	Cgg/Tgg	26/36	0.34482634075024	1	FACETS	1	0.997	1	1	0.999	1	CLONAL	2	TRUE	0	0.34482634075024	1		50	1833	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130120	143130120	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	549	42	1	ENST00000262992.4:c.896del	p.Asn299MetfsTer10	p.N299Mfs*10	ENST00000262992	NM_001101669.1	299	aAt/at	11/24	1	2	FACETS	1	0.995	1	1	0.998	1	CLONAL	2	TRUE	1	0.34482634075024	2		43	1302	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827886	40827886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201911869	NA	P-0054342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	559	92	0	ENST00000373198.4:c.2542G>A	p.Gly848Arg	p.G848R	ENST00000373198	NM_133170.3	848	Gga/Aga	17/32	1	2	FACETS	0.962	0.928	0.997	1	0.998	1	CLONAL	3	TRUE	1	0.34482634075024	2		92	1123	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs371769427	NA	P-0054342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	271	49	0	ENST00000291552.4:c.101C>A	p.Ser34Tyr	p.S34Y	ENST00000291552	NM_006758.2	34	tCt/tAt	2/8	1	2	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	TRUE	1	0.34482634075024	2		49	636	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034491	47034491	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	747	167	0	ENST00000377604.3:c.576G>T	p.Gln192His	p.Q192H	ENST00000377604	NM_001204468.1	192	caG/caT	6/24	0.204005986998829	1	FACETS	1	0.996	1	1	0.998	1	INDETERMINATE	2	TRUE	0	0.34482634075024	1		167	1526	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110165	8110165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774454455	NA	P-0054342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	713	101	0	ENST00000585124.1:c.440G>A	p.Arg147Gln	p.R147Q	ENST00000585124	NM_004217.3	147	cGg/cAg	6/9	1	2	FACETS	0.956	0.925	0.986	1	0.998	1	CLONAL	3	TRUE	1	0.34482634075024	2		101	1442	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220691	1220691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	1363	300	1	ENST00000326873.7:c.709G>A	p.Asp237Asn	p.D237N	ENST00000326873	NM_000455.4	237	Gac/Aac	5/10	0.34482634075024	1	FACETS	0.947	0.927	0.967			1	CLONAL	3	TRUE	0	0.34482634075024	1		301	2302	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031970	10031970	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	775	104	1	ENST00000330684.3:c.853del	p.Asp285ThrfsTer8	p.D285Tfs*8	ENST00000330684	NM_001134407.1	285	Gac/ac	3/13	1	2	FACETS	0.96	0.931	0.99	1	0.998	1	CLONAL	3	TRUE	1	0.34482634075024	2		105	1560	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950285	15950285	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	590	98	0	ENST00000268712.3:c.6659G>T	p.Gly2220Val	p.G2220V	ENST00000268712	NM_006311.3	2220	gGt/gTt	42/46	1	2	FACETS	1	0.996	1	1	0.998	1	CLONAL	2	TRUE	1	0.34482634075024	2		98	1383	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955634	55955634	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs138424770	NA	P-0054342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	411	63	0	ENST00000263923.4:c.3311C>A	p.Ser1104Tyr	p.S1104Y	ENST00000263923	NM_002253.2	1104	tCt/tAt	25/30	1	2	FACETS	0.9	0.861	0.939	1	0.997	1	CLONAL	3	TRUE	1	0.34482634075024	2		63	883	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467545	66467545	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	338	66	0	ENST00000273854.3:c.724G>T	p.Val242Phe	p.V242F	ENST00000273854	NM_004439.5	242	Gtc/Ttc	3/18	1	2	FACETS	0.851	0.81	0.892	1	0.997	1	CLONAL	3	TRUE	1	0.34482634075024	2		66	768	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229491	98229491	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	479	83	0	ENST00000331920.6:c.2467C>A	p.His823Asn	p.H823N	ENST00000331920	NM_000264.3	823	Cac/Aac	15/24	1	2	FACETS	0.887	0.852	0.923	1	0.998	1	CLONAL	3	TRUE	1	0.34482634075024	2		83	1044	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0054343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	308	29	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	1	2	FACETS	0.881	0.837	0.926	1	0.996	1	CLONAL	3	TRUE	1	0.336353365563542	2		29	693	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268419	142268419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs980426116	NA	P-0054343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	408	39	0	ENST00000350721.4:c.3073C>T	p.Arg1025Cys	p.R1025C	ENST00000350721	NM_001184.3	1025	Cgt/Tgt	15/47	1	2	FACETS	0.921	0.881	0.961	1	0.997	1	CLONAL	3	TRUE	1	0.336353365563542	2		39	878	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710627	114710627	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	472	34	0	ENST00000543371.1:c.112G>T	p.Glu38Ter	p.E38*	ENST00000543371	NM_001198531.1	38	Gag/Tag	1/14	1	2	FACETS	0.872	0.836	0.908	1	0.998	1	CLONAL	3	TRUE	1	0.336353365563542	2		34	1073	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982766	7982767	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1285636957	NA	P-0054343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	1133	114	0	ENST00000319144.4:c.1018dup	p.Leu340ProfsTer34	p.L340Pfs*34	ENST00000319144	NM_001139.2	340	ctc/cCtc	8/15	1	2	FACETS	1	0.986	1	1	0.999	1	CLONAL	3	TRUE	1	0.336353365563542	2		114	2208	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808028	1808028	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1261	1260	91	0	ENST00000260795.2:c.2004C>G	p.Asp668Glu	p.D668E	ENST00000260795		668	gaC/gaG	14/17	1	2	FACETS	0.991	0.967	1	1	0.999	1	CLONAL	3	TRUE	1	0.336353365563542	2		91	2521	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958875	38958875	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	271	30	0	ENST00000357387.3:c.2237T>C	p.Phe746Ser	p.F746S	ENST00000357387	NM_152756.3	746	tTc/tCc	23/38	1	2	FACETS	0.869	0.822	0.916	1	0.996	1	CLONAL	3	TRUE	1	0.336353365563542	2		30	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0054344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	1201	812	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.503762902403069	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.521738672859172	2		812	2096	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259166	89259166	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	399	136	1	ENST00000336596.2:c.310C>T	p.Arg104Ter	p.R104*	ENST00000336596	NM_005233.5	104	Cga/Tga	3/17	1	2	FACETS	0.958	0.918	0.999	1	0.997	1	CLONAL	2	TRUE	1	0.521738672859172	2		137	798	SUCCESS
APC	324	MSKCC	GRCh37	5	112175419	112175419	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0054344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	317	106	0	ENST00000257430.4:c.4128T>A	p.Tyr1376Ter	p.Y1376*	ENST00000257430	NM_000038.5	1376	taT/taA	16/16	1	2	FACETS	0.977	0.931	1	1	0.996	1	CLONAL	2	TRUE	1	0.521738672859172	2		106	622	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602601	10602601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751665354	NA	P-0054344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	1112	358	0	ENST00000171111.5:c.977G>A	p.Arg326His	p.R326H	ENST00000171111	NM_203500.1	326	cGc/cAc	3/6	1	2	FACETS	0.943	0.919	0.968	1	0.999	1	CLONAL	2	TRUE	1	0.521738672859172	2		358	2259	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604706	48604706	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	521	172	0	ENST00000342988.3:c.1528G>C	p.Gly510Arg	p.G510R	ENST00000342988	NM_005359.5	510	Gga/Cga	12/12	0.521738672859172	1	FACETS	0.849	0.821	0.877	1	0.997	1	CLONAL	2	TRUE	0	0.521738672859172	1		172	869	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243708834	243708834	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	425	104	0	ENST00000263826.5:c.1229G>C	p.Trp410Ser	p.W410S	ENST00000263826	NM_005465.4	410	tGg/tCg	11/13	1	2	FACETS	0.924	0.885	0.962	1	0.997	1	CLONAL	2	TRUE	1	0.521738672859172	2		104	882	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511512	38511513	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	novel	NA	P-0054344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	740	275	0	ENST00000254066.5:c.1013-2dup		p.X338_splice	ENST00000254066	NM_000964.3	338			0.503762902403069	2	FACETS	0.906	0.877	0.935	0.906	0.877	0.935	CLONAL	2	TRUE	0	0.521738672859172	2		275	1566	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265028	46265028	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1416106002	NA	P-0054344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1442	563	200	0	ENST00000371998.3:c.1898G>T	p.Gly633Val	p.G633V	ENST00000371998		633	gGt/gTt	12/23	0.521738672859172	5	FACETS	0.959	0.919	1	0.64	0.612	0.667	CLONAL	2	TRUE	2	0.521738672859172	5		200	2005	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876413	35876413	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	838	246	0	ENST00000303115.3:c.1205A>G	p.Gln402Arg	p.Q402R	ENST00000303115	NM_002185.3	402	cAg/cGg	8/8	1	2	FACETS	0.919	0.892	0.947	1	0.998	1	CLONAL	2	TRUE	1	0.521738672859172	2		246	1747	SUCCESS
APC	324	MSKCC	GRCh37	5	112174583	112174587	+	frameshift_variant	Frame_Shift_Del	DEL	TGTGT	TGTGT	-	novel	NA	P-0054344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	385	167	0	ENST00000257430.4:c.3293_3297del	p.Cys1098PhefsTer19	p.C1098Ffs*19	ENST00000257430	NM_000038.5	1098	TGTGTt/t	16/16	1	2	FACETS	0.84	0.802	0.879	1	0.996	1	CLONAL	2	TRUE	1	0.521738672859172	2		167	878	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922228	39922228	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	297	407	1	ENST00000378444.4:c.3944C>T	p.Ser1315Phe	p.S1315F	ENST00000378444	NM_001123385.1	1315	tCc/tTc	9/15	0.450288190719942	2	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.521738672859172	2		408	498	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	263	392	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.853	0.809	0.896	1	0.996	1	CLONAL	3	TRUE	1	0.410414351367739	2		392	501	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	769	772	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.977	1	1	0.998	1	CLONAL	3	TRUE	1	0.410414351367739	2		777	1244	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	689	693	4	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.904	0.876	0.931	1	0.998	1	CLONAL	3	TRUE	1	0.410414351367739	2		697	1238	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175857	24175859	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs875989800	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	598	15	0	ENST00000263121.7:c.1091_1093del	p.Lys364del	p.K364del	ENST00000263121	NM_003073.3	362	gAGAag/gag	8/9	1	2	FACETS	0.855	0.826	0.884	1	0.998	1	CLONAL	3	TRUE	1	0.410414351367739	2		15	1136	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	468	38	3	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	1	0.995	1	1	0.997	1	CLONAL	2	TRUE	1	0.410414351367739	2		41	942	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846308	156846308	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	915	145	0	ENST00000524377.1:c.1753del	p.Leu585CysfsTer73	p.L585Cfs*73	ENST00000524377	NM_002529.3	583	cgC/cg	14/17	1	2	FACETS	0.963	0.939	0.988	1	0.999	1	CLONAL	3	TRUE	1	0.410414351367739	2		145	1543	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256768	19256769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1202792889	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	875	52	2	ENST00000162023.5:c.944dup	p.Val316SerfsTer6	p.V316Sfs*6	ENST00000162023		315	cca/ccCa	13/13	1	2	FACETS	0.941	0.916	0.965	1	0.999	1	CLONAL	3	TRUE	1	0.410414351367739	2		54	1511	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201684	67201684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376762664	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	790	137	0	ENST00000312629.5:c.985C>T	p.Arg329Trp	p.R329W	ENST00000312629	NM_003952.2	329	Cgg/Tgg	12/15	1	2	FACETS	0.958	0.932	0.984	1	0.998	1	CLONAL	3	TRUE	1	0.410414351367739	2		137	1339	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	334	47	1	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.901	0.862	0.94	1	0.997	1	CLONAL	3	TRUE	1	0.410414351367739	2		48	602	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390946	89390946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	292	58	0	ENST00000336596.2:c.1012G>A	p.Glu338Lys	p.E338K	ENST00000336596	NM_005233.5	338	Gag/Aag	5/17	1	2	FACETS	0.875	0.834	0.916	1	0.996	1	CLONAL	3	TRUE	1	0.410414351367739	2		58	542	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543828	212543828	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371593463	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	322	98	0	ENST00000342788.4:c.1571G>A	p.Arg524His	p.R524H	ENST00000342788	NM_005235.2	524	cGc/cAc	13/28	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.410414351367739	2		98	704	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664989	138664989	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	292	67	0	ENST00000330315.3:c.576del	p.Lys193SerfsTer78	p.K193Sfs*78	ENST00000330315	NM_023067.3	192	ccC/cc	1/1	1	2	FACETS	0.869	0.827	0.91	1	0.996	1	CLONAL	3	TRUE	1	0.410414351367739	2		67	546	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	1006	203	1	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.927	0.904	0.95	1	0.999	1	CLONAL	3	TRUE	1	0.410414351367739	2		204	1763	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	874	142	3	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.925	0.9	0.949	1	0.999	1	CLONAL	3	TRUE	1	0.410414351367739	2		145	1535	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	674	107	10	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	1	2	FACETS	0.922	0.894	0.949	1	0.998	1	CLONAL	3	TRUE	1	0.410414351367739	2		117	1188	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910411	50910411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762273084	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	850	290	2	ENST00000440232.2:c.1666G>A	p.Val556Ile	p.V556I	ENST00000440232	NM_002691.3	556	Gta/Ata	13/27	1	2	FACETS	0.929	0.904	0.954	1	0.998	1	CLONAL	3	TRUE	1	0.410414351367739	2		292	1486	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200723	128200723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	812	148	3	ENST00000341105.2:c.1082G>A	p.Arg361His	p.R361H	ENST00000341105	NM_032638.4	361	cGc/cAc	5/6	1	2	FACETS	0.907	0.881	0.932	1	0.998	1	CLONAL	3	TRUE	1	0.410414351367739	2		151	1455	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456738	32456738	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	718	142	0	ENST00000332351.3:c.154C>T	p.Arg52Cys	p.R52C	ENST00000332351	NM_024426.4	52	Cgt/Tgt	1/10	1	2	FACETS	0.937	0.909	0.964	1	0.998	1	CLONAL	3	TRUE	1	0.410414351367739	2		142	1245	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822586	72822586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	584	100	0	ENST00000268489.5:c.9589del	p.Gln3197SerfsTer44	p.Q3197Sfs*44	ENST00000268489	NM_006885.3	3197	Cag/ag	10/10	1	2	FACETS	0.957	0.927	0.987	1	0.998	1	CLONAL	3	TRUE	1	0.410414351367739	2		100	991	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136798	2136798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555438551	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	907	170	1	ENST00000219476.3:c.4915C>T	p.Arg1639Cys	p.R1639C	ENST00000219476	NM_000548.3	1639	Cgc/Tgc	38/42	1	2	FACETS	0.856	0.832	0.879	1	0.999	1	CLONAL	3	TRUE	1	0.410414351367739	2		171	1722	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	422	23	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	0.410414351367739	1	FACETS	1	0.982	1	1	0.997	1	CLONAL	2	TRUE	0	0.410414351367739	1		23	786	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228979	36228979	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555734923	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	783	133	2	ENST00000222270.7:c.7759C>T	p.Arg2587Ter	p.R2587*	ENST00000222270	NM_014727.1	2587	Cga/Tga	36/37	1	2	FACETS	0.893	0.867	0.919	1	0.998	1	CLONAL	3	TRUE	1	0.410414351367739	2		135	1424	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326485	62326485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1319765421	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	1083	190	1	ENST00000360203.5:c.3410G>A	p.Gly1137Asp	p.G1137D	ENST00000360203	NM_001283009.1	1137	gGc/gAc	33/35	1	2	FACETS	0.93	0.908	0.952	1	0.999	1	CLONAL	3	TRUE	1	0.410414351367739	2		191	1892	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739024	145739024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371818842	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	801	155	0	ENST00000428558.2:c.2131G>A	p.Glu711Lys	p.E711K	ENST00000428558	NM_004260.3	711	Gag/Aag	13/22	1	2	FACETS	0.888	0.862	0.913	1	0.998	1	CLONAL	3	TRUE	1	0.410414351367739	2		155	1466	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436297	110436302	+	inframe_deletion	In_Frame_Del	DEL	CGGCGG	CGGCGG	-	rs34412495	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	252	19	0	ENST00000375856.3:c.2099_2104del	p.Ala700_Ala701del	p.A700_A701del	ENST00000375856	NM_003749.2	700	gCCGCCGtg/gtg	1/2	1	2	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	TRUE	1	0.410414351367739	2		19	495	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872936	136872936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	293	64	0	ENST00000241393.3:c.562C>T	p.Arg188Cys	p.R188C	ENST00000241393	NM_003467.2	188	Cgc/Tgc	2/2	1	2	FACETS	1	0.992	1	1	0.996	1	CLONAL	2	TRUE	1	0.410414351367739	2		64	581	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035204	6035207	+	frameshift_variant	Frame_Shift_Del	DEL	CTGT	CTGT	-	rs267608154	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	320	87	0	ENST00000265849.7:c.861_864del	p.Arg287SerfsTer19	p.R287Sfs*19	ENST00000265849	NM_000535.5	287	agACAG/ag	8/15	1	2	FACETS	1	0.977	1	1	0.996	1	CLONAL	2	TRUE	1	0.410414351367739	2		87	745	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342999	225342999	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	374	100	0	ENST00000264414.4:c.2093A>G	p.Asp698Gly	p.D698G	ENST00000264414	NM_003590.4	698	gAc/gGc	15/16	1	2	FACETS	1	0.99	1	1	0.997	1	CLONAL	2	TRUE	1	0.410414351367739	2		100	809	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655419	45655419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1181740577	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	672	197	1	ENST00000407780.3:c.433G>A	p.Ala145Thr	p.A145T	ENST00000407780	NM_001283052.1	145	Gcc/Acc	4/7	1	2	FACETS	1	0.996	1	1	0.998	1	CLONAL	2	TRUE	1	0.410414351367739	2		198	1372	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356332	66356332	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs553493695	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	351	87	0	ENST00000273854.3:c.1165G>A	p.Val389Met	p.V389M	ENST00000273854	NM_004439.5	389	Gtg/Atg	5/18	1	2	FACETS	1	0.993	1	1	0.997	1	CLONAL	2	TRUE	1	0.410414351367739	2		87	695	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128201270	128201270	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	572	133	0	ENST00000265960.3:c.1465C>T	p.Arg489Ter	p.R489*	ENST00000265960	NM_001006617.1	489	Cga/Tga	12/12	1	2	FACETS	0.837	0.808	0.866	1	0.998	1	CLONAL	3	TRUE	1	0.410414351367739	2		133	1110	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31504699	31504699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1032572786	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	411	38	1	ENST00000344624.3:c.1631G>A	p.Arg544His	p.R544H	ENST00000344624		544	cGc/cAc	8/33	1	2	FACETS	1	0.975	1	1	0.997	1	CLONAL	2	TRUE	1	0.410414351367739	2		39	973	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652243	36652243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs558863376	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	650	126	0	ENST00000244741.5:c.365G>A	p.Arg122His	p.R122H	ENST00000244741	NM_000389.4	122	cGc/cAc	2/3	1	2	FACETS	0.936	0.907	0.965	1	0.998	1	CLONAL	3	TRUE	1	0.410414351367739	2		126	1128	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324542	31324543	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	418	22	0	ENST00000412585.2:c.265_266del	p.Gln89AspfsTer9	p.Q89Dfs*9	ENST00000412585	NM_005514.6	89	CAg/g	2/8	0.410414351367739	1	FACETS	1	0.991	1	1	0.997	1	CLONAL	2	TRUE	0	0.410414351367739	1		22	733	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046749	180046749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121909657	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	968	148	1	ENST00000261937.6:c.2563G>A	p.Ala855Thr	p.A855T	ENST00000261937	NM_182925.4	855	Gcc/Acc	18/30	1	2	FACETS	0.942	0.918	0.965	1	0.999	1	CLONAL	3	TRUE	1	0.410414351367739	2		149	1670	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42026793	42026793	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	239	54	0	ENST00000219905.7:c.3916+1G>A		p.X1306_splice	ENST00000219905	NM_001164273.1	1306			1	2	FACETS	0.865	0.819	0.91	1	0.996	1	CLONAL	3	TRUE	1	0.410414351367739	2		54	449	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782588	9782588	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	691	171	1	ENST00000377346.4:c.2350C>T	p.Leu784Phe	p.L784F	ENST00000377346	NM_005026.3	784	Ctc/Ttc	19/24	1	2	FACETS	0.928	0.901	0.956	1	0.998	1	CLONAL	3	TRUE	1	0.410414351367739	2		172	1209	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11313963	11313963	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1039496779	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	658	154	0	ENST00000361445.4:c.773A>G	p.Asp258Gly	p.D258G	ENST00000361445	NM_004958.3	258	gAt/gGt	6/58	1	2	FACETS	0.87	0.843	0.898	1	0.998	1	CLONAL	3	TRUE	1	0.410414351367739	2		154	1228	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363823	118363823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377724112	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	404	100	0	ENST00000534358.1:c.5056C>T	p.Arg1686Cys	p.R1686C	ENST00000534358	NM_005933.3	1686	Cgc/Tgc	16/36	1	2	FACETS	0.835	0.8	0.869	1	0.997	1	CLONAL	3	TRUE	1	0.410414351367739	2		100	786	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120785265	120785266	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCCGCTGCC	rs753597947	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	581	66	0	ENST00000257552.2:c.834_842dup	p.Ala279_Ala281dup	p.A279_A281dup	ENST00000257552	NM_002442.3	279	gct/gcGGCAGCGGCt	12/15	1	2	FACETS	1	0.996	1	1	0.998	1	CLONAL	2	TRUE	1	0.410414351367739	2		66	1143	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929235	32929235	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs886038163	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	424	112	0	ENST00000380152.3:c.7248del	p.His2417ThrfsTer50	p.H2417Tfs*50	ENST00000380152		2415	caT/ca	14/27	1	2	FACETS	0.835	0.801	0.869	1	0.997	1	CLONAL	3	TRUE	1	0.410414351367739	2		112	825	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135327	30135327	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	365	91	0	ENST00000331968.5:c.491G>A	p.Gly164Glu	p.G164E	ENST00000331968	NM_002742.2	164	gGa/gAa	3/18	1	2	FACETS	0.847	0.81	0.884	1	0.997	1	CLONAL	3	TRUE	1	0.410414351367739	2		91	700	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707872	43707873	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	684	163	0	ENST00000382044.4:c.5008_5009del	p.Ser1670ArgfsTer9	p.S1670Rfs*9	ENST00000382044	NM_001141980.1	1670	TCa/a	23/28	1	2	FACETS	0.844	0.817	0.87	1	0.998	1	CLONAL	3	TRUE	1	0.410414351367739	2		163	1317	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639089	3639090	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	830	170	0	ENST00000294008.3:c.4549dup	p.Glu1517GlyfsTer33	p.E1517Gfs*33	ENST00000294008	NM_032444.2	1517	gaa/gGaa	12/15	1	2	FACETS	0.927	0.902	0.953	1	0.998	1	CLONAL	3	TRUE	1	0.410414351367739	2		170	1454	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647634	23647634	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1313634930	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	310	66	0	ENST00000261584.4:c.233T>C	p.Val78Ala	p.V78A	ENST00000261584	NM_024675.3	78	gTt/gCt	4/13	1	2	FACETS	0.859	0.819	0.899	1	0.997	1	CLONAL	3	TRUE	1	0.410414351367739	2		66	586	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119722	70119722	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	420	95	0	ENST00000245479.2:c.727del	p.Thr243ProfsTer10	p.T243Pfs*10	ENST00000245479	NM_000346.3	242	Aaa/aa	3/3	1	2	FACETS	0.857	0.823	0.891	1	0.997	1	CLONAL	3	TRUE	1	0.410414351367739	2		95	796	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795424	42795424	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	812	117	0	ENST00000575354.2:c.2504A>T	p.Gln835Leu	p.Q835L	ENST00000575354	NM_015125.3	835	cAg/cTg	10/20	1	2	FACETS	1	0.995	1	1	0.999	1	CLONAL	3	TRUE	1	0.410414351367739	2		117	1229	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42843883	42843883	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	385	79	0	ENST00000398585.3:c.1036A>T	p.Thr346Ser	p.T346S	ENST00000398585	NM_001135099.1	346	Acg/Tcg	10/14	1	2	FACETS	0.885	0.848	0.921	1	0.997	1	CLONAL	3	TRUE	1	0.410414351367739	2		79	707	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12647758	12647758	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	244	59	2	ENST00000251849.4:c.622G>T	p.Ala208Ser	p.A208S	ENST00000251849	NM_002880.3	208	Gca/Tca	6/17	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.410414351367739	2		61	505	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439283	52439283	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	689	132	1	ENST00000460680.1:c.959G>T	p.Cys320Phe	p.C320F	ENST00000460680	NM_004656.3	320	tGc/tTc	11/17	1	2	FACETS	1	0.996	1	1	0.998	1	CLONAL	2	TRUE	1	0.410414351367739	2		133	1409	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976881	55976881	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	523	147	0	ENST00000263923.4:c.1031del	p.Val344GlyfsTer19	p.V344Gfs*19	ENST00000263923	NM_002253.2	344	gTg/gg	8/30	1	2	FACETS	1	0.995	1	1	0.998	1	CLONAL	2	TRUE	1	0.410414351367739	2		147	1073	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270186	66270186	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	173	12	0	ENST00000273854.3:c.1696T>A	p.Ser566Thr	p.S566T	ENST00000273854	NM_004439.5	566	Tcc/Acc	8/18	1	2	FACETS	1	0.975	1	1	0.994	1	CLONAL	2	TRUE	1	0.410414351367739	2		12	385	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66468023	66468023	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	175	20	0	ENST00000273854.3:c.247-1G>A		p.X83_splice	ENST00000273854	NM_004439.5	83			1	2	FACETS	1	0.983	1	1	0.995	1	CLONAL	3	TRUE	1	0.410414351367739	2		20	260	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441602	6441602	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	390	71	0	ENST00000356142.4:c.449A>T	p.Glu150Val	p.E150V	ENST00000356142	NM_018890.3	150	gAg/gTg	6/7	1	2	FACETS	0.97	0.933	1	1	0.997	1	CLONAL	3	TRUE	1	0.410414351367739	2		71	653	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873887	151873887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761131667	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	345	59	0	ENST00000262189.6:c.8651G>A	p.Arg2884Gln	p.R2884Q	ENST00000262189	NM_170606.2	2884	cGa/cAa	38/59	1	2	FACETS	1	0.993	1	1	0.997	1	CLONAL	2	TRUE	1	0.410414351367739	2		59	686	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982040	70982040	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113166129	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	960	174	1	ENST00000276594.2:c.56C>T	p.Pro19Leu	p.P19L	ENST00000276594	NM_024504.3	19	cCg/cTg	2/8	1	2	FACETS	0.941	0.917	0.964	1	0.999	1	CLONAL	3	TRUE	1	0.410414351367739	2		175	1658	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169529	27169529	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1485283183	NA	P-0054345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	489	32	0	ENST00000380036.4:c.530A>C	p.His177Pro	p.H177P	ENST00000380036	NM_000459.3	177	cAc/cCc	4/23	1	2	FACETS	1	0.993	1	1	0.998	1	CLONAL	2	TRUE	1	0.410414351367739	2		32	1039	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	496	375	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.933	0.905	0.96	1	0.998	1	CLONAL	2	TRUE	1	0.745657397102149	2		375	713	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775653	9775653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	963	341	1	ENST00000377346.4:c.196G>A	p.Glu66Lys	p.E66K	ENST00000377346	NM_005026.3	66	Gag/Aag	4/24	1	2	FACETS	0.879	0.858	0.899	1	0.998	1	CLONAL	2	TRUE	1	0.745657397102149	2		342	1470	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808622	1808623	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0054346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	1425	722	1	ENST00000260795.2:c.2235_2236delinsAA	p.Glu746Lys	p.E746K	ENST00000260795		745	gtGGag/gtAAag	16/17	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.745657397102149	NA		723	2029	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184124	123184134	+	frameshift_variant	Frame_Shift_Del	DEL	TATTTAAAATA	TATTTAAAATA	-	novel	NA	P-0054346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	154	144	0	ENST00000218089.9:c.983_993del	p.Tyr328CysfsTer7	p.Y328Cfs*7	ENST00000218089	NM_001042749.1	328	TATTTAAAATAt/t	11/35	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.745657397102149	1		144	184	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0054347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	343	392	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.994	1	1	0.997	1	CLONAL	2	TRUE	1	0.547698884528584	2		392	531	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518190	8518190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	419	91	0	ENST00000356435.5:c.1201C>T	p.Arg401Trp	p.R401W	ENST00000356435		401	Cgg/Tgg	10/35	0.547698884528584	8	FACETS	0.857	0.815	0.9	0.321	0.305	0.338	CLONAL	3	TRUE	0	0.547698884528584	8		91	1573	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0054348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	471	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.987	0.953	1	0.987	0.953	1	CLONAL	1	TRUE	1	1.24	2		248	770	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0054348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	266	169	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.977	0.932	1	0.977	0.932	1	CLONAL	1	TRUE	1	1.24	2		169	439	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0054348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	888	879	2	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	1	0.999	1	1	0.999	1	CLONAL	1	TRUE	1	1.24	2		881	997	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115111972	115111972	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	958	520	0	ENST00000257566.3:c.1768C>T	p.Gln590Ter	p.Q590*	ENST00000257566	NM_016569.3	590	Cag/Tag	7/8	1	2	FACETS	0.997	0.973	1	0.997	0.973	1	CLONAL	1	TRUE	1	1.24	2		520	1550	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445091	89445091	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	371	222	1	ENST00000336596.2:c.1411G>A	p.Glu471Lys	p.E471K	ENST00000336596	NM_005233.5	471	Gag/Aag	6/17	1	2	FACETS	0.911	0.873	0.948	0.911	0.873	0.948	CLONAL	1	TRUE	1	1.24	2		223	657	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445116	49445116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	1037	469	0	ENST00000301067.7:c.2350G>A	p.Glu784Lys	p.E784K	ENST00000301067	NM_003482.3	784	Gag/Aag	10/54	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	1.24	2		469	1673	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448200	49448200	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0054348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	646	332	0	ENST00000301067.7:c.401-1G>A		p.X134_splice	ENST00000301067	NM_003482.3	134			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	1.24	2		332	1040	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445575	49445575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	1214	575	1	ENST00000301067.7:c.1891G>A	p.Glu631Lys	p.E631K	ENST00000301067	NM_003482.3	631	Gag/Aag	10/54	1	2	FACETS	0.991	0.97	1	0.991	0.97	1	CLONAL	1	TRUE	1	1.24	2		576	1976	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444900	49444900	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	1147	540	0	ENST00000301067.7:c.2566G>C	p.Glu856Gln	p.E856Q	ENST00000301067	NM_003482.3	856	Gag/Cag	10/54	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	1.24	2		540	1788	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444927	49444927	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1439134461	NA	P-0054348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	1031	436	0	ENST00000301067.7:c.2539G>A	p.Glu847Lys	p.E847K	ENST00000301067	NM_003482.3	847	Gag/Aag	10/54	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	1.24	2		436	1606	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445035	49445035	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	920	421	1	ENST00000301067.7:c.2431G>T	p.Glu811Ter	p.E811*	ENST00000301067	NM_003482.3	811	Gag/Tag	10/54	1	2	FACETS	0.978	0.953	1	0.978	0.953	1	CLONAL	1	TRUE	1	1.24	2		422	1518	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445143	49445143	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	1145	505	0	ENST00000301067.7:c.2323G>C	p.Glu775Gln	p.E775Q	ENST00000301067	NM_003482.3	775	Gag/Cag	10/54	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	1.24	2		505	1812	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806564	1806564	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	936	59	0	ENST00000260795.2:c.1280C>A	p.Ser427Tyr	p.S427Y	ENST00000260795		427	tCc/tAc	9/17	1	2	FACETS	0.747	0.725	0.769	0.747	0.725	0.769	SUBCLONAL	1	TRUE	1	1.24	2		59	2021	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264609	1264609	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	971	545	1	ENST00000310581.5:c.2753C>A	p.Ala918Asp	p.A918D	ENST00000310581	NM_198253.2	918	gCt/gAt	11/16	1	2	FACETS	0.976	0.952	0.999	0.976	0.952	0.999	CLONAL	1	TRUE	1	1.24	2		546	1605	SUCCESS
APC	324	MSKCC	GRCh37	5	112178951	112178952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0054348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	327	182	0	ENST00000257430.4:c.7660_7661insG	p.His2554ArgfsTer29	p.H2554Rfs*29	ENST00000257430	NM_000038.5	2554	cat/cGat	16/16	1	2	FACETS	0.942	0.902	0.982	0.942	0.902	0.982	CLONAL	1	TRUE	1	1.24	2		182	560	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877161	151877161	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	486	228	0	ENST00000262189.6:c.7200del	p.Ile2400MetfsTer52	p.I2400Mfs*52	ENST00000262189	NM_170606.2	2400	atT/at	37/59	1	2	FACETS	0.892	0.859	0.924	0.892	0.859	0.924	CLONAL	1	TRUE	1	1.24	2		228	879	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181227	123181228	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGAATGTGGCACTAAATCTTAGCATTAATATGGATAATACATAT	novel	NA	P-0054348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	320	83	0	ENST00000218089.9:c.732_733insTATTGAATGTGGCACTAAATCTTAGCATTAATATGGATAATACA	p.Gln245TyrfsTer2	p.Q245Yfs*2	ENST00000218089	NM_001042749.1	231	gtg/gTGAATGTGGCACTAAATCTTAGCATTAATATGGATAATACATATtg	9/35	1	2	FACETS	0.751	0.715	0.788	0.751	0.715	0.788	SUBCLONAL	1	TRUE	1	1.24	2		83	687	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	479	375	0				ENST00000310581	NM_198253.2	-/1132			0.285120134024044	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.460847543899925	3		375	1155	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	698	276	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.460847543899925	1	FACETS	0.952	0.924	0.981	1	0.998	1	CLONAL	2	TRUE	0	0.460847543899925	1		276	1224	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397142	397142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs999945656	NA	P-0054350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	484	87	1	ENST00000380956.4:c.527G>A	p.Arg176Gln	p.R176Q	ENST00000380956	NM_001195286.1	176	cGa/cAa	5/9	0.390585228728136	3	FACETS	0.965	0.924	1	0.965	0.924	1	CLONAL	2	TRUE	1	0.460847543899925	3		88	1339	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331723	8331723	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367558329	NA	P-0054350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	457	79	0	ENST00000356435.5:c.5393G>A	p.Arg1798Gln	p.R1798Q	ENST00000356435		1798	cGa/cAa	33/35	0.164310714593602	3	FACETS	1	0.988	1	1	0.988	1	INDETERMINATE	2	TRUE	1	0.460847543899925	3		79	1130	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101309	27101309	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	1004	442	1	ENST00000324856.7:c.4591G>T	p.Glu1531Ter	p.E1531*	ENST00000324856	NM_006015.4	1531	Gaa/Taa	18/20	0.330860101293047	1	FACETS	0.876	0.853	0.899	1	0.998	1	CLONAL	2	TRUE	0	0.460847543899925	1		443	1914	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711992	89711992	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	318	63	0	ENST00000371953.3:c.611del	p.Pro204GlnfsTer17	p.P204Qfs*17	ENST00000371953	NM_000314.4	204	Cca/ca	6/9	0.460847543899925	1	FACETS	1	0.995	1	1	0.997	1	CLONAL	2	TRUE	0	0.460847543899925	1		63	432	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37863276	37863276	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1567	901	166	1	ENST00000269571.5:c.107C>T	p.Pro36Leu	p.P36L	ENST00000269571		36	cCt/cTt	2/27	0.164310714593602	3	FACETS	0.975	0.944	1	0.975	0.944	1	INDETERMINATE	2	TRUE	1	0.460847543899925	3		167	2468	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347966	70347966	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770988288	NA	P-0054350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	311	103	0	ENST00000374080.3:c.3205G>A	p.Asp1069Asn	p.D1069N	ENST00000374080		1069	Gat/Aat	22/45	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.460847543899925	1		103	812	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720853	89720853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1085308040	NA	P-0054350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	403	82	0	ENST00000371953.3:c.1004G>A	p.Arg335Gln	p.R335Q	ENST00000371953	NM_000314.4	335	cGa/cAa	8/9	0.460847543899925	1	FACETS	1	0.995	1	1	0.997	1	CLONAL	2	TRUE	0	0.460847543899925	1		82	572	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551650	150551650	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2085	676	114	0	ENST00000369026.2:c.357C>G	p.Ile119Met	p.I119M	ENST00000369026	NM_021960.4	119	atC/atG	1/3	0.328103628164833	4	FACETS	0.776	0.745	0.807			1	SUBCLONAL	2	TRUE	NA	0.460847543899925	4		114	2761	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180427	94180427	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	473	69	0	ENST00000323929.3:c.1741G>C	p.Gly581Arg	p.G581R	ENST00000323929	NM_005591.3	581	Ggg/Cgg	15/20	0.102100071562079	0	FACETS	0.883	0.845	0.921			1	INDETERMINATE	1	TRUE	0	0.460847543899925	0		69	1254	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426331	49426331	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs995485937	NA	P-0054350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1296	1106	138	0	ENST00000301067.7:c.12157A>G	p.Thr4053Ala	p.T4053A	ENST00000301067	NM_003482.3	4053	Act/Gct	39/54	0.460847543899925	1	FACETS	0.769	0.748	0.789	1	0.998	1	SUBCLONAL	2	TRUE	0	0.460847543899925	1		138	2402	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911261	32911261	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	487	55	0	ENST00000380152.3:c.2769G>C	p.Lys923Asn	p.K923N	ENST00000380152		923	aaG/aaC	11/27	0.460847543899925	1	FACETS	1	0.993	1	1	0.998	1	CLONAL	2	TRUE	0	0.460847543899925	1		55	741	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913587	32913587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358731	NA	P-0054350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	312	39	0	ENST00000380152.3:c.5095G>A	p.Asp1699Asn	p.D1699N	ENST00000380152		1699	Gat/Aat	11/27	0.460847543899925	1	FACETS	1	0.99	1	1	0.997	1	CLONAL	2	TRUE	0	0.460847543899925	1		39	473	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591633	38591633	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	514	121	0	ENST00000299084.4:c.92G>T	p.Trp31Leu	p.W31L	ENST00000299084	NM_152594.2	31	tGg/tTg	2/7	0.123460441020787	0	FACETS	0.551	0.529	0.572			1	INDETERMINATE	2	TRUE	0	0.460847543899925	0		121	1092	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43699748	43699748	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	496	62	0	ENST00000382044.4:c.5767G>C	p.Asp1923His	p.D1923H	ENST00000382044	NM_001141980.1	1923	Gat/Cat	28/28	0.123460441020787	0	FACETS	0.991	0.951	1			1	INDETERMINATE	1	TRUE	0	0.460847543899925	0		62	1171	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858663	9858663	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0054350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	546	68	0	ENST00000330684.3:c.2738C>G	p.Ser913Ter	p.S913*	ENST00000330684	NM_001134407.1	913	tCa/tGa	13/13	0.424644820767371	4	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.460847543899925	4		68	1557	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627670	37627670	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372766294	NA	P-0054350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	692	93	0	ENST00000447079.4:c.1585C>T	p.Leu529Phe	p.L529F	ENST00000447079	NM_015083.1	529	Ctt/Ttt	2/14	0.164310714593602	3	FACETS	1	0.991	1	1	0.991	1	INDETERMINATE	2	TRUE	1	0.460847543899925	3		93	1722	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40879694	40879694	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	534	46	0	ENST00000428826.2:c.205C>T	p.Gln69Ter	p.Q69*	ENST00000428826		69	Cag/Tag	4/21	0.164310714593602	3	FACETS	1	0.987	1	1	0.987	1	INDETERMINATE	2	TRUE	1	0.460847543899925	3		46	1338	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24129440	24129440	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	534	137	0	ENST00000263121.7:c.84C>G	p.Ile28Met	p.I28M	ENST00000263121	NM_003073.3	28	atC/atG	1/9	0.460847543899925	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.460847543899925	1		137	1405	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924762	49924762	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0054350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1429	1001	140	0	ENST00000296474.3:c.4181C>G	p.Ser1394Ter	p.S1394*	ENST00000296474	NM_002447.2	1394	tCa/tGa	20/20	0.219617335003956	2	FACETS	0.894	0.868	0.92	0.894	0.868	0.92	INDETERMINATE	2	TRUE	0	0.460847543899925	2		140	2430	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294697	1294697	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1457	698	170	0	ENST00000310581.5:c.304G>C	p.Ala102Pro	p.A102P	ENST00000310581	NM_198253.2	102	Gcg/Ccg	2/16	0.285120134024044	3	FACETS	0.865	0.833	0.897	0.865	0.833	0.897	CLONAL	2	TRUE	1	0.460847543899925	3		170	2155	SUCCESS
APC	324	MSKCC	GRCh37	5	112176404	112176404	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1554086453	NA	P-0054350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	227	29	0	ENST00000257430.4:c.5113A>G	p.Thr1705Ala	p.T1705A	ENST00000257430	NM_000038.5	1705	Acc/Gcc	16/16	0.3404718068343	1	FACETS	0.877	0.83	0.925	1	0.995	1	CLONAL	2	TRUE	0	0.460847543899925	1		29	432	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250518	26250518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1554	839	337	1	ENST00000446824.2:c.316G>A	p.Glu106Lys	p.E106K	ENST00000446824	NM_021018.2	106	Gag/Aag	1/1	0.390585228728136	3	FACETS	0.936	0.905	0.967	0.936	0.905	0.967	CLONAL	2	TRUE	1	0.460847543899925	3		338	2393	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27190647	27190647	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	545	83	2	ENST00000380036.4:c.1448A>G	p.Tyr483Cys	p.Y483C	ENST00000380036	NM_000459.3	483	tAc/tGc	10/23	0.164310714593602	3	FACETS	1	0.994	1	1	0.994	1	INDETERMINATE	2	TRUE	1	0.460847543899925	3		85	1238	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430562	80430562	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	443	24	0	ENST00000286548.4:c.446G>C	p.Arg149Pro	p.R149P	ENST00000286548	NM_002072.3	149	cGa/cCa	3/7	1	2	FACETS	0.931	0.9	0.963	1	0.998	1	CLONAL	3	TRUE	1	0.460847543899925	2		24	688	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434676	128434676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	663	110	0	ENST00000265960.3:c.178G>A	p.Glu60Lys	p.E60K	ENST00000265960	NM_001006617.1	60	Gag/Aag	2/12	1	2	FACETS	0.981	0.947	1	1	0.998	1	CLONAL	2	TRUE	1	0.460847543899925	2		110	1467	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787773	135787773	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0054350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	468	74	0	ENST00000298552.3:c.809C>G	p.Ser270Ter	p.S270*	ENST00000298552	NM_001162426.1	270	tCa/tGa	9/23	1	2	FACETS	0.99	0.95	1	1	0.997	1	CLONAL	2	TRUE	1	0.460847543899925	2		74	1026	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139438513	139438513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2000	1137	239	0	ENST00000277541.6:c.103G>A	p.Gly35Arg	p.G35R	ENST00000277541	NM_017617.3	35	Ggg/Agg	2/34	1	2	FACETS	0.786	0.764	0.809	1	0.998	1	SUBCLONAL	2	TRUE	1	0.460847543899925	2		239	3137	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475318	40475318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	593	60	0	ENST00000264657.5:c.1708G>A	p.Asp570Asn	p.D570N	ENST00000264657	NM_139276.2	570	Gac/Aac	19/24	1	2	FACETS	0.994	0.961	1	1	0.998	1	CLONAL	4	TRUE	1	0.279002594653657	2		60	1069	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349778	15349778	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199833114	NA	P-0054352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	1180	103	1	ENST00000263377.2:c.3796G>A	p.Glu1266Lys	p.E1266K	ENST00000263377	NM_058243.2	1266	Gag/Aag	19/20	1	2	FACETS	1	0.996	1			1	CLONAL	4	TRUE	1	0.279002594653657	2		104	1954	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217015	7217015	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1236166735	NA	P-0054352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	683	71	0	ENST00000380728.2:c.506C>T	p.Ala169Val	p.A169V	ENST00000380728		169	gCt/gTt	7/11	0.249258231250953	1	FACETS	0.928	0.901	0.955	1	0.998	1	CLONAL	4	TRUE	0	0.279002594653657	1		71	1135	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984760	11984760	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	282	17	0	ENST00000353533.5:c.306G>C	p.Leu102Phe	p.L102F	ENST00000353533	NM_003010.3	102	ttG/ttC	3/11	0.249258231250953	1	FACETS	1	0.982	1	1	0.997	1	CLONAL	3	TRUE	0	0.279002594653657	1		17	544	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788618	3788618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398124146	NA	P-0054353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	153	493	0	ENST00000262367.5:c.4336C>T	p.Arg1446Cys	p.R1446C	ENST00000262367	NM_004380.2	1446	Cgc/Tgc	26/31	1	2	FACETS	0.95	0.874	1	0.95	0.874	1	CLONAL	1	TRUE	1	0.562947944411928	2		493	572	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797336	135797337	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGAGATAGACTTC	novel	NA	P-0054353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	82	348	0	ENST00000298552.3:c.520_532dup	p.Val178GlyfsTer44	p.V178Gfs*44	ENST00000298552	NM_001162426.1	178	gtc/gGAAGTCTATCTCGtc	7/23	0.562947944411928	1	FACETS	0.691	0.615	0.77	0.691	0.615	0.77	SUBCLONAL	1	TRUE	0	0.562947944411928	1		348	303	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	660	866	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.97	2		867	1136	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	456	90	0	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.97	2		90	827	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	1067	75	0	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	0.147573102929185	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.97	0		75	1705	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447773	49447773	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	478	94	0	ENST00000301067.7:c.661del	p.Ala221LeufsTer40	p.A221Lfs*40	ENST00000301067	NM_003482.3	221	Gct/ct	5/54	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.97	2		94	862	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	460	103	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.3	1	FACETS	0.573	0.551	0.595	0.573	0.551	0.595	INDETERMINATE	1	TRUE	0	0.97	1		103	852	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440489	49440489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910695111	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	751	147	1	ENST00000301067.7:c.4321C>T	p.Arg1441Cys	p.R1441C	ENST00000301067	NM_003482.3	1441	Cgc/Tgc	15/54	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.97	2		148	1312	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526228	31526228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372705339	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	837	175	1	ENST00000344624.3:c.812G>A	p.Arg271Gln	p.R271Q	ENST00000344624		271	cGa/cAa	2/33	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.97	2		176	1500	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	361	37	0	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	1	2	FACETS	0.923	0.881	0.967	0.923	0.881	0.967	CLONAL	1	TRUE	1	0.97	2		37	806	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	362	60	1	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.97	2		61	690	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556463	29556463	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1567849208	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	349	33	0	ENST00000356175.3:c.2835del	p.Phe945LeufsTer9	p.F945Lfs*9	ENST00000356175	NM_000267.3	944	Ttt/tt	21/57	1	2	FACETS	0.962	0.917	1	0.962	0.917	1	CLONAL	1	TRUE	1	0.97	2		33	748	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572649	64572649	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746135199	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	788	124	0	ENST00000312049.6:c.1207G>A	p.Ala403Thr	p.A403T	ENST00000312049	NM_130799.2	403	Gcc/Acc	9/10	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.97	2		124	1391	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020775	112020775	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369151232	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	340	80	0	ENST00000368678.4:c.796C>T	p.Arg266Cys	p.R266C	ENST00000368678		266	Cgt/Tgt	8/13	1	2	FACETS	0.976	0.931	1	0.976	0.931	1	CLONAL	1	TRUE	1	0.97	2		80	718	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998483	100998483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	448	130	2	ENST00000325455.5:c.1319C>T	p.Thr440Met	p.T440M	ENST00000325455	NM_001202474.3	440	aCg/aTg	1/8	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.97	2		132	790	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027087	71027087	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	565	111	1	ENST00000318789.4:c.1240del	p.Leu414Ter	p.L414*	ENST00000318789	NM_032682.5	414	Ctg/tg	15/21	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.97	2		112	1082	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731419	47731419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	60	22	0	ENST00000449228.1:c.373G>A	p.Gly125Arg	p.G125R	ENST00000449228	NM_001127240.2	125	Gga/Aga	2/4	0.109229125303759	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.97	0		22	116	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004601	16004601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1406850631	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	390	36	0	ENST00000268712.3:c.2653G>A	p.Ala885Thr	p.A885T	ENST00000268712	NM_006311.3	885	Gct/Act	20/46	1	2	FACETS	0.994	0.951	1	0.994	0.951	1	CLONAL	1	TRUE	1	0.97	2		36	809	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871044	12871044	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	388	78	0	ENST00000228872.4:c.275del	p.Pro92ArgfsTer27	p.P92Rfs*27	ENST00000228872	NM_004064.3	91	Ccc/cc	1/3	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.97	2		78	692	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752695	42752695	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1366176199	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	873	42	2	ENST00000222329.4:c.1569del	p.Leu525SerfsTer6	p.L525Sfs*6	ENST00000222329	NM_006494.2	523	ggG/gg	4/4	0.109229125303759	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.97	0		44	1584	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731468	47731468	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1284528511	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	54	11	0	ENST00000449228.1:c.324del	p.Phe109SerfsTer120	p.F109Sfs*120	ENST00000449228	NM_001127240.2	108	ggG/gg	2/4	0.109229125303759	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.97	0		11	112	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1918645	1918645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372805518	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	345	19	0	ENST00000382891.5:c.808G>A	p.Ala270Thr	p.A270T	ENST00000382891	NM_133335.3	270	Gcc/Acc	4/22	0.3	1	FACETS	0.532	0.508	0.557	0.532	0.508	0.557	INDETERMINATE	1	TRUE	0	0.97	1		19	688	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347224	89347224	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	743	49	1	ENST00000301030.4:c.5726del	p.Pro1909ArgfsTer54	p.P1909Rfs*54	ENST00000301030	NM_001256183.1	1909	cCg/cg	9/13	0.419188414784313	1	FACETS	0.681	0.663	0.699	0.681	0.663	0.699	INDETERMINATE	1	TRUE	0	0.97	1		50	1158	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964100	28964100	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	380	36	0	ENST00000282397.4:c.1802A>G	p.His601Arg	p.H601R	ENST00000282397	NM_002019.4	601	cAc/cGc	13/30	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.97	2		36	763	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127484	55127484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs538480165	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	446	116	1	ENST00000257290.5:c.272C>T	p.Ser91Leu	p.S91L	ENST00000257290	NM_006206.4	91	tCg/tTg	3/23	1	2	FACETS	0.978	0.938	1	0.978	0.938	1	CLONAL	1	TRUE	1	0.97	2		117	940	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121016	29121016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137853010	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	559	86	2	ENST00000328354.6:c.541C>T	p.Arg181Cys	p.R181C	ENST00000328354	NM_007194.3	181	Cgt/Tgt	4/15	0.109229125303759	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.97	0		88	973	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307172	65307172	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	381	86	0	ENST00000342505.4:c.2516G>A	p.Arg839Gln	p.R839Q	ENST00000342505	NM_002227.2	839	cGa/cAa	18/25	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.97	2		86	698	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625161	69625161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1221660991	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	943	136	1	ENST00000334134.2:c.632G>A	p.Arg211Gln	p.R211Q	ENST00000334134	NM_005247.2	211	cGg/cAg	3/3	0.3	1	FACETS	0.683	0.666	0.699	0.683	0.666	0.699	INDETERMINATE	1	TRUE	0	0.97	1		137	1467	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260470	16260470	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs35184281	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	434	72	0	ENST00000375759.3:c.7739del	p.Lys2580SerfsTer3	p.K2580Sfs*3	ENST00000375759	NM_015001.2	2579	Aaa/aa	11/15	0.109229125303759	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.97	0		72	753	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094312	193094312	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	360	59	0	ENST00000367435.3:c.202C>T	p.His68Tyr	p.H68Y	ENST00000367435	NM_024529.4	68	Cac/Tac	2/17	1	2	FACETS	0.895	0.853	0.938	0.895	0.853	0.938	CLONAL	1	TRUE	1	0.97	2		59	829	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373752	118373752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782199472	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	325	59	0	ENST00000534358.1:c.7145G>A	p.Arg2382Gln	p.R2382Q	ENST00000534358	NM_005933.3	2382	cGa/cAa	27/36	0.3	1	FACETS	0.612	0.585	0.638	0.612	0.585	0.638	INDETERMINATE	1	TRUE	0	0.97	1		59	564	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060742	38060742	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	1020	218	0	ENST00000250448.2:c.1247A>T	p.Asp416Val	p.D416V	ENST00000250448	NM_004496.3	416	gAc/gTc	2/2	1	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	1	0.97	2		218	1845	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060975	38061029	+	frameshift_variant	Frame_Shift_Del	DEL	ACTGTGGTCCAGAGTCTGGGGGCTGGCGGCGGGCCCGGGGGCCGGCGCGCCCTCT	ACTGTGGTCCAGAGTCTGGGGGCTGGCGGCGGGCCCGGGGGCCGGCGCGCCCTCT	-	novel	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	341	124	0	ENST00000250448.2:c.960_1014del	p.Glu321GlyfsTer11	p.E321Gfs*11	ENST00000250448	NM_004496.3	320	ctAGAGGGCGCGCCGGCCCCCGGGCCCGCCGCCAGCCCCCAGACTCTGGACCACAGT/ct	2/2	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.97	2		124	644	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865831	56865831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1171777265	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	270	45	0	ENST00000308159.5:c.1163G>A	p.Arg388Gln	p.R388Q	ENST00000308159	NM_014669.4	388	cGg/cAg	11/22	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.97	2		45	534	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110159	8110159	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	571	89	0	ENST00000585124.1:c.446G>T	p.Arg149Met	p.R149M	ENST00000585124	NM_004217.3	149	aGg/aTg	6/9	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.97	2		89	945	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40876325	40876326	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	390	24	0	ENST00000428826.2:c.363dup	p.Met122TyrfsTer5	p.M122Yfs*5	ENST00000428826		121	-/T	5/21	0.147573102929185	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.97	0		24	704	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753027	42753027	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	866	132	1	ENST00000222329.4:c.1237del	p.Ala413GlnfsTer4	p.A413Qfs*4	ENST00000222329	NM_006494.2	413	Gca/ca	4/4	0.109229125303759	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.97	0		133	1477	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702377	47702377	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	242	38	0	ENST00000233146.2:c.1977del	p.Asp660IlefsTer25	p.D660Ifs*25	ENST00000233146	NM_000251.2	658	gAa/ga	12/16	0.3	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.97	0		38	446	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52661372	52661373	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	295	30	0	ENST00000394830.3:c.1457_1458del	p.Glu486AlafsTer20	p.E486Afs*20	ENST00000394830	NM_018313.4	486	gAG/g	14/30	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.97	2		30	608	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356296	66356296	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	469	168	1	ENST00000273854.3:c.1201C>T	p.His401Tyr	p.H401Y	ENST00000273854	NM_004439.5	401	Cat/Tat	5/18	0.195133489933845	4	FACETS	0.895	0.858	0.932	0.895	0.858	0.932	INDETERMINATE	2	TRUE	2	0.97	4		169	1064	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525729	187525729	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	258	51	0	ENST00000441802.2:c.10351-1G>T		p.X3451_splice	ENST00000441802	NM_005245.3	3451			0.3	2	FACETS	1	0.967	1			1	INDETERMINATE	1	TRUE	NA	0.97	2		51	518	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637090	176637090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	533	77	0	ENST00000439151.2:c.1690G>A	p.Ala564Thr	p.A564T	ENST00000439151	NM_022455.4	564	Gcc/Acc	5/23	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.97	2		77	931	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894931	101894933	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	264	62	0	ENST00000374994.4:c.486_488del	p.Glu162del	p.E162del	ENST00000374994	NM_004612.2	162	GAG/-	3/9	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.97	2		62	538	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390678	139390678	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	912	68	1	ENST00000277541.6:c.7513C>T	p.Pro2505Ser	p.P2505S	ENST00000277541	NM_017617.3	2505	Cct/Tct	34/34	1	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	1	0.97	2		69	1558	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413024	63413024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	459	190	1	ENST00000330258.3:c.143G>A	p.Gly48Asp	p.G48D	ENST00000330258	NM_152424.3	48	gGc/gAc	2/2	1	1	FACETS	0.667	0.644	0.689	0.667	0.644	0.689	SUBCLONAL	1	TRUE	0	0.97	1		191	731	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0054355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	150	817	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.181178861453452	2	FACETS	0.769	0.705	0.836	0.769	0.705	0.836	SUBCLONAL	2	TRUE	0	0.288041242843627	2		817	677	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822351	72822351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs62639993	NA	P-0054355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	108	1059	1	ENST00000268489.5:c.9824C>T	p.Pro3275Leu	p.P3275L	ENST00000268489	NM_006885.3	3275	cCg/cTg	10/10	1	2	FACETS	0.827	0.741	0.918	0.827	0.741	0.918	CLONAL	1	TRUE	1	0.288041242843627	2		1060	907	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279450	1279450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs973201915	NA	P-0054355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	96	1252	0	ENST00000310581.5:c.2086C>T	p.Arg696Cys	p.R696C	ENST00000310581	NM_198253.2	696	Cgt/Tgt	5/16	1	2	FACETS	0.73	0.649	0.816	0.73	0.649	0.816	SUBCLONAL	1	TRUE	1	0.288041242843627	2		1252	913	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523295	9523295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	96	703	0	ENST00000353224.5:c.1942C>T	p.Pro648Ser	p.P648S	ENST00000353224	NM_177990.2	648	Ccc/Tcc	9/10	0.0697199417188352	4	FACETS	0.762	0.681	0.849	0.762	0.681	0.849	INDETERMINATE	2	TRUE	2	0.288041242843627	4		703	563	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057848	27057848	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	89	881	1	ENST00000324856.7:c.1558del	p.Gln520SerfsTer99	p.Q520Sfs*99	ENST00000324856	NM_006015.4	519	tCc/tc	3/20	1	2	FACETS	0.674	0.596	0.757	0.674	0.596	0.757	SUBCLONAL	1	TRUE	1	0.288041242843627	2		882	917	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350272	89350272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1298734986	NA	P-0054355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	128	949	2	ENST00000301030.4:c.2678G>A	p.Arg893Gln	p.R893Q	ENST00000301030	NM_001256183.1	893	cGg/cAg	9/13	1	2	FACETS	0.984	0.891	1	0.984	0.891	1	CLONAL	1	TRUE	1	0.288041242843627	2		951	903	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593388	48593388	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1555686594	NA	P-0054355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	16	297	0	ENST00000342988.3:c.1140-1G>A		p.X380_splice	ENST00000342988	NM_005359.5	380			1	2	FACETS	0.489	0.362	0.641	0.489	0.362	0.641	SUBCLONAL	1	TRUE	1	0.288041242843627	2		297	227	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932904	49932904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	67	817	0	ENST00000296474.3:c.3040G>A	p.Gly1014Ser	p.G1014S	ENST00000296474	NM_002447.2	1014	Ggc/Agc	13/20	0.132840298183321	3	FACETS	0.745	0.647	0.852	0.373	0.323	0.426	INDETERMINATE	1	TRUE	1	0.288041242843627	3		817	714	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591115	67591116	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTATCCAGCTGAGAAAGACGAGAGACCAATACTTGA	novel	NA	P-0054355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	10	250	0	ENST00000274335.5:c.1710_1745dup	p.Leu581_Met582insIleIleGlnLeuArgLysThrArgAspGlnTyrLeu	p.L581_M582insIIQLRKTRDQYL	ENST00000274335		570	ctt/cTTATCCAGCTGAGAAAGACGAGAGACCAATACTTGAtt	12/15	0.240433494919557	3	FACETS	0.337	0.227	0.474	0.168	0.113	0.237	SUBCLONAL	1	TRUE	1	0.288041242843627	3		250	236	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0054356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	293	568	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.345568009115156	2		568	1152	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484634	57484737	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTAGGATGCTGTGGGCTTGGCTGTTCGTAAAGAACGCTTTGCTTCTGTGTTGTTAGGGATCAGGGTCGCTGCTCACGCTCTTGGCTTTGCTCTCTTTGGTTAA	GGTAGGATGCTGTGGGCTTGGCTGTTCGTAAAGAACGCTTTGCTTCTGTGTTGTTAGGGATCAGGGTCGCTGCTCACGCTCTTGGCTTTGCTCTCTTTGGTTAA	-	novel	NA	P-0054356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	148	506	0	ENST00000371085.3:c.718+1_719-1del		p.X240_splice	ENST00000371085	NM_000516.4	240		9/13	0.345568009115156	3	FACETS	0.735	0.669	0.804	0.367	0.334	0.402	SUBCLONAL	1	TRUE	1	0.345568009115156	3		506	1367	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484858	57485003	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTTTGTGGAGTGACCGCCCACCCCCTGCGCTTGCCCAGGAGGCCCTGGTCTGCACTGTTTATAGAGAAGAACCCCGTGCAAGCATTCCAGACCCCTGGCCGAAAGCGCGCTTCTCCCAAGCATTCACACGGCCTCCCTTCTTGT	AGGTTTGTGGAGTGACCGCCCACCCCCTGCGCTTGCCCAGGAGGCCCTGGTCTGCACTGTTTATAGAGAAGAACCCCGTGCAAGCATTCCAGACCCCTGGCCGAAAGCGCGCTTCTCCCAAGCATTCACACGGCCTCCCTTCTTGT	-	novel	NA	P-0054356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1171	165	490	0	ENST00000371085.3:c.839+1_840-1del		p.X280_splice	ENST00000371085	NM_000516.4	280		10/13	0.345568009115156	3	FACETS	0.838	0.768	0.912	0.419	0.384	0.456	CLONAL	1	TRUE	1	0.345568009115156	3		490	1336	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485136	57485387	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTGTGTATGGCTTCCACTCTTGCTGGCTGTTCATTGCGGTGGTTCTTTTTCAAACGGTCAGGCTGAAAACCCCCATCCCCCTCCCACCACCAAACCATAAAGGATCTATAAGAGAAGCAAGAAAAACGCACTCCCACTAATTCTCATATGGAAAAATCAGGGTTTTGAAGACTTCAGGAGCTACAGAGATGCTAGCACCCCAGCTCTGCTTGAATTTTAAATTACATTAATATGTATTCCCTTTTTATATA	GGTGTGTATGGCTTCCACTCTTGCTGGCTGTTCATTGCGGTGGTTCTTTTTCAAACGGTCAGGCTGAAAACCCCCATCCCCCTCCCACCACCAAACCATAAAGGATCTATAAGAGAAGCAAGAAAAACGCACTCCCACTAATTCTCATATGGAAAAATCAGGGTTTTGAAGACTTCAGGAGCTACAGAGATGCTAGCACCCCAGCTCTGCTTGAATTTTAAATTACATTAATATGTATTCCCTTTTTATATA	-	novel	NA	P-0054356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	139	287	0	ENST00000371085.3:c.970+1_971-1del		p.X324_splice	ENST00000371085	NM_000516.4	324		11/13	0.345568009115156	3	FACETS	1	0.971	1	0.578	0.526	0.632	CLONAL	1	TRUE	1	0.345568009115156	3		287	816	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586056	29586056	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1135402857	NA	P-0054356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	100	316	0	ENST00000356175.3:c.4276C>T	p.Gln1426Ter	p.Q1426*	ENST00000356175	NM_000267.3	1426	Cag/Tag	32/57	0.246021500082134	2	FACETS	1	0.979	1	0.686	0.616	0.758	CLONAL	1	TRUE	0	0.345568009115156	2		316	422	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221345	2221347	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0054356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1517	136	828	0	ENST00000326181.6:c.432_434del	p.Thr145del	p.T145del	ENST00000326181	NM_032271.2	143	atCACc/atc	6/21	1	2	FACETS	0.476	0.431	0.524	0.476	0.431	0.524	SUBCLONAL	1	TRUE	1	0.345568009115156	2		828	1653	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713340	40713340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1272852268	NA	P-0054356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1246	129	600	2	ENST00000373198.4:c.4175G>A	p.Arg1392His	p.R1392H	ENST00000373198	NM_133170.3	1392	cGt/cAt	30/32	1	2	FACETS	0.543	0.49	0.599	0.543	0.49	0.599	SUBCLONAL	1	TRUE	1	0.345568009115156	2		602	1375	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974760	21974760	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691186	NA	P-0054356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	103	232	0	ENST00000304494.5:c.67G>T	p.Gly23Cys	p.G23C	ENST00000304494	NM_000077.4	23	Ggt/Tgt	1/3	0.246021500082134	2	FACETS	1	0.98	1	0.69	0.621	0.762	CLONAL	1	TRUE	0	0.345568009115156	2		232	432	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485456	57485736	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTGAGTCGAGCCTGTCTTTAGTTTCCTCTCTTGTTCCTCCTCTTTTTCTCATGGATGTAAATTTACTTAATTCCAAATTCAGGGGTTCAGCTACCCAGTTCCATGGTTTTAGTTCACGCACATCCAGTGTGGATTTGAGCTCTTTGCGCCCCTCTTTTTGCTTTTGTTTTCATATGACATCAGAGGCTGGCTGACAGCCGTCCCTGGTAGGTGTCCCCATCAGGGATAGGGTGGTTCCTGGCGAGGGTGTCACTGACAAGTCCCCTTGTTTGTGCCCGCA	GGTGAGTCGAGCCTGTCTTTAGTTTCCTCTCTTGTTCCTCCTCTTTTTCTCATGGATGTAAATTTACTTAATTCCAAATTCAGGGGTTCAGCTACCCAGTTCCATGGTTTTAGTTCACGCACATCCAGTGTGGATTTGAGCTCTTTGCGCCCCTCTTTTTGCTTTTGTTTTCATATGACATCAGAGGCTGGCTGACAGCCGTCCCTGGTAGGTGTCCCCATCAGGGATAGGGTGGTTCCTGGCGAGGGTGTCACTGACAAGTCCCCTTGTTTGTGCCCGCA	-	novel	NA	P-0054356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	124	281	0	ENST00000371085.3:c.1038+1_1039-1del		p.X346_splice	ENST00000371085	NM_000516.4	346		12/13	0.345568009115156	3	FACETS	0.964	0.872	1	0.482	0.436	0.531	CLONAL	1	TRUE	1	0.345568009115156	3		281	873	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484479	57484575	+	splice_acceptor_variant,splice_donor_variant,intron_variant	Splice_Site	DEL	GTAAGCCAACTGTTACCTTTTTATATAACAGAGATCATGGTTTCTTGACATTCACCCCAGTCCCTCTGGAATAACCAGCTGTCCTCCTCCCCACCAG	GTAAGCCAACTGTTACCTTTTTATATAACAGAGATCATGGTTTCTTGACATTCACCCCAGTCCCTCTGGAATAACCAGCTGTCCTCCTCCCCACCAG	-	novel	NA	P-0054356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	71	381	0	ENST00000371085.3:c.659+1_660-1del		p.X220_splice	ENST00000371085	NM_000516.4	220			0.345568009115156	3	FACETS	0.459	0.399	0.524	0.23	0.199	0.262	SUBCLONAL	1	TRUE	1	0.345568009115156	3		381	1049	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478641	57478726	+	splice_donor_variant,splice_acceptor_variant,intron_variant	Splice_Site	DEL	GTACGTGCTGGCTCCTTGTGCTGTCTGTCTTGTAGCGCCCTCCCAGCCAGTGCTGTTCCCTGACCGCTTTGCTAAATCATTTTCAG	GTACGTGCTGGCTCCTTGTGCTGTCTGTCTTGTAGCGCCCTCCCAGCCAGTGCTGTTCCCTGACCGCTTTGCTAAATCATTTTCAG	-	novel	NA	P-0054356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	111	493	0	ENST00000371085.3:c.312+1_313-1del		p.X104_splice	ENST00000371085	NM_000516.4	104			0.345568009115156	3	FACETS	0.608	0.544	0.675	0.304	0.272	0.338	SUBCLONAL	1	TRUE	1	0.345568009115156	3		493	1240	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156087	106156087	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	111	246	0	ENST00000380013.4:c.988G>C	p.Glu330Gln	p.E330Q	ENST00000380013	NM_001127208.2	330	Gag/Cag	3/11	0.246021500082134	2	FACETS	1	0.977	1	0.642	0.58	0.708	CLONAL	1	TRUE	0	0.345568009115156	2		246	500	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276721	115276721	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	31	249	0	ENST00000438362.2:c.738T>G	p.Ile246Met	p.I246M	ENST00000438362	NM_001242891.1	246	atT/atG	8/20	1	2	FACETS	0.322	0.259	0.392	0.322	0.259	0.392	SUBCLONAL	1	TRUE	1	0.345568009115156	2		249	558	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998697	100998697	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1368	142	798	0	ENST00000325455.5:c.1105C>A	p.Pro369Thr	p.P369T	ENST00000325455	NM_001202474.3	369	Ccc/Acc	1/8	1	2	FACETS	0.544	0.494	0.597	0.544	0.494	0.597	SUBCLONAL	1	TRUE	1	0.345568009115156	2		798	1510	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81960710	81960711	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0054356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	305	564	1	ENST00000359376.3:c.2441_2442delinsTT	p.Arg814Ile	p.R814I	ENST00000359376	NM_002661.3	814	aGG/aTT	23/33	0.345568009115156	2	FACETS	0.842	0.794	0.891	0.842	0.794	0.891	CLONAL	2	TRUE	0	0.345568009115156	2		565	1048	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577595	7577608	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CAGTCAGAGCCAAC	CAGTCAGAGCCAAC	-	novel	NA	P-0054356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	172	483	0	ENST00000269305.4:c.673_686del	p.Val225TyrfsTer10	p.V225Yfs*10	ENST00000269305	NM_001126112.2	225	GTTGGCTCTGACTGt/t	7/11	0.246021500082134	2	FACETS	1	0.967	1	0.547	0.503	0.593	CLONAL	1	TRUE	0	0.345568009115156	2		483	910	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653265	29653265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs370181275	NA	P-0054356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	113	231	0	ENST00000356175.3:c.5200A>G	p.Ile1734Val	p.I1734V	ENST00000356175	NM_000267.3	1734	Att/Gtt	36/57	0.246021500082134	2	FACETS	1	0.983	1	0.714	0.646	0.785	CLONAL	1	TRUE	0	0.345568009115156	2		231	458	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459696	40459696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	312	656	0	ENST00000345506.4:c.1861G>A	p.Asp621Asn	p.D621N	ENST00000345506	NM_003152.3	621	Gac/Aac	16/20	0.246021500082134	2	FACETS	1	0.993	1	0.7	0.66	0.742	CLONAL	1	TRUE	0	0.345568009115156	2		656	1289	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40460198	40460198	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	247	484	1	ENST00000345506.4:c.1909G>T	p.Glu637Ter	p.E637*	ENST00000345506	NM_003152.3	637	Gaa/Taa	17/20	0.246021500082134	2	FACETS	0.769	0.719	0.819	0.769	0.719	0.819	SUBCLONAL	2	TRUE	0	0.345568009115156	2		485	930	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303065	15303065	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2226	514	1122	0	ENST00000263388.2:c.385G>T	p.Ala129Ser	p.A129S	ENST00000263388	NM_000435.2	129	Gcc/Tcc	4/33	0.191159514608536	5	FACETS	0.824	0.786	0.864	0.549	0.524	0.576	INDETERMINATE	2	TRUE	2	0.345568009115156	5		1122	2740	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721182	39721182	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	94	408	0	ENST00000361337.2:c.685C>T	p.Pro229Ser	p.P229S	ENST00000361337	NM_003286.2	229	Cca/Tca	9/21	1	2	FACETS	0.627	0.557	0.702	0.627	0.557	0.702	SUBCLONAL	1	TRUE	1	0.345568009115156	2		408	867	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718109	117718109	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	81	425	0	ENST00000368508.3:c.748T>G	p.Phe250Val	p.F250V	ENST00000368508	NM_002944.2	250	Ttt/Gtt	7/43	1	2	FACETS	0.482	0.423	0.545	0.482	0.423	0.545	SUBCLONAL	1	TRUE	1	0.345568009115156	2		425	973	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92404041	92404041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	89	363	0	ENST00000265734.4:c.338C>T	p.Pro113Leu	p.P113L	ENST00000265734	NM_001259.6	113	cCa/cTa	3/8	1	2	FACETS	0.72	0.639	0.808	0.72	0.639	0.808	SUBCLONAL	1	TRUE	1	0.345568009115156	2		363	715	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	35	304	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.915	0.75	1	0.915	0.75	1	CLONAL	1	TRUE	1	0.17	2		304	450	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609957	81609957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756016910	NA	P-0054357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	29	368	0	ENST00000298171.2:c.1555C>T	p.Arg519Cys	p.R519C	ENST00000298171	NM_000369.2	519	Cgc/Tgc	10/10	1	2	FACETS	0.844	0.678	1	0.844	0.678	1	CLONAL	1	TRUE	1	0.17	2		368	404	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155367	185155367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs902931460	NA	P-0054357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	79	340	0	ENST00000265026.3:c.608C>T	p.Thr203Met	p.T203M	ENST00000265026	NM_004721.4	203	aCg/aTg	3/14	0.3	3	FACETS	0.987	0.87	1	0.987	0.87	1	CLONAL	2	TRUE	1	0.17	3		340	511	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182133	11182133	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	152	693	0	ENST00000361445.4:c.6713G>C	p.Gly2238Ala	p.G2238A	ENST00000361445	NM_004958.3	2238	gGc/gCc	48/58	NA	2	FACETS	1	0.949	1			1	INDETERMINATE	2	TRUE	NA	0.17	2		693	850	SUCCESS
H3C13	653604	MSKCC	GRCh37	1	149784831	149784837	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGCTC	CCCGCTC	-	novel	NA	P-0054357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	28	271	0	ENST00000331491.1:c.400_406del	p.Glu134ProfsTer?	p.E134Pfs*?	ENST00000331491	NM_001123375.2	134	GAGCGGGcc/cc	1/1	1	2	FACETS	0.876	0.7	1	0.876	0.7	1	CLONAL	1	TRUE	1	0.17	2		271	376	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573646	48573662	+	frameshift_variant	Frame_Shift_Del	DEL	CATTGGATGGGAGGCTT	CATTGGATGGGAGGCTT	-	novel	NA	P-0054357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	18	298	0	ENST00000342988.3:c.232_248del	p.Leu78GlyfsTer20	p.L78Gfs*20	ENST00000342988	NM_005359.5	77	aCATTGGATGGGAGGCTT/a	2/12	1	2	FACETS	0.64	0.481	0.828	0.64	0.481	0.828	SUBCLONAL	1	TRUE	1	0.17	2		298	331	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622064	1622064	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	78	783	0	ENST00000344749.5:c.811C>T	p.His271Tyr	p.H271Y	ENST00000344749	NM_001136139.2	271	Cac/Tac	10/19	0.3	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.17	1		783	660	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839872	27839872	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	42	515	0	ENST00000328488.2:c.222G>C	p.Glu74Asp	p.E74D	ENST00000328488	NM_003533.2	74	gaG/gaC	1/1	0.216355335939826	3	FACETS	0.714	0.594	0.847	0.357	0.297	0.424	SUBCLONAL	1	TRUE	1	0.17	3		515	751	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797222	32797222	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	78	692	0	ENST00000374899.4:c.1887C>G	p.Ile629Met	p.I629M	ENST00000374899	NM_018833.2	629	atC/atG	11/12	0.216355335939826	3	FACETS	1	0.882	1	0.503	0.441	0.571	CLONAL	1	TRUE	1	0.17	3		692	989	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955562	48955585	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCCTTGCATGGCTCTCAGTAAGT	TCCCTTGCATGGCTCTCAGTAAGT	-	novel	NA	P-0054358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	79	267	0	ENST00000267163.4:c.1678_1695+6del		p.X560_splice	ENST00000267163	NM_000321.2	560		17/27	0.682178319533019	1	FACETS	0.691	0.618	0.765	0.691	0.618	0.765	SUBCLONAL	1	TRUE	0	0.682178319533019	1		267	221	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577540	7577541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	591	687	0	ENST00000269305.4:c.740dup	p.Asn247LysfsTer17	p.N247Kfs*17	ENST00000269305	NM_001126112.2	247	aac/aaAc	7/11	0.653811909372681	2	FACETS	0.99	0.962	1	0.99	0.962	1	CLONAL	2	TRUE	0	0.682178319533019	2		687	875	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812200	212812200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs953144117	NA	P-0054358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	170	282	0	ENST00000342788.4:c.376G>A	p.Asp126Asn	p.D126N	ENST00000342788	NM_005235.2	126	Gat/Aat	3/28	0.682178319533019	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.682178319533019	1		282	314	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0054359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	345	378	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.581130692183791	3	FACETS	0.866	0.832	0.899	0.866	0.832	0.899	CLONAL	3	TRUE	0	0.660595969406558	3		378	535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0054359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	569	758	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.596917082512654	3	FACETS	0.937	0.911	0.963	0.937	0.911	0.963	CLONAL	3	TRUE	0	0.660595969406558	3		758	815	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519925	NA	P-0054359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	233	504	0	ENST00000263967.3:c.1357G>C	p.Glu453Gln	p.E453Q	ENST00000263967	NM_006218.2	453	Gaa/Caa	8/21	0.581130692183791	3	FACETS	1	0.989	1	0.424	0.397	0.452	CLONAL	1	TRUE	0	0.660595969406558	3		504	738	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78931486	78931486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	293	919	0	ENST00000306801.3:c.3433C>T	p.Arg1145Trp	p.R1145W	ENST00000306801	NM_020761.2	1145	Cgg/Tgg	29/34	0.456759146577601	5	FACETS	1	0.993	1	0.494	0.465	0.525	CLONAL	1	TRUE	2	0.660595969406558	5		919	1191	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115252321	115252321	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	149	358	0	ENST00000369535.4:c.319G>C	p.Asp107His	p.D107H	ENST00000369535	NM_002524.4	107	Gat/Cat	4/7	0.647635550131632	3	FACETS	1	0.978	1	0.587	0.54	0.636	CLONAL	1	TRUE	1	0.660595969406558	3		358	511	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578292	226578292	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	415	713	0	ENST00000366794.5:c.436C>G	p.Pro146Ala	p.P146A	ENST00000366794	NM_001618.3	146	Ccg/Gcg	4/23	0.456759146577601	5	FACETS	0.854	0.817	0.892	0.854	0.817	0.892	CLONAL	3	TRUE	2	0.660595969406558	5		713	976	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040918	42040918	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs777083929	NA	P-0054359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	126	664	0	ENST00000219905.7:c.5296C>G	p.Pro1766Ala	p.P1766A	ENST00000219905	NM_001164273.1	1766	Cca/Gca	16/24	0.647635550131632	3	FACETS	0.587	0.531	0.646	0.293	0.265	0.323	SUBCLONAL	1	TRUE	1	0.660595969406558	3		664	865	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996705	73996705	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	21	124	0	ENST00000318443.5:c.1261G>C	p.Asp421His	p.D421H	ENST00000318443	NM_001024736.1	421	Gat/Cat	6/10	0.647635550131632	3	FACETS	0.622	0.484	0.779	0.311	0.242	0.39	SUBCLONAL	1	TRUE	1	0.660595969406558	3		124	136	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341287	341287	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1177783893	NA	P-0054359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1450	141	1061	0	ENST00000262320.3:c.2197G>C	p.Glu733Gln	p.E733Q	ENST00000262320	NM_003502.3	733	Gag/Cag	9/11	0.652953233438971	5	FACETS	0.534	0.485	0.587	0.107	0.097	0.118	SUBCLONAL	1	TRUE	0	0.660595969406558	5		1061	1591	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343557	343748	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGGTTAGGGGGTTGGGAGCTGGGTGGGGTGGCATGGTGGGGTCTTGGATGAAGAGGTGGGAGGGCTGCACGGAGGTCCGGAGCTGAGGGCCGGCCCAGGGGTGCTCAAGGGACAAGGGTCTGGAGTTCTCATGGGGCTGTGGCTTCCTCGTCCCCGAAGACCTTGGGGAACAAGAGAACAAGTTGTGACTG	TGGGTTAGGGGGTTGGGAGCTGGGTGGGGTGGCATGGTGGGGTCTTGGATGAAGAGGTGGGAGGGCTGCACGGAGGTCCGGAGCTGAGGGCCGGCCCAGGGGTGCTCAAGGGACAAGGGTCTGGAGTTCTCATGGGGCTGTGGCTTCCTCGTCCCCGAAGACCTTGGGGAACAAGAGAACAAGTTGTGACTG	-	novel	NA	P-0054359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	76	767	0	ENST00000262320.3:c.1956-30_2117del		p.X652_splice	ENST00000262320	NM_003502.3	652		8/11	0.652953233438971	5	FACETS	0.425	0.371	0.483	0.085	0.074	0.097	SUBCLONAL	1	TRUE	0	0.660595969406558	5		767	1079	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592264	29592264	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	102	216	0	ENST00000356175.3:c.4679A>T	p.Lys1560Ile	p.K1560I	ENST00000356175	NM_000267.3	1560	aAa/aTa	35/57	0.647635550131632	3	FACETS	1	0.969	1	0.592	0.535	0.651	CLONAL	1	TRUE	1	0.660595969406558	3		216	347	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972830	25972830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	381	506	0	ENST00000435504.4:c.1595G>A	p.Gly532Glu	p.G532E	ENST00000435504		532	gGg/gAg	12/13	0.541578389449398	4	FACETS	1	0.993	1	0.794	0.759	0.829	CLONAL	2	TRUE	1	0.660595969406558	4		506	804	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019126	31019126	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	87	424	0	ENST00000375687.4:c.721C>G	p.Gln241Glu	p.Q241E	ENST00000375687	NM_015338.5	241	Caa/Gaa	9/13	0.427107254184425	5	FACETS	0.701	0.62	0.788	0.234	0.206	0.263	SUBCLONAL	1	TRUE	2	0.660595969406558	5		424	748	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504060	186504063	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CAGG	CAGG	-	novel	NA	P-0054359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	206	235	0	ENST00000323963.5:c.625_627+1del		p.X209_splice	ENST00000323963		209		6/11	0.581130692183791	3	FACETS	0.836	0.792	0.878	0.836	0.792	0.878	CLONAL	3	TRUE	0	0.660595969406558	3		235	331	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955100	55955100	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	368	499	1	ENST00000263923.4:c.3445C>A	p.Gln1149Lys	p.Q1149K	ENST00000263923	NM_002253.2	1149	Cag/Aag	26/30	0.427107254184425	5	FACETS	0.879	0.838	0.92	0.879	0.838	0.92	CLONAL	3	TRUE	2	0.660595969406558	5		500	841	SUCCESS
APC	324	MSKCC	GRCh37	5	112177841	112177841	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794107	NA	P-0054359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	52	251	0	ENST00000257430.4:c.6550G>A	p.Glu2184Lys	p.E2184K	ENST00000257430	NM_000038.5	2184	Gaa/Aaa	16/16	0.201184513519464	2	FACETS	0.549	0.47	0.633	0.274	0.235	0.317	INDETERMINATE	1	TRUE	0	0.660595969406558	2		251	287	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372736	81372736	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	132	363	0	ENST00000222390.5:c.798G>T	p.Gln266His	p.Q266H	ENST00000222390	NM_000601.4	266	caG/caT	7/18	0.181695403983624	4	FACETS	0.815	0.747	0.885	0.815	0.747	0.885	INDETERMINATE	2	TRUE	2	0.660595969406558	4		363	407	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357426	70357426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	427	790	0	ENST00000374080.3:c.5767G>T	p.Gly1923Ter	p.G1923*	ENST00000374080		1923	Gga/Tga	40/45	0.647635550131632	3	FACETS	0.889	0.851	0.928	0.889	0.851	0.928	CLONAL	2	TRUE	1	0.660595969406558	3		790	967	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939939	76939939	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	279	601	0	ENST00000373344.5:c.809C>T	p.Pro270Leu	p.P270L	ENST00000373344	NM_000489.3	270	cCa/cTa	9/35	0.647635550131632	3	FACETS	1	0.986	1	0.576	0.541	0.611	CLONAL	1	TRUE	1	0.660595969406558	3		601	976	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161844	47161844	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	52	385	0	ENST00000409792.3:c.4282del	p.Arg1428GlufsTer4	p.R1428Efs*4	ENST00000409792	NM_014159.6	1428	Aga/ga	3/21	0.30868560253523	1	FACETS	0.816	0.698	0.945	0.816	0.698	0.945	CLONAL	1	TRUE	0	0.30868560253523	1		385	349	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643941	52643941	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	46	412	0	ENST00000394830.3:c.1955C>A	p.Ser652Ter	p.S652*	ENST00000394830	NM_018313.4	652	tCa/tAa	17/30	0.30868560253523	1	FACETS	0.93	0.789	1	0.93	0.789	1	CLONAL	1	TRUE	0	0.30868560253523	1		412	271	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630524	187630524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	80	729	0	ENST00000441802.2:c.458C>T	p.Ser153Leu	p.S153L	ENST00000441802	NM_005245.3	153	tCa/tTa	2/27	1	2	FACETS	0.757	0.666	0.854	0.757	0.666	0.854	SUBCLONAL	1	TRUE	1	0.30868560253523	2		729	685	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227031	53227041	+	frameshift_variant	Frame_Shift_Del	DEL	CATCTGTAGAC	CATCTGTAGAC	-	novel	NA	P-0054360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	111	367	0	ENST00000375401.3:c.2534_2544del	p.Gly845AspfsTer4	p.G845Dfs*4	ENST00000375401	NM_004187.3	845	gGTCTACAGATG/g	18/26	1	1	FACETS	0.768	0.696	0.843	1	0.985	1	SUBCLONAL	2	TRUE	0	0.30868560253523	1		367	396	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	213	375	0				ENST00000310581	NM_198253.2	-/1132			0.338042891660313	5	FACETS	0.997	0.937	1	0.997	0.937	1	CLONAL	4	TRUE	1	0.338042891660313	5		375	476	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981873	201981874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	203	1056	0	ENST00000359651.3:c.585dup	p.Val196ArgfsTer21	p.V196Rfs*21	ENST00000359651		195	gac/gaCc	4/8	0.162661118650989	2	FACETS	0.925	0.855	0.997	0.462	0.427	0.499	INDETERMINATE	1	TRUE	0	0.338042891660313	2		1056	1299	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125523659	125523659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	54	299	0	ENST00000428830.2:c.1252G>A	p.Asp418Asn	p.D418N	ENST00000428830	NM_001114121.2	418	Gat/Aat	12/14	1	2	FACETS	0.88	0.755	1	0.88	0.755	1	CLONAL	1	TRUE	1	0.338042891660313	2		299	363	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811647	102811647	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	65	712	0	ENST00000307046.8:c.537G>T	p.Arg179Ser	p.R179S	ENST00000307046	NM_001111285.1	179	agG/agT	4/4	0.162661118650989	2	FACETS	0.391	0.338	0.449	0.195	0.169	0.225	INDETERMINATE	1	TRUE	0	0.338042891660313	2		712	984	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789693	3789694	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0054361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	47	421	0	ENST00000262367.5:c.4165_4166del	p.Phe1389ProfsTer11	p.F1389Pfs*11	ENST00000262367	NM_004380.2	1389	TTc/c	25/31	0.286382805500132	1	FACETS	0.404	0.34	0.474	0.404	0.34	0.474	SUBCLONAL	1	TRUE	0	0.338042891660313	1		421	572	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665483	138665483	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs111967494	NA	P-0054361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	77	459	0	ENST00000330315.3:c.82G>C	p.Glu28Gln	p.E28Q	ENST00000330315	NM_023067.3	28	Gaa/Caa	1/1	1	2	FACETS	0.806	0.709	0.911	0.806	0.709	0.911	CLONAL	1	TRUE	1	0.338042891660313	2		459	565	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787780	135787780	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	103	348	0	ENST00000298552.3:c.802G>T	p.Glu268Ter	p.E268*	ENST00000298552	NM_001162426.1	268	Gaa/Taa	9/23	0.338042891660313	1	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	0	0.338042891660313	1		348	506	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911143	40911143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370795038	NA	P-0054362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	39	380	0	ENST00000373198.4:c.2162G>A	p.Arg721His	p.R721H	ENST00000373198	NM_133170.3	721	cGt/cAt	13/32	1	2	FACETS	0.811	0.675	0.96	0.811	0.675	0.96	CLONAL	1	TRUE	1	0.346085382949134	2		380	278	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692892	89692892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554898129	NA	P-0054362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	74	391	0	ENST00000371953.3:c.376G>A	p.Ala126Thr	p.A126T	ENST00000371953	NM_000314.4	126	Gct/Act	5/9	0.322038256281293	2	FACETS	0.866	0.768	0.967	0.866	0.768	0.967	CLONAL	2	TRUE	0	0.346085382949134	2		391	247	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981235	201981235	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1481604346	NA	P-0054362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	70	1072	1	ENST00000359651.3:c.314G>T	p.Cys105Phe	p.C105F	ENST00000359651		105	tGt/tTt	2/8	1	2	FACETS	0.366	0.318	0.419	0.366	0.318	0.419	SUBCLONAL	1	TRUE	1	0.346085382949134	2		1073	1104	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961968	41961968	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	80	455	0	ENST00000219905.7:c.877del	p.Arg293ValfsTer36	p.R293Vfs*36	ENST00000219905	NM_001164273.1	292	gtC/gt	2/24	1	2	FACETS	0.925	0.816	1	0.925	0.816	1	CLONAL	1	TRUE	1	0.346085382949134	2		455	500	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028880	42028880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1187276759	NA	P-0054362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	86	491	1	ENST00000219905.7:c.4418C>T	p.Thr1473Ile	p.T1473I	ENST00000219905	NM_001164273.1	1473	aCa/aTa	13/24	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.346085382949134	2		492	473	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591141	67591148	+	frameshift_variant	Frame_Shift_Del	DEL	CCAATACT	CCAATACT	-	novel	NA	P-0054362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	22	325	0	ENST00000274335.5:c.1734_1741del	p.Gln579AspfsTer20	p.Q579Dfs*20	ENST00000274335		578	gaCCAATACTtg/gatg	12/15	1	2	FACETS	0.55	0.428	0.692	0.55	0.428	0.692	SUBCLONAL	1	TRUE	1	0.346085382949134	2		325	231	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591283	67591301	+	frameshift_variant	Frame_Shift_Del	DEL	TGAACGAGTGGTTGGGCAA	TGAACGAGTGGTTGGGCAA	-	novel	NA	P-0054362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	33	352	0	ENST00000274335.5:c.1785_1803del	p.Asn595LysfsTer61	p.N595Kfs*61	ENST00000274335		594	tTGAACGAGTGGTTGGGCAAt/tt	13/15	1	2	FACETS	0.527	0.429	0.636	0.527	0.429	0.636	SUBCLONAL	1	TRUE	1	0.346085382949134	2		352	362	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101067	27101068	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	143	722	0	ENST00000324856.7:c.4354dup	p.Gln1452ProfsTer39	p.Q1452Pfs*39	ENST00000324856	NM_006015.4	1450	ggc/ggCc	18/20	0.296888976914263	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.28	1		722	857	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	125	455	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.975	0.892	1	0.975	0.892	1	CLONAL	1	TRUE	1	0.706563448378844	2		456	363	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462371	89462371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866025221	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	225	509	0	ENST00000336596.2:c.1843G>A	p.Glu615Lys	p.E615K	ENST00000336596	NM_005233.5	615	Gaa/Aaa	10/17	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.706563448378844	2		509	631	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112191	115112191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1275992297	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	319	821	1	ENST00000257566.3:c.1549C>T	p.Pro517Ser	p.P517S	ENST00000257566	NM_016569.3	517	Ccg/Tcg	7/8	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.706563448378844	2		822	783	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418243	139418243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1333041588	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	350	1227	0	ENST00000277541.6:c.329C>T	p.Pro110Leu	p.P110L	ENST00000277541	NM_017617.3	110	cCc/cTc	3/34	0.288664067047894	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.706563448378844	0		1227	991	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587118	189587118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761885185	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	117	292	1	ENST00000264731.3:c.1135C>T	p.Arg379Cys	p.R379C	ENST00000264731	NM_003722.4	379	Cgt/Tgt	9/14	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.706563448378844	2		293	310	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262087	16262087	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1449357349	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	115	395	0	ENST00000375759.3:c.9352C>T	p.His3118Tyr	p.H3118Y	ENST00000375759	NM_015001.2	3118	Cac/Tac	11/15	1	2	FACETS	0.92	0.837	1	0.92	0.837	1	CLONAL	1	TRUE	1	0.706563448378844	2		395	354	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546607	9546607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	185	477	0	ENST00000353224.5:c.1415G>A	p.Gly472Glu	p.G472E	ENST00000353224	NM_177990.2	472	gGg/gAg	5/10	1	2	FACETS	0.894	0.83	0.959	0.894	0.83	0.959	CLONAL	1	TRUE	1	0.706563448378844	2		477	586	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944944	31944944	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144139961	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	161	448	1	ENST00000340398.3:c.157C>T	p.Arg53Cys	p.R53C	ENST00000340398	NM_001013699.2	53	Cgt/Tgt	1/1	1	2	FACETS	0.87	0.803	0.938	0.87	0.803	0.938	CLONAL	1	TRUE	1	0.706563448378844	2		449	524	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566827	212566827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202247795	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	130	261	0	ENST00000342788.4:c.1354G>A	p.Glu452Lys	p.E452K	ENST00000342788	NM_005235.2	452	Gaa/Aaa	12/28	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.706563448378844	2		261	367	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331980	81331980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1383506132	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	114	260	0	ENST00000222390.5:c.2104C>T	p.Arg702Cys	p.R702C	ENST00000222390	NM_000601.4	702	Cgt/Tgt	18/18	1	2	FACETS	0.949	0.865	1	0.949	0.865	1	CLONAL	1	TRUE	1	0.706563448378844	2		260	340	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380279	25380279	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs727503108	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	174	430	0	ENST00000311936.3:c.179G>T	p.Gly60Val	p.G60V	ENST00000311936	NM_004985.3	60	gGt/gTt	3/5	1	2	FACETS	0.817	0.756	0.88	0.817	0.756	0.88	CLONAL	1	TRUE	1	0.706563448378844	2		430	603	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658340	18658340	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	177	361	0	ENST00000266497.5:c.3145C>T	p.His1049Tyr	p.H1049Y	ENST00000266497		1049	Cat/Tat	22/31	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.706563448378844	2		361	473	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426127	47426127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	331	539	0	ENST00000377045.4:c.647C>G	p.Pro216Arg	p.P216R	ENST00000377045	NM_001654.4	216	cCc/cGc	7/16	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.706563448378844	1		539	520	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622446	28622446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	121	428	0	ENST00000241453.7:c.1171C>T	p.Pro391Ser	p.P391S	ENST00000241453	NM_004119.2	391	Cct/Tct	9/24	1	2	FACETS	0.8	0.729	0.875	0.8	0.729	0.875	SUBCLONAL	1	TRUE	1	0.706563448378844	2		428	428	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679274	29679274	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	113	269	0	ENST00000356175.3:c.7395-1G>T		p.X2465_splice	ENST00000356175	NM_000267.3	2465			1	2	FACETS	0.869	0.79	0.951	0.869	0.79	0.951	CLONAL	1	TRUE	1	0.706563448378844	2		269	368	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156345	106156345	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745997182	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	123	290	0	ENST00000380013.4:c.1246C>T	p.Pro416Ser	p.P416S	ENST00000380013	NM_001127208.2	416	Cct/Tct	3/11	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.706563448378844	2		290	337	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492907	8492907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	267	569	0	ENST00000356435.5:c.2422G>A	p.Asp808Asn	p.D808N	ENST00000356435		808	Gat/Aat	16/35	1	2	FACETS	0.96	0.904	1	0.96	0.904	1	CLONAL	1	TRUE	1	0.706563448378844	2		569	787	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223703	36223703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	340	1215	1	ENST00000222270.7:c.6253C>T	p.Pro2085Ser	p.P2085S	ENST00000222270	NM_014727.1	2085	Cct/Tct	28/37	0.185269487269998	3	FACETS	1	0.95	1	0.335	0.317	0.354	INDETERMINATE	1	TRUE	0	0.706563448378844	3		1216	1295	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141545667	141545667	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	291	803	0	ENST00000220592.5:c.2171T>C	p.Val724Ala	p.V724A	ENST00000220592	NM_012154.3	724	gTt/gCt	17/19	1	2	FACETS	0.977	0.923	1	0.977	0.923	1	CLONAL	1	TRUE	1	0.706563448378844	2		803	843	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775521	39775521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	215	567	0	ENST00000288319.7:c.499G>A	p.Glu167Lys	p.E167K	ENST00000288319	NM_182918.3	167	Gaa/Aaa	4/10	1	2	FACETS	0.879	0.821	0.939	0.879	0.821	0.939	CLONAL	1	TRUE	1	0.706563448378844	2		567	692	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117551	4117551	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121434498	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	330	499	0	ENST00000262948.5:c.169T>G	p.Phe57Val	p.F57V	ENST00000262948	NM_030662.3	57	Ttt/Gtt	2/11	0.185269487269998	3	FACETS	1	0.963	1	0.673	0.643	0.704	INDETERMINATE	2	TRUE	0	0.706563448378844	3		499	626	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933782	49933782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769911110	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	256	771	0	ENST00000296474.3:c.2495G>A	p.Arg832Gln	p.R832Q	ENST00000296474	NM_002447.2	832	cGa/cAa	10/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.706563448378844	2		771	703	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325886	30325886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	111	255	0	ENST00000322652.5:c.2084C>T	p.Ser695Phe	p.S695F	ENST00000322652	NM_015355.2	695	tCc/tTc	16/16	1	2	FACETS	0.982	0.894	1	0.982	0.894	1	CLONAL	1	TRUE	1	0.706563448378844	2		255	320	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264421	16264421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	279	869	0	ENST00000375759.3:c.10624G>A	p.Glu3542Lys	p.E3542K	ENST00000375759	NM_015001.2	3542	Gaa/Aaa	13/15	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.706563448378844	2		869	790	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891731	28891732	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	140	521	0	ENST00000282397.4:c.3289_3290delinsAA	p.Gly1097Lys	p.G1097K	ENST00000282397	NM_002019.4	1097	GGg/AAg	25/30	1	2	FACETS	0.826	0.757	0.896	0.826	0.757	0.896	CLONAL	1	TRUE	1	0.706563448378844	2		521	480	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281290	49281290	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	310	752	0	ENST00000282018.3:c.337A>G	p.Ile113Val	p.I113V	ENST00000282018	NM_020377.2	113	Att/Gtt	1/1	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.706563448378844	2		752	842	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348757	89348757	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	368	857	0	ENST00000301030.4:c.4193A>T	p.Glu1398Val	p.E1398V	ENST00000301030	NM_001256183.1	1398	gAg/gTg	9/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.706563448378844	2		857	1016	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15938259	15938259	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1304246858	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	130	301	0	ENST00000268712.3:c.6956-1G>A		p.X2319_splice	ENST00000268712	NM_006311.3	2319			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.706563448378844	2		301	329	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587512	29587512	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567863004	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	126	372	0	ENST00000356175.3:c.4493G>A	p.Gly1498Glu	p.G1498E	ENST00000356175	NM_000267.3	1498	gGg/gAg	33/57	1	2	FACETS	0.868	0.793	0.945	0.868	0.793	0.945	CLONAL	1	TRUE	1	0.706563448378844	2		372	411	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40860047	40860047	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	251	615	0	ENST00000428826.2:c.1589C>T	p.Pro530Leu	p.P530L	ENST00000428826		530	cCc/cTc	15/21	1	2	FACETS	0.891	0.837	0.947	0.891	0.837	0.947	CLONAL	1	TRUE	1	0.706563448378844	2		615	797	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119726	70119726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	160	490	1	ENST00000245479.2:c.728C>T	p.Thr243Ile	p.T243I	ENST00000245479	NM_000346.3	243	aCc/aTc	3/3	1	2	FACETS	0.911	0.842	0.982	0.911	0.842	0.982	CLONAL	1	TRUE	1	0.706563448378844	2		491	497	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896584	78896584	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263566040	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	336	959	0	ENST00000306801.3:c.2581C>T	p.Pro861Ser	p.P861S	ENST00000306801	NM_020761.2	861	Ccc/Tcc	22/34	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.706563448378844	2		959	914	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622359	1622359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	295	1063	0	ENST00000344749.5:c.605C>T	p.Ser202Phe	p.S202F	ENST00000344749	NM_001136139.2	202	tCc/tTc	9/19	0.185269487269998	3	FACETS	1	0.959	1	0.341	0.321	0.362	INDETERMINATE	1	TRUE	0	0.706563448378844	3		1063	1104	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222969	5222969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1385418553	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	595	1130	1	ENST00000357368.4:c.2834C>T	p.Thr945Ile	p.T945I	ENST00000357368	NM_002850.3	945	aCc/aTc	18/38	0.185269487269998	3	FACETS	1	0.976	1	0.675	0.652	0.698	INDETERMINATE	2	TRUE	0	0.706563448378844	3		1131	1126	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094921	11094921	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1304026031	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	551	1120	0	ENST00000358026.2:c.94C>T	p.Pro32Ser	p.P32S	ENST00000358026	NM_001128849.1	32	Ccg/Tcg	2/36	0.185269487269998	3	FACETS	0.941	0.907	0.976	0.628	0.605	0.651	INDETERMINATE	2	TRUE	0	0.706563448378844	3		1120	1121	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36217231	36217231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	520	793	0	ENST00000222270.7:c.3980G>A	p.Arg1327Lys	p.R1327K	ENST00000222270	NM_014727.1	1327	aGg/aAg	14/37	0.185269487269998	3	FACETS	0.994	0.958	1	0.663	0.638	0.687	INDETERMINATE	2	TRUE	0	0.706563448378844	3		793	1002	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909500	50909500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	661	1024	0	ENST00000440232.2:c.1304C>T	p.Ser435Leu	p.S435L	ENST00000440232	NM_002691.3	435	tCa/tTa	11/27	0.185269487269998	3	FACETS	0.941	0.91	0.973	0.628	0.607	0.649	INDETERMINATE	2	TRUE	0	0.706563448378844	3		1024	1345	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645883	215645883	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	169	548	0	ENST00000260947.4:c.715C>A	p.Leu239Met	p.L239M	ENST00000260947	NM_000465.2	239	Ctg/Atg	4/11	1	2	FACETS	0.835	0.772	0.9	0.835	0.772	0.9	CLONAL	1	TRUE	1	0.706563448378844	2		548	573	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016145	31016145	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	186	483	0	ENST00000375687.4:c.391T>A	p.Ser131Thr	p.S131T	ENST00000375687	NM_015338.5	131	Tct/Act	6/13	1	2	FACETS	0.961	0.894	1	0.961	0.894	1	CLONAL	1	TRUE	1	0.706563448378844	2		483	548	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171719	36171719	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	169	436	0	ENST00000300305.3:c.846T>A	p.Asp282Glu	p.D282E	ENST00000300305		282	gaT/gaA	7/8	1	2	FACETS	0.945	0.876	1	0.945	0.876	1	CLONAL	1	TRUE	1	0.706563448378844	2		436	506	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458485	12458485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	246	640	1	ENST00000287820.6:c.1102C>T	p.Leu368Phe	p.L368F	ENST00000287820	NM_015869.4	368	Ctc/Ttc	6/7	1	2	FACETS	0.949	0.891	1	0.949	0.891	1	CLONAL	1	TRUE	1	0.706563448378844	2		641	734	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162479	47162479	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	140	398	0	ENST00000409792.3:c.3647C>T	p.Ser1216Phe	p.S1216F	ENST00000409792	NM_014159.6	1216	tCt/tTt	3/21	1	2	FACETS	0.986	0.907	1	0.986	0.907	1	CLONAL	1	TRUE	1	0.706563448378844	2		398	402	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921398	178921398	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	196	516	0	ENST00000263967.3:c.880T>C	p.Tyr294His	p.Y294H	ENST00000263967	NM_006218.2	294	Tat/Cat	5/21	1	2	FACETS	0.923	0.86	0.988	0.923	0.86	0.988	CLONAL	1	TRUE	1	0.706563448378844	2		516	601	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520677	176520677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	288	906	0	ENST00000292408.4:c.1420G>A	p.Gly474Ser	p.G474S	ENST00000292408	NM_213647.1	474	Ggc/Agc	11/18	NA	2	FACETS	0.904	0.852	0.957			1	INDETERMINATE	1	TRUE	NA	0.706563448378844	2		906	902	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553045	106553045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	242	677	0	ENST00000369096.4:c.1010C>T	p.Pro337Leu	p.P337L	ENST00000369096	NM_001198.3	337	cCc/cTc	5/7	0.706563448378844	1	FACETS	0.895	0.846	0.944	0.895	0.846	0.944	CLONAL	1	TRUE	0	0.706563448378844	1		677	495	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873597	151873597	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	210	498	0	ENST00000262189.6:c.8941C>A	p.His2981Asn	p.H2981N	ENST00000262189	NM_170606.2	2981	Cat/Aat	38/59	1	2	FACETS	0.885	0.825	0.945	0.885	0.825	0.945	CLONAL	1	TRUE	1	0.706563448378844	2		498	672	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873984	151873984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	158	438	0	ENST00000262189.6:c.8554C>T	p.Pro2852Ser	p.P2852S	ENST00000262189	NM_170606.2	2852	Cct/Tct	38/59	1	2	FACETS	0.996	0.921	1	0.996	0.921	1	CLONAL	1	TRUE	1	0.706563448378844	2		438	449	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151882707	151882707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	111	265	0	ENST00000262189.6:c.5018C>T	p.Thr1673Ile	p.T1673I	ENST00000262189	NM_170606.2	1673	aCt/aTt	34/59	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.706563448378844	2		265	281	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923095	39923095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	277	309	0	ENST00000378444.4:c.3613C>T	p.Pro1205Ser	p.P1205S	ENST00000378444	NM_001123385.1	1205	Cct/Tct	8/15	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.706563448378844	1		309	417	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931748	39931750	+	frameshift_variant	Frame_Shift_Del	DEL	CAT	CAT	TA	novel	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	23	377	0	ENST00000378444.4:c.2849_2851delinsTA	p.Asn950IlefsTer6	p.N950Ifs*6	ENST00000378444	NM_001123385.1	950	aATGat/aTAat	4/15	1	1	FACETS	0.092	0.071	0.116	0.092	0.071	0.116	SUBCLONAL	1	TRUE	0	0.706563448378844	1		377	458	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862908	9862910	+	missense_variant	Missense_Mutation	TNP	TCC	TCC	ACT	novel	NA	P-0054367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	185	610	0	ENST00000330684.3:c.2393_2395delinsAGT	p.Gly798_Ile799delinsGluPhe	p.G798_I799delinsEF	ENST00000330684	NM_001134407.1	798	gGGAtc/gAGTtc	12/13	1	2	FACETS	0.854	0.793	0.917	0.854	0.793	0.917	CLONAL	1	TRUE	1	0.706563448378844	2		610	613	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	191	375	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.723812179830482	2		375	503	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0054369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	190	392	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.926	0.862	0.992	0.926	0.862	0.992	CLONAL	1	TRUE	1	0.723812179830482	2		392	567	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820887	3820887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752694988	NA	P-0054369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	498	856	0	ENST00000262367.5:c.2564C>T	p.Pro855Leu	p.P855L	ENST00000262367	NM_004380.2	855	cCa/cTa	14/31	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.723812179830482	2		856	1258	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	18	375	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.801	0.603	1	0.801	0.603	1	CLONAL	1	TRUE	1	0.167065008594485	2		375	269	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094294	27094306	+	frameshift_variant	Frame_Shift_Del	DEL	CTACTACAACCAA	CTACTACAACCAA	-	novel	NA	P-0054384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	26	434	0	ENST00000324856.7:c.3002_3014del	p.Ser1001LeufsTer34	p.S1001Lfs*34	ENST00000324856	NM_006015.4	1001	tCTACTACAACCAAt/tt	11/20	1	2	FACETS	0.64	0.506	0.795	0.64	0.506	0.795	SUBCLONAL	1	TRUE	1	0.167065008594485	2		434	486	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0054385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	326	568	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.975	0.927	1	1	0.996	1	CLONAL	2	TRUE	1	0.439348872420111	2		568	761	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0054385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	267	889	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.784	0.738	0.831	1	0.994	1	SUBCLONAL	2	TRUE	1	0.439348872420111	2		889	775	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0054385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	88	412	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.439348872420111	2		412	362	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0054385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	299	51	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.439348872420111	0	FACETS	0.614	0.584	0.645			1	SUBCLONAL	2	TRUE	0	0.439348872420111	0		51	621	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486542	56486542	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	257	712	3	ENST00000267101.3:c.1121A>T	p.His374Leu	p.H374L	ENST00000267101	NM_001982.3	374	cAc/cTc	10/28	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.439348872420111	2		715	816	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155175	55155175	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0054385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	151	629	0	ENST00000257290.5:c.2775-1G>A		p.X925_splice	ENST00000257290	NM_006206.4	925			1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.439348872420111	2		629	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0054386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	372	801	1	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.715132844354163	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.715132844354163	1		802	628	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590370	67590370	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	39	153	0	ENST00000274335.5:c.1432C>T	p.Gln478Ter	p.Q478*	ENST00000274335		478	Caa/Taa	11/15	1	2	FACETS	0.852	0.722	0.99	0.852	0.722	0.99	CLONAL	1	TRUE	1	0.715132844354163	2		153	128	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs1057519842	NA	P-0054386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	77	356	0	ENST00000274335.5:c.1727_1729del	p.Thr576del	p.T576del	ENST00000274335		575	aaGACg/aag	12/15	1	2	FACETS	0.912	0.814	1	0.912	0.814	1	CLONAL	1	TRUE	1	0.715132844354163	2		356	236	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs121913292	NA	P-0054386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	134	546	0	ENST00000371953.3:c.389del	p.Arg130GlnfsTer4	p.R130Qfs*4	ENST00000371953	NM_000314.4	130	cGa/ca	5/9	0.715132844354163	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.715132844354163	1		546	224	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868610	37868610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769082334	NA	P-0054386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	186	775	0	ENST00000269571.5:c.1057G>A	p.Val353Met	p.V353M	ENST00000269571		353	Gtg/Atg	9/27	1	2	FACETS	0.791	0.733	0.85	0.791	0.733	0.85	SUBCLONAL	1	TRUE	1	0.715132844354163	2		775	658	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0054387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	37	543	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.961	0.792	1	0.961	0.792	1	CLONAL	1	FALSE	1	0.15914142172939	2		543	484	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699534	117699534	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	32	420	0	ENST00000369458.3:c.107C>T	p.Ser36Phe	p.S36F	ENST00000369458	NM_024626.3	36	tCc/tTc	3/6	1	2	FACETS	0.983	0.798	1	0.983	0.798	1	CLONAL	1	FALSE	1	0.15914142172939	2		420	409	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982117	201982117	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	57	1013	0	ENST00000359651.3:c.641G>A	p.Gly214Glu	p.G214E	ENST00000359651		214	gGa/gAa	5/8	1	2	FACETS	0.809	0.693	0.938	0.809	0.693	0.938	CLONAL	1	FALSE	1	0.15914142172939	2		1013	885	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629247	187629247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	58	725	0	ENST00000441802.2:c.1735C>T	p.Pro579Ser	p.P579S	ENST00000441802	NM_005245.3	579	Ccc/Tcc	2/27	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.15914142172939	2		725	494	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460469	8460469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	32	570	0	ENST00000356435.5:c.3817C>T	p.Pro1273Ser	p.P1273S	ENST00000356435		1273	Cct/Tct	22/35	0.15914142172939	1	FACETS	0.689	0.558	0.838	0.689	0.558	0.838	SUBCLONAL	1	FALSE	0	0.15914142172939	1		570	537	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937786	76937786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	24	646	0	ENST00000373344.5:c.2962G>A	p.Gly988Arg	p.G988R	ENST00000373344	NM_000489.3	988	Gga/Aga	9/35	0.15914142172939	1	FACETS	0.831	0.652	1	0.831	0.652	1	CLONAL	1	FALSE	0	0.15914142172939	1		646	334	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284996	15284996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1472208548	NA	P-0054388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	448	1153	1	ENST00000263388.2:c.4619G>A	p.Arg1540His	p.R1540H	ENST00000263388	NM_000435.2	1540	cGc/cAc	25/33	1	2	FACETS	0.996	0.952	1	1	0.998	1	CLONAL	5	FALSE	1	0.158306849155433	2		1154	1137	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061214	38061231	+	inframe_deletion	In_Frame_Del	DEL	AGCAGCCGTTCTCGAACA	AGCAGCCGTTCTCGAACA	-	novel	NA	P-0054388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	301	625	0	ENST00000250448.2:c.758_775del	p.Met253_Tyr259delinsAsn	p.M253_Y259delinsN	ENST00000250448	NM_004496.3	253	aTGTTCGAGAACGGCTGCTac/aac	2/2	0.127021190674833	3	FACETS	0.953	0.903	1	1	0.996	1	CLONAL	6	FALSE	1	0.158306849155433	3		625	718	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618493	37618494	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	331	757	0	ENST00000447079.4:c.174dup	p.Glu59ArgfsTer16	p.E59Rfs*16	ENST00000447079	NM_015083.1	57	acc/aCcc	1/14	1	2	FACETS	1	0.968	1	1	0.997	1	CLONAL	5	FALSE	1	0.158306849155433	2		757	816	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619264	37619265	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	299	775	0	ENST00000447079.4:c.943dup	p.Arg315LysfsTer36	p.R315Kfs*36	ENST00000447079	NM_015083.1	314	gaa/gAaa	1/14	1	2	FACETS	0.909	0.86	0.96	1	0.997	1	CLONAL	5	FALSE	1	0.158306849155433	2		775	831	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686461	37687087	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACCACAGCATGTATATTGTTCCCTCTCATCTTCCTTCCTTCTGCTTTGTTTTAATGTTTCCATCTAACAGCAAAAAGGGGCAGGGAGTCTGCCAACAGCCTGCATGTTAGAACAGTTCTTTAAAGGAAGGAAATGGAGGAAATCTTAGACCAAAATCAGGATAATCATTTGAAACATATGATATTTTTACACTAGCTGTTAGATCCAGGATGCAACTGTTTTACTTTTAATCACTTGATTTATTTATAATTGCAATTTTCTGATCCCAAGATTTTATTCTTTATATATCTGGTTACTTATATTGATATTTGTTTATGTTGCACAGTGTGTGTGTTTGTGTTTATAATCACATGTGCTTTTTAAGATGGTGTTTAAAAGAAGTAACCCTTCCACAGCATGTCCTCCTCACATTCTTCCACCAGAGAAGAGGCCCCCTGAGCCCCCCGGACCTCCACCGCCGCCACCTCCACCCCCTCTGGTTGAAGGCGATCTTTCCAGCGCCCCCCAGGAGTTGAACCCAGCCGTGACAGCCGCCTTGCTGCAACTTTTATCCCAGCCTGAAGCAGAGCCTCCTGGCCACCTGCCACATGAGCACCAGGCCTTGAGACCAATGGAGTACTCCACCC	GACCACAGCATGTATATTGTTCCCTCTCATCTTCCTTCCTTCTGCTTTGTTTTAATGTTTCCATCTAACAGCAAAAAGGGGCAGGGAGTCTGCCAACAGCCTGCATGTTAGAACAGTTCTTTAAAGGAAGGAAATGGAGGAAATCTTAGACCAAAATCAGGATAATCATTTGAAACATATGATATTTTTACACTAGCTGTTAGATCCAGGATGCAACTGTTTTACTTTTAATCACTTGATTTATTTATAATTGCAATTTTCTGATCCCAAGATTTTATTCTTTATATATCTGGTTACTTATATTGATATTTGTTTATGTTGCACAGTGTGTGTGTTTGTGTTTATAATCACATGTGCTTTTTAAGATGGTGTTTAAAAGAAGTAACCCTTCCACAGCATGTCCTCCTCACATTCTTCCACCAGAGAAGAGGCCCCCTGAGCCCCCCGGACCTCCACCGCCGCCACCTCCACCCCCTCTGGTTGAAGGCGATCTTTCCAGCGCCCCCCAGGAGTTGAACCCAGCCGTGACAGCCGCCTTGCTGCAACTTTTATCCCAGCCTGAAGCAGAGCCTCCTGGCCACCTGCCACATGAGCACCAGGCCTTGAGACCAATGGAGTACTCCACCC	-	novel	NA	P-0054388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	140	5	0	ENST00000447079.4:c.3761-392_3995del		p.X1254_splice	ENST00000447079	NM_015083.1	1254		14/14	1	2	FACETS	0.996	0.969	1	1	0.995	1	CLONAL	12	FALSE	1	0.158306849155433	2		5	148	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199711	138199711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368146619	NA	P-0054388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	300	705	0	ENST00000237289.4:c.1129G>A	p.Val377Met	p.V377M	ENST00000237289	NM_001270507.1	377	Gtg/Atg	7/9	0.127021190674833	3	FACETS	0.966	0.916	1	1	0.996	1	CLONAL	6	FALSE	1	0.158306849155433	3		705	706	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0054389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	84	603	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.619469393807094	3	FACETS	0.639	0.565	0.717	0.319	0.282	0.359	SUBCLONAL	1	TRUE	1	0.619469393807094	3		603	556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0054389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	301	750	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.619469393807094	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.619469393807094	1		750	615	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344790	65344790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770735783	NA	P-0054389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	122	378	0	ENST00000342505.4:c.247G>A	p.Glu83Lys	p.E83K	ENST00000342505	NM_002227.2	83	Gag/Aag	4/25	1	2	FACETS	0.749	0.68	0.821	0.749	0.68	0.821	SUBCLONAL	1	TRUE	1	0.619469393807094	2		378	526	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271447	26271447	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	238	737	0	ENST00000305910.3:c.166C>G	p.Gln56Glu	p.Q56E	ENST00000305910	NM_003534.2	56	Cag/Gag	1/1	1	2	FACETS	0.947	0.887	1	0.947	0.887	1	CLONAL	1	TRUE	1	0.619469393807094	2		737	811	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562160	21562160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	436	1049	1	ENST00000382592.4:c.1759G>A	p.Glu587Lys	p.E587K	ENST00000382592	NM_014572.2	587	Gaa/Aaa	4/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.619469393807094	2		1050	1365	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163325209	163325209	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	50	364	0	ENST00000271452.3:c.1345G>C	p.Asp449His	p.D449H	ENST00000271452	NM_145697.2	449	Gat/Cat	14/14	1	2	FACETS	0.74	0.636	0.853	0.74	0.636	0.853	SUBCLONAL	1	TRUE	1	0.619469393807094	2		364	218	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562523	21562523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	37	41	0	ENST00000382592.4:c.1396G>A	p.Val466Met	p.V466M	ENST00000382592	NM_014572.2	466	Gtg/Atg	4/8	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.619469393807094	2		41	83	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672209	86672221	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GTATTTATGCGCT	GTATTTATGCGCT	TCG	novel	NA	P-0054389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	50	356	1	ENST00000274376.6:c.2012-1_2023delinsTCG		p.X671_splice	ENST00000274376	NM_002890.2	671		16/25	0.619469393807094	1	FACETS	0.484	0.415	0.559	0.484	0.415	0.559	SUBCLONAL	1	TRUE	0	0.619469393807094	1		357	230	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	27	304	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.902	0.718	1	0.902	0.718	1	CLONAL	1	TRUE	1	0.17	2		304	352	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519988	NA	P-0054390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	61	772	0	ENST00000269305.4:c.808T>G	p.Phe270Val	p.F270V	ENST00000269305	NM_001126112.2	270	Ttt/Gtt	8/11	1	2	FACETS	0.773	0.665	0.892	0.773	0.665	0.892	SUBCLONAL	1	TRUE	1	0.17	2		772	928	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	89	375	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.871	0.779	0.968	0.871	0.779	0.968	CLONAL	1	TRUE	1	0.588686580732127	2		375	347	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807370	1807370	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs77722678	NA	P-0054391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1338	200	1069	0	ENST00000260795.2:c.1619A>G	p.Asn540Ser	p.N540S	ENST00000260795		540	aAc/aGc	11/17	0.517702335344234	4	FACETS	0.702	0.648	0.758			1	SUBCLONAL	1	TRUE	NA	0.588686580732127	4		1069	1538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0054392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	464	1243	2	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.596117620492205	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.596117620492205	1		1245	1052	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344188	70344188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556335288	NA	P-0054392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	213	338	2	ENST00000374080.3:c.1924G>A	p.Asp642Asn	p.D642N	ENST00000374080		642	Gat/Aat	13/45	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.596117620492205	1		340	360	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672942	30672942	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	174	1049	0	ENST00000376406.3:c.4018C>T	p.Gln1340Ter	p.Q1340*	ENST00000376406	NM_014641.2	1340	Caa/Taa	10/15	0.32917907222366	1	FACETS	0.404	0.372	0.438	0.404	0.372	0.438	INDETERMINATE	1	TRUE	0	0.596117620492205	1		1049	1014	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058546	69058546	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	65	633	0	ENST00000288368.4:c.4190A>G	p.Asn1397Ser	p.N1397S	ENST00000288368	NM_024870.2	1397	aAt/aGt	34/40	0.596117620492205	3	FACETS	0.5	0.434	0.572	0.167	0.144	0.191	SUBCLONAL	1	TRUE	0	0.596117620492205	3		633	566	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0054394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	34	378	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.744	0.608	0.898	0.744	0.608	0.898	SUBCLONAL	1	TRUE	1	0.21	2		378	435	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279527	1279527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767382450	NA	P-0054394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	59	1300	1	ENST00000310581.5:c.2009C>T	p.Ala670Val	p.A670V	ENST00000310581	NM_198253.2	670	gCg/gTg	5/16	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.21	2		1301	560	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218851	36218851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773513850	NA	P-0054394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	36	1176	1	ENST00000222270.7:c.4462C>T	p.Arg1488Trp	p.R1488W	ENST00000222270	NM_014727.1	1488	Cgg/Tgg	18/37	1	2	FACETS	0.588	0.482	0.707	0.588	0.482	0.707	SUBCLONAL	1	TRUE	1	0.21	2		1177	583	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426115	47426115	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	48	1044	0	ENST00000377045.4:c.635C>A	p.Ser212Tyr	p.S212Y	ENST00000377045	NM_001654.4	212	tCc/tAc	7/16	1	2	FACETS	0.672	0.567	0.788	0.672	0.567	0.788	SUBCLONAL	1	TRUE	1	0.21	2		1044	680	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372417	55372417	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	219	1183	0	ENST00000297316.4:c.1107C>A	p.Phe369Leu	p.F369L	ENST00000297316	NM_022454.3	369	ttC/ttA	2/2	0.234806621104374	4	FACETS	1	0.953	1	1	0.953	1	CLONAL	3	TRUE	1	0.21	4		1183	819	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301087	65301087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1413899535	NA	P-0054394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	39	287	0	ENST00000342505.4:c.3361C>T	p.Pro1121Ser	p.P1121S	ENST00000342505	NM_002227.2	1121	Cca/Tca	24/25	0.3	3	FACETS	1	0.901	1			1	CLONAL	1	TRUE	NA	0.21	3		287	365	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615182	43615182	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	43	1016	0	ENST00000355710.3:c.2596G>T	p.Ala866Ser	p.A866S	ENST00000355710	NM_020975.4	866	Gcc/Tcc	14/20	1	2	FACETS	0.729	0.609	0.862	0.729	0.609	0.862	SUBCLONAL	1	TRUE	1	0.21	2		1016	562	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216576	108216576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	35	386	0	ENST00000278616.4:c.8525C>T	p.Pro2842Leu	p.P2842L	ENST00000278616	NM_000051.3	2842	cCa/cTa	58/63	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.21	2		386	309	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15975460	15975460	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	38	506	0	ENST00000268712.3:c.3894G>T	p.Gln1298His	p.Q1298H	ENST00000268712	NM_006311.3	1298	caG/caT	29/46	1	2	FACETS	0.866	0.716	1	0.866	0.716	1	CLONAL	1	TRUE	1	0.21	2		506	418	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201870	152201870	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	46	480	0	ENST00000206249.3:c.724C>G	p.Leu242Val	p.L242V	ENST00000206249	NM_000125.3	242	Ctc/Gtc	3/8	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.21	2		480	430	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729590	41729590	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	78	814	0	ENST00000242208.4:c.939G>T	p.Glu313Asp	p.E313D	ENST00000242208	NM_002192.2	313	gaG/gaT	3/3	0.207942431289603	5	FACETS	1	0.971	1	0.459	0.403	0.52	CLONAL	1	TRUE	2	0.21	5		814	709	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981733	70981733	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	175	1095	2	ENST00000276594.2:c.363C>A	p.Tyr121Ter	p.Y121*	ENST00000276594	NM_024504.3	121	taC/taA	2/8	0.234806621104374	4	FACETS	0.876	0.809	0.947	0.876	0.809	0.947	CLONAL	3	TRUE	1	0.21	4		1097	767	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040794	47040794	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	54	1074	0	ENST00000377604.3:c.1429G>T	p.Gly477Ter	p.G477*	ENST00000377604	NM_001204468.1	477	Gga/Tga	13/24	1	2	FACETS	0.901	0.769	1	0.901	0.769	1	CLONAL	1	TRUE	1	0.21	2		1074	571	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0054395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	116	720	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	0.923	0.834	1	0.923	0.834	1	CLONAL	1	TRUE	1	0.408879419685938	2		720	615	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0054397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	791	865	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.561909286956797	3	FACETS	1	0.995	1	0.742	0.719	0.765	CLONAL	2	TRUE	0	0.559290655392312	3		865	1626	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797291	135797291	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	83	323	0	ENST00000298552.3:c.578G>A	p.Gly193Glu	p.G193E	ENST00000298552	NM_001162426.1	193	gGa/gAa	7/23	0.443927794134931	1	FACETS	0.648	0.577	0.723	0.648	0.577	0.723	SUBCLONAL	1	TRUE	0	0.559290655392312	1		323	330	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401248	139401249	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGGACAG	novel	NA	P-0054397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1500	261	1177	0	ENST00000277541.6:c.3814_3820dup	p.Asn1274ThrfsTer19	p.N1274Tfs*19	ENST00000277541	NM_017617.3	1274	aat/aCTGTCCAat	23/34	0.443927794134931	1	FACETS	0.382	0.356	0.408	0.382	0.356	0.408	SUBCLONAL	1	TRUE	0	0.559290655392312	1		1177	1761	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	156	375	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.602317047458462	2		375	396	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0054398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	143	477	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.926	0.849	1	0.926	0.849	1	CLONAL	1	TRUE	1	0.602317047458462	2		477	513	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0054398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	371	970	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	0.987	0.937	1	0.987	0.937	1	CLONAL	1	TRUE	1	0.602317047458462	2		970	1248	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980421	201980422	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0054398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	297	736	0	ENST00000359651.3:c.158_159dup	p.Thr54ValfsTer102	p.T54Vfs*102	ENST00000359651		53	ggt/gGTgt	1/8	1	2	FACETS	0.931	0.877	0.986	0.931	0.877	0.986	CLONAL	1	TRUE	1	0.602317047458462	2		736	1059	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850825	63850825	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	61	487	0	ENST00000279873.7:c.1603G>C	p.Glu535Gln	p.E535Q	ENST00000279873	NM_032199.2	535	Gag/Cag	10/10	1	2	FACETS	0.266	0.229	0.307	0.266	0.229	0.307	SUBCLONAL	1	TRUE	1	0.602317047458462	2		487	761	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652032	36652032	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	460	1151	0	ENST00000244741.5:c.154G>C	p.Asp52His	p.D52H	ENST00000244741	NM_000389.4	52	Gac/Cac	2/3	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.602317047458462	2		1151	1464	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969378	44969388	+	frameshift_variant	Frame_Shift_Del	DEL	TACATAGTACA	TACATAGTACA	-	novel	NA	P-0054398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	182	285	0	ENST00000377967.4:c.4061_4071del	p.Tyr1354LeufsTer31	p.Y1354Lfs*31	ENST00000377967	NM_021140.2	1354	TACATAGTACAt/t	28/29	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.602317047458462	1		285	313	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217296	123217296	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	185	283	0	ENST00000218089.9:c.2950G>A	p.Glu984Lys	p.E984K	ENST00000218089	NM_001042749.1	984	Gag/Aag	29/35	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.602317047458462	1		283	315	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217347	123217347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	180	309	0	ENST00000218089.9:c.3001G>A	p.Asp1001Asn	p.D1001N	ENST00000218089	NM_001042749.1	1001	Gat/Aat	29/35	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.602317047458462	1		309	342	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217359	123217359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	169	290	0	ENST00000218089.9:c.3013G>A	p.Glu1005Lys	p.E1005K	ENST00000218089	NM_001042749.1	1005	Gaa/Aaa	29/35	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.602317047458462	1		290	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0054399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	577	801	1	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.528451095998439	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.528451095998439	2		802	1049	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867546	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs11466445	NA	P-0054399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	17	44	0	ENST00000374994.4:c.70_78del	p.Ala24_Ala26del	p.A24_A26del	ENST00000374994	NM_004612.2	17	ctGGCGGCGGCg/ctg	1/9	0.528451095998439	2	FACETS	0.804	0.613	1	0.402	0.306	0.51	CLONAL	1	TRUE	0	0.528451095998439	2		44	80	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467086	25467086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757492795	NA	P-0054399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	292	946	2	ENST00000264709.3:c.1789C>T	p.Arg597Trp	p.R597W	ENST00000264709	NM_175629.2	597	Cgg/Tgg	15/23	1	2	FACETS	0.998	0.94	1	0.998	0.94	1	CLONAL	1	TRUE	1	0.528451095998439	2		948	1107	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501213	140501213	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	247	393	0	ENST00000288602.6:c.859G>C	p.Asp287His	p.D287H	ENST00000288602	NM_004333.4	287	Gat/Cat	6/18	0.528451095998439	2	FACETS	0.99	0.938	1	0.99	0.938	1	CLONAL	2	TRUE	0	0.528451095998439	2		393	472	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160520	108160520	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs876659370	NA	P-0054399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	69	447	0	ENST00000278616.4:c.4428C>G	p.Ile1476Met	p.I1476M	ENST00000278616	NM_000051.3	1476	atC/atG	29/63	0.281732490457852	3	FACETS	0.562	0.49	0.641	0.187	0.163	0.214	INDETERMINATE	1	TRUE	0	0.528451095998439	3		447	587	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524717	103524717	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	261	385	0	ENST00000355739.4:c.2848T>G	p.Trp950Gly	p.W950G	ENST00000355739	NM_000123.3	950	Tgg/Ggg	13/15	0.528451095998439	2	FACETS	0.98	0.93	1	0.98	0.93	1	CLONAL	2	TRUE	0	0.528451095998439	2		385	504	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786906	135786943	+	frameshift_variant	Frame_Shift_Del	DEL	ATTTAACAACATCAGCCGAGACGTGGAGTAAGGGGTAG	ATTTAACAACATCAGCCGAGACGTGGAGTAAGGGGTAG	-	novel	NA	P-0054399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	47	489	0	ENST00000298552.3:c.926_963del	p.Ser309TyrfsTer19	p.S309Yfs*19	ENST00000298552	NM_001162426.1	309	tCTACCCCTTACTCCACGTCTCGGCTGATGTTGTTAAAT/t	10/23	0.252804532268216	5	FACETS	0.346	0.291	0.408			1	INDETERMINATE	1	TRUE	NA	0.528451095998439	5		489	921	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417374	139417374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1547	701	1075	1	ENST00000277541.6:c.670C>T	p.Pro224Ser	p.P224S	ENST00000277541	NM_017617.3	224	Ccc/Tcc	4/34	0.456505446593336	5	FACETS	1	0.988	1	0.705	0.679	0.732	CLONAL	2	TRUE	2	0.528451095998439	5		1076	2248	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0054400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	130	455	1				ENST00000310581	NM_198253.2	-/1132			0.452954889929627	3	FACETS	1	0.981	1	0.645	0.588	0.705	CLONAL	1	TRUE	1	0.47043813412608	3		456	529	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651956	36651957	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	326	918	0	ENST00000244741.5:c.79dup	p.Ser27LysfsTer9	p.S27Kfs*9	ENST00000244741	NM_000389.4	26	-/A	2/3	0.277903227525971	3	FACETS	1	0.955	1	0.671	0.637	0.706	INDETERMINATE	2	TRUE	0	0.47043813412608	3		918	850	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528152	103528152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760309416	NA	P-0054400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	44	400	0	ENST00000355739.4:c.3460G>A	p.Asp1154Asn	p.D1154N	ENST00000355739	NM_000123.3	1154	Gat/Aat	15/15	0.264398842429614	6	FACETS	0.574	0.481	0.679	0.144	0.12	0.17	INDETERMINATE	1	TRUE	2	0.47043813412608	6		400	632	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814186	76814186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	23	170	0	ENST00000373344.5:c.6458G>A	p.Arg2153His	p.R2153H	ENST00000373344	NM_000489.3	2153	cGc/cAc	29/35	0.221462908468234	2	FACETS	0.562	0.441	0.699			1	INDETERMINATE	1	TRUE	NA	0.47043813412608	2		170	174	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100344	27100344	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	535	781	0	ENST00000324856.7:c.4059del	p.Phe1354SerfsTer127	p.F1354Sfs*127	ENST00000324856	NM_006015.4	1352	agC/ag	17/20	0.47043813412608	3	FACETS	0.881	0.849	0.913	0.881	0.849	0.913	CLONAL	3	TRUE	0	0.47043813412608	3		781	1063	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797411	45797411	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	140	1050	0	ENST00000450313.1:c.1108del	p.Glu370ArgfsTer38	p.E370Rfs*38	ENST00000450313	NM_012222.2	370	Gag/ag	12/16	0.47043813412608	3	FACETS	0.592	0.537	0.649	0.197	0.179	0.217	SUBCLONAL	1	TRUE	0	0.47043813412608	3		1050	1242	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505366	125505366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	38	376	0	ENST00000428830.2:c.656C>T	p.Ser219Phe	p.S219F	ENST00000428830	NM_001114121.2	219	tCt/tTt	7/14	0.460263328868117	2	FACETS	0.516	0.428	0.614	0.258	0.214	0.307	SUBCLONAL	1	TRUE	0	0.47043813412608	2		376	313	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487891	56487891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	94	679	1	ENST00000267101.3:c.1622G>T	p.Arg541Leu	p.R541L	ENST00000267101	NM_001982.3	541	cGa/cTa	14/28	0.277903227525971	3	FACETS	0.593	0.527	0.663	0.198	0.175	0.221	INDETERMINATE	1	TRUE	0	0.47043813412608	3		680	833	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955481	48955481	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	92	361	1	ENST00000267163.4:c.1597G>T	p.Glu533Ter	p.E533*	ENST00000267163	NM_000321.2	533	Gaa/Taa	17/27	NA	2	FACETS	0.805	0.727	0.884			1	INDETERMINATE	2	TRUE	NA	0.47043813412608	2		362	243	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315405	30315405	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	95	600	0	ENST00000322652.5:c.1090G>C	p.Glu364Gln	p.E364Q	ENST00000322652	NM_015355.2	364	Gag/Cag	10/16	0.257922462932371	5	FACETS	0.853	0.759	0.953	0.171	0.151	0.191	INDETERMINATE	1	TRUE	0	0.47043813412608	5		600	808	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155611	56155611	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	71	445	0	ENST00000399503.3:c.703G>A	p.Glu235Lys	p.E235K	ENST00000399503	NM_005921.1	235	Gag/Aag	3/20	0.452954889929627	3	FACETS	0.749	0.655	0.85	0.374	0.327	0.425	SUBCLONAL	1	TRUE	1	0.47043813412608	3		445	498	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845972	151845972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1019760354	NA	P-0054400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	99	636	0	ENST00000262189.6:c.13040C>T	p.Pro4347Leu	p.P4347L	ENST00000262189	NM_170606.2	4347	cCg/cTg	52/59	0.318253008708209	3	FACETS	0.745	0.665	0.829	0.372	0.332	0.415	SUBCLONAL	1	TRUE	1	0.47043813412608	3		636	698	SUCCESS
AR	367	MSKCC	GRCh37	X	66765955	66765955	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	51	540	0	ENST00000374690.3:c.967G>C	p.Glu323Gln	p.E323Q	ENST00000374690	NM_000044.3	323	Gag/Cag	1/8	0.331672251629669	2	FACETS	0.34	0.289	0.397			1	SUBCLONAL	1	TRUE	NA	0.47043813412608	2		540	637	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0054401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	74	392	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.355863521444864	2		392	362	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0054401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	124	989	1	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.355863521444864	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.355863521444864	1		990	532	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023696	27023696	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	31	482	2	ENST00000324856.7:c.802C>T	p.Gln268Ter	p.Q268*	ENST00000324856	NM_006015.4	268	Cag/Tag	1/20	1	2	FACETS	0.438	0.354	0.533	0.438	0.354	0.533	SUBCLONAL	1	TRUE	1	0.355863521444864	2		484	398	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350062	81350062	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	41	384	0	ENST00000222390.5:c.1270C>A	p.Arg424Ser	p.R424S	ENST00000222390	NM_000601.4	424	Cgt/Agt	10/18	1	2	FACETS	0.666	0.556	0.787	0.666	0.556	0.787	SUBCLONAL	1	TRUE	1	0.355863521444864	2		384	346	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793293	242793293	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	111	1168	1	ENST00000334409.5:c.784C>A	p.Pro262Thr	p.P262T	ENST00000334409	NM_005018.2	262	Ccc/Acc	5/5	0.355863521444864	1	FACETS	0.823	0.742	0.909	0.823	0.742	0.909	CLONAL	1	TRUE	0	0.355863521444864	1		1169	623	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504995	186504995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	65	432	0	ENST00000323963.5:c.851G>A	p.Arg284His	p.R284H	ENST00000323963		284	cGc/cAc	8/11	1	2	FACETS	0.872	0.759	0.994	0.872	0.759	0.994	CLONAL	1	TRUE	1	0.355863521444864	2		432	419	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392119	81392119	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs746355265	NA	P-0054401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	40	382	0	ENST00000222390.5:c.158T>C	p.Ile53Thr	p.I53T	ENST00000222390	NM_000601.4	53	aTa/aCa	2/18	1	2	FACETS	0.698	0.582	0.826	0.698	0.582	0.826	SUBCLONAL	1	TRUE	1	0.355863521444864	2		382	322	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023655	27023655	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	28	435	0	ENST00000324856.7:c.761C>A	p.Ser254Tyr	p.S254Y	ENST00000324856	NM_006015.4	254	tCc/tAc	1/20	1	2	FACETS	0.43	0.344	0.528	0.43	0.344	0.528	SUBCLONAL	1	TRUE	1	0.355863521444864	2		435	366	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134317	2134317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377123510	NA	P-0054401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	45	1206	1	ENST00000219476.3:c.4094C>T	p.Ser1365Leu	p.S1365L	ENST00000219476	NM_000548.3	1365	tCg/tTg	34/42	1	2	FACETS	0.355	0.297	0.419	0.355	0.297	0.419	SUBCLONAL	1	TRUE	1	0.355863521444864	2		1207	713	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923459	9923459	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	75	607	0	ENST00000330684.3:c.1828G>C	p.Gly610Arg	p.G610R	ENST00000330684	NM_001134407.1	610	Ggc/Cgc	9/13	1	2	FACETS	0.987	0.869	1	0.987	0.869	1	CLONAL	1	TRUE	1	0.355863521444864	2		607	427	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17941319	17941319	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	91	796	0	ENST00000458235.1:c.3089C>T	p.Pro1030Leu	p.P1030L	ENST00000458235	NM_000215.3	1030	cCc/cTc	22/24	1	2	FACETS	0.978	0.871	1	0.978	0.871	1	CLONAL	1	TRUE	1	0.355863521444864	2		796	523	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936064	49936064	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	127	983	0	ENST00000296474.3:c.1606T>C	p.Cys536Arg	p.C536R	ENST00000296474	NM_002447.2	536	Tgc/Cgc	4/20	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.355863521444864	2		983	704	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	23	375	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.69	0.539	0.863	0.69	0.539	0.863	SUBCLONAL	1	TRUE	1	0.27	2		375	247	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88428945	88428945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	20	287	0	ENST00000360948.2:c.2155G>A	p.Asp719Asn	p.D719N	ENST00000360948	NM_001012338.2	719	Gat/Aat	17/19	1	2	FACETS	0.686	0.526	0.871	0.686	0.526	0.871	SUBCLONAL	1	TRUE	1	0.27	2		287	216	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554250	29554250	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1567847905	NA	P-0054402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	29	443	0	ENST00000356175.3:c.2266C>T	p.Gln756Ter	p.Q756*	ENST00000356175	NM_000267.3	756	Cag/Tag	19/57	0.215239448082921	3	FACETS	0.592	0.475	0.725	0.296	0.237	0.363	SUBCLONAL	1	TRUE	1	0.27	3		443	412	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905566	50905566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774789534	NA	P-0054402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	74	1302	6	ENST00000440232.2:c.694C>T	p.Arg232Cys	p.R232C	ENST00000440232	NM_002691.3	232	Cgt/Tgt	6/27	1	2	FACETS	0.72	0.63	0.818	0.72	0.63	0.818	SUBCLONAL	1	TRUE	1	0.27	2		1308	761	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152857994	152857994	+	synonymous_variant	Silent	SNP	G	G	A	rs139186601	NA	P-0054402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	27	412	0	ENST00000406277.2:c.621C>T	p.Ala207=	p.A207=	ENST00000406277	NM_152274.4	207	gcC/gcT	6/7	1	2	FACETS	0.725	0.578	0.891	0.725	0.578	0.891	SUBCLONAL	1	TRUE	1	0.27	2		412	276	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109309847	109309847	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757187967	NA	P-0054402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	58	497	1	ENST00000436639.2:c.1468C>T	p.Arg490Cys	p.R490C	ENST00000436639	NM_014454.2	490	Cgt/Tgt	9/10	1	2	FACETS	0.886	0.762	1	0.886	0.762	1	CLONAL	1	TRUE	1	0.27	2		498	485	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927347	245927347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	33	416	0	ENST00000388985.4:c.1181G>A	p.Arg394Lys	p.R394K	ENST00000388985		394	aGa/aAa	11/12	1	2	FACETS	0.689	0.562	0.831	0.689	0.562	0.831	SUBCLONAL	1	TRUE	1	0.27	2		416	355	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949107	71949107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs569502858	NA	P-0054402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	76	938	2	ENST00000298229.2:c.3574C>T	p.Arg1192Trp	p.R1192W	ENST00000298229	NM_001567.3	1192	Cgg/Tgg	27/28	1	2	FACETS	0.931	0.817	1	0.931	0.817	1	CLONAL	1	TRUE	1	0.27	2		940	605	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120811	115120811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1194543955	NA	P-0054402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	39	665	0	ENST00000257566.3:c.195G>A	p.Met65Ile	p.M65I	ENST00000257566	NM_016569.3	65	atG/atA	1/8	1	2	FACETS	0.764	0.635	0.908	0.764	0.635	0.908	CLONAL	1	TRUE	1	0.27	2		665	378	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435174	110435174	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	70	654	0	ENST00000375856.3:c.3227C>T	p.Ala1076Val	p.A1076V	ENST00000375856	NM_003749.2	1076	gCt/gTt	1/2	1	2	FACETS	0.971	0.848	1	0.971	0.848	1	CLONAL	1	TRUE	1	0.27	2		654	534	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223684	36223705	+	frameshift_variant	Frame_Shift_Del	DEL	TCGGGGCCAGGGCACGCCTCCT	TCGGGGCCAGGGCACGCCTCCT	-	novel	NA	P-0054402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	56	1096	1	ENST00000222270.7:c.6245_6266del	p.Gly2082GlufsTer2	p.G2082Efs*2	ENST00000222270	NM_014727.1	2078	ccTCGGGGCCAGGGCACGCCTCCT/cc	28/37	1	2	FACETS	0.561	0.479	0.65	0.561	0.479	0.65	SUBCLONAL	1	TRUE	1	0.27	2		1097	740	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523289	9523289	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	46	587	0	ENST00000353224.5:c.1948C>T	p.Gln650Ter	p.Q650*	ENST00000353224	NM_177990.2	650	Cag/Tag	9/10	1	2	FACETS	0.703	0.592	0.825	0.703	0.592	0.825	SUBCLONAL	1	TRUE	1	0.27	2		587	485	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629794	187629795	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0054402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	61	692	0	ENST00000441802.2:c.1187_1188delinsTT	p.Ser396Phe	p.S396F	ENST00000441802	NM_005245.3	396	tCC/tTT	2/27	1	2	FACETS	0.798	0.689	0.917	0.798	0.689	0.917	CLONAL	1	TRUE	1	0.27	2		692	566	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526421	31526421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1271794085	NA	P-0054402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	71	924	0	ENST00000344624.3:c.619C>T	p.Leu207Phe	p.L207F	ENST00000344624		207	Ctc/Ttc	2/33	1	2	FACETS	0.812	0.708	0.923	0.812	0.708	0.923	CLONAL	1	TRUE	1	0.27	2		924	648	SUCCESS
APC	324	MSKCC	GRCh37	5	112155039	112155039	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	40	431	0	ENST00000257430.4:c.1310C>T	p.Pro437Leu	p.P437L	ENST00000257430	NM_000038.5	437	cCa/cTa	10/16	1	2	FACETS	0.683	0.568	0.811	0.683	0.568	0.811	SUBCLONAL	1	TRUE	1	0.27	2		431	434	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497278	149497278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	81	803	0	ENST00000261799.4:c.3040C>T	p.Pro1014Ser	p.P1014S	ENST00000261799	NM_002609.3	1014	Ccc/Tcc	22/23	1	2	FACETS	0.948	0.836	1	0.948	0.836	1	CLONAL	1	TRUE	1	0.27	2		803	633	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410268	63410268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs968815543	NA	P-0054402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	54	877	4	ENST00000330258.3:c.2899C>T	p.Pro967Ser	p.P967S	ENST00000330258	NM_152424.3	967	Cca/Tca	2/2	1	2	FACETS	0.717	0.612	0.831	0.717	0.612	0.831	SUBCLONAL	1	TRUE	1	0.27	2		881	558	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918940	76918940	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	53	597	0	ENST00000373344.5:c.4051G>A	p.Glu1351Lys	p.E1351K	ENST00000373344	NM_000489.3	1351	Gaa/Aaa	12/35	1	2	FACETS	0.761	0.649	0.883	0.761	0.649	0.883	SUBCLONAL	1	TRUE	1	0.27	2		597	516	SUCCESS
BTK	695	MSKCC	GRCh37	X	100625005	100625005	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	35	553	0	ENST00000308731.7:c.372G>A	p.Trp124Ter	p.W124*	ENST00000308731	NM_000061.2	124	tgG/tgA	5/19	1	2	FACETS	0.524	0.429	0.631	0.524	0.429	0.631	SUBCLONAL	1	TRUE	1	0.27	2		553	495	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	76	375	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.787	0.698	0.881	0.787	0.698	0.881	SUBCLONAL	1	TRUE	1	0.665924903517922	2		375	290	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0054403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	127	456	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.835	0.761	0.911	0.835	0.761	0.911	CLONAL	1	TRUE	1	0.665924903517922	2		456	457	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0054403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	368	913	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.610131362507293	2	FACETS	0.954	0.918	0.99	0.954	0.918	0.99	CLONAL	2	TRUE	0	0.665924903517922	2		913	579	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437507	110437507	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1448817819	NA	P-0054403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	246	897	0	ENST00000375856.3:c.894C>A	p.Phe298Leu	p.F298L	ENST00000375856	NM_003749.2	298	ttC/ttA	1/2	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.665924903517922	2		897	726	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41011012	41011012	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	138	734	0	ENST00000267868.3:c.445G>A	p.Asp149Asn	p.D149N	ENST00000267868	NM_002875.4	149	Gac/Aac	6/10	0.463699299409906	3	FACETS	0.814	0.742	0.889	0.407	0.371	0.445	CLONAL	1	TRUE	1	0.665924903517922	3		734	679	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52661325	52661325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	37	569	0	ENST00000394830.3:c.1505C>T	p.Ser502Leu	p.S502L	ENST00000394830	NM_018313.4	502	tCa/tTa	14/30	1	2	FACETS	0.223	0.183	0.267	0.223	0.183	0.267	SUBCLONAL	1	TRUE	1	0.665924903517922	2		569	499	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997690	149997690	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0054403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	109	397	0	ENST00000253339.5:c.2776+1G>C		p.X926_splice	ENST00000253339		926			1	2	FACETS	0.885	0.802	0.971	0.885	0.802	0.971	CLONAL	1	TRUE	1	0.665924903517922	2		397	370	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776139	135776139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	204	557	0	ENST00000298552.3:c.2588del	p.Leu863TrpfsTer15	p.L863Wfs*15	ENST00000298552	NM_001162426.1	863	tTg/tg	20/23	0.665924903517922	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.665924903517922	1		557	404	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321057	137321074	+	inframe_deletion	In_Frame_Del	DEL	CAGCGCAGGGGTGGGCGC	CAGCGCAGGGGTGGGCGC	-	novel	NA	P-0054403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	205	1047	0	ENST00000481739.1:c.1016_1033del	p.Ser339_Ala344del	p.S339_A344del	ENST00000481739	NM_002957.4	338	caCAGCGCAGGGGTGGGCGCc/cac	7/10	0.665924903517922	1	FACETS	0.933	0.877	0.99	0.933	0.877	0.99	CLONAL	1	TRUE	0	0.665924903517922	1		1047	440	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247197	153247201	+	frameshift_variant	Frame_Shift_Del	DEL	GTGTA	GTGTA	T	novel	NA	P-0054403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	48	431	0	ENST00000281708.4:c.1601_1605delinsA	p.Leu534GlnfsTer21	p.L534Qfs*21	ENST00000281708	NM_033632.3	534	cTACAC/cA	10/12	0.551401034479781	1	FACETS	0.261	0.221	0.305	0.261	0.221	0.305	SUBCLONAL	1	TRUE	0	0.665924903517922	1		431	368	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	121	703	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.49	2		703	463	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	174	801	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.966	0.892	1	0.966	0.892	1	CLONAL	1	TRUE	1	0.49	2		801	735	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	334	772	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.886	0.843	0.93	1	0.996	1	CLONAL	2	TRUE	1	0.49	2		777	769	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380346	14380346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	85	342	0	ENST00000256196.4:c.71G>A	p.Gly24Asp	p.G24D	ENST00000256196		24	gGc/gAc	1/6	1	2	FACETS	0.997	0.889	1	0.997	0.889	1	CLONAL	1	TRUE	1	0.49	2		342	348	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	156	632	1	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	0.912	0.837	0.99	0.912	0.837	0.99	CLONAL	1	TRUE	1	0.49	2		633	698	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413010	49413010	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519952	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	133	577	0	ENST00000418115.1:c.13C>T	p.Arg5Trp	p.R5W	ENST00000418115	NM_001664.2	5	Cgg/Tgg	2/5	1	2	FACETS	0.9	0.82	0.984	0.9	0.82	0.984	CLONAL	1	TRUE	1	0.49	2		577	603	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182637	38182637	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs748659894	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	82	360	0	ENST00000396334.3:c.790C>T	p.Arg264Ter	p.R264*	ENST00000396334	NM_002468.4	264	Cga/Tga	5/5	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.49	2		360	299	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	82	406	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	1	2	FACETS	0.914	0.812	1	0.914	0.812	1	CLONAL	1	TRUE	1	0.49	2		406	366	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	102	103	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.88	0.791	0.974	0.88	0.791	0.974	CLONAL	1	TRUE	1	0.49	2		103	473	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636818	8636818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146973770	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	126	491	0	ENST00000356435.5:c.91G>A	p.Val31Ile	p.V31I	ENST00000356435		31	Gtt/Att	2/35	1	2	FACETS	0.811	0.736	0.89	0.811	0.736	0.89	CLONAL	1	TRUE	1	0.49	2		491	634	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740810	58740810	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1179832290	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	131	538	0	ENST00000305921.3:c.1715G>A	p.Arg572Gln	p.R572Q	ENST00000305921	NM_003620.3	572	cGa/cAa	6/6	1	2	FACETS	0.803	0.73	0.879	0.803	0.73	0.879	CLONAL	1	TRUE	1	0.49	2		538	666	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86668008	86668008	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	53	280	0	ENST00000274376.6:c.1772G>A	p.Arg591His	p.R591H	ENST00000274376	NM_002890.2	591	cGt/cAt	13/25	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.49	2		280	213	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989562	212989562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755026855	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	96	340	0	ENST00000342788.4:c.149G>A	p.Arg50His	p.R50H	ENST00000342788	NM_005235.2	50	cGc/cAc	2/28	1	2	FACETS	0.926	0.83	1	0.926	0.83	1	CLONAL	1	TRUE	1	0.49	2		340	423	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460504	8460504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148300682	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	128	561	0	ENST00000356435.5:c.3782C>T	p.Thr1261Met	p.T1261M	ENST00000356435		1261	aCg/aTg	22/35	1	2	FACETS	0.884	0.804	0.968	0.884	0.804	0.968	CLONAL	1	TRUE	1	0.49	2		561	591	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459687	40459687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	172	717	0	ENST00000345506.4:c.1852C>T	p.Arg618Cys	p.R618C	ENST00000345506	NM_003152.3	618	Cgc/Tgc	16/20	1	2	FACETS	0.902	0.832	0.976	0.902	0.832	0.976	CLONAL	1	TRUE	1	0.49	2		717	778	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805672	89805672	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs17227396	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	113	698	0	ENST00000389301.3:c.4036G>A	p.Ala1346Thr	p.A1346T	ENST00000389301	NM_000135.2	1346	Gcg/Acg	41/43	1	2	FACETS	0.819	0.74	0.903	0.819	0.74	0.903	CLONAL	1	TRUE	1	0.49	2		698	563	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797203	42797203	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202242046	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	165	1084	2	ENST00000575354.2:c.3565G>A	p.Val1189Met	p.V1189M	ENST00000575354	NM_015125.3	1189	Gtg/Atg	15/20	1	2	FACETS	0.818	0.752	0.887	0.818	0.752	0.887	CLONAL	1	TRUE	1	0.49	2		1086	823	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653802	89653802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	72	400	0	ENST00000371953.3:c.100G>A	p.Ala34Thr	p.A34T	ENST00000371953	NM_000314.4	34	Gct/Act	2/9	1	2	FACETS	0.957	0.844	1	0.957	0.844	1	CLONAL	1	TRUE	1	0.49	2		400	307	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803592	1803592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs949596399	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	144	789	0	ENST00000260795.2:c.770C>T	p.Ala257Val	p.A257V	ENST00000260795		257	gCg/gTg	6/17	1	2	FACETS	0.923	0.844	1	0.923	0.844	1	CLONAL	1	TRUE	1	0.49	2		789	637	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131405	202131405	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	92	523	0	ENST00000358485.4:c.373C>A	p.Leu125Ile	p.L125I	ENST00000358485	NM_001080125.1	125	Ctc/Atc	2/9	1	2	FACETS	0.907	0.811	1	0.907	0.811	1	CLONAL	1	TRUE	1	0.49	2		523	414	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711875	89711875	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	rs587782603	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	75	336	0	ENST00000371953.3:c.493G>T	p.Gly165Ter	p.G165*	ENST00000371953	NM_000314.4	165	Gga/Tga	6/9	1	2	FACETS	0.939	0.83	1	0.939	0.83	1	CLONAL	1	TRUE	1	0.49	2		336	326	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845415	151845415	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	142	707	0	ENST00000262189.6:c.13597C>T	p.Arg4533Ter	p.R4533*	ENST00000262189	NM_170606.2	4533	Cga/Tga	52/59	1	2	FACETS	0.805	0.735	0.878	0.805	0.735	0.878	CLONAL	1	TRUE	1	0.49	2		707	720	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65349020	65349020	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754991396	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	116	559	0	ENST00000342505.4:c.145C>T	p.Arg49Trp	p.R49W	ENST00000342505	NM_002227.2	49	Cgg/Tgg	3/25	1	2	FACETS	0.801	0.724	0.882	0.801	0.724	0.882	CLONAL	1	TRUE	1	0.49	2		559	591	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818219	43818219	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	116	636	0	ENST00000372470.3:c.1684G>T	p.Glu562Ter	p.E562*	ENST00000372470	NM_005373.2	562	Gaa/Taa	12/12	1	2	FACETS	0.839	0.759	0.924	0.839	0.759	0.924	CLONAL	1	TRUE	1	0.49	2		636	564	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541507	187541507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758885671	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	62	47	0	ENST00000441802.2:c.6233C>T	p.Ala2078Val	p.A2078V	ENST00000441802	NM_005245.3	2078	gCg/gTg	10/27	1	2	FACETS	0.562	0.487	0.644	0.562	0.487	0.644	SUBCLONAL	1	TRUE	1	0.49	2		47	450	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367350	50367350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369417059	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	101	509	0	ENST00000331340.3:c.157G>A	p.Val53Met	p.V53M	ENST00000331340	NM_006060.4	53	Gtg/Atg	3/8	1	2	FACETS	0.731	0.655	0.811	0.731	0.655	0.811	SUBCLONAL	1	TRUE	1	0.49	2		509	564	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17129521	17129521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	158	772	1	ENST00000285071.4:c.365G>A	p.Arg122His	p.R122H	ENST00000285071	NM_144997.5	122	cGc/cAc	5/14	1	2	FACETS	0.875	0.803	0.95	0.875	0.803	0.95	CLONAL	1	TRUE	1	0.49	2		773	737	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343580	118343580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1368855534	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	125	499	1	ENST00000534358.1:c.1706C>T	p.Pro569Leu	p.P569L	ENST00000534358	NM_005933.3	569	cCg/cTg	3/36	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.49	2		500	501	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351703	89351703	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773132293	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	200	760	0	ENST00000301030.4:c.1247C>T	p.Ala416Val	p.A416V	ENST00000301030	NM_001256183.1	416	gCg/gTg	9/13	1	2	FACETS	0.938	0.87	1	0.938	0.87	1	CLONAL	1	TRUE	1	0.49	2		760	870	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291061	10291061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377146699	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	133	627	0	ENST00000340748.4:c.410C>T	p.Thr137Met	p.T137M	ENST00000340748		137	aCg/aTg	4/40	1	2	FACETS	0.767	0.697	0.839	0.767	0.697	0.839	SUBCLONAL	1	TRUE	1	0.49	2		627	708	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956759	68956759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777080876	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	163	604	0	ENST00000288368.4:c.877C>T	p.Arg293Trp	p.R293W	ENST00000288368	NM_024870.2	293	Cgg/Tgg	8/40	1	2	FACETS	0.899	0.827	0.974	0.899	0.827	0.974	CLONAL	1	TRUE	1	0.49	2		604	740	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226712	2226712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780009010	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	167	990	0	ENST00000398665.3:c.4192G>A	p.Gly1398Arg	p.G1398R	ENST00000398665	NM_032482.2	1398	Ggg/Agg	27/28	1	2	FACETS	0.868	0.799	0.94	0.868	0.799	0.94	CLONAL	1	TRUE	1	0.49	2		990	785	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504591	103504591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778293	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	74	364	0	ENST00000355739.4:c.212G>A	p.Arg71His	p.R71H	ENST00000355739	NM_000123.3	71	cGt/cAt	2/15	1	2	FACETS	0.984	0.869	1	0.984	0.869	1	CLONAL	1	TRUE	1	0.49	2		364	307	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95563031	95563031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776416084	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	84	340	0	ENST00000393063.1:c.4226C>T	p.Ala1409Val	p.A1409V	ENST00000393063	NM_030621.3	1409	gCg/gTg	24/28	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.49	2		340	295	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118954	70118954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555629169	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	182	911	1	ENST00000245479.2:c.526C>T	p.Pro176Ser	p.P176S	ENST00000245479	NM_000346.3	176	Ccg/Tcg	2/3	1	2	FACETS	0.994	0.92	1	0.994	0.92	1	CLONAL	1	TRUE	1	0.49	2		912	747	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021699	69021699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779206847	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	112	484	1	ENST00000288368.4:c.2987C>T	p.Ala996Val	p.A996V	ENST00000288368	NM_024870.2	996	gCg/gTg	25/40	1	2	FACETS	0.833	0.752	0.918	0.833	0.752	0.918	CLONAL	1	TRUE	1	0.49	2		485	549	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573764	64573764	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373135175	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	157	871	0	ENST00000312049.6:c.989G>A	p.Arg330His	p.R330H	ENST00000312049	NM_130799.2	330	cGc/cAc	7/10	1	2	FACETS	0.824	0.755	0.895	0.824	0.755	0.895	CLONAL	1	TRUE	1	0.49	2		871	778	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168724	32168724	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755356228	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	143	829	2	ENST00000375023.3:c.4199G>A	p.Arg1400His	p.R1400H	ENST00000375023	NM_004557.3	1400	cGc/cAc	23/30	1	2	FACETS	0.803	0.733	0.876	0.803	0.733	0.876	CLONAL	1	TRUE	1	0.49	2		831	727	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118339535	118339535	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555034779	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	85	473	3	ENST00000534358.1:c.478C>T	p.Arg160Ter	p.R160*	ENST00000534358	NM_005933.3	160	Cga/Tga	2/36	1	2	FACETS	0.69	0.611	0.773	0.69	0.611	0.773	SUBCLONAL	1	TRUE	1	0.49	2		476	503	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801497	1801497	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774962503	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	181	1006	2	ENST00000260795.2:c.403G>A	p.Glu135Lys	p.E135K	ENST00000260795		135	Gaa/Aaa	3/17	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.49	2		1008	701	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458063	120458063	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	146	707	0	ENST00000256646.2:c.7282T>C	p.Ser2428Pro	p.S2428P	ENST00000256646	NM_024408.3	2428	Tca/Cca	34/34	1	2	FACETS	0.838	0.766	0.913	0.838	0.766	0.913	CLONAL	1	TRUE	1	0.49	2		707	711	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66735688	66735688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	83	356	0	ENST00000307102.5:c.509G>A	p.Ser170Asn	p.S170N	ENST00000307102	NM_002755.3	170	aGc/aAc	4/11	1	2	FACETS	0.878	0.78	0.981	0.878	0.78	0.981	CLONAL	1	TRUE	1	0.49	2		356	386	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128247	30128247	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	160	900	0	ENST00000263025.4:c.985T>C	p.Tyr329His	p.Y329H	ENST00000263025	NM_002746.2	329	Tac/Cac	7/9	1	2	FACETS	0.886	0.814	0.961	0.886	0.814	0.961	CLONAL	1	TRUE	1	0.49	2		900	737	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991443	72991443	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	170	868	0	ENST00000268489.5:c.2602C>G	p.Gln868Glu	p.Q868E	ENST00000268489	NM_006885.3	868	Cag/Gag	2/10	1	2	FACETS	0.901	0.83	0.975	0.901	0.83	0.975	CLONAL	1	TRUE	1	0.49	2		868	770	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350659	89350659	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	230	749	0	ENST00000301030.4:c.2291A>G	p.Glu764Gly	p.E764G	ENST00000301030	NM_001256183.1	764	gAg/gGg	9/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.49	2		749	806	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557860	29557860	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	45	225	0	ENST00000356175.3:c.3114G>T	p.Arg1038Ser	p.R1038S	ENST00000356175	NM_000267.3	1038	agG/agT	24/57	1	2	FACETS	0.947	0.806	1	0.947	0.806	1	CLONAL	1	TRUE	1	0.49	2		225	194	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40461490	40461490	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs529491430	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	178	981	0	ENST00000345506.4:c.2210T>C	p.Met737Thr	p.M737T	ENST00000345506	NM_003152.3	737	aTg/aCg	19/20	1	2	FACETS	0.908	0.838	0.981	0.908	0.838	0.981	CLONAL	1	TRUE	1	0.49	2		981	800	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278125	15278125	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1420105350	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	181	940	0	ENST00000263388.2:c.5297T>C	p.Met1766Thr	p.M1766T	ENST00000263388	NM_000435.2	1766	aTg/aCg	29/33	1	2	FACETS	0.89	0.822	0.961	0.89	0.822	0.961	CLONAL	1	TRUE	1	0.49	2		940	830	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971229	18971229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	159	773	0	ENST00000262803.5:c.2282G>A	p.Gly761Asp	p.G761D	ENST00000262803	NM_002911.3	761	gGc/gAc	16/24	1	2	FACETS	0.882	0.81	0.957	0.882	0.81	0.957	CLONAL	1	TRUE	1	0.49	2		773	736	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134514507	134514507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372758942	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	103	660	3	ENST00000398015.3:c.34G>A	p.Ala12Thr	p.A12T	ENST00000398015	NM_004441.4	12	Gca/Aca	1/16	1	2	FACETS	0.839	0.754	0.929	0.839	0.754	0.929	CLONAL	1	TRUE	1	0.49	2		663	501	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146578	185146578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs548832664	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	139	618	3	ENST00000265026.3:c.209C>T	p.Thr70Met	p.T70M	ENST00000265026	NM_004721.4	70	aCg/aTg	2/14	1	2	FACETS	0.957	0.874	1	0.957	0.874	1	CLONAL	1	TRUE	1	0.49	2		621	593	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38943008	38943008	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	74	330	0	ENST00000357387.3:c.4979T>G	p.Leu1660Arg	p.L1660R	ENST00000357387	NM_152756.3	1660	cTg/cGg	37/38	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.49	2		330	273	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753996	57753996	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	82	311	0	ENST00000274289.3:c.628A>T	p.Asn210Tyr	p.N210Y	ENST00000274289	NM_006622.3	210	Aac/Tac	5/14	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.49	2		311	305	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038452	180038452	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs744282	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	147	944	3	ENST00000261937.6:c.3565C>T	p.Arg1189Cys	p.R1189C	ENST00000261937	NM_182925.4	1189	Cgc/Tgc	27/30	1	2	FACETS	0.804	0.735	0.876	0.804	0.735	0.876	CLONAL	1	TRUE	1	0.49	2		947	746	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675177	30675177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775345865	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	111	573	0	ENST00000376406.3:c.3068C>T	p.Ala1023Val	p.A1023V	ENST00000376406	NM_014641.2	1023	gCt/gTt	9/15	1	2	FACETS	0.833	0.751	0.918	0.833	0.751	0.918	CLONAL	1	TRUE	1	0.49	2		573	544	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273267	55273267	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	134	559	0	ENST00000275493.2:c.3590A>G	p.Tyr1197Cys	p.Y1197C	ENST00000275493	NM_005228.3	1197	tAc/tGc	28/28	0.23255848399267	3	FACETS	1	0.982	1	0.651	0.595	0.71	INDETERMINATE	1	TRUE	1	0.49	3		559	523	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511085	148511085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	130	387	0	ENST00000320356.2:c.1817G>A	p.Cys606Tyr	p.C606Y	ENST00000320356	NM_004456.4	606	tGc/tAc	15/20	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.49	2		387	512	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325665	87325665	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	94	515	1	ENST00000277120.3:c.542G>A	p.Ser181Asn	p.S181N	ENST00000277120		181	aGc/aAc	6/19	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.49	2		516	377	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	201	502	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.994	0.926	1	0.994	0.926	1	CLONAL	1	TRUE	1	0.66	2		502	613	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477807	140477807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs180177038	NA	P-0054405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	218	513	0	ENST00000288602.6:c.1501G>A	p.Glu501Lys	p.E501K	ENST00000288602	NM_004333.4	501	Gaa/Aaa	12/18	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.66	2		513	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0054406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	652	602	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.463934602760444	5	FACETS	1	0.995	1	0.885	0.86	0.908	CLONAL	4	TRUE	0	0.555544990523622	5		602	973	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223306	2223306	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	170	763	1	ENST00000398665.3:c.3417G>T	p.Glu1139Asp	p.E1139D	ENST00000398665	NM_032482.2	1139	gaG/gaT	25/28	1	2	FACETS	0.916	0.846	0.989	0.916	0.846	0.989	CLONAL	1	TRUE	1	0.555544990523622	2		764	668	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264760	46264760	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	80	407	0	ENST00000371998.3:c.1630C>G	p.Pro544Ala	p.P544A	ENST00000371998		544	Cca/Gca	12/23	0.555803871601992	3	FACETS	0.592	0.521	0.667	0.296	0.26	0.334	SUBCLONAL	1	TRUE	1	0.555544990523622	3		407	622	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777867	27777867	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	70	420	2	ENST00000369163.2:c.16C>T	p.Gln6Ter	p.Q6*	ENST00000369163	NM_003536.2	6	Cag/Tag	1/1	0.551468814629687	3	FACETS	0.817	0.716	0.925	0.409	0.358	0.463	CLONAL	1	TRUE	1	0.555544990523622	3		422	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0054409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	219	849	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.438757437505956	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	0	0.438757437505956	3		849	375	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260146	10260146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751754286	NA	P-0054409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	64	810	1	ENST00000340748.4:c.2521G>A	p.Glu841Lys	p.E841K	ENST00000340748		841	Gaa/Aaa	25/40	0.438757437505956	3	FACETS	0.991	0.863	1	0.495	0.431	0.564	CLONAL	1	TRUE	1	0.438757437505956	3		811	359	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89865590	89865591	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0054409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	64	731	0	ENST00000389301.3:c.876_877del	p.His292GlnfsTer46	p.H292Qfs*46	ENST00000389301	NM_000135.2	292	caCAag/caag	10/43	1	2	FACETS	0.917	0.8	1	0.917	0.8	1	CLONAL	1	TRUE	1	0.438757437505956	2		731	318	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0054410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	50	477	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.13895007400954	3	FACETS	0.949	0.804	1	0.475	0.402	0.555	CLONAL	1	TRUE	1	0.16	3		477	711	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149590	61149590	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	29	373	0	ENST00000295025.8:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000295025	NM_002908.2	594	Gat/Aat	11/11	1	2	FACETS	0.68	0.545	0.835	0.68	0.545	0.835	SUBCLONAL	1	TRUE	1	0.16	2		373	533	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270187	198270187	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	23	312	0	ENST00000335508.6:c.1249C>G	p.Pro417Ala	p.P417A	ENST00000335508	NM_012433.2	417	Cct/Gct	10/25	1	2	FACETS	0.633	0.493	0.797	0.633	0.493	0.797	SUBCLONAL	1	TRUE	1	0.16	2		312	454	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956693	93956693	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	32	340	0	ENST00000369303.4:c.2543C>A	p.Ala848Glu	p.A848E	ENST00000369303	NM_004440.3	848	gCa/gAa	15/17	1	2	FACETS	0.813	0.659	0.987	0.813	0.659	0.987	CLONAL	1	TRUE	1	0.16	2		340	492	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132867	152132867	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556229991	NA	P-0054410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	36	540	0	ENST00000262189.6:c.5C>T	p.Ser2Leu	p.S2L	ENST00000262189	NM_170606.2	2	tCg/tTg	1/59	1	2	FACETS	0.758	0.621	0.911	0.758	0.621	0.911	CLONAL	1	TRUE	1	0.16	2		540	594	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359963	87359963	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	29	424	0	ENST00000277120.3:c.1271A>T	p.Asp424Val	p.D424V	ENST00000277120		424	gAt/gTt	11/19	1	2	FACETS	0.704	0.564	0.864	0.704	0.564	0.864	SUBCLONAL	1	TRUE	1	0.16	2		424	515	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432443	49432443	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	44	971	0	ENST00000301067.7:c.8696G>T	p.Gly2899Val	p.G2899V	ENST00000301067	NM_003482.3	2899	gGc/gTc	34/54	1	2	FACETS	0.795	0.665	0.94	0.795	0.665	0.94	CLONAL	1	TRUE	1	0.143777582659175	2		971	770	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533086	63533086	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	46	914	0	ENST00000307078.5:c.1808C>G	p.Ala603Gly	p.A603G	ENST00000307078	NM_004655.3	603	gCt/gGt	7/11	1	2	FACETS	0.947	0.796	1	0.947	0.796	1	CLONAL	1	TRUE	1	0.143777582659175	2		914	676	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753719	42753719	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	53	1175	0	ENST00000222329.4:c.545del	p.Gly182AlafsTer89	p.G182Afs*89	ENST00000222329	NM_006494.2	182	gGc/gc	4/4	1	2	FACETS	0.883	0.751	1	0.883	0.751	1	CLONAL	1	TRUE	1	0.143777582659175	2		1175	835	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912104	50912104	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	55	1090	0	ENST00000440232.2:c.1838C>G	p.Ala613Gly	p.A613G	ENST00000440232	NM_002691.3	613	gCc/gGc	15/27	1	2	FACETS	0.968	0.827	1	0.968	0.827	1	CLONAL	1	TRUE	1	0.143777582659175	2		1090	790	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0054415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	62	696	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	1	0.464027409787676	2		696	243	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752842	128752842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	116	492	0	ENST00000377970.2:c.1003C>T	p.Pro335Ser	p.P335S	ENST00000377970	NM_002467.4	335	Cct/Tct	3/3	0.255424923822269	1	FACETS	0.932	0.847	1	0.932	0.847	1	INDETERMINATE	1	FALSE	0	0.464027409787676	1		492	412	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325101	39325101	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	122	688	0	ENST00000373001.3:c.218G>C	p.Gly73Ala	p.G73A	ENST00000373001	NM_022157.3	73	gGc/gCc	1/7	1	2	FACETS	0.979	0.889	1	0.979	0.889	1	CLONAL	1	FALSE	1	0.464027409787676	2		688	537	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212550	133212550	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	97	664	0	ENST00000320574.5:c.5739del	p.Leu1914PhefsTer85	p.L1914Ffs*85	ENST00000320574	NM_006231.2	1913	ttT/tt	42/49	0.464027409787676	3	FACETS	0.957	0.867	1	0.957	0.867	1	CLONAL	2	FALSE	1	0.464027409787676	3		664	269	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485074	57485074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	74	540	0	ENST00000371085.3:c.908C>T	p.Ala303Val	p.A303V	ENST00000371085	NM_000516.4	303	gCt/gTt	11/13	0.119576566220052	0	FACETS	0.55	0.485	0.618			1	INDETERMINATE	1	FALSE	0	0.464027409787676	0		540	311	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183693	10183693	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs869025615	NA	P-0054415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	155	868	0	ENST00000256474.2:c.163del	p.Glu55ArgfsTer12	p.E55Rfs*12	ENST00000256474	NM_000551.3	54	atG/at	1/3	0.440723192360394	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	0	0.464027409787676	1		868	491	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643575	52643575	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	58	647	0	ENST00000394830.3:c.2321T>A	p.Val774Glu	p.V774E	ENST00000394830	NM_018313.4	774	gTg/gAg	17/30	0.440723192360394	1	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	FALSE	0	0.464027409787676	1		647	189	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0054416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	16	370	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.416	0.306	0.548	0.416	0.306	0.548	SUBCLONAL	1	FALSE	1	0.183084786638225	2		370	420	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0054416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	51	235	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.183084786638225	4	FACETS	1	0.896	1	1	0.896	1	CLONAL	2	FALSE	2	0.183084786638225	4		235	311	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630626	158630626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912678	NA	P-0054416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	12	321	1	ENST00000263640.3:c.617G>A	p.Arg206His	p.R206H	ENST00000263640	NM_001105.4	206	cGc/cAc	6/11	0.148179551614749	3	FACETS	0.532	0.373	0.728	0.266	0.186	0.364	SUBCLONAL	1	FALSE	1	0.183084786638225	3		322	269	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307414	118307416	+	inframe_deletion	In_Frame_Del	DEL	GCG	GCG	-	rs781936420	NA	P-0054416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	11	17	0	ENST00000534358.1:c.200_202del	p.Ala67del	p.A67del	ENST00000534358	NM_005933.3	63	GCG/-	1/36	0.183084786638225	2	FACETS	1	0.742	1	1	0.742	1	CLONAL	2	FALSE	0	0.183084786638225	2		17	57	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165729	108165729	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs762083530	NA	P-0054416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	63	405	0	ENST00000278616.4:c.4852C>T	p.Arg1618Ter	p.R1618*	ENST00000278616	NM_000051.3	1618	Cga/Tga	32/63	0.183084786638225	2	FACETS	0.887	0.781	0.998	1	0.979	1	CLONAL	4	FALSE	0	0.183084786638225	2		405	194	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943788	71943788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771815535	NA	P-0054416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	101	809	0	ENST00000298229.2:c.1831C>T	p.Arg611Cys	p.R611C	ENST00000298229	NM_001567.3	611	Cgc/Tgc	15/28	0.140027197462104	4	FACETS	0.924	0.827	1	0.924	0.827	1	CLONAL	2	FALSE	2	0.183084786638225	4		809	706	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101650	27101669	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTGTTGAAGCCACACAGC	CTCTGTTGAAGCCACACAGC	-	novel	NA	P-0054416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	244	1013	0	ENST00000324856.7:c.4934_4953del	p.Ser1645CysfsTer46	p.S1645Cfs*46	ENST00000324856	NM_006015.4	1644	ggCTCTGTTGAAGCCACACAGCct/ggct	18/20	0.183084786638225	3	FACETS	0.848	0.792	0.907	0.848	0.792	0.907	CLONAL	3	FALSE	0	0.183084786638225	3		1013	1143	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936138	71936143	+	inframe_deletion	In_Frame_Del	DEL	GGGCGG	GGGCGG	-	novel	NA	P-0054416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	69	225	0	ENST00000298229.2:c.111_116del	p.Ala38_Gly39del	p.A38_G39del	ENST00000298229	NM_001567.3	37	cGGGCGGgc/cgc	1/28	0.140027197462104	4	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	FALSE	2	0.183084786638225	4		225	414	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339710	70339736	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACGCAACTAGCCAAAAAGGTAAGGTAC	ACGCAACTAGCCAAAAAGGTAAGGTAC	T	novel	NA	P-0054416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	52	756	0	ENST00000374080.3:c.379_396+9delinsT		p.X127_splice	ENST00000374080		127		3/45	1	2	FACETS	0.912	0.776	1	0.912	0.776	1	CLONAL	1	FALSE	1	0.183084786638225	2		756	623	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711996	89711996	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	21	321	1	ENST00000371953.3:c.614del	p.Met205SerfsTer16	p.M205Sfs*16	ENST00000371953	NM_000314.4	205	aTg/ag	6/9	0.183084786638225	4	FACETS	0.942	0.733	1	0.942	0.733	1	CLONAL	2	FALSE	2	0.183084786638225	4		322	144	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	45	502	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.89	0.756	1	0.89	0.756	1	CLONAL	1	FALSE	1	0.465987018743561	2		502	217	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581229	48581229	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	47	619	0	ENST00000342988.3:c.533C>A	p.Ser178Ter	p.S178*	ENST00000342988	NM_005359.5	178	tCa/tAa	5/12	0.465987018743561	1	FACETS	0.316	0.266	0.37	0.316	0.266	0.37	SUBCLONAL	1	FALSE	0	0.465987018743561	1		619	490	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911593	114911593	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	47	621	0	ENST00000543371.1:c.1111G>T	p.Glu371Ter	p.E371*	ENST00000543371	NM_001198531.1	371	Gag/Tag	10/14	1	2	FACETS	0.239	0.201	0.281	0.239	0.201	0.281	SUBCLONAL	1	FALSE	1	0.465987018743561	2		621	844	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905432	11905432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34966596	NA	P-0054417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	94	564	0	ENST00000396373.4:c.82G>A	p.Ala28Thr	p.A28T	ENST00000396373	NM_001987.4	28	Gct/Act	2/8	0.0641848966645726	4	FACETS	0.67	0.595	0.75	0.335	0.297	0.375	INDETERMINATE	1	FALSE	2	0.465987018743561	4		564	883	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244146	153244146	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	73	609	0	ENST00000281708.4:c.2011G>T	p.Val671Phe	p.V671F	ENST00000281708	NM_033632.3	671	Gtt/Ttt	12/12	1	2	FACETS	0.318	0.277	0.363	0.318	0.277	0.363	SUBCLONAL	1	FALSE	1	0.465987018743561	2		609	984	SUCCESS
APC	324	MSKCC	GRCh37	5	112137071	112137071	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1554076216	NA	P-0054417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	68	473	0	ENST00000257430.4:c.825del	p.Asn276MetfsTer17	p.N276Mfs*17	ENST00000257430	NM_000038.5	275	ggT/gg	8/16	1	2	FACETS	0.853	0.747	0.966	0.853	0.747	0.966	CLONAL	1	FALSE	1	0.465987018743561	2		473	342	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123048	5123048	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	14	548	0	ENST00000381652.3:c.3104C>A	p.Ser1035Ter	p.S1035*	ENST00000381652	NM_004972.3	1035	tCa/tAa	23/25	1	2	FACETS	0.234	0.169	0.313	0.234	0.169	0.313	SUBCLONAL	1	FALSE	1	0.465987018743561	2		548	257	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	123	378	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.291652736880746	2	FACETS	1	0.976	1	0.606	0.552	0.663	CLONAL	1	TRUE	0	0.459921628805	2		378	441	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	397000	397000	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	125	959	0	ENST00000262320.3:c.26C>T	p.Pro9Leu	p.P9L	ENST00000262320	NM_003502.3	9	cCc/cTc	2/11	1	2	FACETS	0.711	0.643	0.781	0.711	0.643	0.781	SUBCLONAL	1	TRUE	1	0.459921628805	2		959	765	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465606	99465606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	39	638	1	ENST00000268035.6:c.2431G>A	p.Glu811Lys	p.E811K	ENST00000268035	NM_000875.3	811	Gag/Aag	11/21	0.221347418882089	3	FACETS	0.374	0.309	0.446	0.187	0.154	0.223	INDETERMINATE	1	TRUE	1	0.459921628805	3		639	558	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928295	69928295	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	79	575	0	ENST00000352241.4:c.115G>T	p.Glu39Ter	p.E39*	ENST00000352241	NM_198159.2	39	Gag/Tag	2/10	1	2	FACETS	0.772	0.682	0.868	0.772	0.682	0.868	SUBCLONAL	1	TRUE	1	0.459921628805	2		575	445	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050701	5050701	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	26	399	0	ENST00000381652.3:c.484G>T	p.Val162Leu	p.V162L	ENST00000381652	NM_004972.3	162	Gtg/Ttg	6/25	1	2	FACETS	0.255	0.201	0.316	0.255	0.201	0.316	SUBCLONAL	1	TRUE	1	0.459921628805	2		399	444	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610576	10610576	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	66	1050	0	ENST00000171111.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000171111	NM_203500.1	45	tCc/tTc	2/6	1	2	FACETS	0.405	0.351	0.463	0.405	0.351	0.463	SUBCLONAL	1	TRUE	1	0.459921628805	2		1050	709	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108225	8108225	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	101	889	1	ENST00000585124.1:c.999G>T	p.Arg333Ser	p.R333S	ENST00000585124	NM_004217.3	333	agG/agT	9/9	1	2	FACETS	0.659	0.59	0.733	0.659	0.59	0.733	SUBCLONAL	1	TRUE	1	0.459921628805	2		890	666	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248580	59248580	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs750731127	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	103	1001	0	ENST00000371222.2:c.163G>T	p.Ala55Ser	p.A55S	ENST00000371222	NM_002228.3	55	Gcc/Tcc	1/1	1	2	FACETS	0.58	0.519	0.645	0.58	0.519	0.645	SUBCLONAL	1	TRUE	1	0.459921628805	2		1001	772	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982073	201982073	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	124	868	0	ENST00000359651.3:c.599-2A>G		p.X200_splice	ENST00000359651		200			0.300578889125811	3	FACETS	0.931	0.844	1	0.466	0.422	0.512	CLONAL	1	TRUE	1	0.459921628805	3		868	712	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70334005	70334005	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	33	267	0	ENST00000373644.4:c.1910T>C	p.Leu637Pro	p.L637P	ENST00000373644	NM_030625.2	637	cTg/cCg	2/12	1	2	FACETS	0.542	0.443	0.651	0.542	0.443	0.651	SUBCLONAL	1	TRUE	1	0.459921628805	2		267	265	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405377	70405377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	58	638	0	ENST00000373644.4:c.2891C>T	p.Ser964Leu	p.S964L	ENST00000373644	NM_030625.2	964	tCa/tTa	4/12	1	2	FACETS	0.387	0.332	0.448	0.387	0.332	0.448	SUBCLONAL	1	TRUE	1	0.459921628805	2		638	651	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573753	64573753	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	113	957	1	ENST00000312049.6:c.1000G>T	p.Val334Leu	p.V334L	ENST00000312049	NM_130799.2	334	Gtg/Ttg	7/10	1	2	FACETS	0.717	0.646	0.792	0.717	0.646	0.792	SUBCLONAL	1	TRUE	1	0.459921628805	2		958	685	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920770	100920770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	71	435	0	ENST00000325455.5:c.2378C>T	p.Ser793Leu	p.S793L	ENST00000325455	NM_001202474.3	793	tCa/tTa	6/8	0.300578889125811	3	FACETS	0.853	0.747	0.967	0.427	0.373	0.484	CLONAL	1	TRUE	1	0.459921628805	3		435	445	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178683	108178683	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1064794105	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	37	269	0	ENST00000278616.4:c.5734G>C	p.Val1912Leu	p.V1912L	ENST00000278616	NM_000051.3	1912	Gtt/Ctt	38/63	0.300578889125811	3	FACETS	0.58	0.479	0.693	0.29	0.239	0.347	SUBCLONAL	1	TRUE	1	0.459921628805	3		269	341	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192067	108192067	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	90	617	1	ENST00000278616.4:c.6492G>T	p.Glu2164Asp	p.E2164D	ENST00000278616	NM_000051.3	2164	gaG/gaT	45/63	0.300578889125811	3	FACETS	0.722	0.641	0.808	0.361	0.32	0.404	SUBCLONAL	1	TRUE	1	0.459921628805	3		618	667	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425910	49425910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369356025	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	91	1077	2	ENST00000301067.7:c.12578C>T	p.Thr4193Met	p.T4193M	ENST00000301067	NM_003482.3	4193	aCg/aTg	39/54	1	2	FACETS	0.562	0.499	0.629	0.562	0.499	0.629	SUBCLONAL	1	TRUE	1	0.459921628805	2		1079	704	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112331	115112331	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	18	186	0	ENST00000257566.3:c.1409C>G	p.Ala470Gly	p.A470G	ENST00000257566	NM_016569.3	470	gCg/gGg	7/8	1	2	FACETS	0.492	0.373	0.631	0.492	0.373	0.631	SUBCLONAL	1	TRUE	1	0.459921628805	2		186	159	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434120	121434120	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	112	946	0	ENST00000257555.6:c.1011C>A	p.Ser337Arg	p.S337R	ENST00000257555		337	agC/agA	5/10	1	2	FACETS	0.74	0.667	0.818	0.74	0.667	0.818	SUBCLONAL	1	TRUE	1	0.459921628805	2		946	658	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623545	28623545	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	26	395	0	ENST00000241453.7:c.1012C>T	p.Gln338Ter	p.Q338*	ENST00000241453	NM_004119.2	338	Caa/Taa	8/24	1	2	FACETS	0.301	0.238	0.373	0.301	0.238	0.373	SUBCLONAL	1	TRUE	1	0.459921628805	2		395	376	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623849	28623849	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	88	676	0	ENST00000241453.7:c.805T>C	p.Trp269Arg	p.W269R	ENST00000241453	NM_004119.2	269	Tgg/Cgg	7/24	1	2	FACETS	0.693	0.615	0.776	0.693	0.615	0.776	SUBCLONAL	1	TRUE	1	0.459921628805	2		676	552	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913308	28913308	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	82	521	0	ENST00000282397.4:c.2485C>G	p.Leu829Val	p.L829V	ENST00000282397	NM_002019.4	829	Ctg/Gtg	17/30	1	2	FACETS	0.679	0.6	0.763	0.679	0.6	0.763	SUBCLONAL	1	TRUE	1	0.459921628805	2		521	525	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930728	32930729	+	missense_variant	Missense_Mutation	DNP	TG	TG	CT	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	65	543	0	ENST00000380152.3:c.7599_7600delinsCT	p.Ala2534Ser	p.A2534S	ENST00000380152		2533	tcTGcg/tcCTcg	15/27	1	2	FACETS	0.499	0.433	0.571	0.499	0.433	0.571	SUBCLONAL	1	TRUE	1	0.459921628805	2		543	566	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515225	103515225	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	55	452	0	ENST00000355739.4:c.1726G>T	p.Glu576Ter	p.E576*	ENST00000355739	NM_000123.3	576	Gaa/Taa	8/15	1	2	FACETS	0.712	0.612	0.82	0.712	0.612	0.82	SUBCLONAL	1	TRUE	1	0.459921628805	2		452	336	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712638	43712638	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	113	895	0	ENST00000382044.4:c.4546G>T	p.Gly1516Ter	p.G1516*	ENST00000382044	NM_001141980.1	1516	Gga/Tga	21/28	1	2	FACETS	0.658	0.592	0.727	0.658	0.592	0.727	SUBCLONAL	1	TRUE	1	0.459921628805	2		895	747	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720216	43720216	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	36	471	0	ENST00000382044.4:c.3826G>A	p.Glu1276Lys	p.E1276K	ENST00000382044	NM_001141980.1	1276	Gag/Aag	18/28	1	2	FACETS	0.368	0.303	0.442	0.368	0.303	0.442	SUBCLONAL	1	TRUE	1	0.459921628805	2		471	425	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985372	60985372	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	53	872	0	ENST00000333681.4:c.528G>A	p.Trp176Ter	p.W176*	ENST00000333681		176	tgG/tgA	2/3	1	2	FACETS	0.341	0.29	0.397	0.341	0.29	0.397	SUBCLONAL	1	TRUE	1	0.459921628805	2		872	676	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556686	41556686	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	68	565	0	ENST00000263253.7:c.3631G>T	p.Glu1211Ter	p.E1211*	ENST00000263253	NM_001429.3	1211	Gag/Tag	20/31	1	2	FACETS	0.578	0.503	0.658	0.578	0.503	0.658	SUBCLONAL	1	TRUE	1	0.459921628805	2		565	512	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170002344	170002344	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	23	229	0	ENST00000295797.4:c.1163C>T	p.Ser388Phe	p.S388F	ENST00000295797	NM_002740.5	388	tCt/tTt	12/18	0.319833480250616	1	FACETS	0.363	0.284	0.454	0.363	0.284	0.454	SUBCLONAL	1	TRUE	0	0.459921628805	1		229	212	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747946	41747946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	34	305	0	ENST00000226382.2:c.823C>A	p.Pro275Thr	p.P275T	ENST00000226382	NM_003924.3	275	Ccc/Acc	3/3	1	2	FACETS	0.548	0.449	0.657	0.548	0.449	0.657	SUBCLONAL	1	TRUE	1	0.459921628805	2		305	270	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217233	66217233	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	76	494	1	ENST00000273854.3:c.2382G>A	p.Met794Ile	p.M794I	ENST00000273854	NM_004439.5	794	atG/atA	14/18	1	2	FACETS	0.787	0.693	0.887	0.787	0.693	0.887	SUBCLONAL	1	TRUE	1	0.459921628805	2		495	420	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155649	106155649	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	25	428	0	ENST00000380013.4:c.550G>C	p.Glu184Gln	p.E184Q	ENST00000380013	NM_001127208.2	184	Gag/Cag	3/11	1	2	FACETS	0.319	0.251	0.397	0.319	0.251	0.397	SUBCLONAL	1	TRUE	1	0.459921628805	2		428	341	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456863	149456864	+	missense_variant	Missense_Mutation	DNP	TG	TG	GT	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	79	800	0	ENST00000286301.3:c.864_865delinsAC	p.Thr289Pro	p.T289P	ENST00000286301	NM_005211.3	288	tcCAcc/tcACcc	6/22	1	2	FACETS	0.538	0.473	0.607	0.538	0.473	0.607	SUBCLONAL	1	TRUE	1	0.459921628805	2		800	639	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043468	180043468	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	34	843	2	ENST00000261937.6:c.3118G>T	p.Ala1040Ser	p.A1040S	ENST00000261937	NM_182925.4	1040	Gct/Tct	23/30	1	2	FACETS	0.262	0.213	0.317	0.262	0.213	0.317	SUBCLONAL	1	TRUE	1	0.459921628805	2		845	565	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469971	157469971	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867133651	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	45	749	0	ENST00000346085.5:c.2765G>A	p.Gly922Asp	p.G922D	ENST00000346085	NM_020732.3	922	gGc/gAc	9/20	1	2	FACETS	0.364	0.305	0.428	0.364	0.305	0.428	SUBCLONAL	1	TRUE	1	0.459921628805	2		749	538	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394339	162394339	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	56	366	0	ENST00000366898.1:c.729C>G	p.Asp243Glu	p.D243E	ENST00000366898	NM_004562.2	243	gaC/gaG	6/12	1	2	FACETS	0.688	0.592	0.792	0.688	0.592	0.792	SUBCLONAL	1	TRUE	1	0.459921628805	2		366	354	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485833	8485833	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	49	468	0	ENST00000356435.5:c.2984G>T	p.Arg995Leu	p.R995L	ENST00000356435		995	cGt/cTt	17/35	1	2	FACETS	0.53	0.45	0.618	0.53	0.45	0.618	SUBCLONAL	1	TRUE	1	0.459921628805	2		468	402	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250493	110250493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	70	789	0	ENST00000374672.4:c.182G>T	p.Arg61Leu	p.R61L	ENST00000374672	NM_004235.4	61	cGc/cTc	3/5	1	2	FACETS	0.62	0.542	0.704	0.62	0.542	0.704	SUBCLONAL	1	TRUE	1	0.459921628805	2		789	491	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922239	39922239	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	59	544	0	ENST00000378444.4:c.3933C>G	p.Cys1311Trp	p.C1311W	ENST00000378444	NM_001123385.1	1311	tgC/tgG	9/15	NA	2	FACETS	0.574	0.495	0.66			1	INDETERMINATE	1	TRUE	NA	0.459921628805	2		544	447	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006788	47006788	+	5_prime_UTR_variant	5'UTR	SNP	G	G	T	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	94	809	0	ENST00000377604.3:c.-93G>T		p.*31*	ENST00000377604	NM_001204468.1	-/852		2/24	1	2	FACETS	0.7	0.624	0.781	0.7	0.624	0.781	SUBCLONAL	1	TRUE	1	0.459921628805	2		809	584	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410289	63410289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	122	979	0	ENST00000330258.3:c.2878G>A	p.Ala960Thr	p.A960T	ENST00000330258	NM_152424.3	960	Gct/Act	2/2	1	2	FACETS	0.792	0.717	0.871	0.792	0.717	0.871	SUBCLONAL	1	TRUE	1	0.459921628805	2		979	670	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875939	76875940	+	missense_variant	Missense_Mutation	DNP	AG	AG	TA	novel	NA	P-0054418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	55	490	2	ENST00000373344.5:c.5195_5196delinsTA	p.Ser1732Leu	p.S1732L	ENST00000373344	NM_000489.3	1732	tCT/tTA	20/35	1	2	FACETS	0.537	0.461	0.621	0.537	0.461	0.621	SUBCLONAL	1	TRUE	1	0.459921628805	2		492	445	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	47	502	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.799	0.676	0.934	0.799	0.676	0.934	CLONAL	1	TRUE	1	0.299430062826272	2		502	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913343	NA	P-0054420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	102	717	0	ENST00000269305.4:c.817C>A	p.Arg273Ser	p.R273S	ENST00000269305	NM_001126112.2	273	Cgt/Agt	8/11	0.248591678787664	1	FACETS	0.967	0.867	1	0.967	0.867	1	CLONAL	1	TRUE	0	0.299430062826272	1		717	599	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0054420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	64	419	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.299430062826272	1	FACETS	0.82	0.713	0.937	0.82	0.713	0.937	CLONAL	1	TRUE	0	0.299430062826272	1		419	443	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0054421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	24	477	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.954	0.748	1	0.954	0.748	1	CLONAL	1	TRUE	1	0.1393494410269	2		477	361	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0054421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	89	364	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.895	1	1	0.989	1	CLONAL	3	TRUE	1	0.1393494410269	2		364	424	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0054421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	56	772	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.1393494410269	2		777	784	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	22	379	2	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.738	0.571	0.933	0.738	0.571	0.933	CLONAL	1	TRUE	1	0.1393494410269	2		381	428	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560476	95560476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	58	464	0	ENST00000393063.1:c.5113G>A	p.Glu1705Lys	p.E1705K	ENST00000393063	NM_030621.3	1705	Gaa/Aaa	25/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.1393494410269	2		464	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs786202525	NA	P-0054421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	32	585	2	ENST00000269305.4:c.532del	p.His178ThrfsTer69	p.H178Tfs*69	ENST00000269305	NM_001126112.2	178	Cac/ac	5/11	1	2	FACETS	0.599	0.484	0.729	0.599	0.484	0.729	SUBCLONAL	1	TRUE	1	0.1393494410269	2		587	767	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114817	108114817	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786204543	NA	P-0054421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	30	460	0	ENST00000278616.4:c.640del	p.Ser214ProfsTer16	p.S214Pfs*16	ENST00000278616	NM_000051.3	212	Ttt/tt	6/63	1	2	FACETS	0.774	0.623	0.948	0.774	0.623	0.948	CLONAL	1	TRUE	1	0.1393494410269	2		460	556	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023482	27023482	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	35	445	0	ENST00000324856.7:c.591del	p.Gln199SerfsTer33	p.Q199Sfs*33	ENST00000324856	NM_006015.4	196	gcG/gc	1/20	1	2	FACETS	0.912	0.746	1	0.912	0.746	1	CLONAL	1	TRUE	1	0.1393494410269	2		445	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578217	7578240	+	inframe_deletion	In_Frame_Del	DEL	GTGTTTCTGTCATCCAAATACTCC	GTGTTTCTGTCATCCAAATACTCC	-	novel	NA	P-0054422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	428	766	1	ENST00000269305.4:c.609_632del	p.Glu204_Thr211del	p.E204_T211del	ENST00000269305	NM_001126112.2	203	gtGGAGTATTTGGATGACAGAAACACt/gtt	6/11	0.610775832324593	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	0	0.610775832324593	3		767	603	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0054423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	12	344	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	NA	2	FACETS	0.128	0.089	0.176			1	INDETERMINATE	1	TRUE	NA	0.34185631684292	2		344	549	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0054423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	54	963	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.422	0.36	0.491	0.422	0.36	0.491	SUBCLONAL	1	TRUE	1	0.34185631684292	2		966	748	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	53	304	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.663	0.566	0.768	0.663	0.566	0.768	SUBCLONAL	1	TRUE	1	0.34185631684292	2		304	468	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	86	632	1	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	0.725	0.641	0.815	0.725	0.641	0.815	SUBCLONAL	1	TRUE	1	0.34185631684292	2		633	694	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0054423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	26	216	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.277936624253825	3	FACETS	0.625	0.496	0.772	0.208	0.165	0.258	SUBCLONAL	1	TRUE	0	0.34185631684292	3		216	285	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954272	32954273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359752	NA	P-0054423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	29	443	0	ENST00000380152.3:c.9253dup	p.Thr3085AsnfsTer26	p.T3085Nfs*26	ENST00000380152		3082	-/A	24/27	1	2	FACETS	0.376	0.301	0.461	0.376	0.301	0.461	SUBCLONAL	1	TRUE	1	0.34185631684292	2		443	451	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249510	153249510	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1157879635	NA	P-0054423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	43	542	1	ENST00000281708.4:c.1268G>T	p.Gly423Val	p.G423V	ENST00000281708	NM_033632.3	423	gGa/gTa	9/12	1	2	FACETS	0.494	0.413	0.584	0.494	0.413	0.584	SUBCLONAL	1	TRUE	1	0.34185631684292	2		543	509	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371799	55371820	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCCGCGCTGGGCCCCGAG	GGCGGCCGCGCTGGGCCCCGAG	-	novel	NA	P-0054423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	31	165	0	ENST00000297316.4:c.499_520del	p.Leu167TrpfsTer213	p.L167Wfs*213	ENST00000297316	NM_022454.3	163	caGGCGGCCGCGCTGGGCCCCGAG/ca	2/2	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.34185631684292	2		165	159	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624297	89624297	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	269	505	0	ENST00000371953.3:c.71A>T	p.Asp24Val	p.D24V	ENST00000371953	NM_000314.4	24	gAc/gTc	1/9	0.277936624253825	3	FACETS	0.876	0.827	0.926	0.876	0.827	0.926	CLONAL	3	TRUE	0	0.34185631684292	3		505	701	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693010	89693010	+	splice_donor_variant	Splice_Site	DEL	T	T	-	rs1060500124	NA	P-0054423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	19	283	0	ENST00000371953.3:c.492+2del		p.X164_splice	ENST00000371953	NM_000314.4	164			0.277936624253825	3	FACETS	0.397	0.301	0.51	0.132	0.1	0.17	SUBCLONAL	1	TRUE	0	0.34185631684292	3		283	328	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924319	11924319	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0054423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	33	113	2	ENST00000353533.5:c.115+1G>T		p.X39_splice	ENST00000353533	NM_003010.3	39			1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.34185631684292	2		115	183	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249873	110249873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	89	600	0	ENST00000374672.4:c.802G>A	p.Gly268Ser	p.G268S	ENST00000374672	NM_004235.4	268	Ggc/Agc	3/5	1	2	FACETS	0.887	0.788	0.993	0.887	0.788	0.993	CLONAL	1	TRUE	1	0.34185631684292	2		600	587	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217333	11217333	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	55	610	0	ENST00000361445.4:c.4345T>C	p.Trp1449Arg	p.W1449R	ENST00000361445	NM_004958.3	1449	Tgg/Cgg	30/58	1	2	FACETS	0.526	0.449	0.61	0.526	0.449	0.61	SUBCLONAL	1	TRUE	1	0.34185631684292	2		610	612	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087381	27087381	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	103	610	0	ENST00000324856.7:c.1955G>T	p.Gly652Val	p.G652V	ENST00000324856	NM_006015.4	652	gGg/gTg	5/20	1	2	FACETS	0.905	0.811	1	0.905	0.811	1	CLONAL	1	TRUE	1	0.34185631684292	2		610	666	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591243	67591267	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCAGGTGGTTGACTCAAAAAGGTG	TTCAGGTGGTTGACTCAAAAAGGTG	-	novel	NA	P-0054423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	11	411	0	ENST00000274335.5:c.1746-2_1768del		p.X582_splice	ENST00000274335		582		13/15	1	2	FACETS	0.154	0.106	0.215	0.154	0.106	0.215	SUBCLONAL	1	TRUE	1	0.34185631684292	2		411	418	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927067	131927067	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	35	296	0	ENST00000265335.6:c.1604G>C	p.Arg535Pro	p.R535P	ENST00000265335		535	cGt/cCt	10/25	1	2	FACETS	0.656	0.539	0.787	0.656	0.539	0.787	SUBCLONAL	1	TRUE	1	0.34185631684292	2		296	312	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589545	67589566	+	protein_altering_variant	In_Frame_Del	DEL	TGTCAAAGAAGATAATATTGAA	TGTCAAAGAAGATAATATTGAA	CGTC	novel	NA	P-0054423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	25	188	1	ENST00000274335.5:c.1308_1329delinsCGTC	p.Lys438_Glu443del	p.K438_E443del	ENST00000274335		436	gtTGTCAAAGAAGATAATATTGAA/gtCGTC	10/15	1	2	FACETS	0.671	0.531	0.83	0.671	0.531	0.83	SUBCLONAL	1	TRUE	1	0.34185631684292	2		189	218	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0054424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	24	455	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.845	0.662	1	0.845	0.662	1	CLONAL	1	TRUE	1	0.16	2		456	355	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0054424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	44	392	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.16	2		392	482	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733217	40733217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	44	590	0	ENST00000373198.4:c.3589G>A	p.Glu1197Lys	p.E1197K	ENST00000373198	NM_133170.3	1197	Gaa/Aaa	26/32	1	2	FACETS	0.713	0.596	0.843	0.713	0.596	0.843	SUBCLONAL	1	TRUE	1	0.16	2		590	771	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0054424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	24	340	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	1	2	FACETS	0.665	0.52	0.833	0.665	0.52	0.833	SUBCLONAL	1	TRUE	1	0.16	2		340	451	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561520	9561520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	56	657	0	ENST00000353224.5:c.262G>A	p.Asp88Asn	p.D88N	ENST00000353224	NM_177990.2	88	Gat/Aat	4/10	1	2	FACETS	0.867	0.741	1	0.867	0.741	1	CLONAL	1	TRUE	1	0.16	2		657	807	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745587	162745587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751660319	NA	P-0054424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	53	551	0	ENST00000367921.3:c.2002C>T	p.Arg668Cys	p.R668C	ENST00000367921	NM_006182.2	668	Cgc/Tgc	15/18	1	2	FACETS	0.886	0.754	1	0.886	0.754	1	CLONAL	1	TRUE	1	0.16	2		551	748	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215889	142215889	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	39	425	0	ENST00000350721.4:c.5704G>T	p.Ala1902Ser	p.A1902S	ENST00000350721	NM_001184.3	1902	Gct/Tct	33/47	1	2	FACETS	0.983	0.814	1	0.983	0.814	1	CLONAL	1	TRUE	1	0.16	2		425	496	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862826	9862826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	56	657	0	ENST00000330684.3:c.2477C>T	p.Ala826Val	p.A826V	ENST00000330684	NM_001134407.1	826	gCc/gTc	12/13	1	2	FACETS	0.874	0.747	1	0.874	0.747	1	CLONAL	1	TRUE	1	0.16	2		657	801	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300488	11300488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1452329078	NA	P-0054424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	80	738	0	ENST00000361445.4:c.1658G>A	p.Arg553His	p.R553H	ENST00000361445	NM_004958.3	553	cGc/cAc	11/58	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.16	2		738	917	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959419	38959419	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	17	317	0	ENST00000357387.3:c.2056C>T	p.Leu686Phe	p.L686F	ENST00000357387	NM_152756.3	686	Ctt/Ttt	22/38	1	2	FACETS	0.675	0.503	0.879	0.675	0.503	0.879	SUBCLONAL	1	TRUE	1	0.16	2		317	315	SUCCESS
APC	324	MSKCC	GRCh37	5	112154766	112154766	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	37	538	2	ENST00000257430.4:c.1037C>T	p.Ser346Phe	p.S346F	ENST00000257430	NM_000038.5	346	tCc/tTc	10/16	1	2	FACETS	0.724	0.595	0.868	0.724	0.595	0.868	SUBCLONAL	1	TRUE	1	0.16	2		540	639	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434474	140434474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520665	NA	P-0054424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	37	407	0	ENST00000288602.6:c.2224G>A	p.Asp742Asn	p.D742N	ENST00000288602	NM_004333.4	742	Gat/Aat	18/18	1	2	FACETS	0.754	0.621	0.905	0.754	0.621	0.905	CLONAL	1	TRUE	1	0.16	2		407	613	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609982	43609982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	70	896	0	ENST00000355710.3:c.1934C>T	p.Ser645Phe	p.S645F	ENST00000355710	NM_020975.4	645	tCc/tTc	11/20	1	2	FACETS	0.801	0.696	0.915	0.801	0.696	0.915	CLONAL	1	TRUE	1	0.16	2		896	1092	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431471	49431471	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1038604121	NA	P-0054424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	70	778	0	ENST00000301067.7:c.9668C>T	p.Pro3223Leu	p.P3223L	ENST00000301067	NM_003482.3	3223	cCt/cTt	34/54	1	2	FACETS	0.935	0.813	1	0.935	0.813	1	CLONAL	1	TRUE	1	0.16	2		778	936	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250985	99250985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	63	678	0	ENST00000268035.6:c.289G>A	p.Gly97Arg	p.G97R	ENST00000268035	NM_000875.3	97	Gga/Aga	2/21	1	2	FACETS	0.863	0.745	0.993	0.863	0.745	0.993	CLONAL	1	TRUE	1	0.16	2		678	912	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134665	2134665	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	95	730	0	ENST00000219476.3:c.4442A>C	p.Lys1481Thr	p.K1481T	ENST00000219476	NM_000548.3	1481	aAg/aCg	34/42	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.16	2		730	973	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132620	11132620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	85	850	0	ENST00000358026.2:c.2836C>T	p.Pro946Ser	p.P946S	ENST00000358026	NM_001128849.1	946	Ccc/Tcc	19/36	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.16	2		850	1045	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300138	15300138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	60	827	0	ENST00000263388.2:c.1138C>T	p.Pro380Ser	p.P380S	ENST00000263388	NM_000435.2	380	Cct/Tct	7/33	1	2	FACETS	0.727	0.624	0.839	0.727	0.624	0.839	SUBCLONAL	1	TRUE	1	0.16	2		827	1032	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211496	36211496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1215639009	NA	P-0054424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	106	659	0	ENST00000222270.7:c.1247C>T	p.Pro416Leu	p.P416L	ENST00000222270	NM_014727.1	416	cCc/cTc	3/37	1	2	FACETS	0.761	0.682	0.846	1	0.982	1	SUBCLONAL	2	TRUE	1	0.16	2		659	870	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715815	61715815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	39	461	0	ENST00000401558.2:c.2114C>T	p.Pro705Leu	p.P705L	ENST00000401558	NM_003400.3	705	cCc/cTc	18/25	1	2	FACETS	0.799	0.661	0.954	0.799	0.661	0.954	CLONAL	1	TRUE	1	0.16	2		461	610	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514521	41514521	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1166281033	NA	P-0054424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	55	576	0	ENST00000373198.4:c.140T>C	p.Leu47Pro	p.L47P	ENST00000373198	NM_133170.3	47	cTa/cCa	2/32	1	2	FACETS	0.886	0.756	1	0.886	0.756	1	CLONAL	1	TRUE	1	0.16	2		576	776	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940610	49940610	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	62	682	0	ENST00000296474.3:c.433del	p.Leu145CysfsTer4	p.L145Cfs*4	ENST00000296474	NM_002447.2	145	Ctg/tg	1/20	1	2	FACETS	0.976	0.842	1	0.976	0.842	1	CLONAL	1	TRUE	1	0.16	2		682	794	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185200167	185200167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	59	584	0	ENST00000265026.3:c.2824G>A	p.Asp942Asn	p.D942N	ENST00000265026	NM_004721.4	942	Gac/Aac	14/14	1	2	FACETS	0.943	0.81	1	0.943	0.81	1	CLONAL	1	TRUE	1	0.16	2		584	782	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1962873	1962873	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	41	442	0	ENST00000382891.5:c.3367G>A	p.Asp1123Asn	p.D1123N	ENST00000382891	NM_133335.3	1123	Gac/Aac	18/22	1	2	FACETS	0.969	0.806	1	0.969	0.806	1	CLONAL	1	TRUE	1	0.16	2		442	529	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628418	86628418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	16	325	1	ENST00000274376.6:c.787C>T	p.Leu263Phe	p.L263F	ENST00000274376	NM_002890.2	263	Ctt/Ttt	3/25	1	2	FACETS	0.66	0.487	0.867	0.66	0.487	0.867	SUBCLONAL	1	TRUE	1	0.16	2		326	303	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149437105	149437105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	86	694	0	ENST00000286301.3:c.2183C>T	p.Pro728Leu	p.P728L	ENST00000286301	NM_005211.3	728	cCt/cTt	16/22	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.16	2		694	935	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168906	32168906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	81	792	0	ENST00000375023.3:c.4127C>T	p.Ser1376Phe	p.S1376F	ENST00000375023	NM_004557.3	1376	tCc/tTc	22/30	1	2	FACETS	0.941	0.827	1	0.941	0.827	1	CLONAL	1	TRUE	1	0.16	2		792	1076	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534765	5534766	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0054424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	27	424	0	ENST00000397747.3:c.76_77delinsTT	p.Pro26Phe	p.P26F	ENST00000397747	NM_025239.3	26	CCt/TTt	3/7	1	2	FACETS	0.668	0.531	0.826	0.668	0.531	0.826	SUBCLONAL	1	TRUE	1	0.16	2		424	505	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020640	37020640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	46	451	0	ENST00000358127.4:c.205C>T	p.Leu69Phe	p.L69F	ENST00000358127	NM_001280556.1	69	Ctt/Ttt	2/10	1	2	FACETS	0.936	0.788	1	0.936	0.788	1	CLONAL	1	TRUE	1	0.16	2		451	614	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913534	39913535	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0054424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	39	588	1	ENST00000378444.4:c.4793_4794delinsAA	p.Trp1598Ter	p.W1598*	ENST00000378444	NM_001123385.1	1598	tGG/tAA	13/15	1	2	FACETS	0.692	0.572	0.827	0.692	0.572	0.827	SUBCLONAL	1	TRUE	1	0.16	2		589	704	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952145	76952146	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0054424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	33	471	2	ENST00000373344.5:c.289_290delinsTT	p.Pro97Phe	p.P97F	ENST00000373344	NM_000489.3	97	CCt/TTt	5/35	1	2	FACETS	0.663	0.539	0.804	0.663	0.539	0.804	SUBCLONAL	1	TRUE	1	0.16	2		473	622	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200078	123200078	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	34	410	0	ENST00000218089.9:c.2150A>G	p.Lys717Arg	p.K717R	ENST00000218089	NM_001042749.1	717	aAa/aGa	22/35	1	2	FACETS	0.835	0.681	1	0.835	0.681	1	CLONAL	1	TRUE	1	0.16	2		410	509	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	303	375	0				ENST00000310581	NM_198253.2	-/1132			0.329576462336062	8	FACETS	0.98	0.932	1	0.98	0.932	1	CLONAL	6	TRUE	2	0.329576462336062	8		375	622	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs11575997	NA	P-0054425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	184	533	0	ENST00000269305.4:c.993+1G>T		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.247296717715474	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	0	0.329576462336062	2		533	552	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261446	16261446	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	81	588	0	ENST00000375759.3:c.8711C>G	p.Ala2904Gly	p.A2904G	ENST00000375759	NM_015001.2	2904	gCc/gGc	11/15	0.110528712699593	3	FACETS	0.946	0.835	1	0.315	0.278	0.356	INDETERMINATE	1	TRUE	0	0.329576462336062	3		588	605	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650157	206650157	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	85	566	1	ENST00000367120.3:c.677G>T	p.Gly226Val	p.G226V	ENST00000367120	NM_014002.3	226	gGg/gTg	7/22	1	2	FACETS	0.948	0.84	1	0.948	0.84	1	CLONAL	1	TRUE	1	0.329576462336062	2		567	544	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955580	48955580	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0054425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	150	292	0	ENST00000267163.4:c.1695+1G>T		p.X565_splice	ENST00000267163	NM_000321.2	565			0.329576462336062	3	FACETS	0.904	0.836	0.973	0.904	0.836	0.973	CLONAL	3	TRUE	0	0.329576462336062	3		292	391	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007730	45007730	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	55	394	0	ENST00000558401.1:c.177A>C	p.Leu59Phe	p.L59F	ENST00000558401	NM_004048.2	59	ttA/ttC	2/4	1	2	FACETS	0.674	0.577	0.78	0.674	0.577	0.78	SUBCLONAL	1	TRUE	1	0.329576462336062	2		394	495	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210596	5210596	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	117	610	0	ENST00000357368.4:c.5371C>A	p.His1791Asn	p.H1791N	ENST00000357368	NM_002850.3	1791	Cac/Aac	35/38	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.329576462336062	2		610	562	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270359	10270359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	142	713	0	ENST00000340748.4:c.1207C>T	p.Pro403Ser	p.P403S	ENST00000340748		403	Ccc/Tcc	16/40	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.329576462336062	2		713	723	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211837	36211837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	470	854	0	ENST00000222270.7:c.1588C>T	p.Pro530Ser	p.P530S	ENST00000222270	NM_014727.1	530	Cct/Tct	3/37	0.329576462336062	6	FACETS	0.938	0.898	0.979			1	CLONAL	4	TRUE	NA	0.329576462336062	6		854	1261	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231825	36231825	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	164	655	0	ENST00000300305.3:c.559G>C	p.Ala187Pro	p.A187P	ENST00000300305		187	Gcc/Ccc	5/8	0.153108984961312	3	FACETS	1	0.987	1	0.706	0.649	0.766	INDETERMINATE	1	TRUE	1	0.329576462336062	3		655	821	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436832	52436832	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs151308667	NA	P-0054425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	100	682	0	ENST00000460680.1:c.1946G>C	p.Cys649Ser	p.C649S	ENST00000460680	NM_004656.3	649	tGc/tCc	15/17	0.329576462336062	3	FACETS	0.948	0.846	1	0.474	0.423	0.528	CLONAL	1	TRUE	1	0.329576462336062	3		682	746	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47604182	47604182	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	18	412	0	ENST00000263735.4:c.521A>G	p.Tyr174Cys	p.Y174C	ENST00000263735	NM_002354.2	174	tAt/tGt	5/9	1	2	FACETS	0.615	0.463	0.794	0.615	0.463	0.794	SUBCLONAL	1	FALSE	1	0.20336559503492	2		412	288	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979307	40979307	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	77	606	0	ENST00000373198.4:c.1826T>C	p.Val609Ala	p.V609A	ENST00000373198	NM_133170.3	609	gTg/gCg	11/32	1	2	FACETS	0.925	0.811	1	0.925	0.811	1	CLONAL	1	FALSE	1	0.20336559503492	2		606	819	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013697	170013697	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0054440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	10	361	0	ENST00000295797.4:c.1418-2A>G		p.X473_splice	ENST00000295797	NM_002740.5	473			1	2	FACETS	0.697	0.474	0.976	0.697	0.474	0.976	SUBCLONAL	1	FALSE	1	0.20336559503492	2		361	141	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979249	93979251	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0054440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	28	329	0	ENST00000369303.4:c.1577_1579del	p.Tyr526_Ser527delinsCys	p.Y526_S527delinsC	ENST00000369303	NM_004440.3	526	tACAgt/tgt	7/17	0.157670919060088	4	FACETS	0.767	0.617	0.936	0.767	0.617	0.936	CLONAL	2	FALSE	2	0.20336559503492	4		329	216	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779745	3779745	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	301	545	0	ENST00000262367.5:c.5303G>A	p.Arg1768His	p.R1768H	ENST00000262367	NM_004380.2	1768	cGc/cAc	31/31	1	2	FACETS	0.891	0.842	0.941	0.891	0.842	0.941	CLONAL	1	TRUE	1	0.782730466697132	2		545	863	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492847	56492848	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	132	383	0	ENST00000407977.2:c.91dup	p.Val31GlyfsTer9	p.V31Gfs*9	ENST00000407977		31	gta/gGta	2/10	0.782730466697132	1	FACETS	0.499	0.457	0.543	0.499	0.457	0.543	SUBCLONAL	1	TRUE	0	0.782730466697132	1		383	411	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0054446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	85	602	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		602	876	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876659802	NA	P-0054446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	43	729	0	ENST00000269305.4:c.833C>A	p.Pro278His	p.P278H	ENST00000269305	NM_001126112.2	278	cCt/cAt	8/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		729	1025	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31472177	31472177	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	254	566	0	ENST00000344624.3:c.2234C>G	p.Pro745Arg	p.P745R	ENST00000344624		745	cCt/cGt	14/33	0.438590785592628	4	FACETS	0.949	0.891	1	0.949	0.891	1	CLONAL	2	TRUE	2	0.458774661663003	4		566	851	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569785	67569785	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1350040171	NA	P-0054447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	95	312	0	ENST00000274335.5:c.446T>C	p.Leu149Pro	p.L149P	ENST00000274335		149	cTa/cCa	3/15	0.438590785592628	4	FACETS	0.872	0.777	0.973	0.436	0.388	0.487	CLONAL	1	TRUE	2	0.458774661663003	4		312	693	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670948	30670948	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536243116	NA	P-0054449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	11	640	1	ENST00000376406.3:c.5798G>A	p.Arg1933Gln	p.R1933Q	ENST00000376406	NM_014641.2	1933	cGg/cAg	12/15	1	2	FACETS	0.489	0.34	0.672	0.489	0.34	0.672	SUBCLONAL	1	TRUE	1	0.390859073822976	2		641	115	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012149	16012149	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	27	575	0	ENST00000268712.3:c.2133T>G	p.Asp711Glu	p.D711E	ENST00000268712	NM_006311.3	711	gaT/gaG	19/46	1	2	FACETS	0.822	0.674	0.981	1	0.95	1	CLONAL	2	TRUE	1	0.390859073822976	2		575	84	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226257	2226257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	10	725	2	ENST00000398665.3:c.3737C>T	p.Ser1246Leu	p.S1246L	ENST00000398665	NM_032482.2	1246	tCg/tTg	27/28	1	2	FACETS	0.419	0.285	0.586	0.419	0.285	0.586	SUBCLONAL	1	TRUE	1	0.390859073822976	2		727	122	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663172	227663172	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	51	625	0	ENST00000305123.5:c.283A>G	p.Ile95Val	p.I95V	ENST00000305123	NM_005544.2	95	Atc/Gtc	1/2	1	2	FACETS	1	0.934	1	1	0.98	1	CLONAL	2	TRUE	1	0.390859073822976	2		625	118	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	348	502	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.924285928280576	3	FACETS	0.962	0.924	1	0.962	0.924	1	CLONAL	2	TRUE	1	0.924285928280576	3		502	572	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092738	27092738	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	165	365	0	ENST00000324856.7:c.2760del	p.Gly922AlafsTer2	p.G922Afs*2	ENST00000324856	NM_006015.4	920	cAa/ca	9/20	1	2	FACETS	0.952	0.887	1	0.952	0.887	1	CLONAL	1	TRUE	1	0.924285928280576	2		365	375	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545676	63545680	+	frameshift_variant	Frame_Shift_Del	DEL	CGCAT	CGCAT	-	novel	NA	P-0054454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	312	523	0	ENST00000307078.5:c.914_918del	p.Asp305AlafsTer4	p.D305Afs*4	ENST00000307078	NM_004655.3	305	gATGCG/g	3/11	0.501236154356031	3	FACETS	0.845	0.806	0.884	0.845	0.806	0.884	INDETERMINATE	2	TRUE	1	0.924285928280576	3		523	584	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117605	70117606	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0054454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	435	715	1	ENST00000245479.2:c.74_75dup	p.Met26ProfsTer36	p.M26Pfs*36	ENST00000245479	NM_000346.3	25	acc/aCCcc	1/3	0.501236154356031	3	FACETS	0.843	0.81	0.876	0.843	0.81	0.876	INDETERMINATE	2	TRUE	1	0.924285928280576	3		716	816	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098559	47098559	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	218	566	1	ENST00000409792.3:c.6715C>T	p.Gln2239Ter	p.Q2239*	ENST00000409792	NM_014159.6	2239	Cag/Tag	15/21	1	2	FACETS	0.947	0.89	1	0.947	0.89	1	CLONAL	1	TRUE	1	0.924285928280576	2		567	498	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465043	120465043	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2911	666	424	1	ENST00000256646.2:c.5029C>T	p.Gln1677Ter	p.Q1677*	ENST00000256646	NM_024408.3	1677	Cag/Tag	28/34	0.916531617843207	10	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	10		425	3577	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955555	90955555	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	300	421	0	ENST00000265433.3:c.2110G>T	p.Gly704Ter	p.G704*	ENST00000265433	NM_002485.4	704	Gga/Tga	14/16	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		421	640	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922871	44922871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	364	507	0	ENST00000377967.4:c.1734del	p.Cys579ValfsTer14	p.C579Vfs*14	ENST00000377967	NM_021140.2	578	Ccc/cc	16/29	0.916531617843207	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		507	461	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0054458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	177	645	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.294255022021278	2		645	1001	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577525	7577527	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0054458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	256	550	0	ENST00000269305.4:c.754_756del	p.Leu252del	p.L252del	ENST00000269305	NM_001126112.2	252	CTC/-	7/11	0.253169650028141	2	FACETS	0.851	0.797	0.907	0.851	0.797	0.907	CLONAL	2	TRUE	0	0.294255022021278	2		550	1022	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11114071	11114071	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	31	443	0	ENST00000358026.2:c.1999G>T	p.Glu667Ter	p.E667*	ENST00000358026	NM_001128849.1	667	Gag/Tag	13/36	0.292951702646552	1	FACETS	0.437	0.353	0.532	0.437	0.353	0.532	SUBCLONAL	1	TRUE	0	0.294255022021278	1		443	411	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276312	15276312	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	110	723	0	ENST00000263388.2:c.5682C>A	p.Asn1894Lys	p.N1894K	ENST00000263388	NM_000435.2	1894	aaC/aaA	31/33	0.292951702646552	1	FACETS	0.686	0.615	0.761	0.686	0.615	0.761	SUBCLONAL	1	TRUE	0	0.294255022021278	1		723	930	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	172	304	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.953	0.881	1	0.953	0.881	1	CLONAL	1	TRUE	1	0.602913166043812	2		304	599	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169935	32169935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142477287	NA	P-0054459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	389	816	3	ENST00000375023.3:c.3673C>T	p.Arg1225Trp	p.R1225W	ENST00000375023	NM_004557.3	1225	Cgg/Tgg	21/30	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.602913166043812	2		819	1008	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	57	502	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.212514233873686	1	FACETS	0.702	0.603	0.81	0.702	0.603	0.81	SUBCLONAL	1	TRUE	0	0.28	1		502	499	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	172	393	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.969	1	1	0.993	1	CLONAL	2	TRUE	1	0.28	2		396	566	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214871	36214871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	125	720	4	ENST00000222270.7:c.3302del	p.Pro1101LeufsTer81	p.P1101Lfs*81	ENST00000222270	NM_014727.1	1099	ggC/gg	8/37	1	2	FACETS	0.813	0.734	0.897	0.813	0.734	0.897	CLONAL	1	TRUE	1	0.28	2		724	1098	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	144	370	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.255257740749307	2	FACETS	0.907	0.831	0.986	0.907	0.831	0.986	CLONAL	2	TRUE	0	0.28	2		370	567	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	57	367	1	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	1	2	FACETS	0.803	0.69	0.927	0.803	0.69	0.927	CLONAL	1	TRUE	1	0.28	2		368	507	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	111	532	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	1	2	FACETS	0.8	0.718	0.887	0.8	0.718	0.887	SUBCLONAL	1	TRUE	1	0.28	2		532	991	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007825	45007825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	97	363	1	ENST00000558401.1:c.276del	p.Thr93LeufsTer10	p.T93Lfs*10	ENST00000558401	NM_004048.2	91	aCc/ac	2/4	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.28	2		364	630	SUCCESS
APC	324	MSKCC	GRCh37	5	112154942	112154942	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779780	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	106	543	0	ENST00000257430.4:c.1213C>T	p.Arg405Ter	p.R405*	ENST00000257430	NM_000038.5	405	Cga/Tga	10/16	1	2	FACETS	0.843	0.755	0.937	0.843	0.755	0.937	CLONAL	1	TRUE	1	0.28	2		543	898	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	22	112	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	0.893	0.697	1	0.893	0.697	1	CLONAL	1	TRUE	1	0.28	2		112	176	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777676	9777676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	128	622	0	ENST00000377346.4:c.1012C>T	p.Arg338Trp	p.R338W	ENST00000377346	NM_005026.3	338	Cgg/Tgg	8/24	1	2	FACETS	0.859	0.777	0.946	0.859	0.777	0.946	CLONAL	1	TRUE	1	0.28	2		622	1064	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219487	133219487	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	145	724	1	ENST00000320574.5:c.4647del	p.Lys1550AsnfsTer12	p.K1550Nfs*12	ENST00000320574	NM_006231.2	1549	ccC/cc	36/49	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.28	2		725	1009	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508234	38508234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367821941	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	122	547	0	ENST00000254066.5:c.542C>T	p.Thr181Met	p.T181M	ENST00000254066	NM_000964.3	181	aCg/aTg	5/9	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.28	2		547	869	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041068	112041068	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs62620251	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	109	561	0	ENST00000368678.4:c.187G>A	p.Val63Ile	p.V63I	ENST00000368678		63	Gtc/Atc	3/13	1	2	FACETS	0.944	0.847	1	0.944	0.847	1	CLONAL	1	TRUE	1	0.28	2		561	825	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783293	9783293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	133	627	1	ENST00000377346.4:c.2537C>T	p.Ala846Val	p.A846V	ENST00000377346	NM_005026.3	846	gCc/gTc	20/24	1	2	FACETS	0.903	0.819	0.992	0.903	0.819	0.992	CLONAL	1	TRUE	1	0.28	2		628	1052	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482607	56482607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs993665271	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	142	582	0	ENST00000267101.3:c.1064C>T	p.Thr355Ile	p.T355I	ENST00000267101	NM_001982.3	355	aCc/aTc	9/28	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.28	2		582	1011	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435345	110435345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	95	345	0	ENST00000375856.3:c.3056C>T	p.Pro1019Leu	p.P1019L	ENST00000375856	NM_003749.2	1019	cCg/cTg	1/2	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.28	2		345	640	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686961	37686961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367703051	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	79	427	0	ENST00000447079.4:c.3865G>A	p.Ala1289Thr	p.A1289T	ENST00000447079	NM_015083.1	1289	Gcc/Acc	14/14	1	2	FACETS	0.802	0.705	0.906	0.802	0.705	0.906	CLONAL	1	TRUE	1	0.28	2		427	704	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070324	37070324	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63749795	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	130	338	0	ENST00000231790.2:c.1459C>T	p.Arg487Ter	p.R487*	ENST00000231790	NM_000249.3	487	Cga/Tga	13/19	0.255257740749307	2	FACETS	0.826	0.752	0.903	0.826	0.752	0.903	CLONAL	2	TRUE	0	0.28	2		338	562	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742931	17742931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	107	690	0	ENST00000250003.3:c.839C>T	p.Pro280Leu	p.P280L	ENST00000250003	NM_002478.4	280	cCg/cTg	3/3	1	2	FACETS	0.843	0.755	0.936	0.843	0.755	0.936	CLONAL	1	TRUE	1	0.28	2		690	907	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347903	347903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376143198	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1265	83	911	0	ENST00000262320.3:c.1603G>A	p.Val535Ile	p.V535I	ENST00000262320	NM_003502.3	535	Gtc/Atc	6/11	1	2	FACETS	0.44	0.386	0.498	0.44	0.386	0.498	SUBCLONAL	1	TRUE	1	0.28	2		911	1348	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436171	110436171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs558236298	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	133	102	0	ENST00000375856.3:c.2230C>T	p.Arg744Cys	p.R744C	ENST00000375856	NM_003749.2	744	Cgc/Tgc	1/2	1	2	FACETS	0.909	0.824	0.999	0.909	0.824	0.999	CLONAL	1	TRUE	1	0.28	2		102	1045	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827948	72827948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746367905	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	132	724	2	ENST00000268489.5:c.8633C>T	p.Ala2878Val	p.A2878V	ENST00000268489	NM_006885.3	2878	gCg/gTg	9/10	1	2	FACETS	0.944	0.856	1	0.944	0.856	1	CLONAL	1	TRUE	1	0.28	2		726	999	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438204	49438204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761386159	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	110	577	1	ENST00000301067.7:c.5065C>T	p.Arg1689Cys	p.R1689C	ENST00000301067	NM_003482.3	1689	Cgt/Tgt	20/54	1	2	FACETS	0.792	0.71	0.879	0.792	0.71	0.879	SUBCLONAL	1	TRUE	1	0.28	2		578	992	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599271	28599271	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs770146088	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	164	715	0	ENST00000253063.3:c.722del	p.Pro241GlnfsTer6	p.P241Qfs*6	ENST00000253063	NM_031459.4	239	agC/ag	5/10	1	2	FACETS	0.98	0.898	1	0.98	0.898	1	CLONAL	1	TRUE	1	0.28	2		715	1195	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645975	215645975	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs587780033	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	61	434	0	ENST00000260947.4:c.623del	p.Lys208ArgfsTer4	p.K208Rfs*4	ENST00000260947	NM_000465.2	208	aAg/ag	4/11	1	2	FACETS	0.768	0.663	0.883	0.768	0.663	0.883	SUBCLONAL	1	TRUE	1	0.28	2		434	567	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948747	71948748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760925109	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	155	1125	14	ENST00000298229.2:c.3466dup	p.Arg1156ProfsTer59	p.R1156Pfs*59	ENST00000298229	NM_001567.3	1153	-/C	26/28	1	2	FACETS	0.951	0.869	1	0.951	0.869	1	CLONAL	1	TRUE	1	0.28	2		1139	1164	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837963	156837963	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	172	822	0	ENST00000524377.1:c.496G>T	p.Gly166Ter	p.G166*	ENST00000524377	NM_002529.3	166	Gga/Tga	5/17	1	2	FACETS	0.926	0.85	1	0.926	0.85	1	CLONAL	1	TRUE	1	0.28	2		822	1327	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211194	2211194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769199900	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	116	742	0	ENST00000398665.3:c.1448C>T	p.Ala483Val	p.A483V	ENST00000398665	NM_032482.2	483	gCg/gTg	15/28	1	2	FACETS	0.755	0.679	0.836	0.755	0.679	0.836	SUBCLONAL	1	TRUE	1	0.28	2		742	1097	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652330	206652330	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	135	757	4	ENST00000367120.3:c.1042del	p.Arg348AspfsTer32	p.R348Dfs*32	ENST00000367120	NM_014002.3	346	gCc/gc	10/22	1	2	FACETS	0.85	0.771	0.934	0.85	0.771	0.934	CLONAL	1	TRUE	1	0.28	2		761	1134	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620366	43620366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758191409	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	101	511	0	ENST00000355710.3:c.2975C>T	p.Pro992Leu	p.P992L	ENST00000355710	NM_020975.4	992	cCg/cTg	18/20	1	2	FACETS	0.932	0.833	1	0.932	0.833	1	CLONAL	1	TRUE	1	0.28	2		511	774	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031657	36031657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1197051295	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	156	832	2	ENST00000358208.4:c.1486G>A	p.Asp496Asn	p.D496N	ENST00000358208		496	Gac/Aac	12/12	1	2	FACETS	0.998	0.913	1	0.998	0.913	1	CLONAL	1	TRUE	1	0.28	2		834	1116	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276950	123276951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	59	296	0	ENST00000358487.5:c.966dup	p.Glu323ArgfsTer3	p.E323Rfs*3	ENST00000358487	NM_000141.4	322	-/A	8/18	1	2	FACETS	0.922	0.795	1	0.922	0.795	1	CLONAL	1	TRUE	1	0.28	2		296	457	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985406	60985406	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	126	640	0	ENST00000333681.4:c.494A>G	p.Glu165Gly	p.E165G	ENST00000333681		165	gAg/gGg	2/3	1	2	FACETS	0.879	0.795	0.968	0.879	0.795	0.968	CLONAL	1	TRUE	1	0.28	2		640	1024	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663016	227663016	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	100	595	0	ENST00000305123.5:c.439del	p.Glu147ArgfsTer3	p.E147Rfs*3	ENST00000305123	NM_005544.2	147	Gag/ag	1/2	1	2	FACETS	0.898	0.802	1	0.898	0.802	1	CLONAL	1	TRUE	1	0.28	2		595	795	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79965968	79965968	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	61	455	0	ENST00000265081.6:c.632A>G	p.Glu211Gly	p.E211G	ENST00000265081	NM_002439.4	211	gAa/gGa	4/24	1	2	FACETS	0.725	0.625	0.833	0.725	0.625	0.833	SUBCLONAL	1	TRUE	1	0.28	2		455	601	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80109533	80109533	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs764871098	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	84	444	0	ENST00000265081.6:c.2786T>C	p.Ile929Thr	p.I929T	ENST00000265081	NM_002439.4	929	aTt/aCt	20/24	1	2	FACETS	0.938	0.829	1	0.938	0.829	1	CLONAL	1	TRUE	1	0.28	2		444	640	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149498361	149498362	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	140	649	0	ENST00000261799.4:c.2852dup	p.Ser952LeufsTer24	p.S952Lfs*24	ENST00000261799	NM_002609.3	951	ttc/ttTc	21/23	1	2	FACETS	0.981	0.893	1	0.981	0.893	1	CLONAL	1	TRUE	1	0.28	2		649	1019	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562339	176562339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	125	499	0	ENST00000439151.2:c.235G>A	p.Ala79Thr	p.A79T	ENST00000439151	NM_022455.4	79	Gcc/Acc	2/23	NA	2	FACETS	0.931	0.842	1			1	INDETERMINATE	1	TRUE	NA	0.28	2		499	959	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001390	150001390	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	83	485	0	ENST00000253339.5:c.2214G>T	p.Lys738Asn	p.K738N	ENST00000253339		738	aaG/aaT	4/7	1	2	FACETS	0.964	0.852	1	0.964	0.852	1	CLONAL	1	TRUE	1	0.28	2		485	615	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859851	117859851	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	43	263	0	ENST00000297338.2:c.1784C>T	p.Ala595Val	p.A595V	ENST00000297338	NM_006265.2	595	gCa/gTa	14/14	1	2	FACETS	0.77	0.645	0.907	0.77	0.645	0.907	CLONAL	1	TRUE	1	0.28	2		263	399	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426786	47426786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	96	620	0	ENST00000377045.4:c.1031C>T	p.Thr344Ile	p.T344I	ENST00000377045	NM_001654.4	344	aCa/aTa	10/16	1	2	FACETS	0.775	0.689	0.866	0.775	0.689	0.866	SUBCLONAL	1	TRUE	1	0.28	2		620	885	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921560	+	protein_altering_variant	In_Frame_Del	DEL	TGTAAATA	TGTAAATA	AT	novel	NA	P-0054460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	30	322	0	ENST00000263967.3:c.1035_1042delinsAT	p.Asn345_Ile348delinsLysPhe	p.N345_I348delinsKF	ENST00000263967	NM_006218.2	345	aaTGTAAATAtt/aaATtt	5/21	1	2	FACETS	0.651	0.526	0.793	0.651	0.526	0.793	SUBCLONAL	1	TRUE	1	0.28	2		322	329	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	115	977	8	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.64	0.576	0.707	0.64	0.576	0.707	SUBCLONAL	1	TRUE	1	0.434842255326782	2		985	827	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665096	138665096	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs758370933	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	133	395	0	ENST00000330315.3:c.469C>G	p.Pro157Ala	p.P157A	ENST00000330315	NM_023067.3	157	Ccc/Gcc	1/1	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.434842255326782	2		395	411	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316397	14316397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782457908	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	70	473	0	ENST00000256196.4:c.208G>A	p.Ala70Thr	p.A70T	ENST00000256196		70	Gca/Aca	3/6	1	2	FACETS	0.912	0.8	1	0.912	0.8	1	CLONAL	1	TRUE	1	0.434842255326782	2		473	353	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200961	108200961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782310	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	63	451	0	ENST00000278616.4:c.7328G>A	p.Arg2443Gln	p.R2443Q	ENST00000278616	NM_000051.3	2443	cGa/cAa	50/63	1	2	FACETS	0.845	0.735	0.962	0.845	0.735	0.962	CLONAL	1	TRUE	1	0.434842255326782	2		451	343	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073804	8073804	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1557463619	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	64	389	0	ENST00000377482.5:c.855del	p.Arg286GlufsTer9	p.R286Efs*9	ENST00000377482	NM_018948.3	285	ccC/cc	4/4	1	2	FACETS	0.932	0.813	1	0.932	0.813	1	CLONAL	1	TRUE	1	0.434842255326782	2		389	316	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775765	9775765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	115	1049	1	ENST00000377346.4:c.308C>T	p.Ala103Val	p.A103V	ENST00000377346	NM_005026.3	103	gCc/gTc	4/24	1	2	FACETS	0.555	0.499	0.614	0.555	0.499	0.614	SUBCLONAL	1	TRUE	1	0.434842255326782	2		1050	953	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023811	27023811	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1470097993	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	82	481	0	ENST00000324856.7:c.920del	p.Gly307AlafsTer56	p.G307Afs*56	ENST00000324856	NM_006015.4	306	cGg/cg	1/20	1	2	FACETS	0.818	0.724	0.918	0.818	0.724	0.918	CLONAL	1	TRUE	1	0.434842255326782	2		481	461	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	68	679	2	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	0.524	0.456	0.598	0.524	0.456	0.598	SUBCLONAL	1	TRUE	1	0.434842255326782	2		681	597	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736510	85736511	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs387906351	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	40	420	5	ENST00000370580.1:c.136dup	p.Ile46AsnfsTer4	p.I46Nfs*4	ENST00000370580	NM_003921.4	46	ata/aAta	2/3	1	2	FACETS	0.611	0.51	0.723	0.611	0.51	0.723	SUBCLONAL	1	TRUE	1	0.434842255326782	2		425	301	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600504	43600504	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	179	894	0	ENST00000355710.3:c.730A>G	p.Thr244Ala	p.T244A	ENST00000355710	NM_020975.4	244	Acc/Gcc	4/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.434842255326782	2		894	777	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852248	63852248	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	90	681	0	ENST00000279873.7:c.3026C>G	p.Ala1009Gly	p.A1009G	ENST00000279873	NM_032199.2	1009	gCg/gGg	10/10	1	2	FACETS	0.545	0.483	0.611	0.545	0.483	0.611	SUBCLONAL	1	TRUE	1	0.434842255326782	2		681	760	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114724384	114724384	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1450688148	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	82	425	0	ENST00000543371.1:c.450+1G>A		p.X150_splice	ENST00000543371	NM_001198531.1	150			1	2	FACETS	0.723	0.639	0.812	0.723	0.639	0.812	SUBCLONAL	1	TRUE	1	0.434842255326782	2		425	522	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256173	123256173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	133	632	0	ENST00000358487.5:c.1736G>A	p.Arg579Gln	p.R579Q	ENST00000358487	NM_000141.4	579	cGg/cAg	13/18	1	2	FACETS	0.905	0.824	0.99	0.905	0.824	0.99	CLONAL	1	TRUE	1	0.434842255326782	2		632	676	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999647	100999647	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	189	1105	2	ENST00000325455.5:c.155C>A	p.Pro52His	p.P52H	ENST00000325455	NM_001202474.3	52	cCt/cAt	1/8	1	2	FACETS	0.973	0.9	1	0.973	0.9	1	CLONAL	1	TRUE	1	0.434842255326782	2		1107	893	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	114	591	15	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	0.92	0.831	1	0.92	0.831	1	CLONAL	1	TRUE	1	0.434842255326782	2		606	570	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691094	18691094	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs201586034	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	55	411	0	ENST00000266497.5:c.3205C>T	p.Arg1069Ter	p.R1069*	ENST00000266497		1069	Cga/Tga	23/31	1	2	FACETS	0.788	0.678	0.907	0.788	0.678	0.907	CLONAL	1	TRUE	1	0.434842255326782	2		411	321	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	108	981	2	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.542	0.486	0.602	0.542	0.486	0.602	SUBCLONAL	1	TRUE	1	0.434842255326782	2		983	916	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492748	50492748	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	114	575	0	ENST00000394963.4:c.1513G>T	p.Glu505Ter	p.E505*	ENST00000394963	NM_003076.4	505	Gaa/Taa	13/13	1	2	FACETS	0.896	0.809	0.988	0.896	0.809	0.988	CLONAL	1	TRUE	1	0.434842255326782	2		575	585	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800850	120800850	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	162	722	0	ENST00000257552.2:c.398G>T	p.Gly133Val	p.G133V	ENST00000257552	NM_002442.3	133	gGg/gTg	6/15	1	2	FACETS	0.84	0.771	0.912	0.84	0.771	0.912	CLONAL	1	TRUE	1	0.434842255326782	2		722	887	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562052	21562052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1359079402	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	213	1009	2	ENST00000382592.4:c.1867C>T	p.Arg623Trp	p.R623W	ENST00000382592	NM_014572.2	623	Cgg/Tgg	4/8	1	2	FACETS	0.979	0.909	1	0.979	0.909	1	CLONAL	1	TRUE	1	0.434842255326782	2		1011	1001	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893590	28893590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752645756	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	111	522	0	ENST00000282397.4:c.3256G>A	p.Gly1086Arg	p.G1086R	ENST00000282397	NM_002019.4	1086	Gga/Aga	24/30	1	2	FACETS	0.961	0.868	1	0.961	0.868	1	CLONAL	1	TRUE	1	0.434842255326782	2		522	531	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434460	110434460	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	122	727	0	ENST00000375856.3:c.3941T>C	p.Leu1314Pro	p.L1314P	ENST00000375856	NM_003749.2	1314	cTg/cCg	1/2	1	2	FACETS	0.682	0.616	0.751	0.682	0.616	0.751	SUBCLONAL	1	TRUE	1	0.434842255326782	2		727	823	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	117	726	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.434842255326782	2		726	488	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457640	67457640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs863223759	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	200	866	2	ENST00000327367.4:c.455del	p.Pro152HisfsTer34	p.P152Hfs*34	ENST00000327367	NM_005902.3	150	ttC/tt	3/9	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.434842255326782	2		868	821	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562747	29562747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137854556	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	101	481	0	ENST00000356175.3:c.3827G>A	p.Arg1276Gln	p.R1276Q	ENST00000356175	NM_000267.3	1276	cGa/cAa	28/57	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.434842255326782	2		481	444	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657517	29657517	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	44	300	0	ENST00000356175.3:c.5749+1G>C		p.X1917_splice	ENST00000356175	NM_000267.3	1917			1	2	FACETS	0.803	0.679	0.938	0.803	0.679	0.938	CLONAL	1	TRUE	1	0.434842255326782	2		300	252	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098425	11098425	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	52	430	1	ENST00000358026.2:c.947del	p.Pro316LeufsTer10	p.P316Lfs*10	ENST00000358026	NM_001128849.1	315	Ccc/cc	6/36	1	2	FACETS	0.506	0.431	0.588	0.506	0.431	0.588	SUBCLONAL	1	TRUE	1	0.434842255326782	2		431	473	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141493	11141493	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	223	887	0	ENST00000358026.2:c.3470G>A	p.Arg1157Gln	p.R1157Q	ENST00000358026	NM_001128849.1	1157	cGg/cAg	25/36	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.434842255326782	2		887	876	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143993	11143993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568509370	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	46	835	1	ENST00000358026.2:c.3574C>T	p.Arg1192Cys	p.R1192C	ENST00000358026	NM_001128849.1	1192	Cgc/Tgc	26/36	1	2	FACETS	0.268	0.225	0.317	0.268	0.225	0.317	SUBCLONAL	1	TRUE	1	0.434842255326782	2		836	788	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284913	15284913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	208	1065	0	ENST00000263388.2:c.4702C>T	p.Arg1568Trp	p.R1568W	ENST00000263388	NM_000435.2	1568	Cgg/Tgg	25/33	1	2	FACETS	0.94	0.872	1	0.94	0.872	1	CLONAL	1	TRUE	1	0.434842255326782	2		1065	1018	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379845	17379845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1175226015	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	199	1053	2	ENST00000359435.4:c.230C>T	p.Pro77Leu	p.P77L	ENST00000359435	NM_001033549.1	77	cCg/cTg	2/9	1	2	FACETS	0.88	0.815	0.948	0.88	0.815	0.948	CLONAL	1	TRUE	1	0.434842255326782	2		1055	1040	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953863	17953863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	168	1104	0	ENST00000458235.1:c.539G>A	p.Arg180Gln	p.R180Q	ENST00000458235	NM_000215.3	180	cGg/cAg	5/24	1	2	FACETS	0.719	0.66	0.781	0.719	0.66	0.781	SUBCLONAL	1	TRUE	1	0.434842255326782	2		1104	1075	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213358	36213359	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	163	969	0	ENST00000222270.7:c.2561_2562del	p.Glu854AlafsTer34	p.E854Afs*34	ENST00000222270	NM_014727.1	852	aAG/a	4/37	1	2	FACETS	0.778	0.713	0.845	0.778	0.713	0.845	SUBCLONAL	1	TRUE	1	0.434842255326782	2		969	964	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794643	42794643	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	169	936	0	ENST00000575354.2:c.1727del	p.Pro576LeufsTer152	p.P576Lfs*152	ENST00000575354	NM_015125.3	575	Ccc/cc	10/20	1	2	FACETS	0.973	0.896	1	0.973	0.896	1	CLONAL	1	TRUE	1	0.434842255326782	2		936	799	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799059	42799059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	222	1040	4	ENST00000575354.2:c.4543C>T	p.Arg1515Cys	p.R1515C	ENST00000575354	NM_015125.3	1515	Cgc/Tgc	20/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.434842255326782	2		1044	914	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912430	50912430	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	128	991	0	ENST00000440232.2:c.1944G>T	p.Lys648Asn	p.K648N	ENST00000440232	NM_002691.3	648	aaG/aaT	16/27	1	2	FACETS	0.628	0.569	0.691	0.628	0.569	0.691	SUBCLONAL	1	TRUE	1	0.434842255326782	2		991	937	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703538	47703538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63749932	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	250	606	0	ENST00000233146.2:c.2038C>T	p.Arg680Ter	p.R680*	ENST00000233146	NM_000251.2	680	Cga/Tga	13/16	0.434842255326782	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.434842255326782	2		606	557	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025942	48025942	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	114	510	0	ENST00000234420.5:c.820A>G	p.Ser274Gly	p.S274G	ENST00000234420	NM_000179.2	274	Agc/Ggc	4/10	0.434842255326782	2	FACETS	1	0.968	1	0.577	0.523	0.634	CLONAL	1	TRUE	0	0.434842255326782	2		510	454	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189310	99189310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	153	588	1	ENST00000074304.5:c.2566C>T	p.Pro856Ser	p.P856S	ENST00000074304	NM_001134224.1	856	Cca/Tca	24/26	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.434842255326782	2		589	672	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719382	190719382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1016802650	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	25	292	0	ENST00000441310.2:c.1384G>A	p.Val462Ile	p.V462I	ENST00000441310	NM_000534.4	462	Gtt/Att	9/13	1	2	FACETS	0.618	0.491	0.762	0.618	0.491	0.762	SUBCLONAL	1	TRUE	1	0.434842255326782	2		292	186	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928074	178928082	+	missense_variant	Missense_Mutation	ONP	GATTAGAAG	GATTAGAAG	AATTAAAAA	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	74	561	1	ENST00000263967.3:c.1352_1360delinsAATTAAAAA	p.Gly451_Asp454delinsGluLeuLysAsn	p.G451_D454delinsELKN	ENST00000263967	NM_006218.2	451	gGATTAGAAGat/gAATTAAAAAat	8/21	1	2	FACETS	0.777	0.683	0.878	0.777	0.683	0.878	SUBCLONAL	1	TRUE	1	0.434842255326782	2		562	438	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535395	66535395	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	73	516	0	ENST00000273854.3:c.66del	p.Ile23SerfsTer39	p.I23Sfs*39	ENST00000273854	NM_004439.5	22	ccC/cc	1/18	1	2	FACETS	0.783	0.687	0.885	0.783	0.687	0.885	SUBCLONAL	1	TRUE	1	0.434842255326782	2		516	429	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	65	283	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.434842255326782	2		283	294	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593244	67593244	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	63	309	0	ENST00000274335.5:c.1990G>T	p.Asp664Tyr	p.D664Y	ENST00000274335		664	Gac/Tac	15/15	1	2	FACETS	0.908	0.791	1	0.908	0.791	1	CLONAL	1	TRUE	1	0.434842255326782	2		309	319	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	147	965	2	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	1	2	FACETS	0.8	0.731	0.873	0.8	0.731	0.873	SUBCLONAL	1	TRUE	1	0.434842255326782	2		967	845	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271362	26271362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781608741	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	160	735	1	ENST00000305910.3:c.251G>A	p.Arg84His	p.R84H	ENST00000305910	NM_003534.2	84	cGc/cAc	1/1	1	2	FACETS	0.992	0.911	1	0.992	0.911	1	CLONAL	1	TRUE	1	0.434842255326782	2		736	742	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163554	32163554	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	74	744	1	ENST00000375023.3:c.5672del	p.Gly1891AlafsTer13	p.G1891Afs*13	ENST00000375023	NM_004557.3	1891	gGc/gc	30/30	1	2	FACETS	0.864	0.76	0.974	0.864	0.76	0.974	CLONAL	1	TRUE	1	0.434842255326782	2		745	394	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288680	33288680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	76	586	1	ENST00000374542.5:c.872G>A	p.Arg291Gln	p.R291Q	ENST00000374542	NM_001141970.1	291	cGg/cAg	3/8	1	2	FACETS	0.703	0.618	0.794	0.703	0.618	0.794	SUBCLONAL	1	TRUE	1	0.434842255326782	2		587	497	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43749781	43749781	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	91	604	1	ENST00000523873.1:c.634C>T	p.Arg212Cys	p.R212C	ENST00000523873		212	Cgt/Tgt	7/8	1	2	FACETS	0.542	0.481	0.608	0.542	0.481	0.608	SUBCLONAL	1	TRUE	1	0.434842255326782	2		605	772	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388065	81388065	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs780541101	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	79	526	0	ENST00000222390.5:c.310A>G	p.Met104Val	p.M104V	ENST00000222390	NM_000601.4	104	Atg/Gtg	3/18	1	2	FACETS	0.861	0.761	0.967	0.861	0.761	0.967	CLONAL	1	TRUE	1	0.434842255326782	2		526	422	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542551	141542551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	170	836	1	ENST00000220592.5:c.2435G>A	p.Arg812Gln	p.R812Q	ENST00000220592	NM_012154.3	812	cGg/cAg	18/19	1	2	FACETS	0.955	0.879	1	0.955	0.879	1	CLONAL	1	TRUE	1	0.434842255326782	2		837	819	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141567294	141567294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	139	786	2	ENST00000220592.5:c.920C>T	p.Thr307Met	p.T307M	ENST00000220592	NM_012154.3	307	aCg/aTg	8/19	1	2	FACETS	0.782	0.712	0.855	0.782	0.712	0.855	SUBCLONAL	1	TRUE	1	0.434842255326782	2		788	818	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231322	98231322	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746898855	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	178	906	1	ENST00000331920.6:c.1961C>T	p.Thr654Met	p.T654M	ENST00000331920	NM_000264.3	654	aCg/aTg	14/24	1	2	FACETS	0.919	0.847	0.993	0.919	0.847	0.993	CLONAL	1	TRUE	1	0.434842255326782	2		907	891	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242255	98242255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs555332902	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	109	597	0	ENST00000331920.6:c.1063G>A	p.Val355Ile	p.V355I	ENST00000331920	NM_000264.3	355	Gtc/Atc	7/24	1	2	FACETS	0.848	0.764	0.937	0.848	0.764	0.937	CLONAL	1	TRUE	1	0.434842255326782	2		597	591	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738360	133738360	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	157	721	0	ENST00000318560.5:c.760G>A	p.Gly254Arg	p.G254R	ENST00000318560	NM_005157.4	254	Ggg/Agg	4/11	1	2	FACETS	0.911	0.835	0.989	0.911	0.835	0.989	CLONAL	1	TRUE	1	0.434842255326782	2		721	793	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402519	139402519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	248	1111	1	ENST00000277541.6:c.3398G>A	p.Cys1133Tyr	p.C1133Y	ENST00000277541	NM_017617.3	1133	tGc/tAc	21/34	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.434842255326782	2		1112	1077	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412672	139412672	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	217	1095	0	ENST00000277541.6:c.1172C>A	p.Pro391His	p.P391H	ENST00000277541	NM_017617.3	391	cCt/cAt	7/34	1	2	FACETS	0.967	0.899	1	0.967	0.899	1	CLONAL	1	TRUE	1	0.434842255326782	2		1095	1032	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223343	53223343	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	73	821	0	ENST00000375401.3:c.4016G>A	p.Gly1339Asp	p.G1339D	ENST00000375401	NM_004187.3	1339	gGc/gAc	23/26	1	2	FACETS	0.435	0.38	0.495	0.435	0.38	0.495	SUBCLONAL	1	TRUE	1	0.434842255326782	2		821	771	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0054463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	66	455	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.975	0.853	1	1	0.981	1	CLONAL	2	FALSE	1	0.215568178316948	2		456	314	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0054463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	105	543	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.773	0.694	0.857	1	0.983	1	SUBCLONAL	2	FALSE	1	0.215568178316948	2		543	630	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608648	189608648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	86	527	0	ENST00000264731.3:c.1723C>T	p.Gln575Ter	p.Q575*	ENST00000264731	NM_003722.4	575	Cag/Tag	13/14	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.215568178316948	2		527	575	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755530	39755530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	71	714	0	ENST00000288319.7:c.1235C>T	p.Pro412Leu	p.P412L	ENST00000288319	NM_182918.3	412	cCc/cTc	10/10	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.215568178316948	2		714	560	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42057198	42057198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	120	632	2	ENST00000219905.7:c.7859C>T	p.Ser2620Phe	p.S2620F	ENST00000219905	NM_001164273.1	2620	tCt/tTt	23/24	1	2	FACETS	0.811	0.734	0.893	1	0.986	1	CLONAL	2	FALSE	1	0.215568178316948	2		634	686	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219985	5219985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	160	914	0	ENST00000357368.4:c.3730C>T	p.Leu1244Phe	p.L1244F	ENST00000357368	NM_002850.3	1244	Ctc/Ttc	22/38	1	2	FACETS	0.915	0.84	0.994	1	0.991	1	CLONAL	2	FALSE	1	0.215568178316948	2		914	811	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715621	30715621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863223850	NA	P-0054463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	54	358	0	ENST00000295754.5:c.1279C>T	p.Pro427Ser	p.P427S	ENST00000295754	NM_003242.5	427	Cca/Tca	5/7	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.215568178316948	2		358	351	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27172728	27172728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	88	550	0	ENST00000380036.4:c.743G>A	p.Gly248Glu	p.G248E	ENST00000380036	NM_000459.3	248	gGa/gAa	5/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.215568178316948	2		550	546	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725060	89725061	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs797045066	NA	P-0054463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	25	182	0	ENST00000371953.3:c.1048dup	p.Thr350AsnfsTer11	p.T350Nfs*11	ENST00000371953	NM_000314.4	348	aca/acAa	9/9	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	FALSE	1	0.215568178316948	2		182	212	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042536	42042536	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	60	546	0	ENST00000219905.7:c.6731G>A	p.Trp2244Ter	p.W2244*	ENST00000219905	NM_001164273.1	2244	tGg/tAg	17/24	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.215568178316948	2		546	412	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726667	46726667	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	82	618	0	ENST00000371975.4:c.746A>T	p.Asp249Val	p.D249V	ENST00000371975	NM_003579.3	249	gAt/gTt	7/18	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.215568178316948	2		618	577	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859582	57859582	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs777509564	NA	P-0054463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	54	804	0	ENST00000228682.2:c.636G>T	p.Leu212Phe	p.L212F	ENST00000228682	NM_005269.2	212	ttG/ttT	7/12	0.109955976207044	3	FACETS	0.801	0.683	0.93	0.4	0.341	0.465	INDETERMINATE	1	FALSE	1	0.215568178316948	3		804	693	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608502	28608502	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	69	661	0	ENST00000241453.7:c.1640C>A	p.Thr547Lys	p.T547K	ENST00000241453	NM_004119.2	547	aCa/aAa	13/24	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.215568178316948	2		661	504	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36989282	36989282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	127	915	0	ENST00000354822.5:c.53G>A	p.Gly18Glu	p.G18E	ENST00000354822	NM_001079668.2	18	gGg/gAg	1/3	1	2	FACETS	0.923	0.839	1	1	0.989	1	CLONAL	2	FALSE	1	0.215568178316948	2		915	638	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341590	89341590	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	120	678	0	ENST00000301030.4:c.7480C>T	p.Pro2494Ser	p.P2494S	ENST00000301030	NM_001256183.1	2494	Cct/Tct	10/13	1	2	FACETS	1	0.925	1	1	0.99	1	CLONAL	2	FALSE	1	0.215568178316948	2		678	544	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244323	5244324	+	missense_variant	Missense_Mutation	DNP	AA	AA	CG	novel	NA	P-0054463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	149	1101	1	ENST00000357368.4:c.1158_1159delinsCG	p.Tyr387Asp	p.Y387D	ENST00000357368	NM_002850.3	386	cgTTac/cgCGac	11/38	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.215568178316948	2		1102	928	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082316	16082316	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	128	1110	0	ENST00000281043.3:c.130C>G	p.Pro44Ala	p.P44A	ENST00000281043	NM_005378.4	44	Ccc/Gcc	2/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.215568178316948	2		1110	793	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259346	36259346	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	100	484	0	ENST00000300305.3:c.145C>T	p.Pro49Ser	p.P49S	ENST00000300305		49	Cca/Tca	3/8	1	2	FACETS	0.845	0.757	0.938	1	0.985	1	CLONAL	2	FALSE	1	0.215568178316948	2		484	549	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980304	55980304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778429	NA	P-0054463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	81	558	0	ENST00000263923.4:c.787C>T	p.Pro263Ser	p.P263S	ENST00000263923	NM_002253.2	263	Cct/Tct	6/30	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.215568178316948	2		558	521	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589312	67589312	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0054463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	31	311	0	ENST00000274335.5:c.1299+1G>T		p.X433_splice	ENST00000274335		433			1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	FALSE	1	0.215568178316948	2		311	263	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	30	304	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.140832611501004	3	FACETS	0.979	0.791	1			1	INDETERMINATE	1	TRUE	NA	0.24	3		304	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs878854073	NA	P-0054464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	26	392	0	ENST00000269305.4:c.673-1G>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			1	2	FACETS	0.727	0.577	0.899	0.727	0.577	0.899	SUBCLONAL	1	TRUE	1	0.24	2		392	298	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912660	NA	P-0054465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	319	781	0	ENST00000269305.4:c.839G>T	p.Arg280Ile	p.R280I	ENST00000269305	NM_001126112.2	280	aGa/aTa	8/11	0.48149499635331	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.61356561422993	4		781	807	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123159694	123159694	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	86	209	0	ENST00000218089.9:c.49T>C	p.Ser17Pro	p.S17P	ENST00000218089	NM_001042749.1	17	Tca/Cca	4/35	0.526827021659311	2	FACETS	0.925	0.876	0.967			1	CLONAL	3	TRUE	NA	0.61356561422993	2		209	101	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578362	7578391	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTGCTCACCATCGCTATCTGAGCAGCGCT	GCTGCTCACCATCGCTATCTGAGCAGCGCT	-	novel	NA	P-0054465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	276	743	0	ENST00000269305.4:c.539_559+9del		p.X180_splice	ENST00000269305	NM_001126112.2	180		5/11	0.48149499635331	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.61356561422993	4		743	692	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560025	29560025	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs878853883	NA	P-0054465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	100	289	0	ENST00000356175.3:c.3502G>C	p.Gly1168Arg	p.G1168R	ENST00000356175	NM_000267.3	1168	Ggt/Cgt	27/57	NA	2	FACETS	1	0.962	1			1	INDETERMINATE	2	TRUE	NA	0.61356561422993	2		289	154	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938800	76938800	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	150	351	0	ENST00000373344.5:c.1948G>T	p.Glu650Ter	p.E650*	ENST00000373344	NM_000489.3	650	Gaa/Taa	9/35	0.526827021659311	2	FACETS	0.849	0.809	0.886			1	CLONAL	3	TRUE	NA	0.61356561422993	2		351	192	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142966	47142966	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1559720382	NA	P-0054466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	197	467	0	ENST00000409792.3:c.4997A>G	p.Tyr1666Cys	p.Y1666C	ENST00000409792	NM_014159.6	1666	tAt/tGt	8/21	0.695431969346268	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.695431969346268	2		467	278	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696241	52696241	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	399	582	0	ENST00000394830.3:c.436C>T	p.Arg146Ter	p.R146*	ENST00000394830	NM_018313.4	146	Cga/Tga	5/30	0.695431969346268	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.695431969346268	2		582	557	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849899	156849899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	76	656	0	ENST00000524377.1:c.2155G>A	p.Glu719Lys	p.E719K	ENST00000524377	NM_002529.3	719	Gag/Aag	16/17	1	2	FACETS	0.698	0.614	0.789	0.698	0.614	0.789	SUBCLONAL	1	TRUE	1	0.408323180764485	2		656	533	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226568	1226568	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	64	682	0	ENST00000326873.7:c.1225del	p.Arg409GlyfsTer101	p.R409Gfs*101	ENST00000326873	NM_000455.4	408	ggC/gg	9/10	0.235002352906303	2	FACETS	0.526	0.455	0.603	0.263	0.227	0.302	INDETERMINATE	1	TRUE	0	0.408323180764485	2		682	596	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077433	30077433	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	39	246	0	ENST00000338641.4:c.1581del	p.Glu527AspfsTer23	p.E527Dfs*23	ENST00000338641	NM_000268.3	527	gAa/ga	15/16	0.408323180764485	1	FACETS	0.889	0.747	1	0.889	0.747	1	CLONAL	1	TRUE	0	0.408323180764485	1		246	171	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156096	106156096	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs748698001	NA	P-0054467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	21	314	0	ENST00000380013.4:c.997C>G	p.Pro333Ala	p.P333A	ENST00000380013	NM_001127208.2	333	Cca/Gca	3/11	1	2	FACETS	0.351	0.27	0.445	0.351	0.27	0.445	SUBCLONAL	1	TRUE	1	0.408323180764485	2		314	293	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0054468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	33	380	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.95	0.774	1	0.95	0.774	1	CLONAL	1	TRUE	1	0.16	2		380	434	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481417	140481417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913348	NA	P-0054468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	16	430	3	ENST00000288602.6:c.1391G>A	p.Gly464Glu	p.G464E	ENST00000288602	NM_004333.4	464	gGa/gAa	11/18	1	2	FACETS	0.402	0.296	0.53	0.402	0.296	0.53	SUBCLONAL	1	TRUE	1	0.16	2		433	497	SUCCESS
APC	324	MSKCC	GRCh37	5	112175578	112175578	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	GAT	novel	NA	P-0054468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	28	389	0	ENST00000257430.4:c.4287delinsGAT	p.Thr1430IlefsTer44	p.T1430Ifs*44	ENST00000257430	NM_000038.5	1429	caA/caGAT	16/16	1	2	FACETS	0.805	0.642	0.99	0.805	0.642	0.99	CLONAL	1	TRUE	1	0.16	2		389	435	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051582	30051582	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1064796632	NA	P-0054469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	14	280	0	ENST00000338641.4:c.517-1G>A		p.X173_splice	ENST00000338641	NM_000268.3	173			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		280	87	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035077	30035090	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGGTACTGGATCAT	AGGTACTGGATCAT	-	novel	NA	P-0054469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	29	291	0	ENST00000338641.4:c.241-2_252del		p.X81_splice	ENST00000338641	NM_000268.3	81		3/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		291	81	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350548	15350548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772431443	NA	P-0054470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	255	789	0	ENST00000263377.2:c.3367G>A	p.Glu1123Lys	p.E1123K	ENST00000263377	NM_058243.2	1123	Gag/Aag	16/20	0.22358563375638	4	FACETS	0.951	0.89	1	0.951	0.89	1	CLONAL	2	TRUE	2	0.305475473219427	4		789	1146	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421555	32421555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	153	641	5	ENST00000332351.3:c.1037C>T	p.Thr346Met	p.T346M	ENST00000332351	NM_024426.4	346	aCg/aTg	6/10	0.200005849521353	3	FACETS	1	0.988	1	0.747	0.684	0.812	CLONAL	1	TRUE	1	0.305475473219427	3		646	773	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740546	145740546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746417965	NA	P-0054470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	489	939	1	ENST00000428558.2:c.1471C>T	p.Arg491Trp	p.R491W	ENST00000428558	NM_004260.3	491	Cgg/Tgg	8/22	0.305475473219427	5	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	2	0.305475473219427	5		940	1481	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573991	7573992	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	489	729	0	ENST00000269305.4:c.1035dup	p.Glu346Ter	p.E346*	ENST00000269305	NM_001126112.2	345	-/T	10/11	0.305475473219427	4	FACETS	0.947	0.909	0.986			1	CLONAL	4	TRUE	NA	0.305475473219427	4		729	1103	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788561	3788561	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	52	310	0	ENST00000262367.5:c.4393G>C	p.Gly1465Arg	p.G1465R	ENST00000262367	NM_004380.2	1465	Ggg/Cgg	26/31	1	2	FACETS	0.903	0.772	1	0.903	0.772	1	CLONAL	1	TRUE	1	0.305475473219427	2		310	377	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858247	9858247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	84	529	0	ENST00000330684.3:c.3154C>T	p.Leu1052Phe	p.L1052F	ENST00000330684	NM_001134407.1	1052	Ctt/Ttt	13/13	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.305475473219427	2		529	525	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907817	76907831	+	inframe_deletion	In_Frame_Del	DEL	TTCCTCCTCTTCTTC	TTCCTCCTCTTCTTC	-	novel	NA	P-0054470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	91	114	0	ENST00000373344.5:c.4330_4344del	p.Glu1444_Glu1448del	p.E1444_E1448del	ENST00000373344	NM_000489.3	1444	GAAGAAGAGGAGGAA/-	15/35	0.305475473219427	2	FACETS	0.937	0.85	1			1	CLONAL	3	TRUE	NA	0.305475473219427	2		114	212	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	98	502	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.935	1	1	0.987	1	CLONAL	2	TRUE	1	0.18	2		502	513	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162475122	162475122	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0054471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	24	447	0	ENST00000366898.1:c.618+1G>T		p.X206_splice	ENST00000366898	NM_004562.2	206			1	2	FACETS	0.639	0.501	0.8	0.639	0.501	0.8	SUBCLONAL	1	TRUE	1	0.18	2		447	417	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741540	17741540	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	34	449	0	ENST00000250003.3:c.211C>A	p.Pro71Thr	p.P71T	ENST00000250003	NM_002478.4	71	Ccg/Acg	1/3	1	2	FACETS	0.902	0.737	1	0.902	0.737	1	CLONAL	1	TRUE	1	0.18	2		449	419	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273868	18273868	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	37	736	0	ENST00000222254.8:c.1201C>G	p.Leu401Val	p.L401V	ENST00000222254	NM_005027.3	401	Ctc/Gtc	10/16	1	2	FACETS	0.616	0.507	0.74	0.616	0.507	0.74	SUBCLONAL	1	TRUE	1	0.18	2		736	667	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570118	212570118	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0054471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	23	319	0	ENST00000342788.4:c.1125-2A>G		p.X375_splice	ENST00000342788	NM_005235.2	375			1	2	FACETS	0.634	0.494	0.797	0.634	0.494	0.797	SUBCLONAL	1	TRUE	1	0.18	2		319	403	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747140	40747140	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	41	434	1	ENST00000373198.4:c.2942G>T	p.Gly981Val	p.G981V	ENST00000373198	NM_133170.3	981	gGt/gTt	22/32	1	2	FACETS	0.961	0.801	1	0.961	0.801	1	CLONAL	1	TRUE	1	0.18	2		435	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574023	+	stop_gained	Nonsense_Mutation	TNP	CAC	CAC	AAA	novel	NA	P-0054471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	81	628	0	ENST00000269305.4:c.1004_1006delinsTTT	p.Arg335_Glu336delinsLeuTer	p.R335_E336delinsL*	ENST00000269305	NM_001126112.2	335	cGTGag/cTTTag	10/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.18	2		628	685	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0054472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	126	602	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.357042984060283	2		602	674	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748309	41748309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs894529129	NA	P-0054472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	145	931	1	ENST00000226382.2:c.460C>T	p.Arg154Cys	p.R154C	ENST00000226382	NM_003924.3	154	Cgc/Tgc	3/3	1	2	FACETS	0.937	0.855	1	0.937	0.855	1	CLONAL	1	TRUE	1	0.357042984060283	2		932	867	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18975049	18975049	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	65	425	0	ENST00000262803.5:c.2846G>T	p.Arg949Leu	p.R949L	ENST00000262803	NM_002911.3	949	cGg/cTg	20/24	1	2	FACETS	0.961	0.837	1	0.961	0.837	1	CLONAL	1	TRUE	1	0.357042984060283	2		425	379	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212252684	212252684	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	30	222	0	ENST00000342788.4:c.3169A>T	p.Thr1057Ser	p.T1057S	ENST00000342788	NM_005235.2	1057	Acc/Tcc	26/28	1	2	FACETS	0.667	0.54	0.81	0.667	0.54	0.81	SUBCLONAL	1	TRUE	1	0.357042984060283	2		222	252	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38991178	38991178	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0054472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	53	337	0	ENST00000357387.3:c.457-1G>T		p.X153_splice	ENST00000357387	NM_152756.3	153			1	2	FACETS	0.805	0.689	0.93	0.805	0.689	0.93	CLONAL	1	TRUE	1	0.357042984060283	2		337	369	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0054473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	41	434	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.864	0.721	1	0.864	0.721	1	CLONAL	1	TRUE	1	0.264426597822957	2		434	359	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577126	7577126	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	109	682	2	ENST00000269305.4:c.812A>T	p.Glu271Val	p.E271V	ENST00000269305	NM_001126112.2	271	gAg/gTg	8/11	0.0966722279661432	3	FACETS	1	0.972	1			1	INDETERMINATE	1	TRUE	NA	0.264426597822957	3		684	759	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955567	55955567	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	46	466	0	ENST00000263923.4:c.3378G>T	p.Arg1126Ser	p.R1126S	ENST00000263923	NM_002253.2	1126	agG/agT	25/30	1	2	FACETS	0.723	0.609	0.849	0.723	0.609	0.849	SUBCLONAL	1	TRUE	1	0.264426597822957	2		466	481	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579547	7579547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567557016	NA	P-0054473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	95	776	0	ENST00000269305.4:c.140del	p.Pro47ArgfsTer76	p.P47Rfs*76	ENST00000269305	NM_001126112.2	47	cCg/cg	4/11	0.0966722279661432	3	FACETS	1	0.935	1			1	INDETERMINATE	1	TRUE	NA	0.264426597822957	3		776	760	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453149	140453149	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913361	NA	P-0054473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	58	380	0	ENST00000288602.6:c.1786G>C	p.Gly596Arg	p.G596R	ENST00000288602	NM_004333.4	596	Ggt/Cgt	15/18	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.264426597822957	2		380	358	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841159	15841159	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752029553	NA	P-0054473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	68	263	0	ENST00000307771.7:c.1243C>T	p.Arg415Trp	p.R415W	ENST00000307771	NM_005089.3	415	Cgg/Tgg	11/11	0.0966722279661432	2	FACETS	0.899	0.79	1			1	INDETERMINATE	2	TRUE	NA	0.264426597822957	2		263	286	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141108	55141108	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1060501505	NA	P-0054473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	46	451	0	ENST00000257290.5:c.1754G>T	p.Arg585Ile	p.R585I	ENST00000257290	NM_006206.4	585	aGa/aTa	12/23	1	2	FACETS	0.87	0.734	1	0.87	0.734	1	CLONAL	1	TRUE	1	0.264426597822957	2		451	400	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023168	27023168	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	12	123	0	ENST00000324856.7:c.275del	p.Gly92AlafsTer9	p.G92Afs*9	ENST00000324856	NM_006015.4	92	Ggc/gc	1/20	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.264426597822957	2		123	67	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956195	175956195	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0054473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	68	397	0	ENST00000367669.3:c.2017A>T	p.Lys673Ter	p.K673*	ENST00000367669	NM_022457.5	673	Aag/Tag	18/20	0.24918457596854	3	FACETS	0.776	0.679	0.881	0.776	0.679	0.881	SUBCLONAL	2	TRUE	1	0.264426597822957	3		397	375	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125523743	125523743	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0054473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	14	205	0	ENST00000428830.2:c.1335+1G>T		p.X445_splice	ENST00000428830	NM_001114121.2	445			1	2	FACETS	0.524	0.379	0.699	0.524	0.379	0.699	SUBCLONAL	1	TRUE	1	0.264426597822957	2		205	202	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152142	11152142	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	96	678	0	ENST00000358026.2:c.4426G>T	p.Gly1476Trp	p.G1476W	ENST00000358026	NM_001128849.1	1476	Ggg/Tgg	31/36	0.264426597822957	1	FACETS	0.899	0.801	1	0.899	0.801	1	CLONAL	1	TRUE	0	0.264426597822957	1		678	701	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285947	39285947	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0054473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	23	320	1	ENST00000402219.2:c.214-2A>T		p.X72_splice	ENST00000402219	NM_005633.3	72			1	2	FACETS	0.559	0.436	0.702	0.559	0.436	0.702	SUBCLONAL	1	TRUE	1	0.264426597822957	2		321	311	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661186	227661186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs765351999	NA	P-0054473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	115	907	0	ENST00000305123.5:c.2269C>T	p.Gln757Ter	p.Q757*	ENST00000305123	NM_005544.2	757	Cag/Tag	1/2	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.264426597822957	2		907	795	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030914	36030914	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	90	800	0	ENST00000358208.4:c.1193G>T	p.Gly398Val	p.G398V	ENST00000358208		398	gGa/gTa	10/12	NA	2	FACETS	0.866	0.768	0.971			1	INDETERMINATE	1	TRUE	NA	0.264426597822957	2		800	786	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213887	66213887	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	51	416	0	ENST00000273854.3:c.2543A>C	p.Glu848Ala	p.E848A	ENST00000273854	NM_004439.5	848	gAa/gCa	15/18	1	2	FACETS	0.972	0.828	1	0.972	0.828	1	CLONAL	1	TRUE	1	0.264426597822957	2		416	397	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975447	13975447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	56	412	0	ENST00000405192.2:c.440C>T	p.Pro147Leu	p.P147L	ENST00000405192	NM_001163147.1	147	cCa/cTa	7/12	1	2	FACETS	0.943	0.81	1	0.943	0.81	1	CLONAL	1	TRUE	1	0.264426597822957	2		412	449	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238432	98238432	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	43	493	0	ENST00000331920.6:c.1612G>T	p.Gly538Trp	p.G538W	ENST00000331920	NM_000264.3	538	Ggg/Tgg	12/24	1	2	FACETS	0.72	0.602	0.849	0.72	0.602	0.849	SUBCLONAL	1	TRUE	1	0.264426597822957	2		493	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0054474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	187	618	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.421414166432745	3	FACETS	1	0.975	1	0.726	0.678	0.774	CLONAL	2	FALSE	0	0.492038479114647	3		618	435	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692889	89692889	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	123	343	0	ENST00000371953.3:c.373A>G	p.Lys125Glu	p.K125E	ENST00000371953	NM_000314.4	125	Aaa/Gaa	5/9	0.492038479114647	3	FACETS	0.966	0.898	1	1	0.989	1	CLONAL	3	FALSE	1	0.492038479114647	3		343	215	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291798	15291798	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs759991207	NA	P-0054474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	153	1264	0	ENST00000263388.2:c.2968G>C	p.Glu990Gln	p.E990Q	ENST00000263388	NM_000435.2	990	Gag/Cag	18/33	0.291283955382769	5	FACETS	1	0.978	1	0.403	0.368	0.439	INDETERMINATE	1	FALSE	2	0.492038479114647	5		1264	894	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260186	149260186	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	295	663	0	ENST00000360632.3:c.707G>T	p.Arg236Leu	p.R236L	ENST00000360632	NM_015472.4	236	cGg/cTg	4/7	0.492038479114647	5	FACETS	0.97	0.919	1	0.97	0.919	1	CLONAL	3	FALSE	2	0.492038479114647	5		663	716	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847395	68847395	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	76	515	0	ENST00000261769.5:c.1319del	p.Lys440ArgfsTer15	p.K440Rfs*15	ENST00000261769	NM_004360.3	439	gcA/gc	9/16	0.454105927748724	3	FACETS	0.745	0.654	0.841	0.248	0.218	0.281	SUBCLONAL	1	FALSE	0	0.492038479114647	3		515	517	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752888	42752888	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	151	1121	0	ENST00000222329.4:c.1376C>G	p.Ala459Gly	p.A459G	ENST00000222329	NM_006494.2	459	gCc/gGc	4/4	0.46535032013695	2	FACETS	0.836	0.766	0.91	0.418	0.383	0.455	CLONAL	1	FALSE	0	0.492038479114647	2		1121	734	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631606	119631607	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0054474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	45	315	1	ENST00000316626.5:c.659_660delinsTT	p.Arg220Leu	p.R220L	ENST00000316626		220	cGG/cTT	6/12	0.492038479114647	5	FACETS	0.955	0.806	1			1	CLONAL	1	FALSE	NA	0.492038479114647	5		316	333	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0054476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	53	372	1	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.816364107108012	2		373	121	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0054476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	262	625	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.816364107108012	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.816364107108012	2		625	292	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063718	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0054476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	115	381	0	ENST00000412916.2:c.165+2dup		p.X55_splice	ENST00000412916		55			0.788998761700233	4	FACETS	0.869	0.785	0.957	0.29	0.261	0.319	CLONAL	1	TRUE	1	0.816364107108012	4		381	589	SUCCESS
APC	324	MSKCC	GRCh37	5	112175324	112175324	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1211642532	NA	P-0054476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	33	250	0	ENST00000257430.4:c.4033G>T	p.Glu1345Ter	p.E1345*	ENST00000257430	NM_000038.5	1345	Gaa/Taa	16/16	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.816364107108012	2		250	65	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0054476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	32	386	0	ENST00000311936.3:c.34_35delinsCT	p.Gly12Leu	p.G12L	ENST00000311936	NM_004985.3	12	GGt/CTt	2/5	0.316904078464439	3	FACETS	0.977	0.811	1	0.488	0.405	0.578	INDETERMINATE	1	TRUE	1	0.816364107108012	3		386	113	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178943755	178943755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200671228	NA	P-0054476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	30	227	0	ENST00000263967.3:c.2422C>T	p.Arg808Trp	p.R808W	ENST00000263967	NM_006218.2	808	Cgg/Tgg	17/21	0.260788933679492	3	FACETS	0.958	0.79	1	0.319	0.263	0.38	INDETERMINATE	1	TRUE	0	0.816364107108012	3		227	108	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524119	187524119	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	115	631	0	ENST00000441802.2:c.11420C>A	p.Ser3807Tyr	p.S3807Y	ENST00000441802	NM_005245.3	3807	tCt/tAt	20/27	0.498905259060863	4	FACETS	1	0.984	1	0.47	0.427	0.514	CLONAL	1	TRUE	1	0.816364107108012	4		631	363	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525003	187525003	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	89	596	0	ENST00000441802.2:c.10677C>A	p.Tyr3559Ter	p.Y3559*	ENST00000441802	NM_005245.3	3559	taC/taA	19/27	0.498905259060863	4	FACETS	1	0.973	1	0.427	0.383	0.474	CLONAL	1	TRUE	1	0.816364107108012	4		596	309	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527322	187527322	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	156	584	0	ENST00000441802.2:c.10252C>T	p.Pro3418Ser	p.P3418S	ENST00000441802	NM_005245.3	3418	Cca/Tca	17/27	0.498905259060863	4	FACETS	1	0.985	1	0.435	0.401	0.47	CLONAL	1	TRUE	1	0.816364107108012	4		584	532	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532552	187532552	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	38	318	0	ENST00000441802.2:c.9841G>C	p.Asp3281His	p.D3281H	ENST00000441802	NM_005245.3	3281	Gat/Cat	14/27	0.498905259060863	4	FACETS	1	0.931	1	0.403	0.339	0.471	CLONAL	1	TRUE	1	0.816364107108012	4		318	140	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80343488	80343488	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	53	374	0	ENST00000286548.4:c.831T>G	p.Asp277Glu	p.D277E	ENST00000286548	NM_002072.3	277	gaT/gaG	6/7	0.579046575712963	5	FACETS	0.969	0.832	1	0.323	0.277	0.373	CLONAL	1	TRUE	2	0.816364107108012	5		374	298	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0054477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	644	963	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.495316659364822	3	FACETS	0.951	0.94	0.962	1	0.998	1	CLONAL	5	TRUE	0	0.495316659364822	3		966	682	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	245	304	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.495316659364822	11	FACETS	0.975	0.932	1			1	CLONAL	9	TRUE	NA	0.495316659364822	11		304	364	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	237	751	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	1	2	FACETS	0.959	0.905	1	1	0.995	1	CLONAL	2	TRUE	1	0.495316659364822	2		751	499	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164611	36164611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	563	666	0	ENST00000300305.3:c.1264G>A	p.Glu422Lys	p.E422K	ENST00000300305		422	Gag/Aag	8/8	0.495316659364822	5	FACETS	1	0.993	1	1	0.997	1	CLONAL	4	TRUE	2	0.495316659364822	5		666	913	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31511216	31511216	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1256	88	624	0	ENST00000344624.3:c.1358G>A	p.Gly453Glu	p.G453E	ENST00000344624		453	gGg/gAg	6/33	0.495316659364822	8	FACETS	0.657	0.58	0.74	0.11	0.096	0.124	SUBCLONAL	1	TRUE	2	0.495316659364822	8		624	1344	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100298	157100298	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	87	303	0	ENST00000346085.5:c.1235C>G	p.Pro412Arg	p.P412R	ENST00000346085	NM_020732.3	412	cCg/cGg	1/20	0.495316659364822	4	FACETS	0.874	0.775	0.98	0.291	0.258	0.327	CLONAL	1	TRUE	1	0.495316659364822	4		303	601	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213611	36213611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757982914	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	494	1025	2	ENST00000222270.7:c.2713G>A	p.Ala905Thr	p.A905T	ENST00000222270	NM_014727.1	905	Gcc/Acc	5/37	1	2	FACETS	0.982	0.943	1	0.982	0.943	1	CLONAL	1	TRUE	1	0.88708228901537	2		1027	1134	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435129	110435129	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	437	916	5	ENST00000375856.3:c.3272del	p.Pro1091ArgfsTer15	p.P1091Rfs*15	ENST00000375856	NM_003749.2	1091	cCg/cg	1/2	1	2	FACETS	0.933	0.892	0.974	0.933	0.892	0.974	CLONAL	1	TRUE	1	0.88708228901537	2		921	1056	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	437	925	3	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.949	0.908	0.991	0.949	0.908	0.991	CLONAL	1	TRUE	1	0.88708228901537	2		928	1038	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	196	358	2	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.896	0.838	0.956	0.896	0.838	0.956	CLONAL	1	TRUE	1	0.88708228901537	2		360	493	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259451	55259451	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761920220	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	285	510	1	ENST00000275493.2:c.2509G>A	p.Asp837Asn	p.D837N	ENST00000275493	NM_005228.3	837	Gac/Aac	21/28	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.88708228901537	2		511	629	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851074	63851074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143074852	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	282	518	0	ENST00000279873.7:c.1852G>A	p.Ala618Thr	p.A618T	ENST00000279873	NM_032199.2	618	Gcc/Acc	10/10	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.88708228901537	2		518	634	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202349	133202349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs552452448	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	308	588	2	ENST00000320574.5:c.6539C>T	p.Ala2180Val	p.A2180V	ENST00000320574	NM_006231.2	2180	gCg/gTg	47/49	1	2	FACETS	0.953	0.904	1	0.953	0.904	1	CLONAL	1	TRUE	1	0.88708228901537	2		590	729	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793238	42793238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763699553	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	441	1001	0	ENST00000575354.2:c.1130C>T	p.Thr377Met	p.T377M	ENST00000575354	NM_015125.3	377	aCg/aTg	7/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.88708228901537	2		1001	947	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795103	242795104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768249210	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	341	971	1	ENST00000334409.5:c.105dup	p.Thr36HisfsTer70	p.T36Hfs*70	ENST00000334409	NM_005018.2	35	-/C	2/5	1	2	FACETS	0.721	0.683	0.759	0.721	0.683	0.759	SUBCLONAL	1	TRUE	1	0.88708228901537	2		972	1067	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553591	106553591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376600972	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	214	459	0	ENST00000369096.4:c.1556C>T	p.Ala519Val	p.A519V	ENST00000369096	NM_001198.3	519	gCg/gTg	5/7	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.88708228901537	2		459	458	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	296	367	8	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	0.97	0.944	0.994	1	0.997	1	CLONAL	2	TRUE	1	0.88708228901537	2		375	344	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138319	2138319	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373365980	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	442	826	8	ENST00000219476.3:c.5252G>A	p.Arg1751His	p.R1751H	ENST00000219476	NM_000548.3	1751	cGc/cAc	41/42	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.88708228901537	2		834	921	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	194	393	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.959	0.898	1	0.959	0.898	1	CLONAL	1	TRUE	1	0.88708228901537	2		396	456	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145645	11145645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	398	909	2	ENST00000358026.2:c.4007G>A	p.Arg1336His	p.R1336H	ENST00000358026	NM_001128849.1	1336	cGc/cAc	29/36	1	2	FACETS	0.949	0.906	0.992	0.949	0.906	0.992	CLONAL	1	TRUE	1	0.88708228901537	2		911	946	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400023	139400023	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	410	998	3	ENST00000277541.6:c.4325del	p.Pro1442ArgfsTer3	p.P1442Rfs*3	ENST00000277541	NM_017617.3	1442	cCg/cg	25/34	1	2	FACETS	0.843	0.804	0.883	0.843	0.804	0.883	CLONAL	1	TRUE	1	0.88708228901537	2		1001	1096	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635188	87635188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	220	541	1	ENST00000277120.3:c.2240C>T	p.Thr747Met	p.T747M	ENST00000277120		747	aCg/aTg	18/19	1	2	FACETS	0.973	0.914	1	0.973	0.914	1	CLONAL	1	TRUE	1	0.88708228901537	2		542	510	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513012	106513012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758968659	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	119	268	0	ENST00000359195.3:c.2026G>A	p.Ala676Thr	p.A676T	ENST00000359195	NM_002649.2	676	Gcc/Acc	3/11	1	2	FACETS	0.928	0.852	1	0.928	0.852	1	CLONAL	1	TRUE	1	0.88708228901537	2		268	289	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743755	46743755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769015770	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	397	751	0	ENST00000371975.4:c.2045G>A	p.Arg682Gln	p.R682Q	ENST00000371975	NM_003579.3	682	cGa/cAa	18/18	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.88708228901537	2		751	835	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89839685	89839685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778312	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	295	561	0	ENST00000389301.3:c.2008C>T	p.Arg670Cys	p.R670C	ENST00000389301	NM_000135.2	670	Cgt/Tgt	22/43	1	2	FACETS	0.961	0.911	1	0.961	0.911	1	CLONAL	1	TRUE	1	0.88708228901537	2		561	692	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568897	212568897	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	192	335	0	ENST00000342788.4:c.1221G>A	p.Trp407Ter	p.W407*	ENST00000342788	NM_005235.2	407	tgG/tgA	11/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.88708228901537	2		335	409	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508614	106508614	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377001952	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	275	504	3	ENST00000359195.3:c.608C>T	p.Thr203Met	p.T203M	ENST00000359195	NM_002649.2	203	aCg/aTg	2/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.88708228901537	2		507	617	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397741	116397741	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	278	497	0	ENST00000397752.3:c.2015G>A	p.Gly672Asp	p.G672D	ENST00000397752	NM_000245.2	672	gGc/gAc	8/21	1	2	FACETS	0.961	0.91	1	0.961	0.91	1	CLONAL	1	TRUE	1	0.88708228901537	2		497	652	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508733	106508733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1207051578	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	283	549	1	ENST00000359195.3:c.727G>A	p.Ala243Thr	p.A243T	ENST00000359195	NM_002649.2	243	Gcc/Acc	2/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.88708228901537	2		550	637	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628340	187628340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536104649	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	299	594	1	ENST00000441802.2:c.2642G>A	p.Arg881His	p.R881H	ENST00000441802	NM_005245.3	881	cGc/cAc	2/27	1	2	FACETS	0.905	0.857	0.953	0.905	0.857	0.953	CLONAL	1	TRUE	1	0.88708228901537	2		595	745	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238329	98238329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1485556285	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	243	477	0	ENST00000331920.6:c.1715C>T	p.Ala572Val	p.A572V	ENST00000331920	NM_000264.3	572	gCg/gTg	12/24	1	2	FACETS	0.994	0.938	1	0.994	0.938	1	CLONAL	1	TRUE	1	0.88708228901537	2		477	551	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804304	43804304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763568293	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	282	574	0	ENST00000372470.3:c.304C>T	p.Arg102Cys	p.R102C	ENST00000372470	NM_005373.2	102	Cgt/Tgt	3/12	1	2	FACETS	0.972	0.92	1	0.972	0.92	1	CLONAL	1	TRUE	1	0.88708228901537	2		574	654	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041630	14041630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368096448	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	201	459	0	ENST00000311895.7:c.2177G>A	p.Arg726His	p.R726H	ENST00000311895	NM_005236.2	726	cGc/cAc	11/11	1	2	FACETS	0.915	0.857	0.975	0.915	0.857	0.975	CLONAL	1	TRUE	1	0.88708228901537	2		459	495	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418670	49418670	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783698	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	256	528	1	ENST00000301067.7:c.15844C>T	p.Arg5282Ter	p.R5282*	ENST00000301067	NM_003482.3	5282	Cga/Tga	49/54	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.88708228901537	2		529	567	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214871	36214871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	402	720	4	ENST00000222270.7:c.3302del	p.Pro1101LeufsTer81	p.P1101Lfs*81	ENST00000222270	NM_014727.1	1099	ggC/gg	8/37	1	2	FACETS	0.947	0.904	0.99	0.947	0.904	0.99	CLONAL	1	TRUE	1	0.88708228901537	2		724	957	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469919	157469919	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	303	630	0	ENST00000346085.5:c.2713C>T	p.Gln905Ter	p.Q905*	ENST00000346085	NM_020732.3	905	Cag/Tag	9/20	1	2	FACETS	0.977	0.927	1	0.977	0.927	1	CLONAL	1	TRUE	1	0.88708228901537	2		630	699	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194790	29194790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773054971	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	493	972	2	ENST00000240100.2:c.938G>A	p.Arg313His	p.R313H	ENST00000240100	NM_001394.6	313	cGc/cAc	4/4	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.88708228901537	2		974	1087	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779258	3779258	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	248	631	0	ENST00000262367.5:c.5790del	p.Thr1931ProfsTer45	p.T1931Pfs*45	ENST00000262367	NM_004380.2	1930	ccC/cc	31/31	1	2	FACETS	0.814	0.765	0.863	0.814	0.765	0.863	CLONAL	1	TRUE	1	0.88708228901537	2		631	687	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420204	49420204	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	375	714	0	ENST00000301067.7:c.15545del	p.Gly5182AlafsTer61	p.G5182Afs*61	ENST00000301067	NM_003482.3	5182	gGc/gc	48/54	1	2	FACETS	0.967	0.923	1	0.967	0.923	1	CLONAL	1	TRUE	1	0.88708228901537	2		714	874	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845702	151845702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771018478	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	316	565	0	ENST00000262189.6:c.13310C>T	p.Thr4437Met	p.T4437M	ENST00000262189	NM_170606.2	4437	aCg/aTg	52/59	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.88708228901537	2		565	694	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918125	50918127	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs763850764	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	411	911	1	ENST00000440232.2:c.2446_2448del	p.Ser816del	p.S816del	ENST00000440232	NM_002691.3	814	ttCTCc/ttc	20/27	1	2	FACETS	0.938	0.896	0.98	0.938	0.896	0.98	CLONAL	1	TRUE	1	0.88708228901537	2		912	988	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212076	5212076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377889959	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	429	896	0	ENST00000357368.4:c.4955G>A	p.Gly1652Asp	p.G1652D	ENST00000357368	NM_002850.3	1652	gGc/gAc	32/38	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.88708228901537	2		896	955	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284906	15284906	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1469453455	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	566	1005	1	ENST00000263388.2:c.4709G>A	p.Arg1570His	p.R1570H	ENST00000263388	NM_000435.2	1570	cGt/cAt	25/33	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.88708228901537	2		1006	1213	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541247	187541247	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	217	389	0	ENST00000441802.2:c.6493del	p.Ser2165GlnfsTer11	p.S2165Qfs*11	ENST00000441802	NM_005245.3	2165	Tca/ca	10/27	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.88708228901537	2		389	489	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225389	26225389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545285022	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	107	209	0	ENST00000360408.1:c.7C>T	p.Arg3Cys	p.R3C	ENST00000360408	NM_003532.2	3	Cgt/Tgt	1/1	1	2	FACETS	0.855	0.779	0.933	0.855	0.779	0.933	CLONAL	1	TRUE	1	0.88708228901537	2		209	282	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570468	39570468	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs267605182	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	141	194	0	ENST00000262039.4:c.664C>T	p.Arg222Ter	p.R222*	ENST00000262039	NM_002647.2	222	Cga/Tga	6/25	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.88708228901537	2		194	276	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053171	180053171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369939230	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	431	983	1	ENST00000261937.6:c.1198G>A	p.Ala400Thr	p.A400T	ENST00000261937	NM_182925.4	400	Gcc/Acc	9/30	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.88708228901537	2		984	959	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224532	36224532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759167832	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	507	1124	4	ENST00000222270.7:c.6994C>T	p.Arg2332Cys	p.R2332C	ENST00000222270	NM_014727.1	2332	Cgt/Tgt	29/37	1	2	FACETS	0.98	0.941	1	0.98	0.941	1	CLONAL	1	TRUE	1	0.88708228901537	2		1128	1166	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793516	42793516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	422	891	2	ENST00000575354.2:c.1318C>T	p.Arg440Cys	p.R440C	ENST00000575354	NM_015125.3	440	Cgc/Tgc	8/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.88708228901537	2		893	907	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942647	71942647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	315	615	1	ENST00000298229.2:c.1603G>A	p.Ala535Thr	p.A535T	ENST00000298229	NM_001567.3	535	Gcc/Acc	13/28	1	2	FACETS	0.996	0.946	1	0.996	0.946	1	CLONAL	1	TRUE	1	0.88708228901537	2		616	713	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446069	49446069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs952760497	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	525	1004	5	ENST00000301067.7:c.1397G>A	p.Arg466His	p.R466H	ENST00000301067	NM_003482.3	466	cGc/cAc	10/54	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.88708228901537	2		1009	1150	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434581	99434581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1461059080	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	339	653	1	ENST00000268035.6:c.668C>T	p.Ala223Val	p.A223V	ENST00000268035	NM_000875.3	223	gCg/gTg	3/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.88708228901537	2		654	744	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650052	206650052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540205249	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	344	663	0	ENST00000367120.3:c.572G>A	p.Arg191Gln	p.R191Q	ENST00000367120	NM_014002.3	191	cGa/cAa	7/22	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.88708228901537	2		663	728	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123752	11123752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568471266	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	265	582	1	ENST00000358026.2:c.2402G>A	p.Arg801His	p.R801H	ENST00000358026	NM_001128849.1	801	cGc/cAc	16/36	1	2	FACETS	0.861	0.812	0.911	0.861	0.812	0.911	CLONAL	1	TRUE	1	0.88708228901537	2		583	694	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019172	31019172	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	281	479	0	ENST00000375687.4:c.767G>T	p.Gly256Val	p.G256V	ENST00000375687	NM_015338.5	256	gGg/gTg	9/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.88708228901537	2		479	608	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322556	39322556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761415462	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	178	367	0	ENST00000373001.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000373001	NM_022157.3	146	Gca/Aca	2/7	1	2	FACETS	0.916	0.854	0.979	0.916	0.854	0.979	CLONAL	1	TRUE	1	0.88708228901537	2		367	438	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40468878	40468878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	216	346	1	ENST00000264657.5:c.2186G>A	p.Arg729His	p.R729H	ENST00000264657	NM_139276.2	729	cGc/cAc	23/24	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.88708228901537	2		347	469	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100004	11100004	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555756272	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	341	640	0	ENST00000358026.2:c.1130G>A	p.Arg377His	p.R377H	ENST00000358026	NM_001128849.1	377	cGc/cAc	7/36	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.88708228901537	2		640	682	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284996	15284996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1472208548	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	529	1153	1	ENST00000263388.2:c.4619G>A	p.Arg1540His	p.R1540H	ENST00000263388	NM_000435.2	1540	cGc/cAc	25/33	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.88708228901537	2		1154	1128	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814535	43814535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1400122324	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	279	553	1	ENST00000372470.3:c.1330G>A	p.Ala444Thr	p.A444T	ENST00000372470	NM_005373.2	444	Gcc/Acc	9/12	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.88708228901537	2		554	609	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211548	98211549	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	255	666	1	ENST00000331920.6:c.3606dup	p.Ser1203GlnfsTer17	p.S1203Qfs*17	ENST00000331920	NM_000264.3	1202	-/C	22/24	1	2	FACETS	0.781	0.735	0.829	0.781	0.735	0.829	SUBCLONAL	1	TRUE	1	0.88708228901537	2		667	736	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263848	16263848	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	348	748	0	ENST00000375759.3:c.10217C>T	p.Ala3406Val	p.A3406V	ENST00000375759	NM_015001.2	3406	gCt/gTt	12/15	1	2	FACETS	0.959	0.913	1	0.959	0.913	1	CLONAL	1	TRUE	1	0.88708228901537	2		748	818	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695968	117695968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	221	476	0	ENST00000369458.3:c.469G>A	p.Val157Met	p.V157M	ENST00000369458	NM_024626.3	157	Gtg/Atg	4/6	1	2	FACETS	0.865	0.811	0.92	0.865	0.811	0.92	CLONAL	1	TRUE	1	0.88708228901537	2		476	576	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480571	120480571	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	240	461	1	ENST00000256646.2:c.3246del	p.Ala1083GlnfsTer25	p.A1083Qfs*25	ENST00000256646	NM_024408.3	1082	aaA/aa	20/34	1	2	FACETS	0.896	0.843	0.95	0.896	0.843	0.95	CLONAL	1	TRUE	1	0.88708228901537	2		462	604	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518547	204518547	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	131	262	0	ENST00000367182.3:c.1210C>A	p.Gln404Lys	p.Q404K	ENST00000367182	NM_001278516.1	404	Caa/Aaa	11/11	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.88708228901537	2		262	295	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533873	533873	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913496	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	422	799	1	ENST00000451590.1:c.183G>T	p.Gln61His	p.Q61H	ENST00000451590	NM_001130442.1	61	caG/caT	3/5	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.88708228901537	2		800	929	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437695	49437695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565802308	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	445	818	1	ENST00000301067.7:c.5275C>T	p.Arg1759Cys	p.R1759C	ENST00000301067	NM_003482.3	1759	Cgc/Tgc	22/54	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.88708228901537	2		819	985	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784078	120784078	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	548	1087	2	ENST00000257552.2:c.907C>T	p.Arg303Cys	p.R303C	ENST00000257552	NM_002442.3	303	Cgc/Tgc	13/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.88708228901537	2		1089	1196	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240999	133240999	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	338	666	0	ENST00000320574.5:c.2518del	p.Ala840ProfsTer10	p.A840Pfs*10	ENST00000320574	NM_006231.2	840	Gcc/cc	22/49	1	2	FACETS	0.968	0.921	1	0.968	0.921	1	CLONAL	1	TRUE	1	0.88708228901537	2		666	787	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562606	21562606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	185	332	0	ENST00000382592.4:c.1313C>T	p.Ala438Val	p.A438V	ENST00000382592	NM_014572.2	438	gCg/gTg	4/8	1	2	FACETS	0.921	0.859	0.983	0.921	0.859	0.983	CLONAL	1	TRUE	1	0.88708228901537	2		332	453	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619853	21619853	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	178	378	1	ENST00000382592.4:c.313C>T	p.Gln105Ter	p.Q105*	ENST00000382592	NM_014572.2	105	Cag/Tag	2/8	1	2	FACETS	0.859	0.8	0.92	0.859	0.8	0.92	CLONAL	1	TRUE	1	0.88708228901537	2		379	467	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967513	26967513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	150	252	0	ENST00000381527.3:c.656C>T	p.Ala219Val	p.A219V	ENST00000381527	NM_001260.1	219	gCt/gTt	7/13	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.88708228901537	2		252	326	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060992	38060992	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	197	509	0	ENST00000250448.2:c.997del	p.Gln333ArgfsTer17	p.Q333Rfs*17	ENST00000250448	NM_004496.3	333	Cag/ag	2/2	1	2	FACETS	0.802	0.748	0.857	0.802	0.748	0.857	CLONAL	1	TRUE	1	0.88708228901537	2		509	554	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644501	3644501	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749913190	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	412	863	0	ENST00000294008.3:c.2113G>A	p.Ala705Thr	p.A705T	ENST00000294008	NM_032444.2	705	Gcc/Acc	10/15	1	2	FACETS	0.995	0.951	1	0.995	0.951	1	CLONAL	1	TRUE	1	0.88708228901537	2		863	934	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348754	89348754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752446167	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	467	874	2	ENST00000301030.4:c.4196C>T	p.Ala1399Val	p.A1399V	ENST00000301030	NM_001256183.1	1399	gCg/gTg	9/13	1	2	FACETS	0.955	0.915	0.995	0.955	0.915	0.995	CLONAL	1	TRUE	1	0.88708228901537	2		876	1103	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89869675	89869675	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	321	596	0	ENST00000389301.3:c.784del	p.Met262CysfsTer13	p.M262Cfs*13	ENST00000389301	NM_000135.2	262	Atg/tg	8/43	1	2	FACETS	0.969	0.92	1	0.969	0.92	1	CLONAL	1	TRUE	1	0.88708228901537	2		596	747	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435824	56435824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	332	643	0	ENST00000407977.2:c.1313C>T	p.Ala438Val	p.A438V	ENST00000407977		438	gCc/gTc	9/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.88708228901537	2		643	710	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227084	2227084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759654625	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	453	903	1	ENST00000398665.3:c.4564G>A	p.Ala1522Thr	p.A1522T	ENST00000398665	NM_032482.2	1522	Gcc/Acc	27/28	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.88708228901537	2		904	940	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210584	5210584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	330	705	1	ENST00000357368.4:c.5383C>T	p.Pro1795Ser	p.P1795S	ENST00000357368	NM_002850.3	1795	Ccg/Tcg	35/38	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.88708228901537	2		706	742	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244152	5244152	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs773187155	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	470	917	0	ENST00000357368.4:c.1330A>G	p.Ile444Val	p.I444V	ENST00000357368	NM_002850.3	444	Att/Gtt	11/38	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.88708228901537	2		917	1040	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945781	17945781	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	462	861	2	ENST00000458235.1:c.2079del	p.Glu694SerfsTer62	p.E694Sfs*62	ENST00000458235	NM_000215.3	693	ccC/cc	16/24	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.88708228901537	2		863	917	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308146	30308146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs574899763	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	345	604	0	ENST00000262643.3:c.283C>T	p.Arg95Trp	p.R95W	ENST00000262643	NM_001238.2	95	Cgg/Tgg	5/12	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.88708228901537	2		604	720	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921169	50921169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755297873	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	417	875	0	ENST00000440232.2:c.3289C>T	p.Arg1097Trp	p.R1097W	ENST00000440232	NM_002691.3	1097	Cgg/Tgg	27/27	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.88708228901537	2		875	936	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873738	151873738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770069367	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	242	466	0	ENST00000262189.6:c.8800C>T	p.Pro2934Ser	p.P2934S	ENST00000262189	NM_170606.2	2934	Cca/Tca	38/59	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.88708228901537	2		466	525	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396481	139396482	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	465	951	0	ENST00000277541.6:c.5443dup	p.Asp1815GlyfsTer19	p.D1815Gfs*19	ENST00000277541	NM_017617.3	1815	gac/gGac	29/34	1	2	FACETS	0.979	0.938	1	0.979	0.938	1	CLONAL	1	TRUE	1	0.88708228901537	2		951	1071	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214728	36214728	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	63	737	0	ENST00000222270.7:c.3159del	p.Arg1055GlyfsTer127	p.R1055Gfs*127	ENST00000222270	NM_014727.1	1052	Ggg/gg	8/37	1	2	FACETS	0.187	0.161	0.215	0.187	0.161	0.215	SUBCLONAL	1	TRUE	1	0.88708228901537	2		737	760	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931452	131931452	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507178	NA	P-0054478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	196	343	7	ENST00000265335.6:c.2165del	p.Lys722ArgfsTer14	p.K722Rfs*14	ENST00000265335		719	ctA/ct	13/25	1	2	FACETS	0.98	0.918	1	0.98	0.918	1	CLONAL	1	TRUE	1	0.88708228901537	2		350	451	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213611	36213611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757982914	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	443	1025	2	ENST00000222270.7:c.2713G>A	p.Ala905Thr	p.A905T	ENST00000222270	NM_014727.1	905	Gcc/Acc	5/37	1	2	FACETS	0.991	0.948	1	0.991	0.948	1	CLONAL	1	TRUE	1	0.858239149938094	2		1027	1042	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435129	110435129	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	332	916	5	ENST00000375856.3:c.3272del	p.Pro1091ArgfsTer15	p.P1091Rfs*15	ENST00000375856	NM_003749.2	1091	cCg/cg	1/2	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.858239149938094	2		921	751	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	341	925	3	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.909	0.864	0.955	0.909	0.864	0.955	CLONAL	1	TRUE	1	0.858239149938094	2		928	874	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	259	358	2	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.858239149938094	2		360	603	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259451	55259451	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761920220	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	283	510	1	ENST00000275493.2:c.2509G>A	p.Asp837Asn	p.D837N	ENST00000275493	NM_005228.3	837	Gac/Aac	21/28	1	2	FACETS	0.981	0.929	1	0.981	0.929	1	CLONAL	1	TRUE	1	0.858239149938094	2		511	672	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851074	63851074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143074852	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	291	518	0	ENST00000279873.7:c.1852G>A	p.Ala618Thr	p.A618T	ENST00000279873	NM_032199.2	618	Gcc/Acc	10/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.858239149938094	2		518	647	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202349	133202349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs552452448	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	317	588	2	ENST00000320574.5:c.6539C>T	p.Ala2180Val	p.A2180V	ENST00000320574	NM_006231.2	2180	gCg/gTg	47/49	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.858239149938094	2		590	685	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793238	42793238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763699553	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	405	1001	0	ENST00000575354.2:c.1130C>T	p.Thr377Met	p.T377M	ENST00000575354	NM_015125.3	377	aCg/aTg	7/20	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.858239149938094	2		1001	842	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795103	242795104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768249210	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	339	971	1	ENST00000334409.5:c.105dup	p.Thr36HisfsTer70	p.T36Hfs*70	ENST00000334409	NM_005018.2	35	-/C	2/5	1	2	FACETS	0.844	0.801	0.888	0.844	0.801	0.888	CLONAL	1	TRUE	1	0.858239149938094	2		972	936	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553591	106553591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376600972	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	204	459	0	ENST00000369096.4:c.1556C>T	p.Ala519Val	p.A519V	ENST00000369096	NM_001198.3	519	gCg/gTg	5/7	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.858239149938094	2		459	451	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	247	367	8	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	1	0.981	1	1	0.996	1	CLONAL	2	TRUE	1	0.858239149938094	2		375	284	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138319	2138319	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373365980	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	319	826	8	ENST00000219476.3:c.5252G>A	p.Arg1751His	p.R1751H	ENST00000219476	NM_000548.3	1751	cGc/cAc	41/42	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.858239149938094	2		834	733	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	212	393	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.974	0.914	1	0.974	0.914	1	CLONAL	1	TRUE	1	0.858239149938094	2		396	507	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145645	11145645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	370	909	2	ENST00000358026.2:c.4007G>A	p.Arg1336His	p.R1336H	ENST00000358026	NM_001128849.1	1336	cGc/cAc	29/36	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.858239149938094	2		911	839	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400023	139400023	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	366	998	3	ENST00000277541.6:c.4325del	p.Pro1442ArgfsTer3	p.P1442Rfs*3	ENST00000277541	NM_017617.3	1442	cCg/cg	25/34	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.858239149938094	2		1001	841	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635188	87635188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	309	541	1	ENST00000277120.3:c.2240C>T	p.Thr747Met	p.T747M	ENST00000277120		747	aCg/aTg	18/19	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.858239149938094	2		542	714	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513012	106513012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758968659	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	87	268	0	ENST00000359195.3:c.2026G>A	p.Ala676Thr	p.A676T	ENST00000359195	NM_002649.2	676	Gcc/Acc	3/11	1	2	FACETS	0.909	0.82	1	0.909	0.82	1	CLONAL	1	TRUE	1	0.858239149938094	2		268	223	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743755	46743755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769015770	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	452	751	0	ENST00000371975.4:c.2045G>A	p.Arg682Gln	p.R682Q	ENST00000371975	NM_003579.3	682	cGa/cAa	18/18	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.858239149938094	2		751	1011	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89839685	89839685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778312	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	338	561	0	ENST00000389301.3:c.2008C>T	p.Arg670Cys	p.R670C	ENST00000389301	NM_000135.2	670	Cgt/Tgt	22/43	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.858239149938094	2		561	731	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568897	212568897	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	112	335	0	ENST00000342788.4:c.1221G>A	p.Trp407Ter	p.W407*	ENST00000342788	NM_005235.2	407	tgG/tgA	11/28	1	2	FACETS	0.974	0.891	1	0.974	0.891	1	CLONAL	1	TRUE	1	0.858239149938094	2		335	268	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508614	106508614	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377001952	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	231	504	3	ENST00000359195.3:c.608C>T	p.Thr203Met	p.T203M	ENST00000359195	NM_002649.2	203	aCg/aTg	2/11	1	2	FACETS	0.982	0.924	1	0.982	0.924	1	CLONAL	1	TRUE	1	0.858239149938094	2		507	548	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397741	116397741	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	158	497	0	ENST00000397752.3:c.2015G>A	p.Gly672Asp	p.G672D	ENST00000397752	NM_000245.2	672	gGc/gAc	8/21	1	2	FACETS	0.977	0.907	1	0.977	0.907	1	CLONAL	1	TRUE	1	0.858239149938094	2		497	377	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508733	106508733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1207051578	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	326	549	1	ENST00000359195.3:c.727G>A	p.Ala243Thr	p.A243T	ENST00000359195	NM_002649.2	243	Gcc/Acc	2/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.858239149938094	2		550	715	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628340	187628340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536104649	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	341	594	1	ENST00000441802.2:c.2642G>A	p.Arg881His	p.R881H	ENST00000441802	NM_005245.3	881	cGc/cAc	2/27	1	2	FACETS	0.951	0.904	0.998	0.951	0.904	0.998	CLONAL	1	TRUE	1	0.858239149938094	2		595	836	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238329	98238329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1485556285	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	186	477	0	ENST00000331920.6:c.1715C>T	p.Ala572Val	p.A572V	ENST00000331920	NM_000264.3	572	gCg/gTg	12/24	1	2	FACETS	0.983	0.918	1	0.983	0.918	1	CLONAL	1	TRUE	1	0.858239149938094	2		477	441	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804304	43804304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763568293	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	364	574	0	ENST00000372470.3:c.304C>T	p.Arg102Cys	p.R102C	ENST00000372470	NM_005373.2	102	Cgt/Tgt	3/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.858239149938094	2		574	826	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041630	14041630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368096448	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	195	459	0	ENST00000311895.7:c.2177G>A	p.Arg726His	p.R726H	ENST00000311895	NM_005236.2	726	cGc/cAc	11/11	1	2	FACETS	0.955	0.893	1	0.955	0.893	1	CLONAL	1	TRUE	1	0.858239149938094	2		459	476	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418670	49418670	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783698	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	303	528	1	ENST00000301067.7:c.15844C>T	p.Arg5282Ter	p.R5282*	ENST00000301067	NM_003482.3	5282	Cga/Tga	49/54	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.858239149938094	2		529	665	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214871	36214871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	405	720	4	ENST00000222270.7:c.3302del	p.Pro1101LeufsTer81	p.P1101Lfs*81	ENST00000222270	NM_014727.1	1099	ggC/gg	8/37	1	2	FACETS	0.922	0.879	0.964	0.922	0.879	0.964	CLONAL	1	TRUE	1	0.858239149938094	2		724	1024	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469919	157469919	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	288	630	0	ENST00000346085.5:c.2713C>T	p.Gln905Ter	p.Q905*	ENST00000346085	NM_020732.3	905	Cag/Tag	9/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.858239149938094	2		630	626	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194790	29194790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773054971	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	442	972	2	ENST00000240100.2:c.938G>A	p.Arg313His	p.R313H	ENST00000240100	NM_001394.6	313	cGc/cAc	4/4	1	2	FACETS	0.993	0.951	1	0.993	0.951	1	CLONAL	1	TRUE	1	0.858239149938094	2		974	1037	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779258	3779258	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	245	631	0	ENST00000262367.5:c.5790del	p.Thr1931ProfsTer45	p.T1931Pfs*45	ENST00000262367	NM_004380.2	1930	ccC/cc	31/31	1	2	FACETS	0.983	0.926	1	0.983	0.926	1	CLONAL	1	TRUE	1	0.858239149938094	2		631	581	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420204	49420204	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	309	714	0	ENST00000301067.7:c.15545del	p.Gly5182AlafsTer61	p.G5182Afs*61	ENST00000301067	NM_003482.3	5182	gGc/gc	48/54	1	2	FACETS	0.854	0.809	0.901	0.854	0.809	0.901	CLONAL	1	TRUE	1	0.858239149938094	2		714	843	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845702	151845702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771018478	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	274	565	0	ENST00000262189.6:c.13310C>T	p.Thr4437Met	p.T4437M	ENST00000262189	NM_170606.2	4437	aCg/aTg	52/59	1	2	FACETS	0.97	0.917	1	0.97	0.917	1	CLONAL	1	TRUE	1	0.858239149938094	2		565	658	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918125	50918127	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs763850764	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	304	911	1	ENST00000440232.2:c.2446_2448del	p.Ser816del	p.S816del	ENST00000440232	NM_002691.3	814	ttCTCc/ttc	20/27	1	2	FACETS	0.952	0.903	1	0.952	0.903	1	CLONAL	1	TRUE	1	0.858239149938094	2		912	744	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212076	5212076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377889959	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	380	896	0	ENST00000357368.4:c.4955G>A	p.Gly1652Asp	p.G1652D	ENST00000357368	NM_002850.3	1652	gGc/gAc	32/38	1	2	FACETS	0.981	0.935	1	0.981	0.935	1	CLONAL	1	TRUE	1	0.858239149938094	2		896	903	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284906	15284906	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1469453455	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	528	1005	1	ENST00000263388.2:c.4709G>A	p.Arg1570His	p.R1570H	ENST00000263388	NM_000435.2	1570	cGt/cAt	25/33	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.858239149938094	2		1006	1133	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541247	187541247	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	204	389	0	ENST00000441802.2:c.6493del	p.Ser2165GlnfsTer11	p.S2165Qfs*11	ENST00000441802	NM_005245.3	2165	Tca/ca	10/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.858239149938094	2		389	433	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225389	26225389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545285022	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	110	209	0	ENST00000360408.1:c.7C>T	p.Arg3Cys	p.R3C	ENST00000360408	NM_003532.2	3	Cgt/Tgt	1/1	1	2	FACETS	0.925	0.845	1	0.925	0.845	1	CLONAL	1	TRUE	1	0.858239149938094	2		209	277	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570468	39570468	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs267605182	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	74	194	0	ENST00000262039.4:c.664C>T	p.Arg222Ter	p.R222*	ENST00000262039	NM_002647.2	222	Cga/Tga	6/25	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.858239149938094	2		194	170	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053171	180053171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369939230	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	393	983	1	ENST00000261937.6:c.1198G>A	p.Ala400Thr	p.A400T	ENST00000261937	NM_182925.4	400	Gcc/Acc	9/30	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.858239149938094	2		984	870	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224532	36224532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759167832	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	504	1124	4	ENST00000222270.7:c.6994C>T	p.Arg2332Cys	p.R2332C	ENST00000222270	NM_014727.1	2332	Cgt/Tgt	29/37	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.858239149938094	2		1128	1153	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793516	42793516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	375	891	2	ENST00000575354.2:c.1318C>T	p.Arg440Cys	p.R440C	ENST00000575354	NM_015125.3	440	Cgc/Tgc	8/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.858239149938094	2		893	823	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942647	71942647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	318	615	1	ENST00000298229.2:c.1603G>A	p.Ala535Thr	p.A535T	ENST00000298229	NM_001567.3	535	Gcc/Acc	13/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.858239149938094	2		616	685	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446069	49446069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs952760497	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	557	1004	5	ENST00000301067.7:c.1397G>A	p.Arg466His	p.R466H	ENST00000301067	NM_003482.3	466	cGc/cAc	10/54	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.858239149938094	2		1009	1172	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434581	99434581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1461059080	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	315	653	1	ENST00000268035.6:c.668C>T	p.Ala223Val	p.A223V	ENST00000268035	NM_000875.3	223	gCg/gTg	3/21	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.858239149938094	2		654	653	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650052	206650052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540205249	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	348	663	0	ENST00000367120.3:c.572G>A	p.Arg191Gln	p.R191Q	ENST00000367120	NM_014002.3	191	cGa/cAa	7/22	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.858239149938094	2		663	757	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123752	11123752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568471266	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	364	582	1	ENST00000358026.2:c.2402G>A	p.Arg801His	p.R801H	ENST00000358026	NM_001128849.1	801	cGc/cAc	16/36	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.858239149938094	2		583	774	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019172	31019172	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	284	479	0	ENST00000375687.4:c.767G>T	p.Gly256Val	p.G256V	ENST00000375687	NM_015338.5	256	gGg/gTg	9/13	1	2	FACETS	0.972	0.92	1	0.972	0.92	1	CLONAL	1	TRUE	1	0.858239149938094	2		479	681	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322556	39322556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761415462	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	153	367	0	ENST00000373001.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000373001	NM_022157.3	146	Gca/Aca	2/7	1	2	FACETS	0.974	0.903	1	0.974	0.903	1	CLONAL	1	TRUE	1	0.858239149938094	2		367	366	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40468878	40468878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	205	346	1	ENST00000264657.5:c.2186G>A	p.Arg729His	p.R729H	ENST00000264657	NM_139276.2	729	cGc/cAc	23/24	1	2	FACETS	0.908	0.85	0.967	0.908	0.85	0.967	CLONAL	1	TRUE	1	0.858239149938094	2		347	526	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100004	11100004	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555756272	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	324	640	0	ENST00000358026.2:c.1130G>A	p.Arg377His	p.R377H	ENST00000358026	NM_001128849.1	377	cGc/cAc	7/36	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.858239149938094	2		640	720	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284996	15284996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1472208548	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	380	1153	1	ENST00000263388.2:c.4619G>A	p.Arg1540His	p.R1540H	ENST00000263388	NM_000435.2	1540	cGc/cAc	25/33	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.858239149938094	2		1154	840	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814535	43814535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1400122324	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	186	553	1	ENST00000372470.3:c.1330G>A	p.Ala444Thr	p.A444T	ENST00000372470	NM_005373.2	444	Gcc/Acc	9/12	1	2	FACETS	0.985	0.92	1	0.985	0.92	1	CLONAL	1	TRUE	1	0.858239149938094	2		554	440	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211548	98211549	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	332	666	1	ENST00000331920.6:c.3606dup	p.Ser1203GlnfsTer17	p.S1203Qfs*17	ENST00000331920	NM_000264.3	1202	-/C	22/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.858239149938094	2		667	758	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263848	16263848	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	360	748	0	ENST00000375759.3:c.10217C>T	p.Ala3406Val	p.A3406V	ENST00000375759	NM_015001.2	3406	gCt/gTt	12/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.858239149938094	2		748	825	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695968	117695968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	212	476	0	ENST00000369458.3:c.469G>A	p.Val157Met	p.V157M	ENST00000369458	NM_024626.3	157	Gtg/Atg	4/6	1	2	FACETS	0.861	0.805	0.917	0.861	0.805	0.917	CLONAL	1	TRUE	1	0.858239149938094	2		476	574	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480571	120480571	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	284	461	1	ENST00000256646.2:c.3246del	p.Ala1083GlnfsTer25	p.A1083Qfs*25	ENST00000256646	NM_024408.3	1082	aaA/aa	20/34	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.858239149938094	2		462	646	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518547	204518547	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	92	262	0	ENST00000367182.3:c.1210C>A	p.Gln404Lys	p.Q404K	ENST00000367182	NM_001278516.1	404	Caa/Aaa	11/11	1	2	FACETS	0.809	0.73	0.891	0.809	0.73	0.891	CLONAL	1	TRUE	1	0.858239149938094	2		262	265	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533873	533873	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913496	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	387	799	1	ENST00000451590.1:c.183G>T	p.Gln61His	p.Q61H	ENST00000451590	NM_001130442.1	61	caG/caT	3/5	1	2	FACETS	0.928	0.884	0.972	0.928	0.884	0.972	CLONAL	1	TRUE	1	0.858239149938094	2		800	972	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437695	49437695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565802308	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	421	818	1	ENST00000301067.7:c.5275C>T	p.Arg1759Cys	p.R1759C	ENST00000301067	NM_003482.3	1759	Cgc/Tgc	22/54	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.858239149938094	2		819	947	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784078	120784078	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	424	1087	2	ENST00000257552.2:c.907C>T	p.Arg303Cys	p.R303C	ENST00000257552	NM_002442.3	303	Cgc/Tgc	13/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.858239149938094	2		1089	942	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240999	133240999	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	314	666	0	ENST00000320574.5:c.2518del	p.Ala840ProfsTer10	p.A840Pfs*10	ENST00000320574	NM_006231.2	840	Gcc/cc	22/49	1	2	FACETS	0.957	0.907	1	0.957	0.907	1	CLONAL	1	TRUE	1	0.858239149938094	2		666	765	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562606	21562606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	137	332	0	ENST00000382592.4:c.1313C>T	p.Ala438Val	p.A438V	ENST00000382592	NM_014572.2	438	gCg/gTg	4/8	1	2	FACETS	0.953	0.879	1	0.953	0.879	1	CLONAL	1	TRUE	1	0.858239149938094	2		332	335	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619853	21619853	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	194	378	1	ENST00000382592.4:c.313C>T	p.Gln105Ter	p.Q105*	ENST00000382592	NM_014572.2	105	Cag/Tag	2/8	1	2	FACETS	0.89	0.831	0.95	0.89	0.831	0.95	CLONAL	1	TRUE	1	0.858239149938094	2		379	508	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967513	26967513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	70	252	0	ENST00000381527.3:c.656C>T	p.Ala219Val	p.A219V	ENST00000381527	NM_001260.1	219	gCt/gTt	7/13	1	2	FACETS	0.748	0.663	0.837	0.748	0.663	0.837	SUBCLONAL	1	TRUE	1	0.858239149938094	2		252	218	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060992	38060992	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	168	509	0	ENST00000250448.2:c.997del	p.Gln333ArgfsTer17	p.Q333Rfs*17	ENST00000250448	NM_004496.3	333	Cag/ag	2/2	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.858239149938094	2		509	354	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644501	3644501	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749913190	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	439	863	0	ENST00000294008.3:c.2113G>A	p.Ala705Thr	p.A705T	ENST00000294008	NM_032444.2	705	Gcc/Acc	10/15	1	2	FACETS	0.97	0.928	1	0.97	0.928	1	CLONAL	1	TRUE	1	0.858239149938094	2		863	1055	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348754	89348754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752446167	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	446	874	2	ENST00000301030.4:c.4196C>T	p.Ala1399Val	p.A1399V	ENST00000301030	NM_001256183.1	1399	gCg/gTg	9/13	1	2	FACETS	0.936	0.896	0.977	0.936	0.896	0.977	CLONAL	1	TRUE	1	0.858239149938094	2		876	1110	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89869675	89869675	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	335	596	0	ENST00000389301.3:c.784del	p.Met262CysfsTer13	p.M262Cfs*13	ENST00000389301	NM_000135.2	262	Atg/tg	8/43	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.858239149938094	2		596	764	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435824	56435824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	245	643	0	ENST00000407977.2:c.1313C>T	p.Ala438Val	p.A438V	ENST00000407977		438	gCc/gTc	9/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.858239149938094	2		643	560	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227084	2227084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759654625	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	358	903	1	ENST00000398665.3:c.4564G>A	p.Ala1522Thr	p.A1522T	ENST00000398665	NM_032482.2	1522	Gcc/Acc	27/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.858239149938094	2		904	810	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210584	5210584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	319	705	1	ENST00000357368.4:c.5383C>T	p.Pro1795Ser	p.P1795S	ENST00000357368	NM_002850.3	1795	Ccg/Tcg	35/38	1	2	FACETS	0.959	0.91	1	0.959	0.91	1	CLONAL	1	TRUE	1	0.858239149938094	2		706	775	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244152	5244152	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs773187155	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	342	917	0	ENST00000357368.4:c.1330A>G	p.Ile444Val	p.I444V	ENST00000357368	NM_002850.3	444	Att/Gtt	11/38	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.858239149938094	2		917	788	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945781	17945781	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	344	861	2	ENST00000458235.1:c.2079del	p.Glu694SerfsTer62	p.E694Sfs*62	ENST00000458235	NM_000215.3	693	ccC/cc	16/24	1	2	FACETS	0.932	0.886	0.979	0.932	0.886	0.979	CLONAL	1	TRUE	1	0.858239149938094	2		863	860	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308146	30308146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs574899763	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	385	604	0	ENST00000262643.3:c.283C>T	p.Arg95Trp	p.R95W	ENST00000262643	NM_001238.2	95	Cgg/Tgg	5/12	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.858239149938094	2		604	850	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921169	50921169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755297873	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	407	875	0	ENST00000440232.2:c.3289C>T	p.Arg1097Trp	p.R1097W	ENST00000440232	NM_002691.3	1097	Cgg/Tgg	27/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.858239149938094	2		875	916	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873738	151873738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770069367	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	252	466	0	ENST00000262189.6:c.8800C>T	p.Pro2934Ser	p.P2934S	ENST00000262189	NM_170606.2	2934	Cca/Tca	38/59	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.858239149938094	2		466	584	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396481	139396482	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	355	951	0	ENST00000277541.6:c.5443dup	p.Asp1815GlyfsTer19	p.D1815Gfs*19	ENST00000277541	NM_017617.3	1815	gac/gGac	29/34	1	2	FACETS	0.926	0.881	0.972	0.926	0.881	0.972	CLONAL	1	TRUE	1	0.858239149938094	2		951	893	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178680	56178680	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054478-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	19	177	0	ENST00000399503.3:c.3653T>A	p.Ile1218Asn	p.I1218N	ENST00000399503	NM_005921.1	1218	aTt/aAt	14/20	1	2	FACETS	0.246	0.187	0.314	0.246	0.187	0.314	SUBCLONAL	1	TRUE	1	0.858239149938094	2		177	180	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0054479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	582	603	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.327267719526111	5	FACETS	0.932	0.9	0.964	1	0.995	1	CLONAL	5	TRUE	1	0.327267719526111	5		603	1138	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0054479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	589	443	1	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.3262915747624	3	FACETS	0.92	0.885	0.955	0.92	0.885	0.955	CLONAL	3	TRUE	0	0.327267719526111	3		444	1518	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780828	9780828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1441813233	NA	P-0054479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	311	837	0	ENST00000377346.4:c.1550G>A	p.Arg517Gln	p.R517Q	ENST00000377346	NM_005026.3	517	cGg/cAg	13/24	0.327267719526111	3	FACETS	0.767	0.722	0.813			1	SUBCLONAL	2	TRUE	NA	0.327267719526111	3		837	1442	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802538	139802538	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756632275	NA	P-0054479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	169	849	0	ENST00000247668.2:c.383G>A	p.Arg128His	p.R128H	ENST00000247668	NM_021138.3	128	cGc/cAc	5/11	0.314549074098614	2	FACETS	0.826	0.758	0.898	0.413	0.379	0.449	CLONAL	1	TRUE	0	0.327267719526111	2		849	1250	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202561	67202561	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1052688	NA	P-0054479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1204	172	984	0	ENST00000312629.5:c.1370C>G	p.Ser457Trp	p.S457W	ENST00000312629	NM_003952.2	457	tCg/tGg	15/15	0.30322457943292	3	FACETS	0.889	0.816	0.966	0.444	0.408	0.483	CLONAL	1	TRUE	1	0.327267719526111	3		984	1376	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609317	39609317	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	74	265	0	ENST00000262039.4:c.1619C>T	p.Ser540Phe	p.S540F	ENST00000262039	NM_002647.2	540	tCt/tTt	15/25	0.205703927978128	4	FACETS	0.997	0.873	1	0.499	0.436	0.565	CLONAL	1	TRUE	2	0.327267719526111	4		265	602	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348568	56348568	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	60	268	0	ENST00000348428.3:c.376G>C	p.Gly126Arg	p.G126R	ENST00000348428	NM_006785.3	126	Gga/Cga	2/17	0.205703927978128	4	FACETS	1	0.876	1	0.508	0.438	0.584	CLONAL	1	TRUE	2	0.327267719526111	4		268	479	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129918	55129918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501501	NA	P-0054479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	216	530	0	ENST00000257290.5:c.452G>A	p.Arg151His	p.R151H	ENST00000257290	NM_006206.4	151	cGc/cAc	4/23	NA	2	FACETS	0.873	0.814	0.933			1	INDETERMINATE	2	TRUE	NA	0.327267719526111	2		530	756	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0054480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	198	758	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.362019348848917	2	FACETS	0.848	0.791	0.907	0.848	0.791	0.907	CLONAL	2	TRUE	0	0.398911155331032	2		758	585	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063718	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0054480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	141	381	0	ENST00000412916.2:c.165+2dup		p.X55_splice	ENST00000412916		55			0.367926459957047	2	FACETS	0.873	0.803	0.944	0.873	0.803	0.944	CLONAL	2	TRUE	0	0.398911155331032	2		381	405	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169355	11169355	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	180	409	0	ENST00000361445.4:c.7520A>G	p.Lys2507Arg	p.K2507R	ENST00000361445	NM_004958.3	2507	aAg/aGg	56/58	0.340167627920307	3	FACETS	0.913	0.846	0.981	0.913	0.846	0.981	CLONAL	2	TRUE	1	0.398911155331032	3		409	593	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120805860	120805860	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	351	987	2	ENST00000257552.2:c.218G>T	p.Gly73Val	p.G73V	ENST00000257552	NM_002442.3	73	gGg/gTg	4/15	0.370705941194105	4	FACETS	0.937	0.887	0.989	0.937	0.887	0.989	CLONAL	2	TRUE	2	0.398911155331032	4		989	1313	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857527	68857528	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	160	387	0	ENST00000261769.5:c.2164dup	p.Ile722AsnfsTer26	p.I722Nfs*26	ENST00000261769	NM_004360.3	721	cta/ctAa	13/16	0.367926459957047	2	FACETS	0.96	0.89	1	0.96	0.89	1	CLONAL	2	TRUE	0	0.398911155331032	2		387	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578538	7578538	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	136	1004	0	ENST00000269305.4:c.392A>G	p.Asn131Ser	p.N131S	ENST00000269305	NM_001126112.2	131	aAc/aGc	5/11	0.131282941938753	3	FACETS	1	0.983	1	0.454	0.412	0.498	INDETERMINATE	1	TRUE	0	0.25	3		1004	899	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0054481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	73	573	0	ENST00000269305.4:c.783-1G>C		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.131282941938753	3	FACETS	1	0.965	1	0.432	0.378	0.489	INDETERMINATE	1	TRUE	0	0.25	3		573	507	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593405	48593405	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	192	249	0	ENST00000342988.3:c.1156G>C	p.Gly386Arg	p.G386R	ENST00000342988	NM_005359.5	386	Ggt/Cgt	10/12	0.519354209963594	2	FACETS	0.902	0.846	0.958	0.902	0.846	0.958	CLONAL	2	TRUE	0	0.521640381090147	2		249	408	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944170	71944170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773191339	NA	P-0054483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	206	743	1	ENST00000298229.2:c.2003G>A	p.Arg668Gln	p.R668Q	ENST00000298229	NM_001567.3	668	cGg/cAg	17/28	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.521640381090147	2		744	766	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579714	7579714	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	199	629	0	ENST00000269305.4:c.82del	p.Glu28LysfsTer16	p.E28Kfs*16	ENST00000269305	NM_001126112.2	28	Gaa/aa	3/11	0.492404232954118	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.521640381090147	1		629	495	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435576	110435576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1450865521	NA	P-0054483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	336	510	2	ENST00000375856.3:c.2825C>T	p.Ala942Val	p.A942V	ENST00000375856	NM_003749.2	942	gCg/gTg	1/2	0.521640381090147	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.521640381090147	3		512	717	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871782	35871782	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	163	544	0	ENST00000216797.5:c.724G>C	p.Asp242His	p.D242H	ENST00000216797	NM_020529.2	242	Gat/Cat	5/6	0.519354209963594	2	FACETS	0.976	0.9	1	0.488	0.45	0.528	CLONAL	1	TRUE	0	0.521640381090147	2		544	640	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306761	41306761	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	328	431	0	ENST00000373198.4:c.898G>C	p.Val300Leu	p.V300L	ENST00000373198	NM_133170.3	300	Gtg/Ctg	7/32	0.376865706566409	3	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.521640381090147	3		431	659	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486202	8486202	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	89	360	0	ENST00000356435.5:c.2615A>C	p.Glu872Ala	p.E872A	ENST00000356435		872	gAg/gCg	17/35	NA	2	FACETS	0.93	0.831	1			1	INDETERMINATE	1	TRUE	NA	0.521640381090147	2		360	367	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920206	76920206	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	119	330	0	ENST00000373344.5:c.3871T>G	p.Ser1291Ala	p.S1291A	ENST00000373344	NM_000489.3	1291	Tct/Gct	11/35	0.134647537909048	0	FACETS	0.441	0.4	0.484			1	INDETERMINATE	1	TRUE	0	0.521640381090147	0		330	495	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664868	29664868	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1193716348	NA	P-0054484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	33	334	0	ENST00000356175.3:c.6611G>A	p.Trp2204Ter	p.W2204*	ENST00000356175	NM_000267.3	2204	tGg/tAg	43/57	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		334	567	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874166	155874166	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs777520196	NA	P-0054485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	262	480	0	ENST00000368323.3:c.365G>T	p.Arg122Leu	p.R122L	ENST00000368323	NM_006912.5	122	cGa/cTa	5/6	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.732385266095942	2		480	657	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724649	43724649	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	316	589	0	ENST00000382044.4:c.3418A>G	p.Asn1140Asp	p.N1140D	ENST00000382044	NM_001141980.1	1140	Aat/Gat	17/28	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.732385266095942	2		589	796	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133546	55133546	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	219	467	0	ENST00000257290.5:c.850G>C	p.Asp284His	p.D284H	ENST00000257290	NM_006206.4	284	Gac/Cac	6/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.732385266095942	2		467	546	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0054487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	150	392	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.437234430104771	2		392	476	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781476	3781476	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0054487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	97	526	0	ENST00000262367.5:c.4891-2A>G		p.X1631_splice	ENST00000262367	NM_004380.2	1631			1	2	FACETS	0.688	0.614	0.766	0.688	0.614	0.766	SUBCLONAL	1	TRUE	1	0.437234430104771	2		526	645	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205108	123205109	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	179	236	0	ENST00000218089.9:c.2469dup	p.Glu824Ter	p.E824*	ENST00000218089	NM_001042749.1	823	tct/tcTt	25/35	1	1	FACETS	1	0.984	1	1	0.994	1	CLONAL	2	TRUE	0	0.437234430104771	1		236	288	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0054488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	113	76	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.536529612657186	2		76	386	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128701	64128701	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	178	722	0	ENST00000334205.4:c.558C>G	p.Phe186Leu	p.F186L	ENST00000334205	NM_003942.2	186	ttC/ttG	5/17	0.218367595991834	3	FACETS	0.836	0.77	0.904	0.418	0.385	0.452	INDETERMINATE	1	TRUE	1	0.536529612657186	3		722	1007	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446931	18446931	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	68	243	0	ENST00000266497.5:c.1016C>A	p.Ser339Tyr	p.S339Y	ENST00000266497		339	tCt/tAt	4/31	1	2	FACETS	0.785	0.688	0.888	0.785	0.688	0.888	SUBCLONAL	1	TRUE	1	0.536529612657186	2		243	323	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428642	49428642	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	160	597	0	ENST00000301067.7:c.10308G>C	p.Lys3436Asn	p.K3436N	ENST00000301067	NM_003482.3	3436	aaG/aaC	35/54	1	2	FACETS	0.718	0.658	0.78	0.718	0.658	0.78	SUBCLONAL	1	TRUE	1	0.536529612657186	2		597	831	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435734	49435734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	92	684	0	ENST00000301067.7:c.6149G>A	p.Arg2050Lys	p.R2050K	ENST00000301067	NM_003482.3	2050	aGa/aAa	29/54	1	2	FACETS	0.399	0.354	0.447	0.399	0.354	0.447	SUBCLONAL	1	TRUE	1	0.536529612657186	2		684	860	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120739	115120740	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0054488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	304	773	0	ENST00000257566.3:c.266dup	p.Leu90PhefsTer21	p.L90Ffs*21	ENST00000257566	NM_016569.3	89	cct/ccCt	1/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.536529612657186	2		773	1040	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216705	7216705	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	149	431	0	ENST00000380728.2:c.718C>T	p.Gln240Ter	p.Q240*	ENST00000380728		240	Cag/Tag	8/11	0.536529612657186	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.536529612657186	1		431	400	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321677	30321677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	149	430	0	ENST00000322652.5:c.1532G>A	p.Gly511Glu	p.G511E	ENST00000322652	NM_015355.2	511	gGa/gAa	13/16	1	2	FACETS	0.803	0.735	0.873	0.803	0.735	0.873	CLONAL	1	TRUE	1	0.536529612657186	2		430	692	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130271	11130271	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	53	525	0	ENST00000358026.2:c.2510C>G	p.Ser837Cys	p.S837C	ENST00000358026	NM_001128849.1	837	tCc/tGc	18/36	1	2	FACETS	0.249	0.211	0.29	0.249	0.211	0.29	SUBCLONAL	1	TRUE	1	0.536529612657186	2		525	795	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610520	215610520	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0054488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	42	359	0	ENST00000260947.4:c.1736C>G	p.Ser579Ter	p.S579*	ENST00000260947	NM_000465.2	579	tCa/tGa	8/11	1	2	FACETS	0.278	0.231	0.329	0.278	0.231	0.329	SUBCLONAL	1	TRUE	1	0.536529612657186	2		359	564	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176576	142176576	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	70	309	0	ENST00000350721.4:c.7525G>C	p.Glu2509Gln	p.E2509Q	ENST00000350721	NM_001184.3	2509	Gaa/Caa	45/47	1	2	FACETS	0.496	0.433	0.564	0.496	0.433	0.564	SUBCLONAL	1	TRUE	1	0.536529612657186	2		309	526	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675556	30675556	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	92	707	0	ENST00000376406.3:c.2800G>C	p.Glu934Gln	p.E934Q	ENST00000376406	NM_014641.2	934	Gaa/Caa	8/15	1	2	FACETS	0.355	0.315	0.398	0.355	0.315	0.398	SUBCLONAL	1	TRUE	1	0.536529612657186	2		707	966	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0054488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	17	423	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	1	2	FACETS	0.107	0.079	0.14	0.107	0.079	0.14	SUBCLONAL	1	TRUE	1	0.536529612657186	2		423	592	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	213	580	0	ENST00000206249.3:c.1607T>A	p.Leu536His	p.L536H	ENST00000206249	NM_000125.3	536	cTc/cAc	8/8	1	2	FACETS	0.944	0.879	1	0.944	0.879	1	CLONAL	1	TRUE	1	0.536529612657186	2		580	841	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	17	584	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	1	2	FACETS	0.075	0.055	0.098	0.075	0.055	0.098	SUBCLONAL	1	TRUE	1	0.536529612657186	2		584	848	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151946996	151946996	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0054488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	44	333	0	ENST00000262189.6:c.1778C>G	p.Ser593Ter	p.S593*	ENST00000262189	NM_170606.2	593	tCa/tGa	13/59	1	2	FACETS	0.359	0.301	0.423	0.359	0.301	0.423	SUBCLONAL	1	TRUE	1	0.536529612657186	2		333	457	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338628	70338628	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	63	735	0	ENST00000374080.3:c.24C>G	p.Ser8Arg	p.S8R	ENST00000374080		8	agC/agG	1/45	1	2	FACETS	0.267	0.23	0.308	0.267	0.23	0.308	SUBCLONAL	1	TRUE	1	0.536529612657186	2		735	878	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0054489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	407	91	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.50195840438355	7	FACETS	1	0.972	1	1	0.972	1	CLONAL	7	TRUE	0	0.50195840438355	7		91	522	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459194	120459194	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1479580345	NA	P-0054489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	76	691	0	ENST00000256646.2:c.6151C>T	p.Arg2051Trp	p.R2051W	ENST00000256646	NM_024408.3	2051	Cgg/Tgg	34/34	0.50195840438355	4	FACETS	1	0.973	1	0.461	0.407	0.517	CLONAL	1	TRUE	1	0.50195840438355	4		691	329	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804951	43804951	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375532666	NA	P-0054489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	97	487	0	ENST00000372470.3:c.401C>T	p.Ala134Val	p.A134V	ENST00000372470	NM_005373.2	134	gCt/gTt	4/12	0.50195840438355	4	FACETS	1	0.974	1	0.806	0.732	0.882	CLONAL	2	TRUE	1	0.50195840438355	4		487	240	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943369	71943369	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	94	759	0	ENST00000298229.2:c.1701G>C	p.Glu567Asp	p.E567D	ENST00000298229	NM_001567.3	567	gaG/gaC	14/28	0.50195840438355	5	FACETS	1	0.978	1	0.465	0.415	0.517	CLONAL	1	TRUE	2	0.50195840438355	5		759	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0054490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	243	708	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	0.67641397527305	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.67641397527305	1		708	410	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198480	108198481	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	73	337	0	ENST00000278616.4:c.7088dup	p.Ala2364GlyfsTer9	p.A2364Gfs*9	ENST00000278616	NM_000051.3	2362	gaa/gAaa	48/63	1	2	FACETS	0.805	0.713	0.903	0.805	0.713	0.903	CLONAL	1	TRUE	1	0.67641397527305	2		337	268	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591725	38591725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	127	415	0	ENST00000299084.4:c.184G>A	p.Gly62Arg	p.G62R	ENST00000299084	NM_152594.2	62	Gga/Aga	2/7	1	2	FACETS	0.884	0.807	0.963	0.884	0.807	0.963	CLONAL	1	TRUE	1	0.67641397527305	2		415	425	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024472	16024487	+	frameshift_variant	Frame_Shift_Del	DEL	CTTACGGCGGCCCTGA	CTTACGGCGGCCCTGA	-	novel	NA	P-0054490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	157	522	0	ENST00000268712.3:c.1731_1746del	p.Ser577ArgfsTer8	p.S577Rfs*8	ENST00000268712	NM_006311.3	577	agTCAGGGCCGCCGTAAG/ag	16/46	0.67641397527305	1	FACETS	0.978	0.913	1	0.978	0.913	1	CLONAL	1	TRUE	0	0.67641397527305	1		522	314	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	55	375	0				ENST00000310581	NM_198253.2	-/1132			0.237471379460041	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	0	0.237471379460041	1		375	305	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188183	11188183	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057524049	NA	P-0054491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	32	445	0	ENST00000361445.4:c.5911G>A	p.Ala1971Thr	p.A1971T	ENST00000361445	NM_004958.3	1971	Gcc/Acc	43/58	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	FALSE	1	0.237471379460041	2		445	224	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584834	52584834	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0054491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	47	566	0	ENST00000394830.3:c.4289-1G>C		p.X1430_splice	ENST00000394830	NM_018313.4	1430			0.206037107114553	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	2	FALSE	0	0.237471379460041	2		566	195	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0054492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	53	720	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	0.619	0.53	0.716	0.619	0.53	0.716	SUBCLONAL	1	TRUE	1	0.451799278310324	2		720	379	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	50	375	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.752	0.641	0.872	1	0.964	1	SUBCLONAL	2	TRUE	1	0.201611009521051	2		375	330	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0054494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	42	477	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.201611009521051	2		477	369	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0054494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	47	465	1	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.911	0.768	1	0.911	0.768	1	CLONAL	1	TRUE	1	0.201611009521051	2		466	512	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149817	202149817	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	65	564	0	ENST00000358485.4:c.1258C>T	p.Gln420Ter	p.Q420*	ENST00000358485	NM_001080125.1	420	Cag/Tag	8/9	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.201611009521051	2		564	594	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0054494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	16	281	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	1	2	FACETS	0.52	0.384	0.684	0.52	0.384	0.684	SUBCLONAL	1	TRUE	1	0.201611009521051	2		281	305	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400022	139400023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0054494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	71	942	1	ENST00000277541.6:c.4325dup	p.Pro1443AlafsTer36	p.P1443Afs*36	ENST00000277541	NM_017617.3	1442	ccg/ccCg	25/34	1	2	FACETS	0.72	0.627	0.822	0.72	0.627	0.822	SUBCLONAL	1	TRUE	1	0.201611009521051	2		943	978	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533881	533881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs727503093	NA	P-0054494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	79	828	2	ENST00000451590.1:c.175G>A	p.Ala59Thr	p.A59T	ENST00000451590	NM_001130442.1	59	Gcc/Acc	3/5	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.201611009521051	2		830	756	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439586	51439586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1372032935	NA	P-0054494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	29	308	0	ENST00000262662.1:c.151G>A	p.Glu51Lys	p.E51K	ENST00000262662		51	Gag/Aag	4/4	1	2	FACETS	0.813	0.653	0.994	0.813	0.653	0.994	CLONAL	1	TRUE	1	0.201611009521051	2		308	354	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119007	3119007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769503200	NA	P-0054494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	88	806	3	ENST00000078429.4:c.691G>A	p.Ala231Thr	p.A231T	ENST00000078429	NM_002067.2	231	Gcc/Acc	5/7	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.201611009521051	2		809	738	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919865	50919866	+	splice_acceptor_variant	Splice_Site	INS	-	-	G	rs756872503	NA	P-0054494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	66	982	7	ENST00000440232.2:c.2959dup		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	0.792	0.686	0.907	0.792	0.686	0.907	CLONAL	1	TRUE	1	0.201611009521051	2		989	827	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600595	43600595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	90	740	2	ENST00000355710.3:c.821C>T	p.Ala274Val	p.A274V	ENST00000355710	NM_020975.4	274	gCg/gTg	4/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.201611009521051	2		742	728	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281803	49281803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	79	639	0	ENST00000282018.3:c.850C>T	p.His284Tyr	p.H284Y	ENST00000282018	NM_020377.2	284	Cat/Tat	1/1	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.201611009521051	2		639	704	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133217	30133217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	65	603	0	ENST00000263025.4:c.281G>A	p.Arg94His	p.R94H	ENST00000263025	NM_002746.2	94	cGc/cAc	2/9	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.201611009521051	2		603	617	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349388	89349388	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs761848111	NA	P-0054494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	128	807	2	ENST00000301030.4:c.3562C>T	p.Arg1188Ter	p.R1188*	ENST00000301030	NM_001256183.1	1188	Cga/Tga	9/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.201611009521051	2		809	992	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288260	21288260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1356309955	NA	P-0054494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	92	673	1	ENST00000354336.3:c.505C>T	p.Arg169Trp	p.R169W	ENST00000354336	NM_005207.3	169	Cgg/Tgg	2/3	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.201611009521051	2		674	726	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067867	30067867	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771675702	NA	P-0054494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	64	470	0	ENST00000338641.4:c.1052G>A	p.Arg351His	p.R351H	ENST00000338641	NM_000268.3	351	cGc/cAc	11/16	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.201611009521051	2		470	553	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530374	187530374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	45	358	1	ENST00000441802.2:c.10169G>T	p.Gly3390Val	p.G3390V	ENST00000441802	NM_005245.3	3390	gGa/gTa	16/27	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.201611009521051	2		359	416	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409977	139409977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774622686	NA	P-0054494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	118	1111	0	ENST00000277541.6:c.1861C>T	p.Arg621Cys	p.R621C	ENST00000277541	NM_017617.3	621	Cgc/Tgc	11/34	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.201611009521051	2		1111	1076	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130334	11130334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1480398200	NA	P-0054496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	211	811	1	ENST00000358026.2:c.2573C>T	p.Thr858Met	p.T858M	ENST00000358026	NM_001128849.1	858	aCg/aTg	18/36	0.280547972528158	3	FACETS	0.844	0.783	0.906	0.844	0.783	0.906	CLONAL	2	TRUE	1	0.283248420493596	3		812	1008	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067836	30067836	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315499	NA	P-0054496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	153	498	0	ENST00000338641.4:c.1021C>T	p.Arg341Ter	p.R341*	ENST00000338641	NM_000268.3	341	Cga/Tga	11/16	0.196719205284039	3	FACETS	1	0.962	1	0.719	0.661	0.779	CLONAL	2	TRUE	0	0.283248420493596	3		498	572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578412	7578412	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519747	NA	P-0054496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	249	823	0	ENST00000269305.4:c.518T>A	p.Val173Glu	p.V173E	ENST00000269305	NM_001126112.2	173	gTg/gAg	5/11	0.244979772088304	2	FACETS	0.849	0.794	0.905	0.849	0.794	0.905	CLONAL	2	TRUE	0	0.283248420493596	2		823	1036	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437266	220437266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753111199	NA	P-0054496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	168	1280	1	ENST00000243786.2:c.170G>A	p.Arg57Gln	p.R57Q	ENST00000243786	NM_002191.3	57	cGg/cAg	1/2	0.280547972528158	3	FACETS	0.994	0.911	1	0.497	0.455	0.541	CLONAL	1	TRUE	1	0.283248420493596	3		1281	1362	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	218478	218482	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTC	GGGTC	-	novel	NA	P-0054496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	70	292	0	ENST00000264932.6:c.8_12del	p.Gly3AlafsTer34	p.G3Afs*34	ENST00000264932	NM_004168.2	3	gGGGTC/g	1/15	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.283248420493596	NA		292	360	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53241028	53241028	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	245	667	1	ENST00000375401.3:c.1183C>T	p.Gln395Ter	p.Q395*	ENST00000375401	NM_004187.3	395	Cag/Tag	9/26	0.239691949435777	2	FACETS	0.89	0.832	0.949	0.89	0.832	0.949	CLONAL	2	TRUE	0	0.283248420493596	2		668	972	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185061	123185061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	95	451	0	ENST00000218089.9:c.1108C>T	p.Arg370Trp	p.R370W	ENST00000218089	NM_001042749.1	370	Cgg/Tgg	12/35	0.195127215013821	3	FACETS	1	0.956	1	0.574	0.51	0.642	CLONAL	1	TRUE	1	0.213405029309217	3		451	858	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100465	102100480	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCAGAACCGTTTCC	CAGCAGAACCGTTTCC	-	novel	NA	P-0054497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	40	473	0	ENST00000282441.5:c.1312_1327del	p.Gln438ThrfsTer21	p.Q438Tfs*21	ENST00000282441	NM_001130145.2	437	CAGCAGAACCGTTTCCca/ca	9/9	0.195127215013821	3	FACETS	0.585	0.485	0.697	0.293	0.242	0.349	SUBCLONAL	1	TRUE	1	0.213405029309217	3		473	709	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21643241	21643241	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	88	640	0	ENST00000421138.2:c.286C>G	p.Gln96Glu	p.Q96E	ENST00000421138		96	Cag/Gag	5/16	1	2	FACETS	0.794	0.701	0.893	0.794	0.701	0.893	SUBCLONAL	1	TRUE	1	0.213405029309217	2		640	1039	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0054498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	426	913	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.208755567707208	2	FACETS	1	0.978	1	1	0.997	1	CLONAL	5	FALSE	0	0.208755567707208	2		913	796	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0054498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	225	816	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.14419955473045	4	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	FALSE	2	0.208755567707208	4		816	1274	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797314	135797314	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	160	333	0	ENST00000298552.3:c.555del	p.Tyr185Ter	p.Y185*	ENST00000298552	NM_001162426.1	185	taC/ta	7/23	0.208755567707208	0	FACETS	0.954	0.908	0.997			1	CLONAL	6	FALSE	0	0.208755567707208	0		333	212	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420411	49420411	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1241895194	NA	P-0054498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	366	710	0	ENST00000301067.7:c.15338A>G	p.Tyr5113Cys	p.Y5113C	ENST00000301067	NM_003482.3	5113	tAc/tGc	48/54	1	2	FACETS	0.969	0.922	1	1	0.997	1	CLONAL	4	FALSE	1	0.208755567707208	2		710	905	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196324	106196324	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	211	364	0	ENST00000380013.4:c.4657C>G	p.Gln1553Glu	p.Q1553E	ENST00000380013	NM_001127208.2	1553	Cag/Gag	11/11	1	2	FACETS	1	0.955	1	1	0.996	1	CLONAL	4	FALSE	1	0.208755567707208	2		364	495	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56882345	56882345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	307	555	0	ENST00000519728.1:c.1043C>T	p.Ser348Phe	p.S348F	ENST00000519728	NM_002350.3	348	tCt/tTt	10/13	1	2	FACETS	0.968	0.917	1	1	0.997	1	CLONAL	4	FALSE	1	0.208755567707208	2		555	760	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522567	187522575	+	frameshift_variant	Frame_Shift_Del	DEL	CATAGATGA	CATAGATGA	T	novel	NA	P-0054498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	206	401	0	ENST00000441802.2:c.11488_11496delinsA	p.Ser3830AsnfsTer16	p.S3830Nfs*16	ENST00000441802	NM_005245.3	3830	TCATCTATG/A	21/27	1	2	FACETS	0.958	0.897	1	1	0.995	1	CLONAL	4	FALSE	1	0.208755567707208	2		401	515	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	60	703	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.673	0.579	0.776	0.673	0.579	0.776	SUBCLONAL	1	TRUE	1	0.23	2		703	775	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794439	42794439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370252719	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	98	1264	0	ENST00000575354.2:c.1519C>T	p.Arg507Cys	p.R507C	ENST00000575354	NM_015125.3	507	Cgc/Tgc	10/20	1	2	FACETS	0.758	0.674	0.848	0.758	0.674	0.848	SUBCLONAL	1	TRUE	1	0.23	2		1264	1124	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	73	415	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.23	2		415	484	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805672	89805672	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs17227396	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	115	698	0	ENST00000389301.3:c.4036G>A	p.Ala1346Thr	p.A1346T	ENST00000389301	NM_000135.2	1346	Gcg/Acg	41/43	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.23	2		698	723	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748272	41748272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774521395	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	71	928	2	ENST00000226382.2:c.497C>T	p.Ala166Val	p.A166V	ENST00000226382	NM_003924.3	166	gCg/gTg	3/3	1	2	FACETS	0.617	0.537	0.704	0.617	0.537	0.704	SUBCLONAL	1	TRUE	1	0.23	2		930	1001	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	12	342	1	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	0.33	0.231	0.453	0.33	0.231	0.453	SUBCLONAL	1	TRUE	1	0.23	2		343	316	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	42	449	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.584	0.487	0.693	0.584	0.487	0.693	SUBCLONAL	1	TRUE	1	0.23	2		450	625	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	56	438	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.23	2		438	360	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404720	70404720	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369109149	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	62	530	0	ENST00000373644.4:c.2234G>A	p.Arg745Gln	p.R745Q	ENST00000373644	NM_030625.2	745	cGa/cAa	4/12	1	2	FACETS	0.911	0.787	1	0.911	0.787	1	CLONAL	1	TRUE	1	0.23	2		530	592	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922294	100922294	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1315135533	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	26	321	1	ENST00000325455.5:c.2218C>T	p.Arg740Ter	p.R740*	ENST00000325455	NM_001202474.3	740	Cga/Tga	5/8	1	2	FACETS	0.756	0.6	0.935	0.756	0.6	0.935	CLONAL	1	TRUE	1	0.23	2		322	299	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341141	8341141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1347452833	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	29	539	1	ENST00000356435.5:c.5075G>A	p.Arg1692His	p.R1692H	ENST00000356435		1692	cGt/cAt	30/35	1	2	FACETS	0.652	0.523	0.798	0.652	0.523	0.798	SUBCLONAL	1	TRUE	1	0.23	2		540	387	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868176	45868176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559154781	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	64	1120	3	ENST00000391945.4:c.514G>A	p.Ala172Thr	p.A172T	ENST00000391945	NM_000400.3	172	Gct/Act	7/23	1	2	FACETS	0.596	0.514	0.685	0.596	0.514	0.685	SUBCLONAL	1	TRUE	1	0.23	2		1123	934	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716329	52716329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863225094	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	41	776	1	ENST00000322088.6:c.773G>A	p.Arg258His	p.R258H	ENST00000322088	NM_014225.5	258	cGc/cAc	6/15	1	2	FACETS	0.436	0.362	0.52	0.436	0.362	0.52	SUBCLONAL	1	TRUE	1	0.23	2		777	817	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692802	89692802	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123320	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	22	386	0	ENST00000371953.3:c.286C>T	p.Pro96Ser	p.P96S	ENST00000371953	NM_000314.4	96	Cca/Tca	5/9	1	2	FACETS	0.543	0.421	0.686	0.543	0.421	0.686	SUBCLONAL	1	TRUE	1	0.23	2		386	352	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508554	106508554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755975307	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	60	470	0	ENST00000359195.3:c.548C>T	p.Pro183Leu	p.P183L	ENST00000359195	NM_002649.2	183	cCg/cTg	2/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.23	2		470	396	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885578	111885578	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs751470371	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	84	1066	0	ENST00000341259.2:c.1355C>G	p.Ala452Gly	p.A452G	ENST00000341259	NM_005475.2	452	gCc/gGc	7/8	1	2	FACETS	0.747	0.658	0.842	0.747	0.658	0.842	SUBCLONAL	1	TRUE	1	0.23	2		1066	978	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107136	27107137	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	133	681	0	ENST00000324856.7:c.6749_6750del	p.Glu2250ValfsTer27	p.E2250Vfs*27	ENST00000324856	NM_006015.4	2249	tcAGag/tcag	20/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.23	2		681	871	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532726	46532726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139871417	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	20	432	1	ENST00000262741.5:c.352C>T	p.Arg118Trp	p.R118W	ENST00000262741	NM_003629.3	118	Cgg/Tgg	4/10	1	2	FACETS	0.464	0.354	0.593	0.464	0.354	0.593	SUBCLONAL	1	TRUE	1	0.23	2		433	375	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576129	88576129	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	53	946	1	ENST00000360948.2:c.1544A>G	p.Gln515Arg	p.Q515R	ENST00000360948	NM_001012338.2	515	cAg/cGg	13/19	1	2	FACETS	0.486	0.413	0.567	0.486	0.413	0.567	SUBCLONAL	1	TRUE	1	0.23	2		947	948	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524541	176524541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759861753	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	112	1194	0	ENST00000292408.4:c.2273G>A	p.Arg758His	p.R758H	ENST00000292408	NM_213647.1	758	cGc/cAc	18/18	1	2	FACETS	0.963	0.865	1	0.963	0.865	1	CLONAL	1	TRUE	1	0.23	2		1194	1011	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461100	120461100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs312262797	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	40	543	0	ENST00000256646.2:c.5858G>A	p.Arg1953His	p.R1953H	ENST00000256646	NM_024408.3	1953	cGc/cAc	32/34	1	2	FACETS	0.629	0.522	0.748	0.629	0.522	0.748	SUBCLONAL	1	TRUE	1	0.23	2		543	553	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261146	16261146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769982439	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	50	652	2	ENST00000375759.3:c.8411C>T	p.Ala2804Val	p.A2804V	ENST00000375759	NM_015001.2	2804	gCg/gTg	11/15	1	2	FACETS	0.683	0.578	0.797	0.683	0.578	0.797	SUBCLONAL	1	TRUE	1	0.23	2		654	637	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88676898	88676898	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747371306	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	62	664	1	ENST00000372037.3:c.683G>A	p.Arg228Gln	p.R228Q	ENST00000372037	NM_004329.2	228	cGa/cAa	9/13	1	2	FACETS	0.681	0.587	0.783	0.681	0.587	0.783	SUBCLONAL	1	TRUE	1	0.23	2		665	792	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316397	14316397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782457908	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	30	473	0	ENST00000256196.4:c.208G>A	p.Ala70Thr	p.A70T	ENST00000256196		70	Gca/Aca	3/6	1	2	FACETS	0.539	0.433	0.659	0.539	0.433	0.659	SUBCLONAL	1	TRUE	1	0.23	2		473	484	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184411	7184411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375845481	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	92	885	1	ENST00000302850.5:c.890G>A	p.Arg297Gln	p.R297Q	ENST00000302850	NM_000208.2	297	cGg/cAg	3/22	1	2	FACETS	0.696	0.616	0.781	0.696	0.616	0.781	SUBCLONAL	1	TRUE	1	0.23	2		886	1150	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190747	11190747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759603938	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	79	1005	3	ENST00000361445.4:c.5452C>T	p.Arg1818Cys	p.R1818C	ENST00000361445	NM_004958.3	1818	Cgt/Tgt	39/58	1	2	FACETS	0.672	0.589	0.762	0.672	0.589	0.762	SUBCLONAL	1	TRUE	1	0.23	2		1008	1022	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097731	8097731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	123	687	1	ENST00000346208.3:c.113C>T	p.Ala38Val	p.A38V	ENST00000346208		38	gCg/gTg	2/6	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.23	2		688	810	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753452	42753452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	51	1082	3	ENST00000222329.4:c.812C>T	p.Thr271Met	p.T271M	ENST00000222329	NM_006494.2	271	aCg/aTg	4/4	1	2	FACETS	0.454	0.384	0.531	0.454	0.384	0.531	SUBCLONAL	1	TRUE	1	0.23	2		1085	977	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182598	99182598	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253335546	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	33	597	3	ENST00000074304.5:c.2401G>A	p.Val801Met	p.V801M	ENST00000074304	NM_001134224.1	801	Gtg/Atg	22/26	1	2	FACETS	0.523	0.425	0.634	0.523	0.425	0.634	SUBCLONAL	1	TRUE	1	0.23	2		600	549	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486587	56486587	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	116	682	0	ENST00000267101.3:c.1166C>G	p.Thr389Arg	p.T389R	ENST00000267101	NM_001982.3	389	aCa/aGa	10/28	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.23	2		682	763	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775497	39775497	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	124	824	2	ENST00000288319.7:c.523G>A	p.Asp175Asn	p.D175N	ENST00000288319	NM_182918.3	175	Gac/Aac	4/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.23	2		826	909	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068421	26068421	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	23	457	0	ENST00000435504.4:c.69del	p.Lys23AsnfsTer7	p.K23Nfs*7	ENST00000435504		23	aaA/aa	2/13	1	2	FACETS	0.442	0.344	0.557	0.442	0.344	0.557	SUBCLONAL	1	TRUE	1	0.23	2		457	452	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120412	70120412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1336660139	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	203	1184	1	ENST00000245479.2:c.1414G>A	p.Ala472Thr	p.A472T	ENST00000245479	NM_000346.3	472	Gct/Act	3/3	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.23	2		1185	1280	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293517	137293517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747209166	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	74	1199	1	ENST00000481739.1:c.68C>T	p.Thr23Met	p.T23M	ENST00000481739	NM_002957.4	23	aCg/aTg	2/10	1	2	FACETS	0.626	0.546	0.712	0.626	0.546	0.712	SUBCLONAL	1	TRUE	1	0.23	2		1200	1028	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993822	72993822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374552910	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	46	701	1	ENST00000268489.5:c.223G>A	p.Ala75Thr	p.A75T	ENST00000268489	NM_006885.3	75	Gcc/Acc	2/10	1	2	FACETS	0.71	0.598	0.835	0.71	0.598	0.835	SUBCLONAL	1	TRUE	1	0.23	2		702	563	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250422	110250422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747921767	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	80	891	1	ENST00000374672.4:c.253G>A	p.Gly85Ser	p.G85S	ENST00000374672	NM_004235.4	85	Ggt/Agt	3/5	1	2	FACETS	0.946	0.833	1	0.946	0.833	1	CLONAL	1	TRUE	1	0.23	2		892	735	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952348	38952348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752956118	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	29	309	0	ENST00000357387.3:c.3077C>T	p.Ser1026Leu	p.S1026L	ENST00000357387	NM_152756.3	1026	tCg/tTg	30/38	1	2	FACETS	0.735	0.591	0.899	0.735	0.591	0.899	SUBCLONAL	1	TRUE	1	0.23	2		309	343	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418387	139418387	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749947050	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	100	1066	0	ENST00000277541.6:c.185C>T	p.Pro62Leu	p.P62L	ENST00000277541	NM_017617.3	62	cCg/cTg	3/34	1	2	FACETS	0.843	0.752	0.941	0.843	0.752	0.941	CLONAL	1	TRUE	1	0.23	2		1066	1031	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920465	50920465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779208942	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	128	790	0	ENST00000440232.2:c.3157C>T	p.Arg1053Cys	p.R1053C	ENST00000440232	NM_002691.3	1053	Cgc/Tgc	26/27	1	2	FACETS	0.807	0.732	0.885	1	0.987	1	CLONAL	2	TRUE	1	0.23	2		790	690	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151932990	151932990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs76844681	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	11	116	1	ENST00000262189.6:c.2681G>A	p.Arg894Gln	p.R894Q	ENST00000262189	NM_170606.2	894	cGg/cAg	16/59	1	2	FACETS	0.778	0.54	1	0.778	0.54	1	CLONAL	1	TRUE	1	0.23	2		117	123	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347562	118347562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	107	571	0	ENST00000534358.1:c.3199C>T	p.Arg1067Trp	p.R1067W	ENST00000534358	NM_005933.3	1067	Cgg/Tgg	4/36	1	2	FACETS	0.758	0.681	0.839	1	0.983	1	SUBCLONAL	2	TRUE	1	0.23	2		571	614	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142540	119142540	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730880431	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	37	399	0	ENST00000264033.4:c.539G>A	p.Arg180Gln	p.R180Q	ENST00000264033	NM_005188.3	180	cGg/cAg	3/16	1	2	FACETS	0.707	0.583	0.846	0.707	0.583	0.846	SUBCLONAL	1	TRUE	1	0.23	2		399	455	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685271	89685271	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	46	222	0	ENST00000371953.3:c.166T>A	p.Phe56Ile	p.F56I	ENST00000371953	NM_000314.4	56	Ttt/Att	3/9	1	2	FACETS	0.784	0.666	0.913	1	0.964	1	CLONAL	2	TRUE	1	0.23	2		222	255	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348479	89348479	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1296165234	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	169	1019	0	ENST00000301030.4:c.4471G>A	p.Glu1491Lys	p.E1491K	ENST00000301030	NM_001256183.1	1491	Gag/Aag	9/13	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.23	2		1019	1062	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440489	49440489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910695111	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	170	147	1	ENST00000301067.7:c.4321C>T	p.Arg1441Cys	p.R1441C	ENST00000301067	NM_003482.3	1441	Cgc/Tgc	15/54	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.23	2		148	1036	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094480	27094480	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	55	598	0	ENST00000324856.7:c.3188G>T	p.Gly1063Val	p.G1063V	ENST00000324856	NM_006015.4	1063	gGa/gTa	11/20	1	2	FACETS	0.846	0.724	0.98	0.846	0.724	0.98	CLONAL	1	TRUE	1	0.23	2		598	565	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521605	46521605	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	81	520	0	ENST00000262741.5:c.803del	p.Gly268ValfsTer10	p.G268Vfs*10	ENST00000262741	NM_003629.3	268	gGt/gt	7/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.23	2		520	531	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933213	100933213	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	44	582	0	ENST00000325455.5:c.2177T>C	p.Leu726Pro	p.L726P	ENST00000325455	NM_001202474.3	726	cTt/cCt	4/8	1	2	FACETS	0.631	0.529	0.745	0.631	0.529	0.745	SUBCLONAL	1	TRUE	1	0.23	2		582	606	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658314	18658314	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	24	529	0	ENST00000266497.5:c.3119T>C	p.Met1040Thr	p.M1040T	ENST00000266497		1040	aTg/aCg	22/31	1	2	FACETS	0.444	0.347	0.556	0.444	0.347	0.556	SUBCLONAL	1	TRUE	1	0.23	2		529	470	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235893	133235894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	34	693	0	ENST00000320574.5:c.3262_3263insT	p.Pro1088LeufsTer36	p.P1088Lfs*36	ENST00000320574	NM_006231.2	1088	cct/cTct	26/49	1	2	FACETS	0.481	0.392	0.581	0.481	0.392	0.581	SUBCLONAL	1	TRUE	1	0.23	2		693	615	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788627	3788627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	54	474	0	ENST00000262367.5:c.4327C>T	p.Arg1443Cys	p.R1443C	ENST00000262367	NM_004380.2	1443	Cgt/Tgt	26/31	1	2	FACETS	0.805	0.688	0.934	0.805	0.688	0.934	CLONAL	1	TRUE	1	0.23	2		474	583	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868091	56868091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1435168393	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	74	645	1	ENST00000308159.5:c.1589G>A	p.Arg530Gln	p.R530Q	ENST00000308159	NM_014669.4	530	cGg/cAg	14/22	1	2	FACETS	0.736	0.643	0.837	0.736	0.643	0.837	SUBCLONAL	1	TRUE	1	0.23	2		646	874	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935782	15935782	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	32	415	0	ENST00000268712.3:c.7151C>A	p.Pro2384His	p.P2384H	ENST00000268712	NM_006311.3	2384	cCt/cAt	46/46	1	2	FACETS	0.656	0.532	0.796	0.656	0.532	0.796	SUBCLONAL	1	TRUE	1	0.23	2		415	424	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553559	29553559	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	51	385	2	ENST00000356175.3:c.2108T>A	p.Val703Asp	p.V703D	ENST00000356175	NM_000267.3	703	gTt/gAt	18/57	1	2	FACETS	0.942	0.801	1	0.942	0.801	1	CLONAL	1	TRUE	1	0.23	2		387	471	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213987	2213987	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	72	629	0	ENST00000398665.3:c.1797+2T>C		p.X599_splice	ENST00000398665	NM_032482.2	599			1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.23	2		629	590	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098378	11098378	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	60	884	0	ENST00000358026.2:c.896C>A	p.Pro299His	p.P299H	ENST00000358026	NM_001128849.1	299	cCt/cAt	6/36	1	2	FACETS	0.709	0.61	0.817	0.709	0.61	0.817	SUBCLONAL	1	TRUE	1	0.23	2		884	736	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297936	15297936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747661515	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	89	1016	2	ENST00000263388.2:c.1820G>A	p.Arg607His	p.R607H	ENST00000263388	NM_000435.2	607	cGc/cAc	11/33	1	2	FACETS	0.796	0.704	0.895	0.796	0.704	0.895	SUBCLONAL	1	TRUE	1	0.23	2		1018	972	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266694	18266694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs978235304	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	139	856	0	ENST00000222254.8:c.5C>T	p.Ala2Val	p.A2V	ENST00000222254	NM_005027.3	2	gCg/gTg	2/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.23	2		856	894	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215904	36215916	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCCCCTTTGCT	TGGCCCCTTTGCT	-	novel	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	69	951	0	ENST00000222270.7:c.3445_3457del	p.Gly1149LeufsTer29	p.G1149Lfs*29	ENST00000222270	NM_014727.1	1148	ccTGGCCCCTTTGCT/cc	10/37	1	2	FACETS	0.588	0.51	0.672	0.588	0.51	0.672	SUBCLONAL	1	TRUE	1	0.23	2		951	1021	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390122	89390122	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	32	387	1	ENST00000336596.2:c.871C>T	p.Pro291Ser	p.P291S	ENST00000336596	NM_005233.5	291	Ccg/Tcg	4/17	1	2	FACETS	0.647	0.525	0.785	0.647	0.525	0.785	SUBCLONAL	1	TRUE	1	0.23	2		388	430	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532890	187532890	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	51	398	0	ENST00000441802.2:c.9503C>T	p.Ala3168Val	p.A3168V	ENST00000441802	NM_005245.3	3168	gCt/gTt	14/27	1	2	FACETS	0.914	0.778	1	0.914	0.778	1	CLONAL	1	TRUE	1	0.23	2		398	485	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502704	149502704	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375978065	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	82	872	3	ENST00000261799.4:c.2084G>A	p.Arg695His	p.R695H	ENST00000261799	NM_002609.3	695	cGc/cAc	15/23	1	2	FACETS	0.841	0.74	0.949	0.841	0.74	0.949	CLONAL	1	TRUE	1	0.23	2		875	848	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040650	47040650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556779016	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	48	894	0	ENST00000377604.3:c.1285G>A	p.Glu429Lys	p.E429K	ENST00000377604	NM_001204468.1	429	Gag/Aag	13/24	1	2	FACETS	0.472	0.397	0.554	0.472	0.397	0.554	SUBCLONAL	1	TRUE	1	0.23	2		894	885	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228071	53228071	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0054499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	41	797	0	ENST00000375401.3:c.2244-1G>T		p.X748_splice	ENST00000375401	NM_004187.3	748			1	2	FACETS	0.501	0.416	0.596	0.501	0.416	0.596	SUBCLONAL	1	TRUE	1	0.23	2		797	712	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0054502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	556	963	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.375017761211102	3	FACETS	0.933	0.9	0.967	0.933	0.9	0.967	CLONAL	3	TRUE	0	0.443987360618108	3		966	1093	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17371320	17371320	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs74315370	NA	P-0054502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	226	662	0	ENST00000375499.3:c.136C>T	p.Arg46Ter	p.R46*	ENST00000375499	NM_003000.2	46	Cga/Tga	2/8	0.202896005457856	3	FACETS	1	0.987	1	0.62	0.578	0.664	INDETERMINATE	1	TRUE	1	0.443987360618108	3		662	1003	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692910	89692910	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	337	634	0	ENST00000371953.3:c.394G>C	p.Gly132Arg	p.G132R	ENST00000371953	NM_000314.4	132	Ggt/Cgt	5/9	0.443987360618108	2	FACETS	0.894	0.849	0.939	0.894	0.849	0.939	CLONAL	2	TRUE	0	0.443987360618108	2		634	849	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828048	3828061	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGCTGAGCCCCC	GGGGCTGAGCCCCC	-	novel	NA	P-0054502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	589	742	0	ENST00000262367.5:c.2064_2077del	p.Gly689CysfsTer32	p.G689Cfs*32	ENST00000262367	NM_004380.2	688	ccGGGGGCTCAGCCCCct/ccct	10/31	0.420392472610358	3	FACETS	0.914	0.882	0.946	0.914	0.882	0.946	CLONAL	3	TRUE	0	0.443987360618108	3		742	1182	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0054503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	23	222	2	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.176424888964717	1	FACETS	0.493	0.39	0.608	0.493	0.39	0.608	INDETERMINATE	1	TRUE	0	0.566722351290447	1		224	118	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335121	65335121	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	17	658	1	ENST00000342505.4:c.520C>T	p.Arg174Ter	p.R174*	ENST00000342505	NM_002227.2	174	Cga/Tga	6/25	0.53078869091208	1	FACETS	0.135	0.1	0.176	0.135	0.1	0.176	SUBCLONAL	1	TRUE	0	0.566722351290447	1		659	319	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521541	8521541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	24	651	0	ENST00000356435.5:c.697C>T	p.Arg233Cys	p.R233C	ENST00000356435		233	Cgt/Tgt	9/35	0.138727621253387	0	FACETS	0.204	0.161	0.253			1	INDETERMINATE	1	TRUE	0	0.566722351290447	0		651	180	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279920	18279920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	84	965	2	ENST00000222254.8:c.2003G>A	p.Cys668Tyr	p.C668Y	ENST00000222254	NM_005027.3	668	tGc/tAc	16/16	1	2	FACETS	0.577	0.511	0.647	0.577	0.511	0.647	SUBCLONAL	1	TRUE	1	0.566722351290447	2		967	514	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687507	37687508	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0054503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	110	543	1	ENST00000447079.4:c.4413_4414del	p.Tyr1472SerfsTer40	p.Y1472Sfs*40	ENST00000447079	NM_015083.1	1471	CTc/c	14/14	0.333900234054993	3	FACETS	1	0.983	1	0.704	0.639	0.771	INDETERMINATE	1	TRUE	1	0.566722351290447	3		544	354	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340408	8340408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775122610	NA	P-0054503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	52	685	0	ENST00000356435.5:c.5188C>T	p.Arg1730Trp	p.R1730W	ENST00000356435		1730	Cgg/Tgg	31/35	0.138727621253387	0	FACETS	0.316	0.271	0.364			1	INDETERMINATE	1	TRUE	0	0.566722351290447	0		685	252	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965459	68965459	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	37	926	0	ENST00000288368.4:c.1071G>T	p.Leu357Phe	p.L357F	ENST00000288368	NM_024870.2	357	ttG/ttT	9/40	0.381082687571433	1	FACETS	0.282	0.233	0.336	0.282	0.233	0.336	SUBCLONAL	1	TRUE	0	0.566722351290447	1		926	332	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453135	140453136	+	missense_variant	Missense_Mutation	DNP	CA	CA	TT	rs121913377	NA	P-0054504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	196	416	1	ENST00000288602.6:c.1799_1800delinsAA	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTG/gAA	15/18	0.506045528860975	3	FACETS	0.866	0.815	0.917	0.866	0.815	0.917	INDETERMINATE	2	TRUE	1	0.864417837525032	3		417	375	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241915	133241915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	123	828	1	ENST00000320574.5:c.2441C>T	p.Ser814Phe	p.S814F	ENST00000320574	NM_006231.2	814	tCc/tTc	21/49	NA	2	FACETS	0.425	0.385	0.468			1	INDETERMINATE	1	TRUE	NA	0.864417837525032	2		829	669	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50818177	50818238	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	AAAAATCTGTTTCTTGAAAAATATGTTTACAGCATGAAGAAAATTATCCTTTTTCTTTTGCA	AAAAATCTGTTTCTTGAAAAATATGTTTACAGCATGAAGAAAATTATCCTTTTTCTTTTGCA	-	novel	NA	P-0054504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	42	156	1	ENST00000398568.2:c.1818-63_1818-2del		p.X606_splice	ENST00000398568	NM_001042412.1	606			0.4407604786743	2	FACETS	0.759	0.649	0.875	0.38	0.324	0.438	INDETERMINATE	1	TRUE	0	0.864417837525032	2		157	128	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322776	30322776	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1434267100	NA	P-0054504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	61	331	0	ENST00000322652.5:c.1789A>G	p.Ile597Val	p.I597V	ENST00000322652	NM_015355.2	597	Att/Gtt	14/16	0.435636153850134	1	FACETS	0.359	0.314	0.407	0.359	0.314	0.407	INDETERMINATE	1	TRUE	0	0.864417837525032	1		331	223	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610339	10610339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	380	1111	1	ENST00000171111.5:c.371C>T	p.Ser124Phe	p.S124F	ENST00000171111	NM_203500.1	124	tCc/tTc	2/6	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.864417837525032	2		1112	806	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098365	11098366	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0054504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	299	866	3	ENST00000358026.2:c.883_884delinsTT	p.Pro295Phe	p.P295F	ENST00000358026	NM_001128849.1	295	CCc/TTc	6/36	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.864417837525032	2		869	666	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624844	9624844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	282	569	0	ENST00000353224.5:c.133G>A	p.Asp45Asn	p.D45N	ENST00000353224	NM_177990.2	45	Gat/Aat	3/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.864417837525032	2		569	642	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000074	30000074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	306	821	0	ENST00000338641.4:c.87G>A	p.Met29Ile	p.M29I	ENST00000338641	NM_000268.3	29	atG/atA	1/16	0.429651496815779	1	FACETS	0.686	0.654	0.718	0.686	0.654	0.718	INDETERMINATE	1	TRUE	0	0.864417837525032	1		821	586	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111995750	111995750	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	237	585	1	ENST00000368678.4:c.1348G>A	p.Gly450Arg	p.G450R	ENST00000368678		450	Gga/Aga	12/13	0.435636153850134	1	FACETS	0.709	0.672	0.746	0.709	0.672	0.746	INDETERMINATE	1	TRUE	0	0.864417837525032	1		586	439	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609855	117609855	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	117	640	3	ENST00000368508.3:c.6844G>A	p.Gly2282Ser	p.G2282S	ENST00000368508	NM_002944.2	2282	Ggc/Agc	43/43	0.435636153850134	1	FACETS	0.375	0.341	0.41	0.375	0.341	0.41	INDETERMINATE	1	TRUE	0	0.864417837525032	1		643	410	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128322047	128322047	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	51	796	0	ENST00000265960.3:c.713A>C	p.Asp238Ala	p.D238A	ENST00000265960	NM_001006617.1	238	gAt/gCt	6/12	0.851406792672937	2	FACETS	0.232	0.197	0.271	0.116	0.098	0.136	SUBCLONAL	1	TRUE	0	0.864417837525032	2		796	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0054506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	174	792	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.475102442021635	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.475102442021635	1		792	531	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9787061	9787061	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	106	714	1	ENST00000377346.4:c.3092T>A	p.Val1031Glu	p.V1031E	ENST00000377346	NM_005026.3	1031	gTg/gAg	24/24	NA	2	FACETS	0.741	0.666	0.821			1	INDETERMINATE	1	TRUE	NA	0.475102442021635	2		715	602	SUCCESS
APC	324	MSKCC	GRCh37	5	112176775	112176775	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	74	337	0	ENST00000257430.4:c.5486del	p.Asn1829IlefsTer34	p.N1829Ifs*34	ENST00000257430	NM_000038.5	1828	ccA/cc	16/16	0.448276814583139	1	FACETS	0.854	0.756	0.957	0.854	0.756	0.957	CLONAL	1	TRUE	0	0.475102442021635	1		337	278	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141036	55141036	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121908586	NA	P-0054507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	16	348	0	ENST00000257290.5:c.1682T>A	p.Val561Asp	p.V561D	ENST00000257290	NM_006206.4	561	gTc/gAc	12/23	1	2	FACETS	0.116	0.085	0.153	0.116	0.085	0.153	SUBCLONAL	1	TRUE	1	0.61570193441842	2		348	449	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911467	39911470	+	frameshift_variant	Frame_Shift_Del	DEL	CTTA	CTTA	-	novel	NA	P-0054507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	225	661	0	ENST00000378444.4:c.5160_5163del	p.Ser1720ArgfsTer4	p.S1720Rfs*4	ENST00000378444	NM_001123385.1	1720	agTAAG/ag	15/15	1	2	FACETS	0.938	0.876	1	0.938	0.876	1	CLONAL	1	TRUE	1	0.61570193441842	2		661	779	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	409	304	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.132521490631268	3	FACETS	1	0.979	1	1	0.997	1	INDETERMINATE	4	TRUE	1	0.305110406676731	3		304	750	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912660	NA	P-0054514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	157	781	0	ENST00000269305.4:c.839G>T	p.Arg280Ile	p.R280I	ENST00000269305	NM_001126112.2	280	aGa/aTa	8/11	0.260036351387217	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.305110406676731	1		781	840	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971124	21971125	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0054514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	66	444	0	ENST00000304494.5:c.233_234del	p.Leu78HisfsTer41	p.L78Hfs*41	ENST00000304494	NM_000077.4	78	cTC/c	2/3	0.305110406676731	1	FACETS	0.785	0.683	0.895	0.785	0.683	0.895	SUBCLONAL	1	TRUE	0	0.305110406676731	1		444	467	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642470	117642470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765146445	NA	P-0054514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	49	694	0	ENST00000368508.3:c.5729G>A	p.Arg1910Gln	p.R1910Q	ENST00000368508	NM_002944.2	1910	cGa/cAa	35/43	0.305110406676731	1	FACETS	0.389	0.328	0.456	0.389	0.328	0.456	SUBCLONAL	1	TRUE	0	0.305110406676731	1		694	700	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183722	10183722	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs104893826	NA	P-0054515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	429	826	0	ENST00000256474.2:c.191G>C	p.Arg64Pro	p.R64P	ENST00000256474	NM_000551.3	64	cGc/cCc	1/3	0.711147887708488	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.711147887708488	1		826	704	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797224	135797234	+	frameshift_variant	Frame_Shift_Del	DEL	AGTCTCCAGGT	AGTCTCCAGGT	-	novel	NA	P-0054515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	91	205	0	ENST00000298552.3:c.635_645del	p.Asn212IlefsTer2	p.N212Ifs*2	ENST00000298552	NM_001162426.1	212	aACCTGGAGACT/a	7/23	0.711147887708488	1	FACETS	0.841	0.765	0.918	0.841	0.765	0.918	CLONAL	1	TRUE	0	0.711147887708488	1		205	196	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	26	502	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.924	0.736	1	0.924	0.736	1	CLONAL	1	TRUE	1	0.25	2		502	225	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001374	150001376	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs753305883	NA	P-0054516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	24	504	0	ENST00000253339.5:c.2228_2230del	p.Leu743del	p.L743del	ENST00000253339		743	cTTCga/cga	4/7	1	2	FACETS	1	0.805	1	1	0.805	1	CLONAL	1	TRUE	1	0.25	2		504	188	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097726	27097726	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	33	561	1	ENST00000324856.7:c.3315C>A	p.Cys1105Ter	p.C1105*	ENST00000324856	NM_006015.4	1105	tgC/tgA	12/20	0.260162056943624	1	FACETS	0.568	0.462	0.686	0.568	0.462	0.686	SUBCLONAL	1	TRUE	0	0.25	1		562	407	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527262	187527262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	47	549	0	ENST00000441802.2:c.10312C>T	p.Pro3438Ser	p.P3438S	ENST00000441802	NM_005245.3	3438	Ccc/Tcc	17/27	1	2	FACETS	0.812	0.686	0.951	0.812	0.686	0.951	CLONAL	1	TRUE	1	0.25	2		549	463	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462065	120462065	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	54	637	0	ENST00000256646.2:c.5651C>A	p.Ala1884Glu	p.A1884E	ENST00000256646	NM_024408.3	1884	gCa/gAa	31/34	0.520203867462451	4	FACETS	0.373	0.317	0.434	0.186	0.158	0.217	SUBCLONAL	1	FALSE	2	0.520203867462451	4		637	847	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0054518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	92	455	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.436052965600616	2		456	352	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0054518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	169	543	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.436052965600616	2		543	580	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164805	47164805	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	73	378	0	ENST00000409792.3:c.1321C>T	p.Arg441Ter	p.R441*	ENST00000409792	NM_014159.6	441	Cga/Tga	3/21	1	2	FACETS	0.841	0.739	0.95	0.841	0.739	0.95	CLONAL	1	FALSE	1	0.436052965600616	2		378	398	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498473	89498473	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	52	316	0	ENST00000336596.2:c.2445G>A	p.Trp815Ter	p.W815*	ENST00000336596	NM_005233.5	815	tgG/tgA	14/17	1	2	FACETS	0.84	0.72	0.969	0.84	0.72	0.969	CLONAL	1	FALSE	1	0.436052965600616	2		316	284	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923102	48923102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	34	294	0	ENST00000267163.4:c.550G>A	p.Glu184Lys	p.E184K	ENST00000267163	NM_000321.2	184	Gaa/Aaa	6/27	1	2	FACETS	0.788	0.65	0.94	0.788	0.65	0.94	CLONAL	1	FALSE	1	0.436052965600616	2		294	198	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24133958	24133958	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	68	336	0	ENST00000263121.7:c.109C>T	p.Arg37Cys	p.R37C	ENST00000263121	NM_003073.3	37	Cgt/Tgt	2/9	0.189390865297971	1	FACETS	0.75	0.658	0.849	0.75	0.658	0.849	INDETERMINATE	1	FALSE	0	0.436052965600616	1		336	325	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406235	70406235	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	92	645	0	ENST00000373644.4:c.3749C>T	p.Ser1250Leu	p.S1250L	ENST00000373644	NM_030625.2	1250	tCa/tTa	4/12	0.156444047056405	3	FACETS	1	0.959	1	0.576	0.514	0.641	INDETERMINATE	1	FALSE	1	0.436052965600616	3		645	446	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373734	118373734	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555046390	NA	P-0054518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	80	423	0	ENST00000534358.1:c.7127G>A	p.Arg2376Lys	p.R2376K	ENST00000534358	NM_005933.3	2376	aGa/aAa	27/36	0.416394138293684	1	FACETS	0.963	0.857	1	0.963	0.857	1	CLONAL	1	FALSE	0	0.436052965600616	1		423	298	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356218	66356218	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	138	644	0	ENST00000273854.3:c.1279A>G	p.Met427Val	p.M427V	ENST00000273854	NM_004439.5	427	Atg/Gtg	5/18	0.135225958479484	3	FACETS	1	0.973	1	0.388	0.354	0.424	INDETERMINATE	1	FALSE	0	0.436052965600616	3		644	662	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816556	32816556	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	263	960	1	ENST00000354258.4:c.1619A>G	p.Glu540Gly	p.E540G	ENST00000354258	NM_000593.5	540	gAg/gGg	7/11	0.156444047056405	3	FACETS	1	0.992	1	0.683	0.64	0.727	INDETERMINATE	1	FALSE	1	0.436052965600616	3		961	1076	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877025	151877026	+	missense_variant	Missense_Mutation	DNP	GA	GA	AC	novel	NA	P-0054518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	70	518	1	ENST00000262189.6:c.7335_7336delinsGT	p.Pro2446Ser	p.P2446S	ENST00000262189	NM_170606.2	2445	tcTCct/tcGTct	37/59	1	2	FACETS	0.776	0.679	0.879	0.776	0.679	0.879	SUBCLONAL	1	FALSE	1	0.436052965600616	2		519	414	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458537	12458537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140204299	NA	P-0054519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	222	686	0	ENST00000287820.6:c.1154G>A	p.Arg385Gln	p.R385Q	ENST00000287820	NM_015869.4	385	cGa/cAa	6/7	1	2	FACETS	0.964	0.901	1	0.964	0.901	1	CLONAL	1	TRUE	1	0.629112842770195	2		686	732	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538909	23538909	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs373263457	NA	P-0054519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	244	644	0	ENST00000380871.4:c.530A>G	p.Tyr177Cys	p.Y177C	ENST00000380871	NM_006167.3	177	tAt/tGt	2/2	1	2	FACETS	0.905	0.848	0.964	0.905	0.848	0.964	CLONAL	1	TRUE	1	0.629112842770195	2		644	857	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256520	115256520	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	157	607	0	ENST00000369535.4:c.191A>G	p.Tyr64Cys	p.Y64C	ENST00000369535	NM_002524.4	64	tAc/tGc	3/7	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.629112842770195	2		607	470	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890140	76890140	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	34	229	0	ENST00000373344.5:c.4754C>G	p.Ser1585Cys	p.S1585C	ENST00000373344	NM_000489.3	1585	tCt/tGt	17/35	1	1	FACETS	0.682	0.561	0.816	0.682	0.561	0.816	SUBCLONAL	1	TRUE	0	0.345253712192722	1		229	239	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041599	47041599	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	292	383	0	ENST00000377604.3:c.1824G>A	p.Trp608Ter	p.W608*	ENST00000377604	NM_001204468.1	608	tgG/tgA	17/24	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.626133613047203	1		383	454	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166251	118166251	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	134	301	0	ENST00000369448.3:c.761A>G	p.Asp254Gly	p.D254G	ENST00000369448	NM_017709.3	254	gAc/gGc	2/2	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.626133613047203	2		301	427	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0054523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	409	477	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.554866752602341	5	FACETS	1	0.992	1	1	0.992	1	CLONAL	4	TRUE	1	0.562928061789452	5		477	616	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184037	123184037	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	38	291	0	ENST00000218089.9:c.895G>A	p.Asp299Asn	p.D299N	ENST00000218089	NM_001042749.1	299	Gat/Aat	11/35	0.470731035257882	4	FACETS	0.52	0.43	0.62	0.26	0.215	0.31	SUBCLONAL	1	TRUE	2	0.562928061789452	4		291	406	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0054524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	14	603	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.074	0.053	0.1	0.074	0.053	0.1	SUBCLONAL	1	TRUE	1	0.776975054917431	2		603	485	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0054524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	9	477	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.056	0.037	0.082	0.056	0.037	0.082	SUBCLONAL	1	TRUE	1	0.776975054917431	2		477	411	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40444023	40444023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218653273	NA	P-0054524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	45	790	0	ENST00000345506.4:c.319C>T	p.Arg107Cys	p.R107C	ENST00000345506	NM_003152.3	107	Cgc/Tgc	5/20	NA	2	FACETS	0.147	0.123	0.174			1	INDETERMINATE	1	TRUE	NA	0.776975054917431	2		790	789	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190348	32190348	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1281	314	846	0	ENST00000375023.3:c.391G>T	p.Gly131Cys	p.G131C	ENST00000375023	NM_004557.3	131	Ggc/Tgc	3/30	0.756204728576175	4	FACETS	0.9	0.847	0.955	0.3	0.282	0.319	CLONAL	1	TRUE	1	0.776975054917431	4		846	1595	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190407	32190407	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1361	342	1036	0	ENST00000375023.3:c.332G>T	p.Gly111Val	p.G111V	ENST00000375023	NM_004557.3	111	gGt/gTt	3/30	0.756204728576175	4	FACETS	0.919	0.867	0.972	0.306	0.289	0.324	CLONAL	1	TRUE	1	0.776975054917431	4		1036	1703	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0054525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	595	568	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.618817178158816	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.618817178158816	2		568	919	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0054525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	302	625	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.618817178158816	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.618817178158816	1		625	666	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73991987	73991987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770116040	NA	P-0054525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	453	854	2	ENST00000318443.5:c.7C>T	p.Arg3Cys	p.R3C	ENST00000318443	NM_001024736.1	3	Cgt/Tgt	2/10	0.618817178158816	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.618817178158816	1		856	987	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437573	56437574	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	79	686	0	ENST00000407977.2:c.888dup	p.Asn297Ter	p.N297*	ENST00000407977		296	-/T	8/10	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.19	2		686	814	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953578	32953643	+	inframe_deletion	In_Frame_Del	DEL	AAGGTTTATCAAGGGATGTCACAACCGTGTGGAAGTTGCGTATTGTAAGCTATTCAAAAAAAGAAA	AAGGTTTATCAAGGGATGTCACAACCGTGTGGAAGTTGCGTATTGTAAGCTATTCAAAAAAAGAAA	-	novel	NA	P-0054527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	28	519	0	ENST00000380152.3:c.8882_8947del	p.Gly2961_Lys2982del	p.G2961_K2982del	ENST00000380152		2960	cAAGGTTTATCAAGGGATGTCACAACCGTGTGGAAGTTGCGTATTGTAAGCTATTCAAAAAAAGAAAaa/caa	22/27	1	2	FACETS	0.534	0.426	0.658	0.534	0.426	0.658	SUBCLONAL	1	TRUE	1	0.19	2		519	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0054528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	257	98	28	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.494969534419669	2		126	907	SUCCESS
APC	324	MSKCC	GRCh37	5	112175198	112175198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	16	233	0	ENST00000257430.4:c.3907C>T	p.Gln1303Ter	p.Q1303*	ENST00000257430	NM_000038.5	1303	Caa/Taa	16/16	1	2	FACETS	0.599	0.448	0.774	0.599	0.448	0.774	SUBCLONAL	1	TRUE	1	0.494969534419669	2		233	108	SUCCESS
APC	324	MSKCC	GRCh37	5	112175351	112175351	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	46	262	0	ENST00000257430.4:c.4063del	p.Ser1355LeufsTer60	p.S1355Lfs*60	ENST00000257430	NM_000038.5	1354	Ttt/tt	16/16	1	2	FACETS	0.999	0.854	1	0.999	0.854	1	CLONAL	1	TRUE	1	0.494969534419669	2		262	186	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	178	833	0	ENST00000269305.4:c.548C>A	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tAa	5/11	1	2	FACETS	0.854	0.788	0.923	0.854	0.788	0.923	CLONAL	1	TRUE	1	0.494969534419669	2		833	842	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117712780	117712780	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	51	360	0	ENST00000369458.3:c.46A>C	p.Ile16Leu	p.I16L	ENST00000369458	NM_024626.3	16	Atc/Ctc	2/6	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.494969534419669	2		360	205	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007318	143007318	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	50	391	0	ENST00000262992.4:c.2466A>C	p.Glu822Asp	p.E822D	ENST00000262992	NM_001101669.1	822	gaA/gaC	22/24	1	2	FACETS	0.771	0.66	0.891	0.771	0.66	0.891	SUBCLONAL	1	TRUE	1	0.494969534419669	2		391	262	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0054529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	281	963	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.220714709966112	3	FACETS	1	0.984	1	0.741	0.699	0.783	INDETERMINATE	2	FALSE	0	0.385650883600031	3		966	782	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	196	502	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.339361354447081	4	FACETS	1	0.975	1	0.809	0.759	0.861	CLONAL	3	FALSE	0	0.385650883600031	4		502	435	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502734	149502734	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	165	545	0	ENST00000261799.4:c.2054G>T	p.Arg685Leu	p.R685L	ENST00000261799	NM_002609.3	685	cGc/cTc	15/23	0.186063068244201	4	FACETS	0.828	0.762	0.896	0.828	0.762	0.896	INDETERMINATE	2	FALSE	2	0.385650883600031	4		545	716	SUCCESS
AR	367	MSKCC	GRCh37	X	66942774	66942774	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	139	189	0	ENST00000374690.3:c.2555C>A	p.Ser852Tyr	p.S852Y	ENST00000374690	NM_000044.3	852	tCc/tAc	7/8	0.385650883600031	2	FACETS	0.89	0.828	0.952			1	CLONAL	3	FALSE	NA	0.385650883600031	2		189	270	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	267	375	0				ENST00000310581	NM_198253.2	-/1132			0.49635386563037	5	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	2	0.49635386563037	5		375	583	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0054530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	409	737	0	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	0.457988728430208	3	FACETS	1	0.994	1	0.803	0.769	0.837	CLONAL	2	TRUE	0	0.49635386563037	3		737	854	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247295	153247295	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	208	368	0	ENST00000281708.4:c.1507G>A	p.Ala503Thr	p.A503T	ENST00000281708	NM_033632.3	503	Gca/Aca	10/12	0.302398783242796	3	FACETS	1	0.984	1	0.76	0.714	0.806	CLONAL	2	TRUE	0	0.49635386563037	3		368	459	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033967	49033967	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1131690865	NA	P-0054530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	161	357	0	ENST00000267163.4:c.2104C>T	p.Gln702Ter	p.Q702*	ENST00000267163	NM_000321.2	702	Caa/Taa	20/27	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.49635386563037	2		357	456	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125513702	125513702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775245290	NA	P-0054530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	87	374	0	ENST00000428830.2:c.830G>A	p.Arg277Gln	p.R277Q	ENST00000428830	NM_001114121.2	277	cGa/cAa	9/14	0.214214207529171	5	FACETS	1	0.954	1	0.382	0.339	0.428	INDETERMINATE	1	TRUE	2	0.49635386563037	5		374	533	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746027	162746027	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	88	381	0	ENST00000367921.3:c.2150T>C	p.Leu717Ser	p.L717S	ENST00000367921	NM_006182.2	717	tTa/tCa	16/18	0.274337301976629	4	FACETS	0.924	0.821	1	0.462	0.41	0.518	INDETERMINATE	1	TRUE	2	0.49635386563037	4		381	574	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439899	49439899	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	144	757	0	ENST00000301067.7:c.4642G>T	p.Asp1548Tyr	p.D1548Y	ENST00000301067	NM_003482.3	1548	Gat/Tat	17/54	0.461642616005283	3	FACETS	0.754	0.687	0.825	0.377	0.343	0.413	SUBCLONAL	1	TRUE	1	0.49635386563037	3		757	960	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646730	23646730	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	85	631	0	ENST00000261584.4:c.1137G>C	p.Lys379Asn	p.K379N	ENST00000261584	NM_024675.3	379	aaG/aaC	4/13	1	2	FACETS	0.513	0.453	0.576	0.513	0.453	0.576	SUBCLONAL	1	TRUE	1	0.49635386563037	2		631	668	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58700899	58700899	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs770546952	NA	P-0054530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	96	521	0	ENST00000305921.3:c.490A>G	p.Met164Val	p.M164V	ENST00000305921	NM_003620.3	164	Atg/Gtg	2/6	0.453484408852534	4	FACETS	0.631	0.561	0.705	0.315	0.28	0.353	SUBCLONAL	1	TRUE	2	0.49635386563037	4		521	918	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246889	10246889	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	179	1148	1	ENST00000340748.4:c.4516C>T	p.Arg1506Trp	p.R1506W	ENST00000340748		1506	Cgg/Tgg	37/40	0.468584333702003	3	FACETS	0.772	0.71	0.836	0.386	0.355	0.418	SUBCLONAL	1	TRUE	1	0.49635386563037	3		1149	1166	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851852	134851852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	122	831	0	ENST00000398015.3:c.1258C>T	p.Pro420Ser	p.P420S	ENST00000398015	NM_004441.4	420	Cca/Tca	5/16	0.226619414058933	4	FACETS	0.752	0.679	0.83	0.376	0.339	0.415	INDETERMINATE	1	TRUE	2	0.49635386563037	4		831	978	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670066	86670067	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	136	432	0	ENST00000274376.6:c.1864dup	p.Ser622LysfsTer24	p.S622Kfs*24	ENST00000274376	NM_002890.2	621	-/A	14/25	0.461642616005283	3	FACETS	1	0.986	1	0.715	0.655	0.778	CLONAL	1	TRUE	1	0.49635386563037	3		432	478	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495457	149495457	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	202	1285	0	ENST00000261799.4:c.3190C>G	p.Leu1064Val	p.L1064V	ENST00000261799	NM_002609.3	1064	Ctg/Gtg	23/23	0.332653507255913	3	FACETS	0.756	0.699	0.815	0.378	0.349	0.408	SUBCLONAL	1	TRUE	1	0.49635386563037	3		1285	1344	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829276	128829276	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	228	956	0	ENST00000249373.3:c.284A>C	p.Asp95Ala	p.D95A	ENST00000249373	NM_005631.4	95	gAc/gCc	1/12	0.49635386563037	4	FACETS	1	0.951	1	0.514	0.478	0.552	CLONAL	1	TRUE	2	0.49635386563037	4		956	1337	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860341	151860341	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	212	528	0	ENST00000262189.6:c.10321A>G	p.Ile3441Val	p.I3441V	ENST00000262189	NM_170606.2	3441	Ata/Gta	43/59	0.49635386563037	4	FACETS	0.824	0.767	0.882	0.824	0.767	0.882	CLONAL	2	TRUE	2	0.49635386563037	4		528	776	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117875410	117875410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	167	393	0	ENST00000297338.2:c.233G>A	p.Cys78Tyr	p.C78Y	ENST00000297338	NM_006265.2	78	tGt/tAt	3/14	0.214214207529171	5	FACETS	1	0.931	1	0.672	0.621	0.725	INDETERMINATE	2	TRUE	2	0.49635386563037	5		393	582	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913315	NA	P-0054532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	56	204	0	ENST00000326873.7:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000326873	NM_000455.4	194	Gac/Tac	4/10	0.289057865025586	1	FACETS	0.542	0.464	0.627	0.542	0.464	0.627	SUBCLONAL	1	TRUE	0	0.289057865025586	1		204	612	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520017	NA	P-0054532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	17	951	1	ENST00000326873.7:c.647C>T	p.Ser216Phe	p.S216F	ENST00000326873	NM_000455.4	216	tCc/tTc	5/10	0.289057865025586	1	FACETS	0.152	0.112	0.199	0.152	0.112	0.199	SUBCLONAL	1	TRUE	0	0.289057865025586	1		952	664	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577111	7577111	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786202082	NA	P-0054532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	112	757	0	ENST00000269305.4:c.827C>A	p.Ala276Asp	p.A276D	ENST00000269305	NM_001126112.2	276	gCc/gAc	8/11	0.289057865025586	1	FACETS	0.971	0.874	1	0.971	0.874	1	CLONAL	1	TRUE	0	0.289057865025586	1		757	683	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094979	11094979	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	119	1204	0	ENST00000358026.2:c.152C>A	p.Ser51Ter	p.S51*	ENST00000358026	NM_001128849.1	51	tCa/tAa	2/36	0.289057865025586	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.289057865025586	1		1204	646	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218948	193218948	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	19	330	0	ENST00000367435.3:c.1506C>A	p.His502Gln	p.H502Q	ENST00000367435	NM_024529.4	502	caC/caA	16/17	1	2	FACETS	0.882	0.675	1	0.882	0.675	1	CLONAL	1	TRUE	1	0.289057865025586	2		330	149	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005555	42005570	+	frameshift_variant	Frame_Shift_Del	DEL	GCATTTTCAGAGGAAG	GCATTTTCAGAGGAAG	-	novel	NA	P-0054532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	60	531	0	ENST00000219905.7:c.3293_3308del	p.His1098LeufsTer30	p.H1098Lfs*30	ENST00000219905	NM_001164273.1	1097	aaGCATTTTCAGAGGAAG/aa	9/24	1	2	FACETS	0.842	0.727	0.967	0.842	0.727	0.967	CLONAL	1	TRUE	1	0.289057865025586	2		531	493	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245414	41245414	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	78	702	0	ENST00000357654.3:c.2134T>G	p.Cys712Gly	p.C712G	ENST00000357654	NM_007294.3	712	Tgt/Ggt	10/23	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.289057865025586	2		702	516	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257150	19257150	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	65	718	0	ENST00000162023.5:c.813G>T	p.Gln271His	p.Q271H	ENST00000162023		271	caG/caT	12/13	0.289057865025586	1	FACETS	0.955	0.831	1	0.955	0.831	1	CLONAL	1	TRUE	0	0.289057865025586	1		718	403	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918622	44918622	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	72	490	1	ENST00000377967.4:c.1105C>T	p.Gln369Ter	p.Q369*	ENST00000377967	NM_021140.2	369	Cag/Tag	12/29	1	2	FACETS	0.512	0.447	0.582	0.512	0.447	0.582	SUBCLONAL	1	TRUE	1	0.413760775912252	2		491	680	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412046	116412046	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	G	novel	NA	P-0054533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	201	660	0	ENST00000397752.3:c.3028+3A>G		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.413760775912252	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.413760775912252	1		660	716	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922136	39922136	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	207	778	0	ENST00000378444.4:c.4036C>A	p.Leu1346Met	p.L1346M	ENST00000378444	NM_001123385.1	1346	Ctg/Atg	9/15	1	2	FACETS	0.953	0.884	1	0.953	0.884	1	CLONAL	1	TRUE	1	0.413760775912252	2		778	1050	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984443	201984443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748296702	NA	P-0054533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	84	614	0	ENST00000359651.3:c.1108C>T	p.Arg370Trp	p.R370W	ENST00000359651		370	Cgg/Tgg	8/8	1	2	FACETS	0.433	0.381	0.488	0.433	0.381	0.488	SUBCLONAL	1	TRUE	1	0.413760775912252	2		614	938	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885436	111885486	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCCCACCATCCTCTCCTCCCACAGCACCTGCGCCTGTCGCTGACAGAGCGG	GCCCACCATCCTCTCCTCCCACAGCACCTGCGCCTGTCGCTGACAGAGCGG	-	novel	NA	P-0054533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	39	648	0	ENST00000341259.2:c.1237-23_1264del		p.X413_splice	ENST00000341259	NM_005475.2	413		7/8	0.212228915950596	1	FACETS	0.194	0.16	0.232	0.194	0.16	0.232	INDETERMINATE	1	TRUE	0	0.413760775912252	1		648	771	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590718	95590718	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	38	278	0	ENST00000393063.1:c.1191C>G	p.Ser397Arg	p.S397R	ENST00000393063	NM_030621.3	397	agC/agG	9/28	0.212228915950596	1	FACETS	0.387	0.321	0.462	0.387	0.321	0.462	INDETERMINATE	1	TRUE	0	0.413760775912252	1		278	376	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993077	72993077	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	118	839	0	ENST00000268489.5:c.968C>G	p.Ser323Cys	p.S323C	ENST00000268489	NM_006885.3	323	tCc/tGc	2/10	0.307557303346216	1	FACETS	0.436	0.392	0.482	0.436	0.392	0.482	SUBCLONAL	1	TRUE	0	0.413760775912252	1		839	1038	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437889	52437890	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0054533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	216	826	0	ENST00000460680.1:c.1271_1272del	p.Gly424GlufsTer10	p.G424Efs*10	ENST00000460680	NM_004656.3	424	gGG/g	13/17	0.413760775912252	1	FACETS	0.884	0.822	0.947	0.884	0.822	0.947	CLONAL	1	TRUE	0	0.413760775912252	1		826	937	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0054534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	342	568	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.507807950017571	2	FACETS	1	0.988	1	0.546	0.521	0.57	INDETERMINATE	1	TRUE	0	0.945121817568054	2		568	663	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	192	568	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.528	0.49	0.568	0.528	0.49	0.568	SUBCLONAL	1	TRUE	1	0.945121817568054	2		568	769	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0054534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	117	292	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	0.484	0.438	0.531	0.484	0.438	0.531	SUBCLONAL	1	TRUE	1	0.945121817568054	2		292	512	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122608	108122608	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	104	349	0	ENST00000278616.4:c.1653del	p.Pro552GlnfsTer4	p.P552Qfs*4	ENST00000278616	NM_000051.3	551	gTt/gt	11/63	1	2	FACETS	0.53	0.478	0.585	0.53	0.478	0.585	SUBCLONAL	1	TRUE	1	0.945121817568054	2		349	415	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957474	1957474	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	208	654	1	ENST00000382891.5:c.2573T>C	p.Leu858Pro	p.L858P	ENST00000382891	NM_133335.3	858	cTg/cCg	14/22	1	2	FACETS	0.501	0.466	0.538	0.501	0.466	0.538	SUBCLONAL	1	TRUE	1	0.945121817568054	2		655	878	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0054535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	162	271	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	NA	2	FACETS	0.83	0.777	0.882			1	INDETERMINATE	2	TRUE	NA	0.648399420186776	2		271	301	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061208	38061208	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1292426539	NA	P-0054535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	454	488	0	ENST00000250448.2:c.781C>G	p.Arg261Gly	p.R261G	ENST00000250448	NM_004496.3	261	Cgc/Ggc	2/2	0.648399420186776	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.648399420186776	3		488	862	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0054536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	34	603	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.892	1	1	0.967	1	CLONAL	2	FALSE	1	0.166960445816193	2		603	183	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0054536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	40	26	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.145842266004515	4	FACETS	0.961	0.808	1	1	0.954	1	CLONAL	3	FALSE	2	0.166960445816193	4		26	194	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0054536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	22	369	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	1	0.801	1	1	0.946	1	CLONAL	2	FALSE	1	0.166960445816193	2		369	129	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263850	133263850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	8	218	1	ENST00000320574.5:c.52G>A	p.Glu18Lys	p.E18K	ENST00000320574	NM_006231.2	18	Gag/Aag	1/49	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.166960445816193	NA		219	169	SUCCESS
APC	324	MSKCC	GRCh37	5	112174262	112174262	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs786202995	NA	P-0054536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	12	308	0	ENST00000257430.4:c.2971G>T	p.Glu991Ter	p.E991*	ENST00000257430	NM_000038.5	991	Gaa/Taa	16/16	1	2	FACETS	0.856	0.61	1	1	0.888	1	CLONAL	2	FALSE	1	0.166960445816193	2		308	84	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239831	41239831	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	145	547	0	ENST00000379561.5:c.519C>G	p.Ile173Met	p.I173M	ENST00000379561	NM_002015.3	173	atC/atG	1/3	0.166960445816193	3	FACETS	0.958	0.876	1	1	0.986	1	CLONAL	3	FALSE	1	0.166960445816193	3		547	655	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	97	375	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.851	0.774	0.93	1	0.99	1	CLONAL	3	TRUE	1	0.32889866879035	2		375	231	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097621	27097622	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	96	427	2	ENST00000324856.7:c.3216dup	p.Trp1073MetfsTer32	p.W1073Mfs*32	ENST00000324856	NM_006015.4	1070	-/A	12/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.32889866879035	2		429	518	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740749	58740749	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs779070661	NA	P-0054538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	240	451	0	ENST00000305921.3:c.1654C>T	p.Arg552Ter	p.R552*	ENST00000305921	NM_003620.3	552	Cga/Tga	6/6	1	2	FACETS	1	0.989	1	1	0.995	1	CLONAL	2	TRUE	1	0.32889866879035	2		451	592	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650077	93650077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	60	469	0	ENST00000375746.1:c.1628G>A	p.Cys543Tyr	p.C543Y	ENST00000375746	NM_001174167.1	543	tGc/tAc	12/14	1	2	FACETS	0.579	0.499	0.667	0.579	0.499	0.667	SUBCLONAL	1	TRUE	1	0.32889866879035	2		469	630	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0054539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	28	696	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	FALSE	1	0.168743309248819	2		696	296	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0054539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	93	376	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	0.144069800569782	2	FACETS	0.975	0.873	1	1	0.98	1	CLONAL	3	FALSE	0	0.168743309248819	2		376	377	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465976	69465976	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	166	796	0	ENST00000227507.2:c.814G>T	p.Glu272Ter	p.E272*	ENST00000227507	NM_053056.2	272	Gag/Tag	5/5	1	2	FACETS	1	0.947	1	1	0.992	1	CLONAL	2	FALSE	1	0.168743309248819	2		796	945	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101259	27101260	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0054539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	73	764	0	ENST00000324856.7:c.4544dup	p.Ser1516LeufsTer16	p.S1516Lfs*16	ENST00000324856	NM_006015.4	1514	acg/acGg	18/20	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	FALSE	1	0.168743309248819	2		764	783	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489811	2489811	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	103	867	0	ENST00000355716.4:c.208C>G	p.Leu70Val	p.L70V	ENST00000355716	NM_003820.2	70	Ctg/Gtg	3/8	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.168743309248819	2		867	1038	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089571	27089574	+	frameshift_variant	Frame_Shift_Del	DEL	GGAC	GGAC	-	novel	NA	P-0054539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	83	756	0	ENST00000324856.7:c.2527_2530del	p.Gly843SerfsTer15	p.G843Sfs*15	ENST00000324856	NM_006015.4	843	GGACag/ag	8/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.168743309248819	2		756	811	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717608	89717608	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0054539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	50	331	0	ENST00000371953.3:c.635-2A>T		p.X212_splice	ENST00000371953	NM_000314.4	212			0.144069800569782	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	FALSE	0	0.168743309248819	2		331	238	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115979	8115980	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0054540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	68	373	0	ENST00000346208.3:c.1328dup	p.Ter444LeufsTer63	p.*444Lfs*63	ENST00000346208		442	atg/atGg	6/6	1	2	FACETS	0.987	0.865	1	0.987	0.865	1	CLONAL	1	TRUE	1	0.407555439667751	2		373	338	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101053	26101053	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	129	738	0	ENST00000435504.4:c.39G>C	p.Trp13Cys	p.W13C	ENST00000435504		13	tgG/tgC	1/13	1	2	FACETS	0.843	0.765	0.925	0.843	0.765	0.925	CLONAL	1	TRUE	1	0.407555439667751	2		738	751	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0054541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	248	643	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.603022063566784	2		643	775	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890149	76890150	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	154	459	0	ENST00000373344.5:c.4744dup	p.Thr1582AsnfsTer19	p.T1582Nfs*19	ENST00000373344	NM_000489.3	1582	aca/aAca	17/35	1	2	FACETS	0.876	0.806	0.949	0.876	0.806	0.949	CLONAL	1	TRUE	1	0.603022063566784	2		459	583	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272121	18272121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	28	30	0	ENST00000222254.8:c.631C>T	p.Pro211Ser	p.P211S	ENST00000222254	NM_005027.3	211	Cca/Tca	6/16	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.603022063566784	2		30	83	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0054543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	716	963	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.995	1	1	0.998	1	CLONAL	2	TRUE	1	0.754304809985557	2		966	904	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	288	502	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.474915944160508	5	FACETS	1	0.986	1			1	CLONAL	3	TRUE	NA	0.754304809985557	5		502	501	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0054543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	70	222	2	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.673393811942967	1	FACETS	0.751	0.673	0.829	0.751	0.673	0.829	SUBCLONAL	1	TRUE	0	0.754304809985557	1		224	154	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0054543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	109	458	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.673393811942967	1	FACETS	0.807	0.742	0.873	0.807	0.742	0.873	CLONAL	1	TRUE	0	0.754304809985557	1		458	223	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368313	45368313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747308534	NA	P-0054543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	69	346	3	ENST00000262160.6:c.1289C>T	p.Thr430Met	p.T430M	ENST00000262160	NM_005901.5	430	aCg/aTg	11/11	0.673393811942967	1	FACETS	0.63	0.56	0.701	0.63	0.56	0.701	SUBCLONAL	1	TRUE	0	0.754304809985557	1		349	181	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	41	632	1	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		633	1085	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	71	375	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.882	0.776	0.994			1	INDETERMINATE	1	TRUE	NA	0.512660364844589	2		375	314	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0054545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	14623	911	2	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.512660364844589	41	FACETS	1	0.999	1	0.983	0.98	0.986	CLONAL	40	TRUE	0	0.512660364844589	41		913	15569	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916226	9916226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	119	493	0	ENST00000330684.3:c.2063G>A	p.Gly688Glu	p.G688E	ENST00000330684	NM_001134407.1	688	gGa/gAa	10/13	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.512660364844589	2		493	440	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509660	106509660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757849968	NA	P-0054545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	141	589	0	ENST00000359195.3:c.1654C>T	p.Arg552Cys	p.R552C	ENST00000359195	NM_002649.2	552	Cgc/Tgc	2/11	0.501060972729071	3	FACETS	0.844	0.769	0.922	0.422	0.384	0.461	CLONAL	1	TRUE	1	0.512660364844589	3		589	819	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685305	89685306	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	104	243	0	ENST00000371953.3:c.201dup	p.Tyr68IlefsTer6	p.Y68Ifs*6	ENST00000371953	NM_000314.4	67	ata/atAa	3/9	0.512660364844589	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.512660364844589	1		243	258	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120759	115120759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	133	899	0	ENST00000257566.3:c.247C>T	p.Pro83Ser	p.P83S	ENST00000257566	NM_016569.3	83	Ccc/Tcc	1/8	1	2	FACETS	0.796	0.724	0.87	0.796	0.724	0.87	SUBCLONAL	1	TRUE	1	0.512660364844589	2		899	652	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	139	375	0				ENST00000310581	NM_198253.2	-/1132			0.193129149967484	2	FACETS	1	0.988	1	0.707	0.653	0.762	INDETERMINATE	1	TRUE	0	0.593665155372857	2		375	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0054546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	234	619	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.942	0.881	1	0.942	0.881	1	CLONAL	1	TRUE	1	0.593665155372857	2		620	837	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0054546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	250	419	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.593665155372857	2		419	690	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0054546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	139	726	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			1	2	FACETS	0.76	0.694	0.829	0.76	0.694	0.829	SUBCLONAL	1	TRUE	1	0.593665155372857	2		726	616	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971209	21971209	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0054546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	203	488	0	ENST00000304494.5:c.151-2A>C		p.X51_splice	ENST00000304494	NM_000077.4	51			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.593665155372857	2		488	607	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414266	32414266	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	110	469	0	ENST00000332351.3:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000332351	NM_024426.4	429	Gaa/Taa	8/10	1	2	FACETS	0.824	0.744	0.906	0.824	0.744	0.906	CLONAL	1	TRUE	1	0.593665155372857	2		469	450	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69456093	69456093	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1356268873	NA	P-0054546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1383	87	724	0	ENST00000227507.2:c.12G>T	p.Gln4His	p.Q4H	ENST00000227507	NM_053056.2	4	caG/caT	1/5	0.593665155372857	7	FACETS	0.495	0.436	0.559	0.083	0.072	0.094	SUBCLONAL	1	TRUE	1	0.593665155372857	7		724	1470	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46254212	46254212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	36	362	0	ENST00000371998.3:c.344C>T	p.Pro115Leu	p.P115L	ENST00000371998		115	cCg/cTg	5/23	1	2	FACETS	0.299	0.246	0.359	0.299	0.246	0.359	SUBCLONAL	1	TRUE	1	0.593665155372857	2		362	405	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202994	27202994	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	37	581	0	ENST00000380036.4:c.2086C>G	p.Gln696Glu	p.Q696E	ENST00000380036	NM_000459.3	696	Cag/Gag	13/23	1	2	FACETS	0.174	0.142	0.209	0.174	0.142	0.209	SUBCLONAL	1	TRUE	1	0.593665155372857	2		581	718	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0054547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	184	455	1				ENST00000310581	NM_198253.2	-/1132			0.297023820863496	5	FACETS	1	0.986	1	0.812	0.757	0.867	INDETERMINATE	2	TRUE	2	0.645127253855633	5		456	461	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	320	1150	1	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.645127253855633	NA		1151	814	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089705	27089706	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1286891446	NA	P-0054547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	398	1040	0	ENST00000324856.7:c.2666dup	p.Met890HisfsTer46	p.M890Hfs*46	ENST00000324856	NM_006015.4	887	-/G	8/20	0.483009930733341	3	FACETS	1	0.993	1	0.773	0.742	0.803	CLONAL	2	TRUE	0	0.645127253855633	3		1040	704	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200961	108200961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782310	NA	P-0054547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	116	451	0	ENST00000278616.4:c.7328G>A	p.Arg2443Gln	p.R2443Q	ENST00000278616	NM_000051.3	2443	cGa/cAa	50/63	0.410999979752793	3	FACETS	0.782	0.715	0.851	0.782	0.715	0.851	SUBCLONAL	2	TRUE	1	0.645127253855633	3		451	304	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866707	37866707	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1481	713	990	0	ENST00000269571.5:c.874G>C	p.Gly292Arg	p.G292R	ENST00000269571		292	Ggc/Cgc	7/27	0.645127253855633	7	FACETS	0.877	0.845	0.91			1	CLONAL	3	TRUE	NA	0.645127253855633	7		990	2194	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264568	1264568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761308654	NA	P-0054547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	223	1026	0	ENST00000310581.5:c.2794G>A	p.Gly932Ser	p.G932S	ENST00000310581	NM_198253.2	932	Ggc/Agc	11/16	NA	2	FACETS	1	0.94	1			1	INDETERMINATE	1	TRUE	NA	0.645127253855633	2		1026	688	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348836	89348836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146474985	NA	P-0054547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	246	1226	0	ENST00000301030.4:c.4114G>A	p.Glu1372Lys	p.E1372K	ENST00000301030	NM_001256183.1	1372	Gag/Aag	9/13	0.540632995177133	1	FACETS	0.622	0.583	0.663	0.622	0.583	0.663	SUBCLONAL	1	TRUE	0	0.645127253855633	1		1226	830	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39251221	39251221	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	366	625	2	ENST00000402219.2:c.1132A>T	p.Thr378Ser	p.T378S	ENST00000402219	NM_005633.3	378	Aca/Tca	9/23	0.630194199666993	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.645127253855633	4		627	889	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915852	127915852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	121	512	0	ENST00000373547.4:c.629G>A	p.Arg210Gln	p.R210Q	ENST00000373547	NM_002721.4	210	cGa/cAa	6/7	0.645127253855633	2	FACETS	1	0.977	1	0.595	0.545	0.646	CLONAL	1	TRUE	0	0.645127253855633	2		512	315	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495438	56495438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1184	79	991	0	ENST00000267101.3:c.3628C>T	p.His1210Tyr	p.H1210Y	ENST00000267101	NM_001982.3	1210	Cat/Tat	28/28	0.450521641581949	6	FACETS	0.444	0.389	0.504	0.111	0.097	0.126	SUBCLONAL	1	TRUE	2	0.645127253855633	6		991	1263	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004348	150004348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766836005	NA	P-0054547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	45	415	0	ENST00000253339.5:c.1877G>A	p.Arg626Gln	p.R626Q	ENST00000253339		626	cGa/cAa	3/7	0.332282161755034	3	FACETS	0.603	0.509	0.706	0.301	0.254	0.353	INDETERMINATE	1	TRUE	1	0.645127253855633	3		415	306	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105740	27105740	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	42	432	0	ENST00000324856.7:c.5351A>G	p.Asn1784Ser	p.N1784S	ENST00000324856	NM_006015.4	1784	aAt/aGt	20/20	0.483009930733341	3	FACETS	0.631	0.53	0.741	0.21	0.176	0.247	SUBCLONAL	1	TRUE	0	0.645127253855633	3		432	273	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201854	67201854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	283	945	0	ENST00000312629.5:c.1054G>A	p.Glu352Lys	p.E352K	ENST00000312629	NM_003952.2	352	Gag/Aag	13/15	0.410999979752793	3	FACETS	1	0.992	1	0.651	0.613	0.69	CLONAL	1	TRUE	1	0.645127253855633	3		945	891	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443583	49443583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	512	1028	0	ENST00000301067.7:c.3788C>T	p.Ser1263Leu	p.S1263L	ENST00000301067	NM_003482.3	1263	tCa/tTa	11/54	0.450521641581949	6	FACETS	1	0.993	1	0.857	0.824	0.889	CLONAL	3	TRUE	2	0.645127253855633	6		1028	1061	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371841	45371841	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	21	377	0	ENST00000262160.6:c.1150A>G	p.Ile384Val	p.I384V	ENST00000262160	NM_005901.5	384	Atc/Gtc	10/11	0.492729285078196	3	FACETS	0.33	0.254	0.418	0.165	0.127	0.209	SUBCLONAL	1	TRUE	1	0.645127253855633	3		377	261	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125347	7125347	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	194	996	0	ENST00000302850.5:c.3205A>T	p.Ile1069Phe	p.I1069F	ENST00000302850	NM_000208.2	1069	Att/Ttt	17/22	1	2	FACETS	0.803	0.745	0.863	0.803	0.745	0.863	CLONAL	1	TRUE	1	0.645127253855633	2		996	749	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45857991	45858052	+	frameshift_variant	Frame_Shift_Del	DEL	CTCATACCAGGAGGCCACGGTGCTCTCCATGTACTGGTAGCTGGTGAAGAAGGCCACGATGC	CTCATACCAGGAGGCCACGGTGCTCTCCATGTACTGGTAGCTGGTGAAGAAGGCCACGATGC	-	novel	NA	P-0054547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	45	777	0	ENST00000391945.4:c.1601_1662del	p.Gly534AlafsTer5	p.G534Afs*5	ENST00000391945	NM_000400.3	534	gGCATCGTGGCCTTCTTCACCAGCTACCAGTACATGGAGAGCACCGTGGCCTCCTGGTATGAG/g	17/23	0.645127253855633	3	FACETS	0.291	0.243	0.343	0.145	0.121	0.172	SUBCLONAL	1	TRUE	1	0.645127253855633	3		777	635	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723020	52723020	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	66	1016	0	ENST00000322088.6:c.1205A>C	p.Gln402Pro	p.Q402P	ENST00000322088	NM_014225.5	402	cAg/cCg	10/15	1	2	FACETS	0.285	0.246	0.326	0.285	0.246	0.326	SUBCLONAL	1	TRUE	1	0.645127253855633	2		1016	719	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495714	72495714	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	223	608	0	ENST00000477973.2:c.358A>G	p.Thr120Ala	p.T120A	ENST00000477973	NM_012234.5	120	Acc/Gcc	1/4	0.410999979752793	3	FACETS	0.833	0.782	0.884	0.833	0.782	0.884	CLONAL	2	TRUE	1	0.645127253855633	3		608	549	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268403	142268403	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	101	404	0	ENST00000350721.4:c.3089T>C	p.Ile1030Thr	p.I1030T	ENST00000350721	NM_001184.3	1030	aTa/aCa	15/47	0.410999979752793	3	FACETS	1	0.96	1	0.564	0.509	0.622	CLONAL	1	TRUE	1	0.645127253855633	3		404	367	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048162	180048162	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	209	1319	0	ENST00000261937.6:c.2111C>A	p.Ala704Glu	p.A704E	ENST00000261937	NM_182925.4	704	gCg/gAg	14/30	1	2	FACETS	0.83	0.772	0.889	0.83	0.772	0.889	CLONAL	1	TRUE	1	0.645127253855633	2		1319	781	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184797	32184797	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	66	795	1	ENST00000375023.3:c.1786G>C	p.Asp596His	p.D596H	ENST00000375023	NM_004557.3	596	Gac/Cac	11/30	0.534651433241919	4	FACETS	0.406	0.351	0.465	0.203	0.175	0.233	SUBCLONAL	1	TRUE	2	0.645127253855633	4		796	829	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099764	157099764	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1010126114	NA	P-0054547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	70	450	0	ENST00000346085.5:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000346085	NM_020732.3	234	tAt/tGt	1/20	0.332282161755034	3	FACETS	1	0.903	1	0.514	0.453	0.579	INDETERMINATE	1	TRUE	1	0.645127253855633	3		450	279	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412038	116412038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760153701	NA	P-0054547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	456	777	0	ENST00000397752.3:c.3023C>T	p.Pro1008Leu	p.P1008L	ENST00000397752	NM_000245.2	1008	cCa/cTa	14/21	0.576715538029137	4	FACETS	0.891	0.857	0.925	0.891	0.857	0.925	CLONAL	3	TRUE	1	0.645127253855633	4		777	870	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850271	128850271	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	69	897	0	ENST00000249373.3:c.1534C>G	p.Arg512Gly	p.R512G	ENST00000249373	NM_005631.4	512	Cgc/Ggc	9/12	0.645127253855633	3	FACETS	0.332	0.288	0.38	0.166	0.144	0.19	SUBCLONAL	1	TRUE	1	0.645127253855633	3		897	852	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38186965	38186965	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	105	794	0	ENST00000317025.8:c.1512A>C	p.Glu504Asp	p.E504D	ENST00000317025	NM_023034.1	504	gaA/gaC	6/24	1	2	FACETS	0.462	0.414	0.513	0.462	0.414	0.513	SUBCLONAL	1	TRUE	1	0.645127253855633	2		794	705	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030630	47030651	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGCCACAGGCAGCCACTGAG	GCTGCCACAGGCAGCCACTGAG	-	novel	NA	P-0054547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	347	645	0	ENST00000377604.3:c.406_427del	p.Leu136MetfsTer19	p.L136Mfs*19	ENST00000377604	NM_001204468.1	135	atGCTGCCACAGGCAGCCACTGAG/at	4/24	0.556189188093172	2	FACETS	1	0.966	1			1	CLONAL	2	TRUE	NA	0.645127253855633	2		645	535	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624240	89624241	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0054548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	157	228	0	ENST00000371953.3:c.14_15del	p.Ile5LysfsTer5	p.I5Kfs*5	ENST00000371953	NM_000314.4	5	aTC/a	1/9	0.750097927777142	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.750097927777142	1		228	247	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439145	52439146	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	463	845	0	ENST00000460680.1:c.1096dup	p.Tyr366LeufsTer32	p.Y366Lfs*32	ENST00000460680	NM_004656.3	366	tat/tTat	11/17	0.750097927777142	1	FACETS	0.963	0.928	0.998	0.963	0.928	0.998	CLONAL	1	TRUE	0	0.750097927777142	1		845	801	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0054550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	342	364	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.636929664025203	2	FACETS	0.88	0.845	0.916	0.88	0.845	0.916	CLONAL	2	TRUE	0	0.692398921100119	2		364	561	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	168	507	1	ENST00000263967.3:c.3012G>A	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atA	21/21	0.37721174032017	1	FACETS	0.631	0.584	0.679	0.631	0.584	0.679	INDETERMINATE	1	TRUE	0	0.692398921100119	1		508	503	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779594	3779594	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	230	1622	0	ENST00000262367.5:c.5454del	p.Cys1819AlafsTer54	p.C1819Afs*54	ENST00000262367	NM_004380.2	1818	gtG/gt	31/31	0.439517072461126	1	FACETS	0.344	0.319	0.369	0.344	0.319	0.369	SUBCLONAL	1	TRUE	0	0.692398921100119	1		1622	1264	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	295	375	0				ENST00000310581	NM_198253.2	-/1132			0.902092704477747	7	FACETS	0.757	0.711	0.804	0.303	0.284	0.322	SUBCLONAL	2	TRUE	2	0.902092704477747	7		375	1406	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371789	55371789	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200011294	NA	P-0054552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	37	348	1	ENST00000297316.4:c.479C>T	p.Ala160Val	p.A160V	ENST00000297316	NM_022454.3	160	gCt/gTt	2/2	0.902092704477747	3	FACETS	0.26	0.214	0.312	0.087	0.071	0.104	SUBCLONAL	1	TRUE	0	0.902092704477747	3		349	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555525857	NA	P-0054552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1228	289	814	0	ENST00000269305.4:c.596G>A	p.Gly199Glu	p.G199E	ENST00000269305	NM_001126112.2	199	gGa/gAa	6/11	0.342383973109431	6	FACETS	1	0.987	1	0.197	0.185	0.21	INDETERMINATE	1	TRUE	0	0.902092704477747	6		814	1517	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149982897	149982897	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	336	372	0	ENST00000253339.5:c.3361G>C	p.Glu1121Gln	p.E1121Q	ENST00000253339		1121	Gag/Cag	7/7	0.894773235319289	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.902092704477747	2		372	367	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156698	106156698	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767778868	NA	P-0054552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	156	368	0	ENST00000380013.4:c.1599G>A	p.Met533Ile	p.M533I	ENST00000380013	NM_001127208.2	533	atG/atA	3/11	0.902092704477747	3	FACETS	0.845	0.777	0.915	0.422	0.388	0.458	CLONAL	1	TRUE	1	0.902092704477747	3		368	594	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969327	44969327	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	330	166	0	ENST00000377967.4:c.4009G>T	p.Glu1337Ter	p.E1337*	ENST00000377967	NM_021140.2	1337	Gag/Tag	28/29	0.83871111422489	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.902092704477747	2		166	347	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376036	8376036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	51	336	2	ENST00000356435.5:c.4561G>A	p.Asp1521Asn	p.D1521N	ENST00000356435		1521	Gat/Aat	28/35	1	2	FACETS	0.272	0.231	0.316	0.272	0.231	0.316	SUBCLONAL	1	TRUE	1	0.902092704477747	2		338	416	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138550	11138550	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	754	674	2	ENST00000358026.2:c.3306C>G	p.Phe1102Leu	p.F1102L	ENST00000358026	NM_001128849.1	1102	ttC/ttG	24/36	0.695168355679244	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	2	0.902092704477747	4		676	1516	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224142	36224142	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	848	971	0	ENST00000222270.7:c.6692C>T	p.Ser2231Phe	p.S2231F	ENST00000222270	NM_014727.1	2231	tCc/tTc	28/37	0.902092704477747	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.902092704477747	2		971	913	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982553	10982553	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	228	230	0	ENST00000327064.4:c.175G>C	p.Glu59Gln	p.E59Q	ENST00000327064	NM_199141.1	59	Gag/Cag	1/16	0.695168355679244	4	FACETS	0.993	0.937	1	0.993	0.937	1	CLONAL	2	TRUE	2	0.902092704477747	4		230	484	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503178	125503178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	365	317	0	ENST00000428830.2:c.545G>A	p.Arg182Lys	p.R182K	ENST00000428830	NM_001114121.2	182	aGa/aAa	6/14	0.902092704477747	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.902092704477747	2		317	391	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95595950	95595950	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0054552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	312	348	0	ENST00000393063.1:c.593C>G	p.Ser198Ter	p.S198*	ENST00000393063	NM_030621.3	198	tCa/tGa	7/28	0.902092704477747	3	FACETS	0.982	0.94	1	0.982	0.94	1	CLONAL	2	TRUE	1	0.902092704477747	3		348	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577548	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0054552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	814	730	3	ENST00000269305.4:c.733_734delinsCT	p.Gly245Leu	p.G245L	ENST00000269305	NM_001126112.2	245	GGc/CTc	7/11	0.342383973109431	6	FACETS	0.911	0.891	0.931	0.759	0.742	0.776	INDETERMINATE	5	TRUE	0	0.902092704477747	6		733	1111	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026144	48026144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766202031	NA	P-0054552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	193	411	0	ENST00000234420.5:c.1022C>T	p.Ser341Phe	p.S341F	ENST00000234420	NM_000179.2	341	tCt/tTt	4/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.902092704477747	2		411	420	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856069	151856069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781280663	NA	P-0054552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	261	509	0	ENST00000262189.6:c.11549G>A	p.Arg3850Gln	p.R3850Q	ENST00000262189	NM_170606.2	3850	cGa/cAa	44/59	0.902092704477747	3	FACETS	0.997	0.937	1	0.499	0.468	0.53	CLONAL	1	TRUE	1	0.902092704477747	3		509	842	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053566	37053568	+	missense_variant	Missense_Mutation	TNP	CCA	CCA	ACG	novel	NA	P-0054552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	271	513	0	ENST00000231790.2:c.653_655delinsACG	p.Ser218_Ile219delinsTyrVal	p.S218_I219delinsYV	ENST00000231790	NM_000249.3	218	tCCAtc/tACGtc	8/19	0.902092704477747	3	FACETS	0.937	0.881	0.995	0.312	0.293	0.332	CLONAL	1	TRUE	0	0.902092704477747	3		513	930	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029477	16029478	+	frameshift_variant	Frame_Shift_Ins	INS	TC	TC	GCTTTATCCTCTG	novel	NA	P-0054552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	167	385	0	ENST00000268712.3:c.1552_1553delinsCAGAGGATAAAGC	p.Glu518GlnfsTer41	p.E518Qfs*41	ENST00000268712	NM_006311.3	518	GAa/CAGAGGATAAAGCa	15/46	0.342383973109431	6	FACETS	1	0.983	1	0.209	0.192	0.227	INDETERMINATE	1	TRUE	0	0.902092704477747	6		385	828	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871012	12871040	+	frameshift_variant	Frame_Shift_Del	DEL	AGAAGGGCAGCTTGCCCGAGTTCTACTAC	AGAAGGGCAGCTTGCCCGAGTTCTACTAC	-	novel	NA	P-0054554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	48	435	0	ENST00000228872.4:c.242_270del	p.Lys81ThrfsTer34	p.K81Tfs*34	ENST00000228872	NM_004064.3	80	gAGAAGGGCAGCTTGCCCGAGTTCTACTAC/g	1/3	0.303765113361376	1	FACETS	0.535	0.453	0.626	0.535	0.453	0.626	SUBCLONAL	1	TRUE	0	0.319378513555445	1		435	472	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593609	55593611	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	rs121913685	NA	P-0054555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	184	397	0	ENST00000288135.5:c.1679_1681del	p.Val560del	p.V560del	ENST00000288135	NM_000222.2	559	GTT/-	11/21	1	2	FACETS	0.979	0.909	1	0.979	0.909	1	CLONAL	1	TRUE	1	0.65950899918747	2		397	570	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828798	3828798	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	110	613	0	ENST00000262367.5:c.1844C>T	p.Thr615Ile	p.T615I	ENST00000262367	NM_004380.2	615	aCa/aTa	9/31	1	2	FACETS	0.349	0.312	0.387	0.349	0.312	0.387	SUBCLONAL	1	TRUE	1	0.65950899918747	2		613	957	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	214	304	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	1	0.968	1			1	INDETERMINATE	2	TRUE	NA	0.359397077933849	2		304	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0054556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	131	817	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.359397077933849	1	FACETS	0.914	0.832	1	0.914	0.832	1	CLONAL	1	TRUE	0	0.359397077933849	1		817	654	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0054556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	52	222	2	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.359397077933849	2		224	289	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149945	99149945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	135	626	1	ENST00000074304.5:c.257C>T	p.Thr86Met	p.T86M	ENST00000074304	NM_001134224.1	86	aCg/aTg	5/26	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.359397077933849	2		627	725	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411576	63411576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	184	902	1	ENST00000330258.3:c.1591C>T	p.Arg531Ter	p.R531*	ENST00000330258	NM_152424.3	531	Cga/Tga	2/2	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.359397077933849	2		903	835	SUCCESS
APC	324	MSKCC	GRCh37	5	112164585	112164585	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123116	NA	P-0054556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	56	197	0	ENST00000257430.4:c.1659G>A	p.Trp553Ter	p.W553*	ENST00000257430	NM_000038.5	553	tgG/tgA	14/16	1	2	FACETS	0.95	0.819	1	0.95	0.819	1	CLONAL	1	TRUE	1	0.359397077933849	2		197	328	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619223	43619223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	89	786	2	ENST00000355710.3:c.2906G>A	p.Arg969Gln	p.R969Q	ENST00000355710	NM_020975.4	969	cGg/cAg	17/20	1	2	FACETS	0.692	0.613	0.776	0.692	0.613	0.776	SUBCLONAL	1	TRUE	1	0.359397077933849	2		788	716	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572532	64572532	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs794728654	NA	P-0054556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	147	1071	2	ENST00000312049.6:c.1324C>T	p.Gln442Ter	p.Q442*	ENST00000312049	NM_130799.2	442	Cag/Tag	9/10	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.359397077933849	2		1073	791	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66520205	66520206	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs281864790	NA	P-0054558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	197	437	0	ENST00000358598.2:c.491_492del	p.Val164AspfsTer5	p.V164Dfs*5	ENST00000358598	NM_212471.2	163	acTGtg/actg	5/11	0.707763634683724	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.707763634683724	1		437	348	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750471	41750563	+	inframe_deletion	In_Frame_Del	DEL	CCCCAAAAGTGGTCCTTATCGGGTTATACTGGAAGCCACTGGCCTGGCTGCAGGAACTGAAGTCAGCATAGGCTGAAGCCAGGCTCGAGGTGT	CCCCAAAAGTGGTCCTTATCGGGTTATACTGGAAGCCACTGGCCTGGCTGCAGGAACTGAAGTCAGCATAGGCTGAAGCCAGGCTCGAGGTGT	-	novel	NA	P-0054558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	196	725	0	ENST00000226382.2:c.65_157del	p.Asp22_Gly52del	p.D22_G52del	ENST00000226382	NM_003924.3	22	gACACCTCGAGCCTGGCTTCAGCCTATGCTGACTTCAGTTCCTGCAGCCAGGCCAGTGGCTTCCAGTATAACCCGATAAGGACCACTTTTGGGGcc/gcc	1/3	1	2	FACETS	0.833	0.774	0.893	0.833	0.774	0.893	CLONAL	1	TRUE	1	0.707763634683724	2		725	665	SUCCESS
APC	324	MSKCC	GRCh37	5	112175769	112175779	+	frameshift_variant	Frame_Shift_Del	DEL	CGGAAAGTACT	CGGAAAGTACT	-	novel	NA	P-0054559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	33	348	0	ENST00000257430.4:c.4479_4489del	p.Glu1494ArgfsTer16	p.E1494Rfs*16	ENST00000257430	NM_000038.5	1493	aCGGAAAGTACT/a	16/16	0.166963639530706	2	FACETS		NA	1			1	NA	NA	FALSE	0	NA	2		348	261	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006159	22006159	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	62	1371	0	ENST00000276925.6:c.244del	p.Arg82AspfsTer83	p.R82Dfs*83	ENST00000276925	NM_004936.3	82	Cga/ga	2/2	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		1371	1119	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979496	7979505	+	frameshift_variant	Frame_Shift_Del	DEL	TCCAGTGCAT	TCCAGTGCAT	-	novel	NA	P-0054561-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	229	523	0	ENST00000319144.4:c.1520_1529del	p.Asn507ArgfsTer4	p.N507Rfs*4	ENST00000319144	NM_001139.2	507	aATGCACTGGAg/ag	11/15	0.85844613418795	3	FACETS	0.971	0.908	1	0.486	0.454	0.518	CLONAL	1	TRUE	1	0.85844613418795	3		523	785	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161790	47161790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054561-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	29	332	0	ENST00000409792.3:c.4336G>A	p.Gly1446Arg	p.G1446R	ENST00000409792	NM_014159.6	1446	Ggg/Agg	3/21	1	2	FACETS	0.176	0.141	0.216	0.176	0.141	0.216	SUBCLONAL	1	TRUE	1	0.85844613418795	2		332	384	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212145	5212145	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs771478606	NA	P-0054564-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	256	956	0	ENST00000357368.4:c.4886A>G	p.Asn1629Ser	p.N1629S	ENST00000357368	NM_002850.3	1629	aAc/aGc	32/38	0.453702814961528	3	FACETS	1	0.937	1	0.334	0.312	0.357	CLONAL	1	TRUE	0	0.443245480083898	3		956	1407	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0054565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	114	889	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	NA	2	FACETS	0.903	0.816	0.995			1	INDETERMINATE	2	FALSE	NA	0.225784109181995	2		889	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574000	7574000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	163	712	0	ENST00000269305.4:c.1027G>T	p.Glu343Ter	p.E343*	ENST00000269305	NM_001126112.2	343	Gag/Tag	10/11	0.174259215666567	3	FACETS	1	0.931	1	0.676	0.621	0.733	CLONAL	2	FALSE	0	0.225784109181995	3		712	792	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589588	67589590	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0054565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	33	217	0	ENST00000274335.5:c.1351_1353del	p.Glu451del	p.E451del	ENST00000274335		451	GAA/-	10/15	0.225784109181995	5	FACETS	1	0.945	1	0.494	0.404	0.594	CLONAL	1	FALSE	2	0.225784109181995	5		217	264	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562711	21562711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054565-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	114	424	1	ENST00000382592.4:c.1208C>T	p.Pro403Leu	p.P403L	ENST00000382592	NM_014572.2	403	cCc/cTc	4/8	0.225784109181995	4	FACETS	0.944	0.856	1	1	0.983	1	CLONAL	3	FALSE	2	0.225784109181995	4		425	437	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717692	89717697	+	frameshift_variant	Frame_Shift_Del	DEL	GTACTT	GTACTT	A	novel	NA	P-0054567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	237	508	1	ENST00000371953.3:c.717_722delinsA	p.Met239IlefsTer2	p.M239Ifs*2	ENST00000371953	NM_000314.4	239	atGTACTTt/atAt	7/9	0.412720267606122	3	FACETS	0.957	0.904	1	1	0.993	1	CLONAL	3	FALSE	1	0.412534058143378	3		509	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0054567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	121	831	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.344699698607223	0	FACETS	0.955	0.872	1			1	CLONAL	1	FALSE	0	0.412534058143378	0		831	361	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339575	70339575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266838743	NA	P-0054567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	208	345	1	ENST00000374080.3:c.244C>T	p.Arg82Cys	p.R82C	ENST00000374080		82	Cgt/Tgt	3/45	0.302355175706226	2	FACETS	1	0.988	1			1	CLONAL	3	FALSE	NA	0.412534058143378	2		346	301	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0054569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	795	76	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.612093410905452	7	FACETS	1	0.98	1			1	CLONAL	6	TRUE	NA	0.612093410905452	7		76	1093	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579359	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587780066	NA	P-0054569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	655	1110	1	ENST00000269305.4:c.328del	p.Arg110ValfsTer13	p.R110Vfs*13	ENST00000269305	NM_001126112.2	110	Cgt/gt	4/11	NA	2	FACETS	0.968	0.938	0.996			1	INDETERMINATE	2	TRUE	NA	0.612093410905452	2		1111	1106	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0054569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	438	316	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	0.612093410905452	7	FACETS	1	0.978	1			1	CLONAL	5	TRUE	NA	0.612093410905452	7		316	711	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422431	225422431	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	179	584	0	ENST00000264414.4:c.209G>C	p.Gly70Ala	p.G70A	ENST00000264414	NM_003590.4	70	gGa/gCa	2/16	1	2	FACETS	0.968	0.897	1	0.968	0.897	1	CLONAL	1	TRUE	1	0.612093410905452	2		584	604	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0054570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	50	564	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.153250224402772	3	FACETS	1	0.901	1	0.533	0.456	0.615	INDETERMINATE	1	TRUE	1	0.480753228755134	3		564	242	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444455	50444455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	55	467	0	ENST00000331340.3:c.385C>T	p.Pro129Ser	p.P129S	ENST00000331340	NM_006060.4	129	Ccc/Tcc	4/8	1	2	FACETS	0.806	0.695	0.925	0.806	0.695	0.925	CLONAL	1	TRUE	1	0.480753228755134	2		467	284	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591825	48591830	+	inframe_deletion	In_Frame_Del	DEL	GAAATG	GAAATG	-	novel	NA	P-0054570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	68	575	0	ENST00000342988.3:c.990_995del	p.Glu330_Met331del	p.E330_M331del	ENST00000342988	NM_005359.5	330	GAAATG/-	9/12	0.467364979963716	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.480753228755134	1		575	189	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575209	48575209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767326	NA	P-0054571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	12	13	0	ENST00000342988.3:c.403C>T	p.Arg135Ter	p.R135*	ENST00000342988	NM_005359.5	135	Cga/Tga	3/12	0.190364640751922	2	FACETS	0.713	0.505	0.964	0.356	0.252	0.482	CLONAL	1	FALSE	0	0.285353878707507	2		13	118	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520008	NA	P-0054571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	71	766	0	ENST00000269305.4:c.613T>C	p.Tyr205His	p.Y205H	ENST00000269305	NM_001126112.2	205	Tat/Cat	6/11	0.285353878707507	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	0	0.285353878707507	1		766	340	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129219	152129219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1199270277	NA	P-0054571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	58	1002	3	ENST00000206249.3:c.172G>A	p.Ala58Thr	p.A58T	ENST00000206249	NM_000125.3	58	Gcc/Acc	1/8	0.277214737228457	3	FACETS	0.999	0.86	1	0.499	0.43	0.575	CLONAL	1	FALSE	1	0.285353878707507	3		1005	465	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986838	36986838	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	50	252	1	ENST00000354822.5:c.851C>T	p.Ser284Leu	p.S284L	ENST00000354822	NM_001079668.2	284	tCg/tTg	3/3	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	FALSE	1	0.285353878707507	2		253	296	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016267	150016267	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	15	490	0	ENST00000253339.5:c.439C>T	p.Arg147Ter	p.R147*	ENST00000253339		147	Cga/Tga	2/7	0.277214737228457	3	FACETS	0.629	0.461	0.829	0.314	0.23	0.415	SUBCLONAL	1	FALSE	1	0.285353878707507	3		490	191	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440940	56440968	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCGCTCACCCGCCATCCGAGCCTGCAGA	CTCGCTCACCCGCCATCCGAGCCTGCAGA	-	novel	NA	P-0054571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	56	821	0	ENST00000407977.2:c.376-7_397del		p.X126_splice	ENST00000407977		126		4/10	0.285353878707507	1	FACETS	0.803	0.69	0.926	0.803	0.69	0.926	CLONAL	1	FALSE	0	0.285353878707507	1		821	419	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	405	502	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.617595164207983	3	FACETS	0.975	0.936	1	0.975	0.936	1	CLONAL	2	TRUE	1	0.740956753434136	3		502	768	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0054572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	397	681	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.740956753434136	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.740956753434136	1		682	614	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604797	48604797	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	216	466	0	ENST00000342988.3:c.1619T>A	p.Leu540His	p.L540H	ENST00000342988	NM_005359.5	540	cTt/cAt	12/12	0.740956753434136	1	FACETS	0.932	0.881	0.982	0.932	0.881	0.982	CLONAL	1	TRUE	0	0.740956753434136	1		466	394	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244107	5244107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	437	993	0	ENST00000357368.4:c.1375G>A	p.Gly459Ser	p.G459S	ENST00000357368	NM_002850.3	459	Ggc/Agc	11/38	1	2	FACETS	0.981	0.937	1	0.981	0.937	1	CLONAL	1	TRUE	1	0.740956753434136	2		993	1202	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435585	56435585	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	436	975	0	ENST00000407977.2:c.1552C>T	p.Gln518Ter	p.Q518*	ENST00000407977		518	Cag/Tag	9/10	0.740956753434136	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.740956753434136	1		975	730	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0054573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	150	817	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.823	0.751	0.898	0.823	0.751	0.898	CLONAL	1	TRUE	1	0.340163572214706	2		817	1072	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978320	2978320	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749237424	NA	P-0054573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	76	778	1	ENST00000396946.4:c.1010G>A	p.Arg337Gln	p.R337Q	ENST00000396946	NM_032415.4	337	cGa/cAa	7/25	1	2	FACETS	0.371	0.324	0.421	0.371	0.324	0.421	SUBCLONAL	1	TRUE	1	0.340163572214706	2		779	1206	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453153	140453153	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913337	NA	P-0054573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	36	346	0	ENST00000288602.6:c.1782T>A	p.Asp594Glu	p.D594E	ENST00000288602	NM_004333.4	594	gaT/gaA	15/18	1	2	FACETS	0.567	0.467	0.68	0.567	0.467	0.68	SUBCLONAL	1	TRUE	1	0.340163572214706	2		346	373	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117677	70117677	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	100	823	0	ENST00000245479.2:c.145C>T	p.Gln49Ter	p.Q49*	ENST00000245479	NM_000346.3	49	Cag/Tag	1/3	1	2	FACETS	0.525	0.467	0.586	0.525	0.467	0.586	SUBCLONAL	1	TRUE	1	0.340163572214706	2		823	1120	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50830354	50830354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121908390	NA	P-0054573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	76	434	0	ENST00000398568.2:c.2797C>T	p.Arg933Ter	p.R933*	ENST00000398568	NM_001042412.1	933	Cga/Tga	18/18	1	2	FACETS	0.627	0.549	0.71	0.627	0.549	0.71	SUBCLONAL	1	TRUE	1	0.340163572214706	2		434	713	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519067	103519067	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	62	599	0	ENST00000355739.4:c.2405A>T	p.Gln802Leu	p.Q802L	ENST00000355739	NM_000123.3	802	cAg/cTg	11/15	0.231068940539026	2	FACETS	0.386	0.332	0.445	0.193	0.166	0.223	SUBCLONAL	1	TRUE	0	0.340163572214706	2		599	944	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672569	30672569	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	56	624	0	ENST00000376406.3:c.4391C>T	p.Pro1464Leu	p.P1464L	ENST00000376406	NM_014641.2	1464	cCt/cTt	10/15	0.13482297335473	3	FACETS	0.376	0.321	0.437	0.125	0.107	0.146	INDETERMINATE	1	TRUE	0	0.340163572214706	3		624	1024	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70353051	70353051	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	44	393	0	ENST00000374080.3:c.4606C>T	p.Arg1536Trp	p.R1536W	ENST00000374080		1536	Cgg/Tgg	33/45	1	2	FACETS	0.36	0.301	0.426	0.36	0.301	0.426	SUBCLONAL	1	TRUE	1	0.340163572214706	2		393	718	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0054574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	82	411	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.374542260857501	1	FACETS	0.917	0.814	1	0.917	0.814	1	CLONAL	1	TRUE	0	0.374542260857501	1		411	388	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592108	67592108	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1419325070	NA	P-0054574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	158	279	0	ENST00000274335.5:c.1924C>T	p.Arg642Ter	p.R642*	ENST00000274335		642	Cga/Tga	14/15	1	2	FACETS	1	0.969	1	1	0.993	1	CLONAL	2	TRUE	1	0.374542260857501	2		279	390	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911107	29911107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45542135	NA	P-0054574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	122	892	0	ENST00000376809.5:c.406G>A	p.Gly136Arg	p.G136R	ENST00000376809	NM_002116.7	136	Ggg/Agg	3/8	0.374542260857501	1	FACETS	0.815	0.738	0.895	0.815	0.738	0.895	CLONAL	1	TRUE	0	0.374542260857501	1		892	650	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845574	128845574	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1405848770	NA	P-0054574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	143	700	1	ENST00000249373.3:c.871C>T	p.Arg291Ter	p.R291*	ENST00000249373	NM_005631.4	291	Cga/Tga	4/12	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.374542260857501	2		701	713	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78921045	78921045	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	135	605	0	ENST00000306801.3:c.3159A>T	p.Lys1053Asn	p.K1053N	ENST00000306801	NM_020761.2	1053	aaA/aaT	27/34	1	2	FACETS	0.977	0.889	1	0.977	0.889	1	CLONAL	1	TRUE	1	0.374542260857501	2		605	738	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572400	41572401	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTT	novel	NA	P-0054574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	345	875	0	ENST00000263253.7:c.4931_4932insTCT	p.Leu1644dup	p.L1644dup	ENST00000263253	NM_001429.3	1644	-/CTT	30/31	0.369685959486859	2	FACETS	0.998	0.948	1	0.998	0.948	1	CLONAL	2	TRUE	0	0.374542260857501	2		875	923	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0054575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	596	963	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.554267366550444	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.554267366550444	3		966	827	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881462	111881462	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs199602272	NA	P-0054575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	224	558	0	ENST00000393256.3:c.140A>G	p.Asn47Ser	p.N47S	ENST00000393256	NM_006538.4	47	aAt/aGt	2/4	0.292454947376991	4	FACETS	0.997	0.934	1	0.665	0.623	0.708	INDETERMINATE	2	TRUE	1	0.554267366550444	4		558	630	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732553	190732553	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781501975	NA	P-0054575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	176	288	0	ENST00000441310.2:c.2371G>A	p.Val791Ile	p.V791I	ENST00000441310	NM_000534.4	791	Gtt/Att	11/13	0.292454947376991	4	FACETS	0.922	0.856	0.991	0.615	0.57	0.661	INDETERMINATE	2	TRUE	1	0.554267366550444	4		288	535	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451206	70451206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	278	594	0	ENST00000373644.4:c.6046G>A	p.Gly2016Ser	p.G2016S	ENST00000373644	NM_030625.2	2016	Ggc/Agc	12/12	0.554267366550444	2	FACETS	1	0.994	1	0.732	0.692	0.773	CLONAL	1	TRUE	0	0.554267366550444	2		594	685	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115524	108115525	+	missense_variant	Missense_Mutation	DNP	GA	GA	TC	novel	NA	P-0054575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	170	320	0	ENST00000278616.4:c.672_673inv	p.Lys224_Ser225delinsAsnArg	p.K224_S225delinsNR	ENST00000278616	NM_000051.3	224	aaGAgc/aaTCgc	7/63	0.52317989734609	4	FACETS	0.818	0.756	0.881	0.818	0.756	0.881	CLONAL	2	TRUE	2	0.554267366550444	4		320	583	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724535	43724535	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	241	747	0	ENST00000382044.4:c.3532A>G	p.Thr1178Ala	p.T1178A	ENST00000382044	NM_001141980.1	1178	Act/Gct	17/28	0.26724957043317	3	FACETS	1	0.986	1	0.596	0.557	0.636	INDETERMINATE	1	TRUE	1	0.554267366550444	3		747	932	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137528134	137528134	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	69	292	0	ENST00000367739.4:c.166G>C	p.Val56Leu	p.V56L	ENST00000367739	NM_000416.2	56	Gtc/Ctc	2/7	0.554267366550444	3	FACETS	0.71	0.62	0.806	0.355	0.31	0.403	SUBCLONAL	1	TRUE	1	0.554267366550444	3		292	448	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581160	48581175	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	GTATGATGGTGAAGGA	GTATGATGGTGAAGGA	TATAGCTCC	novel	NA	P-0054575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	126	264	0	ENST00000342988.3:c.464_479delinsTATAGCTCC	p.Ser155IlefsTer2	p.S155Ifs*2	ENST00000342988	NM_005359.5	155	aGTATGATGGTGAAGGAt/aTATAGCTCCt	5/12	0.531639780498077	2	FACETS	0.851	0.786	0.917	0.851	0.786	0.917	CLONAL	2	TRUE	0	0.554267366550444	2		264	267	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0054577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	70	378	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.118314765420101	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	FALSE	0	0.118314765420101	2		378	512	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104569	193104569	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	24	365	0	ENST00000367435.3:c.356A>C	p.Gln119Pro	p.Q119P	ENST00000367435	NM_024529.4	119	cAg/cCg	4/17	1	2	FACETS	0.849	0.664	1	0.849	0.664	1	CLONAL	1	FALSE	1	0.118314765420101	2		365	478	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244427	46244427	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555154946	NA	P-0054577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	70	433	0	ENST00000334344.6:c.2521C>T	p.Gln841Ter	p.Q841*	ENST00000334344	NM_152641.2	841	Cag/Tag	15/21	0.118314765420101	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	2	FALSE	0	0.118314765420101	2		433	580	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508955	106508955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759136884	NA	P-0054578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	24	570	0	ENST00000359195.3:c.949G>A	p.Glu317Lys	p.E317K	ENST00000359195	NM_002649.2	317	Gag/Aag	2/11	1	2	FACETS	0.276	0.215	0.346	0.276	0.215	0.346	SUBCLONAL	1	TRUE	1	0.370351915414899	2		570	470	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061221	38061235	+	inframe_deletion	In_Frame_Del	DEL	GTTCTCGAACATGTT	GTTCTCGAACATGTT	-	novel	NA	P-0054578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	77	612	0	ENST00000250448.2:c.754_768del	p.Asn252_Asn256del	p.N252_N256del	ENST00000250448	NM_004496.3	252	AACATGTTCGAGAAC/-	2/2	1	2	FACETS	0.863	0.76	0.973	0.863	0.76	0.973	CLONAL	1	TRUE	1	0.370351915414899	2		612	482	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804153	46804153	+	stop_lost	Nonstop_Mutation	SNP	T	T	A	novel	NA	P-0054578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	111	608	0	ENST00000290295.7:c.854A>T	p.Ter285LeuextTer32	p.*285Lext*32	ENST00000290295	NM_006361.5	285	tAa/tTa	2/2	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.370351915414899	2		608	547	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966691	44966694	+	frameshift_variant	Frame_Shift_Del	DEL	ATTG	ATTG	-	novel	NA	P-0054578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	58	236	0	ENST00000377967.4:c.3916_3919del	p.Leu1306GlyfsTer49	p.L1306Gfs*49	ENST00000377967	NM_021140.2	1305	acATTG/ac	27/29	1	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.370351915414899	1		236	188	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	21	632	1	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	0.398	0.305	0.508	0.398	0.305	0.508	SUBCLONAL	1	TRUE	1	0.15	2		633	703	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0054579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	20	655	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	1	2	FACETS	0.437	0.333	0.56	0.437	0.333	0.56	SUBCLONAL	1	TRUE	1	0.15	2		655	610	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210728	2210728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745700742	NA	P-0054579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	54	773	0	ENST00000398665.3:c.1225C>T	p.Arg409Cys	p.R409C	ENST00000398665	NM_032482.2	409	Cgc/Tgc	14/28	1	2	FACETS	0.88	0.75	1	0.88	0.75	1	CLONAL	1	TRUE	1	0.15	2		773	818	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641487	23641487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1462734899	NA	P-0054579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	42	512	0	ENST00000261584.4:c.1988G>A	p.Arg663His	p.R663H	ENST00000261584	NM_024675.3	663	cGc/cAc	5/13	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.15	2		512	437	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846036	68846036	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0054579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	43	550	0	ENST00000261769.5:c.1009-2A>C		p.X337_splice	ENST00000261769	NM_004360.3	337			1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.15	2		550	526	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089582	27089586	+	frameshift_variant	Frame_Shift_Del	DEL	CATCC	CATCC	-	novel	NA	P-0054579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	43	776	0	ENST00000324856.7:c.2540_2544del	p.Ile847ThrfsTer23	p.I847Tfs*23	ENST00000324856	NM_006015.4	846	ggCATCCca/ggca	8/20	1	2	FACETS	0.775	0.647	0.918	0.775	0.647	0.918	CLONAL	1	TRUE	1	0.15	2		776	740	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	51	502	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		502	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0054580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	67	817	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		817	807	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023076	150023076	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs187759014	NA	P-0054580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	39	675	1	ENST00000253339.5:c.187C>T	p.Arg63Ter	p.R63*	ENST00000253339		63	Cga/Tga	1/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		676	687	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0054580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	43	112	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		113	751	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130344	11130345	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0054580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	59	955	0	ENST00000358026.2:c.2583_2584del	p.Tyr862HisfsTer82	p.Y862Hfs*82	ENST00000358026	NM_001128849.1	861	gaGTac/gaac	18/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		955	861	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971100	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGG	CCCGG	-	novel	NA	P-0054580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	24	432	0	ENST00000304494.5:c.258_262del	p.Arg87GlyfsTer31	p.R87Gfs*31	ENST00000304494	NM_000077.4	86	gcCCGGGag/gcag	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		432	346	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054410	13054410	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	211	681	0	ENST00000316448.5:c.1021del	p.Glu341SerfsTer9	p.E341Sfs*9	ENST00000316448	NM_004343.3	340	gaG/ga	8/9	0.477764168337491	1	FACETS	0.894	0.836	0.954	0.894	0.836	0.954	CLONAL	1	TRUE	0	0.557171414750981	1		681	611	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188197	10188197	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0054581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	140	518	0	ENST00000256474.2:c.341-1G>C		p.X114_splice	ENST00000256474	NM_000551.3	114			0.557171414750981	1	FACETS	0.939	0.865	1	0.939	0.865	1	CLONAL	1	TRUE	0	0.557171414750981	1		518	386	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643854	52643854	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	119	491	1	ENST00000394830.3:c.2042G>A	p.Ser681Asn	p.S681N	ENST00000394830	NM_018313.4	681	aGt/aAt	17/30	0.557171414750981	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.557171414750981	1		492	302	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953065	2953065	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1429376486	NA	P-0054581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	209	863	0	ENST00000396946.4:c.2875A>C	p.Ser959Arg	p.S959R	ENST00000396946	NM_032415.4	959	Agc/Cgc	22/25	0.372078006841241	1	FACETS	0.831	0.776	0.888	0.831	0.776	0.888	CLONAL	1	TRUE	0	0.557171414750981	1		863	651	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0054583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	57	603	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.7	0.601	0.808	0.7	0.601	0.808	SUBCLONAL	1	TRUE	1	0.317502389746613	2		603	513	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	99	502	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.317502389746613	2		502	515	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0054583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	99	322	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	0.759	0.677	0.846	0.759	0.677	0.846	SUBCLONAL	1	TRUE	1	0.317502389746613	2		322	822	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0054583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	137	298	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.317502389746613	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.317502389746613	2		298	392	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920422	114920422	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	153	450	1	ENST00000543371.1:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000543371	NM_001198531.1	455	Cga/Tga	13/14	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.317502389746613	2		451	758	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649017	37649017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	51	248	0	ENST00000447079.4:c.2122C>T	p.Arg708Cys	p.R708C	ENST00000447079	NM_015083.1	708	Cgt/Tgt	4/14	1	2	FACETS	0.822	0.7	0.954	0.822	0.7	0.954	CLONAL	1	TRUE	1	0.317502389746613	2		248	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0054584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	41	737	0	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	0.3	1	FACETS	0.978	0.815	1	0.978	0.815	1	CLONAL	1	TRUE	0	0.18	1		737	424	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671400	30671400	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	65	737	0	ENST00000376406.3:c.5560G>C	p.Glu1854Gln	p.E1854Q	ENST00000376406	NM_014641.2	1854	Gag/Cag	10/15	0.106385891241125	4	FACETS	0.989	0.86	1	0.989	0.86	1	INDETERMINATE	2	TRUE	2	0.18	4		737	431	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591925	48591925	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	225	451	0	ENST00000342988.3:c.1088G>T	p.Cys363Phe	p.C363F	ENST00000342988	NM_005359.5	363	tGt/tTt	9/12	0.877349038662475	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.877349038662475	1		451	271	SUCCESS
APC	324	MSKCC	GRCh37	5	112175162	112175162	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561588104	NA	P-0054585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	104	233	0	ENST00000257430.4:c.3871C>T	p.Gln1291Ter	p.Q1291*	ENST00000257430	NM_000038.5	1291	Cag/Tag	16/16	0.877349038662475	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.877349038662475	1		233	132	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	DEL	C	C	-	rs1131691033	NA	P-0054585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	300	713	0	ENST00000269305.4:c.993+1del		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.877349038662475	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.877349038662475	1		713	380	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239423	105239423	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	316	790	0	ENST00000349310.3:c.964G>A	p.Glu322Lys	p.E322K	ENST00000349310	NM_001014432.1	322	Gag/Aag	12/15	1	2	FACETS	0.943	0.895	0.991	0.943	0.895	0.991	CLONAL	1	TRUE	1	0.877349038662475	2		790	764	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197397	27197397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771377363	NA	P-0054585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	46	601	1	ENST00000380036.4:c.1709C>T	p.Ser570Leu	p.S570L	ENST00000380036	NM_000459.3	570	tCg/tTg	12/23	1	2	FACETS	0.152	0.128	0.18	0.152	0.128	0.18	SUBCLONAL	1	TRUE	1	0.877349038662475	2		602	688	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163431	108163432	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0054585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	233	604	0	ENST00000278616.4:c.4523dup	p.Tyr1508Ter	p.Y1508*	ENST00000278616	NM_000051.3	1508	tac/tAac	30/63	1	2	FACETS	0.975	0.918	1	0.975	0.918	1	CLONAL	1	TRUE	1	0.877349038662475	2		604	545	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959410	26959410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	294	519	0	ENST00000381527.3:c.577G>A	p.Val193Met	p.V193M	ENST00000381527	NM_001260.1	193	Gtg/Atg	6/13	0.375351289801259	3	FACETS	1	0.994	1	0.738	0.7	0.776	INDETERMINATE	1	TRUE	1	0.877349038662475	3		519	653	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117850	70117883	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCCCATGAACGCCTTCATGGTGTGGGCGCAG	GCGGCCCATGAACGCCTTCATGGTGTGGGCGCAG	-	novel	NA	P-0054585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	334	740	0	ENST00000245479.2:c.323_356del	p.Pro108ArgfsTer28	p.P108Rfs*28	ENST00000245479	NM_000346.3	106	aaGCGGCCCATGAACGCCTTCATGGTGTGGGCGCAG/aa	1/3	1	2	FACETS	0.922	0.876	0.968	0.922	0.876	0.968	CLONAL	1	TRUE	1	0.877349038662475	2		740	826	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172137	32172137	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	374	798	0	ENST00000375023.3:c.2895C>G	p.Cys965Trp	p.C965W	ENST00000375023	NM_004557.3	965	tgC/tgG	19/30	1	2	FACETS	0.93	0.886	0.974	0.93	0.886	0.974	CLONAL	1	TRUE	1	0.877349038662475	2		798	917	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0054586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	132	51	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.371466930387539	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.371466930387539	1		51	527	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	94	737	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	0.792	0.705	0.884	0.792	0.705	0.884	SUBCLONAL	1	TRUE	1	0.371466930387539	2		737	639	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031873	10031873	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	90	954	0	ENST00000330684.3:c.950A>C	p.Lys317Thr	p.K317T	ENST00000330684	NM_001134407.1	317	aAg/aCg	3/13	0.123479162914214	3	FACETS	0.768	0.681	0.861	0.384	0.34	0.431	INDETERMINATE	1	TRUE	1	0.371466930387539	3		954	748	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118715	115118715	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	157	779	0	ENST00000257566.3:c.626T>G	p.Leu209Arg	p.L209R	ENST00000257566	NM_016569.3	209	cTc/cGc	2/8	0.227179167059012	2	FACETS	0.84	0.775	0.907	0.84	0.775	0.907	CLONAL	2	TRUE	0	0.371466930387539	2		779	503	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480355	89480355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772325232	NA	P-0054586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	31	401	0	ENST00000336596.2:c.2192C>T	p.Ala731Val	p.A731V	ENST00000336596	NM_005233.5	731	gCa/gTa	13/17	1	2	FACETS	0.514	0.416	0.624	0.514	0.416	0.624	SUBCLONAL	1	TRUE	1	0.371466930387539	2		401	325	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44911048	44911048	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1131691535	NA	P-0054586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	29	400	0	ENST00000377967.4:c.748+1G>A		p.X250_splice	ENST00000377967	NM_021140.2	250			1	2	FACETS	0.877	0.711	1	0.877	0.711	1	CLONAL	1	TRUE	1	0.371466930387539	2		400	178	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040911	47040911	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs782684857	NA	P-0054587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	176	623	0	ENST00000377604.3:c.1441G>T	p.Glu481Ter	p.E481*	ENST00000377604	NM_001204468.1	481	Gag/Tag	14/24	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.426344696573474	1		623	462	SUCCESS
BTK	695	MSKCC	GRCh37	X	100625010	100625010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	15	336	0	ENST00000308731.7:c.367C>T	p.Arg123Trp	p.R123W	ENST00000308731	NM_000061.2	123	Cgg/Tgg	5/19	1	1	FACETS	0.203	0.148	0.269	0.203	0.148	0.269	SUBCLONAL	1	TRUE	0	0.426344696573474	1		336	273	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724108	61724109	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0054587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	22	411	0	ENST00000401558.2:c.793_794del	p.Leu265GlufsTer5	p.L265Efs*5	ENST00000401558	NM_003400.3	265	CTg/g	10/25	NA	2	FACETS	0.246	0.19	0.311			1	INDETERMINATE	1	TRUE	NA	0.426344696573474	2		411	420	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259879	16259879	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	167	653	0	ENST00000375759.3:c.7144C>T	p.Gln2382Ter	p.Q2382*	ENST00000375759	NM_015001.2	2382	Cag/Tag	11/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.550058240298672	2		653	572	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061750	38061750	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1670	212	637	0	ENST00000250448.2:c.239G>A	p.Gly80Asp	p.G80D	ENST00000250448	NM_004496.3	80	gGc/gAc	2/2	0.550058240298672	6	FACETS	0.86	0.796	0.928	0.172	0.159	0.186	CLONAL	1	TRUE	1	0.550058240298672	6		637	1882	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085825	16085825	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	35	648	0	ENST00000281043.3:c.1001C>T	p.Ala334Val	p.A334V	ENST00000281043	NM_005378.4	334	gCc/gTc	3/3	1	2	FACETS	0.217	0.177	0.262	0.217	0.177	0.262	SUBCLONAL	1	TRUE	1	0.550058240298672	2		648	586	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085871	16085871	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	40	654	0	ENST00000281043.3:c.1047G>T	p.Lys349Asn	p.K349N	ENST00000281043	NM_005378.4	349	aaG/aaT	3/3	1	2	FACETS	0.241	0.2	0.288	0.241	0.2	0.288	SUBCLONAL	1	TRUE	1	0.550058240298672	2		654	603	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55086978	55086978	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	148	454	2	ENST00000275493.2:c.8C>A	p.Pro3His	p.P3H	ENST00000275493	NM_005228.3	3	cCc/cAc	1/28	1	2	FACETS	0.912	0.837	0.99	0.912	0.837	0.99	CLONAL	1	TRUE	1	0.550058240298672	2		456	590	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027756	152027756	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	46	776	0	ENST00000262189.6:c.319A>G	p.Thr107Ala	p.T107A	ENST00000262189	NM_170606.2	107	Act/Gct	3/59	1	2	FACETS	0.253	0.212	0.298	0.253	0.212	0.298	SUBCLONAL	1	TRUE	1	0.550058240298672	2		776	662	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111468	8111502	+	frameshift_variant	Frame_Shift_Del	DEL	GAACTGTCAGACCACCACAACCACACTCTGGAGGA	GAACTGTCAGACCACCACAACCACACTCTGGAGGA	TAGTGT	novel	NA	P-0054588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	178	751	4	ENST00000346208.3:c.954_988delinsTAGTGT	p.Asn319SerfsTer23	p.N319Sfs*23	ENST00000346208		318	gcGAACTGTCAGACCACCACAACCACACTCTGGAGGAgg/gcTAGTGTgg	5/6	1	2	FACETS	0.814	0.751	0.879	0.814	0.751	0.879	CLONAL	1	TRUE	1	0.550058240298672	2		755	795	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0054589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	260	660	2	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.444987566045772	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.444987566045772	1		662	886	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923126	48923126	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0054589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	133	277	0	ENST00000267163.4:c.574A>T	p.Lys192Ter	p.K192*	ENST00000267163	NM_000321.2	192	Aaa/Taa	6/27	0.444987566045772	2	FACETS	0.993	0.917	1	0.993	0.917	1	CLONAL	2	TRUE	0	0.444987566045772	2		277	301	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100887	27100891	+	frameshift_variant	Frame_Shift_Del	DEL	GCGTG	GCGTG	-	novel	NA	P-0054589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	242	722	0	ENST00000324856.7:c.4169_4173del	p.Ser1390ThrfsTer53	p.S1390Tfs*53	ENST00000324856	NM_006015.4	1390	aGCGTG/a	18/20	1	2	FACETS	0.963	0.899	1	0.963	0.899	1	CLONAL	1	TRUE	1	0.444987566045772	2		722	1129	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893615	28893615	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	291	544	0	ENST00000282397.4:c.3231C>G	p.Ser1077Arg	p.S1077R	ENST00000282397	NM_002019.4	1077	agC/agG	24/30	0.444987566045772	2	FACETS	0.983	0.932	1	0.983	0.932	1	CLONAL	2	TRUE	0	0.444987566045772	2		544	665	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435662	56435662	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	591	846	1	ENST00000407977.2:c.1475G>T	p.Gly492Val	p.G492V	ENST00000407977		492	gGc/gTc	9/10	0.444987566045772	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.444987566045772	2		847	1260	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917772	29917772	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1360	315	933	0	ENST00000389048.3:c.896C>G	p.Ser299Cys	p.S299C	ENST00000389048	NM_004304.4	299	tCc/tGc	3/29	0.436545819568669	3	FACETS	1	0.964	1	0.517	0.486	0.549	CLONAL	1	TRUE	1	0.444987566045772	3		933	1675	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101721	71101722	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	97	327	0	ENST00000318789.4:c.476dup	p.Leu159PhefsTer11	p.L159Ffs*11	ENST00000318789	NM_032682.5	159	tta/ttTa	9/21	0.444987566045772	1	FACETS	0.968	0.872	1	0.968	0.872	1	CLONAL	1	TRUE	0	0.444987566045772	1		327	350	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589789	55589789	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	176	491	0	ENST00000288135.5:c.1271G>T	p.Gly424Val	p.G424V	ENST00000288135	NM_000222.2	424	gGc/gTc	8/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.444987566045772	2		491	717	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0054590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	142	365	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.574669614012067	4	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	2	0.697645957790475	4		365	332	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673775	30673776	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0054590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	92	544	1	ENST00000376406.3:c.3184_3185delinsAT	p.Ala1062Ile	p.A1062I	ENST00000376406	NM_014641.2	1062	GCa/ATa	10/15	0.697645957790475	5	FACETS	0.735	0.653	0.823	0.245	0.217	0.275	SUBCLONAL	1	TRUE	2	0.697645957790475	5		545	734	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821356	32821356	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773916016	NA	P-0054590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	159	1249	0	ENST00000354258.4:c.238C>T	p.Leu80Phe	p.L80F	ENST00000354258	NM_000593.5	80	Ctc/Ttc	1/11	0.697645957790475	5	FACETS	0.955	0.875	1	0.318	0.291	0.347	CLONAL	1	TRUE	2	0.697645957790475	5		1249	977	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511529	38511529	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	61	716	0	ENST00000254066.5:c.1027G>C	p.Glu343Gln	p.E343Q	ENST00000254066	NM_000964.3	343	Gag/Cag	8/9	1	2	FACETS	0.59	0.508	0.681	0.59	0.508	0.681	SUBCLONAL	1	TRUE	1	0.229085116987708	2		716	902	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125726	47125726	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	87	467	0	ENST00000409792.3:c.5544del	p.Ser1849ArgfsTer16	p.S1849Rfs*16	ENST00000409792	NM_014159.6	1848	acA/ac	12/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.229085116987708	2		467	612	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341806	8341806	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs895259059	NA	P-0054591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	71	586	0	ENST00000356435.5:c.4834G>T	p.Ala1612Ser	p.A1612S	ENST00000356435		1612	Gca/Tca	29/35	0.229085116987708	1	FACETS	0.895	0.782	1	0.895	0.782	1	CLONAL	1	TRUE	0	0.229085116987708	1		586	613	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	28	703	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.388	0.309	0.48	0.388	0.309	0.48	SUBCLONAL	1	TRUE	1	0.2	2		703	721	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586470	189586470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147148566	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	48	489	0	ENST00000264731.3:c.1094C>T	p.Ser365Leu	p.S365L	ENST00000264731	NM_003722.4	365	tCg/tTg	8/14	1	2	FACETS	0.876	0.74	1	0.876	0.74	1	CLONAL	1	TRUE	1	0.2	2		489	548	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435317	56435317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200066146	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	77	1054	1	ENST00000407977.2:c.1820C>T	p.Ser607Leu	p.S607L	ENST00000407977		607	tCg/tTg	9/10	1	2	FACETS	0.85	0.745	0.964	0.85	0.745	0.964	CLONAL	1	TRUE	1	0.2	2		1055	906	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994790	73994790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs562558740	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	67	930	1	ENST00000318443.5:c.274C>T	p.Arg92Cys	p.R92C	ENST00000318443	NM_001024736.1	92	Cgc/Tgc	3/10	1	2	FACETS	0.852	0.74	0.975	0.852	0.74	0.975	CLONAL	1	TRUE	1	0.2	2		931	786	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	75	801	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.841	0.735	0.955	0.841	0.735	0.955	CLONAL	1	TRUE	1	0.2	2		801	892	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190321	32190321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1033015617	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	68	780	0	ENST00000375023.3:c.418C>T	p.Arg140Cys	p.R140C	ENST00000375023	NM_004557.3	140	Cgc/Tgc	3/30	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.2	2		780	671	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967279	38967279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746828213	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	23	323	0	ENST00000357387.3:c.1202G>A	p.Arg401His	p.R401H	ENST00000357387	NM_152756.3	401	cGt/cAt	14/38	1	2	FACETS	0.691	0.538	0.867	0.691	0.538	0.867	SUBCLONAL	1	TRUE	1	0.2	2		323	333	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453486	138453486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451809865	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	12	395	0	ENST00000289153.2:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000289153	NM_006219.2	321	cGa/cAa	5/22	1	2	FACETS	0.317	0.222	0.436	0.317	0.222	0.436	SUBCLONAL	1	TRUE	1	0.2	2		395	378	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225959	133225959	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs949243552	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	79	1209	1	ENST00000320574.5:c.3938C>T	p.Thr1313Met	p.T1313M	ENST00000320574	NM_006231.2	1313	aCg/aTg	31/49	0.179484110843656	3	FACETS	0.792	0.695	0.898	0.396	0.347	0.449	SUBCLONAL	1	TRUE	1	0.2	3		1210	1097	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042536	37042536	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63751221	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	46	493	1	ENST00000231790.2:c.298C>T	p.Arg100Ter	p.R100*	ENST00000231790	NM_000249.3	100	Cga/Tga	3/19	1	2	FACETS	0.945	0.796	1	0.945	0.796	1	CLONAL	1	TRUE	1	0.2	2		494	487	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	42	365	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.875	0.731	1	0.875	0.731	1	CLONAL	1	TRUE	1	0.2	2		366	480	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845086	128845086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761395599	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	127	1066	1	ENST00000249373.3:c.580G>A	p.Glu194Lys	p.E194K	ENST00000249373	NM_005631.4	194	Gaa/Aaa	3/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.2	2		1067	1041	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662338	227662338	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147944503	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	69	980	0	ENST00000305123.5:c.1117C>T	p.Arg373Cys	p.R373C	ENST00000305123	NM_005544.2	373	Cgc/Tgc	1/2	1	2	FACETS	0.813	0.706	0.928	0.813	0.706	0.928	CLONAL	1	TRUE	1	0.2	2		980	849	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145588	24145588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762962010	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	75	912	0	ENST00000263121.7:c.607G>A	p.Ala203Thr	p.A203T	ENST00000263121	NM_003073.3	203	Gcc/Acc	5/9	1	2	FACETS	0.798	0.697	0.907	0.798	0.697	0.907	CLONAL	1	TRUE	1	0.2	2		912	940	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990402	69990402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765051386	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	29	318	0	ENST00000394351.3:c.361G>A	p.Asp121Asn	p.D121N	ENST00000394351	NM_000248.3	121	Gat/Aat	4/9	1	2	FACETS	0.918	0.738	1	0.918	0.738	1	CLONAL	1	TRUE	1	0.2	2		318	316	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346205	89346205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202081612	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	33	610	4	ENST00000301030.4:c.6745C>T	p.Arg2249Cys	p.R2249C	ENST00000301030	NM_001256183.1	2249	Cgc/Tgc	9/13	1	2	FACETS	0.676	0.55	0.819	0.676	0.55	0.819	SUBCLONAL	1	TRUE	1	0.2	2		614	488	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921567	178921567	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553821144	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	24	342	1	ENST00000263967.3:c.1049A>G	p.Asp350Gly	p.D350G	ENST00000263967	NM_006218.2	350	gAc/gGc	5/21	1	2	FACETS	0.906	0.712	1	0.906	0.712	1	CLONAL	1	TRUE	1	0.2	2		343	265	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150030	202150030	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs931648756	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	20	705	0	ENST00000358485.4:c.1471C>T	p.Arg491Ter	p.R491*	ENST00000358485	NM_001080125.1	491	Cga/Tga	8/9	1	2	FACETS	0.249	0.189	0.32	0.249	0.189	0.32	SUBCLONAL	1	TRUE	1	0.2	2		705	802	SUCCESS
APC	324	MSKCC	GRCh37	5	112176873	112176873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	34	432	0	ENST00000257430.4:c.5582C>A	p.Ser1861Tyr	p.S1861Y	ENST00000257430	NM_000038.5	1861	tCt/tAt	16/16	1	2	FACETS	0.798	0.652	0.962	0.798	0.652	0.962	CLONAL	1	TRUE	1	0.2	2		432	426	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98222053	98222053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	41	473	0	ENST00000331920.6:c.2716C>T	p.Arg906Cys	p.R906C	ENST00000331920	NM_000264.3	906	Cgt/Tgt	17/24	1	2	FACETS	0.775	0.645	0.92	0.775	0.645	0.92	CLONAL	1	TRUE	1	0.2	2		473	529	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	15	278	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	0.444	0.324	0.589	0.444	0.324	0.589	SUBCLONAL	1	TRUE	1	0.2	2		278	338	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508176	106508176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752039271	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	56	467	0	ENST00000359195.3:c.170C>T	p.Ala57Val	p.A57V	ENST00000359195	NM_002649.2	57	gCg/gTg	2/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.2	2		467	430	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249847	133249847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	70	583	1	ENST00000320574.5:c.1376C>T	p.Ser459Phe	p.S459F	ENST00000320574	NM_006231.2	459	tCt/tTt	14/49	0.179484110843656	3	FACETS	1	0.966	1	0.671	0.585	0.763	CLONAL	1	TRUE	1	0.2	3		584	574	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858370	9858370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760522909	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	48	644	0	ENST00000330684.3:c.3031C>T	p.Arg1011Trp	p.R1011W	ENST00000330684	NM_001134407.1	1011	Cgg/Tgg	13/13	1	2	FACETS	0.767	0.647	0.899	0.767	0.647	0.899	SUBCLONAL	1	TRUE	1	0.2	2		644	626	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430600	181430600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1372564199	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	79	598	2	ENST00000325404.1:c.452C>T	p.Ala151Val	p.A151V	ENST00000325404	NM_003106.3	151	gCg/gTg	1/1	1	2	FACETS	0.839	0.74	0.944	1	0.98	1	CLONAL	2	TRUE	1	0.2	2		600	471	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484814	57484814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	73	787	0	ENST00000371085.3:c.794G>A	p.Arg265His	p.R265H	ENST00000371085	NM_000516.4	265	cGc/cAc	10/13	1	2	FACETS	0.886	0.773	1	0.886	0.773	1	CLONAL	1	TRUE	1	0.2	2		787	824	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522568	106522568	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs754441790	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	24	452	0	ENST00000359195.3:c.2545C>T	p.Arg849Ter	p.R849*	ENST00000359195	NM_002649.2	849	Cga/Tga	7/11	1	2	FACETS	0.708	0.555	0.884	0.708	0.555	0.884	SUBCLONAL	1	TRUE	1	0.2	2		452	339	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907620	76907620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	38	567	1	ENST00000373344.5:c.4541G>A	p.Arg1514Gln	p.R1514Q	ENST00000373344	NM_000489.3	1514	cGa/cAa	15/35	1	2	FACETS	0.586	0.483	0.701	0.586	0.483	0.701	SUBCLONAL	1	TRUE	1	0.2	2		568	649	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211389	98211389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150850039	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	71	1116	4	ENST00000331920.6:c.3766G>A	p.Val1256Met	p.V1256M	ENST00000331920	NM_000264.3	1256	Gtg/Atg	22/24	1	2	FACETS	0.698	0.607	0.797	0.698	0.607	0.797	SUBCLONAL	1	TRUE	1	0.2	2		1120	1017	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273979	10273979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1085307680	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	86	1253	1	ENST00000330684.3:c.290G>A	p.Gly97Asp	p.G97D	ENST00000330684	NM_001134407.1	97	gGc/gAc	2/13	1	2	FACETS	0.747	0.658	0.842	0.747	0.658	0.842	SUBCLONAL	1	TRUE	1	0.2	2		1254	1152	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589618	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519838	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	35	274	0	ENST00000274335.5:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000274335		461	Cga/Tga	10/15	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.2	2		274	292	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428244	47428244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	84	1081	1	ENST00000377045.4:c.1204G>A	p.Asp402Asn	p.D402N	ENST00000377045	NM_001654.4	402	Gac/Aac	11/16	1	2	FACETS	0.824	0.725	0.929	0.824	0.725	0.929	CLONAL	1	TRUE	1	0.2	2		1082	1020	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389107	31389107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749860839	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	51	626	0	ENST00000328111.2:c.2020G>A	p.Glu674Lys	p.E674K	ENST00000328111	NM_006892.3	674	Gaa/Aaa	19/23	1	2	FACETS	0.829	0.704	0.967	0.829	0.704	0.967	CLONAL	1	TRUE	1	0.2	2		626	615	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881594	111881594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778682749	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	79	834	0	ENST00000393256.3:c.272G>A	p.Arg91Gln	p.R91Q	ENST00000393256	NM_006538.4	91	cGa/cAa	2/4	1	2	FACETS	0.87	0.764	0.985	0.87	0.764	0.985	CLONAL	1	TRUE	1	0.2	2		834	908	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533850	63533850	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	57	1067	0	ENST00000307078.5:c.1304C>T	p.Pro435Leu	p.P435L	ENST00000307078	NM_004655.3	435	cCg/cTg	6/11	1	2	FACETS	0.681	0.583	0.789	0.681	0.583	0.789	SUBCLONAL	1	TRUE	1	0.2	2		1067	837	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966270	25966270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759268577	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	52	712	2	ENST00000435504.4:c.2936C>T	p.Thr979Met	p.T979M	ENST00000435504		979	aCg/aTg	13/13	1	2	FACETS	0.758	0.644	0.883	0.758	0.644	0.883	SUBCLONAL	1	TRUE	1	0.2	2		714	686	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849819	156849819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765477124	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	70	747	0	ENST00000524377.1:c.2075G>A	p.Arg692His	p.R692H	ENST00000524377	NM_002529.3	692	cGc/cAc	16/17	1	2	FACETS	0.922	0.803	1	0.922	0.803	1	CLONAL	1	TRUE	1	0.2	2		747	759	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134405	41134405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772929365	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	66	639	0	ENST00000379561.5:c.1223C>T	p.Ala408Val	p.A408V	ENST00000379561	NM_002015.3	408	gCg/gTg	2/3	1	2	FACETS	0.922	0.799	1	0.922	0.799	1	CLONAL	1	TRUE	1	0.2	2		639	716	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610561	10610561	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766652922	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	96	1188	4	ENST00000171111.5:c.149G>A	p.Arg50His	p.R50H	ENST00000171111	NM_203500.1	50	cGc/cAc	2/6	1	2	FACETS	0.873	0.776	0.977	0.873	0.776	0.977	CLONAL	1	TRUE	1	0.2	2		1192	1100	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916935	178916935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	11	433	0	ENST00000263967.3:c.322C>T	p.Arg108Cys	p.R108C	ENST00000263967	NM_006218.2	108	Cgt/Tgt	2/21	1	2	FACETS	0.216	0.148	0.301	0.216	0.148	0.301	SUBCLONAL	1	TRUE	1	0.2	2		433	510	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440334	187440334	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	78	713	1	ENST00000232014.4:c.2033G>A	p.Arg678His	p.R678H	ENST00000232014	NM_001130845.1	678	cGc/cAc	10/10	1	2	FACETS	0.965	0.847	1	0.965	0.847	1	CLONAL	1	TRUE	1	0.2	2		714	808	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021818	71021818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869025203	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	35	274	0	ENST00000318789.4:c.1540C>T	p.Arg514Cys	p.R514C	ENST00000318789	NM_032682.5	514	Cgt/Tgt	18/21	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.2	2		274	289	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550523	29550523	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	34	369	0	ENST00000356175.3:c.1783G>T	p.Glu595Ter	p.E595*	ENST00000356175	NM_000267.3	595	Gaa/Taa	16/57	1	2	FACETS	1	0.833	1	1	0.833	1	CLONAL	1	TRUE	1	0.2	2		369	334	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432738	49432738	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555191203	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	75	815	1	ENST00000301067.7:c.8401C>T	p.Arg2801Ter	p.R2801*	ENST00000301067	NM_003482.3	2801	Cga/Tga	34/54	0.179484110843656	3	FACETS	0.973	0.851	1	0.486	0.425	0.553	CLONAL	1	TRUE	1	0.2	3		816	848	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661632	227661632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893642	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	76	1165	1	ENST00000305123.5:c.1823C>T	p.Thr608Met	p.T608M	ENST00000305123	NM_005544.2	608	aCg/aTg	1/2	1	2	FACETS	0.804	0.704	0.913	0.804	0.704	0.913	CLONAL	1	TRUE	1	0.2	2		1166	945	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126378	5126378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775568041	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	18	402	0	ENST00000381652.3:c.3223G>A	p.Val1075Met	p.V1075M	ENST00000381652	NM_004972.3	1075	Gtg/Atg	24/25	1	2	FACETS	0.545	0.41	0.706	0.545	0.41	0.706	SUBCLONAL	1	TRUE	1	0.2	2		402	330	SUCCESS
AR	367	MSKCC	GRCh37	X	66766334	66766334	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	20	202	0	ENST00000374690.3:c.1346C>T	p.Pro449Leu	p.P449L	ENST00000374690	NM_000044.3	449	cCg/cTg	1/8	1	2	FACETS	0.866	0.664	1	0.866	0.664	1	CLONAL	1	TRUE	1	0.2	2		202	231	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944608	40944608	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs752116362	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	29	418	2	ENST00000373198.4:c.1894C>T	p.Arg632Ter	p.R632*	ENST00000373198	NM_133170.3	632	Cga/Tga	12/32	1	2	FACETS	0.661	0.53	0.81	0.661	0.53	0.81	SUBCLONAL	1	TRUE	1	0.2	2		420	439	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162659	47162659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752223546	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	38	464	0	ENST00000409792.3:c.3467G>A	p.Arg1156His	p.R1156H	ENST00000409792	NM_014159.6	1156	cGc/cAc	3/21	1	2	FACETS	0.931	0.771	1	0.931	0.771	1	CLONAL	1	TRUE	1	0.2	2		464	408	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867227	68867227	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781312	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	63	756	1	ENST00000261769.5:c.2474C>T	p.Pro825Leu	p.P825L	ENST00000261769	NM_004360.3	825	cCg/cTg	16/16	1	2	FACETS	0.804	0.694	0.923	0.804	0.694	0.923	CLONAL	1	TRUE	1	0.2	2		757	784	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352576	89352576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762710349	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	64	751	5	ENST00000301030.4:c.763C>T	p.Arg255Trp	p.R255W	ENST00000301030	NM_001256183.1	255	Cgg/Tgg	8/13	1	2	FACETS	0.893	0.772	1	0.893	0.772	1	CLONAL	1	TRUE	1	0.2	2		756	717	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650842	93650842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	64	522	1	ENST00000375746.1:c.1768C>T	p.Arg590Trp	p.R590W	ENST00000375746	NM_001174167.1	590	Cgg/Tgg	13/14	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.2	2		523	590	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31464432	31464432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771607570	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	70	748	0	ENST00000344624.3:c.2485C>T	p.Arg829Trp	p.R829W	ENST00000344624		829	Cgg/Tgg	17/33	1	2	FACETS	0.834	0.726	0.952	0.834	0.726	0.952	CLONAL	1	TRUE	1	0.2	2		748	839	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660409	227660409	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771924555	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	55	891	1	ENST00000305123.5:c.3046C>T	p.Arg1016Ter	p.R1016*	ENST00000305123	NM_005544.2	1016	Cga/Tga	1/2	1	2	FACETS	0.774	0.661	0.898	0.774	0.661	0.898	SUBCLONAL	1	TRUE	1	0.2	2		892	711	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526271	189526271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	66	799	2	ENST00000264731.3:c.535G>A	p.Val179Met	p.V179M	ENST00000264731	NM_003722.4	179	Gtg/Atg	4/14	1	2	FACETS	0.868	0.753	0.994	0.868	0.753	0.994	CLONAL	1	TRUE	1	0.2	2		801	760	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632477	3632477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371875095	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	79	1206	1	ENST00000294008.3:c.5371C>T	p.Arg1791Cys	p.R1791C	ENST00000294008	NM_032444.2	1791	Cgt/Tgt	15/15	1	2	FACETS	0.712	0.624	0.807	0.712	0.624	0.807	SUBCLONAL	1	TRUE	1	0.2	2		1207	1110	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222242	2222242	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs892092927	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	80	1039	2	ENST00000326181.6:c.526G>A	p.Ala176Thr	p.A176T	ENST00000326181	NM_032271.2	176	Gcg/Acg	8/21	1	2	FACETS	0.802	0.704	0.907	0.802	0.704	0.907	CLONAL	1	TRUE	1	0.2	2		1041	998	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660499	227660499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767686104	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	74	915	2	ENST00000305123.5:c.2956C>T	p.Arg986Trp	p.R986W	ENST00000305123	NM_005544.2	986	Cgg/Tgg	1/2	1	2	FACETS	0.983	0.859	1	0.983	0.859	1	CLONAL	1	TRUE	1	0.2	2		917	753	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139408993	139408993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746313097	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	80	1147	0	ENST00000277541.6:c.2176G>A	p.Val726Ile	p.V726I	ENST00000277541	NM_017617.3	726	Gtc/Atc	13/34	1	2	FACETS	0.794	0.697	0.898	0.794	0.697	0.898	SUBCLONAL	1	TRUE	1	0.2	2		1147	1008	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214792	36214792	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	63	962	0	ENST00000222270.7:c.3218G>A	p.Arg1073His	p.R1073H	ENST00000222270	NM_014727.1	1073	cGc/cAc	8/37	1	2	FACETS	0.692	0.596	0.795	0.692	0.596	0.795	SUBCLONAL	1	TRUE	1	0.2	2		962	911	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215748	133215748	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141519273	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	58	688	0	ENST00000320574.5:c.5515C>T	p.Arg1839Cys	p.R1839C	ENST00000320574	NM_006231.2	1839	Cgc/Tgc	40/49	0.179484110843656	3	FACETS	0.846	0.726	0.978	0.423	0.363	0.489	CLONAL	1	TRUE	1	0.2	3		688	754	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65349019	65349019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137855123	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	65	709	1	ENST00000342505.4:c.146G>A	p.Arg49Gln	p.R49Q	ENST00000342505	NM_002227.2	49	cGg/cAg	3/25	1	2	FACETS	0.931	0.807	1	0.931	0.807	1	CLONAL	1	TRUE	1	0.2	2		710	698	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229009	36229009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	83	1002	1	ENST00000222270.7:c.7789G>A	p.Ala2597Thr	p.A2597T	ENST00000222270	NM_014727.1	2597	Gcg/Acg	36/37	1	2	FACETS	0.818	0.72	0.923	0.818	0.72	0.923	CLONAL	1	TRUE	1	0.2	2		1003	1015	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634786	158634786	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765195676	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	41	500	1	ENST00000263640.3:c.400G>A	p.Ala134Thr	p.A134T	ENST00000263640	NM_001105.4	134	Gca/Aca	5/11	1	2	FACETS	0.83	0.691	0.984	0.83	0.691	0.984	CLONAL	1	TRUE	1	0.2	2		501	494	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569942	95569942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139346443	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	47	519	1	ENST00000393063.1:c.3791C>T	p.Thr1264Met	p.T1264M	ENST00000393063	NM_030621.3	1264	aCg/aTg	22/28	1	2	FACETS	0.927	0.782	1	0.927	0.782	1	CLONAL	1	TRUE	1	0.2	2		520	507	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424741	49424741	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783692	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	92	1021	2	ENST00000301067.7:c.13606C>T	p.Arg4536Ter	p.R4536*	ENST00000301067	NM_003482.3	4536	Cga/Tga	40/54	0.179484110843656	3	FACETS	0.881	0.78	0.989	0.44	0.39	0.495	CLONAL	1	TRUE	1	0.2	3		1023	1149	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542189	141542189	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	75	824	1	ENST00000220592.5:c.2534C>T	p.Ala845Val	p.A845V	ENST00000220592	NM_012154.3	845	gCg/gTg	19/19	1	2	FACETS	0.746	0.652	0.848	0.746	0.652	0.848	SUBCLONAL	1	TRUE	1	0.2	2		825	1005	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656263	18656263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762092026	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	33	523	0	ENST00000266497.5:c.2942G>A	p.Arg981His	p.R981H	ENST00000266497		981	cGc/cAc	21/31	0.179484110843656	3	FACETS	0.772	0.628	0.935	0.386	0.314	0.468	CLONAL	1	TRUE	1	0.2	3		523	470	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779676	3779676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1214172132	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	73	1154	0	ENST00000262367.5:c.5372C>T	p.Ser1791Leu	p.S1791L	ENST00000262367	NM_004380.2	1791	tCg/tTg	31/31	1	2	FACETS	0.734	0.64	0.836	0.734	0.64	0.836	SUBCLONAL	1	TRUE	1	0.2	2		1154	994	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293477	137293477	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	80	1251	0	ENST00000481739.1:c.29-1G>A		p.X10_splice	ENST00000481739	NM_002957.4	10			1	2	FACETS	0.775	0.68	0.877	0.775	0.68	0.877	SUBCLONAL	1	TRUE	1	0.2	2		1251	1032	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727522	66727522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	46	637	1	ENST00000307102.5:c.238G>A	p.Gly80Ser	p.G80S	ENST00000307102	NM_002755.3	80	Ggt/Agt	2/11	1	2	FACETS	0.627	0.526	0.738	0.627	0.526	0.738	SUBCLONAL	1	TRUE	1	0.2	2		638	734	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883623	37883623	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1038581447	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	107	1286	1	ENST00000269571.5:c.3235G>A	p.Glu1079Lys	p.E1079K	ENST00000269571		1079	Gaa/Aaa	26/27	1	2	FACETS	0.977	0.874	1	0.977	0.874	1	CLONAL	1	TRUE	1	0.2	2		1287	1095	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946433	2946433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775862540	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	100	1037	1	ENST00000396946.4:c.3304G>A	p.Val1102Met	p.V1102M	ENST00000396946	NM_032415.4	1102	Gtg/Atg	25/25	1	2	FACETS	0.944	0.842	1	0.944	0.842	1	CLONAL	1	TRUE	1	0.2	2		1038	1059	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907370	32907370	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs431825285	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	34	400	0	ENST00000380152.3:c.1755G>T	p.Lys585Asn	p.K585N	ENST00000380152		585	aaG/aaT	10/27	1	2	FACETS	1	0.84	1	1	0.84	1	CLONAL	1	TRUE	1	0.2	2		400	331	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800486	32800486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773325619	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	136	1076	2	ENST00000374899.4:c.1061G>A	p.Arg354His	p.R354H	ENST00000374899	NM_018833.2	354	cGc/cAc	6/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.2	2		1078	1173	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857016	9857016	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	28	320	0	ENST00000330684.3:c.4385C>A	p.Ser1462Tyr	p.S1462Y	ENST00000330684	NM_001134407.1	1462	tCt/tAt	13/13	1	2	FACETS	1	0.824	1	1	0.824	1	CLONAL	1	TRUE	1	0.2	2		320	272	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659847	227659847	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	32	497	1	ENST00000305123.5:c.3608del	p.Pro1203HisfsTer24	p.P1203Hfs*24	ENST00000305123	NM_005544.2	1203	cCa/ca	1/2	1	2	FACETS	0.737	0.598	0.895	0.737	0.598	0.895	SUBCLONAL	1	TRUE	1	0.2	2		498	434	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552729	226552729	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746139482	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	75	669	1	ENST00000366794.5:c.2632C>T	p.Arg878Trp	p.R878W	ENST00000366794	NM_001618.3	878	Cgg/Tgg	19/23	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.2	2		670	713	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670668	67670668	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1396410914	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	71	653	0	ENST00000264010.4:c.1913C>T	p.Pro638Leu	p.P638L	ENST00000264010	NM_006565.3	638	cCt/cTt	11/12	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.2	2		653	699	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117407	7117407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746000108	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	60	808	0	ENST00000302850.5:c.3809G>A	p.Arg1270His	p.R1270H	ENST00000302850	NM_000208.2	1270	cGc/cAc	22/22	1	2	FACETS	0.845	0.727	0.974	0.845	0.727	0.974	CLONAL	1	TRUE	1	0.2	2		808	710	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68982069	68982069	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	52	607	1	ENST00000288368.4:c.1444-1G>T		p.X482_splice	ENST00000288368	NM_024870.2	482			1	2	FACETS	0.917	0.781	1	0.917	0.781	1	CLONAL	1	TRUE	1	0.2	2		608	567	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846280	156846280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs554180226	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	69	1110	3	ENST00000524377.1:c.1721G>A	p.Arg574His	p.R574H	ENST00000524377	NM_002529.3	574	cGc/cAc	14/17	1	2	FACETS	0.698	0.606	0.798	0.698	0.606	0.798	SUBCLONAL	1	TRUE	1	0.2	2		1113	988	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14300926	14300926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781970568	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	28	306	1	ENST00000256196.4:c.572G>A	p.Arg191Gln	p.R191Q	ENST00000256196		191	cGg/cAg	6/6	1	2	FACETS	0.833	0.667	1	0.833	0.667	1	CLONAL	1	TRUE	1	0.2	2		307	336	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97869368	97869368	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780179187	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	81	885	2	ENST00000289081.3:c.1513G>A	p.Ala505Thr	p.A505T	ENST00000289081	NM_000136.2	505	Gcc/Acc	14/15	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.2	2		887	793	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803247	1803247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778353	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	98	1168	2	ENST00000260795.2:c.599G>A	p.Arg200His	p.R200H	ENST00000260795		200	cGc/cAc	4/17	1	2	FACETS	0.971	0.865	1	0.971	0.865	1	CLONAL	1	TRUE	1	0.2	2		1170	1009	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819721	81819721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370352962	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	61	836	1	ENST00000359376.3:c.127G>A	p.Val43Ile	p.V43I	ENST00000359376	NM_002661.3	43	Gtc/Atc	2/33	1	2	FACETS	0.757	0.651	0.872	0.757	0.651	0.872	SUBCLONAL	1	TRUE	1	0.2	2		837	806	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36823939	36823939	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	72	906	0	ENST00000373129.3:c.243G>T	p.Gln81His	p.Q81H	ENST00000373129	NM_032017.1	81	caG/caT	5/12	1	2	FACETS	0.826	0.72	0.94	0.826	0.72	0.94	CLONAL	1	TRUE	1	0.2	2		906	872	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78422363	78422363	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	38	392	0	ENST00000370768.2:c.1599T>G	p.Asn533Lys	p.N533K	ENST00000370768	NM_003902.3	533	aaT/aaG	17/20	1	2	FACETS	0.696	0.575	0.832	0.696	0.575	0.832	SUBCLONAL	1	TRUE	1	0.2	2		392	546	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685298	89685298	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs587780005	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	42	308	0	ENST00000371953.3:c.193T>G	p.Tyr65Asp	p.Y65D	ENST00000371953	NM_000314.4	65	Tac/Gac	3/9	1	2	FACETS	0.75	0.63	0.882	1	0.958	1	SUBCLONAL	2	TRUE	1	0.2	2		308	280	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711277	114711277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	43	591	2	ENST00000543371.1:c.292C>T	p.Pro98Ser	p.P98S	ENST00000543371	NM_001198531.1	98	Cca/Tca	3/14	1	2	FACETS	0.684	0.571	0.809	0.684	0.571	0.809	SUBCLONAL	1	TRUE	1	0.2	2		593	629	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188193	108188193	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	35	339	0	ENST00000278616.4:c.6292C>A	p.Leu2098Ile	p.L2098I	ENST00000278616	NM_000051.3	2098	Ctt/Att	43/63	1	2	FACETS	0.893	0.732	1	0.893	0.732	1	CLONAL	1	TRUE	1	0.2	2		339	392	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170283	119170283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	31	411	1	ENST00000264033.4:c.2513G>A	p.Gly838Asp	p.G838D	ENST00000264033	NM_005188.3	838	gGc/gAc	16/16	1	2	FACETS	0.675	0.546	0.823	0.675	0.546	0.823	SUBCLONAL	1	TRUE	1	0.2	2		412	459	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385330	4385330	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	36	580	0	ENST00000261254.3:c.355A>G	p.Thr119Ala	p.T119A	ENST00000261254	NM_001759.3	119	Acc/Gcc	2/5	0.183619081820114	3	FACETS	0.619	0.507	0.744	0.309	0.253	0.372	SUBCLONAL	1	TRUE	1	0.2	3		580	640	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18477992	18477993	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	34	578	0	ENST00000266497.5:c.1236dup	p.Tyr413IlefsTer2	p.Y413Ifs*2	ENST00000266497		411	aga/agAa	7/31	0.179484110843656	3	FACETS	0.69	0.563	0.834	0.345	0.281	0.417	SUBCLONAL	1	TRUE	1	0.2	3		578	542	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793419	18793419	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	44	566	0	ENST00000266497.5:c.4116T>G	p.Tyr1372Ter	p.Y1372*	ENST00000266497		1372	taT/taG	30/31	0.179484110843656	3	FACETS	0.863	0.723	1	0.431	0.361	0.509	CLONAL	1	TRUE	1	0.2	3		566	561	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416543	49416543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	74	824	1	ENST00000301067.7:c.16168C>T	p.Arg5390Trp	p.R5390W	ENST00000301067	NM_003482.3	5390	Cgg/Tgg	51/54	0.179484110843656	3	FACETS	0.944	0.825	1	0.472	0.412	0.537	CLONAL	1	TRUE	1	0.2	3		825	862	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432363	49432363	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	80	1123	0	ENST00000301067.7:c.8776G>T	p.Val2926Leu	p.V2926L	ENST00000301067	NM_003482.3	2926	Gta/Tta	34/54	0.179484110843656	3	FACETS	0.879	0.772	0.995	0.44	0.386	0.498	CLONAL	1	TRUE	1	0.2	3		1123	1001	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437528	49437528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779659959	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	73	909	2	ENST00000301067.7:c.5357G>A	p.Arg1786His	p.R1786H	ENST00000301067	NM_003482.3	1786	cGt/cAt	23/54	0.179484110843656	3	FACETS	0.73	0.636	0.832	0.365	0.318	0.416	SUBCLONAL	1	TRUE	1	0.2	3		911	1100	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118740	115118740	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745862855	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	86	760	0	ENST00000257566.3:c.601G>A	p.Val201Ile	p.V201I	ENST00000257566	NM_016569.3	201	Gtc/Atc	2/8	0.179484110843656	3	FACETS	0.985	0.87	1	0.493	0.435	0.555	CLONAL	1	TRUE	1	0.2	3		760	960	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897037	28897037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	60	613	0	ENST00000282397.4:c.2843G>A	p.Gly948Asp	p.G948D	ENST00000282397	NM_002019.4	948	gGc/gAc	21/30	1	2	FACETS	0.834	0.718	0.962	0.834	0.718	0.962	CLONAL	1	TRUE	1	0.2	2		613	719	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906663	32906664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886040342	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	27	489	0	ENST00000380152.3:c.1053dup	p.Tyr352IlefsTer6	p.Y352Ifs*6	ENST00000380152		350	gaa/gAaa	10/27	1	2	FACETS	0.758	0.604	0.935	0.758	0.604	0.935	CLONAL	1	TRUE	1	0.2	2		489	356	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061196	38061196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	60	561	1	ENST00000250448.2:c.793C>T	p.Arg265Cys	p.R265C	ENST00000250448	NM_004496.3	265	Cgc/Tgc	2/2	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.2	2		562	524	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643225	38643225	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	22	435	0	ENST00000299084.4:c.695A>C	p.Lys232Thr	p.K232T	ENST00000299084	NM_152594.2	232	aAa/aCa	7/7	1	2	FACETS	0.615	0.476	0.776	0.615	0.476	0.776	SUBCLONAL	1	TRUE	1	0.2	2		435	358	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99491931	99491931	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	70	788	0	ENST00000268035.6:c.3716A>G	p.Asp1239Gly	p.D1239G	ENST00000268035	NM_000875.3	1239	gAc/gGc	20/21	1	2	FACETS	0.875	0.762	0.998	0.875	0.762	0.998	CLONAL	1	TRUE	1	0.2	2		788	800	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639272	3639272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774858804	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	48	1139	1	ENST00000294008.3:c.4367G>A	p.Arg1456His	p.R1456H	ENST00000294008	NM_032444.2	1456	cGc/cAc	12/15	1	2	FACETS	0.53	0.446	0.623	0.53	0.446	0.623	SUBCLONAL	1	TRUE	1	0.2	2		1140	906	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647610	3647610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1236137552	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	91	1056	1	ENST00000294008.3:c.1453G>A	p.Asp485Asn	p.D485N	ENST00000294008	NM_032444.2	485	Gac/Aac	7/15	1	2	FACETS	0.884	0.783	0.993	0.884	0.783	0.993	CLONAL	1	TRUE	1	0.2	2		1057	1029	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788612	3788612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	38	571	0	ENST00000262367.5:c.4342G>A	p.Ala1448Thr	p.A1448T	ENST00000262367	NM_004380.2	1448	Gcc/Acc	26/31	1	2	FACETS	0.613	0.505	0.733	0.613	0.505	0.733	SUBCLONAL	1	TRUE	1	0.2	2		571	620	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829643	72829643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763494543	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	51	709	2	ENST00000268489.5:c.6938G>A	p.Arg2313His	p.R2313H	ENST00000268489	NM_006885.3	2313	cGt/cAt	9/10	1	2	FACETS	0.711	0.603	0.83	0.711	0.603	0.83	SUBCLONAL	1	TRUE	1	0.2	2		711	717	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347974	89347974	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	96	1089	1	ENST00000301030.4:c.4976C>A	p.Pro1659His	p.P1659H	ENST00000301030	NM_001256183.1	1659	cCt/cAt	9/13	1	2	FACETS	0.898	0.798	1	0.898	0.798	1	CLONAL	1	TRUE	1	0.2	2		1090	1069	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348862	89348862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	90	981	0	ENST00000301030.4:c.4088G>A	p.Arg1363Gln	p.R1363Q	ENST00000301030	NM_001256183.1	1363	cGa/cAa	9/13	1	2	FACETS	0.885	0.783	0.994	0.885	0.783	0.994	CLONAL	1	TRUE	1	0.2	2		981	1017	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838128	89838128	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	77	747	0	ENST00000389301.3:c.2109G>T	p.Gln703His	p.Q703H	ENST00000389301	NM_000135.2	703	caG/caT	23/43	1	2	FACETS	0.965	0.846	1	0.965	0.846	1	CLONAL	1	TRUE	1	0.2	2		747	798	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16041500	16041500	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	34	350	0	ENST00000268712.3:c.1379G>C	p.Gly460Ala	p.G460A	ENST00000268712	NM_006311.3	460	gGa/gCa	13/46	1	2	FACETS	0.89	0.728	1	0.89	0.728	1	CLONAL	1	TRUE	1	0.2	2		350	382	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559884	29559884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	25	327	0	ENST00000356175.3:c.3481C>T	p.Leu1161Phe	p.L1161F	ENST00000356175	NM_000267.3	1161	Ctc/Ttc	26/57	1	2	FACETS	0.762	0.601	0.947	0.762	0.601	0.947	CLONAL	1	TRUE	1	0.2	2		327	328	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618586	37618586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	61	734	1	ENST00000447079.4:c.262G>A	p.Ala88Thr	p.A88T	ENST00000447079	NM_015083.1	88	Gcc/Acc	1/14	1	2	FACETS	0.858	0.739	0.987	0.858	0.739	0.987	CLONAL	1	TRUE	1	0.2	2		735	711	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37865611	37865611	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	85	943	1	ENST00000269571.5:c.480G>T	p.Gln160His	p.Q160H	ENST00000269571		160	caG/caT	4/27	1	2	FACETS	0.928	0.819	1	0.928	0.819	1	CLONAL	1	TRUE	1	0.2	2		944	916	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879595	37879595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	75	950	5	ENST00000269571.5:c.1970C>T	p.Ala657Val	p.A657V	ENST00000269571		657	gCg/gTg	17/27	1	2	FACETS	0.755	0.66	0.858	0.755	0.66	0.858	SUBCLONAL	1	TRUE	1	0.2	2		955	993	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440927	56440927	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	78	923	0	ENST00000407977.2:c.410T>C	p.Val137Ala	p.V137A	ENST00000407977		137	gTc/gCc	4/10	1	2	FACETS	0.861	0.755	0.975	0.861	0.755	0.975	CLONAL	1	TRUE	1	0.2	2		923	906	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387658	17387658	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	59	955	1	ENST00000359435.4:c.726C>A	p.Phe242Leu	p.F242L	ENST00000359435	NM_001033549.1	242	ttC/ttA	8/9	1	2	FACETS	0.642	0.551	0.742	0.642	0.551	0.742	SUBCLONAL	1	TRUE	1	0.2	2		956	919	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118878	61118878	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	39	386	0	ENST00000295025.8:c.71G>T	p.Arg24Ile	p.R24I	ENST00000295025	NM_002908.2	24	aGa/aTa	2/11	1	2	FACETS	0.861	0.714	1	0.861	0.714	1	CLONAL	1	TRUE	1	0.2	2		386	453	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044484	128044484	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	95	897	1	ENST00000285398.2:c.1137G>T	p.Lys379Asn	p.K379N	ENST00000285398	NM_000122.1	379	aaG/aaT	8/15	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.2	2		898	892	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737467	204737467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	30	506	3	ENST00000302823.3:c.604G>A	p.Val202Met	p.V202M	ENST00000302823	NM_005214.4	202	Gtg/Atg	4/4	1	2	FACETS	0.679	0.546	0.829	0.679	0.546	0.829	SUBCLONAL	1	TRUE	1	0.2	2		509	442	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39763592	39763592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759803619	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	45	521	0	ENST00000288319.7:c.860G>A	p.Arg287His	p.R287H	ENST00000288319	NM_182918.3	287	cGt/cAt	8/10	1	2	FACETS	0.852	0.716	1	0.852	0.716	1	CLONAL	1	TRUE	1	0.2	2		521	528	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650340	12650340	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	78	636	0	ENST00000251849.4:c.506G>C	p.Gly169Ala	p.G169A	ENST00000251849	NM_002880.3	169	gGc/gCc	5/17	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.2	2		636	609	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096177	71096177	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	33	473	1	ENST00000318789.4:c.580C>T	p.Gln194Ter	p.Q194*	ENST00000318789	NM_032682.5	194	Cag/Tag	10/21	1	2	FACETS	0.638	0.519	0.773	0.638	0.519	0.773	SUBCLONAL	1	TRUE	1	0.2	2		474	517	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270155	66270155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	41	470	0	ENST00000273854.3:c.1727C>A	p.Ala576Asp	p.A576D	ENST00000273854	NM_004439.5	576	gCt/gAt	8/18	1	2	FACETS	0.844	0.703	1	0.844	0.703	1	CLONAL	1	TRUE	1	0.2	2		470	486	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286200	66286200	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	37	457	0	ENST00000273854.3:c.1486A>G	p.Asn496Asp	p.N496D	ENST00000273854	NM_004439.5	496	Aat/Gat	6/18	1	2	FACETS	0.925	0.763	1	0.925	0.763	1	CLONAL	1	TRUE	1	0.2	2		457	400	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540719	187540719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	30	480	0	ENST00000441802.2:c.7021C>T	p.Leu2341Phe	p.L2341F	ENST00000441802	NM_005245.3	2341	Ctc/Ttc	10/27	1	2	FACETS	0.581	0.467	0.711	0.581	0.467	0.711	SUBCLONAL	1	TRUE	1	0.2	2		480	516	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31423009	31423009	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748009983	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	49	687	0	ENST00000344624.3:c.3304C>T	p.Pro1102Ser	p.P1102S	ENST00000344624		1102	Cca/Tca	26/33	1	2	FACETS	0.77	0.652	0.902	0.77	0.652	0.902	CLONAL	1	TRUE	1	0.2	2		687	636	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591107	67591107	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	52	348	0	ENST00000274335.5:c.1700A>C	p.Lys567Thr	p.K567T	ENST00000274335		567	aAa/aCa	12/15	1	2	FACETS	0.767	0.656	0.887	1	0.967	1	SUBCLONAL	2	TRUE	1	0.2	2		348	339	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721871	176721871	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs950485640	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	67	769	0	ENST00000439151.2:c.7502C>T	p.Pro2501Leu	p.P2501L	ENST00000439151	NM_022455.4	2501	cCg/cTg	23/23	1	2	FACETS	0.831	0.721	0.951	0.831	0.721	0.951	CLONAL	1	TRUE	1	0.2	2		769	806	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815758	32815758	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147741317	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	94	1156	0	ENST00000354258.4:c.1858G>A	p.Gly620Arg	p.G620R	ENST00000354258	NM_000593.5	620	Gga/Aga	8/11	1	2	FACETS	0.939	0.834	1	0.939	0.834	1	CLONAL	1	TRUE	1	0.2	2		1156	1001	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745361	43745361	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	75	917	0	ENST00000523873.1:c.274C>A	p.Leu92Met	p.L92M	ENST00000523873		92	Ctg/Atg	3/8	1	2	FACETS	0.877	0.767	0.996	0.877	0.767	0.996	CLONAL	1	TRUE	1	0.2	2		917	855	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745380	43745380	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	57	817	1	ENST00000523873.1:c.293A>C	p.Glu98Ala	p.E98A	ENST00000523873		98	gAg/gCg	3/8	1	2	FACETS	0.746	0.639	0.864	0.746	0.639	0.864	SUBCLONAL	1	TRUE	1	0.2	2		818	764	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677878	117677878	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	40	502	0	ENST00000368508.3:c.4055T>C	p.Ile1352Thr	p.I1352T	ENST00000368508	NM_002944.2	1352	aTa/aCa	25/43	1	2	FACETS	0.998	0.83	1	0.998	0.83	1	CLONAL	1	TRUE	1	0.2	2		502	401	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469853	157469853	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	87	931	0	ENST00000346085.5:c.2647C>A	p.His883Asn	p.H883N	ENST00000346085	NM_020732.3	883	Cat/Aat	9/20	1	2	FACETS	0.98	0.866	1	0.98	0.866	1	CLONAL	1	TRUE	1	0.2	2		931	888	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984151	2984151	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	66	665	0	ENST00000396946.4:c.379C>A	p.Leu127Ile	p.L127I	ENST00000396946	NM_032415.4	127	Ctc/Atc	5/25	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.2	2		665	657	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38188993	38188993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	40	718	0	ENST00000317025.8:c.1021G>A	p.Ala341Thr	p.A341T	ENST00000317025	NM_023034.1	341	Gct/Act	5/24	1	2	FACETS	0.526	0.435	0.627	0.526	0.435	0.627	SUBCLONAL	1	TRUE	1	0.2	2		718	761	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879322	56879322	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	90	841	0	ENST00000519728.1:c.839G>T	p.Gly280Val	p.G280V	ENST00000519728	NM_002350.3	280	gGa/gTa	9/13	1	2	FACETS	0.964	0.853	1	0.964	0.853	1	CLONAL	1	TRUE	1	0.2	2		841	934	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864684	68864684	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	45	549	0	ENST00000288368.4:c.55A>C	p.Lys19Gln	p.K19Q	ENST00000288368	NM_024870.2	19	Aag/Cag	1/40	1	2	FACETS	0.812	0.682	0.956	0.812	0.682	0.956	CLONAL	1	TRUE	1	0.2	2		549	554	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542168	141542168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	78	793	0	ENST00000220592.5:c.2555C>T	p.Thr852Ile	p.T852I	ENST00000220592	NM_012154.3	852	aCt/aTt	19/19	1	2	FACETS	0.795	0.697	0.901	0.795	0.697	0.901	CLONAL	1	TRUE	1	0.2	2		793	981	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739656	145739656	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	93	1202	0	ENST00000428558.2:c.1795G>T	p.Val599Phe	p.V599F	ENST00000428558	NM_004260.3	599	Gtt/Ttt	11/22	1	2	FACETS	0.883	0.783	0.99	0.883	0.783	0.99	CLONAL	1	TRUE	1	0.2	2		1202	1053	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135804238	135804238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773784532	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	67	674	0	ENST00000298552.3:c.22G>A	p.Gly8Arg	p.G8R	ENST00000298552	NM_001162426.1	8	Ggg/Agg	3/23	1	2	FACETS	0.887	0.77	1	0.887	0.77	1	CLONAL	1	TRUE	1	0.2	2		674	755	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309006	137309006	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1430081220	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	51	1024	0	ENST00000481739.1:c.613G>A	p.Val205Met	p.V205M	ENST00000481739	NM_002957.4	205	Gtg/Atg	5/10	1	2	FACETS	0.576	0.488	0.674	0.576	0.488	0.674	SUBCLONAL	1	TRUE	1	0.2	2		1024	885	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412624	139412624	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	107	1307	0	ENST00000277541.6:c.1220del	p.Pro407ArgfsTer224	p.P407Rfs*224	ENST00000277541	NM_017617.3	407	cCg/cg	7/34	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.2	2		1307	1060	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566396	139566396	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	68	1041	2	ENST00000308874.7:c.655G>A	p.Ala219Thr	p.A219T	ENST00000308874		219	Gcc/Acc	9/10	1	2	FACETS	0.768	0.667	0.879	0.768	0.667	0.879	SUBCLONAL	1	TRUE	1	0.2	2		1043	885	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15833808	15833808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	78	871	0	ENST00000307771.7:c.566G>A	p.Arg189His	p.R189H	ENST00000307771	NM_005089.3	189	cGt/cAt	8/11	1	2	FACETS	0.887	0.778	1	0.887	0.778	1	CLONAL	1	TRUE	1	0.2	2		871	879	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424736	47424736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	59	806	0	ENST00000377045.4:c.544C>T	p.Pro182Ser	p.P182S	ENST00000377045	NM_001654.4	182	Ccc/Tcc	6/16	1	2	FACETS	0.688	0.591	0.795	0.688	0.591	0.795	SUBCLONAL	1	TRUE	1	0.2	2		806	857	SUCCESS
AR	367	MSKCC	GRCh37	X	66766052	66766052	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	82	1075	0	ENST00000374690.3:c.1064A>G	p.Glu355Gly	p.E355G	ENST00000374690	NM_000044.3	355	gAg/gGg	1/8	1	2	FACETS	0.833	0.733	0.941	0.833	0.733	0.941	CLONAL	1	TRUE	1	0.2	2		1075	984	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351403	70351403	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	75	888	0	ENST00000374080.3:c.4051T>G	p.Leu1351Val	p.L1351V	ENST00000374080		1351	Ttg/Gtg	29/45	1	2	FACETS	0.9	0.788	1	0.9	0.788	1	CLONAL	1	TRUE	1	0.2	2		888	833	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438330	110438330	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	18	189	0	ENST00000375856.3:c.71A>G	p.Asn24Ser	p.N24S	ENST00000375856	NM_003749.2	24	aAc/aGc	1/2	1	2	FACETS	0.682	0.514	0.88	0.682	0.514	0.88	SUBCLONAL	1	TRUE	1	0.2	2		189	264	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692940	89692944	+	missense_variant	Missense_Mutation	ONP	CGGGG	CGGGG	TGGGA	novel	NA	P-0054592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	79	636	1	ENST00000371953.3:c.424_428delinsTGGGA	p.Arg142_Gly143delinsTrpAsp	p.R142_G143delinsWD	ENST00000371953	NM_000314.4	142	CGGGGc/TGGGAc	5/9	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.2	2		637	572	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0054593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	71	364	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.290618016863278	2		364	454	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045157	47045157	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	118	878	2	ENST00000377604.3:c.2398G>T	p.Glu800Ter	p.E800*	ENST00000377604	NM_001204468.1	800	Gag/Tag	21/24	1	2	FACETS	0.951	0.857	1	0.951	0.857	1	CLONAL	1	TRUE	1	0.290618016863278	2		880	854	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121856	2121856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745897413	NA	P-0054593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	193	1297	0	ENST00000219476.3:c.2018C>T	p.Ala673Val	p.A673V	ENST00000219476	NM_000548.3	673	gCg/gTg	19/42	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.290618016863278	2		1297	1321	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993554	72993554	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	149	1026	0	ENST00000268489.5:c.491G>T	p.Gly164Val	p.G164V	ENST00000268489	NM_006885.3	164	gGg/gTg	2/10	1	2	FACETS	0.958	0.874	1	0.958	0.874	1	CLONAL	1	TRUE	1	0.290618016863278	2		1026	1070	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750389	133750389	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	125	832	0	ENST00000318560.5:c.1220C>T	p.Ala407Val	p.A407V	ENST00000318560	NM_005157.4	407	gCa/gTa	7/11	1	2	FACETS	0.902	0.815	0.993	0.902	0.815	0.993	CLONAL	1	TRUE	1	0.290618016863278	2		832	954	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70355098	70355098	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0054593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	149	985	0	ENST00000374080.3:c.5020A>T	p.Lys1674Ter	p.K1674*	ENST00000374080		1674	Aag/Tag	36/45	1	2	FACETS	0.971	0.886	1	0.971	0.886	1	CLONAL	1	TRUE	1	0.290618016863278	2		985	1056	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604676	43604676	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	74	554	0	ENST00000355710.3:c.1261C>A	p.Gln421Lys	p.Q421K	ENST00000355710	NM_020975.4	421	Cag/Aag	6/20	NA	2	FACETS	0.419	0.367	0.474			1	INDETERMINATE	1	TRUE	NA	0.618154878650806	2		554	572	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741678	17741678	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	244	387	0	ENST00000250003.3:c.349C>A	p.Arg117Ser	p.R117S	ENST00000250003	NM_002478.4	117	Cgc/Agc	1/3	0.618154878650806	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.618154878650806	1		387	419	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456705	32456705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1353446740	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	195	395	1	ENST00000332351.3:c.187G>A	p.Gly63Arg	p.G63R	ENST00000332351	NM_024426.4	63	Ggg/Agg	1/10	0.618154878650806	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.618154878650806	1		396	359	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200267	67200267	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	691	747	1	ENST00000312629.5:c.575A>T	p.Tyr192Phe	p.Y192F	ENST00000312629	NM_003952.2	192	tAc/tTc	7/15	0.608896430660145	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	0	0.618154878650806	3		748	973	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998525	100998525	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	94	458	0	ENST00000325455.5:c.1277C>G	p.Pro426Arg	p.P426R	ENST00000325455	NM_001202474.3	426	cCg/cGg	1/8	0.608896430660145	3	FACETS	0.591	0.526	0.66	0.197	0.175	0.22	SUBCLONAL	1	TRUE	0	0.618154878650806	3		458	674	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865252	57865252	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	57	635	0	ENST00000228682.2:c.2731del	p.Glu911ArgfsTer35	p.E911Rfs*35	ENST00000228682	NM_005269.2	910	tGg/tg	12/12	0.271969853591641	2	FACETS	0.323	0.277	0.373	0.161	0.138	0.187	INDETERMINATE	1	TRUE	0	0.618154878650806	2		635	571	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249359	133249359	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	302	754	0	ENST00000320574.5:c.1540A>G	p.Ile514Val	p.I514V	ENST00000320574	NM_006231.2	514	Atc/Gtc	15/49	0.462024346368021	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.618154878650806	1		754	610	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256554	133256554	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	46	386	0	ENST00000320574.5:c.409G>T	p.Glu137Ter	p.E137*	ENST00000320574	NM_006231.2	137	Gag/Tag	5/49	0.462024346368021	1	FACETS	0.297	0.251	0.348	0.297	0.251	0.348	SUBCLONAL	1	TRUE	0	0.618154878650806	1		386	346	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046641	30046641	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	84	413	0	ENST00000331968.5:c.2542T>G	p.Leu848Val	p.L848V	ENST00000331968	NM_002742.2	848	Ttg/Gtg	18/18	0.618154878650806	3	FACETS	0.743	0.658	0.833	0.371	0.329	0.417	SUBCLONAL	1	TRUE	1	0.618154878650806	3		413	479	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031961	10031961	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	237	632	0	ENST00000330684.3:c.862C>A	p.Leu288Met	p.L288M	ENST00000330684	NM_001134407.1	288	Ctg/Atg	3/13	0.584254597461707	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.618154878650806	1		632	494	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634390	23634390	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786204248	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	56	397	0	ENST00000261584.4:c.2896A>G	p.Ile966Val	p.I966V	ENST00000261584	NM_024675.3	966	Ata/Gta	9/13	0.584254597461707	1	FACETS	0.396	0.341	0.455	0.396	0.341	0.455	SUBCLONAL	1	TRUE	0	0.618154878650806	1		397	316	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912656	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	279	565	0	ENST00000269305.4:c.734G>C	p.Gly245Ala	p.G245A	ENST00000269305	NM_001126112.2	245	gGc/gCc	7/11	0.618154878650806	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.618154878650806	1		565	523	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40444006	40444006	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	224	595	0	ENST00000345506.4:c.302G>C	p.Cys101Ser	p.C101S	ENST00000345506	NM_003152.3	101	tGc/tCc	5/20	0.195603362179289	5	FACETS	0.89	0.831	0.95	0.593	0.554	0.634	INDETERMINATE	2	TRUE	2	0.618154878650806	5		595	785	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55729517	55729517	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	311	684	2	ENST00000284073.2:c.785G>T	p.Gly262Val	p.G262V	ENST00000284073	NM_138962.2	262	gGa/gTa	11/14	0.195603362179289	5	FACETS	1	0.976	1	0.704	0.666	0.743	INDETERMINATE	2	TRUE	2	0.618154878650806	5		686	918	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58725426	58725426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	180	434	0	ENST00000305921.3:c.1000G>T	p.Glu334Ter	p.E334*	ENST00000305921	NM_003620.3	334	Gag/Tag	4/6	0.195603362179289	5	FACETS	0.926	0.865	0.987	0.926	0.865	0.987	INDETERMINATE	3	TRUE	2	0.618154878650806	5		434	404	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117597	70117597	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	207	770	0	ENST00000245479.2:c.65C>A	p.Pro22His	p.P22H	ENST00000245479	NM_000346.3	22	cCc/cAc	1/3	0.195603362179289	5	FACETS	1	0.99	1	0.472	0.438	0.507	INDETERMINATE	1	TRUE	2	0.618154878650806	5		770	912	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968258	18968258	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	98	821	1	ENST00000262803.5:c.2098G>T	p.Val700Phe	p.V700F	ENST00000262803	NM_002911.3	700	Gtc/Ttc	15/24	0.618154878650806	2	FACETS	0.339	0.302	0.379	0.17	0.151	0.19	SUBCLONAL	1	TRUE	0	0.618154878650806	2		822	935	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791284	42791284	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	283	810	1	ENST00000575354.2:c.344G>T	p.Gly115Val	p.G115V	ENST00000575354	NM_015125.3	115	gGg/gTg	3/20	0.618154878650806	3	FACETS	1	0.988	1	0.398	0.374	0.422	CLONAL	1	TRUE	0	0.618154878650806	3		811	1004	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281192	46281192	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	54	496	0	ENST00000371998.3:c.3989G>C	p.Ser1330Thr	p.S1330T	ENST00000371998		1330	aGt/aCt	21/23	0.302220851465343	3	FACETS	0.428	0.366	0.497	0.143	0.122	0.166	INDETERMINATE	1	TRUE	0	0.618154878650806	3		496	534	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162023	47162023	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	104	340	0	ENST00000409792.3:c.4103A>T	p.Gln1368Leu	p.Q1368L	ENST00000409792	NM_014159.6	1368	cAa/cTa	3/21	0.271969853591641	2	FACETS	1	0.985	1	0.722	0.66	0.785	INDETERMINATE	1	TRUE	0	0.618154878650806	2		340	233	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200016	128200016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	93	786	0	ENST00000341105.2:c.1289C>T	p.Ala430Val	p.A430V	ENST00000341105	NM_032638.4	430	gCa/gTa	6/6	0.271969853591641	2	FACETS	0.43	0.382	0.481	0.215	0.191	0.241	INDETERMINATE	1	TRUE	0	0.618154878650806	2		786	700	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946158	55946158	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	130	392	0	ENST00000263923.4:c.4021del	p.Gln1341ArgfsTer11	p.Q1341Rfs*11	ENST00000263923	NM_002253.2	1341	Cag/ag	30/30	0.618154878650806	3	FACETS	0.722	0.655	0.792			1	SUBCLONAL	1	TRUE	NA	0.618154878650806	3		392	763	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948196	55948196	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	210	386	1	ENST00000263923.4:c.3775G>T	p.Asp1259Tyr	p.D1259Y	ENST00000263923	NM_002253.2	1259	Gac/Tac	29/30	0.618154878650806	3	FACETS	1	0.98	1			1	CLONAL	2	TRUE	NA	0.618154878650806	3		387	409	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356251	66356251	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	146	519	0	ENST00000273854.3:c.1246C>A	p.Pro416Thr	p.P416T	ENST00000273854	NM_004439.5	416	Ccc/Acc	5/18	1	2	FACETS	0.943	0.866	1	0.943	0.866	1	CLONAL	1	TRUE	1	0.618154878650806	2		519	501	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629511	187629511	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs755751300	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	101	544	0	ENST00000441802.2:c.1471G>T	p.Asp491Tyr	p.D491Y	ENST00000441802	NM_005245.3	491	Gat/Tat	2/27	0.389242916274255	1	FACETS	0.676	0.611	0.744	0.676	0.611	0.744	SUBCLONAL	1	TRUE	0	0.618154878650806	1		544	334	SUCCESS
APC	324	MSKCC	GRCh37	5	112173713	112173713	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	29	259	0	ENST00000257430.4:c.2422G>T	p.Asp808Tyr	p.D808Y	ENST00000257430	NM_000038.5	808	Gat/Tat	16/16	0.618154878650806	1	FACETS	0.421	0.342	0.508	0.421	0.342	0.508	SUBCLONAL	1	TRUE	0	0.618154878650806	1		259	154	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176516649	176516649	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	283	642	0	ENST00000292408.4:c.46G>T	p.Gly16Trp	p.G16W	ENST00000292408	NM_213647.1	16	Ggg/Tgg	2/18	0.618154878650806	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.618154878650806	1		642	576	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168727	32168727	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	300	805	2	ENST00000375023.3:c.4196C>A	p.Ser1399Tyr	p.S1399Y	ENST00000375023	NM_004557.3	1399	tCc/tAc	23/30	0.618154878650806	2	FACETS	1	0.988	1	0.581	0.549	0.613	CLONAL	1	TRUE	0	0.618154878650806	2		807	836	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803110	32803110	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	380	539	0	ENST00000374899.4:c.766G>T	p.Asp256Tyr	p.D256Y	ENST00000374899	NM_018833.2	256	Gat/Tat	5/12	0.618154878650806	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.618154878650806	2		539	614	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120576	94120576	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	28	351	0	ENST00000369303.4:c.475G>T	p.Asp159Tyr	p.D159Y	ENST00000369303	NM_004440.3	159	Gac/Tac	3/17	0.618154878650806	1	FACETS	0.415	0.335	0.502	0.415	0.335	0.502	SUBCLONAL	1	TRUE	0	0.618154878650806	1		351	151	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55228014	55228014	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	69	212	0	ENST00000275493.2:c.1481G>T	p.Arg494Ile	p.R494I	ENST00000275493	NM_005228.3	494	aGa/aTa	12/28	0.618154878650806	5	FACETS	0.806	0.71	0.907	0.537	0.473	0.605	CLONAL	2	TRUE	2	0.618154878650806	5		212	267	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339542	81339542	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	94	343	0	ENST00000222390.5:c.1462G>T	p.Ala488Ser	p.A488S	ENST00000222390	NM_000601.4	488	Gcc/Tcc	13/18	0.265503391902931	4	FACETS	0.771	0.694	0.852	0.771	0.694	0.852	INDETERMINATE	2	TRUE	2	0.618154878650806	4		343	319	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852090	128852090	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	412	893	0	ENST00000249373.3:c.2162C>G	p.Ala721Gly	p.A721G	ENST00000249373	NM_005631.4	721	gCt/gGt	12/12	0.265503391902931	4	FACETS	0.98	0.935	1	0.98	0.935	1	INDETERMINATE	2	TRUE	2	0.618154878650806	4		893	1100	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342745	87342745	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	31	354	0	ENST00000277120.3:c.1030G>T	p.Gly344Cys	p.G344C	ENST00000277120		344	Ggc/Tgc	9/19	0.618154878650806	1	FACETS	0.267	0.216	0.323	0.267	0.216	0.323	SUBCLONAL	1	TRUE	0	0.618154878650806	1		354	260	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1315012	1315012	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	171	510	0	ENST00000400841.2:c.649G>T	p.Ala217Ser	p.A217S	ENST00000400841		217	Gcc/Tcc	6/6	0.618154878650806	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.618154878650806	1		510	376	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155526	106155526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749618735	NA	P-0054594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	95	632	0	ENST00000380013.4:c.427G>A	p.Asp143Asn	p.D143N	ENST00000380013	NM_001127208.2	143	Gat/Aat	3/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.618154878650806	2		632	213	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0054595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	32	564	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.738	0.601	0.891	0.738	0.601	0.891	SUBCLONAL	1	TRUE	1	0.318798268234451	2		564	272	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0054595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	36	367	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.318798268234451	1	FACETS	0.581	0.478	0.694	0.581	0.478	0.694	SUBCLONAL	1	TRUE	0	0.318798268234451	1		368	327	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18576895	18576895	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	52	722	0	ENST00000266497.5:c.2303G>A	p.Trp768Ter	p.W768*	ENST00000266497		768	tGg/tAg	16/31	1	2	FACETS	0.948	0.811	1	0.948	0.811	1	CLONAL	1	TRUE	1	0.318798268234451	2		722	344	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	218	502	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.512687088225176	3	FACETS	1	0.99	1	0.802	0.758	0.845	CLONAL	2	TRUE	0	0.597477931940097	3		502	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0054596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	731	1025	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.597477931940097	2	FACETS	0.99	0.962	1	0.99	0.962	1	CLONAL	2	TRUE	0	0.597477931940097	2		1026	1236	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0054596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	155	369	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	0.945	0.87	1	0.945	0.87	1	CLONAL	1	TRUE	1	0.597477931940097	2		369	549	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970927	21970927	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501274	NA	P-0054596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	349	961	3	ENST00000304494.5:c.431G>A	p.Arg144His	p.R144H	ENST00000304494	NM_000077.4	144	cGc/cAc	2/3	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.597477931940097	2		964	1163	SUCCESS
APC	324	MSKCC	GRCh37	5	112162923	112162923	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	75	488	0	ENST00000257430.4:c.1530del	p.Phe510LeufsTer4	p.F510Lfs*4	ENST00000257430	NM_000038.5	509	acT/ac	12/16	1	2	FACETS	0.913	0.809	1	0.913	0.809	1	CLONAL	1	TRUE	1	0.597477931940097	2		488	275	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0054597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	534	926	0	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	0.502806664091153	2	FACETS	0.971	0.935	1	0.971	0.935	1	CLONAL	2	TRUE	0	0.502806664091153	2		926	1094	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978759	13978759	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	116	669	0	ENST00000405192.2:c.348G>C	p.Lys116Asn	p.K116N	ENST00000405192	NM_001163147.1	116	aaG/aaC	6/12	0.481220036136205	3	FACETS	0.727	0.655	0.803	0.364	0.327	0.402	SUBCLONAL	1	TRUE	1	0.502806664091153	3		669	794	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0054598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	489	51	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.58517681726541	2	FACETS	0.977	0.943	1	0.977	0.943	1	CLONAL	2	TRUE	0	0.58517681726541	2		51	855	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515433	103515433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs189280373	NA	P-0054598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	73	378	0	ENST00000355739.4:c.1934C>T	p.Ser645Leu	p.S645L	ENST00000355739	NM_000123.3	645	tCg/tTg	8/15	0.58517681726541	1	FACETS	0.611	0.539	0.686	0.611	0.539	0.686	SUBCLONAL	1	TRUE	0	0.58517681726541	1		378	289	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982996	201982996	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	567	1168	0	ENST00000359651.3:c.845T>A	p.Ile282Asn	p.I282N	ENST00000359651		282	aTc/aAc	7/8	0.482337052412643	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.58517681726541	1		1168	948	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805602	89805602	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	260	1045	0	ENST00000389301.3:c.4106T>G	p.Val1369Gly	p.V1369G	ENST00000389301	NM_000135.2	1369	gTg/gGg	41/43	0.58517681726541	1	FACETS	0.981	0.925	1	0.981	0.925	1	CLONAL	1	TRUE	0	0.58517681726541	1		1045	641	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130285	11130285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	266	1020	0	ENST00000358026.2:c.2524C>T	p.Arg842Trp	p.R842W	ENST00000358026	NM_001128849.1	842	Cgg/Tgg	18/36	1	2	FACETS	0.979	0.919	1	0.979	0.919	1	CLONAL	1	TRUE	1	0.58517681726541	2		1020	929	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662487	227662487	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1232907554	NA	P-0054598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	207	907	0	ENST00000305123.5:c.968C>A	p.Ser323Tyr	p.S323Y	ENST00000305123	NM_005544.2	323	tCc/tAc	1/2	1	2	FACETS	0.914	0.851	0.98	0.914	0.851	0.98	CLONAL	1	TRUE	1	0.58517681726541	2		907	774	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36645651	36645684	+	upstream_gene_variant	5'Flank	DEL	CAAATCCTCCCCTTCCTGGCCAACAAAGCTGCTG	CAAATCCTCCCCTTCCTGGCCAACAAAGCTGCTG	-	novel	NA	P-0054598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	270	775	0				ENST00000244741	NM_000389.4	-/164			1	2	FACETS	0.994	0.935	1	0.994	0.935	1	CLONAL	1	TRUE	1	0.58517681726541	2		775	928	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0054599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	126	817	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.240986580300755	2		817	927	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0054599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	63	703	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.956	0.827	1	0.956	0.827	1	CLONAL	1	TRUE	1	0.240986580300755	2		703	547	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250890	153250890	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0054599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	36	469	0	ENST00000281708.4:c.1170T>A	p.Cys390Ter	p.C390*	ENST00000281708	NM_033632.3	390	tgT/tgA	8/12	1	2	FACETS	0.871	0.718	1	0.871	0.718	1	CLONAL	1	TRUE	1	0.240986580300755	2		469	343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576888	7576888	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0054600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	125	1020	0	ENST00000269305.4:c.958A>T	p.Lys320Ter	p.K320*	ENST00000269305	NM_001126112.2	320	Aag/Tag	9/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.242356747443584	2		1020	818	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509367	106509367	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	182	887	0	ENST00000359195.3:c.1361C>A	p.Ser454Tyr	p.S454Y	ENST00000359195	NM_002649.2	454	tCc/tAc	2/11	0.242356747443584	4	FACETS	0.975	0.899	1	0.975	0.899	1	CLONAL	2	TRUE	2	0.242356747443584	4		887	957	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412023	116412023	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	322	953	0	ENST00000397752.3:c.3008A>T	p.Tyr1003Phe	p.Y1003F	ENST00000397752	NM_000245.2	1003	tAc/tTc	14/21	0.242356747443584	4	FACETS	0.945	0.892	0.998	1	0.994	1	CLONAL	3	TRUE	2	0.242356747443584	4		953	1165	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228340	53228340	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	64	743	0	ENST00000375401.3:c.2062G>T	p.Gly688Cys	p.G688C	ENST00000375401	NM_004187.3	688	Ggt/Tgt	15/26	1	2	FACETS	0.93	0.806	1	0.93	0.806	1	CLONAL	1	TRUE	1	0.242356747443584	2		743	568	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462330	89462330	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	89	675	0	ENST00000336596.2:c.1802C>A	p.Thr601Lys	p.T601K	ENST00000336596	NM_005233.5	601	aCa/aAa	10/17	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.242356747443584	2		675	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578502	7578502	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	57	1309	1	ENST00000269305.4:c.428del	p.Val143GlyfsTer27	p.V143Gfs*27	ENST00000269305	NM_001126112.2	143	gTg/gg	5/11	1	2	FACETS	0.426	0.364	0.495	0.426	0.364	0.495	SUBCLONAL	1	TRUE	1	0.242356747443584	2		1310	1103	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397759	116397760	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	118	786	0	ENST00000397752.3:c.2034dup	p.Gly679TrpfsTer10	p.G679Wfs*10	ENST00000397752	NM_000245.2	678	act/acTt	8/21	0.242356747443584	4	FACETS	1	0.982	1	0.71	0.64	0.784	CLONAL	1	TRUE	2	0.242356747443584	4		786	852	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0054601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	292	1243	2	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.195777519895597	2	FACETS	0.829	0.78	0.88	0.829	0.78	0.88	CLONAL	2	FALSE	0	0.286728440321016	2		1245	1228	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248746	212248746	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762661533	NA	P-0054601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	59	392	0	ENST00000342788.4:c.3521G>A	p.Arg1174Gln	p.R1174Q	ENST00000342788	NM_005235.2	1174	cGg/cAg	28/28	0.272643026356517	2	FACETS	0.962	0.83	1	0.481	0.415	0.552	CLONAL	1	FALSE	0	0.286728440321016	2		392	428	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193889	106193889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395976555	NA	P-0054601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	60	408	0	ENST00000380013.4:c.4351C>T	p.Arg1451Trp	p.R1451W	ENST00000380013	NM_001127208.2	1451	Cgg/Tgg	10/11	0.286728440321016	1	FACETS	0.813	0.702	0.933	0.813	0.702	0.933	CLONAL	1	FALSE	0	0.286728440321016	1		408	441	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175391	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	56	334	0	ENST00000257430.4:c.4100dup	p.Thr1368AspfsTer7	p.T1368Dfs*7	ENST00000257430	NM_000038.5	1367	cag/cAag	16/16	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	FALSE	1	0.286728440321016	2		334	375	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924279	11924279	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	20	111	0	ENST00000353533.5:c.76del	p.Ser26ProfsTer19	p.S26Pfs*19	ENST00000353533	NM_003010.3	26	Tcc/cc	1/11	0.195777519895597	2	FACETS	1	0.817	1	0.532	0.412	0.67	CLONAL	1	FALSE	0	0.286728440321016	2		111	131	SUCCESS
APC	324	MSKCC	GRCh37	5	112177063	112177064	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	29	458	0	ENST00000257430.4:c.5775dup	p.Ile1926HisfsTer23	p.I1926Hfs*23	ENST00000257430	NM_000038.5	1924	-/C	16/16	1	2	FACETS	0.406	0.325	0.499	0.406	0.325	0.499	SUBCLONAL	1	FALSE	1	0.286728440321016	2		458	498	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104386958	104386963	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAAT	GAAAAT	A	novel	NA	P-0054601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	36	451	0	ENST00000369902.3:c.1323_1328delinsA	p.Lys442ValfsTer23	p.K442Vfs*23	ENST00000369902	NM_016169.3	441	gaGAAAATg/gaAg	11/12	1	2	FACETS	0.476	0.39	0.571	0.476	0.39	0.571	SUBCLONAL	1	FALSE	1	0.286728440321016	2		451	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519975	NA	P-0054602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	205	1273	0	ENST00000269305.4:c.403T>C	p.Cys135Arg	p.C135R	ENST00000269305	NM_001126112.2	135	Tgc/Cgc	5/11	0.209867945014224	2	FACETS	1	0.99	1	0.701	0.65	0.753	CLONAL	1	FALSE	0	0.3	2		1273	975	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477136	67477136	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	119	948	0	ENST00000327367.4:c.943G>T	p.Val315Phe	p.V315F	ENST00000327367	NM_005902.3	315	Gtc/Ttc	7/9	0.209867945014224	2	FACETS	1	0.91	1	0.504	0.455	0.556	CLONAL	1	FALSE	0	0.3	2		948	787	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608282	28608282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773466203	NA	P-0054604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	247	722	0	ENST00000241453.7:c.1774G>A	p.Val592Ile	p.V592I	ENST00000241453	NM_004119.2	592	Gtt/Att	14/24	1	2	FACETS	0.91	0.857	0.963	0.91	0.857	0.963	CLONAL	1	TRUE	1	0.888410888772767	2		722	611	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435083	49435087	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGG	CCAGG	-	novel	NA	P-0054604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	333	1118	1	ENST00000301067.7:c.6466_6470del	p.Pro2156Ter	p.P2156*	ENST00000301067	NM_003482.3	2156	CCTGGt/t	31/54	1	2	FACETS	0.851	0.807	0.895	0.851	0.807	0.895	CLONAL	1	TRUE	1	0.888410888772767	2		1119	881	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122963	7122963	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	528	1315	0	ENST00000302850.5:c.3296C>G	p.Thr1099Arg	p.T1099R	ENST00000302850	NM_000208.2	1099	aCg/aGg	18/22	1	2	FACETS	0.977	0.939	1	0.977	0.939	1	CLONAL	1	TRUE	1	0.888410888772767	2		1315	1217	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0054613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	157	76	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.344744162778648	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.344744162778648	3		76	475	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850765	63850765	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	111	444	0	ENST00000279873.7:c.1543G>C	p.Glu515Gln	p.E515Q	ENST00000279873	NM_032199.2	515	Gag/Cag	10/10	0.344744162778648	3	FACETS	1	0.941	1	0.532	0.479	0.589	CLONAL	1	TRUE	1	0.344744162778648	3		444	709	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048602	180048602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778453271	NA	P-0054613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	290	692	0	ENST00000261937.6:c.1960G>A	p.Glu654Lys	p.E654K	ENST00000261937	NM_182925.4	654	Gaa/Aaa	13/30	0.344744162778648	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.344744162778648	3		692	865	SUCCESS
BLM	641	MSKCC	GRCh37	15	91341542	91341542	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	97	457	1	ENST00000355112.3:c.3333G>T	p.Met1111Ile	p.M1111I	ENST00000355112	NM_000057.2	1111	atG/atT	17/22	0.344744162778648	3	FACETS	0.924	0.824	1	0.462	0.412	0.515	CLONAL	1	TRUE	1	0.344744162778648	3		458	714	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443703	49443703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	156	683	0	ENST00000301067.7:c.3668C>T	p.Ser1223Leu	p.S1223L	ENST00000301067	NM_003482.3	1223	tCa/tTa	11/54	0.344744162778648	4	FACETS	1	0.967	1	0.557	0.509	0.607	CLONAL	1	TRUE	2	0.344744162778648	4		683	1093	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123630	46123630	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	51	247	0	ENST00000334344.6:c.11C>G	p.Ser4Trp	p.S4W	ENST00000334344	NM_152641.2	4	tCg/tGg	1/21	0.344744162778648	4	FACETS	0.892	0.759	1	0.446	0.379	0.519	CLONAL	1	TRUE	2	0.344744162778648	4		247	446	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842594	68842594	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0054613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	209	479	0	ENST00000261769.5:c.532-2A>T		p.X178_splice	ENST00000261769	NM_004360.3	178			0.344744162778648	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.344744162778648	2		479	566	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411588	116411588	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	171	358	0	ENST00000397752.3:c.2767G>A	p.Val923Ile	p.V923I	ENST00000397752	NM_000245.2	923	Gta/Ata	13/21	0.344744162778648	4	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	2	0.344744162778648	4		358	640	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	18	375	0				ENST00000310581	NM_198253.2	-/1132			0.35415944552188	0	FACETS	0.394	0.306	0.492			1	SUBCLONAL	1	FALSE	0	0.58415115049764	0		375	65	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913517	NA	P-0054614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	132	543	0	ENST00000288135.5:c.1676T>C	p.Val559Ala	p.V559A	ENST00000288135	NM_000222.2	559	gTt/gCt	11/21	0.58415115049764	6	FACETS	1	0.923	1			1	CLONAL	2	FALSE	NA	0.58415115049764	6		543	485	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230613	46230613	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	150	656	0	ENST00000334344.6:c.862C>T	p.Gln288Ter	p.Q288*	ENST00000334344	NM_152641.2	288	Cag/Tag	8/21	0.285427089806975	6	FACETS	0.97	0.905	1			1	INDETERMINATE	4	FALSE	NA	0.58415115049764	6		656	287	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790684	89790684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1279886870	NA	P-0054614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	86	907	1	ENST00000336032.3:c.71C>T	p.Ser24Phe	p.S24F	ENST00000336032	NM_006813.2	24	tCc/tTc	1/2	0.590580031795124	3	FACETS	0.493	0.436	0.555	0.247	0.218	0.278	SUBCLONAL	1	FALSE	1	0.58415115049764	3		908	771	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148936	119148936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	59	628	0	ENST00000264033.4:c.1156G>A	p.Glu386Lys	p.E386K	ENST00000264033	NM_005188.3	386	Gaa/Aaa	8/16	0.322267807787253	5	FACETS	0.995	0.86	1	0.332	0.286	0.381	INDETERMINATE	1	FALSE	2	0.58415115049764	5		628	381	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576033	29576033	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	132	496	0	ENST00000356175.3:c.4006C>T	p.Gln1336Ter	p.Q1336*	ENST00000356175	NM_000267.3	1336	Cag/Tag	30/57	0.58415115049764	7	FACETS	1	0.977	1			1	CLONAL	2	FALSE	NA	0.58415115049764	7		496	462	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955046	93955046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141581954	NA	P-0054614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	23	336	0	ENST00000369303.4:c.2852C>T	p.Ser951Phe	p.S951F	ENST00000369303	NM_004440.3	951	tCc/tTc	16/17	0.590580031795124	1	FACETS	0.606	0.483	0.741	0.606	0.483	0.741	SUBCLONAL	1	FALSE	0	0.58415115049764	1		336	92	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856398	111856398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769643863	NA	P-0054614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	51	59	1	ENST00000341259.2:c.449C>T	p.Ser150Leu	p.S150L	ENST00000341259	NM_005475.2	150	tCg/tTg	2/8	0.482467413808881	2	FACETS	0.801	0.705	0.898	0.801	0.705	0.898	CLONAL	2	FALSE	0	0.58415115049764	2		60	109	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715780	18715780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745816756	NA	P-0054614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	18	446	0	ENST00000266497.5:c.3611C>T	p.Ser1204Leu	p.S1204L	ENST00000266497		1204	tCg/tTg	25/31	0.590580031795124	1	FACETS	0.383	0.292	0.487	0.383	0.292	0.487	SUBCLONAL	1	FALSE	0	0.58415115049764	1		446	114	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930595	131930595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	21	358	0	ENST00000265335.6:c.1828C>T	p.His610Tyr	p.H610Y	ENST00000265335		610	Cat/Tat	12/25	0.519494416367982	3	FACETS	0.407	0.315	0.515	0.204	0.157	0.258	SUBCLONAL	1	FALSE	1	0.58415115049764	3		358	228	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859006	57859006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	174	879	1	ENST00000228682.2:c.502C>T	p.Pro168Ser	p.P168S	ENST00000228682	NM_005269.2	168	Cct/Tct	5/12	0.58415115049764	7	FACETS	0.962	0.893	1	0.577	0.535	0.62	CLONAL	3	FALSE	2	0.58415115049764	7		880	508	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243924	53243924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	25	467	1	ENST00000375401.3:c.1069C>T	p.Pro357Ser	p.P357S	ENST00000375401	NM_004187.3	357	Cct/Tct	8/26	0.590580031795124	0	FACETS	0.247	0.197	0.303			1	SUBCLONAL	1	FALSE	NA	0.58415115049764	0		468	144	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120324	94120324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	12	423	1	ENST00000369303.4:c.727G>A	p.Glu243Lys	p.E243K	ENST00000369303	NM_004440.3	243	Gaa/Aaa	3/17	0.590580031795124	1	FACETS	0.224	0.158	0.304	0.224	0.158	0.304	SUBCLONAL	1	FALSE	0	0.58415115049764	1		424	130	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588210	69588210	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	32	786	0	ENST00000168712.1:c.488C>T	p.Pro163Leu	p.P163L	ENST00000168712	NM_002007.2	163	cCc/cTc	3/3	0.450508459176486	0	FACETS	0.302	0.248	0.36			1	SUBCLONAL	1	FALSE	0	0.58415115049764	0		786	151	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622517	158622517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906588	NA	P-0054614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	55	633	0	ENST00000263640.3:c.982G>A	p.Gly328Arg	p.G328R	ENST00000263640	NM_001105.4	328	Ggg/Agg	8/11	0.322267807787253	5	FACETS	0.761	0.659	0.871	0.508	0.439	0.581	INDETERMINATE	2	FALSE	2	0.58415115049764	5		633	232	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340252	116340252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773200558	NA	P-0054614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	165	339	1	ENST00000397752.3:c.1114G>A	p.Asp372Asn	p.D372N	ENST00000397752	NM_000245.2	372	Gac/Aac	2/21	0.58415115049764	7	FACETS	1	0.968	1	0.808	0.75	0.867	CLONAL	3	FALSE	3	0.58415115049764	7		340	430	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435826	116435826	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1436537175	NA	P-0054614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	115	798	0	ENST00000397752.3:c.3916G>A	p.Glu1306Lys	p.E1306K	ENST00000397752	NM_000245.2	1306	Gaa/Aaa	20/21	0.58415115049764	7	FACETS	0.765	0.691	0.844	0.383	0.345	0.422	SUBCLONAL	2	FALSE	3	0.58415115049764	7		798	633	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803856	43803856	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	80	767	0	ENST00000372470.3:c.166G>A	p.Glu56Lys	p.E56K	ENST00000372470	NM_005373.2	56	Gag/Aag	2/12	0.266764738080438	5	FACETS	0.834	0.742	0.931	0.556	0.494	0.621	INDETERMINATE	2	FALSE	2	0.58415115049764	5		767	308	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981481	201981481	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377707019	NA	P-0054614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	17	709	0	ENST00000359651.3:c.395C>T	p.Ser132Phe	p.S132F	ENST00000359651		132	tCt/tTt	3/8	0.328192147863465	4	FACETS	0.401	0.299	0.521	0.2	0.149	0.261	INDETERMINATE	1	FALSE	2	0.58415115049764	4		709	230	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948167	71948167	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0054614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	53	907	0	ENST00000298229.2:c.2880-1G>T		p.X960_splice	ENST00000298229	NM_001567.3	960			0.334504673871557	3	FACETS	0.862	0.741	0.992	0.431	0.37	0.496	INDETERMINATE	1	FALSE	1	0.58415115049764	3		907	272	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440103	99440103	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	107	555	0	ENST00000268035.6:c.1071G>C	p.Lys357Asn	p.K357N	ENST00000268035	NM_000875.3	357	aaG/aaC	4/21	0.519494416367982	3	FACETS	0.886	0.809	0.966	0.886	0.809	0.966	CLONAL	2	FALSE	1	0.58415115049764	3		555	267	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976619	7976619	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	103	808	0	ENST00000319144.4:c.1773G>A	p.Trp591Ter	p.W591*	ENST00000319144	NM_001139.2	591	tgG/tgA	14/15	0.27115827081527	6	FACETS	1	0.934	1	0.522	0.472	0.575	INDETERMINATE	2	FALSE	2	0.58415115049764	6		808	366	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222436	2222436	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	30	596	0	ENST00000398665.3:c.3268A>C	p.Lys1090Gln	p.K1090Q	ENST00000398665	NM_032482.2	1090	Aag/Cag	24/28	0.334504673871557	3	FACETS	0.488	0.394	0.593	0.244	0.197	0.297	INDETERMINATE	1	FALSE	1	0.58415115049764	3		596	272	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376814	31376814	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	77	586	0	ENST00000328111.2:c.809C>T	p.Ser270Phe	p.S270F	ENST00000328111	NM_006892.3	270	tCc/tTc	7/23	0.419656436770802	3	FACETS	0.865	0.775	0.957	0.576	0.516	0.638	CLONAL	2	FALSE	0	0.58415115049764	3		586	197	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964385	55964385	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	14	677	0	ENST00000263923.4:c.2428G>A	p.Glu810Lys	p.E810K	ENST00000263923	NM_002253.2	810	Gaa/Aaa	17/30	0.586953318144717	1	FACETS	0.183	0.133	0.245	0.183	0.133	0.245	SUBCLONAL	1	FALSE	0	0.58415115049764	1		677	185	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156439	106156439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	45	463	0	ENST00000380013.4:c.1340G>A	p.Arg447Lys	p.R447K	ENST00000380013	NM_001127208.2	447	aGg/aAg	3/11	0.338659853703186	3	FACETS	1	0.96	1	0.696	0.597	0.8	INDETERMINATE	1	FALSE	1	0.58415115049764	3		463	143	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157521	106157521	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1166110321	NA	P-0054614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	51	410	0	ENST00000380013.4:c.2422G>A	p.Glu808Lys	p.E808K	ENST00000380013	NM_001127208.2	808	Gaa/Aaa	3/11	0.338659853703186	3	FACETS	1	0.96	1	0.667	0.578	0.762	INDETERMINATE	1	FALSE	1	0.58415115049764	3		410	169	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524607	176524607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	46	937	1	ENST00000292408.4:c.2339C>T	p.Ser780Phe	p.S780F	ENST00000292408	NM_213647.1	780	tCt/tTt	18/18	0.519494416367982	3	FACETS	0.817	0.694	0.951	0.409	0.347	0.476	CLONAL	1	FALSE	1	0.58415115049764	3		938	249	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271273	26271273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	100	691	0	ENST00000305910.3:c.340C>T	p.His114Tyr	p.H114Y	ENST00000305910	NM_003534.2	114	Cat/Tat	1/1	0.58415115049764	15	FACETS	0.917	0.818	1	0.229	0.204	0.256	CLONAL	2	FALSE	7	0.58415115049764	15		691	896	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431630	6431630	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	34	387	0	ENST00000356142.4:c.183A>C	p.Gln61His	p.Q61H	ENST00000356142	NM_018890.3	61	caA/caC	3/7	0.266764738080438	5	FACETS	0.786	0.645	0.943	0.262	0.215	0.315	INDETERMINATE	1	FALSE	2	0.58415115049764	5		387	278	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0054615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	216	367	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.293557410942613	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.293557410942613	3		368	744	SUCCESS
APC	324	MSKCC	GRCh37	5	112173801	112173801	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs79512956	NA	P-0054615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	73	411	0	ENST00000257430.4:c.2510C>A	p.Ser837Ter	p.S837*	ENST00000257430	NM_000038.5	837	tCa/tAa	16/16	1	2	FACETS	0.821	0.724	0.922	1	0.979	1	CLONAL	2	TRUE	1	0.293557410942613	2		411	303	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434924	49434924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201190869	NA	P-0054615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	88	754	0	ENST00000301067.7:c.6629C>T	p.Pro2210Leu	p.P2210L	ENST00000301067	NM_003482.3	2210	cCg/cTg	31/54	0.280405901203059	3	FACETS	0.83	0.735	0.933	0.415	0.367	0.467	CLONAL	1	TRUE	1	0.293557410942613	3		754	828	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395213	139395213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751228412	NA	P-0054615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	140	860	0	ENST00000277541.6:c.5725G>A	p.Val1909Ile	p.V1909I	ENST00000277541	NM_017617.3	1909	Gtc/Atc	31/34	0.223464062851017	3	FACETS	1	0.965	1	0.56	0.51	0.614	CLONAL	1	TRUE	1	0.293557410942613	3		860	976	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016570	12016570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	109	416	0	ENST00000353533.5:c.706C>T	p.Leu236Phe	p.L236F	ENST00000353533	NM_003010.3	236	Ctt/Ttt	7/11	0.293557410942613	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.293557410942613	3		416	366	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793238	42793238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763699553	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	215	1001	0	ENST00000575354.2:c.1130C>T	p.Thr377Met	p.T377M	ENST00000575354	NM_015125.3	377	aCg/aTg	7/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.411564415423464	2		1001	899	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	417	772	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	2	TRUE	1	0.411564415423464	2		777	919	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	363	584	2	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.991	1	1	0.997	1	CLONAL	2	TRUE	1	0.411564415423464	2		586	772	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	131	426	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.411564415423464	2		427	544	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574678	41574679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs754418509	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	198	875	4	ENST00000263253.7:c.6970dup	p.His2324ProfsTer55	p.H2324Pfs*55	ENST00000263253	NM_001429.3	2321	-/C	31/31	1	2	FACETS	0.938	0.868	1	0.938	0.868	1	CLONAL	1	TRUE	1	0.411564415423464	2		879	1026	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	125	367	1	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.411564415423464	2		368	513	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	184	693	4	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.411564415423464	2		697	808	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923086	39923087	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	90	375	0	ENST00000378444.4:c.3621dup	p.Gln1208ThrfsTer8	p.Q1208Tfs*8	ENST00000378444	NM_001123385.1	1207	-/A	8/15	1	1	FACETS	0.686	0.611	0.766	0.686	0.611	0.766	SUBCLONAL	1	TRUE	0	0.411564415423464	1		375	506	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044907	47044907	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	181	471	0	ENST00000377604.3:c.2237del	p.Gly746AlafsTer56	p.G746Afs*56	ENST00000377604	NM_001204468.1	745	Ggg/gg	20/24	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.411564415423464	1		471	551	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287446	46287446	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs774801990	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	105	423	0	ENST00000334344.6:c.5305C>T	p.Arg1769Ter	p.R1769*	ENST00000334344	NM_152641.2	1769	Cga/Tga	20/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.411564415423464	2		423	435	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639588	47639588	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63749897	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	36	438	0	ENST00000233146.2:c.687del	p.Ala230LeufsTer16	p.A230Lfs*16	ENST00000233146	NM_000251.2	227	agA/ag	4/16	1	2	FACETS	0.438	0.36	0.526	0.438	0.36	0.526	SUBCLONAL	1	TRUE	1	0.411564415423464	2		438	399	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007901	45007901	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	122	379	0	ENST00000558401.1:c.346+2T>C		p.X116_splice	ENST00000558401	NM_004048.2	116			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.411564415423464	2		379	468	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371807	55371807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	30	59	0	ENST00000297316.4:c.497C>T	p.Ala166Val	p.A166V	ENST00000297316	NM_022454.3	166	gCg/gTg	2/2	0.411564415423464	3	FACETS	1	0.935	1	0.681	0.558	0.815	CLONAL	1	TRUE	1	0.411564415423464	3		59	129	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933594	39933594	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	90	330	0	ENST00000378444.4:c.1005del	p.Ser336ArgfsTer42	p.S336Rfs*42	ENST00000378444	NM_001123385.1	335	ccC/cc	4/15	1	1	FACETS	0.731	0.651	0.816	0.731	0.651	0.816	SUBCLONAL	1	TRUE	0	0.411564415423464	1		330	475	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933617	39933617	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	44	347	0	ENST00000378444.4:c.982del	p.Asp328ThrfsTer50	p.D328Tfs*50	ENST00000378444	NM_001123385.1	328	Gac/ac	4/15	1	1	FACETS	0.39	0.327	0.46	0.39	0.327	0.46	SUBCLONAL	1	TRUE	0	0.411564415423464	1		347	435	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604803	48604803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	74	443	0	ENST00000342988.3:c.1625C>T	p.Thr542Ile	p.T542I	ENST00000342988	NM_005359.5	542	aCc/aTc	12/12	1	2	FACETS	0.748	0.656	0.845	0.748	0.656	0.845	SUBCLONAL	1	TRUE	1	0.411564415423464	2		443	481	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448480	49448480	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	77	684	0	ENST00000301067.7:c.231del	p.His77GlnfsTer53	p.H77Qfs*53	ENST00000301067	NM_003482.3	77	caC/ca	3/54	1	2	FACETS	0.418	0.366	0.474	0.418	0.366	0.474	SUBCLONAL	1	TRUE	1	0.411564415423464	2		684	895	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614463	38614463	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	43	521	0	ENST00000299084.4:c.234del	p.Asp79ThrfsTer42	p.D79Tfs*42	ENST00000299084	NM_152594.2	77	Aaa/aa	3/7	1	2	FACETS	0.626	0.525	0.736	0.626	0.525	0.736	SUBCLONAL	1	TRUE	1	0.411564415423464	2		521	334	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	129	826	0	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	1	2	FACETS	0.609	0.551	0.67	0.609	0.551	0.67	SUBCLONAL	1	TRUE	1	0.411564415423464	2		826	1030	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226576366	226576366	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	77	590	1	ENST00000366794.5:c.708del	p.Ala237ProfsTer2	p.A237Pfs*2	ENST00000366794	NM_001618.3	236	aaA/aa	5/23	1	2	FACETS	0.498	0.437	0.564	0.498	0.437	0.564	SUBCLONAL	1	TRUE	1	0.411564415423464	2		591	751	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347093	347093	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	87	914	3	ENST00000262320.3:c.1918del	p.Glu640LysfsTer65	p.E640Kfs*65	ENST00000262320	NM_003502.3	640	Gaa/aa	7/11	1	2	FACETS	0.397	0.35	0.447	0.397	0.35	0.447	SUBCLONAL	1	TRUE	1	0.411564415423464	2		917	1066	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	64	809	5	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	0.371	0.32	0.426	0.371	0.32	0.426	SUBCLONAL	1	TRUE	1	0.411564415423464	2		814	839	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096313	2096313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774831009	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	233	912	0	ENST00000219066.1:c.194G>A	p.Arg65His	p.R65H	ENST00000219066	NM_002528.5	65	cGt/cAt	2/6	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.411564415423464	2		912	1009	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097749	8097749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1215707952	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	177	604	0	ENST00000346208.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000346208		44	cCg/cTg	2/6	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.411564415423464	2		604	713	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292727	62292727	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763415620	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	48	766	1	ENST00000360203.5:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000360203	NM_001283009.1	60	cGa/cAa	3/35	1	2	FACETS	0.286	0.241	0.336	0.286	0.241	0.336	SUBCLONAL	1	TRUE	1	0.411564415423464	2		767	815	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946337	2946337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759681668	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	228	802	0	ENST00000396946.4:c.3400G>A	p.Val1134Ile	p.V1134I	ENST00000396946	NM_032415.4	1134	Gtt/Att	25/25	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.411564415423464	2		802	979	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213515	36213515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746928288	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	282	979	1	ENST00000222270.7:c.2617C>T	p.Arg873Cys	p.R873C	ENST00000222270	NM_014727.1	873	Cgt/Tgt	5/37	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.411564415423464	2		980	1055	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311605	15311605	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1445073298	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	26	150	1	ENST00000263388.2:c.112del	p.Ala38LeufsTer198	p.A38Lfs*198	ENST00000263388	NM_000435.2	38	Gct/ct	1/33	1	2	FACETS	0.785	0.628	0.96	0.785	0.628	0.96	CLONAL	1	TRUE	1	0.411564415423464	2		151	161	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11168287	11168287	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	185	604	0	ENST00000361445.4:c.7585A>G	p.Ile2529Val	p.I2529V	ENST00000361445	NM_004958.3	2529	Atc/Gtc	57/58	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.411564415423464	2		604	828	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798157	45798157	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782351	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	204	795	0	ENST00000450313.1:c.694A>T	p.Thr232Ser	p.T232S	ENST00000450313	NM_012222.2	232	Acc/Tcc	9/16	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.411564415423464	2		795	954	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726433	46726433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145441107	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	155	564	1	ENST00000371975.4:c.512G>A	p.Arg171Gln	p.R171Q	ENST00000371975	NM_003579.3	171	cGg/cAg	7/18	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.411564415423464	2		565	638	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431177	49431177	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753081311	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	232	781	0	ENST00000301067.7:c.9962G>A	p.Arg3321Gln	p.R3321Q	ENST00000301067	NM_003482.3	3321	cGa/cAa	34/54	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.411564415423464	2		781	911	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249354	133249356	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	novel	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	206	735	0	ENST00000320574.5:c.1543_1545del	p.Ile515del	p.I515del	ENST00000320574	NM_006231.2	515	ATC/-	15/49	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.411564415423464	2		735	900	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748186	43748186	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	68	703	0	ENST00000382044.4:c.2620del	p.Met874TrpfsTer7	p.M874Wfs*7	ENST00000382044	NM_001141980.1	874	Atg/tg	12/28	1	2	FACETS	0.415	0.36	0.475	0.415	0.36	0.475	SUBCLONAL	1	TRUE	1	0.411564415423464	2		703	796	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	364556	364556	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	109	832	0	ENST00000262320.3:c.1006A>G	p.Thr336Ala	p.T336A	ENST00000262320	NM_003502.3	336	Acg/Gcg	3/11	1	2	FACETS	0.537	0.481	0.597	0.537	0.481	0.597	SUBCLONAL	1	TRUE	1	0.411564415423464	2		832	986	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134535	2134535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778925833	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	280	865	2	ENST00000219476.3:c.4312C>T	p.Arg1438Trp	p.R1438W	ENST00000219476	NM_000548.3	1438	Cgg/Tgg	34/42	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.411564415423464	2		867	1080	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779153	3779153	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	175	726	1	ENST00000262367.5:c.5895G>T	p.Glu1965Asp	p.E1965D	ENST00000262367	NM_004380.2	1965	gaG/gaT	31/31	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.411564415423464	2		727	811	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351794	89351794	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	271	861	0	ENST00000301030.4:c.1156del	p.Met386TrpfsTer41	p.M386Wfs*41	ENST00000301030	NM_001256183.1	386	Atg/tg	9/13	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.411564415423464	2		861	1134	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267631	7267631	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	226	784	0	ENST00000302850.5:c.377T>C	p.Val126Ala	p.V126A	ENST00000302850	NM_000208.2	126	gTt/gCt	2/22	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.411564415423464	2		784	869	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121064	11121064	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	127	619	0	ENST00000358026.2:c.2131A>G	p.Lys711Glu	p.K711E	ENST00000358026	NM_001128849.1	711	Aag/Gag	15/36	1	2	FACETS	0.753	0.682	0.827	0.753	0.682	0.827	SUBCLONAL	1	TRUE	1	0.411564415423464	2		619	820	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144003	11144003	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	189	674	0	ENST00000358026.2:c.3584A>G	p.Gln1195Arg	p.Q1195R	ENST00000358026	NM_001128849.1	1195	cAg/cGg	26/36	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.411564415423464	2		674	813	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383757	15383757	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	237	730	0	ENST00000263377.2:c.154A>G	p.Asn52Asp	p.N52D	ENST00000263377	NM_058243.2	52	Aac/Gac	2/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.411564415423464	2		730	990	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256658	19256658	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	170	498	0	ENST00000162023.5:c.1055G>T	p.Arg352Leu	p.R352L	ENST00000162023		352	cGg/cTg	13/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.411564415423464	2		498	654	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209284	36209284	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	130	425	0	ENST00000222270.7:c.363+1G>T		p.X121_splice	ENST00000222270	NM_014727.1	121			1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.411564415423464	2		425	614	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137481	202137481	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	100	580	0	ENST00000358485.4:c.709T>C	p.Tyr237His	p.Y237H	ENST00000358485	NM_001080125.1	237	Tat/Cat	4/9	1	2	FACETS	0.77	0.689	0.856	0.77	0.689	0.856	SUBCLONAL	1	TRUE	1	0.411564415423464	2		580	631	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014283	70014283	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	51	732	0	ENST00000394351.3:c.1144A>C	p.Thr382Pro	p.T382P	ENST00000394351	NM_000248.3	382	Acc/Ccc	9/9	1	2	FACETS	0.293	0.248	0.343	0.293	0.248	0.343	SUBCLONAL	1	TRUE	1	0.411564415423464	2		732	846	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398602	116398602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45446492	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	87	605	0	ENST00000397752.3:c.2192G>A	p.Arg731Gln	p.R731Q	ENST00000397752	NM_000245.2	731	cGa/cAa	9/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.411564415423464	2		605	351	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539069	23539069	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	133	608	0	ENST00000380871.4:c.370C>T	p.Gln124Ter	p.Q124*	ENST00000380871	NM_006167.3	124	Cag/Tag	2/2	0.411564415423464	3	FACETS	0.907	0.824	0.995	0.454	0.412	0.498	CLONAL	1	TRUE	1	0.411564415423464	3		608	859	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981729	70981729	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	241	946	1	ENST00000276594.2:c.367G>T	p.Gly123Cys	p.G123C	ENST00000276594	NM_024504.3	123	Ggt/Tgt	2/8	0.411564415423464	3	FACETS	1	0.988	1	0.627	0.585	0.67	CLONAL	1	TRUE	1	0.411564415423464	3		947	1127	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750738	128750746	+	inframe_deletion	In_Frame_Del	DEL	TCACACCCT	TCACACCCT	-	novel	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	145	731	0	ENST00000377970.2:c.277_285del	p.Thr93_Phe95del	p.T93_F95del	ENST00000377970	NM_002467.4	92	gTCACACCCTtc/gtc	2/3	0.411564415423464	3	FACETS	0.871	0.794	0.952	0.436	0.397	0.476	CLONAL	1	TRUE	1	0.411564415423464	3		731	975	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882041	36882041	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	240	772	0	ENST00000358127.4:c.972G>T	p.Gln324His	p.Q324H	ENST00000358127	NM_001280556.1	324	caG/caT	8/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.411564415423464	2		772	899	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0054617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	247	801	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.965	0.908	1	0.965	0.908	1	CLONAL	1	TRUE	1	0.78596942960247	2		801	651	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0054617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	136	456	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.967	0.89	1	0.967	0.89	1	CLONAL	1	TRUE	1	0.78596942960247	2		456	358	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	17	392	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	0.78596942960247	1	FACETS	0.102	0.076	0.133	0.102	0.076	0.133	SUBCLONAL	1	TRUE	0	0.78596942960247	1		392	257	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0054617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	317	415	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.78596942960247	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.78596942960247	2		415	380	SUCCESS
APC	324	MSKCC	GRCh37	5	112175952	112175952	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587783031	NA	P-0054617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	83	288	0	ENST00000257430.4:c.4666del	p.Thr1556LeufsTer9	p.T1556Lfs*9	ENST00000257430	NM_000038.5	1554	gAa/ga	16/16	0.78596942960247	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.78596942960247	1		288	128	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0054617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	182	802	2	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	0.748715527305245	3	FACETS	0.649	0.598	0.702	0.325	0.299	0.351	SUBCLONAL	1	TRUE	1	0.78596942960247	3		804	994	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143423	108143472	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTTAACCACAGTTCTTTTCCCGTAGGCTGATCCTTATTCAAAATGGGCC	ATTTAACCACAGTTCTTTTCCCGTAGGCTGATCCTTATTCAAAATGGGCC	-	novel	NA	P-0054617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	89	396	0	ENST00000278616.4:c.3154-23_3180del		p.X1052_splice	ENST00000278616	NM_000051.3	1052		22/63	0.78596942960247	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.78596942960247	1		396	128	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574526	41574527	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	326	755	0	ENST00000263253.7:c.6815dup	p.Val2273CysfsTer29	p.V2273Cfs*29	ENST00000263253	NM_001429.3	2271	tcc/tCcc	31/31	0.78596942960247	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.78596942960247	1		755	477	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588969	67588979	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTTTTTGGT	ACCTTTTTGGT	-	novel	NA	P-0054617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	83	333	0	ENST00000274335.5:c.1062_1072del	p.Phe355ArgfsTer5	p.F355Rfs*5	ENST00000274335		354	ACCTTTTTGGTa/a	8/15	0.78596942960247	1	FACETS	0.943	0.865	1	0.943	0.865	1	CLONAL	1	TRUE	0	0.78596942960247	1		333	136	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913583	39913583	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	161	417	0	ENST00000378444.4:c.4745A>T	p.Tyr1582Phe	p.Y1582F	ENST00000378444	NM_001123385.1	1582	tAt/tTt	13/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.78596942960247	2		417	381	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692851	89692851	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121909230	NA	P-0054618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	42	265	0	ENST00000371953.3:c.335T>C	p.Leu112Pro	p.L112P	ENST00000371953	NM_000314.4	112	cTa/cCa	5/9	0.358444711922402	2	FACETS	0.982	0.843	1	0.982	0.843	1	CLONAL	2	TRUE	0	0.378543269027869	2		265	113	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	37	1058	1	ENST00000256196.4:c.68G>A	p.Gly23Asp	p.G23D	ENST00000256196		23	gGc/gAc	1/6	0.16369891940521	0	FACETS	0.538	0.446	0.638			1	INDETERMINATE	1	TRUE	0	0.378543269027869	0		1059	226	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577563	7577564	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0054618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	216	1261	0	ENST00000269305.4:c.717_718del	p.Asn239LysfsTer24	p.N239Kfs*24	ENST00000269305	NM_001126112.2	239	aaCAgt/aagt	7/11	NA	2	FACETS	0.896	0.838	0.955			1	INDETERMINATE	2	TRUE	NA	0.378543269027869	2		1261	637	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0054631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	50	76	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.908	0.776	1	0.908	0.776	1	CLONAL	1	TRUE	1	0.389153241991441	2		76	283	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	202	304	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.237351622466648	3	FACETS	1	0.983	1	0.768	0.718	0.82	CLONAL	2	TRUE	0	0.389153241991441	3		304	538	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164864	36164864	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	199	966	0	ENST00000300305.3:c.1011del	p.Ala338ArgfsTer256	p.A338Rfs*256	ENST00000300305		337	ccC/cc	8/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.389153241991441	2		966	925	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040962	47040963	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0054631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	169	942	0	ENST00000377604.3:c.1495_1496del	p.Ala499ProfsTer18	p.A499Pfs*18	ENST00000377604	NM_001204468.1	498	CGc/c	14/24	0.31181427476023	1	FACETS	0.83	0.764	0.899	0.83	0.764	0.899	CLONAL	1	TRUE	0	0.389153241991441	1		942	843	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805044	89805044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769025633	NA	P-0054631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	78	825	1	ENST00000389301.3:c.4333G>A	p.Asp1445Asn	p.D1445N	ENST00000389301	NM_000135.2	1445	Gac/Aac	43/43	0.267644079473532	3	FACETS	0.48	0.421	0.545	0.16	0.14	0.182	SUBCLONAL	1	TRUE	0	0.389153241991441	3		826	997	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28963952	28963952	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	42	327	0	ENST00000282397.4:c.1950G>T	p.Lys650Asn	p.K650N	ENST00000282397	NM_002019.4	650	aaG/aaT	13/30	0.206043807524466	3	FACETS	0.573	0.479	0.678	0.287	0.239	0.339	INDETERMINATE	1	TRUE	1	0.389153241991441	3		327	450	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348280	70348280	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	62	674	0	ENST00000374080.3:c.3344G>T	p.Cys1115Phe	p.C1115F	ENST00000374080		1115	tGc/tTc	23/45	0.31181427476023	1	FACETS	0.409	0.353	0.47	0.409	0.353	0.47	SUBCLONAL	1	TRUE	0	0.389153241991441	1		674	628	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509377	46509377	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	129	570	0	ENST00000262741.5:c.1354G>T	p.Val452Phe	p.V452F	ENST00000262741	NM_003629.3	452	Gtt/Ttt	10/10	0.31181427476023	1	FACETS	0.905	0.823	0.99	0.905	0.823	0.99	CLONAL	1	TRUE	0	0.389153241991441	1		570	590	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119678	108119678	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0054631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	23	159	0	ENST00000278616.4:c.1084A>T	p.Arg362Ter	p.R362*	ENST00000278616	NM_000051.3	362	Aga/Tga	9/63	0.200268747450973	2	FACETS	0.53	0.415	0.662	0.265	0.207	0.331	INDETERMINATE	1	TRUE	0	0.389153241991441	2		159	223	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023564	31023564	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	111	537	0	ENST00000375687.4:c.3049G>A	p.Asp1017Asn	p.D1017N	ENST00000375687	NM_015338.5	1017	Gac/Aac	13/13	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.389153241991441	2		537	537	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572374	41572374	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	88	748	1	ENST00000263253.7:c.4903A>G	p.Arg1635Gly	p.R1635G	ENST00000263253	NM_001429.3	1635	Agg/Ggg	30/31	0.31181427476023	1	FACETS	0.558	0.494	0.626	0.558	0.494	0.626	SUBCLONAL	1	TRUE	0	0.389153241991441	1		749	653	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488456	20488456	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	83	417	1	ENST00000346618.3:c.1112A>G	p.Asn371Ser	p.N371S	ENST00000346618	NM_001949.4	371	aAt/aGt	6/7	1	2	FACETS	0.88	0.779	0.987	0.88	0.779	0.987	CLONAL	1	TRUE	1	0.389153241991441	2		418	485	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169992	32169992	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1306713027	NA	P-0054631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	185	909	1	ENST00000375023.3:c.3616G>A	p.Gly1206Arg	p.G1206R	ENST00000375023	NM_004557.3	1206	Gga/Aga	21/30	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.389153241991441	2		910	767	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32814940	32814940	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	157	697	0	ENST00000354258.4:c.2125C>A	p.Gln709Lys	p.Q709K	ENST00000354258	NM_000593.5	709	Cag/Aag	10/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.389153241991441	2		697	700	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352346	70352346	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	132	634	0	ENST00000374080.3:c.4373G>T	p.Gly1458Val	p.G1458V	ENST00000374080		1458	gGt/gTt	31/45	0.31181427476023	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.389153241991441	1		634	525	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123041002	123041002	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	14	119	0	ENST00000355640.3:c.1465A>T	p.Thr489Ser	p.T489S	ENST00000355640		489	Act/Tct	7/7	0.280458434855973	4	FACETS	0.476	0.344	0.635	0.119	0.086	0.159	SUBCLONAL	1	TRUE	0	0.389153241991441	4		119	210	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736307	243736308	+	missense_variant	Missense_Mutation	DNP	CG	CG	TT	novel	NA	P-0054631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	32	428	0	ENST00000263826.5:c.739_740delinsAA	p.Arg247Asn	p.R247N	ENST00000263826	NM_005465.4	247	CGc/AAc	8/13	0.267644079473532	3	FACETS	0.31	0.251	0.378	0.103	0.083	0.126	SUBCLONAL	1	TRUE	0	0.389153241991441	3		428	633	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0054632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	35	365	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.739	0.605	0.889	0.739	0.605	0.889	SUBCLONAL	1	TRUE	1	0.207723028574294	2		366	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0054632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	189	1088	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.207723028574294	2		1088	1292	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0054632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	25	336	0	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	1	2	FACETS	0.611	0.481	0.761	0.611	0.481	0.761	SUBCLONAL	1	TRUE	1	0.207723028574294	2		336	394	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962834	2962834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778151	NA	P-0054632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	133	1012	3	ENST00000396946.4:c.2074G>A	p.Val692Met	p.V692M	ENST00000396946	NM_032415.4	692	Gtg/Atg	16/25	1	2	FACETS	0.985	0.892	1	0.985	0.892	1	CLONAL	1	TRUE	1	0.207723028574294	2		1015	1300	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92404064	92404064	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	67	497	0	ENST00000265734.4:c.315G>C	p.Leu105Phe	p.L105F	ENST00000265734	NM_001259.6	105	ttG/ttC	3/8	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.207723028574294	2		497	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0054633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	33	834	2	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.163379111997177	0	FACETS	0.641	0.521	0.777			1	SUBCLONAL	1	FALSE	0	0.163379111997177	0		836	527	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730876	40730876	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372862828	NA	P-0054633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	46	809	2	ENST00000373198.4:c.3659G>A	p.Arg1220Gln	p.R1220Q	ENST00000373198	NM_133170.3	1220	cGg/cAg	27/32	0.163379111997177	3	FACETS	1	0.862	1	0.342	0.288	0.403	CLONAL	1	FALSE	0	0.163379111997177	3		811	593	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582193	189582193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1198643405	NA	P-0054633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	28	447	1	ENST00000264731.3:c.752G>A	p.Arg251His	p.R251H	ENST00000264731	NM_003722.4	251	cGt/cAt	5/14	1	2	FACETS	0.939	0.751	1	0.939	0.751	1	CLONAL	1	FALSE	1	0.163379111997177	2		448	365	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0054634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	90	364	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.242660239299249	NA		364	524	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520166	176520166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs911440999	NA	P-0054634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	161	918	1	ENST00000292408.4:c.1085C>T	p.Ala362Val	p.A362V	ENST00000292408	NM_213647.1	362	gCg/gTg	9/18	0.1870530739362	3	FACETS	1	0.982	1	0.63	0.576	0.686	CLONAL	1	TRUE	1	0.242660239299249	3		919	1181	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857547	57857547	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	50	676	0	ENST00000228682.2:c.73C>T	p.Gln25Ter	p.Q25*	ENST00000228682	NM_005269.2	25	Cag/Tag	2/12	1	2	FACETS	0.523	0.442	0.612	0.523	0.442	0.612	SUBCLONAL	1	TRUE	1	0.242660239299249	2		676	788	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007212	62007212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	165	909	0	ENST00000392795.3:c.470C>T	p.Thr157Met	p.T157M	ENST00000392795	NM_001039933.1	157	aCg/aTg	4/6	0.1870530739362	3	FACETS	1	0.986	1	0.685	0.628	0.745	CLONAL	1	TRUE	1	0.242660239299249	3		909	1113	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471044	8471044	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	61	363	0	ENST00000356435.5:c.3455G>T	p.Gly1152Val	p.G1152V	ENST00000356435		1152	gGg/gTg	20/35	0.242660239299249	1	FACETS	0.977	0.845	1	0.977	0.845	1	CLONAL	1	TRUE	0	0.242660239299249	1		363	452	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221954	1221954	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	146	875	0	ENST00000326873.7:c.869T>G	p.Leu290Arg	p.L290R	ENST00000326873	NM_000455.4	290	cTt/cGt	7/10	0.242660239299249	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.242660239299249	1		875	914	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587782272	NA	P-0054634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	115	628	0	ENST00000269305.4:c.994-1G>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.160016285057684	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.242660239299249	1		628	800	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825539	50825539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762650238	NA	P-0054634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	98	370	0	ENST00000398568.2:c.2170G>A	p.Val724Ile	p.V724I	ENST00000398568	NM_001042412.1	724	Gtt/Att	14/18	1	2	FACETS	0.775	0.694	0.861	1	0.982	1	SUBCLONAL	2	TRUE	1	0.242660239299249	2		370	521	SUCCESS
AR	367	MSKCC	GRCh37	X	66765598	66765598	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	70	998	0	ENST00000374690.3:c.610G>T	p.Glu204Ter	p.E204*	ENST00000374690	NM_000044.3	204	Gaa/Taa	1/8	0.242660239299249	1	FACETS	0.465	0.404	0.531	0.465	0.404	0.531	SUBCLONAL	1	TRUE	0	0.242660239299249	1		998	1091	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106324	27106324	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0054634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	146	673	0	ENST00000324856.7:c.5935A>T	p.Lys1979Ter	p.K1979*	ENST00000324856	NM_006015.4	1979	Aag/Tag	20/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.242660239299249	2		673	871	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008453	71008453	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	43	382	0	ENST00000318789.4:c.1979A>G	p.Asp660Gly	p.D660G	ENST00000318789	NM_032682.5	660	gAt/gGt	21/21	1	2	FACETS	0.636	0.532	0.752	0.636	0.532	0.752	SUBCLONAL	1	TRUE	1	0.242660239299249	2		382	557	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467520	66467520	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	54	307	0	ENST00000273854.3:c.749C>G	p.Ala250Gly	p.A250G	ENST00000273854	NM_004439.5	250	gCt/gGt	3/18	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.242660239299249	2		307	388	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	236	375	0				ENST00000310581	NM_198253.2	-/1132			0.512793850845318	5	FACETS	1	0.989	1	0.808	0.761	0.855	CLONAL	2	TRUE	2	0.764077388773966	5		375	547	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260546	16260546	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	43	618	0	ENST00000375759.3:c.7811C>T	p.Ala2604Val	p.A2604V	ENST00000375759	NM_015001.2	2604	gCt/gTt	11/15	1	2	FACETS	0.196	0.164	0.233	0.196	0.164	0.233	SUBCLONAL	1	TRUE	1	0.764077388773966	2		618	573	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275233	115275233	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	166	471	0	ENST00000438362.2:c.1180C>T	p.Arg394Ter	p.R394*	ENST00000438362	NM_001242891.1	394	Cga/Tga	10/20	0.770548245347102	3	FACETS	0.903	0.832	0.976	0.452	0.416	0.488	CLONAL	1	TRUE	1	0.764077388773966	3		471	665	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101985110	101985111	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0054636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	1014	710	0	ENST00000282441.5:c.560_561del	p.Arg187IlefsTer47	p.R187Ifs*47	ENST00000282441	NM_001130145.2	186	cAG/c	2/9	0.614827667221554	4	FACETS	0.99	0.976	1			1	CLONAL	4	TRUE	NA	0.764077388773966	4		710	1182	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244283	46244283	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	513	413	0	ENST00000334344.6:c.2377C>T	p.Gln793Ter	p.Q793*	ENST00000334344	NM_152641.2	793	Caa/Taa	15/21	0.764077388773966	6	FACETS	0.967	0.934	0.999			1	CLONAL	4	TRUE	NA	0.764077388773966	6		413	878	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245033	46245033	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs139789595	NA	P-0054636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	393	616	0	ENST00000334344.6:c.3127C>T	p.Gln1043Ter	p.Q1043*	ENST00000334344	NM_152641.2	1043	Caa/Taa	15/21	0.764077388773966	6	FACETS	1	0.964	1			1	CLONAL	2	TRUE	NA	0.764077388773966	6		616	1279	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245826	46245826	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1191905912	NA	P-0054636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	506	389	1	ENST00000334344.6:c.3920C>T	p.Ser1307Leu	p.S1307L	ENST00000334344	NM_152641.2	1307	tCa/tTa	15/21	0.764077388773966	6	FACETS	0.959	0.926	0.992			1	CLONAL	4	TRUE	NA	0.764077388773966	6		390	873	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245832	46245832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	492	384	0	ENST00000334344.6:c.3926C>T	p.Ser1309Leu	p.S1309L	ENST00000334344	NM_152641.2	1309	tCa/tTa	15/21	0.764077388773966	6	FACETS	0.971	0.938	1			1	CLONAL	4	TRUE	NA	0.764077388773966	6		384	838	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246186	46246186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	559	417	1	ENST00000334344.6:c.4280C>T	p.Ser1427Phe	p.S1427F	ENST00000334344	NM_152641.2	1427	tCt/tTt	15/21	0.764077388773966	6	FACETS	0.984	0.952	1			1	CLONAL	4	TRUE	NA	0.764077388773966	6		418	940	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426105	49426105	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0054636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	512	796	0	ENST00000301067.7:c.12383C>G	p.Ser4128Ter	p.S4128*	ENST00000301067	NM_003482.3	4128	tCa/tGa	39/54	0.750316057755442	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	2	0.764077388773966	4		796	1095	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426235	49426235	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	590	928	0	ENST00000301067.7:c.12253C>G	p.Gln4085Glu	p.Q4085E	ENST00000301067	NM_003482.3	4085	Cag/Gag	39/54	0.750316057755442	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.764077388773966	4		928	1317	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426459	49426459	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1341534320	NA	P-0054636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	701	1022	1	ENST00000301067.7:c.12029C>G	p.Ser4010Cys	p.S4010C	ENST00000301067	NM_003482.3	4010	tCt/tGt	39/54	0.750316057755442	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	2	0.764077388773966	4		1023	1513	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436996	110436996	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	32	73	0	ENST00000375856.3:c.1405C>G	p.Leu469Val	p.L469V	ENST00000375856	NM_003749.2	469	Ctg/Gtg	1/2	0.326199660879719	5	FACETS	0.936	0.799	1			1	INDETERMINATE	3	TRUE	NA	0.764077388773966	5		73	64	SUCCESS
BLM	641	MSKCC	GRCh37	15	91298106	91298129	+	inframe_deletion	In_Frame_Del	DEL	TGTCAAAACCTGAGAAAATGAGTA	TGTCAAAACCTGAGAAAATGAGTA	-	novel	NA	P-0054636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	28	363	0	ENST00000355112.3:c.1027_1050del	p.Ser343_Met350del	p.S343_M350del	ENST00000355112	NM_000057.2	342	tTGTCAAAACCTGAGAAAATGAGTAtg/ttg	5/22	0.34675146353626	3	FACETS	0.255	0.203	0.313	0.127	0.101	0.157	INDETERMINATE	1	TRUE	1	0.764077388773966	3		363	398	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656488	3656488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	563	808	1	ENST00000294008.3:c.747G>A	p.Met249Ile	p.M249I	ENST00000294008	NM_032444.2	249	atG/atA	3/15	0.76432452501622	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.764077388773966	3		809	982	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0054636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	390	619	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.470854464636234	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.764077388773966	1		620	511	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942864	15942864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	170	555	0	ENST00000268712.3:c.6838G>A	p.Glu2280Lys	p.E2280K	ENST00000268712	NM_006311.3	2280	Gag/Aag	44/46	0.770548245347102	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.764077388773966	1		555	254	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16022772	16022772	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	138	391	0	ENST00000268712.3:c.1880G>C	p.Arg627Pro	p.R627P	ENST00000268712	NM_006311.3	627	cGa/cCa	17/46	0.770548245347102	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.764077388773966	1		391	212	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743085	743085	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	504	587	0	ENST00000314574.4:c.893G>C	p.Gly298Ala	p.G298A	ENST00000314574	NM_005433.3	298	gGa/gCa	8/12	0.552519710055341	5	FACETS	0.842	0.809	0.875	0.842	0.809	0.875	CLONAL	3	TRUE	2	0.764077388773966	5		587	1121	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285135	15285135	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184438857	NA	P-0054636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	419	1042	1	ENST00000263388.2:c.4480G>A	p.Gly1494Ser	p.G1494S	ENST00000263388	NM_000435.2	1494	Ggc/Agc	25/33	0.764523055861778	5	FACETS	0.866	0.824	0.908	0.577	0.549	0.606	CLONAL	2	TRUE	2	0.764077388773966	5		1043	1359	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181946	38181946	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	415	503	0	ENST00000396334.3:c.570G>C	p.Glu190Asp	p.E190D	ENST00000396334	NM_002468.4	190	gaG/gaC	3/5	0.313011228519952	5	FACETS	0.891	0.859	0.923	0.713	0.687	0.738	INDETERMINATE	4	TRUE	0	0.764077388773966	5		503	654	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934956	49934957	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0054636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	93	741	0	ENST00000296474.3:c.2042_2043del	p.Phe681TyrfsTer24	p.F681Yfs*24	ENST00000296474	NM_002447.2	681	tTC/t	6/20	NA	2	FACETS	0.409	0.364	0.457			1	INDETERMINATE	1	TRUE	NA	0.764077388773966	2		741	595	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668732	52668732	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	190	465	0	ENST00000394830.3:c.1187G>C	p.Cys396Ser	p.C396S	ENST00000394830	NM_018313.4	396	tGt/tCt	12/30	0.630387066269328	5	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.764077388773966	5		465	907	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916851	178916851	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	360	612	0	ENST00000263967.3:c.238G>A	p.Glu80Lys	p.E80K	ENST00000263967	NM_006218.2	80	Gaa/Aaa	2/21	0.770548245347102	4	FACETS	0.88	0.837	0.924	0.88	0.837	0.924	CLONAL	2	TRUE	2	0.764077388773966	4		612	944	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916863	178916863	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	381	612	0	ENST00000263967.3:c.250G>A	p.Asp84Asn	p.D84N	ENST00000263967	NM_006218.2	84	Gat/Aat	2/21	0.770548245347102	4	FACETS	0.889	0.846	0.931	0.889	0.846	0.931	CLONAL	2	TRUE	2	0.764077388773966	4		612	990	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225782	26225782	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	360	521	0	ENST00000360408.1:c.400G>T	p.Glu134Ter	p.E134*	ENST00000360408	NM_003532.2	134	Gag/Tag	1/1	0.770548245347102	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.764077388773966	2		521	437	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874923	151874923	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	1007	395	0	ENST00000262189.6:c.7615C>T	p.Gln2539Ter	p.Q2539*	ENST00000262189	NM_170606.2	2539	Cag/Tag	38/59	0.764077388773966	10	FACETS	0.988	0.973	1	0.988	0.973	1	CLONAL	9	TRUE	1	0.764077388773966	10		395	1202	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041550	47041559	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TCCTCCCTCA	TCCTCCCTCA	-	novel	NA	P-0054636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	203	731	0	ENST00000377604.3:c.1786-11_1786-2del		p.X596_splice	ENST00000377604	NM_001204468.1	596			0.770548245347102	3	FACETS	0.902	0.838	0.968			1	CLONAL	1	TRUE	NA	0.764077388773966	3		731	814	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0054637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	265	412	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	0.478394523563388	9	FACETS	0.907	0.853	0.962	0.725	0.682	0.769	CLONAL	4	TRUE	4	0.478394523563388	9		412	817	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0054637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	475	953	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.466649527261609	3	FACETS	0.937	0.903	0.972	0.937	0.903	0.972	CLONAL	3	TRUE	0	0.478394523563388	3		953	875	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453179	140453179	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913340	NA	P-0054637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	209	322	0	ENST00000288602.6:c.1756G>A	p.Glu586Lys	p.E586K	ENST00000288602	NM_004333.4	586	Gaa/Aaa	15/18	0.478394523563388	9	FACETS	1	0.983	1	0.7	0.652	0.748	CLONAL	3	TRUE	4	0.478394523563388	9		322	668	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814542	43814542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561724539	NA	P-0054637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	91	533	1	ENST00000372470.3:c.1337G>A	p.Gly446Glu	p.G446E	ENST00000372470	NM_005373.2	446	gGa/gAa	9/12	0.478394523563388	3	FACETS	0.826	0.735	0.922	0.413	0.367	0.461	CLONAL	1	TRUE	1	0.478394523563388	3		534	571	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643561	52643561	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	39	540	0	ENST00000394830.3:c.2335C>A	p.Gln779Lys	p.Q779K	ENST00000394830	NM_018313.4	779	Caa/Aaa	17/30	0.45581246558295	4	FACETS	0.355	0.293	0.424	0.118	0.097	0.142	SUBCLONAL	1	TRUE	1	0.478394523563388	4		540	679	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186829	142186829	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	46	393	0	ENST00000350721.4:c.6634G>T	p.Val2212Phe	p.V2212F	ENST00000350721	NM_001184.3	2212	Gtt/Ttt	39/47	0.478394523563388	3	FACETS	0.805	0.682	0.94	0.403	0.341	0.47	CLONAL	1	TRUE	1	0.478394523563388	3		393	296	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061180	38061195	+	protein_altering_variant	In_Frame_Del	DEL	TTCTCGCACTTGAAGC	TTCTCGCACTTGAAGC	AAGT	novel	NA	P-0054637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	205	524	2	ENST00000250448.2:c.794_809delinsACTT	p.Arg265_Lys270delinsHisLeu	p.R265_K270delinsHL	ENST00000250448	NM_004496.3	265	cGCTTCAAGTGCGAGAAg/cACTTg	2/2	0.224067854501315	4	FACETS	0.973	0.907	1	0.973	0.907	1	INDETERMINATE	2	TRUE	2	0.478394523563388	4		526	651	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	484	375	0				ENST00000310581	NM_198253.2	-/1132			0.55648744903583	6	FACETS	0.942	0.906	0.979	0.942	0.906	0.979	CLONAL	4	TRUE	2	0.55648744903583	6		375	975	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	29	538	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	0.454468066290301	3	FACETS	0.135	0.108	0.167	0.045	0.036	0.056	SUBCLONAL	1	TRUE	0	0.55648744903583	3		538	985	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201059	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	688	728	0	ENST00000269305.4:c.856G>T	p.Glu286Ter	p.E286*	ENST00000269305	NM_001126112.2	286	Gaa/Taa	8/11	0.454468066290301	3	FACETS	1	0.995	1	0.775	0.75	0.8	CLONAL	2	TRUE	0	0.55648744903583	3		728	1360	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119789	70119789	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	343	680	1	ENST00000245479.2:c.791G>C	p.Arg264Thr	p.R264T	ENST00000245479	NM_000346.3	264	aGa/aCa	3/3	0.402006377011529	4	FACETS	1	0.994	1	0.739	0.698	0.78	CLONAL	1	TRUE	2	0.55648744903583	4		681	1299	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948136	178948136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	65	207	0	ENST00000263967.3:c.2908G>A	p.Glu970Lys	p.E970K	ENST00000263967	NM_006218.2	970	Gaa/Aaa	20/21	0.55648744903583	3	FACETS	0.807	0.713	0.904	0.807	0.713	0.904	CLONAL	2	TRUE	1	0.55648744903583	3		207	185	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411366	63411366	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	83	775	1	ENST00000330258.3:c.1801C>T	p.Arg601Ter	p.R601*	ENST00000330258	NM_152424.3	601	Cga/Tga	2/2	NA	2	FACETS	0.281	0.247	0.318			1	INDETERMINATE	1	TRUE	NA	0.55648744903583	2		776	1061	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056210	26056210	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	58	474	0	ENST00000343677.2:c.447G>C	p.Lys149Asn	p.K149N	ENST00000343677	NM_005319.3	149	aaG/aaC	1/1	0.55648744903583	3	FACETS	0.342	0.293	0.396	0.171	0.146	0.198	SUBCLONAL	1	TRUE	1	0.55648744903583	3		474	779	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502191	157502191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs940353111	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	132	486	1	ENST00000346085.5:c.3224G>A	p.Arg1075Gln	p.R1075Q	ENST00000346085	NM_020732.3	1075	cGa/cAa	12/20	0.55648744903583	3	FACETS	0.745	0.676	0.817	0.372	0.338	0.409	SUBCLONAL	1	TRUE	1	0.55648744903583	3		487	814	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61725838	61725838	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	76	318	0	ENST00000401558.2:c.729G>T	p.Glu243Asp	p.E243D	ENST00000401558	NM_003400.3	243	gaG/gaT	9/25	0.167674220706802	6	FACETS	0.985	0.873	1	0.657	0.582	0.735	INDETERMINATE	2	TRUE	3	0.55648744903583	6		318	293	SUCCESS
APC	324	MSKCC	GRCh37	5	112176962	112176962	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1561601614	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	86	306	0	ENST00000257430.4:c.5671G>A	p.Glu1891Lys	p.E1891K	ENST00000257430	NM_000038.5	1891	Gag/Aag	16/16	0.45416276477209	2	FACETS	1	0.978	1	0.672	0.605	0.741	CLONAL	1	TRUE	0	0.55648744903583	2		306	230	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	17	509	0	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.454468066290301	3	FACETS	0.094	0.069	0.124	0.031	0.023	0.042	SUBCLONAL	1	TRUE	0	0.55648744903583	3		509	829	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179180	123179180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	93	388	0	ENST00000218089.9:c.629C>T	p.Ser210Leu	p.S210L	ENST00000218089	NM_001042749.1	210	tCa/tTa	8/35	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.55648744903583	2		388	229	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028614	12028614	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	92	263	0	ENST00000353533.5:c.817G>C	p.Glu273Gln	p.E273Q	ENST00000353533	NM_003010.3	273	Gaa/Caa	8/11	0.454468066290301	3	FACETS	1	0.93	1	0.35	0.313	0.39	CLONAL	1	TRUE	0	0.55648744903583	3		263	402	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856347	45856347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	532	744	1	ENST00000391945.4:c.1825G>A	p.Asp609Asn	p.D609N	ENST00000391945	NM_000400.3	609	Gac/Aac	19/23	0.402006377011529	4	FACETS	0.893	0.855	0.931	0.893	0.855	0.931	CLONAL	2	TRUE	2	0.55648744903583	4		745	1667	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096652	178096652	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	19	303	0	ENST00000397062.3:c.679C>A	p.His227Asn	p.H227N	ENST00000397062	NM_006164.4	227	Cat/Aat	5/5	0.45416276477209	2	FACETS	0.303	0.231	0.389	0.152	0.115	0.195	SUBCLONAL	1	TRUE	0	0.55648744903583	2		303	225	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100301	157100301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	63	250	0	ENST00000346085.5:c.1238C>T	p.Ser413Leu	p.S413L	ENST00000346085	NM_020732.3	413	tCg/tTg	1/20	0.55648744903583	3	FACETS	0.697	0.605	0.797	0.349	0.302	0.399	SUBCLONAL	1	TRUE	1	0.55648744903583	3		250	415	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830863	156830863	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866270701	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	202	612	3	ENST00000524377.1:c.137C>T	p.Ser46Leu	p.S46L	ENST00000524377	NM_002529.3	46	tCg/tTg	1/17	0.490551372640848	5	FACETS	1	0.961	1			1	CLONAL	1	TRUE	NA	0.55648744903583	5		615	1257	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247977	59247977	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	184	642	0	ENST00000371222.2:c.766G>C	p.Glu256Gln	p.E256Q	ENST00000371222	NM_002228.3	256	Gag/Cag	1/1	0.528327615672315	3	FACETS	0.83	0.766	0.897	0.415	0.383	0.449	CLONAL	1	TRUE	1	0.55648744903583	3		642	1018	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880253	155880253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	302	366	0	ENST00000368323.3:c.151G>A	p.Asp51Asn	p.D51N	ENST00000368323	NM_006912.5	51	Gat/Aat	3/6	0.490551372640848	5	FACETS	0.954	0.911	0.996			1	CLONAL	4	TRUE	NA	0.55648744903583	5		366	522	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233139	46233139	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1434484912	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	176	251	0	ENST00000334344.6:c.1358A>G	p.Asp453Gly	p.D453G	ENST00000334344	NM_152641.2	453	gAt/gGt	11/21	0.55648744903583	3	FACETS	1	0.988	1	0.822	0.771	0.872	CLONAL	2	TRUE	0	0.55648744903583	3		251	328	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817811	3817811	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	270	629	0	ENST00000262367.5:c.3160G>T	p.Glu1054Ter	p.E1054*	ENST00000262367	NM_004380.2	1054	Gaa/Taa	16/31	NA	2	FACETS	0.851	0.807	0.896			1	INDETERMINATE	2	TRUE	NA	0.55648744903583	2		629	570	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944142	81944142	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	132	585	0	ENST00000359376.3:c.1751A>G	p.Gln584Arg	p.Q584R	ENST00000359376	NM_002661.3	584	cAg/cGg	18/33	0.528327615672315	3	FACETS	0.7	0.635	0.768	0.35	0.317	0.384	SUBCLONAL	1	TRUE	1	0.55648744903583	3		585	866	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210395	36210395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	292	656	1	ENST00000222270.7:c.388G>A	p.Glu130Lys	p.E130K	ENST00000222270	NM_014727.1	130	Gaa/Aaa	2/37	0.367482180998683	6	FACETS	0.844	0.793	0.897	0.422	0.396	0.449	CLONAL	2	TRUE	2	0.55648744903583	6		657	1313	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749553	41749553	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	121	554	0	ENST00000301178.4:c.1478A>T	p.Glu493Val	p.E493V	ENST00000301178	NM_021913.4	493	gAa/gTa	12/20	0.402006377011529	4	FACETS	0.555	0.5	0.614	0.278	0.25	0.307	SUBCLONAL	1	TRUE	2	0.55648744903583	4		554	1219	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632375	215632375	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	184	292	0	ENST00000260947.4:c.1399G>T	p.Glu467Ter	p.E467*	ENST00000260947	NM_000465.2	467	Gaa/Taa	6/11	0.45416276477209	2	FACETS	0.953	0.896	1	0.953	0.896	1	CLONAL	2	TRUE	0	0.55648744903583	2		292	347	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161320	55161320	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	120	349	0	ENST00000257290.5:c.3151G>C	p.Glu1051Gln	p.E1051Q	ENST00000257290	NM_006206.4	1051	Gag/Cag	23/23	0.380089963043208	3	FACETS	0.876	0.793	0.964	0.438	0.396	0.482	CLONAL	1	TRUE	1	0.55648744903583	3		349	629	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156529	106156529	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	39	293	0	ENST00000380013.4:c.1430C>G	p.Ser477Cys	p.S477C	ENST00000380013	NM_001127208.2	477	tCt/tGt	3/11	0.288044837160454	6	FACETS	0.8	0.665	0.951	0.2	0.166	0.238	INDETERMINATE	1	TRUE	2	0.55648744903583	6		293	370	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589552	67589552	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	30	150	0	ENST00000274335.5:c.1315G>C	p.Glu439Gln	p.E439Q	ENST00000274335		439	Gaa/Caa	10/15	0.45416276477209	2	FACETS	0.793	0.667	0.921	0.793	0.667	0.921	CLONAL	2	TRUE	0	0.55648744903583	2		150	68	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672132	30672132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	416	676	0	ENST00000376406.3:c.4828G>A	p.Glu1610Lys	p.E1610K	ENST00000376406	NM_014641.2	1610	Gag/Aag	10/15	0.55648744903583	3	FACETS	0.9	0.859	0.941	0.9	0.859	0.941	CLONAL	2	TRUE	1	0.55648744903583	3		676	1062	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188537	32188537	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	141	595	1	ENST00000375023.3:c.918G>A	p.Trp306Ter	p.W306*	ENST00000375023	NM_004557.3	306	tgG/tgA	5/30	0.55648744903583	3	FACETS	0.81	0.738	0.885	0.405	0.369	0.443	CLONAL	1	TRUE	1	0.55648744903583	3		596	800	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709090	117709090	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	129	470	0	ENST00000368508.3:c.1867A>G	p.Thr623Ala	p.T623A	ENST00000368508	NM_002944.2	623	Act/Gct	13/43	0.55648744903583	3	FACETS	0.869	0.789	0.952	0.434	0.394	0.476	CLONAL	1	TRUE	1	0.55648744903583	3		470	682	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940443	13940443	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	170	270	0	ENST00000405192.2:c.1063C>T	p.Gln355Ter	p.Q355*	ENST00000405192	NM_001163147.1	355	Cag/Tag	11/12	0.211496258162852	6	FACETS	0.98	0.911	1	0.98	0.911	1	INDETERMINATE	3	TRUE	3	0.55648744903583	6		270	439	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345830	152345830	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	226	447	0	ENST00000359321.1:c.740C>G	p.Ser247Cys	p.S247C	ENST00000359321	NM_005431.1	247	tCt/tGt	3/3	0.380089963043208	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.55648744903583	3		447	487	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409482	80409482	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	106	430	0	ENST00000286548.4:c.632C>G	p.Ser211Ter	p.S211*	ENST00000286548	NM_002072.3	211	tCa/tGa	5/7	0.211496258162852	6	FACETS	1	0.966	1	0.764	0.692	0.839	INDETERMINATE	2	TRUE	3	0.55648744903583	6		430	351	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941845	44941845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	107	276	0	ENST00000377967.4:c.3169C>T	p.His1057Tyr	p.H1057Y	ENST00000377967	NM_021140.2	1057	Cat/Tat	21/29	0.151504412464048	6	FACETS	1	0.97	1			1	INDETERMINATE	2	TRUE	NA	0.55648744903583	6		276	346	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608215	100608215	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	251	491	0	ENST00000308731.7:c.1875G>T	p.Lys625Asn	p.K625N	ENST00000308731	NM_000061.2	625	aaG/aaT	18/19	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.55648744903583	2		491	644	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179161	123179161	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	104	424	0	ENST00000218089.9:c.610C>A	p.Leu204Ile	p.L204I	ENST00000218089	NM_001042749.1	204	Ctt/Att	8/35	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.55648744903583	2		424	255	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942676	48942677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	C	novel	NA	P-0054638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	59	229	0	ENST00000267163.4:c.1063_1064delinsC	p.Arg355GlnfsTer12	p.R355Qfs*12	ENST00000267163	NM_000321.2	355	AGa/Ca	11/27	0.402006377011529	4	FACETS	1	0.969	1	0.721	0.628	0.819	CLONAL	1	TRUE	2	0.55648744903583	4		229	229	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0054641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2451	654	640	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.577294132880272	19	FACETS	1	0.988	1	0.392	0.375	0.409	CLONAL	4	FALSE	8	0.577294132880272	19		641	3105	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0054641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	420	355	1	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.577294132880272	19	FACETS	0.964	0.92	1	0.701	0.669	0.734	CLONAL	8	FALSE	8	0.577294132880272	19		356	1114	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30103709	30103709	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	14	456	0	ENST00000331968.5:c.1229T>A	p.Val410Glu	p.V410E	ENST00000331968	NM_002742.2	410	gTg/gAg	8/18	0.475772158779849	3	FACETS	0.322	0.233	0.429			1	SUBCLONAL	1	FALSE	NA	0.577294132880272	3		456	194	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618451	37618451	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs746824859	NA	P-0054641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	175	424	0	ENST00000447079.4:c.127A>G	p.Lys43Glu	p.K43E	ENST00000447079	NM_015083.1	43	Aag/Gag	1/14	0.485133159411042	5	FACETS	1	0.987	1			1	CLONAL	1	FALSE	NA	0.577294132880272	5		424	839	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039309	47039315	+	frameshift_variant	Frame_Shift_Del	DEL	GCACCAT	GCACCAT	-	novel	NA	P-0054641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	1053	771	0	ENST00000377604.3:c.933_939del	p.Ser311ArgfsTer22	p.S311Rfs*22	ENST00000377604	NM_001204468.1	311	aGCACCATg/ag	10/24	0.577294132880272	5	FACETS	1	0.995	1			1	CLONAL	3	FALSE	NA	0.577294132880272	5		771	2100	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542191	187542191	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	43	371	0	ENST00000441802.2:c.5549A>G	p.His1850Arg	p.H1850R	ENST00000441802	NM_005245.3	1850	cAt/cGt	10/27	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		371	410	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	99	375	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.538011529607465	2		375	332	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591148	67591154	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TTGATGT	TTGATGT	-	novel	NA	P-0054643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	119	235	0	ENST00000274335.5:c.1741_1745+2del		p.X581_splice	ENST00000274335		581		12/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.538011529607465	2		235	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0054643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	448	509	0	ENST00000269305.4:c.560-1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.538011529607465	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.538011529607465	2		509	777	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717729	89717730	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0054643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	64	355	0	ENST00000371953.3:c.754_755delinsTT	p.Asp252Phe	p.D252F	ENST00000371953	NM_000314.4	252	GAt/TTt	7/9	0.538011529607465	1	FACETS	0.441	0.384	0.503	0.441	0.384	0.503	SUBCLONAL	1	TRUE	0	0.538011529607465	1		355	394	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0054644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	123	217	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.670717982374124	2		217	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0054644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	457	652	0	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.670717982374124	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.670717982374124	2		652	573	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293785	1293785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866101734	NA	P-0054644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	181	905	1	ENST00000310581.5:c.1216G>A	p.Gly406Arg	p.G406R	ENST00000310581	NM_198253.2	406	Ggg/Agg	2/16	1	2	FACETS	0.751	0.694	0.809	0.751	0.694	0.809	SUBCLONAL	1	TRUE	1	0.670717982374124	2		906	719	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354244	70354244	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	22	329	0	ENST00000374080.3:c.4655A>G	p.Gln1552Arg	p.Q1552R	ENST00000374080		1552	cAg/cGg	34/45	1	1	FACETS	0.108	0.083	0.136	0.108	0.083	0.136	SUBCLONAL	1	TRUE	0	0.670717982374124	1		329	405	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849218	76849218	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	179	155	1	ENST00000373344.5:c.6058del	p.Met2020TrpfsTer30	p.M2020Wfs*30	ENST00000373344	NM_000489.3	2020	Atg/tg	26/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.670717982374124	1		156	241	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189585677	189585677	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	191	479	0	ENST00000264731.3:c.938T>C	p.Val313Ala	p.V313A	ENST00000264731	NM_003722.4	313	gTt/gCt	7/14	1	2	FACETS	0.915	0.855	0.976	0.915	0.855	0.976	CLONAL	1	TRUE	1	0.901641863779172	2		479	463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574016	+	frameshift_variant	Frame_Shift_Del	DEL	CGAAG	CGAAG	-	novel	NA	P-0054646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	282	784	0	ENST00000269305.4:c.1011_1015del	p.Phe338AspfsTer7	p.F338Dfs*7	ENST00000269305	NM_001126112.2	337	cgCTTCGag/cgag	10/11	0.597562442107312	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.597562442107312	1		784	560	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326689	62326689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773894104	NA	P-0054646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	198	911	1	ENST00000360203.5:c.3508C>T	p.Arg1170Trp	p.R1170W	ENST00000360203	NM_001283009.1	1170	Cgg/Tgg	34/35	NA	2	FACETS	0.833	0.773	0.894			1	INDETERMINATE	1	TRUE	NA	0.597562442107312	2		912	796	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0054647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	147	603	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.929	0.857	1	0.929	0.857	1	CLONAL	1	TRUE	1	0.791302242927183	2		603	400	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	74	375	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.891	0.794	0.991	0.891	0.794	0.991	CLONAL	1	TRUE	1	0.791302242927183	2		375	210	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0054647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	4173	680	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.791302242927183	23	FACETS	1	0.998	1	0.964	0.958	0.97	CLONAL	21	TRUE	1	0.791302242927183	23		680	4629	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346338	73346338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	61	296	1	ENST00000377767.4:c.1462G>A	p.Asp488Asn	p.D488N	ENST00000377767	NM_014953.3	488	Gat/Aat	10/21	1	2	FACETS	0.724	0.634	0.819	0.724	0.634	0.819	SUBCLONAL	1	TRUE	1	0.791302242927183	2		297	213	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241700	55241700	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	4321	714	0	ENST00000275493.2:c.2148A>C	p.Lys716Asn	p.K716N	ENST00000275493	NM_005228.3	716	aaA/aaC	18/28	0.791302242927183	23	FACETS	1	0.997	1	0.961	0.955	0.967	CLONAL	21	TRUE	1	0.791302242927183	23		714	4809	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099039	27099039	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	137	601	0	ENST00000324856.7:c.3455del	p.Ser1152IlefsTer9	p.S1152Ifs*9	ENST00000324856	NM_006015.4	1152	aGt/at	13/20	1	2	FACETS	0.906	0.834	0.981	0.906	0.834	0.981	CLONAL	1	TRUE	1	0.791302242927183	2		601	382	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27228299	27228299	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	92	386	0	ENST00000380036.4:c.3296G>C	p.Arg1099Pro	p.R1099P	ENST00000380036	NM_000459.3	1099	cGa/cCa	22/23	0.765126665683275	2	FACETS	0.938	0.847	1	0.469	0.423	0.515	CLONAL	1	TRUE	0	0.791302242927183	2		386	248	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0054648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	210	674	0	ENST00000397752.3:c.3028+1G>C		p.X1010_splice	ENST00000397752	NM_000245.2	1010			1	2	FACETS	0.96	0.89	1	1	0.993	1	CLONAL	2	TRUE	1	0.2	2		674	1094	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044472	47044472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556781457	NA	P-0054648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	98	284	2	ENST00000377604.3:c.1969C>T	p.Arg657Cys	p.R657C	ENST00000377604	NM_001204468.1	657	Cgc/Tgc	18/24	1	1	FACETS	0.959	0.86	1	1	0.987	1	CLONAL	2	TRUE	0	0.2	1		286	460	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257536	16257536	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	28	355	0	ENST00000375759.3:c.4801G>C	p.Asp1601His	p.D1601H	ENST00000375759	NM_015001.2	1601	Gac/Cac	11/15	1	2	FACETS	0.535	0.427	0.66	0.535	0.427	0.66	SUBCLONAL	1	TRUE	1	0.2	2		355	523	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916903	178916903	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	80	524	0	ENST00000263967.3:c.290C>A	p.Pro97His	p.P97H	ENST00000263967	NM_006218.2	97	cCc/cAc	2/21	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.2	2		524	710	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435448	18435467	+	frameshift_variant	Frame_Shift_Del	DEL	GCTCCATCATTCACAAGTTT	GCTCCATCATTCACAAGTTT	-	novel	NA	P-0054648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	23	290	0	ENST00000266497.5:c.434_453del	p.Ala145GlyfsTer2	p.A145Gfs*2	ENST00000266497		145	GCTCCATCATTCACAAGTTTg/g	1/31	1	2	FACETS	0.646	0.503	0.811	0.646	0.503	0.811	SUBCLONAL	1	TRUE	1	0.2	2		290	356	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094677	2094677	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1288936702	NA	P-0054648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	99	877	0	ENST00000219066.1:c.503A>G	p.Asp168Gly	p.D168G	ENST00000219066	NM_002528.5	168	gAt/gGt	3/6	1	2	FACETS	0.864	0.769	0.965	0.864	0.769	0.965	CLONAL	1	TRUE	1	0.2	2		877	1146	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943626	9943632	+	frameshift_variant	Frame_Shift_Del	DEL	ACTTCCG	ACTTCCG	-	novel	NA	P-0054648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	86	559	0	ENST00000330684.3:c.1309_1315del	p.Arg437SerfsTer12	p.R437Sfs*12	ENST00000330684	NM_001134407.1	437	CGGAAGTtc/tc	5/13	1	2	FACETS	0.941	0.831	1	0.941	0.831	1	CLONAL	1	TRUE	1	0.2	2		559	914	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383160	42383165	+	inframe_deletion	In_Frame_Del	DEL	CAACGC	CAACGC	-	novel	NA	P-0054648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	126	793	0	ENST00000221972.3:c.185_190del	p.Ala62_Asn63del	p.A62_N63del	ENST00000221972	NM_021601.3	60	aaCAACGCc/aac	2/5	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.2	2		793	1063	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257728	198257728	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	30	332	0	ENST00000335508.6:c.3724G>C	p.Gly1242Arg	p.G1242R	ENST00000335508	NM_012433.2	1242	Gga/Cga	24/25	1	2	FACETS	0.519	0.417	0.635	0.519	0.417	0.635	SUBCLONAL	1	TRUE	1	0.2	2		332	578	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21623968	21623968	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	14	140	0	ENST00000421138.2:c.1732C>A	p.Leu578Ile	p.L578I	ENST00000421138		578	Ctt/Att	15/16	0.703435730430197	1	FACETS	0.516	0.386	0.661	0.516	0.386	0.661	SUBCLONAL	1	TRUE	0	0.703435730430197	1		140	50	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109671	115109671	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	693	832	0	ENST00000257566.3:c.2207A>T	p.Asp736Val	p.D736V	ENST00000257566	NM_016569.3	736	gAc/gTc	8/8	NA	2	FACETS	0.971	0.945	0.995			1	INDETERMINATE	2	TRUE	NA	0.703435730430197	2		832	1015	SUCCESS
BLM	641	MSKCC	GRCh37	15	91306298	91306323	+	frameshift_variant	Frame_Shift_Del	DEL	AATTTGGCCTGCATAATTTTAGAACT	AATTTGGCCTGCATAATTTTAGAACT	-	novel	NA	P-0054649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	57	320	0	ENST00000355112.3:c.1988_2013del	p.Phe663SerfsTer12	p.F663Sfs*12	ENST00000355112	NM_000057.2	662	aAATTTGGCCTGCATAATTTTAGAACT/a	8/22	0.66808475588908	2	FACETS	0.523	0.451	0.6	0.261	0.225	0.3	SUBCLONAL	1	TRUE	0	0.703435730430197	2		320	310	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243777	41243778	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs80357579	NA	P-0054649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	83	479	0	ENST00000357654.3:c.3770_3771del	p.Glu1257GlyfsTer9	p.E1257Gfs*9	ENST00000357654	NM_007294.3	1257	gAG/g	10/23	1	2	FACETS	0.421	0.372	0.473	0.421	0.372	0.473	SUBCLONAL	1	TRUE	1	0.703435730430197	2		479	561	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095893	178095893	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	161	417	0	ENST00000397062.3:c.1438G>A	p.Asp480Asn	p.D480N	ENST00000397062	NM_006164.4	480	Gac/Aac	5/5	0.703046007264133	1	FACETS	0.97	0.907	1	0.97	0.907	1	CLONAL	1	TRUE	0	0.703435730430197	1		417	306	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771244	161771244	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0054649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	169	535	0	ENST00000366898.1:c.1286-1G>T		p.X429_splice	ENST00000366898	NM_004562.2	429			0.659188995584598	2	FACETS	0.743	0.685	0.802	0.371	0.342	0.401	SUBCLONAL	1	TRUE	0	0.703435730430197	2		535	647	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92354923	92354949	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGCACTCTCTCACTCACCACTGAGGTT	AGCACTCTCTCACTCACCACTGAGGTT	-	novel	NA	P-0054649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	97	179	0	ENST00000265734.4:c.528_537+17del		p.X176_splice	ENST00000265734	NM_001259.6	176		4/8	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.703435730430197	2		179	273	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	142	375	0				ENST00000310581	NM_198253.2	-/1132			0.242773383619377	4	FACETS	0.831	0.76	0.904	0.831	0.76	0.904	INDETERMINATE	2	TRUE	2	0.411810038388738	4		375	586	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0054650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	108	112	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.255955948051927	3	FACETS	0.669	0.6	0.743	0.335	0.3	0.372	SUBCLONAL	1	TRUE	1	0.411810038388738	3		113	945	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0054650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	1001	791	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.411810038388738	7	FACETS	1	0.991	1			1	CLONAL	5	TRUE	NA	0.411810038388738	7		791	1905	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245858	46245858	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	125	323	0	ENST00000334344.6:c.3952C>T	p.Gln1318Ter	p.Q1318*	ENST00000334344	NM_152641.2	1318	Cag/Tag	15/21	0.30366784203704	4	FACETS	1	0.986	1	0.749	0.681	0.821	CLONAL	1	TRUE	2	0.411810038388738	4		323	572	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770065	56770065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752608224	NA	P-0054650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	273	582	1	ENST00000337432.4:c.61C>T	p.Pro21Ser	p.P21S	ENST00000337432	NM_058216.2	21	Cca/Tca	1/9	0.255955948051927	3	FACETS	0.835	0.785	0.887	0.835	0.785	0.887	CLONAL	2	TRUE	1	0.411810038388738	3		583	957	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829066	128829066	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs41304185	NA	P-0054650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	19	18	1	ENST00000249373.3:c.74A>G	p.Asp25Gly	p.D25G	ENST00000249373	NM_005631.4	25	gAc/gGc	1/12	0.242773383619377	4	FACETS	0.965	0.771	1	1	0.924	1	INDETERMINATE	3	TRUE	2	0.411810038388738	4		19	45	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867571	45867571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	346	919	0	ENST00000391945.4:c.737C>T	p.Ser246Phe	p.S246F	ENST00000391945	NM_000400.3	246	tCc/tTc	9/23	0.242773383619377	4	FACETS	0.783	0.74	0.828	0.783	0.74	0.828	INDETERMINATE	2	TRUE	2	0.411810038388738	4		919	1515	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058603	47058603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	98	513	0	ENST00000409792.3:c.7675G>A	p.Glu2559Lys	p.E2559K	ENST00000409792	NM_014159.6	2559	Gag/Aag	21/21	0.255955948051927	3	FACETS	0.597	0.532	0.667	0.299	0.266	0.334	SUBCLONAL	1	TRUE	1	0.411810038388738	3		513	961	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268422	198268422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	90	400	0	ENST00000335508.6:c.1606C>T	p.Leu536Phe	p.L536F	ENST00000335508	NM_012433.2	536	Ctt/Ttt	12/25	1	2	FACETS	0.783	0.697	0.876	0.783	0.697	0.876	SUBCLONAL	1	TRUE	1	0.411810038388738	2		400	558	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262259	16262259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	47	257	0	ENST00000375759.3:c.9524C>T	p.Ser3175Leu	p.S3175L	ENST00000375759	NM_015001.2	3175	tCa/tTa	11/15	0.255955948051927	3	FACETS	0.704	0.595	0.823	0.352	0.297	0.412	SUBCLONAL	1	TRUE	1	0.411810038388738	3		257	391	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799812	72799812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	117	565	0	ENST00000325599.8:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000325599	NM_018130.2	453	Gag/Aag	11/11	0.255955948051927	3	FACETS	0.841	0.758	0.928	0.42	0.379	0.464	CLONAL	1	TRUE	1	0.411810038388738	3		565	815	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237712	16237712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	89	483	0	ENST00000375759.3:c.1159G>A	p.Glu387Lys	p.E387K	ENST00000375759	NM_015001.2	387	Gag/Aag	5/15	0.255955948051927	3	FACETS	0.641	0.568	0.72	0.321	0.284	0.36	SUBCLONAL	1	TRUE	1	0.411810038388738	3		483	813	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996885	100996885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748798054	NA	P-0054650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	86	522	0	ENST00000325455.5:c.1642G>A	p.Asp548Asn	p.D548N	ENST00000325455	NM_001202474.3	548	Gat/Aat	2/8	0.255955948051927	3	FACETS	0.721	0.637	0.81	0.36	0.318	0.405	SUBCLONAL	1	TRUE	1	0.411810038388738	3		522	699	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941637	48941649	+	frameshift_variant	Frame_Shift_Del	DEL	ATCTTTCTAAACG	ATCTTTCTAAACG	-	novel	NA	P-0054650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	68	164	0	ENST00000267163.4:c.949_961del	p.Leu317ThrfsTer11	p.L317Tfs*11	ENST00000267163	NM_000321.2	316	aATCTTTCTAAACGa/aa	10/27	0.215093219522113	3	FACETS	0.851	0.751	0.956			1	INDETERMINATE	2	TRUE	NA	0.411810038388738	3		164	234	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816227	89816227	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	139	704	0	ENST00000389301.3:c.3150G>C	p.Glu1050Asp	p.E1050D	ENST00000389301	NM_000135.2	1050	gaG/gaC	32/43	0.286643116916501	3	FACETS	0.737	0.67	0.809	0.369	0.335	0.405	SUBCLONAL	1	TRUE	1	0.411810038388738	3		704	1104	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549719	187549719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	90	386	0	ENST00000441802.2:c.4522G>A	p.Asp1508Asn	p.D1508N	ENST00000441802	NM_005245.3	1508	Gat/Aat	8/27	0.286643116916501	3	FACETS	0.89	0.791	0.996	0.445	0.395	0.498	CLONAL	1	TRUE	1	0.411810038388738	3		386	592	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751973	57751973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs966541733	NA	P-0054650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	71	324	0	ENST00000274289.3:c.1264C>T	p.Pro422Ser	p.P422S	ENST00000274289	NM_006622.3	422	Cca/Tca	10/14	0.242773383619377	4	FACETS	0.82	0.716	0.932	0.41	0.358	0.466	INDETERMINATE	1	TRUE	2	0.411810038388738	4		324	594	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339322	116339322	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	145	353	0	ENST00000397752.3:c.184A>T	p.Ile62Phe	p.I62F	ENST00000397752	NM_000245.2	62	Att/Ttt	2/21	0.242773383619377	4	FACETS	0.902	0.827	0.98	0.902	0.827	0.98	INDETERMINATE	2	TRUE	2	0.411810038388738	4		353	551	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128420000	128420000	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	135	692	0	ENST00000265960.3:c.428C>T	p.Ser143Phe	p.S143F	ENST00000265960	NM_001006617.1	143	tCt/tTt	4/12	1	2	FACETS	0.671	0.609	0.736	0.671	0.609	0.736	SUBCLONAL	1	TRUE	1	0.411810038388738	2		692	977	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0054651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	11	866	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.860290748973652	1	FACETS	0.03	0.02	0.042	0.03	0.02	0.042	SUBCLONAL	1	TRUE	0	0.860290748973652	1		867	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs786203436	NA	P-0054651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	15	850	0	ENST00000269305.4:c.487T>A	p.Tyr163Asn	p.Y163N	ENST00000269305	NM_001126112.2	163	Tac/Aac	5/11	0.860290748973652	1	FACETS	0.035	0.025	0.047	0.035	0.025	0.047	SUBCLONAL	1	TRUE	0	0.860290748973652	1		850	570	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560463	95560463	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555366979	NA	P-0054651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	315	494	0	ENST00000393063.1:c.5126A>G	p.Asp1709Gly	p.D1709G	ENST00000393063	NM_030621.3	1709	gAt/gGt	25/28	0.828839663948223	3	FACETS	0.903	0.862	0.944	0.903	0.862	0.944	CLONAL	2	TRUE	1	0.860290748973652	3		494	580	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396262	139396262	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1266401977	NA	P-0054651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	267	876	0	ENST00000277541.6:c.5576C>T	p.Ala1859Val	p.A1859V	ENST00000277541	NM_017617.3	1859	gCc/gTc	30/34	0.828839663948223	3	FACETS	0.752	0.704	0.801	0.376	0.352	0.401	SUBCLONAL	1	TRUE	1	0.860290748973652	3		876	1181	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0054652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	182	603	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.377588161707417	3	FACETS	0.949	0.879	1	0.475	0.439	0.512	INDETERMINATE	1	TRUE	1	0.7355168651832	3		603	713	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750600586	NA	P-0054652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	434	834	1	ENST00000269305.4:c.413C>T	p.Ala138Val	p.A138V	ENST00000269305	NM_001126112.2	138	gCc/gTc	5/11	0.7355168651832	1	FACETS	0.991	0.954	1	0.991	0.954	1	CLONAL	1	TRUE	0	0.7355168651832	1		835	753	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0054652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	113	370	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.457499125378712	3	FACETS	0.743	0.67	0.818	0.371	0.335	0.409	SUBCLONAL	1	TRUE	1	0.7355168651832	3		370	566	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066745	30066745	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	170	392	1	ENST00000331968.5:c.2386G>A	p.Ala796Thr	p.A796T	ENST00000331968	NM_002742.2	796	Gca/Aca	16/18	1	2	FACETS	0.926	0.859	0.996	0.926	0.859	0.996	CLONAL	1	TRUE	1	0.7355168651832	2		393	499	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945613	38945617	+	frameshift_variant	Frame_Shift_Del	DEL	CTCAG	CTCAG	-	novel	NA	P-0054652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	42	228	0	ENST00000357387.3:c.4609_4613del	p.Leu1537CysfsTer4	p.L1537Cfs*4	ENST00000357387	NM_152756.3	1537	CTGAGt/t	34/38	1	2	FACETS	0.305	0.255	0.36	0.305	0.255	0.36	SUBCLONAL	1	TRUE	1	0.7355168651832	2		228	375	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915168	32915168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775859905	NA	P-0054654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	65	474	0	ENST00000380152.3:c.6676G>A	p.Glu2226Lys	p.E2226K	ENST00000380152		2226	Gaa/Aaa	11/27	0.661300323731074	1	FACETS	0.463	0.405	0.525	0.463	0.405	0.525	SUBCLONAL	1	TRUE	0	0.661300323731074	1		474	284	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65569055	65569055	+	start_lost	Translation_Start_Site	SNP	C	C	A	novel	NA	P-0054654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	38	506	0	ENST00000358664.4:c.3G>T	p.Met1?	p.M1?	ENST00000358664	NM_002382.4	1	atG/atT	1/5	0.341304452078919	1	FACETS	0.134	0.11	0.16	0.134	0.11	0.16	INDETERMINATE	1	TRUE	0	0.661300323731074	1		506	575	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532612	63532612	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555577180	NA	P-0054654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	176	899	2	ENST00000307078.5:c.1967G>A	p.Arg656Gln	p.R656Q	ENST00000307078	NM_004655.3	656	cGa/cAa	8/11	1	2	FACETS	0.451	0.415	0.49	0.451	0.415	0.49	SUBCLONAL	1	TRUE	1	0.661300323731074	2		901	1179	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020450	69020450	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	232	606	0	ENST00000288368.4:c.2822A>C	p.Asn941Thr	p.N941T	ENST00000288368	NM_024870.2	941	aAt/aCt	24/40	1	2	FACETS	0.944	0.884	1	0.944	0.884	1	CLONAL	1	TRUE	1	0.661300323731074	2		606	743	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593603	55593619	+	frameshift_variant	Frame_Shift_Del	DEL	TGGAAGGTTGTTGAGGA	TGGAAGGTTGTTGAGGA	GGT	novel	NA	P-0054654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	110	396	1	ENST00000288135.5:c.1669_1685delinsGGT	p.Trp557GlyfsTer18	p.W557Gfs*18	ENST00000288135	NM_000222.2	557	TGGAAGGTTGTTGAGGAg/GGTg	11/21	1	2	FACETS	0.726	0.656	0.799	0.726	0.656	0.799	SUBCLONAL	1	TRUE	1	0.661300323731074	2		397	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0054655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	48	963	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.766	0.646	0.899	0.766	0.646	0.899	SUBCLONAL	1	TRUE	1	0.16	2		966	783	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	39	502	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.16	2		502	384	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0054655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	22	285	0	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	1	2	FACETS	0.793	0.614	1	0.793	0.614	1	CLONAL	1	TRUE	1	0.16	2		285	347	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0054657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	118	621	1	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.262983082614051	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.262983082614051	1		622	639	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0054657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	66	434	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.262983082614051	2		434	456	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448529	89448529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	151	374	0	ENST00000336596.2:c.1493G>A	p.Ser498Asn	p.S498N	ENST00000336596	NM_005233.5	498	aGc/aAc	7/17	0.262983082614051	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.262983082614051	2		374	550	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140721	55140721	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	104	518	0	ENST00000257290.5:c.1582G>C	p.Ala528Pro	p.A528P	ENST00000257290	NM_006206.4	528	Gct/Cct	11/23	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.262983082614051	2		518	671	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467590	66467590	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746706656	NA	P-0054657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	33	277	0	ENST00000273854.3:c.679C>T	p.Arg227Cys	p.R227C	ENST00000273854	NM_004439.5	227	Cgt/Tgt	3/18	1	2	FACETS	0.602	0.49	0.728	0.602	0.49	0.728	SUBCLONAL	1	TRUE	1	0.262983082614051	2		277	417	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129635	11129635	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	48	551	0	ENST00000358026.2:c.2441C>A	p.Thr814Lys	p.T814K	ENST00000358026	NM_001128849.1	814	aCg/aAg	17/36	0.262983082614051	1	FACETS	0.51	0.43	0.598	0.51	0.43	0.598	SUBCLONAL	1	TRUE	0	0.262983082614051	1		551	622	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709118	117709118	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	97	375	0	ENST00000368508.3:c.1839A>C	p.Lys613Asn	p.K613N	ENST00000368508	NM_002944.2	613	aaA/aaC	13/43	0.250586611651894	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.262983082614051	1		375	470	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129160	64129160	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537223935	NA	P-0054657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	57	787	0	ENST00000334205.4:c.698C>T	p.Thr233Met	p.T233M	ENST00000334205	NM_003942.2	233	aCg/aTg	7/17	1	2	FACETS	0.499	0.427	0.579	0.499	0.427	0.579	SUBCLONAL	1	TRUE	1	0.262983082614051	2		787	868	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336149	73336149	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	38	202	0	ENST00000377767.4:c.2254G>T	p.Val752Leu	p.V752L	ENST00000377767	NM_014953.3	752	Gtg/Ttg	17/21	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.262983082614051	2		202	273	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988659	41988659	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	58	388	0	ENST00000219905.7:c.1451C>T	p.Ser484Phe	p.S484F	ENST00000219905	NM_001164273.1	484	tCt/tTt	3/24	0.248954070029734	0	FACETS	0.793	0.683	0.911			1	CLONAL	1	TRUE	0	0.262983082614051	0		388	410	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602310	10602310	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	167	812	0	ENST00000171111.5:c.1268G>T	p.Gly423Val	p.G423V	ENST00000171111	NM_203500.1	423	gGc/gTc	3/6	0.262983082614051	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.262983082614051	1		812	799	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966145	25966145	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	135	578	0	ENST00000435504.4:c.3061G>T	p.Gly1021Cys	p.G1021C	ENST00000435504		1021	Ggc/Tgc	13/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.262983082614051	2		578	796	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748128	41748128	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	70	207	0	ENST00000226382.2:c.641G>T	p.Gly214Val	p.G214V	ENST00000226382	NM_003924.3	214	gGc/gTc	3/3	1	2	FACETS	0.896	0.789	1	1	0.98	1	CLONAL	2	TRUE	1	0.262983082614051	2		207	297	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156684	106156684	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	71	326	0	ENST00000380013.4:c.1585T>A	p.Cys529Ser	p.C529S	ENST00000380013	NM_001127208.2	529	Tgc/Agc	3/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.262983082614051	2		326	444	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244197	153244197	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	86	437	0	ENST00000281708.4:c.1960G>T	p.Gly654Cys	p.G654C	ENST00000281708	NM_033632.3	654	Ggt/Tgt	12/12	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.262983082614051	2		437	592	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253873	153253873	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	rs1232348209	NA	P-0054657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	40	199	0	ENST00000281708.4:c.862-2A>T		p.X288_splice	ENST00000281708	NM_033632.3	288			1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.262983082614051	2		199	268	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523287	176523287	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0054657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	160	708	0	ENST00000292408.4:c.1945-1G>T		p.X649_splice	ENST00000292408	NM_213647.1	649			1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.262983082614051	2		708	831	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955137	93955137	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	32	455	0	ENST00000369303.4:c.2761G>T	p.Asp921Tyr	p.D921Y	ENST00000369303	NM_004440.3	921	Gat/Tat	16/17	0.250586611651894	1	FACETS	0.513	0.416	0.622	0.513	0.416	0.622	SUBCLONAL	1	TRUE	0	0.262983082614051	1		455	412	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467738	50467738	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	84	577	0	ENST00000331340.3:c.973G>T	p.Glu325Ter	p.E325*	ENST00000331340	NM_006060.4	325	Gag/Tag	8/8	1	2	FACETS	0.854	0.754	0.962	0.854	0.754	0.962	CLONAL	1	TRUE	1	0.262983082614051	2		577	748	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	68	540	0	ENST00000347630.2:c.305T>C	p.Phe102Ser	p.F102S	ENST00000347630	NM_001007230.1	102	tTc/tCc	5/11	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.28	2		540	463	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138762	64138762	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	92	698	0	ENST00000334205.4:c.2129A>C	p.Asn710Thr	p.N710T	ENST00000334205	NM_003942.2	710	aAc/aCc	17/17	1	2	FACETS	0.931	0.827	1	0.931	0.827	1	CLONAL	1	TRUE	1	0.28	2		698	706	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434307	49434307	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	404	988	1	ENST00000301067.7:c.7246C>T	p.Gln2416Ter	p.Q2416*	ENST00000301067	NM_003482.3	2416	Cag/Tag	31/54	0.109054704765234	5	FACETS	0.902	0.858	0.946			1	INDETERMINATE	3	TRUE	NA	0.394142131552092	5		989	1206	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218029	108218029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55798854	NA	P-0054659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	58	268	0	ENST00000278616.4:c.8608G>A	p.Asp2870Asn	p.D2870N	ENST00000278616	NM_000051.3	2870	Gat/Aat	59/63	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.394142131552092	2		268	268	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444053	49444053	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	160	704	0	ENST00000301067.7:c.3318del	p.Ser1107AlafsTer12	p.S1107Afs*12	ENST00000301067	NM_003482.3	1106	ccC/cc	11/54	0.109054704765234	5	FACETS	0.818	0.751	0.888			1	INDETERMINATE	2	TRUE	NA	0.394142131552092	5		704	790	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243778441	243778441	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	92	332	1	ENST00000263826.5:c.584C>A	p.Thr195Asn	p.T195N	ENST00000263826	NM_005465.4	195	aCt/aAt	6/13	0.401115154680552	3	FACETS	0.755	0.676	0.838			1	SUBCLONAL	2	TRUE	NA	0.394142131552092	3		333	370	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158373	108158373	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1565452621	NA	P-0054659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	116	443	0	ENST00000278616.4:c.4040T>A	p.Leu1347Ter	p.L1347*	ENST00000278616	NM_000051.3	1347	tTa/tAa	27/63	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.394142131552092	2		443	485	SUCCESS
BLM	641	MSKCC	GRCh37	15	91341477	91341477	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	74	371	0	ENST00000355112.3:c.3268G>C	p.Glu1090Gln	p.E1090Q	ENST00000355112	NM_000057.2	1090	Gaa/Caa	17/22	0.401115154680552	3	FACETS	0.845	0.741	0.956			1	CLONAL	1	TRUE	NA	0.394142131552092	3		371	532	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094807	143094807	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	74	288	0	ENST00000262992.4:c.1337C>G	p.Ser446Cys	p.S446C	ENST00000262992	NM_001101669.1	446	tCt/tGt	14/24	0.258431293093195	3	FACETS	1	0.969	1	0.663	0.585	0.746	CLONAL	1	TRUE	1	0.394142131552092	3		288	339	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913396	NA	P-0054666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	37	381	0	ENST00000349496.5:c.95A>T	p.Asp32Val	p.D32V	ENST00000349496	NM_001904.3	32	gAc/gTc	3/15	1	2	FACETS	0.22	0.181	0.264	0.22	0.181	0.264	SUBCLONAL	1	TRUE	1	0.646609829759396	2		381	520	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729844	41729844	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs908163566	NA	P-0054666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	163	542	0	ENST00000242208.4:c.685C>T	p.Arg229Trp	p.R229W	ENST00000242208	NM_002192.2	229	Cgg/Tgg	3/3	1	2	FACETS	0.971	0.898	1	0.971	0.898	1	CLONAL	1	TRUE	1	0.646609829759396	2		542	519	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532741	46532741	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	66	365	0	ENST00000262741.5:c.337del	p.Ile113Ter	p.I113*	ENST00000262741	NM_003629.3	113	Ata/ta	4/10	1	2	FACETS	0.765	0.671	0.864	0.765	0.671	0.864	SUBCLONAL	1	TRUE	1	0.646609829759396	2		365	267	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906566	32906566	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359770	NA	P-0054666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	37	354	0	ENST00000380152.3:c.956del	p.Asn319IlefsTer5	p.N319Ifs*5	ENST00000380152		317	acA/ac	10/27	0.646609829759396	1	FACETS	0.833	0.71	0.96	0.833	0.71	0.96	CLONAL	1	TRUE	0	0.646609829759396	1		354	93	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061222	38061222	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	193	561	0	ENST00000250448.2:c.767del	p.Asn256ThrfsTer65	p.N256Tfs*65	ENST00000250448	NM_004496.3	256	aAc/ac	2/2	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.646609829759396	2		561	595	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085851	16085851	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	180	602	0	ENST00000281043.3:c.1027G>T	p.Asp343Tyr	p.D343Y	ENST00000281043	NM_005378.4	343	Gat/Tat	3/3	0.646609829759396	3	FACETS	0.743	0.685	0.804	0.372	0.342	0.402	SUBCLONAL	1	TRUE	1	0.646609829759396	3		602	991	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0054668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	282	381	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.753334309036691	4	FACETS	0.841	0.801	0.882	0.841	0.801	0.882	CLONAL	3	TRUE	1	0.753334309036691	4		381	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578195	7578197	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0054668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	510	723	1	ENST00000269305.4:c.652_654del	p.Val218del	p.V218del	ENST00000269305	NM_001126112.2	218	GTG/-	6/11	0.747782306369718	2	FACETS	0.931	0.904	0.958	0.931	0.904	0.958	CLONAL	2	TRUE	0	0.753334309036691	2		724	727	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097775	27097775	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	183	483	0	ENST00000324856.7:c.3364G>A	p.Asp1122Asn	p.D1122N	ENST00000324856	NM_006015.4	1122	Gat/Aat	12/20	0.753334309036691	3	FACETS	0.934	0.865	1	0.467	0.432	0.503	CLONAL	1	TRUE	1	0.753334309036691	3		483	716	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451203	70451203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	261	648	0	ENST00000373644.4:c.6043C>T	p.His2015Tyr	p.H2015Y	ENST00000373644	NM_030625.2	2015	Cac/Tac	12/12	0.698954608987959	4	FACETS	1	0.97	1	0.53	0.496	0.565	CLONAL	1	TRUE	2	0.753334309036691	4		648	1146	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499384	89499384	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	157	491	0	ENST00000336596.2:c.2554G>C	p.Ala852Pro	p.A852P	ENST00000336596	NM_005233.5	852	Gcc/Ccc	15/17	0.738335861342481	3	FACETS	1	0.954	1	0.525	0.483	0.567	CLONAL	1	TRUE	1	0.753334309036691	3		491	547	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522558	67522558	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	86	299	0	ENST00000274335.5:c.55G>C	p.Glu19Gln	p.E19Q	ENST00000274335		19	Gaa/Caa	1/15	0.753334309036691	4	FACETS	1	0.926	1	0.35	0.312	0.391	CLONAL	1	TRUE	1	0.753334309036691	4		299	381	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	134	502	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.220641730631068	5	FACETS	1	0.926	1	0.676	0.618	0.736	INDETERMINATE	2	TRUE	2	0.446750168255724	5		502	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0054669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	408	868	2	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.429008178092567	3	FACETS	0.888	0.85	0.925	0.888	0.85	0.925	CLONAL	3	TRUE	0	0.446750168255724	3		870	839	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282214	38282214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121909645	NA	P-0054669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	90	587	0	ENST00000425967.3:c.842G>A	p.Arg281Gln	p.R281Q	ENST00000425967	NM_001174067.1	281	cGg/cAg	8/19	0.361722951748594	3	FACETS	0.848	0.754	0.949	0.424	0.377	0.475	CLONAL	1	TRUE	1	0.446750168255724	3		587	581	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881392	37881392	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	182	691	0	ENST00000269571.5:c.2584A>G	p.Thr862Ala	p.T862A	ENST00000269571		862	Aca/Gca	21/27	0.200411253562108	2	FACETS	1	0.983	1	0.616	0.568	0.666	CLONAL	1	TRUE	0	0.31	2		691	953	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0054670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	33	248	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.659	0.538	0.795	0.659	0.538	0.795	SUBCLONAL	1	TRUE	1	0.31	2		248	323	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178165	56178166	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	46	359	0	ENST00000399503.3:c.3139dup	p.Thr1047AsnfsTer10	p.T1047Nfs*10	ENST00000399503	NM_005921.1	1046	-/A	14/20	1	2	FACETS	0.601	0.506	0.705	0.601	0.506	0.705	SUBCLONAL	1	TRUE	1	0.31	2		359	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0054671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	1029	389	1	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.896973718565652	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.896973718565652	3		390	1087	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357502	89357502	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	311	874	0	ENST00000301030.4:c.316C>T	p.Arg106Ter	p.R106*	ENST00000301030	NM_001256183.1	106	Cga/Tga	5/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.896973718565652	2		874	656	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214001	108214001	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	231	336	0	ENST00000278616.4:c.8321del	p.Val2774AlafsTer32	p.V2774Afs*32	ENST00000278616	NM_000051.3	2774	gTc/gc	57/63	0.89695935833398	3	FACETS	0.979	0.931	1	0.979	0.931	1	CLONAL	2	TRUE	1	0.896973718565652	3		336	381	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	17	375	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.556	0.414	0.724	0.556	0.414	0.724	SUBCLONAL	1	TRUE	1	0.19	2		375	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0054672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	78	963	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.934	0.819	1	0.934	0.819	1	CLONAL	1	TRUE	1	0.19	2		966	879	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0054672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	175	378	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.3	3	FACETS	0.917	0.85	0.986	1	0.992	1	CLONAL	4	TRUE	1	0.19	3		378	550	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688753	47688753	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	54	413	0	ENST00000347630.2:c.547G>T	p.Glu183Ter	p.E183*	ENST00000347630	NM_001007230.1	183	Gag/Tag	7/11	1	2	FACETS	0.952	0.813	1	0.952	0.813	1	CLONAL	1	TRUE	1	0.19	2		413	597	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680664	88680664	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	57	639	0	ENST00000360948.2:c.593C>A	p.Pro198His	p.P198H	ENST00000360948	NM_001012338.2	198	cCt/cAt	6/19	1	2	FACETS	0.796	0.681	0.921	0.796	0.681	0.921	CLONAL	1	TRUE	1	0.19	2		639	754	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410126	63410126	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	64	811	1	ENST00000330258.3:c.3041G>T	p.Gly1014Val	p.G1014V	ENST00000330258	NM_152424.3	1014	gGg/gTg	2/2	1	2	FACETS	0.775	0.67	0.89	0.775	0.67	0.89	SUBCLONAL	1	TRUE	1	0.19	2		812	869	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040723	47040723	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	93	831	0	ENST00000377604.3:c.1360del	p.Leu454SerfsTer31	p.L454Sfs*31	ENST00000377604	NM_001204468.1	453	tCc/tc	13/24	1	2	FACETS	0.988	0.877	1	0.988	0.877	1	CLONAL	1	TRUE	1	0.19	2		831	991	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218086	108218086	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	17	268	0	ENST00000278616.4:c.8665G>T	p.Asp2889Tyr	p.D2889Y	ENST00000278616	NM_000051.3	2889	Gat/Tat	59/63	1	2	FACETS	0.688	0.514	0.895	0.688	0.514	0.895	SUBCLONAL	1	TRUE	1	0.19	2		268	260	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557923	21557923	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	35	417	0	ENST00000382592.4:c.1922A>T	p.Gln641Leu	p.Q641L	ENST00000382592	NM_014572.2	641	cAg/cTg	5/8	1	2	FACETS	0.774	0.634	0.931	0.774	0.634	0.931	CLONAL	1	TRUE	1	0.19	2		417	476	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18958603	18958603	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	71	608	0	ENST00000262803.5:c.422A>G	p.Lys141Arg	p.K141R	ENST00000262803	NM_002911.3	141	aAg/aGg	3/24	1	2	FACETS	0.927	0.808	1	0.927	0.808	1	CLONAL	1	TRUE	1	0.19	2		608	806	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535316	66535316	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	70	617	0	ENST00000273854.3:c.145G>C	p.Ala49Pro	p.A49P	ENST00000273854	NM_004439.5	49	Gca/Cca	1/18	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.19	2		617	735	SUCCESS
APC	324	MSKCC	GRCh37	5	112170852	112170852	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	41	423	0	ENST00000257430.4:c.1948G>C	p.Glu650Gln	p.E650Q	ENST00000257430	NM_000038.5	650	Gag/Cag	15/16	1	2	FACETS	0.824	0.686	0.977	0.824	0.686	0.977	CLONAL	1	TRUE	1	0.19	2		423	524	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8733836	8733836	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	95	474	0	ENST00000356435.5:c.8A>C	p.His3Pro	p.H3P	ENST00000356435		3	cAc/cCc	1/35	0.197513189497523	2	FACETS	0.825	0.736	0.92	0.825	0.736	0.92	CLONAL	2	TRUE	0	0.19	2		474	606	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133748421	133748421	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	40	392	0	ENST00000318560.5:c.1082A>G	p.His361Arg	p.H361R	ENST00000318560	NM_005157.4	361	cAc/cGc	6/11	1	2	FACETS	0.796	0.661	0.947	0.796	0.661	0.947	CLONAL	1	TRUE	1	0.19	2		392	529	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028799	47028799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556770750	NA	P-0054672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	81	848	0	ENST00000377604.3:c.103G>A	p.Asp35Asn	p.D35N	ENST00000377604	NM_001204468.1	35	Gac/Aac	3/24	1	2	FACETS	0.898	0.79	1	0.898	0.79	1	CLONAL	1	TRUE	1	0.19	2		848	949	SUCCESS
AR	367	MSKCC	GRCh37	X	66765395	66765395	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	81	807	0	ENST00000374690.3:c.407G>T	p.Gly136Val	p.G136V	ENST00000374690	NM_000044.3	136	gGa/gTa	1/8	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.19	2		807	812	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191480	10191480	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913346	NA	P-0054673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	51	369	0	ENST00000256474.2:c.473T>A	p.Leu158Gln	p.L158Q	ENST00000256474	NM_000551.3	158	cTg/cAg	3/3	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.179955373779041	2		369	492	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637598	52637599	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0054673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	35	457	0	ENST00000394830.3:c.2717_2718del	p.Arg906LysfsTer12	p.R906Kfs*12	ENST00000394830	NM_018313.4	906	aGA/a	18/30	1	2	FACETS	0.922	0.756	1	0.922	0.756	1	CLONAL	1	TRUE	1	0.179955373779041	2		457	422	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11177077	11177077	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	40	341	0	ENST00000361445.4:c.7000T>G	p.Leu2334Val	p.L2334V	ENST00000361445	NM_004958.3	2334	Tta/Gta	50/58	1	2	FACETS	0.896	0.744	1	0.896	0.744	1	CLONAL	1	TRUE	1	0.179955373779041	2		341	496	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858092	9858093	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0054673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	70	499	1	ENST00000330684.3:c.3308_3309del	p.Arg1103HisfsTer11	p.R1103Hfs*11	ENST00000330684	NM_001134407.1	1103	cGC/c	13/13	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.179955373779041	2		500	714	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142981	47142981	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	50	467	0	ENST00000409792.3:c.4982A>T	p.Glu1661Val	p.E1661V	ENST00000409792	NM_014159.6	1661	gAg/gTg	8/21	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.179955373779041	2		467	542	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003191	42003191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs761227360	NA	P-0054689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	69	489	0	ENST00000219905.7:c.2728C>T	p.Arg910Ter	p.R910*	ENST00000219905	NM_001164273.1	910	Cga/Tga	8/24	1	2	FACETS	0.948	0.824	1	0.948	0.824	1	CLONAL	1	TRUE	1	0.17	2		489	856	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404613	70404613	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	59	536	0	ENST00000373644.4:c.2127G>T	p.Lys709Asn	p.K709N	ENST00000373644	NM_030625.2	709	aaG/aaT	4/12	1	2	FACETS	0.917	0.788	1	0.917	0.788	1	CLONAL	1	TRUE	1	0.17	2		536	757	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058279	42058279	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	43	335	0	ENST00000219905.7:c.7999G>C	p.Gly2667Arg	p.G2667R	ENST00000219905	NM_001164273.1	2667	Ggt/Cgt	24/24	1	2	FACETS	0.978	0.819	1	0.978	0.819	1	CLONAL	1	TRUE	1	0.17	2		335	517	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420294	88420294	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	67	489	0	ENST00000360948.2:c.2392G>T	p.Glu798Ter	p.E798*	ENST00000360948	NM_001012338.2	798	Gag/Tag	19/19	1	2	FACETS	0.966	0.838	1	0.966	0.838	1	CLONAL	1	TRUE	1	0.17	2		489	816	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50821707	50821707	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	24	379	0	ENST00000398568.2:c.2043A>C	p.Glu681Asp	p.E681D	ENST00000398568	NM_001042412.1	681	gaA/gaC	13/18	1	2	FACETS	0.749	0.587	0.936	0.749	0.587	0.936	CLONAL	1	TRUE	1	0.17	2		379	377	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220550	1220593	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCCCTGAGGGCTGCACGGCACCGCCACAGGCACTGCACCCGTT	CTCCCTGAGGGCTGCACGGCACCGCCACAGGCACTGCACCCGTT	-	novel	NA	P-0054689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	86	789	0	ENST00000326873.7:c.598-29_612del		p.X200_splice	ENST00000326873	NM_000455.4	200		5/10	1	2	FACETS	0.912	0.805	1	0.912	0.805	1	CLONAL	1	TRUE	1	0.17	2		789	1109	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169530	11169530	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	89	679	1	ENST00000358026.2:c.4696C>T	p.Gln1566Ter	p.Q1566*	ENST00000358026	NM_001128849.1	1566	Cag/Tag	33/36	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.17	2		680	1042	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251802	212251803	+	missense_variant	Missense_Mutation	DNP	CT	CT	AA	novel	NA	P-0054689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	32	330	0	ENST00000342788.4:c.3256_3257delinsTT	p.Ser1086Phe	p.S1086F	ENST00000342788	NM_005235.2	1086	AGc/TTc	27/28	1	2	FACETS	0.646	0.523	0.785	0.646	0.523	0.785	SUBCLONAL	1	TRUE	1	0.17	2		330	583	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391096	89391096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	71	551	0	ENST00000336596.2:c.1162G>A	p.Gly388Arg	p.G388R	ENST00000336596	NM_005233.5	388	Gga/Aga	5/17	1	2	FACETS	0.894	0.779	1	0.894	0.779	1	CLONAL	1	TRUE	1	0.17	2		551	934	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589555	67589557	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	novel	NA	P-0054690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	68	212	0	ENST00000274335.5:c.1318_1320del	p.Asp440del	p.D440del	ENST00000274335		440	GAT/-	10/15	0.454120060803458	4	FACETS	0.85	0.749	0.956	0.85	0.749	0.956	CLONAL	2	TRUE	2	0.476150508342639	4		212	248	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576858	7576858	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	344	601	0	ENST00000269305.4:c.988del	p.Leu330PhefsTer15	p.L330Ffs*15	ENST00000269305	NM_001126112.2	330	Ctt/tt	9/11	0.476150508342639	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.476150508342639	2		601	682	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443512	49443512	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	169	664	0	ENST00000301067.7:c.3859G>T	p.Glu1287Ter	p.E1287*	ENST00000301067	NM_003482.3	1287	Gag/Tag	11/54	0.474142079999041	4	FACETS	0.953	0.875	1			1	CLONAL	1	TRUE	NA	0.476150508342639	4		664	1099	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589181	67589183	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	novel	NA	P-0054690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	162	312	0	ENST00000274335.5:c.1169_1171del	p.Tyr390_Gly391delinsCys	p.Y390_G391delinsC	ENST00000274335		390	tATGgc/tgc	9/15	0.454120060803458	4	FACETS	0.989	0.914	1	0.989	0.914	1	CLONAL	2	TRUE	2	0.476150508342639	4		312	508	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776940	76776940	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	111	446	0	ENST00000373344.5:c.7012G>A	p.Ala2338Thr	p.A2338T	ENST00000373344	NM_000489.3	2338	Gca/Aca	33/35	0.476150508342639	3	FACETS	0.945	0.851	1	0.472	0.425	0.522	CLONAL	1	TRUE	1	0.476150508342639	3		446	611	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0054691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	42	76	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.212497959534756	5	FACETS	1	0.932	1	0.411	0.343	0.486	CLONAL	1	TRUE	2	0.212497959534756	5		76	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0054691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	70	711	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.213133816923094	4	FACETS	1	0.904	1	0.692	0.606	0.783	CLONAL	2	TRUE	1	0.212497959534756	4		712	385	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603041	48603041	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767361	NA	P-0054691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	43	353	0	ENST00000342988.3:c.1342C>T	p.Gln448Ter	p.Q448*	ENST00000342988	NM_005359.5	448	Cag/Tag	11/12	0.127426549759281	3	FACETS	1	0.945	1	0.658	0.553	0.775	INDETERMINATE	1	TRUE	1	0.212497959534756	3		353	340	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272508	11272508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1481267106	NA	P-0054691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	19	469	0	ENST00000361445.4:c.3422G>A	p.Arg1141His	p.R1141H	ENST00000361445	NM_004958.3	1141	cGc/cAc	23/58	0.213133816923094	0	FACETS	0.479	0.363	0.615			1	SUBCLONAL	1	TRUE	0	0.212497959534756	0		469	294	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409422	80409422	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	20	296	0	ENST00000286548.4:c.692del	p.Ala231GlyfsTer43	p.A231Gfs*43	ENST00000286548	NM_002072.3	231	gCg/gg	5/7	0.213133816923094	0	FACETS	0.506	0.387	0.645			1	SUBCLONAL	1	TRUE	0	0.212497959534756	0		296	293	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224461	53224463	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0054691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	19	829	0	ENST00000375401.3:c.3250_3252del	p.Lys1084del	p.K1084del	ENST00000375401	NM_004187.3	1084	AAG/-	21/26	0.213133816923094	0	FACETS	0.643	0.489	0.822			1	SUBCLONAL	1	TRUE	0	0.212497959534756	0		829	219	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0054704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	45	703	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.944	0.793	1	0.944	0.793	1	CLONAL	1	FALSE	1	0.185853013643113	2		703	513	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370985	55370985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	106	929	0	ENST00000297316.4:c.287C>G	p.Ala96Gly	p.A96G	ENST00000297316	NM_022454.3	96	gCc/gGc	1/2	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.185853013643113	2		929	843	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692800	89692800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204856	NA	P-0054704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	62	431	0	ENST00000371953.3:c.284C>T	p.Pro95Leu	p.P95L	ENST00000371953	NM_000314.4	95	cCa/cTa	5/9	0.185853013643113	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	FALSE	0	0.185853013643113	2		431	276	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380338	14380339	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCCCACGCC	novel	NA	P-0054704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	35	427	0	ENST00000256196.4:c.70_78dup	p.Gly24_Gly26dup	p.G24_G26dup	ENST00000256196		24	-/GGCGTGGGC	1/6	1	2	FACETS	0.87	0.713	1	0.87	0.713	1	CLONAL	1	FALSE	1	0.185853013643113	2		427	433	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234309	39234309	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397517159	NA	P-0054704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	39	355	0	ENST00000402219.2:c.2536G>A	p.Glu846Lys	p.E846K	ENST00000402219	NM_005633.3	846	Gaa/Aaa	16/23	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.185853013643113	2		355	311	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428124	47428124	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs756741810	NA	P-0054704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	110	939	0	ENST00000377045.4:c.1084C>T	p.Arg362Ter	p.R362*	ENST00000377045	NM_001654.4	362	Cga/Tga	11/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.185853013643113	2		939	959	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107097	27107098	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0054704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	84	791	0	ENST00000324856.7:c.6709dup	p.Ala2237GlyfsTer41	p.A2237Gfs*41	ENST00000324856	NM_006015.4	2236	-/G	20/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.185853013643113	2		791	729	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14317397	14317397	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	31	373	0	ENST00000256196.4:c.113A>G	p.Tyr38Cys	p.Y38C	ENST00000256196		38	tAt/tGt	2/6	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	FALSE	1	0.185853013643113	2		373	310	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645416	67645416	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	38	500	0	ENST00000264010.4:c.684del	p.Phe228LeufsTer22	p.F228Lfs*22	ENST00000264010	NM_006565.3	227	gaT/ga	3/12	1	2	FACETS	0.897	0.741	1	0.897	0.741	1	CLONAL	1	FALSE	1	0.185853013643113	2		500	456	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0054705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	18	603	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.345536816231272	4	FACETS	0.17	0.127	0.221	0.085	0.063	0.111	SUBCLONAL	1	TRUE	2	0.389573497482227	4		603	757	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578393	7578393	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876660821	NA	P-0054705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	502	876	0	ENST00000269305.4:c.537T>A	p.His179Gln	p.H179Q	ENST00000269305	NM_001126112.2	179	caT/caA	5/11	0.351280811911338	3	FACETS	0.978	0.941	1	0.978	0.941	1	CLONAL	3	TRUE	0	0.389573497482227	3		876	1049	SUCCESS
APC	324	MSKCC	GRCh37	5	112175223	112175223	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	47	218	0	ENST00000257430.4:c.3933del	p.Ile1311MetfsTer10	p.I1311Mfs*10	ENST00000257430	NM_000038.5	1311	aTt/at	16/16	0.383100732819668	3	FACETS	0.765	0.647	0.894	0.382	0.323	0.447	SUBCLONAL	1	TRUE	1	0.389573497482227	3		218	377	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369086	118369086	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	77	322	1	ENST00000534358.1:c.5804G>A	p.Arg1935Lys	p.R1935K	ENST00000534358	NM_005933.3	1935	aGa/aAa	22/36	0.389573497482227	2	FACETS	0.913	0.805	1	0.456	0.402	0.514	CLONAL	1	TRUE	0	0.389573497482227	2		323	433	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366937	15366937	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1412	155	791	0	ENST00000263377.2:c.1689C>G	p.Ser563Arg	p.S563R	ENST00000263377	NM_058243.2	563	agC/agG	9/20	0.302515796681992	5	FACETS	0.805	0.734	0.879	0.268	0.244	0.293	CLONAL	1	TRUE	2	0.389573497482227	5		791	1567	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390186	89390186	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1486190561	NA	P-0054705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	74	406	0	ENST00000336596.2:c.935G>A	p.Arg312Gln	p.R312Q	ENST00000336596	NM_005233.5	312	cGg/cAg	4/17	0.345536816231272	4	FACETS	0.812	0.711	0.921	0.406	0.355	0.461	CLONAL	1	TRUE	2	0.389573497482227	4		406	650	SUCCESS
AR	367	MSKCC	GRCh37	X	66765482	66765482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	177	990	0	ENST00000374690.3:c.494C>T	p.Ser165Phe	p.S165F	ENST00000374690	NM_000044.3	165	tCc/tTc	1/8	0.370632671100707	3	FACETS	0.983	0.905	1	0.328	0.301	0.355	CLONAL	1	TRUE	0	0.389573497482227	3		990	1104	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551854	NA	P-0054706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	182	852	0	ENST00000269305.4:c.592G>T	p.Glu198Ter	p.E198*	ENST00000269305	NM_001126112.2	198	Gaa/Taa	6/11	0.179575930052082	2	FACETS	0.997	0.919	1	0.997	0.919	1	CLONAL	2	FALSE	0	0.179575930052082	2		852	1017	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321304	1321304	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	42	795	0	ENST00000400841.2:c.451C>T	p.Gln151Ter	p.Q151*	ENST00000400841		151	Cag/Tag	4/6	NA	2	FACETS	0.607	0.505	0.72			1	INDETERMINATE	1	FALSE	NA	0.179575930052082	2		795	771	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719794	52719794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	120	748	0	ENST00000322088.6:c.1006G>A	p.Asp336Asn	p.D336N	ENST00000322088	NM_014225.5	336	Gat/Aat	9/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.179575930052082	2		748	1016	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181501	32181501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	72	931	0	ENST00000375023.3:c.2284C>T	p.Pro762Ser	p.P762S	ENST00000375023	NM_004557.3	762	Ccc/Tcc	14/30	1	2	FACETS	0.687	0.598	0.783	0.687	0.598	0.783	SUBCLONAL	1	FALSE	1	0.179575930052082	2		931	1168	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981084	201981084	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0054706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	194	736	0	ENST00000359651.3:c.164-1G>C		p.X55_splice	ENST00000359651		55			0.179575930052082	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	FALSE	0	0.179575930052082	2		736	879	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436941	110436941	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	32	395	0	ENST00000375856.3:c.1460C>G	p.Ser487Cys	p.S487C	ENST00000375856	NM_003749.2	487	tCc/tGc	1/2	1	2	FACETS	0.895	0.727	1	0.895	0.727	1	CLONAL	1	FALSE	1	0.179575930052082	2		395	398	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412986	49412986	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	58	776	0	ENST00000418115.1:c.37G>C	p.Asp13His	p.D13H	ENST00000418115	NM_001664.2	13	Gat/Cat	2/5	1	2	FACETS	0.64	0.548	0.741	0.64	0.548	0.741	SUBCLONAL	1	FALSE	1	0.179575930052082	2		776	1009	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443896	49443896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763628601	NA	P-0054706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1225	137	1073	0	ENST00000301067.7:c.3475G>A	p.Glu1159Lys	p.E1159K	ENST00000301067	NM_003482.3	1159	Gag/Aag	11/54	0.149016692720579	3	FACETS	1	0.975	1	0.61	0.553	0.671	CLONAL	1	FALSE	1	0.179575930052082	3		1073	1362	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109798	115109798	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	53	875	0	ENST00000257566.3:c.2080A>C	p.Ser694Arg	p.S694R	ENST00000257566	NM_016569.3	694	Agc/Cgc	8/8	1	2	FACETS	0.61	0.518	0.711	0.61	0.518	0.711	SUBCLONAL	1	FALSE	1	0.179575930052082	2		875	968	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514695	103514695	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	52	514	0	ENST00000355739.4:c.1196A>G	p.Glu399Gly	p.E399G	ENST00000355739	NM_000123.3	399	gAa/gGa	8/15	1	2	FACETS	0.99	0.842	1	0.99	0.842	1	CLONAL	1	FALSE	1	0.179575930052082	2		514	585	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857340	9857340	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	53	680	0	ENST00000330684.3:c.4061G>A	p.Ser1354Asn	p.S1354N	ENST00000330684	NM_001134407.1	1354	aGc/aAc	13/13	1	2	FACETS	0.648	0.551	0.755	0.648	0.551	0.755	SUBCLONAL	1	FALSE	1	0.179575930052082	2		680	911	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622352	1622352	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	201	1100	0	ENST00000344749.5:c.612G>C	p.Lys204Asn	p.K204N	ENST00000344749	NM_001136139.2	204	aaG/aaC	9/19	1	2	FACETS	0.849	0.785	0.916	1	0.992	1	CLONAL	2	FALSE	1	0.179575930052082	2		1100	1318	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741879	40741879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	76	1129	0	ENST00000392038.2:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000392038	NM_001626.4	365	Gaa/Aaa	11/14	1	2	FACETS	0.641	0.56	0.729	0.641	0.56	0.729	SUBCLONAL	1	FALSE	1	0.179575930052082	2		1129	1321	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198262807	198262807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	39	392	0	ENST00000335508.6:c.3168G>A	p.Met1056Ile	p.M1056I	ENST00000335508	NM_012433.2	1056	atG/atA	22/25	1	2	FACETS	0.864	0.715	1	0.864	0.715	1	CLONAL	1	FALSE	1	0.179575930052082	2		392	503	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46270964	46270964	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1168539147	NA	P-0054706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	50	602	0	ENST00000371998.3:c.3088C>G	p.Leu1030Val	p.L1030V	ENST00000371998		1030	Ctt/Gtt	17/23	1	2	FACETS	0.677	0.572	0.792	0.677	0.572	0.792	SUBCLONAL	1	FALSE	1	0.179575930052082	2		602	823	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46271054	46271054	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	64	618	0	ENST00000371998.3:c.3178C>G	p.Leu1060Val	p.L1060V	ENST00000371998		1060	Ctt/Gtt	17/23	1	2	FACETS	0.826	0.714	0.948	0.826	0.714	0.948	CLONAL	1	FALSE	1	0.179575930052082	2		618	863	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643503	52643503	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	56	560	0	ENST00000394830.3:c.2393G>C	p.Arg798Thr	p.R798T	ENST00000394830	NM_018313.4	798	aGa/aCa	17/30	1	2	FACETS	0.845	0.723	0.979	0.845	0.723	0.979	CLONAL	1	FALSE	1	0.179575930052082	2		560	738	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643871	52643871	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	35	516	0	ENST00000394830.3:c.2025G>T	p.Lys675Asn	p.K675N	ENST00000394830	NM_018313.4	675	aaG/aaT	17/30	1	2	FACETS	0.639	0.522	0.771	0.639	0.522	0.771	SUBCLONAL	1	FALSE	1	0.179575930052082	2		516	610	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490560	20490560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	54	675	0	ENST00000346618.3:c.1297G>A	p.Asp433Asn	p.D433N	ENST00000346618	NM_001949.4	433	Gac/Aac	7/7	1	2	FACETS	0.687	0.585	0.8	0.687	0.585	0.8	SUBCLONAL	1	FALSE	1	0.179575930052082	2		675	875	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852058	128852058	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1276	95	1247	0	ENST00000249373.3:c.2130G>C	p.Gln710His	p.Q710H	ENST00000249373	NM_005631.4	710	caG/caC	12/12	1	2	FACETS	0.772	0.685	0.865	0.772	0.685	0.865	SUBCLONAL	1	FALSE	1	0.179575930052082	2		1247	1371	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5081725	5081738	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	ATTATGAACTATTA	ATTATGAACTATTA	-	novel	NA	P-0054706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	19	233	0	ENST00000381652.3:c.2436_2449del	p.Tyr813ArgfsTer3	p.Y813Rfs*3	ENST00000381652	NM_004972.3	812	gATTATGAACTATTA/g	19/25	NA	2	FACETS	0.799	0.607	1			1	INDETERMINATE	1	FALSE	NA	0.179575930052082	2		233	265	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772695	135772695	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	144	659	0	ENST00000298552.3:c.2851C>T	p.Gln951Ter	p.Q951*	ENST00000298552	NM_001162426.1	951	Cag/Tag	22/23	0.179575930052082	2	FACETS	0.947	0.864	1	0.947	0.864	1	CLONAL	2	FALSE	0	0.179575930052082	2		659	847	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949164	44949164	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	92	500	0	ENST00000377967.4:c.3725G>A	p.Gly1242Asp	p.G1242D	ENST00000377967	NM_021140.2	1242	gGt/gAt	25/29	NA	2	FACETS	0.811	0.721	0.906			1	INDETERMINATE	2	FALSE	NA	0.179575930052082	2		500	632	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224478	53224478	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	155	954	0	ENST00000375401.3:c.3235C>T	p.His1079Tyr	p.H1079Y	ENST00000375401	NM_004187.3	1079	Cac/Tac	21/26	NA	2	FACETS	0.793	0.725	0.865			1	INDETERMINATE	2	FALSE	NA	0.179575930052082	2		954	1088	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939771	76939771	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	60	738	0	ENST00000373344.5:c.977G>C	p.Gly326Ala	p.G326A	ENST00000373344	NM_000489.3	326	gGa/gCa	9/35	1	2	FACETS	0.693	0.595	0.8	0.693	0.595	0.8	SUBCLONAL	1	FALSE	1	0.179575930052082	2		738	964	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	127	375	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.935	0.864	1			1	INDETERMINATE	2	TRUE	NA	0.504690304958851	2		375	269	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0054707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	260	324	1	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	0.504690304958851	6	FACETS	0.931	0.877	0.987	0.698	0.657	0.74	CLONAL	3	TRUE	2	0.504690304958851	6		325	741	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42384773	42384773	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782714583	NA	P-0054707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	91	426	0	ENST00000221972.3:c.535G>A	p.Gly179Arg	p.G179R	ENST00000221972	NM_021601.3	179	Ggg/Agg	4/5	0.369699265375667	3	FACETS	0.832	0.74	0.929			1	CLONAL	1	TRUE	NA	0.504690304958851	3		426	543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579503	7579503	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567556752	NA	P-0054707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	532	910	0	ENST00000269305.4:c.184G>T	p.Glu62Ter	p.E62*	ENST00000269305	NM_001126112.2	62	Gaa/Taa	4/11	0.453371092894639	3	FACETS	0.967	0.935	0.999	0.967	0.935	0.999	CLONAL	3	TRUE	0	0.504690304958851	3		910	910	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100919	27100919	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	261	695	0	ENST00000324856.7:c.4201C>T	p.Gln1401Ter	p.Q1401*	ENST00000324856	NM_006015.4	1401	Cag/Tag	18/20	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.504690304958851	2		695	703	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890189	76890189	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	111	211	0	ENST00000373344.5:c.4705C>T	p.Gln1569Ter	p.Q1569*	ENST00000373344	NM_000489.3	1569	Cag/Tag	17/35	0.319012693725595	2	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.504690304958851	2		211	353	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187812	11187812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	92	600	0	ENST00000361445.4:c.6085G>A	p.Glu2029Lys	p.E2029K	ENST00000361445	NM_004958.3	2029	Gaa/Aaa	44/58	0.369607667821578	3	FACETS	0.666	0.592	0.745	0.333	0.296	0.373	SUBCLONAL	1	TRUE	1	0.504690304958851	3		600	686	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114724371	114724371	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	129	460	0	ENST00000543371.1:c.438G>C	p.Gln146His	p.Q146H	ENST00000543371	NM_001198531.1	146	caG/caC	4/14	0.504690304958851	2	FACETS	1	0.941	1	0.521	0.475	0.568	CLONAL	1	TRUE	0	0.504690304958851	2		460	491	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514014	125514014	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	126	441	0	ENST00000428830.2:c.952C>A	p.Gln318Lys	p.Q318K	ENST00000428830	NM_001114121.2	318	Cag/Aag	10/14	0.130851176729877	6	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.504690304958851	6		441	700	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042387	42042387	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	191	569	0	ENST00000219905.7:c.6582G>C	p.Lys2194Asn	p.K2194N	ENST00000219905	NM_001164273.1	2194	aaG/aaC	17/24	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.504690304958851	2		569	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579491	7579491	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	503	897	0	ENST00000269305.4:c.196A>C	p.Met66Leu	p.M66L	ENST00000269305	NM_001126112.2	66	Atg/Ctg	4/11	0.453371092894639	3	FACETS	0.958	0.924	0.991	0.958	0.924	0.991	CLONAL	3	TRUE	0	0.504690304958851	3		897	869	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15938159	15938159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	49	465	0	ENST00000268712.3:c.7055C>T	p.Ser2352Leu	p.S2352L	ENST00000268712	NM_006311.3	2352	tCa/tTa	45/46	0.453371092894639	3	FACETS	0.447	0.378	0.523	0.149	0.126	0.175	SUBCLONAL	1	TRUE	0	0.504690304958851	3		465	544	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677317	29677317	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	57	352	0	ENST00000356175.3:c.7375C>G	p.His2459Asp	p.H2459D	ENST00000356175	NM_000267.3	2459	Cat/Gat	49/57	0.504690304958851	6	FACETS	0.68	0.583	0.787	0.17	0.145	0.197	SUBCLONAL	1	TRUE	2	0.504690304958851	6		352	667	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679327	29679327	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs876658333	NA	P-0054707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	105	405	0	ENST00000356175.3:c.7447C>G	p.Leu2483Val	p.L2483V	ENST00000356175	NM_000267.3	2483	Ctt/Gtt	50/57	0.504690304958851	6	FACETS	0.905	0.81	1	0.226	0.202	0.252	CLONAL	1	TRUE	2	0.504690304958851	6		405	924	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2208937	2208937	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	223	456	0	ENST00000398665.3:c.967G>A	p.Glu323Lys	p.E323K	ENST00000398665	NM_032482.2	323	Gaa/Aaa	12/28	0.385879369585197	4	FACETS	0.902	0.843	0.963	0.902	0.843	0.963	CLONAL	2	TRUE	2	0.504690304958851	4		456	737	SUCCESS
REL	5966	MSKCC	GRCh37	2	61128157	61128157	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	59	257	0	ENST00000295025.8:c.333G>C	p.Lys111Asn	p.K111N	ENST00000295025	NM_002908.2	111	aaG/aaC	4/11	0.43448652751314	4	FACETS	0.747	0.644	0.859	0.373	0.322	0.43	SUBCLONAL	1	TRUE	2	0.504690304958851	4		257	471	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536199	106536199	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	144	449	0	ENST00000369096.4:c.166G>C	p.Glu56Gln	p.E56Q	ENST00000369096	NM_001198.3	56	Gag/Cag	2/7	0.159327276883691	5	FACETS	0.787	0.72	0.857			1	INDETERMINATE	2	TRUE	NA	0.504690304958851	5		449	637	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069067	5069067	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	85	284	0	ENST00000381652.3:c.1372G>C	p.Glu458Gln	p.E458Q	ENST00000381652	NM_004972.3	458	Gag/Cag	11/25	0.504690304958851	3	FACETS	0.979	0.87	1	0.489	0.435	0.547	CLONAL	1	TRUE	1	0.504690304958851	3		284	431	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209367	98209367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45535032	NA	P-0054708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1490	117	1147	4	ENST00000331920.6:c.4171C>T	p.Arg1391Trp	p.R1391W	ENST00000331920	NM_000264.3	1391	Cgg/Tgg	23/24	0.316782939642289	5	FACETS	0.678	0.609	0.752	0.17	0.152	0.188	SUBCLONAL	1	TRUE	1	0.316782939642289	5		1151	1607	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962550	100962550	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	93	623	0	ENST00000325455.5:c.1847G>T	p.Arg616Ile	p.R616I	ENST00000325455	NM_001202474.3	616	aGa/aTa	3/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.316782939642289	2		623	506	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730823	40730823	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	93	728	0	ENST00000373198.4:c.3712C>T	p.Pro1238Ser	p.P1238S	ENST00000373198	NM_133170.3	1238	Ccc/Tcc	27/32	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.18	2		728	891	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279674	123279674	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs77543610	NA	P-0054709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	55	454	0	ENST00000358487.5:c.758C>G	p.Pro253Arg	p.P253R	ENST00000358487	NM_000141.4	253	cCt/cGt	7/18	1	2	FACETS	0.959	0.82	1	0.959	0.82	1	CLONAL	1	TRUE	1	0.18	2		454	637	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692791	89692791	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	38	365	0	ENST00000371953.3:c.275A>T	p.Asp92Val	p.D92V	ENST00000371953	NM_000314.4	92	gAc/gTc	5/9	1	2	FACETS	0.757	0.625	0.905	0.757	0.625	0.905	CLONAL	1	TRUE	1	0.18	2		365	558	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883981	37883981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1357550606	NA	P-0054709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	80	815	2	ENST00000269571.5:c.3452C>T	p.Ser1151Leu	p.S1151L	ENST00000269571		1151	tCg/tTg	27/27	1	2	FACETS	0.928	0.815	1	0.928	0.815	1	CLONAL	1	TRUE	1	0.18	2		817	958	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830136	72830136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	68	690	1	ENST00000268489.5:c.6445C>T	p.Arg2149Cys	p.R2149C	ENST00000268489	NM_006885.3	2149	Cgc/Tgc	9/10	1	2	FACETS	0.769	0.667	0.88	0.769	0.667	0.88	SUBCLONAL	1	TRUE	1	0.18	2		691	983	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0054709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	77	800	7	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.931	0.816	1	0.931	0.816	1	CLONAL	1	TRUE	1	0.18	2		807	919	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211138	36211138	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	142	1026	0	ENST00000222270.7:c.889C>T	p.Arg297Ter	p.R297*	ENST00000222270	NM_014727.1	297	Cga/Tga	3/37	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.18	2		1026	1351	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023708	27023708	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	50	474	0	ENST00000324856.7:c.817del	p.Ala273ProfsTer90	p.A273Pfs*90	ENST00000324856	NM_006015.4	272	Ggg/gg	1/20	1	2	FACETS	0.903	0.766	1	0.903	0.766	1	CLONAL	1	TRUE	1	0.18	2		474	615	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213611	36213611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757982914	NA	P-0054709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	102	1025	2	ENST00000222270.7:c.2713G>A	p.Ala905Thr	p.A905T	ENST00000222270	NM_014727.1	905	Gcc/Acc	5/37	1	2	FACETS	0.979	0.873	1	0.979	0.873	1	CLONAL	1	TRUE	1	0.18	2		1027	1158	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435129	110435129	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	56	916	5	ENST00000375856.3:c.3272del	p.Pro1091ArgfsTer15	p.P1091Rfs*15	ENST00000375856	NM_003749.2	1091	cCg/cg	1/2	1	2	FACETS	0.645	0.551	0.748	0.645	0.551	0.748	SUBCLONAL	1	TRUE	1	0.18	2		921	965	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803721	1803721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780313125	NA	P-0054709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	81	888	0	ENST00000260795.2:c.899C>T	p.Pro300Leu	p.P300L	ENST00000260795		300	cCg/cTg	6/17	1	2	FACETS	0.856	0.752	0.968	0.856	0.752	0.968	CLONAL	1	TRUE	1	0.18	2		888	1052	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088658	27088659	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	66	784	1	ENST00000324856.7:c.2272dup	p.Gln758ProfsTer59	p.Q758Pfs*59	ENST00000324856	NM_006015.4	756	aac/aaCc	7/20	1	2	FACETS	0.72	0.623	0.826	0.72	0.623	0.826	SUBCLONAL	1	TRUE	1	0.18	2		785	1018	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439302	149439302	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	72	767	0	ENST00000286301.3:c.2093A>G	p.Asp698Gly	p.D698G	ENST00000286301	NM_005211.3	698	gAc/gGc	15/22	1	2	FACETS	0.854	0.744	0.973	0.854	0.744	0.973	CLONAL	1	TRUE	1	0.18	2		767	937	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948280	71948280	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	84	939	1	ENST00000298229.2:c.2996del	p.Pro999ArgfsTer132	p.P999Rfs*132	ENST00000298229	NM_001567.3	998	Ccc/cc	26/28	1	2	FACETS	0.834	0.734	0.942	0.834	0.734	0.942	CLONAL	1	TRUE	1	0.18	2		940	1119	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923700	39923700	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372187961	NA	P-0054709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	101	816	0	ENST00000378444.4:c.3391C>T	p.Arg1131Trp	p.R1131W	ENST00000378444	NM_001123385.1	1131	Cgg/Tgg	7/15	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.18	2		816	1041	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447880	49447880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771025627	NA	P-0054709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	60	675	1	ENST00000301067.7:c.554G>A	p.Arg185His	p.R185H	ENST00000301067	NM_003482.3	185	cGc/cAc	5/54	1	2	FACETS	0.774	0.665	0.893	0.774	0.665	0.893	SUBCLONAL	1	TRUE	1	0.18	2		676	861	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566433	41566433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769217956	NA	P-0054709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	35	416	0	ENST00000263253.7:c.4310C>T	p.Ala1437Val	p.A1437V	ENST00000263253	NM_001429.3	1437	gCa/gTa	27/31	1	2	FACETS	0.685	0.56	0.825	0.685	0.56	0.825	SUBCLONAL	1	TRUE	1	0.18	2		416	568	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256410	16256411	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	62	576	0	ENST00000375759.3:c.3680dup	p.Lys1228GlufsTer9	p.K1228Efs*9	ENST00000375759	NM_015001.2	1225	-/A	11/15	1	2	FACETS	0.771	0.665	0.888	0.771	0.665	0.888	SUBCLONAL	1	TRUE	1	0.18	2		576	893	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175858	176175858	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1431484004	NA	P-0054709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	22	295	0	ENST00000367669.3:c.257T>C	p.Leu86Pro	p.L86P	ENST00000367669	NM_022457.5	86	cTg/cCg	1/20	1	2	FACETS	0.837	0.649	1	0.837	0.649	1	CLONAL	1	TRUE	1	0.18	2		295	292	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567708	226567708	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	66	599	0	ENST00000366794.5:c.1458G>T	p.Lys486Asn	p.K486N	ENST00000366794	NM_001618.3	486	aaG/aaT	10/23	0.152549540058345	3	FACETS	0.911	0.789	1	0.456	0.394	0.522	CLONAL	1	TRUE	1	0.18	3		599	877	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682479	37682479	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	66	484	0	ENST00000447079.4:c.3670G>A	p.Ala1224Thr	p.A1224T	ENST00000447079	NM_015083.1	1224	Gca/Aca	13/14	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.18	2		484	659	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40857188	40857188	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	39	384	0	ENST00000428826.2:c.1853C>T	p.Ala618Val	p.A618V	ENST00000428826		618	gCc/gTc	17/21	1	2	FACETS	0.788	0.652	0.94	0.788	0.652	0.94	CLONAL	1	TRUE	1	0.18	2		384	550	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885878	59885878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145601931	NA	P-0054709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	53	630	1	ENST00000259008.2:c.868G>A	p.Gly290Ser	p.G290S	ENST00000259008	NM_032043.2	290	Ggt/Agt	7/20	1	2	FACETS	0.771	0.656	0.897	0.771	0.656	0.897	SUBCLONAL	1	TRUE	1	0.18	2		631	764	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291959	15291959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	80	795	0	ENST00000263388.2:c.2807G>A	p.Gly936Asp	p.G936D	ENST00000263388	NM_000435.2	936	gGc/gAc	18/33	1	2	FACETS	0.917	0.806	1	0.917	0.806	1	CLONAL	1	TRUE	1	0.18	2		795	969	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36217256	36217256	+	splice_donor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0054709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	59	647	0	ENST00000222270.7:c.4003+2del		p.X1335_splice	ENST00000222270	NM_014727.1	1335			1	2	FACETS	0.807	0.693	0.932	0.807	0.693	0.932	CLONAL	1	TRUE	1	0.18	2		647	812	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573830	41573830	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs764896987	NA	P-0054709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	71	860	0	ENST00000263253.7:c.6115A>G	p.Ser2039Gly	p.S2039G	ENST00000263253	NM_001429.3	2039	Agc/Ggc	31/31	1	2	FACETS	0.783	0.682	0.894	0.783	0.682	0.894	SUBCLONAL	1	TRUE	1	0.18	2		860	1007	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979581	55979581	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	59	659	0	ENST00000263923.4:c.866del	p.Leu289Ter	p.L289*	ENST00000263923	NM_002253.2	289	tTg/tg	7/30	1	2	FACETS	0.745	0.639	0.861	0.745	0.639	0.861	SUBCLONAL	1	TRUE	1	0.18	2		659	880	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591274	67591317	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	AAAAGAAGTTGAACGAGTGGTTGGGCAATGAAAACACTGAAGAG	AAAAGAAGTTGAACGAGTGGTTGGGCAATGAAAACACTGAAGAG	-	novel	NA	P-0054709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	42	440	0	ENST00000274335.5:c.1772_1814+1del		p.X591_splice	ENST00000274335		591		13/15	1	2	FACETS	0.667	0.555	0.791	0.667	0.555	0.791	SUBCLONAL	1	TRUE	1	0.18	2		440	700	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29197674	29197674	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	64	711	0	ENST00000240100.2:c.520A>C	p.Ser174Arg	p.S174R	ENST00000240100	NM_001394.6	174	Agt/Cgt	2/4	1	2	FACETS	0.723	0.624	0.831	0.723	0.624	0.831	SUBCLONAL	1	TRUE	1	0.18	2		711	983	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970946	21970946	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs145012438	NA	P-0054709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	86	676	0	ENST00000304494.5:c.412A>G	p.Arg138Gly	p.R138G	ENST00000304494	NM_000077.4	138	Aga/Gga	2/3	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.18	2		676	913	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781504	NA	P-0054710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	225	780	1	ENST00000269305.4:c.314G>T	p.Gly105Val	p.G105V	ENST00000269305	NM_001126112.2	105	gGc/gTc	4/11	0.243900406209765	2	FACETS	0.755	0.705	0.807	0.755	0.705	0.807	SUBCLONAL	2	TRUE	0	0.374672816784174	2		781	795	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023116	48023116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569728764	NA	P-0054710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	66	423	0	ENST00000234420.5:c.541G>A	p.Glu181Lys	p.E181K	ENST00000234420	NM_000179.2	181	Gaa/Aaa	3/10	0.251069566463409	3	FACETS	0.659	0.572	0.753	0.329	0.286	0.377	SUBCLONAL	1	TRUE	1	0.374672816784174	3		423	635	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118856	115118856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1565861840	NA	P-0054710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	140	513	0	ENST00000257566.3:c.485G>A	p.Arg162His	p.R162H	ENST00000257566	NM_016569.3	162	cGt/cAt	2/8	0.251069566463409	3	FACETS	1	0.986	1	0.716	0.654	0.78	CLONAL	1	TRUE	1	0.374672816784174	3		513	620	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687021	37687021	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1387854042	NA	P-0054710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	46	540	0	ENST00000447079.4:c.3925G>A	p.Glu1309Lys	p.E1309K	ENST00000447079	NM_015083.1	1309	Gaa/Aaa	14/14	0.243900406209765	2	FACETS	0.397	0.333	0.467	0.198	0.166	0.234	SUBCLONAL	1	TRUE	0	0.374672816784174	2		540	619	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0054711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	195	439	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	0.914	0.85	0.98	0.914	0.85	0.98	CLONAL	1	TRUE	1	0.677153312975133	2		439	630	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439874	52439874	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	316	597	0	ENST00000460680.1:c.838C>T	p.Gln280Ter	p.Q280*	ENST00000460680	NM_004656.3	280	Cag/Tag	10/17	0.632936358860909	1	FACETS	0.89	0.846	0.934	0.89	0.846	0.934	CLONAL	1	TRUE	0	0.677153312975133	1		597	694	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56859022	56859022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1249	70	495	0	ENST00000519728.1:c.148C>T	p.Leu50Phe	p.L50F	ENST00000519728	NM_002350.3	50	Ctt/Ttt	3/13	0.342584402773243	6	FACETS	0.369	0.32	0.422	0.062	0.053	0.071	INDETERMINATE	1	TRUE	0	0.677153312975133	6		495	1319	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248998	55248999	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCAGCG	rs727504263	NA	P-0054712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	235	472	0	ENST00000275493.2:c.2300_2308dup	p.Ala767_Val769dup	p.A767_V769dup	ENST00000275493	NM_005228.3	767	atg/aTGGCCAGCGtg	20/28	0.523669882319631	4	FACETS	1	0.99	1	0.668	0.624	0.715	CLONAL	1	TRUE	2	0.525210471875777	4		472	1021	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155583	56155583	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs373481385	NA	P-0054712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	43	351	0	ENST00000399503.3:c.675G>T	p.Met225Ile	p.M225I	ENST00000399503	NM_005921.1	225	atG/atT	3/20	0.522001494775779	2	FACETS	0.296	0.247	0.35	0.148	0.123	0.175	SUBCLONAL	1	TRUE	0	0.525210471875777	2		351	553	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0054713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	53	477	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.852	0.729	0.986	0.852	0.729	0.986	CLONAL	1	TRUE	1	0.324815249353116	2		477	383	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867300	68867317	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCTCAGAGTCAGACAA	CTCCTCAGAGTCAGACAA	TC	novel	NA	P-0054713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	120	598	3	ENST00000261769.5:c.2547_2564delinsTC	p.Ser850GlnfsTer8	p.S850Qfs*8	ENST00000261769	NM_004360.3	849	aaCTCCTCAGAGTCAGACAAa/aaTCa	16/16	0.324815249353116	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.324815249353116	1		601	602	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851286	156851286	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745776726	NA	P-0000391-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	311	936	0	ENST00000524377.1:c.2243G>A	p.Arg748Gln	p.R748Q	ENST00000524377	NM_002529.3	748	cGg/cAg	17/17	1	2	FACETS	0.957	0.905	1	0.957	0.905	1	CLONAL	1	TRUE	1	0.687851658083342	2		936	945	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793008	33793010	+	inframe_deletion	In_Frame_Del	DEL	CGC	CGC	-	rs780345232	NA	P-0000391-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	9	129	1	ENST00000498907.2:c.311_313del	p.Gly104del	p.G104del	ENST00000498907	NM_004364.3	104	gGCGac/gac	1/1	1	2	FACETS	0.182	0.12	0.259	0.182	0.12	0.259	SUBCLONAL	1	TRUE	1	0.687851658083342	2		130	144	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724380	117724380	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs769105985	NA	P-0000391-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	304	673	1	ENST00000368508.3:c.499C>T	p.Arg167Ter	p.R167*	ENST00000368508	NM_002944.2	167	Cga/Tga	6/43	0.687851658083342	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.687851658083342	1		674	557	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946428	71946429	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000391-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	368	867	0	ENST00000298229.2:c.2594dup	p.Asn865LysfsTer19	p.N865Kfs*19	ENST00000298229	NM_001567.3	864	-/A	23/28	0.687851658083342	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.687851658083342	1		867	638	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435890	49435890	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000391-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	126	699	0	ENST00000301067.7:c.6091del	p.Leu2031SerfsTer16	p.L2031Sfs*16	ENST00000301067	NM_003482.3	2031	Ctc/tc	28/54	1	2	FACETS	0.451	0.408	0.496	0.451	0.408	0.496	SUBCLONAL	1	TRUE	1	0.687851658083342	2		699	812	SUCCESS
AR	367	MSKCC	GRCh37	X	66765461	66765461	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000391-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	42	415	0	ENST00000374690.3:c.473C>A	p.Ser158Ter	p.S158*	ENST00000374690	NM_000044.3	158	tCa/tAa	1/8	1	1	FACETS	0.19	0.158	0.225	0.19	0.158	0.225	SUBCLONAL	1	TRUE	0	0.687851658083342	1		415	422	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519886	NA	P-0001244-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	224	405	1	ENST00000349496.5:c.97T>C	p.Ser33Pro	p.S33P	ENST00000349496	NM_001904.3	33	Tct/Cct	3/15	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.83150846123507	2		406	539	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716327	52716327	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001244-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	401	820	0	ENST00000322088.6:c.771G>T	p.Trp257Cys	p.W257C	ENST00000322088	NM_014225.5	257	tgG/tgT	6/15	1	2	FACETS	0.989	0.944	1	0.989	0.944	1	CLONAL	1	TRUE	1	0.83150846123507	2		820	975	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288495	15288495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001244-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	173	345	0	ENST00000263388.2:c.4244G>A	p.Gly1415Asp	p.G1415D	ENST00000263388	NM_000435.2	1415	gGc/gAc	24/33	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.83150846123507	2		345	409	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0003309-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	1020	603	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.3	8	FACETS	1	0.987	1	1	0.998	1	CLONAL	11	TRUE	1	0.12	8		603	2057	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577520	7577520	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003309-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	63	724	0	ENST00000269305.4:c.761T>C	p.Ile254Thr	p.I254T	ENST00000269305	NM_001126112.2	254	aTc/aCc	7/11	1	2	FACETS	0.926	0.798	1	0.926	0.798	1	CLONAL	1	TRUE	1	0.12	2		724	1134	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141545650	141545650	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003309-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1226	87	807	0	ENST00000220592.5:c.2188A>G	p.Ile730Val	p.I730V	ENST00000220592	NM_012154.3	730	Att/Gtt	17/19	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.12	2		807	1313	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004226-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	270	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.958	0.908	1	0.958	0.908	1	CLONAL	1	TRUE	1	0.954917653612947	2		276	590	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0004226-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	177	464	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.946	0.884	1	0.946	0.884	1	CLONAL	1	TRUE	1	0.954917653612947	2		464	392	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398262	25398262	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913538	NA	P-0004226-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	204	551	0	ENST00000311936.3:c.57G>C	p.Leu19Phe	p.L19F	ENST00000311936	NM_004985.3	19	ttG/ttC	2/5	1	2	FACETS	0.952	0.893	1	0.952	0.893	1	CLONAL	1	TRUE	1	0.954917653612947	2		551	449	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158626	26158626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772836222	NA	P-0004226-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	261	309	0	ENST00000289316.2:c.229G>A	p.Glu77Lys	p.E77K	ENST00000289316	NM_138720.2	77	Gag/Aag	1/2	0.399865424084485	4	FACETS	0.988	0.935	1	0.988	0.935	1	INDETERMINATE	2	TRUE	2	0.954917653612947	4		309	541	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645693	12645693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397516827	NA	P-0004226-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	298	392	1	ENST00000251849.4:c.776C>T	p.Ser259Phe	p.S259F	ENST00000251849	NM_002880.3	259	tCc/tTc	7/17	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.954917653612947	2		393	622	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230772	46230772	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004226-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	174	330	0	ENST00000334344.6:c.1021G>C	p.Glu341Gln	p.E341Q	ENST00000334344	NM_152641.2	341	Gag/Cag	8/21	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.954917653612947	2		330	356	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588849	69588849	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004226-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2441	672	1037	0	ENST00000168712.1:c.387C>A	p.Phe129Leu	p.F129L	ENST00000168712	NM_002007.2	129	ttC/ttA	2/3	0.905657242829737	4	FACETS	0.884	0.848	0.92	0.295	0.282	0.307	CLONAL	1	TRUE	1	0.954917653612947	4		1037	3113	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168983	11168983	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004226-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	541	801	0	ENST00000358026.2:c.4573G>C	p.Glu1525Gln	p.E1525Q	ENST00000358026	NM_001128849.1	1525	Gag/Cag	32/36	1	2	FACETS	0.887	0.853	0.922	0.887	0.853	0.922	CLONAL	1	TRUE	1	0.954917653612947	2		801	1277	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170834	11170834	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004226-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	546	1022	0	ENST00000358026.2:c.4978G>A	p.Asp1660Asn	p.D1660N	ENST00000358026	NM_001128849.1	1660	Gac/Aac	35/36	1	2	FACETS	0.837	0.804	0.87	0.837	0.804	0.87	CLONAL	1	TRUE	1	0.954917653612947	2		1022	1366	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170861	11170861	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1298648044	NA	P-0004226-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	442	845	2	ENST00000358026.2:c.5005G>A	p.Glu1669Lys	p.E1669K	ENST00000358026	NM_001128849.1	1669	Gag/Aag	35/36	1	2	FACETS	0.824	0.788	0.861	0.824	0.788	0.861	CLONAL	1	TRUE	1	0.954917653612947	2		847	1123	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004757-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	30	276	0				ENST00000310581	NM_198253.2	-/1132			0.15261105090099	1	FACETS	0.858	0.694	1	1	0.951	1	CLONAL	2	TRUE	0	0.12	1		276	274	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983036	201983036	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004757-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	37	710	0	ENST00000359651.3:c.885G>T	p.Trp295Cys	p.W295C	ENST00000359651		295	tgG/tgT	7/8	1	2	FACETS	1	0.833	1	1	0.833	1	CLONAL	1	TRUE	1	0.12	2		710	609	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23625392	23625392	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004757-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	19	348	0	ENST00000261584.4:c.3134T>C	p.Leu1045Pro	p.L1045P	ENST00000261584	NM_024675.3	1045	cTc/cCc	11/13	1	2	FACETS	0.974	0.739	1	0.974	0.739	1	CLONAL	1	TRUE	1	0.12	2		348	325	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412945	49412945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004757-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	48	620	0	ENST00000418115.1:c.78C>G	p.Ser26Arg	p.S26R	ENST00000418115	NM_001664.2	26	agC/agG	2/5	1	2	FACETS	0.94	0.792	1	0.94	0.792	1	CLONAL	1	TRUE	1	0.12	2		620	851	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530336	187530336	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004757-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	22	289	0	ENST00000441802.2:c.10206+1G>A		p.X3402_splice	ENST00000441802	NM_005245.3	3402			1	2	FACETS	1	0.817	1	1	0.817	1	CLONAL	1	TRUE	1	0.12	2		289	345	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593667	55593669	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	rs1060502543	NA	P-0006104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	98	402	0	ENST00000288135.5:c.1735_1737del	p.Asp579del	p.D579del	ENST00000288135	NM_000222.2	578	tATGat/tat	11/21	1	2	FACETS	0.309	0.276	0.345	0.309	0.276	0.345	SUBCLONAL	1	TRUE	1	0.890829480756745	2		402	711	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692901	89692901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786204929	NA	P-0006104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	326	460	0	ENST00000371953.3:c.385G>A	p.Gly129Arg	p.G129R	ENST00000371953	NM_000314.4	129	Gga/Aga	5/9	0.890829480756745	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.890829480756745	1		460	394	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599334	55599334	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	322	407	0	ENST00000288135.5:c.2460T>G	p.Asp820Glu	p.D820E	ENST00000288135	NM_000222.2	820	gaT/gaG	17/21	1	2	FACETS	0.966	0.918	1	0.966	0.918	1	CLONAL	1	TRUE	1	0.890829480756745	2		407	748	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593607	55593615	+	inframe_deletion	In_Frame_Del	DEL	AGGTTGTTG	AGGTTGTTG	-	novel	NA	P-0006104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	227	402	0	ENST00000288135.5:c.1676_1684del	p.Val559_Glu561del	p.V559_E561del	ENST00000288135	NM_000222.2	558	aAGGTTGTTGag/aag	11/21	1	2	FACETS	0.753	0.705	0.802	0.753	0.705	0.802	SUBCLONAL	1	TRUE	1	0.890829480756745	2		402	677	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593652	55593652	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	167	424	0	ENST00000288135.5:c.1718C>A	p.Pro573Gln	p.P573Q	ENST00000288135	NM_000222.2	573	cCa/cAa	11/21	1	2	FACETS	0.507	0.466	0.549	0.507	0.466	0.549	SUBCLONAL	1	TRUE	1	0.890829480756745	2		424	740	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593631	55593654	+	inframe_deletion	In_Frame_Del	DEL	ACAATTATGTTTACATAGACCCAA	ACAATTATGTTTACATAGACCCAA	-	novel	NA	P-0006120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	190	438	0	ENST00000288135.5:c.1697_1720del	p.Asn566_Pro573del	p.N566_P573del	ENST00000288135	NM_000222.2	566	aACAATTATGTTTACATAGACCCAAca/aca	11/21	1	2	FACETS	0.937	0.873	1	0.937	0.873	1	CLONAL	1	TRUE	1	0.752032665248212	2		438	539	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213973	2213979	+	frameshift_variant	Frame_Shift_Del	DEL	AATCTTC	AATCTTC	-	novel	NA	P-0006120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	42	515	0	ENST00000326181.6:c.52_58del	p.Asn18ProfsTer108	p.N18Pfs*108	ENST00000326181	NM_032271.2	18	AATCTTCcc/cc	2/21	1	2	FACETS	0.248	0.207	0.294	0.248	0.207	0.294	SUBCLONAL	1	TRUE	1	0.752032665248212	2		515	450	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442054	52442054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006419-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	90	577	1	ENST00000460680.1:c.295G>A	p.Val99Met	p.V99M	ENST00000460680	NM_004656.3	99	Gtg/Atg	5/17	1	2	FACETS	0.807	0.715	0.905	0.807	0.715	0.905	CLONAL	1	TRUE	1	0.267743317887543	2		578	833	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067836	30067836	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315499	NA	P-0006419-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	76	517	1	ENST00000338641.4:c.1021C>T	p.Arg341Ter	p.R341*	ENST00000338641	NM_000268.3	341	Cga/Tga	11/16	0.267743317887543	1	FACETS	0.82	0.719	0.927	0.82	0.719	0.927	CLONAL	1	TRUE	0	0.267743317887543	1		518	600	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442054	52442054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	110	577	1	ENST00000460680.1:c.295G>A	p.Val99Met	p.V99M	ENST00000460680	NM_004656.3	99	Gtg/Atg	5/17	0.203249017936103	1	FACETS	0.843	0.764	0.925	0.843	0.764	0.925	INDETERMINATE	1	FALSE	0	0.495678246741158	1		578	396	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067836	30067836	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315499	NA	P-0006419-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	68	517	1	ENST00000338641.4:c.1021C>T	p.Arg341Ter	p.R341*	ENST00000338641	NM_000268.3	341	Cga/Tga	11/16	0.36384912303835	0	FACETS	0.685	0.606	0.767			1	SUBCLONAL	1	FALSE	0	0.495678246741158	0		518	202	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125269	47125269	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0008084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	207	502	0	ENST00000409792.3:c.6001A>T	p.Lys2001Ter	p.K2001*	ENST00000409792	NM_014159.6	2001	Aaa/Taa	12/21	0.842543272023341	1	FACETS	0.971	0.926	1	0.971	0.926	1	CLONAL	1	TRUE	0	0.842543272023341	1		502	293	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920432	134920432	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	121	625	0	ENST00000398015.3:c.2247C>G	p.Asn749Lys	p.N749K	ENST00000398015	NM_004441.4	749	aaC/aaG	12/16	0.0812844479975652	5	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.842543272023341	5		625	553	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593609	55593653	+	inframe_deletion	In_Frame_Del	DEL	GTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCCA	GTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCCA	-	novel	NA	P-0008084-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	179	566	0	ENST00000288135.5:c.1675_1719del	p.Val559_Pro573del	p.V559_P573del	ENST00000288135	NM_000222.2	559	GTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCCA/-	11/21	1	2	FACETS	0.555	0.513	0.599	0.555	0.513	0.599	SUBCLONAL	1	TRUE	1	0.842543272023341	2		566	765	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125269	47125269	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0008084-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	576	502	0	ENST00000409792.3:c.6001A>T	p.Lys2001Ter	p.K2001*	ENST00000409792	NM_014159.6	2001	Aaa/Taa	12/21	0.840917790194582	1	FACETS	0.999	0.972	1	0.999	0.972	1	CLONAL	1	TRUE	0	0.840917790194582	1		502	795	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920432	134920432	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008084-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1174	461	625	0	ENST00000398015.3:c.2247C>G	p.Asn749Lys	p.N749K	ENST00000398015	NM_004441.4	749	aaC/aaG	12/16	0.840917790194582	3	FACETS	0.953	0.908	0.998	0.318	0.302	0.333	CLONAL	1	TRUE	0	0.840917790194582	3		625	1635	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593609	55593653	+	inframe_deletion	In_Frame_Del	DEL	GTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCCA	GTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCCA	-	novel	NA	P-0008084-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	251	566	0	ENST00000288135.5:c.1675_1719del	p.Val559_Pro573del	p.V559_P573del	ENST00000288135	NM_000222.2	559	GTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCCA/-	11/21	1	2	FACETS	0.668	0.626	0.711	0.668	0.626	0.711	SUBCLONAL	1	TRUE	1	0.840917790194582	2		566	894	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0008084-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	18	383	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.061	0.045	0.079	0.061	0.045	0.079	SUBCLONAL	1	TRUE	1	0.840917790194582	2		383	707	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0008084-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	297	498	0	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	1	2	FACETS	0.974	0.923	1	0.974	0.923	1	CLONAL	1	TRUE	1	0.840917790194582	2		498	725	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125269	47125269	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0008084-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	73	502	0	ENST00000409792.3:c.6001A>T	p.Lys2001Ter	p.K2001*	ENST00000409792	NM_014159.6	2001	Aaa/Taa	12/21	0.430889541144846	1	FACETS	0.889	0.785	0.999	0.889	0.785	0.999	CLONAL	1	TRUE	0	0.430889541144846	1		502	299	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920432	134920432	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008084-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	90	625	0	ENST00000398015.3:c.2247C>G	p.Asn749Lys	p.N749K	ENST00000398015	NM_004441.4	749	aaC/aaG	12/16	0.430889541144846	3	FACETS	0.772	0.685	0.864	0.257	0.228	0.288	SUBCLONAL	1	TRUE	0	0.430889541144846	3		625	658	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593609	55593653	+	inframe_deletion	In_Frame_Del	DEL	GTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCCA	GTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCCA	-	novel	NA	P-0008084-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	64	566	0	ENST00000288135.5:c.1675_1719del	p.Val559_Pro573del	p.V559_P573del	ENST00000288135	NM_000222.2	559	GTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCCA/-	11/21	1	2	FACETS	0.632	0.548	0.722	0.632	0.548	0.722	SUBCLONAL	1	TRUE	1	0.430889541144846	2		566	470	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0008084-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	98	498	0	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.430889541144846	2		498	436	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280661	41280668	+	frameshift_variant	Frame_Shift_Del	DEL	GCCAGGAT	GCCAGGAT	-	novel	NA	P-0008084-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	89	641	0	ENST00000349496.5:c.2177_2184del	p.Gln726LeufsTer10	p.Q726Lfs*10	ENST00000349496	NM_001904.3	725	gGCCAGGAT/g	15/15	0.430889541144846	1	FACETS	0.792	0.707	0.883	0.792	0.707	0.883	SUBCLONAL	1	TRUE	0	0.430889541144846	1		641	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0008846-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	231	563	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.332987380569765	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.332987380569765	2		564	687	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0008880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	13	258	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.822	0.594	1	0.822	0.594	1	CLONAL	1	TRUE	1	0.34	2		258	93	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866444	37866444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	31	753	0	ENST00000269571.5:c.749C>T	p.Ser250Phe	p.S250F	ENST00000269571		250	tCt/tTt	6/27	1	2	FACETS	0.996	0.814	1	0.996	0.814	1	CLONAL	1	TRUE	1	0.34	2		753	183	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263850	133263850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	14	273	0	ENST00000320574.5:c.52G>A	p.Glu18Lys	p.E18K	ENST00000320574	NM_006231.2	18	Gag/Aag	1/49	1	2	FACETS	0.487	0.353	0.648	0.487	0.353	0.648	SUBCLONAL	1	TRUE	1	0.34	2		273	169	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321245	65321245	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771960711	NA	P-0008880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	21	490	1	ENST00000342505.4:c.1595G>A	p.Arg532His	p.R532H	ENST00000342505	NM_002227.2	532	cGc/cAc	11/25	1	2	FACETS	0.65	0.503	0.819	0.65	0.503	0.819	SUBCLONAL	1	TRUE	1	0.34	2		491	190	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843447	3843447	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783461	NA	P-0008880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	22	436	1	ENST00000262367.5:c.1156C>T	p.Arg386Ter	p.R386*	ENST00000262367	NM_004380.2	386	Cga/Tga	4/31	1	2	FACETS	0.88	0.689	1	0.88	0.689	1	CLONAL	1	TRUE	1	0.34	2		437	147	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860556	45860556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	33	726	0	ENST00000391945.4:c.1451C>T	p.Thr484Met	p.T484M	ENST00000391945	NM_000400.3	484	aCg/aTg	15/23	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.34	2		726	168	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190656538	190656538	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0008880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	11	159	0	ENST00000441310.2:c.3G>A	p.Met1?	p.M1?	ENST00000441310	NM_000534.4	1	atG/atA	2/13	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.34	2		159	45	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183665	10183665	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs199583685	NA	P-0008880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	16	627	0	ENST00000256474.2:c.134C>G	p.Pro45Arg	p.P45R	ENST00000256474	NM_000551.3	45	cCg/cGg	1/3	1	2	FACETS	0.607	0.451	0.791	0.607	0.451	0.791	SUBCLONAL	1	TRUE	1	0.34	2		627	155	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430398	181430398	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	29	585	0	ENST00000325404.1:c.250G>A	p.Glu84Lys	p.E84K	ENST00000325404	NM_003106.3	84	Gag/Aag	1/1	1	2	FACETS	1	0.828	1	1	0.828	1	CLONAL	1	TRUE	1	0.34	2		585	167	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84390185	84390185	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1060503253	NA	P-0008880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	13	412	0	ENST00000321945.7:c.596G>A	p.Ser199Asn	p.S199N	ENST00000321945	NM_139076.2	199	aGc/aAc	6/9	1	2	FACETS	0.98	0.712	1	0.98	0.712	1	CLONAL	1	TRUE	1	0.34	2		412	78	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245404	153245404	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	13	510	0	ENST00000281708.4:c.1787C>G	p.Ser596Cys	p.S596C	ENST00000281708	NM_033632.3	596	tCt/tGt	11/12	1	2	FACETS	0.735	0.53	0.98	0.735	0.53	0.98	CLONAL	1	TRUE	1	0.34	2		510	104	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163813	32163813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	25	508	0	ENST00000375023.3:c.5413G>A	p.Asp1805Asn	p.D1805N	ENST00000375023	NM_004557.3	1805	Gac/Aac	30/30	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.34	2		508	116	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510845	157510845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	16	518	0	ENST00000346085.5:c.3620C>T	p.Pro1207Leu	p.P1207L	ENST00000346085	NM_020732.3	1207	cCa/cTa	14/20	1	2	FACETS	0.632	0.47	0.822	0.632	0.47	0.822	SUBCLONAL	1	TRUE	1	0.34	2		518	149	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915874	127915874	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	17	515	1	ENST00000373547.4:c.607G>A	p.Asp203Asn	p.D203N	ENST00000373547	NM_002721.4	203	Gat/Aat	6/7	1	2	FACETS	0.84	0.634	1	0.84	0.634	1	CLONAL	1	TRUE	1	0.34	2		516	119	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799278	88799278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	11	419	0	ENST00000360948.2:c.107G>A	p.Cys36Tyr	p.C36Y	ENST00000360948	NM_001012338.2	36	tGt/tAt	2/19	0.108957616825657	0	FACETS	0.375	0.26	0.514			1	INDETERMINATE	1	TRUE	0	0.34	0		419	114	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827870	72827870	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs777143827	NA	P-0008880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	25	546	1	ENST00000268489.5:c.8711A>G	p.Lys2904Arg	p.K2904R	ENST00000268489	NM_006885.3	2904	aAg/aGg	9/10	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.34	2		547	117	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701088	29701088	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	23	389	0	ENST00000356175.3:c.8372G>A	p.Arg2791Gln	p.R2791Q	ENST00000356175	NM_000267.3	2791	cGa/cAa	57/57	1	2	FACETS	0.966	0.762	1	0.966	0.762	1	CLONAL	1	TRUE	1	0.34	2		389	140	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584739	48584739	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	17	496	0	ENST00000342988.3:c.817A>T	p.Thr273Ser	p.T273S	ENST00000342988	NM_005359.5	273	Act/Tct	7/12	0.108957616825657	0	FACETS	0.733	0.557	0.934			1	INDETERMINATE	1	TRUE	0	0.34	0		496	90	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039647	47039647	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556778363	NA	P-0008880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	14	292	0	ENST00000377604.3:c.1099C>T	p.His367Tyr	p.H367Y	ENST00000377604	NM_001204468.1	367	Cac/Tac	11/24	1	1	FACETS	1	0.754	1	1	0.754	1	CLONAL	1	TRUE	0	0.34	1		292	67	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106497	27106498	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0008880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	16	718	0	ENST00000324856.7:c.6109dup	p.Gln2037ProfsTer62	p.Q2037Pfs*62	ENST00000324856	NM_006015.4	2036	-/C	20/20	1	2	FACETS	0.547	0.406	0.714	0.547	0.406	0.714	SUBCLONAL	1	TRUE	1	0.34	2		718	172	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58701089	58701089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	10	455	0	ENST00000305921.3:c.680G>A	p.Arg227Gln	p.R227Q	ENST00000305921	NM_003620.3	227	cGa/cAa	2/6	1	2	FACETS	0.361	0.245	0.506	0.361	0.245	0.506	SUBCLONAL	1	TRUE	1	0.34	2		455	163	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212191	36212191	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1313945983	NA	P-0008880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	11	415	0	ENST00000222270.7:c.1942C>T	p.Arg648Trp	p.R648W	ENST00000222270	NM_014727.1	648	Cgg/Tgg	3/37	1	2	FACETS	0.539	0.375	0.741	0.539	0.375	0.741	SUBCLONAL	1	TRUE	1	0.34	2		415	120	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180229	38180229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	11	577	0	ENST00000396334.3:c.77C>T	p.Pro26Leu	p.P26L	ENST00000396334	NM_002468.4	26	cCg/cTg	1/5	1	2	FACETS	0.376	0.26	0.52	0.376	0.26	0.52	SUBCLONAL	1	TRUE	1	0.34	2		577	172	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870903	12870903	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	19	359	0	ENST00000228872.4:c.130G>A	p.Asp44Asn	p.D44N	ENST00000228872	NM_004064.3	44	Gac/Aac	1/3	1	2	FACETS	1	0.795	1	1	0.795	1	CLONAL	1	TRUE	1	0.34	2		359	108	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753518	42753518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	10	747	1	ENST00000222329.4:c.746C>T	p.Pro249Leu	p.P249L	ENST00000222329	NM_006494.2	249	cCt/cTt	4/4	1	2	FACETS	0.359	0.243	0.503	0.359	0.243	0.503	SUBCLONAL	1	TRUE	1	0.34	2		748	164	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098762	178098762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	11	518	0	ENST00000397062.3:c.283G>A	p.Glu95Lys	p.E95K	ENST00000397062	NM_006164.4	95	Gaa/Aaa	2/5	1	2	FACETS	0.696	0.486	0.95	0.696	0.486	0.95	SUBCLONAL	1	TRUE	1	0.34	2		518	93	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22008946	22008946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	17	464	0	ENST00000276925.6:c.7G>A	p.Glu3Lys	p.E3K	ENST00000276925	NM_004936.3	3	Gag/Aag	1/2	1	2	FACETS	0.602	0.452	0.779	0.602	0.452	0.779	SUBCLONAL	1	TRUE	1	0.34	2		464	166	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0010079-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	363	646	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.738409474097012	4	FACETS	0.805	0.765	0.847			1	CLONAL	2	TRUE	NA	0.738409474097012	4		646	1061	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031889	26031889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010079-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	29	546	0	ENST00000244661.2:c.400G>A	p.Glu134Lys	p.E134K	ENST00000244661	NM_003537.3	134	Gaa/Aaa	1/1	0.68860548111632	3	FACETS	0.206	0.164	0.253	0.069	0.054	0.085	SUBCLONAL	1	TRUE	0	0.738409474097012	3		546	523	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371986	55371986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1339233187	NA	P-0010079-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	23	341	0	ENST00000297316.4:c.676C>T	p.Pro226Ser	p.P226S	ENST00000297316	NM_022454.3	226	Ccg/Tcg	2/2	0.387276987040523	3	FACETS	0.234	0.182	0.295	0.078	0.06	0.099	INDETERMINATE	1	TRUE	0	0.738409474097012	3		341	364	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657384	29657384	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs774893767	NA	P-0010079-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	125	459	0	ENST00000356175.3:c.5617G>C	p.Glu1873Gln	p.E1873Q	ENST00000356175	NM_000267.3	1873	Gag/Cag	38/57	0.345307336761958	6	FACETS	0.889	0.804	0.979	0.222	0.201	0.245	INDETERMINATE	1	TRUE	2	0.738409474097012	6		459	943	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021784	71021784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553663084	NA	P-0010079-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	125	397	0	ENST00000318789.4:c.1574G>A	p.Arg525Gln	p.R525Q	ENST00000318789	NM_032682.5	525	cGa/cAa	18/21	0.564212007908136	4	FACETS	0.946	0.859	1	0.473	0.429	0.519	CLONAL	1	TRUE	2	0.738409474097012	4		397	622	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497704	125497704	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010079-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	85	238	0	ENST00000428830.2:c.268G>A	p.Gly90Arg	p.G90R	ENST00000428830	NM_001114121.2	90	Gga/Aga	3/14	0.636363422916237	3	FACETS	0.568	0.503	0.637			1	SUBCLONAL	1	TRUE	NA	0.738409474097012	3		238	555	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023085	150023085	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010079-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	42	642	0	ENST00000253339.5:c.178G>T	p.Glu60Ter	p.E60*	ENST00000253339		60	Gaa/Taa	1/7	0.68860548111632	3	FACETS	0.199	0.165	0.237	0.066	0.055	0.079	SUBCLONAL	1	TRUE	0	0.738409474097012	3		642	783	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073619	8073619	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010079-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	44	578	0	ENST00000377482.5:c.1040C>G	p.Pro347Arg	p.P347R	ENST00000377482	NM_018948.3	347	cCc/cGc	4/4	0.66863933799595	3	FACETS	0.223	0.186	0.264	0.111	0.093	0.132	SUBCLONAL	1	TRUE	1	0.738409474097012	3		578	732	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983056	201983058	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0010079-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	248	721	0	ENST00000359651.3:c.907_909del	p.Phe303del	p.F303del	ENST00000359651		302	gTCTtc/gtc	7/8	NA	2	FACETS	1	0.944	1			1	INDETERMINATE	1	TRUE	NA	0.738409474097012	2		721	669	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943284	71943284	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010079-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	42	615	0	ENST00000298229.2:c.1616G>A	p.Gly539Glu	p.G539E	ENST00000298229	NM_001567.3	539	gGg/gAg	14/28	0.66863933799595	3	FACETS	0.195	0.162	0.232	0.098	0.081	0.116	SUBCLONAL	1	TRUE	1	0.738409474097012	3		615	798	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531906	41531906	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010079-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	185	341	0	ENST00000263253.7:c.1618C>G	p.Gln540Glu	p.Q540E	ENST00000263253	NM_001429.3	540	Caa/Gaa	7/31	0.738409474097012	3	FACETS	0.99	0.917	1	0.495	0.458	0.533	CLONAL	1	TRUE	1	0.738409474097012	3		341	693	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144155	55144155	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010079-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	50	589	0	ENST00000257290.5:c.1984G>C	p.Gly662Arg	p.G662R	ENST00000257290	NM_006206.4	662	Gga/Cga	14/23	0.738409474097012	3	FACETS	0.208	0.176	0.244	0.104	0.088	0.122	SUBCLONAL	1	TRUE	1	0.738409474097012	3		589	890	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92244513	92244513	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010079-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	73	553	0	ENST00000265734.4:c.922G>C	p.Glu308Gln	p.E308Q	ENST00000265734	NM_001259.6	308	Gaa/Caa	8/8	0.738409474097012	3	FACETS	0.344	0.3	0.391	0.172	0.15	0.196	SUBCLONAL	1	TRUE	1	0.738409474097012	3		553	788	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836768	151836768	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010079-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	168	490	0	ENST00000262189.6:c.14452G>C	p.Glu4818Gln	p.E4818Q	ENST00000262189	NM_170606.2	4818	Gag/Cag	56/59	0.738409474097012	3	FACETS	0.975	0.9	1	0.488	0.45	0.527	CLONAL	1	TRUE	1	0.738409474097012	3		490	639	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652129	36652129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34916193	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1332	400	1230	0	ENST00000244741.5:c.251G>A	p.Arg84Gln	p.R84Q	ENST00000244741	NM_000389.4	84	cGa/cAa	2/3	0.285470550776315	3	FACETS	0.924	0.877	0.973	0.924	0.877	0.973	CLONAL	2	TRUE	1	0.285470550776315	3		1230	1732	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959144	28959144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767259336	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	78	484	0	ENST00000282397.4:c.1994G>A	p.Arg665Gln	p.R665Q	ENST00000282397	NM_002019.4	665	cGa/cAa	14/30	0.285470550776315	3	FACETS	0.896	0.787	1	0.448	0.393	0.507	CLONAL	1	TRUE	1	0.285470550776315	3		484	697	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279766	46279766	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	233	670	0	ENST00000371998.3:c.3692G>C	p.Arg1231Thr	p.R1231T	ENST00000371998		1231	aGa/aCa	20/23	0.271341092969023	4	FACETS	1	0.933	1	1	0.933	1	CLONAL	2	TRUE	2	0.285470550776315	4		670	1049	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459852	149459852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1475	216	1202	1	ENST00000286301.3:c.355G>A	p.Glu119Lys	p.E119K	ENST00000286301	NM_005211.3	119	Gag/Aag	4/22	0.285470550776315	3	FACETS	1	0.944	1	0.511	0.473	0.551	CLONAL	1	TRUE	1	0.285470550776315	3		1203	1691	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280122	142280122	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	109	620	0	ENST00000350721.4:c.1312C>G	p.Leu438Val	p.L438V	ENST00000350721	NM_001184.3	438	Cta/Gta	5/47	1	2	FACETS	0.975	0.876	1	0.975	0.876	1	CLONAL	1	TRUE	1	0.285470550776315	2		620	783	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155749	106155749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	212	538	0	ENST00000380013.4:c.650C>T	p.Ser217Phe	p.S217F	ENST00000380013	NM_001127208.2	217	tCc/tTc	3/11	0.285470550776315	3	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	1	0.285470550776315	3		538	843	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875677	35875677	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	113	372	0	ENST00000303115.3:c.864G>C	p.Lys288Asn	p.K288N	ENST00000303115	NM_002185.3	288	aaG/aaC	7/8	0.285470550776315	3	FACETS	0.839	0.758	0.924	0.839	0.758	0.924	CLONAL	2	TRUE	1	0.285470550776315	3		372	539	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177920	56177920	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	179	541	0	ENST00000399503.3:c.2893C>T	p.Gln965Ter	p.Q965*	ENST00000399503	NM_005921.1	965	Cag/Tag	14/20	0.285470550776315	3	FACETS	0.826	0.762	0.893	0.826	0.762	0.893	CLONAL	2	TRUE	1	0.285470550776315	3		541	867	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721675	176721675	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	86	666	0	ENST00000439151.2:c.7306G>C	p.Glu2436Gln	p.E2436Q	ENST00000439151	NM_022455.4	2436	Gaa/Caa	23/23	0.285470550776315	3	FACETS	0.674	0.595	0.76	0.337	0.297	0.38	SUBCLONAL	1	TRUE	1	0.285470550776315	3		666	1021	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020937	26020937	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	204	708	0	ENST00000357647.3:c.220G>C	p.Glu74Gln	p.E74Q	ENST00000357647	NM_003529.2	74	Gag/Cag	1/1	0.285470550776315	3	FACETS	0.866	0.803	0.931	0.866	0.803	0.931	CLONAL	2	TRUE	1	0.285470550776315	3		708	943	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839699	27839699	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	225	637	0	ENST00000328488.2:c.395G>C	p.Arg132Pro	p.R132P	ENST00000328488	NM_003533.2	132	cGa/cCa	1/1	0.285470550776315	3	FACETS	0.988	0.921	1	0.988	0.921	1	CLONAL	2	TRUE	1	0.285470550776315	3		637	912	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528327	157528327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776894668	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	300	1050	2	ENST00000346085.5:c.6052G>A	p.Glu2018Lys	p.E2018K	ENST00000346085	NM_020732.3	2018	Gag/Aag	20/20	0.285470550776315	3	FACETS	0.884	0.831	0.938	0.884	0.831	0.938	CLONAL	2	TRUE	1	0.285470550776315	3		1052	1359	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974152	2974152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	416	1024	0	ENST00000396946.4:c.1453G>A	p.Glu485Lys	p.E485K	ENST00000396946	NM_032415.4	485	Gaa/Aaa	10/25	0.285470550776315	5	FACETS	0.886	0.842	0.931	0.886	0.842	0.931	CLONAL	3	TRUE	2	0.285470550776315	5		1024	1566	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186589	108186589	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	130	429	0	ENST00000278616.4:c.6046G>C	p.Asp2016His	p.D2016H	ENST00000278616	NM_000051.3	2016	Gat/Cat	41/63	0.285470550776315	2	FACETS	0.872	0.795	0.952	0.872	0.795	0.952	CLONAL	2	TRUE	0	0.285470550776315	2		429	522	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427557	427557	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs760471868	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	236	578	0	ENST00000399788.2:c.2612C>G	p.Ser871Cys	p.S871C	ENST00000399788	NM_001042603.1	871	tCt/tGt	19/28	0.285470550776315	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.285470550776315	2		578	718	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961377	41961377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	168	613	0	ENST00000219905.7:c.285G>A	p.Met95Ile	p.M95I	ENST00000219905	NM_001164273.1	95	atG/atA	2/24	0.271341092969023	4	FACETS	0.779	0.716	0.845	0.779	0.716	0.845	SUBCLONAL	2	TRUE	2	0.285470550776315	4		613	971	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42057177	42057177	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	116	727	0	ENST00000219905.7:c.7838C>G	p.Ser2613Ter	p.S2613*	ENST00000219905	NM_001164273.1	2613	tCa/tGa	23/24	0.271341092969023	4	FACETS	0.93	0.836	1	0.465	0.418	0.515	CLONAL	1	TRUE	2	0.285470550776315	4		727	1123	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496932	29496932	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	70	247	0	ENST00000356175.3:c.503C>A	p.Ser168Ter	p.S168*	ENST00000356175	NM_000267.3	168	tCa/tAa	5/57	0.285470550776315	2	FACETS	1	0.971	1	0.699	0.613	0.79	CLONAL	1	TRUE	0	0.285470550776315	2		247	351	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775238	73775238	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	223	765	0	ENST00000254810.4:c.18G>T	p.Gln6His	p.Q6H	ENST00000254810	NM_005324.3	6	caG/caT	2/4	0.271341092969023	4	FACETS	0.841	0.782	0.902	0.841	0.782	0.902	CLONAL	2	TRUE	2	0.285470550776315	4		765	1194	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2225391	2225391	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	150	525	0	ENST00000398665.3:c.3601G>C	p.Glu1201Gln	p.E1201Q	ENST00000398665	NM_032482.2	1201	Gag/Cag	26/28	0.285470550776315	3	FACETS	0.824	0.754	0.896	0.824	0.754	0.896	CLONAL	2	TRUE	1	0.285470550776315	3		525	729	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943403	17943403	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	400	1152	0	ENST00000458235.1:c.2605C>T	p.Gln869Ter	p.Q869*	ENST00000458235	NM_000215.3	869	Cag/Tag	19/24	0.285470550776315	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.285470550776315	3		1152	1578	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038877	47038877	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	186	525	0	ENST00000377604.3:c.884C>T	p.Ser295Leu	p.S295L	ENST00000377604	NM_001204468.1	295	tCa/tTa	9/24	1	1	FACETS	0.78	0.723	0.839	1	0.991	1	SUBCLONAL	2	TRUE	0	0.285470550776315	1		525	716	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961361	54961362	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	197	596	0	ENST00000312783.6:c.270dup	p.Pro91AlafsTer4	p.P91Afs*4	ENST00000312783	NM_198436.1	90	-/G	4/10	0.271341092969023	4	FACETS	0.908	0.841	0.978	0.908	0.841	0.978	CLONAL	2	TRUE	2	0.285470550776315	4		596	977	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938404	44938404	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	72	241	0	ENST00000377967.4:c.2952C>G	p.Phe984Leu	p.F984L	ENST00000377967	NM_021140.2	984	ttC/ttG	20/29	1	1	FACETS	0.759	0.67	0.852	1	0.977	1	SUBCLONAL	2	TRUE	0	0.285470550776315	1		241	285	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257238	16257238	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	123	596	0	ENST00000375759.3:c.4503G>C	p.Arg1501Ser	p.R1501S	ENST00000375759	NM_015001.2	1501	agG/agC	11/15	0.285470550776315	3	FACETS	1	0.936	1	0.524	0.473	0.578	CLONAL	1	TRUE	1	0.285470550776315	3		596	940	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151725	108151725	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	51	272	0	ENST00000278616.4:c.3406C>A	p.His1136Asn	p.H1136N	ENST00000278616	NM_000051.3	1136	Cat/Aat	24/63	0.285470550776315	2	FACETS	0.953	0.813	1	0.476	0.406	0.553	CLONAL	1	TRUE	0	0.285470550776315	2		272	375	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375067	118375068	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	95	533	0	ENST00000534358.1:c.8464_8465dup	p.Asn2822LysfsTer12	p.N2822Kfs*12	ENST00000534358	NM_005933.3	2820	-/AA	27/36	0.285470550776315	2	FACETS	0.945	0.842	1	0.473	0.421	0.528	CLONAL	1	TRUE	0	0.285470550776315	2		533	704	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111855996	111855996	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1437	172	1004	0	ENST00000341259.2:c.47C>G	p.Ser16Ter	p.S16*	ENST00000341259	NM_005475.2	16	tCa/tGa	2/8	0.285470550776315	5	FACETS	1	0.958	1	0.267	0.245	0.291	CLONAL	1	TRUE	1	0.285470550776315	5		1004	1609	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954192	32954192	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1420447960	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	98	584	0	ENST00000380152.3:c.9166C>T	p.His3056Tyr	p.H3056Y	ENST00000380152		3056	Cac/Tac	24/27	0.285470550776315	3	FACETS	0.937	0.836	1	0.469	0.418	0.523	CLONAL	1	TRUE	1	0.285470550776315	3		584	837	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748549	43748549	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	384	916	0	ENST00000382044.4:c.2257G>C	p.Glu753Gln	p.E753Q	ENST00000382044	NM_001141980.1	753	Gaa/Caa	12/28	0.271341092969023	4	FACETS	0.856	0.813	0.901	1	0.993	1	CLONAL	3	TRUE	2	0.285470550776315	4		916	1346	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906327	50906327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501813	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1300	191	1193	0	ENST00000440232.2:c.988G>A	p.Glu330Lys	p.E330K	ENST00000440232	NM_002691.3	330	Gag/Aag	9/27	0.285470550776315	3	FACETS	1	0.942	1	0.513	0.472	0.555	CLONAL	1	TRUE	1	0.285470550776315	3		1193	1491	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610482	215610482	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	85	509	0	ENST00000260947.4:c.1774C>G	p.Leu592Val	p.L592V	ENST00000260947	NM_000465.2	592	Ctt/Gtt	8/11	0.285470550776315	3	FACETS	1	0.911	1	0.518	0.458	0.582	CLONAL	1	TRUE	1	0.285470550776315	3		509	657	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69788781	69788781	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	71	632	0	ENST00000352241.4:c.33C>G	p.Phe11Leu	p.F11L	ENST00000352241	NM_198159.2	11	ttC/ttG	1/10	1	2	FACETS	0.764	0.667	0.869	0.764	0.667	0.869	SUBCLONAL	1	TRUE	1	0.285470550776315	2		632	651	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55154999	55154999	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	103	678	0	ENST00000257290.5:c.2708C>T	p.Ser903Phe	p.S903F	ENST00000257290	NM_006206.4	903	tCt/tTt	20/23	0.285470550776315	3	FACETS	0.875	0.782	0.975	0.438	0.391	0.488	CLONAL	1	TRUE	1	0.285470550776315	3		678	942	SUCCESS
APC	324	MSKCC	GRCh37	5	112177400	112177400	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	66	401	0	ENST00000257430.4:c.6109G>T	p.Asp2037Tyr	p.D2037Y	ENST00000257430	NM_000038.5	2037	Gac/Tac	16/16	0.253693017689029	4	FACETS	0.943	0.819	1	0.314	0.273	0.36	CLONAL	1	TRUE	1	0.285470550776315	4		401	630	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915052	131915052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	97	532	0	ENST00000265335.6:c.409G>A	p.Asp137Asn	p.D137N	ENST00000265335		137	Gac/Aac	4/25	0.253693017689029	4	FACETS	0.98	0.873	1	0.327	0.291	0.365	CLONAL	1	TRUE	1	0.285470550776315	4		532	891	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721249	176721249	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	89	664	0	ENST00000439151.2:c.6880G>C	p.Asp2294His	p.D2294H	ENST00000439151	NM_022455.4	2294	Gat/Cat	23/23	0.285470550776315	3	FACETS	0.787	0.697	0.884	0.394	0.348	0.442	SUBCLONAL	1	TRUE	1	0.285470550776315	3		664	905	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192435	138192435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	51	371	0	ENST00000237289.4:c.71G>A	p.Arg24Lys	p.R24K	ENST00000237289	NM_001270507.1	24	aGa/aAa	2/9	0.285470550776315	3	FACETS	0.773	0.657	0.901	0.387	0.328	0.451	CLONAL	1	TRUE	1	0.285470550776315	3		371	528	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5064926	5064926	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	85	375	0	ENST00000381652.3:c.1100C>G	p.Ser367Ter	p.S367*	ENST00000381652	NM_004972.3	367	tCa/tGa	9/25	0.285470550776315	3	FACETS	1	0.944	1	0.555	0.491	0.624	CLONAL	1	TRUE	1	0.285470550776315	3		375	613	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434609	128434609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	194	657	0	ENST00000265960.3:c.245G>A	p.Arg82Lys	p.R82K	ENST00000265960	NM_001006617.1	82	aGa/aAa	2/12	0.285470550776315	3	FACETS	0.858	0.794	0.924	0.858	0.794	0.924	CLONAL	2	TRUE	1	0.285470550776315	3		657	905	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717717	89717717	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011363-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	268	444	0	ENST00000371953.3:c.743del	p.Pro248LeufsTer8	p.P248Lfs*8	ENST00000371953	NM_000314.4	248	Cct/ct	7/9	0.642367035181783	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.642367035181783	1		444	525	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441795	49441795	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011363-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	289	684	1	ENST00000301067.7:c.4189T>A	p.Cys1397Ser	p.C1397S	ENST00000301067	NM_003482.3	1397	Tgt/Agt	14/54	0.106746398430166	3	FACETS	1	0.99	1	0.61	0.574	0.646	INDETERMINATE	1	TRUE	1	0.642367035181783	3		685	975	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445017	49445017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011363-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	293	814	1	ENST00000301067.7:c.2449C>T	p.Pro817Ser	p.P817S	ENST00000301067	NM_003482.3	817	Cct/Tct	10/54	0.106746398430166	3	FACETS	1	0.991	1	0.628	0.592	0.665	INDETERMINATE	1	TRUE	1	0.642367035181783	3		815	959	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061212	38061212	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0011363-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	317	608	0	ENST00000250448.2:c.777C>G	p.Tyr259Ter	p.Y259*	ENST00000250448	NM_004496.3	259	taC/taG	2/2	0.106746398430166	3	FACETS	0.764	0.724	0.805	0.764	0.724	0.805	INDETERMINATE	2	TRUE	1	0.642367035181783	3		608	853	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55962458	55962458	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011363-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	233	486	1	ENST00000263923.4:c.2666T>C	p.Leu889Pro	p.L889P	ENST00000263923	NM_002253.2	889	cTc/cCc	19/30	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.642367035181783	2		487	674	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932611	39932611	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011363-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	334	512	1	ENST00000378444.4:c.1988C>T	p.Pro663Leu	p.P663L	ENST00000378444	NM_001123385.1	663	cCt/cTt	4/15	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.642367035181783	1		513	509	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124448	94124449	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAAA	novel	NA	P-0011363-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	195	412	0	ENST00000369303.4:c.134_135insTTTT	p.Leu45PhefsTer16	p.L45Ffs*16	ENST00000369303	NM_004440.3	45	ttg/ttTTTTg	2/17	0.642367035181783	1	FACETS	0.818	0.764	0.873	0.818	0.764	0.873	CLONAL	1	TRUE	0	0.642367035181783	1		412	504	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124441	94124443	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	TCC	TCC	CT	novel	NA	P-0011363-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	188	403	0	ENST00000369303.4:c.140_142delinsAG	p.Trp47Ter	p.W47*	ENST00000369303	NM_004440.3	47	tGGAtt/tAGtt	2/17	0.642367035181783	1	FACETS	0.853	0.796	0.91	0.853	0.796	0.91	CLONAL	1	TRUE	0	0.642367035181783	1		403	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579362	7579362	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057523496	NA	P-0012403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	141	688	0	ENST00000269305.4:c.325T>G	p.Phe109Val	p.F109V	ENST00000269305	NM_001126112.2	109	Ttc/Gtc	4/11	0.475049040594966	1	FACETS	0.983	0.905	1	0.983	0.905	1	CLONAL	1	TRUE	0	0.530722464402396	1		688	397	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593629	55593652	+	inframe_deletion	In_Frame_Del	DEL	AAACAATTATGTTTACATAGACCC	AAACAATTATGTTTACATAGACCC	-	novel	NA	P-0012403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	130	458	0	ENST00000288135.5:c.1697_1720del	p.Asn566_Pro573del	p.N566_P573del	ENST00000288135	NM_000222.2	565	ggAAACAATTATGTTTACATAGACCCa/gga	11/21	1	2	FACETS	0.88	0.801	0.961	0.88	0.801	0.961	CLONAL	1	TRUE	1	0.530722464402396	2		458	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579362	7579362	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057523496	NA	P-0012403-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	367	688	0	ENST00000269305.4:c.325T>G	p.Phe109Val	p.F109V	ENST00000269305	NM_001126112.2	109	Ttc/Gtc	4/11	0.682111428578384	1	FACETS	0.996	0.953	1	0.996	0.953	1	CLONAL	1	TRUE	0	0.682111428578384	1		688	712	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593629	55593652	+	inframe_deletion	In_Frame_Del	DEL	AAACAATTATGTTTACATAGACCC	AAACAATTATGTTTACATAGACCC	-	novel	NA	P-0012403-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	206	458	0	ENST00000288135.5:c.1697_1720del	p.Asn566_Pro573del	p.N566_P573del	ENST00000288135	NM_000222.2	565	ggAAACAATTATGTTTACATAGACCCa/gga	11/21	1	2	FACETS	0.859	0.8	0.92	0.859	0.8	0.92	CLONAL	1	TRUE	1	0.682111428578384	2		458	703	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599320	55599321	+	protein_altering_variant	In_Frame_Ins	INS	-	-	AAATCA	novel	NA	P-0012403-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	192	403	0	ENST00000288135.5:c.2447_2448insAATCAA	p.Asp816delinsGluIleAsn	p.D816delinsEIN	ENST00000288135	NM_000222.2	816	gac/gAAATCAac	17/21	1	2	FACETS	0.865	0.803	0.928	0.865	0.803	0.928	CLONAL	1	TRUE	1	0.682111428578384	2		403	651	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0012403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	208	498	0	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	1	2	FACETS	0.856	0.799	0.915	0.856	0.799	0.915	CLONAL	1	TRUE	1	0.738308117610279	2		498	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579362	7579362	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057523496	NA	P-0012403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	237	688	0	ENST00000269305.4:c.325T>G	p.Phe109Val	p.F109V	ENST00000269305	NM_001126112.2	109	Ttc/Gtc	4/11	0.731600496455184	1	FACETS	0.88	0.833	0.928	0.88	0.833	0.928	CLONAL	1	TRUE	0	0.738308117610279	1		688	460	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593629	55593652	+	inframe_deletion	In_Frame_Del	DEL	AAACAATTATGTTTACATAGACCC	AAACAATTATGTTTACATAGACCC	-	novel	NA	P-0012403-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	162	458	0	ENST00000288135.5:c.1697_1720del	p.Asn566_Pro573del	p.N566_P573del	ENST00000288135	NM_000222.2	565	ggAAACAATTATGTTTACATAGACCCa/gga	11/21	1	2	FACETS	0.817	0.754	0.882	0.817	0.754	0.882	CLONAL	1	TRUE	1	0.738308117610279	2		458	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579362	7579362	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057523496	NA	P-0012403-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	565	688	0	ENST00000269305.4:c.325T>G	p.Phe109Val	p.F109V	ENST00000269305	NM_001126112.2	109	Ttc/Gtc	4/11	0.788702919477972	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.788702919477972	1		688	820	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593629	55593652	+	inframe_deletion	In_Frame_Del	DEL	AAACAATTATGTTTACATAGACCC	AAACAATTATGTTTACATAGACCC	-	novel	NA	P-0012403-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	143	458	0	ENST00000288135.5:c.1697_1720del	p.Asn566_Pro573del	p.N566_P573del	ENST00000288135	NM_000222.2	565	ggAAACAATTATGTTTACATAGACCCa/gga	11/21	1	2	FACETS	0.436	0.397	0.476	0.436	0.397	0.476	SUBCLONAL	1	TRUE	1	0.788702919477972	2		458	832	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599320	55599321	+	protein_altering_variant	In_Frame_Ins	INS	-	-	AAATCA	novel	NA	P-0012403-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	252	403	0	ENST00000288135.5:c.2447_2448insAATCAA	p.Asp816delinsGluIleAsn	p.D816delinsEIN	ENST00000288135	NM_000222.2	816	gac/gAAATCAac	17/21	1	2	FACETS	0.708	0.663	0.753	0.708	0.663	0.753	SUBCLONAL	1	TRUE	1	0.788702919477972	2		403	903	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593629	55593652	+	inframe_deletion	In_Frame_Del	DEL	AAACAATTATGTTTACATAGACCC	AAACAATTATGTTTACATAGACCC	-	novel	NA	P-0012403-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	120	458	0	ENST00000288135.5:c.1697_1720del	p.Asn566_Pro573del	p.N566_P573del	ENST00000288135	NM_000222.2	565	ggAAACAATTATGTTTACATAGACCCa/gga	11/21	1	2	FACETS	0.414	0.374	0.456	0.414	0.374	0.456	SUBCLONAL	1	TRUE	1	0.882147681878876	2		458	657	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0012824-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	63	329	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	1	2	FACETS	0.52	0.45	0.595	0.52	0.45	0.595	SUBCLONAL	1	TRUE	1	0.507395641745541	2		329	478	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012824-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	65	784	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.284	0.245	0.326	0.284	0.245	0.326	SUBCLONAL	1	TRUE	1	0.507395641745541	2		784	902	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593652	55593652	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	694	511	0	ENST00000288135.5:c.1718C>G	p.Pro573Arg	p.P573R	ENST00000288135	NM_000222.2	573	cCa/cGa	11/21	0.599211506866686	6	FACETS	1	0.994	1			1	CLONAL	5	TRUE	NA	0.599211506866686	6		511	963	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692830	89692830	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016625-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	36	276	0	ENST00000371953.3:c.314G>T	p.Cys105Phe	p.C105F	ENST00000371953	NM_000314.4	105	tGt/tTt	5/9	0.34154981660926	2	FACETS	1	0.945	1	0.655	0.553	0.762	CLONAL	1	TRUE	0	0.513912744121462	2		276	107	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827927	40827927	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536150112	NA	P-0016625-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	115	297	1	ENST00000373198.4:c.2501G>A	p.Arg834His	p.R834H	ENST00000373198	NM_133170.3	834	cGc/cAc	17/32	0.419814706441419	3	FACETS	0.705	0.635	0.779	0.352	0.317	0.39	SUBCLONAL	1	TRUE	1	0.513912744121462	3		298	798	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209504	98209504	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766315655	NA	P-0016625-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	393	443	0	ENST00000331920.6:c.4034G>A	p.Arg1345His	p.R1345H	ENST00000331920	NM_000264.3	1345	cGt/cAt	23/24	0.267241278233706	4	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.513912744121462	4		443	943	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271490	26271492	+	missense_variant	Missense_Mutation	TNP	GCG	GCG	CGA	novel	NA	P-0016625-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	234	837	1	ENST00000305910.3:c.121_123delinsTCG	p.Arg41Ser	p.R41S	ENST00000305910	NM_003534.2	41	CGC/TCG	1/1	0.513912744121462	7	FACETS	1	0.965	1	0.525	0.49	0.562	CLONAL	2	TRUE	3	0.513912744121462	7		838	990	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363312	40363350	+	inframe_deletion	In_Frame_Del	DEL	TCAGAACTGACAGGTTTGGGGTGGCAGGACTGGGCAGCC	TCAGAACTGACAGGTTTGGGGTGGCAGGACTGGGCAGCC	-	novel	NA	P-0016625-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	127	313	0	ENST00000397332.2:c.879_917del	p.Glu293_Ser305del	p.E293_S305del	ENST00000397332	NM_001033082.2	293	gaGGCTGCCCAGTCCTGCCACCCCAAACCTGTCAGTTCTGAt/gat	3/3	0.446931608999582	3	FACETS	0.607	0.549	0.668	0.303	0.274	0.334	SUBCLONAL	1	TRUE	1	0.513912744121462	3		313	1024	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937462	32937462	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1566245492	NA	P-0016625-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	73	632	0	ENST00000380152.3:c.8123C>T	p.Thr2708Ile	p.T2708I	ENST00000380152		2708	aCt/aTt	18/27	0.34154981660926	2	FACETS	0.742	0.652	0.837	0.371	0.326	0.419	SUBCLONAL	1	TRUE	0	0.513912744121462	2		632	383	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23652435	23652436	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0016625-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	193	525	0	ENST00000261584.4:c.43_44delinsAT	p.Glu15Ile	p.E15I	ENST00000261584	NM_024675.3	15	GAa/ATa	1/13	0.495850158329062	3	FACETS	0.877	0.811	0.947	0.439	0.405	0.474	CLONAL	1	TRUE	1	0.513912744121462	3		525	1076	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634813	158634813	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016625-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	76	442	0	ENST00000263640.3:c.373G>C	p.Gly125Arg	p.G125R	ENST00000263640	NM_001105.4	125	Ggc/Cgc	5/11	0.313578719005689	5	FACETS	1	0.911	1	0.348	0.306	0.393	CLONAL	1	TRUE	2	0.513912744121462	5		442	502	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217245	66217245	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs761764875	NA	P-0016625-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	71	508	0	ENST00000273854.3:c.2370C>A	p.Tyr790Ter	p.Y790*	ENST00000273854	NM_004439.5	790	taC/taA	14/18	0.513912744121462	3	FACETS	0.744	0.651	0.843	0.372	0.325	0.422	SUBCLONAL	1	TRUE	1	0.513912744121462	3		508	467	SUCCESS
MET	4233	MSKCC	GRCh37	7	116381073	116381073	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016625-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	267	634	0	ENST00000397752.3:c.1695C>G	p.Ile565Met	p.I565M	ENST00000397752	NM_000245.2	565	atC/atG	5/21	0.415946679686123	5	FACETS	1	0.992	1	0.48	0.449	0.512	CLONAL	1	TRUE	2	0.513912744121462	5		634	1278	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486028	8486028	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016625-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	91	577	0	ENST00000356435.5:c.2789C>T	p.Thr930Ile	p.T930I	ENST00000356435		930	aCc/aTc	17/35	0.415946679686123	5	FACETS	0.88	0.781	0.985	0.293	0.26	0.329	CLONAL	1	TRUE	2	0.513912744121462	5		577	713	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349180	70349180	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016625-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	139	342	0	ENST00000374080.3:c.3592G>C	p.Gly1198Arg	p.G1198R	ENST00000374080		1198	Gga/Cga	26/45	NA	2	FACETS	0.739	0.674	0.807			1	INDETERMINATE	1	TRUE	NA	0.513912744121462	2		342	732	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124370	2124381	+	frameshift_variant	Frame_Shift_Del	DEL	CACTGCTGGAGT	CACTGCTGGAGT	TGTCCAGTGAG	novel	NA	P-0016625-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	152	250	1	ENST00000219476.3:c.2525_2536delinsTGTCCAGTGAG	p.Pro842LeufsTer52	p.P842Lfs*52	ENST00000219476	NM_000548.3	842	cCACTGCTGGAGTtc/cTGTCCAGTGAGtc	22/42	0.495850158329062	3	FACETS	0.63	0.575	0.688	0.315	0.287	0.344	SUBCLONAL	1	TRUE	1	0.513912744121462	3		251	1180	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23652461	23652462	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0016625-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	176	490	0	ENST00000261584.4:c.17_18delinsTT	p.Gly6Val	p.G6V	ENST00000261584	NM_024675.3	6	gGG/gTT	1/13	0.495850158329062	3	FACETS	0.874	0.805	0.946	0.437	0.402	0.473	CLONAL	1	TRUE	1	0.513912744121462	3		490	985	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0016764-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	263	546	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.618138752833643	1	FACETS	0.903	0.855	0.952	0.903	0.855	0.952	CLONAL	1	FALSE	0	0.676122046734273	1		546	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519988	NA	P-0016764-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	297	656	0	ENST00000269305.4:c.808T>C	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	Ttt/Ctt	8/11	0.618138752833643	1	FACETS	0.891	0.845	0.936	0.891	0.845	0.936	CLONAL	1	FALSE	0	0.676122046734273	1		656	653	SUCCESS
APC	324	MSKCC	GRCh37	5	112157682	112157682	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1060503340	NA	P-0016764-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	285	289	0	ENST00000257430.4:c.1402G>T	p.Glu468Ter	p.E468*	ENST00000257430	NM_000038.5	468	Gaa/Taa	11/16	0.632621199892915	2	FACETS	0.846	0.807	0.885	0.846	0.807	0.885	CLONAL	2	FALSE	0	0.676122046734273	2		289	498	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411777	63411777	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016764-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	471	847	0	ENST00000330258.3:c.1390del	p.Ala464ProfsTer77	p.A464Pfs*77	ENST00000330258	NM_152424.3	464	Gcc/cc	2/2	NA	2	FACETS	0.898	0.857	0.94			1	INDETERMINATE	1	FALSE	NA	0.676122046734273	2		847	1551	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164929	47164930	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0016764-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	125	290	0	ENST00000409792.3:c.1196_1197del	p.Glu399AlafsTer9	p.E399Afs*9	ENST00000409792	NM_014159.6	399	gAG/g	3/21	1	2	FACETS	0.922	0.842	1	0.922	0.842	1	CLONAL	1	FALSE	1	0.676122046734273	2		290	401	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920251	76920251	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016764-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	116	300	0	ENST00000373344.5:c.3826C>A	p.Leu1276Ile	p.L1276I	ENST00000373344	NM_000489.3	1276	Ctt/Att	11/35	0.305234139026603	5	FACETS	1	0.954	1	0.365	0.329	0.402	INDETERMINATE	1	FALSE	2	0.676122046734273	5		300	632	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456341	32456341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017717-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	110	741	2	ENST00000332351.3:c.551C>T	p.Pro184Leu	p.P184L	ENST00000332351	NM_024426.4	184	cCg/cTg	1/10	0.861375380819176	3	FACETS	0.502	0.451	0.556	0.251	0.225	0.278	SUBCLONAL	1	TRUE	1	0.861375380819176	3		743	728	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858288	9858288	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017717-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	102	405	0	ENST00000330684.3:c.3113C>G	p.Thr1038Arg	p.T1038R	ENST00000330684	NM_001134407.1	1038	aCa/aGa	13/13	0.486014669737552	1	FACETS	0.616	0.563	0.669	0.616	0.563	0.669	INDETERMINATE	1	TRUE	0	0.861375380819176	1		405	219	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859555	151859555	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017717-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	485	462	0	ENST00000262189.6:c.11107G>T	p.Glu3703Ter	p.E3703*	ENST00000262189	NM_170606.2	3703	Gaa/Taa	43/59	0.861375380819176	3	FACETS	0.936	0.915	0.955	0.936	0.915	0.955	CLONAL	3	TRUE	0	0.861375380819176	3		462	574	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098955	+	protein_altering_variant	In_Frame_Ins	INS	CCA	CCA	TTGGAGGCAAGATAT	novel	NA	P-0017717-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	184	231	0	ENST00000397062.3:c.90_92delinsATATCTTGCCTCCAA	p.Gly31delinsTyrLeuAlaSerLys	p.G31delinsYLASK	ENST00000397062	NM_006164.4	30	ctTGGa/ctATATCTTGCCTCCAAa	2/5	0.783242759624681	2	FACETS	0.841	0.801	0.879	0.841	0.801	0.879	CLONAL	2	TRUE	0	0.861375380819176	2		231	254	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0017717-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	99	844	0	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	0.358259505191627	3	FACETS	0.446	0.398	0.497	0.223	0.199	0.249	INDETERMINATE	1	TRUE	1	0.861375380819176	3		844	737	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222494	2222494	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017717-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	62	829	0	ENST00000326181.6:c.688C>A	p.Pro230Thr	p.P230T	ENST00000326181	NM_032271.2	230	Cct/Act	9/21	0.486014669737552	1	FACETS	0.188	0.162	0.215	0.188	0.162	0.215	INDETERMINATE	1	TRUE	0	0.861375380819176	1		829	437	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	134	670	3	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.947	0.864	1	0.947	0.864	1	CLONAL	1	TRUE	1	0.50823075090913	2		673	557	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	67	397	3	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	0.906	0.795	1	0.906	0.795	1	CLONAL	1	TRUE	1	0.50823075090913	2		400	291	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	64	436	2	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.95	0.832	1	0.95	0.832	1	CLONAL	1	TRUE	1	0.50823075090913	2		438	265	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	108	720	10	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.738	0.664	0.816	0.738	0.664	0.816	SUBCLONAL	1	TRUE	1	0.50823075090913	2		730	576	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	63	465	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.50823075090913	2		465	215	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	52	383	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.50823075090913	2		383	199	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	294	721	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.991	0.942	1	1	0.996	1	CLONAL	2	TRUE	1	0.50823075090913	2		728	584	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	79	296	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.797	0.716	0.88	1	0.982	1	SUBCLONAL	2	TRUE	1	0.50823075090913	2		296	195	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	41	343	1	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	0.13757489380031	0	FACETS	0.606	0.516	0.701			1	INDETERMINATE	1	TRUE	0	0.50823075090913	0		344	131	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	38	250	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	0.845	0.707	0.994	0.845	0.707	0.994	CLONAL	1	TRUE	1	0.50823075090913	2		250	177	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	100	719	1	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	0.939	0.845	1	0.939	0.845	1	CLONAL	1	TRUE	1	0.50823075090913	2		720	419	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372337	55372337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1281266243	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	140	692	2	ENST00000297316.4:c.1027C>T	p.Arg343Trp	p.R343W	ENST00000297316	NM_022454.3	343	Cgg/Tgg	2/2	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.50823075090913	2		694	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519986	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	136	570	0	ENST00000269305.4:c.809T>C	p.Phe270Ser	p.F270S	ENST00000269305	NM_001126112.2	270	tTt/tCt	8/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.50823075090913	2		570	492	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937659	17937659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144968714	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	127	666	2	ENST00000458235.1:c.3268G>A	p.Ala1090Thr	p.A1090T	ENST00000458235	NM_000215.3	1090	Gcc/Acc	24/24	1	2	FACETS	0.932	0.849	1	0.932	0.849	1	CLONAL	1	TRUE	1	0.50823075090913	2		668	536	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	63	443	2	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	0.8	0.697	0.91	0.8	0.697	0.91	CLONAL	1	TRUE	1	0.50823075090913	2		445	310	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984762	72984762	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1224592041	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	198	695	0	ENST00000268489.5:c.2822C>T	p.Ser941Leu	p.S941L	ENST00000268489	NM_006885.3	941	tCg/tTg	3/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.50823075090913	2		695	567	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	65	474	5	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	0.954	0.836	1	0.954	0.836	1	CLONAL	1	TRUE	1	0.50823075090913	2		479	268	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519886	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	64	328	0	ENST00000349496.5:c.97T>G	p.Ser33Ala	p.S33A	ENST00000349496	NM_001904.3	33	Tct/Gct	3/15	1	2	FACETS	0.94	0.822	1	0.94	0.822	1	CLONAL	1	TRUE	1	0.50823075090913	2		328	268	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	109	562	6	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.50823075090913	2		568	428	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219487	133219487	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	145	764	1	ENST00000320574.5:c.4647del	p.Lys1550AsnfsTer12	p.K1550Nfs*12	ENST00000320574	NM_006231.2	1549	ccC/cc	36/49	1	2	FACETS	0.922	0.844	1	0.922	0.844	1	CLONAL	1	TRUE	1	0.50823075090913	2		765	619	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460476	149460476	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	103	718	0	ENST00000286301.3:c.161del	p.Pro54HisfsTer58	p.P54Hfs*58	ENST00000286301	NM_005211.3	54	cCa/ca	3/22	1	2	FACETS	0.862	0.776	0.953	0.862	0.776	0.953	CLONAL	1	TRUE	1	0.50823075090913	2		718	470	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610522	10610522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	138	774	0	ENST00000171111.5:c.188C>T	p.Ala63Val	p.A63V	ENST00000171111	NM_203500.1	63	gCc/gTc	2/6	1	2	FACETS	0.977	0.893	1	0.977	0.893	1	CLONAL	1	TRUE	1	0.50823075090913	2		774	556	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048668	180048668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1158883745	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	118	810	1	ENST00000261937.6:c.1894C>T	p.Arg632Cys	p.R632C	ENST00000261937	NM_182925.4	632	Cgc/Tgc	13/30	1	2	FACETS	0.934	0.847	1	0.934	0.847	1	CLONAL	1	TRUE	1	0.50823075090913	2		811	497	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920173	76920173	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	52	431	1	ENST00000373344.5:c.3904del	p.Arg1302GlufsTer44	p.R1302Efs*44	ENST00000373344	NM_000489.3	1302	Aga/ga	11/35	0.13757489380031	0	FACETS	0.343	0.294	0.397			1	INDETERMINATE	1	TRUE	0	0.50823075090913	0		432	293	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795608	42795609	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1555770200	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	142	782	1	ENST00000575354.2:c.2694dup	p.Lys899GlnfsTer32	p.K899Qfs*32	ENST00000575354	NM_015125.3	896	-/C	10/20	1	2	FACETS	0.93	0.851	1	0.93	0.851	1	CLONAL	1	TRUE	1	0.50823075090913	2		783	601	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395186	139395186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	181	993	3	ENST00000277541.6:c.5752G>A	p.Ala1918Thr	p.A1918T	ENST00000277541	NM_017617.3	1918	Gcc/Acc	31/34	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.50823075090913	2		996	640	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188294	32188295	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs766348245	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	149	773	3	ENST00000375023.3:c.1046dup	p.Thr350HisfsTer4	p.T350Hfs*4	ENST00000375023	NM_004557.3	349	ggc/ggGc	6/30	0.50823075090913	2	FACETS	1	0.923	1	0.503	0.461	0.546	CLONAL	1	TRUE	0	0.50823075090913	2		776	583	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937673	17937673	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	160	624	0	ENST00000458235.1:c.3254G>A	p.Arg1085Gln	p.R1085Q	ENST00000458235	NM_000215.3	1085	cGg/cAg	24/24	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.50823075090913	2		624	515	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	146	760	1	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.969	0.888	1	0.969	0.888	1	CLONAL	1	TRUE	1	0.50823075090913	2		761	593	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	132	1094	5	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.986	0.899	1	0.986	0.899	1	CLONAL	1	TRUE	1	0.50823075090913	2		1099	527	SUCCESS
YES1	7525	MSKCC	GRCh37	18	732914	732914	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1384930568	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	67	456	0	ENST00000314574.4:c.1343G>A	p.Arg448Gln	p.R448Q	ENST00000314574	NM_005433.3	448	cGg/cAg	11/12	1	2	FACETS	0.928	0.815	1	0.928	0.815	1	CLONAL	1	TRUE	1	0.50823075090913	2		456	284	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460527	149460527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139635308	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	120	730	1	ENST00000286301.3:c.110C>T	p.Thr37Met	p.T37M	ENST00000286301	NM_005211.3	37	aCg/aTg	3/22	1	2	FACETS	0.862	0.781	0.946	0.862	0.781	0.946	CLONAL	1	TRUE	1	0.50823075090913	2		731	548	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399278	139399278	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778271353	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	132	747	0	ENST00000277541.6:c.4865G>A	p.Arg1622His	p.R1622H	ENST00000277541	NM_017617.3	1622	cGc/cAc	26/34	1	2	FACETS	0.893	0.813	0.975	0.893	0.813	0.975	CLONAL	1	TRUE	1	0.50823075090913	2		747	582	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061725	38061726	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs766493600	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	57	500	0	ENST00000250448.2:c.263dup	p.Ser89LeufsTer138	p.S89Lfs*138	ENST00000250448	NM_004496.3	88	ggc/ggGc	2/2	1	2	FACETS	0.859	0.744	0.982	0.859	0.744	0.982	CLONAL	1	TRUE	1	0.50823075090913	2		500	261	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912367	29912367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	64	525	0	ENST00000376809.5:c.986C>T	p.Ala329Val	p.A329V	ENST00000376809	NM_002116.7	329	gCc/gTc	5/8	0.50823075090913	2	FACETS	0.766	0.667	0.87	0.383	0.333	0.435	SUBCLONAL	1	TRUE	0	0.50823075090913	2		525	329	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43733757	43733757	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	81	326	0	ENST00000382044.4:c.3065del	p.Asn1022MetfsTer20	p.N1022Mfs*20	ENST00000382044	NM_001141980.1	1022	aAt/at	15/28	1	2	FACETS	0.963	0.856	1	0.963	0.856	1	CLONAL	1	TRUE	1	0.50823075090913	2		326	331	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432420	49432420	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	129	710	0	ENST00000301067.7:c.8719del	p.Tyr2907ThrfsTer3	p.Y2907Tfs*3	ENST00000301067	NM_003482.3	2907	Tac/ac	34/54	1	2	FACETS	0.98	0.893	1	0.98	0.893	1	CLONAL	1	TRUE	1	0.50823075090913	2		710	518	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100120	27100120	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	92	664	0	ENST00000324856.7:c.3916C>T	p.Gln1306Ter	p.Q1306*	ENST00000324856	NM_006015.4	1306	Cag/Tag	16/20	1	2	FACETS	0.864	0.772	0.961	0.864	0.772	0.961	CLONAL	1	TRUE	1	0.50823075090913	2		664	419	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36940986	36940986	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	121	569	0	ENST00000361632.4:c.353G>C	p.Arg118Pro	p.R118P	ENST00000361632		118	cGc/cCc	3/16	1	2	FACETS	0.978	0.888	1	0.978	0.888	1	CLONAL	1	TRUE	1	0.50823075090913	2		569	487	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097730	8097730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747477962	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	125	565	0	ENST00000346208.3:c.112G>A	p.Ala38Thr	p.A38T	ENST00000346208		38	Gcg/Acg	2/6	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.50823075090913	2		565	483	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404591	70404591	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	66	435	0	ENST00000373644.4:c.2105T>C	p.Met702Thr	p.M702T	ENST00000373644	NM_030625.2	702	aTg/aCg	4/12	1	2	FACETS	0.902	0.79	1	0.902	0.79	1	CLONAL	1	TRUE	1	0.50823075090913	2		435	288	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441816	49441816	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	152	618	1	ENST00000301067.7:c.4168del	p.Ala1390GlnfsTer27	p.A1390Qfs*27	ENST00000301067	NM_003482.3	1390	Gca/ca	14/54	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.50823075090913	2		619	544	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420285	88420285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199690201	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	88	532	0	ENST00000360948.2:c.2401G>A	p.Asp801Asn	p.D801N	ENST00000360948	NM_001012338.2	801	Gat/Aat	19/19	1	2	FACETS	0.851	0.758	0.948	0.851	0.758	0.948	CLONAL	1	TRUE	1	0.50823075090913	2		532	407	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213967	2213967	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1188110300	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	164	758	1	ENST00000326181.6:c.46C>G	p.Pro16Ala	p.P16A	ENST00000326181	NM_032271.2	16	Ccc/Gcc	2/21	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.50823075090913	2		759	607	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129821	30129821	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	85	518	0	ENST00000263025.4:c.392A>G	p.Lys131Arg	p.K131R	ENST00000263025	NM_002746.2	131	aAg/aGg	3/9	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.50823075090913	2		518	315	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821382	72821382	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs774585182	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	53	470	0	ENST00000268489.5:c.10793del	p.Pro3598LeufsTer96	p.P3598Lfs*96	ENST00000268489	NM_006885.3	3598	cCt/ct	10/10	1	2	FACETS	0.63	0.54	0.728	0.63	0.54	0.728	SUBCLONAL	1	TRUE	1	0.50823075090913	2		470	331	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357502	89357502	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	141	778	0	ENST00000301030.4:c.316C>T	p.Arg106Ter	p.R106*	ENST00000301030	NM_001256183.1	106	Cga/Tga	5/13	0.50823075090913	3	FACETS	1	0.93	1	0.51	0.466	0.557	CLONAL	1	TRUE	1	0.50823075090913	3		778	682	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858926	89858927	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	114	486	0	ENST00000389301.3:c.1034_1035dup	p.Trp346SerfsTer20	p.W346Sfs*20	ENST00000389301	NM_000135.2	345	-/AG	12/43	0.50823075090913	3	FACETS	0.789	0.711	0.871	0.395	0.355	0.436	SUBCLONAL	1	TRUE	1	0.50823075090913	3		486	713	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369448	40369448	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	124	718	1	ENST00000293328.3:c.1204G>A	p.Val402Ile	p.V402I	ENST00000293328	NM_012448.3	402	Gtc/Atc	10/19	1	2	FACETS	0.899	0.817	0.984	0.899	0.817	0.984	CLONAL	1	TRUE	1	0.50823075090913	2		719	543	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734161	58734161	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	96	512	0	ENST00000305921.3:c.1219T>A	p.Cys407Ser	p.C407S	ENST00000305921	NM_003620.3	407	Tgt/Agt	5/6	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.50823075090913	2		512	331	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121133	11121133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	133	690	0	ENST00000358026.2:c.2200G>A	p.Val734Met	p.V734M	ENST00000358026	NM_001128849.1	734	Gtg/Atg	15/36	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.50823075090913	2		690	507	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051211	13051211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200173883	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	111	544	0	ENST00000316448.5:c.647C>T	p.Pro216Leu	p.P216L	ENST00000316448	NM_004343.3	216	cCg/cTg	5/9	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.50823075090913	2		544	418	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967800	18967800	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	191	739	0	ENST00000262803.5:c.1939A>G	p.Met647Val	p.M647V	ENST00000262803	NM_002911.3	647	Atg/Gtg	14/24	1	2	FACETS	0.944	0.875	1	0.944	0.875	1	CLONAL	1	TRUE	1	0.50823075090913	2		739	796	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416583	29416583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs112657055	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	106	579	2	ENST00000389048.3:c.4370C>T	p.Thr1457Ile	p.T1457I	ENST00000389048	NM_004304.4	1457	aCa/aTa	29/29	1	2	FACETS	0.903	0.814	0.996	0.903	0.814	0.996	CLONAL	1	TRUE	1	0.50823075090913	2		581	462	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275661	41275661	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	99	409	0	ENST00000349496.5:c.1556T>C	p.Leu519Pro	p.L519P	ENST00000349496	NM_001904.3	519	cTt/cCt	10/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.50823075090913	2		409	340	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940484	49940484	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	152	895	1	ENST00000296474.3:c.559A>G	p.Thr187Ala	p.T187A	ENST00000296474	NM_002447.2	187	Act/Gct	1/20	1	2	FACETS	0.922	0.846	1	0.922	0.846	1	CLONAL	1	TRUE	1	0.50823075090913	2		896	649	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286255	66286255	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	31	279	0	ENST00000273854.3:c.1431del	p.Ile480LeufsTer21	p.I480Lfs*21	ENST00000273854	NM_004439.5	477	aaA/aa	6/18	1	2	FACETS	0.709	0.58	0.852	0.709	0.58	0.852	SUBCLONAL	1	TRUE	1	0.50823075090913	2		279	172	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196731	106196731	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	45	418	0	ENST00000380013.4:c.5067del	p.Phe1689LeufsTer6	p.F1689Lfs*6	ENST00000380013	NM_001127208.2	1688	agT/ag	11/11	1	2	FACETS	0.831	0.706	0.966	0.831	0.706	0.966	CLONAL	1	TRUE	1	0.50823075090913	2		418	213	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687113	176687113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	82	436	0	ENST00000439151.2:c.5090G>A	p.Arg1697Gln	p.R1697Q	ENST00000439151	NM_022455.4	1697	cGg/cAg	14/23	1	2	FACETS	0.99	0.881	1	0.99	0.881	1	CLONAL	1	TRUE	1	0.50823075090913	2		436	326	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323362	31323363	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748204482	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	82	379	0	ENST00000412585.2:c.626dup	p.Thr211AspfsTer10	p.T211Dfs*10	ENST00000412585	NM_005514.6	209	cca/ccCa	4/8	0.50823075090913	2	FACETS	1	0.978	1	0.698	0.626	0.773	CLONAL	1	TRUE	0	0.50823075090913	2		379	231	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372133	55372133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161016147	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	92	409	1	ENST00000297316.4:c.823G>A	p.Gly275Ser	p.G275S	ENST00000297316	NM_022454.3	275	Ggc/Agc	2/2	1	2	FACETS	0.948	0.848	1	0.948	0.848	1	CLONAL	1	TRUE	1	0.50823075090913	2		410	382	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485280	8485280	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329600473	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	66	428	0	ENST00000356435.5:c.3100G>A	p.Val1034Met	p.V1034M	ENST00000356435		1034	Gtg/Atg	18/35	1	2	FACETS	0.938	0.822	1	0.938	0.822	1	CLONAL	1	TRUE	1	0.50823075090913	2		428	277	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390984	139390984	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	167	944	0	ENST00000277541.6:c.7207C>A	p.Gln2403Lys	p.Q2403K	ENST00000277541	NM_017617.3	2403	Cag/Aag	34/34	1	2	FACETS	0.994	0.917	1	0.994	0.917	1	CLONAL	1	TRUE	1	0.50823075090913	2		944	661	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841240	15841240	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746842789	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	82	264	1	ENST00000307771.7:c.1324C>T	p.Arg442Trp	p.R442W	ENST00000307771	NM_005089.3	442	Cgg/Tgg	11/11	0.13757489380031	0	FACETS	0.731	0.657	0.808			1	INDETERMINATE	1	TRUE	0	0.50823075090913	0		265	217	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041170	47041170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	116	731	0	ENST00000377604.3:c.1598C>T	p.Ala533Val	p.A533V	ENST00000377604	NM_001204468.1	533	gCt/gTt	15/24	0.13757489380031	0	FACETS	0.477	0.432	0.523			1	INDETERMINATE	1	TRUE	0	0.50823075090913	0		731	471	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411852	63411852	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	147	745	2	ENST00000330258.3:c.1315C>A	p.Leu439Ile	p.L439I	ENST00000330258	NM_152424.3	439	Ctt/Att	2/2	0.13757489380031	0	FACETS	0.495	0.454	0.537			1	INDETERMINATE	1	TRUE	0	0.50823075090913	0		747	575	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982123	93982123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769773179	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	50	357	0	ENST00000369303.4:c.1342G>A	p.Gly448Arg	p.G448R	ENST00000369303	NM_004440.3	448	Gga/Aga	6/17	1	2	FACETS	0.734	0.628	0.849	0.734	0.628	0.849	SUBCLONAL	1	TRUE	1	0.50823075090913	2		357	268	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86637110	86637110	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	19	257	0	ENST00000274376.6:c.1021C>T	p.Arg341Trp	p.R341W	ENST00000274376	NM_002890.2	341	Cgg/Tgg	6/25	1	2	FACETS	0.554	0.425	0.702	0.554	0.425	0.702	SUBCLONAL	1	TRUE	1	0.50823075090913	2		257	135	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131495	202131495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	57	378	0	ENST00000358485.4:c.463G>A	p.Ala155Thr	p.A155T	ENST00000358485	NM_001080125.1	155	Gct/Act	2/9	1	2	FACETS	0.743	0.642	0.851	0.743	0.642	0.851	SUBCLONAL	1	TRUE	1	0.50823075090913	2		378	302	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739470	145739470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747895651	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	138	782	3	ENST00000428558.2:c.1900G>A	p.Val634Met	p.V634M	ENST00000428558	NM_004260.3	634	Gtg/Atg	12/22	1	2	FACETS	0.893	0.816	0.974	0.893	0.816	0.974	CLONAL	1	TRUE	1	0.50823075090913	2		785	608	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371677	55371677	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	45	660	0	ENST00000297316.4:c.367C>T	p.Arg123Trp	p.R123W	ENST00000297316	NM_022454.3	123	Cgg/Tgg	2/2	1	2	FACETS	0.345	0.289	0.406	0.345	0.289	0.406	SUBCLONAL	1	TRUE	1	0.50823075090913	2		660	514	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442809	99442809	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	73	485	0	ENST00000268035.6:c.1211del	p.Asn404ThrfsTer6	p.N404Tfs*6	ENST00000268035	NM_000875.3	402	ctA/ct	5/21	1	2	FACETS	0.93	0.82	1	0.93	0.82	1	CLONAL	1	TRUE	1	0.50823075090913	2		485	309	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688734	47688734	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	69	405	0	ENST00000347630.2:c.566A>T	p.Glu189Val	p.E189V	ENST00000347630	NM_001007230.1	189	gAg/gTg	7/11	1	2	FACETS	0.73	0.639	0.827	0.73	0.639	0.827	SUBCLONAL	1	TRUE	1	0.50823075090913	2		405	372	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418643	49418643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs936142615	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	109	502	0	ENST00000301067.7:c.15871G>A	p.Glu5291Lys	p.E5291K	ENST00000301067	NM_003482.3	5291	Gag/Aag	49/54	1	2	FACETS	0.881	0.795	0.971	0.881	0.795	0.971	CLONAL	1	TRUE	1	0.50823075090913	2		502	487	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40444065	40444065	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	99	564	0	ENST00000345506.4:c.361C>T	p.Arg121Ter	p.R121*	ENST00000345506	NM_003152.3	121	Cga/Tga	5/20	1	2	FACETS	0.91	0.818	1	0.91	0.818	1	CLONAL	1	TRUE	1	0.50823075090913	2		564	428	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467373	66467373	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	19	229	0	ENST00000273854.3:c.896del	p.Asn299MetfsTer123	p.N299Mfs*123	ENST00000273854	NM_004439.5	299	aAt/at	3/18	1	2	FACETS	0.523	0.4	0.664	0.523	0.4	0.664	SUBCLONAL	1	TRUE	1	0.50823075090913	2		229	143	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793708	89793709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	41	327	0	ENST00000336032.3:c.782dup	p.Asn261LysfsTer12	p.N261Kfs*12	ENST00000336032	NM_006813.2	259	-/A	2/2	1	2	FACETS	0.836	0.705	0.978	0.836	0.705	0.978	CLONAL	1	TRUE	1	0.50823075090913	2		327	193	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120452	70120452	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	158	715	0	ENST00000245479.2:c.1454G>T	p.Gly485Val	p.G485V	ENST00000245479	NM_000346.3	485	gGg/gTg	3/3	1	2	FACETS	0.925	0.85	1	0.925	0.85	1	CLONAL	1	TRUE	1	0.50823075090913	2		715	672	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822441	72822441	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	130	782	0	ENST00000268489.5:c.9734A>C	p.Lys3245Thr	p.K3245T	ENST00000268489	NM_006885.3	3245	aAg/aCg	10/10	1	2	FACETS	0.946	0.862	1	0.946	0.862	1	CLONAL	1	TRUE	1	0.50823075090913	2		782	541	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645139	86645139	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1175378445	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	29	260	0	ENST00000274376.6:c.1211C>T	p.Thr404Met	p.T404M	ENST00000274376	NM_002890.2	404	aCg/aTg	8/25	1	2	FACETS	0.839	0.684	1	0.839	0.684	1	CLONAL	1	TRUE	1	0.50823075090913	2		260	136	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739102	46739102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	100	538	0	ENST00000371975.4:c.1451G>A	p.Gly484Asp	p.G484D	ENST00000371975	NM_003579.3	484	gGt/gAt	13/18	1	2	FACETS	0.911	0.819	1	0.911	0.819	1	CLONAL	1	TRUE	1	0.50823075090913	2		538	432	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117838	108117838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375049090	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	31	303	1	ENST00000278616.4:c.1049C>T	p.Ala350Val	p.A350V	ENST00000278616	NM_000051.3	350	gCa/gTa	8/63	1	2	FACETS	0.777	0.637	0.931	0.777	0.637	0.931	CLONAL	1	TRUE	1	0.50823075090913	2		304	157	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427404	427404	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	98	537	0	ENST00000399788.2:c.2765T>C	p.Met922Thr	p.M922T	ENST00000399788	NM_001042603.1	922	aTg/aCg	19/28	1	2	FACETS	0.989	0.889	1	0.989	0.889	1	CLONAL	1	TRUE	1	0.50823075090913	2		537	390	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911458	32911458	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	29	371	0	ENST00000380152.3:c.2966A>G	p.Tyr989Cys	p.Y989C	ENST00000380152		989	tAc/tGc	11/27	1	2	FACETS	0.92	0.752	1	0.92	0.752	1	CLONAL	1	TRUE	1	0.50823075090913	2		371	124	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801789	3801789	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	106	434	0	ENST00000262367.5:c.3717G>T	p.Lys1239Asn	p.K1239N	ENST00000262367	NM_004380.2	1239	aaG/aaT	20/31	1	2	FACETS	0.988	0.892	1	0.988	0.892	1	CLONAL	1	TRUE	1	0.50823075090913	2		434	422	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993765	72993765	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	87	663	0	ENST00000268489.5:c.280T>C	p.Tyr94His	p.Y94H	ENST00000268489	NM_006885.3	94	Tac/Cac	2/10	1	2	FACETS	0.941	0.839	1	0.941	0.839	1	CLONAL	1	TRUE	1	0.50823075090913	2		663	364	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245914	41245914	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	77	490	0	ENST00000357654.3:c.1634T>C	p.Val545Ala	p.V545A	ENST00000357654	NM_007294.3	545	gTg/gCg	10/23	1	2	FACETS	0.981	0.869	1	0.981	0.869	1	CLONAL	1	TRUE	1	0.50823075090913	2		490	309	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226618	1226618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881992	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	97	428	0	ENST00000326873.7:c.1274G>A	p.Arg425His	p.R425H	ENST00000326873	NM_000455.4	425	cGc/cAc	9/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.50823075090913	2		428	297	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611789	1611789	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	137	698	0	ENST00000344749.5:c.1873G>T	p.Gly625Cys	p.G625C	ENST00000344749	NM_001136139.2	625	Ggt/Tgt	19/19	1	2	FACETS	0.806	0.735	0.88	0.806	0.735	0.88	CLONAL	1	TRUE	1	0.50823075090913	2		698	669	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141468	11141468	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	130	679	0	ENST00000358026.2:c.3445T>C	p.Tyr1149His	p.Y1149H	ENST00000358026	NM_001128849.1	1149	Tac/Cac	25/36	1	2	FACETS	0.894	0.814	0.978	0.894	0.814	0.978	CLONAL	1	TRUE	1	0.50823075090913	2		679	572	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910406	50910406	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	150	856	0	ENST00000440232.2:c.1661A>C	p.Lys554Thr	p.K554T	ENST00000440232	NM_002691.3	554	aAg/aCg	13/27	1	2	FACETS	0.972	0.892	1	0.972	0.892	1	CLONAL	1	TRUE	1	0.50823075090913	2		856	607	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860360	42860360	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760565628	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	147	682	2	ENST00000398585.3:c.517G>A	p.Val173Met	p.V173M	ENST00000398585	NM_001135099.1	173	Gtg/Atg	5/14	1	2	FACETS	0.91	0.833	0.989	0.91	0.833	0.989	CLONAL	1	TRUE	1	0.50823075090913	2		684	636	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670484	134670484	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs746739761	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	88	529	1	ENST00000398015.3:c.395C>G	p.Ala132Gly	p.A132G	ENST00000398015	NM_004441.4	132	gCc/gGc	3/16	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.50823075090913	2		530	344	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604248	189604248	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	81	490	0	ENST00000264731.3:c.1415T>C	p.Met472Thr	p.M472T	ENST00000264731	NM_003722.4	472	aTg/aCg	11/14	1	2	FACETS	0.888	0.788	0.993	0.888	0.788	0.993	CLONAL	1	TRUE	1	0.50823075090913	2		490	359	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94129055	94129055	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	69	296	0	ENST00000369303.4:c.5T>G	p.Val2Gly	p.V2G	ENST00000369303	NM_004440.3	2	gTt/gGt	1/17	1	2	FACETS	0.92	0.809	1	0.92	0.809	1	CLONAL	1	TRUE	1	0.50823075090913	2		296	295	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553212	106553212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755211447	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	106	612	1	ENST00000369096.4:c.1177G>A	p.Ala393Thr	p.A393T	ENST00000369096	NM_001198.3	393	Gca/Aca	5/7	1	2	FACETS	0.838	0.754	0.925	0.838	0.754	0.925	CLONAL	1	TRUE	1	0.50823075090913	2		613	498	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309019	137309019	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	132	776	3	ENST00000481739.1:c.626G>A	p.Arg209Gln	p.R209Q	ENST00000481739	NM_002957.4	209	cGg/cAg	5/10	1	2	FACETS	0.953	0.869	1	0.953	0.869	1	CLONAL	1	TRUE	1	0.50823075090913	2		779	545	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411474	63411474	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	107	744	1	ENST00000330258.3:c.1693C>T	p.Gln565Ter	p.Q565*	ENST00000330258	NM_152424.3	565	Cag/Tag	2/2	0.13757489380031	0	FACETS	0.42	0.378	0.464			1	INDETERMINATE	1	TRUE	0	0.50823075090913	0		745	493	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938064	76938064	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	59	517	0	ENST00000373344.5:c.2684T>G	p.Val895Gly	p.V895G	ENST00000373344	NM_000489.3	895	gTt/gGt	9/35	0.13757489380031	0	FACETS	0.323	0.279	0.371			1	INDETERMINATE	1	TRUE	0	0.50823075090913	0		517	353	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593656	55593657	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAACTTCCTTATGATCACAAATGGGAGTTTCCCAGAAACAGGCTGAGTTTTGGT	novel	NA	P-0019583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	203	656	0	ENST00000288135.5:c.1725_1774+4dup		p.Q575_G592dup	ENST00000288135	NM_000222.2	575	-/CAACTTCCTTATGATCACAAATGGGAGTTTCCCAGAAACAGGCTGAGTTTTGGT	11/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		656	1283	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486102	29486102	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0021753-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	64	347	0	ENST00000356175.3:c.279T>A	p.Cys93Ter	p.C93*	ENST00000356175	NM_000267.3	93	tgT/tgA	3/57	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.692709231343221	2		347	184	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654533	29654533	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1555533550	NA	P-0021753-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	132	229	0	ENST00000356175.3:c.5222T>A	p.Val1741Asp	p.V1741D	ENST00000356175	NM_000267.3	1741	gTc/gAc	37/57	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.692709231343221	2		229	377	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021753-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	429	715	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.692709231343221	2		715	1154	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057269	30057270	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0021753-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	310	560	0	ENST00000338641.4:c.756dup	p.Lys253GlnfsTer8	p.K253Qfs*8	ENST00000338641	NM_000268.3	251	acc/aCcc	8/16	0.692709231343221	1	FACETS	0.992	0.945	1	0.992	0.945	1	CLONAL	1	TRUE	0	0.692709231343221	1		560	590	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167796	56167796	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021753-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	226	431	0	ENST00000399503.3:c.1361A>G	p.Glu454Gly	p.E454G	ENST00000399503	NM_005921.1	454	gAa/gGa	7/20	0.127889609820412	4	FACETS	0.942	0.885	1	0.942	0.885	1	INDETERMINATE	2	TRUE	2	0.692709231343221	4		431	586	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508832	106508832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773933093	NA	P-0021753-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	318	538	1	ENST00000359195.3:c.826G>A	p.Gly276Ser	p.G276S	ENST00000359195	NM_002649.2	276	Ggc/Agc	2/11	0.692709231343221	3	FACETS	0.995	0.939	1	0.498	0.469	0.527	CLONAL	1	TRUE	1	0.692709231343221	3		539	1242	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56911005	56911005	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021753-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	712	504	1	ENST00000519728.1:c.1151C>A	p.Ala384Glu	p.A384E	ENST00000519728	NM_002350.3	384	gCa/gAa	11/13	0.681312801069471	4	FACETS	0.933	0.906	0.96	0.933	0.906	0.96	CLONAL	3	TRUE	1	0.692709231343221	4		505	1243	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141570544	141570544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021753-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	1336	758	1	ENST00000220592.5:c.584G>A	p.Gly195Asp	p.G195D	ENST00000220592	NM_012154.3	195	gGc/gAc	5/19	0.681312801069471	4	FACETS	0.982	0.962	1	0.982	0.962	1	CLONAL	3	TRUE	1	0.692709231343221	4		759	2216	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857538	9857538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778951185	NA	P-0021978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	22	470	0	ENST00000330684.3:c.3863G>A	p.Arg1288His	p.R1288H	ENST00000330684	NM_001134407.1	1288	cGt/cAt	13/13	1	2	FACETS	0.37	0.286	0.468	0.37	0.286	0.468	SUBCLONAL	1	TRUE	1	0.3	2		470	396	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593602	55593652	+	inframe_deletion	In_Frame_Del	DEL	GTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCC	GTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCC	-	novel	NA	P-0021978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	59	379	0	ENST00000288135.5:c.1668_1718del	p.Trp557_Pro573del	p.W557_P573del	ENST00000288135	NM_000222.2	556	caGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCCa/caa	11/21	1	2	FACETS	0.908	0.784	1	0.908	0.784	1	CLONAL	1	TRUE	1	0.3	2		379	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0024083-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	418	649	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.620247360976373	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.636475672699087	2		649	650	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936091	71936091	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024083-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	16	27	0	ENST00000298229.2:c.63G>A	p.Trp21Ter	p.W21*	ENST00000298229	NM_001567.3	21	tgG/tgA	1/28	1	2	FACETS	0.967	0.742	1	0.967	0.742	1	CLONAL	1	TRUE	1	0.636475672699087	2		27	52	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149793	202149793	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs773127303	NA	P-0024083-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	229	784	2	ENST00000358485.4:c.1234A>G	p.Lys412Glu	p.K412E	ENST00000358485	NM_001080125.1	412	Aaa/Gaa	8/9	1	2	FACETS	0.765	0.713	0.818	0.765	0.713	0.818	SUBCLONAL	1	TRUE	1	0.636475672699087	2		786	941	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730904	40730904	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024083-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	207	682	0	ENST00000373198.4:c.3631G>C	p.Glu1211Gln	p.E1211Q	ENST00000373198	NM_133170.3	1211	Gag/Cag	27/32	1	2	FACETS	0.999	0.932	1	0.999	0.932	1	CLONAL	1	TRUE	1	0.636475672699087	2		682	651	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186507023	186507023	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024083-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	106	284	0	ENST00000323963.5:c.1189G>T	p.Glu397Ter	p.E397*	ENST00000323963		397	Gag/Tag	11/11	0.559471348853565	3	FACETS	1	0.956	1	0.367	0.331	0.404	CLONAL	1	TRUE	0	0.636475672699087	3		284	399	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161984	47161984	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024888-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	205	244	0	ENST00000409792.3:c.4142del	p.Leu1381Ter	p.L1381*	ENST00000409792	NM_014159.6	1381	tTa/ta	3/21	0.304324159795822	1	FACETS	0.82	0.766	0.876	0.82	0.766	0.876	INDETERMINATE	1	TRUE	0	0.592882509891816	1		244	593	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468318	50468318	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024888-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	194	255	0	ENST00000331340.3:c.1553T>C	p.Met518Thr	p.M518T	ENST00000331340	NM_006060.4	518	aTg/aCg	8/8	1	2	FACETS	0.992	0.922	1	0.992	0.922	1	CLONAL	1	TRUE	1	0.592882509891816	2		255	660	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593648	55593649	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACCCAACACAACTTCCTTATGATCACAAATGGGAGTTTCCCAGAA	novel	NA	P-0024888-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	115	354	0	ENST00000288135.5:c.1717_1761dup	p.Pro573_Asn587dup	p.P573_N587dup	ENST00000288135	NM_000222.2	573	gac/gACCCAACACAACTTCCTTATGATCACAAATGGGAGTTTCCCAGAAac	11/21	0.304324159795822	1	FACETS	0.293	0.264	0.325	0.293	0.264	0.325	INDETERMINATE	1	TRUE	0	0.592882509891816	1		354	930	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0025546-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	329	470	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.408559288082571	4	FACETS	1	0.99	1	0.831	0.795	0.866	CLONAL	3	TRUE	0	0.52648946870031	4		470	574	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0025546-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	270	848	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.52648946870031	1	FACETS	0.987	0.93	1	0.987	0.93	1	CLONAL	1	TRUE	0	0.52648946870031	1		848	766	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732484	74732519	+	inframe_deletion	In_Frame_Del	DEL	GATCGGCTGCGAGACCTGGAACGACTCCGACTCCGG	GATCGGCTGCGAGACCTGGAACGACTCCGACTCCGG	-	rs1270919613	NA	P-0025546-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	23	261	0	ENST00000359995.5:c.390_425del	p.Ser132_Arg143del	p.S132_R143del	ENST00000359995	NM_001195427.1	130	tcCCGGAGTCGGAGTCGTTCCAGGTCTCGCAGCCGATCt/tct	2/3	0.388675771265794	3	FACETS	0.296	0.23	0.372	0.148	0.115	0.186	SUBCLONAL	1	TRUE	1	0.52648946870031	3		261	373	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941668	48941669	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025546-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	113	88	0	ENST00000267163.4:c.983dup	p.Asn328LysfsTer2	p.N328Kfs*2	ENST00000267163	NM_000321.2	326	-/A	10/27	0.52648946870031	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.52648946870031	1		88	277	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444666	78444666	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025546-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	136	507	0	ENST00000370768.2:c.23del	p.Pro8LeufsTer46	p.P8Lfs*46	ENST00000370768	NM_003902.3	8	cCt/ct	1/20	0.164153136408026	2	FACETS	0.732	0.666	0.8	0.366	0.333	0.4	INDETERMINATE	1	TRUE	0	0.52648946870031	2		507	706	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720717	89720717	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025546-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	88	63	0	ENST00000371953.3:c.868del	p.Val290Ter	p.V290*	ENST00000371953	NM_000314.4	290	Gta/ta	8/9	0.52648946870031	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.52648946870031	1		63	213	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426578	49426592	+	inframe_deletion	In_Frame_Del	DEL	CTGCTGCTGTTGAAA	CTGCTGCTGTTGAAA	-	rs1195849154	NA	P-0025546-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	426	809	0	ENST00000301067.7:c.11896_11910del	p.Phe3966_Gln3970del	p.F3966_Q3970del	ENST00000301067	NM_003482.3	3966	TTTCAACAGCAGCAG/-	39/54	0.197933681124059	3	FACETS	0.776	0.739	0.813	0.517	0.493	0.542	INDETERMINATE	2	TRUE	0	0.52648946870031	3		809	1317	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865120	57865120	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025546-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	540	847	1	ENST00000228682.2:c.2597C>A	p.Thr866Asn	p.T866N	ENST00000228682	NM_005269.2	866	aCc/aAc	12/12	0.197933681124059	3	FACETS	1	0.993	1	0.75	0.722	0.778	INDETERMINATE	2	TRUE	0	0.52648946870031	3		848	1152	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631604	119631604	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025546-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	61	202	1	ENST00000316626.5:c.662A>T	p.Tyr221Phe	p.Y221F	ENST00000316626		221	tAc/tTc	6/12	0.171524339753022	4	FACETS	0.665	0.574	0.764	0.166	0.143	0.191	INDETERMINATE	1	TRUE	0	0.52648946870031	4		203	532	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176940	56176940	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025546-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	68	152	0	ENST00000399503.3:c.2210T>A	p.Val737Asp	p.V737D	ENST00000399503	NM_005921.1	737	gTc/gAc	13/20	0.168174273108195	1	FACETS	0.489	0.427	0.555	0.489	0.427	0.555	INDETERMINATE	1	TRUE	0	0.52648946870031	1		152	389	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465563	8465563	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025546-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	176	347	0	ENST00000356435.5:c.3617G>T	p.Gly1206Val	p.G1206V	ENST00000356435		1206	gGg/gTg	21/35	0.248666821619923	3	FACETS	1	0.983	1	0.612	0.565	0.66	INDETERMINATE	1	TRUE	1	0.52648946870031	3		347	690	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197720	123197720	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025546-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	119	204	1	ENST00000218089.9:c.1844A>G	p.Gln615Arg	p.Q615R	ENST00000218089	NM_001042749.1	615	cAg/cGg	20/35	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.52648946870031	2		205	432	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52722992	52722992	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1362406458	NA	P-0025546-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	79	786	0	ENST00000322088.6:c.1177G>A	p.Glu393Lys	p.E393K	ENST00000322088	NM_014225.5	393	Gag/Aag	10/15	0.274894086880402	4	FACETS	0.415	0.364	0.471	0.208	0.182	0.236	INDETERMINATE	1	TRUE	2	0.52648946870031	4		786	1103	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271162	38271162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437821654	NA	P-0025546-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	75	691	0	ENST00000425967.3:c.2546G>A	p.Gly849Glu	p.G849E	ENST00000425967	NM_001174067.1	849	gGa/gAa	19/19	1	2	FACETS	0.372	0.326	0.423	0.372	0.326	0.423	SUBCLONAL	1	TRUE	1	0.52648946870031	2		691	765	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0025739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	234	482	0	ENST00000288602.6:c.1397G>T	p.Gly466Val	p.G466V	ENST00000288602	NM_004333.4	466	gGa/gTa	11/18	0.391769954068194	4	FACETS	0.952	0.896	1	0.952	0.896	1	CLONAL	3	TRUE	1	0.414915066573545	4		482	559	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430422	181430422	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	184	677	2	ENST00000325404.1:c.274G>T	p.Asp92Tyr	p.D92Y	ENST00000325404	NM_003106.3	92	Gac/Tac	1/1	0.205362196442286	2	FACETS	0.882	0.821	0.944	0.882	0.821	0.944	INDETERMINATE	2	TRUE	0	0.414915066573545	2		679	503	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346947	73346947	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	49	345	0	ENST00000377767.4:c.1270G>T	p.Gly424Ter	p.G424*	ENST00000377767	NM_014953.3	424	Gga/Tga	9/21	0.414915066573545	1	FACETS	0.755	0.645	0.873	0.755	0.645	0.873	SUBCLONAL	1	TRUE	0	0.414915066573545	1		345	248	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390201	89390201	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1167543166	NA	P-0025739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	37	368	0	ENST00000336596.2:c.950C>A	p.Pro317His	p.P317H	ENST00000336596	NM_005233.5	317	cCt/cAt	4/17	0.253889482223654	2	FACETS	0.433	0.357	0.518	0.216	0.178	0.259	SUBCLONAL	1	TRUE	0	0.414915066573545	2		368	412	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894934	101894934	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	79	399	0	ENST00000374994.4:c.487G>T	p.Asp163Tyr	p.D163Y	ENST00000374994	NM_004612.2	163	Gac/Tac	3/9	1	2	FACETS	0.962	0.851	1	0.962	0.851	1	CLONAL	1	TRUE	1	0.414915066573545	2		399	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0025739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	37	527	0	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.299432219155891	0	FACETS	0.278	0.229	0.333			1	SUBCLONAL	1	TRUE	0	0.414915066573545	0		527	375	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264360	30264360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	21	164	0	ENST00000322652.5:c.95C>T	p.Ala32Val	p.A32V	ENST00000322652	NM_015355.2	32	gCg/gTg	1/16	1	2	FACETS	0.511	0.395	0.645	0.511	0.395	0.645	SUBCLONAL	1	TRUE	1	0.414915066573545	2		164	198	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546326	46546326	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	63	444	0	ENST00000262741.5:c.203G>T	p.Gly68Val	p.G68V	ENST00000262741	NM_003629.3	68	gGg/gTg	2/10	1	2	FACETS	0.752	0.653	0.858	0.752	0.653	0.858	SUBCLONAL	1	TRUE	1	0.414915066573545	2		444	404	SUCCESS
FH	2271	MSKCC	GRCh37	1	241671911	241671911	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	31	470	0	ENST00000366560.3:c.730C>G	p.Leu244Val	p.L244V	ENST00000366560	NM_000143.3	244	Ctt/Gtt	5/10	0.21146372795508	3	FACETS	0.347	0.28	0.423	0.173	0.14	0.212	INDETERMINATE	1	TRUE	1	0.414915066573545	3		470	520	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941007	71941007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1179011278	NA	P-0025739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	59	912	1	ENST00000298229.2:c.883C>T	p.Pro295Ser	p.P295S	ENST00000298229	NM_001567.3	295	Cca/Tca	8/28	0.351978389573054	2	FACETS	0.403	0.346	0.465	0.201	0.173	0.233	SUBCLONAL	1	TRUE	0	0.414915066573545	2		913	706	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28624231	28624231	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1214984827	NA	P-0025739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	44	472	0	ENST00000241453.7:c.742+1G>T		p.X248_splice	ENST00000241453	NM_004119.2	248			0.414915066573545	1	FACETS	0.459	0.386	0.54	0.459	0.386	0.54	SUBCLONAL	1	TRUE	0	0.414915066573545	1		472	366	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81558891	81558891	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121908863	NA	P-0025739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	134	511	0	ENST00000298171.2:c.484C>A	p.Pro162Thr	p.P162T	ENST00000298171	NM_000369.2	162	Cct/Act	6/10	0.21146372795508	3	FACETS	0.791	0.723	0.861	0.791	0.723	0.861	INDETERMINATE	2	TRUE	1	0.414915066573545	3		511	493	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246696	41246696	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	52	498	0	ENST00000357654.3:c.852G>C	p.Gln284His	p.Q284H	ENST00000357654	NM_007294.3	284	caG/caC	10/23	1	2	FACETS	0.427	0.363	0.497	0.427	0.363	0.497	SUBCLONAL	1	TRUE	1	0.414915066573545	2		498	587	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214607	5214607	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1326918817	NA	P-0025739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	144	643	0	ENST00000357368.4:c.4459A>G	p.Ile1487Val	p.I1487V	ENST00000357368	NM_002850.3	1487	Atc/Gtc	29/38	0.414915066573545	1	FACETS	0.934	0.855	1	0.934	0.855	1	CLONAL	1	TRUE	0	0.414915066573545	1		643	589	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155386	99155386	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	30	523	0	ENST00000074304.5:c.612G>T	p.Glu204Asp	p.E204D	ENST00000074304	NM_001134224.1	204	gaG/gaT	9/26	1	2	FACETS	0.271	0.217	0.332	0.271	0.217	0.332	SUBCLONAL	1	TRUE	1	0.414915066573545	2		523	534	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739113	40739113	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	319	556	0	ENST00000373198.4:c.3171G>C	p.Glu1057Asp	p.E1057D	ENST00000373198	NM_133170.3	1057	gaG/gaC	24/32	0.414915066573545	3	FACETS	0.938	0.893	0.983	0.938	0.893	0.983	CLONAL	3	TRUE	0	0.414915066573545	3		556	660	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564533	41564533	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	42	564	0	ENST00000263253.7:c.3955G>C	p.Gly1319Arg	p.G1319R	ENST00000263253	NM_001429.3	1319	Gga/Cga	24/31	0.304514250716062	2	FACETS	0.332	0.276	0.394	0.166	0.138	0.197	SUBCLONAL	1	TRUE	0	0.414915066573545	2		564	610	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713741	30713742	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	33	461	0	ENST00000295754.5:c.1071dup	p.Ile358AspfsTer7	p.I358Dfs*7	ENST00000295754	NM_003242.5	356	cgg/cGgg	4/7	0.205362196442286	2	FACETS	0.388	0.316	0.469	0.194	0.158	0.235	INDETERMINATE	1	TRUE	0	0.414915066573545	2		461	410	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799503	72799503	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	64	692	0	ENST00000325599.8:c.1666A>G	p.Lys556Glu	p.K556E	ENST00000325599	NM_018130.2	556	Aag/Gag	11/11	0.205362196442286	2	FACETS	0.512	0.443	0.586	0.256	0.221	0.293	INDETERMINATE	1	TRUE	0	0.414915066573545	2		692	603	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957019	1957019	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	97	527	0	ENST00000382891.5:c.2470C>T	p.Arg824Ter	p.R824*	ENST00000382891	NM_133335.3	824	Cga/Tga	13/22	0.272294675697724	1	FACETS	0.727	0.65	0.807	0.727	0.65	0.807	SUBCLONAL	1	TRUE	0	0.414915066573545	1		527	510	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564574	55564574	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	146	624	0	ENST00000288135.5:c.462G>C	p.Lys154Asn	p.K154N	ENST00000288135	NM_000222.2	154	aaG/aaC	3/21	0.272294675697724	1	FACETS	0.975	0.894	1	0.975	0.894	1	CLONAL	1	TRUE	0	0.414915066573545	1		624	572	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31451746	31451746	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0025739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	68	295	0	ENST00000344624.3:c.2576del	p.His859LeufsTer3	p.H859Lfs*3	ENST00000344624		859	cAt/ct	18/33	1	2	FACETS	0.876	0.767	0.994	0.876	0.767	0.994	CLONAL	1	TRUE	1	0.414915066573545	2		295	374	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876395	35876395	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	43	579	0	ENST00000303115.3:c.1187A>G	p.Asn396Ser	p.N396S	ENST00000303115	NM_002185.3	396	aAt/aGt	8/8	1	2	FACETS	0.299	0.249	0.354	0.299	0.249	0.354	SUBCLONAL	1	TRUE	1	0.414915066573545	2		579	693	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853063	151853063	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	116	437	0	ENST00000262189.6:c.11892G>T	p.Gln3964His	p.Q3964H	ENST00000262189	NM_170606.2	3964	caG/caT	46/59	0.391769954068194	4	FACETS	1	0.977	1	0.424	0.383	0.467	CLONAL	1	TRUE	1	0.414915066573545	4		437	622	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992720	68992720	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	120	652	1	ENST00000288368.4:c.1685G>T	p.Arg562Leu	p.R562L	ENST00000288368	NM_024870.2	562	cGt/cTt	16/40	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.414915066573545	2		653	522	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868981	117868981	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	59	427	0	ENST00000297338.2:c.718G>T	p.Gly240Cys	p.G240C	ENST00000297338	NM_006265.2	240	Ggt/Tgt	7/14	1	2	FACETS	0.553	0.476	0.637	0.553	0.476	0.637	SUBCLONAL	1	TRUE	1	0.414915066573545	2		427	514	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742488	145742501	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCTGGCGGCTCC	GCCCTGGCGGCTCC	-	novel	NA	P-0025739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	43	718	0	ENST00000428558.2:c.287_300del	p.Arg96LeufsTer36	p.R96Lfs*36	ENST00000428558	NM_004260.3	96	cGGAGCCGCCAGGGC/c	4/22	1	2	FACETS	0.306	0.255	0.362	0.306	0.255	0.362	SUBCLONAL	1	TRUE	1	0.414915066573545	2		718	678	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486097	8486097	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	70	496	0	ENST00000356435.5:c.2720T>A	p.Met907Lys	p.M907K	ENST00000356435		907	aTg/aAg	17/35	1	2	FACETS	0.589	0.514	0.67	0.589	0.514	0.67	SUBCLONAL	1	TRUE	1	0.414915066573545	2		496	573	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106512	108106513	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0027224-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	64	412	0	ENST00000278616.4:c.447_448delinsAT	p.Leu150Phe	p.L150F	ENST00000278616	NM_000051.3	149	atTCtt/atATtt	5/63	0.411462407676401	2	FACETS	0.852	0.742	0.971	0.426	0.371	0.486	CLONAL	1	TRUE	0	0.411462407676401	2		412	365	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954337	48954337	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027224-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	103	390	0	ENST00000267163.4:c.1458A>T	p.Leu486Phe	p.L486F	ENST00000267163	NM_000321.2	486	ttA/ttT	16/27	0.411462407676401	3	FACETS	1	0.954	1	0.556	0.499	0.616	CLONAL	1	TRUE	1	0.411462407676401	3		390	543	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360646	70360646	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027224-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	75	357	0	ENST00000374080.3:c.6206A>C	p.Gln2069Pro	p.Q2069P	ENST00000374080		2069	cAa/cCa	42/45	0.395033690197882	3	FACETS	0.916	0.805	1	0.458	0.402	0.517	CLONAL	1	TRUE	1	0.411462407676401	3		357	480	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207162	1207162	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs137853076	NA	P-0027822-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	65	844	0	ENST00000326873.7:c.250A>T	p.Lys84Ter	p.K84*	ENST00000326873	NM_000455.4	84	Aag/Tag	1/10	1	2	FACETS	0.609	0.528	0.698	0.609	0.528	0.698	SUBCLONAL	1	TRUE	1	0.318445991527981	2		844	670	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218090	108218090	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027822-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	21	243	0	ENST00000278616.4:c.8669T>C	p.Leu2890Pro	p.L2890P	ENST00000278616	NM_000051.3	2890	cTa/cCa	59/63	1	2	FACETS	0.554	0.428	0.701	0.554	0.428	0.701	SUBCLONAL	1	TRUE	1	0.318445991527981	2		243	238	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664524	29664525	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0027822-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	104	497	0	ENST00000356175.3:c.6503_6504del	p.Pro2168ArgfsTer4	p.P2168Rfs*4	ENST00000356175	NM_000267.3	2168	cCT/c	42/57	0.318445991527981	3	FACETS	0.76	0.684	0.841	0.507	0.456	0.561	SUBCLONAL	2	TRUE	0	0.318445991527981	3		497	498	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17389792	17389792	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027822-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	61	994	0	ENST00000359435.4:c.925A>G	p.Ser309Gly	p.S309G	ENST00000359435	NM_001033549.1	309	Agc/Ggc	9/9	1	2	FACETS	0.563	0.485	0.647	0.563	0.485	0.647	SUBCLONAL	1	TRUE	1	0.318445991527981	2		994	681	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566759	212566759	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027822-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	32	381	0	ENST00000342788.4:c.1422G>T	p.Trp474Cys	p.W474C	ENST00000342788	NM_005235.2	474	tgG/tgT	12/28	1	2	FACETS	0.476	0.386	0.578	0.476	0.386	0.578	SUBCLONAL	1	TRUE	1	0.318445991527981	2		381	422	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0027898-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	50	836	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.240432222274597	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.240432222274597	1		836	305	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063335	67063368	+	frameshift_variant	Frame_Shift_Del	DEL	AGAAGCAAGTTCGAGAACGAGGAGTTTTTTAGGA	AGAAGCAAGTTCGAGAACGAGGAGTTTTTTAGGA	-	novel	NA	P-0027898-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	11	232	0	ENST00000412916.2:c.27_60del	p.Arg9SerfsTer2	p.R9Sfs*2	ENST00000412916		9	AGAAGCAAGTTCGAGAACGAGGAGTTTTTTAGGAag/ag	1/6	0.240432222274597	1	FACETS	0.383	0.265	0.531	0.383	0.265	0.531	SUBCLONAL	1	TRUE	0	0.240432222274597	1		232	210	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846076	68846076	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027898-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	47	387	0	ENST00000261769.5:c.1048del	p.Leu350PhefsTer6	p.L350Ffs*6	ENST00000261769	NM_004360.3	349	gaC/ga	8/16	0.240432222274597	1	FACETS	0.9	0.762	1	0.9	0.762	1	CLONAL	1	TRUE	0	0.240432222274597	1		387	382	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031120	11031120	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	63	650	0	ENST00000327064.4:c.1205T>A	p.Val402Glu	p.V402E	ENST00000327064	NM_199141.1	402	gTg/gAg	11/16	1	2	FACETS	0.206	0.177	0.237	0.206	0.177	0.237	SUBCLONAL	1	TRUE	1	0.854541286899741	2		650	717	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366187	15366187	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	140	634	0	ENST00000263377.2:c.1968del	p.Phe656LeufsTer4	p.F656Lfs*4	ENST00000263377	NM_058243.2	656	ttT/tt	10/20	1	2	FACETS	0.477	0.435	0.521	0.477	0.435	0.521	SUBCLONAL	1	TRUE	1	0.854541286899741	2		634	687	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164298	47164298	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	130	358	0	ENST00000409792.3:c.1828G>T	p.Glu610Ter	p.E610*	ENST00000409792	NM_014159.6	610	Gaa/Taa	3/21	0.157492739145347	2	FACETS	0.554	0.505	0.606	0.277	0.252	0.303	INDETERMINATE	1	TRUE	0	0.854541286899741	2		358	549	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593648	55593649	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACCCAACACAACTTCCTTATGATC	novel	NA	P-0030447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	174	537	0	ENST00000288135.5:c.1717_1740dup	p.Pro573_His580dup	p.P573_H580dup	ENST00000288135	NM_000222.2	573	gac/gACCCAACACAACTTCCTTATGATCac	11/21	1	2	FACETS	0.534	0.493	0.578	0.534	0.493	0.578	SUBCLONAL	1	TRUE	1	0.854541286899741	2		537	762	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	81	386	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.197958496180069	3	FACETS	1	0.977	1	0.7	0.624	0.779	INDETERMINATE	1	TRUE	1	0.516248363395545	3		386	282	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	16	329	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.399275612897023	1	FACETS	0.568	0.428	0.727	0.568	0.428	0.727	SUBCLONAL	1	TRUE	0	0.516248363395545	1		329	81	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248773	212248773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	23	237	0	ENST00000342788.4:c.3494C>T	p.Pro1165Leu	p.P1165L	ENST00000342788	NM_005235.2	1165	cCa/cTa	28/28	1	2	FACETS	0.882	0.702	1	0.882	0.702	1	CLONAL	1	TRUE	1	0.516248363395545	2		237	101	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	94	547	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.516248363395545	2		547	299	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	55	496	4	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.679	0.584	0.781	0.679	0.584	0.781	SUBCLONAL	1	TRUE	1	0.516248363395545	2		500	314	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	28	538	8	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.516248363395545	2		546	101	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	44	285	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.399275612897023	1	FACETS	0.626	0.531	0.728	0.626	0.531	0.728	SUBCLONAL	1	TRUE	0	0.516248363395545	1		285	202	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	125	888	3	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.516248363395545	2		891	448	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	51	397	3	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	NA	2	FACETS	0.827	0.71	0.952			1	INDETERMINATE	1	TRUE	NA	0.516248363395545	2		400	239	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	155	473	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.967	1	1	0.993	1	CLONAL	2	TRUE	1	0.516248363395545	2		478	285	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123788	11123788	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1064795105	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	96	508	0	ENST00000358026.2:c.2438C>T	p.Ser813Leu	p.S813L	ENST00000358026	NM_001128849.1	813	tCa/tTa	16/36	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.516248363395545	2		508	314	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806180	1806181	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760502257	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	107	898	1	ENST00000260795.2:c.1206dup	p.Lys403GlnfsTer93	p.K403Qfs*93	ENST00000260795		400	agc/agCc	8/17	1	2	FACETS	0.992	0.896	1	0.992	0.896	1	CLONAL	1	TRUE	1	0.516248363395545	2		899	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579439	7579439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201717599	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	140	769	1	ENST00000269305.4:c.248C>T	p.Ala83Val	p.A83V	ENST00000269305	NM_001126112.2	83	gCg/gTg	4/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.516248363395545	2		770	523	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199945	138199945	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	77	468	1	ENST00000237289.4:c.1368del	p.Pro457LeufsTer20	p.P457Lfs*20	ENST00000237289	NM_001270507.1	455	Ggg/gg	7/9	0.133128013348729	4	FACETS	1	0.926	1	0.535	0.471	0.602	INDETERMINATE	1	TRUE	2	0.516248363395545	4		469	423	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783347	9783347	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148984508	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	100	574	0	ENST00000377346.4:c.2591C>T	p.Pro864Leu	p.P864L	ENST00000377346	NM_005026.3	864	cCg/cTg	20/24	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.516248363395545	2		574	353	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319965	8319965	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs141403124	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	35	225	0	ENST00000356435.5:c.5536G>A	p.Ala1846Thr	p.A1846T	ENST00000356435		1846	Gcg/Acg	34/35	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.516248363395545	2		225	111	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	84	436	2	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.925	0.823	1	0.925	0.823	1	CLONAL	1	TRUE	1	0.516248363395545	2		438	352	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916730	178916730	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	37	340	0	ENST00000263967.3:c.117G>T	p.Glu39Asp	p.E39D	ENST00000263967	NM_006218.2	39	gaG/gaT	2/21	0.516248363395545	2	FACETS	1	0.92	1	0.578	0.487	0.675	CLONAL	1	TRUE	0	0.516248363395545	2		340	124	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800902	120800903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748469666	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	136	759	4	ENST00000257552.2:c.345dup	p.Leu116AlafsTer15	p.L116Afs*15	ENST00000257552	NM_002442.3	115	-/G	6/15	0.399275612897023	1	FACETS	0.759	0.694	0.826	0.759	0.694	0.826	SUBCLONAL	1	TRUE	0	0.516248363395545	1		763	515	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	351	885	1	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	0.144973636921636	4	FACETS	1	0.973	1	1	0.996	1	INDETERMINATE	3	TRUE	2	0.516248363395545	4		886	671	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953115	81953115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1336595726	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	69	342	0	ENST00000359376.3:c.2081G>A	p.Arg694His	p.R694H	ENST00000359376	NM_002661.3	694	cGc/cAc	20/33	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.516248363395545	2		342	254	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458270	12458270	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	100	501	0	ENST00000287820.6:c.892del	p.Leu298CysfsTer38	p.L298Cfs*38	ENST00000287820	NM_015869.4	296	aCc/ac	6/7	0.516248363395545	2	FACETS	0.95	0.854	1	0.475	0.427	0.525	CLONAL	1	TRUE	0	0.516248363395545	2		501	408	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366987	40366987	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	154	856	1	ENST00000397332.2:c.210del	p.Thr71ArgfsTer69	p.T71Rfs*69	ENST00000397332	NM_001033082.2	70	ccC/cc	2/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.516248363395545	2		857	530	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223175	36223175	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	180	1039	1	ENST00000222270.7:c.5730del	p.Arg1911AspfsTer23	p.R1911Dfs*23	ENST00000222270	NM_014727.1	1909	Ccc/cc	28/37	1	2	FACETS	0.961	0.888	1	0.961	0.888	1	CLONAL	1	TRUE	1	0.516248363395545	2		1040	726	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99452077	99452077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1441621301	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	90	370	0	ENST00000268035.6:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000268035	NM_000875.3	471	Cgc/Tgc	6/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.516248363395545	2		370	273	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027436	48027436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750138	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	41	394	0	ENST00000234420.5:c.2314C>T	p.Arg772Trp	p.R772W	ENST00000234420	NM_000179.2	772	Cgg/Tgg	4/10	1	2	FACETS	0.79	0.666	0.925	0.79	0.666	0.925	CLONAL	1	TRUE	1	0.516248363395545	2		394	201	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133968	41133968	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767908809	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	29	561	1	ENST00000379561.5:c.1660C>T	p.Arg554Cys	p.R554C	ENST00000379561	NM_002015.3	554	Cgc/Tgc	2/3	1	2	FACETS	0.304	0.244	0.373	0.304	0.244	0.373	SUBCLONAL	1	TRUE	1	0.516248363395545	2		562	369	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022998	27022999	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	21	49	0	ENST00000324856.7:c.110dup	p.Glu38ArgfsTer73	p.E38Rfs*73	ENST00000324856	NM_006015.4	35	gcg/gcGg	1/20	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.516248363395545	2		49	64	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467774	50467774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148169768	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	23	573	1	ENST00000331340.3:c.1009G>A	p.Gly337Ser	p.G337S	ENST00000331340	NM_006060.4	337	Ggt/Agt	8/8	1	2	FACETS	0.236	0.184	0.297	0.236	0.184	0.297	SUBCLONAL	1	TRUE	1	0.516248363395545	2		574	377	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100452	8100452	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	149	924	2	ENST00000346208.3:c.431del	p.Gly144AlafsTer51	p.G144Afs*51	ENST00000346208		142	tcG/tc	3/6	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.516248363395545	2		926	513	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006636	62006636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369201285	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	86	701	4	ENST00000392795.3:c.643C>T	p.Arg215Trp	p.R215W	ENST00000392795	NM_001039933.1	215	Cgg/Tgg	6/6	1	2	FACETS	0.893	0.796	0.996	0.893	0.796	0.996	CLONAL	1	TRUE	1	0.516248363395545	2		705	373	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59820423	59820423	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747568830	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	69	416	0	ENST00000259008.2:c.2330G>A	p.Arg777His	p.R777H	ENST00000259008	NM_032043.2	777	cGt/cAt	16/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.516248363395545	2		416	238	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923438	9923438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	79	568	1	ENST00000330684.3:c.1849G>A	p.Val617Met	p.V617M	ENST00000330684	NM_001134407.1	617	Gtg/Atg	9/13	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.516248363395545	2		569	297	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905545	50905545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763249087	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	130	973	1	ENST00000440232.2:c.673C>T	p.Arg225Cys	p.R225C	ENST00000440232	NM_002691.3	225	Cgt/Tgt	6/27	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.516248363395545	2		974	490	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112472	115112472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145432134	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	185	735	0	ENST00000257566.3:c.1268G>A	p.Arg423Gln	p.R423Q	ENST00000257566	NM_016569.3	423	cGg/cAg	7/8	0.399275612897023	1	FACETS	0.969	0.901	1	0.969	0.901	1	CLONAL	1	TRUE	0	0.516248363395545	1		735	549	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740393	145740393	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762113412	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	188	943	0	ENST00000428558.2:c.1547C>T	p.Ala516Val	p.A516V	ENST00000428558	NM_004260.3	516	gCg/gTg	9/22	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.516248363395545	2		943	605	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699457	117699457	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	103	449	0	ENST00000369458.3:c.184A>G	p.Ile62Val	p.I62V	ENST00000369458	NM_024626.3	62	Atc/Gtc	3/6	0.516248363395545	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.516248363395545	1		449	213	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741628	17741628	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	106	535	1	ENST00000250003.3:c.299C>T	p.Ala100Val	p.A100V	ENST00000250003	NM_002478.4	100	gCg/gTg	1/3	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.516248363395545	2		536	284	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988629	41988629	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	41	436	0	ENST00000219905.7:c.1421G>A	p.Cys474Tyr	p.C474Y	ENST00000219905	NM_001164273.1	474	tGt/tAt	3/24	1	2	FACETS	0.918	0.776	1	0.918	0.776	1	CLONAL	1	TRUE	1	0.516248363395545	2		436	173	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003375	42003375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762161367	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	72	375	0	ENST00000219905.7:c.2912G>A	p.Arg971Gln	p.R971Q	ENST00000219905	NM_001164273.1	971	cGg/cAg	8/24	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.516248363395545	2		375	274	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720366	43720366	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	90	551	0	ENST00000382044.4:c.3676G>A	p.Gly1226Arg	p.G1226R	ENST00000382044	NM_001141980.1	1226	Gga/Aga	18/28	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.516248363395545	2		551	266	SUCCESS
BLM	641	MSKCC	GRCh37	15	91337570	91337570	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	32	267	0	ENST00000355112.3:c.3193A>G	p.Asn1065Asp	p.N1065D	ENST00000355112	NM_000057.2	1065	Aat/Gat	16/22	1	2	FACETS	0.79	0.649	0.943	0.79	0.649	0.943	CLONAL	1	TRUE	1	0.516248363395545	2		267	157	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639812	3639812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756389198	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	154	871	0	ENST00000294008.3:c.3827G>A	p.Ser1276Asn	p.S1276N	ENST00000294008	NM_032444.2	1276	aGc/aAc	12/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.516248363395545	2		871	500	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829688	72829688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	99	722	0	ENST00000268489.5:c.6893G>A	p.Arg2298Lys	p.R2298K	ENST00000268489	NM_006885.3	2298	aGg/aAg	9/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.516248363395545	2		722	309	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346141	89346141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1045721935	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	31	382	0	ENST00000301030.4:c.6809C>T	p.Ala2270Val	p.A2270V	ENST00000301030	NM_001256183.1	2270	gCc/gTc	9/13	1	2	FACETS	0.938	0.773	1	0.938	0.773	1	CLONAL	1	TRUE	1	0.516248363395545	2		382	128	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119902	70119902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1414403898	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	67	650	2	ENST00000245479.2:c.904G>A	p.Gly302Ser	p.G302S	ENST00000245479	NM_000346.3	302	Ggc/Agc	3/3	1	2	FACETS	0.503	0.438	0.574	0.503	0.438	0.574	SUBCLONAL	1	TRUE	1	0.516248363395545	2		652	516	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611797	1611797	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	191	902	0	ENST00000344749.5:c.1865A>G	p.Lys622Arg	p.K622R	ENST00000344749	NM_001136139.2	622	aAg/aGg	19/19	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.516248363395545	2		902	641	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7123000	7123000	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	116	718	0	ENST00000302850.5:c.3259G>A	p.Val1087Met	p.V1087M	ENST00000302850	NM_000208.2	1087	Gtg/Atg	18/22	1	2	FACETS	0.96	0.871	1	0.96	0.871	1	CLONAL	1	TRUE	1	0.516248363395545	2		718	468	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47205399	47205404	+	inframe_deletion	In_Frame_Del	DEL	GCTGCA	GCTGCA	-	novel	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	99	497	0	ENST00000409792.3:c.11_16del	p.Leu4_Gln5del	p.L4_Q5del	ENST00000409792	NM_014159.6	4	cTGCAGCcg/ccg	1/21	0.516248363395545	2	FACETS	0.764	0.685	0.848	0.382	0.342	0.424	SUBCLONAL	1	TRUE	0	0.516248363395545	2		497	502	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928054	49928054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	45	620	3	ENST00000296474.3:c.3674C>T	p.Ala1225Val	p.A1225V	ENST00000296474	NM_002447.2	1225	gCt/gTt	18/20	0.516248363395545	2	FACETS	0.42	0.353	0.494	0.21	0.176	0.247	SUBCLONAL	1	TRUE	0	0.516248363395545	2		623	415	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102878	71102878	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	122	368	0	ENST00000318789.4:c.329A>G	p.Gln110Arg	p.Q110R	ENST00000318789	NM_032682.5	110	cAg/cGg	8/21	0.516248363395545	2	FACETS	1	0.98	1	0.635	0.58	0.692	CLONAL	1	TRUE	0	0.516248363395545	2		368	372	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902558	1902558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	135	799	0	ENST00000382891.5:c.181del	p.Val61SerfsTer19	p.V61Sfs*19	ENST00000382891	NM_133335.3	59	gaG/ga	2/22	1	2	FACETS	0.96	0.876	1	0.96	0.876	1	CLONAL	1	TRUE	1	0.516248363395545	2		799	545	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233123	66233123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1288176462	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	58	437	0	ENST00000273854.3:c.1876G>A	p.Ala626Thr	p.A626T	ENST00000273854	NM_004439.5	626	Gca/Aca	10/18	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.516248363395545	2		437	222	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515215	31515215	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	100	842	2	ENST00000344624.3:c.1170del	p.Glu391SerfsTer87	p.E391Sfs*87	ENST00000344624		390	aaA/aa	5/33	0.241040189870342	0	FACETS	0.412	0.37	0.456			1	INDETERMINATE	1	TRUE	0	0.516248363395545	0		844	455	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189499	56189499	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	46	349	0	ENST00000399503.3:c.4531A>G	p.Thr1511Ala	p.T1511A	ENST00000399503	NM_005921.1	1511	Aca/Gca	20/20	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.516248363395545	2		349	173	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066437	94066437	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	21	186	0	ENST00000369303.4:c.1322C>T	p.Ala441Val	p.A441V	ENST00000369303	NM_004440.3	441	gCa/gTa	5/17	1	2	FACETS	0.856	0.673	1	0.856	0.673	1	CLONAL	1	TRUE	1	0.516248363395545	2		186	95	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975350	13975350	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	73	469	1	ENST00000405192.2:c.537C>A	p.Ser179Arg	p.S179R	ENST00000405192	NM_001163147.1	179	agC/agA	7/12	1	2	FACETS	0.918	0.81	1	0.918	0.81	1	CLONAL	1	TRUE	1	0.516248363395545	2		470	308	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151871274	151871274	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	59	410	0	ENST00000262189.6:c.9316G>T	p.Gly3106Cys	p.G3106C	ENST00000262189	NM_170606.2	3106	Ggt/Tgt	39/59	1	2	FACETS	0.964	0.84	1	0.964	0.84	1	CLONAL	1	TRUE	1	0.516248363395545	2		410	237	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194907	29194907	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	188	837	1	ENST00000240100.2:c.821G>T	p.Gly274Val	p.G274V	ENST00000240100	NM_001394.6	274	gGg/gTg	4/4	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.516248363395545	2		838	609	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738044	145738044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	164	915	0	ENST00000428558.2:c.2866C>T	p.Leu956Phe	p.L956F	ENST00000428558	NM_004260.3	956	Ctc/Ttc	17/22	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.516248363395545	2		915	582	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507345	8507345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	31	341	0	ENST00000356435.5:c.1633G>A	p.Ala545Thr	p.A545T	ENST00000356435		545	Gcc/Acc	11/35	1	2	FACETS	0.6	0.49	0.724	0.6	0.49	0.724	SUBCLONAL	1	TRUE	1	0.516248363395545	2		341	200	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239939	98239939	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	77	420	0	ENST00000331920.6:c.1393T>C	p.Ser465Pro	p.S465P	ENST00000331920	NM_000264.3	465	Tcc/Ccc	10/24	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.516248363395545	2		420	277	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245720	46245720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030967-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	233	429	2	ENST00000334344.6:c.3814C>T	p.Arg1272Ter	p.R1272*	ENST00000334344	NM_152641.2	1272	Cga/Tga	15/21	0.802350808200386	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.84862984278688	1		431	308	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533078	63533078	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030967-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	322	783	2	ENST00000307078.5:c.1816C>A	p.Leu606Met	p.L606M	ENST00000307078	NM_004655.3	606	Ctg/Atg	7/11	0.164195227111312	3	FACETS	1	0.994	1	0.674	0.639	0.709	INDETERMINATE	1	TRUE	1	0.84862984278688	3		785	802	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106385	27106386	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0030967-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	309	537	2	ENST00000324856.7:c.5996_5997insC	p.Glu2000Ter	p.E2000*	ENST00000324856	NM_006015.4	1999	ttt/ttCt	20/20	0.802350808200386	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.84862984278688	1		539	396	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356193	66356193	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030967-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	267	564	2	ENST00000273854.3:c.1304C>G	p.Thr435Arg	p.T435R	ENST00000273854	NM_004439.5	435	aCa/aGa	5/18	0.84862984278688	1	FACETS	0.984	0.946	1	0.984	0.946	1	CLONAL	1	TRUE	0	0.84862984278688	1		566	368	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628915	187628915	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030967-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	46	590	0	ENST00000441802.2:c.2067G>T	p.Gln689His	p.Q689H	ENST00000441802	NM_005245.3	689	caG/caT	2/27	NA	2	FACETS	0.151	0.127	0.178			1	INDETERMINATE	1	TRUE	NA	0.84862984278688	2		590	717	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945719	17945719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140655992	NA	P-0031583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	250	1388	2	ENST00000458235.1:c.2141C>T	p.Thr714Met	p.T714M	ENST00000458235	NM_000215.3	714	aCg/aTg	16/24	0.467194732686642	3	FACETS	0.97	0.905	1	0.485	0.452	0.518	CLONAL	1	TRUE	1	0.494338756704782	3		1390	1301	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578565	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTACTGTAGGAAGA	AGTACTGTAGGAAGA	-	novel	NA	P-0031583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	426	1218	0	ENST00000269305.4:c.376-11_379del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	0.37393638855577	3	FACETS	1	0.99	1	0.744	0.712	0.776	CLONAL	2	TRUE	0	0.494338756704782	3		1218	963	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413009	49413009	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519953	NA	P-0031583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	230	943	1	ENST00000418115.1:c.14G>T	p.Arg5Leu	p.R5L	ENST00000418115	NM_001664.2	5	cGg/cTg	2/5	0.494338756704782	3	FACETS	1	0.98	1	0.376	0.35	0.403	CLONAL	1	TRUE	0	0.494338756704782	3		944	1028	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502855	186502856	+	inframe_insertion	In_Frame_Ins	INS	-	-	TAG	novel	NA	P-0031583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	186	810	0	ENST00000323963.5:c.316_318dup	p.Val106dup	p.V106dup	ENST00000323963		106	cta/cTAGta	4/11	0.494338756704782	3	FACETS	1	0.933	1	0.337	0.311	0.364	CLONAL	1	TRUE	0	0.494338756704782	3		810	929	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0032790-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	329	470	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.86423344645921	4	FACETS	0.988	0.942	1	0.988	0.942	1	CLONAL	2	FALSE	2	0.962028896368068	4		470	679	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105841	27105841	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032790-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	362	583	0	ENST00000324856.7:c.5452C>T	p.Gln1818Ter	p.Q1818*	ENST00000324856	NM_006015.4	1818	Cag/Tag	20/20	0.54263234971873	6	FACETS	0.896	0.854	0.938	0.896	0.854	0.938	INDETERMINATE	3	FALSE	3	0.962028896368068	6		583	819	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28934577	NA	P-0032790-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	516	683	0	ENST00000269305.4:c.770T>C	p.Leu257Pro	p.L257P	ENST00000269305	NM_001126112.2	257	cTg/cCg	7/11	0.922130998275902	2	FACETS	0.968	0.954	0.981	0.968	0.954	0.981	CLONAL	2	FALSE	0	0.962028896368068	2		683	554	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152357845	152357845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032790-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	419	443	0	ENST00000359321.1:c.62G>A	p.Arg21Lys	p.R21K	ENST00000359321	NM_005431.1	21	aGa/aAa	2/3	0.916326390583821	2	FACETS	0.977	0.961	0.99	0.977	0.961	0.99	CLONAL	2	FALSE	0	0.962028896368068	2		443	446	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416064	49416064	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032790-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	561	736	0	ENST00000301067.7:c.16411A>G	p.Arg5471Gly	p.R5471G	ENST00000301067	NM_003482.3	5471	Agg/Ggg	52/54	0.86423344645921	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	FALSE	2	0.962028896368068	4		736	1039	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467644	66467644	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032790-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	415	449	0	ENST00000273854.3:c.625G>T	p.Gly209Ter	p.G209*	ENST00000273854	NM_004439.5	209	Gga/Tga	3/18	0.924831763711828	2	FACETS	0.967	0.951	0.982	0.967	0.951	0.982	CLONAL	2	FALSE	0	0.962028896368068	2		449	446	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0034103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	272	761	0	ENST00000269305.4:c.560-1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.586091389827221	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.586091389827221	1		761	530	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665044	29665044	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	258	474	0	ENST00000356175.3:c.6645del	p.Phe2215LeufsTer29	p.F2215Lfs*29	ENST00000356175	NM_000267.3	2215	Ttt/tt	44/57	0.586091389827221	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.586091389827221	1		474	499	SUCCESS
AR	367	MSKCC	GRCh37	X	66942744	66942744	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	29	437	0	ENST00000374690.3:c.2525T>A	p.Ile842Asn	p.I842N	ENST00000374690	NM_000044.3	842	aTc/aAc	7/8	0.524260149110803	1	FACETS	0.195	0.156	0.239	0.195	0.156	0.239	SUBCLONAL	1	TRUE	0	0.586091389827221	1		437	359	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577525	7577527	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0034914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	211	690	0	ENST00000269305.4:c.754_756del	p.Leu252del	p.L252del	ENST00000269305	NM_001126112.2	252	CTC/-	7/11	0.163143874364522	2	FACETS	1	0.983	1	0.6	0.556	0.645	INDETERMINATE	1	TRUE	0	0.287507053557593	2		690	1224	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120460335	120460335	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	90	554	0	ENST00000256646.2:c.5980C>G	p.Leu1994Val	p.L1994V	ENST00000256646	NM_024408.3	1994	Ctt/Gtt	33/34	0.163143874364522	2	FACETS	0.685	0.607	0.769	0.342	0.303	0.385	INDETERMINATE	1	TRUE	0	0.287507053557593	2		554	914	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431975	121431975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	201	845	0	ENST00000257555.6:c.722G>A	p.Cys241Tyr	p.C241Y	ENST00000257555		241	tGc/tAc	4/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.287507053557593	2		845	991	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028610	42028610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761482641	NA	P-0035107-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	72	684	0	ENST00000219905.7:c.4148G>A	p.Arg1383Gln	p.R1383Q	ENST00000219905	NM_001164273.1	1383	cGg/cAg	13/24	1	2	FACETS	0.678	0.593	0.77	0.678	0.593	0.77	SUBCLONAL	1	TRUE	1	0.348155261309872	2		684	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578476	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0035107-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	181	1045	0	ENST00000269305.4:c.454_455del	p.Pro152AlafsTer28	p.P152Afs*28	ENST00000269305	NM_001126112.2	152	CCg/g	5/11	0.348155261309872	1	FACETS	0.911	0.84	0.984	0.911	0.84	0.984	CLONAL	1	TRUE	0	0.348155261309872	1		1045	943	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593648	55593649	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACCCAACACAACTTCCTTATGATC	novel	NA	P-0035148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	107	537	0	ENST00000288135.5:c.1717_1740dup	p.Pro573_His580dup	p.P573_H580dup	ENST00000288135	NM_000222.2	573	gac/gACCCAACACAACTTCCTTATGATCac	11/21	1	2	FACETS	0.49	0.44	0.542	0.49	0.44	0.542	SUBCLONAL	1	TRUE	1	0.771910262955171	2		537	566	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743763	46743763	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	224	684	0	ENST00000371975.4:c.2053G>C	p.Val685Leu	p.V685L	ENST00000371975	NM_003579.3	685	Gtc/Ctc	18/18	0.771910262955171	1	FACETS	0.895	0.848	0.942	0.895	0.848	0.942	CLONAL	1	TRUE	0	0.771910262955171	1		684	398	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560495	65560495	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	218	561	0	ENST00000358664.4:c.102del	p.Lys34AsnfsTer31	p.K34Nfs*31	ENST00000358664	NM_002382.4	34	aaA/aa	3/5	0.771910262955171	1	FACETS	0.935	0.886	0.983	0.935	0.886	0.983	CLONAL	1	TRUE	0	0.771910262955171	1		561	371	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077589	30077589	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	13	319	0	ENST00000338641.4:c.1736A>T	p.Lys579Met	p.K579M	ENST00000338641	NM_000268.3	579	aAg/aTg	15/16	0.771910262955171	1	FACETS	0.096	0.068	0.13	0.096	0.068	0.13	SUBCLONAL	1	TRUE	0	0.771910262955171	1		319	216	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059132	47059132	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	197	505	0	ENST00000409792.3:c.7529G>T	p.Arg2510Leu	p.R2510L	ENST00000409792	NM_014159.6	2510	cGc/cTc	20/21	0.771910262955171	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.771910262955171	1		505	306	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599341	55599341	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	162	527	1	ENST00000288135.5:c.2467T>A	p.Tyr823Asn	p.Y823N	ENST00000288135	NM_000222.2	823	Tat/Aat	17/21	1	2	FACETS	0.945	0.876	1	0.945	0.876	1	CLONAL	1	TRUE	1	0.771910262955171	2		528	444	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035168-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	77	276	0				ENST00000310581	NM_198253.2	-/1132			0.168171145156367	3	FACETS	1	0.965	1	0.606	0.54	0.675	INDETERMINATE	1	TRUE	1	0.731671008095779	3		276	237	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0035168-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	131	239	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.731671008095779	2		239	332	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412252	139412252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057523819	NA	P-0035168-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	282	842	6	ENST00000277541.6:c.1393G>A	p.Ala465Thr	p.A465T	ENST00000277541	NM_017617.3	465	Gcc/Acc	8/34	0.359787000937147	2	FACETS	1	0.968	1	0.518	0.489	0.547	INDETERMINATE	1	TRUE	0	0.731671008095779	2		848	744	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692895	89692895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781255	NA	P-0035168-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	69	305	0	ENST00000371953.3:c.379G>A	p.Gly127Arg	p.G127R	ENST00000371953	NM_000314.4	127	Gga/Aga	5/9	1	2	FACETS	0.387	0.338	0.44	0.387	0.338	0.44	SUBCLONAL	1	TRUE	1	0.731671008095779	2		305	487	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793165	42793165	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1135401823	NA	P-0035168-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	153	859	1	ENST00000575354.2:c.1057C>T	p.Arg353Ter	p.R353*	ENST00000575354	NM_015125.3	353	Cga/Tga	7/20	0.731671008095779	1	FACETS	0.554	0.51	0.598	0.554	0.51	0.598	SUBCLONAL	1	TRUE	0	0.731671008095779	1		860	479	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058054	27058054	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035168-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	86	448	0	ENST00000324856.7:c.1762C>T	p.Gln588Ter	p.Q588*	ENST00000324856	NM_006015.4	588	Cag/Tag	3/20	0.731671008095779	1	FACETS	0.463	0.413	0.515	0.463	0.413	0.515	SUBCLONAL	1	TRUE	0	0.731671008095779	1		448	322	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182068	11182068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035168-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	98	645	0	ENST00000361445.4:c.6778C>T	p.Leu2260Phe	p.L2260F	ENST00000361445	NM_004958.3	2260	Ctt/Ttt	48/58	0.731671008095779	1	FACETS	0.501	0.451	0.553	0.501	0.451	0.553	SUBCLONAL	1	TRUE	0	0.731671008095779	1		645	339	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555730	21555730	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035168-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	142	713	0	ENST00000382592.4:c.2540A>G	p.Asn847Ser	p.N847S	ENST00000382592	NM_014572.2	847	aAc/aGc	6/8	NA	2	FACETS	0.588	0.537	0.641			1	INDETERMINATE	1	TRUE	NA	0.731671008095779	2		713	660	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434524	121434524	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035168-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	126	754	0	ENST00000257555.6:c.1288G>C	p.Gly430Arg	p.G430R	ENST00000257555		430	Ggt/Cgt	6/10	0.359787000937147	2	FACETS	0.541	0.491	0.593	0.27	0.245	0.297	INDETERMINATE	1	TRUE	0	0.731671008095779	2		754	637	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514571	103514571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035168-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	45	322	0	ENST00000355739.4:c.1072G>A	p.Glu358Lys	p.E358K	ENST00000355739	NM_000123.3	358	Gaa/Aaa	8/15	0.121812297381659	4	FACETS	0.593	0.5	0.696	0.297	0.25	0.348	INDETERMINATE	1	TRUE	2	0.731671008095779	4		322	359	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714325	43714325	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0035168-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	80	364	0	ENST00000382044.4:c.3829-1G>A		p.X1277_splice	ENST00000382044	NM_001141980.1	1277			1	2	FACETS	0.498	0.44	0.56	0.498	0.44	0.56	SUBCLONAL	1	TRUE	1	0.731671008095779	2		364	439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0035466-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	310	866	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.487931591566442	2	FACETS	0.828	0.785	0.871	0.828	0.785	0.871	CLONAL	2	TRUE	0	0.49995705738948	2		867	749	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0035466-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	130	455	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.49995705738948	6	FACETS	1	0.974	1	0.301	0.273	0.331	CLONAL	1	TRUE	2	0.49995705738948	6		455	863	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641180	3641180	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035466-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	489	1096	0	ENST00000294008.3:c.2459G>C	p.Arg820Thr	p.R820T	ENST00000294008	NM_032444.2	820	aGg/aCg	12/15	0.49995705738948	5	FACETS	1	0.984	1	0.708	0.676	0.74	CLONAL	2	TRUE	2	0.49995705738948	5		1096	1612	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022653	36022653	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035466-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	184	827	0	ENST00000358208.4:c.526C>G	p.Leu176Val	p.L176V	ENST00000358208		176	Ctc/Gtc	5/12	0.204500017189892	3	FACETS	1	0.982	1	0.601	0.555	0.647	INDETERMINATE	1	TRUE	1	0.49995705738948	3		827	766	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905275	50905275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035466-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	203	1265	1	ENST00000440232.2:c.483G>A	p.Met161Ile	p.M161I	ENST00000440232	NM_002691.3	161	atG/atA	5/27	0.44655358552581	2	FACETS	0.993	0.922	1	0.496	0.461	0.533	CLONAL	1	TRUE	0	0.49995705738948	2		1266	818	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0035547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	24	570	2	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.675083242242326	1	FACETS	0.961	0.797	1	0.961	0.797	1	CLONAL	1	TRUE	0	0.675083242242326	1		572	49	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0035547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	40	464	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.287291925757759	3	FACETS	1	0.956	1	0.695	0.593	0.802	INDETERMINATE	1	TRUE	1	0.675083242242326	3		464	114	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584709	48584709	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0035547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	27	332	0	ENST00000342988.3:c.788-1G>C		p.X263_splice	ENST00000342988	NM_005359.5	263			0.663974550414606	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.675083242242326	1		332	36	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203722	94203723	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0035768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	72	305	0	ENST00000323929.3:c.931_932delinsTT	p.Asp311Phe	p.D311F	ENST00000323929	NM_005591.3	311	GAt/TTt	9/20	0.529754414801999	4	FACETS	0.887	0.779	1	0.443	0.389	0.501	CLONAL	1	TRUE	2	0.719783056587692	4		305	388	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856595	111856595	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	43	126	0	ENST00000341259.2:c.646C>A	p.Arg216Ser	p.R216S	ENST00000341259	NM_005475.2	216	Cgc/Agc	2/8	0.712995640786272	3	FACETS	1	0.96	1	0.694	0.597	0.796	CLONAL	1	TRUE	1	0.719783056587692	3		126	117	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33446185	33446185	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	133	555	0	ENST00000345365.6:c.89A>C	p.Asp30Ala	p.D30A	ENST00000345365	NM_002878.3	30	gAc/gCc	2/10	0.677670092379544	4	FACETS	0.878	0.798	0.961	0.293	0.266	0.321	CLONAL	1	TRUE	1	0.719783056587692	4		555	724	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057049	180057754	+	splice_acceptor_variant,splice_donor_variant,frameshift_variant,stop_lost,intron_variant	Splice_Site	DEL	GCCCCGCCGGTCATCCCACACCACCTCCTGCCCGTCTGGCCACAGCACCGAGCTTTGCTGGAGGGACAAGGCCACCATCATTGCCCAGCTGCCCCTTGCTCCTGGCCAGACAGGCGGCCGCCTTTCCCAGGGGTGGGATGGGAGGGTCGGATGCTGGGGTTGGGGTGGGGCCGTACCGAGCGCAGCGTGACATTGAGGCCGGGGATGGACACCAGACAGGGCACCCACATGGCGTCCTTCCTGTTGACCAAGAGCGTGTCAGGCTTGTTGATGAATGGCTGCTCAAAGTCTATGGAGAGGGAGCAAGCTGTTGGGGAAGGGACGTGGCGGCCAGGCTGGGGGAGGGCTCCACGGGGCTGGGTGGTGCTGGTCCTGAACCAGCCACCCGCTGGAGCAGGTAGGGCCCCGTTCTCTCCTCCTGCCAGCCCAGGGTCCACAGGCTGGGGGCGGTGTGGGCCCCAGCTGCCCGGGACCCTGCTCCAGCCTGGCCCGCCTCCAAGTCTCACCTCTCACGAACACGTAGGAGCTGGCGGCCGTGGTGCCCTCGATGCGTGCCTTGATGTACTTGTAGTAGCAGACGTAGCTGCCTGTGTCGTTGGCATGTACCTCGTGCAGCAGCAACACCTTGCAGTAGGGCCTGGCGTCTGTGCCCTCGCAGTCTCGCACCACCCCCGTGTCCTCGCTGTCCTTGTCTCCGGTGGCTGGC	GCCCCGCCGGTCATCCCACACCACCTCCTGCCCGTCTGGCCACAGCACCGAGCTTTGCTGGAGGGACAAGGCCACCATCATTGCCCAGCTGCCCCTTGCTCCTGGCCAGACAGGCGGCCGCCTTTCCCAGGGGTGGGATGGGAGGGTCGGATGCTGGGGTTGGGGTGGGGCCGTACCGAGCGCAGCGTGACATTGAGGCCGGGGATGGACACCAGACAGGGCACCCACATGGCGTCCTTCCTGTTGACCAAGAGCGTGTCAGGCTTGTTGATGAATGGCTGCTCAAAGTCTATGGAGAGGGAGCAAGCTGTTGGGGAAGGGACGTGGCGGCCAGGCTGGGGGAGGGCTCCACGGGGCTGGGTGGTGCTGGTCCTGAACCAGCCACCCGCTGGAGCAGGTAGGGCCCCGTTCTCTCCTCCTGCCAGCCCAGGGTCCACAGGCTGGGGGCGGTGTGGGCCCCAGCTGCCCGGGACCCTGCTCCAGCCTGGCCCGCCTCCAAGTCTCACCTCTCACGAACACGTAGGAGCTGGCGGCCGTGGTGCCCTCGATGCGTGCCTTGATGTACTTGTAGTAGCAGACGTAGCTGCCTGTGTCGTTGGCATGTACCTCGTGCAGCAGCAACACCTTGCAGTAGGGCCTGGCGTCTGTGCCCTCGCAGTCTCGCACCACCCCCGTGTCCTCGCTGTCCTTGTCTCCGGTGGCTGGC	-	novel	NA	P-0035768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	132	1198	0	ENST00000261937.6:c.201_570del		p.X67_splice	ENST00000261937	NM_182925.4	67	gcGCCAGCCACCGGAGACAAGGACAGCGAGGACACGGGGGTGGTGCGAGACTGCGAGGGCACAGACGCCAGGCCCTACTGCAAGGTGTTGCTGCTGCACGAGGTACATGCCAACGACACAGGCAGCTACGTCTGCTACTACAAGTACATCAAGGCACGCATCGAGGGCACCACGGCCGCCAGCTCCTACGTGTTCGTGAGAGGTGAGACTTGGAGGCGGGCCAGGCTGGAGCAGGGTCCCGGGCAGCTGGGGCCCACACCGCCCCCAGCCTGTGGACCCTGGGCTGGCAGGAGGAGAGAACGGGGCCCTACCTGCTCCAGCGGGTGGCTGGTTCAGGACCAGCACCACCCAGCCCCGTGGAGCCCTCCCCCAGCCTGGCCGCCACGTCCCTTCCCCAACAGCTTGCTCCCTCTCCATAGACTTTGAGCAGCCATTCATCAACAAGCCTGACACGCTCTTGGTCAACAGGAAGGACGCCATGTGGGTGCCCTGTCTGGTGTCCATCCCCGGCCTCAATGTCACGCTGCGCTCGGTACGGCCCCACCCCAACCCCAGCATCCGACCCTCCCATCCCACCCCTGGGAAAGGCGGCCGCCTGTCTGGCCAGGAGCAAGGGGCAGCTGGGCAATGATGGTGGCCTTGTCCCTCCAGCAAAGCTCGGTGCTGTGGCCAGACGGGCAGGAGGTGGTGTGGGATGACCGGCGGGGC/gc	3-5/30	0.719783056587692	4	FACETS	0.518	0.469	0.57	0.13	0.117	0.143	SUBCLONAL	1	TRUE	0	0.719783056587692	4		1198	1217	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265588	152265589	+	missense_variant	Missense_Mutation	DNP	CA	CA	AC	novel	NA	P-0035768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	140	610	0	ENST00000206249.3:c.1041_1042delinsAC	p.Asn348His	p.N348H	ENST00000206249	NM_000125.3	347	acCAac/acACac	4/8	0.576981120660695	5	FACETS	0.967	0.88	1	0.322	0.293	0.353	CLONAL	1	TRUE	2	0.719783056587692	5		610	837	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593650	55593651	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCAACACAACTTCCTTATGATCACAAATGGGAGTTTCCCAGA	novel	NA	P-0035810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	135	390	0	ENST00000288135.5:c.1717_1758dup	p.Pro573_Arg586dup	p.P573_R586dup	ENST00000288135	NM_000222.2	573	-/CCAACACAACTTCCTTATGATCACAAATGGGAGTTTCCCAGA	11/21	1	2	FACETS	0.418	0.38	0.457	0.418	0.38	0.457	SUBCLONAL	1	TRUE	1	0.898504453860765	2		390	719	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0035964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	185	478	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.705159311349517	2		478	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0035964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	260	583	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	0.667058837070995	1	FACETS	0.951	0.902	1	0.951	0.902	1	CLONAL	1	TRUE	0	0.705159311349517	1		583	502	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692850	89692850	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	71	162	0	ENST00000371953.3:c.334C>G	p.Leu112Val	p.L112V	ENST00000371953	NM_000314.4	112	Cta/Gta	5/9	0.705159311349517	1	FACETS	0.938	0.846	1	0.938	0.846	1	CLONAL	1	TRUE	0	0.705159311349517	1		162	139	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988430	41988430	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	235	481	0	ENST00000219905.7:c.1222G>C	p.Asp408His	p.D408H	ENST00000219905	NM_001164273.1	408	Gat/Cat	3/24	1	2	FACETS	0.97	0.91	1	0.97	0.91	1	CLONAL	1	TRUE	1	0.705159311349517	2		481	687	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853197	68853197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	256	467	0	ENST00000261769.5:c.1580G>A	p.Arg527Lys	p.R527K	ENST00000261769	NM_004360.3	527	aGa/aAa	11/16	0.705159311349517	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.705159311349517	1		467	441	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805789	46805789	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	334	846	0	ENST00000290295.7:c.167C>G	p.Ser56Trp	p.S56W	ENST00000290295	NM_006361.5	56	tCg/tGg	1/2	1	2	FACETS	0.941	0.891	0.991	0.941	0.891	0.991	CLONAL	1	TRUE	1	0.705159311349517	2		846	1007	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031275	36031275	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	237	531	0	ENST00000358208.4:c.1394C>G	p.Pro465Arg	p.P465R	ENST00000358208		465	cCc/cGc	11/12	1	2	FACETS	0.977	0.917	1	0.977	0.917	1	CLONAL	1	TRUE	1	0.705159311349517	2		531	688	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098655	47098655	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	281	627	0	ENST00000409792.3:c.6619C>G	p.Gln2207Glu	p.Q2207E	ENST00000409792	NM_014159.6	2207	Cag/Gag	15/21	1	2	FACETS	0.911	0.858	0.965	0.911	0.858	0.965	CLONAL	1	TRUE	1	0.705159311349517	2		627	875	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498519	89498519	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	30	317	0	ENST00000336596.2:c.2491C>T	p.Gln831Ter	p.Q831*	ENST00000336596	NM_005233.5	831	Cag/Tag	14/17	1	2	FACETS	0.204	0.164	0.249	0.204	0.164	0.249	SUBCLONAL	1	TRUE	1	0.705159311349517	2		317	417	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287392	38287392	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1034848904	NA	P-0035964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1917	330	728	0	ENST00000425967.3:c.265C>T	p.Arg89Trp	p.R89W	ENST00000425967	NM_001174067.1	89	Cgg/Tgg	4/19	0.705159311349517	6	FACETS	1	0.944	1			1	CLONAL	1	TRUE	NA	0.705159311349517	6		728	2247	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751173	128751173	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	311	583	0	ENST00000377970.2:c.710C>G	p.Ser237Cys	p.S237C	ENST00000377970	NM_002467.4	237	tCt/tGt	2/3	0.705159311349517	3	FACETS	1	0.979	1	0.537	0.506	0.568	CLONAL	1	TRUE	1	0.705159311349517	3		583	1111	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953752	48953766	+	frameshift_variant	Frame_Shift_Ins	INS	TGTATTACCGAGTAA	TGTATTACCGAGTAA	ACAAGTTCGCTTCAAGTTCGCTACT	novel	NA	P-0035964-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	97	235	0	ENST00000267163.4:c.1355_1369delinsACAAGTTCGCTTCAAGTTCGCTACT	p.Leu452TyrfsTer14	p.L452Yfs*14	ENST00000267163	NM_000321.2	452	tTGTATTACCGAGTAAtg/tACAAGTTCGCTTCAAGTTCGCTACTtg	14/27	0.699128291303881	2	FACETS	1	0.982	1	0.668	0.609	0.726	CLONAL	1	TRUE	0	0.705159311349517	2		235	206	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711927	89711928	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554900593	NA	P-0036294-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	419	612	0	ENST00000371953.3:c.548dup	p.Asn184GlufsTer6	p.N184Efs*6	ENST00000371953	NM_000314.4	182	tta/ttAa	6/9	0.516126823321416	6	FACETS	0.886	0.846	0.926	0.886	0.846	0.926	CLONAL	3	TRUE	3	0.801957873851935	6		612	1024	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210058	55210058	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036294-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	232	720	0	ENST00000275493.2:c.168T>G	p.Asn56Lys	p.N56K	ENST00000275493	NM_005228.3	56	aaT/aaG	2/28	0.584384565316281	4	FACETS	1	0.985	1	0.392	0.366	0.419	CLONAL	1	TRUE	1	0.801957873851935	4		720	886	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0036721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	170	424	1	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.362520071677902	2		425	924	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032748	30032748	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	131	572	0	ENST00000338641.4:c.123G>A	p.Trp41Ter	p.W41*	ENST00000338641	NM_000268.3	41	tgG/tgA	2/16	0.362520071677902	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.362520071677902	1		572	564	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030308	180030308	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1180832689	NA	P-0036721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1431	91	1094	0	ENST00000261937.6:c.3976G>C	p.Ala1326Pro	p.A1326P	ENST00000261937	NM_182925.4	1326	Gcc/Ccc	30/30	1	2	FACETS	0.33	0.291	0.371	0.33	0.291	0.371	SUBCLONAL	1	TRUE	1	0.362520071677902	2		1094	1522	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280164	142280164	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	55	663	0	ENST00000350721.4:c.1270A>T	p.Ser424Cys	p.S424C	ENST00000350721	NM_001184.3	424	Agt/Tgt	5/47	1	2	FACETS	0.347	0.296	0.403	0.347	0.296	0.403	SUBCLONAL	1	TRUE	1	0.362520071677902	2		663	875	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0037409-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	113	879	3	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.19	2		882	1154	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186501402	186501402	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0037409-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	78	516	0	ENST00000323963.5:c.3G>A	p.Met1?	p.M1?	ENST00000323963		1	atG/atA	1/11	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.19	2		516	806	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038879-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	151	276	0				ENST00000310581	NM_198253.2	-/1132			0.795750508054273	3	FACETS	0.929	0.854	1	0.465	0.427	0.504	CLONAL	1	TRUE	1	0.795750508054273	3		276	571	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0038879-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	426	981	2	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.795750508054273	3	FACETS	1	0.973	1	0.516	0.491	0.541	CLONAL	1	TRUE	1	0.795750508054273	3		983	1451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0038879-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	538	583	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	0.795750508054273	3	FACETS	0.981	0.948	1	0.981	0.948	1	CLONAL	2	TRUE	1	0.795750508054273	3		583	963	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050363	176050363	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1301409514	NA	P-0038879-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	150	580	0	ENST00000367669.3:c.1202G>A	p.Arg401Gln	p.R401Q	ENST00000367669	NM_022457.5	401	cGa/cAa	11/20	0.619007194836505	4	FACETS	0.917	0.84	0.998	0.459	0.42	0.499	CLONAL	1	TRUE	2	0.795750508054273	4		580	738	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692794	89692794	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121909238	NA	P-0038879-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	302	381	0	ENST00000371953.3:c.278A>G	p.His93Arg	p.H93R	ENST00000371953	NM_000314.4	93	cAt/cGt	5/9	0.795750508054273	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.795750508054273	2		381	373	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143293	30143293	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs748978993	NA	P-0038879-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	686	804	2	ENST00000389048.3:c.233C>G	p.Ser78Trp	p.S78W	ENST00000389048	NM_004304.4	78	tCg/tGg	1/29	0.795750508054273	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.795750508054273	3		806	1159	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158629	26158629	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038879-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	225	296	0	ENST00000289316.2:c.232G>A	p.Ala78Thr	p.A78T	ENST00000289316	NM_138720.2	78	Gct/Act	1/2	0.795750508054273	3	FACETS	0.976	0.924	1	0.976	0.924	1	CLONAL	2	TRUE	1	0.795750508054273	3		296	405	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309890	65309890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038879-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	228	563	0	ENST00000342505.4:c.2260G>A	p.Glu754Lys	p.E754K	ENST00000342505	NM_002227.2	754	Gaa/Aaa	17/25	0.795750508054273	4	FACETS	1	0.964	1	0.526	0.49	0.563	CLONAL	1	TRUE	2	0.795750508054273	4		563	979	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829847	72829847	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750842718	NA	P-0038879-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	321	880	0	ENST00000268489.5:c.6734C>T	p.Ser2245Leu	p.S2245L	ENST00000268489	NM_006885.3	2245	tCa/tTa	9/10	0.795750508054273	2	FACETS	1	0.988	1	0.559	0.532	0.587	CLONAL	1	TRUE	0	0.795750508054273	2		880	721	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107122	27107122	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038879-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	605	686	0	ENST00000324856.7:c.6733G>T	p.Asp2245Tyr	p.D2245Y	ENST00000324856	NM_006015.4	2245	Gac/Tac	20/20	0.795750508054273	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	2	0.795750508054273	4		686	1274	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447000	49447000	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038879-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	195	501	0	ENST00000301067.7:c.944G>C	p.Trp315Ser	p.W315S	ENST00000301067	NM_003482.3	315	tGg/tCg	7/54	0.795750508054273	3	FACETS	0.948	0.88	1	0.474	0.44	0.509	CLONAL	1	TRUE	1	0.795750508054273	3		501	723	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032558	12032558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1355543573	NA	P-0038879-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	368	492	0	ENST00000353533.5:c.994G>A	p.Glu332Lys	p.E332K	ENST00000353533	NM_003010.3	332	Gag/Aag	9/11	0.795750508054273	3	FACETS	0.985	0.945	1	0.985	0.945	1	CLONAL	2	TRUE	1	0.795750508054273	3		492	656	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547861	41547861	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038879-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	413	540	0	ENST00000263253.7:c.2842G>C	p.Glu948Gln	p.E948Q	ENST00000263253	NM_001429.3	948	Gaa/Caa	15/31	0.795750508054273	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.795750508054273	2		540	518	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259063	89259063	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038879-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	124	350	0	ENST00000336596.2:c.207G>T	p.Gln69His	p.Q69H	ENST00000336596	NM_005233.5	69	caG/caT	3/17	0.750243247244414	3	FACETS	0.911	0.83	0.996	0.456	0.415	0.498	CLONAL	1	TRUE	1	0.795750508054273	3		350	478	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998990	169998990	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038879-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	124	412	0	ENST00000295797.4:c.919G>C	p.Glu307Gln	p.E307Q	ENST00000295797	NM_002740.5	307	Gag/Cag	10/18	0.750243247244414	3	FACETS	0.839	0.763	0.919	0.42	0.381	0.46	CLONAL	1	TRUE	1	0.795750508054273	3		412	519	SUCCESS
APC	324	MSKCC	GRCh37	5	112178697	112178697	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1561615265	NA	P-0038879-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	136	436	0	ENST00000257430.4:c.7406C>G	p.Ser2469Cys	p.S2469C	ENST00000257430	NM_000038.5	2469	tCt/tGt	16/16	0.795750508054273	3	FACETS	0.835	0.763	0.911	0.418	0.381	0.456	CLONAL	1	TRUE	1	0.795750508054273	3		436	572	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652094	36652101	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGCCCA	CCTGCCCA	-	novel	NA	P-0038879-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	795	1099	0	ENST00000244741.5:c.216_223del	p.Leu73AlafsTer13	p.L73Afs*13	ENST00000244741	NM_000389.4	72	ggCCTGCCCAag/ggag	2/3	0.795750508054273	3	FACETS	0.954	0.926	0.981	0.954	0.926	0.981	CLONAL	2	TRUE	1	0.795750508054273	3		1099	1464	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415150	116415150	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038879-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	472	626	0	ENST00000397752.3:c.3244G>A	p.Glu1082Lys	p.E1082K	ENST00000397752	NM_000245.2	1082	Gaa/Aaa	15/21	0.795750508054273	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.795750508054273	3		626	821	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87322782	87322782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201256653	NA	P-0038879-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	402	480	0	ENST00000277120.3:c.383C>T	p.Thr128Met	p.T128M	ENST00000277120		128	aCg/aTg	5/19	0.660581106782774	4	FACETS	0.96	0.917	1	0.96	0.917	1	CLONAL	2	TRUE	2	0.795750508054273	4		480	945	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552891	106552891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771056895	NA	P-0039177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	163	763	1	ENST00000369096.4:c.856C>T	p.Arg286Cys	p.R286C	ENST00000369096	NM_001198.3	286	Cgt/Tgt	5/7	0.285674172798618	3	FACETS	0.89	0.816	0.967	0.445	0.408	0.484	CLONAL	1	TRUE	1	0.43678324170415	3		764	1022	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0039177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	75	283	0	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	0.303214868964144	2	FACETS	1	0.978	1	0.747	0.664	0.832	CLONAL	1	TRUE	0	0.43678324170415	2		283	230	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0039177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	64	444	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.43678324170415	1	FACETS	0.815	0.713	0.924	0.815	0.713	0.924	CLONAL	1	TRUE	0	0.43678324170415	1		444	281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579355	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519997	NA	P-0039177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	294	806	0	ENST00000269305.4:c.332T>A	p.Leu111Gln	p.L111Q	ENST00000269305	NM_001126112.2	111	cTg/cAg	4/11	0.416743845944619	2	FACETS	0.944	0.894	0.994	0.944	0.894	0.994	CLONAL	2	TRUE	0	0.43678324170415	2		806	713	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247294	153247294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	41	305	0	ENST00000281708.4:c.1508C>T	p.Ala503Val	p.A503V	ENST00000281708	NM_033632.3	503	gCa/gTa	10/12	1	2	FACETS	0.519	0.433	0.613	0.519	0.433	0.613	SUBCLONAL	1	TRUE	1	0.43678324170415	2		305	362	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741443	145741443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs551940973	NA	P-0039177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	170	1101	0	ENST00000428558.2:c.1060G>A	p.Val354Ile	p.V354I	ENST00000428558	NM_004260.3	354	Gta/Ata	5/22	0.43678324170415	4	FACETS	0.844	0.774	0.917	0.281	0.258	0.306	CLONAL	1	TRUE	1	0.43678324170415	4		1101	1325	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524363	187524363	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774876308	NA	P-0039177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	93	453	0	ENST00000441802.2:c.11317C>T	p.Arg3773Cys	p.R3773C	ENST00000441802	NM_005245.3	3773	Cgc/Tgc	19/27	1	2	FACETS	0.944	0.844	1	0.944	0.844	1	CLONAL	1	TRUE	1	0.43678324170415	2		453	451	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545635	63545636	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	novel	NA	P-0039177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	36	344	0	ENST00000307078.5:c.956+2_956+3del		p.X319_splice	ENST00000307078	NM_004655.3	319			0.43678324170415	1	FACETS	0.369	0.304	0.442	0.369	0.304	0.442	SUBCLONAL	1	TRUE	0	0.43678324170415	1		344	349	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0040055-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	306	501	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.372816117133083	3	FACETS	0.83	0.788	0.872	0.83	0.788	0.872	INDETERMINATE	2	TRUE	1	0.710975087491268	3		501	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0040055-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	593	741	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	0.66162042739551	2	FACETS	0.908	0.881	0.934	0.908	0.881	0.934	CLONAL	2	TRUE	0	0.710975087491268	2		741	919	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254724	46254743	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGTAAAAAGTAAATGGCAA	TTGTAAAAAGTAAATGGCAA	-	novel	NA	P-0040055-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	156	237	1	ENST00000334344.6:c.4916_4922+13del		p.X1639_splice	ENST00000334344	NM_152641.2	1639		16/21	0.710975087491268	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.710975087491268	1		238	262	SUCCESS
APC	324	MSKCC	GRCh37	5	112163652	112163652	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040055-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	111	226	0	ENST00000257430.4:c.1575C>A	p.Cys525Ter	p.C525*	ENST00000257430	NM_000038.5	525	tgC/tgA	13/16	0.710975087491268	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.710975087491268	1		226	195	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340823	70340823	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040055-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	261	480	0	ENST00000374080.3:c.556T>C	p.Trp186Arg	p.W186R	ENST00000374080		186	Tgg/Cgg	5/45	0.641402231111614	1	FACETS	0.816	0.771	0.861	0.816	0.771	0.861	CLONAL	1	TRUE	0	0.710975087491268	1		480	580	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655415	45655415	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040055-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	203	668	1	ENST00000407780.3:c.437C>T	p.Pro146Leu	p.P146L	ENST00000407780	NM_001283052.1	146	cCc/cTc	4/7	1	2	FACETS	0.497	0.46	0.535	0.497	0.46	0.535	SUBCLONAL	1	TRUE	1	0.710975087491268	2		669	1150	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325780	30325780	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041074-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	36	277	0	ENST00000322652.5:c.1978C>G	p.Leu660Val	p.L660V	ENST00000322652	NM_015355.2	660	Cta/Gta	16/16	1	2	FACETS	1	0.842	1	1	0.842	1	CLONAL	1	TRUE	1	0.25	2		277	282	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62323153	62323155	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs1568715177	NA	P-0041074-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	74	604	0	ENST00000360203.5:c.2619_2621del	p.Gly874del	p.G874del	ENST00000360203	NM_001283009.1	872	cGAGga/cga	28/35	1	2	FACETS	0.774	0.677	0.879	0.774	0.677	0.879	SUBCLONAL	1	TRUE	1	0.25	2		604	765	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0041149-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	319	777	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.600358195698208	3	FACETS	1	0.964	1	0.515	0.485	0.545	CLONAL	1	TRUE	1	0.646210097559689	3		777	1269	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442059	52442059	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041149-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	288	714	0	ENST00000460680.1:c.290T>G	p.Leu97Arg	p.L97R	ENST00000460680	NM_004656.3	97	cTg/cGg	5/17	0.630951706148471	1	FACETS	0.949	0.9	0.998	0.949	0.9	0.998	CLONAL	1	TRUE	0	0.646210097559689	1		714	636	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604642	48604653	+	inframe_deletion	In_Frame_Del	DEL	TGGAATTGGTGT	TGGAATTGGTGT	-	novel	NA	P-0041149-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	129	408	0	ENST00000342988.3:c.1466_1477del	p.Gly489_Val492del	p.G489_V492del	ENST00000342988	NM_005359.5	488	gcTGGAATTGGTGTt/gct	12/12	0.626283911070027	1	FACETS	0.866	0.798	0.936	0.866	0.798	0.936	CLONAL	1	TRUE	0	0.646210097559689	1		408	312	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244261	98244261	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041149-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	225	736	0	ENST00000331920.6:c.716C>A	p.Ala239Glu	p.A239E	ENST00000331920	NM_000264.3	239	gCg/gAg	5/24	1	2	FACETS	0.89	0.832	0.951	0.89	0.832	0.951	CLONAL	1	TRUE	1	0.646210097559689	2		736	782	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0041265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	116	464	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.324383387407489	2		464	638	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604778	48604778	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767383	NA	P-0041265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	27	474	0	ENST00000342988.3:c.1600C>T	p.Gln534Ter	p.Q534*	ENST00000342988	NM_005359.5	534	Cag/Tag	12/12	0.324383387407489	1	FACETS	0.327	0.259	0.404	0.327	0.259	0.404	SUBCLONAL	1	FALSE	0	0.324383387407489	1		474	427	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032045	26032045	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	122	569	0	ENST00000244661.2:c.244G>C	p.Asp82His	p.D82H	ENST00000244661	NM_003537.3	82	Gat/Cat	1/1	0.218024348772241	3	FACETS	1	0.977	1	0.628	0.568	0.691	CLONAL	1	FALSE	1	0.324383387407489	3		569	696	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591916	48591916	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	31	449	0	ENST00000342988.3:c.1079A>T	p.Asp360Val	p.D360V	ENST00000342988	NM_005359.5	360	gAt/gTt	9/12	0.324383387407489	1	FACETS	0.314	0.253	0.383	0.314	0.253	0.383	SUBCLONAL	1	FALSE	0	0.324383387407489	1		449	510	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913783	32913784	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1555284157	NA	P-0041265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	106	352	0	ENST00000380152.3:c.5297dup	p.Asn1766LysfsTer2	p.N1766Kfs*2	ENST00000380152		1764	tca/tcAa	11/27	0.324383387407489	5	FACETS	1	0.91	1	0.673	0.606	0.743	CLONAL	2	FALSE	2	0.324383387407489	5		352	481	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682338	37682338	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	31	699	0	ENST00000447079.4:c.3529G>T	p.Glu1177Ter	p.E1177*	ENST00000447079	NM_015083.1	1177	Gag/Tag	13/14	1	2	FACETS	0.312	0.252	0.381	0.312	0.252	0.381	SUBCLONAL	1	FALSE	1	0.324383387407489	2		699	612	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295669	212295703	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CCTTTCCTCCATCAGCATTGTACTCTTTTTCATCT	CCTTTCCTCCATCAGCATTGTACTCTTTTTCATCT	-	novel	NA	P-0041265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	117	405	0	ENST00000342788.4:c.2610_2643+1del		p.X870_splice	ENST00000342788	NM_005235.2	870		21/28	0.324383387407489	3	FACETS	0.809	0.733	0.889	0.809	0.733	0.889	CLONAL	2	FALSE	1	0.324383387407489	3		405	518	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139794937	139794937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772816687	NA	P-0041265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	88	692	0	ENST00000247668.2:c.331G>A	p.Gly111Arg	p.G111R	ENST00000247668	NM_021138.3	111	Gga/Aga	4/11	0.324383387407489	1	FACETS	0.774	0.687	0.867	0.774	0.687	0.867	SUBCLONAL	1	FALSE	0	0.324383387407489	1		692	587	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0042002-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	54	721	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	0.286	0.243	0.333	0.286	0.243	0.333	SUBCLONAL	1	TRUE	1	0.439663892267627	2		721	860	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936096	178936096	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519940	NA	P-0042002-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	758	592	2	ENST00000263967.3:c.1638G>T	p.Gln546His	p.Q546H	ENST00000263967	NM_006218.2	546	caG/caT	10/21	0.439663892267627	8	FACETS	1	0.994	1			1	CLONAL	6	TRUE	NA	0.439663892267627	8		594	1247	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042002-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	827	458	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	0.439663892267627	8	FACETS	1	0.977	1			1	CLONAL	7	TRUE	NA	0.439663892267627	8		458	1245	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61708412	61708412	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042002-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	25	325	0	ENST00000401558.2:c.2977C>G	p.Gln993Glu	p.Q993E	ENST00000401558	NM_003400.3	993	Caa/Gaa	24/25	1	2	FACETS	0.29	0.228	0.361	0.29	0.228	0.361	SUBCLONAL	1	TRUE	1	0.439663892267627	2		325	392	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158610	26158610	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042002-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	32	473	0	ENST00000289316.2:c.213C>G	p.Phe71Leu	p.F71L	ENST00000289316	NM_138720.2	71	ttC/ttG	1/2	0.266975124429202	3	FACETS	0.352	0.285	0.428	0.176	0.142	0.214	SUBCLONAL	1	TRUE	1	0.439663892267627	3		473	504	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903779	41903779	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042002-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	98	1088	0	ENST00000372991.4:c.778C>T	p.Gln260Ter	p.Q260*	ENST00000372991	NM_001760.3	260	Cag/Tag	5/5	1	2	FACETS	0.405	0.36	0.453	0.405	0.36	0.453	SUBCLONAL	1	TRUE	1	0.439663892267627	2		1088	1100	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445424	29445424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762571775	NA	P-0042002-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	76	1051	1	ENST00000389048.3:c.3409G>A	p.Gly1137Arg	p.G1137R	ENST00000389048	NM_004304.4	1137	Gga/Aga	21/29	1	2	FACETS	0.351	0.306	0.398	0.351	0.306	0.398	SUBCLONAL	1	TRUE	1	0.439663892267627	2		1052	986	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010560	48010560	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587779920	NA	P-0042002-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	53	778	0	ENST00000234420.5:c.188C>G	p.Ser63Cys	p.S63C	ENST00000234420	NM_000179.2	63	tCc/tGc	1/10	1	2	FACETS	0.295	0.25	0.344	0.295	0.25	0.344	SUBCLONAL	1	TRUE	1	0.439663892267627	2		778	818	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932974	39932974	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042002-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	98	1142	1	ENST00000378444.4:c.1625C>T	p.Ser542Leu	p.S542L	ENST00000378444	NM_001123385.1	542	tCa/tTa	4/15	1	2	FACETS	0.459	0.408	0.513	0.459	0.408	0.513	SUBCLONAL	1	TRUE	1	0.439663892267627	2		1143	972	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645450	67645450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042002-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	48	481	0	ENST00000264010.4:c.715G>A	p.Glu239Lys	p.E239K	ENST00000264010	NM_006565.3	239	Gag/Aag	3/12	1	2	FACETS	0.405	0.342	0.475	0.405	0.342	0.475	SUBCLONAL	1	TRUE	1	0.439663892267627	2		481	539	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431655	431655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373480934	NA	P-0042002-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	57	630	0	ENST00000399788.2:c.2354G>A	p.Arg785Lys	p.R785K	ENST00000399788	NM_001042603.1	785	aGg/aAg	17/28	1	2	FACETS	0.344	0.294	0.398	0.344	0.294	0.398	SUBCLONAL	1	TRUE	1	0.439663892267627	2		630	754	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62290847	62290847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042002-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	42	548	0	ENST00000360203.5:c.92G>A	p.Cys31Tyr	p.C31Y	ENST00000360203	NM_001283009.1	31	tGt/tAt	2/35	0.439663892267627	3	FACETS	0.372	0.309	0.441	0.186	0.154	0.221	SUBCLONAL	1	TRUE	1	0.439663892267627	3		548	627	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206646604	206646604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042002-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1646	97	1254	1	ENST00000367120.3:c.34G>A	p.Asp12Asn	p.D12N	ENST00000367120	NM_014002.3	12	Gat/Aat	3/22	0.439663892267627	5	FACETS	0.42	0.373	0.471	0.14	0.124	0.157	SUBCLONAL	1	TRUE	2	0.439663892267627	5		1255	1743	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307526	118307526	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042002-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	56	772	0	ENST00000534358.1:c.299C>G	p.Ser100Cys	p.S100C	ENST00000534358	NM_005933.3	100	tCt/tGt	1/36	1	2	FACETS	0.367	0.313	0.425	0.367	0.313	0.425	SUBCLONAL	1	TRUE	1	0.439663892267627	2		772	695	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588663	28588663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042002-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	43	488	0	ENST00000241453.7:c.2785G>A	p.Asp929Asn	p.D929N	ENST00000241453	NM_004119.2	929	Gac/Aac	23/24	1	2	FACETS	0.413	0.345	0.487	0.413	0.345	0.487	SUBCLONAL	1	TRUE	1	0.439663892267627	2		488	474	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481784	40481784	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042002-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	47	540	0	ENST00000264657.5:c.1120G>C	p.Asp374His	p.D374H	ENST00000264657	NM_139276.2	374	Gac/Cac	12/24	NA	2	FACETS	0.428	0.361	0.501			1	INDETERMINATE	1	TRUE	NA	0.439663892267627	2		540	500	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770065	56770065	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042002-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3391	77	935	1	ENST00000337432.4:c.61C>A	p.Pro21Thr	p.P21T	ENST00000337432	NM_058216.2	21	Cca/Aca	1/9	0.439663892267627	16	FACETS	0.412	0.359	0.469			1	SUBCLONAL	1	TRUE	NA	0.439663892267627	16		936	3468	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61708356	61708356	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042002-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	37	398	0	ENST00000401558.2:c.3033C>G	p.Phe1011Leu	p.F1011L	ENST00000401558	NM_003400.3	1011	ttC/ttG	24/25	1	2	FACETS	0.348	0.286	0.417	0.348	0.286	0.417	SUBCLONAL	1	TRUE	1	0.439663892267627	2		398	484	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388699	31388699	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0042002-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	75	835	0	ENST00000328111.2:c.1964C>G	p.Ser655Ter	p.S655*	ENST00000328111	NM_006892.3	655	tCa/tGa	18/23	0.439663892267627	3	FACETS	0.417	0.364	0.474	0.209	0.182	0.237	SUBCLONAL	1	TRUE	1	0.439663892267627	3		835	998	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670768	134670768	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042002-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	68	788	0	ENST00000398015.3:c.679C>A	p.Pro227Thr	p.P227T	ENST00000398015	NM_004441.4	227	Ccc/Acc	3/16	0.439663892267627	4	FACETS	0.436	0.378	0.499			1	SUBCLONAL	1	TRUE	NA	0.439663892267627	4		788	1022	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502264	186502264	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042002-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	39	505	0	ENST00000323963.5:c.73G>A	p.Glu25Lys	p.E25K	ENST00000323963		25	Gag/Aag	2/11	1	2	FACETS	0.355	0.294	0.423	0.355	0.294	0.423	SUBCLONAL	1	TRUE	1	0.439663892267627	2		505	500	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032069	26032069	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042002-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	65	828	0	ENST00000244661.2:c.220G>T	p.Glu74Ter	p.E74*	ENST00000244661	NM_003537.3	74	Gaa/Taa	1/1	0.266975124429202	3	FACETS	0.461	0.399	0.529	0.231	0.199	0.265	SUBCLONAL	1	TRUE	1	0.439663892267627	3		828	782	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793620	89793620	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042002-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	44	381	0	ENST00000336032.3:c.689G>C	p.Arg230Thr	p.R230T	ENST00000336032	NM_006813.2	230	aGa/aCa	2/2	1	2	FACETS	0.428	0.359	0.504	0.428	0.359	0.504	SUBCLONAL	1	TRUE	1	0.439663892267627	2		381	468	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467780	50467780	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042002-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	61	961	0	ENST00000331340.3:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000331340	NM_006060.4	339	Gag/Tag	8/8	0.372039366182028	3	FACETS	0.337	0.29	0.39	0.169	0.145	0.195	SUBCLONAL	1	TRUE	1	0.439663892267627	3		961	1003	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457310	5457310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042002-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	34	410	0	ENST00000381577.3:c.284G>A	p.Gly95Glu	p.G95E	ENST00000381577	NM_014143.3	95	gGa/gAa	3/7	1	2	FACETS	0.335	0.274	0.405	0.335	0.274	0.405	SUBCLONAL	1	TRUE	1	0.439663892267627	2		410	461	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224592	123224592	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042002-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	56	655	0	ENST00000218089.9:c.3445del	p.His1149IlefsTer11	p.H1149Ifs*11	ENST00000218089	NM_001042749.1	1149	Cat/at	31/35	1	2	FACETS	0.445	0.381	0.514	0.445	0.381	0.514	SUBCLONAL	1	TRUE	1	0.439663892267627	2		655	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579409	7579409	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1567556114	NA	P-0042868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	391	897	1	ENST00000269305.4:c.278del	p.Leu93ArgfsTer30	p.L93Rfs*30	ENST00000269305	NM_001126112.2	93	cTg/cg	4/11	0.457503247987012	2	FACETS	0.957	0.914	1	0.957	0.914	1	CLONAL	2	TRUE	0	0.457503247987012	2		898	893	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939109	48939109	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0042868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	70	273	1	ENST00000267163.4:c.939+2T>A		p.X313_splice	ENST00000267163	NM_000321.2	313			0.380674910791361	3	FACETS	0.942	0.851	1	0.942	0.851	1	CLONAL	3	TRUE	0	0.457503247987012	3		274	133	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38506044	38506044	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	296	585	1	ENST00000254066.5:c.336C>G	p.Phe112Leu	p.F112L	ENST00000254066	NM_000964.3	112	ttC/ttG	4/9	0.457503247987012	2	FACETS	0.846	0.8	0.892	0.846	0.8	0.892	CLONAL	2	TRUE	0	0.457503247987012	2		586	765	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271826	15271826	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1424	1067	1065	2	ENST00000263388.2:c.6613C>T	p.Gln2205Ter	p.Q2205*	ENST00000263388	NM_000435.2	2205	Cag/Tag	33/33	0.457503247987012	8	FACETS	1	0.996	1	0.74	0.72	0.761	CLONAL	4	TRUE	2	0.457503247987012	8		1067	2491	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503772	186503772	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	204	505	0	ENST00000323963.5:c.449C>T	p.Ala150Val	p.A150V	ENST00000323963		150	gCt/gTt	5/11	0.440186899006288	4	FACETS	0.847	0.788	0.909	0.847	0.788	0.909	CLONAL	2	TRUE	2	0.457503247987012	4		505	767	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624621	93624621	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	208	474	0	ENST00000375746.1:c.712T>A	p.Trp238Arg	p.W238R	ENST00000375746	NM_001174167.1	238	Tgg/Agg	4/14	0.457503247987012	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.457503247987012	2		474	432	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397639	139397639	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043104-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	521	1119	0	ENST00000277541.6:c.5162T>G	p.Val1721Gly	p.V1721G	ENST00000277541	NM_017617.3	1721	gTg/gGg	27/34	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.84	2		1119	1232	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087932	27087932	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043104-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	406	858	0	ENST00000324856.7:c.2220del	p.Met741Ter	p.M741*	ENST00000324856	NM_006015.4	740	tCc/tc	6/20	1	2	FACETS	0.946	0.903	0.989	0.946	0.903	0.989	CLONAL	1	TRUE	1	0.84	2		858	1022	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390906	139390909	+	frameshift_variant	Frame_Shift_Del	DEL	GGTG	GGTG	-	novel	NA	P-0043104-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	491	1163	0	ENST00000277541.6:c.7282_7285del	p.His2428TrpfsTer6	p.H2428Wfs*6	ENST00000277541	NM_017617.3	2428	CACCtg/tg	34/34	1	2	FACETS	0.918	0.879	0.957	0.918	0.879	0.957	CLONAL	1	TRUE	1	0.84	2		1163	1274	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820587	44820593	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTTTG	TCTTTTG	-	novel	NA	P-0043104-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	55	90	0	ENST00000377967.4:c.286_292del	p.Phe96AsnfsTer2	p.F96Nfs*2	ENST00000377967	NM_021140.2	95	tTCTTTTGt/tt	3/29	1	2	FACETS	0.784	0.684	0.889	0.784	0.684	0.889	SUBCLONAL	1	TRUE	1	0.84	2		90	167	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974744	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAGCAGCGCCCGCA	CCTCCAGCAGCGCCCGCA	-	novel	NA	P-0043534-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	206	418	0	ENST00000304494.5:c.83_100del	p.Val28_Glu33del	p.V28_E33del	ENST00000304494	NM_000077.4	28	gTGCGGGCGCTGCTGGAGGcg/gcg	1/3	0.628699038691314	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.628699038691314	1		418	439	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0043534-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	211	386	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.96	0.896	1	0.96	0.896	1	CLONAL	1	TRUE	1	0.628699038691314	2		386	699	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0043534-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	236	424	1	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.628699038691314	2		425	711	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	rs786202799	NA	P-0043534-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	363	803	0	ENST00000269305.4:c.376-2A>C		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.628699038691314	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.628699038691314	1		803	763	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426844	70426844	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043534-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	34	388	0	ENST00000373644.4:c.4504G>T	p.Val1502Phe	p.V1502F	ENST00000373644	NM_030625.2	1502	Gtc/Ttc	7/12	1	2	FACETS	0.183	0.149	0.222	0.183	0.149	0.222	SUBCLONAL	1	TRUE	1	0.628699038691314	2		388	590	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066874	30066874	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043534-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	225	573	0	ENST00000331968.5:c.2257G>A	p.Glu753Lys	p.E753K	ENST00000331968	NM_002742.2	753	Gag/Aag	16/18	0.606320719580781	4	FACETS	0.922	0.857	0.989	0.307	0.285	0.33	CLONAL	1	TRUE	1	0.628699038691314	4		573	1265	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457352	67457353	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043534-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	697	772	0	ENST00000327367.4:c.327dup	p.Glu110Ter	p.E110*	ENST00000327367	NM_005902.3	109	tgt/tgTt	2/9	0.628699038691314	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.628699038691314	2		772	1100	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0043877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	149	377	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.680836158165818	4	FACETS	0.836	0.764	0.912	0.418	0.382	0.456	CLONAL	1	TRUE	2	0.680836158165818	4		377	880	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0043877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	800	1064	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.680836158165818	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.680836158165818	2		1064	1154	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105709	27105709	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	112	394	2	ENST00000324856.7:c.5320G>C	p.Glu1774Gln	p.E1774Q	ENST00000324856	NM_006015.4	1774	Gaa/Caa	20/20	1	2	FACETS	0.922	0.838	1	0.922	0.838	1	CLONAL	1	TRUE	1	0.680836158165818	2		396	357	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602799	10602799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	841	1200	0	ENST00000171111.5:c.779G>T	p.Arg260Leu	p.R260L	ENST00000171111	NM_203500.1	260	cGa/cTa	3/6	0.680836158165818	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.680836158165818	2		1200	1188	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541542	29541542	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137854557	NA	P-0043877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	14	430	0	ENST00000356175.3:c.1466A>G	p.Tyr489Cys	p.Y489C	ENST00000356175	NM_000267.3	489	tAt/tGt	13/57	0.680836158165818	2	FACETS	0.249	0.181	0.332	0.125	0.09	0.166	SUBCLONAL	1	TRUE	0	0.680836158165818	2		430	165	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149011	61149011	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	309	373	0	ENST00000295025.8:c.1201C>T	p.His401Tyr	p.H401Y	ENST00000295025	NM_002908.2	401	Cat/Tat	11/11	0.680836158165818	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.680836158165818	3		373	589	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852298	63852298	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs752506951	NA	P-0043877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	217	697	0	ENST00000279873.7:c.3076A>G	p.Lys1026Glu	p.K1026E	ENST00000279873	NM_032199.2	1026	Aaa/Gaa	10/10	0.680836158165818	2	FACETS	0.92	0.859	0.982	0.46	0.429	0.491	CLONAL	1	TRUE	0	0.680836158165818	2		697	693	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106159	27106159	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375952330	NA	P-0043877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	219	609	0	ENST00000324856.7:c.5770G>A	p.Glu1924Lys	p.E1924K	ENST00000324856	NM_006015.4	1924	Gag/Aag	20/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.680836158165818	2		609	617	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105796	27105796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	178	518	0	ENST00000324856.7:c.5407G>A	p.Glu1803Lys	p.E1803K	ENST00000324856	NM_006015.4	1803	Gag/Aag	20/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.680836158165818	2		518	512	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105614	27105614	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	181	536	0	ENST00000324856.7:c.5225G>C	p.Arg1742Thr	p.R1742T	ENST00000324856	NM_006015.4	1742	aGa/aCa	20/20	1	2	FACETS	0.946	0.878	1	0.946	0.878	1	CLONAL	1	TRUE	1	0.680836158165818	2		536	562	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105727	27105727	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	114	413	0	ENST00000324856.7:c.5338G>C	p.Glu1780Gln	p.E1780Q	ENST00000324856	NM_006015.4	1780	Gaa/Caa	20/20	1	2	FACETS	0.928	0.844	1	0.928	0.844	1	CLONAL	1	TRUE	1	0.680836158165818	2		413	361	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105895	27105895	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	194	609	0	ENST00000324856.7:c.5506G>C	p.Glu1836Gln	p.E1836Q	ENST00000324856	NM_006015.4	1836	Gag/Cag	20/20	1	2	FACETS	0.905	0.841	0.969	0.905	0.841	0.969	CLONAL	1	TRUE	1	0.680836158165818	2		609	630	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106166	27106166	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	224	613	0	ENST00000324856.7:c.5777G>T	p.Gly1926Val	p.G1926V	ENST00000324856	NM_006015.4	1926	gGa/gTa	20/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.680836158165818	2		613	634	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106279	27106279	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	266	737	1	ENST00000324856.7:c.5890G>A	p.Glu1964Lys	p.E1964K	ENST00000324856	NM_006015.4	1964	Gag/Aag	20/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.680836158165818	2		738	768	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100664	8100664	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1506	724	1075	0	ENST00000346208.3:c.638C>G	p.Ser213Trp	p.S213W	ENST00000346208		213	tCg/tGg	3/6	0.521976860005301	6	FACETS	1	0.994	1	0.751	0.723	0.778	CLONAL	2	TRUE	3	0.680836158165818	6		1075	2230	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435176	18435176	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	245	273	1	ENST00000266497.5:c.161A>G	p.Tyr54Cys	p.Y54C	ENST00000266497		54	tAc/tGc	1/31	0.680836158165818	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.680836158165818	3		274	468	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705394	43705394	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	598	927	0	ENST00000382044.4:c.5228T>G	p.Met1743Arg	p.M1743R	ENST00000382044	NM_001141980.1	1743	aTg/aGg	24/28	0.680836158165818	4	FACETS	0.976	0.939	1	0.976	0.939	1	CLONAL	2	TRUE	2	0.680836158165818	4		927	1513	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134529	2134529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	863	1271	0	ENST00000219476.3:c.4306G>A	p.Asp1436Asn	p.D1436N	ENST00000219476	NM_000548.3	1436	Gac/Aac	34/42	0.680836158165818	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.680836158165818	2		1271	1232	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40859977	40859977	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	867	502	0	ENST00000428826.2:c.1659C>G	p.Asp553Glu	p.D553E	ENST00000428826		553	gaC/gaG	15/21	0.665864994750572	5	FACETS	0.975	0.958	0.992	0.975	0.958	0.992	CLONAL	5	TRUE	0	0.680836158165818	5		502	1056	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306619	41306619	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	467	823	0	ENST00000373198.4:c.1040T>A	p.Leu347Gln	p.L347Q	ENST00000373198	NM_133170.3	347	cTg/cAg	7/32	NA	2	FACETS	0.932	0.901	0.963			1	INDETERMINATE	2	TRUE	NA	0.680836158165818	2		823	736	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050650	30050650	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	387	393	0	ENST00000338641.4:c.452G>T	p.Gly151Val	p.G151V	ENST00000338641	NM_000268.3	151	gGt/gTt	5/16	0.674585529391698	3	FACETS	0.955	0.924	0.985	0.955	0.924	0.985	CLONAL	3	TRUE	0	0.680836158165818	3		393	532	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269060	142269060	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	304	422	1	ENST00000350721.4:c.2890G>T	p.Val964Leu	p.V964L	ENST00000350721	NM_001184.3	964	Gtg/Ttg	14/47	0.680836158165818	4	FACETS	0.876	0.828	0.924	0.876	0.828	0.924	CLONAL	2	TRUE	2	0.680836158165818	4		423	857	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535384	66535384	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs888131597	NA	P-0043877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	317	467	0	ENST00000273854.3:c.77C>G	p.Ala26Gly	p.A26G	ENST00000273854	NM_004439.5	26	gCg/gGg	1/18	0.680836158165818	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.680836158165818	2		467	452	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539015	187539015	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	366	507	0	ENST00000441802.2:c.8725A>G	p.Thr2909Ala	p.T2909A	ENST00000441802	NM_005245.3	2909	Acc/Gcc	10/27	0.680836158165818	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.680836158165818	2		507	530	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562666	176562666	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	373	492	0	ENST00000439151.2:c.562C>G	p.Gln188Glu	p.Q188E	ENST00000439151	NM_022455.4	188	Cag/Gag	2/23	0.678701243893269	4	FACETS	0.967	0.921	1	0.484	0.46	0.507	CLONAL	2	TRUE	0	0.680836158165818	4		492	952	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346592	81346592	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	178	340	0	ENST00000222390.5:c.1361C>G	p.Thr454Arg	p.T454R	ENST00000222390	NM_000601.4	454	aCg/aGg	11/18	0.379727595700606	5	FACETS	1	0.956	1	0.692	0.643	0.742	INDETERMINATE	2	TRUE	2	0.680836158165818	5		340	509	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81399214	81399214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	482	693	0	ENST00000222390.5:c.74C>T	p.Ala25Val	p.A25V	ENST00000222390	NM_000601.4	25	gCc/gTc	1/18	0.379727595700606	5	FACETS	0.862	0.827	0.897	0.862	0.827	0.897	INDETERMINATE	3	TRUE	2	0.680836158165818	5		693	1107	SUCCESS
AR	367	MSKCC	GRCh37	X	66766355	66766355	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	66	46	0	ENST00000374690.3:c.1367G>T	p.Gly456Val	p.G456V	ENST00000374690	NM_000044.3	456	gGt/gTt	1/8	1	1	FACETS		NA	1	1	0.986	1	NA	2	TRUE	0	0.680836158165818	1		46	82	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433979	49433979	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	98	1236	0	ENST00000301067.7:c.7574G>T	p.Gly2525Val	p.G2525V	ENST00000301067	NM_003482.3	2525	gGt/gTt	31/54	NA	2	FACETS	0.251	0.223	0.282			1	INDETERMINATE	1	TRUE	NA	0.680836158165818	2		1236	1145	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257867	133257867	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0043877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	91	396	0	ENST00000320574.5:c.63-2A>G		p.X21_splice	ENST00000320574	NM_006231.2	21			0.496538386863691	3	FACETS	0.711	0.633	0.793	0.355	0.316	0.397	SUBCLONAL	1	TRUE	1	0.680836158165818	3		396	504	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993552	72993552	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	187	907	0	ENST00000268489.5:c.493C>G	p.Pro165Ala	p.P165A	ENST00000268489	NM_006885.3	165	Cct/Gct	2/10	0.680836158165818	2	FACETS	0.573	0.529	0.619	0.287	0.264	0.31	SUBCLONAL	1	TRUE	0	0.680836158165818	2		907	958	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660583	190660583	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	60	274	0	ENST00000441310.2:c.221A>G	p.Tyr74Cys	p.Y74C	ENST00000441310	NM_000534.4	74	tAc/tGc	3/13	0.455754599337265	6	FACETS	0.708	0.61	0.815			1	SUBCLONAL	1	TRUE	NA	0.680836158165818	6		274	588	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030317	180030322	+	protein_altering_variant	In_Frame_Del	DEL	CAGGCC	CAGGCC	GAG	novel	NA	P-0043877-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	1371	1168	2	ENST00000261937.6:c.3962_3967delinsCTC	p.Arg1321_Glu1323delinsProGln	p.R1321_E1323delinsPQ	ENST00000261937	NM_182925.4	1321	cGGCCTGag/cCTCag	30/30	0.678701243893269	4	FACETS	0.998	0.983	1	0.998	0.983	1	CLONAL	4	TRUE	0	0.680836158165818	4		1170	1696	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0043969-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	148	562	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.313599625686782	3	FACETS	1	0.98	1	0.618	0.564	0.674	CLONAL	1	TRUE	1	0.33779685931607	3		562	829	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268361	46268362	+	missense_variant	Missense_Mutation	DNP	CT	CT	TC	novel	NA	P-0043969-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	35	388	1	ENST00000371998.3:c.2748_2749delinsTC	p.Ser917Pro	p.S917P	ENST00000371998		916	tcCTca/tcTCca	15/23	1	2	FACETS	0.376	0.307	0.453	0.376	0.307	0.453	SUBCLONAL	1	TRUE	1	0.33779685931607	2		389	551	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0045112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	126	258	0				ENST00000310581	NM_198253.2	-/1132			0.181838263207857	2	FACETS	0.968	0.886	1	0.968	0.886	1	INDETERMINATE	2	TRUE	0	0.341596597112027	2		258	381	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224504	108224504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	44	317	0	ENST00000278616.4:c.8683G>A	p.Glu2895Lys	p.E2895K	ENST00000278616	NM_000051.3	2895	Gaa/Aaa	60/63	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.341596597112027	2		317	249	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118307	17118309	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs879255681	NA	P-0045112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	63	770	1	ENST00000285071.4:c.1528_1530del	p.Glu510del	p.E510del	ENST00000285071	NM_144997.5	510	GAG/-	13/14	0.341596597112027	3	FACETS	0.63	0.545	0.724	0.315	0.272	0.362	SUBCLONAL	1	TRUE	1	0.341596597112027	3		771	685	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440302	52440303	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	63	693	0	ENST00000460680.1:c.749dup	p.Asn251GlufsTer33	p.N251Efs*33	ENST00000460680	NM_004656.3	250	gtg/gtTg	9/17	0.341596597112027	3	FACETS	0.601	0.519	0.69	0.3	0.259	0.345	SUBCLONAL	1	TRUE	1	0.341596597112027	3		693	719	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0045484-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	101	470	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.210278362408981	3	FACETS	1	0.947	1	0.547	0.489	0.608	CLONAL	1	TRUE	1	0.319279501484894	3		470	671	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2115571	2115571	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs149877669	NA	P-0045484-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	74	798	0	ENST00000219476.3:c.1651G>T	p.Ala551Ser	p.A551S	ENST00000219476	NM_000548.3	551	Gcc/Tcc	16/42	1	2	FACETS	0.586	0.512	0.666	0.586	0.512	0.666	SUBCLONAL	1	TRUE	1	0.319279501484894	2		798	791	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267360	198267360	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs374250186	NA	P-0045484-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	17	525	0	ENST00000335508.6:c.1997A>C	p.Lys666Thr	p.K666T	ENST00000335508	NM_012433.2	666	aAg/aCg	14/25	1	2	FACETS	0.174	0.129	0.228	0.174	0.129	0.228	SUBCLONAL	1	TRUE	1	0.319279501484894	2		525	612	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600336	10600336	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs751088754	NA	P-0045484-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	75	770	0	ENST00000171111.5:c.1519C>T	p.Arg507Ter	p.R507*	ENST00000171111	NM_203500.1	507	Cga/Tga	4/6	0.319279501484894	1	FACETS	0.605	0.53	0.685	0.605	0.53	0.685	SUBCLONAL	1	TRUE	0	0.319279501484894	1		770	653	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1206990	1206990	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045484-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	107	837	0	ENST00000326873.7:c.79del	p.His27ThrfsTer24	p.H27Tfs*24	ENST00000326873	NM_000455.4	26	atC/at	1/10	0.319279501484894	1	FACETS	0.672	0.602	0.746	0.672	0.602	0.746	SUBCLONAL	1	TRUE	0	0.319279501484894	1		837	838	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552630	18552630	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045484-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	50	546	0	ENST00000266497.5:c.2041C>A	p.Arg681Ser	p.R681S	ENST00000266497		681	Cgc/Agc	14/31	0.210278362408981	3	FACETS	0.675	0.573	0.788	0.338	0.286	0.394	SUBCLONAL	1	TRUE	1	0.319279501484894	3		546	538	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820881	3820881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766086544	NA	P-0045484-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	94	865	1	ENST00000262367.5:c.2570C>T	p.Pro857Leu	p.P857L	ENST00000262367	NM_004380.2	857	cCg/cTg	14/31	1	2	FACETS	0.622	0.552	0.696	0.622	0.552	0.696	SUBCLONAL	1	TRUE	1	0.319279501484894	2		866	947	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56377242	56377242	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045484-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	33	369	0	ENST00000348428.3:c.863A>T	p.Tyr288Phe	p.Y288F	ENST00000348428	NM_006785.3	288	tAc/tTc	6/17	1	2	FACETS	0.557	0.454	0.673	0.557	0.454	0.673	SUBCLONAL	1	TRUE	1	0.319279501484894	2		369	371	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097049	11097050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045484-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	113	1017	0	ENST00000358026.2:c.541dup	p.Arg181LysfsTer106	p.R181Kfs*106	ENST00000358026	NM_001128849.1	180	-/A	4/36	0.319279501484894	1	FACETS	0.787	0.708	0.87	0.787	0.708	0.87	SUBCLONAL	1	TRUE	0	0.319279501484894	1		1017	756	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513251	44513251	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045484-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	59	614	0	ENST00000291552.4:c.684G>T	p.Arg228Ser	p.R228S	ENST00000291552	NM_006758.2	228	agG/agT	8/8	1	2	FACETS	0.631	0.542	0.727	0.631	0.542	0.727	SUBCLONAL	1	TRUE	1	0.319279501484894	2		614	586	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101910013	101910013	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045484-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	31	283	0	ENST00000374994.4:c.1333G>T	p.Val445Phe	p.V445F	ENST00000374994	NM_004612.2	445	Gtt/Ttt	8/9	0.294432245897721	1	FACETS	0.551	0.447	0.669	0.551	0.447	0.669	SUBCLONAL	1	TRUE	0	0.319279501484894	1		283	296	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932797	39932797	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045484-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	91	865	0	ENST00000378444.4:c.1802C>A	p.Pro601His	p.P601H	ENST00000378444	NM_001123385.1	601	cCc/cAc	4/15	0.294432245897721	1	FACETS	0.541	0.48	0.607	0.541	0.48	0.607	SUBCLONAL	1	TRUE	0	0.319279501484894	1		865	885	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0045811-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	103	478	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.341872358432137	2		478	513	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579349	7579349	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045811-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	170	724	0	ENST00000269305.4:c.338T>C	p.Phe113Ser	p.F113S	ENST00000269305	NM_001126112.2	113	tTc/tCc	4/11	0.341872358432137	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.341872358432137	1		724	730	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528441	29528441	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045811-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	78	408	1	ENST00000356175.3:c.1198C>T	p.Gln400Ter	p.Q400*	ENST00000356175	NM_000267.3	400	Cag/Tag	11/57	0.341872358432137	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.341872358432137	1		409	368	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339017	225339017	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045811-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	91	498	0	ENST00000264414.4:c.2252G>C	p.Arg751Thr	p.R751T	ENST00000264414	NM_003590.4	751	aGa/aCa	16/16	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.341872358432137	2		498	511	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921559	178921559	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045811-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	54	324	0	ENST00000263967.3:c.1041T>G	p.Asn347Lys	p.N347K	ENST00000263967	NM_006218.2	347	aaT/aaG	5/21	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.341872358432137	2		324	302	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845419	156845419	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045811-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	204	949	0	ENST00000524377.1:c.1462G>T	p.Gly488Cys	p.G488C	ENST00000524377	NM_002529.3	488	Ggc/Tgc	12/17	0.250422384970839	3	FACETS	1	0.985	1	0.618	0.573	0.666	CLONAL	1	TRUE	1	0.341872358432137	3		949	1130	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007462	62007462	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045811-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1479	110	628	0	ENST00000392795.3:c.405G>C	p.Gln135His	p.Q135H	ENST00000392795	NM_001039933.1	135	caG/caC	3/6	0.341872358432137	7	FACETS	0.751	0.672	0.836			1	SUBCLONAL	1	TRUE	NA	0.341872358432137	7		628	1589	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007612	62007612	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045811-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1725	144	806	1	ENST00000392795.3:c.255G>C	p.Glu85Asp	p.E85D	ENST00000392795	NM_001039933.1	85	gaG/gaC	3/6	0.341872358432137	7	FACETS	0.836	0.759	0.918			1	CLONAL	1	TRUE	NA	0.341872358432137	7		807	1869	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250110	39250110	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057517897	NA	P-0045811-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	147	721	1	ENST00000402219.2:c.1459G>A	p.Glu487Lys	p.E487K	ENST00000402219	NM_005633.3	487	Gaa/Aaa	10/23	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.341872358432137	2		722	756	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442557	52442557	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747311942	NA	P-0045811-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	50	491	0	ENST00000460680.1:c.188C>T	p.Ser63Phe	p.S63F	ENST00000460680	NM_004656.3	63	tCt/tTt	4/17	1	2	FACETS	0.523	0.444	0.611	0.523	0.444	0.611	SUBCLONAL	1	TRUE	1	0.341872358432137	2		491	559	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820911	32820911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045811-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	91	977	2	ENST00000354258.4:c.683G>A	p.Gly228Asp	p.G228D	ENST00000354258	NM_000593.5	228	gGc/gAc	1/11	0.250422384970839	3	FACETS	0.578	0.512	0.649	0.289	0.256	0.325	SUBCLONAL	1	TRUE	1	0.341872358432137	3		979	1078	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0046278-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	944	987	1	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	0.648403396549877	4	FACETS	0.943	0.921	0.964	0.943	0.921	0.964	CLONAL	3	TRUE	1	0.882913230978441	4		988	1424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577095	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519984	NA	P-0046278-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	695	904	0	ENST00000269305.4:c.843C>G	p.Asp281Glu	p.D281E	ENST00000269305	NM_001126112.2	281	gaC/gaG	8/11	0.882913230978441	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.882913230978441	2		904	760	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974744	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAGCAGCGCCCGCA	CCTCCAGCAGCGCCCGCA	-	novel	NA	P-0046278-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	297	418	0	ENST00000304494.5:c.83_100del	p.Val28_Glu33del	p.V28_E33del	ENST00000304494	NM_000077.4	28	gTGCGGGCGCTGCTGGAGGcg/gcg	1/3	0.882913230978441	2	FACETS	0.94	0.912	0.966	0.94	0.912	0.966	CLONAL	2	TRUE	0	0.882913230978441	2		418	358	SUCCESS
APC	324	MSKCC	GRCh37	5	112176520	112176521	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554086550	NA	P-0046278-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	150	432	0	ENST00000257430.4:c.5234dup	p.Ile1746AspfsTer23	p.I1746Dfs*23	ENST00000257430	NM_000038.5	1743	-/A	16/16	0.882913230978441	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.882913230978441	1		432	188	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210689	36210689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754616271	NA	P-0046278-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	847	821	0	ENST00000222270.7:c.440G>A	p.Arg147Gln	p.R147Q	ENST00000222270	NM_014727.1	147	cGa/cAa	3/37	0.648403396549877	4	FACETS	0.96	0.937	0.983	0.96	0.937	0.983	CLONAL	3	TRUE	1	0.882913230978441	4		821	1254	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57567463	57567464	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046278-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	266	575	2	ENST00000316660.6:c.55dup	p.Ala19GlyfsTer69	p.A19Gfs*69	ENST00000316660	NM_021127.2	18	-/G	1/2	0.882913230978441	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.882913230978441	1		577	316	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266229	41266229	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046278-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	251	490	1	ENST00000349496.5:c.226C>G	p.Gln76Glu	p.Q76E	ENST00000349496	NM_001904.3	76	Caa/Gaa	3/15	0.527600349546671	6	FACETS	1	0.986	1	0.578	0.544	0.613	INDETERMINATE	2	TRUE	2	0.882913230978441	6		491	680	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665207	138665207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046278-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	361	991	0	ENST00000330315.3:c.358G>A	p.Gly120Ser	p.G120S	ENST00000330315	NM_023067.3	120	Ggc/Agc	1/1	0.527600349546671	6	FACETS	0.758	0.718	0.8	0.379	0.359	0.4	INDETERMINATE	2	TRUE	2	0.882913230978441	6		991	1491	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001064	150001064	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046278-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	233	607	0	ENST00000253339.5:c.2540T>G	p.Phe847Cys	p.F847C	ENST00000253339		847	tTt/tGt	4/7	0.44935732217655	4	FACETS	0.864	0.813	0.916	0.432	0.406	0.458	INDETERMINATE	2	TRUE	0	0.882913230978441	4		607	575	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729420	41729420	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046278-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	298	820	0	ENST00000242208.4:c.1109C>T	p.Ser370Leu	p.S370L	ENST00000242208	NM_002192.2	370	tCa/tTa	3/3	0.604861047260171	4	FACETS	1	0.99	1	0.405	0.381	0.429	CLONAL	1	TRUE	1	0.882913230978441	4		820	1047	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0046530-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	186	949	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.537753706573251	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.529540912343262	1		949	354	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100117	157100119	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs797045268	NA	P-0046530-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	10	57	0	ENST00000346085.5:c.1069_1071del	p.Gly357del	p.G357del	ENST00000346085	NM_020732.3	352	GGC/-	1/20	0.324356662621068	3	FACETS	0.31	0.21	0.435	0.155	0.105	0.218	SUBCLONAL	1	TRUE	1	0.529540912343262	3		57	154	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591104	67591115	+	inframe_deletion	In_Frame_Del	DEL	TTAAACCAGACC	TTAAACCAGACC	-	novel	NA	P-0046530-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	63	383	0	ENST00000274335.5:c.1700_1711del	p.Lys567_Leu570del	p.K567_L570del	ENST00000274335		566	aTTAAACCAGACCtt/att	12/15	0.324356662621068	3	FACETS	0.85	0.75	0.953	0.85	0.75	0.953	CLONAL	2	TRUE	1	0.529540912343262	3		383	177	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950724	79950725	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCGCAGCGC	rs1554066076	NA	P-0046530-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	16	194	1	ENST00000265081.6:c.181_189dup	p.Ala61_Pro63dup	p.A61_P63dup	ENST00000265081	NM_002439.4	61	gcc/gCCGCAGCGCcc	1/24	0.324356662621068	3	FACETS	0.271	0.2	0.356	0.136	0.1	0.178	SUBCLONAL	1	TRUE	1	0.529540912343262	3		195	282	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456266	32456266	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs771024882	NA	P-0046530-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1998	251	1100	0	ENST00000332351.3:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000332351	NM_024426.4	209	cAg/cCg	1/10	0.537753706573251	4	FACETS	0.645	0.6	0.691			1	SUBCLONAL	1	TRUE	NA	0.529540912343262	4		1100	2249	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046752-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	66	276	0				ENST00000310581	NM_198253.2	-/1132			0.288658948725069	3	FACETS	1	0.966	1	0.671	0.585	0.763	CLONAL	1	FALSE	1	0.288658948725069	3		276	390	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023696	27023696	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046752-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	85	517	0	ENST00000324856.7:c.802C>T	p.Gln268Ter	p.Q268*	ENST00000324856	NM_006015.4	268	Cag/Tag	1/20	0.184667430067886	3	FACETS	1	0.97	1	0.43	0.381	0.483	CLONAL	1	FALSE	0	0.288658948725069	3		517	522	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983114	201983114	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046752-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	201	653	0	ENST00000359651.3:c.963del	p.Asn321LysfsTer4	p.N321Kfs*4	ENST00000359651		321	aaC/aa	7/8	0.184667430067886	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	3	FALSE	0	0.288658948725069	3		653	518	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390691	118390691	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046752-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	26	326	0	ENST00000534358.1:c.11343del	p.Phe3781LeufsTer26	p.F3781Lfs*26	ENST00000534358	NM_005933.3	3781	Ttt/tt	33/36	0.195522509895606	3	FACETS	0.95	0.757	1	0.475	0.378	0.585	CLONAL	1	FALSE	1	0.288658948725069	3		326	217	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060821	38060822	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046752-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	123	940	0	ENST00000250448.2:c.1167dup	p.Gly390ArgfsTer25	p.G390Rfs*25	ENST00000250448	NM_004496.3	389	-/A	2/2	0.250992808939114	3	FACETS	1	0.984	1	0.725	0.656	0.796	CLONAL	1	FALSE	1	0.288658948725069	3		940	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578538	7578538	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046752-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	118	915	0	ENST00000269305.4:c.392A>C	p.Asn131Thr	p.N131T	ENST00000269305	NM_001126112.2	131	aAc/aCc	5/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.288658948725069	2		915	579	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412947	49412947	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046752-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	46	736	0	ENST00000418115.1:c.76A>C	p.Ser26Arg	p.S26R	ENST00000418115	NM_001664.2	26	Agc/Cgc	2/5	0.250992808939114	3	FACETS	0.907	0.766	1	0.454	0.383	0.532	CLONAL	1	FALSE	1	0.288658948725069	3		736	402	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908892	101908892	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0046752-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	41	471	0	ENST00000374994.4:c.1255+1G>T		p.X419_splice	ENST00000374994	NM_004612.2	419			0.288658948725069	1	FACETS	0.769	0.643	0.908	0.769	0.643	0.908	CLONAL	1	FALSE	0	0.288658948725069	1		471	316	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942708	44942708	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046752-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	24	348	0	ENST00000377967.4:c.3288G>A	p.Trp1096Ter	p.W1096*	ENST00000377967	NM_021140.2	1096	tgG/tgA	23/29	0.288658948725069	1	FACETS	0.722	0.57	0.896	0.722	0.57	0.896	SUBCLONAL	1	FALSE	0	0.288658948725069	1		348	197	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	60	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.338795725003966	2		276	352	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0047087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	155	881	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	0.961	0.879	1	0.961	0.879	1	CLONAL	1	TRUE	1	0.338795725003966	2		881	952	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047122-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	45	276	0				ENST00000310581	NM_198253.2	-/1132			0.223267763677477	3	FACETS	1	0.882	1	0.525	0.444	0.613	INDETERMINATE	1	TRUE	1	0.394634327952525	3		276	260	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0047122-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1652	6541	907	0	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.394634327952525	45	FACETS	1	0.997	1			1	CLONAL	38	TRUE	NA	0.394634327952525	45		907	8193	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575507	67575507	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047122-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	84	434	0	ENST00000274335.5:c.581del	p.Pro194GlnfsTer13	p.P194Qfs*13	ENST00000274335		194	Cca/ca	4/15	0.223267763677477	3	FACETS	1	0.961	1	0.595	0.528	0.666	INDETERMINATE	1	TRUE	1	0.394634327952525	3		434	428	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417862	138417862	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047122-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	98	530	0	ENST00000289153.2:c.1657A>G	p.Asn553Asp	p.N553D	ENST00000289153	NM_006219.2	553	Aat/Gat	11/22	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.394634327952525	2		530	488	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591281	67591292	+	inframe_deletion	In_Frame_Del	DEL	GTTGAACGAGTG	GTTGAACGAGTG	-	novel	NA	P-0047122-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	46	378	0	ENST00000274335.5:c.1783_1794del	p.Asn595_Leu598del	p.N595_L598del	ENST00000274335		593	aaGTTGAACGAGTGg/aag	13/15	0.223267763677477	3	FACETS	0.843	0.713	0.986	0.422	0.356	0.493	INDETERMINATE	1	TRUE	1	0.394634327952525	3		378	331	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144049	11144051	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0047310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	127	938	2	ENST00000358026.2:c.3634_3636del	p.Glu1212del	p.E1212del	ENST00000358026	NM_001128849.1	1210	gtGGAg/gtg	26/36	0.127281311027287	0	FACETS	0.348	0.316	0.382			1	INDETERMINATE	1	TRUE	0	0.541323092519012	0		940	618	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919601	96919601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144326855	NA	P-0047310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	146	807	0	ENST00000258439.3:c.662C>T	p.Pro221Leu	p.P221L	ENST00000258439	NM_001193304.2	221	cCg/cTg	4/4	1	2	FACETS	0.91	0.834	0.989	0.91	0.834	0.989	CLONAL	1	TRUE	1	0.541323092519012	2		807	593	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188207	10188207	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs869025640	NA	P-0047310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	142	612	2	ENST00000256474.2:c.351del	p.Trp117CysfsTer42	p.W117Cfs*42	ENST00000256474	NM_000551.3	117	tGg/tg	2/3	0.479449626696023	1	FACETS	0.797	0.732	0.865	0.797	0.732	0.865	SUBCLONAL	1	TRUE	0	0.541323092519012	1		614	480	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0047455-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	57	470	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.96	0.823	1	0.96	0.823	1	CLONAL	1	TRUE	1	0.197267507461873	2		470	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912664	NA	P-0047455-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	19	741	0	ENST00000269305.4:c.1010G>C	p.Arg337Pro	p.R337P	ENST00000269305	NM_001126112.2	337	cGc/cCc	10/11	1	2	FACETS	0.251	0.189	0.324	0.251	0.189	0.324	SUBCLONAL	1	TRUE	1	0.197267507461873	2		741	768	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786795	3786795	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047455-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	19	454	0	ENST00000262367.5:c.4416G>T	p.Trp1472Cys	p.W1472C	ENST00000262367	NM_004380.2	1472	tgG/tgT	27/31	1	2	FACETS	0.389	0.294	0.502	0.389	0.294	0.502	SUBCLONAL	1	TRUE	1	0.197267507461873	2		454	495	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045116	47045116	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047455-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	81	358	0	ENST00000377604.3:c.2360del	p.Asn787ThrfsTer15	p.N787Tfs*15	ENST00000377604	NM_001204468.1	786	cAa/ca	21/24	1	1	FACETS	1	0.925	1	1	0.985	1	CLONAL	2	TRUE	0	0.197267507461873	1		358	351	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220388	1220388	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1131690938	NA	P-0047455-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	71	665	0	ENST00000326873.7:c.481A>T	p.Ile161Phe	p.I161F	ENST00000326873	NM_000455.4	161	Att/Ttt	4/10	0.197267507461873	1	FACETS	0.991	0.864	1	0.991	0.864	1	CLONAL	1	TRUE	0	0.197267507461873	1		665	655	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602698	10602698	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047455-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	97	874	0	ENST00000171111.5:c.880G>T	p.Asp294Tyr	p.D294Y	ENST00000171111	NM_203500.1	294	Gac/Tac	3/6	0.197267507461873	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.197267507461873	1		874	771	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161294	55161294	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs764265933	NA	P-0047455-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	62	406	0	ENST00000257290.5:c.3125C>T	p.Ser1042Leu	p.S1042L	ENST00000257290	NM_006206.4	1042	tCg/tTg	23/23	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.197267507461873	2		406	428	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406228	406228	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047455-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	56	447	0	ENST00000399788.2:c.4213G>T	p.Ala1405Ser	p.A1405S	ENST00000399788	NM_001042603.1	1405	Gct/Tct	25/28	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.197267507461873	2		447	520	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39233668	39233668	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047455-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	64	389	0	ENST00000402219.2:c.2676A>T	p.Gln892His	p.Q892H	ENST00000402219	NM_005633.3	892	caA/caT	17/23	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.197267507461873	2		389	623	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877339	40877339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047455-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	46	496	0	ENST00000373198.4:c.2357C>T	p.Thr786Ile	p.T786I	ENST00000373198	NM_133170.3	786	aCc/aTc	15/32	0.197267507461873	0	FACETS	0.783	0.66	0.919			1	CLONAL	1	TRUE	0	0.197267507461873	0		496	478	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876316	35876316	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047455-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	53	557	0	ENST00000303115.3:c.1108C>G	p.Leu370Val	p.L370V	ENST00000303115	NM_002185.3	370	Ctg/Gtg	8/8	0.14889583474476	4	FACETS	1	0.936	1	0.592	0.505	0.688	CLONAL	1	TRUE	2	0.197267507461873	4		557	543	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528780	8528780	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0047455-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	55	398	0	ENST00000356435.5:c.353-1G>T		p.X118_splice	ENST00000356435		118			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.197267507461873	2		398	445	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520017	NA	P-0047455-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	251	834	3	ENST00000326873.7:c.647C>T	p.Ser216Phe	p.S216F	ENST00000326873	NM_000455.4	216	tCc/tTc	5/10	0.303584494829662	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.31	2		837	795	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912664	NA	P-0047455-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	301	741	0	ENST00000269305.4:c.1010G>C	p.Arg337Pro	p.R337P	ENST00000269305	NM_001126112.2	337	cGc/cCc	10/11	0.258410419571278	3	FACETS	1	0.99	1	0.806	0.761	0.852	CLONAL	2	TRUE	0	0.31	3		741	928	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206843	162206843	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047455-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	65	475	0	ENST00000366898.1:c.832G>T	p.Val278Phe	p.V278F	ENST00000366898	NM_004562.2	278	Gtt/Ttt	7/12	0.303584494829662	9	FACETS	0.852	0.737	0.978			1	CLONAL	1	TRUE	NA	0.31	9		475	1026	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355206	81355206	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047455-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	25	261	1	ENST00000222390.5:c.1168G>T	p.Asp390Tyr	p.D390Y	ENST00000222390	NM_000601.4	390	Gat/Tat	9/18	0.251175824621643	3	FACETS	0.891	0.707	1	0.446	0.353	0.551	CLONAL	1	TRUE	1	0.31	3		262	209	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105657	11105657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047455-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	98	761	0	ENST00000358026.2:c.1573G>T	p.Glu525Ter	p.E525*	ENST00000358026	NM_001128849.1	525	Gag/Tag	9/36	0.303584494829662	2	FACETS	0.876	0.781	0.976	0.438	0.39	0.488	CLONAL	1	TRUE	0	0.31	2		761	722	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912069	32912069	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047455-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	57	626	1	ENST00000380152.3:c.3577G>T	p.Ala1193Ser	p.A1193S	ENST00000380152		1193	Gct/Tct	11/27	1	2	FACETS	0.707	0.607	0.816	0.707	0.607	0.816	SUBCLONAL	1	TRUE	1	0.31	2		627	520	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786795	3786795	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047455-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	176	454	0	ENST00000262367.5:c.4416G>T	p.Trp1472Cys	p.W1472C	ENST00000262367	NM_004380.2	1472	tgG/tgT	27/31	0.258410419571278	3	FACETS	0.915	0.85	0.98	0.915	0.85	0.98	CLONAL	3	TRUE	0	0.31	3		454	478	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277036	18277036	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047455-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	86	671	0	ENST00000222254.8:c.1483G>T	p.Gly495Cys	p.G495C	ENST00000222254	NM_005027.3	495	Ggc/Tgc	12/16	0.303584494829662	2	FACETS	0.928	0.822	1	0.464	0.411	0.521	CLONAL	1	TRUE	0	0.31	2		671	598	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268853	115268853	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047455-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	117	559	0	ENST00000438362.2:c.1757A>C	p.Lys586Thr	p.K586T	ENST00000438362	NM_001242891.1	586	aAg/aCg	14/20	0.246914790645613	2	FACETS	0.785	0.711	0.861	0.785	0.711	0.861	SUBCLONAL	2	TRUE	0	0.31	2		559	481	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465000	120465000	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047455-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	110	561	0	ENST00000256646.2:c.5072T>G	p.Phe1691Cys	p.F1691C	ENST00000256646	NM_024408.3	1691	tTt/tGt	28/34	0.246914790645613	2	FACETS	0.785	0.71	0.864	0.785	0.71	0.864	SUBCLONAL	2	TRUE	0	0.31	2		561	452	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600411	43600411	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047455-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	71	443	0	ENST00000355710.3:c.639del	p.Phe214SerfsTer10	p.F214Sfs*10	ENST00000355710	NM_020975.4	213	Ccc/cc	4/20	0.137038200285463	3	FACETS	1	0.964	1	0.428	0.375	0.485	INDETERMINATE	1	TRUE	0	0.31	3		443	412	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691219	18691219	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1303514822	NA	P-0047455-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	69	373	0	ENST00000266497.5:c.3330C>A	p.Ser1110Arg	p.S1110R	ENST00000266497		1110	agC/agA	23/31	0.165476526771322	5	FACETS	0.908	0.796	1	0.606	0.53	0.686	INDETERMINATE	2	TRUE	2	0.31	5		373	359	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860111	57860111	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047455-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	168	898	0	ENST00000228682.2:c.851C>A	p.Ala284Asp	p.A284D	ENST00000228682	NM_005269.2	284	gCc/gAc	8/12	0.303584494829662	3	FACETS	1	0.98	1	0.604	0.555	0.656	CLONAL	1	TRUE	1	0.31	3		898	1036	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562203	21562203	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047455-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	127	1233	1	ENST00000382592.4:c.1716G>T	p.Gln572His	p.Q572H	ENST00000382592	NM_014572.2	572	caG/caT	4/8	1	2	FACETS	0.71	0.642	0.783	0.71	0.642	0.783	SUBCLONAL	1	TRUE	1	0.31	2		1234	1154	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248566	212248566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1210422013	NA	P-0047455-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	208	633	0	ENST00000342788.4:c.3701A>G	p.Lys1234Arg	p.K1234R	ENST00000342788	NM_005235.2	1234	aAg/aGg	28/28	0.228268563379552	3	FACETS	1	0.981	1	0.76	0.708	0.813	CLONAL	2	TRUE	0	0.31	3		633	680	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880893	134880893	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047455-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	141	672	0	ENST00000398015.3:c.1456A>T	p.Ser486Cys	p.S486C	ENST00000398015	NM_004441.4	486	Agt/Tgt	7/16	0.251175824621643	3	FACETS	0.788	0.719	0.859	0.788	0.719	0.859	SUBCLONAL	2	TRUE	1	0.31	3		672	667	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230896	66230896	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047455-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	54	346	0	ENST00000273854.3:c.2075G>T	p.Gly692Val	p.G692V	ENST00000273854	NM_004439.5	692	gGa/gTa	12/18	0.0642990469725331	3	FACETS	0.756	0.652	0.869	0.756	0.652	0.869	INDETERMINATE	2	TRUE	1	0.31	3		346	266	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517382	157517382	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs199674889	NA	P-0047455-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	74	614	0	ENST00000346085.5:c.3946G>T	p.Gly1316Ter	p.G1316*	ENST00000346085	NM_020732.3	1316	Gga/Tga	16/20	0.0642990469725331	3	FACETS	0.933	0.817	1	0.467	0.408	0.529	INDETERMINATE	1	TRUE	1	0.31	3		614	591	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468101	50468101	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047455-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	58	591	0	ENST00000331340.3:c.1336C>A	p.Gln446Lys	p.Q446K	ENST00000331340	NM_006060.4	446	Cag/Aag	8/8	0.251175824621643	3	FACETS	0.856	0.736	0.986	0.428	0.368	0.493	CLONAL	1	TRUE	1	0.31	3		591	505	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55272981	55272981	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1268506326	NA	P-0047455-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	160	688	0	ENST00000275493.2:c.3304G>T	p.Ala1102Ser	p.A1102S	ENST00000275493	NM_005228.3	1102	Gct/Tct	28/28	0.251175824621643	3	FACETS	1	0.986	1	0.693	0.636	0.753	CLONAL	1	TRUE	1	0.31	3		688	860	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624416	140624416	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047455-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	12	60	0	ENST00000288602.6:c.88G>C	p.Gly30Arg	p.G30R	ENST00000288602	NM_004333.4	30	Ggc/Cgc	1/18	0.251175824621643	3	FACETS	0.951	0.676	1	0.476	0.338	0.64	CLONAL	1	TRUE	1	0.31	3		60	94	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211418	98211418	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047455-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	123	844	0	ENST00000331920.6:c.3737G>T	p.Gly1246Val	p.G1246V	ENST00000331920	NM_000264.3	1246	gGc/gTc	22/24	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.31	2		844	747	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27217747	27217747	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047455-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	65	595	0	ENST00000380036.4:c.3053A>C	p.Asn1018Thr	p.N1018T	ENST00000380036	NM_000459.3	1018	aAc/aCc	19/23	0.303584494829662	0	FACETS	0.571	0.495	0.652			1	SUBCLONAL	1	TRUE	0	0.31	0		595	507	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982641	90982641	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047996-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	158	280	0	ENST00000265433.3:c.847C>T	p.Pro283Ser	p.P283S	ENST00000265433	NM_002485.4	283	Cct/Tct	7/16	0.105677098413514	4	FACETS	1	0.966	1	1	0.966	1	INDETERMINATE	2	TRUE	2	0.950114992924007	4		280	308	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906928	32906928	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047996-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	109	341	0	ENST00000380152.3:c.1313A>T	p.Asp438Val	p.D438V	ENST00000380152		438	gAt/gTt	10/27	0.950114992924007	4	FACETS	0.499	0.447	0.554			1	SUBCLONAL	1	TRUE	NA	0.950114992924007	4		341	897	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0048404-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	82	465	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.685442556100898	5	FACETS	0.978	0.902	1	0.978	0.902	1	CLONAL	4	TRUE	1	0.685442556100898	5		465	124	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424958105	NA	P-0048404-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	39	423	0	ENST00000334344.6:c.940C>T	p.Arg314Cys	p.R314C	ENST00000334344	NM_152641.2	314	Cgt/Tgt	8/21	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.685442556100898	2		423	90	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0048404-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	39	440	0				ENST00000310581	NM_198253.2	-/1132			0.473837287359031	4	FACETS	0.927	0.81	1	0.927	0.81	1	CLONAL	3	TRUE	1	0.685442556100898	4		440	69	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857524	9857524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778230379	NA	P-0048404-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	15	494	0	ENST00000330684.3:c.3877G>A	p.Asp1293Asn	p.D1293N	ENST00000330684	NM_001134407.1	1293	Gat/Aat	13/13	1	2	FACETS	0.768	0.579	0.979	0.768	0.579	0.979	CLONAL	1	TRUE	1	0.685442556100898	2		494	57	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686267	117686267	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048404-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	41	412	0	ENST00000368508.3:c.3074G>A	p.Gly1025Glu	p.G1025E	ENST00000368508	NM_002944.2	1025	gGa/gAa	20/43	0.514044241623261	4	FACETS	0.96	0.825	1			1	CLONAL	2	TRUE	NA	0.685442556100898	4		412	105	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0048404-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	23	513	0	ENST00000304494.5:c.151-1G>A		p.X51_splice	ENST00000304494	NM_000077.4	51			0.680229024957323	1	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	0	0.685442556100898	1		513	41	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665464	138665540	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCTCGGCGGCGGCCCTTCTGGCTCCTTGACTGTGCGACCGGTCTCTGGGGCCAGCAGGGCCCCCGCCGCGTCCTC	GGGCTCGGCGGCGGCCCTTCTGGCTCCTTGACTGTGCGACCGGTCTCTGGGGCCAGCAGGGCCCCCGCCGCGTCCTC	-	novel	NA	P-0048404-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	13	736	3	ENST00000330315.3:c.25_101del	p.Glu9ArgfsTer61	p.E9Rfs*61	ENST00000330315	NM_023067.3	9	GAGGACGCGGCGGGGGCCCTGCTGGCCCCAGAGACCGGTCGCACAGTCAAGGAGCCAGAAGGGCCGCCGCCGAGCCCa/a	1/1	0.685442556100898	3	FACETS	0.679	0.493	0.896	0.34	0.246	0.448	SUBCLONAL	1	TRUE	1	0.685442556100898	3		739	75	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121566	2121566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750663771	NA	P-0048404-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	15	952	0	ENST00000219476.3:c.1895C>T	p.Pro632Leu	p.P632L	ENST00000219476	NM_000548.3	632	cCc/cTc	18/42	1	2	FACETS	0.742	0.559	0.947	0.742	0.559	0.947	CLONAL	1	TRUE	1	0.685442556100898	2		952	59	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612015	189612016	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0048404-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	28	494	0	ENST00000264731.3:c.1767_1768delinsTT	p.Pro590Ser	p.P590S	ENST00000264731	NM_003722.4	589	atCCct/atTTct	14/14	0.685442556100898	3	FACETS	0.831	0.693	0.973	0.831	0.693	0.973	CLONAL	2	TRUE	1	0.685442556100898	3		494	66	SUCCESS
APC	324	MSKCC	GRCh37	5	112174563	112174563	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048404-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	23	456	1	ENST00000257430.4:c.3272C>A	p.Pro1091Gln	p.P1091Q	ENST00000257430	NM_000038.5	1091	cCa/cAa	16/16	0.280023005222565	3	FACETS	1	0.925	1	0.683	0.552	0.822	INDETERMINATE	1	TRUE	1	0.685442556100898	3		457	66	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543672	148543672	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1199671048	NA	P-0048404-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	39	415	0	ENST00000320356.2:c.136C>T	p.Arg46Cys	p.R46C	ENST00000320356	NM_004456.4	46	Cgt/Tgt	3/20	0.68294600341297	5	FACETS	1	0.932	1			1	CLONAL	1	TRUE	NA	0.685442556100898	5		415	188	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	42	276	0				ENST00000310581	NM_198253.2	-/1132			0.201908380907352	3	FACETS	1	0.911	1	0.564	0.474	0.661	INDETERMINATE	1	TRUE	1	0.348714973129047	3		276	251	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087458	27087458	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	123	675	0	ENST00000324856.7:c.2032C>T	p.Gln678Ter	p.Q678*	ENST00000324856	NM_006015.4	678	Cag/Tag	5/20	0.201908380907352	3	FACETS	0.95	0.859	1	0.475	0.429	0.524	INDETERMINATE	1	TRUE	1	0.348714973129047	3		675	872	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143341	30143341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	188	449	0	ENST00000389048.3:c.185C>T	p.Ser62Leu	p.S62L	ENST00000389048	NM_004304.4	62	tCg/tTg	1/29	0.289755057420995	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.348714973129047	3		449	539	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978935	25978935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	76	368	0	ENST00000435504.4:c.988G>A	p.Glu330Lys	p.E330K	ENST00000435504		330	Gaa/Aaa	10/13	0.289755057420995	3	FACETS	1	0.929	1	0.54	0.475	0.609	CLONAL	1	TRUE	1	0.348714973129047	3		368	474	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856617	111856617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1364785726	NA	P-0048590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	46	135	1	ENST00000341259.2:c.668C>T	p.Ala223Val	p.A223V	ENST00000341259	NM_005475.2	223	gCg/gTg	2/8	0.289755057420995	3	FACETS	0.807	0.689	0.934	0.807	0.689	0.934	CLONAL	2	TRUE	1	0.348714973129047	3		136	192	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696719	47696719	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	132	356	0	ENST00000347630.2:c.229G>C	p.Asp77His	p.D77H	ENST00000347630	NM_001007230.1	77	Gat/Cat	5/11	0.348714973129047	3	FACETS	0.872	0.796	0.95	0.872	0.796	0.95	CLONAL	2	TRUE	1	0.348714973129047	3		356	510	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665280	138665280	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	143	716	0	ENST00000330315.3:c.285G>C	p.Lys95Asn	p.K95N	ENST00000330315	NM_023067.3	95	aaG/aaC	1/1	0.289755057420995	3	FACETS	1	0.975	1	0.591	0.539	0.645	CLONAL	1	TRUE	1	0.348714973129047	3		716	815	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577572	7577572	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882004	NA	P-0048590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	180	543	0	ENST00000269305.4:c.709A>G	p.Met237Val	p.M237V	ENST00000269305	NM_001126112.2	237	Atg/Gtg	7/11	0.348714973129047	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.348714973129047	2		543	498	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564485	41564485	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	52	327	0	ENST00000263253.7:c.3907G>C	p.Glu1303Gln	p.E1303Q	ENST00000263253	NM_001429.3	1303	Gag/Cag	24/31	1	2	FACETS	0.838	0.716	0.97	0.838	0.716	0.97	CLONAL	1	TRUE	1	0.348714973129047	2		327	356	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793041	33793041	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	32	157	0	ENST00000498907.2:c.280G>C	p.Ala94Pro	p.A94P	ENST00000498907	NM_004364.3	94	Gcc/Ccc	1/1	0.253012697585165	4	FACETS	0.887	0.723	1	0.296	0.241	0.357	CLONAL	1	TRUE	1	0.348714973129047	4		157	279	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006068	22006068	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	109	584	0	ENST00000276925.6:c.335G>T	p.Trp112Leu	p.W112L	ENST00000276925	NM_004936.3	112	tGg/tTg	2/2	0.348714973129047	2	FACETS	1	0.967	1	0.585	0.527	0.646	CLONAL	1	TRUE	0	0.348714973129047	2		584	534	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303244	11303244	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1392170596	NA	P-0048590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	110	655	1	ENST00000361445.4:c.1339G>A	p.Glu447Lys	p.E447K	ENST00000361445	NM_004958.3	447	Gag/Aag	9/58	0.185652124976249	2	FACETS	0.89	0.8	0.985	0.445	0.4	0.493	INDETERMINATE	1	TRUE	0	0.348714973129047	2		656	709	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105238746	105238746	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749544983	NA	P-0048590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	265	809	1	ENST00000349310.3:c.1216C>T	p.Arg406Cys	p.R406C	ENST00000349310	NM_001014432.1	406	Cgc/Tgc	13/15	0.348714973129047	1	FACETS	0.971	0.917	1	1	0.995	1	CLONAL	2	TRUE	0	0.348714973129047	1		810	646	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519518	137519518	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs963564493	NA	P-0048590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	50	331	0	ENST00000367739.4:c.1120A>G	p.Ile374Val	p.I374V	ENST00000367739	NM_000416.2	374	Ata/Gta	7/7	1	2	FACETS	0.801	0.682	0.931	0.801	0.682	0.931	CLONAL	1	TRUE	1	0.348714973129047	2		331	358	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366994	40366994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1300	116	789	2	ENST00000397332.2:c.203C>T	p.Ser68Leu	p.S68L	ENST00000397332	NM_001033082.2	68	tCg/tTg	2/3	0.2705142429406	2	FACETS	0.47	0.422	0.521	0.235	0.211	0.261	SUBCLONAL	1	TRUE	0	0.348714973129047	2		791	1416	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521497	46521497	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	94	385	1	ENST00000262741.5:c.911A>C	p.Gln304Pro	p.Q304P	ENST00000262741	NM_003629.3	304	cAg/cCg	7/10	0.2705142429406	2	FACETS	1	0.955	1	0.564	0.504	0.627	CLONAL	1	TRUE	0	0.348714973129047	2		386	478	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307496	118307496	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	86	278	0	ENST00000534358.1:c.269C>A	p.Ser90Ter	p.S90*	ENST00000534358	NM_005933.3	90	tCg/tAg	1/36	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.348714973129047	2		278	384	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041099	29041099	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	99	504	0	ENST00000282397.4:c.329T>A	p.Leu110Gln	p.L110Q	ENST00000282397	NM_002019.4	110	cTa/cAa	3/30	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.348714973129047	2		504	500	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43700276	43700276	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	58	547	0	ENST00000382044.4:c.5611G>T	p.Glu1871Ter	p.E1871*	ENST00000382044	NM_001141980.1	1871	Gaa/Taa	27/28	0.289755057420995	3	FACETS	0.718	0.617	0.828	0.359	0.308	0.414	SUBCLONAL	1	TRUE	1	0.348714973129047	3		547	544	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944155	81944155	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	99	680	0	ENST00000359376.3:c.1764C>G	p.Ile588Met	p.I588M	ENST00000359376	NM_002661.3	588	atC/atG	18/33	0.159630086879718	3	FACETS	0.865	0.772	0.964	0.288	0.257	0.322	INDETERMINATE	1	TRUE	0	0.348714973129047	3		680	771	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217814	2217814	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	124	886	1	ENST00000398665.3:c.2588C>A	p.Thr863Asn	p.T863N	ENST00000398665	NM_032482.2	863	aCc/aAc	22/28	0.341684052418577	2	FACETS	0.978	0.886	1	0.489	0.443	0.538	CLONAL	1	TRUE	0	0.348714973129047	2		887	727	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291246	10291246	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0048590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	74	506	1	ENST00000340748.4:c.226-1G>T		p.X76_splice	ENST00000340748		76			0.341684052418577	2	FACETS	1	0.956	1	0.591	0.521	0.666	CLONAL	1	TRUE	0	0.348714973129047	2		507	359	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292665	62292665	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	56	682	0	ENST00000360203.5:c.117C>G	p.Ile39Met	p.I39M	ENST00000360203	NM_001283009.1	39	atC/atG	3/35	0.320898178602413	4	FACETS	0.644	0.551	0.746	0.215	0.183	0.249	SUBCLONAL	1	TRUE	1	0.348714973129047	4		682	673	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196871	106196871	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	33	311	0	ENST00000380013.4:c.5204G>C	p.Gly1735Ala	p.G1735A	ENST00000380013	NM_001127208.2	1735	gGa/gCa	11/11	1	2	FACETS	0.834	0.684	1	0.834	0.684	1	CLONAL	1	TRUE	1	0.348714973129047	2		311	227	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584759	187584759	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	48	240	0	ENST00000441802.2:c.3274G>C	p.Glu1092Gln	p.E1092Q	ENST00000441802	NM_005245.3	1092	Gag/Cag	3/27	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.348714973129047	2		240	254	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933101	39933101	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	65	390	0	ENST00000378444.4:c.1498G>C	p.Glu500Gln	p.E500Q	ENST00000378444	NM_001123385.1	500	Gaa/Caa	4/15	0.103022896665629	2	FACETS	1	0.92	1			1	INDETERMINATE	1	TRUE	NA	0.348714973129047	2		390	347	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0048696-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	90	501	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.0870288033778046	5	FACETS	0.781	0.692	0.875	0.52	0.461	0.583	INDETERMINATE	2	TRUE	2	0.206266661115628	5		501	732	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048841-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	26	276	0				ENST00000310581	NM_198253.2	-/1132			0.185939271225466	1	FACETS	0.876	0.694	1	0.876	0.694	1	CLONAL	1	TRUE	0	0.15	1		276	366	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578175	7578175	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0048841-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	60	588	0	ENST00000269305.4:c.672+2T>C		p.X224_splice	ENST00000269305	NM_001126112.2	224			1	2	FACETS	0.938	0.806	1	0.938	0.806	1	CLONAL	1	TRUE	1	0.15	2		588	853	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220692	1220692	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555738459	NA	P-0048841-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	78	1040	0	ENST00000326873.7:c.710A>G	p.Asp237Gly	p.D237G	ENST00000326873	NM_000455.4	237	gAc/gGc	5/10	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.15	2		1040	1008	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049044-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	161	276	0				ENST00000310581	NM_198253.2	-/1132			0.348111955805837	6	FACETS	0.996	0.925	1	0.996	0.925	1	CLONAL	4	FALSE	2	0.348111955805837	6		276	394	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166231	118166231	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049044-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	61	464	0	ENST00000369448.3:c.741C>A	p.Tyr247Ter	p.Y247*	ENST00000369448	NM_017709.3	247	taC/taA	2/2	0.246636491526913	4	FACETS	1	0.899	1	0.524	0.453	0.601	CLONAL	1	FALSE	2	0.348111955805837	4		464	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0049560-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	73	832	0	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	0.237773634080374	1	FACETS	0.875	0.766	0.993	0.875	0.766	0.993	CLONAL	1	TRUE	0	0.237773634080374	1		832	618	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346158	89346158	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs878855327	NA	P-0049560-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	8	417	0	ENST00000301030.4:c.6792del	p.Ala2265ProfsTer72	p.A2265Pfs*72	ENST00000301030	NM_001256183.1	2264	ccC/cc	9/13	0.237773634080374	1	FACETS	0.174	0.111	0.256	0.174	0.111	0.256	SUBCLONAL	1	TRUE	0	0.237773634080374	1		417	340	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627654	14627654	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs774560970	NA	P-0049560-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	80	717	0	ENST00000254322.2:c.416G>T	p.Gly139Val	p.G139V	ENST00000254322	NM_006145.1	139	gGt/gTt	2/3	0.210234412183381	3	FACETS	0.891	0.783	1	0.446	0.391	0.504	CLONAL	1	TRUE	1	0.237773634080374	3		717	845	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056100	26056100	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049560-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	53	467	0	ENST00000343677.2:c.557C>A	p.Ala186Asp	p.A186D	ENST00000343677	NM_005319.3	186	gCc/gAc	1/1	0.237773634080374	1	FACETS	0.81	0.691	0.94	0.81	0.691	0.94	CLONAL	1	TRUE	0	0.237773634080374	1		467	485	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	50	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.862	0.746	0.983	0.862	0.746	0.983	CLONAL	1	TRUE	1	0.753571271494996	2		276	154	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0049797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	257	1039	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	0.27184119880946	2	FACETS	1	0.992	1	0.653	0.619	0.688	INDETERMINATE	1	TRUE	0	0.753571271494996	2		1039	522	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415856	49415858	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	rs587783704	NA	P-0049797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	163	413	0	ENST00000301067.7:c.16489_16491del	p.Ile5497del	p.I5497del	ENST00000301067	NM_003482.3	5497	ATC/-	53/54	1	2	FACETS	0.93	0.862	1	0.93	0.862	1	CLONAL	1	TRUE	1	0.753571271494996	2		413	465	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0050586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	91	478	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.661	0.591	0.736	0.661	0.591	0.736	SUBCLONAL	1	TRUE	1	0.682783247034737	2		478	403	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259759	16259759	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	253	404	0	ENST00000375759.3:c.7024C>T	p.Arg2342Ter	p.R2342*	ENST00000375759	NM_015001.2	2342	Cga/Tga	11/15	0.580703642370697	3	FACETS	1	0.992	1	0.818	0.78	0.855	CLONAL	2	TRUE	0	0.682783247034737	3		404	405	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061217	38061217	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	129	505	0	ENST00000250448.2:c.772T>C	p.Cys258Arg	p.C258R	ENST00000250448	NM_004496.3	258	Tgc/Cgc	2/2	1	2	FACETS	0.661	0.601	0.723	0.661	0.601	0.723	SUBCLONAL	1	TRUE	1	0.682783247034737	2		505	572	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060801	38060801	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	347	840	1	ENST00000250448.2:c.1188del	p.Phe396LeufsTer44	p.F396Lfs*44	ENST00000250448	NM_004496.3	396	ttC/tt	2/2	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.682783247034737	2		841	906	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665110	29665110	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658541	NA	P-0050865-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	24	676	1	ENST00000356175.3:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000356175	NM_000267.3	2237	Cga/Tga	44/57	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		677	145	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0050979-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	237	478	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.322922802559319	4	FACETS	0.902	0.847	0.958	0.902	0.847	0.958	CLONAL	3	TRUE	1	0.368782950728805	4		478	650	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955381	48955381	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0050979-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	3	0	0	ENST00000267163.4:c.1499-2A>G		p.X500_splice	ENST00000267163	NM_000321.2	500			0.368782950728805	1	FACETS	0.082	0.038	0.15	0.082	0.038	0.15	SUBCLONAL	1	TRUE	0	0.368782950728805	1		0	162	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579527	7579528	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0050979-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	246	907	0	ENST00000269305.4:c.159dup	p.Phe54ValfsTer3	p.F54Vfs*3	ENST00000269305	NM_001126112.2	53	-/G	4/11	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	2	TRUE	NA	0.368782950728805	2		907	642	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934530	9934530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050979-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	47	616	0	ENST00000330684.3:c.1625G>A	p.Gly542Asp	p.G542D	ENST00000330684	NM_001134407.1	542	gGc/gAc	7/13	0.368782950728805	3	FACETS	0.547	0.461	0.642	0.273	0.23	0.321	SUBCLONAL	1	TRUE	1	0.368782950728805	3		616	552	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051006-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	85	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.644942911755291	2		276	240	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0051006-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	226	836	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.945	0.883	1	0.945	0.883	1	CLONAL	1	TRUE	1	0.644942911755291	2		836	742	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5055739	5055739	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0051006-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	75	339	0	ENST00000381652.3:c.1007C>G	p.Ser336Ter	p.S336*	ENST00000381652	NM_004972.3	336	tCa/tGa	8/25	0.644942911755291	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.644942911755291	1		339	153	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984412	201984413	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0051006-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	265	817	0	ENST00000359651.3:c.1079dup	p.Trp361LeufsTer110	p.W361Lfs*110	ENST00000359651		359	-/G	8/8	1	2	FACETS	0.804	0.763	0.845	1	0.995	1	CLONAL	2	TRUE	1	0.644942911755291	2		817	511	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093424	30093424	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051006-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	134	455	0	ENST00000331968.5:c.1839C>G	p.Ile613Met	p.I613M	ENST00000331968	NM_002742.2	613	atC/atG	13/18	1	2	FACETS	0.987	0.905	1	0.987	0.905	1	CLONAL	1	TRUE	1	0.644942911755291	2		455	421	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217258	7217259	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CTGTCAGCTGCCATGAGGGTGC	novel	NA	P-0051006-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	129	702	0	ENST00000380728.2:c.425_446dup	p.Ala150HisfsTer6	p.A150Hfs*6	ENST00000380728		149	aga/agGCACCCTCATGGCAGCTGACAGa	6/11	0.644942911755291	1	FACETS	0.63	0.576	0.686	0.63	0.576	0.686	SUBCLONAL	1	TRUE	0	0.644942911755291	1		702	430	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947180	178947180	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051006-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	97	276	0	ENST00000263967.3:c.2616C>A	p.Phe872Leu	p.F872L	ENST00000263967	NM_006218.2	872	ttC/ttA	18/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.644942911755291	2		276	273	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612132	43612132	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	196	420	0	ENST00000355710.3:c.2237T>G	p.Leu746Arg	p.L746R	ENST00000355710	NM_020975.4	746	cTg/cGg	12/20	0.942631022935736	1	FACETS	0.901	0.869	0.93	0.901	0.869	0.93	CLONAL	1	TRUE	0	0.967806075209498	1		420	232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578448	7578448	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1064795691	NA	P-0051131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	1026	826	0	ENST00000269305.4:c.482C>A	p.Ala161Asp	p.A161D	ENST00000269305	NM_001126112.2	161	gCc/gAc	5/11	0.92976764483494	2	FACETS	0.97	0.96	0.979	0.97	0.96	0.979	CLONAL	2	TRUE	0	0.967806075209498	2		826	1093	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257940	19257940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	557	914	0	ENST00000162023.5:c.446C>T	p.Pro149Leu	p.P149L	ENST00000162023		149	cCa/cTa	9/13	0.104867886212906	3	FACETS	1	0.997	1	0.709	0.683	0.736	INDETERMINATE	1	TRUE	1	0.967806075209498	3		914	1204	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702337	47702337	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs267607982	NA	P-0051131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	286	394	0	ENST00000233146.2:c.1933C>G	p.Gln645Glu	p.Q645E	ENST00000233146	NM_000251.2	645	Caa/Gaa	12/16	1	2	FACETS	0.961	0.912	1	0.961	0.912	1	CLONAL	1	TRUE	1	0.967806075209498	2		394	615	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023938	31023938	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	424	606	0	ENST00000375687.4:c.3423C>G	p.Asp1141Glu	p.D1141E	ENST00000375687	NM_015338.5	1141	gaC/gaG	13/13	0.788066090261647	3	FACETS	1	0.961	1	0.504	0.48	0.529	CLONAL	1	TRUE	1	0.967806075209498	3		606	1289	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200681	128200681	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	761	726	0	ENST00000341105.2:c.1124T>A	p.Leu375His	p.L375H	ENST00000341105	NM_032638.4	375	cTc/cAc	5/6	0.842801037739241	3	FACETS	0.939	0.913	0.964	0.939	0.913	0.964	CLONAL	2	TRUE	1	0.967806075209498	3		726	1243	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270102	66270103	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAGGACGCC	novel	NA	P-0051131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	212	381	2	ENST00000273854.3:c.1771_1779dup	p.Gly591_Leu593dup	p.G591_L593dup	ENST00000273854	NM_004439.5	591	-/GGCGTCCTC	8/18	0.967806075209498	1	FACETS	0.734	0.7	0.767	0.734	0.7	0.767	SUBCLONAL	1	TRUE	0	0.967806075209498	1		383	308	SUCCESS
APC	324	MSKCC	GRCh37	5	112175876	112175876	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085992	NA	P-0051131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	173	274	0	ENST00000257430.4:c.4585C>T	p.Gln1529Ter	p.Q1529*	ENST00000257430	NM_000038.5	1529	Cag/Tag	16/16	0.920835147418565	1	FACETS	0.961	0.931	0.986	0.961	0.931	0.986	CLONAL	1	TRUE	0	0.967806075209498	1		274	192	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848666	151848666	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	151	238	0	ENST00000262189.6:c.12527G>A	p.Gly4176Asp	p.G4176D	ENST00000262189	NM_170606.2	4176	gGt/gAt	50/59	0.92976764483494	2	FACETS	0.943	0.876	1	0.471	0.438	0.505	CLONAL	1	TRUE	0	0.967806075209498	2		238	331	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328431	137328431	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	535	707	0	ENST00000481739.1:c.1360A>T	p.Met454Leu	p.M454L	ENST00000481739	NM_002957.4	454	Atg/Ttg	10/10	0.935459782683525	2	FACETS	0.978	0.941	1	0.489	0.47	0.507	CLONAL	1	TRUE	0	0.967806075209498	2		707	1131	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0051548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	25	465	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.43	0.338	0.535	0.43	0.338	0.535	SUBCLONAL	1	TRUE	1	0.29	2		465	401	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247376	153247376	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	24	314	0	ENST00000281708.4:c.1426A>G	p.Ser476Gly	p.S476G	ENST00000281708	NM_033632.3	476	Agc/Ggc	10/12	1	2	FACETS	0.639	0.502	0.796	0.639	0.502	0.796	SUBCLONAL	1	TRUE	1	0.29	2		314	259	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0051548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	40	533	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.108409044194965	3	FACETS	0.814	0.678	0.966	0.407	0.339	0.483	INDETERMINATE	1	TRUE	1	0.29	3		533	388	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007825	45007825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	33	488	0	ENST00000558401.1:c.276del	p.Thr93LeufsTer10	p.T93Lfs*10	ENST00000558401	NM_004048.2	91	aCc/ac	2/4	1	2	FACETS	0.406	0.329	0.492	0.406	0.329	0.492	SUBCLONAL	1	TRUE	1	0.29	2		488	561	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161907	47161907	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	28	413	0	ENST00000409792.3:c.4219del	p.Arg1407GlyfsTer5	p.R1407Gfs*5	ENST00000409792	NM_014159.6	1407	Agg/gg	3/21	1	2	FACETS	0.536	0.429	0.659	0.536	0.429	0.659	SUBCLONAL	1	TRUE	1	0.29	2		413	360	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589575	67589576	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0051548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	20	115	0	ENST00000274335.5:c.1344dup	p.Leu449IlefsTer3	p.L449Ifs*3	ENST00000274335		446	-/A	10/15	0.166227025275268	3	FACETS	0.603	0.462	0.768	0.301	0.231	0.384	INDETERMINATE	1	TRUE	1	0.29	3		115	262	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682399	52682400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0051548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	37	347	0	ENST00000394830.3:c.773dup	p.Asn258LysfsTer6	p.N258Kfs*6	ENST00000394830	NM_018313.4	258	aat/aaAt	8/30	1	2	FACETS	0.57	0.469	0.682	0.57	0.469	0.682	SUBCLONAL	1	TRUE	1	0.29	2		347	448	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151289	202151290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0051548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	29	412	0	ENST00000358485.4:c.1596dup	p.Leu533ThrfsTer6	p.L533Tfs*6	ENST00000358485	NM_001080125.1	530	aga/agAa	9/9	1	2	FACETS	0.639	0.514	0.781	0.639	0.514	0.781	SUBCLONAL	1	TRUE	1	0.29	2		412	313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0051548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	57	795	0	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	1	2	FACETS	0.643	0.552	0.744	0.643	0.552	0.744	SUBCLONAL	1	TRUE	1	0.29	2		795	611	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0051548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	44	320	0	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	1	2	FACETS	0.988	0.833	1	0.988	0.833	1	CLONAL	1	TRUE	1	0.29	2		320	307	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170313	32170313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201260854	NA	P-0051548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	57	1074	2	ENST00000375023.3:c.3295G>A	p.Gly1099Arg	p.G1099R	ENST00000375023	NM_004557.3	1099	Gga/Aga	21/30	1	2	FACETS	0.662	0.568	0.765	0.662	0.568	0.765	SUBCLONAL	1	TRUE	1	0.29	2		1076	594	SUCCESS
APC	324	MSKCC	GRCh37	5	112175969	112175970	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1114167552	NA	P-0051548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	20	231	0	ENST00000257430.4:c.4682dup	p.Asp1562GlyfsTer5	p.D1562Gfs*5	ENST00000257430	NM_000038.5	1560	gaa/gAaa	16/16	0.166227025275268	3	FACETS	0.731	0.561	0.929	0.366	0.28	0.465	INDETERMINATE	1	TRUE	1	0.29	3		231	216	SUCCESS
APC	324	MSKCC	GRCh37	5	112164565	112164566	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1554082091	NA	P-0051548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	11	249	0	ENST00000257430.4:c.1643dup	p.Leu548PhefsTer12	p.L548Ffs*12	ENST00000257430	NM_000038.5	547	gtt/gTtt	14/16	0.166227025275268	3	FACETS	0.395	0.272	0.547	0.197	0.136	0.274	INDETERMINATE	1	TRUE	1	0.29	3		249	220	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974676	21974676	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0051548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	38	650	1	ENST00000304494.5:c.150+1G>T		p.X50_splice	ENST00000304494	NM_000077.4	50			1	2	FACETS	0.598	0.495	0.714	0.598	0.495	0.714	SUBCLONAL	1	TRUE	1	0.29	2		651	438	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948279	71948280	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0051548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	33	1052	0	ENST00000298229.2:c.2996dup	p.Glu1000GlyfsTer43	p.E1000Gfs*43	ENST00000298229	NM_001567.3	997	-/C	26/28	1	2	FACETS	0.398	0.323	0.482	0.398	0.323	0.482	SUBCLONAL	1	TRUE	1	0.29	2		1052	572	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70442680	70442680	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	44	493	0	ENST00000373644.4:c.5002T>C	p.Cys1668Arg	p.C1668R	ENST00000373644	NM_030625.2	1668	Tgt/Cgt	10/12	0.3	3	FACETS	0.783	0.657	0.921			1	CLONAL	1	TRUE	NA	0.29	3		493	444	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101985013	101985013	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs746188462	NA	P-0051548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	62	640	0	ENST00000282441.5:c.460A>G	p.Thr154Ala	p.T154A	ENST00000282441	NM_001130145.2	154	Aca/Gca	2/9	1	2	FACETS	0.736	0.636	0.845	0.736	0.636	0.845	SUBCLONAL	1	TRUE	1	0.29	2		640	581	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342640	118342640	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	20	281	0	ENST00000534358.1:c.766A>T	p.Ile256Phe	p.I256F	ENST00000534358	NM_005933.3	256	Att/Ttt	3/36	1	2	FACETS	0.539	0.413	0.686	0.539	0.413	0.686	SUBCLONAL	1	TRUE	1	0.29	2		281	256	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831300	3831300	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	22	330	0	ENST00000262367.5:c.1581T>A	p.Asn527Lys	p.N527K	ENST00000262367	NM_004380.2	527	aaT/aaA	7/31	1	2	FACETS	0.581	0.451	0.732	0.581	0.451	0.732	SUBCLONAL	1	TRUE	1	0.29	2		330	261	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50788312	50788312	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	44	620	0	ENST00000398568.2:c.890T>C	p.Leu297Ser	p.L297S	ENST00000398568	NM_001042412.1	297	tTg/tCg	5/18	1	2	FACETS	0.528	0.442	0.623	0.528	0.442	0.623	SUBCLONAL	1	TRUE	1	0.29	2		620	575	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16001790	16001790	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	28	533	1	ENST00000268712.3:c.2711A>T	p.Lys904Met	p.K904M	ENST00000268712	NM_006311.3	904	aAg/aTg	21/46	1	2	FACETS	0.423	0.338	0.521	0.423	0.338	0.521	SUBCLONAL	1	TRUE	1	0.29	2		534	456	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226409	41226409	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	48	672	0	ENST00000357654.3:c.4614G>T	p.Gln1538His	p.Q1538H	ENST00000357654	NM_007294.3	1538	caG/caT	14/23	1	2	FACETS	0.534	0.451	0.626	0.534	0.451	0.626	SUBCLONAL	1	TRUE	1	0.29	2		672	620	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226412	2226412	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	46	1175	1	ENST00000398665.3:c.3892G>T	p.Gly1298Cys	p.G1298C	ENST00000398665	NM_032482.2	1298	Ggc/Tgc	27/28	1	2	FACETS	0.513	0.431	0.603	0.513	0.431	0.603	SUBCLONAL	1	TRUE	1	0.29	2		1176	619	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248686	10248686	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0051548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	20	558	0	ENST00000340748.4:c.4068-1G>T		p.X1356_splice	ENST00000340748		1356			1	2	FACETS	0.396	0.303	0.506	0.396	0.303	0.506	SUBCLONAL	1	TRUE	1	0.29	2		558	348	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42384996	42384996	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	48	830	1	ENST00000221972.3:c.630C>A	p.Tyr210Ter	p.Y210*	ENST00000221972	NM_021601.3	210	taC/taA	5/5	0.108409044194965	0	FACETS	0.454	0.383	0.531			1	INDETERMINATE	1	TRUE	0	0.29	0		831	518	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449520	31449520	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1360547844	NA	P-0051548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	14	296	0	ENST00000344624.3:c.2689A>G	p.Met897Val	p.M897V	ENST00000344624		897	Atg/Gtg	19/33	1	2	FACETS	0.5	0.362	0.667	0.5	0.362	0.667	SUBCLONAL	1	TRUE	1	0.29	2		296	193	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776996	135776996	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	29	527	0	ENST00000298552.3:c.2482C>G	p.Leu828Val	p.L828V	ENST00000298552	NM_001162426.1	828	Ctc/Gtc	19/23	1	2	FACETS	0.469	0.376	0.576	0.469	0.376	0.576	SUBCLONAL	1	TRUE	1	0.29	2		527	426	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663815	241663817	+	missense_variant	Missense_Mutation	TNP	TTC	TTC	ATA	novel	NA	P-0051548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	24	258	1	ENST00000366560.3:c.1310_1312delinsTAT	p.Gly437_Ile438delinsValPhe	p.G437_I438delinsVF	ENST00000366560	NM_000143.3	437	gGAAtc/gTATtc	9/10	1	2	FACETS	0.823	0.649	1	0.823	0.649	1	CLONAL	1	TRUE	1	0.29	2		259	201	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0051626-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	154	478	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.907	0.842	0.974	1	0.994	1	CLONAL	4	FALSE	1	0.231876959318308	2		478	366	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533661	41533661	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs142823793	NA	P-0051626-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	203	546	0	ENST00000263253.7:c.1627A>G	p.Met543Val	p.M543V	ENST00000263253	NM_001429.3	543	Atg/Gtg	8/31	1	2	FACETS	0.875	0.82	0.932	1	0.995	1	CLONAL	4	FALSE	1	0.231876959318308	2		546	500	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3929881	3929881	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587783484	NA	P-0051626-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	428	561	0	ENST00000262367.5:c.37A>G	p.Lys13Glu	p.K13E	ENST00000262367	NM_004380.2	13	Aaa/Gaa	1/31	1	2	FACETS	0.99	0.948	1	1	0.998	1	CLONAL	4	FALSE	1	0.231876959318308	2		561	932	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533656	41533656	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0051626-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	192	515	0	ENST00000263253.7:c.1623-1G>T		p.X541_splice	ENST00000263253	NM_001429.3	541			1	2	FACETS	0.888	0.83	0.947	1	0.995	1	CLONAL	4	FALSE	1	0.231876959318308	2		515	466	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69027999	69027999	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051626-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	51	455	0	ENST00000288368.4:c.3158C>A	p.Ser1053Ter	p.S1053*	ENST00000288368	NM_024870.2	1053	tCa/tAa	26/40	1	2	FACETS	1	0.942	1	1	0.983	1	CLONAL	3	FALSE	1	0.231876959318308	2		455	128	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390628	139390628	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051626-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	796	995	0	ENST00000277541.6:c.7563del	p.Ser2522AlafsTer67	p.S2522Afs*67	ENST00000277541	NM_017617.3	2521	tcC/tc	34/34	1	2	FACETS	0.996	0.965	1	1	0.998	1	CLONAL	4	FALSE	1	0.231876959318308	2		995	1723	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397632	139397633	+	splice_donor_variant	Splice_Site	INS	-	-	CTCTGCACGGCCTCGATCTTGTAGGGGATGTTGAGGCTG	novel	NA	P-0051626-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1289	268	953	0	ENST00000277541.6:c.5130_5167+1dup		p.X1710_splice	ENST00000277541	NM_017617.3	1710			1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	FALSE	1	0.231876959318308	2		953	1557	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0051695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	2268	646	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.768886697844875	10	FACETS	0.968	0.957	0.978			1	CLONAL	9	TRUE	NA	0.768886697844875	10		646	2761	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451217	70451217	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	359	709	0	ENST00000373644.4:c.6057G>C	p.Leu2019Phe	p.L2019F	ENST00000373644	NM_030625.2	2019	ttG/ttC	12/12	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.768886697844875	2		709	934	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076636	102076636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	224	368	0	ENST00000282441.5:c.815G>A	p.Arg272Lys	p.R272K	ENST00000282441	NM_001130145.2	272	aGa/aAa	5/9	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.768886697844875	2		368	576	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448103	49448103	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0051695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	288	575	0	ENST00000301067.7:c.497C>G	p.Ser166Ter	p.S166*	ENST00000301067	NM_003482.3	166	tCa/tGa	4/54	1	2	FACETS	0.978	0.924	1	0.978	0.924	1	CLONAL	1	TRUE	1	0.768886697844875	2		575	766	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28979931	28979931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	238	458	0	ENST00000282397.4:c.1537G>A	p.Glu513Lys	p.E513K	ENST00000282397	NM_002019.4	513	Gaa/Aaa	11/30	1	2	FACETS	0.931	0.874	0.989	0.931	0.874	0.989	CLONAL	1	TRUE	1	0.768886697844875	2		458	665	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004835	16004835	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	341	694	0	ENST00000268712.3:c.2419G>C	p.Glu807Gln	p.E807Q	ENST00000268712	NM_006311.3	807	Gag/Cag	20/46	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.768886697844875	2		694	876	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665029	29665061	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTTTTAATTGCAGATTTGCATTCCAATATAAT	TCTTTTAATTGCAGATTTGCATTCCAATATAAT	-	novel	NA	P-0051695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	216	347	0	ENST00000356175.3:c.6642-14_6660del		p.X2214_splice	ENST00000356175	NM_000267.3	2214		44/57	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.768886697844875	NA		347	632	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256228	41256228	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659315	NA	P-0051695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	236	408	0	ENST00000357654.3:c.352C>G	p.Leu118Val	p.L118V	ENST00000357654	NM_007294.3	118	Cta/Gta	6/23	1	2	FACETS	0.934	0.877	0.993	0.934	0.877	0.993	CLONAL	1	TRUE	1	0.768886697844875	2		408	657	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223403	2223403	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	293	784	0	ENST00000398665.3:c.3514C>G	p.Leu1172Val	p.L1172V	ENST00000398665	NM_032482.2	1172	Ctg/Gtg	25/28	0.175521648986272	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.768886697844875	0		784	787	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197196	26197196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	333	696	0	ENST00000356476.2:c.283G>A	p.Glu95Lys	p.E95K	ENST00000356476		95	Gag/Aag	1/1	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.768886697844875	2		696	858	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109309886	109309886	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	227	377	0	ENST00000436639.2:c.1429G>C	p.Asp477His	p.D477H	ENST00000436639	NM_014454.2	477	Gat/Cat	9/10	1	2	FACETS	0.943	0.884	1	0.943	0.884	1	CLONAL	1	TRUE	1	0.768886697844875	2		377	626	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398560	116398560	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0051695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	269	431	0	ENST00000397752.3:c.2150C>G	p.Ser717Ter	p.S717*	ENST00000397752	NM_000245.2	717	tCa/tGa	9/21	1	2	FACETS	0.961	0.906	1	0.961	0.906	1	CLONAL	1	TRUE	1	0.768886697844875	2		431	728	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779172	135779173	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0051695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	169	463	0	ENST00000298552.3:c.2073_2074delinsTT	p.Arg692Ter	p.R692*	ENST00000298552	NM_001162426.1	691	ctCCga/ctTTga	17/23	0.768886697844875	1	FACETS	0.867	0.813	0.921	0.867	0.813	0.921	CLONAL	1	TRUE	0	0.768886697844875	1		463	312	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0051883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	40	288	0	ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	4/10	0.187603664973491	4	FACETS	0.912	0.765	1	0.912	0.765	1	CLONAL	2	TRUE	2	0.251744169995532	4		288	218	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239453	123239453	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	67	597	0	ENST00000358487.5:c.2384A>G	p.Asp795Gly	p.D795G	ENST00000358487	NM_000141.4	795	gAt/gGt	18/18	0.175551309243388	3	FACETS	0.805	0.704	0.914	0.805	0.704	0.914	CLONAL	2	TRUE	1	0.251744169995532	3		597	372	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474044	29474044	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1166188112	NA	P-0051883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	115	951	0	ENST00000389048.3:c.2131A>C	p.Ser711Arg	p.S711R	ENST00000389048	NM_004304.4	711	Agc/Cgc	12/29	0.187603664973491	4	FACETS	0.882	0.796	0.973	0.882	0.796	0.973	CLONAL	2	TRUE	2	0.251744169995532	4		951	648	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940137	31940137	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs756226200	NA	P-0051883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	47	907	0	ENST00000375333.2:c.279G>T	p.Arg93Ser	p.R93S	ENST00000375333	NM_032454.1	93	agG/agT	2/8	0.242571793251344	4	FACETS	0.55	0.462	0.647	0.275	0.231	0.324	SUBCLONAL	1	TRUE	2	0.251744169995532	4		907	850	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0051890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	151	646	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.936	0.867	1	0.936	0.867	1	CLONAL	1	TRUE	1	0.86	2		646	375	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78865601	78865601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	164	720	0	ENST00000306801.3:c.2065G>A	p.Glu689Lys	p.E689K	ENST00000306801	NM_020761.2	689	Gaa/Aaa	18/34	1	2	FACETS	0.803	0.743	0.864	0.803	0.743	0.864	CLONAL	1	TRUE	1	0.86	2		720	475	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339968	116339968	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	130	469	0	ENST00000397752.3:c.830G>C	p.Arg277Thr	p.R277T	ENST00000397752	NM_000245.2	277	aGa/aCa	2/21	1	2	FACETS	0.96	0.884	1	0.96	0.884	1	CLONAL	1	TRUE	1	0.86	2		469	315	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339220	116339220	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	162	445	0	ENST00000397752.3:c.82G>C	p.Glu28Gln	p.E28Q	ENST00000397752	NM_000245.2	28	Gag/Cag	2/21	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.86	2		445	375	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44948987	44948987	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs796568156	NA	P-0051890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	102	403	0	ENST00000377967.4:c.3549-1G>A		p.X1183_splice	ENST00000377967	NM_021140.2	1183			1	2	FACETS	0.976	0.89	1	0.976	0.89	1	CLONAL	1	TRUE	1	0.86	2		403	243	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0051890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	151	258	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.86	2		258	298	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47108581	47108581	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	35	369	0	ENST00000409792.3:c.6088C>T	p.Gln2030Ter	p.Q2030*	ENST00000409792	NM_014159.6	2030	Caa/Taa	13/21	1	2	FACETS	0.271	0.223	0.325	0.271	0.223	0.325	SUBCLONAL	1	TRUE	1	0.86	2		369	300	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845321	76845322	+	missense_variant	Missense_Mutation	DNP	TT	TT	GG	novel	NA	P-0051890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	13	280	0	ENST00000373344.5:c.6199_6200delinsCC	p.Lys2067Pro	p.K2067P	ENST00000373344	NM_000489.3	2067	AAa/CCa	27/35	1	2	FACETS	0.123	0.087	0.166	0.123	0.087	0.166	SUBCLONAL	1	TRUE	1	0.86	2		280	246	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333717	70333717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	58	623	0	ENST00000373644.4:c.1622C>T	p.Ser541Leu	p.S541L	ENST00000373644	NM_030625.2	541	tCa/tTa	2/12	1	2	FACETS	0.323	0.278	0.371	0.323	0.278	0.371	SUBCLONAL	1	TRUE	1	0.86	2		623	418	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912061	32912061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358605	NA	P-0051890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	27	774	1	ENST00000380152.3:c.3569G>A	p.Arg1190Gln	p.R1190Q	ENST00000380152		1190	cGg/cAg	11/27	1	2	FACETS	0.185	0.147	0.229	0.185	0.147	0.229	SUBCLONAL	1	TRUE	1	0.86	2		775	339	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159027	143159027	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	34	291	0	ENST00000262992.4:c.826G>C	p.Asp276His	p.D276H	ENST00000262992	NM_001101669.1	276	Gat/Cat	10/24	1	2	FACETS	0.405	0.334	0.484	0.405	0.334	0.484	SUBCLONAL	1	TRUE	1	0.86	2		291	195	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44911033	44911036	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0051890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	21	337	0	ENST00000377967.4:c.734_737del	p.Val245AspfsTer4	p.V245Dfs*4	ENST00000377967	NM_021140.2	245	gTCTTa/ga	9/29	1	2	FACETS	0.178	0.137	0.225	0.178	0.137	0.225	SUBCLONAL	1	TRUE	1	0.86	2		337	275	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215341	123215341	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	167	531	0	ENST00000218089.9:c.2887C>T	p.Gln963Ter	p.Q963*	ENST00000218089	NM_001042749.1	963	Cag/Tag	28/35	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.86	2		531	370	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807973	3807991	+	protein_altering_variant	In_Frame_Del	DEL	TCTTGGTATTGCCCTGTGT	TCTTGGTATTGCCCTGTGT	AATA	novel	NA	P-0051890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	198	712	2	ENST00000262367.5:c.3428_3446delinsTATT	p.Asp1143_Glu1149delinsValLeu	p.D1143_E1149delinsVL	ENST00000262367	NM_004380.2	1143	gACACAGGGCAATACCAAGAg/gTATTg	18/31	1	2	FACETS	0.919	0.859	0.98	0.919	0.859	0.98	CLONAL	1	TRUE	1	0.86	2		714	501	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0052009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	133	501	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.307892331394837	3	FACETS	0.943	0.856	1	0.472	0.428	0.518	CLONAL	1	TRUE	1	0.337246128731188	3		501	977	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934574	NA	P-0052009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	81	767	0	ENST00000269305.4:c.844C>G	p.Arg282Gly	p.R282G	ENST00000269305	NM_001126112.2	282	Cgg/Ggg	8/11	1	2	FACETS	0.397	0.349	0.45	0.397	0.349	0.45	SUBCLONAL	1	TRUE	1	0.337246128731188	2		767	1209	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77070044	77070044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	65	544	2	ENST00000356341.3:c.496G>A	p.Glu166Lys	p.E166K	ENST00000356341	NM_002576.4	166	Gag/Aag	6/15	1	2	FACETS	0.441	0.381	0.506	0.441	0.381	0.506	SUBCLONAL	1	TRUE	1	0.337246128731188	2		546	875	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878093	48878138	+	frameshift_variant	Frame_Shift_Del	DEL	TGCCGCCGCGGAACCCCCGGCACCGCCGCCGCCGCCCCCTCCTGAG	TGCCGCCGCGGAACCCCCGGCACCGCCGCCGCCGCCCCCTCCTGAG	-	novel	NA	P-0052059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	176	54	0	ENST00000267163.4:c.45_90del	p.Ala16ArgfsTer34	p.A16Rfs*34	ENST00000267163	NM_000321.2	15	gcTGCCGCCGCGGAACCCCCGGCACCGCCGCCGCCGCCCCCTCCTGAG/gc	1/27	0.910191290917936	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.910191290917936	2		54	184	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643612	38643612	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	74	390	1	ENST00000299084.4:c.1082G>T	p.Arg361Ile	p.R361I	ENST00000299084	NM_152594.2	361	aGa/aTa	7/7	0.910191290917936	1	FACETS	0.41	0.365	0.457	0.41	0.365	0.457	SUBCLONAL	1	TRUE	0	0.910191290917936	1		391	216	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005375	42005376	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	243	316	0	ENST00000219905.7:c.3112dup	p.Thr1038AsnfsTer13	p.T1038Nfs*13	ENST00000219905	NM_001164273.1	1037	-/A	9/24	0.910191290917936	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.910191290917936	1		316	266	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593646	55593647	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGACCC	novel	NA	P-0052059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	297	395	0	ENST00000288135.5:c.1714_1719dup	p.Asp572_Pro573dup	p.D572_P573dup	ENST00000288135	NM_000222.2	572	ata/atAGACCCa	11/21	0.465827309116458	4	FACETS	0.888	0.842	0.935	0.888	0.842	0.935	INDETERMINATE	2	TRUE	2	0.910191290917936	4		395	702	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0052166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	178	533	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.577249836094006	2		533	489	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0052166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	222	444	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.577249836094006	2		444	659	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602620	10602620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	352	823	1	ENST00000171111.5:c.958C>T	p.Arg320Trp	p.R320W	ENST00000171111	NM_203500.1	320	Cgg/Tgg	3/6	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.577249836094006	2		824	1092	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089489	27089489	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0052166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	348	761	0	ENST00000324856.7:c.2445T>G	p.Tyr815Ter	p.Y815*	ENST00000324856	NM_006015.4	815	taT/taG	8/20	0.577249836094006	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.577249836094006	1		761	747	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491277	2491277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374643973	NA	P-0052166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	411	863	0	ENST00000355716.4:c.320C>T	p.Ala107Val	p.A107V	ENST00000355716	NM_003820.2	107	gCg/gTg	4/8	0.577249836094006	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.577249836094006	1		863	896	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692961	89692961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060500122	NA	P-0052248-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	36	486	0	ENST00000371953.3:c.445C>T	p.Gln149Ter	p.Q149*	ENST00000371953	NM_000314.4	149	Caa/Taa	5/9	0.362919152071274	2	FACETS	0.699	0.577	0.834	0.349	0.288	0.417	SUBCLONAL	1	TRUE	0	0.384355272961935	2		486	268	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576851	7576851	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0052248-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	208	824	0	ENST00000269305.4:c.993+2T>C		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.384355272961935	4	FACETS	0.942	0.877	1	0.942	0.877	1	CLONAL	2	TRUE	2	0.384355272961935	4		824	795	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434289	49434289	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052248-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	429	1266	1	ENST00000301067.7:c.7264C>T	p.Gln2422Ter	p.Q2422*	ENST00000301067	NM_003482.3	2422	Cag/Tag	31/54	0.384355272961935	3	FACETS	0.95	0.905	0.996	0.95	0.905	0.996	CLONAL	2	TRUE	1	0.384355272961935	3		1267	1401	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599916	10599916	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs946921406	NA	P-0052248-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	786	1032	2	ENST00000171111.5:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000171111	NM_203500.1	554	Cga/Tga	5/6	0.379128468096928	4	FACETS	0.994	0.966	1	0.994	0.966	1	CLONAL	4	TRUE	0	0.384355272961935	4		1034	1424	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497683	120497747	+	frameshift_variant	Frame_Shift_Del	DEL	GTTTCCATGGATGCAGGGATTGCTCAGGCATTCGTTCACCTGTGAGTAGCAGCTGGGGTGATGGG	GTTTCCATGGATGCAGGGATTGCTCAGGCATTCGTTCACCTGTGAGTAGCAGCTGGGGTGATGGG	-	novel	NA	P-0052248-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	178	499	0	ENST00000256646.2:c.2135_2199del	p.Pro712LeufsTer9	p.P712Lfs*9	ENST00000256646	NM_024408.3	712	cCCCATCACCCCAGCTGCTACTCACAGGTGAACGAATGCCTGAGCAATCCCTGCATCCATGGAAAC/c	13/34	0.306764776811354	3	FACETS	1	0.983	1	0.788	0.733	0.844	CLONAL	2	TRUE	0	0.384355272961935	3		499	467	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204651	108204651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052248-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	38	212	0	ENST00000278616.4:c.7966C>T	p.Leu2656Phe	p.L2656F	ENST00000278616	NM_000051.3	2656	Ctt/Ttt	54/63	0.346433280794526	4	FACETS	0.931	0.783	1	0.931	0.783	1	CLONAL	2	TRUE	2	0.384355272961935	4		212	147	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041977	14041977	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052248-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	94	492	1	ENST00000311895.7:c.2524G>T	p.Glu842Ter	p.E842*	ENST00000311895	NM_005236.2	842	Gag/Tag	11/11	0.175400026027941	5	FACETS	0.78	0.697	0.869	0.52	0.465	0.579	INDETERMINATE	2	TRUE	2	0.384355272961935	5		493	494	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654634	67654634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052248-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	122	608	0	ENST00000264010.4:c.1121C>T	p.Thr374Ile	p.T374I	ENST00000264010	NM_006565.3	374	aCt/aTt	6/12	0.175400026027941	5	FACETS	0.816	0.74	0.897	0.544	0.493	0.598	INDETERMINATE	2	TRUE	2	0.384355272961935	5		608	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577133	7577146	+	frameshift_variant	Frame_Shift_Del	DEL	TGTTCCGTCCCAGT	TGTTCCGTCCCAGT	-	novel	NA	P-0052248-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	215	841	0	ENST00000269305.4:c.792_805del	p.Gly266Ter	p.G266*	ENST00000269305	NM_001126112.2	264	ctACTGGGACGGAACAgc/ctgc	8/11	0.384355272961935	4	FACETS	1	0.991	1	0.732	0.68	0.786	CLONAL	1	TRUE	2	0.384355272961935	4		841	1058	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99850117	99850117	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052248-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	401	1057	0	ENST00000280892.6:c.7G>T	p.Asp3Tyr	p.D3Y	ENST00000280892	NM_001130678.1	3	Gac/Tac	1/7	0.384355272961935	2	FACETS	0.991	0.945	1	0.991	0.945	1	CLONAL	2	TRUE	0	0.384355272961935	2		1057	1053	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541408	187541409	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052248-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	133	452	0	ENST00000441802.2:c.6331_6332insT	p.Gly2111ValfsTer15	p.G2111Vfs*15	ENST00000441802	NM_005245.3	2111	ggc/gTgc	10/27	0.384355272961935	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.384355272961935	2		452	326	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250524	26250524	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052248-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	368	1030	0	ENST00000446824.2:c.310C>A	p.Leu104Ile	p.L104I	ENST00000446824	NM_021018.2	104	Ctc/Atc	1/1	0.384355272961935	3	FACETS	0.91	0.863	0.957	0.91	0.863	0.957	CLONAL	2	TRUE	1	0.384355272961935	3		1030	1255	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519739	137519739	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052248-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	46	308	0	ENST00000367739.4:c.899C>T	p.Pro300Leu	p.P300L	ENST00000367739	NM_000416.2	300	cCt/cTt	7/7	0.308285743396987	3	FACETS	1	0.885	1	0.526	0.446	0.614	CLONAL	1	TRUE	1	0.384355272961935	3		308	271	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871906	45871906	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	111	748	0	ENST00000391945.4:c.342C>A	p.Asn114Lys	p.N114K	ENST00000391945	NM_000400.3	114	aaC/aaA	5/23	1	2	FACETS	0.91	0.816	1	0.91	0.816	1	CLONAL	1	TRUE	1	0.221329523820265	2		748	1102	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165458	47165486	+	frameshift_variant	Frame_Shift_Del	DEL	ATTAGAACTGTTATTGGTGTATGTGGCAA	ATTAGAACTGTTATTGGTGTATGTGGCAA	-	novel	NA	P-0052297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	57	590	0	ENST00000409792.3:c.640_668del	p.Leu214GlyfsTer13	p.L214Gfs*13	ENST00000409792	NM_014159.6	214	TTGCCACATACACCAATAACAGTTCTAATg/g	3/21	1	2	FACETS	0.692	0.593	0.801	0.692	0.593	0.801	SUBCLONAL	1	TRUE	1	0.221329523820265	2		590	744	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647558	117647558	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs766461873	NA	P-0052297-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	85	566	0	ENST00000368508.3:c.5386T>G	p.Leu1796Val	p.L1796V	ENST00000368508	NM_002944.2	1796	Tta/Gta	33/43	0.221329523820265	1	FACETS	0.848	0.748	0.954	0.848	0.748	0.954	CLONAL	1	TRUE	0	0.221329523820265	1		566	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579349	7579349	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	71	724	0	ENST00000269305.4:c.338T>C	p.Phe113Ser	p.F113S	ENST00000269305	NM_001126112.2	113	tTc/tCc	4/11	0.3	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.14	1		724	692	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0052310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	31	501	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	0.789	0.637	0.963	0.789	0.637	0.963	CLONAL	1	TRUE	1	0.14	2		501	561	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872380	45872380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	116	829	1	ENST00000391945.4:c.131C>T	p.Ser44Leu	p.S44L	ENST00000391945	NM_000400.3	44	tCa/tTa	3/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.202373448845901	2		830	956	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045190	47045190	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0052369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	42	702	0	ENST00000377604.3:c.2430+1G>T		p.X810_splice	ENST00000377604	NM_001204468.1	810			1	2	FACETS	0.539	0.449	0.64	0.539	0.449	0.64	SUBCLONAL	1	TRUE	1	0.202373448845901	2		702	770	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482870	67482870	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	92	519	0	ENST00000327367.4:c.1274C>G	p.Ser425Cys	p.S425C	ENST00000327367	NM_005902.3	425	tCt/tGt	9/9	0.202373448845901	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.202373448845901	1		519	566	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398282	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0052369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	273	435	1	ENST00000311936.3:c.37_38delinsTT	p.Gly13Phe	p.G13F	ENST00000311936	NM_004985.3	13	GGc/TTc	2/5	0.202373448845901	6	FACETS	0.91	0.857	0.964			1	CLONAL	5	TRUE	NA	0.202373448845901	6		436	833	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979530	2979530	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868565027	NA	P-0052369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	51	495	0	ENST00000396946.4:c.717G>A	p.Met239Ile	p.M239I	ENST00000396946	NM_032415.4	239	atG/atA	6/25	NA	2	FACETS	0.746	0.633	0.87			1	INDETERMINATE	1	TRUE	NA	0.202373448845901	2		495	676	SUCCESS
ALK	238	MSKCC	GRCh37	2	29420436	29420436	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs368744524	NA	P-0052369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	51	625	0	ENST00000389048.3:c.4045G>C	p.Asp1349His	p.D1349H	ENST00000389048	NM_004304.4	1349	Gac/Cac	27/29	1	2	FACETS	0.585	0.495	0.683	0.585	0.495	0.683	SUBCLONAL	1	TRUE	1	0.202373448845901	2		625	862	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931652	39931652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	54	616	1	ENST00000378444.4:c.2947G>A	p.Glu983Lys	p.E983K	ENST00000378444	NM_001123385.1	983	Gaa/Aaa	4/15	1	2	FACETS	0.648	0.552	0.754	0.648	0.552	0.754	SUBCLONAL	1	TRUE	1	0.202373448845901	2		617	823	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215817	133215817	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	138	648	0	ENST00000320574.5:c.5446A>C	p.Asn1816His	p.N1816H	ENST00000320574	NM_006231.2	1816	Aac/Cac	40/49	0.202373448845901	1	FACETS	0.911	0.831	0.994	1	0.99	1	CLONAL	2	TRUE	0	0.202373448845901	1		648	673	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573529	48573529	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	27	298	0	ENST00000342988.3:c.113G>C	p.Arg38Thr	p.R38T	ENST00000342988	NM_005359.5	38	aGa/aCa	2/12	1	2	FACETS	0.729	0.58	0.899	0.729	0.58	0.899	SUBCLONAL	1	TRUE	1	0.202373448845901	2		298	366	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253766	153253766	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	68	371	0	ENST00000281708.4:c.967G>C	p.Glu323Gln	p.E323Q	ENST00000281708	NM_033632.3	323	Gag/Cag	6/12	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.202373448845901	2		371	525	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332791	152332791	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	65	487	0	ENST00000206249.3:c.1097G>T	p.Gly366Val	p.G366V	ENST00000206249	NM_000125.3	366	gGc/gTc	5/8	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.202373448845901	2		487	633	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63760074	63760074	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	51	290	0	ENST00000279873.7:c.727G>C	p.Glu243Gln	p.E243Q	ENST00000279873	NM_032199.2	243	Gag/Cag	4/10	0.202373448845901	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.202373448845901	1		290	368	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165773	108165774	+	stop_gained	Nonsense_Mutation	DNP	GA	GA	TT	novel	NA	P-0052369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	38	363	0	ENST00000278616.4:c.4896_4897delinsTT	p.Met1632_Arg1633delinsIleTer	p.M1632_R1633delinsI*	ENST00000278616	NM_000051.3	1632	atGAga/atTTga	32/63	1	2	FACETS	0.745	0.615	0.89	0.745	0.615	0.89	SUBCLONAL	1	TRUE	1	0.202373448845901	2		363	504	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375587	118375587	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	29	310	0	ENST00000534358.1:c.8980C>G	p.Pro2994Ala	p.P2994A	ENST00000534358	NM_005933.3	2994	Cct/Gct	27/36	1	2	FACETS	0.671	0.538	0.823	0.671	0.538	0.823	SUBCLONAL	1	TRUE	1	0.202373448845901	2		310	427	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093420	30093420	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	48	508	0	ENST00000331968.5:c.1843G>C	p.Asp615His	p.D615H	ENST00000331968	NM_002742.2	615	Gac/Cac	13/18	1	2	FACETS	0.974	0.824	1	0.974	0.824	1	CLONAL	1	TRUE	1	0.202373448845901	2		508	487	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000301	42000301	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0052369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	42	325	0	ENST00000219905.7:c.2321-1G>A		p.X774_splice	ENST00000219905	NM_001164273.1	774			0.202373448845901	1	FACETS	0.84	0.702	0.993	0.84	0.702	0.993	CLONAL	1	TRUE	0	0.202373448845901	1		325	444	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256204	41256204	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1085307902	NA	P-0052369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	93	587	1	ENST00000357654.3:c.376C>T	p.Gln126Ter	p.Q126*	ENST00000357654	NM_007294.3	126	Caa/Taa	6/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.202373448845901	2		588	753	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265433	10265433	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	104	770	0	ENST00000340748.4:c.1613C>G	p.Ser538Cys	p.S538C	ENST00000340748		538	tCt/tGt	20/40	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.202373448845901	2		770	838	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918208	50918208	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	120	1019	0	ENST00000440232.2:c.2525A>C	p.Asn842Thr	p.N842T	ENST00000440232	NM_002691.3	842	aAc/aCc	20/27	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.202373448845901	2		1019	1029	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994346	25994346	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	78	436	0	ENST00000435504.4:c.467C>T	p.Ser156Phe	p.S156F	ENST00000435504		156	tCt/tTt	6/13	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.202373448845901	2		436	643	SUCCESS
ALK	238	MSKCC	GRCh37	2	29497991	29497991	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	109	598	0	ENST00000389048.3:c.2015G>C	p.Arg672Thr	p.R672T	ENST00000389048	NM_004304.4	672	aGa/aCa	11/29	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.202373448845901	2		598	878	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572904	41572904	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	116	775	0	ENST00000263253.7:c.5189C>G	p.Ser1730Cys	p.S1730C	ENST00000263253	NM_001429.3	1730	tCt/tGt	31/31	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.202373448845901	2		775	920	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456647	138456647	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	53	515	0	ENST00000289153.2:c.703C>G	p.His235Asp	p.H235D	ENST00000289153	NM_006219.2	235	Cat/Gat	4/22	1	2	FACETS	0.674	0.573	0.785	0.674	0.573	0.785	SUBCLONAL	1	TRUE	1	0.202373448845901	2		515	777	SUCCESS
MET	4233	MSKCC	GRCh37	7	116381062	116381062	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1204728771	NA	P-0052369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	73	643	0	ENST00000397752.3:c.1684C>G	p.Leu562Val	p.L562V	ENST00000397752	NM_000245.2	562	Ctg/Gtg	5/21	1	2	FACETS	0.729	0.636	0.83	0.729	0.636	0.83	SUBCLONAL	1	TRUE	1	0.202373448845901	2		643	990	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247478	53247478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	89	624	1	ENST00000375401.3:c.331G>A	p.Asp111Asn	p.D111N	ENST00000375401	NM_004187.3	111	Gac/Aac	3/26	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.202373448845901	2		625	810	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	77	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.540831798941026	2		276	201	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268805	41268805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	41	438	0	ENST00000349496.5:c.1043C>T	p.Ser348Phe	p.S348F	ENST00000349496	NM_001904.3	348	tCt/tTt	7/15	0.540831798941026	3	FACETS	0.978	0.824	1	0.489	0.412	0.572	CLONAL	1	TRUE	1	0.540831798941026	3		438	197	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0052440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	178	948	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.444890323975553	3	FACETS	0.937	0.873	1	0.937	0.873	1	CLONAL	2	TRUE	1	0.540831798941026	3		948	446	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	61	702	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.444890323975553	3	FACETS	1	0.953	1	0.602	0.526	0.683	CLONAL	1	TRUE	1	0.540831798941026	3		702	238	SUCCESS
FH	2271	MSKCC	GRCh37	1	241676905	241676905	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	13	355	0	ENST00000366560.3:c.376G>A	p.Glu126Lys	p.E126K	ENST00000366560	NM_000143.3	126	Gag/Aag	3/10	0.540831798941026	3	FACETS	0.671	0.485	0.891	0.336	0.242	0.446	SUBCLONAL	1	TRUE	1	0.540831798941026	3		355	91	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953761	48953761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769425649	NA	P-0052440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	10	283	0	ENST00000267163.4:c.1364G>A	p.Arg455Gln	p.R455Q	ENST00000267163	NM_000321.2	455	cGa/cAa	14/27	0.540831798941026	3	FACETS	0.242	0.164	0.341	0.121	0.082	0.171	SUBCLONAL	1	TRUE	1	0.540831798941026	3		283	194	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446976	187446976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369842677	NA	P-0052440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	95	1081	2	ENST00000232014.4:c.1217G>A	p.Arg406Gln	p.R406Q	ENST00000232014	NM_001130845.1	406	cGa/cAa	5/10	0.540831798941026	3	FACETS	0.946	0.846	1	0.473	0.423	0.526	CLONAL	1	TRUE	1	0.540831798941026	3		1083	472	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106953	27106954	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	104	838	0	ENST00000324856.7:c.6566dup	p.Ser2191GlnfsTer34	p.S2191Qfs*34	ENST00000324856	NM_006015.4	2188	-/A	20/20	0.344843585262568	3	FACETS	0.962	0.877	1	0.962	0.877	1	CLONAL	2	TRUE	1	0.540831798941026	3		838	254	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912486	32912486	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs863224588	NA	P-0052440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	49	215	0	ENST00000380152.3:c.3994C>G	p.His1332Asp	p.H1332D	ENST00000380152		1332	Cat/Gat	11/27	0.540831798941026	3	FACETS	0.921	0.802	1	0.921	0.802	1	CLONAL	2	TRUE	1	0.540831798941026	3		215	125	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438207	110438207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	29	234	0	ENST00000375856.3:c.194G>A	p.Gly65Glu	p.G65E	ENST00000375856	NM_003749.2	65	gGg/gAg	1/2	0.540831798941026	3	FACETS	0.902	0.734	1	0.451	0.367	0.545	CLONAL	1	TRUE	1	0.540831798941026	3		234	151	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991400	72991400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201144589	NA	P-0052440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	114	1044	0	ENST00000268489.5:c.2645C>T	p.Ser882Leu	p.S882L	ENST00000268489	NM_006885.3	882	tCg/tTg	2/10	0.478284360980141	2	FACETS	1	0.967	1	0.57	0.518	0.623	CLONAL	1	TRUE	0	0.540831798941026	2		1044	370	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993631	72993631	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	95	1050	0	ENST00000268489.5:c.414C>G	p.Asp138Glu	p.D138E	ENST00000268489	NM_006885.3	138	gaC/gaG	2/10	0.478284360980141	2	FACETS	0.925	0.83	1	0.462	0.415	0.512	CLONAL	1	TRUE	0	0.540831798941026	2		1050	380	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435860	149435861	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0052440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	86	1027	0	ENST00000286301.3:c.2363_2364del	p.Asn788ArgfsTer13	p.N788Rfs*13	ENST00000286301	NM_005211.3	788	aAT/a	18/22	1	2	FACETS	0.947	0.845	1	0.947	0.845	1	CLONAL	1	TRUE	1	0.540831798941026	2		1027	336	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858354	27858354	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	96	1132	4	ENST00000359303.2:c.217C>T	p.Arg73Ter	p.R73*	ENST00000359303	NM_003535.2	73	Cga/Tga	1/1	0.444890323975553	3	FACETS	0.888	0.794	0.987	0.444	0.397	0.494	CLONAL	1	TRUE	1	0.540831798941026	3		1136	508	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651984	36651994	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCTAATGGC	GCGCTAATGGC	-	novel	NA	P-0052440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	197	1130	0	ENST00000244741.5:c.107_117del	p.Ala36GlyfsTer8	p.A36Gfs*8	ENST00000244741	NM_000389.4	36	GCGCTAATGGCg/g	2/3	0.444890323975553	3	FACETS	0.806	0.752	0.862	0.806	0.752	0.862	CLONAL	2	TRUE	1	0.540831798941026	3		1130	574	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652118	36652131	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGCCCCGGCGAG	GGGGCCCCGGCGAG	-	novel	NA	P-0052440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	142	1212	0	ENST00000244741.5:c.241_254del	p.Gly81ProfsTer3	p.G81Pfs*3	ENST00000244741	NM_000389.4	80	acGGGGCCCCGGCGAGgc/acgc	2/3	0.444890323975553	3	FACETS	1	0.953	1	0.531	0.485	0.579	CLONAL	1	TRUE	1	0.540831798941026	3		1212	628	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612057	43612057	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356141763	NA	P-0052497-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	215	724	0	ENST00000355710.3:c.2162G>A	p.Arg721Gln	p.R721Q	ENST00000355710	NM_020975.4	721	cGg/cAg	12/20	0.463575962478591	3	FACETS	1	0.99	1	0.652	0.611	0.694	INDETERMINATE	1	TRUE	1	0.841021962504447	3		724	557	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434507	49434508	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0052497-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	711	925	0	ENST00000301067.7:c.7044_7045dup	p.Pro2349ArgfsTer36	p.P2349Rfs*36	ENST00000301067	NM_003482.3	2349	ccc/cGCcc	31/54	0.841021962504447	3	FACETS	0.888	0.869	0.906	0.888	0.869	0.906	CLONAL	3	TRUE	0	0.841021962504447	3		925	902	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578187	7578187	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs878854071	NA	P-0052497-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	1170	649	0	ENST00000269305.4:c.662del	p.Glu221GlyfsTer26	p.E221Gfs*26	ENST00000269305	NM_001126112.2	221	gAg/gg	6/11	0.841021962504447	3	FACETS	1	0.998	1	1	0.998	1	CLONAL	3	TRUE	0	0.841021962504447	3		649	1252	SUCCESS
ALK	238	MSKCC	GRCh37	2	29541229	29541229	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052497-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	72	494	0	ENST00000389048.3:c.1588G>T	p.Glu530Ter	p.E530*	ENST00000389048	NM_004304.4	530	Gaa/Taa	8/29	0.287097438645729	5	FACETS	0.598	0.522	0.679	0.199	0.174	0.227	INDETERMINATE	1	TRUE	2	0.841021962504447	5		494	648	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262563	39262566	+	frameshift_variant	Frame_Shift_Del	DEL	ACTG	ACTG	-	novel	NA	P-0052497-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	191	374	0	ENST00000402219.2:c.940_943del	p.Gln314TyrfsTer13	p.Q314Yfs*13	ENST00000402219	NM_005633.3	314	CAGTta/ta	7/23	0.287097438645729	5	FACETS	1	0.974	1	0.722	0.675	0.771	INDETERMINATE	2	TRUE	2	0.841021962504447	5		374	474	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139648	202139648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052497-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	52	314	0	ENST00000358485.4:c.809C>T	p.Ser270Phe	p.S270F	ENST00000358485	NM_001080125.1	270	tCt/tTt	6/9	0.841021962504447	3	FACETS	0.405	0.345	0.47	0.202	0.172	0.235	SUBCLONAL	1	TRUE	1	0.841021962504447	3		314	434	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884888	134884888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1320801657	NA	P-0052497-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	62	582	0	ENST00000398015.3:c.1664C>T	p.Ser555Phe	p.S555F	ENST00000398015	NM_004441.4	555	tCc/tTc	8/16	0.295313504628125	2	FACETS	0.256	0.221	0.295	0.128	0.11	0.148	INDETERMINATE	1	TRUE	0	0.841021962504447	2		582	575	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38968093	38968093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1020349804	NA	P-0052497-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	36	285	0	ENST00000357387.3:c.1012C>T	p.Pro338Ser	p.P338S	ENST00000357387	NM_152756.3	338	Cct/Tct	12/38	0.841021962504447	5	FACETS	0.41	0.337	0.493	0.137	0.112	0.165	SUBCLONAL	1	TRUE	2	0.841021962504447	5		285	472	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38968099	38968099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052497-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	40	282	0	ENST00000357387.3:c.1006C>T	p.Arg336Cys	p.R336C	ENST00000357387	NM_152756.3	336	Cgt/Tgt	12/38	0.841021962504447	5	FACETS	0.458	0.38	0.544	0.153	0.126	0.182	SUBCLONAL	1	TRUE	2	0.841021962504447	5		282	470	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052552-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	58	703	0	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.14	2		703	816	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867571	45867571	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052552-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	49	842	0	ENST00000391945.4:c.737C>A	p.Ser246Tyr	p.S246Y	ENST00000391945	NM_000400.3	246	tCc/tAc	9/23	1	2	FACETS	0.806	0.681	0.945	0.806	0.681	0.945	CLONAL	1	TRUE	1	0.14	2		842	868	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229415	36229415	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052552-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	41	475	0	ENST00000222270.7:c.8105C>A	p.Pro2702His	p.P2702H	ENST00000222270	NM_014727.1	2702	cCc/cAc	37/37	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.14	2		475	569	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0052615-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	176	533	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.31972865952003	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.31972865952003	4		533	620	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225060	NA	P-0052615-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	186	384	0	ENST00000263967.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000263967	NM_006218.2	104	cCa/cTa	2/21	0.31972865952003	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.31972865952003	4		384	682	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028614	12028614	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052615-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	116	327	0	ENST00000353533.5:c.817G>A	p.Glu273Lys	p.E273K	ENST00000353533	NM_003010.3	273	Gaa/Aaa	8/11	0.31972865952003	2	FACETS	0.852	0.773	0.933	0.852	0.773	0.933	CLONAL	2	TRUE	0	0.31972865952003	2		327	426	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196186	108196186	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786202583	NA	P-0052615-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	30	0	0	ENST00000278616.4:c.6722A>G	p.Asn2241Ser	p.N2241S	ENST00000278616	NM_000051.3	2241	aAc/aGc	46/63	0.31972865952003	2	FACETS	0.284	0.228	0.348	0.142	0.114	0.174	SUBCLONAL	1	TRUE	0	0.31972865952003	2		0	661	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0052694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	183	377	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.417887352385002	4	FACETS	1	0.951	1	1	0.951	1	CLONAL	3	TRUE	1	0.417625510311472	4		377	406	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0052694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	109	533	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.417887352385002	4	FACETS	0.856	0.781	0.934	0.856	0.781	0.934	CLONAL	3	TRUE	1	0.417625510311472	4		533	288	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0052694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	151	357	1	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.417887352385002	3	FACETS	0.989	0.912	1	0.989	0.912	1	CLONAL	2	TRUE	1	0.417625510311472	3		358	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0052694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	170	641	5	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.417625510311472	2	FACETS	0.947	0.88	1	0.947	0.88	1	CLONAL	2	TRUE	0	0.417625510311472	2		646	430	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615083	43615083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377767422	NA	P-0052694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	200	814	3	ENST00000355710.3:c.2497C>T	p.Arg833Cys	p.R833C	ENST00000355710	NM_020975.4	833	Cgc/Tgc	14/20	0.417887352385002	3	FACETS	0.895	0.833	0.958	0.895	0.833	0.958	CLONAL	2	TRUE	1	0.417625510311472	3		817	647	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176104189	176104189	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	23	310	0	ENST00000367669.3:c.925G>C	p.Asp309His	p.D309H	ENST00000367669	NM_022457.5	309	Gat/Cat	8/20	0.417887352385002	4	FACETS	0.556	0.434	0.696	0.278	0.217	0.348	SUBCLONAL	1	TRUE	2	0.417625510311472	4		310	281	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509890	106509890	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	108	529	0	ENST00000359195.3:c.1884G>T	p.Met628Ile	p.M628I	ENST00000359195	NM_002649.2	628	atG/atT	2/11	0.417887352385002	3	FACETS	1	0.975	1	0.625	0.564	0.69	CLONAL	1	TRUE	1	0.417625510311472	3		529	500	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0052702-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	167	651	2	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.577464766214356	2		653	570	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439229	52439229	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052702-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	318	1087	8	ENST00000460680.1:c.1013del	p.Pro338LeufsTer24	p.P338Lfs*24	ENST00000460680	NM_004656.3	338	cCt/ct	11/17	0.553690987865237	1	FACETS	0.861	0.815	0.908	0.861	0.815	0.908	CLONAL	1	TRUE	0	0.577464766214356	1		1095	910	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829040	128829042	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	rs570242755	NA	P-0052731-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	14	47	0	ENST00000249373.3:c.67_69del	p.Leu23del	p.L23del	ENST00000249373	NM_005631.4	16	ggGCTg/ggg	1/12	0.384588016636389	6	FACETS	0.599	0.434	0.796	0.15	0.108	0.199	SUBCLONAL	1	FALSE	2	0.611939082532479	6		47	170	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152566	56152566	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052731-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	94	295	0	ENST00000399503.3:c.622C>T	p.Arg208Ter	p.R208*	ENST00000399503	NM_005921.1	208	Cga/Tga	2/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.611939082532479	2		295	278	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78933956	78933956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771660225	NA	P-0052731-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	119	816	1	ENST00000306801.3:c.3556G>A	p.Gly1186Ser	p.G1186S	ENST00000306801	NM_020761.2	1186	Ggt/Agt	30/34	0.293331633846791	3	FACETS	0.755	0.682	0.831	0.377	0.341	0.416	INDETERMINATE	1	FALSE	1	0.611939082532479	3		817	673	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610247	10610247	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780079329	NA	P-0052731-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	21	988	2	ENST00000171111.5:c.463G>A	p.Val155Ile	p.V155I	ENST00000171111	NM_203500.1	155	Gtc/Atc	2/6	0.195513259067182	4	FACETS	0.112	0.086	0.144	0.056	0.043	0.072	INDETERMINATE	1	FALSE	2	0.611939082532479	4		990	986	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971101	55971101	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052731-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	31	516	0	ENST00000263923.4:c.1696A>G	p.Ser566Gly	p.S566G	ENST00000263923	NM_002253.2	566	Agc/Ggc	13/30	0.138761881153006	0	FACETS	0.157	0.127	0.19			1	INDETERMINATE	1	FALSE	0	0.611939082532479	0		516	251	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167805	56167805	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052731-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	138	411	0	ENST00000399503.3:c.1370del	p.Thr457LysfsTer30	p.T457Kfs*30	ENST00000399503	NM_005921.1	457	aCa/aa	7/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.611939082532479	2		411	381	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860530	45860530	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs769095908	NA	P-0052756-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	245	794	0	ENST00000391945.4:c.1477A>G	p.Met493Val	p.M493V	ENST00000391945	NM_000400.3	493	Atg/Gtg	15/23	0.728626535621038	2	FACETS	1	0.974	1	0.532	0.5	0.564	CLONAL	1	TRUE	0	0.733887884578778	2		794	628	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190461	32190461	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052756-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	243	977	0	ENST00000375023.3:c.278C>T	p.Ser93Phe	p.S93F	ENST00000375023	NM_004557.3	93	tCt/tTt	3/30	1	2	FACETS	0.922	0.866	0.98	0.922	0.866	0.98	CLONAL	1	TRUE	1	0.733887884578778	2		977	718	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052853-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	33	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	TRUE	1	0.12	2		276	530	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052853-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	38	250	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	1	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.12	1		250	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578513	7578513	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052853-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1282	51	796	0	ENST00000269305.4:c.417G>C	p.Lys139Asn	p.K139N	ENST00000269305	NM_001126112.2	139	aaG/aaC	5/11	1	2	FACETS	0.638	0.539	0.747	0.638	0.539	0.747	SUBCLONAL	1	TRUE	1	0.12	2		796	1333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0052853-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	41	671	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	1	2	FACETS	0.604	0.501	0.72	0.604	0.501	0.72	SUBCLONAL	1	TRUE	1	0.12	2		671	1131	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0052853-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	13	0	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	1	2	FACETS	0.218	0.154	0.297	0.218	0.154	0.297	SUBCLONAL	1	TRUE	1	0.12	2		0	992	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030378	49030378	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs267603840	NA	P-0052853-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	17	0	0	ENST00000267163.4:c.1853C>A	p.Ser618Ter	p.S618*	ENST00000267163	NM_000321.2	618	tCa/tAa	19/27	1	2	FACETS	0.441	0.328	0.578	0.441	0.328	0.578	SUBCLONAL	1	TRUE	1	0.12	2		0	642	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024678	14024678	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052853-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	19	0	0	ENST00000311895.7:c.904G>C	p.Asp302His	p.D302H	ENST00000311895	NM_005236.2	302	Gat/Cat	5/11	0.165372778240566	3	FACETS	0.417	0.315	0.539	0.209	0.157	0.27	SUBCLONAL	1	TRUE	1	0.12	3		0	804	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39567798	39567798	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052853-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	10	0	0	ENST00000262039.4:c.554G>A	p.Gly185Glu	p.G185E	ENST00000262039	NM_002647.2	185	gGa/gAa	5/25	1	2	FACETS	0.345	0.232	0.488	0.345	0.232	0.488	SUBCLONAL	1	TRUE	1	0.12	2		0	483	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0053147-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	172	650	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.215663293493826	7	FACETS	0.994	0.929	1	1	0.99	1	CLONAL	7	TRUE	2	0.215663293493826	7		650	353	SUCCESS
APC	324	MSKCC	GRCh37	5	112174096	112174096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs137854575	NA	P-0053147-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	62	438	0	ENST00000257430.4:c.2805C>A	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	taC/taA	16/16	1	2	FACETS	0.968	0.85	1	1	0.984	1	CLONAL	3	TRUE	1	0.215663293493826	2		438	198	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482425	56482425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053147-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	161	735	0	ENST00000267101.3:c.973G>A	p.Gly325Arg	p.G325R	ENST00000267101	NM_001982.3	325	Gga/Aga	8/28	0.215663293493826	7	FACETS	1	0.976	1	0.69	0.635	0.747	CLONAL	3	TRUE	2	0.215663293493826	7		735	666	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120121	70120121	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053147-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	135	268	0	ENST00000245479.2:c.1123C>T	p.Gln375Ter	p.Q375*	ENST00000245479	NM_000346.3	375	Cag/Tag	3/3	0.215663293493826	6	FACETS	0.974	0.909	1	1	0.991	1	CLONAL	8	TRUE	1	0.215663293493826	6		268	230	SUCCESS
APC	324	MSKCC	GRCh37	5	112175493	112175493	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053147-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	82	431	0	ENST00000257430.4:c.4203del	p.Ile1401MetfsTer14	p.I1401Mfs*14	ENST00000257430	NM_000038.5	1401	aTt/at	16/16	1	2	FACETS	0.893	0.796	0.993	1	0.988	1	CLONAL	3	TRUE	1	0.215663293493826	2		431	284	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645765	12645765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053147-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	138	460	0	ENST00000251849.4:c.704C>T	p.Pro235Leu	p.P235L	ENST00000251849	NM_002880.3	235	cCt/cTt	7/17	1	2	FACETS	1	0.97	1	1	0.993	1	CLONAL	3	TRUE	1	0.215663293493826	2		460	384	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0053188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	102	249	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.878	0.792	0.969	0.878	0.792	0.969	CLONAL	1	TRUE	1	0.589503930045697	2		249	394	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420204	49420204	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	204	637	1	ENST00000301067.7:c.15545del	p.Gly5182AlafsTer61	p.G5182Afs*61	ENST00000301067	NM_003482.3	5182	gGc/gc	48/54	1	2	FACETS	0.948	0.882	1	0.948	0.882	1	CLONAL	1	TRUE	1	0.589503930045697	2		638	730	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106648	27106648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553153748	NA	P-0053188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	177	632	0	ENST00000324856.7:c.6259G>A	p.Gly2087Arg	p.G2087R	ENST00000324856	NM_006015.4	2087	Gga/Aga	20/20	1	2	FACETS	0.918	0.849	0.989	0.918	0.849	0.989	CLONAL	1	TRUE	1	0.589503930045697	2		632	654	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0053188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	96	269	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.839	0.754	0.929	0.839	0.754	0.929	CLONAL	1	TRUE	1	0.589503930045697	2		269	388	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552144	29552144	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	81	200	0	ENST00000356175.3:c.1882del	p.Tyr628ThrfsTer3	p.Y628Tfs*3	ENST00000356175	NM_000267.3	626	cTt/ct	17/57	1	2	FACETS	0.948	0.844	1	0.948	0.844	1	CLONAL	1	TRUE	1	0.589503930045697	2		200	290	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390617	139390617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567323027	NA	P-0053188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	280	930	0	ENST00000277541.6:c.7574C>T	p.Pro2525Leu	p.P2525L	ENST00000277541	NM_017617.3	2525	cCg/cTg	34/34	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.589503930045697	2		930	930	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0053188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	42	100	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.589503930045697	2		100	128	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557331	29557332	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0053188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	101	281	0	ENST00000356175.3:c.3047_3048del	p.Cys1016SerfsTer4	p.C1016Sfs*4	ENST00000356175	NM_000267.3	1015	cTG/c	23/57	1	2	FACETS	0.85	0.766	0.939	0.85	0.766	0.939	CLONAL	1	TRUE	1	0.589503930045697	2		281	403	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	171	548	1	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	0.809	0.746	0.874	0.809	0.746	0.874	CLONAL	1	TRUE	1	0.589503930045697	2		549	717	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46252810	46252810	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751452957	NA	P-0053188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	80	206	0	ENST00000371998.3:c.239G>A	p.Arg80His	p.R80H	ENST00000371998		80	cGt/cAt	4/23	0.575932746120629	3	FACETS	0.965	0.856	1	0.483	0.428	0.541	CLONAL	1	TRUE	1	0.589503930045697	3		206	364	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223358	36223358	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	269	975	0	ENST00000222270.7:c.5908C>T	p.Pro1970Ser	p.P1970S	ENST00000222270	NM_014727.1	1970	Cct/Tct	28/37	1	2	FACETS	0.941	0.884	0.999	0.941	0.884	0.999	CLONAL	1	TRUE	1	0.589503930045697	2		975	970	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0053188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	308	362	7	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	1	2	FACETS	0.869	0.828	0.911	1	0.996	1	CLONAL	2	TRUE	1	0.589503930045697	2		369	601	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202925	27202925	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	167	469	0	ENST00000380036.4:c.2017C>A	p.Arg673Ser	p.R673S	ENST00000380036	NM_000459.3	673	Cgt/Agt	13/23	1	2	FACETS	0.954	0.881	1	0.954	0.881	1	CLONAL	1	TRUE	1	0.589503930045697	2		469	594	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267849	46267849	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	177	515	0	ENST00000371998.3:c.2615del	p.Asn872IlefsTer20	p.N872Ifs*20	ENST00000371998		870	gtA/gt	14/23	0.575932746120629	3	FACETS	0.905	0.835	0.978	0.453	0.417	0.489	CLONAL	1	TRUE	1	0.589503930045697	3		515	859	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946238	81946238	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	207	702	0	ENST00000359376.3:c.1971G>T	p.Glu657Asp	p.E657D	ENST00000359376	NM_002661.3	657	gaG/gaT	19/33	1	2	FACETS	0.9	0.838	0.965	0.9	0.838	0.965	CLONAL	1	TRUE	1	0.589503930045697	2		702	780	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65323386	65323386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1387066409	NA	P-0053188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	171	527	0	ENST00000342505.4:c.1411G>A	p.Asp471Asn	p.D471N	ENST00000342505	NM_002227.2	471	Gac/Aac	10/25	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.589503930045697	2		527	566	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4094470	4094470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	490	810	3	ENST00000262948.5:c.1073C>T	p.Ala358Val	p.A358V	ENST00000262948	NM_030662.3	358	gCg/gTg	10/11	0.589503930045697	2	FACETS	0.976	0.941	1	0.976	0.941	1	CLONAL	2	TRUE	0	0.589503930045697	2		813	852	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668809	52668810	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0053188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	101	278	0	ENST00000394830.3:c.1109_1110del	p.Glu370ValfsTer21	p.E370Vfs*21	ENST00000394830	NM_018313.4	370	gAG/g	12/30	0.573268038960222	1	FACETS	0.974	0.887	1	0.974	0.887	1	CLONAL	1	TRUE	0	0.589503930045697	1		278	248	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527298	187527298	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772835024	NA	P-0053188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	156	478	2	ENST00000441802.2:c.10276G>A	p.Val3426Met	p.V3426M	ENST00000441802	NM_005245.3	3426	Gtg/Atg	17/27	1	2	FACETS	0.927	0.853	1	0.927	0.853	1	CLONAL	1	TRUE	1	0.589503930045697	2		480	571	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984070	2984070	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	175	488	0	ENST00000396946.4:c.460G>T	p.Ala154Ser	p.A154S	ENST00000396946	NM_032415.4	154	Gcc/Tcc	5/25	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.589503930045697	2		488	569	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145728	11145728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	224	802	0	ENST00000358026.2:c.4090G>A	p.Glu1364Lys	p.E1364K	ENST00000358026	NM_001128849.1	1364	Gag/Aag	29/36	1	2	FACETS	0.95	0.887	1	0.95	0.887	1	CLONAL	1	TRUE	1	0.589503930045697	2		802	800	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50821745	50821765	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	AACCTTTGCTAAAAATAAGGT	AACCTTTGCTAAAAATAAGGT	-	novel	NA	P-0053202-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	133	426	1	ENST00000398568.2:c.2088_2099+9del		p.X696_splice	ENST00000398568	NM_001042412.1	696		13/18	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		427	324	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0053218-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	205	646	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.58307703679698	4	FACETS	1	0.991	1	0.736	0.686	0.786	CLONAL	1	TRUE	2	0.823398667707251	4		646	617	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0053218-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	165	258	0				ENST00000310581	NM_198253.2	-/1132			0.265950860563271	2	FACETS	0.842	0.798	0.884	0.842	0.798	0.884	INDETERMINATE	2	TRUE	0	0.823398667707251	2		258	238	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031889	26031889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053218-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	417	546	0	ENST00000244661.2:c.400G>A	p.Glu134Lys	p.E134K	ENST00000244661	NM_003537.3	134	Gaa/Aaa	1/1	0.821237173773944	4	FACETS	0.982	0.962	1	0.982	0.962	1	CLONAL	4	TRUE	0	0.823398667707251	4		546	470	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095917	29095917	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780192	NA	P-0053218-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	1049	554	0	ENST00000328354.6:c.917G>A	p.Gly306Glu	p.G306E	ENST00000328354	NM_007194.3	306	gGg/gAg	9/15	0.823398667707251	8	FACETS	1	0.997	1			1	CLONAL	8	TRUE	NA	0.823398667707251	8		554	1093	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165924	47165924	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053218-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	277	261	0	ENST00000409792.3:c.202C>T	p.Gln68Ter	p.Q68*	ENST00000409792	NM_014159.6	68	Cag/Tag	3/21	0.768845739178342	3	FACETS	0.961	0.916	1	0.961	0.916	1	CLONAL	2	TRUE	1	0.823398667707251	3		261	494	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683487	29683487	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053218-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	177	127	0	ENST00000356175.3:c.7562A>G	p.Lys2521Arg	p.K2521R	ENST00000356175	NM_000267.3	2521	aAa/aGa	51/57	0.763669409520268	5	FACETS	1	0.952	1			1	CLONAL	2	TRUE	NA	0.823398667707251	5		127	467	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115272901	115272901	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs767985022	NA	P-0053218-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	322	251	0	ENST00000438362.2:c.1472G>T	p.Ser491Ile	p.S491I	ENST00000438362	NM_001242891.1	491	aGc/aTc	12/20	0.803877967202882	3	FACETS	0.957	0.914	0.999	0.957	0.914	0.999	CLONAL	2	TRUE	1	0.823398667707251	3		251	577	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786818	3786818	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0053218-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	149	503	0	ENST00000262367.5:c.4395-2A>C		p.X1465_splice	ENST00000262367	NM_004380.2	1465			0.58307703679698	4	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	2	0.823398667707251	4		503	321	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029368	14029368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053218-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	174	312	0	ENST00000311895.7:c.1579G>A	p.Glu527Lys	p.E527K	ENST00000311895	NM_005236.2	527	Gaa/Aaa	8/11	0.58307703679698	4	FACETS	0.935	0.872	1	0.935	0.872	1	CLONAL	2	TRUE	2	0.823398667707251	4		312	412	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741858	17741858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053278-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	21	147	0	ENST00000250003.3:c.529G>A	p.Ala177Thr	p.A177T	ENST00000250003	NM_002478.4	177	Gcc/Acc	1/3	1	2	FACETS	0.652	0.504	0.824	0.652	0.504	0.824	SUBCLONAL	1	TRUE	1	0.29	2		147	222	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053278-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	320	522	0	ENST00000397752.3:c.3028G>A	p.Asp1010Asn	p.D1010N	ENST00000397752	NM_000245.2	1010	Gat/Aat	14/21	0.291977453108632	3	FACETS	0.957	0.912	1	1	0.993	1	CLONAL	4	TRUE	0	0.29	3		522	660	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044971	47044971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053278-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	113	867	0	ENST00000377604.3:c.2297G>A	p.Arg766His	p.R766H	ENST00000377604	NM_001204468.1	766	cGc/cAc	20/24	1	2	FACETS	0.68	0.61	0.754	0.68	0.61	0.754	SUBCLONAL	1	TRUE	1	0.29	2		867	1146	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578198	7578202	+	frameshift_variant	Frame_Shift_Del	DEL	CACCA	CACCA	-	novel	NA	P-0053278-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	153	617	0	ENST00000269305.4:c.647_651del	p.Val216GlyfsTer4	p.V216Gfs*4	ENST00000269305	NM_001126112.2	216	gTGGTG/g	6/11	0.295288252580333	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.29	1		617	850	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233597	69233597	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053278-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	16	304	0	ENST00000462284.1:c.1462A>G	p.Ile488Val	p.I488V	ENST00000462284	NM_002392.5	488	Att/Gtt	11/11	1	2	FACETS	0.369	0.272	0.485	0.369	0.272	0.485	SUBCLONAL	1	TRUE	1	0.29	2		304	299	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267761	7267761	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053278-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	151	609	0	ENST00000302850.5:c.247A>G	p.Met83Val	p.M83V	ENST00000302850	NM_000208.2	83	Atg/Gtg	2/22	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.29	2		609	794	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879465	151879471	+	frameshift_variant	Frame_Shift_Del	DEL	TTATGGA	TTATGGA	-	novel	NA	P-0053278-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	160	501	0	ENST00000262189.6:c.5474_5480del	p.Phe1825Ter	p.F1825*	ENST00000262189	NM_170606.2	1825	tTCCATAAa/ta	36/59	0.291977453108632	3	FACETS	0.785	0.72	0.852	0.523	0.48	0.568	SUBCLONAL	2	TRUE	0	0.29	3		501	805	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0053281-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	187	781	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.311319495632863	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.311319495632863	1		782	947	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0053281-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	116	563	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.197769980951805	1	FACETS	0.842	0.76	0.93	0.842	0.76	0.93	CLONAL	1	TRUE	0	0.311319495632863	1		563	747	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974768	21974768	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053281-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	101	275	0	ENST00000304494.5:c.59C>A	p.Ala20Glu	p.A20E	ENST00000304494	NM_000077.4	20	gCg/gAg	1/3	0.311319495632863	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.311319495632863	1		275	435	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298704	15298704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1202763005	NA	P-0053281-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1335	106	797	3	ENST00000263388.2:c.1594C>T	p.Arg532Cys	p.R532C	ENST00000263388	NM_000435.2	532	Cgc/Tgc	10/33	1	2	FACETS	0.473	0.422	0.527	0.473	0.422	0.527	SUBCLONAL	1	TRUE	1	0.311319495632863	2		800	1441	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326717	62326717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1350306450	NA	P-0053281-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	244	903	0	ENST00000360203.5:c.3536G>A	p.Ser1179Asn	p.S1179N	ENST00000360203	NM_001283009.1	1179	aGc/aAc	34/35	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.311319495632863	2		903	1476	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0053282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	63	470	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.225869826422171	2		470	486	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236153	108236153	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876658529	NA	P-0053282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	106	624	1	ENST00000278616.4:c.9089G>T	p.Gly3030Val	p.G3030V	ENST00000278616	NM_000051.3	3030	gGa/gTa	63/63	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.225869826422171	2		625	667	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483934	88483934	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	154	701	0	ENST00000360948.2:c.1636G>T	p.Glu546Ter	p.E546*	ENST00000360948	NM_001012338.2	546	Gag/Tag	14/19	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.225869826422171	2		701	1010	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106530	108106530	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	27	349	0	ENST00000278616.4:c.465C>A	p.Tyr155Ter	p.Y155*	ENST00000278616	NM_000051.3	155	taC/taA	5/63	1	2	FACETS	0.781	0.623	0.962	0.781	0.623	0.962	CLONAL	1	TRUE	1	0.225869826422171	2		349	306	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082484	16082484	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	182	608	0	ENST00000281043.3:c.298G>T	p.Gly100Trp	p.G100W	ENST00000281043	NM_005378.4	100	Ggg/Tgg	2/3	1	2	FACETS	0.754	0.695	0.815	1	0.99	1	SUBCLONAL	2	TRUE	1	0.225869826422171	2		608	1069	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874278	155874278	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	75	493	0	ENST00000368323.3:c.253A>G	p.Met85Val	p.M85V	ENST00000368323	NM_006912.5	85	Atg/Gtg	5/6	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.225869826422171	2		493	574	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715613	30715613	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs878854610	NA	P-0053282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	18	301	0	ENST00000295754.5:c.1271A>T	p.Tyr424Phe	p.Y424F	ENST00000295754	NM_003242.5	424	tAc/tTc	5/7	0.225869826422171	1	FACETS	0.423	0.318	0.548	0.423	0.318	0.548	SUBCLONAL	1	TRUE	0	0.225869826422171	1		301	334	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514027	125514027	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs761313560	NA	P-0053282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	61	473	2	ENST00000428830.2:c.965G>T	p.Arg322Leu	p.R322L	ENST00000428830	NM_001114121.2	322	cGc/cTc	10/14	1	2	FACETS	0.951	0.821	1	0.951	0.821	1	CLONAL	1	TRUE	1	0.225869826422171	2		475	568	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680789	88680789	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	66	659	0	ENST00000360948.2:c.468G>T	p.Gln156His	p.Q156H	ENST00000360948	NM_001012338.2	156	caG/caT	6/19	1	2	FACETS	0.543	0.47	0.623	0.543	0.47	0.623	SUBCLONAL	1	TRUE	1	0.225869826422171	2		659	1076	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226761	2226761	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs772356994	NA	P-0053282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	69	621	2	ENST00000398665.3:c.4241G>T	p.Arg1414Leu	p.R1414L	ENST00000398665	NM_032482.2	1414	cGg/cTg	27/28	1	2	FACETS	0.61	0.53	0.698	0.61	0.53	0.698	SUBCLONAL	1	TRUE	1	0.225869826422171	2		623	1001	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523289	9523289	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	73	619	0	ENST00000353224.5:c.1948C>A	p.Gln650Lys	p.Q650K	ENST00000353224	NM_177990.2	650	Cag/Aag	9/10	1	2	FACETS	0.68	0.593	0.774	0.68	0.593	0.774	SUBCLONAL	1	TRUE	1	0.225869826422171	2		619	951	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867410	35867410	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	145	406	1	ENST00000303115.3:c.224G>T	p.Gly75Val	p.G75V	ENST00000303115	NM_002185.3	75	gGg/gTg	3/8	0.225869826422171	5	FACETS	1	0.925	1	1	0.925	1	CLONAL	4	TRUE	1	0.225869826422171	5		407	428	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878400	151878400	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	114	626	0	ENST00000262189.6:c.6545G>C	p.Arg2182Thr	p.R2182T	ENST00000262189	NM_170606.2	2182	aGa/aCa	36/59	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.225869826422171	2		626	831	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006890	47006890	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	108	754	0	ENST00000377604.3:c.10G>T	p.Glu4Ter	p.E4*	ENST00000377604	NM_001204468.1	4	Gaa/Taa	2/24	0.140209138199969	0	FACETS	0.747	0.669	0.83			1	SUBCLONAL	1	TRUE	0	0.225869826422171	0		754	991	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519337	176519338	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	A	novel	NA	P-0053282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	74	737	0	ENST00000292408.4:c.743_744delinsA	p.Arg248HisfsTer37	p.R248Hfs*37	ENST00000292408	NM_213647.1	248	cGG/cA	7/18	0.198186973654768	1	FACETS	0.499	0.435	0.569	0.499	0.435	0.569	SUBCLONAL	1	TRUE	0	0.225869826422171	1		737	1164	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0053285-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	137	650	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.872	0.795	0.952	0.872	0.795	0.952	CLONAL	1	TRUE	1	0.491049199062389	2		650	640	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053285-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	255	618	0	ENST00000304494.5:c.322G>C	p.Asp108His	p.D108H	ENST00000304494	NM_000077.4	108	Gat/Cat	2/3	0.491049199062389	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.491049199062389	1		618	782	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220410	1220410	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053285-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	311	857	0	ENST00000326873.7:c.503A>G	p.His168Arg	p.H168R	ENST00000326873	NM_000455.4	168	cAt/cGt	4/10	0.451212603764427	1	FACETS	0.878	0.829	0.929	0.878	0.829	0.929	CLONAL	1	TRUE	0	0.491049199062389	1		857	1088	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610417	10610417	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053285-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	340	918	0	ENST00000171111.5:c.293T>A	p.Val98Glu	p.V98E	ENST00000171111	NM_203500.1	98	gTg/gAg	2/6	0.451212603764427	1	FACETS	0.965	0.914	1	0.965	0.914	1	CLONAL	1	TRUE	0	0.491049199062389	1		918	1083	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121194	11121194	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053285-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	193	639	0	ENST00000358026.2:c.2261T>G	p.Leu754Arg	p.L754R	ENST00000358026	NM_001128849.1	754	cTc/cGc	15/36	0.451212603764427	1	FACETS	0.761	0.706	0.819	0.761	0.706	0.819	SUBCLONAL	1	TRUE	0	0.491049199062389	1		639	779	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753968	57753968	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053292-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	40	584	0	ENST00000274289.3:c.656T>G	p.Leu219Arg	p.L219R	ENST00000274289	NM_006622.3	219	cTa/cGa	5/14	0.184428413648273	3	FACETS	0.649	0.539	0.773	0.325	0.269	0.387	SUBCLONAL	1	FALSE	1	0.235328302571072	3		584	585	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548947	29548978	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTATATGTACTTTTATTTTTTAAATTCAACT	GGTATATGTACTTTTATTTTTTAAATTCAACT	CCTAATCTCCC	novel	NA	P-0053292-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	29	333	1	ENST00000356175.3:c.1721_1721+31delinsCCTAATCTCCC		p.X574_splice	ENST00000356175	NM_000267.3	574		15/57	0.214674565151874	1	FACETS	0.918	0.74	1	0.918	0.74	1	CLONAL	1	FALSE	0	0.235328302571072	1		334	237	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0053345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	48	650	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.14	2		650	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0053345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	34	848	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	0.655	0.534	0.793	0.655	0.534	0.793	SUBCLONAL	1	TRUE	1	0.14	2		848	741	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419882	41419883	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0053345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	38	774	1	ENST00000373198.4:c.438_439delinsTT	p.Trp146_Val147delinsCysLeu	p.W146_V147delinsCL	ENST00000373198	NM_133170.3	146	tgGGtg/tgTTtg	3/32	1	2	FACETS	0.858	0.707	1	0.858	0.707	1	CLONAL	1	TRUE	1	0.14	2		775	633	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524960	8524960	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	29	466	0	ENST00000356435.5:c.644C>A	p.Thr215Asn	p.T215N	ENST00000356435		215	aCt/aAt	7/35	0.181585067149298	3	FACETS	0.925	0.742	1	0.463	0.371	0.568	CLONAL	1	TRUE	1	0.14	3		466	479	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	35	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.294376830169541	2		276	230	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0053362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	79	798	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.294376830169541	1	FACETS	0.806	0.71	0.909	0.806	0.71	0.909	CLONAL	1	TRUE	0	0.294376830169541	1		798	568	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485917	8485917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757868633	NA	P-0053362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	21	441	0	ENST00000356435.5:c.2900C>T	p.Pro967Leu	p.P967L	ENST00000356435		967	cCg/cTg	17/35	1	2	FACETS	0.377	0.29	0.48	0.377	0.29	0.48	SUBCLONAL	1	TRUE	1	0.294376830169541	2		441	378	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234535	41234535	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519558	NA	P-0053362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	58	555	0	ENST00000357654.3:c.4243G>C	p.Glu1415Gln	p.E1415Q	ENST00000357654	NM_007294.3	1415	Gaa/Caa	12/23	1	2	FACETS	0.761	0.654	0.877	0.761	0.654	0.877	SUBCLONAL	1	TRUE	1	0.294376830169541	2		555	518	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56401549	56401551	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	novel	NA	P-0053362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	21	383	1	ENST00000348428.3:c.1414_1416del	p.Asp472del	p.D472del	ENST00000348428	NM_006785.3	471	GAT/-	12/17	1	2	FACETS	0.353	0.271	0.449	0.353	0.271	0.449	SUBCLONAL	1	TRUE	1	0.294376830169541	2		384	404	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56411670	56411670	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	65	434	0	ENST00000348428.3:c.1854A>G	p.Ile618Met	p.I618M	ENST00000348428	NM_006785.3	618	atA/atG	15/17	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.294376830169541	2		434	441	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38991087	38991087	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	67	445	0	ENST00000357387.3:c.547A>G	p.Met183Val	p.M183V	ENST00000357387	NM_152756.3	183	Atg/Gtg	7/38	1	2	FACETS	0.87	0.757	0.992	0.87	0.757	0.992	CLONAL	1	TRUE	1	0.294376830169541	2		445	523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0053369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	113	929	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.27603696445689	2	FACETS	1	0.979	1	0.655	0.594	0.72	CLONAL	1	TRUE	0	0.386566817367118	2		929	446	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0053369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	45	419	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.23457639644345	4	FACETS	1	0.857	1	1	0.857	1	CLONAL	2	TRUE	2	0.386566817367118	4		419	161	SUCCESS
APC	324	MSKCC	GRCh37	5	112173848	112173848	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	43	307	1	ENST00000257430.4:c.2557G>T	p.Glu853Ter	p.E853*	ENST00000257430	NM_000038.5	853	Gag/Tag	16/16	0.3094453201307	2	FACETS	0.856	0.733	0.985	0.856	0.733	0.985	CLONAL	2	TRUE	0	0.386566817367118	2		308	130	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239351	105239351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1168658858	NA	P-0053369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	100	860	0	ENST00000349310.3:c.1036C>T	p.Arg346Cys	p.R346C	ENST00000349310	NM_001014432.1	346	Cgc/Tgc	12/15	0.197060094321898	5	FACETS	0.811	0.727	0.899	0.541	0.485	0.6	INDETERMINATE	2	TRUE	2	0.386566817367118	5		860	504	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38616990	38616990	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	96	417	1	ENST00000299084.4:c.403G>T	p.Glu135Ter	p.E135*	ENST00000299084	NM_152594.2	135	Gaa/Taa	4/7	0.36906781216491	4	FACETS	0.838	0.757	0.921	1	0.975	1	CLONAL	3	TRUE	2	0.386566817367118	4		418	274	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779037	3779037	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	112	825	1	ENST00000262367.5:c.6011G>T	p.Arg2004Leu	p.R2004L	ENST00000262367	NM_004380.2	2004	cGa/cTa	31/31	0.134526280832751	4	FACETS	0.901	0.815	0.99	0.901	0.815	0.99	INDETERMINATE	2	TRUE	2	0.386566817367118	4		826	446	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965200	81965200	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	84	655	0	ENST00000359376.3:c.2680G>T	p.Glu894Ter	p.E894*	ENST00000359376	NM_002661.3	894	Gag/Tag	25/33	0.134526280832751	4	FACETS	1	0.978	1	0.744	0.661	0.832	INDETERMINATE	1	TRUE	2	0.386566817367118	4		655	405	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41251818	41251818	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1567806035	NA	P-0053369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	98	616	0	ENST00000357654.3:c.521A>C	p.Gln174Pro	p.Q174P	ENST00000357654	NM_007294.3	174	cAa/cCa	7/23	0.366753112131859	3	FACETS	0.807	0.726	0.891	0.807	0.726	0.891	CLONAL	2	TRUE	1	0.386566817367118	3		616	375	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530023	212530071	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCCCTTGGCCAGCAAGAATGCTTACCCTTGGGTGCAGTTTGGATGGCAT	GCCCTTGGCCAGCAAGAATGCTTACCCTTGGGTGCAGTTTGGATGGCAT	-	novel	NA	P-0053369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	36	207	0	ENST00000342788.4:c.1848_1871+25del		p.X616_splice	ENST00000342788	NM_005235.2	616		15/28	0.23457639644345	4	FACETS	0.936	0.783	1	0.936	0.783	1	CLONAL	2	TRUE	2	0.386566817367118	4		207	138	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119595278	119595278	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	33	282	0	ENST00000316626.5:c.891G>T	p.Lys297Asn	p.K297N	ENST00000316626		297	aaG/aaT	8/12	0.23457639644345	4	FACETS	0.97	0.807	1	0.97	0.807	1	CLONAL	2	TRUE	2	0.386566817367118	4		282	122	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555015	106555015	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	89	507	0	ENST00000369096.4:c.2132C>T	p.Ala711Val	p.A711V	ENST00000369096	NM_001198.3	711	gCt/gTt	7/7	0.3094453201307	2	FACETS	1	0.98	1	0.719	0.644	0.798	CLONAL	1	TRUE	0	0.386566817367118	2		507	320	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053385-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	95	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.888	0.798	0.981	0.888	0.798	0.981	CLONAL	1	TRUE	1	0.640785452309525	2		276	334	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0053385-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	233	563	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.640785452309525	2		563	656	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480335	56480335	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053385-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	172	422	0	ENST00000267101.3:c.442T>C	p.Tyr148His	p.Y148H	ENST00000267101	NM_001982.3	148	Tat/Cat	4/28	1	2	FACETS	0.91	0.842	0.98	0.91	0.842	0.98	CLONAL	1	TRUE	1	0.640785452309525	2		422	590	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94129030	94129030	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053385-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	168	387	0	ENST00000369303.4:c.30G>C	p.Trp10Cys	p.W10C	ENST00000369303	NM_004440.3	10	tgG/tgC	1/17	1	2	FACETS	0.898	0.83	0.968	0.898	0.83	0.968	CLONAL	1	TRUE	1	0.640785452309525	2		387	584	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188361	32188361	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053385-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	202	741	0	ENST00000375023.3:c.980G>A	p.Arg327Lys	p.R327K	ENST00000375023	NM_004557.3	327	aGa/aAa	6/30	1	2	FACETS	0.805	0.748	0.864	0.805	0.748	0.864	CLONAL	1	TRUE	1	0.640785452309525	2		741	783	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106417	27106418	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0053385-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	204	560	0	ENST00000324856.7:c.6028_6029del	p.Ile2010ProfsTer22	p.I2010Pfs*22	ENST00000324856	NM_006015.4	2010	ATc/c	20/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.640785452309525	2		560	623	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781900	3781900	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053385-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	220	539	0	ENST00000262367.5:c.4767del	p.Asn1589LysfsTer46	p.N1589Kfs*46	ENST00000262367	NM_004380.2	1589	aaC/aa	29/31	1	2	FACETS	0.951	0.888	1	0.951	0.888	1	CLONAL	1	TRUE	1	0.640785452309525	2		539	722	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881636	37881636	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193920750	NA	P-0053385-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	203	589	0	ENST00000269571.5:c.2706G>C	p.Gln902His	p.Q902H	ENST00000269571		902	caG/caC	22/27	0.640785452309525	3	FACETS	0.98	0.91	1	0.49	0.455	0.526	CLONAL	1	TRUE	1	0.640785452309525	3		589	854	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40856620	40856620	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053385-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	310	402	0	ENST00000428826.2:c.2017G>T	p.Asp673Tyr	p.D673Y	ENST00000428826		673	Gat/Tat	18/21	0.640785452309525	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.640785452309525	3		402	616	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752920	57752920	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0053385-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	104	344	0	ENST00000274289.3:c.1009-1G>C		p.X337_splice	ENST00000274289	NM_006622.3	337			1	2	FACETS	0.606	0.544	0.67	0.606	0.544	0.67	SUBCLONAL	1	TRUE	1	0.640785452309525	2		344	536	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188346	32188346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053385-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	218	784	1	ENST00000375023.3:c.995G>A	p.Cys332Tyr	p.C332Y	ENST00000375023	NM_004557.3	332	tGc/tAc	6/30	1	2	FACETS	0.787	0.733	0.842	0.787	0.733	0.842	SUBCLONAL	1	TRUE	1	0.640785452309525	2		785	865	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15818036	15818036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555899273	NA	P-0053385-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	119	250	0	ENST00000307771.7:c.163G>A	p.Glu55Lys	p.E55K	ENST00000307771	NM_005089.3	55	Gaa/Aaa	3/11	NA	2	FACETS	0.919	0.837	1			1	INDETERMINATE	1	TRUE	NA	0.640785452309525	2		250	404	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941654	48941654	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs776534331	NA	P-0053391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2	67	115	0	ENST00000267163.4:c.964G>T	p.Glu322Ter	p.E322*	ENST00000267163	NM_000321.2	322	Gaa/Taa	10/27	0.952561884883503	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.952561884883503	1		115	69	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934576	NA	P-0053391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	658	715	0	ENST00000269305.4:c.818G>C	p.Arg273Pro	p.R273P	ENST00000269305	NM_001126112.2	273	cGt/cCt	8/11	0.952561884883503	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.952561884883503	1		715	709	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204515950	204515950	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	310	357	0	ENST00000367182.3:c.848A>G	p.Asp283Gly	p.D283G	ENST00000367182	NM_001278516.1	283	gAc/gGc	10/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.952561884883503	2		357	646	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622117	43622117	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	261	628	0	ENST00000355710.3:c.3134A>T	p.Asn1045Ile	p.N1045I	ENST00000355710	NM_020975.4	1045	aAt/aTt	19/20	0.198197532872142	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.952561884883503	0		628	920	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417842	32417842	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0053391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	477	524	0	ENST00000332351.3:c.1210A>T	p.Lys404Ter	p.K404*	ENST00000332351	NM_024426.4	404	Aag/Tag	7/10	0.116136602307951	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.952561884883503	0		524	1004	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658343	18658343	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	382	431	0	ENST00000266497.5:c.3148A>G	p.Ile1050Val	p.I1050V	ENST00000266497		1050	Att/Gtt	22/31	0.913287134005775	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.952561884883503	1		431	394	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221572	2221572	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0053391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	769	894	2	ENST00000326181.6:c.442-1G>A		p.X148_splice	ENST00000326181	NM_032271.2	148			1	2	FACETS	0.991	0.96	1	0.991	0.96	1	CLONAL	1	TRUE	1	0.952561884883503	2		896	1629	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020551	14020551	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	405	411	0	ENST00000311895.7:c.526del	p.Cys176ValfsTer6	p.C176Vfs*6	ENST00000311895	NM_005236.2	174	ggT/gg	3/11	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.952561884883503	2		411	749	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864616	37864629	+	frameshift_variant	Frame_Shift_Del	DEL	CAAGTGAGGCAGGT	CAAGTGAGGCAGGT	-	novel	NA	P-0053391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	623	758	0	ENST00000269571.5:c.269_282del	p.Gln90ProfsTer15	p.Q90Pfs*15	ENST00000269571		90	CAAGTGAGGCAGGTc/c	3/27	1	2	FACETS	0.93	0.897	0.964	0.93	0.897	0.964	CLONAL	1	TRUE	1	0.952561884883503	2		758	1406	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896569	78896569	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	856	947	0	ENST00000306801.3:c.2566C>G	p.Leu856Val	p.L856V	ENST00000306801	NM_020761.2	856	Ctc/Gtc	22/34	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.952561884883503	2		947	1716	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224586	36224586	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	1260	965	0	ENST00000222270.7:c.7048G>C	p.Gly2350Arg	p.G2350R	ENST00000222270	NM_014727.1	2350	Ggg/Cgg	29/37	0.648020268985511	3	FACETS	0.948	0.928	0.968	0.948	0.928	0.968	CLONAL	2	TRUE	1	0.952561884883503	3		965	2059	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141582935	141582935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	619	663	1	ENST00000220592.5:c.312G>T	p.Met104Ile	p.M104I	ENST00000220592	NM_012154.3	104	atG/atT	3/19	1	2	FACETS	0.987	0.952	1	0.987	0.952	1	CLONAL	1	TRUE	1	0.952561884883503	2		664	1317	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950021	44950021	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	309	491	0	ENST00000377967.4:c.3790G>C	p.Val1264Leu	p.V1264L	ENST00000377967	NM_021140.2	1264	Gtg/Ctg	26/29	0.150039313143712	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.952561884883503	0		491	701	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855994	76855995	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0053391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	165	502	0	ENST00000373344.5:c.5605_5606delinsTT	p.Gly1869Phe	p.G1869F	ENST00000373344	NM_000489.3	1869	GGt/TTt	23/35	0.150039313143712	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.952561884883503	0		502	505	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359419	118359421	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	rs1555041617	NA	P-0053401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	482	433	0	ENST00000534358.1:c.4426_4428del	p.Cys1476del	p.C1476del	ENST00000534358	NM_005933.3	1475	TGT/-	11/36	0.80094376277961	2	FACETS	0.963	0.938	0.988	0.963	0.938	0.988	CLONAL	2	TRUE	0	0.804652520632127	2		433	622	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2114323	2114324	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0053401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	527	994	0	ENST00000219476.3:c.1494_1495delinsAT	p.Asp499Tyr	p.D499Y	ENST00000219476	NM_000548.3	498	gaGGat/gaATat	15/42	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.804652520632127	2		994	1187	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641513	23641513	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	461	719	0	ENST00000261584.4:c.1962T>G	p.Ile654Met	p.I654M	ENST00000261584	NM_024675.3	654	atT/atG	5/13	0.358473309414336	3	FACETS	0.875	0.841	0.91	0.875	0.841	0.91	INDETERMINATE	2	TRUE	1	0.804652520632127	3		719	918	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480499	57480499	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1329	96	370	0	ENST00000371085.3:c.494G>T	p.Arg165Leu	p.R165L	ENST00000371085	NM_000516.4	165	cGc/cTc	6/13	0.804652520632127	6	FACETS	0.437	0.388	0.49			1	SUBCLONAL	1	TRUE	NA	0.804652520632127	6		370	1425	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478057	138478057	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	102	462	0	ENST00000289153.2:c.129G>C	p.Gln43His	p.Q43H	ENST00000289153	NM_006219.2	43	caG/caC	1/22	1	2	FACETS	0.448	0.401	0.497	0.448	0.401	0.497	SUBCLONAL	1	TRUE	1	0.804652520632127	2		462	566	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009384	69009384	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	128	516	0	ENST00000288368.4:c.2501A>G	p.Asn834Ser	p.N834S	ENST00000288368	NM_024870.2	834	aAt/aGt	22/40	0.388784162931343	5	FACETS	0.618	0.558	0.68	0.206	0.186	0.227	INDETERMINATE	1	TRUE	2	0.804652520632127	5		516	1137	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778134	135778134	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	122	599	0	ENST00000298552.3:c.2249G>T	p.Trp750Leu	p.W750L	ENST00000298552	NM_001162426.1	750	tGg/tTg	18/23	0.553172018812198	1	FACETS	0.347	0.314	0.38	0.347	0.314	0.38	SUBCLONAL	1	TRUE	0	0.804652520632127	1		599	523	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413124	63413124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	203	862	1	ENST00000330258.3:c.43G>A	p.Ala15Thr	p.A15T	ENST00000330258	NM_152424.3	15	Gca/Aca	2/2	0.804652520632127	1	FACETS	0.48	0.447	0.514	0.48	0.447	0.514	SUBCLONAL	1	TRUE	0	0.804652520632127	1		863	628	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053447-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	211	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.873234478176738	2		276	459	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0053447-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	251	533	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.873234478176738	2		533	565	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0053447-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	874	478	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	NA	2	FACETS	1	0.997	1			1	INDETERMINATE	2	TRUE	NA	0.873234478176738	2		478	953	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952138	178952138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053447-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	110	316	0	ENST00000263967.3:c.3193C>T	p.His1065Tyr	p.H1065Y	ENST00000263967	NM_006218.2	1065	Cat/Tat	21/21	1	2	FACETS	0.577	0.521	0.634	0.577	0.521	0.634	SUBCLONAL	1	TRUE	1	0.873234478176738	2		316	437	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161751	47161751	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053447-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	233	417	1	ENST00000409792.3:c.4375C>T	p.Arg1459Ter	p.R1459*	ENST00000409792	NM_014159.6	1459	Cga/Tga	3/21	1	2	FACETS	0.864	0.811	0.917	0.864	0.811	0.917	CLONAL	1	TRUE	1	0.873234478176738	2		418	618	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609462	81609462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200523471	NA	P-0053447-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	126	590	1	ENST00000298171.2:c.1060G>A	p.Val354Ile	p.V354I	ENST00000298171	NM_000369.2	354	Gtc/Atc	10/10	1	2	FACETS	0.395	0.358	0.434	0.395	0.358	0.434	SUBCLONAL	1	TRUE	1	0.873234478176738	2		591	731	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0053487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	224	494	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.716006592191861	2		494	608	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0053487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	129	352	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.716006592191861	2	FACETS	0.875	0.8	0.951	0.437	0.4	0.476	CLONAL	1	TRUE	0	0.716006592191861	2		352	412	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720732	89720733	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs587780006	NA	P-0053487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	39	130	0	ENST00000371953.3:c.884dup	p.Cys296MetfsTer2	p.C296Mfs*2	ENST00000371953	NM_000314.4	295	cta/cTta	8/9	0.716006592191861	2	FACETS	1	0.965	1	0.726	0.631	0.821	CLONAL	1	TRUE	0	0.716006592191861	2		130	75	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056319	27056319	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	174	396	1	ENST00000324856.7:c.1315C>T	p.Gln439Ter	p.Q439*	ENST00000324856	NM_006015.4	439	Cag/Tag	2/20	1	2	FACETS	0.978	0.908	1	0.978	0.908	1	CLONAL	1	TRUE	1	0.716006592191861	2		397	497	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94963961	94963961	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	140	249	0	ENST00000536441.1:c.64A>G	p.Lys22Glu	p.K22E	ENST00000536441	NM_144665.3	22	Aaa/Gaa	1/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.716006592191861	2		249	341	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244007	41244007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56336919	NA	P-0053487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	187	496	0	ENST00000357654.3:c.3541G>A	p.Val1181Ile	p.V1181I	ENST00000357654	NM_007294.3	1181	Gtc/Atc	10/23	1	2	FACETS	0.966	0.899	1	0.966	0.899	1	CLONAL	1	TRUE	1	0.716006592191861	2		496	541	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732932	74732932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	128	232	0	ENST00000359995.5:c.311G>A	p.Gly104Glu	p.G104E	ENST00000359995	NM_001195427.1	104	gGa/gAa	1/3	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.716006592191861	2		232	328	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252871	36252871	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	128	306	0	ENST00000300305.3:c.491T>C	p.Val164Ala	p.V164A	ENST00000300305		164	gTc/gCc	4/8	1	2	FACETS	0.996	0.913	1	0.996	0.913	1	CLONAL	1	TRUE	1	0.716006592191861	2		306	359	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589636	67589659	+	inframe_deletion	In_Frame_Del	DEL	TATGAAGAATATACCCGCACATCC	TATGAAGAATATACCCGCACATCC	-	novel	NA	P-0053487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	12	222	0	ENST00000274335.5:c.1399_1422del	p.Tyr467_Ser474del	p.Y467_S474del	ENST00000274335		467	TATGAAGAATATACCCGCACATCC/-	10/15	1	2	FACETS	0.302	0.214	0.408	0.302	0.214	0.408	SUBCLONAL	1	TRUE	1	0.716006592191861	2		222	111	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	56	276	0				ENST00000310581	NM_198253.2	-/1132			0.0841461652227515	6	FACETS	1	0.939	1	0.767	0.665	0.875	INDETERMINATE	2	TRUE	3	0.378601606653802	6		276	226	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	254	420	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.378601606653802	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	1	0.378601606653802	4		420	539	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	187	498	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.986	1	1	0.994	1	CLONAL	2	TRUE	1	0.378601606653802	2		498	411	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509639	29509639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	110	301	0	ENST00000356175.3:c.844C>T	p.Gln282Ter	p.Q282*	ENST00000356175	NM_000267.3	282	Cag/Tag	8/57	0.378601606653802	3	FACETS	1	0.979	1	0.67	0.604	0.738	CLONAL	1	TRUE	1	0.378601606653802	3		301	516	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750818	57750818	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	157	279	0	ENST00000274289.3:c.1786C>T	p.Arg596Ter	p.R596*	ENST00000274289	NM_006622.3	596	Cga/Tga	13/14	0.378601606653802	5	FACETS	0.842	0.776	0.909	0.842	0.776	0.909	CLONAL	3	TRUE	2	0.378601606653802	5		279	515	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335121	65335121	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	130	360	0	ENST00000342505.4:c.520C>T	p.Arg174Ter	p.R174*	ENST00000342505	NM_002227.2	174	Cga/Tga	6/25	0.378601606653802	2	FACETS	0.951	0.873	1	0.951	0.873	1	CLONAL	2	TRUE	0	0.378601606653802	2		360	361	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735525	204735525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144988077	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	57	313	0	ENST00000302823.3:c.326G>A	p.Gly109Glu	p.G109E	ENST00000302823	NM_005214.4	109	gGa/gAa	2/4	0.378601606653802	3	FACETS	0.955	0.823	1	0.477	0.411	0.549	CLONAL	1	TRUE	1	0.378601606653802	3		313	375	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367321	50367321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	163	307	2	ENST00000331340.3:c.128G>A	p.Gly43Glu	p.G43E	ENST00000331340	NM_006060.4	43	gGa/gAa	3/8	0.378601606653802	5	FACETS	0.846	0.781	0.912	0.846	0.781	0.912	CLONAL	3	TRUE	2	0.378601606653802	5		309	532	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713147	30713147	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886058303	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	32	217	0	ENST00000295754.5:c.472C>T	p.Pro158Ser	p.P158S	ENST00000295754	NM_003242.5	158	Cct/Tct	4/7	0.378601606653802	4	FACETS	0.647	0.526	0.784	0.216	0.175	0.262	SUBCLONAL	1	TRUE	1	0.378601606653802	4		217	360	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482301	87482301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	128	389	0	ENST00000277120.3:c.1588C>T	p.Pro530Ser	p.P530S	ENST00000277120		530	Ccc/Tcc	14/19	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.378601606653802	2		389	473	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056291	180056291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199942873	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	173	685	1	ENST00000261937.6:c.953G>A	p.Arg318Gln	p.R318Q	ENST00000261937	NM_182925.4	318	cGa/cAa	7/30	0.0841461652227515	6	FACETS	0.897	0.83	0.966	0.897	0.83	0.966	INDETERMINATE	3	TRUE	3	0.378601606653802	6		686	597	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207816	102207816	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	75	162	0	ENST00000263464.3:c.1798C>T	p.Arg600Cys	p.R600C	ENST00000263464	NM_001165.4	600	Cgt/Tgt	9/9	0.378601606653802	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.378601606653802	2		162	177	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715647	18715647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	56	170	0	ENST00000266497.5:c.3478G>A	p.Glu1160Lys	p.E1160K	ENST00000266497		1160	Gaa/Aaa	25/31	0.378601606653802	5	FACETS	0.794	0.686	0.911	0.529	0.457	0.608	CLONAL	2	TRUE	2	0.378601606653802	5		170	292	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519776	176519776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	180	692	1	ENST00000292408.4:c.1048G>A	p.Val350Met	p.V350M	ENST00000292408	NM_213647.1	350	Gtg/Atg	8/18	0.0841461652227515	6	FACETS	1	0.954	1	1	0.954	1	INDETERMINATE	3	TRUE	3	0.378601606653802	6		693	538	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572484	95572484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	145	240	0	ENST00000393063.1:c.2881C>T	p.Pro961Ser	p.P961S	ENST00000393063	NM_030621.3	961	Cct/Tct	19/28	0.378601606653802	4	FACETS	0.97	0.896	1	0.97	0.896	1	CLONAL	3	TRUE	1	0.378601606653802	4		240	363	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55130049	55130049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	116	374	0	ENST00000257290.5:c.583G>A	p.Gly195Arg	p.G195R	ENST00000257290	NM_006206.4	195	Gga/Aga	4/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.378601606653802	2		374	454	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859899	151859899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148585727	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	154	275	0	ENST00000262189.6:c.10763C>T	p.Ser3588Leu	p.S3588L	ENST00000262189	NM_170606.2	3588	tCg/tTg	43/59	0.378601606653802	5	FACETS	0.977	0.903	1	0.977	0.903	1	CLONAL	3	TRUE	2	0.378601606653802	5		275	435	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932925	49932925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	276	582	1	ENST00000296474.3:c.3019C>T	p.Pro1007Ser	p.P1007S	ENST00000296474	NM_002447.2	1007	Ccc/Tcc	13/20	0.378601606653802	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	1	0.378601606653802	4		583	578	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222928	36222928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	239	685	0	ENST00000222270.7:c.5557C>T	p.Pro1853Ser	p.P1853S	ENST00000222270	NM_014727.1	1853	Cct/Tct	27/37	0.0841461652227515	6	FACETS	1	0.976	1	1	0.976	1	INDETERMINATE	3	TRUE	3	0.378601606653802	6		685	686	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169601	27169601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540914328	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	167	487	1	ENST00000380036.4:c.602C>T	p.Ser201Leu	p.S201L	ENST00000380036	NM_000459.3	201	tCg/tTg	4/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.378601606653802	2		488	736	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246490517	246490517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	176	282	1	ENST00000388985.4:c.517G>A	p.Glu173Lys	p.E173K	ENST00000388985		173	Gaa/Aaa	5/12	0.139880093198702	6	FACETS	0.914	0.846	0.983	0.914	0.846	0.983	INDETERMINATE	3	TRUE	3	0.378601606653802	6		283	596	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171914	32171914	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	82	352	0	ENST00000375023.3:c.3118G>A	p.Gly1040Ser	p.G1040S	ENST00000375023	NM_004557.3	1040	Ggc/Agc	19/30	0.139880093198702	6	FACETS	1	0.961	1	0.788	0.701	0.879	INDETERMINATE	2	TRUE	3	0.378601606653802	6		352	322	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934843	9934843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	104	369	0	ENST00000330684.3:c.1447G>A	p.Gly483Arg	p.G483R	ENST00000330684	NM_001134407.1	483	Ggg/Agg	6/13	0.0723302168133348	3	FACETS	1	0.976	1	0.644	0.579	0.713	INDETERMINATE	1	TRUE	1	0.378601606653802	3		369	507	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255394	16255394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	54	351	0	ENST00000375759.3:c.2659G>A	p.Glu887Lys	p.E887K	ENST00000375759	NM_015001.2	887	Gag/Aag	11/15	0.378601606653802	3	FACETS	0.714	0.611	0.827	0.357	0.305	0.414	SUBCLONAL	1	TRUE	1	0.378601606653802	3		351	475	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112764467	112764467	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	66	285	0	ENST00000369452.4:c.1076C>T	p.Ser359Phe	p.S359F	ENST00000369452	NM_007373.3	359	tCc/tTc	5/9	0.378601606653802	3	FACETS	0.911	0.793	1	0.304	0.264	0.346	CLONAL	1	TRUE	0	0.378601606653802	3		285	455	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196039	108196039	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	112	178	0	ENST00000278616.4:c.6575C>T	p.Ser2192Leu	p.S2192L	ENST00000278616	NM_000051.3	2192	tCa/tTa	46/63	0.378601606653802	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	0	0.378601606653802	2		178	287	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148875	119148876	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AC	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	67	187	0	ENST00000264033.4:c.1096-1_1096delinsAC		p.X366_splice	ENST00000264033	NM_005188.3	366		8/16	0.378601606653802	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	0	0.378601606653802	2		187	164	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426528	49426528	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	140	625	0	ENST00000301067.7:c.11960C>T	p.Pro3987Leu	p.P3987L	ENST00000301067	NM_003482.3	3987	cCt/cTt	39/54	0.378601606653802	5	FACETS	1	0.985	1	0.473	0.43	0.517	CLONAL	1	TRUE	2	0.378601606653802	5		625	818	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115389	115115389	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	405	305	0	ENST00000257566.3:c.937A>T	p.Lys313Ter	p.K313*	ENST00000257566	NM_016569.3	313	Aaa/Taa	5/8	0.378601606653802	5	FACETS	0.911	0.87	0.951	1	0.993	1	CLONAL	4	TRUE	2	0.378601606653802	5		305	921	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953532	32953532	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	54	356	0	ENST00000380152.3:c.8833C>T	p.Gln2945Ter	p.Q2945*	ENST00000380152		2945	Cag/Tag	22/27	0.276550579660599	2	FACETS	0.598	0.511	0.693	0.299	0.255	0.347	SUBCLONAL	1	TRUE	0	0.378601606653802	2		356	477	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590744	95590744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	175	230	0	ENST00000393063.1:c.1165C>T	p.Pro389Ser	p.P389S	ENST00000393063	NM_030621.3	389	Cca/Tca	9/28	0.378601606653802	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	1	0.378601606653802	4		230	391	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457689	67457689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	109	523	0	ENST00000327367.4:c.499C>T	p.Pro167Ser	p.P167S	ENST00000327367	NM_005902.3	167	Ccc/Tcc	3/9	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.378601606653802	2		523	469	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996029	73996029	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	109	648	0	ENST00000318443.5:c.763C>G	p.Pro255Ala	p.P255A	ENST00000318443	NM_001024736.1	255	Ccg/Gcg	5/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.378601606653802	2		648	495	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576133	88576133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	128	556	0	ENST00000360948.2:c.1540C>T	p.Pro514Ser	p.P514S	ENST00000360948	NM_001012338.2	514	Ccc/Tcc	13/19	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.378601606653802	2		556	469	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020598	14020598	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs756024042	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	54	247	0	ENST00000311895.7:c.569T>C	p.Leu190Pro	p.L190P	ENST00000311895	NM_005236.2	190	cTg/cCg	3/11	0.0723302168133348	3	FACETS	0.817	0.7	0.945	0.409	0.35	0.473	INDETERMINATE	1	TRUE	1	0.378601606653802	3		247	415	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8111131	8111131	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	113	500	1	ENST00000585124.1:c.76C>T	p.Gln26Ter	p.Q26*	ENST00000585124	NM_004217.3	26	Cag/Tag	3/9	0.374307244150638	2	FACETS	1	0.928	1	0.517	0.467	0.57	CLONAL	1	TRUE	0	0.378601606653802	2		501	577	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652965	29652965	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	149	308	0	ENST00000356175.3:c.4900A>T	p.Lys1634Ter	p.K1634*	ENST00000356175	NM_000267.3	1634	Aaa/Taa	36/57	0.378601606653802	3	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	1	0.378601606653802	3		308	462	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362285	40362285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	85	339	0	ENST00000293328.3:c.1810C>T	p.His604Tyr	p.H604Y	ENST00000293328	NM_012448.3	604	Cat/Tat	15/19	0.378601606653802	3	FACETS	1	0.965	1	0.612	0.544	0.685	CLONAL	1	TRUE	1	0.378601606653802	3		339	436	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105563	11105564	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	80	476	0	ENST00000358026.2:c.1481_1482del	p.Thr494ArgfsTer39	p.T494Rfs*39	ENST00000358026	NM_001128849.1	493	gtCAca/gtca	9/36	0.378601606653802	1	FACETS	0.81	0.716	0.909	0.81	0.716	0.909	CLONAL	1	TRUE	0	0.378601606653802	1		476	423	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211744	36211744	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	189	564	0	ENST00000222270.7:c.1495C>T	p.Pro499Ser	p.P499S	ENST00000222270	NM_014727.1	499	Ccc/Tcc	3/37	0.0841461652227515	6	FACETS	1	0.975	1	1	0.975	1	INDETERMINATE	3	TRUE	3	0.378601606653802	6		564	533	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216518	36216518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	186	688	1	ENST00000222270.7:c.3781G>A	p.Gly1261Arg	p.G1261R	ENST00000222270	NM_014727.1	1261	Gga/Aga	12/37	0.0841461652227515	6	FACETS	0.849	0.787	0.913	0.849	0.787	0.913	INDETERMINATE	3	TRUE	3	0.378601606653802	6		689	678	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793103	42793104	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	205	613	0	ENST00000575354.2:c.995_996delinsAA	p.Gly332Glu	p.G332E	ENST00000575354	NM_015125.3	332	gGG/gAA	7/20	0.0841461652227515	6	FACETS	0.874	0.813	0.936	0.874	0.813	0.936	INDETERMINATE	3	TRUE	3	0.378601606653802	6		613	726	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574038	46574038	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	84	482	0	ENST00000263734.3:c.53A>G	p.Lys18Arg	p.K18R	ENST00000263734	NM_001430.4	18	aAg/aGg	2/16	0.378601606653802	3	FACETS	0.975	0.864	1	0.488	0.432	0.548	CLONAL	1	TRUE	1	0.378601606653802	3		482	541	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793317	242793317	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	168	701	2	ENST00000334409.5:c.760C>T	p.Pro254Ser	p.P254S	ENST00000334409	NM_005018.2	254	Cct/Tct	5/5	0.378601606653802	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.378601606653802	3		703	495	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794365	242794365	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	138	626	0	ENST00000334409.5:c.577T>A	p.Ser193Thr	p.S193T	ENST00000334409	NM_005018.2	193	Tcc/Acc	3/5	0.378601606653802	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.378601606653802	3		626	396	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979296	40979296	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	124	402	0	ENST00000373198.4:c.1837C>T	p.Pro613Ser	p.P613S	ENST00000373198	NM_133170.3	613	Ccc/Tcc	11/32	0.0883482931502777	4	FACETS	0.787	0.714	0.862	0.787	0.714	0.862	INDETERMINATE	2	TRUE	2	0.378601606653802	4		402	574	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268741	46268741	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	119	437	0	ENST00000371998.3:c.3026C>T	p.Ser1009Phe	p.S1009F	ENST00000371998		1009	tCc/tTc	16/23	0.0883482931502777	4	FACETS	0.764	0.692	0.84	0.764	0.692	0.84	INDETERMINATE	2	TRUE	2	0.378601606653802	4		437	567	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267311	41267311	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	165	199	0	ENST00000349496.5:c.895G>A	p.Asp299Asn	p.D299N	ENST00000349496	NM_001904.3	299	Gac/Aac	6/15	0.378601606653802	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	3	TRUE	1	0.378601606653802	4		199	377	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186900	142186900	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	154	251	0	ENST00000350721.4:c.6563C>T	p.Pro2188Leu	p.P2188L	ENST00000350721	NM_001184.3	2188	cCc/cTc	39/47	0.378601606653802	4	FACETS	1	0.945	1	1	0.945	1	CLONAL	3	TRUE	1	0.378601606653802	4		251	366	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1962777	1962777	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	51	291	0	ENST00000382891.5:c.3271G>A	p.Glu1091Lys	p.E1091K	ENST00000382891	NM_133335.3	1091	Gag/Aag	18/22	1	2	FACETS	0.939	0.803	1	0.939	0.803	1	CLONAL	1	TRUE	1	0.378601606653802	2		291	287	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271228	153271228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	60	170	0	ENST00000281708.4:c.550G>A	p.Gly184Arg	p.G184R	ENST00000281708	NM_033632.3	184	Gga/Aga	3/12	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.378601606653802	2		170	269	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31483664	31483664	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	113	223	0	ENST00000344624.3:c.2068C>T	p.Pro690Ser	p.P690S	ENST00000344624		690	Cca/Tca	13/33	0.0841461652227515	6	FACETS	0.838	0.76	0.92	0.838	0.76	0.92	INDETERMINATE	3	TRUE	3	0.378601606653802	6		223	417	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939146	131939146	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	183	339	0	ENST00000265335.6:c.2362T>C	p.Cys788Arg	p.C788R	ENST00000265335		788	Tgc/Cgc	14/25	0.0841461652227515	6	FACETS	0.874	0.81	0.94	0.874	0.81	0.94	INDETERMINATE	3	TRUE	3	0.378601606653802	6		339	648	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058728	180058728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1268376969	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	142	636	1	ENST00000261937.6:c.109G>A	p.Glu37Lys	p.E37K	ENST00000261937	NM_182925.4	37	Gag/Aag	2/30	0.0841461652227515	6	FACETS	1	0.972	1	0.761	0.697	0.829	INDETERMINATE	2	TRUE	3	0.378601606653802	6		637	577	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109315790	109315790	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	145	354	0	ENST00000436639.2:c.995T>C	p.Val332Ala	p.V332A	ENST00000436639	NM_014454.2	332	gTt/gCt	6/10	0.139880093198702	6	FACETS	0.996	0.911	1	0.664	0.607	0.723	INDETERMINATE	2	TRUE	3	0.378601606653802	6		354	676	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117632270	117632270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	141	291	0	ENST00000368508.3:c.6146C>T	p.Pro2049Leu	p.P2049L	ENST00000368508	NM_002944.2	2049	cCt/cTt	39/43	0.139880093198702	6	FACETS	0.985	0.905	1	0.985	0.905	1	INDETERMINATE	3	TRUE	3	0.378601606653802	6		291	443	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641159	117641159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	216	469	0	ENST00000368508.3:c.5812C>T	p.Pro1938Ser	p.P1938S	ENST00000368508	NM_002944.2	1938	Cct/Tct	36/43	0.139880093198702	6	FACETS	0.877	0.818	0.938	0.877	0.818	0.938	INDETERMINATE	3	TRUE	3	0.378601606653802	6		469	762	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884803	151884803	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	103	249	0	ENST00000262189.6:c.4790C>G	p.Ala1597Gly	p.A1597G	ENST00000262189	NM_170606.2	1597	gCc/gGc	32/59	0.378601606653802	5	FACETS	1	0.929	1	0.692	0.624	0.763	CLONAL	2	TRUE	2	0.378601606653802	5		249	411	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29197682	29197682	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	222	513	0	ENST00000240100.2:c.512T>C	p.Val171Ala	p.V171A	ENST00000240100	NM_001394.6	171	gTt/gCt	2/4	0.0841461652227515	6	FACETS	1	0.948	1	1	0.948	1	INDETERMINATE	3	TRUE	3	0.378601606653802	6		513	677	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212737	27212737	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	134	485	0	ENST00000380036.4:c.2719C>T	p.His907Tyr	p.H907Y	ENST00000380036	NM_000459.3	907	Cat/Tat	17/23	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.378601606653802	2		485	654	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249422	110249422	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	205	661	1	ENST00000374672.4:c.1151G>T	p.Gly384Val	p.G384V	ENST00000374672	NM_004235.4	384	gGa/gTa	4/5	1	2	FACETS	0.8	0.745	0.856	1	0.992	1	SUBCLONAL	2	TRUE	1	0.378601606653802	2		662	677	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426078	47426078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	204	297	0	ENST00000377045.4:c.598C>T	p.Pro200Ser	p.P200S	ENST00000377045	NM_001654.4	200	Cct/Tct	7/16	0.186908075351796	3	FACETS	1	0.986	1			1	INDETERMINATE	3	TRUE	NA	0.378601606653802	3		297	372	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342611	70342611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	188	221	0	ENST00000374080.3:c.1372C>T	p.His458Tyr	p.H458Y	ENST00000374080		458	Cat/Tat	10/45	0.186908075351796	3	FACETS	1	0.985	1			1	INDETERMINATE	3	TRUE	NA	0.378601606653802	3		221	342	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249134	55249136	+	stop_gained	Nonsense_Mutation	TNP	CCC	CCC	ACT	novel	NA	P-0053511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	174	459	0	ENST00000275493.2:c.2432_2434delinsACT	p.Ser811_Gln812delinsTyrTer	p.S811_Q812delinsY*	ENST00000275493	NM_005228.3	811	tCCCag/tACTag	20/28	0.378601606653802	5	FACETS	1	0.98	1	0.78	0.721	0.84	CLONAL	2	TRUE	2	0.378601606653802	5		459	616	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248633	59248634	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0053512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	207	737	0	ENST00000371222.2:c.109_110del	p.Ser37HisfsTer69	p.S37Hfs*69	ENST00000371222	NM_002228.3	37	AGc/c	1/1	0.578294451711207	3	FACETS	1	0.939	1	0.506	0.47	0.543	CLONAL	1	TRUE	1	0.578294451711207	3		737	912	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435619	110435620	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0053512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	20	410	0	ENST00000375856.3:c.2781dup	p.Gly928ArgfsTer63	p.G928Rfs*63	ENST00000375856	NM_003749.2	927	-/C	1/2	0.578294451711207	3	FACETS	0.239	0.182	0.306	0.12	0.091	0.153	SUBCLONAL	1	TRUE	1	0.578294451711207	3		410	373	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351476	89351476	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	137	633	0	ENST00000301030.4:c.1474G>T	p.Asp492Tyr	p.D492Y	ENST00000301030	NM_001256183.1	492	Gac/Tac	9/13	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.578294451711207	2		633	468	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	94	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.953	1	1	0.988	1	CLONAL	2	TRUE	1	0.306500469081402	2		276	280	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0053514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	38	533	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.458	0.378	0.548	0.458	0.378	0.548	SUBCLONAL	1	TRUE	1	0.306500469081402	2		533	541	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0053514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	455	1176	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	0.306500469081402	1	FACETS	0.889	0.859	0.918	1	0.998	1	CLONAL	4	TRUE	0	0.306500469081402	1		1176	707	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188222	108188223	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGTGGGA	novel	NA	P-0053514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	38	348	0	ENST00000278616.4:c.6323_6330dup	p.His2111SerfsTer12	p.H2111Sfs*12	ENST00000278616	NM_000051.3	2107	-/CAGTGGGA	43/63	1	2	FACETS	0.539	0.445	0.644	0.539	0.445	0.644	SUBCLONAL	1	TRUE	1	0.306500469081402	2		348	460	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188236	108188236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	32	319	0	ENST00000278616.4:c.6335G>A	p.Cys2112Tyr	p.C2112Y	ENST00000278616	NM_000051.3	2112	tGc/tAc	43/63	1	2	FACETS	0.522	0.424	0.633	0.522	0.424	0.633	SUBCLONAL	1	TRUE	1	0.306500469081402	2		319	400	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473748	67473748	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	268	860	0	ENST00000327367.4:c.828T>A	p.Asn276Lys	p.N276K	ENST00000327367	NM_005902.3	276	aaT/aaA	6/9	0.306500469081402	2	FACETS	0.993	0.94	1	1	0.994	1	CLONAL	3	TRUE	0	0.306500469081402	2		860	587	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246810	41246810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs768416164	NA	P-0053514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	60	615	0	ENST00000357654.3:c.738G>C	p.Leu246Phe	p.L246F	ENST00000357654	NM_007294.3	246	ttG/ttC	10/23	1	2	FACETS	0.604	0.52	0.696	0.604	0.52	0.696	SUBCLONAL	1	TRUE	1	0.306500469081402	2		615	648	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564792	41564792	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	50	852	0	ENST00000263253.7:c.4093G>T	p.Glu1365Ter	p.E1365*	ENST00000263253	NM_001429.3	1365	Gaa/Taa	25/31	1	2	FACETS	0.431	0.365	0.504	0.431	0.365	0.504	SUBCLONAL	1	TRUE	1	0.306500469081402	2		852	757	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564837	41564837	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	62	773	0	ENST00000263253.7:c.4138G>C	p.Glu1380Gln	p.E1380Q	ENST00000263253	NM_001429.3	1380	Gag/Cag	25/31	1	2	FACETS	0.527	0.455	0.607	0.527	0.455	0.607	SUBCLONAL	1	TRUE	1	0.306500469081402	2		773	767	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402809	20402809	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	87	179	0	ENST00000346618.3:c.346C>T	p.Pro116Ser	p.P116S	ENST00000346618	NM_001949.4	116	Cca/Tca	1/7	1	2	FACETS	0.991	0.899	1	1	0.989	1	CLONAL	3	TRUE	1	0.306500469081402	2		179	191	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176458	123176459	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	45	384	0	ENST00000218089.9:c.426dup	p.Glu143Ter	p.E143*	ENST00000218089	NM_001042749.1	142	tct/tcTt	7/35	1	2	FACETS	0.421	0.353	0.496	0.421	0.353	0.496	SUBCLONAL	1	TRUE	1	0.306500469081402	2		384	698	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224458	123224458	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0053514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	209	740	0	ENST00000218089.9:c.3311T>A	p.Leu1104Ter	p.L1104*	ENST00000218089	NM_001042749.1	1104	tTa/tAa	31/35	1	2	FACETS	0.912	0.849	0.976	1	0.993	1	CLONAL	2	TRUE	1	0.306500469081402	2		740	748	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0053516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	205	866	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.330809517280646	2		867	1078	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0053516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	135	882	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.846	0.768	0.928	0.846	0.768	0.928	CLONAL	1	TRUE	1	0.330809517280646	2		883	965	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0053516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	82	270	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.223779277214174	2	FACETS	0.77	0.685	0.859	0.77	0.685	0.859	SUBCLONAL	2	TRUE	0	0.330809517280646	2		270	322	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006632	62006632	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	107	873	0	ENST00000392795.3:c.647C>G	p.Thr216Arg	p.T216R	ENST00000392795	NM_001039933.1	216	aCa/aGa	6/6	1	2	FACETS	0.726	0.65	0.806	0.726	0.65	0.806	SUBCLONAL	1	TRUE	1	0.330809517280646	2		873	891	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516881	187516881	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	150	550	0	ENST00000441802.2:c.13100C>G	p.Ser4367Cys	p.S4367C	ENST00000441802	NM_005245.3	4367	tCt/tGt	26/27	0.330809517280646	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.330809517280646	1		550	626	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817489	39817489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763409220	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	107	713	1	ENST00000288319.7:c.74C>T	p.Thr25Met	p.T25M	ENST00000288319	NM_182918.3	25	aCg/aTg	2/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.28	2		714	691	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233751	233751	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	170	719	0	ENST00000264932.6:c.1055G>T	p.Arg352Leu	p.R352L	ENST00000264932	NM_004168.2	352	cGa/cTa	8/15	0.277265163619093	3	FACETS	0.761	0.699	0.824	0.507	0.466	0.55	SUBCLONAL	2	TRUE	0	0.28	3		719	910	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588943	67588943	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	47	258	0	ENST00000274335.5:c.1034A>G	p.Glu345Gly	p.E345G	ENST00000274335		345	gAa/gGa	8/15	0.3	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.28	1		258	242	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792100	42792100	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	50	803	1	ENST00000575354.2:c.904G>T	p.Glu302Ter	p.E302*	ENST00000575354	NM_015125.3	302	Gag/Tag	6/20	0.244740546141769	1	FACETS	0.458	0.388	0.536	0.458	0.388	0.536	SUBCLONAL	1	TRUE	0	0.28	1		804	670	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195364	102195364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	42	481	0	ENST00000263464.3:c.124G>A	p.Gly42Arg	p.G42R	ENST00000263464	NM_001165.4	42	Ggg/Agg	2/9	0.219503284912364	3	FACETS	0.669	0.558	0.792	0.335	0.279	0.396	SUBCLONAL	1	TRUE	1	0.28	3		481	511	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340976	70340976	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	58	399	0	ENST00000374080.3:c.709G>T	p.Glu237Ter	p.E237*	ENST00000374080		237	Gag/Tag	5/45	1	1	FACETS	0.871	0.751	1	0.871	0.751	1	CLONAL	1	TRUE	0	0.28	1		399	409	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520192	9520192	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	40	597	0	ENST00000353224.5:c.2077G>T	p.Glu693Ter	p.E693*	ENST00000353224	NM_177990.2	693	Gaa/Taa	10/10	0.219503284912364	3	FACETS	0.591	0.49	0.703	0.296	0.245	0.352	SUBCLONAL	1	TRUE	1	0.28	3		597	551	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169953064	169953064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	42	577	0	ENST00000295797.4:c.148C>T	p.Leu50Phe	p.L50F	ENST00000295797	NM_002740.5	50	Ctt/Ttt	2/18	1	2	FACETS	0.503	0.419	0.596	0.503	0.419	0.596	SUBCLONAL	1	TRUE	1	0.28	2		577	597	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491669	56491669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	84	557	0	ENST00000267101.3:c.2561G>T	p.Gly854Val	p.G854V	ENST00000267101	NM_001982.3	854	gGt/gTt	21/28	0.3	5	FACETS	1	0.925	1			1	CLONAL	1	TRUE	NA	0.28	5		557	800	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555725	21555725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778450722	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	120	889	1	ENST00000382592.4:c.2545C>T	p.Arg849Trp	p.R849W	ENST00000382592	NM_014572.2	849	Cgg/Tgg	6/8	0.3	1	FACETS	0.901	0.814	0.994	0.901	0.814	0.994	CLONAL	1	TRUE	0	0.28	1		890	818	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729355	41729355	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	44	643	0	ENST00000242208.4:c.1174G>T	p.Val392Leu	p.V392L	ENST00000242208	NM_002192.2	392	Gtg/Ttg	3/3	0.152749102285	2	FACETS	0.452	0.378	0.534	0.226	0.189	0.267	INDETERMINATE	1	TRUE	0	0.28	2		643	696	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193204	11193204	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	76	778	0	ENST00000361445.4:c.5297A>C	p.Glu1766Ala	p.E1766A	ENST00000361445	NM_004958.3	1766	gAg/gCg	38/58	0.219503284912364	3	FACETS	0.658	0.576	0.747	0.329	0.288	0.374	SUBCLONAL	1	TRUE	1	0.28	3		778	940	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254785	16254785	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	40	587	0	ENST00000375759.3:c.2050A>G	p.Arg684Gly	p.R684G	ENST00000375759	NM_015001.2	684	Agg/Ggg	11/15	0.219503284912364	3	FACETS	0.503	0.417	0.599	0.251	0.208	0.3	SUBCLONAL	1	TRUE	1	0.28	3		587	648	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28586425	28586425	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	83	782	0	ENST00000253063.3:c.67G>T	p.Val23Phe	p.V23F	ENST00000253063	NM_031459.4	23	Gtc/Ttc	1/10	0.219503284912364	3	FACETS	0.869	0.766	0.979	0.434	0.383	0.49	CLONAL	1	TRUE	1	0.28	3		782	778	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36934765	36934765	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	101	824	1	ENST00000361632.4:c.1568A>T	p.Gln523Leu	p.Q523L	ENST00000361632		523	cAa/cTa	11/16	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.28	2		825	712	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805132	43805132	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs769674316	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	101	745	0	ENST00000372470.3:c.582C>A	p.Cys194Ter	p.C194*	ENST00000372470	NM_005373.2	194	tgC/tgA	4/12	1	2	FACETS	0.963	0.861	1	0.963	0.861	1	CLONAL	1	TRUE	1	0.28	2		745	749	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521639	46521639	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	35	329	0	ENST00000262741.5:c.769A>T	p.Met257Leu	p.M257L	ENST00000262741	NM_003629.3	257	Atg/Ttg	7/10	1	2	FACETS	0.704	0.578	0.845	0.704	0.578	0.845	SUBCLONAL	1	TRUE	1	0.28	2		329	355	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695937	117695937	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs771525947	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	48	661	0	ENST00000369458.3:c.500G>T	p.Arg167Leu	p.R167L	ENST00000369458	NM_024626.3	167	cGg/cTg	4/6	1	2	FACETS	0.412	0.347	0.484	0.412	0.347	0.484	SUBCLONAL	1	TRUE	1	0.28	2		661	833	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506254	120506254	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	28	492	0	ENST00000256646.2:c.1858G>T	p.Gly620Cys	p.G620C	ENST00000256646	NM_024408.3	620	Ggt/Tgt	11/34	1	2	FACETS	0.364	0.29	0.448	0.364	0.29	0.448	SUBCLONAL	1	TRUE	1	0.28	2		492	550	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844747	156844747	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	168	884	1	ENST00000524377.1:c.1301C>A	p.Thr434Lys	p.T434K	ENST00000524377	NM_002529.3	434	aCg/aAg	11/17	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.28	2		885	969	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176055022	176055022	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	30	485	1	ENST00000367669.3:c.1031A>T	p.Lys344Met	p.K344M	ENST00000367669	NM_022457.5	344	aAg/aTg	10/20	1	2	FACETS	0.455	0.366	0.556	0.455	0.366	0.556	SUBCLONAL	1	TRUE	1	0.28	2		486	471	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245912945	245912945	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	32	421	0	ENST00000388985.4:c.1207A>T	p.Thr403Ser	p.T403S	ENST00000388985		403	Aca/Tca	12/12	1	2	FACETS	0.49	0.398	0.596	0.49	0.398	0.596	SUBCLONAL	1	TRUE	1	0.28	2		421	466	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332742	70332742	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	65	612	0	ENST00000373644.4:c.647G>T	p.Gly216Val	p.G216V	ENST00000373644	NM_030625.2	216	gGg/gTg	2/12	1	2	FACETS	0.715	0.62	0.819	0.715	0.62	0.819	SUBCLONAL	1	TRUE	1	0.28	2		612	649	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406297	70406297	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	85	711	0	ENST00000373644.4:c.3811G>T	p.Glu1271Ter	p.E1271*	ENST00000373644	NM_030625.2	1271	Gaa/Taa	4/12	1	2	FACETS	0.979	0.866	1	0.979	0.866	1	CLONAL	1	TRUE	1	0.28	2		711	620	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625313	69625313	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	74	1107	2	ENST00000334134.2:c.480G>T	p.Lys160Asn	p.K160N	ENST00000334134	NM_005247.2	160	aaG/aaT	3/3	0.219503284912364	3	FACETS	0.528	0.46	0.601	0.264	0.23	0.301	SUBCLONAL	1	TRUE	1	0.28	3		1109	1142	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998255	100998255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	22	354	0	ENST00000325455.5:c.1547G>T	p.Gly516Val	p.G516V	ENST00000325455	NM_001202474.3	516	gGc/gTc	1/8	0.219503284912364	3	FACETS	0.417	0.322	0.527	0.208	0.161	0.264	SUBCLONAL	1	TRUE	1	0.28	3		354	430	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164150	108164150	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	42	296	0	ENST00000278616.4:c.4722G>T	p.Leu1574Phe	p.L1574F	ENST00000278616	NM_000051.3	1574	ttG/ttT	31/63	0.219503284912364	3	FACETS	0.974	0.816	1	0.487	0.408	0.575	CLONAL	1	TRUE	1	0.28	3		296	351	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170274	119170274	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	27	330	1	ENST00000264033.4:c.2504G>T	p.Arg835Leu	p.R835L	ENST00000264033	NM_005188.3	835	cGg/cTg	16/16	0.219503284912364	3	FACETS	0.475	0.377	0.587	0.237	0.188	0.294	SUBCLONAL	1	TRUE	1	0.28	3		331	463	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421872	49421872	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	136	1008	0	ENST00000301067.7:c.14435C>G	p.Pro4812Arg	p.P4812R	ENST00000301067	NM_003482.3	4812	cCc/cGc	46/54	0.221675617408904	2	FACETS	1	0.971	1	0.581	0.528	0.636	CLONAL	1	TRUE	0	0.28	2		1008	836	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426495	49426495	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	144	1050	0	ENST00000301067.7:c.11993G>T	p.Gly3998Val	p.G3998V	ENST00000301067	NM_003482.3	3998	gGc/gTc	39/54	0.221675617408904	2	FACETS	1	0.913	1	0.501	0.456	0.549	CLONAL	1	TRUE	0	0.28	2		1050	1026	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861891	57861891	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	67	763	0	ENST00000228682.2:c.1192C>A	p.Arg398Ser	p.R398S	ENST00000228682	NM_005269.2	398	Cgt/Agt	10/12	0.0816545206000918	3	FACETS	0.631	0.547	0.723			1	INDETERMINATE	1	TRUE	NA	0.28	3		763	864	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865344	57865344	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	324	989	1	ENST00000228682.2:c.2821G>T	p.Ala941Ser	p.A941S	ENST00000228682	NM_005269.2	941	Gct/Tct	12/12	0.0816545206000918	3	FACETS	0.861	0.815	0.909			1	INDETERMINATE	3	TRUE	NA	0.28	3		990	1021	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32899229	32899229	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	19	321	0	ENST00000380152.3:c.333T>A	p.Asn111Lys	p.N111K	ENST00000380152		111	aaT/aaA	4/27	0.3	1	FACETS	0.396	0.3	0.508	0.396	0.3	0.508	SUBCLONAL	1	TRUE	0	0.28	1		321	295	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73351584	73351584	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	18	272	0	ENST00000377767.4:c.628C>A	p.Arg210Ser	p.R210S	ENST00000377767	NM_014953.3	210	Cgt/Agt	4/21	0.3	1	FACETS	0.336	0.253	0.435	0.336	0.253	0.435	SUBCLONAL	1	TRUE	0	0.28	1		272	329	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675520	40675520	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1333298727	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	52	672	1	ENST00000249776.8:c.301G>T	p.Ala101Ser	p.A101S	ENST00000249776	NM_033286.3	101	Gca/Tca	2/9	0.3	1	FACETS	0.644	0.549	0.748	0.644	0.549	0.748	SUBCLONAL	1	TRUE	0	0.28	1		673	496	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678353	88678353	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	128	791	1	ENST00000360948.2:c.1183T>A	p.Phe395Ile	p.F395I	ENST00000360948	NM_001012338.2	395	Ttc/Atc	9/19	0.3	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.28	1		792	757	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679246	88679247	+	missense_variant	Missense_Mutation	DNP	TG	TG	AT	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	48	736	0	ENST00000360948.2:c.790_791delinsAT	p.His264Ile	p.H264I	ENST00000360948	NM_001012338.2	264	CAt/ATt	8/19	0.3	1	FACETS	0.401	0.338	0.471	0.401	0.338	0.471	SUBCLONAL	1	TRUE	0	0.28	1		736	735	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106216	2106216	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	44	854	0	ENST00000219476.3:c.619G>T	p.Val207Phe	p.V207F	ENST00000219476	NM_000548.3	207	Gtc/Ttc	7/42	0.244740546141769	1	FACETS	0.324	0.271	0.384	0.324	0.271	0.384	SUBCLONAL	1	TRUE	0	0.28	1		854	834	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857524	9857524	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs778230379	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	58	540	0	ENST00000330684.3:c.3877G>C	p.Asp1293His	p.D1293H	ENST00000330684	NM_001134407.1	1293	Gat/Cat	13/13	0.244740546141769	1	FACETS	0.739	0.636	0.851	0.739	0.636	0.851	SUBCLONAL	1	TRUE	0	0.28	1		540	482	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032334	10032334	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	44	539	0	ENST00000330684.3:c.489G>T	p.Gln163His	p.Q163H	ENST00000330684	NM_001134407.1	163	caG/caT	3/13	0.244740546141769	1	FACETS	0.464	0.389	0.548	0.464	0.389	0.548	SUBCLONAL	1	TRUE	0	0.28	1		539	582	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273854	10273854	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	105	847	0	ENST00000330684.3:c.414+1G>C		p.X138_splice	ENST00000330684	NM_001134407.1	138			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.28	NA		847	829	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832447	72832447	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	85	529	0	ENST00000268489.5:c.4134G>C	p.Gln1378His	p.Q1378H	ENST00000268489	NM_006885.3	1378	caG/caC	9/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.28	2		529	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	131	1037	1	ENST00000269305.4:c.473del	p.Arg158ProfsTer12	p.R158Pfs*12	ENST00000269305	NM_001126112.2	158	cGc/cc	5/11	0.3	1	FACETS	0.899	0.815	0.987	0.899	0.815	0.987	CLONAL	1	TRUE	0	0.28	1		1038	895	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667664	29667664	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	35	392	0	ENST00000356175.3:c.6999+1G>T		p.X2333_splice	ENST00000356175	NM_000267.3	2333			1	2	FACETS	0.579	0.474	0.696	0.579	0.474	0.696	SUBCLONAL	1	TRUE	1	0.28	2		392	432	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627521	37627521	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	48	654	0	ENST00000447079.4:c.1436G>T	p.Gly479Val	p.G479V	ENST00000447079	NM_015083.1	479	gGg/gTg	2/14	1	2	FACETS	0.514	0.434	0.603	0.514	0.434	0.603	SUBCLONAL	1	TRUE	1	0.28	2		654	667	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354419	40354419	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	158	1485	0	ENST00000293328.3:c.2176A>G	p.Met726Val	p.M726V	ENST00000293328	NM_012448.3	726	Atg/Gtg	18/19	1	2	FACETS	0.981	0.898	1	0.981	0.898	1	CLONAL	1	TRUE	1	0.28	2		1485	1150	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276767	15276767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1206434921	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	96	944	0	ENST00000263388.2:c.5498C>T	p.Ala1833Val	p.A1833V	ENST00000263388	NM_000435.2	1833	gCa/gTa	30/33	1	2	FACETS	0.789	0.702	0.882	0.789	0.702	0.882	SUBCLONAL	1	TRUE	1	0.28	2		944	869	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942482	17942482	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	60	1063	0	ENST00000458235.1:c.2805+1G>T		p.X935_splice	ENST00000458235	NM_000215.3	935			1	2	FACETS	0.466	0.4	0.538	0.466	0.4	0.538	SUBCLONAL	1	TRUE	1	0.28	2		1063	920	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948832	17948832	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	77	824	0	ENST00000458235.1:c.1610G>T	p.Arg537Leu	p.R537L	ENST00000458235	NM_000215.3	537	cGg/cTg	12/24	1	2	FACETS	0.597	0.523	0.677	0.597	0.523	0.677	SUBCLONAL	1	TRUE	1	0.28	2		824	921	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257874	19257874	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	125	1117	0	ENST00000162023.5:c.512G>C	p.Arg171Pro	p.R171P	ENST00000162023		171	cGa/cCa	9/13	1	2	FACETS	0.852	0.77	0.939	0.852	0.77	0.939	CLONAL	1	TRUE	1	0.28	2		1117	1048	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40740985	40740985	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	89	1042	0	ENST00000392038.2:c.1333G>T	p.Ala445Ser	p.A445S	ENST00000392038	NM_001626.4	445	Gcc/Tcc	13/14	0.244740546141769	1	FACETS	0.657	0.582	0.738	0.657	0.582	0.738	SUBCLONAL	1	TRUE	0	0.28	1		1042	832	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160393	99160393	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	63	664	1	ENST00000074304.5:c.872G>T	p.Arg291Leu	p.R291L	ENST00000074304	NM_001134224.1	291	cGg/cTg	11/26	1	2	FACETS	0.568	0.49	0.653	0.568	0.49	0.653	SUBCLONAL	1	TRUE	1	0.28	2		665	792	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248567	212248567	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	43	588	1	ENST00000342788.4:c.3700A>T	p.Lys1234Ter	p.K1234*	ENST00000342788	NM_005235.2	1234	Aag/Tag	28/28	0.219503284912364	3	FACETS	0.554	0.463	0.656	0.277	0.231	0.328	SUBCLONAL	1	TRUE	1	0.28	3		589	632	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662503	227662503	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	87	779	0	ENST00000305123.5:c.952G>T	p.Gly318Cys	p.G318C	ENST00000305123	NM_005544.2	318	Ggc/Tgc	1/2	0.244740546141769	1	FACETS	0.781	0.692	0.877	0.781	0.692	0.877	SUBCLONAL	1	TRUE	0	0.28	1		779	684	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546826	9546826	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	42	545	0	ENST00000353224.5:c.1196C>A	p.Ser399Tyr	p.S399Y	ENST00000353224	NM_177990.2	399	tCc/tAc	5/10	0.219503284912364	3	FACETS	0.708	0.591	0.838	0.354	0.295	0.419	SUBCLONAL	1	TRUE	1	0.28	3		545	483	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247417	71247417	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	165	773	1	ENST00000318789.4:c.116G>T	p.Gly39Val	p.G39V	ENST00000318789	NM_032682.5	39	gGa/gTa	6/21	0.3	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.28	1		774	686	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200703	128200703	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	70	1036	3	ENST00000341105.2:c.1102C>A	p.Pro368Thr	p.P368T	ENST00000341105	NM_032638.4	368	Cct/Act	5/6	0.3	1	FACETS	0.494	0.429	0.564	0.494	0.429	0.564	SUBCLONAL	1	TRUE	0	0.28	1		1039	871	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920370	134920370	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	37	620	0	ENST00000398015.3:c.2185G>T	p.Ala729Ser	p.A729S	ENST00000398015	NM_004441.4	729	Gct/Tct	12/16	0.3	1	FACETS	0.41	0.337	0.492	0.41	0.337	0.492	SUBCLONAL	1	TRUE	0	0.28	1		620	554	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461400	138461400	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	26	315	0	ENST00000289153.2:c.621G>T	p.Gln207His	p.Q207H	ENST00000289153	NM_006219.2	207	caG/caT	3/22	1	2	FACETS	0.607	0.481	0.75	0.607	0.481	0.75	SUBCLONAL	1	TRUE	1	0.28	2		315	306	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269131	142269131	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	26	364	0	ENST00000350721.4:c.2819C>T	p.Ser940Phe	p.S940F	ENST00000350721	NM_001184.3	940	tCc/tTc	14/47	1	2	FACETS	0.432	0.341	0.536	0.432	0.341	0.536	SUBCLONAL	1	TRUE	1	0.28	2		364	430	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138653	55138653	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs745702167	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	55	567	0	ENST00000257290.5:c.1330G>C	p.Asp444His	p.D444H	ENST00000257290	NM_006206.4	444	Gat/Cat	9/23	0.244740546141769	1	FACETS	0.53	0.453	0.615	0.53	0.453	0.615	SUBCLONAL	1	TRUE	0	0.28	1		567	637	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946130	55946130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	34	446	0	ENST00000263923.4:c.4049C>A	p.Thr1350Lys	p.T1350K	ENST00000263923	NM_002253.2	1350	aCa/aAa	30/30	0.244740546141769	1	FACETS	0.494	0.403	0.595	0.494	0.403	0.595	SUBCLONAL	1	TRUE	0	0.28	1		446	423	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356247	66356247	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs199614818	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	49	679	0	ENST00000273854.3:c.1250G>T	p.Arg417Leu	p.R417L	ENST00000273854	NM_004439.5	417	cGg/cTg	5/18	0.244740546141769	1	FACETS	0.425	0.359	0.498	0.425	0.359	0.498	SUBCLONAL	1	TRUE	0	0.28	1		679	708	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245548	153245548	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	33	293	0	ENST00000281708.4:c.1645-2A>T		p.X549_splice	ENST00000281708	NM_033632.3	549			0.244740546141769	1	FACETS	0.719	0.588	0.865	0.719	0.588	0.865	SUBCLONAL	1	TRUE	0	0.28	1		293	282	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247158	153247158	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	50	321	0	ENST00000281708.4:c.1644G>T	p.Gln548His	p.Q548H	ENST00000281708	NM_033632.3	548	caG/caT	10/12	0.244740546141769	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.28	1		321	273	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517870	187517870	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	41	519	0	ENST00000441802.2:c.12824G>T	p.Gly4275Val	p.G4275V	ENST00000441802	NM_005245.3	4275	gGa/gTa	25/27	0.244740546141769	1	FACETS	0.507	0.422	0.601	0.507	0.422	0.601	SUBCLONAL	1	TRUE	0	0.28	1		519	497	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627885	187627885	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs752785176	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	58	703	0	ENST00000441802.2:c.3097G>T	p.Val1033Leu	p.V1033L	ENST00000441802	NM_005245.3	1033	Gtg/Ttg	2/27	0.244740546141769	1	FACETS	0.533	0.457	0.615	0.533	0.457	0.615	SUBCLONAL	1	TRUE	0	0.28	1		703	669	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032255	26032255	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	36	447	0	ENST00000244661.2:c.34A>T	p.Thr12Ser	p.T12S	ENST00000244661	NM_003537.3	12	Acc/Tcc	1/1	1	2	FACETS	0.522	0.428	0.626	0.522	0.428	0.626	SUBCLONAL	1	TRUE	1	0.28	2		447	493	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673583	30673583	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	75	957	0	ENST00000376406.3:c.3377A>T	p.Glu1126Val	p.E1126V	ENST00000376406	NM_014641.2	1126	gAg/gTg	10/15	1	2	FACETS	0.597	0.522	0.679	0.597	0.522	0.679	SUBCLONAL	1	TRUE	1	0.28	2		957	897	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166499	32166499	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	43	750	0	ENST00000375023.3:c.4544A>T	p.Lys1515Met	p.K1515M	ENST00000375023	NM_004557.3	1515	aAg/aTg	25/30	1	2	FACETS	0.424	0.354	0.503	0.424	0.354	0.503	SUBCLONAL	1	TRUE	1	0.28	2		750	724	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188018	32188018	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	74	1002	1	ENST00000375023.3:c.1203C>A	p.Cys401Ter	p.C401*	ENST00000375023	NM_004557.3	401	tgC/tgA	7/30	1	2	FACETS	0.551	0.481	0.627	0.551	0.481	0.627	SUBCLONAL	1	TRUE	1	0.28	2		1003	959	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843371	128843371	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	110	858	0	ENST00000249373.3:c.478G>T	p.Glu160Ter	p.E160*	ENST00000249373	NM_005631.4	160	Gag/Tag	2/12	0.219503284912364	3	FACETS	1	0.924	1	0.518	0.465	0.574	CLONAL	1	TRUE	1	0.28	3		858	865	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140508777	140508777	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1554404622	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	58	382	0	ENST00000288602.6:c.523G>T	p.Val175Phe	p.V175F	ENST00000288602	NM_004333.4	175	Gtt/Ttt	4/18	0.219503284912364	3	FACETS	1	0.894	1	0.522	0.45	0.601	CLONAL	1	TRUE	1	0.28	3		382	452	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148544317	148544317	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	48	541	0	ENST00000320356.2:c.74G>T	p.Arg25Leu	p.R25L	ENST00000320356	NM_004456.4	25	cGa/cTa	2/20	0.219503284912364	3	FACETS	0.56	0.472	0.657	0.28	0.236	0.329	SUBCLONAL	1	TRUE	1	0.28	3		541	698	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008883	152008883	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	35	364	0	ENST00000262189.6:c.739G>T	p.Gly247Cys	p.G247C	ENST00000262189	NM_170606.2	247	Ggc/Tgc	5/59	0.219503284912364	3	FACETS	0.658	0.539	0.792	0.329	0.269	0.396	SUBCLONAL	1	TRUE	1	0.28	3		364	433	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372417	55372417	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	65	1099	3	ENST00000297316.4:c.1107C>A	p.Phe369Leu	p.F369L	ENST00000297316	NM_022454.3	369	ttC/ttA	2/2	0.174354361421395	3	FACETS	0.505	0.436	0.58	0.168	0.145	0.194	SUBCLONAL	1	TRUE	0	0.28	3		1102	1048	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485849	8485849	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	30	496	0	ENST00000356435.5:c.2968T>A	p.Tyr990Asn	p.Y990N	ENST00000356435		990	Tac/Aac	17/35	0.3	1	FACETS	0.521	0.42	0.635	0.521	0.42	0.635	SUBCLONAL	1	TRUE	0	0.28	1		496	354	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486113	8486113	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	70	631	0	ENST00000356435.5:c.2704G>C	p.Gly902Arg	p.G902R	ENST00000356435		902	Ggc/Cgc	17/35	0.3	1	FACETS	0.966	0.845	1	0.966	0.845	1	CLONAL	1	TRUE	0	0.28	1		631	445	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486344	8486344	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	24	334	0	ENST00000356435.5:c.2473G>T	p.Gly825Trp	p.G825W	ENST00000356435		825	Ggg/Tgg	17/35	0.3	1	FACETS	0.664	0.523	0.825	0.664	0.523	0.825	SUBCLONAL	1	TRUE	0	0.28	1		334	222	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321342	1321342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	53	731	0	ENST00000400841.2:c.413G>A	p.Cys138Tyr	p.C138Y	ENST00000400841		138	tGt/tAt	4/6	1	1	FACETS	0.462	0.393	0.538	0.462	0.393	0.538	SUBCLONAL	1	TRUE	0	0.28	1		731	705	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007808	45007808	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	TT	novel	NA	P-0053517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	44	487	0	ENST00000558401.1:c.255delinsTT	p.Leu85PhefsTer5	p.L85Ffs*5	ENST00000558401	NM_004048.2	85	ttG/ttTT	2/4	0.3	1	FACETS	0.658	0.552	0.774	0.658	0.552	0.774	SUBCLONAL	1	TRUE	0	0.28	1		487	411	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426908	6426908	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	35	504	0	ENST00000356142.4:c.101C>G	p.Pro34Arg	p.P34R	ENST00000356142	NM_018890.3	34	cCt/cGt	2/7	1	2	FACETS	0.595	0.486	0.719	0.595	0.486	0.719	SUBCLONAL	1	TRUE	1	0.13	2		504	905	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258744	115258744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434596	NA	P-0053518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	17	367	2	ENST00000369535.4:c.38G>A	p.Gly13Asp	p.G13D	ENST00000369535	NM_002524.4	13	gGt/gAt	2/7	1	2	FACETS	0.401	0.297	0.524	0.401	0.297	0.524	SUBCLONAL	1	TRUE	1	0.13	2		369	653	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974795	21974818	+	inframe_deletion	In_Frame_Del	DEL	GGCTCCATGCTGCTCCCCGCCGCC	GGCTCCATGCTGCTCCCCGCCGCC	-	rs587780668	NA	P-0053518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	14	215	0	ENST00000304494.5:c.9_32del	p.Ala4_Pro11del	p.A4_P11del	ENST00000304494	NM_000077.4	3	ccGGCGGCGGGGAGCAGCATGGAGCCt/cct	1/3	1	2	FACETS	0.78	0.563	1	0.78	0.563	1	CLONAL	1	TRUE	1	0.13	2		215	276	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144106	11144106	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	64	815	0	ENST00000358026.2:c.3687C>G	p.Ile1229Met	p.I1229M	ENST00000358026	NM_001128849.1	1229	atC/atG	26/36	0.112753518068971	0	FACETS	0.923	0.797	1			1	CLONAL	1	TRUE	0	0.13	0		815	928	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357107	89357107	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	51	823	1	ENST00000301030.4:c.527C>T	p.Ala176Val	p.A176V	ENST00000301030	NM_001256183.1	176	gCc/gTc	6/13	1	2	FACETS	0.789	0.668	0.922	0.789	0.668	0.922	CLONAL	1	TRUE	1	0.13	2		824	995	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587385	29587385	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0053518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	31	359	0	ENST00000356175.3:c.4368-2A>G		p.X1456_splice	ENST00000356175	NM_000267.3	1456			1	2	FACETS	0.882	0.712	1	0.882	0.712	1	CLONAL	1	TRUE	1	0.13	2		359	541	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955135	17955135	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	62	843	0	ENST00000458235.1:c.92C>A	p.Pro31His	p.P31H	ENST00000458235	NM_000215.3	31	cCc/cAc	2/24	1	2	FACETS	0.954	0.821	1	0.954	0.821	1	CLONAL	1	TRUE	1	0.13	2		843	1000	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395603	31395603	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1348564459	NA	P-0053518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	43	623	0	ENST00000328111.2:c.2456C>T	p.Ser819Phe	p.S819F	ENST00000328111	NM_006892.3	819	tCc/tTc	23/23	1	2	FACETS	0.797	0.665	0.945	0.797	0.665	0.945	CLONAL	1	TRUE	1	0.13	2		623	830	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643665	52643666	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	AAGACTC	novel	NA	P-0053518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	37	475	0	ENST00000394830.3:c.2224_2230dup	p.Leu744Ter	p.L744*	ENST00000394830	NM_018313.4	744	ttg/tGAGTCTTtg	17/30	1	2	FACETS	0.811	0.667	0.973	0.811	0.667	0.973	CLONAL	1	TRUE	1	0.13	2		475	702	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674330	86674330	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	30	358	0	ENST00000274376.6:c.2462T>A	p.Ile821Lys	p.I821K	ENST00000274376	NM_002890.2	821	aTa/aAa	18/25	1	2	FACETS	0.974	0.784	1	0.974	0.784	1	CLONAL	1	TRUE	1	0.13	2		358	474	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006173	22006174	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0053518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	89	850	2	ENST00000276925.6:c.229_230delinsAA	p.Pro77Asn	p.P77N	ENST00000276925	NM_004936.3	77	CCt/AAt	2/2	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.13	2		852	936	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577577	+	protein_altering_variant	In_Frame_Del	DEL	TACACATGTAGT	TACACATGTAGT	ATG	novel	NA	P-0053519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	171	703	3	ENST00000269305.4:c.704_715delinsCAT	p.Asn235_Asn239delinsThrTyr	p.N235_N239delinsTY	ENST00000269305	NM_001126112.2	235	aACTACATGTGTAac/aCATac	7/11	0.347995358337112	1	FACETS	0.976	0.898	1	0.976	0.898	1	CLONAL	1	TRUE	0	0.347995358337112	1		706	832	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0053520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	156	468	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.443860452664847	3	FACETS	0.849	0.783	0.917	0.849	0.783	0.917	CLONAL	2	TRUE	1	0.443860452664847	3		468	506	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs770248150	NA	P-0053520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	111	536	0	ENST00000311936.3:c.351A>C	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaC	4/5	1	2	FACETS	0.973	0.879	1	0.973	0.879	1	CLONAL	1	TRUE	1	0.443860452664847	2		536	514	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40364153	40364153	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200200711	NA	P-0053520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	86	471	0	ENST00000293328.3:c.1529C>T	p.Ala510Val	p.A510V	ENST00000293328	NM_012448.3	510	gCg/gTg	13/19	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.443860452664847	2		471	379	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624263	89624263	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	247	406	0	ENST00000371953.3:c.37A>G	p.Lys13Glu	p.K13E	ENST00000371953	NM_000314.4	13	Aaa/Gaa	1/9	0.443860452664847	3	FACETS	0.975	0.924	1	0.975	0.924	1	CLONAL	3	TRUE	0	0.443860452664847	3		406	465	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564710	55564710	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	103	619	0	ENST00000288135.5:c.598T>C	p.Phe200Leu	p.F200L	ENST00000288135	NM_000222.2	200	Ttc/Ctc	3/21	1	2	FACETS	0.806	0.723	0.893	0.806	0.723	0.893	CLONAL	1	TRUE	1	0.443860452664847	2		619	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0053521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	372	879	3	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.298412938726366	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	0	0.29	3		882	937	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713475	30713479	+	frameshift_variant	Frame_Shift_Del	DEL	CTTCA	CTTCA	TCT	novel	NA	P-0053521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	136	752	1	ENST00000295754.5:c.800_804delinsTCT	p.Thr267IlefsTer2	p.T267Ifs*2	ENST00000295754	NM_003242.5	267	aCTTCA/aTCT	4/7	0.242967296829048	2	FACETS	0.791	0.722	0.863	0.791	0.722	0.863	SUBCLONAL	2	TRUE	0	0.29	2		753	593	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542504	187542506	+	frameshift_variant	Frame_Shift_Del	DEL	ACA	ACA	CC	novel	NA	P-0053521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	305	715	1	ENST00000441802.2:c.5234_5236delinsGG	p.Leu1745TrpfsTer8	p.L1745Wfs*8	ENST00000441802	NM_005245.3	1745	tTGTcc/tGGcc	10/27	0.298412938726366	3	FACETS	0.974	0.922	1	0.974	0.922	1	CLONAL	3	TRUE	0	0.29	3		716	824	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0053522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	313	721	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.653083610333127	2		721	949	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244785	46244785	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	221	564	0	ENST00000334344.6:c.2880del	p.Gln961SerfsTer2	p.Q961Sfs*2	ENST00000334344	NM_152641.2	960	gTt/gt	15/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.653083610333127	2		564	642	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	23	276	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		276	378	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0053524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	163	470	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.660332535646591	2		470	446	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0053524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	16	356	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.131	0.096	0.173	0.131	0.096	0.173	SUBCLONAL	1	TRUE	1	0.660332535646591	2		356	369	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041195	29041195	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1412106014	NA	P-0053524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	170	672	0	ENST00000282397.4:c.233A>C	p.Lys78Thr	p.K78T	ENST00000282397	NM_002019.4	78	aAa/aCa	3/30	NA	2	FACETS	1	0.963	1			1	INDETERMINATE	1	TRUE	NA	0.660332535646591	2		672	485	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023169	33023169	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	163	719	0	ENST00000300177.4:c.278G>T	p.Trp93Leu	p.W93L	ENST00000300177	NM_001191322.1	93	tGg/tTg	2/2	1	2	FACETS	0.97	0.897	1	0.97	0.897	1	CLONAL	1	TRUE	1	0.660332535646591	2		719	509	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140734	55140734	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	205	628	0	ENST00000257290.5:c.1595T>A	p.Leu532Gln	p.L532Q	ENST00000257290	NM_006206.4	532	cTg/cAg	11/23	1	2	FACETS	0.879	0.819	0.942	0.879	0.819	0.942	CLONAL	1	TRUE	1	0.660332535646591	2		628	706	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564615	55564615	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	182	718	0	ENST00000288135.5:c.503C>G	p.Ala168Gly	p.A168G	ENST00000288135	NM_000222.2	168	gCg/gGg	3/21	1	2	FACETS	0.824	0.763	0.887	0.824	0.763	0.887	CLONAL	1	TRUE	1	0.660332535646591	2		718	669	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520208	176520208	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	215	1012	0	ENST00000292408.4:c.1127G>T	p.Gly376Val	p.G376V	ENST00000292408	NM_213647.1	376	gGc/gTc	9/18	1	2	FACETS	0.61	0.567	0.655	0.61	0.567	0.655	SUBCLONAL	1	TRUE	1	0.660332535646591	2		1012	1067	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0053526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	118	678	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.34	0.306	0.377	0.34	0.306	0.377	SUBCLONAL	1	TRUE	1	0.617924971505283	2		678	1122	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0053526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	61	738	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.179	0.153	0.207	0.179	0.153	0.207	SUBCLONAL	1	TRUE	1	0.617924971505283	2		738	1103	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591111	67591137	+	inframe_deletion	In_Frame_Del	DEL	AGACCTTATCCAGCTGAGAAAGACGAG	AGACCTTATCCAGCTGAGAAAGACGAG	-	novel	NA	P-0053526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	22	298	0	ENST00000274335.5:c.1709_1735del	p.Leu570_Asp578del	p.L570_D578del	ENST00000274335		568	ccAGACCTTATCCAGCTGAGAAAGACGAGa/cca	12/15	1	2	FACETS	0.204	0.158	0.258	0.204	0.158	0.258	SUBCLONAL	1	TRUE	1	0.617924971505283	2		298	349	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	11	386	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.374236655768449	7	FACETS	1	0.82	1			1	CLONAL	1	FALSE	NA	0.374236655768449	7		386	89	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519998	NA	P-0053527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	43	644	0	ENST00000269305.4:c.581T>A	p.Leu194His	p.L194H	ENST00000269305	NM_001126112.2	194	cTt/cAt	6/11	0.374359313432672	3	FACETS	0.874	0.756	0.996	1	0.957	1	CLONAL	3	FALSE	1	0.374236655768449	3		644	104	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569289	67569289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs539374043	NA	P-0053527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	26	360	0	ENST00000274335.5:c.406G>A	p.Val136Met	p.V136M	ENST00000274335		136	Gtg/Atg	2/15	0.374359313432672	3	FACETS	0.994	0.81	1	0.994	0.81	1	CLONAL	2	FALSE	1	0.374236655768449	3		360	83	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782177	NA	P-0053528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	173	680	0	ENST00000269305.4:c.644G>T	p.Ser215Ile	p.S215I	ENST00000269305	NM_001126112.2	215	aGt/aTt	6/11	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.234335313177587	2		680	1069	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420213	49420213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267607237	NA	P-0053528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	88	653	2	ENST00000301067.7:c.15536G>A	p.Arg5179His	p.R5179H	ENST00000301067	NM_003482.3	5179	cGt/cAt	48/54	1	2	FACETS	0.733	0.647	0.824	0.733	0.647	0.824	SUBCLONAL	1	TRUE	1	0.234335313177587	2		655	1025	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433768	49433778	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCAGGGGGC	CCCCAGGGGGC	-	novel	NA	P-0053528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1376	143	1007	0	ENST00000301067.7:c.7775_7785del	p.Ser2592ThrfsTer59	p.S2592Tfs*59	ENST00000301067	NM_003482.3	2592	aGCCCCCTGGGG/a	31/54	1	2	FACETS	0.803	0.73	0.881	0.803	0.73	0.881	CLONAL	1	TRUE	1	0.234335313177587	2		1007	1519	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426670	121426670	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	61	686	0	ENST00000257555.6:c.361T>G	p.Ser121Ala	p.S121A	ENST00000257555		121	Tcc/Gcc	2/10	1	2	FACETS	0.468	0.402	0.54	0.468	0.402	0.54	SUBCLONAL	1	TRUE	1	0.234335313177587	2		686	1113	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939539	68939539	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	29	355	0	ENST00000288368.4:c.524A>T	p.Lys175Met	p.K175M	ENST00000288368	NM_024870.2	175	aAg/aTg	5/40	0.234335313177587	1	FACETS	0.407	0.326	0.5	0.407	0.326	0.5	SUBCLONAL	1	TRUE	0	0.234335313177587	1		355	537	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36846845	36846845	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	38	412	0	ENST00000358127.4:c.1094T>A	p.Leu365Gln	p.L365Q	ENST00000358127	NM_001280556.1	365	cTg/cAg	9/10	0.234335313177587	1	FACETS	0.519	0.428	0.62	0.519	0.428	0.62	SUBCLONAL	1	TRUE	0	0.234335313177587	1		412	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0053530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	278	817	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.178131230611044	2	FACETS	0.939	0.885	0.994	0.939	0.885	0.994	INDETERMINATE	2	TRUE	0	0.350720662379342	2		819	844	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972628	32972630	+	missense_variant	Missense_Mutation	TNP	AAA	AAA	TAT	novel	NA	P-0053530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	56	455	1	ENST00000380152.3:c.9978_9980delinsTAT	p.Lys3326_Lys3327delinsAsnIle	p.K3326_K3327delinsNI	ENST00000380152		3326	aaAAAa/aaTATa	27/27	0.350720662379342	3	FACETS	0.554	0.473	0.641	0.277	0.236	0.321	SUBCLONAL	1	TRUE	1	0.350720662379342	3		456	678	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007825	45007825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	205	488	0	ENST00000558401.1:c.276del	p.Thr93LeufsTer10	p.T93Lfs*10	ENST00000558401	NM_004048.2	91	aCc/ac	2/4	0.294827352779022	2	FACETS	0.889	0.827	0.953	0.889	0.827	0.953	CLONAL	2	TRUE	0	0.294827352779022	2		488	782	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1359	260	1030	0	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.294827352779022	2		1030	1619	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106497	27106498	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	361	718	0	ENST00000324856.7:c.6109dup	p.Gln2037ProfsTer62	p.Q2037Pfs*62	ENST00000324856	NM_006015.4	2036	-/C	20/20	0.294827352779022	2	FACETS	0.962	0.911	1	0.962	0.911	1	CLONAL	2	TRUE	0	0.294827352779022	2		718	1273	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735470	40735470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761910971	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	184	674	0	ENST00000373198.4:c.3403G>A	p.Val1135Met	p.V1135M	ENST00000373198	NM_133170.3	1135	Gtg/Atg	25/32	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.294827352779022	2		674	1127	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156742	20156742	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	87	358	0	ENST00000379607.5:c.17-2A>G		p.X6_splice	ENST00000379607	NM_001412.3	6			1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.294827352779022	2		358	586	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132428	11132428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	216	890	2	ENST00000358026.2:c.2644G>A	p.Glu882Lys	p.E882K	ENST00000358026	NM_001128849.1	882	Gaa/Aaa	19/36	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.294827352779022	2		892	1364	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866987936	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	74	297	0	ENST00000281708.4:c.1436G>T	p.Arg479Leu	p.R479L	ENST00000281708	NM_033632.3	479	cGa/cTa	10/12	1	2	FACETS	0.979	0.859	1	0.979	0.859	1	CLONAL	1	TRUE	1	0.294827352779022	2		297	513	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119794	70119794	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	160	686	0	ENST00000245479.2:c.800del	p.Pro267LeufsTer12	p.P267Lfs*12	ENST00000245479	NM_000346.3	266	Ccc/cc	3/3	1	2	FACETS	0.922	0.844	1	0.922	0.844	1	CLONAL	1	TRUE	1	0.294827352779022	2		686	1177	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589576	67589576	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1289537429	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	42	286	0	ENST00000274335.5:c.1344del	p.Lys448AsnfsTer32	p.K448Nfs*32	ENST00000274335		447	Aaa/aa	10/15	1	2	FACETS	0.65	0.543	0.769	0.65	0.543	0.769	SUBCLONAL	1	TRUE	1	0.294827352779022	2		286	438	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324220	31324220	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	34	116	0	ENST00000412585.2:c.344-1G>A		p.X115_splice	ENST00000412585	NM_005514.6	115			1	2	FACETS	0.887	0.739	1	1	0.961	1	CLONAL	2	TRUE	1	0.294827352779022	2		116	130	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562146	21562147	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1363	235	998	0	ENST00000382592.4:c.1772_1773del	p.Glu591ValfsTer12	p.E591Vfs*12	ENST00000382592	NM_014572.2	591	gAG/g	4/8	1	2	FACETS	0.998	0.928	1	0.998	0.928	1	CLONAL	1	TRUE	1	0.294827352779022	2		998	1598	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1273	247	960	1	ENST00000227507.2:c.859C>A	p.Pro287Thr	p.P287T	ENST00000227507	NM_053056.2	287	Ccc/Acc	5/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.294827352779022	2		961	1520	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467921	50467921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	124	563	3	ENST00000331340.3:c.1156C>T	p.Arg386Cys	p.R386C	ENST00000331340	NM_006060.4	386	Cgc/Tgc	8/8	1	2	FACETS	0.878	0.793	0.968	0.878	0.793	0.968	CLONAL	1	TRUE	1	0.294827352779022	2		566	958	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210893	36210893	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1345	201	1026	1	ENST00000222270.7:c.649del	p.Arg217GlyfsTer22	p.R217Gfs*22	ENST00000222270	NM_014727.1	215	aCc/ac	3/37	1	2	FACETS	0.882	0.815	0.952	0.882	0.815	0.952	CLONAL	1	TRUE	1	0.294827352779022	2		1027	1546	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599907	10599907	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1361	88	879	0	ENST00000171111.5:c.1669C>A	p.Leu557Met	p.L557M	ENST00000171111	NM_203500.1	557	Ctg/Atg	5/6	1	2	FACETS	0.412	0.363	0.465	0.412	0.363	0.465	SUBCLONAL	1	TRUE	1	0.294827352779022	2		879	1449	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346428	152346428	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	103	455	0	ENST00000359321.1:c.142G>T	p.Gly48Cys	p.G48C	ENST00000359321	NM_005431.1	48	Ggc/Tgc	3/3	1	2	FACETS	0.955	0.854	1	0.955	0.854	1	CLONAL	1	TRUE	1	0.294827352779022	2		455	732	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983146	201983146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	177	640	2	ENST00000359651.3:c.995C>T	p.Ala332Val	p.A332V	ENST00000359651		332	gCc/gTc	7/8	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.294827352779022	2		642	1035	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380343	14380344	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGCCGCCCC	novel	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	83	376	0	ENST00000256196.4:c.65_73dup	p.Gly22_Gly24dup	p.G22_G24dup	ENST00000256196		22	gtg/gGGGGCGGCGtg	1/6	0.294827352779022	2	FACETS	1	0.889	1	0.503	0.444	0.565	CLONAL	1	TRUE	0	0.294827352779022	2		376	560	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663328	227663328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	147	555	1	ENST00000305123.5:c.127C>T	p.Arg43Cys	p.R43C	ENST00000305123	NM_005544.2	43	Cgc/Tgc	1/2	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.294827352779022	2		556	948	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225648	26225648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770438126	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	195	877	0	ENST00000360408.1:c.266C>T	p.Ala89Val	p.A89V	ENST00000360408	NM_003532.2	89	gCg/gTg	1/1	1	2	FACETS	0.984	0.908	1	0.984	0.908	1	CLONAL	1	TRUE	1	0.294827352779022	2		877	1345	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94200986	94200986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140528613	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	81	368	0	ENST00000323929.3:c.1091G>A	p.Arg364Gln	p.R364Q	ENST00000323929	NM_005591.3	364	cGa/cAa	10/20	1	2	FACETS	0.839	0.739	0.946	0.839	0.739	0.946	CLONAL	1	TRUE	1	0.294827352779022	2		368	655	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905402	11905402	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	90	433	1	ENST00000396373.4:c.52A>G	p.Thr18Ala	p.T18A	ENST00000396373	NM_001987.4	18	Aca/Gca	2/8	1	2	FACETS	0.872	0.774	0.977	0.872	0.774	0.977	CLONAL	1	TRUE	1	0.294827352779022	2		434	700	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435991	49435992	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	171	794	0	ENST00000301067.7:c.5989_5990del	p.Ser1997LeufsTer2	p.S1997Lfs*2	ENST00000301067	NM_003482.3	1997	TCc/c	28/54	1	2	FACETS	0.895	0.821	0.972	0.895	0.821	0.972	CLONAL	1	TRUE	1	0.294827352779022	2		794	1296	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122967	2122967	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	177	729	0	ENST00000219476.3:c.2338C>A	p.Leu780Met	p.L780M	ENST00000219476	NM_000548.3	780	Ctg/Atg	21/42	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.294827352779022	2		729	1188	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279543	18279543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	107	468	0	ENST00000222254.8:c.1816G>A	p.Ala606Thr	p.A606T	ENST00000222254	NM_005027.3	606	Gca/Aca	15/16	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.294827352779022	2		468	708	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919960	50919960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1440946792	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1239	147	843	2	ENST00000440232.2:c.3047G>A	p.Arg1016His	p.R1016H	ENST00000440232	NM_002691.3	1016	cGc/cAc	24/27	1	2	FACETS	0.719	0.655	0.788	0.719	0.655	0.788	SUBCLONAL	1	TRUE	1	0.294827352779022	2		845	1386	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46602870	46602870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	211	806	2	ENST00000263734.3:c.928C>T	p.Leu310Phe	p.L310F	ENST00000263734	NM_001430.4	310	Ctc/Ttc	8/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.294827352779022	2		808	1301	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193566	99193566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	164	769	0	ENST00000074304.5:c.2761G>A	p.Ala921Thr	p.A921T	ENST00000074304	NM_001134224.1	921	Gcc/Acc	25/26	1	2	FACETS	0.94	0.861	1	0.94	0.861	1	CLONAL	1	TRUE	1	0.294827352779022	2		769	1184	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119562111	119562111	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781064367	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	97	391	0	ENST00000316626.5:c.1225G>A	p.Ala409Thr	p.A409T	ENST00000316626		409	Gca/Aca	11/12	1	2	FACETS	0.958	0.854	1	0.958	0.854	1	CLONAL	1	TRUE	1	0.294827352779022	2		391	687	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813432	32813432	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1291	195	938	1	ENST00000354258.4:c.2351del	p.Gly784GlufsTer75	p.G784Efs*75	ENST00000354258	NM_000593.5	784	gGa/ga	11/11	1	2	FACETS	0.89	0.821	0.962	0.89	0.821	0.962	CLONAL	1	TRUE	1	0.294827352779022	2		939	1486	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793471	89793471	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	58	264	2	ENST00000336032.3:c.541-1G>T		p.X181_splice	ENST00000336032	NM_006813.2	181			1	2	FACETS	0.874	0.753	1	0.874	0.753	1	CLONAL	1	TRUE	1	0.294827352779022	2		266	450	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674161	117674161	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	145	532	0	ENST00000368508.3:c.4313C>A	p.Pro1438His	p.P1438H	ENST00000368508	NM_002944.2	1438	cCt/cAt	26/43	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.294827352779022	2		532	824	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949145	44949170	+	frameshift_variant	Frame_Shift_Del	DEL	AACATTGCTTGGAATGTTGGTCCACT	AACATTGCTTGGAATGTTGGTCCACT	-	novel	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	68	512	0	ENST00000377967.4:c.3706_3731del	p.Asn1236TyrfsTer6	p.N1236Yfs*6	ENST00000377967	NM_021140.2	1236	AACATTGCTTGGAATGTTGGTCCACTt/t	25/29	1	2	FACETS	0.565	0.491	0.646	0.565	0.491	0.646	SUBCLONAL	1	TRUE	1	0.294827352779022	2		512	816	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589588	67589591	+	protein_altering_variant	In_Frame_Del	DEL	GAAT	GAAT	C	novel	NA	P-0053531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	60	292	0	ENST00000274335.5:c.1351_1354delinsC	p.Glu451_Tyr452delinsHis	p.E451_Y452delinsH	ENST00000274335		451	GAATat/Cat	10/15	1	2	FACETS	0.906	0.783	1	0.906	0.783	1	CLONAL	1	TRUE	1	0.294827352779022	2		292	449	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371708	225371708	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	88	200	1	ENST00000264414.4:c.896T>G	p.Met299Arg	p.M299R	ENST00000264414	NM_003590.4	299	aTg/aGg	7/16	1	2	FACETS	0.823	0.73	0.921	0.823	0.73	0.921	CLONAL	1	TRUE	1	0.353687659407603	2		201	605	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870935	12870945	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGAGCCAGC	GGCGAGCCAGC	-	novel	NA	P-0053554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	52	393	1	ENST00000228872.4:c.163_173del	p.Ala55GlnfsTer66	p.A55Qfs*66	ENST00000228872	NM_004064.3	54	gaGGCGAGCCAGCgc/gagc	1/3	1	2	FACETS	0.987	0.846	1	0.987	0.846	1	CLONAL	1	TRUE	1	0.353687659407603	2		394	298	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474311	40474311	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	73	468	2	ENST00000264657.5:c.2090C>T	p.Ala697Val	p.A697V	ENST00000264657	NM_139276.2	697	gCt/gTt	21/24	1	2	FACETS	0.901	0.791	1	0.901	0.791	1	CLONAL	1	TRUE	1	0.353687659407603	2		470	458	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468121	25468121	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0053554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	42	996	0	ENST00000264709.3:c.1554+1G>T		p.X518_splice	ENST00000264709	NM_175629.2	518			1	2	FACETS	0.311	0.259	0.37	0.311	0.259	0.37	SUBCLONAL	1	TRUE	1	0.353687659407603	2		996	763	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0053555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	110	290	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.491524213673345	2		290	415	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0053555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	143	420	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.491524213673345	2		420	561	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0053555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	63	265	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.697	0.605	0.794	0.697	0.605	0.794	SUBCLONAL	1	TRUE	1	0.491524213673345	2		265	368	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	71	281	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	0.775	0.68	0.875	0.775	0.68	0.875	SUBCLONAL	1	TRUE	1	0.491524213673345	2		281	373	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106093	8106093	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	116	402	0	ENST00000346208.3:c.913C>T	p.Arg305Ter	p.R305*	ENST00000346208		305	Cga/Tga	4/6	1	2	FACETS	0.99	0.897	1	0.99	0.897	1	CLONAL	1	TRUE	1	0.491524213673345	2		402	477	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0053555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	241	385	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	0.491524213673345	3	FACETS	0.92	0.864	0.977	0.92	0.864	0.977	CLONAL	2	TRUE	1	0.491524213673345	3		385	664	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554161	63554161	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	195	597	0	ENST00000307078.5:c.578C>A	p.Ser193Tyr	p.S193Y	ENST00000307078	NM_004655.3	193	tCt/tAt	2/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.491524213673345	2		597	660	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748129	41748129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776131193	NA	P-0053555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	64	253	1	ENST00000226382.2:c.640G>A	p.Gly214Ser	p.G214S	ENST00000226382	NM_003924.3	214	Ggc/Agc	3/3	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.491524213673345	2		254	206	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201786	66201786	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	119	404	0	ENST00000273854.3:c.2716G>T	p.Ala906Ser	p.A906S	ENST00000273854	NM_004439.5	906	Gct/Tct	16/18	1	2	FACETS	0.929	0.843	1	0.929	0.843	1	CLONAL	1	TRUE	1	0.491524213673345	2		404	521	SUCCESS
APC	324	MSKCC	GRCh37	5	112170762	112170765	+	frameshift_variant	Frame_Shift_Del	DEL	CTTA	CTTA	-	novel	NA	P-0053555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	176	500	0	ENST00000257430.4:c.1863_1866del	p.Tyr622GlyfsTer7	p.Y622Gfs*7	ENST00000257430	NM_000038.5	620	CTTAct/ct	15/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.491524213673345	2		500	686	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494163	140494163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	202	576	1	ENST00000288602.6:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000288602	NM_004333.4	362	cGa/cAa	8/18	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.491524213673345	2		577	769	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411246	63411246	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	310	763	1	ENST00000330258.3:c.1921C>T	p.Arg641Ter	p.R641*	ENST00000330258	NM_152424.3	641	Cga/Tga	2/2	0.491524213673345	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.491524213673345	3		764	770	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0053556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	230	470	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.473433559836776	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.531203851962513	1		470	458	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488718	212488718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267599191	NA	P-0053556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	74	564	0	ENST00000342788.4:c.2131C>T	p.Arg711Cys	p.R711C	ENST00000342788	NM_005235.2	711	Cgt/Tgt	18/28	1	2	FACETS	0.525	0.46	0.594	0.525	0.46	0.594	SUBCLONAL	1	TRUE	1	0.531203851962513	2		564	531	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846212	156846212	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	65	694	0	ENST00000524377.1:c.1653G>C	p.Glu551Asp	p.E551D	ENST00000524377	NM_002529.3	551	gaG/gaC	14/17	0.402041686061787	5	FACETS	0.47	0.406	0.539	0.157	0.135	0.18	SUBCLONAL	1	TRUE	2	0.531203851962513	5		694	936	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828330	50828330	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	66	364	0	ENST00000398568.2:c.2668G>T	p.Asp890Tyr	p.D890Y	ENST00000398568	NM_001042412.1	890	Gat/Tat	17/18	0.225756197882012	2	FACETS	0.558	0.486	0.636	0.279	0.243	0.318	INDETERMINATE	1	TRUE	0	0.531203851962513	2		364	445	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830448	72830448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	37	276	0	ENST00000268489.5:c.6133C>T	p.Pro2045Ser	p.P2045S	ENST00000268489	NM_006885.3	2045	Cca/Tca	9/10	0.225756197882012	2	FACETS	0.651	0.541	0.771	0.325	0.27	0.386	INDETERMINATE	1	TRUE	0	0.531203851962513	2		276	214	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845246	89845246	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	91	547	0	ENST00000389301.3:c.1789C>T	p.Pro597Ser	p.P597S	ENST00000389301	NM_000135.2	597	Cct/Tct	20/43	0.225756197882012	2	FACETS	0.62	0.551	0.692	0.31	0.275	0.346	INDETERMINATE	1	TRUE	0	0.531203851962513	2		547	553	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295177	15295177	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	81	830	0	ENST00000263388.2:c.2495G>A	p.Ser832Asn	p.S832N	ENST00000263388	NM_000435.2	832	aGt/aAt	16/33	0.531203851962513	1	FACETS	0.385	0.339	0.434	0.385	0.339	0.434	SUBCLONAL	1	TRUE	0	0.531203851962513	1		830	582	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200278	138200278	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1307820633	NA	P-0053556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	52	489	0	ENST00000237289.4:c.1696G>C	p.Asp566His	p.D566H	ENST00000237289	NM_001270507.1	566	Gat/Cat	7/9	0.531203851962513	1	FACETS	0.406	0.347	0.47	0.406	0.347	0.47	SUBCLONAL	1	TRUE	0	0.531203851962513	1		489	354	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141545605	141545605	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	321	877	0	ENST00000220592.5:c.2233G>T	p.Glu745Ter	p.E745*	ENST00000220592	NM_012154.3	745	Gag/Tag	17/19	0.250225147054455	3	FACETS	0.805	0.762	0.849	0.805	0.762	0.849	INDETERMINATE	2	TRUE	1	0.531203851962513	3		877	950	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507340	8507341	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	33	347	0	ENST00000356435.5:c.1637dup	p.Asn546LysfsTer3	p.N546Kfs*3	ENST00000356435		546	aac/aaAc	11/35	0.504700559833707	1	FACETS	0.318	0.26	0.383	0.318	0.26	0.383	SUBCLONAL	1	TRUE	0	0.531203851962513	1		347	287	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517972	8517972	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	48	408	0	ENST00000356435.5:c.1419C>G	p.Asp473Glu	p.D473E	ENST00000356435		473	gaC/gaG	10/35	0.504700559833707	1	FACETS	0.434	0.368	0.505	0.434	0.368	0.505	SUBCLONAL	1	TRUE	0	0.531203851962513	1		408	306	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778755	76778755	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	110	471	0	ENST00000373344.5:c.6824G>T	p.Trp2275Leu	p.W2275L	ENST00000373344	NM_000489.3	2275	tGg/tTg	31/35	0.225756197882012	2	FACETS	0.67	0.603	0.741	0.335	0.301	0.371	INDETERMINATE	1	TRUE	0	0.531203851962513	2		471	618	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937573	76937573	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	71	441	0	ENST00000373344.5:c.3175G>C	p.Glu1059Gln	p.E1059Q	ENST00000373344	NM_000489.3	1059	Gaa/Caa	9/35	0.225756197882012	2	FACETS	0.667	0.584	0.754	0.333	0.292	0.377	INDETERMINATE	1	TRUE	0	0.531203851962513	2		441	401	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030478	49030479	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1566234123	NA	P-0053557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	115	275	1	ENST00000267163.4:c.1959dup	p.Val654SerfsTer14	p.V654Sfs*14	ENST00000267163	NM_000321.2	651	-/A	19/27	0.63254826624444	1	FACETS	0.882	0.807	0.957	0.882	0.807	0.957	CLONAL	1	TRUE	0	0.63254826624444	1		276	282	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891415	76891415	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	194	149	0	ENST00000373344.5:c.4690C>A	p.Gln1564Lys	p.Q1564K	ENST00000373344	NM_000489.3	1564	Caa/Aaa	16/35	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.63254826624444	1		149	321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577091	7577109	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGGTCTCTCCCAGGACA	GCCGGTCTCTCCCAGGACA	CACCG	novel	NA	P-0053557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	325	724	0	ENST00000269305.4:c.829_847delinsCGGTG	p.Cys277ArgfsTer24	p.C277Rfs*24	ENST00000269305	NM_001126112.2	277	TGTCCTGGGAGAGACCGGCgc/CGGTGgc	8/11	0.63254826624444	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.63254826624444	1		724	694	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0053558-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	107	650	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.32	2		650	630	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100520	8100520	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053558-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	73	704	0	ENST00000346208.3:c.494C>A	p.Pro165Gln	p.P165Q	ENST00000346208		165	cCa/cAa	3/6	1	2	FACETS	0.697	0.609	0.791	0.697	0.609	0.791	SUBCLONAL	1	TRUE	1	0.32	2		704	655	SUCCESS
APC	324	MSKCC	GRCh37	5	112177865	112177865	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053558-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	53	257	0	ENST00000257430.4:c.6574A>C	p.Lys2192Gln	p.K2192Q	ENST00000257430	NM_000038.5	2192	Aaa/Caa	16/16	0.104530198412204	4	FACETS	1	0.863	1	0.505	0.431	0.585	INDETERMINATE	1	TRUE	2	0.32	4		257	433	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163299	32163299	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053558-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	41	755	0	ENST00000375023.3:c.5927C>G	p.Pro1976Arg	p.P1976R	ENST00000375023	NM_004557.3	1976	cCg/cGg	30/30	1	2	FACETS	0.279	0.232	0.333	0.279	0.232	0.333	SUBCLONAL	1	TRUE	1	0.32	2		755	917	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87356809	87356809	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053558-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	46	346	0	ENST00000277120.3:c.1162G>A	p.Ala388Thr	p.A388T	ENST00000277120		388	Gca/Aca	10/19	1	2	FACETS	0.489	0.411	0.575	0.489	0.411	0.575	SUBCLONAL	1	TRUE	1	0.32	2		346	588	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347204	70347204	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053558-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	86	454	0	ENST00000374080.3:c.2868G>T	p.Lys956Asn	p.K956N	ENST00000374080		956	aaG/aaT	21/45	1	2	FACETS	0.97	0.86	1	0.97	0.86	1	CLONAL	1	TRUE	1	0.32	2		454	554	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0053558-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	17	444	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.291	0.216	0.379	0.291	0.216	0.379	SUBCLONAL	1	TRUE	1	0.36	2		444	325	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0053558-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	58	650	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.36	2		650	319	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100520	8100520	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053558-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	156	704	0	ENST00000346208.3:c.494C>A	p.Pro165Gln	p.P165Q	ENST00000346208		165	cCa/cAa	3/6	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.36	2		704	828	SUCCESS
APC	324	MSKCC	GRCh37	5	112177865	112177865	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053558-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	32	257	0	ENST00000257430.4:c.6574A>C	p.Lys2192Gln	p.K2192Q	ENST00000257430	NM_000038.5	2192	Aaa/Caa	16/16	1	2	FACETS	0.921	0.755	1	0.921	0.755	1	CLONAL	1	TRUE	1	0.36	2		257	193	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163299	32163299	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053558-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	83	755	0	ENST00000375023.3:c.5927C>G	p.Pro1976Arg	p.P1976R	ENST00000375023	NM_004557.3	1976	cCg/cGg	30/30	0.184519503389121	0	FACETS	0.279	0.246	0.316			1	INDETERMINATE	1	TRUE	0	0.36	0		755	1056	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87356809	87356809	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053558-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	22	346	0	ENST00000277120.3:c.1162G>A	p.Ala388Thr	p.A388T	ENST00000277120		388	Gca/Aca	10/19	0.252081281328313	1	FACETS	0.491	0.382	0.616	0.491	0.382	0.616	SUBCLONAL	1	TRUE	0	0.36	1		346	204	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347204	70347204	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053558-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	123	454	0	ENST00000374080.3:c.2868G>T	p.Lys956Asn	p.K956N	ENST00000374080		956	aaG/aaT	21/45	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.36	2		454	668	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536164	106536164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	27	314	0	ENST00000369096.4:c.131C>T	p.Ala44Val	p.A44V	ENST00000369096	NM_001198.3	44	gCg/gTg	2/7	0.262080323978354	4	FACETS	0.306	0.242	0.378	0.076	0.06	0.095	INDETERMINATE	1	TRUE	0	0.512842196702314	4		314	521	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77085409	77085409	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	19	311	0	ENST00000356341.3:c.441T>G	p.Asp147Glu	p.D147E	ENST00000356341	NM_002576.4	147	gaT/gaG	5/15	0.343817605149766	3	FACETS	0.256	0.194	0.329	0.128	0.097	0.165	SUBCLONAL	1	TRUE	1	0.512842196702314	3		311	364	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56801452	56801452	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	47	368	0	ENST00000337432.4:c.956G>T	p.Arg319Leu	p.R319L	ENST00000337432	NM_058216.2	319	cGa/cTa	7/9	0.207503594960933	5	FACETS	0.568	0.479	0.667	0.189	0.159	0.223	INDETERMINATE	1	TRUE	2	0.512842196702314	5		368	571	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374948	149374948	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	258	562	0	ENST00000360632.3:c.146C>G	p.Pro49Arg	p.P49R	ENST00000360632	NM_015472.4	49	cCg/cGg	2/7	0.343817605149766	3	FACETS	0.971	0.916	1	0.971	0.916	1	CLONAL	2	TRUE	1	0.512842196702314	3		562	651	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965545	93965545	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0053559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	227	270	0	ENST00000369303.4:c.2382+1G>C		p.X794_splice	ENST00000369303	NM_004440.3	794			0.262080323978354	4	FACETS	1	0.966	1	0.771	0.729	0.813	INDETERMINATE	3	TRUE	0	0.512842196702314	4		270	434	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0053560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	54	563	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		563	321	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581268	48581268	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	26	426	0	ENST00000342988.3:c.572C>A	p.Ser191Ter	p.S191*	ENST00000342988	NM_005359.5	191	tCg/tAg	5/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		426	321	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971176	21971176	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	46	453	0	ENST00000304494.5:c.182del	p.Glu61GlyfsTer85	p.E61Gfs*85	ENST00000304494	NM_000077.4	61	gAg/gg	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		453	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576829	7576859	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATAAGAGGTCCCAAGACTTAGTACCTGAAGG	ATAAGAGGTCCCAAGACTTAGTACCTGAAGG	CTAA	novel	NA	P-0053560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	60	560	2	ENST00000269305.4:c.987_993+24delinsTTAG		p.X329_splice	ENST00000269305	NM_001126112.2	329		9/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		562	383	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0053561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	41	420	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.375317236405871	2		420	195	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0053561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	165	742	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	0.168987346114662	2	FACETS	1	0.978	1	0.585	0.538	0.633	INDETERMINATE	1	TRUE	0	0.375317236405871	2		742	752	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0053561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	109	674	1	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.375317236405871	1	FACETS	0.991	0.895	1	0.991	0.895	1	CLONAL	1	TRUE	0	0.375317236405871	1		675	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0053561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	80	762	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.168987346114662	2	FACETS	0.57	0.501	0.644	0.285	0.25	0.322	INDETERMINATE	1	TRUE	0	0.375317236405871	2		762	748	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942761	44942761	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0053561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	102	250	0	ENST00000377967.4:c.3341C>G	p.Ser1114Ter	p.S1114*	ENST00000377967	NM_021140.2	1114	tCa/tGa	23/29	1	1	FACETS	0.824	0.749	0.901	1	0.986	1	CLONAL	2	TRUE	0	0.375317236405871	1		250	268	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774771	73774771	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	52	497	0	ENST00000254810.4:c.316G>C	p.Glu106Gln	p.E106Q	ENST00000254810	NM_005324.3	106	Gaa/Caa	4/4	0.195874342491848	1	FACETS	0.347	0.295	0.404	0.347	0.295	0.404	INDETERMINATE	1	TRUE	0	0.375317236405871	1		497	649	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347299	89347299	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0053561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	156	763	0	ENST00000301030.4:c.5651C>G	p.Ser1884Ter	p.S1884*	ENST00000301030	NM_001256183.1	1884	tCa/tGa	9/13	0.310202698442627	1	FACETS	0.986	0.905	1	0.986	0.905	1	CLONAL	1	TRUE	0	0.375317236405871	1		763	685	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426694	49426694	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	98	466	0	ENST00000301067.7:c.11794C>T	p.Gln3932Ter	p.Q3932*	ENST00000301067	NM_003482.3	3932	Caa/Taa	39/54	1	2	FACETS	0.91	0.814	1	0.91	0.814	1	CLONAL	1	TRUE	1	0.375317236405871	2		466	574	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288399	15288399	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	173	675	0	ENST00000263388.2:c.4340G>C	p.Ser1447Thr	p.S1447T	ENST00000263388	NM_000435.2	1447	aGc/aCc	24/33	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.375317236405871	2		675	807	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715708	30715708	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	76	292	0	ENST00000295754.5:c.1366G>C	p.Glu456Gln	p.E456Q	ENST00000295754	NM_003242.5	456	Gaa/Caa	5/7	0.375317236405871	1	FACETS	0.951	0.84	1	0.951	0.84	1	CLONAL	1	TRUE	0	0.375317236405871	1		292	346	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504426	186504426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	98	460	0	ENST00000323963.5:c.763G>A	p.Glu255Lys	p.E255K	ENST00000323963		255	Gag/Aag	7/11	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.375317236405871	2		460	474	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636828	176636828	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	82	419	0	ENST00000439151.2:c.1428G>C	p.Leu476Phe	p.L476F	ENST00000439151	NM_022455.4	476	ttG/ttC	5/23	1	2	FACETS	0.95	0.841	1	0.95	0.841	1	CLONAL	1	TRUE	1	0.375317236405871	2		419	460	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683510	29683511	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0053561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	16	339	0	ENST00000356175.3:c.7585_7586delinsTT	p.Asp2529Phe	p.D2529F	ENST00000356175	NM_000267.3	2529	GAc/TTc	51/57	0.168987346114662	2	FACETS	0.329	0.243	0.432	0.165	0.121	0.216	INDETERMINATE	1	TRUE	0	0.375317236405871	2		339	259	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294106	1294106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756624928	NA	P-0053561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	54	1072	0	ENST00000310581.5:c.895G>A	p.Val299Met	p.V299M	ENST00000310581	NM_198253.2	299	Gtg/Atg	2/16	0.168987346114662	2	FACETS	0.311	0.265	0.363	0.156	0.132	0.182	INDETERMINATE	1	TRUE	0	0.375317236405871	2		1072	924	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0053561-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	191	420	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.658287777738545	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.658287777738545	4		420	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0053561-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	346	742	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	0.658287777738545	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.658287777738545	3		742	656	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0053561-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	218	674	1	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.657470850635347	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.658287777738545	2		675	320	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0053561-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	159	762	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.658287777738545	3	FACETS	0.966	0.888	1	0.483	0.444	0.523	CLONAL	1	TRUE	1	0.658287777738545	3		762	665	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942761	44942761	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0053561-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	244	250	0	ENST00000377967.4:c.3341C>G	p.Ser1114Ter	p.S1114*	ENST00000377967	NM_021140.2	1114	tCa/tGa	23/29	0.573880624885354	2	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.658287777738545	2		250	315	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774771	73774771	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053561-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	112	497	0	ENST00000254810.4:c.316G>C	p.Glu106Gln	p.E106Q	ENST00000254810	NM_005324.3	106	Gaa/Caa	4/4	0.658287777738545	3	FACETS	0.964	0.872	1	0.482	0.436	0.53	CLONAL	1	TRUE	1	0.658287777738545	3		497	469	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347299	89347299	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0053561-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	334	763	0	ENST00000301030.4:c.5651C>G	p.Ser1884Ter	p.S1884*	ENST00000301030	NM_001256183.1	1884	tCa/tGa	9/13	0.628674987818223	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.658287777738545	3		763	628	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426694	49426694	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053561-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	204	466	0	ENST00000301067.7:c.11794C>T	p.Gln3932Ter	p.Q3932*	ENST00000301067	NM_003482.3	3932	Caa/Taa	39/54	0.540332318821443	4	FACETS	0.946	0.885	1	0.946	0.885	1	CLONAL	2	TRUE	2	0.658287777738545	4		466	543	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543648	9543648	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053561-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	83	438	0	ENST00000353224.5:c.1506C>A	p.His502Gln	p.H502Q	ENST00000353224	NM_177990.2	502	caC/caA	6/10	0.601879316196115	4	FACETS	0.899	0.797	1	0.45	0.398	0.504	CLONAL	1	TRUE	2	0.658287777738545	4		438	465	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288399	15288399	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053561-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	250	675	0	ENST00000263388.2:c.4340G>C	p.Ser1447Thr	p.S1447T	ENST00000263388	NM_000435.2	1447	aGc/aCc	24/33	0.324019714854697	5	FACETS	1	0.958	1	0.683	0.641	0.725	INDETERMINATE	2	TRUE	2	0.658287777738545	5		675	737	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715708	30715708	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053561-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	146	292	0	ENST00000295754.5:c.1366G>C	p.Glu456Gln	p.E456Q	ENST00000295754	NM_003242.5	456	Gaa/Caa	5/7	0.655158039190265	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.658287777738545	2		292	209	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504426	186504426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053561-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	187	460	0	ENST00000323963.5:c.763G>A	p.Glu255Lys	p.E255K	ENST00000323963		255	Gag/Aag	7/11	0.658287777738545	4	FACETS	0.863	0.803	0.924	0.863	0.803	0.924	CLONAL	2	TRUE	2	0.658287777738545	4		460	546	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636828	176636828	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053561-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	226	419	0	ENST00000439151.2:c.1428G>C	p.Leu476Phe	p.L476F	ENST00000439151	NM_022455.4	476	ttG/ttC	5/23	0.540332318821443	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.658287777738545	4		419	523	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253388	226253389	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0053561-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	58	209	1	ENST00000366813.1:c.160_161delinsAA	p.Arg54Asn	p.R54N	ENST00000366813		54	CGt/AAt	2/3	0.627571425499724	5	FACETS	1	0.899	1	0.35	0.302	0.401	CLONAL	1	TRUE	2	0.658287777738545	5		210	334	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066909	30066909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053561-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	115	503	0	ENST00000331968.5:c.2222G>A	p.Arg741Lys	p.R741K	ENST00000331968	NM_002742.2	741	aGg/aAg	16/18	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.658287777738545	2		503	316	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0053581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	109	302	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.532917598788928	2		302	363	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs17849781	NA	P-0053582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	445	834	0	ENST00000269305.4:c.832C>G	p.Pro278Ala	p.P278A	ENST00000269305	NM_001126112.2	278	Cct/Gct	8/11	0.440494297160601	2	FACETS	0.958	0.917	0.998	0.958	0.917	0.998	CLONAL	2	TRUE	0	0.46234232821552	2		834	1005	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861939	57861939	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	53	722	0	ENST00000228682.2:c.1240C>A	p.Pro414Thr	p.P414T	ENST00000228682	NM_005269.2	414	Ccc/Acc	10/12	0.331818529464705	2	FACETS	0.251	0.213	0.293	0.126	0.106	0.147	SUBCLONAL	1	TRUE	0	0.46234232821552	2		722	912	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134640	41134640	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	136	501	0	ENST00000379561.5:c.988C>A	p.Pro330Thr	p.P330T	ENST00000379561	NM_002015.3	330	Ccc/Acc	2/3	0.461246164843675	3	FACETS	0.974	0.886	1	0.487	0.443	0.533	CLONAL	1	TRUE	1	0.46234232821552	3		501	744	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440653	56440653	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0053582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	458	822	0	ENST00000407977.2:c.565A>T	p.Lys189Ter	p.K189*	ENST00000407977		189	Aag/Tag	5/10	0.440494297160601	2	FACETS	0.999	0.958	1	0.999	0.958	1	CLONAL	2	TRUE	0	0.46234232821552	2		822	992	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288564	198288564	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	140	530	0	ENST00000335508.6:c.163G>C	p.Val55Leu	p.V55L	ENST00000335508	NM_012433.2	55	Gtg/Ctg	2/25	0.461246164843675	3	FACETS	0.839	0.764	0.918	0.419	0.382	0.459	CLONAL	1	TRUE	1	0.46234232821552	3		530	889	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144567	55144567	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	32	519	0	ENST00000257290.5:c.2041G>T	p.Asp681Tyr	p.D681Y	ENST00000257290	NM_006206.4	681	Gat/Tat	15/23	NA	2	FACETS	0.226	0.183	0.275			1	INDETERMINATE	1	TRUE	NA	0.46234232821552	2		519	612	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	33	386	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.735	0.598	0.891	0.735	0.598	0.891	SUBCLONAL	1	TRUE	1	0.17	2		386	528	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0053583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	64	547	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.88	0.76	1	0.88	0.76	1	CLONAL	1	TRUE	1	0.17	2		547	856	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0053583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	47	533	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.17	2		533	510	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0053583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	62	494	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.982	0.847	1	0.982	0.847	1	CLONAL	1	TRUE	1	0.17	2		494	743	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0053584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	23	469	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.483	0.376	0.607	0.483	0.376	0.607	SUBCLONAL	1	FALSE	1	0.223077083504214	2		470	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0053584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	145	895	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	1	0.223077083504214	2		895	1238	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266605	198266605	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs754077338	NA	P-0053584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	21	354	3	ENST00000335508.6:c.2231C>A	p.Ala744Asp	p.A744D	ENST00000335508	NM_012433.2	744	gCt/gAt	16/25	1	2	FACETS	0.59	0.454	0.749	0.59	0.454	0.749	SUBCLONAL	1	FALSE	1	0.223077083504214	2		357	319	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435470	110435470	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	102	584	0	ENST00000375856.3:c.2931del	p.Tyr978ThrfsTer2	p.Y978Tfs*2	ENST00000375856	NM_003749.2	977	gaC/ga	1/2	1	2	FACETS	0.94	0.839	1	0.94	0.839	1	CLONAL	1	FALSE	1	0.223077083504214	2		584	973	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37876050	37876050	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5258	537	757	0	ENST00000269571.5:c.1909C>G	p.Leu637Val	p.L637V	ENST00000269571		637	Ctg/Gtg	16/27	0.223077083504214	40	FACETS	1	0.986	1			1	CLONAL	4	FALSE	NA	0.223077083504214	40		757	5795	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319860	8319860	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	54	416	0	ENST00000356435.5:c.5641A>C	p.Thr1881Pro	p.T1881P	ENST00000356435		1881	Aca/Cca	34/35	1	2	FACETS	0.848	0.724	0.984	0.848	0.724	0.984	CLONAL	1	FALSE	1	0.223077083504214	2		416	571	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	61	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.983	0.848	1	0.983	0.848	1	CLONAL	1	FALSE	1	0.210281426512098	2		276	590	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0053586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	10	420	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.0990972975889766	3	FACETS	0.4	0.27	0.563	0.2	0.135	0.282	INDETERMINATE	1	FALSE	1	0.210281426512098	3		420	263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764146326	NA	P-0053586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	99	1085	2	ENST00000269305.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000269305	NM_001126112.2	281	Gac/Aac	8/11	0.0990972975889766	3	FACETS	0.936	0.833	1	0.468	0.416	0.523	INDETERMINATE	1	FALSE	1	0.210281426512098	3		1087	1112	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699360	47699360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	35	695	0	ENST00000347630.2:c.148G>A	p.Glu50Lys	p.E50K	ENST00000347630	NM_001007230.1	50	Gaa/Aaa	4/11	0.0990972975889766	3	FACETS	0.889	0.729	1	0.444	0.364	0.534	INDETERMINATE	1	FALSE	1	0.210281426512098	3		695	414	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs121913468	NA	P-0053586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	63	690	0	ENST00000269571.5:c.2305G>C	p.Asp769His	p.D769H	ENST00000269571		769	Gac/Cac	19/27	0.0990972975889766	3	FACETS	0.849	0.733	0.975	0.424	0.366	0.488	INDETERMINATE	1	FALSE	1	0.210281426512098	3		690	780	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040979	42040979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781312897	NA	P-0053586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	62	953	1	ENST00000219905.7:c.5357G>A	p.Arg1786Gln	p.R1786Q	ENST00000219905	NM_001164273.1	1786	cGg/cAg	16/24	0.21033845996759	3	FACETS	0.647	0.557	0.746	0.324	0.278	0.373	SUBCLONAL	1	FALSE	1	0.210281426512098	3		954	1007	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984409	201984409	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	80	968	0	ENST00000359651.3:c.1075del	p.Ser359AlafsTer88	p.S359Afs*88	ENST00000359651		358	tcA/tc	8/8	1	2	FACETS	0.762	0.669	0.863	0.762	0.669	0.863	SUBCLONAL	1	FALSE	1	0.210281426512098	2		968	998	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358414	91358414	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	58	937	0	ENST00000355112.3:c.4159C>G	p.Gln1387Glu	p.Q1387E	ENST00000355112	NM_000057.2	1387	Caa/Gaa	22/22	0.21033845996759	3	FACETS	0.626	0.536	0.725			1	SUBCLONAL	1	FALSE	NA	0.210281426512098	3		937	974	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40490801	40490801	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555568530	NA	P-0053586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	37	645	0	ENST00000264657.5:c.498G>C	p.Glu166Asp	p.E166D	ENST00000264657	NM_139276.2	166	gaG/gaC	6/24	0.0990972975889766	3	FACETS	0.607	0.499	0.728	0.303	0.249	0.364	INDETERMINATE	1	FALSE	1	0.210281426512098	3		645	641	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31025054	31025054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	78	695	1	ENST00000375687.4:c.4539G>A	p.Met1513Ile	p.M1513I	ENST00000375687	NM_015338.5	1513	atG/atA	13/13	1	2	FACETS	0.904	0.793	1	0.904	0.793	1	CLONAL	1	FALSE	1	0.210281426512098	2		696	821	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890230	72890230	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	36	739	1	ENST00000325599.8:c.452G>T	p.Gly151Val	p.G151V	ENST00000325599	NM_018130.2	151	gGa/gTa	4/11	0.0990972975889766	3	FACETS	0.604	0.495	0.726	0.302	0.247	0.363	INDETERMINATE	1	FALSE	1	0.210281426512098	3		740	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577093	7577093	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882008	NA	P-0053587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	359	1006	0	ENST00000269305.4:c.845G>C	p.Arg282Pro	p.R282P	ENST00000269305	NM_001126112.2	282	cGg/cCg	8/11	0.291403650419125	3	FACETS	0.925	0.879	0.972	0.925	0.879	0.972	CLONAL	3	TRUE	0	0.29478753266308	3		1006	1007	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339267	70339267	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	66	790	0	ENST00000374080.3:c.144G>C	p.Gln48His	p.Q48H	ENST00000374080		48	caG/caC	2/45	0.29478753266308	3	FACETS	0.582	0.504	0.667	0.291	0.252	0.334	SUBCLONAL	1	TRUE	1	0.29478753266308	3		790	883	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	89	386	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.109767088496218	3	FACETS	0.882	0.781	0.989	0.882	0.781	0.989	CLONAL	2	TRUE	1	0.140123130337704	3		386	771	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256298	16256298	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	107	728	0	ENST00000375759.3:c.3563A>T	p.Lys1188Met	p.K1188M	ENST00000375759	NM_015001.2	1188	aAg/aTg	11/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.140123130337704	2		728	1026	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070823	30070823	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0053588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	64	574	0	ENST00000338641.4:c.1341-2A>G		p.X447_splice	ENST00000338641	NM_000268.3	447			0.140123130337704	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.140123130337704	1		574	646	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0053589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	102	563	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.152657310891508	3	FACETS	0.906	0.813	1	1	0.978	1	CLONAL	3	TRUE	1	0.152657310891508	3		563	529	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974715	21974732	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCCCCCGCCTCCA	GCAGCGCCCCCGCCTCCA	-	novel	NA	P-0053589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	38	486	0	ENST00000304494.5:c.95_112del	p.Leu32_Leu37del	p.L32_L37del	ENST00000304494	NM_000077.4	32	cTGGAGGCGGGGGCGCTGCcc/ccc	1/3	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.152657310891508	2		486	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	91	1000	0	ENST00000269305.4:c.470T>G	p.Val157Gly	p.V157G	ENST00000269305	NM_001126112.2	157	gTc/gGc	5/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.152657310891508	2		1000	808	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46543188	46543188	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1341157816	NA	P-0053589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	21	544	0	ENST00000262741.5:c.313C>T	p.Arg105Trp	p.R105W	ENST00000262741	NM_003629.3	105	Cgg/Tgg	3/10	1	2	FACETS	0.66	0.507	0.839	0.66	0.507	0.839	SUBCLONAL	1	TRUE	1	0.152657310891508	2		544	417	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61727010	61727010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	28	577	0	ENST00000401558.2:c.428C>T	p.Pro143Leu	p.P143L	ENST00000401558	NM_003400.3	143	cCc/cTc	7/25	1	2	FACETS	0.776	0.619	0.955	0.776	0.619	0.955	CLONAL	1	TRUE	1	0.152657310891508	2		577	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0053590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	249	608	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.588481581822095	1	FACETS	0.995	0.938	1	0.995	0.938	1	CLONAL	1	TRUE	0	0.588481581822095	1		608	600	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720803	89720805	+	inframe_deletion	In_Frame_Del	DEL	TAC	TAC	-	novel	NA	P-0053590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	73	391	0	ENST00000371953.3:c.955_957del	p.Thr319del	p.T319del	ENST00000371953	NM_000314.4	318	ctTACt/ctt	8/9	1	2	FACETS	0.743	0.655	0.836	0.743	0.655	0.836	SUBCLONAL	1	TRUE	1	0.588481581822095	2		391	334	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741353	17741353	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	284	914	0	ENST00000250003.3:c.25del	p.Arg9AlafsTer3	p.R9Afs*3	ENST00000250003	NM_002478.4	8	ctC/ct	1/3	1	2	FACETS	0.897	0.843	0.952	0.897	0.843	0.952	CLONAL	1	TRUE	1	0.588481581822095	2		914	1076	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008296	29008296	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	157	452	0	ENST00000282397.4:c.575T>C	p.Phe192Ser	p.F192S	ENST00000282397	NM_002019.4	192	tTc/tCc	5/30	0.588481581822095	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.588481581822095	1		452	352	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941739	48941739	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	119	250	0	ENST00000267163.4:c.1049G>C	p.Ser350Thr	p.S350T	ENST00000267163	NM_000321.2	350	aGt/aCt	10/27	0.588481581822095	1	FACETS	0.961	0.881	1	0.961	0.881	1	CLONAL	1	TRUE	0	0.588481581822095	1		250	297	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127670	2127671	+	missense_variant	Missense_Mutation	DNP	CT	CT	TC	novel	NA	P-0053590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	281	885	0	ENST00000219476.3:c.2909_2910delinsTC	p.Ser970Phe	p.S970F	ENST00000219476	NM_000548.3	970	tCT/tTC	26/42	1	2	FACETS	0.917	0.862	0.973	0.917	0.862	0.973	CLONAL	1	TRUE	1	0.588481581822095	2		885	1042	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052981	180052981	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	372	1103	0	ENST00000261937.6:c.1309C>A	p.Arg437Ser	p.R437S	ENST00000261937	NM_182925.4	437	Cgt/Agt	10/30	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.588481581822095	2		1103	1244	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97887444	97887444	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	227	735	0	ENST00000289081.3:c.920G>C	p.Gly307Ala	p.G307A	ENST00000289081	NM_000136.2	307	gGg/gCg	10/15	1	2	FACETS	0.897	0.837	0.959	0.897	0.837	0.959	CLONAL	1	TRUE	1	0.588481581822095	2		735	860	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843487	3843490	+	frameshift_variant	Frame_Shift_Del	DEL	TTGC	TTGC	AA	novel	NA	P-0053590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	238	682	0	ENST00000262367.5:c.1113_1116delinsTT	p.Glu371AspfsTer55	p.E371Dfs*55	ENST00000262367	NM_004380.2	371	gaGCAA/gaTT	4/31	1	2	FACETS	0.877	0.82	0.936	0.877	0.82	0.936	CLONAL	1	TRUE	1	0.588481581822095	2		682	922	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	157	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.60269730632677	2		276	500	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653808	89653808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	274	467	0	ENST00000371953.3:c.106G>A	p.Gly36Arg	p.G36R	ENST00000371953	NM_000314.4	36	Gga/Aga	2/9	0.60269730632677	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.60269730632677	1		467	606	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147534	47147534	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	252	457	1	ENST00000409792.3:c.4792C>T	p.Arg1598Ter	p.R1598*	ENST00000409792	NM_014159.6	1598	Cga/Tga	6/21	1	2	FACETS	0.974	0.913	1	0.974	0.913	1	CLONAL	1	TRUE	1	0.60269730632677	2		458	859	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138383915	138383915	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	325	626	0	ENST00000289153.2:c.2635G>C	p.Asp879His	p.D879H	ENST00000289153	NM_006219.2	879	Gat/Cat	18/22	1	2	FACETS	0.989	0.935	1	0.989	0.935	1	CLONAL	1	TRUE	1	0.60269730632677	2		626	1090	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66777357	66777358	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0053591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	336	815	0	ENST00000307102.5:c.725_726del	p.Val242AlafsTer43	p.V242Afs*43	ENST00000307102	NM_002755.3	241	tcTGtg/tctg	7/11	0.219691786684856	1	FACETS	0.689	0.652	0.727	0.689	0.652	0.727	INDETERMINATE	1	TRUE	0	0.60269730632677	1		815	1130	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578502	7578502	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	484	1036	0	ENST00000269305.4:c.428T>A	p.Val143Glu	p.V143E	ENST00000269305	NM_001126112.2	143	gTg/gAg	5/11	0.60269730632677	1	FACETS	0.987	0.947	1	0.987	0.947	1	CLONAL	1	TRUE	0	0.60269730632677	1		1036	1137	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504333	8504333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754609275	NA	P-0053592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	195	610	0	ENST00000356435.5:c.1750C>T	p.Arg584Cys	p.R584C	ENST00000356435		584	Cgt/Tgt	12/35	0.505458410147569	1	FACETS	0.936	0.871	1	0.936	0.871	1	CLONAL	1	TRUE	0	0.505458410147569	1		610	616	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0053593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	347	866	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.298844923444592	2	FACETS	0.925	0.877	0.974	0.925	0.877	0.974	CLONAL	2	TRUE	0	0.345026646632684	2		867	1087	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	344	386	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.345026646632684	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	TRUE	1	0.345026646632684	4		386	870	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0053593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	288	547	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.345026646632684	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.345026646632684	2		547	762	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176662842	176662842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779028625	NA	P-0053593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	201	490	1	ENST00000439151.2:c.3817C>T	p.Arg1273Cys	p.R1273C	ENST00000439151	NM_022455.4	1273	Cgc/Tgc	6/23	0.345026646632684	3	FACETS	0.986	0.917	1	0.986	0.917	1	CLONAL	2	TRUE	1	0.345026646632684	3		491	693	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031883	26031884	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs758780418	NA	P-0053593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	84	407	0	ENST00000244661.2:c.405_406del	p.Arg135SerfsTer12	p.R135Sfs*12	ENST00000244661	NM_003537.3	135	agAGcg/agcg	1/1	0.345026646632684	3	FACETS	0.79	0.697	0.889	0.395	0.348	0.445	SUBCLONAL	1	TRUE	1	0.345026646632684	3		407	723	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437548	52437575	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCTGTCATCCTCTCCAAAAAGCACCT	AGGCTGTCATCCTCTCCAAAAAGCACCT	-	novel	NA	P-0053594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	29	833	0	ENST00000460680.1:c.1586_1613del	p.Lys529SerfsTer33	p.K529Sfs*33	ENST00000460680	NM_004656.3	529	aAGGTGCTTTTTGGAGAGGATGACAGCCTg/ag	13/17	1	2	FACETS	1	0.824	1	1	0.824	1	CLONAL	1	TRUE	1	0.12	2		833	469	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	69	276	0				ENST00000310581	NM_198253.2	-/1132			0.192014662613053	1	FACETS	1	0.906	1	1	0.982	1	CLONAL	2	TRUE	0	0.192014662613053	1		276	313	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0053595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	50	465	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.111497801082979	3	FACETS	0.844	0.72	0.98	0.844	0.72	0.98	INDETERMINATE	2	TRUE	1	0.192014662613053	3		465	338	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0053595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	92	948	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.192014662613053	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.192014662613053	1		948	628	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0053596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	100	470	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.167700209475455	2	FACETS	1	0.975	1	0.653	0.585	0.726	CLONAL	1	TRUE	0	0.250046363300826	2		470	612	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038902	12038902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159945	NA	P-0053596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	105	496	1	ENST00000396373.4:c.1195C>T	p.Arg399Cys	p.R399C	ENST00000396373	NM_001987.4	399	Cgc/Tgc	7/8	0.167700209475455	2	FACETS	1	0.978	1	0.673	0.604	0.746	CLONAL	1	TRUE	0	0.250046363300826	2		497	624	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435068	18435068	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	80	403	0	ENST00000266497.5:c.53A>T	p.Gln18Leu	p.Q18L	ENST00000266497		18	cAg/cTg	1/31	0.167700209475455	2	FACETS	1	0.96	1	0.606	0.534	0.682	CLONAL	1	TRUE	0	0.250046363300826	2		403	528	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000306	42000306	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	39	557	0	ENST00000219905.7:c.2327del	p.Gly776AspfsTer41	p.G776Dfs*41	ENST00000219905	NM_001164273.1	775	gcG/gc	7/24	0.163695596266943	1	FACETS	0.481	0.398	0.574	0.481	0.398	0.574	SUBCLONAL	1	TRUE	0	0.250046363300826	1		557	567	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578549	7578565	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGAGTACTGTAGGAAGA	GGAGTACTGTAGGAAGA	-	novel	NA	P-0053596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	120	1151	2	ENST00000269305.4:c.376-11_381del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	1	2	FACETS	0.848	0.764	0.937	0.848	0.764	0.937	CLONAL	1	TRUE	1	0.250046363300826	2		1153	1132	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791554	42791554	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	77	916	0	ENST00000575354.2:c.535A>C	p.Lys179Gln	p.K179Q	ENST00000575354	NM_015125.3	179	Aag/Cag	4/20	1	2	FACETS	0.582	0.509	0.661	0.582	0.509	0.661	SUBCLONAL	1	TRUE	1	0.250046363300826	2		916	1058	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872807	136872807	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	73	649	0	ENST00000241393.3:c.691G>T	p.Gly231Cys	p.G231C	ENST00000241393	NM_003467.2	231	Ggc/Tgc	2/2	1	2	FACETS	0.912	0.798	1	0.912	0.798	1	CLONAL	1	TRUE	1	0.250046363300826	2		649	640	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884416	151884416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1405466580	NA	P-0053596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	33	438	0	ENST00000262189.6:c.4939G>A	p.Glu1647Lys	p.E1647K	ENST00000262189	NM_170606.2	1647	Gaa/Aaa	33/59	1	2	FACETS	0.471	0.382	0.57	0.471	0.382	0.57	SUBCLONAL	1	TRUE	1	0.250046363300826	2		438	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0053597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	270	651	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.408251771230718	2	FACETS	0.912	0.86	0.965	0.912	0.86	0.965	CLONAL	2	TRUE	0	0.408251771230718	2		651	725	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799994	45800067	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACAATCCCTTCCCAGCCTGAATCTGCCTTTCATGGCCAATGAGCCTTGGGCCACAACCTAGTTCCTTACCATCA	ACAATCCCTTCCCAGCCTGAATCTGCCTTTCATGGCCAATGAGCCTTGGGCCACAACCTAGTTCCTTACCATCA	-	novel	NA	P-0053597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	117	324	0	ENST00000450313.1:c.153_157+69del		p.X51_splice	ENST00000450313	NM_012222.2	51		2/16	0.388804746273402	3	FACETS	1	0.984	1	0.736	0.667	0.807	CLONAL	1	TRUE	1	0.408251771230718	3		324	469	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976572	7976572	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	125	806	0	ENST00000319144.4:c.1820A>T	p.Lys607Met	p.K607M	ENST00000319144	NM_001139.2	607	aAg/aTg	14/15	0.408251771230718	2	FACETS	0.686	0.62	0.755	0.343	0.31	0.378	SUBCLONAL	1	TRUE	0	0.408251771230718	2		806	893	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15967440	15967445	+	inframe_deletion	In_Frame_Del	DEL	CTCCCG	CTCCCG	-	rs1289562742	NA	P-0053597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	145	663	0	ENST00000268712.3:c.5158_5163del	p.Arg1720_Glu1721del	p.R1720_E1721del	ENST00000268712	NM_006311.3	1720	CGGGAG/-	35/46	0.408251771230718	2	FACETS	0.91	0.831	0.992	0.455	0.415	0.496	CLONAL	1	TRUE	0	0.408251771230718	2		663	781	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391492	84391492	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	217	371	0	ENST00000321945.7:c.340G>C	p.Glu114Gln	p.E114Q	ENST00000321945	NM_139076.2	114	Gag/Cag	5/9	0.408251771230718	2	FACETS	0.836	0.789	0.883	1	0.99	1	CLONAL	3	TRUE	0	0.408251771230718	2		371	424	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859820	151859821	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCATC	novel	NA	P-0053597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	77	477	0	ENST00000262189.6:c.10837_10841dup	p.Asp3614GlufsTer18	p.D3614Efs*18	ENST00000262189	NM_170606.2	3614	gat/gaGATGAt	43/59	0.408251771230718	4	FACETS	0.83	0.729	0.939	0.277	0.243	0.313	CLONAL	1	TRUE	1	0.408251771230718	4		477	640	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884505	151884505	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	104	478	0	ENST00000262189.6:c.4850C>A	p.Ser1617Ter	p.S1617*	ENST00000262189	NM_170606.2	1617	tCa/tAa	33/59	0.408251771230718	4	FACETS	1	0.914	1	0.341	0.305	0.379	CLONAL	1	TRUE	1	0.408251771230718	4		478	702	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	30	386	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.34	0.273	0.416	0.34	0.273	0.416	SUBCLONAL	1	TRUE	1	0.336222153063298	2		386	525	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0053598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	34	674	1	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	0.507	0.414	0.611	0.507	0.414	0.611	SUBCLONAL	1	TRUE	1	0.336222153063298	2		675	399	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178655	108178656	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587781730	NA	P-0053598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	20	381	0	ENST00000278616.4:c.5712dup	p.Ser1905IlefsTer25	p.S1905Ifs*25	ENST00000278616	NM_000051.3	1902	-/A	38/63	1	2	FACETS	0.417	0.319	0.532	0.417	0.319	0.532	SUBCLONAL	1	TRUE	1	0.336222153063298	2		381	285	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0053600-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	152	465	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.818	0.754	0.884	0.818	0.754	0.884	CLONAL	1	TRUE	1	0.783786479201639	2		465	474	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032866	30032866	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0053600-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	28	348	0	ENST00000338641.4:c.240+1G>A		p.X80_splice	ENST00000338641	NM_000268.3	80			0.783786479201639	1	FACETS	0.131	0.105	0.162	0.131	0.105	0.162	SUBCLONAL	1	TRUE	0	0.783786479201639	1		348	331	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038226	30038226	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053600-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	29	456	0	ENST00000338641.4:c.399C>G	p.Cys133Trp	p.C133W	ENST00000338641	NM_000268.3	133	tgC/tgG	4/16	0.783786479201639	1	FACETS	0.104	0.083	0.128	0.104	0.083	0.128	SUBCLONAL	1	TRUE	0	0.783786479201639	1		456	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0053613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	98	586	1	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	1	2	FACETS	0.841	0.75	0.938	0.841	0.75	0.938	CLONAL	1	TRUE	1	0.288795855746084	2		587	807	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089640	27089640	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	135	832	0	ENST00000324856.7:c.2596C>T	p.Arg866Trp	p.R866W	ENST00000324856	NM_006015.4	866	Cgg/Tgg	8/20	0.288795855746084	1	FACETS	0.82	0.745	0.9	0.82	0.745	0.9	CLONAL	1	TRUE	0	0.288795855746084	1		832	975	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375526	40375526	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	48	696	0	ENST00000293328.3:c.424C>G	p.Leu142Val	p.L142V	ENST00000293328	NM_012448.3	142	Ctc/Gtc	5/19	1	2	FACETS	0.367	0.309	0.432	0.367	0.309	0.432	SUBCLONAL	1	TRUE	1	0.288795855746084	2		696	905	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385159	41385159	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	57	855	2	ENST00000373198.4:c.802G>T	p.Val268Leu	p.V268L	ENST00000373198	NM_133170.3	268	Gtg/Ttg	6/32	NA	2	FACETS	0.354	0.302	0.411			1	INDETERMINATE	1	TRUE	NA	0.288795855746084	2		857	1115	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419935	41419935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1232162514	NA	P-0053613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	110	735	0	ENST00000373198.4:c.386G>A	p.Gly129Asp	p.G129D	ENST00000373198	NM_133170.3	129	gGc/gAc	3/32	NA	2	FACETS	0.766	0.687	0.85			1	INDETERMINATE	1	TRUE	NA	0.288795855746084	2		735	995	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003228	143003228	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs148929063	NA	P-0053613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	87	464	0	ENST00000262992.4:c.2598G>T	p.Gln866His	p.Q866H	ENST00000262992	NM_001101669.1	866	caG/caT	23/24	1	2	FACETS	0.955	0.846	1	0.955	0.846	1	CLONAL	1	TRUE	1	0.288795855746084	2		464	631	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038867	47038868	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	63	459	0	ENST00000377604.3:c.874_875insT	p.Glu292ValfsTer9	p.E292Vfs*9	ENST00000377604	NM_001204468.1	292	gag/gTag	9/24	1	1	FACETS	0.67	0.58	0.768	0.67	0.58	0.768	SUBCLONAL	1	TRUE	0	0.288795855746084	1		459	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0053615-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	132	678	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.190104625439265	2	FACETS	1	0.985	1	0.735	0.668	0.806	CLONAL	1	TRUE	0	0.235106625793262	2		678	764	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562482	21562483	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGGCG	rs550642106	NA	P-0053615-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	9	101	0	ENST00000382592.4:c.1431_1436dup	p.Pro479_Ala480dup	p.P479_A480dup	ENST00000382592	NM_014572.2	479	ccg/ccCGCCCCg	4/8	0.190104625439265	2	FACETS	0.709	0.472	1	0.354	0.236	0.503	CLONAL	1	TRUE	0	0.235106625793262	2		101	108	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249013	55249014	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACCCCC	novel	NA	P-0053615-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	218	736	0	ENST00000275493.2:c.2314_2319dup	p.Pro772_His773dup	p.P772_H773dup	ENST00000275493	NM_005228.3	772	aac/aACCCCCac	20/28	0.235106625793262	4	FACETS	0.896	0.835	0.959	0.896	0.835	0.959	CLONAL	3	TRUE	1	0.235106625793262	4		736	852	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641126	3641126	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053615-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	68	977	0	ENST00000294008.3:c.2513A>T	p.Asp838Val	p.D838V	ENST00000294008	NM_032444.2	838	gAc/gTc	12/15	1	2	FACETS	0.518	0.449	0.594	0.518	0.449	0.594	SUBCLONAL	1	TRUE	1	0.235106625793262	2		977	1116	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013734	12013734	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053615-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	40	215	0	ENST00000353533.5:c.676A>T	p.Ile226Phe	p.I226F	ENST00000353533	NM_003010.3	226	Att/Ttt	6/11	0.190104625439265	2	FACETS	0.629	0.522	0.748	0.314	0.261	0.374	SUBCLONAL	1	TRUE	0	0.235106625793262	2		215	541	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538907	23538907	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1462337389	NA	P-0053615-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	54	673	0	ENST00000380871.4:c.532A>G	p.Lys178Glu	p.K178E	ENST00000380871	NM_006167.3	178	Aag/Gag	2/2	0.235106625793262	1	FACETS	0.656	0.56	0.761	0.656	0.56	0.761	SUBCLONAL	1	TRUE	0	0.235106625793262	1		673	618	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0053618-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	119	470	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.493550820018164	2	FACETS	0.908	0.841	0.973	0.908	0.841	0.973	CLONAL	2	TRUE	0	0.604224203305422	2		470	217	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89791020	89791020	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053618-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	14	146	0	ENST00000336032.3:c.407G>A	p.Gly136Glu	p.G136E	ENST00000336032	NM_006813.2	136	gGa/gAa	1/2	0.604224203305422	1	FACETS	0.173	0.125	0.231	0.173	0.125	0.231	SUBCLONAL	1	TRUE	0	0.604224203305422	1		146	187	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361157	66361157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053618-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	26	360	0	ENST00000273854.3:c.1015G>A	p.Glu339Lys	p.E339K	ENST00000273854	NM_004439.5	339	Gaa/Aaa	4/18	0.273626073357944	1	FACETS	0.328	0.262	0.403	0.328	0.262	0.403	INDETERMINATE	1	TRUE	0	0.604224203305422	1		360	183	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850857	128850857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053618-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	52	494	0	ENST00000249373.3:c.1704G>A	p.Met568Ile	p.M568I	ENST00000249373	NM_005631.4	568	atG/atA	10/12	0.604224203305422	3	FACETS	0.239	0.203	0.28	0.12	0.101	0.14	SUBCLONAL	1	TRUE	1	0.604224203305422	3		494	937	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574027	7574027	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882028	NA	P-0053618-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	214	464	0	ENST00000269305.4:c.1000G>T	p.Gly334Trp	p.G334W	ENST00000269305	NM_001126112.2	334	Ggg/Tgg	10/11	0.37871805143789	2	FACETS	1	0.988	1	0.619	0.58	0.659	CLONAL	1	TRUE	0	0.604224203305422	2		464	572	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640737	3640737	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs777514343	NA	P-0053618-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	52	407	0	ENST00000294008.3:c.2902G>C	p.Glu968Gln	p.E968Q	ENST00000294008	NM_032444.2	968	Gag/Cag	12/15	0.202274393472402	5	FACETS	0.49	0.416	0.571	0.163	0.138	0.191	INDETERMINATE	1	TRUE	2	0.604224203305422	5		407	670	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711918	89711918	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053618-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	106	628	0	ENST00000371953.3:c.536G>C	p.Ser179Thr	p.S179T	ENST00000371953	NM_000314.4	179	aGc/aCc	6/9	0.496466845156215	3	FACETS	0.767	0.697	0.838	0.767	0.697	0.838	SUBCLONAL	2	TRUE	1	0.604224203305422	3		628	298	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572625	64572625	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs757179911	NA	P-0053618-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	152	359	0	ENST00000312049.6:c.1231G>T	p.Ala411Ser	p.A411S	ENST00000312049	NM_130799.2	411	Gcc/Tcc	9/10	0.223543437386948	4	FACETS	1	0.945	1	0.521	0.477	0.567	INDETERMINATE	1	TRUE	2	0.604224203305422	4		359	775	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245514	133245514	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053618-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	40	324	0	ENST00000320574.5:c.1806G>C	p.Glu602Asp	p.E602D	ENST00000320574	NM_006231.2	602	gaG/gaC	17/49	0.604224203305422	1	FACETS	0.227	0.189	0.27	0.227	0.189	0.27	SUBCLONAL	1	TRUE	0	0.604224203305422	1		324	407	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023009	33023009	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053618-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	32	363	0	ENST00000300177.4:c.118C>T	p.Gln40Ter	p.Q40*	ENST00000300177	NM_001191322.1	40	Cag/Tag	2/2	0.516254628938668	1	FACETS	0.173	0.14	0.21	0.173	0.14	0.21	SUBCLONAL	1	TRUE	0	0.604224203305422	1		363	428	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005538	42005538	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053618-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	120	540	0	ENST00000219905.7:c.3274G>T	p.Gly1092Ter	p.G1092*	ENST00000219905	NM_001164273.1	1092	Gga/Tga	9/24	0.516254628938668	1	FACETS	0.82	0.75	0.892	0.82	0.75	0.892	CLONAL	1	TRUE	0	0.604224203305422	1		540	338	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639366	3639366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053618-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	163	490	1	ENST00000294008.3:c.4273G>T	p.Asp1425Tyr	p.D1425Y	ENST00000294008	NM_032444.2	1425	Gac/Tac	12/15	0.202274393472402	5	FACETS	1	0.986	1	0.455	0.418	0.494	INDETERMINATE	1	TRUE	2	0.604224203305422	5		491	753	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944174	81944174	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053618-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	121	503	0	ENST00000359376.3:c.1783G>T	p.Gly595Trp	p.G595W	ENST00000359376	NM_002661.3	595	Ggg/Tgg	18/33	1	2	FACETS	0.719	0.652	0.789	0.719	0.652	0.789	SUBCLONAL	1	TRUE	1	0.604224203305422	2		503	557	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288838	15288838	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053618-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	30	120	0	ENST00000263388.2:c.3901G>T	p.Gly1301Cys	p.G1301C	ENST00000263388	NM_000435.2	1301	Ggc/Tgc	24/33	0.604224203305422	4	FACETS	0.339	0.272	0.415	0.169	0.136	0.208	SUBCLONAL	1	TRUE	2	0.604224203305422	4		120	470	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645844	215645844	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053618-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	21	670	0	ENST00000260947.4:c.754C>G	p.Pro252Ala	p.P252A	ENST00000260947	NM_000465.2	252	Cct/Gct	4/11	1	2	FACETS	0.234	0.18	0.297	0.234	0.18	0.297	SUBCLONAL	1	TRUE	1	0.604224203305422	2		670	297	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510144	187510144	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053618-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	97	420	0	ENST00000441802.2:c.13369A>C	p.Asn4457His	p.N4457H	ENST00000441802	NM_005245.3	4457	Aat/Cat	27/27	0.496466845156215	3	FACETS	0.86	0.77	0.955	0.43	0.385	0.478	CLONAL	1	TRUE	1	0.604224203305422	3		420	486	SUCCESS
APC	324	MSKCC	GRCh37	5	112174823	112174823	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053618-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	11	248	0	ENST00000257430.4:c.3532G>T	p.Asp1178Tyr	p.D1178Y	ENST00000257430	NM_000038.5	1178	Gat/Tat	16/16	0.496466845156215	3	FACETS	0.341	0.236	0.47	0.171	0.118	0.235	SUBCLONAL	1	TRUE	1	0.604224203305422	3		248	139	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372293	55372293	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053618-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	27	528	0	ENST00000297316.4:c.983C>A	p.Pro328Gln	p.P328Q	ENST00000297316	NM_022454.3	328	cCg/cAg	2/2	NA	2	FACETS	0.172	0.136	0.213			1	INDETERMINATE	1	TRUE	NA	0.604224203305422	2		528	521	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0053619-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	458	603	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.209272529473597	3	FACETS	1	0.996	1	0.709	0.679	0.74	INDETERMINATE	1	TRUE	1	0.800225226669191	3		603	1130	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0053619-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	526	777	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.209272529473597	3	FACETS	1	0.997	1	0.748	0.718	0.777	INDETERMINATE	1	TRUE	1	0.800225226669191	3		777	1231	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0053619-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	367	483	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.800225226669191	2		483	862	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0053619-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	436	686	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.800225226669191	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.800225226669191	1		686	635	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41228505	41228505	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs80357389	NA	P-0053619-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	250	216	0	ENST00000357654.3:c.4484G>T	p.Arg1495Met	p.R1495M	ENST00000357654	NM_007294.3	1495	aGg/aTg	13/23	0.226904237312318	4	FACETS	0.928	0.875	0.982	0.928	0.875	0.982	INDETERMINATE	2	TRUE	2	0.800225226669191	4		216	606	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033840	49033840	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0053619-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	272	230	0	ENST00000267163.4:c.1977T>A	p.Tyr659Ter	p.Y659*	ENST00000267163	NM_000321.2	659	taT/taA	20/27	0.800225226669191	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.800225226669191	1		230	364	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053626-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	145	276	0				ENST00000310581	NM_198253.2	-/1132			0.316003947779487	1	FACETS	0.655	0.608	0.702	0.655	0.608	0.702	INDETERMINATE	1	TRUE	0	0.836564011361481	1		276	308	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981167	201981168	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053626-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	446	1250	1	ENST00000359651.3:c.248dup	p.Asn83LysfsTer9	p.N83Kfs*9	ENST00000359651		82	-/A	2/8	0.275575073299036	2	FACETS	1	0.995	1	0.618	0.593	0.642	INDETERMINATE	1	TRUE	0	0.836564011361481	2		1251	863	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375991	118375991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781853027	NA	P-0053626-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	301	734	0	ENST00000534358.1:c.9384G>A	p.Met3128Ile	p.M3128I	ENST00000534358	NM_005933.3	3128	atG/atA	27/36	0.836564011361481	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.836564011361481	1		734	385	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030468	49030468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053626-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	151	451	0	ENST00000267163.4:c.1943C>T	p.Ser648Leu	p.S648L	ENST00000267163	NM_000321.2	648	tCa/tTa	19/27	0.320619165814752	1	FACETS	0.609	0.565	0.653	0.609	0.565	0.653	INDETERMINATE	1	TRUE	0	0.836564011361481	1		451	345	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655488	67655488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053626-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	176	543	1	ENST00000264010.4:c.1351G>A	p.Asp451Asn	p.D451N	ENST00000264010	NM_006565.3	451	Gat/Aat	7/12	1	2	FACETS	0.888	0.825	0.951	0.888	0.825	0.951	CLONAL	1	TRUE	1	0.836564011361481	2		544	474	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16062082	16062082	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053626-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	220	564	0	ENST00000268712.3:c.724G>T	p.Glu242Ter	p.E242*	ENST00000268712	NM_006311.3	242	Gag/Tag	6/46	0.169265905320275	3	FACETS	1	0.992	1	0.719	0.675	0.763	INDETERMINATE	1	TRUE	1	0.836564011361481	3		564	519	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871714	37871714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053626-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	424	1109	0	ENST00000269571.5:c.1238C>T	p.Ser413Leu	p.S413L	ENST00000269571		413	tCa/tTa	11/27	0.188480180353994	4	FACETS	0.936	0.896	0.978	0.936	0.896	0.978	INDETERMINATE	2	TRUE	2	0.836564011361481	4		1109	994	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873699	37873699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766029214	NA	P-0053626-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	194	1094	0	ENST00000269571.5:c.1864G>A	p.Ala622Thr	p.A622T	ENST00000269571		622	Gca/Aca	15/27	0.188480180353994	4	FACETS	0.804	0.744	0.867	0.402	0.372	0.434	INDETERMINATE	1	TRUE	2	0.836564011361481	4		1094	1059	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166387	7166387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747554207	NA	P-0053626-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	302	902	0	ENST00000302850.5:c.1639G>A	p.Gly547Arg	p.G547R	ENST00000302850	NM_000208.2	547	Ggg/Agg	8/22	1	2	FACETS	0.969	0.918	1	0.969	0.918	1	CLONAL	1	TRUE	1	0.836564011361481	2		902	745	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643408	52643408	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053626-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	16	612	0	ENST00000394830.3:c.2488G>T	p.Glu830Ter	p.E830*	ENST00000394830	NM_018313.4	830	Gaa/Taa	17/30	0.836564011361481	1	FACETS	0.101	0.074	0.133	0.101	0.074	0.133	SUBCLONAL	1	TRUE	0	0.836564011361481	1		612	220	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643678	52643678	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053626-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	147	649	0	ENST00000394830.3:c.2218G>T	p.Glu740Ter	p.E740*	ENST00000394830	NM_018313.4	740	Gag/Tag	17/30	0.836564011361481	1	FACETS	0.811	0.76	0.862	0.811	0.76	0.862	CLONAL	1	TRUE	0	0.836564011361481	1		649	252	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0053626-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	20	478	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.420906042906283	3	FACETS	0.119	0.09	0.153	0.06	0.045	0.077	INDETERMINATE	1	TRUE	1	0.836564011361481	3		478	569	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191804	123191805	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1392503050	NA	P-0053626-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	124	205	0	ENST00000218089.9:c.1400dup	p.Phe468LeufsTer5	p.F468Lfs*5	ENST00000218089	NM_001042749.1	465	gtt/gTtt	15/35	1	1	FACETS	0.917	0.859	0.973	0.917	0.859	0.973	CLONAL	1	TRUE	0	0.836564011361481	1		205	188	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0053627-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	600	1034	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.608070101531631	3	FACETS	0.984	0.949	1	0.656	0.632	0.68	CLONAL	2	TRUE	0	0.608070101531631	3		1034	1308	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163807	32163807	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs751250725	NA	P-0053627-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	489	949	0	ENST00000375023.3:c.5419G>C	p.Ala1807Pro	p.A1807P	ENST00000375023	NM_004557.3	1807	Gct/Cct	30/30	0.370052542364842	4	FACETS	0.895	0.856	0.934	0.895	0.856	0.934	CLONAL	2	TRUE	2	0.608070101531631	4		949	1445	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356113	66356113	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053627-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	266	546	0	ENST00000273854.3:c.1384G>A	p.Val462Ile	p.V462I	ENST00000273854	NM_004439.5	462	Gta/Ata	5/18	0.477902360185041	2	FACETS	0.758	0.718	0.799	0.758	0.718	0.799	SUBCLONAL	2	TRUE	0	0.608070101531631	2		546	577	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100407	157101301	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCCGCCGTCGCAGCCCCAGTCCCAGGCGGCGGCGGCGGGGGCGGCGGCGGGCGGCCAGCAGGCGGCCGCGGGCATGGGCTTGGGCAAGGACATGGGCGCCCAGTACGCCGCTGCCAGCCCGGCCTGGGCGGCCGCGCAACAAAGGAGTCACCCGGCGATGAGCCCCGGCACCCCCGGACCGACCATGGGCAGATCCCAGGTAACCCTCGCGCCAGCCGGGCCTGCTTCCGCCCGGCGGCCTCGCCGCGCCGCGAGCCTGAGTTTCTTTCTTTGCCGCGTACTTTTCCCCGTCTTCCCGCGGGGGCGGCGGGGGCGCGGCGCCCAAAGCCATCTTGACGGGCGGCCGCCTCCCGCCGCGGTCGGGGCGCCCCGGGGGCCGGCGCGCTGTCCAGGCCTGGGAGGGCTTCGCCGGGCCGGGCCGGGCCGGGTGGCTTCTACCCCGCCGGCCCGCACCCGCGTCCCCCCCCTCCCCCAGGCCCGGGAACGCGAAGCGAGATCCCGAGGCGCCACCCGCGCGGTCGCCGTTTGGGGCGGCGGGGACCGTTCGGGTGCTTTTGTAACAAATAGGCTCTCCCGGCCAGGACGGCTGGGGCGAAGAGCCACCCGATCGGTTCTGGGAGCGCCCACAATGTGCTTTAACGGGGGAAAGAATGAGGAACTTTCTCACACCTTTAGCCACAGCACGTTCCCTCTTGGCTTCCGAGGTCCAGGCAGGGAAAATAGGTTAGCTTTGTGACAAGCGAGTGGGTTTTTCCTACTTAGGGAGAGCCATTCAGAGACACTCGGTGCGGGCTTCGAGCTCGAACGTTTGCTGGTAGGAATAATAACAAAATTTACAACGACATGGAGGTGCAATATTGTAAAATACATCGATTCGTTCCTTAGAATAGCCAGG	GCCGCCGTCGCAGCCCCAGTCCCAGGCGGCGGCGGCGGGGGCGGCGGCGGGCGGCCAGCAGGCGGCCGCGGGCATGGGCTTGGGCAAGGACATGGGCGCCCAGTACGCCGCTGCCAGCCCGGCCTGGGCGGCCGCGCAACAAAGGAGTCACCCGGCGATGAGCCCCGGCACCCCCGGACCGACCATGGGCAGATCCCAGGTAACCCTCGCGCCAGCCGGGCCTGCTTCCGCCCGGCGGCCTCGCCGCGCCGCGAGCCTGAGTTTCTTTCTTTGCCGCGTACTTTTCCCCGTCTTCCCGCGGGGGCGGCGGGGGCGCGGCGCCCAAAGCCATCTTGACGGGCGGCCGCCTCCCGCCGCGGTCGGGGCGCCCCGGGGGCCGGCGCGCTGTCCAGGCCTGGGAGGGCTTCGCCGGGCCGGGCCGGGCCGGGTGGCTTCTACCCCGCCGGCCCGCACCCGCGTCCCCCCCCTCCCCCAGGCCCGGGAACGCGAAGCGAGATCCCGAGGCGCCACCCGCGCGGTCGCCGTTTGGGGCGGCGGGGACCGTTCGGGTGCTTTTGTAACAAATAGGCTCTCCCGGCCAGGACGGCTGGGGCGAAGAGCCACCCGATCGGTTCTGGGAGCGCCCACAATGTGCTTTAACGGGGGAAAGAATGAGGAACTTTCTCACACCTTTAGCCACAGCACGTTCCCTCTTGGCTTCCGAGGTCCAGGCAGGGAAAATAGGTTAGCTTTGTGACAAGCGAGTGGGTTTTTCCTACTTAGGGAGAGCCATTCAGAGACACTCGGTGCGGGCTTCGAGCTCGAACGTTTGCTGGTAGGAATAATAACAAAATTTACAACGACATGGAGGTGCAATATTGTAAAATACATCGATTCGTTCCTTAGAATAGCCAGG	-	novel	NA	P-0053627-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	102	140	0	ENST00000346085.5:c.1345_1542+697del		p.X449_splice	ENST00000346085	NM_020732.3	449		1/20	0.275108583472456		FACETS		0.817	0.977				INDETERMINATE	2	TRUE	NA	0.608070101531631	3		140	244	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460522	8460546	+	frameshift_variant	Frame_Shift_Del	DEL	AGATCCATTGACACCACGGGGTCGG	AGATCCATTGACACCACGGGGTCGG	-	novel	NA	P-0053627-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	257	622	0	ENST00000356435.5:c.3740_3764del	p.Ser1247TrpfsTer13	p.S1247Wfs*13	ENST00000356435		1247	tCCGACCCCGTGGTGTCAATGGATCTg/tg	22/35	0.477902360185041	2	FACETS	1	0.993	1	0.71	0.671	0.75	CLONAL	1	TRUE	0	0.608070101531631	2		622	595	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053630-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	43	276	0				ENST00000310581	NM_198253.2	-/1132			0.321825558020526	4	FACETS	0.813	0.687	0.948	0.813	0.687	0.948	CLONAL	2	TRUE	2	0.341171949097201	4		276	208	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144880	47144880	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053630-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	17	114	0	ENST00000409792.3:c.4873C>A	p.Arg1625Ser	p.R1625S	ENST00000409792	NM_014159.6	1625	Cgt/Agt	7/21	0.341171949097201	4	FACETS	0.189	0.14	0.248			1	SUBCLONAL	1	TRUE	NA	0.341171949097201	4		114	708	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876660825	NA	P-0053630-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	241	662	0	ENST00000269305.4:c.569C>G	p.Pro190Arg	p.P190R	ENST00000269305	NM_001126112.2	190	cCt/cGt	6/11	0.341171949097201	1	FACETS	0.964	0.907	1	1	0.995	1	CLONAL	2	TRUE	0	0.341171949097201	1		662	608	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420213	49420213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267607237	NA	P-0053630-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	184	653	2	ENST00000301067.7:c.15536G>A	p.Arg5179His	p.R5179H	ENST00000301067	NM_003482.3	5179	cGt/cAt	48/54	1	2	FACETS	0.759	0.702	0.817	1	0.99	1	SUBCLONAL	2	TRUE	1	0.341171949097201	2		655	711	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027210	49027210	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053630-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	183	104	0	ENST00000267163.4:c.1778del	p.Asn593IlefsTer18	p.N593Ifs*18	ENST00000267163	NM_000321.2	593	Aat/at	18/27	0.341171949097201	3	FACETS	0.9	0.839	0.962	0.9	0.839	0.962	CLONAL	3	TRUE	0	0.341171949097201	3		104	465	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696689	47696689	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519972	NA	P-0053644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	143	410	0	ENST00000347630.2:c.259T>A	p.Tyr87Asn	p.Y87N	ENST00000347630	NM_001007230.1	87	Tac/Aac	5/11	0.183370781340404	2	FACETS	0.813	0.748	0.879	0.813	0.748	0.879	INDETERMINATE	2	TRUE	0	0.412064015242997	2		410	427	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246961	10246961	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs768764350	NA	P-0053644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	37	533	0	ENST00000340748.4:c.4444G>A	p.Gly1482Ser	p.G1482S	ENST00000340748		1482	Ggc/Agc	37/40	0.257882065566955	1	FACETS	0.5	0.414	0.596	0.5	0.414	0.596	SUBCLONAL	1	TRUE	0	0.412064015242997	1		533	285	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061114	38061190	+	protein_altering_variant	In_Frame_Del	DEL	TCAGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTT	TCAGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTT	GCGGG	novel	NA	P-0053644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	134	427	2	ENST00000250448.2:c.799_875delinsCCCGC	p.Lys267_Glu292delinsProAla	p.K267_E292delinsPA	ENST00000250448	NM_004496.3	267	AAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGGCGCCAAGGGCGGCCCTGAg/CCCGCg	2/2	0.15525651827869	5	FACETS	0.897	0.824	0.973	0.897	0.824	0.973	INDETERMINATE	3	TRUE	2	0.412064015242997	5		429	391	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936983	48936983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690863	NA	P-0053645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	125	448	1	ENST00000267163.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000267163	NM_000321.2	251	Cga/Tga	8/27	0.38377058857585	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.38377058857585	1		449	504	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0053645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	70	286	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	0.38377058857585	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.38377058857585	1		286	279	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934571	NA	P-0053645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	165	646	0	ENST00000269305.4:c.747G>C	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agC	7/11	0.38377058857585	1	FACETS	0.923	0.849	0.999	0.923	0.849	0.999	CLONAL	1	TRUE	0	0.38377058857585	1		646	753	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598192	28598192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776410096	NA	P-0053645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	188	763	2	ENST00000253063.3:c.164G>A	p.Arg55Gln	p.R55Q	ENST00000253063	NM_031459.4	55	cGg/cAg	3/10	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.38377058857585	2		765	961	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927450	245927450	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	146	607	0	ENST00000388985.4:c.1078A>T	p.Ile360Phe	p.I360F	ENST00000388985		360	Att/Ttt	11/12	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.38377058857585	2		607	745	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274641	198274641	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	201	659	0	ENST00000335508.6:c.757A>T	p.Ile253Leu	p.I253L	ENST00000335508	NM_012433.2	253	Ata/Tta	7/25	0.137410197203625	3	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.38377058857585	3		659	957	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509436	106509436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200175951	NA	P-0053646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	144	701	1	ENST00000359195.3:c.1430G>A	p.Arg477His	p.R477H	ENST00000359195	NM_002649.2	477	cGt/cAt	2/11	1	2	FACETS	0.42	0.382	0.459	0.42	0.382	0.459	SUBCLONAL	1	TRUE	1	0.722296603252542	2		702	950	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875687	56875687	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	623	712	0	ENST00000308159.5:c.2291A>G	p.Lys764Arg	p.K764R	ENST00000308159	NM_014669.4	764	aAg/aGg	21/22	0.139363241490154	4	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.722296603252542	4		712	1237	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509919	187509919	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	130	574	0	ENST00000441802.2:c.13594G>C	p.Val4532Leu	p.V4532L	ENST00000441802	NM_005245.3	4532	Gtc/Ctc	27/27	0.397936868436354	1	FACETS	0.388	0.353	0.425	0.388	0.353	0.425	INDETERMINATE	1	TRUE	0	0.722296603252542	1		574	592	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499822	8499822	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	142	610	1	ENST00000356435.5:c.2147G>T	p.Arg716Leu	p.R716L	ENST00000356435		716	cGc/cTc	14/35	0.397936868436354	1	FACETS	0.391	0.357	0.427	0.391	0.357	0.427	INDETERMINATE	1	TRUE	0	0.722296603252542	1		611	642	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0053648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	39	757	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.434104144979863	2	FACETS	0.23	0.19	0.275	0.115	0.095	0.138	SUBCLONAL	1	TRUE	0	0.441832318872545	2		757	768	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579346	7579346	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	423	820	0	ENST00000269305.4:c.341del	p.Leu114CysfsTer9	p.L114Cfs*9	ENST00000269305	NM_001126112.2	114	tTg/tg	4/11	0.434104144979863	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.441832318872545	2		820	874	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980364	201980398	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTTTGGGGCCGATGACTTGGTACTGACCCTGAG	ACCTTTGGGGCCGATGACTTGGTACTGACCCTGAG	-	novel	NA	P-0053648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	513	793	0	ENST00000359651.3:c.100_134del	p.Thr34GlnfsTer46	p.T34Qfs*46	ENST00000359651		34	ACCTTTGGGGCCGATGACTTGGTACTGACCCTGAGc/c	1/8	0.187502241805647	3	FACETS	0.887	0.853	0.92	0.887	0.853	0.92	INDETERMINATE	3	TRUE	0	0.441832318872545	3		793	1066	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0053649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	289	781	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.384965901351401	2	FACETS	0.846	0.8	0.893	0.846	0.8	0.893	CLONAL	2	TRUE	0	0.447673522613884	2		782	763	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0053649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	63	545	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.264174651970465	1	FACETS	0.508	0.441	0.581	0.508	0.441	0.581	INDETERMINATE	1	TRUE	0	0.447673522613884	1		545	430	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519920	NA	P-0053649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	76	371	0	ENST00000397062.3:c.85G>T	p.Asp29Tyr	p.D29Y	ENST00000397062	NM_006164.4	29	Gat/Tat	2/5	0.195958417544429	3	FACETS	0.944	0.832	1	0.472	0.416	0.533	INDETERMINATE	1	TRUE	1	0.447673522613884	3		371	440	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473672	67473672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	152	829	0	ENST00000327367.4:c.752C>T	p.Ser251Leu	p.S251L	ENST00000327367	NM_005902.3	251	tCg/tTg	6/9	1	2	FACETS	0.839	0.768	0.914	0.839	0.768	0.914	CLONAL	1	TRUE	1	0.447673522613884	2		829	809	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982463	25982463	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	87	469	0	ENST00000435504.4:c.827C>T	p.Ser276Phe	p.S276F	ENST00000435504		276	tCc/tTc	9/13	0.447673522613884	3	FACETS	0.654	0.579	0.735	0.327	0.289	0.368	SUBCLONAL	1	TRUE	1	0.447673522613884	3		469	727	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249810	133249810	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	132	756	0	ENST00000320574.5:c.1413G>C	p.Met471Ile	p.M471I	ENST00000320574	NM_006231.2	471	atG/atC	14/49	0.337860198545494	1	FACETS	0.984	0.9	1	0.984	0.9	1	CLONAL	1	TRUE	0	0.447673522613884	1		756	465	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042283	42042283	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	32	614	0	ENST00000219905.7:c.6478G>C	p.Glu2160Gln	p.E2160Q	ENST00000219905	NM_001164273.1	2160	Gag/Cag	17/24	1	2	FACETS	0.271	0.219	0.329	0.271	0.219	0.329	SUBCLONAL	1	TRUE	1	0.447673522613884	2		614	528	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646559	23646559	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	69	605	0	ENST00000261584.4:c.1308G>C	p.Lys436Asn	p.K436N	ENST00000261584	NM_024675.3	436	aaG/aaC	4/13	0.264174651970465	1	FACETS	0.531	0.463	0.603	0.531	0.463	0.603	INDETERMINATE	1	TRUE	0	0.447673522613884	1		605	451	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836606	89836606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1387374844	NA	P-0053649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	155	1042	1	ENST00000389301.3:c.2284C>T	p.Leu762Phe	p.L762F	ENST00000389301	NM_000135.2	762	Ctc/Ttc	25/43	1	2	FACETS	0.815	0.746	0.886	0.815	0.746	0.886	CLONAL	1	TRUE	1	0.447673522613884	2		1043	850	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122397	17122397	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0053649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	157	883	1	ENST00000285071.4:c.998C>G	p.Ser333Ter	p.S333*	ENST00000285071	NM_144997.5	333	tCa/tGa	9/14	1	2	FACETS	0.882	0.809	0.959	0.882	0.809	0.959	CLONAL	1	TRUE	1	0.447673522613884	2		884	795	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312713	30312713	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	80	675	0	ENST00000262643.3:c.694A>G	p.Met232Val	p.M232V	ENST00000262643	NM_001238.2	232	Atg/Gtg	8/12	0.447673522613884	4	FACETS	0.583	0.512	0.66	0.194	0.17	0.22	SUBCLONAL	1	TRUE	1	0.447673522613884	4		675	887	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793340	42793340	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	317	936	0	ENST00000575354.2:c.1142C>G	p.Ser381Cys	p.S381C	ENST00000575354	NM_015125.3	381	tCt/tGt	8/20	0.447673522613884	4	FACETS	0.924	0.872	0.976	0.616	0.581	0.651	CLONAL	2	TRUE	1	0.447673522613884	4		936	1110	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549385	5549385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	165	751	0	ENST00000397747.3:c.412G>A	p.Glu138Lys	p.E138K	ENST00000397747	NM_025239.3	138	Gag/Aag	4/7	0.43553555979125	1	FACETS	0.85	0.783	0.92	0.85	0.783	0.92	CLONAL	1	TRUE	0	0.447673522613884	1		751	673	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998582	100998582	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	504	860	5	ENST00000325455.5:c.1220C>A	p.Ala407Asp	p.A407D	ENST00000325455	NM_001202474.3	407	gCc/gAc	1/8	0.580837022983052	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	2	0.743635728224412	4		865	1065	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022681	12022681	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	621	663	6	ENST00000396373.4:c.787A>T	p.Thr263Ser	p.T263S	ENST00000396373	NM_001987.4	263	Aca/Tca	5/8	0.469606823985998	5	FACETS	1	0.995	1			1	CLONAL	3	TRUE	NA	0.743635728224412	5		669	1049	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432202	49432214	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAGGATTGGGG	CAGAGGATTGGGG	-	novel	NA	P-0053650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	355	867	1	ENST00000301067.7:c.8925_8937del	p.Asn2977TrpfsTer23	p.N2977Wfs*23	ENST00000301067	NM_003482.3	2975	cgCCCCAATCCTCTG/cg	34/54	0.519572768392931	4	FACETS	1	0.991	1	0.405	0.383	0.427	CLONAL	1	TRUE	1	0.743635728224412	4		868	1371	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416655	121416655	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	391	928	0	ENST00000257555.6:c.84G>T	p.Gln28His	p.Q28H	ENST00000257555		28	caG/caT	1/10	0.748007751328699	3	FACETS	1	0.986	1	0.549	0.521	0.577	CLONAL	1	TRUE	1	0.743635728224412	3		928	1315	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959479	26959479	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	162	384	2	ENST00000381527.3:c.646G>A	p.Asp216Asn	p.D216N	ENST00000381527	NM_001260.1	216	Gat/Aat	6/13	0.748007751328699	3	FACETS	1	0.957	1	0.527	0.486	0.569	CLONAL	1	TRUE	1	0.743635728224412	3		386	567	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540652	NA	P-0053650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	676	743	5	ENST00000269305.4:c.743G>C	p.Arg248Pro	p.R248P	ENST00000269305	NM_001126112.2	248	cGg/cCg	7/11	0.748007751328699	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.743635728224412	2		748	879	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010554	48010554	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	342	708	0	ENST00000234420.5:c.182C>G	p.Ala61Gly	p.A61G	ENST00000234420	NM_000179.2	61	gCg/gGg	1/10	0.748007751328699	2	FACETS	1	0.983	1	0.537	0.51	0.564	CLONAL	1	TRUE	0	0.743635728224412	2		708	857	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215633994	215633994	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	295	536	2	ENST00000260947.4:c.1357G>T	p.Asp453Tyr	p.D453Y	ENST00000260947	NM_000465.2	453	Gat/Tat	5/11	0.748007751328699	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.743635728224412	3		538	536	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37083820	37083820	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	305	464	2	ENST00000231790.2:c.1729T>A	p.Ser577Thr	p.S577T	ENST00000231790	NM_000249.3	577	Tcg/Acg	15/19	0.748007751328699	2	FACETS	0.967	0.932	1	0.967	0.932	1	CLONAL	2	TRUE	0	0.743635728224412	2		466	424	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058704	47058704	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	237	591	2	ENST00000409792.3:c.7574A>G	p.Lys2525Arg	p.K2525R	ENST00000409792	NM_014159.6	2525	aAg/aGg	21/21	0.748007751328699	2	FACETS	0.921	0.864	0.979	0.461	0.432	0.49	CLONAL	1	TRUE	0	0.743635728224412	2		593	692	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751561	57751561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	171	426	1	ENST00000274289.3:c.1430G>A	p.Arg477Lys	p.R477K	ENST00000274289	NM_006622.3	477	aGg/aAg	11/14	0.748007751328699	2	FACETS	1	0.972	1	0.544	0.506	0.582	CLONAL	1	TRUE	0	0.743635728224412	2		427	423	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894992	101894992	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	135	330	0	ENST00000374994.4:c.545A>G	p.Tyr182Cys	p.Y182C	ENST00000374994	NM_004612.2	182	tAt/tGt	3/9	0.748007751328699	3	FACETS	1	0.915	1	0.5	0.457	0.545	CLONAL	1	TRUE	1	0.743635728224412	3		330	498	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	77	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.45000751209795	2		276	331	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0053658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	80	375	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.912	0.807	1	0.912	0.807	1	CLONAL	1	TRUE	1	0.45000751209795	2		375	390	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652248	48652248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057518396	NA	P-0053658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	158	695	0	ENST00000376670.3:c.919C>T	p.Arg307Cys	p.R307C	ENST00000376670	NM_002049.3	307	Cgc/Tgc	6/6	0.45000751209795	1	FACETS	0.854	0.786	0.925	0.854	0.786	0.925	CLONAL	1	TRUE	0	0.45000751209795	1		695	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578429	7578429	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1567553148	NA	P-0053658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	461	822	0	ENST00000269305.4:c.501del	p.Gln167HisfsTer3	p.Q167Hfs*3	ENST00000269305	NM_001126112.2	167	caG/ca	5/11	0.45000751209795	2	FACETS	0.998	0.957	1	0.998	0.957	1	CLONAL	2	TRUE	0	0.45000751209795	2		822	1026	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637008	93637008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201479078	NA	P-0053658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	135	467	0	ENST00000375746.1:c.1058C>T	p.Ala353Val	p.A353V	ENST00000375746	NM_001174167.1	353	gCg/gTg	9/14	1	2	FACETS	0.968	0.882	1	0.968	0.882	1	CLONAL	1	TRUE	1	0.45000751209795	2		467	620	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692874	89692875	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCAATTC	novel	NA	P-0053658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	52	259	0	ENST00000371953.3:c.359_367dup	p.Ile122_His123insProAlaIle	p.I122_H123insPAI	ENST00000371953	NM_000314.4	120	gca/gCAGCAATTCca	5/9	0.45000751209795	1	FACETS	0.782	0.673	0.899	0.782	0.673	0.899	SUBCLONAL	1	TRUE	0	0.45000751209795	1		259	229	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0053659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	85	478	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.36	2		478	402	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0053659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	110	290	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.36	2		290	504	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692961	89692961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060500122	NA	P-0053659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	92	486	0	ENST00000371953.3:c.445C>T	p.Gln149Ter	p.Q149*	ENST00000371953	NM_000314.4	149	Caa/Taa	5/9	0.374305778686358	1	FACETS	0.835	0.744	0.931	0.835	0.744	0.931	CLONAL	1	TRUE	0	0.36	1		486	502	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	120	419	0	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	0.374305778686358	1	FACETS	0.976	0.885	1	0.976	0.885	1	CLONAL	1	TRUE	0	0.36	1		419	560	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913250	NA	P-0053659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	91	407	0	ENST00000369535.4:c.34G>A	p.Gly12Ser	p.G12S	ENST00000369535	NM_002524.4	12	Ggt/Agt	2/7	1	2	FACETS	0.845	0.752	0.945	0.845	0.752	0.945	CLONAL	1	TRUE	1	0.36	2		407	598	SUCCESS
APC	324	MSKCC	GRCh37	5	112175530	112175530	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	100	385	0	ENST00000257430.4:c.4240del	p.Val1414Ter	p.V1414*	ENST00000257430	NM_000038.5	1413	atG/at	16/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.36	2		385	486	SUCCESS
APC	324	MSKCC	GRCh37	5	112173590	112173590	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561575998	NA	P-0053659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	67	350	0	ENST00000257430.4:c.2299C>T	p.Gln767Ter	p.Q767*	ENST00000257430	NM_000038.5	767	Cag/Tag	16/16	1	2	FACETS	0.838	0.731	0.954	0.838	0.731	0.954	CLONAL	1	TRUE	1	0.36	2		350	444	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331718	68331718	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs766149487	NA	P-0053659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	38	124	1	ENST00000487270.1:c.316-2A>T		p.X106_splice	ENST00000487270	NM_133509.3	106			1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.36	2		125	155	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522130	157522130	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758892744	NA	P-0053659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	203	690	0	ENST00000346085.5:c.4402C>T	p.Arg1468Cys	p.R1468C	ENST00000346085	NM_020732.3	1468	Cgc/Tgc	18/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.36	2		690	996	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984363	201984363	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	179	660	0	ENST00000359651.3:c.1028A>G	p.Glu343Gly	p.E343G	ENST00000359651		343	gAa/gGa	8/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.36	2		660	885	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054559	13054560	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAG	novel	NA	P-0053659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	103	487	0	ENST00000316448.5:c.1090_1092dup	p.Glu364dup	p.E364dup	ENST00000316448	NM_004343.3	364	-/GAG	9/9	1	2	FACETS	0.811	0.726	0.9	0.811	0.726	0.9	CLONAL	1	TRUE	1	0.36	2		487	706	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547389	106547389	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	107	410	0	ENST00000369096.4:c.626A>T	p.His209Leu	p.H209L	ENST00000369096	NM_001198.3	209	cAc/cTc	4/7	1	2	FACETS	0.948	0.852	1	0.948	0.852	1	CLONAL	1	TRUE	1	0.36	2		410	627	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	165	386	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.92	0.848	0.994	0.92	0.848	0.994	CLONAL	1	TRUE	1	0.561355375316539	2		386	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0053660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	103	601	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.454895730541063	1	FACETS	0.5	0.449	0.554	0.5	0.449	0.554	SUBCLONAL	1	TRUE	0	0.561355375316539	1		601	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	178	621	0	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	0.454895730541063	1	FACETS	0.753	0.697	0.81	0.753	0.697	0.81	SUBCLONAL	1	TRUE	0	0.561355375316539	1		621	606	SUCCESS
APC	324	MSKCC	GRCh37	5	112128187	112128187	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	187	364	0	ENST00000257430.4:c.690del	p.Ile231TyrfsTer62	p.I231Yfs*62	ENST00000257430	NM_000038.5	230	cgT/cg	7/16	0.561355375316539	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.561355375316539	1		364	438	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129867	55129867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373126818	NA	P-0053660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	178	483	0	ENST00000257290.5:c.401C>T	p.Thr134Met	p.T134M	ENST00000257290	NM_006206.4	134	aCg/aTg	4/23	1	2	FACETS	0.982	0.909	1	0.982	0.909	1	CLONAL	1	TRUE	1	0.561355375316539	2		483	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	625	599	0	ENST00000269305.4:c.731del	p.Gly244AlafsTer3	p.G244Afs*3	ENST00000269305	NM_001126112.2	244	gGc/gc	7/11	0.927328417491251	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.927328417491251	2		599	644	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267359	198267359	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs377023736	NA	P-0053661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	250	516	0	ENST00000335508.6:c.1998G>T	p.Lys666Asn	p.K666N	ENST00000335508	NM_012433.2	666	aaG/aaT	14/25	0.922991584270653	3	FACETS	1	0.966	1	0.521	0.489	0.553	CLONAL	1	TRUE	1	0.927328417491251	3		516	758	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674234	86674234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	325	383	0	ENST00000274376.6:c.2366G>A	p.Arg789Gln	p.R789Q	ENST00000274376	NM_002890.2	789	cGa/cAa	18/25	0.927328417491251	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.927328417491251	2		383	350	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045025	47045025	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	800	429	0	ENST00000377604.3:c.2351A>G	p.His784Arg	p.H784R	ENST00000377604	NM_001204468.1	784	cAc/cGc	20/24	0.899469194813403	2	FACETS	1	0.998	1			1	CLONAL	2	TRUE	NA	0.927328417491251	2		429	815	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615611	43615611	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	521	583	0	ENST00000355710.3:c.2690G>T	p.Arg897Leu	p.R897L	ENST00000355710	NM_020975.4	897	cGa/cTa	15/20	0.922991584270653	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.927328417491251	3		583	819	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405403	70405403	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	213	605	0	ENST00000373644.4:c.2917C>G	p.Gln973Glu	p.Q973E	ENST00000373644	NM_030625.2	973	Caa/Gaa	4/12	0.922991584270653	3	FACETS	0.832	0.775	0.891	0.416	0.387	0.446	CLONAL	1	TRUE	1	0.927328417491251	3		605	808	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919223	48919223	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	108	180	0	ENST00000267163.4:c.390del	p.Lys130AsnfsTer6	p.K130Nfs*6	ENST00000267163	NM_000321.2	130	Aaa/aa	4/27	0.927328417491251	2	FACETS	0.971	0.932	1	0.971	0.932	1	CLONAL	2	TRUE	0	0.927328417491251	2		180	120	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871543	37871543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	695	704	0	ENST00000269571.5:c.1153C>T	p.Pro385Ser	p.P385S	ENST00000269571		385	Cca/Tca	10/27	0.922991584270653	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.927328417491251	3		704	1075	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582019	189582019	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0053661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	355	371	0	ENST00000264731.3:c.580-2A>T		p.X194_splice	ENST00000264731	NM_003722.4	194			0.906606601304644	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.927328417491251	4		371	732	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908798	101908798	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	165	420	0	ENST00000374994.4:c.1162A>G	p.Ile388Val	p.I388V	ENST00000374994	NM_004612.2	388	Ata/Gta	7/9	0.922991584270653	3	FACETS	1	0.925	1	0.5	0.462	0.539	CLONAL	1	TRUE	1	0.927328417491251	3		420	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0053662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	30	848	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	0.394	0.316	0.484	0.394	0.316	0.484	SUBCLONAL	1	TRUE	1	0.17	2		848	895	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	116	386	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.305919959035693	1	FACETS	0.799	0.721	0.881	0.799	0.721	0.881	SUBCLONAL	1	TRUE	0	0.357843722130303	1		386	666	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155164	108155165	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0053664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	124	485	0	ENST00000278616.4:c.3958dup	p.Asp1320GlyfsTer4	p.D1320Gfs*4	ENST00000278616	NM_000051.3	1319	-/G	26/63	1	2	FACETS	0.977	0.886	1	0.977	0.886	1	CLONAL	1	TRUE	1	0.357843722130303	2		485	709	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307321	118307321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	14	17	0	ENST00000534358.1:c.94C>T	p.Arg32Trp	p.R32W	ENST00000534358	NM_005933.3	32	Cgg/Tgg	1/36	1	2	FACETS	1	0.855	1	1	0.935	1	CLONAL	2	TRUE	1	0.47756665526615	2		17	26	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696644	47696644	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519964	NA	P-0053666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	291	562	0	ENST00000347630.2:c.304T>G	p.Phe102Val	p.F102V	ENST00000347630	NM_001007230.1	102	Ttc/Gtc	5/11	1	2	FACETS	0.987	0.931	1	0.987	0.931	1	CLONAL	1	TRUE	1	0.692376473529052	2		562	852	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591826	48591826	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs281875324	NA	P-0053666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	247	560	0	ENST00000342988.3:c.989A>C	p.Glu330Ala	p.E330A	ENST00000342988	NM_005359.5	330	gAa/gCa	9/12	0.655068977207258	1	FACETS	0.931	0.881	0.981	0.931	0.881	0.981	CLONAL	1	TRUE	0	0.692376473529052	1		560	501	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0053667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	99	948	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.246786404448948	2		948	708	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	29	419	0	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	1	2	FACETS	0.717	0.576	0.876	0.717	0.576	0.876	SUBCLONAL	1	FALSE	1	0.246786404448948	2		419	328	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573977	41573977	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201569846	NA	P-0053667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	40	613	1	ENST00000263253.7:c.6262C>T	p.Arg2088Trp	p.R2088W	ENST00000263253	NM_001429.3	2088	Cgg/Tgg	31/31	1	2	FACETS	0.566	0.469	0.673	0.566	0.469	0.673	SUBCLONAL	1	FALSE	1	0.246786404448948	2		614	573	SUCCESS
EED	8726	MSKCC	GRCh37	11	85967495	85967495	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	29	371	0	ENST00000263360.6:c.493G>C	p.Val165Leu	p.V165L	ENST00000263360	NM_003797.3	165	Gta/Cta	5/12	0.152673347978344	3	FACETS	1	0.818	1	0.508	0.409	0.619	CLONAL	1	FALSE	1	0.246786404448948	3		371	260	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251531	251531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	41	444	0	ENST00000264932.6:c.1742G>A	p.Gly581Glu	p.G581E	ENST00000264932	NM_004168.2	581	gGa/gAa	13/15	0.239584264728245	1	FACETS	0.757	0.631	0.895	0.757	0.631	0.895	SUBCLONAL	1	FALSE	0	0.246786404448948	1		444	385	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0053673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	264	563	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.578444873486599	2		563	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0053673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	1371	771	5	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.578444873486599	6	FACETS	0.961	0.945	0.975			1	CLONAL	6	TRUE	NA	0.578444873486599	6		776	1774	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656921	45656921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369596621	NA	P-0053673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	557	857	0	ENST00000407780.3:c.235C>T	p.Arg79Cys	p.R79C	ENST00000407780	NM_001283052.1	79	Cgc/Tgc	3/7	0.513404274134272	3	FACETS	0.868	0.839	0.896	0.868	0.839	0.896	CLONAL	3	TRUE	0	0.578444873486599	3		857	954	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867567	35867567	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0053677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	63	306	0	ENST00000303115.3:c.379+2T>A		p.X127_splice	ENST00000303115	NM_002185.3	127			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		306	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780071	NA	P-0053678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	379	833	2	ENST00000269305.4:c.580C>T	p.Leu194Phe	p.L194F	ENST00000269305	NM_001126112.2	194	Ctt/Ttt	6/11	0.625970940619544	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.625970940619544	1		835	794	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176104194	176104194	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	232	443	0	ENST00000367669.3:c.920G>C	p.Ser307Thr	p.S307T	ENST00000367669	NM_022457.5	307	aGt/aCt	8/20	0.527454728212755	3	FACETS	0.782	0.734	0.831	0.782	0.734	0.831	SUBCLONAL	2	TRUE	1	0.625970940619544	3		443	622	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	48	329	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.631	0.535	0.735	0.631	0.535	0.735	SUBCLONAL	1	TRUE	1	0.43	2		329	354	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	192	473	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.43	2		478	892	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778972	9778972	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1214315014	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	194	617	1	ENST00000377346.4:c.1241C>T	p.Ala414Val	p.A414V	ENST00000377346	NM_005026.3	414	gCg/gTg	9/24	1	2	FACETS	0.869	0.804	0.937	0.869	0.804	0.937	CLONAL	1	TRUE	1	0.43	2		618	1038	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	42	445	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.262	0.218	0.311	0.262	0.218	0.311	SUBCLONAL	1	TRUE	1	0.43	2		445	746	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	152	623	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.957	0.876	1	0.957	0.876	1	CLONAL	1	TRUE	1	0.43	2		623	739	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466000	69466000	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	366	894	0	ENST00000227507.2:c.838G>T	p.Glu280Ter	p.E280*	ENST00000227507	NM_053056.2	280	Gag/Tag	5/5	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.43	2		894	1451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	220	590	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	1	2	FACETS	0.937	0.871	1	0.937	0.871	1	CLONAL	1	TRUE	1	0.43	2		590	1092	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913396	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	27	393	0	ENST00000349496.5:c.95A>T	p.Asp32Val	p.D32V	ENST00000349496	NM_001904.3	32	gAc/gTc	3/15	1	2	FACETS	0.163	0.129	0.203	0.163	0.129	0.203	SUBCLONAL	1	TRUE	1	0.43	2		393	770	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653796	89653798	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	rs1554893765	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	62	412	0	ENST00000371953.3:c.97_99del	p.Ile33del	p.I33del	ENST00000371953	NM_000314.4	32	ATT/-	2/9	1	2	FACETS	0.901	0.784	1	0.901	0.784	1	CLONAL	1	TRUE	1	0.43	2		412	320	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	185	352	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.995	0.919	1	0.995	0.919	1	CLONAL	1	TRUE	1	0.43	2		352	865	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638899	176638899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750922390	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	280	613	0	ENST00000439151.2:c.3499C>T	p.Arg1167Cys	p.R1167C	ENST00000439151	NM_022455.4	1167	Cgc/Tgc	5/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.43	2		613	1192	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404893	70404893	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765094207	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	117	563	1	ENST00000373644.4:c.2407G>A	p.Ala803Thr	p.A803T	ENST00000373644	NM_030625.2	803	Gct/Act	4/12	1	2	FACETS	0.838	0.758	0.924	0.838	0.758	0.924	CLONAL	1	TRUE	1	0.43	2		564	649	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149945	99149945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	254	654	0	ENST00000074304.5:c.257C>T	p.Thr86Met	p.T86M	ENST00000074304	NM_001134224.1	86	aCg/aTg	5/26	1	2	FACETS	0.95	0.888	1	0.95	0.888	1	CLONAL	1	TRUE	1	0.43	2		654	1243	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	216	572	2	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	0.832	0.773	0.894	0.832	0.773	0.894	CLONAL	1	TRUE	1	0.43	2		574	1207	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	287	682	6	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.43	2		688	1321	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	206	407	1	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.43	2		408	811	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030692	48030692	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs267608092	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	123	431	2	ENST00000234420.5:c.3312del	p.Phe1104LeufsTer11	p.F1104Lfs*11	ENST00000234420	NM_000179.2	1102	acT/ac	5/10	1	2	FACETS	0.844	0.764	0.927	0.844	0.764	0.927	CLONAL	1	TRUE	1	0.43	2		433	678	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081511	143081511	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	122	486	0	ENST00000262992.4:c.1563G>T	p.Trp521Cys	p.W521C	ENST00000262992	NM_001101669.1	521	tgG/tgT	15/24	1	2	FACETS	0.944	0.856	1	0.944	0.856	1	CLONAL	1	TRUE	1	0.43	2		486	601	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241993	133241993	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500813	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	322	659	2	ENST00000320574.5:c.2363C>T	p.Ala788Val	p.A788V	ENST00000320574	NM_006231.2	788	gCg/gTg	21/49	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.43	2		661	1398	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655272	45655272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764295138	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	286	796	0	ENST00000407780.3:c.580C>T	p.Arg194Trp	p.R194W	ENST00000407780	NM_001283052.1	194	Cgg/Tgg	4/7	1	2	FACETS	0.956	0.897	1	0.956	0.897	1	CLONAL	1	TRUE	1	0.43	2		796	1392	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231233	98231233	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs62637629	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	309	707	3	ENST00000331920.6:c.2050G>A	p.Glu684Lys	p.E684K	ENST00000331920	NM_000264.3	684	Gag/Aag	14/24	1	2	FACETS	0.993	0.935	1	0.993	0.935	1	CLONAL	1	TRUE	1	0.43	2		710	1447	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434182	12434182	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776687	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	159	483	1	ENST00000287820.6:c.556del	p.Ser186ValfsTer47	p.S186Vfs*47	ENST00000287820	NM_015869.4	184	Aaa/aa	4/7	1	2	FACETS	0.991	0.91	1	0.991	0.91	1	CLONAL	1	TRUE	1	0.43	2		484	746	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	300	796	8	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.43	2		804	1369	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720808	89720808	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1114167667	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	42	290	1	ENST00000371953.3:c.959T>A	p.Leu320Ter	p.L320*	ENST00000371953	NM_000314.4	320	tTa/tAa	8/9	1	2	FACETS	0.754	0.634	0.886	0.754	0.634	0.886	SUBCLONAL	1	TRUE	1	0.43	2		291	259	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925402	114925402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748822481	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	243	442	5	ENST00000543371.1:c.1485del	p.Ser496ProfsTer5	p.S496Pfs*5	ENST00000543371	NM_001198531.1	494	Ccc/cc	14/14	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.43	2		447	969	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873598	37873598	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	331	829	1	ENST00000269571.5:c.1763C>T	p.Ala588Val	p.A588V	ENST00000269571		588	gCc/gTc	15/27	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.43	2		830	1467	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351594	89351595	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	219	742	0	ENST00000301030.4:c.1355dup	p.Asn452LysfsTer2	p.N452Kfs*2	ENST00000301030	NM_001256183.1	452	aat/aaAt	9/13	1	2	FACETS	0.832	0.772	0.893	0.832	0.772	0.893	CLONAL	1	TRUE	1	0.43	2		742	1225	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919879	50919879	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866317622	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1345	139	875	0	ENST00000440232.2:c.2966C>T	p.Thr989Met	p.T989M	ENST00000440232	NM_002691.3	989	aCg/aTg	24/27	1	2	FACETS	0.436	0.395	0.479	0.436	0.395	0.479	SUBCLONAL	1	TRUE	1	0.43	2		875	1484	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954698	17954698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs992942163	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	291	742	1	ENST00000458235.1:c.196G>A	p.Val66Met	p.V66M	ENST00000458235	NM_000215.3	66	Gtg/Atg	3/24	1	2	FACETS	0.972	0.913	1	0.972	0.913	1	CLONAL	1	TRUE	1	0.43	2		743	1392	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100376	27100376	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	246	598	0	ENST00000324856.7:c.4089del	p.Gln1363HisfsTer118	p.Q1363Hfs*118	ENST00000324856	NM_006015.4	1363	cAa/ca	17/20	1	2	FACETS	0.976	0.912	1	0.976	0.912	1	CLONAL	1	TRUE	1	0.43	2		598	1172	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101495	27101495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201556442	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	113	759	2	ENST00000324856.7:c.4777C>T	p.Arg1593Trp	p.R1593W	ENST00000324856	NM_006015.4	1593	Cgg/Tgg	18/20	1	2	FACETS	0.424	0.38	0.471	0.424	0.38	0.471	SUBCLONAL	1	TRUE	1	0.43	2		761	1239	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818214	43818214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	180	605	0	ENST00000372470.3:c.1679G>A	p.Cys560Tyr	p.C560Y	ENST00000372470	NM_005373.2	560	tGt/tAt	12/12	1	2	FACETS	0.873	0.805	0.944	0.873	0.805	0.944	CLONAL	1	TRUE	1	0.43	2		605	959	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339128	65339129	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	175	602	0	ENST00000342505.4:c.407dup	p.Asn136LysfsTer16	p.N136Kfs*16	ENST00000342505	NM_002227.2	136	aat/aaAt	5/25	1	2	FACETS	0.895	0.825	0.969	0.895	0.825	0.969	CLONAL	1	TRUE	1	0.43	2		602	909	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114905851	114905851	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	92	496	1	ENST00000543371.1:c.870G>A	p.Met290Ile	p.M290I	ENST00000543371	NM_001198531.1	290	atG/atA	8/14	1	2	FACETS	0.465	0.412	0.522	0.465	0.412	0.522	SUBCLONAL	1	TRUE	1	0.43	2		497	920	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633484	69633484	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	33	239	0	ENST00000334134.2:c.218A>T	p.Tyr73Phe	p.Y73F	ENST00000334134	NM_005247.2	73	tAc/tTc	1/3	1	2	FACETS	0.323	0.263	0.391	0.323	0.263	0.391	SUBCLONAL	1	TRUE	1	0.43	2		239	475	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103189	119103189	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757898729	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	128	525	0	ENST00000264033.4:c.227C>T	p.Ala76Val	p.A76V	ENST00000264033	NM_005188.3	76	gCg/gTg	2/16	1	2	FACETS	0.611	0.553	0.672	0.611	0.553	0.672	SUBCLONAL	1	TRUE	1	0.43	2		525	975	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503153	125503153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	115	417	0	ENST00000428830.2:c.520G>A	p.Val174Ile	p.V174I	ENST00000428830	NM_001114121.2	174	Gtt/Att	6/14	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.43	2		417	477	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415595	49415596	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	171	508	0	ENST00000301067.7:c.16581_16582del	p.Cys5527TrpfsTer38	p.C5527Wfs*38	ENST00000301067	NM_003482.3	5527	tgTGga/tgga	54/54	1	2	FACETS	0.912	0.839	0.988	0.912	0.839	0.988	CLONAL	1	TRUE	1	0.43	2		508	872	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856052	111856052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758024019	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	321	546	1	ENST00000341259.2:c.103G>A	p.Val35Ile	p.V35I	ENST00000341259	NM_005475.2	35	Gta/Ata	2/8	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.43	2		547	1177	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120805858	120805858	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1332	160	764	1	ENST00000257552.2:c.220del	p.Val74TrpfsTer32	p.V74Wfs*32	ENST00000257552	NM_002442.3	74	Gtg/tg	4/15	1	2	FACETS	0.499	0.456	0.544	0.499	0.456	0.544	SUBCLONAL	1	TRUE	1	0.43	2		765	1492	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712532	43712532	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	260	710	1	ENST00000382044.4:c.4652C>T	p.Ala1551Val	p.A1551V	ENST00000382044	NM_001141980.1	1551	gCc/gTc	21/28	1	2	FACETS	0.893	0.835	0.953	0.893	0.835	0.953	CLONAL	1	TRUE	1	0.43	2		711	1354	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865812	56865812	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	144	363	0	ENST00000308159.5:c.1144A>G	p.Asn382Asp	p.N382D	ENST00000308159	NM_014669.4	382	Aat/Gat	11/22	1	2	FACETS	0.917	0.838	1	0.917	0.838	1	CLONAL	1	TRUE	1	0.43	2		363	730	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828655	72828659	+	frameshift_variant	Frame_Shift_Del	DEL	CTTGT	CTTGT	-	novel	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	316	662	0	ENST00000268489.5:c.7922_7926del	p.Asp2641AlafsTer85	p.D2641Afs*85	ENST00000268489	NM_006885.3	2641	gACAAG/g	9/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.43	2		662	1330	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745815	745815	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	42	593	0	ENST00000314574.4:c.617del	p.Gly206ValfsTer4	p.G206Vfs*4	ENST00000314574	NM_005433.3	206	gGt/gt	6/12	1	2	FACETS	0.393	0.328	0.465	0.393	0.328	0.465	SUBCLONAL	1	TRUE	1	0.43	2		593	497	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143093	7143093	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	241	601	1	ENST00000302850.5:c.2276G>T	p.Arg759Leu	p.R759L	ENST00000302850	NM_000208.2	759	cGg/cTg	12/22	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.43	2		602	1064	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219065	36219066	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	315	716	0	ENST00000222270.7:c.4564_4565del	p.Leu1522AlafsTer155	p.L1522Afs*155	ENST00000222270	NM_014727.1	1522	CTg/g	19/37	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.43	2		716	1198	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131370	202131370	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	174	556	0	ENST00000358485.4:c.338T>C	p.Leu113Ser	p.L113S	ENST00000358485	NM_001080125.1	113	tTg/tCg	2/9	1	2	FACETS	0.948	0.873	1	0.948	0.873	1	CLONAL	1	TRUE	1	0.43	2		556	854	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119595356	119595356	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	68	285	0	ENST00000316626.5:c.814-1G>A		p.X272_splice	ENST00000316626		272			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.43	2		285	261	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280176	142280176	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	121	522	0	ENST00000350721.4:c.1258C>A	p.Leu420Ile	p.L420I	ENST00000350721	NM_001184.3	420	Ctc/Atc	5/47	1	2	FACETS	0.697	0.63	0.769	0.697	0.63	0.769	SUBCLONAL	1	TRUE	1	0.43	2		522	807	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921518	178921518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	43	424	0	ENST00000263967.3:c.1000C>T	p.Leu334Phe	p.L334F	ENST00000263967	NM_006218.2	334	Ctc/Ttc	5/21	1	2	FACETS	0.439	0.367	0.518	0.439	0.367	0.518	SUBCLONAL	1	TRUE	1	0.43	2		424	456	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294199	1294199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749827230	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1303	124	793	1	ENST00000310581.5:c.802C>T	p.Arg268Cys	p.R268C	ENST00000310581	NM_198253.2	268	Cgt/Tgt	2/16	1	2	FACETS	0.404	0.364	0.447	0.404	0.364	0.447	SUBCLONAL	1	TRUE	1	0.43	2		794	1427	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200339	138200339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756832433	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	107	578	0	ENST00000237289.4:c.1757C>T	p.Ala586Val	p.A586V	ENST00000237289	NM_001270507.1	586	gCc/gTc	7/9	1	2	FACETS	0.461	0.413	0.513	0.461	0.413	0.513	SUBCLONAL	1	TRUE	1	0.43	2		578	1079	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133901	38133901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	252	742	1	ENST00000317025.8:c.3985G>A	p.Asp1329Asn	p.D1329N	ENST00000317025	NM_023034.1	1329	Gat/Aat	23/24	1	2	FACETS	0.929	0.868	0.992	0.929	0.868	0.992	CLONAL	1	TRUE	1	0.43	2		743	1262	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239118	98239119	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	90	502	0	ENST00000331920.6:c.1524dup	p.Gly509TrpfsTer6	p.G509Wfs*6	ENST00000331920	NM_000264.3	508	-/T	11/24	1	2	FACETS	0.519	0.46	0.582	0.519	0.46	0.582	SUBCLONAL	1	TRUE	1	0.43	2		502	807	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222247	53222247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	294	784	2	ENST00000375401.3:c.4585G>A	p.Ala1529Thr	p.A1529T	ENST00000375401	NM_004187.3	1529	Gcg/Acg	26/26	1	2	FACETS	0.977	0.918	1	0.977	0.918	1	CLONAL	1	TRUE	1	0.43	2		786	1400	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224172	53224172	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1362	133	806	1	ENST00000375401.3:c.3379A>T	p.Lys1127Ter	p.K1127*	ENST00000375401	NM_004187.3	1127	Aaa/Taa	22/26	1	2	FACETS	0.414	0.374	0.456	0.414	0.374	0.456	SUBCLONAL	1	TRUE	1	0.43	2		807	1495	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210299	123210299	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	24	464	0	ENST00000218089.9:c.2651A>T	p.Asp884Val	p.D884V	ENST00000218089	NM_001042749.1	884	gAt/gTt	26/35	1	2	FACETS	0.269	0.21	0.337	0.269	0.21	0.337	SUBCLONAL	1	TRUE	1	0.43	2		464	415	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0053680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	198	470	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.4974994581767	3	FACETS	0.936	0.874	0.999	0.936	0.874	0.999	CLONAL	2	TRUE	1	0.4974994581767	3		470	531	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597395	10597395	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	192	851	0	ENST00000171111.5:c.1808G>T	p.Gly603Val	p.G603V	ENST00000171111	NM_203500.1	603	gGg/gTg	6/6	0.4974994581767	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.4974994581767	1		851	569	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380245	25380245	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	141	565	1	ENST00000311936.3:c.213C>A	p.Tyr71Ter	p.Y71*	ENST00000311936	NM_004985.3	71	taC/taA	3/5	0.4974994581767	3	FACETS	1	0.976	1	0.59	0.539	0.643	CLONAL	1	TRUE	1	0.4974994581767	3		566	600	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416503	49416503	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	332	670	0	ENST00000301067.7:c.16208G>C	p.Arg5403Pro	p.R5403P	ENST00000301067	NM_003482.3	5403	cGc/cCc	51/54	0.4974994581767	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.4974994581767	3		670	804	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097035	11097035	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	185	917	0	ENST00000358026.2:c.526C>T	p.Gln176Ter	p.Q176*	ENST00000358026	NM_001128849.1	176	Cag/Tag	4/36	0.4974994581767	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.4974994581767	1		917	535	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868492	117868492	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	93	459	0	ENST00000297338.2:c.850G>T	p.Val284Phe	p.V284F	ENST00000297338	NM_006265.2	284	Gtt/Ttt	8/14	0.4974994581767	4	FACETS	0.909	0.809	1	0.303	0.269	0.339	CLONAL	1	TRUE	1	0.4974994581767	4		459	616	SUCCESS
AR	367	MSKCC	GRCh37	X	66766583	66766583	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	141	808	0	ENST00000374690.3:c.1595C>A	p.Ser532Tyr	p.S532Y	ENST00000374690	NM_000044.3	532	tCc/tAc	1/8	1	2	FACETS	0.984	0.9	1	0.984	0.9	1	CLONAL	1	TRUE	1	0.4974994581767	2		808	576	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0053681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	187	603	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.322047705220095	3	FACETS	1	0.983	1	0.613	0.565	0.662	CLONAL	1	TRUE	1	0.322047705220095	3		603	1100	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781371	NA	P-0053681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	147	768	3	ENST00000269305.4:c.328C>T	p.Arg110Cys	p.R110C	ENST00000269305	NM_001126112.2	110	Cgt/Tgt	4/11	0.322047705220095	1	FACETS	0.813	0.742	0.888	0.813	0.742	0.888	CLONAL	1	TRUE	0	0.322047705220095	1		771	942	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6438294	6438294	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	124	463	0	ENST00000356142.4:c.227T>C	p.Val76Ala	p.V76A	ENST00000356142	NM_018890.3	76	gTt/gCt	4/7	0.322047705220095	3	FACETS	1	0.957	1	0.551	0.499	0.607	CLONAL	1	TRUE	1	0.322047705220095	3		463	811	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249028	55249028	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	181	698	0	ENST00000275493.2:c.2326C>A	p.Arg776Ser	p.R776S	ENST00000275493	NM_005228.3	776	Cgc/Agc	20/28	0.322047705220095	3	FACETS	1	0.983	1	0.616	0.568	0.667	CLONAL	1	TRUE	1	0.322047705220095	3		698	1059	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0053681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	19	409	1	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.303703198515117	1	FACETS	0.188	0.142	0.242	0.188	0.142	0.242	SUBCLONAL	1	TRUE	0	0.322047705220095	1		410	527	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593492	48593492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	32	320	1	ENST00000342988.3:c.1243G>A	p.Asp415Asn	p.D415N	ENST00000342988	NM_005359.5	415	Gac/Aac	10/12	0.303703198515117	1	FACETS	0.296	0.24	0.36	0.296	0.24	0.36	SUBCLONAL	1	TRUE	0	0.322047705220095	1		321	563	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0053681-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	192	603	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.489372842089712	3	FACETS	1	0.942	1	0.511	0.472	0.551	CLONAL	1	TRUE	1	0.489857102787895	3		603	955	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781371	NA	P-0053681-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	216	768	3	ENST00000269305.4:c.328C>T	p.Arg110Cys	p.R110C	ENST00000269305	NM_001126112.2	110	Cgt/Tgt	4/11	0.489857102787895	1	FACETS	0.945	0.882	1	0.945	0.882	1	CLONAL	1	TRUE	0	0.489857102787895	1		771	705	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6438294	6438294	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053681-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	141	463	0	ENST00000356142.4:c.227T>C	p.Val76Ala	p.V76A	ENST00000356142	NM_018890.3	76	gTt/gCt	4/7	0.489372842089712	3	FACETS	0.984	0.898	1	0.492	0.449	0.538	CLONAL	1	TRUE	1	0.489857102787895	3		463	728	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249028	55249028	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053681-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	170	698	0	ENST00000275493.2:c.2326C>A	p.Arg776Ser	p.R776S	ENST00000275493	NM_005228.3	776	Cgc/Agc	20/28	0.489372842089712	3	FACETS	0.905	0.832	0.981	0.452	0.416	0.491	CLONAL	1	TRUE	1	0.489857102787895	3		698	955	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0053682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	35	817	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.555279566897217	1	FACETS	0.796	0.699	0.887	1	0.969	1	SUBCLONAL	2	TRUE	0	0.578461936468776	1		819	54	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0053682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	13	464	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.578461936468776	2		464	34	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054402	42054402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752413385	NA	P-0053682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	10	448	0	ENST00000219905.7:c.7586G>A	p.Arg2529Lys	p.R2529K	ENST00000219905	NM_001164273.1	2529	aGa/aAa	22/24	0.198766993212993	3	FACETS	0.464	0.317	0.645	0.232	0.158	0.323	INDETERMINATE	1	TRUE	1	0.578461936468776	3		448	96	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661393	227661393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751466820	NA	P-0053682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	25	703	1	ENST00000305123.5:c.2062G>A	p.Ala688Thr	p.A688T	ENST00000305123	NM_005544.2	688	Gcc/Acc	1/2	0.210961317197949	5	FACETS	0.854	0.702	1	0.854	0.702	1	INDETERMINATE	3	TRUE	2	0.578461936468776	5		704	63	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574638	41574638	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759647202	NA	P-0053682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	12	901	2	ENST00000263253.7:c.6923G>A	p.Arg2308His	p.R2308H	ENST00000263253	NM_001429.3	2308	cGc/cAc	31/31	0.228637126800441	1	FACETS	0.238	0.168	0.322	0.238	0.168	0.322	INDETERMINATE	1	TRUE	0	0.578461936468776	1		903	124	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	36	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.754	0.624	0.897	0.754	0.624	0.897	SUBCLONAL	1	TRUE	1	0.394771789230712	2		276	242	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0053683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	225	781	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.394771789230712	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.394771789230712	1		782	632	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690819	89690820	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0053683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	86	408	0	ENST00000371953.3:c.227_228del	p.Tyr76Ter	p.Y76*	ENST00000371953	NM_000314.4	76	TAt/t	4/9	0.394771789230712	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.394771789230712	1		408	312	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779129	135779129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	110	579	1	ENST00000298552.3:c.2117G>A	p.Arg706His	p.R706H	ENST00000298552	NM_001162426.1	706	cGt/cAt	17/23	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.394771789230712	2		580	546	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955593	55955593	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs373654225	NA	P-0053683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	65	552	0	ENST00000263923.4:c.3352C>T	p.Arg1118Ter	p.R1118*	ENST00000263923	NM_002253.2	1118	Cga/Tga	25/30	1	2	FACETS	0.73	0.635	0.833	0.73	0.635	0.833	SUBCLONAL	1	TRUE	1	0.394771789230712	2		552	451	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934263	48934263	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0053683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	111	514	0	ENST00000267163.4:c.718A>T	p.Lys240Ter	p.K240*	ENST00000267163	NM_000321.2	240	Aaa/Taa	7/27	0.394771789230712	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.394771789230712	1		514	359	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347699	89347699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201278036	NA	P-0053683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	77	857	2	ENST00000301030.4:c.5251G>A	p.Ala1751Thr	p.A1751T	ENST00000301030	NM_001256183.1	1751	Gct/Act	9/13	1	2	FACETS	0.747	0.657	0.844	0.747	0.657	0.844	SUBCLONAL	1	TRUE	1	0.394771789230712	2		859	522	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158245	47158245	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0053683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	59	370	0	ENST00000409792.3:c.4455-1G>A		p.X1485_splice	ENST00000409792	NM_014159.6	1485			1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.394771789230712	2		370	269	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930142	68930142	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs774177545	NA	P-0053683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	85	504	0	ENST00000288368.4:c.203A>G	p.Glu68Gly	p.E68G	ENST00000288368	NM_024870.2	68	gAa/gGa	2/40	1	2	FACETS	0.865	0.767	0.969	0.865	0.767	0.969	CLONAL	1	TRUE	1	0.394771789230712	2		504	498	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	37	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.288	0.237	0.345	0.288	0.237	0.345	SUBCLONAL	1	TRUE	1	0.571596676951573	2		276	449	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643474	38643474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115440602	NA	P-0053693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	72	535	0	ENST00000299084.4:c.944C>T	p.Pro315Leu	p.P315L	ENST00000299084	NM_152594.2	315	cCt/cTt	7/7	1	2	FACETS	0.869	0.767	0.976	0.869	0.767	0.976	CLONAL	1	TRUE	1	0.571596676951573	2		535	290	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17125845	17125845	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	306	791	0	ENST00000285071.4:c.749T>G	p.Leu250Arg	p.L250R	ENST00000285071	NM_144997.5	250	cTg/cGg	7/14	1	2	FACETS	0.948	0.893	1	0.948	0.893	1	CLONAL	1	TRUE	1	0.571596676951573	2		791	1130	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212651	36212651	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	272	918	0	ENST00000222270.7:c.2402T>A	p.Val801Glu	p.V801E	ENST00000222270	NM_014727.1	801	gTg/gAg	3/37	1	2	FACETS	0.94	0.882	0.998	0.94	0.882	0.998	CLONAL	1	TRUE	1	0.571596676951573	2		918	1013	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225449662	225449662	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	255	481	0	ENST00000264414.4:c.65del	p.Pro22ArgfsTer2	p.P22Rfs*2	ENST00000264414	NM_003590.4	22	cCg/cg	1/16	0.571596676951573	2	FACETS	0.898	0.851	0.944	0.898	0.851	0.944	CLONAL	2	TRUE	0	0.571596676951573	2		481	497	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	143	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.902	0.828	0.978	0.902	0.828	0.978	CLONAL	1	TRUE	1	0.666138612113521	2		276	476	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440372	52440372	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	301	578	0	ENST00000460680.1:c.680G>C	p.Arg227Pro	p.R227P	ENST00000460680	NM_004656.3	227	cGc/cCc	9/17	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.666138612113521	2		578	875	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797314	135797314	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	279	271	0	ENST00000298552.3:c.555del	p.Tyr185Ter	p.Y185*	ENST00000298552	NM_001162426.1	185	taC/ta	7/23	0.634146849367567	2	FACETS	0.965	0.923	1	0.965	0.923	1	CLONAL	2	TRUE	0	0.666138612113521	2		271	434	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709524	176709524	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587784169	NA	P-0053694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	155	310	1	ENST00000439151.2:c.5951G>A	p.Arg1984Gln	p.R1984Q	ENST00000439151	NM_022455.4	1984	cGa/cAa	19/23	1	2	FACETS	0.952	0.878	1	0.952	0.878	1	CLONAL	1	TRUE	1	0.666138612113521	2		311	489	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652037	36652041	+	frameshift_variant	Frame_Shift_Del	DEL	TGTCA	TGTCA	-	novel	NA	P-0053694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	439	956	0	ENST00000244741.5:c.159_163del	p.Val54ArgfsTer7	p.V54Rfs*7	ENST00000244741	NM_000389.4	53	ttTGTCAcc/ttcc	2/3	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.666138612113521	2		956	1302	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971138	21971142	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CGGCG	CGGCG	-	novel	NA	P-0053694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	298	529	0	ENST00000304494.5:c.216_220del	p.Cys72Ter	p.C72*	ENST00000304494	NM_000077.4	72	tgCGCCGac/tgac	2/3	0.609970077517547	1	FACETS	0.967	0.919	1	0.967	0.919	1	CLONAL	1	TRUE	0	0.666138612113521	1		529	617	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651970	36651971	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0053694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	316	764	0	ENST00000244741.5:c.92_93insAC	p.Ser31ArgfsTer8	p.S31Rfs*8	ENST00000244741	NM_000389.4	31	agc/agACc	2/3	1	2	FACETS	0.866	0.818	0.916	0.866	0.818	0.916	CLONAL	1	TRUE	1	0.666138612113521	2		764	1095	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	175	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.767379081269754	2		276	364	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008549	70008549	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775320252	NA	P-0053694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	76	237	0	ENST00000394351.3:c.836G>A	p.Arg279Gln	p.R279Q	ENST00000394351	NM_000248.3	279	cGg/cAg	8/9	1	2	FACETS	0.377	0.331	0.426	0.377	0.331	0.426	SUBCLONAL	1	TRUE	1	0.767379081269754	2		237	526	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0053695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	969	836	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.491737747514168	4	FACETS	0.885	0.864	0.906			1	CLONAL	4	FALSE	NA	0.551712923785769	4		836	1539	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482438	56482438	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	312	557	0	ENST00000267101.3:c.986A>C	p.Lys329Thr	p.K329T	ENST00000267101	NM_001982.3	329	aAa/aCa	8/28	0.222635525660042	3	FACETS	0.933	0.885	0.982	0.933	0.885	0.982	INDETERMINATE	2	FALSE	1	0.551712923785769	3		557	773	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991721	72991721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370398587	NA	P-0053695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	361	461	2	ENST00000268489.5:c.2324C>T	p.Ala775Val	p.A775V	ENST00000268489	NM_006885.3	775	gCg/gTg	2/10	0.561673581874855	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	FALSE	0	0.551712923785769	2		463	594	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618689	37618690	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	599	560	0	ENST00000447079.4:c.366dup	p.Leu123ThrfsTer4	p.L123Tfs*4	ENST00000447079	NM_015083.1	122	tta/ttAa	1/14	0.491737747514168	4	FACETS	1	0.991	1			1	CLONAL	3	FALSE	NA	0.551712923785769	4		560	1053	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650879	37650879	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	328	347	1	ENST00000447079.4:c.2351del	p.Arg784GlnfsTer6	p.R784Qfs*6	ENST00000447079	NM_015083.1	784	cGa/ca	5/14	0.491737747514168	4	FACETS	0.875	0.828	0.923			1	CLONAL	2	FALSE	NA	0.551712923785769	4		348	1054	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015067	71015067	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	236	432	0	ENST00000318789.4:c.1863T>G	p.Ser621Arg	p.S621R	ENST00000318789	NM_032682.5	621	agT/agG	20/21	NA	2	FACETS	0.807	0.761	0.854			1	INDETERMINATE	2	FALSE	NA	0.551712923785769	2		432	530	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	98	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.951	1	1	0.988	1	CLONAL	2	TRUE	1	0.1639603891856	2		276	539	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0053696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	492	1039	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	0.109939268032671	4	FACETS	0.949	0.912	0.987	1	0.998	1	CLONAL	7	TRUE	2	0.1639603891856	4		1039	1051	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445235	49445235	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1233	278	1478	0	ENST00000301067.7:c.2231C>A	p.Ser744Ter	p.S744*	ENST00000301067	NM_003482.3	744	tCa/tAa	10/54	1	2	FACETS	1	0.982	1	1	0.995	1	CLONAL	2	TRUE	1	0.1639603891856	2		1478	1511	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0053697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	35	373	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	0.26869861105691	3	FACETS	0.722	0.592	0.867	0.361	0.296	0.434	SUBCLONAL	1	TRUE	1	0.29	3		373	383	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750827	57750827	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	48	392	0	ENST00000274289.3:c.1777A>G	p.Thr593Ala	p.T593A	ENST00000274289	NM_006622.3	593	Act/Gct	13/14	0.270707865730244	3	FACETS	0.974	0.826	1	0.487	0.413	0.569	CLONAL	1	TRUE	1	0.29	3		392	389	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	162	670	3	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.348538181460015	2		673	858	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	124	397	3	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	0.348538181460015	1	FACETS	0.939	0.851	1	0.939	0.851	1	CLONAL	1	FALSE	0	0.348538181460015	1		400	626	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	131	436	2	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.348538181460015	2		438	652	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	114	465	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.348538181460015	2		465	499	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882049	36882050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs780753361	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	231	1072	8	ENST00000358127.4:c.963dup	p.Ala322ArgfsTer19	p.A322Rfs*19	ENST00000358127	NM_001280556.1	321	-/C	8/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.348538181460015	2		1080	1084	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	154	418	1	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.348538181460015	2		419	647	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	178	904	4	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.348538181460015	2		908	826	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	90	573	4	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.856	0.761	0.958	0.856	0.761	0.958	CLONAL	1	FALSE	1	0.348538181460015	2		577	603	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778972	9778972	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1214315014	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	139	617	1	ENST00000377346.4:c.1241C>T	p.Ala414Val	p.A414V	ENST00000377346	NM_005026.3	414	gCg/gTg	9/24	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.348538181460015	2		618	749	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	10	328	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.127	0.085	0.18	0.127	0.085	0.18	SUBCLONAL	1	FALSE	1	0.348538181460015	2		328	451	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266134	41266136	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs587776850	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	11	360	0	ENST00000349496.5:c.133_135del	p.Ser45del	p.S45del	ENST00000349496	NM_001904.3	44	cCTTct/cct	3/15	1	2	FACETS	0.146	0.1	0.204	0.146	0.1	0.204	SUBCLONAL	1	FALSE	1	0.348538181460015	2		360	432	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	171	823	1	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.348538181460015	2		824	825	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913253	39913253	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	58	647	0	ENST00000378444.4:c.4862del	p.Pro1621GlnfsTer53	p.P1621Qfs*53	ENST00000378444	NM_001123385.1	1621	cCa/ca	14/15	1	2	FACETS	0.525	0.451	0.606	0.525	0.451	0.606	SUBCLONAL	1	FALSE	1	0.348538181460015	2		647	634	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	115	495	2	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.348538181460015	2		497	548	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513282	44513287	+	inframe_deletion	In_Frame_Del	DEL	CCACCG	CCACCG	-	rs745888281	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	191	706	1	ENST00000291552.4:c.648_653del	p.Gly222_Gly223del	p.G222_G223del	ENST00000291552	NM_006758.2	216	ggCGGTGGt/ggt	8/8	1	2	FACETS	0.972	0.898	1	0.972	0.898	1	CLONAL	1	FALSE	1	0.348538181460015	2		707	1127	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505443	157505443	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554231830	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	64	518	0	ENST00000346085.5:c.3428del	p.Lys1143SerfsTer68	p.K1143Sfs*68	ENST00000346085	NM_020732.3	1142	Aaa/aa	13/20	1	2	FACETS	0.575	0.497	0.659	0.575	0.497	0.659	SUBCLONAL	1	FALSE	1	0.348538181460015	2		518	639	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003779	45003779	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	44	707	0	ENST00000558401.1:c.35T>C	p.Leu12Pro	p.L12P	ENST00000558401	NM_004048.2	12	cTa/cCa	1/4	1	2	FACETS	0.378	0.316	0.447	0.378	0.316	0.447	SUBCLONAL	1	FALSE	1	0.348538181460015	2		707	668	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119024	70119024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	181	907	1	ENST00000245479.2:c.600del	p.Asn201ThrfsTer18	p.N201Tfs*18	ENST00000245479	NM_000346.3	199	tCc/tc	2/3	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.348538181460015	2		908	914	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	71	1075	1	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.373	0.325	0.427	0.373	0.325	0.427	SUBCLONAL	1	FALSE	1	0.348538181460015	2		1076	1091	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527398	157527398	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	34	439	0	ENST00000346085.5:c.5127del	p.Ala1710HisfsTer56	p.A1710Hfs*56	ENST00000346085	NM_020732.3	1708	cAa/ca	20/20	1	2	FACETS	0.366	0.298	0.442	0.366	0.298	0.442	SUBCLONAL	1	FALSE	1	0.348538181460015	2		439	533	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738979	145738979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766748490	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	214	846	2	ENST00000428558.2:c.2176G>A	p.Ala726Thr	p.A726T	ENST00000428558	NM_004260.3	726	Gca/Aca	13/22	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.348538181460015	2		848	900	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599271	28599271	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs770146088	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	222	1070	0	ENST00000253063.3:c.722del	p.Pro241GlnfsTer6	p.P241Qfs*6	ENST00000253063	NM_031459.4	239	agC/ag	5/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.348538181460015	2		1070	1135	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216189	36216189	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	248	976	2	ENST00000222270.7:c.3602del	p.Pro1201ArgfsTer154	p.P1201Rfs*154	ENST00000222270	NM_014727.1	1199	ggC/gg	11/37	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	1	0.348538181460015	2		978	1004	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413578	32413578	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121907909	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	125	490	0	ENST00000332351.3:c.1372C>T	p.Arg458Ter	p.R458*	ENST00000332351	NM_024426.4	458	Cga/Tga	9/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.348538181460015	2		490	641	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087346	27087346	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	103	436	0	ENST00000324856.7:c.1921-1G>T		p.X641_splice	ENST00000324856	NM_006015.4	641			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.348538181460015	2		436	470	SUCCESS
AR	367	MSKCC	GRCh37	X	66765635	66765635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	217	1084	0	ENST00000374690.3:c.647G>A	p.Gly216Glu	p.G216E	ENST00000374690	NM_000044.3	216	gGg/gAg	1/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.348538181460015	2		1084	972	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007642	45007642	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	27	297	0	ENST00000558401.1:c.89A>G	p.Tyr30Cys	p.Y30C	ENST00000558401	NM_004048.2	30	tAc/tGc	2/4	1	2	FACETS	0.489	0.389	0.602	0.489	0.389	0.602	SUBCLONAL	1	FALSE	1	0.348538181460015	2		297	317	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428598	78428598	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	72	463	0	ENST00000370768.2:c.1201del	p.Ser401AlafsTer2	p.S401Afs*2	ENST00000370768	NM_003902.3	401	Agc/gc	14/20	1	2	FACETS	0.968	0.849	1	0.968	0.849	1	CLONAL	1	FALSE	1	0.348538181460015	2		463	427	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244243	5244243	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1390768500	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	103	1026	0	ENST00000357368.4:c.1239del	p.Ser414AlafsTer30	p.S414Afs*30	ENST00000357368	NM_002850.3	413	ccC/cc	11/38	1	2	FACETS	0.559	0.499	0.623	0.559	0.499	0.623	SUBCLONAL	1	FALSE	1	0.348538181460015	2		1026	1058	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139642	202139642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1351320412	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	139	428	0	ENST00000358485.4:c.803C>T	p.Ser268Leu	p.S268L	ENST00000358485	NM_001080125.1	268	tCg/tTg	6/9	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.348538181460015	2		428	622	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713851	30713853	+	inframe_deletion	In_Frame_Del	DEL	CTG	CTG	-	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	173	820	0	ENST00000295754.5:c.1180_1182del	p.Cys394del	p.C394del	ENST00000295754	NM_003242.5	392	acCTGc/acc	4/7	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.348538181460015	2		820	913	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940100	31940100	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	89	1033	0	ENST00000375333.2:c.242T>C	p.Val81Ala	p.V81A	ENST00000375333	NM_032454.1	81	gTa/gCa	2/8	1	2	FACETS	0.522	0.461	0.586	0.522	0.461	0.586	SUBCLONAL	1	FALSE	1	0.348538181460015	2		1033	979	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226573273	226573273	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	184	723	0	ENST00000366794.5:c.943G>A	p.Val315Ile	p.V315I	ENST00000366794	NM_001618.3	315	Gtc/Atc	7/23	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.348538181460015	2		723	851	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130264	2130264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1265032446	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	111	1140	0	ENST00000219476.3:c.3496C>T	p.Pro1166Ser	p.P1166S	ENST00000219476	NM_000548.3	1166	Cct/Tct	30/42	1	2	FACETS	0.584	0.523	0.648	0.584	0.523	0.648	SUBCLONAL	1	FALSE	1	0.348538181460015	2		1140	1091	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820852	3820852	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	251	1061	3	ENST00000262367.5:c.2599C>T	p.Pro867Ser	p.P867S	ENST00000262367	NM_004380.2	867	Cca/Tca	14/31	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.348538181460015	2		1064	1221	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123875183	123875183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751091053	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	97	509	0	ENST00000330479.4:c.139G>A	p.Val47Ile	p.V47I	ENST00000330479	NM_020382.3	47	Gta/Ata	3/9	1	2	FACETS	0.978	0.874	1	0.978	0.874	1	CLONAL	1	FALSE	1	0.348538181460015	2		509	569	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864534	57864534	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	187	959	0	ENST00000228682.2:c.2015del	p.Gly672GlufsTer47	p.G672Efs*47	ENST00000228682	NM_005269.2	671	Ggg/gg	12/12	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.348538181460015	2		959	871	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11269492	11269492	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	114	531	0	ENST00000361445.4:c.3678G>T	p.Glu1226Asp	p.E1226D	ENST00000361445	NM_004958.3	1226	gaG/gaT	25/58	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.348538181460015	2		531	559	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873131	71873131	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	25	313	0	ENST00000357731.5:c.1063T>C	p.Ter355GlnextTer9	p.*355Qext*9	ENST00000357731	NM_173808.2	355	Taa/Caa	7/7	1	2	FACETS	0.47	0.371	0.584	0.47	0.371	0.584	SUBCLONAL	1	FALSE	1	0.348538181460015	2		313	305	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595972	43595972	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	206	990	0	ENST00000355710.3:c.139G>T	p.Gly47Cys	p.G47C	ENST00000355710	NM_020975.4	47	Ggc/Tgc	2/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.348538181460015	2		990	1095	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	430217	430217	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	61	372	0	ENST00000399788.2:c.2485T>G	p.Phe829Val	p.F829V	ENST00000399788	NM_001042603.1	829	Ttt/Gtt	18/28	0.348538181460015	1	FACETS	0.503	0.434	0.578	0.503	0.434	0.578	SUBCLONAL	1	FALSE	0	0.348538181460015	1		372	575	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871025	12871025	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	83	459	0	ENST00000228872.4:c.252del	p.Leu84PhefsTer35	p.L84Ffs*35	ENST00000228872	NM_004064.3	84	ttG/tt	1/3	0.101809538392556	4	FACETS	1	0.976	1	0.712	0.631	0.798	INDETERMINATE	1	FALSE	2	0.348538181460015	4		459	451	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552780	18552780	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	79	389	0	ENST00000266497.5:c.2191A>C	p.Ser731Arg	p.S731R	ENST00000266497		731	Agt/Cgt	14/31	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.348538181460015	2		389	381	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243902	46243902	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	75	354	0	ENST00000334344.6:c.1996C>T	p.Gln666Ter	p.Q666*	ENST00000334344	NM_152641.2	666	Caa/Taa	15/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.348538181460015	2		354	363	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495462	56495464	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	182	813	0	ENST00000267101.3:c.3655_3657del	p.Glu1219del	p.E1219del	ENST00000267101	NM_001982.3	1218	GAG/-	28/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.348538181460015	2		813	906	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244151	133244153	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs878854850	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	208	692	0	ENST00000320574.5:c.2255_2257del	p.Ser752del	p.S752del	ENST00000320574	NM_006231.2	752	tCCTtc/ttc	20/49	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.348538181460015	2		692	883	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524671	103524671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	168	492	0	ENST00000355739.4:c.2802G>T	p.Glu934Asp	p.E934D	ENST00000355739	NM_000123.3	934	gaG/gaT	13/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.348538181460015	2		492	723	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36989334	36989334	+	start_lost	Translation_Start_Site	SNP	T	T	A	rs747000470	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	149	724	1	ENST00000354822.5:c.1A>T	p.Met1?	p.M1?	ENST00000354822	NM_001079668.2	1	Atg/Ttg	1/3	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.348538181460015	2		725	706	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058861	42058861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749267770	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	112	408	0	ENST00000219905.7:c.8581C>T	p.Arg2861Trp	p.R2861W	ENST00000219905	NM_001164273.1	2861	Cgg/Tgg	24/24	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.348538181460015	2		408	480	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358487	91358487	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	30	518	0	ENST00000355112.3:c.4232A>G	p.Lys1411Arg	p.K1411R	ENST00000355112	NM_000057.2	1411	aAg/aGg	22/22	1	2	FACETS	0.308	0.247	0.377	0.308	0.247	0.377	SUBCLONAL	1	FALSE	1	0.348538181460015	2		518	559	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467812	99467812	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1451794305	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	110	476	0	ENST00000268035.6:c.2681A>G	p.Asn894Ser	p.N894S	ENST00000268035	NM_000875.3	894	aAc/aGc	13/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.348538181460015	2		476	578	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274025	10274025	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	109	1059	0	ENST00000330684.3:c.244C>A	p.Leu82Ile	p.L82I	ENST00000330684	NM_001134407.1	82	Ctc/Atc	2/13	1	2	FACETS	0.583	0.522	0.648	0.583	0.522	0.648	SUBCLONAL	1	FALSE	1	0.348538181460015	2		1059	1073	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128235	30128235	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	76	875	0	ENST00000263025.4:c.997T>C	p.Tyr333His	p.Y333H	ENST00000263025	NM_002746.2	333	Tac/Cac	7/9	1	2	FACETS	0.457	0.399	0.519	0.457	0.399	0.519	SUBCLONAL	1	FALSE	1	0.348538181460015	2		875	955	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858081	40858081	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	94	831	0	ENST00000428826.2:c.1783T>C	p.Trp595Arg	p.W595R	ENST00000428826		595	Tgg/Cgg	16/21	1	2	FACETS	0.501	0.444	0.561	0.501	0.444	0.561	SUBCLONAL	1	FALSE	1	0.348538181460015	2		831	1077	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870056	40870056	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1220002873	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	139	503	0	ENST00000428826.2:c.961C>T	p.Arg321Cys	p.R321C	ENST00000428826		321	Cgc/Tgc	10/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.348538181460015	2		503	627	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229358	36229359	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTT	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	178	693	0	ENST00000222270.7:c.8049_8050insTTT	p.Gly2683_Glu2684insPhe	p.G2683_E2684insF	ENST00000222270	NM_014727.1	2683	ggt/ggTTTt	37/37	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.348538181460015	2		693	842	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982370	25982370	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	41	270	0	ENST00000435504.4:c.920T>A	p.Leu307His	p.L307H	ENST00000435504		307	cTc/cAc	9/13	1	2	FACETS	0.572	0.477	0.678	0.572	0.477	0.678	SUBCLONAL	1	FALSE	1	0.348538181460015	2		270	411	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568632	41568632	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	77	437	0	ENST00000263253.7:c.4582A>G	p.Lys1528Glu	p.K1528E	ENST00000263253	NM_001429.3	1528	Aaa/Gaa	28/31	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	FALSE	1	0.348538181460015	2		437	430	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598150	52598151	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	154	619	0	ENST00000394830.3:c.3715_3716del	p.Ser1239ArgfsTer18	p.S1239Rfs*18	ENST00000394830	NM_018313.4	1239	AGc/c	24/30	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.348538181460015	2		619	711	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133520	55133520	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1433722204	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	41	633	0	ENST00000257290.5:c.824T>C	p.Leu275Ser	p.L275S	ENST00000257290	NM_006206.4	275	tTg/tCg	6/23	1	2	FACETS	0.325	0.27	0.387	0.325	0.27	0.387	SUBCLONAL	1	FALSE	1	0.348538181460015	2		633	724	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293709	1293709	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1164823749	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	71	1249	0	ENST00000310581.5:c.1292C>T	p.Pro431Leu	p.P431L	ENST00000310581	NM_198253.2	431	cCc/cTc	2/16	1	2	FACETS	0.36	0.313	0.412	0.36	0.313	0.412	SUBCLONAL	1	FALSE	1	0.348538181460015	2		1249	1131	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166731	32166731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	236	1037	0	ENST00000375023.3:c.4507C>T	p.Pro1503Ser	p.P1503S	ENST00000375023	NM_004557.3	1503	Cca/Tca	24/30	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.348538181460015	2		1037	1268	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969142	93969143	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	38	373	0	ENST00000369303.4:c.1853dup	p.Asn618LysfsTer2	p.N618Kfs*2	ENST00000369303	NM_004440.3	618	aat/aaAt	10/17	1	2	FACETS	0.499	0.412	0.596	0.499	0.412	0.596	SUBCLONAL	1	FALSE	1	0.348538181460015	2		373	437	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552960	106552960	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	83	823	0	ENST00000369096.4:c.925T>C	p.Phe309Leu	p.F309L	ENST00000369096	NM_001198.3	309	Ttt/Ctt	5/7	1	2	FACETS	0.522	0.46	0.589	0.522	0.46	0.589	SUBCLONAL	1	FALSE	1	0.348538181460015	2		823	912	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023199	150023199	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	42	576	0	ENST00000253339.5:c.64A>G	p.Asn22Asp	p.N22D	ENST00000253339		22	Aac/Gac	1/7	1	2	FACETS	0.43	0.358	0.509	0.43	0.358	0.509	SUBCLONAL	1	FALSE	1	0.348538181460015	2		576	561	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874886	151874886	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	101	377	0	ENST00000262189.6:c.7652A>G	p.His2551Arg	p.H2551R	ENST00000262189	NM_170606.2	2551	cAc/cGc	38/59	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.348538181460015	2		377	470	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521385	8521385	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	107	611	1	ENST00000356435.5:c.853G>T	p.Gly285Ter	p.G285*	ENST00000356435		285	Gga/Tga	9/35	1	2	FACETS	0.937	0.842	1	0.937	0.842	1	CLONAL	1	FALSE	1	0.348538181460015	2		612	655	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760480	133760480	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1230752004	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	193	867	0	ENST00000318560.5:c.2803A>G	p.Thr935Ala	p.T935A	ENST00000318560	NM_005157.4	935	Acg/Gcg	11/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.348538181460015	2		867	937	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932877	39932877	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	122	884	0	ENST00000378444.4:c.1722del	p.Asn575MetfsTer14	p.N575Mfs*14	ENST00000378444	NM_001123385.1	574	ccC/cc	4/15	1	2	FACETS	0.882	0.797	0.971	0.882	0.797	0.971	CLONAL	1	FALSE	1	0.348538181460015	2		884	794	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228029	53228029	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	151	935	0	ENST00000375401.3:c.2285A>C	p.Lys762Thr	p.K762T	ENST00000375401	NM_004187.3	762	aAg/aCg	16/26	1	2	FACETS	0.918	0.839	1	0.918	0.839	1	CLONAL	1	FALSE	1	0.348538181460015	2		935	944	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0053699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	137	328	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.254327157127603	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.254327157127603	2		328	483	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0053699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	36	316	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.672	0.553	0.806	0.672	0.553	0.806	SUBCLONAL	1	TRUE	1	0.254327157127603	2		316	421	SUCCESS
APC	324	MSKCC	GRCh37	5	112174112	112174112	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	43	280	0	ENST00000257430.4:c.2821G>T	p.Glu941Ter	p.E941*	ENST00000257430	NM_000038.5	941	Gaa/Taa	16/16	1	2	FACETS	0.79	0.662	0.932	0.79	0.662	0.932	CLONAL	1	TRUE	1	0.254327157127603	2		280	428	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143981	11143981	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	63	589	2	ENST00000358026.2:c.3562G>T	p.Asp1188Tyr	p.D1188Y	ENST00000358026	NM_001128849.1	1188	Gac/Tac	26/36	1	2	FACETS	0.615	0.531	0.707	0.615	0.531	0.707	SUBCLONAL	1	TRUE	1	0.254327157127603	2		591	805	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798461	45798461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779997419	NA	P-0053699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	78	926	1	ENST00000450313.1:c.550C>T	p.Arg184Trp	p.R184W	ENST00000450313	NM_012222.2	184	Cgg/Tgg	7/16	1	2	FACETS	0.515	0.45	0.584	0.515	0.45	0.584	SUBCLONAL	1	TRUE	1	0.254327157127603	2		927	1192	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748602	40748602	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	73	452	0	ENST00000373198.4:c.2914C>T	p.Arg972Ter	p.R972*	ENST00000373198	NM_133170.3	972	Cga/Tga	21/32	0.254327157127603	1	FACETS	0.916	0.802	1	0.916	0.802	1	CLONAL	1	TRUE	0	0.254327157127603	1		452	547	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0053700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	1020	444	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.395418791772078	3	FACETS	1	0.997	1	1	0.998	1	CLONAL	4	TRUE	0	0.435899866679653	3		444	1317	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0053700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	318	879	3	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.435899866679653	1	FACETS	0.852	0.81	0.893	1	0.996	1	CLONAL	2	TRUE	0	0.435899866679653	1		882	670	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15365046	15365046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200802400	NA	P-0053700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1960	128	732	1	ENST00000263377.2:c.2075C>T	p.Ser692Phe	p.S692F	ENST00000263377	NM_058243.2	692	tCc/tTc	11/20	0.435899866679653	9	FACETS	0.71	0.641	0.785	0.089	0.08	0.099	SUBCLONAL	1	TRUE	1	0.435899866679653	9		733	2088	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435027	110435028	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0053700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	138	881	0	ENST00000375856.3:c.3373dup	p.Gln1125ProfsTer200	p.Q1125Pfs*200	ENST00000375856	NM_003749.2	1125	cag/cCag	1/2	1	2	FACETS	0.72	0.655	0.789	0.72	0.655	0.789	SUBCLONAL	1	TRUE	1	0.435899866679653	2		881	879	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141567303	141567304	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCGTCTGC	novel	NA	P-0053700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	207	676	0	ENST00000220592.5:c.903_910dup	p.Val304GlyfsTer56	p.V304Gfs*56	ENST00000220592	NM_012154.3	304	gtg/gGCAGACGGtg	8/19	0.435899866679653	3	FACETS	1	0.947	1	0.513	0.475	0.552	CLONAL	1	TRUE	1	0.435899866679653	3		676	1127	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	119	386	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.881	0.8	0.964	0.881	0.8	0.964	CLONAL	1	TRUE	1	0.608782972437048	2		386	444	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0053701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	169	289	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.608782972437048	2	FACETS	0.964	0.907	1	0.964	0.907	1	CLONAL	2	TRUE	0	0.608782972437048	2		289	288	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119104	70119104	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	141	533	0	ENST00000245479.2:c.676G>T	p.Glu226Ter	p.E226*	ENST00000245479	NM_000346.3	226	Gag/Tag	2/3	1	2	FACETS	0.983	0.903	1	0.983	0.903	1	CLONAL	1	TRUE	1	0.608782972437048	2		533	471	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178713	108178713	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0053701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	60	258	0	ENST00000278616.4:c.5762+2T>G		p.X1921_splice	ENST00000278616	NM_000051.3	1921			0.608782972437048	1	FACETS	0.926	0.819	1	0.926	0.819	1	CLONAL	1	TRUE	0	0.608782972437048	1		258	148	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096192	71096193	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0053701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	142	428	0	ENST00000318789.4:c.564dup	p.Gln189AlafsTer106	p.Q189Afs*106	ENST00000318789	NM_032682.5	188	-/G	10/21	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.608782972437048	2		428	435	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797254	32797254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772061173	NA	P-0053701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	305	1069	0	ENST00000374899.4:c.1855C>T	p.Arg619Trp	p.R619W	ENST00000374899	NM_018833.2	619	Cgg/Tgg	11/12	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.608782972437048	2		1069	932	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476826	140476826	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	49	563	0	ENST00000288602.6:c.1580T>C	p.Ile527Thr	p.I527T	ENST00000288602	NM_004333.4	527	aTt/aCt	13/18	0.322195178971619	3	FACETS	0.409	0.346	0.478	0.136	0.115	0.16	INDETERMINATE	1	TRUE	0	0.608782972437048	3		563	513	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578369	7578369	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0053702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	576	666	0	ENST00000269305.4:c.559+2T>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.594484621803789	3	FACETS	1	0.996	1			1	CLONAL	3	TRUE	NA	0.594484621803789	3		666	742	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944729	206944731	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	rs1473801814	NA	P-0053702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	97	504	0	ENST00000423557.1:c.195_197del	p.Leu66del	p.L66del	ENST00000423557	NM_000572.2	65	ttGTTa/tta	2/5	0.594484621803789	3	FACETS	0.855	0.766	0.95	0.428	0.383	0.475	CLONAL	1	TRUE	1	0.594484621803789	3		504	495	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562303	95562303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1372597986	NA	P-0053703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	129	447	0	ENST00000393063.1:c.4954C>T	p.His1652Tyr	p.H1652Y	ENST00000393063	NM_030621.3	1652	Cat/Tat	24/28	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.681002007546743	2		447	347	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0053703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	243	908	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.681002007546743	2		908	671	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931967	39931967	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	274	1038	0	ENST00000378444.4:c.2632del	p.Val878Ter	p.V878*	ENST00000378444	NM_001123385.1	878	Gta/ta	4/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.681002007546743	2		1038	716	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591270	67591270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1289880098	NA	P-0053704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	21	435	0	ENST00000274335.5:c.1768C>T	p.Arg590Trp	p.R590W	ENST00000274335		590	Cgg/Tgg	13/15	0.394703229431127	1	FACETS	0.178	0.137	0.226	0.178	0.137	0.226	SUBCLONAL	1	TRUE	0	0.555702126409299	1		435	307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs786203436	NA	P-0053704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	413	825	0	ENST00000269305.4:c.487T>A	p.Tyr163Asn	p.Y163N	ENST00000269305	NM_001126112.2	163	Tac/Aac	5/11	0.502522457029481	1	FACETS	0.961	0.917	1	0.961	0.917	1	CLONAL	1	TRUE	0	0.555702126409299	1		825	1117	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729775	41729775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	51	511	0	ENST00000242208.4:c.754G>A	p.Ala252Thr	p.A252T	ENST00000242208	NM_002192.2	252	Gcc/Acc	3/3	1	2	FACETS	0.342	0.291	0.399	0.342	0.291	0.399	SUBCLONAL	1	TRUE	1	0.555702126409299	2		511	536	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624291	89624292	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0053704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	76	579	0	ENST00000371953.3:c.65_66del	p.Asp22ValfsTer21	p.D22Vfs*21	ENST00000371953	NM_000314.4	22	gAC/g	1/9	0.51979539476177	1	FACETS	0.258	0.225	0.292	0.258	0.225	0.292	SUBCLONAL	1	TRUE	0	0.555702126409299	1		579	767	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629615	187629615	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	201	564	1	ENST00000441802.2:c.1367C>T	p.Ala456Val	p.A456V	ENST00000441802	NM_005245.3	456	gCa/gTa	2/27	0.40799666607483	1	FACETS	0.715	0.664	0.766	0.715	0.664	0.766	SUBCLONAL	1	TRUE	0	0.555702126409299	1		565	731	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs786203436	NA	P-0053704-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	69	825	0	ENST00000269305.4:c.487T>A	p.Tyr163Asn	p.Y163N	ENST00000269305	NM_001126112.2	163	Tac/Aac	5/11	1	2	FACETS	0.92	0.799	1	0.92	0.799	1	CLONAL	1	TRUE	1	0.15	2		825	1000	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629615	187629615	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053704-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	50	564	1	ENST00000441802.2:c.1367C>T	p.Ala456Val	p.A456V	ENST00000441802	NM_005245.3	456	gCa/gTa	2/27	1	2	FACETS	0.782	0.662	0.916	0.782	0.662	0.916	CLONAL	1	TRUE	1	0.15	2		565	852	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	54	276	0				ENST00000310581	NM_198253.2	-/1132			0.366240336724582	3	FACETS	0.844	0.725	0.973	0.422	0.362	0.487	CLONAL	1	TRUE	1	0.499565155091689	3		276	320	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586422	189586422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866267914	NA	P-0053705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	120	417	0	ENST00000264731.3:c.1046G>A	p.Gly349Glu	p.G349E	ENST00000264731	NM_003722.4	349	gGa/gAa	8/14	1	2	FACETS	0.885	0.802	0.971	0.885	0.802	0.971	CLONAL	1	TRUE	1	0.499565155091689	2		417	543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0053705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	277	799	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.499565155091689	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.499565155091689	1		799	799	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	116	755	0	ENST00000267101.3:c.273G>A	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atA	3/28	0.178424187241924	2	FACETS	0.614	0.554	0.678	0.307	0.277	0.339	INDETERMINATE	1	TRUE	0	0.499565155091689	2		755	756	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204864	NA	P-0053705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	86	506	2	ENST00000371953.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000371953	NM_000314.4	171	Cag/Tag	6/9	1	2	FACETS	0.931	0.829	1	0.931	0.829	1	CLONAL	1	TRUE	1	0.499565155091689	2		508	370	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974792	21974792	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs141798398	NA	P-0053705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	134	222	0	ENST00000304494.5:c.35C>A	p.Ser12Ter	p.S12*	ENST00000304494	NM_000077.4	12	tCg/tAg	1/3	0.490711253335493	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.499565155091689	2		222	215	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441262	52441262	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	94	651	0	ENST00000460680.1:c.508T>G	p.Phe170Val	p.F170V	ENST00000460680	NM_004656.3	170	Ttt/Gtt	7/17	1	2	FACETS	0.734	0.655	0.817	0.734	0.655	0.817	SUBCLONAL	1	TRUE	1	0.499565155091689	2		651	513	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526285	31526285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201151813	NA	P-0053705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	406	923	1	ENST00000344624.3:c.755G>A	p.Arg252Gln	p.R252Q	ENST00000344624		252	cGa/cAa	2/33	0.366240336724582	3	FACETS	0.861	0.821	0.903	0.861	0.821	0.903	CLONAL	2	TRUE	1	0.499565155091689	3		924	1179	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958587	38958587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs532413623	NA	P-0053705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	67	251	0	ENST00000357387.3:c.2378C>T	p.Ala793Val	p.A793V	ENST00000357387	NM_152756.3	793	gCg/gTg	24/38	0.366240336724582	3	FACETS	1	0.945	1	0.572	0.502	0.647	CLONAL	1	TRUE	1	0.499565155091689	3		251	293	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729662	162729662	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1484743299	NA	P-0053705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	130	568	0	ENST00000367921.3:c.748G>A	p.Val250Met	p.V250M	ENST00000367921	NM_006182.2	250	Gtg/Atg	8/18	0.337753770961073	1	FACETS	0.713	0.649	0.779	0.713	0.649	0.779	SUBCLONAL	1	TRUE	0	0.499565155091689	1		568	548	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138623	11138623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	39	518	1	ENST00000358026.2:c.3379G>A	p.Asp1127Asn	p.D1127N	ENST00000358026	NM_001128849.1	1127	Gat/Aat	24/36	0.464944391611561	1	FACETS	0.268	0.222	0.319	0.268	0.222	0.319	SUBCLONAL	1	TRUE	0	0.499565155091689	1		519	437	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184818	32184818	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	92	678	0	ENST00000375023.3:c.1765G>C	p.Glu589Gln	p.E589Q	ENST00000375023	NM_004557.3	589	Gag/Cag	11/30	1	2	FACETS	0.623	0.555	0.696	0.623	0.555	0.696	SUBCLONAL	1	TRUE	1	0.499565155091689	2		678	591	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163307814	163307814	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	38	281	1	ENST00000271452.3:c.440C>T	p.Ser147Phe	p.S147F	ENST00000271452	NM_145697.2	147	tCc/tTc	7/14	0.337753770961073	1	FACETS	0.431	0.358	0.511	0.431	0.358	0.511	SUBCLONAL	1	TRUE	0	0.499565155091689	1		282	265	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123353247	123353247	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	142	580	0	ENST00000358487.5:c.85G>C	p.Glu29Gln	p.E29Q	ENST00000358487	NM_000141.4	29	Gag/Cag	2/18	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.499565155091689	2		580	525	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56477614	56477614	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	77	639	0	ENST00000267101.3:c.162G>C	p.Glu54Asp	p.E54D	ENST00000267101	NM_001982.3	54	gaG/gaC	2/28	0.178424187241924	2	FACETS	0.449	0.394	0.508	0.224	0.197	0.254	INDETERMINATE	1	TRUE	0	0.499565155091689	2		639	687	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936950	48936950	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0053705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	45	307	0	ENST00000267163.4:c.719-1G>T		p.X240_splice	ENST00000267163	NM_000321.2	240			1	2	FACETS	0.862	0.733	1	0.862	0.733	1	CLONAL	1	TRUE	1	0.499565155091689	2		307	209	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508723	38508723	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	224	685	0	ENST00000254066.5:c.771G>C	p.Gln257His	p.Q257H	ENST00000254066	NM_000964.3	257	caG/caC	6/9	0.499565155091689	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.499565155091689	1		685	633	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138584	11138584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	50	672	0	ENST00000358026.2:c.3340G>A	p.Asp1114Asn	p.D1114N	ENST00000358026	NM_001128849.1	1114	Gat/Aat	24/36	0.464944391611561	1	FACETS	0.257	0.218	0.301	0.257	0.218	0.301	SUBCLONAL	1	TRUE	0	0.499565155091689	1		672	584	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797954	42797954	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	75	1103	0	ENST00000575354.2:c.4006C>T	p.Pro1336Ser	p.P1336S	ENST00000575354	NM_015125.3	1336	Ccg/Tcg	16/20	0.194337330867704	2	FACETS	0.333	0.291	0.379	0.167	0.145	0.19	INDETERMINATE	1	TRUE	0	0.499565155091689	2		1103	901	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646072	215646072	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	62	584	0	ENST00000260947.4:c.526C>G	p.Gln176Glu	p.Q176E	ENST00000260947	NM_000465.2	176	Cag/Gag	4/11	0.337753770961073	1	FACETS	0.455	0.394	0.521	0.455	0.394	0.521	SUBCLONAL	1	TRUE	0	0.499565155091689	1		584	409	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646149	215646149	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	71	510	0	ENST00000260947.4:c.449G>T	p.Arg150Leu	p.R150L	ENST00000260947	NM_000465.2	150	cGa/cTa	4/11	0.337753770961073	1	FACETS	0.608	0.534	0.686	0.608	0.534	0.686	SUBCLONAL	1	TRUE	0	0.499565155091689	1		510	351	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928837	49928837	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	168	896	0	ENST00000296474.3:c.3529C>T	p.Gln1177Ter	p.Q1177*	ENST00000296474	NM_002447.2	1177	Cag/Tag	16/20	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.499565155091689	2		896	667	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205167	128205167	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	206	957	0	ENST00000341105.2:c.274A>G	p.Ser92Gly	p.S92G	ENST00000341105	NM_032638.4	92	Agc/Ggc	3/6	1	2	FACETS	0.96	0.892	1	0.96	0.892	1	CLONAL	1	TRUE	1	0.499565155091689	2		957	859	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562499	176562499	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28932174	NA	P-0053705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	53	660	0	ENST00000439151.2:c.395G>C	p.Cys132Ser	p.C132S	ENST00000439151	NM_022455.4	132	tGt/tCt	2/23	0.194337330867704	2	FACETS	0.379	0.323	0.44	0.189	0.161	0.22	INDETERMINATE	1	TRUE	0	0.499565155091689	2		660	560	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923024	44923024	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	236	635	0	ENST00000377967.4:c.1885G>T	p.Glu629Ter	p.E629*	ENST00000377967	NM_021140.2	629	Gag/Tag	16/29	0.470158503362784	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.499565155091689	1		635	662	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928882	44928882	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	158	430	0	ENST00000377967.4:c.1982C>G	p.Ser661Cys	p.S661C	ENST00000377967	NM_021140.2	661	tCt/tGt	17/29	0.470158503362784	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.499565155091689	1		430	380	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202485	123202492	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	GAATACTA	GAATACTA	TAAGGAACTGACTAACCTTACCTGACTAAC	novel	NA	P-0053705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	42	386	0	ENST00000218089.9:c.2337_2344delinsTAAGGAACTGACTAACCTTACCTGACTAAC	p.Asn780LysfsTer8	p.N780Kfs*8	ENST00000218089	NM_001042749.1	779	gtGAATACTAct/gtTAAGGAACTGACTAACCTTACCTGACTAACct	24/35	0.470158503362784	1	FACETS	0.571	0.481	0.668	0.571	0.481	0.668	SUBCLONAL	1	TRUE	0	0.499565155091689	1		386	221	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86637110	86637110	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	28	257	0	ENST00000274376.6:c.1021C>T	p.Arg341Trp	p.R341W	ENST00000274376	NM_002890.2	341	Cgg/Tgg	6/25	1	2	FACETS	0.375	0.299	0.46	0.375	0.299	0.46	SUBCLONAL	1	TRUE	1	0.437063799077093	2		257	342	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913403	NA	P-0053706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	9	345	0	ENST00000349496.5:c.110C>A	p.Ser37Tyr	p.S37Y	ENST00000349496	NM_001904.3	37	tCt/tAt	3/15	1	2	FACETS	0.106	0.07	0.153	0.106	0.07	0.153	SUBCLONAL	1	TRUE	1	0.437063799077093	2		345	388	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913338	NA	P-0053706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	119	386	0	ENST00000288602.6:c.1781A>C	p.Asp594Ala	p.D594A	ENST00000288602	NM_004333.4	594	gAt/gCt	15/18	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.437063799077093	2		386	472	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466000	69466000	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	183	894	0	ENST00000227507.2:c.838G>T	p.Glu280Ter	p.E280*	ENST00000227507	NM_053056.2	280	Gag/Tag	5/5	1	2	FACETS	0.92	0.85	0.994	0.92	0.85	0.994	CLONAL	1	TRUE	1	0.437063799077093	2		894	910	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164727	36164727	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	145	963	0	ENST00000300305.3:c.1148C>T	p.Pro383Leu	p.P383L	ENST00000300305		383	cCg/cTg	8/8	1	2	FACETS	0.768	0.701	0.839	0.768	0.701	0.839	SUBCLONAL	1	TRUE	1	0.437063799077093	2		963	864	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602679	10602679	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	281	1115	0	ENST00000171111.5:c.899A>G	p.Tyr300Cys	p.Y300C	ENST00000171111	NM_203500.1	300	tAc/tGc	3/6	0.437063799077093	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.437063799077093	1		1115	843	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115272916	115272916	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs149300730	NA	P-0053706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	125	669	0	ENST00000438362.2:c.1457A>G	p.Asn486Ser	p.N486S	ENST00000438362	NM_001242891.1	486	aAt/aGt	12/20	1	2	FACETS	0.803	0.728	0.883	0.803	0.728	0.883	CLONAL	1	TRUE	1	0.437063799077093	2		669	712	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588860	69588860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1401631287	NA	P-0053706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	183	945	0	ENST00000168712.1:c.376G>A	p.Val126Met	p.V126M	ENST00000168712	NM_002007.2	126	Gtg/Atg	2/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.437063799077093	2		945	760	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708616	43708616	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0053706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	125	454	0	ENST00000382044.4:c.4682-2A>C		p.X1561_splice	ENST00000382044	NM_001141980.1	1561			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.437063799077093	2		454	464	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221994	1221994	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1064793427	NA	P-0053706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	205	825	0	ENST00000326873.7:c.910del	p.Arg304GlyfsTer32	p.R304Gfs*32	ENST00000326873	NM_000455.4	303	atC/at	7/10	0.437063799077093	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.437063799077093	1		825	680	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026107	36026107	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	260	1073	0	ENST00000358208.4:c.709G>T	p.Ala237Ser	p.A237S	ENST00000358208		237	Gcc/Tcc	7/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.437063799077093	2		1073	976	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0053707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	257	444	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.172352132832689	3	FACETS	1	0.993	1	0.702	0.662	0.742	INDETERMINATE	1	TRUE	1	0.845798846199632	3		444	616	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220640	1220640	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690940	NA	P-0053707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	361	1056	0	ENST00000326873.7:c.658C>T	p.Gln220Ter	p.Q220*	ENST00000326873	NM_000455.4	220	Cag/Tag	5/10	0.845798846199632	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.845798846199632	1		1056	466	SUCCESS
BTK	695	MSKCC	GRCh37	X	100629541	100629541	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	214	703	0	ENST00000308731.7:c.223C>A	p.Pro75Thr	p.P75T	ENST00000308731	NM_000061.2	75	Cca/Aca	3/19	1	2	FACETS	0.767	0.716	0.818	0.767	0.716	0.818	SUBCLONAL	1	TRUE	1	0.845798846199632	2		703	660	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609534	81609534	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	238	571	0	ENST00000298171.2:c.1132C>G	p.Leu378Val	p.L378V	ENST00000298171	NM_000369.2	378	Cta/Gta	10/10	0.845798846199632	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.845798846199632	1		571	316	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832143	72832143	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	182	611	0	ENST00000268489.5:c.4438A>T	p.Thr1480Ser	p.T1480S	ENST00000268489	NM_006885.3	1480	Act/Tct	9/10	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.845798846199632	2		611	423	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610073	10610073	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	rs758477344	NA	P-0053707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	281	759	0	ENST00000171111.5:c.637del	p.Glu213ArgfsTer17	p.E213Rfs*17	ENST00000171111	NM_203500.1	213	Gag/ag	2/6	0.845798846199632	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.845798846199632	1		759	376	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165755	47165755	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0053707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	242	573	0	ENST00000409792.3:c.371T>G	p.Leu124Ter	p.L124*	ENST00000409792	NM_014159.6	124	tTa/tGa	3/21	0.845798846199632	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.845798846199632	1		573	315	SUCCESS
APC	324	MSKCC	GRCh37	5	112176434	112176434	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	136	336	0	ENST00000257430.4:c.5143del	p.Asp1715ThrfsTer29	p.D1715Tfs*29	ENST00000257430	NM_000038.5	1715	Gac/ac	16/16	0.172352132832689	3	FACETS	1	0.986	1	0.675	0.622	0.729	INDETERMINATE	1	TRUE	1	0.845798846199632	3		336	339	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149450097	149450097	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	275	989	0	ENST00000286301.3:c.1120T>A	p.Ser374Thr	p.S374T	ENST00000286301	NM_005211.3	374	Tct/Act	8/22	0.256108495811084	1	FACETS	0.56	0.529	0.591	0.56	0.529	0.591	INDETERMINATE	1	TRUE	0	0.845798846199632	1		989	670	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036043	180036043	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	188	790	0	ENST00000261937.6:c.3818C>A	p.Thr1273Lys	p.T1273K	ENST00000261937	NM_182925.4	1273	aCa/aAa	29/30	0.221557662811339	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.845798846199632	0		790	502	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139034	37139034	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	227	893	1	ENST00000373509.5:c.374C>T	p.Pro125Leu	p.P125L	ENST00000373509	NM_002648.3	125	cCg/cTg	4/6	1	2	FACETS	0.886	0.831	0.941	0.886	0.831	0.941	CLONAL	1	TRUE	1	0.845798846199632	2		894	606	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410026	139410026	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	357	1251	2	ENST00000277541.6:c.1812C>G	p.Ile604Met	p.I604M	ENST00000277541	NM_017617.3	604	atC/atG	11/34	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.845798846199632	2		1253	760	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410060	139410060	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	335	1207	0	ENST00000277541.6:c.1778C>G	p.Pro593Arg	p.P593R	ENST00000277541	NM_017617.3	593	cCa/cGa	11/34	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.845798846199632	2		1207	741	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360639	70360640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	117	532	0	ENST00000374080.3:c.6201dup	p.Gln2068ThrfsTer97	p.Q2068Tfs*97	ENST00000374080		2067	caa/cAaa	42/45	1	2	FACETS	0.67	0.609	0.733	0.67	0.609	0.733	SUBCLONAL	1	TRUE	1	0.845798846199632	2		532	413	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519889	NA	P-0053708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	21	413	1	ENST00000263253.7:c.4195G>T	p.Asp1399Tyr	p.D1399Y	ENST00000263253	NM_001429.3	1399	Gat/Tat	26/31	1	2	FACETS	0.275	0.211	0.349	0.275	0.211	0.349	SUBCLONAL	1	TRUE	1	0.432548346445966	2		414	353	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368526	225368526	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	35	361	0	ENST00000264414.4:c.1220A>T	p.Glu407Val	p.E407V	ENST00000264414	NM_003590.4	407	gAa/gTa	9/16	1	2	FACETS	0.418	0.343	0.503	0.418	0.343	0.503	SUBCLONAL	1	TRUE	1	0.432548346445966	2		361	387	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910577	29910600	+	inframe_deletion	In_Frame_Del	DEL	CGGCCGCGGGGAGCCCCGCTTCAT	CGGCCGCGGGGAGCCCCGCTTCAT	-	novel	NA	P-0053708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	255	1268	0	ENST00000376809.5:c.119_142del	p.Gly40_Ile47del	p.G40_I47del	ENST00000376809	NM_002116.7	39	ccCGGCCGCGGGGAGCCCCGCTTCATc/ccc	2/8	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.432548346445966	2		1268	801	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348280	70348280	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	36	417	0	ENST00000374080.3:c.3344G>T	p.Cys1115Phe	p.C1115F	ENST00000374080		1115	tGc/tTc	23/45	1	1	FACETS	0.432	0.356	0.516	0.432	0.356	0.516	SUBCLONAL	1	TRUE	0	0.432548346445966	1		417	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0053710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	177	649	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.256857703632632	3	FACETS	0.988	0.916	1	0.659	0.61	0.709	CLONAL	2	TRUE	0	0.355785848049583	3		649	593	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941876	44941876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	85	383	0	ENST00000377967.4:c.3200C>T	p.Ser1067Leu	p.S1067L	ENST00000377967	NM_021140.2	1067	tCg/tTg	21/29	1	2	FACETS	0.752	0.666	0.845	0.752	0.666	0.845	SUBCLONAL	1	TRUE	1	0.355785848049583	2		383	635	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362516	118362516	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	103	420	0	ENST00000534358.1:c.4877A>C	p.Asn1626Thr	p.N1626T	ENST00000534358	NM_005933.3	1626	aAc/aCc	15/36	0.355785848049583	3	FACETS	0.927	0.829	1	0.463	0.414	0.515	CLONAL	1	TRUE	1	0.355785848049583	3		420	736	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433029	49433029	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	138	896	1	ENST00000301067.7:c.8342C>A	p.Pro2781His	p.P2781H	ENST00000301067	NM_003482.3	2781	cCt/cAt	33/54	0.239737618211545	5	FACETS	1	0.949	1	0.356	0.323	0.39	CLONAL	1	TRUE	2	0.355785848049583	5		897	1115	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609474	81609474	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	98	440	0	ENST00000298171.2:c.1072G>T	p.Glu358Ter	p.E358*	ENST00000298171	NM_000369.2	358	Gaa/Taa	10/10	1	2	FACETS	0.909	0.813	1	0.909	0.813	1	CLONAL	1	TRUE	1	0.355785848049583	2		440	606	SUCCESS
MET	4233	MSKCC	GRCh37	7	116417524	116417524	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0053710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	57	235	0	ENST00000397752.3:c.3340+1G>C		p.X1114_splice	ENST00000397752	NM_000245.2	1114			0.12772189997418	3	FACETS	1	0.927	1	0.558	0.481	0.641	INDETERMINATE	1	TRUE	1	0.355785848049583	3		235	338	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0053717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	285	817	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.526793341127848	1	FACETS	0.999	0.943	1	0.999	0.943	1	CLONAL	1	TRUE	0	0.526793341127848	1		819	798	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192660	94192660	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1376550081	NA	P-0053717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	124	435	1	ENST00000323929.3:c.1414G>T	p.Glu472Ter	p.E472*	ENST00000323929	NM_005591.3	472	Gaa/Taa	13/20	0.526793341127848	3	FACETS	0.501	0.452	0.553			1	SUBCLONAL	1	TRUE	NA	0.526793341127848	3		436	1187	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265592	152265592	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	249	477	0	ENST00000206249.3:c.1045C>G	p.Leu349Val	p.L349V	ENST00000206249	NM_000125.3	349	Ctg/Gtg	4/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.526793341127848	2		477	861	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0053719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	25	478	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.376028801117058	4	FACETS	0.253	0.199	0.317	0.127	0.099	0.159	SUBCLONAL	1	TRUE	2	0.376028801117058	4		478	722	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0053719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	256	558	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.324780294618033	2	FACETS	0.781	0.733	0.83	0.781	0.733	0.83	SUBCLONAL	2	TRUE	0	0.376028801117058	2		558	872	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731139	162731139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	262	580	0	ENST00000367921.3:c.994C>T	p.Arg332Trp	p.R332W	ENST00000367921	NM_006182.2	332	Cgg/Tgg	9/18	0.196656803600789	3	FACETS	0.903	0.847	0.959	0.903	0.847	0.959	INDETERMINATE	2	TRUE	1	0.376028801117058	3		580	917	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849828	156849828	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121964868	NA	P-0053719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	229	681	0	ENST00000524377.1:c.2084C>T	p.Pro695Leu	p.P695L	ENST00000524377	NM_002529.3	695	cCg/cTg	16/17	0.196656803600789	3	FACETS	1	0.992	1	0.733	0.683	0.784	INDETERMINATE	1	TRUE	1	0.376028801117058	3		681	987	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961116	55961116	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	51	339	0	ENST00000263923.4:c.2824G>T	p.Gly942Trp	p.G942W	ENST00000263923	NM_002253.2	942	Ggg/Tgg	21/30	1	2	FACETS	0.332	0.281	0.388	0.332	0.281	0.388	SUBCLONAL	1	TRUE	1	0.376028801117058	2		339	818	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0053720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	256	478	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.831730208057676	5	FACETS	0.758	0.711	0.806	0.379	0.355	0.403	SUBCLONAL	2	TRUE	1	0.831730208057676	5		478	913	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202349	133202349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs552452448	NA	P-0053720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	431	683	1	ENST00000320574.5:c.6539C>T	p.Ala2180Val	p.A2180V	ENST00000320574	NM_006231.2	2180	gCg/gTg	47/49	1	2	FACETS	0.997	0.953	1	0.997	0.953	1	CLONAL	1	TRUE	1	0.831730208057676	2		684	1040	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053150	180053150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	522	874	0	ENST00000261937.6:c.1219G>A	p.Gly407Ser	p.G407S	ENST00000261937	NM_182925.4	407	Ggc/Agc	9/30	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.831730208057676	2		874	1248	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874261	155874261	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs483352822	NA	P-0053720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	244	551	1	ENST00000368323.3:c.270G>C	p.Met90Ile	p.M90I	ENST00000368323	NM_006912.5	90	atG/atC	5/6	NA	2	FACETS	0.863	0.811	0.916			1	INDETERMINATE	1	TRUE	NA	0.831730208057676	2		552	680	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500901	8500901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	372	495	1	ENST00000356435.5:c.1981G>A	p.Glu661Lys	p.E661K	ENST00000356435		661	Gag/Aag	13/35	0.831730208057676	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.831730208057676	1		496	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574035	7574035	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs867389695	NA	P-0053720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	426	600	0	ENST00000269305.4:c.994-2A>G		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.831730208057676	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.831730208057676	1		600	588	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445463	29445463	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	413	611	2	ENST00000389048.3:c.3370C>T	p.His1124Tyr	p.H1124Y	ENST00000389048	NM_004304.4	1124	Cat/Tat	21/29	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.831730208057676	2		613	948	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072612	5072613	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0053720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	147	354	0	ENST00000381652.3:c.1763_1764del	p.Arg588LysfsTer8	p.R588Kfs*8	ENST00000381652	NM_004972.3	588	AGa/a	13/25	0.831730208057676	1	FACETS	0.988	0.934	1	0.988	0.934	1	CLONAL	1	TRUE	0	0.831730208057676	1		354	209	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564853	41564853	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	462	541	0	ENST00000263253.7:c.4154G>T	p.Cys1385Phe	p.C1385F	ENST00000263253	NM_001429.3	1385	tGc/tTc	25/31	1	2	FACETS	0.954	0.914	0.996	0.954	0.914	0.996	CLONAL	1	TRUE	1	0.831730208057676	2		541	1164	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262741	16262741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369486221	NA	P-0053720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	276	425	0	ENST00000375759.3:c.10006C>T	p.Arg3336Trp	p.R3336W	ENST00000375759	NM_015001.2	3336	Cgg/Tgg	11/15	1	2	FACETS	0.931	0.879	0.983	0.931	0.879	0.983	CLONAL	1	TRUE	1	0.831730208057676	2		425	713	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939087	36939087	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	592	873	0	ENST00000361632.4:c.622G>C	p.Ala208Pro	p.A208P	ENST00000361632		208	Gcg/Ccg	5/16	1	2	FACETS	0.972	0.936	1	0.972	0.936	1	CLONAL	1	TRUE	1	0.831730208057676	2		873	1464	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797148	45797148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	576	830	2	ENST00000450313.1:c.1267G>A	p.Glu423Lys	p.E423K	ENST00000450313	NM_012222.2	423	Gaa/Aaa	13/16	0.281232668419008	1	FACETS	0.592	0.569	0.615	0.592	0.569	0.615	INDETERMINATE	1	TRUE	0	0.831730208057676	1		832	1367	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647673	206647673	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0053720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	189	448	0	ENST00000367120.3:c.88-1G>C		p.X30_splice	ENST00000367120	NM_014002.3	30			0.831730208057676	1	FACETS	0.55	0.513	0.587	0.55	0.513	0.587	SUBCLONAL	1	TRUE	0	0.831730208057676	1		448	483	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783961	50783962	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0053720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	346	556	1	ENST00000398568.2:c.353_354del	p.Arg118ThrfsTer3	p.R118Tfs*3	ENST00000398568	NM_001042412.1	118	AGa/a	3/18	0.831730208057676	1	FACETS	0.974	0.939	1	0.974	0.939	1	CLONAL	1	TRUE	0	0.831730208057676	1		557	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573998	7573998	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	569	711	0	ENST00000269305.4:c.1029G>C	p.Glu343Asp	p.E343D	ENST00000269305	NM_001126112.2	343	gaG/gaC	10/11	0.831730208057676	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.831730208057676	1		711	780	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944587	40944587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1054630078	NA	P-0053720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	303	435	0	ENST00000373198.4:c.1915G>A	p.Ala639Thr	p.A639T	ENST00000373198	NM_133170.3	639	Gca/Aca	12/32	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.831730208057676	2		435	723	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845313	42845313	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	582	927	0	ENST00000398585.3:c.949G>T	p.Val317Leu	p.V317L	ENST00000398585	NM_001135099.1	317	Gtg/Ttg	9/14	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.831730208057676	2		927	1307	SUCCESS
ATR	545	MSKCC	GRCh37	3	142257400	142257400	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	674	435	0	ENST00000350721.4:c.3649G>T	p.Val1217Leu	p.V1217L	ENST00000350721	NM_001184.3	1217	Gta/Tta	19/47	0.827633982941051	4	FACETS	0.94	0.914	0.966	0.94	0.914	0.966	CLONAL	3	TRUE	1	0.831730208057676	4		435	1053	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939634	131939634	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	173	328	0	ENST00000265335.6:c.2420G>C	p.Arg807Thr	p.R807T	ENST00000265335		807	aGa/aCa	15/25	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.831730208057676	2		328	393	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197059	26197188	+	coding_sequence_variant,3_prime_UTR_variant	Frame_Shift_Del	DEL	CAAGACAATTTACGCCCTCTCCCCACGAATGCGGCGAGCAAGCTGGATGTCCTTGGGCATGATAGTCACTCGCTTGGCGTGAATGGCGCATAGGTTGGTGTCCTCAAACAGCCCCACCAGGTAGGCCTCG	CAAGACAATTTACGCCCTCTCCCCACGAATGCGGCGAGCAAGCTGGATGTCCTTGGGCATGATAGTCACTCGCTTGGCGTGAATGGCGCATAGGTTGGTGTCCTCAAACAGCCCCACCAGGTAGGCCTCG	-	novel	NA	P-0053720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	526	260	0				ENST00000356476		97		1/1	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.831730208057676	2		260	1097	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288804	33288804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751767798	NA	P-0053720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	459	520	0	ENST00000374542.5:c.748G>A	p.Gly250Ser	p.G250S	ENST00000374542	NM_001141970.1	250	Ggc/Agc	3/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.831730208057676	2		520	1028	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525935	148525935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	265	434	0	ENST00000320356.2:c.522G>T	p.Leu174Phe	p.L174F	ENST00000320356	NM_004456.4	174	ttG/ttT	6/20	1	2	FACETS	0.973	0.918	1	0.973	0.918	1	CLONAL	1	TRUE	1	0.831730208057676	2		434	655	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128246848	128246848	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	504	610	0	ENST00000265960.3:c.1081G>C	p.Gly361Arg	p.G361R	ENST00000265960	NM_001006617.1	361	Ggg/Cgg	9/12	0.19834314535428	3	FACETS	0.758	0.728	0.788	0.758	0.728	0.788	INDETERMINATE	2	TRUE	1	0.831730208057676	3		610	1132	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228045	53228045	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	521	734	0	ENST00000375401.3:c.2269C>A	p.Pro757Thr	p.P757T	ENST00000375401	NM_004187.3	757	Cct/Act	16/26	0.831730208057676	1	FACETS	0.994	0.966	1	0.994	0.966	1	CLONAL	1	TRUE	0	0.831730208057676	1		734	736	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0053720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1279	397	478	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.817881374539979	6	FACETS	0.763	0.724	0.804	0.305	0.289	0.322	SUBCLONAL	2	TRUE	1	0.817881374539979	6		478	1676	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202349	133202349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs552452448	NA	P-0053720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	349	683	1	ENST00000320574.5:c.6539C>T	p.Ala2180Val	p.A2180V	ENST00000320574	NM_006231.2	2180	gCg/gTg	47/49	0.116276287434717	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.817881374539979	0		684	738	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053150	180053150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	358	874	0	ENST00000261937.6:c.1219G>A	p.Gly407Ser	p.G407S	ENST00000261937	NM_182925.4	407	Ggc/Agc	9/30	0.116276287434717	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.817881374539979	0		874	892	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874261	155874261	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs483352822	NA	P-0053720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	205	551	1	ENST00000368323.3:c.270G>C	p.Met90Ile	p.M90I	ENST00000368323	NM_006912.5	90	atG/atC	5/6	NA	2	FACETS	0.742	0.691	0.794			1	INDETERMINATE	1	TRUE	NA	0.817881374539979	2		552	676	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500901	8500901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	319	495	1	ENST00000356435.5:c.1981G>A	p.Glu661Lys	p.E661K	ENST00000356435		661	Gag/Aag	13/35	0.817881374539979	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.817881374539979	1		496	446	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574035	7574035	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs867389695	NA	P-0053720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	364	600	0	ENST00000269305.4:c.994-2A>G		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.817881374539979	1	FACETS	0.976	0.941	1	0.976	0.941	1	CLONAL	1	TRUE	0	0.817881374539979	1		600	539	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445463	29445463	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	304	611	2	ENST00000389048.3:c.3370C>T	p.His1124Tyr	p.H1124Y	ENST00000389048	NM_004304.4	1124	Cat/Tat	21/29	1	2	FACETS	0.933	0.883	0.983	0.933	0.883	0.983	CLONAL	1	TRUE	1	0.817881374539979	2		613	797	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072612	5072613	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0053720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	227	354	0	ENST00000381652.3:c.1763_1764del	p.Arg588LysfsTer8	p.R588Kfs*8	ENST00000381652	NM_004972.3	588	AGa/a	13/25	0.814022470129417	1	FACETS	0.875	0.831	0.918	0.875	0.831	0.918	CLONAL	1	TRUE	0	0.817881374539979	1		354	375	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564853	41564853	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	470	541	0	ENST00000263253.7:c.4154G>T	p.Cys1385Phe	p.C1385F	ENST00000263253	NM_001429.3	1385	tGc/tTc	25/31	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.817881374539979	2		541	1057	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262741	16262741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369486221	NA	P-0053720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	232	425	0	ENST00000375759.3:c.10006C>T	p.Arg3336Trp	p.R3336W	ENST00000375759	NM_015001.2	3336	Cgg/Tgg	11/15	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.817881374539979	2		425	563	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939087	36939087	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	401	873	0	ENST00000361632.4:c.622G>C	p.Ala208Pro	p.A208P	ENST00000361632		208	Gcg/Ccg	5/16	0.176484238524069	1	FACETS	0.561	0.535	0.588	0.561	0.535	0.588	INDETERMINATE	1	TRUE	0	0.817881374539979	1		873	1033	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797148	45797148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	389	830	2	ENST00000450313.1:c.1267G>A	p.Glu423Lys	p.E423K	ENST00000450313	NM_012222.2	423	Gaa/Aaa	13/16	1	2	FACETS	0.901	0.858	0.944	0.901	0.858	0.944	CLONAL	1	TRUE	1	0.817881374539979	2		832	1056	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647673	206647673	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0053720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	168	448	0	ENST00000367120.3:c.88-1G>C		p.X30_splice	ENST00000367120	NM_014002.3	30			0.817881374539979	1	FACETS	0.606	0.563	0.648	0.606	0.563	0.648	SUBCLONAL	1	TRUE	0	0.817881374539979	1		448	401	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783961	50783962	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0053720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	407	556	1	ENST00000398568.2:c.353_354del	p.Arg118ThrfsTer3	p.R118Tfs*3	ENST00000398568	NM_001042412.1	118	AGa/a	3/18	0.817881374539979	1	FACETS	0.95	0.917	0.983	0.95	0.917	0.983	CLONAL	1	TRUE	0	0.817881374539979	1		557	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573998	7573998	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	473	711	0	ENST00000269305.4:c.1029G>C	p.Glu343Asp	p.E343D	ENST00000269305	NM_001126112.2	343	gaG/gaC	10/11	0.817881374539979	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.817881374539979	1		711	671	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944587	40944587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1054630078	NA	P-0053720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	246	435	0	ENST00000373198.4:c.1915G>A	p.Ala639Thr	p.A639T	ENST00000373198	NM_133170.3	639	Gca/Aca	12/32	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.817881374539979	2		435	601	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845313	42845313	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	439	927	0	ENST00000398585.3:c.949G>T	p.Val317Leu	p.V317L	ENST00000398585	NM_001135099.1	317	Gtg/Ttg	9/14	0.380422461258081	1	FACETS	0.772	0.742	0.802	0.772	0.742	0.802	INDETERMINATE	1	TRUE	0	0.817881374539979	1		927	822	SUCCESS
ATR	545	MSKCC	GRCh37	3	142257400	142257400	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	958	435	0	ENST00000350721.4:c.3649G>T	p.Val1217Leu	p.V1217L	ENST00000350721	NM_001184.3	1217	Gta/Tta	19/47	0.353000504287212	6	FACETS	0.907	0.887	0.926	0.756	0.739	0.772	INDETERMINATE	5	TRUE	0	0.817881374539979	6		435	1362	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939634	131939634	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	233	328	0	ENST00000265335.6:c.2420G>C	p.Arg807Thr	p.R807T	ENST00000265335		807	aGa/aCa	15/25	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.817881374539979	2		328	544	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197059	26197188	+	coding_sequence_variant,3_prime_UTR_variant	Frame_Shift_Del	DEL	CAAGACAATTTACGCCCTCTCCCCACGAATGCGGCGAGCAAGCTGGATGTCCTTGGGCATGATAGTCACTCGCTTGGCGTGAATGGCGCATAGGTTGGTGTCCTCAAACAGCCCCACCAGGTAGGCCTCG	CAAGACAATTTACGCCCTCTCCCCACGAATGCGGCGAGCAAGCTGGATGTCCTTGGGCATGATAGTCACTCGCTTGGCGTGAATGGCGCATAGGTTGGTGTCCTCAAACAGCCCCACCAGGTAGGCCTCG	-	novel	NA	P-0053720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	584	260	0				ENST00000356476		97		1/1	1	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	1	0.817881374539979	2		260	1037	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288804	33288804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751767798	NA	P-0053720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	288	520	0	ENST00000374542.5:c.748G>A	p.Gly250Ser	p.G250S	ENST00000374542	NM_001141970.1	250	Ggc/Agc	3/8	1	2	FACETS	0.881	0.832	0.931	0.881	0.832	0.931	CLONAL	1	TRUE	1	0.817881374539979	2		520	799	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525935	148525935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	291	434	0	ENST00000320356.2:c.522G>T	p.Leu174Phe	p.L174F	ENST00000320356	NM_004456.4	174	ttG/ttT	6/20	1	2	FACETS	0.928	0.877	0.979	0.928	0.877	0.979	CLONAL	1	TRUE	1	0.817881374539979	2		434	767	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128246848	128246848	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	416	610	0	ENST00000265960.3:c.1081G>C	p.Gly361Arg	p.G361R	ENST00000265960	NM_001006617.1	361	Ggg/Cgg	9/12	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.817881374539979	2		610	1010	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228045	53228045	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053720-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	417	734	0	ENST00000375401.3:c.2269C>A	p.Pro757Thr	p.P757T	ENST00000375401	NM_004187.3	757	Cct/Act	16/26	0.817881374539979	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.817881374539979	1		734	563	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0053721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	102	258	0				ENST00000310581	NM_198253.2	-/1132			0.169841990011277	0	FACETS	0.45	0.407	0.494			1	INDETERMINATE	1	FALSE	0	0.596156230702129	0		258	307	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249017	55249018	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCA	rs1554350381	NA	P-0053721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	284	764	0	ENST00000275493.2:c.2317_2319dup	p.His773dup	p.H773dup	ENST00000275493	NM_005228.3	773	ccc/ccCCAc	20/28	0.549758880353657	3	FACETS	1	0.949	1	0.506	0.475	0.538	CLONAL	1	FALSE	1	0.596156230702129	3		764	1223	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692830	89692830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782343	NA	P-0053721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	96	184	1	ENST00000371953.3:c.314G>A	p.Cys105Tyr	p.C105Y	ENST00000371953	NM_000314.4	105	tGt/tAt	5/9	0.596156230702129	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	FALSE	0	0.596156230702129	1		185	214	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026675	6026675	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1259	303	908	0	ENST00000265849.7:c.1721C>T	p.Pro574Leu	p.P574L	ENST00000265849	NM_000535.5	574	cCa/cTa	11/15	0.549758880353657	3	FACETS	0.845	0.794	0.897	0.422	0.397	0.449	CLONAL	1	FALSE	1	0.596156230702129	3		908	1562	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136832	55136833	+	missense_variant	Missense_Mutation	DNP	AG	AG	TA	novel	NA	P-0053722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	585	432	0	ENST00000257290.5:c.1154_1155delinsTA	p.Lys385Ile	p.K385I	ENST00000257290	NM_006206.4	385	aAG/aTA	8/23	0.674529432401381	3	FACETS	0.952	0.929	0.974	0.952	0.929	0.974	CLONAL	3	TRUE	0	0.731458273040704	3		432	765	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593613	55593614	+	missense_variant	Missense_Mutation	DNP	TT	TT	AG	novel	NA	P-0053723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	191	441	0	ENST00000288135.5:c.1679_1680delinsAG	p.Val560Glu	p.V560E	ENST00000288135	NM_000222.2	560	gTT/gAG	11/21	1	2	FACETS	0.851	0.793	0.911	0.851	0.793	0.911	CLONAL	1	TRUE	1	0.836999343162037	2		441	536	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0053725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	16	623	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.339	0.249	0.448	0.339	0.249	0.448	SUBCLONAL	1	TRUE	1	0.13	2		623	726	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0053725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	79	1094	5	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.79	0.694	0.894	1	0.978	1	SUBCLONAL	2	TRUE	1	0.13	2		1099	769	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0053725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	25	478	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	0.754	0.593	0.94	0.754	0.593	0.94	CLONAL	1	TRUE	1	0.13	2		478	510	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0053725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	43	444	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.13	2		444	450	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557639	95557639	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	17	543	0	ENST00000393063.1:c.5428G>T	p.Asp1810Tyr	p.D1810Y	ENST00000393063	NM_030621.3	1810	Gat/Tat	26/28	1	2	FACETS	0.449	0.334	0.588	0.449	0.334	0.588	SUBCLONAL	1	TRUE	1	0.13	2		543	582	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574406	95574406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	26	278	0	ENST00000393063.1:c.2461C>T	p.Arg821Cys	p.R821C	ENST00000393063	NM_030621.3	821	Cgc/Tgc	17/28	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.13	2		278	274	SUCCESS
APC	324	MSKCC	GRCh37	5	112111364	112111364	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554071529	NA	P-0053725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	24	342	0	ENST00000257430.4:c.465del	p.Asp156ThrfsTer14	p.D156Tfs*14	ENST00000257430	NM_000038.5	154	gAa/ga	5/16	1	2	FACETS	0.977	0.765	1	0.977	0.765	1	CLONAL	1	TRUE	1	0.13	2		342	378	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123022508	123022508	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	37	632	0	ENST00000355640.3:c.917G>T	p.Gly306Val	p.G306V	ENST00000355640		306	gGg/gTg	3/7	1	2	FACETS	0.887	0.729	1	0.887	0.729	1	CLONAL	1	TRUE	1	0.13	2		632	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0053726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	363	608	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.856744004842173	2	FACETS	0.995	0.97	1	0.995	0.97	1	CLONAL	2	TRUE	0	0.856744004842173	2		608	426	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395496	116395496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	93	343	0	ENST00000397752.3:c.1789G>A	p.Asp597Asn	p.D597N	ENST00000397752	NM_000245.2	597	Gat/Aat	6/21	0.411641974427194	5	FACETS	1	0.974	1	0.428	0.383	0.476	INDETERMINATE	1	TRUE	2	0.856744004842173	5		343	386	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433903	49433904	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0053726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	603	1156	0	ENST00000301067.7:c.7649dup	p.Val2551CysfsTer104	p.V2551Cfs*104	ENST00000301067	NM_003482.3	2550	cct/ccCt	31/54	0.856744004842173	3	FACETS	0.888	0.858	0.918	0.888	0.858	0.918	CLONAL	2	TRUE	1	0.856744004842173	3		1156	1132	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096312	178096312	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs755229916	NA	P-0053726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	389	482	0	ENST00000397062.3:c.1019A>G	p.Asn340Ser	p.N340S	ENST00000397062	NM_006164.4	340	aAt/aGt	5/5	0.851776277335457	3	FACETS	0.905	0.867	0.941	0.905	0.867	0.941	CLONAL	2	TRUE	1	0.856744004842173	3		482	717	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933686	39933686	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	182	320	0	ENST00000378444.4:c.913C>T	p.Pro305Ser	p.P305S	ENST00000378444	NM_001123385.1	305	Cct/Tct	4/15	0.351427827942071	2	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.49257632236312	2		320	593	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842726	68842726	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	183	417	0	ENST00000261769.5:c.662A>C	p.Asp221Ala	p.D221A	ENST00000261769	NM_004360.3	221	gAt/gCt	5/16	0.49428464041261	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.49257632236312	1		417	519	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845947	151845947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	153	394	1	ENST00000262189.6:c.13065G>A	p.Met4355Ile	p.M4355I	ENST00000262189	NM_170606.2	4355	atG/atA	52/59	0.494637834770587	4	FACETS	0.986	0.902	1	0.247	0.225	0.269	CLONAL	1	TRUE	0	0.49257632236312	4		395	940	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759816	133759816	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	328	735	0	ENST00000318560.5:c.2140del	p.Leu714CysfsTer62	p.L714Cfs*62	ENST00000318560	NM_005157.4	713	ttC/tt	11/11	0.494637834770587	3	FACETS	0.801	0.758	0.845			1	CLONAL	2	TRUE	NA	0.49257632236312	3		735	1036	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060912	38060912	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	50	672	1	ENST00000250448.2:c.1077del	p.Ile360Ter	p.I360*	ENST00000250448	NM_004496.3	359	ccC/cc	2/2	1	2	FACETS	0.691	0.586	0.807	0.691	0.586	0.807	SUBCLONAL	1	TRUE	1	0.25	2		673	579	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061334	38061334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	93	704	0	ENST00000250448.2:c.655C>A	p.Arg219Ser	p.R219S	ENST00000250448	NM_004496.3	219	Cgc/Agc	2/2	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.25	2		704	715	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579361	7579361	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1064796722	NA	P-0053730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	92	900	0	ENST00000269305.4:c.326T>G	p.Phe109Cys	p.F109C	ENST00000269305	NM_001126112.2	109	tTc/tGc	4/11	1	2	FACETS	0.952	0.846	1	0.952	0.846	1	CLONAL	1	TRUE	1	0.25	2		900	773	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518109	69518109	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	176	888	1	ENST00000294312.3:c.256G>T	p.Ala86Ser	p.A86S	ENST00000294312	NM_005117.2	86	Gct/Tct	2/3	1	2	FACETS	0.968	0.894	1	1	0.992	1	CLONAL	2	TRUE	1	0.25	2		889	727	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48921986	48921987	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	112	359	1	ENST00000267163.4:c.528dup	p.Pro177ThrfsTer8	p.P177Tfs*8	ENST00000267163	NM_000321.2	176	caa/cAaa	5/27	0.757085563538225	1	FACETS	0.888	0.821	0.955	0.888	0.821	0.955	CLONAL	1	TRUE	0	0.757085563538225	1		360	207	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0053731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	440	590	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.757085563538225	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.757085563538225	1		590	712	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0053732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	68	469	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.891163595116067	4	FACETS	1	0.955	1	0.393	0.346	0.442	CLONAL	1	TRUE	1	0.89767722771073	4		470	244	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414400	6414400	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	174	143	0	ENST00000356142.4:c.34G>A	p.Gly12Arg	p.G12R	ENST00000356142	NM_018890.3	12	Gga/Aga	1/7	0.89767722771073	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.89767722771073	4		143	349	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114160	73114160	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	158	349	1	ENST00000356692.5:c.796A>G	p.Ser266Gly	p.S266G	ENST00000356692		266	Agc/Ggc	8/9	0.89767722771073	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.89767722771073	2		350	175	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	30	386	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.917	0.739	1	0.917	0.739	1	CLONAL	1	TRUE	1	0.15	2		386	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578451	7578459	+	inframe_deletion	In_Frame_Del	DEL	ATGGCGCGG	ATGGCGCGG	-	novel	NA	P-0053733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1434	111	675	0	ENST00000269305.4:c.471_479del	p.Arg158_Met160del	p.R158_M160del	ENST00000269305	NM_001126112.2	157	gtCCGCGCCATg/gtg	5/11	1	2	FACETS	0.958	0.858	1	0.958	0.858	1	CLONAL	1	TRUE	1	0.15	2		675	1545	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430653	181430653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771393751	NA	P-0053733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1205	124	532	0	ENST00000325404.1:c.505G>A	p.Gly169Ser	p.G169S	ENST00000325404	NM_003106.3	169	Ggc/Agc	1/1	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.15	2		532	1329	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0053734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	179	346	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.381859506898682	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.381859506898682	3		346	531	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0053734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	236	533	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.381859506898682	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.381859506898682	3		533	648	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181765	56181765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1287268127	NA	P-0053734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	70	301	4	ENST00000399503.3:c.3989C>T	p.Ser1330Leu	p.S1330L	ENST00000399503	NM_005921.1	1330	tCg/tTg	17/20	0.381859506898682	4	FACETS	0.854	0.745	0.972	0.285	0.248	0.324	CLONAL	1	TRUE	1	0.381859506898682	4		305	593	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912798	100912798	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	123	438	1	ENST00000325455.5:c.2524G>T	p.Glu842Ter	p.E842*	ENST00000325455	NM_001202474.3	842	Gag/Tag	7/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.381859506898682	2		439	568	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160681	56160681	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	346	444	0	ENST00000399503.3:c.955del	p.Leu319CysfsTer4	p.L319Cfs*4	ENST00000399503	NM_005921.1	319	Ctg/tg	4/20	0.381859506898682	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	1	0.381859506898682	4		444	783	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512319	120512319	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	130	629	1	ENST00000256646.2:c.923C>T	p.Ala308Val	p.A308V	ENST00000256646	NM_024408.3	308	gCc/gTc	6/34	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.26957786344926	2		630	910	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743258	162743258	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0053736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	41	277	0	ENST00000367921.3:c.1729-1G>A		p.X577_splice	ENST00000367921	NM_006182.2	577			1	2	FACETS	0.782	0.652	0.925	0.782	0.652	0.925	CLONAL	1	TRUE	1	0.26957786344926	2		277	389	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445020	89445020	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs925530491	NA	P-0053736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	53	489	0	ENST00000336596.2:c.1340G>A	p.Arg447Gln	p.R447Q	ENST00000336596	NM_005233.5	447	cGg/cAg	6/17	1	2	FACETS	0.68	0.58	0.79	0.68	0.58	0.79	SUBCLONAL	1	TRUE	1	0.26957786344926	2		489	578	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519893	NA	P-0053738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	27	723	0	ENST00000267101.3:c.310G>T	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ttg	3/28	1	2	FACETS	0.363	0.287	0.45	0.363	0.287	0.45	SUBCLONAL	1	TRUE	1	0.12	2		723	1241	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0053738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	28	646	1	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	1	2	FACETS	0.401	0.319	0.496	0.401	0.319	0.496	SUBCLONAL	1	TRUE	1	0.12	2		647	1163	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0053738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	51	743	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	1	2	FACETS	0.713	0.603	0.835	0.713	0.603	0.835	SUBCLONAL	1	TRUE	1	0.12	2		743	1192	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0053738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	22	615	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	1	2	FACETS	0.342	0.264	0.435	0.342	0.264	0.435	SUBCLONAL	1	TRUE	1	0.12	2		615	1071	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100366	8100366	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1239	70	922	0	ENST00000346208.3:c.340C>G	p.Leu114Val	p.L114V	ENST00000346208		114	Ctc/Gtc	3/6	1	2	FACETS	0.891	0.774	1	0.891	0.774	1	CLONAL	1	TRUE	1	0.12	2		922	1309	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599961	10599961	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1253	66	813	0	ENST00000171111.5:c.1615G>T	p.Val539Leu	p.V539L	ENST00000171111	NM_203500.1	539	Gtg/Ttg	5/6	1	2	FACETS	0.834	0.721	0.958	0.834	0.721	0.958	CLONAL	1	TRUE	1	0.12	2		813	1319	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796903	42796903	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs779481484	NA	P-0053738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1422	102	911	0	ENST00000575354.2:c.3361A>G	p.Thr1121Ala	p.T1121A	ENST00000575354	NM_015125.3	1121	Act/Gct	14/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.12	2		911	1524	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855817	45855818	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0053738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1265	97	909	2	ENST00000391945.4:c.1992_1993delinsAT	p.Gly665Cys	p.G665C	ENST00000391945	NM_000400.3	664	gtGGgt/gtATgt	21/23	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.12	2		911	1362	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287429	38287429	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	61	736	0	ENST00000425967.3:c.228C>A	p.Phe76Leu	p.F76L	ENST00000425967	NM_001174067.1	76	ttC/ttA	4/19	1	2	FACETS	0.964	0.829	1	0.964	0.829	1	CLONAL	1	TRUE	1	0.12	2		736	1055	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949156	44949156	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398122929	NA	P-0053738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	53	493	0	ENST00000377967.4:c.3717G>A	p.Trp1239Ter	p.W1239*	ENST00000377967	NM_021140.2	1239	tgG/tgA	25/29	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.12	2		493	812	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0053739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	338	915	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.361373993251066	2	FACETS	0.801	0.758	0.845	0.801	0.758	0.845	CLONAL	2	TRUE	0	0.361373993251066	2		915	1168	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690810	89690813	+	frameshift_variant	Frame_Shift_Del	DEL	GAAA	GAAA	-	novel	NA	P-0053739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	50	217	0	ENST00000371953.3:c.219_222del	p.Glu73AspfsTer25	p.E73Dfs*25	ENST00000371953	NM_000314.4	73	GAAAga/ga	4/9	0.361373993251066	3	FACETS	1	0.907	1	0.707	0.612	0.807	CLONAL	2	TRUE	0	0.361373993251066	3		217	154	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099436	27099440	+	frameshift_variant	Frame_Shift_Del	DEL	TCCTA	TCCTA	-	novel	NA	P-0053739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	115	585	0	ENST00000324856.7:c.3674_3678del	p.Ser1225Ter	p.S1225*	ENST00000324856	NM_006015.4	1225	TCCTAt/t	14/20	0.327633364837945	3	FACETS	1	0.956	1	0.553	0.498	0.61	CLONAL	1	TRUE	1	0.361373993251066	3		585	680	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115279421	115279422	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCAGCTGAACGTTCCCTTCG	novel	NA	P-0053739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	38	374	0	ENST00000438362.2:c.576_595dup	p.Glu199AlafsTer13	p.E199Afs*13	ENST00000438362	NM_001242891.1	199	gaa/gCGAAGGGAACGTTCAGCTGGaa	6/20	0.308408433293252	4	FACETS	0.666	0.551	0.794	0.333	0.275	0.397	SUBCLONAL	1	TRUE	2	0.361373993251066	4		374	430	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134713	2134713	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs45497997	NA	P-0053739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1274	124	801	0	ENST00000219476.3:c.4490C>G	p.Pro1497Arg	p.P1497R	ENST00000219476	NM_000548.3	1497	cCc/cGc	34/42	0.361373993251066	4	FACETS	0.668	0.602	0.738			1	SUBCLONAL	1	TRUE	NA	0.361373993251066	4		801	1398	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976854	18976855	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0053739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1419	95	577	1	ENST00000262803.5:c.3240_3241del	p.Asp1080GlufsTer5	p.D1080Efs*5	ENST00000262803	NM_002911.3	1080	gAC/g	23/24	0.361373993251066	5	FACETS	0.536	0.475	0.601			1	SUBCLONAL	1	TRUE	NA	0.361373993251066	5		578	1514	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750769	57750769	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	41	338	0	ENST00000274289.3:c.1835T>A	p.Leu612Gln	p.L612Q	ENST00000274289	NM_006622.3	612	cTa/cAa	13/14	0.361373993251066	2	FACETS	0.69	0.576	0.815	0.345	0.288	0.408	SUBCLONAL	1	TRUE	0	0.361373993251066	2		338	329	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592090	67592109	+	frameshift_variant	Frame_Shift_Del	DEL	AACCTGTTGCGAGGGAAGCG	AACCTGTTGCGAGGGAAGCG	-	novel	NA	P-0053739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	31	335	0	ENST00000274335.5:c.1907_1926del	p.Asn636ArgfsTer11	p.N636Rfs*11	ENST00000274335		636	AACCTGTTGCGAGGGAAGCGa/a	14/15	0.361373993251066	2	FACETS	0.366	0.295	0.446	0.183	0.147	0.223	SUBCLONAL	1	TRUE	0	0.361373993251066	2		335	469	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564365	86564365	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	128	637	0	ENST00000274376.6:c.97G>C	p.Val33Leu	p.V33L	ENST00000274376	NM_002890.2	33	Gtg/Ctg	1/25	0.361373993251066	2	FACETS	0.782	0.708	0.86	0.391	0.354	0.43	SUBCLONAL	1	TRUE	0	0.361373993251066	2		637	906	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339538	116339538	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	73	365	0	ENST00000397752.3:c.400G>C	p.Gly134Arg	p.G134R	ENST00000397752	NM_000245.2	134	Ggc/Cgc	2/21	0.341955953718231	4	FACETS	0.868	0.759	0.985	0.289	0.253	0.329	CLONAL	1	TRUE	1	0.361373993251066	4		365	634	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900083	151900083	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	17	281	0	ENST00000262189.6:c.4028A>T	p.Lys1343Ile	p.K1343I	ENST00000262189	NM_170606.2	1343	aAa/aTa	26/59	0.361373993251066	6	FACETS	0.849	0.636	1			1	CLONAL	1	TRUE	NA	0.361373993251066	6		281	191	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591220	67591247	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	GCGTTCTCTTTTCAAAACTGTTTTTCAG	GCGTTCTCTTTTCAAAACTGTTTTTCAG	-	novel	NA	P-0053739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	45	313	0	ENST00000274335.5:c.1746-27_1746del		p.X582_splice	ENST00000274335		582			0.361373993251066	2	FACETS	1	0.905	1	0.546	0.463	0.636	CLONAL	1	TRUE	0	0.361373993251066	2		313	228	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	191	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.967	0.905	1	0.967	0.905	1	CLONAL	1	TRUE	1	0.895988424895044	2		276	441	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956221	55956221	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs767542615	NA	P-0053745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5969	191	457	1	ENST00000263923.4:c.3094C>T	p.Arg1032Ter	p.R1032*	ENST00000263923	NM_002253.2	1032	Cga/Tga	23/30	0.895988424895044	21	FACETS	0.658	0.604	0.716	0.033	0.03	0.036	SUBCLONAL	1	TRUE	1	0.895988424895044	21		458	6160	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	103	386	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.862	0.778	0.949	0.862	0.778	0.949	CLONAL	1	TRUE	1	0.64060416369359	2		386	373	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	70	329	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.938	0.83	1	0.938	0.83	1	CLONAL	1	TRUE	1	0.64060416369359	2		329	233	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	145	473	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.999	0.919	1	0.999	0.919	1	CLONAL	1	TRUE	1	0.64060416369359	2		478	453	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	203	436	2	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.64060416369359	2		438	530	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	323	757	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.64060416369359	2		757	940	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	315	721	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.64060416369359	2		728	925	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	109	394	1	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.978	0.888	1	0.978	0.888	1	CLONAL	1	TRUE	1	0.64060416369359	2		395	348	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	151	495	2	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	0.152983954758156	0	FACETS	0.386	0.356	0.417			1	INDETERMINATE	1	TRUE	0	0.64060416369359	0		497	439	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	80	377	1	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.827	0.736	0.923	0.827	0.736	0.923	CLONAL	1	TRUE	1	0.64060416369359	2		378	302	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	293	760	1	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.64060416369359	2		761	904	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	178	444	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.64060416369359	2		444	459	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099982	157099987	+	inframe_deletion	In_Frame_Del	DEL	GGCGGC	GGCGGC	-	rs587779747	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	135	316	3	ENST00000346085.5:c.939_944del	p.Gly318_Gly319del	p.G318_G319del	ENST00000346085	NM_020732.3	307	GGCGGC/-	1/20	1	2	FACETS	0.812	0.742	0.885	0.812	0.742	0.885	CLONAL	1	TRUE	1	0.64060416369359	2		319	519	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	275	550	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	0.213279765960762	4	FACETS	0.843	0.794	0.893	0.843	0.794	0.893	INDETERMINATE	2	TRUE	2	0.64060416369359	4		550	835	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	68	359	0	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	1	2	FACETS	0.823	0.724	0.927	0.823	0.724	0.927	CLONAL	1	TRUE	1	0.64060416369359	2		359	258	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	87	288	1	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.64060416369359	2		289	226	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	227	757	4	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.64060416369359	2		761	687	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911588	134911588	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	165	468	0	ENST00000398015.3:c.2053G>T	p.Gly685Cys	p.G685C	ENST00000398015	NM_004441.4	685	Ggt/Tgt	11/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.64060416369359	2		468	463	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354008	15354008	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	79	274	2	ENST00000263377.2:c.2872del	p.Leu958CysfsTer110	p.L958Cfs*110	ENST00000263377	NM_058243.2	958	Ctg/tg	14/20	0.144041328816602	4	FACETS	0.769	0.685	0.857	0.769	0.685	0.857	INDETERMINATE	2	TRUE	2	0.64060416369359	4		276	263	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	242	372	9	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	0.984	0.938	1	1	0.996	1	CLONAL	2	TRUE	1	0.64060416369359	2		381	384	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	191	602	7	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	1	2	FACETS	0.817	0.758	0.878	0.817	0.758	0.878	CLONAL	1	TRUE	1	0.64060416369359	2		609	730	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717778	89717778	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	101	281	0	ENST00000371953.3:c.801+2T>G		p.X267_splice	ENST00000371953	NM_000314.4	267			1	2	FACETS	0.964	0.872	1	0.964	0.872	1	CLONAL	1	TRUE	1	0.64060416369359	2		281	327	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086002	16086002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893646	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	209	529	0	ENST00000281043.3:c.1178G>A	p.Arg393His	p.R393H	ENST00000281043	NM_005378.4	393	cGc/cAc	3/3	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.64060416369359	2		529	592	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932085	39932085	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	275	344	0	ENST00000378444.4:c.2514del	p.Lys839SerfsTer17	p.K839Sfs*17	ENST00000378444	NM_001123385.1	838	ccC/cc	4/15	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.64060416369359	1		344	440	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270530	98270530	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs751977093	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	115	347	3	ENST00000331920.6:c.114del	p.Leu39CysfsTer41	p.L39Cfs*41	ENST00000331920	NM_000264.3	38	ggG/gg	1/24	1	2	FACETS	0.835	0.758	0.915	0.835	0.758	0.915	CLONAL	1	TRUE	1	0.64060416369359	2		350	430	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132542	11132542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	365	768	1	ENST00000358026.2:c.2758G>A	p.Glu920Lys	p.E920K	ENST00000358026	NM_001128849.1	920	Gag/Aag	19/36	0.144041328816602	4	FACETS	0.95	0.903	0.997	0.95	0.903	0.997	INDETERMINATE	2	TRUE	2	0.64060416369359	4		769	984	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191437	185191437	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs374399820	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	237	608	0	ENST00000265026.3:c.2318C>A	p.Ser773Tyr	p.S773Y	ENST00000265026	NM_004721.4	773	tCt/tAt	11/14	1	2	FACETS	0.966	0.905	1	0.966	0.905	1	CLONAL	1	TRUE	1	0.64060416369359	2		608	766	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268985	142268985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs911751877	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	134	332	0	ENST00000350721.4:c.2965C>T	p.Arg989Cys	p.R989C	ENST00000350721	NM_001184.3	989	Cgt/Tgt	14/47	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.64060416369359	2		332	370	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627306	37627307	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs755536892	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	216	563	0	ENST00000447079.4:c.1233_1235dup	p.Ala413dup	p.A413dup	ENST00000447079	NM_015083.1	413	-/GCT	2/14	1	2	FACETS	0.892	0.832	0.954	0.892	0.832	0.954	CLONAL	1	TRUE	1	0.64060416369359	2		563	756	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723126	49723128	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs751306787	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	339	514	0	ENST00000449682.2:c.1288_1290del	p.Glu430del	p.E430del	ENST00000449682	NM_020998.3	430	GAG/-	11/18	0.295090837966091	4	FACETS	1	0.974	1			1	INDETERMINATE	2	TRUE	NA	0.64060416369359	4		514	837	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540634	187540634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201741692	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	159	414	0	ENST00000441802.2:c.7106C>T	p.Thr2369Met	p.T2369M	ENST00000441802	NM_005245.3	2369	aCg/aTg	10/27	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.64060416369359	2		414	423	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428258	33428258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782129	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	238	583	1	ENST00000345365.6:c.865G>A	p.Gly289Ser	p.G289S	ENST00000345365	NM_002878.3	289	Ggc/Agc	9/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.64060416369359	2		584	680	SUCCESS
APC	324	MSKCC	GRCh37	5	112175039	112175040	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs1114167583	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	60	220	0	ENST00000257430.4:c.3749_3750del	p.Lys1250SerfsTer5	p.K1250Sfs*5	ENST00000257430	NM_000038.5	1250	AAa/a	16/16	1	2	FACETS	0.966	0.846	1	0.966	0.846	1	CLONAL	1	TRUE	1	0.64060416369359	2		220	194	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	138	502	5	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.921	0.844	1	0.921	0.844	1	CLONAL	1	TRUE	1	0.64060416369359	2		507	468	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300040	137300040	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	295	739	2	ENST00000481739.1:c.331del	p.Leu111TrpfsTer57	p.L111Wfs*57	ENST00000481739	NM_002957.4	109	Ccc/cc	3/10	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.64060416369359	2		741	916	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874147	151874148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs747256476	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	153	439	9	ENST00000262189.6:c.8390dup	p.Glu2798GlyfsTer11	p.E2798Gfs*11	ENST00000262189	NM_170606.2	2797	aag/aaAg	38/59	0.144041328816602	4	FACETS	1	0.987	1	0.712	0.655	0.771	INDETERMINATE	1	TRUE	2	0.64060416369359	4		448	550	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948483	71948484	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	311	841	0	ENST00000298229.2:c.3201dup	p.Ser1068GlnfsTer17	p.S1068Qfs*17	ENST00000298229	NM_001567.3	1065	-/C	26/28	1	2	FACETS	0.941	0.888	0.994	0.941	0.888	0.994	CLONAL	1	TRUE	1	0.64060416369359	2		841	1032	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146944	38146945	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	209	557	1	ENST00000317025.8:c.3197dup	p.Asn1066LysfsTer14	p.N1066Kfs*14	ENST00000317025	NM_023034.1	1066	aac/aaAc	18/24	0.64060416369359	3	FACETS	1	0.949	1	0.341	0.317	0.366	CLONAL	1	TRUE	0	0.64060416369359	3		558	841	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537237	80537237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	221	484	1	ENST00000286548.4:c.161C>T	p.Thr54Met	p.T54M	ENST00000286548	NM_002072.3	54	aCg/aTg	2/7	0.247381625921241	0	FACETS	0.425	0.398	0.452			1	INDETERMINATE	1	TRUE	0	0.64060416369359	0		485	584	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928358	69928358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774545277	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	138	479	0	ENST00000352241.4:c.178C>T	p.Arg60Cys	p.R60C	ENST00000352241	NM_198159.2	60	Cgc/Tgc	2/10	1	2	FACETS	0.993	0.911	1	0.993	0.911	1	CLONAL	1	TRUE	1	0.64060416369359	2		479	434	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944878	31944878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141415515	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	160	339	0	ENST00000340398.3:c.223G>A	p.Ala75Thr	p.A75T	ENST00000340398	NM_001013699.2	75	Gcg/Acg	1/1	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.64060416369359	2		339	420	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187222	38187222	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	252	667	1	ENST00000317025.8:c.1255del	p.Thr419ProfsTer8	p.T419Pfs*8	ENST00000317025	NM_023034.1	419	Acc/cc	6/24	0.64060416369359	3	FACETS	0.886	0.829	0.946	0.295	0.276	0.316	CLONAL	1	TRUE	0	0.64060416369359	3		668	1172	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883774	37883774	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	358	788	0	ENST00000269571.5:c.3391del	p.Leu1131Ter	p.L1131*	ENST00000269571		1129	gCc/gc	26/27	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.64060416369359	2		788	1098	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238359	98238359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	222	537	0	ENST00000331920.6:c.1685C>T	p.Ala562Val	p.A562V	ENST00000331920	NM_000264.3	562	gCc/gTc	12/24	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.64060416369359	2		537	592	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821889	72821890	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	118	416	0	ENST00000268489.5:c.10285dup	p.Arg3429ProfsTer2	p.R3429Pfs*2	ENST00000268489	NM_006885.3	3429	cgt/cCgt	10/10	1	2	FACETS	0.815	0.74	0.893	0.815	0.74	0.893	CLONAL	1	TRUE	1	0.64060416369359	2		416	452	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98011462	98011462	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778951584	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	197	496	0	ENST00000289081.3:c.112G>A	p.Val38Met	p.V38M	ENST00000289081	NM_000136.2	38	Gtg/Atg	2/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.64060416369359	2		496	576	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323123	31323123	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	373	981	0	ENST00000412585.2:c.866G>T	p.Gly289Val	p.G289V	ENST00000412585	NM_005514.6	289	gGg/gTg	4/8	0.144041328816602	4	FACETS	0.83	0.788	0.872	0.83	0.788	0.872	INDETERMINATE	2	TRUE	2	0.64060416369359	4		981	1151	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047918	180047918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770591360	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	253	896	2	ENST00000261937.6:c.2257G>A	p.Ala753Thr	p.A753T	ENST00000261937	NM_182925.4	753	Gcc/Acc	15/30	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.64060416369359	2		898	726	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268341	142268341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367641692	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	94	351	0	ENST00000350721.4:c.3151C>T	p.Arg1051Cys	p.R1051C	ENST00000350721	NM_001184.3	1051	Cgt/Tgt	15/47	1	2	FACETS	0.897	0.807	0.992	0.897	0.807	0.992	CLONAL	1	TRUE	1	0.64060416369359	2		351	327	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946451	71946451	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	296	694	0	ENST00000298229.2:c.2615T>C	p.Val872Ala	p.V872A	ENST00000298229	NM_001567.3	872	gTg/gCg	23/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.64060416369359	2		694	913	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999569	100999569	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	234	802	0	ENST00000325455.5:c.233A>G	p.Gln78Arg	p.Q78R	ENST00000325455	NM_001202474.3	78	cAg/cGg	1/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.64060416369359	2		802	658	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153438	108153438	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	116	259	0	ENST00000278616.4:c.3578T>G	p.Val1193Gly	p.V1193G	ENST00000278616	NM_000051.3	1193	gTt/gGt	25/63	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.64060416369359	2		259	335	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244600	46244600	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	216	490	1	ENST00000334344.6:c.2697del	p.Lys899AsnfsTer28	p.K899Nfs*28	ENST00000334344	NM_152641.2	898	ccA/cc	15/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.64060416369359	2		491	576	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007647	45007647	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	120	279	0	ENST00000558401.1:c.94del	p.Arg32ValfsTer12	p.R32Vfs*12	ENST00000558401	NM_004048.2	32	Cgt/gt	2/4	0.213279765960762	4	FACETS	0.837	0.764	0.913	0.837	0.764	0.913	INDETERMINATE	2	TRUE	2	0.64060416369359	4		279	367	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032186	10032186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	207	587	0	ENST00000330684.3:c.637G>A	p.Ala213Thr	p.A213T	ENST00000330684	NM_001134407.1	213	Gca/Aca	3/13	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.64060416369359	2		587	518	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020613	14020613	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	106	337	0	ENST00000311895.7:c.584G>T	p.Arg195Met	p.R195M	ENST00000311895	NM_005236.2	195	aGg/aTg	3/11	1	2	FACETS	0.991	0.898	1	0.991	0.898	1	CLONAL	1	TRUE	1	0.64060416369359	2		337	334	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858262	59858264	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs1355330975	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	177	476	0	ENST00000259008.2:c.1731_1733del	p.Lys578del	p.K578del	ENST00000259008	NM_032043.2	577	aaGAAa/aaa	12/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.64060416369359	2		476	533	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861776	59861776	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	124	316	0	ENST00000259008.2:c.1483del	p.Ser495LeufsTer31	p.S495Lfs*31	ENST00000259008	NM_032043.2	495	Tct/ct	11/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.64060416369359	2		316	323	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222329	2222329	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	390	778	1	ENST00000398665.3:c.3161G>A	p.Gly1054Asp	p.G1054D	ENST00000398665	NM_032482.2	1054	gGc/gAc	24/28	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.64060416369359	2		779	989	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170447	11170447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555795880	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	320	652	0	ENST00000358026.2:c.4750G>A	p.Val1584Ile	p.V1584I	ENST00000358026	NM_001128849.1	1584	Gtc/Atc	34/36	0.144041328816602	4	FACETS	0.881	0.834	0.929	0.881	0.834	0.929	INDETERMINATE	2	TRUE	2	0.64060416369359	4		652	930	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291543	15291543	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1285584068	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	263	693	0	ENST00000263388.2:c.3091C>T	p.Arg1031Cys	p.R1031C	ENST00000263388	NM_000435.2	1031	Cgc/Tgc	19/33	0.144041328816602	4	FACETS	0.796	0.748	0.845	0.796	0.748	0.845	INDETERMINATE	2	TRUE	2	0.64060416369359	4		693	846	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211062	36211063	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	335	789	0	ENST00000222270.7:c.816dup	p.Gly273ArgfsTer61	p.G273Rfs*61	ENST00000222270	NM_014727.1	271	-/C	3/37	0.144041328816602	4	FACETS	0.769	0.728	0.812	0.769	0.728	0.812	INDETERMINATE	2	TRUE	2	0.64060416369359	4		789	1115	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223961	36223961	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	348	805	0	ENST00000222270.7:c.6514del	p.Val2172SerfsTer4	p.V2172Sfs*4	ENST00000222270	NM_014727.1	2171	Ggg/gg	28/37	0.144041328816602	4	FACETS	0.879	0.834	0.925	0.879	0.834	0.925	INDETERMINATE	2	TRUE	2	0.64060416369359	4		805	1014	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791471	42791471	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	322	618	0	ENST00000575354.2:c.453-1G>A		p.X151_splice	ENST00000575354	NM_015125.3	151			0.144041328816602	4	FACETS	0.974	0.923	1	0.974	0.923	1	INDETERMINATE	2	TRUE	2	0.64060416369359	4		618	847	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466902	57466902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	125	174	0	ENST00000371085.3:c.121C>T	p.His41Tyr	p.H41Y	ENST00000371085	NM_000516.4	41	Cac/Tac	1/13	0.144041328816602	4	FACETS	0.87	0.796	0.946	0.87	0.796	0.946	INDETERMINATE	2	TRUE	2	0.64060416369359	4		174	368	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961355	1961355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745664737	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	302	517	1	ENST00000382891.5:c.3143C>T	p.Ala1048Val	p.A1048V	ENST00000382891	NM_133335.3	1048	gCg/gTg	17/22	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.64060416369359	2		518	797	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293976	1293976	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	294	837	2	ENST00000310581.5:c.1025G>T	p.Arg342Leu	p.R342L	ENST00000310581	NM_198253.2	342	cGg/cTg	2/16	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.64060416369359	2		839	790	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31485063	31485063	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	78	284	0	ENST00000344624.3:c.1921del	p.Cys641ValfsTer2	p.C641Vfs*2	ENST00000344624		641	Tgt/gt	12/33	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.64060416369359	2		284	225	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86658402	86658402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	61	168	0	ENST00000274376.6:c.1367G>A	p.Gly456Asp	p.G456D	ENST00000274376	NM_002890.2	456	gGc/gAc	10/25	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.64060416369359	2		168	186	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680164	30680164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	342	619	0	ENST00000376406.3:c.1555G>A	p.Val519Met	p.V519M	ENST00000376406	NM_014641.2	519	Gtg/Atg	5/15	0.144041328816602	4	FACETS	0.913	0.867	0.961	0.913	0.867	0.961	INDETERMINATE	2	TRUE	2	0.64060416369359	4		619	959	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87322816	87322817	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	147	335	0	ENST00000277120.3:c.419dup	p.Leu140PhefsTer3	p.L140Ffs*3	ENST00000277120		139	-/T	5/19	0.247381625921241	0	FACETS	0.408	0.377	0.441			1	INDETERMINATE	1	TRUE	0	0.64060416369359	0		335	404	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755920	133755920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765425928	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	293	599	1	ENST00000318560.5:c.1547G>A	p.Arg516His	p.R516H	ENST00000318560	NM_005157.4	516	cGt/cAt	10/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.64060416369359	2		600	812	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932902	39932902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180666937	NA	P-0053748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	247	350	1	ENST00000378444.4:c.1697G>A	p.Arg566His	p.R566H	ENST00000378444	NM_001123385.1	566	cGc/cAc	4/15	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.64060416369359	1		351	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0053751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	32	693	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		693	1008	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	24	647	0	ENST00000269571.5:c.829G>T	p.Asp277Tyr	p.D277Y	ENST00000269571		277	Gac/Tac	7/27	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		647	815	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	197	276	0				ENST00000310581	NM_198253.2	-/1132			0.330165139956841	6	FACETS	1	0.971	1	0.852	0.798	0.907	CLONAL	4	FALSE	1	0.330165139956841	6		276	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0053751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	403	693	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.260824588130277	3	FACETS	0.941	0.898	0.984	0.941	0.898	0.984	CLONAL	3	FALSE	0	0.330165139956841	3		693	1008	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	143	647	0	ENST00000269571.5:c.829G>T	p.Asp277Tyr	p.D277Y	ENST00000269571		277	Gac/Tac	7/27	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.330165139956841	2		647	727	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347552	89347552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369218399	NA	P-0053751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	56	714	0	ENST00000301030.4:c.5398G>A	p.Glu1800Lys	p.E1800K	ENST00000301030	NM_001256183.1	1800	Gag/Aag	9/13	NA	2	FACETS	0.563	0.482	0.651			1	INDETERMINATE	1	FALSE	NA	0.330165139956841	2		714	603	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947585	48947585	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0053751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	72	265	0	ENST00000267163.4:c.1172C>G	p.Ser391Ter	p.S391*	ENST00000267163	NM_000321.2	391	tCa/tGa	12/27	0.179617573180081	4	FACETS	1	0.968	1	0.671	0.589	0.76	INDETERMINATE	1	FALSE	2	0.330165139956841	4		265	432	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197187	26197187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	48	577	0	ENST00000356476.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000356476		98	Gag/Aag	1/1	0.330165139956841	6	FACETS	0.607	0.512	0.713	0.121	0.102	0.143	SUBCLONAL	1	FALSE	1	0.330165139956841	6		577	795	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550913	150550913	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	84	437	0	ENST00000369026.2:c.743G>C	p.Arg248Pro	p.R248P	ENST00000369026	NM_021960.4	248	cGa/cCa	2/3	0.267424342857916	4	FACETS	1	0.9	1	0.51	0.451	0.574	CLONAL	1	FALSE	2	0.330165139956841	4		437	663	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15840904	15840904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	45	293	0	ENST00000307771.7:c.988C>T	p.His330Tyr	p.H330Y	ENST00000307771	NM_005089.3	330	Cat/Tat	11/11	1	2	FACETS	0.735	0.619	0.862	0.735	0.619	0.862	SUBCLONAL	1	FALSE	1	0.330165139956841	2		293	371	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249752	133249752	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs776770625	NA	P-0053751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	29	366	1	ENST00000320574.5:c.1471G>A	p.Glu491Lys	p.E491K	ENST00000320574	NM_006231.2	491	Gag/Aag	14/49	1	2	FACETS	0.563	0.453	0.688	0.563	0.453	0.688	SUBCLONAL	1	FALSE	1	0.330165139956841	2		367	312	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866671	37866671	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	144	780	0	ENST00000269571.5:c.838G>C	p.Glu280Gln	p.E280Q	ENST00000269571		280	Gag/Cag	7/27	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.330165139956841	2		780	801	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990459	69990459	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749465060	NA	P-0053751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	30	256	0	ENST00000394351.3:c.418C>T	p.Pro140Ser	p.P140S	ENST00000394351	NM_000248.3	140	Cct/Tct	4/9	0.118845256470669	4	FACETS	0.597	0.481	0.729	0.298	0.24	0.365	INDETERMINATE	1	FALSE	2	0.330165139956841	4		256	405	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023667	27023667	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	51	330	0	ENST00000324856.7:c.773C>A	p.Ser258Tyr	p.S258Y	ENST00000324856	NM_006015.4	258	tCc/tAc	1/20	0.267424342857916	4	FACETS	0.721	0.612	0.84	0.36	0.306	0.42	SUBCLONAL	1	FALSE	2	0.330165139956841	4		330	570	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056269	27056275	+	frameshift_variant	Frame_Shift_Del	DEL	ACGGGTC	ACGGGTC	-	novel	NA	P-0053751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	177	503	0	ENST00000324856.7:c.1265_1271del	p.Tyr422SerfsTer9	p.Y422Sfs*9	ENST00000324856	NM_006015.4	422	tACGGGTCc/tc	2/20	0.267424342857916	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	FALSE	2	0.330165139956841	4		503	624	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954220	48954252	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTAAATTTTTTACTTTTAGTAAAAAATTTTTT	GGTAAATTTTTTACTTTTAGTAAAAAATTTTTT	-	novel	NA	P-0053751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	62	117	0	ENST00000267163.4:c.1421_1421+32del		p.X474_splice	ENST00000267163	NM_000321.2	474		15/27	0.179617573180081	4	FACETS	1	0.96	1	0.645	0.56	0.738	INDETERMINATE	1	FALSE	2	0.330165139956841	4		117	387	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346655	89346655	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	33	564	0	ENST00000301030.4:c.6295G>T	p.Glu2099Ter	p.E2099*	ENST00000301030	NM_001256183.1	2099	Gaa/Taa	9/13	NA	2	FACETS	0.494	0.402	0.597			1	INDETERMINATE	1	FALSE	NA	0.330165139956841	2		564	405	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348669	89348669	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	67	824	0	ENST00000301030.4:c.4281G>C	p.Lys1427Asn	p.K1427N	ENST00000301030	NM_001256183.1	1427	aaG/aaC	9/13	NA	2	FACETS	0.393	0.34	0.45			1	INDETERMINATE	1	FALSE	NA	0.330165139956841	2		824	1034	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033984	48033984	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs192740549	NA	P-0053751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	45	274	0	ENST00000234420.5:c.4068G>C	p.Leu1356Phe	p.L1356F	ENST00000234420	NM_000179.2	1356	ttG/ttC	10/10	1	2	FACETS	0.501	0.421	0.59	0.501	0.421	0.59	SUBCLONAL	1	FALSE	1	0.330165139956841	2		274	544	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259216	89259216	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	26	375	0	ENST00000336596.2:c.360C>G	p.Phe120Leu	p.F120L	ENST00000336596	NM_005233.5	120	ttC/ttG	3/17	0.118845256470669	4	FACETS	0.667	0.529	0.825	0.334	0.264	0.413	INDETERMINATE	1	FALSE	2	0.330165139956841	4		375	314	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205200	128205201	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0053751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	105	631	0	ENST00000341105.2:c.240dup	p.Gly81ArgfsTer104	p.G81Rfs*104	ENST00000341105	NM_032638.4	80	-/C	3/6	0.118845256470669	4	FACETS	1	0.977	1	0.665	0.597	0.737	INDETERMINATE	1	FALSE	2	0.330165139956841	4		631	636	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884893	134884893	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	156	497	0	ENST00000398015.3:c.1669G>T	p.Val557Leu	p.V557L	ENST00000398015	NM_004441.4	557	Gtg/Ttg	8/16	0.118845256470669	4	FACETS	0.994	0.914	1	0.994	0.914	1	INDETERMINATE	2	FALSE	2	0.330165139956841	4		497	632	SUCCESS
ATR	545	MSKCC	GRCh37	3	142254026	142254026	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	32	293	0	ENST00000350721.4:c.3841C>T	p.Leu1281Phe	p.L1281F	ENST00000350721	NM_001184.3	1281	Ctt/Ttt	21/47	0.118845256470669	4	FACETS	0.617	0.5	0.748	0.308	0.25	0.374	INDETERMINATE	1	FALSE	2	0.330165139956841	4		293	418	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56911007	56911007	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	51	480	0	ENST00000519728.1:c.1153G>C	p.Asp385His	p.D385H	ENST00000519728	NM_002350.3	385	Gat/Cat	11/13	0.214799652079631	1	FACETS	0.406	0.344	0.473	0.406	0.344	0.473	SUBCLONAL	1	FALSE	0	0.330165139956841	1		480	636	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981788	70981788	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	67	914	0	ENST00000276594.2:c.308C>G	p.Pro103Arg	p.P103R	ENST00000276594	NM_024504.3	103	cCa/cGa	2/8	0.214799652079631	1	FACETS	0.501	0.435	0.573	0.501	0.435	0.573	SUBCLONAL	1	FALSE	0	0.330165139956841	1		914	676	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652126	36652144	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGAGGCCGGGATGAGTT	GGCGAGGCCGGGATGAGTT	TCGTC	novel	NA	P-0053751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	124	779	2	ENST00000244741.5:c.248_266delinsTCGTC	p.Arg83LeufsTer41	p.R83Lfs*41	ENST00000244741	NM_000389.4	83	cGGCGAGGCCGGGATGAGTTg/cTCGTCg	2/3	0.330165139956841	4	FACETS	1	0.967	1	0.385	0.348	0.424	CLONAL	1	FALSE	1	0.330165139956841	4		781	865	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035307	42035307	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	248	530	0	ENST00000219905.7:c.5149C>G	p.Leu1717Val	p.L1717V	ENST00000219905	NM_001164273.1	1717	Ctg/Gtg	15/24	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.81836248550926	2		530	601	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	183	316	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.510970239498479	4	FACETS	1	0.988	1	0.445	0.413	0.478	CLONAL	1	TRUE	1	0.81836248550926	4		316	609	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	152	785	0	ENST00000269571.5:c.829G>C	p.Asp277His	p.D277H	ENST00000269571		277	Gac/Cac	7/27	1	2	FACETS	0.416	0.381	0.454	0.416	0.381	0.454	SUBCLONAL	1	TRUE	1	0.81836248550926	2		785	892	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	344	819	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.81836248550926	2		819	779	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	331	646	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.81836248550926	2		646	762	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880257	37880257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	201	466	0	ENST00000269571.5:c.2301C>G	p.Ile767Met	p.I767M	ENST00000269571		767	atC/atG	19/27	1	2	FACETS	0.979	0.916	1	0.979	0.916	1	CLONAL	1	TRUE	1	0.81836248550926	2		466	502	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	56	451	0	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	1	2	FACETS	0.291	0.25	0.337	0.291	0.25	0.337	SUBCLONAL	1	TRUE	1	0.81836248550926	2		451	470	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112569	115112569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180836314	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	367	853	2	ENST00000257566.3:c.1171G>A	p.Asp391Asn	p.D391N	ENST00000257566	NM_016569.3	391	Gac/Aac	7/8	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.81836248550926	2		855	809	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039133	49039133	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	155	260	0	ENST00000267163.4:c.2212-1G>C		p.X738_splice	ENST00000267163	NM_000321.2	738			0.81836248550926	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.81836248550926	1		260	198	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572904	41572904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	317	773	0	ENST00000263253.7:c.5189C>T	p.Ser1730Phe	p.S1730F	ENST00000263253	NM_001429.3	1730	tCt/tTt	31/31	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.81836248550926	2		773	755	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143332	108143332	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs774935453	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	227	402	0	ENST00000278616.4:c.3151G>C	p.Glu1051Gln	p.E1051Q	ENST00000278616	NM_000051.3	1051	Gag/Cag	21/63	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.81836248550926	2		402	504	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961930	41961930	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	196	441	0	ENST00000219905.7:c.838G>C	p.Glu280Gln	p.E280Q	ENST00000219905	NM_001164273.1	280	Gaa/Caa	2/24	1	2	FACETS	0.984	0.92	1	0.984	0.92	1	CLONAL	1	TRUE	1	0.81836248550926	2		441	487	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642800	3642800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747832147	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	403	788	0	ENST00000294008.3:c.2227G>A	p.Val743Met	p.V743M	ENST00000294008	NM_032444.2	743	Gtg/Atg	11/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.81836248550926	2		788	914	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166449	32166449	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	344	707	0	ENST00000375023.3:c.4594G>C	p.Glu1532Gln	p.E1532Q	ENST00000375023	NM_004557.3	1532	Gag/Cag	25/30	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.81836248550926	2		707	814	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701200	43701200	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	328	617	0	ENST00000382044.4:c.5495C>T	p.Ser1832Phe	p.S1832F	ENST00000382044	NM_001141980.1	1832	tCt/tTt	26/28	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.81836248550926	2		617	709	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247174	153247174	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	53	343	0	ENST00000281708.4:c.1628G>C	p.Arg543Thr	p.R543T	ENST00000281708	NM_033632.3	543	aGa/aCa	10/12	1	2	FACETS	0.279	0.238	0.323	0.279	0.238	0.323	SUBCLONAL	1	TRUE	1	0.81836248550926	2		343	465	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879590	37879590	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	346	659	0	ENST00000269571.5:c.1965C>G	p.Ile655Met	p.I655M	ENST00000269571		655	atC/atG	17/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.81836248550926	2		659	808	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035101	42035101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	350	670	0	ENST00000219905.7:c.4943C>T	p.Ser1648Phe	p.S1648F	ENST00000219905	NM_001164273.1	1648	tCt/tTt	15/24	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.81836248550926	2		670	813	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927451	178927451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	194	441	0	ENST00000263967.3:c.1214C>T	p.Ser405Phe	p.S405F	ENST00000263967	NM_006218.2	405	tCc/tTc	7/21	0.512272826459587	3	FACETS	1	0.986	1	0.41	0.382	0.439	CLONAL	1	TRUE	0	0.81836248550926	3		441	543	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195769	102195769	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	229	435	0	ENST00000263464.3:c.529C>T	p.Gln177Ter	p.Q177*	ENST00000263464	NM_001165.4	177	Cag/Tag	2/9	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.81836248550926	2		435	462	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244235	153244235	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	28	397	1	ENST00000281708.4:c.1922C>G	p.Ser641Ter	p.S641*	ENST00000281708	NM_033632.3	641	tCa/tGa	12/12	1	2	FACETS	0.127	0.101	0.157	0.127	0.101	0.157	SUBCLONAL	1	TRUE	1	0.81836248550926	2		398	538	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258630	16258630	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	297	682	0	ENST00000375759.3:c.5895G>C	p.Glu1965Asp	p.E1965D	ENST00000375759	NM_015001.2	1965	gaG/gaC	11/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.81836248550926	2		682	695	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935343	36935343	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	103	812	0	ENST00000361632.4:c.1384G>C	p.Glu462Gln	p.E462Q	ENST00000361632		462	Gag/Cag	10/16	1	2	FACETS	0.319	0.285	0.355	0.319	0.285	0.355	SUBCLONAL	1	TRUE	1	0.81836248550926	2		812	789	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436169	51436169	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	219	384	0	ENST00000262662.1:c.129G>C	p.Gln43His	p.Q43H	ENST00000262662		43	caG/caC	3/4	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.81836248550926	2		384	467	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275438	115275438	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	180	369	0	ENST00000438362.2:c.976-1G>C		p.X326_splice	ENST00000438362	NM_001242891.1	326			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.81836248550926	2		369	406	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551334	150551334	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	395	836	0	ENST00000369026.2:c.673G>C	p.Glu225Gln	p.E225Q	ENST00000369026	NM_021960.4	225	Gag/Cag	1/3	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.81836248550926	2		836	931	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246290	46246290	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	196	441	0	ENST00000334344.6:c.4384C>G	p.Gln1462Glu	p.Q1462E	ENST00000334344	NM_152641.2	1462	Cag/Gag	15/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.81836248550926	2		441	430	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425030	49425034	+	frameshift_variant	Frame_Shift_Del	DEL	CTCAG	CTCAG	-	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	359	788	0	ENST00000301067.7:c.13454_13458del	p.Ala4485AspfsTer6	p.A4485Dfs*6	ENST00000301067	NM_003482.3	4485	gCTGAG/g	39/54	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.81836248550926	2		788	862	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446025	49446025	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	407	920	0	ENST00000301067.7:c.1441G>T	p.Glu481Ter	p.E481*	ENST00000301067	NM_003482.3	481	Gag/Tag	10/54	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.81836248550926	2		920	923	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41962056	41962056	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	261	520	0	ENST00000219905.7:c.964G>C	p.Glu322Gln	p.E322Q	ENST00000219905	NM_001164273.1	322	Gag/Cag	2/24	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.81836248550926	2		520	581	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021497	42021497	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	301	598	1	ENST00000219905.7:c.3793C>T	p.Gln1265Ter	p.Q1265*	ENST00000219905	NM_001164273.1	1265	Cag/Tag	11/24	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.81836248550926	2		599	642	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035332	42035332	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	186	477	0	ENST00000219905.7:c.5174C>G	p.Ser1725Ter	p.S1725*	ENST00000219905	NM_001164273.1	1725	tCa/tGa	15/24	1	2	FACETS	0.926	0.863	0.99	0.926	0.863	0.99	CLONAL	1	TRUE	1	0.81836248550926	2		477	491	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2224033	2224033	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	357	797	0	ENST00000326181.6:c.1247C>G	p.Ser416Cys	p.S416C	ENST00000326181	NM_032271.2	416	tCt/tGt	13/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.81836248550926	2		797	836	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89866024	89866024	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	272	519	0	ENST00000389301.3:c.815G>C	p.Arg272Thr	p.R272T	ENST00000389301	NM_000135.2	272	aGa/aCa	9/43	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.81836248550926	2		519	631	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37863257	37863257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	40	715	0	ENST00000269571.5:c.88G>A	p.Asp30Asn	p.D30N	ENST00000269571		30	Gac/Aac	2/27	1	2	FACETS	0.124	0.102	0.148	0.124	0.102	0.148	SUBCLONAL	1	TRUE	1	0.81836248550926	2		715	788	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858048	45858048	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	382	866	0	ENST00000391945.4:c.1605C>G	p.Ile535Met	p.I535M	ENST00000391945	NM_000400.3	535	atC/atG	17/23	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.81836248550926	2		866	813	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715311	61715311	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	277	567	0	ENST00000401558.2:c.2302G>A	p.Asp768Asn	p.D768N	ENST00000401558	NM_003400.3	768	Gat/Aat	19/25	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.81836248550926	2		567	637	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096331	178096331	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	320	554	0	ENST00000397062.3:c.1000G>T	p.Glu334Ter	p.E334*	ENST00000397062	NM_006164.4	334	Gaa/Taa	5/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.81836248550926	2		554	731	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952463	38952463	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	204	407	0	ENST00000357387.3:c.2962C>T	p.His988Tyr	p.H988Y	ENST00000357387	NM_152756.3	988	Cac/Tac	30/38	1	2	FACETS	0.978	0.915	1	0.978	0.915	1	CLONAL	1	TRUE	1	0.81836248550926	2		407	510	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950766	79950766	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs751800062	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	117	388	0	ENST00000265081.6:c.220C>T	p.Gln74Ter	p.Q74*	ENST00000265081	NM_002439.4	74	Cag/Tag	1/24	1	2	FACETS	0.745	0.678	0.814	0.745	0.678	0.814	SUBCLONAL	1	TRUE	1	0.81836248550926	2		388	384	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911529	131911529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	258	481	0	ENST00000265335.6:c.274G>A	p.Glu92Lys	p.E92K	ENST00000265335		92	Gaa/Aaa	3/25	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.81836248550926	2		481	607	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563506	87563506	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	290	686	0	ENST00000277120.3:c.1894G>T	p.Val632Phe	p.V632F	ENST00000277120		632	Gtc/Ttc	16/19	1	2	FACETS	0.948	0.896	1	0.948	0.896	1	CLONAL	1	TRUE	1	0.81836248550926	2		686	748	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97933389	97933389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	209	399	0	ENST00000289081.3:c.493C>T	p.His165Tyr	p.H165Y	ENST00000289081	NM_000136.2	165	Cat/Tat	6/15	1	2	FACETS	0.998	0.935	1	0.998	0.935	1	CLONAL	1	TRUE	1	0.81836248550926	2		399	512	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938800	76938800	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	257	297	0	ENST00000373344.5:c.1948G>A	p.Glu650Lys	p.E650K	ENST00000373344	NM_000489.3	650	Gaa/Aaa	9/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.81836248550926	1		297	283	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374244	138374244	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	31	446	1	ENST00000289153.2:c.3200A>T	p.Asp1067Val	p.D1067V	ENST00000289153	NM_006219.2	1067	gAc/gTc	22/22	1	2	FACETS	0.731	0.591	0.89	0.731	0.591	0.89	SUBCLONAL	1	TRUE	1	0.2	2		447	424	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481600	56481600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1176464861	NA	P-0053754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	51	586	0	ENST00000267101.3:c.635C>T	p.Pro212Leu	p.P212L	ENST00000267101	NM_001982.3	212	cCt/cTt	6/28	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.2	2		586	510	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692839	89692839	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1064793243	NA	P-0053754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	14	158	0	ENST00000371953.3:c.323T>C	p.Leu108Pro	p.L108P	ENST00000371953	NM_000314.4	108	cTt/cCt	5/9	0.22432161933911	3	FACETS	0.994	0.722	1	0.497	0.361	0.66	CLONAL	1	TRUE	1	0.2	3		158	155	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087568	27087568	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	47	622	0	ENST00000324856.7:c.2142del	p.Ser715ArgfsTer27	p.S715Rfs*27	ENST00000324856	NM_006015.4	714	ctC/ct	5/20	1	2	FACETS	0.87	0.734	1	0.87	0.734	1	CLONAL	1	TRUE	1	0.2	2		622	540	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692803	89692803	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1554898074	NA	P-0053754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	59	278	0	ENST00000371953.3:c.287C>G	p.Pro96Arg	p.P96R	ENST00000371953	NM_000314.4	96	cCa/cGa	5/9	0.22432161933911	3	FACETS	1	0.913	1	1	0.913	1	CLONAL	2	TRUE	1	0.2	3		278	303	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644979	67644980	+	stop_gained	Nonsense_Mutation	DNP	GT	GT	TA	novel	NA	P-0053754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	37	598	1	ENST00000264010.4:c.244_245delinsTA	p.Val82Ter	p.V82*	ENST00000264010	NM_006565.3	82	GTg/TAg	3/12	1	2	FACETS	0.824	0.679	0.986	0.824	0.679	0.986	CLONAL	1	TRUE	1	0.2	2		599	449	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89478319	89478319	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0053754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	28	358	0	ENST00000336596.2:c.2136+2T>C		p.X712_splice	ENST00000336596	NM_005233.5	712			1	2	FACETS	1	0.816	1	1	0.816	1	CLONAL	1	TRUE	1	0.2	2		358	275	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0053755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	331	726	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.658083672368484	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.658303558641295	3		726	424	SUCCESS
AR	367	MSKCC	GRCh37	X	66863125	66863125	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139524801	NA	P-0053755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	19	572	0	ENST00000374690.3:c.1644G>T	p.Leu548Phe	p.L548F	ENST00000374690	NM_000044.3	548	ttG/ttT	2/8	0.613727449677248	1	FACETS	0.139	0.105	0.179	0.139	0.105	0.179	SUBCLONAL	1	TRUE	0	0.658303558641295	1		572	278	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951955	178951955	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	126	443	0	ENST00000263967.3:c.3010A>G	p.Met1004Val	p.M1004V	ENST00000263967	NM_006218.2	1004	Atg/Gtg	21/21	0.658303558641295	4	FACETS	1	0.936	1	0.346	0.314	0.38	CLONAL	1	TRUE	1	0.658303558641295	4		443	611	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779620	3779620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	48	1010	0	ENST00000262367.5:c.5428C>T	p.Arg1810Cys	p.R1810C	ENST00000262367	NM_004380.2	1810	Cgc/Tgc	31/31	0.252318860606649	3	FACETS	0.433	0.366	0.506	0.216	0.183	0.253	INDETERMINATE	1	TRUE	1	0.658303558641295	3		1010	448	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206941983	206941983	+	stop_lost	Nonstop_Mutation	SNP	A	A	C	novel	NA	P-0053755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	28	285	0	ENST00000423557.1:c.535T>G	p.Ter179GlyextTer8	p.*179Gext*8	ENST00000423557	NM_000572.2	179	Tga/Gga	5/5	0.26297925621182	4	FACETS	0.562	0.451	0.688	0.281	0.225	0.344	INDETERMINATE	1	TRUE	2	0.658303558641295	4		285	251	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572121	64572121	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	127	765	0	ENST00000312049.6:c.1518del	p.Gly507AlafsTer52	p.G507Afs*52	ENST00000312049	NM_130799.2	506	acC/ac	10/10	0.155231783522101	2	FACETS	1	0.961	1	0.542	0.497	0.588	INDETERMINATE	1	TRUE	0	0.658303558641295	2		765	356	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444390	49444400	+	frameshift_variant	Frame_Shift_Del	DEL	TCAGGGTCAGT	TCAGGGTCAGT	-	novel	NA	P-0053755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	33	718	0	ENST00000301067.7:c.2971_2981del	p.Thr991AlafsTer73	p.T991Afs*73	ENST00000301067	NM_003482.3	991	ACTGACCCTGAg/g	11/54	0.658303558641295	3	FACETS	0.285	0.232	0.346	0.143	0.116	0.173	SUBCLONAL	1	TRUE	1	0.658303558641295	3		718	467	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858226	9858226	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	79	510	0	ENST00000330684.3:c.3175T>G	p.Ser1059Ala	p.S1059A	ENST00000330684	NM_001134407.1	1059	Tct/Gct	13/13	0.252318860606649	3	FACETS	1	0.904	1	0.51	0.452	0.57	INDETERMINATE	1	TRUE	1	0.658303558641295	3		510	313	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277048	18277048	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	88	563	0	ENST00000222254.8:c.1495G>C	p.Glu499Gln	p.E499Q	ENST00000222254	NM_005027.3	499	Gag/Cag	12/16	0.474877984365063	2	FACETS	0.715	0.638	0.796	0.357	0.319	0.398	SUBCLONAL	1	TRUE	0	0.658303558641295	2		563	374	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643401	52643401	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	161	491	0	ENST00000394830.3:c.2495A>T	p.Asn832Ile	p.N832I	ENST00000394830	NM_018313.4	832	aAt/aTt	17/30	0.658303558641295	2	FACETS	0.923	0.868	0.976	0.923	0.868	0.976	CLONAL	2	TRUE	0	0.658303558641295	2		491	265	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190797	185190797	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	51	583	1	ENST00000265026.3:c.1678A>T	p.Thr560Ser	p.T560S	ENST00000265026	NM_004721.4	560	Aca/Tca	11/14	0.658303558641295	4	FACETS	0.383	0.325	0.448	0.128	0.108	0.15	SUBCLONAL	1	TRUE	1	0.658303558641295	4		584	670	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729883	41729883	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	33	578	0	ENST00000242208.4:c.646A>T	p.Ser216Cys	p.S216C	ENST00000242208	NM_002192.2	216	Agc/Tgc	3/3	0.280038891985297	5	FACETS	0.514	0.418	0.621	0.171	0.139	0.207	INDETERMINATE	1	TRUE	2	0.658303558641295	5		578	388	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0053757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	20	533	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.538	0.41	0.688	0.538	0.41	0.688	SUBCLONAL	1	TRUE	1	0.16	2		533	465	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0053757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	43	392	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	1	0.16	2		392	526	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100693	67100693	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	65	604	0	ENST00000412916.2:c.391C>T	p.Arg131Ter	p.R131*	ENST00000412916		131	Cga/Tga	4/6	0.3	1	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	0	0.16	1		604	734	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578499	7578499	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs786203071	NA	P-0053759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	383	1045	0	ENST00000269305.4:c.431A>C	p.Gln144Pro	p.Q144P	ENST00000269305	NM_001126112.2	144	cAg/cCg	5/11	0.345512524859269	2	FACETS	1	0.995	1	0.694	0.659	0.729	CLONAL	1	TRUE	0	0.447290664088758	2		1045	1234	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918125	50918127	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs763850764	NA	P-0053759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	135	944	0	ENST00000440232.2:c.2446_2448del	p.Ser816del	p.S816del	ENST00000440232	NM_002691.3	814	ttCTCc/ttc	20/27	1	2	FACETS	0.722	0.656	0.791	0.722	0.656	0.791	SUBCLONAL	1	TRUE	1	0.447290664088758	2		944	836	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673701	37673701	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	200	568	0	ENST00000447079.4:c.2855G>T	p.Cys952Phe	p.C952F	ENST00000447079	NM_015083.1	952	tGt/tTt	10/14	0.345512524859269	2	FACETS	0.757	0.705	0.809	0.757	0.705	0.809	SUBCLONAL	2	TRUE	0	0.447290664088758	2		568	591	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	170	880	1	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.891	0.818	0.967	0.891	0.818	0.967	CLONAL	1	TRUE	1	0.338763740876831	2		881	1127	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	103	473	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.928	0.832	1	0.928	0.832	1	CLONAL	1	TRUE	1	0.338763740876831	2		478	655	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	69	444	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.794	0.693	0.903	0.794	0.693	0.903	CLONAL	1	TRUE	1	0.338763740876831	2		444	513	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	103	495	2	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.338763740876831	2		497	577	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	68	265	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.929	0.811	1	0.929	0.811	1	CLONAL	1	TRUE	1	0.338763740876831	2		265	432	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099980	27099981	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	167	747	0	ENST00000324856.7:c.3861_3862del	p.Arg1287SerfsTer10	p.R1287Sfs*10	ENST00000324856	NM_006015.4	1287	AGa/a	15/20	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.338763740876831	2		747	975	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	190	766	1	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.338763740876831	2		767	926	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513243	44513243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200044775	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	85	427	0	ENST00000291552.4:c.692C>T	p.Ser231Leu	p.S231L	ENST00000291552	NM_006758.2	231	tCg/tTg	8/8	0.19831206159063	4	FACETS	0.949	0.839	1	0.474	0.419	0.534	INDETERMINATE	1	TRUE	2	0.338763740876831	4		427	708	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562387	21562387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764960515	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	190	834	1	ENST00000382592.4:c.1532G>A	p.Arg511Gln	p.R511Q	ENST00000382592	NM_014572.2	511	cGg/cAg	4/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.338763740876831	2		835	934	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131282	17131282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749770193	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	212	967	0	ENST00000285071.4:c.170G>A	p.Arg57Gln	p.R57Q	ENST00000285071	NM_144997.5	57	cGg/cAg	4/14	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.338763740876831	2		967	1187	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430771	47430771	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764281834	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	254	942	2	ENST00000377045.4:c.1736G>A	p.Arg579Gln	p.R579Q	ENST00000377045	NM_001654.4	579	cGg/cAg	16/16	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.338763740876831	2		944	1130	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967308	134967308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201143675	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	131	625	0	ENST00000398015.3:c.2647C>T	p.Arg883Trp	p.R883W	ENST00000398015	NM_004441.4	883	Cgg/Tgg	14/16	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.338763740876831	2		625	759	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027196	48027196	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs267608083	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	76	450	0	ENST00000234420.5:c.2079del	p.Lys693AsnfsTer43	p.K693Nfs*43	ENST00000234420	NM_000179.2	692	Aaa/aa	4/10	0.338763740876831	2	FACETS	0.865	0.76	0.977	0.432	0.38	0.489	CLONAL	1	TRUE	0	0.338763740876831	2		450	519	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474041	29474041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs78723472	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	150	1001	2	ENST00000389048.3:c.2134G>A	p.Val712Met	p.V712M	ENST00000389048	NM_004304.4	712	Gtg/Atg	12/29	0.338763740876831	2	FACETS	0.872	0.796	0.951	0.436	0.398	0.476	CLONAL	1	TRUE	0	0.338763740876831	2		1003	1016	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574679	41574679	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	136	930	1	ENST00000263253.7:c.6970del	p.His2324ThrfsTer29	p.H2324Tfs*29	ENST00000263253	NM_001429.3	2322	Ccc/cc	31/31	1	2	FACETS	0.692	0.627	0.759	0.692	0.627	0.759	SUBCLONAL	1	TRUE	1	0.338763740876831	2		931	1161	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514591	44514591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	129	452	0	ENST00000291552.4:c.565C>T	p.Arg189Cys	p.R189C	ENST00000291552	NM_006758.2	189	Cgt/Tgt	7/8	0.19831206159063	4	FACETS	1	0.984	1	0.72	0.654	0.79	INDETERMINATE	1	TRUE	2	0.338763740876831	4		452	708	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025857	48025857	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs267608041	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	68	318	0	ENST00000234420.5:c.741del	p.Lys247AsnfsTer32	p.K247Nfs*32	ENST00000234420	NM_000179.2	245	atA/at	4/10	0.338763740876831	2	FACETS	0.945	0.825	1	0.472	0.412	0.537	CLONAL	1	TRUE	0	0.338763740876831	2		318	425	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324892	31324892	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs765875917	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	45	643	1	ENST00000412585.2:c.44del	p.Ala15GlyfsTer5	p.A15Gfs*5	ENST00000412585	NM_005514.6	15	gCg/gg	1/8	0.330554017417222	2	FACETS	0.398	0.334	0.47	0.199	0.167	0.235	SUBCLONAL	1	TRUE	0	0.338763740876831	2		644	667	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948778	71948778	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377556632	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	237	968	4	ENST00000298229.2:c.3490C>T	p.Arg1164Trp	p.R1164W	ENST00000298229	NM_001567.3	1164	Cgg/Tgg	26/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.338763740876831	2		972	1195	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591246	67591246	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	29	383	1	ENST00000274335.5:c.1746-2A>G		p.X582_splice	ENST00000274335		582			1	2	FACETS	0.387	0.31	0.475	0.387	0.31	0.475	SUBCLONAL	1	TRUE	1	0.338763740876831	2		384	442	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437163	121437163	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1421619915	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	220	1046	1	ENST00000257555.6:c.1594G>A	p.Ala532Thr	p.A532T	ENST00000257555		532	Gcc/Acc	8/10	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.338763740876831	2		1047	1246	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155420	99155420	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	49	410	0	ENST00000074304.5:c.646C>T	p.Arg216Ter	p.R216*	ENST00000074304	NM_001134224.1	216	Cga/Tga	9/26	1	2	FACETS	0.415	0.351	0.486	0.415	0.351	0.486	SUBCLONAL	1	TRUE	1	0.338763740876831	2		410	697	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370686	225370686	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1232071537	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	31	308	1	ENST00000264414.4:c.1193del	p.Lys398ArgfsTer6	p.K398Rfs*6	ENST00000264414	NM_003590.4	398	aAg/ag	8/16	0.338763740876831	2	FACETS	0.541	0.438	0.658	0.271	0.219	0.329	SUBCLONAL	1	TRUE	0	0.338763740876831	2		309	338	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760790	133760790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367600262	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	185	793	1	ENST00000318560.5:c.3113C>T	p.Ala1038Val	p.A1038V	ENST00000318560	NM_005157.4	1038	gCg/gTg	11/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.338763740876831	2		794	861	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281305	15281305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	234	963	0	ENST00000263388.2:c.4951G>A	p.Ala1651Thr	p.A1651T	ENST00000263388	NM_000435.2	1651	Gct/Act	27/33	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.338763740876831	2		963	1184	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422682	47422682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	146	805	2	ENST00000377045.4:c.154C>T	p.Arg52Trp	p.R52W	ENST00000377045	NM_001654.4	52	Cgg/Tgg	3/16	1	2	FACETS	0.921	0.84	1	0.921	0.84	1	CLONAL	1	TRUE	1	0.338763740876831	2		807	936	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917083	50917083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747996611	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	242	931	0	ENST00000440232.2:c.2335G>A	p.Ala779Thr	p.A779T	ENST00000440232	NM_002691.3	779	Gcg/Acg	19/27	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.338763740876831	2		931	1262	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951811	2951811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146334064	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	161	695	1	ENST00000396946.4:c.3139G>A	p.Ala1047Thr	p.A1047T	ENST00000396946	NM_032415.4	1047	Gcc/Acc	23/25	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.338763740876831	2		696	942	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438655	49438655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1268188754	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	196	681	0	ENST00000301067.7:c.4835G>A	p.Arg1612His	p.R1612H	ENST00000301067	NM_003482.3	1612	cGc/cAc	19/54	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.338763740876831	2		681	1012	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17125885	17125885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257705335	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	223	808	2	ENST00000285071.4:c.709G>A	p.Ala237Thr	p.A237T	ENST00000285071	NM_144997.5	237	Gcc/Acc	7/14	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.338763740876831	2		810	1120	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572273	64572273	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765306552	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	161	697	2	ENST00000312049.6:c.1366C>T	p.Arg456Cys	p.R456C	ENST00000312049	NM_130799.2	456	Cgc/Tgc	10/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.338763740876831	2		699	893	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341631	70341631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	185	732	0	ENST00000374080.3:c.1066C>T	p.Arg356Trp	p.R356W	ENST00000374080		356	Cgg/Tgg	7/45	1	2	FACETS	0.997	0.919	1	0.997	0.919	1	CLONAL	1	TRUE	1	0.338763740876831	2		732	1096	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480346	89480346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748206093	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	59	308	0	ENST00000336596.2:c.2183G>A	p.Arg728Gln	p.R728Q	ENST00000336596	NM_005233.5	728	cGa/cAa	13/17	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.338763740876831	2		308	315	SUCCESS
APC	324	MSKCC	GRCh37	5	112162923	112162923	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	61	343	0	ENST00000257430.4:c.1530del	p.Phe510LeufsTer4	p.F510Lfs*4	ENST00000257430	NM_000038.5	509	acT/ac	12/16	1	2	FACETS	0.933	0.808	1	0.933	0.808	1	CLONAL	1	TRUE	1	0.338763740876831	2		343	386	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639605	3639605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757202686	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	98	1067	0	ENST00000294008.3:c.4034G>A	p.Arg1345His	p.R1345H	ENST00000294008	NM_032444.2	1345	cGt/cAt	12/15	1	2	FACETS	0.479	0.426	0.536	0.479	0.426	0.536	SUBCLONAL	1	TRUE	1	0.338763740876831	2		1067	1207	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614539	38614539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754706111	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	77	587	1	ENST00000299084.4:c.305C>T	p.Thr102Met	p.T102M	ENST00000299084	NM_152594.2	102	aCg/aTg	3/7	1	2	FACETS	0.736	0.646	0.832	0.736	0.646	0.832	SUBCLONAL	1	TRUE	1	0.338763740876831	2		588	618	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172515	108172515	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	54	205	0	ENST00000278616.4:c.5318A>G	p.Lys1773Arg	p.K1773R	ENST00000278616	NM_000051.3	1773	aAg/aGg	35/63	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.338763740876831	2		205	261	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187221	38187222	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	168	822	1	ENST00000317025.8:c.1255dup	p.Thr419AsnfsTer28	p.T419Nfs*28	ENST00000317025	NM_023034.1	419	acc/aAcc	6/24	1	2	FACETS	0.777	0.712	0.845	0.777	0.712	0.845	SUBCLONAL	1	TRUE	1	0.338763740876831	2		823	1277	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118391551	118391551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	107	343	0	ENST00000534358.1:c.11464C>T	p.Arg3822Cys	p.R3822C	ENST00000534358	NM_005933.3	3822	Cgc/Tgc	34/36	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.338763740876831	2		343	600	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1905952	1905955	+	frameshift_variant	Frame_Shift_Del	DEL	AAGA	AAGA	-	novel	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	147	521	0	ENST00000382891.5:c.611_614del	p.Lys204SerfsTer14	p.K204Sfs*14	ENST00000382891	NM_133335.3	203	AAGAaa/aa	3/22	1	2	FACETS	0.983	0.897	1	0.983	0.897	1	CLONAL	1	TRUE	1	0.338763740876831	2		521	883	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419965	152419965	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200128829	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	175	712	0	ENST00000206249.3:c.1652C>T	p.Ala551Val	p.A551V	ENST00000206249	NM_000125.3	551	gCg/gTg	8/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.338763740876831	2		712	889	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332336	70332336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775380660	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	89	522	0	ENST00000373644.4:c.241C>T	p.Arg81Cys	p.R81C	ENST00000373644	NM_030625.2	81	Cgc/Tgc	2/12	1	2	FACETS	0.825	0.732	0.924	0.825	0.732	0.924	CLONAL	1	TRUE	1	0.338763740876831	2		522	637	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374487	118374487	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	100	487	1	ENST00000534358.1:c.7880G>A	p.Arg2627His	p.R2627H	ENST00000534358	NM_005933.3	2627	cGt/cAt	27/36	1	2	FACETS	0.981	0.878	1	0.981	0.878	1	CLONAL	1	TRUE	1	0.338763740876831	2		488	602	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261373	16261373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773726905	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	181	665	2	ENST00000375759.3:c.8638G>A	p.Val2880Met	p.V2880M	ENST00000375759	NM_015001.2	2880	Gtg/Atg	11/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.338763740876831	2		667	823	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627289	37627289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	221	989	2	ENST00000249071.6:c.430G>A	p.Ala144Thr	p.A144T	ENST00000249071	NM_002872.4	144	Gca/Aca	5/7	1	2	FACETS	0.972	0.902	1	0.972	0.902	1	CLONAL	1	TRUE	1	0.338763740876831	2		991	1343	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730388	133730388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	122	582	0	ENST00000318560.5:c.454C>T	p.Arg152Cys	p.R152C	ENST00000318560	NM_005157.4	152	Cgt/Tgt	3/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.338763740876831	2		582	658	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780192	9780192	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	167	878	0	ENST00000377346.4:c.1365del	p.Thr456ArgfsTer91	p.T456Rfs*91	ENST00000377346	NM_005026.3	454	aaC/aa	11/24	1	2	FACETS	0.887	0.814	0.964	0.887	0.814	0.964	CLONAL	1	TRUE	1	0.338763740876831	2		878	1111	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344375	118344375	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	59	370	0	ENST00000534358.1:c.2501C>A	p.Pro834His	p.P834H	ENST00000534358	NM_005933.3	834	cCt/cAt	3/36	1	2	FACETS	0.968	0.837	1	0.968	0.837	1	CLONAL	1	TRUE	1	0.338763740876831	2		370	360	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022865	12022865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1274778570	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	142	781	1	ENST00000396373.4:c.971C>T	p.Pro324Leu	p.P324L	ENST00000396373	NM_001987.4	324	cCg/cTg	5/8	0.256959229291168	4	FACETS	1	0.984	1	0.681	0.621	0.744	CLONAL	1	TRUE	2	0.338763740876831	4		782	824	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499641	18499641	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	98	455	0	ENST00000266497.5:c.1496A>G	p.Asn499Ser	p.N499S	ENST00000266497		499	aAc/aGc	10/31	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.338763740876831	2		455	557	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858504	57858504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1289476480	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	196	759	1	ENST00000228682.2:c.242G>A	p.Arg81Gln	p.R81Q	ENST00000228682	NM_005269.2	81	cGg/cAg	4/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.338763740876831	2		760	1003	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32969036	32969036	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	63	352	0	ENST00000380152.3:c.9467A>T	p.Gln3156Leu	p.Q3156L	ENST00000380152		3156	cAa/cTa	25/27	1	2	FACETS	0.956	0.831	1	0.956	0.831	1	CLONAL	1	TRUE	1	0.338763740876831	2		352	389	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609672	81609672	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778742	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	106	588	0	ENST00000298171.2:c.1270G>A	p.Val424Ile	p.V424I	ENST00000298171	NM_000369.2	424	Gtt/Att	10/10	1	2	FACETS	0.85	0.762	0.943	0.85	0.762	0.943	CLONAL	1	TRUE	1	0.338763740876831	2		588	736	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631703	90631703	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	188	751	0	ENST00000330062.3:c.566C>A	p.Ala189Asp	p.A189D	ENST00000330062	NM_002168.2	189	gCc/gAc	5/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.338763740876831	2		751	943	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641027	3641027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138259798	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1261	148	895	3	ENST00000294008.3:c.2612C>T	p.Ala871Val	p.A871V	ENST00000294008	NM_032444.2	871	gCg/gTg	12/15	1	2	FACETS	0.62	0.564	0.679	0.62	0.564	0.679	SUBCLONAL	1	TRUE	1	0.338763740876831	2		898	1409	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829779	72829779	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	152	692	0	ENST00000268489.5:c.6802A>G	p.Lys2268Glu	p.K2268E	ENST00000268489	NM_006885.3	2268	Aag/Gag	9/10	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.338763740876831	2		692	886	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830420	72830420	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765590881	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	70	379	0	ENST00000268489.5:c.6161C>T	p.Ala2054Val	p.A2054V	ENST00000268489	NM_006885.3	2054	gCg/gTg	9/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.338763740876831	2		379	340	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37856505	37856505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	60	374	0	ENST00000269571.5:c.14C>T	p.Ala5Val	p.A5V	ENST00000269571		5	gCc/gTc	1/27	1	2	FACETS	0.62	0.534	0.714	0.62	0.534	0.714	SUBCLONAL	1	TRUE	1	0.338763740876831	2		374	571	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533009	63533009	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	149	860	1	ENST00000307078.5:c.1885C>T	p.Gln629Ter	p.Q629*	ENST00000307078	NM_004655.3	629	Cag/Tag	7/11	1	2	FACETS	0.953	0.87	1	0.953	0.87	1	CLONAL	1	TRUE	1	0.338763740876831	2		861	923	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554182	63554182	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757415705	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	158	691	0	ENST00000307078.5:c.557C>T	p.Ala186Val	p.A186V	ENST00000307078	NM_004655.3	186	gCc/gTc	2/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.338763740876831	2		691	771	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280055	18280055	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763521018	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	91	281	0	ENST00000222254.8:c.2138C>T	p.Ala713Val	p.A713V	ENST00000222254	NM_005027.3	713	gCg/gTg	16/16	1	2	FACETS	0.752	0.674	0.835	1	0.981	1	SUBCLONAL	2	TRUE	1	0.338763740876831	2		281	357	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965448	18965448	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751561543	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	138	555	0	ENST00000262803.5:c.1195G>A	p.Val399Met	p.V399M	ENST00000262803	NM_002911.3	399	Gtg/Atg	9/24	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.338763740876831	2		555	769	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531083	187531083	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	113	515	0	ENST00000441802.2:c.9940del	p.Ser3314HisfsTer2	p.S3314Hfs*2	ENST00000441802	NM_005245.3	3314	Tca/ca	15/27	1	2	FACETS	0.977	0.88	1	0.977	0.88	1	CLONAL	1	TRUE	1	0.338763740876831	2		515	683	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526537	31526537	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	58	703	0	ENST00000344624.3:c.503A>G	p.Tyr168Cys	p.Y168C	ENST00000344624		168	tAc/tGc	2/33	0.338763740876831	1	FACETS	0.335	0.287	0.388	0.335	0.287	0.388	SUBCLONAL	1	TRUE	0	0.338763740876831	1		703	849	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393165	393165	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	223	453	0	ENST00000380956.4:c.13G>T	p.Gly5Cys	p.G5C	ENST00000380956	NM_001195286.1	5	Ggc/Tgc	2/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.338763740876831	NA		453	543	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324464	31324464	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1168937188	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	80	658	0	ENST00000412585.2:c.343+1G>A		p.X115_splice	ENST00000412585	NM_005514.6	115			0.330554017417222	2	FACETS	0.566	0.498	0.64	0.283	0.249	0.32	SUBCLONAL	1	TRUE	0	0.338763740876831	2		658	834	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141570530	141570530	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	284	741	0	ENST00000220592.5:c.598T>C	p.Phe200Leu	p.F200L	ENST00000220592	NM_012154.3	200	Ttt/Ctt	5/19	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.338763740876831	2		741	1205	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390774	139390774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358523874	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	248	1006	0	ENST00000277541.6:c.7417G>A	p.Val2473Ile	p.V2473I	ENST00000277541	NM_017617.3	2473	Gtc/Atc	34/34	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.338763740876831	2		1006	1266	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045495	47045495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	142	804	1	ENST00000377604.3:c.2462G>A	p.Arg821His	p.R821H	ENST00000377604	NM_001204468.1	821	cGc/cAc	22/24	1	2	FACETS	0.892	0.812	0.976	0.892	0.812	0.976	CLONAL	1	TRUE	1	0.338763740876831	2		805	940	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	100	478	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.364397125912568	6	FACETS	1	0.982	1	0.375	0.335	0.417	CLONAL	1	FALSE	2	0.415252847775167	6		478	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	362	804	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.415252847775167	3	FACETS	0.886	0.845	0.927	1	0.994	1	CLONAL	3	FALSE	1	0.415252847775167	3		804	792	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	148	879	3	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.415252847775167	3	FACETS	1	0.982	1	0.639	0.585	0.695	CLONAL	1	FALSE	1	0.415252847775167	3		882	674	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979257	93979257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	93	448	0	ENST00000369303.4:c.1571G>A	p.Gly524Glu	p.G524E	ENST00000369303	NM_004440.3	524	gGa/gAa	7/17	0.415252847775167	7	FACETS	0.856	0.764	0.955	0.428	0.382	0.478	CLONAL	2	FALSE	3	0.415252847775167	7		448	533	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937556	17937556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	169	1092	0	ENST00000458235.1:c.3371C>T	p.Ser1124Leu	p.S1124L	ENST00000458235	NM_000215.3	1124	tCa/tTa	24/24	0.415252847775167	5	FACETS	0.796	0.732	0.862	0.796	0.732	0.862	SUBCLONAL	2	FALSE	3	0.415252847775167	5		1092	830	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63537656	63537656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201387209	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	144	715	0	ENST00000307078.5:c.976C>T	p.Arg326Cys	p.R326C	ENST00000307078	NM_004655.3	326	Cgt/Tgt	4/11	0.415252847775167	3	FACETS	0.838	0.776	0.901	1	0.985	1	CLONAL	3	FALSE	1	0.415252847775167	3		715	333	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230641	46230641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	72	553	0	ENST00000334344.6:c.890C>T	p.Ser297Phe	p.S297F	ENST00000334344	NM_152641.2	297	tCc/tTc	8/21	0.415252847775167	8	FACETS	0.808	0.708	0.915	0.404	0.354	0.458	CLONAL	2	FALSE	4	0.415252847775167	8		553	482	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271734	38271734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	306	1258	0	ENST00000425967.3:c.2215G>A	p.Glu739Lys	p.E739K	ENST00000425967	NM_001174067.1	739	Gaa/Aaa	17/19	0.415252847775167	7	FACETS	1	0.98	1			1	CLONAL	3	FALSE	NA	0.415252847775167	7		1258	928	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663346	227663346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024227751	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	120	714	2	ENST00000305123.5:c.109G>A	p.Glu37Lys	p.E37K	ENST00000305123	NM_005544.2	37	Gag/Aag	1/2	0.415252847775167	6	FACETS	0.895	0.816	0.977	0.895	0.816	0.977	CLONAL	3	FALSE	3	0.415252847775167	6		716	394	SUCCESS
BTK	695	MSKCC	GRCh37	X	100625055	100625055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	83	519	0	ENST00000308731.7:c.322G>A	p.Glu108Lys	p.E108K	ENST00000308731	NM_000061.2	108	Gaa/Aaa	5/19	0.366930175702635	3	FACETS	1	0.979	1	0.491	0.437	0.547	CLONAL	1	FALSE	0	0.415252847775167	3		519	328	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526197	189526197	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	271	969	1	ENST00000264731.3:c.461C>G	p.Ser154Cys	p.S154C	ENST00000264731	NM_003722.4	154	tCc/tGc	4/14	0.364397125912568	6	FACETS	0.894	0.845	0.944	0.894	0.845	0.944	CLONAL	4	FALSE	2	0.415252847775167	6		970	668	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036019	180036019	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	112	965	1	ENST00000261937.6:c.3842C>T	p.Ser1281Leu	p.S1281L	ENST00000261937	NM_182925.4	1281	tCg/tTg	29/30	0.415252847775167	0	FACETS	0.722	0.654	0.793			1	SUBCLONAL	1	FALSE	0	0.415252847775167	0		966	437	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801727	3801727	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs777015995	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	93	598	0	ENST00000262367.5:c.3779C>T	p.Thr1260Met	p.T1260M	ENST00000262367	NM_004380.2	1260	aCg/aTg	20/31	0.415252847775167	0	FACETS	0.837	0.752	0.925			1	CLONAL	1	FALSE	0	0.415252847775167	0		598	313	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771344	68771344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555509646	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	81	436	3	ENST00000261769.5:c.26C>T	p.Ser9Leu	p.S9L	ENST00000261769	NM_004360.3	9	tCg/tTg	1/16	1	2	FACETS	0.806	0.721	0.894	1	0.982	1	CLONAL	2	FALSE	1	0.415252847775167	2		439	242	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864883	57864883	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	157	989	0	ENST00000228682.2:c.2360C>G	p.Ser787Cys	p.S787C	ENST00000228682	NM_005269.2	787	tCt/tGt	12/12	0.415252847775167	8	FACETS	1	0.949	1	0.523	0.48	0.569	CLONAL	2	FALSE	4	0.415252847775167	8		989	811	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850981	63850981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	109	730	1	ENST00000279873.7:c.1759G>A	p.Glu587Lys	p.E587K	ENST00000279873	NM_032199.2	587	Gaa/Aaa	10/10	0.415252847775167	5	FACETS	0.776	0.699	0.857	0.517	0.466	0.571	SUBCLONAL	2	FALSE	2	0.415252847775167	5		731	549	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90634846	90634846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	295	809	0	ENST00000330062.3:c.146C>T	p.Pro49Leu	p.P49L	ENST00000330062	NM_002168.2	49	cCc/cTc	2/11	0.415252847775167	6	FACETS	0.924	0.88	0.968	1	0.99	1	CLONAL	5	FALSE	2	0.415252847775167	6		809	563	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197187	26197187	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	218	946	0	ENST00000356476.2:c.292G>C	p.Glu98Gln	p.E98Q	ENST00000356476		98	Gag/Cag	1/1	0.415252847775167	12	FACETS	0.84	0.779	0.902			1	CLONAL	3	FALSE	NA	0.415252847775167	12		946	1282	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743871	40743871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	109	683	1	ENST00000373198.4:c.3124G>A	p.Glu1042Lys	p.E1042K	ENST00000373198	NM_133170.3	1042	Gaa/Aaa	23/32	0.199090091483538	6	FACETS	1	0.921	1	0.682	0.615	0.751	INDETERMINATE	2	FALSE	3	0.415252847775167	6		684	470	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399456	139399456	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	154	1141	0	ENST00000277541.6:c.4687G>C	p.Glu1563Gln	p.E1563Q	ENST00000277541	NM_017617.3	1563	Gag/Cag	26/34	0.415252847775167	5	FACETS	1	0.988	1	0.295	0.27	0.322	CLONAL	1	FALSE	0	0.415252847775167	5		1141	815	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951053	48951053	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	126	255	0	ENST00000267163.4:c.1216-1G>C		p.X406_splice	ENST00000267163	NM_000321.2	406			0.415252847775167	5	FACETS	0.958	0.886	1	0.766	0.709	0.824	CLONAL	4	FALSE	0	0.415252847775167	5		255	257	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870853	12870853	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	76	358	0	ENST00000228872.4:c.80C>A	p.Ser27Ter	p.S27*	ENST00000228872	NM_004064.3	27	tCg/tAg	1/3	0.415252847775167	6	FACETS	1	0.972	1	0.466	0.41	0.526	CLONAL	1	FALSE	3	0.415252847775167	6		358	479	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324579	62324579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144034326	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	166	1112	0	ENST00000360203.5:c.2935C>T	p.Arg979Trp	p.R979W	ENST00000360203	NM_001283009.1	979	Cgg/Tgg	30/35	0.199090091483538	6	FACETS	0.9	0.828	0.975	0.6	0.552	0.65	INDETERMINATE	2	FALSE	3	0.415252847775167	6		1112	813	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556714	41556714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1176732027	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	87	546	1	ENST00000263253.7:c.3659C>T	p.Ser1220Phe	p.S1220F	ENST00000263253	NM_001429.3	1220	tCc/tTc	20/31	0.415252847775167	3	FACETS	1	0.979	1	0.729	0.651	0.811	CLONAL	1	FALSE	1	0.415252847775167	3		547	347	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495208	212495208	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	154	573	0	ENST00000342788.4:c.2058G>C	p.Leu686Phe	p.L686F	ENST00000342788	NM_005235.2	686	ttG/ttC	17/28	0.415252847775167	6	FACETS	1	0.979	1	0.794	0.73	0.86	CLONAL	2	FALSE	3	0.415252847775167	6		573	570	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211707	5211707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145108936	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	286	962	2	ENST00000357368.4:c.5128C>T	p.Arg1710Cys	p.R1710C	ENST00000357368	NM_002850.3	1710	Cgc/Tgc	33/38	0.415252847775167	5	FACETS	1	0.985	1	1	0.995	1	CLONAL	3	FALSE	3	0.415252847775167	5		964	675	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976689	55976689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747477930	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	64	665	2	ENST00000263923.4:c.1136C>T	p.Ala379Val	p.A379V	ENST00000263923	NM_002253.2	379	gCg/gTg	9/30	0.135457351342667	4	FACETS	1	0.901	1	0.522	0.453	0.596	INDETERMINATE	1	FALSE	2	0.415252847775167	4		667	418	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981298	201981298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs79918642	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	155	979	0	ENST00000359651.3:c.377G>A	p.Arg126Gln	p.R126Q	ENST00000359651		126	cGa/cAa	2/8	0.415252847775167	7	FACETS	0.819	0.749	0.892	0.409	0.374	0.446	CLONAL	2	FALSE	3	0.415252847775167	7		979	929	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462948	120462948	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	87	657	0	ENST00000256646.2:c.5383G>C	p.Glu1795Gln	p.E1795Q	ENST00000256646	NM_024408.3	1795	Gaa/Caa	30/34	0.168032450704719	6	FACETS	0.825	0.733	0.922			1	INDETERMINATE	2	FALSE	NA	0.415252847775167	6		657	465	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37622806	37622806	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	155	1163	0	ENST00000249071.6:c.486G>C	p.Gln162His	p.Q162H	ENST00000249071	NM_002872.4	162	caG/caC	6/7	0.415252847775167	3	FACETS	1	0.988	1	0.737	0.677	0.798	CLONAL	1	FALSE	1	0.415252847775167	3		1163	612	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472571	88472571	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	100	782	1	ENST00000360948.2:c.1984C>T	p.Gln662Ter	p.Q662*	ENST00000360948	NM_001012338.2	662	Cag/Tag	16/19	0.415252847775167	5	FACETS	1	0.982	1	0.374	0.335	0.415	CLONAL	1	FALSE	1	0.415252847775167	5		783	523	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858351	27858351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	193	969	1	ENST00000359303.2:c.220G>A	p.Glu74Lys	p.E74K	ENST00000359303	NM_003535.2	74	Gaa/Aaa	1/1	0.415252847775167	6	FACETS	0.905	0.837	0.975	0.603	0.558	0.65	CLONAL	2	FALSE	3	0.415252847775167	6		970	940	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031679	69031679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1294114324	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	139	511	0	ENST00000288368.4:c.3434C>T	p.Pro1145Leu	p.P1145L	ENST00000288368	NM_024870.2	1145	cCc/cTc	28/40	0.415252847775167	5	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	FALSE	3	0.415252847775167	5		511	458	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673637	30673637	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	148	948	0	ENST00000376406.3:c.3323G>C	p.Arg1108Thr	p.R1108T	ENST00000376406	NM_014641.2	1108	aGa/aCa	10/15	0.415252847775167	10	FACETS	1	0.917	1			1	CLONAL	2	FALSE	NA	0.415252847775167	10		948	944	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864860	117864860	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1236205322	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	187	637	0	ENST00000297338.2:c.1249C>T	p.Leu417Phe	p.L417F	ENST00000297338	NM_006265.2	417	Ctc/Ttc	10/14	0.415252847775167	5	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	FALSE	3	0.415252847775167	5		637	665	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748026	72748026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	137	881	1	ENST00000357731.5:c.152G>A	p.Arg51Lys	p.R51K	ENST00000357731	NM_173808.2	51	aGa/aAa	1/7	0.415252847775167	5	FACETS	0.834	0.761	0.91	0.556	0.507	0.607	CLONAL	2	FALSE	2	0.415252847775167	5		882	642	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445325	49445325	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747636808	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	181	1402	1	ENST00000301067.7:c.2141C>T	p.Ser714Leu	p.S714L	ENST00000301067	NM_003482.3	714	tCg/tTg	10/54	0.415252847775167	8	FACETS	0.949	0.874	1	0.474	0.437	0.513	CLONAL	2	FALSE	4	0.415252847775167	8		1403	1032	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223667	36223667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	163	1363	1	ENST00000222270.7:c.6217G>A	p.Glu2073Lys	p.E2073K	ENST00000222270	NM_014727.1	2073	Gag/Aag	28/37	0.415252847775167	5	FACETS	1	0.988	1	0.367	0.337	0.399	CLONAL	1	FALSE	1	0.415252847775167	5		1364	868	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853389	151853389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	76	494	0	ENST00000262189.6:c.11713C>T	p.Pro3905Ser	p.P3905S	ENST00000262189	NM_170606.2	3905	Cct/Tct	45/59	0.415252847775167	5	FACETS	0.849	0.75	0.953	0.566	0.5	0.636	CLONAL	2	FALSE	2	0.415252847775167	5		494	350	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666636	206666636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782318549	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	390	903	0	ENST00000367120.3:c.1970G>A	p.Arg657Gln	p.R657Q	ENST00000367120	NM_014002.3	657	cGa/cAa	20/22	0.415252847775167	7	FACETS	0.949	0.908	0.99	1	0.993	1	CLONAL	5	FALSE	3	0.415252847775167	7		903	807	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570805	226570805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	142	848	0	ENST00000366794.5:c.1091C>T	p.Ser364Phe	p.S364F	ENST00000366794	NM_001618.3	364	tCc/tTc	8/23	0.415252847775167	7	FACETS	0.777	0.708	0.85	0.388	0.354	0.425	SUBCLONAL	2	FALSE	3	0.415252847775167	7		848	897	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139033	37139033	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	133	905	0	ENST00000373509.5:c.373C>G	p.Pro125Ala	p.P125A	ENST00000373509	NM_002648.3	125	Ccg/Gcg	4/6	0.415252847775167	7	FACETS	0.778	0.707	0.853	0.389	0.353	0.427	SUBCLONAL	2	FALSE	3	0.415252847775167	7		905	839	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222412	53222413	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	95	1188	3	ENST00000375401.3:c.4419_4420delinsTT	p.Arg1474Ter	p.R1474*	ENST00000375401	NM_004187.3	1473	gcCCga/gcTTga	26/26	0.415252847775167	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	FALSE	0	0.415252847775167	1		1191	335	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541619	187541619	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372908534	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	84	423	0	ENST00000441802.2:c.6121C>T	p.Arg2041Cys	p.R2041C	ENST00000441802	NM_005245.3	2041	Cgt/Tgt	10/27	0.415252847775167	6	FACETS	0.972	0.864	1	0.648	0.576	0.724	CLONAL	2	FALSE	3	0.415252847775167	6		423	381	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387701	17387701	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	102	715	1	ENST00000359435.4:c.769G>A	p.Glu257Lys	p.E257K	ENST00000359435	NM_001033549.1	257	Gag/Aag	8/9	0.415252847775167	5	FACETS	1	0.974	1	0.64	0.573	0.711	CLONAL	1	FALSE	3	0.415252847775167	5		716	623	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780063	9780064	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	210	1033	3	ENST00000377346.4:c.1327_1328delinsTT	p.Pro443Phe	p.P443F	ENST00000377346	NM_005026.3	443	CCc/TTc	10/24	0.415252847775167	5	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	FALSE	2	0.415252847775167	5		1036	474	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259987	16259987	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	106	721	0	ENST00000375759.3:c.7252G>A	p.Glu2418Lys	p.E2418K	ENST00000375759	NM_015001.2	2418	Gag/Aag	11/15	0.415252847775167	5	FACETS	1	0.982	1	0.492	0.442	0.545	CLONAL	1	FALSE	2	0.415252847775167	5		721	561	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088697	27088697	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	167	952	0	ENST00000324856.7:c.2306C>T	p.Ser769Leu	p.S769L	ENST00000324856	NM_006015.4	769	tCa/tTa	7/20	0.415252847775167	5	FACETS	0.875	0.806	0.947	0.583	0.537	0.631	CLONAL	2	FALSE	2	0.415252847775167	5		952	746	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462204	120462205	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	145	704	0	ENST00000256646.2:c.5511_5512delinsTT	p.Arg1838Ter	p.R1838*	ENST00000256646	NM_024408.3	1837	ctCCga/ctTTga	31/34	0.168032450704719	6	FACETS	1	0.971	1			1	INDETERMINATE	3	FALSE	NA	0.415252847775167	6		704	384	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669425	241669425	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	77	420	0	ENST00000366560.3:c.782G>A	p.Arg261Lys	p.R261K	ENST00000366560	NM_000143.3	261	aGa/aAa	6/10	0.415252847775167	7	FACETS	1	0.976	1	0.375	0.33	0.423	CLONAL	1	FALSE	3	0.415252847775167	7		420	504	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852407	63852407	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	131	907	2	ENST00000279873.7:c.3185C>T	p.Ser1062Phe	p.S1062F	ENST00000279873	NM_032199.2	1062	tCc/tTc	10/10	0.415252847775167	5	FACETS	1	0.985	1	0.486	0.441	0.532	CLONAL	1	FALSE	2	0.415252847775167	5		909	703	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279624	123279624	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	106	761	0	ENST00000358487.5:c.808G>T	p.Val270Phe	p.V270F	ENST00000358487	NM_000141.4	270	Gtc/Ttc	7/18	0.415252847775167	3	FACETS	1	0.97	1	0.603	0.543	0.667	CLONAL	1	FALSE	1	0.415252847775167	3		761	511	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218029	108218029	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	44	450	0	ENST00000278616.4:c.8608G>C	p.Asp2870His	p.D2870H	ENST00000278616	NM_000051.3	2870	Gat/Cat	59/63	0.364397125912568	6	FACETS	1	0.879	1	0.264	0.221	0.31	CLONAL	1	FALSE	2	0.415252847775167	6		450	368	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343798	118343798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	104	616	1	ENST00000534358.1:c.1924C>T	p.Leu642Phe	p.L642F	ENST00000534358	NM_005933.3	642	Ctt/Ttt	3/36	0.364397125912568	6	FACETS	0.982	0.884	1	0.491	0.442	0.542	CLONAL	2	FALSE	2	0.415252847775167	6		617	467	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420718	49420718	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs777295270	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	138	873	0	ENST00000301067.7:c.15031G>C	p.Glu5011Gln	p.E5011Q	ENST00000301067	NM_003482.3	5011	Gag/Cag	48/54	0.415252847775167	8	FACETS	0.883	0.804	0.967	0.442	0.402	0.484	CLONAL	2	FALSE	4	0.415252847775167	8		873	845	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440150	49440150	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	139	881	0	ENST00000301067.7:c.4476G>T	p.Gln1492His	p.Q1492H	ENST00000301067	NM_003482.3	1492	caG/caT	16/54	0.415252847775167	8	FACETS	0.92	0.838	1	0.46	0.419	0.503	CLONAL	2	FALSE	4	0.415252847775167	8		881	817	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562666	21562667	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	85	671	3	ENST00000382592.4:c.1252_1253delinsTT	p.Pro418Leu	p.P418L	ENST00000382592	NM_014572.2	418	CCg/TTg	4/8	0.415252847775167	3	FACETS	1	0.929	1			1	CLONAL	1	FALSE	NA	0.415252847775167	3		674	465	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599001	28599001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	79	550	0	ENST00000241453.7:c.2287G>A	p.Glu763Lys	p.E763K	ENST00000241453	NM_004119.2	763	Gaa/Aaa	18/24	0.415252847775167	2	FACETS	1	0.971	1	0.649	0.577	0.725	CLONAL	1	FALSE	0	0.415252847775167	2		550	293	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061401	38061401	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	149	724	0	ENST00000250448.2:c.588C>G	p.Ile196Met	p.I196M	ENST00000250448	NM_004496.3	196	atC/atG	2/2	0.415252847775167	7	FACETS	1	0.933	1	0.511	0.467	0.556	CLONAL	2	FALSE	3	0.415252847775167	7		724	716	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68878153	68878153	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	141	455	0	ENST00000487270.1:c.866C>A	p.Ser289Tyr	p.S289Y	ENST00000487270	NM_133509.3	289	tCc/tAc	9/11	0.415252847775167	7	FACETS	0.889	0.815	0.966	0.667	0.611	0.725	CLONAL	3	FALSE	3	0.415252847775167	7		455	519	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041410	42041410	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	100	640	0	ENST00000219905.7:c.5605C>T	p.Gln1869Ter	p.Q1869*	ENST00000219905	NM_001164273.1	1869	Caa/Taa	17/24	0.415252847775167	6	FACETS	0.812	0.727	0.901	0.406	0.363	0.451	CLONAL	2	FALSE	2	0.415252847775167	6		640	543	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43733733	43733733	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	69	529	0	ENST00000382044.4:c.3089C>G	p.Ser1030Cys	p.S1030C	ENST00000382044	NM_001141980.1	1030	tCt/tGt	15/28	0.415252847775167	6	FACETS	1	0.963	1	0.322	0.28	0.366	CLONAL	1	FALSE	2	0.415252847775167	6		529	473	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99472815	99472815	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	106	529	0	ENST00000268035.6:c.2811C>G	p.Ile937Met	p.I937M	ENST00000268035	NM_000875.3	937	atC/atG	14/21	0.415252847775167	6	FACETS	0.799	0.718	0.884	0.399	0.359	0.442	SUBCLONAL	2	FALSE	2	0.415252847775167	6		529	585	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632573	3632573	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	137	1212	0	ENST00000294008.3:c.5275T>G	p.Tyr1759Asp	p.Y1759D	ENST00000294008	NM_032444.2	1759	Tac/Gac	15/15	0.415252847775167	0	FACETS	1	0.929	1			1	CLONAL	1	FALSE	0	0.415252847775167	0		1212	382	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346420	89346420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	116	983	0	ENST00000301030.4:c.6530G>A	p.Gly2177Glu	p.G2177E	ENST00000301030	NM_001256183.1	2177	gGg/gAg	9/13	1	2	FACETS	0.751	0.684	0.821	1	0.986	1	SUBCLONAL	2	FALSE	1	0.415252847775167	2		983	372	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347804	89347804	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	115	1004	0	ENST00000301030.4:c.5146G>C	p.Glu1716Gln	p.E1716Q	ENST00000301030	NM_001256183.1	1716	Gag/Cag	9/13	1	2	FACETS	0.815	0.742	0.889	1	0.987	1	CLONAL	2	FALSE	1	0.415252847775167	2		1004	340	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831401	89831401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	146	914	0	ENST00000389301.3:c.2675C>T	p.Ser892Phe	p.S892F	ENST00000389301	NM_000135.2	892	tCc/tTc	28/43	1	2	FACETS	0.821	0.757	0.888	1	0.99	1	CLONAL	2	FALSE	1	0.415252847775167	2		914	428	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108266	8108267	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	364	1085	1	ENST00000585124.1:c.957_958delinsTT	p.Gln320Ter	p.Q320*	ENST00000585124	NM_004217.3	319	gcCCag/gcTTag	9/9	0.415252847775167	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	FALSE	1	0.415252847775167	3		1086	908	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40864389	40864389	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	170	931	0	ENST00000428826.2:c.1319C>G	p.Ser440Cys	p.S440C	ENST00000428826		440	tCt/tGt	12/21	0.415252847775167	3	FACETS	1	0.987	1	0.67	0.617	0.724	CLONAL	1	FALSE	1	0.415252847775167	3		931	738	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40872447	40872447	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	117	725	0	ENST00000428826.2:c.508C>G	p.Leu170Val	p.L170V	ENST00000428826		170	Ctg/Gtg	7/21	0.415252847775167	3	FACETS	1	0.966	1	0.576	0.521	0.634	CLONAL	1	FALSE	1	0.415252847775167	3		725	591	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243743	41243743	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	83	757	0	ENST00000357654.3:c.3805G>C	p.Asp1269His	p.D1269H	ENST00000357654	NM_007294.3	1269	Gac/Cac	10/23	0.415252847775167	3	FACETS	0.966	0.855	1	0.483	0.427	0.542	CLONAL	1	FALSE	1	0.415252847775167	3		757	500	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733066	74733066	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	172	891	0	ENST00000359995.5:c.177del	p.Phe59LeufsTer173	p.F59Lfs*173	ENST00000359995	NM_001195427.1	59	ttC/tt	1/3	0.415252847775167	3	FACETS	1	0.988	1	0.699	0.644	0.755	CLONAL	1	FALSE	1	0.415252847775167	3		891	716	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78921049	78921049	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	90	837	0	ENST00000306801.3:c.3163G>T	p.Glu1055Ter	p.E1055*	ENST00000306801	NM_020761.2	1055	Gag/Tag	27/34	0.415252847775167	3	FACETS	1	0.969	1	0.622	0.555	0.692	CLONAL	1	FALSE	1	0.415252847775167	3		837	421	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985728	60985728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	37	254	0	ENST00000333681.4:c.172C>T	p.His58Tyr	p.H58Y	ENST00000333681		58	Cat/Tat	2/3	0.415252847775167	5	FACETS	0.773	0.645	0.913	0.387	0.322	0.457	CLONAL	2	FALSE	1	0.415252847775167	5		254	187	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208295	5208295	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	147	1078	0	ENST00000357368.4:c.5595G>C	p.Lys1865Asn	p.K1865N	ENST00000357368	NM_002850.3	1865	aaG/aaC	36/38	0.415252847775167	5	FACETS	0.82	0.75	0.892	0.82	0.75	0.892	CLONAL	2	FALSE	3	0.415252847775167	5		1078	701	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184517	7184517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141484557	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	128	848	0	ENST00000302850.5:c.784G>A	p.Gly262Ser	p.G262S	ENST00000302850	NM_000208.2	262	Ggc/Agc	3/22	0.415252847775167	5	FACETS	1	0.984	1	0.709	0.643	0.777	CLONAL	1	FALSE	3	0.415252847775167	5		848	706	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251541	10251541	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	131	1032	0	ENST00000340748.4:c.3391G>C	p.Glu1131Gln	p.E1131Q	ENST00000340748		1131	Gag/Cag	31/40	0.415252847775167	5	FACETS	1	0.983	1	0.693	0.629	0.759	CLONAL	1	FALSE	3	0.415252847775167	5		1032	739	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145621	11145621	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	307	1043	0	ENST00000358026.2:c.3983C>T	p.Ala1328Val	p.A1328V	ENST00000358026	NM_001128849.1	1328	gCc/gTc	29/36	0.415252847775167	5	FACETS	0.972	0.92	1	1	0.994	1	CLONAL	3	FALSE	3	0.415252847775167	5		1043	823	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942118	17942118	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	183	1129	3	ENST00000458235.1:c.2897C>T	p.Ala966Val	p.A966V	ENST00000458235	NM_000215.3	966	gCt/gTt	21/24	0.415252847775167	5	FACETS	0.805	0.744	0.87	0.805	0.744	0.87	CLONAL	2	FALSE	3	0.415252847775167	5		1132	888	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976381	18976381	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	145	1177	0	ENST00000262803.5:c.3031C>T	p.Pro1011Ser	p.P1011S	ENST00000262803	NM_002911.3	1011	Ccg/Tcg	22/24	0.415252847775167	5	FACETS	1	0.986	1	0.706	0.644	0.77	CLONAL	1	FALSE	3	0.415252847775167	5		1177	803	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797398	42797398	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	202	1185	0	ENST00000575354.2:c.3760G>A	p.Glu1254Lys	p.E1254K	ENST00000575354	NM_015125.3	1254	Gag/Aag	15/20	0.415252847775167	8	FACETS	1	0.979	1			1	CLONAL	2	FALSE	NA	0.415252847775167	8		1185	953	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46603694	46603694	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	70	709	1	ENST00000263734.3:c.1051G>A	p.Asp351Asn	p.D351N	ENST00000263734	NM_001430.4	351	Gac/Aac	9/16	0.415252847775167	5	FACETS	1	0.963	1	0.319	0.279	0.362	CLONAL	1	FALSE	1	0.415252847775167	5		710	429	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033468	48033468	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs63750554	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	83	598	0	ENST00000234420.5:c.3772C>G	p.Gln1258Glu	p.Q1258E	ENST00000234420	NM_000179.2	1258	Caa/Gaa	8/10	0.415252847775167	5	FACETS	1	0.969	1	0.321	0.284	0.361	CLONAL	1	FALSE	1	0.415252847775167	5		598	505	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872894	136872894	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	124	467	0	ENST00000241393.3:c.604C>G	p.Gln202Glu	p.Q202E	ENST00000241393	NM_003467.2	202	Cag/Gag	2/2	0.415252847775167	6	FACETS	0.92	0.84	1	0.92	0.84	1	CLONAL	3	FALSE	3	0.415252847775167	6		467	396	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136284	202136284	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	131	701	0	ENST00000358485.4:c.528G>C	p.Leu176Phe	p.L176F	ENST00000358485	NM_001080125.1	176	ttG/ttC	3/9	0.415252847775167	6	FACETS	1	0.979	1	0.819	0.748	0.892	CLONAL	2	FALSE	3	0.415252847775167	6		701	470	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016136	31016136	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1247216500	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	77	741	0	ENST00000375687.4:c.382G>C	p.Asp128His	p.D128H	ENST00000375687	NM_015338.5	128	Gat/Cat	6/13	0.199090091483538	6	FACETS	1	0.961	1	0.411	0.361	0.464	INDETERMINATE	1	FALSE	3	0.415252847775167	6		741	551	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36024680	36024680	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs761890358	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	118	1010	1	ENST00000358208.4:c.669C>G	p.Phe223Leu	p.F223L	ENST00000358208		223	ttC/ttG	6/12	0.199090091483538	6	FACETS	0.788	0.712	0.868	0.525	0.475	0.579	INDETERMINATE	2	FALSE	3	0.415252847775167	6		1011	660	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46275818	46275818	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	89	570	0	ENST00000371998.3:c.3254G>A	p.Gly1085Glu	p.G1085E	ENST00000371998		1085	gGa/gAa	18/23	0.199090091483538	6	FACETS	0.966	0.862	1	0.644	0.575	0.718	INDETERMINATE	2	FALSE	3	0.415252847775167	6		570	406	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958213	54958213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	68	502	0	ENST00000312783.6:c.394G>A	p.Asp132Asn	p.D132N	ENST00000312783	NM_198436.1	132	Gac/Aac	6/10	0.199090091483538	6	FACETS	0.806	0.705	0.914	0.537	0.47	0.609	INDETERMINATE	2	FALSE	3	0.415252847775167	6		502	372	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162749	47162749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774939342	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	49	537	0	ENST00000409792.3:c.3377C>T	p.Pro1126Leu	p.P1126L	ENST00000409792	NM_014159.6	1126	cCt/cTt	3/21	0.415252847775167	3	FACETS	1	0.88	1	0.345	0.294	0.401	CLONAL	1	FALSE	0	0.415252847775167	3		537	275	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720961	119720961	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	98	633	0	ENST00000316626.5:c.214C>G	p.Gln72Glu	p.Q72E	ENST00000316626		72	Caa/Gaa	2/12	0.415252847775167	5	FACETS	0.897	0.805	0.993			1	CLONAL	2	FALSE	NA	0.415252847775167	5		633	427	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506930	186506930	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1213509261	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	74	287	0	ENST00000323963.5:c.1096C>T	p.Arg366Ter	p.R366*	ENST00000323963		366	Cga/Tga	11/11	0.364397125912568	6	FACETS	1	0.934	1	0.542	0.479	0.608	CLONAL	2	FALSE	2	0.415252847775167	6		287	301	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189585730	189585730	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	58	467	0	ENST00000264731.3:c.991G>C	p.Asp331His	p.D331H	ENST00000264731	NM_003722.4	331	Gat/Cat	7/14	0.364397125912568	6	FACETS	1	0.968	1	0.368	0.318	0.423	CLONAL	1	FALSE	2	0.415252847775167	6		467	347	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747927	41747927	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	200	530	1	ENST00000226382.2:c.842C>T	p.Thr281Ile	p.T281I	ENST00000226382	NM_003924.3	281	aCc/aTc	3/3	0.415252847775167	7	FACETS	1	0.965	1	1	0.965	1	CLONAL	4	FALSE	3	0.415252847775167	7		531	470	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808266	99808266	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	77	467	0	ENST00000280892.6:c.423G>C	p.Gln141His	p.Q141H	ENST00000280892	NM_001130678.1	141	caG/caC	5/7	0.415252847775167	6	FACETS	0.758	0.668	0.854	0.505	0.445	0.569	SUBCLONAL	2	FALSE	3	0.415252847775167	6		467	448	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958798	38958798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	58	351	0	ENST00000357387.3:c.2314G>A	p.Asp772Asn	p.D772N	ENST00000357387	NM_152756.3	772	Gat/Aat	23/38	0.415252847775167	5	FACETS	0.758	0.656	0.867	0.505	0.437	0.578	SUBCLONAL	2	FALSE	2	0.415252847775167	5		351	299	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722176	176722176	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs765511629	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	102	638	0	ENST00000439151.2:c.7807C>G	p.Leu2603Val	p.L2603V	ENST00000439151	NM_022455.4	2603	Ctc/Gtc	23/23	0.415252847775167	5	FACETS	0.794	0.713	0.879	0.529	0.475	0.586	SUBCLONAL	2	FALSE	2	0.415252847775167	5		638	502	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048882	180048882	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs372330214	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	108	1235	0	ENST00000261937.6:c.1680C>G	p.Ile560Met	p.I560M	ENST00000261937	NM_182925.4	560	atC/atG	13/30	0.415252847775167	0	FACETS	0.696	0.629	0.766			1	SUBCLONAL	1	FALSE	0	0.415252847775167	0		1235	437	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323157	31323157	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	127	1114	0	ENST00000412585.2:c.832G>C	p.Glu278Gln	p.E278Q	ENST00000412585	NM_005514.6	278	Gag/Cag	4/8	0.415252847775167	7	FACETS	0.841	0.763	0.924	0.421	0.381	0.462	CLONAL	2	FALSE	3	0.415252847775167	7		1114	741	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908144	41908144	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	120	1020	0	ENST00000372991.4:c.378C>G	p.Ile126Met	p.I126M	ENST00000372991	NM_001760.3	126	atC/atG	2/5	0.415252847775167	7	FACETS	0.844	0.763	0.929	0.422	0.381	0.465	CLONAL	2	FALSE	3	0.415252847775167	7		1020	698	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553447	106553447	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	66	576	0	ENST00000369096.4:c.1412C>T	p.Pro471Leu	p.P471L	ENST00000369096	NM_001198.3	471	cCc/cTc	5/7	0.415252847775167	7	FACETS	0.755	0.658	0.86	0.378	0.329	0.43	SUBCLONAL	2	FALSE	3	0.415252847775167	7		576	429	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005381	150005381	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	99	725	0	ENST00000253339.5:c.844G>T	p.Glu282Ter	p.E282*	ENST00000253339		282	Gaa/Taa	3/7	0.415252847775167	7	FACETS	1	0.98	1	0.362	0.323	0.403	CLONAL	1	FALSE	3	0.415252847775167	7		725	671	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265500	152265501	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	100	756	0	ENST00000206249.3:c.953_954delinsTT	p.Ala318Val	p.A318V	ENST00000206249	NM_000125.3	318	gCC/gTT	4/8	0.415252847775167	7	FACETS	0.801	0.716	0.89	0.4	0.358	0.445	CLONAL	2	FALSE	3	0.415252847775167	7		756	613	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157192752	157192752	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	82	537	0	ENST00000346085.5:c.1742C>T	p.Ser581Phe	p.S581F	ENST00000346085	NM_020732.3	581	tCt/tTt	3/20	0.415252847775167	7	FACETS	0.815	0.721	0.915	0.407	0.36	0.458	CLONAL	2	FALSE	3	0.415252847775167	7		537	494	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987374	2987374	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	107	833	1	ENST00000396946.4:c.55G>A	p.Glu19Lys	p.E19K	ENST00000396946	NM_032415.4	19	Gag/Aag	3/25	0.109117556630046	6	FACETS	0.806	0.725	0.892	0.538	0.483	0.595	INDETERMINATE	2	FALSE	3	0.415252847775167	6		834	585	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846362	128846362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766211091	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	205	923	1	ENST00000249373.3:c.1198C>T	p.Arg400Cys	p.R400C	ENST00000249373	NM_005631.4	400	Cgt/Tgt	6/12	0.415252847775167	5	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	FALSE	2	0.415252847775167	5		924	479	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140507785	140507785	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	126	466	0	ENST00000288602.6:c.686A>G	p.Asn229Ser	p.N229S	ENST00000288602	NM_004333.4	229	aAt/aGt	5/18	0.415252847775167	5	FACETS	1	0.919	1	1	0.919	1	CLONAL	3	FALSE	2	0.415252847775167	5		466	328	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874737	151874737	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	75	558	0	ENST00000262189.6:c.7801G>A	p.Gly2601Ser	p.G2601S	ENST00000262189	NM_170606.2	2601	Ggc/Agc	38/59	0.415252847775167	5	FACETS	1	0.974	1	0.478	0.42	0.539	CLONAL	1	FALSE	2	0.415252847775167	5		558	409	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151893073	151893073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	50	390	0	ENST00000262189.6:c.4297G>A	p.Asp1433Asn	p.D1433N	ENST00000262189	NM_170606.2	1433	Gat/Aat	28/59	0.415252847775167	5	FACETS	1	0.961	1	0.475	0.406	0.55	CLONAL	1	FALSE	2	0.415252847775167	5		390	274	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741631	145741631	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	230	1236	1	ENST00000428558.2:c.872C>T	p.Ala291Val	p.A291V	ENST00000428558	NM_004260.3	291	gCt/gTt	5/22	0.415252847775167	7	FACETS	0.947	0.885	1	0.71	0.664	0.758	CLONAL	3	FALSE	3	0.415252847775167	7		1237	795	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8338945	8338945	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	81	534	0	ENST00000356435.5:c.5356G>C	p.Glu1786Gln	p.E1786Q	ENST00000356435		1786	Gaa/Caa	32/35	0.415252847775167	4	FACETS	1	0.977	1	0.365	0.324	0.409	CLONAL	1	FALSE	0	0.415252847775167	4		534	378	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537128	80537128	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	87	704	0	ENST00000286548.4:c.270G>T	p.Met90Ile	p.M90I	ENST00000286548	NM_002072.3	90	atG/atT	2/7	0.415252847775167	6	FACETS	1	0.941	1	0.22	0.194	0.247	CLONAL	1	FALSE	1	0.415252847775167	6		704	697	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549184	87549184	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	66	586	0	ENST00000277120.3:c.1741G>C	p.Asp581His	p.D581H	ENST00000277120		581	Gac/Cac	15/19	0.415252847775167	6	FACETS	1	0.966	1	0.271	0.235	0.309	CLONAL	1	FALSE	1	0.415252847775167	6		586	430	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97933360	97933361	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	47	416	1	ENST00000289081.3:c.521_521+1delinsAA		p.X174_splice	ENST00000289081	NM_000136.2	174		6/15	0.415252847775167	6	FACETS	0.834	0.704	0.977	0.167	0.14	0.196	CLONAL	1	FALSE	1	0.415252847775167	6		417	497	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218625	98218625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781188522	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	131	685	1	ENST00000331920.6:c.3239C>T	p.Ala1080Val	p.A1080V	ENST00000331920	NM_000264.3	1080	gCc/gTc	19/24	0.415252847775167	6	FACETS	0.798	0.725	0.874	0.319	0.29	0.35	SUBCLONAL	2	FALSE	1	0.415252847775167	6		686	724	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231234	98231235	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	490	1029	0	ENST00000331920.6:c.2048_2049delinsTT	p.Ser683Phe	p.S683F	ENST00000331920	NM_000264.3	683	tCC/tTT	14/24	0.415252847775167	6	FACETS	0.917	0.887	0.947	1	0.993	1	CLONAL	6	FALSE	1	0.415252847775167	6		1029	785	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759713	133759713	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	104	952	0	ENST00000318560.5:c.2036C>G	p.Ser679Ter	p.S679*	ENST00000318560	NM_005157.4	679	tCa/tGa	11/11	0.415252847775167	5	FACETS	1	0.982	1	0.297	0.267	0.329	CLONAL	1	FALSE	0	0.415252847775167	5		952	547	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393596	139393596	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	162	1221	0	ENST00000277541.6:c.6050C>A	p.Ser2017Ter	p.S2017*	ENST00000277541	NM_017617.3	2017	tCa/tAa	32/34	0.415252847775167	5	FACETS	0.82	0.754	0.889	0.328	0.301	0.356	CLONAL	2	FALSE	0	0.415252847775167	5		1221	772	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396800	139396801	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	510	1061	1	ENST00000277541.6:c.5307_5308delinsTT	p.Pro1770Ser	p.P1770S	ENST00000277541	NM_017617.3	1769	ttCCct/ttTTct	28/34	0.415252847775167	5	FACETS	1	0.985	1	1	0.997	1	CLONAL	6	FALSE	0	0.415252847775167	5		1062	655	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185169	123185169	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	82	473	0	ENST00000218089.9:c.1121G>C	p.Arg374Thr	p.R374T	ENST00000218089	NM_001042749.1	374	aGa/aCa	13/35	0.366930175702635	3	FACETS	1	0.975	1	0.458	0.407	0.512	CLONAL	1	FALSE	0	0.415252847775167	3		473	347	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197881	123197881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	30	507	0	ENST00000218089.9:c.2005C>T	p.Leu669Phe	p.L669F	ENST00000218089	NM_001042749.1	669	Ctt/Ttt	20/35	0.366930175702635	3	FACETS	0.524	0.423	0.639	0.175	0.141	0.213	SUBCLONAL	1	FALSE	0	0.415252847775167	3		507	333	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918620	44918622	+	stop_gained	Nonsense_Mutation	TNP	CTC	CTC	TTT	novel	NA	P-0053761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	174	642	1	ENST00000377967.4:c.1103_1105delinsTTT	p.Pro368_Gln369delinsLeuTer	p.P368_Q369delinsL*	ENST00000377967	NM_021140.2	368	cCTCag/cTTTag	12/29	0.415252847775167	2	FACETS	0.834	0.782	0.886	1	0.988	1	CLONAL	3	FALSE	0	0.415252847775167	2		643	335	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0053762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	48	478	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.276928723511785	3	FACETS	0.763	0.646	0.89	0.381	0.323	0.445	SUBCLONAL	1	TRUE	1	0.379084778642196	3		478	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0053762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	334	866	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.304936669279623	2	FACETS	0.842	0.797	0.888	0.842	0.797	0.888	CLONAL	2	TRUE	0	0.379084778642196	2		867	1046	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584513	48584514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs377767334	NA	P-0053762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	172	558	0	ENST00000342988.3:c.692dup	p.Ser232GlnfsTer3	p.S232Qfs*3	ENST00000342988	NM_005359.5	229	ctg/ctGg	6/12	0.295983179080585	2	FACETS	0.854	0.792	0.919	0.854	0.792	0.919	CLONAL	2	TRUE	0	0.379084778642196	2		558	531	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214395	5214395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772384138	NA	P-0053762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	92	747	1	ENST00000357368.4:c.4591G>A	p.Val1531Ile	p.V1531I	ENST00000357368	NM_002850.3	1531	Gtc/Atc	30/38	0.155285093512613	2	FACETS	0.641	0.569	0.718	0.321	0.284	0.359	INDETERMINATE	1	TRUE	0	0.379084778642196	2		748	757	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256264	16256264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1409348994	NA	P-0053762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	110	695	1	ENST00000375759.3:c.3529C>T	p.Arg1177Cys	p.R1177C	ENST00000375759	NM_015001.2	1177	Cgt/Tgt	11/15	1	2	FACETS	0.842	0.758	0.932	0.842	0.758	0.932	CLONAL	1	TRUE	1	0.379084778642196	2		696	689	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843717	156843717	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs374700842	NA	P-0053762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	335	1368	0	ENST00000524377.1:c.1143C>A	p.Asn381Lys	p.N381K	ENST00000524377	NM_002529.3	381	aaC/aaA	8/17	0.276928723511785	3	FACETS	0.754	0.712	0.797	0.754	0.712	0.797	SUBCLONAL	2	TRUE	1	0.379084778642196	3		1368	1394	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235875	108235875	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555151352	NA	P-0053762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	72	536	0	ENST00000278616.4:c.8917A>G	p.Arg2973Gly	p.R2973G	ENST00000278616	NM_000051.3	2973	Agg/Ggg	62/63	0.276928723511785	3	FACETS	0.846	0.74	0.96	0.423	0.37	0.48	CLONAL	1	TRUE	1	0.379084778642196	3		536	534	SUCCESS
REL	5966	MSKCC	GRCh37	2	61148938	61148938	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	58	385	0	ENST00000295025.8:c.1128G>T	p.Met376Ile	p.M376I	ENST00000295025	NM_002908.2	376	atG/atT	11/11	0.293689704282146	3	FACETS	0.802	0.69	0.923	0.401	0.345	0.462	CLONAL	1	TRUE	1	0.379084778642196	3		385	454	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983459	90983459	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753718	NA	P-0053762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	74	429	0	ENST00000265433.3:c.644G>A	p.Arg215Gln	p.R215Q	ENST00000265433	NM_002485.4	215	cGg/cAg	6/16	0.216519375446376	4	FACETS	0.776	0.684	0.873	0.776	0.684	0.873	INDETERMINATE	2	TRUE	2	0.379084778642196	4		429	347	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0053763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	81	478	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.410689156695227	3	FACETS	0.796	0.702	0.896	0.398	0.351	0.448	SUBCLONAL	1	TRUE	1	0.447098782645528	3		478	557	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715721	30715721	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs104893816	NA	P-0053763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	31	416	2	ENST00000295754.5:c.1379G>T	p.Arg460Leu	p.R460L	ENST00000295754	NM_003242.5	460	cGc/cTc	5/7	1	2	FACETS	0.383	0.31	0.466	0.383	0.31	0.466	SUBCLONAL	1	TRUE	1	0.447098782645528	2		418	362	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223927	2223927	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs928579907	NA	P-0053763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	41	1010	0	ENST00000326181.6:c.1141G>A	p.Asp381Asn	p.D381N	ENST00000326181	NM_032271.2	381	Gac/Aac	13/21	1	2	FACETS	0.259	0.215	0.308	0.259	0.215	0.308	SUBCLONAL	1	TRUE	1	0.447098782645528	2		1010	708	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56409144	56409144	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	39	396	1	ENST00000348428.3:c.1651C>T	p.Arg551Ter	p.R551*	ENST00000348428	NM_006785.3	551	Cga/Tga	14/17	0.391254879242405	1	FACETS	0.401	0.332	0.477	0.401	0.332	0.477	SUBCLONAL	1	TRUE	0	0.391254879242405	1		397	400	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348859	118348859	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	29	303	0	ENST00000534358.1:c.3512C>A	p.Thr1171Asn	p.T1171N	ENST00000534358	NM_005933.3	1171	aCt/aAt	5/36	0.293532454998593	3	FACETS	0.326	0.261	0.4			1	SUBCLONAL	1	TRUE	NA	0.391254879242405	3		303	544	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750396	133750397	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGCC	novel	NA	P-0053771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	220	606	0	ENST00000318560.5:c.1228_1231dup	p.Leu411GlnfsTer35	p.L411Qfs*35	ENST00000318560	NM_005157.4	409	-/AGCC	7/11	0.391254879242405	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.391254879242405	1		606	786	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0053773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	28	563	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.318	0.253	0.391	0.318	0.253	0.391	SUBCLONAL	1	TRUE	1	0.354738102250487	2		563	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0053773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	84	726	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	1	2	FACETS	0.487	0.429	0.549	0.487	0.429	0.549	SUBCLONAL	1	TRUE	1	0.354738102250487	2		726	973	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398262	25398262	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913538	NA	P-0053773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	28	492	0	ENST00000311936.3:c.57G>T	p.Leu19Phe	p.L19F	ENST00000311936	NM_004985.3	19	ttG/ttT	2/5	1	2	FACETS	0.297	0.237	0.367	0.297	0.237	0.367	SUBCLONAL	1	TRUE	1	0.354738102250487	2		492	531	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866562	78866562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778224744	NA	P-0053773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	83	849	2	ENST00000306801.3:c.2135C>T	p.Pro712Leu	p.P712L	ENST00000306801	NM_020761.2	712	cCg/cTg	19/34	1	2	FACETS	0.484	0.426	0.547	0.484	0.426	0.547	SUBCLONAL	1	TRUE	1	0.354738102250487	2		851	966	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	60	386	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.186717175682514	4	FACETS	0.795	0.689	0.909	0.795	0.689	0.909	CLONAL	2	TRUE	2	0.280987934195891	4		386	344	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602932	10602932	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0053774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	220	880	2	ENST00000171111.5:c.646A>T	p.Lys216Ter	p.K216*	ENST00000171111	NM_203500.1	216	Aag/Tag	3/6	0.233203957358934	2	FACETS	0.759	0.706	0.814	0.759	0.706	0.814	SUBCLONAL	2	TRUE	0	0.280987934195891	2		882	1031	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221994	1221994	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	214	859	0	ENST00000326873.7:c.909C>G	p.Ile303Met	p.I303M	ENST00000326873	NM_000455.4	303	atC/atG	7/10	0.233203957358934	2	FACETS	0.841	0.782	0.901	0.841	0.782	0.901	CLONAL	2	TRUE	0	0.280987934195891	2		859	906	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984435	201984436	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0053774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	160	646	0	ENST00000359651.3:c.1102dup	p.Gln368ProfsTer103	p.Q368Pfs*103	ENST00000359651		367	ctc/ctCc	8/8	0.280987934195891	5	FACETS	1	0.987	1	0.477	0.436	0.519	CLONAL	1	TRUE	2	0.280987934195891	5		646	1132	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844109	68844110	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	337	527	0	ENST00000261769.5:c.698dup	p.His233GlnfsTer11	p.H233Qfs*11	ENST00000261769	NM_004360.3	233	cac/cAac	6/16	0.600283559662794	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.600283559662794	1		527	704	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0053777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	54	443	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	0.16968443780463	3	FACETS	0.251	0.213	0.292	0.125	0.106	0.146	INDETERMINATE	1	TRUE	1	0.600283559662794	3		443	932	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0053777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1373	37	1069	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.600283559662794	1	FACETS	0.061	0.05	0.074	0.061	0.05	0.074	SUBCLONAL	1	TRUE	0	0.600283559662794	1		1069	1410	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	30	649	3	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	0.600283559662794	2	FACETS	0.088	0.07	0.108	0.044	0.035	0.054	SUBCLONAL	1	TRUE	0	0.600283559662794	2		652	1136	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0053777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	285	443	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	0.16968443780463	3	FACETS	1	0.992	1	0.676	0.637	0.716	INDETERMINATE	1	TRUE	1	0.600283559662794	3		443	913	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139135	108139135	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0053777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	275	435	0	ENST00000278616.4:c.2639-2A>C		p.X880_splice	ENST00000278616	NM_000051.3	880			0.600283559662794	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.600283559662794	1		435	578	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878473	151878473	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	376	693	0	ENST00000262189.6:c.6472C>T	p.Pro2158Ser	p.P2158S	ENST00000262189	NM_170606.2	2158	Cct/Tct	36/59	1	2	FACETS	0.993	0.943	1	0.993	0.943	1	CLONAL	1	TRUE	1	0.600283559662794	2		693	1261	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729153	66729153	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519856	NA	P-0053780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	21	323	0	ENST00000307102.5:c.361T>A	p.Cys121Ser	p.C121S	ENST00000307102	NM_002755.3	121	Tgc/Agc	3/11	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.252838860849897	2		323	143	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222987	1222987	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	15	240	0	ENST00000326873.7:c.924G>T	p.Trp308Cys	p.W308C	ENST00000326873	NM_000455.4	308	tgG/tgT	8/10	0.252838860849897	1	FACETS	1	0.753	1	1	0.753	1	CLONAL	1	TRUE	0	0.252838860849897	1		240	102	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737130	162737130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	30	179	0	ENST00000367921.3:c.1274G>T	p.Trp425Leu	p.W425L	ENST00000367921	NM_006182.2	425	tGg/tTg	11/18	0.252838860849897	3	FACETS	0.841	0.693	0.999	1	0.926	1	CLONAL	3	TRUE	1	0.252838860849897	3		179	106	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216316	2216316	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	13	297	0	ENST00000398665.3:c.1960C>T	p.Gln654Ter	p.Q654*	ENST00000398665	NM_032482.2	654	Cag/Tag	20/28	0.252838860849897	1	FACETS	0.864	0.623	1	0.864	0.623	1	CLONAL	1	TRUE	0	0.252838860849897	1		297	104	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599927	10599928	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	20	320	0	ENST00000171111.5:c.1648dup	p.Met550AsnfsTer24	p.M550Nfs*24	ENST00000171111	NM_203500.1	550	atg/aAtg	5/6	0.252838860849897	1	FACETS	0.921	0.711	1	0.921	0.711	1	CLONAL	1	TRUE	0	0.252838860849897	1		320	150	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713385	40713385	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	18	296	0	ENST00000373198.4:c.4130G>T	p.Arg1377Leu	p.R1377L	ENST00000373198	NM_133170.3	1377	cGa/cTa	30/32	1	2	FACETS	0.884	0.67	1	0.884	0.67	1	CLONAL	1	TRUE	1	0.252838860849897	2		296	161	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372342	55372342	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	22	279	0	ENST00000297316.4:c.1032C>A	p.Asp344Glu	p.D344E	ENST00000297316	NM_022454.3	344	gaC/gaA	2/2	0.252838860849897	1	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	0	0.252838860849897	1		279	124	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578471	7578471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	291	1046	0	ENST00000269305.4:c.459del	p.Gly154AlafsTer16	p.G154Afs*16	ENST00000269305	NM_001126112.2	153	ccC/cc	5/11	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.287508689115499	2		1046	1448	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141557610	141557610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1226849588	NA	P-0053784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1392	368	1165	0	ENST00000220592.5:c.1705G>A	p.Val569Ile	p.V569I	ENST00000220592	NM_012154.3	569	Gtc/Atc	13/19	0.124736956186942	4	FACETS	0.936	0.885	0.989	0.936	0.885	0.989	INDETERMINATE	2	TRUE	2	0.287508689115499	4		1165	1760	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0053785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	42	464	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.683971785537192	2		464	117	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0053785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	81	771	5	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.677946900348527	1	FACETS	0.956	0.867	1	0.956	0.867	1	CLONAL	1	TRUE	0	0.683971785537192	1		776	163	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247492	71247492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	60	548	0	ENST00000318789.4:c.41C>T	p.Ser14Leu	p.S14L	ENST00000318789	NM_032682.5	14	tCa/tTa	6/21	1	2	FACETS	0.75	0.654	0.851	0.75	0.654	0.851	SUBCLONAL	1	TRUE	1	0.683971785537192	2		548	234	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103380	119103380	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	27	385	0	ENST00000264033.4:c.418A>G	p.Met140Val	p.M140V	ENST00000264033	NM_005188.3	140	Atg/Gtg	2/16	1	2	FACETS	0.907	0.743	1	0.907	0.743	1	CLONAL	1	TRUE	1	0.683971785537192	2		385	87	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	75	276	0				ENST00000310581	NM_198253.2	-/1132			0.344967746343232	5	FACETS	0.887	0.788	0.99	0.887	0.788	0.99	CLONAL	3	TRUE	2	0.344967746343232	5		276	248	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0053786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	241	799	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.284030107525105	2	FACETS	0.925	0.868	0.984	0.925	0.868	0.984	CLONAL	2	TRUE	0	0.344967746343232	2		799	755	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576882	7576883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	239	770	0	ENST00000269305.4:c.963dup	p.Pro322ThrfsTer15	p.P322Tfs*15	ENST00000269305	NM_001126112.2	321	-/A	9/11	0.284030107525105	2	FACETS	0.836	0.782	0.891	0.836	0.782	0.891	CLONAL	2	TRUE	0	0.344967746343232	2		770	829	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341976	8341976	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs377463668	NA	P-0053786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	48	363	0	ENST00000356435.5:c.4664C>T	p.Ala1555Val	p.A1555V	ENST00000356435		1555	gCg/gTg	29/35	0.332417963594495	3	FACETS	0.98	0.832	1	0.49	0.416	0.571	CLONAL	1	TRUE	1	0.344967746343232	3		363	333	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242872	142242872	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0053786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	72	497	0	ENST00000350721.4:c.4115C>G	p.Ser1372Ter	p.S1372*	ENST00000350721	NM_001184.3	1372	tCa/tGa	22/47	0.344967746343232	4	FACETS	0.681	0.594	0.776	0.227	0.198	0.259	SUBCLONAL	1	TRUE	1	0.344967746343232	4		497	824	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89842194	89842194	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	270	650	0	ENST00000389301.3:c.1856C>G	p.Ser619Cys	p.S619C	ENST00000389301	NM_000135.2	619	tCc/tGc	21/43	0.344967746343232	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.344967746343232	3		650	836	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200957	108200957	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	83	360	0	ENST00000278616.4:c.7324C>T	p.Gln2442Ter	p.Q2442*	ENST00000278616	NM_000051.3	2442	Cag/Tag	50/63	0.344967746343232	1	FACETS	0.901	0.799	1	0.901	0.799	1	CLONAL	1	TRUE	0	0.344967746343232	1		360	442	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201130	108201732	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTCAATGGCATGATGAAGGCAAGTGTTACTCAGCCCAATATTCTACCCTGTGCTTGAAAAACTTAGACATAAGCCCCTTGATGTCAGGAATCGTGTATACCTCTTTGTATTCCTAGCACTTGGTCCAGTGCTCTACACATAAGTAGCATTTTGTAGTTTTCTAAACTTTGATCCATATTTAGGATTATTTACAAGTTCTAGTCTTGTTTCTACAAAAGTTCCTTTGTATTATATAAGCTGACAAGCTGTAAATGATGCAAGTTTGTGTGGAGGTGATAGAATTTAGCTTGGTCCTATGTCTTTGCAGTTACCATAGGAGAGGGTCTAGAATGGGGCATTAGATTGGAGGATTTAGAAAGCAGTTAAAGATGATGTGATCACAGGTGGGTTTTCCCCCTGCTGCAGAAATATGGGATTTTTACAATAAATTACTTTTGTAAGTAGAGAAAATATATTTTTCAGAAAATGTCAAGACAGCAGTATTGTATAAGTTTTTCTTTGAAAACCTTAGATTATAGTGATGACACCTAATATTAAATTTAAGTTGACAAGCTATATATTGTTAGTCAATTTGAAGGTTAGAGATAAAATGTTTCTCCTGC	AGTCAATGGCATGATGAAGGCAAGTGTTACTCAGCCCAATATTCTACCCTGTGCTTGAAAAACTTAGACATAAGCCCCTTGATGTCAGGAATCGTGTATACCTCTTTGTATTCCTAGCACTTGGTCCAGTGCTCTACACATAAGTAGCATTTTGTAGTTTTCTAAACTTTGATCCATATTTAGGATTATTTACAAGTTCTAGTCTTGTTTCTACAAAAGTTCCTTTGTATTATATAAGCTGACAAGCTGTAAATGATGCAAGTTTGTGTGGAGGTGATAGAATTTAGCTTGGTCCTATGTCTTTGCAGTTACCATAGGAGAGGGTCTAGAATGGGGCATTAGATTGGAGGATTTAGAAAGCAGTTAAAGATGATGTGATCACAGGTGGGTTTTCCCCCTGCTGCAGAAATATGGGATTTTTACAATAAATTACTTTTGTAAGTAGAGAAAATATATTTTTCAGAAAATGTCAAGACAGCAGTATTGTATAAGTTTTTCTTTGAAAACCTTAGATTATAGTGATGACACCTAATATTAAATTTAAGTTGACAAGCTATATATTGTTAGTCAATTTGAAGGTTAGAGATAAAATGTTTCTCCTGC	-	novel	NA	P-0053786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	36	435	0	ENST00000278616.4:c.7499_7516-437del		p.X2500_splice	ENST00000278616	NM_000051.3	2500		50/63	0.344967746343232	1	FACETS	0.468	0.385	0.561	0.468	0.385	0.561	SUBCLONAL	1	TRUE	0	0.344967746343232	1		435	369	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864253	57864253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764155302	NA	P-0053786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	98	835	0	ENST00000228682.2:c.1730C>A	p.Ser577Tyr	p.S577Y	ENST00000228682	NM_005269.2	577	tCc/tAc	12/12	0.300804947758661	4	FACETS	0.911	0.812	1	0.228	0.203	0.254	CLONAL	1	TRUE	0	0.344967746343232	4		835	839	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050948	49050948	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	200	382	0	ENST00000267163.4:c.2632G>C	p.Asp878His	p.D878H	ENST00000267163	NM_000321.2	878	Gat/Cat	25/27	0.344967746343232	3	FACETS	0.858	0.802	0.916	1	0.989	1	CLONAL	3	TRUE	1	0.344967746343232	3		382	528	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3634845	3634845	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775232005	NA	P-0053786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	123	811	0	ENST00000294008.3:c.4664C>T	p.Pro1555Leu	p.P1555L	ENST00000294008	NM_032444.2	1555	cCc/cTc	13/15	1	2	FACETS	0.89	0.805	0.98	0.89	0.805	0.98	CLONAL	1	TRUE	1	0.344967746343232	2		811	801	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258581	19258581	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs761470340	NA	P-0053786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	99	975	0	ENST00000162023.5:c.319G>C	p.Glu107Gln	p.E107Q	ENST00000162023		107	Gag/Cag	8/13	0.290330119580626	2	FACETS	0.697	0.622	0.778	0.349	0.311	0.389	SUBCLONAL	1	TRUE	0	0.344967746343232	2		975	823	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258599	19258599	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	83	939	0	ENST00000162023.5:c.301G>C	p.Glu101Gln	p.E101Q	ENST00000162023		101	Gag/Cag	8/13	0.290330119580626	2	FACETS	0.636	0.56	0.716	0.318	0.28	0.358	SUBCLONAL	1	TRUE	0	0.344967746343232	2		939	757	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52685767	52685767	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	60	422	0	ENST00000394830.3:c.705G>C	p.Gln235His	p.Q235H	ENST00000394830	NM_018313.4	235	caG/caC	7/30	0.110348122426616	4	FACETS	0.745	0.641	0.858	0.372	0.32	0.429	INDETERMINATE	1	TRUE	2	0.344967746343232	4		422	628	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651934	36651935	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0053786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	228	781	0	ENST00000244741.5:c.57_58dup	p.Arg20ProfsTer12	p.R20Pfs*12	ENST00000244741	NM_000389.4	19	cgc/cgCCc	2/3	0.283297256856859	3	FACETS	1	0.944	1	0.674	0.63	0.719	CLONAL	2	TRUE	0	0.344967746343232	3		781	767	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0053787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	96	464	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.834	0.744	0.929	1	0.983	1	CLONAL	2	TRUE	1	0.19	2		464	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578213	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs864309495	NA	P-0053787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	59	847	0	ENST00000269305.4:c.636del	p.Arg213AspfsTer34	p.R213Dfs*34	ENST00000269305	NM_001126112.2	212	ttT/tt	6/11	1	2	FACETS	0.711	0.61	0.821	0.711	0.61	0.821	SUBCLONAL	1	TRUE	1	0.19	2		847	874	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	51	386	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.592	0.503	0.69	0.592	0.503	0.69	SUBCLONAL	1	TRUE	1	0.32	2		386	538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0053788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	172	570	2	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.892	0.819	0.968	0.892	0.819	0.968	CLONAL	1	TRUE	1	0.32	2		572	1205	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291828	15291828	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376187165	NA	P-0053788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1926	121	1060	1	ENST00000263388.2:c.2938G>A	p.Ala980Thr	p.A980T	ENST00000263388	NM_000435.2	980	Gcc/Acc	18/33	0.204599209180789	3	FACETS	0.429	0.385	0.475	0.214	0.192	0.238	SUBCLONAL	1	TRUE	1	0.32	3		1061	2047	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060853	38060859	+	frameshift_variant	Frame_Shift_Del	DEL	AAGCCGT	AAGCCGT	-	novel	NA	P-0053789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	111	861	0	ENST00000250448.2:c.1130_1136del	p.His377ArgfsTer10	p.H377Rfs*10	ENST00000250448	NM_004496.3	377	cACGGCTTg/cg	2/2	1	2	FACETS	0.844	0.757	0.938	0.844	0.757	0.938	CLONAL	1	FALSE	1	0.224896479928143	2		861	1169	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439930	56439930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2285990	NA	P-0053789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	132	707	2	ENST00000407977.2:c.662G>A	p.Arg221Gln	p.R221Q	ENST00000407977		221	cGg/cAg	6/10	1	2	FACETS	0.902	0.816	0.992	0.902	0.816	0.992	CLONAL	1	FALSE	1	0.224896479928143	2		709	1302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519990	NA	P-0053789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	100	690	0	ENST00000269305.4:c.796G>C	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Cga	8/11	1	2	FACETS	0.955	0.852	1	0.955	0.852	1	CLONAL	1	FALSE	1	0.224896479928143	2		690	931	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696165	52696165	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs758198630	NA	P-0053789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	118	682	0	ENST00000394830.3:c.512G>T	p.Gly171Val	p.G171V	ENST00000394830	NM_018313.4	171	gGc/gTc	5/30	0.110860032565051	3	FACETS	0.998	0.898	1	0.499	0.449	0.552	INDETERMINATE	1	FALSE	1	0.224896479928143	3		682	1170	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670545	30670545	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	89	575	0	ENST00000376406.3:c.5975A>G	p.Glu1992Gly	p.E1992G	ENST00000376406	NM_014641.2	1992	gAg/gGg	13/15	1	2	FACETS	0.843	0.746	0.947	0.843	0.746	0.947	CLONAL	1	FALSE	1	0.224896479928143	2		575	939	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828743	72828745	+	frameshift_variant	Frame_Shift_Ins	INS	GTG	GTG	AACAC	novel	NA	P-0053789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	82	533	0	ENST00000268489.5:c.7836_7838delinsGTGTT	p.Asn2612LysfsTer34	p.N2612Kfs*34	ENST00000268489	NM_006885.3	2612	aaCACt/aaGTGTTt	9/10	1	2	FACETS	0.838	0.738	0.946	0.838	0.738	0.946	CLONAL	1	FALSE	1	0.224896479928143	2		533	870	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	249	436	2	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.681634784371438	2		438	687	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	785	721	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.681634784371438	3	FACETS	0.926	0.904	0.947	1	0.998	1	CLONAL	3	TRUE	1	0.681634784371438	3		728	1112	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	216	495	2	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.681634784371438	2		497	605	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783245	9783245	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756497515	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	250	734	1	ENST00000377346.4:c.2489G>A	p.Arg830His	p.R830H	ENST00000377346	NM_005026.3	830	cGt/cAt	20/24	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.681634784371438	2		735	728	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11167558	11167558	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	130	307	0	ENST00000361445.4:c.7635-1G>T		p.X2545_splice	ENST00000361445	NM_004958.3	2545			1	2	FACETS	0.926	0.847	1	0.926	0.847	1	CLONAL	1	TRUE	1	0.681634784371438	2		307	412	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182095	11182095	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1365408542	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	270	669	1	ENST00000361445.4:c.6751C>T	p.Arg2251Trp	p.R2251W	ENST00000361445	NM_004958.3	2251	Cgg/Tgg	48/58	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.681634784371438	2		670	752	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023162	27023162	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs752026201	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	17	60	0	ENST00000324856.7:c.268A>G	p.Ser90Gly	p.S90G	ENST00000324856	NM_006015.4	90	Agc/Ggc	1/20	1	2	FACETS	0.703	0.538	0.887	0.703	0.538	0.887	SUBCLONAL	1	TRUE	1	0.681634784371438	2		60	71	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023805	27023805	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	173	391	0	ENST00000324856.7:c.911C>A	p.Ser304Ter	p.S304*	ENST00000324856	NM_006015.4	304	tCg/tAg	1/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.681634784371438	2		391	449	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023831	27023831	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1415214478	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	121	321	0	ENST00000324856.7:c.941del	p.Gly314AlafsTer49	p.G314Afs*49	ENST00000324856	NM_006015.4	313	Ggg/gg	1/20	1	2	FACETS	0.826	0.752	0.902	0.826	0.752	0.902	CLONAL	1	TRUE	1	0.681634784371438	2		321	430	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46543287	46543287	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs762631338	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	155	368	0	ENST00000262741.5:c.216-2A>G		p.X72_splice	ENST00000262741	NM_003629.3	72			1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.681634784371438	2		368	450	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	152	445	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.935	0.862	1	0.935	0.862	1	CLONAL	1	TRUE	1	0.681634784371438	2		445	477	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981111	201981111	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	279	790	1	ENST00000359651.3:c.193del	p.Gln65SerfsTer90	p.Q65Sfs*90	ENST00000359651		64	Ccc/cc	2/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.681634784371438	2		791	788	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612164	43612164	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	104	310	1	ENST00000355710.3:c.2269G>A	p.Val757Met	p.V757M	ENST00000355710	NM_020975.4	757	Gtg/Atg	12/20	0.681634784371438	3	FACETS	1	0.955	1	0.548	0.495	0.604	CLONAL	1	TRUE	1	0.681634784371438	3		311	373	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137065	64137065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767134558	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	180	455	0	ENST00000334205.4:c.1576G>A	p.Val526Met	p.V526M	ENST00000334205	NM_003942.2	526	Gtg/Atg	13/17	1	2	FACETS	0.966	0.897	1	0.966	0.897	1	CLONAL	1	TRUE	1	0.681634784371438	2		455	547	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518488	69518488	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	145	421	0	ENST00000294312.3:c.157del	p.His53ThrfsTer93	p.H53Tfs*93	ENST00000294312	NM_005117.2	53	Cac/ac	1/3	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.681634784371438	2		421	418	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417081	417081	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373321785	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	203	390	0	ENST00000399788.2:c.3469C>T	p.Arg1157Cys	p.R1157C	ENST00000399788	NM_001042603.1	1157	Cgc/Tgc	23/28	0.195230631582016	3	FACETS	0.774	0.724	0.825	0.774	0.724	0.825	INDETERMINATE	2	TRUE	1	0.681634784371438	3		390	516	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245465	46245465	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	29	359	0	ENST00000334344.6:c.3559G>A	p.Val1187Met	p.V1187M	ENST00000334344	NM_152641.2	1187	Gtg/Atg	15/21	0.195230631582016	3	FACETS	0.259	0.208	0.318	0.13	0.104	0.159	INDETERMINATE	1	TRUE	1	0.681634784371438	3		359	440	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420204	49420204	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	56	637	1	ENST00000301067.7:c.15545del	p.Gly5182AlafsTer61	p.G5182Afs*61	ENST00000301067	NM_003482.3	5182	gGc/gc	48/54	0.195230631582016	3	FACETS	0.286	0.244	0.332	0.143	0.122	0.166	INDETERMINATE	1	TRUE	1	0.681634784371438	3		638	770	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424442	49424443	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs797044740	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	266	809	0	ENST00000301067.7:c.13780dup	p.Ala4594GlyfsTer12	p.A4594Gfs*12	ENST00000301067	NM_003482.3	4594	gcc/gGcc	41/54	0.195230631582016	3	FACETS	1	0.988	1	0.599	0.563	0.636	INDETERMINATE	1	TRUE	1	0.681634784371438	3		809	874	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	86	680	2	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	0.195230631582016	3	FACETS	0.402	0.355	0.453	0.201	0.177	0.227	INDETERMINATE	1	TRUE	1	0.681634784371438	3		682	841	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	367	758	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	0.195230631582016	3	FACETS	0.77	0.733	0.808	0.77	0.733	0.808	INDETERMINATE	2	TRUE	1	0.681634784371438	3		758	937	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434595	110434595	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs555841746	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	187	598	0	ENST00000375856.3:c.3806A>C	p.Gln1269Pro	p.Q1269P	ENST00000375856	NM_003749.2	1269	cAg/cCg	1/2	1	2	FACETS	0.905	0.841	0.972	0.905	0.841	0.972	CLONAL	1	TRUE	1	0.681634784371438	2		598	606	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435444	110435444	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	231	632	0	ENST00000375856.3:c.2957C>A	p.Pro986His	p.P986H	ENST00000375856	NM_003749.2	986	cCc/cAc	1/2	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.681634784371438	2		632	643	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986889	36986889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	165	317	3	ENST00000354822.5:c.800G>A	p.Gly267Glu	p.G267E	ENST00000354822	NM_001079668.2	267	gGg/gAg	3/3	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.681634784371438	2		320	412	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061519	38061522	+	missense_variant	Missense_Mutation	ONP	CCGC	CCGC	GCGT	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	18	324	0	ENST00000250448.2:c.467_470delinsACGC	p.Gly156_Gly157delinsAspAla	p.G156_G157delinsDA	ENST00000250448	NM_004496.3	156	gGCGGc/gACGCc	2/2	1	2	FACETS	0.172	0.129	0.223	0.172	0.129	0.223	SUBCLONAL	1	TRUE	1	0.681634784371438	2		324	307	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	211	607	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.95	0.887	1	0.95	0.887	1	CLONAL	1	TRUE	1	0.681634784371438	2		607	652	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007789	45007789	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	157	417	0	ENST00000558401.1:c.236A>T	p.Asp79Val	p.D79V	ENST00000558401	NM_004048.2	79	gAc/gTc	2/4	1	2	FACETS	0.931	0.859	1	0.931	0.859	1	CLONAL	1	TRUE	1	0.681634784371438	2		417	495	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007825	45007825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	195	488	0	ENST00000558401.1:c.276del	p.Thr93LeufsTer10	p.T93Lfs*10	ENST00000558401	NM_004048.2	91	aCc/ac	2/4	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.681634784371438	2		488	500	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	328	797	1	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.681634784371438	2		798	920	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500456	99500456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	269	831	0	ENST00000268035.6:c.3889C>T	p.Pro1297Ser	p.P1297S	ENST00000268035	NM_000875.3	1297	Cca/Tca	21/21	1	2	FACETS	0.929	0.874	0.985	0.929	0.874	0.985	CLONAL	1	TRUE	1	0.681634784371438	2		831	850	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135314	2135316	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs137854146	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	257	754	0	ENST00000219476.3:c.4655_4657del	p.Glu1552del	p.E1552del	ENST00000219476	NM_000548.3	1551	ggAGAa/gga	36/42	1	2	FACETS	0.967	0.909	1	0.967	0.909	1	CLONAL	1	TRUE	1	0.681634784371438	2		754	780	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	188	414	0	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.681634784371438	2		414	519	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026013	14026013	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	116	241	0	ENST00000311895.7:c.974-1G>T		p.X325_splice	ENST00000311895	NM_005236.2	325			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.681634784371438	2		241	310	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347194	89347194	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773848887	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	252	730	0	ENST00000301030.4:c.5756C>T	p.Ala1919Val	p.A1919V	ENST00000301030	NM_001256183.1	1919	gCg/gTg	9/13	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.681634784371438	2		730	738	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349604	89349604	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs924589358	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	280	790	0	ENST00000301030.4:c.3346G>A	p.Ala1116Thr	p.A1116T	ENST00000301030	NM_001256183.1	1116	Gca/Aca	9/13	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.681634784371438	2		790	816	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	312	678	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.681634784371438	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.681634784371438	1		678	568	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15967447	15967452	+	inframe_deletion	In_Frame_Del	DEL	TCCCGT	TCCCGT	-	rs770726844	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	37	581	0	ENST00000268712.3:c.5151_5156del	p.Arg1720_Glu1721del	p.R1720_E1721del	ENST00000268712	NM_006311.3	1717	gaACGGGAg/gag	35/46	0.681634784371438	1	FACETS	0.14	0.115	0.168	0.14	0.115	0.168	SUBCLONAL	1	TRUE	0	0.681634784371438	1		581	510	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983785	15983785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs772070121	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	204	503	0	ENST00000268712.3:c.3337C>T	p.Arg1113Ter	p.R1113*	ENST00000268712	NM_006311.3	1113	Cga/Tga	25/46	0.681634784371438	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.681634784371438	1		503	365	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30326004	30326005	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs769517721	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	113	288	0	ENST00000322652.5:c.2208dup	p.Gln737ThrfsTer20	p.Q737Tfs*20	ENST00000322652	NM_015355.2	734	-/A	16/16	0.681634784371438	3	FACETS	0.971	0.879	1	0.485	0.439	0.533	CLONAL	1	TRUE	1	0.681634784371438	3		288	458	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40497642	40497642	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408283351	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	238	640	1	ENST00000264657.5:c.307C>T	p.Arg103Trp	p.R103W	ENST00000264657	NM_139276.2	103	Cgg/Tgg	4/24	0.681634784371438	3	FACETS	0.98	0.916	1	0.49	0.458	0.524	CLONAL	1	TRUE	1	0.681634784371438	3		641	955	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234420	41234420	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs80358027	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	179	397	1	ENST00000357654.3:c.4357+1G>A		p.X1453_splice	ENST00000357654	NM_007294.3	1453			0.681634784371438	3	FACETS	1	0.935	1	0.506	0.468	0.545	CLONAL	1	TRUE	1	0.681634784371438	3		398	696	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245803	41245803	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786202386	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	211	555	0	ENST00000357654.3:c.1745C>T	p.Thr582Met	p.T582M	ENST00000357654	NM_007294.3	582	aCg/aTg	10/23	0.681634784371438	3	FACETS	1	0.971	1	0.539	0.502	0.577	CLONAL	1	TRUE	1	0.681634784371438	3		555	770	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414763	56414763	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	251	619	0	ENST00000348428.3:c.2164G>T	p.Gly722Ter	p.G722*	ENST00000348428	NM_006785.3	722	Gga/Tga	17/17	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.681634784371438	2		619	712	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100001	11100001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	256	714	1	ENST00000358026.2:c.1127C>T	p.Ala376Val	p.A376V	ENST00000358026	NM_001128849.1	376	gCt/gTt	7/36	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.681634784371438	2		715	682	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296358	15296358	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	356	1058	1	ENST00000263388.2:c.2084del	p.Pro695ArgfsTer165	p.P695Rfs*165	ENST00000263388	NM_000435.2	695	cCg/cg	13/33	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.681634784371438	2		1059	930	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	318	984	3	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.681634784371438	2		987	926	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215969	36215969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1313553140	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	295	931	0	ENST00000222270.7:c.3509G>A	p.Arg1170His	p.R1170H	ENST00000222270	NM_014727.1	1170	cGc/cAc	10/37	1	2	FACETS	0.979	0.924	1	0.979	0.924	1	CLONAL	1	TRUE	1	0.681634784371438	2		931	884	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	337	1030	0	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.969	0.918	1	0.969	0.918	1	CLONAL	1	TRUE	1	0.681634784371438	2		1030	1020	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249954	39249954	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	197	560	0	ENST00000402219.2:c.1615G>A	p.Ala539Thr	p.A539T	ENST00000402219	NM_005633.3	539	Gca/Aca	10/23	1	2	FACETS	0.97	0.904	1	0.97	0.904	1	CLONAL	1	TRUE	1	0.681634784371438	2		560	596	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661579	227661579	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs993467904	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	251	807	0	ENST00000305123.5:c.1876C>T	p.Arg626Ter	p.R626*	ENST00000305123	NM_005544.2	626	Cga/Tga	1/2	1	2	FACETS	0.949	0.891	1	0.949	0.891	1	CLONAL	1	TRUE	1	0.681634784371438	2		807	776	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	235	806	3	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	1	2	FACETS	0.943	0.884	1	0.943	0.884	1	CLONAL	1	TRUE	1	0.681634784371438	2		809	731	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101104	41101104	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	232	745	0	ENST00000373198.4:c.1252C>A	p.His418Asn	p.H418N	ENST00000373198	NM_133170.3	418	Cat/Aat	8/32	1	2	FACETS	0.895	0.837	0.953	0.895	0.837	0.953	CLONAL	1	TRUE	1	0.681634784371438	2		745	761	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265378	46265378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs894357444	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	126	258	1	ENST00000371998.3:c.2248G>A	p.Ala750Thr	p.A750T	ENST00000371998		750	Gca/Aca	12/23	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.681634784371438	2		259	353	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	294	296	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	0.681634784371438	2	FACETS	0.936	0.896	0.974	0.936	0.896	0.974	CLONAL	2	TRUE	0	0.681634784371438	2		296	461	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067281	37067281	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750483	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	391	456	0	ENST00000231790.2:c.1192C>T	p.Gln398Ter	p.Q398*	ENST00000231790	NM_000249.3	398	Cag/Tag	12/19	0.681634784371438	2	FACETS	0.974	0.939	1	0.974	0.939	1	CLONAL	2	TRUE	0	0.681634784371438	2		456	589	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725181	49725181	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	162	449	0	ENST00000449682.2:c.242+2T>C		p.X81_splice	ENST00000449682	NM_020998.3	81			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.681634784371438	2		449	457	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	97	304	0	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	1	2	FACETS	0.85	0.765	0.937	0.85	0.765	0.937	CLONAL	1	TRUE	1	0.681634784371438	2		304	335	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928506	69928506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	261	731	0	ENST00000352241.4:c.326C>T	p.Ala109Val	p.A109V	ENST00000352241	NM_198159.2	109	gCc/gTc	2/10	1	2	FACETS	0.948	0.891	1	0.948	0.891	1	CLONAL	1	TRUE	1	0.681634784371438	2		731	808	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114265	73114267	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs1366197239	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	96	237	0	ENST00000356692.5:c.906_908del	p.Glu303del	p.E303del	ENST00000356692		301	GAA/-	8/9	1	2	FACETS	0.802	0.722	0.887	0.802	0.722	0.887	CLONAL	1	TRUE	1	0.681634784371438	2		237	351	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451396	187451396	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	200	429	1	ENST00000232014.4:c.86A>G	p.Asp29Gly	p.D29G	ENST00000232014	NM_001130845.1	29	gAc/gGc	3/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.681634784371438	2		430	541	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920105	1920105	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1338705176	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	135	684	0	ENST00000382891.5:c.1165T>C	p.Ser389Pro	p.S389P	ENST00000382891	NM_133335.3	389	Tct/Cct	5/22	1	2	FACETS	0.48	0.436	0.526	0.48	0.436	0.526	SUBCLONAL	1	TRUE	1	0.681634784371438	2		684	825	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525646	187525648	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs1454581466	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	118	469	0	ENST00000441802.2:c.10431_10433del	p.Phe3478del	p.F3478del	ENST00000441802	NM_005245.3	3477	ttCTTt/ttt	18/27	1	2	FACETS	0.536	0.484	0.59	0.536	0.484	0.59	SUBCLONAL	1	TRUE	1	0.681634784371438	2		469	646	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251207	251207	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs181238392	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	147	362	0	ENST00000264932.6:c.1652C>T	p.Thr551Met	p.T551M	ENST00000264932	NM_004168.2	551	aCg/aTg	12/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.681634784371438	2		362	405	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	148	377	1	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.681634784371438	2		378	430	SUCCESS
APC	324	MSKCC	GRCh37	5	112102960	112102960	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139196838	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	168	396	2	ENST00000257430.4:c.295C>T	p.Arg99Trp	p.R99W	ENST00000257430	NM_000038.5	99	Cgg/Tgg	4/16	1	2	FACETS	0.98	0.908	1	0.98	0.908	1	CLONAL	1	TRUE	1	0.681634784371438	2		398	503	SUCCESS
APC	324	MSKCC	GRCh37	5	112154849	112154849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs947634162	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	238	601	0	ENST00000257430.4:c.1120C>T	p.Arg374Trp	p.R374W	ENST00000257430	NM_000038.5	374	Cgg/Tgg	10/16	1	2	FACETS	0.981	0.92	1	0.981	0.92	1	CLONAL	1	TRUE	1	0.681634784371438	2		601	712	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271605	26271605	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	150	432	0	ENST00000305910.3:c.8G>T	p.Arg3Leu	p.R3L	ENST00000305910	NM_003534.2	3	cGc/cTc	1/1	1	2	FACETS	0.982	0.906	1	0.982	0.906	1	CLONAL	1	TRUE	1	0.681634784371438	2		432	448	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	170	603	2	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	0.781	0.721	0.842	0.781	0.721	0.842	SUBCLONAL	1	TRUE	1	0.681634784371438	2		605	639	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32191659	32191664	+	inframe_deletion	In_Frame_Del	DEL	AGCAGC	AGCAGC	-	rs35795312	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	172	701	14	ENST00000375023.3:c.42_47del	p.Leu15_Leu16del	p.L15_L16del	ENST00000375023	NM_004557.3	14	ctGCTGCTa/cta	1/30	1	2	FACETS	0.609	0.561	0.659	0.609	0.561	0.659	SUBCLONAL	1	TRUE	1	0.681634784371438	2		715	829	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200285	138200285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374368025	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	202	504	0	ENST00000237289.4:c.1703C>T	p.Ser568Leu	p.S568L	ENST00000237289	NM_001270507.1	568	tCg/tTg	7/9	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.681634784371438	2		504	580	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100462	157100466	+	stop_gained	Nonsense_Mutation	ONP	CAGCA	CAGCA	TAGCT	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	16	19	0	ENST00000346085.5:c.1399_1403delinsTAGCT	p.Gln467_Gln468delinsTer	p.Q467_Q468delins*	ENST00000346085	NM_020732.3	467	CAGCAg/TAGCTg	1/20	1	2	FACETS	0.782	0.625	0.937	1	0.927	1	CLONAL	2	TRUE	1	0.681634784371438	2		19	30	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510824	157510824	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	232	629	0	ENST00000346085.5:c.3599G>T	p.Ser1200Ile	p.S1200I	ENST00000346085	NM_020732.3	1200	aGc/aTc	14/20	1	2	FACETS	0.977	0.915	1	0.977	0.915	1	CLONAL	1	TRUE	1	0.681634784371438	2		629	697	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962853	2962854	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	269	821	1	ENST00000396946.4:c.2054dup	p.Asn686GlnfsTer23	p.N686Qfs*23	ENST00000396946	NM_032415.4	685	ggc/ggGc	16/25	0.681634784371438	3	FACETS	0.889	0.833	0.946	0.444	0.416	0.473	CLONAL	1	TRUE	1	0.681634784371438	3		822	1191	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739618	41739618	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	305	461	3	ENST00000242208.4:c.355C>T	p.Gln119Ter	p.Q119*	ENST00000242208	NM_002192.2	119	Cag/Tag	2/3	0.681634784371438	3	FACETS	0.984	0.936	1	0.984	0.936	1	CLONAL	2	TRUE	1	0.681634784371438	3		464	610	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444275	50444275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	274	317	2	ENST00000331340.3:c.205C>T	p.Arg69Cys	p.R69C	ENST00000331340	NM_006060.4	69	Cgt/Tgt	4/8	0.681634784371438	3	FACETS	0.993	0.942	1	0.993	0.942	1	CLONAL	2	TRUE	1	0.681634784371438	3		319	543	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346220	152346220	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	227	569	5	ENST00000359321.1:c.350del	p.Leu117TrpfsTer17	p.L117Wfs*17	ENST00000359321	NM_005431.1	117	tTg/tg	3/3	0.681634784371438	3	FACETS	0.964	0.899	1	0.482	0.449	0.516	CLONAL	1	TRUE	1	0.681634784371438	3		574	926	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285580	38285580	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	175	478	1	ENST00000425967.3:c.573G>T	p.Lys191Asn	p.K191N	ENST00000425967	NM_001174067.1	191	aaG/aaT	6/19	0.681634784371438	3	FACETS	0.922	0.851	0.995	0.461	0.425	0.498	CLONAL	1	TRUE	1	0.681634784371438	3		479	747	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738404	145738404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1291628811	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	319	1008	1	ENST00000428558.2:c.2581C>T	p.Pro861Ser	p.P861S	ENST00000428558	NM_004260.3	861	Ccc/Tcc	16/22	0.681634784371438	3	FACETS	0.995	0.939	1	0.498	0.469	0.527	CLONAL	1	TRUE	1	0.681634784371438	3		1009	1261	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336379	80336379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	144	444	0	ENST00000286548.4:c.940G>A	p.Val314Met	p.V314M	ENST00000286548	NM_002072.3	314	Gtg/Atg	7/7	0.647813476331174	3	FACETS	0.839	0.767	0.914	0.42	0.383	0.457	CLONAL	1	TRUE	1	0.681634784371438	3		444	675	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128246855	128246855	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	205	608	0	ENST00000265960.3:c.1074G>T	p.Arg358Ser	p.R358S	ENST00000265960	NM_001006617.1	358	agG/agT	9/12	0.647813476331174	3	FACETS	0.986	0.916	1	0.493	0.458	0.529	CLONAL	1	TRUE	1	0.681634784371438	3		608	818	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224238	53224238	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	261	859	0	ENST00000375401.3:c.3313T>C	p.Cys1105Arg	p.C1105R	ENST00000375401	NM_004187.3	1105	Tgt/Cgt	22/26	0.681634784371438	2	FACETS	0.951	0.894	1	0.476	0.447	0.505	CLONAL	1	TRUE	0	0.681634784371438	2		859	805	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412628	63412628	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755983037	NA	P-0053790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	37	722	2	ENST00000330258.3:c.539G>A	p.Arg180Gln	p.R180Q	ENST00000330258	NM_152424.3	180	cGg/cAg	2/2	0.681634784371438	2	FACETS	0.15	0.123	0.18	0.075	0.061	0.09	SUBCLONAL	1	TRUE	0	0.681634784371438	2		724	725	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220370	1220370	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0053791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	20	640	1	ENST00000326873.7:c.465-2A>T		p.X155_splice	ENST00000326873	NM_000455.4	155			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		641	855	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	61	691	1	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.347	0.298	0.401	0.347	0.298	0.401	SUBCLONAL	1	TRUE	1	0.34	2		692	1033	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	122	563	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.808	0.736	0.883	1	0.987	1	CLONAL	2	TRUE	1	0.34	2		563	444	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	236	494	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.825	0.772	0.88	1	0.993	1	CLONAL	2	TRUE	1	0.34	2		494	841	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	81	418	1	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	0.716	0.631	0.808	0.716	0.631	0.808	SUBCLONAL	1	TRUE	1	0.34	2		419	665	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	93	445	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.826	0.735	0.923	0.826	0.735	0.923	CLONAL	1	TRUE	1	0.34	2		445	662	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	205	623	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.895	0.834	0.957	1	0.993	1	CLONAL	2	TRUE	1	0.34	2		623	674	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	144	419	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.844	0.774	0.915	1	0.99	1	CLONAL	2	TRUE	1	0.34	2		419	502	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717769	89717770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	107	299	0	ENST00000371953.3:c.800dup	p.Asp268GlyfsTer30	p.D268Gfs*30	ENST00000371953	NM_000314.4	265	cta/ctAa	7/9	1	2	FACETS	0.766	0.692	0.843	1	0.984	1	SUBCLONAL	2	TRUE	1	0.34	2		299	411	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	26	329	1	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	0.284	0.224	0.353	0.284	0.224	0.353	SUBCLONAL	1	TRUE	1	0.34	2		330	538	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936093	178936093	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913275	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	159	536	3	ENST00000263967.3:c.1635G>T	p.Glu545Asp	p.E545D	ENST00000263967	NM_006218.2	545	gaG/gaT	10/21	1	2	FACETS	0.834	0.768	0.901	1	0.991	1	CLONAL	2	TRUE	1	0.34	2		539	561	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	77	527	1	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.552	0.483	0.625	0.552	0.483	0.625	SUBCLONAL	1	TRUE	1	0.34	2		528	821	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444659	78444659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs908264837	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	119	460	1	ENST00000370768.2:c.30del	p.Ser11LeufsTer43	p.S11Lfs*43	ENST00000370768	NM_003902.3	10	ccC/cc	1/20	1	2	FACETS	0.793	0.715	0.875	0.793	0.715	0.875	SUBCLONAL	1	TRUE	1	0.34	2		461	883	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164778	106164778	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1009194427	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	51	484	1	ENST00000380013.4:c.3646C>T	p.Arg1216Ter	p.R1216*	ENST00000380013	NM_001127208.2	1216	Cga/Tga	6/11	1	2	FACETS	0.33	0.279	0.386	0.33	0.279	0.386	SUBCLONAL	1	TRUE	1	0.34	2		485	910	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820617	3820617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	381	835	0	ENST00000262367.5:c.2834C>T	p.Ser945Leu	p.S945L	ENST00000262367	NM_004380.2	945	tCg/tTg	14/31	1	2	FACETS	0.841	0.798	0.884	1	0.996	1	CLONAL	2	TRUE	1	0.34	2		835	1333	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159748	20159748	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	250	635	0	ENST00000379607.5:c.11A>G	p.Asn4Ser	p.N4S	ENST00000379607	NM_001412.3	4	aAt/aGt	1/7	1	2	FACETS	0.923	0.866	0.981	1	0.995	1	CLONAL	2	TRUE	1	0.34	2		635	797	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101117	27101117	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	170	814	1	ENST00000324856.7:c.4403del	p.Pro1468LeufsTer13	p.P1468Lfs*13	ENST00000324856	NM_006015.4	1467	Ccc/cc	18/20	1	2	FACETS	0.978	0.899	1	0.978	0.899	1	CLONAL	1	TRUE	1	0.34	2		815	1022	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435971	56435971	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780893183	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	53	595	0	ENST00000407977.2:c.1166G>A	p.Arg389His	p.R389H	ENST00000407977		389	cGc/cAc	9/10	1	2	FACETS	0.394	0.335	0.459	0.394	0.335	0.459	SUBCLONAL	1	TRUE	1	0.34	2		595	792	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165283	47165283	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	85	370	0	ENST00000409792.3:c.843del	p.Glu282LysfsTer19	p.E282Kfs*19	ENST00000409792	NM_014159.6	281	aaA/aa	3/21	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.34	2		370	490	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947119	178947119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199943173	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	42	341	0	ENST00000263967.3:c.2555G>A	p.Arg852Gln	p.R852Q	ENST00000263967	NM_006218.2	852	cGa/cAa	18/21	1	2	FACETS	0.419	0.349	0.497	0.419	0.349	0.497	SUBCLONAL	1	TRUE	1	0.34	2		341	589	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466022	69466022	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	367	1034	0	ENST00000227507.2:c.860C>A	p.Pro287His	p.P287H	ENST00000227507	NM_053056.2	287	cCc/cAc	5/5	1	2	FACETS	0.815	0.773	0.859	1	0.995	1	CLONAL	2	TRUE	1	0.34	2		1034	1324	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491283	2491283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776730987	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	225	904	1	ENST00000355716.4:c.326G>A	p.Arg109Gln	p.R109Q	ENST00000355716	NM_003820.2	109	cGg/cAg	4/8	1	2	FACETS	0.98	0.911	1	0.98	0.911	1	CLONAL	1	TRUE	1	0.34	2		905	1350	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140449169	140449169	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	35	401	0	ENST00000288602.6:c.1910C>T	p.Ser637Leu	p.S637L	ENST00000288602	NM_004333.4	637	tCa/tTa	16/18	1	2	FACETS	0.412	0.337	0.496	0.412	0.337	0.496	SUBCLONAL	1	TRUE	1	0.34	2		401	500	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339110	65339111	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	122	526	4	ENST00000342505.4:c.425dup	p.Ile143AspfsTer9	p.I143Dfs*9	ENST00000342505	NM_002227.2	142	aag/aaAg	5/25	1	2	FACETS	0.818	0.739	0.902	0.818	0.739	0.902	CLONAL	1	TRUE	1	0.34	2		530	877	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376248	15376248	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	113	616	1	ENST00000263377.2:c.766del	p.Gln256SerfsTer27	p.Q256Sfs*27	ENST00000263377	NM_058243.2	256	Cag/ag	5/20	1	2	FACETS	0.776	0.697	0.858	0.776	0.697	0.858	SUBCLONAL	1	TRUE	1	0.34	2		617	857	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815713	32815713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1168560265	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	100	819	0	ENST00000354258.4:c.1903C>T	p.Arg635Cys	p.R635C	ENST00000354258	NM_000593.5	635	Cgc/Tgc	8/11	1	2	FACETS	0.505	0.45	0.565	0.505	0.45	0.565	SUBCLONAL	1	TRUE	1	0.34	2		819	1164	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391424	139391424	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759225800	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	384	902	1	ENST00000277541.6:c.6767C>T	p.Ala2256Val	p.A2256V	ENST00000277541	NM_017617.3	2256	gCg/gTg	34/34	1	2	FACETS	0.914	0.868	0.96	1	0.996	1	CLONAL	2	TRUE	1	0.34	2		903	1236	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073946	8073946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	43	482	0	ENST00000377482.5:c.713C>A	p.Pro238His	p.P238H	ENST00000377482	NM_018948.3	238	cCt/cAt	4/4	1	2	FACETS	0.314	0.262	0.373	0.314	0.262	0.373	SUBCLONAL	1	TRUE	1	0.34	2		482	805	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100813	27100818	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	GCCTTA	GCCTTA	-	novel	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	178	479	0	ENST00000324856.7:c.4102-6_4102-1del		p.X1368_splice	ENST00000324856	NM_006015.4	1368			1	2	FACETS	0.853	0.79	0.917	1	0.992	1	CLONAL	2	TRUE	1	0.34	2		479	614	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129204	64129204	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	82	923	2	ENST00000334205.4:c.742G>A	p.Ala248Thr	p.A248T	ENST00000334205	NM_003942.2	248	Gct/Act	7/17	1	2	FACETS	0.377	0.331	0.427	0.377	0.331	0.427	SUBCLONAL	1	TRUE	1	0.34	2		925	1278	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195927	102195927	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	164	381	0	ENST00000263464.3:c.687T>A	p.Phe229Leu	p.F229L	ENST00000263464	NM_001165.4	229	ttT/ttA	2/9	1	2	FACETS	0.903	0.835	0.974	1	0.992	1	CLONAL	2	TRUE	1	0.34	2		381	534	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865708	57865708	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	306	822	1	ENST00000228682.2:c.3185C>A	p.Pro1062His	p.P1062H	ENST00000228682	NM_005269.2	1062	cCt/cAt	12/12	1	2	FACETS	0.787	0.741	0.833	1	0.994	1	SUBCLONAL	2	TRUE	1	0.34	2		823	1144	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900281	32900281	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	66	303	0	ENST00000380152.3:c.469A>G	p.Lys157Glu	p.K157E	ENST00000380152		157	Aag/Gag	5/27	1	2	FACETS	0.988	0.861	1	0.988	0.861	1	CLONAL	1	TRUE	1	0.34	2		303	393	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110159	3110159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	155	576	0	ENST00000078429.4:c.149G>A	p.Ser50Asn	p.S50N	ENST00000078429	NM_002067.2	50	aGc/aAc	2/7	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.34	2		576	826	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3113425	3113425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	189	790	0	ENST00000078429.4:c.419G>A	p.Gly140Asp	p.G140D	ENST00000078429	NM_002067.2	140	gGc/gAc	3/7	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.34	2		790	1095	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284895	15284895	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1182	252	957	0	ENST00000263388.2:c.4720G>C	p.Ala1574Pro	p.A1574P	ENST00000263388	NM_000435.2	1574	Gcc/Ccc	25/33	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.34	2		957	1434	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753549	42753549	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754203690	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1281	72	1047	0	ENST00000222329.4:c.715C>T	p.Arg239Trp	p.R239W	ENST00000222329	NM_006494.2	239	Cgg/Tgg	4/4	1	2	FACETS	0.313	0.272	0.358	0.313	0.272	0.358	SUBCLONAL	1	TRUE	1	0.34	2		1047	1353	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250549	110250549	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	111	534	0	ENST00000374672.4:c.127-1G>A		p.X43_splice	ENST00000374672	NM_004235.4	43			1	2	FACETS	0.953	0.858	1	0.953	0.858	1	CLONAL	1	TRUE	1	0.34	2		534	685	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771862	135771862	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	282	672	1	ENST00000298552.3:c.3255A>C	p.Lys1085Asn	p.K1085N	ENST00000298552	NM_001162426.1	1085	aaA/aaC	23/23	1	2	FACETS	0.838	0.788	0.889	1	0.994	1	CLONAL	2	TRUE	1	0.34	2		673	990	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417545	139417545	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	202	1041	0	ENST00000277541.6:c.499C>A	p.Pro167Thr	p.P167T	ENST00000277541	NM_017617.3	167	Cca/Aca	4/34	1	2	FACETS	0.846	0.782	0.912	0.846	0.782	0.912	CLONAL	1	TRUE	1	0.34	2		1041	1405	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0053794-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	30	603	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		603	934	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210075	55210075	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053794-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	28	630	0	ENST00000275493.2:c.185T>G	p.Leu62Arg	p.L62R	ENST00000275493	NM_005228.3	62	cTt/cGt	2/28	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		630	759	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050864	49050864	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886042935	NA	P-0053797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	52	516	1	ENST00000267163.4:c.2548C>T	p.Gln850Ter	p.Q850*	ENST00000267163	NM_000321.2	850	Cag/Tag	25/27	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.18	2		517	574	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0053797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	99	873	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.18	2		873	1020	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244778	46244778	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057524391	NA	P-0053797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	76	836	0	ENST00000334344.6:c.2872C>T	p.Gln958Ter	p.Q958*	ENST00000334344	NM_152641.2	958	Cag/Tag	15/21	1	2	FACETS	0.947	0.829	1	0.947	0.829	1	CLONAL	1	TRUE	1	0.18	2		836	892	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871147	12871148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	63	503	0	ENST00000228872.4:c.375dup	p.Glu126Ter	p.E126*	ENST00000228872	NM_004064.3	125	tct/tcTt	1/3	0.176930247822392	3	FACETS	1	0.94	1	0.581	0.502	0.667	CLONAL	1	TRUE	1	0.18	3		503	657	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701889	43701889	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	39	396	1	ENST00000382044.4:c.5356C>T	p.Arg1786Ter	p.R1786*	ENST00000382044	NM_001141980.1	1786	Cga/Tga	25/28	1	2	FACETS	0.912	0.756	1	0.912	0.756	1	CLONAL	1	TRUE	1	0.18	2		397	475	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589550	67589606	+	inframe_deletion	In_Frame_Del	DEL	AAGAAGATAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACACTCAGTTTC	AAGAAGATAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACACTCAGTTTC	-	novel	NA	P-0053797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	13	319	0	ENST00000274335.5:c.1318_1374del	p.Asp440_Glu458del	p.D440_E458del	ENST00000274335		438	aAAGAAGATAATATTGAAGCTGTAGGGAAAAAATTACATGAATATAACACTCAGTTTCaa/aaa	10/15	1	2	FACETS	0.639	0.456	0.862	0.639	0.456	0.862	SUBCLONAL	1	TRUE	1	0.18	2		319	226	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148513777	148513777	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1462379572	NA	P-0053797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	57	804	2	ENST00000320356.2:c.1504C>T	p.Arg502Trp	p.R502W	ENST00000320356	NM_004456.4	502	Cgg/Tgg	12/20	1	2	FACETS	0.662	0.566	0.767	0.662	0.566	0.767	SUBCLONAL	1	TRUE	1	0.18	2		806	957	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0053805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	103	258	0				ENST00000310581	NM_198253.2	-/1132			0.18010008603895	3	FACETS	0.939	0.847	1	0.313	0.282	0.345	INDETERMINATE	1	TRUE	0	0.782942755794887	3		258	390	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0053805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	336	470	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.407240406981885	2	FACETS	1	0.996	1	0.748	0.716	0.779	INDETERMINATE	1	TRUE	0	0.782942755794887	2		470	574	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777978	27777978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	515	952	0	ENST00000369163.2:c.127C>T	p.Arg43Trp	p.R43W	ENST00000369163	NM_003536.2	43	Cgg/Tgg	1/1	0.23416773751334	6	FACETS	1	0.987	1	1	0.987	1	INDETERMINATE	3	TRUE	3	0.782942755794887	6		952	1065	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514547	149514547	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	183	698	1	ENST00000261799.4:c.397G>A	p.Glu133Lys	p.E133K	ENST00000261799	NM_002609.3	133	Gag/Aag	4/23	0.355933127787075	1	FACETS	0.494	0.458	0.53	0.494	0.458	0.53	INDETERMINATE	1	TRUE	0	0.782942755794887	1		699	576	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067048	143067048	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	81	583	0	ENST00000262992.4:c.1665C>A	p.Asn555Lys	p.N555K	ENST00000262992	NM_001101669.1	555	aaC/aaA	16/24	0.26846285801137	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.782942755794887	0		583	458	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249241	133249241	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	140	1071	0	ENST00000320574.5:c.1658G>T	p.Arg553Leu	p.R553L	ENST00000320574	NM_006231.2	553	cGc/cTc	15/49	0.406202080802157	2	FACETS	0.466	0.424	0.509	0.233	0.212	0.255	INDETERMINATE	1	TRUE	0	0.782942755794887	2		1071	768	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134563	41134563	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	68	760	0	ENST00000379561.5:c.1065G>A	p.Met355Ile	p.M355I	ENST00000379561	NM_002015.3	355	atG/atA	2/3	0.459559307377821	2	FACETS	0.373	0.325	0.424	0.186	0.162	0.212	INDETERMINATE	1	TRUE	0	0.782942755794887	2		760	466	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663300	67663300	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0053805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	194	488	0	ENST00000264010.4:c.1702-1G>C		p.X568_splice	ENST00000264010	NM_006565.3	568			0.412690735920521	1	FACETS	0.775	0.728	0.822	0.775	0.728	0.822	INDETERMINATE	1	TRUE	0	0.782942755794887	1		488	389	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117725	70117725	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	435	1319	0	ENST00000245479.2:c.193G>C	p.Glu65Gln	p.E65Q	ENST00000245479	NM_000346.3	65	Gag/Cag	1/3	0.325550926230543	3	FACETS	1	0.991	1	0.58	0.553	0.608	INDETERMINATE	1	TRUE	1	0.782942755794887	3		1319	1333	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867313	45867313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1169596580	NA	P-0053805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	643	1378	0	ENST00000391945.4:c.880G>A	p.Glu294Lys	p.E294K	ENST00000391945	NM_000400.3	294	Gag/Aag	10/23	0.782942755794887	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.782942755794887	1		1378	826	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536300	106536300	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	201	617	0	ENST00000369096.4:c.267C>G	p.Phe89Leu	p.F89L	ENST00000369096	NM_001198.3	89	ttC/ttG	2/7	0.782942755794887	1	FACETS	0.967	0.917	1	0.967	0.917	1	CLONAL	1	TRUE	0	0.782942755794887	1		617	323	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100301	157100301	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	116	325	0	ENST00000346085.5:c.1238C>A	p.Ser413Ter	p.S413*	ENST00000346085	NM_020732.3	413	tCg/tAg	1/20	0.355933127787075	1	FACETS	0.615	0.563	0.669	0.615	0.563	0.669	INDETERMINATE	1	TRUE	0	0.782942755794887	1		325	293	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937227	76937227	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	311	320	0	ENST00000373344.5:c.3521C>G	p.Ser1174Cys	p.S1174C	ENST00000373344	NM_000489.3	1174	tCt/tGt	9/35	0.607504226646813	2	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.782942755794887	2		320	373	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436527	49436530	+	frameshift_variant	Frame_Shift_Del	DEL	GAAG	GAAG	AAA	novel	NA	P-0053805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	480	1118	1	ENST00000301067.7:c.5776_5779delinsTTT	p.Leu1926PhefsTer121	p.L1926Ffs*121	ENST00000301067	NM_003482.3	1926	CTTCaa/TTTaa	26/54	0.407240406981885	2	FACETS	1	0.997	1	0.736	0.71	0.762	INDETERMINATE	1	TRUE	0	0.782942755794887	2		1119	833	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867295	45867297	+	missense_variant	Missense_Mutation	TNP	CCC	CCC	TTT	novel	NA	P-0053805-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	588	1382	0	ENST00000391945.4:c.896_898delinsAAA	p.Arg299_Glu300delinsGlnLys	p.R299_E300delinsQK	ENST00000391945	NM_000400.3	299	cGGGag/cAAAag	10/23	0.782942755794887	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.782942755794887	1		1382	780	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0053816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	82	494	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	1	FACETS	0.797	0.707	0.893	1	0.98	1	SUBCLONAL	2	TRUE	0	0.22	1		494	416	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0053816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	96	562	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.22	2		562	754	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0053816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	131	781	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.22	2		781	890	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604656	48604656	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	27	415	0	ENST00000342988.3:c.1478A>G	p.Asp493Gly	p.D493G	ENST00000342988	NM_005359.5	493	gAt/gGt	12/12	1	2	FACETS	0.559	0.444	0.691	0.559	0.444	0.691	SUBCLONAL	1	TRUE	1	0.22	2		415	439	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	81	386	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.334831049291285	3	FACETS	1	0.963	1	0.773	0.694	0.853	CLONAL	2	TRUE	0	0.408628098604938	3		386	206	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0053818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	107	804	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.393272013670331	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.408628098604938	1		804	358	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0053818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	41	270	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	0.283009704697195	2	FACETS	1	0.954	1	0.692	0.587	0.803	CLONAL	1	TRUE	0	0.408628098604938	2		270	145	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604701	48604701	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	38	486	0	ENST00000342988.3:c.1523G>T	p.Gly508Val	p.G508V	ENST00000342988	NM_005359.5	508	gGc/gTc	12/12	0.408628098604938	1	FACETS	0.736	0.615	0.869	0.736	0.615	0.869	SUBCLONAL	1	TRUE	0	0.408628098604938	1		486	201	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011106	12011106	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0053818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	34	316	0	ENST00000353533.5:c.514-1G>C		p.X172_splice	ENST00000353533	NM_003010.3	172			0.393272013670331	1	FACETS	0.901	0.748	1	0.901	0.748	1	CLONAL	1	TRUE	0	0.408628098604938	1		316	147	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0053819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	91	798	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.40062411660216	2		798	380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	144	952	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.32689176638299	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.40062411660216	2		952	341	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545855	41545855	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867077693	NA	P-0053819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	489	1008	1	ENST00000263253.7:c.2470C>T	p.Gln824Ter	p.Q824*	ENST00000263253	NM_001429.3	824	Caa/Taa	14/31	0.40062411660216	9	FACETS	1	0.982	1			1	CLONAL	7	TRUE	NA	0.40062411660216	9		1009	816	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0053819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	46	598	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	0.186871213651968	1	FACETS	0.982	0.839	1	0.982	0.839	1	INDETERMINATE	1	TRUE	0	0.40062411660216	1		598	187	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345969	70345969	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	67	413	0	ENST00000374080.3:c.2506C>T	p.Leu836Phe	p.L836F	ENST00000374080		836	Ctt/Ttt	18/45	0.266301703890887	2	FACETS	1	0.906	1			1	CLONAL	2	TRUE	NA	0.40062411660216	2		413	164	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881425	37881425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	105	896	1	ENST00000269571.5:c.2617G>A	p.Asp873Asn	p.D873N	ENST00000269571		873	Gac/Aac	21/27	0.40062411660216	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.40062411660216	1		897	377	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983120	201983121	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0053819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	58	853	0	ENST00000359651.3:c.970_971dup	p.Met324IlefsTer2	p.M324Ifs*2	ENST00000359651		323	-/AT	7/8	1	2	FACETS	0.88	0.761	1	0.88	0.761	1	CLONAL	1	TRUE	1	0.40062411660216	2		853	329	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49430916	49430916	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	38	548	0	ENST00000301067.7:c.10223C>G	p.Pro3408Arg	p.P3408R	ENST00000301067	NM_003482.3	3408	cCa/cGa	34/54	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.40062411660216	2		548	166	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041459	42041459	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1389544895	NA	P-0053819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	127	726	0	ENST00000219905.7:c.5654C>G	p.Ser1885Ter	p.S1885*	ENST00000219905	NM_001164273.1	1885	tCa/tGa	17/24	0.32689176638299	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.40062411660216	2		726	276	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041720	42041720	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	73	573	0	ENST00000219905.7:c.5915C>A	p.Ser1972Tyr	p.S1972Y	ENST00000219905	NM_001164273.1	1972	tCt/tAt	17/24	0.32689176638299	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	2	TRUE	0	0.40062411660216	2		573	177	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339468	339468	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	79	1170	0	ENST00000262320.3:c.2434G>C	p.Glu812Gln	p.E812Q	ENST00000262320	NM_003502.3	812	Gag/Cag	10/11	0.186871213651968	1	FACETS	0.746	0.659	0.838	0.746	0.659	0.838	INDETERMINATE	1	TRUE	0	0.40062411660216	1		1170	423	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339557	339557	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1269809545	NA	P-0053819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	90	1162	1	ENST00000262320.3:c.2345G>A	p.Ser782Asn	p.S782N	ENST00000262320	NM_003502.3	782	aGc/aAc	10/11	0.186871213651968	1	FACETS	0.802	0.715	0.894	0.802	0.715	0.894	INDETERMINATE	1	TRUE	0	0.40062411660216	1		1163	448	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545837	41545837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	478	1013	0	ENST00000263253.7:c.2452C>T	p.His818Tyr	p.H818Y	ENST00000263253	NM_001429.3	818	Cac/Tac	14/31	0.40062411660216	9	FACETS	1	0.982	1			1	CLONAL	7	TRUE	NA	0.40062411660216	9		1013	798	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393285	393285	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs934099606	NA	P-0053819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	43	752	1	ENST00000380956.4:c.133G>C	p.Glu45Gln	p.E45Q	ENST00000380956	NM_001195286.1	45	Gag/Cag	2/9	1	2	FACETS	0.665	0.558	0.781	0.665	0.558	0.781	SUBCLONAL	1	TRUE	1	0.40062411660216	2		753	323	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724721	112724743	+	frameshift_variant	Frame_Shift_Del	DEL	ATCGTATAACTACTGTGGAAAAG	ATCGTATAACTACTGTGGAAAAG	TAC	novel	NA	P-0053819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	42	558	2	ENST00000369452.4:c.605_627delinsTAC	p.Asn202IlefsTer13	p.N202Ifs*13	ENST00000369452	NM_007373.3	202	aATCGTATAACTACTGTGGAAAAG/aTAC	2/9	0.399198111997094	1	FACETS	0.798	0.674	0.934	0.798	0.674	0.934	CLONAL	1	TRUE	0	0.40062411660216	1		560	210	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0053820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	343	465	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.656890167311914	4	FACETS	0.908	0.878	0.937	0.908	0.878	0.937	CLONAL	4	TRUE	0	0.691586250261667	4		465	462	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114229	115114229	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	419	531	0	ENST00000257566.3:c.988A>G	p.Lys330Glu	p.K330E	ENST00000257566	NM_016569.3	330	Aaa/Gaa	6/8	0.656890167311914	4	FACETS	0.832	0.793	0.872	0.416	0.396	0.436	CLONAL	2	TRUE	0	0.691586250261667	4		531	1232	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639116	3639116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs112694849	NA	P-0053820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	343	760	0	ENST00000294008.3:c.4523C>T	p.Ser1508Leu	p.S1508L	ENST00000294008	NM_032444.2	1508	tCg/tTg	12/15	0.691586250261667	3	FACETS	0.875	0.826	0.925	0.437	0.413	0.463	CLONAL	1	TRUE	1	0.691586250261667	3		760	1526	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858531	9858531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	189	488	0	ENST00000330684.3:c.2870G>A	p.Gly957Glu	p.G957E	ENST00000330684	NM_001134407.1	957	gGa/gAa	13/13	0.691586250261667	3	FACETS	0.895	0.828	0.964	0.447	0.414	0.482	CLONAL	1	TRUE	1	0.691586250261667	3		488	822	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348566	56348566	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	52	253	0	ENST00000348428.3:c.374C>T	p.Pro125Leu	p.P125L	ENST00000348428	NM_006785.3	125	cCa/cTa	2/17	0.404305832574329	2	FACETS	0.414	0.354	0.48	0.207	0.177	0.24	INDETERMINATE	1	TRUE	0	0.691586250261667	2		253	363	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368203	31368203	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	713	717	0	ENST00000328111.2:c.74G>A	p.Gly25Glu	p.G25E	ENST00000328111	NM_006892.3	25	gGg/gAg	2/23	0.444812934622397	5	FACETS	1	0.994	1	0.75	0.723	0.776	CLONAL	2	TRUE	2	0.691586250261667	5		717	1868	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961525	54961525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763948949	NA	P-0053820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	207	442	0	ENST00000312783.6:c.107C>T	p.Pro36Leu	p.P36L	ENST00000312783	NM_198436.1	36	cCa/cTa	4/10	0.691586250261667	4	FACETS	0.799	0.74	0.861	0.4	0.37	0.431	SUBCLONAL	1	TRUE	2	0.691586250261667	4		442	1267	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960059	134960059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	264	560	0	ENST00000398015.3:c.2416G>A	p.Asp806Asn	p.D806N	ENST00000398015	NM_004441.4	806	Gac/Aac	13/16	0.5180061116789	1	FACETS	0.697	0.656	0.738	0.697	0.656	0.738	SUBCLONAL	1	TRUE	0	0.691586250261667	1		560	717	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261523	142261523	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs377698546	NA	P-0053820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	83	247	0	ENST00000350721.4:c.3434T>C	p.Ile1145Thr	p.I1145T	ENST00000350721	NM_001184.3	1145	aTt/aCt	17/47	1	2	FACETS	0.762	0.679	0.849	0.762	0.679	0.849	SUBCLONAL	1	TRUE	1	0.691586250261667	2		247	315	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0053820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	273	440	0				ENST00000310581	NM_198253.2	-/1132			0.679172878700955	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.691586250261667	2		440	368	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190369	32190369	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	466	745	0	ENST00000375023.3:c.370C>T	p.Pro124Ser	p.P124S	ENST00000375023	NM_004557.3	124	Ccc/Tcc	3/30	0.23947165125434	4	FACETS	0.935	0.895	0.976	0.935	0.895	0.976	INDETERMINATE	2	TRUE	2	0.691586250261667	4		745	1219	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760714	133760714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755821709	NA	P-0053820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	203	881	2	ENST00000318560.5:c.3037C>T	p.Arg1013Trp	p.R1013W	ENST00000318560	NM_005157.4	1013	Cgg/Tgg	11/11	0.691586250261667	1	FACETS	0.4	0.371	0.431	0.4	0.371	0.431	SUBCLONAL	1	TRUE	0	0.691586250261667	1		883	959	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0053821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	45	478	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.509	0.429	0.598	0.509	0.429	0.598	SUBCLONAL	1	TRUE	1	0.45197318328108	2		478	391	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0053821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	47	533	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.7	0.594	0.816	0.7	0.594	0.816	SUBCLONAL	1	TRUE	1	0.45197318328108	2		533	297	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	100	755	0	ENST00000267101.3:c.273G>A	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atA	3/28	1	2	FACETS	0.492	0.439	0.549	0.492	0.439	0.549	SUBCLONAL	1	TRUE	1	0.45197318328108	2		755	899	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682991	241682991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226883651	NA	P-0053821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	123	606	0	ENST00000366560.3:c.32C>T	p.Ser11Leu	p.S11L	ENST00000366560	NM_000143.3	11	tCg/tTg	1/10	0.45197318328108	3	FACETS	0.8	0.723	0.881	0.4	0.361	0.441	SUBCLONAL	1	TRUE	1	0.45197318328108	3		606	834	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120842	115120842	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	84	645	0	ENST00000257566.3:c.164C>T	p.Ser55Leu	p.S55L	ENST00000257566	NM_016569.3	55	tCg/tTg	1/8	1	2	FACETS	0.589	0.521	0.662	0.589	0.521	0.662	SUBCLONAL	1	TRUE	1	0.45197318328108	2		645	631	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860254	151860254	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	148	532	0	ENST00000262189.6:c.10408C>T	p.Gln3470Ter	p.Q3470*	ENST00000262189	NM_170606.2	3470	Cag/Tag	43/59	NA	2	FACETS	1	0.96	1			1	INDETERMINATE	1	TRUE	NA	0.45197318328108	2		532	608	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526886	31526886	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	102	891	0	ENST00000344624.3:c.154C>T	p.Gln52Ter	p.Q52*	ENST00000344624		52	Caa/Taa	2/33	1	2	FACETS	0.474	0.423	0.528	0.474	0.423	0.528	SUBCLONAL	1	TRUE	1	0.45197318328108	2		891	953	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40685704	40685704	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	50	389	0	ENST00000249776.8:c.857G>C	p.Arg286Thr	p.R286T	ENST00000249776	NM_033286.3	286	aGa/aCa	9/9	1	2	FACETS	0.515	0.437	0.599	0.515	0.437	0.599	SUBCLONAL	1	TRUE	1	0.45197318328108	2		389	430	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352537	89352537	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1029611205	NA	P-0053821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	123	748	0	ENST00000301030.4:c.802G>A	p.Glu268Lys	p.E268K	ENST00000301030	NM_001256183.1	268	Gag/Aag	8/13	1	2	FACETS	0.59	0.533	0.651	0.59	0.533	0.651	SUBCLONAL	1	TRUE	1	0.45197318328108	2		748	922	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552237	29552237	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	48	411	0	ENST00000356175.3:c.1970C>T	p.Ser657Phe	p.S657F	ENST00000356175	NM_000267.3	657	tCt/tTt	17/57	1	2	FACETS	0.472	0.399	0.552	0.472	0.399	0.552	SUBCLONAL	1	TRUE	1	0.45197318328108	2		411	450	SUCCESS
APC	324	MSKCC	GRCh37	5	112175084	112175084	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	35	164	0	ENST00000257430.4:c.3793G>C	p.Glu1265Gln	p.E1265Q	ENST00000257430	NM_000038.5	1265	Gaa/Caa	16/16	1	2	FACETS	0.714	0.59	0.851	0.714	0.59	0.851	SUBCLONAL	1	TRUE	1	0.45197318328108	2		164	217	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845784	151845784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	100	740	0	ENST00000262189.6:c.13228G>A	p.Asp4410Asn	p.D4410N	ENST00000262189	NM_170606.2	4410	Gat/Aat	52/59	NA	2	FACETS	0.539	0.481	0.601			1	INDETERMINATE	1	TRUE	NA	0.45197318328108	2		740	821	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0053823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	155	762	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	1	2	FACETS	0.806	0.737	0.879	0.806	0.737	0.879	CLONAL	1	TRUE	1	0.359764634725565	2		762	1069	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0053823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	18	359	1	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	0.322	0.242	0.416	0.322	0.242	0.416	SUBCLONAL	1	TRUE	1	0.359764634725565	2		360	311	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101228	27101229	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0053823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	81	591	0	ENST00000324856.7:c.4510_4511del	p.Met1504AspfsTer3	p.M1504Dfs*3	ENST00000324856	NM_006015.4	1504	ATg/g	18/20	1	2	FACETS	0.476	0.418	0.538	0.476	0.418	0.538	SUBCLONAL	1	TRUE	1	0.359764634725565	2		591	946	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33446588	33446588	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	141	708	0	ENST00000345365.6:c.45G>C	p.Glu15Asp	p.E15D	ENST00000345365	NM_002878.3	15	gaG/gaC	1/10	1	2	FACETS	0.737	0.67	0.807	0.737	0.67	0.807	SUBCLONAL	1	TRUE	1	0.359764634725565	2		708	1064	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80149965	80149966	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0053823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	13	263	0	ENST00000265081.6:c.2831_2832insGA	p.Asn944LysfsTer14	p.N944Kfs*14	ENST00000265081	NM_002439.4	944	aat/aAGat	21/24	1	2	FACETS	0.321	0.229	0.434	0.321	0.229	0.434	SUBCLONAL	1	TRUE	1	0.359764634725565	2		263	225	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508121	106508121	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	107	226	0	ENST00000359195.3:c.115C>A	p.Pro39Thr	p.P39T	ENST00000359195	NM_002649.2	39	Ccc/Acc	2/11	0.326805042487688	3	FACETS	0.751	0.678	0.829	0.751	0.678	0.829	SUBCLONAL	2	TRUE	1	0.359764634725565	3		226	467	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	110	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.965	0.883	1	1	0.991	1	CLONAL	3	TRUE	1	0.29	2		276	262	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	90	547	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.637238040941711	1	FACETS	0.983	0.874	1	0.983	0.874	1	CLONAL	1	TRUE	0	0.29	1		547	540	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440372	52440372	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	95	578	0	ENST00000460680.1:c.680G>C	p.Arg227Pro	p.R227P	ENST00000460680	NM_004656.3	227	cGc/cCc	9/17	1	2	FACETS	0.788	0.701	0.881	0.788	0.701	0.881	SUBCLONAL	1	TRUE	1	0.29	2		578	831	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	404	1176	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	1	0.29	2		1176	1164	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652097	36652098	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	151	874	0	ENST00000244741.5:c.222dup	p.Lys75GlnfsTer14	p.K75Qfs*14	ENST00000244741	NM_000389.4	73	-/C	2/3	1	2	FACETS	0.851	0.777	0.93	0.851	0.777	0.93	CLONAL	1	TRUE	1	0.29	2		874	1223	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872213	45872213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	439	687	0	ENST00000391945.4:c.221C>T	p.Ser74Leu	p.S74L	ENST00000391945	NM_000400.3	74	tCa/tTa	4/23	1	2	FACETS	1	0.987	1	1	0.998	1	CLONAL	3	TRUE	1	0.29	2		687	946	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481620	56481620	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	344	635	0	ENST00000267101.3:c.655T>C	p.Phe219Leu	p.F219L	ENST00000267101	NM_001982.3	219	Ttt/Ctt	6/28	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.29	2		635	1033	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807335	1807335	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1448843898	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	115	857	0	ENST00000260795.2:c.1584G>A	p.Met528Ile	p.M528I	ENST00000260795		528	atG/atA	11/17	1	2	FACETS	0.743	0.667	0.822	0.743	0.667	0.822	SUBCLONAL	1	TRUE	1	0.29	2		857	1068	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112602	115112602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs865915137	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	181	799	3	ENST00000257566.3:c.1138G>A	p.Glu380Lys	p.E380K	ENST00000257566	NM_016569.3	380	Gag/Aag	7/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.29	2		802	1187	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243472	46243472	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	113	348	0	ENST00000334344.6:c.1825C>T	p.Gln609Ter	p.Q609*	ENST00000334344	NM_152641.2	609	Cag/Tag	14/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.29	2		348	689	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502191	157502191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs940353111	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	111	473	0	ENST00000346085.5:c.3224G>A	p.Arg1075Gln	p.R1075Q	ENST00000346085	NM_020732.3	1075	cGa/cAa	12/20	1	2	FACETS	0.93	0.836	1	0.93	0.836	1	CLONAL	1	TRUE	1	0.29	2		473	823	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627685	14627685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	107	648	0	ENST00000254322.2:c.385G>A	p.Asp129Asn	p.D129N	ENST00000254322	NM_006145.1	129	Gac/Aac	2/3	1	2	FACETS	0.793	0.711	0.882	0.793	0.711	0.882	SUBCLONAL	1	TRUE	1	0.29	2		648	930	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	39	481	0	ENST00000346208.3:c.878T>G	p.Met293Arg	p.M293R	ENST00000346208		293	aTg/aGg	4/6	1	2	FACETS	0.34	0.281	0.407	0.34	0.281	0.407	SUBCLONAL	1	TRUE	1	0.29	2		481	791	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626694	28626694	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	41	390	0	ENST00000241453.7:c.602C>T	p.Ser201Leu	p.S201L	ENST00000241453	NM_004119.2	201	tCa/tTa	5/24	1	2	FACETS	0.45	0.374	0.535	0.45	0.374	0.535	SUBCLONAL	1	TRUE	1	0.29	2		390	628	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836762	151836762	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	60	408	0	ENST00000262189.6:c.14458C>T	p.Gln4820Ter	p.Q4820*	ENST00000262189	NM_170606.2	4820	Cag/Tag	56/59	1	2	FACETS	0.629	0.541	0.724	0.629	0.541	0.724	SUBCLONAL	1	TRUE	1	0.29	2		408	658	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983049	201983049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	136	851	0	ENST00000359651.3:c.898G>A	p.Glu300Lys	p.E300K	ENST00000359651		300	Gaa/Aaa	7/8	1	2	FACETS	0.746	0.676	0.819	0.746	0.676	0.819	SUBCLONAL	1	TRUE	1	0.29	2		851	1258	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008964	152008964	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	73	404	0	ENST00000262189.6:c.658C>T	p.Gln220Ter	p.Q220*	ENST00000262189	NM_170606.2	220	Caa/Taa	5/59	1	2	FACETS	0.75	0.656	0.852	0.75	0.656	0.852	SUBCLONAL	1	TRUE	1	0.29	2		404	671	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624446	21624446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775015037	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	319	529	0	ENST00000421138.2:c.1583G>A	p.Arg528Lys	p.R528K	ENST00000421138		528	aGa/aAa	14/16	1	2	FACETS	1	0.98	1	1	0.996	1	CLONAL	2	TRUE	1	0.29	2		529	1024	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212200	36212200	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	260	621	0	ENST00000222270.7:c.1951C>T	p.Gln651Ter	p.Q651*	ENST00000222270	NM_014727.1	651	Cag/Tag	3/37	1	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	2	TRUE	1	0.29	2		621	782	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046415	128046415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749390618	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	50	340	0	ENST00000285398.2:c.848G>A	p.Arg283His	p.R283H	ENST00000285398	NM_000122.1	283	cGt/cAt	7/15	1	2	FACETS	0.657	0.557	0.766	0.657	0.557	0.766	SUBCLONAL	1	TRUE	1	0.29	2		340	525	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440379	52440379	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	43	540	0	ENST00000460680.1:c.673G>T	p.Asp225Tyr	p.D225Y	ENST00000460680	NM_004656.3	225	Gac/Tac	9/17	1	2	FACETS	0.38	0.317	0.451	0.38	0.317	0.451	SUBCLONAL	1	TRUE	1	0.29	2		540	780	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727095	40727095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	204	534	0	ENST00000373198.4:c.3869C>T	p.Ser1290Phe	p.S1290F	ENST00000373198	NM_133170.3	1290	tCt/tTt	28/32	0.3	1	FACETS	0.815	0.758	0.873	1	0.992	1	CLONAL	2	TRUE	0	0.29	1		534	738	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699388	117699388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	90	485	0	ENST00000369458.3:c.253G>A	p.Glu85Lys	p.E85K	ENST00000369458	NM_024626.3	85	Gaa/Aaa	3/6	1	2	FACETS	0.717	0.635	0.804	0.717	0.635	0.804	SUBCLONAL	1	TRUE	1	0.29	2		485	866	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551858	150551858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	42	259	0	ENST00000369026.2:c.149G>A	p.Gly50Glu	p.G50E	ENST00000369026	NM_021960.4	50	gGa/gAa	1/3	1	2	FACETS	0.83	0.695	0.979	0.83	0.695	0.979	CLONAL	1	TRUE	1	0.29	2		259	349	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851289	156851289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	407	825	0	ENST00000524377.1:c.2246C>T	p.Pro749Leu	p.P749L	ENST00000524377	NM_002529.3	749	cCa/cTa	17/17	1	2	FACETS	1	0.993	1	1	0.997	1	CLONAL	2	TRUE	1	0.29	2		825	1141	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918476	94918476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	134	455	0	ENST00000536441.1:c.706G>A	p.Asp236Asn	p.D236N	ENST00000536441	NM_144665.3	236	Gat/Aat	5/10	0.292682724622842	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.29	1		455	634	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307487	118307487	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	141	396	0	ENST00000534358.1:c.260C>A	p.Ser87Ter	p.S87*	ENST00000534358	NM_005933.3	87	tCg/tAg	1/36	0.292682724622842	1	FACETS	1	0.969	1	1	0.992	1	CLONAL	2	TRUE	0	0.29	1		396	378	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359353	118359353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	61	248	0	ENST00000534358.1:c.4357G>A	p.Glu1453Lys	p.E1453K	ENST00000534358	NM_005933.3	1453	Gag/Aag	11/36	0.292682724622842	1	FACETS	0.871	0.754	0.997	0.871	0.754	0.997	CLONAL	1	TRUE	0	0.29	1		248	413	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433938	49433938	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	84	993	0	ENST00000301067.7:c.7615C>T	p.Pro2539Ser	p.P2539S	ENST00000301067	NM_003482.3	2539	Cct/Tct	31/54	1	2	FACETS	0.511	0.45	0.577	0.511	0.45	0.577	SUBCLONAL	1	TRUE	1	0.29	2		993	1133	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355826	73355831	+	inframe_deletion	In_Frame_Del	DEL	CCAGGG	CCAGGG	-	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	70	402	0	ENST00000377767.4:c.140_145del	p.Ala47_Leu48del	p.A47_L48del	ENST00000377767	NM_014953.3	47	gCCCTGGag/gag	1/21	1	2	FACETS	0.848	0.74	0.965	0.848	0.74	0.965	CLONAL	1	TRUE	1	0.29	2		402	569	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131638	2131638	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	234	834	0	ENST00000219476.3:c.3653C>G	p.Pro1218Arg	p.P1218R	ENST00000219476	NM_000548.3	1218	cCt/cGt	31/42	0.216153940998459	2	FACETS	0.798	0.745	0.853	0.798	0.745	0.853	SUBCLONAL	2	TRUE	0	0.29	2		834	1011	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785714	50785714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	66	497	1	ENST00000398568.2:c.704G>A	p.Arg235Lys	p.R235K	ENST00000398568	NM_001042412.1	235	aGa/aAa	4/18	1	2	FACETS	0.586	0.507	0.671	0.586	0.507	0.671	SUBCLONAL	1	TRUE	1	0.29	2		498	777	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004928	16004928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	104	667	0	ENST00000268712.3:c.2326G>A	p.Glu776Lys	p.E776K	ENST00000268712	NM_006311.3	776	Gaa/Aaa	20/46	1	2	FACETS	0.733	0.655	0.816	0.733	0.655	0.816	SUBCLONAL	1	TRUE	1	0.29	2		667	979	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068390	16068390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	44	40	0	ENST00000268712.3:c.521C>T	p.Ser174Leu	p.S174L	ENST00000268712	NM_006311.3	174	tCa/tTa	5/46	1	2	FACETS	1	0.901	1	1	0.98	1	CLONAL	3	TRUE	1	0.29	2		40	97	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677896	58677896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	226	519	0	ENST00000305921.3:c.121C>T	p.Pro41Ser	p.P41S	ENST00000305921	NM_003620.3	41	Ccg/Tcg	1/6	1	2	FACETS	1	0.983	1	1	0.995	1	CLONAL	2	TRUE	1	0.29	2		519	681	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62009557	62009557	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	84	704	0	ENST00000392795.3:c.65C>T	p.Ser22Leu	p.S22L	ENST00000392795	NM_001039933.1	22	tCa/tTa	1/6	1	2	FACETS	0.629	0.554	0.709	0.629	0.554	0.709	SUBCLONAL	1	TRUE	1	0.29	2		704	921	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211945	36211945	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	425	821	0	ENST00000222270.7:c.1696C>A	p.Pro566Thr	p.P566T	ENST00000222270	NM_014727.1	566	Ccc/Acc	3/37	1	2	FACETS	1	0.993	1	1	0.997	1	CLONAL	2	TRUE	1	0.29	2		821	1194	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143084	30143084	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	133	881	1	ENST00000389048.3:c.442G>A	p.Glu148Lys	p.E148K	ENST00000389048	NM_004304.4	148	Gag/Aag	1/29	1	2	FACETS	0.752	0.681	0.827	0.752	0.681	0.827	SUBCLONAL	1	TRUE	1	0.29	2		882	1220	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96930972	96930972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437924634	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	80	615	1	ENST00000258439.3:c.148G>A	p.Glu50Lys	p.E50K	ENST00000258439	NM_001193304.2	50	Gag/Aag	2/4	1	2	FACETS	0.626	0.55	0.708	0.626	0.55	0.708	SUBCLONAL	1	TRUE	1	0.29	2		616	881	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266144	198266144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	200	418	0	ENST00000335508.6:c.2476G>A	p.Asp826Asn	p.D826N	ENST00000335508	NM_012433.2	826	Gat/Aat	17/25	1	2	FACETS	1	0.953	1	1	0.994	1	CLONAL	2	TRUE	1	0.29	2		418	669	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346698	225346704	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTTTG	TCTTTTG	-	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	38	392	0	ENST00000264414.4:c.1934_1940del	p.Thr645AsnfsTer7	p.T645Nfs*7	ENST00000264414	NM_003590.4	645	aCAAAAGAa/aa	14/16	1	2	FACETS	0.373	0.307	0.447	0.373	0.307	0.447	SUBCLONAL	1	TRUE	1	0.29	2		392	702	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661114	227661114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1427555970	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	123	873	0	ENST00000305123.5:c.2341G>A	p.Glu781Lys	p.E781K	ENST00000305123	NM_005544.2	781	Gag/Aag	1/2	1	2	FACETS	0.732	0.66	0.808	0.732	0.66	0.808	SUBCLONAL	1	TRUE	1	0.29	2		873	1159	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72842103	72842103	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754326459	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	38	237	0	ENST00000325599.8:c.1145A>G	p.Tyr382Cys	p.Y382C	ENST00000325599	NM_018130.2	382	tAc/tGc	10/11	1	2	FACETS	0.644	0.533	0.768	0.644	0.533	0.768	SUBCLONAL	1	TRUE	1	0.29	2		237	407	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374784	149374784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1487193626	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	59	341	0	ENST00000360632.3:c.310G>A	p.Gly104Ser	p.G104S	ENST00000360632	NM_015472.4	104	Ggt/Agt	2/7	1	2	FACETS	0.809	0.697	0.931	0.809	0.697	0.931	CLONAL	1	TRUE	1	0.29	2		341	503	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806119	1806119	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28931614	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	180	933	0	ENST00000260795.2:c.1138G>C	p.Gly380Arg	p.G380R	ENST00000260795		380	Ggg/Cgg	8/17	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.29	2		933	1201	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040097	180040097	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	96	718	0	ENST00000261937.6:c.3345C>G	p.Tyr1115Ter	p.Y1115*	ENST00000261937	NM_182925.4	1115	taC/taG	25/30	0.0818490631562951	0	FACETS	0.57	0.507	0.637			1	INDETERMINATE	1	TRUE	0	0.29	0		718	825	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501213	140501213	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	54	290	0	ENST00000288602.6:c.859G>C	p.Asp287His	p.D287H	ENST00000288602	NM_004333.4	287	Gat/Cat	6/18	1	2	FACETS	0.776	0.663	0.899	0.776	0.663	0.899	SUBCLONAL	1	TRUE	1	0.29	2		290	480	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950407	68950407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757702693	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	50	319	0	ENST00000288368.4:c.719C>T	p.Thr240Ile	p.T240I	ENST00000288368	NM_024870.2	240	aCt/aTt	7/40	1	2	FACETS	0.569	0.482	0.665	0.569	0.482	0.665	SUBCLONAL	1	TRUE	1	0.29	2		319	606	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781040	135781040	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	74	617	0	ENST00000298552.3:c.1925C>T	p.Ser642Phe	p.S642F	ENST00000298552	NM_001162426.1	642	tCt/tTt	15/23	0.292682724622842	1	FACETS	0.551	0.481	0.626	0.551	0.481	0.626	SUBCLONAL	1	TRUE	0	0.29	1		617	792	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328433	137328441	+	inframe_deletion	In_Frame_Del	DEL	GCTGGAGGC	GCTGGAGGC	-	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	245	844	0	ENST00000481739.1:c.1364_1372del	p.Leu455_Ala457del	p.L455_A457del	ENST00000481739	NM_002957.4	454	atGCTGGAGGCg/atg	10/10	0.292682724622842	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.29	1		844	1026	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942728	44942728	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	296	217	0	ENST00000377967.4:c.3308T>C	p.Leu1103Pro	p.L1103P	ENST00000377967	NM_021140.2	1103	cTg/cCg	23/29	1	1	FACETS	1	0.975	1	1	0.997	1	CLONAL	4	TRUE	0	0.29	1		217	428	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195168	123195168	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	24	215	0	ENST00000218089.9:c.1512del	p.Glu505SerfsTer9	p.E505Sfs*9	ENST00000218089	NM_001042749.1	504	gAa/ga	16/35	1	1	FACETS	0.358	0.28	0.448	0.358	0.28	0.448	SUBCLONAL	1	TRUE	0	0.29	1		215	395	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200230	123200244	+	inframe_deletion	In_Frame_Del	DEL	ACTCACTATGTAATC	ACTCACTATGTAATC	-	novel	NA	P-0053825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	86	231	0	ENST00000218089.9:c.2209_2223del	p.Thr737_Ile741del	p.T737_I741del	ENST00000218089	NM_001042749.1	737	ACTCACTATGTAATC/-	23/35	1	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.29	1		231	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882025	NA	P-0053826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	257	785	0	ENST00000269305.4:c.646G>T	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ttg	6/11	0.116635038875769	3	FACETS	1	0.969	1			1	INDETERMINATE	2	TRUE	NA	0.27000831224128	3		785	1023	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984661	72984661	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780299674	NA	P-0053826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	94	877	0	ENST00000268489.5:c.2923G>A	p.Glu975Lys	p.E975K	ENST00000268489	NM_006885.3	975	Gag/Aag	3/10	0.163527486638273	4	FACETS	0.701	0.621	0.786	0.35	0.31	0.393	SUBCLONAL	1	TRUE	2	0.27000831224128	4		877	1262	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881324	111881324	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0053826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	41	369	0	ENST00000393256.3:c.2T>C	p.Met1?	p.M1?	ENST00000393256	NM_006538.4	1	aTg/aCg	2/4	0.18555926865904	3	FACETS	0.8	0.667	0.947	0.4	0.333	0.474	CLONAL	1	TRUE	1	0.27000831224128	3		369	431	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417551	139417564	+	frameshift_variant	Frame_Shift_Del	DEL	GGCAGATGTAGGAG	GGCAGATGTAGGAG	-	novel	NA	P-0053826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	283	1026	0	ENST00000277541.6:c.480_493del	p.Ser161LeufsTer90	p.S161Lfs*90	ENST00000277541	NM_017617.3	160	gcCTCCTACATCTGCCac/gcac	4/34	0.27000831224128	3	FACETS	0.882	0.827	0.938	0.882	0.827	0.938	CLONAL	2	TRUE	1	0.27000831224128	3		1026	1349	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888779	76888779	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	22	491	1	ENST00000373344.5:c.5050G>A	p.Glu1684Lys	p.E1684K	ENST00000373344	NM_000489.3	1684	Gag/Aag	19/35	0.116635038875769	3	FACETS	0.573	0.444	0.722			1	INDETERMINATE	1	TRUE	NA	0.27000831224128	3		492	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0053827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	160	866	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.170972320482112	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.170972320482112	1		867	1280	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0053827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	43	570	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.170972320482112	2		570	414	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0053827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	39	334	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.170972320482112	2		334	361	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0053827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	30	248	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.170972320482112	2		248	241	SUCCESS
APC	324	MSKCC	GRCh37	5	112173968	112173968	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs199740875	NA	P-0053827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	25	305	0	ENST00000257430.4:c.2677G>T	p.Glu893Ter	p.E893*	ENST00000257430	NM_000038.5	893	Gaa/Taa	16/16	1	2	FACETS	0.991	0.783	1	0.991	0.783	1	CLONAL	1	TRUE	1	0.170972320482112	2		305	295	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9770571	9770571	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143116020	NA	P-0053827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	122	849	0	ENST00000377346.4:c.58G>A	p.Val20Ile	p.V20I	ENST00000377346	NM_005026.3	20	Gtt/Att	3/24	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.170972320482112	2		849	1182	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	32	556	1	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	1	2	FACETS	0.875	0.71	1	0.875	0.71	1	CLONAL	1	TRUE	1	0.170972320482112	2		557	428	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857020	9857020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555481892	NA	P-0053827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	31	259	1	ENST00000330684.3:c.4381G>A	p.Glu1461Lys	p.E1461K	ENST00000330684	NM_001134407.1	1461	Gaa/Aaa	13/13	1	2	FACETS	0.759	0.617	0.917	1	0.944	1	CLONAL	2	TRUE	1	0.170972320482112	2		260	239	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160414	108160414	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1469317936	NA	P-0053827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	26	272	0	ENST00000278616.4:c.4322T>C	p.Ile1441Thr	p.I1441T	ENST00000278616	NM_000051.3	1441	aTa/aCa	29/63	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.170972320482112	2		272	250	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0053828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	128	258	0				ENST00000310581	NM_198253.2	-/1132			0.63157107633209	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.63157107633209	1		258	203	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976476	25976476	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	204	357	0	ENST00000435504.4:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000435504		357	Cga/Tga	11/13	0.380435146006255	3	FACETS	0.91	0.854	0.967	0.91	0.854	0.967	CLONAL	2	TRUE	1	0.63157107633209	3		357	467	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0053828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	932	614	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.63157107633209	7	FACETS	1	0.996	1			1	CLONAL	5	TRUE	NA	0.63157107633209	7		614	1410	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811664	102811664	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0053828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	101	764	0	ENST00000307046.8:c.520A>T	p.Lys174Ter	p.K174*	ENST00000307046	NM_001111285.1	174	Aag/Tag	4/4	0.314519079681617	2	FACETS	0.479	0.428	0.532	0.239	0.214	0.266	INDETERMINATE	1	TRUE	0	0.63157107633209	2		764	668	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024380	31024380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201302084	NA	P-0053828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	200	689	0	ENST00000375687.4:c.3865C>T	p.Arg1289Trp	p.R1289W	ENST00000375687	NM_015338.5	1289	Cgg/Tgg	13/13	0.255308784224641	4	FACETS	0.906	0.846	0.968	0.906	0.846	0.968	INDETERMINATE	2	TRUE	2	0.63157107633209	4		689	570	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705240	52705240	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	152	604	0	ENST00000322088.6:c.122C>T	p.Ala41Val	p.A41V	ENST00000322088	NM_014225.5	41	gCc/gTc	2/15	0.214541482214029	3	FACETS	1	0.981	1	0.605	0.557	0.655	INDETERMINATE	1	TRUE	1	0.63157107633209	3		604	523	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667405	241667405	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1254962869	NA	P-0053828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	201	462	0	ENST00000366560.3:c.1045C>G	p.Pro349Ala	p.P349A	ENST00000366560	NM_000143.3	349	Cct/Gct	7/10	0.291844422095884	4	FACETS	0.898	0.838	0.96	0.898	0.838	0.96	INDETERMINATE	2	TRUE	2	0.63157107633209	4		462	578	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8252031	8252031	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	229	788	0	ENST00000335790.3:c.46C>T	p.Gln16Ter	p.Q16*	ENST00000335790	NM_002315.2	16	Cag/Tag	2/4	0.17380469633256	4	FACETS	0.984	0.924	1	0.984	0.924	1	INDETERMINATE	2	TRUE	2	0.63157107633209	4		788	601	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005586	42005586	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	263	407	0	ENST00000219905.7:c.3322C>T	p.Pro1108Ser	p.P1108S	ENST00000219905	NM_001164273.1	1108	Cca/Tca	9/24	0.63157107633209	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.63157107633209	2		407	387	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701210	43701210	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	259	587	0	ENST00000382044.4:c.5485C>T	p.Pro1829Ser	p.P1829S	ENST00000382044	NM_001141980.1	1829	Cct/Tct	26/28	0.63157107633209	2	FACETS	0.972	0.927	1	0.972	0.927	1	CLONAL	2	TRUE	0	0.63157107633209	2		587	422	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9927991	9927991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	147	414	0	ENST00000330684.3:c.1748G>A	p.Gly583Glu	p.G583E	ENST00000330684	NM_001134407.1	583	gGa/gAa	8/13	0.255308784224641	4	FACETS	0.844	0.777	0.913	0.844	0.777	0.913	INDETERMINATE	2	TRUE	2	0.63157107633209	4		414	450	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422973	45422973	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	57	370	0	ENST00000262160.6:c.155T>A	p.Leu52Gln	p.L52Q	ENST00000262160	NM_005901.5	52	cTa/cAa	2/11	0.300907320010056	1	FACETS	0.417	0.36	0.478	0.417	0.36	0.478	INDETERMINATE	1	TRUE	0	0.63157107633209	1		370	296	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226266	2226266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	204	955	0	ENST00000398665.3:c.3746C>T	p.Ser1249Phe	p.S1249F	ENST00000398665	NM_032482.2	1249	tCc/tTc	27/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.63157107633209	2		955	564	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300135	15300135	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	251	773	0	ENST00000263388.2:c.1141C>T	p.Pro381Ser	p.P381S	ENST00000263388	NM_000435.2	381	Ccc/Tcc	7/33	0.214541482214029	3	FACETS	0.795	0.748	0.842	0.795	0.748	0.842	INDETERMINATE	2	TRUE	1	0.63157107633209	3		773	658	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458480	12458480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	190	650	0	ENST00000287820.6:c.1097G>A	p.Gly366Glu	p.G366E	ENST00000287820	NM_015869.4	366	gGg/gAg	6/7	1	2	FACETS	0.969	0.9	1	0.969	0.9	1	CLONAL	1	TRUE	1	0.63157107633209	2		650	621	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752758	128752758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	165	207	0	ENST00000377970.2:c.919C>T	p.His307Tyr	p.H307Y	ENST00000377970	NM_002467.4	307	Cac/Tac	3/3	0.63157107633209	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.63157107633209	3		207	303	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555525585	NA	P-0053829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	165	464	0	ENST00000269305.4:c.673-2A>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.612172739283874	1	FACETS	0.995	0.926	1	0.995	0.926	1	CLONAL	1	TRUE	0	0.612172739283874	1		464	376	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711311	114711311	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	107	393	0	ENST00000543371.1:c.326C>T	p.Pro109Leu	p.P109L	ENST00000543371	NM_001198531.1	109	cCc/cTc	3/14	1	2	FACETS	0.846	0.765	0.932	0.846	0.765	0.932	CLONAL	1	TRUE	1	0.612172739283874	2		393	413	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573583	48573591	+	inframe_deletion	In_Frame_Del	DEL	CTTTAATAA	CTTTAATAA	-	novel	NA	P-0053829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	68	287	0	ENST00000342988.3:c.168_176del	p.Leu57_Thr59del	p.L57_T59del	ENST00000342988	NM_005359.5	56	tCTTTAATAAca/tca	2/12	0.612172739283874	1	FACETS	0.816	0.724	0.911	0.816	0.724	0.911	CLONAL	1	TRUE	0	0.612172739283874	1		287	189	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103775	47103777	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0053829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	209	497	0	ENST00000409792.3:c.6169_6171del	p.Pro2057del	p.P2057del	ENST00000409792	NM_014159.6	2057	CCT/-	14/21	1	2	FACETS	0.917	0.854	0.981	0.917	0.854	0.981	CLONAL	1	TRUE	1	0.612172739283874	2		497	745	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86642514	86642514	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	84	292	0	ENST00000274376.6:c.1075C>T	p.Gln359Ter	p.Q359*	ENST00000274376	NM_002890.2	359	Cag/Tag	7/25	0.612172739283874	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.612172739283874	1		292	151	SUCCESS
YES1	7525	MSKCC	GRCh37	18	742954	742954	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	70	311	0	ENST00000314574.4:c.1024G>T	p.Glu342Ter	p.E342*	ENST00000314574	NM_005433.3	342	Gaa/Taa	8/12	1	2	FACETS	0.775	0.679	0.878	0.775	0.679	0.878	SUBCLONAL	1	TRUE	1	0.453685123485747	2		311	398	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0053830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	106	650	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.453685123485747	2		650	427	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222983	1222983	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs398123406	NA	P-0053830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	139	697	1	ENST00000326873.7:c.921-1G>T		p.X307_splice	ENST00000326873	NM_000455.4	307			0.453685123485747	1	FACETS	0.997	0.915	1	0.997	0.915	1	CLONAL	1	TRUE	0	0.453685123485747	1		698	475	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600326	10600326	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	135	792	0	ENST00000171111.5:c.1529C>T	p.Ala510Val	p.A510V	ENST00000171111	NM_203500.1	510	gCa/gTa	4/6	0.453685123485747	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.453685123485747	1		792	442	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111965564	111965564	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	55	222	0	ENST00000375549.3:c.350G>T	p.Gly117Val	p.G117V	ENST00000375549	NM_003002.3	117	gGg/gTg	4/4	1	2	FACETS	0.99	0.855	1	0.99	0.855	1	CLONAL	1	TRUE	1	0.453685123485747	2		222	245	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175891	24175891	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1555881586	NA	P-0053830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	93	585	0	ENST00000263121.7:c.1118+1G>A		p.X373_splice	ENST00000263121	NM_003073.3	373			0.453685123485747	1	FACETS	0.868	0.779	0.962	0.868	0.779	0.962	CLONAL	1	TRUE	0	0.453685123485747	1		585	365	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163837	32163837	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	113	694	0	ENST00000375023.3:c.5389G>T	p.Asp1797Tyr	p.D1797Y	ENST00000375023	NM_004557.3	1797	Gac/Tac	30/30	1	2	FACETS	0.88	0.795	0.97	0.88	0.795	0.97	CLONAL	1	TRUE	1	0.453685123485747	2		694	566	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347845	128347845	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	192	670	1	ENST00000265960.3:c.660G>T	p.Glu220Asp	p.E220D	ENST00000265960	NM_001006617.1	220	gaG/gaT	5/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.453685123485747	2		671	651	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0053831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	190	720	10	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.581	0.537	0.627	0.581	0.537	0.627	SUBCLONAL	1	TRUE	1	0.703625354976406	2		730	929	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821890	72821890	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	168	445	1	ENST00000268489.5:c.10285del	p.Arg3429ValfsTer56	p.R3429Vfs*56	ENST00000268489	NM_006885.3	3429	Cgt/gt	10/10	1	2	FACETS	0.708	0.653	0.766	0.708	0.653	0.766	SUBCLONAL	1	TRUE	1	0.703625354976406	2		446	674	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	120	484	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.582	0.527	0.64	0.582	0.527	0.64	SUBCLONAL	1	TRUE	1	0.703625354976406	2		484	586	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	154	445	0	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.725	0.666	0.786	0.725	0.666	0.786	SUBCLONAL	1	TRUE	1	0.703625354976406	2		445	604	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	215	445	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.703625354976406	2		445	475	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0053831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	104	680	2	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.347	0.31	0.387	0.347	0.31	0.387	SUBCLONAL	1	TRUE	1	0.703625354976406	2		682	851	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0053831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	235	1094	5	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.673	0.628	0.72	0.673	0.628	0.72	SUBCLONAL	1	TRUE	1	0.703625354976406	2		1099	992	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0053831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	249	933	5	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	0.559	0.521	0.597	0.559	0.521	0.597	SUBCLONAL	1	TRUE	1	0.703625354976406	2		938	1267	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0053831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	123	299	0	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	1	2	FACETS	0.75	0.683	0.82	0.75	0.683	0.82	SUBCLONAL	1	TRUE	1	0.703625354976406	2		299	466	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389203	31389203	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs996239307	NA	P-0053831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	162	578	0	ENST00000328111.2:c.2116G>A	p.Asp706Asn	p.D706N	ENST00000328111	NM_006892.3	706	Gac/Aac	19/23	1	2	FACETS	0.606	0.557	0.657	0.606	0.557	0.657	SUBCLONAL	1	TRUE	1	0.703625354976406	2		578	760	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681119	117681120	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs748436511	NA	P-0053831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	115	420	0	ENST00000368508.3:c.3500dup	p.Leu1167PhefsTer26	p.L1167Ffs*26	ENST00000368508	NM_002944.2	1167	tta/ttTa	23/43	1	2	FACETS	0.668	0.605	0.735	0.668	0.605	0.735	SUBCLONAL	1	TRUE	1	0.703625354976406	2		420	489	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0053831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1297	89	924	4	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	1	2	FACETS	0.183	0.161	0.206	0.183	0.161	0.206	SUBCLONAL	1	TRUE	1	0.703625354976406	2		928	1386	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99175934	99175934	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	160	477	1	ENST00000074304.5:c.1850del	p.Pro617LeufsTer18	p.P617Lfs*18	ENST00000074304	NM_001134224.1	616	Ccc/cc	18/26	1	2	FACETS	0.631	0.58	0.684	0.631	0.58	0.684	SUBCLONAL	1	TRUE	1	0.703625354976406	2		478	721	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106543549	106543549	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs139534654	NA	P-0053831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	79	248	0	ENST00000369096.4:c.351A>G	p.Ile117Met	p.I117M	ENST00000369096	NM_001198.3	117	atA/atG	3/7	1	2	FACETS	0.727	0.645	0.812	0.727	0.645	0.812	SUBCLONAL	1	TRUE	1	0.703625354976406	2		248	309	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750390	41750390	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	171	474	2	ENST00000226382.2:c.238G>A	p.Ala80Thr	p.A80T	ENST00000226382	NM_003924.3	80	Gca/Aca	1/3	1	2	FACETS	0.756	0.698	0.816	0.756	0.698	0.816	SUBCLONAL	1	TRUE	1	0.703625354976406	2		476	643	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527742	157527742	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	69	490	1	ENST00000346085.5:c.5471del	p.Gly1824ValfsTer27	p.G1824Vfs*27	ENST00000346085	NM_020732.3	1823	Ggg/gg	20/20	1	2	FACETS	0.281	0.244	0.32	0.281	0.244	0.32	SUBCLONAL	1	TRUE	1	0.703625354976406	2		491	699	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100095	157100116	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCGGCGGCAGCAGCAGGA	GGCGGCGGCGGCAGCAGCAGGA	-	novel	NA	P-0053831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	25	33	0	ENST00000346085.5:c.1044_1065del	p.Gly351MetfsTer11	p.G351Mfs*11	ENST00000346085	NM_020732.3	344	gcGGCGGCGGCGGCAGCAGCAGGA/gc	1/20	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.703625354976406	2		33	64	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288811	15288811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	108	164	0	ENST00000263388.2:c.3928G>A	p.Gly1310Arg	p.G1310R	ENST00000263388	NM_000435.2	1310	Ggg/Agg	24/33	1	2	FACETS	0.916	0.832	1	0.916	0.832	1	CLONAL	1	TRUE	1	0.703625354976406	2		164	335	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371604	225371606	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0053831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	58	437	0	ENST00000264414.4:c.998_1000del	p.Gly333del	p.G333del	ENST00000264414	NM_003590.4	333	gGAGaa/gaa	7/16	1	2	FACETS	0.494	0.426	0.566	0.494	0.426	0.566	SUBCLONAL	1	TRUE	1	0.703625354976406	2		437	334	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76949318	76949318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	70	358	0	ENST00000373344.5:c.479G>A	p.Arg160His	p.R160H	ENST00000373344	NM_000489.3	160	cGc/cAc	6/35	1	2	FACETS	0.786	0.694	0.883	0.786	0.694	0.883	SUBCLONAL	1	TRUE	1	0.703625354976406	2		358	253	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458902	120458903	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0053831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	153	745	1	ENST00000256646.2:c.6442_6443del	p.Leu2148IlefsTer4	p.L2148Ifs*4	ENST00000256646	NM_024408.3	2148	TTa/a	34/34	1	2	FACETS	0.527	0.482	0.574	0.527	0.482	0.574	SUBCLONAL	1	TRUE	1	0.703625354976406	2		746	825	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099980	27099981	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0053831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	238	747	0	ENST00000324856.7:c.3861_3862del	p.Arg1287SerfsTer10	p.R1287Sfs*10	ENST00000324856	NM_006015.4	1287	AGa/a	15/20	1	2	FACETS	0.733	0.685	0.782	0.733	0.685	0.782	SUBCLONAL	1	TRUE	1	0.703625354976406	2		747	923	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190641	11190641	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	291	660	0	ENST00000361445.4:c.5558C>T	p.Ala1853Val	p.A1853V	ENST00000361445	NM_004958.3	1853	gCc/gTc	39/58	1	2	FACETS	0.75	0.706	0.795	0.75	0.706	0.795	SUBCLONAL	1	TRUE	1	0.703625354976406	2		660	1103	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692916	89692917	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	317	499	0	ENST00000371953.3:c.401dup	p.Met134IlefsTer46	p.M134Ifs*46	ENST00000371953	NM_000314.4	134	atg/aTtg	5/9	0.491603184016925	3	FACETS	1	0.992	1	0.779	0.746	0.812	CLONAL	2	TRUE	0	0.703625354976406	3		499	521	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066743	77066743	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	119	378	0	ENST00000356341.3:c.742del	p.Met248CysfsTer13	p.M248Cfs*13	ENST00000356341	NM_002576.4	248	Atg/tg	7/15	1	2	FACETS	0.671	0.609	0.736	0.671	0.609	0.736	SUBCLONAL	1	TRUE	1	0.703625354976406	2		378	504	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377230	118377230	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	157	402	1	ENST00000534358.1:c.10627del	p.Thr3543ProfsTer8	p.T3543Pfs*8	ENST00000534358	NM_005933.3	3541	ccA/cc	27/36	1	2	FACETS	0.704	0.647	0.763	0.704	0.647	0.763	SUBCLONAL	1	TRUE	1	0.703625354976406	2		403	634	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218123	36218123	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	140	468	0	ENST00000222270.7:c.4070del	p.Cys1357SerfsTer49	p.C1357Sfs*49	ENST00000222270	NM_014727.1	1357	tGc/tc	15/37	1	2	FACETS	0.64	0.584	0.697	0.64	0.584	0.697	SUBCLONAL	1	TRUE	1	0.703625354976406	2		468	622	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905304	50905304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	314	959	2	ENST00000440232.2:c.512C>T	p.Ala171Val	p.A171V	ENST00000440232	NM_002691.3	171	gCc/gTc	5/27	1	2	FACETS	0.675	0.636	0.715	0.675	0.636	0.715	SUBCLONAL	1	TRUE	1	0.703625354976406	2		961	1323	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143047	30143047	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	232	835	0	ENST00000389048.3:c.479A>G	p.Glu160Gly	p.E160G	ENST00000389048	NM_004304.4	160	gAg/gGg	1/29	1	2	FACETS	0.567	0.528	0.607	0.567	0.528	0.607	SUBCLONAL	1	TRUE	1	0.703625354976406	2		835	1164	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589221	67589226	+	inframe_deletion	In_Frame_Del	DEL	ATTAAT	ATTAAT	-	novel	NA	P-0053831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	57	253	0	ENST00000274335.5:c.1210_1215del	p.Leu404_Ile405del	p.L404_I405del	ENST00000274335		403	gaATTAATa/gaa	9/15	1	2	FACETS	0.681	0.591	0.777	0.681	0.591	0.777	SUBCLONAL	1	TRUE	1	0.703625354976406	2		253	238	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109311935	109311938	+	frameshift_variant	Frame_Shift_Del	DEL	TAAG	TAAG	-	rs1484471803	NA	P-0053831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	126	507	0	ENST00000436639.2:c.1334_1337del	p.Thr445IlefsTer29	p.T445Ifs*29	ENST00000436639	NM_014454.2	445	aCTTAt/at	8/10	1	2	FACETS	0.677	0.616	0.741	0.677	0.616	0.741	SUBCLONAL	1	TRUE	1	0.703625354976406	2		507	529	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	244	276	0				ENST00000310581	NM_198253.2	-/1132			0.500946667344917	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.599840035574218	4		276	565	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	422	386	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.599840035574218	4	FACETS	0.962	0.932	0.991	0.962	0.932	0.991	CLONAL	4	TRUE	0	0.599840035574218	4		386	585	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788618	3788618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398124146	NA	P-0053832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	264	421	0	ENST00000262367.5:c.4336C>T	p.Arg1446Cys	p.R1446C	ENST00000262367	NM_004380.2	1446	Cgc/Tgc	26/31	0.599840035574218	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.599840035574218	2		421	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579547	7579547	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	389	840	0	ENST00000269305.4:c.140C>G	p.Pro47Arg	p.P47R	ENST00000269305	NM_001126112.2	47	cCg/cGg	4/11	0.599840035574218	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.599840035574218	2		840	602	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980741	201981763	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTAATCCCAGCACTTTGGGAGGCTGAGCTGAGCGGATCACCTGAGGTCAAGAGTTCGAGACCAGCCTAGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAAAAAATTTATCCCAGCGTGGTGGTGGGCACCTATAATCCCAGCTACTGGGGAGGCTGACGCAGGAGTATCGCTTGAACCTGGGAGGTGGAGGTTGCTGTGAGCCGAGATTGTGCCATTGCACCCCAGCCTAGGTGACAGGAGTGAGACTCCATCTCAAAAAAAAAAAAAAAAATGGGGCTGTAAGGTCTGCTGGGTGGCCTGAGCTGAGCCTGTTTCCCTGCCTGGCCCTTGCAGAGAAGGCCAGCTGGTTGGGGGAACAGCCCCAGTTCTGGTCGAAGACGCAGGTTCTGGACTGGATCAGCTACCAAGTGGAGAAGAACAAGTACGACGCAAGCGCCATTGACTTCTCACGATGTGACATGGATGGCGCCACCCTCTGCAATTGTGCCCTTGAGGAGCTGCGTCTGGTCTTTGGGCCTCTGGGGGACCAACTCCATGCCCAGCTGCGAGACCTCAGTGAGTCCAGGCCCCTGGAGGCTGGGGAGCAGCTCCACATGTTGAGCTGAGTCGAGTTCAGTGTGGCCGTAGGCAGGCCCTGGAGCTCTGGGCCAGCTGCACAGCCAGAGAGAGCCCTTGAGGGAGGGATTAGGGGAGTGTGACCCTTCCTTCCTTCCTTGTCAGCTTCCAGCTCTTCTGATGAGCTCAGTTGGATCATTGAGCTGCTGGAGAAGGATGGCATGGCCTTCCAGGAGGCCCTAGACCCAGGGCCCTTTGGTGAGAACCCGTTTTCTCCTTCCTTCCCCAGCCTGTCTTGTCCCATCCCTGCCCCTCCACAGAGTGCTAGAGATGACCCCCTCCCCAGACTTCTTCCTCCCTCAATTAGAAAAATTGCAGCAGGTCATCAGACCCATGGGCAGCATCACCTGTCCTGGTCTGGTCCCCTGAGCCCTCTCTGAGTTCTCACCTCCTCTTC	TGTAATCCCAGCACTTTGGGAGGCTGAGCTGAGCGGATCACCTGAGGTCAAGAGTTCGAGACCAGCCTAGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAAAAAATTTATCCCAGCGTGGTGGTGGGCACCTATAATCCCAGCTACTGGGGAGGCTGACGCAGGAGTATCGCTTGAACCTGGGAGGTGGAGGTTGCTGTGAGCCGAGATTGTGCCATTGCACCCCAGCCTAGGTGACAGGAGTGAGACTCCATCTCAAAAAAAAAAAAAAAAATGGGGCTGTAAGGTCTGCTGGGTGGCCTGAGCTGAGCCTGTTTCCCTGCCTGGCCCTTGCAGAGAAGGCCAGCTGGTTGGGGGAACAGCCCCAGTTCTGGTCGAAGACGCAGGTTCTGGACTGGATCAGCTACCAAGTGGAGAAGAACAAGTACGACGCAAGCGCCATTGACTTCTCACGATGTGACATGGATGGCGCCACCCTCTGCAATTGTGCCCTTGAGGAGCTGCGTCTGGTCTTTGGGCCTCTGGGGGACCAACTCCATGCCCAGCTGCGAGACCTCAGTGAGTCCAGGCCCCTGGAGGCTGGGGAGCAGCTCCACATGTTGAGCTGAGTCGAGTTCAGTGTGGCCGTAGGCAGGCCCTGGAGCTCTGGGCCAGCTGCACAGCCAGAGAGAGCCCTTGAGGGAGGGATTAGGGGAGTGTGACCCTTCCTTCCTTCCTTGTCAGCTTCCAGCTCTTCTGATGAGCTCAGTTGGATCATTGAGCTGCTGGAGAAGGATGGCATGGCCTTCCAGGAGGCCCTAGACCCAGGGCCCTTTGGTGAGAACCCGTTTTCTCCTTCCTTCCCCAGCCTGTCTTGTCCCATCCCTGCCCCTCCACAGAGTGCTAGAGATGACCCCCTCCCCAGACTTCTTCCTCCCTCAATTAGAAAAATTGCAGCAGGTCATCAGACCCATGGGCAGCATCACCTGTCCTGGTCTGGTCCCCTGAGCCCTCTCTGAGTTCTCACCTCCTCTTC	-	novel	NA	P-0053832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	0	127	11	0	ENST00000359651.3:c.163+314_479-5del		p.X55_splice	ENST00000359651		55		2-3/8	0.599840035574218	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.599840035574218	2		11	127	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124617	108124617	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	209	403	0	ENST00000278616.4:c.1976del	p.Lys659ArgfsTer5	p.K659Rfs*5	ENST00000278616	NM_000051.3	659	Aag/ag	13/63	0.570603776602766	4	FACETS	0.963	0.9	1	0.963	0.9	1	CLONAL	2	TRUE	2	0.599840035574218	4		403	579	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075184	16075185	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGACACGCTGAAAA	novel	NA	P-0053832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	169	423	0	ENST00000268712.3:c.354_367dup	p.Ser123IlefsTer12	p.S123Ifs*12	ENST00000268712	NM_006311.3	123	agt/aTTTTCAGCGTGTCAgt	4/46	0.599840035574218	2	FACETS	1	0.991	1	0.738	0.687	0.788	CLONAL	1	TRUE	0	0.599840035574218	2		423	382	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391186	89391186	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	193	461	0	ENST00000336596.2:c.1252C>A	p.Leu418Met	p.L418M	ENST00000336596	NM_005233.5	418	Ctg/Atg	5/17	0.599840035574218	3	FACETS	0.875	0.818	0.933	0.875	0.818	0.933	CLONAL	2	TRUE	1	0.599840035574218	3		461	478	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141426	11141426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0121550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	20	770	1	ENST00000358026.2:c.3403C>T	p.Arg1135Trp	p.R1135W	ENST00000358026	NM_001128849.1	1135	Cgg/Tgg	25/36	1	2	FACETS	0.091	0.069	0.117	0.091	0.069	0.117	SUBCLONAL	1	NA	1	0.6606860031149	2		771	665	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831869	72831869	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0121550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	311	857	1	ENST00000268489.5:c.4712A>T	p.His1571Leu	p.H1571L	ENST00000268489	NM_006885.3	1571	cAt/cTt	9/10	1	2	FACETS	0.998	0.944	1	0.998	0.944	1	CLONAL	1	NA	1	0.6606860031149	2		858	943	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221229	1221229	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	92	745	0	ENST00000326873.7:c.752G>T	p.Gly251Val	p.G251V	ENST00000326873	NM_000455.4	251	gGt/gTt	6/10	0.216429077349428	1	FACETS	0.984	0.874	1	0.984	0.874	1	CLONAL	1	TRUE	0	0.21	1		745	797	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600006	10600006	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	85	757	0	ENST00000171111.5:c.1570G>T	p.Gly524Cys	p.G524C	ENST00000171111	NM_203500.1	524	Ggc/Tgc	5/6	0.216429077349428	1	FACETS	0.978	0.864	1	0.978	0.864	1	CLONAL	1	TRUE	0	0.21	1		757	741	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085992	16085992	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	59	527	0	ENST00000281043.3:c.1168G>C	p.Glu390Gln	p.E390Q	ENST00000281043	NM_005378.4	390	Gag/Cag	3/3	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.21	2		527	524	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155778	106155778	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	23	365	0	ENST00000380013.4:c.679G>T	p.Glu227Ter	p.E227*	ENST00000380013	NM_001127208.2	227	Gaa/Taa	3/11	1	2	FACETS	0.484	0.376	0.609	0.484	0.376	0.609	SUBCLONAL	1	TRUE	1	0.21	2		365	453	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143326460	143326460	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	33	292	0	ENST00000262992.4:c.154G>T	p.Ala52Ser	p.A52S	ENST00000262992	NM_001101669.1	52	Gct/Tct	4/24	1	2	FACETS	0.919	0.75	1	0.919	0.75	1	CLONAL	1	TRUE	1	0.21	2		292	342	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435632	149435632	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	54	654	0	ENST00000286301.3:c.2511C>A	p.Asp837Glu	p.D837E	ENST00000286301	NM_005211.3	837	gaC/gaA	19/22	1	2	FACETS	0.836	0.714	0.971	0.836	0.714	0.971	CLONAL	1	TRUE	1	0.21	2		654	615	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509714	106509714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	86	512	0	ENST00000359195.3:c.1708G>A	p.Glu570Lys	p.E570K	ENST00000359195	NM_002649.2	570	Gag/Aag	2/11	0.216429077349428	3	FACETS	0.795	0.705	0.892	0.795	0.705	0.892	SUBCLONAL	2	TRUE	1	0.21	3		512	569	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53253977	53253977	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	54	329	0	ENST00000375401.3:c.95C>G	p.Ala32Gly	p.A32G	ENST00000375401	NM_004187.3	32	gCg/gGg	1/26	1	1	FACETS	0.919	0.785	1	0.919	0.785	1	CLONAL	1	TRUE	0	0.21	1		329	501	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546043	29546044	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	T	novel	NA	P-0053835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	64	447	0	ENST00000356175.3:c.1548_1549delinsT	p.Glu517LysfsTer9	p.E517Kfs*9	ENST00000356175	NM_000267.3	516	ccCGaa/ccTaa	14/57	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.21	2		447	600	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	76	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.943	0.84	1	0.943	0.84	1	CLONAL	1	TRUE	1	0.707269157270895	2		276	228	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711973	89711975	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	rs1064793244	NA	P-0053837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	304	421	0	ENST00000371953.3:c.595_597del	p.Met199del	p.M199del	ENST00000371953	NM_000314.4	197	aaGATg/aag	6/9	0.707269157270895	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.707269157270895	1		421	553	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62305395	62305395	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	215	864	0	ENST00000360203.5:c.868G>T	p.Ala290Ser	p.A290S	ENST00000360203	NM_001283009.1	290	Gcg/Tcg	10/35	1	2	FACETS	0.615	0.572	0.66	0.615	0.572	0.66	SUBCLONAL	1	TRUE	1	0.707269157270895	2		864	988	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221716	55221716	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	256	545	0	ENST00000275493.2:c.760T>A	p.Phe254Ile	p.F254I	ENST00000275493	NM_005228.3	254	Ttc/Atc	7/28	0.707269157270895	3	FACETS	1	0.989	1	0.619	0.582	0.658	CLONAL	1	TRUE	1	0.707269157270895	3		545	791	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0053838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	66	726	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.160848945416899	2	FACETS	0.818	0.716	0.926	0.818	0.716	0.926	INDETERMINATE	2	TRUE	0	0.27	2		726	299	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880244	155880244	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	75	469	0	ENST00000368323.3:c.160A>T	p.Ile54Phe	p.I54F	ENST00000368323	NM_006912.5	54	Att/Ttt	3/6	0.222378568191632	3	FACETS	1	0.972	1	0.693	0.609	0.782	CLONAL	1	TRUE	1	0.27	3		469	455	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95598906	95598906	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	91	503	0	ENST00000393063.1:c.253A>G	p.Ile85Val	p.I85V	ENST00000393063	NM_030621.3	85	Atc/Gtc	4/28	0.117056398961216	4	FACETS	1	0.975	1	0.682	0.606	0.762	INDETERMINATE	1	TRUE	2	0.27	4		503	628	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119721006	119721006	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	126	615	0	ENST00000316626.5:c.169A>G	p.Thr57Ala	p.T57A	ENST00000316626		57	Aca/Gca	2/12	1	2	FACETS	0.837	0.758	0.919	1	0.987	1	CLONAL	2	TRUE	1	0.205159027959665	2		615	734	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0053840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	73	465	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.338817592931385	3	FACETS	0.913	0.814	1	0.609	0.543	0.677	CLONAL	2	TRUE	0	0.505917980842036	3		465	198	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0053840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	129	766	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.505917980842036	1	FACETS	0.984	0.902	1	0.984	0.902	1	CLONAL	1	TRUE	0	0.505917980842036	1		766	387	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912580	NA	P-0053840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	31	408	0	ENST00000342988.3:c.1157G>A	p.Gly386Asp	p.G386D	ENST00000342988	NM_005359.5	386	gGt/gAt	10/12	0.505917980842036	1	FACETS	0.721	0.594	0.859	0.721	0.594	0.859	SUBCLONAL	1	TRUE	0	0.505917980842036	1		408	127	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965475	68965475	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760923944	NA	P-0053840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	35	524	0	ENST00000288368.4:c.1087C>T	p.Arg363Trp	p.R363W	ENST00000288368	NM_024870.2	363	Cgg/Tgg	9/40	0.170229890676064	4	FACETS	0.808	0.666	0.965	0.404	0.333	0.483	INDETERMINATE	1	TRUE	2	0.505917980842036	4		524	258	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999302	100999302	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	73	1027	0	ENST00000325455.5:c.500G>T	p.Arg167Leu	p.R167L	ENST00000325455	NM_001202474.3	167	cGg/cTg	1/8	1	2	FACETS	0.411	0.359	0.467	0.411	0.359	0.467	SUBCLONAL	1	TRUE	1	0.505917980842036	2		1027	702	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134817	41134817	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	20	520	1	ENST00000379561.5:c.811G>T	p.Ala271Ser	p.A271S	ENST00000379561	NM_002015.3	271	Gcc/Tcc	2/3	0.170229890676064	4	FACETS	0.492	0.377	0.626	0.246	0.188	0.313	INDETERMINATE	1	TRUE	2	0.505917980842036	4		521	242	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741531	39741531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	17	522	0	ENST00000361337.2:c.1418G>A	p.Arg473Gln	p.R473Q	ENST00000361337	NM_003286.2	473	cGg/cAg	14/21	0.338817592931385	3	FACETS	0.29	0.216	0.378	0.097	0.072	0.126	SUBCLONAL	1	TRUE	0	0.505917980842036	3		522	290	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564516	55564516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1174814949	NA	P-0053842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	57	549	1	ENST00000288135.5:c.404G>A	p.Arg135His	p.R135H	ENST00000288135	NM_000222.2	135	cGc/cAc	3/21	1	2	FACETS	0.754	0.647	0.87	0.754	0.647	0.87	SUBCLONAL	1	TRUE	1	0.28	2		550	540	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875627	35875627	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369971728	NA	P-0053842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	78	426	0	ENST00000303115.3:c.814G>A	p.Val272Ile	p.V272I	ENST00000303115	NM_002185.3	272	Gta/Ata	7/8	0.223110891252033	3	FACETS	1	0.94	1	0.371	0.326	0.419	CLONAL	1	TRUE	0	0.28	3		426	571	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500886	8500886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	51	643	0	ENST00000356435.5:c.1996C>T	p.Pro666Ser	p.P666S	ENST00000356435		666	Cct/Tct	13/35	0.3	1	FACETS	0.588	0.499	0.685	0.588	0.499	0.685	SUBCLONAL	1	TRUE	0	0.28	1		643	533	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346550	81346550	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs148293411	NA	P-0053842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	114	385	0	ENST00000222390.5:c.1403G>A	p.Arg468His	p.R468H	ENST00000222390	NM_000601.4	468	cGt/cAt	11/18	0.3	3	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	1	0.28	3		385	450	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670540	134670540	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	118	940	0	ENST00000398015.3:c.451T>C	p.Phe151Leu	p.F151L	ENST00000398015	NM_004441.4	151	Ttt/Ctt	3/16	1	2	FACETS	0.978	0.882	1	0.978	0.882	1	CLONAL	1	TRUE	1	0.28	2		940	862	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727138	40727138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375402843	NA	P-0053842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	202	695	1	ENST00000373198.4:c.3826G>A	p.Val1276Met	p.V1276M	ENST00000373198	NM_133170.3	1276	Gtg/Atg	28/32	0.134301117745212	3	FACETS	1	0.972	1	0.725	0.674	0.778	INDETERMINATE	2	TRUE	0	0.28	3		696	756	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	125	984	0	ENST00000269305.4:c.476C>A	p.Ala159Asp	p.A159D	ENST00000269305	NM_001126112.2	159	gCc/gAc	5/11	0.3	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.28	1		984	700	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682908	241682908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	23	263	1	ENST00000366560.3:c.115C>T	p.Pro39Ser	p.P39S	ENST00000366560	NM_000143.3	39	Ccg/Tcg	1/10	0.254634582928718	1	FACETS	0.614	0.481	0.768	0.614	0.481	0.768	SUBCLONAL	1	TRUE	0	0.28	1		264	230	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649978	88649978	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786201792	NA	P-0053842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	140	703	0	ENST00000372037.3:c.227G>A	p.Cys76Tyr	p.C76Y	ENST00000372037	NM_004329.2	76	tGc/tAc	4/13	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.28	2		703	774	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145781	11145781	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	51	840	0	ENST00000358026.2:c.4143C>G	p.Asp1381Glu	p.D1381E	ENST00000358026	NM_001128849.1	1381	gaC/gaG	29/36	0.3	1	FACETS	0.547	0.464	0.637	0.547	0.464	0.637	SUBCLONAL	1	TRUE	0	0.28	1		840	573	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47604169	47604169	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	78	507	1	ENST00000263735.4:c.508A>T	p.Ile170Phe	p.I170F	ENST00000263735	NM_002354.2	170	Atc/Ttc	5/9	0.243022430267367	3	FACETS	0.739	0.648	0.837	0.369	0.324	0.419	SUBCLONAL	1	TRUE	1	0.28	3		508	860	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637449	176637449	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	101	591	0	ENST00000439151.2:c.2049G>C	p.Lys683Asn	p.K683N	ENST00000439151	NM_022455.4	683	aaG/aaC	5/23	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.28	2		591	618	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045534	47045534	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	52	383	0	ENST00000377604.3:c.2501A>C	p.Lys834Thr	p.K834T	ENST00000377604	NM_001204468.1	834	aAg/aCg	22/24	1	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.28	1		383	274	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409759	63409759	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0053842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	62	244	0	ENST00000330258.3:c.3408G>C	p.Ter1136TyrextTer7	p.*1136Yext*7	ENST00000330258	NM_152424.3	1136	taG/taC	2/2	1	1	FACETS	0.858	0.751	0.97	1	0.978	1	CLONAL	2	TRUE	0	0.28	1		244	222	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347218	70347218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766598254	NA	P-0053842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	115	399	0	ENST00000374080.3:c.2882G>A	p.Arg961Gln	p.R961Q	ENST00000374080		961	cGg/cAg	21/45	0.169507722335392	2	FACETS	1	0.973	1			1	CLONAL	2	TRUE	NA	0.28	2		399	349	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448353	49448353	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	166	734	0	ENST00000301067.7:c.358T>G	p.Phe120Val	p.F120V	ENST00000301067	NM_003482.3	120	Ttc/Gtc	3/54	0.136568222690347	4	FACETS	0.826	0.765	0.89	0.826	0.765	0.89	INDETERMINATE	2	TRUE	2	0.649945327767589	4		734	510	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577138	+	inframe_deletion	In_Frame_Del	DEL	CACGCACCTCAAAGCTGTTCC	CACGCACCTCAAAGCTGTTCC	-	novel	NA	P-0053844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	163	823	0	ENST00000269305.4:c.800_820del	p.Arg267_Val274delinsLeu	p.R267_V274delinsL	ENST00000269305	NM_001126112.2	267	cGGAACAGCTTTGAGGTGCGTGtt/ctt	8/11	0.649945327767589	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.649945327767589	1		823	323	SUCCESS
APC	324	MSKCC	GRCh37	5	112174675	112174676	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0053844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	39	412	0	ENST00000257430.4:c.3385_3386del	p.Leu1129ValfsTer5	p.L1129Vfs*5	ENST00000257430	NM_000038.5	1128	tcTTtg/tctg	16/16	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.649945327767589	2		412	116	SUCCESS
APC	324	MSKCC	GRCh37	5	112174733	112174773	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGAAGAAGAACAGCATGAAGAAGAAGAGAGACCAACAAA	TCTGAAGAAGAACAGCATGAAGAAGAAGAGAGACCAACAAA	-	novel	NA	P-0053844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	29	330	0	ENST00000257430.4:c.3443_3483del	p.Ser1148LeufsTer2	p.S1148Lfs*2	ENST00000257430	NM_000038.5	1148	TCTGAAGAAGAACAGCATGAAGAAGAAGAGAGACCAACAAAt/t	16/16	1	2	FACETS	0.992	0.819	1	0.992	0.819	1	CLONAL	1	TRUE	1	0.649945327767589	2		330	90	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0053848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	30	333	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	1	2	FACETS	0.332	0.268	0.404	0.332	0.268	0.404	SUBCLONAL	1	TRUE	1	0.642324432515936	2		333	281	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696688	47696688	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519971	NA	P-0053848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	130	492	0	ENST00000347630.2:c.260A>G	p.Tyr87Cys	p.Y87C	ENST00000347630	NM_001007230.1	87	tAc/tGc	5/11	1	2	FACETS	0.944	0.863	1	0.944	0.863	1	CLONAL	1	TRUE	1	0.642324432515936	2		492	429	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526176	189526176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747354750	NA	P-0053848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	99	841	0	ENST00000264731.3:c.440C>T	p.Ser147Leu	p.S147L	ENST00000264731	NM_003722.4	147	tCg/tTg	4/14	1	2	FACETS	0.311	0.277	0.348	0.311	0.277	0.348	SUBCLONAL	1	TRUE	1	0.642324432515936	2		841	991	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969401	44969401	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	131	261	0	ENST00000377967.4:c.4083T>G	p.Cys1361Trp	p.C1361W	ENST00000377967	NM_021140.2	1361	tgT/tgG	28/29	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.642324432515936	1		261	193	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543860	212543860	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	205	434	1	ENST00000342788.4:c.1539G>T	p.Trp513Cys	p.W513C	ENST00000342788	NM_005235.2	513	tgG/tgT	13/28	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.642324432515936	2		435	631	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748599	40748599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	178	488	0	ENST00000373198.4:c.2917C>T	p.Pro973Ser	p.P973S	ENST00000373198	NM_133170.3	973	Cct/Tct	21/32	1	2	FACETS	0.93	0.862	1	0.93	0.862	1	CLONAL	1	TRUE	1	0.642324432515936	2		488	596	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249580	110249580	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0053848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	387	1204	0	ENST00000374672.4:c.1095C>G	p.Tyr365Ter	p.Y365*	ENST00000374672	NM_004235.4	365	taC/taG	3/5	1	2	FACETS	0.996	0.947	1	0.996	0.947	1	CLONAL	1	TRUE	1	0.642324432515936	2		1204	1210	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307316	118307316	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs9332745	NA	P-0053849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	14	2	0	ENST00000534358.1:c.89C>G	p.Ala30Gly	p.A30G	ENST00000534358	NM_005933.3	30	gCc/gGc	1/36	1	2	FACETS	0.96	0.752	1	1	0.944	1	CLONAL	4	TRUE	1	0.27	2		2	27	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589615	67589616	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTCGAGAAT	novel	NA	P-0053849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	15	195	0	ENST00000274335.5:c.1379_1387dup	p.Glu462_Tyr463insCysArgGlu	p.E462_Y463insCRE	ENST00000274335		460	agt/aGTCGAGAATgt	10/15	1	2	FACETS	0.389	0.284	0.515	0.389	0.284	0.515	SUBCLONAL	1	TRUE	1	0.27	2		195	286	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589625	67589625	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	22	201	0	ENST00000274335.5:c.1388A>G	p.Tyr463Cys	p.Y463C	ENST00000274335		463	tAt/tGt	10/15	1	2	FACETS	0.568	0.44	0.715	0.568	0.44	0.715	SUBCLONAL	1	TRUE	1	0.27	2		201	287	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520008	NA	P-0053850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	87	734	0	ENST00000269305.4:c.613T>G	p.Tyr205Asp	p.Y205D	ENST00000269305	NM_001126112.2	205	Tat/Gat	6/11	1	2	FACETS	0.8	0.708	0.898	0.8	0.708	0.898	SUBCLONAL	1	FALSE	1	0.3	2		734	725	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833909	44833909	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0053850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	31	153	1	ENST00000377967.4:c.335-2A>T		p.X112_splice	ENST00000377967	NM_021140.2	112			0.242862435824295	2	FACETS	0.783	0.644	0.934			1	CLONAL	2	FALSE	NA	0.3	2		154	132	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202421	123202421	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0053850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	23	114	0	ENST00000218089.9:c.2273T>A	p.Leu758Ter	p.L758*	ENST00000218089	NM_001042749.1	758	tTg/tAg	24/35	1	1	FACETS	1	0.816	1	1	0.816	1	CLONAL	1	FALSE	0	0.3	1		114	126	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0053851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	54	470	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.138905614054101	4	FACETS	0.751	0.643	0.869	0.751	0.643	0.869	SUBCLONAL	2	TRUE	2	0.196272655013439	4		470	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0053851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	359	879	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.125090967034388	4	FACETS	0.991	0.94	1			1	CLONAL	4	TRUE	NA	0.196272655013439	4		879	1104	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687550	29687550	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	37	413	0	ENST00000356175.3:c.8143G>C	p.Asp2715His	p.D2715H	ENST00000356175	NM_000267.3	2715	Gat/Cat	56/57	1	2	FACETS	0.748	0.616	0.896	0.748	0.616	0.896	SUBCLONAL	1	TRUE	1	0.196272655013439	2		413	504	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	105	636	0	ENST00000267101.3:c.850G>C	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Cga	7/28	0.138905614054101	4	FACETS	0.757	0.678	0.842	0.757	0.678	0.842	SUBCLONAL	2	TRUE	2	0.196272655013439	4		636	845	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291056	15291056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	61	862	0	ENST00000263388.2:c.3154G>A	p.Glu1052Lys	p.E1052K	ENST00000263388	NM_000435.2	1052	Gag/Aag	20/33	0.173733620226043	2	FACETS	0.753	0.648	0.868	0.377	0.324	0.434	SUBCLONAL	1	TRUE	0	0.196272655013439	2		862	825	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560838	9560838	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	32	476	0	ENST00000353224.5:c.944C>T	p.Ser315Phe	p.S315F	ENST00000353224	NM_177990.2	315	tCc/tTc	4/10	1	2	FACETS	0.578	0.468	0.703	0.578	0.468	0.703	SUBCLONAL	1	TRUE	1	0.196272655013439	2		476	564	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970971	21970971	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0053851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	218	570	0	ENST00000304494.5:c.387C>G	p.Tyr129Ter	p.Y129*	ENST00000304494	NM_000077.4	129	taC/taG	2/3	0.163194915639699	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	3	TRUE	0	0.196272655013439	3		570	772	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290990	15290990	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	71	910	0	ENST00000263388.2:c.3220G>C	p.Glu1074Gln	p.E1074Q	ENST00000263388	NM_000435.2	1074	Gag/Cag	20/33	0.173733620226043	2	FACETS	0.892	0.777	1	0.446	0.388	0.508	CLONAL	1	TRUE	0	0.196272655013439	2		910	811	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103552	77103552	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	32	312	0	ENST00000356341.3:c.14G>T	p.Gly5Val	p.G5V	ENST00000356341	NM_002576.4	5	gGc/gTc	2/15	0.196272655013439	3	FACETS	0.947	0.77	1	0.474	0.385	0.574	CLONAL	1	TRUE	1	0.196272655013439	3		312	378	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416617	49416617	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	105	532	0	ENST00000301067.7:c.16094A>T	p.Gln5365Leu	p.Q5365L	ENST00000301067	NM_003482.3	5365	cAg/cTg	51/54	0.138905614054101	4	FACETS	0.977	0.877	1	0.977	0.877	1	CLONAL	2	TRUE	2	0.196272655013439	4		532	655	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102874141	102874141	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	25	237	0	ENST00000307046.8:c.19C>G	p.Leu7Val	p.L7V	ENST00000307046	NM_001111285.1	7	Ctt/Gtt	1/4	0.138905614054101	4	FACETS	1	0.794	1	0.503	0.397	0.625	CLONAL	1	TRUE	2	0.196272655013439	4		237	303	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608514	28608514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774257127	NA	P-0053851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	40	517	0	ENST00000241453.7:c.1628C>T	p.Ser543Leu	p.S543L	ENST00000241453	NM_004119.2	543	tCa/tTa	13/24	1	2	FACETS	0.748	0.621	0.89	0.748	0.621	0.89	SUBCLONAL	1	TRUE	1	0.196272655013439	2		517	545	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670679	134670679	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	55	638	0	ENST00000398015.3:c.590C>G	p.Pro197Arg	p.P197R	ENST00000398015	NM_004441.4	197	cCc/cGc	3/16	1	2	FACETS	0.87	0.744	1	0.87	0.744	1	CLONAL	1	TRUE	1	0.196272655013439	2		638	644	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441317	149441317	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	83	700	0	ENST00000286301.3:c.1722G>T	p.Lys574Asn	p.K574N	ENST00000286301	NM_005211.3	574	aaG/aaT	12/22	0.127272945805543	3	FACETS	1	0.967	1	0.641	0.566	0.723	CLONAL	1	TRUE	1	0.196272655013439	3		700	724	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377148	118377151	+	frameshift_variant	Frame_Shift_Del	DEL	CTCC	CTCC	TT	novel	NA	P-0053851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	88	472	1	ENST00000534358.1:c.10541_10544delinsTT	p.Ser3514PhefsTer24	p.S3514Ffs*24	ENST00000534358	NM_005933.3	3514	tCTCCt/tTTt	27/36	0.196272655013439	3	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	1	0.196272655013439	3		473	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578397	7578398	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0053852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	593	797	0	ENST00000269305.4:c.532dup	p.His178ProfsTer3	p.H178Pfs*3	ENST00000269305	NM_001126112.2	178	cac/cCac	5/11	0.909333028608473	1	FACETS	0.931	0.909	0.952	0.931	0.909	0.952	CLONAL	1	TRUE	0	0.909333028608473	1		797	764	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923059	39923059	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	600	392	0	ENST00000378444.4:c.3649C>T	p.Arg1217Ter	p.R1217*	ENST00000378444	NM_001123385.1	1217	Cga/Tga	8/15	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.909333028608473	1		392	653	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142001	108142001	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749471737	NA	P-0053852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	192	472	0	ENST00000278616.4:c.2945G>A	p.Arg982His	p.R982H	ENST00000278616	NM_000051.3	982	cGt/cAt	20/63	1	2	FACETS	0.96	0.898	1	0.96	0.898	1	CLONAL	1	TRUE	1	0.909333028608473	2		472	440	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	97	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.507633381568465	2		276	305	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206941988	206941988	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376415487	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	80	233	1	ENST00000423557.1:c.530G>A	p.Arg177Gln	p.R177Q	ENST00000423557	NM_000572.2	177	cGa/cAa	5/5	1	2	FACETS	0.861	0.763	0.965	0.861	0.763	0.965	CLONAL	1	TRUE	1	0.507633381568465	2		234	366	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645132	67645132	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	209	677	0	ENST00000264010.4:c.397G>A	p.Glu133Lys	p.E133K	ENST00000264010	NM_006565.3	133	Gaa/Aaa	3/12	1	2	FACETS	0.979	0.911	1	0.979	0.911	1	CLONAL	1	TRUE	1	0.507633381568465	2		677	841	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352343	143352343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	155	453	0	ENST00000262992.4:c.70C>T	p.Pro24Ser	p.P24S	ENST00000262992	NM_001101669.1	24	Ccc/Tcc	2/24	0.21504703608644	3	FACETS	0.954	0.874	1	0.477	0.437	0.519	INDETERMINATE	1	TRUE	1	0.507633381568465	3		453	803	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658469	117658469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	152	501	0	ENST00000368508.3:c.5114C>T	p.Ser1705Leu	p.S1705L	ENST00000368508	NM_002944.2	1705	tCa/tTa	31/43	0.244599218715757	3	FACETS	0.942	0.862	1	0.471	0.431	0.513	INDETERMINATE	1	TRUE	1	0.507633381568465	3		501	797	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467500	66467500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757521167	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	98	321	0	ENST00000273854.3:c.769G>A	p.Glu257Lys	p.E257K	ENST00000273854	NM_004439.5	257	Gaa/Aaa	3/18	0.507633381568465	3	FACETS	0.953	0.853	1	0.476	0.426	0.529	CLONAL	1	TRUE	1	0.507633381568465	3		321	508	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124437	94124437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	142	396	0	ENST00000369303.4:c.146C>T	p.Ser49Phe	p.S49F	ENST00000369303	NM_004440.3	49	tCc/tTc	2/17	0.244599218715757	3	FACETS	1	0.952	1	0.531	0.485	0.579	INDETERMINATE	1	TRUE	1	0.507633381568465	3		396	660	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251859	212251859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147514533	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	98	280	0	ENST00000342788.4:c.3200G>A	p.Arg1067Gln	p.R1067Q	ENST00000342788	NM_005235.2	1067	cGa/cAa	27/28	0.409317225514171	4	FACETS	1	0.974	1	0.426	0.381	0.472	CLONAL	1	TRUE	1	0.507633381568465	4		280	456	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142982	30142982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1229550831	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	618	883	0	ENST00000389048.3:c.544G>A	p.Glu182Lys	p.E182K	ENST00000389048	NM_004304.4	182	Gaa/Aaa	1/29	0.485814791046324	3	FACETS	0.97	0.94	1	0.97	0.94	1	CLONAL	3	TRUE	0	0.507633381568465	3		883	1049	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710984	117710984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	113	234	0	ENST00000368508.3:c.1288G>A	p.Gly430Ser	p.G430S	ENST00000368508	NM_002944.2	430	Ggc/Agc	12/43	0.244599218715757	3	FACETS	0.872	0.795	0.951	0.872	0.795	0.951	INDETERMINATE	2	TRUE	1	0.507633381568465	3		234	320	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217251	66217251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1281456118	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	100	378	0	ENST00000273854.3:c.2364G>A	p.Met788Ile	p.M788I	ENST00000273854	NM_004439.5	788	atG/atA	14/18	0.507633381568465	3	FACETS	0.762	0.682	0.848	0.381	0.341	0.424	SUBCLONAL	1	TRUE	1	0.507633381568465	3		378	648	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250440	26250440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	123	465	0	ENST00000446824.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000446824	NM_021018.2	132	Cgc/Tgc	1/1	0.244599218715757	3	FACETS	0.919	0.833	1	0.46	0.416	0.505	INDETERMINATE	1	TRUE	1	0.507633381568465	3		465	661	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250755	26250755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	141	464	0	ENST00000446824.2:c.79C>T	p.Arg27Cys	p.R27C	ENST00000446824	NM_021018.2	27	Cgc/Tgc	1/1	0.244599218715757	3	FACETS	1	0.977	1	0.596	0.545	0.649	INDETERMINATE	1	TRUE	1	0.507633381568465	3		464	584	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93953241	93953241	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267601169	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	176	365	0	ENST00000369303.4:c.2900G>A	p.Gly967Glu	p.G967E	ENST00000369303	NM_004440.3	967	gGg/gAg	17/17	0.244599218715757	3	FACETS	0.755	0.699	0.812	0.755	0.699	0.812	INDETERMINATE	2	TRUE	1	0.507633381568465	3		365	576	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530954	187530954	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	163	371	0	ENST00000441802.2:c.10068+1G>A		p.X3356_splice	ENST00000441802	NM_005245.3	3356			0.21504703608644	3	FACETS	1	0.988	1	0.713	0.658	0.769	INDETERMINATE	1	TRUE	1	0.507633381568465	3		371	565	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042523	42042523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	189	454	0	ENST00000219905.7:c.6718G>A	p.Glu2240Lys	p.E2240K	ENST00000219905	NM_001164273.1	2240	Gaa/Aaa	17/24	0.507633381568465	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.507633381568465	1		454	495	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271561	15271561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	292	1079	2	ENST00000263388.2:c.6878C>T	p.Pro2293Leu	p.P2293L	ENST00000263388	NM_000435.2	2293	cCc/cTc	33/33	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.507633381568465	2		1081	1124	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31429584	31429584	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1354342796	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	132	316	2	ENST00000344624.3:c.3214C>T	p.Pro1072Ser	p.P1072S	ENST00000344624		1072	Ccg/Tcg	24/33	1	2	FACETS	0.974	0.889	1	0.974	0.889	1	CLONAL	1	TRUE	1	0.507633381568465	2		318	534	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524565	176524565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	274	1066	0	ENST00000292408.4:c.2297C>T	p.Pro766Leu	p.P766L	ENST00000292408	NM_213647.1	766	cCc/cTc	18/18	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.507633381568465	2		1066	1073	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021912	246021912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	213	672	0	ENST00000388985.4:c.962C>T	p.Pro321Leu	p.P321L	ENST00000388985		321	cCc/cTc	10/12	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.507633381568465	2		672	832	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706929	117706929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777867372	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	169	482	0	ENST00000368508.3:c.2221C>T	p.His741Tyr	p.H741Y	ENST00000368508	NM_002944.2	741	Cac/Tac	15/43	0.244599218715757	3	FACETS	1	0.957	1	0.529	0.487	0.573	INDETERMINATE	1	TRUE	1	0.507633381568465	3		482	789	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12393108	12393108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	272	541	1	ENST00000287820.6:c.17G>A	p.Gly6Glu	p.G6E	ENST00000287820	NM_015869.4	6	gGa/gAa	1/7	0.244599218715757	3	FACETS	0.874	0.823	0.925	0.874	0.823	0.925	INDETERMINATE	2	TRUE	1	0.507633381568465	3		542	769	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106513	108106513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	98	248	0	ENST00000278616.4:c.448C>T	p.Leu150Phe	p.L150F	ENST00000278616	NM_000051.3	150	Ctt/Ttt	5/63	1	2	FACETS	0.858	0.77	0.951	0.858	0.77	0.951	CLONAL	1	TRUE	1	0.507633381568465	2		248	450	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11269485	11269485	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	150	496	0	ENST00000361445.4:c.3685C>T	p.Pro1229Ser	p.P1229S	ENST00000361445	NM_004958.3	1229	Cct/Tct	25/58	1	2	FACETS	0.943	0.865	1	0.943	0.865	1	CLONAL	1	TRUE	1	0.507633381568465	2		496	627	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304231	65304232	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	157	394	1	ENST00000342505.4:c.2883_2884delinsAA	p.Gly962Arg	p.G962R	ENST00000342505	NM_002227.2	961	tcGGga/tcAAga	21/25	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.507633381568465	2		395	587	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695990	117695991	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	135	428	2	ENST00000369458.3:c.446_447delinsTT	p.Ala149Val	p.A149V	ENST00000369458	NM_024626.3	149	gCC/gTT	4/6	1	2	FACETS	0.951	0.869	1	0.951	0.869	1	CLONAL	1	TRUE	1	0.507633381568465	2		430	559	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939459	71939459	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1415623678	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	310	908	0	ENST00000298229.2:c.314C>T	p.Pro105Leu	p.P105L	ENST00000298229	NM_001567.3	105	cCc/cTc	3/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.507633381568465	2		908	1100	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207701	102207701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1477953478	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	146	297	0	ENST00000263464.3:c.1683G>A	p.Met561Ile	p.M561I	ENST00000263464	NM_001165.4	561	atG/atA	9/9	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.507633381568465	2		297	544	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366590	118366590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs551537456	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	98	350	0	ENST00000534358.1:c.5539C>T	p.Pro1847Ser	p.P1847S	ENST00000534358	NM_005933.3	1847	Cct/Tct	19/36	1	2	FACETS	0.852	0.764	0.945	0.852	0.764	0.945	CLONAL	1	TRUE	1	0.507633381568465	2		350	453	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871086	12871086	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	109	319	0	ENST00000228872.4:c.313G>A	p.Glu105Lys	p.E105K	ENST00000228872	NM_004064.3	105	Gag/Aag	1/3	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.507633381568465	2		319	411	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495085	56495085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	197	725	3	ENST00000267101.3:c.3442C>T	p.Pro1148Ser	p.P1148S	ENST00000267101	NM_001982.3	1148	Cca/Tca	27/28	1	2	FACETS	0.941	0.873	1	0.941	0.873	1	CLONAL	1	TRUE	1	0.507633381568465	2		728	825	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885014	111885014	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	175	632	0	ENST00000341259.2:c.1012C>T	p.Leu338Phe	p.L338F	ENST00000341259	NM_005475.2	338	Ctt/Ttt	5/8	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.507633381568465	2		632	689	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396758	396758	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	190	617	1	ENST00000262320.3:c.268C>A	p.His90Asn	p.H90N	ENST00000262320	NM_003502.3	90	Cat/Aat	2/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.507633381568465	2		618	705	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639143	3639143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1231411840	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	222	779	0	ENST00000294008.3:c.4496G>A	p.Gly1499Glu	p.G1499E	ENST00000294008	NM_032444.2	1499	gGg/gAg	12/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.507633381568465	2		779	828	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577092	7577100	+	inframe_deletion	In_Frame_Del	DEL	CCGGTCTCT	CCGGTCTCT	-	rs1555525215	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	659	803	0	ENST00000269305.4:c.838_846del	p.Asp281_Arg283del	p.D281_R283del	ENST00000269305	NM_001126112.2	280	AGAGACCGG/-	8/11	0.485814791046324	3	FACETS	0.971	0.942	1	0.971	0.942	1	CLONAL	3	TRUE	0	0.507633381568465	3		803	1117	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223207	41223207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	266	566	0	ENST00000357654.3:c.4724C>T	p.Pro1575Leu	p.P1575L	ENST00000357654	NM_007294.3	1575	cCt/cTt	15/23	0.244599218715757	3	FACETS	0.883	0.832	0.935	0.883	0.832	0.935	INDETERMINATE	2	TRUE	1	0.507633381568465	3		566	744	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533911	63533911	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	239	503	1	ENST00000307078.5:c.1243G>T	p.Glu415Ter	p.E415*	ENST00000307078	NM_004655.3	415	Gag/Tag	6/11	0.244599218715757	3	FACETS	0.921	0.865	0.977	0.921	0.865	0.977	INDETERMINATE	2	TRUE	1	0.507633381568465	3		504	641	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726667	41726667	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	246	822	0	ENST00000301178.4:c.212G>C	p.Arg71Pro	p.R71P	ENST00000301178	NM_021913.4	71	cGg/cCg	2/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.507633381568465	2		822	894	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193502	99193503	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	459	765	1	ENST00000074304.5:c.2697_2698delinsAA	p.Asp900Asn	p.D900N	ENST00000074304	NM_001134224.1	899	aaGGac/aaAAac	25/26	0.409317225514171	4	FACETS	0.839	0.804	0.875	0.839	0.804	0.875	CLONAL	3	TRUE	1	0.507633381568465	4		766	1083	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495203	212495203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	151	442	0	ENST00000342788.4:c.2063G>A	p.Arg688Lys	p.R688K	ENST00000342788	NM_005235.2	688	aGa/aAa	17/28	0.409317225514171	4	FACETS	1	0.948	1	0.35	0.32	0.382	CLONAL	1	TRUE	1	0.507633381568465	4		442	854	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520237	9520237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1345841620	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	139	481	0	ENST00000353224.5:c.2032G>A	p.Asp678Asn	p.D678N	ENST00000353224	NM_177990.2	678	Gac/Aac	10/10	1	2	FACETS	0.952	0.871	1	0.952	0.871	1	CLONAL	1	TRUE	1	0.507633381568465	2		481	575	SUCCESS
ATR	545	MSKCC	GRCh37	3	142218484	142218484	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	112	337	0	ENST00000350721.4:c.5365A>C	p.Asn1789His	p.N1789H	ENST00000350721	NM_001184.3	1789	Aac/Cac	31/47	1	2	FACETS	0.769	0.693	0.848	0.769	0.693	0.848	SUBCLONAL	1	TRUE	1	0.507633381568465	2		337	574	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628794	187628794	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	214	564	1	ENST00000441802.2:c.2188C>T	p.Gln730Ter	p.Q730*	ENST00000441802	NM_005245.3	730	Cag/Tag	2/27	0.21504703608644	3	FACETS	1	0.98	1	0.568	0.528	0.61	INDETERMINATE	1	TRUE	1	0.507633381568465	3		565	930	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131895017	131895018	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	111	294	0	ENST00000265335.6:c.171_172delinsTT	p.Pro58Ser	p.P58S	ENST00000265335		57	ttCCct/ttTTct	2/25	1	2	FACETS	0.805	0.727	0.888	0.805	0.727	0.888	CLONAL	1	TRUE	1	0.507633381568465	2		294	543	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047913	180047913	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	255	947	0	ENST00000261937.6:c.2262G>T	p.Lys754Asn	p.K754N	ENST00000261937	NM_182925.4	754	aaG/aaT	15/30	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.507633381568465	2		947	984	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948293	31948293	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	313	904	0	ENST00000375333.2:c.881G>A	p.Gly294Glu	p.G294E	ENST00000375333	NM_032454.1	294	gGa/gAa	6/8	0.244599218715757	3	FACETS	0.782	0.739	0.826	0.782	0.739	0.826	INDETERMINATE	2	TRUE	1	0.507633381568465	3		904	988	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166847	32166847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	369	871	1	ENST00000375023.3:c.4391C>T	p.Ala1464Val	p.A1464V	ENST00000375023	NM_004557.3	1464	gCt/gTt	24/30	0.244599218715757	3	FACETS	0.898	0.854	0.943	0.898	0.854	0.943	INDETERMINATE	2	TRUE	1	0.507633381568465	3		872	1015	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505384	157505384	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	206	384	0	ENST00000346085.5:c.3365G>T	p.Trp1122Leu	p.W1122L	ENST00000346085	NM_020732.3	1122	tGg/tTg	13/20	0.244599218715757	3	FACETS	0.837	0.781	0.894	0.837	0.781	0.894	INDETERMINATE	2	TRUE	1	0.507633381568465	3		384	608	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355233	81355233	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	153	273	0	ENST00000222390.5:c.1141C>A	p.Pro381Thr	p.P381T	ENST00000222390	NM_000601.4	381	Cca/Aca	9/18	0.244599218715757	3	FACETS	0.809	0.746	0.874	0.809	0.746	0.874	INDETERMINATE	2	TRUE	1	0.507633381568465	3		273	467	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509198	106509198	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	193	602	1	ENST00000359195.3:c.1192A>T	p.Arg398Ter	p.R398*	ENST00000359195	NM_002649.2	398	Aga/Tga	2/11	0.244599218715757	3	FACETS	1	0.96	1	0.527	0.488	0.568	INDETERMINATE	1	TRUE	1	0.507633381568465	3		603	904	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526703	106526703	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775602332	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	147	404	0	ENST00000359195.3:c.2996G>A	p.Gly999Glu	p.G999E	ENST00000359195	NM_002649.2	999	gGa/gAa	10/11	0.244599218715757	3	FACETS	1	0.968	1	0.559	0.511	0.608	INDETERMINATE	1	TRUE	1	0.507633381568465	3		404	650	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845463	151845463	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	292	683	0	ENST00000262189.6:c.13549A>G	p.Ser4517Gly	p.S4517G	ENST00000262189	NM_170606.2	4517	Agt/Ggt	52/59	0.244599218715757	3	FACETS	0.867	0.819	0.916	0.867	0.819	0.916	INDETERMINATE	2	TRUE	1	0.507633381568465	3		683	832	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971016	21971017	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	242	344	1	ENST00000304494.5:c.341_342delinsAT	p.Pro114His	p.P114H	ENST00000304494	NM_000077.4	114	cCC/cAT	2/3	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.507633381568465	2		345	429	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359945	87359945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	121	355	0	ENST00000277120.3:c.1253C>T	p.Pro418Leu	p.P418L	ENST00000277120		418	cCt/cTt	11/19	0.507633381568465	2	FACETS	0.987	0.897	1	0.494	0.448	0.541	CLONAL	1	TRUE	0	0.507633381568465	2		355	483	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	37	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.485	0.4	0.58	0.485	0.4	0.58	SUBCLONAL	1	TRUE	1	0.388043865682695	2		276	393	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266102	+	inframe_deletion	In_Frame_Del	DEL	GACTCT	GACTCT	-	novel	NA	P-0053854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	22	320	0	ENST00000349496.5:c.95_100del	p.Asp32_Ser33del	p.D32_S33del	ENST00000349496	NM_001904.3	32	GACTCT/-	3/15	1	2	FACETS	0.225	0.174	0.285	0.225	0.174	0.285	SUBCLONAL	1	TRUE	1	0.388043865682695	2		320	504	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251644	212251644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368679346	NA	P-0053854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	52	536	2	ENST00000342788.4:c.3415C>T	p.Arg1139Trp	p.R1139W	ENST00000342788	NM_005235.2	1139	Cgg/Tgg	27/28	1	2	FACETS	0.428	0.364	0.499	0.428	0.364	0.499	SUBCLONAL	1	TRUE	1	0.388043865682695	2		538	626	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193181546	193181546	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1305485686	NA	P-0053854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	28	379	0	ENST00000367435.3:c.1093C>A	p.Pro365Thr	p.P365T	ENST00000367435	NM_024529.4	365	Cct/Act	13/17	0.375893500473078	3	FACETS	0.357	0.285	0.44	0.179	0.142	0.22	SUBCLONAL	1	TRUE	1	0.388043865682695	3		379	482	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652092	36652102	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCTGCCCAA	GGCCTGCCCAA	-	novel	NA	P-0053854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	303	911	0	ENST00000244741.5:c.215_225del	p.Gly72AlafsTer13	p.G72Afs*13	ENST00000244741	NM_000389.4	72	GGCCTGCCCAAg/g	2/3	0.388043865682695	3	FACETS	1	0.993	1	0.687	0.646	0.729	CLONAL	1	TRUE	1	0.388043865682695	3		911	1358	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559295	141559295	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	263	853	0	ENST00000220592.5:c.1506G>C	p.Glu502Asp	p.E502D	ENST00000220592	NM_012154.3	502	gaG/gaC	12/19	0.216745904233164	3	FACETS	1	0.99	1	0.643	0.601	0.685	INDETERMINATE	1	TRUE	1	0.388043865682695	3		853	1259	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060780	38060781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	16	1099	0	ENST00000250448.2:c.1208dup	p.Asn403LysfsTer12	p.N403Kfs*12	ENST00000250448	NM_004496.3	403	aac/aaAc	2/2	1	2	FACETS	0.103	0.075	0.137	0.103	0.075	0.137	SUBCLONAL	1	FALSE	1	0.392912941606849	2		1099	790	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272036	15272036	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	42	651	1	ENST00000263388.2:c.6403G>T	p.Val2135Leu	p.V2135L	ENST00000263388	NM_000435.2	2135	Gtg/Ttg	33/33	1	2	FACETS	0.331	0.275	0.393	0.331	0.275	0.393	SUBCLONAL	1	FALSE	1	0.392912941606849	2		652	646	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101750	71101751	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	42	264	0	ENST00000318789.4:c.447dup	p.Gln150ThrfsTer20	p.Q150Tfs*20	ENST00000318789	NM_032682.5	149	-/A	9/21	1	2	FACETS	0.722	0.605	0.851	0.722	0.605	0.851	SUBCLONAL	1	FALSE	1	0.345345698722967	2		264	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578512	7578512	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	73	940	0	ENST00000269305.4:c.418del	p.Thr140ProfsTer30	p.T140Pfs*30	ENST00000269305	NM_001126112.2	140	Acc/cc	5/11	0.163593918753299	1	FACETS	0.65	0.569	0.737	0.65	0.569	0.737	INDETERMINATE	1	FALSE	0	0.345345698722967	1		940	538	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755705	39755705	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs547051424	NA	P-0053859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	10	678	2	ENST00000288319.7:c.1060C>T	p.Arg354Trp	p.R354W	ENST00000288319	NM_182918.3	354	Cgg/Tgg	10/10	1	2	FACETS	0.143	0.096	0.202	0.143	0.096	0.202	SUBCLONAL	1	FALSE	1	0.345345698722967	2		680	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0053861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	299	770	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.413396415324703	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.413396415324703	2		770	713	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137323821	137323821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769209021	NA	P-0053861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	75	826	3	ENST00000481739.1:c.1114G>A	p.Ala372Thr	p.A372T	ENST00000481739	NM_002957.4	372	Gcc/Acc	8/10	0.413396415324703	2	FACETS	0.522	0.457	0.592	0.261	0.228	0.296	SUBCLONAL	1	TRUE	0	0.413396415324703	2		829	695	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778143	27778143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	54	722	2	ENST00000369163.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000369163	NM_003536.2	98	Gag/Aag	1/1	0.247644859144129	3	FACETS	0.415	0.353	0.482	0.207	0.176	0.241	INDETERMINATE	1	TRUE	1	0.413396415324703	3		724	760	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845523	151845524	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	136	662	0	ENST00000262189.6:c.13488dup	p.Lys4497Ter	p.K4497*	ENST00000262189	NM_170606.2	4496	-/T	52/59	0.247644859144129	3	FACETS	1	0.961	1	0.55	0.501	0.601	INDETERMINATE	1	TRUE	1	0.413396415324703	3		662	722	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540670	187540670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530876083	NA	P-0053861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	42	385	0	ENST00000441802.2:c.7070C>T	p.Thr2357Met	p.T2357M	ENST00000441802	NM_005245.3	2357	aCg/aTg	10/27	0.294144297018744	0	FACETS	0.41	0.344	0.482			1	SUBCLONAL	1	TRUE	0	0.413396415324703	0		385	291	SUCCESS
FH	2271	MSKCC	GRCh37	1	241672007	241672007	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	46	454	0	ENST00000366560.3:c.634C>A	p.Gln212Lys	p.Q212K	ENST00000366560	NM_000143.3	212	Cag/Aag	5/10	0.413396415324703	3	FACETS	0.371	0.311	0.437	0.185	0.155	0.219	SUBCLONAL	1	TRUE	1	0.413396415324703	3		454	724	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246490627	246490630	+	frameshift_variant	Frame_Shift_Del	DEL	AGTT	AGTT	-	novel	NA	P-0053861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	52	400	0	ENST00000388985.4:c.404_407del	p.Lys135ArgfsTer13	p.K135Rfs*13	ENST00000388985		135	aAACTg/ag	5/12	0.413396415324703	3	FACETS	0.482	0.41	0.561	0.241	0.205	0.281	SUBCLONAL	1	TRUE	1	0.413396415324703	3		400	630	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871044	12871044	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769828807	NA	P-0053861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	45	337	1	ENST00000228872.4:c.271C>A	p.Pro91Thr	p.P91T	ENST00000228872	NM_004064.3	91	Ccc/Acc	1/3	0.222730828231946	3	FACETS	0.571	0.48	0.672	0.19	0.16	0.224	INDETERMINATE	1	TRUE	0	0.413396415324703	3		338	460	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031909	10031909	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	56	649	0	ENST00000330684.3:c.914C>A	p.Ser305Tyr	p.S305Y	ENST00000330684	NM_001134407.1	305	tCt/tAt	3/13	0.216876683352602	6	FACETS	0.537	0.458	0.623			1	INDETERMINATE	1	TRUE	NA	0.413396415324703	6		649	922	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026996	48026996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773927995	NA	P-0053861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	44	371	0	ENST00000234420.5:c.1874C>T	p.Ser625Phe	p.S625F	ENST00000234420	NM_000179.2	625	tCc/tTc	4/10	1	2	FACETS	0.517	0.434	0.608	0.517	0.434	0.608	SUBCLONAL	1	TRUE	1	0.413396415324703	2		371	412	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916932	+	inframe_deletion	In_Frame_Del	DEL	CAGTAGGCA	CAGTAGGCA	-	novel	NA	P-0053861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	148	457	0	ENST00000263967.3:c.311_319del	p.Pro104_Asn107delinsHis	p.P104_N107delinsH	ENST00000263967	NM_006218.2	104	cCAGTAGGCAac/cac	2/21	0.205222918745736	4	FACETS	1	0.986	1	0.708	0.648	0.77	INDETERMINATE	1	TRUE	2	0.413396415324703	4		457	715	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0053862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	449	776	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.638464056757751	2	FACETS	0.916	0.885	0.946	0.916	0.885	0.946	CLONAL	2	FALSE	0	0.722070084791922	2		779	679	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132552	11132552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	455	737	0	ENST00000358026.2:c.2768C>T	p.Ala923Val	p.A923V	ENST00000358026	NM_001128849.1	923	gCg/gTg	19/36	0.722070084791922	3	FACETS	0.874	0.838	0.91	0.874	0.838	0.91	CLONAL	2	FALSE	1	0.722070084791922	3		737	981	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578466	7578466	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786202752	NA	P-0053863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	443	991	1	ENST00000269305.4:c.464C>A	p.Thr155Asn	p.T155N	ENST00000269305	NM_001126112.2	155	aCc/aAc	5/11	0.540550163092196	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.540550163092196	1		992	1112	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004242	29004242	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766441216	NA	P-0053863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	269	401	2	ENST00000282397.4:c.1051C>T	p.Arg351Trp	p.R351W	ENST00000282397	NM_002019.4	351	Cgg/Tgg	8/30	0.540550163092196	3	FACETS	0.852	0.803	0.902	0.852	0.803	0.902	CLONAL	2	TRUE	1	0.540550163092196	3		403	742	SUCCESS
APC	324	MSKCC	GRCh37	5	112174437	112174437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs876658667	NA	P-0053863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	90	244	0	ENST00000257430.4:c.3146G>A	p.Trp1049Ter	p.W1049*	ENST00000257430	NM_000038.5	1049	tGg/tAg	16/16	0.540550163092196	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.540550163092196	1		244	223	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541975	187541975	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	113	539	0	ENST00000441802.2:c.5765A>G	p.Asn1922Ser	p.N1922S	ENST00000441802	NM_005245.3	1922	aAc/aGc	10/27	NA	2	FACETS	0.62	0.559	0.685			1	INDETERMINATE	1	TRUE	NA	0.540550163092196	2		539	674	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848088	151848088	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	214	313	0	ENST00000262189.6:c.12671C>T	p.Ser4224Phe	p.S4224F	ENST00000262189	NM_170606.2	4224	tCc/tTc	51/59	0.326824617363959	3	FACETS	0.892	0.835	0.949	0.892	0.835	0.949	CLONAL	2	TRUE	1	0.540550163092196	3		313	564	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	36	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.337626295669328	2		276	202	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579419	7579420	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs587783062	NA	P-0053864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	61	1001	0	ENST00000269305.4:c.267dup	p.Ser90LeufsTer59	p.S90Lfs*59	ENST00000269305	NM_001126112.2	89	-/C	4/11	0.337626295669328	1	FACETS	0.545	0.47	0.626	0.545	0.47	0.626	SUBCLONAL	1	TRUE	0	0.337626295669328	1		1001	551	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480335	56480335	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	118	422	0	ENST00000267101.3:c.442T>C	p.Tyr148His	p.Y148H	ENST00000267101	NM_001982.3	148	Tat/Cat	4/28	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.337626295669328	2		422	472	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983019	201983019	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	132	977	1	ENST00000359651.3:c.868G>T	p.Glu290Ter	p.E290*	ENST00000359651		290	Gag/Tag	7/8	1	2	FACETS	0.758	0.692	0.826	1	0.987	1	SUBCLONAL	2	TRUE	1	0.337626295669328	2		978	516	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488281	56488281	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	144	711	0	ENST00000267101.3:c.1800C>G	p.Ile600Met	p.I600M	ENST00000267101	NM_001982.3	600	atC/atG	15/28	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.337626295669328	2		711	631	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488300	56488300	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	120	677	1	ENST00000267101.3:c.1819C>G	p.Gln607Glu	p.Q607E	ENST00000267101	NM_001982.3	607	Cag/Gag	15/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.337626295669328	2		678	594	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81557471	81557471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	37	380	1	ENST00000298171.2:c.451G>A	p.Asp151Asn	p.D151N	ENST00000298171	NM_000369.2	151	Gat/Aat	5/10	1	2	FACETS	0.483	0.398	0.578	0.483	0.398	0.578	SUBCLONAL	1	TRUE	1	0.337626295669328	2		381	454	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591588	38591588	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	64	517	0	ENST00000299084.4:c.47G>C	p.Arg16Pro	p.R16P	ENST00000299084	NM_152594.2	16	cGa/cCa	2/7	1	2	FACETS	0.761	0.66	0.87	0.761	0.66	0.87	SUBCLONAL	1	TRUE	1	0.337626295669328	2		517	498	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37882884	37882884	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	68	883	1	ENST00000269571.5:c.2942G>A	p.Arg981Lys	p.R981K	ENST00000269571		981	aGg/aAg	24/27	1	2	FACETS	0.71	0.618	0.81	0.71	0.618	0.81	SUBCLONAL	1	TRUE	1	0.337626295669328	2		884	567	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350574	15350574	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	59	1061	0	ENST00000263377.2:c.3341A>T	p.Lys1114Met	p.K1114M	ENST00000263377	NM_058243.2	1114	aAg/aTg	16/20	0.337626295669328	1	FACETS	0.514	0.442	0.592	0.514	0.442	0.592	SUBCLONAL	1	TRUE	0	0.337626295669328	1		1061	565	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798876	135798876	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	25	241	0	ENST00000298552.3:c.367G>T	p.Asp123Tyr	p.D123Y	ENST00000298552	NM_001162426.1	123	Gac/Tac	6/23	0.337626295669328	1	FACETS	0.688	0.546	0.847	0.688	0.546	0.847	SUBCLONAL	1	TRUE	0	0.337626295669328	1		241	179	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0053865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	68	776	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.202197645339639	1	FACETS	0.89	0.774	1	0.89	0.774	1	CLONAL	1	FALSE	0	0.202197645339639	1		779	679	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0053865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	47	464	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.114458109795679	3	FACETS	1	0.844	1			1	INDETERMINATE	1	FALSE	NA	0.202197645339639	3		464	512	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115269632	115269632	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	77	707	1	ENST00000438362.2:c.1574G>T	p.Gly525Val	p.G525V	ENST00000438362	NM_001242891.1	525	gGa/gTa	13/20	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	1	0.202197645339639	2		708	683	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733237	40733237	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	131	641	0	ENST00000373198.4:c.3569A>T	p.Asn1190Ile	p.N1190I	ENST00000373198	NM_133170.3	1190	aAc/aTc	26/32	1	2	FACETS	0.83	0.753	0.91	1	0.988	1	CLONAL	2	FALSE	1	0.202197645339639	2		641	781	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	45	276	0				ENST00000310581	NM_198253.2	-/1132			0.462053835995113	4	FACETS	1	0.917	1	1	0.917	1	CLONAL	2	TRUE	2	0.462053835995113	4		276	130	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	114	804	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.369805651613952	2	FACETS	0.931	0.854	1	0.931	0.854	1	CLONAL	2	TRUE	0	0.462053835995113	2		804	265	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11167552	11167552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	48	327	0	ENST00000361445.4:c.7640C>T	p.Pro2547Leu	p.P2547L	ENST00000361445	NM_004958.3	2547	cCt/cTt	58/58	0.264976732948816	4	FACETS	1	0.95	1	0.644	0.549	0.745	INDETERMINATE	1	TRUE	2	0.462053835995113	4		327	236	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272496	11272496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	41	545	0	ENST00000361445.4:c.3434C>T	p.Ser1145Phe	p.S1145F	ENST00000361445	NM_004958.3	1145	tCc/tTc	23/58	0.264976732948816	4	FACETS	0.904	0.757	1	0.452	0.378	0.533	INDETERMINATE	1	TRUE	2	0.462053835995113	4		545	287	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099852	27099852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	50	573	1	ENST00000324856.7:c.3731C>T	p.Pro1244Leu	p.P1244L	ENST00000324856	NM_006015.4	1244	cCc/cTc	15/20	0.264976732948816	4	FACETS	1	0.862	1	0.505	0.431	0.586	INDETERMINATE	1	TRUE	2	0.462053835995113	4		574	313	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797445	45797446	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	109	929	0	ENST00000450313.1:c.1073_1074delinsAT	p.Phe358Tyr	p.F358Y	ENST00000450313	NM_012222.2	358	tTC/tAT	12/16	0.264976732948816	4	FACETS	0.988	0.897	1	0.988	0.897	1	INDETERMINATE	2	TRUE	2	0.462053835995113	4		929	349	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313349	65313349	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	41	540	0	ENST00000342505.4:c.1765C>T	p.Leu589Phe	p.L589F	ENST00000342505	NM_002227.2	589	Ctt/Ttt	13/25	0.264976732948816	4	FACETS	0.944	0.791	1	0.472	0.395	0.556	INDETERMINATE	1	TRUE	2	0.462053835995113	4		540	275	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843670	156843670	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751741388	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	132	1033	1	ENST00000524377.1:c.1096C>T	p.Pro366Ser	p.P366S	ENST00000524377	NM_002529.3	366	Ccc/Tcc	8/17	0.264976732948816	4	FACETS	1	0.969	1	1	0.969	1	INDETERMINATE	2	TRUE	2	0.462053835995113	4		1034	375	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850793	63850793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537465187	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	113	498	1	ENST00000279873.7:c.1571C>T	p.Ser524Phe	p.S524F	ENST00000279873	NM_032199.2	524	tCc/tTc	10/10	0.462053835995113	3	FACETS	1	0.977	1	0.79	0.725	0.856	CLONAL	2	TRUE	0	0.462053835995113	3		499	254	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977128	85977128	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	27	272	0	ENST00000263360.6:c.730T>C	p.Tyr244His	p.Y244H	ENST00000263360	NM_003797.3	244	Tat/Cat	8/12	0.428519770729677	4	FACETS	1	0.842	1			1	CLONAL	1	TRUE	NA	0.462053835995113	4		272	162	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922293	100922293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149186732	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	65	330	0	ENST00000325455.5:c.2219G>A	p.Arg740Gln	p.R740Q	ENST00000325455	NM_001202474.3	740	cGa/cAa	5/8	0.428519770729677	4	FACETS	0.839	0.737	0.948			1	CLONAL	2	TRUE	NA	0.462053835995113	4		330	245	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375063	118375064	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	73	428	0	ENST00000534358.1:c.8456_8457delinsAA	p.Ser2819Ter	p.S2819*	ENST00000534358	NM_005933.3	2819	tCC/tAA	27/36	0.394088197121827	2	FACETS	0.778	0.693	0.866	0.778	0.693	0.866	SUBCLONAL	2	TRUE	0	0.462053835995113	2		428	203	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149244	119149244	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	90	573	0	ENST00000264033.4:c.1252T>A	p.Phe418Ile	p.F418I	ENST00000264033	NM_005188.3	418	Ttc/Atc	9/16	0.394088197121827	2	FACETS	1	0.979	1	0.701	0.63	0.774	CLONAL	1	TRUE	0	0.462053835995113	2		573	278	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21639499	21639499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	35	335	0	ENST00000421138.2:c.415C>T	p.Pro139Ser	p.P139S	ENST00000421138		139	Cca/Tca	6/16	0.415754285805201	3	FACETS	1	0.852	1	0.515	0.427	0.612	CLONAL	1	TRUE	1	0.462053835995113	3		335	181	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424958105	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	76	423	0	ENST00000334344.6:c.940C>T	p.Arg314Cys	p.R314C	ENST00000334344	NM_152641.2	314	Cgt/Tgt	8/21	0.442562638034579	4	FACETS	0.838	0.743	0.938	0.838	0.743	0.938	CLONAL	2	TRUE	2	0.462053835995113	4		423	287	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425613	49425613	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	88	900	1	ENST00000301067.7:c.12875C>T	p.Pro4292Leu	p.P4292L	ENST00000301067	NM_003482.3	4292	cCa/cTa	39/54	0.442562638034579	4	FACETS	1	0.977	1	0.694	0.619	0.774	CLONAL	1	TRUE	2	0.462053835995113	4		901	401	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434175	49434175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs570260017	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	126	1075	0	ENST00000301067.7:c.7378C>T	p.Arg2460Cys	p.R2460C	ENST00000301067	NM_003482.3	2460	Cgt/Tgt	31/54	0.442562638034579	4	FACETS	0.846	0.771	0.924	0.846	0.771	0.924	CLONAL	2	TRUE	2	0.462053835995113	4		1075	471	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109830	115109830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	67	470	0	ENST00000257566.3:c.2048C>T	p.Ser683Leu	p.S683L	ENST00000257566	NM_016569.3	683	tCg/tTg	8/8	0.442562638034579	4	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	2	0.462053835995113	4		470	198	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426647	121426647	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	82	667	0	ENST00000257555.6:c.338G>A	p.Trp113Ter	p.W113*	ENST00000257555		113	tGg/tAg	2/10	0.442562638034579	4	FACETS	0.765	0.681	0.855	0.765	0.681	0.855	SUBCLONAL	2	TRUE	2	0.462053835995113	4		667	339	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226444	133226444	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772686048	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	78	630	0	ENST00000320574.5:c.3614C>T	p.Pro1205Leu	p.P1205L	ENST00000320574	NM_006231.2	1205	cCg/cTg	30/49	0.442562638034579	4	FACETS	0.809	0.718	0.905	0.809	0.718	0.905	CLONAL	2	TRUE	2	0.462053835995113	4		630	305	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896476	28896476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	60	430	0	ENST00000282397.4:c.2974G>A	p.Glu992Lys	p.E992K	ENST00000282397	NM_002019.4	992	Gag/Aag	22/30	0.394293742768195	4	FACETS	0.804	0.702	0.913	0.804	0.702	0.913	CLONAL	2	TRUE	2	0.462053835995113	4		430	236	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066720	30066720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	87	435	0	ENST00000331968.5:c.2411C>T	p.Pro804Leu	p.P804L	ENST00000331968	NM_002742.2	804	cCc/cTc	16/18	0.264976732948816	4	FACETS	0.85	0.767	0.934	1	0.975	1	INDETERMINATE	3	TRUE	2	0.462053835995113	4		435	216	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562258	95562258	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	33	443	0	ENST00000393063.1:c.4999G>C	p.Glu1667Gln	p.E1667Q	ENST00000393063	NM_030621.3	1667	Gaa/Caa	24/28	0.264976732948816	4	FACETS	0.825	0.676	0.992	0.413	0.338	0.496	INDETERMINATE	1	TRUE	2	0.462053835995113	4		443	253	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40991033	40991033	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180753546	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	149	581	0	ENST00000267868.3:c.77C>T	p.Ser26Leu	p.S26L	ENST00000267868	NM_002875.4	26	tCa/tTa	2/10	0.415468785574563	3	FACETS	0.837	0.778	0.897	0.837	0.778	0.897	CLONAL	3	TRUE	0	0.462053835995113	3		581	316	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110689	2110689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs911600402	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	55	871	0	ENST00000219476.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000219476	NM_000548.3	332	Gag/Aag	11/42	0.415754285805201	3	FACETS	0.84	0.722	0.967	0.42	0.361	0.484	CLONAL	1	TRUE	1	0.462053835995113	3		871	349	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2115586	2115586	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	68	841	0	ENST00000219476.3:c.1666T>A	p.Ser556Thr	p.S556T	ENST00000219476	NM_000548.3	556	Tcc/Acc	16/42	0.415754285805201	3	FACETS	0.931	0.814	1	0.466	0.407	0.529	CLONAL	1	TRUE	1	0.462053835995113	3		841	389	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130174	2130174	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	52	833	0	ENST00000219476.3:c.3406G>A	p.Gly1136Ser	p.G1136S	ENST00000219476	NM_000548.3	1136	Ggt/Agt	30/42	0.415754285805201	3	FACETS	0.832	0.712	0.962	0.416	0.356	0.481	CLONAL	1	TRUE	1	0.462053835995113	3		833	333	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779379	3779379	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	66	808	1	ENST00000262367.5:c.5669C>T	p.Pro1890Leu	p.P1890L	ENST00000262367	NM_004380.2	1890	cCc/cTc	31/31	0.415754285805201	3	FACETS	1	0.885	1	0.507	0.442	0.575	CLONAL	1	TRUE	1	0.462053835995113	3		809	347	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274097	10274097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143833346	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	44	827	0	ENST00000330684.3:c.172G>A	p.Glu58Lys	p.E58K	ENST00000330684	NM_001134407.1	58	Gag/Aag	2/13	0.415754285805201	3	FACETS	0.849	0.717	0.994	0.425	0.358	0.497	CLONAL	1	TRUE	1	0.462053835995113	3		827	276	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274114	10274114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	49	802	0	ENST00000330684.3:c.155G>A	p.Arg52Gln	p.R52Q	ENST00000330684	NM_001134407.1	52	cGa/cAa	2/13	0.415754285805201	3	FACETS	0.903	0.77	1	0.452	0.385	0.524	CLONAL	1	TRUE	1	0.462053835995113	3		802	289	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029554	14029554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147105770	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	29	356	0	ENST00000311895.7:c.1765C>T	p.Arg589Trp	p.R589W	ENST00000311895	NM_005236.2	589	Cgg/Tgg	8/11	0.415754285805201	3	FACETS	0.681	0.549	0.828	0.34	0.274	0.414	SUBCLONAL	1	TRUE	1	0.462053835995113	3		356	227	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041543	14041543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	63	498	0	ENST00000311895.7:c.2090C>T	p.Ser697Phe	p.S697F	ENST00000311895	NM_005236.2	697	tCt/tTt	11/11	0.415754285805201	3	FACETS	1	0.971	1	0.711	0.623	0.804	CLONAL	1	TRUE	1	0.462053835995113	3		498	236	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868136	56868136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	110	691	0	ENST00000308159.5:c.1634G>A	p.Arg545Lys	p.R545K	ENST00000308159	NM_014669.4	545	aGg/aAg	14/22	0.429493317356108	2	FACETS	0.888	0.812	0.966	0.888	0.812	0.966	CLONAL	2	TRUE	0	0.462053835995113	2		691	268	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576032	29576033	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	70	493	1	ENST00000356175.3:c.4005_4006delinsTT	p.Gln1336Ter	p.Q1336*	ENST00000356175	NM_000267.3	1335	aaCCag/aaTTag	30/57	0.442562638034579	4	FACETS	0.78	0.687	0.878	0.78	0.687	0.878	SUBCLONAL	2	TRUE	2	0.462053835995113	4		494	284	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652837	29652837	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1057518326	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	52	232	0	ENST00000356175.3:c.4773-1G>A		p.X1591_splice	ENST00000356175	NM_000267.3	1591			0.442562638034579	4	FACETS	0.914	0.791	1	0.914	0.791	1	CLONAL	2	TRUE	2	0.462053835995113	4		232	180	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526441	66526441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	82	451	2	ENST00000358598.2:c.997C>T	p.Arg333Cys	p.R333C	ENST00000358598	NM_212471.2	333	Cgt/Tgt	11/11	0.442562638034579	4	FACETS	0.856	0.763	0.954	0.856	0.763	0.954	CLONAL	2	TRUE	2	0.462053835995113	4		453	303	SUCCESS
YES1	7525	MSKCC	GRCh37	18	747962	747962	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	85	539	0	ENST00000314574.4:c.428C>T	p.Pro143Leu	p.P143L	ENST00000314574	NM_005433.3	143	cCg/cTg	4/12	0.428519770729677	4	FACETS	0.789	0.703	0.879			1	SUBCLONAL	2	TRUE	NA	0.462053835995113	4		539	341	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56415027	56415027	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	85	424	0	ENST00000348428.3:c.2428G>T	p.Glu810Ter	p.E810*	ENST00000348428	NM_006785.3	810	Gaa/Taa	17/17	0.369805651613952	2	FACETS	0.773	0.695	0.854	0.773	0.695	0.854	SUBCLONAL	2	TRUE	0	0.462053835995113	2		424	238	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134236	11134236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	46	661	0	ENST00000358026.2:c.2902C>T	p.Leu968Phe	p.L968F	ENST00000358026	NM_001128849.1	968	Ctc/Ttc	20/36	1	2	FACETS	0.809	0.687	0.942	0.809	0.687	0.942	CLONAL	1	TRUE	1	0.462053835995113	2		661	246	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291825	15291825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143695196	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	50	1018	0	ENST00000263388.2:c.2941C>T	p.His981Tyr	p.H981Y	ENST00000263388	NM_000435.2	981	Cac/Tac	18/33	1	2	FACETS	0.79	0.675	0.914	0.79	0.675	0.914	CLONAL	1	TRUE	1	0.462053835995113	2		1018	274	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17949200	17949200	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	64	709	0	ENST00000458235.1:c.1442-1G>A		p.X481_splice	ENST00000458235	NM_000215.3	481			1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.462053835995113	2		709	266	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210859	36210859	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	103	899	1	ENST00000222270.7:c.610C>T	p.Gln204Ter	p.Q204*	ENST00000222270	NM_014727.1	204	Caa/Taa	3/37	0.415754285805201	3	FACETS	0.775	0.7	0.853	0.775	0.7	0.853	SUBCLONAL	2	TRUE	1	0.462053835995113	3		900	354	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910390	50910390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775734510	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	118	907	0	ENST00000440232.2:c.1645C>T	p.Arg549Cys	p.R549C	ENST00000440232	NM_002691.3	549	Cgt/Tgt	13/27	0.462053835995113	3	FACETS	0.995	0.91	1	0.663	0.607	0.721	CLONAL	2	TRUE	0	0.462053835995113	3		907	316	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46611688	46611689	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AG	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	52	960	1	ENST00000263734.3:c.2502_2503delinsAG	p.Tyr834_Leu835delinsTer	p.Y834_L835delins*	ENST00000263734	NM_001430.4	834	taCCtg/taAGtg	16/16	0.264976732948816	4	FACETS	0.914	0.781	1	0.457	0.39	0.529	INDETERMINATE	1	TRUE	2	0.462053835995113	4		961	360	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690188	47690188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	49	443	0	ENST00000233146.2:c.1405C>T	p.Leu469Phe	p.L469F	ENST00000233146	NM_000251.2	469	Ctt/Ttt	9/16	0.264976732948816	4	FACETS	1	0.898	1	0.535	0.456	0.62	INDETERMINATE	1	TRUE	2	0.462053835995113	4		443	290	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99180054	99180054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	84	716	0	ENST00000074304.5:c.1997C>T	p.Thr666Ile	p.T666I	ENST00000074304	NM_001134224.1	666	aCc/aTc	19/26	0.264976732948816	4	FACETS	0.88	0.786	0.979	0.88	0.786	0.979	INDETERMINATE	2	TRUE	2	0.462053835995113	4		716	302	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266513	198266513	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	40	382	1	ENST00000335508.6:c.2323C>T	p.Arg775Ter	p.R775*	ENST00000335508	NM_012433.2	775	Cga/Tga	16/25	0.315899540477352	4	FACETS	1	0.894	1	0.546	0.457	0.642	CLONAL	1	TRUE	2	0.462053835995113	4		383	232	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274595	198274595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	45	629	0	ENST00000335508.6:c.803C>T	p.Pro268Leu	p.P268L	ENST00000335508	NM_012433.2	268	cCt/cTt	7/25	0.315899540477352	4	FACETS	0.863	0.728	1	0.431	0.364	0.506	CLONAL	1	TRUE	2	0.462053835995113	4		629	330	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251853	212251853	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	36	311	0	ENST00000342788.4:c.3206G>A	p.Gly1069Glu	p.G1069E	ENST00000342788	NM_005235.2	1069	gGa/gAa	27/28	0.427438510921924	3	FACETS	1	0.912	1	0.578	0.481	0.683	CLONAL	1	TRUE	1	0.462053835995113	3		311	166	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212522507	212522507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	50	406	0	ENST00000342788.4:c.1918G>A	p.Gly640Ser	p.G640S	ENST00000342788	NM_005235.2	640	Ggc/Agc	16/28	0.427438510921924	3	FACETS	1	0.96	1	0.68	0.585	0.781	CLONAL	1	TRUE	1	0.462053835995113	3		406	196	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576779	212576779	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	53	412	0	ENST00000342788.4:c.1120C>T	p.His374Tyr	p.H374Y	ENST00000342788	NM_005235.2	374	Cat/Tat	9/28	0.427438510921924	3	FACETS	1	0.961	1	0.672	0.581	0.77	CLONAL	1	TRUE	1	0.462053835995113	3		412	210	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632221	215632221	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758139986	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	56	368	0	ENST00000260947.4:c.1553C>T	p.Ala518Val	p.A518V	ENST00000260947	NM_000465.2	518	gCc/gTc	6/11	0.427438510921924	3	FACETS	0.811	0.707	0.92	0.811	0.707	0.92	CLONAL	2	TRUE	1	0.462053835995113	3		368	184	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520219	9520219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867360779	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	90	572	0	ENST00000353224.5:c.2050G>A	p.Glu684Lys	p.E684K	ENST00000353224	NM_177990.2	684	Gag/Aag	10/10	0.442562638034579	4	FACETS	1	0.921	1	1	0.921	1	CLONAL	2	TRUE	2	0.462053835995113	4		572	277	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546781	9546781	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	57	408	0	ENST00000353224.5:c.1241C>G	p.Pro414Arg	p.P414R	ENST00000353224	NM_177990.2	414	cCc/cGc	5/10	0.442562638034579	4	FACETS	0.781	0.678	0.89	0.781	0.678	0.89	SUBCLONAL	2	TRUE	2	0.462053835995113	4		408	231	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560902	9560902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756198440	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	88	566	0	ENST00000353224.5:c.880G>A	p.Glu294Lys	p.E294K	ENST00000353224	NM_177990.2	294	Gaa/Aaa	4/10	0.442562638034579	4	FACETS	0.89	0.797	0.987	0.89	0.797	0.987	CLONAL	2	TRUE	2	0.462053835995113	4		566	313	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561435	9561436	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	88	682	1	ENST00000353224.5:c.346_347delinsAA	p.Gly116Asn	p.G116N	ENST00000353224	NM_177990.2	116	GGt/AAt	4/10	0.442562638034579	4	FACETS	0.791	0.707	0.88	0.791	0.707	0.88	SUBCLONAL	2	TRUE	2	0.462053835995113	4		683	352	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62293892	62293892	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	121	1039	1	ENST00000360203.5:c.396-7C>T		p.X132_splice	ENST00000360203	NM_001283009.1	132			0.442562638034579	4	FACETS	0.938	0.855	1	0.938	0.855	1	CLONAL	2	TRUE	2	0.462053835995113	4		1040	408	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275037	41275038	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	112	459	0	ENST00000349496.5:c.1203_1204delinsTA	p.Leu402Ile	p.L402I	ENST00000349496	NM_001904.3	401	ctCCtt/ctTAtt	9/15	0.462053835995113	5	FACETS	0.897	0.818	0.978	0.897	0.818	0.978	CLONAL	3	TRUE	2	0.462053835995113	5		459	305	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164307	47164307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	69	369	1	ENST00000409792.3:c.1819C>T	p.Pro607Ser	p.P607S	ENST00000409792	NM_014159.6	607	Cct/Tct	3/21	0.462053835995113	5	FACETS	0.857	0.753	0.967	0.571	0.502	0.645	CLONAL	2	TRUE	2	0.462053835995113	5		370	295	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259197	89259197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	64	438	0	ENST00000336596.2:c.341G>A	p.Gly114Glu	p.G114E	ENST00000336596	NM_005233.5	114	gGa/gAa	3/17	0.415754285805201	3	FACETS	1	0.956	1	0.611	0.534	0.693	CLONAL	1	TRUE	1	0.462053835995113	3		438	279	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670724	134670724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	47	603	0	ENST00000398015.3:c.635G>A	p.Gly212Glu	p.G212E	ENST00000398015	NM_004441.4	212	gGg/gAg	3/16	0.415754285805201	3	FACETS	0.967	0.822	1	0.483	0.411	0.562	CLONAL	1	TRUE	1	0.462053835995113	3		603	259	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851568	134851568	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	23	544	0	ENST00000398015.3:c.974G>A	p.Gly325Asp	p.G325D	ENST00000398015	NM_004441.4	325	gGt/gAt	5/16	0.415754285805201	3	FACETS	0.479	0.374	0.599	0.239	0.187	0.3	SUBCLONAL	1	TRUE	1	0.462053835995113	3		544	256	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155243	185155243	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	36	444	0	ENST00000265026.3:c.484G>T	p.Glu162Ter	p.E162*	ENST00000265026	NM_004721.4	162	Gaa/Taa	3/14	0.415754285805201	3	FACETS	0.864	0.716	1	0.432	0.358	0.514	CLONAL	1	TRUE	1	0.462053835995113	3		444	222	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612250	189612250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749906547	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	71	543	2	ENST00000264731.3:c.2002C>T	p.Arg668Cys	p.R668C	ENST00000264731	NM_003722.4	668	Cgc/Tgc	14/14	0.415754285805201	3	FACETS	0.918	0.816	1	0.918	0.816	1	CLONAL	2	TRUE	1	0.462053835995113	3		545	206	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902463	1902463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	127	648	1	ENST00000382891.5:c.82C>T	p.Leu28Phe	p.L28F	ENST00000382891	NM_133335.3	28	Ctc/Ttc	2/22	0.462053835995113	3	FACETS	0.912	0.835	0.991			1	CLONAL	2	TRUE	NA	0.462053835995113	3		649	371	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955923	55955923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	97	544	0	ENST00000263923.4:c.3239G>A	p.Arg1080Lys	p.R1080K	ENST00000263923	NM_002253.2	1080	aGa/aAa	24/30	0.169875515753477	5	FACETS	1	0.965	1			1	INDETERMINATE	2	TRUE	NA	0.462053835995113	5		544	307	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280155	66280155	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	40	286	0	ENST00000273854.3:c.1534G>A	p.Glu512Lys	p.E512K	ENST00000273854	NM_004439.5	512	Gag/Aag	7/18	0.427438510921924	3	FACETS	0.82	0.696	0.951	0.82	0.696	0.951	CLONAL	2	TRUE	1	0.462053835995113	3		286	130	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294342	1294342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	94	410	0	ENST00000310581.5:c.659G>A	p.Gly220Asp	p.G220D	ENST00000310581	NM_198253.2	220	gGt/gAt	2/16	0.462053835995113	4	FACETS	0.847	0.768	0.928	1	0.977	1	CLONAL	3	TRUE	2	0.462053835995113	4		410	234	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750513	57750513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	77	528	0	ENST00000274289.3:c.1955C>T	p.Ser652Phe	p.S652F	ENST00000274289	NM_006622.3	652	tCt/tTt	14/14	0.462053835995113	4	FACETS	0.807	0.715	0.903	0.807	0.715	0.903	CLONAL	2	TRUE	2	0.462053835995113	4		528	302	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80168953	80168953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	95	779	0	ENST00000265081.6:c.3149C>T	p.Pro1050Leu	p.P1050L	ENST00000265081	NM_002439.4	1050	cCt/cTt	23/24	0.462053835995113	4	FACETS	0.84	0.754	0.929	0.84	0.754	0.929	CLONAL	2	TRUE	2	0.462053835995113	4		779	358	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459696	149459696	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	84	828	0	ENST00000286301.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000286301	NM_005211.3	171	Cag/Tag	4/22	0.394293742768195	4	FACETS	0.762	0.678	0.849	0.762	0.678	0.849	SUBCLONAL	2	TRUE	2	0.462053835995113	4		828	349	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047951	180047951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	103	923	0	ENST00000261937.6:c.2224G>A	p.Asp742Asn	p.D742N	ENST00000261937	NM_182925.4	742	Gat/Aat	15/30	0.394293742768195	4	FACETS	0.886	0.8	0.975	0.886	0.8	0.975	CLONAL	2	TRUE	2	0.462053835995113	4		923	368	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056258	180056258	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	108	778	2	ENST00000261937.6:c.985+1G>A		p.X329_splice	ENST00000261937	NM_182925.4	329			0.394293742768195	4	FACETS	1	0.912	1	1	0.912	1	CLONAL	2	TRUE	2	0.462053835995113	4		780	340	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183149	32183149	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	62	948	0	ENST00000375023.3:c.1875G>C	p.Glu625Asp	p.E625D	ENST00000375023	NM_004557.3	625	gaG/gaC	12/30	0.442562638034579	4	FACETS	0.886	0.767	1	0.443	0.383	0.507	CLONAL	1	TRUE	2	0.462053835995113	4		948	443	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43749695	43749696	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	47	448	0	ENST00000523873.1:c.548_549delinsTT	p.Pro183Leu	p.P183L	ENST00000523873		183	cCC/cTT	7/8	0.462053835995113	4	FACETS	1	0.901	1	0.541	0.459	0.629	CLONAL	1	TRUE	2	0.462053835995113	4		448	275	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969140	93969140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	86	434	1	ENST00000369303.4:c.1856G>A	p.Arg619Lys	p.R619K	ENST00000369303	NM_004440.3	619	aGa/aAa	10/17	0.315899540477352	4	FACETS	1	0.904	1	1	0.904	1	CLONAL	2	TRUE	2	0.462053835995113	4		435	270	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066699	94066699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	63	546	0	ENST00000369303.4:c.1060C>T	p.Pro354Ser	p.P354S	ENST00000369303	NM_004440.3	354	Cct/Tct	5/17	0.315899540477352	4	FACETS	0.761	0.665	0.863	0.761	0.665	0.863	SUBCLONAL	2	TRUE	2	0.462053835995113	4		546	262	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552985	106552985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	80	771	0	ENST00000369096.4:c.950G>A	p.Gly317Glu	p.G317E	ENST00000369096	NM_001198.3	317	gGg/gAg	5/7	0.315899540477352	4	FACETS	0.76	0.675	0.85	0.76	0.675	0.85	SUBCLONAL	2	TRUE	2	0.462053835995113	4		771	333	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117737452	117737452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	70	422	0	ENST00000368508.3:c.197C>T	p.Ser66Phe	p.S66F	ENST00000368508	NM_002944.2	66	tCt/tTt	3/43	0.315899540477352	4	FACETS	0.879	0.776	0.987	0.879	0.776	0.987	CLONAL	2	TRUE	2	0.462053835995113	4		422	252	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117737471	117737471	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	71	437	0	ENST00000368508.3:c.178G>A	p.Gly60Arg	p.G60R	ENST00000368508	NM_002944.2	60	Gga/Aga	3/43	0.315899540477352	4	FACETS	0.874	0.772	0.981	0.874	0.772	0.981	CLONAL	2	TRUE	2	0.462053835995113	4		437	257	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511284	157511284	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773135175	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	85	537	2	ENST00000346085.5:c.3802G>A	p.Asp1268Asn	p.D1268N	ENST00000346085	NM_020732.3	1268	Gat/Aat	15/20	0.429493317356108	2	FACETS	0.829	0.746	0.913	0.829	0.746	0.913	CLONAL	2	TRUE	0	0.462053835995113	2		539	222	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971370	13971370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748346103	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	49	372	1	ENST00000405192.2:c.559C>T	p.Arg187Cys	p.R187C	ENST00000405192	NM_001163147.1	187	Cgc/Tgc	8/12	0.427438510921924	3	FACETS	1	0.964	1	0.721	0.62	0.828	CLONAL	1	TRUE	1	0.462053835995113	3		373	181	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450328	50450328	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	38	692	0	ENST00000331340.3:c.512A>G	p.Lys171Arg	p.K171R	ENST00000331340	NM_006060.4	171	aAg/aGg	5/8	0.442562638034579	4	FACETS	0.781	0.648	0.928	0.39	0.324	0.464	CLONAL	1	TRUE	2	0.462053835995113	4		692	308	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397510	116397510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	39	484	0	ENST00000397752.3:c.1882C>T	p.Pro628Ser	p.P628S	ENST00000397752	NM_000245.2	628	Cct/Tct	7/21	0.415754285805201	3	FACETS	0.787	0.656	0.931	0.394	0.328	0.466	CLONAL	1	TRUE	1	0.462053835995113	3		484	264	SUCCESS
MET	4233	MSKCC	GRCh37	7	116414965	116414965	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	61	800	1	ENST00000397752.3:c.3059C>T	p.Ser1020Leu	p.S1020L	ENST00000397752	NM_000245.2	1020	tCa/tTa	15/21	0.415754285805201	3	FACETS	0.821	0.711	0.939	0.41	0.355	0.47	CLONAL	1	TRUE	1	0.462053835995113	3		801	396	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434422	140434422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	31	440	0	ENST00000288602.6:c.2276G>A	p.Gly759Glu	p.G759E	ENST00000288602	NM_004333.4	759	gGa/gAa	18/18	0.415754285805201	3	FACETS	0.653	0.53	0.79	0.326	0.265	0.395	SUBCLONAL	1	TRUE	1	0.462053835995113	3		440	253	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151893093	151893093	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	28	232	0	ENST00000262189.6:c.4277C>T	p.Pro1426Leu	p.P1426L	ENST00000262189	NM_170606.2	1426	cCt/cTt	28/59	0.415754285805201	3	FACETS	1	0.841	1	0.522	0.422	0.631	CLONAL	1	TRUE	1	0.462053835995113	3		232	143	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540141	23540141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1280668959	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	33	136	0	ENST00000380871.4:c.262G>A	p.Glu88Lys	p.E88K	ENST00000380871	NM_006167.3	88	Gag/Aag	1/2	0.394293742768195	4	FACETS	1	0.869	1	1	0.869	1	CLONAL	2	TRUE	2	0.462053835995113	4		136	100	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950517	68950517	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	50	380	0	ENST00000288368.4:c.829A>T	p.Arg277Ter	p.R277*	ENST00000288368	NM_024870.2	277	Aga/Tga	7/40	0.137970596645072	4	FACETS	0.753	0.647	0.867	0.753	0.647	0.867	INDETERMINATE	2	TRUE	2	0.462053835995113	4		380	210	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981315	68981315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866864487	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	47	364	0	ENST00000288368.4:c.1387C>T	p.Arg463Cys	p.R463C	ENST00000288368	NM_024870.2	463	Cgc/Tgc	12/40	0.137970596645072	4	FACETS	1	0.962	1	0.725	0.62	0.839	INDETERMINATE	1	TRUE	2	0.462053835995113	4		364	205	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020470	69020470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760670689	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	88	707	0	ENST00000288368.4:c.2842C>T	p.Pro948Ser	p.P948S	ENST00000288368	NM_024870.2	948	Ccc/Tcc	24/40	0.137970596645072	4	FACETS	0.884	0.791	0.981	0.884	0.791	0.981	INDETERMINATE	2	TRUE	2	0.462053835995113	4		707	315	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046410	69046410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868582467	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	66	649	0	ENST00000288368.4:c.3883G>A	p.Glu1295Lys	p.E1295K	ENST00000288368	NM_024870.2	1295	Gaa/Aaa	32/40	0.137970596645072	4	FACETS	1	0.968	1	0.68	0.595	0.771	INDETERMINATE	1	TRUE	2	0.462053835995113	4		649	307	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050714	69050714	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	63	449	1	ENST00000288368.4:c.4049T>A	p.Phe1350Tyr	p.F1350Y	ENST00000288368	NM_024870.2	1350	tTt/tAt	33/40	0.137970596645072	4	FACETS	0.902	0.791	1	0.902	0.791	1	INDETERMINATE	2	TRUE	2	0.462053835995113	4		450	221	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534946	5534946	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762936264	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	76	613	0	ENST00000397747.3:c.257C>T	p.Ser86Leu	p.S86L	ENST00000397747	NM_025239.3	86	tCg/tTg	3/7	0.462053835995113	4	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.462053835995113	4		613	328	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534978	5534978	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201840318	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	71	565	0	ENST00000397747.3:c.289G>A	p.Glu97Lys	p.E97K	ENST00000397747	NM_025239.3	97	Gaa/Aaa	3/7	0.462053835995113	4	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.462053835995113	4		565	314	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341785	8341785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776356704	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	79	679	0	ENST00000356435.5:c.4855G>A	p.Glu1619Lys	p.E1619K	ENST00000356435		1619	Gaa/Aaa	29/35	0.382341627629959	3	FACETS	1	0.968	1			1	CLONAL	1	TRUE	NA	0.462053835995113	3		679	333	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484129	8484129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	58	417	0	ENST00000356435.5:c.3403G>A	p.Glu1135Lys	p.E1135K	ENST00000356435		1135	Gag/Aag	19/35	0.382341627629959	3	FACETS	1	0.942	1			1	CLONAL	1	TRUE	NA	0.462053835995113	3		417	266	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485927	8485927	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	57	437	0	ENST00000356435.5:c.2890C>T	p.Pro964Ser	p.P964S	ENST00000356435		964	Ccc/Tcc	17/35	0.382341627629959	3	FACETS	1	0.961	1			1	CLONAL	1	TRUE	NA	0.462053835995113	3		437	232	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8525030	8525030	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	46	322	2	ENST00000356435.5:c.574C>T	p.Leu192Phe	p.L192F	ENST00000356435		192	Ctt/Ttt	7/35	0.382341627629959	3	FACETS	1	0.951	1			1	CLONAL	1	TRUE	NA	0.462053835995113	3		324	189	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180318	27180318	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	91	633	0	ENST00000380036.4:c.982G>A	p.Gly328Arg	p.G328R	ENST00000380036	NM_000459.3	328	Gga/Aga	7/23	0.315899540477352	4	FACETS	0.966	0.868	1	0.966	0.868	1	CLONAL	2	TRUE	2	0.462053835995113	4		633	298	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180351	27180351	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	73	537	0	ENST00000380036.4:c.1015C>T	p.Gln339Ter	p.Q339*	ENST00000380036	NM_000459.3	339	Cag/Tag	7/23	0.315899540477352	4	FACETS	0.859	0.76	0.963	0.859	0.76	0.963	CLONAL	2	TRUE	2	0.462053835995113	4		537	269	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27183591	27183591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	73	524	1	ENST00000380036.4:c.1165G>A	p.Asp389Asn	p.D389N	ENST00000380036	NM_000459.3	389	Gat/Aat	8/23	0.315899540477352	4	FACETS	0.928	0.822	1	0.928	0.822	1	CLONAL	2	TRUE	2	0.462053835995113	4		525	249	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206581	27206581	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs759734452	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	65	404	0	ENST00000380036.4:c.2366G>A	p.Arg789Lys	p.R789K	ENST00000380036	NM_000459.3	789	aGg/aAg	15/23	0.315899540477352	4	FACETS	0.979	0.863	1	0.979	0.863	1	CLONAL	2	TRUE	2	0.462053835995113	4		404	210	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250225	110250225	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	32	599	0	ENST00000374672.4:c.450C>G	p.Phe150Leu	p.F150L	ENST00000374672	NM_004235.4	150	ttC/ttG	3/5	0.415468785574563	3	FACETS	0.666	0.543	0.803	0.222	0.181	0.268	SUBCLONAL	1	TRUE	0	0.462053835995113	3		599	256	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760687	133760687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	157	1167	2	ENST00000318560.5:c.3010C>T	p.Pro1004Ser	p.P1004S	ENST00000318560	NM_005157.4	1004	Cct/Tct	11/11	0.415468785574563	3	FACETS	1	0.981	1	0.775	0.72	0.83	CLONAL	2	TRUE	0	0.462053835995113	3		1169	360	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404342	139404342	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs554142958	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	167	930	3	ENST00000277541.6:c.2812C>T	p.Arg938Trp	p.R938W	ENST00000277541	NM_017617.3	938	Cgg/Tgg	18/34	0.415468785574563	3	FACETS	0.857	0.801	0.914	0.857	0.801	0.914	CLONAL	3	TRUE	0	0.462053835995113	3		933	346	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1327709	1327709	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	83	727	0	ENST00000400841.2:c.172T>G	p.Phe58Val	p.F58V	ENST00000400841		58	Ttc/Gtc	2/6	0.257170600387608	4	FACETS	0.85	0.758	0.946	0.85	0.758	0.946	INDETERMINATE	2	TRUE	2	0.462053835995113	4		727	309	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041355	47041355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	103	864	0	ENST00000377604.3:c.1699C>T	p.Pro567Ser	p.P567S	ENST00000377604	NM_001204468.1	567	Ccc/Tcc	16/24	0.257170600387608	4	FACETS	0.905	0.818	0.996	0.905	0.818	0.996	INDETERMINATE	2	TRUE	2	0.462053835995113	4		864	360	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239729	53239729	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780372	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	84	703	0	ENST00000375401.3:c.1613C>T	p.Pro538Leu	p.P538L	ENST00000375401	NM_004187.3	538	cCc/cTc	12/26	0.257170600387608	4	FACETS	1	0.973	1	0.664	0.59	0.743	INDETERMINATE	1	TRUE	2	0.462053835995113	4		703	400	SUCCESS
AR	367	MSKCC	GRCh37	X	66765922	66765922	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	103	972	0	ENST00000374690.3:c.934T>C	p.Phe312Leu	p.F312L	ENST00000374690	NM_000044.3	312	Ttc/Ctc	1/8	0.257170600387608	4	FACETS	0.893	0.806	0.983	0.893	0.806	0.983	INDETERMINATE	2	TRUE	2	0.462053835995113	4		972	365	SUCCESS
AR	367	MSKCC	GRCh37	X	66863196	66863196	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	73	617	0	ENST00000374690.3:c.1715A>T	p.Tyr572Phe	p.Y572F	ENST00000374690	NM_000044.3	572	tAt/tTt	2/8	0.257170600387608	4	FACETS	0.783	0.692	0.88	0.783	0.692	0.88	INDETERMINATE	2	TRUE	2	0.462053835995113	4		617	295	SUCCESS
AR	367	MSKCC	GRCh37	X	66937404	66937404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057523747	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	90	691	4	ENST00000374690.3:c.2258G>A	p.Arg753Gln	p.R753Q	ENST00000374690	NM_000044.3	753	cGa/cAa	5/8	0.257170600387608	4	FACETS	1	0.919	1	1	0.919	1	INDETERMINATE	2	TRUE	2	0.462053835995113	4		695	278	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341237	70341237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1222426673	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	92	676	0	ENST00000374080.3:c.796C>T	p.Arg266Cys	p.R266C	ENST00000374080		266	Cgc/Tgc	6/45	0.257170600387608	4	FACETS	0.872	0.782	0.965	0.872	0.782	0.965	INDETERMINATE	2	TRUE	2	0.462053835995113	4		676	334	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939247	76939247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	80	827	0	ENST00000373344.5:c.1501G>A	p.Glu501Lys	p.E501K	ENST00000373344	NM_000489.3	501	Gaa/Aaa	9/35	0.427438510921924	3	FACETS	1	0.973	1	0.672	0.597	0.751	CLONAL	1	TRUE	1	0.462053835995113	3		827	317	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220527	123220527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	34	624	0	ENST00000218089.9:c.3184G>A	p.Gly1062Arg	p.G1062R	ENST00000218089	NM_001042749.1	1062	Gga/Aga	30/35	0.427438510921924	3	FACETS	0.596	0.488	0.716	0.298	0.244	0.358	SUBCLONAL	1	TRUE	1	0.462053835995113	3		624	304	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946460	2946460	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764955786	NA	P-0053866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	75	694	0	ENST00000396946.4:c.3277C>T	p.Pro1093Ser	p.P1093S	ENST00000396946	NM_032415.4	1093	Cct/Tct	25/25	0.427438510921924	3	FACETS	1	0.978	1	0.748	0.664	0.837	CLONAL	1	TRUE	1	0.462053835995113	3		694	267	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0053871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	218	748	0	ENST00000269305.4:c.376-1G>T		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.220066262641438	2	FACETS	1	0.991	1	0.737	0.686	0.79	CLONAL	1	TRUE	0	0.31	2		748	954	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123705	11123705	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	194	595	0	ENST00000358026.2:c.2355G>C	p.Lys785Asn	p.K785N	ENST00000358026	NM_001128849.1	785	aaG/aaC	16/36	0.220066262641438	2	FACETS	0.759	0.703	0.816	0.759	0.703	0.816	SUBCLONAL	2	TRUE	0	0.31	2		595	825	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0053871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	105	424	1	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.220066262641438	2	FACETS	1	0.968	1	0.596	0.536	0.66	CLONAL	1	TRUE	0	0.31	2		425	568	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339299	116339299	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	97	368	0	ENST00000397752.3:c.161A>T	p.Asn54Ile	p.N54I	ENST00000397752	NM_000245.2	54	aAt/aTt	2/21	0.206979685418185	4	FACETS	1	0.98	1	0.729	0.652	0.811	CLONAL	1	TRUE	2	0.31	4		368	562	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs730881677	NA	P-0053871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	138	454	0	ENST00000304494.5:c.151-1G>C		p.X51_splice	ENST00000304494	NM_000077.4	51			0.220066262641438	2	FACETS	0.782	0.715	0.852	0.782	0.715	0.852	SUBCLONAL	2	TRUE	0	0.31	2		454	569	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400125	41400125	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	162	514	0	ENST00000373198.4:c.634C>T	p.Gln212Ter	p.Q212*	ENST00000373198	NM_133170.3	212	Cag/Tag	5/32	0.206979685418185	4	FACETS	1	0.988	1	0.724	0.664	0.786	CLONAL	1	TRUE	2	0.31	4		514	946	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26956953	26956953	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	67	244	0	ENST00000381527.3:c.459A>T	p.Lys153Asn	p.K153N	ENST00000381527	NM_001260.1	153	aaA/aaT	5/13	0.220066262641438	2	FACETS	1	0.947	1	0.581	0.507	0.66	CLONAL	1	TRUE	0	0.31	2		244	372	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994830	73994830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	82	309	0	ENST00000318443.5:c.314C>T	p.Ala105Val	p.A105V	ENST00000318443	NM_001024736.1	105	gCa/gTa	3/10	0.218161500894306	3	FACETS	0.779	0.691	0.872	0.779	0.691	0.872	SUBCLONAL	2	TRUE	1	0.31	3		309	392	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607219	189607219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1360624743	NA	P-0053871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1512	81	722	0	ENST00000264731.3:c.1598C>T	p.Ser533Phe	p.S533F	ENST00000264731	NM_003722.4	533	tCc/tTc	12/14	0.297622880470869	6	FACETS	0.531	0.466	0.602	0.177	0.155	0.201	SUBCLONAL	1	TRUE	3	0.31	6		722	1593	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993122	90993122	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0053871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	33	277	0	ENST00000265433.3:c.321-1G>A		p.X107_splice	ENST00000265433	NM_002485.4	107			0.218161500894306	3	FACETS	0.705	0.575	0.85	0.352	0.287	0.425	SUBCLONAL	1	TRUE	1	0.31	3		277	349	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932017	39932017	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053871-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	89	303	0	ENST00000378444.4:c.2582G>C	p.Arg861Pro	p.R861P	ENST00000378444	NM_001123385.1	861	cGc/cCc	4/15	1	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.31	1		303	440	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0053887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	50	725	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	1	2	FACETS	0.685	0.58	0.802	0.685	0.58	0.802	SUBCLONAL	1	TRUE	1	0.18	2		725	811	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520008	NA	P-0053887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	41	690	0	ENST00000269305.4:c.613T>C	p.Tyr205His	p.Y205H	ENST00000269305	NM_001126112.2	205	Tat/Cat	6/11	1	2	FACETS	0.509	0.422	0.606	0.509	0.422	0.606	SUBCLONAL	1	TRUE	1	0.18	2		690	895	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222002	1222002	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	65	628	0	ENST00000326873.7:c.917A>G	p.His306Arg	p.H306R	ENST00000326873	NM_000455.4	306	cAc/cGc	7/10	1	2	FACETS	0.822	0.711	0.943	0.822	0.711	0.943	CLONAL	1	TRUE	1	0.18	2		628	879	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66520220	66520220	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0053888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	87	389	0	ENST00000358598.2:c.502+2T>G		p.X168_splice	ENST00000358598	NM_212471.2	168			1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.553330335475944	2		389	302	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450267	50450267	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	249	776	0	ENST00000331340.3:c.451G>T	p.Gly151Trp	p.G151W	ENST00000331340	NM_006060.4	151	Ggg/Tgg	5/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.553330335475944	2		776	746	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349232	70349232	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	363	477	0	ENST00000374080.3:c.3644T>A	p.Ile1215Asn	p.I1215N	ENST00000374080		1215	aTc/aAc	26/45	1	1	FACETS	0.802	0.77	0.833	1	0.996	1	CLONAL	2	TRUE	0	0.553330335475944	1		477	592	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923064	44923065	+	splice_donor_variant,intron_variant	Splice_Site	DEL	TA	TA	G	novel	NA	P-0053888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	138	277	0	ENST00000377967.4:c.1923+2_1923+3delinsG		p.X641_splice	ENST00000377967	NM_021140.2	641			1	1	FACETS	0.813	0.761	0.862	1	0.992	1	CLONAL	2	TRUE	0	0.553330335475944	1		277	222	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519998	NA	P-0053889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	81	607	0	ENST00000269305.4:c.581T>C	p.Leu194Pro	p.L194P	ENST00000269305	NM_001126112.2	194	cTt/cCt	6/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.26	2		607	535	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989536	85989536	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	56	317	0	ENST00000263360.6:c.1295C>T	p.Ala432Val	p.A432V	ENST00000263360	NM_003797.3	432	gCc/gTc	12/12	0.287619190636705	3	FACETS	0.882	0.756	1	0.441	0.378	0.51	CLONAL	1	TRUE	1	0.26	3		317	552	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803199	1803199	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	69	816	0	ENST00000260795.2:c.551C>G	p.Pro184Arg	p.P184R	ENST00000260795		184	cCc/cGc	4/17	1	2	FACETS	0.876	0.763	0.998	0.876	0.763	0.998	CLONAL	1	TRUE	1	0.26	2		816	606	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176686988	176686988	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs587784133	NA	P-0053889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	21	314	0	ENST00000439151.2:c.4967-2A>T		p.X1656_splice	ENST00000439151	NM_022455.4	1656			1	2	FACETS	0.408	0.313	0.518	0.408	0.313	0.518	SUBCLONAL	1	TRUE	1	0.26	2		314	396	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1327795	1327795	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs370595721	NA	P-0053889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	64	462	0	ENST00000400841.2:c.86G>C	p.Gly29Ala	p.G29A	ENST00000400841		29	gGa/gCa	2/6	0.174320170184739	2	FACETS	1	0.948	1			1	CLONAL	1	TRUE	NA	0.26	2		462	415	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0053890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	410	646	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	3	TRUE	1	0.26	2		646	911	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0053890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	231	258	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.92	0.868	0.972	1	0.996	1	CLONAL	4	TRUE	1	0.26	2		258	483	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195112	123195112	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	130	463	0	ENST00000218089.9:c.1455G>A	p.Trp485Ter	p.W485*	ENST00000218089	NM_001042749.1	485	tgG/tgA	16/35	1	2	FACETS	1	0.958	1	1	0.993	1	CLONAL	3	TRUE	1	0.26	2		463	314	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442667	442667	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	236	500	0	ENST00000399788.2:c.1639G>A	p.Glu547Lys	p.E547K	ENST00000399788	NM_001042603.1	547	Gag/Aag	12/28	1	2	FACETS	1	0.981	1	1	0.996	1	CLONAL	3	TRUE	1	0.26	2		500	553	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427447	49427447	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	535	803	0	ENST00000301067.7:c.11041C>T	p.Gln3681Ter	p.Q3681*	ENST00000301067	NM_003482.3	3681	Cag/Tag	39/54	1	2	FACETS	1	0.993	1	1	0.998	1	CLONAL	3	TRUE	1	0.26	2		803	1201	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427964	49427965	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	418	673	2	ENST00000301067.7:c.10625dup	p.Cys3543ValfsTer13	p.C3543Vfs*13	ENST00000301067	NM_003482.3	3542	ctg/ctTg	38/54	1	2	FACETS	1	0.991	1	1	0.997	1	CLONAL	3	TRUE	1	0.26	2		675	953	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848560	151848565	+	inframe_deletion	In_Frame_Del	DEL	CCGCAC	CCGCAC	-	novel	NA	P-0053890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	70	323	0	ENST00000262189.6:c.12628_12633del	p.Val4210_Arg4211del	p.V4210_R4211del	ENST00000262189	NM_170606.2	4210	GTGCGG/-	50/59	1	2	FACETS	0.851	0.754	0.951	1	0.985	1	CLONAL	3	TRUE	1	0.26	2		323	211	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599321	55599321	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913507	NA	P-0053891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	265	455	0	ENST00000288135.5:c.2447A>T	p.Asp816Val	p.D816V	ENST00000288135	NM_000222.2	816	gAc/gTc	17/21	0.409108514853666	5	FACETS	1	0.981	1			1	CLONAL	3	TRUE	NA	0.459082377806092	5		455	600	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916851	178916851	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	106	483	0	ENST00000263967.3:c.238G>A	p.Glu80Lys	p.E80K	ENST00000263967	NM_006218.2	80	Gaa/Aaa	2/21	0.459082377806092	3	FACETS	0.94	0.845	1	0.47	0.422	0.521	CLONAL	1	TRUE	1	0.459082377806092	3		483	604	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148546	119148546	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	210	308	0	ENST00000264033.4:c.1087G>C	p.Val363Leu	p.V363L	ENST00000264033	NM_005188.3	363	Gtg/Ctg	7/16	0.459082377806092	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	3	TRUE	0	0.459082377806092	3		308	367	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134757	41134757	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	145	390	1	ENST00000379561.5:c.871C>T	p.Gln291Ter	p.Q291*	ENST00000379561	NM_002015.3	291	Cag/Tag	2/3	0.459082377806092	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.459082377806092	2		391	298	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579579	7579580	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	T	novel	NA	P-0053891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	266	667	0	ENST00000269305.4:c.107_108delinsA	p.Pro36HisfsTer8	p.P36Hfs*8	ENST00000269305	NM_001126112.2	36	cCG/cA	4/11	0.459082377806092	3	FACETS	0.973	0.925	1	0.973	0.925	1	CLONAL	3	TRUE	0	0.459082377806092	3		667	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0053893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	886	558	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.903345373112443	3	FACETS	1	0.996	1			1	CLONAL	3	TRUE	NA	0.903345373112443	3		558	935	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434844	110434844	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	673	597	0	ENST00000375856.3:c.3557G>T	p.Ser1186Ile	p.S1186I	ENST00000375856	NM_003749.2	1186	aGc/aTc	1/2	0.903345373112443	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.903345373112443	2		597	724	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39647446	39647446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	197	448	0	ENST00000262039.4:c.2618C>T	p.Ala873Val	p.A873V	ENST00000262039	NM_002647.2	873	gCa/gTa	24/25	0.750363620729297	4	FACETS	1	0.967	1	0.358	0.332	0.384	CLONAL	1	TRUE	1	0.903345373112443	4		448	774	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635598	47635598	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	139	301	0	ENST00000233146.2:c.270A>C	p.Lys90Asn	p.K90N	ENST00000233146	NM_000251.2	90	aaA/aaC	2/16	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.903345373112443	2		301	305	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719148	190719148	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	66	213	1	ENST00000441310.2:c.1150G>A	p.Asp384Asn	p.D384N	ENST00000441310	NM_000534.4	384	Gat/Aat	9/13	1	2	FACETS	0.931	0.829	1	0.931	0.829	1	CLONAL	1	TRUE	1	0.903345373112443	2		214	157	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212522503	212522503	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	177	377	0	ENST00000342788.4:c.1922A>T	p.His641Leu	p.H641L	ENST00000342788	NM_005235.2	641	cAt/cTt	16/28	1	2	FACETS	0.963	0.899	1	0.963	0.899	1	CLONAL	1	TRUE	1	0.903345373112443	2		377	407	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294279	1294279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1338516048	NA	P-0053893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	348	571	4	ENST00000310581.5:c.722G>A	p.Gly241Asp	p.G241D	ENST00000310581	NM_198253.2	241	gGc/gAc	2/16	0.808326122382651	4	FACETS	0.995	0.94	1	0.497	0.47	0.526	CLONAL	1	TRUE	2	0.903345373112443	4		575	1474	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	111	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	1	0.851227032970388	2		276	253	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0053894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	299	646	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.747	0.705	0.789	0.747	0.705	0.789	SUBCLONAL	1	FALSE	1	0.851227032970388	2		646	941	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022253	26022253	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0053894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	304	426	1	ENST00000435504.4:c.403+1G>A		p.X135_splice	ENST00000435504		135			0.814243249214431	1	FACETS	0.916	0.88	0.951	0.916	0.88	0.951	CLONAL	1	FALSE	0	0.851227032970388	1		427	448	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465994	69465994	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	977	656	0	ENST00000227507.2:c.832G>T	p.Glu278Ter	p.E278*	ENST00000227507	NM_053056.2	278	Gag/Tag	5/5	0.85050913425727	2	FACETS	0.979	0.963	0.995	0.979	0.963	0.995	CLONAL	2	FALSE	0	0.851227032970388	2		656	1172	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352534	118352534	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	633	425	0	ENST00000534358.1:c.3739del	p.Ser1247GlnfsTer109	p.S1247Qfs*109	ENST00000534358	NM_005933.3	1247	Tca/ca	7/36	0.85050913425727	2	FACETS	0.94	0.92	0.96	0.94	0.92	0.96	CLONAL	2	FALSE	0	0.851227032970388	2		425	791	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435810	110435810	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	140	227	0	ENST00000375856.3:c.2591del	p.Pro864LeufsTer2	p.P864Lfs*2	ENST00000375856	NM_003749.2	864	cCt/ct	1/2	1	2	FACETS	0.988	0.913	1	0.988	0.913	1	CLONAL	1	FALSE	1	0.851227032970388	2		227	333	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210023	55210023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	273	365	0	ENST00000275493.2:c.133G>A	p.Glu45Lys	p.E45K	ENST00000275493	NM_005228.3	45	Gaa/Aaa	2/28	1	2	FACETS	0.903	0.853	0.955	0.903	0.853	0.955	CLONAL	1	FALSE	1	0.851227032970388	2		365	710	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	46	496	4	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.471	0.395	0.554	0.471	0.395	0.554	SUBCLONAL	1	TRUE	1	0.32	2		500	611	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	106	397	3	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.32	2		400	607	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	117	436	2	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.958	0.865	1	0.958	0.865	1	CLONAL	1	TRUE	1	0.32	2		438	763	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	212	721	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.304904567224238	2	FACETS	0.836	0.779	0.896	0.836	0.779	0.896	CLONAL	2	TRUE	0	0.32	2		728	792	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497950	25497950	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	84	734	0	ENST00000264709.3:c.499C>T	p.Arg167Trp	p.R167W	ENST00000264709	NM_175629.2	167	Cgg/Tgg	6/23	1	2	FACETS	0.855	0.756	0.961	0.855	0.756	0.961	CLONAL	1	TRUE	1	0.32	2		734	614	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435300	110435302	+	inframe_deletion	In_Frame_Del	DEL	GGT	GGT	-	rs765493638	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	69	333	0	ENST00000375856.3:c.3099_3101del	p.Pro1036del	p.P1036del	ENST00000375856	NM_003749.2	1033	ccACCg/ccg	1/2	0.267166222707556	4	FACETS	1	0.961	1	0.633	0.552	0.718	CLONAL	1	TRUE	2	0.32	4		333	450	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521299	187521299	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1166479124	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	85	621	0	ENST00000441802.2:c.11856del	p.Phe3952LeufsTer31	p.F3952Lfs*31	ENST00000441802	NM_005245.3	3952	ttT/tt	22/27	0.304904567224238	2	FACETS	0.799	0.706	0.898	0.399	0.353	0.449	SUBCLONAL	1	TRUE	0	0.32	2		621	665	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852118	63852118	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	63	542	0	ENST00000279873.7:c.2901del	p.Lys967AsnfsTer15	p.K967Nfs*15	ENST00000279873	NM_032199.2	966	Aaa/aa	10/10	1	2	FACETS	0.671	0.58	0.769	0.671	0.58	0.769	SUBCLONAL	1	TRUE	1	0.32	2		542	587	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419951	41419951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	94	616	0	ENST00000373198.4:c.370G>A	p.Val124Met	p.V124M	ENST00000373198	NM_133170.3	124	Gtg/Atg	3/32	0.257673508960684	0	FACETS	0.597	0.532	0.667			1	SUBCLONAL	1	TRUE	0	0.32	0		616	669	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058747	180058748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755445139	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	92	803	6	ENST00000261937.6:c.89dup	p.Thr31AspfsTer15	p.T31Dfs*15	ENST00000261937	NM_182925.4	30	ccg/ccCg	2/30	0.304904567224238	1	FACETS	0.689	0.612	0.771	0.689	0.612	0.771	SUBCLONAL	1	TRUE	0	0.32	1		809	701	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165720	185165720	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	28	325	0	ENST00000265026.3:c.999del	p.Val334LeufsTer14	p.V334Lfs*14	ENST00000265026	NM_004721.4	332	gAa/ga	5/14	1	2	FACETS	0.349	0.278	0.43	0.349	0.278	0.43	SUBCLONAL	1	TRUE	1	0.32	2		325	502	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557927	187557927	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs369805914	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	174	488	0	ENST00000441802.2:c.3784C>T	p.Arg1262Ter	p.R1262*	ENST00000441802	NM_005245.3	1262	Cga/Tga	5/27	0.304904567224238	2	FACETS	0.876	0.81	0.943	0.876	0.81	0.943	CLONAL	2	TRUE	0	0.32	2		488	621	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054541	42054541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1458609443	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	57	362	0	ENST00000219905.7:c.7731del	p.Asp2578ThrfsTer10	p.D2578Tfs*10	ENST00000219905	NM_001164273.1	2575	agA/ag	22/24	1	2	FACETS	0.848	0.73	0.977	0.848	0.73	0.977	CLONAL	1	TRUE	1	0.32	2		362	420	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	250	1067	2	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.833	0.78	0.887	1	0.994	1	CLONAL	2	TRUE	1	0.32	2		1069	938	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222730	5222731	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs756013055	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	65	919	7	ENST00000357368.4:c.3072dup	p.Val1025ArgfsTer34	p.V1025Rfs*34	ENST00000357368	NM_002850.3	1024	-/C	18/38	1	2	FACETS	0.532	0.46	0.61	0.532	0.46	0.61	SUBCLONAL	1	TRUE	1	0.32	2		926	764	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447773	49447773	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	32	493	0	ENST00000301067.7:c.661del	p.Ala221LeufsTer40	p.A221Lfs*40	ENST00000301067	NM_003482.3	221	Gct/ct	5/54	1	2	FACETS	0.317	0.256	0.386	0.317	0.256	0.386	SUBCLONAL	1	TRUE	1	0.32	2		493	631	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214398	36214398	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs868041281	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	88	643	4	ENST00000222270.7:c.3057del	p.Gly1020AlafsTer4	p.G1020Afs*4	ENST00000222270	NM_014727.1	1018	Aaa/aa	7/37	1	2	FACETS	0.881	0.782	0.988	0.881	0.782	0.988	CLONAL	1	TRUE	1	0.32	2		647	624	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025856	48025857	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs267608041	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	48	276	0	ENST00000234420.5:c.741dup	p.Arg248ThrfsTer8	p.R248Tfs*8	ENST00000234420	NM_000179.2	245	ata/atAa	4/10	1	2	FACETS	0.746	0.632	0.871	0.746	0.632	0.871	SUBCLONAL	1	TRUE	1	0.32	2		276	402	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467175	99467175	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	26	499	0	ENST00000268035.6:c.2556G>A	p.Trp852Ter	p.W852*	ENST00000268035	NM_000875.3	852	tgG/tgA	12/21	1	2	FACETS	0.341	0.27	0.424	0.341	0.27	0.424	SUBCLONAL	1	TRUE	1	0.32	2		499	476	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120257	70120257	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	143	758	0	ENST00000245479.2:c.1259A>G	p.Tyr420Cys	p.Y420C	ENST00000245479	NM_000346.3	420	tAc/tGc	3/3	0.304904567224238	2	FACETS	1	0.968	1	0.563	0.513	0.615	CLONAL	1	TRUE	0	0.32	2		758	794	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524759	187524759	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	108	709	0	ENST00000441802.2:c.10921C>A	p.His3641Asn	p.H3641N	ENST00000441802	NM_005245.3	3641	Cac/Aac	19/27	0.304904567224238	2	FACETS	0.836	0.75	0.928	0.418	0.375	0.464	CLONAL	1	TRUE	0	0.32	2		709	807	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637540	52637540	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	90	341	0	ENST00000394830.3:c.2776del	p.Arg926GlufsTer82	p.R926Efs*82	ENST00000394830	NM_018313.4	926	Aga/ga	18/30	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.32	2		341	547	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478757	57478757	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	58	423	0	ENST00000371085.3:c.348del	p.Val117TrpfsTer16	p.V117Wfs*16	ENST00000371085	NM_000516.4	115	Ccc/cc	5/13	1	2	FACETS	0.783	0.674	0.901	0.783	0.674	0.901	CLONAL	1	TRUE	1	0.32	2		423	463	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888304	112888304	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	66	367	0	ENST00000351677.2:c.320C>A	p.Pro107His	p.P107H	ENST00000351677	NM_002834.3	107	cCt/cAt	3/16	1	2	FACETS	0.868	0.756	0.99	0.868	0.756	0.99	CLONAL	1	TRUE	1	0.32	2		367	475	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360600	70360608	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAA	CAGCAGCAA	-	rs762261992	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	57	517	0	ENST00000374080.3:c.6174_6182del	p.Gln2074_Gln2076del	p.Q2074_Q2076del	ENST00000374080		2054	CAGCAGCAA/-	42/45	1	2	FACETS	0.632	0.542	0.73	0.632	0.542	0.73	SUBCLONAL	1	TRUE	1	0.32	2		517	564	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646190	3646190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376620029	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	99	1024	0	ENST00000294008.3:c.1888G>A	p.Gly630Ser	p.G630S	ENST00000294008	NM_032444.2	630	Ggc/Agc	8/15	1	2	FACETS	0.791	0.706	0.882	0.791	0.706	0.882	SUBCLONAL	1	TRUE	1	0.32	2		1024	782	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90970987	90970987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765403660	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	72	345	1	ENST00000265433.3:c.1090G>A	p.Val364Ile	p.V364I	ENST00000265433	NM_002485.4	364	Gta/Ata	9/16	0.298490802250406	2	FACETS	0.798	0.698	0.906	0.399	0.349	0.453	CLONAL	1	TRUE	0	0.32	2		346	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578464	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs563378859	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	138	963	3	ENST00000269305.4:c.466C>T	p.Arg156Cys	p.R156C	ENST00000269305	NM_001126112.2	156	Cgc/Tgc	5/11	1	2	FACETS	0.825	0.75	0.905	0.825	0.75	0.905	CLONAL	1	TRUE	1	0.32	2		966	1045	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659847	227659847	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	52	353	0	ENST00000305123.5:c.3608del	p.Pro1203HisfsTer24	p.P1203Hfs*24	ENST00000305123	NM_005544.2	1203	cCa/ca	1/2	1	2	FACETS	0.979	0.838	1	0.979	0.838	1	CLONAL	1	TRUE	1	0.32	2		353	332	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754580	42754580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	110	852	0	ENST00000222329.4:c.160G>A	p.Glu54Lys	p.E54K	ENST00000222329	NM_006494.2	54	Gaa/Aaa	2/4	1	2	FACETS	0.879	0.79	0.974	0.879	0.79	0.974	CLONAL	1	TRUE	1	0.32	2		852	782	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023864	27023913	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGCCGGCAAGGGCCCGGCGGACATGGCCTCGCAGTGTTGGGGGGCTGC	GGCGCCGGCAAGGGCCCGGCGGACATGGCCTCGCAGTGTTGGGGGGCTGC	-	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	60	361	0	ENST00000324856.7:c.974_1023del	p.Ala325GlyfsTer58	p.A325Gfs*58	ENST00000324856	NM_006015.4	324	GGCGCCGGCAAGGGCCCGGCGGACATGGCCTCGCAGTGTTGGGGGGCTGCg/g	1/20	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.32	2		361	340	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28586383	28586383	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	121	847	0	ENST00000253063.3:c.25C>A	p.Arg9Ser	p.R9S	ENST00000253063	NM_031459.4	9	Cgc/Agc	1/10	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.32	2		847	707	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330567	65330567	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290427088	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	116	440	0	ENST00000342505.4:c.1079G>A	p.Arg360Gln	p.R360Q	ENST00000342505	NM_002227.2	360	cGg/cAg	8/25	1	2	FACETS	0.946	0.853	1	0.946	0.853	1	CLONAL	1	TRUE	1	0.32	2		440	766	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514070	69514070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	119	766	1	ENST00000294312.3:c.611C>T	p.Thr204Ile	p.T204I	ENST00000294312	NM_005117.2	204	aCc/aTc	3/3	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.32	2		767	724	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589639	69589639	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	53	317	0	ENST00000168712.1:c.214G>A	p.Gly72Ser	p.G72S	ENST00000168712	NM_002007.2	72	Ggc/Agc	1/3	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.32	2		317	321	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999062	100999062	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	102	943	0	ENST00000325455.5:c.740C>G	p.Ala247Gly	p.A247G	ENST00000325455	NM_001202474.3	247	gCg/gGg	1/8	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.32	2		943	613	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377315	118377315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	29	352	0	ENST00000534358.1:c.10708G>A	p.Ala3570Thr	p.A3570T	ENST00000534358	NM_005933.3	3570	Gca/Aca	27/36	1	2	FACETS	0.338	0.27	0.415	0.338	0.27	0.415	SUBCLONAL	1	TRUE	1	0.32	2		352	537	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442505	49442505	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs763491594	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	88	452	0	ENST00000301067.7:c.4068T>A	p.Asp1356Glu	p.D1356E	ENST00000301067	NM_003482.3	1356	gaT/gaA	13/54	1	2	FACETS	0.996	0.885	1	0.996	0.885	1	CLONAL	1	TRUE	1	0.32	2		452	552	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202800	133202800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770009143	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	109	798	1	ENST00000320574.5:c.6434G>A	p.Arg2145Gln	p.R2145Q	ENST00000320574	NM_006231.2	2145	cGa/cAa	46/49	1	2	FACETS	0.871	0.782	0.965	0.871	0.782	0.965	CLONAL	1	TRUE	1	0.32	2		799	782	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626685	28626685	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	159	419	0	ENST00000241453.7:c.611A>G	p.Glu204Gly	p.E204G	ENST00000241453	NM_004119.2	204	gAa/gGa	5/24	0.267166222707556	4	FACETS	0.925	0.85	1	0.925	0.85	1	CLONAL	2	TRUE	2	0.32	4		419	709	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857484	9857484	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	65	521	0	ENST00000330684.3:c.3917G>T	p.Arg1306Met	p.R1306M	ENST00000330684	NM_001134407.1	1306	aGg/aTg	13/13	1	2	FACETS	0.87	0.756	0.993	0.87	0.756	0.993	CLONAL	1	TRUE	1	0.32	2		521	467	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862787	9862787	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	82	715	0	ENST00000330684.3:c.2516A>C	p.His839Pro	p.H839P	ENST00000330684	NM_001134407.1	839	cAc/cCc	12/13	1	2	FACETS	0.771	0.68	0.868	0.771	0.68	0.868	SUBCLONAL	1	TRUE	1	0.32	2		715	665	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976202	7976202	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	118	801	0	ENST00000319144.4:c.1993T>C	p.Phe665Leu	p.F665L	ENST00000319144	NM_001139.2	665	Ttc/Ctc	15/15	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.32	2		801	710	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968186	15968186	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1486743506	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	52	260	0	ENST00000268712.3:c.5099C>T	p.Pro1700Leu	p.P1700L	ENST00000268712	NM_006311.3	1700	cCa/cTa	34/46	1	2	FACETS	0.926	0.792	1	0.926	0.792	1	CLONAL	1	TRUE	1	0.32	2		260	351	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127295	17127295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	119	773	1	ENST00000285071.4:c.559C>T	p.Pro187Ser	p.P187S	ENST00000285071	NM_144997.5	187	Ccc/Tcc	6/14	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.32	2		774	728	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584410	39584410	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	56	333	0	ENST00000262039.4:c.1075G>C	p.Asp359His	p.D359H	ENST00000262039	NM_002647.2	359	Gat/Cat	10/25	1	2	FACETS	0.795	0.683	0.918	0.795	0.683	0.918	CLONAL	1	TRUE	1	0.32	2		333	440	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395655	45395655	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	85	347	0	ENST00000262160.6:c.479T>C	p.Val160Ala	p.V160A	ENST00000262160	NM_005901.5	160	gTa/gCa	4/11	1	2	FACETS	0.893	0.79	1	0.893	0.79	1	CLONAL	1	TRUE	1	0.32	2		347	595	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226944	2226944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	117	619	0	ENST00000398665.3:c.4424C>T	p.Ala1475Val	p.A1475V	ENST00000398665	NM_032482.2	1475	gCg/gTg	27/28	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.32	2		619	699	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212471	5212471	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	101	745	0	ENST00000357368.4:c.4646A>G	p.Gln1549Arg	p.Q1549R	ENST00000357368	NM_002850.3	1549	cAg/cGg	31/38	1	2	FACETS	0.882	0.788	0.981	0.882	0.788	0.981	CLONAL	1	TRUE	1	0.32	2		745	716	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61708347	61708347	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	40	239	0	ENST00000401558.2:c.3042T>G	p.His1014Gln	p.H1014Q	ENST00000401558	NM_003400.3	1014	caT/caG	24/25	1	2	FACETS	0.566	0.47	0.672	0.566	0.47	0.672	SUBCLONAL	1	TRUE	1	0.32	2		239	442	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735445	40735445	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	94	666	1	ENST00000373198.4:c.3428T>A	p.Val1143Asp	p.V1143D	ENST00000373198	NM_133170.3	1143	gTc/gAc	25/32	0.257673508960684	0	FACETS	0.636	0.567	0.71			1	SUBCLONAL	1	TRUE	0	0.32	0		667	628	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42843748	42843748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	68	414	0	ENST00000398585.3:c.1171C>T	p.Pro391Ser	p.P391S	ENST00000398585	NM_001135099.1	391	Cct/Tct	10/14	1	2	FACETS	0.742	0.646	0.845	0.742	0.646	0.845	SUBCLONAL	1	TRUE	1	0.32	2		414	573	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437314	52437314	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	32	630	0	ENST00000460680.1:c.1730A>G	p.Glu577Gly	p.E577G	ENST00000460680	NM_004656.3	577	gAg/gGg	14/17	1	2	FACETS	0.353	0.285	0.429	0.353	0.285	0.429	SUBCLONAL	1	TRUE	1	0.32	2		630	567	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651399	52651399	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	36	505	0	ENST00000394830.3:c.1697T>C	p.Met566Thr	p.M566T	ENST00000394830	NM_018313.4	566	aTg/aCg	15/30	1	2	FACETS	0.369	0.303	0.444	0.369	0.303	0.444	SUBCLONAL	1	TRUE	1	0.32	2		505	609	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157678	106157678	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1423923476	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	55	233	0	ENST00000380013.4:c.2582del	p.Asn861ThrfsTer12	p.N861Tfs*12	ENST00000380013	NM_001127208.2	860	cAa/ca	3/11	1	2	FACETS	0.853	0.732	0.984	0.853	0.732	0.984	CLONAL	1	TRUE	1	0.32	2		233	403	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180076487	180076487	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	59	241	0	ENST00000261937.6:c.58+1G>A		p.X20_splice	ENST00000261937	NM_182925.4	20			0.304904567224238	1	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	0	0.32	1		241	301	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43746637	43746638	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	107	538	0	ENST00000523873.1:c.405_406del	p.Asp135GlufsTer26	p.D135Efs*26	ENST00000523873		135	gAT/g	5/8	1	2	FACETS	0.899	0.806	0.997	0.899	0.806	0.997	CLONAL	1	TRUE	1	0.32	2		538	744	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849882	151849882	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143770207	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	46	410	1	ENST00000262189.6:c.12434G>A	p.Arg4145His	p.R4145H	ENST00000262189	NM_170606.2	4145	cGt/cAt	49/59	1	2	FACETS	0.566	0.476	0.665	0.566	0.476	0.665	SUBCLONAL	1	TRUE	1	0.32	2		411	508	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873878	151873878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	30	399	0	ENST00000262189.6:c.8660C>T	p.Ala2887Val	p.A2887V	ENST00000262189	NM_170606.2	2887	gCt/gTt	38/59	1	2	FACETS	0.369	0.297	0.452	0.369	0.297	0.452	SUBCLONAL	1	TRUE	1	0.32	2		399	508	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922991	39922991	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	105	640	1	ENST00000378444.4:c.3717G>T	p.Gln1239His	p.Q1239H	ENST00000378444	NM_001123385.1	1239	caG/caT	8/15	1	2	FACETS	0.859	0.77	0.954	0.859	0.77	0.954	CLONAL	1	TRUE	1	0.32	2		641	764	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	31	309	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	1	2	FACETS	0.959	0.781	1	0.959	0.781	1	CLONAL	1	TRUE	1	0.29	2		309	223	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	96	473	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.29	2		478	607	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	68	436	2	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.987	0.861	1	0.987	0.861	1	CLONAL	1	TRUE	1	0.29	2		438	475	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	39	444	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.978	0.815	1	0.978	0.815	1	CLONAL	1	TRUE	1	0.29	2		444	275	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	25	533	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.787	0.624	0.973	0.787	0.624	0.973	CLONAL	1	TRUE	1	0.29	2		533	219	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	53	284	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.29	2		284	277	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	35	545	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.871	0.717	1	0.871	0.717	1	CLONAL	1	TRUE	1	0.29	2		545	277	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965666	90965666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	21	374	1	ENST00000265433.3:c.1651del	p.Arg551GlyfsTer8	p.R551Gfs*8	ENST00000265433	NM_002485.4	551	Agg/gg	11/16	1	2	FACETS	0.641	0.495	0.81	0.641	0.495	0.81	SUBCLONAL	1	TRUE	1	0.29	2		375	226	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	85	475	0	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	0.949	0.839	1	0.949	0.839	1	CLONAL	1	TRUE	1	0.29	2		475	618	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244968	133244968	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567031389	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	175	895	0	ENST00000320574.5:c.2147C>T	p.Ala716Val	p.A716V	ENST00000320574	NM_006231.2	716	gCg/gTg	19/49	1	2	FACETS	0.944	0.867	1	0.944	0.867	1	CLONAL	1	TRUE	1	0.29	2		895	1279	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	216	1072	4	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.29	2		1076	1361	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191488	10191488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs5030818	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	93	401	0	ENST00000256474.2:c.481C>T	p.Arg161Ter	p.R161*	ENST00000256474	NM_000551.3	161	Cga/Tga	3/3	0.239065860565717	2	FACETS	0.936	0.833	1	0.468	0.416	0.523	CLONAL	1	TRUE	0	0.29	2		401	685	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	30	279	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	1	2	FACETS	0.953	0.773	1	0.953	0.773	1	CLONAL	1	TRUE	1	0.29	2		279	217	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732279	74732279	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	73	433	0	ENST00000359995.5:c.630del	p.Lys211SerfsTer21	p.K211Sfs*21	ENST00000359995	NM_001195427.1	210	ccC/cc	2/3	1	2	FACETS	0.95	0.832	1	0.95	0.832	1	CLONAL	1	TRUE	1	0.29	2		433	530	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233195	69233195	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	25	271	0	ENST00000462284.1:c.1060G>A	p.Glu354Lys	p.E354K	ENST00000462284	NM_002392.5	354	Gaa/Aaa	11/11	1	2	FACETS	0.763	0.604	0.944	0.763	0.604	0.944	CLONAL	1	TRUE	1	0.29	2		271	226	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436148	56436148	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760556127	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	116	699	0	ENST00000407977.2:c.989G>A	p.Arg330Gln	p.R330Q	ENST00000407977		330	cGa/cAa	9/10	1	2	FACETS	0.947	0.853	1	0.947	0.853	1	CLONAL	1	TRUE	1	0.29	2		699	845	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782159	9782159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	136	869	0	ENST00000377346.4:c.2182C>T	p.Leu728Phe	p.L728F	ENST00000377346	NM_005026.3	728	Ctc/Ttc	17/24	1	2	FACETS	0.963	0.875	1	0.963	0.875	1	CLONAL	1	TRUE	1	0.29	2		869	974	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068078	94068078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765322526	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	36	279	0	ENST00000369303.4:c.884G>A	p.Arg295His	p.R295H	ENST00000369303	NM_004440.3	295	cGt/cAt	4/17	1	2	FACETS	0.9	0.743	1	0.9	0.743	1	CLONAL	1	TRUE	1	0.29	2		279	276	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217215	11217215	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	101	525	0	ENST00000361445.4:c.4463G>T	p.Gly1488Val	p.G1488V	ENST00000361445	NM_004958.3	1488	gGg/gTg	30/58	1	2	FACETS	0.836	0.747	0.931	0.836	0.747	0.931	CLONAL	1	TRUE	1	0.29	2		525	833	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135334	30135334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	75	435	0	ENST00000331968.5:c.484C>T	p.His162Tyr	p.H162Y	ENST00000331968	NM_002742.2	162	Cac/Tac	3/18	1	2	FACETS	0.884	0.776	1	0.884	0.776	1	CLONAL	1	TRUE	1	0.29	2		435	585	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090446	37090446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750217	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	74	418	0	ENST00000231790.2:c.2041G>A	p.Ala681Thr	p.A681T	ENST00000231790	NM_000249.3	681	Gct/Act	18/19	0.239065860565717	2	FACETS	0.77	0.674	0.873	0.385	0.337	0.437	SUBCLONAL	1	TRUE	0	0.29	2		418	663	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517762	187517762	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	57	324	1	ENST00000441802.2:c.12932del	p.Pro4311HisfsTer38	p.P4311Hfs*38	ENST00000441802	NM_005245.3	4311	cCa/ca	25/27	1	2	FACETS	0.904	0.777	1	0.904	0.777	1	CLONAL	1	TRUE	1	0.29	2		325	435	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475586	12475586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201781800	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	103	496	0	ENST00000287820.6:c.1460C>T	p.Thr487Met	p.T487M	ENST00000287820	NM_015869.4	487	aCg/aTg	7/7	0.239065860565717	2	FACETS	0.943	0.844	1	0.472	0.422	0.525	CLONAL	1	TRUE	0	0.29	2		496	753	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647460	3647460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776394340	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	151	910	0	ENST00000294008.3:c.1603G>A	p.Ala535Thr	p.A535T	ENST00000294008	NM_032444.2	535	Gca/Aca	7/15	1	2	FACETS	0.873	0.796	0.954	0.873	0.796	0.954	CLONAL	1	TRUE	1	0.29	2		910	1193	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333442	70333442	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	105	626	0	ENST00000373644.4:c.1347G>A	p.Trp449Ter	p.W449*	ENST00000373644	NM_030625.2	449	tgG/tgA	2/12	1	2	FACETS	0.94	0.843	1	0.94	0.843	1	CLONAL	1	TRUE	1	0.29	2		626	770	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443835	49443835	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	159	940	1	ENST00000301067.7:c.3536G>A	p.Gly1179Asp	p.G1179D	ENST00000301067	NM_003482.3	1179	gGc/gAc	11/54	1	2	FACETS	0.94	0.86	1	0.94	0.86	1	CLONAL	1	TRUE	1	0.29	2		941	1167	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432170	121432170	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	155	936	0	ENST00000257555.6:c.917G>A	p.Gly306Asp	p.G306D	ENST00000257555		306	gGc/gAc	4/10	1	2	FACETS	0.989	0.904	1	0.989	0.904	1	CLONAL	1	TRUE	1	0.29	2		936	1081	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434749	110434749	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	156	1065	2	ENST00000375856.3:c.3652C>T	p.Arg1218Trp	p.R1218W	ENST00000375856	NM_003749.2	1218	Cgg/Tgg	1/2	1	2	FACETS	0.968	0.885	1	0.968	0.885	1	CLONAL	1	TRUE	1	0.29	2		1067	1112	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831093	72831093	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	118	541	0	ENST00000268489.5:c.5488G>T	p.Gly1830Cys	p.G1830C	ENST00000268489	NM_006885.3	1830	Ggc/Tgc	9/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.29	2		541	744	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924296	11924296	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	35	175	0	ENST00000353533.5:c.95del	p.Pro32ArgfsTer13	p.P32Rfs*13	ENST00000353533	NM_003010.3	31	caC/ca	1/11	1	2	FACETS	0.789	0.649	0.945	0.789	0.649	0.945	CLONAL	1	TRUE	1	0.29	2		175	306	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637944	39637944	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	72	536	1	ENST00000262039.4:c.2366del	p.Gly789AlafsTer27	p.G789Afs*27	ENST00000262039	NM_002647.2	787	atG/at	22/25	1	2	FACETS	0.911	0.797	1	0.911	0.797	1	CLONAL	1	TRUE	1	0.29	2		537	545	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56377251	56377251	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	40	300	0	ENST00000348428.3:c.872A>G	p.His291Arg	p.H291R	ENST00000348428	NM_006785.3	291	cAt/cGt	6/17	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.29	2		300	222	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110146	3110146	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	84	506	0	ENST00000078429.4:c.137-1G>A		p.X46_splice	ENST00000078429	NM_002067.2	46			1	2	FACETS	0.875	0.773	0.984	0.875	0.773	0.984	CLONAL	1	TRUE	1	0.29	2		506	662	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538338	9538338	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	66	433	0	ENST00000353224.5:c.1660A>G	p.Arg554Gly	p.R554G	ENST00000353224	NM_177990.2	554	Aga/Gga	7/10	1	2	FACETS	0.814	0.707	0.93	0.814	0.707	0.93	CLONAL	1	TRUE	1	0.29	2		433	559	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39706253	39706255	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	52	223	0	ENST00000361337.2:c.313_315del	p.Glu105del	p.E105del	ENST00000361337	NM_003286.2	104	aAGGag/aag	5/21	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.29	2		223	326	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177826	142177826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	18	274	0	ENST00000350721.4:c.7477G>A	p.Val2493Ile	p.V2493I	ENST00000350721	NM_001184.3	2493	Gta/Ata	44/47	1	2	FACETS	0.839	0.637	1	0.839	0.637	1	CLONAL	1	TRUE	1	0.29	2		274	148	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964339	55964339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771563961	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	63	477	0	ENST00000263923.4:c.2474G>A	p.Ser825Asn	p.S825N	ENST00000263923	NM_002253.2	825	aGc/aAc	17/30	1	2	FACETS	0.844	0.731	0.966	0.844	0.731	0.966	CLONAL	1	TRUE	1	0.29	2		477	515	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542783	187542783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	45	413	0	ENST00000441802.2:c.4957G>A	p.Val1653Met	p.V1653M	ENST00000441802	NM_005245.3	1653	Gtg/Atg	10/27	1	2	FACETS	0.946	0.799	1	0.946	0.799	1	CLONAL	1	TRUE	1	0.29	2		413	328	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38968045	38968045	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	30	251	0	ENST00000357387.3:c.1060G>T	p.Asp354Tyr	p.D354Y	ENST00000357387	NM_152756.3	354	Gat/Tat	12/38	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.29	2		251	177	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80074657	80074657	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	52	306	0	ENST00000265081.6:c.2435+2T>C		p.X812_splice	ENST00000265081	NM_002439.4	812			1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.29	2		306	342	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680350	30680350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773991078	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	126	627	1	ENST00000376406.3:c.1369G>A	p.Val457Met	p.V457M	ENST00000376406	NM_014641.2	457	Gtg/Atg	5/15	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.29	2		628	855	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665266	117665266	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs142098208	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	37	320	0	ENST00000368508.3:c.4481T>C	p.Val1494Ala	p.V1494A	ENST00000368508	NM_002944.2	1494	gTt/gCt	27/43	1	2	FACETS	0.889	0.736	1	0.889	0.736	1	CLONAL	1	TRUE	1	0.29	2		320	287	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467769	50467769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749767946	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	124	723	1	ENST00000331340.3:c.1004C>T	p.Pro335Leu	p.P335L	ENST00000331340	NM_006060.4	335	cCg/cTg	8/8	1	2	FACETS	0.915	0.827	1	0.915	0.827	1	CLONAL	1	TRUE	1	0.29	2		724	935	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012377	152012377	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	36	321	0	ENST00000262189.6:c.436G>T	p.Gly146Ter	p.G146*	ENST00000262189	NM_170606.2	146	Gga/Tga	4/59	1	2	FACETS	0.937	0.774	1	0.937	0.774	1	CLONAL	1	TRUE	1	0.29	2		321	265	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0053904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	67	470	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.951	0.83	1	0.951	0.83	1	CLONAL	1	TRUE	1	0.350363567759695	2		470	402	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207071	1207088	+	inframe_deletion	In_Frame_Del	DEL	CCTGCTGGGGGAAGGCTC	CCTGCTGGGGGAAGGCTC	-	novel	NA	P-0053904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	136	901	0	ENST00000326873.7:c.159_176del	p.Leu54_Ser59del	p.L54_S59del	ENST00000326873	NM_000455.4	53	gaCCTGCTGGGGGAAGGCTCt/gat	1/10	0.350363567759695	1	FACETS	0.916	0.835	1	0.916	0.835	1	CLONAL	1	TRUE	0	0.350363567759695	1		901	699	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602278	10602279	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACCGT	novel	NA	P-0053904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	151	839	0	ENST00000171111.5:c.1299_1300insACGGT	p.Cys434ThrfsTer26	p.C434Tfs*26	ENST00000171111	NM_203500.1	433	-/ACGGT	3/6	0.350363567759695	1	FACETS	0.978	0.896	1	0.978	0.896	1	CLONAL	1	TRUE	0	0.350363567759695	1		839	727	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905511	50905512	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0053904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	102	1026	0	ENST00000440232.2:c.640dup	p.Val214GlyfsTer38	p.V214Gfs*38	ENST00000440232	NM_002691.3	213	-/G	6/27	NA	2	FACETS	0.489	0.436	0.546			1	INDETERMINATE	1	TRUE	NA	0.350363567759695	2		1026	1190	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920195	1920195	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	115	601	0	ENST00000382891.5:c.1255G>A	p.Gly419Arg	p.G419R	ENST00000382891	NM_133335.3	419	Ggg/Agg	5/22	0.154496885434918	3	FACETS	0.868	0.781	0.96			1	INDETERMINATE	1	TRUE	NA	0.350363567759695	3		601	889	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987398	2987398	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	192	466	0	ENST00000396946.4:c.31T>A	p.Tyr11Asn	p.Y11N	ENST00000396946	NM_032415.4	11	Tac/Aac	3/25	0.15496404543136	0	FACETS	0.335	0.311	0.36			1	INDETERMINATE	1	TRUE	0	0.637100399846741	0		466	652	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0053906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	203	929	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.177076170406525	3	FACETS	1	0.933	1	1	0.991	1	CLONAL	3	TRUE	1	0.177076170406525	3		929	828	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717615	89717615	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909227	NA	P-0053906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	34	346	0	ENST00000371953.3:c.640C>T	p.Gln214Ter	p.Q214*	ENST00000371953	NM_000314.4	214	Cag/Tag	7/9	0.177076170406525	1	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	TRUE	0	0.177076170406525	1		346	340	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679274	29679274	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0053906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	16	284	0	ENST00000356175.3:c.7395-1G>A		p.X2465_splice	ENST00000356175	NM_000267.3	2465			0.146716860585519	2	FACETS	0.7	0.518	0.918	0.35	0.259	0.459	SUBCLONAL	1	TRUE	0	0.177076170406525	2		284	258	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306605	41306605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	72	693	1	ENST00000373198.4:c.1054C>T	p.Pro352Ser	p.P352S	ENST00000373198	NM_133170.3	352	Ccc/Tcc	7/32	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.177076170406525	2		694	652	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435971	49435971	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	46	845	0	ENST00000301067.7:c.6010C>T	p.Gln2004Ter	p.Q2004*	ENST00000301067	NM_003482.3	2004	Cag/Tag	28/54	1	2	FACETS	0.757	0.636	0.891	0.757	0.636	0.891	SUBCLONAL	1	TRUE	1	0.177076170406525	2		845	686	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589548	69589548	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	67	290	0	ENST00000168712.1:c.305G>T	p.Gly102Val	p.G102V	ENST00000168712	NM_002007.2	102	gGc/gTc	1/3	0.177076170406525	3	FACETS	0.869	0.761	0.984	1	0.965	1	CLONAL	3	TRUE	1	0.177076170406525	3		290	316	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992062	72992062	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	50	767	0	ENST00000268489.5:c.1983G>C	p.Met661Ile	p.M661I	ENST00000268489	NM_006885.3	661	atG/atC	2/10	1	2	FACETS	0.935	0.793	1	0.935	0.793	1	CLONAL	1	TRUE	1	0.177076170406525	2		767	604	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245410	41245410	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs80357233	NA	P-0053906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	75	552	0	ENST00000357654.3:c.2138C>G	p.Ser713Ter	p.S713*	ENST00000357654	NM_007294.3	713	tCa/tGa	10/23	0.146716860585519	2	FACETS	0.844	0.741	0.954	0.844	0.741	0.954	CLONAL	2	TRUE	0	0.177076170406525	2		552	502	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164625	36164625	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	97	792	0	ENST00000300305.3:c.1250C>G	p.Ser417Cys	p.S417C	ENST00000300305		417	tCc/tGc	8/8	0.177076170406525	1	FACETS	0.835	0.746	0.929	1	0.984	1	CLONAL	2	TRUE	0	0.177076170406525	1		792	598	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072594	5072594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	15	326	0	ENST00000381652.3:c.1744G>A	p.Val582Ile	p.V582I	ENST00000381652	NM_004972.3	582	Gtt/Att	13/25	0.177076170406525	1	FACETS	0.568	0.415	0.752	0.568	0.415	0.752	SUBCLONAL	1	TRUE	0	0.177076170406525	1		326	272	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285738	87285738	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	91	840	0	ENST00000277120.3:c.75C>G	p.Phe25Leu	p.F25L	ENST00000277120		25	ttC/ttG	2/19	0.177076170406525	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.177076170406525	1		840	671	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0053907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	273	563	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.586405694190128	5	FACETS	0.987	0.935	1	0.987	0.935	1	CLONAL	3	TRUE	2	0.586405694190128	5		563	591	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420025	49420025	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	382	506	0	ENST00000301067.7:c.15724G>C	p.Val5242Leu	p.V5242L	ENST00000301067	NM_003482.3	5242	Gta/Cta	48/54	0.586405694190128	5	FACETS	1	0.986	1	0.729	0.694	0.766	CLONAL	2	TRUE	2	0.586405694190128	5		506	1119	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0053908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	50	470	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.166139131867977	2	FACETS	0.953	0.81	1	0.476	0.405	0.555	CLONAL	1	TRUE	0	0.248124585632034	2		470	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0053908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	99	742	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	0.248124585632034	1	FACETS	0.956	0.854	1	0.956	0.854	1	CLONAL	1	TRUE	0	0.248124585632034	1		742	731	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576121	88576121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374272958	NA	P-0053908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	106	671	3	ENST00000360948.2:c.1552C>T	p.Arg518Cys	p.R518C	ENST00000360948	NM_001012338.2	518	Cgt/Tgt	13/19	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.248124585632034	2		674	790	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741690	17741690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	73	546	0	ENST00000250003.3:c.361C>T	p.Arg121Cys	p.R121C	ENST00000250003	NM_002478.4	121	Cgc/Tgc	1/3	1	2	FACETS	0.996	0.871	1	0.996	0.871	1	CLONAL	1	TRUE	1	0.248124585632034	2		546	591	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259605	11259605	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	47	529	0	ENST00000361445.4:c.4100G>T	p.Ser1367Ile	p.S1367I	ENST00000361445	NM_004958.3	1367	aGt/aTt	27/58	1	2	FACETS	0.683	0.576	0.801	0.683	0.576	0.801	SUBCLONAL	1	TRUE	1	0.248124585632034	2		529	555	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893603	28893603	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	56	372	0	ENST00000282397.4:c.3243C>A	p.Asp1081Glu	p.D1081E	ENST00000282397	NM_002019.4	1081	gaC/gaA	24/30	1	2	FACETS	0.861	0.738	0.996	0.861	0.738	0.996	CLONAL	1	TRUE	1	0.248124585632034	2		372	524	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665117	29665117	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	76	435	0	ENST00000356175.3:c.6716C>G	p.Ser2239Cys	p.S2239C	ENST00000356175	NM_000267.3	2239	tCt/tGt	44/57	1	2	FACETS	0.982	0.862	1	0.982	0.862	1	CLONAL	1	TRUE	1	0.248124585632034	2		435	624	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983905	2983905	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	100	664	0	ENST00000396946.4:c.625G>T	p.Ala209Ser	p.A209S	ENST00000396946	NM_032415.4	209	Gca/Tca	5/25	0.232648231622866	0	FACETS	0.728	0.649	0.811			1	SUBCLONAL	1	TRUE	0	0.248124585632034	0		664	833	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467623	50467623	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	54	377	0	ENST00000331340.3:c.858G>T	p.Lys286Asn	p.K286N	ENST00000331340	NM_006060.4	286	aaG/aaT	8/8	0.156820147749159	3	FACETS	1	0.951	1	0.634	0.543	0.732	CLONAL	1	TRUE	1	0.248124585632034	3		377	386	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148526880	148526880	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	54	293	0	ENST00000320356.2:c.424G>C	p.Asp142His	p.D142H	ENST00000320356	NM_004456.4	142	Gat/Cat	5/20	0.156820147749159	3	FACETS	0.967	0.827	1	0.483	0.413	0.56	CLONAL	1	TRUE	1	0.248124585632034	3		293	506	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972982	68972982	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	49	315	0	ENST00000288368.4:c.1307A>T	p.Gln436Leu	p.Q436L	ENST00000288368	NM_024870.2	436	cAa/cTa	11/40	0.156820147749159	3	FACETS	0.874	0.74	1	0.437	0.37	0.511	CLONAL	1	TRUE	1	0.248124585632034	3		315	508	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760375	133760375	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	47	729	0	ENST00000318560.5:c.2698C>G	p.Pro900Ala	p.P900A	ENST00000318560	NM_005157.4	900	Ccg/Gcg	11/11	1	2	FACETS	0.655	0.552	0.769	0.655	0.552	0.769	SUBCLONAL	1	TRUE	1	0.248124585632034	2		729	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	8	725	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.170169267634005	2	FACETS	0.171	0.109	0.251	0.085	0.054	0.126	SUBCLONAL	1	TRUE	0	0.252531850369202	2		725	371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	23	969	2	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	0.170169267634005	2	FACETS	0.342	0.266	0.431	0.171	0.133	0.216	SUBCLONAL	1	TRUE	0	0.252531850369202	2		971	532	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913384	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	54	812	0	ENST00000304494.5:c.262G>T	p.Glu88Ter	p.E88*	ENST00000304494	NM_000077.4	88	Gag/Tag	2/3	0.252531850369202	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.252531850369202	1		812	297	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056305	26056305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1256677846	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	53	579	0	ENST00000343677.2:c.352C>T	p.Pro118Ser	p.P118S	ENST00000343677	NM_005319.3	118	Ccc/Tcc	1/1	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.252531850369202	2		579	386	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310208	91310208	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs747341586	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	12	264	2	ENST00000355112.3:c.2268del	p.Asp757ThrfsTer4	p.D757Tfs*4	ENST00000355112	NM_000057.2	754	tcA/tc	10/22	0.252531850369202	1	FACETS	0.624	0.441	0.847	0.624	0.441	0.847	SUBCLONAL	1	TRUE	0	0.252531850369202	1		266	133	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276860	15276861	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs753725730	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	26	784	4	ENST00000263388.2:c.5404dup	p.Ala1802GlyfsTer8	p.A1802Gfs*8	ENST00000263388	NM_000435.2	1802	gct/gGct	30/33	0.252531850369202	1	FACETS	0.463	0.366	0.573	0.463	0.366	0.573	SUBCLONAL	1	TRUE	0	0.252531850369202	1		788	389	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522521	187522521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	30	517	0	ENST00000441802.2:c.11542G>T	p.Glu3848Ter	p.E3848*	ENST00000441802	NM_005245.3	3848	Gaa/Taa	21/27	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.252531850369202	2		517	217	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100947	41100947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372070542	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	38	742	1	ENST00000373198.4:c.1409G>A	p.Arg470Gln	p.R470Q	ENST00000373198	NM_133170.3	470	cGa/cAa	8/32	0.239990760337276	3	FACETS	0.854	0.707	1	0.427	0.353	0.509	CLONAL	1	TRUE	1	0.252531850369202	3		743	397	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40468879	40468879	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	22	421	3	ENST00000264657.5:c.2185del	p.Arg729AlafsTer3	p.R729Afs*3	ENST00000264657	NM_139276.2	729	Cgc/gc	23/24	0.252531850369202	1	FACETS	0.546	0.423	0.687	0.546	0.423	0.687	SUBCLONAL	1	TRUE	0	0.252531850369202	1		424	279	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852188	128852188	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	27	1052	3	ENST00000249373.3:c.2260G>A	p.Ala754Thr	p.A754T	ENST00000249373	NM_005631.4	754	Gcc/Acc	12/12	1	2	FACETS	0.465	0.369	0.575	0.465	0.369	0.575	SUBCLONAL	1	TRUE	1	0.252531850369202	2		1055	460	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99460038	99460038	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	38	498	0	ENST00000268035.6:c.2134G>A	p.Glu712Lys	p.E712K	ENST00000268035	NM_000875.3	712	Gag/Aag	10/21	0.252531850369202	1	FACETS	0.819	0.679	0.974	0.819	0.679	0.974	CLONAL	1	TRUE	0	0.252531850369202	1		498	321	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	17	737	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	0.467	0.349	0.609	0.467	0.349	0.609	SUBCLONAL	1	TRUE	1	0.252531850369202	2		737	288	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424178	49424178	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs886040960	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	38	445	0	ENST00000301067.7:c.13884del	p.Thr4629ProfsTer11	p.T4629Pfs*11	ENST00000301067	NM_003482.3	4628	ccC/cc	42/54	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.252531850369202	2		445	250	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	22	1005	2	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	0.463	0.359	0.585	0.463	0.359	0.585	SUBCLONAL	1	TRUE	1	0.252531850369202	2		1007	376	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612347	1612347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200962332	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	49	1094	2	ENST00000344749.5:c.1672C>T	p.Arg558Cys	p.R558C	ENST00000344749	NM_001136139.2	558	Cgc/Tgc	18/19	0.252531850369202	1	FACETS	0.66	0.559	0.771	0.66	0.559	0.771	SUBCLONAL	1	TRUE	0	0.252531850369202	1		1096	514	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593308	67593308	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	27	325	0	ENST00000274335.5:c.2054A>G	p.Tyr685Cys	p.Y685C	ENST00000274335		685	tAt/tGt	15/15	1	2	FACETS	1	0.815	1	1	0.815	1	CLONAL	1	TRUE	1	0.252531850369202	2		325	210	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349508	89349508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143417087	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	25	746	0	ENST00000301030.4:c.3442G>A	p.Gly1148Ser	p.G1148S	ENST00000301030	NM_001256183.1	1148	Ggc/Agc	9/13	1	2	FACETS	0.542	0.427	0.675	0.542	0.427	0.675	SUBCLONAL	1	TRUE	1	0.252531850369202	2		746	365	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436674	52436676	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	31	678	0	ENST00000460680.1:c.1998_2000del	p.Arg667del	p.R667del	ENST00000460680	NM_004656.3	666	agAAGg/agg	16/17	0.252531850369202	1	FACETS	0.825	0.67	0.999	0.825	0.67	0.999	CLONAL	1	TRUE	0	0.252531850369202	1		678	260	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137439	202137440	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	23	386	0	ENST00000358485.4:c.669_670del	p.Ala224ProfsTer14	p.A224Pfs*14	ENST00000358485	NM_001080125.1	223	TGt/t	4/9	1	2	FACETS	0.915	0.718	1	0.915	0.718	1	CLONAL	1	TRUE	1	0.252531850369202	2		386	199	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111051	193111051	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	11	225	0	ENST00000367435.3:c.584C>T	p.Ser195Phe	p.S195F	ENST00000367435	NM_024529.4	195	tCt/tTt	7/17	1	2	FACETS	0.917	0.64	1	0.917	0.64	1	CLONAL	1	TRUE	1	0.252531850369202	2		225	95	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406663	70406663	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	10	511	0	ENST00000373644.4:c.4181del	p.Asn1394IlefsTer7	p.N1394Ifs*7	ENST00000373644	NM_030625.2	1393	Aaa/aa	4/12	1	2	FACETS	0.412	0.279	0.58	0.412	0.279	0.58	SUBCLONAL	1	TRUE	1	0.252531850369202	2		511	192	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1022565	1022565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	22	583	0	ENST00000358495.3:c.1249C>T	p.Pro417Ser	p.P417S	ENST00000358495	NM_134424.2	417	Cca/Tca	12/12	1	2	FACETS	0.799	0.622	1	0.799	0.622	1	CLONAL	1	TRUE	1	0.252531850369202	2		583	218	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225573	133225573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369171111	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	21	943	0	ENST00000320574.5:c.4091G>A	p.Arg1364His	p.R1364H	ENST00000320574	NM_006231.2	1364	cGt/cAt	32/49	1	2	FACETS	0.4	0.307	0.508	0.4	0.307	0.508	SUBCLONAL	1	TRUE	1	0.252531850369202	2		943	416	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240667	133240667	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	16	659	0	ENST00000320574.5:c.2629G>C	p.Val877Leu	p.V877L	ENST00000320574	NM_006231.2	877	Gtc/Ctc	23/49	1	2	FACETS	0.44	0.325	0.578	0.44	0.325	0.578	SUBCLONAL	1	TRUE	1	0.252531850369202	2		659	288	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134697	41134697	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	35	397	0	ENST00000379561.5:c.931A>T	p.Ser311Cys	p.S311C	ENST00000379561	NM_002015.3	311	Agt/Tgt	2/3	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.252531850369202	2		397	258	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576870	7576871	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCCA	novel	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	55	750	0	ENST00000269305.4:c.972_975dup	p.Glu326TrpfsTer12	p.E326Wfs*12	ENST00000269305	NM_001126112.2	325	-/TGGA	9/11	0.170169267634005	2	FACETS	0.807	0.696	0.925	0.807	0.696	0.925	CLONAL	2	TRUE	0	0.252531850369202	2		750	270	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240289	5240289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368361739	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	104	1055	0	ENST00000357368.4:c.1625C>T	p.Thr542Met	p.T542M	ENST00000357368	NM_002850.3	542	aCg/aTg	12/38	0.252531850369202	1	FACETS	0.786	0.707	0.868	1	0.984	1	SUBCLONAL	2	TRUE	0	0.252531850369202	1		1055	458	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14628971	14628971	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	25	874	0	ENST00000254322.2:c.191T>C	p.Phe64Ser	p.F64S	ENST00000254322	NM_006145.1	64	tTc/tCc	1/3	0.252531850369202	1	FACETS	0.379	0.298	0.473	0.379	0.298	0.473	SUBCLONAL	1	TRUE	0	0.252531850369202	1		874	456	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149597	61149597	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	22	316	0	ENST00000295025.8:c.1787A>G	p.Gln596Arg	p.Q596R	ENST00000295025	NM_002908.2	596	cAg/cGg	11/11	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.252531850369202	2		316	156	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916857	178916857	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs141098973	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	15	569	0	ENST00000263967.3:c.249del	p.Phe83LeufsTer17	p.F83Lfs*17	ENST00000263967	NM_006218.2	82	Ttt/tt	2/21	0.173766425715633	4	FACETS	0.639	0.467	0.844	0.319	0.233	0.422	SUBCLONAL	1	TRUE	2	0.252531850369202	4		569	233	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332747	153332747	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	12	484	0	ENST00000281708.4:c.209del	p.Asn70MetfsTer18	p.N70Mfs*18	ENST00000281708	NM_033632.3	70	aAt/at	2/12	1	2	FACETS	0.49	0.344	0.668	0.49	0.344	0.668	SUBCLONAL	1	TRUE	1	0.252531850369202	2		484	194	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339394	116339394	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	22	391	0	ENST00000397752.3:c.256A>G	p.Thr86Ala	p.T86A	ENST00000397752	NM_000245.2	86	Act/Gct	2/21	1	2	FACETS	0.932	0.727	1	0.932	0.727	1	CLONAL	1	TRUE	1	0.252531850369202	2		391	187	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009251	69009251	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	23	341	0	ENST00000288368.4:c.2369-1G>C		p.X790_splice	ENST00000288368	NM_024870.2	790			1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.252531850369202	2		341	136	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418186	139418186	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	67	1020	1	ENST00000277541.6:c.386G>T	p.Cys129Phe	p.C129F	ENST00000277541	NM_017617.3	129	tGc/tTc	3/34	0.252531850369202	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.252531850369202	1		1021	434	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928995	44928996	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	33	318	0	ENST00000377967.4:c.2098_2099del	p.Ser700LeufsTer29	p.S700Lfs*29	ENST00000377967	NM_021140.2	699	CTc/c	17/29	1	1	FACETS	0.782	0.647	0.929	1	0.953	1	CLONAL	2	TRUE	0	0.252531850369202	1		318	146	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347294	70347294	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	25	300	0	ENST00000374080.3:c.2958G>C	p.Lys986Asn	p.K986N	ENST00000374080		986	aaG/aaC	21/45	1	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.252531850369202	1		300	119	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0053909-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	595	892	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.528234030123	4	FACETS	0.908	0.882	0.933	0.908	0.882	0.933	CLONAL	4	TRUE	0	0.573716260244133	4		892	899	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0053909-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	146	265	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.393197130100913	4	FACETS	1	0.934	1	0.75	0.7	0.799	CLONAL	3	TRUE	0	0.573716260244133	4		265	267	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442854	187442854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867576130	NA	P-0053909-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	8	515	1	ENST00000232014.4:c.1852C>T	p.Arg618Cys	p.R618C	ENST00000232014	NM_001130845.1	618	Cgt/Tgt	9/10	0.25515924797549	5	FACETS	0.162	0.103	0.238	0.054	0.034	0.08	INDETERMINATE	1	TRUE	2	0.573716260244133	5		516	321	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955484	48955484	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053909-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	42	466	0	ENST00000267163.4:c.1600A>C	p.Ser534Arg	p.S534R	ENST00000267163	NM_000321.2	534	Agt/Cgt	17/27	0.573716260244133	6	FACETS	0.576	0.48	0.682	0.144	0.12	0.171	SUBCLONAL	1	TRUE	2	0.573716260244133	6		466	546	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954991	2954991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053909-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	67	895	1	ENST00000396946.4:c.2719G>A	p.Glu907Lys	p.E907K	ENST00000396946	NM_032415.4	907	Gag/Aag	21/25	0.538845164496832	3	FACETS	0.344	0.298	0.394			1	SUBCLONAL	1	TRUE	NA	0.573716260244133	3		896	873	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952076	178952076	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1064793838	NA	P-0053909-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	44	432	0	ENST00000263967.3:c.3131A>G	p.Asn1044Ser	p.N1044S	ENST00000263967	NM_006218.2	1044	aAt/aGt	21/21	0.25515924797549	5	FACETS	1	0.913	1	0.375	0.316	0.438	INDETERMINATE	1	TRUE	2	0.573716260244133	5		432	254	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129205	152129205	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053909-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	126	1197	0	ENST00000206249.3:c.158A>T	p.Asn53Ile	p.N53I	ENST00000206249	NM_000125.3	53	aAc/aTc	1/8	0.573716260244133	4	FACETS	0.999	0.906	1	0.333	0.302	0.366	CLONAL	1	TRUE	1	0.573716260244133	4		1197	692	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0053911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	39	375	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.766	0.635	0.912	0.766	0.635	0.912	CLONAL	1	TRUE	1	0.235685305389631	2		375	432	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624297	89624297	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs797044910	NA	P-0053911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	232	485	0	ENST00000371953.3:c.71A>G	p.Asp24Gly	p.D24G	ENST00000371953	NM_000314.4	24	gAc/gGc	1/9	0.212515930746821	3	FACETS	0.924	0.864	0.985	0.924	0.864	0.985	CLONAL	3	TRUE	0	0.235685305389631	3		485	794	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092917	29092917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908703	NA	P-0053911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	47	411	0	ENST00000328354.6:c.1067C>T	p.Ser356Leu	p.S356L	ENST00000328354	NM_007194.3	356	tCa/tTa	10/15	1	2	FACETS	0.79	0.666	0.926	0.79	0.666	0.926	CLONAL	1	TRUE	1	0.235685305389631	2		411	505	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716329	52716329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863225094	NA	P-0053911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	123	734	1	ENST00000322088.6:c.773G>A	p.Arg258His	p.R258H	ENST00000322088	NM_014225.5	258	cGc/cAc	6/15	1	2	FACETS	0.989	0.893	1	0.989	0.893	1	CLONAL	1	TRUE	1	0.235685305389631	2		735	1055	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256219	123256219	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	50	340	0	ENST00000358487.5:c.1690G>C	p.Val564Leu	p.V564L	ENST00000358487	NM_000141.4	564	Gtt/Ctt	13/18	0.212515930746821	3	FACETS	0.792	0.671	0.925	0.264	0.223	0.309	CLONAL	1	TRUE	0	0.235685305389631	3		340	599	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370912	55370912	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	118	833	0	ENST00000297316.4:c.214A>G	p.Met72Val	p.M72V	ENST00000297316	NM_022454.3	72	Atg/Gtg	1/2	1	2	FACETS	0.976	0.879	1	0.976	0.879	1	CLONAL	1	TRUE	1	0.235685305389631	2		833	1026	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481625	20481627	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0053911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	33	215	0	ENST00000346618.3:c.700_702del	p.Lys234del	p.K234del	ENST00000346618	NM_001949.4	232	AAG/-	3/7	1	2	FACETS	0.875	0.715	1	0.875	0.715	1	CLONAL	1	TRUE	1	0.235685305389631	2		215	320	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097788	27097788	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	61	418	0	ENST00000324856.7:c.3379del	p.Gln1127SerfsTer34	p.Q1127Sfs*34	ENST00000324856	NM_006015.4	1126	tCc/tc	12/20	1	2	FACETS	0.793	0.683	0.912	0.793	0.683	0.912	CLONAL	1	TRUE	1	0.235685305389631	2		418	653	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274768	123274788	+	inframe_deletion	In_Frame_Del	DEL	CTATGCAGTAAATGGCTATCT	CTATGCAGTAAATGGCTATCT	-	novel	NA	P-0053911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	213	539	0	ENST00000358487.5:c.1130_1150del	p.Glu377_Ile383del	p.E377_I383del	ENST00000358487	NM_000141.4	377	gAGATAGCCATTTACTGCATAGgg/ggg	9/18	0.212515930746821	3	FACETS	0.839	0.781	0.898	0.839	0.781	0.898	CLONAL	3	TRUE	0	0.235685305389631	3		539	803	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933372	100933372	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	79	425	0	ENST00000325455.5:c.2018del	p.Phe673SerfsTer11	p.F673Sfs*11	ENST00000325455	NM_001202474.3	673	tTc/tc	4/8	1	2	FACETS	0.883	0.776	0.999	0.883	0.776	0.999	CLONAL	1	TRUE	1	0.235685305389631	2		425	759	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	69	386	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.966	0.844	1	1	0.981	1	CLONAL	2	TRUE	1	0.169303774982174	2		386	422	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0053913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	34	424	1	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	1	0.821	1	1	0.821	1	CLONAL	1	TRUE	1	0.169303774982174	2		425	400	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0053913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	45	249	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	0.169303774982174	1	FACETS	0.882	0.746	1	1	0.968	1	CLONAL	2	TRUE	0	0.169303774982174	1		249	276	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0053913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	64	334	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	1	0.928	1	1	0.982	1	CLONAL	2	TRUE	1	0.169303774982174	2		334	344	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755554	39755554	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	36	558	3	ENST00000288319.7:c.1211del	p.Pro404ArgfsTer25	p.P404Rfs*25	ENST00000288319	NM_182918.3	404	cCg/cg	10/10	1	2	FACETS	0.832	0.683	0.999	0.832	0.683	0.999	CLONAL	1	TRUE	1	0.169303774982174	2		561	511	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0053913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	16	354	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	0.509	0.376	0.67	0.509	0.376	0.67	SUBCLONAL	1	TRUE	1	0.169303774982174	2		354	371	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252865	36252865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060499616	NA	P-0053913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	41	313	0	ENST00000300305.3:c.497G>A	p.Arg166Gln	p.R166Q	ENST00000300305		166	cGa/cAa	4/8	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.169303774982174	2		313	435	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446270	187446270	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	41	701	1	ENST00000232014.4:c.1418del	p.Pro473ArgfsTer117	p.P473Rfs*117	ENST00000232014	NM_001130845.1	473	cCg/cg	6/10	1	2	FACETS	0.721	0.599	0.857	0.721	0.599	0.857	SUBCLONAL	1	TRUE	1	0.169303774982174	2		702	672	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682810	190682810	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	17	297	0	ENST00000441310.2:c.492del	p.Lys164AsnfsTer6	p.K164Nfs*6	ENST00000441310	NM_000534.4	162	gcA/gc	5/13	1	2	FACETS	0.601	0.448	0.784	0.601	0.448	0.784	SUBCLONAL	1	TRUE	1	0.169303774982174	2		297	334	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27217701	27217701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772600804	NA	P-0053913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	61	550	1	ENST00000380036.4:c.3007C>T	p.Arg1003Cys	p.R1003C	ENST00000380036	NM_000459.3	1003	Cgc/Tgc	19/23	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.169303774982174	2		551	660	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481838	56481838	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	151	621	1	ENST00000267101.3:c.766G>T	p.Val256Leu	p.V256L	ENST00000267101	NM_001982.3	256	Gta/Tta	7/28	1	2	FACETS	0.836	0.766	0.909	1	0.993	1	CLONAL	3	TRUE	1	0.169303774982174	2		622	711	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359435	118359435	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	72	452	0	ENST00000534358.1:c.4439A>C	p.Lys1480Thr	p.K1480T	ENST00000534358	NM_005933.3	1480	aAa/aCa	11/36	1	2	FACETS	0.939	0.823	1	1	0.981	1	CLONAL	2	TRUE	1	0.169303774982174	2		452	453	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641236	3641236	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	77	814	1	ENST00000294008.3:c.2403G>T	p.Glu801Asp	p.E801D	ENST00000294008	NM_032444.2	801	gaG/gaT	12/15	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.169303774982174	2		815	841	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821859	72821859	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	49	467	1	ENST00000268489.5:c.10316C>A	p.Pro3439His	p.P3439H	ENST00000268489	NM_006885.3	3439	cCt/cAt	10/10	1	2	FACETS	0.981	0.83	1	0.981	0.83	1	CLONAL	1	TRUE	1	0.169303774982174	2		468	590	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682212	37682212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	45	610	2	ENST00000447079.4:c.3403G>A	p.Ala1135Thr	p.A1135T	ENST00000447079	NM_015083.1	1135	Gca/Aca	13/14	1	2	FACETS	0.931	0.782	1	0.931	0.782	1	CLONAL	1	TRUE	1	0.169303774982174	2		612	571	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688779	47688779	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	50	347	0	ENST00000347630.2:c.521A>G	p.Asn174Ser	p.N174S	ENST00000347630	NM_001007230.1	174	aAt/aGt	7/11	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.169303774982174	2		347	480	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37036969	37037991	+	intron_variant	Intron	DEL	CTGCCTCAGCCTCCCGAGTAGCTGGGAGTACAGGCGTGCATGACCACACCCGGCTAATTTTTTTATTTTTAGTAGAGACGGGGTTTCTCCATGTTGGCCGGGCTGGTCTTGAACTCCTGACCTCAGGTGATCCGCCCACCTCAGCCTCCCCAAGTGTTGGGATTACAGGTGTGAGCCCCCGTGCCCAGCCTATTATCTTATTTCTGAATAAAGAATTGTCTGTGTGGGGAATAGATAACTCTTTCTCATGCAGCCCCTGCTAGAAAATTTGTTTTCTCTAGCAGTTGGTCTGTGCTTATAGGCTACTCTTTGAAAGCACAAAAAATTTATTGACTTCTTTTTTTTGGGTTTTTTTTTTTTTTTGAGACAGAGTTTTGCCCTTGTTGCCCAGGTTGGAGTGCAATGGCGCGATCTCAGCTCACCGCAACCTCCACCTCCTGGGTTCAAGTGATTCTCCTGCCTTAGCCTCCTGAGTAGCTGGGATTACAGGCATGCGTCACCATGCCTGGCTAATTTTGTATTTTTAGTACAAATGGGGTTTCTCCATGTTGGTCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCCACCCGCCTTGGCCTCCCAAAGTGCTGGGATTATGGGTGTGAGCCATTGCGCCTGGCCAGAAAATTCATTGACTTCCTAAAGATTTATTAACTTTCTGCATTACTTTTTTTTTTCCCCTCCATCGTAAATATAAAAGGGAATAGTAGAGAAAATCATTCAGAATTTTATTTTTTAGTGACATTATTTAGTGACATTTTATTAGAGTCACTTAGGAACCTGAGGCTGAATAAAGTTCAGGTAAAAGTAAAATTAGTTGAGAAGAGACATCTGCCAAAAGAAATCTATTTTTAACTTCACTTGCTGTCTTTCCTAGAGGAACAGAAATAGTGCTGAATGTCCTATTAGAAATGATGGTTGCTCTGCCCGTCTCTTCCCTCTCTCTCACACAATATGTAAACTCATACAGTGTATGAGCCTGTAAGACAAAGGAAAAAC	CTGCCTCAGCCTCCCGAGTAGCTGGGAGTACAGGCGTGCATGACCACACCCGGCTAATTTTTTTATTTTTAGTAGAGACGGGGTTTCTCCATGTTGGCCGGGCTGGTCTTGAACTCCTGACCTCAGGTGATCCGCCCACCTCAGCCTCCCCAAGTGTTGGGATTACAGGTGTGAGCCCCCGTGCCCAGCCTATTATCTTATTTCTGAATAAAGAATTGTCTGTGTGGGGAATAGATAACTCTTTCTCATGCAGCCCCTGCTAGAAAATTTGTTTTCTCTAGCAGTTGGTCTGTGCTTATAGGCTACTCTTTGAAAGCACAAAAAATTTATTGACTTCTTTTTTTTGGGTTTTTTTTTTTTTTTGAGACAGAGTTTTGCCCTTGTTGCCCAGGTTGGAGTGCAATGGCGCGATCTCAGCTCACCGCAACCTCCACCTCCTGGGTTCAAGTGATTCTCCTGCCTTAGCCTCCTGAGTAGCTGGGATTACAGGCATGCGTCACCATGCCTGGCTAATTTTGTATTTTTAGTACAAATGGGGTTTCTCCATGTTGGTCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCCACCCGCCTTGGCCTCCCAAAGTGCTGGGATTATGGGTGTGAGCCATTGCGCCTGGCCAGAAAATTCATTGACTTCCTAAAGATTTATTAACTTTCTGCATTACTTTTTTTTTTCCCCTCCATCGTAAATATAAAAGGGAATAGTAGAGAAAATCATTCAGAATTTTATTTTTTAGTGACATTATTTAGTGACATTTTATTAGAGTCACTTAGGAACCTGAGGCTGAATAAAGTTCAGGTAAAAGTAAAATTAGTTGAGAAGAGACATCTGCCAAAAGAAATCTATTTTTAACTTCACTTGCTGTCTTTCCTAGAGGAACAGAAATAGTGCTGAATGTCCTATTAGAAATGATGGTTGCTCTGCCCGTCTCTTCCCTCTCTCTCACACAATATGTAAACTCATACAGTGTATGAGCCTGTAAGACAAAGGAAAAAC	-	novel	NA	P-0053913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	0	45	0	0	ENST00000231790.2:c.117-1141_117-119del		p.*39*	ENST00000231790	NM_000249.3	-/756			0.169303774982174	2	FACETS		NA	1	1	0.984	1	NA	12	TRUE	0	0.169303774982174	2		0	45	SUCCESS
APC	324	MSKCC	GRCh37	5	112174110	112174110	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	62	250	0	ENST00000257430.4:c.2819C>A	p.Ser940Ter	p.S940*	ENST00000257430	NM_000038.5	940	tCg/tAg	16/16	1	2	FACETS	1	0.93	1	1	0.981	1	CLONAL	2	TRUE	1	0.169303774982174	2		250	330	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164218	47164218	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	80	344	0	ENST00000409792.3:c.1908del	p.Phe636LeufsTer6	p.F636Lfs*6	ENST00000409792	NM_014159.6	636	ttT/tt	3/21	0.368812407219736	1	FACETS	0.869	0.769	0.975	0.869	0.769	0.975	CLONAL	1	TRUE	0	0.368812407219736	1		344	407	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226566916	226566916	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	157	635	0	ENST00000366794.5:c.1672G>C	p.Gly558Arg	p.G558R	ENST00000366794	NM_001618.3	558	Ggc/Cgc	12/23	1	2	FACETS	0.961	0.88	1	0.961	0.88	1	CLONAL	1	TRUE	1	0.368812407219736	2		635	886	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691130	18691130	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	96	421	0	ENST00000266497.5:c.3241T>A	p.Phe1081Ile	p.F1081I	ENST00000266497		1081	Ttt/Att	23/31	0.368812407219736	4	FACETS	1	0.96	1	0.387	0.345	0.431	CLONAL	1	TRUE	1	0.368812407219736	4		421	614	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486275	99486275	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	155	565	0	ENST00000268035.6:c.3581A>G	p.Asp1194Gly	p.D1194G	ENST00000268035	NM_000875.3	1194	gAc/gGc	19/21	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.368812407219736	2		565	792	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619071	37619071	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	163	681	0	ENST00000447079.4:c.747T>A	p.Ser249Arg	p.S249R	ENST00000447079	NM_015083.1	249	agT/agA	1/14	1	2	FACETS	0.918	0.842	0.997	0.918	0.842	0.997	CLONAL	1	TRUE	1	0.368812407219736	2		681	963	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183762	10183762	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	264	1133	0	ENST00000256474.2:c.231C>A	p.Cys77Ter	p.C77*	ENST00000256474	NM_000551.3	77	tgC/tgA	1/3	0.368812407219736	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.368812407219736	1		1133	1042	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436794	52436794	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0053914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	180	728	0	ENST00000460680.1:c.1983+1G>A		p.X661_splice	ENST00000460680	NM_004656.3	661			0.368812407219736	1	FACETS	0.985	0.91	1	0.985	0.91	1	CLONAL	1	TRUE	0	0.368812407219736	1		728	808	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164010	47164010	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	65	321	0	ENST00000409792.3:c.2116del	p.Glu706AsnfsTer61	p.E706Nfs*61	ENST00000409792	NM_014159.6	706	Gaa/aa	3/21	1	2	FACETS	0.867	0.758	0.983	1	0.978	1	CLONAL	2	TRUE	1	0.25	2		321	300	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0053920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	123	563	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.405506772167206	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.405506772167206	1		563	458	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913273	NA	P-0053920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	9	222	0	ENST00000263967.3:c.1624G>C	p.Glu542Gln	p.E542Q	ENST00000263967	NM_006218.2	542	Gaa/Caa	10/21	0.405506772167206	1	FACETS	0.116	0.076	0.167	0.116	0.076	0.167	SUBCLONAL	1	TRUE	0	0.405506772167206	1		222	305	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577562	7577563	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGT	novel	NA	P-0053920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	205	862	0	ENST00000269305.4:c.716_718dup	p.Asn239dup	p.N239dup	ENST00000269305	NM_001126112.2	239	agt/aACAgt	7/11	0.405506772167206	1	FACETS	0.921	0.856	0.989	0.921	0.856	0.989	CLONAL	1	TRUE	0	0.405506772167206	1		862	875	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691763	30691763	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	97	359	0	ENST00000295754.5:c.265A>G	p.Arg89Gly	p.R89G	ENST00000295754	NM_003242.5	89	Aga/Gga	3/7	0.405506772167206	1	FACETS	0.842	0.755	0.934	0.842	0.755	0.934	CLONAL	1	TRUE	0	0.405506772167206	1		359	453	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114790	108114790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	294	452	0	ENST00000278616.4:c.607G>A	p.Asp203Asn	p.D203N	ENST00000278616	NM_000051.3	203	Gac/Aac	6/63	1	2	FACETS	0.968	0.917	1	0.968	0.917	1	CLONAL	1	TRUE	1	0.907048458306448	2		452	670	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720807	89720807	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	106	264	0	ENST00000371953.3:c.958T>A	p.Leu320Ile	p.L320I	ENST00000371953	NM_000314.4	320	Tta/Ata	8/9	1	2	FACETS	0.814	0.741	0.89	0.814	0.741	0.89	CLONAL	1	TRUE	1	0.907048458306448	2		264	287	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593605	55593611	+	protein_altering_variant	In_Frame_Del	DEL	GAAGGTT	GAAGGTT	TAAG	novel	NA	P-0053921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	273	417	1	ENST00000288135.5:c.1671_1677delinsTAAG	p.Trp557_Val559delinsCysLys	p.W557_V559delinsCK	ENST00000288135	NM_000222.2	557	tgGAAGGTT/tgTAAG	11/21	0.907048458306448	1	FACETS	0.985	0.953	1	0.985	0.953	1	CLONAL	1	TRUE	0	0.907048458306448	1		418	334	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0053925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	183	444	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.178417301836455	4	FACETS	0.94	0.873	1			1	CLONAL	4	TRUE	NA	0.204711006713559	4		444	573	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0053925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	19	420	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.204711006713559	3	FACETS	0.701	0.532	0.899	0.234	0.177	0.3	SUBCLONAL	1	TRUE	0	0.204711006713559	3		420	292	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	32	281	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	0.204711006713559	5	FACETS	1	0.872	1			1	CLONAL	2	TRUE	NA	0.204711006713559	5		281	189	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967270	134967270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374549505	NA	P-0053925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	86	699	1	ENST00000398015.3:c.2609G>A	p.Arg870Gln	p.R870Q	ENST00000398015	NM_004441.4	870	cGg/cAg	14/16	0.204711006713559	3	FACETS	0.882	0.778	0.994	0.294	0.259	0.332	CLONAL	1	TRUE	0	0.204711006713559	3		700	1050	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196879	108196880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs773570504	NA	P-0053925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	91	340	0	ENST00000278616.4:c.6908dup	p.Glu2304GlyfsTer69	p.E2304Gfs*69	ENST00000278616	NM_000051.3	2301	gca/gcAa	47/63	0.204711006713559	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.204711006713559	2		340	370	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955513	90955513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	65	421	0	ENST00000265433.3:c.2152G>A	p.Glu718Lys	p.E718K	ENST00000265433	NM_002485.4	718	Gaa/Aaa	14/16	0.197246424310789	4	FACETS	1	0.968	1	0.707	0.614	0.808	CLONAL	1	TRUE	2	0.204711006713559	4		421	541	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266050	41266639	+	splice_donor_variant,splice_acceptor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	CAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCAAGATGATG	CAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCAAGATGATG	-	novel	NA	P-0053925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	30	320	0	ENST00000349496.5:c.51_440del		p.X17_splice	ENST00000349496	NM_001904.3	17	cCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCAAGATGATGca/cca	3-4/15	1	2	FACETS	0.761	0.614	0.929	0.761	0.614	0.929	CLONAL	1	TRUE	1	0.204711006713559	2		320	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0053926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	299	747	1	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.795856356321518	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.809319798601504	1		748	423	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0053926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	163	402	1	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.809319798601504	1	FACETS	0.926	0.873	0.978	0.926	0.873	0.978	CLONAL	1	TRUE	0	0.809319798601504	1		403	259	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417865	138417865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	371	418	0	ENST00000289153.2:c.1654G>A	p.Glu552Lys	p.E552K	ENST00000289153	NM_006219.2	552	Gaa/Aaa	11/22	0.744954170029196	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.809319798601504	3		418	632	SUCCESS
APC	324	MSKCC	GRCh37	5	112175907	112175907	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0053926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	90	189	1	ENST00000257430.4:c.4616C>G	p.Ser1539Ter	p.S1539*	ENST00000257430	NM_000038.5	1539	tCa/tGa	16/16	0.809319798601504	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.809319798601504	1		190	132	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317700	163317700	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	75	148	0	ENST00000271452.3:c.1096G>T	p.Val366Phe	p.V366F	ENST00000271452	NM_145697.2	366	Gtt/Ttt	12/14	0.399684931412208	3	FACETS	1	0.892	1	0.506	0.446	0.571	CLONAL	1	TRUE	1	0.482409289393828	3		148	381	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992003	72992004	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0053927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	159	713	0	ENST00000268489.5:c.2040_2041dup	p.Lys681IlefsTer11	p.K681Ifs*11	ENST00000268489	NM_006885.3	681	aag/aTAag	2/10	0.482409289393828	1	FACETS	0.775	0.713	0.84	0.775	0.713	0.84	SUBCLONAL	1	TRUE	0	0.482409289393828	1		713	645	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449747	149449747	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	161	693	0	ENST00000286301.3:c.1317T>G	p.Asp439Glu	p.D439E	ENST00000286301	NM_005211.3	439	gaT/gaG	9/22	0.408845635322595	1	FACETS	0.695	0.638	0.753	0.695	0.638	0.753	SUBCLONAL	1	TRUE	0	0.482409289393828	1		693	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0053928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	555	748	0	ENST00000269305.4:c.376-1G>T		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.914242060889972	1	FACETS	0.999	0.981	1	0.999	0.981	1	CLONAL	1	TRUE	0	0.937088859763207	1		748	630	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163671	32163671	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1257471825	NA	P-0053928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	233	419	0	ENST00000375023.3:c.5555del	p.Pro1852ArgfsTer33	p.P1852Rfs*33	ENST00000375023	NM_004557.3	1852	cCg/cg	30/30	0.457504427372556	1	FACETS	0.382	0.358	0.407	0.382	0.358	0.407	INDETERMINATE	1	TRUE	0	0.937088859763207	1		419	691	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119502	193119502	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	97	235	3	ENST00000367435.3:c.897A>C	p.Lys299Asn	p.K299N	ENST00000367435	NM_024529.4	299	aaA/aaC	9/17	0.476693241795981	1	FACETS	0.307	0.276	0.34	0.307	0.276	0.34	INDETERMINATE	1	TRUE	0	0.937088859763207	1		238	358	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398059	4398059	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	443	512	10	ENST00000261254.3:c.623G>T	p.Gly208Val	p.G208V	ENST00000261254	NM_001759.3	208	gGa/gTa	4/5	NA	2	FACETS	0.977	0.936	1			1	INDETERMINATE	1	TRUE	NA	0.937088859763207	2		522	968	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881471	48881471	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0053928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	201	210	4	ENST00000267163.4:c.193A>T	p.Lys65Ter	p.K65*	ENST00000267163	NM_000321.2	65	Aag/Tag	2/27	0.937088859763207	1	FACETS	0.983	0.951	1	0.983	0.951	1	CLONAL	1	TRUE	0	0.937088859763207	1		214	232	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059200	42059200	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1423994019	NA	P-0053928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	353	359	13	ENST00000219905.7:c.8920G>C	p.Glu2974Gln	p.E2974Q	ENST00000219905	NM_001164273.1	2974	Gag/Cag	24/24	1	2	FACETS	0.965	0.92	1	0.965	0.92	1	CLONAL	1	TRUE	1	0.937088859763207	2		372	781	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783821	50783821	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	390	443	5	ENST00000398568.2:c.212G>C	p.Gly71Ala	p.G71A	ENST00000398568	NM_001042412.1	71	gGa/gCa	3/18	0.937088859763207	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.937088859763207	1		448	437	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923853	72923853	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs745635132	NA	P-0053928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	421	389	15	ENST00000268489.5:c.3225G>T	p.Gln1075His	p.Q1075H	ENST00000268489	NM_006885.3	1075	caG/caT	4/10	0.937088859763207	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.937088859763207	1		404	468	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62008721	62008721	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs750544228	NA	P-0053928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	925	677	56	ENST00000392795.3:c.95C>G	p.Ser32Trp	p.S32W	ENST00000392795	NM_001039933.1	32	tCg/tGg	2/6	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.937088859763207	NA		733	1659	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467160	25467160	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	530	580	8	ENST00000264709.3:c.1715C>G	p.Ala572Gly	p.A572G	ENST00000264709	NM_175629.2	572	gCc/gGc	15/23	1	2	FACETS	0.91	0.874	0.946	0.91	0.874	0.946	CLONAL	1	TRUE	1	0.937088859763207	2		588	1243	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342933	225342933	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs775596955	NA	P-0053928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	293	346	7	ENST00000264414.4:c.2159A>G	p.Asn720Ser	p.N720S	ENST00000264414	NM_003590.4	720	aAt/aGt	15/16	1	2	FACETS	0.958	0.908	1	0.958	0.908	1	CLONAL	1	TRUE	1	0.937088859763207	2		353	653	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706902	117706902	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	335	348	4	ENST00000368508.3:c.2248G>T	p.Ala750Ser	p.A750S	ENST00000368508	NM_002944.2	750	Gct/Tct	15/43	1	2	FACETS	0.983	0.937	1	0.983	0.937	1	CLONAL	1	TRUE	1	0.937088859763207	2		352	727	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396208	139396208	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	688	762	19	ENST00000277541.6:c.5630G>T	p.Arg1877Leu	p.R1877L	ENST00000277541	NM_017617.3	1877	cGc/cTc	30/34	1	2	FACETS	0.964	0.932	0.997	0.964	0.932	0.997	CLONAL	1	TRUE	1	0.937088859763207	2		781	1523	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410670	63410670	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	283	691	10	ENST00000330258.3:c.2497G>T	p.Asp833Tyr	p.D833Y	ENST00000330258	NM_152424.3	833	Gat/Tat	2/2	0.5878300421536	1	FACETS	0.36	0.339	0.382	0.36	0.339	0.382	SUBCLONAL	1	TRUE	0	0.937088859763207	1		701	891	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937084	76937084	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	125	360	6	ENST00000373344.5:c.3664G>T	p.Asp1222Tyr	p.D1222Y	ENST00000373344	NM_000489.3	1222	Gat/Tat	9/35	0.5878300421536	1	FACETS	0.353	0.322	0.384	0.353	0.322	0.384	SUBCLONAL	1	TRUE	0	0.937088859763207	1		366	402	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0053929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	145	470	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.443701868231548	3	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	TRUE	1	0.443701868231548	3		470	399	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117746808	117746808	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	96	264	0	ENST00000368508.3:c.12T>G	p.Ile4Met	p.I4M	ENST00000368508	NM_002944.2	4	atT/atG	1/43	1	2	FACETS	0.801	0.725	0.88	1	0.985	1	CLONAL	2	TRUE	1	0.443701868231548	2		264	270	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390143	89390143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	31	315	0	ENST00000336596.2:c.892G>A	p.Glu298Lys	p.E298K	ENST00000336596	NM_005233.5	298	Gaa/Aaa	4/17	0.226254584060751	1	FACETS	0.299	0.241	0.363	0.299	0.241	0.363	INDETERMINATE	1	TRUE	0	0.443701868231548	1		315	364	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729094	66729099	+	inframe_deletion	In_Frame_Del	DEL	TGGAGA	TGGAGA	-	novel	NA	P-0053931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	54	514	0	ENST00000307102.5:c.303_308del	p.Glu102_Ile103del	p.E102_I103del	ENST00000307102	NM_002755.3	101	cTGGAGAtc/ctc	3/11	1	2	FACETS	0.82	0.699	0.953	0.82	0.699	0.953	CLONAL	1	TRUE	1	0.18	2		514	732	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0053932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	103	258	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.899	0.81	0.992	0.899	0.81	0.992	CLONAL	1	TRUE	1	0.54415862770668	2		258	421	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0053932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	78	935	2	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	0.539083563458998	3	FACETS	0.284	0.248	0.322	0.142	0.124	0.161	SUBCLONAL	1	TRUE	1	0.54415862770668	3		937	1285	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538374	9538374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868564987	NA	P-0053932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	86	344	0	ENST00000353224.5:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000353224	NM_177990.2	542	Gaa/Aaa	7/10	1	2	FACETS	0.898	0.801	1	0.898	0.801	1	CLONAL	1	TRUE	1	0.54415862770668	2		344	352	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871292	35871292	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	93	336	0	ENST00000303115.3:c.514G>A	p.Glu172Lys	p.E172K	ENST00000303115	NM_002185.3	172	Gaa/Aaa	4/8	1	2	FACETS	0.886	0.793	0.982	0.886	0.793	0.982	CLONAL	1	TRUE	1	0.54415862770668	2		336	386	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435420	110435420	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1049519615	NA	P-0053932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	268	594	1	ENST00000375856.3:c.2981C>T	p.Pro994Leu	p.P994L	ENST00000375856	NM_003749.2	994	cCg/cTg	1/2	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.54415862770668	2		595	882	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088672	27088672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	242	797	0	ENST00000324856.7:c.2281C>T	p.Gln761Ter	p.Q761*	ENST00000324856	NM_006015.4	761	Cag/Tag	7/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.54415862770668	2		797	855	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187456	32187456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	231	893	0	ENST00000375023.3:c.1423G>A	p.Asp475Asn	p.D475N	ENST00000375023	NM_004557.3	475	Gat/Aat	8/30	0.539083563458998	3	FACETS	0.983	0.916	1	0.491	0.458	0.526	CLONAL	1	TRUE	1	0.54415862770668	3		893	1099	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298174	123298174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	116	555	0	ENST00000358487.5:c.680G>A	p.Gly227Glu	p.G227E	ENST00000358487	NM_000141.4	227	gGa/gAa	6/18	0.54415862770668	1	FACETS	0.766	0.696	0.839	0.766	0.696	0.839	SUBCLONAL	1	TRUE	0	0.54415862770668	1		555	405	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631415	117631415	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	127	390	0	ENST00000368508.3:c.6263C>T	p.Ser2088Phe	p.S2088F	ENST00000368508	NM_002944.2	2088	tCc/tTc	40/43	0.523207876990058	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.54415862770668	1		390	319	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488718	212488718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267599191	NA	P-0053932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	19	564	0	ENST00000342788.4:c.2131C>T	p.Arg711Cys	p.R711C	ENST00000342788	NM_005235.2	711	Cgt/Tgt	18/28	1	2	FACETS	0.128	0.096	0.165	0.128	0.096	0.165	SUBCLONAL	1	TRUE	1	0.54415862770668	2		564	546	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463566	25463566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	188	765	0	ENST00000264709.3:c.2116G>A	p.Gly706Arg	p.G706R	ENST00000264709	NM_175629.2	706	Ggg/Agg	18/23	1	2	FACETS	0.916	0.849	0.986	0.916	0.849	0.986	CLONAL	1	TRUE	1	0.54415862770668	2		765	754	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375978	8375978	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556078617	NA	P-0053932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	110	424	0	ENST00000356435.5:c.4619C>T	p.Thr1540Ile	p.T1540I	ENST00000356435		1540	aCc/aTc	28/35	1	2	FACETS	0.883	0.798	0.971	0.883	0.798	0.971	CLONAL	1	TRUE	1	0.54415862770668	2		424	458	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69456187	69456187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746088878	NA	P-0053932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	83	875	0	ENST00000227507.2:c.106G>A	p.Glu36Lys	p.E36K	ENST00000227507	NM_053056.2	36	Gag/Aag	1/5	1	2	FACETS	0.353	0.31	0.398	0.353	0.31	0.398	SUBCLONAL	1	TRUE	1	0.54415862770668	2		875	865	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727456	66727470	+	inframe_deletion	In_Frame_Del	DEL	CAGAAGGTGGGAGAA	CAGAAGGTGGGAGAA	-	novel	NA	P-0053932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	137	565	0	ENST00000307102.5:c.173_187del	p.Gln58_Glu62del	p.Q58_E62del	ENST00000307102	NM_002755.3	58	CAGAAGGTGGGAGAA/-	2/11	1	2	FACETS	0.874	0.798	0.953	0.874	0.798	0.953	CLONAL	1	TRUE	1	0.54415862770668	2		565	576	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258102	123258102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868142351	NA	P-0053932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	79	461	0	ENST00000358487.5:c.1579G>A	p.Asp527Asn	p.D527N	ENST00000358487	NM_000141.4	527	Gac/Aac	12/18	0.54415862770668	1	FACETS	0.582	0.515	0.653	0.582	0.515	0.653	SUBCLONAL	1	TRUE	0	0.54415862770668	1		461	363	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964398	70964398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1289330671	NA	P-0053932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	106	531	0	ENST00000276594.2:c.1630G>A	p.Asp544Asn	p.D544N	ENST00000276594	NM_024504.3	544	Gat/Aat	8/8	1	2	FACETS	0.832	0.75	0.919	0.832	0.75	0.919	CLONAL	1	TRUE	1	0.54415862770668	2		531	468	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812236	212812236	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	98	380	0	ENST00000342788.4:c.340C>T	p.Arg114Ter	p.R114*	ENST00000342788	NM_005235.2	114	Cga/Tga	3/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.54415862770668	2		380	328	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533851	63533851	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1451720453	NA	P-0053932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	198	849	0	ENST00000307078.5:c.1303C>T	p.Pro435Ser	p.P435S	ENST00000307078	NM_004655.3	435	Ccg/Tcg	6/11	1	2	FACETS	0.922	0.856	0.991	0.922	0.856	0.991	CLONAL	1	TRUE	1	0.54415862770668	2		849	789	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468028	120468028	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	240	751	1	ENST00000256646.2:c.4411C>T	p.Pro1471Ser	p.P1471S	ENST00000256646	NM_024408.3	1471	Ccc/Tcc	25/34	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.54415862770668	2		752	820	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195383	102195383	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1215021212	NA	P-0053932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	107	380	0	ENST00000263464.3:c.143G>A	p.Arg48Lys	p.R48K	ENST00000263464	NM_001165.4	48	aGg/aAg	2/9	1	2	FACETS	0.925	0.836	1	0.925	0.836	1	CLONAL	1	TRUE	1	0.54415862770668	2		380	425	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366557	118366557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	43	415	0	ENST00000534358.1:c.5506G>A	p.Gly1836Arg	p.G1836R	ENST00000534358	NM_005933.3	1836	Gga/Aga	19/36	1	2	FACETS	0.321	0.268	0.379	0.321	0.268	0.379	SUBCLONAL	1	TRUE	1	0.54415862770668	2		415	493	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377073	118377073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376937581	NA	P-0053932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	123	487	0	ENST00000534358.1:c.10466C>T	p.Thr3489Met	p.T3489M	ENST00000534358	NM_005933.3	3489	aCg/aTg	27/36	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.54415862770668	2		487	438	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573944	18573945	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	71	332	0	ENST00000266497.5:c.2262_2263delinsAA	p.Glu755Lys	p.E755K	ENST00000266497		754	ctGGaa/ctAAaa	15/31	1	2	FACETS	0.897	0.79	1	0.897	0.79	1	CLONAL	1	TRUE	1	0.54415862770668	2		332	291	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058885	42058885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1346242175	NA	P-0053932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	112	374	0	ENST00000219905.7:c.8605C>T	p.Pro2869Ser	p.P2869S	ENST00000219905	NM_001164273.1	2869	Cct/Tct	24/24	1	2	FACETS	0.96	0.869	1	0.96	0.869	1	CLONAL	1	TRUE	1	0.54415862770668	2		374	429	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358477	91358477	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	151	498	0	ENST00000355112.3:c.4222C>T	p.Pro1408Ser	p.P1408S	ENST00000355112	NM_000057.2	1408	Ccg/Tcg	22/22	1	2	FACETS	0.873	0.801	0.948	0.873	0.801	0.948	CLONAL	1	TRUE	1	0.54415862770668	2		498	636	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40745991	40745991	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	220	901	0	ENST00000392038.2:c.600G>C	p.Glu200Asp	p.E200D	ENST00000392038	NM_001626.4	200	gaG/gaC	7/14	1	2	FACETS	0.866	0.806	0.927	0.866	0.806	0.927	CLONAL	1	TRUE	1	0.54415862770668	2		901	934	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295747	212295747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	141	558	1	ENST00000342788.4:c.2566C>T	p.His856Tyr	p.H856Y	ENST00000342788	NM_005235.2	856	Cat/Tat	21/28	1	2	FACETS	0.871	0.797	0.948	0.871	0.797	0.948	CLONAL	1	TRUE	1	0.54415862770668	2		559	595	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400181	41400181	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	146	515	0	ENST00000373198.4:c.578C>A	p.Pro193His	p.P193H	ENST00000373198	NM_133170.3	193	cCt/cAt	5/32	1	2	FACETS	0.935	0.857	1	0.935	0.857	1	CLONAL	1	TRUE	1	0.54415862770668	2		515	574	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326096	62326096	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs755886610	NA	P-0053932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	48	894	0	ENST00000360203.5:c.3112G>A	p.Asp1038Asn	p.D1038N	ENST00000360203	NM_001283009.1	1038	Gac/Aac	32/35	1	2	FACETS	0.197	0.165	0.231	0.197	0.165	0.231	SUBCLONAL	1	TRUE	1	0.54415862770668	2		894	897	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673038	30673038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745572919	NA	P-0053932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	159	798	0	ENST00000376406.3:c.3922C>T	p.Arg1308Trp	p.R1308W	ENST00000376406	NM_014641.2	1308	Cgg/Tgg	10/15	0.539083563458998	3	FACETS	0.767	0.703	0.835	0.384	0.351	0.418	SUBCLONAL	1	TRUE	1	0.54415862770668	3		798	969	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169165	32169165	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	236	974	0	ENST00000375023.3:c.3868G>A	p.Asp1290Asn	p.D1290N	ENST00000375023	NM_004557.3	1290	Gac/Aac	22/30	0.539083563458998	3	FACETS	1	0.954	1	0.514	0.479	0.55	CLONAL	1	TRUE	1	0.54415862770668	3		974	1073	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862949	117862949	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	134	549	0	ENST00000297338.2:c.1528C>T	p.Pro510Ser	p.P510S	ENST00000297338	NM_006265.2	510	Cca/Tca	12/14	1	2	FACETS	0.968	0.884	1	0.968	0.884	1	CLONAL	1	TRUE	1	0.54415862770668	2		549	509	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410122	139410123	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	246	1016	0	ENST00000277541.6:c.1715_1716delinsTT	p.Pro572Leu	p.P572L	ENST00000277541	NM_017617.3	572	cCC/cTT	11/34	1	2	FACETS	0.904	0.846	0.964	0.904	0.846	0.964	CLONAL	1	TRUE	1	0.54415862770668	2		1016	1000	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0053933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	238	378	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.819245159195569	2		378	550	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859593	151859593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	268	529	1	ENST00000262189.6:c.11069C>T	p.Ser3690Leu	p.S3690L	ENST00000262189	NM_170606.2	3690	tCa/tTa	43/59	1	2	FACETS	0.94	0.887	0.994	0.94	0.887	0.994	CLONAL	1	TRUE	1	0.819245159195569	2		530	696	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62322280	62322280	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	491	904	0	ENST00000360203.5:c.2536G>A	p.Gly846Arg	p.G846R	ENST00000360203	NM_001283009.1	846	Ggg/Agg	27/35	1	2	FACETS	0.931	0.891	0.97	0.931	0.891	0.97	CLONAL	1	TRUE	1	0.819245159195569	2		904	1288	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0053934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	292	603	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.272544007310853	3	FACETS	0.851	0.802	0.901	1	0.991	1	CLONAL	3	TRUE	1	0.272526485790629	3		603	954	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039356	47039358	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0053934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	94	729	0	ENST00000377604.3:c.985_987del	p.Ser329del	p.S329del	ENST00000377604	NM_001204468.1	327	TCC/-	10/24	1	2	FACETS	0.793	0.705	0.887	0.793	0.705	0.887	SUBCLONAL	1	TRUE	1	0.272526485790629	2		729	870	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982387	201982387	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	89	823	0	ENST00000359651.3:c.766G>A	p.Glu256Lys	p.E256K	ENST00000359651		256	Gag/Aag	6/8	1	2	FACETS	0.692	0.612	0.777	0.692	0.612	0.777	SUBCLONAL	1	TRUE	1	0.272526485790629	2		823	944	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179127	123179127	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0053934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	44	471	0	ENST00000218089.9:c.576T>A	p.Tyr192Ter	p.Y192*	ENST00000218089	NM_001042749.1	192	taT/taA	8/35	1	2	FACETS	0.617	0.517	0.728	0.617	0.517	0.728	SUBCLONAL	1	TRUE	1	0.272526485790629	2		471	523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577587	7577587	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	169	588	0	ENST00000269305.4:c.694A>T	p.Ile232Phe	p.I232F	ENST00000269305	NM_001126112.2	232	Atc/Ttc	7/11	0.437349561985453	1	FACETS	0.808	0.745	0.874	0.808	0.745	0.874	CLONAL	1	TRUE	0	0.461488890338017	1		588	697	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798128	32798128	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	204	801	0	ENST00000374899.4:c.1551G>C	p.Gln517His	p.Q517H	ENST00000374899	NM_018833.2	517	caG/caC	9/12	1	2	FACETS	0.813	0.753	0.875	0.813	0.753	0.875	CLONAL	1	TRUE	1	0.461488890338017	2		801	1088	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136276	2136276	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	302	1056	2	ENST00000219476.3:c.4745del	p.Ile1582ThrfsTer3	p.I1582Tfs*3	ENST00000219476	NM_000548.3	1582	aTc/ac	37/42	0.437349561985453	1	FACETS	0.941	0.887	0.996	0.941	0.887	0.996	CLONAL	1	TRUE	0	0.461488890338017	1		1058	1070	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688781	47688781	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	152	370	0	ENST00000347630.2:c.519G>C	p.Gln173His	p.Q173H	ENST00000347630	NM_001007230.1	173	caG/caC	7/11	1	2	FACETS	0.906	0.83	0.985	0.906	0.83	0.985	CLONAL	1	TRUE	1	0.461488890338017	2		370	727	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248587	10248587	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	278	992	0	ENST00000340748.4:c.4166A>G	p.Asn1389Ser	p.N1389S	ENST00000340748		1389	aAc/aGc	35/40	1	2	FACETS	0.952	0.893	1	0.952	0.893	1	CLONAL	1	TRUE	1	0.461488890338017	2		992	1265	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795141	42795141	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	271	1032	0	ENST00000575354.2:c.2221G>T	p.Ala741Ser	p.A741S	ENST00000575354	NM_015125.3	741	Gcc/Tcc	10/20	1	2	FACETS	0.846	0.792	0.901	0.846	0.792	0.901	CLONAL	1	TRUE	1	0.461488890338017	2		1032	1389	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661685	227661685	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs541467189	NA	P-0053935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	210	833	0	ENST00000305123.5:c.1770C>A	p.His590Gln	p.H590Q	ENST00000305123	NM_005544.2	590	caC/caA	1/2	1	2	FACETS	0.802	0.744	0.862	0.802	0.744	0.862	CLONAL	1	TRUE	1	0.461488890338017	2		833	1135	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165726	47165726	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0053935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	155	448	0	ENST00000409792.3:c.400A>T	p.Lys134Ter	p.K134*	ENST00000409792	NM_014159.6	134	Aag/Tag	3/21	0.437349561985453	1	FACETS	0.873	0.803	0.945	0.873	0.803	0.945	CLONAL	1	TRUE	0	0.461488890338017	1		448	592	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636808	8636808	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	185	569	0	ENST00000356435.5:c.101C>A	p.Thr34Lys	p.T34K	ENST00000356435		34	aCa/aAa	2/35	1	2	FACETS	0.972	0.899	1	0.972	0.899	1	CLONAL	1	TRUE	1	0.461488890338017	2		569	825	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0053936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	208	467	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.287436820976974	3	FACETS	0.977	0.915	1	0.977	0.915	1	CLONAL	3	TRUE	0	0.31	3		467	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782177	NA	P-0053936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	235	680	0	ENST00000269305.4:c.644G>T	p.Ser215Ile	p.S215I	ENST00000269305	NM_001126112.2	215	aGt/aTt	6/11	NA	2	FACETS	0.789	0.736	0.843			1	INDETERMINATE	2	TRUE	NA	0.31	2		680	961	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524486	44524486	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	94	257	0	ENST00000291552.4:c.71T>C	p.Ile24Thr	p.I24T	ENST00000291552	NM_006758.2	24	aTt/aCt	2/8	0.269162122367586	3	FACETS	0.846	0.763	0.931	1	0.975	1	CLONAL	3	TRUE	1	0.31	3		257	276	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900164	101900164	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	85	299	0	ENST00000374994.4:c.598A>G	p.Thr200Ala	p.T200A	ENST00000374994	NM_004612.2	200	Aca/Gca	4/9	0.296010402376395	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.31	2		299	233	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984938	101984938	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	143	310	0	ENST00000282441.5:c.385C>G	p.Pro129Ala	p.P129A	ENST00000282441	NM_001130145.2	129	Cca/Gca	2/9	0.269162122367586	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.31	3		310	486	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22008921	22008921	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	277	735	1	ENST00000276925.6:c.32G>T	p.Gly11Val	p.G11V	ENST00000276925	NM_004936.3	11	gGg/gTg	1/2	0.296010402376395	2	FACETS	1	0.992	1	0.678	0.636	0.722	CLONAL	1	TRUE	0	0.31	2		736	1317	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691022	NA	P-0053937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	218	799	0	ENST00000269305.4:c.1024del	p.Arg342GlufsTer3	p.R342Efs*3	ENST00000269305	NM_001126112.2	342	Cga/ga	10/11	0.39902788098559	1	FACETS	0.962	0.896	1	0.962	0.896	1	CLONAL	1	TRUE	0	0.39902788098559	1		799	909	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774100	56774100	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753912045	NA	P-0053937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	146	482	0	ENST00000337432.4:c.451G>A	p.Val151Met	p.V151M	ENST00000337432	NM_058216.2	151	Gtg/Atg	3/9	0.39902788098559	1	FACETS	0.959	0.878	1	0.959	0.878	1	CLONAL	1	TRUE	0	0.39902788098559	1		482	611	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129287	152129287	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	233	846	0	ENST00000206249.3:c.240C>A	p.Tyr80Ter	p.Y80*	ENST00000206249	NM_000125.3	80	taC/taA	1/8	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.39902788098559	2		846	1013	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294392	1294392	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	98	604	0	ENST00000310581.5:c.609G>A	p.Trp203Ter	p.W203*	ENST00000310581	NM_198253.2	203	tgG/tgA	2/16	0.268925487356483	3	FACETS	0.559	0.497	0.625	0.28	0.248	0.313	SUBCLONAL	1	TRUE	1	0.39902788098559	3		604	1054	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916529	39916529	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs781170619	NA	P-0053937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	221	715	0	ENST00000378444.4:c.4474C>G	p.His1492Asp	p.H1492D	ENST00000378444	NM_001123385.1	1492	Cat/Gat	11/15	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.39902788098559	2		715	1006	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	50	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.201921706362997	2		276	416	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	209	446	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.201921706362997	1	FACETS	0.903	0.838	0.97	1	0.993	1	CLONAL	2	TRUE	0	0.201921706362997	1		446	1031	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254644	16254644	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	111	398	0	ENST00000375759.3:c.1909C>T	p.Arg637Ter	p.R637*	ENST00000375759	NM_015001.2	637	Cga/Tga	11/15	0.052257195537857	4	FACETS	0.945	0.851	1	0.945	0.851	1	INDETERMINATE	2	TRUE	2	0.201921706362997	4		398	699	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971199	21971199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894095	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	133	427	0	ENST00000304494.5:c.159G>A	p.Met53Ile	p.M53I	ENST00000304494	NM_000077.4	53	atG/atA	2/3	0.201921706362997	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.201921706362997	1		427	816	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	65	356	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.052257195537857	4	FACETS	1	0.956	1	0.625	0.542	0.715	INDETERMINATE	1	TRUE	2	0.201921706362997	4		356	619	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251668	212251668	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1401131440	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	108	486	1	ENST00000342788.4:c.3391G>A	p.Asp1131Asn	p.D1131N	ENST00000342788	NM_005235.2	1131	Gac/Aac	27/28	1	2	FACETS	0.796	0.715	0.881	1	0.984	1	SUBCLONAL	2	TRUE	1	0.201921706362997	2		487	672	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923318	9923318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867335598	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	48	572	0	ENST00000330684.3:c.1969G>A	p.Glu657Lys	p.E657K	ENST00000330684	NM_001134407.1	657	Gaa/Aaa	9/13	0.052257195537857	4	FACETS	0.781	0.658	0.916	0.39	0.329	0.458	INDETERMINATE	1	TRUE	2	0.201921706362997	4		572	732	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176561	142176561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	65	402	0	ENST00000350721.4:c.7540C>T	p.Arg2514Cys	p.R2514C	ENST00000350721	NM_001184.3	2514	Cgc/Tgc	45/47	1	2	FACETS	0.917	0.8	1	1	0.979	1	CLONAL	2	TRUE	1	0.201921706362997	2		402	351	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729535	41729535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	76	588	0	ENST00000242208.4:c.994G>A	p.Asp332Asn	p.D332N	ENST00000242208	NM_002192.2	332	Gac/Aac	3/3	1	2	FACETS	0.818	0.716	0.929	0.818	0.716	0.929	CLONAL	1	TRUE	1	0.201921706362997	2		588	920	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554305	81554305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777252114	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	29	351	0	ENST00000298171.2:c.325C>T	p.Arg109Trp	p.R109W	ENST00000298171	NM_000369.2	109	Cgg/Tgg	4/10	1	2	FACETS	0.86	0.691	1	0.86	0.691	1	CLONAL	1	TRUE	1	0.201921706362997	2		351	334	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101327	27101327	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1313	310	756	0	ENST00000324856.7:c.4609C>T	p.Gln1537Ter	p.Q1537*	ENST00000324856	NM_006015.4	1537	Cag/Tag	18/20	0.052257195537857	4	FACETS	1	0.985	1	1	0.985	1	INDETERMINATE	2	TRUE	2	0.201921706362997	4		756	1623	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102882	71102882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	85	341	1	ENST00000318789.4:c.325C>T	p.Pro109Ser	p.P109S	ENST00000318789	NM_032682.5	109	Ccc/Tcc	8/21	0.052257195537857	4	FACETS	0.812	0.718	0.912	0.812	0.718	0.912	INDETERMINATE	2	TRUE	2	0.201921706362997	4		342	623	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576024	29576024	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	65	359	0	ENST00000356175.3:c.3997G>T	p.Glu1333Ter	p.E1333*	ENST00000356175	NM_000267.3	1333	Gag/Tag	30/57	0.193593893890774	3	FACETS	1	0.904	1	0.695	0.606	0.79	CLONAL	2	TRUE	0	0.201921706362997	3		359	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576891	7576891	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	272	624	1	ENST00000269305.4:c.955A>T	p.Lys319Ter	p.K319*	ENST00000269305	NM_001126112.2	319	Aag/Tag	9/11	0.193593893890774	3	FACETS	0.982	0.922	1	0.982	0.922	1	CLONAL	3	TRUE	0	0.201921706362997	3		625	1007	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552922	106552922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1214061937	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1174	114	726	0	ENST00000369096.4:c.887G>A	p.Arg296Gln	p.R296Q	ENST00000369096	NM_001198.3	296	cGg/cAg	5/7	1	2	FACETS	0.877	0.787	0.972	0.877	0.787	0.972	CLONAL	1	TRUE	1	0.201921706362997	2		726	1288	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383226	31383226	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs376213530	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	56	436	1	ENST00000328111.2:c.1138C>T	p.Arg380Ter	p.R380*	ENST00000328111	NM_006892.3	380	Cga/Tga	11/23	1	2	FACETS	0.669	0.572	0.776	0.669	0.572	0.776	SUBCLONAL	1	TRUE	1	0.201921706362997	2		437	829	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453115	140453115	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	15	293	0	ENST00000288602.6:c.1820C>T	p.Ser607Phe	p.S607F	ENST00000288602	NM_004333.4	607	tCc/tTc	15/18	1	2	FACETS	0.721	0.528	0.952	0.721	0.528	0.952	CLONAL	1	TRUE	1	0.201921706362997	2		293	206	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987076	36987076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	79	774	0	ENST00000354822.5:c.613G>A	p.Glu205Lys	p.E205K	ENST00000354822	NM_001079668.2	205	Gag/Aag	3/3	1	2	FACETS	0.772	0.677	0.874	0.772	0.677	0.874	SUBCLONAL	1	TRUE	1	0.201921706362997	2		774	1014	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257832	198257832	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	53	390	2	ENST00000335508.6:c.3620C>T	p.Ser1207Leu	p.S1207L	ENST00000335508	NM_012433.2	1207	tCg/tTg	24/25	1	2	FACETS	0.974	0.831	1	0.974	0.831	1	CLONAL	1	TRUE	1	0.201921706362997	2		392	539	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964502	93964502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	34	357	0	ENST00000369303.4:c.2395C>T	p.Pro799Ser	p.P799S	ENST00000369303	NM_004440.3	799	Cca/Tca	14/17	1	2	FACETS	0.798	0.657	0.953	1	0.953	1	CLONAL	2	TRUE	1	0.201921706362997	2		357	211	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710649	40710649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	45	464	0	ENST00000373198.4:c.4202G>A	p.Gly1401Glu	p.G1401E	ENST00000373198	NM_133170.3	1401	gGa/gAa	31/32	0.201921706362997	0	FACETS	0.572	0.48	0.674			1	SUBCLONAL	1	TRUE	0	0.201921706362997	0		464	622	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518223	8518223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	32	347	0	ENST00000356435.5:c.1168G>A	p.Glu390Lys	p.E390K	ENST00000356435		390	Gaa/Aaa	10/35	0.201921706362997	1	FACETS	0.652	0.529	0.791	0.652	0.529	0.791	SUBCLONAL	1	TRUE	0	0.201921706362997	1		347	437	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581261	48581261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140743238	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	62	428	0	ENST00000342988.3:c.565C>T	p.Arg189Cys	p.R189C	ENST00000342988	NM_005359.5	189	Cgt/Tgt	5/12	0.201921706362997	3	FACETS	0.893	0.77	1	0.298	0.256	0.343	CLONAL	1	TRUE	0	0.201921706362997	3		428	757	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43739672	43739672	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761309980	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	27	157	0	ENST00000382044.4:c.2728C>T	p.His910Tyr	p.H910Y	ENST00000382044	NM_001141980.1	910	Cat/Tat	13/28	0.139620748366515	5	FACETS	1	0.934	1	0.494	0.395	0.607	CLONAL	1	TRUE	2	0.201921706362997	5		157	235	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808888	1808888	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1388	139	995	0	ENST00000260795.2:c.2320G>A	p.Gly774Ser	p.G774S	ENST00000260795		774	Ggc/Agc	17/17	0.201921706362997	1	FACETS	0.811	0.735	0.89	0.811	0.735	0.89	CLONAL	1	TRUE	0	0.201921706362997	1		995	1527	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729723	41729723	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779220866	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	132	545	0	ENST00000242208.4:c.806G>A	p.Gly269Glu	p.G269E	ENST00000242208	NM_002192.2	269	gGg/gAg	3/3	1	2	FACETS	0.802	0.728	0.88	1	0.987	1	CLONAL	2	TRUE	1	0.201921706362997	2		545	815	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841434	156841434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	90	585	0	ENST00000524377.1:c.737C>T	p.Ser246Phe	p.S246F	ENST00000524377	NM_002529.3	246	tCc/tTc	7/17	0.052257195537857	4	FACETS	1	0.963	1	0.606	0.537	0.68	INDETERMINATE	1	TRUE	2	0.201921706362997	4		585	884	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332279	70332279	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	78	315	0	ENST00000373644.4:c.184A>T	p.Thr62Ser	p.T62S	ENST00000373644	NM_030625.2	62	Aca/Tca	2/12	1	2	FACETS	0.855	0.754	0.962	1	0.981	1	CLONAL	2	TRUE	1	0.201921706362997	2		315	452	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274630	123274630	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	34	315	0	ENST00000358487.5:c.1287+1G>A		p.X429_splice	ENST00000358487	NM_000141.4	429			1	2	FACETS	0.653	0.532	0.788	0.653	0.532	0.788	SUBCLONAL	1	TRUE	1	0.201921706362997	2		315	516	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342745	118342745	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	48	251	0	ENST00000534358.1:c.871C>T	p.Gln291Ter	p.Q291*	ENST00000534358	NM_005933.3	291	Caa/Taa	3/36	0.201921706362997	4	FACETS	0.965	0.821	1			1	CLONAL	2	TRUE	NA	0.201921706362997	4		251	296	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254249	133254249	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	87	522	0	ENST00000320574.5:c.635C>T	p.Ala212Val	p.A212V	ENST00000320574	NM_006231.2	212	gCt/gTt	7/49	1	2	FACETS	0.922	0.814	1	0.922	0.814	1	CLONAL	1	TRUE	1	0.201921706362997	2		522	935	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562825	21562825	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	73	554	0	ENST00000382592.4:c.1094C>T	p.Thr365Ile	p.T365I	ENST00000382592	NM_014572.2	365	aCc/aTc	4/8	1	2	FACETS	0.753	0.657	0.857	0.753	0.657	0.857	SUBCLONAL	1	TRUE	1	0.201921706362997	2		554	960	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243018	105243019	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	210	856	1	ENST00000349310.3:c.264_265delinsTT	p.His89Tyr	p.H89Y	ENST00000349310	NM_001014432.1	88	ttCCat/ttTTat	5/15	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.201921706362997	2		857	1440	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041804	42041804	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	38	393	0	ENST00000219905.7:c.5999C>T	p.Ala2000Val	p.A2000V	ENST00000219905	NM_001164273.1	2000	gCt/gTt	17/24	0.139620748366515	5	FACETS	0.971	0.802	1	0.324	0.267	0.387	CLONAL	1	TRUE	2	0.201921706362997	5		393	505	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857451	9857451	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	75	529	0	ENST00000330684.3:c.3950A>G	p.Glu1317Gly	p.E1317G	ENST00000330684	NM_001134407.1	1317	gAa/gGa	13/13	0.052257195537857	4	FACETS	1	0.965	1	0.648	0.567	0.735	INDETERMINATE	1	TRUE	2	0.201921706362997	4		529	689	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990636	7990636	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	280	594	0	ENST00000319144.4:c.125G>A	p.Gly42Glu	p.G42E	ENST00000319144	NM_001139.2	42	gGg/gAg	1/15	0.193593893890774	3	FACETS	0.865	0.813	0.92	0.865	0.813	0.92	CLONAL	3	TRUE	0	0.201921706362997	3		594	1176	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686952	37686952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	108	467	0	ENST00000447079.4:c.3856C>T	p.Leu1286Phe	p.L1286F	ENST00000447079	NM_015083.1	1286	Ctt/Ttt	14/14	0.139620748366515	5	FACETS	1	0.972	1	0.416	0.372	0.463	CLONAL	1	TRUE	2	0.201921706362997	5		467	1117	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10286236	10286236	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	184	587	0	ENST00000340748.4:c.580A>G	p.Lys194Glu	p.K194E	ENST00000340748		194	Aag/Gag	6/40	0.052257195537857	4	FACETS	1	0.951	1	1	0.951	1	INDETERMINATE	2	TRUE	2	0.201921706362997	4		587	1051	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295124	15295124	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1304	88	746	0	ENST00000263388.2:c.2548A>C	p.Ile850Leu	p.I850L	ENST00000263388	NM_000435.2	850	Atc/Ctc	16/33	0.052257195537857	4	FACETS	0.753	0.664	0.848	0.376	0.332	0.424	INDETERMINATE	1	TRUE	2	0.201921706362997	4		746	1392	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082893	16082893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759545096	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	23	148	0	ENST00000281043.3:c.707C>T	p.Pro236Leu	p.P236L	ENST00000281043	NM_005378.4	236	cCt/cTt	2/3	1	2	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	1	0.201921706362997	2		148	204	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607810	46607810	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1362	116	812	0	ENST00000263734.3:c.1999T>A	p.Leu667Met	p.L667M	ENST00000263734	NM_001430.4	667	Ttg/Atg	12/16	1	2	FACETS	0.777	0.698	0.862	0.777	0.698	0.862	SUBCLONAL	1	TRUE	1	0.201921706362997	2		812	1478	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113152	209113153	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	40	294	0	ENST00000345146.2:c.354_355delinsAT	p.Arg119Trp	p.R119W	ENST00000345146	NM_005896.2	118	ccCCgg/ccATgg	4/10	1	2	FACETS	0.869	0.722	1	0.869	0.722	1	CLONAL	1	TRUE	1	0.201921706362997	2		294	456	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566727	212566727	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	20	300	0	ENST00000342788.4:c.1454T>A	p.Ile485Lys	p.I485K	ENST00000342788	NM_005235.2	485	aTa/aAa	12/28	1	2	FACETS	0.71	0.543	0.905	0.71	0.543	0.905	CLONAL	1	TRUE	1	0.201921706362997	2		300	279	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440138	220440138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1381075326	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1278	92	812	0	ENST00000243786.2:c.991C>T	p.Leu331Phe	p.L331F	ENST00000243786	NM_002191.3	331	Ctc/Ttc	2/2	1	2	FACETS	0.665	0.589	0.747	0.665	0.589	0.747	SUBCLONAL	1	TRUE	1	0.201921706362997	2		812	1370	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561040	9561041	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	31	439	0	ENST00000353224.5:c.741_742delinsAA	p.Glu248Lys	p.E248K	ENST00000353224	NM_177990.2	247	aaGGag/aaAAag	4/10	1	2	FACETS	0.528	0.426	0.645	0.528	0.426	0.645	SUBCLONAL	1	TRUE	1	0.201921706362997	2		439	581	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723064	49723064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778896456	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	29	131	0	ENST00000449682.2:c.1352G>A	p.Arg451Lys	p.R451K	ENST00000449682	NM_020998.3	451	aGg/aAg	11/18	0.052257195537857	4	FACETS	1	0.922	1	0.661	0.533	0.806	INDETERMINATE	1	TRUE	2	0.201921706362997	4		131	261	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890335	72890336	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	59	280	0	ENST00000325599.8:c.346_347delinsTT	p.Pro116Phe	p.P116F	ENST00000325599	NM_018130.2	116	CCt/TTt	4/11	0.052257195537857	4	FACETS	0.973	0.841	1	0.973	0.841	1	INDETERMINATE	2	TRUE	2	0.201921706362997	4		280	361	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967198	134967198	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753554755	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	117	496	0	ENST00000398015.3:c.2537C>T	p.Pro846Leu	p.P846L	ENST00000398015	NM_004441.4	846	cCc/cTc	14/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.201921706362997	2		496	789	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803561	1803561	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	150	620	0	ENST00000260795.2:c.740-1G>A		p.X247_splice	ENST00000260795		247			0.201921706362997	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.201921706362997	1		620	950	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	223673	223673	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	34	285	0	ENST00000264932.6:c.140T>C	p.Val47Ala	p.V47A	ENST00000264932	NM_004168.2	47	gTt/gCt	2/15	1	2	FACETS	0.629	0.513	0.76	0.629	0.513	0.76	SUBCLONAL	1	TRUE	1	0.201921706362997	2		285	535	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637651	176637651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775181583	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	59	463	0	ENST00000439151.2:c.2251C>T	p.Leu751Phe	p.L751F	ENST00000439151	NM_022455.4	751	Ctc/Ttc	5/23	1	2	FACETS	0.961	0.827	1	0.961	0.827	1	CLONAL	1	TRUE	1	0.201921706362997	2		463	608	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638234	176638234	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	105	553	0	ENST00000439151.2:c.2834C>T	p.Ser945Phe	p.S945F	ENST00000439151	NM_022455.4	945	tCt/tTt	5/23	1	2	FACETS	0.973	0.87	1	0.973	0.87	1	CLONAL	1	TRUE	1	0.201921706362997	2		553	1069	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707813	176707814	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	54	323	0	ENST00000439151.2:c.5870_5871delinsAA	p.Arg1957Gln	p.R1957Q	ENST00000439151	NM_022455.4	1957	cGG/cAA	18/23	1	2	FACETS	0.987	0.843	1	0.987	0.843	1	CLONAL	1	TRUE	1	0.201921706362997	2		323	542	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056298	26056298	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	226	479	0	ENST00000343677.2:c.359T>G	p.Val120Gly	p.V120G	ENST00000343677	NM_005319.3	120	gTt/gGt	1/1	0.201921706362997	5	FACETS	1	0.986	1	0.823	0.766	0.883	CLONAL	2	TRUE	2	0.201921706362997	5		479	1181	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181902	32181902	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1474	126	729	1	ENST00000375023.3:c.2152C>T	p.Pro718Ser	p.P718S	ENST00000375023	NM_004557.3	718	Cct/Tct	13/30	0.201921706362997	5	FACETS	1	0.915	1	0.339	0.305	0.374	CLONAL	1	TRUE	2	0.201921706362997	5		730	1600	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004337	150004337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767993990	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	34	348	0	ENST00000253339.5:c.1888C>T	p.Arg630Cys	p.R630C	ENST00000253339		630	Cgt/Tgt	3/7	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.201921706362997	2		348	317	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976754	2976754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772685938	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	140	679	1	ENST00000396946.4:c.1258G>A	p.Glu420Lys	p.E420K	ENST00000396946	NM_032415.4	420	Gag/Aag	9/25	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.201921706362997	2		680	1253	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045937	47045938	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	212	383	1	ENST00000377604.3:c.2732_2733delinsTT	p.Thr911Ile	p.T911I	ENST00000377604	NM_001204468.1	911	aCC/aTT	24/24	0.125673436505036	2	FACETS	0.984	0.918	1			1	CLONAL	3	TRUE	NA	0.201921706362997	2		384	711	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056296	26056298	+	stop_gained	Nonsense_Mutation	TNP	TAA	TAA	AAC	novel	NA	P-0053938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	231	480	0	ENST00000343677.2:c.359_361delinsGTT	p.Val120_Lys121delinsGlyTer	p.V120_K121delinsG*	ENST00000343677	NM_005319.3	120	gTTAaa/gGTTaa	1/1	0.201921706362997	5	FACETS	1	0.987	1	0.823	0.766	0.881	CLONAL	2	TRUE	2	0.201921706362997	5		480	1208	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	110	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.754477359515538	2		276	273	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0053939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	127	533	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.754477359515538	2		533	302	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942124	81942124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781434235	NA	P-0053939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	323	659	0	ENST00000359376.3:c.1661C>T	p.Thr554Met	p.T554M	ENST00000359376	NM_002661.3	554	aCg/aTg	17/33	0.63225557521001	1	FACETS	0.884	0.844	0.924	0.884	0.844	0.924	CLONAL	1	TRUE	0	0.754477359515538	1		659	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0053940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	955	866	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.683233221703067	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.683233221703067	2		867	1389	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0053940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	528	432	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	0.683233221703067	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.683233221703067	2		432	762	SUCCESS
APC	324	MSKCC	GRCh37	5	112176029	112176029	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	177	319	0	ENST00000257430.4:c.4738del	p.Ile1580PhefsTer70	p.I1580Ffs*70	ENST00000257430	NM_000038.5	1580	Att/tt	16/16	1	2	FACETS	0.858	0.794	0.923	0.858	0.794	0.923	CLONAL	1	TRUE	1	0.683233221703067	2		319	604	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268147	153268147	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	287	395	1	ENST00000281708.4:c.661C>T	p.Gln221Ter	p.Q221*	ENST00000281708	NM_033632.3	221	Caa/Taa	4/12	0.683233221703067	1	FACETS	0.969	0.921	1	0.969	0.921	1	CLONAL	1	TRUE	0	0.683233221703067	1		396	571	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038902	12038902	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs724159945	NA	P-0053940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	234	340	0	ENST00000396373.4:c.1195C>A	p.Arg399Ser	p.R399S	ENST00000396373	NM_001987.4	399	Cgc/Agc	7/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.683233221703067	2		340	636	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443493	49443506	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCGCCGCCGCCC	CTGCGCCGCCGCCC	-	novel	NA	P-0053940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	399	607	0	ENST00000301067.7:c.3865_3878del	p.Gly1289LeufsTer31	p.G1289Lfs*31	ENST00000301067	NM_003482.3	1289	GGGCGGCGGCGCAGc/c	11/54	1	2	FACETS	0.988	0.941	1	0.988	0.941	1	CLONAL	1	TRUE	1	0.683233221703067	2		607	1182	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599985	10599985	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	1070	811	1	ENST00000171111.5:c.1591C>A	p.Leu531Met	p.L531M	ENST00000171111	NM_203500.1	531	Ctg/Atg	5/6	0.683233221703067	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.683233221703067	3		812	2095	SUCCESS
APC	324	MSKCC	GRCh37	5	112173561	112173561	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	188	317	0	ENST00000257430.4:c.2274del	p.Ala759ProfsTer2	p.A759Pfs*2	ENST00000257430	NM_000038.5	757	cAa/ca	16/16	1	2	FACETS	0.939	0.873	1	0.939	0.873	1	CLONAL	1	TRUE	1	0.683233221703067	2		317	586	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781180	161781180	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1554252213	NA	P-0053940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	401	638	0	ENST00000366898.1:c.1225G>T	p.Glu409Ter	p.E409*	ENST00000366898	NM_004562.2	409	Gaa/Taa	11/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.683233221703067	2		638	1169	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289247	33289247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1455644209	NA	P-0053942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	256	534	0	ENST00000374542.5:c.305C>T	p.Ser102Leu	p.S102L	ENST00000374542	NM_001141970.1	102	tCg/tTg	3/8	0.470364620122778	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.470364620122778	1		534	782	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100211	30100211	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	29	431	0	ENST00000331968.5:c.1409A>C	p.Glu470Ala	p.E470A	ENST00000331968	NM_002742.2	470	gAa/gCa	10/18	1	2	FACETS	0.251	0.2	0.308	0.251	0.2	0.308	SUBCLONAL	1	TRUE	1	0.470364620122778	2		431	492	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577167	64577167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	107	738	0	ENST00000312049.6:c.415C>T	p.His139Tyr	p.H139Y	ENST00000312049	NM_130799.2	139	Cac/Tac	2/10	0.470364620122778	1	FACETS	0.414	0.371	0.46	0.414	0.371	0.46	SUBCLONAL	1	TRUE	0	0.470364620122778	1		738	840	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0053943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	56	866	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.707	0.603	0.821	0.707	0.603	0.821	SUBCLONAL	1	TRUE	1	0.13	2		867	1219	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0053943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1261	50	757	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.587	0.495	0.688	0.587	0.495	0.688	SUBCLONAL	1	TRUE	1	0.13	2		757	1311	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	20	357	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	1	2	FACETS	0.602	0.459	0.771	0.602	0.459	0.771	SUBCLONAL	1	TRUE	1	0.13	2		357	511	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349914	89349916	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs761762028	NA	P-0053943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1276	34	929	0	ENST00000301030.4:c.3034_3036del	p.Lys1012del	p.K1012del	ENST00000301030	NM_001256183.1	1012	AAG/-	9/13	1	2	FACETS	0.399	0.324	0.485	0.399	0.324	0.485	SUBCLONAL	1	TRUE	1	0.13	2		929	1310	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032136	26032136	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	29	622	0	ENST00000244661.2:c.153G>C	p.Glu51Asp	p.E51D	ENST00000244661	NM_003537.3	51	gaG/gaC	1/1	1	2	FACETS	0.469	0.375	0.578	0.469	0.375	0.578	SUBCLONAL	1	TRUE	1	0.13	2		622	951	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239420	105239420	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1181	37	816	1	ENST00000349310.3:c.967G>T	p.Asp323Tyr	p.D323Y	ENST00000349310	NM_001014432.1	323	Gac/Tac	12/15	1	2	FACETS	0.467	0.383	0.562	0.467	0.383	0.562	SUBCLONAL	1	TRUE	1	0.13	2		817	1218	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112359	115112359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1239750042	NA	P-0053943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	20	222	2	ENST00000257566.3:c.1381G>A	p.Gly461Ser	p.G461S	ENST00000257566	NM_016569.3	461	Ggc/Agc	7/8	1	2	FACETS	0.921	0.704	1	0.921	0.704	1	CLONAL	1	TRUE	1	0.13	2		224	334	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348523	56348523	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	34	356	0	ENST00000348428.3:c.331C>T	p.Gln111Ter	p.Q111*	ENST00000348428	NM_006785.3	111	Cag/Tag	2/17	1	2	FACETS	0.832	0.678	1	0.832	0.678	1	CLONAL	1	TRUE	1	0.13	2		356	629	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447761	187447779	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGAACTCTTCACGAGGA	GAGGAACTCTTCACGAGGA	-	novel	NA	P-0053943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	62	598	0	ENST00000232014.4:c.414_432del	p.Pro139ThrfsTer5	p.P139Tfs*5	ENST00000232014	NM_001130845.1	138	ccTCCTCGTGAAGAGTTCCTC/cc	5/10	1	2	FACETS	0.932	0.803	1	0.932	0.803	1	CLONAL	1	TRUE	1	0.13	2		598	1023	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	229	781	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.324280679485967	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.324280679485967	1		782	1130	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46543204	46543204	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1612	86	478	0	ENST00000262741.5:c.297T>G	p.Asp99Glu	p.D99E	ENST00000262741	NM_003629.3	99	gaT/gaG	3/10	0.324280679485967	6	FACETS	0.515	0.453	0.582	0.103	0.09	0.117	SUBCLONAL	1	TRUE	1	0.324280679485967	6		478	1698	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325870	65325870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	118	572	0	ENST00000342505.4:c.1252G>A	p.Asp418Asn	p.D418N	ENST00000342505	NM_002227.2	418	Gat/Aat	9/25	1	2	FACETS	0.586	0.527	0.649	0.586	0.527	0.649	SUBCLONAL	1	TRUE	1	0.324280679485967	2		572	1241	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550959	150550959	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	55	352	1	ENST00000369026.2:c.697C>T	p.Arg233Trp	p.R233W	ENST00000369026	NM_021960.4	233	Cgg/Tgg	2/3	1	2	FACETS	0.426	0.363	0.494	0.426	0.363	0.494	SUBCLONAL	1	TRUE	1	0.324280679485967	2		353	797	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518089	69518089	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1339752006	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1287	105	950	0	ENST00000294312.3:c.276C>G	p.Ile92Met	p.I92M	ENST00000294312	NM_005117.2	92	atC/atG	2/3	1	2	FACETS	0.465	0.415	0.519	0.465	0.415	0.519	SUBCLONAL	1	TRUE	1	0.324280679485967	2		950	1392	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18473929	18473929	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	36	287	0	ENST00000266497.5:c.1171C>T	p.Gln391Ter	p.Q391*	ENST00000266497		391	Caa/Taa	6/31	1	2	FACETS	0.748	0.617	0.893	0.748	0.617	0.893	SUBCLONAL	1	TRUE	1	0.324280679485967	2		287	297	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246324	46246324	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	42	408	0	ENST00000334344.6:c.4418C>G	p.Ser1473Cys	p.S1473C	ENST00000334344	NM_152641.2	1473	tCt/tGt	15/21	0.320831638484736	3	FACETS	0.385	0.321	0.458	0.193	0.16	0.229	SUBCLONAL	1	TRUE	1	0.324280679485967	3		408	781	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061115	38061115	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1016447126	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	21	79	0	ENST00000250448.2:c.874G>A	p.Glu292Lys	p.E292K	ENST00000250448	NM_004496.3	292	Gag/Aag	2/2	1	2	FACETS	0.795	0.617	0.998	0.795	0.617	0.998	CLONAL	1	TRUE	1	0.324280679485967	2		79	163	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701853	43701853	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	36	314	0	ENST00000382044.4:c.5392G>A	p.Glu1798Lys	p.E1798K	ENST00000382044	NM_001141980.1	1798	Gaa/Aaa	25/28	0.324280679485967	1	FACETS	0.409	0.336	0.491	0.409	0.336	0.491	SUBCLONAL	1	TRUE	0	0.324280679485967	1		314	455	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855984	68855984	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121964877	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	95	593	0	ENST00000261769.5:c.1792C>T	p.Arg598Ter	p.R598*	ENST00000261769	NM_004360.3	598	Cga/Tga	12/16	0.324280679485967	1	FACETS	0.542	0.482	0.607	0.542	0.482	0.607	SUBCLONAL	1	TRUE	0	0.324280679485967	1		593	905	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474318	40474318	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	63	474	0	ENST00000264657.5:c.2083C>G	p.Pro695Ala	p.P695A	ENST00000264657	NM_139276.2	695	Cct/Gct	21/24	0.324280679485967	1	FACETS	0.399	0.344	0.459	0.399	0.344	0.459	SUBCLONAL	1	TRUE	0	0.324280679485967	1		474	816	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40879727	40879727	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	90	582	0	ENST00000428826.2:c.172G>T	p.Glu58Ter	p.E58*	ENST00000428826		58	Gaa/Taa	4/21	0.324280679485967	1	FACETS	0.524	0.464	0.588	0.524	0.464	0.588	SUBCLONAL	1	TRUE	0	0.324280679485967	1		582	888	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40880910	40880910	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	101	550	0	ENST00000428826.2:c.50del	p.Arg17LysfsTer3	p.R17Kfs*3	ENST00000428826		17	aGa/aa	3/21	0.324280679485967	1	FACETS	0.568	0.507	0.633	0.568	0.507	0.633	SUBCLONAL	1	TRUE	0	0.324280679485967	1		550	919	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770110	56770110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773998134	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	81	652	0	ENST00000337432.4:c.106G>A	p.Glu36Lys	p.E36K	ENST00000337432	NM_058216.2	36	Gag/Aag	1/9	0.324280679485967	1	FACETS	0.443	0.39	0.501	0.443	0.39	0.501	SUBCLONAL	1	TRUE	0	0.324280679485967	1		652	944	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62009583	62009583	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	106	768	0	ENST00000392795.3:c.39G>A	p.Trp13Ter	p.W13*	ENST00000392795	NM_001039933.1	13	tgG/tgA	1/6	0.324280679485967	1	FACETS	0.499	0.446	0.556	0.499	0.446	0.556	SUBCLONAL	1	TRUE	0	0.324280679485967	1		768	1097	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118903	70118903	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	102	883	0	ENST00000245479.2:c.475G>A	p.Glu159Lys	p.E159K	ENST00000245479	NM_000346.3	159	Gag/Aag	2/3	0.324280679485967	1	FACETS	0.485	0.432	0.541	0.485	0.432	0.541	SUBCLONAL	1	TRUE	0	0.324280679485967	1		883	1087	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56376768	56376768	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	59	440	0	ENST00000348428.3:c.808G>C	p.Glu270Gln	p.E270Q	ENST00000348428	NM_006785.3	270	Gag/Cag	5/17	0.20028408447929	0	FACETS	0.465	0.4	0.535			1	SUBCLONAL	1	TRUE	0	0.324280679485967	0		440	529	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223186	5223186	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1213	129	689	0	ENST00000357368.4:c.2617G>C	p.Glu873Gln	p.E873Q	ENST00000357368	NM_002850.3	873	Gag/Cag	18/38	1	2	FACETS	0.593	0.536	0.653	0.593	0.536	0.653	SUBCLONAL	1	TRUE	1	0.324280679485967	2		689	1342	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117318	7117318	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1288	98	777	0	ENST00000302850.5:c.3898G>C	p.Glu1300Gln	p.E1300Q	ENST00000302850	NM_000208.2	1300	Gag/Cag	22/22	1	2	FACETS	0.436	0.387	0.488	0.436	0.387	0.488	SUBCLONAL	1	TRUE	1	0.324280679485967	2		777	1386	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168953	11168953	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303255317	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	74	580	0	ENST00000358026.2:c.4543G>A	p.Glu1515Lys	p.E1515K	ENST00000358026	NM_001128849.1	1515	Gag/Aag	32/36	1	2	FACETS	0.428	0.373	0.487	0.428	0.373	0.487	SUBCLONAL	1	TRUE	1	0.324280679485967	2		580	1067	SUCCESS
CALR	811	MSKCC	GRCh37	19	13049987	13049987	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	85	628	0	ENST00000316448.5:c.131C>T	p.Ser44Leu	p.S44L	ENST00000316448	NM_004343.3	44	tCa/tTa	2/9	1	2	FACETS	0.411	0.362	0.465	0.411	0.362	0.465	SUBCLONAL	1	TRUE	1	0.324280679485967	2		628	1274	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271771	18271771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770445875	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1430	133	888	2	ENST00000222254.8:c.458C>T	p.Pro153Leu	p.P153L	ENST00000222254	NM_005027.3	153	cCg/cTg	4/16	1	2	FACETS	0.525	0.475	0.578	0.525	0.475	0.578	SUBCLONAL	1	TRUE	1	0.324280679485967	2		890	1563	SUCCESS
AXL	558	MSKCC	GRCh37	19	41737159	41737159	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1409	118	884	0	ENST00000301178.4:c.739C>G	p.Pro247Ala	p.P247A	ENST00000301178	NM_021913.4	247	Cca/Gca	6/20	1	2	FACETS	0.477	0.428	0.528	0.477	0.428	0.528	SUBCLONAL	1	TRUE	1	0.324280679485967	2		884	1527	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906429	50906429	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2040	158	1055	0	ENST00000440232.2:c.1090C>G	p.Leu364Val	p.L364V	ENST00000440232	NM_002691.3	364	Ctg/Gtg	9/27	0.324280679485967	3	FACETS	0.515	0.47	0.564	0.258	0.235	0.282	SUBCLONAL	1	TRUE	1	0.324280679485967	3		1055	2198	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52693404	52693404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2149	154	925	0	ENST00000322088.6:c.55G>A	p.Glu19Lys	p.E19K	ENST00000322088	NM_014225.5	19	Gaa/Aaa	1/15	0.324280679485967	3	FACETS	0.479	0.436	0.525	0.24	0.218	0.263	SUBCLONAL	1	TRUE	1	0.324280679485967	3		925	2303	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160365	99160365	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	87	600	0	ENST00000074304.5:c.844G>A	p.Glu282Lys	p.E282K	ENST00000074304	NM_001134224.1	282	Gag/Aag	11/26	1	2	FACETS	0.459	0.404	0.517	0.459	0.404	0.517	SUBCLONAL	1	TRUE	1	0.324280679485967	2		600	1170	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264697	46264697	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	63	423	0	ENST00000371998.3:c.1567C>G	p.Leu523Val	p.L523V	ENST00000371998		523	Ctc/Gtc	12/23	0.324280679485967	1	FACETS	0.427	0.369	0.491	0.427	0.369	0.491	SUBCLONAL	1	TRUE	0	0.324280679485967	1		423	762	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321741	62321741	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1696	689	576	0	ENST00000360203.5:c.2360G>C	p.Arg787Thr	p.R787T	ENST00000360203	NM_001283009.1	787	aGg/aCg	26/35	0.324280679485967	5	FACETS	0.883	0.849	0.917			1	CLONAL	3	TRUE	NA	0.324280679485967	5		576	2385	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527502	41527502	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	99	545	0	ENST00000263253.7:c.1393G>C	p.Glu465Gln	p.E465Q	ENST00000263253	NM_001429.3	465	Gaa/Caa	6/31	0.291293650625763	4	FACETS	0.676	0.601	0.755			1	SUBCLONAL	1	TRUE	NA	0.324280679485967	4		545	1197	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139450	47139450	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	72	414	0	ENST00000409792.3:c.5137G>C	p.Asp1713His	p.D1713H	ENST00000409792	NM_014159.6	1713	Gat/Cat	9/21	1	2	FACETS	0.572	0.498	0.651	0.572	0.498	0.651	SUBCLONAL	1	TRUE	1	0.324280679485967	2		414	777	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49399935	49399935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	66	538	0	ENST00000418115.1:c.402G>A	p.Met134Ile	p.M134I	ENST00000418115	NM_001664.2	134	atG/atA	4/5	1	2	FACETS	0.408	0.353	0.468	0.408	0.353	0.468	SUBCLONAL	1	TRUE	1	0.324280679485967	2		538	997	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630006	187630006	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	117	697	0	ENST00000441802.2:c.976G>C	p.Asp326His	p.D326H	ENST00000441802	NM_005245.3	326	Gac/Cac	2/27	0.324280679485967	1	FACETS	0.627	0.565	0.694	0.627	0.565	0.694	SUBCLONAL	1	TRUE	0	0.324280679485967	1		697	964	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952360	38952360	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	51	322	0	ENST00000357387.3:c.3065T>C	p.Leu1022Pro	p.L1022P	ENST00000357387	NM_152756.3	1022	cTa/cCa	30/38	0.324280679485967	1	FACETS	0.558	0.475	0.65	0.558	0.475	0.65	SUBCLONAL	1	TRUE	0	0.324280679485967	1		322	472	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752417	57752417	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	20	208	0	ENST00000274289.3:c.1157-1G>A		p.X386_splice	ENST00000274289	NM_006622.3	386			0.324280679485967	1	FACETS	0.459	0.352	0.584	0.459	0.352	0.584	SUBCLONAL	1	TRUE	0	0.324280679485967	1		208	225	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057783	180057783	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148126951	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	89	705	0	ENST00000261937.6:c.172G>A	p.Glu58Lys	p.E58K	ENST00000261937	NM_182925.4	58	Gag/Aag	3/30	0.324280679485967	1	FACETS	0.52	0.46	0.584	0.52	0.46	0.584	SUBCLONAL	1	TRUE	0	0.324280679485967	1		705	884	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790788	89790788	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1676	129	869	0	ENST00000336032.3:c.175C>G	p.His59Asp	p.H59D	ENST00000336032	NM_006813.2	59	Cat/Gat	1/2	0.188494993286312	3	FACETS	0.512	0.462	0.565	0.256	0.231	0.283	INDETERMINATE	1	TRUE	1	0.324280679485967	3		869	1805	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980758	70980758	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	70	487	0	ENST00000276594.2:c.710C>G	p.Ser237Cys	p.S237C	ENST00000276594	NM_024504.3	237	tCt/tGt	3/8	1	2	FACETS	0.536	0.466	0.611	0.536	0.466	0.611	SUBCLONAL	1	TRUE	1	0.324280679485967	2		487	806	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787755	135787755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	82	514	0	ENST00000298552.3:c.827C>T	p.Ser276Phe	p.S276F	ENST00000298552	NM_001162426.1	276	tCt/tTt	9/23	1	2	FACETS	0.526	0.463	0.595	0.526	0.463	0.595	SUBCLONAL	1	TRUE	1	0.324280679485967	2		514	961	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53244001	53244004	+	missense_variant	Missense_Mutation	ONP	GAAC	GAAC	AAAA	novel	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	100	666	1	ENST00000375401.3:c.989_992delinsTTTT	p.Cys330_Ser331delinsPhePhe	p.C330_S331delinsFF	ENST00000375401	NM_004187.3	330	tGTTCt/tTTTTt	8/26	1	2	FACETS	0.495	0.44	0.553	0.495	0.44	0.553	SUBCLONAL	1	TRUE	1	0.324280679485967	2		667	1247	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608938	100608938	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	147	609	0	ENST00000308731.7:c.1670C>G	p.Ser557Cys	p.S557C	ENST00000308731	NM_000061.2	557	tCc/tGc	17/19	1	2	FACETS	0.764	0.696	0.836	0.764	0.696	0.836	SUBCLONAL	1	TRUE	1	0.324280679485967	2		609	1187	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	23	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.801	1	1	0.801	1	CLONAL	1	TRUE	1	0.16	2		276	280	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340057	116340057	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0053946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	33	257	0	ENST00000397752.3:c.919A>T	p.Arg307Ter	p.R307*	ENST00000397752	NM_000245.2	307	Aga/Tga	2/21	1	2	FACETS	0.876	0.713	1	0.876	0.713	1	CLONAL	1	TRUE	1	0.16	2		257	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579406	7579406	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0053947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	698	1047	1	ENST00000269305.4:c.281C>G	p.Ser94Ter	p.S94*	ENST00000269305	NM_001126112.2	94	tCa/tGa	4/11	0.714811216469061	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.722554533466999	2		1048	947	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0053947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	202	533	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.528403346136291	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.722554533466999	4		533	453	SUCCESS
BLM	641	MSKCC	GRCh37	15	91337546	91337546	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	20	448	0	ENST00000355112.3:c.3169A>G	p.Lys1057Glu	p.K1057E	ENST00000355112	NM_000057.2	1057	Aaa/Gaa	16/22	0.41641841208465	1	FACETS	0.131	0.1	0.168	0.131	0.1	0.168	INDETERMINATE	1	TRUE	0	0.722554533466999	1		448	269	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435704	56435739	+	inframe_deletion	In_Frame_Del	DEL	GAGTCACTGGAAGAGCCATGACAGGGCCCTGAGCTG	GAGTCACTGGAAGAGCCATGACAGGGCCCTGAGCTG	-	novel	NA	P-0053947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	90	906	0	ENST00000407977.2:c.1398_1433del	p.Ser467_Ser478del	p.S467_S478del	ENST00000407977		466	tcCAGCTCAGGGCCCTGTCATGGCTCTTCCAGTGACTCt/tct	9/10	0.322593516505304	3	FACETS	0.427	0.378	0.479	0.142	0.126	0.16	INDETERMINATE	1	TRUE	0	0.722554533466999	3		906	795	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157834	106157834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs4145756	NA	P-0053949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	94	339	1	ENST00000380013.4:c.2735C>T	p.Ala912Val	p.A912V	ENST00000380013	NM_001127208.2	912	gCg/gTg	3/11	0.688955329711463	2	FACETS	0.968	0.873	1	0.484	0.436	0.533	CLONAL	1	TRUE	0	0.688955329711463	2		340	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs530941076	NA	P-0053949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	548	825	0	ENST00000269305.4:c.658T>G	p.Tyr220Asp	p.Y220D	ENST00000269305	NM_001126112.2	220	Tat/Gat	6/11	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	2	TRUE	NA	0.688955329711463	2		825	781	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480411	89480411	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	145	385	0	ENST00000336596.2:c.2248C>T	p.Arg750Trp	p.R750W	ENST00000336596	NM_005233.5	750	Cgg/Tgg	13/17	0.51077715828184	4	FACETS	1	0.986	1	0.457	0.419	0.496	CLONAL	1	TRUE	1	0.688955329711463	4		385	519	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374280	15374280	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	204	632	0	ENST00000263377.2:c.1292A>C	p.Lys431Thr	p.K431T	ENST00000263377	NM_058243.2	431	aAg/aCg	7/20	0.68902313918709	3	FACETS	1	0.976	1	0.553	0.514	0.593	CLONAL	1	TRUE	1	0.688955329711463	3		632	720	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015094	37015094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	197	797	1	ENST00000358127.4:c.310C>T	p.Arg104Cys	p.R104C	ENST00000358127	NM_001280556.1	104	Cgc/Tgc	3/10	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.39002072618749	2		798	1002	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578514	7578550	+	frameshift_variant	Frame_Shift_Del	DEL	TTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGG	TTGGCCAGTTGGCAAAACATCTTGTTGAGGGCAGGGG	-	novel	NA	P-0053950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	210	1013	0	ENST00000269305.4:c.380_416del	p.Ser127Ter	p.S127*	ENST00000269305	NM_001126112.2	127	tCCCCTGCCCTCAACAAGATGTTTTGCCAACTGGCCAAg/tg	5/11	0.39002072618749	1	FACETS	0.915	0.85	0.983	0.915	0.85	0.983	CLONAL	1	TRUE	0	0.39002072618749	1		1013	947	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332653	70332653	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	46	541	0	ENST00000373644.4:c.558A>T	p.Gln186His	p.Q186H	ENST00000373644	NM_030625.2	186	caA/caT	2/12	1	2	FACETS	0.304	0.255	0.358	0.304	0.255	0.358	SUBCLONAL	1	TRUE	1	0.39002072618749	2		541	776	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434629	99434629	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	182	889	0	ENST00000268035.6:c.716G>T	p.Cys239Phe	p.C239F	ENST00000268035	NM_000875.3	239	tGc/tTc	3/21	1	2	FACETS	0.827	0.762	0.895	0.827	0.762	0.895	CLONAL	1	TRUE	1	0.39002072618749	2		889	1128	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546725	9546725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210292896	NA	P-0053952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	27	549	0	ENST00000353224.5:c.1297C>T	p.Arg433Trp	p.R433W	ENST00000353224	NM_177990.2	433	Cgg/Tgg	5/10	0.517338337447537	3	FACETS	0.28	0.222	0.346	0.14	0.111	0.173	SUBCLONAL	1	TRUE	1	0.526769021852689	3		549	463	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991718	72991718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs544025035	NA	P-0053952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	92	393	0	ENST00000268489.5:c.2327C>T	p.Ala776Val	p.A776V	ENST00000268489	NM_006885.3	776	gCg/gTg	2/10	0.526769021852689	2	FACETS	1	0.971	1	0.609	0.548	0.672	CLONAL	1	TRUE	0	0.526769021852689	2		393	287	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878530	151878530	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1396109953	NA	P-0053952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	117	741	1	ENST00000262189.6:c.6415C>T	p.Arg2139Ter	p.R2139*	ENST00000262189	NM_170606.2	2139	Cga/Tga	36/59	0.526773618085399	3	FACETS	0.748	0.675	0.826	0.374	0.337	0.413	SUBCLONAL	1	TRUE	1	0.526769021852689	3		742	750	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849586	68849586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567508990	NA	P-0053952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	222	873	0	ENST00000261769.5:c.1489G>A	p.Glu497Lys	p.E497K	ENST00000261769	NM_004360.3	497	Gag/Aag	10/16	0.526769021852689	2	FACETS	1	0.966	1	0.528	0.493	0.565	CLONAL	1	TRUE	0	0.526769021852689	2		873	798	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101064	41101064	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	167	964	0	ENST00000373198.4:c.1292A>C	p.Asn431Thr	p.N431T	ENST00000373198	NM_133170.3	431	aAc/aCc	8/32	0.517338337447537	3	FACETS	0.924	0.849	1	0.462	0.424	0.501	CLONAL	1	TRUE	1	0.526769021852689	3		964	867	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73991988	73991988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775892211	NA	P-0053952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	126	1111	2	ENST00000318443.5:c.8G>A	p.Arg3His	p.R3H	ENST00000318443	NM_001024736.1	3	cGt/cAt	2/10	1	2	FACETS	0.591	0.535	0.65	0.591	0.535	0.65	SUBCLONAL	1	TRUE	1	0.526769021852689	2		1113	810	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819267	3819267	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	164	794	0	ENST00000262367.5:c.2968C>G	p.Pro990Ala	p.P990A	ENST00000262367	NM_004380.2	990	Cct/Gct	15/31	0.526769021852689	2	FACETS	0.938	0.864	1	0.469	0.432	0.507	CLONAL	1	TRUE	0	0.526769021852689	2		794	664	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579383	7579384	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTTC	novel	NA	P-0053952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	345	1018	0	ENST00000269305.4:c.300_303dup	p.Thr102GlufsTer48	p.T102Efs*48	ENST00000269305	NM_001126112.2	101	-/GAAA	4/11	0.492027823595188	2	FACETS	0.89	0.848	0.932	0.89	0.848	0.932	CLONAL	2	TRUE	0	0.526769021852689	2		1018	736	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142938	7142938	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35045353	NA	P-0053952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	105	992	0	ENST00000302850.5:c.2431G>A	p.Gly811Ser	p.G811S	ENST00000302850	NM_000208.2	811	Ggc/Agc	12/22	0.526773618085399	1	FACETS	0.391	0.35	0.434	0.391	0.35	0.434	SUBCLONAL	1	TRUE	0	0.526769021852689	1		992	752	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497853	25497853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55710413	NA	P-0053952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	170	965	0	ENST00000264709.3:c.596G>A	p.Ser199Asn	p.S199N	ENST00000264709	NM_175629.2	199	aGc/aAc	6/23	0.526773618085399	3	FACETS	0.933	0.858	1	0.467	0.429	0.506	CLONAL	1	TRUE	1	0.526769021852689	3		965	874	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	218495	218495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776218604	NA	P-0053952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	104	236	0	ENST00000264932.6:c.25C>T	p.Arg9Trp	p.R9W	ENST00000264932	NM_004168.2	9	Cgg/Tgg	1/15	0.517338337447537	3	FACETS	0.967	0.881	1	0.967	0.881	1	CLONAL	2	TRUE	1	0.526769021852689	3		236	258	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	55	276	0				ENST00000310581	NM_198253.2	-/1132			0.226922099559718	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.891721196910967	0		276	126	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0053953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	197	646	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.891721196910967	2		646	400	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480459	89480459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	120	366	0	ENST00000336596.2:c.2296G>A	p.Gly766Arg	p.G766R	ENST00000336596	NM_005233.5	766	Gga/Aga	13/17	1	2	FACETS	0.979	0.9	1	0.979	0.9	1	CLONAL	1	TRUE	1	0.891721196910967	2		366	275	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269101	142269101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146041880	NA	P-0053953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	155	443	0	ENST00000350721.4:c.2849C>T	p.Pro950Leu	p.P950L	ENST00000350721	NM_001184.3	950	cCg/cTg	14/47	1	2	FACETS	0.94	0.872	1	0.94	0.872	1	CLONAL	1	TRUE	1	0.891721196910967	2		443	370	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966654	44966654	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0053953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	112	169	0	ENST00000377967.4:c.3879-1G>C		p.X1293_splice	ENST00000377967	NM_021140.2	1293			1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.891721196910967	1		169	120	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857980	9857980	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	50	692	0	ENST00000330684.3:c.3421C>G	p.Leu1141Val	p.L1141V	ENST00000330684	NM_001134407.1	1141	Ctg/Gtg	13/13	1	2	FACETS	0.409	0.35	0.474	0.409	0.35	0.474	SUBCLONAL	1	TRUE	1	0.891721196910967	2		692	274	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58700911	58700911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	201	560	1	ENST00000305921.3:c.502C>T	p.Pro168Ser	p.P168S	ENST00000305921	NM_003620.3	168	Cct/Tct	2/6	1	2	FACETS	0.949	0.889	1	0.949	0.889	1	CLONAL	1	TRUE	1	0.891721196910967	2		561	475	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815565	139815565	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	257	917	0	ENST00000247668.2:c.1036G>C	p.Glu346Gln	p.E346Q	ENST00000247668	NM_021138.3	346	Gag/Cag	9/11	0.891721196910967	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.891721196910967	1		917	297	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171447	123171459	+	frameshift_variant	Frame_Shift_Del	DEL	TTTTTATTCAGTG	TTTTTATTCAGTG	-	novel	NA	P-0053953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	113	221	0	ENST00000218089.9:c.361_373del	p.Phe121GlnfsTer20	p.F121Qfs*20	ENST00000218089	NM_001042749.1	120	tTTTTTATTCAGTGt/tt	6/35	1	1	FACETS	0.962	0.909	1	0.962	0.909	1	CLONAL	1	TRUE	0	0.891721196910967	1		221	146	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0053954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	11	663	0	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	0.877303635268581	1	FACETS	0.027	0.018	0.038	0.027	0.018	0.038	SUBCLONAL	1	TRUE	0	0.877303635268581	1		663	519	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842625	68842626	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0053954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	391	733	0	ENST00000261769.5:c.562_563dup	p.Tyr190SerfsTer26	p.Y190Sfs*26	ENST00000261769	NM_004360.3	187	-/GT	5/16	0.877303635268581	1	FACETS	0.987	0.958	1	0.987	0.958	1	CLONAL	1	TRUE	0	0.877303635268581	1		733	507	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765488	41765507	+	frameshift_variant	Frame_Shift_Del	DEL	AAATCCCCAGGACCGGCCAA	AAATCCCCAGGACCGGCCAA	-	novel	NA	P-0053954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	411	835	0	ENST00000301178.4:c.2364_2383del	p.Asn789PhefsTer22	p.N789Ffs*22	ENST00000301178	NM_021913.4	788	ctAAATCCCCAGGACCGGCCAAgt/ctgt	20/20	1	2	FACETS	0.911	0.87	0.953	0.911	0.87	0.953	CLONAL	1	TRUE	1	0.877303635268581	2		835	1028	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs967461896	NA	P-0053956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	397	1063	0	ENST00000269305.4:c.526T>G	p.Cys176Gly	p.C176G	ENST00000269305	NM_001126112.2	176	Tgc/Ggc	5/11	0.326496918693215	3	FACETS	0.84	0.801	0.88	0.84	0.801	0.88	CLONAL	3	TRUE	0	0.358883972829985	3		1063	1035	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045919	26045919	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	142	921	0	ENST00000540144.1:c.281A>G	p.Gln94Arg	p.Q94R	ENST00000540144	NM_003531.2	94	cAg/cGg	1/1	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.358883972829985	2		921	771	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920660	127920660	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	86	421	0	ENST00000373547.4:c.239G>T	p.Gly80Val	p.G80V	ENST00000373547	NM_002721.4	80	gGt/gTt	4/7	0.358883972829985	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.358883972829985	1		421	363	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0053957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	464	771	5	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.546772792929957	2	FACETS	0.98	0.943	1	0.98	0.943	1	CLONAL	2	TRUE	0	0.546772792929957	2		776	866	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509841	106509841	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	210	637	2	ENST00000359195.3:c.1835C>T	p.Ala612Val	p.A612V	ENST00000359195	NM_002649.2	612	gCc/gTc	2/11	0.546893984805254	4	FACETS	1	0.936	1	0.505	0.468	0.544	CLONAL	1	TRUE	2	0.546772792929957	4		639	1176	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534749	18534749	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	143	499	0	ENST00000266497.5:c.1807C>G	p.Pro603Ala	p.P603A	ENST00000266497		603	Cct/Gct	12/31	0.546893984805254	3	FACETS	0.984	0.899	1	0.492	0.449	0.536	CLONAL	1	TRUE	1	0.546772792929957	3		499	677	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0053960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	217	547	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.489563952817096	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.489563952817096	2		547	372	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	141	784	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.489563952817096	2		784	487	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188100	11188100	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	108	686	0	ENST00000361445.4:c.5994G>T	p.Met1998Ile	p.M1998I	ENST00000361445	NM_004958.3	1998	atG/atT	43/58	1	2	FACETS	0.974	0.879	1	0.974	0.879	1	CLONAL	1	TRUE	1	0.489563952817096	2		686	453	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149707	202149707	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	113	616	0	ENST00000358485.4:c.1148A>G	p.Tyr383Cys	p.Y383C	ENST00000358485	NM_001080125.1	383	tAt/tGt	8/9	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.489563952817096	2		616	357	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176551	56176558	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTCCAT	CTGTCCAT	-	novel	NA	P-0053960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	53	506	0	ENST00000399503.3:c.2101_2108del	p.Leu701IlefsTer32	p.L701Ifs*32	ENST00000399503	NM_005921.1	701	CTGTCCATa/a	12/20	0.489563952817096	3	FACETS	0.884	0.758	1	0.442	0.379	0.51	CLONAL	1	TRUE	1	0.489563952817096	3		506	305	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189443	56189443	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	174	588	0	ENST00000399503.3:c.4475A>C	p.Gln1492Pro	p.Q1492P	ENST00000399503	NM_005921.1	1492	cAa/cCa	20/20	0.489563952817096	3	FACETS	0.958	0.89	1	0.958	0.89	1	CLONAL	2	TRUE	1	0.489563952817096	3		588	462	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189470	56189470	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	160	548	0	ENST00000399503.3:c.4502A>G	p.Glu1501Gly	p.E1501G	ENST00000399503	NM_005921.1	1501	gAg/gGg	20/20	0.489563952817096	3	FACETS	0.992	0.92	1	0.992	0.92	1	CLONAL	2	TRUE	1	0.489563952817096	3		548	410	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845896	151845899	+	frameshift_variant	Frame_Shift_Del	DEL	TTTA	TTTA	-	novel	NA	P-0053960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	195	743	0	ENST00000262189.6:c.13113_13116del	p.Lys4372HisfsTer7	p.K4372Hfs*7	ENST00000262189	NM_170606.2	4371	ttTAAA/tt	52/59	0.489563952817096	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.489563952817096	3		743	432	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220475	123220486	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CCGAAATTCTTT	CCGAAATTCTTT	G	novel	NA	P-0053960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	172	683	0	ENST00000218089.9:c.3132_3143delinsG	p.Tyr1044Ter	p.Y1044*	ENST00000218089	NM_001042749.1	1044	taCCGAAATTCTTTg/taGg	30/35	0.350408259609836	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.489563952817096	4		683	457	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	54	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.992	0.85	1	0.992	0.85	1	CLONAL	1	TRUE	1	0.270879108664651	2		276	402	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0053971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	85	470	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.270879108664651	2		470	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0053971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	163	1978	1	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.270879108664651	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.270879108664651	1		1979	974	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720670	89720670	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	72	397	0	ENST00000371953.3:c.823del	p.Val275Ter	p.V275*	ENST00000371953	NM_000314.4	274	tGg/tg	8/9	0.270879108664651	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.270879108664651	1		397	412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578491	7578491	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	260	2374	0	ENST00000269305.4:c.439G>C	p.Val147Leu	p.V147L	ENST00000269305	NM_001126112.2	147	Gtt/Ctt	5/11	0.270879108664651	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.270879108664651	1		2374	1165	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254699	16254699	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	48	994	0	ENST00000375759.3:c.1964G>C	p.Arg655Thr	p.R655T	ENST00000375759	NM_015001.2	655	aGa/aCa	11/15	1	2	FACETS	0.484	0.408	0.568	0.484	0.408	0.568	SUBCLONAL	1	TRUE	1	0.270879108664651	2		994	732	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254840	16254840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1361099404	NA	P-0053971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	50	933	0	ENST00000375759.3:c.2105G>A	p.Arg702Gln	p.R702Q	ENST00000375759	NM_015001.2	702	cGa/cAa	11/15	1	2	FACETS	0.485	0.41	0.568	0.485	0.41	0.568	SUBCLONAL	1	TRUE	1	0.270879108664651	2		933	761	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402320	402320	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	92	649	0	ENST00000399788.2:c.4471G>C	p.Glu1491Gln	p.E1491Q	ENST00000399788	NM_001042603.1	1491	Gag/Cag	27/28	0.248339766469496	3	FACETS	1	0.944	1	0.551	0.489	0.616	CLONAL	1	TRUE	1	0.270879108664651	3		649	700	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899040	40899040	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	102	1160	0	ENST00000373198.4:c.2230A>C	p.Thr744Pro	p.T744P	ENST00000373198	NM_133170.3	744	Aca/Cca	14/32	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.270879108664651	2		1160	634	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505670	186505670	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0053971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	39	401	0	ENST00000323963.5:c.1078A>T	p.Arg360Ter	p.R360*	ENST00000323963		360	Aga/Tga	10/11	0.248339766469496	3	FACETS	1	0.887	1	0.543	0.452	0.644	CLONAL	1	TRUE	1	0.270879108664651	3		401	301	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800541	32800541	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	177	2126	0	ENST00000374899.4:c.1006G>T	p.Val336Phe	p.V336F	ENST00000374899	NM_018833.2	336	Gtt/Ttt	6/12	0.270879108664651	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.270879108664651	1		2126	995	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0053972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	51	464	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.599	0.509	0.698	0.599	0.509	0.698	SUBCLONAL	1	TRUE	1	0.31	2		464	549	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0053972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	141	1211	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.303987246019565	1	FACETS	0.797	0.726	0.873	0.797	0.726	0.873	SUBCLONAL	1	TRUE	0	0.31	1		1211	964	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097639	27097640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0053972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	99	666	0	ENST00000324856.7:c.3229dup	p.Ala1077GlyfsTer28	p.A1077Gfs*28	ENST00000324856	NM_006015.4	1076	-/G	12/20	0.303987246019565	1	FACETS	0.804	0.719	0.895	0.804	0.719	0.895	CLONAL	1	TRUE	0	0.31	1		666	671	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971005	21971009	+	frameshift_variant	Frame_Shift_Del	DEL	GCCAG	GCCAG	-	novel	NA	P-0053972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	97	1119	0	ENST00000304494.5:c.349_353del	p.Leu117Ter	p.L117*	ENST00000304494	NM_000077.4	117	CTGGCt/t	2/3	0.303987246019565	1	FACETS	0.722	0.644	0.806	0.722	0.644	0.806	SUBCLONAL	1	TRUE	0	0.31	1		1119	732	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	147	276	0				ENST00000310581	NM_198253.2	-/1132			0.344665605515217	3	FACETS	0.755	0.691	0.822	0.755	0.691	0.822	SUBCLONAL	2	TRUE	1	0.344665605515217	3		276	662	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839699	27839699	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	73	637	0	ENST00000328488.2:c.395G>C	p.Arg132Pro	p.R132P	ENST00000328488	NM_003533.2	132	cGa/cCa	1/1	1	2	FACETS	0.473	0.413	0.539	0.473	0.413	0.539	SUBCLONAL	1	TRUE	1	0.344665605515217	2		637	895	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120535135	120535135	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1192955368	NA	P-0053973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	121	685	0	ENST00000229340.5:c.520G>C	p.Asp174His	p.D174H	ENST00000229340	NM_006861.6	174	Gac/Cac	6/6	1	2	FACETS	0.668	0.602	0.738	0.668	0.602	0.738	SUBCLONAL	1	TRUE	1	0.344665605515217	2		685	1051	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941720	48941720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	37	182	0	ENST00000267163.4:c.1030C>T	p.Gln344Ter	p.Q344*	ENST00000267163	NM_000321.2	344	Cag/Tag	10/27	1	2	FACETS	0.542	0.447	0.648	0.542	0.447	0.648	SUBCLONAL	1	TRUE	1	0.344665605515217	2		182	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0053973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	116	764	0	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.244756708987014	1	FACETS	0.63	0.567	0.696	0.63	0.567	0.696	SUBCLONAL	1	TRUE	0	0.344665605515217	1		764	885	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208001	5208001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	136	966	0	ENST00000357368.4:c.5710G>A	p.Gly1904Ser	p.G1904S	ENST00000357368	NM_002850.3	1904	Ggc/Agc	37/38	0.298389984833814	1	FACETS	0.576	0.523	0.633	0.576	0.523	0.633	SUBCLONAL	1	TRUE	0	0.344665605515217	1		966	1133	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707951	47707951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63749830	NA	P-0053973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	68	441	1	ENST00000233146.2:c.2575G>A	p.Glu859Lys	p.E859K	ENST00000233146	NM_000251.2	859	Gaa/Aaa	15/16	1	2	FACETS	0.578	0.502	0.66	0.578	0.502	0.66	SUBCLONAL	1	TRUE	1	0.344665605515217	2		442	683	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707961	47707961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1216558739	NA	P-0053973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	61	421	1	ENST00000233146.2:c.2585G>A	p.Gly862Glu	p.G862E	ENST00000233146	NM_000251.2	862	gGa/gAa	15/16	1	2	FACETS	0.526	0.453	0.605	0.526	0.453	0.605	SUBCLONAL	1	TRUE	1	0.344665605515217	2		422	673	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665213	138665213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1311	146	897	0	ENST00000330315.3:c.352G>A	p.Glu118Lys	p.E118K	ENST00000330315	NM_023067.3	118	Gag/Aag	1/1	1	2	FACETS	0.581	0.529	0.637	0.581	0.529	0.637	SUBCLONAL	1	TRUE	1	0.344665605515217	2		897	1457	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280447	1280447	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	108	781	0	ENST00000310581.5:c.1776C>A	p.His592Gln	p.H592Q	ENST00000310581	NM_198253.2	592	caC/caA	4/16	0.344665605515217	3	FACETS	0.581	0.519	0.646	0.29	0.259	0.323	SUBCLONAL	1	TRUE	1	0.344665605515217	3		781	1265	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128322044	128322044	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	104	656	0	ENST00000265960.3:c.716G>T	p.Gly239Val	p.G239V	ENST00000265960	NM_001006617.1	239	gGg/gTg	6/12	1	2	FACETS	0.605	0.54	0.673	0.605	0.54	0.673	SUBCLONAL	1	TRUE	1	0.344665605515217	2		656	998	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0053974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1182	1580	603	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.239941601953596	5	FACETS	1	0.997	1	1	0.998	1	CLONAL	6	TRUE	0	0.239941601953596	5		603	2762	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0053974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	139	813	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.239941601953596	2		813	1069	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991519	72991519	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1554	119	836	0	ENST00000268489.5:c.2526C>G	p.Ile842Met	p.I842M	ENST00000268489	NM_006885.3	842	atC/atG	2/10	1	2	FACETS	0.593	0.533	0.657	0.593	0.533	0.657	SUBCLONAL	1	TRUE	1	0.239941601953596	2		836	1673	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426641	212426641	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	46	635	0	ENST00000342788.4:c.2474T>C	p.Val825Ala	p.V825A	ENST00000342788	NM_005235.2	825	gTc/gCc	20/28	1	2	FACETS	0.454	0.381	0.536	0.454	0.381	0.536	SUBCLONAL	1	TRUE	1	0.239941601953596	2		635	844	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814214	76814214	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	13	198	0	ENST00000373344.5:c.6430del	p.Asp2144ThrfsTer23	p.D2144Tfs*23	ENST00000373344	NM_000489.3	2144	Gac/ac	29/35	NA	2	FACETS	0.82	0.595	1			1	INDETERMINATE	2	TRUE	NA	0.200760377026914	2		198	79	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215356	123215356	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	21	239	0	ENST00000218089.9:c.2902G>T	p.Glu968Ter	p.E968*	ENST00000218089	NM_001042749.1	968	Gaa/Taa	28/35	NA	2	FACETS	0.864	0.675	1			1	INDETERMINATE	2	TRUE	NA	0.200760377026914	2		239	121	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	69	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.823	0.719	0.934	0.823	0.719	0.934	CLONAL	1	TRUE	1	0.386316044114704	2		276	434	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0053979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	85	465	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.364009771232903	3	FACETS	1	0.898	1	0.507	0.449	0.568	CLONAL	1	TRUE	1	0.386316044114704	3		465	518	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0053979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	80	420	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.386316044114704	2		420	394	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61197647	61197647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	156	831	0	ENST00000301761.2:c.29C>T	p.Ser10Leu	p.S10L	ENST00000301761	NM_017841.2	10	tCg/tTg	1/4	1	2	FACETS	0.914	0.837	0.994	0.914	0.837	0.994	CLONAL	1	TRUE	1	0.386316044114704	2		831	884	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422253	422253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374400044	NA	P-0053979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	128	327	0	ENST00000399788.2:c.3005G>A	p.Arg1002Gln	p.R1002Q	ENST00000399788	NM_001042603.1	1002	cGa/cAa	20/28	NA	2	FACETS	0.832	0.755	0.914			1	INDETERMINATE	1	TRUE	NA	0.386316044114704	2		327	796	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965571	25965571	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0053979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	187	618	0	ENST00000435504.4:c.3635C>G	p.Ser1212Ter	p.S1212*	ENST00000435504		1212	tCa/tGa	13/13	1	2	FACETS	0.985	0.91	1	0.985	0.91	1	CLONAL	1	TRUE	1	0.386316044114704	2		618	983	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572976	41572976	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0053979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	237	1138	0	ENST00000263253.7:c.5261C>G	p.Ser1754Ter	p.S1754*	ENST00000263253	NM_001429.3	1754	tCa/tGa	31/31	1	2	FACETS	0.946	0.881	1	0.946	0.881	1	CLONAL	1	TRUE	1	0.386316044114704	2		1138	1297	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156625	106156625	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs771408533	NA	P-0053979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	112	244	0	ENST00000380013.4:c.1526C>G	p.Ser509Ter	p.S509*	ENST00000380013	NM_001127208.2	509	tCa/tGa	3/11	0.386316044114704	3	FACETS	1	0.968	1			1	CLONAL	1	TRUE	NA	0.386316044114704	3		244	590	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156810	106156810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1472426057	NA	P-0053979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	132	390	0	ENST00000380013.4:c.1711C>T	p.Arg571Cys	p.R571C	ENST00000380013	NM_001127208.2	571	Cgt/Tgt	3/11	0.386316044114704	3	FACETS	1	0.947	1			1	CLONAL	1	TRUE	NA	0.386316044114704	3		390	768	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156862	106156862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	127	364	0	ENST00000380013.4:c.1763C>T	p.Ser588Leu	p.S588L	ENST00000380013	NM_001127208.2	588	tCa/tTa	3/11	0.386316044114704	3	FACETS	1	0.958	1			1	CLONAL	1	TRUE	NA	0.386316044114704	3		364	715	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923699	39923699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758883383	NA	P-0053979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	230	579	0	ENST00000378444.4:c.3392G>A	p.Arg1131Gln	p.R1131Q	ENST00000378444	NM_001123385.1	1131	cGg/cAg	7/15	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.386316044114704	1		579	657	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0053980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	43	533	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.212500413762757	4	FACETS	0.882	0.756	1	0.882	0.756	1	INDETERMINATE	2	TRUE	2	0.64833107575076	4		533	124	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294237	11294237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	219	680	0	ENST00000361445.4:c.2294C>T	p.Pro765Leu	p.P765L	ENST00000361445	NM_004958.3	765	cCc/cTc	14/58	0.480110957736767	5	FACETS	1	0.987	1	0.797	0.748	0.848	CLONAL	2	TRUE	2	0.64833107575076	5		680	557	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29115439	29115440	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	55	238	0	ENST00000328354.6:c.626dup	p.Ser210ValfsTer5	p.S210Vfs*5	ENST00000328354	NM_007194.3	209	cag/caAg	5/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.64833107575076	2		238	140	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191487	10191487	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	40	420	0	ENST00000256474.2:c.480G>C	p.Glu160Asp	p.E160D	ENST00000256474	NM_000551.3	160	gaG/gaC	3/3	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	1	0.166553651416838	2		420	353	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156629	55156629	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	121	725	0	ENST00000257290.5:c.3030G>C	p.Gln1010His	p.Q1010H	ENST00000257290	NM_006206.4	1010	caG/caC	22/23	0.145353927962956	4	FACETS	1	0.926	1	1	0.986	1	CLONAL	3	FALSE	2	0.166553651416838	4		725	552	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0053982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	106	373	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	0.215894263931577	2	FACETS	1	0.98	1	0.695	0.625	0.769	CLONAL	1	TRUE	0	0.269098295542591	2		373	567	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514525	149514525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138830253	NA	P-0053982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	186	564	0	ENST00000261799.4:c.419C>T	p.Thr140Met	p.T140M	ENST00000261799	NM_002609.3	140	aCg/aTg	4/23	0.215894263931577	2	FACETS	0.797	0.737	0.86	0.797	0.737	0.86	SUBCLONAL	2	TRUE	0	0.269098295542591	2		564	867	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022582	12022582	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1260	97	834	0	ENST00000396373.4:c.688C>T	p.Gln230Ter	p.Q230*	ENST00000396373	NM_001987.4	230	Cag/Tag	5/8	0.193005999786257	4	FACETS	0.674	0.599	0.755	0.337	0.299	0.378	SUBCLONAL	1	TRUE	2	0.269098295542591	4		834	1357	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646305	23646305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555461218	NA	P-0053982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	113	669	0	ENST00000261584.4:c.1562C>T	p.Thr521Ile	p.T521I	ENST00000261584	NM_024675.3	521	aCc/aTc	4/13	0.215894263931577	2	FACETS	0.704	0.632	0.781	0.352	0.316	0.391	SUBCLONAL	1	TRUE	0	0.269098295542591	2		669	1193	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546586	9546586	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	49	657	1	ENST00000353224.5:c.1436A>T	p.Lys479Ile	p.K479I	ENST00000353224	NM_177990.2	479	aAa/aTa	5/10	0.269098295542591	1	FACETS	0.357	0.301	0.419	0.357	0.301	0.419	SUBCLONAL	1	TRUE	0	0.269098295542591	1		658	882	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878815	151878815	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0053982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	94	585	0	ENST00000262189.6:c.6130A>T	p.Lys2044Ter	p.K2044*	ENST00000262189	NM_170606.2	2044	Aag/Tag	36/59	NA	2	FACETS	0.831	0.738	0.929			1	INDETERMINATE	1	TRUE	NA	0.269098295542591	2		585	841	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061225	38061242	+	inframe_deletion	In_Frame_Del	DEL	TCGAACATGTTGCCGGAG	TCGAACATGTTGCCGGAG	-	novel	NA	P-0053983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	87	660	0	ENST00000250448.2:c.747_764del	p.Asp249_Phe254del	p.D249_F254del	ENST00000250448	NM_004496.3	249	gaCTCCGGCAACATGTTCGAg/gag	2/2	1	2	FACETS	0.964	0.856	1	1	0.985	1	CLONAL	2	TRUE	1	0.17	2		660	531	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696449	47696449	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	79	442	0	ENST00000347630.2:c.374T>G	p.Phe125Cys	p.F125C	ENST00000347630	NM_001007230.1	125	tTt/tGt	6/11	1	2	FACETS	0.835	0.733	0.945	0.835	0.733	0.945	CLONAL	1	TRUE	1	0.231050794116383	2		442	819	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434357	49434357	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778813102	NA	P-0053985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1290	180	819	1	ENST00000301067.7:c.7196C>T	p.Pro2399Leu	p.P2399L	ENST00000301067	NM_003482.3	2399	cCc/cTc	31/54	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.231050794116383	2		820	1470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0053986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	274	586	1	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.478198708584979	2	FACETS	0.82	0.778	0.862	0.82	0.778	0.862	CLONAL	2	TRUE	0	0.589396771254014	2		587	567	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902581	1902581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	136	850	0	ENST00000382891.5:c.200G>A	p.Gly67Asp	p.G67D	ENST00000382891	NM_133335.3	67	gGc/gAc	2/22	0.343492443864524	4	FACETS	0.74	0.672	0.812	0.37	0.336	0.406	INDETERMINATE	1	TRUE	2	0.589396771254014	4		850	991	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096273	178096273	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs759117836	NA	P-0053986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	103	538	0	ENST00000397062.3:c.1058G>C	p.Ser353Thr	p.S353T	ENST00000397062	NM_006164.4	353	aGt/aCt	5/5	0.589396771254014	4	FACETS	0.633	0.565	0.704	0.211	0.188	0.235	SUBCLONAL	1	TRUE	1	0.589396771254014	4		538	878	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033494	48033547	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TATGGTATGTGCAAATTGTTTTTTTCCACAAATTCGGTTTTTTGAGAGGGCACT	TATGGTATGTGCAAATTGTTTTTTTCCACAAATTCGGTTTTTTGAGAGGGCACT	-	novel	NA	P-0053986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	135	513	0	ENST00000234420.5:c.3799_3802-43del		p.X1267_splice	ENST00000234420	NM_000179.2	1267		8/10	0.589396771254014	4	FACETS	0.863	0.791	0.936	0.575	0.527	0.624	CLONAL	2	TRUE	1	0.589396771254014	4		513	422	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419861	41419861	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	90	651	0	ENST00000373198.4:c.460A>T	p.Ser154Cys	p.S154C	ENST00000373198	NM_133170.3	154	Agc/Tgc	3/32	0.311174233746878	6	FACETS	0.871	0.772	0.976	0.218	0.193	0.244	INDETERMINATE	1	TRUE	2	0.589396771254014	6		651	764	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960053	134960053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	107	640	0	ENST00000398015.3:c.2410G>A	p.Ala804Thr	p.A804T	ENST00000398015	NM_004441.4	804	Gcc/Acc	13/16	0.589396771254014	3	FACETS	0.656	0.588	0.727	0.328	0.294	0.364	SUBCLONAL	1	TRUE	1	0.589396771254014	3		640	717	SUCCESS
AR	367	MSKCC	GRCh37	X	66931391	66931391	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	65	735	0	ENST00000374690.3:c.2033T>A	p.Leu678Gln	p.L678Q	ENST00000374690	NM_000044.3	678	cTg/cAg	4/8	0.589396771254014	3	FACETS	0.439	0.38	0.503	0.22	0.19	0.252	SUBCLONAL	1	TRUE	1	0.589396771254014	3		735	650	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519893	NA	P-0053987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1162	299	723	0	ENST00000267101.3:c.310G>T	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ttg	3/28	0.172179491540984	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.222644786596442	3		723	1461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579716	7579716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1192416464	NA	P-0053987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	139	823	1	ENST00000269305.4:c.80del	p.Pro27LeufsTer17	p.P27Lfs*17	ENST00000269305	NM_001126112.2	27	cCt/ct	3/11	0.173138876896512	2	FACETS	0.762	0.694	0.834	0.762	0.694	0.834	SUBCLONAL	2	TRUE	0	0.222644786596442	2		824	819	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912733	32912733	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs70953664	NA	P-0053987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	47	501	0	ENST00000380152.3:c.4241C>T	p.Thr1414Met	p.T1414M	ENST00000380152		1414	aCg/aTg	11/27	1	2	FACETS	0.592	0.498	0.696	0.592	0.498	0.696	SUBCLONAL	1	TRUE	1	0.222644786596442	2		501	713	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	22	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.805	1	1	0.805	1	CLONAL	1	TRUE	1	0.23	2		276	185	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562627	21562627	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754998895	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	19	147	0	ENST00000382592.4:c.1292C>T	p.Thr431Ile	p.T431I	ENST00000382592	NM_014572.2	431	aCc/aTc	4/8	1	2	FACETS	0.545	0.414	0.7	0.545	0.414	0.7	SUBCLONAL	1	TRUE	1	0.23	2		147	303	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620593	52620593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766154467	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	120	478	0	ENST00000394830.3:c.3160C>T	p.Pro1054Ser	p.P1054S	ENST00000394830	NM_018313.4	1054	Ccc/Tcc	21/30	0.11882099007519	4	FACETS	1	0.962	1	0.567	0.511	0.627	INDETERMINATE	1	TRUE	2	0.23	4		478	1131	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244997	46244997	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs868082376	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	181	589	0	ENST00000334344.6:c.3091C>T	p.Gln1031Ter	p.Q1031*	ENST00000334344	NM_152641.2	1031	Cag/Tag	15/21	1	2	FACETS	0.773	0.712	0.836	1	0.99	1	SUBCLONAL	2	TRUE	1	0.23	2		589	1018	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547022	9547022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs58486349	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	61	276	0	ENST00000353224.5:c.1000G>A	p.Asp334Asn	p.D334N	ENST00000353224	NM_177990.2	334	Gat/Aat	5/10	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.23	2		276	473	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590732	189590732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	109	535	0	ENST00000264731.3:c.1297G>A	p.Glu433Lys	p.E433K	ENST00000264731	NM_003722.4	433	Gaa/Aaa	10/14	0.126558599368198	3	FACETS	1	0.941	1	0.536	0.481	0.596	INDETERMINATE	1	TRUE	1	0.23	3		535	985	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459867	149459867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1386	95	902	1	ENST00000286301.3:c.340G>A	p.Glu114Lys	p.E114K	ENST00000286301	NM_005211.3	114	Gag/Aag	4/22	1	2	FACETS	0.558	0.494	0.626	0.558	0.494	0.626	SUBCLONAL	1	TRUE	1	0.23	2		903	1481	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	66	266	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.23	2		266	521	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713358	30713358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	106	522	1	ENST00000295754.5:c.683G>A	p.Ser228Asn	p.S228N	ENST00000295754	NM_003242.5	228	aGc/aAc	4/7	0.11882099007519	4	FACETS	1	0.959	1	0.572	0.512	0.636	INDETERMINATE	1	TRUE	2	0.23	4		523	991	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871777	37871777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147382623	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	211	654	0	ENST00000269571.5:c.1301G>A	p.Arg434Gln	p.R434Q	ENST00000269571		434	cGa/cAa	11/27	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.23	2		654	1235	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577106	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	133	658	2	ENST00000269305.4:c.832_833delinsTT	p.Pro278Phe	p.P278F	ENST00000269305	NM_001126112.2	278	CCt/TTt	8/11	1	2	FACETS	0.957	0.867	1	0.957	0.867	1	CLONAL	1	TRUE	1	0.23	2		660	1209	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522194	157522194	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	110	687	0	ENST00000346085.5:c.4466C>T	p.Pro1489Leu	p.P1489L	ENST00000346085	NM_020732.3	1489	cCt/cTt	18/20	1	2	FACETS	0.863	0.773	0.958	0.863	0.773	0.958	CLONAL	1	TRUE	1	0.23	2		687	1109	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858735	9858735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	71	358	1	ENST00000330684.3:c.2666G>A	p.Gly889Glu	p.G889E	ENST00000330684	NM_001134407.1	889	gGa/gAa	13/13	1	2	FACETS	0.899	0.784	1	0.899	0.784	1	CLONAL	1	TRUE	1	0.23	2		359	687	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390995	89390995	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144727411	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	106	483	0	ENST00000336596.2:c.1061G>A	p.Arg354Gln	p.R354Q	ENST00000336596	NM_005233.5	354	cGg/cAg	5/17	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.23	2		483	829	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8338945	8338945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	61	405	0	ENST00000356435.5:c.5356G>A	p.Glu1786Lys	p.E1786K	ENST00000356435		1786	Gaa/Aaa	32/35	1	2	FACETS	0.629	0.541	0.725	0.629	0.541	0.725	SUBCLONAL	1	TRUE	1	0.23	2		405	843	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591270	67591270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1289880098	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	56	435	0	ENST00000274335.5:c.1768C>T	p.Arg590Trp	p.R590W	ENST00000274335		590	Cgg/Tgg	13/15	1	2	FACETS	0.645	0.551	0.748	0.645	0.551	0.748	SUBCLONAL	1	TRUE	1	0.23	2		435	755	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39706225	39706225	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	38	200	0	ENST00000361337.2:c.283C>T	p.Arg95Ter	p.R95*	ENST00000361337	NM_003286.2	95	Cga/Tga	5/21	1	2	FACETS	0.69	0.57	0.824	0.69	0.57	0.824	SUBCLONAL	1	TRUE	1	0.23	2		200	479	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924327	112924327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	209	789	1	ENST00000351677.2:c.1273G>A	p.Asp425Asn	p.D425N	ENST00000351677	NM_002834.3	425	Gac/Aac	11/16	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.23	2		790	1386	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492945	8492945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759831182	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	53	511	1	ENST00000356435.5:c.2384C>T	p.Ser795Phe	p.S795F	ENST00000356435		795	tCc/tTc	16/35	1	2	FACETS	0.516	0.438	0.601	0.516	0.438	0.601	SUBCLONAL	1	TRUE	1	0.23	2		512	894	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589165	67589165	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	39	270	0	ENST00000274335.5:c.1153C>T	p.His385Tyr	p.H385Y	ENST00000274335		385	Cat/Tat	9/15	1	2	FACETS	0.551	0.456	0.658	0.551	0.456	0.658	SUBCLONAL	1	TRUE	1	0.23	2		270	615	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860333	42860333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758778273	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	115	593	0	ENST00000398585.3:c.544G>A	p.Glu182Lys	p.E182K	ENST00000398585	NM_001135099.1	182	Gag/Aag	5/14	1	2	FACETS	0.898	0.807	0.995	0.898	0.807	0.995	CLONAL	1	TRUE	1	0.23	2		593	1113	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562629	95562629	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	74	358	0	ENST00000393063.1:c.4628C>T	p.Ser1543Phe	p.S1543F	ENST00000393063	NM_030621.3	1543	tCc/tTc	24/28	1	2	FACETS	0.867	0.758	0.985	0.867	0.758	0.985	CLONAL	1	TRUE	1	0.23	2		358	742	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486104	8486104	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369780691	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	96	584	0	ENST00000356435.5:c.2713G>A	p.Glu905Lys	p.E905K	ENST00000356435		905	Gag/Aag	17/35	1	2	FACETS	0.863	0.768	0.966	0.863	0.768	0.966	CLONAL	1	TRUE	1	0.23	2		584	967	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484270	8484270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867884876	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	69	480	0	ENST00000356435.5:c.3262C>T	p.Arg1088Cys	p.R1088C	ENST00000356435		1088	Cgt/Tgt	19/35	1	2	FACETS	0.708	0.615	0.808	0.708	0.615	0.808	SUBCLONAL	1	TRUE	1	0.23	2		480	848	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522604	106522604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	74	372	0	ENST00000359195.3:c.2581G>A	p.Asp861Asn	p.D861N	ENST00000359195	NM_002649.2	861	Gat/Aat	7/11	0.126558599368198	3	FACETS	0.814	0.711	0.926	0.407	0.355	0.463	INDETERMINATE	1	TRUE	1	0.23	3		372	881	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670340	134670340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415689583	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	99	456	1	ENST00000398015.3:c.251G>A	p.Arg84His	p.R84H	ENST00000398015	NM_004441.4	84	cGc/cAc	3/16	1	2	FACETS	0.991	0.883	1	0.991	0.883	1	CLONAL	1	TRUE	1	0.23	2		457	869	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650169	93650169	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	71	407	0	ENST00000375746.1:c.1720C>T	p.Arg574Ter	p.R574*	ENST00000375746	NM_001174167.1	574	Cga/Tga	12/14	1	2	FACETS	0.751	0.654	0.856	0.751	0.654	0.856	SUBCLONAL	1	TRUE	1	0.23	2		407	822	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058471	69058471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	84	368	0	ENST00000288368.4:c.4115G>A	p.Gly1372Glu	p.G1372E	ENST00000288368	NM_024870.2	1372	gGa/gAa	34/40	0.126558599368198	3	FACETS	1	0.916	1	0.523	0.462	0.59	INDETERMINATE	1	TRUE	1	0.23	3		368	778	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519343	137519343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	67	337	0	ENST00000367739.4:c.1295C>T	p.Pro432Leu	p.P432L	ENST00000367739	NM_000416.2	432	cCa/cTa	7/7	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.23	2		337	554	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654784	29654784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769843989	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	65	435	1	ENST00000356175.3:c.5473C>T	p.Arg1825Trp	p.R1825W	ENST00000356175	NM_000267.3	1825	Cgg/Tgg	37/57	1	2	FACETS	0.844	0.731	0.966	0.844	0.731	0.966	CLONAL	1	TRUE	1	0.23	2		436	670	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995553	68995553	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771763123	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	154	532	1	ENST00000288368.4:c.1957G>A	p.Asp653Asn	p.D653N	ENST00000288368	NM_024870.2	653	Gat/Aat	18/40	0.126558599368198	3	FACETS	1	0.983	1	0.661	0.604	0.722	INDETERMINATE	1	TRUE	1	0.23	3		533	1129	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356425	66356425	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762220456	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	50	285	1	ENST00000273854.3:c.1072C>T	p.Pro358Ser	p.P358S	ENST00000273854	NM_004439.5	358	Ccc/Tcc	5/18	1	2	FACETS	0.747	0.633	0.872	0.747	0.633	0.872	SUBCLONAL	1	TRUE	1	0.23	2		286	582	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934560	9934560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	105	469	0	ENST00000330684.3:c.1595G>A	p.Gly532Glu	p.G532E	ENST00000330684	NM_001134407.1	532	gGa/gAa	7/13	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.23	2		469	912	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233099	69233099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1221150148	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	109	294	0	ENST00000462284.1:c.964C>T	p.Pro322Ser	p.P322S	ENST00000462284	NM_002392.5	322	Cca/Tca	11/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.23	2		294	691	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775521	39775521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	80	615	0	ENST00000288319.7:c.499G>A	p.Glu167Lys	p.E167K	ENST00000288319	NM_182918.3	167	Gaa/Aaa	4/10	1	2	FACETS	0.654	0.574	0.741	0.654	0.574	0.741	SUBCLONAL	1	TRUE	1	0.23	2		615	1063	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166271	118166271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	50	367	0	ENST00000369448.3:c.781G>A	p.Glu261Lys	p.E261K	ENST00000369448	NM_017709.3	261	Gaa/Aaa	2/2	1	2	FACETS	0.664	0.562	0.776	0.664	0.562	0.776	SUBCLONAL	1	TRUE	1	0.23	2		367	655	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864574	37864574	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	152	541	0	ENST00000269571.5:c.226G>A	p.Asp76Asn	p.D76N	ENST00000269571		76	Gat/Aat	3/27	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.23	2		541	972	SUCCESS
MET	4233	MSKCC	GRCh37	7	116381005	116381005	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763991073	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	127	599	1	ENST00000397752.3:c.1627G>A	p.Asp543Asn	p.D543N	ENST00000397752	NM_000245.2	543	Gac/Aac	5/21	0.126558599368198	3	FACETS	1	0.944	1	0.532	0.481	0.587	INDETERMINATE	1	TRUE	1	0.23	3		600	1157	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294150	1294150	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1279190294	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1319	88	802	0	ENST00000310581.5:c.851C>T	p.Ser284Phe	p.S284F	ENST00000310581	NM_198253.2	284	tCt/tTt	2/16	1	2	FACETS	0.544	0.48	0.613	0.544	0.48	0.613	SUBCLONAL	1	TRUE	1	0.23	2		802	1407	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244232	41244232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45599040	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	55	492	0	ENST00000357654.3:c.3316C>T	p.Pro1106Ser	p.P1106S	ENST00000357654	NM_007294.3	1106	Cct/Tct	10/23	1	2	FACETS	0.481	0.41	0.56	0.481	0.41	0.56	SUBCLONAL	1	TRUE	1	0.23	2		492	994	SUCCESS
BLM	641	MSKCC	GRCh37	15	91337531	91337531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	85	323	0	ENST00000355112.3:c.3154C>T	p.Pro1052Ser	p.P1052S	ENST00000355112	NM_000057.2	1052	Cct/Tct	16/22	1	2	FACETS	0.87	0.768	0.979	0.87	0.768	0.979	CLONAL	1	TRUE	1	0.23	2		323	850	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261923	16261923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	102	511	0	ENST00000375759.3:c.9188C>T	p.Pro3063Leu	p.P3063L	ENST00000375759	NM_015001.2	3063	cCa/cTa	11/15	1	2	FACETS	0.919	0.821	1	0.919	0.821	1	CLONAL	1	TRUE	1	0.23	2		511	965	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690358	117690358	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	102	526	0	ENST00000369458.3:c.771G>C	p.Lys257Asn	p.K257N	ENST00000369458	NM_024626.3	257	aaG/aaC	5/6	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.23	2		526	866	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980403	201980403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	86	756	0	ENST00000359651.3:c.139C>T	p.Pro47Ser	p.P47S	ENST00000359651		47	Ccc/Tcc	1/8	1	2	FACETS	0.608	0.536	0.686	0.608	0.536	0.686	SUBCLONAL	1	TRUE	1	0.23	2		756	1229	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983004	201983004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1201	85	754	0	ENST00000359651.3:c.853C>T	p.His285Tyr	p.H285Y	ENST00000359651		285	Cac/Tac	7/8	1	2	FACETS	0.575	0.506	0.649	0.575	0.506	0.649	SUBCLONAL	1	TRUE	1	0.23	2		754	1286	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615167	43615167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	92	811	1	ENST00000355710.3:c.2581G>A	p.Gly861Arg	p.G861R	ENST00000355710	NM_020975.4	861	Ggg/Agg	14/20	1	2	FACETS	0.61	0.54	0.686	0.61	0.54	0.686	SUBCLONAL	1	TRUE	1	0.23	2		812	1311	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114799863	114799863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	100	520	0	ENST00000543371.1:c.530C>T	p.Ser177Phe	p.S177F	ENST00000543371	NM_001198531.1	177	tCc/tTc	5/14	1	2	FACETS	0.857	0.764	0.956	0.857	0.764	0.956	CLONAL	1	TRUE	1	0.23	2		520	1015	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925577	114925577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	71	701	0	ENST00000543371.1:c.1655C>T	p.Pro552Leu	p.P552L	ENST00000543371	NM_001198531.1	552	cCc/cTc	14/14	1	2	FACETS	0.529	0.46	0.604	0.529	0.46	0.604	SUBCLONAL	1	TRUE	1	0.23	2		701	1168	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111886026	111886026	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	202	656	0	ENST00000341259.2:c.1648G>A	p.Ala550Thr	p.A550T	ENST00000341259	NM_005475.2	550	Gcc/Acc	8/8	1	2	FACETS	0.758	0.702	0.817	1	0.991	1	SUBCLONAL	2	TRUE	1	0.23	2		656	1158	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120858	115120858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	70	253	1	ENST00000257566.3:c.148G>A	p.Gly50Ser	p.G50S	ENST00000257566	NM_016569.3	50	Ggc/Agc	1/8	1	2	FACETS	0.78	0.684	0.884	1	0.976	1	SUBCLONAL	2	TRUE	1	0.23	2		254	390	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434172	121434172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	236	820	0	ENST00000257555.6:c.1063G>A	p.Gly355Ser	p.G355S	ENST00000257555		355	Ggc/Agc	5/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.23	2		820	1397	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571420	95571420	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	45	230	0	ENST00000393063.1:c.3257C>T	p.Pro1086Leu	p.P1086L	ENST00000393063	NM_030621.3	1086	cCt/cTt	21/28	1	2	FACETS	0.794	0.667	0.934	0.794	0.667	0.934	CLONAL	1	TRUE	1	0.23	2		230	493	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348166	348166	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1304	149	907	0	ENST00000262320.3:c.1340T>C	p.Phe447Ser	p.F447S	ENST00000262320	NM_003502.3	447	tTc/tCc	6/11	1	2	FACETS	0.892	0.812	0.976	0.892	0.812	0.976	CLONAL	1	TRUE	1	0.23	2		907	1453	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658524	3658524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	144	724	1	ENST00000294008.3:c.442C>T	p.Pro148Ser	p.P148S	ENST00000294008	NM_032444.2	148	Cca/Tca	2/15	1	2	FACETS	0.96	0.873	1	0.96	0.873	1	CLONAL	1	TRUE	1	0.23	2		725	1304	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78829263	78829263	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	56	483	0	ENST00000306801.3:c.1315-1G>A		p.X439_splice	ENST00000306801	NM_020761.2	439			1	2	FACETS	0.478	0.408	0.555	0.478	0.408	0.555	SUBCLONAL	1	TRUE	1	0.23	2		483	1019	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122778	7122778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	126	699	1	ENST00000302850.5:c.3376C>T	p.Pro1126Ser	p.P1126S	ENST00000302850	NM_000208.2	1126	Cct/Tct	19/22	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.23	2		700	974	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227879	36227879	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1206264437	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1269	166	796	0	ENST00000222270.7:c.7364C>T	p.Ser2455Phe	p.S2455F	ENST00000222270	NM_014727.1	2455	tCc/tTc	32/37	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.23	2		796	1435	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743894	41743894	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1258	164	859	1	ENST00000301178.4:c.829G>A	p.Asp277Asn	p.D277N	ENST00000301178	NM_021913.4	277	Gac/Aac	7/20	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.23	2		860	1422	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469032	25469032	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	73	672	0	ENST00000264709.3:c.1426A>G	p.Arg476Gly	p.R476G	ENST00000264709	NM_175629.2	476	Aga/Gga	11/23	1	2	FACETS	0.578	0.504	0.659	0.578	0.504	0.659	SUBCLONAL	1	TRUE	1	0.23	2		672	1098	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46588177	46588177	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1152	70	642	0	ENST00000263734.3:c.727A>C	p.Thr243Pro	p.T243P	ENST00000263734	NM_001430.4	243	Acc/Ccc	6/16	1	2	FACETS	0.498	0.432	0.57	0.498	0.432	0.57	SUBCLONAL	1	TRUE	1	0.23	2		642	1222	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251752	212251752	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	59	375	0	ENST00000342788.4:c.3307G>A	p.Asp1103Asn	p.D1103N	ENST00000342788	NM_005235.2	1103	Gat/Aat	27/28	1	2	FACETS	0.803	0.69	0.926	0.803	0.69	0.926	CLONAL	1	TRUE	1	0.23	2		375	639	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281601	142281601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1464478582	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	81	440	0	ENST00000350721.4:c.643C>T	p.Arg215Cys	p.R215C	ENST00000350721	NM_001184.3	215	Cgt/Tgt	4/47	0.126558599368198	3	FACETS	0.894	0.787	1	0.447	0.393	0.506	INDETERMINATE	1	TRUE	1	0.23	3		440	878	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998141	169998141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1428010723	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	141	484	0	ENST00000295797.4:c.832C>T	p.Arg278Cys	p.R278C	ENST00000295797	NM_002740.5	278	Cgt/Tgt	9/18	0.126558599368198	3	FACETS	1	0.973	1	0.591	0.537	0.648	INDETERMINATE	1	TRUE	1	0.23	3		484	1156	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146457	185146457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	70	392	0	ENST00000265026.3:c.88G>A	p.Glu30Lys	p.E30K	ENST00000265026	NM_004721.4	30	Gag/Aag	2/14	0.126558599368198	3	FACETS	0.911	0.793	1	0.456	0.396	0.519	INDETERMINATE	1	TRUE	1	0.23	3		392	745	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127432	55127432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	124	533	0	ENST00000257290.5:c.220G>A	p.Glu74Lys	p.E74K	ENST00000257290	NM_006206.4	74	Gaa/Aaa	3/23	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.23	2		533	1042	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133824	55133824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	115	400	0	ENST00000257290.5:c.1037G>A	p.Arg346Lys	p.R346K	ENST00000257290	NM_006206.4	346	aGg/aAg	7/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.23	2		400	756	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55962485	55962485	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368407075	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	76	437	0	ENST00000263923.4:c.2639G>A	p.Arg880Gln	p.R880Q	ENST00000263923	NM_002253.2	880	cGa/cAa	19/30	1	2	FACETS	0.873	0.765	0.99	0.873	0.765	0.99	CLONAL	1	TRUE	1	0.23	2		437	757	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513213	106513213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	64	311	0	ENST00000359195.3:c.2117C>T	p.Ser706Phe	p.S706F	ENST00000359195	NM_002649.2	706	tCc/tTc	4/11	0.126558599368198	3	FACETS	0.929	0.804	1	0.464	0.402	0.533	INDETERMINATE	1	TRUE	1	0.23	3		311	668	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371858	116371858	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	90	421	0	ENST00000397752.3:c.1337T>A	p.Ile446Asn	p.I446N	ENST00000397752	NM_000245.2	446	aTt/aAt	3/21	0.126558599368198	3	FACETS	1	0.935	1	0.54	0.478	0.606	INDETERMINATE	1	TRUE	1	0.23	3		421	808	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850236	128850236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	129	642	1	ENST00000249373.3:c.1499C>T	p.Thr500Ile	p.T500I	ENST00000249373	NM_005631.4	500	aCc/aTc	9/12	0.126558599368198	3	FACETS	1	0.94	1	0.526	0.476	0.58	INDETERMINATE	1	TRUE	1	0.23	3		643	1188	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277110	38277110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	160	569	0	ENST00000425967.3:c.1318C>T	p.His440Tyr	p.H440Y	ENST00000425967	NM_001174067.1	440	Cac/Tac	10/19	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.23	2		569	1072	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212813	27212813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	88	710	0	ENST00000380036.4:c.2795C>T	p.Thr932Ile	p.T932I	ENST00000380036	NM_000459.3	932	aCc/aTc	17/23	1	2	FACETS	0.613	0.541	0.69	0.613	0.541	0.69	SUBCLONAL	1	TRUE	1	0.23	2		710	1249	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606517	93606517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1229812218	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1250	141	894	0	ENST00000375746.1:c.337G>A	p.Val113Met	p.V113M	ENST00000375746	NM_001174167.1	113	Gtg/Atg	2/14	1	2	FACETS	0.881	0.8	0.967	0.881	0.8	0.967	CLONAL	1	TRUE	1	0.23	2		894	1391	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729927	41729931	+	missense_variant	Missense_Mutation	ONP	CTCTC	CTCTC	TTCTT	novel	NA	P-0053989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	109	677	0	ENST00000242208.4:c.598_602delinsAAGAA	p.Glu200_Arg201delinsLysLys	p.E200_R201delinsKK	ENST00000242208	NM_002192.2	200	GAGAGg/AAGAAg	3/3	1	2	FACETS	0.864	0.774	0.96	0.864	0.774	0.96	CLONAL	1	TRUE	1	0.23	2		677	1097	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115947	8115948	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0053990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	370	501	0	ENST00000346208.3:c.1294_1295dup	p.His434ThrfsTer42	p.H434Tfs*42	ENST00000346208		431	-/CC	6/6	1	2	FACETS	0.962	0.914	1	0.962	0.914	1	CLONAL	1	TRUE	1	0.700847466979222	2		501	1098	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512600	148512600	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	9	284	0	ENST00000320356.2:c.1544A>G	p.Lys515Arg	p.K515R	ENST00000320356	NM_004456.4	515	aAg/aGg	13/20	1	2	FACETS	0.065	0.042	0.094	0.065	0.042	0.094	SUBCLONAL	1	TRUE	1	0.655206020074411	2		284	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0053992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	498	678	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.826387282440054	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.826362226323871	2		678	594	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024758	31024758	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs754129466	NA	P-0053992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	126	811	0	ENST00000375687.4:c.4243C>T	p.Arg1415Ter	p.R1415*	ENST00000375687	NM_015338.5	1415	Cga/Tga	13/13	0.368922833520702	5	FACETS	0.813	0.736	0.894	0.271	0.245	0.298	INDETERMINATE	1	TRUE	2	0.826362226323871	5		811	840	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797235	32797235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768383489	NA	P-0053992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	245	1010	1	ENST00000374899.4:c.1874C>T	p.Pro625Leu	p.P625L	ENST00000374899	NM_018833.2	625	cCg/cTg	11/12	0.814637350237445	5	FACETS	1	0.971	1	0.214	0.2	0.229	CLONAL	1	TRUE	0	0.826362226323871	5		1011	1240	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129405	64129405	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	136	1124	0	ENST00000334205.4:c.837G>T	p.Lys279Asn	p.K279N	ENST00000334205	NM_003942.2	279	aaG/aaT	8/17	0.826387282440054	3	FACETS	0.521	0.474	0.572	0.261	0.237	0.286	SUBCLONAL	1	TRUE	1	0.826362226323871	3		1124	892	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845135	151845135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	170	669	0	ENST00000262189.6:c.13877G>A	p.Ser4626Asn	p.S4626N	ENST00000262189	NM_170606.2	4626	aGt/aAt	52/59	0.533481462184604	6	FACETS	1	0.989	1	0.494	0.455	0.534	CLONAL	1	TRUE	3	0.826362226323871	6		669	737	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0053993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	189	832	0	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	0.792449148195233	4	FACETS	0.904	0.872	0.932	0.904	0.872	0.932	CLONAL	4	TRUE	0	0.898106369700904	4		832	221	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371903	116371903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs544274181	NA	P-0053993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	70	496	0	ENST00000397752.3:c.1382G>A	p.Arg461His	p.R461H	ENST00000397752	NM_000245.2	461	cGc/cAc	3/21	0.898106369700904	3	FACETS	0.859	0.758	0.965	0.286	0.252	0.322	CLONAL	1	TRUE	0	0.898106369700904	3		496	263	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101560	27101560	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	112	948	1	ENST00000324856.7:c.4842G>T	p.Gln1614His	p.Q1614H	ENST00000324856	NM_006015.4	1614	caG/caT	18/20	0.532866392705972	4	FACETS	1	0.982	1	0.456	0.415	0.499	INDETERMINATE	1	TRUE	1	0.898106369700904	4		949	346	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741827	17741827	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	43	446	0	ENST00000250003.3:c.498C>A	p.Asp166Glu	p.D166E	ENST00000250003	NM_002478.4	166	gaC/gaA	1/3	0.546748311559959	6	FACETS	0.842	0.717	0.976	0.561	0.478	0.651	CLONAL	2	TRUE	3	0.898106369700904	6		446	159	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025895	48025895	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	196	411	0	ENST00000234420.5:c.773T>A	p.Ile258Asn	p.I258N	ENST00000234420	NM_000179.2	258	aTt/aAt	4/10	0.818267161668661	4	FACETS	0.911	0.865	0.957	0.684	0.648	0.718	CLONAL	3	TRUE	0	0.898106369700904	4		411	303	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025916	48025916	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs63749890	NA	P-0053993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	217	448	0	ENST00000234420.5:c.794T>G	p.Phe265Cys	p.F265C	ENST00000234420	NM_000179.2	265	tTt/tGt	4/10	0.818267161668661	4	FACETS	0.889	0.845	0.932	0.667	0.633	0.699	CLONAL	3	TRUE	0	0.898106369700904	4		448	344	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACA	novel	NA	P-0053993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	2756	851	0	ENST00000275493.2:c.2311_2313dup	p.Asn771dup	p.N771dup	ENST00000275493	NM_005228.3	771	gac/gACAac	20/28	0.898106369700904	29	FACETS	1	0.99	1			1	CLONAL	22	TRUE	NA	0.898106369700904	29		851	3656	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0053994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	114	469	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.835	0.756	0.918	0.835	0.756	0.918	CLONAL	1	TRUE	1	0.554703960643492	2		470	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0053994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	327	754	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.554703960643492	1	FACETS	0.976	0.926	1	0.976	0.926	1	CLONAL	1	TRUE	0	0.554703960643492	1		754	873	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913283	NA	P-0053994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	121	352	0	ENST00000263967.3:c.3129G>T	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atT	21/21	0.180496596152446	3	FACETS	1	0.985	1	0.709	0.646	0.774	INDETERMINATE	1	TRUE	1	0.554703960643492	3		352	393	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916957	178916957	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200018596	NA	P-0053994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	83	239	0	ENST00000263967.3:c.344G>T	p.Arg115Leu	p.R115L	ENST00000263967	NM_006218.2	115	cGa/cTa	2/21	0.180496596152446	3	FACETS	1	0.976	1	0.688	0.614	0.764	INDETERMINATE	1	TRUE	1	0.554703960643492	3		239	278	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049703	16049703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	29	371	0	ENST00000268712.3:c.1069G>A	p.Glu357Lys	p.E357K	ENST00000268712	NM_006311.3	357	Gaa/Aaa	10/46	0.554703960643492	1	FACETS	0.212	0.17	0.26	0.212	0.17	0.26	SUBCLONAL	1	TRUE	0	0.554703960643492	1		371	356	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0053995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	72	329	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.200348736010131	4	FACETS	1	0.969	1	0.681	0.597	0.77	CLONAL	1	TRUE	2	0.33125912726587	4		329	425	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0053995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	81	805	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.891	0.786	1	0.891	0.786	1	CLONAL	1	TRUE	1	0.33125912726587	2		805	549	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0053995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	149	419	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.33125912726587	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.33125912726587	2		419	429	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254644	16254644	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	151	398	0	ENST00000375759.3:c.1909C>T	p.Arg637Ter	p.R637*	ENST00000375759	NM_015001.2	637	Cga/Tga	11/15	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.33125912726587	2		398	782	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891277	101891277	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	140	718	0	ENST00000374994.4:c.238C>T	p.Arg80Ter	p.R80*	ENST00000374994	NM_004612.2	80	Cga/Tga	2/9	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.33125912726587	2		718	757	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495220	212495220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	64	595	0	ENST00000342788.4:c.2046G>T	p.Lys682Asn	p.K682N	ENST00000342788	NM_005235.2	682	aaG/aaT	17/28	1	2	FACETS	0.647	0.56	0.741	0.647	0.56	0.741	SUBCLONAL	1	TRUE	1	0.33125912726587	2		595	597	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202926	27202926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772637203	NA	P-0053995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	118	649	1	ENST00000380036.4:c.2018G>A	p.Arg673His	p.R673H	ENST00000380036	NM_000459.3	673	cGt/cAt	13/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.33125912726587	2		650	641	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981797	201981798	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	534	1522	1	ENST00000359651.3:c.509dup	p.Asp171GlyfsTer25	p.D171Gfs*25	ENST00000359651		170	ctg/cTtg	4/8	0.33125912726587	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.33125912726587	2		1523	1367	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244217	46244217	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	215	583	1	ENST00000334344.6:c.2311C>T	p.Gln771Ter	p.Q771*	ENST00000334344	NM_152641.2	771	Cag/Tag	15/21	0.33125912726587	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.33125912726587	2		584	627	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233460	69233460	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	220	621	0	ENST00000462284.1:c.1325A>G	p.Glu442Gly	p.E442G	ENST00000462284	NM_002392.5	442	gAa/gGa	11/11	0.33125912726587	2	FACETS	0.996	0.931	1	0.996	0.931	1	CLONAL	2	TRUE	0	0.33125912726587	2		621	667	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872999	136872999	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	152	706	0	ENST00000241393.3:c.499C>A	p.Leu167Met	p.L167M	ENST00000241393	NM_003467.2	167	Ctg/Atg	2/2	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.33125912726587	2		706	793	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904977	101904977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223833	NA	P-0053995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	89	486	0	ENST00000374994.4:c.965G>A	p.Gly322Asp	p.G322D	ENST00000374994	NM_004612.2	322	gGt/gAt	5/9	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.33125912726587	2		486	492	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	414	258	0				ENST00000310581	NM_198253.2	-/1132			0.684090086221173	7	FACETS	1	0.99	1	0.458	0.436	0.482	CLONAL	2	TRUE	2	0.684090086221173	7		258	1431	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	1382	798	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.684090086221173	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	4	TRUE	0	0.684090086221173	4		798	1696	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	618	903	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.684090086221173	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.684090086221173	2		903	892	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812197	43812197	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	255	704	0	ENST00000372470.3:c.1062C>G	p.Phe354Leu	p.F354L	ENST00000372470	NM_005373.2	354	ttC/ttG	7/12	0.684090086221173	4	FACETS	0.994	0.929	1			1	CLONAL	1	TRUE	NA	0.684090086221173	4		704	1263	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	615	1032	5	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	0.483851635366176	5	FACETS	1	0.991	1	0.726	0.698	0.754	CLONAL	2	TRUE	2	0.684090086221173	5		1037	1673	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240171	41240171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1291996842	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	82	155	1	ENST00000379561.5:c.179C>T	p.Ser60Leu	p.S60L	ENST00000379561	NM_002015.3	60	tCg/tTg	1/3	0.684090086221173	6	FACETS	1	0.972	1	0.333	0.295	0.374	CLONAL	1	TRUE	2	0.684090086221173	6		156	426	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923060	44923060	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	404	356	0	ENST00000377967.4:c.1921C>T	p.Gln641Ter	p.Q641*	ENST00000377967	NM_021140.2	641	Cag/Tag	16/29	0.628820047473748	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.684090086221173	2		356	492	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789627	3789627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201186078	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	175	634	0	ENST00000262367.5:c.4232G>A	p.Gly1411Glu	p.G1411E	ENST00000262367	NM_004380.2	1411	gGa/gAa	25/31	1	2	FACETS	0.87	0.806	0.936	0.87	0.806	0.936	CLONAL	1	TRUE	1	0.684090086221173	2		634	588	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966955	25966955	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs773343381	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	309	912	0	ENST00000435504.4:c.2251C>G	p.Gln751Glu	p.Q751E	ENST00000435504		751	Cag/Gag	13/13	0.683270554717092	3	FACETS	1	0.959	1	0.511	0.481	0.541	CLONAL	1	TRUE	1	0.684090086221173	3		912	1187	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413042	63413042	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	613	511	0	ENST00000330258.3:c.125C>G	p.Ser42Ter	p.S42*	ENST00000330258	NM_152424.3	42	tCa/tGa	2/2	0.628820047473748	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.684090086221173	2		511	748	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658353	18658353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868506094	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	292	423	0	ENST00000266497.5:c.3158G>A	p.Gly1053Glu	p.G1053E	ENST00000266497		1053	gGa/gAa	22/31	0.649761766411408	4	FACETS	0.989	0.936	1	0.989	0.936	1	CLONAL	2	TRUE	2	0.684090086221173	4		423	727	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830976	72830976	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	212	611	1	ENST00000268489.5:c.5605C>T	p.Gln1869Ter	p.Q1869*	ENST00000268489	NM_006885.3	1869	Cag/Tag	9/10	0.684090086221173	3	FACETS	0.988	0.919	1	0.494	0.459	0.53	CLONAL	1	TRUE	1	0.684090086221173	3		612	842	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035307	42035307	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	219	530	0	ENST00000219905.7:c.5149C>G	p.Leu1717Val	p.L1717V	ENST00000219905	NM_001164273.1	1717	Ctg/Gtg	15/24	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.684090086221173	2		530	628	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772605	135772605	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	809	574	0	ENST00000298552.3:c.2941G>C	p.Glu981Gln	p.E981Q	ENST00000298552	NM_001162426.1	981	Gaa/Caa	22/23	0.684090086221173	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	4	TRUE	0	0.684090086221173	4		574	995	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056240	26056240	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs547786942	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	234	716	0	ENST00000343677.2:c.417G>C	p.Lys139Asn	p.K139N	ENST00000343677	NM_005319.3	139	aaG/aaC	1/1	0.684090086221173	3	FACETS	0.994	0.928	1	0.497	0.464	0.531	CLONAL	1	TRUE	1	0.684090086221173	3		716	924	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144732	119144732	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	116	385	0	ENST00000264033.4:c.745C>G	p.Gln249Glu	p.Q249E	ENST00000264033	NM_005188.3	249	Cag/Gag	4/16	0.683270554717092	3	FACETS	0.925	0.838	1	0.463	0.419	0.508	CLONAL	1	TRUE	1	0.684090086221173	3		385	492	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639697	47639697	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	127	403	0	ENST00000233146.2:c.790C>G	p.Gln264Glu	p.Q264E	ENST00000233146	NM_000251.2	264	Cag/Gag	4/16	0.683270554717092	3	FACETS	1	0.958	1	0.542	0.494	0.591	CLONAL	1	TRUE	1	0.684090086221173	3		403	460	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190754	11190754	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	724	958	0	ENST00000361445.4:c.5445G>C	p.Lys1815Asn	p.K1815N	ENST00000361445	NM_004958.3	1815	aaG/aaC	39/58	0.684090086221173	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	1	0.684090086221173	3		958	1264	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22413001	22413001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	58	178	0	ENST00000344548.3:c.248C>T	p.Ser83Leu	p.S83L	ENST00000344548	NM_001039802.1	83	tCa/tTa	5/7	0.684090086221173	3	FACETS	0.921	0.8	1	0.461	0.4	0.525	CLONAL	1	TRUE	1	0.684090086221173	3		178	247	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258033	123258034	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	158	588	0	ENST00000358487.5:c.1647_1648delinsAT	p.Asn549_Leu550delinsLysPhe	p.N549_L550delinsKF	ENST00000358487	NM_000141.4	549	aaTCtt/aaATtt	12/18	0.684090086221173	2	FACETS	0.792	0.73	0.857	0.396	0.365	0.429	SUBCLONAL	1	TRUE	0	0.684090086221173	2		588	583	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857871	57857871	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	520	755	0	ENST00000228682.2:c.190G>T	p.Glu64Ter	p.E64*	ENST00000228682	NM_005269.2	64	Gag/Tag	3/12	0.483851635366176	5	FACETS	1	0.992	1	0.749	0.718	0.78	CLONAL	2	TRUE	2	0.684090086221173	5		755	1371	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914890	32914890	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	310	422	0	ENST00000380152.3:c.6398C>G	p.Ser2133Ter	p.S2133*	ENST00000380152		2133	tCa/tGa	11/27	0.684090086221173	6	FACETS	0.953	0.91	0.996	0.953	0.91	0.996	CLONAL	4	TRUE	2	0.684090086221173	6		422	563	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40682124	40682124	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	206	594	0	ENST00000249776.8:c.679G>C	p.Asp227His	p.D227H	ENST00000249776	NM_033286.3	227	Gat/Cat	6/9	1	2	FACETS	0.917	0.855	0.98	0.917	0.855	0.98	CLONAL	1	TRUE	1	0.684090086221173	2		594	657	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41001231	41001231	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	137	500	0	ENST00000267868.3:c.352G>T	p.Glu118Ter	p.E118*	ENST00000267868	NM_002875.4	118	Gag/Tag	5/10	1	2	FACETS	0.912	0.837	0.99	0.912	0.837	0.99	CLONAL	1	TRUE	1	0.684090086221173	2		500	439	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021457	42021457	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1332012274	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	194	571	0	ENST00000219905.7:c.3753G>C	p.Gln1251His	p.Q1251H	ENST00000219905	NM_001164273.1	1251	caG/caC	11/24	1	2	FACETS	0.952	0.886	1	0.952	0.886	1	CLONAL	1	TRUE	1	0.684090086221173	2		571	596	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641786	23641786	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	95	262	0	ENST00000261584.4:c.1689G>C	p.Lys563Asn	p.K563N	ENST00000261584	NM_024675.3	563	aaG/aaC	5/13	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.684090086221173	2		262	232	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993096	72993096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	625	900	0	ENST00000268489.5:c.949C>G	p.Leu317Val	p.L317V	ENST00000268489	NM_006885.3	317	Ctt/Gtt	2/10	0.684090086221173	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.684090086221173	3		900	1188	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422944	45422944	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	116	482	0	ENST00000262160.6:c.184G>C	p.Glu62Gln	p.E62Q	ENST00000262160	NM_005901.5	62	Gag/Cag	2/11	0.684090086221173	2	FACETS	0.821	0.746	0.899	0.411	0.373	0.45	CLONAL	1	TRUE	0	0.684090086221173	2		482	413	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229017	36229017	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1567	317	971	0	ENST00000222270.7:c.7797G>C	p.Glu2599Asp	p.E2599D	ENST00000222270	NM_014727.1	2599	gaG/gaC	36/37	0.684090086221173	5	FACETS	0.997	0.937	1	0.332	0.312	0.353	CLONAL	1	TRUE	2	0.684090086221173	5		971	1884	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719457	190719457	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	223	289	0	ENST00000441310.2:c.1459C>G	p.Leu487Val	p.L487V	ENST00000441310	NM_000534.4	487	Ctt/Gtt	9/13	0.684090086221173	4	FACETS	1	0.981	1	0.732	0.689	0.776	CLONAL	2	TRUE	1	0.684090086221173	4		289	500	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421325	12421325	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	524	790	0	ENST00000287820.6:c.205G>C	p.Asp69His	p.D69H	ENST00000287820	NM_015869.4	69	Gac/Cac	2/7	0.684090086221173	3	FACETS	0.942	0.907	0.978	0.628	0.604	0.652	CLONAL	2	TRUE	0	0.684090086221173	3		790	1091	SUCCESS
APC	324	MSKCC	GRCh37	5	112179309	112179309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	147	386	0	ENST00000257430.4:c.8018G>A	p.Arg2673Lys	p.R2673K	ENST00000257430	NM_000038.5	2673	aGa/aAa	16/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.684090086221173	2		386	385	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509480	106509480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	224	709	0	ENST00000359195.3:c.1474G>A	p.Glu492Lys	p.E492K	ENST00000359195	NM_002649.2	492	Gaa/Aaa	2/11	0.684090086221173	3	FACETS	0.967	0.901	1	0.322	0.3	0.345	CLONAL	1	TRUE	0	0.684090086221173	3		709	909	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56910947	56910947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	441	675	0	ENST00000519728.1:c.1093C>T	p.His365Tyr	p.H365Y	ENST00000519728	NM_002350.3	365	Cac/Tac	11/13	0.684090086221173	6	FACETS	0.968	0.922	1	0.484	0.461	0.508	CLONAL	2	TRUE	2	0.684090086221173	6		675	1577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0053997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	340	693	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.403319955561936	1	FACETS	0.991	0.937	1	0.991	0.937	1	CLONAL	1	TRUE	0	0.409077380227713	1		693	1334	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0053997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	124	623	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.703	0.636	0.774	0.703	0.636	0.774	SUBCLONAL	1	TRUE	1	0.409077380227713	2		623	862	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266831	18266831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1011337615	NA	P-0053997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	282	864	0	ENST00000222254.8:c.142G>A	p.Glu48Lys	p.E48K	ENST00000222254	NM_005027.3	48	Gag/Aag	2/16	1	2	FACETS	0.923	0.866	0.983	0.923	0.866	0.983	CLONAL	1	TRUE	1	0.409077380227713	2		864	1493	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778863	9778863	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1453300166	NA	P-0053997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1477	141	926	2	ENST00000377346.4:c.1132G>A	p.Asp378Asn	p.D378N	ENST00000377346	NM_005026.3	378	Gac/Aac	9/24	1	2	FACETS	0.426	0.386	0.468	0.426	0.386	0.468	SUBCLONAL	1	TRUE	1	0.409077380227713	2		928	1618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576870	7576870	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs876659384	NA	P-0053998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	201	987	0	ENST00000269305.4:c.976G>T	p.Glu326Ter	p.E326*	ENST00000269305	NM_001126112.2	326	Gaa/Taa	9/11	0.388403649414357	1	FACETS	0.975	0.905	1	0.975	0.905	1	CLONAL	1	TRUE	0	0.388403649414357	1		987	855	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249022	55249022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567477136	NA	P-0053998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	195	1059	0	ENST00000275493.2:c.2320G>A	p.Val774Met	p.V774M	ENST00000275493	NM_005228.3	774	Gtg/Atg	20/28	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.388403649414357	2		1059	935	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0053998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	182	972	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.388403649414357	2		972	858	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47108598	47108598	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	108	436	2	ENST00000409792.3:c.6071G>A	p.Arg2024Gln	p.R2024Q	ENST00000409792	NM_014159.6	2024	cGa/cAa	13/21	0.388403649414357	1	FACETS	0.887	0.8	0.979	0.887	0.8	0.979	CLONAL	1	TRUE	0	0.388403649414357	1		438	505	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059476	42059476	+	stop_lost	Nonstop_Mutation	SNP	T	T	C	novel	NA	P-0053998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	97	521	0	ENST00000219905.7:c.9196T>C	p.Ter3066ArgextTer51	p.*3066Rext*51	ENST00000219905	NM_001164273.1	3066	Tga/Cga	24/24	0.388403649414357	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.388403649414357	1		521	390	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490546	20490546	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	139	773	0	ENST00000346618.3:c.1283C>T	p.Pro428Leu	p.P428L	ENST00000346618	NM_001949.4	428	cCc/cTc	7/7	1	2	FACETS	0.89	0.811	0.974	0.89	0.811	0.974	CLONAL	1	TRUE	1	0.388403649414357	2		773	804	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263760	16263760	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	153	993	1	ENST00000375759.3:c.10129C>A	p.Pro3377Thr	p.P3377T	ENST00000375759	NM_015001.2	3377	Ccc/Acc	12/15	1	2	FACETS	0.956	0.875	1	0.956	0.875	1	CLONAL	1	TRUE	1	0.388403649414357	2		994	824	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440372	52440372	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	182	578	0	ENST00000460680.1:c.680G>C	p.Arg227Pro	p.R227P	ENST00000460680	NM_004656.3	227	cGc/cCc	9/17	0.485830064397594	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	0	0.485830064397594	1		578	482	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355282	15355282	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572537806	NA	P-0053999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	14	502	0	ENST00000263377.2:c.2341C>T	p.Pro781Ser	p.P781S	ENST00000263377	NM_058243.2	781	Ccc/Tcc	13/20	1	2	FACETS	0.237	0.171	0.317	0.237	0.171	0.317	SUBCLONAL	1	FALSE	1	0.485830064397594	2		502	243	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188264	10188265	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	112	802	0	ENST00000256474.2:c.407_408insA	p.Phe136LeufsTer8	p.F136Lfs*8	ENST00000256474	NM_000551.3	136	ttt/ttAt	2/3	0.485830064397594	1	FACETS	0.986	0.896	1	0.986	0.896	1	CLONAL	1	FALSE	0	0.485830064397594	1		802	354	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	35	276	0				ENST00000310581	NM_198253.2	-/1132			0.320273003759525	1	FACETS	0.675	0.556	0.807	0.675	0.556	0.807	SUBCLONAL	1	TRUE	0	0.320273003759525	1		276	272	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222733	5222733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202163446	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	144	1515	1	ENST00000357368.4:c.3070C>T	p.Pro1024Ser	p.P1024S	ENST00000357368	NM_002850.3	1024	Ccc/Tcc	18/38	0.320273003759525	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.320273003759525	1		1516	571	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546761	9546761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768724288	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	50	740	1	ENST00000353224.5:c.1261G>A	p.Asp421Asn	p.D421N	ENST00000353224	NM_177990.2	421	Gac/Aac	5/10	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.320273003759525	2		741	306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577544	7577544	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587780074	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	131	871	0	ENST00000269305.4:c.737T>C	p.Met246Thr	p.M246T	ENST00000269305	NM_001126112.2	246	aTg/aCg	7/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.320273003759525	2		871	549	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509639	29509639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	61	301	0	ENST00000356175.3:c.844C>T	p.Gln282Ter	p.Q282*	ENST00000356175	NM_000267.3	282	Cag/Tag	8/57	1	2	FACETS	0.95	0.823	1	0.95	0.823	1	CLONAL	1	TRUE	1	0.320273003759525	2		301	401	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40376853	40376853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1177773526	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	71	789	1	ENST00000293328.3:c.319C>T	p.Arg107Cys	p.R107C	ENST00000293328	NM_012448.3	107	Cgc/Tgc	4/19	1	2	FACETS	0.771	0.674	0.876	0.771	0.674	0.876	SUBCLONAL	1	TRUE	1	0.320273003759525	2		790	575	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134123	41134123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751383976	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	56	659	0	ENST00000379561.5:c.1505C>T	p.Ser502Leu	p.S502L	ENST00000379561	NM_002015.3	502	tCg/tTg	2/3	1	2	FACETS	0.996	0.858	1	0.996	0.858	1	CLONAL	1	TRUE	1	0.320273003759525	2		659	351	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341914	8341914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	98	227	0	ENST00000356435.5:c.4726G>A	p.Glu1576Lys	p.E1576K	ENST00000356435		1576	Gaa/Aaa	29/35	0.320273003759525	5	FACETS	1	0.936	1			1	CLONAL	2	TRUE	NA	0.320273003759525	5		227	428	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412109	63412109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157288902	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	87	468	0	ENST00000330258.3:c.1058G>A	p.Arg353Gln	p.R353Q	ENST00000330258	NM_152424.3	353	cGa/cAa	2/2	0.272586037662752	2	FACETS	0.852	0.762	0.946			1	CLONAL	2	TRUE	NA	0.320273003759525	2		468	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578196	7578196	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555525743	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	94	905	0	ENST00000269305.4:c.653T>G	p.Val218Gly	p.V218G	ENST00000269305	NM_001126112.2	218	gTg/gGg	6/11	1	2	FACETS	0.806	0.717	0.901	0.806	0.717	0.901	CLONAL	1	TRUE	1	0.320273003759525	2		905	728	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653001	29653001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs865781825	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	97	270	0	ENST00000356175.3:c.4936C>T	p.Pro1646Ser	p.P1646S	ENST00000356175	NM_000267.3	1646	Cct/Tct	36/57	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.320273003759525	2		270	484	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955046	93955046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141581954	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	38	99	0	ENST00000369303.4:c.2852C>T	p.Ser951Phe	p.S951F	ENST00000369303	NM_004440.3	951	tCc/tTc	16/17	0.267459269890995	4	FACETS	1	0.952	1	0.725	0.605	0.857	CLONAL	1	TRUE	2	0.320273003759525	4		99	216	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350062	81350062	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs759145490	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	53	117	0	ENST00000222390.5:c.1270C>T	p.Arg424Cys	p.R424C	ENST00000222390	NM_000601.4	424	Cgt/Tgt	10/18	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.320273003759525	2		117	278	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150039	202150039	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1368296717	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	69	499	0	ENST00000358485.4:c.1480C>T	p.Arg494Ter	p.R494*	ENST00000358485	NM_001080125.1	494	Cga/Tga	8/9	1	2	FACETS	0.807	0.704	0.918	0.807	0.704	0.918	CLONAL	1	TRUE	1	0.320273003759525	2		499	534	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963988	2963988	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755527825	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	69	971	0	ENST00000396946.4:c.1819G>A	p.Glu607Lys	p.E607K	ENST00000396946	NM_032415.4	607	Gaa/Aaa	15/25	0.235491806437053	1	FACETS	0.733	0.639	0.833	0.733	0.639	0.833	SUBCLONAL	1	TRUE	0	0.320273003759525	1		971	494	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389318	8389318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	306	261	0	ENST00000356435.5:c.4300G>A	p.Glu1434Lys	p.E1434K	ENST00000356435		1434	Gaa/Aaa	26/35	0.320273003759525	5	FACETS	0.907	0.863	0.951			1	CLONAL	5	TRUE	NA	0.320273003759525	5		261	624	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416152	29416152	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376702277	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	52	724	0	ENST00000389048.3:c.4801G>A	p.Ala1601Thr	p.A1601T	ENST00000389048	NM_004304.4	1601	Gct/Act	29/29	0.135274286442777	0	FACETS	0.46	0.392	0.534			1	INDETERMINATE	1	TRUE	0	0.320273003759525	0		724	480	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954199	48954199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	28	95	0	ENST00000267163.4:c.1400G>A	p.Arg467Gln	p.R467Q	ENST00000267163	NM_000321.2	467	cGa/cAa	15/27	1	2	FACETS	0.64	0.513	0.784	0.64	0.513	0.784	SUBCLONAL	1	TRUE	1	0.320273003759525	2		95	273	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845361	42845361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	105	1436	0	ENST00000398585.3:c.901C>T	p.Pro301Ser	p.P301S	ENST00000398585	NM_001135099.1	301	Ccg/Tcg	9/14	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.320273003759525	2		1436	644	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351694	89351694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373149812	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	90	965	1	ENST00000301030.4:c.1256C>T	p.Thr419Ile	p.T419I	ENST00000301030	NM_001256183.1	419	aCc/aTc	9/13	0.320273003759525	1	FACETS	0.634	0.562	0.71	0.634	0.562	0.71	SUBCLONAL	1	TRUE	0	0.320273003759525	1		966	745	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069435	30069435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs992662337	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	31	1061	1	ENST00000338641.4:c.1300G>A	p.Glu434Lys	p.E434K	ENST00000338641	NM_000268.3	434	Gag/Aag	12/16	1	2	FACETS	0.364	0.293	0.444	0.364	0.293	0.444	SUBCLONAL	1	TRUE	1	0.320273003759525	2		1062	532	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793166	42793166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778778296	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	55	1466	2	ENST00000575354.2:c.1058G>A	p.Arg353Gln	p.R353Q	ENST00000575354	NM_015125.3	353	cGa/cAa	7/20	0.320273003759525	1	FACETS	0.402	0.343	0.466	0.402	0.343	0.466	SUBCLONAL	1	TRUE	0	0.320273003759525	1		1468	718	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50788288	50788288	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	57	238	0	ENST00000398568.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000398568	NM_001042412.1	289	gCg/gTg	5/18	0.320273003759525	1	FACETS	0.56	0.48	0.646	0.56	0.48	0.646	SUBCLONAL	1	TRUE	0	0.320273003759525	1		238	534	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960002	134960002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	72	602	1	ENST00000398015.3:c.2359C>T	p.Pro787Ser	p.P787S	ENST00000398015	NM_004441.4	787	Cct/Tct	13/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.320273003759525	2		603	379	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961373	15961373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	56	365	0	ENST00000268712.3:c.6016C>T	p.Pro2006Ser	p.P2006S	ENST00000268712	NM_006311.3	2006	Cct/Tct	39/46	1	2	FACETS	0.868	0.746	1	0.868	0.746	1	CLONAL	1	TRUE	1	0.320273003759525	2		365	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579875	7579875	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854070	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	146	1057	0	ENST00000269305.4:c.38C>T	p.Pro13Leu	p.P13L	ENST00000269305	NM_001126112.2	13	cCt/cTt	2/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.320273003759525	2		1057	623	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713697	52713697	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	67	420	0	ENST00000394830.3:c.31C>T	p.Pro11Ser	p.P11S	ENST00000394830	NM_018313.4	11	Cct/Tct	2/30	1	2	FACETS	0.825	0.718	0.94	0.825	0.718	0.94	CLONAL	1	TRUE	1	0.320273003759525	2		420	507	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459318	120459318	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	31	346	0	ENST00000256646.2:c.6028-1G>A		p.X2010_splice	ENST00000256646	NM_024408.3	2010			1	2	FACETS	0.694	0.563	0.841	0.694	0.563	0.841	SUBCLONAL	1	TRUE	1	0.320273003759525	2		346	279	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992790	72992790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	71	1032	1	ENST00000268489.5:c.1255C>T	p.Pro419Ser	p.P419S	ENST00000268489	NM_006885.3	419	Ccc/Tcc	2/10	0.320273003759525	1	FACETS	0.727	0.636	0.825	0.727	0.636	0.825	SUBCLONAL	1	TRUE	0	0.320273003759525	1		1033	512	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177624	56177624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	55	402	0	ENST00000399503.3:c.2597C>T	p.Ala866Val	p.A866V	ENST00000399503	NM_005921.1	866	gCc/gTc	14/20	0.134462044338668	4	FACETS	1	0.958	1	0.661	0.568	0.761	INDETERMINATE	1	TRUE	2	0.320273003759525	4		402	343	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031889	26031889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	95	546	0	ENST00000244661.2:c.400G>A	p.Glu134Lys	p.E134K	ENST00000244661	NM_003537.3	134	Gaa/Aaa	1/1	1	2	FACETS	0.774	0.695	0.858	1	0.983	1	SUBCLONAL	2	TRUE	1	0.320273003759525	2		546	383	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974676	21974677	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	48	959	0	ENST00000304494.5:c.150_150+1delinsAA		p.X50_splice	ENST00000304494	NM_000077.4	50		1/3	0.320273003759525	1	FACETS	0.721	0.612	0.841	0.721	0.612	0.841	SUBCLONAL	1	TRUE	0	0.320273003759525	1		959	349	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272443	11272443	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	81	638	0	ENST00000361445.4:c.3487C>G	p.Leu1163Val	p.L1163V	ENST00000361445	NM_004958.3	1163	Ctg/Gtg	23/58	1	2	FACETS	0.923	0.815	1	0.923	0.815	1	CLONAL	1	TRUE	1	0.320273003759525	2		638	548	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461492	138461492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758175087	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	69	208	0	ENST00000289153.2:c.529C>T	p.Pro177Ser	p.P177S	ENST00000289153	NM_006219.2	177	Cca/Tca	3/22	1	2	FACETS	0.801	0.698	0.911	0.801	0.698	0.911	CLONAL	1	TRUE	1	0.320273003759525	2		208	538	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502614	149502614	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	32	724	0	ENST00000261799.4:c.2174C>T	p.Pro725Leu	p.P725L	ENST00000261799	NM_002609.3	725	cCc/cTc	15/23	0.320273003759525	0	FACETS	0.373	0.303	0.452			1	SUBCLONAL	1	TRUE	0	0.320273003759525	0		724	364	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16174568	16174569	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	39	635	2	ENST00000375759.3:c.6_7delinsTT	p.Arg3Trp	p.R3W	ENST00000375759	NM_015001.2	2	gtCCgg/gtTTgg	1/15	1	2	FACETS	0.57	0.473	0.679	0.57	0.473	0.679	SUBCLONAL	1	TRUE	1	0.320273003759525	2		637	427	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733411	85733411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	67	326	0	ENST00000370580.1:c.601C>T	p.Pro201Ser	p.P201S	ENST00000370580	NM_003921.4	201	Cct/Tct	3/3	1	2	FACETS	0.98	0.855	1	0.98	0.855	1	CLONAL	1	TRUE	1	0.320273003759525	2		326	427	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459007	120459008	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	77	748	1	ENST00000256646.2:c.6337_6338delinsTT	p.Pro2113Phe	p.P2113F	ENST00000256646	NM_024408.3	2113	CCt/TTt	34/34	1	2	FACETS	0.839	0.738	0.948	0.839	0.738	0.948	CLONAL	1	TRUE	1	0.320273003759525	2		749	573	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462102	120462103	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	100	1120	1	ENST00000256646.2:c.5613_5614delinsTT	p.Gln1872Ter	p.Q1872*	ENST00000256646	NM_024408.3	1871	gcCCag/gcTTag	31/34	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.320273003759525	2		1121	578	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943776	71943776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	81	1087	0	ENST00000298229.2:c.1819G>A	p.Asp607Asn	p.D607N	ENST00000298229	NM_001567.3	607	Gac/Aac	15/28	0.235491806437053	1	FACETS	0.696	0.614	0.785	0.696	0.614	0.785	SUBCLONAL	1	TRUE	0	0.320273003759525	1		1087	610	SUCCESS
ATM	472	MSKCC	GRCh37	11	108127035	108127035	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786201866	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	67	229	0	ENST00000278616.4:c.2218G>A	p.Ala740Thr	p.A740T	ENST00000278616	NM_000051.3	740	Gca/Aca	14/63	1	2	FACETS	0.953	0.831	1	0.953	0.831	1	CLONAL	1	TRUE	1	0.320273003759525	2		229	439	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620044	21620044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	89	774	0	ENST00000382592.4:c.122C>T	p.Pro41Leu	p.P41L	ENST00000382592	NM_014572.2	41	cCa/cTa	2/8	1	2	FACETS	0.898	0.797	1	0.898	0.797	1	CLONAL	1	TRUE	1	0.320273003759525	2		774	619	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066828	30066828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	85	438	0	ENST00000331968.5:c.2303C>T	p.Ser768Phe	p.S768F	ENST00000331968	NM_002742.2	768	tCt/tTt	16/18	0.134462044338668	4	FACETS	0.765	0.679	0.856	0.765	0.679	0.856	INDETERMINATE	2	TRUE	2	0.320273003759525	4		438	458	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828048	3828048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776122323	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	67	772	0	ENST00000262367.5:c.2077C>T	p.Pro693Ser	p.P693S	ENST00000262367	NM_004380.2	693	Cct/Tct	10/31	0.320273003759525	1	FACETS	0.546	0.475	0.624	0.546	0.475	0.624	SUBCLONAL	1	TRUE	0	0.320273003759525	1		772	643	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510627	38510628	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	137	1226	3	ENST00000254066.5:c.881_882delinsAA	p.Arg294Gln	p.R294Q	ENST00000254066	NM_000964.3	294	cGG/cAA	7/9	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.320273003759525	2		1229	708	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59820399	59820400	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	51	181	0	ENST00000259008.2:c.2353_2354delinsTT	p.Pro785Phe	p.P785F	ENST00000259008	NM_032043.2	785	CCt/TTt	16/20	0.235491806437053	1	FACETS	0.729	0.622	0.846	0.729	0.622	0.846	SUBCLONAL	1	TRUE	0	0.320273003759525	1		181	367	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11018787	11018788	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	46	1317	3	ENST00000327064.4:c.419_420delinsAA	p.Arg140Gln	p.R140Q	ENST00000327064	NM_199141.1	140	cGG/cAA	3/16	0.320273003759525	1	FACETS	0.322	0.27	0.38	0.322	0.27	0.38	SUBCLONAL	1	TRUE	0	0.320273003759525	1		1320	749	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798209	42798209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	92	1345	1	ENST00000575354.2:c.4163G>A	p.Gly1388Asp	p.G1388D	ENST00000575354	NM_015125.3	1388	gGc/gAc	17/20	0.320273003759525	1	FACETS	0.9	0.802	1	0.9	0.802	1	CLONAL	1	TRUE	0	0.320273003759525	1		1346	536	SUCCESS
ALK	238	MSKCC	GRCh37	2	29450503	29450503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	85	757	0	ENST00000389048.3:c.2851G>A	p.Asp951Asn	p.D951N	ENST00000389048	NM_004304.4	951	Gat/Aat	17/29	0.135274286442777	0	FACETS	0.642	0.568	0.72			1	INDETERMINATE	1	TRUE	0	0.320273003759525	0		757	562	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543670	29543670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	114	844	1	ENST00000389048.3:c.1493C>T	p.Thr498Ile	p.T498I	ENST00000389048	NM_004304.4	498	aCt/aTt	7/29	0.135274286442777	0	FACETS	0.771	0.695	0.85			1	INDETERMINATE	1	TRUE	0	0.320273003759525	0		845	628	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224554	39224554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	37	119	0	ENST00000402219.2:c.2804C>T	p.Thr935Ile	p.T935I	ENST00000402219	NM_005633.3	935	aCt/aTt	18/23	1	2	FACETS	0.831	0.689	0.989	0.831	0.689	0.989	CLONAL	1	TRUE	1	0.320273003759525	2		119	278	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047352	128047352	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	57	531	0	ENST00000285398.2:c.570G>T	p.Gln190His	p.Q190H	ENST00000285398	NM_000122.1	190	caG/caT	5/15	1	2	FACETS	0.708	0.608	0.816	0.708	0.608	0.816	SUBCLONAL	1	TRUE	1	0.320273003759525	2		531	503	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022551	31022551	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	57	852	0	ENST00000375687.4:c.2036G>A	p.Gly679Glu	p.G679E	ENST00000375687	NM_015338.5	679	gGa/gAa	13/13	1	2	FACETS	0.839	0.722	0.967	0.839	0.722	0.967	CLONAL	1	TRUE	1	0.320273003759525	2		852	424	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026176	36026176	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	106	1577	0	ENST00000358208.4:c.778A>T	p.Lys260Ter	p.K260*	ENST00000358208		260	Aag/Tag	7/12	1	2	FACETS	0.87	0.78	0.965	0.87	0.78	0.965	CLONAL	1	TRUE	1	0.320273003759525	2		1577	761	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266145	41266145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	46	265	0	ENST00000349496.5:c.142G>A	p.Gly48Ser	p.G48S	ENST00000349496	NM_001904.3	48	Ggt/Agt	3/15	1	2	FACETS	0.774	0.654	0.906	0.774	0.654	0.906	CLONAL	1	TRUE	1	0.320273003759525	2		265	371	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281784	142281784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	58	250	0	ENST00000350721.4:c.460G>A	p.Glu154Lys	p.E154K	ENST00000350721	NM_001184.3	154	Gaa/Aaa	4/47	1	2	FACETS	0.803	0.691	0.924	0.803	0.691	0.924	CLONAL	1	TRUE	1	0.320273003759525	2		250	451	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169999699	169999699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	48	109	0	ENST00000295797.4:c.1010G>A	p.Gly337Glu	p.G337E	ENST00000295797	NM_002740.5	337	gGa/gAa	11/18	1	2	FACETS	0.94	0.798	1	0.94	0.798	1	CLONAL	1	TRUE	1	0.320273003759525	2		109	319	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99850105	99850105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766662779	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	68	1282	3	ENST00000280892.6:c.19C>T	p.Arg7Cys	p.R7C	ENST00000280892	NM_001130678.1	7	Cgc/Tgc	1/7	0.235491806437053	1	FACETS	0.677	0.589	0.771	0.677	0.589	0.771	SUBCLONAL	1	TRUE	0	0.320273003759525	1		1285	527	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156479	106156480	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	30	249	0	ENST00000380013.4:c.1380_1381delinsTT	p.Gln461Ter	p.Q461*	ENST00000380013	NM_001127208.2	460	tcCCag/tcTTag	3/11	0.235491806437053	1	FACETS	0.523	0.422	0.636	0.523	0.422	0.636	SUBCLONAL	1	TRUE	0	0.320273003759525	1		249	301	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530474	187530475	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	31	295	0	ENST00000441802.2:c.10069-1_10069delinsAA		p.X3357_splice	ENST00000441802	NM_005245.3	3357		16/27	0.235491806437053	1	FACETS	0.643	0.522	0.778	0.643	0.522	0.778	SUBCLONAL	1	TRUE	0	0.320273003759525	1		295	253	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628809	187628809	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	46	404	0	ENST00000441802.2:c.2173C>T	p.Gln725Ter	p.Q725*	ENST00000441802	NM_005245.3	725	Cag/Tag	2/27	0.235491806437053	1	FACETS	0.518	0.436	0.608	0.518	0.436	0.608	SUBCLONAL	1	TRUE	0	0.320273003759525	1		404	466	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679547	86679547	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	42	161	0	ENST00000274376.6:c.2708G>C	p.Arg903Pro	p.R903P	ENST00000274376	NM_002890.2	903	cGa/cCa	21/25	0.134462044338668	4	FACETS	0.921	0.771	1	0.46	0.385	0.544	INDETERMINATE	1	TRUE	2	0.320273003759525	4		161	376	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490459	20490459	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	90	466	0	ENST00000346618.3:c.1196C>T	p.Pro399Leu	p.P399L	ENST00000346618	NM_001949.4	399	cCt/cTt	7/7	1	2	FACETS	0.969	0.861	1	0.969	0.861	1	CLONAL	1	TRUE	1	0.320273003759525	2		466	580	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041112	112041112	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	155	888	0	ENST00000368678.4:c.143C>T	p.Pro48Leu	p.P48L	ENST00000368678		48	cCc/cTc	3/13	0.267459269890995	4	FACETS	0.884	0.811	0.96	0.884	0.811	0.96	CLONAL	2	TRUE	2	0.320273003759525	4		888	723	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878966	151878966	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	41	394	0	ENST00000262189.6:c.5979A>T	p.Gln1993His	p.Q1993H	ENST00000262189	NM_170606.2	1993	caA/caT	36/59	1	2	FACETS	0.512	0.426	0.608	0.512	0.426	0.608	SUBCLONAL	1	TRUE	1	0.320273003759525	2		394	500	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752857	128752857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	49	515	0	ENST00000377970.2:c.1018G>A	p.Val340Ile	p.V340I	ENST00000377970	NM_002467.4	340	Gtc/Atc	3/3	1	2	FACETS	0.843	0.716	0.981	0.843	0.716	0.981	CLONAL	1	TRUE	1	0.320273003759525	2		515	363	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465656	8465656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	204	183	0	ENST00000356435.5:c.3524G>A	p.Arg1175Lys	p.R1175K	ENST00000356435		1175	aGg/aAg	21/35	0.320273003759525	5	FACETS	0.902	0.849	0.956			1	CLONAL	5	TRUE	NA	0.320273003759525	5		183	418	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412689	139412690	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	257	1525	2	ENST00000277541.6:c.1154_1155delinsTT	p.Ser385Phe	p.S385F	ENST00000277541	NM_017617.3	385	tCC/tTT	7/34	0.320273003759525	1	FACETS	0.887	0.834	0.941	1	0.995	1	CLONAL	2	TRUE	0	0.320273003759525	1		1527	760	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433059	49433060	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	A	novel	NA	P-0054000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	65	1390	1	ENST00000301067.7:c.8311_8312delinsT	p.Arg2771TyrfsTer16	p.R2771Yfs*16	ENST00000301067	NM_003482.3	2771	CGa/Ta	33/54	0.134462044338668	4	FACETS	0.89	0.772	1	0.445	0.386	0.509	INDETERMINATE	1	TRUE	2	0.320273003759525	4		1391	602	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	114	386	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.281021967280507	3	FACETS	0.95	0.86	1	0.95	0.86	1	CLONAL	2	TRUE	1	0.29	3		386	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0054001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	257	781	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.289995135577718	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	0	0.29	2		782	878	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022914	27022945	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCCGCCGCCAGCAGCCTGGGCAACCCGCCG	CCGCCGCCGCCAGCAGCCTGGGCAACCCGCCG	-	novel	NA	P-0054001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	12	24	0	ENST00000324856.7:c.31_62del	p.Ser11LeufsTer89	p.S11Lfs*89	ENST00000324856	NM_006015.4	7	cCCGCCGCCGCCAGCAGCCTGGGCAACCCGCCG/c	1/20	0.281021967280507	3	FACETS	0.803	0.578	1	0.803	0.578	1	CLONAL	2	TRUE	1	0.29	3		24	59	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575209	48575210	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0054001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	92	281	1	ENST00000342988.3:c.405_406dup	p.Val136GlufsTer12	p.V136Efs*12	ENST00000342988	NM_005359.5	135	cga/cGAga	3/12	0.289995135577718	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	0	0.29	2		282	306	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342812	87342812	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	49	496	1	ENST00000277120.3:c.1097A>T	p.Glu366Val	p.E366V	ENST00000277120		366	gAg/gTg	9/19	1	2	FACETS	0.667	0.565	0.779	0.667	0.565	0.779	SUBCLONAL	1	TRUE	1	0.29	2		497	507	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057781	27057781	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	C	C	TA	novel	NA	P-0054001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	179	842	0	ENST00000324856.7:c.1489delinsTA	p.Gln497Ter	p.Q497*	ENST00000324856	NM_006015.4	497	Caa/TAaa	3/20	0.281021967280507	3	FACETS	1	0.979	1	0.591	0.544	0.64	CLONAL	1	TRUE	1	0.29	3		842	1196	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115980	8116077	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	GGGTTAGAGCCCTGCTCGATGCTCACAGGGCCCCCAGCGAGAGTCCCTGCAGTCCCTTTCGACTTGCATTTTTGCAGGAGCAGTATCATGAAGCCTAA	GGGTTAGAGCCCTGCTCGATGCTCACAGGGCCCCCAGCGAGAGTCCCTGCAGTCCCTTTCGACTTGCATTTTTGCAGGAGCAGTATCATGAAGCCTAA	-	novel	NA	P-0054002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	65	344	0	ENST00000346208.3:c.1326_*91del		p.*442*	ENST00000346208		442		6/6	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		344	183	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0054003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	48	329	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.53545635795887	1	FACETS	0.918	0.794	1	0.918	0.794	1	CLONAL	1	TRUE	0	0.53545635795887	1		329	143	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435041	18435041	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	70	237	0	ENST00000266497.5:c.26C>A	p.Pro9Gln	p.P9Q	ENST00000266497		9	cCa/cAa	1/31	0.486184883426402	1	FACETS	0.866	0.767	0.97	0.866	0.767	0.97	CLONAL	1	TRUE	0	0.53545635795887	1		237	221	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696688	47696688	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	156	454	0	ENST00000347630.2:c.260A>T	p.Tyr87Phe	p.Y87F	ENST00000347630	NM_001007230.1	87	tAc/tTc	5/11	1	2	FACETS	0.905	0.831	0.981	0.905	0.831	0.981	CLONAL	1	TRUE	1	0.53545635795887	2		454	644	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295675	212295675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	93	410	0	ENST00000342788.4:c.2638G>A	p.Gly880Arg	p.G880R	ENST00000342788	NM_005235.2	880	Gga/Aga	21/28	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.36839325444248	2		410	492	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587235	212587235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1443253742	NA	P-0054004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	96	407	0	ENST00000342788.4:c.766G>A	p.Gly256Arg	p.G256R	ENST00000342788	NM_005235.2	256	Gga/Aga	7/28	1	2	FACETS	0.927	0.828	1	0.927	0.828	1	CLONAL	1	TRUE	1	0.36839325444248	2		407	562	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0054005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	90	888	3	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.471	0.417	0.528	0.471	0.417	0.528	SUBCLONAL	1	TRUE	1	0.458660151813696	2		891	834	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0054005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	194	720	10	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.843	0.779	0.908	0.843	0.779	0.908	CLONAL	1	TRUE	1	0.458660151813696	2		730	1004	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021817	71021817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs797045586	NA	P-0054005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	47	245	1	ENST00000318789.4:c.1541G>A	p.Arg514His	p.R514H	ENST00000318789	NM_032682.5	514	cGt/cAt	18/21	0.458660151813696	1	FACETS	0.752	0.642	0.87	0.752	0.642	0.87	SUBCLONAL	1	TRUE	0	0.458660151813696	1		246	210	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821890	72821890	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	138	445	1	ENST00000268489.5:c.10285del	p.Arg3429ValfsTer56	p.R3429Vfs*56	ENST00000268489	NM_006885.3	3429	Cgt/gt	10/10	1	2	FACETS	0.884	0.806	0.965	0.884	0.806	0.965	CLONAL	1	TRUE	1	0.458660151813696	2		446	681	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306996	65306997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	95	480	7	ENST00000342505.4:c.2580dup	p.Pro861ThrfsTer4	p.P861Tfs*4	ENST00000342505	NM_002227.2	860	-/A	19/25	0.458660151813696	1	FACETS	0.887	0.797	0.981	0.887	0.797	0.981	CLONAL	1	TRUE	0	0.458660151813696	1		487	360	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	103	746	3	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	0.458660151813696	1	FACETS	0.762	0.686	0.843	0.762	0.686	0.843	SUBCLONAL	1	TRUE	0	0.458660151813696	1		749	454	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527817	157527817	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	107	607	0	ENST00000346085.5:c.5547del	p.Leu1850Ter	p.L1850*	ENST00000346085	NM_020732.3	1848	Ccc/cc	20/20	1	2	FACETS	0.877	0.79	0.969	0.877	0.79	0.969	CLONAL	1	TRUE	1	0.458660151813696	2		607	532	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681432	30681432	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	32	456	0	ENST00000376406.3:c.580C>A	p.Pro194Thr	p.P194T	ENST00000376406	NM_014641.2	194	Cca/Aca	4/15	1	2	FACETS	0.345	0.28	0.419	0.345	0.28	0.419	SUBCLONAL	1	TRUE	1	0.458660151813696	2		456	404	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638345	176638345	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779087886	NA	P-0054005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	56	891	0	ENST00000439151.2:c.2945G>T	p.Gly982Val	p.G982V	ENST00000439151	NM_022455.4	982	gGg/gTg	5/23	0.385206212748131	3	FACETS	0.305	0.26	0.354	0.153	0.13	0.177	SUBCLONAL	1	TRUE	1	0.458660151813696	3		891	984	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974254	18974254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149336516	NA	P-0054005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	140	710	0	ENST00000262803.5:c.2608G>A	p.Val870Ile	p.V870I	ENST00000262803	NM_002911.3	870	Gtc/Atc	19/24	1	2	FACETS	0.922	0.842	1	0.922	0.842	1	CLONAL	1	TRUE	1	0.458660151813696	2		710	662	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439913	51439913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs956412807	NA	P-0054005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	21	411	0	ENST00000262662.1:c.478G>A	p.Gly160Arg	p.G160R	ENST00000262662		160	Ggg/Agg	4/4	0.458660151813696	1	FACETS	0.255	0.196	0.323	0.255	0.196	0.323	SUBCLONAL	1	TRUE	0	0.458660151813696	1		411	277	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420694	49420694	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	164	957	0	ENST00000301067.7:c.15055G>A	p.Ala5019Thr	p.A5019T	ENST00000301067	NM_003482.3	5019	Gcc/Acc	48/54	1	2	FACETS	0.912	0.839	0.989	0.912	0.839	0.989	CLONAL	1	TRUE	1	0.458660151813696	2		957	784	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562370	21562370	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	258	1009	1	ENST00000382592.4:c.1549C>T	p.Pro517Ser	p.P517S	ENST00000382592	NM_014572.2	517	Ccc/Tcc	4/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.458660151813696	2		1010	1057	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563444	21563444	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0054005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	238	1257	0	ENST00000382592.4:c.476-1G>T		p.X159_splice	ENST00000382592	NM_014572.2	159			1	2	FACETS	0.943	0.879	1	0.943	0.879	1	CLONAL	1	TRUE	1	0.458660151813696	2		1257	1101	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117864	70117865	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTTT	novel	NA	P-0054005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	158	722	0	ENST00000245479.2:c.332_333insGTTT	p.Met113LeufsTer140	p.M113Lfs*140	ENST00000245479	NM_000346.3	111	gcc/gcGTTTc	1/3	0.458660151813696	1	FACETS	0.96	0.885	1	0.96	0.885	1	CLONAL	1	TRUE	0	0.458660151813696	1		722	553	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117680991	117680991	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	16	363	0	ENST00000368508.3:c.3629A>G	p.His1210Arg	p.H1210R	ENST00000368508	NM_002944.2	1210	cAc/cGc	23/43	1	2	FACETS	0.236	0.174	0.31	0.236	0.174	0.31	SUBCLONAL	1	TRUE	1	0.458660151813696	2		363	296	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738349	145738349	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1215700016	NA	P-0054005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	269	1406	1	ENST00000428558.2:c.2636del	p.Pro879LeufsTer69	p.P879Lfs*69	ENST00000428558	NM_004260.3	879	cCt/ct	16/22	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.458660151813696	2		1407	1172	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87338544	87338544	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	38	633	0	ENST00000277120.3:c.640A>T	p.Ile214Phe	p.I214F	ENST00000277120		214	Atc/Ttc	7/19	1	2	FACETS	0.287	0.237	0.344	0.287	0.237	0.344	SUBCLONAL	1	TRUE	1	0.458660151813696	2		633	577	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0054007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	191	310	1	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	0.917985356676998	5	FACETS	1	0.961	1			1	CLONAL	2	TRUE	NA	0.917985356676998	5		311	475	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913237	NA	P-0054007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	116	359	0	ENST00000369535.4:c.35G>C	p.Gly12Ala	p.G12A	ENST00000369535	NM_002524.4	12	gGt/gCt	2/7	0.917985356676998	3	FACETS	0.917	0.834	1	0.459	0.417	0.502	CLONAL	1	TRUE	1	0.917985356676998	3		359	402	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588172	69588172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550329316	NA	P-0054007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	231	761	2	ENST00000168712.1:c.526G>A	p.Gly176Ser	p.G176S	ENST00000168712	NM_002007.2	176	Ggc/Agc	3/3	0.407119026072102	6	FACETS	0.843	0.787	0.899	0.562	0.525	0.6	INDETERMINATE	2	TRUE	3	0.917985356676998	6		763	847	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982957	201982957	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs374568591	NA	P-0054007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	180	798	1	ENST00000359651.3:c.806C>T	p.Ala269Val	p.A269V	ENST00000359651		269	gCg/gTg	7/8	0.917985356676998	6	FACETS	1	0.942	1	0.343	0.315	0.371	CLONAL	1	TRUE	3	0.917985356676998	6		799	1082	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155013	108155013	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs146017595	NA	P-0054007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	139	394	0	ENST00000278616.4:c.3806A>G	p.Lys1269Arg	p.K1269R	ENST00000278616	NM_000051.3	1269	aAg/aGg	26/63	0.917985356676998	4	FACETS	0.919	0.85	0.989	0.919	0.85	0.989	CLONAL	2	TRUE	2	0.917985356676998	4		394	316	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960156	151960156	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	139	382	0	ENST00000262189.6:c.1244C>A	p.Thr415Asn	p.T415N	ENST00000262189	NM_170606.2	415	aCt/aAt	9/59	0.917985356676998	4	FACETS	0.968	0.897	1	0.968	0.897	1	CLONAL	2	TRUE	2	0.917985356676998	4		382	300	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159755	20159755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	312	610	2	ENST00000379607.5:c.4C>T	p.Pro2Ser	p.P2S	ENST00000379607	NM_001412.3	2	Ccc/Tcc	1/7	0.509674859934486	5	FACETS	0.869	0.827	0.91			1	INDETERMINATE	3	TRUE	NA	0.917985356676998	5		612	620	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939232	76939232	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	87	660	0	ENST00000373344.5:c.1516C>A	p.Pro506Thr	p.P506T	ENST00000373344	NM_000489.3	506	Cct/Act	9/35	0.804536414927534	3	FACETS	0.881	0.788	0.978	0.44	0.394	0.489	CLONAL	1	TRUE	1	0.917985356676998	3		660	314	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593605	55593661	+	inframe_deletion	In_Frame_Del	DEL	GAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAACT	GAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAACT	-	novel	NA	P-0054008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	222	462	0	ENST00000288135.5:c.1671_1727del	p.Trp557_Leu576delinsCys	p.W557_L576delinsC	ENST00000288135	NM_000222.2	557	tgGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGACCCAACACAACTt/tgt	11/21	0.795890576915552	3	FACETS	0.817	0.77	0.865	0.817	0.77	0.865	CLONAL	2	TRUE	1	0.795890576915552	3		462	477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs17849781	NA	P-0054009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	211	779	1	ENST00000269305.4:c.832C>A	p.Pro278Thr	p.P278T	ENST00000269305	NM_001126112.2	278	Cct/Act	8/11	0.360983445468016	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.360983445468016	1		780	895	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028668	12028668	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	90	360	1	ENST00000353533.5:c.871T>C	p.Trp291Arg	p.W291R	ENST00000353533	NM_003010.3	291	Tgg/Cgg	8/11	0.360983445468016	1	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	0	0.360983445468016	1		361	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579415	7579415	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	492	859	6	ENST00000269305.4:c.272G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tGg/tAg	4/11	0.611028539352982	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.611028539352982	2		865	771	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348566	89348568	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs753054998	NA	P-0054011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	50	805	1	ENST00000301030.4:c.4382_4384del	p.Lys1461del	p.K1461del	ENST00000301030	NM_001256183.1	1461	aAGAga/aga	9/13	1	2	FACETS	0.186	0.157	0.218	0.186	0.157	0.218	SUBCLONAL	1	TRUE	1	0.611028539352982	2		806	881	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491732	120491735	+	frameshift_variant	Frame_Shift_Del	DEL	CTGT	CTGT	-	novel	NA	P-0054011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	93	257	2	ENST00000256646.2:c.2494_2497del	p.Thr832TyrfsTer51	p.T832Yfs*51	ENST00000256646	NM_024408.3	832	ACAGta/ta	16/34	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.611028539352982	2		259	299	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138947	64138947	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	38	265	1	ENST00000334205.4:c.2314del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	772	Tcc/cc	17/17	0.581341900078526	4	FACETS	0.739	0.615	0.877	0.185	0.153	0.22	SUBCLONAL	1	TRUE	0	0.611028539352982	4		266	271	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241967	39241967	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	88	217	1	ENST00000402219.2:c.1879T>A	p.Phe627Ile	p.F627I	ENST00000402219	NM_005633.3	627	Ttt/Att	11/23	0.611028539352982	3	FACETS	0.933	0.832	1	0.467	0.416	0.52	CLONAL	1	TRUE	1	0.611028539352982	3		218	403	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80071513	80071513	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	160	202	0	ENST00000265081.6:c.2256del	p.Phe752LeufsTer2	p.F752Lfs*2	ENST00000265081	NM_002439.4	752	Ttt/tt	16/24	0.533439512014547	2	FACETS	0.882	0.825	0.938	0.882	0.825	0.938	CLONAL	2	TRUE	0	0.611028539352982	2		202	297	SUCCESS
APC	324	MSKCC	GRCh37	5	112176879	112176879	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	153	237	2	ENST00000257430.4:c.5588G>T	p.Ser1863Ile	p.S1863I	ENST00000257430	NM_000038.5	1863	aGt/aTt	16/16	0.567144684666018	3	FACETS	1	0.938	1	0.673	0.626	0.72	CLONAL	2	TRUE	0	0.611028539352982	3		239	324	SUCCESS
AR	367	MSKCC	GRCh37	X	66765179	66765180	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGAGACTAGCCCCAG	novel	NA	P-0054011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	25	183	1	ENST00000374690.3:c.191_192insAGAGACTAGCCCCAG	p.Gln64_Gln65insGluThrSerProArg	p.Q64_Q65insETSPR	ENST00000374690	NM_000044.3	64	cag/caAGAGACTAGCCCCAGg	1/8	0.461575981547994	2	FACETS	0.525	0.418	0.645			1	SUBCLONAL	1	TRUE	NA	0.611028539352982	2		184	156	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	79	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.978	0.869	1	0.978	0.869	1	CLONAL	1	TRUE	1	0.53334446327398	2		276	303	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0054012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	141	570	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.858	0.785	0.935	0.858	0.785	0.935	CLONAL	1	TRUE	1	0.53334446327398	2		570	616	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397710	49397710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	127	425	0	ENST00000418115.1:c.514G>A	p.Glu172Lys	p.E172K	ENST00000418115	NM_001664.2	172	Gaa/Aaa	5/5	1	2	FACETS	0.945	0.861	1	0.945	0.861	1	CLONAL	1	TRUE	1	0.53334446327398	2		425	504	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0054012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	190	798	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.53334446327398	1	FACETS	0.917	0.853	0.982	0.917	0.853	0.982	CLONAL	1	TRUE	0	0.53334446327398	1		798	570	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023212	27023225	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGGGCCCTAGGC	CGCGGGCCCTAGGC	-	novel	NA	P-0054012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	34	161	0	ENST00000324856.7:c.319_332del	p.Ala107ArgfsTer5	p.A107Rfs*5	ENST00000324856	NM_006015.4	106	aaCGCGGGCCCTAGGCcc/aacc	1/20	1	2	FACETS	0.577	0.475	0.69	0.577	0.475	0.69	SUBCLONAL	1	TRUE	1	0.53334446327398	2		161	221	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370847	55370847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	112	667	0	ENST00000297316.4:c.149C>T	p.Ala50Val	p.A50V	ENST00000297316	NM_022454.3	50	gCg/gTg	1/2	1	2	FACETS	0.595	0.535	0.658	0.595	0.535	0.658	SUBCLONAL	1	TRUE	1	0.53334446327398	2		667	706	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197834	123197834	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	133	120	0	ENST00000218089.9:c.1958C>A	p.Ser653Ter	p.S653*	ENST00000218089	NM_001042749.1	653	tCa/tAa	20/35	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.53334446327398	1		120	270	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259162	16259162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	55	467	1	ENST00000375759.3:c.6427G>A	p.Asp2143Asn	p.D2143N	ENST00000375759	NM_015001.2	2143	Gat/Aat	11/15	1	2	FACETS	0.371	0.317	0.43	0.371	0.317	0.43	SUBCLONAL	1	TRUE	1	0.53334446327398	2		468	556	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416461	49416461	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	164	509	0	ENST00000301067.7:c.16250T>C	p.Leu5417Pro	p.L5417P	ENST00000301067	NM_003482.3	5417	cTa/cCa	51/54	1	2	FACETS	0.978	0.901	1	0.978	0.901	1	CLONAL	1	TRUE	1	0.53334446327398	2		509	629	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807314	3807314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	101	295	0	ENST00000262367.5:c.3673del	p.Ala1225LeufsTer25	p.A1225Lfs*25	ENST00000262367	NM_004380.2	1225	Gct/ct	19/31	1	2	FACETS	0.904	0.813	0.999	0.904	0.813	0.999	CLONAL	1	TRUE	1	0.53334446327398	2		295	419	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11019818	11019818	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	62	506	0	ENST00000327064.4:c.493G>C	p.Asp165His	p.D165H	ENST00000327064	NM_199141.1	165	Gac/Cac	4/16	1	2	FACETS	0.399	0.345	0.459	0.399	0.345	0.459	SUBCLONAL	1	TRUE	1	0.53334446327398	2		506	582	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131462	202131462	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	38	379	0	ENST00000358485.4:c.430G>T	p.Glu144Ter	p.E144*	ENST00000358485	NM_001080125.1	144	Gag/Tag	2/9	1	2	FACETS	0.308	0.254	0.368	0.308	0.254	0.368	SUBCLONAL	1	TRUE	1	0.53334446327398	2		379	463	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845745	151845745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388579933	NA	P-0054012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	159	481	0	ENST00000262189.6:c.13267G>A	p.Asp4423Asn	p.D4423N	ENST00000262189	NM_170606.2	4423	Gac/Aac	52/59	1	2	FACETS	0.916	0.842	0.992	0.916	0.842	0.992	CLONAL	1	TRUE	1	0.53334446327398	2		481	651	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846123	151846123	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	123	402	0	ENST00000262189.6:c.12889G>T	p.Glu4297Ter	p.E4297*	ENST00000262189	NM_170606.2	4297	Gag/Tag	52/59	1	2	FACETS	0.908	0.825	0.994	0.908	0.825	0.994	CLONAL	1	TRUE	1	0.53334446327398	2		402	508	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772934	135772934	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203727	NA	P-0054012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	69	459	3	ENST00000298552.3:c.2689C>T	p.Gln897Ter	p.Q897*	ENST00000298552	NM_001162426.1	897	Cag/Tag	21/23	0.414306844310674	0	FACETS	0.352	0.308	0.398			1	SUBCLONAL	1	TRUE	0	0.53334446327398	0		462	343	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272140	15272140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	254	845	0	ENST00000263388.2:c.6299C>T	p.Ser2100Leu	p.S2100L	ENST00000263388	NM_000435.2	2100	tCg/tTg	33/33	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.413405562190536	2		845	1045	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0054013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	199	663	1	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.413405562190536	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.413405562190536	1		664	742	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929412	44929415	+	frameshift_variant	Frame_Shift_Del	DEL	ACAA	ACAA	-	rs786205676	NA	P-0054013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	174	308	0	ENST00000377967.4:c.2515_2518del	p.Asn839ValfsTer27	p.N839Vfs*27	ENST00000377967	NM_021140.2	838	ACAAac/ac	17/29	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.413405562190536	1		308	451	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298639	11298639	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	174	561	0	ENST00000361445.4:c.1822G>C	p.Asp608His	p.D608H	ENST00000361445	NM_004958.3	608	Gat/Cat	12/58	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.413405562190536	2		561	771	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832518	72832518	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	101	451	0	ENST00000268489.5:c.4063A>G	p.Arg1355Gly	p.R1355G	ENST00000268489	NM_006885.3	1355	Aga/Gga	9/10	1	2	FACETS	0.798	0.715	0.887	0.798	0.715	0.887	SUBCLONAL	1	TRUE	1	0.413405562190536	2		451	612	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030464	47030464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	257	455	0	ENST00000377604.3:c.239G>A	p.Arg80His	p.R80H	ENST00000377604	NM_001204468.1	80	cGt/cAt	4/24	1	1	FACETS	0.827	0.781	0.874	1	0.994	1	CLONAL	2	TRUE	0	0.413405562190536	1		455	596	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	160	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.749144723475571	2		276	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0054014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	344	882	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.732456008243286	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.749144723475571	1		883	559	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932242	36932242	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	170	737	1	ENST00000361632.4:c.2227C>T	p.Gln743Ter	p.Q743*	ENST00000361632		743	Cag/Tag	16/16	0.384613567589615	1	FACETS	0.364	0.335	0.394	0.364	0.335	0.394	INDETERMINATE	1	TRUE	0	0.749144723475571	1		738	780	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740381	46740381	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	92	405	0	ENST00000371975.4:c.1861C>A	p.Leu621Met	p.L621M	ENST00000371975	NM_003579.3	621	Ctg/Atg	16/18	NA	2	FACETS	0.407	0.362	0.455			1	INDETERMINATE	1	TRUE	NA	0.749144723475571	2		405	603	SUCCESS
ATR	545	MSKCC	GRCh37	3	142184082	142184082	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	120	173	0	ENST00000350721.4:c.6898G>T	p.Val2300Leu	p.V2300L	ENST00000350721	NM_001184.3	2300	Gtg/Ttg	41/47	1	2	FACETS	0.91	0.831	0.991	0.91	0.831	0.991	CLONAL	1	TRUE	1	0.749144723475571	2		173	352	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220494	123220494	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	274	432	0	ENST00000218089.9:c.3151G>T	p.Gly1051Cys	p.G1051C	ENST00000218089	NM_001042749.1	1051	Ggt/Tgt	30/35	0.503764838829049	1	FACETS	0.839	0.797	0.882	0.839	0.797	0.882	CLONAL	1	TRUE	0	0.749144723475571	1		432	545	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546377	46546377	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs558585498	NA	P-0054015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	173	334	0	ENST00000262741.5:c.152A>G	p.Asn51Ser	p.N51S	ENST00000262741	NM_003629.3	51	aAt/aGt	2/10	0.385797549515853	2	FACETS	1	0.931	1	0.503	0.465	0.541	CLONAL	1	FALSE	0	0.624555189829689	2		334	551	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612798	228612798	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	162	855	2	ENST00000366696.1:c.229C>A	p.Gln77Lys	p.Q77K	ENST00000366696	NM_003493.2	77	Cag/Aag	1/1	1	2	FACETS	0.439	0.402	0.478	0.439	0.402	0.478	SUBCLONAL	1	FALSE	1	0.624555189829689	2		857	1181	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170606	108170606	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	97	213	0	ENST00000278616.4:c.5171A>G	p.Glu1724Gly	p.E1724G	ENST00000278616	NM_000051.3	1724	gAa/gGa	34/63	1	2	FACETS	0.977	0.881	1	0.977	0.881	1	CLONAL	1	FALSE	1	0.624555189829689	2		213	318	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606199	81606199	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs752683894	NA	P-0054015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	234	298	0	ENST00000298171.2:c.869A>T	p.Lys290Met	p.K290M	ENST00000298171	NM_000369.2	290	aAg/aTg	9/10	0.624555189829689	2	FACETS	0.755	0.713	0.798	0.755	0.713	0.798	SUBCLONAL	2	FALSE	0	0.624555189829689	2		298	496	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462572	29462572	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1266	223	685	0	ENST00000389048.3:c.2329C>A	p.Gln777Lys	p.Q777K	ENST00000389048	NM_004304.4	777	Cag/Aag	13/29	0.267796736261069	4	FACETS	0.779	0.723	0.837	0.39	0.361	0.419	INDETERMINATE	1	FALSE	2	0.624555189829689	4		685	1489	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180076490	180076490	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	113	114	0	ENST00000261937.6:c.56A>G	p.Asp19Gly	p.D19G	ENST00000261937	NM_182925.4	19	gAc/gGc	1/30	0.624555189829689	5	FACETS	1	0.978	1	0.433	0.391	0.477	CLONAL	1	FALSE	2	0.624555189829689	5		114	540	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662324	117662324	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs775601610	NA	P-0054015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	194	417	1	ENST00000368508.3:c.5053A>C	p.Ile1685Leu	p.I1685L	ENST00000368508	NM_002944.2	1685	Atc/Ctc	30/43	0.624555189829689	1	FACETS	0.984	0.922	1	0.984	0.922	1	CLONAL	1	FALSE	0	0.624555189829689	1		418	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	93	817	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.462	0.411	0.516	0.462	0.411	0.516	SUBCLONAL	1	TRUE	1	0.62	2		819	650	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	41	383	0	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	0.342	0.285	0.405	0.342	0.285	0.405	SUBCLONAL	1	TRUE	1	0.62	2		383	387	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170136	32170136	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771019003	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	129	1005	1	ENST00000375023.3:c.3472C>T	p.Arg1158Ter	p.R1158*	ENST00000375023	NM_004557.3	1158	Cga/Tga	21/30	1	2	FACETS	0.501	0.454	0.551	0.501	0.454	0.551	SUBCLONAL	1	TRUE	1	0.62	2		1006	830	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341902	8341902	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	25	330	0	ENST00000356435.5:c.4738G>T	p.Asp1580Tyr	p.D1580Y	ENST00000356435		1580	Gat/Tat	29/35	1	2	FACETS	0.263	0.207	0.327	0.263	0.207	0.327	SUBCLONAL	1	TRUE	1	0.62	2		330	307	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936983	48936983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690863	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	24	448	1	ENST00000267163.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000267163	NM_000321.2	251	Cga/Tga	8/27	1	2	FACETS	0.226	0.177	0.283	0.226	0.177	0.283	SUBCLONAL	1	TRUE	1	0.62	2		449	342	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945092	38945092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769767383	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	107	274	0	ENST00000357387.3:c.4712C>T	p.Ser1571Leu	p.S1571L	ENST00000357387	NM_152756.3	1571	tCg/tTg	35/38	1	2	FACETS	0.992	0.899	1	0.992	0.899	1	CLONAL	1	TRUE	1	0.62	2		274	348	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589168	67589168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	77	245	0	ENST00000274335.5:c.1156C>T	p.Arg386Ter	p.R386*	ENST00000274335		386	Cga/Tga	9/15	1	2	FACETS	0.941	0.837	1	0.941	0.837	1	CLONAL	1	TRUE	1	0.62	2		245	264	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407570	407570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	32	328	0	ENST00000380956.4:c.1328C>T	p.Ser443Phe	p.S443F	ENST00000380956	NM_001195286.1	443	tCt/tTt	9/9	1	2	FACETS	0.297	0.241	0.359	0.297	0.241	0.359	SUBCLONAL	1	TRUE	1	0.62	2		328	348	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518099	8518099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764400127	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	9	399	0	ENST00000356435.5:c.1292C>T	p.Ser431Leu	p.S431L	ENST00000356435		431	tCg/tTg	10/35	1	2	FACETS	0.07	0.046	0.101	0.07	0.046	0.101	SUBCLONAL	1	TRUE	1	0.62	2		399	416	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426123	138426123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217537873	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	31	269	0	ENST00000289153.2:c.1408G>A	p.Glu470Lys	p.E470K	ENST00000289153	NM_006219.2	470	Gaa/Aaa	9/22	1	2	FACETS	0.347	0.281	0.421	0.347	0.281	0.421	SUBCLONAL	1	TRUE	1	0.62	2		269	288	SUCCESS
APC	324	MSKCC	GRCh37	5	112177677	112177677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782301	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	97	245	0	ENST00000257430.4:c.6386C>T	p.Ser2129Leu	p.S2129L	ENST00000257430	NM_000038.5	2129	tCg/tTg	16/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.62	2		245	277	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	149	446	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.62	2		446	412	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916248	9916248	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397518472	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	113	357	0	ENST00000330684.3:c.2041C>T	p.Arg681Ter	p.R681*	ENST00000330684	NM_001134407.1	681	Cga/Tga	10/13	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.62	2		357	354	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	29	286	0	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	1	2	FACETS	0.459	0.371	0.557	0.459	0.371	0.557	SUBCLONAL	1	TRUE	1	0.62	2		286	204	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86686647	86686647	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	70	150	0	ENST00000274376.6:c.3091G>T	p.Glu1031Ter	p.E1031*	ENST00000274376	NM_002890.2	1031	Gaa/Taa	25/25	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.62	2		150	200	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97897674	97897674	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	51	369	0	ENST00000289081.3:c.797G>T	p.Arg266Ile	p.R266I	ENST00000289081	NM_000136.2	266	aGa/aTa	8/15	1	2	FACETS	0.402	0.342	0.467	0.402	0.342	0.467	SUBCLONAL	1	TRUE	1	0.62	2		369	409	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119325	3119325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	132	776	0	ENST00000078429.4:c.857C>T	p.Ser286Leu	p.S286L	ENST00000078429	NM_002067.2	286	tCg/tTg	6/7	1	2	FACETS	0.698	0.636	0.763	0.698	0.636	0.763	SUBCLONAL	1	TRUE	1	0.62	2		776	610	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14027732	14027732	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	18	277	0	ENST00000405192.2:c.112G>T	p.Asp38Tyr	p.D38Y	ENST00000405192	NM_001163147.1	38	Gat/Tat	3/12	1	2	FACETS	0.185	0.139	0.239	0.185	0.139	0.239	SUBCLONAL	1	TRUE	1	0.62	2		277	314	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881438	48881438	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	49	132	1	ENST00000267163.4:c.160G>T	p.Glu54Ter	p.E54*	ENST00000267163	NM_000321.2	54	Gaa/Taa	2/27	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.62	2		133	136	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645156	67645156	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	87	566	2	ENST00000264010.4:c.421G>T	p.Glu141Ter	p.E141*	ENST00000264010	NM_006565.3	141	Gaa/Taa	3/12	1	2	FACETS	0.461	0.408	0.517	0.461	0.408	0.517	SUBCLONAL	1	TRUE	1	0.62	2		568	609	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867343	68867343	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142927667	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	112	439	0	ENST00000261769.5:c.2590G>A	p.Glu864Lys	p.E864K	ENST00000261769	NM_004360.3	864	Gaa/Aaa	16/16	1	2	FACETS	0.798	0.722	0.877	0.798	0.722	0.877	SUBCLONAL	1	TRUE	1	0.62	2		439	453	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685316	89685316	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs878853937	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	68	171	0	ENST00000371953.3:c.209+2T>C		p.X70_splice	ENST00000371953	NM_000314.4	70			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.62	2		171	190	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748047	72748047	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	51	538	2	ENST00000357731.5:c.131C>T	p.Ala44Val	p.A44V	ENST00000357731	NM_173808.2	44	gCc/gTc	1/7	1	2	FACETS	0.254	0.215	0.296	0.254	0.215	0.296	SUBCLONAL	1	TRUE	1	0.62	2		540	648	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812293	212812293	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569995088	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	68	281	1	ENST00000342788.4:c.283C>T	p.Arg95Cys	p.R95C	ENST00000342788	NM_005235.2	95	Cgt/Tgt	3/28	1	2	FACETS	0.751	0.66	0.848	0.751	0.66	0.848	SUBCLONAL	1	TRUE	1	0.62	2		282	292	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518437	204518437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201947927	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	18	287	0	ENST00000367182.3:c.1100C>T	p.Ser367Leu	p.S367L	ENST00000367182	NM_001278516.1	367	tCg/tTg	11/11	1	2	FACETS	0.17	0.128	0.221	0.17	0.128	0.221	SUBCLONAL	1	TRUE	1	0.62	2		287	341	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703632	47703632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138465383	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	161	377	0	ENST00000233146.2:c.2132G>A	p.Arg711Gln	p.R711Q	ENST00000233146	NM_000251.2	711	cGa/cAa	13/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.62	2		377	465	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922294	100922294	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1315135533	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	39	214	0	ENST00000325455.5:c.2218C>T	p.Arg740Ter	p.R740*	ENST00000325455	NM_001202474.3	740	Cga/Tga	5/8	1	2	FACETS	0.466	0.388	0.552	0.466	0.388	0.552	SUBCLONAL	1	TRUE	1	0.62	2		214	270	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441986	6441986	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	71	549	0	ENST00000356142.4:c.545G>A	p.Arg182Gln	p.R182Q	ENST00000356142	NM_018890.3	182	cGa/cAa	7/7	1	2	FACETS	0.401	0.35	0.456	0.401	0.35	0.456	SUBCLONAL	1	TRUE	1	0.62	2		549	571	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144446	58144446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140644696	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	75	223	0	ENST00000257904.6:c.625C>T	p.Arg209Cys	p.R209C	ENST00000257904	NM_000075.3	209	Cgt/Tgt	5/8	1	2	FACETS	0.941	0.836	1	0.941	0.836	1	CLONAL	1	TRUE	1	0.62	2		223	257	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928872	44928872	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs755440519	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	111	343	0	ENST00000377967.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000377967	NM_021140.2	658	Cga/Tga	17/29	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.62	2		343	349	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532825	187532825	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	54	410	0	ENST00000441802.2:c.9568G>T	p.Glu3190Ter	p.E3190*	ENST00000441802	NM_005245.3	3190	Gaa/Taa	14/27	1	2	FACETS	0.331	0.282	0.383	0.331	0.282	0.383	SUBCLONAL	1	TRUE	1	0.62	2		410	527	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188288	142188288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1470834016	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	121	273	0	ENST00000350721.4:c.6443G>A	p.Arg2148Gln	p.R2148Q	ENST00000350721	NM_001184.3	2148	cGa/cAa	38/47	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.62	2		273	311	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915943	127915943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781486938	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	159	393	0	ENST00000373547.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000373547	NM_002721.4	180	Gaa/Aaa	6/7	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.62	2		393	428	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141989	108141989	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	41	358	0	ENST00000278616.4:c.2933C>A	p.Ser978Tyr	p.S978Y	ENST00000278616	NM_000051.3	978	tCt/tAt	20/63	1	2	FACETS	0.331	0.276	0.392	0.331	0.276	0.392	SUBCLONAL	1	TRUE	1	0.62	2		358	400	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435061	18435061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603400	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	23	232	0	ENST00000266497.5:c.46G>A	p.Glu16Lys	p.E16K	ENST00000266497		16	Gaa/Aaa	1/31	1	2	FACETS	0.327	0.256	0.409	0.327	0.256	0.409	SUBCLONAL	1	TRUE	1	0.62	2		232	227	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218483	1218483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775595174	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	188	458	1	ENST00000326873.7:c.358G>A	p.Glu120Lys	p.E120K	ENST00000326873	NM_000455.4	120	Gaa/Aaa	2/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.62	2		459	506	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841178	15841178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753128407	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	37	376	1	ENST00000307771.7:c.1262G>A	p.Arg421Gln	p.R421Q	ENST00000307771	NM_005089.3	421	cGa/cAa	11/11	1	2	FACETS	0.287	0.236	0.343	0.287	0.236	0.343	SUBCLONAL	1	TRUE	1	0.62	2		377	416	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916220	9916220	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1445802934	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	141	423	0	ENST00000330684.3:c.2069C>T	p.Thr690Met	p.T690M	ENST00000330684	NM_001134407.1	690	aCg/aTg	10/13	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.62	2		423	409	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746018	162746018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	108	327	1	ENST00000367921.3:c.2141G>A	p.Arg714Gln	p.R714Q	ENST00000367921	NM_006182.2	714	cGa/cAa	16/18	1	2	FACETS	0.987	0.895	1	0.987	0.895	1	CLONAL	1	TRUE	1	0.62	2		328	353	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286805	212286805	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	84	226	0	ENST00000342788.4:c.2891G>T	p.Arg964Ile	p.R964I	ENST00000342788	NM_005235.2	964	aGa/aTa	24/28	1	2	FACETS	0.839	0.748	0.934	0.839	0.748	0.934	CLONAL	1	TRUE	1	0.62	2		226	323	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11167549	11167549	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	19	222	0	ENST00000361445.4:c.7643T>C	p.Phe2548Ser	p.F2548S	ENST00000361445	NM_004958.3	2548	tTc/tCc	58/58	1	2	FACETS	0.275	0.209	0.352	0.275	0.209	0.352	SUBCLONAL	1	TRUE	1	0.62	2		222	223	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851255	156851255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1480681042	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	50	842	0	ENST00000524377.1:c.2212G>A	p.Asp738Asn	p.D738N	ENST00000524377	NM_002529.3	738	Gac/Aac	17/17	1	2	FACETS	0.246	0.208	0.288	0.246	0.208	0.288	SUBCLONAL	1	TRUE	1	0.62	2		842	656	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131106	55131106	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	35	411	0	ENST00000257290.5:c.649G>T	p.Glu217Ter	p.E217*	ENST00000257290	NM_006206.4	217	Gaa/Taa	5/23	1	2	FACETS	0.251	0.206	0.303	0.251	0.206	0.303	SUBCLONAL	1	TRUE	1	0.62	2		411	449	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134988	41134988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	22	194	0	ENST00000379561.5:c.640C>T	p.Arg214Cys	p.R214C	ENST00000379561	NM_002015.3	214	Cgt/Tgt	2/3	1	2	FACETS	0.305	0.237	0.383	0.305	0.237	0.383	SUBCLONAL	1	TRUE	1	0.62	2		194	233	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916843	48916843	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	16	233	0	ENST00000267163.4:c.373G>T	p.Glu125Ter	p.E125*	ENST00000267163	NM_000321.2	125	Gaa/Taa	3/27	1	2	FACETS	0.204	0.15	0.268	0.204	0.15	0.268	SUBCLONAL	1	TRUE	1	0.62	2		233	253	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412095	63412095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852217	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	273	802	1	ENST00000330258.3:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000330258	NM_152424.3	358	Cga/Tga	2/2	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.62	2		803	767	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	25	250	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.279	0.22	0.347	0.279	0.22	0.347	SUBCLONAL	1	TRUE	1	0.62	2		250	289	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149129	61149129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144119768	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	46	319	0	ENST00000295025.8:c.1319C>T	p.Ser440Leu	p.S440L	ENST00000295025	NM_002908.2	440	tCg/tTg	11/11	1	2	FACETS	0.366	0.309	0.43	0.366	0.309	0.43	SUBCLONAL	1	TRUE	1	0.62	2		319	405	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589298	28589298	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	29	239	0	ENST00000241453.7:c.2749G>T	p.Glu917Ter	p.E917*	ENST00000241453	NM_004119.2	917	Gaa/Taa	22/24	1	2	FACETS	0.331	0.266	0.404	0.331	0.266	0.404	SUBCLONAL	1	TRUE	1	0.62	2		239	283	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914478	32914478	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358833	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	27	401	1	ENST00000380152.3:c.5986G>A	p.Ala1996Thr	p.A1996T	ENST00000380152		1996	Gca/Aca	11/27	1	2	FACETS	0.206	0.164	0.255	0.206	0.164	0.255	SUBCLONAL	1	TRUE	1	0.62	2		402	422	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961330	41961330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	43	339	0	ENST00000219905.7:c.238G>A	p.Asp80Asn	p.D80N	ENST00000219905	NM_001164273.1	80	Gat/Aat	2/24	1	2	FACETS	0.362	0.303	0.427	0.362	0.303	0.427	SUBCLONAL	1	TRUE	1	0.62	2		339	383	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937587	76937587	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	118	320	0	ENST00000373344.5:c.3161C>A	p.Ser1054Tyr	p.S1054Y	ENST00000373344	NM_000489.3	1054	tCt/tAt	9/35	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.62	2		320	321	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350146	89350146	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs575811373	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	282	836	0	ENST00000301030.4:c.2804C>T	p.Ser935Leu	p.S935L	ENST00000301030	NM_001256183.1	935	tCg/tTg	9/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.62	2		836	814	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131412	202131412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339962485	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	99	408	0	ENST00000358485.4:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000358485	NM_001080125.1	127	cGa/cAa	2/9	1	2	FACETS	0.741	0.665	0.82	0.741	0.665	0.82	SUBCLONAL	1	TRUE	1	0.62	2		408	431	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812335	212812335	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	25	220	0	ENST00000342788.4:c.241C>T	p.Arg81Ter	p.R81*	ENST00000342788	NM_005235.2	81	Cga/Tga	3/28	1	2	FACETS	0.32	0.253	0.397	0.32	0.253	0.397	SUBCLONAL	1	TRUE	1	0.62	2		220	252	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763965	76763965	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	237	587	0	ENST00000373344.5:c.7343C>A	p.Pro2448His	p.P2448H	ENST00000373344	NM_000489.3	2448	cCt/cAt	35/35	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.62	2		587	584	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698180	47698180	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63751411	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	8	187	0	ENST00000233146.2:c.1738G>T	p.Glu580Ter	p.E580*	ENST00000233146	NM_000251.2	580	Gaa/Taa	11/16	1	2	FACETS	0.101	0.064	0.148	0.101	0.064	0.148	SUBCLONAL	1	TRUE	1	0.62	2		187	256	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510153	187510153	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367799188	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	170	493	0	ENST00000441802.2:c.13360G>A	p.Glu4454Lys	p.E4454K	ENST00000441802	NM_005245.3	4454	Gaa/Aaa	27/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.62	2		493	482	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715410	117715410	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769599473	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	122	245	0	ENST00000368508.3:c.1079G>T	p.Arg360Ile	p.R360I	ENST00000368508	NM_002944.2	360	aGa/aTa	10/43	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.62	2		245	308	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545740	106545740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	145	416	0	ENST00000359195.3:c.3217G>A	p.Glu1073Lys	p.E1073K	ENST00000359195	NM_002649.2	1073	Gaa/Aaa	11/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.62	2		416	460	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609467	81609467	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	151	353	1	ENST00000298171.2:c.1065C>A	p.Phe355Leu	p.F355L	ENST00000298171	NM_000369.2	355	ttC/ttA	10/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.62	2		354	360	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245825	41245825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397508902	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	174	436	1	ENST00000357654.3:c.1723G>A	p.Glu575Lys	p.E575K	ENST00000357654	NM_007294.3	575	Gaa/Aaa	10/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.62	2		437	453	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306638	41306638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	217	786	0	ENST00000373198.4:c.1021G>A	p.Asp341Asn	p.D341N	ENST00000373198	NM_133170.3	341	Gac/Aac	7/32	0.121113281179045	0	FACETS	0.429	0.401	0.457			1	INDETERMINATE	1	TRUE	0	0.62	0		786	620	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876618	59876618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	22	321	0	ENST00000259008.2:c.1183G>A	p.Ala395Thr	p.A395T	ENST00000259008	NM_032043.2	395	Gct/Act	9/20	1	2	FACETS	0.192	0.148	0.243	0.192	0.148	0.243	SUBCLONAL	1	TRUE	1	0.62	2		321	370	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61709651	61709651	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	65	155	0	ENST00000401558.2:c.2836C>A	p.Leu946Ile	p.L946I	ENST00000401558	NM_003400.3	946	Ctt/Att	23/25	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.62	2		155	202	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197845	66197845	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	78	203	0	ENST00000273854.3:c.2854G>T	p.Val952Leu	p.V952L	ENST00000273854	NM_004439.5	952	Gta/Tta	17/18	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.62	2		203	219	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808917	3808917	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	169	564	0	ENST00000262367.5:c.3307C>T	p.Arg1103Ter	p.R1103*	ENST00000262367	NM_004380.2	1103	Cga/Tga	17/31	1	2	FACETS	0.829	0.764	0.895	0.829	0.764	0.895	CLONAL	1	TRUE	1	0.62	2		564	658	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15978955	15978955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779823128	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	54	428	0	ENST00000268712.3:c.3563C>T	p.Ser1188Leu	p.S1188L	ENST00000268712	NM_006311.3	1188	tCg/tTg	27/46	1	2	FACETS	0.354	0.302	0.41	0.354	0.302	0.41	SUBCLONAL	1	TRUE	1	0.62	2		428	492	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765576	41765576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763066660	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	85	653	0	ENST00000301178.4:c.2452G>A	p.Glu818Lys	p.E818K	ENST00000301178	NM_021913.4	818	Gaa/Aaa	20/20	1	2	FACETS	0.439	0.389	0.494	0.439	0.389	0.494	SUBCLONAL	1	TRUE	1	0.62	2		653	624	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39706272	39706272	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	57	206	0	ENST00000361337.2:c.330C>A	p.Phe110Leu	p.F110L	ENST00000361337	NM_003286.2	110	ttC/ttA	5/21	0.121113281179045	0	FACETS	0.356	0.31	0.405			1	INDETERMINATE	1	TRUE	0	0.62	0		206	196	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164712	36164712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	295	991	1	ENST00000300305.3:c.1163C>T	p.Ser388Leu	p.S388L	ENST00000300305		388	tCg/tTg	8/8	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.62	2		992	834	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681437	88681437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35619497	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	66	610	1	ENST00000372037.3:c.1327C>T	p.Arg443Cys	p.R443C	ENST00000372037	NM_004329.2	443	Cgt/Tgt	11/13	1	2	FACETS	0.283	0.245	0.324	0.283	0.245	0.324	SUBCLONAL	1	TRUE	1	0.62	2		611	753	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87322770	87322770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781137734	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	24	306	0	ENST00000277120.3:c.371G>A	p.Arg124Gln	p.R124Q	ENST00000277120		124	cGa/cAa	5/19	1	2	FACETS	0.212	0.165	0.265	0.212	0.165	0.265	SUBCLONAL	1	TRUE	1	0.62	2		306	366	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348715	89348715	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs578198369	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	301	786	0	ENST00000301030.4:c.4235T>C	p.Ile1412Thr	p.I1412T	ENST00000301030	NM_001256183.1	1412	aTa/aCa	9/13	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.62	2		786	857	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685281	89685281	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	51	144	0	ENST00000371953.3:c.176C>A	p.Ser59Ter	p.S59*	ENST00000371953	NM_000314.4	59	tCa/tAa	3/9	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.62	2		144	147	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956553	93956553	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1035177735	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	38	267	0	ENST00000369303.4:c.2683C>T	p.Arg895Ter	p.R895*	ENST00000369303	NM_004440.3	895	Cga/Tga	15/17	1	2	FACETS	0.395	0.328	0.47	0.395	0.328	0.47	SUBCLONAL	1	TRUE	1	0.62	2		267	310	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696421	47696421	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	144	415	1	ENST00000347630.2:c.402G>T	p.Lys134Asn	p.K134N	ENST00000347630	NM_001007230.1	134	aaG/aaT	6/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.62	2		416	402	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374251	138374251	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	150	438	0	ENST00000289153.2:c.3193C>T	p.Arg1065Trp	p.R1065W	ENST00000289153	NM_006219.2	1065	Cgg/Tgg	22/22	0.3	1	FACETS	0.701	0.646	0.758	0.701	0.646	0.758	INDETERMINATE	1	TRUE	0	0.62	1		438	476	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250046	53250046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1569282235	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	67	545	0	ENST00000375401.3:c.203G>A	p.Arg68Gln	p.R68Q	ENST00000375401	NM_004187.3	68	cGa/cAa	2/26	1	2	FACETS	0.334	0.29	0.382	0.334	0.29	0.382	SUBCLONAL	1	TRUE	1	0.62	2		545	647	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549127	87549127	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	47	457	0	ENST00000277120.3:c.1684G>A	p.Glu562Lys	p.E562K	ENST00000277120		562	Gaa/Aaa	15/19	1	2	FACETS	0.33	0.278	0.386	0.33	0.278	0.386	SUBCLONAL	1	TRUE	1	0.62	2		457	460	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714387	40714387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1441976520	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	129	432	2	ENST00000373198.4:c.4010G>A	p.Arg1337His	p.R1337H	ENST00000373198	NM_133170.3	1337	cGc/cAc	29/32	0.121113281179045	0	FACETS	0.379	0.347	0.413			1	INDETERMINATE	1	TRUE	0	0.62	0		434	417	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589618	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519838	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	66	161	0	ENST00000274335.5:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000274335		461	Cga/Tga	10/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.62	2		161	174	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212216	98212216	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	23	197	0	ENST00000331920.6:c.3456C>A	p.Phe1152Leu	p.F1152L	ENST00000331920	NM_000264.3	1152	ttC/ttA	21/24	1	2	FACETS	0.34	0.266	0.425	0.34	0.266	0.425	SUBCLONAL	1	TRUE	1	0.62	2		197	218	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363589	40363589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1328955180	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	63	503	0	ENST00000397332.2:c.640C>T	p.Arg214Trp	p.R214W	ENST00000397332	NM_001033082.2	214	Cgg/Tgg	3/3	1	2	FACETS	0.397	0.343	0.455	0.397	0.343	0.455	SUBCLONAL	1	TRUE	1	0.62	2		503	512	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291528	10291528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755995375	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	155	410	0	ENST00000340748.4:c.151G>A	p.Glu51Lys	p.E51K	ENST00000340748		51	Gaa/Aaa	3/40	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.62	2		410	407	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922300	178922300	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	20	269	0	ENST00000263967.3:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000263967	NM_006218.2	357	Cga/Tga	6/21	1	2	FACETS	0.171	0.13	0.218	0.171	0.13	0.218	SUBCLONAL	1	TRUE	1	0.62	2		269	378	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181425	185181425	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1435276633	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	166	354	0	ENST00000265026.3:c.1366C>T	p.Arg456Ter	p.R456*	ENST00000265026	NM_004721.4	456	Cga/Tga	8/14	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.62	2		354	391	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55603385	55603385	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	29	264	0	ENST00000288135.5:c.2741G>T	p.Arg914Ile	p.R914I	ENST00000288135	NM_000222.2	914	aGa/aTa	20/21	1	2	FACETS	0.482	0.39	0.585	0.482	0.39	0.585	SUBCLONAL	1	TRUE	1	0.62	2		264	194	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793432	18793432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187869576	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	28	305	0	ENST00000266497.5:c.4129C>T	p.Arg1377Cys	p.R1377C	ENST00000266497		1377	Cgt/Tgt	30/31	1	2	FACETS	0.232	0.185	0.286	0.232	0.185	0.286	SUBCLONAL	1	TRUE	1	0.62	2		305	389	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763428	59763428	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	50	454	0	ENST00000259008.2:c.2674C>A	p.Leu892Ile	p.L892I	ENST00000259008	NM_032043.2	892	Ctt/Att	19/20	1	2	FACETS	0.334	0.283	0.39	0.334	0.283	0.39	SUBCLONAL	1	TRUE	1	0.62	2		454	483	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39713125	39713125	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	13	115	0	ENST00000361337.2:c.531G>T	p.Lys177Asn	p.K177N	ENST00000361337	NM_003286.2	177	aaG/aaT	8/21	0.121113281179045	0	FACETS	0.112	0.08	0.151			1	INDETERMINATE	1	TRUE	0	0.62	0		115	142	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157539	106157539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs192553789	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	52	213	0	ENST00000380013.4:c.2440C>T	p.Arg814Cys	p.R814C	ENST00000380013	NM_001127208.2	814	Cgt/Tgt	3/11	1	2	FACETS	0.674	0.579	0.775	0.674	0.579	0.775	SUBCLONAL	1	TRUE	1	0.62	2		213	249	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194110	94194110	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773469981	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	30	297	0	ENST00000323929.3:c.1318G>A	p.Ala440Thr	p.A440T	ENST00000323929	NM_005591.3	440	Gca/Aca	12/20	1	2	FACETS	0.232	0.186	0.283	0.232	0.186	0.283	SUBCLONAL	1	TRUE	1	0.62	2		297	418	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696653	47696653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866898949	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	137	390	0	ENST00000347630.2:c.295C>T	p.Arg99Trp	p.R99W	ENST00000347630	NM_001007230.1	99	Cgg/Tgg	5/11	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.62	2		390	442	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050414	176050414	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148950158	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	103	253	0	ENST00000367669.3:c.1151G>A	p.Arg384Gln	p.R384Q	ENST00000367669	NM_022457.5	384	cGa/cAa	11/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.62	2		253	279	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562984	176562984	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	69	311	0	ENST00000439151.2:c.880G>T	p.Glu294Ter	p.E294*	ENST00000439151	NM_022455.4	294	Gaa/Taa	2/23	1	2	FACETS	0.484	0.422	0.55	0.484	0.422	0.55	SUBCLONAL	1	TRUE	1	0.62	2		311	460	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285871	87285871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408094711	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	140	466	0	ENST00000277120.3:c.208G>A	p.Glu70Lys	p.E70K	ENST00000277120		70	Gaa/Aaa	2/19	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.62	2		466	440	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845627	63845627	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	55	162	0	ENST00000279873.7:c.1366G>T	p.Glu456Ter	p.E456*	ENST00000279873	NM_032199.2	456	Gaa/Taa	9/10	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.62	2		162	176	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864193	57864193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746398371	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	70	638	1	ENST00000228682.2:c.1670G>A	p.Arg557His	p.R557H	ENST00000228682	NM_005269.2	557	cGc/cAc	12/12	1	2	FACETS	0.368	0.32	0.419	0.368	0.32	0.419	SUBCLONAL	1	TRUE	1	0.62	2		639	614	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549116	21549116	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	50	488	1	ENST00000382592.4:c.3160C>T	p.Arg1054Ter	p.R1054*	ENST00000382592	NM_014572.2	1054	Cga/Tga	8/8	1	2	FACETS	0.33	0.28	0.385	0.33	0.28	0.385	SUBCLONAL	1	TRUE	1	0.62	2		489	489	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541679	187541679	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs185406112	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	115	288	0	ENST00000441802.2:c.6061C>T	p.Arg2021Cys	p.R2021C	ENST00000441802	NM_005245.3	2021	Cgc/Tgc	10/27	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.62	2		288	312	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61713094	61713094	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1272790060	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	14	209	0	ENST00000401558.2:c.2317G>A	p.Ala773Thr	p.A773T	ENST00000401558	NM_003400.3	773	Gct/Act	20/25	1	2	FACETS	0.229	0.166	0.306	0.229	0.166	0.306	SUBCLONAL	1	TRUE	1	0.62	2		209	197	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763235	59763235	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	165	446	0	ENST00000259008.2:c.2867C>A	p.Ser956Ter	p.S956*	ENST00000259008	NM_032043.2	956	tCa/tAa	19/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.62	2		446	459	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945543	54945543	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs774552788	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	262	768	2	ENST00000312783.6:c.1027C>T	p.Arg343Trp	p.R343W	ENST00000312783	NM_198436.1	343	Cgg/Tgg	9/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.62	2		770	793	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740750	58740750	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760201595	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	30	455	0	ENST00000305921.3:c.1655G>A	p.Arg552Gln	p.R552Q	ENST00000305921	NM_003620.3	552	cGa/cAa	6/6	1	2	FACETS	0.19	0.152	0.232	0.19	0.152	0.232	SUBCLONAL	1	TRUE	1	0.62	2		455	510	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465049	120465049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	25	341	1	ENST00000256646.2:c.5023C>T	p.Arg1675Cys	p.R1675C	ENST00000256646	NM_024408.3	1675	Cgc/Tgc	28/34	1	2	FACETS	0.242	0.191	0.301	0.242	0.191	0.301	SUBCLONAL	1	TRUE	1	0.62	2		342	333	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275649	41275649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	151	356	0	ENST00000349496.5:c.1544G>A	p.Arg515Gln	p.R515Q	ENST00000349496	NM_001904.3	515	cGa/cAa	10/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.62	2		356	418	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692978	89692978	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	104	419	0	ENST00000371953.3:c.462C>A	p.Phe154Leu	p.F154L	ENST00000371953	NM_000314.4	154	ttC/ttA	5/9	1	2	FACETS	0.826	0.745	0.911	0.826	0.745	0.911	CLONAL	1	TRUE	1	0.62	2		419	406	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044542	47044542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782739450	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	48	798	0	ENST00000377604.3:c.2039G>A	p.Arg680Gln	p.R680Q	ENST00000377604	NM_001204468.1	680	cGa/cAa	18/24	1	2	FACETS	0.231	0.195	0.271	0.231	0.195	0.271	SUBCLONAL	1	TRUE	1	0.62	2		798	670	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137360	202137360	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	21	227	0	ENST00000358485.4:c.589-1G>T		p.X197_splice	ENST00000358485	NM_001080125.1	197			1	2	FACETS	0.287	0.221	0.363	0.287	0.221	0.363	SUBCLONAL	1	TRUE	1	0.62	2		227	236	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39725963	39725963	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	22	205	0	ENST00000361337.2:c.834C>A	p.Phe278Leu	p.F278L	ENST00000361337	NM_003286.2	278	ttC/ttA	10/21	0.121113281179045	0	FACETS	0.102	0.079	0.129			1	INDETERMINATE	1	TRUE	0	0.62	0		205	264	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582935	95582935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs965350808	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	89	297	0	ENST00000393063.1:c.1607G>A	p.Arg536His	p.R536H	ENST00000393063	NM_030621.3	536	cGt/cAt	11/28	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.62	2		297	287	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134955	41134955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	36	263	0	ENST00000379561.5:c.673C>T	p.Arg225Cys	p.R225C	ENST00000379561	NM_002015.3	225	Cgt/Tgt	2/3	1	2	FACETS	0.387	0.319	0.463	0.387	0.319	0.463	SUBCLONAL	1	TRUE	1	0.62	2		263	300	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100016	11100016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749059769	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	224	677	1	ENST00000358026.2:c.1142G>A	p.Arg381Gln	p.R381Q	ENST00000358026	NM_001128849.1	381	cGa/cAa	7/36	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.62	2		678	682	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754304	57754304	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	122	328	0	ENST00000274289.3:c.547C>T	p.Arg183Ter	p.R183*	ENST00000274289	NM_006622.3	183	Cga/Tga	4/14	1	2	FACETS	0.984	0.897	1	0.984	0.897	1	CLONAL	1	TRUE	1	0.62	2		328	400	SUCCESS
APC	324	MSKCC	GRCh37	5	112176278	112176278	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758987855	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	35	305	0	ENST00000257430.4:c.4987G>A	p.Glu1663Lys	p.E1663K	ENST00000257430	NM_000038.5	1663	Gaa/Aaa	16/16	1	2	FACETS	0.346	0.284	0.416	0.346	0.284	0.416	SUBCLONAL	1	TRUE	1	0.62	2		305	326	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047941	180047941	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs184409663	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	122	953	1	ENST00000261937.6:c.2234G>A	p.Arg745His	p.R745H	ENST00000261937	NM_182925.4	745	cGc/cAc	15/30	1	2	FACETS	0.457	0.413	0.504	0.457	0.413	0.504	SUBCLONAL	1	TRUE	1	0.62	2		954	861	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340344	8340344	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	44	386	0	ENST00000356435.5:c.5252G>T	p.Arg1751Ile	p.R1751I	ENST00000356435		1751	aGa/aTa	31/35	1	2	FACETS	0.318	0.267	0.375	0.318	0.267	0.375	SUBCLONAL	1	TRUE	1	0.62	2		386	446	SUCCESS
CBL	867	MSKCC	GRCh37	11	119145620	119145620	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755244263	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	121	318	1	ENST00000264033.4:c.826G>A	p.Glu276Lys	p.E276K	ENST00000264033	NM_005188.3	276	Gaa/Aaa	5/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.62	2		319	350	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86648999	86648999	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs975191415	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	75	225	0	ENST00000274376.6:c.1279C>T	p.Arg427Ter	p.R427*	ENST00000274376	NM_002890.2	427	Cga/Tga	9/25	1	2	FACETS	0.979	0.87	1	0.979	0.87	1	CLONAL	1	TRUE	1	0.62	2		225	247	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123040864	123040864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1489246570	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	235	727	0	ENST00000355640.3:c.1327C>T	p.Arg443Cys	p.R443C	ENST00000355640		443	Cgc/Tgc	7/7	1	2	FACETS	0.972	0.91	1	0.972	0.91	1	CLONAL	1	TRUE	1	0.62	2		727	780	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971099	21971099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749714198	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	87	481	0	ENST00000304494.5:c.259C>T	p.Arg87Trp	p.R87W	ENST00000304494	NM_000077.4	87	Cgg/Tgg	2/3	1	2	FACETS	0.509	0.452	0.571	0.509	0.452	0.571	SUBCLONAL	1	TRUE	1	0.62	2		481	551	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220555	123220555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	175	481	0	ENST00000218089.9:c.3212G>A	p.Arg1071Gln	p.R1071Q	ENST00000218089	NM_001042749.1	1071	cGg/cAg	30/35	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.62	2		481	471	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128989	64128989	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	60	755	0	ENST00000334205.4:c.619G>A	p.Glu207Lys	p.E207K	ENST00000334205	NM_003942.2	207	Gaa/Aaa	6/17	1	2	FACETS	0.283	0.243	0.326	0.283	0.243	0.326	SUBCLONAL	1	TRUE	1	0.62	2		755	684	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937220	76937220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	166	446	0	ENST00000373344.5:c.3528G>T	p.Lys1176Asn	p.K1176N	ENST00000373344	NM_000489.3	1176	aaG/aaT	9/35	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.62	2		446	431	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40789994	40789994	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs746391800	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	57	470	2	ENST00000373198.4:c.2737G>A	p.Glu913Lys	p.E913K	ENST00000373198	NM_133170.3	913	Gag/Aag	18/32	0.121113281179045	0	FACETS	0.17	0.146	0.196			1	INDETERMINATE	1	TRUE	0	0.62	0		472	411	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526582	106526582	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	101	295	0	ENST00000359195.3:c.2875A>C	p.Asn959His	p.N959H	ENST00000359195	NM_002649.2	959	Aac/Cac	10/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.62	2		295	292	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212215	36212215	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1010777622	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	37	733	0	ENST00000222270.7:c.1966G>A	p.Glu656Lys	p.E656K	ENST00000222270	NM_014727.1	656	Gaa/Aaa	3/37	1	2	FACETS	0.192	0.157	0.23	0.192	0.157	0.23	SUBCLONAL	1	TRUE	1	0.62	2		733	623	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020225	123020225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	34	515	1	ENST00000355640.3:c.713G>A	p.Arg238Gln	p.R238Q	ENST00000355640		238	cGa/cAa	2/7	1	2	FACETS	0.209	0.17	0.253	0.209	0.17	0.253	SUBCLONAL	1	TRUE	1	0.62	2		516	524	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536873	120536873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	41	688	1	ENST00000229340.5:c.313G>A	p.Glu105Lys	p.E105K	ENST00000229340	NM_006861.6	105	Gaa/Aaa	4/6	1	2	FACETS	0.197	0.163	0.234	0.197	0.163	0.234	SUBCLONAL	1	TRUE	1	0.62	2		689	672	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36014498	36014498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	39	610	2	ENST00000358208.4:c.271G>A	p.Ala91Thr	p.A91T	ENST00000358208		91	Gcc/Acc	3/12	0.121113281179045	0	FACETS	0.077	0.063	0.092			1	INDETERMINATE	1	TRUE	0	0.62	0		612	624	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193116996	193116996	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	116	218	0	ENST00000367435.3:c.730-1G>T		p.X244_splice	ENST00000367435	NM_024529.4	244			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.62	2		218	309	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134924	41134924	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	29	321	0	ENST00000379561.5:c.704C>A	p.Ser235Tyr	p.S235Y	ENST00000379561	NM_002015.3	235	tCt/tAt	2/3	1	2	FACETS	0.261	0.209	0.319	0.261	0.209	0.319	SUBCLONAL	1	TRUE	1	0.62	2		321	359	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276929	123276929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200204947	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	129	280	0	ENST00000358487.5:c.988C>T	p.Arg330Trp	p.R330W	ENST00000358487	NM_000141.4	330	Cgg/Tgg	8/18	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.62	2		280	348	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050676	30050676	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150667239	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	133	395	0	ENST00000338641.4:c.478C>T	p.Arg160Trp	p.R160W	ENST00000338641	NM_000268.3	160	Cgg/Tgg	5/16	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.62	2		395	406	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931826	68931826	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs759461290	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	68	447	0	ENST00000288368.4:c.256G>T	p.Glu86Ter	p.E86*	ENST00000288368	NM_024870.2	86	Gaa/Taa	3/40	1	2	FACETS	0.402	0.35	0.459	0.402	0.35	0.459	SUBCLONAL	1	TRUE	1	0.62	2		447	545	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745581	162745581	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	131	398	0	ENST00000367921.3:c.1996C>A	p.Leu666Ile	p.L666I	ENST00000367921	NM_006182.2	666	Ctt/Att	15/18	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.62	2		398	408	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915295	32915295	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	174	545	1	ENST00000380152.3:c.6803G>T	p.Arg2268Ile	p.R2268I	ENST00000380152		2268	aGa/aTa	11/27	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.62	2		546	503	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271269	153271269	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	19	149	0	ENST00000281708.4:c.509G>T	p.Arg170Ile	p.R170I	ENST00000281708	NM_033632.3	170	aGa/aTa	3/12	1	2	FACETS	0.35	0.267	0.447	0.35	0.267	0.447	SUBCLONAL	1	TRUE	1	0.62	2		149	175	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176469	123176469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	23	215	0	ENST00000218089.9:c.436C>T	p.Arg146Ter	p.R146*	ENST00000218089	NM_001042749.1	146	Cga/Tga	7/35	1	2	FACETS	0.257	0.2	0.322	0.257	0.2	0.322	SUBCLONAL	1	TRUE	1	0.62	2		215	289	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273878	10273878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	233	762	3	ENST00000330684.3:c.391G>A	p.Ala131Thr	p.A131T	ENST00000330684	NM_001134407.1	131	Gca/Aca	2/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.62	2		765	702	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344458	118344458	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	33	230	0	ENST00000534358.1:c.2584C>T	p.Arg862Ter	p.R862*	ENST00000534358	NM_005933.3	862	Cga/Tga	3/36	1	2	FACETS	0.406	0.332	0.489	0.406	0.332	0.489	SUBCLONAL	1	TRUE	1	0.62	2		230	262	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910306	50910306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1341055535	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	202	919	1	ENST00000440232.2:c.1561C>T	p.Arg521Trp	p.R521W	ENST00000440232	NM_002691.3	521	Cgg/Tgg	13/27	1	2	FACETS	0.813	0.756	0.873	0.813	0.756	0.873	CLONAL	1	TRUE	1	0.62	2		920	801	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248565	212248565	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	190	519	0	ENST00000342788.4:c.3702G>T	p.Lys1234Asn	p.K1234N	ENST00000342788	NM_005235.2	1234	aaG/aaT	28/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.62	2		519	557	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934254	48934254	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1131690904	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	23	294	0	ENST00000267163.4:c.709G>T	p.Glu237Ter	p.E237*	ENST00000267163	NM_000321.2	237	Gaa/Taa	7/27	1	2	FACETS	0.232	0.18	0.291	0.232	0.18	0.291	SUBCLONAL	1	TRUE	1	0.62	2		294	320	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716095	243716095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	29	381	0	ENST00000263826.5:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000263826	NM_005465.4	367	Cga/Tga	10/13	1	2	FACETS	0.207	0.165	0.254	0.207	0.165	0.254	SUBCLONAL	1	TRUE	1	0.62	2		381	453	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652274	48652274	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	244	794	1	ENST00000376670.3:c.945G>T	p.Lys315Asn	p.K315N	ENST00000376670	NM_002049.3	315	aaG/aaT	6/6	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.62	2		795	734	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197281	106197281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	97	309	0	ENST00000380013.4:c.5614C>T	p.Leu1872Phe	p.L1872F	ENST00000380013	NM_001127208.2	1872	Ctc/Ttc	11/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.62	2		309	282	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349688	70349688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	62	581	0	ENST00000374080.3:c.3850C>T	p.Arg1284Cys	p.R1284C	ENST00000374080		1284	Cgc/Tgc	27/45	1	2	FACETS	0.385	0.333	0.442	0.385	0.333	0.442	SUBCLONAL	1	TRUE	1	0.62	2		581	519	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192078	108192078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200431631	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	177	432	1	ENST00000278616.4:c.6503C>T	p.Ser2168Leu	p.S2168L	ENST00000278616	NM_000051.3	2168	tCg/tTg	45/63	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.62	2		433	555	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828372	72828372	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	225	488	0	ENST00000268489.5:c.8209G>T	p.Glu2737Ter	p.E2737*	ENST00000268489	NM_006885.3	2737	Gaa/Taa	9/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.62	2		488	590	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230538	46230538	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	92	302	0	ENST00000334344.6:c.787G>T	p.Glu263Ter	p.E263*	ENST00000334344	NM_152641.2	263	Gaa/Taa	8/21	1	2	FACETS	0.813	0.728	0.902	0.813	0.728	0.902	CLONAL	1	TRUE	1	0.62	2		302	365	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741894	40741894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs930976777	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	99	830	3	ENST00000392038.2:c.1078G>A	p.Glu360Lys	p.E360K	ENST00000392038	NM_001626.4	360	Gag/Aag	11/14	1	2	FACETS	0.442	0.394	0.492	0.442	0.394	0.492	SUBCLONAL	1	TRUE	1	0.62	2		833	723	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244451	41244451	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs273899698	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	33	476	0	ENST00000357654.3:c.3097G>T	p.Glu1033Ter	p.E1033*	ENST00000357654	NM_007294.3	1033	Gaa/Taa	10/23	1	2	FACETS	0.212	0.172	0.257	0.212	0.172	0.257	SUBCLONAL	1	TRUE	1	0.62	2		476	503	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406078	70406078	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	36	450	0	ENST00000373644.4:c.3592T>G	p.Phe1198Val	p.F1198V	ENST00000373644	NM_030625.2	1198	Ttt/Gtt	4/12	1	2	FACETS	0.236	0.194	0.284	0.236	0.194	0.284	SUBCLONAL	1	TRUE	1	0.62	2		450	492	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990354	81990354	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	41	457	0	ENST00000359376.3:c.3625G>T	p.Glu1209Ter	p.E1209*	ENST00000359376	NM_002661.3	1209	Gaa/Taa	32/33	1	2	FACETS	0.277	0.23	0.328	0.277	0.23	0.328	SUBCLONAL	1	TRUE	1	0.62	2		457	478	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515591	31515591	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	19	299	0	ENST00000344624.3:c.1028C>A	p.Ser343Tyr	p.S343Y	ENST00000344624		343	tCt/tAt	4/33	1	2	FACETS	0.169	0.128	0.217	0.169	0.128	0.217	SUBCLONAL	1	TRUE	1	0.62	2		299	363	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729363	41729363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	58	537	0	ENST00000242208.4:c.1166C>T	p.Ser389Leu	p.S389L	ENST00000242208	NM_002192.2	389	tCg/tTg	3/3	1	2	FACETS	0.339	0.291	0.391	0.339	0.291	0.391	SUBCLONAL	1	TRUE	1	0.62	2		537	552	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458329	12458329	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1364613522	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	79	561	0	ENST00000287820.6:c.946C>T	p.Arg316Cys	p.R316C	ENST00000287820	NM_015869.4	316	Cgc/Tgc	6/7	1	2	FACETS	0.442	0.389	0.499	0.442	0.389	0.499	SUBCLONAL	1	TRUE	1	0.62	2		561	576	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146680	185146680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770162461	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	48	482	1	ENST00000265026.3:c.311C>T	p.Thr104Met	p.T104M	ENST00000265026	NM_004721.4	104	aCg/aTg	2/14	1	2	FACETS	0.298	0.251	0.349	0.298	0.251	0.349	SUBCLONAL	1	TRUE	1	0.62	2		483	520	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816896	32816896	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1159721335	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	216	375	0	ENST00000354258.4:c.1429-1G>T		p.X477_splice	ENST00000354258	NM_000593.5	477			1	2	FACETS	0.937	0.887	0.985	1	0.995	1	CLONAL	2	TRUE	1	0.62	2		375	372	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70967581	70967581	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	49	508	2	ENST00000276594.2:c.1442G>A	p.Arg481Gln	p.R481Q	ENST00000276594	NM_024504.3	481	cGa/cAa	7/8	1	2	FACETS	0.292	0.247	0.342	0.292	0.247	0.342	SUBCLONAL	1	TRUE	1	0.62	2		510	541	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528496	157528496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149978361	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	230	542	1	ENST00000346085.5:c.6221C>T	p.Ser2074Leu	p.S2074L	ENST00000346085	NM_020732.3	2074	tCg/tTg	20/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.62	2		543	581	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267470	7267470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1240458376	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	58	501	0	ENST00000302850.5:c.538G>A	p.Glu180Lys	p.E180K	ENST00000302850	NM_000208.2	180	Gag/Aag	2/22	1	2	FACETS	0.315	0.27	0.364	0.315	0.27	0.364	SUBCLONAL	1	TRUE	1	0.62	2		501	594	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241717	55241717	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762494280	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	199	540	0	ENST00000275493.2:c.2165C>T	p.Ala722Val	p.A722V	ENST00000275493	NM_005228.3	722	gCg/gTg	18/28	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.62	2		540	530	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273210	55273210	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	150	528	0	ENST00000275493.2:c.3533C>T	p.Pro1178Leu	p.P1178L	ENST00000275493	NM_005228.3	1178	cCc/cTc	28/28	1	2	FACETS	0.903	0.83	0.978	0.903	0.83	0.978	CLONAL	1	TRUE	1	0.62	2		528	536	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453494	138453494	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1291010707	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	18	298	0	ENST00000289153.2:c.954G>T	p.Lys318Asn	p.K318N	ENST00000289153	NM_006219.2	318	aaG/aaT	5/22	1	2	FACETS	0.173	0.13	0.225	0.173	0.13	0.225	SUBCLONAL	1	TRUE	1	0.62	2		298	335	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818213	32818213	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs143800384	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	65	606	0	ENST00000354258.4:c.1312C>T	p.Arg438Ter	p.R438*	ENST00000354258	NM_000593.5	438	Cga/Tga	5/11	1	2	FACETS	0.332	0.287	0.38	0.332	0.287	0.38	SUBCLONAL	1	TRUE	1	0.62	2		606	632	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217654	7217654	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	54	397	0	ENST00000380728.2:c.273G>T	p.Lys91Asn	p.K91N	ENST00000380728		91	aaG/aaT	4/11	1	2	FACETS	0.358	0.306	0.415	0.358	0.306	0.415	SUBCLONAL	1	TRUE	1	0.62	2		397	487	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80021297	80021297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs963234468	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	29	295	0	ENST00000265081.6:c.1366G>A	p.Glu456Lys	p.E456K	ENST00000265081	NM_002439.4	456	Gaa/Aaa	9/24	1	2	FACETS	0.228	0.183	0.28	0.228	0.183	0.28	SUBCLONAL	1	TRUE	1	0.62	2		295	410	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916624	178916624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749956691	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	21	229	0	ENST00000263967.3:c.11G>A	p.Arg4Gln	p.R4Q	ENST00000263967	NM_006218.2	4	cGa/cAa	2/21	1	2	FACETS	0.271	0.209	0.343	0.271	0.209	0.343	SUBCLONAL	1	TRUE	1	0.62	2		229	250	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938397	76938397	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	37	509	0	ENST00000373344.5:c.2351C>A	p.Ser784Tyr	p.S784Y	ENST00000373344	NM_000489.3	784	tCt/tAt	9/35	1	2	FACETS	0.192	0.157	0.231	0.192	0.157	0.231	SUBCLONAL	1	TRUE	1	0.62	2		509	622	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277233	41277233	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	20	304	0	ENST00000349496.5:c.1702G>T	p.Glu568Ter	p.E568*	ENST00000349496	NM_001904.3	568	Gaa/Taa	11/15	1	2	FACETS	0.187	0.143	0.239	0.187	0.143	0.239	SUBCLONAL	1	TRUE	1	0.62	2		304	345	SUCCESS
APC	324	MSKCC	GRCh37	5	112175925	112175925	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs863225356	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	20	151	0	ENST00000257430.4:c.4634C>A	p.Ser1545Ter	p.S1545*	ENST00000257430	NM_000038.5	1545	tCa/tAa	16/16	1	2	FACETS	0.283	0.217	0.36	0.283	0.217	0.36	SUBCLONAL	1	TRUE	1	0.62	2		151	228	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864023	97864023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881729	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	46	462	0	ENST00000289081.3:c.1643G>A	p.Arg548Gln	p.R548Q	ENST00000289081	NM_000136.2	548	cGa/cAa	15/15	1	2	FACETS	0.274	0.23	0.322	0.274	0.23	0.322	SUBCLONAL	1	TRUE	1	0.62	2		462	542	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992692	68992692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529924687	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	45	411	0	ENST00000288368.4:c.1657G>A	p.Glu553Lys	p.E553K	ENST00000288368	NM_024870.2	553	Gaa/Aaa	16/40	1	2	FACETS	0.319	0.268	0.375	0.319	0.268	0.375	SUBCLONAL	1	TRUE	1	0.62	2		411	455	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28971138	28971138	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	16	290	0	ENST00000282397.4:c.1619A>C	p.Lys540Thr	p.K540T	ENST00000282397	NM_002019.4	540	aAa/aCa	12/30	1	2	FACETS	0.181	0.133	0.238	0.181	0.133	0.238	SUBCLONAL	1	TRUE	1	0.62	2		290	285	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90627542	90627542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1222149957	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	39	689	0	ENST00000330062.3:c.1315G>A	p.Asp439Asn	p.D439N	ENST00000330062	NM_002168.2	439	Gac/Aac	11/11	1	2	FACETS	0.2	0.165	0.239	0.2	0.165	0.239	SUBCLONAL	1	TRUE	1	0.62	2		689	630	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429003	47429003	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	245	730	1	ENST00000377045.4:c.1366C>T	p.Arg456Ter	p.R456*	ENST00000377045	NM_001654.4	456	Cga/Tga	13/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.62	2		731	709	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781260	3781260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1275659601	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	126	1069	1	ENST00000262367.5:c.5105G>A	p.Arg1702His	p.R1702H	ENST00000262367	NM_004380.2	1702	cGc/cAc	30/31	1	2	FACETS	0.417	0.377	0.459	0.417	0.377	0.459	SUBCLONAL	1	TRUE	1	0.62	2		1070	975	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243030	105243030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1566818890	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	340	899	1	ENST00000349310.3:c.253G>A	p.Glu85Lys	p.E85K	ENST00000349310	NM_001014432.1	85	Gaa/Aaa	5/15	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.62	2		900	916	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321378	1321378	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	57	433	0	ENST00000400841.2:c.377G>T	p.Arg126Ile	p.R126I	ENST00000400841		126	aGa/aTa	4/6	1	2	FACETS	0.382	0.328	0.441	0.382	0.328	0.441	SUBCLONAL	1	TRUE	1	0.62	2		433	481	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198253	185198253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370479462	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	70	522	0	ENST00000265026.3:c.2735C>T	p.Ala912Val	p.A912V	ENST00000265026	NM_004721.4	912	gCc/gTc	13/14	1	2	FACETS	0.395	0.345	0.45	0.395	0.345	0.45	SUBCLONAL	1	TRUE	1	0.62	2		522	571	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29197723	29197723	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs774219516	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	48	811	0	ENST00000240100.2:c.471C>A	p.Phe157Leu	p.F157L	ENST00000240100	NM_001394.6	157	ttC/ttA	2/4	1	2	FACETS	0.213	0.179	0.25	0.213	0.179	0.25	SUBCLONAL	1	TRUE	1	0.62	2		811	727	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29083926	29083926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781710	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	48	245	0	ENST00000328354.6:c.1591G>A	p.Glu531Lys	p.E531K	ENST00000328354	NM_007194.3	531	Gag/Aag	15/15	1	2	FACETS	0.662	0.565	0.766	0.662	0.565	0.766	SUBCLONAL	1	TRUE	1	0.62	2		245	234	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62309674	62309674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs116495318	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	207	658	0	ENST00000360203.5:c.1012G>A	p.Asp338Asn	p.D338N	ENST00000360203	NM_001283009.1	338	Gac/Aac	12/35	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.62	2		658	582	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294126	1294126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	112	1114	1	ENST00000310581.5:c.875C>T	p.Thr292Met	p.T292M	ENST00000310581	NM_198253.2	292	aCg/aTg	2/16	1	2	FACETS	0.361	0.324	0.401	0.361	0.324	0.401	SUBCLONAL	1	TRUE	1	0.62	2		1115	1000	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988918	41988918	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	144	378	0	ENST00000219905.7:c.1710G>T	p.Lys570Asn	p.K570N	ENST00000219905	NM_001164273.1	570	aaG/aaT	3/24	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.62	2		378	453	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150022982	150022982	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	52	414	0	ENST00000253339.5:c.281C>A	p.Ser94Tyr	p.S94Y	ENST00000253339		94	tCt/tAt	1/7	1	2	FACETS	0.337	0.287	0.392	0.337	0.287	0.392	SUBCLONAL	1	TRUE	1	0.62	2		414	498	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243904	46243904	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	30	270	0	ENST00000334344.6:c.1998A>C	p.Gln666His	p.Q666H	ENST00000334344	NM_152641.2	666	caA/caC	15/21	1	2	FACETS	0.312	0.252	0.38	0.312	0.252	0.38	SUBCLONAL	1	TRUE	1	0.62	2		270	310	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740814	58740814	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	64	422	0	ENST00000305921.3:c.1719G>T	p.Lys573Asn	p.K573N	ENST00000305921	NM_003620.3	573	aaG/aaT	6/6	1	2	FACETS	0.401	0.347	0.459	0.401	0.347	0.459	SUBCLONAL	1	TRUE	1	0.62	2		422	515	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445055	89445055	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	102	360	0	ENST00000336596.2:c.1375G>T	p.Glu459Ter	p.E459*	ENST00000336596	NM_005233.5	459	Gaa/Taa	6/17	1	2	FACETS	0.88	0.794	0.969	0.88	0.794	0.969	CLONAL	1	TRUE	1	0.62	2		360	374	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22417932	22417932	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	17	172	0	ENST00000344548.3:c.498G>T	p.Lys166Asn	p.K166N	ENST00000344548	NM_001039802.1	166	aaG/aaT	7/7	1	2	FACETS	0.264	0.197	0.342	0.264	0.197	0.342	SUBCLONAL	1	TRUE	1	0.62	2		172	208	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243927	41243927	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	64	461	0	ENST00000357654.3:c.3621G>T	p.Lys1207Asn	p.K1207N	ENST00000357654	NM_007294.3	1207	aaG/aaT	10/23	1	2	FACETS	0.381	0.33	0.436	0.381	0.33	0.436	SUBCLONAL	1	TRUE	1	0.62	2		461	542	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202122998	202122998	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	57	427	0	ENST00000358485.4:c.44G>T	p.Arg15Ile	p.R15I	ENST00000358485	NM_001080125.1	15	aGa/aTa	1/9	1	2	FACETS	0.382	0.328	0.441	0.382	0.328	0.441	SUBCLONAL	1	TRUE	1	0.62	2		427	481	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190670376	190670376	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs760336651	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	80	229	0	ENST00000441310.2:c.316-2A>G		p.X106_splice	ENST00000441310	NM_000534.4	106			1	2	FACETS	0.893	0.795	0.996	0.893	0.795	0.996	CLONAL	1	TRUE	1	0.62	2		229	289	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80071530	80071530	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	25	206	0	ENST00000265081.6:c.2271G>T	p.Lys757Asn	p.K757N	ENST00000265081	NM_002439.4	757	aaG/aaT	16/24	1	2	FACETS	0.293	0.231	0.364	0.293	0.231	0.364	SUBCLONAL	1	TRUE	1	0.62	2		206	275	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170426	119170426	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1435757249	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	38	307	0	ENST00000264033.4:c.2656G>A	p.Glu886Lys	p.E886K	ENST00000264033	NM_005188.3	886	Gag/Aag	16/16	1	2	FACETS	0.304	0.251	0.363	0.304	0.251	0.363	SUBCLONAL	1	TRUE	1	0.62	2		307	403	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315354	30315354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1480541649	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	130	301	0	ENST00000322652.5:c.1039G>A	p.Glu347Lys	p.E347K	ENST00000322652	NM_015355.2	347	Gaa/Aaa	10/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.62	2		301	387	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321352	65321352	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	222	539	0	ENST00000342505.4:c.1488G>T	p.Lys496Asn	p.K496N	ENST00000342505	NM_002227.2	496	aaG/aaT	11/25	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.62	2		539	585	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551328	29551328	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	209	615	1	ENST00000389048.3:c.1302G>T	p.Lys434Asn	p.K434N	ENST00000389048	NM_004304.4	434	aaG/aaT	6/29	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.62	2		616	610	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29106017	29106017	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs749963436	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	26	253	1	ENST00000328354.6:c.823G>T	p.Glu275Ter	p.E275*	ENST00000328354	NM_007194.3	275	Gaa/Taa	7/15	1	2	FACETS	0.279	0.221	0.345	0.279	0.221	0.345	SUBCLONAL	1	TRUE	1	0.62	2		254	301	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026567	48026567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773226008	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	131	365	0	ENST00000234420.5:c.1445G>A	p.Arg482Gln	p.R482Q	ENST00000234420	NM_000179.2	482	cGa/cAa	4/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.62	2		365	345	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665375	182665375	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	18	160	0	ENST00000292782.4:c.566G>T	p.Arg189Ile	p.R189I	ENST00000292782	NM_020640.2	189	aGa/aTa	5/7	1	2	FACETS	0.274	0.207	0.353	0.274	0.207	0.353	SUBCLONAL	1	TRUE	1	0.62	2		160	212	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542914	187542914	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	18	179	0	ENST00000441802.2:c.4826C>A	p.Ser1609Tyr	p.S1609Y	ENST00000441802	NM_005245.3	1609	tCt/tAt	10/27	1	2	FACETS	0.237	0.178	0.306	0.237	0.178	0.306	SUBCLONAL	1	TRUE	1	0.62	2		179	245	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181803	56181803	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	103	248	0	ENST00000399503.3:c.4027G>T	p.Glu1343Ter	p.E1343*	ENST00000399503	NM_005921.1	1343	Gaa/Taa	17/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.62	2		248	296	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972606	32972606	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778694116	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	54	329	0	ENST00000380152.3:c.9956C>A	p.Ser3319Tyr	p.S3319Y	ENST00000380152		3319	tCt/tAt	27/27	1	2	FACETS	0.417	0.357	0.482	0.417	0.357	0.482	SUBCLONAL	1	TRUE	1	0.62	2		329	418	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191026	185191026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	233	679	0	ENST00000265026.3:c.1907C>A	p.Ser636Tyr	p.S636Y	ENST00000265026	NM_004721.4	636	tCt/tAt	11/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.62	2		679	679	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185512	27185512	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	37	432	0	ENST00000380036.4:c.1212C>A	p.Phe404Leu	p.F404L	ENST00000380036	NM_000459.3	404	ttC/ttA	9/23	1	2	FACETS	0.225	0.185	0.27	0.225	0.185	0.27	SUBCLONAL	1	TRUE	1	0.62	2		432	530	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541439	187541439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1246955615	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	22	284	0	ENST00000441802.2:c.6301C>T	p.Arg2101Cys	p.R2101C	ENST00000441802	NM_005245.3	2101	Cgc/Tgc	10/27	1	2	FACETS	0.198	0.153	0.25	0.198	0.153	0.25	SUBCLONAL	1	TRUE	1	0.62	2		284	359	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953926	32953926	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587780664	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	26	292	0	ENST00000380152.3:c.8993C>A	p.Ser2998Tyr	p.S2998Y	ENST00000380152		2998	tCt/tAt	23/27	1	2	FACETS	0.305	0.242	0.377	0.305	0.242	0.377	SUBCLONAL	1	TRUE	1	0.62	2		292	275	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31422949	31422949	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1257594254	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	35	478	0	ENST00000344624.3:c.3364C>T	p.Arg1122Ter	p.R1122*	ENST00000344624		1122	Cga/Tga	26/33	1	2	FACETS	0.197	0.161	0.238	0.197	0.161	0.238	SUBCLONAL	1	TRUE	1	0.62	2		478	573	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957774	1957774	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	73	603	1	ENST00000382891.5:c.2740G>A	p.Glu914Lys	p.E914K	ENST00000382891	NM_133335.3	914	Gag/Aag	15/22	1	2	FACETS	0.323	0.282	0.368	0.323	0.282	0.368	SUBCLONAL	1	TRUE	1	0.62	2		604	728	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763495	41763495	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868015563	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	40	447	0	ENST00000301178.4:c.2294G>A	p.Gly765Glu	p.G765E	ENST00000301178	NM_021913.4	765	gGa/gAa	19/20	1	2	FACETS	0.276	0.229	0.328	0.276	0.229	0.328	SUBCLONAL	1	TRUE	1	0.62	2		447	468	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176484	123176484	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	25	205	0	ENST00000218089.9:c.451G>T	p.Glu151Ter	p.E151*	ENST00000218089	NM_001042749.1	151	Gaa/Taa	7/35	1	2	FACETS	0.293	0.231	0.364	0.293	0.231	0.364	SUBCLONAL	1	TRUE	1	0.62	2		205	275	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467623	66467623	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	25	276	0	ENST00000273854.3:c.646G>T	p.Asp216Tyr	p.D216Y	ENST00000273854	NM_004439.5	216	Gat/Tat	3/18	1	2	FACETS	0.271	0.213	0.336	0.271	0.213	0.336	SUBCLONAL	1	TRUE	1	0.62	2		276	298	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020196	123020196	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	198	543	0	ENST00000355640.3:c.684C>A	p.Phe228Leu	p.F228L	ENST00000355640		228	ttC/ttA	2/7	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.62	2		543	587	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873204	71873204	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	116	331	0	ENST00000357731.5:c.990C>A	p.Phe330Leu	p.F330L	ENST00000357731	NM_173808.2	330	ttC/ttA	7/7	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.62	2		331	338	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920289	1920289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146822227	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	69	569	0	ENST00000382891.5:c.1349G>A	p.Arg450Gln	p.R450Q	ENST00000382891	NM_133335.3	450	cGa/cAa	5/22	1	2	FACETS	0.351	0.305	0.4	0.351	0.305	0.4	SUBCLONAL	1	TRUE	1	0.62	2		569	634	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488706	212488706	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	50	427	0	ENST00000342788.4:c.2143G>T	p.Glu715Ter	p.E715*	ENST00000342788	NM_005235.2	715	Gaa/Taa	18/28	1	2	FACETS	0.304	0.257	0.355	0.304	0.257	0.355	SUBCLONAL	1	TRUE	1	0.62	2		427	531	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266472	41266472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	122	314	0	ENST00000349496.5:c.269G>A	p.Arg90Gln	p.R90Q	ENST00000349496	NM_001904.3	90	cGa/cAa	4/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.62	2		314	341	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095761	178095761	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	51	323	0	ENST00000397062.3:c.1570G>T	p.Glu524Ter	p.E524*	ENST00000397062	NM_006164.4	524	Gaa/Taa	5/5	1	2	FACETS	0.467	0.399	0.542	0.467	0.399	0.542	SUBCLONAL	1	TRUE	1	0.62	2		323	352	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590878	95590878	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	25	271	0	ENST00000393063.1:c.1031T>G	p.Phe344Cys	p.F344C	ENST00000393063	NM_030621.3	344	tTt/tGt	9/28	1	2	FACETS	0.277	0.218	0.344	0.277	0.218	0.344	SUBCLONAL	1	TRUE	1	0.62	2		271	291	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903815	41903815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	32	686	0	ENST00000372991.4:c.742G>A	p.Glu248Lys	p.E248K	ENST00000372991	NM_001760.3	248	Gaa/Aaa	5/5	1	2	FACETS	0.17	0.137	0.207	0.17	0.137	0.207	SUBCLONAL	1	TRUE	1	0.62	2		686	608	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376302	118376302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1052748793	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	86	383	0	ENST00000534358.1:c.9695G>A	p.Arg3232Gln	p.R3232Q	ENST00000534358	NM_005933.3	3232	cGa/cAa	27/36	1	2	FACETS	0.633	0.563	0.708	0.633	0.563	0.708	SUBCLONAL	1	TRUE	1	0.62	2		383	438	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514277	69514277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147498407	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	83	673	0	ENST00000294312.3:c.404G>A	p.Arg135Gln	p.R135Q	ENST00000294312	NM_005117.2	135	cGa/cAa	3/3	1	2	FACETS	0.449	0.397	0.505	0.449	0.397	0.505	SUBCLONAL	1	TRUE	1	0.62	2		673	596	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230825	53230825	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	58	812	0	ENST00000375401.3:c.1968G>T	p.Glu656Asp	p.E656D	ENST00000375401	NM_004187.3	656	gaG/gaT	14/26	1	2	FACETS	0.25	0.214	0.289	0.25	0.214	0.289	SUBCLONAL	1	TRUE	1	0.62	2		812	749	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805081	43805081	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	222	663	0	ENST00000372470.3:c.531G>T	p.Lys177Asn	p.K177N	ENST00000372470	NM_005373.2	177	aaG/aaT	4/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.62	2		663	581	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465499	8465499	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	148	375	1	ENST00000356435.5:c.3681C>A	p.Phe1227Leu	p.F1227L	ENST00000356435		1227	ttC/ttA	21/35	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.62	2		376	420	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197739	123197739	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	27	322	1	ENST00000218089.9:c.1863G>T	p.Glu621Asp	p.E621D	ENST00000218089	NM_001042749.1	621	gaG/gaT	20/35	1	2	FACETS	0.238	0.189	0.294	0.238	0.189	0.294	SUBCLONAL	1	TRUE	1	0.62	2		323	366	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138402565	138402565	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1178994056	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	22	299	0	ENST00000289153.2:c.2380G>T	p.Val794Leu	p.V794L	ENST00000289153	NM_006219.2	794	Gta/Tta	16/22	1	2	FACETS	0.186	0.143	0.235	0.186	0.143	0.235	SUBCLONAL	1	TRUE	1	0.62	2		299	382	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863334	57863334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	84	755	1	ENST00000228682.2:c.1429G>A	p.Asp477Asn	p.D477N	ENST00000228682	NM_005269.2	477	Gac/Aac	11/12	1	2	FACETS	0.37	0.326	0.416	0.37	0.326	0.416	SUBCLONAL	1	TRUE	1	0.62	2		756	733	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602916	55602916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372795544	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	106	345	0	ENST00000288135.5:c.2626G>A	p.Asp876Asn	p.D876N	ENST00000288135	NM_000222.2	876	Gat/Aat	19/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.62	2		345	298	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829616	72829616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745878919	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	55	538	0	ENST00000268489.5:c.6965G>A	p.Arg2322Gln	p.R2322Q	ENST00000268489	NM_006885.3	2322	cGa/cAa	9/10	1	2	FACETS	0.307	0.263	0.357	0.307	0.263	0.357	SUBCLONAL	1	TRUE	1	0.62	2		538	577	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073413	8073413	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	175	404	0	ENST00000377482.5:c.1246G>T	p.Glu416Ter	p.E416*	ENST00000377482	NM_018948.3	416	Gaa/Taa	4/4	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.62	2		404	501	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828135	3828135	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	35	476	1	ENST00000262367.5:c.1990G>T	p.Glu664Ter	p.E664*	ENST00000262367	NM_004380.2	664	Gaa/Taa	10/31	1	2	FACETS	0.222	0.182	0.268	0.222	0.182	0.268	SUBCLONAL	1	TRUE	1	0.62	2		477	508	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20486949	20486949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188266138	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	25	226	0	ENST00000346618.3:c.914G>A	p.Arg305Gln	p.R305Q	ENST00000346618	NM_001949.4	305	cGa/cAa	5/7	1	2	FACETS	0.284	0.224	0.353	0.284	0.224	0.353	SUBCLONAL	1	TRUE	1	0.62	2		226	284	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217835	7217835	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	66	568	0	ENST00000380728.2:c.176G>T	p.Arg59Ile	p.R59I	ENST00000380728		59	aGa/aTa	3/11	1	2	FACETS	0.3	0.26	0.343	0.3	0.26	0.343	SUBCLONAL	1	TRUE	1	0.62	2		568	710	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163935	47163935	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs933495344	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	23	309	0	ENST00000409792.3:c.2191G>T	p.Asp731Tyr	p.D731Y	ENST00000409792	NM_014159.6	731	Gac/Tac	3/21	1	2	FACETS	0.222	0.173	0.279	0.222	0.173	0.279	SUBCLONAL	1	TRUE	1	0.62	2		309	334	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952119	76952119	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	101	352	0	ENST00000373344.5:c.316G>T	p.Asp106Tyr	p.D106Y	ENST00000373344	NM_000489.3	106	Gat/Tat	5/35	1	2	FACETS	0.869	0.783	0.958	0.869	0.783	0.958	CLONAL	1	TRUE	1	0.62	2		352	375	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532921	187532921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	26	198	0	ENST00000441802.2:c.9472C>T	p.Arg3158Trp	p.R3158W	ENST00000441802	NM_005245.3	3158	Cgg/Tgg	14/27	1	2	FACETS	0.293	0.232	0.363	0.293	0.232	0.363	SUBCLONAL	1	TRUE	1	0.62	2		198	286	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955965	55955965	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754208569	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	106	354	0	ENST00000263923.4:c.3197G>A	p.Arg1066His	p.R1066H	ENST00000263923	NM_002253.2	1066	cGc/cAc	24/30	1	2	FACETS	0.83	0.749	0.914	0.83	0.749	0.914	CLONAL	1	TRUE	1	0.62	2		354	412	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229269	123229269	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	25	233	1	ENST00000218089.9:c.3753C>A	p.Phe1251Leu	p.F1251L	ENST00000218089	NM_001042749.1	1251	ttC/ttA	34/35	1	2	FACETS	0.27	0.213	0.335	0.27	0.213	0.335	SUBCLONAL	1	TRUE	1	0.62	2		234	299	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591612	38591612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057518150	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	47	378	0	ENST00000299084.4:c.71G>A	p.Arg24Gln	p.R24Q	ENST00000299084	NM_152594.2	24	cGa/cAa	2/7	1	2	FACETS	0.31	0.261	0.364	0.31	0.261	0.364	SUBCLONAL	1	TRUE	1	0.62	2		378	489	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46527637	46527637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778971217	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	38	377	0	ENST00000262741.5:c.728G>A	p.Arg243Gln	p.R243Q	ENST00000262741	NM_003629.3	243	cGa/cAa	6/10	1	2	FACETS	0.248	0.204	0.296	0.248	0.204	0.296	SUBCLONAL	1	TRUE	1	0.62	2		377	495	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350972	89350972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276054196	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	50	812	0	ENST00000301030.4:c.1978G>A	p.Glu660Lys	p.E660K	ENST00000301030	NM_001256183.1	660	Gaa/Aaa	9/13	1	2	FACETS	0.184	0.155	0.215	0.184	0.155	0.215	SUBCLONAL	1	TRUE	1	0.62	2		812	878	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737651	145737651	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763078132	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	73	911	0	ENST00000428558.2:c.3112C>T	p.Arg1038Cys	p.R1038C	ENST00000428558	NM_004260.3	1038	Cgc/Tgc	19/22	1	2	FACETS	0.275	0.24	0.314	0.275	0.24	0.314	SUBCLONAL	1	TRUE	1	0.62	2		911	855	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246078852	246078852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150058397	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	209	600	0	ENST00000388985.4:c.793C>T	p.Arg265Cys	p.R265C	ENST00000388985		265	Cgt/Tgt	8/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.62	2		600	628	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190069	123190069	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	23	345	1	ENST00000218089.9:c.1288G>T	p.Glu430Ter	p.E430*	ENST00000218089	NM_001042749.1	430	Gaa/Taa	14/35	1	2	FACETS	0.214	0.166	0.269	0.214	0.166	0.269	SUBCLONAL	1	TRUE	1	0.62	2		346	347	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024540	16024540	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	139	467	1	ENST00000268712.3:c.1678G>T	p.Glu560Ter	p.E560*	ENST00000268712	NM_006311.3	560	Gaa/Taa	16/46	1	2	FACETS	0.785	0.718	0.855	0.785	0.718	0.855	SUBCLONAL	1	TRUE	1	0.62	2		468	571	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961766	55961766	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	21	368	1	ENST00000263923.4:c.2795G>A	p.Arg932Lys	p.R932K	ENST00000263923	NM_002253.2	932	aGa/aAa	20/30	1	2	FACETS	0.189	0.145	0.241	0.189	0.145	0.241	SUBCLONAL	1	TRUE	1	0.62	2		369	358	SUCCESS
APC	324	MSKCC	GRCh37	5	112176882	112176882	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	18	264	0	ENST00000257430.4:c.5591C>A	p.Ser1864Tyr	p.S1864Y	ENST00000257430	NM_000038.5	1864	tCt/tAt	16/16	1	2	FACETS	0.179	0.134	0.231	0.179	0.134	0.231	SUBCLONAL	1	TRUE	1	0.62	2		264	325	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725590	117725590	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	108	342	0	ENST00000368508.3:c.291A>T	p.Glu97Asp	p.E97D	ENST00000368508	NM_002944.2	97	gaA/gaT	5/43	1	2	FACETS	0.995	0.903	1	0.995	0.903	1	CLONAL	1	TRUE	1	0.62	2		342	350	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104572	193104572	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	107	262	1	ENST00000367435.3:c.359G>A	p.Arg120Gln	p.R120Q	ENST00000367435	NM_024529.4	120	cGa/cAa	4/17	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.62	2		263	335	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589809	212589809	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	114	344	0	ENST00000342788.4:c.733G>T	p.Asp245Tyr	p.D245Y	ENST00000342788	NM_005235.2	245	Gac/Tac	6/28	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.62	2		344	351	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719941	18719941	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1234321768	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	27	302	0	ENST00000266497.5:c.3838C>A	p.Leu1280Ile	p.L1280I	ENST00000266497		1280	Cta/Ata	27/31	1	2	FACETS	0.23	0.183	0.285	0.23	0.183	0.285	SUBCLONAL	1	TRUE	1	0.62	2		302	378	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253835	153253835	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	15	220	0	ENST00000281708.4:c.898G>T	p.Asp300Tyr	p.D300Y	ENST00000281708	NM_033632.3	300	Gac/Tac	6/12	1	2	FACETS	0.18	0.131	0.238	0.18	0.131	0.238	SUBCLONAL	1	TRUE	1	0.62	2		220	269	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028618	12028618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	20	274	0	ENST00000353533.5:c.821G>A	p.Arg274Lys	p.R274K	ENST00000353533	NM_003010.3	274	aGa/aAa	8/11	1	2	FACETS	0.176	0.134	0.226	0.176	0.134	0.226	SUBCLONAL	1	TRUE	1	0.62	2		274	366	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715947	52715947	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1029209344	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	197	569	1	ENST00000322088.6:c.512G>A	p.Arg171Gln	p.R171Q	ENST00000322088	NM_014225.5	171	cGg/cAg	5/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.62	2		570	561	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634684	158634684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764097240	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	129	297	0	ENST00000263640.3:c.502G>A	p.Glu168Lys	p.E168K	ENST00000263640	NM_001105.4	168	Gaa/Aaa	5/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.62	2		297	362	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50481242	50481242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	57	382	0	ENST00000394963.4:c.628C>T	p.Arg210Trp	p.R210W	ENST00000394963	NM_003076.4	210	Cgg/Tgg	5/13	1	2	FACETS	0.412	0.354	0.475	0.412	0.354	0.475	SUBCLONAL	1	TRUE	1	0.62	2		382	446	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032279	10032279	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1555455742	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	45	562	0	ENST00000330684.3:c.544G>T	p.Glu182Ter	p.E182*	ENST00000330684	NM_001134407.1	182	Gaa/Taa	3/13	1	2	FACETS	0.313	0.263	0.368	0.313	0.263	0.368	SUBCLONAL	1	TRUE	1	0.62	2		562	464	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679176	88679176	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	179	503	0	ENST00000360948.2:c.861G>T	p.Glu287Asp	p.E287D	ENST00000360948	NM_001012338.2	287	gaG/gaT	8/19	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.62	2		503	484	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855911	76855911	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	24	332	0	ENST00000373344.5:c.5689G>T	p.Glu1897Ter	p.E1897*	ENST00000373344	NM_000489.3	1897	Gaa/Taa	23/35	1	2	FACETS	0.261	0.204	0.325	0.261	0.204	0.325	SUBCLONAL	1	TRUE	1	0.62	2		332	297	SUCCESS
YES1	7525	MSKCC	GRCh37	18	742954	742954	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	42	311	0	ENST00000314574.4:c.1024G>T	p.Glu342Ter	p.E342*	ENST00000314574	NM_005433.3	342	Gaa/Taa	8/12	1	2	FACETS	0.367	0.307	0.434	0.367	0.307	0.434	SUBCLONAL	1	TRUE	1	0.62	2		311	369	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073686	8073686	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	45	370	0	ENST00000377482.5:c.973T>G	p.Leu325Val	p.L325V	ENST00000377482	NM_018948.3	325	Ttg/Gtg	4/4	1	2	FACETS	0.339	0.285	0.399	0.339	0.285	0.399	SUBCLONAL	1	TRUE	1	0.62	2		370	428	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294232	11294232	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	67	567	0	ENST00000361445.4:c.2299C>G	p.Leu767Val	p.L767V	ENST00000361445	NM_004958.3	767	Ctc/Gtc	14/58	1	2	FACETS	0.388	0.337	0.443	0.388	0.337	0.443	SUBCLONAL	1	TRUE	1	0.62	2		567	557	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11308139	11308139	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	31	462	0	ENST00000361445.4:c.853G>T	p.Glu285Ter	p.E285*	ENST00000361445	NM_004958.3	285	Gaa/Taa	7/58	1	2	FACETS	0.211	0.17	0.257	0.211	0.17	0.257	SUBCLONAL	1	TRUE	1	0.62	2		462	474	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11318602	11318602	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	44	386	0	ENST00000361445.4:c.211A>C	p.Ile71Leu	p.I71L	ENST00000361445	NM_004958.3	71	Att/Ctt	3/58	1	2	FACETS	0.312	0.261	0.368	0.312	0.261	0.368	SUBCLONAL	1	TRUE	1	0.62	2		386	455	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261283	16261283	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	189	563	0	ENST00000375759.3:c.8548T>C	p.Ser2850Pro	p.S2850P	ENST00000375759	NM_015001.2	2850	Tca/Cca	11/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.62	2		563	539	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105554	27105554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	49	409	1	ENST00000324856.7:c.5165G>A	p.Arg1722Gln	p.R1722Q	ENST00000324856	NM_006015.4	1722	cGa/cAa	20/20	1	2	FACETS	0.328	0.278	0.383	0.328	0.278	0.383	SUBCLONAL	1	TRUE	1	0.62	2		410	482	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28595727	28595727	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1160838878	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	108	813	0	ENST00000253063.3:c.124C>T	p.Arg42Ter	p.R42*	ENST00000253063	NM_031459.4	42	Cga/Tga	2/10	1	2	FACETS	0.401	0.36	0.446	0.401	0.36	0.446	SUBCLONAL	1	TRUE	1	0.62	2		813	868	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937918	36937918	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	57	1045	2	ENST00000361632.4:c.918G>T	p.Gln306His	p.Q306H	ENST00000361632		306	caG/caT	7/16	1	2	FACETS	0.209	0.178	0.242	0.209	0.178	0.242	SUBCLONAL	1	TRUE	1	0.62	2		1047	881	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941044	36941044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	53	735	0	ENST00000361632.4:c.295C>T	p.Leu99Phe	p.L99F	ENST00000361632		99	Ctc/Ttc	3/16	1	2	FACETS	0.256	0.218	0.298	0.256	0.218	0.298	SUBCLONAL	1	TRUE	1	0.62	2		735	667	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322740	39322740	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	36	334	0	ENST00000373001.3:c.252G>T	p.Lys84Asn	p.K84N	ENST00000373001	NM_022157.3	84	aaG/aaT	2/7	1	2	FACETS	0.302	0.248	0.362	0.302	0.248	0.362	SUBCLONAL	1	TRUE	1	0.62	2		334	385	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363181	40363181	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	59	578	0	ENST00000397332.2:c.1048G>T	p.Val350Leu	p.V350L	ENST00000397332	NM_001033082.2	350	Gta/Tta	3/3	1	2	FACETS	0.376	0.324	0.433	0.376	0.324	0.433	SUBCLONAL	1	TRUE	1	0.62	2		578	506	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363601	40363601	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	68	465	0	ENST00000397332.2:c.628T>C	p.Ser210Pro	p.S210P	ENST00000397332	NM_001033082.2	210	Tct/Cct	3/3	1	2	FACETS	0.447	0.389	0.509	0.447	0.389	0.509	SUBCLONAL	1	TRUE	1	0.62	2		465	491	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43806086	43806086	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	99	630	0	ENST00000372470.3:c.882G>T	p.Leu294Phe	p.L294F	ENST00000372470	NM_005373.2	294	ttG/ttT	6/12	1	2	FACETS	0.51	0.456	0.568	0.51	0.456	0.568	SUBCLONAL	1	TRUE	1	0.62	2		630	626	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531757	46531757	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	21	254	0	ENST00000262741.5:c.590G>A	p.Arg197Lys	p.R197K	ENST00000262741	NM_003629.3	197	aGg/aAg	5/10	1	2	FACETS	0.245	0.189	0.311	0.245	0.189	0.311	SUBCLONAL	1	TRUE	1	0.62	2		254	276	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306954	65306954	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	44	350	0	ENST00000342505.4:c.2623C>A	p.Leu875Ile	p.L875I	ENST00000342505	NM_002227.2	875	Cta/Ata	19/25	1	2	FACETS	0.396	0.333	0.466	0.396	0.333	0.466	SUBCLONAL	1	TRUE	1	0.62	2		350	358	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736353	85736353	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762156408	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	37	242	0	ENST00000370580.1:c.294G>T	p.Lys98Asn	p.K98N	ENST00000370580	NM_003921.4	98	aaG/aaT	2/3	1	2	FACETS	0.363	0.3	0.433	0.363	0.3	0.433	SUBCLONAL	1	TRUE	1	0.62	2		242	329	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736375	85736376	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1027681039	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	56	280	0	ENST00000370580.1:c.271dup	p.Thr91AsnfsTer12	p.T91Nfs*12	ENST00000370580	NM_003921.4	91	aca/aAca	2/3	1	2	FACETS	0.473	0.406	0.545	0.473	0.406	0.545	SUBCLONAL	1	TRUE	1	0.62	2		280	382	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256456	115256456	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	30	315	0	ENST00000369535.4:c.255T>G	p.Asn85Lys	p.N85K	ENST00000369535	NM_002524.4	85	aaT/aaG	3/7	1	2	FACETS	0.247	0.199	0.302	0.247	0.199	0.302	SUBCLONAL	1	TRUE	1	0.62	2		315	392	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115284243	115284243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	119	377	0	ENST00000438362.2:c.43C>T	p.Pro15Ser	p.P15S	ENST00000438362	NM_001242891.1	15	Cct/Tct	2/20	1	2	FACETS	0.941	0.856	1	0.941	0.856	1	CLONAL	1	TRUE	1	0.62	2		377	408	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459112	120459112	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	134	588	0	ENST00000256646.2:c.6233C>T	p.Ser2078Phe	p.S2078F	ENST00000256646	NM_024408.3	2078	tCt/tTt	34/34	1	2	FACETS	0.799	0.729	0.871	0.799	0.729	0.871	SUBCLONAL	1	TRUE	1	0.62	2		588	541	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466606	120466606	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	112	304	0	ENST00000256646.2:c.4513T>C	p.Tyr1505His	p.Y1505H	ENST00000256646	NM_024408.3	1505	Tat/Cat	26/34	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.62	2		304	336	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471740	120471740	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782797192	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	55	439	0	ENST00000256646.2:c.3751C>T	p.Arg1251Cys	p.R1251C	ENST00000256646	NM_024408.3	1251	Cgc/Tgc	23/34	1	2	FACETS	0.341	0.291	0.394	0.341	0.291	0.394	SUBCLONAL	1	TRUE	1	0.62	2		439	521	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120496256	120496256	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	143	339	0	ENST00000256646.2:c.2275A>C	p.Asn759His	p.N759H	ENST00000256646	NM_024408.3	759	Aat/Cat	14/34	1	2	FACETS	0.986	0.906	1	0.986	0.906	1	CLONAL	1	TRUE	1	0.62	2		339	468	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510699	120510699	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	73	507	0	ENST00000256646.2:c.1264+1G>A		p.X422_splice	ENST00000256646	NM_024408.3	422			1	2	FACETS	0.418	0.365	0.474	0.418	0.365	0.474	SUBCLONAL	1	TRUE	1	0.62	2		507	564	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870393	155870393	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	38	409	0	ENST00000368323.3:c.446G>T	p.Gly149Val	p.G149V	ENST00000368323	NM_006912.5	149	gGa/gTa	6/6	1	2	FACETS	0.262	0.217	0.314	0.262	0.217	0.314	SUBCLONAL	1	TRUE	1	0.62	2		409	467	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724979	162724979	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	113	368	0	ENST00000367921.3:c.451T>G	p.Phe151Val	p.F151V	ENST00000367921	NM_006182.2	151	Ttc/Gtc	6/18	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.62	2		368	332	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731237	162731237	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	59	252	0	ENST00000367921.3:c.1092C>A	p.Phe364Leu	p.F364L	ENST00000367921	NM_006182.2	364	ttC/ttA	9/18	1	2	FACETS	0.894	0.78	1	0.894	0.78	1	CLONAL	1	TRUE	1	0.62	2		252	213	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111030	193111030	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	63	169	0	ENST00000367435.3:c.563A>C	p.Lys188Thr	p.K188T	ENST00000367435	NM_024529.4	188	aAa/aCa	7/17	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.62	2		169	177	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206646604	206646604	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	95	939	1	ENST00000367120.3:c.34G>T	p.Asp12Tyr	p.D12Y	ENST00000367120	NM_014002.3	12	Gat/Tat	3/22	1	2	FACETS	0.349	0.31	0.391	0.349	0.31	0.391	SUBCLONAL	1	TRUE	1	0.62	2		940	878	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206943230	206943230	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	33	312	0	ENST00000423557.1:c.388C>A	p.Leu130Ile	p.L130I	ENST00000423557	NM_000572.2	130	Ctt/Att	4/5	1	2	FACETS	0.324	0.264	0.391	0.324	0.264	0.391	SUBCLONAL	1	TRUE	1	0.62	2		312	329	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858991	243858991	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	27	298	0	ENST00000263826.5:c.74G>T	p.Arg25Ile	p.R25I	ENST00000263826	NM_005465.4	25	aGa/aTa	2/13	1	2	FACETS	0.325	0.259	0.4	0.325	0.259	0.4	SUBCLONAL	1	TRUE	1	0.62	2		298	268	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623687	43623688	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	42	386	3	ENST00000355710.3:c.3315_3316delinsAA	p.Ala1106Thr	p.A1106T	ENST00000355710	NM_020975.4	1105	gcGGca/gcAAca	20/20	1	2	FACETS	0.31	0.259	0.367	0.31	0.259	0.367	SUBCLONAL	1	TRUE	1	0.62	2		389	437	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63661966	63661966	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	117	349	0	ENST00000279873.7:c.70G>A	p.Ala24Thr	p.A24T	ENST00000279873	NM_032199.2	24	Gct/Act	2/10	1	2	FACETS	0.973	0.885	1	0.973	0.885	1	CLONAL	1	TRUE	1	0.62	2		349	388	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845577	63845577	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	16	186	0	ENST00000279873.7:c.1316C>A	p.Ser439Tyr	p.S439Y	ENST00000279873	NM_032199.2	439	tCt/tAt	9/10	1	2	FACETS	0.241	0.178	0.316	0.241	0.178	0.316	SUBCLONAL	1	TRUE	1	0.62	2		186	214	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850648	63850648	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	18	173	0	ENST00000279873.7:c.1426G>T	p.Glu476Ter	p.E476*	ENST00000279873	NM_032199.2	476	Gag/Tag	10/10	1	2	FACETS	0.259	0.195	0.334	0.259	0.195	0.334	SUBCLONAL	1	TRUE	1	0.62	2		173	224	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852230	63852230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1367766830	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	44	502	0	ENST00000279873.7:c.3008C>T	p.Pro1003Leu	p.P1003L	ENST00000279873	NM_032199.2	1003	cCg/cTg	10/10	1	2	FACETS	0.253	0.212	0.299	0.253	0.212	0.299	SUBCLONAL	1	TRUE	1	0.62	2		502	561	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332282	70332282	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	38	295	0	ENST00000373644.4:c.187G>T	p.Glu63Ter	p.E63*	ENST00000373644	NM_030625.2	63	Gaa/Taa	2/12	1	2	FACETS	0.394	0.327	0.469	0.394	0.327	0.469	SUBCLONAL	1	TRUE	1	0.62	2		295	311	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404873	70404873	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	45	396	0	ENST00000373644.4:c.2387A>G	p.Asp796Gly	p.D796G	ENST00000373644	NM_030625.2	796	gAc/gGc	4/12	1	2	FACETS	0.346	0.291	0.406	0.346	0.291	0.406	SUBCLONAL	1	TRUE	1	0.62	2		396	420	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426826	70426826	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	51	265	0	ENST00000373644.4:c.4486G>T	p.Glu1496Ter	p.E1496*	ENST00000373644	NM_030625.2	1496	Gaa/Taa	7/12	1	2	FACETS	0.426	0.363	0.495	0.426	0.363	0.495	SUBCLONAL	1	TRUE	1	0.62	2		265	386	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104359205	104359205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770246373	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	37	418	1	ENST00000369902.3:c.926G>A	p.Arg309Gln	p.R309Q	ENST00000369902	NM_016169.3	309	cGg/cAg	8/12	1	2	FACETS	0.303	0.25	0.362	0.303	0.25	0.362	SUBCLONAL	1	TRUE	1	0.62	2		419	394	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724784	112724784	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	22	225	0	ENST00000369452.4:c.668G>A	p.Arg223Gln	p.R223Q	ENST00000369452	NM_007373.3	223	cGa/cAa	2/9	1	2	FACETS	0.259	0.201	0.326	0.259	0.201	0.326	SUBCLONAL	1	TRUE	1	0.62	2		225	274	SUCCESS
EED	8726	MSKCC	GRCh37	11	85963193	85963193	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	22	204	0	ENST00000263360.6:c.271G>T	p.Asp91Tyr	p.D91Y	ENST00000263360	NM_003797.3	91	Gat/Tat	3/12	1	2	FACETS	0.291	0.226	0.366	0.291	0.226	0.366	SUBCLONAL	1	TRUE	1	0.62	2		204	244	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999500	100999500	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs573557192	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	112	979	0	ENST00000325455.5:c.302C>A	p.Ser101Tyr	p.S101Y	ENST00000325455	NM_001202474.3	101	tCt/tAt	1/8	1	2	FACETS	0.421	0.378	0.467	0.421	0.378	0.467	SUBCLONAL	1	TRUE	1	0.62	2		979	858	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984966	101984966	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	21	305	0	ENST00000282441.5:c.413C>A	p.Ser138Tyr	p.S138Y	ENST00000282441	NM_001130145.2	138	tCt/tAt	2/9	1	2	FACETS	0.202	0.155	0.257	0.202	0.155	0.257	SUBCLONAL	1	TRUE	1	0.62	2		305	335	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101985035	101985035	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1222855372	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	48	700	0	ENST00000282441.5:c.482G>A	p.Arg161Gln	p.R161Q	ENST00000282441	NM_001130145.2	161	cGa/cAa	2/9	1	2	FACETS	0.192	0.161	0.225	0.192	0.161	0.225	SUBCLONAL	1	TRUE	1	0.62	2		700	808	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102098289	102098289	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	45	404	0	ENST00000282441.5:c.1253A>G	p.Asn418Ser	p.N418S	ENST00000282441	NM_001130145.2	418	aAc/aGc	8/9	1	2	FACETS	0.262	0.219	0.308	0.262	0.219	0.308	SUBCLONAL	1	TRUE	1	0.62	2		404	555	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206711	102206711	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	39	223	0	ENST00000263464.3:c.1339A>C	p.Ile447Leu	p.I447L	ENST00000263464	NM_001165.4	447	Atc/Ctc	7/9	1	2	FACETS	0.408	0.34	0.485	0.408	0.34	0.485	SUBCLONAL	1	TRUE	1	0.62	2		223	308	SUCCESS
ATM	472	MSKCC	GRCh37	11	108183179	108183179	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	22	178	0	ENST00000278616.4:c.5960C>A	p.Ser1987Tyr	p.S1987Y	ENST00000278616	NM_000051.3	1987	tCt/tAt	40/63	1	2	FACETS	0.315	0.245	0.396	0.315	0.245	0.396	SUBCLONAL	1	TRUE	1	0.62	2		178	225	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344845	118344845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	87	273	0	ENST00000534358.1:c.2971C>T	p.Leu991Phe	p.L991F	ENST00000534358	NM_005933.3	991	Ctt/Ttt	3/36	1	2	FACETS	0.902	0.807	1	0.902	0.807	1	CLONAL	1	TRUE	1	0.62	2		273	311	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352580	118352580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	37	426	0	ENST00000534358.1:c.3785C>T	p.Pro1262Leu	p.P1262L	ENST00000534358	NM_005933.3	1262	cCt/cTt	7/36	1	2	FACETS	0.241	0.198	0.289	0.241	0.198	0.289	SUBCLONAL	1	TRUE	1	0.62	2		426	496	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374377	118374377	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	32	279	0	ENST00000534358.1:c.7770C>A	p.Asn2590Lys	p.N2590K	ENST00000534358	NM_005933.3	2590	aaC/aaA	27/36	1	2	FACETS	0.3	0.244	0.364	0.3	0.244	0.364	SUBCLONAL	1	TRUE	1	0.62	2		279	344	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103396	119103396	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1383200629	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	84	292	0	ENST00000264033.4:c.434C>T	p.Ser145Phe	p.S145F	ENST00000264033	NM_005188.3	145	tCt/tTt	2/16	1	2	FACETS	0.978	0.875	1	0.978	0.875	1	CLONAL	1	TRUE	1	0.62	2		292	277	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148881	119148881	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs760326164	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	65	209	0	ENST00000264033.4:c.1101A>C	p.Gln367His	p.Q367H	ENST00000264033	NM_005188.3	367	caA/caC	8/16	1	2	FACETS	0.856	0.751	0.966	0.856	0.751	0.966	CLONAL	1	TRUE	1	0.62	2		209	245	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025946	1025946	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	34	548	0	ENST00000358495.3:c.584A>C	p.Asp195Ala	p.D195A	ENST00000358495	NM_134424.2	195	gAt/gCt	8/12	1	2	FACETS	0.207	0.169	0.251	0.207	0.169	0.251	SUBCLONAL	1	TRUE	1	0.62	2		548	529	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037459	12037459	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	120	401	0	ENST00000396373.4:c.1090G>T	p.Glu364Ter	p.E364*	ENST00000396373	NM_001987.4	364	Gaa/Taa	6/8	1	2	FACETS	0.795	0.722	0.871	0.795	0.722	0.871	SUBCLONAL	1	TRUE	1	0.62	2		401	487	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443805	18443805	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	38	238	0	ENST00000266497.5:c.778C>A	p.His260Asn	p.H260N	ENST00000266497		260	Cat/Aat	3/31	1	2	FACETS	0.511	0.425	0.605	0.511	0.425	0.605	SUBCLONAL	1	TRUE	1	0.62	2		238	240	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246119	46246119	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	33	279	0	ENST00000334344.6:c.4213G>T	p.Asp1405Tyr	p.D1405Y	ENST00000334344	NM_152641.2	1405	Gat/Tat	15/21	1	2	FACETS	0.355	0.29	0.428	0.355	0.29	0.428	SUBCLONAL	1	TRUE	1	0.62	2		279	300	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434572	49434572	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	94	803	0	ENST00000301067.7:c.6981C>A	p.Phe2327Leu	p.F2327L	ENST00000301067	NM_003482.3	2327	ttC/ttA	31/54	1	2	FACETS	0.392	0.348	0.438	0.392	0.348	0.438	SUBCLONAL	1	TRUE	1	0.62	2		803	774	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446779	49446779	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	68	580	0	ENST00000301067.7:c.1031C>A	p.Ser344Tyr	p.S344Y	ENST00000301067	NM_003482.3	344	tCt/tAt	8/54	1	2	FACETS	0.352	0.306	0.401	0.352	0.306	0.401	SUBCLONAL	1	TRUE	1	0.62	2		580	624	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488220	56488220	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200350558	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	32	451	0	ENST00000267101.3:c.1739G>A	p.Arg580Gln	p.R580Q	ENST00000267101	NM_001982.3	580	cGa/cAa	15/28	1	2	FACETS	0.218	0.177	0.265	0.218	0.177	0.265	SUBCLONAL	1	TRUE	1	0.62	2		451	473	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865476	57865476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	92	744	1	ENST00000228682.2:c.2953G>A	p.Ala985Thr	p.A985T	ENST00000228682	NM_005269.2	985	Gca/Aca	12/12	1	2	FACETS	0.452	0.402	0.506	0.452	0.402	0.506	SUBCLONAL	1	TRUE	1	0.62	2		745	656	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869559	102869559	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	40	526	0	ENST00000307046.8:c.82T>C	p.Ser28Pro	p.S28P	ENST00000307046	NM_001111285.1	28	Tcc/Ccc	2/4	1	2	FACETS	0.229	0.19	0.273	0.229	0.19	0.273	SUBCLONAL	1	TRUE	1	0.62	2		526	563	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112893815	112893815	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	155	366	0	ENST00000351677.2:c.704A>C	p.Lys235Thr	p.K235T	ENST00000351677	NM_002834.3	235	aAa/aCa	6/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.62	2		366	410	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597512	28597512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	49	379	0	ENST00000241453.7:c.2393G>A	p.Gly798Glu	p.G798E	ENST00000241453	NM_004119.2	798	gGa/gAa	19/24	1	2	FACETS	0.323	0.274	0.378	0.323	0.274	0.378	SUBCLONAL	1	TRUE	1	0.62	2		379	489	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608493	28608493	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	30	424	0	ENST00000241453.7:c.1649T>C	p.Val550Ala	p.V550A	ENST00000241453	NM_004119.2	550	gTt/gCt	13/24	1	2	FACETS	0.233	0.187	0.284	0.233	0.187	0.284	SUBCLONAL	1	TRUE	1	0.62	2		424	416	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931742	28931742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	55	416	0	ENST00000282397.4:c.2197G>A	p.Ala733Thr	p.A733T	ENST00000282397	NM_002019.4	733	Gcc/Acc	15/30	1	2	FACETS	0.423	0.363	0.489	0.423	0.363	0.489	SUBCLONAL	1	TRUE	1	0.62	2		416	419	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041184	29041184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	171	524	0	ENST00000282397.4:c.244G>A	p.Gly82Arg	p.G82R	ENST00000282397	NM_002019.4	82	Gga/Aga	3/30	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.62	2		524	521	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907340	32907340	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	31	324	0	ENST00000380152.3:c.1725G>T	p.Lys575Asn	p.K575N	ENST00000380152		575	aaG/aaT	10/27	1	2	FACETS	0.31	0.251	0.376	0.31	0.251	0.376	SUBCLONAL	1	TRUE	1	0.62	2		324	323	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911343	32911343	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	37	379	0	ENST00000380152.3:c.2851C>A	p.Leu951Ile	p.L951I	ENST00000380152		951	Ctt/Att	11/27	1	2	FACETS	0.308	0.254	0.369	0.308	0.254	0.369	SUBCLONAL	1	TRUE	1	0.62	2		379	387	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912318	32912318	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	35	309	0	ENST00000380152.3:c.3826G>T	p.Glu1276Ter	p.E1276*	ENST00000380152		1276	Gaa/Taa	11/27	1	2	FACETS	0.351	0.288	0.421	0.351	0.288	0.421	SUBCLONAL	1	TRUE	1	0.62	2		309	322	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913936	32913936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782031	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	137	348	0	ENST00000380152.3:c.5444C>T	p.Thr1815Ile	p.T1815I	ENST00000380152		1815	aCt/aTt	11/27	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.62	2		348	351	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914063	32914063	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	33	360	0	ENST00000380152.3:c.5571A>C	p.Glu1857Asp	p.E1857D	ENST00000380152		1857	gaA/gaC	11/27	1	2	FACETS	0.283	0.23	0.342	0.283	0.23	0.342	SUBCLONAL	1	TRUE	1	0.62	2		360	376	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914368	32914368	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	27	365	0	ENST00000380152.3:c.5876A>C	p.Lys1959Thr	p.K1959T	ENST00000380152		1959	aAa/aCa	11/27	1	2	FACETS	0.251	0.199	0.31	0.251	0.199	0.31	SUBCLONAL	1	TRUE	1	0.62	2		365	347	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914935	32914935	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs80358880	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	24	297	0	ENST00000380152.3:c.6443C>A	p.Ser2148Tyr	p.S2148Y	ENST00000380152		2148	tCt/tAt	11/27	1	2	FACETS	0.256	0.2	0.319	0.256	0.2	0.319	SUBCLONAL	1	TRUE	1	0.62	2		297	303	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929011	32929011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41293505	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	29	324	1	ENST00000380152.3:c.7021C>T	p.Arg2341Cys	p.R2341C	ENST00000380152		2341	Cgt/Tgt	14/27	1	2	FACETS	0.265	0.213	0.325	0.265	0.213	0.325	SUBCLONAL	1	TRUE	1	0.62	2		325	353	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972645	32972645	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876658246	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	49	300	1	ENST00000380152.3:c.9995C>A	p.Ser3332Tyr	p.S3332Y	ENST00000380152		3332	tCt/tAt	27/27	1	2	FACETS	0.374	0.317	0.436	0.374	0.317	0.436	SUBCLONAL	1	TRUE	1	0.62	2		301	423	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281039	49281039	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	59	492	0	ENST00000282018.3:c.86G>T	p.Arg29Met	p.R29M	ENST00000282018	NM_020377.2	29	aGg/aTg	1/1	1	2	FACETS	0.398	0.343	0.458	0.398	0.343	0.458	SUBCLONAL	1	TRUE	1	0.62	2		492	478	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73348179	73348179	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757537527	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	32	213	0	ENST00000377767.4:c.1006G>A	p.Glu336Lys	p.E336K	ENST00000377767	NM_014953.3	336	Gag/Aag	7/21	1	2	FACETS	0.355	0.289	0.429	0.355	0.289	0.429	SUBCLONAL	1	TRUE	1	0.62	2		213	291	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355062	73355062	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1367047317	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	116	330	0	ENST00000377767.4:c.308C>T	p.Ala103Val	p.A103V	ENST00000377767	NM_014953.3	103	gCc/gTc	2/21	1	2	FACETS	0.985	0.896	1	0.985	0.896	1	CLONAL	1	TRUE	1	0.62	2		330	380	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355069	73355069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775752957	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	30	343	0	ENST00000377767.4:c.301C>T	p.Arg101Cys	p.R101C	ENST00000377767	NM_014953.3	101	Cgc/Tgc	2/21	1	2	FACETS	0.255	0.205	0.311	0.255	0.205	0.311	SUBCLONAL	1	TRUE	1	0.62	2		343	380	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514679	103514679	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1190190828	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	42	263	0	ENST00000355739.4:c.1180G>T	p.Ala394Ser	p.A394S	ENST00000355739	NM_000123.3	394	Gct/Tct	8/15	1	2	FACETS	0.401	0.336	0.473	0.401	0.336	0.473	SUBCLONAL	1	TRUE	1	0.62	2		263	338	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	69061235	69061235	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	51	290	0	ENST00000487270.1:c.1070T>G	p.Leu357Arg	p.L357R	ENST00000487270	NM_133509.3	357	cTg/cGg	11/11	1	2	FACETS	0.55	0.47	0.637	0.55	0.47	0.637	SUBCLONAL	1	TRUE	1	0.62	2		290	299	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95599745	95599745	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	34	310	0	ENST00000393063.1:c.51G>T	p.Met17Ile	p.M17I	ENST00000393063	NM_030621.3	17	atG/atT	3/28	1	2	FACETS	0.249	0.203	0.3	0.249	0.203	0.3	SUBCLONAL	1	TRUE	1	0.62	2		310	441	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643251	38643251	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	18	238	0	ENST00000299084.4:c.721G>A	p.Asp241Asn	p.D241N	ENST00000299084	NM_152594.2	241	Gat/Aat	7/7	1	2	FACETS	0.212	0.159	0.274	0.212	0.159	0.274	SUBCLONAL	1	TRUE	1	0.62	2		238	274	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41021019	41021019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	60	456	0	ENST00000267868.3:c.641C>A	p.Ser214Tyr	p.S214Y	ENST00000267868	NM_002875.4	214	tCt/tAt	7/10	1	2	FACETS	0.389	0.335	0.447	0.389	0.335	0.447	SUBCLONAL	1	TRUE	1	0.62	2		456	498	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991276	41991276	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	163	351	0	ENST00000219905.7:c.2107A>C	p.Ile703Leu	p.I703L	ENST00000219905	NM_001164273.1	703	Att/Ctt	5/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.62	2		351	433	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762120	43762120	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	80	697	1	ENST00000382044.4:c.1325C>A	p.Ser442Tyr	p.S442Y	ENST00000382044	NM_001141980.1	442	tCt/tAt	11/28	1	2	FACETS	0.356	0.313	0.403	0.356	0.313	0.403	SUBCLONAL	1	TRUE	1	0.62	2		698	724	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43772127	43772127	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	256	676	0	ENST00000382044.4:c.588C>G	p.Asp196Glu	p.D196E	ENST00000382044	NM_001141980.1	196	gaC/gaG	6/28	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.62	2		676	720	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43773168	43773168	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	36	467	0	ENST00000382044.4:c.424G>T	p.Glu142Ter	p.E142*	ENST00000382044	NM_001141980.1	142	Gaa/Taa	5/28	1	2	FACETS	0.237	0.194	0.284	0.237	0.194	0.284	SUBCLONAL	1	TRUE	1	0.62	2		467	491	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576154	88576154	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548610351	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	235	669	0	ENST00000360948.2:c.1519C>T	p.Arg507Cys	p.R507C	ENST00000360948	NM_001012338.2	507	Cgc/Tgc	13/19	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.62	2		669	678	SUCCESS
BLM	641	MSKCC	GRCh37	15	91326134	91326134	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	32	267	0	ENST00000355112.3:c.2638G>T	p.Glu880Ter	p.E880*	ENST00000355112	NM_000057.2	880	Gaa/Taa	13/22	1	2	FACETS	0.354	0.288	0.427	0.354	0.288	0.427	SUBCLONAL	1	TRUE	1	0.62	2		267	292	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250988	99250988	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1460703226	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	143	547	1	ENST00000268035.6:c.292G>T	p.Asp98Tyr	p.D98Y	ENST00000268035	NM_000875.3	98	Gac/Tac	2/21	1	2	FACETS	0.785	0.718	0.853	0.785	0.718	0.853	SUBCLONAL	1	TRUE	1	0.62	2		548	588	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454654	99454654	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	57	449	1	ENST00000268035.6:c.1573G>T	p.Val525Phe	p.V525F	ENST00000268035	NM_000875.3	525	Gtt/Ttt	7/21	1	2	FACETS	0.346	0.297	0.4	0.346	0.297	0.4	SUBCLONAL	1	TRUE	1	0.62	2		450	531	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104363	2104363	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	96	659	1	ENST00000219476.3:c.403G>T	p.Asp135Tyr	p.D135Y	ENST00000219476	NM_000548.3	135	Gac/Tac	5/42	1	2	FACETS	0.444	0.395	0.495	0.444	0.395	0.495	SUBCLONAL	1	TRUE	1	0.62	2		660	698	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641082	3641082	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	318	880	0	ENST00000294008.3:c.2557G>T	p.Glu853Ter	p.E853*	ENST00000294008	NM_032444.2	853	Gaa/Taa	12/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.62	2		880	923	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781414	3781414	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1488071616	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	63	787	0	ENST00000262367.5:c.4951G>A	p.Asp1651Asn	p.D1651N	ENST00000262367	NM_004380.2	1651	Gac/Aac	30/31	1	2	FACETS	0.294	0.253	0.337	0.294	0.253	0.337	SUBCLONAL	1	TRUE	1	0.62	2		787	692	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790499	3790499	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	64	609	0	ENST00000262367.5:c.4034T>G	p.Phe1345Cys	p.F1345C	ENST00000262367	NM_004380.2	1345	tTt/tGt	24/31	1	2	FACETS	0.321	0.277	0.368	0.321	0.277	0.368	SUBCLONAL	1	TRUE	1	0.62	2		609	644	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029171	14029171	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	14	201	0	ENST00000311895.7:c.1382G>T	p.Arg461Ile	p.R461I	ENST00000311895	NM_005236.2	461	aGa/aTa	8/11	1	2	FACETS	0.189	0.136	0.253	0.189	0.136	0.253	SUBCLONAL	1	TRUE	1	0.62	2		201	239	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647326	23647326	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs864622280	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	59	521	0	ENST00000261584.4:c.541G>T	p.Glu181Ter	p.E181*	ENST00000261584	NM_024675.3	181	Gaa/Taa	4/13	1	2	FACETS	0.365	0.314	0.421	0.365	0.314	0.421	SUBCLONAL	1	TRUE	1	0.62	2		521	521	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129405	30129405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754076411	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	36	697	0	ENST00000263025.4:c.623G>A	p.Arg208His	p.R208H	ENST00000263025	NM_002746.2	208	cGc/cAc	4/9	1	2	FACETS	0.164	0.134	0.198	0.164	0.134	0.198	SUBCLONAL	1	TRUE	1	0.62	2		697	707	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813597	50813597	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	52	404	0	ENST00000398568.2:c.1151C>A	p.Ser384Tyr	p.S384Y	ENST00000398568	NM_001042412.1	384	tCt/tAt	8/18	1	2	FACETS	0.356	0.303	0.414	0.356	0.303	0.414	SUBCLONAL	1	TRUE	1	0.62	2		404	471	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984574	72984574	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	115	833	0	ENST00000268489.5:c.3010A>G	p.Lys1004Glu	p.K1004E	ENST00000268489	NM_006885.3	1004	Aag/Gag	3/10	1	2	FACETS	0.411	0.369	0.455	0.411	0.369	0.455	SUBCLONAL	1	TRUE	1	0.62	2		833	903	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346968	89346968	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	176	567	0	ENST00000301030.4:c.5982C>A	p.Phe1994Leu	p.F1994L	ENST00000301030	NM_001256183.1	1994	ttC/ttA	9/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.62	2		567	462	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357166	89357166	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	231	718	0	ENST00000301030.4:c.468A>C	p.Lys156Asn	p.K156N	ENST00000301030	NM_001256183.1	156	aaA/aaC	6/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.62	2		718	715	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217890	7217890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	51	382	0	ENST00000380728.2:c.121G>A	p.Glu41Lys	p.E41K	ENST00000380728		41	Gaa/Aaa	3/11	1	2	FACETS	0.355	0.301	0.413	0.355	0.301	0.413	SUBCLONAL	1	TRUE	1	0.62	2		382	464	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965098	15965098	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	36	335	0	ENST00000268712.3:c.5498A>G	p.Gln1833Arg	p.Q1833R	ENST00000268712	NM_006311.3	1833	cAg/cGg	37/46	1	2	FACETS	0.315	0.259	0.377	0.315	0.259	0.377	SUBCLONAL	1	TRUE	1	0.62	2		335	369	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29579968	29579968	+	intron_variant	Intron	SNP	T	T	C	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	82	284	0	ENST00000356175.3:c.4110+3831T>C		p.*1370*	ENST00000356175	NM_000267.3	1375/2839			1	2	FACETS	0.754	0.67	0.842	0.754	0.67	0.842	SUBCLONAL	1	TRUE	1	0.62	2		284	351	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325751	30325751	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	23	196	0	ENST00000322652.5:c.1949A>T	p.Lys650Met	p.K650M	ENST00000322652	NM_015355.2	650	aAg/aTg	16/16	1	2	FACETS	0.32	0.25	0.4	0.32	0.25	0.4	SUBCLONAL	1	TRUE	1	0.62	2		196	232	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33430330	33430330	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	219	669	1	ENST00000345365.6:c.681G>T	p.Met227Ile	p.M227I	ENST00000345365	NM_002878.3	227	atG/atT	8/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.62	2		670	631	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492701	56492701	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	65	421	0	ENST00000407977.2:c.238G>T	p.Gly80Ter	p.G80*	ENST00000407977		80	Gga/Tga	2/10	1	2	FACETS	0.484	0.421	0.552	0.484	0.421	0.552	SUBCLONAL	1	TRUE	1	0.62	2		421	433	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56798152	56798152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746571208	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	101	254	1	ENST00000337432.4:c.883G>A	p.Ala295Thr	p.A295T	ENST00000337432	NM_058216.2	295	Gcc/Acc	6/9	1	2	FACETS	0.936	0.845	1	0.936	0.845	1	CLONAL	1	TRUE	1	0.62	2		255	348	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811494	56811494	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1555605533	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	21	261	0	ENST00000337432.4:c.1042G>T	p.Asp348Tyr	p.D348Y	ENST00000337432	NM_058216.2	348	Gat/Tat	9/9	1	2	FACETS	0.206	0.158	0.262	0.206	0.158	0.262	SUBCLONAL	1	TRUE	1	0.62	2		261	329	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923323	78923323	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	74	525	0	ENST00000306801.3:c.3346T>C	p.Ser1116Pro	p.S1116P	ENST00000306801	NM_020761.2	1116	Tcg/Ccg	28/34	1	2	FACETS	0.486	0.426	0.55	0.486	0.426	0.55	SUBCLONAL	1	TRUE	1	0.62	2		525	491	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743317	743317	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	51	444	0	ENST00000314574.4:c.823G>T	p.Glu275Ter	p.E275*	ENST00000314574	NM_005433.3	275	Gaa/Taa	7/12	1	2	FACETS	0.279	0.236	0.325	0.279	0.236	0.325	SUBCLONAL	1	TRUE	1	0.62	2		444	590	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400658	56400658	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	21	229	0	ENST00000348428.3:c.1252G>T	p.Glu418Ter	p.E418*	ENST00000348428	NM_006785.3	418	Gaa/Taa	11/17	1	2	FACETS	0.266	0.205	0.336	0.266	0.205	0.336	SUBCLONAL	1	TRUE	1	0.62	2		229	255	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400661	56400661	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	19	238	0	ENST00000348428.3:c.1255A>C	p.Asn419His	p.N419H	ENST00000348428	NM_006785.3	419	Aat/Cat	11/17	1	2	FACETS	0.234	0.177	0.3	0.234	0.177	0.3	SUBCLONAL	1	TRUE	1	0.62	2		238	262	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216395	2216395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1294685607	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	70	914	2	ENST00000398665.3:c.2039G>A	p.Gly680Asp	p.G680D	ENST00000398665	NM_032482.2	680	gGc/gAc	20/28	1	2	FACETS	0.284	0.247	0.325	0.284	0.247	0.325	SUBCLONAL	1	TRUE	1	0.62	2		916	794	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262158	10262158	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	68	718	1	ENST00000340748.4:c.2133G>T	p.Glu711Asp	p.E711D	ENST00000340748		711	gaG/gaT	23/40	1	2	FACETS	0.317	0.275	0.362	0.317	0.275	0.362	SUBCLONAL	1	TRUE	1	0.62	2		719	693	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030327	11030327	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	40	575	0	ENST00000327064.4:c.1077C>A	p.Phe359Leu	p.F359L	ENST00000327064	NM_199141.1	359	ttC/ttA	9/16	1	2	FACETS	0.238	0.197	0.283	0.238	0.197	0.283	SUBCLONAL	1	TRUE	1	0.62	2		575	543	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130329	11130329	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	81	629	0	ENST00000358026.2:c.2568G>T	p.Leu856Phe	p.L856F	ENST00000358026	NM_001128849.1	856	ttG/ttT	18/36	1	2	FACETS	0.372	0.327	0.42	0.372	0.327	0.42	SUBCLONAL	1	TRUE	1	0.62	2		629	703	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054382	13054382	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	93	532	0	ENST00000316448.5:c.992T>G	p.Leu331Arg	p.L331R	ENST00000316448	NM_004343.3	331	cTc/cGc	8/9	1	2	FACETS	0.426	0.379	0.477	0.426	0.379	0.477	SUBCLONAL	1	TRUE	1	0.62	2		532	704	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355371	15355371	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	77	558	0	ENST00000263377.2:c.2252C>T	p.Ala751Val	p.A751V	ENST00000263377	NM_058243.2	751	gCt/gTt	13/20	1	2	FACETS	0.46	0.404	0.52	0.46	0.404	0.52	SUBCLONAL	1	TRUE	1	0.62	2		558	540	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741001	40741001	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	44	845	0	ENST00000392038.2:c.1317C>A	p.Phe439Leu	p.F439L	ENST00000392038	NM_001626.4	439	ttC/ttA	13/14	1	2	FACETS	0.193	0.161	0.229	0.193	0.161	0.229	SUBCLONAL	1	TRUE	1	0.62	2		845	734	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762843	40762843	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	128	570	0	ENST00000392038.2:c.165C>A	p.Phe55Leu	p.F55L	ENST00000392038	NM_001626.4	55	ttC/ttA	3/14	1	2	FACETS	0.723	0.658	0.791	0.723	0.658	0.791	SUBCLONAL	1	TRUE	1	0.62	2		570	571	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752731	42752731	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	85	780	1	ENST00000222329.4:c.1533G>T	p.Lys511Asn	p.K511N	ENST00000222329	NM_006494.2	511	aaG/aaT	4/4	1	2	FACETS	0.376	0.332	0.423	0.376	0.332	0.423	SUBCLONAL	1	TRUE	1	0.62	2		781	729	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855550	45855550	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1568531345	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	98	960	0	ENST00000391945.4:c.2107G>T	p.Asp703Tyr	p.D703Y	ENST00000391945	NM_000400.3	703	Gat/Tat	22/23	1	2	FACETS	0.432	0.385	0.482	0.432	0.385	0.482	SUBCLONAL	1	TRUE	1	0.62	2		960	732	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716041	52716041	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	87	760	1	ENST00000322088.6:c.606G>T	p.Lys202Asn	p.K202N	ENST00000322088	NM_014225.5	202	aaG/aaT	5/15	1	2	FACETS	0.37	0.327	0.416	0.37	0.327	0.416	SUBCLONAL	1	TRUE	1	0.62	2		761	758	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719287	52719287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760606403	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	161	592	1	ENST00000322088.6:c.953G>A	p.Arg318Gln	p.R318Q	ENST00000322088	NM_014225.5	318	cGg/cAg	8/15	1	2	FACETS	0.886	0.817	0.958	0.886	0.817	0.958	CLONAL	1	TRUE	1	0.62	2		593	586	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25458690	25458690	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs867632277	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	35	418	0	ENST00000264709.3:c.2483G>T	p.Ser828Ile	p.S828I	ENST00000264709	NM_175629.2	828	aGc/aTc	22/23	1	2	FACETS	0.268	0.22	0.323	0.268	0.22	0.323	SUBCLONAL	1	TRUE	1	0.62	2		418	421	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455205	29455205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528844155	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	218	590	1	ENST00000389048.3:c.2597C>T	p.Ser866Leu	p.S866L	ENST00000389048	NM_004304.4	866	tCg/tTg	15/29	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.62	2		591	621	SUCCESS
ALK	238	MSKCC	GRCh37	2	29541231	29541231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	43	428	0	ENST00000389048.3:c.1586C>T	p.Ser529Phe	p.S529F	ENST00000389048	NM_004304.4	529	tCt/tTt	8/29	1	2	FACETS	0.309	0.258	0.365	0.309	0.258	0.365	SUBCLONAL	1	TRUE	1	0.62	2		428	449	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39239267	39239267	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	49	322	0	ENST00000402219.2:c.2390G>A	p.Arg797Gln	p.R797Q	ENST00000402219	NM_005633.3	797	cGa/cAa	14/23	1	2	FACETS	0.404	0.343	0.471	0.404	0.343	0.471	SUBCLONAL	1	TRUE	1	0.62	2		322	391	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583908	46583908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	57	366	0	ENST00000263734.3:c.415G>A	p.Asp139Asn	p.D139N	ENST00000263734	NM_001430.4	139	Gac/Aac	4/16	1	2	FACETS	0.418	0.359	0.482	0.418	0.359	0.482	SUBCLONAL	1	TRUE	1	0.62	2		366	440	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027508	48027508	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1558665297	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	28	310	0	ENST00000234420.5:c.2386G>T	p.Glu796Ter	p.E796*	ENST00000234420	NM_000179.2	796	Gaa/Taa	4/10	1	2	FACETS	0.295	0.236	0.362	0.295	0.236	0.362	SUBCLONAL	1	TRUE	1	0.62	2		310	306	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719719	61719719	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	34	453	1	ENST00000401558.2:c.1549C>A	p.Leu517Ile	p.L517I	ENST00000401558	NM_003400.3	517	Ctt/Att	14/25	1	2	FACETS	0.207	0.169	0.251	0.207	0.169	0.251	SUBCLONAL	1	TRUE	1	0.62	2		454	529	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99203955	99203955	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	56	271	0	ENST00000074304.5:c.2818G>T	p.Glu940Ter	p.E940*	ENST00000074304	NM_001134224.1	940	Gaa/Taa	26/26	1	2	FACETS	0.638	0.551	0.732	0.638	0.551	0.732	SUBCLONAL	1	TRUE	1	0.62	2		271	283	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267295	198267295	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	23	242	0	ENST00000335508.6:c.2062G>A	p.Glu688Lys	p.E688K	ENST00000335508	NM_012433.2	688	Gaa/Aaa	14/25	1	2	FACETS	0.252	0.196	0.316	0.252	0.196	0.316	SUBCLONAL	1	TRUE	1	0.62	2		242	295	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139677	202139677	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	26	193	0	ENST00000358485.4:c.837+1G>A		p.X279_splice	ENST00000358485	NM_001080125.1	279			1	2	FACETS	0.32	0.254	0.395	0.32	0.254	0.395	SUBCLONAL	1	TRUE	1	0.62	2		193	262	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285303	212285303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	14	317	0	ENST00000342788.4:c.2998G>A	p.Asp1000Asn	p.D1000N	ENST00000342788	NM_005235.2	1000	Gac/Aac	25/28	1	2	FACETS	0.176	0.127	0.236	0.176	0.127	0.236	SUBCLONAL	1	TRUE	1	0.62	2		317	256	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593656	215593656	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	143	296	0	ENST00000260947.4:c.2078A>C	p.Lys693Thr	p.K693T	ENST00000260947	NM_000465.2	693	aAg/aCg	11/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.62	2		296	362	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646084	215646084	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	35	415	0	ENST00000260947.4:c.514G>T	p.Asp172Tyr	p.D172Y	ENST00000260947	NM_000465.2	172	Gat/Tat	4/11	1	2	FACETS	0.226	0.185	0.272	0.226	0.185	0.272	SUBCLONAL	1	TRUE	1	0.62	2		415	500	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378252	225378252	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	83	198	0	ENST00000264414.4:c.643G>T	p.Glu215Ter	p.E215*	ENST00000264414	NM_003590.4	215	Gaa/Taa	5/16	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.62	2		198	259	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022987	31022987	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	37	468	0	ENST00000375687.4:c.2472G>T	p.Glu824Asp	p.E824D	ENST00000375687	NM_015338.5	824	gaG/gaT	13/13	1	2	FACETS	0.241	0.198	0.289	0.241	0.198	0.289	SUBCLONAL	1	TRUE	1	0.62	2		468	496	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39709861	39709861	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	24	150	0	ENST00000361337.2:c.488G>T	p.Arg163Ile	p.R163I	ENST00000361337	NM_003286.2	163	aGa/aTa	7/21	0.121113281179045	0	FACETS	0.161	0.127	0.2			1	INDETERMINATE	1	TRUE	0	0.62	0		150	183	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728729	39728729	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	33	245	2	ENST00000361337.2:c.1009G>T	p.Glu337Ter	p.E337*	ENST00000361337	NM_003286.2	337	Gaa/Taa	12/21	0.121113281179045	0	FACETS	0.148	0.121	0.179			1	INDETERMINATE	1	TRUE	0	0.62	0		247	273	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076952	41076952	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	28	449	0	ENST00000373198.4:c.1468C>A	p.Leu490Ile	p.L490I	ENST00000373198	NM_133170.3	490	Cta/Ata	9/32	0.121113281179045	0	FACETS	0.09	0.071	0.111			1	INDETERMINATE	1	TRUE	0	0.62	0		449	383	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478757	57478757	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	21	338	0	ENST00000371085.3:c.343C>T	p.Pro115Ser	p.P115S	ENST00000371085	NM_000516.4	115	Ccc/Tcc	5/13	1	2	FACETS	0.182	0.139	0.231	0.182	0.139	0.231	SUBCLONAL	1	TRUE	1	0.62	2		338	373	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574836	41574836	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	234	644	0	ENST00000263253.7:c.7121C>A	p.Ser2374Tyr	p.S2374Y	ENST00000263253	NM_001429.3	2374	tCt/tAt	31/31	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.62	2		644	704	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729884	30729884	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	26	264	0	ENST00000295754.5:c.1405G>T	p.Asp469Tyr	p.D469Y	ENST00000295754	NM_003242.5	469	Gat/Tat	6/7	1	2	FACETS	0.255	0.202	0.316	0.255	0.202	0.316	SUBCLONAL	1	TRUE	1	0.62	2		264	329	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267292	41267292	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	8	288	0	ENST00000349496.5:c.876A>C	p.Lys292Asn	p.K292N	ENST00000349496	NM_001904.3	292	aaA/aaC	6/15	1	2	FACETS	0.071	0.045	0.105	0.071	0.045	0.105	SUBCLONAL	1	TRUE	1	0.62	2		288	363	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058720	47058720	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	118	357	0	ENST00000409792.3:c.7558G>A	p.Glu2520Lys	p.E2520K	ENST00000409792	NM_014159.6	2520	Gag/Aag	21/21	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.62	2		357	371	SUCCESS
ATR	545	MSKCC	GRCh37	3	142184042	142184042	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1446847444	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	25	309	0	ENST00000350721.4:c.6938C>A	p.Ser2313Tyr	p.S2313Y	ENST00000350721	NM_001184.3	2313	tCt/tAt	41/47	1	2	FACETS	0.268	0.211	0.333	0.268	0.211	0.333	SUBCLONAL	1	TRUE	1	0.62	2		309	301	SUCCESS
ATR	545	MSKCC	GRCh37	3	142234315	142234315	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	27	318	0	ENST00000350721.4:c.4425G>T	p.Lys1475Asn	p.K1475N	ENST00000350721	NM_001184.3	1475	aaG/aaT	25/47	1	2	FACETS	0.238	0.189	0.294	0.238	0.189	0.294	SUBCLONAL	1	TRUE	1	0.62	2		318	366	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259780	142259780	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	128	353	0	ENST00000350721.4:c.3547C>T	p.Arg1183Ter	p.R1183*	ENST00000350721	NM_001184.3	1183	Cga/Tga	18/47	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.62	2		353	386	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277601	142277601	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	70	236	0	ENST00000350721.4:c.1750G>T	p.Asp584Tyr	p.D584Y	ENST00000350721	NM_001184.3	584	Gat/Tat	8/47	1	2	FACETS	0.903	0.798	1	0.903	0.798	1	CLONAL	1	TRUE	1	0.62	2		236	250	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951956	178951956	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	151	321	0	ENST00000263967.3:c.3011T>G	p.Met1004Arg	p.M1004R	ENST00000263967	NM_006218.2	1004	aTg/aGg	21/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.62	2		321	396	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430418	181430418	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	251	727	0	ENST00000325404.1:c.270C>A	p.Phe90Leu	p.F90L	ENST00000325404	NM_003106.3	90	ttC/ttA	1/1	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.62	2		727	740	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502470	186502470	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs750238082	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	84	208	0	ENST00000323963.5:c.193A>C	p.Ile65Leu	p.I65L	ENST00000323963		65	Att/Ctt	3/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.62	2		208	237	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446847	187446847	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	67	595	0	ENST00000232014.4:c.1346T>G	p.Ile449Ser	p.I449S	ENST00000232014	NM_001130845.1	449	aTc/aGc	5/10	1	2	FACETS	0.354	0.308	0.405	0.354	0.308	0.405	SUBCLONAL	1	TRUE	1	0.62	2		595	610	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902508	1902508	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1165866735	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	254	616	0	ENST00000382891.5:c.127G>A	p.Glu43Lys	p.E43K	ENST00000382891	NM_133335.3	43	Gag/Aag	2/22	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.62	2		616	687	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133720	55133720	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	52	373	0	ENST00000257290.5:c.933G>T	p.Glu311Asp	p.E311D	ENST00000257290	NM_006206.4	311	gaG/gaT	7/23	1	2	FACETS	0.431	0.368	0.5	0.431	0.368	0.5	SUBCLONAL	1	TRUE	1	0.62	2		373	389	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151650	55151650	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	28	361	0	ENST00000257290.5:c.2436A>C	p.Lys812Asn	p.K812N	ENST00000257290	NM_006206.4	812	aaA/aaC	17/23	1	2	FACETS	0.185	0.148	0.229	0.185	0.148	0.229	SUBCLONAL	1	TRUE	1	0.62	2		361	487	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564530	55564530	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	65	497	0	ENST00000288135.5:c.418G>T	p.Asp140Tyr	p.D140Y	ENST00000288135	NM_000222.2	140	Gac/Tac	3/21	1	2	FACETS	0.403	0.35	0.461	0.403	0.35	0.461	SUBCLONAL	1	TRUE	1	0.62	2		497	520	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602754	55602754	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	21	397	0	ENST00000288135.5:c.2575C>A	p.Leu859Ile	p.L859I	ENST00000288135	NM_000222.2	859	Ctt/Att	18/21	1	2	FACETS	0.181	0.139	0.23	0.181	0.139	0.23	SUBCLONAL	1	TRUE	1	0.62	2		397	374	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602969	55602969	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	102	279	0	ENST00000288135.5:c.2679A>C	p.Glu893Asp	p.E893D	ENST00000288135	NM_000222.2	893	gaA/gaC	19/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.62	2		279	279	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946206	55946206	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	38	424	0	ENST00000263923.4:c.3973G>T	p.Glu1325Ter	p.E1325*	ENST00000263923	NM_002253.2	1325	Gaa/Taa	30/30	1	2	FACETS	0.297	0.245	0.354	0.297	0.245	0.354	SUBCLONAL	1	TRUE	1	0.62	2		424	413	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971140	55971140	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	59	406	0	ENST00000263923.4:c.1657A>T	p.Ile553Phe	p.I553F	ENST00000263923	NM_002253.2	553	Att/Ttt	13/30	1	2	FACETS	0.392	0.337	0.451	0.392	0.337	0.451	SUBCLONAL	1	TRUE	1	0.62	2		406	486	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361240	66361240	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	18	295	0	ENST00000273854.3:c.932A>C	p.Lys311Thr	p.K311T	ENST00000273854	NM_004439.5	311	aAa/aCa	4/18	1	2	FACETS	0.185	0.139	0.239	0.185	0.139	0.239	SUBCLONAL	1	TRUE	1	0.62	2		295	314	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467547	66467547	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	13	257	0	ENST00000273854.3:c.722C>A	p.Ala241Asp	p.A241D	ENST00000273854	NM_004439.5	241	gCt/gAt	3/18	1	2	FACETS	0.17	0.121	0.231	0.17	0.121	0.231	SUBCLONAL	1	TRUE	1	0.62	2		257	246	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142949980	142949980	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	41	400	0	ENST00000262992.4:c.2730G>T	p.Lys910Asn	p.K910N	ENST00000262992	NM_001101669.1	910	aaG/aaT	24/24	1	2	FACETS	0.37	0.309	0.438	0.37	0.309	0.438	SUBCLONAL	1	TRUE	1	0.62	2		400	357	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540193	187540193	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	41	413	1	ENST00000441802.2:c.7547C>A	p.Thr2516Asn	p.T2516N	ENST00000441802	NM_005245.3	2516	aCt/aAt	10/27	1	2	FACETS	0.292	0.243	0.346	0.292	0.243	0.346	SUBCLONAL	1	TRUE	1	0.62	2		414	453	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540254	187540254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1221380402	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	31	350	0	ENST00000441802.2:c.7486G>A	p.Glu2496Lys	p.E2496K	ENST00000441802	NM_005245.3	2496	Gaa/Aaa	10/27	1	2	FACETS	0.253	0.204	0.307	0.253	0.204	0.307	SUBCLONAL	1	TRUE	1	0.62	2		350	396	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557968	187557968	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	48	374	0	ENST00000441802.2:c.3743A>C	p.Lys1248Thr	p.K1248T	ENST00000441802	NM_005245.3	1248	aAg/aCg	5/27	1	2	FACETS	0.35	0.296	0.409	0.35	0.296	0.409	SUBCLONAL	1	TRUE	1	0.62	2		374	443	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876205	35876205	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	36	402	0	ENST00000303115.3:c.997G>T	p.Glu333Ter	p.E333*	ENST00000303115	NM_002185.3	333	Gaa/Taa	8/8	1	2	FACETS	0.278	0.229	0.334	0.278	0.229	0.334	SUBCLONAL	1	TRUE	1	0.62	2		402	417	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876298	35876298	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	66	450	0	ENST00000303115.3:c.1090G>T	p.Asp364Tyr	p.D364Y	ENST00000303115	NM_002185.3	364	Gat/Tat	8/8	1	2	FACETS	0.491	0.427	0.559	0.491	0.427	0.559	SUBCLONAL	1	TRUE	1	0.62	2		450	434	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751114	57751114	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	18	207	0	ENST00000274289.3:c.1753G>A	p.Asp585Asn	p.D585N	ENST00000274289	NM_006622.3	585	Gat/Aat	12/14	1	2	FACETS	0.249	0.188	0.322	0.249	0.188	0.322	SUBCLONAL	1	TRUE	1	0.62	2		207	233	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751979	57751979	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	34	319	0	ENST00000274289.3:c.1258C>A	p.Leu420Ile	p.L420I	ENST00000274289	NM_006622.3	420	Ctc/Atc	10/14	1	2	FACETS	0.312	0.255	0.376	0.312	0.255	0.376	SUBCLONAL	1	TRUE	1	0.62	2		319	351	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80160683	80160683	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	53	491	0	ENST00000265081.6:c.3052G>T	p.Glu1018Ter	p.E1018*	ENST00000265081	NM_002439.4	1018	Gaa/Taa	22/24	1	2	FACETS	0.267	0.227	0.31	0.267	0.227	0.31	SUBCLONAL	1	TRUE	1	0.62	2		491	641	SUCCESS
APC	324	MSKCC	GRCh37	5	112102967	112102967	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs954713888	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	53	355	1	ENST00000257430.4:c.302G>A	p.Gly101Glu	p.G101E	ENST00000257430	NM_000038.5	101	gGa/gAa	4/16	1	2	FACETS	0.361	0.308	0.419	0.361	0.308	0.419	SUBCLONAL	1	TRUE	1	0.62	2		356	474	SUCCESS
APC	324	MSKCC	GRCh37	5	112178394	112178394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs547564330	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	26	278	0	ENST00000257430.4:c.7103C>T	p.Ser2368Phe	p.S2368F	ENST00000257430	NM_000038.5	2368	tCt/tTt	16/16	1	2	FACETS	0.269	0.213	0.333	0.269	0.213	0.333	SUBCLONAL	1	TRUE	1	0.62	2		278	312	SUCCESS
APC	324	MSKCC	GRCh37	5	112179153	112179153	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	24	182	0	ENST00000257430.4:c.7862C>A	p.Ser2621Tyr	p.S2621Y	ENST00000257430	NM_000038.5	2621	tCt/tAt	16/16	1	2	FACETS	0.324	0.255	0.403	0.324	0.255	0.403	SUBCLONAL	1	TRUE	1	0.62	2		182	239	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925377	131925377	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	52	137	0	ENST00000265335.6:c.1300G>T	p.Asp434Tyr	p.D434Y	ENST00000265335		434	Gat/Tat	9/25	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.62	2		137	151	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944349	131944349	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	14	138	0	ENST00000265335.6:c.2761A>C	p.Lys921Gln	p.K921Q	ENST00000265335		921	Aag/Cag	17/25	1	2	FACETS	0.208	0.15	0.278	0.208	0.15	0.278	SUBCLONAL	1	TRUE	1	0.62	2		138	217	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953913	131953913	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	116	218	0	ENST00000265335.6:c.3316G>T	p.Glu1106Ter	p.E1106*	ENST00000265335		1106	Gaa/Taa	21/25	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.62	2		218	350	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433968	149433968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	188	790	2	ENST00000286301.3:c.2680G>A	p.Ala894Thr	p.A894T	ENST00000286301	NM_005211.3	894	Gcc/Acc	21/22	1	2	FACETS	0.799	0.74	0.86	0.799	0.74	0.86	SUBCLONAL	1	TRUE	1	0.62	2		792	759	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671591	30671591	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	61	616	0	ENST00000376406.3:c.5369A>C	p.Lys1790Thr	p.K1790T	ENST00000376406	NM_014641.2	1790	aAg/aCg	10/15	1	2	FACETS	0.281	0.242	0.323	0.281	0.242	0.323	SUBCLONAL	1	TRUE	1	0.62	2		616	701	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673643	30673643	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	237	651	0	ENST00000376406.3:c.3317A>C	p.Lys1106Thr	p.K1106T	ENST00000376406	NM_014641.2	1106	aAa/aCa	10/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.62	2		651	673	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680847	30680847	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	72	561	1	ENST00000376406.3:c.872G>T	p.Arg291Met	p.R291M	ENST00000376406	NM_014641.2	291	aGg/aTg	5/15	1	2	FACETS	0.36	0.314	0.409	0.36	0.314	0.409	SUBCLONAL	1	TRUE	1	0.62	2		562	646	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31939804	31939804	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	67	924	1	ENST00000375333.2:c.31G>T	p.Ala11Ser	p.A11S	ENST00000375333	NM_032454.1	11	Gca/Tca	1/8	1	2	FACETS	0.247	0.214	0.283	0.247	0.214	0.283	SUBCLONAL	1	TRUE	1	0.62	2		925	875	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288839	33288839	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	30	432	1	ENST00000374542.5:c.713G>A	p.Arg238Gln	p.R238Q	ENST00000374542	NM_001141970.1	238	cGa/cAa	3/8	1	2	FACETS	0.211	0.169	0.258	0.211	0.169	0.258	SUBCLONAL	1	TRUE	1	0.62	2		433	459	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289535	33289535	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	93	777	0	ENST00000374542.5:c.168G>T	p.Lys56Asn	p.K56N	ENST00000374542	NM_001141970.1	56	aaG/aaT	2/8	1	2	FACETS	0.376	0.334	0.422	0.376	0.334	0.422	SUBCLONAL	1	TRUE	1	0.62	2		777	797	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106534465	106534465	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	75	195	0	ENST00000369096.4:c.37A>C	p.Thr13Pro	p.T13P	ENST00000369096	NM_001198.3	13	Acc/Ccc	1/7	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.62	2		195	235	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106543506	106543506	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	26	175	0	ENST00000369096.4:c.308G>T	p.Ser103Ile	p.S103I	ENST00000369096	NM_001198.3	103	aGt/aTt	3/7	1	2	FACETS	0.34	0.27	0.419	0.34	0.27	0.419	SUBCLONAL	1	TRUE	1	0.62	2		175	247	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554354	106554354	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	61	365	0	ENST00000369096.4:c.1882G>T	p.Glu628Ter	p.E628*	ENST00000369096	NM_001198.3	628	Gaa/Taa	6/7	1	2	FACETS	0.498	0.431	0.57	0.498	0.431	0.57	SUBCLONAL	1	TRUE	1	0.62	2		365	395	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555110	106555110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141223053	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	98	525	0	ENST00000369096.4:c.2227G>A	p.Glu743Lys	p.E743K	ENST00000369096	NM_001198.3	743	Gag/Aag	7/7	1	2	FACETS	0.608	0.544	0.675	0.608	0.544	0.675	SUBCLONAL	1	TRUE	1	0.62	2		525	520	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109319765	109319765	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	40	410	0	ENST00000436639.2:c.923G>T	p.Gly308Val	p.G308V	ENST00000436639	NM_014454.2	308	gGc/gTc	5/10	1	2	FACETS	0.294	0.244	0.349	0.294	0.244	0.349	SUBCLONAL	1	TRUE	1	0.62	2		410	439	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109321725	109321725	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	204	505	0	ENST00000436639.2:c.698G>T	p.Arg233Ile	p.R233I	ENST00000436639	NM_014454.2	233	aGa/aTa	4/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.62	2		505	554	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609891	117609891	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	137	394	0	ENST00000368508.3:c.6808G>T	p.Glu2270Ter	p.E2270*	ENST00000368508	NM_002944.2	2270	Gaa/Taa	43/43	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.62	2		394	428	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658376	117658376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	41	549	0	ENST00000368508.3:c.5207G>A	p.Gly1736Glu	p.G1736E	ENST00000368508	NM_002944.2	1736	gGa/gAa	31/43	1	2	FACETS	0.246	0.205	0.293	0.246	0.205	0.293	SUBCLONAL	1	TRUE	1	0.62	2		549	537	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658406	117658406	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	38	473	0	ENST00000368508.3:c.5177A>C	p.Asn1726Thr	p.N1726T	ENST00000368508	NM_002944.2	1726	aAt/aCt	31/43	1	2	FACETS	0.258	0.212	0.308	0.258	0.212	0.308	SUBCLONAL	1	TRUE	1	0.62	2		473	476	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662399	117662399	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	58	383	0	ENST00000368508.3:c.4978G>T	p.Glu1660Ter	p.E1660*	ENST00000368508	NM_002944.2	1660	Gag/Tag	30/43	1	2	FACETS	0.451	0.388	0.519	0.451	0.388	0.519	SUBCLONAL	1	TRUE	1	0.62	2		383	415	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674297	117674297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	33	381	0	ENST00000368508.3:c.4177G>A	p.Asp1393Asn	p.D1393N	ENST00000368508	NM_002944.2	1393	Gat/Aat	26/43	1	2	FACETS	0.278	0.226	0.336	0.278	0.226	0.336	SUBCLONAL	1	TRUE	1	0.62	2		381	383	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709042	117709042	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	40	478	0	ENST00000368508.3:c.1915C>A	p.Leu639Met	p.L639M	ENST00000368508	NM_002944.2	639	Ctg/Atg	13/43	1	2	FACETS	0.284	0.236	0.338	0.284	0.236	0.338	SUBCLONAL	1	TRUE	1	0.62	2		478	454	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117746761	117746761	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	98	305	0	ENST00000368508.3:c.59T>C	p.Leu20Pro	p.L20P	ENST00000368508	NM_002944.2	20	cTa/cCa	1/43	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.62	2		305	304	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137522142	137522142	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	51	123	0	ENST00000367739.4:c.737C>A	p.Ser246Tyr	p.S246Y	ENST00000367739	NM_000416.2	246	tCt/tAt	6/7	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.62	2		123	140	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527383	137527383	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	52	388	0	ENST00000367739.4:c.263C>A	p.Ser88Tyr	p.S88Y	ENST00000367739	NM_000416.2	88	tCt/tAt	3/7	1	2	FACETS	0.436	0.372	0.505	0.436	0.372	0.505	SUBCLONAL	1	TRUE	1	0.62	2		388	385	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150392	157150392	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	55	525	1	ENST00000346085.5:c.1574G>T	p.Arg525Ile	p.R525I	ENST00000346085	NM_020732.3	525	aGa/aTa	2/20	1	2	FACETS	0.326	0.278	0.377	0.326	0.278	0.377	SUBCLONAL	1	TRUE	1	0.62	2		526	545	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469965	157469965	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	65	538	0	ENST00000346085.5:c.2759C>A	p.Ser920Tyr	p.S920Y	ENST00000346085	NM_020732.3	920	tCt/tAt	9/20	1	2	FACETS	0.392	0.34	0.448	0.392	0.34	0.448	SUBCLONAL	1	TRUE	1	0.62	2		538	535	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2955005	2955005	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	162	557	0	ENST00000396946.4:c.2705T>C	p.Phe902Ser	p.F902S	ENST00000396946	NM_032415.4	902	tTc/tCc	21/25	0.3	1	FACETS	0.691	0.638	0.745	0.691	0.638	0.745	INDETERMINATE	1	TRUE	0	0.62	1		557	522	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2966418	2966418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	46	641	1	ENST00000396946.4:c.1762G>A	p.Glu588Lys	p.E588K	ENST00000396946	NM_032415.4	588	Gaa/Aaa	14/25	0.3	1	FACETS	0.149	0.125	0.176	0.149	0.125	0.176	INDETERMINATE	1	TRUE	0	0.62	1		642	685	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946173	13946173	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	58	364	1	ENST00000405192.2:c.923G>T	p.Arg308Leu	p.R308L	ENST00000405192	NM_001163147.1	308	cGg/cTg	10/12	1	2	FACETS	0.363	0.312	0.418	0.363	0.312	0.418	SUBCLONAL	1	TRUE	1	0.62	2		365	516	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346613	81346613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1033158417	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	14	268	0	ENST00000222390.5:c.1340C>T	p.Ala447Val	p.A447V	ENST00000222390	NM_000601.4	447	gCt/gTt	11/18	1	2	FACETS	0.162	0.117	0.218	0.162	0.117	0.218	SUBCLONAL	1	TRUE	1	0.62	2		268	278	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509823	106509823	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	55	535	0	ENST00000359195.3:c.1817A>C	p.Lys606Thr	p.K606T	ENST00000359195	NM_002649.2	606	aAa/aCa	2/11	1	2	FACETS	0.323	0.276	0.375	0.323	0.276	0.375	SUBCLONAL	1	TRUE	1	0.62	2		535	549	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514482	148514482	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	35	242	0	ENST00000320356.2:c.1242A>C	p.Glu414Asp	p.E414D	ENST00000320356	NM_004456.4	414	gaA/gaC	11/20	1	2	FACETS	0.365	0.3	0.438	0.365	0.3	0.438	SUBCLONAL	1	TRUE	1	0.62	2		242	309	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148526862	148526862	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	89	266	0	ENST00000320356.2:c.442G>T	p.Glu148Ter	p.E148*	ENST00000320356	NM_004456.4	148	Gaa/Taa	5/20	1	2	FACETS	0.867	0.776	0.962	0.867	0.776	0.962	CLONAL	1	TRUE	1	0.62	2		266	331	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148544290	148544290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	46	376	0	ENST00000320356.2:c.101G>A	p.Arg34Gln	p.R34Q	ENST00000320356	NM_004456.4	34	cGa/cAa	2/20	1	2	FACETS	0.321	0.27	0.377	0.321	0.27	0.377	SUBCLONAL	1	TRUE	1	0.62	2		376	462	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873390	151873390	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	23	269	0	ENST00000262189.6:c.9148G>T	p.Glu3050Ter	p.E3050*	ENST00000262189	NM_170606.2	3050	Gaa/Taa	38/59	1	2	FACETS	0.214	0.167	0.27	0.214	0.167	0.27	SUBCLONAL	1	TRUE	1	0.62	2		269	346	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874231	151874231	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	30	277	0	ENST00000262189.6:c.8307G>T	p.Lys2769Asn	p.K2769N	ENST00000262189	NM_170606.2	2769	aaG/aaT	38/59	1	2	FACETS	0.306	0.247	0.373	0.306	0.247	0.373	SUBCLONAL	1	TRUE	1	0.62	2		277	316	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38176411	38176411	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	103	274	0	ENST00000317025.8:c.1855+2T>C		p.X619_splice	ENST00000317025	NM_023034.1	619			1	2	FACETS	0.835	0.753	0.92	0.835	0.753	0.92	CLONAL	1	TRUE	1	0.62	2		274	398	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205252	38205252	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	102	786	0	ENST00000317025.8:c.438G>T	p.Lys146Asn	p.K146N	ENST00000317025	NM_023034.1	146	aaG/aaT	2/24	1	2	FACETS	0.357	0.319	0.398	0.357	0.319	0.398	SUBCLONAL	1	TRUE	1	0.62	2		786	921	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931887	68931887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	156	502	0	ENST00000288368.4:c.317G>A	p.Gly106Glu	p.G106E	ENST00000288368	NM_024870.2	106	gGa/gAa	3/40	1	2	FACETS	0.84	0.773	0.91	0.84	0.773	0.91	CLONAL	1	TRUE	1	0.62	2		502	599	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117870608	117870608	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	28	218	0	ENST00000297338.2:c.464T>C	p.Leu155Ser	p.L155S	ENST00000297338	NM_006265.2	155	tTa/tCa	5/14	1	2	FACETS	0.309	0.248	0.379	0.309	0.248	0.379	SUBCLONAL	1	TRUE	1	0.62	2		218	292	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752720	128752720	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	24	215	0	ENST00000377970.2:c.881C>A	p.Ser294Tyr	p.S294Y	ENST00000377970	NM_002467.4	294	tCt/tAt	3/3	1	2	FACETS	0.323	0.254	0.402	0.323	0.254	0.402	SUBCLONAL	1	TRUE	1	0.62	2		215	240	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022214	5022214	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	30	334	0	ENST00000381652.3:c.226+1G>T		p.X76_splice	ENST00000381652	NM_004972.3	76			1	2	FACETS	0.273	0.22	0.334	0.273	0.22	0.334	SUBCLONAL	1	TRUE	1	0.62	2		334	354	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072581	5072581	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	78	293	0	ENST00000381652.3:c.1731A>C	p.Glu577Asp	p.E577D	ENST00000381652	NM_004972.3	577	gaA/gaC	13/25	1	2	FACETS	0.742	0.657	0.832	0.742	0.657	0.832	SUBCLONAL	1	TRUE	1	0.62	2		293	339	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317909	8317909	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	19	263	0	ENST00000356435.5:c.5704G>T	p.Glu1902Ter	p.E1902*	ENST00000356435		1902	Gag/Tag	35/35	1	2	FACETS	0.192	0.145	0.247	0.192	0.145	0.247	SUBCLONAL	1	TRUE	1	0.62	2		263	319	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375987	8375987	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs773293867	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	35	326	0	ENST00000356435.5:c.4610G>T	p.Arg1537Ile	p.R1537I	ENST00000356435		1537	aGa/aTa	28/35	1	2	FACETS	0.336	0.276	0.403	0.336	0.276	0.403	SUBCLONAL	1	TRUE	1	0.62	2		326	336	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485270	8485270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	83	393	0	ENST00000356435.5:c.3110C>T	p.Ser1037Phe	p.S1037F	ENST00000356435		1037	tCt/tTt	18/35	1	2	FACETS	0.631	0.56	0.707	0.631	0.56	0.707	SUBCLONAL	1	TRUE	1	0.62	2		393	424	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492966	8492966	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	93	389	0	ENST00000356435.5:c.2363C>A	p.Ser788Tyr	p.S788Y	ENST00000356435		788	tCt/tAt	16/35	1	2	FACETS	0.759	0.68	0.843	0.759	0.68	0.843	SUBCLONAL	1	TRUE	1	0.62	2		389	395	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020640	37020640	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	38	354	0	ENST00000358127.4:c.205C>A	p.Leu69Ile	p.L69I	ENST00000358127	NM_001280556.1	69	Ctt/Att	2/10	1	2	FACETS	0.314	0.259	0.374	0.314	0.259	0.374	SUBCLONAL	1	TRUE	1	0.62	2		354	391	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87322794	87322794	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	28	302	0	ENST00000277120.3:c.395G>T	p.Arg132Met	p.R132M	ENST00000277120		132	aGg/aTg	5/19	1	2	FACETS	0.226	0.18	0.278	0.226	0.18	0.278	SUBCLONAL	1	TRUE	1	0.62	2		302	400	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482331	87482331	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	37	447	0	ENST00000277120.3:c.1618C>T	p.Leu540Phe	p.L540F	ENST00000277120		540	Ctc/Ttc	14/19	1	2	FACETS	0.295	0.243	0.353	0.295	0.243	0.353	SUBCLONAL	1	TRUE	1	0.62	2		447	405	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563530	87563530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	44	456	1	ENST00000277120.3:c.1918G>A	p.Asp640Asn	p.D640N	ENST00000277120		640	Gac/Aac	16/19	1	2	FACETS	0.332	0.278	0.391	0.332	0.278	0.391	SUBCLONAL	1	TRUE	1	0.62	2		457	428	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98011468	98011468	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	51	422	0	ENST00000289081.3:c.106C>A	p.Leu36Ile	p.L36I	ENST00000289081	NM_000136.2	36	Ctt/Att	2/15	1	2	FACETS	0.326	0.277	0.38	0.326	0.277	0.38	SUBCLONAL	1	TRUE	1	0.62	2		422	505	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434811	128434811	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	43	521	0	ENST00000265960.3:c.43C>T	p.Arg15Ter	p.R15*	ENST00000265960	NM_001006617.1	15	Cga/Tga	2/12	1	2	FACETS	0.247	0.206	0.292	0.247	0.206	0.292	SUBCLONAL	1	TRUE	1	0.62	2		521	562	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802623	135802623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	39	270	0	ENST00000298552.3:c.175C>T	p.His59Tyr	p.H59Y	ENST00000298552	NM_001162426.1	59	Cac/Tac	4/23	1	2	FACETS	0.385	0.32	0.457	0.385	0.32	0.457	SUBCLONAL	1	TRUE	1	0.62	2		270	327	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922911	39922911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	216	623	0	ENST00000378444.4:c.3797G>A	p.Gly1266Asp	p.G1266D	ENST00000378444	NM_001123385.1	1266	gGc/gAc	8/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.62	2		623	660	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820634	44820634	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	20	248	0	ENST00000377967.4:c.331A>T	p.Lys111Ter	p.K111*	ENST00000377967	NM_021140.2	111	Aaa/Taa	3/29	1	2	FACETS	0.232	0.177	0.296	0.232	0.177	0.296	SUBCLONAL	1	TRUE	1	0.62	2		248	278	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879950	44879950	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	154	383	0	ENST00000377967.4:c.539A>G	p.Asn180Ser	p.N180S	ENST00000377967	NM_021140.2	180	aAc/aGc	6/29	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.62	2		383	484	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44921958	44921958	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	45	332	0	ENST00000377967.4:c.1492C>G	p.Leu498Val	p.L498V	ENST00000377967	NM_021140.2	498	Ctg/Gtg	15/29	1	2	FACETS	0.354	0.298	0.416	0.354	0.298	0.416	SUBCLONAL	1	TRUE	1	0.62	2		332	410	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949001	44949001	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	140	297	0	ENST00000377967.4:c.3562T>G	p.Phe1188Val	p.F1188V	ENST00000377967	NM_021140.2	1188	Ttc/Gtc	25/29	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.62	2		297	411	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426817	47426817	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	45	512	0	ENST00000377045.4:c.1062G>T	p.Glu354Asp	p.E354D	ENST00000377045	NM_001654.4	354	gaG/gaT	10/16	1	2	FACETS	0.298	0.25	0.351	0.298	0.25	0.351	SUBCLONAL	1	TRUE	1	0.62	2		512	487	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225976	53225976	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	355	1079	0	ENST00000375401.3:c.2873C>T	p.Ala958Val	p.A958V	ENST00000375401	NM_004187.3	958	gCc/gTc	19/26	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.62	2		1079	908	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410280	63410280	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	261	800	0	ENST00000330258.3:c.2887C>A	p.Pro963Thr	p.P963T	ENST00000330258	NM_152424.3	963	Ccc/Acc	2/2	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.62	2		800	674	SUCCESS
AR	367	MSKCC	GRCh37	X	66765736	66765736	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	107	1022	0	ENST00000374690.3:c.748G>A	p.Gly250Ser	p.G250S	ENST00000374690	NM_000044.3	250	Ggt/Agt	1/8	1	2	FACETS	0.355	0.318	0.395	0.355	0.318	0.395	SUBCLONAL	1	TRUE	1	0.62	2		1022	972	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348980	70348980	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	218	516	0	ENST00000374080.3:c.3492C>G	p.Asp1164Glu	p.D1164E	ENST00000374080		1164	gaC/gaG	25/45	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.62	2		516	665	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845363	76845363	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	20	273	0	ENST00000373344.5:c.6158T>G	p.Phe2053Cys	p.F2053C	ENST00000373344	NM_000489.3	2053	tTt/tGt	27/35	1	2	FACETS	0.208	0.159	0.266	0.208	0.159	0.266	SUBCLONAL	1	TRUE	1	0.62	2		273	310	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918901	76918901	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	68	521	1	ENST00000373344.5:c.4090A>T	p.Lys1364Ter	p.K1364*	ENST00000373344	NM_000489.3	1364	Aaa/Taa	12/35	1	2	FACETS	0.358	0.311	0.408	0.358	0.311	0.408	SUBCLONAL	1	TRUE	1	0.62	2		522	613	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76919041	76919041	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	17	216	0	ENST00000373344.5:c.3950A>T	p.Lys1317Ile	p.K1317I	ENST00000373344	NM_000489.3	1317	aAa/aTa	12/35	1	2	FACETS	0.248	0.185	0.322	0.248	0.185	0.322	SUBCLONAL	1	TRUE	1	0.62	2		216	221	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938634	76938634	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs781804632	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	125	393	0	ENST00000373344.5:c.2114A>G	p.Asp705Gly	p.D705G	ENST00000373344	NM_000489.3	705	gAc/gGc	9/35	1	2	FACETS	0.828	0.754	0.905	0.828	0.754	0.905	CLONAL	1	TRUE	1	0.62	2		393	487	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626624	100626624	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	38	303	0	ENST00000308731.7:c.306C>A	p.Phe102Leu	p.F102L	ENST00000308731	NM_000061.2	102	ttC/ttA	4/19	1	2	FACETS	0.385	0.319	0.459	0.385	0.319	0.459	SUBCLONAL	1	TRUE	1	0.62	2		303	318	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215311	123215311	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	28	380	1	ENST00000218089.9:c.2857C>T	p.Arg953Ter	p.R953*	ENST00000218089	NM_001042749.1	953	Cga/Tga	28/35	1	2	FACETS	0.182	0.145	0.225	0.182	0.145	0.225	SUBCLONAL	1	TRUE	1	0.62	2		381	496	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341701	8341704	+	missense_variant	Missense_Mutation	ONP	CGAG	CGAG	TGAT	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	25	393	0	ENST00000356435.5:c.4936_4939delinsATCA	p.Leu1646_Glu1647delinsIleLys	p.L1646_E1647delinsIK	ENST00000356435		1646	CTCGaa/ATCAaa	29/35	1	2	FACETS	0.209	0.165	0.261	0.209	0.165	0.261	SUBCLONAL	1	TRUE	1	0.62	2		393	385	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178217	56178218	+	missense_variant	Missense_Mutation	DNP	AG	AG	CA	novel	NA	P-0054016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	27	246	0	ENST00000399503.3:c.3190_3191delinsCA	p.Arg1064Gln	p.R1064Q	ENST00000399503	NM_005921.1	1064	AGa/CAa	14/20	1	2	FACETS	0.265	0.211	0.326	0.265	0.211	0.326	SUBCLONAL	1	TRUE	1	0.62	2		246	329	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0054019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	232	1978	1	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.367108296687651	2	FACETS	0.872	0.818	0.928	0.872	0.818	0.928	CLONAL	2	TRUE	0	0.394107652727827	2		1979	675	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344204	70344223	+	frameshift_variant	Frame_Shift_Del	DEL	AGGAGGCTGAAGGCAGCAGC	AGGAGGCTGAAGGCAGCAGC	-	novel	NA	P-0054019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	80	416	0	ENST00000374080.3:c.1942_1961del	p.Glu648GlnfsTer15	p.E648Qfs*15	ENST00000374080		647	aAGGAGGCTGAAGGCAGCAGC/a	13/45	0.300677887055536	4	FACETS	1	0.97	1	0.657	0.581	0.737	CLONAL	1	TRUE	2	0.394107652727827	4		416	431	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	93	563	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.34699823727186	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.352184611383348	2		563	227	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0054020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	136	892	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.34699823727186	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.352184611383348	2		892	352	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954211	48954211	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	87	218	0	ENST00000267163.4:c.1415del	p.Asn472IlefsTer6	p.N472Ifs*6	ENST00000267163	NM_000321.2	471	cAa/ca	15/27	0.352184611383348	4	FACETS	1	0.964	1	0.852	0.772	0.933	CLONAL	3	TRUE	0	0.352184611383348	4		218	196	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831413	89831413	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	133	577	0	ENST00000389301.3:c.2663T>C	p.Val888Ala	p.V888A	ENST00000389301	NM_000135.2	888	gTa/gCa	28/43	0.349128720513355	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.352184611383348	3		577	381	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157470037	157470037	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	42	476	0	ENST00000346085.5:c.2831A>C	p.Glu944Ala	p.E944A	ENST00000346085	NM_020732.3	944	gAg/gCg	9/20	0.352184611383348	3	FACETS	0.917	0.769	1	0.458	0.384	0.54	CLONAL	1	TRUE	1	0.352184611383348	3		476	306	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0054021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	133	465	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.354568960744786	3	FACETS	0.83	0.759	0.904	0.83	0.759	0.904	CLONAL	2	TRUE	1	0.407678690163038	3		465	473	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143030	47143030	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	114	356	0	ENST00000409792.3:c.4933C>T	p.Gln1645Ter	p.Q1645*	ENST00000409792	NM_014159.6	1645	Caa/Taa	8/21	1	2	FACETS	0.963	0.869	1	0.963	0.869	1	CLONAL	1	TRUE	1	0.407678690163038	2		356	581	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162156	47162156	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	92	353	0	ENST00000409792.3:c.3970C>T	p.Gln1324Ter	p.Q1324*	ENST00000409792	NM_014159.6	1324	Caa/Taa	3/21	1	2	FACETS	0.876	0.781	0.977	0.876	0.781	0.977	CLONAL	1	TRUE	1	0.407678690163038	2		353	515	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860887	151860888	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATGTT	novel	NA	P-0054021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	64	261	0	ENST00000262189.6:c.9770_9774dup	p.Ala3259AsnfsTer5	p.A3259Nfs*5	ENST00000262189	NM_170606.2	3258	-/AACAT	43/59	0.354568960744786	3	FACETS	0.738	0.64	0.844	0.369	0.32	0.422	SUBCLONAL	1	TRUE	1	0.407678690163038	3		261	512	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236087	108236087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781894	NA	P-0054022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	255	443	1	ENST00000278616.4:c.9023G>A	p.Arg3008His	p.R3008H	ENST00000278616	NM_000051.3	3008	cGt/cAt	63/63	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.807607731841416	2		444	561	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0054022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	66	97	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	0.784844800580355	3	FACETS	1	0.906	1	0.517	0.455	0.581	CLONAL	1	TRUE	1	0.807607731841416	3		97	222	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814225	76814225	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	226	141	0	ENST00000373344.5:c.6419A>G	p.Asn2140Ser	p.N2140S	ENST00000373344	NM_000489.3	2140	aAt/aGt	29/35	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.807607731841416	1		141	257	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228801	36228801	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	385	869	1	ENST00000222270.7:c.7700G>T	p.Arg2567Leu	p.R2567L	ENST00000222270	NM_014727.1	2567	cGt/cTt	35/37	0.427201386968975	1	FACETS	0.653	0.623	0.682	0.653	0.623	0.682	INDETERMINATE	1	TRUE	0	0.807607731841416	1		870	871	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0054023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	330	882	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.535419754988811	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.535419754988811	1		883	839	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201089	108201089	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779865	NA	P-0054024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	52	319	0	ENST00000278616.4:c.7456C>T	p.Arg2486Ter	p.R2486*	ENST00000278616	NM_000051.3	2486	Cga/Tga	50/63	0.376290588354809	1	FACETS	0.738	0.632	0.852	0.738	0.632	0.852	SUBCLONAL	1	TRUE	0	0.385767503410897	1		319	295	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045136	47045136	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	470	343	0	ENST00000377604.3:c.2377C>T	p.Arg793Ter	p.R793*	ENST00000377604	NM_001204468.1	793	Cga/Tga	21/24	0.385767503410897	3	FACETS	1	0.993	1			1	CLONAL	4	TRUE	NA	0.385767503410897	3		343	669	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148861	119148887	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTTTTAATCAAAGGAACAATATGAA	TTTTTTTAATCAAAGGAACAATATGAA	-	novel	NA	P-0054024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	466	187	0	ENST00000264033.4:c.1096-13_1109del		p.X366_splice	ENST00000264033	NM_005188.3	366		8/16	0.385767503410897	9	FACETS	1	0.991	1			1	CLONAL	9	TRUE	NA	0.385767503410897	9		187	604	SUCCESS
APC	324	MSKCC	GRCh37	5	112175122	112175124	+	inframe_deletion	In_Frame_Del	DEL	ATC	ATC	-	rs1257663822	NA	P-0054024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	36	171	0	ENST00000257430.4:c.3834_3836del	p.Ser1279del	p.S1279del	ENST00000257430	NM_000038.5	1277	ttATCa/tta	16/16	0.35746225528854	4	FACETS	0.895	0.739	1	0.447	0.369	0.534	CLONAL	1	TRUE	2	0.385767503410897	4		171	289	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217705	7217707	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs757139280	NA	P-0054025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	314	701	0	ENST00000380728.2:c.220_222del	p.Glu74del	p.E74del	ENST00000380728		74	GAG/-	4/11	0.7933763305692	1	FACETS	0.995	0.955	1	0.995	0.955	1	CLONAL	1	TRUE	0	0.7933763305692	1		701	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	487	1005	0	ENST00000269305.4:c.388del	p.Leu130SerfsTer40	p.L130Sfs*40	ENST00000269305	NM_001126112.2	130	Ctc/tc	5/11	0.7933763305692	1	FACETS	0.982	0.95	1	0.982	0.95	1	CLONAL	1	TRUE	0	0.7933763305692	1		1005	754	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564739	86564742	+	frameshift_variant	Frame_Shift_Del	DEL	CTCT	CTCT	-	novel	NA	P-0054025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	308	1014	0	ENST00000274376.6:c.473_476del	p.Ser158TrpfsTer15	p.S158Wfs*15	ENST00000274376	NM_002890.2	157	gaCTCT/ga	1/25	0.7933763305692	1	FACETS	0.892	0.853	0.931	0.892	0.853	0.931	CLONAL	1	TRUE	0	0.7933763305692	1		1014	525	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659314	86659315	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0054025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	113	265	0	ENST00000274376.6:c.1604_1605del	p.Phe535TrpfsTer14	p.F535Wfs*14	ENST00000274376	NM_002890.2	535	TTt/t	11/25	0.7933763305692	1	FACETS	0.971	0.905	1	0.971	0.905	1	CLONAL	1	TRUE	0	0.7933763305692	1		265	177	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672431	30672431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	350	967	0	ENST00000376406.3:c.4529C>T	p.Pro1510Leu	p.P1510L	ENST00000376406	NM_014641.2	1510	cCc/cTc	10/15	1	2	FACETS	0.917	0.871	0.964	0.917	0.871	0.964	CLONAL	1	TRUE	1	0.7933763305692	2		967	962	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407890	139407891	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0054025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	431	1131	0	ENST00000277541.6:c.2306_2307del	p.Lys769ArgfsTer39	p.K769Rfs*39	ENST00000277541	NM_017617.3	769	aAA/a	14/34	1	2	FACETS	0.952	0.909	0.996	0.952	0.909	0.996	CLONAL	1	TRUE	1	0.7933763305692	2		1131	1141	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	88	276	0				ENST00000310581	NM_198253.2	-/1132			0.260222825723883	5	FACETS	0.922	0.824	1	0.922	0.824	1	CLONAL	3	TRUE	2	0.260222825723883	5		276	340	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462371	89462371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866025221	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	210	612	1	ENST00000336596.2:c.1843G>A	p.Glu615Lys	p.E615K	ENST00000336596	NM_005233.5	615	Gaa/Aaa	10/17	0.260222825723883	3	FACETS	0.864	0.805	0.924	1	0.989	1	CLONAL	3	TRUE	1	0.260222825723883	3		613	704	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508728	148508728	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs267601395	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	131	451	0	ENST00000320356.2:c.1936T>A	p.Tyr646Asn	p.Y646N	ENST00000320356	NM_004456.4	646	Tac/Aac	16/20	0.260222825723883	5	FACETS	0.855	0.779	0.933	0.855	0.779	0.933	CLONAL	3	TRUE	2	0.260222825723883	5		451	546	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	145	571	1	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	0.100894788391346	5	FACETS	0.852	0.781	0.927	0.852	0.781	0.927	INDETERMINATE	3	TRUE	2	0.260222825723883	5		572	606	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374404	81374404	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1486090533	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	109	503	0	ENST00000222390.5:c.658C>T	p.Arg220Ter	p.R220*	ENST00000222390	NM_000601.4	220	Cga/Tga	6/18	0.260222825723883	5	FACETS	1	0.965	1	0.77	0.695	0.85	CLONAL	2	TRUE	2	0.260222825723883	5		503	504	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286830	33286830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775787032	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	91	901	0	ENST00000374542.5:c.2107C>T	p.Pro703Ser	p.P703S	ENST00000374542	NM_001141970.1	703	Cca/Tca	7/8	0.260222825723883	5	FACETS	1	0.962	1	0.3	0.266	0.337	CLONAL	1	TRUE	1	0.260222825723883	5		901	810	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636727	8636727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159852	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	52	422	0	ENST00000356435.5:c.182G>A	p.Gly61Glu	p.G61E	ENST00000356435		61	gGa/gAa	2/35	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.260222825723883	2		422	310	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979257	93979257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	45	448	0	ENST00000369303.4:c.1571G>A	p.Gly524Glu	p.G524E	ENST00000369303	NM_004440.3	524	gGa/gAa	7/17	0.225503474515734	3	FACETS	0.841	0.707	0.988	0.42	0.353	0.494	CLONAL	1	TRUE	1	0.260222825723883	3		448	465	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939048	36939048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	102	996	0	ENST00000361632.4:c.661C>T	p.Pro221Ser	p.P221S	ENST00000361632		221	Ccc/Tcc	5/16	0.225503474515734	3	FACETS	1	0.978	1	0.683	0.611	0.758	CLONAL	1	TRUE	1	0.260222825723883	3		996	649	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521384	8521384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777779009	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	60	738	1	ENST00000356435.5:c.854G>A	p.Gly285Glu	p.G285E	ENST00000356435		285	gGa/gAa	9/35	1	2	FACETS	0.895	0.772	1	0.895	0.772	1	CLONAL	1	TRUE	1	0.260222825723883	2		739	515	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821601	72821618	+	inframe_deletion	In_Frame_Del	DEL	CCGCCGCCGCCGCCGCCA	CCGCCGCCGCCGCCGCCA	-	rs778016374	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	22	131	0	ENST00000268489.5:c.10557_10574del	p.Gly3522_Gly3527del	p.G3522_G3527del	ENST00000268489	NM_006885.3	3519	ggTGGCGGCGGCGGCGGCGGc/ggc	10/10	0.260222825723883	3	FACETS	1	0.847	1	1	0.847	1	CLONAL	2	TRUE	1	0.260222825723883	3		131	88	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279483	1279483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	184	1297	0	ENST00000310581.5:c.2053G>A	p.Asp685Asn	p.D685N	ENST00000310581	NM_198253.2	685	Gat/Aat	5/16	0.260222825723883	5	FACETS	1	0.98	1	0.783	0.724	0.845	CLONAL	2	TRUE	2	0.260222825723883	5		1297	837	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971178	13971178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs904139873	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	212	535	0	ENST00000405192.2:c.751C>T	p.Pro251Ser	p.P251S	ENST00000405192	NM_001163147.1	251	Ccc/Tcc	8/12	0.260222825723883	5	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	2	0.260222825723883	5		535	684	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584747	187584747	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1358297166	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	119	418	0	ENST00000441802.2:c.3286C>T	p.Arg1096Ter	p.R1096*	ENST00000441802	NM_005245.3	1096	Cga/Tga	3/27	0.100894788391346	5	FACETS	0.9	0.817	0.986	0.9	0.817	0.986	INDETERMINATE	3	TRUE	2	0.260222825723883	5		418	471	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662625	117662625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	79	682	0	ENST00000368508.3:c.4840C>T	p.Pro1614Ser	p.P1614S	ENST00000368508	NM_002944.2	1614	Cca/Tca	29/43	0.225503474515734	3	FACETS	1	0.954	1	0.587	0.517	0.663	CLONAL	1	TRUE	1	0.260222825723883	3		682	584	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	124	935	2	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	0.260222825723883	5	FACETS	1	0.98	1	0.334	0.302	0.369	CLONAL	1	TRUE	1	0.260222825723883	5		937	991	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004206	29004206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	74	491	0	ENST00000282397.4:c.1087C>T	p.Pro363Ser	p.P363S	ENST00000282397	NM_002019.4	363	Ccc/Tcc	8/30	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.260222825723883	2		491	388	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608604	189608604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	231	737	0	ENST00000264731.3:c.1679C>T	p.Ser560Leu	p.S560L	ENST00000264731	NM_003722.4	560	tCa/tTa	13/14	0.260222825723883	3	FACETS	0.926	0.867	0.987	1	0.991	1	CLONAL	3	TRUE	1	0.260222825723883	3		737	722	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622151	43622151	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	159	801	0	ENST00000355710.3:c.3168G>A	p.Trp1056Ter	p.W1056*	ENST00000355710	NM_020975.4	1056	tgG/tgA	19/20	0.100894788391346	5	FACETS	1	0.981	1	0.817	0.751	0.886	INDETERMINATE	2	TRUE	2	0.260222825723883	5		801	693	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857917	9857917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	97	820	1	ENST00000330684.3:c.3484G>A	p.Asp1162Asn	p.D1162N	ENST00000330684	NM_001134407.1	1162	Gac/Aac	13/13	0.260222825723883	3	FACETS	1	0.975	1	0.659	0.588	0.734	CLONAL	1	TRUE	1	0.260222825723883	3		821	639	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455135	50455135	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	89	493	0	ENST00000331340.3:c.682G>C	p.Glu228Gln	p.E228Q	ENST00000331340	NM_006060.4	228	Gaa/Caa	6/8	0.260222825723883	5	FACETS	0.855	0.76	0.957	0.57	0.506	0.638	CLONAL	2	TRUE	2	0.260222825723883	5		493	556	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033209	69033209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	169	655	0	ENST00000288368.4:c.3649C>T	p.His1217Tyr	p.H1217Y	ENST00000288368	NM_024870.2	1217	Cat/Tat	30/40	0.260222825723883	3	FACETS	0.849	0.785	0.916	1	0.985	1	CLONAL	3	TRUE	1	0.260222825723883	3		655	576	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381528	81381528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776090604	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	123	431	3	ENST00000222390.5:c.533G>A	p.Arg178Gln	p.R178Q	ENST00000222390	NM_000601.4	178	cGa/cAa	5/18	0.260222825723883	5	FACETS	0.894	0.813	0.978	0.894	0.813	0.978	CLONAL	3	TRUE	2	0.260222825723883	5		434	490	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1268746	1268746	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	158	1050	0	ENST00000310581.5:c.2471C>T	p.Ser824Phe	p.S824F	ENST00000310581	NM_198253.2	824	tCc/tTc	9/16	0.260222825723883	5	FACETS	1	0.925	1	0.673	0.617	0.732	CLONAL	2	TRUE	2	0.260222825723883	5		1050	836	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857956	9857956	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	81	793	1	ENST00000330684.3:c.3445G>A	p.Asp1149Asn	p.D1149N	ENST00000330684	NM_001134407.1	1149	Gac/Aac	13/13	0.260222825723883	3	FACETS	1	0.955	1	0.585	0.516	0.659	CLONAL	1	TRUE	1	0.260222825723883	3		794	601	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660282	227660282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	145	1052	0	ENST00000305123.5:c.3173C>T	p.Ser1058Phe	p.S1058F	ENST00000305123	NM_005544.2	1058	tCc/tTc	1/2	0.260222825723883	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.260222825723883	3		1052	577	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202869	16202869	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757023093	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	116	766	1	ENST00000375759.3:c.577C>T	p.Arg193Cys	p.R193C	ENST00000375759	NM_015001.2	193	Cgc/Tgc	3/15	0.225503474515734	3	FACETS	0.807	0.729	0.889	0.807	0.729	0.889	CLONAL	2	TRUE	1	0.260222825723883	3		767	624	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588138	69588138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	100	881	0	ENST00000168712.1:c.560C>T	p.Thr187Ile	p.T187I	ENST00000168712	NM_002007.2	187	aCc/aTc	3/3	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.260222825723883	2		881	582	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343583	118343583	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	83	667	0	ENST00000534358.1:c.1709C>T	p.Pro570Leu	p.P570L	ENST00000534358	NM_005933.3	570	cCa/cTa	3/36	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.260222825723883	2		667	431	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66777418	66777418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	180	1000	0	ENST00000307102.5:c.784C>T	p.Pro262Ser	p.P262S	ENST00000307102	NM_002755.3	262	Ccc/Tcc	7/11	0.127703199294092	4	FACETS	1	0.977	1	1	0.977	1	INDETERMINATE	2	TRUE	2	0.260222825723883	4		1000	761	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657350	29657350	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	105	722	0	ENST00000356175.3:c.5583T>A	p.Cys1861Ter	p.C1861*	ENST00000356175	NM_000267.3	1861	tgT/tgA	38/57	0.260222825723883	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.260222825723883	1		722	503	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758815	41758815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	157	995	0	ENST00000301178.4:c.1869G>A	p.Met623Ile	p.M623I	ENST00000301178	NM_021913.4	623	atG/atA	16/20	0.0770234575102562	3	FACETS	0.931	0.855	1	0.931	0.855	1	INDETERMINATE	2	TRUE	1	0.260222825723883	3		995	732	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543900	212543900	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	86	528	0	ENST00000342788.4:c.1499G>A	p.Gly500Glu	p.G500E	ENST00000342788	NM_005235.2	500	gGa/gAa	13/28	0.260222825723883	3	FACETS	0.798	0.709	0.893	0.798	0.709	0.893	SUBCLONAL	2	TRUE	1	0.260222825723883	3		528	468	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375178	31375178	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	234	1031	0	ENST00000328111.2:c.575C>T	p.Ala192Val	p.A192V	ENST00000328111	NM_006892.3	192	gCc/gTc	6/23	0.225503474515734	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.260222825723883	3		1031	892	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733220	40733220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	147	798	0	ENST00000373198.4:c.3586G>A	p.Asp1196Asn	p.D1196N	ENST00000373198	NM_133170.3	1196	Gat/Aat	26/32	0.225503474515734	3	FACETS	0.994	0.911	1	0.994	0.911	1	CLONAL	2	TRUE	1	0.260222825723883	3		798	642	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458384	12458384	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	182	813	1	ENST00000287820.6:c.1001T>A	p.Phe334Tyr	p.F334Y	ENST00000287820	NM_015869.4	334	tTt/tAt	6/7	0.260222825723883	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.260222825723883	3		814	637	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446310	187446310	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	88	856	0	ENST00000232014.4:c.1378A>G	p.Ser460Gly	p.S460G	ENST00000232014	NM_001130845.1	460	Agc/Ggc	6/10	0.260222825723883	3	FACETS	1	0.963	1	0.605	0.536	0.678	CLONAL	1	TRUE	1	0.260222825723883	3		856	632	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721484	176721484	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	160	886	0	ENST00000439151.2:c.7115C>T	p.Pro2372Leu	p.P2372L	ENST00000439151	NM_022455.4	2372	cCc/cTc	23/23	0.260222825723883	5	FACETS	1	0.978	1	0.785	0.721	0.851	CLONAL	2	TRUE	2	0.260222825723883	5		886	726	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184980	32184980	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1182535525	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	85	1054	0	ENST00000375023.3:c.1688G>A	p.Gly563Asp	p.G563D	ENST00000375023	NM_004557.3	563	gGt/gAt	10/30	0.260222825723883	5	FACETS	1	0.922	1	0.264	0.233	0.298	CLONAL	1	TRUE	1	0.260222825723883	5		1054	859	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27190599	27190599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	74	742	0	ENST00000380036.4:c.1400C>T	p.Ser467Phe	p.S467F	ENST00000380036	NM_000459.3	467	tCt/tTt	10/23	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.260222825723883	2		742	518	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426115	47426115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	227	538	0	ENST00000377045.4:c.635C>T	p.Ser212Phe	p.S212F	ENST00000377045	NM_001654.4	212	tCc/tTc	7/16	0.260222825723883	2	FACETS	1	0.965	1			1	CLONAL	4	TRUE	NA	0.260222825723883	2		538	425	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	100	378	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.410202600383257	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	0	0.410202600383257	1		378	280	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	45	538	8	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.751	0.635	0.878	0.751	0.635	0.878	SUBCLONAL	1	FALSE	1	0.410202600383257	2		546	292	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	71	397	3	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	0.368746665929881	0	FACETS	0.514	0.451	0.582			1	SUBCLONAL	1	FALSE	0	0.410202600383257	0		400	397	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	139	473	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.869	0.8	0.94	1	0.99	1	CLONAL	2	FALSE	1	0.410202600383257	2		478	390	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	76	436	2	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.410202600383257	2		438	285	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446283	70446284	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	130	824	3	ENST00000373644.4:c.5230dup	p.Arg1744LysfsTer26	p.R1744Kfs*26	ENST00000373644	NM_030625.2	1741	-/A	11/12	1	2	FACETS	0.997	0.906	1	0.997	0.906	1	CLONAL	1	FALSE	1	0.410202600383257	2		827	636	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	59	424	1	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	FALSE	1	0.410202600383257	2		425	260	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	160	757	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	1	0.410202600383257	2		757	740	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606272	93606273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1182878074	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	156	1246	3	ENST00000375746.1:c.98dup	p.Met34HisfsTer3	p.M34Hfs*3	ENST00000375746	NM_001174167.1	31	cag/caGg	2/14	0.136670585581068	0	FACETS	0.532	0.487	0.578			1	INDETERMINATE	1	FALSE	0	0.410202600383257	0		1249	844	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	146	721	7	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.959	0.877	1	0.959	0.877	1	CLONAL	1	FALSE	1	0.410202600383257	2		728	742	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	22	394	1	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.526	0.409	0.66	0.526	0.409	0.66	SUBCLONAL	1	FALSE	1	0.410202600383257	2		395	204	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	179	1312	2	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	FALSE	1	0.410202600383257	2		1314	852	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692981	89692982	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	16	737	0	ENST00000371953.3:c.469dup	p.Glu157GlyfsTer23	p.E157Gfs*23	ENST00000371953	NM_000314.4	155	-/G	5/9	1	2	FACETS	0.302	0.223	0.397	0.302	0.223	0.397	SUBCLONAL	1	FALSE	1	0.410202600383257	2		737	258	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	8	538	1	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	1	2	FACETS	0.155	0.099	0.228	0.155	0.099	0.228	SUBCLONAL	1	FALSE	1	0.410202600383257	2		539	251	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	192	1124	9	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	0.136670585581068	0	FACETS	0.601	0.556	0.648			1	INDETERMINATE	1	FALSE	0	0.410202600383257	0		1133	918	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279861	46279866	+	inframe_deletion	In_Frame_Del	DEL	CAGCAA	CAGCAA	-	rs748517056	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	57	853	0	ENST00000371998.3:c.3810_3815del	p.Gln1275_Gln1276del	p.Q1275_Q1276del	ENST00000371998		1263	CAGCAA/-	20/23	1	2	FACETS	0.43	0.369	0.498	0.43	0.369	0.498	SUBCLONAL	1	FALSE	1	0.410202600383257	2		853	646	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772951	135772951	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs118203724	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	46	672	0	ENST00000298552.3:c.2672del	p.Asn891ThrfsTer40	p.N891Tfs*40	ENST00000298552	NM_001162426.1	891	aAc/ac	21/23	0.136670585581068	0	FACETS	0.438	0.371	0.512			1	INDETERMINATE	1	FALSE	0	0.410202600383257	0		672	302	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882049	36882050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs780753361	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	160	1072	8	ENST00000358127.4:c.963dup	p.Ala322ArgfsTer19	p.A322Rfs*19	ENST00000358127	NM_001280556.1	321	-/C	8/10	0.136670585581068	0	FACETS	0.484	0.443	0.526			1	INDETERMINATE	1	FALSE	0	0.410202600383257	0		1080	951	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399409	139399411	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	rs761020817	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	186	1321	20	ENST00000277541.6:c.4732_4734del	p.Val1578del	p.V1578del	ENST00000277541	NM_017617.3	1578	GTG/-	26/34	0.136670585581068	0	FACETS	0.558	0.515	0.603			1	INDETERMINATE	1	FALSE	0	0.410202600383257	0		1341	958	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81941311	81941311	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	94	966	2	ENST00000359376.3:c.1489G>A	p.Ala497Thr	p.A497T	ENST00000359376	NM_002661.3	497	Gcc/Acc	16/33	1	2	FACETS	0.917	0.819	1	0.917	0.819	1	CLONAL	1	FALSE	1	0.410202600383257	2		968	500	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257365	19257366	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	124	1255	3	ENST00000162023.5:c.767dup	p.Glu257ArgfsTer28	p.E257Rfs*28	ENST00000162023		256	cca/ccCa	11/13	1	2	FACETS	0.853	0.772	0.937	0.853	0.772	0.937	CLONAL	1	FALSE	1	0.410202600383257	2		1258	709	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120115	70120115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	35	264	1	ENST00000245479.2:c.1121del	p.Pro374ArgfsTer9	p.P374Rfs*9	ENST00000245479	NM_000346.3	373	Ccc/cc	3/3	1	2	FACETS	0.922	0.764	1	0.922	0.764	1	CLONAL	1	FALSE	1	0.410202600383257	2		265	185	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808898	1808898	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1416045205	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	138	1442	1	ENST00000260795.2:c.2334del	p.Ser779AlafsTer41	p.S779Afs*41	ENST00000260795		777	aCc/ac	17/17	1	2	FACETS	0.764	0.695	0.836	0.764	0.695	0.836	SUBCLONAL	1	FALSE	1	0.410202600383257	2		1443	881	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	185	484	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.84	0.781	0.9	1	0.992	1	CLONAL	2	FALSE	1	0.410202600383257	2		484	537	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143043366	143043366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199940140	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	26	567	0	ENST00000262992.4:c.2050G>A	p.Val684Ile	p.V684I	ENST00000262992	NM_001101669.1	684	Gtt/Att	19/24	1	2	FACETS	0.664	0.529	0.815	0.664	0.529	0.815	SUBCLONAL	1	FALSE	1	0.410202600383257	2		567	191	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104698	209104698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766985383	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	72	586	0	ENST00000345146.2:c.880G>A	p.Val294Met	p.V294M	ENST00000345146	NM_005896.2	294	Gtg/Atg	8/10	0.101569264791678	4	FACETS	1	0.942	1	0.564	0.494	0.638	INDETERMINATE	1	FALSE	2	0.410202600383257	4		586	439	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591247	67591247	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	35	554	0	ENST00000274335.5:c.1746-1G>C		p.X582_splice	ENST00000274335		582			1	2	FACETS	0.649	0.534	0.776	0.649	0.534	0.776	SUBCLONAL	1	FALSE	1	0.410202600383257	2		554	263	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674316	86674317	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs886041400	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	33	471	0	ENST00000274376.6:c.2450_2451del	p.Ser817TyrfsTer12	p.S817Yfs*12	ENST00000274376	NM_002890.2	816	gaCTct/gact	18/25	1	2	FACETS	0.829	0.682	0.992	0.829	0.682	0.992	CLONAL	1	FALSE	1	0.410202600383257	2		471	194	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505508	25505508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753287419	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	151	1099	5	ENST00000264709.3:c.250G>A	p.Ala84Thr	p.A84T	ENST00000264709	NM_175629.2	84	Gcc/Acc	4/23	0.136670585581068	0	FACETS	0.505	0.462	0.551			1	INDETERMINATE	1	FALSE	0	0.410202600383257	0		1104	859	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100487	8100487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	191	1416	1	ENST00000346208.3:c.461C>T	p.Pro154Leu	p.P154L	ENST00000346208		154	cCg/cTg	3/6	1	2	FACETS	0.952	0.88	1	0.952	0.88	1	CLONAL	1	FALSE	1	0.410202600383257	2		1417	978	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629108	86629108	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853218	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	37	458	0	ENST00000274376.6:c.853C>T	p.Arg285Ter	p.R285*	ENST00000274376	NM_002890.2	285	Cga/Tga	4/25	1	2	FACETS	0.893	0.744	1	0.893	0.744	1	CLONAL	1	FALSE	1	0.410202600383257	2		458	202	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665285	117665285	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	38	566	0	ENST00000368508.3:c.4462C>A	p.Leu1488Met	p.L1488M	ENST00000368508	NM_002944.2	1488	Ctg/Atg	27/43	0.101569264791678	4	FACETS	1	0.927	1	0.608	0.507	0.718	INDETERMINATE	1	FALSE	2	0.410202600383257	4		566	215	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251949	153251949	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	44	742	0	ENST00000281708.4:c.1057del	p.Ser353ValfsTer24	p.S353Vfs*24	ENST00000281708	NM_033632.3	353	Agt/gt	7/12	1	2	FACETS	0.701	0.591	0.822	0.701	0.591	0.822	SUBCLONAL	1	FALSE	1	0.410202600383257	2		742	306	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295098	1295098	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1166646936	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	71	196	0	ENST00000310581.5:c.7C>T	p.Arg3Cys	p.R3C	ENST00000310581	NM_198253.2	3	Cgc/Tgc	1/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.410202600383257	2		196	261	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs753143066	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	68	848	6	ENST00000295797.4:c.826dup	p.Thr276AsnfsTer16	p.T276Nfs*16	ENST00000295797	NM_002740.5	273	tta/ttAa	9/18	1	2	FACETS	0.882	0.771	1	0.882	0.771	1	CLONAL	1	FALSE	1	0.410202600383257	2		854	376	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522693	67522693	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	25	420	0	ENST00000274335.5:c.193del	p.Glu65LysfsTer10	p.E65Kfs*10	ENST00000274335		64	Ggg/gg	1/15	1	2	FACETS	0.622	0.493	0.768	0.622	0.493	0.768	SUBCLONAL	1	FALSE	1	0.410202600383257	2		420	196	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546784	9546784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1252319558	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	91	643	0	ENST00000353224.5:c.1238C>T	p.Pro413Leu	p.P413L	ENST00000353224	NM_177990.2	413	cCg/cTg	5/10	1	2	FACETS	0.96	0.857	1	0.96	0.857	1	CLONAL	1	FALSE	1	0.410202600383257	2		643	462	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258977	16258977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751501193	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	96	850	1	ENST00000375759.3:c.6242G>A	p.Arg2081Gln	p.R2081Q	ENST00000375759	NM_015001.2	2081	cGa/cAa	11/15	1	2	FACETS	0.895	0.8	0.995	0.895	0.8	0.995	CLONAL	1	FALSE	1	0.410202600383257	2		851	523	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114169	115114169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773465537	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	159	1040	1	ENST00000257566.3:c.1048G>A	p.Ala350Thr	p.A350T	ENST00000257566	NM_016569.3	350	Gcc/Acc	6/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.410202600383257	2		1041	701	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101967	11101967	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779161503	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	195	1235	2	ENST00000358026.2:c.1387G>A	p.Glu463Lys	p.E463K	ENST00000358026	NM_001128849.1	463	Gag/Aag	8/36	1	2	FACETS	0.973	0.901	1	0.973	0.901	1	CLONAL	1	FALSE	1	0.410202600383257	2		1237	977	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660093	227660093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143913301	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	125	1121	2	ENST00000305123.5:c.3362C>T	p.Ala1121Val	p.A1121V	ENST00000305123	NM_005544.2	1121	gCg/gTg	1/2	1	2	FACETS	0.833	0.754	0.915	0.833	0.754	0.915	CLONAL	1	FALSE	1	0.410202600383257	2		1123	732	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677249	29677250	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	51	601	0	ENST00000356175.3:c.7308_7309del	p.His2436GlnfsTer8	p.H2436Qfs*8	ENST00000356175	NM_000267.3	2436	cAT/c	49/57	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	FALSE	1	0.410202600383257	2		601	247	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528504	29528504	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs267606603	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	49	564	0	ENST00000356175.3:c.1260+1G>A		p.X420_splice	ENST00000356175	NM_000267.3	420			1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	FALSE	1	0.410202600383257	2		564	229	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14015970	14015970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768270013	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	24	461	0	ENST00000311895.7:c.290G>A	p.Arg97His	p.R97H	ENST00000311895	NM_005236.2	97	cGc/cAc	2/11	1	2	FACETS	0.563	0.443	0.698	0.563	0.443	0.698	SUBCLONAL	1	FALSE	1	0.410202600383257	2		461	208	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199492	16199492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	76	703	2	ENST00000375759.3:c.265C>T	p.Arg89Trp	p.R89W	ENST00000375759	NM_015001.2	89	Cgg/Tgg	2/15	1	2	FACETS	0.88	0.776	0.992	0.88	0.776	0.992	CLONAL	1	FALSE	1	0.410202600383257	2		705	421	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49430944	49430944	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	80	930	0	ENST00000301067.7:c.10195C>T	p.Gln3399Ter	p.Q3399*	ENST00000301067	NM_003482.3	3399	Cag/Tag	34/54	1	2	FACETS	0.736	0.649	0.829	0.736	0.649	0.829	SUBCLONAL	1	FALSE	1	0.410202600383257	2		930	530	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252027	133252027	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1475049831	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	161	1156	0	ENST00000320574.5:c.1183G>T	p.Gly395Trp	p.G395W	ENST00000320574	NM_006231.2	395	Ggg/Tgg	12/49	1	2	FACETS	0.999	0.917	1	0.999	0.917	1	CLONAL	1	FALSE	1	0.410202600383257	2		1156	786	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42050037	42050037	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	30	433	0	ENST00000219905.7:c.7191G>T	p.Lys2397Asn	p.K2397N	ENST00000219905	NM_001164273.1	2397	aaG/aaT	19/24	1	2	FACETS	0.86	0.701	1	0.86	0.701	1	CLONAL	1	FALSE	1	0.410202600383257	2		433	170	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74000695	74000696	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs745883489	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	188	1092	3	ENST00000318443.5:c.1391dup	p.Glu465ArgfsTer33	p.E465Rfs*33	ENST00000318443	NM_001024736.1	462	ttc/ttCc	7/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.410202600383257	2		1095	884	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864471	56864471	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1015912856	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	127	861	0	ENST00000308159.5:c.959C>T	p.Ala320Val	p.A320V	ENST00000308159	NM_014669.4	320	gCg/gTg	10/22	1	2	FACETS	0.964	0.876	1	0.964	0.876	1	CLONAL	1	FALSE	1	0.410202600383257	2		861	642	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645932	67645932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	94	814	0	ENST00000264010.4:c.860G>A	p.Ser287Asn	p.S287N	ENST00000264010	NM_006565.3	287	aGc/aAc	4/12	1	2	FACETS	0.85	0.759	0.947	0.85	0.759	0.947	CLONAL	1	FALSE	1	0.410202600383257	2		814	539	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935629	15935629	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	94	596	0	ENST00000268712.3:c.7304T>C	p.Leu2435Pro	p.L2435P	ENST00000268712	NM_006311.3	2435	cTg/cCg	46/46	1	2	FACETS	0.965	0.862	1	0.965	0.862	1	CLONAL	1	FALSE	1	0.410202600383257	2		596	475	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965431	15965431	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1159031268	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	47	569	0	ENST00000268712.3:c.5375A>G	p.Gln1792Arg	p.Q1792R	ENST00000268712	NM_006311.3	1792	cAg/cGg	36/46	1	2	FACETS	0.744	0.631	0.867	0.744	0.631	0.867	SUBCLONAL	1	FALSE	1	0.410202600383257	2		569	308	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18963029	18963029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	209	1204	2	ENST00000262803.5:c.896C>T	p.Ala299Val	p.A299V	ENST00000262803	NM_002911.3	299	gCc/gTc	6/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.410202600383257	2		1206	852	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303601	30303601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242761919	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	87	683	5	ENST00000262643.3:c.29C>T	p.Ala10Val	p.A10V	ENST00000262643	NM_001238.2	10	gCg/gTg	3/12	1	2	FACETS	0.759	0.673	0.85	0.759	0.673	0.85	SUBCLONAL	1	FALSE	1	0.410202600383257	2		688	559	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793071	33793071	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	140	636	0	ENST00000498907.2:c.250C>G	p.His84Asp	p.H84D	ENST00000498907	NM_004364.3	84	Cac/Gac	1/1	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.410202600383257	2		636	545	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222902	36222902	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	185	1375	1	ENST00000222270.7:c.5531C>A	p.Pro1844Gln	p.P1844Q	ENST00000222270	NM_014727.1	1844	cCa/cAa	27/37	1	2	FACETS	0.942	0.869	1	0.942	0.869	1	CLONAL	1	FALSE	1	0.410202600383257	2		1376	958	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426656	212426656	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	73	823	0	ENST00000342788.4:c.2459T>C	p.Leu820Pro	p.L820P	ENST00000342788	NM_005235.2	820	cTg/cCg	20/28	0.101569264791678	4	FACETS	1	0.964	1	0.634	0.557	0.716	INDETERMINATE	1	FALSE	2	0.410202600383257	4		823	396	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957464	1957464	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	127	982	0	ENST00000382891.5:c.2563C>A	p.Pro855Thr	p.P855T	ENST00000382891	NM_133335.3	855	Cct/Act	14/22	1	2	FACETS	0.823	0.746	0.904	0.823	0.746	0.904	CLONAL	1	FALSE	1	0.410202600383257	2		982	752	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86667992	86667992	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	17	521	0	ENST00000274376.6:c.1756T>C	p.Ser586Pro	p.S586P	ENST00000274376	NM_002890.2	586	Tcc/Ccc	13/25	1	2	FACETS	0.466	0.349	0.603	0.466	0.349	0.603	SUBCLONAL	1	FALSE	1	0.410202600383257	2		521	178	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508757	148508757	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	34	586	0	ENST00000320356.2:c.1907C>A	p.Pro636His	p.P636H	ENST00000320356	NM_004456.4	636	cCt/cAt	16/20	1	2	FACETS	0.682	0.561	0.817	0.682	0.561	0.817	SUBCLONAL	1	FALSE	1	0.410202600383257	2		586	243	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995496	68995496	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	41	737	5	ENST00000288368.4:c.1904del	p.Lys635ArgfsTer9	p.K635Rfs*9	ENST00000288368	NM_024870.2	634	Aaa/aa	18/40	1	2	FACETS	0.766	0.642	0.902	0.766	0.642	0.902	CLONAL	1	FALSE	1	0.410202600383257	2		742	261	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117870628	117870628	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	45	571	0	ENST00000297338.2:c.444A>C	p.Glu148Asp	p.E148D	ENST00000297338	NM_006265.2	148	gaA/gaC	5/14	1	2	FACETS	0.874	0.741	1	0.874	0.741	1	CLONAL	1	FALSE	1	0.410202600383257	2		571	251	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87322777	87322777	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	51	676	0	ENST00000277120.3:c.378A>C	p.Lys126Asn	p.K126N	ENST00000277120		126	aaA/aaC	5/19	0.136670585581068	0	FACETS	0.529	0.453	0.612			1	INDETERMINATE	1	FALSE	0	0.410202600383257	0		676	277	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637032	93637032	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	103	730	0	ENST00000375746.1:c.1082A>C	p.Lys361Thr	p.K361T	ENST00000375746	NM_001174167.1	361	aAg/aCg	9/14	0.136670585581068	0	FACETS	0.504	0.452	0.559			1	INDETERMINATE	1	FALSE	0	0.410202600383257	0		730	588	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760373	133760373	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	126	1210	0	ENST00000318560.5:c.2696C>A	p.Pro899Gln	p.P899Q	ENST00000318560	NM_005157.4	899	cCg/cAg	11/11	0.136670585581068	0	FACETS	0.521	0.473	0.573			1	INDETERMINATE	1	FALSE	0	0.410202600383257	0		1210	695	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	155	670	3	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	0.120210469455878	3	FACETS	1	0.982	1	0.429	0.392	0.468	INDETERMINATE	1	TRUE	0	0.252518433097526	3		673	1074	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306996	65306997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	97	480	7	ENST00000342505.4:c.2580dup	p.Pro861ThrfsTer4	p.P861Tfs*4	ENST00000342505	NM_002227.2	860	-/A	19/25	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.252518433097526	2		487	529	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851255	156851255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1480681042	NA	P-0054032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	179	842	0	ENST00000524377.1:c.2212G>A	p.Asp738Asn	p.D738N	ENST00000524377	NM_002529.3	738	Gac/Aac	17/17	1	2	FACETS	0.786	0.725	0.849	1	0.99	1	SUBCLONAL	2	TRUE	1	0.252518433097526	2		842	902	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1232964733	NA	P-0054032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	58	149	0	ENST00000324856.7:c.1015del	p.Ala339LeufsTer24	p.A339Lfs*24	ENST00000324856	NM_006015.4	337	tGg/tg	1/20	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.252518433097526	2		149	424	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0054032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	147	612	0	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.252518433097526	2		612	846	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247515	123247515	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	97	513	1	ENST00000358487.5:c.1976del	p.Lys659ArgfsTer34	p.K659Rfs*34	ENST00000358487	NM_000141.4	659	aAg/ag	14/18	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.252518433097526	2		514	596	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118365422	118365422	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	90	373	0	ENST00000534358.1:c.5307del	p.Pro1770HisfsTer53	p.P1770Hfs*53	ENST00000534358	NM_005933.3	1768	gTt/gt	18/36	1	2	FACETS	0.812	0.724	0.905	1	0.982	1	CLONAL	2	TRUE	1	0.252518433097526	2		373	439	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445041	49445041	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	83	771	2	ENST00000301067.7:c.2425del	p.Gln809ArgfsTer121	p.Q809Rfs*121	ENST00000301067	NM_003482.3	809	Cag/ag	10/54	0.0966523789976608	4	FACETS	0.8	0.704	0.904	0.4	0.352	0.452	INDETERMINATE	1	TRUE	2	0.252518433097526	4		773	1029	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123889545	123889545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1176879178	NA	P-0054032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	27	76	0	ENST00000330479.4:c.772C>T	p.Arg258Trp	p.R258W	ENST00000330479	NM_020382.3	258	Cgg/Tgg	7/9	1	2	FACETS	0.938	0.761	1	1	0.954	1	CLONAL	2	TRUE	1	0.252518433097526	2		76	114	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913837	32913837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359507	NA	P-0054032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	109	381	3	ENST00000380152.3:c.5351del	p.Asn1784ThrfsTer7	p.N1784Tfs*7	ENST00000380152		1782	cAa/ca	11/27	0.111736043360197	3	FACETS	1	0.917	1			1	INDETERMINATE	2	TRUE	NA	0.252518433097526	3		384	478	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028815	42028815	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	161	667	1	ENST00000219905.7:c.4357del	p.Tyr1453MetfsTer27	p.Y1453Mfs*27	ENST00000219905	NM_001164273.1	1451	ccT/cc	13/24	1	2	FACETS	0.763	0.7	0.828	1	0.989	1	SUBCLONAL	2	TRUE	1	0.252518433097526	2		668	836	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052635	42052635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	140	500	0	ENST00000219905.7:c.7306C>T	p.Arg2436Cys	p.R2436C	ENST00000219905	NM_001164273.1	2436	Cgt/Tgt	20/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.252518433097526	2		500	780	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478220	99478220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	88	435	0	ENST00000268035.6:c.3124C>T	p.Arg1042Cys	p.R1042C	ENST00000268035	NM_000875.3	1042	Cgt/Tgt	16/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.252518433097526	2		435	504	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2090159	2090159	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2233522	NA	P-0054032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	284	1072	0	ENST00000219066.1:c.790G>A	p.Ala264Thr	p.A264T	ENST00000219066	NM_002528.5	264	Gcc/Acc	5/6	1	2	FACETS	0.829	0.778	0.882	1	0.994	1	CLONAL	2	TRUE	1	0.252518433097526	2		1072	1357	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828110	3828110	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	159	660	0	ENST00000262367.5:c.2015G>A	p.Arg672His	p.R672H	ENST00000262367	NM_004380.2	672	cGt/cAt	10/31	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.252518433097526	2		660	988	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647146	23647146	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs113217267	NA	P-0054032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	174	792	0	ENST00000261584.4:c.721A>G	p.Asn241Asp	p.N241D	ENST00000261584	NM_024675.3	241	Aat/Gat	4/13	1	2	FACETS	0.806	0.743	0.872	1	0.99	1	CLONAL	2	TRUE	1	0.252518433097526	2		792	855	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830471	72830471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	141	588	2	ENST00000268489.5:c.6110del	p.Pro2037GlnfsTer64	p.P2037Qfs*64	ENST00000268489	NM_006885.3	2037	cCa/ca	9/10	1	2	FACETS	0.929	0.85	1	1	0.99	1	CLONAL	2	TRUE	1	0.252518433097526	2		590	601	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	92	445	0	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.252518433097526	2		445	560	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119780	70119781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0054032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	41	696	0	ENST00000245479.2:c.788dup	p.Arg264GlnfsTer32	p.R264Qfs*32	ENST00000245479	NM_000346.3	261	gag/gaGg	3/3	1	2	FACETS	0.473	0.393	0.562	0.473	0.393	0.562	SUBCLONAL	1	TRUE	1	0.252518433097526	2		696	687	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030342	11030344	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0054032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	172	667	0	ENST00000327064.4:c.1094_1096del	p.Gly365del	p.G365del	ENST00000327064	NM_199141.1	364	gaAGGa/gaa	9/16	0.252518433097526	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.252518433097526	1		667	811	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752695	42752695	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1366176199	NA	P-0054032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	241	993	2	ENST00000222329.4:c.1569del	p.Leu525SerfsTer6	p.L525Sfs*6	ENST00000222329	NM_006494.2	523	ggG/gg	4/4	0.0239251323600638	3	FACETS	0.802	0.748	0.859	0.802	0.748	0.859	INDETERMINATE	2	TRUE	1	0.252518433097526	3		995	1340	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753479	42753479	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555750721	NA	P-0054032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	301	1164	1	ENST00000222329.4:c.785del	p.Pro262LeufsTer9	p.P262Lfs*9	ENST00000222329	NM_006494.2	262	cCt/ct	4/4	0.0239251323600638	3	FACETS	0.911	0.857	0.968	0.911	0.857	0.968	INDETERMINATE	2	TRUE	1	0.252518433097526	3		1165	1473	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108211	209108211	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	148	472	4	ENST00000345146.2:c.638del	p.Asn213ThrfsTer4	p.N213Tfs*4	ENST00000345146	NM_005896.2	213	aAc/ac	6/10	0.252518433097526	1	FACETS	0.983	0.903	1	1	0.991	1	CLONAL	2	TRUE	0	0.252518433097526	1		476	521	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538287	9538287	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0054032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	153	578	0	ENST00000353224.5:c.1711del	p.Ser571ValfsTer6	p.S571Vfs*6	ENST00000353224	NM_177990.2	571	Agt/gt	7/10	1	2	FACETS	0.939	0.862	1	1	0.991	1	CLONAL	2	TRUE	1	0.252518433097526	2		578	645	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967347	134967347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749600936	NA	P-0054032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	50	522	0	ENST00000398015.3:c.2686G>A	p.Ala896Thr	p.A896T	ENST00000398015	NM_004441.4	896	Gcc/Acc	14/16	0.252518433097526	0	FACETS	0.565	0.479	0.659			1	SUBCLONAL	1	TRUE	0	0.252518433097526	0		522	524	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964872	55964872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374386254	NA	P-0054032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	32	324	0	ENST00000263923.4:c.2365G>A	p.Val789Ile	p.V789I	ENST00000263923	NM_002253.2	789	Gtt/Att	16/30	0.252518433097526	1	FACETS	0.51	0.414	0.619	0.51	0.414	0.619	SUBCLONAL	1	TRUE	0	0.252518433097526	1		324	434	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270158	66270159	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	114	372	0	ENST00000273854.3:c.1723dup	p.Ile575AsnfsTer65	p.I575Nfs*65	ENST00000273854	NM_004439.5	575	att/aAtt	8/18	0.252518433097526	1	FACETS	0.863	0.782	0.948	1	0.987	1	CLONAL	2	TRUE	0	0.252518433097526	1		372	457	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240767	55240767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770193776	NA	P-0054032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	175	905	1	ENST00000275493.2:c.2011C>T	p.Arg671Cys	p.R671C	ENST00000275493	NM_005228.3	671	Cgc/Tgc	17/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.252518433097526	2		906	1218	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966682	36966682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1220530661	NA	P-0054032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	207	674	2	ENST00000358127.4:c.644C>T	p.Pro215Leu	p.P215L	ENST00000358127	NM_001280556.1	215	cCg/cTg	6/10	0.120210469455878	3	FACETS	0.916	0.854	0.98	0.916	0.854	0.98	INDETERMINATE	3	TRUE	0	0.252518433097526	3		676	672	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395158	139395158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554826860	NA	P-0054032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1291	164	1180	1	ENST00000277541.6:c.5780C>T	p.Thr1927Met	p.T1927M	ENST00000277541	NM_017617.3	1927	aCg/aTg	31/34	0.120210469455878	3	FACETS	1	0.92	1	0.335	0.306	0.365	INDETERMINATE	1	TRUE	0	0.252518433097526	3		1181	1455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577543	7577551	+	inframe_deletion	In_Frame_Del	DEL	CATGCCGCC	CATGCCGCC	-	novel	NA	P-0054034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	131	683	0	ENST00000269305.4:c.730_738del	p.Gly244_Met246del	p.G244_M246del	ENST00000269305	NM_001126112.2	244	GGCGGCATG/-	7/11	0.711975904262574	1	FACETS	0.837	0.774	0.901	0.837	0.774	0.901	CLONAL	1	TRUE	0	0.711975904262574	1		683	283	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143994	11143994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	23	758	0	ENST00000358026.2:c.3575G>A	p.Arg1192His	p.R1192H	ENST00000358026	NM_001128849.1	1192	cGc/cAc	26/36	1	2	FACETS	0.243	0.188	0.307	0.243	0.188	0.307	SUBCLONAL	1	TRUE	1	0.2	2		758	947	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0054035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	47	866	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.381	0.32	0.449	0.381	0.32	0.449	SUBCLONAL	1	TRUE	1	0.2	2		867	1234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0054035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	75	760	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	1	2	FACETS	0.64	0.559	0.728	0.64	0.559	0.728	SUBCLONAL	1	TRUE	1	0.2	2		760	1172	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0054035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	107	498	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.2	2		498	916	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023905	27023905	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	64	123	2	ENST00000324856.7:c.1011G>A	p.Trp337Ter	p.W337*	ENST00000324856	NM_006015.4	337	tgG/tgA	1/20	0.18096543718761	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	0	0.2	2		125	291	SUCCESS
BTK	695	MSKCC	GRCh37	X	100625010	100625010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	38	596	0	ENST00000308731.7:c.367C>T	p.Arg123Trp	p.R123W	ENST00000308731	NM_000061.2	123	Cgg/Tgg	5/19	1	2	FACETS	0.5	0.412	0.599	0.5	0.412	0.599	SUBCLONAL	1	TRUE	1	0.2	2		596	760	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244358	5244358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	201	983	3	ENST00000357368.4:c.1124C>T	p.Pro375Leu	p.P375L	ENST00000357368	NM_002850.3	375	cCg/cTg	11/38	1	2	FACETS	0.84	0.777	0.906	1	0.992	1	CLONAL	2	TRUE	1	0.2	2		986	1196	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348110	89348110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1170699512	NA	P-0054035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	95	907	1	ENST00000301030.4:c.4840C>T	p.Arg1614Trp	p.R1614W	ENST00000301030	NM_001256183.1	1614	Cgg/Tgg	9/13	1	2	FACETS	0.752	0.667	0.843	0.752	0.667	0.843	SUBCLONAL	1	TRUE	1	0.2	2		908	1264	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95597936	95597936	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	39	426	0	ENST00000393063.1:c.348T>G	p.His116Gln	p.H116Q	ENST00000393063	NM_030621.3	116	caT/caG	5/28	1	2	FACETS	0.653	0.54	0.78	0.653	0.54	0.78	SUBCLONAL	1	TRUE	1	0.2	2		426	597	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456411	99456411	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	88	641	0	ENST00000268035.6:c.1728G>C	p.Gln576His	p.Q576H	ENST00000268035	NM_000875.3	576	caG/caC	8/21	1	2	FACETS	0.909	0.804	1	0.909	0.804	1	CLONAL	1	TRUE	1	0.2	2		641	968	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041672	14041672	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758565772	NA	P-0054035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	47	550	0	ENST00000311895.7:c.2219G>A	p.Arg740His	p.R740H	ENST00000311895	NM_005236.2	740	cGc/cAc	11/11	1	2	FACETS	0.633	0.533	0.745	0.633	0.533	0.745	SUBCLONAL	1	TRUE	1	0.2	2		550	742	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508261	38508278	+	inframe_deletion	In_Frame_Del	DEL	AGGTGCGCAAAGCGCACC	AGGTGCGCAAAGCGCACC	-	novel	NA	P-0054035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	141	819	0	ENST00000254066.5:c.572_589del	p.Val191_Gln196del	p.V191_Q196del	ENST00000254066	NM_000964.3	190	aAGGTGCGCAAAGCGCACCag/aag	5/9	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.2	2		819	1057	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222020	2222020	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764430547	NA	P-0054035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	93	1103	0	ENST00000398665.3:c.2852G>A	p.Gly951Asp	p.G951D	ENST00000398665	NM_032482.2	951	gGc/gAc	24/28	1	2	FACETS	0.739	0.655	0.83	0.739	0.655	0.83	SUBCLONAL	1	TRUE	1	0.2	2		1103	1258	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201731	66201731	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	64	504	0	ENST00000273854.3:c.2771A>T	p.Lys924Met	p.K924M	ENST00000273854	NM_004439.5	924	aAg/aTg	16/18	1	2	FACETS	0.934	0.808	1	0.934	0.808	1	CLONAL	1	TRUE	1	0.2	2		504	685	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971098	21971103	+	frameshift_variant	Frame_Shift_Del	DEL	CGGGCA	CGGGCA	GGGG	novel	NA	P-0054035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	61	722	2	ENST00000304494.5:c.255_260delinsCCCC	p.Ala86ProfsTer33	p.A86Pfs*33	ENST00000304494	NM_000077.4	85	gcTGCCCGg/gcCCCCg	2/3	1	2	FACETS	0.737	0.634	0.849	0.737	0.634	0.849	SUBCLONAL	1	TRUE	1	0.2	2		724	828	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143994	11143994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	31	758	0	ENST00000358026.2:c.3575G>A	p.Arg1192His	p.R1192H	ENST00000358026	NM_001128849.1	1192	cGc/cAc	26/36	0.3	1	FACETS	0.474	0.384	0.576	0.474	0.384	0.576	SUBCLONAL	1	TRUE	0	0.32	1		758	343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0054035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	55	866	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.32	2		867	341	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348471	70348471	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	54	623	0	ENST00000374080.3:c.3378C>A	p.Asp1126Glu	p.D1126E	ENST00000374080		1126	gaC/gaA	24/45	1	2	FACETS	0.893	0.765	1	0.893	0.765	1	CLONAL	1	TRUE	1	0.32	2		623	378	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121569	193121574	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GTAACG	GTAACG	-	novel	NA	P-0054035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	25	337	0	ENST00000367435.3:c.971_972+4del		p.VTdel	ENST00000367435	NM_024529.4	323	GTAACG/-	10/17	1	2	FACETS	0.526	0.415	0.653	0.526	0.415	0.653	SUBCLONAL	1	TRUE	1	0.32	2		337	297	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490313	56490327	+	inframe_deletion	In_Frame_Del	DEL	GAAGGCTAACAAAGT	GAAGGCTAACAAAGT	-	novel	NA	P-0054035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	75	433	0	ENST00000267101.3:c.2082_2096del	p.Glu694_Val699delinsAsp	p.E694_V699delinsD	ENST00000267101	NM_001982.3	694	gaGAAGGCTAACAAAGTc/gac	18/28	0.169754356193295	4	FACETS	0.988	0.874	1	0.659	0.583	0.74	INDETERMINATE	2	TRUE	1	0.32	4		433	313	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650846	37650846	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	70	668	0	ENST00000447079.4:c.2318G>C	p.Arg773Pro	p.R773P	ENST00000447079	NM_015083.1	773	cGt/cCt	5/14	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.32	2		668	432	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218521	5218521	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772880114	NA	P-0054035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	26	871	0	ENST00000357368.4:c.3958C>T	p.Arg1320Cys	p.R1320C	ENST00000357368	NM_002850.3	1320	Cgc/Tgc	25/38	0.3	1	FACETS	0.344	0.272	0.426	0.344	0.272	0.426	SUBCLONAL	1	TRUE	0	0.32	1		871	397	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056108	26056867	+	coding_sequence_variant,5_prime_UTR_variant	Frame_Shift_Del	DEL	CTTGGGCTTCGCAACCTTGGCCTTCTTTGGGCTCTTAGCCACTTTCTTGGTTACAGTGGCCGCGGCCGGCTTCTTCGCTTTCTTCGGTGTTTTCTTAGCGCTCTTCTTCGGAGTTGCGCCGCCAGCCGCCTTCTTGGGCTTCTTGGCTGCCCCAACTGGCTTCTTAGGTTTGGTTCCGCCCGCCTTTTTAACCTTGGGCTTGGCTTCCCCGGAGGCTGCCTTCTTGTTGAGTTTAAAGGAGCCAGAAGCACCGGTGCCTTTCGTTTGCACCAGAGTGCCCTTGCTCACCAGGCTCTTGAGACCAAGTTTGATACGGCTGTTGTTTTTCTCCACATCATAGCCGGCGGCAGCCAACGCTTTTTTCAGAGCAGCCAGAGAAACTCCGCTACGCTCTTTAGAGGCGGCCACAGCCTTGGTGATGAGCTCTGACACCGGGGGACCAGACGCCTTACGAGGCGTACCCCCAGCCTTTTTGGCCGCCTTCTTCTTTACAGGGGCCTTCTCCGCAGGAGGCGCGGCAGCGGGAGCGGCAGGAGCAGTCTCGGACATGTTGAGAATCAAAAACTCGGGTACAAGTGGCAAAGCGCCGATGAAGCAGCGCCTGGGCAGGGCCGCTGTATATATAGAGCGCAGGCGCGCTCTGATTGGTGCTCTGGTCGCCCGCCTGGCTGGCAGGCTCTGAGCCGCTGCGCTGCTCCCAAGTTGTGTTTGTTCCACCTCACAAAAGGGGAAAAATATTAAAATTCCCCGCACCAAATCA	CTTGGGCTTCGCAACCTTGGCCTTCTTTGGGCTCTTAGCCACTTTCTTGGTTACAGTGGCCGCGGCCGGCTTCTTCGCTTTCTTCGGTGTTTTCTTAGCGCTCTTCTTCGGAGTTGCGCCGCCAGCCGCCTTCTTGGGCTTCTTGGCTGCCCCAACTGGCTTCTTAGGTTTGGTTCCGCCCGCCTTTTTAACCTTGGGCTTGGCTTCCCCGGAGGCTGCCTTCTTGTTGAGTTTAAAGGAGCCAGAAGCACCGGTGCCTTTCGTTTGCACCAGAGTGCCCTTGCTCACCAGGCTCTTGAGACCAAGTTTGATACGGCTGTTGTTTTTCTCCACATCATAGCCGGCGGCAGCCAACGCTTTTTTCAGAGCAGCCAGAGAAACTCCGCTACGCTCTTTAGAGGCGGCCACAGCCTTGGTGATGAGCTCTGACACCGGGGGACCAGACGCCTTACGAGGCGTACCCCCAGCCTTTTTGGCCGCCTTCTTCTTTACAGGGGCCTTCTCCGCAGGAGGCGCGGCAGCGGGAGCGGCAGGAGCAGTCTCGGACATGTTGAGAATCAAAAACTCGGGTACAAGTGGCAAAGCGCCGATGAAGCAGCGCCTGGGCAGGGCCGCTGTATATATAGAGCGCAGGCGCGCTCTGATTGGTGCTCTGGTCGCCCGCCTGGCTGGCAGGCTCTGAGCCGCTGCGCTGCTCCCAAGTTGTGTTTGTTCCACCTCACAAAAGGGGAAAAATATTAAAATTCCCCGCACCAAATCA	-	novel	NA	P-0054035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	546	20	0				ENST00000343677	NM_005319.3	?-183/213		1/1	1	2	FACETS	1	0.991	1	1	0.998	1	CLONAL	4	TRUE	1	0.32	2		20	809	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	57	563	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.947	0.812	1	0.947	0.812	1	CLONAL	1	TRUE	1	0.205751597983229	2		563	585	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094409	27094409	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	78	648	1	ENST00000324856.7:c.3119del	p.Asn1040IlefsTer19	p.N1040Ifs*19	ENST00000324856	NM_006015.4	1039	acA/ac	11/20	0.205751597983229	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.205751597983229	1		649	656	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204627	108204627	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	62	241	0	ENST00000278616.4:c.7943del	p.Pro2648GlnfsTer12	p.P2648Qfs*12	ENST00000278616	NM_000051.3	2648	Cca/ca	54/63	0.199744598660481	2	FACETS	1	0.97	1	0.737	0.639	0.843	CLONAL	1	TRUE	0	0.205751597983229	2		241	409	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649405	23649405	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs151316635	NA	P-0054036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	51	441	0	ENST00000261584.4:c.94C>G	p.Leu32Val	p.L32V	ENST00000261584	NM_024675.3	32	Cta/Gta	2/13	1	2	FACETS	0.793	0.673	0.925	0.793	0.673	0.925	CLONAL	1	TRUE	1	0.205751597983229	2		441	625	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054036-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	54	563	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	FALSE	1	0.162499804792435	2		563	631	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094409	27094409	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054036-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	101	648	1	ENST00000324856.7:c.3119del	p.Asn1040IlefsTer19	p.N1040Ifs*19	ENST00000324856	NM_006015.4	1039	acA/ac	11/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.162499804792435	2		649	952	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204627	108204627	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054036-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	45	241	0	ENST00000278616.4:c.7943del	p.Pro2648GlnfsTer12	p.P2648Qfs*12	ENST00000278616	NM_000051.3	2648	Cca/ca	54/63	0.144820364555245	2	FACETS	0.796	0.671	0.933	0.796	0.671	0.933	CLONAL	2	FALSE	0	0.162499804792435	2		241	348	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649405	23649405	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs151316635	NA	P-0054036-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	55	441	0	ENST00000261584.4:c.94C>G	p.Leu32Val	p.L32V	ENST00000261584	NM_024675.3	32	Cta/Gta	2/13	1	2	FACETS	0.911	0.778	1	0.911	0.778	1	CLONAL	1	FALSE	1	0.162499804792435	2		441	743	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0054037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	81	439	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.79	0.696	0.89	1	0.979	1	SUBCLONAL	2	TRUE	1	0.16	2		439	641	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	55	576	4	ENST00000304494.5:c.143C>T	p.Pro48Leu	p.P48L	ENST00000304494	NM_000077.4	48	cCg/cTg	1/3	0.209657580511388	1	FACETS	0.812	0.693	0.943	0.812	0.693	0.943	CLONAL	1	TRUE	0	0.16	1		580	779	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774154	56774154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	49	524	2	ENST00000337432.4:c.505G>A	p.Val169Met	p.V169M	ENST00000337432	NM_058216.2	169	Gtg/Atg	3/9	1	2	FACETS	0.834	0.705	0.977	0.834	0.705	0.977	CLONAL	1	TRUE	1	0.16	2		526	734	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303461	91303461	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	39	401	0	ENST00000355112.3:c.1172T>C	p.Leu391Pro	p.L391P	ENST00000355112	NM_000057.2	391	cTg/cCg	6/22	1	2	FACETS	0.822	0.68	0.981	0.822	0.68	0.981	CLONAL	1	TRUE	1	0.16	2		401	593	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927477	178927477	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	260	367	0	ENST00000263967.3:c.1240G>C	p.Gly414Arg	p.G414R	ENST00000263967	NM_006218.2	414	Ggt/Cgt	7/21	0.737922339077811	5	FACETS	1	0.97	1	0.696	0.656	0.736	CLONAL	2	TRUE	2	0.857476058967748	5		367	664	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0054038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	549	736	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.850445387127806	2	FACETS	0.991	0.971	1	0.991	0.971	1	CLONAL	2	TRUE	0	0.857476058967748	2		736	646	SUCCESS
APC	324	MSKCC	GRCh37	5	112179432	112179432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747362422	NA	P-0054038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	173	516	0	ENST00000257430.4:c.8141G>A	p.Arg2714His	p.R2714H	ENST00000257430	NM_000038.5	2714	cGt/cAt	16/16	0.843998344358231	3	FACETS	0.919	0.85	0.991	0.46	0.425	0.496	CLONAL	1	TRUE	1	0.857476058967748	3		516	627	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249511	153249511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	312	514	0	ENST00000281708.4:c.1267G>A	p.Gly423Arg	p.G423R	ENST00000281708	NM_033632.3	423	Gga/Aga	9/12	0.843998344358231	3	FACETS	0.88	0.839	0.92	0.88	0.839	0.92	CLONAL	2	TRUE	1	0.857476058967748	3		514	591	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281814	46281814	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1953	385	585	0	ENST00000371998.3:c.4261C>G	p.Gln1421Glu	p.Q1421E	ENST00000371998		1421	Cag/Gag	22/23	0.857476058967748	9	FACETS	0.768	0.726	0.812			1	SUBCLONAL	2	TRUE	NA	0.857476058967748	9		585	2338	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0054039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	57	650	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.284	0.243	0.329	0.284	0.243	0.329	SUBCLONAL	1	TRUE	1	0.667814225585855	2		650	601	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436410	49436410	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs756972898	NA	P-0054039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	46	611	0	ENST00000301067.7:c.5801A>G	p.Asn1934Ser	p.N1934S	ENST00000301067	NM_003482.3	1934	aAt/aGt	27/54	1	2	FACETS	0.233	0.196	0.274	0.233	0.196	0.274	SUBCLONAL	1	TRUE	1	0.667814225585855	2		611	591	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871256	35871256	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	46	411	0	ENST00000216797.5:c.917A>C	p.Asp306Ala	p.D306A	ENST00000216797	NM_020529.2	306	gAt/gCt	6/6	0.233105616602967	1	FACETS	0.143	0.12	0.169	0.143	0.12	0.169	INDETERMINATE	1	TRUE	0	0.667814225585855	1		411	641	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295212	1295212	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0054039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	140	334	1				ENST00000310581	NM_198253.2	-/1132			0.667814225585855	3	FACETS	1	0.967	1	0.554	0.507	0.602	CLONAL	1	TRUE	1	0.667814225585855	3		335	505	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295225	1295225	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0054039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	114	389	1				ENST00000310581	NM_198253.2	-/1132			0.667814225585855	3	FACETS	0.9	0.814	0.99	0.45	0.407	0.495	CLONAL	1	TRUE	1	0.667814225585855	3		390	506	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949065	44949065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	46	501	0	ENST00000377967.4:c.3626G>A	p.Arg1209Lys	p.R1209K	ENST00000377967	NM_021140.2	1209	aGg/aAg	25/29	1	2	FACETS	0.174	0.146	0.206	0.174	0.146	0.206	SUBCLONAL	1	TRUE	1	0.667814225585855	2		501	791	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	292	918	0	ENST00000269305.4:c.383del	p.Pro128LeufsTer42	p.P128Lfs*42	ENST00000269305	NM_001126112.2	128	cCt/ct	5/11	0.305678705668841	1	FACETS	0.92	0.868	0.972	1	0.995	1	CLONAL	2	FALSE	0	0.305678705668841	1		918	880	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2220201	2220201	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	163	971	0	ENST00000398665.3:c.2786G>A	p.Ser929Asn	p.S929N	ENST00000398665	NM_032482.2	929	aGc/aAc	23/28	0.27551869477753	1	FACETS	0.794	0.727	0.864	0.794	0.727	0.864	SUBCLONAL	1	FALSE	0	0.305678705668841	1		971	1138	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	48	386	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.347378587012059	1	FACETS	0.878	0.748	1	0.878	0.748	1	CLONAL	1	TRUE	0	0.347378587012059	1		386	260	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248444	212248444	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397514263	NA	P-0054041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	62	400	2	ENST00000342788.4:c.3823C>T	p.Arg1275Trp	p.R1275W	ENST00000342788	NM_005235.2	1275	Cgg/Tgg	28/28	1	2	FACETS	0.848	0.735	0.97	0.848	0.735	0.97	CLONAL	1	TRUE	1	0.347378587012059	2		402	421	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727829	41727829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs545028002	NA	P-0054041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	108	942	4	ENST00000301178.4:c.454G>A	p.Ala152Thr	p.A152T	ENST00000301178	NM_021913.4	152	Gcc/Acc	4/20	1	2	FACETS	0.852	0.765	0.944	0.852	0.765	0.944	CLONAL	1	TRUE	1	0.347378587012059	2		946	730	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186742	108186742	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs532480170	NA	P-0054041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	78	423	0	ENST00000278616.4:c.6100C>T	p.Arg2034Ter	p.R2034*	ENST00000278616	NM_000051.3	2034	Cga/Tga	42/63	0.347378587012059	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.347378587012059	1		423	260	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988452	41988455	+	frameshift_variant	Frame_Shift_Del	DEL	CAAA	CAAA	-	novel	NA	P-0054042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	97	375	0	ENST00000219905.7:c.1246_1249del	p.Asn416ValfsTer7	p.N416Vfs*7	ENST00000219905	NM_001164273.1	415	tCAAAc/tc	3/24	1	2	FACETS	0.821	0.733	0.915	0.821	0.733	0.915	CLONAL	1	TRUE	1	0.357874835341318	2		375	660	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060912	38060912	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	133	672	1	ENST00000250448.2:c.1077del	p.Ile360Ter	p.I360*	ENST00000250448	NM_004496.3	359	ccC/cc	2/2	0.357874835341318	3	FACETS	0.925	0.84	1	0.463	0.42	0.508	CLONAL	1	TRUE	1	0.357874835341318	3		673	947	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578181	7578192	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCTCATAG	GGCGGCTCATAG	-	rs876660749	NA	P-0054042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	155	689	0	ENST00000269305.4:c.657_668del	p.Tyr220_Pro223del	p.Y220_P223del	ENST00000269305	NM_001126112.2	219	ccCTATGAGCCGCCt/cct	6/11	0.292603709620474	1	FACETS	0.992	0.91	1	0.992	0.91	1	CLONAL	1	TRUE	0	0.357874835341318	1		689	717	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347610	118347610	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs782451966	NA	P-0054042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	199	456	1	ENST00000534358.1:c.3247C>T	p.Arg1083Ter	p.R1083*	ENST00000534358	NM_005933.3	1083	Cga/Tga	4/36	0.199530020853088	3	FACETS	0.831	0.771	0.892	0.831	0.771	0.892	INDETERMINATE	2	TRUE	1	0.357874835341318	3		457	789	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858456	57858456	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	237	484	0	ENST00000228682.2:c.194G>A	p.Gly65Asp	p.G65D	ENST00000228682	NM_005269.2	65	gGc/gAc	4/12	0.357874835341318	3	FACETS	0.945	0.884	1	0.945	0.884	1	CLONAL	2	TRUE	1	0.357874835341318	3		484	826	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920410	134920410	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	116	487	0	ENST00000398015.3:c.2225A>C	p.His742Pro	p.H742P	ENST00000398015	NM_004441.4	742	cAt/cCt	12/16	0.357874835341318	3	FACETS	0.932	0.84	1	0.466	0.42	0.515	CLONAL	1	TRUE	1	0.357874835341318	3		487	820	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041698	42041704	+	frameshift_variant	Frame_Shift_Del	DEL	TCCCTTC	TCCCTTC	GA	novel	NA	P-0054042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	96	402	1	ENST00000219905.7:c.5893_5899delinsGA	p.Ser1965GlufsTer14	p.S1965Efs*14	ENST00000219905	NM_001164273.1	1965	TCCCTTCag/GAag	17/24	1	2	FACETS	0.992	0.886	1	0.992	0.886	1	CLONAL	1	TRUE	1	0.357874835341318	2		403	541	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830806	72830807	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	49	779	0	ENST00000268489.5:c.5774dup	p.Gly1926TrpfsTer3	p.G1926Wfs*3	ENST00000268489	NM_006885.3	1925	ggt/ggGt	9/10	0.3	1	FACETS	0.69	0.584	0.806	0.69	0.584	0.806	SUBCLONAL	1	TRUE	0	0.24	1		779	521	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720675	89720675	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	59	436	0	ENST00000371953.3:c.826A>G	p.Asn276Asp	p.N276D	ENST00000371953	NM_000314.4	276	Aat/Gat	8/9	1	2	FACETS	0.873	0.752	1	0.873	0.752	1	CLONAL	1	TRUE	1	0.24	2		436	563	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670256	134670256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	24	503	0	ENST00000398015.3:c.167G>A	p.Arg56His	p.R56H	ENST00000398015	NM_004441.4	56	cGc/cAc	3/16	1	2	FACETS	0.513	0.402	0.641	0.513	0.402	0.641	SUBCLONAL	1	TRUE	1	0.24	2		503	390	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870258	155870258	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	76	669	0	ENST00000368323.3:c.581A>G	p.Glu194Gly	p.E194G	ENST00000368323	NM_006912.5	194	gAg/gGg	6/6	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.24	2		669	626	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661358	227661358	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	76	829	0	ENST00000305123.5:c.2097G>A	p.Trp699Ter	p.W699*	ENST00000305123	NM_005544.2	699	tgG/tgA	1/2	1	2	FACETS	0.961	0.843	1	0.961	0.843	1	CLONAL	1	TRUE	1	0.24	2		829	659	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123260408	123260408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	121	690	0	ENST00000358487.5:c.1493C>T	p.Ala498Val	p.A498V	ENST00000358487	NM_000141.4	498	gCg/gTg	11/18	0.358118957426997	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	0	0.358118957426997	1		690	443	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279449	1279449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756152343	NA	P-0054044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	160	1136	2	ENST00000310581.5:c.2087G>A	p.Arg696His	p.R696H	ENST00000310581	NM_198253.2	696	cGt/cAt	5/16	0.358118957426997	0	FACETS	1	0.976	1			1	CLONAL	1	FALSE	0	0.358118957426997	0		1138	505	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011162	12011163	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0054044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	28	298	0	ENST00000353533.5:c.572_573dup	p.Val192MetfsTer6	p.V192Mfs*6	ENST00000353533	NM_003010.3	190	aaa/aaATa	5/11	0.358118957426997	1	FACETS	0.773	0.637	0.917	1	0.948	1	CLONAL	2	FALSE	0	0.358118957426997	1		298	83	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271274	38271274	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2326	169	1030	1	ENST00000425967.3:c.2434C>A	p.Pro812Thr	p.P812T	ENST00000425967	NM_001174067.1	812	Ccc/Acc	19/19	0.358118957426997	15	FACETS	1	0.981	1			1	CLONAL	1	FALSE	NA	0.358118957426997	15		1031	2495	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250041	110250041	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	128	735	0	ENST00000374672.4:c.634T>C	p.Tyr212His	p.Y212H	ENST00000374672	NM_004235.4	212	Tac/Cac	3/5	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.358118957426997	2		735	527	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0054045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	65	496	4	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.89	0.772	1	0.89	0.772	1	CLONAL	1	TRUE	1	0.27	2		500	541	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0054045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	131	473	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.976	1	1	0.992	1	CLONAL	2	TRUE	1	0.27	2		478	411	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0054045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	61	290	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.27	2		290	397	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053022	180053023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750808726	NA	P-0054045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	97	1088	4	ENST00000261937.6:c.1267dup	p.Gln423ProfsTer4	p.Q423Pfs*4	ENST00000261937	NM_182925.4	423	cag/cCag	10/30	0.3	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.27	1		1092	602	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446283	70446284	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	91	824	3	ENST00000373644.4:c.5230dup	p.Arg1744LysfsTer26	p.R1744Kfs*26	ENST00000373644	NM_030625.2	1741	-/A	11/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.27	2		827	536	SUCCESS
APC	324	MSKCC	GRCh37	5	112128161	112128161	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	59	281	0	ENST00000257430.4:c.664C>T	p.Gln222Ter	p.Q222*	ENST00000257430	NM_000038.5	222	Cag/Tag	7/16	1	2	FACETS	0.934	0.805	1	0.934	0.805	1	CLONAL	1	TRUE	1	0.27	2		281	468	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274172	10274173	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1555491538	NA	P-0054045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	67	652	0	ENST00000330684.3:c.96dup	p.Ala33ArgfsTer105	p.A33Rfs*105	ENST00000330684	NM_001134407.1	32	-/C	2/13	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.27	2		652	450	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220098	133220099	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	rs758487568	NA	P-0054045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	93	925	1	ENST00000320574.5:c.4337_4338dup	p.Val1447TrpfsTer7	p.V1447Wfs*7	ENST00000320574	NM_006231.2	1446	-/TG	34/49	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.27	2		926	680	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271304	18271304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs553673157	NA	P-0054045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	107	882	0	ENST00000222254.8:c.346G>A	p.Glu116Lys	p.E116K	ENST00000222254	NM_005027.3	116	Gag/Aag	3/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.27	2		882	732	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799130	42799131	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	86	965	1	ENST00000575354.2:c.4620dup	p.Thr1541HisfsTer18	p.T1541Hfs*18	ENST00000575354	NM_015125.3	1538	-/C	20/20	1	2	FACETS	0.991	0.877	1	0.991	0.877	1	CLONAL	1	TRUE	1	0.27	2		966	643	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186839	108186839	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1565500074	NA	P-0054045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	64	337	0	ENST00000278616.4:c.6197A>G	p.Gln2066Arg	p.Q2066R	ENST00000278616	NM_000051.3	2066	cAg/cGg	42/63	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.27	2		337	413	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128420046	128420047	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	102	550	4	ENST00000265960.3:c.381dup	p.Ser128IlefsTer28	p.S128Ifs*28	ENST00000265960	NM_001006617.1	127	-/A	4/12	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.27	2		554	608	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927420	245927420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	63	445	0	ENST00000388985.4:c.1108G>A	p.Gly370Arg	p.G370R	ENST00000388985		370	Ggg/Agg	11/12	1	2	FACETS	0.879	0.761	1	0.879	0.761	1	CLONAL	1	TRUE	1	0.27	2		445	531	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514782	103514782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	39	353	1	ENST00000355739.4:c.1283G>A	p.Ser428Asn	p.S428N	ENST00000355739	NM_000123.3	428	aGt/aAt	8/15	1	2	FACETS	0.821	0.682	0.975	0.821	0.682	0.975	CLONAL	1	TRUE	1	0.27	2		354	352	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438222	110438222	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	28	113	0	ENST00000375856.3:c.179C>A	p.Ala60Glu	p.A60E	ENST00000375856	NM_003749.2	60	gCg/gAg	1/2	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.27	2		113	139	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350379	89350379	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	101	681	0	ENST00000301030.4:c.2571C>A	p.Ser857Arg	p.S857R	ENST00000301030	NM_001256183.1	857	agC/agA	9/13	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.27	2		681	666	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715967	52715968	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	109	768	0	ENST00000322088.6:c.537dup	p.Met180HisfsTer25	p.M180Hfs*25	ENST00000322088	NM_014225.5	178	acc/aCcc	5/15	0.23103058577943	0	FACETS	0.982	0.884	1			1	CLONAL	1	TRUE	0	0.27	0		768	600	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084118	47084118	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	84	587	0	ENST00000409792.3:c.7171T>G	p.Leu2391Val	p.L2391V	ENST00000409792	NM_014159.6	2391	Tta/Gta	17/21	1	2	FACETS	0.956	0.845	1	0.956	0.845	1	CLONAL	1	TRUE	1	0.27	2		587	651	SUCCESS
APC	324	MSKCC	GRCh37	5	112173860	112173875	+	frameshift_variant	Frame_Shift_Del	DEL	GGAATTGGTCTAGGCA	GGAATTGGTCTAGGCA	-	novel	NA	P-0054045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	33	293	0	ENST00000257430.4:c.2569_2584del	p.Gly857ThrfsTer54	p.G857Tfs*54	ENST00000257430	NM_000038.5	857	GGAATTGGTCTAGGCAac/ac	16/16	1	2	FACETS	0.721	0.588	0.87	0.721	0.588	0.87	SUBCLONAL	1	TRUE	1	0.27	2		293	339	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64290000	64290000	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	83	456	0	ENST00000370651.3:c.443A>G	p.Tyr148Cys	p.Y148C	ENST00000370651	NM_003463.4	148	tAt/tGt	6/6	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.27	2		456	560	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6045558	6045558	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	142	395	0	ENST00000265849.7:c.128T>G	p.Val43Gly	p.V43G	ENST00000265849	NM_000535.5	43	gTa/gGa	2/15	0.3	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.27	2		395	430	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739031	40739031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358914349	NA	P-0054046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	139	692	1	ENST00000373198.4:c.3253G>A	p.Val1085Ile	p.V1085I	ENST00000373198	NM_133170.3	1085	Gtc/Atc	24/32	0.258561633811904	3	FACETS	1	0.951	1			1	CLONAL	1	TRUE	NA	0.27477513412227	3		693	1076	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127739	64127739	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	155	949	0	ENST00000334205.4:c.232A>G	p.Thr78Ala	p.T78A	ENST00000334205	NM_003942.2	78	Acg/Gcg	3/17	0.262685528418665	3	FACETS	0.973	0.888	1	0.486	0.444	0.531	CLONAL	1	TRUE	1	0.27477513412227	3		949	1319	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122911	2122911	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	147	825	0	ENST00000219476.3:c.2282A>T	p.Asp761Val	p.D761V	ENST00000219476	NM_000548.3	761	gAc/gTc	21/42	1	2	FACETS	0.993	0.906	1	0.993	0.906	1	CLONAL	1	TRUE	1	0.27477513412227	2		825	1077	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37680977	37680977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751631029	NA	P-0054046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	152	492	1	ENST00000447079.4:c.3146G>A	p.Arg1049His	p.R1049H	ENST00000447079	NM_015083.1	1049	cGt/cAt	12/14	0.273675009865503	2	FACETS	0.91	0.836	0.987	0.91	0.836	0.987	CLONAL	2	TRUE	0	0.27477513412227	2		493	608	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099403	157099435	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAGCAACAGCAGCAG	CAGCAGCAGCAGCAGCAGCAGCAACAGCAGCAG	-	novel	NA	P-0054046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	58	350	0	ENST00000346085.5:c.354_386del	p.Gln121_Gln131del	p.Q121_Q131del	ENST00000346085	NM_020732.3	114	CAGCAGCAGCAGCAGCAGCAGCAACAGCAGCAG/-	1/20	0.262685528418665	3	FACETS	0.964	0.829	1	0.482	0.414	0.556	CLONAL	1	TRUE	1	0.27477513412227	3		350	498	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5463050	5463050	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	52	257	0	ENST00000381577.3:c.611A>T	p.Asn204Ile	p.N204I	ENST00000381577	NM_014143.3	204	aAt/aTt	4/7	0.262685528418665	3	FACETS	1	0.908	1	0.544	0.464	0.63	CLONAL	1	TRUE	1	0.27477513412227	3		257	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577146	7577153	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TAGATTAC	TAGATTAC	GAA	novel	NA	P-0054046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	216	721	2	ENST00000269305.4:c.785_792delinsTTC	p.Gly262ValfsTer8	p.G262Vfs*8	ENST00000269305	NM_001126112.2	262	gGTAATCTA/gTTC	8/11	0.273675009865503	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.27477513412227	2		723	747	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0054047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	56	570	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.701	0.6	0.811	0.701	0.6	0.811	SUBCLONAL	1	TRUE	1	0.268655546773615	2		570	595	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023408	27023408	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	36	384	0	ENST00000324856.7:c.514C>T	p.Gln172Ter	p.Q172*	ENST00000324856	NM_006015.4	172	Caa/Taa	1/20	1	2	FACETS	0.662	0.544	0.793	0.662	0.544	0.793	SUBCLONAL	1	TRUE	1	0.268655546773615	2		384	405	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016679	12016679	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0054047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	35	316	0	ENST00000353533.5:c.813+2T>G		p.X271_splice	ENST00000353533	NM_003010.3	271			1	2	FACETS	0.782	0.643	0.938	0.782	0.643	0.938	CLONAL	1	TRUE	1	0.268655546773615	2		316	333	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	92	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.947	1	1	0.99	1	CLONAL	3	TRUE	1	0.281833478954411	2		276	205	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557630	95557630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	197	526	0	ENST00000393063.1:c.5437G>A	p.Glu1813Lys	p.E1813K	ENST00000393063	NM_030621.3	1813	Gag/Aag	26/28	1	2	FACETS	0.987	0.924	1	1	0.995	1	CLONAL	3	TRUE	1	0.281833478954411	2		526	472	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222406	2222406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755921261	NA	P-0054049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	166	864	0	ENST00000398665.3:c.3238G>A	p.Gly1080Arg	p.G1080R	ENST00000398665	NM_032482.2	1080	Ggg/Agg	24/28	1	2	FACETS	1	0.928	1	1	0.992	1	CLONAL	2	TRUE	1	0.281833478954411	2		864	586	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95579452	95579452	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	95	294	0	ENST00000393063.1:c.2017del	p.Ser673HisfsTer12	p.S673Hfs*12	ENST00000393063	NM_030621.3	673	Tca/ca	13/28	1	2	FACETS	0.895	0.811	0.982	1	0.99	1	CLONAL	3	TRUE	1	0.281833478954411	2		294	251	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498060	29498060	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	33	713	0	ENST00000389048.3:c.1946C>G	p.Ala649Gly	p.A649G	ENST00000389048	NM_004304.4	649	gCa/gGa	11/29	1	2	FACETS	0.401	0.326	0.486	0.401	0.326	0.486	SUBCLONAL	1	TRUE	1	0.281833478954411	2		713	584	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514789	44514789	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	28	660	0	ENST00000291552.4:c.458C>A	p.Ala153Asp	p.A153D	ENST00000291552	NM_006758.2	153	gCc/gAc	6/8	1	2	FACETS	0.373	0.298	0.46	0.373	0.298	0.46	SUBCLONAL	1	TRUE	1	0.281833478954411	2		660	532	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	332	276	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.800056898104357	NA		276	586	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0054066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	249	465	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.564432118250578	6	FACETS	0.911	0.866	0.957	0.911	0.866	0.957	CLONAL	4	TRUE	2	0.800056898104357	6		465	444	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589610	67589612	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	novel	NA	P-0054066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	47	188	0	ENST00000274335.5:c.1376_1378del	p.Lys459del	p.K459del	ENST00000274335		458	gAAAaa/gaa	10/15	0.512552774959748	4	FACETS	1	0.928	1	0.381	0.326	0.44	CLONAL	1	TRUE	1	0.800056898104357	4		188	185	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001303	29001303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201407326	NA	P-0054066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	182	224	0	ENST00000282397.4:c.1429G>A	p.Glu477Lys	p.E477K	ENST00000282397	NM_002019.4	477	Gaa/Aaa	10/30	0.536057018981476	4	FACETS	1	0.957	1			1	CLONAL	2	TRUE	NA	0.800056898104357	4		224	398	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526316	189526316	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0054066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	305	316	0	ENST00000264731.3:c.579+1G>A		p.X193_splice	ENST00000264731	NM_003722.4	193			0.638995139330652	4	FACETS	0.873	0.834	0.911	0.873	0.834	0.911	CLONAL	3	TRUE	1	0.800056898104357	4		316	524	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955863	55955863	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868047715	NA	P-0054066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	177	295	0	ENST00000263923.4:c.3299C>T	p.Ser1100Phe	p.S1100F	ENST00000263923	NM_002253.2	1100	tCc/tTc	24/30	0.512552774959748	4	FACETS	0.846	0.795	0.895	0.846	0.795	0.895	CLONAL	3	TRUE	1	0.800056898104357	4		295	314	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274712	198274712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	136	309	1	ENST00000335508.6:c.686C>T	p.Ser229Phe	p.S229F	ENST00000335508	NM_012433.2	229	tCc/tTc	7/25	0.18995064132625	4	FACETS	0.944	0.872	1	0.944	0.872	1	INDETERMINATE	2	TRUE	2	0.800056898104357	4		310	324	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521723	89521723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767387399	NA	P-0054066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	267	271	2	ENST00000336596.2:c.2800G>A	p.Gly934Ser	p.G934S	ENST00000336596	NM_005233.5	934	Ggt/Agt	16/17	0.800056898104357	3	FACETS	0.957	0.91	1	0.957	0.91	1	CLONAL	2	TRUE	1	0.800056898104357	3		273	488	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419834	41419834	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0054066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	126	356	0	ENST00000373198.4:c.486+1G>A		p.X162_splice	ENST00000373198	NM_133170.3	162			0.798380407347537	3	FACETS	1	0.964	1	0.551	0.504	0.6	CLONAL	1	TRUE	1	0.800056898104357	3		356	400	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805729	43805729	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	261	782	0	ENST00000372470.3:c.785G>A	p.Gly262Glu	p.G262E	ENST00000372470	NM_005373.2	262	gGg/gAg	5/12	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.800056898104357	2		782	586	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720758	89720771	+	frameshift_variant	Frame_Shift_Del	DEL	TTGCAGTATAGAGC	TTGCAGTATAGAGC	-	novel	NA	P-0054066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	11	145	0	ENST00000371953.3:c.909_922del	p.Ile303MetfsTer4	p.I303Mfs*4	ENST00000371953	NM_000314.4	303	atTTGCAGTATAGAGCgt/atgt	8/9	0.783881609438957	2	FACETS	0.561	0.399	0.749	0.281	0.199	0.375	SUBCLONAL	1	TRUE	0	0.800056898104357	2		145	49	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106396	108106396	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs747855862	NA	P-0054066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	42	85	0	ENST00000278616.4:c.332-1G>A		p.X111_splice	ENST00000278616	NM_000051.3	111			0.783881609438957	2	FACETS	0.972	0.883	1	0.972	0.883	1	CLONAL	2	TRUE	0	0.800056898104357	2		85	54	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633221	3633221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	523	1289	0	ENST00000294008.3:c.5030C>T	p.Pro1677Leu	p.P1677L	ENST00000294008	NM_032444.2	1677	cCc/cTc	14/15	0.497264841681559	3	FACETS	0.945	0.912	0.979			1	CLONAL	2	TRUE	NA	0.800056898104357	3		1289	968	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803376	1803377	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0054066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	200	1174	1	ENST00000260795.2:c.645_646delinsAA	p.Met215_Glu216delinsIleLys	p.M215_E216delinsIK	ENST00000260795		215	atGGaa/atAAaa	5/17	0.197703372604771	3	FACETS	0.884	0.821	0.949			1	INDETERMINATE	1	TRUE	NA	0.800056898104357	3		1175	792	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979305	93979305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	204	243	0	ENST00000369303.4:c.1523G>A	p.Gly508Glu	p.G508E	ENST00000369303	NM_004440.3	508	gGa/gAa	7/17	0.728621236440852	3	FACETS	1	0.992	1	0.832	0.794	0.869	CLONAL	2	TRUE	0	0.800056898104357	3		243	286	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002883	69002883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	122	221	4	ENST00000288368.4:c.2183G>A	p.Ser728Asn	p.S728N	ENST00000288368	NM_024870.2	728	aGc/aAc	20/40	0.260054164081751	4	FACETS	0.877	0.804	0.951	0.877	0.804	0.951	INDETERMINATE	2	TRUE	2	0.800056898104357	4		225	313	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8527352	8527352	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	39	158	0	ENST00000356435.5:c.543A>T	p.Glu181Asp	p.E181D	ENST00000356435		181	gaA/gaT	5/35	0.783881609438957	2	FACETS	0.819	0.696	0.949	0.41	0.348	0.475	CLONAL	1	TRUE	0	0.800056898104357	2		158	119	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0054067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	26	465	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.18	2		465	265	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0054067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	26	461	1	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	1	2	FACETS	0.929	0.737	1	0.929	0.737	1	CLONAL	1	TRUE	1	0.18	2		462	311	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155043	108155043	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587779836	NA	P-0054067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	21	482	0	ENST00000278616.4:c.3836G>A	p.Trp1279Ter	p.W1279*	ENST00000278616	NM_000051.3	1279	tGg/tAg	26/63	1	2	FACETS	0.775	0.597	0.983	0.775	0.597	0.983	CLONAL	1	TRUE	1	0.18	2		482	301	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192134	108192134	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	31	517	0	ENST00000278616.4:c.6559G>T	p.Glu2187Ter	p.E2187*	ENST00000278616	NM_000051.3	2187	Gag/Tag	45/63	1	2	FACETS	0.721	0.582	0.878	0.721	0.582	0.878	SUBCLONAL	1	TRUE	1	0.18	2		517	478	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579170	7579474	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CATTAAGTGGGTAAACTATAAAAAAACACTGACAGGAAGCCAAAGGGTGAAGAGGAATCCCAAAGTTCCAAACAAAAGAAATGCAGGGGGATACGGCCAGGCATTGAAGTCTCATGGAAGCCAGCCCCTCAGGGCAACTGACCGTGCAAGTCACAGACTTGGCTGTCCCAGAATGCAAGAAGCCCAGACGGAAACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGGACAGAAGATGACAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTGCAGGGGCCACGGGG	CATTAAGTGGGTAAACTATAAAAAAACACTGACAGGAAGCCAAAGGGTGAAGAGGAATCCCAAAGTTCCAAACAAAAGAAATGCAGGGGGATACGGCCAGGCATTGAAGTCTCATGGAAGCCAGCCCCTCAGGGCAACTGACCGTGCAAGTCACAGACTTGGCTGTCCCAGAATGCAAGAAGCCCAGACGGAAACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGGACAGAAGATGACAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTGCAGGGGCCACGGGG	-	novel	NA	P-0054067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	47	130	0	ENST00000269305.4:c.213_375+142del		p.X71_splice	ENST00000269305	NM_001126112.2	71		4/11	1	2	FACETS	1	0.876	1	1	0.982	1	CLONAL	4	TRUE	1	0.18	2		130	129	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	43	563	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.95	0.795	1	0.95	0.795	1	CLONAL	1	TRUE	1	0.199913485790365	2		563	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0054069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	88	877	1	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	1	2	FACETS	0.75	0.662	0.844	0.75	0.662	0.844	SUBCLONAL	1	TRUE	1	0.199913485790365	2		878	1174	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578175	7578175	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0054070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	50	588	0	ENST00000269305.4:c.672+2T>C		p.X224_splice	ENST00000269305	NM_001126112.2	224			1	2	FACETS	0.521	0.442	0.609	0.521	0.442	0.609	SUBCLONAL	1	FALSE	1	0.316494080354686	2		588	606	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738714	145738714	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753386714	NA	P-0054070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	132	727	1	ENST00000428558.2:c.2350C>T	p.Arg784Trp	p.R784W	ENST00000428558	NM_004260.3	784	Cgg/Tgg	15/22	0.316494080354686	4	FACETS	1	0.954	1	0.361	0.327	0.397	CLONAL	1	FALSE	1	0.316494080354686	4		728	1013	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975614	26975614	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	16	270	0	ENST00000381527.3:c.1122G>T	p.Gln374His	p.Q374H	ENST00000381527	NM_001260.1	374	caG/caT	12/13	0.26487897335508	0	FACETS	0.427	0.317	0.556			1	SUBCLONAL	1	FALSE	0	0.316494080354686	0		270	162	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28929495	NA	P-0054070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	20	502	0	ENST00000275493.2:c.2155G>C	p.Gly719Arg	p.G719R	ENST00000275493	NM_005228.3	719	Ggc/Cgc	18/28	1	2	FACETS	0.299	0.228	0.383	0.299	0.228	0.383	SUBCLONAL	1	FALSE	1	0.316494080354686	2		502	422	SUCCESS
APC	324	MSKCC	GRCh37	5	112179437	112179437	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778044	NA	P-0054071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	88	520	1	ENST00000257430.4:c.8146G>A	p.Val2716Met	p.V2716M	ENST00000257430	NM_000038.5	2716	Gtg/Atg	16/16	1	2	FACETS	0.772	0.686	0.864	0.772	0.686	0.864	SUBCLONAL	1	TRUE	1	0.439949124055985	2		521	518	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652932	29652932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	255	434	0	ENST00000356175.3:c.4867G>A	p.Asp1623Asn	p.D1623N	ENST00000356175	NM_000267.3	1623	Gac/Aac	36/57	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	2	TRUE	NA	0.439949124055985	2		434	549	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418394	49418394	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	163	611	0	ENST00000301067.7:c.16019G>T	p.Arg5340Leu	p.R5340L	ENST00000301067	NM_003482.3	5340	cGa/cTa	50/54	0.122634016649963	4	FACETS	0.765	0.704	0.829	0.765	0.704	0.829	INDETERMINATE	2	TRUE	2	0.439949124055985	4		611	697	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433553	49433553	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	343	1077	1	ENST00000301067.7:c.8000del	p.Pro2667GlnfsTer24	p.P2667Qfs*24	ENST00000301067	NM_003482.3	2667	cCa/ca	31/54	0.122634016649963	4	FACETS	0.955	0.904	1	0.955	0.904	1	INDETERMINATE	2	TRUE	2	0.439949124055985	4		1078	1176	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041932	42041932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	138	467	0	ENST00000219905.7:c.6127G>A	p.Ala2043Thr	p.A2043T	ENST00000219905	NM_001164273.1	2043	Gca/Aca	17/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.439949124055985	2		467	549	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0054074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	411	563	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.491630094379777	3	FACETS	1	0.994	1	0.796	0.763	0.829	CLONAL	2	TRUE	0	0.529602887391312	3		564	822	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	125	465	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	0.529602887391312	3	FACETS	0.936	0.859	1	0.936	0.859	1	CLONAL	2	TRUE	1	0.529602887391312	3		465	319	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032271	26032271	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	26	276	0	ENST00000244661.2:c.18G>T	p.Gln6His	p.Q6H	ENST00000244661	NM_003537.3	6	caG/caT	1/1	0.529602887391312	3	FACETS	0.306	0.242	0.379	0.153	0.121	0.19	SUBCLONAL	1	TRUE	1	0.529602887391312	3		276	406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578476	7578476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767328513	NA	P-0054075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	370	914	0	ENST00000269305.4:c.454C>T	p.Pro152Ser	p.P152S	ENST00000269305	NM_001126112.2	152	Ccg/Tcg	5/11	0.548247572003686	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.548247572003686	1		914	852	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0054075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	214	575	0	ENST00000269305.4:c.375+1del		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.548247572003686	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.548247572003686	1		575	541	SUCCESS
APC	324	MSKCC	GRCh37	5	112164609	112164609	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	81	263	0	ENST00000257430.4:c.1683del	p.Thr562ArgfsTer8	p.T562Rfs*8	ENST00000257430	NM_000038.5	561	aaG/aa	14/16	0.548247572003686	1	FACETS	0.633	0.562	0.707	0.633	0.562	0.707	SUBCLONAL	1	TRUE	0	0.548247572003686	1		263	339	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218085	108218085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs769052707	NA	P-0054075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	125	252	0	ENST00000278616.4:c.8664A>G	p.Ile2888Met	p.I2888M	ENST00000278616	NM_000051.3	2888	atA/atG	59/63	1	2	FACETS	0.95	0.865	1	0.95	0.865	1	CLONAL	1	TRUE	1	0.548247572003686	2		252	480	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426285	49426285	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	318	965	0	ENST00000301067.7:c.12203C>A	p.Ser4068Ter	p.S4068*	ENST00000301067	NM_003482.3	4068	tCa/tAa	39/54	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.548247572003686	2		965	1138	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145701	11145701	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	295	842	1	ENST00000358026.2:c.4063G>T	p.Glu1355Ter	p.E1355*	ENST00000358026	NM_001128849.1	1355	Gag/Tag	29/36	0.548247572003686	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.548247572003686	1		843	692	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17389673	17389673	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	223	662	0	ENST00000359435.4:c.806G>T	p.Gly269Val	p.G269V	ENST00000359435	NM_001033549.1	269	gGc/gTc	9/9	0.548247572003686	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.548247572003686	1		662	571	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223823	36223823	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	357	1012	0	ENST00000222270.7:c.6373G>C	p.Gly2125Arg	p.G2125R	ENST00000222270	NM_014727.1	2125	Ggg/Cgg	28/37	0.426444415016389	3	FACETS	1	0.987	1	0.563	0.533	0.595	CLONAL	1	TRUE	1	0.548247572003686	3		1012	1473	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884864	134884864	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	394	559	0	ENST00000398015.3:c.1640C>A	p.Ala547Glu	p.A547E	ENST00000398015	NM_004441.4	547	gCg/gAg	8/16	NA	2	FACETS	0.816	0.779	0.852			1	INDETERMINATE	2	TRUE	NA	0.548247572003686	2		559	881	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225552	225552	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	101	144	0	ENST00000264932.6:c.331C>G	p.Leu111Val	p.L111V	ENST00000264932	NM_004168.2	111	Ctg/Gtg	4/15	0.426444415016389	3	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	1	0.548247572003686	3		144	228	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157256686	157256686	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	118	256	0	ENST00000346085.5:c.2013G>T	p.Gln671His	p.Q671H	ENST00000346085	NM_020732.3	671	caG/caT	5/20	1	2	FACETS	0.895	0.812	0.981	0.895	0.812	0.981	CLONAL	1	TRUE	1	0.548247572003686	2		256	481	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878200	151878200	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	242	543	0	ENST00000262189.6:c.6745C>A	p.Pro2249Thr	p.P2249T	ENST00000262189	NM_170606.2	2249	Cct/Act	36/59	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.548247572003686	2		543	855	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922601	56922601	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	205	508	0	ENST00000519728.1:c.1471G>T	p.Asp491Tyr	p.D491Y	ENST00000519728	NM_002350.3	491	Gac/Tac	13/13	0.548247572003686	1	FACETS	0.922	0.861	0.984	0.922	0.861	0.984	CLONAL	1	TRUE	0	0.548247572003686	1		508	589	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499724	8499724	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs759878846	NA	P-0054075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	184	523	0	ENST00000356435.5:c.2245G>T	p.Val749Leu	p.V749L	ENST00000356435		749	Gtg/Ttg	14/35	0.548247572003686	1	FACETS	0.935	0.87	1	0.935	0.87	1	CLONAL	1	TRUE	0	0.548247572003686	1		523	521	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652437	48652437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	285	476	1	ENST00000376670.3:c.1108G>A	p.Val370Met	p.V370M	ENST00000376670	NM_002049.3	370	Gtg/Atg	6/6	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.548247572003686	1		477	547	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0054088-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	56	377	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.515	0.441	0.597	0.515	0.441	0.597	SUBCLONAL	1	TRUE	1	0.313082973994238	2		377	694	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0054088-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	88	420	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.889	0.789	0.997	0.889	0.789	0.997	CLONAL	1	TRUE	1	0.313082973994238	2		420	632	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054088-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1600	90	385	0	ENST00000425967.3:c.1731C>G	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaG	13/19	0.313082973994238	14	FACETS	0.979	0.865	1			1	CLONAL	1	TRUE	NA	0.313082973994238	14		385	1690	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0054088-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	168	736	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.313082973994238	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.313082973994238	1		736	802	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117782	108117782	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054088-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	30	254	0	ENST00000278616.4:c.993G>C	p.Lys331Asn	p.K331N	ENST00000278616	NM_000051.3	331	aaG/aaC	8/63	0.299414204505925	1	FACETS	0.405	0.326	0.495	0.405	0.326	0.495	SUBCLONAL	1	TRUE	0	0.313082973994238	1		254	399	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440867	52440867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054088-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	110	607	0	ENST00000460680.1:c.637C>T	p.Arg213Cys	p.R213C	ENST00000460680	NM_004656.3	213	Cgt/Tgt	8/17	0.299414204505925	1	FACETS	0.825	0.742	0.914	0.825	0.742	0.914	CLONAL	1	TRUE	0	0.313082973994238	1		607	718	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900243	101900243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054088-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	73	279	0	ENST00000374994.4:c.677G>A	p.Gly226Glu	p.G226E	ENST00000374994	NM_004612.2	226	gGa/gAa	4/9	1	2	FACETS	0.856	0.749	0.97	0.856	0.749	0.97	CLONAL	1	TRUE	1	0.313082973994238	2		279	545	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11210264	11210264	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	47	407	0	ENST00000361445.4:c.4489T>C	p.Cys1497Arg	p.C1497R	ENST00000361445	NM_004958.3	1497	Tgc/Cgc	31/58	0.177318460527208	2	FACETS	0.519	0.437	0.61	0.26	0.218	0.305	SUBCLONAL	1	TRUE	0	0.24307845087201	2		407	745	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448536	49448536	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0054091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	55	379	0	ENST00000301067.7:c.177-2A>G		p.X59_splice	ENST00000301067	NM_003482.3	59			1	2	FACETS	0.64	0.547	0.743	0.64	0.547	0.743	SUBCLONAL	1	TRUE	1	0.24307845087201	2		379	707	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252058	133252058	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	198	622	0	ENST00000320574.5:c.1152G>T	p.Gln384His	p.Q384H	ENST00000320574	NM_006231.2	384	caG/caT	12/49	0.24307845087201	2	FACETS	0.892	0.827	0.96	0.892	0.827	0.96	CLONAL	2	TRUE	0	0.24307845087201	2		622	913	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857902	89857902	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	86	452	0	ENST00000389301.3:c.1268A>T	p.Gln423Leu	p.Q423L	ENST00000389301	NM_000135.2	423	cAg/cTg	14/43	0.24307845087201	2	FACETS	0.884	0.782	0.995	0.442	0.391	0.498	CLONAL	1	TRUE	0	0.24307845087201	2		452	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0054091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	271	776	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.24307845087201	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.24307845087201	2		779	1074	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016559	12016559	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	80	190	0	ENST00000353533.5:c.695C>T	p.Pro232Leu	p.P232L	ENST00000353533	NM_003010.3	232	cCt/cTt	7/11	0.24307845087201	2	FACETS	0.932	0.827	1	0.932	0.827	1	CLONAL	2	TRUE	0	0.24307845087201	2		190	353	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40371839	40371839	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	136	828	0	ENST00000293328.3:c.572A>C	p.Gln191Pro	p.Q191P	ENST00000293328	NM_012448.3	191	cAg/cCg	6/19	0.177318460527208	2	FACETS	0.9	0.816	0.988	0.45	0.408	0.494	CLONAL	1	TRUE	0	0.24307845087201	2		828	1244	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246397	41246397	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	85	400	0	ENST00000357654.3:c.1151A>G	p.Glu384Gly	p.E384G	ENST00000357654	NM_007294.3	384	gAg/gGg	10/23	0.177318460527208	2	FACETS	0.996	0.881	1	0.498	0.44	0.56	CLONAL	1	TRUE	0	0.24307845087201	2		400	702	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223159	1223159	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	86	511	0	ENST00000326873.7:c.1096T>A	p.Phe366Ile	p.F366I	ENST00000326873	NM_000455.4	366	Ttc/Atc	8/10	1	2	FACETS	0.802	0.708	0.903	0.802	0.708	0.903	CLONAL	1	TRUE	1	0.24307845087201	2		511	882	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719176	190719176	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs766742199	NA	P-0054091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	37	168	0	ENST00000441310.2:c.1178A>T	p.Asp393Val	p.D393V	ENST00000441310	NM_000534.4	393	gAt/gTt	9/13	0.186928061620254	3	FACETS	1	0.863	1	0.525	0.434	0.627	CLONAL	1	TRUE	1	0.24307845087201	3		168	325	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980892	40980892	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	65	374	0	ENST00000373198.4:c.1594A>C	p.Ser532Arg	p.S532R	ENST00000373198	NM_133170.3	532	Agt/Cgt	10/32	0.24307845087201	3	FACETS	0.817	0.708	0.936	0.409	0.354	0.468	CLONAL	1	TRUE	1	0.24307845087201	3		374	734	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182679084	182679084	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	36	339	0	ENST00000292782.4:c.450A>C	p.Glu150Asp	p.E150D	ENST00000292782	NM_020640.2	150	gaA/gaC	4/7	0.186928061620254	3	FACETS	0.552	0.453	0.664	0.276	0.226	0.332	SUBCLONAL	1	TRUE	1	0.24307845087201	3		339	602	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467826	66467826	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	56	221	0	ENST00000273854.3:c.443A>C	p.Lys148Thr	p.K148T	ENST00000273854	NM_004439.5	148	aAg/aCg	3/18	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.24307845087201	2		221	417	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271248	153271248	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	14	142	0	ENST00000281708.4:c.530A>C	p.Glu177Ala	p.E177A	ENST00000281708	NM_033632.3	177	gAg/gCg	3/12	1	2	FACETS	0.478	0.345	0.638	0.478	0.345	0.638	SUBCLONAL	1	TRUE	1	0.24307845087201	2		142	241	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526435	31526435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1368902815	NA	P-0054091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	139	768	1	ENST00000344624.3:c.605C>T	p.Pro202Leu	p.P202L	ENST00000344624		202	cCt/cTt	2/33	1	2	FACETS	0.913	0.829	1	0.913	0.829	1	CLONAL	1	TRUE	1	0.24307845087201	2		769	1252	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345949	152345949	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	74	398	0	ENST00000359321.1:c.621A>C	p.Glu207Asp	p.E207D	ENST00000359321	NM_005431.1	207	gaA/gaC	3/3	1	2	FACETS	0.947	0.829	1	0.947	0.829	1	CLONAL	1	TRUE	1	0.24307845087201	2		398	643	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518109	8518109	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	58	332	0	ENST00000356435.5:c.1282A>C	p.Met428Leu	p.M428L	ENST00000356435		428	Atg/Ctg	10/35	0.24307845087201	2	FACETS	0.966	0.831	1	0.483	0.415	0.557	CLONAL	1	TRUE	0	0.24307845087201	2		332	494	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436681	52436681	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	218	434	1	ENST00000460680.1:c.1993C>T	p.Gln665Ter	p.Q665*	ENST00000460680	NM_004656.3	665	Cag/Tag	16/17	0.768618922092048	1	FACETS	0.891	0.843	0.939	0.891	0.843	0.939	CLONAL	1	TRUE	0	0.768618922092048	1		435	392	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	51	603	1	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.259221634846726	1	FACETS	0.463	0.392	0.541	0.463	0.392	0.541	SUBCLONAL	1	TRUE	0	0.259221634846726	1		604	740	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0054095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	91	465	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.977	0.877	1	0.977	0.877	1	CLONAL	1	TRUE	1	0.585990144469293	2		465	318	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349753	89349753	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	179	717	0	ENST00000301030.4:c.3197A>C	p.His1066Pro	p.H1066P	ENST00000301030	NM_001256183.1	1066	cAt/cCt	9/13	0.0957046326958091	3	FACETS	0.574	0.528	0.622			1	INDETERMINATE	1	TRUE	NA	0.720804438616658	3		717	1177	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577607	7577608	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	373	426	0	ENST00000269305.4:c.673dup	p.Val225GlyfsTer4	p.V225Gfs*4	ENST00000269305	NM_001126112.2	225	gtt/gGtt	7/11	0.711571955925118	2	FACETS	0.976	0.943	1	0.976	0.943	1	CLONAL	2	TRUE	0	0.720804438616658	2		426	530	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0054099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	149	258	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.546873295178187	2		258	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0054099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	840	948	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.509879596145674	3	FACETS	0.972	0.948	0.997	0.972	0.948	0.997	CLONAL	3	TRUE	0	0.546873295178187	3		948	1341	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	188	250	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.546873295178187	1		250	349	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397738	49397738	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	229	549	0	ENST00000418115.1:c.486G>C	p.Lys162Asn	p.K162N	ENST00000418115	NM_001664.2	162	aaG/aaC	5/5	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.546873295178187	2		549	822	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120523	2120523	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45517199	NA	P-0054099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	244	1135	2	ENST00000219476.3:c.1783C>T	p.Gln595Ter	p.Q595*	ENST00000219476	NM_000548.3	595	Cag/Tag	17/42	0.546873295178187	1	FACETS	0.668	0.624	0.712	0.668	0.624	0.712	SUBCLONAL	1	TRUE	0	0.546873295178187	1		1137	971	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100988	27100988	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	180	740	0	ENST00000324856.7:c.4270C>T	p.Gln1424Ter	p.Q1424*	ENST00000324856	NM_006015.4	1424	Cag/Tag	18/20	1	2	FACETS	0.743	0.685	0.803	0.743	0.685	0.803	SUBCLONAL	1	TRUE	1	0.546873295178187	2		740	886	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006363	12006363	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	101	363	0	ENST00000396373.4:c.331G>A	p.Asp111Asn	p.D111N	ENST00000396373	NM_001987.4	111	Gat/Aat	4/8	1	2	FACETS	0.755	0.678	0.837	0.755	0.678	0.837	SUBCLONAL	1	TRUE	1	0.546873295178187	2		363	489	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101195	27101195	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	230	857	0	ENST00000324856.7:c.4477C>G	p.Gln1493Glu	p.Q1493E	ENST00000324856	NM_006015.4	1493	Cag/Gag	18/20	1	2	FACETS	0.913	0.852	0.976	0.913	0.852	0.976	CLONAL	1	TRUE	1	0.546873295178187	2		857	921	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142479	119142479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	142	430	0	ENST00000264033.4:c.478C>T	p.His160Tyr	p.H160Y	ENST00000264033	NM_005188.3	160	Cac/Tac	3/16	1	2	FACETS	0.838	0.766	0.912	0.838	0.766	0.912	CLONAL	1	TRUE	1	0.546873295178187	2		430	620	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418594	49418594	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0054099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	172	577	0	ENST00000301067.7:c.15920C>G	p.Ser5307Ter	p.S5307*	ENST00000301067	NM_003482.3	5307	tCa/tGa	49/54	1	2	FACETS	0.913	0.843	0.986	0.913	0.843	0.986	CLONAL	1	TRUE	1	0.546873295178187	2		577	689	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444136	49444136	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0054099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	271	938	0	ENST00000301067.7:c.3235del	p.Ser1079GlnfsTer40	p.S1079Qfs*40	ENST00000301067	NM_003482.3	1079	Tca/ca	11/54	1	2	FACETS	0.987	0.927	1	0.987	0.927	1	CLONAL	1	TRUE	1	0.546873295178187	2		938	1004	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133854	2134800	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGGGGCTCCTTAGGGGAGGCAGGGCTCTGCGTGGGTGTGCCTGCACCCTGGGAACTGGCTCTGAACTTGGGGGAGATGTTCTTCCACATCCCTCGTGCACAGACGGTCTGCACTTTGCAGCCATCCACCTGGGCCGGCCCTGGCTGCTGGGCAGCCTGTGGTCTCAGGGGATGCTGATACCTCTGCTCACGCAGTGTGGGGCACAGCTGGTGGCAGTGCTGCTGCGTCAACGGGCGGGGGCCGTAGCCTGGTGCTCGGGCTGGTCTGTGGCCCTGGGATGGAGGACAGATAGGGCCTCACCACCTCCAGGTCAACCCCAGGTGGGCTCGAGGGTGCCTGCTGACAGGGGTTCTCTTTGGGATGGTCCTTTCTAGTCGTCCTCAGTCTCCAGCCAGGAGGAGAAGTCGCTCCACGCGGAGGAGCTGGTTGGCAGGGGCATCCCCATCGAGCGAGTCGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCTTCCAGCCCTCGCAGCCCCTGAGCAAGTCCAGCTCCTCTCCCGAGCTGCAGACTCTGCAGGACATCCTCGGGGACCCTGGGGACAAGGCCGACGTGGGCCGGCTGAGCCCTGAGGTTAAGGCCCGGTCACAGTCAGGGACCCTGGACGGGGAAAGTGCTGCCTGGTCGGCCTCGGGCGAAGACAGTCGGGGCCAGCCCGAGGGTCCCTTGCCTTCCAGCTCCCCCCGCTCGCCCAGTGGCCTCCGGCCCCGAGGTTACACCATCTCCGACTCGGCCCCATCACGCAGGGGCAAGAGAGTAGAGAGGGACGCCTTAAAGAGCAGAGCCACAGCCTCCAATGCAGAGAAAGTGCCAGGCATCAACCCCAGGTGGGCCTCTTGCTTCCGGGCGGGGCTCCTGACACCTCTCCTGCGGGAACCTGGTGCCTCACTTGCCCCAGGCCGAGCGGGCTG	GGGGGGCTCCTTAGGGGAGGCAGGGCTCTGCGTGGGTGTGCCTGCACCCTGGGAACTGGCTCTGAACTTGGGGGAGATGTTCTTCCACATCCCTCGTGCACAGACGGTCTGCACTTTGCAGCCATCCACCTGGGCCGGCCCTGGCTGCTGGGCAGCCTGTGGTCTCAGGGGATGCTGATACCTCTGCTCACGCAGTGTGGGGCACAGCTGGTGGCAGTGCTGCTGCGTCAACGGGCGGGGGCCGTAGCCTGGTGCTCGGGCTGGTCTGTGGCCCTGGGATGGAGGACAGATAGGGCCTCACCACCTCCAGGTCAACCCCAGGTGGGCTCGAGGGTGCCTGCTGACAGGGGTTCTCTTTGGGATGGTCCTTTCTAGTCGTCCTCAGTCTCCAGCCAGGAGGAGAAGTCGCTCCACGCGGAGGAGCTGGTTGGCAGGGGCATCCCCATCGAGCGAGTCGTCTCCTCGGAGGGTGGCCGGCCCTCTGTGGACCTCTCCTTCCAGCCCTCGCAGCCCCTGAGCAAGTCCAGCTCCTCTCCCGAGCTGCAGACTCTGCAGGACATCCTCGGGGACCCTGGGGACAAGGCCGACGTGGGCCGGCTGAGCCCTGAGGTTAAGGCCCGGTCACAGTCAGGGACCCTGGACGGGGAAAGTGCTGCCTGGTCGGCCTCGGGCGAAGACAGTCGGGGCCAGCCCGAGGGTCCCTTGCCTTCCAGCTCCCCCCGCTCGCCCAGTGGCCTCCGGCCCCGAGGTTACACCATCTCCGACTCGGCCCCATCACGCAGGGGCAAGAGAGTAGAGAGGGACGCCTTAAAGAGCAGAGCCACAGCCTCCAATGCAGAGAAAGTGCCAGGCATCAACCCCAGGTGGGCCTCTTGCTTCCGGGCGGGGCTCCTGACACCTCTCCTGCGGGAACCTGGTGCCTCACTTGCCCCAGGCCGAGCGGGCTG	-	novel	NA	P-0054099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	149	560	0	ENST00000219476.3:c.4005+40_4493+87del		p.X1335_splice	ENST00000219476	NM_000548.3	1335		34/42	0.546873295178187	1	FACETS	0.938	0.866	1	0.938	0.866	1	CLONAL	1	TRUE	0	0.546873295178187	1		560	422	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974821	15974821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	173	444	0	ENST00000268712.3:c.4054C>T	p.His1352Tyr	p.H1352Y	ENST00000268712	NM_006311.3	1352	Cat/Tat	30/46	0.546873295178187	1	FACETS	0.997	0.927	1	0.997	0.927	1	CLONAL	1	TRUE	0	0.546873295178187	1		444	461	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2208937	2208937	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	169	474	0	ENST00000398665.3:c.967G>C	p.Glu323Gln	p.E323Q	ENST00000398665	NM_032482.2	323	Gaa/Caa	12/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.546873295178187	2		474	592	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907686	111907686	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	180	394	0	ENST00000393256.3:c.460C>G	p.Arg154Gly	p.R154G	ENST00000393256	NM_006538.4	154	Cgt/Ggt	3/4	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.546873295178187	2		394	580	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645784	12645784	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	108	336	0	ENST00000251849.4:c.685C>T	p.Gln229Ter	p.Q229*	ENST00000251849	NM_002880.3	229	Cag/Tag	7/17	1	2	FACETS	0.839	0.757	0.924	0.839	0.757	0.924	CLONAL	1	TRUE	1	0.546873295178187	2		336	471	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675202	30675202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	227	621	0	ENST00000376406.3:c.3043G>A	p.Glu1015Lys	p.E1015K	ENST00000376406	NM_014641.2	1015	Gag/Aag	9/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.546873295178187	2		621	800	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679876	30679876	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	186	661	0	ENST00000376406.3:c.1843C>G	p.Leu615Val	p.L615V	ENST00000376406	NM_014641.2	615	Ctt/Gtt	5/15	1	2	FACETS	0.942	0.873	1	0.942	0.873	1	CLONAL	1	TRUE	1	0.546873295178187	2		661	722	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2969666	2969666	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747866557	NA	P-0054099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	301	928	0	ENST00000396946.4:c.1613C>G	p.Ser538Cys	p.S538C	ENST00000396946	NM_032415.4	538	tCc/tGc	12/25	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.546873295178187	2		928	998	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409014	139409014	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	332	1097	0	ENST00000277541.6:c.2155G>A	p.Glu719Lys	p.E719K	ENST00000277541	NM_017617.3	719	Gag/Aag	13/34	1	2	FACETS	0.997	0.942	1	0.997	0.942	1	CLONAL	1	TRUE	1	0.546873295178187	2		1097	1218	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820205	139820205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	238	804	0	ENST00000247668.2:c.1358C>T	p.Ser453Leu	p.S453L	ENST00000247668	NM_021138.3	453	tCa/tTa	11/11	1	2	FACETS	0.959	0.896	1	0.959	0.896	1	CLONAL	1	TRUE	1	0.546873295178187	2		804	908	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0054101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	135	470	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.368607061797481	5	FACETS	1	0.966	1	0.731	0.672	0.791	INDETERMINATE	2	TRUE	2	0.661561440798982	5		470	371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578281	7578281	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660254	NA	P-0054101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	319	655	0	ENST00000269305.4:c.568C>A	p.Pro190Thr	p.P190T	ENST00000269305	NM_001126112.2	190	Cct/Act	6/11	0.268284404948919	5	FACETS	1	0.992	1	0.829	0.786	0.871	INDETERMINATE	2	TRUE	2	0.661561440798982	5		655	773	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128018	64128018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781570977	NA	P-0054101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	203	758	1	ENST00000334205.4:c.416G>A	p.Arg139His	p.R139H	ENST00000334205	NM_003942.2	139	cGc/cAc	4/17	0.341565813175744	3	FACETS	0.988	0.917	1	0.494	0.458	0.53	INDETERMINATE	1	TRUE	1	0.661561440798982	3		759	827	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578471	7578471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	340	1046	0	ENST00000269305.4:c.459del	p.Gly154AlafsTer16	p.G154Afs*16	ENST00000269305	NM_001126112.2	153	ccC/cc	5/11	0.268284404948919	5	FACETS	0.905	0.857	0.955	0.604	0.571	0.637	INDETERMINATE	2	TRUE	2	0.661561440798982	5		1046	1131	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975360	13975360	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	27	389	0	ENST00000405192.2:c.527C>A	p.Pro176Gln	p.P176Q	ENST00000405192	NM_001163147.1	176	cCa/cAa	7/12	0.268284404948919	5	FACETS	0.333	0.264	0.411	0.111	0.088	0.137	INDETERMINATE	1	TRUE	2	0.661561440798982	5		389	489	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211685	36211685	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	256	678	0	ENST00000222270.7:c.1436G>T	p.Arg479Leu	p.R479L	ENST00000222270	NM_014727.1	479	cGg/cTg	3/37	0.249669445379532	3	FACETS	1	0.993	1	0.745	0.702	0.79	INDETERMINATE	1	TRUE	1	0.661561440798982	3		678	691	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143431	30143431	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759748510	NA	P-0054101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	264	538	0	ENST00000389048.3:c.95C>T	p.Pro32Leu	p.P32L	ENST00000389048	NM_004304.4	32	cCa/cTa	1/29	0.268284404948919	5	FACETS	1	0.986	1	0.757	0.714	0.801	INDETERMINATE	2	TRUE	2	0.661561440798982	5		538	700	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629505	187629505	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	303	543	0	ENST00000441802.2:c.1477G>T	p.Gly493Cys	p.G493C	ENST00000441802	NM_005245.3	493	Ggt/Tgt	2/27	0.574220907463718	2	FACETS	0.9	0.86	0.939	0.9	0.86	0.939	CLONAL	2	TRUE	0	0.661561440798982	2		543	509	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31511190	31511190	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	301	580	0	ENST00000344624.3:c.1384G>T	p.Ala462Ser	p.A462S	ENST00000344624		462	Gct/Tct	6/33	0.307937563944544	4	FACETS	0.908	0.858	0.958	0.908	0.858	0.958	INDETERMINATE	2	TRUE	2	0.661561440798982	4		580	833	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0054102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	258	929	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.347282058681373	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.413182198972544	2		929	620	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230641	46230641	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	65	352	1	ENST00000334344.6:c.890C>A	p.Ser297Tyr	p.S297Y	ENST00000334344	NM_152641.2	297	tCc/tAc	8/21	0.413182198972544	3	FACETS	1	0.959	1	0.624	0.546	0.708	CLONAL	1	TRUE	1	0.413182198972544	3		353	304	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436344	110436344	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	85	530	1	ENST00000375856.3:c.2057C>G	p.Pro686Arg	p.P686R	ENST00000375856	NM_003749.2	686	cCc/cGc	1/2	0.413182198972544	6	FACETS	1	0.947	1	0.281	0.248	0.316	CLONAL	1	TRUE	2	0.413182198972544	6		531	668	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588830	52588831	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0054102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	170	523	0	ENST00000394830.3:c.4197dup	p.Met1400HisfsTer109	p.M1400Hfs*109	ENST00000394830	NM_018313.4	1399	-/C	27/30	0.413182198972544	2	FACETS	0.991	0.923	1	0.991	0.923	1	CLONAL	2	TRUE	0	0.413182198972544	2		523	415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0054103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	255	651	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.407249926820474	2	FACETS	0.999	0.942	1	0.999	0.942	1	CLONAL	2	TRUE	0	0.407249926820474	2		651	627	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557846	21557847	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0054103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	308	551	0	ENST00000382592.4:c.1998dup	p.Met667TyrfsTer21	p.M667Yfs*21	ENST00000382592	NM_014572.2	666	-/T	5/8	0.386408429795295	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.407249926820474	2		551	755	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067082	143067085	+	frameshift_variant	Frame_Shift_Del	DEL	TCAA	TCAA	-	novel	NA	P-0054103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	207	381	0	ENST00000262992.4:c.1628_1631del	p.Ile543LysfsTer21	p.I543Kfs*21	ENST00000262992	NM_001101669.1	543	aTTGAa/aa	16/24	0.407249926820474	2	FACETS	0.941	0.881	1	0.941	0.881	1	CLONAL	2	TRUE	0	0.407249926820474	2		381	540	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061334	38061334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	30	599	0	ENST00000250448.2:c.655C>T	p.Arg219Cys	p.R219C	ENST00000250448	NM_004496.3	219	Cgc/Tgc	2/2	0.229984722169709	3	FACETS	0.9	0.727	1	0.45	0.363	0.548	CLONAL	1	FALSE	1	0.244353826562424	3		599	306	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170894	99170894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770046161	NA	P-0054104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	16	701	0	ENST00000074304.5:c.1523G>A	p.Arg508Gln	p.R508Q	ENST00000074304	NM_001134224.1	508	cGg/cAg	16/26	1	2	FACETS	0.562	0.416	0.736	0.562	0.416	0.736	SUBCLONAL	1	FALSE	1	0.244353826562424	2		701	233	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845232	151845239	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	TATTGGCA	TATTGGCA	-	novel	NA	P-0054104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	13	478	0	ENST00000262189.6:c.13773_13780del	p.Tyr4591Ter	p.Y4591*	ENST00000262189	NM_170606.2	4591	taTGCCAATAgg/tagg	52/59	1	2	FACETS	0.486	0.347	0.656	0.486	0.347	0.656	SUBCLONAL	1	FALSE	1	0.244353826562424	2		478	219	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	75	276	0				ENST00000310581	NM_198253.2	-/1132			0.312418695164049	5	FACETS	1	0.936	1	0.72	0.639	0.803	CLONAL	2	TRUE	2	0.49352714721412	5		276	245	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0054106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	110	465	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.148158237162704	6	FACETS	0.858	0.78	0.939	0.858	0.78	0.939	INDETERMINATE	3	TRUE	3	0.49352714721412	6		465	344	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999605	100999605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	170	1133	0	ENST00000325455.5:c.197G>A	p.Gly66Glu	p.G66E	ENST00000325455	NM_001202474.3	66	gGa/gAa	1/8	0.478016516650953	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.49352714721412	1		1133	463	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336071	73336071	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	27	173	0	ENST00000377767.4:c.2332C>T	p.Pro778Ser	p.P778S	ENST00000377767	NM_014953.3	778	Ccc/Tcc	17/21	0.475470975960646	3	FACETS	1	0.9	1	0.593	0.481	0.716	CLONAL	1	TRUE	1	0.49352714721412	3		173	115	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059055	42059056	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0054106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	54	384	1	ENST00000219905.7:c.8775_8776delinsTT	p.Leu2926Phe	p.L2926F	ENST00000219905	NM_001164273.1	2925	gtCCtt/gtTTtt	24/24	1	2	FACETS	0.787	0.678	0.905	0.787	0.678	0.905	CLONAL	1	TRUE	1	0.49352714721412	2		385	278	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729162	66729162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519732	NA	P-0054106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	137	714	0	ENST00000307102.5:c.370C>T	p.Pro124Ser	p.P124S	ENST00000307102	NM_002755.3	124	Ccg/Tcg	3/11	0.412346502381967	4	FACETS	0.995	0.906	1	0.332	0.302	0.364	CLONAL	1	TRUE	1	0.49352714721412	4		714	833	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211160	2211160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	185	1098	0	ENST00000398665.3:c.1414C>T	p.Pro472Ser	p.P472S	ENST00000398665	NM_032482.2	472	Ccc/Tcc	15/28	0.475470975960646	3	FACETS	0.913	0.842	0.986	0.456	0.421	0.493	CLONAL	1	TRUE	1	0.49352714721412	3		1098	1024	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961612	18961612	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	268	746	0	ENST00000262803.5:c.745C>T	p.Gln249Ter	p.Q249*	ENST00000262803	NM_002911.3	249	Cag/Tag	5/24	0.475470975960646	3	FACETS	0.97	0.915	1	0.97	0.915	1	CLONAL	2	TRUE	1	0.49352714721412	3		746	698	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686345	117686345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	27	205	0	ENST00000368508.3:c.2996C>T	p.Ser999Phe	p.S999F	ENST00000368508	NM_002944.2	999	tCt/tTt	20/43	0.475470975960646	3	FACETS	0.832	0.669	1	0.416	0.334	0.507	CLONAL	1	TRUE	1	0.49352714721412	3		205	164	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974715	21974732	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCCCCCGCCTCCA	GCAGCGCCCCCGCCTCCA	-	novel	NA	P-0054106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	93	486	0	ENST00000304494.5:c.95_112del	p.Leu32_Leu37del	p.L32_L37del	ENST00000304494	NM_000077.4	32	cTGGAGGCGGGGGCGCTGCcc/ccc	1/3	0.49352714721412	2	FACETS	1	0.982	1	0.736	0.665	0.809	CLONAL	1	TRUE	0	0.49352714721412	2		486	256	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930404	39930404	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	60	342	0	ENST00000378444.4:c.3060G>A	p.Met1020Ile	p.M1020I	ENST00000378444	NM_001123385.1	1020	atG/atA	6/15	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.49352714721412	2		342	231	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360684	70360684	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	42	249	0	ENST00000374080.3:c.6244C>T	p.Gln2082Ter	p.Q2082*	ENST00000374080		2082	Cag/Tag	42/45	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.49352714721412	2		249	160	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0054107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	70	470	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.263378981514667	2		470	439	SUCCESS
APC	324	MSKCC	GRCh37	5	112175513	112175513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	51	292	0	ENST00000257430.4:c.4222G>T	p.Glu1408Ter	p.E1408*	ENST00000257430	NM_000038.5	1408	Gaa/Taa	16/16	0.263378981514667	3	FACETS	1	0.884	1	0.522	0.444	0.606	CLONAL	1	TRUE	1	0.263378981514667	3		292	420	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591125	67591125	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	107	217	0	ENST00000274335.5:c.1718T>C	p.Leu573Pro	p.L573P	ENST00000274335		573	cTg/cCg	12/15	0.263378981514667	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.263378981514667	3		217	391	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733321	40733321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	155	416	1	ENST00000373198.4:c.3485C>T	p.Ala1162Val	p.A1162V	ENST00000373198	NM_133170.3	1162	gCg/gTg	26/32	0.263378981514667	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.263378981514667	3		417	610	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644599	21644599	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	105	453	0	ENST00000421138.2:c.68T>C	p.Ile23Thr	p.I23T	ENST00000421138		23	aTt/aCt	4/16	0.257169505423125	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.263378981514667	1		453	559	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304213	65304213	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	85	424	0	ENST00000342505.4:c.2902C>A	p.Leu968Ile	p.L968I	ENST00000342505	NM_002227.2	968	Ctt/Att	21/25	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.263378981514667	2		424	551	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989503	212989503	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	61	315	0	ENST00000342788.4:c.208C>A	p.His70Asn	p.H70N	ENST00000342788	NM_005235.2	70	Cac/Aac	2/28	0.106732931772807	3	FACETS	1	0.918	1	0.544	0.47	0.624	INDETERMINATE	1	TRUE	1	0.263378981514667	3		315	482	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974709	21974709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	133	451	1	ENST00000304494.5:c.118G>A	p.Ala40Thr	p.A40T	ENST00000304494	NM_000077.4	40	Gca/Aca	1/3	1	2	FACETS	0.825	0.752	0.902	1	0.988	1	CLONAL	2	TRUE	1	0.263378981514667	2		452	612	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0054108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	13	478	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.0157744972102511	3	FACETS	0.219	0.155	0.298	0.109	0.077	0.149	INDETERMINATE	1	TRUE	1	0.226093592217769	3		478	585	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0054108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	92	470	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.0617417089140266	4	FACETS	1	0.959	1	1	0.959	1	INDETERMINATE	2	TRUE	2	0.226093592217769	4		470	433	SUCCESS
APC	324	MSKCC	GRCh37	5	112175246	112175246	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1057517558	NA	P-0054108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	118	209	0	ENST00000257430.4:c.3956del	p.Pro1319LeufsTer2	p.P1319Lfs*2	ENST00000257430	NM_000038.5	1319	Cct/ct	16/16	0.226093592217769	2	FACETS	0.985	0.913	1	1	0.992	1	CLONAL	5	TRUE	0	0.226093592217769	2		209	212	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371942	55371942	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	17	295	0	ENST00000297316.4:c.632C>T	p.Ala211Val	p.A211V	ENST00000297316	NM_022454.3	211	gCg/gTg	2/2	1	2	FACETS	0.488	0.364	0.636	0.488	0.364	0.636	SUBCLONAL	1	TRUE	1	0.226093592217769	2		295	308	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435086	49435086	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	52	835	0	ENST00000301067.7:c.6467C>T	p.Pro2156Leu	p.P2156L	ENST00000301067	NM_003482.3	2156	cCt/cTt	31/54	0.0617417089140266	4	FACETS	0.869	0.739	1	0.435	0.369	0.506	INDETERMINATE	1	TRUE	2	0.226093592217769	4		835	649	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068909	30068909	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	51	569	0	ENST00000331968.5:c.2020G>T	p.Glu674Ter	p.E674*	ENST00000331968	NM_002742.2	674	Gaa/Taa	14/18	1	2	FACETS	0.861	0.732	1	0.861	0.732	1	CLONAL	1	TRUE	1	0.226093592217769	2		569	524	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678342	88678342	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	166	695	0	ENST00000360948.2:c.1194G>T	p.Glu398Asp	p.E398D	ENST00000360948	NM_001012338.2	398	gaG/gaT	9/19	1	2	FACETS	1	0.965	1	1	0.994	1	CLONAL	3	TRUE	1	0.226093592217769	2		695	458	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047353	128047353	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	97	478	0	ENST00000285398.2:c.569A>T	p.Gln190Leu	p.Q190L	ENST00000285398	NM_000122.1	190	cAg/cTg	5/15	1	2	FACETS	1	0.921	1	1	0.987	1	CLONAL	2	TRUE	1	0.226093592217769	2		478	416	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875950	76875950	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	19	387	0	ENST00000373344.5:c.5185T>C	p.Ser1729Pro	p.S1729P	ENST00000373344	NM_000489.3	1729	Tct/Cct	20/35	0.226093592217769	1	FACETS	0.459	0.348	0.589	0.459	0.348	0.589	SUBCLONAL	1	TRUE	0	0.226093592217769	1		387	325	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936983	48936983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690863	NA	P-0054109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	310	448	1	ENST00000267163.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000267163	NM_000321.2	251	Cga/Tga	8/27	0.396738134329691	5	FACETS	0.921	0.877	0.966			1	INDETERMINATE	3	TRUE	NA	0.756572324400586	5		449	633	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413009	49413009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519953	NA	P-0054109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	313	584	0	ENST00000418115.1:c.14G>A	p.Arg5Gln	p.R5Q	ENST00000418115	NM_001664.2	5	cGg/cAg	2/5	1	2	FACETS	0.886	0.838	0.935	0.886	0.838	0.935	CLONAL	1	TRUE	1	0.756572324400586	2		584	934	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259449	55259449	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146121458	NA	P-0054109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	308	524	0	ENST00000275493.2:c.2507G>A	p.Arg836His	p.R836H	ENST00000275493	NM_005228.3	836	cGc/cAc	21/28	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.756572324400586	2		524	735	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0054110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	66	420	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.258735170874269	3	FACETS	1	0.883	1	0.509	0.442	0.582	CLONAL	1	TRUE	1	0.258735170874269	3		420	566	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955108	17955108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56384680	NA	P-0054110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	196	861	0	ENST00000458235.1:c.119G>A	p.Arg40His	p.R40H	ENST00000458235	NM_000215.3	40	cGc/cAc	2/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.258735170874269	2		861	1309	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977198	85977198	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0054110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	43	220	0	ENST00000263360.6:c.800C>G	p.Ser267Ter	p.S267*	ENST00000263360	NM_003797.3	267	tCa/tGa	8/12	0.258735170874269	1	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	0	0.258735170874269	1		220	286	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547942	41547942	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	106	397	0	ENST00000263253.7:c.2923G>T	p.Glu975Ter	p.E975*	ENST00000263253	NM_001429.3	975	Gaa/Taa	15/31	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.258735170874269	2		397	756	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828723	3828724	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0054110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	204	472	0	ENST00000262367.5:c.1918_1919del	p.Met640ValfsTer9	p.M640Vfs*9	ENST00000262367	NM_004380.2	640	ATg/g	9/31	1	2	FACETS	0.871	0.809	0.936	1	0.993	1	CLONAL	2	TRUE	1	0.258735170874269	2		472	905	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303064	15303064	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	170	944	0	ENST00000263388.2:c.386C>G	p.Ala129Gly	p.A129G	ENST00000263388	NM_000435.2	129	gCc/gGc	4/33	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.258735170874269	2		944	1223	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056069	26056107	+	inframe_deletion	In_Frame_Del	DEL	CTTGGGCTTCACAGCCTTAGCAGCACTTTTGGCAGCTTT	CTTGGGCTTCACAGCCTTAGCAGCACTTTTGGCAGCTTT	-	novel	NA	P-0054110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	68	331	0	ENST00000343677.2:c.550_588del	p.Lys184_Lys196del	p.K184_K196del	ENST00000343677	NM_005319.3	184	AAAGCTGCCAAAAGTGCTGCTAAGGCTGTGAAGCCCAAG/-	1/1	0.173809696798524	3	FACETS	0.953	0.829	1	0.476	0.414	0.544	CLONAL	1	TRUE	1	0.258735170874269	3		331	623	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0054145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	69	570	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.179871395405355	1	FACETS	0.971	0.845	1	0.971	0.845	1	CLONAL	1	FALSE	0	0.179871395405355	1		570	719	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604764	48604765	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs377767376	NA	P-0054145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	44	587	0	ENST00000342988.3:c.1587dup	p.His530ThrfsTer47	p.H530Tfs*47	ENST00000342988	NM_005359.5	529	tta/ttAa	12/12	0.179871395405355	1	FACETS	0.861	0.722	1	0.861	0.722	1	CLONAL	1	FALSE	0	0.179871395405355	1		587	517	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716141	243716141	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	33	693	0	ENST00000263826.5:c.1053T>G	p.His351Gln	p.H351Q	ENST00000263826	NM_005465.4	351	caT/caG	10/13	0.179871395405355	1	FACETS	0.621	0.505	0.752	0.621	0.505	0.752	SUBCLONAL	1	FALSE	0	0.179871395405355	1		693	538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579494	7579495	+	stop_gained	Nonsense_Mutation	DNP	TG	TG	AT	novel	NA	P-0054145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	104	993	0	ENST00000269305.4:c.192_193delinsAT	p.Arg65Ter	p.R65*	ENST00000269305	NM_001126112.2	64	ccCAga/ccATga	4/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.179871395405355	2		993	857	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386587	81386587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1032300573	NA	P-0054146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	181	498	0	ENST00000222390.5:c.400C>T	p.Arg134Cys	p.R134C	ENST00000222390	NM_000601.4	134	Cgc/Tgc	4/18	0.813765077355514	1	FACETS	0.885	0.836	0.934	0.885	0.836	0.934	CLONAL	1	TRUE	0	0.813765077355514	1		498	298	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098910	47098910	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	361	769	0	ENST00000409792.3:c.6364C>G	p.Arg2122Gly	p.R2122G	ENST00000409792	NM_014159.6	2122	Cgg/Ggg	15/21	1	2	FACETS	0.981	0.934	1	0.981	0.934	1	CLONAL	1	TRUE	1	0.813765077355514	2		769	904	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913914	32914141	+	inframe_deletion	In_Frame_Del	DEL	ATTTGCGTTGAGGAACTTGTGACTAGCTCTTCACCCTGCAAAAATAAAAATGCAGCCATTAAATTGTCCATATCTAATAGTAATAATTTTGAGGTAGGGCCACCTGCATTTAGGATAGCCAGTGGTAAAATCGTTTGTGTTTCACATGAAACAATTAAAAAAGTGAAAGACATATTTACAGACAGTTTCAGTAAAGTAATTAAGGAAAACAACGAGAATAAATCAAAA	ATTTGCGTTGAGGAACTTGTGACTAGCTCTTCACCCTGCAAAAATAAAAATGCAGCCATTAAATTGTCCATATCTAATAGTAATAATTTTGAGGTAGGGCCACCTGCATTTAGGATAGCCAGTGGTAAAATCGTTTGTGTTTCACATGAAACAATTAAAAAAGTGAAAGACATATTTACAGACAGTTTCAGTAAAGTAATTAAGGAAAACAACGAGAATAAATCAAAA	-	novel	NA	P-0054146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	188	527	1	ENST00000380152.3:c.5428_5655del	p.Val1810_Cys1885del	p.V1810_C1885del	ENST00000380152		1808	ATTTGCGTTGAGGAACTTGTGACTAGCTCTTCACCCTGCAAAAATAAAAATGCAGCCATTAAATTGTCCATATCTAATAGTAATAATTTTGAGGTAGGGCCACCTGCATTTAGGATAGCCAGTGGTAAAATCGTTTGTGTTTCACATGAAACAATTAAAAAAGTGAAAGACATATTTACAGACAGTTTCAGTAAAGTAATTAAGGAAAACAACGAGAATAAATCAAAA/-	11/27	0.813765077355514	1	FACETS	0.816	0.768	0.862	0.816	0.768	0.862	CLONAL	1	TRUE	0	0.813765077355514	1		528	336	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246783	41246783	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	278	574	0	ENST00000357654.3:c.765G>C	p.Glu255Asp	p.E255D	ENST00000357654	NM_007294.3	255	gaG/gaC	10/23	1	2	FACETS	0.973	0.92	1	0.973	0.92	1	CLONAL	1	TRUE	1	0.813765077355514	2		574	702	SUCCESS
ALK	238	MSKCC	GRCh37	2	29497965	29497965	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	224	497	0	ENST00000389048.3:c.2041G>C	p.Val681Leu	p.V681L	ENST00000389048	NM_004304.4	681	Gtt/Ctt	11/29	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.813765077355514	2		497	533	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	62	386	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.195929483296675	4	FACETS	0.865	0.75	0.988	0.865	0.75	0.988	CLONAL	2	TRUE	2	0.229642415949583	4		386	384	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0054147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	22	329	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	1	0.833	1	1	0.833	1	CLONAL	1	TRUE	1	0.229642415949583	2		329	177	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579575	7579575	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	115	852	0	ENST00000269305.4:c.112C>T	p.Gln38Ter	p.Q38*	ENST00000269305	NM_001126112.2	38	Caa/Taa	4/11	1	2	FACETS	0.885	0.8	0.974	1	0.987	1	CLONAL	2	TRUE	1	0.229642415949583	2		852	566	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189849	66189849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139793674	NA	P-0054147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	36	578	1	ENST00000273854.3:c.3097G>A	p.Gly1033Arg	p.G1033R	ENST00000273854	NM_004439.5	1033	Gga/Aga	18/18	1	2	FACETS	0.782	0.643	0.937	0.782	0.643	0.937	CLONAL	1	TRUE	1	0.229642415949583	2		579	401	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927978	178927986	+	inframe_deletion	In_Frame_Del	DEL	ACTGTCCAT	ACTGTCCAT	-	novel	NA	P-0054147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	45	350	0	ENST00000263967.3:c.1256_1264del	p.His419_Pro421del	p.H419_P421del	ENST00000263967	NM_006218.2	419	cACTGTCCATtg/ctg	8/21	1	2	FACETS	0.879	0.746	1	1	0.969	1	CLONAL	2	TRUE	1	0.229642415949583	2		350	223	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578196	7578197	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCACC	novel	NA	P-0054147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	66	879	0	ENST00000269305.4:c.648_652dup	p.Val218GlyfsTer31	p.V218Gfs*31	ENST00000269305	NM_001126112.2	218	gtg/gGGTGGtg	6/11	1	2	FACETS	0.844	0.732	0.966	0.844	0.732	0.966	CLONAL	1	TRUE	1	0.229642415949583	2		879	681	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046253	128046253	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	51	584	0	ENST00000285398.2:c.1010T>C	p.Val337Ala	p.V337A	ENST00000285398	NM_000122.1	337	gTc/gCc	7/15	1	2	FACETS	0.826	0.702	0.962	0.826	0.702	0.962	CLONAL	1	TRUE	1	0.229642415949583	2		584	538	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151833963	151833963	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	56	640	0	ENST00000262189.6:c.14690T>G	p.Ile4897Ser	p.I4897S	ENST00000262189	NM_170606.2	4897	aTt/aGt	59/59	0.229642415949583	3	FACETS	0.926	0.793	1	0.463	0.396	0.536	CLONAL	1	TRUE	1	0.229642415949583	3		640	587	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778771	76778771	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	25	617	0	ENST00000373344.5:c.6808G>T	p.Glu2270Ter	p.E2270*	ENST00000373344	NM_000489.3	2270	Gaa/Taa	31/35	1	2	FACETS	0.458	0.36	0.572	0.458	0.36	0.572	SUBCLONAL	1	TRUE	1	0.229642415949583	2		617	475	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519996	NA	P-0054148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	154	981	1	ENST00000269305.4:c.395A>T	p.Lys132Met	p.K132M	ENST00000269305	NM_001126112.2	132	aAg/aTg	5/11	0.426807227767871	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.434558441471641	2		982	348	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142954	7142954	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	58	907	0	ENST00000302850.5:c.2415G>T	p.Glu805Asp	p.E805D	ENST00000302850	NM_000208.2	805	gaG/gaT	12/22	0.424716890368092	3	FACETS	0.77	0.663	0.885			1	SUBCLONAL	1	TRUE	NA	0.434558441471641	3		907	422	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584497	187584497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	32	505	0	ENST00000441802.2:c.3536C>T	p.Thr1179Ile	p.T1179I	ENST00000441802	NM_005245.3	1179	aCa/aTa	3/27	0.434558441471641	1	FACETS	0.801	0.66	0.954	0.801	0.66	0.954	CLONAL	1	TRUE	0	0.434558441471641	1		505	144	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579319	7579319	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	338	752	0	ENST00000269305.4:c.368del	p.Thr123IlefsTer47	p.T123Ifs*47	ENST00000269305	NM_001126112.2	123	aCt/at	4/11	0.667535473566816	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.667535473566816	1		752	656	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0054151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	368	570	2	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.546672962325011	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.546672962325011	2		572	596	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277980	18277980	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	304	702	0	ENST00000222254.8:c.1600G>A	p.Glu534Lys	p.E534K	ENST00000222254	NM_005027.3	534	Gag/Aag	13/16	0.546672962325011	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.546672962325011	3		702	680	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728714	190728714	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	82	285	0	ENST00000441310.2:c.2102T>G	p.Phe701Cys	p.F701C	ENST00000441310	NM_000534.4	701	tTt/tGt	10/13	0.546672962325011	3	FACETS	0.91	0.806	1	0.455	0.403	0.51	CLONAL	1	TRUE	1	0.546672962325011	3		285	420	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440078	220440078	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	208	1099	0	ENST00000243786.2:c.931C>G	p.Pro311Ala	p.P311A	ENST00000243786	NM_002191.3	311	Ccc/Gcc	2/2	0.546672962325011	3	FACETS	1	0.974	1	0.549	0.51	0.589	CLONAL	1	TRUE	1	0.546672962325011	3		1099	883	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0054152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	641	570	2	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.64508143521496	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.64508143521496	2		572	901	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451784	29451784	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs772809305	NA	P-0054152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	47	533	3	ENST00000389048.3:c.2781del	p.Cys928AlafsTer11	p.C928Afs*11	ENST00000389048	NM_004304.4	927	ggG/gg	16/29	0.249390075211819	4	FACETS	0.338	0.284	0.398	0.169	0.142	0.199	INDETERMINATE	1	TRUE	2	0.64508143521496	4		536	709	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578441	7578441	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1567553246	NA	P-0054152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	191	1184	0	ENST00000269305.4:c.489C>G	p.Tyr163Ter	p.Y163*	ENST00000269305	NM_001126112.2	163	taC/taG	5/11	0.64508143521496	2	FACETS	0.442	0.408	0.478	0.221	0.204	0.239	SUBCLONAL	1	TRUE	0	0.64508143521496	2		1184	1339	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805712	32805712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760254380	NA	P-0054152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1253	149	906	0	ENST00000374899.4:c.299G>A	p.Ser100Asn	p.S100N	ENST00000374899	NM_018833.2	100	aGc/aAc	2/12	0.64508143521496	5	FACETS	0.648	0.59	0.71	0.216	0.196	0.237	SUBCLONAL	1	TRUE	2	0.64508143521496	5		906	1402	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62322267	62322267	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	575	1257	0	ENST00000360203.5:c.2523C>G	p.Ser841Arg	p.S841R	ENST00000360203	NM_001283009.1	841	agC/agG	27/35	0.382402911647682	5	FACETS	0.835	0.803	0.867	0.835	0.803	0.867	INDETERMINATE	3	TRUE	2	0.64508143521496	5		1257	1400	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11210243	11210243	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	152	770	0	ENST00000361445.4:c.4510G>C	p.Val1504Leu	p.V1504L	ENST00000361445	NM_004958.3	1504	Gtt/Ctt	31/58	0.576899428631248	3	FACETS	0.664	0.607	0.724	0.221	0.202	0.242	SUBCLONAL	1	TRUE	0	0.64508143521496	3		770	939	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258157	16258157	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	112	713	0	ENST00000375759.3:c.5422G>T	p.Asp1808Tyr	p.D1808Y	ENST00000375759	NM_015001.2	1808	Gat/Tat	11/15	0.576899428631248	3	FACETS	0.571	0.513	0.632	0.19	0.171	0.211	SUBCLONAL	1	TRUE	0	0.64508143521496	3		713	804	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567820	226567820	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	89	968	0	ENST00000366794.5:c.1346C>G	p.Ala449Gly	p.A449G	ENST00000366794	NM_001618.3	449	gCc/gGc	10/23	0.468620364952035	3	FACETS	0.347	0.306	0.39	0.173	0.153	0.195	SUBCLONAL	1	TRUE	1	0.64508143521496	3		968	1052	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926974	112926974	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	56	660	0	ENST00000351677.2:c.1594G>T	p.Glu532Ter	p.E532*	ENST00000351677	NM_002834.3	532	Gag/Tag	13/16	NA	2	FACETS	0.238	0.203	0.276			1	INDETERMINATE	1	TRUE	NA	0.64508143521496	2		660	729	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756736	756736	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs771024922	NA	P-0054152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	103	776	0	ENST00000314574.4:c.92A>G	p.His31Arg	p.H31R	ENST00000314574	NM_005433.3	31	cAt/cGt	2/12	0.305489812570143	3	FACETS	0.626	0.56	0.695	0.313	0.28	0.348	INDETERMINATE	1	TRUE	1	0.64508143521496	3		776	675	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050291	13050291	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11547568	NA	P-0054152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	355	772	0	ENST00000316448.5:c.243C>G	p.Phe81Leu	p.F81L	ENST00000316448	NM_004343.3	81	ttC/ttG	3/9	0.397777397082233	6	FACETS	0.949	0.898	1	0.633	0.599	0.667	CLONAL	2	TRUE	3	0.64508143521496	6		772	1328	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61729383	61729383	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0054152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	35	537	0	ENST00000401558.2:c.363+1G>T		p.X121_splice	ENST00000401558	NM_003400.3	121			0.249390075211819	4	FACETS	0.371	0.304	0.447	0.186	0.152	0.224	INDETERMINATE	1	TRUE	2	0.64508143521496	4		537	481	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632375	215632375	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	37	432	0	ENST00000260947.4:c.1399G>A	p.Glu467Lys	p.E467K	ENST00000260947	NM_000465.2	467	Gaa/Aaa	6/11	0.374939334154114	5	FACETS	0.453	0.373	0.543	0.151	0.124	0.181	INDETERMINATE	1	TRUE	2	0.64508143521496	5		432	498	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164444	36164444	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	87	374	0	ENST00000300305.3:c.1431G>T	p.Trp477Cys	p.W477C	ENST00000300305		477	tgG/tgT	8/8	0.581401765926258	3	FACETS	0.761	0.676	0.85	0.38	0.338	0.425	SUBCLONAL	1	TRUE	1	0.64508143521496	3		374	469	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294196	1294196	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	148	1054	0	ENST00000310581.5:c.805G>T	p.Gly269Cys	p.G269C	ENST00000310581	NM_198253.2	269	Ggt/Tgt	2/16	0.301894662296281	3	FACETS	0.515	0.469	0.563	0.172	0.156	0.188	INDETERMINATE	1	TRUE	0	0.64508143521496	3		1054	1178	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045663	26045663	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	40	477	0	ENST00000540144.1:c.25C>G	p.Arg9Gly	p.R9G	ENST00000540144	NM_003531.2	9	Cgc/Ggc	1/1	0.604008878003951	6	FACETS	0.412	0.341	0.491	0.103	0.085	0.123	SUBCLONAL	1	TRUE	2	0.64508143521496	6		477	689	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459525	50459525	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	29	417	0	ENST00000331340.3:c.814G>C	p.Ala272Pro	p.A272P	ENST00000331340	NM_006060.4	272	Gcc/Ccc	7/8	0.374939334154114	5	FACETS	0.371	0.297	0.455	0.124	0.099	0.152	INDETERMINATE	1	TRUE	2	0.64508143521496	5		417	477	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8501056	8501224	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCTCTTATTTTGGTAGTGAGTTAAAGGAGGATTTAAGTGAAAGGACAGGAGTGGTTGAAAAAAAAAATGATAAAACAAAAGAAAAGGCAAAAATAAATAAACGAACAATAAGGACAAAATGAAAATAAGGCTTTGAAACTTAAATTCTAATGACAAATTATGTACCTT	GGCTCTTATTTTGGTAGTGAGTTAAAGGAGGATTTAAGTGAAAGGACAGGAGTGGTTGAAAAAAAAAATGATAAAACAAAAGAAAAGGCAAAAATAAATAAACGAACAATAAGGACAAAATGAAAATAAGGCTTTGAAACTTAAATTCTAATGACAAATTATGTACCTT	-	novel	NA	P-0054152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	41	406	0	ENST00000356435.5:c.1823-165_1826del		p.X608_splice	ENST00000356435		608		13/35	0.515873128598831	4	FACETS	0.531	0.443	0.628	0.177	0.147	0.21	SUBCLONAL	1	TRUE	1	0.64508143521496	4		406	394	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430766	47430766	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	181	1145	0	ENST00000377045.4:c.1731T>G	p.Ile577Met	p.I577M	ENST00000377045	NM_001654.4	577	atT/atG	16/16	0.249390075211819	4	FACETS	0.679	0.625	0.736	0.34	0.312	0.368	INDETERMINATE	1	TRUE	2	0.64508143521496	4		1145	1359	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	255	258	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.68368072191909	2		258	574	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	331	804	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	1	2	FACETS	0.858	0.812	0.906	0.858	0.812	0.906	CLONAL	1	TRUE	1	0.68368072191909	2		804	1128	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	310	446	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	1	2	FACETS	0.993	0.939	1	0.993	0.939	1	CLONAL	1	TRUE	1	0.68368072191909	2		446	913	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335667	81335667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	150	578	2	ENST00000222390.5:c.1693C>T	p.Leu565Phe	p.L565F	ENST00000222390	NM_000601.4	565	Ctc/Ttc	15/18	NA	2	FACETS	0.869	0.8	0.94			1	INDETERMINATE	1	TRUE	NA	0.68368072191909	2		580	505	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271975	15271975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs567953412	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	392	1218	1	ENST00000263388.2:c.6464G>A	p.Gly2155Glu	p.G2155E	ENST00000263388	NM_000435.2	2155	gGa/gAa	33/33	1	2	FACETS	0.886	0.841	0.93	0.886	0.841	0.93	CLONAL	1	TRUE	1	0.68368072191909	2		1219	1295	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780068	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	479	1076	2	ENST00000269305.4:c.472C>T	p.Arg158Cys	p.R158C	ENST00000269305	NM_001126112.2	158	Cgc/Tgc	5/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.68368072191909	2		1078	1382	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888303	112888303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	160	484	0	ENST00000351677.2:c.319C>T	p.Pro107Ser	p.P107S	ENST00000351677	NM_002834.3	107	Cct/Tct	3/16	1	2	FACETS	0.881	0.813	0.952	0.881	0.813	0.952	CLONAL	1	TRUE	1	0.68368072191909	2		484	531	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858255	9858255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	196	613	0	ENST00000330684.3:c.3146C>T	p.Pro1049Leu	p.P1049L	ENST00000330684	NM_001134407.1	1049	cCt/cTt	13/13	1	2	FACETS	0.957	0.891	1	0.957	0.891	1	CLONAL	1	TRUE	1	0.68368072191909	2		613	599	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024150	31024150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542568224	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	307	802	0	ENST00000375687.4:c.3635C>T	p.Ser1212Phe	p.S1212F	ENST00000375687	NM_015338.5	1212	tCc/tTc	13/13	1	2	FACETS	0.949	0.897	1	0.949	0.897	1	CLONAL	1	TRUE	1	0.68368072191909	2		802	946	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993791	72993791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371690491	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	305	904	2	ENST00000268489.5:c.254C>T	p.Ser85Leu	p.S85L	ENST00000268489	NM_006885.3	85	tCg/tTg	2/10	1	2	FACETS	0.904	0.853	0.956	0.904	0.853	0.956	CLONAL	1	TRUE	1	0.68368072191909	2		906	987	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212173	98212173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1131690985	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	245	485	0	ENST00000331920.6:c.3499G>A	p.Gly1167Arg	p.G1167R	ENST00000331920	NM_000264.3	1167	Ggg/Agg	21/24	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.68368072191909	2		485	626	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	254	334	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.68368072191909	2		335	512	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849089	156849089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	399	1044	0	ENST00000524377.1:c.1981G>A	p.Gly661Arg	p.G661R	ENST00000524377	NM_002529.3	661	Gga/Aga	15/17	1	2	FACETS	0.921	0.875	0.966	0.921	0.875	0.966	CLONAL	1	TRUE	1	0.68368072191909	2		1044	1268	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723473	52723473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	257	676	1	ENST00000322088.6:c.1334C>T	p.Ser445Phe	p.S445F	ENST00000322088	NM_014225.5	445	tCc/tTc	11/15	1	2	FACETS	0.865	0.812	0.92	0.865	0.812	0.92	CLONAL	1	TRUE	1	0.68368072191909	2		677	869	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722252	176722252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	281	763	3	ENST00000439151.2:c.7883G>A	p.Gly2628Glu	p.G2628E	ENST00000439151	NM_022455.4	2628	gGa/gAa	23/23	1	2	FACETS	0.924	0.87	0.978	0.924	0.87	0.978	CLONAL	1	TRUE	1	0.68368072191909	2		766	890	SUCCESS
APC	324	MSKCC	GRCh37	5	112178303	112178303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs571304880	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	176	489	0	ENST00000257430.4:c.7012C>T	p.Pro2338Ser	p.P2338S	ENST00000257430	NM_000038.5	2338	Cct/Tct	16/16	1	2	FACETS	0.919	0.852	0.988	0.919	0.852	0.988	CLONAL	1	TRUE	1	0.68368072191909	2		489	560	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224140	98224140	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs1064796618	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	192	363	0	ENST00000331920.6:c.2701C>T	p.Gln901Ter	p.Q901*	ENST00000331920	NM_000264.3	901	Cag/Tag	16/24	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.68368072191909	2		363	542	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264964	46264964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	211	554	0	ENST00000371998.3:c.1834C>T	p.Pro612Ser	p.P612S	ENST00000371998		612	Cct/Tct	12/23	1	2	FACETS	0.932	0.87	0.996	0.932	0.87	0.996	CLONAL	1	TRUE	1	0.68368072191909	2		554	662	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156836701	156836701	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	395	994	0	ENST00000524377.1:c.360-1G>A		p.X120_splice	ENST00000524377	NM_002529.3	120			1	2	FACETS	0.955	0.908	1	0.955	0.908	1	CLONAL	1	TRUE	1	0.68368072191909	2		994	1210	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738415	133738415	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	277	607	0	ENST00000318560.5:c.815C>T	p.Thr272Ile	p.T272I	ENST00000318560	NM_005157.4	272	aCc/aTc	4/11	1	2	FACETS	0.976	0.92	1	0.976	0.92	1	CLONAL	1	TRUE	1	0.68368072191909	2		607	830	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023511	31023511	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778222400	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	282	658	2	ENST00000375687.4:c.2996C>T	p.Thr999Met	p.T999M	ENST00000375687	NM_015338.5	999	aCg/aTg	13/13	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.68368072191909	2		660	792	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226553753	226553753	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	133	374	0	ENST00000366794.5:c.2407G>A	p.Val803Met	p.V803M	ENST00000366794	NM_001618.3	803	Gtg/Atg	18/23	1	2	FACETS	0.849	0.777	0.924	0.849	0.777	0.924	CLONAL	1	TRUE	1	0.68368072191909	2		374	458	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49423020	49423020	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	348	909	0	ENST00000301067.7:c.14076-1G>A		p.X4692_splice	ENST00000301067	NM_003482.3	4692			1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.68368072191909	2		909	837	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434149	121434149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	457	1093	0	ENST00000257555.6:c.1040C>T	p.Pro347Leu	p.P347L	ENST00000257555		347	cCc/cTc	5/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.68368072191909	2		1093	1268	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590606	95590606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1222748384	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	125	291	0	ENST00000393063.1:c.1303C>T	p.Pro435Ser	p.P435S	ENST00000393063	NM_030621.3	435	Cct/Tct	9/28	1	2	FACETS	0.975	0.892	1	0.975	0.892	1	CLONAL	1	TRUE	1	0.68368072191909	2		291	375	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034759	42034759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	209	582	0	ENST00000219905.7:c.4601C>T	p.Pro1534Leu	p.P1534L	ENST00000219905	NM_001164273.1	1534	cCt/cTt	15/24	1	2	FACETS	0.841	0.783	0.9	0.841	0.783	0.9	CLONAL	1	TRUE	1	0.68368072191909	2		582	727	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43739680	43739680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750921505	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	108	258	0	ENST00000382044.4:c.2720C>T	p.Thr907Ile	p.T907I	ENST00000382044	NM_001141980.1	907	aCc/aTc	13/28	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.68368072191909	2		258	305	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348180	348181	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	386	1233	1	ENST00000262320.3:c.1325_1326delinsTT	p.Pro442Leu	p.P442L	ENST00000262320	NM_003502.3	442	cCC/cTT	6/11	1	2	FACETS	0.848	0.805	0.892	0.848	0.805	0.892	CLONAL	1	TRUE	1	0.68368072191909	2		1234	1331	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124369	2124370	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	397	1072	1	ENST00000219476.3:c.2524_2525delinsTT	p.Pro842Leu	p.P842L	ENST00000219476	NM_000548.3	842	CCa/TTa	22/42	1	2	FACETS	0.909	0.865	0.955	0.909	0.865	0.955	CLONAL	1	TRUE	1	0.68368072191909	2		1073	1277	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220640	2220641	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	336	945	2	ENST00000326181.6:c.257_258delinsTT	p.Ser86Phe	p.S86F	ENST00000326181	NM_032271.2	86	tCC/tTT	5/21	1	2	FACETS	0.868	0.821	0.915	0.868	0.821	0.915	CLONAL	1	TRUE	1	0.68368072191909	2		947	1133	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993836	72993836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	293	897	0	ENST00000268489.5:c.209C>T	p.Pro70Leu	p.P70L	ENST00000268489	NM_006885.3	70	cCc/cTc	2/10	1	2	FACETS	0.934	0.881	0.988	0.934	0.881	0.988	CLONAL	1	TRUE	1	0.68368072191909	2		897	918	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81979782	81979782	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	208	522	0	ENST00000359376.3:c.3484T>A	p.Phe1162Ile	p.F1162I	ENST00000359376	NM_002661.3	1162	Ttc/Atc	31/33	1	2	FACETS	0.884	0.824	0.946	0.884	0.824	0.946	CLONAL	1	TRUE	1	0.68368072191909	2		522	688	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646983	37646983	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	216	500	0	ENST00000447079.4:c.2105C>T	p.Pro702Leu	p.P702L	ENST00000447079	NM_015083.1	702	cCa/cTa	3/14	1	2	FACETS	0.952	0.889	1	0.952	0.889	1	CLONAL	1	TRUE	1	0.68368072191909	2		500	664	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60795946	60795946	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	328	733	0	ENST00000333681.4:c.632A>G	p.Asp211Gly	p.D211G	ENST00000333681		211	gAt/gGt	3/3	1	2	FACETS	0.974	0.922	1	0.974	0.922	1	CLONAL	1	TRUE	1	0.68368072191909	2		733	985	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119247	3119248	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	288	1045	0	ENST00000078429.4:c.779_780delinsTT	p.Thr260Ile	p.T260I	ENST00000078429	NM_002067.2	260	aCC/aTT	6/7	1	2	FACETS	0.776	0.73	0.824	0.776	0.73	0.824	SUBCLONAL	1	TRUE	1	0.68368072191909	2		1045	1085	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211689	5211689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	375	917	0	ENST00000357368.4:c.5146C>T	p.Pro1716Ser	p.P1716S	ENST00000357368	NM_002850.3	1716	Ccc/Tcc	33/38	1	2	FACETS	0.975	0.927	1	0.975	0.927	1	CLONAL	1	TRUE	1	0.68368072191909	2		917	1125	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626862	14626862	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370674842	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	378	895	0	ENST00000254322.2:c.913C>T	p.Pro305Ser	p.P305S	ENST00000254322	NM_006145.1	305	Ccc/Tcc	3/3	1	2	FACETS	0.989	0.94	1	0.989	0.94	1	CLONAL	1	TRUE	1	0.68368072191909	2		895	1118	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792534	33792535	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	118	250	0	ENST00000498907.2:c.786_787delinsTT	p.Leu263Phe	p.L263F	ENST00000498907	NM_004364.3	262	gaCCtc/gaTTtc	1/1	1	2	FACETS	0.995	0.908	1	0.995	0.908	1	CLONAL	1	TRUE	1	0.68368072191909	2		250	347	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714526	52714526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148604195	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	331	812	0	ENST00000322088.6:c.284C>T	p.Ser95Leu	p.S95L	ENST00000322088	NM_014225.5	95	tCg/tTg	4/15	1	2	FACETS	0.987	0.935	1	0.987	0.935	1	CLONAL	1	TRUE	1	0.68368072191909	2		812	981	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737525	204737525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	106	306	0	ENST00000302823.3:c.662C>T	p.Pro221Leu	p.P221L	ENST00000302823	NM_005214.4	221	cCc/cTc	4/4	0.68368072191909	1	FACETS	0.887	0.813	0.963	0.887	0.813	0.963	CLONAL	1	TRUE	0	0.68368072191909	1		306	230	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670679	134670679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369940583	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	311	794	0	ENST00000398015.3:c.590C>T	p.Pro197Leu	p.P197L	ENST00000398015	NM_004441.4	197	cCc/cTc	3/16	0.329742272670505	1	FACETS	0.655	0.619	0.691	0.655	0.619	0.691	INDETERMINATE	1	TRUE	0	0.68368072191909	1		794	914	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595521	55595521	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	99	428	0	ENST00000288135.5:c.2011G>A	p.Glu671Lys	p.E671K	ENST00000288135	NM_000222.2	671	Gaa/Aaa	14/21	0.236779244273562	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.68368072191909	0		428	415	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459719	149459719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	384	1023	0	ENST00000286301.3:c.488C>T	p.Thr163Ile	p.T163I	ENST00000286301	NM_005211.3	163	aCc/aTc	4/22	1	2	FACETS	0.932	0.886	0.979	0.932	0.886	0.979	CLONAL	1	TRUE	1	0.68368072191909	2		1023	1205	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522441	176522441	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs745431924	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	342	1032	0	ENST00000292408.4:c.1630G>A	p.Gly544Arg	p.G544R	ENST00000292408	NM_213647.1	544	Ggg/Agg	12/18	1	2	FACETS	0.921	0.873	0.971	0.921	0.873	0.971	CLONAL	1	TRUE	1	0.68368072191909	2		1032	1086	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336634	81336634	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	84	390	0	ENST00000222390.5:c.1588C>T	p.Leu530Phe	p.L530F	ENST00000222390	NM_000601.4	530	Ctt/Ttt	14/18	NA	2	FACETS	0.8	0.714	0.89			1	INDETERMINATE	1	TRUE	NA	0.68368072191909	2		390	307	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981645	70981645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs916090052	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	397	1125	0	ENST00000276594.2:c.451C>T	p.Pro151Ser	p.P151S	ENST00000276594	NM_024504.3	151	Cca/Tca	2/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.68368072191909	2		1125	1150	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410816	63410816	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	318	425	0	ENST00000330258.3:c.2351C>T	p.Ser784Phe	p.S784F	ENST00000330258	NM_152424.3	784	tCc/tTc	2/2	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.68368072191909	1		425	504	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508856	106508856	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376958957	NA	P-0054154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	184	760	1	ENST00000359195.3:c.850G>A	p.Glu284Lys	p.E284K	ENST00000359195	NM_002649.2	284	Gaa/Aaa	2/11	1	2	FACETS	0.641	0.592	0.693	0.641	0.592	0.693	SUBCLONAL	1	TRUE	1	0.599431362308802	2		761	957	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060780	38060780	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	343	1065	0	ENST00000250448.2:c.1209C>G	p.Asn403Lys	p.N403K	ENST00000250448	NM_004496.3	403	aaC/aaG	2/2	1	2	FACETS	0.916	0.867	0.967	0.916	0.867	0.967	CLONAL	1	TRUE	1	0.599431362308802	2		1065	1249	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819932	170819934	+	inframe_deletion	In_Frame_Del	DEL	TGC	TGC	-	rs587778581	NA	P-0054154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	116	360	0	ENST00000296930.5:c.479_481del	p.Ala160del	p.A160del	ENST00000296930	NM_002520.6	158	ctTGCt/ctt	6/11	1	2	FACETS	0.858	0.779	0.941	0.858	0.779	0.941	CLONAL	1	TRUE	1	0.599431362308802	2		360	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0054155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	187	781	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.250513216775705	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	0	0.250513216775705	1		782	941	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0054155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	62	499	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.92	0.795	1	0.92	0.795	1	CLONAL	1	FALSE	1	0.250513216775705	2		499	538	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149290746	149290746	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775570561	NA	P-0054155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	140	652	0	ENST00000360632.3:c.473C>T	p.Ala158Val	p.A158V	ENST00000360632	NM_015472.4	158	gCg/gTg	3/7	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.250513216775705	2		652	851	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488226	56488226	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	169	737	2	ENST00000267101.3:c.1745G>T	p.Gly582Val	p.G582V	ENST00000267101	NM_001982.3	582	gGg/gTg	15/28	0.250513216775705	1	FACETS	0.776	0.715	0.84	1	0.99	1	SUBCLONAL	2	FALSE	0	0.250513216775705	1		739	760	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	149	258	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.829640333913265	2		258	324	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	313	670	3	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.953	0.903	1	0.953	0.903	1	CLONAL	1	TRUE	1	0.829640333913265	2		673	792	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023559	27023560	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	115	605	1	ENST00000324856.7:c.671dup	p.Pro225AlafsTer175	p.P225Afs*175	ENST00000324856	NM_006015.4	222	tac/taCc	1/20	1	2	FACETS	0.676	0.614	0.741	0.676	0.614	0.741	SUBCLONAL	1	TRUE	1	0.829640333913265	2		606	410	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	231	691	1	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.829640333913265	2		692	540	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846398	128846398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879255280	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	507	822	0	ENST00000249373.3:c.1234C>T	p.Leu412Phe	p.L412F	ENST00000249373	NM_005631.4	412	Ctc/Ttc	6/12	0.830563828212396	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	1	0.829640333913265	3		822	774	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391340	139391340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1341934554	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	271	1284	0	ENST00000277541.6:c.6851C>T	p.Thr2284Ile	p.T2284I	ENST00000277541	NM_017617.3	2284	aCc/aTc	34/34	0.830563828212396	2	FACETS	1	0.962	1	0.511	0.483	0.54	CLONAL	1	TRUE	0	0.829640333913265	2		1284	639	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268793	98268793	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1554708751	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	219	732	1	ENST00000331920.6:c.290del	p.Asn97ThrfsTer20	p.N97Tfs*20	ENST00000331920	NM_000264.3	97	aAc/ac	2/24	1	2	FACETS	0.928	0.87	0.987	0.928	0.87	0.987	CLONAL	1	TRUE	1	0.829640333913265	2		733	569	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983275	149983275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	357	740	0	ENST00000253339.5:c.2983C>T	p.Arg995Cys	p.R995C	ENST00000253339		995	Cgc/Tgc	7/7	0.829640333913265	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.829640333913265	2		740	424	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467824	66467824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	71	433	0	ENST00000273854.3:c.445G>A	p.Glu149Lys	p.E149K	ENST00000273854	NM_004439.5	149	Gaa/Aaa	3/18	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.829640333913265	2		433	171	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351422	70351422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	218	438	1	ENST00000374080.3:c.4070G>A	p.Arg1357His	p.R1357H	ENST00000374080		1357	cGc/cAc	29/45	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.829640333913265	1		439	246	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505385	157505385	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	210	587	0	ENST00000346085.5:c.3366G>A	p.Trp1122Ter	p.W1122*	ENST00000346085	NM_020732.3	1122	tgG/tgA	13/20	0.829640333913265	2	FACETS	1	0.967	1	0.523	0.491	0.556	CLONAL	1	TRUE	0	0.829640333913265	2		587	484	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593663	55593663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	111	598	0	ENST00000288135.5:c.1729C>T	p.Pro577Ser	p.P577S	ENST00000288135	NM_000222.2	577	Cct/Tct	11/21	1	2	FACETS	0.88	0.802	0.96	0.88	0.802	0.96	CLONAL	1	TRUE	1	0.829640333913265	2		598	304	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	227	880	1	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.759	0.71	0.809	0.759	0.71	0.809	SUBCLONAL	1	TRUE	1	0.829640333913265	2		881	721	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228800	36228800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393734909	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	258	1119	2	ENST00000222270.7:c.7699C>T	p.Arg2567Cys	p.R2567C	ENST00000222270	NM_014727.1	2567	Cgt/Tgt	35/37	1	2	FACETS	0.992	0.936	1	0.992	0.936	1	CLONAL	1	TRUE	1	0.829640333913265	2		1121	627	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410945	63410945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	147	510	1	ENST00000330258.3:c.2222C>T	p.Pro741Leu	p.P741L	ENST00000330258	NM_152424.3	741	cCc/cTc	2/2	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.829640333913265	1		511	181	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945118	151945118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774935898	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	32	558	0	ENST00000262189.6:c.2401C>T	p.Pro801Ser	p.P801S	ENST00000262189	NM_170606.2	801	Cct/Tct	14/59	0.830563828212396	3	FACETS	0.62	0.509	0.743	0.31	0.254	0.372	SUBCLONAL	1	TRUE	1	0.829640333913265	3		558	176	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11015633	11015634	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	179	727	0	ENST00000327064.4:c.235_236dup	p.Phe80SerfsTer46	p.F80Sfs*46	ENST00000327064	NM_199141.1	76	gat/gaTGt	2/16	1	2	FACETS	0.888	0.826	0.951	0.888	0.826	0.951	CLONAL	1	TRUE	1	0.829640333913265	2		727	486	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268805	41268805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	121	438	0	ENST00000349496.5:c.1043C>T	p.Ser348Phe	p.S348F	ENST00000349496	NM_001904.3	348	tCt/tTt	7/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.829640333913265	2		438	275	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112566	115112566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	325	1072	2	ENST00000257566.3:c.1174G>A	p.Ala392Thr	p.A392T	ENST00000257566	NM_016569.3	392	Gcg/Acg	7/8	1	2	FACETS	0.985	0.936	1	0.985	0.936	1	CLONAL	1	TRUE	1	0.829640333913265	2		1074	795	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149440428	149440428	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	221	849	0	ENST00000286301.3:c.1966G>A	p.Gly656Arg	p.G656R	ENST00000286301	NM_005211.3	656	Gga/Aga	14/22	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.829640333913265	2		849	479	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270102	66270102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	103	468	0	ENST00000273854.3:c.1780C>T	p.Leu594Phe	p.L594F	ENST00000273854	NM_004439.5	594	Ctc/Ttc	8/18	1	2	FACETS	0.926	0.843	1	0.926	0.843	1	CLONAL	1	TRUE	1	0.829640333913265	2		468	268	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248543	212248543	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	206	770	0	ENST00000342788.4:c.3724T>A	p.Tyr1242Asn	p.Y1242N	ENST00000342788	NM_005235.2	1242	Tac/Aac	28/28	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.829640333913265	2		770	477	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272278	18272278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	14	36	0	ENST00000222254.8:c.788C>T	p.Ser263Leu	p.S263L	ENST00000222254	NM_005027.3	263	tCg/tTg	6/16	1	2	FACETS	0.767	0.616	0.904	1	0.923	1	CLONAL	2	TRUE	1	0.829640333913265	2		36	22	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120509002	120509002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	183	612	0	ENST00000256646.2:c.1564C>T	p.Pro522Ser	p.P522S	ENST00000256646	NM_024408.3	522	Cct/Tct	9/34	1	2	FACETS	0.998	0.932	1	0.998	0.932	1	CLONAL	1	TRUE	1	0.829640333913265	2		612	442	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104377175	104377175	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	246	1143	0	ENST00000369902.3:c.1286C>T	p.Pro429Leu	p.P429L	ENST00000369902	NM_016169.3	429	cCc/cTc	10/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.829640333913265	2		1143	566	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424168	49424168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	170	698	0	ENST00000301067.7:c.13894C>T	p.Pro4632Ser	p.P4632S	ENST00000301067	NM_003482.3	4632	Cca/Tca	42/54	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.829640333913265	2		698	406	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427126	49427126	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	213	1078	0	ENST00000301067.7:c.11362C>T	p.Gln3788Ter	p.Q3788*	ENST00000301067	NM_003482.3	3788	Cag/Tag	39/54	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.829640333913265	2		1078	486	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486532	56486532	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	158	756	0	ENST00000267101.3:c.1111G>A	p.Asp371Asn	p.D371N	ENST00000267101	NM_001982.3	371	Gac/Aac	10/28	1	2	FACETS	0.89	0.824	0.957	0.89	0.824	0.957	CLONAL	1	TRUE	1	0.829640333913265	2		756	428	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495624	56495624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	144	761	0	ENST00000267101.3:c.3814C>T	p.Pro1272Ser	p.P1272S	ENST00000267101	NM_001982.3	1272	Cct/Tct	28/28	1	2	FACETS	0.962	0.889	1	0.962	0.889	1	CLONAL	1	TRUE	1	0.829640333913265	2		761	361	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143283	58143283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	78	521	0	ENST00000257904.6:c.637C>T	p.Leu213Phe	p.L213F	ENST00000257904	NM_000075.3	213	Ctc/Ttc	6/8	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.829640333913265	2		521	186	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784102	120784102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	315	1289	0	ENST00000257552.2:c.883C>T	p.Pro295Ser	p.P295S	ENST00000257552	NM_002442.3	295	Ccc/Tcc	13/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.829640333913265	2		1289	694	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281441	49281441	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	140	833	0	ENST00000282018.3:c.488G>A	p.Trp163Ter	p.W163*	ENST00000282018	NM_020377.2	163	tGg/tAg	1/1	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.829640333913265	2		833	291	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436551	110436551	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	353	1214	0	ENST00000375856.3:c.1850C>T	p.Pro617Leu	p.P617L	ENST00000375856	NM_003749.2	617	cCc/cTc	1/2	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.829640333913265	2		1214	746	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003356	42003356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	165	645	0	ENST00000219905.7:c.2893C>T	p.Pro965Ser	p.P965S	ENST00000219905	NM_001164273.1	965	Cca/Tca	8/24	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.829640333913265	2		645	394	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832690	3832690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	145	634	0	ENST00000262367.5:c.1568C>T	p.Pro523Leu	p.P523L	ENST00000262367	NM_004380.2	523	cCc/cTc	6/31	1	2	FACETS	0.93	0.859	1	0.93	0.859	1	CLONAL	1	TRUE	1	0.829640333913265	2		634	376	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828155	72828155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756200766	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	151	779	0	ENST00000268489.5:c.8426G>A	p.Gly2809Glu	p.G2809E	ENST00000268489	NM_006885.3	2809	gGg/gAg	9/10	1	2	FACETS	0.943	0.873	1	0.943	0.873	1	CLONAL	1	TRUE	1	0.829640333913265	2		779	386	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974872	15974872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	128	597	0	ENST00000268712.3:c.4003G>A	p.Gly1335Arg	p.G1335R	ENST00000268712	NM_006311.3	1335	Gga/Aga	30/46	1	2	FACETS	0.949	0.873	1	0.949	0.873	1	CLONAL	1	TRUE	1	0.829640333913265	2		597	325	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234490	41234490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357466	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	159	769	0	ENST00000357654.3:c.4288C>T	p.Pro1430Ser	p.P1430S	ENST00000357654	NM_007294.3	1430	Cct/Tct	12/23	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.829640333913265	2		769	374	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245423	41245423	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	148	834	0	ENST00000357654.3:c.2125T>C	p.Phe709Leu	p.F709L	ENST00000357654	NM_007294.3	709	Ttt/Ctt	10/23	1	2	FACETS	0.838	0.772	0.904	0.838	0.772	0.904	CLONAL	1	TRUE	1	0.829640333913265	2		834	426	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805925	46805925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	129	792	0	ENST00000290295.7:c.31G>A	p.Gly11Arg	p.G11R	ENST00000290295	NM_006361.5	11	Gga/Aga	1/2	1	2	FACETS	0.997	0.918	1	0.997	0.918	1	CLONAL	1	TRUE	1	0.829640333913265	2		792	312	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604677	48604677	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs281875321	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	139	549	1	ENST00000342988.3:c.1499T>C	p.Ile500Thr	p.I500T	ENST00000342988	NM_005359.5	500	aTa/aCa	12/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.829640333913265	2		550	309	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244361	5244361	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	315	1156	1	ENST00000357368.4:c.1121G>A	p.Gly374Glu	p.G374E	ENST00000357368	NM_002850.3	374	gGg/gAg	11/38	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.829640333913265	2		1157	680	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172341	7172341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747657283	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	154	663	0	ENST00000302850.5:c.1228C>T	p.Arg410Trp	p.R410W	ENST00000302850	NM_000208.2	410	Cgg/Tgg	5/22	1	2	FACETS	0.952	0.882	1	0.952	0.882	1	CLONAL	1	TRUE	1	0.829640333913265	2		663	390	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272110	15272110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	290	1140	0	ENST00000263388.2:c.6329C>T	p.Pro2110Leu	p.P2110L	ENST00000263388	NM_000435.2	2110	cCt/cTt	33/33	1	2	FACETS	0.941	0.89	0.993	0.941	0.89	0.993	CLONAL	1	TRUE	1	0.829640333913265	2		1140	743	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302244	15302244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	247	1022	0	ENST00000263388.2:c.1027G>A	p.Gly343Ser	p.G343S	ENST00000263388	NM_000435.2	343	Ggc/Agc	6/33	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.829640333913265	2		1022	574	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015005	27015005	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	165	556	0	ENST00000335756.4:c.107C>A	p.Ser36Tyr	p.S36Y	ENST00000335756	NM_001809.3	36	tCc/tAc	2/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.829640333913265	2		556	366	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420076	41420076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	140	711	0	ENST00000373198.4:c.245G>A	p.Arg82Lys	p.R82K	ENST00000373198	NM_133170.3	82	aGa/aAa	3/32	0.763263553216651	3	FACETS	0.936	0.858	1	0.468	0.429	0.509	CLONAL	1	TRUE	1	0.829640333913265	3		711	510	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164472	36164472	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1034562071	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	186	636	0	ENST00000300305.3:c.1403C>T	p.Pro468Leu	p.P468L	ENST00000300305		468	cCc/cTc	8/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.829640333913265	2		636	420	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523616	41523617	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	255	1032	1	ENST00000263253.7:c.1032_1033delinsTT	p.Leu345Phe	p.L345F	ENST00000263253	NM_001429.3	344	ctCCtt/ctTTtt	4/31	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.829640333913265	2		1033	612	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12632343	12632343	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	267	866	0	ENST00000251849.4:c.1324A>C	p.Met442Leu	p.M442L	ENST00000251849	NM_002880.3	442	Atg/Ctg	12/17	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.829640333913265	2		866	579	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723381	49723381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1440228604	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	221	890	0	ENST00000449682.2:c.1162G>A	p.Ala388Thr	p.A388T	ENST00000449682	NM_020998.3	388	Gca/Aca	10/18	1	2	FACETS	0.981	0.921	1	0.981	0.921	1	CLONAL	1	TRUE	1	0.829640333913265	2		890	543	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932713	49932713	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	259	1210	0	ENST00000296474.3:c.3158G>T	p.Arg1053Leu	p.R1053L	ENST00000296474	NM_002447.2	1053	cGg/cTg	14/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.829640333913265	2		1210	558	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427619	72427619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	145	604	0	ENST00000477973.2:c.871G>A	p.Gly291Arg	p.G291R	ENST00000477973	NM_012234.5	291	Ggg/Agg	4/4	1	2	FACETS	0.94	0.868	1	0.94	0.868	1	CLONAL	1	TRUE	1	0.829640333913265	2		604	372	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169985735	169985735	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	214	693	0	ENST00000295797.4:c.397A>G	p.Arg133Gly	p.R133G	ENST00000295797	NM_002740.5	133	Aga/Gga	5/18	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.829640333913265	2		693	485	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1978230	1978230	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	286	973	0	ENST00000382891.5:c.3650A>G	p.Lys1217Arg	p.K1217R	ENST00000382891	NM_133335.3	1217	aAg/aGg	21/22	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.829640333913265	2		973	655	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468092	31468092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	183	772	0	ENST00000344624.3:c.2320C>T	p.His774Tyr	p.H774Y	ENST00000344624		774	Cac/Tac	15/33	1	2	FACETS	0.897	0.835	0.96	0.897	0.835	0.96	CLONAL	1	TRUE	1	0.829640333913265	2		772	492	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38966766	38966766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1274268930	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	74	321	0	ENST00000357387.3:c.1276C>T	p.Leu426Phe	p.L426F	ENST00000357387	NM_152756.3	426	Ctt/Ttt	15/38	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.829640333913265	2		321	177	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638711	176638712	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs797045812	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	34	864	0	ENST00000439151.2:c.3316dup	p.Ser1106PhefsTer2	p.S1106Ffs*2	ENST00000439151	NM_022455.4	1104	cat/caTt	5/23	1	2	FACETS	0.196	0.16	0.237	0.196	0.16	0.237	SUBCLONAL	1	TRUE	1	0.829640333913265	2		864	418	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848049	151848049	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	77	414	0	ENST00000262189.6:c.12710T>A	p.Phe4237Tyr	p.F4237Y	ENST00000262189	NM_170606.2	4237	tTc/tAc	51/59	0.830563828212396	3	FACETS	0.796	0.704	0.892	0.398	0.352	0.446	SUBCLONAL	1	TRUE	1	0.829640333913265	3		414	330	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457342	5457342	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	82	365	0	ENST00000381577.3:c.316T>A	p.Leu106Met	p.L106M	ENST00000381577	NM_014143.3	106	Ttg/Atg	3/7	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.829640333913265	2		365	185	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27173310	27173310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	208	934	0	ENST00000380036.4:c.851C>T	p.Pro284Leu	p.P284L	ENST00000380036	NM_000459.3	284	cCc/cTc	6/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.829640333913265	2		934	480	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139408969	139408969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1292975359	NA	P-0054156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	287	1045	0	ENST00000277541.6:c.2200C>T	p.Leu734Phe	p.L734F	ENST00000277541	NM_017617.3	734	Ctc/Ttc	13/34	0.830563828212396	2	FACETS	1	0.961	1	0.509	0.481	0.536	CLONAL	1	TRUE	0	0.829640333913265	2		1045	680	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974744	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAGCAGCGCCCGCA	CCTCCAGCAGCGCCCGCA	-	novel	NA	P-0054158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	150	418	0	ENST00000304494.5:c.83_100del	p.Val28_Glu33del	p.V28_E33del	ENST00000304494	NM_000077.4	28	gTGCGGGCGCTGCTGGAGGcg/gcg	1/3	0.247648424871121	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.247648424871121	1		418	774	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281506	49281506	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	59	837	0	ENST00000282018.3:c.553A>T	p.Thr185Ser	p.T185S	ENST00000282018	NM_020377.2	185	Aca/Tca	1/1	0.247648424871121	1	FACETS	0.461	0.396	0.533	0.461	0.396	0.533	SUBCLONAL	1	TRUE	0	0.247648424871121	1		837	905	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244164	5244164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1016675364	NA	P-0054158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1294	217	1289	0	ENST00000357368.4:c.1318G>A	p.Ala440Thr	p.A440T	ENST00000357368	NM_002850.3	440	Gcg/Acg	11/38	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.247648424871121	2		1289	1511	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235975	133235975	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	95	987	0	ENST00000320574.5:c.3181G>T	p.Ala1061Ser	p.A1061S	ENST00000320574	NM_006231.2	1061	Gcc/Tcc	26/49	0.247648424871121	1	FACETS	0.604	0.536	0.677	0.604	0.536	0.677	SUBCLONAL	1	TRUE	0	0.247648424871121	1		987	1113	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220660	2220660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1466445292	NA	P-0054158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	237	1036	0	ENST00000326181.6:c.277C>T	p.Arg93Cys	p.R93C	ENST00000326181	NM_032271.2	93	Cgc/Tgc	5/21	0.247648424871121	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.247648424871121	1		1036	1373	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828231	50828231	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	109	683	0	ENST00000398568.2:c.2569G>T	p.Glu857Ter	p.E857*	ENST00000398568	NM_001042412.1	857	Gag/Tag	17/18	NA	2	FACETS	0.949	0.851	1			1	INDETERMINATE	1	TRUE	NA	0.247648424871121	2		683	928	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285692	87285692	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1432834509	NA	P-0054158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	81	1081	1	ENST00000277120.3:c.29C>A	p.Pro10His	p.P10H	ENST00000277120		10	cCc/cAc	2/19	0.211165905394331	2	FACETS	0.521	0.457	0.59	0.26	0.228	0.295	SUBCLONAL	1	TRUE	0	0.247648424871121	2		1082	1256	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820193	139820193	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	64	1030	1	ENST00000247668.2:c.1346C>G	p.Pro449Arg	p.P449R	ENST00000247668	NM_021138.3	449	cCc/cGc	11/11	0.240553263525084	1	FACETS	0.392	0.338	0.451	0.392	0.338	0.451	SUBCLONAL	1	TRUE	0	0.247648424871121	1		1031	1156	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577564	7577565	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	37	720	0	ENST00000269305.4:c.716dup	p.Asn239LysfsTer25	p.N239Kfs*25	ENST00000269305	NM_001126112.2	239	aac/aaAc	7/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		720	271	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56873501	56873501	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0054159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	16	474	0	ENST00000308159.5:c.2205A>C	p.Arg735Ser	p.R735S	ENST00000308159	NM_014669.4	735	agA/agC	20/22	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		474	307	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	28	276	0				ENST00000310581	NM_198253.2	-/1132			0.138576310899643	3	FACETS	0.989	0.789	1	0.494	0.394	0.609	CLONAL	1	TRUE	1	0.13	3		276	464	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0054160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	16	329	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	1	2	FACETS	0.673	0.496	0.885	0.673	0.496	0.885	SUBCLONAL	1	TRUE	1	0.13	2		329	366	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163720	32163720	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	57	929	0	ENST00000375023.3:c.5506G>C	p.Glu1836Gln	p.E1836Q	ENST00000375023	NM_004557.3	1836	Gag/Cag	30/30	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.13	2		929	764	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023447	27023447	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	42	714	1	ENST00000324856.7:c.553C>T	p.Gln185Ter	p.Q185*	ENST00000324856	NM_006015.4	185	Cag/Tag	1/20	1	2	FACETS	0.88	0.733	1	0.88	0.733	1	CLONAL	1	TRUE	1	0.13	2		715	734	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802635	135802635	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203343	NA	P-0054160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	26	429	0	ENST00000298552.3:c.163C>T	p.Gln55Ter	p.Q55*	ENST00000298552	NM_001162426.1	55	Cag/Tag	4/23	1	2	FACETS	0.777	0.614	0.964	0.777	0.614	0.964	CLONAL	1	TRUE	1	0.13	2		429	515	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244401	46244401	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	35	553	0	ENST00000334344.6:c.2495C>T	p.Ser832Leu	p.S832L	ENST00000334344	NM_152641.2	832	tCa/tTa	15/21	1	2	FACETS	0.849	0.694	1	0.849	0.694	1	CLONAL	1	TRUE	1	0.13	2		553	634	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245486	46245486	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	26	451	0	ENST00000334344.6:c.3580C>T	p.Gln1194Ter	p.Q1194*	ENST00000334344	NM_152641.2	1194	Cag/Tag	15/21	1	2	FACETS	0.839	0.663	1	0.839	0.663	1	CLONAL	1	TRUE	1	0.13	2		451	477	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11273609	11273609	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532979867	NA	P-0054160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	30	441	0	ENST00000361445.4:c.3132G>A	p.Met1044Ile	p.M1044I	ENST00000361445	NM_004958.3	1044	atG/atA	21/58	1	2	FACETS	1	0.829	1	1	0.829	1	CLONAL	1	TRUE	1	0.13	2		441	447	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246113	46246113	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	28	514	0	ENST00000334344.6:c.4207C>A	p.Gln1403Lys	p.Q1403K	ENST00000334344	NM_152641.2	1403	Cag/Aag	15/21	1	2	FACETS	0.951	0.759	1	0.951	0.759	1	CLONAL	1	TRUE	1	0.13	2		514	453	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873688	35873688	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	42	708	0	ENST00000216797.5:c.163G>C	p.Glu55Gln	p.E55Q	ENST00000216797	NM_020529.2	55	Gag/Cag	1/6	1	2	FACETS	0.978	0.815	1	0.978	0.815	1	CLONAL	1	TRUE	1	0.13	2		708	661	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873733	35873733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	41	787	6	ENST00000216797.5:c.118G>A	p.Glu40Lys	p.E40K	ENST00000216797	NM_020529.2	40	Gag/Aag	1/6	1	2	FACETS	0.888	0.738	1	0.888	0.738	1	CLONAL	1	TRUE	1	0.13	2		793	710	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873677	37873677	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	55	1015	0	ENST00000269571.5:c.1842G>C	p.Trp614Cys	p.W614C	ENST00000269571		614	tgG/tgC	15/27	1	2	FACETS	0.805	0.686	0.936	0.805	0.686	0.936	CLONAL	1	TRUE	1	0.13	2		1015	1051	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0054161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	199	378	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		378	443	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051639	30051639	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	76	427	0	ENST00000338641.4:c.573G>A	p.Trp191Ter	p.W191*	ENST00000338641	NM_000268.3	191	tgG/tgA	6/16	0.565144152670805	1	FACETS	0.399	0.351	0.451	0.399	0.351	0.451	SUBCLONAL	1	TRUE	0	0.565144152670805	1		427	483	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549311	21549312	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0054162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	105	1042	0	ENST00000382592.4:c.2963_2964dup	p.Tyr989ProfsTer18	p.Y989Pfs*18	ENST00000382592	NM_014572.2	988	-/CC	8/8	0.565144152670805	1	FACETS	0.295	0.264	0.328	0.295	0.264	0.328	SUBCLONAL	1	TRUE	0	0.565144152670805	1		1042	904	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55991411	55991411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	138	1094	0	ENST00000263923.4:c.50C>T	p.Thr17Ile	p.T17I	ENST00000263923	NM_002253.2	17	aCc/aTc	1/30	1	2	FACETS	0.376	0.341	0.413	0.376	0.341	0.413	SUBCLONAL	1	TRUE	1	0.565144152670805	2		1094	1298	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001104	150001106	+	inframe_deletion	In_Frame_Del	DEL	TAT	TAT	-	novel	NA	P-0054162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	43	481	0	ENST00000253339.5:c.2498_2500del	p.Asn833del	p.N833del	ENST00000253339		833	aATAtt/att	4/7	0.266965982352071	1	FACETS	0.201	0.167	0.238	0.201	0.167	0.238	INDETERMINATE	1	TRUE	0	0.565144152670805	1		481	544	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0054163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	117	516	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.334009093494036	3	FACETS	1	0.983	1	0.717	0.649	0.787	CLONAL	1	TRUE	1	0.362578482623857	3		516	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0054163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	338	760	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.348264699105304	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.362578482623857	2		760	890	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467632	66467632	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	57	469	0	ENST00000273854.3:c.637G>T	p.Ala213Ser	p.A213S	ENST00000273854	NM_004439.5	213	Gct/Tct	3/18	1	2	FACETS	0.959	0.827	1	0.959	0.827	1	CLONAL	1	TRUE	1	0.362578482623857	2		469	328	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28901615	28901615	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	255	355	0	ENST00000282397.4:c.2780T>C	p.Leu927Ser	p.L927S	ENST00000282397	NM_002019.4	927	tTa/tCa	20/30	0.480102087715526	6	FACETS	1	0.956	1	0.511	0.48	0.544	CLONAL	2	FALSE	2	0.761412543033279	6		355	826	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435652	110435652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753831518	NA	P-0054168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	145	438	2	ENST00000375856.3:c.2749G>A	p.Gly917Ser	p.G917S	ENST00000375856	NM_003749.2	917	Ggc/Agc	1/2	0.118953735901911	4	FACETS	0.936	0.877	0.993			1	INDETERMINATE	3	FALSE	NA	0.761412543033279	4		440	239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0054168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	891	675	0	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.772320689152894	4	FACETS	1	0.998	1	1	0.998	1	CLONAL	4	FALSE	0	0.761412543033279	4		675	945	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984384	201984395	+	inframe_deletion	In_Frame_Del	DEL	TCGTCTACAAGT	TCGTCTACAAGT	-	novel	NA	P-0054168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1700	281	646	1	ENST00000359651.3:c.1050_1061del	p.Val351_Phe354del	p.V351_F354del	ENST00000359651		350	cTCGTCTACAAGTtt/ctt	8/8	0.761412543033279	8	FACETS	1	0.988	1	0.175	0.163	0.187	CLONAL	1	FALSE	1	0.761412543033279	8		647	1981	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914482	32914482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793478	NA	P-0054168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	300	476	0	ENST00000380152.3:c.5990G>A	p.Arg1997Lys	p.R1997K	ENST00000380152		1997	aGa/aAa	11/27	0.480102087715526	6	FACETS	1	0.944	1	0.501	0.472	0.53	CLONAL	2	FALSE	2	0.761412543033279	6		476	993	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472655	88472655	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	280	373	0	ENST00000360948.2:c.1900C>G	p.Pro634Ala	p.P634A	ENST00000360948	NM_001012338.2	634	Cca/Gca	16/19	0.772320689152894	3	FACETS	0.818	0.775	0.861	0.545	0.516	0.574	CLONAL	2	FALSE	0	0.761412543033279	3		373	621	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245833	5245833	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs924726109	NA	P-0054168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	409	826	0	ENST00000357368.4:c.942G>T	p.Met314Ile	p.M314I	ENST00000357368	NM_002850.3	314	atG/atT	10/38	0.772320689152894	3	FACETS	0.831	0.795	0.867	0.554	0.53	0.578	CLONAL	2	FALSE	0	0.761412543033279	3		826	893	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745141	41745141	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	532	731	2	ENST00000301178.4:c.1207A>G	p.Thr403Ala	p.T403A	ENST00000301178	NM_021913.4	403	Aca/Gca	9/20	0.772320689152894	3	FACETS	0.844	0.812	0.876	0.563	0.541	0.584	CLONAL	2	FALSE	0	0.761412543033279	3		733	1143	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189349317	189349317	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	325	273	0	ENST00000264731.3:c.13A>T	p.Thr5Ser	p.T5S	ENST00000264731	NM_003722.4	5	Act/Tct	1/14	0.761412543033279	7	FACETS	1	0.991	1	0.402	0.38	0.425	CLONAL	2	FALSE	1	0.761412543033279	7		273	1027	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158540	26158540	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	173	567	1	ENST00000289316.2:c.143A>T	p.Gln48Leu	p.Q48L	ENST00000289316	NM_138720.2	48	cAg/cTg	1/2	0.63953652129367	6	FACETS	1	0.989	1	0.297	0.273	0.321	CLONAL	1	FALSE	1	0.761412543033279	6		568	773	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350116	81350116	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	150	362	0	ENST00000222390.5:c.1216A>C	p.Thr406Pro	p.T406P	ENST00000222390	NM_000601.4	406	Aca/Cca	10/18	0.761412543033279	6	FACETS	0.772	0.708	0.838	0.386	0.354	0.419	SUBCLONAL	2	FALSE	2	0.761412543033279	6		362	644	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891165	151891165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	184	445	0	ENST00000262189.6:c.4589C>T	p.Pro1530Leu	p.P1530L	ENST00000262189	NM_170606.2	1530	cCt/cTt	31/59	0.772320689152894	3	FACETS	1	0.991	1	0.488	0.455	0.521	CLONAL	1	FALSE	0	0.761412543033279	3		445	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0054171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	26	781	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.625	0.493	0.776	0.625	0.493	0.776	SUBCLONAL	1	TRUE	1	0.15	2		782	555	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841117	15841117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773402194	NA	P-0054171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	11	323	0	ENST00000307771.7:c.1201C>T	p.Arg401Cys	p.R401C	ENST00000307771	NM_005089.3	401	Cgt/Tgt	11/11	1	1	FACETS	0.622	0.43	0.862	0.622	0.43	0.862	SUBCLONAL	1	TRUE	0	0.15	1		323	218	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	18	450	0	ENST00000371953.3:c.511C>G	p.Gln171Glu	p.Q171E	ENST00000371953	NM_000314.4	171	Cag/Gag	6/9	1	2	FACETS	1	0.833	1	1	0.833	1	CLONAL	1	TRUE	1	0.15	2		450	211	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061287	38061288	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0054171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	20	857	0	ENST00000250448.2:c.701_702insA	p.Asp236GlyfsTer57	p.D236Gfs*57	ENST00000250448	NM_004496.3	234	tcc/tcAc	2/2	1	2	FACETS	0.53	0.404	0.679	0.53	0.404	0.679	SUBCLONAL	1	TRUE	1	0.15	2		857	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0054174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	106	726	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.259935368509769	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.259935368509769	1		726	635	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872910	35872910	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	87	504	0	ENST00000216797.5:c.322A>T	p.Asn108Tyr	p.N108Y	ENST00000216797	NM_020529.2	108	Aac/Tac	2/6	0.259935368509769	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.259935368509769	1		504	451	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822030	72822031	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCC	rs1161154125	NA	P-0054174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	32	528	0	ENST00000268489.5:c.10142_10144dup	p.Arg3381dup	p.R3381dup	ENST00000268489	NM_006885.3	3381	caa/cGGCaa	10/10	1	2	FACETS	0.603	0.49	0.732	0.603	0.49	0.732	SUBCLONAL	1	TRUE	1	0.259935368509769	2		528	408	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467038	25467038	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	165	654	1	ENST00000264709.3:c.1837C>T	p.His613Tyr	p.H613Y	ENST00000264709	NM_175629.2	613	Cac/Tac	15/23	0.259935368509769	3	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	1	0.259935368509769	3		655	703	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156453	106156453	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	50	345	1	ENST00000380013.4:c.1354G>T	p.Glu452Ter	p.E452*	ENST00000380013	NM_001127208.2	452	Gag/Tag	3/11	1	2	FACETS	0.962	0.818	1	0.962	0.818	1	CLONAL	1	TRUE	1	0.259935368509769	2		346	400	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356212	66356212	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	132	598	0	ENST00000273854.3:c.1285G>T	p.Val429Leu	p.V429L	ENST00000273854	NM_004439.5	429	Gtg/Ttg	5/18	0.459092731414906	5	FACETS	0.904	0.826	0.984	0.603	0.551	0.656	CLONAL	2	TRUE	2	0.570619801723223	5		598	475	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597858	43597858	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs79014735	NA	P-0054175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	197	918	1	ENST00000355710.3:c.406G>A	p.Glu136Lys	p.E136K	ENST00000355710	NM_020975.4	136	Gag/Aag	3/20	0.548312061237616	3	FACETS	0.98	0.918	1	0.98	0.918	1	CLONAL	2	TRUE	1	0.570619801723223	3		919	453	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95579443	95579443	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	32	293	0	ENST00000393063.1:c.2026C>G	p.Arg676Gly	p.R676G	ENST00000393063	NM_030621.3	676	Cga/Gga	13/28	0.570619801723223	6	FACETS	1	0.893	1	0.228	0.186	0.274	CLONAL	1	TRUE	1	0.570619801723223	6		293	211	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247376	153247376	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	88	314	0	ENST00000281708.4:c.1426A>G	p.Ser476Gly	p.S476G	ENST00000281708	NM_033632.3	476	Agc/Ggc	10/12	0.570619801723223	4	FACETS	0.944	0.861	1			1	CLONAL	3	TRUE	NA	0.570619801723223	4		314	171	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579479	7579479	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0054175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	395	879	0	ENST00000269305.4:c.208del	p.Ala70LeufsTer53	p.A70Lfs*53	ENST00000269305	NM_001126112.2	70	Gct/ct	4/11	0.570619801723223	4	FACETS	0.978	0.946	1	0.978	0.946	1	CLONAL	4	TRUE	0	0.570619801723223	4		879	556	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144473	11144473	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	164	802	0	ENST00000358026.2:c.3805G>T	p.Ala1269Ser	p.A1269S	ENST00000358026	NM_001128849.1	1269	Gcc/Tcc	27/36	0.388718965850898	6	FACETS	1	0.924	1	0.501	0.462	0.542	CLONAL	2	TRUE	2	0.570619801723223	6		802	614	SUCCESS
AXL	558	MSKCC	GRCh37	19	41759611	41759611	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	74	671	2	ENST00000301178.4:c.2034C>A	p.Cys678Ter	p.C678*	ENST00000301178	NM_021913.4	678	tgC/tgA	17/20	0.474031039043025	4	FACETS	0.826	0.725	0.935	0.413	0.362	0.468	CLONAL	1	TRUE	2	0.570619801723223	4		673	493	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607678	46607678	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	100	855	2	ENST00000263734.3:c.1867C>T	p.Gln623Ter	p.Q623*	ENST00000263734	NM_001430.4	623	Cag/Tag	12/16	0.548312061237616	3	FACETS	1	0.954	1	0.552	0.496	0.61	CLONAL	1	TRUE	1	0.570619801723223	3		857	408	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40864891	40864891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	40	372	0	ENST00000373198.4:c.2377G>A	p.Ala793Thr	p.A793T	ENST00000373198	NM_133170.3	793	Gct/Act	16/32	0.570619801723223	3	FACETS	0.754	0.631	0.888			1	SUBCLONAL	1	TRUE	NA	0.570619801723223	3		372	239	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536145	41536145	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1457616974	NA	P-0054175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	100	439	0	ENST00000263253.7:c.1762G>A	p.Val588Ile	p.V588I	ENST00000263253	NM_001429.3	588	Gtc/Atc	9/31	0.570619801723223	4	FACETS	0.952	0.863	1	0.952	0.863	1	CLONAL	2	TRUE	2	0.570619801723223	4		439	289	SUCCESS
APC	324	MSKCC	GRCh37	5	112090700	112090700	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	10	248	0	ENST00000257430.4:c.113A>T	p.Glu38Val	p.E38V	ENST00000257430	NM_000038.5	38	gAa/gTa	2/16	0.570619801723223	4	FACETS	0.338	0.229	0.474	0.113	0.076	0.158	SUBCLONAL	1	TRUE	1	0.570619801723223	4		248	163	SUCCESS
APC	324	MSKCC	GRCh37	5	112103071	112103071	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	94	272	0	ENST00000257430.4:c.406G>C	p.Glu136Gln	p.E136Q	ENST00000257430	NM_000038.5	136	Gaa/Caa	4/16	0.570619801723223	4	FACETS	1	0.93	1	1	0.93	1	CLONAL	3	TRUE	1	0.570619801723223	4		272	170	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508722	106508722	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	72	611	0	ENST00000359195.3:c.716A>G	p.Asp239Gly	p.D239G	ENST00000359195	NM_002649.2	239	gAc/gGc	2/11	0.564738964412205	2	FACETS	0.952	0.842	1	0.476	0.421	0.534	CLONAL	1	TRUE	0	0.570619801723223	2		611	265	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	58	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.382497703871944	2		276	298	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	88	478	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.382497703871944	2		478	452	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	62	346	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.876	0.761	1	0.876	0.761	1	CLONAL	1	TRUE	1	0.382497703871944	2		346	370	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633620	69633620	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	15	79	0	ENST00000334134.2:c.82G>C	p.Asp28His	p.D28H	ENST00000334134	NM_005247.2	28	Gat/Cat	1/3	1	2	FACETS	0.923	0.687	1	0.923	0.687	1	CLONAL	1	TRUE	1	0.382497703871944	2		79	85	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276653	15276653	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	309	907	1	ENST00000263388.2:c.5612C>G	p.Ser1871Ter	p.S1871*	ENST00000263388	NM_000435.2	1871	tCa/tGa	30/33	0.208852099914678	2	FACETS	0.949	0.898	1	0.949	0.898	1	INDETERMINATE	2	TRUE	0	0.382497703871944	2		908	851	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987214	2987214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	85	489	0	ENST00000396946.4:c.215G>A	p.Arg72Gln	p.R72Q	ENST00000396946	NM_032415.4	72	cGa/cAa	3/25	0.382497703871944	3	FACETS	1	0.904	1	0.511	0.453	0.573	CLONAL	1	TRUE	1	0.382497703871944	3		489	518	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684326	29684326	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201367	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	70	428	0	ENST00000356175.3:c.7846C>T	p.Arg2616Ter	p.R2616*	ENST00000356175	NM_000267.3	2616	Cga/Tga	53/57	1	2	FACETS	0.884	0.774	1	0.884	0.774	1	CLONAL	1	TRUE	1	0.382497703871944	2		428	414	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332882	153332882	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	79	421	0	ENST00000281708.4:c.74C>G	p.Ser25Ter	p.S25*	ENST00000281708	NM_033632.3	25	tCa/tGa	2/12	1	2	FACETS	0.804	0.709	0.905	0.804	0.709	0.905	CLONAL	1	TRUE	1	0.382497703871944	2		421	514	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879838	37879838	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	140	829	0	ENST00000269571.5:c.2133G>C	p.Gln711His	p.Q711H	ENST00000269571		711	caG/caC	18/27	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.382497703871944	2		829	641	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579406	7579406	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	165	1047	1	ENST00000269305.4:c.281C>G	p.Ser94Ter	p.S94*	ENST00000269305	NM_001126112.2	94	tCa/tGa	4/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.382497703871944	2		1048	626	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193995	106193995	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1376289450	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	70	224	0	ENST00000380013.4:c.4457C>G	p.Ser1486Ter	p.S1486*	ENST00000380013	NM_001127208.2	1486	tCa/tGa	10/11	0.0712551740793748	3	FACETS	1	0.968	1	0.665	0.584	0.751	INDETERMINATE	1	TRUE	1	0.382497703871944	3		224	328	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586422	189586422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866267914	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	146	417	0	ENST00000264731.3:c.1046G>A	p.Gly349Glu	p.G349E	ENST00000264731	NM_003722.4	349	gGa/gAa	8/14	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.382497703871944	2		417	607	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641214	3641214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs546657275	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	50	873	1	ENST00000294008.3:c.2425G>A	p.Glu809Lys	p.E809K	ENST00000294008	NM_032444.2	809	Gaa/Aaa	12/15	1	2	FACETS	0.333	0.282	0.39	0.333	0.282	0.39	SUBCLONAL	1	TRUE	1	0.382497703871944	2		874	785	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515295	31515295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756537138	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	120	589	0	ENST00000344624.3:c.1090C>T	p.Arg364Cys	p.R364C	ENST00000344624		364	Cgt/Tgt	5/33	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.382497703871944	2		589	612	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010560	48010560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	107	630	1	ENST00000234420.5:c.188C>T	p.Ser63Phe	p.S63F	ENST00000234420	NM_000179.2	63	tCc/tTc	1/10	1	2	FACETS	0.894	0.803	0.989	0.894	0.803	0.989	CLONAL	1	TRUE	1	0.382497703871944	2		631	626	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662301	227662301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1289819083	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	202	832	1	ENST00000305123.5:c.1154C>T	p.Ser385Leu	p.S385L	ENST00000305123	NM_005544.2	385	tCg/tTg	1/2	0.382497703871944	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.382497703871944	1		833	633	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216125	7216125	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	112	459	0	ENST00000380728.2:c.934C>G	p.Arg312Gly	p.R312G	ENST00000380728		312	Cgg/Ggg	11/11	1	2	FACETS	0.968	0.873	1	0.968	0.873	1	CLONAL	1	TRUE	1	0.382497703871944	2		459	605	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214377	36214377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	110	664	0	ENST00000222270.7:c.3031C>T	p.Arg1011Trp	p.R1011W	ENST00000222270	NM_014727.1	1011	Cgg/Tgg	7/37	0.382497703871944	3	FACETS	0.883	0.793	0.978	0.441	0.396	0.489	CLONAL	1	TRUE	1	0.382497703871944	3		664	776	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225784	26225784	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	103	502	0	ENST00000360408.1:c.402G>C	p.Glu134Asp	p.E134D	ENST00000360408	NM_003532.2	134	gaG/gaC	1/1	1	2	FACETS	0.765	0.685	0.85	0.765	0.685	0.85	SUBCLONAL	1	TRUE	1	0.382497703871944	2		502	704	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151866334	151866334	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	72	353	0	ENST00000262189.6:c.9454G>C	p.Asp3152His	p.D3152H	ENST00000262189	NM_170606.2	3152	Gat/Cat	41/59	0.382497703871944	3	FACETS	1	0.974	1	0.723	0.637	0.814	CLONAL	1	TRUE	1	0.382497703871944	3		353	310	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941234	71941234	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	166	1050	0	ENST00000298229.2:c.1009G>C	p.Asp337His	p.D337H	ENST00000298229	NM_001567.3	337	Gat/Cat	9/28	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.382497703871944	2		1050	858	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426859	49426859	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	99	600	0	ENST00000301067.7:c.11629C>T	p.Gln3877Ter	p.Q3877*	ENST00000301067	NM_003482.3	3877	Cag/Tag	39/54	1	2	FACETS	0.962	0.862	1	0.962	0.862	1	CLONAL	1	TRUE	1	0.382497703871944	2		600	538	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536260	41536260	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	70	363	1	ENST00000263253.7:c.1877G>A	p.Arg626Gln	p.R626Q	ENST00000263253	NM_001429.3	626	cGa/cAa	9/31	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.382497703871944	2		364	363	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845334	151845334	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	105	649	0	ENST00000262189.6:c.13678C>T	p.Gln4560Ter	p.Q4560*	ENST00000262189	NM_170606.2	4560	Cag/Tag	52/59	0.382497703871944	3	FACETS	0.965	0.865	1	0.482	0.432	0.535	CLONAL	1	TRUE	1	0.382497703871944	3		649	678	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16062082	16062082	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	56	400	0	ENST00000268712.3:c.724G>C	p.Glu242Gln	p.E242Q	ENST00000268712	NM_006311.3	242	Gag/Cag	6/46	1	2	FACETS	0.769	0.661	0.885	0.769	0.661	0.885	SUBCLONAL	1	TRUE	1	0.382497703871944	2		400	381	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426223	49426223	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	48	862	0	ENST00000301067.7:c.12265C>G	p.Leu4089Val	p.L4089V	ENST00000301067	NM_003482.3	4089	Ctg/Gtg	39/54	1	2	FACETS	0.307	0.258	0.361	0.307	0.258	0.361	SUBCLONAL	1	TRUE	1	0.382497703871944	2		862	818	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243390	46243390	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	40	258	0	ENST00000334344.6:c.1743G>C	p.Lys581Asn	p.K581N	ENST00000334344	NM_152641.2	581	aaG/aaC	14/21	1	2	FACETS	0.898	0.752	1	0.898	0.752	1	CLONAL	1	TRUE	1	0.382497703871944	2		258	233	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349241	11349241	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	18	182	0	ENST00000332029.2:c.95C>T	p.Ser32Leu	p.S32L	ENST00000332029	NM_003745.1	32	tCg/tTg	2/2	1	2	FACETS	0.475	0.359	0.612	0.475	0.359	0.612	SUBCLONAL	1	TRUE	1	0.382497703871944	2		182	198	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11177134	11177134	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	57	438	0	ENST00000361445.4:c.6943G>C	p.Asp2315His	p.D2315H	ENST00000361445	NM_004958.3	2315	Gac/Cac	50/58	1	2	FACETS	0.882	0.761	1	0.882	0.761	1	CLONAL	1	TRUE	1	0.382497703871944	2		438	338	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850858	63850858	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs971439856	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	105	494	0	ENST00000279873.7:c.1636C>T	p.Pro546Ser	p.P546S	ENST00000279873	NM_032199.2	546	Cct/Tct	10/10	1	2	FACETS	0.965	0.867	1	0.965	0.867	1	CLONAL	1	TRUE	1	0.382497703871944	2		494	569	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263980	104263980	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754218597	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	36	354	0	ENST00000369902.3:c.71C>T	p.Pro24Leu	p.P24L	ENST00000369902	NM_016169.3	24	cCg/cTg	1/12	1	2	FACETS	0.451	0.371	0.541	0.451	0.371	0.541	SUBCLONAL	1	TRUE	1	0.382497703871944	2		354	417	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941221	71941221	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1262263936	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	180	1040	0	ENST00000298229.2:c.996C>G	p.Phe332Leu	p.F332L	ENST00000298229	NM_001567.3	332	ttC/ttG	9/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.382497703871944	2		1040	847	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442507	49442507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	79	490	0	ENST00000301067.7:c.4066G>A	p.Asp1356Asn	p.D1356N	ENST00000301067	NM_003482.3	1356	Gat/Aat	13/54	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.382497703871944	2		490	385	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493443	56493443	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	70	454	0	ENST00000267101.3:c.2851G>A	p.Asp951Asn	p.D951N	ENST00000267101	NM_001982.3	951	Gat/Aat	24/28	1	2	FACETS	0.878	0.768	0.995	0.878	0.768	0.995	CLONAL	1	TRUE	1	0.382497703871944	2		454	417	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906531	32906531	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	20	336	0	ENST00000380152.3:c.916G>C	p.Asp306His	p.D306H	ENST00000380152		306	Gat/Cat	10/27	1	2	FACETS	0.412	0.315	0.524	0.412	0.315	0.524	SUBCLONAL	1	TRUE	1	0.382497703871944	2		336	254	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134649	2134649	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs376946970	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	154	1017	0	ENST00000219476.3:c.4426G>C	p.Glu1476Gln	p.E1476Q	ENST00000219476	NM_000548.3	1476	Gag/Cag	34/42	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.382497703871944	2		1017	759	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786674	3786674	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	137	655	0	ENST00000262367.5:c.4537G>C	p.Glu1513Gln	p.E1513Q	ENST00000262367	NM_004380.2	1513	Gag/Cag	27/31	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.382497703871944	2		655	631	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349253	11349253	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	35	235	0	ENST00000332029.2:c.83C>G	p.Ser28Cys	p.S28C	ENST00000332029	NM_003745.1	28	tCt/tGt	2/2	1	2	FACETS	0.642	0.528	0.769	0.642	0.528	0.769	SUBCLONAL	1	TRUE	1	0.382497703871944	2		235	285	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128320	30128330	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGGGCTATGG	AAGGGCTATGG	-	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	92	653	0	ENST00000263025.4:c.908-6_912del		p.X303_splice	ENST00000263025	NM_002746.2	303		7/9	1	2	FACETS	0.904	0.806	1	0.904	0.806	1	CLONAL	1	TRUE	1	0.382497703871944	2		653	532	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662312	67662312	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	129	532	0	ENST00000264010.4:c.1558G>A	p.Glu520Lys	p.E520K	ENST00000264010	NM_006565.3	520	Gag/Aag	9/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.382497703871944	2		532	569	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89335015	89335015	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	20	177	0	ENST00000301030.4:c.7863G>C	p.Arg2621Ser	p.R2621S	ENST00000301030	NM_001256183.1	2621	agG/agC	13/13	1	2	FACETS	0.559	0.43	0.709	0.559	0.43	0.709	SUBCLONAL	1	TRUE	1	0.382497703871944	2		177	187	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346060	89346060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1472989420	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	10	91	0	ENST00000301030.4:c.6890C>T	p.Ser2297Phe	p.S2297F	ENST00000301030	NM_001256183.1	2297	tCc/tTc	9/13	1	2	FACETS	1	0.827	1	1	0.827	1	CLONAL	1	TRUE	1	0.382497703871944	2		91	40	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845216	89845216	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	56	482	1	ENST00000389301.3:c.1819C>G	p.Leu607Val	p.L607V	ENST00000389301	NM_000135.2	607	Ctg/Gtg	20/43	1	2	FACETS	0.595	0.51	0.688	0.595	0.51	0.688	SUBCLONAL	1	TRUE	1	0.382497703871944	2		483	492	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108641	8108641	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	34	771	0	ENST00000585124.1:c.754G>C	p.Glu252Gln	p.E252Q	ENST00000585124	NM_004217.3	252	Gag/Cag	8/9	1	2	FACETS	0.261	0.213	0.317	0.261	0.213	0.317	SUBCLONAL	1	TRUE	1	0.382497703871944	2		771	680	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453447	40453447	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	143	851	0	ENST00000345506.4:c.1144C>G	p.Leu382Val	p.L382V	ENST00000345506	NM_003152.3	382	Ctg/Gtg	10/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.382497703871944	2		851	674	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462677	40462677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758087729	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	111	567	0	ENST00000345506.4:c.2375C>T	p.Ser792Phe	p.S792F	ENST00000345506	NM_003152.3	792	tCc/tTc	20/20	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.382497703871944	2		567	550	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59793421	59793421	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	32	307	0	ENST00000259008.2:c.2383G>C	p.Glu795Gln	p.E795Q	ENST00000259008	NM_032043.2	795	Gaa/Caa	17/20	1	2	FACETS	0.706	0.576	0.85	0.706	0.576	0.85	SUBCLONAL	1	TRUE	1	0.382497703871944	2		307	237	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581177	48581177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1183671082	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	49	368	0	ENST00000342988.3:c.481G>A	p.Glu161Lys	p.E161K	ENST00000342988	NM_005359.5	161	Gaa/Aaa	5/12	0.0712551740793748	3	FACETS	0.781	0.663	0.909	0.39	0.331	0.455	INDETERMINATE	1	TRUE	1	0.382497703871944	3		368	391	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296422	15296422	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	56	999	0	ENST00000263388.2:c.2020G>C	p.Asp674His	p.D674H	ENST00000263388	NM_000435.2	674	Gat/Cat	13/33	0.208852099914678	2	FACETS	0.374	0.319	0.434	0.187	0.159	0.217	INDETERMINATE	1	TRUE	0	0.382497703871944	2		999	783	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224574	36224574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	130	970	0	ENST00000222270.7:c.7036G>A	p.Glu2346Lys	p.E2346K	ENST00000222270	NM_014727.1	2346	Gaa/Aaa	29/37	0.382497703871944	3	FACETS	0.869	0.787	0.955	0.434	0.393	0.478	CLONAL	1	TRUE	1	0.382497703871944	3		970	932	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796832	42796832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	175	994	0	ENST00000575354.2:c.3290C>T	p.Ser1097Phe	p.S1097F	ENST00000575354	NM_015125.3	1097	tCt/tTt	14/20	0.382497703871944	3	FACETS	1	0.978	1	0.585	0.539	0.634	CLONAL	1	TRUE	1	0.382497703871944	3		994	931	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096682	178096682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	17	319	0	ENST00000397062.3:c.649G>A	p.Glu217Lys	p.E217K	ENST00000397062	NM_006164.4	217	Gaa/Aaa	5/5	0.382497703871944	1	FACETS	0.219	0.163	0.286	0.219	0.163	0.286	SUBCLONAL	1	TRUE	0	0.382497703871944	1		319	328	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790128	40790128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	130	669	0	ENST00000373198.4:c.2603C>T	p.Pro868Leu	p.P868L	ENST00000373198	NM_133170.3	868	cCc/cTc	18/32	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.382497703871944	2		669	628	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485404	57485404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	70	375	0	ENST00000371085.3:c.986G>A	p.Gly329Glu	p.G329E	ENST00000371085	NM_000516.4	329	gGa/gAa	12/13	1	2	FACETS	0.794	0.694	0.901	0.794	0.694	0.901	CLONAL	1	TRUE	1	0.382497703871944	2		375	461	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000002	30000002	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs998779035	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	69	419	0	ENST00000338641.4:c.15C>G	p.Ile5Met	p.I5M	ENST00000338641	NM_000268.3	5	atC/atG	1/16	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.382497703871944	2		419	317	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430967	181430967	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	181	950	2	ENST00000325404.1:c.819G>T	p.Met273Ile	p.M273I	ENST00000325404	NM_003106.3	273	atG/atT	1/1	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.382497703871944	2		952	846	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189349314	189349314	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	81	330	0	ENST00000264731.3:c.10G>C	p.Glu4Gln	p.E4Q	ENST00000264731	NM_003722.4	4	Gaa/Caa	1/14	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.382497703871944	2		330	315	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935565	13935565	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs770880512	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	36	475	0	ENST00000405192.2:c.1291G>C	p.Asp431His	p.D431H	ENST00000405192	NM_001163147.1	431	Gat/Cat	12/12	0.382497703871944	3	FACETS	0.349	0.286	0.42	0.175	0.143	0.21	SUBCLONAL	1	TRUE	1	0.382497703871944	3		475	642	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459453	50459453	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	24	289	0	ENST00000331340.3:c.742G>A	p.Glu248Lys	p.E248K	ENST00000331340	NM_006060.4	248	Gaa/Aaa	7/8	0.382497703871944	3	FACETS	0.591	0.464	0.736	0.295	0.232	0.368	SUBCLONAL	1	TRUE	1	0.382497703871944	3		289	253	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140507856	140507856	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	28	326	0	ENST00000288602.6:c.615G>C	p.Lys205Asn	p.K205N	ENST00000288602	NM_004333.4	205	aaG/aaC	5/18	0.382497703871944	3	FACETS	0.658	0.528	0.806	0.329	0.264	0.403	SUBCLONAL	1	TRUE	1	0.382497703871944	3		326	265	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282083	38282083	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	159	899	0	ENST00000425967.3:c.973G>C	p.Glu325Gln	p.E325Q	ENST00000425967	NM_001174067.1	325	Gag/Cag	8/19	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.382497703871944	2		899	759	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654793	29654795	+	missense_variant	Missense_Mutation	TNP	GAT	GAT	AAA	novel	NA	P-0054176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	64	398	0	ENST00000356175.3:c.5482_5484delinsAAA	p.Asp1828Lys	p.D1828K	ENST00000356175	NM_000267.3	1828	GAT/AAA	37/57	1	2	FACETS	0.726	0.63	0.829	0.726	0.63	0.829	SUBCLONAL	1	TRUE	1	0.382497703871944	2		398	461	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	99	276	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.922	0.837	1			1	INDETERMINATE	1	TRUE	NA	0.819752728466437	2		276	262	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204849	128204849	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	303	904	0	ENST00000341105.2:c.592G>A	p.Ala198Thr	p.A198T	ENST00000341105	NM_032638.4	198	Gcg/Acg	3/6	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.819752728466437	2		904	638	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047192	77047192	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	206	740	0	ENST00000356341.3:c.1352G>A	p.Gly451Asp	p.G451D	ENST00000356341	NM_002576.4	451	gGc/gAc	13/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.819752728466437	2		740	486	SUCCESS
MET	4233	MSKCC	GRCh37	7	116399515	116399515	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1562923583	NA	P-0054189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	32	535	0	ENST00000397752.3:c.2335G>A	p.Val779Met	p.V779M	ENST00000397752	NM_000245.2	779	Gtg/Atg	10/21	0.797091152695831	3	FACETS	0.218	0.176	0.265	0.109	0.088	0.133	SUBCLONAL	1	TRUE	1	0.819752728466437	3		535	506	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874416	76874416	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	71	400	0	ENST00000373344.5:c.5306T>C	p.Leu1769Ser	p.L1769S	ENST00000373344	NM_000489.3	1769	tTa/tCa	21/35	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.819752728466437	2		400	166	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221319	1221319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913322	NA	P-0054190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	606	729	0	ENST00000326873.7:c.842C>T	p.Pro281Leu	p.P281L	ENST00000326873	NM_000455.4	281	cCg/cTg	6/10	0.534625284708944	2	FACETS	0.88	0.856	0.903	1	0.997	1	CLONAL	3	TRUE	0	0.534625284708944	2		729	859	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962834	2962834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778151	NA	P-0054190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	136	755	0	ENST00000396946.4:c.2074G>A	p.Val692Met	p.V692M	ENST00000396946	NM_032415.4	692	Gtg/Atg	16/25	0.53464630669045	3	FACETS	0.856	0.779	0.937	0.428	0.389	0.469	CLONAL	1	TRUE	1	0.534625284708944	3		755	753	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221318	1221319	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	T	novel	NA	P-0054190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	576	728	1	ENST00000326873.7:c.841_842delinsT	p.Pro281CysfsTer6	p.P281Cfs*6	ENST00000326873	NM_000455.4	281	CCg/Tg	6/10	0.534625284708944	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.534625284708944	2		729	882	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691039	NA	P-0054190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	347	782	1	ENST00000269305.4:c.919+1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			NA	2	FACETS	0.976	0.933	1			1	INDETERMINATE	2	TRUE	NA	0.534625284708944	2		783	665	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504384	8504384	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	252	541	0	ENST00000356435.5:c.1699G>T	p.Gly567Trp	p.G567W	ENST00000356435		567	Ggg/Tgg	12/35	0.534625284708944	2	FACETS	0.96	0.91	1	0.96	0.91	1	CLONAL	2	TRUE	0	0.534625284708944	2		541	491	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420245	88420245	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0054190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	239	607	0	ENST00000360948.2:c.2441G>T	p.Arg814Leu	p.R814L	ENST00000360948	NM_001012338.2	814	cGg/cTg	19/19	0.153877618978995	3	FACETS	0.887	0.833	0.941	0.591	0.555	0.627	INDETERMINATE	2	TRUE	0	0.534625284708944	3		607	639	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	364588	364588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	200	891	1	ENST00000262320.3:c.974G>A	p.Ser325Asn	p.S325N	ENST00000262320	NM_003502.3	325	aGc/aAc	3/11	0.118863465161469	6	FACETS	1	0.99	1	0.474	0.439	0.511	INDETERMINATE	1	TRUE	3	0.534625284708944	6		892	1088	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89345505	89345505	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0054190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	211	506	1	ENST00000301030.4:c.7445C>A	p.Pro2482Gln	p.P2482Q	ENST00000301030	NM_001256183.1	2482	cCg/cAg	9/13	0.123856967627176	6	FACETS	0.924	0.864	0.985	0.924	0.864	0.985	INDETERMINATE	3	TRUE	3	0.534625284708944	6		507	589	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610482	10610499	+	inframe_deletion	In_Frame_Del	DEL	CAGCTGCTGGCTGAGCCG	CAGCTGCTGGCTGAGCCG	-	novel	NA	P-0054190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	375	823	1	ENST00000171111.5:c.211_228del	p.Arg71_Leu76del	p.R71_L76del	ENST00000171111	NM_203500.1	71	CGGCTCAGCCAGCAGCTG/-	2/6	0.534625284708944	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.534625284708944	2		824	643	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970825	55970825	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	207	524	0	ENST00000263923.4:c.1972C>T	p.Gln658Ter	p.Q658*	ENST00000263923	NM_002253.2	658	Cag/Tag	13/30	0.51049349678912	3	FACETS	0.875	0.818	0.933	0.875	0.818	0.933	CLONAL	2	TRUE	1	0.534625284708944	3		524	561	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120638	94120638	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	240	526	0	ENST00000369303.4:c.413T>C	p.Ile138Thr	p.I138T	ENST00000369303	NM_004440.3	138	aTa/aCa	3/17	0.520937589287842	2	FACETS	0.97	0.918	1	0.97	0.918	1	CLONAL	2	TRUE	0	0.534625284708944	2		526	463	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566477	139566477	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	418	823	0	ENST00000308874.7:c.736C>G	p.Gln246Glu	p.Q246E	ENST00000308874		246	Cag/Gag	9/10	0.386078945718846	3	FACETS	0.924	0.889	0.958			1	CLONAL	3	TRUE	NA	0.534625284708944	3		823	715	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	74	276	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		276	375	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0054193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	281	386	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.315560343728774	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.334098448159644	2		386	752	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0054193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	166	547	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.258641114292004	2	FACETS	0.808	0.745	0.872	0.808	0.745	0.872	CLONAL	2	TRUE	0	0.334098448159644	2		547	615	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188865	32188865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138205668	NA	P-0054193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	136	784	1	ENST00000375023.3:c.689G>A	p.Arg230His	p.R230H	ENST00000375023	NM_004557.3	230	cGt/cAt	4/30	1	2	FACETS	0.973	0.885	1	0.973	0.885	1	CLONAL	1	TRUE	1	0.334098448159644	2		785	837	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0054193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	144	915	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.334098448159644	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.334098448159644	1		915	678	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992764	68992764	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs769067107	NA	P-0054193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	320	821	0	ENST00000288368.4:c.1729C>T	p.Arg577Ter	p.R577*	ENST00000288368	NM_024870.2	577	Cga/Tga	16/40	0.290940687599431	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.334098448159644	3		821	1095	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033682	48033682	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786202520	NA	P-0054193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	121	647	0	ENST00000234420.5:c.3893A>G	p.Tyr1298Cys	p.Y1298C	ENST00000234420	NM_000179.2	1298	tAt/tGt	9/10	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.334098448159644	2		647	722	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850832	128850832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	60	817	0	ENST00000249373.3:c.1679C>T	p.Pro560Leu	p.P560L	ENST00000249373	NM_005631.4	560	cCa/cTa	10/12	0.290940687599431	3	FACETS	0.473	0.406	0.546	0.236	0.203	0.273	SUBCLONAL	1	TRUE	1	0.334098448159644	3		817	887	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	44	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.84	0.707	0.988	0.84	0.707	0.988	CLONAL	1	TRUE	1	0.28	2		276	374	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866444	37866444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	178	753	0	ENST00000269571.5:c.749C>T	p.Ser250Phe	p.S250F	ENST00000269571		250	tCt/tTt	6/27	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.28	2		753	994	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984096	7984096	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs959284348	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	78	527	0	ENST00000319144.4:c.530G>A	p.Trp177Ter	p.W177*	ENST00000319144	NM_001139.2	177	tGg/tAg	5/15	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.28	2		527	528	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976476	25976476	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	77	357	0	ENST00000435504.4:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000435504		357	Cga/Tga	11/13	1	2	FACETS	0.841	0.738	0.951	0.841	0.738	0.951	CLONAL	1	TRUE	1	0.28	2		357	654	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248773	212248773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	66	237	0	ENST00000342788.4:c.3494C>T	p.Pro1165Leu	p.P1165L	ENST00000342788	NM_005235.2	1165	cCa/cTa	28/28	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.28	2		237	392	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874636	35874636	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	90	687	0	ENST00000303115.3:c.792G>A	p.Trp264Ter	p.W264*	ENST00000303115	NM_002185.3	264	tgG/tgA	6/8	1	2	FACETS	0.897	0.796	1	0.897	0.796	1	CLONAL	1	TRUE	1	0.28	2		687	717	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491450	18491450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	71	534	0	ENST00000266497.5:c.1363G>A	p.Glu455Lys	p.E455K	ENST00000266497		455	Gaa/Aaa	8/31	1	2	FACETS	0.694	0.605	0.79	0.694	0.605	0.79	SUBCLONAL	1	TRUE	1	0.28	2		534	731	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	100	449	0	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	1	2	FACETS	0.866	0.773	0.965	0.866	0.773	0.965	CLONAL	1	TRUE	1	0.28	2		449	825	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811603	102811603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	112	780	1	ENST00000307046.8:c.581G>A	p.Gly194Glu	p.G194E	ENST00000307046	NM_001111285.1	194	gGa/gAa	4/4	1	2	FACETS	0.985	0.886	1	0.985	0.886	1	CLONAL	1	TRUE	1	0.28	2		781	812	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022289	31022289	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs951716574	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	144	624	0	ENST00000375687.4:c.1774C>T	p.Gln592Ter	p.Q592*	ENST00000375687	NM_015338.5	592	Cag/Tag	13/13	0.277488749561442	3	FACETS	0.909	0.832	0.99	0.909	0.832	0.99	CLONAL	2	TRUE	1	0.28	3		624	645	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574015	7574015	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	146	863	0	ENST00000269305.4:c.1012T>C	p.Phe338Leu	p.F338L	ENST00000269305	NM_001126112.2	338	Ttc/Ctc	10/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.28	2		863	959	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921533	178921533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	74	531	0	ENST00000263967.3:c.1015C>T	p.Leu339Phe	p.L339F	ENST00000263967	NM_006218.2	339	Ctt/Ttt	5/21	1	2	FACETS	0.846	0.741	0.959	0.846	0.741	0.959	CLONAL	1	TRUE	1	0.28	2		531	625	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27183486	27183486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	99	594	1	ENST00000380036.4:c.1060G>A	p.Asp354Asn	p.D354N	ENST00000380036	NM_000459.3	354	Gat/Aat	8/23	1	2	FACETS	0.982	0.877	1	0.982	0.877	1	CLONAL	1	TRUE	1	0.28	2		595	720	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781113	135781113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	120	883	1	ENST00000298552.3:c.1852C>T	p.His618Tyr	p.H618Y	ENST00000298552	NM_001162426.1	618	Cat/Tat	15/23	1	2	FACETS	0.994	0.897	1	0.994	0.897	1	CLONAL	1	TRUE	1	0.28	2		884	862	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538885	23538885	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	108	677	0	ENST00000380871.4:c.554C>T	p.Ser185Phe	p.S185F	ENST00000380871	NM_006167.3	185	tCc/tTc	2/2	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.28	2		677	689	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279768	46279768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	213	651	1	ENST00000371998.3:c.3694G>A	p.Glu1232Lys	p.E1232K	ENST00000371998		1232	Gag/Aag	20/23	0.277488749561442	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.28	3		652	776	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656215	18656215	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	70	491	0	ENST00000266497.5:c.2894G>A	p.Gly965Glu	p.G965E	ENST00000266497		965	gGa/gAa	21/31	1	2	FACETS	0.856	0.747	0.974	0.856	0.747	0.974	CLONAL	1	TRUE	1	0.28	2		491	584	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770617	40770617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749916516	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	72	634	0	ENST00000373198.4:c.2765C>T	p.Ser922Leu	p.S922L	ENST00000373198	NM_133170.3	922	tCg/tTg	19/32	NA	2	FACETS	0.809	0.706	0.919			1	INDETERMINATE	1	TRUE	NA	0.28	2		634	636	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818393	43818393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	135	906	0	ENST00000372470.3:c.1858C>T	p.His620Tyr	p.H620Y	ENST00000372470	NM_005373.2	620	Cac/Tac	12/12	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.28	2		906	805	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726224	46726224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	84	716	1	ENST00000371975.4:c.418C>T	p.Pro140Ser	p.P140S	ENST00000371975	NM_003579.3	140	Cct/Tct	6/18	1	2	FACETS	0.838	0.74	0.943	0.838	0.74	0.943	CLONAL	1	TRUE	1	0.28	2		717	716	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458906	120458906	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	163	1008	0	ENST00000256646.2:c.6439A>C	p.Thr2147Pro	p.T2147P	ENST00000256646	NM_024408.3	2147	Act/Cct	34/34	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.28	2		1008	944	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457832	69457832	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	81	531	0	ENST00000227507.2:c.232T>C	p.Phe78Leu	p.F78L	ENST00000227507	NM_053056.2	78	Ttc/Ctc	2/5	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.28	2		531	507	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428670	49428670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	106	893	1	ENST00000301067.7:c.10280C>T	p.Ala3427Val	p.A3427V	ENST00000301067	NM_003482.3	3427	gCc/gTc	35/54	1	2	FACETS	0.88	0.789	0.978	0.88	0.789	0.978	CLONAL	1	TRUE	1	0.28	2		894	860	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109691	115109691	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs774611046	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	141	885	0	ENST00000257566.3:c.2187C>G	p.Ser729Arg	p.S729R	ENST00000257566	NM_016569.3	729	agC/agG	8/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.28	2		885	815	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553539	29553540	+	inframe_insertion	In_Frame_Ins	INS	-	-	AACCCT	novel	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	57	419	1	ENST00000356175.3:c.2089_2094dup	p.Asn697_Pro698dup	p.N697_P698dup	ENST00000356175	NM_000267.3	697	-/AACCCT	18/57	1	2	FACETS	0.94	0.809	1	0.94	0.809	1	CLONAL	1	TRUE	1	0.28	2		420	433	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654736	29654736	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs797045139	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	88	564	0	ENST00000356175.3:c.5425C>G	p.Arg1809Gly	p.R1809G	ENST00000356175	NM_000267.3	1809	Cgc/Ggc	37/57	1	2	FACETS	0.972	0.861	1	0.972	0.861	1	CLONAL	1	TRUE	1	0.28	2		564	647	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646971	37646971	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs145090341	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	132	688	0	ENST00000447079.4:c.2093A>G	p.Tyr698Cys	p.Y698C	ENST00000447079	NM_015083.1	698	tAt/tGt	3/14	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.28	2		688	836	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546585	9546585	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	99	702	2	ENST00000353224.5:c.1437A>T	p.Lys479Asn	p.K479N	ENST00000353224	NM_177990.2	479	aaA/aaT	5/10	0.277488749561442	3	FACETS	0.757	0.674	0.846	0.378	0.337	0.423	SUBCLONAL	1	TRUE	1	0.28	3		704	1065	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434113	12434113	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	84	480	0	ENST00000287820.6:c.481G>A	p.Gly161Ser	p.G161S	ENST00000287820	NM_015869.4	161	Ggt/Agt	4/7	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.28	2		480	562	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936687	49936687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	101	746	0	ENST00000296474.3:c.1240G>A	p.Glu414Lys	p.E414K	ENST00000296474	NM_002447.2	414	Gaa/Aaa	2/20	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.28	2		746	683	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52621385	52621385	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	100	741	0	ENST00000394830.3:c.3032T>A	p.Val1011Glu	p.V1011E	ENST00000394830	NM_018313.4	1011	gTg/gAg	20/30	1	2	FACETS	0.805	0.718	0.898	0.805	0.718	0.898	CLONAL	1	TRUE	1	0.28	2		741	887	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911418	134911418	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	106	565	0	ENST00000398015.3:c.1883G>A	p.Gly628Glu	p.G628E	ENST00000398015	NM_004441.4	628	gGg/gAg	11/16	0.276764538022464	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.28	1		565	583	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158192	106158192	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	67	480	0	ENST00000380013.4:c.3093T>A	p.His1031Gln	p.H1031Q	ENST00000380013	NM_001127208.2	1031	caT/caA	3/11	1	2	FACETS	0.946	0.823	1	0.946	0.823	1	CLONAL	1	TRUE	1	0.28	2		480	506	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867454	35867454	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	97	507	0	ENST00000303115.3:c.268G>A	p.Glu90Lys	p.E90K	ENST00000303115	NM_002185.3	90	Gag/Aag	3/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.28	2		507	619	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505023	149505023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370532697	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	66	535	1	ENST00000261799.4:c.1792G>A	p.Asp598Asn	p.D598N	ENST00000261799	NM_002609.3	598	Gac/Aac	12/23	1	2	FACETS	0.901	0.784	1	0.901	0.784	1	CLONAL	1	TRUE	1	0.28	2		536	523	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520553	176520553	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1425958556	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	114	869	1	ENST00000292408.4:c.1397+1G>A		p.X466_splice	ENST00000292408	NM_213647.1	466			1	2	FACETS	0.953	0.858	1	0.953	0.858	1	CLONAL	1	TRUE	1	0.28	2		870	854	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109309807	109309807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	135	802	1	ENST00000436639.2:c.1508C>T	p.Pro503Leu	p.P503L	ENST00000436639	NM_014454.2	503	cCt/cTt	9/10	0.3	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.28	1		803	802	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528883	157528883	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	122	701	0	ENST00000346085.5:c.6608T>A	p.Leu2203Gln	p.L2203Q	ENST00000346085	NM_020732.3	2203	cTa/cAa	20/20	0.3	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.28	1		701	622	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55087048	55087049	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	66	336	1	ENST00000275493.2:c.78_79delinsAA	p.Glu27Lys	p.E27K	ENST00000275493	NM_005228.3	26	gaGGaa/gaAAaa	1/28	0.277488749561442	3	FACETS	1	0.973	1	0.746	0.652	0.848	CLONAL	1	TRUE	1	0.28	3		337	360	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97873813	97873814	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	122	824	4	ENST00000289081.3:c.1260_1261delinsTA	p.Ala421Thr	p.A421T	ENST00000289081	NM_000136.2	420	acGGcc/acTAcc	13/15	1	2	FACETS	0.968	0.874	1	0.968	0.874	1	CLONAL	1	TRUE	1	0.28	2		828	900	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652267	48652267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	155	501	0	ENST00000376670.3:c.938G>A	p.Gly313Glu	p.G313E	ENST00000376670	NM_002049.3	313	gGg/gAg	6/6	1	1	FACETS	0.984	0.908	1	1	0.992	1	CLONAL	2	TRUE	0	0.28	1		501	484	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0054195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	21	563	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.558	0.429	0.709	0.558	0.429	0.709	SUBCLONAL	1	TRUE	1	0.19	2		563	396	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729932	30729932	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0054195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	71	544	0	ENST00000295754.5:c.1453G>T	p.Glu485Ter	p.E485*	ENST00000295754	NM_003242.5	485	Gaa/Taa	6/7	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.19	2		544	647	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923037	44923038	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAACC	novel	NA	P-0054195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	52	719	0	ENST00000377967.4:c.1901_1905dup	p.Leu636ThrfsTer57	p.L636Tfs*57	ENST00000377967	NM_021140.2	633	aaa/aaAAACCa	16/29	0.0930119069915034	0	FACETS	0.572	0.486	0.667			1	INDETERMINATE	1	TRUE	0	0.19	0		719	775	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044541	47044541	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0054195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	44	804	3	ENST00000377604.3:c.2038C>T	p.Arg680Ter	p.R680*	ENST00000377604	NM_001204468.1	680	Cga/Tga	18/24	0.0930119069915034	0	FACETS	0.516	0.431	0.61			1	INDETERMINATE	1	TRUE	0	0.19	0		807	727	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0054196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	52	346	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.877	0.75	1	0.877	0.75	1	CLONAL	1	FALSE	1	0.343691092893831	2		346	345	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0054196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	186	643	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.343691092893831	2		643	768	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0054196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	32	309	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	1	2	FACETS	0.945	0.774	1	0.945	0.774	1	CLONAL	1	FALSE	1	0.343691092893831	2		309	197	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597493	52597493	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0054196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	60	456	0	ENST00000394830.3:c.3817C>T	p.Gln1273Ter	p.Q1273*	ENST00000394830	NM_018313.4	1273	Cag/Tag	25/30	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	FALSE	1	0.343691092893831	2		456	317	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023685	27023685	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0054196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	84	414	1	ENST00000324856.7:c.791C>A	p.Ser264Ter	p.S264*	ENST00000324856	NM_006015.4	264	tCg/tAg	1/20	1	2	FACETS	0.912	0.807	1	0.912	0.807	1	CLONAL	1	FALSE	1	0.343691092893831	2		415	536	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927477	178927477	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0054196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	26	367	0	ENST00000263967.3:c.1240G>C	p.Gly414Arg	p.G414R	ENST00000263967	NM_006218.2	414	Ggt/Cgt	7/21	1	2	FACETS	0.694	0.553	0.854	0.694	0.553	0.854	SUBCLONAL	1	FALSE	1	0.343691092893831	2		367	218	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246490514	246490514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0054196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	25	550	0	ENST00000388985.4:c.520G>A	p.Ala174Thr	p.A174T	ENST00000388985		174	Gcc/Acc	5/12	1	2	FACETS	0.543	0.429	0.673	0.543	0.429	0.673	SUBCLONAL	1	FALSE	1	0.343691092893831	2		550	268	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405950	49405950	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0054196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	127	697	0	ENST00000418115.1:c.188A>G	p.Gln63Arg	p.Q63R	ENST00000418115	NM_001664.2	63	cAg/cGg	3/5	1	2	FACETS	0.898	0.813	0.987	0.898	0.813	0.987	CLONAL	1	FALSE	1	0.343691092893831	2		697	823	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813446	32813462	+	frameshift_variant	Frame_Shift_Del	DEL	AGCGCCTCCTTCCAGAA	AGCGCCTCCTTCCAGAA	-	novel	NA	P-0054196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	143	912	0	ENST00000354258.4:c.2321_2337del	p.Phe774TyrfsTer56	p.F774Yfs*56	ENST00000354258	NM_000593.5	774	tTTCTGGAAGGAGGCGCT/t	11/11	0.184028774362405	2	FACETS	0.945	0.861	1	0.472	0.43	0.516	INDETERMINATE	1	FALSE	0	0.343691092893831	2		912	881	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971142	21971157	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGTTGGGCTCCGCG	GCAGTTGGGCTCCGCG	-	novel	NA	P-0054196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	86	452	0	ENST00000304494.5:c.201_216del	p.Ala68ProfsTer73	p.A68Pfs*73	ENST00000304494	NM_000077.4	67	ggCGCGGAGCCCAACTGC/gg	2/3	0.343691092893831	1	FACETS	0.723	0.641	0.811	0.723	0.641	0.811	SUBCLONAL	1	FALSE	0	0.343691092893831	1		452	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0054197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	579	981	2	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.623763337817947	2	FACETS	0.882	0.856	0.907	0.882	0.856	0.907	CLONAL	2	TRUE	0	0.751900725972914	2		983	873	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528086	29528086	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs864622107	NA	P-0054197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	365	306	0	ENST00000356175.3:c.1094C>G	p.Ser365Ter	p.S365*	ENST00000356175	NM_000267.3	365	tCa/tGa	10/57	0.751900725972914	7	FACETS	1	0.983	1	1	0.983	1	CLONAL	6	TRUE	1	0.751900725972914	7		306	458	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445302	49445302	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0054197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	575	799	1	ENST00000301067.7:c.2164G>C	p.Glu722Gln	p.E722Q	ENST00000301067	NM_003482.3	722	Gag/Cag	10/54	0.381484692371532	6	FACETS	1	0.984	1	0.778	0.75	0.807	INDETERMINATE	3	TRUE	2	0.751900725972914	6		800	1230	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117493	4117493	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0054197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	120	447	0	ENST00000262948.5:c.227C>G	p.Ser76Ter	p.S76*	ENST00000262948	NM_030662.3	76	tCa/tGa	2/11	0.581463000140502	4	FACETS	0.9	0.815	0.99	0.45	0.407	0.495	CLONAL	1	TRUE	2	0.751900725972914	4		447	621	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266498	198266498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0054197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	191	438	0	ENST00000335508.6:c.2338C>T	p.Pro780Ser	p.P780S	ENST00000335508	NM_012433.2	780	Cct/Tct	16/25	0.751900725972914	5	FACETS	1	0.988	1	0.452	0.419	0.487	CLONAL	1	TRUE	2	0.751900725972914	5		438	797	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212190	98212190	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0054197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	240	359	0	ENST00000331920.6:c.3482T>A	p.Ile1161Asn	p.I1161N	ENST00000331920	NM_000264.3	1161	aTc/aAc	21/24	0.558495237779116	4	FACETS	1	0.976	1	0.707	0.667	0.748	CLONAL	2	TRUE	1	0.751900725972914	4		359	527	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920154	76920154	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004109-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	83	602	0	ENST00000373344.5:c.3923A>G	p.Glu1308Gly	p.E1308G	ENST00000373344	NM_000489.3	1308	gAa/gGa	11/35	0.415784159704465	1	FACETS	0.519	0.459	0.584	0.519	0.459	0.584	SUBCLONAL	1	TRUE	0	0.415784159704465	1		602	609	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0004939-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	25	575	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.613	0.481	0.765	0.613	0.481	0.765	SUBCLONAL	1	TRUE	1	0.12	2		576	680	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913136	44913136	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004939-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	17	0	0	ENST00000377967.4:c.811C>T	p.Gln271Ter	p.Q271*	ENST00000377967	NM_021140.2	271	Cag/Tag	10/29	1	2	FACETS	0.465	0.345	0.609	0.465	0.345	0.609	SUBCLONAL	1	TRUE	1	0.12	2		0	609	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268401	46268401	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004939-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	11	0	0	ENST00000371998.3:c.2788A>G	p.Met930Val	p.M930V	ENST00000371998		930	Atg/Gtg	15/23	1	2	FACETS	0.38	0.261	0.529	0.38	0.261	0.529	SUBCLONAL	1	TRUE	1	0.12	2		0	483	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524567	187524567	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004939-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	34	527	0	ENST00000441802.2:c.11113C>T	p.Gln3705Ter	p.Q3705*	ENST00000441802	NM_005245.3	3705	Cag/Tag	19/27	1	2	FACETS	0.877	0.715	1	0.877	0.715	1	CLONAL	1	TRUE	1	0.12	2		527	646	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188200	10188200	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs5030811	NA	P-0005596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	254	491	0	ENST00000256474.2:c.343C>T	p.His115Tyr	p.H115Y	ENST00000256474	NM_000551.3	115	Cac/Tac	2/3	0.514575108867137	2	FACETS	0.799	0.755	0.843	0.799	0.755	0.843	SUBCLONAL	2	TRUE	0	0.568518457873481	2		491	559	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129075	30129075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1289763589	NA	P-0005596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	155	705	0	ENST00000263025.4:c.691G>A	p.Val231Met	p.V231M	ENST00000263025	NM_002746.2	231	Gtg/Atg	5/9	1	2	FACETS	0.838	0.769	0.909	0.838	0.769	0.909	CLONAL	1	TRUE	1	0.568518457873481	2		705	651	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705470	47705470	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs780448421	NA	P-0005596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	103	435	0	ENST00000233146.2:c.2270A>G	p.Tyr757Cys	p.Y757C	ENST00000233146	NM_000251.2	757	tAc/tGc	14/16	1	2	FACETS	0.82	0.738	0.905	0.82	0.738	0.905	CLONAL	1	TRUE	1	0.568518457873481	2		435	442	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231114	53231149	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGATGACAAACTCTCCTGCACACTGGTTTGTGCG	GGTGATGACAAACTCTCCTGCACACTGGTTTGTGCG	C	novel	NA	P-0005596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	100	390	0	ENST00000375401.3:c.1753_1788delinsG	p.Arg585ValfsTer25	p.R585Vfs*25	ENST00000375401	NM_004187.3	585	CGCACAAACCAGTGTGCAGGAGAGTTTGTCATCACC/G	13/26	1	1	FACETS	0.929	0.843	1	0.929	0.843	1	CLONAL	1	TRUE	0	0.568518457873481	1		390	271	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0012076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1395	754	297	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.437878188534548	11	FACETS	0.952	0.919	0.986	0.793	0.766	0.821	CLONAL	5	TRUE	5	0.437878188534548	11		297	2149	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047507	49047507	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0012076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	177	279	0	ENST00000267163.4:c.2501C>G	p.Ser834Ter	p.S834*	ENST00000267163	NM_000321.2	834	tCa/tGa	24/27	0.414066609239834	3	FACETS	0.905	0.847	0.963	0.905	0.847	0.963	CLONAL	3	TRUE	0	0.437878188534548	3		279	363	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0012076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	668	856	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	0.437878188534548	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	0	0.437878188534548	3		856	1198	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888102	81888102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	267	563	0	ENST00000359376.3:c.247G>A	p.Glu83Lys	p.E83K	ENST00000359376	NM_002661.3	83	Gag/Aag	3/33	0.437878188534548	2	FACETS	0.957	0.904	1	0.957	0.904	1	CLONAL	2	TRUE	0	0.437878188534548	2		563	637	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45649965	45649966	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0012076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	286	674	0	ENST00000407780.3:c.869_870delinsTT	p.Trp290Phe	p.W290F	ENST00000407780	NM_001283052.1	290	tGG/tTT	6/7	0.437878188534548	4	FACETS	0.908	0.855	0.963	0.908	0.855	0.963	CLONAL	2	TRUE	2	0.437878188534548	4		674	1034	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098636	2098636	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	199	605	0	ENST00000219476.3:c.20A>T	p.Lys7Ile	p.K7I	ENST00000219476	NM_000548.3	7	aAa/aTa	2/42	0.437878188534548	5	FACETS	1	0.987	1	0.434	0.401	0.468	CLONAL	1	TRUE	2	0.437878188534548	5		605	1157	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793540	42793540	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1417	113	935	0	ENST00000575354.2:c.1342G>A	p.Gly448Arg	p.G448R	ENST00000575354	NM_015125.3	448	Ggg/Agg	8/20	0.423834674308983	5	FACETS	0.559	0.501	0.621	0.14	0.125	0.156	SUBCLONAL	1	TRUE	1	0.437878188534548	5		935	1530	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066760	5066763	+	frameshift_variant	Frame_Shift_Del	DEL	AATA	AATA	-	novel	NA	P-0012076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	34	251	0	ENST00000381652.3:c.1301_1304del	p.Lys434IlefsTer3	p.K434Ifs*3	ENST00000381652	NM_004972.3	433	AATAaa/aa	10/25	0.326825332802058	4	FACETS	0.576	0.47	0.693	0.288	0.235	0.347	SUBCLONAL	1	TRUE	2	0.437878188534548	4		251	388	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0012436-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1768	18	441	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.3	10	FACETS	0.111	0.082	0.145	0.012	0.009	0.017	INDETERMINATE	1	TRUE	1	0.67	10		441	1786	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0012436-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	19	388	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.101	0.076	0.131	0.101	0.076	0.131	SUBCLONAL	1	TRUE	1	0.67	2		388	559	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829227	72829227	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012436-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	50	0	0	ENST00000268489.5:c.7354C>T	p.Pro2452Ser	p.P2452S	ENST00000268489	NM_006885.3	2452	Cca/Tca	9/10	1	2	FACETS	0.136	0.115	0.16	0.136	0.115	0.16	SUBCLONAL	1	TRUE	1	0.67	2		0	1096	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575055	48575055	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0012436-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	25	282	0	ENST00000342988.3:c.250-1G>A		p.X84_splice	ENST00000342988	NM_005359.5	84			1	2	FACETS	0.192	0.151	0.239	0.192	0.151	0.239	SUBCLONAL	1	TRUE	1	0.67	2		282	389	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242729	46242729	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012436-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	32	215	0	ENST00000334344.6:c.1691del	p.Ser564Ter	p.S564*	ENST00000334344	NM_152641.2	564	tCa/ta	13/21	1	2	FACETS	0.157	0.126	0.191	0.157	0.126	0.191	SUBCLONAL	1	TRUE	1	0.67	2		215	610	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0015989-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	192	353	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.145406328975505	3	FACETS	1	0.974	1	1	0.992	1	CLONAL	3	TRUE	1	0.145406328975505	3		353	849	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0015989-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	26	572	1	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	0.422	0.333	0.526	0.422	0.333	0.526	SUBCLONAL	1	TRUE	1	0.145406328975505	2		573	847	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859638	57859638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777659251	NA	P-0015989-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	57	667	0	ENST00000228682.2:c.692C>T	p.Ser231Phe	p.S231F	ENST00000228682	NM_005269.2	231	tCt/tTt	7/12	1	2	FACETS	0.75	0.641	0.869	0.75	0.641	0.869	SUBCLONAL	1	TRUE	1	0.145406328975505	2		667	1046	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652882	212652882	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015989-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	24	261	0	ENST00000342788.4:c.424A>G	p.Ile142Val	p.I142V	ENST00000342788	NM_005235.2	142	Atc/Gtc	4/28	1	2	FACETS	0.885	0.694	1	0.885	0.694	1	CLONAL	1	TRUE	1	0.145406328975505	2		261	373	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798810	135798810	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203382	NA	P-0016762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	280	274	8	ENST00000298552.3:c.433C>T	p.Gln145Ter	p.Q145*	ENST00000298552	NM_001162426.1	145	Cag/Tag	6/23	0.3	1	FACETS	1	0.989	1	1	0.997	1	CLONAL	4	FALSE	0	0.3	1		282	371	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0017194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	420	1153	1	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.993	0.95	1	0.993	0.95	1	CLONAL	1	TRUE	1	0.883731675567697	2		1154	957	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932463	39932464	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0017194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	442	931	0	ENST00000378444.4:c.2135_2136del	p.Glu712ValfsTer27	p.E712Vfs*27	ENST00000378444	NM_001123385.1	712	gAG/g	4/15	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.883731675567697	1		931	521	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0019667-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	212	508	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.701515869163633	2	FACETS	0.771	0.728	0.813	0.771	0.728	0.813	SUBCLONAL	2	TRUE	0	0.701661968705291	2		508	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578463	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371524413	NA	P-0019667-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	288	848	0	ENST00000269305.4:c.467G>C	p.Arg156Pro	p.R156P	ENST00000269305	NM_001126112.2	156	cGc/cCc	5/11	0.601808241025829	1	FACETS	0.932	0.886	0.978	0.932	0.886	0.978	CLONAL	1	TRUE	0	0.701661968705291	1		848	572	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022279	31022279	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019667-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	157	652	0	ENST00000375687.4:c.1764G>C	p.Gln588His	p.Q588H	ENST00000375687	NM_015338.5	588	caG/caC	13/13	0.368622328231178	3	FACETS	1	0.985	1	0.64	0.591	0.691	INDETERMINATE	1	TRUE	1	0.701661968705291	3		652	472	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514451	149514469	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTCTTCTCGTGCAGTGT	CTTTCTTCTCGTGCAGTGT	-	novel	NA	P-0019667-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	215	882	0	ENST00000261799.4:c.475_493del	p.Thr159GlyfsTer54	p.T159Gfs*54	ENST00000261799	NM_002609.3	159	ACACTGCACGAGAAGAAAGgg/gg	4/23	1	2	FACETS	0.938	0.877	1	0.938	0.877	1	CLONAL	1	TRUE	1	0.701661968705291	2		882	653	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627744	37627744	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021620-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	129	374	0	ENST00000447079.4:c.1661del	p.Leu554CysfsTer56	p.L554Cfs*56	ENST00000447079	NM_015083.1	553	ccT/cc	2/14	1	2	FACETS	0.478	0.434	0.524	0.478	0.434	0.524	SUBCLONAL	1	FALSE	1	0.816492237110011	2		374	661	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061221	38061232	+	inframe_deletion	In_Frame_Del	DEL	GTTCTCGAACAT	GTTCTCGAACAT	-	novel	NA	P-0021620-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	110	393	0	ENST00000250448.2:c.757_768del	p.Met253_Asn256del	p.M253_N256del	ENST00000250448	NM_004496.3	253	ATGTTCGAGAAC/-	2/2	1	2	FACETS	0.393	0.353	0.435	0.393	0.353	0.435	SUBCLONAL	1	FALSE	1	0.816492237110011	2		393	686	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37055943	37055943	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021620-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	76	218	0	ENST00000231790.2:c.698G>A	p.Cys233Tyr	p.C233Y	ENST00000231790	NM_000249.3	233	tGt/tAt	9/19	1	2	FACETS	0.44	0.388	0.496	0.44	0.388	0.496	SUBCLONAL	1	FALSE	1	0.816492237110011	2		218	423	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627446	37627452	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAATC	AAAAATC	-	novel	NA	P-0021620-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	150	357	0	ENST00000447079.4:c.1361_1367del	p.Glu454ValfsTer8	p.E454Vfs*8	ENST00000447079	NM_015083.1	454	gAAAAATCt/gt	2/14	1	2	FACETS	0.434	0.397	0.474	0.434	0.397	0.474	SUBCLONAL	1	FALSE	1	0.816492237110011	2		357	846	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250264	110250265	+	stop_gained	Nonsense_Mutation	DNP	CG	CG	TC	novel	NA	P-0021620-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	163	511	1	ENST00000374672.4:c.410_411delinsGA	p.Ser137Ter	p.S137*	ENST00000374672	NM_004235.4	137	tCG/tGA	3/5	1	2	FACETS	0.454	0.416	0.493	0.454	0.416	0.493	SUBCLONAL	1	FALSE	1	0.816492237110011	2		512	880	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444488	49444488	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021620-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	191	622	0	ENST00000301067.7:c.2883del	p.Phe961LeufsTer39	p.F961Lfs*39	ENST00000301067	NM_003482.3	961	ttT/tt	11/54	1	2	FACETS	0.504	0.466	0.544	0.504	0.466	0.544	SUBCLONAL	1	FALSE	1	0.816492237110011	2		622	928	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875645	35875645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201449880	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	49	159	0	ENST00000303115.3:c.832G>A	p.Asp278Asn	p.D278N	ENST00000303115	NM_002185.3	278	Gat/Aat	7/8	1	2	FACETS	0.79	0.678	0.91	0.79	0.678	0.91	CLONAL	1	TRUE	1	0.61075584490485	2		159	203	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857692	9857692	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1389208302	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	120	210	0	ENST00000330684.3:c.3709G>A	p.Asp1237Asn	p.D1237N	ENST00000330684	NM_001134407.1	1237	Gat/Aat	13/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.61075584490485	2		210	337	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313222	30313222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	87	265	0	ENST00000262643.3:c.916C>T	p.His306Tyr	p.H306Y	ENST00000262643	NM_001238.2	306	Cat/Tat	10/12	1	2	FACETS	0.91	0.814	1	0.91	0.814	1	CLONAL	1	TRUE	1	0.61075584490485	2		265	313	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954188	48954188	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	35	116	0	ENST00000267163.4:c.1390-1G>A		p.X464_splice	ENST00000267163	NM_000321.2	464			1	2	FACETS	0.69	0.573	0.818	0.69	0.573	0.818	SUBCLONAL	1	TRUE	1	0.61075584490485	2		116	166	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39613898	39613898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	36	150	0	ENST00000262039.4:c.1816C>T	p.Pro606Ser	p.P606S	ENST00000262039	NM_002647.2	606	Ccg/Tcg	16/25	0.125977957269541	4	FACETS	1	0.935	1	0.633	0.529	0.746	INDETERMINATE	1	TRUE	2	0.61075584490485	4		150	150	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175874	24175874	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	139	241	0	ENST00000263121.7:c.1102C>T	p.Gln368Ter	p.Q368*	ENST00000263121	NM_003073.3	368	Cag/Tag	8/9	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.61075584490485	2		241	406	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92252390	92252390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373488172	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	30	94	0	ENST00000265734.4:c.658C>T	p.Arg220Cys	p.R220C	ENST00000265734	NM_001259.6	220	Cgt/Tgt	6/8	1	2	FACETS	0.571	0.465	0.689	0.571	0.465	0.689	SUBCLONAL	1	TRUE	1	0.61075584490485	2		94	172	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778251	27778251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761484168	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	111	229	0	ENST00000369163.2:c.400G>A	p.Glu134Lys	p.E134K	ENST00000369163	NM_003536.2	134	Gag/Aag	1/1	0.61075584490485	3	FACETS	1	0.976	1	0.616	0.559	0.676	CLONAL	1	TRUE	1	0.61075584490485	3		229	385	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436671	110436671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	152	391	0	ENST00000375856.3:c.1730C>T	p.Ser577Phe	p.S577F	ENST00000375856	NM_003749.2	577	tCc/tTc	1/2	1	2	FACETS	0.92	0.846	0.996	0.92	0.846	0.996	CLONAL	1	TRUE	1	0.61075584490485	2		391	541	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232137	98232137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1382474804	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	89	157	0	ENST00000331920.6:c.1805G>A	p.Arg602Gln	p.R602Q	ENST00000331920	NM_000264.3	602	cGa/cAa	13/24	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.61075584490485	2		157	278	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273096	198273096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	77	246	0	ENST00000335508.6:c.1114C>T	p.Pro372Ser	p.P372S	ENST00000335508	NM_012433.2	372	Cca/Tca	8/25	1	2	FACETS	0.813	0.721	0.911	0.813	0.721	0.911	CLONAL	1	TRUE	1	0.61075584490485	2		246	310	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271633	15271633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	151	482	0	ENST00000263388.2:c.6806C>T	p.Ser2269Phe	p.S2269F	ENST00000263388	NM_000435.2	2269	tCc/tTc	33/33	1	2	FACETS	0.907	0.834	0.983	0.907	0.834	0.983	CLONAL	1	TRUE	1	0.61075584490485	2		482	545	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730938	40730938	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	220	235	0	ENST00000373198.4:c.3598-1G>A		p.X1200_splice	ENST00000373198	NM_133170.3	1200			0.61075584490485	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.61075584490485	3		235	426	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169286	99169286	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	116	237	0	ENST00000074304.5:c.1216C>T	p.Gln406Ter	p.Q406*	ENST00000074304	NM_001134224.1	406	Cag/Tag	15/26	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.61075584490485	2		237	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573976	7573976	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	321	359	0	ENST00000269305.4:c.1051A>T	p.Lys351Ter	p.K351*	ENST00000269305	NM_001126112.2	351	Aag/Tag	10/11	NA	2	FACETS	0.99	0.948	1			1	INDETERMINATE	2	TRUE	NA	0.61075584490485	2		359	531	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45800147	45800147	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764645557	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	279	292	0	ENST00000450313.1:c.73G>A	p.Gly25Ser	p.G25S	ENST00000450313	NM_012222.2	25	Ggt/Agt	2/16	0.61075584490485	3	FACETS	0.965	0.914	1	0.965	0.914	1	CLONAL	2	TRUE	1	0.61075584490485	3		292	618	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63700047	63700048	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	39	109	0	ENST00000279873.7:c.382_383delinsTT	p.Pro128Leu	p.P128L	ENST00000279873	NM_032199.2	128	CCa/TTa	3/10	1	2	FACETS	0.55	0.46	0.65	0.55	0.46	0.65	SUBCLONAL	1	TRUE	1	0.61075584490485	2		109	232	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446380	70446380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	92	252	0	ENST00000373644.4:c.5320G>A	p.Glu1774Lys	p.E1774K	ENST00000373644	NM_030625.2	1774	Gaa/Aaa	11/12	1	2	FACETS	0.819	0.733	0.908	0.819	0.733	0.908	CLONAL	1	TRUE	1	0.61075584490485	2		252	368	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201913	102201913	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs369562282	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	36	181	0	ENST00000263464.3:c.1265A>G	p.Asn422Ser	p.N422S	ENST00000263464	NM_001165.4	422	aAt/aGt	6/9	0.534189906185836	1	FACETS	0.598	0.5	0.702	0.598	0.5	0.702	SUBCLONAL	1	TRUE	0	0.61075584490485	1		181	137	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037391	12037391	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	103	319	0	ENST00000396373.4:c.1022T>C	p.Leu341Pro	p.L341P	ENST00000396373	NM_001987.4	341	cTt/cCt	6/8	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.61075584490485	NA		319	392	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244039	46244039	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	62	209	0	ENST00000334344.6:c.2133T>A	p.Cys711Ter	p.C711*	ENST00000334344	NM_152641.2	711	tgT/tgA	15/21	1	2	FACETS	0.778	0.679	0.883	0.778	0.679	0.883	SUBCLONAL	1	TRUE	1	0.61075584490485	2		209	261	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435231	49435231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	143	325	0	ENST00000301067.7:c.6322C>T	p.Pro2108Ser	p.P2108S	ENST00000301067	NM_003482.3	2108	Ccg/Tcg	31/54	1	2	FACETS	0.922	0.846	1	0.922	0.846	1	CLONAL	1	TRUE	1	0.61075584490485	2		325	508	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447796	49447796	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	143	214	0	ENST00000301067.7:c.638T>A	p.Leu213Gln	p.L213Q	ENST00000301067	NM_003482.3	213	cTa/cAa	5/54	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.61075584490485	2		214	436	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226464	133226465	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	81	234	0	ENST00000320574.5:c.3593_3594delinsTT	p.Ala1198Val	p.A1198V	ENST00000320574	NM_006231.2	1198	gCC/gTT	30/49	1	2	FACETS	0.837	0.744	0.934	0.837	0.744	0.934	CLONAL	1	TRUE	1	0.61075584490485	2		234	317	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434487	110434487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	153	228	0	ENST00000375856.3:c.3914G>A	p.Gly1305Glu	p.G1305E	ENST00000375856	NM_003749.2	1305	gGg/gAg	1/2	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.61075584490485	2		228	445	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42384766	42384767	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	75	194	0	ENST00000221972.3:c.528_529delinsAA	p.Asp177Asn	p.D177N	ENST00000221972	NM_021601.3	176	ttGGat/ttAAat	4/5	1	2	FACETS	0.85	0.753	0.952	0.85	0.753	0.952	CLONAL	1	TRUE	1	0.61075584490485	2		194	289	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147744	61147744	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749138316	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	46	163	0	ENST00000295025.8:c.1054G>A	p.Gly352Ser	p.G352S	ENST00000295025	NM_002908.2	352	Ggt/Agt	10/11	1	2	FACETS	0.679	0.577	0.788	0.679	0.577	0.788	SUBCLONAL	1	TRUE	1	0.61075584490485	2		163	222	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147745	61147745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	70	173	0	ENST00000295025.8:c.1055G>A	p.Gly352Asp	p.G352D	ENST00000295025	NM_002908.2	352	gGt/gAt	10/11	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.61075584490485	2		173	220	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439851	220439851	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	152	428	0	ENST00000243786.2:c.704C>T	p.Pro235Leu	p.P235L	ENST00000243786	NM_002191.3	235	cCc/cTc	2/2	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.61075584490485	2		428	488	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662578	227662578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1175926903	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	118	331	0	ENST00000305123.5:c.877C>T	p.Pro293Ser	p.P293S	ENST00000305123	NM_005544.2	293	Ccg/Tcg	1/2	1	2	FACETS	0.916	0.833	1	0.916	0.833	1	CLONAL	1	TRUE	1	0.61075584490485	2		331	422	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62298874	62298874	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	289	338	0	ENST00000360203.5:c.667T>A	p.Phe223Ile	p.F223I	ENST00000360203	NM_001283009.1	223	Ttc/Atc	8/35	0.61075584490485	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.61075584490485	3		338	587	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124431	94124431	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	46	189	1	ENST00000369303.4:c.152C>A	p.Pro51Gln	p.P51Q	ENST00000369303	NM_004440.3	51	cCa/cAa	2/17	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.61075584490485	2		190	115	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129292	152129292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	106	339	0	ENST00000206249.3:c.245C>T	p.Pro82Leu	p.P82L	ENST00000206249	NM_000125.3	82	cCc/cTc	1/8	1	2	FACETS	0.883	0.798	0.972	0.883	0.798	0.972	CLONAL	1	TRUE	1	0.61075584490485	2		339	393	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509214	106509214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	106	312	1	ENST00000359195.3:c.1208C>T	p.Pro403Leu	p.P403L	ENST00000359195	NM_002649.2	403	cCc/cTc	2/11	1	2	FACETS	0.87	0.786	0.957	0.87	0.786	0.957	CLONAL	1	TRUE	1	0.61075584490485	2		313	399	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829108	128829108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1413825142	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	26	10	0	ENST00000249373.3:c.116C>T	p.Pro39Leu	p.P39L	ENST00000249373	NM_005631.4	39	cCt/cTt	1/12	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.61075584490485	2		10	71	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874454	151874454	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	57	207	0	ENST00000262189.6:c.8084C>T	p.Ser2695Phe	p.S2695F	ENST00000262189	NM_170606.2	2695	tCt/tTt	38/59	0.125977957269541	4	FACETS	1	0.957	1	0.634	0.55	0.724	INDETERMINATE	1	TRUE	2	0.61075584490485	4		207	237	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412658	139412659	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	141	481	0	ENST00000277541.6:c.1185_1186delinsAT	p.Ala396Ser	p.A396S	ENST00000277541	NM_017617.3	395	aaGGcc/aaATcc	7/34	1	2	FACETS	0.788	0.721	0.858	0.788	0.721	0.858	SUBCLONAL	1	TRUE	1	0.61075584490485	2		481	586	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933557	39933557	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	156	162	0	ENST00000378444.4:c.1042C>T	p.Gln348Ter	p.Q348*	ENST00000378444	NM_001123385.1	348	Cag/Tag	4/15	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.61075584490485	1		162	272	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411168	63411169	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	79	139	0	ENST00000330258.3:c.1998_1999delinsAA	p.Ala667Thr	p.A667T	ENST00000330258	NM_152424.3	666	ctGGca/ctAAca	2/2	1	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.61075584490485	1		139	170	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271209	26271209	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1318299590	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	84	213	0	ENST00000305910.3:c.404G>A	p.Arg135Lys	p.R135K	ENST00000305910	NM_003534.2	135	aGa/aAa	1/1	0.61075584490485	3	FACETS	1	0.96	1	0.581	0.518	0.647	CLONAL	1	TRUE	1	0.61075584490485	3		213	309	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094915	11094915	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	175	462	0	ENST00000358026.2:c.88C>T	p.Pro30Ser	p.P30S	ENST00000358026	NM_001128849.1	30	Cct/Tct	2/36	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.61075584490485	2		462	533	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237745	16237746	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	79	243	1	ENST00000375759.3:c.1192_1193delinsAA	p.Gly398Lys	p.G398K	ENST00000375759	NM_015001.2	398	GGa/AAa	5/15	0.61075584490485	3	FACETS	0.938	0.831	1	0.469	0.415	0.526	CLONAL	1	TRUE	1	0.61075584490485	3		244	360	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021913	246021913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	182	287	0	ENST00000388985.4:c.961C>T	p.Pro321Ser	p.P321S	ENST00000388985		321	Ccc/Tcc	10/12	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.61075584490485	2		287	496	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625377	69625377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	140	390	0	ENST00000334134.2:c.416G>A	p.Ser139Asn	p.S139N	ENST00000334134	NM_005247.2	139	aGt/aAt	3/3	1	2	FACETS	0.936	0.858	1	0.936	0.858	1	CLONAL	1	TRUE	1	0.61075584490485	2		390	490	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719878	61719878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	39	197	0	ENST00000401558.2:c.1390C>T	p.Leu464Phe	p.L464F	ENST00000401558	NM_003400.3	464	Ctt/Ttt	14/25	1	2	FACETS	0.694	0.582	0.815	0.694	0.582	0.815	SUBCLONAL	1	TRUE	1	0.61075584490485	2		197	184	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920187	1920188	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	113	375	0	ENST00000382891.5:c.1247_1248delinsTT	p.Pro416Leu	p.P416L	ENST00000382891	NM_133335.3	416	cCC/cTT	5/22	1	2	FACETS	0.843	0.764	0.925	0.843	0.764	0.925	CLONAL	1	TRUE	1	0.61075584490485	2		375	439	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522497	157522497	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	155	370	0	ENST00000346085.5:c.4769C>T	p.Ser1590Phe	p.S1590F	ENST00000346085	NM_020732.3	1590	tCc/tTc	18/20	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.61075584490485	2		370	507	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341192	8341192	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	57	206	0	ENST00000356435.5:c.5024T>G	p.Leu1675Arg	p.L1675R	ENST00000356435		1675	cTt/cGt	30/35	1	2	FACETS	0.977	0.852	1	0.977	0.852	1	CLONAL	1	TRUE	1	0.61075584490485	2		206	191	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827757	72827757	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021648-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	118	258	0	ENST00000268489.5:c.8824G>A	p.Asp2942Asn	p.D2942N	ENST00000268489	NM_006885.3	2942	Gat/Aat	9/10	1	2	FACETS	0.931	0.847	1	0.931	0.847	1	CLONAL	1	TRUE	1	0.61075584490485	2		258	415	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754484	42754484	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777008	NA	P-0021939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	386	1090	1	ENST00000222329.4:c.256C>T	p.Arg86Cys	p.R86C	ENST00000222329	NM_006494.2	86	Cgc/Tgc	2/4	1	2	FACETS	0.858	0.819	0.898	1	0.996	1	CLONAL	2	TRUE	1	0.481027372116253	2		1091	935	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427016	49427016	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0021939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	254	761	0	ENST00000301067.7:c.11472del	p.His3824GlnfsTer6	p.H3824Qfs*6	ENST00000301067	NM_003482.3	3824	caC/ca	39/54	1	2	FACETS	0.867	0.818	0.917	1	0.995	1	CLONAL	2	TRUE	1	0.481027372116253	2		761	609	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778117	27778117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1396125926	NA	P-0021939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	345	898	2	ENST00000369163.2:c.266C>T	p.Ala89Val	p.A89V	ENST00000369163	NM_003536.2	89	gCg/gTg	1/1	1	2	FACETS	0.844	0.802	0.886	1	0.996	1	CLONAL	2	TRUE	1	0.481027372116253	2		900	850	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039481	49039481	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022721-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	95	412	0	ENST00000267163.4:c.2467del	p.Thr823GlnfsTer3	p.T823Qfs*3	ENST00000267163	NM_000321.2	822	ccA/cc	23/27	0.28304415255294	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.28304415255294	1		412	536	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030367	49030368	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023399-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	157	283	0	ENST00000267163.4:c.1848dup	p.Gly617ArgfsTer36	p.G617Rfs*36	ENST00000267163	NM_000321.2	614	-/A	19/27	0.721324290591182	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.721324290591182	1		283	265	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911143	40911143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370795038	NA	P-0023399-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	313	306	0	ENST00000373198.4:c.2162G>A	p.Arg721His	p.R721H	ENST00000373198	NM_133170.3	721	cGt/cAt	13/32	0.657620734507413	3	FACETS	0.928	0.896	0.96	0.928	0.896	0.96	CLONAL	3	TRUE	0	0.721324290591182	3		306	424	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505121	149505121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140081345	NA	P-0023399-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	155	617	0	ENST00000261799.4:c.1694G>A	p.Arg565Gln	p.R565Q	ENST00000261799	NM_002609.3	565	cGa/cAa	12/23	0.721324290591182	3	FACETS	0.686	0.628	0.747	0.343	0.314	0.374	SUBCLONAL	1	TRUE	1	0.721324290591182	3		617	852	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50827484	50827484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1460880286	NA	P-0023399-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	101	426	0	ENST00000398568.2:c.2369G>A	p.Gly790Glu	p.G790E	ENST00000398568	NM_001042412.1	790	gGg/gAg	16/18	0.691230178861909	2	FACETS	0.582	0.523	0.645	0.291	0.261	0.323	SUBCLONAL	1	TRUE	0	0.721324290591182	2		426	481	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719732	61719732	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025414-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	280	885	2	ENST00000401558.2:c.1536C>A	p.Asp512Glu	p.D512E	ENST00000401558	NM_003400.3	512	gaC/gaA	14/25	1	2	FACETS	0.907	0.855	0.959	0.907	0.855	0.959	CLONAL	1	TRUE	1	0.761396505927992	2		887	811	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0025531-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	111	297	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.200503027892261	0	FACETS	1	0.909	1			1	CLONAL	1	TRUE	0	0.200503027892261	0		297	874	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242470	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs397517097	NA	P-0025531-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	90	513	0	ENST00000275493.2:c.2240T>C	p.Leu747Ser	p.L747S	ENST00000275493	NM_005228.3	747	tTa/tCa	19/28	0.200503027892261	0	FACETS	1	0.91	1			1	CLONAL	1	TRUE	0	0.200503027892261	0		513	697	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745624	162745624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765562219	NA	P-0025531-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	47	443	2	ENST00000367921.3:c.2039G>A	p.Arg680His	p.R680H	ENST00000367921	NM_006182.2	680	cGc/cAc	15/18	1	2	FACETS	0.759	0.639	0.891	0.759	0.639	0.891	SUBCLONAL	1	TRUE	1	0.200503027892261	2		445	618	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044494	12044494	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1300593472	NA	P-0025531-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	23	331	0	ENST00000353533.5:c.1117C>T	p.Arg373Cys	p.R373C	ENST00000353533	NM_003010.3	373	Cgt/Tgt	11/11	1	2	FACETS	0.524	0.407	0.659	0.524	0.407	0.659	SUBCLONAL	1	TRUE	1	0.200503027892261	2		331	438	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637498	47637498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025629-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	77	422	0	ENST00000233146.2:c.632G>A	p.Gly211Glu	p.G211E	ENST00000233146	NM_000251.2	211	gGg/gAg	3/16	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.25	2		422	510	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0025812-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	316	575	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.498914803389069	2		576	946	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0025812-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	38	439	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.498914803389069	2		439	122	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0025812-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	94	395	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	1	2	FACETS	0.779	0.705	0.854	1	0.984	1	SUBCLONAL	2	TRUE	1	0.498914803389069	2		395	242	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249013	55249014	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACCCCC	novel	NA	P-0025812-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	806	706	0	ENST00000275493.2:c.2314_2319dup	p.Pro772_His773dup	p.P772_H773dup	ENST00000275493	NM_005228.3	772	aac/aACCCCCac	20/28	0.498914803389069	6	FACETS	1	0.994	1	0.826	0.799	0.853	CLONAL	3	TRUE	2	0.498914803389069	6		706	1954	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121909229	NA	P-0025812-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	147	479	0	ENST00000371953.3:c.389G>C	p.Arg130Pro	p.R130P	ENST00000371953	NM_000314.4	130	cGa/cCa	5/9	0.498914803389069	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.498914803389069	3		479	316	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0025812-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	130	117	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.498914803389069	2		117	425	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711906	89711906	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025812-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	86	623	0	ENST00000371953.3:c.524T>A	p.Val175Glu	p.V175E	ENST00000371953	NM_000314.4	175	gTg/gAg	6/9	0.498914803389069	3	FACETS	1	0.954	1	0.567	0.505	0.632	CLONAL	1	TRUE	1	0.498914803389069	3		623	380	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485984	40485984	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025812-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	233	709	1	ENST00000264657.5:c.881A>T	p.Lys294Ile	p.K294I	ENST00000264657	NM_139276.2	294	aAa/aTa	9/24	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.498914803389069	2		710	768	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0026112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	55	411	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.227646421909163	1	FACETS	0.841	0.73	0.959	0.841	0.73	0.959	INDETERMINATE	1	TRUE	0	0.483659811870503	1		411	205	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971082	21971083	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0026112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	174	468	0	ENST00000304494.5:c.275dup	p.Asp92GlufsTer28	p.D92Efs*28	ENST00000304494	NM_000077.4	92	gac/gaAc	2/3	0.446280741445522	2	FACETS	1	0.989	1	0.695	0.644	0.746	CLONAL	1	TRUE	0	0.483659811870503	2		468	518	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986699	36986709	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCGCCTGCG	CGCCGCCTGCG	-	novel	NA	P-0026112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	57	39	0	ENST00000354822.5:c.980_990del	p.Ala327GlyfsTer108	p.A327Gfs*108	ENST00000354822	NM_001079668.2	327	gCGCAGGCGGCG/g	3/3	0.459338174822898	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.483659811870503	1		39	120	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0026513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	329	364	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.412802167480051	5	FACETS	0.923	0.878	0.968	0.923	0.878	0.968	CLONAL	3	TRUE	2	0.622466864708662	5		364	738	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0026513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	153	322	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.412802167480051	5	FACETS	1	0.984	1	0.823	0.762	0.885	CLONAL	2	TRUE	2	0.622466864708662	5		322	385	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411768	139411768	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201768800	NA	P-0026513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	90	956	4	ENST00000277541.6:c.1511G>A	p.Arg504His	p.R504H	ENST00000277541	NM_017617.3	504	cGc/cAc	9/34	0.346706655138822	3	FACETS	0.566	0.502	0.634	0.189	0.167	0.212	INDETERMINATE	1	TRUE	0	0.622466864708662	3		960	670	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056209	26056211	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs779842031	NA	P-0026513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	42	507	0	ENST00000343677.2:c.446_448del	p.Lys149del	p.K149del	ENST00000343677	NM_005319.3	149	aAGAgc/agc	1/1	0.359768831896705	6	FACETS	0.537	0.448	0.637	0.134	0.112	0.16	INDETERMINATE	1	TRUE	2	0.622466864708662	6		507	564	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684357	29684363	+	frameshift_variant	Frame_Shift_Del	DEL	GTGTTGT	GTGTTGT	-	novel	NA	P-0026513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	127	504	0	ENST00000356175.3:c.7879_7885del	p.Val2627PhefsTer29	p.V2627Ffs*29	ENST00000356175	NM_000267.3	2626	aGTGTTGTg/ag	53/57	0.622466864708662	1	FACETS	0.931	0.857	1	0.931	0.857	1	CLONAL	1	TRUE	0	0.622466864708662	1		504	302	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732984	74732984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1314	60	0	0	ENST00000359995.5:c.259G>A	p.Val87Met	p.V87M	ENST00000359995	NM_001195427.1	87	Gtg/Atg	1/3	0.622466864708662	6	FACETS	0.315	0.27	0.365	0.079	0.067	0.092	SUBCLONAL	1	TRUE	2	0.622466864708662	6		0	1374	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948166	55948166	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	122	595	0	ENST00000263923.4:c.3805C>A	p.Leu1269Met	p.L1269M	ENST00000263923	NM_002253.2	1269	Ctg/Atg	29/30	0.341580649766645	5	FACETS	1	0.949	1	0.358	0.324	0.395	INDETERMINATE	1	TRUE	2	0.622466864708662	5		595	705	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032279	10032279	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1555455742	NA	P-0026513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	56	628	0	ENST00000330684.3:c.544G>T	p.Glu182Ter	p.E182*	ENST00000330684	NM_001134407.1	182	Gaa/Taa	3/13	0.37050076040458	5	FACETS	0.417	0.356	0.484			1	INDETERMINATE	1	TRUE	NA	0.622466864708662	5		628	834	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466859	57466859	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	38	381	0	ENST00000371085.3:c.78C>G	p.Ile26Met	p.I26M	ENST00000371085	NM_000516.4	26	atC/atG	1/13	0.622466864708662	4	FACETS	0.307	0.253	0.368	0.102	0.084	0.123	SUBCLONAL	1	TRUE	1	0.622466864708662	4		381	645	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630195	100630195	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	44	568	0	ENST00000308731.7:c.78G>C	p.Lys26Asn	p.K26N	ENST00000308731	NM_000061.2	26	aaG/aaC	2/19	0.403639677556084	2	FACETS	0.273	0.229	0.323	0.137	0.114	0.162	SUBCLONAL	1	TRUE	0	0.622466864708662	2		568	517	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955432	48955432	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028050-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	62	249	0	ENST00000267163.4:c.1548G>A	p.Trp516Ter	p.W516*	ENST00000267163	NM_000321.2	516	tgG/tgA	17/27	0.34954891052934	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.34954891052934	1		249	256	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665476	138665476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1264132565	NA	P-0028050-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	34	161	0	ENST00000330315.3:c.89C>T	p.Pro30Leu	p.P30L	ENST00000330315	NM_023067.3	30	cCg/cTg	1/1	1	2	FACETS	0.721	0.591	0.864	0.721	0.591	0.864	SUBCLONAL	1	TRUE	1	0.34954891052934	2		161	270	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778090	135778090	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203673	NA	P-0028050-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	131	367	0	ENST00000298552.3:c.2293C>T	p.Gln765Ter	p.Q765*	ENST00000298552	NM_001162426.1	765	Cag/Tag	18/23	0.34954891052934	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.34954891052934	1		367	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	300	827	0	ENST00000269305.4:c.403del	p.Cys135AlafsTer35	p.C135Afs*35	ENST00000269305	NM_001126112.2	135	Tgc/gc	5/11	0.558738425769588	1	FACETS	0.946	0.895	0.998	0.946	0.895	0.998	CLONAL	1	TRUE	0	0.558738425769588	1		827	818	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890169	76890169	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	153	327	0	ENST00000373344.5:c.4725C>A	p.Cys1575Ter	p.C1575*	ENST00000373344	NM_000489.3	1575	tgC/tgA	17/35	1	2	FACETS	0.964	0.887	1	0.964	0.887	1	CLONAL	1	TRUE	1	0.558738425769588	2		327	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0028513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	355	574	3	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.325108820641067	3	FACETS	0.895	0.85	0.94			1	CLONAL	3	TRUE	NA	0.325108820641067	3		577	946	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0028909-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	414	1171	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.82619536333264	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.82619536333264	2		1171	473	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547022	9547022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs58486349	NA	P-0028909-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	69	280	1	ENST00000353224.5:c.1000G>A	p.Asp334Asn	p.D334N	ENST00000353224	NM_177990.2	334	Gat/Aat	5/10	NA	2	FACETS	1	0.962	1			1	INDETERMINATE	1	TRUE	NA	0.82619536333264	2		281	144	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717777	89717777	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs786204873	NA	P-0028909-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	193	208	0	ENST00000371953.3:c.801+1G>A		p.X267_splice	ENST00000371953	NM_000314.4	267			0.825212016601359	2	FACETS	0.946	0.907	0.982	0.946	0.907	0.982	CLONAL	2	TRUE	0	0.82619536333264	2		208	247	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659647	88659647	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028909-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	341	421	0	ENST00000372037.3:c.430G>T	p.Gly144Cys	p.G144C	ENST00000372037	NM_004329.2	144	Ggt/Tgt	6/13	0.825212016601359	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.82619536333264	2		421	410	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161390	2161390	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028909-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	369	460	1	ENST00000434045.2:c.137G>A	p.Arg46His	p.R46H	ENST00000434045	NM_001127598.1	46	cGc/cAc	2/5	0.82619536333264	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.82619536333264	2		461	436	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293796	1293796	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029239-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	218	1049	1	ENST00000310581.5:c.1205A>T	p.Gln402Leu	p.Q402L	ENST00000310581	NM_198253.2	402	cAg/cTg	2/16	0.585338798899817	4	FACETS	0.972	0.903	1	0.243	0.225	0.261	CLONAL	1	TRUE	0	0.644940505529958	4		1050	1144	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467726	50467726	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029239-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	148	797	0	ENST00000331340.3:c.961T>A	p.Tyr321Asn	p.Y321N	ENST00000331340	NM_006060.4	321	Tac/Aac	8/8	0.644940505529958	6	FACETS	0.963	0.878	1	0.193	0.175	0.211	CLONAL	1	TRUE	1	0.644940505529958	6		797	1091	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772011	135772011	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029239-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	110	612	0	ENST00000298552.3:c.3106G>T	p.Gly1036Ter	p.G1036*	ENST00000298552	NM_001162426.1	1036	Gga/Tga	23/23	0.642170304146328	3	FACETS	0.885	0.798	0.975	0.442	0.399	0.488	CLONAL	1	TRUE	1	0.644940505529958	3		612	510	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0029340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	71	388	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.149347150084752	3	FACETS	0.86	0.755	0.972	1	0.965	1	CLONAL	3	TRUE	1	0.163006559231254	3		388	365	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922294	100922294	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1315135533	NA	P-0029340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	11	297	0	ENST00000325455.5:c.2218C>T	p.Arg740Ter	p.R740*	ENST00000325455	NM_001202474.3	740	Cga/Tga	5/8	1	2	FACETS	0.675	0.466	0.934	0.675	0.466	0.934	SUBCLONAL	1	TRUE	1	0.163006559231254	2		297	200	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599107	28599108	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0029340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	108	1028	0	ENST00000253063.3:c.555_556dup	p.Glu186AlafsTer62	p.E186Afs*62	ENST00000253063	NM_031459.4	185	ggc/gGCgc	5/10	0.163006559231254	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.163006559231254	1		1028	1018	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252845	10252845	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	85	816	0	ENST00000340748.4:c.3120C>A	p.Asn1040Lys	p.N1040K	ENST00000340748		1040	aaC/aaA	29/40	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.163006559231254	2		816	927	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426744	212426744	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs879103900	NA	P-0029340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	42	656	0	ENST00000342788.4:c.2371A>G	p.Thr791Ala	p.T791A	ENST00000342788	NM_005235.2	791	Acc/Gcc	20/28	0.149347150084752	3	FACETS	0.715	0.595	0.849	0.358	0.297	0.425	SUBCLONAL	1	TRUE	1	0.163006559231254	3		656	779	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143994	11143994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029655-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	9	791	1	ENST00000358026.2:c.3575G>A	p.Arg1192His	p.R1192H	ENST00000358026	NM_001128849.1	1192	cGc/cAc	26/36	0.271905887781553	1	FACETS	0.131	0.086	0.188	0.131	0.086	0.188	SUBCLONAL	1	TRUE	0	0.271905887781553	1		792	438	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs869025608	NA	P-0029655-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	109	707	0	ENST00000307102.5:c.171G>C	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaC	2/11	1	2	FACETS	1	0.944	1	1	0.989	1	CLONAL	2	TRUE	1	0.271905887781553	2		707	379	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394045	31394045	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029655-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	141	452	0	ENST00000328111.2:c.2332T>C	p.Ser778Pro	p.S778P	ENST00000328111	NM_006892.3	778	Tcg/Ccg	22/23	0.271905887781553	4	FACETS	0.932	0.866	0.998	1	0.99	1	CLONAL	5	TRUE	1	0.271905887781553	4		452	283	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447144	187447144	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029655-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	141	895	0	ENST00000232014.4:c.1049G>C	p.Ser350Thr	p.S350T	ENST00000232014	NM_001130845.1	350	aGt/aCt	5/10	1	2	FACETS	1	0.981	1	1	0.992	1	CLONAL	2	TRUE	1	0.271905887781553	2		895	424	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	113	429	0				ENST00000310581	NM_198253.2	-/1132			0.282304650641288	4	FACETS	0.947	0.862	1	0.947	0.862	1	CLONAL	3	TRUE	1	0.312848333661577	4		429	334	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0030136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	90	482	1	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.303698835832933	3	FACETS	0.777	0.693	0.866	0.777	0.693	0.866	SUBCLONAL	2	TRUE	1	0.312848333661577	3		483	428	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981761	101981761	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	88	624	0	ENST00000282441.5:c.182C>G	p.Ser61Trp	p.S61W	ENST00000282441	NM_001130145.2	61	tCg/tGg	1/9	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.312848333661577	2		624	554	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0030136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	108	515	0	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	0.312848333661577	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.312848333661577	1		515	414	SUCCESS
ATM	472	MSKCC	GRCh37	11	108183205	108183205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	24	291	0	ENST00000278616.4:c.5986G>A	p.Glu1996Lys	p.E1996K	ENST00000278616	NM_000051.3	1996	Gaa/Aaa	40/63	1	2	FACETS	0.609	0.479	0.758	0.609	0.479	0.758	SUBCLONAL	1	TRUE	1	0.312848333661577	2		291	252	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148931	119148931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs985412813	NA	P-0030136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	9	483	2	ENST00000264033.4:c.1151G>A	p.Cys384Tyr	p.C384Y	ENST00000264033	NM_005188.3	384	tGt/tAt	8/16	1	2	FACETS	0.133	0.087	0.192	0.133	0.087	0.192	SUBCLONAL	1	TRUE	1	0.312848333661577	2		485	433	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984923	101984923	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	79	489	0	ENST00000282441.5:c.370C>G	p.Arg124Gly	p.R124G	ENST00000282441	NM_001130145.2	124	Cga/Gga	2/9	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.312848333661577	2		489	485	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913277	NA	P-0030136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	43	386	0	ENST00000263967.3:c.3145G>A	p.Gly1049Ser	p.G1049S	ENST00000263967	NM_006218.2	1049	Ggt/Agt	21/21	1	2	FACETS	0.741	0.622	0.873	0.741	0.622	0.873	SUBCLONAL	1	TRUE	1	0.312848333661577	2		386	371	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188187	32188187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754712190	NA	P-0030136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	123	828	2	ENST00000375023.3:c.1154G>A	p.Arg385His	p.R385H	ENST00000375023	NM_004557.3	385	cGc/cAc	6/30	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.312848333661577	2		830	687	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102098231	102098231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	75	470	0	ENST00000282441.5:c.1195G>A	p.Asp399Asn	p.D399N	ENST00000282441	NM_001130145.2	399	Gac/Aac	8/9	1	2	FACETS	0.896	0.787	1	0.896	0.787	1	CLONAL	1	TRUE	1	0.312848333661577	2		470	535	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857517	57857517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs890327478	NA	P-0030136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	270	979	0	ENST00000228682.2:c.43G>A	p.Glu15Lys	p.E15K	ENST00000228682	NM_005269.2	15	Gag/Aag	2/12	0.303698835832933	3	FACETS	0.886	0.831	0.942	0.886	0.831	0.942	CLONAL	2	TRUE	1	0.312848333661577	3		979	1127	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260162	10260162	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	129	765	0	ENST00000340748.4:c.2505C>G	p.Ile835Met	p.I835M	ENST00000340748		835	atC/atG	25/40	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.312848333661577	2		765	816	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143318	30143345	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGGGCGTAGACACGGAAGAGCGAGGG	CCCGGGCGTAGACACGGAAGAGCGAGGG	-	novel	NA	P-0030136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	75	640	0	ENST00000389048.3:c.181_208del	p.Pro61ThrfsTer11	p.P61Tfs*11	ENST00000389048	NM_004304.4	61	CCCTCGCTCTTCCGTGTCTACGCCCGGGac/ac	1/29	1	2	FACETS	0.731	0.64	0.828	0.731	0.64	0.828	SUBCLONAL	1	TRUE	1	0.312848333661577	2		640	656	SUCCESS
REL	5966	MSKCC	GRCh37	2	61148952	61148952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	65	393	0	ENST00000295025.8:c.1142C>T	p.Ser381Leu	p.S381L	ENST00000295025	NM_002908.2	381	tCa/tTa	11/11	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.312848333661577	2		393	388	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151181	202151181	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs1354563506	NA	P-0030136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	66	268	0	ENST00000358485.4:c.1482-1G>C		p.X494_splice	ENST00000358485	NM_001080125.1	494			0.278886204094252	2	FACETS	0.898	0.79	1	0.898	0.79	1	CLONAL	2	TRUE	0	0.312848333661577	2		268	235	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538328	9538328	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	105	530	0	ENST00000353224.5:c.1670C>G	p.Ser557Cys	p.S557C	ENST00000353224	NM_177990.2	557	tCc/tGc	7/10	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.312848333661577	2		530	655	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260707	1260707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755707625	NA	P-0030136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	117	646	2	ENST00000310581.5:c.2852G>A	p.Arg951Gln	p.R951Q	ENST00000310581	NM_198253.2	951	cGg/cAg	12/16	0.282304650641288	4	FACETS	1	0.95	1	0.363	0.327	0.401	CLONAL	1	TRUE	1	0.312848333661577	4		648	902	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672638	30672638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	133	870	0	ENST00000376406.3:c.4322C>T	p.Ser1441Phe	p.S1441F	ENST00000376406	NM_014641.2	1441	tCt/tTt	10/15	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.312848333661577	2		870	849	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324218	31325240	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	CCCTGGCCCCGGCCCCGCGGTCAGCCCAGTCCCCCGAGCCCCGCCCCGCCCCGACCAACCCGCGGGGATTTTGGCCTCAACTGAAAATGAAACCGGGTAAACGCGCCTGGGGCTCTCGCCGGTCGAGGGTCTGGGCGGGTCCCGCGGCCTCAGGGAGGCGGATCTCGGACCCGGAGACTCGGGGCGACCCGGGCCGTACGTGGGGGATGGGGAGTCGTGACCTGCGCCCCGGGCCGGGGTCACTCACCGGCCTCGCTCTGGTTGTAGTAGCCGCGCAGGTTCCGCAGGCTCTCTCGGTCAGTCTGTGCCTGGGCCTTGTAGATCTGTGTGTTCCGGTCCCAATACTCCGGCCCCTCCTGCTCTATCCACGGCGCCCGCGGCTCCTCTCTCGGACTCGCGGCGTCGCTGTCGAACCTCACGAACTGGGTGTCGTCCACGTAGCCCACTGAGATGAAGCGGGGCTCCCCGCGGCCGGGCCGGGACACGGAGGTGTAGAAATACCTCATGGAGTGGGAGCCTGGGGGTGAGGAGGGGCTGAGACCCGCCCGACCCTCCTCCCGGCGCGGCTCCTCAGGTCCTGCGCCCCCGCCTGCGGTCCCCTCGCTCCTCCCGGCAGAGGCCATTTCCCTCCCGACCCGCACTCACCGGCCCAGGTCTCGGTCAGGGCCAGGGCCGCCGAGAGCAGCAGGAGGACGGTTCGGGGCGCCATGACCAGCATCTCGGCGTCTGAGGAGACTCTGAGTCCGGGTGGGTGCGTGGGGACTTTAGAACTGGGACCGCGGCGACGCTGATTGGCTTCTCTAGATATCCAATACCCAATGGGAGTGGGAAGTGGGGACGCGTCACGAGTATCCTGGAAGAAGGACCCGACACAAGTTGGGAGAAGAAGTGAAACTCAGGGGAGTGGGGAATCCCCAACGCTGCGCCTCCCCATTGCAGACGCGGCCCTCGGAGCCTGAGACCCTGAGAGCCCCGTCCGGGACCTGGGACTTCGTCCTGATCCCTCTTCTCCTACACCAAGCC	CCCTGGCCCCGGCCCCGCGGTCAGCCCAGTCCCCCGAGCCCCGCCCCGCCCCGACCAACCCGCGGGGATTTTGGCCTCAACTGAAAATGAAACCGGGTAAACGCGCCTGGGGCTCTCGCCGGTCGAGGGTCTGGGCGGGTCCCGCGGCCTCAGGGAGGCGGATCTCGGACCCGGAGACTCGGGGCGACCCGGGCCGTACGTGGGGGATGGGGAGTCGTGACCTGCGCCCCGGGCCGGGGTCACTCACCGGCCTCGCTCTGGTTGTAGTAGCCGCGCAGGTTCCGCAGGCTCTCTCGGTCAGTCTGTGCCTGGGCCTTGTAGATCTGTGTGTTCCGGTCCCAATACTCCGGCCCCTCCTGCTCTATCCACGGCGCCCGCGGCTCCTCTCTCGGACTCGCGGCGTCGCTGTCGAACCTCACGAACTGGGTGTCGTCCACGTAGCCCACTGAGATGAAGCGGGGCTCCCCGCGGCCGGGCCGGGACACGGAGGTGTAGAAATACCTCATGGAGTGGGAGCCTGGGGGTGAGGAGGGGCTGAGACCCGCCCGACCCTCCTCCCGGCGCGGCTCCTCAGGTCCTGCGCCCCCGCCTGCGGTCCCCTCGCTCCTCCCGGCAGAGGCCATTTCCCTCCCGACCCGCACTCACCGGCCCAGGTCTCGGTCAGGGCCAGGGCCGCCGAGAGCAGCAGGAGGACGGTTCGGGGCGCCATGACCAGCATCTCGGCGTCTGAGGAGACTCTGAGTCCGGGTGGGTGCGTGGGGACTTTAGAACTGGGACCGCGGCGACGCTGATTGGCTTCTCTAGATATCCAATACCCAATGGGAGTGGGAAGTGGGGACGCGTCACGAGTATCCTGGAAGAAGGACCCGACACAAGTTGGGAGAAGAAGTGAAACTCAGGGGAGTGGGGAATCCCCAACGCTGCGCCTCCCCATTGCAGACGCGGCCCTCGGAGCCTGAGACCCTGAGAGCCCCGTCCGGGACCTGGGACTTCGTCCTGATCCCTCTTCTCCTACACCAAGCC	-	novel	NA	P-0030136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	363	34	0				ENST00000412585	NM_005514.6	?-115/362		1-3/8	1	2	FACETS	0.915	0.877	0.952	1	0.997	1	CLONAL	4	TRUE	1	0.312848333661577	2		34	634	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700262	117700262	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	42	532	0	ENST00000368508.3:c.2557C>T	p.Gln853Ter	p.Q853*	ENST00000368508	NM_002944.2	853	Caa/Taa	17/43	1	2	FACETS	0.655	0.547	0.774	0.655	0.547	0.774	SUBCLONAL	1	TRUE	1	0.312848333661577	2		532	410	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412690	139412690	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	479	1226	0	ENST00000277541.6:c.1154C>G	p.Ser385Cys	p.S385C	ENST00000277541	NM_017617.3	385	tCc/tGc	7/34	0.312848333661577	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	TRUE	0	0.312848333661577	3		1226	1167	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266604	41266614	+	frameshift_variant	Frame_Shift_Del	DEL	ATGCAGTTGTA	ATGCAGTTGTA	-	novel	NA	P-0030136-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	77	509	0	ENST00000349496.5:c.402_412del	p.His134GlnfsTer4	p.H134Qfs*4	ENST00000349496	NM_001904.3	134	cATGCAGTTGTA/c	4/15	1	2	FACETS	0.849	0.746	0.959	0.849	0.746	0.959	CLONAL	1	TRUE	1	0.312848333661577	2		509	580	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272308	38272308	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs869320694	NA	P-0030349-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	242	655	0	ENST00000425967.3:c.2059A>G	p.Lys687Glu	p.K687E	ENST00000425967	NM_001174067.1	687	Aag/Gag	15/19	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.589177965834013	2		655	783	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191636	10191636	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030349-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	203	582	0	ENST00000256474.2:c.629G>T	p.Arg210Leu	p.R210L	ENST00000256474	NM_000551.3	210	cGg/cTg	3/3	1	2	FACETS	0.961	0.894	1	0.961	0.894	1	CLONAL	1	TRUE	1	0.589177965834013	2		582	717	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0121475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	158	768	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.906	0.841	0.971	0.906	0.841	0.971	CLONAL	1	NA	1	0.91821728462455	2		768	380	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46736330	46736330	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0121475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	26	445	0	ENST00000371975.4:c.1043-1G>T		p.X348_splice	ENST00000371975	NM_003579.3	348			1	2	FACETS	0.195	0.154	0.241	0.195	0.154	0.241	SUBCLONAL	1	NA	1	0.91821728462455	2		445	291	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958594	175958594	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0121475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	80	466	0	ENST00000367669.3:c.1751A>T	p.Asp584Val	p.D584V	ENST00000367669	NM_022457.5	584	gAt/gTt	16/20	1	2	FACETS	0.968	0.873	1	0.968	0.873	1	CLONAL	1	NA	1	0.91821728462455	2		466	180	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380719	118380719	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	44	419	0	ENST00000534358.1:c.10957C>A	p.Leu3653Ile	p.L3653I	ENST00000534358	NM_005933.3	3653	Ctt/Att	30/36	1	2	FACETS	0.819	0.706	0.936	0.819	0.706	0.936	CLONAL	1	NA	1	0.91821728462455	2		419	117	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117707003	117707003	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0121475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	162	635	0	ENST00000368508.3:c.2147G>C	p.Ser716Thr	p.S716T	ENST00000368508	NM_002944.2	716	aGc/aCc	15/43	0.564634328846095	4	FACETS	1	0.987	1	0.449	0.414	0.484	CLONAL	1	NA	1	0.91821728462455	4		635	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577112	7577112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	717	654	0	ENST00000269305.4:c.826G>A	p.Ala276Thr	p.A276T	ENST00000269305	NM_001126112.2	276	Gcc/Acc	8/11	0.957256266239688	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.957256266239688	1		654	775	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032677-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	513	430	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.204737477344433	7	FACETS	0.939	0.902	0.976	0.939	0.902	0.976	CLONAL	7	TRUE	0	0.204737477344433	7		430	1153	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0032677-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	248	1171	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.204737477344433	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.204737477344433	3		1171	1176	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962529	100962529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767360879	NA	P-0032677-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	150	552	2	ENST00000325455.5:c.1868G>A	p.Arg623His	p.R623H	ENST00000325455	NM_001202474.3	623	cGc/cAc	3/8	0.204737477344433	4	FACETS	0.857	0.782	0.935	0.857	0.782	0.935	CLONAL	2	TRUE	2	0.204737477344433	4		554	1030	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425572	49425572	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032677-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	151	976	2	ENST00000301067.7:c.12916C>T	p.His4306Tyr	p.H4306Y	ENST00000301067	NM_003482.3	4306	Cat/Tat	39/54	0.197165292697203	3	FACETS	1	0.975	1	0.397	0.362	0.434	CLONAL	1	TRUE	0	0.204737477344433	3		978	1365	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438302	110438302	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032677-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	27	290	0	ENST00000375856.3:c.99G>C	p.Lys33Asn	p.K33N	ENST00000375856	NM_003749.2	33	aaG/aaC	1/2	0.204737477344433	6	FACETS	0.801	0.637	0.99	0.2	0.159	0.248	CLONAL	1	TRUE	2	0.204737477344433	6		290	464	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457820	69457822	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0035085-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	30	505	0	ENST00000227507.2:c.227_229del	p.Glu76del	p.E76del	ENST00000227507	NM_053056.2	74	GAG/-	2/5	0.160013491175645	3	FACETS	1	0.842	1	0.526	0.424	0.642	CLONAL	1	TRUE	1	0.160013491175645	3		505	385	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030479	49030479	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035085-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	11	282	0	ENST00000267163.4:c.1959del	p.Val654CysfsTer4	p.V654Cfs*4	ENST00000267163	NM_000321.2	652	Aaa/aa	19/27	0.160013491175645	1	FACETS	1	0.709	1	1	0.709	1	CLONAL	1	TRUE	0	0.160013491175645	1		282	124	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443613	29443613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519783	NA	P-0035085-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	31	867	2	ENST00000389048.3:c.3604G>A	p.Gly1202Arg	p.G1202R	ENST00000389048	NM_004304.4	1202	Gga/Aga	23/29	0.160013491175645	3	FACETS	0.978	0.791	1	0.489	0.395	0.595	CLONAL	1	TRUE	1	0.160013491175645	3		869	428	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057937	27057937	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035085-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	56	719	0	ENST00000324856.7:c.1650del	p.Tyr551ThrfsTer68	p.Y551Tfs*68	ENST00000324856	NM_006015.4	549	Ccc/cc	3/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.160013491175645	2		719	525	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631917	90631918	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs747216375	NA	P-0035085-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	56	956	4	ENST00000330062.3:c.435dup	p.Thr146AspfsTer126	p.T146Dfs*126	ENST00000330062	NM_002168.2	145	-/G	4/11	1	2	FACETS	0.79	0.678	0.912	1	0.97	1	CLONAL	2	TRUE	1	0.160013491175645	2		960	443	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11181418	11181418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761004954	NA	P-0035085-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	30	818	1	ENST00000361445.4:c.6818C>T	p.Pro2273Leu	p.P2273L	ENST00000361445	NM_004958.3	2273	cCg/cTg	49/58	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.160013491175645	2		819	322	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089123	37089125	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs63751247	NA	P-0035085-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	14	501	0	ENST00000231790.2:c.1852_1854del	p.Lys618del	p.K618del	ENST00000231790	NM_000249.3	615	ctGAAg/ctg	16/19	1	2	FACETS	0.72	0.52	0.962	0.72	0.52	0.962	CLONAL	1	TRUE	1	0.160013491175645	2		501	243	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440320	187440320	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1230004461	NA	P-0035085-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	40	716	2	ENST00000232014.4:c.2047G>A	p.Ala683Thr	p.A683T	ENST00000232014	NM_001130845.1	683	Gcc/Acc	10/10	0.160013491175645	5	FACETS	1	0.953	1	0.74	0.615	0.878	CLONAL	1	TRUE	3	0.160013491175645	5		718	419	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444987	49444987	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035085-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	42	801	1	ENST00000301067.7:c.2479del	p.Gln827AsnfsTer103	p.Q827Nfs*103	ENST00000301067	NM_003482.3	827	Caa/aa	10/54	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.160013491175645	2		802	496	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781860	3781860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375557093	NA	P-0035085-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	40	844	2	ENST00000262367.5:c.4807G>A	p.Ala1603Thr	p.A1603T	ENST00000262367	NM_004380.2	1603	Gcc/Acc	29/31	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.160013491175645	2		846	460	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035206	6035206	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035085-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	22	541	0	ENST00000265849.7:c.862C>T	p.Gln288Ter	p.Q288*	ENST00000265849	NM_000535.5	288	Cag/Tag	8/15	1	2	FACETS	1	0.806	1	1	0.806	1	CLONAL	1	TRUE	1	0.160013491175645	2		541	264	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883774	37883774	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035085-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	50	1073	0	ENST00000269571.5:c.3391del	p.Leu1131Ter	p.L1131*	ENST00000269571		1129	gCc/gc	26/27	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.160013491175645	2		1073	525	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317915	8317915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748481193	NA	P-0035085-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	12	507	0	ENST00000356435.5:c.5698G>A	p.Ala1900Thr	p.A1900T	ENST00000356435		1900	Gca/Aca	35/35	1	2	FACETS	0.725	0.509	0.989	0.725	0.509	0.989	CLONAL	1	TRUE	1	0.160013491175645	2		507	207	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434973	110434973	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035085-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	40	1026	4	ENST00000375856.3:c.3428del	p.Gly1143AlafsTer116	p.G1143Afs*116	ENST00000375856	NM_003749.2	1143	gGc/gc	1/2	NA	2	FACETS	1	0.921	1			1	INDETERMINATE	1	TRUE	NA	0.160013491175645	2		1030	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578436	7578439	+	frameshift_variant	Frame_Shift_Del	DEL	TGCT	TGCT	-	novel	NA	P-0035085-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	86	1109	0	ENST00000269305.4:c.491_494del	p.Lys164SerfsTer5	p.K164Sfs*5	ENST00000269305	NM_001126112.2	164	aAGCAg/ag	5/11	1	2	FACETS	1	0.955	1	1	0.987	1	CLONAL	2	TRUE	1	0.160013491175645	2		1109	467	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739002	145739002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769675968	NA	P-0035085-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	46	931	0	ENST00000428558.2:c.2153C>T	p.Ala718Val	p.A718V	ENST00000428558	NM_004260.3	718	gCg/gTg	13/22	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.160013491175645	2		931	556	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446827	49446827	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373271756	NA	P-0035085-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	28	896	2	ENST00000301067.7:c.983C>T	p.Ala328Val	p.A328V	ENST00000301067	NM_003482.3	328	gCg/gTg	8/54	1	2	FACETS	0.738	0.589	0.909	0.738	0.589	0.909	CLONAL	1	TRUE	1	0.160013491175645	2		898	474	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610403	10610403	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035085-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	67	1021	0	ENST00000171111.5:c.307T>C	p.Ser103Pro	p.S103P	ENST00000171111	NM_203500.1	103	Tcc/Ccc	2/6	0.160013491175645	1	FACETS	0.757	0.659	0.863	1	0.973	1	SUBCLONAL	2	TRUE	0	0.160013491175645	1		1021	509	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540560	187540560	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035085-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	27	544	0	ENST00000441802.2:c.7180A>T	p.Ile2394Phe	p.I2394F	ENST00000441802	NM_005245.3	2394	Att/Ttt	10/27	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.160013491175645	2		544	229	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119809	70119809	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771635102	NA	P-0035085-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	50	786	0	ENST00000245479.2:c.811C>T	p.Arg271Cys	p.R271C	ENST00000245479	NM_000346.3	271	Cgc/Tgc	3/3	1	2	FACETS	0.933	0.795	1	1	0.973	1	CLONAL	2	TRUE	1	0.160013491175645	2		786	335	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500304	99500304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45512296	NA	P-0035085-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	34	860	1	ENST00000268035.6:c.3737G>A	p.Arg1246His	p.R1246H	ENST00000268035	NM_000875.3	1246	cGc/cAc	21/21	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.160013491175645	2		861	392	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427784	72427784	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035085-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	25	441	0	ENST00000477973.2:c.704del	p.Arg236GlyfsTer2	p.R236Gfs*2	ENST00000477973	NM_012234.5	236	Cgg/gg	4/4	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.160013491175645	2		441	256	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210687	2210687	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745691240	NA	P-0035085-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	44	935	2	ENST00000398665.3:c.1184G>A	p.Arg395His	p.R395H	ENST00000398665	NM_032482.2	395	cGc/cAc	14/28	0.160013491175645	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.160013491175645	1		937	404	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50483699	50483699	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035085-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	19	613	0	ENST00000394963.4:c.804T>A	p.Asp268Glu	p.D268E	ENST00000394963	NM_003076.4	268	gaT/gaA	7/13	1	2	FACETS	0.679	0.514	0.872	0.679	0.514	0.872	SUBCLONAL	1	TRUE	1	0.160013491175645	2		613	350	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640830	3640830	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776329769	NA	P-0035085-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	36	957	0	ENST00000294008.3:c.2809G>A	p.Gly937Arg	p.G937R	ENST00000294008	NM_032444.2	937	Ggg/Agg	12/15	1	2	FACETS	0.93	0.764	1	0.93	0.764	1	CLONAL	1	TRUE	1	0.160013491175645	2		957	484	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17124937	17124937	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035085-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	36	718	0	ENST00000285071.4:c.785T>C	p.Leu262Pro	p.L262P	ENST00000285071	NM_144997.5	262	cTg/cCg	8/14	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.160013491175645	2		718	371	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370172	40370172	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035085-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	30	1054	3	ENST00000293328.3:c.1166G>A	p.Arg389His	p.R389H	ENST00000293328	NM_012448.3	389	cGc/cAc	9/19	1	2	FACETS	0.942	0.759	1	0.942	0.759	1	CLONAL	1	TRUE	1	0.160013491175645	2		1057	398	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41228566	41228566	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035085-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	12	576	0	ENST00000357654.3:c.4423G>C	p.Asp1475His	p.D1475H	ENST00000357654	NM_007294.3	1475	Gac/Cac	13/23	1	2	FACETS	0.937	0.661	1	0.937	0.661	1	CLONAL	1	TRUE	1	0.160013491175645	2		576	160	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626953	158626955	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0035085-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	22	583	0	ENST00000263640.3:c.715_717del	p.Ser239del	p.S239del	ENST00000263640	NM_001105.4	239	TCC/-	7/11	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.160013491175645	2		583	229	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582156	189582156	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035085-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	37	643	0	ENST00000264731.3:c.715G>C	p.Glu239Gln	p.E239Q	ENST00000264731	NM_003722.4	239	Gag/Cag	5/14	0.160013491175645	5	FACETS	1	0.945	1	0.706	0.583	0.844	CLONAL	1	TRUE	3	0.160013491175645	5		643	406	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876582	35876582	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035085-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	19	591	0	ENST00000303115.3:c.1374C>A	p.Asn458Lys	p.N458K	ENST00000303115	NM_002185.3	458	aaC/aaA	8/8	0.160013491175645	5	FACETS	1	0.808	1	0.358	0.272	0.46	CLONAL	1	TRUE	2	0.160013491175645	5		591	274	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180241	27180241	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035085-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	24	656	0	ENST00000380036.4:c.905G>A	p.Cys302Tyr	p.C302Y	ENST00000380036	NM_000459.3	302	tGc/tAc	7/23	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.160013491175645	2		656	245	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631839	90631839	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519906	NA	P-0035161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	111	749	0	ENST00000330062.3:c.514A>T	p.Arg172Trp	p.R172W	ENST00000330062	NM_002168.2	172	Agg/Tgg	4/11	1	2	FACETS	0.877	0.787	0.972	0.877	0.787	0.972	CLONAL	1	TRUE	1	0.289712089783853	2		749	874	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0035161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	19	426	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	1	2	FACETS	0.917	0.703	1	0.917	0.703	1	CLONAL	1	TRUE	1	0.289712089783853	2		426	143	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52621447	52621447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035831-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	70	421	0	ENST00000394830.3:c.2970del	p.Glu991LysfsTer17	p.E991Kfs*17	ENST00000394830	NM_018313.4	990	aaA/aa	20/30	0.384046400187758	1	FACETS	0.923	0.812	1	0.923	0.812	1	CLONAL	1	TRUE	0	0.384046400187758	1		421	319	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058642	47058647	+	inframe_deletion	In_Frame_Del	DEL	TCTTAA	TCTTAA	-	novel	NA	P-0035831-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	187	631	0	ENST00000409792.3:c.7631_7636del	p.Ile2544_Lys2545del	p.I2544_K2545del	ENST00000409792	NM_014159.6	2544	aTTAAGAag/aag	21/21	0.384046400187758	1	FACETS	0.904	0.836	0.975	0.904	0.836	0.975	CLONAL	1	TRUE	0	0.384046400187758	1		631	870	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	179	429	0				ENST00000310581	NM_198253.2	-/1132			0.342418794774764	1	FACETS	0.642	0.6	0.685	0.642	0.6	0.685	INDETERMINATE	1	TRUE	0	0.823611303577791	1		429	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0036851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	328	691	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.823611303577791	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.823611303577791	1		691	411	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303212	11303212	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	277	530	0	ENST00000361445.4:c.1371C>A	p.Asp457Glu	p.D457E	ENST00000361445	NM_004958.3	457	gaC/gaA	9/58	0.579605421168081	3	FACETS	0.816	0.774	0.858	0.816	0.774	0.858	CLONAL	2	TRUE	1	0.823611303577791	3		530	582	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543654	9543654	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1215512353	NA	P-0036851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	138	474	0	ENST00000353224.5:c.1500T>A	p.Asp500Glu	p.D500E	ENST00000353224	NM_177990.2	500	gaT/gaA	6/10	1	2	FACETS	0.926	0.853	1	0.926	0.853	1	CLONAL	1	TRUE	1	0.823611303577791	2		474	362	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724133	61724133	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036851-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	90	296	0	ENST00000401558.2:c.769G>T	p.Val257Phe	p.V257F	ENST00000401558	NM_003400.3	257	Gtt/Ttt	10/25	0.680114713951807	6	FACETS	1	0.917	1	0.512	0.46	0.566	CLONAL	2	FALSE	2	0.756669878472354	6		296	292	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0036946-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	135	411	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.327258950698421	4	FACETS	0.854	0.779	0.932	0.854	0.779	0.932	CLONAL	2	TRUE	2	0.360879963791807	4		411	596	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0036946-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	149	784	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.360879963791807	3	FACETS	0.894	0.816	0.977	0.447	0.408	0.489	CLONAL	1	TRUE	1	0.360879963791807	3		784	1090	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026078	48026078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs188252826	NA	P-0036946-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	141	256	1	ENST00000234420.5:c.956C>T	p.Thr319Met	p.T319M	ENST00000234420	NM_000179.2	319	aCg/aTg	4/10	0.327258950698421	4	FACETS	0.849	0.776	0.926	0.849	0.776	0.926	CLONAL	2	TRUE	2	0.360879963791807	4		257	626	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849152	156849152	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs768180688	NA	P-0036946-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	239	524	0	ENST00000524377.1:c.2044C>T	p.Arg682Cys	p.R682C	ENST00000524377	NM_002529.3	682	Cgt/Tgt	15/17	0.360879963791807	3	FACETS	0.966	0.905	1	0.966	0.905	1	CLONAL	2	TRUE	1	0.360879963791807	3		524	809	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036946-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	286	571	0	ENST00000269305.4:c.569del	p.Pro190LeufsTer57	p.P190Lfs*57	ENST00000269305	NM_001126112.2	190	cCt/ct	6/11	0.352731916634405	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.360879963791807	2		571	774	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604703	48604703	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036946-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	214	284	0	ENST00000342988.3:c.1525T>C	p.Trp509Arg	p.W509R	ENST00000342988	NM_005359.5	509	Tgg/Cgg	12/12	0.352731916634405	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.360879963791807	2		284	552	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420213	49420213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267607237	NA	P-0036946-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	326	653	1	ENST00000301067.7:c.15536G>A	p.Arg5179His	p.R5179H	ENST00000301067	NM_003482.3	5179	cGt/cAt	48/54	0.327258950698421	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.360879963791807	4		654	1170	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106561	27106561	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036946-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	322	654	0	ENST00000324856.7:c.6172G>T	p.Glu2058Ter	p.E2058*	ENST00000324856	NM_006015.4	2058	Gaa/Taa	20/20	0.360879963791807	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	1	0.360879963791807	3		654	1048	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630125	187630125	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs201488687	NA	P-0036946-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	456	464	0	ENST00000441802.2:c.857A>G	p.Asn286Ser	p.N286S	ENST00000441802	NM_005245.3	286	aAt/aGt	2/27	0.360879963791807	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	1	0.360879963791807	4		464	1083	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945478	151945478	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036946-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	68	275	0	ENST00000262189.6:c.2041G>T	p.Glu681Ter	p.E681*	ENST00000262189	NM_170606.2	681	Gaa/Taa	14/59	0.360879963791807	3	FACETS	0.963	0.84	1	0.481	0.42	0.548	CLONAL	1	TRUE	1	0.360879963791807	3		275	462	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953083	2953083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1322611135	NA	P-0036946-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	60	696	0	ENST00000396946.4:c.2857G>A	p.Glu953Lys	p.E953K	ENST00000396946	NM_032415.4	953	Gag/Aag	22/25	0.360879963791807	3	FACETS	0.364	0.313	0.421	0.182	0.156	0.211	SUBCLONAL	1	TRUE	1	0.360879963791807	3		696	1077	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221616	36221616	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036946-T08-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	154	667	0	ENST00000222270.7:c.5285G>A	p.Arg1762His	p.R1762H	ENST00000222270	NM_014727.1	1762	cGt/cAt	26/37	0.360879963791807	3	FACETS	0.947	0.865	1	0.473	0.432	0.516	CLONAL	1	TRUE	1	0.360879963791807	3		667	1064	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710903	117710903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	44	434	0	ENST00000368508.3:c.1369G>A	p.Asp457Asn	p.D457N	ENST00000368508	NM_002944.2	457	Gac/Aac	12/43	1	2	FACETS	0.162	0.135	0.192	0.162	0.135	0.192	SUBCLONAL	1	TRUE	1	0.918031512974916	2		434	591	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888166	112888166	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121918461	NA	P-0037271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	297	593	0	ENST00000351677.2:c.182A>C	p.Asp61Ala	p.D61A	ENST00000351677	NM_002834.3	61	gAt/gCt	3/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.918031512974916	2		593	629	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920337	134920337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141607080	NA	P-0037271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	49	534	1	ENST00000398015.3:c.2152G>A	p.Val718Met	p.V718M	ENST00000398015	NM_004441.4	718	Gtg/Atg	12/16	1	2	FACETS	0.172	0.145	0.202	0.172	0.145	0.202	SUBCLONAL	1	TRUE	1	0.918031512974916	2		535	619	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514616	103514616	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	91	381	0	ENST00000355739.4:c.1117A>G	p.Asn373Asp	p.N373D	ENST00000355739	NM_000123.3	373	Aac/Gac	8/15	0.864257499634391	3	FACETS	0.435	0.386	0.487	0.217	0.193	0.244	SUBCLONAL	1	TRUE	1	0.918031512974916	3		381	665	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574235	95574235	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	170	365	0	ENST00000393063.1:c.2632G>A	p.Val878Ile	p.V878I	ENST00000393063	NM_030621.3	878	Gtt/Att	17/28	1	2	FACETS	0.942	0.878	1	0.942	0.878	1	CLONAL	1	TRUE	1	0.918031512974916	2		365	393	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10305569	10305569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	41	221	0	ENST00000340748.4:c.7G>A	p.Ala3Thr	p.A3T	ENST00000340748		3	Gcg/Acg	1/40	1	2	FACETS	0.25	0.208	0.295	0.25	0.208	0.295	SUBCLONAL	1	TRUE	1	0.918031512974916	2		221	358	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211972	36211972	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	496	828	0	ENST00000222270.7:c.1723C>A	p.Gln575Lys	p.Q575K	ENST00000222270	NM_014727.1	575	Cag/Aag	3/37	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.918031512974916	2		828	1027	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375172	31375172	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	115	573	0	ENST00000328111.2:c.569G>T	p.Arg190Leu	p.R190L	ENST00000328111	NM_006892.3	190	cGc/cTc	6/23	0.777973648021066	3	FACETS	0.336	0.302	0.373	0.168	0.151	0.187	SUBCLONAL	1	TRUE	1	0.918031512974916	3		573	1087	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380514	31380514	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	531	487	0	ENST00000328111.2:c.1004G>C	p.Trp335Ser	p.W335S	ENST00000328111	NM_006892.3	335	tGg/tCg	9/23	0.777973648021066	3	FACETS	0.946	0.915	0.977	0.946	0.915	0.977	CLONAL	2	TRUE	1	0.918031512974916	3		487	892	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250831	26250831	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0037271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	29	323	0	ENST00000446824.2:c.3G>A	p.Met1?	p.M1?	ENST00000446824	NM_021018.2	1	atG/atA	1/1	1	2	FACETS	0.183	0.146	0.224	0.183	0.146	0.224	SUBCLONAL	1	TRUE	1	0.918031512974916	2		323	346	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039822	47039822	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	56	731	0	ENST00000377604.3:c.1165A>G	p.Met389Val	p.M389V	ENST00000377604	NM_001204468.1	389	Atg/Gtg	12/24	0.863847525978857	1	FACETS	0.132	0.113	0.153	0.132	0.113	0.153	SUBCLONAL	1	TRUE	0	0.918031512974916	1		731	501	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918982	76918982	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0037271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	64	519	1	ENST00000373344.5:c.4009A>T	p.Arg1337Ter	p.R1337*	ENST00000373344	NM_000489.3	1337	Aga/Tga	12/35	0.863847525978857	1	FACETS	0.175	0.151	0.2	0.175	0.151	0.2	SUBCLONAL	1	TRUE	0	0.918031512974916	1		520	432	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937656	76937656	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	247	601	0	ENST00000373344.5:c.3092del	p.Gly1031AlafsTer2	p.G1031Afs*2	ENST00000373344	NM_000489.3	1031	gGc/gc	9/35	0.863847525978857	1	FACETS	0.776	0.741	0.81	0.776	0.741	0.81	SUBCLONAL	1	TRUE	0	0.918031512974916	1		601	375	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519896	NA	P-0037436-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	303	406	0	ENST00000281708.4:c.1514G>T	p.Arg505Leu	p.R505L	ENST00000281708	NM_033632.3	505	cGc/cTc	10/12	1	2	FACETS	0.874	0.83	0.919	1	0.996	1	CLONAL	2	TRUE	1	0.5	2		406	693	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0037730-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	33	441	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.392523955872447	4	FACETS	1	0.854	1	1	0.854	1	CLONAL	2	TRUE	2	0.392523955872447	4		441	114	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268970	115268970	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037730-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	26	435	0	ENST00000438362.2:c.1640A>T	p.Gln547Leu	p.Q547L	ENST00000438362	NM_001242891.1	547	cAg/cTg	14/20	0.351989329280495	4	FACETS	1	0.874	1	0.566	0.453	0.693	CLONAL	1	TRUE	2	0.392523955872447	4		435	163	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948520	71948532	+	frameshift_variant	Frame_Shift_Del	DEL	CGGGGCCGTGGTG	CGGGGCCGTGGTG	-	novel	NA	P-0037730-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	31	1087	0	ENST00000298229.2:c.3232_3244del	p.Arg1078GlyfsTer49	p.R1078Gfs*49	ENST00000298229	NM_001567.3	1078	CGGGGCCGTGGTGgg/gg	26/28	0.392523955872447	3	FACETS	0.652	0.529	0.79	0.326	0.264	0.395	SUBCLONAL	1	TRUE	1	0.392523955872447	3		1087	290	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120554432	120554432	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037730-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	15	135	0	ENST00000229340.5:c.23T>C	p.Leu8Pro	p.L8P	ENST00000229340	NM_006861.6	8	cTc/cCc	1/6	1	2	FACETS	0.346	0.253	0.457	0.346	0.253	0.457	SUBCLONAL	1	TRUE	1	0.392523955872447	2		135	221	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240220	41240220	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037730-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	10	139	0	ENST00000379561.5:c.130C>T	p.Pro44Ser	p.P44S	ENST00000379561	NM_002015.3	44	Ccg/Tcg	1/3	0.392523955872447	3	FACETS	0.321	0.217	0.451	0.16	0.108	0.226	SUBCLONAL	1	TRUE	1	0.392523955872447	3		139	190	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911258	29911258	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037730-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	10	528	2	ENST00000376809.5:c.557G>T	p.Gly186Val	p.G186V	ENST00000376809	NM_002116.7	186	gGc/gTc	3/8	0.392523955872447	7	FACETS	0.612	0.415	0.858	0.122	0.083	0.172	SUBCLONAL	1	TRUE	2	0.392523955872447	7		530	165	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0038280-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	168	848	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.400414973392039	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.400414973392039	1		848	619	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0038280-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	132	286	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.400414973392039	2		286	599	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038280-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	132	741	2	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	0.400414973392039	1	FACETS	0.975	0.889	1	0.975	0.889	1	CLONAL	1	TRUE	0	0.400414973392039	1		743	541	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0038280-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	132	696	1	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	0.400414973392039	1	FACETS	0.917	0.836	1	0.917	0.836	1	CLONAL	1	TRUE	0	0.400414973392039	1		697	575	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138570	2138570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45517423	NA	P-0038280-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	149	862	0	ENST00000219476.3:c.5383C>T	p.Arg1795Cys	p.R1795C	ENST00000219476	NM_000548.3	1795	Cgc/Tgc	42/42	1	2	FACETS	0.822	0.751	0.897	0.822	0.751	0.897	CLONAL	1	TRUE	1	0.400414973392039	2		862	905	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744385	41744385	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038280-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	147	864	1	ENST00000301178.4:c.1010del	p.Pro337LeufsTer29	p.P337Lfs*29	ENST00000301178	NM_021913.4	335	ggC/gg	8/20	1	2	FACETS	0.969	0.886	1	0.969	0.886	1	CLONAL	1	TRUE	1	0.400414973392039	2		865	758	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772951	135772951	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs118203724	NA	P-0038280-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	99	469	0	ENST00000298552.3:c.2672del	p.Asn891ThrfsTer40	p.N891Tfs*40	ENST00000298552	NM_001162426.1	891	aAc/ac	21/23	1	2	FACETS	0.762	0.681	0.848	0.762	0.681	0.848	SUBCLONAL	1	TRUE	1	0.400414973392039	2		469	649	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038280-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	139	625	1	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.400414973392039	2		626	558	SUCCESS
YES1	7525	MSKCC	GRCh37	18	751726	751726	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1010928891	NA	P-0038280-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	91	238	0	ENST00000314574.4:c.350G>T	p.Arg117Ile	p.R117I	ENST00000314574	NM_005433.3	117	aGa/aTa	3/12	0.0916596772184868	4	FACETS	1	0.952	1	0.564	0.502	0.63	INDETERMINATE	1	TRUE	2	0.400414973392039	4		238	564	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396839	396839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145608130	NA	P-0038280-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	193	962	1	ENST00000262320.3:c.187C>T	p.Arg63Cys	p.R63C	ENST00000262320	NM_003502.3	63	Cgc/Tgc	2/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.400414973392039	2		963	915	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439770	51439772	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0038280-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	135	539	0	ENST00000262662.1:c.338_340del	p.Glu113del	p.E113del	ENST00000262662		112	aAAGaa/aaa	4/4	0.400414973392039	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.400414973392039	1		539	425	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863054	56863054	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1266824391	NA	P-0038280-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	78	509	0	ENST00000519728.1:c.327del	p.Glu110LysfsTer15	p.E110Kfs*15	ENST00000519728	NM_002350.3	107	acA/ac	5/13	1	2	FACETS	0.494	0.433	0.559	0.494	0.433	0.559	SUBCLONAL	1	TRUE	1	0.400414973392039	2		509	789	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056047	26056047	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038280-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	111	502	0	ENST00000343677.2:c.610A>G	p.Lys204Glu	p.K204E	ENST00000343677	NM_005319.3	204	Aag/Gag	1/1	0.190527762282824	4	FACETS	1	0.98	1	0.675	0.609	0.745	INDETERMINATE	1	TRUE	2	0.400414973392039	4		502	575	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681031	117681031	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038280-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	126	518	0	ENST00000368508.3:c.3589T>C	p.Tyr1197His	p.Y1197H	ENST00000368508	NM_002944.2	1197	Tat/Cat	23/43	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.400414973392039	2		518	569	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911423	39911424	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0038280-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	173	685	0	ENST00000378444.4:c.5206_5207del	p.Leu1736AlafsTer12	p.L1736Afs*12	ENST00000378444	NM_001123385.1	1736	CTg/g	15/15	0.400414973392039	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.400414973392039	1		685	669	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281045	49281045	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200483129	NA	P-0038280-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	42	624	0	ENST00000282018.3:c.92G>A	p.Cys31Tyr	p.C31Y	ENST00000282018	NM_020377.2	31	tGc/tAc	1/1	1	2	FACETS	0.255	0.212	0.303	0.255	0.212	0.303	SUBCLONAL	1	TRUE	1	0.400414973392039	2		624	824	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40860078	40860078	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038280-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	149	639	1	ENST00000428826.2:c.1558A>G	p.Asn520Asp	p.N520D	ENST00000428826		520	Aac/Gac	15/21	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.400414973392039	2		640	709	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4094483	4094483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038280-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	211	970	0	ENST00000262948.5:c.1060C>T	p.Pro354Ser	p.P354S	ENST00000262948	NM_030662.3	354	Cca/Tca	10/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.400414973392039	2		970	862	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113790	11113790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038280-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	199	850	0	ENST00000358026.2:c.1898C>T	p.Ala633Val	p.A633V	ENST00000358026	NM_001128849.1	633	gCc/gTc	12/36	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.400414973392039	2		850	869	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130319	11130319	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038280-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	199	843	0	ENST00000358026.2:c.2558T>C	p.Phe853Ser	p.F853S	ENST00000358026	NM_001128849.1	853	tTc/tCc	18/36	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.400414973392039	2		843	933	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610656	52610656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038280-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	184	568	0	ENST00000394830.3:c.3517C>T	p.His1173Tyr	p.H1173Y	ENST00000394830	NM_018313.4	1173	Cac/Tac	23/30	0.400414973392039	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.400414973392039	1		568	556	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039575	180039575	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038280-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	190	993	0	ENST00000261937.6:c.3468del	p.Lys1157ArgfsTer96	p.K1157Rfs*96	ENST00000261937	NM_182925.4	1156	ccC/cc	26/30	1	2	FACETS	0.985	0.911	1	0.985	0.911	1	CLONAL	1	TRUE	1	0.400414973392039	2		993	963	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	21	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.989	0.77	1	0.989	0.77	1	CLONAL	1	TRUE	1	0.305421691742676	2		429	139	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983113	201983127	+	inframe_deletion	In_Frame_Del	DEL	ACAGCAACATGACCT	ACAGCAACATGACCT	-	novel	NA	P-0040185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	124	661	0	ENST00000359651.3:c.964_978del	p.Ser322_Tyr326del	p.S322_Y326del	ENST00000359651		321	aACAGCAACATGACCTac/aac	7/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.305421691742676	2		661	702	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984406	201984407	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCAAGCGG	novel	NA	P-0040185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	121	660	0	ENST00000359651.3:c.1072_1079dup	p.Trp361GlnfsTer89	p.W361Qfs*89	ENST00000359651		357	-/TCAAGCGG	8/8	1	2	FACETS	0.937	0.846	1	0.937	0.846	1	CLONAL	1	TRUE	1	0.305421691742676	2		660	846	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244137	46244137	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	70	449	0	ENST00000334344.6:c.2231T>G	p.Val744Gly	p.V744G	ENST00000334344	NM_152641.2	744	gTt/gGt	15/21	1	2	FACETS	0.871	0.761	0.99	0.871	0.761	0.99	CLONAL	1	TRUE	1	0.305421691742676	2		449	526	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435120	49435136	+	frameshift_variant	Frame_Shift_Del	DEL	GCTTCAGGAACCCGTCC	GCTTCAGGAACCCGTCC	-	novel	NA	P-0040185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	116	706	0	ENST00000301067.7:c.6417_6433del	p.Asp2140AlafsTer9	p.D2140Afs*9	ENST00000301067	NM_003482.3	2139	gcGGACGGGTTCCTGAAGCcg/gccg	31/54	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.305421691742676	2		706	661	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919281	48919281	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs587778870	NA	P-0040185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	128	274	0	ENST00000267163.4:c.446C>G	p.Ser149Ter	p.S149*	ENST00000267163	NM_000321.2	149	tCa/tGa	4/27	0.217587675634846	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.305421691742676	4		274	483	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939033	48939033	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1160807049	NA	P-0040185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	112	283	0	ENST00000267163.4:c.865A>T	p.Lys289Ter	p.K289*	ENST00000267163	NM_000321.2	289	Aaa/Taa	9/27	0.217587675634846	4	FACETS	0.867	0.783	0.956	0.867	0.783	0.956	CLONAL	2	TRUE	2	0.305421691742676	4		283	552	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281106	49281106	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	179	585	0	ENST00000282018.3:c.153G>A	p.Trp51Ter	p.W51*	ENST00000282018	NM_020377.2	51	tgG/tgA	1/1	0.217587675634846	4	FACETS	0.904	0.835	0.977	0.904	0.835	0.977	CLONAL	2	TRUE	2	0.305421691742676	4		585	846	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250833	99250860	+	frameshift_variant	Frame_Shift_Del	DEL	TGAAGCGCCTGGAGAACTGCACGGTGAT	TGAAGCGCCTGGAGAACTGCACGGTGAT	ATCAC	novel	NA	P-0040185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	139	566	2	ENST00000268035.6:c.137_164delinsATCAC	p.Leu46HisfsTer91	p.L46Hfs*91	ENST00000268035	NM_000875.3	46	cTGAAGCGCCTGGAGAACTGCACGGTGATc/cATCACc	2/21	0.112022763274317	3	FACETS	1	0.986	1	0.717	0.653	0.783	INDETERMINATE	1	TRUE	1	0.305421691742676	3		568	732	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81973562	81973562	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762731399	NA	P-0040185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	86	615	0	ENST00000359376.3:c.3379C>A	p.Pro1127Thr	p.P1127T	ENST00000359376	NM_002661.3	1127	Cca/Aca	30/33	0.305421691742676	3	FACETS	0.751	0.664	0.846	0.376	0.332	0.423	SUBCLONAL	1	TRUE	1	0.305421691742676	3		615	864	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618622	37618622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	56	543	0	ENST00000447079.4:c.298C>T	p.Arg100Cys	p.R100C	ENST00000447079	NM_015083.1	100	Cgt/Tgt	1/14	0.305421691742676	1	FACETS	0.458	0.391	0.53	0.458	0.391	0.53	SUBCLONAL	1	TRUE	0	0.305421691742676	1		543	679	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129695	11129695	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	121	634	2	ENST00000358026.2:c.2501A>G	p.Tyr834Cys	p.Y834C	ENST00000358026	NM_001128849.1	834	tAc/tGc	17/36	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.305421691742676	2		636	755	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872207	45872207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	148	754	0	ENST00000391945.4:c.227C>T	p.Thr76Ile	p.T76I	ENST00000391945	NM_000400.3	76	aCt/aTt	4/23	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.305421691742676	2		754	821	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609664	46609664	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	77	763	0	ENST00000263734.3:c.2388G>C	p.Lys796Asn	p.K796N	ENST00000263734	NM_001430.4	796	aaG/aaC	15/16	1	2	FACETS	0.585	0.512	0.663	0.585	0.512	0.663	SUBCLONAL	1	TRUE	1	0.305421691742676	2		763	862	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46271023	46271023	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	146	583	0	ENST00000371998.3:c.3147C>G	p.Asp1049Glu	p.D1049E	ENST00000371998		1049	gaC/gaG	17/23	0.112022763274317	3	FACETS	1	0.985	1	0.689	0.629	0.751	INDETERMINATE	1	TRUE	1	0.305421691742676	3		583	800	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412982	49412982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	111	660	0	ENST00000418115.1:c.41G>A	p.Gly14Glu	p.G14E	ENST00000418115	NM_001664.2	14	gGa/gAa	2/5	1	2	FACETS	0.898	0.807	0.995	0.898	0.807	0.995	CLONAL	1	TRUE	1	0.305421691742676	2		660	809	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426844	6426845	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0040185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	48	414	0	ENST00000356142.4:c.37_38delinsTT	p.Ala13Phe	p.A13F	ENST00000356142	NM_018890.3	13	GCt/TTt	2/7	0.305421691742676	3	FACETS	0.524	0.442	0.614	0.262	0.221	0.307	SUBCLONAL	1	TRUE	1	0.305421691742676	3		414	692	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199469669	NA	P-0040185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	180	268	0	ENST00000374080.3:c.130G>T	p.Gly44Cys	p.G44C	ENST00000374080		44	Ggt/Tgt	2/45	0.173722447528223	2	FACETS	0.856	0.797	0.915			1	INDETERMINATE	3	TRUE	NA	0.305421691742676	2		268	459	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040843-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	20	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	TRUE	1	0.231563448619535	2		429	153	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040843-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	147	738	1	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.174669835791257	2	FACETS	0.781	0.713	0.852	0.781	0.713	0.852	SUBCLONAL	2	TRUE	0	0.231563448619535	2		739	813	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101612	27101612	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040843-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	75	824	0	ENST00000324856.7:c.4899del	p.Met1634Ter	p.M1634*	ENST00000324856	NM_006015.4	1632	Ccc/cc	18/20	1	2	FACETS	0.7	0.612	0.796	0.7	0.612	0.796	SUBCLONAL	1	TRUE	1	0.231563448619535	2		824	925	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033967	49033967	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1131690865	NA	P-0040843-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	71	394	0	ENST00000267163.4:c.2104C>T	p.Gln702Ter	p.Q702*	ENST00000267163	NM_000321.2	702	Caa/Taa	20/27	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.231563448619535	2		394	509	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553117	106553117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750485966	NA	P-0040843-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	85	630	1	ENST00000369096.4:c.1082C>T	p.Ser361Phe	p.S361F	ENST00000369096	NM_001198.3	361	tCc/tTc	5/7	1	2	FACETS	0.873	0.771	0.983	0.873	0.771	0.983	CLONAL	1	TRUE	1	0.231563448619535	2		631	841	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630263	100630265	+	missense_variant	Missense_Mutation	TNP	CTG	CTG	TTT	novel	NA	P-0040843-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	21	208	1	ENST00000308731.7:c.8_10delinsAAA	p.Ala3_Val4delinsGluMet	p.A3_V4delinsEM	ENST00000308731	NM_000061.2	3	gCAGtg/gAAAtg	2/19	1	1	FACETS	0.619	0.478	0.784	0.619	0.478	0.784	SUBCLONAL	1	TRUE	0	0.231563448619535	1		209	259	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0042807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	104	305	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.925	1			1	INDETERMINATE	1	FALSE	NA	0.76252640822501	2		305	268	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0042807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14662	1854	536	0	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.76252640822501	47	FACETS	1	0.995	1			1	CLONAL	5	FALSE	NA	0.76252640822501	47		536	16516	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259397	11259397	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	196	702	0	ENST00000361445.4:c.4171C>G	p.Arg1391Gly	p.R1391G	ENST00000361445	NM_004958.3	1391	Cga/Gga	28/58	0.76252640822501	1	FACETS	0.782	0.734	0.829	0.782	0.734	0.829	SUBCLONAL	1	FALSE	0	0.76252640822501	1		702	407	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981164	55981164	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	198	533	0	ENST00000263923.4:c.535T>A	p.Trp179Arg	p.W179R	ENST00000263923	NM_002253.2	179	Tgg/Agg	5/30	1	2	FACETS	0.666	0.618	0.715	0.666	0.618	0.715	SUBCLONAL	1	FALSE	1	0.76252640822501	2		533	780	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0043051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	148	415	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.92636229636143	2		416	286	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043526-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	96	523	0	ENST00000425967.3:c.1731C>G	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaG	13/19	1	2	FACETS	0.909	0.815	1	1	0.986	1	CLONAL	2	FALSE	1	0.24566828331616	2		523	430	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209065	133209065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs58916399	NA	P-0043526-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	157	502	0	ENST00000320574.5:c.6166G>A	p.Ala2056Thr	p.A2056T	ENST00000320574	NM_006231.2	2056	Gca/Aca	45/49	0.158348062348483	1	FACETS	1	0.94	1	1	0.994	1	CLONAL	3	FALSE	0	0.24566828331616	1		502	369	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562980	95562980	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043526-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	68	354	0	ENST00000393063.1:c.4277G>C	p.Ser1426Thr	p.S1426T	ENST00000393063	NM_030621.3	1426	aGc/aCc	24/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.24566828331616	2		354	384	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118535	17118535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043526-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	34	713	0	ENST00000285071.4:c.1396G>A	p.Val466Met	p.V466M	ENST00000285071	NM_144997.5	466	Gtg/Atg	12/14	1	2	FACETS	0.518	0.423	0.626	0.518	0.423	0.626	SUBCLONAL	1	FALSE	1	0.24566828331616	2		713	534	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044014-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	337	429	0				ENST00000310581	NM_198253.2	-/1132			0.646295097821661	8	FACETS	0.988	0.95	1	0.988	0.95	1	CLONAL	6	TRUE	2	0.646295097821661	8		429	517	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799254	42799254	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044014-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	656	1053	0	ENST00000575354.2:c.4738G>C	p.Glu1580Gln	p.E1580Q	ENST00000575354	NM_015125.3	1580	Gag/Cag	20/20	0.646295097821661	6	FACETS	1	0.994	1			1	CLONAL	3	TRUE	NA	0.646295097821661	6		1053	1366	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200023	123200023	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0044014-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	143	0	0	ENST00000218089.9:c.2097-2A>G		p.X699_splice	ENST00000218089	NM_001042749.1	699			0.569618850948007	2	FACETS	1	0.985	1			1	CLONAL	2	TRUE	NA	0.646295097821661	2		0	197	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295295	1295295	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0044014-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	260	615	1				ENST00000310581	NM_198253.2	-/1132			0.646295097821661	8	FACETS	1	0.983	1	0.379	0.354	0.403	CLONAL	2	TRUE	2	0.646295097821661	8		616	1041	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344087	70344087	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044014-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	196	469	0	ENST00000374080.3:c.1823T>A	p.Val608Asp	p.V608D	ENST00000374080		608	gTt/gAt	13/45	0.569618850948007	2	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.646295097821661	2		469	547	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724829	43724829	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044014-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	147	773	0	ENST00000382044.4:c.3238G>C	p.Glu1080Gln	p.E1080Q	ENST00000382044	NM_001141980.1	1080	Gaa/Caa	17/28	0.646295097821661	3	FACETS	0.963	0.882	1	0.482	0.441	0.524	CLONAL	1	TRUE	1	0.646295097821661	3		773	625	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439798	52439798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1462186340	NA	P-0044014-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	139	850	0	ENST00000460680.1:c.914C>T	p.Ser305Phe	p.S305F	ENST00000460680	NM_004656.3	305	tCt/tTt	10/17	0.646295097821661	4	FACETS	0.884	0.805	0.967	0.442	0.402	0.484	CLONAL	1	TRUE	2	0.646295097821661	4		850	801	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044119-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	12	429	0				ENST00000310581	NM_198253.2	-/1132			0.3	0	FACETS	0.488	0.345	0.662			1	SUBCLONAL	1	TRUE	0	0.27	0		429	133	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519893	NA	P-0044119-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	96	727	0	ENST00000267101.3:c.310G>T	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ttg	3/28	0.241508857893378	4	FACETS	1	0.972	1	0.639	0.569	0.713	CLONAL	1	TRUE	2	0.27	4		727	707	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651906	36651906	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044119-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	83	645	0	ENST00000244741.5:c.28C>T	p.Gln10Ter	p.Q10*	ENST00000244741	NM_000389.4	10	Cag/Tag	2/3	1	2	FACETS	0.987	0.872	1	0.987	0.872	1	CLONAL	1	TRUE	1	0.27	2		645	623	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47601015	47601015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044119-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	62	541	0	ENST00000263735.4:c.253G>A	p.Glu85Lys	p.E85K	ENST00000263735	NM_002354.2	85	Gaa/Aaa	3/9	0.18481471840371	1	FACETS	0.758	0.656	0.869	0.758	0.656	0.869	SUBCLONAL	1	TRUE	0	0.27	1		541	524	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937706	44937707	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0044119-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	63	227	0	ENST00000377967.4:c.2897dup	p.Val967CysfsTer12	p.V967Cfs*12	ENST00000377967	NM_021140.2	965	aac/aaCc	19/29	0.152238431574741	2	FACETS	0.933	0.817	1			1	INDETERMINATE	2	TRUE	NA	0.27	2		227	250	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270095	66270096	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0044119-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	32	324	1	ENST00000273854.3:c.1786_1787delinsTT	p.Gly596Leu	p.G596L	ENST00000273854	NM_004439.5	596	GGa/TTa	8/18	1	2	FACETS	0.666	0.541	0.806	0.666	0.541	0.806	SUBCLONAL	1	TRUE	1	0.27	2		325	356	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	41	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.429092006453323	2		429	157	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0044511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	42	485	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.429092006453323	1	FACETS	0.22	0.183	0.261	0.22	0.183	0.261	SUBCLONAL	1	TRUE	0	0.429092006453323	1		486	699	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0044511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	187	840	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.429092006453323	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.429092006453323	1		840	680	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867546	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs11466445	NA	P-0044511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	10	22	0	ENST00000374994.4:c.70_78del	p.Ala24_Ala26del	p.A24_A26del	ENST00000374994	NM_004612.2	17	ctGGCGGCGGCg/ctg	1/9	0.429092006453323	1	FACETS	0.989	0.698	1	0.989	0.698	1	CLONAL	1	TRUE	0	0.429092006453323	1		22	37	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107180	27107180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1308037041	NA	P-0044511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	76	572	0	ENST00000324856.7:c.6791C>T	p.Ser2264Leu	p.S2264L	ENST00000324856	NM_006015.4	2264	tCa/tTa	20/20	0.290515911775806	1	FACETS	0.375	0.329	0.426	0.375	0.329	0.426	SUBCLONAL	1	TRUE	0	0.429092006453323	1		572	741	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652203	36652203	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	210	820	0	ENST00000244741.5:c.325G>C	p.Asp109His	p.D109H	ENST00000244741	NM_000389.4	109	Gac/Cac	2/3	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.429092006453323	2		820	928	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970944	55970944	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	102	571	0	ENST00000263923.4:c.1853C>G	p.Ser618Cys	p.S618C	ENST00000263923	NM_002253.2	618	tCt/tGt	13/30	1	2	FACETS	0.758	0.679	0.842	0.758	0.679	0.842	SUBCLONAL	1	TRUE	1	0.429092006453323	2		571	627	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308431	30308431	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	112	495	0	ENST00000262643.3:c.445C>G	p.Leu149Val	p.L149V	ENST00000262643	NM_001238.2	149	Ctg/Gtg	6/12	0.243531550685576	2	FACETS	0.765	0.689	0.846	0.383	0.344	0.423	INDETERMINATE	1	TRUE	0	0.429092006453323	2		495	682	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802635	135802635	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203343	NA	P-0044511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	100	365	0	ENST00000298552.3:c.163C>T	p.Gln55Ter	p.Q55*	ENST00000298552	NM_001162426.1	55	Cag/Tag	4/23	0.429092006453323	1	FACETS	0.878	0.789	0.971	0.878	0.789	0.971	CLONAL	1	TRUE	0	0.429092006453323	1		365	417	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061171	38061171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024200279	NA	P-0044511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	60	273	0	ENST00000250448.2:c.818G>A	p.Gly273Glu	p.G273E	ENST00000250448	NM_004496.3	273	gGg/gAg	2/2	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.429092006453323	2		273	244	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095967	11095967	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	177	763	0	ENST00000358026.2:c.241G>T	p.Glu81Ter	p.E81*	ENST00000358026	NM_001128849.1	81	Gag/Tag	3/36	0.429092006453323	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.429092006453323	1		763	636	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444053	49444053	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	126	756	0	ENST00000301067.7:c.3318del	p.Ser1107AlafsTer12	p.S1107Afs*12	ENST00000301067	NM_003482.3	1106	ccC/cc	11/54	1	2	FACETS	0.743	0.673	0.817	0.743	0.673	0.817	SUBCLONAL	1	TRUE	1	0.429092006453323	2		756	790	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226858	142226858	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	104	511	0	ENST00000350721.4:c.4946A>C	p.Lys1649Thr	p.K1649T	ENST00000350721	NM_001184.3	1649	aAa/aCa	28/47	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.429092006453323	2		511	450	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856583	45856583	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1427879797	NA	P-0044511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	127	567	1	ENST00000391945.4:c.1675G>C	p.Glu559Gln	p.E559Q	ENST00000391945	NM_000400.3	559	Gag/Cag	18/23	0.243531550685576	2	FACETS	0.842	0.764	0.924	0.421	0.382	0.462	INDETERMINATE	1	TRUE	0	0.429092006453323	2		568	703	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534289	187534289	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	181	505	0	ENST00000441802.2:c.9437G>C	p.Arg3146Thr	p.R3146T	ENST00000441802	NM_005245.3	3146	aGa/aCa	13/27	0.429092006453323	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.429092006453323	1		505	586	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176176047	176176047	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	134	606	0	ENST00000367669.3:c.68C>G	p.Ser23Trp	p.S23W	ENST00000367669	NM_022457.5	23	tCg/tGg	1/20	1	2	FACETS	0.998	0.909	1	0.998	0.909	1	CLONAL	1	TRUE	1	0.429092006453323	2		606	626	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946434	71946434	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	143	727	0	ENST00000298229.2:c.2598C>G	p.Ile866Met	p.I866M	ENST00000298229	NM_001567.3	866	atC/atG	23/28	1	2	FACETS	0.808	0.737	0.882	0.808	0.737	0.882	CLONAL	1	TRUE	1	0.429092006453323	2		727	825	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103182	119103182	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	109	502	0	ENST00000264033.4:c.220A>G	p.Lys74Glu	p.K74E	ENST00000264033	NM_005188.3	74	Aag/Gag	2/16	1	2	FACETS	0.898	0.809	0.991	0.898	0.809	0.991	CLONAL	1	TRUE	1	0.429092006453323	2		502	566	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562591	95562591	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	113	470	0	ENST00000393063.1:c.4666G>A	p.Asp1556Asn	p.D1556N	ENST00000393063	NM_030621.3	1556	Gac/Aac	24/28	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.429092006453323	2		470	523	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15943757	15943757	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	96	404	0	ENST00000268712.3:c.6731C>T	p.Ser2244Leu	p.S2244L	ENST00000268712	NM_006311.3	2244	tCa/tTa	43/46	0.429092006453323	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.429092006453323	1		404	320	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16056710	16056710	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0044511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	42	304	0	ENST00000268712.3:c.733-1G>C		p.X245_splice	ENST00000268712	NM_006311.3	245			0.429092006453323	1	FACETS	0.84	0.711	0.98	0.84	0.711	0.98	CLONAL	1	TRUE	0	0.429092006453323	1		304	183	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724573	724573	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	172	381	0	ENST00000314574.4:c.1483C>G	p.Gln495Glu	p.Q495E	ENST00000314574	NM_005433.3	495	Cag/Gag	12/12	1	2	FACETS	0.802	0.744	0.861	1	0.991	1	CLONAL	2	TRUE	1	0.429092006453323	2		381	500	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758777	41758777	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	93	815	0	ENST00000301178.4:c.1831G>C	p.Glu611Gln	p.E611Q	ENST00000301178	NM_021913.4	611	Gag/Cag	16/20	0.243531550685576	2	FACETS	0.462	0.41	0.518	0.231	0.205	0.259	INDETERMINATE	1	TRUE	0	0.429092006453323	2		815	938	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921797	111921805	+	inframe_deletion	In_Frame_Del	DEL	AGAATGCAT	AGAATGCAT	-	novel	NA	P-0044511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	130	365	0	ENST00000393256.3:c.586_594del	p.Arg196_His198del	p.R196_H198del	ENST00000393256	NM_006538.4	196	AGAATGCAT/-	4/4	0.429092006453323	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.429092006453323	1		365	377	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380455	31380455	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	151	656	0	ENST00000328111.2:c.945G>C	p.Lys315Asn	p.K315N	ENST00000328111	NM_006892.3	315	aaG/aaC	9/23	1	2	FACETS	0.952	0.872	1	0.952	0.872	1	CLONAL	1	TRUE	1	0.429092006453323	2		656	739	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127528	55127528	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	109	364	0	ENST00000257290.5:c.316C>G	p.Gln106Glu	p.Q106E	ENST00000257290	NM_006206.4	106	Cag/Gag	3/23	1	2	FACETS	0.929	0.837	1	0.929	0.837	1	CLONAL	1	TRUE	1	0.429092006453323	2		364	547	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630417	187630427	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	TAAAACTGTAG	TAAAACTGTAG	-	novel	NA	P-0044511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	46	662	0	ENST00000441802.2:c.555_565del	p.Tyr185Ter	p.Y185*	ENST00000441802	NM_005245.3	185	taCTACAGTTTTAaa/taaa	2/27	0.429092006453323	1	FACETS	0.265	0.222	0.312	0.265	0.222	0.312	SUBCLONAL	1	TRUE	0	0.429092006453323	1		662	636	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945368	151945368	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1200279994	NA	P-0044511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	11	227	0	ENST00000262189.6:c.2151A>G	p.Ile717Met	p.I717M	ENST00000262189	NM_170606.2	717	atA/atG	14/59	1	2	FACETS	0.286	0.198	0.396	0.286	0.198	0.396	SUBCLONAL	1	TRUE	1	0.429092006453323	2		227	179	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080330	5080330	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044511-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	47	303	1	ENST00000381652.3:c.2233G>T	p.Glu745Ter	p.E745*	ENST00000381652	NM_004972.3	745	Gaa/Taa	17/25	0.429092006453323	1	FACETS	0.768	0.655	0.89	0.768	0.655	0.89	SUBCLONAL	1	TRUE	0	0.429092006453323	1		304	224	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658388	18658388	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	55	349	0	ENST00000266497.5:c.3193A>T	p.Ile1065Leu	p.I1065L	ENST00000266497		1065	Ata/Tta	22/31	0.610017305514698	3	FACETS	0.659	0.566	0.76	0.33	0.283	0.38	SUBCLONAL	1	TRUE	1	0.610017305514698	3		349	357	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436203	110436203	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	168	547	0	ENST00000375856.3:c.2198C>G	p.Ala733Gly	p.A733G	ENST00000375856	NM_003749.2	733	gCc/gGc	1/2	0.610017305514698	3	FACETS	0.728	0.669	0.79	0.243	0.223	0.264	SUBCLONAL	1	TRUE	0	0.610017305514698	3		547	987	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578202	7578235	+	frameshift_variant	Frame_Shift_Del	DEL	ACACTATGTCGAAAAGTGTTTCTGTCATCCAAAT	ACACTATGTCGAAAAGTGTTTCTGTCATCCAAAT	-	novel	NA	P-0044517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	386	664	1	ENST00000269305.4:c.614_647del	p.Tyr205TrpfsTer31	p.Y205Wfs*31	ENST00000269305	NM_001126112.2	205	tATTTGGATGACAGAAACACTTTTCGACATAGTGTg/tg	6/11	0.551015887668551	2	FACETS	0.86	0.824	0.896	0.86	0.824	0.896	CLONAL	2	TRUE	0	0.610017305514698	2		665	736	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772041	135772041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs533565295	NA	P-0044517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	116	499	1	ENST00000298552.3:c.3076G>A	p.Ala1026Thr	p.A1026T	ENST00000298552	NM_001162426.1	1026	Gcc/Acc	23/23	0.517493047009314	2	FACETS	0.52	0.468	0.574	0.26	0.234	0.287	SUBCLONAL	1	TRUE	0	0.610017305514698	2		500	732	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0044602-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	108	284	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.894	0.819	0.971	1	0.991	1	CLONAL	3	TRUE	1	0.33	2		284	244	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0044602-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	315	682	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	0.924	0.878	0.969	1	0.997	1	CLONAL	3	TRUE	1	0.33	2		682	689	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579310	7579310	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1555526469	NA	P-0044602-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	241	638	0	ENST00000269305.4:c.375+2T>C		p.X125_splice	ENST00000269305	NM_001126112.2	125			1	2	FACETS	0.882	0.832	0.933	1	0.996	1	CLONAL	3	TRUE	1	0.33	2		638	552	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447395	12447395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044602-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	138	629	1	ENST00000287820.6:c.634C>T	p.Arg212Trp	p.R212W	ENST00000287820	NM_015869.4	212	Cgg/Tgg	5/7	1	2	FACETS	0.868	0.803	0.935	1	0.993	1	CLONAL	3	TRUE	1	0.33	2		630	321	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918978	76918981	+	frameshift_variant	Frame_Shift_Del	DEL	TGTC	TGTC	-	novel	NA	P-0044602-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	136	475	0	ENST00000373344.5:c.4010_4013del	p.Arg1337IlefsTer8	p.R1337Ifs*8	ENST00000373344	NM_000489.3	1337	aGACAt/at	12/35	0.24959356921539	0	FACETS	0.7	0.65	0.749			1	SUBCLONAL	3	TRUE	0	0.33	0		475	263	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638929	176638929	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044602-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	18	0	0	ENST00000439151.2:c.3529T>C	p.Phe1177Leu	p.F1177L	ENST00000439151	NM_022455.4	1177	Ttt/Ctt	5/23	0.296565531647143	1	FACETS	0.16	0.12	0.209	0.16	0.12	0.209	SUBCLONAL	1	TRUE	0	0.33	1		0	568	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0044938-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	15	768	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	NA	2	FACETS	0.06	0.043	0.08			1	INDETERMINATE	1	TRUE	NA	0.76541027729016	2		768	655	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0044938-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	342	690	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.737463587955272	2	FACETS	0.937	0.904	0.968	0.937	0.904	0.968	CLONAL	2	TRUE	0	0.76541027729016	2		690	477	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114682	73114682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747658097	NA	P-0044938-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	405	304	0	ENST00000356692.5:c.1063G>A	p.Glu355Lys	p.E355K	ENST00000356692		355	Gag/Aag	9/9	0.68952024249077	5	FACETS	0.968	0.928	1			1	CLONAL	3	TRUE	NA	0.76541027729016	5		304	783	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972633	25972633	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1304291937	NA	P-0044938-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1349	157	452	0	ENST00000435504.4:c.1792C>G	p.Gln598Glu	p.Q598E	ENST00000435504		598	Cag/Gag	12/13	0.76541027729016	7	FACETS	0.794	0.724	0.867	0.159	0.144	0.174	SUBCLONAL	1	TRUE	2	0.76541027729016	7		452	1506	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984428	201984428	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044938-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	654	615	0	ENST00000359651.3:c.1093G>T	p.Glu365Ter	p.E365*	ENST00000359651		365	Gag/Tag	8/8	0.704898965028277	5	FACETS	0.973	0.942	1	0.73	0.706	0.754	CLONAL	3	TRUE	1	0.76541027729016	5		615	1257	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513224	106513224	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044938-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	133	328	0	ENST00000359195.3:c.2128C>T	p.Gln710Ter	p.Q710*	ENST00000359195	NM_002649.2	710	Cag/Tag	4/11	0.71705557383955	3	FACETS	1	0.951	1	0.528	0.483	0.575	CLONAL	1	TRUE	1	0.76541027729016	3		328	455	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968832	32968832	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044938-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	103	268	0	ENST00000380152.3:c.9266del	p.Pro3089LeufsTer15	p.P3089Lfs*15	ENST00000380152		3088	gCc/gc	25/27	1	2	FACETS	0.838	0.759	0.92	0.838	0.759	0.92	CLONAL	1	TRUE	1	0.76541027729016	2		268	321	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027697	48027697	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044938-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	122	316	0	ENST00000234420.5:c.2575C>T	p.Leu859Phe	p.L859F	ENST00000234420	NM_000179.2	859	Ctt/Ttt	4/10	0.736246191556143	2	FACETS	0.932	0.853	1	0.466	0.426	0.507	CLONAL	1	TRUE	0	0.76541027729016	2		316	342	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799185	45799185	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs370124822	NA	P-0044938-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	223	670	0	ENST00000450313.1:c.248C>G	p.Ser83Ter	p.S83*	ENST00000450313	NM_012222.2	83	tCa/tGa	3/16	0.71705557383955	3	FACETS	0.997	0.931	1	0.499	0.465	0.533	CLONAL	1	TRUE	1	0.76541027729016	3		670	808	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233186	46233186	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044938-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	293	361	0	ENST00000334344.6:c.1405G>T	p.Glu469Ter	p.E469*	ENST00000334344	NM_152641.2	469	Gaa/Taa	11/21	0.737463587955272	2	FACETS	0.969	0.934	1	0.969	0.934	1	CLONAL	2	TRUE	0	0.76541027729016	2		361	395	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427871	49427871	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044938-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	213	654	0	ENST00000301067.7:c.10719G>C	p.Lys3573Asn	p.K3573N	ENST00000301067	NM_003482.3	3573	aaG/aaC	38/54	0.737463587955272	2	FACETS	0.978	0.916	1	0.489	0.458	0.521	CLONAL	1	TRUE	0	0.76541027729016	2		654	569	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514958	103514958	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044938-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	152	347	1	ENST00000355739.4:c.1459C>T	p.Pro487Ser	p.P487S	ENST00000355739	NM_000123.3	487	Ccg/Tcg	8/15	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.76541027729016	2		348	294	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319885	62319885	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs115423936	NA	P-0044938-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	495	780	0	ENST00000360203.5:c.1727G>T	p.Arg576Leu	p.R576L	ENST00000360203	NM_001283009.1	576	cGc/cTc	21/35	0.76541027729016	6	FACETS	1	0.977	1			1	CLONAL	2	TRUE	NA	0.76541027729016	6		780	1583	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184808	32184808	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044938-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	80	610	0	ENST00000375023.3:c.1775A>C	p.Glu592Ala	p.E592A	ENST00000375023	NM_004557.3	592	gAg/gCg	11/30	0.760172178100969	3	FACETS	0.454	0.399	0.512	0.227	0.199	0.256	SUBCLONAL	1	TRUE	1	0.76541027729016	3		610	637	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0045733-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	144	430	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.227115382041724	3	FACETS	1	0.979	1	0.613	0.56	0.669	CLONAL	1	FALSE	1	0.361120926430889	3		430	768	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597883	43597883	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs551142665	NA	P-0045733-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	422	1017	2	ENST00000355710.3:c.431G>A	p.Arg144His	p.R144H	ENST00000355710	NM_020975.4	144	cGc/cAc	3/20	0.361120926430889	3	FACETS	0.993	0.945	1	0.993	0.945	1	CLONAL	2	FALSE	1	0.361120926430889	3		1019	1390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577497	7577497	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0045733-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	280	747	1	ENST00000269305.4:c.782+2T>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.290841494447454	2	FACETS	0.874	0.823	0.926	0.874	0.823	0.926	CLONAL	2	FALSE	0	0.361120926430889	2		748	887	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46733203	46733203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045733-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	79	744	0	ENST00000371975.4:c.964C>T	p.Leu322Phe	p.L322F	ENST00000371975	NM_003579.3	322	Ctc/Ttc	9/18	0.189196488854266	2	FACETS	0.517	0.454	0.585	0.259	0.227	0.293	INDETERMINATE	1	FALSE	0	0.361120926430889	2		744	846	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599341	55599341	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519761	NA	P-0045947-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	240	401	0	ENST00000288135.5:c.2467T>G	p.Tyr823Asp	p.Y823D	ENST00000288135	NM_000222.2	823	Tat/Gat	17/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.795859512876029	2		401	602	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593608	55593613	+	inframe_deletion	In_Frame_Del	DEL	GGTTGT	GGTTGT	-	novel	NA	P-0045947-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	178	368	0	ENST00000288135.5:c.1674_1679del	p.Lys558_Val560delinsAsn	p.K558_V560delinsN	ENST00000288135	NM_000222.2	558	aaGGTTGTt/aat	11/21	1	2	FACETS	0.896	0.833	0.961	0.896	0.833	0.961	CLONAL	1	TRUE	1	0.795859512876029	2		368	499	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	59	507	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	1	2	FACETS	0.964	0.83	1	0.964	0.83	1	CLONAL	1	FALSE	1	0.24589881780836	2		507	498	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0047187-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	138	967	0	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	0.187253880241966	2	FACETS	0.843	0.767	0.923	0.843	0.767	0.923	CLONAL	2	TRUE	0	0.187253880241966	2		967	874	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970969	21970969	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047187-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	106	677	0	ENST00000304494.5:c.389T>A	p.Leu130Gln	p.L130Q	ENST00000304494	NM_000077.4	130	cTg/cAg	2/3	0.187253880241966	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	0	0.187253880241966	2		677	541	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0047459-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	116	411	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.36035258292252	2		411	519	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438170	56438170	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047459-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	248	848	0	ENST00000407977.2:c.823T>G	p.Cys275Gly	p.C275G	ENST00000407977		275	Tgt/Ggt	7/10	0.36035258292252	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	FALSE	0	0.36035258292252	2		848	601	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524472	44524472	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047459-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	65	276	0	ENST00000291552.4:c.85C>A	p.His29Asn	p.H29N	ENST00000291552	NM_006758.2	29	Cat/Aat	2/8	1	2	FACETS	0.949	0.827	1	0.949	0.827	1	CLONAL	1	FALSE	1	0.36035258292252	2		276	380	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047847-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	207	430	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.281958450376906	3	FACETS	0.87	0.811	0.93	0.87	0.811	0.93	CLONAL	3	TRUE	0	0.281958450376906	3		430	642	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0047847-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	114	286	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.175550910326907	4	FACETS	0.919	0.83	1	0.919	0.83	1	CLONAL	2	TRUE	2	0.281958450376906	4		286	564	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181846	56181846	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047847-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	193	303	0	ENST00000399503.3:c.4072del	p.Ser1358ArgfsTer19	p.S1358Rfs*19	ENST00000399503	NM_005921.1	1357	cTt/ct	17/20	0.268296955976429	3	FACETS	0.984	0.918	1	0.984	0.918	1	CLONAL	3	TRUE	0	0.281958450376906	3		303	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0048318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	433	833	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.88	2		837	971	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141426	11141426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	355	705	0	ENST00000358026.2:c.3403C>T	p.Arg1135Trp	p.R1135W	ENST00000358026	NM_001128849.1	1135	Cgg/Tgg	25/36	1	2	FACETS	0.924	0.879	0.969	0.924	0.879	0.969	CLONAL	1	TRUE	1	0.88	2		705	873	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022468	31022468	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	158	384	0	ENST00000375687.4:c.1953del	p.Gly652AlafsTer51	p.G652Afs*51	ENST00000375687	NM_015338.5	651	ggC/gg	13/13	1	2	FACETS	0.981	0.912	1	0.981	0.912	1	CLONAL	1	TRUE	1	0.88	2		384	366	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918292	44918293	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	173	287	0	ENST00000377967.4:c.919dup	p.Tyr307LeufsTer6	p.Y307Lfs*6	ENST00000377967	NM_021140.2	306	tct/tcTt	11/29	1	2	FACETS	0.809	0.751	0.868	0.809	0.751	0.868	CLONAL	1	TRUE	1	0.88	2		287	486	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048778-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	41	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.371574694454778	2		429	193	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048778-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	102	330	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.371574694454778	2		330	547	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0048778-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	307	784	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.328679160828286	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.371574694454778	2		784	793	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0048778-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	41	288	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.869	0.729	1	0.869	0.729	1	CLONAL	1	TRUE	1	0.371574694454778	2		288	254	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652171	36652171	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048778-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	121	574	0	ENST00000244741.5:c.293C>A	p.Ser98Ter	p.S98*	ENST00000244741	NM_000389.4	98	tCa/tAa	2/3	1	2	FACETS	0.943	0.853	1	0.943	0.853	1	CLONAL	1	TRUE	1	0.371574694454778	2		574	691	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131205	17131205	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs757060348	NA	P-0048778-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	62	635	0	ENST00000285071.4:c.247G>A	p.Glu83Lys	p.E83K	ENST00000285071	NM_144997.5	83	Gag/Aag	4/14	0.34225050085837	1	FACETS	0.455	0.393	0.523	0.455	0.393	0.523	SUBCLONAL	1	TRUE	0	0.371574694454778	1		635	597	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175942	176175942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs964768927	NA	P-0048778-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	13	17	0	ENST00000367669.3:c.173C>T	p.Ser58Leu	p.S58L	ENST00000367669	NM_022457.5	58	tCg/tTg	1/20	1	2	FACETS	0.777	0.576	1	1	0.893	1	CLONAL	2	TRUE	1	0.371574694454778	2		17	45	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719107	52719107	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048778-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	46	552	0	ENST00000322088.6:c.883G>A	p.Glu295Lys	p.E295K	ENST00000322088	NM_014225.5	295	Gag/Aag	7/15	1	2	FACETS	0.326	0.274	0.384	0.326	0.274	0.384	SUBCLONAL	1	TRUE	1	0.371574694454778	2		552	759	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004817	16004817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048778-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	78	548	1	ENST00000268712.3:c.2437C>T	p.Pro813Ser	p.P813S	ENST00000268712	NM_006311.3	813	Ccc/Tcc	20/46	0.34225050085837	1	FACETS	0.659	0.58	0.743	0.659	0.58	0.743	SUBCLONAL	1	TRUE	0	0.371574694454778	1		549	519	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004664	16004664	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048778-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	74	503	0	ENST00000268712.3:c.2590C>T	p.Gln864Ter	p.Q864*	ENST00000268712	NM_006311.3	864	Cag/Tag	20/46	0.34225050085837	1	FACETS	0.546	0.478	0.619	0.546	0.478	0.619	SUBCLONAL	1	TRUE	0	0.371574694454778	1		503	594	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426859	49426859	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048778-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	97	444	0	ENST00000301067.7:c.11629C>T	p.Gln3877Ter	p.Q3877*	ENST00000301067	NM_003482.3	3877	Cag/Tag	39/54	1	2	FACETS	0.9	0.804	1	0.9	0.804	1	CLONAL	1	TRUE	1	0.371574694454778	2		444	580	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871770	12871770	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048778-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	58	202	0	ENST00000228872.4:c.487C>G	p.Gln163Glu	p.Q163E	ENST00000228872	NM_004064.3	163	Caa/Gaa	2/3	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.371574694454778	2		202	306	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909973	100909973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048778-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	56	419	0	ENST00000325455.5:c.2676G>C	p.Leu892Phe	p.L892F	ENST00000325455	NM_001202474.3	892	ttG/ttC	8/8	0.27659138128058	1	FACETS	0.487	0.417	0.563	0.487	0.417	0.563	SUBCLONAL	1	TRUE	0	0.371574694454778	1		419	504	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131214	17131214	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048778-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	66	662	0	ENST00000285071.4:c.238G>C	p.Asp80His	p.D80H	ENST00000285071	NM_144997.5	80	Gac/Cac	4/14	0.34225050085837	1	FACETS	0.461	0.4	0.528	0.461	0.4	0.528	SUBCLONAL	1	TRUE	0	0.371574694454778	1		662	627	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42759149	42759149	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0048778-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	55	216	0	ENST00000222329.4:c.3G>A	p.Met1?	p.M1?	ENST00000222329	NM_006494.2	1	atG/atA	1/4	1	2	FACETS	0.977	0.842	1	0.977	0.842	1	CLONAL	1	TRUE	1	0.371574694454778	2		216	303	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159072	24159072	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048778-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	54	514	0	ENST00000263121.7:c.747del	p.Thr250ArgfsTer17	p.T250Rfs*17	ENST00000263121	NM_003073.3	248	taC/ta	6/9	0.198046402982585	0	FACETS	0.33	0.281	0.383			1	INDETERMINATE	1	TRUE	0	0.371574694454778	0		514	554	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205751	128205751	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048778-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	102	401	0	ENST00000341105.2:c.124C>G	p.Pro42Ala	p.P42A	ENST00000341105	NM_032638.4	42	Cca/Gca	2/6	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.371574694454778	2		401	526	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2966410	2966410	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048778-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	54	601	0	ENST00000396946.4:c.1770C>G	p.Asp590Glu	p.D590E	ENST00000396946	NM_032415.4	590	gaC/gaG	14/25	0.34225050085837	1	FACETS	0.312	0.265	0.363	0.312	0.265	0.363	SUBCLONAL	1	TRUE	0	0.371574694454778	1		601	759	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918338	44918338	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048778-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	101	177	0	ENST00000377967.4:c.963G>A	p.Trp321Ter	p.W321*	ENST00000377967	NM_021140.2	321	tgG/tgA	11/29	1	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.371574694454778	1		177	298	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001155	150001155	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048778-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	47	507	0	ENST00000253339.5:c.2449G>C	p.Glu817Gln	p.E817Q	ENST00000253339		817	Gaa/Caa	4/7	1	2	FACETS	0.374	0.315	0.44	0.374	0.315	0.44	SUBCLONAL	1	TRUE	1	0.371574694454778	2		507	676	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0049062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	44	305	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.929	0.78	1	0.929	0.78	1	CLONAL	1	TRUE	1	0.21	2		305	451	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521522	46521522	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	61	399	0	ENST00000262741.5:c.886A>G	p.Asn296Asp	p.N296D	ENST00000262741	NM_003629.3	296	Aat/Gat	7/10	1	2	FACETS	0.988	0.852	1	0.988	0.852	1	CLONAL	1	TRUE	1	0.21	2		399	588	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265130	198265130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	28	306	0	ENST00000335508.6:c.2747C>A	p.Thr916Lys	p.T916K	ENST00000335508	NM_012433.2	916	aCa/aAa	19/25	1	2	FACETS	0.57	0.455	0.702	0.57	0.455	0.702	SUBCLONAL	1	TRUE	1	0.21	2		306	468	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662892	227662892	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	40	546	0	ENST00000305123.5:c.563C>G	p.Thr188Ser	p.T188S	ENST00000305123	NM_005544.2	188	aCc/aGc	1/2	1	2	FACETS	0.48	0.397	0.572	0.48	0.397	0.572	SUBCLONAL	1	TRUE	1	0.21	2		546	794	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839822	27839822	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	64	576	0	ENST00000328488.2:c.272T>C	p.Met91Thr	p.M91T	ENST00000328488	NM_003533.2	91	aTg/aCg	1/1	1	2	FACETS	0.687	0.593	0.789	0.687	0.593	0.789	SUBCLONAL	1	TRUE	1	0.21	2		576	887	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0049305-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	299	671	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.631995941148734	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.631995941148734	1		671	576	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248573	8248573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780757257	NA	P-0049305-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	133	957	1	ENST00000335790.3:c.314G>A	p.Arg105Gln	p.R105Q	ENST00000335790	NM_002315.2	105	cGg/cAg	3/4	0.413006149920149	0	FACETS	0.23	0.209	0.252			1	SUBCLONAL	1	TRUE	0	0.631995941148734	0		958	673	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120732	94120732	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049305-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	296	561	0	ENST00000369303.4:c.319A>T	p.Arg107Trp	p.R107W	ENST00000369303	NM_004440.3	107	Agg/Tgg	3/17	0.353696296841823	2	FACETS	0.915	0.873	0.956	0.915	0.873	0.956	INDETERMINATE	2	TRUE	0	0.631995941148734	2		561	512	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220463	1220464	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049305-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	327	1010	0	ENST00000326873.7:c.558dup	p.Gly187ArgfsTer79	p.G187Rfs*79	ENST00000326873	NM_000455.4	186	acc/aCcc	4/10	0.631995941148734	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.631995941148734	1		1010	700	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589779	55589779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1560414379	NA	P-0049305-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	202	439	0	ENST00000288135.5:c.1261C>T	p.Leu421Phe	p.L421F	ENST00000288135	NM_000222.2	421	Ctc/Ttc	8/21	0.631995941148734	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.631995941148734	1		439	392	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600015	10600015	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049305-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	379	996	0	ENST00000171111.5:c.1561G>C	p.Ala521Pro	p.A521P	ENST00000171111	NM_203500.1	521	Gct/Cct	5/6	0.631995941148734	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.631995941148734	1		996	700	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834536	156834536	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049305-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	207	926	1	ENST00000524377.1:c.304G>T	p.Gly102Cys	p.G102C	ENST00000524377	NM_002529.3	102	Ggt/Tgt	3/17	NA	2	FACETS	0.924	0.861	0.989			1	INDETERMINATE	1	TRUE	NA	0.631995941148734	2		927	709	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498388	89498388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049305-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	105	244	0	ENST00000336596.2:c.2360C>T	p.Pro787Leu	p.P787L	ENST00000336596	NM_005233.5	787	cCa/cTa	14/17	0.631995941148734	1	FACETS	0.924	0.844	1	0.924	0.844	1	CLONAL	1	TRUE	0	0.631995941148734	1		244	246	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967332	134967332	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049305-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	55	612	1	ENST00000398015.3:c.2671G>T	p.Val891Leu	p.V891L	ENST00000398015	NM_004441.4	891	Gtg/Ttg	14/16	0.292886765148277	2	FACETS	0.37	0.316	0.428	0.185	0.158	0.214	INDETERMINATE	1	TRUE	0	0.631995941148734	2		613	471	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149375020	149375020	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049305-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	111	988	0	ENST00000360632.3:c.74A>T	p.Asp25Val	p.D25V	ENST00000360632	NM_015472.4	25	gAc/gTc	2/7	0.292886765148277	2	FACETS	0.386	0.346	0.428	0.193	0.173	0.214	INDETERMINATE	1	TRUE	0	0.631995941148734	2		988	910	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143066998	143066998	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1561280492	NA	P-0049305-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	170	422	0	ENST00000262992.4:c.1715C>G	p.Pro572Arg	p.P572R	ENST00000262992	NM_001101669.1	572	cCa/cGa	16/24	0.631995941148734	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.631995941148734	1		422	351	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38978707	38978707	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049305-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	185	381	0	ENST00000357387.3:c.799G>T	p.Asp267Tyr	p.D267Y	ENST00000357387	NM_152756.3	267	Gat/Tat	9/38	0.233967819660325	3	FACETS	1	0.985	1	0.622	0.577	0.669	INDETERMINATE	1	TRUE	1	0.631995941148734	3		381	619	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564587	86564587	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138308013	NA	P-0049305-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	79	899	0	ENST00000274376.6:c.319G>C	p.Val107Leu	p.V107L	ENST00000274376	NM_002890.2	107	Gtt/Ctt	1/25	0.328031724967715	0	FACETS	0.219	0.193	0.246			1	INDETERMINATE	1	TRUE	0	0.631995941148734	0		899	421	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951932	2951932	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0049305-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	210	618	0	ENST00000396946.4:c.3020-2A>T		p.X1007_splice	ENST00000396946	NM_032415.4	1007			0.149497172413998	2	FACETS	1	0.988	1	0.621	0.582	0.661	INDETERMINATE	1	TRUE	0	0.631995941148734	2		618	535	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443679	29443679	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049375-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	109	644	0	ENST00000389048.3:c.3538G>C	p.Val1180Leu	p.V1180L	ENST00000389048	NM_004304.4	1180	Gtt/Ctt	23/29	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.445510050485716	2		644	450	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590777	95590778	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0049375-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	72	369	0	ENST00000393063.1:c.1131_1132del	p.Ile378GlnfsTer10	p.I378Qfs*10	ENST00000393063	NM_030621.3	377	gtAAtc/gttc	9/28	1	2	FACETS	0.864	0.759	0.976	0.864	0.759	0.976	CLONAL	1	TRUE	1	0.445510050485716	2		369	374	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069458	30069458	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049375-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	121	693	0	ENST00000338641.4:c.1323del	p.Glu442ArgfsTer13	p.E442Rfs*13	ENST00000338641	NM_000268.3	441	gcT/gc	12/16	0.445510050485716	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.445510050485716	1		693	391	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0049540-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	20	284	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		284	190	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0049600-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	160	548	0	ENST00000269305.4:c.375+1G>T		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.387805627308465	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.388658819056267	1		548	561	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819743	81819743	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370242901	NA	P-0049600-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	128	533	0	ENST00000359376.3:c.149G>A	p.Arg50Gln	p.R50Q	ENST00000359376	NM_002661.3	50	cGg/cAg	2/33	1	2	FACETS	0.906	0.822	0.994	0.906	0.822	0.994	CLONAL	1	TRUE	1	0.388658819056267	2		533	727	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197789	123197789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049600-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	68	439	0	ENST00000218089.9:c.1913C>T	p.Ala638Val	p.A638V	ENST00000218089	NM_001042749.1	638	gCa/gTa	20/35	1	2	FACETS	0.967	0.846	1	0.967	0.846	1	CLONAL	1	TRUE	1	0.388658819056267	2		439	362	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317658	163317658	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049600-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	62	287	0	ENST00000271452.3:c.1054C>T	p.Leu352Phe	p.L352F	ENST00000271452	NM_145697.2	352	Ctt/Ttt	12/14	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.388658819056267	2		287	286	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28963969	28963969	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049600-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	46	319	0	ENST00000282397.4:c.1933del	p.Glu645LysfsTer36	p.E645Kfs*36	ENST00000282397	NM_002019.4	645	Gaa/aa	13/30	0.388658819056267	1	FACETS	0.734	0.622	0.854	0.734	0.622	0.854	SUBCLONAL	1	TRUE	0	0.388658819056267	1		319	260	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993957	72993957	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049600-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	142	623	0	ENST00000268489.5:c.88A>C	p.Thr30Pro	p.T30P	ENST00000268489	NM_006885.3	30	Acc/Ccc	2/10	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.388658819056267	2		623	698	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486051	29486061	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAAATTTAT	AAAAAATTTAT	-	novel	NA	P-0049600-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	40	309	0	ENST00000356175.3:c.229_239del	p.Lys77SerfsTer26	p.K77Sfs*26	ENST00000356175	NM_000267.3	76	gaAAAAAATTTATat/gaat	3/57	0.387805627308465	1	FACETS	0.706	0.591	0.831	0.706	0.591	0.831	SUBCLONAL	1	TRUE	0	0.388658819056267	1		309	235	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220418	1220419	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCATTGTGCACAAGGACATCAA	novel	NA	P-0049600-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	32	774	1	ENST00000326873.7:c.514_535dup	p.Pro179HisfsTer94	p.P179Hfs*94	ENST00000326873	NM_000455.4	171	ggc/gGCATTGTGCACAAGGACATCAAgc	4/10	0.388658819056267	1	FACETS	0.209	0.169	0.255	0.209	0.169	0.255	SUBCLONAL	1	TRUE	0	0.388658819056267	1		775	635	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223024	1223024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049600-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	39	691	0	ENST00000326873.7:c.963del	p.Ile322SerfsTer14	p.I322Sfs*14	ENST00000326873	NM_000455.4	321	Ccc/cc	8/10	0.388658819056267	1	FACETS	0.232	0.191	0.277	0.232	0.191	0.277	SUBCLONAL	1	TRUE	0	0.388658819056267	1		691	697	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600477	10600477	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049600-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	68	669	0	ENST00000171111.5:c.1378A>T	p.Arg460Trp	p.R460W	ENST00000171111	NM_203500.1	460	Agg/Tgg	4/6	0.388658819056267	1	FACETS	0.434	0.377	0.495	0.434	0.377	0.495	SUBCLONAL	1	TRUE	0	0.388658819056267	1		669	650	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39239266	39239266	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0049600-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	21	314	0	ENST00000402219.2:c.2390+1G>C		p.X797_splice	ENST00000402219	NM_005633.3	797			1	2	FACETS	0.303	0.233	0.385	0.303	0.233	0.385	SUBCLONAL	1	TRUE	1	0.388658819056267	2		314	357	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643915	52643916	+	stop_gained	Nonsense_Mutation	DNP	TC	TC	AA	novel	NA	P-0049600-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	64	385	0	ENST00000394830.3:c.1980_1981delinsTT	p.Gln660_Lys661delinsHisTer	p.Q660_K661delinsH*	ENST00000394830	NM_018313.4	660	caGAaa/caTTaa	17/30	0.388658819056267	1	FACETS	0.792	0.69	0.901	0.792	0.69	0.901	CLONAL	1	TRUE	0	0.388658819056267	1		385	335	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066525	94066525	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049600-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	86	299	0	ENST00000369303.4:c.1234A>G	p.Thr412Ala	p.T412A	ENST00000369303	NM_004440.3	412	Act/Gct	5/17	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.388658819056267	2		299	393	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317912	8317912	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs769140839	NA	P-0049600-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	64	304	0	ENST00000356435.5:c.5701C>G	p.Leu1901Val	p.L1901V	ENST00000356435		1901	Cta/Gta	35/35	0.388658819056267	1	FACETS	0.893	0.78	1	0.893	0.78	1	CLONAL	1	TRUE	0	0.388658819056267	1		304	297	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482244	87482244	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049600-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	28	557	0	ENST00000277120.3:c.1531G>T	p.Glu511Ter	p.E511*	ENST00000277120		511	Gaa/Taa	14/19	0.388658819056267	1	FACETS	0.27	0.215	0.332	0.27	0.215	0.332	SUBCLONAL	1	TRUE	0	0.388658819056267	1		557	430	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076929	41076929	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049600-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	60	451	0	ENST00000373198.4:c.1491del	p.Phe498LeufsTer103	p.F498Lfs*103	ENST00000373198	NM_133170.3	497	ccC/cc	9/32	1	2	FACETS	0.68	0.587	0.781	0.68	0.587	0.781	SUBCLONAL	1	TRUE	1	0.388658819056267	2		451	454	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910371	29910372	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0049737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	39	1128	0	ENST00000376809.5:c.46dup	p.Ala16GlyfsTer83	p.A16Gfs*83	ENST00000376809	NM_002116.7	14	tcg/tcGg	1/8	1	2	FACETS	0.412	0.341	0.492	0.412	0.341	0.492	SUBCLONAL	1	TRUE	1	0.359634317006566	2		1128	526	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570064	212570064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55671017	NA	P-0049737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	15	482	1	ENST00000342788.4:c.1177C>T	p.Arg393Trp	p.R393W	ENST00000342788	NM_005235.2	393	Cgg/Tgg	10/28	1	2	FACETS	0.328	0.24	0.435	0.328	0.24	0.435	SUBCLONAL	1	TRUE	1	0.359634317006566	2		483	254	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220437	1220437	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	106	910	0	ENST00000326873.7:c.530T>C	p.Ile177Thr	p.I177T	ENST00000326873	NM_000455.4	177	aTc/aCc	4/10	0.359634317006566	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.359634317006566	1		910	448	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439754	51439754	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	22	452	0	ENST00000262662.1:c.319T>A	p.Leu107Met	p.L107M	ENST00000262662		107	Ttg/Atg	4/4	1	2	FACETS	0.409	0.317	0.516	0.409	0.317	0.516	SUBCLONAL	1	TRUE	1	0.359634317006566	2		452	299	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650821	37650821	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	75	760	0	ENST00000447079.4:c.2293G>C	p.Glu765Gln	p.E765Q	ENST00000447079	NM_015083.1	765	Gag/Cag	5/14	0.359634317006566	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	0	0.359634317006566	1		760	331	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540830	187540830	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	36	406	1	ENST00000441802.2:c.6910C>T	p.Gln2304Ter	p.Q2304*	ENST00000441802	NM_005245.3	2304	Caa/Taa	10/27	0.229738980077691	1	FACETS	0.944	0.786	1	0.944	0.786	1	CLONAL	1	TRUE	0	0.359634317006566	1		407	174	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651897	36651897	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	49	840	0	ENST00000244741.5:c.19G>T	p.Asp7Tyr	p.D7Y	ENST00000244741	NM_000389.4	7	Gat/Tat	2/3	1	2	FACETS	0.508	0.43	0.594	0.508	0.43	0.594	SUBCLONAL	1	TRUE	1	0.359634317006566	2		840	536	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0049751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	373	550	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.275538936679696	4	FACETS	0.879	0.837	0.922	1	0.991	1	CLONAL	4	TRUE	1	0.275538936679696	4		550	982	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576857	7576857	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	111	604	0	ENST00000269305.4:c.989T>G	p.Leu330Arg	p.L330R	ENST00000269305	NM_001126112.2	330	cTt/cGt	9/11	0.216473070593125	2	FACETS	1	0.957	1	0.558	0.502	0.617	CLONAL	1	TRUE	0	0.275538936679696	2		604	722	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602404	10602404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1432914621	NA	P-0049751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	435	891	0	ENST00000171111.5:c.1174G>A	p.Ala392Thr	p.A392T	ENST00000171111	NM_203500.1	392	Gcc/Acc	3/6	0.275538936679696	5	FACETS	0.874	0.831	0.917	0.874	0.831	0.917	CLONAL	3	TRUE	2	0.275538936679696	5		891	1702	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589841	55589841	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	145	387	0	ENST00000288135.5:c.1327del	p.Cys443ValfsTer20	p.C443Vfs*20	ENST00000288135	NM_000222.2	441	taT/ta	8/21	0.275538936679696	6	FACETS	0.965	0.88	1	0.643	0.587	0.702	CLONAL	2	TRUE	3	0.275538936679696	6		387	846	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39239341	39239341	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1176763588	NA	P-0049751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	34	450	0	ENST00000402219.2:c.2316G>C	p.Glu772Asp	p.E772D	ENST00000402219	NM_005633.3	772	gaG/gaC	14/23	0.275538936679696	3	FACETS	0.446	0.363	0.539	0.223	0.181	0.27	SUBCLONAL	1	TRUE	1	0.275538936679696	3		450	630	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	36	411	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.883	0.726	1	0.883	0.726	1	CLONAL	1	TRUE	1	0.18	2		411	453	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495360	149495360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs114435947	NA	P-0049781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	77	818	2	ENST00000261799.4:c.3287C>T	p.Ala1096Val	p.A1096V	ENST00000261799	NM_002609.3	1096	gCg/gTg	23/23	1	2	FACETS	0.991	0.869	1	0.991	0.869	1	CLONAL	1	TRUE	1	0.18	2		820	863	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579433	7579433	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1064793279	NA	P-0049781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	77	836	0	ENST00000269305.4:c.254del	p.Pro85LeufsTer38	p.P85Lfs*38	ENST00000269305	NM_001126112.2	85	cCt/ct	4/11	NA	2	FACETS	0.956	0.838	1			1	INDETERMINATE	1	TRUE	NA	0.18	2		836	895	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981170	201981171	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0049781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	88	842	0	ENST00000359651.3:c.249_250insG	p.Lys84GlufsTer8	p.K84Efs*8	ENST00000359651		83	-/G	2/8	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.18	2		842	934	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772951	135772951	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs118203724	NA	P-0050474-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	262	469	0	ENST00000298552.3:c.2672del	p.Asn891ThrfsTer40	p.N891Tfs*40	ENST00000298552	NM_001162426.1	891	aAc/ac	21/23	0.533687695323882	3	FACETS	0.838	0.795	0.88	0.838	0.795	0.88	CLONAL	3	TRUE	0	0.533687695323882	3		469	495	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077427	30077427	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0050474-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	62	321	0	ENST00000338641.4:c.1575-1G>A		p.X525_splice	ENST00000338641	NM_000268.3	525			0.145108461346445	3	FACETS	0.911	0.793	1	0.304	0.264	0.346	INDETERMINATE	1	TRUE	0	0.533687695323882	3		321	323	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189358	56189358	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050474-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	265	543	0	ENST00000399503.3:c.4390A>C	p.Ile1464Leu	p.I1464L	ENST00000399503	NM_005921.1	1464	Att/Ctt	20/20	0.533687695323882	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.533687695323882	3		543	595	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593405	48593405	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	71	310	0	ENST00000342988.3:c.1156G>C	p.Gly386Arg	p.G386R	ENST00000342988	NM_005359.5	386	Ggt/Cgt	10/12	0.33218171301352	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.33218171301352	1		310	332	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107095	27107096	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0050682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	103	516	1	ENST00000324856.7:c.6711_6712del	p.Leu2238AlafsTer39	p.L2238Afs*39	ENST00000324856	NM_006015.4	2236	CGc/c	20/20	0.33218171301352	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.33218171301352	1		517	512	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672758	86672758	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1204340475	NA	P-0050682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	70	364	0	ENST00000274376.6:c.2245C>T	p.Arg749Ter	p.R749*	ENST00000274376	NM_002890.2	749	Cga/Tga	17/25	0.33218171301352	1	FACETS	0.932	0.817	1	0.932	0.817	1	CLONAL	1	TRUE	0	0.33218171301352	1		364	377	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034489	47034489	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	121	306	0	ENST00000377604.3:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000377604	NM_001204468.1	192	Cag/Tag	6/24	1	1	FACETS	1	0.956	1	1	0.991	1	CLONAL	2	TRUE	0	0.33218171301352	1		306	286	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30103742	30103742	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0050682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	72	326	0	ENST00000331968.5:c.1196C>G	p.Ser399Ter	p.S399*	ENST00000331968	NM_002742.2	399	tCa/tGa	8/18	1	2	FACETS	0.915	0.801	1	0.915	0.801	1	CLONAL	1	TRUE	1	0.33218171301352	2		326	474	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727457	66727459	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs869025339	NA	P-0050682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	93	439	0	ENST00000307102.5:c.175_177del	p.Lys59del	p.K59del	ENST00000307102	NM_002755.3	58	cAGAag/cag	2/11	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.33218171301352	2		439	527	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729093	66729098	+	inframe_deletion	In_Frame_Del	DEL	CTGGAG	CTGGAG	-	novel	NA	P-0050682-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	108	503	0	ENST00000307102.5:c.301_306del	p.Leu101_Glu102del	p.L101_E102del	ENST00000307102	NM_002755.3	101	CTGGAG/-	3/11	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.33218171301352	2		503	621	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86667940	86667940	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	13	286	0	ENST00000274376.6:c.1704G>A	p.Trp568Ter	p.W568*	ENST00000274376	NM_002890.2	568	tgG/tgA	13/25	0.721083605357865	1	FACETS	0.64	0.481	0.813	0.64	0.481	0.813	SUBCLONAL	1	TRUE	0	0.721083605357865	1		286	36	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578493	7578493	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1206165503	NA	P-0050879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	248	917	0	ENST00000269305.4:c.437G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tGg/tAg	5/11	0.721083605357865	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.721083605357865	1		917	388	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482843	67482843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	182	603	0	ENST00000327367.4:c.1247C>T	p.Ser416Phe	p.S416F	ENST00000327367	NM_005902.3	416	tCc/tTc	9/9	0.721083605357865	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.721083605357865	1		603	302	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979979	7979979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	172	732	0	ENST00000319144.4:c.1358C>T	p.Ala453Val	p.A453V	ENST00000319144	NM_001139.2	453	gCc/gTc	10/15	0.721083605357865	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.721083605357865	1		732	297	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245404	153245404	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	82	510	0	ENST00000281708.4:c.1787C>G	p.Ser596Cys	p.S596C	ENST00000281708	NM_033632.3	596	tCt/tGt	11/12	0.721083605357865	1	FACETS	0.841	0.761	0.921	0.841	0.761	0.921	CLONAL	1	TRUE	0	0.721083605357865	1		510	173	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61197647	61197647	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	75	484	0	ENST00000301761.2:c.29C>A	p.Ser10Ter	p.S10*	ENST00000301761	NM_017841.2	10	tCg/tAg	1/4	0.412676694458388	1	FACETS	0.389	0.343	0.437	0.389	0.343	0.437	INDETERMINATE	1	TRUE	0	0.721083605357865	1		484	342	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967255	134967255	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	217	696	0	ENST00000398015.3:c.2594G>T	p.Arg865Leu	p.R865L	ENST00000398015	NM_004441.4	865	cGg/cTg	14/16	0.379866896723016	1	FACETS	0.85	0.8	0.899	0.85	0.8	0.899	INDETERMINATE	1	TRUE	0	0.721083605357865	1		696	453	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456504	32456504	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	27	113	0	ENST00000332351.3:c.388C>A	p.Pro130Thr	p.P130T	ENST00000332351	NM_024426.4	130	Cca/Aca	1/10	0.412676694458388	1	FACETS	0.55	0.45	0.658	0.55	0.45	0.658	INDETERMINATE	1	TRUE	0	0.721083605357865	1		113	87	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733286	40733286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	142	583	0	ENST00000373198.4:c.3520G>A	p.Glu1174Lys	p.E1174K	ENST00000373198	NM_133170.3	1174	Gag/Aag	26/32	0.379866896723016	1	FACETS	0.739	0.683	0.795	0.739	0.683	0.795	INDETERMINATE	1	TRUE	0	0.721083605357865	1		583	341	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135695	64135695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	83	759	0	ENST00000334205.4:c.1163C>T	p.Pro388Leu	p.P388L	ENST00000334205	NM_003942.2	388	cCa/cTa	10/17	0.412676694458388	1	FACETS	0.372	0.33	0.416	0.372	0.33	0.416	INDETERMINATE	1	TRUE	0	0.721083605357865	1		759	396	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037483	12037483	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	121	434	0	ENST00000396373.4:c.1114G>T	p.Asp372Tyr	p.D372Y	ENST00000396373	NM_001987.4	372	Gat/Tat	6/8	1	2	FACETS	0.925	0.844	1	0.925	0.844	1	CLONAL	1	TRUE	1	0.721083605357865	2		434	363	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937061	48937061	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	23	290	0	ENST00000267163.4:c.829del	p.Leu277SerfsTer9	p.L277Sfs*9	ENST00000267163	NM_000321.2	277	Ctc/tc	8/27	0.721083605357865	1	FACETS	0.85	0.701	1	0.85	0.701	1	CLONAL	1	TRUE	0	0.721083605357865	1		290	48	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961374	41961374	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	85	466	2	ENST00000219905.7:c.282G>T	p.Glu94Asp	p.E94D	ENST00000219905	NM_001164273.1	94	gaG/gaT	2/24	0.721083605357865	1	FACETS	0.847	0.769	0.926	0.847	0.769	0.926	CLONAL	1	TRUE	0	0.721083605357865	1		468	178	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007703	62007703	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	147	548	0	ENST00000392795.3:c.164C>A	p.Ala55Asp	p.A55D	ENST00000392795	NM_001039933.1	55	gCc/gAc	3/6	1	2	FACETS	0.985	0.908	1	0.985	0.908	1	CLONAL	1	TRUE	1	0.721083605357865	2		548	414	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733065	74733065	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	163	608	0	ENST00000359995.5:c.178G>T	p.Val60Phe	p.V60F	ENST00000359995	NM_001195427.1	60	Gtt/Ttt	1/3	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.721083605357865	2		608	424	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354043	15354043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	141	470	0	ENST00000263377.2:c.2837C>T	p.Pro946Leu	p.P946L	ENST00000263377	NM_058243.2	946	cCt/cTt	14/20	1	2	FACETS	0.942	0.867	1	0.942	0.867	1	CLONAL	1	TRUE	1	0.721083605357865	2		470	415	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967056	25967056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	196	713	0	ENST00000435504.4:c.2150C>T	p.Ser717Leu	p.S717L	ENST00000435504		717	tCa/tTa	13/13	0.412676694458388	1	FACETS	0.805	0.754	0.855	0.805	0.754	0.855	INDETERMINATE	1	TRUE	0	0.721083605357865	1		713	432	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096117	71096117	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	155	422	0	ENST00000318789.4:c.640C>G	p.Leu214Val	p.L214V	ENST00000318789	NM_032682.5	214	Ctt/Gtt	10/21	0.698024904786092	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.721083605357865	1		422	249	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096207	71096207	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	144	384	1	ENST00000318789.4:c.550C>T	p.Gln184Ter	p.Q184*	ENST00000318789	NM_032682.5	184	Cag/Tag	10/21	0.698024904786092	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.721083605357865	1		385	242	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920521	134920521	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	163	521	0	ENST00000398015.3:c.2336C>A	p.Thr779Asn	p.T779N	ENST00000398015	NM_004441.4	779	aCc/aAc	12/16	0.379866896723016	1	FACETS	0.786	0.731	0.84	0.786	0.731	0.84	INDETERMINATE	1	TRUE	0	0.721083605357865	1		521	368	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143043285	143043285	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	64	391	0	ENST00000262992.4:c.2131A>G	p.Arg711Gly	p.R711G	ENST00000262992	NM_001101669.1	711	Aga/Gga	19/24	0.721083605357865	1	FACETS	0.841	0.751	0.931	0.841	0.751	0.931	CLONAL	1	TRUE	0	0.721083605357865	1		391	135	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402742	139402742	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	340	871	1	ENST00000277541.6:c.3267G>T	p.Trp1089Cys	p.W1089C	ENST00000277541	NM_017617.3	1089	tgG/tgT	20/34	0.721083605357865	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.721083605357865	1		872	485	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0050979-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	719	330	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.698163956273371	5	FACETS	1	0.979	1	1	0.979	1	CLONAL	4	TRUE	1	0.698163956273371	5		330	1049	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955381	48955381	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0050979-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	17	199	0	ENST00000267163.4:c.1499-2A>G		p.X500_splice	ENST00000267163	NM_000321.2	500			0.677613657011417	0	FACETS		NA	1			1	NA	1	TRUE	0	0.698163956273371	0		199	94	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579527	7579528	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0050979-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	692	745	0	ENST00000269305.4:c.159dup	p.Phe54ValfsTer3	p.F54Vfs*3	ENST00000269305	NM_001126112.2	53	-/G	4/11	NA	2	FACETS	0.994	0.969	1			1	INDETERMINATE	2	TRUE	NA	0.698163956273371	2		745	997	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934530	9934530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050979-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	31	0	0	ENST00000330684.3:c.1625G>A	p.Gly542Asp	p.G542D	ENST00000330684	NM_001134407.1	542	gGc/gAc	7/13	0.698163956273371	3	FACETS	0.143	0.115	0.176	0.072	0.057	0.088	SUBCLONAL	1	TRUE	1	0.698163956273371	3		0	835	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0051170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	66	388	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.976	0.862	1	0.976	0.862	1	CLONAL	1	TRUE	1	0.676385363243294	2		388	200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0051170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	250	633	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.660641342638595	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.676385363243294	2		633	351	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918950	76918951	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0051170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	126	504	0	ENST00000373344.5:c.4040_4041del	p.Val1347GlufsTer2	p.V1347Efs*2	ENST00000373344	NM_000489.3	1347	gTG/g	12/35	0.287409481767565	1	FACETS	0.683	0.626	0.742	0.683	0.626	0.742	INDETERMINATE	1	TRUE	0	0.676385363243294	1		504	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882000	NA	P-0051170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	8	861	0	ENST00000269305.4:c.475G>A	p.Ala159Thr	p.A159T	ENST00000269305	NM_001126112.2	159	Gcc/Acc	5/11	0.660641342638595	2	FACETS	0.06	0.038	0.088	0.03	0.019	0.044	SUBCLONAL	1	TRUE	0	0.676385363243294	2		861	396	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344917	70344917	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051170-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	89	663	0	ENST00000374080.3:c.2147A>G	p.Glu716Gly	p.E716G	ENST00000374080		716	gAg/gGg	15/45	0.287409481767565	1	FACETS	0.638	0.573	0.705	0.638	0.573	0.705	INDETERMINATE	1	TRUE	0	0.676385363243294	1		663	273	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051210-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	30	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.756	0.612	0.916	0.756	0.612	0.916	CLONAL	1	TRUE	1	0.34227479563898	2		429	232	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562738	29562739	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555615472	NA	P-0051210-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	104	520	0	ENST00000356175.3:c.3822_3823del	p.Phe1275ProfsTer8	p.F1275Pfs*8	ENST00000356175	NM_000267.3	1273	aCT/a	28/57	0.31667265187264	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.34227479563898	1		520	470	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624537	93624537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237227040	NA	P-0051210-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	219	616	0	ENST00000375746.1:c.628G>A	p.Glu210Lys	p.E210K	ENST00000375746	NM_001174167.1	210	Gaa/Aaa	4/14	0.34227479563898	2	FACETS	0.881	0.823	0.941	0.881	0.823	0.941	CLONAL	2	TRUE	0	0.34227479563898	2		616	726	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069437	30069437	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051210-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	51	718	0	ENST00000338641.4:c.1303del	p.Val435CysfsTer4	p.V435Cfs*4	ENST00000338641	NM_000268.3	434	gaG/ga	12/16	0.34227479563898	1	FACETS	0.341	0.289	0.398	0.341	0.289	0.398	SUBCLONAL	1	TRUE	0	0.34227479563898	1		718	725	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182277	38182277	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051210-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	109	629	1	ENST00000396334.3:c.713A>T	p.Asp238Val	p.D238V	ENST00000396334	NM_002468.4	238	gAt/gTt	4/5	1	2	FACETS	0.777	0.697	0.861	0.777	0.697	0.861	SUBCLONAL	1	TRUE	1	0.34227479563898	2		630	820	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144146	11144146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1171	89	764	1	ENST00000358026.2:c.3727C>T	p.Arg1243Trp	p.R1243W	ENST00000358026	NM_001128849.1	1243	Cgg/Tgg	26/36	1	2	FACETS	0.633	0.559	0.713	0.633	0.559	0.713	SUBCLONAL	1	TRUE	1	0.223153496386145	2		765	1260	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534444	140534444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1258111302	NA	P-0051268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	84	376	0	ENST00000288602.6:c.469G>A	p.Val157Ile	p.V157I	ENST00000288602	NM_004333.4	157	Gtt/Att	3/18	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.223153496386145	2		376	713	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378639	25378639	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	76	422	0	ENST00000311936.3:c.359T>C	p.Leu120Ser	p.L120S	ENST00000311936	NM_004985.3	120	tTg/tCg	4/5	1	2	FACETS	1	0.958	1	1	0.986	1	CLONAL	2	TRUE	1	0.223153496386145	2		422	290	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900408	3900408	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	132	719	0	ENST00000262367.5:c.688G>C	p.Ala230Pro	p.A230P	ENST00000262367	NM_004380.2	230	Gcc/Ccc	2/31	1	2	FACETS	0.967	0.875	1	0.967	0.875	1	CLONAL	1	TRUE	1	0.223153496386145	2		719	1224	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786002	135786002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769331772	NA	P-0051268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1206	137	751	1	ENST00000298552.3:c.1219G>A	p.Val407Met	p.V407M	ENST00000298552	NM_001162426.1	407	Gtg/Atg	12/23	1	2	FACETS	0.914	0.829	1	0.914	0.829	1	CLONAL	1	TRUE	1	0.223153496386145	2		752	1343	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	114	411	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.355831140026389	2		411	539	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0051286-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	84	364	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.355831140026389	2		364	344	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0051294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	302	330	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.89811606584615	2		330	623	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251839	212251839	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	209	281	0	ENST00000342788.4:c.3220G>A	p.Glu1074Lys	p.E1074K	ENST00000342788	NM_005235.2	1074	Gaa/Aaa	27/28	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.89811606584615	2		281	462	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458878	120458878	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	375	586	2	ENST00000256646.2:c.6467C>G	p.Ser2156Cys	p.S2156C	ENST00000256646	NM_024408.3	2156	tCt/tGt	34/34	0.859323961434985	3	FACETS	1	0.955	1			1	CLONAL	1	TRUE	NA	0.89811606584615	3		588	1203	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256735	16256735	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	346	471	1	ENST00000375759.3:c.4000G>T	p.Glu1334Ter	p.E1334*	ENST00000375759	NM_015001.2	1334	Gaa/Taa	11/15	0.225504715967559	1	FACETS	0.625	0.597	0.653	0.625	0.597	0.653	INDETERMINATE	1	TRUE	0	0.89811606584615	1		472	679	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799201	45799201	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	246	542	3	ENST00000450313.1:c.232C>T	p.Gln78Ter	p.Q78*	ENST00000450313	NM_012222.2	78	Cag/Tag	3/16	0.225504715967559	1	FACETS	0.472	0.444	0.501	0.472	0.444	0.501	INDETERMINATE	1	TRUE	0	0.89811606584615	1		545	639	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425263	49425263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	799	598	6	ENST00000301067.7:c.13225G>A	p.Glu4409Lys	p.E4409K	ENST00000301067	NM_003482.3	4409	Gag/Aag	39/54	0.879384730082152	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.89811606584615	3		604	1273	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249332	133249332	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1275423655	NA	P-0051294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	375	571	0	ENST00000320574.5:c.1567G>C	p.Glu523Gln	p.E523Q	ENST00000320574	NM_006231.2	523	Gag/Cag	15/49	0.879384730082152	3	FACETS	0.917	0.87	0.965	0.458	0.435	0.483	CLONAL	1	TRUE	1	0.89811606584615	3		571	1320	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954040	32954040	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	268	411	0	ENST00000380152.3:c.9107A>C	p.Gln3036Pro	p.Q3036P	ENST00000380152		3036	cAa/cCa	23/27	0.89811606584615	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.89811606584615	1		411	321	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350954	89350954	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs747922528	NA	P-0051294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	502	643	0	ENST00000301030.4:c.1996C>T	p.Gln666Ter	p.Q666*	ENST00000301030	NM_001256183.1	666	Cag/Tag	9/13	0.89811606584615	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.89811606584615	1		643	587	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528752	157528752	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	303	416	0	ENST00000346085.5:c.6477G>C	p.Leu2159Phe	p.L2159F	ENST00000346085	NM_020732.3	2159	ttG/ttC	20/20	0.89811606584615	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.89811606584615	1		416	344	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946451	2946451	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	322	528	0	ENST00000396946.4:c.3286G>C	p.Glu1096Gln	p.E1096Q	ENST00000396946	NM_032415.4	1096	Gag/Cag	25/25	0.225504715967559	1	FACETS	0.546	0.519	0.574	0.546	0.519	0.574	INDETERMINATE	1	TRUE	0	0.89811606584615	1		528	723	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877808	151877808	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs767671441	NA	P-0051294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	30	267	0	ENST00000262189.6:c.7137G>T	p.Glu2379Asp	p.E2379D	ENST00000262189	NM_170606.2	2379	gaG/gaT	36/59	0.521501709707977	3	FACETS	0.178	0.142	0.218	0.089	0.071	0.109	INDETERMINATE	1	TRUE	1	0.89811606584615	3		267	545	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080539	5080539	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	15	268	0	ENST00000381652.3:c.2290C>G	p.Gln764Glu	p.Q764E	ENST00000381652	NM_004972.3	764	Caa/Gaa	18/25	0.89811606584615	1	FACETS	0.081	0.059	0.107	0.081	0.059	0.107	SUBCLONAL	1	TRUE	0	0.89811606584615	1		268	228	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813107	76813107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	276	396	0	ENST00000373344.5:c.6514G>A	p.Glu2172Lys	p.E2172K	ENST00000373344	NM_000489.3	2172	Gaa/Aaa	30/35	1	2	FACETS	0.977	0.925	1	0.977	0.925	1	CLONAL	1	TRUE	1	0.89811606584615	2		396	629	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0051317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	12	79	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	0.27317604062443	3	FACETS	1	0.872	1	0.738	0.532	0.977	CLONAL	1	TRUE	1	0.33250640908079	3		79	57	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29563039	29563039	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	53	310	0	ENST00000356175.3:c.3974+1del		p.R1325fs	ENST00000356175	NM_000267.3	1325	aGg/ag	29/57	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.33250640908079	2		310	228	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592318	29592318	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	54	461	1	ENST00000356175.3:c.4734del	p.Ala1580LeufsTer23	p.A1580Lfs*23	ENST00000356175	NM_000267.3	1578	tCc/tc	35/57	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.33250640908079	2		462	311	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875971	76875971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	61	337	0	ENST00000373344.5:c.5164C>T	p.His1722Tyr	p.H1722Y	ENST00000373344	NM_000489.3	1722	Cat/Tat	20/35	0.266327929049406	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.33250640908079	1		337	225	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0051487-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	12	286	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.197	0.138	0.269	0.197	0.138	0.269	SUBCLONAL	1	TRUE	1	0.624552348444386	2		286	195	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140449202	140449202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051487-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	4	0	0	ENST00000288602.6:c.1877G>A	p.Arg626Lys	p.R626K	ENST00000288602	NM_004333.4	626	aGa/aAa	16/18	0.10348825863345	4	FACETS	0.165	0.086	0.28	0.083	0.043	0.14	INDETERMINATE	1	TRUE	2	0.624552348444386	4		0	126	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867292	68867292	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051487-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	25	547	0	ENST00000261769.5:c.2539del	p.Ser847ProfsTer2	p.S847Pfs*2	ENST00000261769	NM_004360.3	847	Tcc/cc	16/16	0.624552348444386	1	FACETS	0.199	0.157	0.248	0.199	0.157	0.248	SUBCLONAL	1	TRUE	0	0.624552348444386	1		547	276	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592199	55592199	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051487-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	33	481	0	ENST00000288135.5:c.1523T>A	p.Phe508Tyr	p.F508Y	ENST00000288135	NM_000222.2	508	tTt/tAt	9/21	1	2	FACETS	0.433	0.355	0.521	0.433	0.355	0.521	SUBCLONAL	1	TRUE	1	0.624552348444386	2		481	244	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954379	48954379	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0051536-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	116	101	0	ENST00000267163.4:c.1498+2T>C		p.X500_splice	ENST00000267163	NM_000321.2	500			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		101	140	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0051902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	250	430	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.527732467318951	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.546768283608953	3		430	555	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0051902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	76	205	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.88	0.779	0.986	0.88	0.779	0.986	CLONAL	1	TRUE	1	0.546768283608953	2		205	316	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519757	NA	P-0051902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	85	146	0	ENST00000274335.5:c.1126G>C	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Cga	9/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.546768283608953	2		146	262	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696462	47696462	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	257	275	0	ENST00000347630.2:c.361C>G	p.Arg121Gly	p.R121G	ENST00000347630	NM_001007230.1	121	Cgg/Ggg	6/11	0.546768283608953	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.546768283608953	2		275	461	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424062	49424062	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs886041779	NA	P-0051902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	220	527	0	ENST00000301067.7:c.13999+1G>A		p.X4667_splice	ENST00000301067	NM_003482.3	4667			1	2	FACETS	0.958	0.893	1	0.958	0.893	1	CLONAL	1	TRUE	1	0.546768283608953	2		527	840	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059244	27059245	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0051902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	154	326	0	ENST00000324856.7:c.1882dup	p.Met628AsnfsTer14	p.M628Nfs*14	ENST00000324856	NM_006015.4	627	-/A	4/20	1	2	FACETS	0.933	0.857	1	0.933	0.857	1	CLONAL	1	TRUE	1	0.546768283608953	2		326	604	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106580	27106580	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	203	388	1	ENST00000324856.7:c.6191T>A	p.Leu2064His	p.L2064H	ENST00000324856	NM_006015.4	2064	cTc/cAc	20/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.546768283608953	2		389	668	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973051	25973057	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGAAG	GGAGAAG	-	novel	NA	P-0051902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	134	285	0	ENST00000435504.4:c.1368_1374del	p.Asn456LysfsTer64	p.N456Kfs*64	ENST00000435504		456	aaCTTCTCC/aa	12/13	1	2	FACETS	0.994	0.909	1	0.994	0.909	1	CLONAL	1	TRUE	1	0.546768283608953	2		285	493	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374661	149374661	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0051902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	177	346	0	ENST00000360632.3:c.431+2T>G		p.X144_splice	ENST00000360632	NM_015472.4	144			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.546768283608953	2		346	598	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1978220	1978220	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	180	469	0	ENST00000382891.5:c.3640T>A	p.Ser1214Thr	p.S1214T	ENST00000382891	NM_133335.3	1214	Tca/Aca	21/22	1	2	FACETS	0.833	0.77	0.899	0.833	0.77	0.899	CLONAL	1	TRUE	1	0.546768283608953	2		469	790	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183871	10183871	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs869025636	NA	P-0051958-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	191	647	0	ENST00000256474.2:c.340G>C	p.Gly114Arg	p.G114R	ENST00000256474	NM_000551.3	114	Ggt/Cgt	1/3	0.495315579919049	1	FACETS	0.976	0.908	1	0.976	0.908	1	CLONAL	1	TRUE	0	0.497033101012762	1		647	592	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856302	111856302	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051958-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	29	57	0	ENST00000341259.2:c.353C>A	p.Ala118Asp	p.A118D	ENST00000341259	NM_005475.2	118	gCc/gAc	2/8	1	2	FACETS	0.81	0.676	0.95	1	0.955	1	CLONAL	2	TRUE	1	0.497033101012762	2		57	72	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668720	52668742	+	frameshift_variant	Frame_Shift_Del	DEL	TGGTTATTCCGACAACTCCTAAC	TGGTTATTCCGACAACTCCTAAC	-	novel	NA	P-0051958-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	146	458	0	ENST00000394830.3:c.1177_1199del	p.Val393ArgfsTer6	p.V393Rfs*6	ENST00000394830	NM_018313.4	393	GTTAGGAGTTGTCGGAATAACCAa/a	12/30	0.495315579919049	1	FACETS	0.941	0.866	1	0.941	0.866	1	CLONAL	1	TRUE	0	0.497033101012762	1		458	469	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682377	52682377	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051958-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	103	334	0	ENST00000394830.3:c.796G>C	p.Gly266Arg	p.G266R	ENST00000394830	NM_018313.4	266	Ggc/Cgc	8/30	0.495315579919049	1	FACETS	0.908	0.821	0.998	0.908	0.821	0.998	CLONAL	1	TRUE	0	0.497033101012762	1		334	343	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0051958-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	132	353	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.952	0.87	1	0.952	0.87	1	CLONAL	1	TRUE	1	0.596643001250842	2		353	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0051958-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	258	928	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	0.596643001250842	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.596643001250842	1		928	557	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259557	89259557	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051958-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	130	440	0	ENST00000336596.2:c.701C>T	p.Ser234Phe	p.S234F	ENST00000336596	NM_005233.5	234	tCt/tTt	3/17	0.596643001250842	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.596643001250842	1		440	295	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992211	11992211	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051958-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	178	508	0	ENST00000396373.4:c.301G>A	p.Asp101Asn	p.D101N	ENST00000396373	NM_001987.4	101	Gac/Aac	3/8	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.596643001250842	2		508	580	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219405	1219406	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0051958-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	147	589	1	ENST00000326873.7:c.457_458delinsTT	p.Ala153Phe	p.A153F	ENST00000326873	NM_000455.4	153	GCc/TTc	3/10	0.596643001250842	1	FACETS	0.999	0.926	1	0.999	0.926	1	CLONAL	1	TRUE	0	0.596643001250842	1		590	346	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597373	10597373	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1389853223	NA	P-0051958-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	259	917	0	ENST00000171111.5:c.1830G>T	p.Met610Ile	p.M610I	ENST00000171111	NM_203500.1	610	atG/atT	6/6	0.571694060256712	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.596643001250842	1		917	552	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172205	99172205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775377216	NA	P-0051958-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	203	765	1	ENST00000074304.5:c.1771G>A	p.Asp591Asn	p.D591N	ENST00000074304	NM_001134224.1	591	Gat/Aat	17/26	1	2	FACETS	0.976	0.909	1	0.976	0.909	1	CLONAL	1	TRUE	1	0.596643001250842	2		766	697	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651477	52651477	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051958-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	147	528	0	ENST00000394830.3:c.1619G>C	p.Arg540Thr	p.R540T	ENST00000394830	NM_018313.4	540	aGa/aCa	15/30	0.596643001250842	1	FACETS	0.947	0.876	1	0.947	0.876	1	CLONAL	1	TRUE	0	0.596643001250842	1		528	365	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876953	151876953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051958-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	109	368	0	ENST00000262189.6:c.7408G>A	p.Val2470Ile	p.V2470I	ENST00000262189	NM_170606.2	2470	Gtt/Att	37/59	0.171136512141789	3	FACETS	1	0.965	1	0.573	0.518	0.63	INDETERMINATE	1	TRUE	1	0.596643001250842	3		368	414	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549202	87549202	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051958-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	141	394	0	ENST00000277120.3:c.1759G>T	p.Val587Leu	p.V587L	ENST00000277120		587	Gtg/Ttg	15/19	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.596643001250842	2		394	404	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	84	411	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.48671298066646	2		411	306	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584542	48584543	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0051965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	162	516	0	ENST00000342988.3:c.717_718dup	p.Ile240ArgfsTer2	p.I240Rfs*2	ENST00000342988	NM_005359.5	239	cag/cAGag	6/12	0.48671298066646	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.48671298066646	1		516	418	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197321	26197321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	216	787	1	ENST00000356476.2:c.158G>A	p.Arg53His	p.R53H	ENST00000356476		53	cGc/cAc	1/1	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.48671298066646	2		788	866	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0052004-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	111	411	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.816	0.737	0.899	0.816	0.737	0.899	CLONAL	1	TRUE	1	0.537787689165292	2		411	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0052004-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	300	833	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.537787689165292	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.537787689165292	1		837	742	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905873	50905873	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756829126	NA	P-0052004-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	308	799	0	ENST00000440232.2:c.845C>T	p.Thr282Met	p.T282M	ENST00000440232	NM_002691.3	282	aCg/aTg	8/27	1	2	FACETS	0.984	0.928	1	0.984	0.928	1	CLONAL	1	TRUE	1	0.537787689165292	2		799	1164	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972585	25972585	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052004-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	129	335	0	ENST00000435504.4:c.1840C>T	p.Arg614Ter	p.R614*	ENST00000435504		614	Cga/Tga	12/13	1	2	FACETS	0.933	0.851	1	0.933	0.851	1	CLONAL	1	TRUE	1	0.537787689165292	2		335	514	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021232	31021232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148964601	NA	P-0052004-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	193	504	0	ENST00000375687.4:c.1231C>T	p.Arg411Cys	p.R411C	ENST00000375687	NM_015338.5	411	Cgc/Tgc	12/13	0.537787689165292	3	FACETS	0.883	0.816	0.952	0.441	0.408	0.476	CLONAL	1	TRUE	1	0.537787689165292	3		504	1032	SUCCESS
APC	324	MSKCC	GRCh37	5	112175912	112175912	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201801	NA	P-0052004-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	72	271	0	ENST00000257430.4:c.4621C>T	p.Gln1541Ter	p.Q1541*	ENST00000257430	NM_000038.5	1541	Cag/Tag	16/16	0.394949839891733	1	FACETS	0.866	0.769	0.968	0.866	0.769	0.968	CLONAL	1	TRUE	0	0.537787689165292	1		271	226	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441414	52441414	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1553645838	NA	P-0052004-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	206	593	0	ENST00000460680.1:c.437+1G>T		p.X146_splice	ENST00000460680	NM_004656.3	146			1	2	FACETS	0.967	0.9	1	0.967	0.9	1	CLONAL	1	TRUE	1	0.537787689165292	2		593	792	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276974	123276974	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052004-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	67	290	0	ENST00000358487.5:c.943G>C	p.Ala315Pro	p.A315P	ENST00000358487	NM_000141.4	315	Gcc/Ccc	8/18	0.124087059755848	5	FACETS	0.798	0.694	0.911			1	INDETERMINATE	1	TRUE	NA	0.537787689165292	5		290	564	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229387	36229405	+	frameshift_variant	Frame_Shift_Del	DEL	CCCATCGAGGATGCCAGCA	CCCATCGAGGATGCCAGCA	-	novel	NA	P-0052004-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	222	672	0	ENST00000222270.7:c.8077_8095del	p.Pro2693ThrfsTer39	p.P2693Tfs*39	ENST00000222270	NM_014727.1	2693	CCCATCGAGGATGCCAGCAac/ac	37/37	1	2	FACETS	0.933	0.87	0.998	0.933	0.87	0.998	CLONAL	1	TRUE	1	0.537787689165292	2		672	885	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280139	142280139	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052004-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	164	439	0	ENST00000350721.4:c.1295G>T	p.Arg432Leu	p.R432L	ENST00000350721	NM_001184.3	432	cGt/cTt	5/47	1	2	FACETS	0.871	0.802	0.943	0.871	0.802	0.943	CLONAL	1	TRUE	1	0.537787689165292	2		439	700	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348105	89348106	+	frameshift_variant	Frame_Shift_Ins	INS	GG	GG	AAC	novel	NA	P-0052004-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	335	705	2	ENST00000301030.4:c.4844_4845delinsGTT	p.Ser1615CysfsTer26	p.S1615Cfs*26	ENST00000301030	NM_001256183.1	1615	tCC/tGTT	9/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.537787689165292	2		707	1139	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0052008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	465	460	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.74848372095192	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.770400906217395	3		460	798	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980862	40980862	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	288	619	1	ENST00000373198.4:c.1624G>T	p.Val542Leu	p.V542L	ENST00000373198	NM_133170.3	542	Gtg/Ttg	10/32	NA	2	FACETS	0.994	0.94	1			1	INDETERMINATE	1	TRUE	NA	0.770400906217395	2		620	752	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984856	9984856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	293	608	1	ENST00000330684.3:c.1109G>A	p.Arg370Gln	p.R370Q	ENST00000330684	NM_001134407.1	370	cGg/cAg	4/13	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.770400906217395	2		609	661	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574931	41574931	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	680	665	0	ENST00000263253.7:c.7216C>G	p.Leu2406Val	p.L2406V	ENST00000263253	NM_001429.3	2406	Ctc/Gtc	31/31	0.770400906217395	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.770400906217395	2		665	850	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259268	89259268	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	157	465	0	ENST00000336596.2:c.412C>A	p.His138Asn	p.H138N	ENST00000336596	NM_005233.5	138	Cat/Aat	3/17	1	2	FACETS	0.984	0.912	1	0.984	0.912	1	CLONAL	1	TRUE	1	0.770400906217395	2		465	414	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149290708	149290708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	65	720	2	ENST00000360632.3:c.511G>A	p.Ala171Thr	p.A171T	ENST00000360632	NM_015472.4	171	Gcc/Acc	3/7	1	2	FACETS	0.183	0.158	0.21	0.183	0.158	0.21	SUBCLONAL	1	TRUE	1	0.770400906217395	2		722	924	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0052016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	635	738	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.350844721353172	7	FACETS	0.935	0.902	0.969	0.935	0.902	0.969	CLONAL	5	TRUE	2	0.350844721353172	7		738	1453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	348	1099	0	ENST00000269305.4:c.469G>C	p.Val157Leu	p.V157L	ENST00000269305	NM_001126112.2	157	Gtc/Ctc	5/11	0.277105172406071	2	FACETS	1	0.995	1	0.746	0.705	0.787	CLONAL	1	TRUE	0	0.350844721353172	2		1099	1330	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551889	150551889	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs755460962	NA	P-0052016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	195	504	0	ENST00000369026.2:c.118A>G	p.Lys40Glu	p.K40E	ENST00000369026	NM_021960.4	40	Aag/Gag	1/3	0.276972620221022	3	FACETS	1	0.979	1	0.748	0.697	0.801	CLONAL	2	TRUE	0	0.350844721353172	3		504	582	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927943	49927943	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs368569784	NA	P-0052016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	142	865	1	ENST00000296474.3:c.3785A>G	p.Tyr1262Cys	p.Y1262C	ENST00000296474	NM_002447.2	1262	tAt/tGt	18/20	1	2	FACETS	0.77	0.701	0.843	0.77	0.701	0.843	SUBCLONAL	1	TRUE	1	0.350844721353172	2		866	1051	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151866306	151866306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	47	580	0	ENST00000262189.6:c.9482G>A	p.Arg3161Lys	p.R3161K	ENST00000262189	NM_170606.2	3161	aGg/aAg	41/59	0.350844721353172	3	FACETS	0.34	0.286	0.401	0.17	0.143	0.201	SUBCLONAL	1	TRUE	1	0.350844721353172	3		580	925	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0052022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	47	561	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.24322494531035	1	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	0	0.24322494531035	1		561	338	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0052022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	110	872	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.15358375006666	2	FACETS	0.765	0.689	0.845	0.765	0.689	0.845	SUBCLONAL	2	TRUE	0	0.24322494531035	2		873	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0052022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	35	795	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.15358375006666	2	FACETS	0.5	0.409	0.602	0.25	0.204	0.301	SUBCLONAL	1	TRUE	0	0.24322494531035	2		795	576	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916947	178916947	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	38	350	0	ENST00000263967.3:c.334A>T	p.Ile112Phe	p.I112F	ENST00000263967	NM_006218.2	112	Atc/Ttc	2/21	1	2	FACETS	0.827	0.684	0.985	0.827	0.684	0.985	CLONAL	1	TRUE	1	0.24322494531035	2		350	378	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868216	37868216	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	595	645	0	ENST00000269571.5:c.937C>G	p.Leu313Val	p.L313V	ENST00000269571		313	Ctc/Gtc	8/27	0.24322494531035	5	FACETS	0.93	0.9	0.959			1	CLONAL	7	TRUE	NA	0.24322494531035	5		645	1026	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266579	198266579	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	31	326	1	ENST00000335508.6:c.2257C>T	p.Leu753Phe	p.L753F	ENST00000335508	NM_012433.2	753	Ctt/Ttt	16/25	1	2	FACETS	0.6	0.485	0.73	0.6	0.485	0.73	SUBCLONAL	1	TRUE	1	0.24322494531035	2		327	425	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861170	57861170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764293116	NA	P-0052022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	27	585	0	ENST00000228682.2:c.967C>T	p.Arg323Trp	p.R323W	ENST00000228682	NM_005269.2	323	Cgg/Tgg	9/12	1	2	FACETS	0.453	0.36	0.56	0.453	0.36	0.56	SUBCLONAL	1	TRUE	1	0.24322494531035	2		585	490	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912758	32912758	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	33	362	0	ENST00000380152.3:c.4266G>C	p.Glu1422Asp	p.E1422D	ENST00000380152		1422	gaG/gaC	11/27	0.24322494531035	1	FACETS	0.632	0.515	0.764	0.632	0.515	0.764	SUBCLONAL	1	TRUE	0	0.24322494531035	1		362	377	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349586	70349586	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	32	592	0	ENST00000374080.3:c.3748C>T	p.Pro1250Ser	p.P1250S	ENST00000374080		1250	Cca/Tca	27/45	1	2	FACETS	0.49	0.397	0.596	0.49	0.397	0.596	SUBCLONAL	1	TRUE	1	0.24322494531035	2		592	537	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107147	27107147	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	111	648	0	ENST00000324856.7:c.6758T>C	p.Leu2253Pro	p.L2253P	ENST00000324856	NM_006015.4	2253	cTg/cCg	20/20	0.204354950442025	3	FACETS	1	0.966	1	0.59	0.529	0.654	CLONAL	1	TRUE	1	0.232646704458849	3		648	903	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453987	140453987	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs180177040	NA	P-0052127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	8	0	0	ENST00000288602.6:c.1741A>C	p.Asn581His	p.N581H	ENST00000288602	NM_004333.4	581	Aat/Cat	14/18	1	2	FACETS	0.226	0.144	0.332	0.226	0.144	0.332	SUBCLONAL	1	TRUE	1	0.16	2		0	443	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396401	396401	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	69	835	0	ENST00000262320.3:c.625G>T	p.Glu209Ter	p.E209*	ENST00000262320	NM_003502.3	209	Gaa/Taa	2/11	1	2	FACETS	0.976	0.848	1	0.976	0.848	1	CLONAL	1	TRUE	1	0.16	2		835	884	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0052147-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	76	525	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.324750776675463	2		525	440	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134266	11134266	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064796254	NA	P-0052147-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	104	700	1	ENST00000358026.2:c.2932C>T	p.Arg978Ter	p.R978*	ENST00000358026	NM_001128849.1	978	Cga/Tga	20/36	0.324750776675463	1	FACETS	0.858	0.77	0.952	0.858	0.77	0.952	CLONAL	1	TRUE	0	0.324750776675463	1		701	625	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599958	10599971	+	frameshift_variant	Frame_Shift_Del	DEL	CCACATCGTAGCGC	CCACATCGTAGCGC	-	novel	NA	P-0052147-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	136	807	0	ENST00000171111.5:c.1605_1618del	p.Arg536AsnfsTer33	p.R536Nfs*33	ENST00000171111	NM_203500.1	535	gaGCGCTACGATGTGGaa/gaaa	5/6	0.324750776675463	1	FACETS	0.862	0.784	0.944	0.862	0.784	0.944	CLONAL	1	TRUE	0	0.324750776675463	1		807	814	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219352	1219366	+	inframe_deletion	In_Frame_Del	DEL	GCATGCAGGAAATGC	GCATGCAGGAAATGC	-	novel	NA	P-0052147-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	145	812	0	ENST00000326873.7:c.404_418del	p.Gly135_Leu140delinsVal	p.G135_L140delinsV	ENST00000326873	NM_000455.4	135	gGCATGCAGGAAATGCtg/gtg	3/10	0.324750776675463	1	FACETS	0.999	0.912	1	0.999	0.912	1	CLONAL	1	TRUE	0	0.324750776675463	1		812	749	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567272	226567272	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0052147-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	67	528	2	ENST00000366794.5:c.1612+2T>C		p.X538_splice	ENST00000366794	NM_001618.3	538			0.29629139838874	3	FACETS	0.88	0.766	1	0.44	0.383	0.502	CLONAL	1	TRUE	1	0.324750776675463	3		530	545	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494878	56494895	+	inframe_deletion	In_Frame_Del	DEL	CCCCGTCCAGTCTCTCTA	CCCCGTCCAGTCTCTCTA	-	novel	NA	P-0052147-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	119	561	1	ENST00000267101.3:c.3236_3253del	p.Pro1079_Leu1084del	p.P1079_L1084del	ENST00000267101	NM_001982.3	1079	CCCCGTCCAGTCTCTCTA/-	27/28	0.287786070780554	4	FACETS	1	0.974	1	0.618	0.557	0.681	CLONAL	1	TRUE	2	0.324750776675463	4		562	786	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417499	139417499	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052147-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	167	850	0	ENST00000277541.6:c.545G>T	p.Cys182Phe	p.C182F	ENST00000277541	NM_017617.3	182	tGt/tTt	4/34	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.324750776675463	2		850	967	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1331482	1331482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052147-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	139	598	0	ENST00000400841.2:c.46G>A	p.Gly16Arg	p.G16R	ENST00000400841		16	Gga/Aga	1/6	0.166291871343426	2	FACETS	0.934	0.849	1			1	INDETERMINATE	1	TRUE	NA	0.324750776675463	2		598	917	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0052150-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	385	813	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.64434894646177	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.670565401773077	2		813	573	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910398	29910398	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052150-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	388	930	0	ENST00000376809.5:c.68G>C	p.Trp23Ser	p.W23S	ENST00000376809	NM_002116.7	23	tGg/tCg	1/8	0.670565401773077	5	FACETS	0.987	0.939	1	0.658	0.626	0.691	CLONAL	2	TRUE	2	0.670565401773077	5		930	1176	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433787	149433787	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052213-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	298	817	0	ENST00000286301.3:c.2764G>A	p.Asp922Asn	p.D922N	ENST00000286301	NM_005211.3	922	Gac/Aac	22/22	0.522810351146045	4	FACETS	1	0.967	1	0.521	0.49	0.554	CLONAL	1	TRUE	2	0.655051712954127	4		817	1444	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098760	47098763	+	frameshift_variant	Frame_Shift_Del	DEL	GATA	GATA	TT	novel	NA	P-0052213-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	562	756	1	ENST00000409792.3:c.6511_6514delinsAA	p.Tyr2171AsnfsTer12	p.Y2171Nfs*12	ENST00000409792	NM_014159.6	2171	TATCcc/AAcc	15/21	0.655051712954127	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.655051712954127	2		757	826	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	38	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.897	0.751	1	0.897	0.751	1	CLONAL	1	TRUE	1	0.4897703763992	2		429	173	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0052220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	31	250	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.4897703763992	3	FACETS	0.312	0.252	0.381	0.156	0.126	0.191	SUBCLONAL	1	TRUE	1	0.4897703763992	3		250	505	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552152	29552152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199474738	NA	P-0052220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	67	192	0	ENST00000356175.3:c.1885G>A	p.Gly629Arg	p.G629R	ENST00000356175	NM_000267.3	629	Ggg/Agg	17/57	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.4897703763992	2		192	254	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166184	118166184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371434677	NA	P-0052220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	90	292	0	ENST00000369448.3:c.694G>A	p.Ala232Thr	p.A232T	ENST00000369448	NM_017709.3	232	Gcc/Acc	2/2	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.4897703763992	2		292	340	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692910	89692910	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	107	362	0	ENST00000371953.3:c.394G>C	p.Gly132Arg	p.G132R	ENST00000371953	NM_000314.4	132	Ggt/Cgt	5/9	0.4897703763992	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.4897703763992	1		362	305	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0052248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	15	280	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.475082396612126	7	FACETS	0.25	0.182	0.333	0.05	0.036	0.067	SUBCLONAL	1	TRUE	2	0.475082396612126	7		280	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576851	7576851	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0052248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	268	893	0	ENST00000269305.4:c.993+2T>C		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.114446693440985	6	FACETS	1	0.983	1	0.748	0.703	0.795	INDETERMINATE	2	TRUE	3	0.475082396612126	6		893	980	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434289	49434289	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	369	1225	1	ENST00000301067.7:c.7264C>T	p.Gln2422Ter	p.Q2422*	ENST00000301067	NM_003482.3	2422	Cag/Tag	31/54	0.433054266375836	3	FACETS	0.889	0.845	0.934	0.889	0.845	0.934	CLONAL	2	TRUE	1	0.475082396612126	3		1226	1081	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599916	10599916	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs946921406	NA	P-0052248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	716	1152	1	ENST00000171111.5:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000171111	NM_203500.1	554	Cga/Tga	5/6	0.465745844717045	4	FACETS	0.896	0.87	0.922	0.896	0.87	0.922	CLONAL	4	TRUE	0	0.475082396612126	4		1153	1240	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497683	120497747	+	frameshift_variant	Frame_Shift_Del	DEL	GTTTCCATGGATGCAGGGATTGCTCAGGCATTCGTTCACCTGTGAGTAGCAGCTGGGGTGATGGG	GTTTCCATGGATGCAGGGATTGCTCAGGCATTCGTTCACCTGTGAGTAGCAGCTGGGGTGATGGG	-	novel	NA	P-0052248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	232	676	0	ENST00000256646.2:c.2135_2199del	p.Pro712LeufsTer9	p.P712Lfs*9	ENST00000256646	NM_024408.3	712	cCCCATCACCCCAGCTGCTACTCACAGGTGAACGAATGCCTGAGCAATCCCTGCATCCATGGAAAC/c	13/34	0.429416866327169	2	FACETS	0.913	0.859	0.967	0.913	0.859	0.967	CLONAL	2	TRUE	0	0.475082396612126	2		676	535	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204651	108204651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	93	214	0	ENST00000278616.4:c.7966C>T	p.Leu2656Phe	p.L2656F	ENST00000278616	NM_000051.3	2656	Ctt/Ttt	54/63	0.114446693440985	6	FACETS	1	0.965	1	0.783	0.704	0.866	INDETERMINATE	2	TRUE	3	0.475082396612126	6		214	325	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041977	14041977	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	185	634	0	ENST00000311895.7:c.2524G>T	p.Glu842Ter	p.E842*	ENST00000311895	NM_005236.2	842	Gag/Tag	11/11	0.114446693440985	6	FACETS	1	0.971	1	0.727	0.674	0.783	INDETERMINATE	2	TRUE	3	0.475082396612126	6		634	696	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654634	67654634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	241	732	1	ENST00000264010.4:c.1121C>T	p.Thr374Ile	p.T374I	ENST00000264010	NM_006565.3	374	aCt/aTt	6/12	0.114446693440985	6	FACETS	1	0.944	1	0.674	0.63	0.72	INDETERMINATE	2	TRUE	3	0.475082396612126	6		733	978	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577133	7577146	+	frameshift_variant	Frame_Shift_Del	DEL	TGTTCCGTCCCAGT	TGTTCCGTCCCAGT	-	novel	NA	P-0052248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	279	923	0	ENST00000269305.4:c.792_805del	p.Gly266Ter	p.G266*	ENST00000269305	NM_001126112.2	264	ctACTGGGACGGAACAgc/ctgc	8/11	0.114446693440985	6	FACETS	1	0.968	1	0.698	0.656	0.741	INDETERMINATE	2	TRUE	3	0.475082396612126	6		923	1094	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99850117	99850117	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	273	1067	1	ENST00000280892.6:c.7G>T	p.Asp3Tyr	p.D3Y	ENST00000280892	NM_001130678.1	3	Gac/Tac	1/7	0.415098941720354	2	FACETS	0.877	0.829	0.926	0.877	0.829	0.926	CLONAL	2	TRUE	0	0.475082396612126	2		1068	655	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541408	187541409	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	205	559	0	ENST00000441802.2:c.6331_6332insT	p.Gly2111ValfsTer15	p.G2111Vfs*15	ENST00000441802	NM_005245.3	2111	ggc/gTgc	10/27	0.415098941720354	2	FACETS	0.848	0.794	0.902	0.848	0.794	0.902	CLONAL	2	TRUE	0	0.475082396612126	2		559	509	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250524	26250524	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	323	1129	0	ENST00000446824.2:c.310C>A	p.Leu104Ile	p.L104I	ENST00000446824	NM_021018.2	104	Ctc/Atc	1/1	0.340211809039967	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.475082396612126	1		1129	862	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519739	137519739	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	68	407	0	ENST00000367739.4:c.899C>T	p.Pro300Leu	p.P300L	ENST00000367739	NM_000416.2	300	cCt/cTt	7/7	0.461433242044997	3	FACETS	0.87	0.761	0.988	0.435	0.38	0.494	CLONAL	1	TRUE	1	0.475082396612126	3		407	407	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285830	39285830	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052248-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	62	505	0	ENST00000402219.2:c.329T>G	p.Ile110Ser	p.I110S	ENST00000402219	NM_005633.3	110	aTt/aGt	3/23	0.475082396612126	4	FACETS	0.666	0.575	0.765	0.222	0.191	0.255	SUBCLONAL	1	TRUE	1	0.475082396612126	4		505	578	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0052258-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	199	430	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.100482211568958	3	FACETS	1	0.983	1	0.79	0.735	0.848	INDETERMINATE	2	TRUE	0	0.267718095468111	3		430	711	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795109	242795109	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs763228671	NA	P-0052258-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	96	999	0	ENST00000334409.5:c.100C>A	p.Pro34Thr	p.P34T	ENST00000334409	NM_005018.2	34	Ccc/Acc	2/5	1	2	FACETS	0.774	0.688	0.865	0.774	0.688	0.865	SUBCLONAL	1	TRUE	1	0.267718095468111	2		999	927	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511641	66511641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052258-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	57	430	0	ENST00000358598.2:c.101C>T	p.Ser34Phe	p.S34F	ENST00000358598	NM_212471.2	34	tCt/tTt	2/11	0.100482211568958	3	FACETS	0.655	0.561	0.758	0.218	0.187	0.253	INDETERMINATE	1	TRUE	0	0.267718095468111	3		430	737	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555646	21555646	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052258-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	71	798	0	ENST00000382592.4:c.2624G>T	p.Gly875Val	p.G875V	ENST00000382592	NM_014572.2	875	gGg/gTg	6/8	1	2	FACETS	0.718	0.626	0.817	0.718	0.626	0.817	SUBCLONAL	1	TRUE	1	0.267718095468111	2		798	739	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961093	41961093	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0052258-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	27	238	0	ENST00000219905.7:c.1A>G	p.Met1?	p.M1?	ENST00000219905	NM_001164273.1	1	Atg/Gtg	2/24	1	2	FACETS	0.67	0.534	0.825	0.67	0.534	0.825	SUBCLONAL	1	TRUE	1	0.267718095468111	2		238	301	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113113	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0052258-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	35	258	0	ENST00000345146.2:c.394_395delinsTT	p.Arg132Phe	p.R132F	ENST00000345146	NM_005896.2	132	CGt/TTt	4/10	1	2	FACETS	0.812	0.667	0.973	0.812	0.667	0.973	CLONAL	1	TRUE	1	0.267718095468111	2		258	322	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191561	10191561	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs561874453	NA	P-0052258-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	113	508	0	ENST00000256474.2:c.554A>G	p.Tyr185Cys	p.Y185C	ENST00000256474	NM_000551.3	185	tAc/tGc	3/3	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.267718095468111	2		508	736	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691839	30691839	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052258-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	42	411	0	ENST00000295754.5:c.341A>T	p.Glu114Val	p.E114V	ENST00000295754	NM_003242.5	114	gAa/gTa	3/7	1	2	FACETS	0.577	0.481	0.683	0.577	0.481	0.683	SUBCLONAL	1	TRUE	1	0.267718095468111	2		411	544	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200036	128200036	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052258-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	132	912	0	ENST00000341105.2:c.1269G>T	p.Glu423Asp	p.E423D	ENST00000341105	NM_032638.4	423	gaG/gaT	6/6	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.267718095468111	2		912	914	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0052263-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	97	286	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.222495227003996	3	FACETS	1	0.968	1	0.61	0.545	0.679	CLONAL	1	TRUE	1	0.315035709203975	3		286	584	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056500	26056500	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs372319415	NA	P-0052263-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	41	354	0	ENST00000343677.2:c.157G>C	p.Glu53Gln	p.E53Q	ENST00000343677	NM_005319.3	53	Gag/Cag	1/1	1	2	FACETS	0.611	0.509	0.724	0.611	0.509	0.724	SUBCLONAL	1	TRUE	1	0.315035709203975	2		354	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577560	7577560	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520002	NA	P-0052263-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	202	591	1	ENST00000269305.4:c.721T>C	p.Ser241Pro	p.S241P	ENST00000269305	NM_001126112.2	241	Tcc/Ccc	7/11	0.25479057661635	2	FACETS	0.819	0.761	0.879	0.819	0.761	0.879	CLONAL	2	TRUE	0	0.315035709203975	2		592	783	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714415	40714415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765339833	NA	P-0052263-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	115	571	0	ENST00000373198.4:c.3982G>A	p.Asp1328Asn	p.D1328N	ENST00000373198	NM_133170.3	1328	Gac/Aac	29/32	0.315035709203975	6	FACETS	1	0.955	1	0.278	0.25	0.308	CLONAL	1	TRUE	2	0.315035709203975	6		571	1070	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724175	112724175	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052263-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	88	369	1	ENST00000369452.4:c.59C>T	p.Ser20Leu	p.S20L	ENST00000369452	NM_007373.3	20	tCa/tTa	2/9	0.222495227003996	3	FACETS	0.999	0.886	1	0.5	0.443	0.56	CLONAL	1	TRUE	1	0.315035709203975	3		370	647	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687075	37687075	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052263-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	222	593	0	ENST00000447079.4:c.3979G>C	p.Glu1327Gln	p.E1327Q	ENST00000447079	NM_015083.1	1327	Gag/Cag	14/14	0.198460592621056	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.315035709203975	4		593	849	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422666	47422666	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052263-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	98	693	0	ENST00000377045.4:c.138C>A	p.Asp46Glu	p.D46E	ENST00000377045	NM_001654.4	46	gaC/gaA	3/16	0.315035709203975	3	FACETS	0.774	0.69	0.865	0.387	0.345	0.433	SUBCLONAL	1	TRUE	1	0.315035709203975	3		693	930	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304138	91304138	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052263-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	41	452	0	ENST00000355112.3:c.1535G>T	p.Gly512Val	p.G512V	ENST00000355112	NM_000057.2	512	gGa/gTa	7/22	0.209542656730489	3	FACETS	0.433	0.359	0.515	0.216	0.179	0.258	SUBCLONAL	1	TRUE	1	0.315035709203975	3		452	696	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449441	149449441	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052263-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	40	473	0	ENST00000286301.3:c.1505C>G	p.Ser502Cys	p.S502C	ENST00000286301	NM_005211.3	502	tCt/tGt	10/22	0.118109859845242	3	FACETS	0.458	0.379	0.546	0.153	0.126	0.182	INDETERMINATE	1	TRUE	0	0.315035709203975	3		473	642	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643744	52643744	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052309-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	54	501	0	ENST00000394830.3:c.2152T>C	p.Tyr718His	p.Y718H	ENST00000394830	NM_018313.4	718	Tac/Cac	17/30	0.195841042490512	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		501	466	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0052444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	511	330	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.755240662673631	8	FACETS	0.97	0.941	0.999	0.832	0.806	0.857	CLONAL	6	TRUE	1	0.755240662673631	8		330	759	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350783	89350783	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	251	788	0	ENST00000301030.4:c.2167G>C	p.Asp723His	p.D723H	ENST00000301030	NM_001256183.1	723	Gac/Cac	9/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.755240662673631	2		788	594	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233100	69233100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867680779	NA	P-0052444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	124	502	0	ENST00000462284.1:c.965C>T	p.Pro322Leu	p.P322L	ENST00000462284	NM_002392.5	322	cCa/cTa	11/11	1	2	FACETS	0.895	0.818	0.973	0.895	0.818	0.973	CLONAL	1	TRUE	1	0.755240662673631	2		502	367	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859639	151859639	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	207	579	0	ENST00000262189.6:c.11023C>T	p.Gln3675Ter	p.Q3675*	ENST00000262189	NM_170606.2	3675	Cag/Tag	43/59	0.755240662673631	1	FACETS	0.989	0.937	1	0.989	0.937	1	CLONAL	1	TRUE	0	0.755240662673631	1		579	345	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871751	35871751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	362	685	0	ENST00000216797.5:c.755C>T	p.Ser252Phe	p.S252F	ENST00000216797	NM_020529.2	252	tCt/tTt	5/6	1	2	FACETS	0.982	0.934	1	0.982	0.934	1	CLONAL	1	TRUE	1	0.755240662673631	2		685	976	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268857	115268857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	187	583	0	ENST00000438362.2:c.1753G>A	p.Asp585Asn	p.D585N	ENST00000438362	NM_001242891.1	585	Gat/Aat	14/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.755240662673631	2		583	447	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944756	31944756	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	111	198	0	ENST00000340398.3:c.345G>C	p.Lys115Asn	p.K115N	ENST00000340398	NM_001013699.2	115	aaG/aaC	1/1	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.755240662673631	2		198	275	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235916	133235916	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs769386598	NA	P-0052444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	357	774	0	ENST00000320574.5:c.3240C>G	p.Ile1080Met	p.I1080M	ENST00000320574	NM_006231.2	1080	atC/atG	26/49	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.755240662673631	2		774	868	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629038	14629038	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	279	584	0	ENST00000254322.2:c.124G>C	p.Glu42Gln	p.E42Q	ENST00000254322	NM_006145.1	42	Gag/Cag	1/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.755240662673631	2		584	706	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226131	53226131	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	368	837	0	ENST00000375401.3:c.2718G>C	p.Glu906Asp	p.E906D	ENST00000375401	NM_004187.3	906	gaG/gaC	19/26	0.755240662673631	3	FACETS	1	0.986	1	0.552	0.524	0.581	CLONAL	1	TRUE	1	0.755240662673631	3		837	1216	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939613	76939613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	243	619	0	ENST00000373344.5:c.1135G>A	p.Asp379Asn	p.D379N	ENST00000373344	NM_000489.3	379	Gat/Aat	9/35	0.211340898167653	3	FACETS	0.92	0.87	0.969	0.613	0.58	0.646	INDETERMINATE	2	TRUE	0	0.755240662673631	3		619	482	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0052472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	194	768	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.639862837418584	2		768	585	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687306	37687306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1172789499	NA	P-0052472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	185	756	2	ENST00000447079.4:c.4210C>T	p.Arg1404Cys	p.R1404C	ENST00000447079	NM_015083.1	1404	Cgt/Tgt	14/14	1	2	FACETS	0.945	0.877	1	0.945	0.877	1	CLONAL	1	TRUE	1	0.639862837418584	2		758	612	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041375	42041375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764277967	NA	P-0052472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	134	625	0	ENST00000219905.7:c.5570C>T	p.Ser1857Leu	p.S1857L	ENST00000219905	NM_001164273.1	1857	tCg/tTg	17/24	1	2	FACETS	0.792	0.723	0.863	0.792	0.723	0.863	SUBCLONAL	1	TRUE	1	0.639862837418584	2		625	529	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259244	89259244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	123	460	0	ENST00000336596.2:c.388G>A	p.Asp130Asn	p.D130N	ENST00000336596	NM_005233.5	130	Gat/Aat	3/17	0.639862837418584	3	FACETS	1	0.944	1			1	CLONAL	1	TRUE	NA	0.639862837418584	3		460	483	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916903	178916903	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	191	611	1	ENST00000263967.3:c.290C>A	p.Pro97His	p.P97H	ENST00000263967	NM_006218.2	97	cCc/cAc	2/21	1	2	FACETS	0.954	0.886	1	0.954	0.886	1	CLONAL	1	TRUE	1	0.639862837418584	2		612	626	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0052472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	49	186	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.982	0.848	1	0.982	0.848	1	CLONAL	1	TRUE	1	0.639862837418584	2		187	156	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076945	41076945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767453141	NA	P-0052472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	123	603	0	ENST00000373198.4:c.1475C>T	p.Ser492Phe	p.S492F	ENST00000373198	NM_133170.3	492	tCc/tTc	9/32	0.639862837418584	1	FACETS	0.646	0.589	0.704	0.646	0.589	0.704	SUBCLONAL	1	TRUE	0	0.639862837418584	1		603	405	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545734	106545734	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	127	668	0	ENST00000359195.3:c.3211C>T	p.Gln1071Ter	p.Q1071*	ENST00000359195	NM_002649.2	1071	Cag/Tag	11/11	0.1454876115986	3	FACETS	1	0.966	1	0.561	0.511	0.612	INDETERMINATE	1	TRUE	1	0.639862837418584	3		668	467	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595821	52595821	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	347	601	0	ENST00000394830.3:c.4094G>A	p.Trp1365Ter	p.W1365*	ENST00000394830	NM_018313.4	1365	tGg/tAg	26/30	0.608902125070385	2	FACETS	0.977	0.939	1	0.977	0.939	1	CLONAL	2	TRUE	0	0.639862837418584	2		601	555	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631107	69631107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782695249	NA	P-0052472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	129	834	0	ENST00000334134.2:c.305G>A	p.Arg102Lys	p.R102K	ENST00000334134	NM_005247.2	102	aGg/aAg	2/3	1	2	FACETS	0.996	0.911	1	0.996	0.911	1	CLONAL	1	TRUE	1	0.639862837418584	2		834	405	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106208	27106208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773088565	NA	P-0052472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	159	703	1	ENST00000324856.7:c.5819C>T	p.Pro1940Leu	p.P1940L	ENST00000324856	NM_006015.4	1940	cCa/cTa	20/20	1	2	FACETS	0.919	0.847	0.992	0.919	0.847	0.992	CLONAL	1	TRUE	1	0.639862837418584	2		704	541	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210790	36210790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	166	1151	1	ENST00000222270.7:c.541C>T	p.Arg181Trp	p.R181W	ENST00000222270	NM_014727.1	181	Cgg/Tgg	3/37	1	2	FACETS	0.804	0.742	0.869	0.804	0.742	0.869	CLONAL	1	TRUE	1	0.639862837418584	2		1152	645	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40684192	40684192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199907924	NA	P-0052472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	142	530	0	ENST00000249776.8:c.790G>A	p.Glu264Lys	p.E264K	ENST00000249776	NM_033286.3	264	Gaa/Aaa	8/9	1	2	FACETS	0.87	0.798	0.945	0.87	0.798	0.945	CLONAL	1	TRUE	1	0.639862837418584	2		530	510	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125513777	125513777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1363144435	NA	P-0052472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	161	444	0	ENST00000428830.2:c.905C>T	p.Pro302Leu	p.P302L	ENST00000428830	NM_001114121.2	302	cCa/cTa	9/14	NA	2	FACETS	1	0.932	1			1	INDETERMINATE	1	TRUE	NA	0.639862837418584	2		444	499	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437498	49437498	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223905716	NA	P-0052472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	151	908	1	ENST00000301067.7:c.5387G>A	p.Arg1796Gln	p.R1796Q	ENST00000301067	NM_003482.3	1796	cGg/cAg	23/54	1	2	FACETS	0.877	0.807	0.95	0.877	0.807	0.95	CLONAL	1	TRUE	1	0.639862837418584	2		909	538	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748290	43748290	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	193	870	1	ENST00000382044.4:c.2516C>T	p.Ser839Phe	p.S839F	ENST00000382044	NM_001141980.1	839	tCc/tTc	12/28	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.639862837418584	2		871	599	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66525086	66525086	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	125	389	0	ENST00000358598.2:c.845T>C	p.Ile282Thr	p.I282T	ENST00000358598	NM_212471.2	282	aTt/aCt	9/11	1	2	FACETS	0.809	0.737	0.884	0.809	0.737	0.884	CLONAL	1	TRUE	1	0.639862837418584	2		389	483	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252762	10252762	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	155	937	0	ENST00000340748.4:c.3203T>A	p.Leu1068Gln	p.L1068Q	ENST00000340748		1068	cTg/cAg	29/40	1	2	FACETS	0.832	0.766	0.901	0.832	0.766	0.901	CLONAL	1	TRUE	1	0.639862837418584	2		937	582	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968261	18968261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	125	1010	1	ENST00000262803.5:c.2101C>T	p.Gln701Ter	p.Q701*	ENST00000262803	NM_002911.3	701	Cag/Tag	15/24	1	2	FACETS	0.955	0.872	1	0.955	0.872	1	CLONAL	1	TRUE	1	0.639862837418584	2		1011	409	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705553	47705553	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553369759	NA	P-0052472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	137	393	0	ENST00000233146.2:c.2353C>T	p.His785Tyr	p.H785Y	ENST00000233146	NM_000251.2	785	Cat/Tat	14/16	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.639862837418584	2		393	419	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770617	40770617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749916516	NA	P-0052472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	90	505	0	ENST00000373198.4:c.2765C>T	p.Ser922Leu	p.S922L	ENST00000373198	NM_133170.3	922	tCg/tTg	19/32	0.639862837418584	1	FACETS	0.623	0.559	0.69	0.623	0.559	0.69	SUBCLONAL	1	TRUE	0	0.639862837418584	1		505	307	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775479	39775479	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	113	709	0	ENST00000288319.7:c.541C>T	p.Pro181Ser	p.P181S	ENST00000288319	NM_182918.3	181	Ccc/Tcc	4/10	1	2	FACETS	0.795	0.721	0.874	0.795	0.721	0.874	SUBCLONAL	1	TRUE	1	0.639862837418584	2		709	444	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589818	55589818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	170	483	0	ENST00000288135.5:c.1300C>T	p.Pro434Ser	p.P434S	ENST00000288135	NM_000222.2	434	Cca/Tca	8/21	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.639862837418584	2		483	510	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249505	153249505	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	160	534	0	ENST00000281708.4:c.1273T>G	p.Trp425Gly	p.W425G	ENST00000281708	NM_033632.3	425	Tgg/Ggg	9/12	0.1454876115986	3	FACETS	1	0.982	1	0.611	0.564	0.66	INDETERMINATE	1	TRUE	1	0.639862837418584	3		534	540	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978432	2978432	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	110	925	0	ENST00000396946.4:c.898G>A	p.Ala300Thr	p.A300T	ENST00000396946	NM_032415.4	300	Gcc/Acc	7/25	0.157800798936488	0	FACETS	0.253	0.228	0.279			1	INDETERMINATE	1	TRUE	0	0.639862837418584	0		925	490	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729382	41729382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	125	746	0	ENST00000242208.4:c.1147C>T	p.Pro383Ser	p.P383S	ENST00000242208	NM_002192.2	383	Ccc/Tcc	3/3	1	2	FACETS	0.911	0.831	0.993	0.911	0.831	0.993	CLONAL	1	TRUE	1	0.639862837418584	2		746	429	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250527	110250527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	139	676	0	ENST00000374672.4:c.148C>T	p.His50Tyr	p.H50Y	ENST00000374672	NM_004235.4	50	Cac/Tac	3/5	1	2	FACETS	0.983	0.902	1	0.983	0.902	1	CLONAL	1	TRUE	1	0.639862837418584	2		676	442	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128246859	128246859	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052472-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	145	624	1	ENST00000265960.3:c.1070C>T	p.Ser357Leu	p.S357L	ENST00000265960	NM_001006617.1	357	tCa/tTa	9/12	1	2	FACETS	0.906	0.833	0.983	0.906	0.833	0.983	CLONAL	1	TRUE	1	0.639862837418584	2		625	500	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0052481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	326	550	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	NA	2	FACETS	1	0.961	1			1	INDETERMINATE	2	TRUE	NA	0.379312414602582	2		550	846	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578512	7578532	+	inframe_deletion	In_Frame_Del	DEL	TCTTGGCCAGTTGGCAAAACA	TCTTGGCCAGTTGGCAAAACA	-	novel	NA	P-0052481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	196	960	0	ENST00000269305.4:c.398_418del	p.Met133_Lys139del	p.M133_K139del	ENST00000269305	NM_001126112.2	133	aTGTTTTGCCAACTGGCCAAGAcc/acc	5/11	0.379312414602582	1	FACETS	0.996	0.923	1	0.996	0.923	1	CLONAL	1	TRUE	0	0.379312414602582	1		960	841	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310824	123310824	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	161	713	0	ENST00000358487.5:c.604C>G	p.His202Asp	p.H202D	ENST00000358487	NM_000141.4	202	Cat/Gat	5/18	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.379312414602582	2		713	763	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938499	44938499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	165	610	0	ENST00000377967.4:c.3047G>A	p.Gly1016Glu	p.G1016E	ENST00000377967	NM_021140.2	1016	gGa/gAa	20/29	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.379312414602582	2		610	798	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163903	47163908	+	frameshift_variant	Frame_Shift_Ins	INS	CTTCTT	CTTCTT	GACGGGCGGATCACCCGTCTTGG	novel	NA	P-0052481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	90	552	0	ENST00000409792.3:c.2218_2223delinsCCAAGACGGGTGATCCGCCCGTC	p.Lys740ProfsTer33	p.K740Pfs*33	ENST00000409792	NM_014159.6	740	AAGAAG/CCAAGACGGGTGATCCGCCCGTC	3/21	1	2	FACETS	0.695	0.617	0.778	0.695	0.617	0.778	SUBCLONAL	1	TRUE	1	0.379312414602582	2		552	683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0052483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	42	840	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	1	2	FACETS	0.708	0.589	0.841	0.708	0.589	0.841	SUBCLONAL	1	TRUE	1	0.14	2		840	847	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155046	55155046	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	34	502	0	ENST00000257290.5:c.2755G>C	p.Asp919His	p.D919H	ENST00000257290	NM_006206.4	919	Gac/Cac	20/23	1	2	FACETS	0.895	0.73	1	0.895	0.73	1	CLONAL	1	TRUE	1	0.14	2		502	543	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118697	115118697	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052549-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	166	359	0	ENST00000257566.3:c.644A>G	p.Asp215Gly	p.D215G	ENST00000257566	NM_016569.3	215	gAc/gGc	2/8	0.295401613641458	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	1	0.304456157028815	3		359	612	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0052564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	196	286	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.412340655748317	4	FACETS	1	0.941	1	1	0.941	1	CLONAL	3	TRUE	1	0.476531844545113	4		286	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	458	728	18	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	0.476531844545113	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.476531844545113	2		746	851	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939408	36939408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	336	854	32	ENST00000361632.4:c.442C>T	p.Pro148Ser	p.P148S	ENST00000361632		148	Cct/Tct	4/16	0.476531844545113	2	FACETS	1	0.991	1	0.608	0.575	0.642	CLONAL	1	TRUE	0	0.476531844545113	2		886	1160	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925341	131925341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	21	199	1	ENST00000265335.6:c.1264G>A	p.Glu422Lys	p.E422K	ENST00000265335		422	Gag/Aag	9/25	1	2	FACETS	0.639	0.497	0.8	0.639	0.497	0.8	SUBCLONAL	1	TRUE	1	0.476531844545113	2		200	138	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169377	11169377	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519916	NA	P-0052613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	140	461	0	ENST00000361445.4:c.7498A>T	p.Ile2500Phe	p.I2500F	ENST00000361445	NM_004958.3	2500	Att/Ttt	56/58	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.316444912194371	2		461	651	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115830	8115837	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGGCCG	CCCGGCCG	-	novel	NA	P-0052613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	116	560	0	ENST00000346208.3:c.1179_1186del	p.Ala394LeufsTer110	p.A394Lfs*110	ENST00000346208		392	aaCCCGGCCGcc/aacc	6/6	NA	2	FACETS	1	0.912	1			1	INDETERMINATE	1	TRUE	NA	0.316444912194371	2		560	725	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808932	3808933	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0052613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	145	565	1	ENST00000262367.5:c.3291_3292delinsAG	p.Leu1098Val	p.L1098V	ENST00000262367	NM_004380.2	1097	acCCta/acAGta	17/31	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.316444912194371	2		566	780	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545922	41545922	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1029166382	NA	P-0052613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	121	665	1	ENST00000263253.7:c.2537C>T	p.Pro846Leu	p.P846L	ENST00000263253	NM_001429.3	846	cCc/cTc	14/31	1	2	FACETS	0.974	0.88	1	0.974	0.88	1	CLONAL	1	TRUE	1	0.316444912194371	2		666	785	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170009677	170009677	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	97	360	0	ENST00000295797.4:c.1239C>A	p.Phe413Leu	p.F413L	ENST00000295797	NM_002740.5	413	ttC/ttA	13/18	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.316444912194371	2		360	574	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879670	151879670	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	56	208	0	ENST00000262189.6:c.5275C>T	p.Gln1759Ter	p.Q1759*	ENST00000262189	NM_170606.2	1759	Cag/Tag	36/59	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.316444912194371	2		208	334	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945601	151945606	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	CGCCAC	CGCCAC	-	novel	NA	P-0052613-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	91	308	0	ENST00000262189.6:c.1913_1918del	p.Cys638_Glu640delinsTer	p.C638_E640delins*	ENST00000262189	NM_170606.2	638	tGTGGCGaa/taa	14/59	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.316444912194371	2		308	499	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0052615-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	103	286	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.36021733353774	5	FACETS	1	0.974	1	0.798	0.726	0.871	INDETERMINATE	2	FALSE	2	0.662404307841441	5		286	259	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225060	NA	P-0052615-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	110	510	0	ENST00000263967.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000263967	NM_006218.2	104	cCa/cTa	2/21	0.36021733353774	5	FACETS	1	0.953	1	0.714	0.65	0.78	INDETERMINATE	2	FALSE	2	0.662404307841441	5		510	309	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196186	108196186	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786202583	NA	P-0052615-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	129	541	0	ENST00000278616.4:c.6722A>G	p.Asn2241Ser	p.N2241S	ENST00000278616	NM_000051.3	2241	aAc/aGc	46/63	0.316682393840114	6	FACETS	0.999	0.921	1	0.999	0.921	1	INDETERMINATE	3	FALSE	3	0.662404307841441	6		541	302	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115731	8115732	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0052615-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	41	375	0	ENST00000346208.3:c.1078_1079dup	p.Ile361AlafsTer44	p.I361Afs*44	ENST00000346208		359	-/GG	6/6	0.662404307841441	4	FACETS	0.53	0.442	0.628	0.265	0.221	0.314	SUBCLONAL	1	FALSE	2	0.662404307841441	4		375	388	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041624	14041624	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052615-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	44	491	0	ENST00000311895.7:c.2171T>C	p.Val724Ala	p.V724A	ENST00000311895	NM_005236.2	724	gTg/gCg	11/11	0.295076063390532	5	FACETS	0.686	0.577	0.807	0.229	0.192	0.269	INDETERMINATE	1	FALSE	2	0.662404307841441	5		491	386	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0052639-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	388	441	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.497463858102967	3	FACETS	0.866	0.826	0.906	0.866	0.826	0.906	CLONAL	2	TRUE	1	0.634915432348306	3		441	930	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853277	68853277	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs566103420	NA	P-0052639-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	297	746	0	ENST00000261769.5:c.1660G>C	p.Glu554Gln	p.E554Q	ENST00000261769	NM_004360.3	554	Gag/Cag	11/16	NA	2	FACETS	0.985	0.929	1			1	INDETERMINATE	1	TRUE	NA	0.634915432348306	2		746	950	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874466	151874466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753744599	NA	P-0052639-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	390	577	0	ENST00000262189.6:c.8072C>T	p.Ser2691Phe	p.S2691F	ENST00000262189	NM_170606.2	2691	tCt/tTt	38/59	0.634915432348306	2	FACETS	0.929	0.893	0.965	0.929	0.893	0.965	CLONAL	2	TRUE	0	0.634915432348306	2		577	661	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	461445	461445	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052639-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	100	637	0	ENST00000399788.2:c.1075C>G	p.Arg359Gly	p.R359G	ENST00000399788	NM_001042603.1	359	Cga/Gga	9/28	0.634915432348306	1	FACETS	0.332	0.297	0.37	0.332	0.297	0.37	SUBCLONAL	1	TRUE	0	0.634915432348306	1		637	647	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579426	7579427	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0052639-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	438	925	0	ENST00000269305.4:c.260_261del	p.Pro87ArgfsTer61	p.P87Rfs*61	ENST00000269305	NM_001126112.2	87	cCA/c	4/11	0.616306598131781	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.634915432348306	1		925	899	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953869	17953869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052639-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	401	1023	0	ENST00000458235.1:c.533C>T	p.Ala178Val	p.A178V	ENST00000458235	NM_000215.3	178	gCc/gTc	5/24	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.634915432348306	2		1023	1231	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520200	9520200	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052639-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	245	671	2	ENST00000353224.5:c.2069C>T	p.Thr690Ile	p.T690I	ENST00000353224	NM_177990.2	690	aCa/aTa	10/10	0.610222806199847	3	FACETS	0.982	0.918	1	0.491	0.459	0.524	CLONAL	1	TRUE	1	0.634915432348306	3		673	1035	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037378	12037378	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0052639-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	75	857	0	ENST00000396373.4:c.1010-1G>C		p.X337_splice	ENST00000396373	NM_001987.4	337			0.634915432348306	1	FACETS	0.177	0.154	0.201	0.177	0.154	0.201	SUBCLONAL	1	TRUE	0	0.634915432348306	1		857	912	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953127	17953127	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs776551276	NA	P-0052639-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	190	534	0	ENST00000458235.1:c.859G>A	p.Glu287Lys	p.E287K	ENST00000458235	NM_000215.3	287	Gag/Aag	6/24	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.634915432348306	2		534	593	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981172	55981172	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052639-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	250	602	0	ENST00000263923.4:c.527G>C	p.Arg176Thr	p.R176T	ENST00000263923	NM_002253.2	176	aGa/aCa	5/30	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.634915432348306	2		602	785	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658354	206658354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs52817862	NA	P-0052698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	132	840	1	ENST00000367120.3:c.1448C>T	p.Thr483Met	p.T483M	ENST00000367120	NM_014002.3	483	aCg/aTg	14/22	0.443664401695485	3	FACETS	0.855	0.777	0.938	0.428	0.388	0.469	CLONAL	1	TRUE	1	0.458841820585072	3		841	827	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0052698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	292	761	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.368494157562027	2	FACETS	0.912	0.864	0.96	0.912	0.864	0.96	CLONAL	2	TRUE	0	0.458841820585072	2		761	698	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602493	10602493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	431	1126	0	ENST00000171111.5:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000171111	NM_203500.1	362	cGg/cAg	3/6	0.42982273921005	2	FACETS	0.946	0.905	0.987	0.946	0.905	0.987	CLONAL	2	TRUE	0	0.458841820585072	2		1126	993	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314572	30314572	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	247	771	1	ENST00000262643.3:c.1121G>T	p.Arg374Leu	p.R374L	ENST00000262643	NM_001238.2	374	cGa/cTa	12/12	0.42982273921005	2	FACETS	0.878	0.827	0.93	0.878	0.827	0.93	CLONAL	2	TRUE	0	0.458841820585072	2		772	613	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750502	41750502	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	207	751	1	ENST00000226382.2:c.126C>A	p.Phe42Leu	p.F42L	ENST00000226382	NM_003924.3	42	ttC/ttA	1/3	0.427020443177967	2	FACETS	0.921	0.863	0.979	0.921	0.863	0.979	CLONAL	2	TRUE	0	0.458841820585072	2		752	490	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386569	81386569	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	209	661	0	ENST00000222390.5:c.418G>T	p.Val140Leu	p.V140L	ENST00000222390	NM_000601.4	140	Gta/Tta	4/18	0.19993538963972	1	FACETS	1	0.989	1	1	0.989	1	INDETERMINATE	1	TRUE	0	0.458841820585072	1		661	547	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587386	29587386	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0052698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	167	408	0	ENST00000356175.3:c.4368-1G>T		p.X1456_splice	ENST00000356175	NM_000267.3	1456			0.368494157562027	2	FACETS	0.948	0.883	1	0.948	0.883	1	CLONAL	2	TRUE	0	0.458841820585072	2		408	384	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52685769	52685769	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	188	582	0	ENST00000394830.3:c.703C>T	p.Gln235Ter	p.Q235*	ENST00000394830	NM_018313.4	235	Cag/Tag	7/30	0.42982273921005	2	FACETS	0.897	0.837	0.956	0.897	0.837	0.956	CLONAL	2	TRUE	0	0.458841820585072	2		582	457	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538254	9538254	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0052698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	197	608	0	ENST00000353224.5:c.1743+1del		p.X581_splice	ENST00000353224	NM_177990.2	581			0.368494157562027	2	FACETS	1	0.991	1	0.724	0.674	0.775	CLONAL	1	TRUE	0	0.458841820585072	2		608	593	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412698	63412698	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	105	853	1	ENST00000330258.3:c.469G>T	p.Glu157Ter	p.E157*	ENST00000330258	NM_152424.3	157	Gag/Tag	2/2	0.458841820585072	1	FACETS	0.818	0.738	0.902	0.818	0.738	0.902	CLONAL	1	TRUE	0	0.458841820585072	1		854	431	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464892	120464892	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	96	679	0	ENST00000256646.2:c.5180G>T	p.Arg1727Leu	p.R1727L	ENST00000256646	NM_024408.3	1727	cGt/cTt	28/34	1	2	FACETS	0.799	0.714	0.888	0.799	0.714	0.888	SUBCLONAL	1	TRUE	1	0.458841820585072	2		679	524	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771377	112771377	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	199	617	0	ENST00000369452.4:c.1550A>G	p.Glu517Gly	p.E517G	ENST00000369452	NM_007373.3	517	gAg/gGg	9/9	0.458841820585072	3	FACETS	0.863	0.804	0.923	0.863	0.804	0.923	CLONAL	2	TRUE	1	0.458841820585072	3		617	618	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343345	118343345	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	82	491	0	ENST00000534358.1:c.1471C>T	p.Gln491Ter	p.Q491*	ENST00000534358	NM_005933.3	491	Cag/Tag	3/36	0.429109399977432	4	FACETS	0.933	0.824	1	0.311	0.274	0.35	CLONAL	1	TRUE	1	0.458841820585072	4		491	559	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582002	95582002	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0052698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	82	368	0	ENST00000393063.1:c.1907+2T>A		p.X636_splice	ENST00000393063	NM_030621.3	636			1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.458841820585072	2		368	319	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726721	88726721	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0052698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	195	609	1	ENST00000360948.2:c.324-1G>T		p.X108_splice	ENST00000360948	NM_001012338.2	108			0.42982273921005	2	FACETS	0.936	0.876	0.996	0.936	0.876	0.996	CLONAL	2	TRUE	0	0.458841820585072	2		610	454	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819742	81819742	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	399	831	0	ENST00000359376.3:c.148C>G	p.Arg50Gly	p.R50G	ENST00000359376	NM_002661.3	50	Cgg/Ggg	2/33	0.382281324939248	3	FACETS	0.899	0.861	0.937	0.899	0.861	0.937	CLONAL	3	TRUE	0	0.458841820585072	3		831	793	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965158	81965158	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs3189935	NA	P-0052698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	421	883	0	ENST00000359376.3:c.2638C>G	p.Gln880Glu	p.Q880E	ENST00000359376	NM_002661.3	880	Cag/Gag	25/33	0.382281324939248	3	FACETS	0.948	0.91	0.986	0.948	0.91	0.986	CLONAL	3	TRUE	0	0.458841820585072	3		883	793	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696656	47696656	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	321	648	0	ENST00000347630.2:c.292G>T	p.Val98Phe	p.V98F	ENST00000347630	NM_001007230.1	98	Gtt/Ttt	5/11	0.427891392787262	3	FACETS	0.856	0.815	0.897	0.856	0.815	0.897	CLONAL	3	TRUE	0	0.458841820585072	3		648	670	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281275	46281275	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	181	477	0	ENST00000371998.3:c.4072C>G	p.Gln1358Glu	p.Q1358E	ENST00000371998		1358	Cag/Gag	21/23	0.42982273921005	2	FACETS	0.979	0.915	1	0.979	0.915	1	CLONAL	2	TRUE	0	0.458841820585072	2		477	403	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691911	30691911	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	179	510	0	ENST00000295754.5:c.413G>T	p.Cys138Phe	p.C138F	ENST00000295754	NM_003242.5	138	tGt/tTt	3/7	0.42982273921005	2	FACETS	0.92	0.858	0.982	0.92	0.858	0.982	CLONAL	2	TRUE	0	0.458841820585072	2		510	424	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631628	119631628	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	140	417	0	ENST00000316626.5:c.638A>T	p.Asn213Ile	p.N213I	ENST00000316626		213	aAt/aTt	6/12	0.458841820585072	2	FACETS	0.784	0.722	0.848	0.784	0.722	0.848	SUBCLONAL	2	TRUE	0	0.458841820585072	2		417	389	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138452282	138452282	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0052698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	159	348	0	ENST00000289153.2:c.973-2A>T		p.X325_splice	ENST00000289153	NM_006219.2	325			0.42982273921005	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.458841820585072	2		348	335	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449478	31449478	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	213	526	0	ENST00000344624.3:c.2731del	p.Asp911IlefsTer35	p.D911Ifs*35	ENST00000344624		911	Gat/at	19/33	0.458841820585072	5	FACETS	1	0.957	1	0.69	0.643	0.739	CLONAL	2	TRUE	2	0.458841820585072	5		526	757	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752778	128752778	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	98	398	0	ENST00000377970.2:c.939G>C	p.Lys313Asn	p.K313N	ENST00000377970	NM_002467.4	313	aaG/aaC	3/3	0.448529927689912	4	FACETS	1	0.935	1	0.266	0.237	0.296	CLONAL	1	TRUE	0	0.458841820585072	4		398	586	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911553	101911553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	112	540	0	ENST00000374994.4:c.1478C>T	p.Ser493Leu	p.S493L	ENST00000374994	NM_004612.2	493	tCg/tTg	9/9	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.458841820585072	2		540	487	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0052725-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	87	430	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.846	0.749	0.95	0.846	0.749	0.95	CLONAL	1	TRUE	1	0.273861373673977	2		430	751	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4090603	4090603	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs912154933	NA	P-0052725-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	56	656	0	ENST00000262948.5:c.1196C>T	p.Ala399Val	p.A399V	ENST00000262948	NM_030662.3	399	gCc/gTc	11/11	1	2	FACETS	0.435	0.371	0.505	0.435	0.371	0.505	SUBCLONAL	1	TRUE	1	0.273861373673977	2		656	941	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629513	187629513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052725-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	119	629	0	ENST00000441802.2:c.1469C>T	p.Pro490Leu	p.P490L	ENST00000441802	NM_005245.3	490	cCt/cTt	2/27	1	2	FACETS	0.895	0.807	0.989	0.895	0.807	0.989	CLONAL	1	TRUE	1	0.273861373673977	2		629	971	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982136	201982136	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052725-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1216	74	710	0	ENST00000359651.3:c.660T>G	p.Asp220Glu	p.D220E	ENST00000359651		220	gaT/gaG	5/8	0.260652530039472	3	FACETS	0.476	0.415	0.543	0.238	0.207	0.272	SUBCLONAL	1	TRUE	1	0.273861373673977	3		710	1290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0052740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	874	649	1	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.877335871420607	2		650	995	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420314	88420314	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	307	516	0	ENST00000360948.2:c.2372G>T	p.Arg791Leu	p.R791L	ENST00000360948	NM_001012338.2	791	cGg/cTg	19/19	1	2	FACETS	0.996	0.945	1	0.996	0.945	1	CLONAL	1	TRUE	1	0.877335871420607	2		516	703	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874274	155874274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1185965337	NA	P-0052740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	696	649	1	ENST00000368323.3:c.257G>A	p.Arg86Gln	p.R86Q	ENST00000368323	NM_006912.5	86	cGg/cAg	5/6	0.87607980651314	3	FACETS	0.991	0.962	1	0.991	0.962	1	CLONAL	2	TRUE	1	0.877335871420607	3		650	1152	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129184	2129184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	585	932	1	ENST00000219476.3:c.3118G>A	p.Ala1040Thr	p.A1040T	ENST00000219476	NM_000548.3	1040	Gct/Act	27/42	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.877335871420607	2		933	1302	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456456	89456456	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	180	550	1	ENST00000336596.2:c.1632G>T	p.Met544Ile	p.M544I	ENST00000336596	NM_005233.5	544	atG/atT	8/17	0.877335871420607	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.877335871420607	1		551	226	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851294	156851294	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	1142	1036	0	ENST00000524377.1:c.2251G>T	p.Ala751Ser	p.A751S	ENST00000524377	NM_002529.3	751	Gcc/Tcc	17/17	0.87607980651314	3	FACETS	0.978	0.956	1	0.978	0.956	1	CLONAL	2	TRUE	1	0.877335871420607	3		1036	1915	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405421	70405421	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	301	684	0	ENST00000373644.4:c.2935A>G	p.Asn979Asp	p.N979D	ENST00000373644	NM_030625.2	979	Aac/Gac	4/12	1	2	FACETS	0.952	0.902	1	0.952	0.902	1	CLONAL	1	TRUE	1	0.877335871420607	2		684	721	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432373	432373	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0052740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	234	147	0	ENST00000399788.2:c.2151-1G>C		p.X717_splice	ENST00000399788	NM_001042603.1	717			0.877422218075823	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	TRUE	1	0.877335871420607	4		147	325	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257758	133257758	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	869	653	0	ENST00000320574.5:c.170G>T	p.Gly57Val	p.G57V	ENST00000320574	NM_006231.2	57	gGt/gTt	2/49	0.445296589067495	4	FACETS	1	0.997	1	0.83	0.808	0.852	INDETERMINATE	2	TRUE	1	0.877335871420607	4		653	1494	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782924	66782924	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1199306921	NA	P-0052740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	264	486	0	ENST00000307102.5:c.1153A>C	p.Ser385Arg	p.S385R	ENST00000307102	NM_002755.3	385	Agc/Cgc	11/11	1	2	FACETS	0.801	0.755	0.849	0.801	0.755	0.849	CLONAL	1	TRUE	1	0.877335871420607	2		486	751	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223789	2223789	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	527	884	1	ENST00000326181.6:c.1087G>T	p.Asp363Tyr	p.D363Y	ENST00000326181	NM_032271.2	363	Gac/Tac	12/21	1	2	FACETS	0.944	0.907	0.982	0.944	0.907	0.982	CLONAL	1	TRUE	1	0.877335871420607	2		885	1272	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925191	81925191	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	334	552	0	ENST00000359376.3:c.982A>T	p.Asn328Tyr	p.N328Y	ENST00000359376	NM_002661.3	328	Aac/Tac	11/33	0.877422218075823	1	FACETS	0.999	0.967	1	0.999	0.967	1	CLONAL	1	TRUE	0	0.877335871420607	1		552	428	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390432	56390432	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	140	404	0	ENST00000348428.3:c.1171A>T	p.Met391Leu	p.M391L	ENST00000348428	NM_006785.3	391	Atg/Ttg	10/17	0.867272132824171	3	FACETS	0.915	0.838	0.994	0.457	0.419	0.497	CLONAL	1	TRUE	1	0.877335871420607	3		404	502	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520152	9520152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201686986	NA	P-0052740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	343	601	0	ENST00000353224.5:c.2117C>T	p.Pro706Leu	p.P706L	ENST00000353224	NM_177990.2	706	cCg/cTg	10/10	0.107059553615745	3	FACETS	1	0.995	1	0.491	0.467	0.515	INDETERMINATE	1	TRUE	0	0.877335871420607	3		601	764	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385152	41385152	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs751630191	NA	P-0052740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	527	792	1	ENST00000373198.4:c.809G>T	p.Arg270Leu	p.R270L	ENST00000373198	NM_133170.3	270	cGc/cTc	6/32	0.107059553615745	3	FACETS	1	0.997	1	0.486	0.467	0.505	INDETERMINATE	1	TRUE	0	0.877335871420607	3		793	1185	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31504699	31504699	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1032572786	NA	P-0052740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	323	692	0	ENST00000344624.3:c.1631G>T	p.Arg544Leu	p.R544L	ENST00000344624		544	cGc/cTc	8/33	1	2	FACETS	0.93	0.883	0.977	0.93	0.883	0.977	CLONAL	1	TRUE	1	0.877335871420607	2		692	792	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576525	67576525	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	146	456	0	ENST00000274335.5:c.804C>G	p.Phe268Leu	p.F268L	ENST00000274335		268	ttC/ttG	5/15	1	2	FACETS	0.895	0.827	0.964	0.895	0.827	0.964	CLONAL	1	TRUE	1	0.877335871420607	2		456	372	SUCCESS
APC	324	MSKCC	GRCh37	5	112177358	112177358	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0052740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	71	378	0	ENST00000257430.4:c.6067A>T	p.Arg2023Ter	p.R2023*	ENST00000257430	NM_000038.5	2023	Aga/Tga	16/16	0.613106380092291	1	FACETS	0.313	0.276	0.353	0.313	0.276	0.353	SUBCLONAL	1	TRUE	0	0.877335871420607	1		378	290	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813546	32813546	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	413	596	0	ENST00000354258.4:c.2237A>G	p.Tyr746Cys	p.Y746C	ENST00000354258	NM_000593.5	746	tAc/tGc	11/11	1	2	FACETS	0.976	0.933	1	0.976	0.933	1	CLONAL	1	TRUE	1	0.877335871420607	2		596	965	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972955	68972955	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	206	557	0	ENST00000288368.4:c.1280G>C	p.Arg427Thr	p.R427T	ENST00000288368	NM_024870.2	427	aGg/aCg	11/40	1	2	FACETS	0.928	0.869	0.988	0.928	0.869	0.988	CLONAL	1	TRUE	1	0.877335871420607	2		557	506	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015040	37015040	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	463	655	0	ENST00000358127.4:c.364C>G	p.Arg122Gly	p.R122G	ENST00000358127	NM_001280556.1	122	Cgg/Ggg	3/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.877335871420607	2		655	1044	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285753	87285753	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	479	848	0	ENST00000277120.3:c.90C>G	p.Phe30Leu	p.F30L	ENST00000277120		30	ttC/ttG	2/19	1	2	FACETS	0.948	0.909	0.987	0.948	0.909	0.987	CLONAL	1	TRUE	1	0.877335871420607	2		848	1152	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933511	39933511	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1305	409	834	0	ENST00000378444.4:c.1088G>T	p.Arg363Met	p.R363M	ENST00000378444	NM_001123385.1	363	aGg/aTg	4/15	0.877422218075823	3	FACETS	0.783	0.743	0.823	0.391	0.371	0.412	SUBCLONAL	1	TRUE	1	0.877335871420607	3		834	1714	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426823	47426823	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	696	531	1	ENST00000377045.4:c.1068G>T	p.Gln356His	p.Q356H	ENST00000377045	NM_001654.4	356	caG/caT	10/16	0.877422218075823	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	1	0.877335871420607	3		532	1056	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410971	63410971	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	305	858	0	ENST00000330258.3:c.2196G>T	p.Met732Ile	p.M732I	ENST00000330258	NM_152424.3	732	atG/atT	2/2	0.3311022711878	3	FACETS	0.797	0.75	0.845	0.266	0.25	0.282	INDETERMINATE	1	TRUE	0	0.877335871420607	3		858	1255	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411069	63411069	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	336	811	0	ENST00000330258.3:c.2098C>A	p.Pro700Thr	p.P700T	ENST00000330258	NM_152424.3	700	Cct/Act	2/2	0.3311022711878	3	FACETS	0.888	0.839	0.938	0.296	0.279	0.313	INDETERMINATE	1	TRUE	0	0.877335871420607	3		811	1241	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340908	70340908	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1404	441	863	0	ENST00000374080.3:c.641G>T	p.Gly214Val	p.G214V	ENST00000374080		214	gGc/gTc	5/45	0.3311022711878	3	FACETS	0.784	0.746	0.823	0.261	0.248	0.275	INDETERMINATE	1	TRUE	0	0.877335871420607	3		863	1845	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343027	70343027	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	1036	716	0	ENST00000374080.3:c.1568T>C	p.Met523Thr	p.M523T	ENST00000374080		523	aTg/aCg	11/45	0.3311022711878	3	FACETS	1	0.993	1	0.69	0.674	0.706	INDETERMINATE	2	TRUE	0	0.877335871420607	3		716	1641	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937491	76937491	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	69	563	1	ENST00000373344.5:c.3257C>A	p.Ala1086Glu	p.A1086E	ENST00000373344	NM_000489.3	1086	gCa/gAa	9/35	0.3311022711878	3	FACETS	0.721	0.633	0.814	0.24	0.211	0.272	INDETERMINATE	1	TRUE	0	0.877335871420607	3		564	314	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551290	29551290	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	537	816	0	ENST00000389048.3:c.1340C>G	p.Thr447Arg	p.T447R	ENST00000389048	NM_004304.4	447	aCa/aGa	6/29	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.877335871420607	2		816	1205	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031557	11031566	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCCTCGGA	CTCCCTCGGA	GTTCCACT	novel	NA	P-0052740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1924	334	1033	3	ENST00000327064.4:c.1472_1481delinsGTTCCACT	p.Ser491CysfsTer28	p.S491Cfs*28	ENST00000327064	NM_199141.1	491	tCTCCCTCGGAa/tGTTCCACTa	13/16	0.877422218075823	3	FACETS	0.485	0.456	0.515	0.162	0.152	0.172	SUBCLONAL	1	TRUE	0	0.877335871420607	3		1036	2258	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0052781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	887	330	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.865808587280119	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	4	TRUE	0	0.865808587280119	4		330	947	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0052781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	523	377	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.265331551380075	5	FACETS	0.905	0.878	0.932	0.724	0.702	0.745	INDETERMINATE	4	TRUE	0	0.865808587280119	5		377	767	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0052781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	357	562	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.865808587280119	2		562	745	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0052781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	718	638	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	0.265331551380075	5	FACETS	0.943	0.92	0.965	0.754	0.736	0.772	INDETERMINATE	4	TRUE	0	0.865808587280119	5		638	1011	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750639	128750639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775522201	NA	P-0052781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	319	823	0	ENST00000377970.2:c.176C>T	p.Ala59Val	p.A59V	ENST00000377970	NM_002467.4	59	gCg/gTg	2/3	1	2	FACETS	0.893	0.847	0.94	0.893	0.847	0.94	CLONAL	1	TRUE	1	0.865808587280119	2		823	825	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239419	105239419	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	390	841	0	ENST00000349310.3:c.968A>G	p.Asp323Gly	p.D323G	ENST00000349310	NM_001014432.1	323	gAc/gGc	12/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.865808587280119	2		841	885	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274196	10274196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	287	638	0	ENST00000330684.3:c.73G>A	p.Ala25Thr	p.A25T	ENST00000330684	NM_001134407.1	25	Gcg/Acg	2/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.865808587280119	2		638	638	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406445	70406445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781773145	NA	P-0052781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	355	771	1	ENST00000373644.4:c.3959G>A	p.Arg1320Gln	p.R1320Q	ENST00000373644	NM_030625.2	1320	cGg/cAg	4/12	0.865808587280119	3	FACETS	0.967	0.916	1	0.484	0.458	0.51	CLONAL	1	TRUE	1	0.865808587280119	3		772	1215	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384940	17384940	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	306	975	0	ENST00000359435.4:c.490C>T	p.Arg164Cys	p.R164C	ENST00000359435	NM_001033549.1	164	Cgc/Tgc	5/9	1	2	FACETS	0.667	0.63	0.706	0.667	0.63	0.706	SUBCLONAL	1	TRUE	1	0.865808587280119	2		975	1059	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521992	157521992	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554235619	NA	P-0052781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	340	730	0	ENST00000346085.5:c.4264C>T	p.Gln1422Ter	p.Q1422*	ENST00000346085	NM_020732.3	1422	Cag/Tag	18/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.865808587280119	2		730	740	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776975	135776975	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0052781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	225	440	1	ENST00000298552.3:c.2502+1G>T		p.X834_splice	ENST00000298552	NM_001162426.1	834			1	2	FACETS	0.986	0.927	1	0.986	0.927	1	CLONAL	1	TRUE	1	0.865808587280119	2		441	527	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059195	27059196	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	C	novel	NA	P-0052781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	263	537	0	ENST00000324856.7:c.1832_1833delinsC	p.Gln611ProfsTer8	p.Q611Pfs*8	ENST00000324856	NM_006015.4	611	cAG/cC	4/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.865808587280119	2		537	591	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870848	12870849	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0052782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	260	273	0	ENST00000228872.4:c.78dup	p.Ser27LeufsTer98	p.S27Lfs*98	ENST00000228872	NM_004064.3	25	-/C	1/3	0.842666098204063	2	FACETS	0.941	0.908	0.971	0.941	0.908	0.971	CLONAL	2	TRUE	0	0.842666098204063	2		273	328	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73350222	73350222	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	57	191	0	ENST00000377767.4:c.663A>G	p.Ile221Met	p.I221M	ENST00000377767	NM_014953.3	221	atA/atG	5/21	1	2	FACETS	0.84	0.737	0.948	0.84	0.737	0.948	CLONAL	1	TRUE	1	0.842666098204063	2		191	161	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0052783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	198	354	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.845477014640125	1	FACETS	0.907	0.862	0.951	0.907	0.862	0.951	CLONAL	1	TRUE	0	0.845477014640125	1		354	298	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574494	64574494	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	599	841	1	ENST00000312049.6:c.901del	p.Leu301SerfsTer67	p.L301Sfs*67	ENST00000312049	NM_130799.2	301	Ctc/tc	6/10	0.845477014640125	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.845477014640125	1		842	812	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855208	76855209	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	T	novel	NA	P-0052783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	321	241	0	ENST00000373344.5:c.5778_5779delinsA	p.Asp1926GlufsTer29	p.D1926Efs*29	ENST00000373344	NM_000489.3	1926	gaTTat/gaAat	24/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.845477014640125	1		241	393	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0052784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	20	330	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.394	0.3	0.506	0.394	0.3	0.506	SUBCLONAL	1	TRUE	1	0.13	2		330	780	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0052784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	57	795	1	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	1	2	FACETS	0.841	0.719	0.975	0.841	0.719	0.975	CLONAL	1	TRUE	1	0.13	2		796	1043	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881488	48881489	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0052784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	34	128	0	ENST00000267163.4:c.219_220dup	p.Ala74GlufsTer4	p.A74Efs*4	ENST00000267163	NM_000321.2	70	-/AG	2/27	1	2	FACETS	1	0.834	1	1	0.834	1	CLONAL	1	TRUE	1	0.13	2		128	511	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982964	201982965	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0052784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	102	791	0	ENST00000359651.3:c.815dup	p.Thr273HisfsTer28	p.T273Hfs*28	ENST00000359651		271	-/G	7/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.13	2		791	1183	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249404	153249404	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	41	563	0	ENST00000281708.4:c.1374del	p.Tyr458Ter	p.Y458*	ENST00000281708	NM_033632.3	458	taT/ta	9/12	1	2	FACETS	0.82	0.681	0.976	0.82	0.681	0.976	CLONAL	1	TRUE	1	0.13	2		563	769	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0052786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	191	550	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.357775298586405	6	FACETS	0.976	0.93	1	1	0.989	1	CLONAL	7	FALSE	0	0.357775298586405	6		550	268	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883212	37883212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs566053951	NA	P-0052786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	10	932	0	ENST00000269571.5:c.3115G>A	p.Ala1039Thr	p.A1039T	ENST00000269571		1039	Gct/Act	25/27	0.301216483959726	2	FACETS	0.304	0.206	0.427	0.152	0.103	0.214	SUBCLONAL	1	FALSE	0	0.357775298586405	2		932	184	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962899	2962899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3735134	NA	P-0052786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	11	1194	1	ENST00000396946.4:c.2009C>T	p.Thr670Met	p.T670M	ENST00000396946	NM_032415.4	670	aCg/aTg	16/25	0.257836078506274	3	FACETS	0.361	0.249	0.499	0.12	0.083	0.167	SUBCLONAL	1	FALSE	0	0.357775298586405	3		1195	201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576853	7576862	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CTGAAGGGTG	CTGAAGGGTG	-	novel	NA	P-0052786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	46	735	0	ENST00000269305.4:c.984_993del	p.Phe328LeufsTer14	p.F328Lfs*14	ENST00000269305	NM_001126112.2	328	ttCACCCTTCAG/tt	9/11	0.301216483959726	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	2	FALSE	0	0.357775298586405	2		735	119	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729847	47729847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	10	522	1	ENST00000449228.1:c.542G>A	p.Arg181Gln	p.R181Q	ENST00000449228	NM_001127240.2	181	cGa/cAa	3/4	0.247005199701041	2	FACETS	0.321	0.218	0.451	0.161	0.109	0.226	SUBCLONAL	1	FALSE	0	0.357775298586405	2		523	174	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713590	52713591	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0052786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	21	477	0	ENST00000394830.3:c.137dup	p.Ile47TyrfsTer6	p.I47Yfs*6	ENST00000394830	NM_018313.4	46	cct/ccCt	2/30	0.357775298586405	3	FACETS	0.948	0.737	1	0.316	0.245	0.396	CLONAL	1	FALSE	0	0.357775298586405	3		477	146	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117875444	117875444	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	32	512	0	ENST00000297338.2:c.199T>G	p.Tyr67Asp	p.Y67D	ENST00000297338	NM_006265.2	67	Tat/Gat	3/14	0.357775298586405	5	FACETS	1	0.875	1	0.43	0.355	0.51	CLONAL	2	FALSE	0	0.357775298586405	5		512	128	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163262	32163286	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGGGACCACAGTCAAGTTGAGGT	TGGGGGACCACAGTCAAGTTGAGGT	GA	novel	NA	P-0052786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	41	1240	0	ENST00000375023.3:c.5940_5964delinsTC	p.Pro1981ArgfsTer14	p.P1981Rfs*14	ENST00000375023	NM_004557.3	1980	tcACCTCAACTTGACTGTGGTCCCCCA/tcTC	30/30	0.251701996417287	5	FACETS	0.804	0.676	0.943	0.322	0.27	0.378	CLONAL	2	FALSE	0	0.357775298586405	5		1240	219	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249017	55249018	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCA	rs1554350381	NA	P-0052787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	406	692	0	ENST00000275493.2:c.2317_2319dup	p.His773dup	p.H773dup	ENST00000275493	NM_005228.3	773	ccc/ccCCAc	20/28	0.245400700515595	5	FACETS	0.882	0.843	0.922	0.882	0.843	0.922	INDETERMINATE	3	TRUE	2	0.617908020153625	5		692	957	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574026	+	inframe_deletion	In_Frame_Del	DEL	CACGCC	CACGCC	-	novel	NA	P-0052787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	482	739	0	ENST00000269305.4:c.1001_1006del	p.Gly334_Arg335del	p.G334_R335del	ENST00000269305	NM_001126112.2	334	gGGCGTGag/gag	10/11	0.617908020153625	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.617908020153625	2		739	730	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431388	49431388	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	285	683	1	ENST00000301067.7:c.9751G>T	p.Asp3251Tyr	p.D3251Y	ENST00000301067	NM_003482.3	3251	Gac/Tac	34/54	0.380371439935758	3	FACETS	0.865	0.818	0.912	0.865	0.818	0.912	CLONAL	2	TRUE	1	0.617908020153625	3		684	698	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431772	49431772	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	321	812	1	ENST00000301067.7:c.9367G>T	p.Glu3123Ter	p.E3123*	ENST00000301067	NM_003482.3	3123	Gag/Tag	34/54	0.380371439935758	3	FACETS	0.881	0.836	0.926	0.881	0.836	0.926	CLONAL	2	TRUE	1	0.617908020153625	3		813	772	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38955725	38955725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	243	409	0	ENST00000357387.3:c.2581G>A	p.Asp861Asn	p.D861N	ENST00000357387	NM_152756.3	861	Gat/Aat	26/38	0.617908020153625	4	FACETS	1	0.99	1	0.445	0.416	0.475	CLONAL	1	TRUE	1	0.617908020153625	4		409	953	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338702	70338702	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	194	585	0	ENST00000374080.3:c.98A>T	p.Glu33Val	p.E33V	ENST00000374080		33	gAg/gTg	1/45	0.617908020153625	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.617908020153625	1		585	314	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626364	12626364	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	86	603	0	ENST00000251849.4:c.1785G>C	p.Glu595Asp	p.E595D	ENST00000251849	NM_002880.3	595	gaG/gaC	16/17	0.617908020153625	3	FACETS	0.44	0.388	0.495	0.22	0.194	0.248	SUBCLONAL	1	TRUE	1	0.617908020153625	3		603	829	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94926622	94926622	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	70	493	0	ENST00000536441.1:c.143A>G	p.Glu48Gly	p.E48G	ENST00000536441	NM_144665.3	48	gAa/gGa	2/10	1	2	FACETS	0.288	0.25	0.328	0.288	0.25	0.328	SUBCLONAL	1	TRUE	1	0.617908020153625	2		493	788	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911134	40911134	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1476533276	NA	P-0052787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	46	380	0	ENST00000373198.4:c.2171C>A	p.Thr724Lys	p.T724K	ENST00000373198	NM_133170.3	724	aCa/aAa	13/32	NA	2	FACETS	0.216	0.181	0.254			1	INDETERMINATE	1	TRUE	NA	0.617908020153625	2		380	690	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017489	112017489	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1326474009	NA	P-0052787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	86	387	0	ENST00000368678.4:c.1024A>G	p.Met342Val	p.M342V	ENST00000368678		342	Atg/Gtg	9/13	0.242980860545389	2	FACETS	0.74	0.659	0.825	0.37	0.329	0.413	INDETERMINATE	1	TRUE	0	0.617908020153625	2		387	376	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249017	55249018	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCA	rs1554350381	NA	P-0052787-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	29	692	0	ENST00000275493.2:c.2317_2319dup	p.His773dup	p.H773dup	ENST00000275493	NM_005228.3	773	ccc/ccCCAc	20/28	1	2	FACETS	0.598	0.478	0.734	0.598	0.478	0.734	SUBCLONAL	1	TRUE	1	0.17	2		692	571	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574026	+	inframe_deletion	In_Frame_Del	DEL	CACGCC	CACGCC	-	novel	NA	P-0052787-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	71	739	0	ENST00000269305.4:c.1001_1006del	p.Gly334_Arg335del	p.G334_R335del	ENST00000269305	NM_001126112.2	334	gGGCGTGag/gag	10/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.17	2		739	582	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431388	49431388	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052787-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	49	683	1	ENST00000301067.7:c.9751G>T	p.Asp3251Tyr	p.D3251Y	ENST00000301067	NM_003482.3	3251	Gac/Tac	34/54	0.157793511831835	3	FACETS	1	0.911	1	0.556	0.471	0.651	CLONAL	1	TRUE	1	0.17	3		684	562	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431772	49431772	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052787-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	57	812	1	ENST00000301067.7:c.9367G>T	p.Glu3123Ter	p.E3123*	ENST00000301067	NM_003482.3	3123	Gag/Tag	34/54	0.157793511831835	3	FACETS	1	0.916	1	0.55	0.471	0.636	CLONAL	1	TRUE	1	0.17	3		813	662	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38955725	38955725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052787-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	34	409	0	ENST00000357387.3:c.2581G>A	p.Asp861Asn	p.D861N	ENST00000357387	NM_152756.3	861	Gat/Aat	26/38	0.201407148517222	4	FACETS	0.806	0.657	0.974	0.403	0.328	0.487	CLONAL	1	TRUE	2	0.17	4		409	581	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338702	70338702	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052787-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	27	585	0	ENST00000374080.3:c.98A>T	p.Glu33Val	p.E33V	ENST00000374080		33	gAg/gTg	1/45	1	2	FACETS	0.682	0.541	0.842	0.682	0.541	0.842	SUBCLONAL	1	TRUE	1	0.17	2		585	466	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	93	151	0				ENST00000310581	NM_198253.2	-/1132			0.283437660245206	3	FACETS	0.974	0.882	1	0.974	0.882	1	INDETERMINATE	2	TRUE	1	0.515682123479166	3		151	233	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	234	1171	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.502538233449997	3	FACETS	1	0.961	1	0.522	0.487	0.559	CLONAL	1	TRUE	1	0.515682123479166	3		1171	1093	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631443	117631443	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	101	290	0	ENST00000368508.3:c.6235G>A	p.Asp2079Asn	p.D2079N	ENST00000368508	NM_002944.2	2079	Gat/Aat	40/43	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.515682123479166	2		290	360	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	94	137	0				ENST00000310581	NM_198253.2	-/1132			0.283437660245206	3	FACETS	0.988	0.896	1	0.988	0.896	1	INDETERMINATE	2	TRUE	1	0.515682123479166	3		137	232	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798245	45798246	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	315	873	2	ENST00000450313.1:c.690_690+1delinsAA		p.X230_splice	ENST00000450313	NM_012222.2	230		8/16	0.515682123479166	4	FACETS	0.918	0.868	0.97	0.918	0.868	0.97	CLONAL	2	TRUE	2	0.515682123479166	4		875	1008	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244982	123244982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	267	708	0	ENST00000358487.5:c.2122C>T	p.Pro708Ser	p.P708S	ENST00000358487	NM_000141.4	708	Ccc/Tcc	16/18	0.296352888200504	3	FACETS	0.926	0.874	0.98			1	INDETERMINATE	2	TRUE	NA	0.515682123479166	3		708	703	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154225	2154225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1014211286	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	291	889	1	ENST00000434045.2:c.703C>T	p.Arg235Trp	p.R235W	ENST00000434045	NM_001127598.1	235	Cgg/Tgg	5/5	0.222803963233872	5	FACETS	1	0.98	1	0.723	0.682	0.765	INDETERMINATE	2	TRUE	2	0.515682123479166	5		890	923	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457992	69457992	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759551813	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	112	465	0	ENST00000227507.2:c.392C>T	p.Ser131Phe	p.S131F	ENST00000227507	NM_053056.2	131	tCc/tTc	2/5	0.283437660245206	3	FACETS	1	0.908	1	0.503	0.454	0.555	INDETERMINATE	1	TRUE	1	0.515682123479166	3		465	543	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	430229	430229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	188	414	0	ENST00000399788.2:c.2473G>A	p.Glu825Lys	p.E825K	ENST00000399788	NM_001042603.1	825	Gaa/Aaa	18/28	0.385729238309428	4	FACETS	0.961	0.894	1	0.961	0.894	1	CLONAL	2	TRUE	2	0.515682123479166	4		414	575	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28883012	28883012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	220	574	0	ENST00000282397.4:c.3688G>A	p.Glu1230Lys	p.E1230K	ENST00000282397	NM_002019.4	1230	Gaa/Aaa	28/30	0.385729238309428	4	FACETS	0.986	0.922	1	0.986	0.922	1	CLONAL	2	TRUE	2	0.515682123479166	4		574	656	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912874	32912874	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	171	382	0	ENST00000380152.3:c.4382C>T	p.Ser1461Phe	p.S1461F	ENST00000380152		1461	tCc/tTc	11/27	0.385729238309428	4	FACETS	0.985	0.914	1	0.985	0.914	1	CLONAL	2	TRUE	2	0.515682123479166	4		382	510	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028529	42028530	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	121	593	2	ENST00000219905.7:c.4067_4068delinsTT	p.Ser1356Phe	p.S1356F	ENST00000219905	NM_001164273.1	1356	tCC/tTT	13/24	0.515682123479166	3	FACETS	0.965	0.874	1	0.482	0.437	0.53	CLONAL	1	TRUE	1	0.515682123479166	3		595	612	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994895	73994895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150953383	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	12	64	0	ENST00000318443.5:c.379C>T	p.Arg127Trp	p.R127W	ENST00000318443	NM_001024736.1	127	Cgg/Tgg	3/10	0.515682123479166	3	FACETS	1	0.804	1	0.574	0.415	0.756	CLONAL	1	TRUE	1	0.515682123479166	3		64	51	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641206	3641207	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	192	1025	3	ENST00000294008.3:c.2432_2433delinsAA	p.Arg811Lys	p.R811K	ENST00000294008	NM_032444.2	811	aGG/aAA	12/15	0.515682123479166	3	FACETS	0.827	0.764	0.893	0.414	0.382	0.447	CLONAL	1	TRUE	1	0.515682123479166	3		1028	1132	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953147	81953147	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	200	379	0	ENST00000359376.3:c.2113G>A	p.Gly705Arg	p.G705R	ENST00000359376	NM_002661.3	705	Ggg/Agg	20/33	0.515682123479166	3	FACETS	0.992	0.928	1	0.992	0.928	1	CLONAL	2	TRUE	1	0.515682123479166	3		379	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577548	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	325	701	2	ENST00000269305.4:c.733_734delinsAA	p.Gly245Asn	p.G245N	ENST00000269305	NM_001126112.2	245	GGc/AAc	7/11	0.502538233449997	3	FACETS	0.937	0.889	0.986	0.937	0.889	0.986	CLONAL	2	TRUE	1	0.515682123479166	3		703	846	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496908	29496908	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	109	222	0	ENST00000356175.3:c.480-1G>A		p.X160_splice	ENST00000356175	NM_000267.3	160			0.515682123479166	2	FACETS	0.935	0.859	1	0.935	0.859	1	CLONAL	2	TRUE	0	0.515682123479166	2		222	226	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40491346	40491347	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	293	644	0	ENST00000264657.5:c.453_454delinsTT	p.Arg152Trp	p.R152W	ENST00000264657	NM_139276.2	151	gtCCgg/gtTTgg	5/24	0.515682123479166	2	FACETS	0.938	0.891	0.984	0.938	0.891	0.984	CLONAL	2	TRUE	0	0.515682123479166	2		644	606	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752378	55752378	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	550	1217	4	ENST00000284073.2:c.836C>T	p.Pro279Leu	p.P279L	ENST00000284073	NM_138962.2	279	cCa/cTa	12/14	0.515682123479166	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.515682123479166	2		1221	1007	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678125	58678126	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	290	687	1	ENST00000305921.3:c.350_351delinsAA	p.Arg117Gln	p.R117Q	ENST00000305921	NM_003620.3	117	cGG/cAA	1/6	0.515682123479166	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.515682123479166	2		688	531	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775164	73775164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867543814	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	358	723	0	ENST00000254810.4:c.92C>T	p.Pro31Leu	p.P31L	ENST00000254810	NM_005324.3	31	cCc/cTc	2/4	0.385729238309428	4	FACETS	0.948	0.899	0.997	0.948	0.899	0.997	CLONAL	2	TRUE	2	0.515682123479166	4		723	1110	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745837	745837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1050998183	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	122	562	0	ENST00000314574.4:c.595C>T	p.Arg199Cys	p.R199C	ENST00000314574	NM_005433.3	199	Cgt/Tgt	6/12	0.2425017996574	4	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.515682123479166	4		562	520	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793026	33793027	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	77	233	2	ENST00000498907.2:c.294_295delinsAA	p.Gly99Ser	p.G99S	ENST00000498907	NM_004364.3	98	acGGgc/acAAgc	1/1	0.385729238309428	4	FACETS	1	0.898	1	1	0.898	1	CLONAL	2	TRUE	2	0.515682123479166	4		235	225	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228053	36228054	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	422	979	1	ENST00000222270.7:c.7439_7440delinsTT	p.Pro2480Leu	p.P2480L	ENST00000222270	NM_014727.1	2480	cCC/cTT	33/37	0.385729238309428	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.515682123479166	4		980	1161	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723443	52723443	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	276	533	0	ENST00000322088.6:c.1304G>A	p.Gly435Glu	p.G435E	ENST00000322088	NM_014225.5	435	gGa/gAa	11/15	0.385729238309428	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	2	0.515682123479166	4		533	797	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973212	25973212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	222	512	0	ENST00000435504.4:c.1213C>T	p.Pro405Ser	p.P405S	ENST00000435504		405	Cca/Tca	12/13	0.385729238309428	4	FACETS	0.964	0.902	1	0.964	0.902	1	CLONAL	2	TRUE	2	0.515682123479166	4		512	677	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285854	39285854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	184	578	1	ENST00000402219.2:c.305C>T	p.Pro102Leu	p.P102L	ENST00000402219	NM_005633.3	102	cCt/cTt	3/23	0.385729238309428	4	FACETS	0.849	0.787	0.913	0.849	0.787	0.913	CLONAL	2	TRUE	2	0.515682123479166	4		579	637	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99180007	99180008	+	missense_variant	Missense_Mutation	DNP	GG	GG	TA	novel	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	326	814	1	ENST00000074304.5:c.1950_1951delinsTA	p.Lys650_Ala651delinsAsnThr	p.K650_A651delinsNT	ENST00000074304	NM_001134224.1	650	aaGGcc/aaTAcc	19/26	0.385729238309428	4	FACETS	0.904	0.855	0.954	0.904	0.855	0.954	CLONAL	2	TRUE	2	0.515682123479166	4		815	1060	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182228	99182228	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs267599505	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	302	627	0	ENST00000074304.5:c.2293C>T	p.Arg765Cys	p.R765C	ENST00000074304	NM_001134224.1	765	Cgc/Tgc	21/26	0.385729238309428	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.515682123479166	4		627	860	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574182	41574182	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	320	740	0	ENST00000263253.7:c.6467C>T	p.Pro2156Leu	p.P2156L	ENST00000263253	NM_001429.3	2156	cCa/cTa	31/31	0.502538233449997	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.515682123479166	3		740	693	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434123	12434123	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	170	392	0	ENST00000287820.6:c.491G>A	p.Arg164Gln	p.R164Q	ENST00000287820	NM_015869.4	164	cGg/cAg	4/7	0.222803963233872	5	FACETS	0.868	0.806	0.931	0.868	0.806	0.931	INDETERMINATE	3	TRUE	2	0.515682123479166	5		392	449	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851885	134851885	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	267	598	1	ENST00000398015.3:c.1291C>T	p.Gln431Ter	p.Q431*	ENST00000398015	NM_004441.4	431	Caa/Taa	5/16	0.515682123479166	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.515682123479166	2		599	497	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510103	187510104	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	225	490	0	ENST00000441802.2:c.13409_13410delinsTT	p.Ala4470Val	p.A4470V	ENST00000441802	NM_005245.3	4470	gCC/gTT	27/27	0.385729238309428	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	2	0.515682123479166	4		490	640	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729673	41729673	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	342	718	0	ENST00000242208.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000242208	NM_002192.2	286	Gag/Aag	3/3	0.385729238309428	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.515682123479166	4		718	946	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339968	116339968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	183	405	0	ENST00000397752.3:c.830G>A	p.Arg277Lys	p.R277K	ENST00000397752	NM_000245.2	277	aGa/aAa	2/21	0.515682123479166	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.515682123479166	3		405	425	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849886	151849886	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148110224	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	112	476	0	ENST00000262189.6:c.12430C>T	p.Leu4144Phe	p.L4144F	ENST00000262189	NM_170606.2	4144	Ctc/Ttc	49/59	0.515682123479166	3	FACETS	1	0.946	1	0.535	0.483	0.589	CLONAL	1	TRUE	1	0.515682123479166	3		476	511	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971207	21971208	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	182	470	0	ENST00000304494.5:c.151-1_151delinsAA		p.X51_splice	ENST00000304494	NM_000077.4	51		2/3	0.515682123479166	2	FACETS	0.931	0.872	0.99	0.931	0.872	0.99	CLONAL	2	TRUE	0	0.515682123479166	2		470	379	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232138	98232138	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs863224650	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	180	422	1	ENST00000331920.6:c.1804C>T	p.Arg602Ter	p.R602*	ENST00000331920	NM_000264.3	602	Cga/Tga	13/24	0.515682123479166	3	FACETS	0.919	0.855	0.983	0.919	0.855	0.983	CLONAL	2	TRUE	1	0.515682123479166	3		423	478	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391527	139391527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	446	1153	0	ENST00000277541.6:c.6664C>T	p.Pro2222Ser	p.P2222S	ENST00000277541	NM_017617.3	2222	Ccg/Tcg	34/34	0.515682123479166	3	FACETS	0.97	0.927	1	0.97	0.927	1	CLONAL	2	TRUE	1	0.515682123479166	3		1153	1122	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620470	52620470	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	38	529	0	ENST00000394830.3:c.3283C>T	p.Arg1095Ter	p.R1095*	ENST00000394830	NM_018313.4	1095	Cga/Tga	21/30	1	2	FACETS	0.757	0.624	0.907	0.757	0.624	0.907	CLONAL	1	TRUE	1	0.14	2		529	717	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610561	10610561	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766652922	NA	P-0052789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	50	1172	0	ENST00000171111.5:c.149G>A	p.Arg50His	p.R50H	ENST00000171111	NM_203500.1	50	cGc/cAc	2/6	1	2	FACETS	0.719	0.608	0.843	0.719	0.608	0.843	SUBCLONAL	1	TRUE	1	0.14	2		1172	993	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944413	40944414	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0052789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	38	641	0	ENST00000373198.4:c.2088_2089del	p.Leu698GlufsTer54	p.L698Efs*54	ENST00000373198	NM_133170.3	696	tcTCcc/tccc	12/32	1	2	FACETS	0.731	0.602	0.875	0.731	0.602	0.875	SUBCLONAL	1	TRUE	1	0.14	2		641	743	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508656	38508656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	48	882	1	ENST00000254066.5:c.704G>A	p.Cys235Tyr	p.C235Y	ENST00000254066	NM_000964.3	235	tGc/tAc	6/9	1	2	FACETS	0.811	0.683	0.952	0.811	0.683	0.952	CLONAL	1	TRUE	1	0.14	2		883	846	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738694	43738694	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	64	591	0	ENST00000382044.4:c.2931del	p.Asp979IlefsTer14	p.D979Ifs*14	ENST00000382044	NM_001141980.1	977	aaA/aa	14/28	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.14	2		591	762	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0052790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	139	353	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.514365825747362	3	FACETS	0.827	0.76	0.895	0.827	0.76	0.895	CLONAL	2	TRUE	1	0.514365825747362	3		353	411	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0052790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	143	474	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	NA	2	FACETS	0.921	0.855	0.987			1	INDETERMINATE	2	TRUE	NA	0.514365825747362	2		474	302	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391214	89391214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs530556931	NA	P-0052790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	88	507	0	ENST00000336596.2:c.1280C>T	p.Ala427Val	p.A427V	ENST00000336596	NM_005233.5	427	gCg/gTg	5/17	1	2	FACETS	0.815	0.726	0.909	0.815	0.726	0.909	CLONAL	1	TRUE	1	0.514365825747362	2		507	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0052790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	208	1371	5	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.514365825747362	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.514365825747362	1		1376	581	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443618	29443618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200585833	NA	P-0052790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	162	1074	3	ENST00000389048.3:c.3599C>T	p.Ala1200Val	p.A1200V	ENST00000389048	NM_004304.4	1200	gCg/gTg	23/29	1	2	FACETS	0.998	0.92	1	0.998	0.92	1	CLONAL	1	TRUE	1	0.514365825747362	2		1077	631	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100286	8100286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241255776	NA	P-0052790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	60	1201	0	ENST00000346208.3:c.260C>T	p.Pro87Leu	p.P87L	ENST00000346208		87	cCg/cTg	3/6	1	2	FACETS	0.37	0.319	0.427	0.37	0.319	0.427	SUBCLONAL	1	TRUE	1	0.514365825747362	2		1201	630	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026110	36026110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1433113895	NA	P-0052790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	124	1508	0	ENST00000358208.4:c.712G>A	p.Asp238Asn	p.D238N	ENST00000358208		238	Gat/Aat	7/12	0.514365825747362	5	FACETS	0.684	0.617	0.756	0.171	0.154	0.189	SUBCLONAL	1	TRUE	1	0.514365825747362	5		1508	1248	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	203	1003	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.796	0.741	0.852	1	0.992	1	SUBCLONAL	2	FALSE	1	0.3830535278892	2		1007	666	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	14	561	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.158	0.113	0.212	0.158	0.113	0.212	SUBCLONAL	1	FALSE	1	0.3830535278892	2		561	463	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	79	455	3	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.701	0.618	0.791	0.701	0.618	0.791	SUBCLONAL	1	FALSE	1	0.3830535278892	2		458	588	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	43	587	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.110357829085189	3	FACETS	0.39	0.325	0.462	0.195	0.162	0.231	INDETERMINATE	1	FALSE	1	0.3830535278892	3		587	686	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	55	315	3	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.3830535278892	2		318	224	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168910	32168910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1220425760	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	118	831	4	ENST00000375023.3:c.4123G>A	p.Asp1375Asn	p.D1375N	ENST00000375023	NM_004557.3	1375	Gac/Aac	22/30	1	2	FACETS	0.803	0.725	0.886	0.803	0.725	0.886	CLONAL	1	FALSE	1	0.3830535278892	2		835	767	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397743	49397743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	144	556	0	ENST00000418115.1:c.481G>A	p.Ala161Thr	p.A161T	ENST00000418115	NM_001664.2	161	Gca/Aca	5/5	1	2	FACETS	0.973	0.888	1	0.973	0.888	1	CLONAL	1	FALSE	1	0.3830535278892	2		556	773	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	199	508	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.878	0.818	0.938	1	0.993	1	CLONAL	2	FALSE	1	0.3830535278892	2		508	592	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030479	49030479	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	59	282	0	ENST00000267163.4:c.1959del	p.Val654CysfsTer4	p.V654Cfs*4	ENST00000267163	NM_000321.2	652	Aaa/aa	19/27	1	2	FACETS	0.922	0.798	1	0.922	0.798	1	CLONAL	1	FALSE	1	0.3830535278892	2		282	334	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518992	103518992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	84	519	0	ENST00000355739.4:c.2330G>A	p.Arg777His	p.R777H	ENST00000355739	NM_000123.3	777	cGc/cAc	11/15	1	2	FACETS	0.91	0.807	1	0.91	0.807	1	CLONAL	1	FALSE	1	0.3830535278892	2		519	482	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	31	639	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	1	2	FACETS	0.286	0.231	0.35	0.286	0.231	0.35	SUBCLONAL	1	FALSE	1	0.3830535278892	2		639	565	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965666	90965666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	81	395	0	ENST00000265433.3:c.1651del	p.Arg551GlyfsTer8	p.R551Gfs*8	ENST00000265433	NM_002485.4	551	Agg/gg	11/16	0.2350033748151	3	FACETS	1	0.975	1	0.696	0.618	0.779	CLONAL	1	FALSE	1	0.3830535278892	3		395	362	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs767894241	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	91	524	1	ENST00000358127.4:c.76dup	p.Val26GlyfsTer49	p.V26Gfs*49	ENST00000358127	NM_001280556.1	26	gtt/gGtt	2/10	0.185969755347049	0	FACETS	0.517	0.46	0.578			1	INDETERMINATE	1	FALSE	0	0.3830535278892	0		525	567	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103755	47103756	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	92	507	1	ENST00000409792.3:c.6190_6191del	p.Asp2064ProfsTer8	p.D2064Pfs*8	ENST00000409792	NM_014159.6	2064	GAc/c	14/21	1	2	FACETS	0.77	0.685	0.86	0.77	0.685	0.86	SUBCLONAL	1	FALSE	1	0.3830535278892	2		508	624	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11177103	11177103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	74	474	2	ENST00000361445.4:c.6974C>T	p.Ala2325Val	p.A2325V	ENST00000361445	NM_004958.3	2325	gCg/gTg	50/58	1	2	FACETS	0.678	0.594	0.768	0.678	0.594	0.768	SUBCLONAL	1	FALSE	1	0.3830535278892	2		476	570	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044348	128044348	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913047	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	98	724	1	ENST00000285398.2:c.1273C>T	p.Arg425Ter	p.R425*	ENST00000285398	NM_000122.1	425	Cga/Tga	8/15	1	2	FACETS	0.827	0.739	0.92	0.827	0.739	0.92	CLONAL	1	FALSE	1	0.3830535278892	2		725	619	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89806477	89806477	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs17227354	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	96	565	0	ENST00000389301.3:c.3859G>A	p.Val1287Ile	p.V1287I	ENST00000389301	NM_000135.2	1287	Gtt/Att	39/43	1	2	FACETS	0.757	0.675	0.844	0.757	0.675	0.844	SUBCLONAL	1	FALSE	1	0.3830535278892	2		565	662	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100425	8100425	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	129	926	3	ENST00000346208.3:c.404del	p.Pro135ArgfsTer60	p.P135Rfs*60	ENST00000346208		133	taC/ta	3/6	1	2	FACETS	0.896	0.813	0.983	0.896	0.813	0.983	CLONAL	1	FALSE	1	0.3830535278892	2		929	752	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118988	70118988	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	149	820	1	ENST00000245479.2:c.560C>T	p.Ala187Val	p.A187V	ENST00000245479	NM_000346.3	187	gCg/gTg	2/3	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	FALSE	1	0.3830535278892	2		821	756	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522601	176522601	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	112	1000	3	ENST00000292408.4:c.1703del	p.Pro568GlnfsTer53	p.P568Qfs*53	ENST00000292408	NM_213647.1	566	cgC/cg	13/18	1	2	FACETS	0.833	0.75	0.921	0.833	0.75	0.921	CLONAL	1	FALSE	1	0.3830535278892	2		1003	702	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	117	679	3	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	1	2	FACETS	0.799	0.72	0.881	0.799	0.72	0.881	SUBCLONAL	1	FALSE	1	0.3830535278892	2		682	765	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309776	104309776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202247756	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	115	684	1	ENST00000369902.3:c.367C>T	p.Arg123Cys	p.R123C	ENST00000369902	NM_016169.3	123	Cgt/Tgt	3/12	1	2	FACETS	0.875	0.789	0.966	0.875	0.789	0.966	CLONAL	1	FALSE	1	0.3830535278892	2		685	686	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794441	42794441	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	125	1039	2	ENST00000575354.2:c.1526del	p.Pro509HisfsTer14	p.P509Hfs*14	ENST00000575354	NM_015125.3	507	cgC/cg	10/20	1	2	FACETS	0.776	0.702	0.854	0.776	0.702	0.854	SUBCLONAL	1	FALSE	1	0.3830535278892	2		1041	841	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821959	72821960	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762108866	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	57	442	0	ENST00000268489.5:c.10215dup	p.Gly3406ArgfsTer25	p.G3406Rfs*25	ENST00000268489	NM_006885.3	3405	-/C	10/10	1	2	FACETS	0.672	0.578	0.774	0.672	0.578	0.774	SUBCLONAL	1	FALSE	1	0.3830535278892	2		442	443	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131277	17131277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778275358	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	163	961	0	ENST00000285071.4:c.175C>T	p.Arg59Cys	p.R59C	ENST00000285071	NM_144997.5	59	Cgt/Tgt	4/14	1	2	FACETS	0.904	0.83	0.982	0.904	0.83	0.982	CLONAL	1	FALSE	1	0.3830535278892	2		961	941	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs770248150	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	19	477	0	ENST00000311936.3:c.351A>T	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaT	4/5	1	2	FACETS	0.223	0.168	0.287	0.223	0.168	0.287	SUBCLONAL	1	FALSE	1	0.3830535278892	2		477	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579329	7579329	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912658	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	246	808	0	ENST00000269305.4:c.358A>G	p.Lys120Glu	p.K120E	ENST00000269305	NM_001126112.2	120	Aag/Gag	4/11	0.301192354393991	2	FACETS	0.943	0.886	1	0.943	0.886	1	CLONAL	2	FALSE	0	0.3830535278892	2		808	681	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245378	53245378	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	85	491	0	ENST00000375401.3:c.659C>T	p.Pro220Leu	p.P220L	ENST00000375401	NM_004187.3	220	cCg/cTg	6/26	0.3830535278892	1	FACETS	0.858	0.763	0.959	0.858	0.763	0.959	CLONAL	1	FALSE	0	0.3830535278892	1		491	418	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921765	111921765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572257286	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	75	377	0	ENST00000393256.3:c.554G>A	p.Arg185Gln	p.R185Q	ENST00000393256	NM_006538.4	185	cGa/cAa	4/4	1	2	FACETS	0.786	0.691	0.889	0.786	0.691	0.889	SUBCLONAL	1	FALSE	1	0.3830535278892	2		377	498	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40738973	40738973	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	44	481	0	ENST00000373198.4:c.3311G>T	p.Ser1104Ile	p.S1104I	ENST00000373198	NM_133170.3	1104	aGt/aTt	24/32	1	2	FACETS	0.485	0.406	0.571	0.485	0.406	0.571	SUBCLONAL	1	FALSE	1	0.3830535278892	2		481	474	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439906	56439906	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs763974538	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	127	662	0	ENST00000407977.2:c.686C>T	p.Pro229Leu	p.P229L	ENST00000407977		229	cCg/cTg	6/10	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	FALSE	1	0.3830535278892	2		662	661	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830441	72830441	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	35	255	0	ENST00000268489.5:c.6140del	p.Pro2047LeufsTer54	p.P2047Lfs*54	ENST00000268489	NM_006885.3	2047	cCt/ct	9/10	1	2	FACETS	0.795	0.656	0.948	0.795	0.656	0.948	CLONAL	1	FALSE	1	0.3830535278892	2		255	230	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262483	16262483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369155141	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	29	268	0	ENST00000375759.3:c.9748G>A	p.Val3250Ile	p.V3250I	ENST00000375759	NM_015001.2	3250	Gtc/Atc	11/15	1	2	FACETS	0.797	0.645	0.966	0.797	0.645	0.966	CLONAL	1	FALSE	1	0.3830535278892	2		268	190	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325846	30325846	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763509688	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	63	362	1	ENST00000322652.5:c.2044C>T	p.Arg682Cys	p.R682C	ENST00000322652	NM_015355.2	682	Cgt/Tgt	16/16	1	2	FACETS	0.891	0.775	1	0.891	0.775	1	CLONAL	1	FALSE	1	0.3830535278892	2		363	369	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945008	31945008	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	133	887	0	ENST00000340398.3:c.93del	p.Ser32LeufsTer5	p.S32Lfs*5	ENST00000340398	NM_001013699.2	31	ccC/cc	1/1	1	2	FACETS	0.784	0.711	0.86	0.784	0.711	0.86	SUBCLONAL	1	FALSE	1	0.3830535278892	2		887	886	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98003011	98003011	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	19	304	1	ENST00000289081.3:c.265del	p.Ile89PhefsTer2	p.I89Ffs*2	ENST00000289081	NM_000136.2	89	Att/tt	4/15	1	2	FACETS	0.268	0.203	0.345	0.268	0.203	0.345	SUBCLONAL	1	FALSE	1	0.3830535278892	2		305	370	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103525641	103525641	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750643985	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	70	407	0	ENST00000355739.4:c.2912C>T	p.Thr971Met	p.T971M	ENST00000355739	NM_000123.3	971	aCg/aTg	14/15	1	2	FACETS	0.81	0.709	0.919	0.81	0.709	0.919	CLONAL	1	FALSE	1	0.3830535278892	2		407	451	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518900	187518900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745695748	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	54	468	2	ENST00000441802.2:c.12304G>A	p.Gly4102Arg	p.G4102R	ENST00000441802	NM_005245.3	4102	Gga/Aga	24/27	1	2	FACETS	0.464	0.396	0.538	0.464	0.396	0.538	SUBCLONAL	1	FALSE	1	0.3830535278892	2		470	608	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112422	115112422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775182377	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	104	602	2	ENST00000257566.3:c.1318G>A	p.Ala440Thr	p.A440T	ENST00000257566	NM_016569.3	440	Gcc/Acc	7/8	1	2	FACETS	0.966	0.868	1	0.966	0.868	1	CLONAL	1	FALSE	1	0.3830535278892	2		604	562	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686961	37686961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367703051	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	76	538	0	ENST00000447079.4:c.3865G>A	p.Ala1289Thr	p.A1289T	ENST00000447079	NM_015083.1	1289	Gcc/Acc	14/14	1	2	FACETS	0.716	0.629	0.81	0.716	0.629	0.81	SUBCLONAL	1	FALSE	1	0.3830535278892	2		538	554	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190872	185190872	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	159	623	0	ENST00000265026.3:c.1753C>T	p.Arg585Ter	p.R585*	ENST00000265026	NM_004721.4	585	Cga/Tga	11/14	0.110357829085189	3	FACETS	1	0.986	1	0.685	0.629	0.743	INDETERMINATE	1	FALSE	1	0.3830535278892	3		623	722	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552143	29552144	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1555613558	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	26	243	0	ENST00000356175.3:c.1882dup	p.Tyr628LeufsTer6	p.Y628Lfs*6	ENST00000356175	NM_000267.3	626	ctt/cTtt	17/57	1	2	FACETS	0.583	0.463	0.718	0.583	0.463	0.718	SUBCLONAL	1	FALSE	1	0.3830535278892	2		243	233	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271813	15271813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs541716070	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	127	1105	0	ENST00000263388.2:c.6626C>T	p.Pro2209Leu	p.P2209L	ENST00000263388	NM_000435.2	2209	cCg/cTg	33/33	1	2	FACETS	0.856	0.775	0.94	0.856	0.775	0.94	CLONAL	1	FALSE	1	0.3830535278892	2		1105	775	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919882	50919882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771789997	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	141	884	2	ENST00000440232.2:c.2969G>A	p.Arg990His	p.R990H	ENST00000440232	NM_002691.3	990	cGc/cAc	24/27	1	2	FACETS	0.926	0.844	1	0.926	0.844	1	CLONAL	1	FALSE	1	0.3830535278892	2		886	795	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748583	40748583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444440253	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	60	458	1	ENST00000373198.4:c.2933C>T	p.Ala978Val	p.A978V	ENST00000373198	NM_133170.3	978	gCg/gTg	21/32	1	2	FACETS	0.675	0.583	0.775	0.675	0.583	0.775	SUBCLONAL	1	FALSE	1	0.3830535278892	2		459	464	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180951	32180951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs978741176	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	104	779	1	ENST00000375023.3:c.2399C>T	p.Pro800Leu	p.P800L	ENST00000375023	NM_004557.3	800	cCg/cTg	15/30	1	2	FACETS	0.922	0.828	1	0.922	0.828	1	CLONAL	1	FALSE	1	0.3830535278892	2		780	589	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538941	187538941	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs113224498	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	78	395	0	ENST00000441802.2:c.8799del	p.Gly2934ValfsTer3	p.G2934Vfs*3	ENST00000441802	NM_005245.3	2933	caA/ca	10/27	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	FALSE	1	0.3830535278892	2		395	390	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652147	3652147	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775151113	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	113	822	1	ENST00000294008.3:c.922G>A	p.Val308Met	p.V308M	ENST00000294008	NM_032444.2	308	Gtg/Atg	4/15	1	2	FACETS	0.763	0.687	0.844	0.763	0.687	0.844	SUBCLONAL	1	FALSE	1	0.3830535278892	2		823	773	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300040	137300040	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	102	924	0	ENST00000481739.1:c.331del	p.Leu111TrpfsTer57	p.L111Wfs*57	ENST00000481739	NM_002957.4	109	Ccc/cc	3/10	1	2	FACETS	0.635	0.567	0.707	0.635	0.567	0.707	SUBCLONAL	1	FALSE	1	0.3830535278892	2		924	839	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991508	72991508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755878058	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	105	706	2	ENST00000268489.5:c.2537G>A	p.Arg846His	p.R846H	ENST00000268489	NM_006885.3	846	cGc/cAc	2/10	1	2	FACETS	0.795	0.712	0.881	0.795	0.712	0.881	SUBCLONAL	1	FALSE	1	0.3830535278892	2		708	690	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007182	62007182	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147194821	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	118	793	1	ENST00000392795.3:c.500C>T	p.Thr167Met	p.T167M	ENST00000392795	NM_001039933.1	167	aCg/aTg	4/6	1	2	FACETS	0.97	0.877	1	0.97	0.877	1	CLONAL	1	FALSE	1	0.3830535278892	2		794	635	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188143	11188143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772288758	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	104	547	0	ENST00000361445.4:c.5951C>T	p.Thr1984Met	p.T1984M	ENST00000361445	NM_004958.3	1984	aCg/aTg	43/58	1	2	FACETS	0.866	0.777	0.96	0.866	0.777	0.96	CLONAL	1	FALSE	1	0.3830535278892	2		547	627	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658354	206658354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs52817862	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	95	840	1	ENST00000367120.3:c.1448C>T	p.Thr483Met	p.T483M	ENST00000367120	NM_014002.3	483	aCg/aTg	14/22	1	2	FACETS	0.792	0.706	0.884	0.792	0.706	0.884	SUBCLONAL	1	FALSE	1	0.3830535278892	2		841	626	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274740	142274741	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	45	259	1	ENST00000350721.4:c.2319_2320del	p.Lys773AsnfsTer3	p.K773Nfs*3	ENST00000350721	NM_001184.3	773	aaAAta/aata	10/47	1	2	FACETS	0.775	0.655	0.907	0.775	0.655	0.907	CLONAL	1	FALSE	1	0.3830535278892	2		260	303	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31521250	31521250	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	93	494	0	ENST00000344624.3:c.927del	p.Glu310SerfsTer42	p.E310Sfs*42	ENST00000344624		309	aaA/aa	3/33	1	2	FACETS	0.812	0.723	0.906	0.812	0.723	0.906	CLONAL	1	FALSE	1	0.3830535278892	2		494	598	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432116	121432116	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1565885932	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	101	881	0	ENST00000257555.6:c.863G>C	p.Gly288Ala	p.G288A	ENST00000257555		288	gGg/gCg	4/10	1	2	FACETS	0.752	0.673	0.837	0.752	0.673	0.837	SUBCLONAL	1	FALSE	1	0.3830535278892	2		881	701	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412634	63412634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753930754	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	96	734	0	ENST00000330258.3:c.533G>A	p.Arg178His	p.R178H	ENST00000330258	NM_152424.3	178	cGt/cAt	2/2	0.3830535278892	1	FACETS	0.781	0.698	0.868	0.781	0.698	0.868	SUBCLONAL	1	FALSE	0	0.3830535278892	1		734	519	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660879	227660879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756434990	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	96	798	1	ENST00000305123.5:c.2576C>T	p.Thr859Met	p.T859M	ENST00000305123	NM_005544.2	859	aCg/aTg	1/2	1	2	FACETS	0.926	0.828	1	0.926	0.828	1	CLONAL	1	FALSE	1	0.3830535278892	2		799	541	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343913	118343913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264831726	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	62	404	0	ENST00000534358.1:c.2039C>T	p.Ser680Leu	p.S680L	ENST00000534358	NM_005933.3	680	tCg/tTg	3/36	1	2	FACETS	0.698	0.604	0.799	0.698	0.604	0.799	SUBCLONAL	1	FALSE	1	0.3830535278892	2		404	464	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449396	31449396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	71	400	2	ENST00000344624.3:c.2813G>A	p.Arg938Gln	p.R938Q	ENST00000344624		938	cGg/cAg	19/33	1	2	FACETS	0.941	0.825	1	0.941	0.825	1	CLONAL	1	FALSE	1	0.3830535278892	2		402	394	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418931	116418931	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879254336	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	59	361	0	ENST00000397752.3:c.3442C>T	p.Arg1148Ter	p.R1148*	ENST00000397752	NM_000245.2	1148	Cga/Tga	17/21	1	2	FACETS	0.835	0.722	0.957	0.835	0.722	0.957	CLONAL	1	FALSE	1	0.3830535278892	2		361	369	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944836	31944836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148314204	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	102	724	0	ENST00000340398.3:c.265G>A	p.Val89Ile	p.V89I	ENST00000340398	NM_001013699.2	89	Gtc/Atc	1/1	1	2	FACETS	0.632	0.564	0.703	0.632	0.564	0.703	SUBCLONAL	1	FALSE	1	0.3830535278892	2		724	843	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611358	28611358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200949858	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	128	566	0	ENST00000241453.7:c.1273G>A	p.Ala425Thr	p.A425T	ENST00000241453	NM_004119.2	425	Gcc/Acc	10/24	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	FALSE	1	0.3830535278892	2		566	666	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15952264	15952264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779213445	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	130	716	1	ENST00000268712.3:c.6431C>T	p.Ser2144Leu	p.S2144L	ENST00000268712	NM_006311.3	2144	tCg/tTg	41/46	1	2	FACETS	0.929	0.843	1	0.929	0.843	1	CLONAL	1	FALSE	1	0.3830535278892	2		717	731	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845839	72845839	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	110	652	2	ENST00000268489.5:c.3628C>T	p.Arg1210Ter	p.R1210*	ENST00000268489	NM_006885.3	1210	Cga/Tga	6/10	1	2	FACETS	0.84	0.755	0.929	0.84	0.755	0.929	CLONAL	1	FALSE	1	0.3830535278892	2		654	684	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302983	15302983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142492710	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	156	1014	3	ENST00000263388.2:c.467G>A	p.Arg156Gln	p.R156Q	ENST00000263388	NM_000435.2	156	cGa/cAa	4/33	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	FALSE	1	0.3830535278892	2		1017	805	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681003	37681003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1225789669	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	105	519	0	ENST00000447079.4:c.3172G>A	p.Glu1058Lys	p.E1058K	ENST00000447079	NM_015083.1	1058	Gaa/Aaa	12/14	1	2	FACETS	0.854	0.766	0.947	0.854	0.766	0.947	CLONAL	1	FALSE	1	0.3830535278892	2		519	642	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560133	29560133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199474732	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	65	326	0	ENST00000356175.3:c.3610C>T	p.Arg1204Trp	p.R1204W	ENST00000356175	NM_000267.3	1204	Cgg/Tgg	27/57	1	2	FACETS	0.795	0.691	0.906	0.795	0.691	0.906	CLONAL	1	FALSE	1	0.3830535278892	2		326	427	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433848	49433848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201507971	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	152	1127	1	ENST00000301067.7:c.7705G>A	p.Gly2569Ser	p.G2569S	ENST00000301067	NM_003482.3	2569	Ggc/Agc	31/54	1	2	FACETS	0.901	0.824	0.981	0.901	0.824	0.981	CLONAL	1	FALSE	1	0.3830535278892	2		1128	881	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210015	55210015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	79	494	1	ENST00000275493.2:c.125G>A	p.Gly42Asp	p.G42D	ENST00000275493	NM_005228.3	42	gGc/gAc	2/28	1	2	FACETS	0.697	0.613	0.786	0.697	0.613	0.786	SUBCLONAL	1	FALSE	1	0.3830535278892	2		495	592	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78617605	78617605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	71	356	0	ENST00000306801.3:c.343C>T	p.Pro115Ser	p.P115S	ENST00000306801	NM_020761.2	115	Cca/Tca	3/34	1	2	FACETS	0.843	0.738	0.954	0.843	0.738	0.954	CLONAL	1	FALSE	1	0.3830535278892	2		356	440	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651622	48651622	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557020433	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	114	734	1	ENST00000376670.3:c.788C>T	p.Thr263Met	p.T263M	ENST00000376670	NM_002049.3	263	aCg/aTg	5/6	0.3830535278892	1	FACETS	0.757	0.683	0.835	0.757	0.683	0.835	SUBCLONAL	1	FALSE	0	0.3830535278892	1		735	636	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528451	157528451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	93	545	1	ENST00000346085.5:c.6176C>T	p.Pro2059Leu	p.P2059L	ENST00000346085	NM_020732.3	2059	cCg/cTg	20/20	1	2	FACETS	0.853	0.76	0.952	0.853	0.76	0.952	CLONAL	1	FALSE	1	0.3830535278892	2		546	569	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118806	115118806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754023417	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	82	474	1	ENST00000257566.3:c.535G>A	p.Glu179Lys	p.E179K	ENST00000257566	NM_016569.3	179	Gaa/Aaa	2/8	1	2	FACETS	0.806	0.713	0.906	0.806	0.713	0.906	CLONAL	1	FALSE	1	0.3830535278892	2		475	531	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37856539	37856540	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	50	392	2	ENST00000269571.5:c.54dup	p.Gly19ArgfsTer91	p.G19Rfs*91	ENST00000269571		16	-/C	1/27	1	2	FACETS	0.864	0.738	1	0.864	0.738	1	CLONAL	1	FALSE	1	0.3830535278892	2		394	302	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448552	89448552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	81	483	0	ENST00000336596.2:c.1516G>A	p.Val506Ile	p.V506I	ENST00000336596	NM_005233.5	506	Gta/Ata	7/17	1	2	FACETS	0.737	0.65	0.83	0.737	0.65	0.83	SUBCLONAL	1	FALSE	1	0.3830535278892	2		483	574	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049809	16049809	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	75	379	0	ENST00000268712.3:c.963del	p.Val322TrpfsTer4	p.V322Wfs*4	ENST00000268712	NM_006311.3	321	aaA/aa	10/46	1	2	FACETS	0.915	0.805	1	0.915	0.805	1	CLONAL	1	FALSE	1	0.3830535278892	2		379	428	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1978316	1978316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1424067803	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	111	934	2	ENST00000382891.5:c.3736G>A	p.Gly1246Ser	p.G1246S	ENST00000382891	NM_133335.3	1246	Ggt/Agt	21/22	1	2	FACETS	0.586	0.526	0.65	0.586	0.526	0.65	SUBCLONAL	1	FALSE	1	0.3830535278892	2		936	989	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097604	11097604	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	107	1048	1	ENST00000358026.2:c.788del	p.Pro263GlnfsTer40	p.P263Qfs*40	ENST00000358026	NM_001128849.1	262	Ccc/cc	5/36	1	2	FACETS	0.764	0.686	0.847	0.764	0.686	0.847	SUBCLONAL	1	FALSE	1	0.3830535278892	2		1049	731	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300927	137300927	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1564289265	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	127	843	1	ENST00000481739.1:c.572G>A	p.Arg191His	p.R191H	ENST00000481739	NM_002957.4	191	cGc/cAc	4/10	1	2	FACETS	0.773	0.7	0.85	0.773	0.7	0.85	SUBCLONAL	1	FALSE	1	0.3830535278892	2		844	858	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054396	42054396	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	46	318	1	ENST00000219905.7:c.7585del	p.Arg2529GlufsTer28	p.R2529Efs*28	ENST00000219905	NM_001164273.1	2527	cAa/ca	22/24	1	2	FACETS	0.751	0.635	0.877	0.751	0.635	0.877	SUBCLONAL	1	FALSE	1	0.3830535278892	2		319	320	SUCCESS
APC	324	MSKCC	GRCh37	5	112175504	112175504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761966904	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	53	318	1	ENST00000257430.4:c.4213G>A	p.Val1405Ile	p.V1405I	ENST00000257430	NM_000038.5	1405	Gtt/Att	16/16	1	2	FACETS	0.836	0.717	0.965	0.836	0.717	0.965	CLONAL	1	FALSE	1	0.3830535278892	2		319	331	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989642	68989642	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767992923	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	71	465	1	ENST00000288368.4:c.1580G>A	p.Arg527His	p.R527H	ENST00000288368	NM_024870.2	527	cGc/cAc	15/40	1	2	FACETS	0.734	0.642	0.833	0.734	0.642	0.833	SUBCLONAL	1	FALSE	1	0.3830535278892	2		466	505	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862712	9862712	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	66	475	0	ENST00000330684.3:c.2591G>A	p.Ser864Asn	p.S864N	ENST00000330684	NM_001134407.1	864	aGc/aAc	12/13	1	2	FACETS	0.766	0.667	0.873	0.766	0.667	0.873	SUBCLONAL	1	FALSE	1	0.3830535278892	2		475	450	SUCCESS
EED	8726	MSKCC	GRCh37	11	85979605	85979605	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	24	313	0	ENST00000263360.6:c.966+2T>C		p.X322_splice	ENST00000263360	NM_003797.3	322			1	2	FACETS	0.306	0.239	0.383	0.306	0.239	0.383	SUBCLONAL	1	FALSE	1	0.3830535278892	2		313	410	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575113	64575113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1225847249	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	116	639	2	ENST00000312049.6:c.694C>T	p.Arg232Cys	p.R232C	ENST00000312049	NM_130799.2	232	Cgc/Tgc	4/10	1	2	FACETS	0.864	0.78	0.953	0.864	0.78	0.953	CLONAL	1	FALSE	1	0.3830535278892	2		641	701	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225768	26225768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	83	628	1	ENST00000360408.1:c.386G>A	p.Arg129His	p.R129H	ENST00000360408	NM_003532.2	129	cGc/cAc	1/1	1	2	FACETS	0.716	0.633	0.806	0.716	0.633	0.806	SUBCLONAL	1	FALSE	1	0.3830535278892	2		629	605	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521066	187521066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572074365	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	62	446	0	ENST00000441802.2:c.12089C>T	p.Pro4030Leu	p.P4030L	ENST00000441802	NM_005245.3	4030	cCg/cTg	22/27	1	2	FACETS	0.859	0.745	0.981	0.859	0.745	0.981	CLONAL	1	FALSE	1	0.3830535278892	2		446	377	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276215	15276215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748889237	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	120	760	2	ENST00000263388.2:c.5779G>A	p.Ala1927Thr	p.A1927T	ENST00000263388	NM_000435.2	1927	Gcc/Acc	31/33	1	2	FACETS	0.879	0.794	0.968	0.879	0.794	0.968	CLONAL	1	FALSE	1	0.3830535278892	2		762	713	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101510	27101510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781689378	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	120	909	0	ENST00000324856.7:c.4792C>T	p.Arg1598Cys	p.R1598C	ENST00000324856	NM_006015.4	1598	Cgc/Tgc	18/20	1	2	FACETS	0.829	0.749	0.913	0.829	0.749	0.913	CLONAL	1	FALSE	1	0.3830535278892	2		909	756	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193181576	193181576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	71	385	0	ENST00000367435.3:c.1123C>T	p.Leu375Phe	p.L375F	ENST00000367435	NM_024529.4	375	Ctt/Ttt	13/17	1	2	FACETS	0.774	0.677	0.878	0.774	0.677	0.878	SUBCLONAL	1	FALSE	1	0.3830535278892	2		385	479	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246498751	246498751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1431606369	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	117	563	0	ENST00000388985.4:c.254G>A	p.Arg85Gln	p.R85Q	ENST00000388985		85	cGg/cAg	3/12	1	2	FACETS	0.902	0.815	0.994	0.902	0.815	0.994	CLONAL	1	FALSE	1	0.3830535278892	2		563	677	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972470	32972470	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs80359244	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	61	545	0	ENST00000380152.3:c.9820T>G	p.Leu3274Val	p.L3274V	ENST00000380152		3274	Ttg/Gtg	27/27	1	2	FACETS	0.479	0.413	0.551	0.479	0.413	0.551	SUBCLONAL	1	FALSE	1	0.3830535278892	2		545	665	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41001222	41001222	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	93	445	0	ENST00000267868.3:c.344-1G>T		p.X115_splice	ENST00000267868	NM_002875.4	115			1	2	FACETS	0.855	0.762	0.954	0.855	0.762	0.954	CLONAL	1	FALSE	1	0.3830535278892	2		445	568	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456302	99456302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	112	365	0	ENST00000268035.6:c.1619G>T	p.Gly540Val	p.G540V	ENST00000268035	NM_000875.3	540	gGg/gTg	8/21	0.2350033748151	3	FACETS	1	0.982	1	0.701	0.633	0.772	CLONAL	1	FALSE	1	0.3830535278892	3		365	497	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014110	14014110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	99	731	2	ENST00000311895.7:c.88G>A	p.Asp30Asn	p.D30N	ENST00000311895	NM_005236.2	30	Gac/Aac	1/11	1	2	FACETS	0.847	0.758	0.942	0.847	0.758	0.942	CLONAL	1	FALSE	1	0.3830535278892	2		733	610	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020501	14020501	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746296279	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	26	406	2	ENST00000311895.7:c.472C>T	p.Arg158Cys	p.R158C	ENST00000311895	NM_005236.2	158	Cgt/Tgt	3/11	1	2	FACETS	0.294	0.232	0.365	0.294	0.232	0.365	SUBCLONAL	1	FALSE	1	0.3830535278892	2		408	462	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40460265	40460265	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138484872	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	35	612	1	ENST00000345506.4:c.1976G>A	p.Arg659Gln	p.R659Q	ENST00000345506	NM_003152.3	659	cGg/cAg	17/20	1	2	FACETS	0.287	0.235	0.347	0.287	0.235	0.347	SUBCLONAL	1	FALSE	1	0.3830535278892	2		613	636	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245007	41245007	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	107	641	1	ENST00000357654.3:c.2541G>T	p.Met847Ile	p.M847I	ENST00000357654	NM_007294.3	847	atG/atT	10/23	1	2	FACETS	0.869	0.781	0.962	0.869	0.781	0.962	CLONAL	1	FALSE	1	0.3830535278892	2		642	643	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375319	15375319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1196808917	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	113	756	2	ENST00000263377.2:c.1108G>A	p.Ala370Thr	p.A370T	ENST00000263377	NM_058243.2	370	Gcc/Acc	6/20	1	2	FACETS	0.759	0.683	0.84	0.759	0.683	0.84	SUBCLONAL	1	FALSE	1	0.3830535278892	2		758	777	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214635	36214635	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs753991431	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	109	869	2	ENST00000222270.7:c.3061C>T	p.Arg1021Trp	p.R1021W	ENST00000222270	NM_014727.1	1021	Cgg/Tgg	8/37	1	2	FACETS	0.741	0.665	0.821	0.741	0.665	0.821	SUBCLONAL	1	FALSE	1	0.3830535278892	2		871	768	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219063	36219063	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556493224	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	115	803	0	ENST00000222270.7:c.4562G>A	p.Arg1521Gln	p.R1521Q	ENST00000222270	NM_014727.1	1521	cGg/cAg	19/37	1	2	FACETS	0.871	0.786	0.962	0.871	0.786	0.962	CLONAL	1	FALSE	1	0.3830535278892	2		803	689	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082356	16082356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	124	973	0	ENST00000281043.3:c.170C>T	p.Pro57Leu	p.P57L	ENST00000281043	NM_005378.4	57	cCc/cTc	2/3	1	2	FACETS	0.821	0.743	0.903	0.821	0.743	0.903	CLONAL	1	FALSE	1	0.3830535278892	2		973	789	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707987	47707987	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	68	432	0	ENST00000233146.2:c.2611A>T	p.Lys871Ter	p.K871*	ENST00000233146	NM_000251.2	871	Aag/Tag	15/16	1	2	FACETS	0.839	0.733	0.953	0.839	0.733	0.953	CLONAL	1	FALSE	1	0.3830535278892	2		432	423	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47709936	47709936	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750808	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	79	288	0	ENST00000233146.2:c.2653C>T	p.Gln885Ter	p.Q885*	ENST00000233146	NM_000251.2	885	Cag/Tag	16/16	1	2	FACETS	0.931	0.822	1	0.931	0.822	1	CLONAL	1	FALSE	1	0.3830535278892	2		288	443	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169355	99169355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745803782	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	95	489	0	ENST00000074304.5:c.1285G>A	p.Ala429Thr	p.A429T	ENST00000074304	NM_001134224.1	429	Gca/Aca	15/26	1	2	FACETS	0.915	0.817	1	0.915	0.817	1	CLONAL	1	FALSE	1	0.3830535278892	2		489	542	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661789	227661789	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	114	900	1	ENST00000305123.5:c.1666C>T	p.Pro556Ser	p.P556S	ENST00000305123	NM_005544.2	556	Cct/Tct	1/2	1	2	FACETS	0.931	0.84	1	0.931	0.84	1	CLONAL	1	FALSE	1	0.3830535278892	2		901	639	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021635	31021635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149449801	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	105	502	1	ENST00000375687.4:c.1634G>A	p.Arg545His	p.R545H	ENST00000375687	NM_015338.5	545	cGt/cAt	12/13	1	2	FACETS	0.894	0.803	0.991	0.894	0.803	0.991	CLONAL	1	FALSE	1	0.3830535278892	2		503	613	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940479	49940480	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	121	1032	0	ENST00000296474.3:c.563_564del	p.Val188GlyfsTer2	p.V188Gfs*2	ENST00000296474	NM_002447.2	188	gTG/g	1/20	1	2	FACETS	0.734	0.662	0.809	0.734	0.662	0.809	SUBCLONAL	1	FALSE	1	0.3830535278892	2		1032	861	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188405	142188405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755849743	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	77	287	0	ENST00000350721.4:c.6326G>A	p.Arg2109His	p.R2109H	ENST00000350721	NM_001184.3	2109	cGc/cAc	38/47	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.3830535278892	2		287	351	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374668	149374668	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	133	666	0	ENST00000360632.3:c.426C>A	p.Phe142Leu	p.F142L	ENST00000360632	NM_015472.4	142	ttC/ttA	2/7	0.110357829085189	3	FACETS	1	0.954	1	0.539	0.489	0.59	INDETERMINATE	1	FALSE	1	0.3830535278892	3		666	768	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157588	106157588	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	57	310	0	ENST00000380013.4:c.2489T>G	p.Ile830Arg	p.I830R	ENST00000380013	NM_001127208.2	830	aTa/aGa	3/11	1	2	FACETS	0.838	0.723	0.963	0.838	0.723	0.963	CLONAL	1	FALSE	1	0.3830535278892	2		310	355	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143235878	143235878	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	76	352	0	ENST00000262992.4:c.410del	p.Pro137ArgfsTer20	p.P137Rfs*20	ENST00000262992	NM_001101669.1	137	cCg/cg	6/24	1	2	FACETS	0.914	0.805	1	0.914	0.805	1	CLONAL	1	FALSE	1	0.3830535278892	2		352	434	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449403	31449403	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	80	434	0	ENST00000344624.3:c.2806C>T	p.His936Tyr	p.H936Y	ENST00000344624		936	Cac/Tac	19/33	1	2	FACETS	0.954	0.843	1	0.954	0.843	1	CLONAL	1	FALSE	1	0.3830535278892	2		434	438	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839754	27839754	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	105	584	0	ENST00000328488.2:c.340C>A	p.His114Asn	p.H114N	ENST00000328488	NM_003533.2	114	Cac/Aac	1/1	1	2	FACETS	0.798	0.716	0.885	0.798	0.716	0.885	SUBCLONAL	1	FALSE	1	0.3830535278892	2		584	687	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679695	30679696	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	88	675	0	ENST00000376406.3:c.2023_2024del	p.Glu675ThrfsTer10	p.E675Tfs*10	ENST00000376406	NM_014641.2	675	GAa/a	5/15	1	2	FACETS	0.718	0.636	0.805	0.718	0.636	0.805	SUBCLONAL	1	FALSE	1	0.3830535278892	2		675	640	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952945	2952945	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	100	839	0	ENST00000396946.4:c.2995A>G	p.Met999Val	p.M999V	ENST00000396946	NM_032415.4	999	Atg/Gtg	22/25	1	2	FACETS	0.75	0.67	0.835	0.75	0.67	0.835	SUBCLONAL	1	FALSE	1	0.3830535278892	2		839	696	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55231511	55231511	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	85	521	0	ENST00000275493.2:c.1717G>T	p.Gly573Ter	p.G573*	ENST00000275493	NM_005228.3	573	Gga/Tga	14/28	1	2	FACETS	0.852	0.755	0.955	0.852	0.755	0.955	CLONAL	1	FALSE	1	0.3830535278892	2		521	521	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462493	92462493	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	97	667	0	ENST00000265734.4:c.145A>G	p.Thr49Ala	p.T49A	ENST00000265734	NM_001259.6	49	Acc/Gcc	2/8	1	2	FACETS	0.858	0.767	0.955	0.858	0.767	0.955	CLONAL	1	FALSE	1	0.3830535278892	2		667	590	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878091	151878091	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	69	499	0	ENST00000262189.6:c.6854A>G	p.Asp2285Gly	p.D2285G	ENST00000262189	NM_170606.2	2285	gAc/gGc	36/59	1	2	FACETS	0.725	0.633	0.824	0.725	0.633	0.824	SUBCLONAL	1	FALSE	1	0.3830535278892	2		499	497	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133244	38133244	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	144	583	0	ENST00000317025.8:c.4229C>A	p.Pro1410His	p.P1410H	ENST00000317025	NM_023034.1	1410	cCc/cAc	24/24	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	FALSE	1	0.3830535278892	2		583	730	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133868	38133869	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	129	787	0	ENST00000317025.8:c.4017dup	p.Asp1340ArgfsTer12	p.D1340Rfs*12	ENST00000317025	NM_023034.1	1339	-/A	23/24	1	2	FACETS	0.797	0.723	0.876	0.797	0.723	0.876	SUBCLONAL	1	FALSE	1	0.3830535278892	2		787	845	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995563	68995563	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1157862775	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	117	558	0	ENST00000288368.4:c.1967T>C	p.Leu656Pro	p.L656P	ENST00000288368	NM_024870.2	656	cTg/cCg	18/40	1	2	FACETS	0.952	0.86	1	0.952	0.86	1	CLONAL	1	FALSE	1	0.3830535278892	2		558	642	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5077560	5077560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	37	463	0	ENST00000381652.3:c.1972G>A	p.Ala658Thr	p.A658T	ENST00000381652	NM_004972.3	658	Gca/Aca	15/25	0.185969755347049	0	FACETS	0.295	0.243	0.353			1	INDETERMINATE	1	FALSE	0	0.3830535278892	0		463	404	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27204908	27204908	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0052791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	32	439	0	ENST00000380036.4:c.2210-1G>A		p.X737_splice	ENST00000380036	NM_000459.3	737			0.185969755347049	0	FACETS	0.273	0.222	0.332			1	INDETERMINATE	1	FALSE	0	0.3830535278892	0		439	377	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	54	1003	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.163	0.138	0.19	0.163	0.138	0.19	SUBCLONAL	1	TRUE	1	0.68	2		1007	974	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	209	561	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.846	0.788	0.905	0.846	0.788	0.905	CLONAL	1	TRUE	1	0.68	2		561	727	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	317	942	4	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.68	2		946	918	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	248	711	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	0.988	0.928	1	0.988	0.928	1	CLONAL	1	TRUE	1	0.68	2		711	738	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	305	624	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	1	2	FACETS	0.988	0.934	1	0.988	0.934	1	CLONAL	1	TRUE	1	0.68	2		624	908	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	211	500	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.868	0.809	0.928	0.868	0.809	0.928	CLONAL	1	TRUE	1	0.68	2		500	715	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	150	369	1	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.829	0.762	0.898	0.829	0.762	0.898	CLONAL	1	TRUE	1	0.68	2		370	532	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027422	48027422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781462	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	196	435	0	ENST00000234420.5:c.2300C>T	p.Thr767Ile	p.T767I	ENST00000234420	NM_000179.2	767	aCt/aTt	4/10	1	2	FACETS	0.966	0.899	1	0.966	0.899	1	CLONAL	1	TRUE	1	0.68	2		435	597	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	107	258	0	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	1	2	FACETS	0.934	0.847	1	0.934	0.847	1	CLONAL	1	TRUE	1	0.68	2		258	337	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433745	149433745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537011691	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	334	1024	1	ENST00000286301.3:c.2806G>A	p.Gly936Ser	p.G936S	ENST00000286301	NM_005211.3	936	Ggc/Agc	22/22	0.0946658792058589	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.68	0		1025	1085	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821890	72821890	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	222	582	0	ENST00000268489.5:c.10285del	p.Arg3429ValfsTer56	p.R3429Vfs*56	ENST00000268489	NM_006885.3	3429	Cgt/gt	10/10	1	2	FACETS	0.922	0.862	0.984	0.922	0.862	0.984	CLONAL	1	TRUE	1	0.68	2		582	708	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582168	189582168	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121908835	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	240	560	1	ENST00000264731.3:c.727C>T	p.Arg243Trp	p.R243W	ENST00000264731	NM_003722.4	243	Cgg/Tgg	5/14	1	2	FACETS	0.934	0.875	0.993	0.934	0.875	0.993	CLONAL	1	TRUE	1	0.68	2		561	756	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89815155	89815155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376089640	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	342	923	1	ENST00000389301.3:c.3260C>T	p.Ser1087Leu	p.S1087L	ENST00000389301	NM_000135.2	1087	tCg/tTg	33/43	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.68	2		924	983	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165602	118165602	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs921184290	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	32	517	0	ENST00000369448.3:c.112C>T	p.Arg38Ter	p.R38*	ENST00000369448	NM_017709.3	38	Cga/Tga	2/2	1	2	FACETS	0.148	0.119	0.18	0.148	0.119	0.18	SUBCLONAL	1	TRUE	1	0.68	2		517	637	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115727	108115727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747727055	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	127	250	0	ENST00000278616.4:c.875C>T	p.Pro292Leu	p.P292L	ENST00000278616	NM_000051.3	292	cCg/cTg	7/63	1	2	FACETS	0.996	0.912	1	0.996	0.912	1	CLONAL	1	TRUE	1	0.68	2		250	375	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098912	47098912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	59	707	0	ENST00000409792.3:c.6362G>A	p.Arg2121His	p.R2121H	ENST00000409792	NM_014159.6	2121	cGc/cAc	15/21	1	2	FACETS	0.148	0.127	0.172	0.148	0.127	0.172	SUBCLONAL	1	TRUE	1	0.68	2		707	1170	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912188	114912188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	256	680	1	ENST00000543371.1:c.1258C>T	p.Arg420Trp	p.R420W	ENST00000543371	NM_001198531.1	420	Cgg/Tgg	11/14	1	2	FACETS	0.828	0.777	0.881	0.828	0.777	0.881	CLONAL	1	TRUE	1	0.68	2		681	909	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473648	67473648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223736	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	272	856	0	ENST00000327367.4:c.728G>A	p.Arg243His	p.R243H	ENST00000327367	NM_005902.3	243	cGc/cAc	6/9	0.154183054834926	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.68	0		856	894	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261038	16261038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144525015	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	225	721	4	ENST00000375759.3:c.8303C>T	p.Ala2768Val	p.A2768V	ENST00000375759	NM_015001.2	2768	gCg/gTg	11/15	1	2	FACETS	0.854	0.798	0.912	0.854	0.798	0.912	CLONAL	1	TRUE	1	0.68	2		725	775	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938230	76938230	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	274	648	3	ENST00000373344.5:c.2518del	p.Arg840GlufsTer29	p.R840Efs*29	ENST00000373344	NM_000489.3	840	Aga/ga	9/35	1	2	FACETS	0.797	0.749	0.847	0.797	0.749	0.847	SUBCLONAL	1	TRUE	1	0.68	2		651	1011	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916124	9916124	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376029542	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	168	543	0	ENST00000330684.3:c.2165C>T	p.Thr722Met	p.T722M	ENST00000330684	NM_001134407.1	722	aCg/aTg	10/13	1	2	FACETS	0.853	0.789	0.92	0.853	0.789	0.92	CLONAL	1	TRUE	1	0.68	2		543	579	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839700	27839700	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	245	653	0	ENST00000328488.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000328488	NM_003533.2	132	Cga/Tga	1/1	1	2	FACETS	0.986	0.925	1	0.986	0.925	1	CLONAL	1	TRUE	1	0.68	2		653	731	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944381	131944382	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs748536322	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	131	234	5	ENST00000265335.6:c.2801dup	p.Asn934LysfsTer10	p.N934Kfs*10	ENST00000265335		931	-/A	17/25	1	2	FACETS	0.838	0.766	0.912	0.838	0.766	0.912	CLONAL	1	TRUE	1	0.68	2		239	460	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076740	102076740	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	303	750	4	ENST00000282441.5:c.919C>T	p.Arg307Ter	p.R307*	ENST00000282441	NM_001130145.2	307	Cga/Tga	5/9	1	2	FACETS	0.864	0.815	0.915	0.864	0.815	0.915	CLONAL	1	TRUE	1	0.68	2		754	1031	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158212	47158212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553699111	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	227	465	2	ENST00000409792.3:c.4487G>A	p.Arg1496Gln	p.R1496Q	ENST00000409792	NM_014159.6	1496	cGa/cAa	4/21	1	2	FACETS	0.872	0.815	0.93	0.872	0.815	0.93	CLONAL	1	TRUE	1	0.68	2		467	766	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435971	56435971	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780893183	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	186	702	0	ENST00000407977.2:c.1166G>A	p.Arg389His	p.R389H	ENST00000407977		389	cGc/cAc	9/10	1	2	FACETS	0.995	0.925	1	0.995	0.925	1	CLONAL	1	TRUE	1	0.68	2		702	550	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451546	70451546	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768089885	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	306	716	0	ENST00000373644.4:c.6386C>T	p.Ala2129Val	p.A2129V	ENST00000373644	NM_030625.2	2129	gCg/gTg	12/12	1	2	FACETS	0.977	0.923	1	0.977	0.923	1	CLONAL	1	TRUE	1	0.68	2		716	921	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164875	36164875	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	248	1123	0	ENST00000300305.3:c.1000C>T	p.Arg334Cys	p.R334C	ENST00000300305		334	Cgc/Tgc	8/8	1	2	FACETS	0.744	0.696	0.794	0.744	0.696	0.794	SUBCLONAL	1	TRUE	1	0.68	2		1123	980	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657002	45657002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	310	766	0	ENST00000407780.3:c.154G>A	p.Val52Ile	p.V52I	ENST00000407780	NM_001283052.1	52	Gta/Ata	3/7	1	2	FACETS	0.995	0.941	1	0.995	0.941	1	CLONAL	1	TRUE	1	0.68	2		766	916	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687001	176687001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	210	484	1	ENST00000439151.2:c.4978C>T	p.Arg1660Cys	p.R1660C	ENST00000439151	NM_022455.4	1660	Cgc/Tgc	14/23	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.68	2		485	585	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827892	40827892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573377632	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	198	654	3	ENST00000373198.4:c.2536G>A	p.Val846Ile	p.V846I	ENST00000373198	NM_133170.3	846	Gtc/Atc	17/32	0.3	1	FACETS	0.559	0.519	0.599	0.559	0.519	0.599	INDETERMINATE	1	TRUE	0	0.68	1		657	688	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912094	114912094	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	195	520	0	ENST00000543371.1:c.1164G>A	p.Trp388Ter	p.W388*	ENST00000543371	NM_001198531.1	388	tgG/tgA	11/14	1	2	FACETS	0.942	0.877	1	0.942	0.877	1	CLONAL	1	TRUE	1	0.68	2		520	609	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	75	415	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.951	0.846	1	0.951	0.846	1	CLONAL	1	TRUE	1	0.68	2		416	232	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780277	9780277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	223	981	0	ENST00000377346.4:c.1447G>A	p.Val483Met	p.V483M	ENST00000377346	NM_005026.3	483	Gtg/Atg	11/24	1	2	FACETS	0.773	0.721	0.827	0.773	0.721	0.827	SUBCLONAL	1	TRUE	1	0.68	2		981	848	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376268	15376268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536634033	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	186	857	0	ENST00000263377.2:c.746C>T	p.Thr249Met	p.T249M	ENST00000263377	NM_058243.2	249	aCg/aTg	5/20	1	2	FACETS	0.846	0.784	0.909	0.846	0.784	0.909	CLONAL	1	TRUE	1	0.68	2		857	647	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057304	180057304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140347743	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	309	1027	1	ENST00000261937.6:c.434C>T	p.Thr145Met	p.T145M	ENST00000261937	NM_182925.4	145	aCg/aTg	4/30	0.154183054834926	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.68	0		1028	901	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041121	180041121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770869636	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	358	1320	0	ENST00000261937.6:c.3278C>T	p.Thr1093Met	p.T1093M	ENST00000261937	NM_182925.4	1093	aCg/aTg	24/30	0.154183054834926	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.68	0		1320	1109	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440951	56440951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777370273	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	263	817	3	ENST00000407977.2:c.386C>T	p.Ala129Val	p.A129V	ENST00000407977		129	gCg/gTg	4/10	1	2	FACETS	0.891	0.837	0.946	0.891	0.837	0.946	CLONAL	1	TRUE	1	0.68	2		820	868	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035930	47035930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1308446046	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	52	942	2	ENST00000377604.3:c.608C>T	p.Ser203Leu	p.S203L	ENST00000377604	NM_001204468.1	203	tCg/tTg	7/24	1	2	FACETS	0.149	0.126	0.174	0.149	0.126	0.174	SUBCLONAL	1	TRUE	1	0.68	2		944	1029	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808001	3808001	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	244	605	0	ENST00000262367.5:c.3418C>T	p.Arg1140Trp	p.R1140W	ENST00000262367	NM_004380.2	1140	Cgg/Tgg	18/31	1	2	FACETS	0.906	0.849	0.964	0.906	0.849	0.964	CLONAL	1	TRUE	1	0.68	2		605	792	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072540	5072540	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	236	401	0	ENST00000381652.3:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000381652	NM_004972.3	564	Cga/Tga	13/25	1	2	FACETS	0.997	0.935	1	0.997	0.935	1	CLONAL	1	TRUE	1	0.68	2		401	696	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469073	25469073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200845575	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	310	991	2	ENST00000264709.3:c.1385C>T	p.Ala462Val	p.A462V	ENST00000264709	NM_175629.2	462	gCg/gTg	11/23	1	2	FACETS	0.988	0.934	1	0.988	0.934	1	CLONAL	1	TRUE	1	0.68	2		993	923	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740749	58740749	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs779070661	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	316	616	0	ENST00000305921.3:c.1654C>T	p.Arg552Ter	p.R552*	ENST00000305921	NM_003620.3	552	Cga/Tga	6/6	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.68	2		616	851	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317533	1317533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199794164	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	293	748	1	ENST00000400841.2:c.532G>A	p.Glu178Lys	p.E178K	ENST00000400841		178	Gag/Aag	5/6	0.3	2	FACETS	0.98	0.925	1			1	INDETERMINATE	1	TRUE	NA	0.68	2		749	879	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617690	39617690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141329274	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	192	413	0	ENST00000262039.4:c.1874C>T	p.Thr625Met	p.T625M	ENST00000262039	NM_002647.2	625	aCg/aTg	17/25	1	2	FACETS	0.901	0.837	0.966	0.901	0.837	0.966	CLONAL	1	TRUE	1	0.68	2		413	627	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655328	45655328	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776339033	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	368	1090	0	ENST00000407780.3:c.524C>T	p.Thr175Met	p.T175M	ENST00000407780	NM_001283052.1	175	aCg/aTg	4/7	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.68	2		1090	1054	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346961	89346961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775491352	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	144	616	2	ENST00000301030.4:c.5989G>A	p.Ala1997Thr	p.A1997T	ENST00000301030	NM_001256183.1	1997	Gcg/Acg	9/13	1	2	FACETS	0.927	0.852	1	0.927	0.852	1	CLONAL	1	TRUE	1	0.68	2		618	457	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302857	15302857	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140914494	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	59	1207	1	ENST00000263388.2:c.593C>T	p.Ala198Val	p.A198V	ENST00000263388	NM_000435.2	198	gCg/gTg	4/33	1	2	FACETS	0.151	0.129	0.175	0.151	0.129	0.175	SUBCLONAL	1	TRUE	1	0.68	2		1208	1147	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132498	11132498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	77	1103	0	ENST00000358026.2:c.2714G>A	p.Arg905His	p.R905H	ENST00000358026	NM_001128849.1	905	cGc/cAc	19/36	1	2	FACETS	0.21	0.183	0.239	0.21	0.183	0.239	SUBCLONAL	1	TRUE	1	0.68	2		1103	1079	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922222	39922222	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780412607	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	36	592	0	ENST00000378444.4:c.3950C>T	p.Pro1317Leu	p.P1317L	ENST00000378444	NM_001123385.1	1317	cCg/cTg	9/15	0.3	2	FACETS	0.151	0.123	0.182			1	INDETERMINATE	1	TRUE	NA	0.68	2		592	703	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169624	27169624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762239847	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	291	745	0	ENST00000380036.4:c.625C>T	p.Arg209Trp	p.R209W	ENST00000380036	NM_000459.3	209	Cgg/Tgg	4/23	1	2	FACETS	0.923	0.871	0.977	0.923	0.871	0.977	CLONAL	1	TRUE	1	0.68	2		745	927	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434581	99434581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1461059080	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	52	790	1	ENST00000268035.6:c.668C>T	p.Ala223Val	p.A223V	ENST00000268035	NM_000875.3	223	gCg/gTg	3/21	0.3	2	FACETS	0.169	0.143	0.198			1	INDETERMINATE	1	TRUE	NA	0.68	2		791	904	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434270	49434270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776887182	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	431	1216	1	ENST00000301067.7:c.7283G>A	p.Arg2428Gln	p.R2428Q	ENST00000301067	NM_003482.3	2428	cGg/cAg	31/54	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.68	2		1217	1247	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788626	3788626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	259	535	0	ENST00000262367.5:c.4328G>A	p.Arg1443His	p.R1443H	ENST00000262367	NM_004380.2	1443	cGt/cAt	26/31	1	2	FACETS	0.957	0.9	1	0.957	0.9	1	CLONAL	1	TRUE	1	0.68	2		535	796	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751225	57751225	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358636691	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	37	372	1	ENST00000274289.3:c.1642G>A	p.Ala548Thr	p.A548T	ENST00000274289	NM_006622.3	548	Gca/Aca	12/14	1	2	FACETS	0.186	0.152	0.223	0.186	0.152	0.223	SUBCLONAL	1	TRUE	1	0.68	2		373	586	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022694	31022694	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1264581343	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	42	788	2	ENST00000375687.4:c.2179G>T	p.Glu727Ter	p.E727*	ENST00000375687	NM_015338.5	727	Gag/Tag	13/13	1	2	FACETS	0.154	0.128	0.184	0.154	0.128	0.184	SUBCLONAL	1	TRUE	1	0.68	2		790	801	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442932	49442932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886049484	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	262	788	2	ENST00000301067.7:c.3976C>T	p.Arg1326Trp	p.R1326W	ENST00000301067	NM_003482.3	1326	Cgg/Tgg	12/54	1	2	FACETS	0.939	0.882	0.996	0.939	0.882	0.996	CLONAL	1	TRUE	1	0.68	2		790	821	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020396	69020396	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	275	650	0	ENST00000288368.4:c.2768C>A	p.Ser923Tyr	p.S923Y	ENST00000288368	NM_024870.2	923	tCt/tAt	24/40	1	2	FACETS	0.974	0.918	1	0.974	0.918	1	CLONAL	1	TRUE	1	0.68	2		650	830	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937223	36937223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768170625	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	316	1054	0	ENST00000361632.4:c.1096G>A	p.Gly366Arg	p.G366R	ENST00000361632		366	Gga/Aga	9/16	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.68	2		1054	923	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543892	41543892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746729196	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	305	680	0	ENST00000263253.7:c.2183G>A	p.Arg728Gln	p.R728Q	ENST00000263253	NM_001429.3	728	cGg/cAg	12/31	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.68	2		680	862	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199706	11199706	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1190108406	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	55	672	0	ENST00000361445.4:c.4882C>T	p.Arg1628Cys	p.R1628C	ENST00000361445	NM_004958.3	1628	Cgt/Tgt	35/58	1	2	FACETS	0.239	0.203	0.277	0.239	0.203	0.277	SUBCLONAL	1	TRUE	1	0.68	2		672	678	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258772	16258772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766851755	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	235	705	0	ENST00000375759.3:c.6037G>A	p.Ala2013Thr	p.A2013T	ENST00000375759	NM_015001.2	2013	Gcc/Acc	11/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.68	2		705	655	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262334	16262334	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs757613816	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	97	463	0	ENST00000375759.3:c.9599A>G	p.His3200Arg	p.H3200R	ENST00000375759	NM_015001.2	3200	cAt/cGt	11/15	1	2	FACETS	0.829	0.747	0.916	0.829	0.747	0.916	CLONAL	1	TRUE	1	0.68	2		463	344	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63829468	63829468	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1001964542	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	207	399	1	ENST00000279873.7:c.1111C>T	p.Arg371Cys	p.R371C	ENST00000279873	NM_032199.2	371	Cgc/Tgc	8/10	1	2	FACETS	0.947	0.883	1	0.947	0.883	1	CLONAL	1	TRUE	1	0.68	2		400	643	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333374	70333374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	315	892	0	ENST00000373644.4:c.1279C>A	p.Pro427Thr	p.P427T	ENST00000373644	NM_030625.2	427	Cca/Aca	2/12	1	2	FACETS	0.949	0.897	1	0.949	0.897	1	CLONAL	1	TRUE	1	0.68	2		892	976	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325026	123325026	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	78	757	0	ENST00000358487.5:c.302A>G	p.Asp101Gly	p.D101G	ENST00000358487	NM_000141.4	101	gAc/gGc	3/18	1	2	FACETS	0.25	0.219	0.284	0.25	0.219	0.284	SUBCLONAL	1	TRUE	1	0.68	2		757	918	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457976	69457976	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	193	531	0	ENST00000227507.2:c.376A>G	p.Ile126Val	p.I126V	ENST00000227507	NM_053056.2	126	Atc/Gtc	2/5	1	2	FACETS	0.962	0.896	1	0.962	0.896	1	CLONAL	1	TRUE	1	0.68	2		531	590	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188228	108188228	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs867760244	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	140	273	0	ENST00000278616.4:c.6327G>T	p.Trp2109Cys	p.W2109C	ENST00000278616	NM_000051.3	2109	tgG/tgT	43/63	1	2	FACETS	0.844	0.774	0.916	0.844	0.774	0.916	CLONAL	1	TRUE	1	0.68	2		273	488	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495532	56495532	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	45	739	0	ENST00000267101.3:c.3722G>A	p.Cys1241Tyr	p.C1241Y	ENST00000267101	NM_001982.3	1241	tGc/tAc	28/28	1	2	FACETS	0.183	0.153	0.216	0.183	0.153	0.216	SUBCLONAL	1	TRUE	1	0.68	2		739	724	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437385	110437385	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	53	228	0	ENST00000375856.3:c.1016T>C	p.Val339Ala	p.V339A	ENST00000375856	NM_003749.2	339	gTg/gCg	1/2	1	2	FACETS	0.739	0.638	0.846	0.739	0.638	0.846	SUBCLONAL	1	TRUE	1	0.68	2		228	211	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131695	2131695	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753907159	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	313	1105	1	ENST00000219476.3:c.3710C>T	p.Ala1237Val	p.A1237V	ENST00000219476	NM_000548.3	1237	gCg/gTg	31/42	1	2	FACETS	0.903	0.853	0.954	0.903	0.853	0.954	CLONAL	1	TRUE	1	0.68	2		1106	1019	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511586	38511586	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	307	975	0	ENST00000254066.5:c.1084T>C	p.Tyr362His	p.Y362H	ENST00000254066	NM_000964.3	362	Tac/Cac	8/9	1	2	FACETS	0.91	0.859	0.962	0.91	0.859	0.962	CLONAL	1	TRUE	1	0.68	2		975	992	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40876343	40876343	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	254	664	1	ENST00000428826.2:c.346C>A	p.Pro116Thr	p.P116T	ENST00000428826		116	Cct/Act	5/21	1	2	FACETS	0.963	0.905	1	0.963	0.905	1	CLONAL	1	TRUE	1	0.68	2		665	776	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622124	1622124	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	276	1153	1	ENST00000344749.5:c.751C>T	p.Pro251Ser	p.P251S	ENST00000344749	NM_001136139.2	251	Ccc/Tcc	10/19	1	2	FACETS	0.902	0.849	0.956	0.902	0.849	0.956	CLONAL	1	TRUE	1	0.68	2		1154	900	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3113454	3113454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752848608	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	257	659	0	ENST00000078429.4:c.448G>A	p.Glu150Lys	p.E150K	ENST00000078429	NM_002067.2	150	Gag/Aag	3/7	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.68	2		659	730	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905082	50905082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141579552	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	283	1098	2	ENST00000440232.2:c.364G>A	p.Val122Met	p.V122M	ENST00000440232	NM_002691.3	122	Gtg/Atg	4/27	1	2	FACETS	0.869	0.818	0.921	0.869	0.818	0.921	CLONAL	1	TRUE	1	0.68	2		1100	958	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248530	212248530	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	201	640	0	ENST00000342788.4:c.3737G>C	p.Ser1246Thr	p.S1246T	ENST00000342788	NM_005235.2	1246	aGc/aCc	28/28	1	2	FACETS	0.789	0.734	0.847	0.789	0.734	0.847	SUBCLONAL	1	TRUE	1	0.68	2		640	749	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662775	227662775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	369	1049	0	ENST00000305123.5:c.680G>A	p.Arg227His	p.R227H	ENST00000305123	NM_005544.2	227	cGt/cAt	1/2	1	2	FACETS	0.973	0.924	1	0.973	0.924	1	CLONAL	1	TRUE	1	0.68	2		1049	1115	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385062	31385062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	296	977	0	ENST00000328111.2:c.1447G>A	p.Glu483Lys	p.E483K	ENST00000328111	NM_006892.3	483	Gag/Aag	14/23	1	2	FACETS	0.913	0.861	0.965	0.913	0.861	0.965	CLONAL	1	TRUE	1	0.68	2		977	954	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817454	39817455	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGACGC	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	40	691	1	ENST00000288319.7:c.103_108dup	p.Ala35_Ser36dup	p.A35_S36dup	ENST00000288319	NM_182918.3	35	-/GCGTCC	2/10	1	2	FACETS	0.161	0.133	0.192	0.161	0.133	0.192	SUBCLONAL	1	TRUE	1	0.68	2		692	730	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573336	41573336	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	294	1040	2	ENST00000263253.7:c.5621A>G	p.Gln1874Arg	p.Q1874R	ENST00000263253	NM_001429.3	1874	cAg/cGg	31/31	1	2	FACETS	0.912	0.86	0.965	0.912	0.86	0.965	CLONAL	1	TRUE	1	0.68	2		1042	948	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574268	41574268	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	259	822	0	ENST00000263253.7:c.6553C>T	p.Arg2185Ter	p.R2185*	ENST00000263253	NM_001429.3	2185	Cga/Tga	31/31	1	2	FACETS	0.944	0.887	1	0.944	0.887	1	CLONAL	1	TRUE	1	0.68	2		822	807	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71019918	71019918	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	143	305	2	ENST00000318789.4:c.1691C>T	p.Ala564Val	p.A564V	ENST00000318789	NM_032682.5	564	gCc/gTc	19/21	1	2	FACETS	0.985	0.907	1	0.985	0.907	1	CLONAL	1	TRUE	1	0.68	2		307	427	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1962831	1962831	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	234	612	1	ENST00000382891.5:c.3325G>A	p.Ala1109Thr	p.A1109T	ENST00000382891	NM_133335.3	1109	Gca/Aca	18/22	1	2	FACETS	0.938	0.878	0.998	0.938	0.878	0.998	CLONAL	1	TRUE	1	0.68	2		613	734	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748144	41748144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	122	434	0	ENST00000226382.2:c.625G>A	p.Gly209Arg	p.G209R	ENST00000226382	NM_003924.3	209	Ggg/Agg	3/3	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.68	2		434	347	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160667	56160667	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	212	477	0	ENST00000399503.3:c.941C>T	p.Ala314Val	p.A314V	ENST00000399503	NM_005921.1	314	gCc/gTc	4/20	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.68	2		477	621	SUCCESS
APC	324	MSKCC	GRCh37	5	112175840	112175840	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1114167596	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	134	301	0	ENST00000257430.4:c.4549C>T	p.Gln1517Ter	p.Q1517*	ENST00000257430	NM_000038.5	1517	Cag/Tag	16/16	1	2	FACETS	0.985	0.904	1	0.985	0.904	1	CLONAL	1	TRUE	1	0.68	2		301	400	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953880	131953880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	218	340	0	ENST00000265335.6:c.3283C>T	p.Pro1095Ser	p.P1095S	ENST00000265335		1095	Cca/Tca	21/25	1	2	FACETS	0.893	0.834	0.954	0.893	0.834	0.954	CLONAL	1	TRUE	1	0.68	2		340	718	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940087	31940087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	57	889	0	ENST00000375333.2:c.229C>T	p.Pro77Ser	p.P77S	ENST00000375333	NM_032454.1	77	Ccc/Tcc	2/8	1	2	FACETS	0.177	0.151	0.205	0.177	0.151	0.205	SUBCLONAL	1	TRUE	1	0.68	2		889	948	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815720	32815721	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	343	1059	0	ENST00000354258.4:c.1895_1896del	p.Tyr632Ter	p.Y632*	ENST00000354258	NM_000593.5	632	tAT/t	8/11	1	2	FACETS	0.924	0.875	0.973	0.924	0.875	0.973	CLONAL	1	TRUE	1	0.68	2		1059	1092	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816538	32816538	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	376	1036	1	ENST00000354258.4:c.1637del	p.Pro546LeufsTer9	p.P546Lfs*9	ENST00000354258	NM_000593.5	546	cCt/ct	7/11	1	2	FACETS	0.836	0.793	0.88	0.836	0.793	0.88	CLONAL	1	TRUE	1	0.68	2		1037	1323	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289611	33289611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766116335	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	275	778	1	ENST00000374542.5:c.92C>T	p.Ala31Val	p.A31V	ENST00000374542	NM_001141970.1	31	gCg/gTg	2/8	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.68	2		779	808	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200414	138200414	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	320	691	0	ENST00000237289.4:c.1832G>A	p.Gly611Asp	p.G611D	ENST00000237289	NM_001270507.1	611	gGc/gAc	7/9	1	2	FACETS	0.956	0.904	1	0.956	0.904	1	CLONAL	1	TRUE	1	0.68	2		691	985	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028064	69028064	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs556672943	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	269	581	0	ENST00000288368.4:c.3223A>G	p.Asn1075Asp	p.N1075D	ENST00000288368	NM_024870.2	1075	Aat/Gat	26/40	1	2	FACETS	0.908	0.854	0.964	0.908	0.854	0.964	CLONAL	1	TRUE	1	0.68	2		581	871	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128321915	128321915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1008519449	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	239	575	2	ENST00000265960.3:c.845G>A	p.Arg282Gln	p.R282Q	ENST00000265960	NM_001006617.1	282	cGa/cAa	6/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.68	2		577	660	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393422	139393422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	326	1115	1	ENST00000277541.6:c.6109G>A	p.Ala2037Thr	p.A2037T	ENST00000277541	NM_017617.3	2037	Gcc/Acc	33/34	1	2	FACETS	0.895	0.847	0.945	0.895	0.847	0.945	CLONAL	1	TRUE	1	0.68	2		1116	1071	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321322	1321322	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	47	755	0	ENST00000400841.2:c.433del	p.Asp145IlefsTer28	p.D145Ifs*28	ENST00000400841		145	Gat/at	4/6	0.3	2	FACETS	0.186	0.156	0.219			1	INDETERMINATE	1	TRUE	NA	0.68	2		755	743	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0052793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	382	1171	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.557895244352685	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.557895244352685	1		1171	951	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434682	110434682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	384	902	0	ENST00000375856.3:c.3719G>A	p.Arg1240His	p.R1240H	ENST00000375856	NM_003749.2	1240	cGc/cAc	1/2	0.471525967825063	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.557895244352685	1		902	886	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943701	71943701	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	328	1108	0	ENST00000298229.2:c.1744C>G	p.Leu582Val	p.L582V	ENST00000298229	NM_001567.3	582	Ctg/Gtg	15/28	0.511661086286158	3	FACETS	1	0.96	1	0.512	0.482	0.542	CLONAL	1	TRUE	1	0.557895244352685	3		1108	1470	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245471	46245471	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	141	517	0	ENST00000334344.6:c.3565C>T	p.Gln1189Ter	p.Q1189*	ENST00000334344	NM_152641.2	1189	Cag/Tag	15/21	0.557895244352685	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.557895244352685	1		517	364	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032348	42032348	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs763367691	NA	P-0052793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	210	767	0	ENST00000219905.7:c.4532C>G	p.Thr1511Arg	p.T1511R	ENST00000219905	NM_001164273.1	1511	aCa/aGa	14/24	1	2	FACETS	0.893	0.831	0.957	0.893	0.831	0.957	CLONAL	1	TRUE	1	0.557895244352685	2		767	843	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843480	3843480	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	532	706	0	ENST00000262367.5:c.1123G>T	p.Gly375Ter	p.G375*	ENST00000262367	NM_004380.2	375	Gga/Tga	4/31	0.557895244352685	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.557895244352685	2		706	939	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509684	29509684	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0052793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	92	443	0	ENST00000356175.3:c.888+1G>T		p.X296_splice	ENST00000356175	NM_000267.3	296			0.557895244352685	1	FACETS	0.604	0.54	0.671	0.604	0.54	0.671	SUBCLONAL	1	TRUE	0	0.557895244352685	1		443	394	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61729417	61729417	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	193	443	0	ENST00000401558.2:c.330T>G	p.Ile110Met	p.I110M	ENST00000401558	NM_003400.3	110	atT/atG	5/25	1	2	FACETS	0.987	0.916	1	0.987	0.916	1	CLONAL	1	TRUE	1	0.557895244352685	2		443	701	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270043	198270043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	114	510	0	ENST00000335508.6:c.1393C>T	p.Pro465Ser	p.P465S	ENST00000335508	NM_012433.2	465	Cca/Tca	10/25	1	2	FACETS	0.564	0.508	0.624	0.564	0.508	0.624	SUBCLONAL	1	TRUE	1	0.557895244352685	2		510	724	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794389	242794389	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	135	1403	0	ENST00000334409.5:c.553G>A	p.Val185Ile	p.V185I	ENST00000334409	NM_005018.2	185	Gtc/Atc	3/5	0.557895244352685	1	FACETS	0.289	0.262	0.318	0.289	0.262	0.318	SUBCLONAL	1	TRUE	0	0.557895244352685	1		1403	1207	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205046	128205046	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	313	1338	0	ENST00000341105.2:c.395G>C	p.Gly132Ala	p.G132A	ENST00000341105	NM_032638.4	132	gGa/gCa	3/6	0.234299210309692	1	FACETS	0.635	0.598	0.672	0.635	0.598	0.672	INDETERMINATE	1	TRUE	0	0.557895244352685	1		1338	1275	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165660	185165660	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	174	635	0	ENST00000265026.3:c.935C>A	p.Ser312Ter	p.S312*	ENST00000265026	NM_004721.4	312	tCa/tAa	5/14	0.270611485417836	3	FACETS	1	0.967	1	0.544	0.502	0.588	INDETERMINATE	1	TRUE	1	0.557895244352685	3		635	733	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31511253	31511253	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	140	782	2	ENST00000344624.3:c.1321C>T	p.Leu441Phe	p.L441F	ENST00000344624		441	Ctt/Ttt	6/33	1	2	FACETS	0.497	0.452	0.545	0.497	0.452	0.545	SUBCLONAL	1	TRUE	1	0.557895244352685	2		784	1009	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245515	153245515	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	59	449	0	ENST00000281708.4:c.1676T>C	p.Leu559Pro	p.L559P	ENST00000281708	NM_033632.3	559	cTt/cCt	11/12	0.587045235691209	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.587045235691209	1		449	119	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52621397	52621397	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	58	532	0	ENST00000394830.3:c.3020T>C	p.Leu1007Pro	p.L1007P	ENST00000394830	NM_018313.4	1007	cTa/cCa	20/30	0.587045235691209	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.587045235691209	1		532	114	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151833973	151833973	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	137	671	0	ENST00000262189.6:c.14680C>G	p.Gln4894Glu	p.Q4894E	ENST00000262189	NM_170606.2	4894	Cag/Gag	59/59	0.198766384081594	3	FACETS	0.755	0.693	0.817	0.755	0.693	0.817	INDETERMINATE	2	TRUE	1	0.587045235691209	3		671	400	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560464	95560464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	560	600	1	ENST00000393063.1:c.5125G>A	p.Asp1709Asn	p.D1709N	ENST00000393063	NM_030621.3	1709	Gat/Aat	25/28	0.845796429071226	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.845796429071226	2		601	646	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0052797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	384	658	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.602553489594414	2	FACETS	0.82	0.789	0.85	0.82	0.789	0.85	CLONAL	2	TRUE	0	0.774130351356222	2		658	605	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0052797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	488	633	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.774130351356222	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.774130351356222	1		633	690	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938577	44938577	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0052797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	302	566	0	ENST00000377967.4:c.3125C>G	p.Ser1042Ter	p.S1042*	ENST00000377967	NM_021140.2	1042	tCa/tGa	20/29	0.467482577090461	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.774130351356222	1		566	436	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416398	49416399	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0052797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	362	681	0	ENST00000301067.7:c.16312dup	p.Arg5438ProfsTer21	p.R5438Pfs*21	ENST00000301067	NM_003482.3	5438	cgg/cCgg	51/54	0.251628012320407	4	FACETS	0.873	0.831	0.917	0.873	0.831	0.917	INDETERMINATE	2	TRUE	2	0.774130351356222	4		681	950	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467665	66467665	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	36	424	0	ENST00000273854.3:c.604G>T	p.Val202Leu	p.V202L	ENST00000273854	NM_004439.5	202	Gta/Tta	3/18	1	2	FACETS	0.204	0.167	0.245	0.204	0.167	0.245	SUBCLONAL	1	TRUE	1	0.774130351356222	2		424	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0052798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	110	1171	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.448525723896109	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.450369788909581	1		1171	368	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0052798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	144	525	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.441378894959281	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.450369788909581	2		525	264	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974793	21974799	+	frameshift_variant	Frame_Shift_Del	DEL	AAGGCTC	AAGGCTC	-	novel	NA	P-0052798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	13	196	0	ENST00000304494.5:c.28_34del	p.Glu10ArgfsTer14	p.E10Rfs*14	ENST00000304494	NM_000077.4	10	GAGCCTTcg/cg	1/3	0.448525723896109	1	FACETS	0.581	0.422	0.767	0.581	0.422	0.767	SUBCLONAL	1	TRUE	0	0.450369788909581	1		196	77	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	131	411	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.508	0.462	0.556	0.508	0.462	0.556	SUBCLONAL	1	TRUE	1	0.86391036694067	2		411	597	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	137	725	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	NA	2	FACETS	0.608	0.556	0.662			1	INDETERMINATE	1	TRUE	NA	0.86391036694067	2		725	522	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	40	1072	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.116	0.096	0.139	0.116	0.096	0.139	SUBCLONAL	1	TRUE	1	0.86391036694067	2		1073	797	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	78	288	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.417279550557781	2	FACETS	0.618	0.549	0.691	0.309	0.274	0.346	INDETERMINATE	1	TRUE	0	0.86391036694067	2		288	292	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789591	3789591	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	98	473	0	ENST00000262367.5:c.4268del	p.Pro1423LeufsTer36	p.P1423Lfs*36	ENST00000262367	NM_004380.2	1423	cCt/ct	25/31	1	2	FACETS	0.431	0.386	0.479	0.431	0.386	0.479	SUBCLONAL	1	TRUE	1	0.86391036694067	2		473	526	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	178	987	1	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.448	0.413	0.485	0.448	0.413	0.485	SUBCLONAL	1	TRUE	1	0.86391036694067	2		988	919	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	102	386	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	NA	2	FACETS	0.514	0.462	0.569			1	INDETERMINATE	1	TRUE	NA	0.86391036694067	2		386	459	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	117	496	7	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.434	0.392	0.478	0.434	0.392	0.478	SUBCLONAL	1	TRUE	1	0.86391036694067	2		503	624	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884218	37884218	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	142	821	0	ENST00000269571.5:c.3694del	p.Ala1232LeufsTer70	p.A1232Lfs*70	ENST00000269571		1230	cGg/cg	27/27	1	2	FACETS	0.493	0.45	0.537	0.493	0.45	0.537	SUBCLONAL	1	TRUE	1	0.86391036694067	2		821	667	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591135	67591136	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	82	318	0	ENST00000274335.5:c.1732_1733del	p.Asp578ProfsTer23	p.D578Pfs*23	ENST00000274335		576	acGAga/acga	12/15	1	2	FACETS	0.432	0.383	0.485	0.432	0.383	0.485	SUBCLONAL	1	TRUE	1	0.86391036694067	2		318	439	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2492096	2492097	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs772088410	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	46	885	2	ENST00000355716.4:c.500dup	p.Thr169AspfsTer65	p.T169Dfs*65	ENST00000355716	NM_003820.2	165	tgc/tgCc	5/8	1	2	FACETS	0.131	0.11	0.155	0.131	0.11	0.155	SUBCLONAL	1	TRUE	1	0.86391036694067	2		887	812	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955111	17955112	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755706305	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	86	959	7	ENST00000458235.1:c.115dup	p.Gln39ProfsTer13	p.Q39Pfs*13	ENST00000458235	NM_000215.3	39	cag/cCag	2/24	1	2	FACETS	0.215	0.19	0.243	0.215	0.19	0.243	SUBCLONAL	1	TRUE	1	0.86391036694067	2		966	925	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548269	41548269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	105	332	0	ENST00000263253.7:c.3061del	p.Thr1021LeufsTer3	p.T1021Lfs*3	ENST00000263253	NM_001429.3	1019	ttA/tt	16/31	1	2	FACETS	0.546	0.492	0.603	0.546	0.492	0.603	SUBCLONAL	1	TRUE	1	0.86391036694067	2		332	445	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942053	71942053	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	86	833	0	ENST00000298229.2:c.1322del	p.Asn441ThrfsTer2	p.N441Tfs*2	ENST00000298229	NM_001567.3	439	ccA/cc	12/28	1	2	FACETS	0.229	0.202	0.259	0.229	0.202	0.259	SUBCLONAL	1	TRUE	1	0.86391036694067	2		833	868	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652397	48652397	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	169	1025	0	ENST00000376670.3:c.1073del	p.Pro358GlnfsTer74	p.P358Qfs*74	ENST00000376670	NM_002049.3	356	ggC/gg	6/6	1	2	FACETS	0.524	0.482	0.567	0.524	0.482	0.567	SUBCLONAL	1	TRUE	1	0.86391036694067	2		1025	747	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	104	731	2	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.351	0.314	0.39	0.351	0.314	0.39	SUBCLONAL	1	TRUE	1	0.86391036694067	2		733	686	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457615	67457615	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	137	759	1	ENST00000327367.4:c.425G>A	p.Arg142His	p.R142H	ENST00000327367	NM_005902.3	142	cGc/cAc	3/9	1	2	FACETS	0.442	0.402	0.483	0.442	0.402	0.483	SUBCLONAL	1	TRUE	1	0.86391036694067	2		760	718	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435129	110435129	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	131	560	3	ENST00000375856.3:c.3272del	p.Pro1091ArgfsTer15	p.P1091Rfs*15	ENST00000375856	NM_003749.2	1091	cCg/cg	1/2	1	2	FACETS	0.475	0.432	0.52	0.475	0.432	0.52	SUBCLONAL	1	TRUE	1	0.86391036694067	2		563	638	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593270	67593273	+	frameshift_variant	Frame_Shift_Del	DEL	AAAC	AAAC	-	novel	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	76	280	0	ENST00000274335.5:c.2019_2022del	p.Asn673LysfsTer18	p.N673Kfs*18	ENST00000274335		672	atAAAC/at	15/15	1	2	FACETS	0.45	0.397	0.507	0.45	0.397	0.507	SUBCLONAL	1	TRUE	1	0.86391036694067	2		280	391	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984671	11984672	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	novel	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	18	313	0	ENST00000353533.5:c.224_225del		p.X75_splice	ENST00000353533	NM_003010.3	75			1	2	FACETS	0.124	0.093	0.161	0.124	0.093	0.161	SUBCLONAL	1	TRUE	1	0.86391036694067	2		313	336	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993593	72993593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	36	812	0	ENST00000268489.5:c.452C>T	p.Thr151Ile	p.T151I	ENST00000268489	NM_006885.3	151	aCc/aTc	2/10	1	2	FACETS	0.124	0.101	0.149	0.124	0.101	0.149	SUBCLONAL	1	TRUE	1	0.86391036694067	2		812	674	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100991	27100991	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	144	738	0	ENST00000324856.7:c.4273C>T	p.Gln1425Ter	p.Q1425*	ENST00000324856	NM_006015.4	1425	Caa/Taa	18/20	1	2	FACETS	0.465	0.425	0.507	0.465	0.425	0.507	SUBCLONAL	1	TRUE	1	0.86391036694067	2		738	717	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461946	120461946	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	83	525	0	ENST00000256646.2:c.5770G>T	p.Gly1924Cys	p.G1924C	ENST00000256646	NM_024408.3	1924	Ggt/Tgt	31/34	1	2	FACETS	0.392	0.347	0.44	0.392	0.347	0.44	SUBCLONAL	1	TRUE	1	0.86391036694067	2		525	490	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601891	43601891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	214	887	2	ENST00000355710.3:c.935G>T	p.Arg312Met	p.R312M	ENST00000355710	NM_020975.4	312	aGg/aTg	5/20	0.417279550557781	2	FACETS	0.571	0.532	0.612	0.286	0.266	0.306	INDETERMINATE	1	TRUE	0	0.86391036694067	2		889	867	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518518	69518518	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1162715075	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	103	320	0	ENST00000294312.3:c.127C>T	p.Arg43Cys	p.R43C	ENST00000294312	NM_005117.2	43	Cgc/Tgc	1/3	1	2	FACETS	0.65	0.587	0.715	0.65	0.587	0.715	SUBCLONAL	1	TRUE	1	0.86391036694067	2		320	367	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041887	42041888	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	34	487	0	ENST00000219905.7:c.6082_6083insT	p.Arg2028MetfsTer3	p.R2028Mfs*3	ENST00000219905	NM_001164273.1	2028	agg/aTgg	17/24	1	2	FACETS	0.135	0.109	0.163	0.135	0.109	0.163	SUBCLONAL	1	TRUE	1	0.86391036694067	2		487	585	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831741	72831741	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	123	621	0	ENST00000268489.5:c.4840C>A	p.His1614Asn	p.H1614N	ENST00000268489	NM_006885.3	1614	Cat/Aat	9/10	1	2	FACETS	0.421	0.381	0.463	0.421	0.381	0.463	SUBCLONAL	1	TRUE	1	0.86391036694067	2		621	676	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229019	36229019	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	181	794	0	ENST00000222270.7:c.7799T>G	p.Met2600Arg	p.M2600R	ENST00000222270	NM_014727.1	2600	aTg/aGg	36/37	1	2	FACETS	0.484	0.446	0.523	0.484	0.446	0.523	SUBCLONAL	1	TRUE	1	0.86391036694067	2		794	866	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755717	39755717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1333152977	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	72	609	0	ENST00000288319.7:c.1048C>T	p.Arg350Cys	p.R350C	ENST00000288319	NM_182918.3	350	Cgc/Tgc	10/10	1	2	FACETS	0.275	0.24	0.313	0.275	0.24	0.313	SUBCLONAL	1	TRUE	1	0.86391036694067	2		609	606	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713243	30713243	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758703490	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	65	412	0	ENST00000295754.5:c.568C>T	p.Arg190Cys	p.R190C	ENST00000295754	NM_003242.5	190	Cgc/Tgc	4/7	1	2	FACETS	0.294	0.255	0.336	0.294	0.255	0.336	SUBCLONAL	1	TRUE	1	0.86391036694067	2		412	512	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163868	47163868	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	38	489	0	ENST00000409792.3:c.2258T>C	p.Val753Ala	p.V753A	ENST00000409792	NM_014159.6	753	gTg/gCg	3/21	1	2	FACETS	0.138	0.113	0.166	0.138	0.113	0.166	SUBCLONAL	1	TRUE	1	0.86391036694067	2		489	637	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652294	36652294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	106	750	0	ENST00000244741.5:c.416G>A	p.Gly139Asp	p.G139D	ENST00000244741	NM_000389.4	139	gGt/gAt	2/3	1	2	FACETS	0.38	0.341	0.422	0.38	0.341	0.422	SUBCLONAL	1	TRUE	1	0.86391036694067	2		750	645	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979544	2979544	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766516628	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	117	460	0	ENST00000396946.4:c.703C>T	p.Arg235Trp	p.R235W	ENST00000396946	NM_032415.4	235	Cgg/Tgg	6/25	0.83233925126677	1	FACETS	0.28	0.253	0.308	0.28	0.253	0.308	SUBCLONAL	1	TRUE	0	0.86391036694067	1		460	550	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739951	41739951	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	95	483	0	ENST00000242208.4:c.22G>T	p.Gly8Ter	p.G8*	ENST00000242208	NM_002192.2	8	Gga/Tga	2/3	1	2	FACETS	0.417	0.372	0.465	0.417	0.372	0.465	SUBCLONAL	1	TRUE	1	0.86391036694067	2		483	527	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424450	47424450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs62636600	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	187	744	1	ENST00000377045.4:c.370C>T	p.Arg124Cys	p.R124C	ENST00000377045	NM_001654.4	124	Cgt/Tgt	5/16	1	2	FACETS	0.505	0.466	0.544	0.505	0.466	0.544	SUBCLONAL	1	TRUE	1	0.86391036694067	2		745	858	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76919015	76919015	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	95	359	0	ENST00000373344.5:c.3976T>C	p.Ser1326Pro	p.S1326P	ENST00000373344	NM_000489.3	1326	Tca/Cca	12/35	1	2	FACETS	0.479	0.429	0.533	0.479	0.429	0.533	SUBCLONAL	1	TRUE	1	0.86391036694067	2		359	459	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0052800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	97	430	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.16867950648995	3	FACETS	0.929	0.829	1	0.929	0.829	1	CLONAL	2	FALSE	1	0.16867950648995	3		430	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0052800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	118	795	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.160427318013467	2	FACETS	0.984	0.889	1	0.984	0.889	1	CLONAL	2	FALSE	0	0.16867950648995	2		795	711	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735470	40735470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761910971	NA	P-0052800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	116	757	0	ENST00000373198.4:c.3403G>A	p.Val1135Met	p.V1135M	ENST00000373198	NM_133170.3	1135	Gtg/Atg	25/32	NA	2	FACETS	0.881	0.794	0.972			1	INDETERMINATE	2	FALSE	NA	0.16867950648995	2		757	781	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416416	49416416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123734	NA	P-0052800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	90	666	0	ENST00000301067.7:c.16295G>A	p.Arg5432Gln	p.R5432Q	ENST00000301067	NM_003482.3	5432	cGg/cAg	51/54	0.16867950648995	3	FACETS	0.864	0.767	0.967	0.864	0.767	0.967	CLONAL	2	FALSE	1	0.16867950648995	3		666	670	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974701	21974701	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	49	443	0	ENST00000304494.5:c.126T>G	p.Asn42Lys	p.N42K	ENST00000304494	NM_000077.4	42	aaT/aaG	1/3	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.16867950648995	2		443	399	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273989	10273989	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1282664179	NA	P-0052800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	73	1013	0	ENST00000330684.3:c.280C>T	p.Arg94Cys	p.R94C	ENST00000330684	NM_001134407.1	94	Cgc/Tgc	2/13	0.16867950648995	3	FACETS	1	0.925	1	0.543	0.473	0.617	CLONAL	1	FALSE	1	0.16867950648995	3		1013	865	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89851361	89851361	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	39	600	0	ENST00000389301.3:c.1371del	p.Ser458AlafsTer68	p.S458Afs*68	ENST00000389301	NM_000135.2	457	ggG/gg	15/43	1	2	FACETS	0.772	0.639	0.921	0.772	0.639	0.921	CLONAL	1	FALSE	1	0.16867950648995	2		600	599	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402475	139402475	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	1382	1303	126	ENST00000277541.6:c.3442G>T	p.Glu1148Ter	p.E1148*	ENST00000277541	NM_017617.3	1148	Gag/Tag	21/34	0.770239088738377	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.770239088738377	2		1429	1728	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826618	50826618	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0052801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	163	209	3	ENST00000398568.2:c.2341+2T>C		p.X781_splice	ENST00000398568	NM_001042412.1	781			0.770239088738377	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.770239088738377	1		212	252	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0052802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	594	872	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.523758646302007	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	FALSE	0	0.523758646302007	3		873	865	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0052802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3345	80	476	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.523758646302007	37	FACETS	0.907	0.793	1			1	CLONAL	1	FALSE	NA	0.523758646302007	37		476	3425	SUCCESS
APC	324	MSKCC	GRCh37	5	112173830	112173831	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	107	395	0	ENST00000257430.4:c.2544dup	p.Asp849ArgfsTer2	p.D849Rfs*2	ENST00000257430	NM_000038.5	847	gaa/gAaa	16/16	0.462278735386718	3	FACETS	0.832	0.756	0.91	0.832	0.756	0.91	CLONAL	2	FALSE	1	0.523758646302007	3		395	310	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175481	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0052802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	87	411	0	ENST00000257430.4:c.4192_4193del	p.Arg1399PhefsTer9	p.R1399Ffs*9	ENST00000257430	NM_000038.5	1397	GAg/g	16/16	0.462278735386718	3	FACETS	1	0.957	1	0.573	0.511	0.638	CLONAL	1	FALSE	1	0.523758646302007	3		411	366	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261683	16261683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149575630	NA	P-0052802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	86	742	1	ENST00000375759.3:c.8948C>T	p.Thr2983Met	p.T2983M	ENST00000375759	NM_015001.2	2983	aCg/aTg	11/15	0.523758646302007	3	FACETS	0.811	0.719	0.908	0.27	0.239	0.303	CLONAL	1	FALSE	0	0.523758646302007	3		743	511	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615045	43615045	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	159	1124	3	ENST00000355710.3:c.2459G>A	p.Arg820His	p.R820H	ENST00000355710	NM_020975.4	820	cGc/cAc	14/20	0.523758646302007	3	FACETS	0.911	0.836	0.99	0.455	0.418	0.495	CLONAL	1	FALSE	1	0.523758646302007	3		1127	841	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242716	98242716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767601899	NA	P-0052802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	47	610	2	ENST00000331920.6:c.901G>A	p.Asp301Asn	p.D301N	ENST00000331920	NM_000264.3	301	Gat/Aat	6/24	0.523758646302007	5	FACETS	0.363	0.305	0.428	0.121	0.101	0.143	SUBCLONAL	1	FALSE	2	0.523758646302007	5		612	882	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	36	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.289362232763487	2		429	194	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935438	36935438	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	117	877	1	ENST00000361632.4:c.1289C>T	p.Pro430Leu	p.P430L	ENST00000361632		430	cCa/cTa	10/16	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.289362232763487	2		878	796	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578499	7578499	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs786203071	NA	P-0052803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	333	1059	0	ENST00000269305.4:c.431A>C	p.Gln144Pro	p.Q144P	ENST00000269305	NM_001126112.2	144	cAg/cCg	5/11	0.231949792864948	2	FACETS	0.994	0.94	1	0.994	0.94	1	CLONAL	2	TRUE	0	0.289362232763487	2		1059	1158	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293816	1293816	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	142	1066	0	ENST00000310581.5:c.1185G>C	p.Glu395Asp	p.E395D	ENST00000310581	NM_198253.2	395	gaG/gaC	2/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.289362232763487	2		1066	896	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	61	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.973	0.85	1	0.973	0.85	1	CLONAL	1	TRUE	1	0.520095465269972	2		429	241	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0052804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	596	833	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.520095465269972	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.520095465269972	2		837	1071	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0052804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	262	624	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	0.520095465269972	2	FACETS	1	0.963	1	0.518	0.486	0.551	CLONAL	1	TRUE	0	0.520095465269972	2		624	972	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264821	46264821	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs764548730	NA	P-0052804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	633	452	0	ENST00000371998.3:c.1691A>G	p.Asn564Ser	p.N564S	ENST00000371998		564	aAt/aGt	12/23	0.520095465269972	5	FACETS	1	0.983	1			1	CLONAL	4	TRUE	NA	0.520095465269972	5		452	1062	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274172	10274172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567354612	NA	P-0052804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	1576	624	0	ENST00000330684.3:c.97G>A	p.Ala33Thr	p.A33T	ENST00000330684	NM_001134407.1	33	Gcg/Acg	2/13	0.520095465269972	8	FACETS	1	0.997	1			1	CLONAL	7	TRUE	NA	0.520095465269972	8		624	2108	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038864	12038864	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	103	279	0	ENST00000396373.4:c.1157G>C	p.Arg386Thr	p.R386T	ENST00000396373	NM_001987.4	386	aGa/aCa	7/8	1	2	FACETS	0.863	0.776	0.954	0.863	0.776	0.954	CLONAL	1	TRUE	1	0.520095465269972	2		279	459	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936949	48936949	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0052804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	140	254	0	ENST00000267163.4:c.719-2A>G		p.X240_splice	ENST00000267163	NM_000321.2	240			0.481517478189849	2	FACETS	0.818	0.756	0.881	0.818	0.756	0.881	CLONAL	2	TRUE	0	0.520095465269972	2		254	329	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438047	110438070	+	inframe_deletion	In_Frame_Del	DEL	CTTGGTGTAGAGGGCGATCAGGTA	CTTGGTGTAGAGGGCGATCAGGTA	-	novel	NA	P-0052804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	71	469	0	ENST00000375856.3:c.331_354del	p.Tyr111_Lys118del	p.Y111_K118del	ENST00000375856	NM_003749.2	111	TACCTGATCGCCCTCTACACCAAG/-	1/2	0.388829993984592	3	FACETS	0.473	0.412	0.539	0.237	0.206	0.27	SUBCLONAL	1	TRUE	1	0.520095465269972	3		469	727	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678416	88678416	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	311	749	0	ENST00000360948.2:c.1120G>A	p.Gly374Ser	p.G374S	ENST00000360948	NM_001012338.2	374	Ggc/Agc	9/19	0.388829993984592	3	FACETS	1	0.989	1	0.598	0.563	0.634	CLONAL	1	TRUE	1	0.520095465269972	3		749	1260	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683571	29683571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	61	304	0	ENST00000356175.3:c.7646G>A	p.Arg2549Lys	p.R2549K	ENST00000356175	NM_000267.3	2549	aGg/aAg	51/57	1	2	FACETS	0.506	0.437	0.58	0.506	0.437	0.58	SUBCLONAL	1	TRUE	1	0.520095465269972	2		304	464	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624402	140624412	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGGCGCCGG	CGCGGCGCCGG	-	novel	NA	P-0052804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	106	111	0	ENST00000288602.6:c.92_102del	p.Ala31GlyfsTer21	p.A31Gfs*21	ENST00000288602	NM_004333.4	31	gCCGGCGCCGCG/g	1/18	1	2	FACETS	0.802	0.733	0.873	1	0.987	1	CLONAL	2	TRUE	1	0.520095465269972	2		111	254	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200226	123200238	+	frameshift_variant	Frame_Shift_Del	DEL	GTGTACTCACTAT	GTGTACTCACTAT	-	novel	NA	P-0052804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	140	205	0	ENST00000218089.9:c.2207_2219del	p.Cys736Ter	p.C736*	ENST00000218089	NM_001042749.1	735	caGTGTACTCACTAT/ca	23/35	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.520095465269972	1		205	305	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	170	429	0				ENST00000310581	NM_198253.2	-/1132			0.499191007507801	3	FACETS	1	0.976	1	0.56	0.519	0.601	INDETERMINATE	1	TRUE	1	0.908903596282822	3		429	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0052805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	592	885	2	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.908903596282822	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.908903596282822	1		887	675	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0052805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	199	426	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	0.467698396918099	3	FACETS	0.877	0.827	0.927	0.877	0.827	0.927	INDETERMINATE	2	TRUE	1	0.908903596282822	3		426	363	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837979	156837979	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1428	474	1278	0	ENST00000524377.1:c.512C>A	p.Pro171His	p.P171H	ENST00000524377	NM_002529.3	171	cCt/cAt	5/17	0.461823784264855	2	FACETS	0.548	0.522	0.575	0.274	0.261	0.288	INDETERMINATE	1	TRUE	0	0.908903596282822	2		1278	1902	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667374	241667374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	146	560	0	ENST00000366560.3:c.1076C>T	p.Pro359Leu	p.P359L	ENST00000366560	NM_000143.3	359	cCt/cTt	7/10	0.461823784264855	2	FACETS	0.45	0.411	0.49	0.225	0.205	0.245	INDETERMINATE	1	TRUE	0	0.908903596282822	2		560	714	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033928	49033928	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1566235470	NA	P-0052805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	192	423	1	ENST00000267163.4:c.2065C>T	p.Gln689Ter	p.Q689*	ENST00000267163	NM_000321.2	689	Cag/Tag	20/27	0.908903596282822	1	FACETS	0.998	0.961	1	0.998	0.961	1	CLONAL	1	TRUE	0	0.908903596282822	1		424	231	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944623	40944623	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	200	324	0	ENST00000373198.4:c.1879G>T	p.Val627Phe	p.V627F	ENST00000373198	NM_133170.3	627	Gtt/Ttt	12/32	0.908903596282822	2	FACETS	0.812	0.758	0.867	0.406	0.379	0.434	CLONAL	1	TRUE	0	0.908903596282822	2		324	542	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331911	81331911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1487303636	NA	P-0052805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	77	253	0	ENST00000222390.5:c.2173G>A	p.Val725Ile	p.V725I	ENST00000222390	NM_000601.4	725	Gta/Ata	18/18	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.908903596282822	2		253	167	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8339007	8339007	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	202	488	0	ENST00000356435.5:c.5294G>C	p.Arg1765Thr	p.R1765T	ENST00000356435		1765	aGa/aCa	32/35	1	2	FACETS	0.95	0.89	1	0.95	0.89	1	CLONAL	1	TRUE	1	0.908903596282822	2		488	468	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15821827	15821827	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	40	242	0	ENST00000307771.7:c.220G>T	p.Glu74Ter	p.E74*	ENST00000307771	NM_005089.3	74	Gag/Tag	4/11	0.733817161928807	1	FACETS	0.239	0.2	0.281	0.239	0.2	0.281	SUBCLONAL	1	TRUE	0	0.908903596282822	1		242	201	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176490	123176491	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0052805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	34	357	0	ENST00000218089.9:c.457_458delinsTT	p.Asp153Phe	p.D153F	ENST00000218089	NM_001042749.1	153	GAt/TTt	7/35	0.733817161928807	1	FACETS	0.213	0.175	0.254	0.213	0.175	0.254	SUBCLONAL	1	TRUE	0	0.908903596282822	1		357	192	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0052806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	46	778	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		779	969	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0052808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	427	885	2	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.7462018466455	2	FACETS	0.972	0.943	1	0.972	0.943	1	CLONAL	2	TRUE	0	0.759706369705703	2		887	578	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321784	62321784	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1219370345	NA	P-0052808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	95	477	0	ENST00000360203.5:c.2403G>C	p.Gln801His	p.Q801H	ENST00000360203	NM_001283009.1	801	caG/caC	26/35	0.56171580921171	4	FACETS	0.882	0.788	0.981			1	CLONAL	1	TRUE	NA	0.759706369705703	4		477	499	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484198	120484198	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	147	720	0	ENST00000256646.2:c.2932G>C	p.Gly978Arg	p.G978R	ENST00000256646	NM_024408.3	978	Gga/Cga	18/34	0.624297220568715	4	FACETS	0.82	0.749	0.895	0.41	0.374	0.448	CLONAL	1	TRUE	2	0.759706369705703	4		720	830	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46255875	46255875	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	116	366	0	ENST00000371998.3:c.487G>T	p.Glu163Ter	p.E163*	ENST00000371998		163	Gaa/Taa	6/23	0.759706369705703	7	FACETS	0.892	0.802	0.986			1	CLONAL	1	TRUE	NA	0.759706369705703	7		366	993	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0052817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	247	431	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.486261693295823	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.486261693295823	1		431	599	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864328	57864328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201538749	NA	P-0052817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	166	491	0	ENST00000228682.2:c.1805C>T	p.Ser602Leu	p.S602L	ENST00000228682	NM_005269.2	602	tCg/tTg	12/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.486261693295823	2		491	621	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213952	2213952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770881335	NA	P-0052817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	341	499	0	ENST00000326181.6:c.31C>T	p.Arg11Cys	p.R11C	ENST00000326181	NM_032271.2	11	Cgc/Tgc	2/21	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.486261693295823	2		499	983	SUCCESS
APC	324	MSKCC	GRCh37	5	112175517	112175518	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATGCAGTGGA	novel	NA	P-0052817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	77	214	0	ENST00000257430.4:c.4230_4239dup	p.Val1414GlnfsTer12	p.V1414Qfs*12	ENST00000257430	NM_000038.5	1409	cca/ccATGCAGTGGAa	16/16	0.486261693295823	1	FACETS	0.841	0.747	0.94	0.841	0.747	0.94	CLONAL	1	TRUE	0	0.486261693295823	1		214	285	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0052818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	356	602	1	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	0.769958479298491	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.777029555273331	2		603	447	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170655	7170655	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	260	511	0	ENST00000302850.5:c.1376C>A	p.Pro459His	p.P459H	ENST00000302850	NM_000208.2	459	cCc/cAc	6/22	0.475266918196849	4	FACETS	0.95	0.897	1	0.95	0.897	1	CLONAL	2	TRUE	2	0.777029555273331	4		511	626	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32921008	32921008	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	235	325	0	ENST00000380152.3:c.6982G>C	p.Glu2328Gln	p.E2328Q	ENST00000380152		2328	Gag/Cag	13/27	NA	2	FACETS	0.985	0.947	1			1	INDETERMINATE	2	TRUE	NA	0.777029555273331	2		325	307	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937518	32937518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	111	439	0	ENST00000380152.3:c.8179G>A	p.Ala2727Thr	p.A2727T	ENST00000380152		2727	Gct/Act	18/27	0.275418496393493	3	FACETS	1	0.968	1	0.592	0.532	0.656	CLONAL	1	TRUE	1	0.275418496393493	3		439	774	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0052819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	154	561	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.275418496393493	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.275418496393493	1		561	837	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528450	29528450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	79	318	0	ENST00000356175.3:c.1207C>T	p.Pro403Ser	p.P403S	ENST00000356175	NM_000267.3	403	Cct/Tct	11/57	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.275418496393493	2		318	469	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354260	15354260	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	129	610	1	ENST00000263377.2:c.2620A>G	p.Ser874Gly	p.S874G	ENST00000263377	NM_058243.2	874	Agc/Ggc	14/20	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.275418496393493	2		611	898	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770570	40770570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1468460412	NA	P-0052819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	82	333	0	ENST00000373198.4:c.2812G>A	p.Gly938Arg	p.G938R	ENST00000373198	NM_133170.3	938	Ggg/Agg	19/32	1	2	FACETS	0.978	0.863	1	0.978	0.863	1	CLONAL	1	TRUE	1	0.275418496393493	2		333	609	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917576	178917576	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	202	374	0	ENST00000263967.3:c.451G>T	p.Val151Leu	p.V151L	ENST00000263967	NM_006218.2	151	Gtg/Ttg	3/21	0.274979650276872	4	FACETS	0.979	0.912	1			1	CLONAL	3	TRUE	NA	0.275418496393493	4		374	637	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163488	32163488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	116	421	3	ENST00000375023.3:c.5738G>A	p.Gly1913Asp	p.G1913D	ENST00000375023	NM_004557.3	1913	gGc/gAc	30/30	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.275418496393493	2		424	776	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180941	32180941	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	90	437	0	ENST00000375023.3:c.2409G>C	p.Glu803Asp	p.E803D	ENST00000375023	NM_004557.3	803	gaG/gaC	15/30	1	2	FACETS	0.927	0.823	1	0.927	0.823	1	CLONAL	1	TRUE	1	0.275418496393493	2		437	705	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542217	141542217	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	175	410	0	ENST00000220592.5:c.2506G>T	p.Gly836Trp	p.G836W	ENST00000220592	NM_012154.3	836	Ggg/Tgg	19/19	0.252482647789386	2	FACETS	0.991	0.917	1	0.991	0.917	1	CLONAL	2	TRUE	0	0.275418496393493	2		410	641	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933127	39933127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	123	513	0	ENST00000378444.4:c.1472G>C	p.Gly491Ala	p.G491A	ENST00000378444	NM_001123385.1	491	gGa/gCa	4/15	0.275418496393493	3	FACETS	1	0.964	1	0.57	0.515	0.628	CLONAL	1	TRUE	1	0.275418496393493	3		513	892	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76777853	76777853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1135401774	NA	P-0052819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	90	400	0	ENST00000373344.5:c.6863G>A	p.Arg2288His	p.R2288H	ENST00000373344	NM_000489.3	2288	cGt/cAt	32/35	0.23290718991423	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.275418496393493	1		400	552	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854890	76854890	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	48	390	0	ENST00000373344.5:c.5946A>T	p.Lys1982Asn	p.K1982N	ENST00000373344	NM_000489.3	1982	aaA/aaT	25/35	0.23290718991423	1	FACETS	0.598	0.505	0.699	0.598	0.505	0.699	SUBCLONAL	1	TRUE	0	0.275418496393493	1		390	503	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0052820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	28	350	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.701145554676897	4	FACETS	0.879	0.729	1	0.879	0.729	1	CLONAL	2	TRUE	2	0.774141206041206	4		350	73	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579716	7579716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1192416464	NA	P-0052820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	102	481	1	ENST00000269305.4:c.80del	p.Pro27LeufsTer17	p.P27Lfs*17	ENST00000269305	NM_001126112.2	27	cCt/ct	3/11	0.774141206041206	2	FACETS	0.983	0.925	1	0.983	0.925	1	CLONAL	2	TRUE	0	0.774141206041206	2		482	134	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954327	48954328	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0052820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	19	200	0	ENST00000267163.4:c.1450_1451del	p.Met484ValfsTer8	p.M484Vfs*8	ENST00000267163	NM_000321.2	483	cAT/c	16/27	0.774141206041206	3	FACETS	0.841	0.71	0.955	0.841	0.71	0.955	CLONAL	3	TRUE	0	0.774141206041206	3		200	27	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111794	56111794	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs557606535	NA	P-0052820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	42	7	0	ENST00000399503.3:c.394G>C	p.Asp132His	p.D132H	ENST00000399503	NM_005921.1	132	Gac/Cac	1/20	0.396936457628465	5	FACETS	1	0.878	1	1	0.878	1	INDETERMINATE	3	TRUE	2	0.774141206041206	5		7	78	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220691	1220691	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs878853247	NA	P-0052820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	220	472	0	ENST00000326873.7:c.709G>C	p.Asp237His	p.D237H	ENST00000326873	NM_000455.4	237	Gac/Cac	5/10	0.774141206041206	6	FACETS	1	0.948	1			1	CLONAL	2	TRUE	NA	0.774141206041206	6		472	712	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993741	72993741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544655521	NA	P-0052820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	164	376	0	ENST00000268489.5:c.304G>A	p.Ala102Thr	p.A102T	ENST00000268489	NM_006885.3	102	Gcg/Acg	2/10	0.701145554676897	4	FACETS	0.956	0.889	1	0.956	0.889	1	CLONAL	2	TRUE	2	0.774141206041206	4		376	393	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412723	63412745	+	frameshift_variant	Frame_Shift_Del	DEL	AGCCACAGATGTCTTACATCTGG	AGCCACAGATGTCTTACATCTGG	-	novel	NA	P-0052820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	60	211	0	ENST00000330258.3:c.422_444del	p.Ser141TrpfsTer9	p.S141Wfs*9	ENST00000330258	NM_152424.3	141	tCCAGATGTAAGACATCTGTGGCT/t	2/2	0.774141206041206	2	FACETS	1	0.979	1			1	CLONAL	2	TRUE	NA	0.774141206041206	2		211	68	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	60	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.915	0.795	1	0.915	0.795	1	CLONAL	1	TRUE	1	0.458429340477185	2		429	286	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0052821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	467	315	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.458429340477185	8	FACETS	1	0.988	1	1	0.988	1	CLONAL	6	TRUE	2	0.458429340477185	8		315	767	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687605	29687605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	213	364	0	ENST00000356175.3:c.8198C>T	p.Ser2733Phe	p.S2733F	ENST00000356175	NM_000267.3	2733	tCc/tTc	56/57	0.443600816405957	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.458429340477185	3		364	521	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599206	28599207	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0052821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	116	523	1	ENST00000253063.3:c.652_653delinsTT	p.Pro218Phe	p.P218F	ENST00000253063	NM_031459.4	218	CCt/TTt	5/10	0.443600816405957	3	FACETS	0.991	0.895	1	0.495	0.447	0.546	CLONAL	1	TRUE	1	0.458429340477185	3		524	628	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150224	108150225	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0052821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	129	283	0	ENST00000278616.4:c.3291_3292delinsTT	p.Gln1098Ter	p.Q1098*	ENST00000278616	NM_000051.3	1097	ttCCag/ttTTag	23/63	0.458429340477185	2	FACETS	0.947	0.874	1	0.947	0.874	1	CLONAL	2	TRUE	0	0.458429340477185	2		283	297	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858065	9858066	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0052821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	94	392	0	ENST00000330684.3:c.3335_3336delinsTT	p.Ser1112Phe	p.S1112F	ENST00000330684	NM_001134407.1	1112	tCC/tTT	13/13	0.223236792169551	5	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.458429340477185	5		392	618	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858321	9858321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	102	265	0	ENST00000330684.3:c.3080C>T	p.Ser1027Phe	p.S1027F	ENST00000330684	NM_001134407.1	1027	tCc/tTc	13/13	0.223236792169551	5	FACETS	0.991	0.894	1			1	INDETERMINATE	2	TRUE	NA	0.458429340477185	5		265	379	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029422	16029422	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	185	312	0	ENST00000268712.3:c.1608G>T	p.Glu536Asp	p.E536D	ENST00000268712	NM_006311.3	536	gaG/gaT	15/46	0.443600816405957	3	FACETS	0.959	0.893	1	0.959	0.893	1	CLONAL	2	TRUE	1	0.458429340477185	3		312	517	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563425	87563425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	199	428	0	ENST00000277120.3:c.1813G>A	p.Ala605Thr	p.A605T	ENST00000277120		605	Gcc/Acc	16/19	0.458429340477185	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.458429340477185	2		428	426	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453136	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	rs397516897	NA	P-0052822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	52	168	0	ENST00000288602.6:c.1799_1801del	p.Val600_Lys601delinsGlu	p.V600_K601delinsE	ENST00000288602	NM_004333.4	600	gTGAaa/gaa	15/18	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.224595479242	2		168	414	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643446	38643446	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1300035418	NA	P-0052822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	32	296	0	ENST00000299084.4:c.916A>G	p.Lys306Glu	p.K306E	ENST00000299084	NM_152594.2	306	Aaa/Gaa	7/7	1	2	FACETS	0.584	0.473	0.709	0.584	0.473	0.709	SUBCLONAL	1	TRUE	1	0.224595479242	2		296	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577505	7577506	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTTCC	novel	NA	P-0052822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	72	396	0	ENST00000269305.4:c.771_775dup	p.Asp259GlyfsTer88	p.D259Gfs*88	ENST00000269305	NM_001126112.2	259	gac/gGGAAGac	7/11	0.224595479242	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.224595479242	1		396	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578218	7578218	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1060501198	NA	P-0052824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	23	457	0	ENST00000269305.4:c.631A>C	p.Thr211Pro	p.T211P	ENST00000269305	NM_001126112.2	211	Act/Cct	6/11	1	2	FACETS	0.408	0.317	0.515	0.408	0.317	0.515	SUBCLONAL	1	TRUE	1	0.19	2		457	593	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0052827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	1447	297	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.849794276456518	12	FACETS	1	0.993	1	1	0.993	1	CLONAL	11	FALSE	1	0.849794276456518	12		297	1617	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0052827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	323	633	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.849794276456518	3	FACETS	0.973	0.949	0.996	0.973	0.949	0.996	CLONAL	3	FALSE	0	0.849794276456518	3		633	371	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564570	55564570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	95	341	0	ENST00000288135.5:c.458G>A	p.Gly153Glu	p.G153E	ENST00000288135	NM_000222.2	153	gGg/gAg	3/21	0.841916051684882	4	FACETS	0.574	0.511	0.641			1	SUBCLONAL	1	FALSE	NA	0.849794276456518	4		341	721	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695938	117695938	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142973937	NA	P-0052827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	72	417	1	ENST00000369458.3:c.499C>T	p.Arg167Trp	p.R167W	ENST00000369458	NM_024626.3	167	Cgg/Tgg	4/6	0.347508048182084	4	FACETS	0.75	0.658	0.848			1	INDETERMINATE	1	FALSE	NA	0.849794276456518	4		418	418	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932050	39932050	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs923387791	NA	P-0052827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	45	208	0	ENST00000378444.4:c.2549G>A	p.Arg850His	p.R850H	ENST00000378444	NM_001123385.1	850	cGt/cAt	4/15	0.834879757344615	2	FACETS	0.273	0.23	0.321			1	SUBCLONAL	1	FALSE	NA	0.849794276456518	2		208	388	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437871	110437871	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	36	71	0	ENST00000375856.3:c.530C>T	p.Ala177Val	p.A177V	ENST00000375856	NM_003749.2	177	gCc/gTc	1/2	0.849794276456518	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	0	0.849794276456518	1		71	43	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249441	153249441	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	169	605	0	ENST00000281708.4:c.1337G>T	p.Trp446Leu	p.W446L	ENST00000281708	NM_033632.3	446	tGg/tTg	9/12	0.222599664730946	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.222599664730946	3		605	790	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795082	242795082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368829632	NA	P-0052831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	169	948	0	ENST00000334409.5:c.127G>A	p.Val43Met	p.V43M	ENST00000334409	NM_005018.2	43	Gtg/Atg	2/5	0.210585320230679	3	FACETS	0.896	0.823	0.971	0.896	0.823	0.971	CLONAL	2	TRUE	1	0.222599664730946	3		948	942	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052602	42052602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	125	538	0	ENST00000219905.7:c.7273C>T	p.Arg2425Cys	p.R2425C	ENST00000219905	NM_001164273.1	2425	Cgc/Tgc	20/24	0.216786729149347	3	FACETS	0.853	0.772	0.937	0.853	0.772	0.937	CLONAL	2	TRUE	1	0.222599664730946	3		538	732	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930087	68930087	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	53	475	0	ENST00000288368.4:c.148T>G	p.Leu50Val	p.L50V	ENST00000288368	NM_024870.2	50	Tta/Gta	2/40	1	2	FACETS	0.774	0.66	0.9	0.774	0.66	0.9	SUBCLONAL	1	TRUE	1	0.222599664730946	2		475	615	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711026	114711028	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0052831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	34	279	0	ENST00000543371.1:c.254_256del	p.Glu85del	p.E85del	ENST00000543371	NM_001198531.1	84	GAA/-	2/14	0.222599664730946	3	FACETS	1	0.865	1	0.534	0.437	0.642	CLONAL	1	TRUE	1	0.222599664730946	3		279	318	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577067	7577067	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0052831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	162	809	0	ENST00000269305.4:c.871A>T	p.Lys291Ter	p.K291*	ENST00000269305	NM_001126112.2	291	Aag/Tag	8/11	NA	2	FACETS	0.857	0.787	0.931			1	INDETERMINATE	2	TRUE	NA	0.222599664730946	2		809	849	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201138	108201138	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	69	409	0	ENST00000278616.4:c.7505G>C	p.Gly2502Ala	p.G2502A	ENST00000278616	NM_000051.3	2502	gGc/gCc	50/63	0.203537683503995	2	FACETS	1	0.946	1	0.58	0.506	0.661	CLONAL	1	TRUE	0	0.222599664730946	2		409	534	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039158	49039158	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs958914211	NA	P-0052831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	41	337	0	ENST00000267163.4:c.2236G>C	p.Glu746Gln	p.E746Q	ENST00000267163	NM_000321.2	746	Gaa/Caa	22/27	0.222599664730946	3	FACETS	0.825	0.687	0.979	0.413	0.343	0.49	CLONAL	1	TRUE	1	0.222599664730946	3		337	496	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144164	11144164	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	77	680	0	ENST00000358026.2:c.3745G>T	p.Ala1249Ser	p.A1249S	ENST00000358026	NM_001128849.1	1249	Gcc/Tcc	26/36	0.216786729149347	3	FACETS	0.859	0.753	0.974	0.43	0.376	0.487	CLONAL	1	TRUE	1	0.222599664730946	3		680	895	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955161	93955168	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTTATT	GGCTTATT	-	novel	NA	P-0052831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	45	556	0	ENST00000369303.4:c.2730_2737del	p.Ile911SerfsTer8	p.I911Sfs*8	ENST00000369303	NM_004440.3	910	ccAATAAGCCct/ccct	16/17	0.216786729149347	3	FACETS	0.687	0.576	0.81	0.344	0.288	0.405	SUBCLONAL	1	TRUE	1	0.222599664730946	3		556	654	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518362	204518362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746628364	NA	P-0052833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	107	463	0	ENST00000367182.3:c.1025C>T	p.Ser342Phe	p.S342F	ENST00000367182	NM_001278516.1	342	tCc/tTc	11/11	0.379157528626324	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	3	TRUE	0	0.379157528626324	3		463	208	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711873	89711873	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	rs587781784	NA	P-0052833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	19	376	0	ENST00000371953.3:c.493-2A>C		p.X165_splice	ENST00000371953	NM_000314.4	165			0.349180076012055	0	FACETS	0.566	0.435	0.714			1	SUBCLONAL	1	TRUE	0	0.379157528626324	0		376	110	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165306	47165306	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs869025571	NA	P-0052833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	26	382	0	ENST00000409792.3:c.820C>T	p.Gln274Ter	p.Q274*	ENST00000409792	NM_014159.6	274	Caa/Taa	3/21	0.379157528626324	1	FACETS	0.992	0.801	1	0.992	0.801	1	CLONAL	1	TRUE	0	0.379157528626324	1		382	112	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0052834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	239	411	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.48006320300539	4	FACETS	0.934	0.881	0.986	0.934	0.881	0.986	CLONAL	3	TRUE	1	0.491375553198616	4		411	518	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584513	48584514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs377767334	NA	P-0052834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	192	571	0	ENST00000342988.3:c.692dup	p.Ser232GlnfsTer3	p.S232Qfs*3	ENST00000342988	NM_005359.5	229	ctg/ctGg	6/12	0.480826178874062	1	FACETS	0.724	0.671	0.779	0.724	0.671	0.779	SUBCLONAL	1	TRUE	0	0.491375553198616	1		571	814	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0052834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	225	548	1	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.491375553198616	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.491375553198616	1		549	673	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031708	69031708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	102	485	0	ENST00000288368.4:c.3463C>T	p.Gln1155Ter	p.Q1155*	ENST00000288368	NM_024870.2	1155	Cag/Tag	28/40	1	2	FACETS	0.959	0.863	1	0.959	0.863	1	CLONAL	1	TRUE	1	0.491375553198616	2		485	433	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435927	56435927	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767761157	NA	P-0052835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	354	447	0	ENST00000407977.2:c.1210C>T	p.Arg404Cys	p.R404C	ENST00000407977		404	Cgc/Tgc	9/10	0.816515325105262	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	1	0.816515325105262	3		447	500	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0052836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	150	768	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.569	0.521	0.62	0.569	0.521	0.62	SUBCLONAL	1	TRUE	1	0.72	2		768	732	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068067	94068067	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	27	251	0	ENST00000369303.4:c.895C>A	p.His299Asn	p.H299N	ENST00000369303	NM_004440.3	299	Cac/Aac	4/17	1	2	FACETS	0.17	0.134	0.21	0.17	0.134	0.21	SUBCLONAL	1	TRUE	1	0.72	2		251	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578237	7578241	+	protein_altering_variant	In_Frame_Ins	INS	CTCCA	CTCCA	GTGGAAGGAAATTT	novel	NA	P-0052837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	331	592	0	ENST00000269305.4:c.608_612delinsAAATTTCCTTCCAC	p.Val203_Glu204delinsGluIleSerPheHis	p.V203_E204delinsEISFH	ENST00000269305	NM_001126112.2	203	gTGGAG/gAAATTTCCTTCCAC	6/11	0.543030220118398	2	FACETS	0.902	0.861	0.942	0.902	0.861	0.942	CLONAL	2	TRUE	0	0.575437805013982	2		592	638	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883171	37883171	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1508	80	752	0	ENST00000269571.5:c.3074T>C	p.Val1025Ala	p.V1025A	ENST00000269571		1025	gTa/gCa	25/27	0.575437805013982	5	FACETS	0.326	0.286	0.37			1	SUBCLONAL	1	TRUE	NA	0.575437805013982	5		752	1588	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55607060	55607060	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	149	450	0	ENST00000284073.2:c.429T>G	p.Phe143Leu	p.F143L	ENST00000284073	NM_138962.2	143	ttT/ttG	7/14	0.477591688197466	5	FACETS	0.906	0.826	0.99	0.302	0.275	0.33	CLONAL	1	TRUE	2	0.575437805013982	5		450	1065	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275834	38275834	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749903780	NA	P-0052837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	235	601	1	ENST00000425967.3:c.1435C>T	p.Arg479Trp	p.R479W	ENST00000425967	NM_001174067.1	479	Cgg/Tgg	11/19	0.575437805013982	5	FACETS	1	0.968	1	0.356	0.331	0.382	CLONAL	1	TRUE	2	0.575437805013982	5		602	1425	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0052838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	191	305	0				ENST00000310581	NM_198253.2	-/1132			0.289309721660345	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.96	0		305	377	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0052838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	140	97	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.812	0.749	0.877	0.812	0.749	0.877	CLONAL	1	TRUE	1	0.96	2		97	359	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653833	89653833	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	109	75	0	ENST00000371953.3:c.131G>T	p.Gly44Val	p.G44V	ENST00000371953	NM_000314.4	44	gGc/gTc	2/9	1	2	FACETS	0.797	0.727	0.869	0.797	0.727	0.869	SUBCLONAL	1	TRUE	1	0.96	2		75	285	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711900	+	missense_variant	Missense_Mutation	DNP	CG	CG	TT	novel	NA	P-0052838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	183	123	0	ENST00000371953.3:c.517_518delinsTT	p.Arg173Phe	p.R173F	ENST00000371953	NM_000314.4	173	CGc/TTc	6/9	1	2	FACETS	0.857	0.799	0.915	0.857	0.799	0.915	CLONAL	1	TRUE	1	0.96	2		123	445	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711931	89711932	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554900606	NA	P-0052838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	239	136	0	ENST00000371953.3:c.551dup	p.Asn184LysfsTer6	p.N184Kfs*6	ENST00000371953	NM_000314.4	183	-/A	6/9	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.96	2		136	496	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	232	560	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.225997965956385	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	1	0.225997965956385	4		560	744	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121912651	NA	P-0052839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	121	581	0	ENST00000269305.4:c.742C>G	p.Arg248Gly	p.R248G	ENST00000269305	NM_001126112.2	248	Cgg/Ggg	7/11	0.225997965956385	1	FACETS	0.833	0.755	0.915	1	0.987	1	CLONAL	2	TRUE	0	0.225997965956385	1		581	570	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692887	89692887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660535	NA	P-0052839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	125	370	0	ENST00000371953.3:c.371G>A	p.Cys124Tyr	p.C124Y	ENST00000371953	NM_000314.4	124	tGt/tAt	5/9	0.173434905054006	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.225997965956385	4		370	600	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692820	89692820	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0052839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	79	219	0	ENST00000371953.3:c.304A>T	p.Lys102Ter	p.K102*	ENST00000371953	NM_000314.4	102	Aaa/Taa	5/9	0.173434905054006	4	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	2	0.225997965956385	4		219	399	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478815	56478815	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	74	570	1	ENST00000267101.3:c.271A>G	p.Met91Val	p.M91V	ENST00000267101	NM_001982.3	91	Atg/Gtg	3/28	1	2	FACETS	0.81	0.708	0.921	0.81	0.708	0.921	CLONAL	1	TRUE	1	0.225997965956385	2		571	808	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238183	133238184	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	72	529	0	ENST00000320574.5:c.2793dup	p.Glu932Ter	p.E932*	ENST00000320574	NM_006231.2	931	-/T	24/49	0.168083666253446	3	FACETS	0.852	0.743	0.969	0.284	0.247	0.323	CLONAL	1	TRUE	0	0.252869289716872	3		529	753	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs985033810	NA	P-0052840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	199	608	0	ENST00000269305.4:c.731G>T	p.Gly244Val	p.G244V	ENST00000269305	NM_001126112.2	244	gGc/gTc	7/11	0.235772044750898	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.252869289716872	2		608	755	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3901006	3901006	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1555496732	NA	P-0052840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	55	338	0	ENST00000262367.5:c.90del	p.Phe30LeufsTer15	p.F30Lfs*15	ENST00000262367	NM_004380.2	30	ttT/tt	2/31	0.252869289716872	1	FACETS	0.768	0.657	0.888	0.768	0.657	0.888	SUBCLONAL	1	TRUE	0	0.252869289716872	1		338	495	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930927	39930927	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	81	180	0	ENST00000378444.4:c.3014A>G	p.Glu1005Gly	p.E1005G	ENST00000378444	NM_001123385.1	1005	gAg/gGg	5/15	0.233219026576068	4	FACETS	1	0.949	1	0.572	0.503	0.645	CLONAL	1	TRUE	2	0.252869289716872	4		180	702	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0052842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	95	548	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	0.979	0.872	1	0.979	0.872	1	CLONAL	1	TRUE	1	0.247777587734939	2		548	783	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385104	31385104	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs757998715	NA	P-0052842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	75	442	0	ENST00000328111.2:c.1489C>T	p.Arg497Trp	p.R497W	ENST00000328111	NM_006892.3	497	Cgg/Tgg	14/23	1	2	FACETS	0.916	0.802	1	0.916	0.802	1	CLONAL	1	TRUE	1	0.247777587734939	2		442	661	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657614	37657614	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	63	561	0	ENST00000447079.4:c.2531T>C	p.Met844Thr	p.M844T	ENST00000447079	NM_015083.1	844	aTg/aCg	6/14	0.247777587734939	1	FACETS	0.651	0.563	0.748	0.651	0.563	0.748	SUBCLONAL	1	TRUE	0	0.247777587734939	1		561	684	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106528	27106528	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	62	711	1	ENST00000324856.7:c.6139G>T	p.Glu2047Ter	p.E2047*	ENST00000324856	NM_006015.4	2047	Gag/Tag	20/20	1	2	FACETS	0.628	0.541	0.723	0.628	0.541	0.723	SUBCLONAL	1	TRUE	1	0.231615816119221	2		712	853	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11172458	11172458	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0052843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	50	666	0	ENST00000358026.2:c.5008-2A>C		p.X1670_splice	ENST00000358026	NM_001128849.1	1670			0.231615816119221	1	FACETS	0.559	0.473	0.653	0.559	0.473	0.653	SUBCLONAL	1	TRUE	0	0.231615816119221	1		666	683	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0052846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	35	350	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.898	0.735	1	0.898	0.735	1	CLONAL	1	TRUE	1	0.14	2		350	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0052846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	43	656	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	TRUE	1	0.14	2		656	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577148	7577148	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	35	610	0	ENST00000269305.4:c.790C>G	p.Leu264Val	p.L264V	ENST00000269305	NM_001126112.2	264	Cta/Gta	8/11	1	2	FACETS	1	0.824	1	1	0.824	1	CLONAL	1	TRUE	1	0.14	2		610	497	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0052849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	28	411	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.3	4	FACETS	0.916	0.733	1			1	CLONAL	1	TRUE	NA	0.22	4		411	339	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254858	16254858	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	34	164	1	ENST00000375759.3:c.2123G>T	p.Arg708Ile	p.R708I	ENST00000375759	NM_015001.2	708	aGa/aTa	11/15	0.209201325589935	3	FACETS	0.713	0.582	0.861	0.357	0.291	0.431	SUBCLONAL	1	TRUE	1	0.22	3		165	481	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653075	29653076	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	232	454	0	ENST00000356175.3:c.5011dup	p.Tyr1671LeufsTer3	p.Y1671Lfs*3	ENST00000356175	NM_000267.3	1670	-/T	36/57	0.815210546232939	1	FACETS	0.939	0.895	0.982	0.939	0.895	0.982	CLONAL	1	TRUE	0	0.815210546232939	1		454	359	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782082	NA	P-0052852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	327	690	0	ENST00000269305.4:c.745A>T	p.Arg249Trp	p.R249W	ENST00000269305	NM_001126112.2	249	Agg/Tgg	7/11	0.729584469629473	1	FACETS	0.987	0.944	1	0.987	0.944	1	CLONAL	1	TRUE	0	0.729584469629473	1		690	577	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5466823	5466863	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAAAGTGGTAAGAATATCAGAAGGAATTGGGAAGTAAAAGT	CAAAGTGGTAAGAATATCAGAAGGAATTGGGAAGTAAAAGT	-	novel	NA	P-0052852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	23	153	0	ENST00000381577.3:c.849_850+39del		p.X283_splice	ENST00000381577	NM_014143.3	283		6/7	1	2	FACETS	0.45	0.355	0.558	0.45	0.355	0.558	SUBCLONAL	1	TRUE	1	0.729584469629473	2		153	140	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759710	133759710	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	55	654	0	ENST00000318560.5:c.2033G>C	p.Gly678Ala	p.G678A	ENST00000318560	NM_005157.4	678	gGc/gCc	11/11	0.727874427488313	1	FACETS	0.186	0.158	0.215	0.186	0.158	0.215	SUBCLONAL	1	TRUE	0	0.729584469629473	1		654	516	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	101	429	0				ENST00000310581	NM_198253.2	-/1132			0.341410584878325	5	FACETS	1	0.925	1	0.683	0.618	0.749	INDETERMINATE	2	TRUE	2	0.680070705016771	5		429	293	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	117	213	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	0.64177864699553	2	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.680070705016771	2		213	141	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0052853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	177	920	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.680070705016771	2		920	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578513	7578513	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	211	1039	1	ENST00000269305.4:c.417G>C	p.Lys139Asn	p.K139N	ENST00000269305	NM_001126112.2	139	aaG/aaC	5/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.680070705016771	2		1040	542	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0052853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	87	624	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	0.290004754146631	3	FACETS	0.877	0.781	0.977	0.292	0.26	0.326	INDETERMINATE	1	TRUE	0	0.680070705016771	3		624	391	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030378	49030378	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs267603840	NA	P-0052853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	141	285	0	ENST00000267163.4:c.1853C>A	p.Ser618Ter	p.S618*	ENST00000267163	NM_000321.2	618	tCa/tAa	19/27	0.54625052436645	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.680070705016771	2		285	192	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670622	67670622	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	81	522	0	ENST00000264010.4:c.1867G>T	p.Glu623Ter	p.E623*	ENST00000264010	NM_006565.3	623	Gag/Tag	11/12	0.188346758081094	2	FACETS	0.824	0.734	0.918	0.412	0.367	0.459	INDETERMINATE	1	TRUE	0	0.680070705016771	2		522	289	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309740	104309740	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	58	654	0	ENST00000369902.3:c.331G>C	p.Asp111His	p.D111H	ENST00000369902	NM_016169.3	111	Gat/Cat	3/12	0.478952592009011	1	FACETS	0.285	0.245	0.328	0.285	0.245	0.328	SUBCLONAL	1	TRUE	0	0.680070705016771	1		654	395	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024678	14024678	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	111	298	0	ENST00000311895.7:c.904G>C	p.Asp302His	p.D302H	ENST00000311895	NM_005236.2	302	Gat/Cat	5/11	0.680070705016771	7	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.680070705016771	7		298	648	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244528	41244528	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs80357168	NA	P-0052853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	58	369	0	ENST00000357654.3:c.3020C>G	p.Ser1007Ter	p.S1007*	ENST00000357654	NM_007294.3	1007	tCa/tGa	10/23	0.354406936251657	3	FACETS	0.625	0.539	0.717	0.208	0.179	0.239	INDETERMINATE	1	TRUE	0	0.680070705016771	3		369	366	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39567798	39567798	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	42	187	0	ENST00000262039.4:c.554G>A	p.Gly185Glu	p.G185E	ENST00000262039	NM_002647.2	185	gGa/gAa	5/25	0.589771825697086	3	FACETS	0.618	0.519	0.726	0.309	0.259	0.363	SUBCLONAL	1	TRUE	1	0.680070705016771	3		187	268	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030613	11030613	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	85	802	0	ENST00000327064.4:c.1167C>G	p.Phe389Leu	p.F389L	ENST00000327064	NM_199141.1	389	ttC/ttG	10/16	1	2	FACETS	0.602	0.535	0.673	0.602	0.535	0.673	SUBCLONAL	1	TRUE	1	0.680070705016771	2		802	415	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740561	145740561	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs768311526	NA	P-0052853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	59	979	0	ENST00000428558.2:c.1456G>C	p.Glu486Gln	p.E486Q	ENST00000428558	NM_004260.3	486	Gag/Cag	8/22	0.341410584878325	5	FACETS	0.637	0.548	0.734	0.212	0.182	0.245	INDETERMINATE	1	TRUE	2	0.680070705016771	5		979	550	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	34	299	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	1	2	FACETS	0.915	0.748	1	0.915	0.748	1	CLONAL	1	TRUE	1	0.17	2		299	437	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	40	376	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.908	0.754	1	0.908	0.754	1	CLONAL	1	TRUE	1	0.17	2		376	518	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	57	587	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.897	0.768	1	0.897	0.768	1	CLONAL	1	TRUE	1	0.17	2		587	748	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	72	443	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.175265740638735	3	FACETS	0.836	0.731	0.948	0.836	0.731	0.948	CLONAL	2	TRUE	1	0.17	3		443	550	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828699	72828699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762362472	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	47	596	1	ENST00000268489.5:c.7882G>A	p.Glu2628Lys	p.E2628K	ENST00000268489	NM_006885.3	2628	Gaa/Aaa	9/10	1	2	FACETS	0.659	0.554	0.775	0.659	0.554	0.775	SUBCLONAL	1	TRUE	1	0.17	2		597	839	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	58	424	0	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	1	2	FACETS	0.92	0.789	1	0.92	0.789	1	CLONAL	1	TRUE	1	0.17	2		424	742	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	46	1153	1	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.808	0.679	0.951	0.808	0.679	0.951	CLONAL	1	TRUE	1	0.17	2		1154	670	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39311616	39311616	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	35	448	0	ENST00000373001.3:c.1043G>T	p.Arg348Ile	p.R348I	ENST00000373001	NM_022157.3	348	aGa/aTa	6/7	1	2	FACETS	0.787	0.644	0.948	0.787	0.644	0.948	CLONAL	1	TRUE	1	0.17	2		448	523	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818403	43818403	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	51	574	0	ENST00000372470.3:c.1868A>G	p.Asn623Ser	p.N623S	ENST00000372470	NM_005373.2	623	aAc/aGc	12/12	1	2	FACETS	0.776	0.658	0.906	0.776	0.658	0.906	CLONAL	1	TRUE	1	0.17	2		574	773	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46543272	46543272	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	45	384	0	ENST00000262741.5:c.229G>T	p.Asp77Tyr	p.D77Y	ENST00000262741	NM_003629.3	77	Gac/Tac	3/10	1	2	FACETS	0.771	0.646	0.909	0.771	0.646	0.909	CLONAL	1	TRUE	1	0.17	2		384	687	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321352	65321352	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	58	493	0	ENST00000342505.4:c.1488G>T	p.Lys496Asn	p.K496N	ENST00000342505	NM_002227.2	496	aaG/aaT	11/25	1	2	FACETS	0.809	0.694	0.936	0.809	0.694	0.936	CLONAL	1	TRUE	1	0.17	2		493	843	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330517	65330517	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	60	468	0	ENST00000342505.4:c.1129A>G	p.Ile377Val	p.I377V	ENST00000342505	NM_002227.2	377	Ata/Gta	8/25	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.17	2		468	673	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241956	72241956	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	22	245	0	ENST00000357731.5:c.434C>A	p.Ser145Ter	p.S145*	ENST00000357731	NM_173808.2	145	tCa/tAa	3/7	1	2	FACETS	0.599	0.463	0.758	0.599	0.463	0.758	SUBCLONAL	1	TRUE	1	0.17	2		245	432	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745581	162745581	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	45	514	0	ENST00000367921.3:c.1996C>A	p.Leu666Ile	p.L666I	ENST00000367921	NM_006182.2	666	Ctt/Att	15/18	1	2	FACETS	0.73	0.612	0.861	0.73	0.612	0.861	SUBCLONAL	1	TRUE	1	0.17	2		514	725	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663891	241663891	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	29	329	0	ENST00000366560.3:c.1237-1G>T		p.X413_splice	ENST00000366560	NM_000143.3	413			1	2	FACETS	0.677	0.542	0.831	0.677	0.542	0.831	SUBCLONAL	1	TRUE	1	0.17	2		329	504	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667422	241667422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756990249	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	39	420	1	ENST00000366560.3:c.1028G>A	p.Arg343Gln	p.R343Q	ENST00000366560	NM_000143.3	343	cGa/cAa	7/10	1	2	FACETS	0.656	0.543	0.784	0.656	0.543	0.784	SUBCLONAL	1	TRUE	1	0.17	2		421	699	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606814	43606814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746512075	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	60	693	0	ENST00000355710.3:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000355710	NM_020975.4	475	Cgg/Tgg	7/20	0.175265740638735	3	FACETS	0.766	0.658	0.884	0.383	0.329	0.442	SUBCLONAL	1	TRUE	1	0.17	3		693	1000	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63661997	63661997	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	46	339	0	ENST00000279873.7:c.101G>T	p.Arg34Ile	p.R34I	ENST00000279873	NM_032199.2	34	aGa/aTa	2/10	0.175265740638735	3	FACETS	0.88	0.74	1	0.44	0.37	0.518	CLONAL	1	TRUE	1	0.17	3		339	667	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406666	70406666	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs752300962	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	41	490	0	ENST00000373644.4:c.4180A>C	p.Asn1394His	p.N1394H	ENST00000373644	NM_030625.2	1394	Aat/Cat	4/12	0.175265740638735	3	FACETS	0.663	0.551	0.789	0.332	0.275	0.395	SUBCLONAL	1	TRUE	1	0.17	3		490	789	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	32	448	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	0.175265740638735	3	FACETS	0.689	0.558	0.838	0.344	0.279	0.419	SUBCLONAL	1	TRUE	1	0.17	3		448	593	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720859	89720859	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	28	257	0	ENST00000371953.3:c.1010T>G	p.Phe337Cys	p.F337C	ENST00000371953	NM_000314.4	337	tTt/tGt	8/9	0.175265740638735	3	FACETS	0.857	0.685	1	0.429	0.342	0.527	CLONAL	1	TRUE	1	0.17	3		257	417	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104352402	104352402	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587778697	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	60	601	0	ENST00000369902.3:c.518G>T	p.Arg173Ile	p.R173I	ENST00000369902	NM_016169.3	173	aGa/aTa	4/12	0.175265740638735	3	FACETS	0.839	0.721	0.968	0.419	0.36	0.484	CLONAL	1	TRUE	1	0.17	3		601	913	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104357036	104357036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374946819	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	48	468	1	ENST00000369902.3:c.896G>A	p.Arg299Gln	p.R299Q	ENST00000369902	NM_016169.3	299	cGa/cAa	7/12	0.175265740638735	3	FACETS	0.873	0.736	1	0.436	0.368	0.512	CLONAL	1	TRUE	1	0.17	3		469	702	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925719	114925719	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	49	490	0	ENST00000543371.1:c.1797G>T	p.Lys599Asn	p.K599N	ENST00000543371	NM_001198531.1	599	aaG/aaT	14/14	0.175265740638735	3	FACETS	0.733	0.619	0.86	0.367	0.309	0.43	SUBCLONAL	1	TRUE	1	0.17	3		490	853	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518641	69518641	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1001998520	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	64	414	1	ENST00000294312.3:c.4C>T	p.Arg2Trp	p.R2W	ENST00000294312	NM_005117.2	2	Cgg/Tgg	1/3	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.17	2		415	597	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933477	100933477	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	23	234	0	ENST00000325455.5:c.1913A>C	p.Lys638Thr	p.K638T	ENST00000325455	NM_001202474.3	638	aAa/aCa	4/8	1	2	FACETS	0.835	0.651	1	0.835	0.651	1	CLONAL	1	TRUE	1	0.17	2		234	324	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139287	108139287	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs786203309	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	57	507	0	ENST00000278616.4:c.2789T>G	p.Leu930Ter	p.L930*	ENST00000278616	NM_000051.3	930	tTa/tGa	18/63	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.17	2		507	634	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402318	402318	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1055745005	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	34	391	1	ENST00000399788.2:c.4473G>T	p.Glu1491Asp	p.E1491D	ENST00000399788	NM_001042603.1	1491	gaG/gaT	27/28	0.3	2	FACETS	0.657	0.535	0.794			1	SUBCLONAL	1	TRUE	NA	0.17	2		392	609	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438054	438054	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	37	359	0	ENST00000399788.2:c.1915T>G	p.Leu639Val	p.L639V	ENST00000399788	NM_001042603.1	639	Ttg/Gtg	14/28	0.3	2	FACETS	0.635	0.522	0.762			1	SUBCLONAL	1	TRUE	NA	0.17	2		359	686	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691118	18691118	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	46	365	0	ENST00000266497.5:c.3229G>T	p.Glu1077Ter	p.E1077*	ENST00000266497		1077	Gag/Tag	23/31	0.175265740638735	3	FACETS	1	0.935	1	0.612	0.515	0.718	CLONAL	1	TRUE	1	0.17	3		365	480	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420934	49420934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs569620684	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	43	548	2	ENST00000301067.7:c.14815G>A	p.Glu4939Lys	p.E4939K	ENST00000301067	NM_003482.3	4939	Gaa/Aaa	48/54	0.175265740638735	3	FACETS	0.751	0.627	0.889	0.375	0.313	0.445	SUBCLONAL	1	TRUE	1	0.17	3		550	731	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426544	49426544	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555188379	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1252	101	884	2	ENST00000301067.7:c.11944C>T	p.Arg3982Ter	p.R3982*	ENST00000301067	NM_003482.3	3982	Cga/Tga	39/54	0.175265740638735	3	FACETS	0.953	0.849	1	0.476	0.424	0.532	CLONAL	1	TRUE	1	0.17	3		886	1353	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432408	49432408	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	77	753	0	ENST00000301067.7:c.8731G>T	p.Glu2911Ter	p.E2911*	ENST00000301067	NM_003482.3	2911	Gag/Tag	34/54	0.175265740638735	3	FACETS	0.982	0.86	1	0.491	0.43	0.557	CLONAL	1	TRUE	1	0.17	3		753	1001	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447266	49447266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	61	550	0	ENST00000301067.7:c.832G>A	p.Ala278Thr	p.A278T	ENST00000301067	NM_003482.3	278	Gcc/Acc	6/54	0.175265740638735	3	FACETS	0.865	0.744	0.997	0.433	0.372	0.499	CLONAL	1	TRUE	1	0.17	3		550	900	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484097	50484097	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	69	577	2	ENST00000394963.4:c.947T>C	p.Ile316Thr	p.I316T	ENST00000394963	NM_003076.4	316	aTc/aCc	8/13	0.175265740638735	3	FACETS	0.93	0.808	1	0.465	0.404	0.532	CLONAL	1	TRUE	1	0.17	3		579	947	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233505	69233505	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	30	386	0	ENST00000462284.1:c.1370T>C	p.Val457Ala	p.V457A	ENST00000462284	NM_002392.5	457	gTc/gCc	11/11	0.175265740638735	3	FACETS	0.745	0.599	0.911	0.373	0.299	0.456	CLONAL	1	TRUE	1	0.17	3		386	514	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249857	133249857	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1565972665	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	97	441	0	ENST00000320574.5:c.1366G>C	p.Ala456Pro	p.A456P	ENST00000320574	NM_006231.2	456	Gcc/Ccc	14/49	0.175265740638735	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.17	3		441	566	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911697	32911697	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	24	460	0	ENST00000380152.3:c.3205T>G	p.Ser1069Ala	p.S1069A	ENST00000380152		1069	Tct/Gct	11/27	1	2	FACETS	0.619	0.484	0.775	0.619	0.484	0.775	SUBCLONAL	1	TRUE	1	0.17	2		460	456	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912357	32912357	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786201943	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	19	348	0	ENST00000380152.3:c.3865A>G	p.Lys1289Glu	p.K1289E	ENST00000380152		1289	Aaa/Gaa	11/27	1	2	FACETS	0.677	0.514	0.87	0.677	0.514	0.87	SUBCLONAL	1	TRUE	1	0.17	2		348	330	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954021	32954021	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	32	412	0	ENST00000380152.3:c.9088A>G	p.Thr3030Ala	p.T3030A	ENST00000380152		3030	Aca/Gca	23/27	1	2	FACETS	0.826	0.67	1	0.826	0.67	1	CLONAL	1	TRUE	1	0.17	2		412	456	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346314	73346314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs575448022	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	24	266	0	ENST00000377767.4:c.1486G>A	p.Glu496Lys	p.E496K	ENST00000377767	NM_014953.3	496	Gaa/Aaa	10/21	1	2	FACETS	0.877	0.688	1	0.877	0.688	1	CLONAL	1	TRUE	1	0.17	2		266	322	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73350160	73350160	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	41	321	0	ENST00000377767.4:c.725A>C	p.Lys242Thr	p.K242T	ENST00000377767	NM_014953.3	242	aAa/aCa	5/21	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.17	2		321	385	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435774	110435774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1428455100	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	11	96	0	ENST00000375856.3:c.2627G>A	p.Arg876His	p.R876H	ENST00000375856	NM_003749.2	876	cGc/cAc	1/2	1	2	FACETS	0.84	0.582	1	0.84	0.582	1	CLONAL	1	TRUE	1	0.17	2		96	154	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331809	68331809	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	42	456	0	ENST00000487270.1:c.405A>C	p.Glu135Asp	p.E135D	ENST00000487270	NM_133509.3	135	gaA/gaC	5/11	1	2	FACETS	0.737	0.614	0.875	0.737	0.614	0.875	SUBCLONAL	1	TRUE	1	0.17	2		456	670	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021510	42021510	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	54	536	1	ENST00000219905.7:c.3806C>A	p.Ser1269Ter	p.S1269*	ENST00000219905	NM_001164273.1	1269	tCa/tAa	11/24	1	2	FACETS	0.811	0.691	0.943	0.811	0.691	0.943	CLONAL	1	TRUE	1	0.17	2		537	783	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058770	42058770	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	34	307	0	ENST00000219905.7:c.8490T>G	p.Ile2830Met	p.I2830M	ENST00000219905	NM_001164273.1	2830	atT/atG	24/24	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.17	2		307	335	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712646	43712646	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146431821	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	97	734	0	ENST00000382044.4:c.4538G>A	p.Arg1513Gln	p.R1513Q	ENST00000382044	NM_001141980.1	1513	cGa/cAa	21/28	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.17	2		734	1106	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727452	66727452	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	18	516	0	ENST00000307102.5:c.168G>T	p.Gln56His	p.Q56H	ENST00000307102	NM_002755.3	56	caG/caT	2/11	1	2	FACETS	0.28	0.21	0.364	0.28	0.21	0.364	SUBCLONAL	1	TRUE	1	0.17	2		516	756	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679176	88679176	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	71	475	0	ENST00000360948.2:c.861G>T	p.Glu287Asp	p.E287D	ENST00000360948	NM_001012338.2	287	gaG/gaT	8/19	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.17	2		475	759	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858337	9858337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560057284	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	28	383	0	ENST00000330684.3:c.3064C>T	p.Arg1022Cys	p.R1022C	ENST00000330684	NM_001134407.1	1022	Cgc/Tgc	13/13	1	2	FACETS	0.676	0.54	0.833	0.676	0.54	0.833	SUBCLONAL	1	TRUE	1	0.17	2		383	487	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828362	72828362	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	81	591	0	ENST00000268489.5:c.8219G>T	p.Arg2740Ile	p.R2740I	ENST00000268489	NM_006885.3	2740	aGa/aTa	9/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.17	2		591	783	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576028	29576028	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	41	399	0	ENST00000356175.3:c.4001A>G	p.Glu1334Gly	p.E1334G	ENST00000356175	NM_000267.3	1334	gAa/gGa	30/57	1	2	FACETS	0.861	0.717	1	0.861	0.717	1	CLONAL	1	TRUE	1	0.17	2		399	560	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	34	320	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.17	2		320	363	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321692	30321692	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	52	477	1	ENST00000322652.5:c.1547G>A	p.Arg516His	p.R516H	ENST00000322652	NM_015355.2	516	cGc/cAc	13/16	1	2	FACETS	0.832	0.707	0.97	0.832	0.707	0.97	CLONAL	1	TRUE	1	0.17	2		478	735	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618727	37618727	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	49	510	0	ENST00000447079.4:c.403G>T	p.Glu135Ter	p.E135*	ENST00000447079	NM_015083.1	135	Gaa/Taa	1/14	1	2	FACETS	0.777	0.656	0.91	0.777	0.656	0.91	CLONAL	1	TRUE	1	0.17	2		510	742	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438156	56438156	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs141997049	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	74	719	0	ENST00000407977.2:c.837C>A	p.Phe279Leu	p.F279L	ENST00000407977		279	ttC/ttA	7/10	1	2	FACETS	0.972	0.849	1	0.972	0.849	1	CLONAL	1	TRUE	1	0.17	2		719	896	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740436	58740436	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs769061997	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	37	522	0	ENST00000305921.3:c.1341G>T	p.Glu447Asp	p.E447D	ENST00000305921	NM_003620.3	447	gaG/gaT	6/6	1	2	FACETS	0.606	0.498	0.728	0.606	0.498	0.728	SUBCLONAL	1	TRUE	1	0.17	2		522	718	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59820444	59820444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555590457	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	39	418	0	ENST00000259008.2:c.2309A>G	p.Asp770Gly	p.D770G	ENST00000259008	NM_032043.2	770	gAt/gGt	16/20	1	2	FACETS	0.741	0.613	0.885	0.741	0.613	0.885	SUBCLONAL	1	TRUE	1	0.17	2		418	619	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56415044	56415044	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs772139375	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	35	377	0	ENST00000348428.3:c.2445C>A	p.Phe815Leu	p.F815L	ENST00000348428	NM_006785.3	815	ttC/ttA	17/17	1	2	FACETS	0.827	0.677	0.995	0.827	0.677	0.995	CLONAL	1	TRUE	1	0.17	2		377	498	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117382	7117382	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	64	620	0	ENST00000302850.5:c.3834G>T	p.Lys1278Asn	p.K1278N	ENST00000302850	NM_000208.2	1278	aaG/aaT	22/22	1	2	FACETS	0.877	0.757	1	0.877	0.757	1	CLONAL	1	TRUE	1	0.17	2		620	859	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138486	11138486	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	63	505	0	ENST00000358026.2:c.3242A>C	p.Lys1081Thr	p.K1081T	ENST00000358026	NM_001128849.1	1081	aAa/aCa	24/36	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.17	2		505	720	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152033	11152033	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1384070535	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	52	555	0	ENST00000358026.2:c.4317G>T	p.Lys1439Asn	p.K1439N	ENST00000358026	NM_001128849.1	1439	aaG/aaT	31/36	1	2	FACETS	0.873	0.742	1	0.873	0.742	1	CLONAL	1	TRUE	1	0.17	2		555	701	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794440	42794440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776806622	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	74	832	0	ENST00000575354.2:c.1520G>A	p.Arg507His	p.R507H	ENST00000575354	NM_015125.3	507	cGc/cAc	10/20	1	2	FACETS	0.885	0.772	1	0.885	0.772	1	CLONAL	1	TRUE	1	0.17	2		832	984	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855769	45855769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913023	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	57	547	0	ENST00000391945.4:c.2041G>A	p.Asp681Asn	p.D681N	ENST00000391945	NM_000400.3	681	Gac/Aac	21/23	1	2	FACETS	0.862	0.738	0.998	0.862	0.738	0.998	CLONAL	1	TRUE	1	0.17	2		547	778	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855837	45855837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762141272	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	92	714	0	ENST00000391945.4:c.1973G>A	p.Arg658His	p.R658H	ENST00000391945	NM_000400.3	658	cGc/cAc	21/23	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.17	2		714	1038	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976426	25976426	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	52	476	0	ENST00000435504.4:c.1119C>A	p.Phe373Leu	p.F373L	ENST00000435504		373	ttC/ttA	11/13	1	2	FACETS	0.951	0.809	1	0.951	0.809	1	CLONAL	1	TRUE	1	0.17	2		476	643	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262578	39262578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867539471	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	42	438	0	ENST00000402219.2:c.928C>T	p.Arg310Cys	p.R310C	ENST00000402219	NM_005633.3	310	Cgt/Tgt	7/23	1	2	FACETS	0.815	0.68	0.967	0.815	0.68	0.967	CLONAL	1	TRUE	1	0.17	2		438	606	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574151	46574151	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	66	641	0	ENST00000263734.3:c.166A>G	p.Ile56Val	p.I56V	ENST00000263734	NM_001430.4	56	Atc/Gtc	2/16	1	2	FACETS	0.949	0.822	1	0.949	0.822	1	CLONAL	1	TRUE	1	0.17	2		641	818	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027837	48027837	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	32	415	0	ENST00000234420.5:c.2715G>T	p.Leu905Phe	p.L905F	ENST00000234420	NM_000179.2	905	ttG/ttT	4/10	1	2	FACETS	0.697	0.565	0.847	0.697	0.565	0.847	SUBCLONAL	1	TRUE	1	0.17	2		415	540	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	20	483	0	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	0.423	0.322	0.542	0.423	0.322	0.542	SUBCLONAL	1	TRUE	1	0.17	2		483	556	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630638	158630638	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs387906591	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	33	273	0	ENST00000263640.3:c.605G>T	p.Arg202Ile	p.R202I	ENST00000263640	NM_001105.4	202	aGa/aTa	6/11	1	2	FACETS	0.824	0.671	0.998	0.824	0.671	0.998	CLONAL	1	TRUE	1	0.17	2		273	471	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519920	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	24	265	0	ENST00000397062.3:c.85G>T	p.Asp29Tyr	p.D29Y	ENST00000397062	NM_006164.4	29	Gat/Tat	2/5	1	2	FACETS	0.761	0.596	0.951	0.761	0.596	0.951	CLONAL	1	TRUE	1	0.17	2		265	371	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149771	202149771	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	53	545	0	ENST00000358485.4:c.1212C>G	p.Cys404Trp	p.C404W	ENST00000358485	NM_001080125.1	404	tgC/tgG	8/9	1	2	FACETS	0.818	0.696	0.953	0.818	0.696	0.953	CLONAL	1	TRUE	1	0.17	2		545	762	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736158	204736158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs963824682	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	51	415	0	ENST00000302823.3:c.515C>T	p.Ser172Leu	p.S172L	ENST00000302823	NM_005214.4	172	tCg/tTg	3/4	1	2	FACETS	0.828	0.702	0.966	0.828	0.702	0.966	CLONAL	1	TRUE	1	0.17	2		415	725	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440178	220440178	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1025309043	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	66	764	0	ENST00000243786.2:c.1031C>T	p.Ser344Leu	p.S344L	ENST00000243786	NM_002191.3	344	tCg/tTg	2/2	1	2	FACETS	0.887	0.768	1	0.887	0.768	1	CLONAL	1	TRUE	1	0.17	2		764	875	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253883	30253883	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	40	445	0	ENST00000307677.4:c.571T>G	p.Phe191Val	p.F191V	ENST00000307677	NM_138578.1	191	Ttt/Gtt	3/3	1	2	FACETS	0.783	0.649	0.932	0.783	0.649	0.932	CLONAL	1	TRUE	1	0.17	2		445	601	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031657	36031657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1197051295	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	71	684	0	ENST00000358208.4:c.1486G>A	p.Asp496Asn	p.D496N	ENST00000358208		496	Gac/Aac	12/12	1	2	FACETS	0.871	0.758	0.993	0.871	0.758	0.993	CLONAL	1	TRUE	1	0.17	2		684	959	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739099	40739099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536918490	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	33	511	0	ENST00000373198.4:c.3185G>A	p.Arg1062His	p.R1062H	ENST00000373198	NM_133170.3	1062	cGc/cAc	24/32	1	2	FACETS	0.59	0.479	0.716	0.59	0.479	0.716	SUBCLONAL	1	TRUE	1	0.17	2		511	658	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46255777	46255777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769864577	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	34	410	0	ENST00000371998.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371998		130	cGa/cAa	6/23	1	2	FACETS	0.901	0.736	1	0.901	0.736	1	CLONAL	1	TRUE	1	0.17	2		410	444	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24135796	24135796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	60	550	0	ENST00000263121.7:c.283G>A	p.Glu95Lys	p.E95K	ENST00000263121	NM_003073.3	95	Gaa/Aaa	3/9	1	2	FACETS	0.85	0.731	0.981	0.85	0.731	0.981	CLONAL	1	TRUE	1	0.17	2		550	830	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092966	29092966	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	51	456	0	ENST00000328354.6:c.1018G>T	p.Glu340Ter	p.E340*	ENST00000328354	NM_007194.3	340	Gaa/Taa	10/15	1	2	FACETS	0.968	0.822	1	0.968	0.822	1	CLONAL	1	TRUE	1	0.17	2		456	620	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713129	30713129	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	27	261	0	ENST00000295754.5:c.455-1G>T		p.X152_splice	ENST00000295754	NM_003242.5	152			1	2	FACETS	0.767	0.61	0.947	0.767	0.61	0.947	CLONAL	1	TRUE	1	0.17	2		261	414	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163233	47163233	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	49	428	0	ENST00000409792.3:c.2893G>T	p.Glu965Ter	p.E965*	ENST00000409792	NM_014159.6	965	Gaa/Taa	3/21	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.17	2		428	531	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595813	52595813	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	69	457	0	ENST00000394830.3:c.4102C>A	p.Leu1368Ile	p.L1368I	ENST00000394830	NM_018313.4	1368	Ctt/Att	26/30	1	2	FACETS	0.953	0.828	1	0.953	0.828	1	CLONAL	1	TRUE	1	0.17	2		457	852	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205748	128205748	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	49	543	0	ENST00000341105.2:c.127G>T	p.Asp43Tyr	p.D43Y	ENST00000341105	NM_032638.4	43	Gac/Tac	2/6	1	2	FACETS	0.73	0.616	0.855	0.73	0.616	0.855	SUBCLONAL	1	TRUE	1	0.17	2		543	790	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670674	134670674	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	59	642	0	ENST00000398015.3:c.585G>T	p.Lys195Asn	p.K195N	ENST00000398015	NM_004441.4	195	aaG/aaT	3/16	1	2	FACETS	0.791	0.678	0.913	0.791	0.678	0.913	CLONAL	1	TRUE	1	0.17	2		642	878	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873100	134873100	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	42	554	2	ENST00000398015.3:c.1404G>T	p.Glu468Asp	p.E468D	ENST00000398015	NM_004441.4	468	gaG/gaT	6/16	1	2	FACETS	0.81	0.675	0.96	0.81	0.675	0.96	CLONAL	1	TRUE	1	0.17	2		556	610	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433378	138433378	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	57	487	0	ENST00000289153.2:c.1234A>C	p.Lys412Gln	p.K412Q	ENST00000289153	NM_006219.2	412	Aaa/Caa	7/22	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.17	2		487	567	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186875	142186875	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	17	308	0	ENST00000350721.4:c.6588A>C	p.Glu2196Asp	p.E2196D	ENST00000350721	NM_001184.3	2196	gaA/gaC	39/47	1	2	FACETS	0.599	0.446	0.781	0.599	0.446	0.781	SUBCLONAL	1	TRUE	1	0.17	2		308	334	SUCCESS
ATR	545	MSKCC	GRCh37	3	142285095	142285095	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	37	287	1	ENST00000350721.4:c.160G>T	p.Glu54Ter	p.E54*	ENST00000350721	NM_001184.3	54	Gaa/Taa	3/47	1	2	FACETS	1	0.842	1	1	0.842	1	CLONAL	1	TRUE	1	0.17	2		288	426	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	32	323	0	ENST00000263967.3:c.333G>T	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaT	2/21	1	2	FACETS	0.789	0.64	0.958	0.789	0.64	0.958	CLONAL	1	TRUE	1	0.17	2		323	477	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1919902	1919902	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	48	480	0	ENST00000382891.5:c.962A>G	p.Gln321Arg	p.Q321R	ENST00000382891	NM_133335.3	321	cAg/cGg	5/22	1	2	FACETS	0.795	0.671	0.933	0.795	0.671	0.933	CLONAL	1	TRUE	1	0.17	2		480	710	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133718	55133718	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	38	413	0	ENST00000257290.5:c.932-1G>T		p.X311_splice	ENST00000257290	NM_006206.4	311			1	2	FACETS	0.767	0.633	0.917	0.767	0.633	0.917	CLONAL	1	TRUE	1	0.17	2		413	583	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146567	55146567	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	30	397	0	ENST00000257290.5:c.2241A>C	p.Glu747Asp	p.E747D	ENST00000257290	NM_006206.4	747	gaA/gaC	16/23	1	2	FACETS	0.702	0.564	0.858	0.702	0.564	0.858	SUBCLONAL	1	TRUE	1	0.17	2		397	503	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156639	55156639	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768291477	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	43	530	1	ENST00000257290.5:c.3040G>A	p.Ala1014Thr	p.A1014T	ENST00000257290	NM_006206.4	1014	Gct/Act	22/23	1	2	FACETS	0.638	0.532	0.756	0.638	0.532	0.756	SUBCLONAL	1	TRUE	1	0.17	2		531	793	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961766	55961766	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	45	466	0	ENST00000263923.4:c.2795G>T	p.Arg932Ile	p.R932I	ENST00000263923	NM_002253.2	932	aGa/aTa	20/30	1	2	FACETS	0.811	0.68	0.956	0.811	0.68	0.956	CLONAL	1	TRUE	1	0.17	2		466	653	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213898	66213898	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	30	399	0	ENST00000273854.3:c.2532G>A	p.Trp844Ter	p.W844*	ENST00000273854	NM_004439.5	844	tgG/tgA	15/18	1	2	FACETS	0.634	0.509	0.775	0.634	0.509	0.775	SUBCLONAL	1	TRUE	1	0.17	2		399	557	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231769	66231769	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	27	283	0	ENST00000273854.3:c.1931T>A	p.Leu644Gln	p.L644Q	ENST00000273854	NM_004439.5	644	cTg/cAg	11/18	1	2	FACETS	1	0.818	1	1	0.818	1	CLONAL	1	TRUE	1	0.17	2		283	309	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233094	66233094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	36	350	0	ENST00000273854.3:c.1905G>A	p.Met635Ile	p.M635I	ENST00000273854	NM_004439.5	635	atG/atA	10/18	1	2	FACETS	0.759	0.623	0.912	0.759	0.623	0.912	CLONAL	1	TRUE	1	0.17	2		350	558	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286229	66286229	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	24	325	0	ENST00000273854.3:c.1457C>A	p.Ser486Tyr	p.S486Y	ENST00000273854	NM_004439.5	486	tCt/tAt	6/18	1	2	FACETS	0.63	0.493	0.789	0.63	0.493	0.789	SUBCLONAL	1	TRUE	1	0.17	2		325	448	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467378	66467378	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	16	223	0	ENST00000273854.3:c.891G>T	p.Glu297Asp	p.E297D	ENST00000273854	NM_004439.5	297	gaG/gaT	3/18	1	2	FACETS	0.605	0.447	0.795	0.605	0.447	0.795	SUBCLONAL	1	TRUE	1	0.17	2		223	311	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143129578	143129578	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	27	255	0	ENST00000262992.4:c.1072G>T	p.Asp358Tyr	p.D358Y	ENST00000262992	NM_001101669.1	358	Gat/Tat	12/24	1	2	FACETS	0.951	0.758	1	0.951	0.758	1	CLONAL	1	TRUE	1	0.17	2		255	334	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176614	56176614	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	46	354	0	ENST00000399503.3:c.2164G>T	p.Glu722Ter	p.E722*	ENST00000399503	NM_005921.1	722	Gaa/Taa	12/20	1	2	FACETS	0.87	0.732	1	0.87	0.732	1	CLONAL	1	TRUE	1	0.17	2		354	622	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177954	56177954	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	55	408	0	ENST00000399503.3:c.2927C>A	p.Ser976Tyr	p.S976Y	ENST00000399503	NM_005921.1	976	tCc/tAc	14/20	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.17	2		408	589	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754855	57754855	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	30	321	0	ENST00000274289.3:c.335T>G	p.Ile112Ser	p.I112S	ENST00000274289	NM_006622.3	112	aTt/aGt	2/14	1	2	FACETS	0.661	0.531	0.809	0.661	0.531	0.809	SUBCLONAL	1	TRUE	1	0.17	2		321	534	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592171	67592171	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	14	192	0	ENST00000274335.5:c.1985+2T>G		p.X662_splice	ENST00000274335		662			1	2	FACETS	0.622	0.449	0.831	0.622	0.449	0.831	SUBCLONAL	1	TRUE	1	0.17	2		192	265	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80040402	80040402	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	38	381	0	ENST00000265081.6:c.1731G>T	p.Lys577Asn	p.K577N	ENST00000265081	NM_002439.4	577	aaG/aaT	12/24	1	2	FACETS	0.81	0.669	0.968	0.81	0.669	0.968	CLONAL	1	TRUE	1	0.17	2		381	552	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675572	86675572	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	22	257	0	ENST00000274376.6:c.2508A>C	p.Glu836Asp	p.E836D	ENST00000274376	NM_002890.2	836	gaA/gaC	19/25	1	2	FACETS	0.915	0.71	1	0.915	0.71	1	CLONAL	1	TRUE	1	0.17	2		257	283	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267600319	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	33	305	0	ENST00000257430.4:c.4199C>T	p.Ser1400Leu	p.S1400L	ENST00000257430	NM_000038.5	1400	tCg/tTg	16/16	1	2	FACETS	0.761	0.619	0.922	0.761	0.619	0.922	CLONAL	1	TRUE	1	0.17	2		305	510	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923370	131923370	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1441715028	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	26	205	0	ENST00000265335.6:c.873G>T	p.Glu291Asp	p.E291D	ENST00000265335		291	gaG/gaT	6/25	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.17	2		205	270	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176684115	176684115	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	50	417	0	ENST00000439151.2:c.4929T>G	p.Cys1643Trp	p.C1643W	ENST00000439151	NM_022455.4	1643	tgT/tgG	13/23	1	2	FACETS	0.839	0.711	0.981	0.839	0.711	0.981	CLONAL	1	TRUE	1	0.17	2		417	701	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052875	180052875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143813005	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	53	719	0	ENST00000261937.6:c.1415G>A	p.Arg472His	p.R472H	ENST00000261937	NM_182925.4	472	cGt/cAt	10/30	1	2	FACETS	0.785	0.668	0.914	0.785	0.668	0.914	CLONAL	1	TRUE	1	0.17	2		719	794	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288896	33288896	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	32	440	0	ENST00000374542.5:c.656A>G	p.Asp219Gly	p.D219G	ENST00000374542	NM_001141970.1	219	gAc/gGc	3/8	1	2	FACETS	0.751	0.609	0.913	0.751	0.609	0.913	CLONAL	1	TRUE	1	0.17	2		440	501	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109308751	109308751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	22	271	0	ENST00000436639.2:c.1652C>T	p.Thr551Ile	p.T551I	ENST00000436639	NM_014454.2	551	aCc/aTc	10/10	1	2	FACETS	0.822	0.637	1	0.822	0.637	1	CLONAL	1	TRUE	1	0.17	2		271	315	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710770	117710770	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1310552526	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	58	378	0	ENST00000368508.3:c.1502G>A	p.Ser501Asn	p.S501N	ENST00000368508	NM_002944.2	501	aGt/aAt	12/43	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.17	2		378	500	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718123	117718123	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	44	530	0	ENST00000368508.3:c.734G>T	p.Arg245Ile	p.R245I	ENST00000368508	NM_002944.2	245	aGa/aTa	7/43	1	2	FACETS	0.778	0.651	0.92	0.778	0.651	0.92	CLONAL	1	TRUE	1	0.17	2		530	665	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001305	150001305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568586257	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	33	555	0	ENST00000253339.5:c.2299C>T	p.Arg767Cys	p.R767C	ENST00000253339		767	Cgt/Tgt	4/7	1	2	FACETS	0.778	0.633	0.942	0.778	0.633	0.942	CLONAL	1	TRUE	1	0.17	2		555	499	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528608	157528608	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	49	646	0	ENST00000346085.5:c.6333C>A	p.Phe2111Leu	p.F2111L	ENST00000346085	NM_020732.3	2111	ttC/ttA	20/20	1	2	FACETS	0.691	0.584	0.81	0.691	0.584	0.81	SUBCLONAL	1	TRUE	1	0.17	2		646	834	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14026311	14026311	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	23	219	0	ENST00000405192.2:c.134-1G>T		p.X45_splice	ENST00000405192	NM_001163147.1	45			1	2	FACETS	0.808	0.63	1	0.808	0.63	1	CLONAL	1	TRUE	1	0.17	2		219	335	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509660	106509660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757849968	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	41	511	0	ENST00000359195.3:c.1654C>T	p.Arg552Cys	p.R552C	ENST00000359195	NM_002649.2	552	Cgc/Tgc	2/11	1	2	FACETS	0.728	0.605	0.865	0.728	0.605	0.865	SUBCLONAL	1	TRUE	1	0.17	2		511	663	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411694	116411694	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	80	679	1	ENST00000397752.3:c.2873G>T	p.Arg958Ile	p.R958I	ENST00000397752	NM_000245.2	958	aGa/aTa	13/21	1	2	FACETS	0.977	0.858	1	0.977	0.858	1	CLONAL	1	TRUE	1	0.17	2		680	963	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845550	151845550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753793539	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	56	681	1	ENST00000262189.6:c.13462G>A	p.Ala4488Thr	p.A4488T	ENST00000262189	NM_170606.2	4488	Gcc/Acc	52/59	1	2	FACETS	0.812	0.694	0.942	0.812	0.694	0.942	CLONAL	1	TRUE	1	0.17	2		682	811	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345765	152345765	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	39	306	0	ENST00000359321.1:c.805T>G	p.Phe269Val	p.F269V	ENST00000359321	NM_005431.1	269	Ttt/Gtt	3/3	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.17	2		306	437	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345770	152345770	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	39	313	0	ENST00000359321.1:c.800A>T	p.Lys267Ile	p.K267I	ENST00000359321	NM_005431.1	267	aAa/aTa	3/3	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.17	2		313	438	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189002	38189002	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	58	580	0	ENST00000317025.8:c.1012G>T	p.Glu338Ter	p.E338*	ENST00000317025	NM_023034.1	338	Gaa/Taa	5/24	1	2	FACETS	0.733	0.628	0.848	0.733	0.628	0.848	SUBCLONAL	1	TRUE	1	0.17	2		580	931	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931880	68931880	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	49	522	0	ENST00000288368.4:c.310G>T	p.Glu104Ter	p.E104*	ENST00000288368	NM_024870.2	104	Gaa/Taa	3/40	1	2	FACETS	0.798	0.675	0.935	0.798	0.675	0.935	CLONAL	1	TRUE	1	0.17	2		522	722	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066740	5066740	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777015472	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	26	298	0	ENST00000381652.3:c.1277G>A	p.Arg426Gln	p.R426Q	ENST00000381652	NM_004972.3	426	cGa/cAa	10/25	1	2	FACETS	0.894	0.709	1	0.894	0.709	1	CLONAL	1	TRUE	1	0.17	2		298	342	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436620	8436620	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	25	407	0	ENST00000356435.5:c.4058A>T	p.Asp1353Val	p.D1353V	ENST00000356435		1353	gAc/gTc	24/35	1	2	FACETS	0.605	0.476	0.755	0.605	0.476	0.755	SUBCLONAL	1	TRUE	1	0.17	2		407	486	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518099	8518099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764400127	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	39	395	0	ENST00000356435.5:c.1292C>T	p.Ser431Leu	p.S431L	ENST00000356435		431	tCg/tTg	10/35	1	2	FACETS	0.837	0.693	0.998	0.837	0.693	0.998	CLONAL	1	TRUE	1	0.17	2		395	548	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916549	39916549	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	51	579	0	ENST00000378444.4:c.4454A>G	p.Asn1485Ser	p.N1485S	ENST00000378444	NM_001123385.1	1485	aAc/aGc	11/15	1	2	FACETS	0.632	0.535	0.739	0.632	0.535	0.739	SUBCLONAL	1	TRUE	1	0.17	2		579	949	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932599	39932599	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	66	712	0	ENST00000378444.4:c.2000C>A	p.Ala667Asp	p.A667D	ENST00000378444	NM_001123385.1	667	gCt/gAt	4/15	1	2	FACETS	0.704	0.609	0.808	0.704	0.609	0.808	SUBCLONAL	1	TRUE	1	0.17	2		712	1103	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650283	48650283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	47	651	0	ENST00000376670.3:c.253G>A	p.Glu85Lys	p.E85K	ENST00000376670	NM_002049.3	85	Gag/Aag	3/6	1	2	FACETS	0.653	0.549	0.768	0.653	0.549	0.768	SUBCLONAL	1	TRUE	1	0.17	2		651	847	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352995	70352995	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	47	588	0	ENST00000374080.3:c.4550A>G	p.Asp1517Gly	p.D1517G	ENST00000374080		1517	gAc/gGc	33/45	1	2	FACETS	0.641	0.539	0.754	0.641	0.539	0.754	SUBCLONAL	1	TRUE	1	0.17	2		588	863	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855911	76855911	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	23	322	0	ENST00000373344.5:c.5689G>T	p.Glu1897Ter	p.E1897*	ENST00000373344	NM_000489.3	1897	Gaa/Taa	23/35	1	2	FACETS	0.605	0.471	0.762	0.605	0.471	0.762	SUBCLONAL	1	TRUE	1	0.17	2		322	447	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937351	76937351	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	27	398	0	ENST00000373344.5:c.3397G>T	p.Glu1133Ter	p.E1133*	ENST00000373344	NM_000489.3	1133	Gaa/Taa	9/35	1	2	FACETS	0.73	0.58	0.902	0.73	0.58	0.902	CLONAL	1	TRUE	1	0.17	2		398	435	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611923	100611923	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	64	567	0	ENST00000308731.7:c.1198A>C	p.Lys400Gln	p.K400Q	ENST00000308731	NM_000061.2	400	Aag/Cag	14/19	1	2	FACETS	0.889	0.768	1	0.889	0.768	1	CLONAL	1	TRUE	1	0.17	2		567	847	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599333	55599333	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913682	NA	P-0052855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	44	575	0	ENST00000288135.5:c.2459A>T	p.Asp820Val	p.D820V	ENST00000288135	NM_000222.2	820	gAt/gTt	17/21	0.449765170576581	1	FACETS	0.548	0.466	0.635	0.548	0.466	0.635	SUBCLONAL	1	TRUE	0	0.631633864998539	1		575	174	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148875	119148875	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs397517076	NA	P-0052855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	41	334	0	ENST00000264033.4:c.1096-1G>T		p.X366_splice	ENST00000264033	NM_005188.3	366			0.631633864998539	1	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	0	0.631633864998539	1		334	86	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0052856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	118	431	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.163142150968939	3	FACETS	1	0.978	1	0.427	0.386	0.47	INDETERMINATE	1	FALSE	0	0.34693791129105	3		431	623	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0052856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	35	426	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	0.171439587112551	3	FACETS	0.415	0.339	0.5	0.138	0.113	0.167	INDETERMINATE	1	FALSE	0	0.34693791129105	3		426	571	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912149	114912149	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	101	508	0	ENST00000543371.1:c.1219C>T	p.Arg407Ter	p.R407*	ENST00000543371	NM_001198531.1	407	Cga/Tga	11/14	0.163713868589246	4	FACETS	1	0.938	1	0.535	0.478	0.595	INDETERMINATE	1	FALSE	2	0.34693791129105	4		508	733	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651549	206651550	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	94	567	4	ENST00000367120.3:c.860dup	p.Glu288GlyfsTer17	p.E288Gfs*17	ENST00000367120	NM_014002.3	287	gtg/gTtg	9/22	0.13177822013955	3	FACETS	1	0.959	1	0.578	0.516	0.644	INDETERMINATE	1	FALSE	1	0.34693791129105	3		571	550	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230394	46230394	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	94	395	0	ENST00000334344.6:c.728A>G	p.Asp243Gly	p.D243G	ENST00000334344	NM_152641.2	243	gAt/gGt	7/21	0.34693791129105	5	FACETS	1	0.977	1	0.465	0.414	0.518	CLONAL	1	FALSE	2	0.34693791129105	5		395	591	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130337	11130337	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	126	591	0	ENST00000358026.2:c.2576C>A	p.Thr859Lys	p.T859K	ENST00000358026	NM_001128849.1	859	aCg/aAg	18/36	0.199349574668437	2	FACETS	1	0.966	1	0.568	0.516	0.624	INDETERMINATE	1	FALSE	0	0.34693791129105	2		591	639	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801095	135801095	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	53	508	0	ENST00000298552.3:c.242G>C	p.Gly81Ala	p.G81A	ENST00000298552	NM_001162426.1	81	gGc/gCc	5/23	1	2	FACETS	0.773	0.66	0.896	0.773	0.66	0.896	SUBCLONAL	1	FALSE	1	0.306103891767523	2		508	448	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627686	37627686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	93	668	3	ENST00000447079.4:c.1601C>T	p.Ser534Phe	p.S534F	ENST00000447079	NM_015083.1	534	tCt/tTt	2/14	0.306103891767523	4	FACETS	1	0.927	1			1	CLONAL	1	FALSE	NA	0.306103891767523	4		671	752	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587781845	NA	P-0052869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	294	823	0	ENST00000269305.4:c.511G>T	p.Glu171Ter	p.E171*	ENST00000269305	NM_001126112.2	171	Gag/Tag	5/11	0.258000435504756	1	FACETS	1	0.992	1	1	0.992	1	INDETERMINATE	1	TRUE	0	0.471298265573307	1		823	742	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441821	49441821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202217665	NA	P-0052869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	170	546	3	ENST00000301067.7:c.4163G>A	p.Arg1388Gln	p.R1388Q	ENST00000301067	NM_003482.3	1388	cGg/cAg	14/54	0.297778422005592	3	FACETS	1	0.98	1	0.596	0.549	0.645	CLONAL	1	TRUE	1	0.471298265573307	3		549	748	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865041	57865041	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	67	759	0	ENST00000228682.2:c.2518G>T	p.Gly840Trp	p.G840W	ENST00000228682	NM_005269.2	840	Ggg/Tgg	12/12	0.297778422005592	3	FACETS	0.384	0.333	0.44	0.192	0.166	0.22	SUBCLONAL	1	TRUE	1	0.471298265573307	3		759	914	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120824	115120839	+	frameshift_variant	Frame_Shift_Del	DEL	GCCAGGGCGCCCGGCA	GCCAGGGCGCCCGGCA	-	rs774642194	NA	P-0052869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	164	525	0	ENST00000257566.3:c.167_182del	p.Leu56ProfsTer27	p.L56Pfs*27	ENST00000257566	NM_016569.3	56	cTGCCGGGCGCCCTGGCc/cc	1/8	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.471298265573307	2		525	556	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119721071	119721086	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CTGCCGTCCTTGTCTC	CTGCCGTCCTTGTCTC	-	novel	NA	P-0052869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	25	394	0	ENST00000316626.5:c.89_104del	p.Arg30ThrfsTer3	p.R30Tfs*3	ENST00000316626		30	aGAGACAAGGACGGCAGc/ac	2/12	NA	2	FACETS	0.231	0.181	0.288			1	INDETERMINATE	1	TRUE	NA	0.471298265573307	2		394	459	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984333	72984369	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAGAGCGCCTGAGCCATAAGGAGCTGGGCCTTACCT	AAAGAGCGCCTGAGCCATAAGGAGCTGGGCCTTACCT	CC	novel	NA	P-0052869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	78	279	0	ENST00000268489.5:c.3215_3216+35delinsGG		p.X1072_splice	ENST00000268489	NM_006885.3	1072		3/10	0.471298265573307	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	0	0.471298265573307	1		279	247	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0052870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	52	305	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.830257213473151	2		305	123	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0052870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	216	658	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.830257213473151	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.830257213473151	2		658	256	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355963	73355964	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0052870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	61	591	0	ENST00000377767.4:c.7_8del	p.Lys3ValfsTer68	p.K3Vfs*68	ENST00000377767	NM_014953.3	3	AAg/g	1/21	1	2	FACETS	0.474	0.412	0.541	0.474	0.412	0.541	SUBCLONAL	1	TRUE	1	0.830257213473151	2		591	310	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564599	41564599	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	55	599	0	ENST00000263253.7:c.4021G>C	p.Ala1341Pro	p.A1341P	ENST00000263253	NM_001429.3	1341	Gca/Cca	24/31	1	2	FACETS	0.399	0.343	0.46	0.399	0.343	0.46	SUBCLONAL	1	TRUE	1	0.830257213473151	2		599	332	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158446	106158446	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	25	256	0	ENST00000380013.4:c.3347T>C	p.Ile1116Thr	p.I1116T	ENST00000380013	NM_001127208.2	1116	aTa/aCa	3/11	0.830257213473151	2	FACETS	0.312	0.247	0.385	0.156	0.123	0.193	SUBCLONAL	1	TRUE	0	0.830257213473151	2		256	193	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870265	44870265	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0052870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	119	185	0	ENST00000377967.4:c.443+1G>T		p.X148_splice	ENST00000377967	NM_021140.2	148			1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.830257213473151	1		185	133	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720877	89720879	+	splice_donor_variant,intron_variant	Splice_Site	DEL	TCA	TCA	-	novel	NA	P-0052870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	55	369	0	ENST00000371953.3:c.1026+2_1026+4del		p.X342_splice	ENST00000371953	NM_000314.4	342			0.830257213473151	1	FACETS	0.934	0.845	1	0.934	0.845	1	CLONAL	1	TRUE	0	0.830257213473151	1		369	83	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	588	634	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.561446232114158	3	FACETS	0.9	0.873	0.927			1	CLONAL	3	TRUE	NA	0.60713839197389	3		634	935	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371709	89371709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1010844836	NA	P-0052871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	164	683	0	ENST00000301030.4:c.131G>A	p.Arg44His	p.R44H	ENST00000301030	NM_001256183.1	44	cGt/cAt	4/13	1	2	FACETS	0.76	0.699	0.823	0.76	0.699	0.823	SUBCLONAL	1	TRUE	1	0.60713839197389	2		683	711	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73340165	73340165	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1234341757	NA	P-0052871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	68	177	0	ENST00000377767.4:c.1915T>G	p.Phe639Val	p.F639V	ENST00000377767	NM_014953.3	639	Ttc/Gtc	15/21	0.563824623658008	3	FACETS	0.882	0.773	0.998	0.441	0.386	0.499	CLONAL	1	TRUE	1	0.60713839197389	3		177	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0052872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	167	608	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.590996910958336	2	FACETS	0.883	0.832	0.934	0.883	0.832	0.934	CLONAL	2	TRUE	0	0.684887738690364	2		608	276	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710626	114710627	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0052872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	298	409	0	ENST00000543371.1:c.115_116del	p.Arg39GlyfsTer4	p.R39Gfs*4	ENST00000543371	NM_001198531.1	37	gcAGag/gcag	1/14	0.556686657810039	4	FACETS	0.953	0.91	0.995	0.953	0.91	0.995	CLONAL	3	TRUE	1	0.684887738690364	4		409	513	SUCCESS
APC	324	MSKCC	GRCh37	5	112155042	112155042	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0052872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	152	386	0	ENST00000257430.4:c.1312+1G>C		p.X438_splice	ENST00000257430	NM_000038.5	438			0.684887738690364	3	FACETS	0.955	0.906	1	0.955	0.906	1	CLONAL	3	TRUE	0	0.684887738690364	3		386	208	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056080	26056080	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	107	420	0	ENST00000343677.2:c.577G>T	p.Val193Leu	p.V193L	ENST00000343677	NM_005319.3	193	Gtg/Ttg	1/1	0.559510562827346	6	FACETS	0.979	0.886	1			1	CLONAL	2	TRUE	NA	0.684887738690364	6		420	378	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	40	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.747597038314434	2		429	100	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0052873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	74	117	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.975	0.87	1	0.975	0.87	1	CLONAL	1	TRUE	1	0.747597038314434	2		117	203	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023805	27023805	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	85	150	0	ENST00000324856.7:c.911C>A	p.Ser304Ter	p.S304*	ENST00000324856	NM_006015.4	304	tCg/tAg	1/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.747597038314434	2		150	203	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533012	63533012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200201811	NA	P-0052873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	127	323	2	ENST00000307078.5:c.1882C>T	p.Arg628Trp	p.R628W	ENST00000307078	NM_004655.3	628	Cgg/Tgg	7/11	0.748135372836508	3	FACETS	1	0.941	1	0.52	0.474	0.567	CLONAL	1	TRUE	1	0.747597038314434	3		325	449	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087955	27087955	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	119	250	0	ENST00000324856.7:c.2242C>T	p.Gln748Ter	p.Q748*	ENST00000324856	NM_006015.4	748	Caa/Taa	6/20	1	2	FACETS	0.989	0.905	1	0.989	0.905	1	CLONAL	1	TRUE	1	0.747597038314434	2		250	322	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098589	108098590	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0052873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	67	36	0	ENST00000278616.4:c.161_162del	p.Tyr54PhefsTer8	p.Y54Ffs*8	ENST00000278616	NM_000051.3	53	aaATat/aaat	3/63	1	2	FACETS	0.919	0.814	1	0.919	0.814	1	CLONAL	1	TRUE	1	0.747597038314434	2		36	195	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229321	36229321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	118	328	0	ENST00000222270.7:c.8011C>T	p.His2671Tyr	p.H2671Y	ENST00000222270	NM_014727.1	2671	Cac/Tac	37/37	1	2	FACETS	0.957	0.874	1	0.957	0.874	1	CLONAL	1	TRUE	1	0.747597038314434	2		328	330	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015156	37015156	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	130	218	0	ENST00000358127.4:c.248T>C	p.Ile83Thr	p.I83T	ENST00000358127	NM_001280556.1	83	aTt/aCt	3/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.747597038314434	2		218	304	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771894	135771894	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	82	270	0	ENST00000298552.3:c.3223C>G	p.Pro1075Ala	p.P1075A	ENST00000298552	NM_001162426.1	1075	Ccc/Gcc	23/23	1	2	FACETS	0.719	0.641	0.802	0.719	0.641	0.802	SUBCLONAL	1	TRUE	1	0.747597038314434	2		270	305	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0052874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	12	550	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.175	0.122	0.241	0.175	0.122	0.241	SUBCLONAL	1	FALSE	1	0.383645361133451	2		550	357	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0052874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	32	778	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.363042341792946	1	FACETS	0.255	0.206	0.31	0.255	0.206	0.31	SUBCLONAL	1	FALSE	0	0.383645361133451	1		779	529	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410928	31410928	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	55	635	0	ENST00000344624.3:c.3592G>C	p.Glu1198Gln	p.E1198Q	ENST00000344624		1198	Gag/Cag	28/33	1	2	FACETS	0.427	0.364	0.495	0.427	0.364	0.495	SUBCLONAL	1	FALSE	1	0.383645361133451	2		635	672	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499382	89499382	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	130	420	0	ENST00000336596.2:c.2552C>G	p.Ala851Gly	p.A851G	ENST00000336596	NM_005233.5	851	gCt/gGt	15/17	0.466554762036589	2	FACETS	0.997	0.908	1	0.498	0.454	0.545	CLONAL	1	TRUE	0	0.469148742722102	2		420	556	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346219	152346220	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs764640893	NA	P-0052875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	147	527	3	ENST00000359321.1:c.350dup	p.Leu117PhefsTer6	p.L117Ffs*6	ENST00000359321	NM_005431.1	117	ttg/ttTg	3/3	0.469148742722102	3	FACETS	0.911	0.832	0.994	0.456	0.416	0.497	CLONAL	1	TRUE	1	0.469148742722102	3		530	849	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578476	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0052875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	469	1022	0	ENST00000269305.4:c.454_455del	p.Pro152AlafsTer28	p.P152Afs*28	ENST00000269305	NM_001126112.2	152	CCg/g	5/11	0.466554762036589	2	FACETS	0.97	0.93	1	0.97	0.93	1	CLONAL	2	TRUE	0	0.469148742722102	2		1022	1031	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094873	11094873	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	462	1164	0	ENST00000358026.2:c.46C>G	p.Pro16Ala	p.P16A	ENST00000358026	NM_001128849.1	16	Cct/Gct	2/36	0.466554762036589	2	FACETS	0.938	0.899	0.977	0.938	0.899	0.977	CLONAL	2	TRUE	0	0.469148742722102	2		1164	1050	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245023	53245023	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	179	705	0	ENST00000375401.3:c.917C>G	p.Thr306Ser	p.T306S	ENST00000375401	NM_004187.3	306	aCc/aGc	7/26	0.469148742722102	3	FACETS	0.847	0.78	0.917	0.424	0.39	0.459	CLONAL	1	TRUE	1	0.469148742722102	3		705	1112	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs786202525	NA	P-0052876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	46	875	7	ENST00000269305.4:c.532del	p.His178ThrfsTer69	p.H178Tfs*69	ENST00000269305	NM_001126112.2	178	Cac/ac	5/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		882	338	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591104	67591115	+	inframe_deletion	In_Frame_Del	DEL	TTAAACCAGACC	TTAAACCAGACC	-	novel	NA	P-0052876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	23	286	1	ENST00000274335.5:c.1700_1711del	p.Lys567_Leu570del	p.K567_L570del	ENST00000274335		566	aTTAAACCAGACCtt/att	12/15	0.19249603440299	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		287	253	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720855	89720856	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0052876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	31	426	1	ENST00000371953.3:c.1007dup	p.Tyr336Ter	p.Y336*	ENST00000371953	NM_000314.4	336	tac/tAac	8/9	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		427	291	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0052877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	32	411	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.909	0.738	1	0.909	0.738	1	CLONAL	1	TRUE	1	0.18	2		411	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0052877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	42	509	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.18	2		509	446	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0052878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	63	430	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.261059590919033	4	FACETS	1	0.902	1	1	0.902	1	CLONAL	3	FALSE	1	0.321175470341112	4		430	169	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0052878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	27	316	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.337264013456337	3	FACETS	1	0.883	1	0.574	0.461	0.7	CLONAL	1	FALSE	1	0.321175470341112	3		316	170	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0052878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	143	633	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.275526205158786	3	FACETS	1	0.935	1	0.681	0.625	0.739	CLONAL	2	FALSE	0	0.321175470341112	3		633	506	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0052878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	13	194	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.337264013456337	3	FACETS	1	0.786	1	0.553	0.4	0.732	CLONAL	1	FALSE	1	0.321175470341112	3		194	85	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587781525	NA	P-0052879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	139	653	0	ENST00000269305.4:c.842A>G	p.Asp281Gly	p.D281G	ENST00000269305	NM_001126112.2	281	gAc/gGc	8/11	0.221741413488016	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.222849635295342	1		653	899	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876472	35876472	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	89	443	0	ENST00000303115.3:c.1264C>T	p.Gln422Ter	p.Q422*	ENST00000303115	NM_002185.3	422	Caa/Taa	8/8	1	2	FACETS	0.978	0.866	1	0.978	0.866	1	CLONAL	1	TRUE	1	0.222849635295342	2		443	817	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0052880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	230	411	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.1460433902526	6	FACETS	0.896	0.844	0.947			1	INDETERMINATE	4	TRUE	NA	0.541382874718786	6		411	494	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936528	49936528	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	69	653	0	ENST00000296474.3:c.1399A>C	p.Met467Leu	p.M467L	ENST00000296474	NM_002447.2	467	Atg/Ctg	2/20	1	2	FACETS	0.301	0.262	0.344	0.301	0.262	0.344	SUBCLONAL	1	TRUE	1	0.541382874718786	2		653	846	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792731	33792732	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCGGGT	rs762459325	NA	P-0052882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	18	55	2	ENST00000498907.2:c.584_589dup	p.His195_Pro196dup	p.H195_P196dup	ENST00000498907	NM_004364.3	195	ccg/cACCCGCcg	1/1	1	2	FACETS	0.945	0.725	1	0.945	0.725	1	CLONAL	1	TRUE	1	0.418530491666007	2		57	91	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879796	37879798	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0052882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	1569	520	0	ENST00000269571.5:c.2092_2094del	p.Glu698del	p.E698del	ENST00000269571		697	gtGGAg/gtg	18/27	0.418530491666007	18	FACETS	1	0.994	1			1	CLONAL	16	TRUE	NA	0.418530491666007	18		520	2004	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102098286	102098286	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	67	367	0	ENST00000282441.5:c.1250T>G	p.Leu417Arg	p.L417R	ENST00000282441	NM_001130145.2	417	cTg/cGg	8/9	1	2	FACETS	0.536	0.466	0.612	0.536	0.466	0.612	SUBCLONAL	1	TRUE	1	0.418530491666007	2		367	597	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89871715	89871715	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	70	493	0	ENST00000389301.3:c.682G>T	p.Ala228Ser	p.A228S	ENST00000389301	NM_000135.2	228	Gct/Tct	7/43	1	2	FACETS	0.506	0.441	0.577	0.506	0.441	0.577	SUBCLONAL	1	TRUE	1	0.418530491666007	2		493	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577503	7577508	+	inframe_deletion	In_Frame_Del	DEL	AGTCTT	AGTCTT	-	novel	NA	P-0052882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	143	521	0	ENST00000269305.4:c.773_778del	p.Glu258_Ser260delinsAla	p.E258_S260delinsA	ENST00000269305	NM_001126112.2	258	gAAGACTcc/gcc	7/11	0.386805670549898	1	FACETS	0.917	0.84	0.998	0.917	0.84	0.998	CLONAL	1	TRUE	0	0.418530491666007	1		521	589	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0052884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	105	551	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.224772572580735	2		551	930	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032404	10032404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142566406	NA	P-0052884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	18	224	1	ENST00000330684.3:c.419C>T	p.Pro140Leu	p.P140L	ENST00000330684	NM_001134407.1	140	cCg/cTg	3/13	1	2	FACETS	0.46	0.346	0.596	0.46	0.346	0.596	SUBCLONAL	1	TRUE	1	0.224772572580735	2		225	348	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839943	27839943	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	155	648	0	ENST00000328488.2:c.151G>T	p.Glu51Ter	p.E51*	ENST00000328488	NM_003533.2	51	Gag/Tag	1/1	0.106068309125226	4	FACETS	1	0.982	1	0.65	0.593	0.709	INDETERMINATE	1	TRUE	2	0.224772572580735	4		648	1300	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644524	3644524	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs554989399	NA	P-0052884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	82	653	0	ENST00000294008.3:c.2090C>T	p.Thr697Met	p.T697M	ENST00000294008	NM_032444.2	697	aCg/aTg	10/15	1	2	FACETS	0.616	0.541	0.696	0.616	0.541	0.696	SUBCLONAL	1	TRUE	1	0.224772572580735	2		653	1185	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060712	38060748	+	frameshift_variant	Frame_Shift_Del	DEL	TATTGCAGTGCCTGTTCGTATGCCTTGAAGTCCAGCT	TATTGCAGTGCCTGTTCGTATGCCTTGAAGTCCAGCT	-	novel	NA	P-0052884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1276	106	813	0	ENST00000250448.2:c.1241_1277del	p.Lys414ThrfsTer14	p.K414Tfs*14	ENST00000250448	NM_004496.3	414	aAGCTGGACTTCAAGGCATACGAACAGGCACTGCAATAc/ac	2/2	1	2	FACETS	0.682	0.609	0.76	0.682	0.609	0.76	SUBCLONAL	1	TRUE	1	0.224772572580735	2		813	1382	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971164	21971166	+	inframe_deletion	In_Frame_Del	DEL	AGC	AGC	-	novel	NA	P-0052884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	69	405	0	ENST00000304494.5:c.192_194del	p.Leu65del	p.L65del	ENST00000304494	NM_000077.4	64	ctGCTc/ctc	2/3	0.224772572580735	1	FACETS	0.827	0.72	0.943	0.827	0.72	0.943	CLONAL	1	TRUE	0	0.224772572580735	1		405	659	SUCCESS
APC	324	MSKCC	GRCh37	5	112176863	112176863	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1270783041	NA	P-0052885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	173	303	4	ENST00000257430.4:c.5572C>T	p.Arg1858Ter	p.R1858*	ENST00000257430	NM_000038.5	1858	Cga/Tga	16/16	0.841792922290119	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.841792922290119	1		307	233	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155491	106155491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	178	302	1	ENST00000380013.4:c.392G>A	p.Arg131Lys	p.R131K	ENST00000380013	NM_001127208.2	131	aGa/aAa	3/11	0.431823994384853	1	FACETS	0.71	0.666	0.754	0.71	0.666	0.754	INDETERMINATE	1	TRUE	0	0.841792922290119	1		303	345	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416197	416197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	210	325	7	ENST00000399788.2:c.3989C>T	p.Ser1330Phe	p.S1330F	ENST00000399788	NM_001042603.1	1330	tCt/tTt	24/28	NA	2	FACETS	1	0.957	1			1	INDETERMINATE	1	TRUE	NA	0.841792922290119	2		332	487	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0052890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	243	784	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	0.753	0.705	0.803	1	0.993	1	SUBCLONAL	2	TRUE	1	0.352955569320775	2		784	914	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0052890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	101	305	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.352955569320775	2		305	394	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	99	213	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	1	1	FACETS	0.875	0.794	0.958	1	0.987	1	CLONAL	2	TRUE	0	0.352955569320775	1		213	264	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949124	44949124	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	88	225	0	ENST00000377967.4:c.3685C>T	p.Gln1229Ter	p.Q1229*	ENST00000377967	NM_021140.2	1229	Cag/Tag	25/29	1	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.352955569320775	1		225	309	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0052890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	95	234	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.767	0.689	0.848	1	0.983	1	SUBCLONAL	2	TRUE	1	0.352955569320775	2		234	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0052890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	288	555	0	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	0.25613780498177	3	FACETS	0.85	0.803	0.897	0.85	0.803	0.897	CLONAL	3	TRUE	0	0.352955569320775	3		555	753	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458591	120458591	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	115	574	0	ENST00000256646.2:c.6754G>A	p.Asp2252Asn	p.D2252N	ENST00000256646	NM_024408.3	2252	Gat/Aat	34/34	1	2	FACETS	0.957	0.863	1	0.957	0.863	1	CLONAL	1	TRUE	1	0.352955569320775	2		574	681	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253446	226253446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	31	68	0	ENST00000366813.1:c.218G>A	p.Arg73Gln	p.R73Q	ENST00000366813		73	cGa/cAa	2/3	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.352955569320775	2		68	133	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727920	41727920	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138094666	NA	P-0052890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	68	782	2	ENST00000301178.4:c.545C>T	p.Thr182Met	p.T182M	ENST00000301178	NM_021913.4	182	aCg/aTg	4/20	1	2	FACETS	0.52	0.452	0.594	0.52	0.452	0.594	SUBCLONAL	1	TRUE	1	0.352955569320775	2		784	741	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858353	27858353	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138060838	NA	P-0052890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	291	768	0	ENST00000359303.2:c.218G>A	p.Arg73Gln	p.R73Q	ENST00000359303	NM_003535.2	73	cGa/cAa	1/1	0.352955569320775	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.352955569320775	3		768	896	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101089	26101089	+	start_lost	Translation_Start_Site	SNP	C	C	T	rs1559535727	NA	P-0052890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	105	593	0	ENST00000435504.4:c.3G>A	p.Met1?	p.M1?	ENST00000435504		1	atG/atA	1/13	0.251790537246495	3	FACETS	0.997	0.894	1	0.499	0.447	0.553	CLONAL	1	TRUE	1	0.352955569320775	3		593	702	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872210	45872210	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	162	670	0	ENST00000391945.4:c.224G>A	p.Arg75Lys	p.R75K	ENST00000391945	NM_000400.3	75	aGa/aAa	4/23	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.352955569320775	2		670	877	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244139	46244139	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	47	370	1	ENST00000334344.6:c.2233C>T	p.Gln745Ter	p.Q745*	ENST00000334344	NM_152641.2	745	Cag/Tag	15/21	0.352955569320775	3	FACETS	0.595	0.501	0.697			1	SUBCLONAL	1	TRUE	NA	0.352955569320775	3		371	527	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224384	36224384	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	165	871	1	ENST00000222270.7:c.6934C>T	p.Gln2312Ter	p.Q2312*	ENST00000222270	NM_014727.1	2312	Cag/Tag	28/37	1	2	FACETS	0.906	0.831	0.984	0.906	0.831	0.984	CLONAL	1	TRUE	1	0.352955569320775	2		872	1032	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023210	27023229	+	frameshift_variant	Frame_Shift_Del	DEL	AACGCGGGCCCTAGGCCCGC	AACGCGGGCCCTAGGCCCGC	-	novel	NA	P-0052890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	16	130	0	ENST00000324856.7:c.316_335del	p.Asn106ProfsTer4	p.N106Pfs*4	ENST00000324856	NM_006015.4	106	AACGCGGGCCCTAGGCCCGCc/c	1/20	1	2	FACETS	0.383	0.283	0.501	0.383	0.283	0.501	SUBCLONAL	1	TRUE	1	0.352955569320775	2		130	237	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101985049	101985049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	106	609	1	ENST00000282441.5:c.496G>A	p.Glu166Lys	p.E166K	ENST00000282441	NM_001130145.2	166	Gag/Aag	2/9	1	2	FACETS	0.722	0.647	0.802	0.722	0.647	0.802	SUBCLONAL	1	TRUE	1	0.352955569320775	2		610	832	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482785	67482785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	78	459	0	ENST00000327367.4:c.1189G>A	p.Glu397Lys	p.E397K	ENST00000327367	NM_005902.3	397	Gag/Aag	9/9	0.306171258773238	1	FACETS	0.581	0.51	0.656	0.581	0.51	0.656	SUBCLONAL	1	TRUE	0	0.352955569320775	1		459	627	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807926	3807926	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	133	450	0	ENST00000262367.5:c.3493T>A	p.Trp1165Arg	p.W1165R	ENST00000262367	NM_004380.2	1165	Tgg/Agg	18/31	0.352955569320775	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.352955569320775	1		450	578	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341600	89341600	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1400747745	NA	P-0052890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	70	536	0	ENST00000301030.4:c.7471-1G>A		p.X2491_splice	ENST00000301030	NM_001256183.1	2491			1	2	FACETS	0.69	0.602	0.785	0.69	0.602	0.785	SUBCLONAL	1	TRUE	1	0.352955569320775	2		536	575	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372171	45372171	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	212	332	0	ENST00000262160.6:c.998G>A	p.Gly333Glu	p.G333E	ENST00000262160	NM_005901.5	333	gGa/gAa	9/11	0.352955569320775	3	FACETS	0.869	0.814	0.925			1	CLONAL	3	TRUE	NA	0.352955569320775	3		332	542	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026581	48026581	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1469561474	NA	P-0052890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	83	380	1	ENST00000234420.5:c.1459G>A	p.Glu487Lys	p.E487K	ENST00000234420	NM_000179.2	487	Gag/Aag	4/10	0.251790537246495	3	FACETS	1	0.955	1	0.58	0.514	0.651	CLONAL	1	TRUE	1	0.352955569320775	3		381	477	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805482	1805482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	98	721	0	ENST00000260795.2:c.994G>A	p.Glu332Lys	p.E332K	ENST00000260795		332	Gag/Aag	7/17	1	2	FACETS	0.698	0.622	0.778	0.698	0.622	0.778	SUBCLONAL	1	TRUE	1	0.352955569320775	2		721	796	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157780	106157780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	23	288	0	ENST00000380013.4:c.2681C>T	p.Ser894Leu	p.S894L	ENST00000380013	NM_001127208.2	894	tCa/tTa	3/11	1	2	FACETS	0.449	0.351	0.563	0.449	0.351	0.563	SUBCLONAL	1	TRUE	1	0.352955569320775	2		288	290	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038436	180038436	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	138	815	1	ENST00000261937.6:c.3581C>T	p.Ser1194Leu	p.S1194L	ENST00000261937	NM_182925.4	1194	tCa/tTa	27/30	1	2	FACETS	0.875	0.796	0.958	0.875	0.796	0.958	CLONAL	1	TRUE	1	0.352955569320775	2		816	894	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56860182	56860182	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773485609	NA	P-0052890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	84	484	0	ENST00000519728.1:c.184G>A	p.Glu62Lys	p.E62K	ENST00000519728	NM_002350.3	62	Gag/Aag	4/13	0.251790537246495	3	FACETS	1	0.897	1	0.507	0.449	0.57	CLONAL	1	TRUE	1	0.352955569320775	3		484	552	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220350	98220350	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	63	470	0	ENST00000331920.6:c.3113G>T	p.Cys1038Phe	p.C1038F	ENST00000331920	NM_000264.3	1038	tGc/tTc	18/24	1	2	FACETS	0.766	0.664	0.876	0.766	0.664	0.876	SUBCLONAL	1	TRUE	1	0.352955569320775	2		470	466	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904974	101904974	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	79	264	0	ENST00000374994.4:c.962T>C	p.Val321Ala	p.V321A	ENST00000374994	NM_004612.2	321	gTt/gCt	5/9	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.352955569320775	2		264	411	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568571	41568575	+	frameshift_variant	Frame_Shift_Del	DEL	TTTCT	TTTCT	G	novel	NA	P-0052890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	69	485	0	ENST00000263253.7:c.4521_4525delinsG	p.Asp1507GlufsTer33	p.D1507Efs*33	ENST00000263253	NM_001429.3	1507	gaTTTCTgg/gaGgg	28/31	1	2	FACETS	0.776	0.677	0.882	0.776	0.677	0.882	SUBCLONAL	1	TRUE	1	0.352955569320775	2		485	504	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607823	46607824	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0052905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	123	750	0	ENST00000263734.3:c.2016_2017del	p.Pro673ThrfsTer42	p.P673Tfs*42	ENST00000263734	NM_001430.4	671	gTC/g	12/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.25	2		750	698	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916942	178916944	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	novel	NA	P-0052905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	78	376	0	ENST00000263967.3:c.330_332del	p.Lys111del	p.K111del	ENST00000263967	NM_006218.2	110	gAAAag/gag	2/21	0.282224396186018	3	FACETS	0.883	0.786	0.984	1	0.973	1	CLONAL	3	TRUE	1	0.25	3		376	265	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	25	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.678	0.538	0.836	0.678	0.538	0.836	SUBCLONAL	1	TRUE	1	0.384332556449875	2		429	192	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0052906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	109	741	0	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.384332556449875	3	FACETS	0.85	0.763	0.942	0.425	0.381	0.471	CLONAL	1	TRUE	1	0.384332556449875	3		741	796	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540977	187540977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200488891	NA	P-0052906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	61	363	0	ENST00000441802.2:c.6763C>T	p.Arg2255Cys	p.R2255C	ENST00000441802	NM_005245.3	2255	Cgc/Tgc	10/27	1	2	FACETS	0.939	0.815	1	0.939	0.815	1	CLONAL	1	TRUE	1	0.384332556449875	2		363	338	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711908	89711910	+	inframe_deletion	In_Frame_Del	DEL	TAT	TAT	-	rs587780711	NA	P-0052906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	50	514	0	ENST00000371953.3:c.532_534del	p.Tyr178del	p.Y178del	ENST00000371953	NM_000314.4	176	TAT/-	6/9	0.384332556449875	1	FACETS	0.553	0.471	0.643	0.553	0.471	0.643	SUBCLONAL	1	TRUE	0	0.384332556449875	1		514	380	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911305	32911305	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs55773834	NA	P-0052906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	103	546	0	ENST00000380152.3:c.2813C>A	p.Ala938Glu	p.A938E	ENST00000380152		938	gCa/gAa	11/27	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.384332556449875	2		546	491	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266460	41266460	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1223771101	NA	P-0052906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	73	388	0	ENST00000349496.5:c.257A>G	p.Tyr86Cys	p.Y86C	ENST00000349496	NM_001904.3	86	tAt/tGt	4/15	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.384332556449875	2		388	372	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0052908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	81	482	1	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.56771574046767	2	FACETS	0.864	0.784	0.944	0.864	0.784	0.944	CLONAL	2	TRUE	0	0.582472198392811	2		483	161	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882019	NA	P-0052908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	141	880	1	ENST00000269305.4:c.455del	p.Pro152ArgfsTer18	p.P152Rfs*18	ENST00000269305	NM_001126112.2	152	cCg/cg	5/11	0.367154136066128	3	FACETS	1	0.966	1	0.714	0.662	0.765	CLONAL	2	TRUE	0	0.582472198392811	3		881	292	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274897	41274897	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	74	462	0	ENST00000349496.5:c.1147T>C	p.Trp383Arg	p.W383R	ENST00000349496	NM_001904.3	383	Tgg/Cgg	8/15	0.494736873102679	3	FACETS	1	0.974	1	0.822	0.746	0.897	CLONAL	2	TRUE	0	0.582472198392811	3		462	133	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653803	89653810	+	frameshift_variant	Frame_Shift_Del	DEL	CTATGGGA	CTATGGGA	-	novel	NA	P-0052908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	15	345	0	ENST00000371953.3:c.101_108del	p.Ala34ValfsTer7	p.A34Vfs*7	ENST00000371953	NM_000314.4	34	gCTATGGGA/g	2/9	0.566900895201913	2	FACETS	0.92	0.729	1	0.92	0.729	1	CLONAL	2	TRUE	0	0.582472198392811	2		345	28	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	465682	465682	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	93	528	0	ENST00000399788.2:c.694A>G	p.Arg232Gly	p.R232G	ENST00000399788	NM_001042603.1	232	Aga/Gga	6/28	0.582472198392811	7	FACETS	1	0.931	1	0.778	0.703	0.855	CLONAL	3	TRUE	3	0.582472198392811	7		528	252	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424780	49424780	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0052908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	279	703	0	ENST00000301067.7:c.13567A>T	p.Lys4523Ter	p.K4523*	ENST00000301067	NM_003482.3	4523	Aag/Tag	40/54	0.514859776453368	5	FACETS	1	0.99	1	0.88	0.844	0.915	CLONAL	4	TRUE	0	0.582472198392811	5		703	408	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785814	50785814	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	12	366	0	ENST00000398568.2:c.804C>G	p.Asp268Glu	p.D268E	ENST00000398568	NM_001042412.1	268	gaC/gaG	4/18	0.543081185177594	3	FACETS	0.858	0.617	1	0.429	0.308	0.57	CLONAL	1	TRUE	1	0.582472198392811	3		366	62	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984427	72984427	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	67	705	1	ENST00000268489.5:c.3157G>T	p.Glu1053Ter	p.E1053*	ENST00000268489	NM_006885.3	1053	Gag/Tag	3/10	0.543081185177594	3	FACETS	1	0.886	1	0.505	0.443	0.571	CLONAL	1	TRUE	1	0.582472198392811	3		706	294	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227037	2227037	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	110	644	0	ENST00000398665.3:c.4517G>T	p.Gly1506Val	p.G1506V	ENST00000398665	NM_032482.2	1506	gGc/gTc	27/28	0.400879637520092	4	FACETS	0.859	0.78	0.94	0.859	0.78	0.94	CLONAL	2	TRUE	2	0.582472198392811	4		644	348	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225343033	225343033	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	52	510	0	ENST00000264414.4:c.2059G>T	p.Glu687Ter	p.E687*	ENST00000264414	NM_003590.4	687	Gag/Tag	15/16	0.467667438935253	3	FACETS	0.922	0.808	1	0.922	0.808	1	CLONAL	2	TRUE	1	0.582472198392811	3		510	125	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074284	30074284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762588182	NA	P-0052908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	76	420	1	ENST00000338641.4:c.1546C>T	p.Arg516Trp	p.R516W	ENST00000338641	NM_000268.3	516	Cgg/Tgg	14/16	0.551289551280176	4	FACETS	0.875	0.779	0.974			1	CLONAL	2	TRUE	NA	0.582472198392811	4		421	236	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39021158	39021158	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	28	354	0	ENST00000357387.3:c.178C>G	p.Leu60Val	p.L60V	ENST00000357387	NM_152756.3	60	Ctg/Gtg	3/38	0.509272040259733	4	FACETS	0.885	0.728	1	0.885	0.728	1	CLONAL	2	TRUE	2	0.582472198392811	4		354	86	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287622	33287622	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	91	542	0	ENST00000374542.5:c.1475G>T	p.Gly492Val	p.G492V	ENST00000374542	NM_001141970.1	492	gGa/gTa	6/8	0.588322261750328	5	FACETS	1	0.97	1	0.797	0.719	0.876	CLONAL	2	TRUE	2	0.582472198392811	5		542	245	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367288	50367288	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	54	429	1	ENST00000331340.3:c.95C>A	p.Pro32Gln	p.P32Q	ENST00000331340	NM_006060.4	32	cCg/cAg	3/8	0.509272040259733	4	FACETS	0.756	0.656	0.862	0.756	0.656	0.862	SUBCLONAL	2	TRUE	2	0.582472198392811	4		430	194	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737421	145737421	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	148	934	0	ENST00000428558.2:c.3266T>A	p.Leu1089Gln	p.L1089Q	ENST00000428558	NM_004260.3	1089	cTg/cAg	20/22	0.588322261750328	3	FACETS	0.812	0.75	0.876	0.541	0.5	0.584	CLONAL	2	TRUE	0	0.582472198392811	3		934	404	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519803	29519803	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	CAGGC	novel	NA	P-0052908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	16	600	0	ENST00000389048.3:c.1768delinsGCCTG	p.Leu590AlafsTer17	p.L590Afs*17	ENST00000389048	NM_004304.4	590	Ttg/GCCTGtg	9/29	0.467667438935253	3	FACETS	0.392	0.291	0.512	0.196	0.145	0.256	SUBCLONAL	1	TRUE	1	0.582472198392811	3		600	181	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0052909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	8	432	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.4	0.256	0.587	0.4	0.256	0.587	SUBCLONAL	1	TRUE	1	0.11	2		432	364	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0052909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	15	393	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.937	0.685	1	0.937	0.685	1	CLONAL	1	TRUE	1	0.11	2		393	291	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0052909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	18	377	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.839	0.631	1	0.839	0.631	1	CLONAL	1	TRUE	1	0.11	2		377	390	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0052909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	16	562	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.591	0.435	0.779	0.591	0.435	0.779	SUBCLONAL	1	TRUE	1	0.11	2		562	492	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087328	27087348	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTTATATATATGTTCTAGGA	TCTTATATATATGTTCTAGGA	-	novel	NA	P-0052909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	16	248	1	ENST00000324856.7:c.1921-16_1925del		p.X641_splice	ENST00000324856	NM_006015.4	641		5/20	1	2	FACETS	1	0.828	1	1	0.828	1	CLONAL	1	TRUE	1	0.11	2		249	249	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257148	198257148	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs765885503	NA	P-0052910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	17	359	0	ENST00000335508.6:c.3794A>G	p.Tyr1265Cys	p.Y1265C	ENST00000335508	NM_012433.2	1265	tAt/tGt	25/25	1	2	FACETS	0.786	0.591	1	0.786	0.591	1	CLONAL	1	TRUE	1	0.273633808395389	2		359	158	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0052911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	56	452	0	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	1	2	FACETS	0.821	0.703	0.948	0.821	0.703	0.948	CLONAL	1	TRUE	1	0.26	2		452	525	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443729	52443729	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0052911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	80	691	0	ENST00000460680.1:c.67+1G>T		p.X23_splice	ENST00000460680	NM_004656.3	23			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.26	2		691	524	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366536	118366536	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	30	361	0	ENST00000534358.1:c.5485G>T	p.Ala1829Ser	p.A1829S	ENST00000534358	NM_005933.3	1829	Gct/Tct	19/36	1	2	FACETS	0.671	0.541	0.818	0.671	0.541	0.818	SUBCLONAL	1	TRUE	1	0.26	2		361	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0052912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	162	656	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA	2	FACETS	0.874	0.806	0.943			1	INDETERMINATE	2	TRUE	NA	0.332310639545863	2		656	558	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3113454	3113454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752848608	NA	P-0052912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	67	659	0	ENST00000078429.4:c.448G>A	p.Glu150Lys	p.E150K	ENST00000078429	NM_002067.2	150	Gag/Aag	3/7	1	2	FACETS	0.718	0.624	0.819	0.718	0.624	0.819	SUBCLONAL	1	TRUE	1	0.332310639545863	2		659	562	SUCCESS
APC	324	MSKCC	GRCh37	5	112175206	112175206	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	16	212	0	ENST00000257430.4:c.3915del	p.Glu1306LysfsTer2	p.E1306Kfs*2	ENST00000257430	NM_000038.5	1305	gcA/gc	16/16	0.332310639545863	1	FACETS	0.743	0.556	0.961	0.743	0.556	0.961	CLONAL	1	TRUE	0	0.332310639545863	1		212	108	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027158	49027158	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	76	269	0	ENST00000267163.4:c.1725A>T	p.Gln575His	p.Q575H	ENST00000267163	NM_000321.2	575	caA/caT	18/27	0.294822202486202	4	FACETS	0.923	0.824	1	0.923	0.824	1	CLONAL	3	TRUE	1	0.332310639545863	4		269	220	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0052913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	102	441	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.191696381141053	7	FACETS	1	0.923	1			1	CLONAL	5	TRUE	NA	0.191696381141053	7		441	308	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519988	NA	P-0052913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	60	632	0	ENST00000269305.4:c.808T>G	p.Phe270Val	p.F270V	ENST00000269305	NM_001126112.2	270	Ttt/Gtt	8/11	0.191696381141053	3	FACETS	1	0.896	1	1	0.973	1	CLONAL	3	TRUE	1	0.191696381141053	3		632	222	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932433	39932433	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	49	771	0	ENST00000378444.4:c.2166G>T	p.Leu722Phe	p.L722F	ENST00000378444	NM_001123385.1	722	ttG/ttT	4/15	0.191696381141053	3	FACETS	0.979	0.835	1	0.979	0.835	1	CLONAL	2	TRUE	1	0.191696381141053	3		771	286	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233349	69233349	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	10	276	0	ENST00000462284.1:c.1214C>G	p.Thr405Ser	p.T405S	ENST00000462284	NM_002392.5	405	aCt/aGt	11/11	0.191696381141053	2	FACETS	0.632	0.429	0.887	0.316	0.214	0.444	SUBCLONAL	1	TRUE	0	0.191696381141053	2		276	165	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856229	111856229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	13	175	0	ENST00000341259.2:c.280C>T	p.Arg94Cys	p.R94C	ENST00000341259	NM_005475.2	94	Cgt/Tgt	2/8	0.191696381141053	2	FACETS	0.699	0.499	0.942	0.35	0.249	0.471	SUBCLONAL	1	TRUE	0	0.191696381141053	2		175	194	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005546	150005546	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	10	362	0	ENST00000253339.5:c.679C>A	p.His227Asn	p.H227N	ENST00000253339		227	Cac/Aac	3/7	0.191696381141053	3	FACETS	0.635	0.431	0.892	0.318	0.215	0.446	SUBCLONAL	1	TRUE	1	0.191696381141053	3		362	180	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0052914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	10	592	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.275	0.185	0.39	0.275	0.185	0.39	SUBCLONAL	1	TRUE	1	0.15	2		592	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0052915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	338	632	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.586441018982875	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.605315468395455	2		632	546	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937526	32937526	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs80359065	NA	P-0052915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	230	508	0	ENST00000380152.3:c.8187G>T	p.Lys2729Asn	p.K2729N	ENST00000380152		2729	aaG/aaT	18/27	0.373448494349288	3	FACETS	0.767	0.72	0.816	0.767	0.72	0.816	SUBCLONAL	2	TRUE	1	0.605315468395455	3		508	645	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675359	241675359	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	443	367	0	ENST00000366560.3:c.463G>T	p.Glu155Ter	p.E155*	ENST00000366560	NM_000143.3	155	Gaa/Taa	4/10	0.58925058326083	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	0	0.605315468395455	3		367	629	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132971	176132971	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	278	328	0	ENST00000367669.3:c.622G>C	p.Asp208His	p.D208H	ENST00000367669	NM_022457.5	208	Gac/Cac	4/20	0.58925058326083	3	FACETS	0.784	0.74	0.829	0.523	0.493	0.553	SUBCLONAL	2	TRUE	0	0.605315468395455	3		328	763	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50488239	50488240	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0052915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	60	486	0	ENST00000394963.4:c.1156_1157del	p.Lys386AspfsTer5	p.K386Dfs*5	ENST00000394963	NM_003076.4	385	AAa/a	10/13	0.605315468395455	3	FACETS	0.417	0.359	0.481	0.209	0.179	0.241	SUBCLONAL	1	TRUE	1	0.605315468395455	3		486	619	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865551	57865551	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	139	728	0	ENST00000228682.2:c.3028A>T	p.Ser1010Cys	p.S1010C	ENST00000228682	NM_005269.2	1010	Agc/Tgc	12/12	0.605315468395455	3	FACETS	0.953	0.87	1	0.476	0.435	0.52	CLONAL	1	TRUE	1	0.605315468395455	3		728	628	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112470	115112470	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	112	705	0	ENST00000257566.3:c.1270del	p.Asp424ThrfsTer208	p.D424Tfs*208	ENST00000257566	NM_016569.3	424	Gac/ac	7/8	0.18819200475355	3	FACETS	0.923	0.834	1	0.308	0.278	0.339	INDETERMINATE	1	TRUE	0	0.605315468395455	3		705	522	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105634	30105634	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs762691633	NA	P-0052915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	327	573	0	ENST00000331968.5:c.1052A>G	p.Glu351Gly	p.E351G	ENST00000331968	NM_002742.2	351	gAa/gGa	7/18	0.56518436830857	2	FACETS	0.905	0.865	0.945	0.905	0.865	0.945	CLONAL	2	TRUE	0	0.605315468395455	2		573	597	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9928049	9928049	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	88	275	0	ENST00000330684.3:c.1690A>T	p.Met564Leu	p.M564L	ENST00000330684	NM_001134407.1	564	Atg/Ttg	8/13	0.18819200475355	3	FACETS	0.992	0.885	1	0.331	0.295	0.368	INDETERMINATE	1	TRUE	0	0.605315468395455	3		275	382	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983595	7983595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1220054227	NA	P-0052915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	328	590	0	ENST00000319144.4:c.712G>A	p.Asp238Asn	p.D238N	ENST00000319144	NM_001139.2	238	Gac/Aac	6/15	0.586441018982875	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.605315468395455	2		590	500	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983324	15983324	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	258	324	0	ENST00000268712.3:c.3455A>G	p.Lys1152Arg	p.K1152R	ENST00000268712	NM_006311.3	1152	aAa/aGa	26/46	0.586441018982875	2	FACETS	0.982	0.935	1	0.982	0.935	1	CLONAL	2	TRUE	0	0.605315468395455	2		324	434	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259228	89259228	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	200	321	0	ENST00000336596.2:c.372C>A	p.Tyr124Ter	p.Y124*	ENST00000336596	NM_005233.5	124	taC/taA	3/17	0.56518436830857	2	FACETS	0.883	0.833	0.934	0.883	0.833	0.934	CLONAL	2	TRUE	0	0.605315468395455	2		321	374	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55524186	55524187	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0052915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	38	550	0	ENST00000288135.5:c.5_6delinsTT	p.Arg2Ile	p.R2I	ENST00000288135	NM_000222.2	2	aGA/aTT	1/21	0.476444466959423	1	FACETS	0.265	0.219	0.315	0.265	0.219	0.315	SUBCLONAL	1	TRUE	0	0.605315468395455	1		550	331	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004219	150004219	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	86	290	0	ENST00000253339.5:c.2006T>A	p.Met669Lys	p.M669K	ENST00000253339		669	aTg/aAg	3/7	0.605315468395455	3	FACETS	0.898	0.799	1	0.449	0.399	0.502	CLONAL	1	TRUE	1	0.605315468395455	3		290	412	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513374	106513374	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	24	268	0	ENST00000359195.3:c.2278A>C	p.Ser760Arg	p.S760R	ENST00000359195	NM_002649.2	760	Agt/Cgt	4/11	0.597542668603855	3	FACETS	0.271	0.212	0.339	0.136	0.106	0.17	SUBCLONAL	1	TRUE	1	0.605315468395455	3		268	381	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0052916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	105	353	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.199702930127408	3	FACETS	0.922	0.827	1	0.922	0.827	1	CLONAL	2	TRUE	1	0.201619131962402	3		353	622	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074183	8074183	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	33	382	0	ENST00000377482.5:c.476C>A	p.Ser159Tyr	p.S159Y	ENST00000377482	NM_018948.3	159	tCt/tAt	4/4	1	2	FACETS	0.686	0.558	0.831	0.686	0.558	0.831	SUBCLONAL	1	TRUE	1	0.201619131962402	2		382	477	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36808967	36808967	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	67	636	0	ENST00000373129.3:c.1087G>T	p.Glu363Ter	p.E363*	ENST00000373129	NM_032017.1	363	Gag/Tag	11/12	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.201619131962402	2		636	593	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054956	176054956	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	149	412	0	ENST00000367669.3:c.1097A>G	p.Asp366Gly	p.D366G	ENST00000367669	NM_022457.5	366	gAc/gGc	10/20	0.156001243082568	3	FACETS	0.964	0.881	1	0.964	0.881	1	CLONAL	2	TRUE	1	0.201619131962402	3		412	844	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683184	88683184	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	49	285	0	ENST00000372037.3:c.1394C>A	p.Pro465Gln	p.P465Q	ENST00000372037	NM_004329.2	465	cCg/cAg	12/13	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.201619131962402	2		285	415	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524151	18524151	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	126	352	0	ENST00000266497.5:c.1663G>T	p.Glu555Ter	p.E555*	ENST00000266497		555	Gaa/Taa	11/31	0.199702930127408	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.201619131962402	3		352	609	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905607	50905607	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	101	961	0	ENST00000440232.2:c.735G>T	p.Glu245Asp	p.E245D	ENST00000440232	NM_002691.3	245	gaG/gaT	6/27	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.201619131962402	2		961	870	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384997	31384997	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	41	548	1	ENST00000328111.2:c.1382G>T	p.Arg461Leu	p.R461L	ENST00000328111	NM_006892.3	461	cGc/cTc	14/23	1	2	FACETS	0.755	0.628	0.896	0.755	0.628	0.896	SUBCLONAL	1	TRUE	1	0.201619131962402	2		549	539	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242714	66242714	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0052916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	40	250	0	ENST00000273854.3:c.1856+2T>C		p.X619_splice	ENST00000273854	NM_004439.5	619			1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.201619131962402	2		250	351	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179495	56179496	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0052916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	29	244	0	ENST00000399503.3:c.3808_3809delinsTT	p.Ala1270Phe	p.A1270F	ENST00000399503	NM_005921.1	1270	GCt/TTt	15/20	1	2	FACETS	0.859	0.69	1	0.859	0.69	1	CLONAL	1	TRUE	1	0.201619131962402	2		244	335	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435635	149435635	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	54	639	1	ENST00000286301.3:c.2508C>A	p.Ser836Arg	p.S836R	ENST00000286301	NM_005211.3	836	agC/agA	19/22	0.201619131962402	0	FACETS	0.7	0.597	0.812			1	SUBCLONAL	1	TRUE	0	0.201619131962402	0		640	611	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324500	31324501	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCAGGCTCT	novel	NA	P-0052916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	21	418	0	ENST00000412585.2:c.299_307dup	p.Leu102_Arg103insGlnSerLeu	p.L102_R103insQSL	ENST00000412585	NM_005514.6	103	cgg/cAGAGCCTGCgg	2/8	1	2	FACETS	0.651	0.501	0.826	0.651	0.501	0.826	SUBCLONAL	1	TRUE	1	0.201619131962402	2		418	320	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993111	90993111	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1306328242	NA	P-0052916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	47	222	0	ENST00000265433.3:c.331G>A	p.Glu111Lys	p.E111K	ENST00000265433	NM_002485.4	111	Gag/Aag	4/16	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.201619131962402	2		222	414	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309141	137309141	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs767968089	NA	P-0052916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	43	781	1	ENST00000481739.1:c.748G>T	p.Val250Leu	p.V250L	ENST00000481739	NM_002957.4	250	Gtg/Ttg	5/10	0.201619131962402	1	FACETS	0.516	0.431	0.612	0.516	0.431	0.612	SUBCLONAL	1	TRUE	0	0.201619131962402	1		782	743	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403467	139403467	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	91	1060	0	ENST00000277541.6:c.3026G>T	p.Cys1009Phe	p.C1009F	ENST00000277541	NM_017617.3	1009	tGt/tTt	19/34	0.201619131962402	1	FACETS	0.909	0.806	1	0.909	0.806	1	CLONAL	1	TRUE	0	0.201619131962402	1		1060	893	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576883	7576883	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	798	701	0	ENST00000269305.4:c.963del	p.Lys321AsnfsTer24	p.K321Nfs*24	ENST00000269305	NM_001126112.2	321	aaA/aa	9/11	0.779075058053326	4	FACETS	0.95	0.933	0.967	0.95	0.933	0.967	CLONAL	4	FALSE	0	0.772896224167032	4		701	963	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061334	38061334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4487	679	643	0	ENST00000250448.2:c.655C>A	p.Arg219Ser	p.R219S	ENST00000250448	NM_004496.3	219	Cgc/Agc	2/2	0.772896224167032	14	FACETS	0.959	0.918	1	0.192	0.183	0.2	CLONAL	2	FALSE	4	0.772896224167032	14		643	5166	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780684	9780684	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	614	679	2	ENST00000377346.4:c.1486C>T	p.Arg496Ter	p.R496*	ENST00000377346	NM_005026.3	496	Cga/Tga	12/24	0.74514710052299	5	FACETS	0.994	0.961	1	0.994	0.961	1	CLONAL	3	FALSE	2	0.772896224167032	5		681	1151	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713343	40713343	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	423	656	0	ENST00000373198.4:c.4172G>T	p.Gly1391Val	p.G1391V	ENST00000373198	NM_133170.3	1391	gGa/gTa	30/32	0.74514710052299	5	FACETS	1	0.972	1	0.683	0.652	0.715	CLONAL	2	FALSE	2	0.772896224167032	5		656	1153	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324521	62324521	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs373996455	NA	P-0052917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1918	247	978	0	ENST00000360203.5:c.2877C>A	p.His959Gln	p.H959Q	ENST00000360203	NM_001283009.1	959	caC/caA	30/35	0.772896224167032	6	FACETS	0.752	0.699	0.806	0.251	0.233	0.269	SUBCLONAL	1	FALSE	3	0.772896224167032	6		978	2165	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707576	176707576	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	426	481	0	ENST00000439151.2:c.5633C>G	p.Pro1878Arg	p.P1878R	ENST00000439151	NM_022455.4	1878	cCt/cGt	18/23	0.725161441563546	5	FACETS	1	0.977	1			1	CLONAL	3	FALSE	NA	0.772896224167032	5		481	775	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469669	NA	P-0052919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	25	698	1	ENST00000374080.3:c.130G>A	p.Gly44Ser	p.G44S	ENST00000374080		44	Ggt/Agt	2/45	1	2	FACETS	0.246	0.193	0.308	0.246	0.193	0.308	SUBCLONAL	1	TRUE	1	0.22	2		699	923	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0052919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	18	351	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	0.511	0.385	0.661	0.511	0.385	0.661	SUBCLONAL	1	TRUE	1	0.22	2		351	320	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692836	89692836	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs786204858	NA	P-0052919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	20	202	0	ENST00000371953.3:c.320A>T	p.Asp107Val	p.D107V	ENST00000371953	NM_000314.4	107	gAt/gTt	5/9	1	2	FACETS	1	0.842	1	1	0.842	1	CLONAL	1	TRUE	1	0.22	2		202	162	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481838	56481838	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	43	777	0	ENST00000267101.3:c.766G>T	p.Val256Leu	p.V256L	ENST00000267101	NM_001982.3	256	Gta/Tta	7/28	1	2	FACETS	0.458	0.382	0.543	0.458	0.382	0.543	SUBCLONAL	1	TRUE	1	0.22	2		777	854	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074121	8074122	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	53	439	0	ENST00000377482.5:c.537dup	p.Asp180ArgfsTer11	p.D180Rfs*11	ENST00000377482	NM_018948.3	179	-/A	4/4	1	2	FACETS	0.871	0.743	1	0.871	0.743	1	CLONAL	1	TRUE	1	0.22	2		439	553	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087465	27087466	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	114	918	0	ENST00000324856.7:c.2042dup	p.Ser682LeufsTer135	p.S682Lfs*135	ENST00000324856	NM_006015.4	680	cct/ccTt	5/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.22	2		918	962	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371859	55371859	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	24	241	0	ENST00000297316.4:c.552del	p.Glu185SerfsTer202	p.E185Sfs*202	ENST00000297316	NM_022454.3	183	ttC/tt	2/2	1	2	FACETS	0.887	0.698	1	0.887	0.698	1	CLONAL	1	TRUE	1	0.22	2		241	246	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696644	47696644	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519964	NA	P-0052920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	119	418	0	ENST00000347630.2:c.304T>G	p.Phe102Val	p.F102V	ENST00000347630	NM_001007230.1	102	Ttc/Gtc	5/11	1	2	FACETS	0.968	0.879	1	0.968	0.879	1	CLONAL	1	TRUE	1	0.504910567618005	2		418	487	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531004	187531004	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	72	505	0	ENST00000441802.2:c.10019A>G	p.Tyr3340Cys	p.Y3340C	ENST00000441802	NM_005245.3	3340	tAc/tGc	15/27	0.382309788155446	2	FACETS	0.737	0.645	0.836	0.369	0.322	0.418	SUBCLONAL	1	TRUE	0	0.382309788155446	2		505	511	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136030	64136030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1380280944	NA	P-0052921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	149	855	2	ENST00000334205.4:c.1291C>T	p.Arg431Cys	p.R431C	ENST00000334205	NM_003942.2	431	Cgc/Tgc	11/17	0.382309788155446	4	FACETS	1	0.976	1	0.395	0.361	0.431	CLONAL	1	TRUE	1	0.382309788155446	4		857	909	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410378	63410378	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1196061753	NA	P-0052921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	15	417	0	ENST00000330258.3:c.2789A>T	p.Glu930Val	p.E930V	ENST00000330258	NM_152424.3	930	gAg/gTg	2/2	0.0825823606729483	2	FACETS	0.27	0.197	0.358			1	INDETERMINATE	1	TRUE	NA	0.382309788155446	2		417	291	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829040	128829042	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	rs570242755	NA	P-0052922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	15	52	0	ENST00000249373.3:c.67_69del	p.Leu23del	p.L23del	ENST00000249373	NM_005631.4	16	ggGCTg/ggg	1/12	0.320773335502175	3	FACETS	0.714	0.526	0.935	0.357	0.263	0.468	CLONAL	1	TRUE	1	0.382198555258422	3		52	131	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246078852	246078852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150058397	NA	P-0052922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	140	554	0	ENST00000388985.4:c.793C>T	p.Arg265Cys	p.R265C	ENST00000388985		265	Cgt/Tgt	8/12	NA	2	FACETS	0.738	0.671	0.808			1	INDETERMINATE	1	TRUE	NA	0.382198555258422	2		554	993	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503839	149503839	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	68	615	0	ENST00000261799.4:c.1997A>C	p.Asn666Thr	p.N666T	ENST00000261799	NM_002609.3	666	aAc/aCc	14/23	1	2	FACETS	0.425	0.369	0.486	0.425	0.369	0.486	SUBCLONAL	1	TRUE	1	0.382198555258422	2		615	837	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505055	149505055	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	113	455	0	ENST00000261799.4:c.1760T>C	p.Leu587Pro	p.L587P	ENST00000261799	NM_002609.3	587	cTg/cCg	12/23	1	2	FACETS	0.762	0.686	0.843	0.762	0.686	0.843	SUBCLONAL	1	TRUE	1	0.382198555258422	2		455	776	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335705	81335705	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	95	384	0	ENST00000222390.5:c.1655A>G	p.Asp552Gly	p.D552G	ENST00000222390	NM_000601.4	552	gAt/gGt	15/18	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.382198555258422	2		384	455	SUCCESS
AR	367	MSKCC	GRCh37	X	66943618	66943618	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	170	553	0	ENST00000374690.3:c.2698A>G	p.Ile900Val	p.I900V	ENST00000374690	NM_000044.3	900	Atc/Gtc	8/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.382198555258422	2		553	779	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265443	198265464	+	protein_altering_variant	In_Frame_Del	DEL	GTAGTCTGTTCTTGGAAAGCAT	GTAGTCTGTTCTTGGAAAGCAT	AAGAACAGACTAC	novel	NA	P-0052922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	71	384	2	ENST00000335508.6:c.2693_2714delinsGTAGTCTGTTCTT	p.Tyr898_Thr905delinsCysSerLeuPheLeu	p.Y898_T905delinsCSLFL	ENST00000335508	NM_012433.2	898	tATGCTTTCCAAGAACAGACTACa/tGTAGTCTGTTCTTa	18/25	1	2	FACETS	0.804	0.704	0.912	0.804	0.704	0.912	CLONAL	1	TRUE	1	0.382198555258422	2		386	462	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0052923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	243	364	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.560979336204224	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.560979336204224	3		364	493	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0052923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	190	427	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.560979336204224	2		427	570	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	169	476	0	ENST00000206249.3:c.1610A>G	p.Tyr537Cys	p.Y537C	ENST00000206249	NM_000125.3	537	tAt/tGt	8/8	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.560979336204224	2		476	575	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942685	48942685	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913301	NA	P-0052923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	95	232	0	ENST00000267163.4:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000267163	NM_000321.2	358	Cga/Tga	11/27	0.482894984486892	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	0	0.560979336204224	1		232	243	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164611	36164611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	353	476	0	ENST00000300305.3:c.1264G>A	p.Glu422Lys	p.E422K	ENST00000300305		422	Gag/Aag	8/8	0.366727147311882	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.560979336204224	2		476	531	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942852	68942852	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	119	504	0	ENST00000288368.4:c.664G>A	p.Glu222Lys	p.E222K	ENST00000288368	NM_024870.2	222	Gaa/Aaa	6/40	0.319728166805865	4	FACETS	0.869	0.785	0.958	0.435	0.392	0.479	INDETERMINATE	1	TRUE	2	0.560979336204224	4		504	762	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271525	26271525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	187	408	1	ENST00000305910.3:c.88G>A	p.Ala30Thr	p.A30T	ENST00000305910	NM_003534.2	30	Gcg/Acg	1/1	0.538018262919147	4	FACETS	0.759	0.703	0.816	0.759	0.703	0.816	SUBCLONAL	2	TRUE	2	0.560979336204224	4		409	686	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943699	71943699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766706961	NA	P-0052923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	328	552	0	ENST00000298229.2:c.1742G>A	p.Arg581Gln	p.R581Q	ENST00000298229	NM_001567.3	581	cGg/cAg	15/28	0.311731647438301	5	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.560979336204224	5		552	941	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013741	12013741	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	186	240	0	ENST00000353533.5:c.683G>A	p.Arg228Lys	p.R228K	ENST00000353533	NM_003010.3	228	aGa/aAa	6/11	0.560979336204224	2	FACETS	0.981	0.923	1	0.981	0.923	1	CLONAL	2	TRUE	0	0.560979336204224	2		240	338	SUCCESS
APC	324	MSKCC	GRCh37	5	112175424	112175424	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	163	248	0	ENST00000257430.4:c.4133del	p.Gln1378ArgfsTer37	p.Q1378Rfs*37	ENST00000257430	NM_000038.5	1378	cAg/cg	16/16	0.560979336204224	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.560979336204224	3		248	346	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528505	157528505	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1554237979	NA	P-0052923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	157	494	0	ENST00000346085.5:c.6230C>A	p.Ser2077Ter	p.S2077*	ENST00000346085	NM_020732.3	2077	tCg/tAg	20/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.560979336204224	2		494	501	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023620	27023642	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGGCGGCGGCTGCCGGCTCCA	CGCGGCGGCGGCTGCCGGCTCCA	AGCCGGC	novel	NA	P-0052924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	97	311	3	ENST00000324856.7:c.726_748delinsAGCCGGC	p.Ala244GlyfsTer114	p.A244Gfs*114	ENST00000324856	NM_006015.4	242	ggCGCGGCGGCGGCTGCCGGCTCCAag/ggAGCCGGCag	1/20	0.196500345278645	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.216309817235161	3		314	430	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	51	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.865	0.754	0.98	0.865	0.754	0.98	CLONAL	1	FALSE	1	0.873363164423679	2		429	135	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416698	29416698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56181542	NA	P-0052927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	134	568	0	ENST00000389048.3:c.4255G>A	p.Glu1419Lys	p.E1419K	ENST00000389048	NM_004304.4	1419	Gag/Aag	29/29	0.164351506241066	3	FACETS	1	0.983	1	0.421	0.387	0.455	INDETERMINATE	1	FALSE	0	0.873363164423679	3		568	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	465	892	0	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	1	2	FACETS	1	0.994	1	1	0.998	1	CLONAL	2	FALSE	1	0.873363164423679	2		892	515	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221987	1221987	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370222210	NA	P-0052927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	184	954	0	ENST00000326873.7:c.902G>A	p.Arg301Gln	p.R301Q	ENST00000326873	NM_000455.4	301	cGg/cAg	7/10	1	2	FACETS	0.938	0.876	1	0.938	0.876	1	CLONAL	1	FALSE	1	0.873363164423679	2		954	449	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143341	30143341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	33	779	0	ENST00000389048.3:c.185C>T	p.Ser62Leu	p.S62L	ENST00000389048	NM_004304.4	62	tCg/tTg	1/29	0.164351506241066	3	FACETS	0.265	0.215	0.32	0.088	0.071	0.107	INDETERMINATE	1	FALSE	0	0.873363164423679	3		779	410	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030485	49030485	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	98	334	0	ENST00000267163.4:c.1960G>T	p.Val654Leu	p.V654L	ENST00000267163	NM_000321.2	654	Gtg/Ttg	19/27	0.873363164423679	1	FACETS	0.988	0.928	1	0.988	0.928	1	CLONAL	1	FALSE	0	0.873363164423679	1		334	128	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023943	27023943	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	24	121	0	ENST00000324856.7:c.1049C>A	p.Ser350Ter	p.S350*	ENST00000324856	NM_006015.4	350	tCg/tAg	1/20	1	2	FACETS	0.393	0.311	0.484	0.393	0.311	0.484	SUBCLONAL	1	FALSE	1	0.873363164423679	2		121	140	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876137	35876137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	119	616	0	ENST00000303115.3:c.929G>A	p.Arg310Lys	p.R310K	ENST00000303115	NM_002185.3	310	aGg/aAg	8/8	1	2	FACETS	0.876	0.802	0.952	0.876	0.802	0.952	CLONAL	1	FALSE	1	0.873363164423679	2		616	311	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441813	49441813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	38	793	0	ENST00000301067.7:c.4171G>A	p.Glu1391Lys	p.E1391K	ENST00000301067	NM_003482.3	1391	Gag/Aag	14/54	0.133726664669997	4	FACETS	0.315	0.26	0.376	0.157	0.13	0.188	INDETERMINATE	1	FALSE	2	0.873363164423679	4		793	518	SUCCESS
APC	324	MSKCC	GRCh37	5	112175921	112175921	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	11	264	0	ENST00000257430.4:c.4630G>C	p.Glu1544Gln	p.E1544Q	ENST00000257430	NM_000038.5	1544	Gaa/Caa	16/16	NA	2	FACETS	0.187	0.129	0.257			1	INDETERMINATE	1	FALSE	NA	0.873363164423679	2		264	135	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260917	16260917	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	110	666	2	ENST00000375759.3:c.8182G>T	p.Ala2728Ser	p.A2728S	ENST00000375759	NM_015001.2	2728	Gct/Tct	11/15	0.502190081224615	4	FACETS	0.911	0.834	0.99			1	INDETERMINATE	2	FALSE	NA	0.873363164423679	4		668	259	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107087	27107087	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	175	614	0	ENST00000324856.7:c.6700del	p.Ala2234LeufsTer33	p.A2234Lfs*33	ENST00000324856	NM_006015.4	2233	cGg/cg	20/20	1	2	FACETS	0.932	0.868	0.997	0.932	0.868	0.997	CLONAL	1	FALSE	1	0.873363164423679	2		614	430	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724610	162724610	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	116	621	0	ENST00000367921.3:c.382C>G	p.Arg128Gly	p.R128G	ENST00000367921	NM_006182.2	128	Cgc/Ggc	5/18	1	2	FACETS	0.803	0.732	0.875	0.803	0.732	0.875	CLONAL	1	FALSE	1	0.873363164423679	2		621	331	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518041	69518041	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	125	1078	0	ENST00000294312.3:c.324G>C	p.Lys108Asn	p.K108N	ENST00000294312	NM_005117.2	108	aaG/aaC	2/3	1	2	FACETS	0.827	0.758	0.898	0.827	0.758	0.898	CLONAL	1	FALSE	1	0.873363164423679	2		1078	346	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986803	36986803	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	66	224	0	ENST00000354822.5:c.886G>C	p.Asp296His	p.D296H	ENST00000354822	NM_001079668.2	296	Gac/Cac	3/3	1	2	FACETS	0.752	0.664	0.843	0.752	0.664	0.843	SUBCLONAL	1	FALSE	1	0.873363164423679	2		224	201	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63553937	63553937	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	107	538	0	ENST00000307078.5:c.802G>C	p.Asp268His	p.D268H	ENST00000307078	NM_004655.3	268	Gac/Cac	2/11	0.129394500240849	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.873363164423679	0		538	314	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366215	15366215	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	217	881	0	ENST00000263377.2:c.1940C>G	p.Ser647Cys	p.S647C	ENST00000263377	NM_058243.2	647	tCc/tGc	10/20	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	1	0.873363164423679	2		881	492	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227707	36227707	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	180	825	0	ENST00000222270.7:c.7276G>C	p.Val2426Leu	p.V2426L	ENST00000222270	NM_014727.1	2426	Gtt/Ctt	31/37	1	2	FACETS	0.988	0.923	1	0.988	0.923	1	CLONAL	1	FALSE	1	0.873363164423679	2		825	417	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047315	128047315	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	117	588	0	ENST00000285398.2:c.607G>A	p.Glu203Lys	p.E203K	ENST00000285398	NM_000122.1	203	Gaa/Aaa	5/15	0.873363164423679	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	0	0.873363164423679	1		588	144	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021451	31021451	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1388025911	NA	P-0052927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	56	715	0	ENST00000375687.4:c.1450G>C	p.Glu484Gln	p.E484Q	ENST00000375687	NM_015338.5	484	Gag/Cag	12/13	0.3943168567636	3	FACETS	0.394	0.338	0.455	0.131	0.112	0.152	INDETERMINATE	1	FALSE	0	0.873363164423679	3		715	468	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672450	30672450	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	201	880	0	ENST00000376406.3:c.4510C>T	p.Gln1504Ter	p.Q1504*	ENST00000376406	NM_014641.2	1504	Cag/Tag	10/15	1	2	FACETS	0.936	0.876	0.996	0.936	0.876	0.996	CLONAL	1	FALSE	1	0.873363164423679	2		880	492	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178635	32178635	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	61	1038	0	ENST00000375023.3:c.2759C>G	p.Pro920Arg	p.P920R	ENST00000375023	NM_004557.3	920	cCt/cGt	18/30	1	2	FACETS	0.296	0.255	0.34	0.296	0.255	0.34	SUBCLONAL	1	FALSE	1	0.873363164423679	2		1038	472	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752948	128752948	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	116	432	0	ENST00000377970.2:c.1109A>G	p.Lys370Arg	p.K370R	ENST00000377970	NM_002467.4	370	aAg/aGg	3/3	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	FALSE	1	0.873363164423679	2		432	261	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045025	47045025	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	190	523	0	ENST00000377604.3:c.2351A>G	p.His784Arg	p.H784R	ENST00000377604	NM_001204468.1	784	cAc/cGc	20/24	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	0	0.873363164423679	1		523	226	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907608	76907608	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	135	246	0	ENST00000373344.5:c.4553G>C	p.Arg1518Thr	p.R1518T	ENST00000373344	NM_000489.3	1518	aGa/aCa	15/35	1	1	FACETS	0.862	0.81	0.912	0.862	0.81	0.912	CLONAL	1	FALSE	0	0.873363164423679	1		246	202	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061202	38061204	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	novel	NA	P-0052928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	86	538	1	ENST00000250448.2:c.785_787del	p.Arg262del	p.R262del	ENST00000250448	NM_004496.3	262	cGCCag/cag	2/2	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.27	2		539	600	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618543	37618543	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0052928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	122	589	0	ENST00000447079.4:c.219T>G	p.Tyr73Ter	p.Y73*	ENST00000447079	NM_015083.1	73	taT/taG	1/14	0.184944337820384	2	FACETS	1	0.974	1	0.61	0.551	0.671	CLONAL	1	TRUE	0	0.27	2		589	741	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0052929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	63	460	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.397	0.343	0.456	0.397	0.343	0.456	SUBCLONAL	1	TRUE	1	0.492789100028878	2		460	644	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069363	30069363	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1556000842	NA	P-0052929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	79	952	6	ENST00000338641.4:c.1228C>T	p.Gln410Ter	p.Q410*	ENST00000338641	NM_000268.3	410	Cag/Tag	12/16	0.48846486866774	1	FACETS	0.407	0.358	0.459	0.407	0.358	0.459	SUBCLONAL	1	TRUE	0	0.492789100028878	1		958	594	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635191	87635191	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367769334	NA	P-0052929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	61	668	1	ENST00000277120.3:c.2243C>T	p.Thr748Met	p.T748M	ENST00000277120		748	aCg/aTg	18/19	1	2	FACETS	0.322	0.277	0.371	0.322	0.277	0.371	SUBCLONAL	1	TRUE	1	0.492789100028878	2		669	770	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059186	27059192	+	frameshift_variant	Frame_Shift_Del	DEL	TTGGGTC	TTGGGTC	-	novel	NA	P-0052929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	55	441	0	ENST00000324856.7:c.1824_1830del	p.Gly609ArgfsTer8	p.G609Rfs*8	ENST00000324856	NM_006015.4	608	tTTGGGTCt/tt	4/20	1	2	FACETS	0.404	0.345	0.468	0.404	0.345	0.468	SUBCLONAL	1	TRUE	1	0.492789100028878	2		441	553	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117614	70117614	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	179	943	0	ENST00000245479.2:c.82G>A	p.Glu28Lys	p.E28K	ENST00000245479	NM_000346.3	28	Gag/Aag	1/3	1	2	FACETS	0.923	0.853	0.996	0.923	0.853	0.996	CLONAL	1	TRUE	1	0.492789100028878	2		943	787	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0052930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	443	833	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.762754789491954	1	FACETS	0.981	0.946	1	0.981	0.946	1	CLONAL	1	TRUE	0	0.771572013364009	1		837	719	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910549	29910549	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45585732	NA	P-0052930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	31	1125	8	ENST00000376809.5:c.89G>A	p.Arg30Lys	p.R30K	ENST00000376809	NM_002116.7	30	aGg/aAg	2/8	0.771572013364009	0	FACETS		NA	1			1	NA	1	TRUE	0	0.771572013364009	0		1133	261	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980783	40980783	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	238	669	1	ENST00000373198.4:c.1703C>A	p.Ala568Asp	p.A568D	ENST00000373198	NM_133170.3	568	gCc/gAc	10/32	0.771572013364009	1	FACETS	0.568	0.533	0.604	0.568	0.533	0.604	SUBCLONAL	1	TRUE	0	0.771572013364009	1		670	667	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164467	36164467	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	232	397	3	ENST00000300305.3:c.1408G>A	p.Ala470Thr	p.A470T	ENST00000300305		470	Gcg/Acg	8/8	1	2	FACETS	0.958	0.899	1	0.958	0.899	1	CLONAL	1	TRUE	1	0.771572013364009	2		400	628	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844722	156844722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs986498490	NA	P-0052930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	262	975	0	ENST00000524377.1:c.1276G>A	p.Val426Ile	p.V426I	ENST00000524377	NM_002529.3	426	Gtc/Atc	11/17	0.375575027212725	3	FACETS	0.739	0.691	0.788	0.246	0.23	0.263	INDETERMINATE	1	TRUE	0	0.771572013364009	3		975	1274	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350972	89350972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276054196	NA	P-0052930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	302	887	2	ENST00000301030.4:c.1978G>A	p.Glu660Lys	p.E660K	ENST00000301030	NM_001256183.1	660	Gaa/Aaa	9/13	0.304965920238656	1	FACETS	0.532	0.502	0.562	0.532	0.502	0.562	INDETERMINATE	1	TRUE	0	0.771572013364009	1		889	904	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950626	38950626	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	191	454	0	ENST00000357387.3:c.3324del	p.Lys1108AsnfsTer52	p.K1108Nfs*52	ENST00000357387	NM_152756.3	1108	aaA/aa	31/38	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.771572013364009	2		454	422	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498229	498229	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs547859375	NA	P-0052930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	120	398	0	ENST00000399788.2:c.29C>T	p.Ala10Val	p.A10V	ENST00000399788	NM_001042603.1	10	gCg/gTg	1/28	0.556941922216394	1	FACETS	0.4	0.363	0.438	0.4	0.363	0.438	SUBCLONAL	1	TRUE	0	0.771572013364009	1		398	478	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713259	43713259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	860	1028	1	ENST00000382044.4:c.4214G>A	p.Arg1405Gln	p.R1405Q	ENST00000382044	NM_001141980.1	1405	cGa/cAa	20/28	0.771572013364009	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.771572013364009	2		1029	1072	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028009	48028009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	155	346	0	ENST00000234420.5:c.2887G>A	p.Gly963Ser	p.G963S	ENST00000234420	NM_000179.2	963	Ggc/Agc	4/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.771572013364009	2		346	389	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713271	30713286	+	frameshift_variant	Frame_Shift_Del	DEL	CAACCTGGGAAACCGG	CAACCTGGGAAACCGG	-	novel	NA	P-0052930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	147	474	0	ENST00000295754.5:c.599_614del	p.Thr200ArgfsTer59	p.T200Rfs*59	ENST00000295754	NM_003242.5	199	tCAACCTGGGAAACCGGc/tc	4/7	0.325030168595031	1	FACETS	0.487	0.447	0.527	0.487	0.447	0.527	INDETERMINATE	1	TRUE	0	0.771572013364009	1		474	481	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323100	31323114	+	inframe_deletion	In_Frame_Del	DEL	TCAGGGTGAGGGGCT	TCAGGGTGAGGGGCT	-	novel	NA	P-0052930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	273	1371	0	ENST00000412585.2:c.875_889del	p.Lys292_Leu296del	p.K292_L296del	ENST00000412585	NM_005514.6	292	aAGCCCCTCACCCTGAga/aga	4/8	0.722994083675518	1	FACETS	0.642	0.606	0.678	0.642	0.606	0.678	SUBCLONAL	1	TRUE	0	0.771572013364009	1		1371	677	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0052931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	54	286	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.203579849545473	4	FACETS	1	0.919	1	0.555	0.475	0.642	CLONAL	1	TRUE	2	0.31	4		286	411	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	52	285	0	ENST00000397062.3:c.92G>A	p.Gly31Glu	p.G31E	ENST00000397062	NM_006164.4	31	gGa/gAa	2/5	0.203579849545473	4	FACETS	1	0.96	1	0.693	0.593	0.801	CLONAL	1	TRUE	2	0.31	4		285	317	SUCCESS
AR	367	MSKCC	GRCh37	X	66766357	66766389	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	-	rs746853821	NA	P-0052931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	28	87	0	ENST00000374690.3:c.1388_1420del	p.Gly463_Gly473del	p.G463_G473del	ENST00000374690	NM_000044.3	457	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC/-	1/8	1	2	FACETS	0.886	0.724	1	1	0.954	1	CLONAL	2	TRUE	1	0.31	2		87	102	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs371769427	NA	P-0052931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	43	325	0	ENST00000291552.4:c.101C>A	p.Ser34Tyr	p.S34Y	ENST00000291552	NM_006758.2	34	tCt/tAt	2/8	0.135214021147074	3	FACETS	0.898	0.753	1	0.449	0.376	0.528	INDETERMINATE	1	TRUE	1	0.31	3		325	357	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	70	350	0	ENST00000256196.4:c.68G>A	p.Gly23Asp	p.G23D	ENST00000256196		23	gGc/gAc	1/6	0.203579849545473	4	FACETS	1	0.96	1	0.628	0.549	0.713	CLONAL	1	TRUE	2	0.31	4		350	471	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106342	27106342	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	109	761	0	ENST00000324856.7:c.5953T>C	p.Ser1985Pro	p.S1985P	ENST00000324856	NM_006015.4	1985	Tcc/Ccc	20/20	0.203579849545473	4	FACETS	1	0.978	1	0.662	0.595	0.733	CLONAL	1	TRUE	2	0.31	4		761	696	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481403	140481403	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913357	NA	P-0052931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	37	326	0	ENST00000288602.6:c.1405G>C	p.Gly469Arg	p.G469R	ENST00000288602	NM_004333.4	469	Gga/Cga	11/18	0.203579849545473	5	FACETS	1	0.878	1	0.36	0.297	0.429	CLONAL	1	TRUE	2	0.31	5		326	324	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058013	27058014	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0052931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	91	664	0	ENST00000324856.7:c.1722_1723del	p.Gln575AlafsTer47	p.Q575Afs*47	ENST00000324856	NM_006015.4	574	tCC/t	3/20	0.203579849545473	4	FACETS	1	0.933	1	0.536	0.475	0.6	CLONAL	1	TRUE	2	0.31	4		664	718	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157519999	157520000	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0052931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	89	827	0	ENST00000346085.5:c.4070dup	p.Tyr1358ValfsTer101	p.Y1358Vfs*101	ENST00000346085	NM_020732.3	1356	-/C	17/20	0.345727553425632	4	FACETS	0.863	0.764	0.969	0.431	0.382	0.485	CLONAL	1	TRUE	2	0.31	4		827	872	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205605	38205606	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	GATGTTGGCGGAGTCA	novel	NA	P-0052931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	139	798	0	ENST00000317025.8:c.69_84dup	p.Arg29Ter	p.R29*	ENST00000317025	NM_023034.1	28	-/TGACTCCGCCAACATC	2/24	0.203579849545473	5	FACETS	1	0.984	1	0.468	0.426	0.513	CLONAL	1	TRUE	2	0.31	5		798	935	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492910	8492910	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	102	668	0	ENST00000356435.5:c.2419G>C	p.Gly807Arg	p.G807R	ENST00000356435		807	Gga/Cga	16/35	1	2	FACETS	0.803	0.717	0.893	0.803	0.717	0.893	CLONAL	1	TRUE	1	0.31	2		668	820	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0052932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	207	460	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.58	2		460	706	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916929	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519931	NA	P-0052932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	152	466	0	ENST00000263967.3:c.316G>C	p.Gly106Arg	p.G106R	ENST00000263967	NM_006218.2	106	Ggc/Cgc	2/21	1	2	FACETS	0.902	0.829	0.978	0.902	0.829	0.978	CLONAL	1	TRUE	1	0.58	2		466	581	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557629	95557629	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	160	465	0	ENST00000393063.1:c.5438A>G	p.Glu1813Gly	p.E1813G	ENST00000393063	NM_030621.3	1813	gAg/gGg	26/28	1	2	FACETS	0.83	0.763	0.899	0.83	0.763	0.899	CLONAL	1	TRUE	1	0.58	2		465	665	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572535	95572535	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852978	NA	P-0052932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	109	317	0	ENST00000393063.1:c.2830C>T	p.Arg944Ter	p.R944*	ENST00000393063	NM_030621.3	944	Cga/Tga	19/28	1	2	FACETS	0.94	0.851	1	0.94	0.851	1	CLONAL	1	TRUE	1	0.58	2		317	400	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0052933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	87	305	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.31	2		305	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0052933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	236	833	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.2643355573183	2	FACETS	0.855	0.799	0.913	0.855	0.799	0.913	CLONAL	2	TRUE	0	0.31	2		837	890	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971080	21971081	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0052933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	118	416	0	ENST00000304494.5:c.277_278del	p.Thr93AlafsTer26	p.T93Afs*26	ENST00000304494	NM_000077.4	93	ACg/g	2/3	0.29988036653151	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.31	1		416	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0052934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	1281	1094	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.799736629622773	4	FACETS	1	0.998	1			1	CLONAL	4	TRUE	NA	0.868459496924813	4		1094	1335	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436393	52436393	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1244342890	NA	P-0052934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	398	868	3	ENST00000460680.1:c.2101C>T	p.Arg701Cys	p.R701C	ENST00000460680	NM_004656.3	701	Cgc/Tgc	17/17	0.881151119135434	5	FACETS	0.918	0.874	0.963	0.612	0.583	0.642	CLONAL	2	TRUE	2	0.868459496924813	5		871	1149	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5216750	5216750	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	27	645	0	ENST00000357368.4:c.4077G>C	p.Glu1359Asp	p.E1359D	ENST00000357368	NM_002850.3	1359	gaG/gaC	26/38	0.881151119135434	1	FACETS	0.11	0.087	0.136	0.11	0.087	0.136	SUBCLONAL	1	TRUE	0	0.868459496924813	1		645	320	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557639	95557639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775912475	NA	P-0052967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	77	574	1	ENST00000393063.1:c.5428G>A	p.Asp1810Asn	p.D1810N	ENST00000393063	NM_030621.3	1810	Gat/Aat	26/28	1	2	FACETS	0.993	0.871	1	0.993	0.871	1	CLONAL	1	TRUE	1	0.19	2		575	816	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783807	50783807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	68	626	1	ENST00000398568.2:c.198G>T	p.Lys66Asn	p.K66N	ENST00000398568	NM_001042412.1	66	aaG/aaT	3/18	1	2	FACETS	0.8	0.694	0.915	0.8	0.694	0.915	CLONAL	1	TRUE	1	0.19	2		627	895	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578178	7578192	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TCAGGCGGCTCATAG	TCAGGCGGCTCATAG	-	novel	NA	P-0052967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	235	736	0	ENST00000269305.4:c.657_671del	p.Tyr220_Glu224del	p.Y220_E224del	ENST00000269305	NM_001126112.2	219	ccCTATGAGCCGCCTGAg/ccg	6/11	0.225651672443384	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.19	2		736	1042	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732997	30732997	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057524810	NA	P-0052967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	59	552	0	ENST00000295754.5:c.1610G>A	p.Arg537His	p.R537H	ENST00000295754	NM_003242.5	537	cGc/cAc	7/7	1	2	FACETS	0.762	0.654	0.88	0.762	0.654	0.88	SUBCLONAL	1	TRUE	1	0.19	2		552	815	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260151	149260151	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1307297959	NA	P-0052967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	65	578	2	ENST00000360632.3:c.742C>T	p.Arg248Ter	p.R248*	ENST00000360632	NM_015472.4	248	Cga/Tga	4/7	1	2	FACETS	0.811	0.701	0.93	0.811	0.701	0.93	CLONAL	1	TRUE	1	0.19	2		580	844	SUCCESS
APC	324	MSKCC	GRCh37	5	112170648	112170648	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	47	382	0	ENST00000257430.4:c.1744G>T	p.Glu582Ter	p.E582*	ENST00000257430	NM_000038.5	582	Gaa/Taa	15/16	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.19	2		382	491	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205046	38205046	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1200854666	NA	P-0052967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	66	655	0	ENST00000317025.8:c.644A>G	p.Lys215Arg	p.K215R	ENST00000317025	NM_023034.1	215	aAa/aGa	2/24	1	2	FACETS	0.811	0.702	0.929	0.811	0.702	0.929	CLONAL	1	TRUE	1	0.19	2		655	857	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562487	21562487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	44	179	0	ENST00000382592.4:c.1432G>A	p.Ala478Thr	p.A478T	ENST00000382592	NM_014572.2	478	Gcc/Acc	4/8	0.230496028412878	3	FACETS	0.831	0.701	0.975	0.831	0.701	0.975	CLONAL	2	TRUE	1	0.19	3		179	305	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74003499	74003500	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	230	725	0	ENST00000318443.5:c.1571dup	p.Asp524GlufsTer6	p.D524Efs*6	ENST00000318443	NM_001024736.1	524	gac/gAac	9/10	1	2	FACETS	0.961	0.899	1	0.961	0.899	1	CLONAL	1	TRUE	1	0.61931914545519	2		725	773	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676253	37676253	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	227	637	0	ENST00000447079.4:c.3008T>G	p.Leu1003Arg	p.L1003R	ENST00000447079	NM_015083.1	1003	cTa/cGa	11/14	1	2	FACETS	0.974	0.91	1	0.974	0.91	1	CLONAL	1	TRUE	1	0.61931914545519	2		637	753	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676309	37676309	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	172	585	0	ENST00000447079.4:c.3064del	p.Asp1022MetfsTer35	p.D1022Mfs*35	ENST00000447079	NM_015083.1	1022	Gat/at	11/14	1	2	FACETS	0.799	0.738	0.863	0.799	0.738	0.863	SUBCLONAL	1	TRUE	1	0.61931914545519	2		585	695	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350770	15350770	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	283	806	0	ENST00000263377.2:c.3233G>C	p.Ser1078Thr	p.S1078T	ENST00000263377	NM_058243.2	1078	aGc/aCc	15/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.61931914545519	2		806	897	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989217	41989217	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0052970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	71	614	0	ENST00000219905.7:c.2009C>G	p.Ser670Ter	p.S670*	ENST00000219905	NM_001164273.1	670	tCa/tGa	3/24	1	2	FACETS	0.464	0.405	0.528	0.464	0.405	0.528	SUBCLONAL	1	TRUE	1	0.505700585383436	2		614	605	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0052971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	188	411	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.925	0.862	0.989	0.925	0.862	0.989	CLONAL	1	TRUE	1	0.817898065972896	2		411	497	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231506	5231506	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1386910242	NA	P-0052971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	272	829	1	ENST00000357368.4:c.1970G>A	p.Arg657His	p.R657H	ENST00000357368	NM_002850.3	657	cGc/cAc	14/38	0.126556488984927	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.817898065972896	0		830	778	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0052971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	354	766	0	ENST00000269305.4:c.560-1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.780638605750732	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.817898065972896	1		766	477	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219979	5219979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	262	869	1	ENST00000357368.4:c.3736G>A	p.Val1246Met	p.V1246M	ENST00000357368	NM_002850.3	1246	Gtg/Atg	22/38	0.126556488984927	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.817898065972896	0		870	767	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0052972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	36	529	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	1	2	FACETS	0.524	0.429	0.63	0.524	0.429	0.63	SUBCLONAL	1	TRUE	1	0.189692849067494	2		529	725	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682514	37682514	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	57	644	0	ENST00000447079.4:c.3705C>G	p.Asn1235Lys	p.N1235K	ENST00000447079	NM_015083.1	1235	aaC/aaG	13/14	0.127834195257527	3	FACETS	0.85	0.728	0.984	0.283	0.242	0.328	CLONAL	1	TRUE	0	0.189692849067494	3		644	774	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170015111	170015111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	99	816	0	ENST00000295797.4:c.1517G>A	p.Gly506Asp	p.G506D	ENST00000295797	NM_002740.5	506	gGt/gAt	16/18	0.160264266651684	3	FACETS	1	0.953	1	0.565	0.503	0.631	CLONAL	1	TRUE	1	0.189692849067494	3		816	1012	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440336	187440336	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	58	736	0	ENST00000232014.4:c.2031G>C	p.Leu677Phe	p.L677F	ENST00000232014	NM_001130845.1	677	ttG/ttC	10/10	1	2	FACETS	0.745	0.638	0.861	0.745	0.638	0.861	SUBCLONAL	1	TRUE	1	0.189692849067494	2		736	821	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540767	187540767	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	44	585	0	ENST00000441802.2:c.6973A>G	p.Asn2325Asp	p.N2325D	ENST00000441802	NM_005245.3	2325	Aat/Gat	10/27	1	2	FACETS	0.724	0.606	0.855	0.724	0.606	0.855	SUBCLONAL	1	TRUE	1	0.189692849067494	2		585	641	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97869442	97869442	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	59	1015	0	ENST00000289081.3:c.1439G>C	p.Arg480Thr	p.R480T	ENST00000289081	NM_000136.2	480	aGa/aCa	14/15	1	2	FACETS	0.613	0.526	0.709	0.613	0.526	0.709	SUBCLONAL	1	TRUE	1	0.189692849067494	2		1015	1014	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	59	429	0				ENST00000310581	NM_198253.2	-/1132			0.3	3	FACETS	1	0.961	1	0.669	0.578	0.766	CLONAL	1	TRUE	1	0.27	3		429	371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0052973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	149	833	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.286243114401546	3	FACETS	0.812	0.743	0.885	0.812	0.743	0.885	CLONAL	2	TRUE	1	0.27	3		837	771	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092965	27092965	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	25	444	0	ENST00000324856.7:c.2896G>A	p.Glu966Lys	p.E966K	ENST00000324856	NM_006015.4	966	Gag/Aag	10/20	1	2	FACETS	0.414	0.326	0.516	0.414	0.326	0.516	SUBCLONAL	1	TRUE	1	0.27	2		444	447	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550818	150550818	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	41	501	0	ENST00000369026.2:c.838A>T	p.Thr280Ser	p.T280S	ENST00000369026	NM_021960.4	280	Acc/Tcc	2/3	0.286243114401546	3	FACETS	0.563	0.468	0.669	0.282	0.234	0.335	SUBCLONAL	1	TRUE	1	0.27	3		501	612	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012365	176012365	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	71	487	0	ENST00000367669.3:c.1569G>C	p.Leu523Phe	p.L523F	ENST00000367669	NM_022457.5	523	ttG/ttC	14/20	0.286243114401546	3	FACETS	0.85	0.742	0.968	0.425	0.371	0.484	CLONAL	1	TRUE	1	0.27	3		487	702	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976618	7976618	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	39	738	0	ENST00000319144.4:c.1774A>G	p.Met592Val	p.M592V	ENST00000319144	NM_001139.2	592	Atg/Gtg	14/15	0.286243114401546	3	FACETS	0.466	0.385	0.557	0.233	0.192	0.279	SUBCLONAL	1	TRUE	1	0.27	3		738	704	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727101	40727101	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	38	682	0	ENST00000373198.4:c.3863G>T	p.Cys1288Phe	p.C1288F	ENST00000373198	NM_133170.3	1288	tGc/tTc	28/32	1	2	FACETS	0.408	0.336	0.489	0.408	0.336	0.489	SUBCLONAL	1	TRUE	1	0.27	2		682	690	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495716	72495716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	38	597	1	ENST00000477973.2:c.356G>A	p.Cys119Tyr	p.C119Y	ENST00000477973	NM_012234.5	119	tGc/tAc	1/4	1	2	FACETS	0.373	0.307	0.447	0.373	0.307	0.447	SUBCLONAL	1	TRUE	1	0.27	2		598	754	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948043	178948043	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	34	306	0	ENST00000263967.3:c.2815G>C	p.Asp939His	p.D939H	ENST00000263967	NM_006218.2	939	Gat/Cat	20/21	1	2	FACETS	0.521	0.425	0.63	0.521	0.425	0.63	SUBCLONAL	1	TRUE	1	0.27	2		306	483	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271220	38271220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	66	782	0	ENST00000425967.3:c.2488G>A	p.Glu830Lys	p.E830K	ENST00000425967	NM_001174067.1	830	Gag/Aag	19/19	1	2	FACETS	0.741	0.643	0.847	0.741	0.643	0.847	SUBCLONAL	1	TRUE	1	0.27	2		782	660	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0052974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	321	430	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.1636383838278	2	FACETS	1	0.992	1	0.598	0.57	0.626	INDETERMINATE	1	TRUE	0	0.853400535247888	2		430	629	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0052974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	315	656	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.85	0.805	0.896	0.85	0.805	0.896	CLONAL	1	TRUE	1	0.853400535247888	2		656	868	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0052974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	350	485	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.853400535247888	2		486	808	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0052974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	324	727	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.915	0.868	0.962	0.915	0.868	0.962	CLONAL	1	TRUE	1	0.853400535247888	2		727	830	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353767	40353767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760771231	NA	P-0052974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	46	722	1	ENST00000293328.3:c.2353G>A	p.Ala785Thr	p.A785T	ENST00000293328	NM_012448.3	785	Gca/Aca	19/19	NA	2	FACETS	0.13	0.109	0.154			1	INDETERMINATE	1	TRUE	NA	0.853400535247888	2		723	828	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105724	27105724	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	110	416	1	ENST00000324856.7:c.5335G>T	p.Glu1779Ter	p.E1779*	ENST00000324856	NM_006015.4	1779	Gag/Tag	20/20	0.333483768468733	1	FACETS	0.322	0.291	0.355	0.322	0.291	0.355	INDETERMINATE	1	TRUE	0	0.853400535247888	1		417	459	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935406	36935406	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	287	802	0	ENST00000361632.4:c.1321G>C	p.Asp441His	p.D441H	ENST00000361632		441	Gac/Cac	10/16	0.333483768468733	1	FACETS	0.491	0.463	0.518	0.491	0.463	0.518	INDETERMINATE	1	TRUE	0	0.853400535247888	1		802	786	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564795	41564795	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	94	705	0	ENST00000263253.7:c.4096A>T	p.Ile1366Phe	p.I1366F	ENST00000263253	NM_001429.3	1366	Att/Ttt	25/31	1	2	FACETS	0.238	0.211	0.267	0.238	0.211	0.267	SUBCLONAL	1	TRUE	1	0.853400535247888	2		705	925	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0052975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	115	574	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.435609598696558	1	FACETS	0.566	0.51	0.625	0.566	0.51	0.625	SUBCLONAL	1	TRUE	0	0.435609598696558	1		574	730	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421519	32421519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	92	692	0	ENST00000332351.3:c.1073C>T	p.Thr358Met	p.T358M	ENST00000332351	NM_024426.4	358	aCg/aTg	6/10	1	2	FACETS	0.618	0.549	0.691	0.618	0.549	0.691	SUBCLONAL	1	TRUE	1	0.435609598696558	2		692	684	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554308	29554308	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	210	695	0	ENST00000356175.3:c.2324A>T	p.Glu775Val	p.E775V	ENST00000356175	NM_000267.3	775	gAg/gTg	19/57	0.435609598696558	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.435609598696558	1		695	636	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602511	10602511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754728119	NA	P-0052975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	57	1066	0	ENST00000171111.5:c.1067C>T	p.Ala356Val	p.A356V	ENST00000171111	NM_203500.1	356	gCg/gTg	3/6	1	2	FACETS	0.32	0.274	0.371	0.32	0.274	0.371	SUBCLONAL	1	TRUE	1	0.435609598696558	2		1066	817	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070557	67070557	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	135	319	0	ENST00000412916.2:c.181G>C	p.Gly61Arg	p.G61R	ENST00000412916		61	Gga/Cga	3/6	0.435609598696558	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.435609598696558	1		319	342	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	53	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.425574211465142	2		429	229	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233037	55233037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1477025000	NA	P-0052976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9342	2861	615	0	ENST00000275493.2:c.1787C>T	p.Pro596Leu	p.P596L	ENST00000275493	NM_005228.3	596	cCg/cTg	15/28	0.425574211465142	53	FACETS	1	0.984	1	0.272	0.266	0.278	CLONAL	13	TRUE	5	0.425574211465142	53		615	12203	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717739	89717739	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	23	448	0	ENST00000371953.3:c.764T>C	p.Val255Ala	p.V255A	ENST00000371953	NM_000314.4	255	gTa/gCa	7/9	0.425574211465142	1	FACETS	0.198	0.154	0.25	0.198	0.154	0.25	SUBCLONAL	1	TRUE	0	0.425574211465142	1		448	429	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087333	27087346	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TATATATGTTCTAG	TATATATGTTCTAG	-	novel	NA	P-0052976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	62	362	0	ENST00000324856.7:c.1921-14_1921-1del		p.X641_splice	ENST00000324856	NM_006015.4	641			1	2	FACETS	0.745	0.646	0.852	0.745	0.646	0.852	SUBCLONAL	1	TRUE	1	0.425574211465142	2		362	391	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55225428	55225429	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0052976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9719	726	504	2	ENST00000275493.2:c.1280_1281delinsTT	p.Arg427Leu	p.R427L	ENST00000275493	NM_005228.3	427	cGC/cTT	11/28	0.425574211465142	53	FACETS	0.968	0.927	1	0.081	0.077	0.085	CLONAL	4	TRUE	5	0.425574211465142	53		506	10445	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241895	133241895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483635586	NA	P-0052978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	132	611	0	ENST00000320574.5:c.2461C>T	p.Arg821Cys	p.R821C	ENST00000320574	NM_006231.2	821	Cgc/Tgc	21/49	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.39960973365009	2		611	638	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685314	89685315	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TG	TG	-	rs1564826836	NA	P-0052978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	92	291	0	ENST00000371953.3:c.209+1_209+2del		p.X70_splice	ENST00000371953	NM_000314.4	70		3/9	0.39960973365009	1	FACETS	0.853	0.762	0.949	0.853	0.762	0.949	CLONAL	1	TRUE	0	0.39960973365009	1		291	432	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575671	48575671	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0052978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	85	499	0	ENST00000342988.3:c.431C>G	p.Ser144Ter	p.S144*	ENST00000342988	NM_005359.5	144	tCa/tGa	4/12	0.39960973365009	1	FACETS	0.618	0.547	0.693	0.618	0.547	0.693	SUBCLONAL	1	TRUE	0	0.39960973365009	1		499	551	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274192	10274192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765986049	NA	P-0052978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	96	653	1	ENST00000330684.3:c.77C>T	p.Ala26Val	p.A26V	ENST00000330684	NM_001134407.1	26	gCg/gTg	2/13	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.39960973365009	2		654	467	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591888	48591888	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519739	NA	P-0052978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	17	520	0	ENST00000342988.3:c.1051G>C	p.Asp351His	p.D351H	ENST00000342988	NM_005359.5	351	Gat/Cat	9/12	0.39960973365009	1	FACETS	0.131	0.097	0.171	0.131	0.097	0.171	SUBCLONAL	1	TRUE	0	0.39960973365009	1		520	521	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031939	26031939	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	39	569	0	ENST00000244661.2:c.350G>C	p.Arg117Pro	p.R117P	ENST00000244661	NM_003537.3	117	cGa/cCa	1/1	0.324372160667716	2	FACETS	0.365	0.302	0.435	0.182	0.151	0.218	SUBCLONAL	1	TRUE	0	0.39960973365009	2		569	535	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060745	38060772	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTTATGCTGCTGCTCCGAGGAGGACA	AGCTTATGCTGCTGCTCCGAGGAGGACA	-	novel	NA	P-0052978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	133	879	1	ENST00000250448.2:c.1217_1244del	p.Met406ArgfsTer25	p.M406Rfs*25	ENST00000250448	NM_004496.3	406	aTGTCCTCCTCGGAGCAGCAGCATAAGCTg/ag	2/2	1	2	FACETS	0.791	0.719	0.868	0.791	0.719	0.868	SUBCLONAL	1	TRUE	1	0.39960973365009	2		880	841	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254497	10254497	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	167	670	0	ENST00000340748.4:c.3013A>T	p.Ser1005Cys	p.S1005C	ENST00000340748		1005	Agc/Tgc	28/40	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.39960973365009	2		670	737	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375463	15375469	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGCTG	GCCGCTG	-	novel	NA	P-0052978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	141	856	0	ENST00000263377.2:c.958_964del	p.Gln320GlyfsTer7	p.Q320Gfs*7	ENST00000263377	NM_058243.2	320	CAGCGGCgg/gg	6/20	1	2	FACETS	0.959	0.875	1	0.959	0.875	1	CLONAL	1	TRUE	1	0.39960973365009	2		856	736	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098929	178098949	+	inframe_deletion	In_Frame_Del	DEL	AAGTCAAATACTTCTCGACTT	AAGTCAAATACTTCTCGACTT	-	novel	NA	P-0052978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	85	439	0	ENST00000397062.3:c.96_116del	p.Arg34_Ser40del	p.R34_S40del	ENST00000397062	NM_006164.4	32	gtAAGTCGAGAAGTATTTGACTTc/gtc	2/5	1	2	FACETS	0.854	0.757	0.957	0.854	0.757	0.957	CLONAL	1	TRUE	1	0.39960973365009	2		439	498	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144912	47144912	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	108	448	0	ENST00000409792.3:c.4841T>C	p.Ile1614Thr	p.I1614T	ENST00000409792	NM_014159.6	1614	aTa/aCa	7/21	0.39960973365009	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.39960973365009	1		448	421	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589594	67589611	+	inframe_deletion	In_Frame_Del	DEL	AACACTCAGTTTCAAGAA	AACACTCAGTTTCAAGAA	-	novel	NA	P-0052978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	83	302	0	ENST00000274335.5:c.1359_1376del	p.Asn453_Glu458del	p.N453_E458del	ENST00000274335		453	AACACTCAGTTTCAAGAA/-	10/15	0.39960973365009	1	FACETS	0.913	0.812	1	0.913	0.812	1	CLONAL	1	TRUE	0	0.39960973365009	1		302	364	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	179	429	0				ENST00000310581	NM_198253.2	-/1132			0.643724791169963	4	FACETS	0.982	0.918	1	0.982	0.918	1	CLONAL	2	TRUE	2	0.878192355441678	4		429	390	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864328	57864328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201538749	NA	P-0052980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	304	491	0	ENST00000228682.2:c.1805C>T	p.Ser602Leu	p.S602L	ENST00000228682	NM_005269.2	602	tCg/tTg	12/12	0.878192355441678	3	FACETS	0.942	0.888	0.996	0.471	0.444	0.498	CLONAL	1	TRUE	1	0.878192355441678	3		491	1058	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416698	29416698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56181542	NA	P-0052980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	251	568	0	ENST00000389048.3:c.4255G>A	p.Glu1419Lys	p.E1419K	ENST00000389048	NM_004304.4	1419	Gag/Aag	29/29	0.878192355441678	3	FACETS	1	0.979	1	0.365	0.342	0.387	CLONAL	1	TRUE	0	0.878192355441678	3		568	752	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176715849	176715849	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	260	619	1	ENST00000439151.2:c.6181G>A	p.Glu2061Lys	p.E2061K	ENST00000439151	NM_022455.4	2061	Gaa/Aaa	21/23	0.878192355441678	2	FACETS	1	0.945	1	0.5	0.472	0.528	CLONAL	1	TRUE	0	0.878192355441678	2		620	592	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955569	48955569	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	440	471	0	ENST00000267163.4:c.1685C>A	p.Ala562Glu	p.A562E	ENST00000267163	NM_000321.2	562	gCa/gAa	17/27	0.878192355441678	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.878192355441678	3		471	476	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784109	9784109	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	311	958	1	ENST00000377346.4:c.2677G>A	p.Asp893Asn	p.D893N	ENST00000377346	NM_005026.3	893	Gat/Aat	21/24	0.878192355441678	2	FACETS	1	0.967	1	0.512	0.486	0.538	CLONAL	1	TRUE	0	0.878192355441678	2		959	692	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102094442	102094442	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	208	651	0	ENST00000282441.5:c.1122G>C	p.Leu374Phe	p.L374F	ENST00000282441	NM_001130145.2	374	ttG/ttC	7/9	1	2	FACETS	0.864	0.809	0.921	0.864	0.809	0.921	CLONAL	1	TRUE	1	0.878192355441678	2		651	548	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400030	49400030	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	256	762	0	ENST00000418115.1:c.307G>T	p.Val103Phe	p.V103F	ENST00000418115	NM_001664.2	103	Gtc/Ttc	4/5	1	2	FACETS	0.992	0.936	1	0.992	0.936	1	CLONAL	1	TRUE	1	0.878192355441678	2		762	588	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535346	66535346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1180540482	NA	P-0052980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	284	675	0	ENST00000273854.3:c.115C>T	p.Pro39Ser	p.P39S	ENST00000273854	NM_004439.5	39	Ccc/Tcc	1/18	0.878192355441678	2	FACETS	1	0.968	1	0.514	0.487	0.541	CLONAL	1	TRUE	0	0.878192355441678	2		675	629	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0052981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	88	525	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.242484993847169	2		525	652	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287197	38287203	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AACCTGA	AACCTGA	-	novel	NA	P-0052981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	61	914	0	ENST00000425967.3:c.454_457+3del		p.X152_splice	ENST00000425967	NM_001174067.1	152		4/19	1	2	FACETS	0.809	0.698	0.93	0.809	0.698	0.93	CLONAL	1	TRUE	1	0.242484993847169	2		914	622	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040688	47040689	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0052981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	87	480	0	ENST00000377604.3:c.1324dup	p.Glu442GlyfsTer76	p.E442Gfs*76	ENST00000377604	NM_001204468.1	441	-/G	13/24	1	1	FACETS	0.861	0.768	0.959	1	0.983	1	CLONAL	2	TRUE	0	0.242484993847169	1		480	366	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	135	429	0				ENST00000310581	NM_198253.2	-/1132			0.562759972920553	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	2	0.634595368800741	4		429	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0052982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	454	872	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.634347390381581	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.634595368800741	3		873	922	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0052982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	290	880	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.634347390381581	3	FACETS	1	0.986	1	0.572	0.538	0.606	CLONAL	1	TRUE	1	0.634595368800741	3		881	1053	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912133	50912133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768773535	NA	P-0052982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	534	1042	2	ENST00000440232.2:c.1867C>T	p.Arg623Trp	p.R623W	ENST00000440232	NM_002691.3	623	Cgg/Tgg	15/27	0.383141654516016	3	FACETS	1	0.974	1			1	CLONAL	2	TRUE	NA	0.634595368800741	3		1044	1094	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241964	133241964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	202	838	0	ENST00000320574.5:c.2392G>A	p.Glu798Lys	p.E798K	ENST00000320574	NM_006231.2	798	Gag/Aag	21/49	0.620425349976272	3	FACETS	0.908	0.842	0.976	0.454	0.421	0.488	CLONAL	1	TRUE	1	0.634595368800741	3		838	924	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259828	16259828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754902694	NA	P-0052982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	232	706	0	ENST00000375759.3:c.7093G>A	p.Glu2365Lys	p.E2365K	ENST00000375759	NM_015001.2	2365	Gag/Aag	11/15	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.634595368800741	2		706	680	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087944	27087944	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	181	743	1	ENST00000324856.7:c.2231C>A	p.Ser744Ter	p.S744*	ENST00000324856	NM_006015.4	744	tCa/tAa	6/20	NA	2	FACETS	0.854	0.791	0.919			1	INDETERMINATE	1	TRUE	NA	0.634595368800741	2		744	668	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375527	118375527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	124	463	0	ENST00000534358.1:c.8920G>A	p.Glu2974Lys	p.E2974K	ENST00000534358	NM_005933.3	2974	Gaa/Aaa	27/36	0.620425349976272	3	FACETS	1	0.909	1	0.5	0.454	0.547	CLONAL	1	TRUE	1	0.634595368800741	3		463	515	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955446	48955446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	440	523	0	ENST00000267163.4:c.1563del	p.Asn522IlefsTer2	p.N522Ifs*2	ENST00000267163	NM_000321.2	521	cTt/ct	17/27	0.614657102438826	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.634595368800741	3		523	587	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43699714	43699714	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1423123951	NA	P-0052982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	207	764	0	ENST00000382044.4:c.5801C>T	p.Ser1934Leu	p.S1934L	ENST00000382044	NM_001141980.1	1934	tCg/tTg	28/28	0.620425349976272	3	FACETS	1	0.968	1	0.534	0.497	0.573	CLONAL	1	TRUE	1	0.634595368800741	3		764	804	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217677	7217677	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	188	665	0	ENST00000380728.2:c.250C>G	p.His84Asp	p.H84D	ENST00000380728		84	Cac/Gac	4/11	0.634347390381581	3	FACETS	1	0.962	1	0.53	0.49	0.57	CLONAL	1	TRUE	1	0.634595368800741	3		665	737	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462559	40462559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs780160492	NA	P-0052982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	191	801	0	ENST00000345506.4:c.2257G>C	p.Asp753His	p.D753H	ENST00000345506	NM_003152.3	753	Gac/Cac	20/20	0.634347390381581	3	FACETS	0.907	0.84	0.977	0.454	0.42	0.489	CLONAL	1	TRUE	1	0.634595368800741	3		801	874	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3094469	3094670	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	GCGGGGACCCGGCGGCTCGCCAGGCGGCGGCCGAGGCGGGGCGGGCCGGCCCGGGGCCGAGGGCCGGTGGCCGAGGCCGGAGGGCCGCGGCGGGCGGCGGCCGAGGCGGCTCCGGCCAGGGCCGGGCCGGGGGCCGGGGGGCGGCGGCGGGCAGGCGGCCGCGTCGGCCGGGGCCGGGACGATGACTCTGGAGTCCATGATG	GCGGGGACCCGGCGGCTCGCCAGGCGGCGGCCGAGGCGGGGCGGGCCGGCCCGGGGCCGAGGGCCGGTGGCCGAGGCCGGAGGGCCGCGGCGGGCGGCGGCCGAGGCGGCTCCGGCCAGGGCCGGGCCGGGGGCCGGGGGGCGGCGGCGGGCAGGCGGCCGCGTCGGCCGGGGCCGGGACGATGACTCTGGAGTCCATGATG	-	novel	NA	P-0052982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1	62	0	0	ENST00000078429.4:c.-178_24del		p.*60*	ENST00000078429	NM_002067.2	?-7/359		1/7	0.621461815752691	4	FACETS	1	0.981	1	1	0.988	1	CLONAL	5	TRUE	2	0.634595368800741	4		0	63	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587123	212587123	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	263	446	0	ENST00000342788.4:c.878G>A	p.Cys293Tyr	p.C293Y	ENST00000342788	NM_005235.2	293	tGt/tAt	7/28	0.620425349976272	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.634595368800741	3		446	535	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12393168	12393168	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	150	626	0	ENST00000287820.6:c.77C>T	p.Ser26Leu	p.S26L	ENST00000287820	NM_015869.4	26	tCa/tTa	1/7	1	2	FACETS	0.907	0.834	0.983	0.907	0.834	0.983	CLONAL	1	TRUE	1	0.634595368800741	2		626	521	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456460	89456460	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	125	545	0	ENST00000336596.2:c.1636G>C	p.Ala546Pro	p.A546P	ENST00000336596	NM_005233.5	546	Gcc/Ccc	8/17	0.272541607093162	5	FACETS	1	0.942	1			1	INDETERMINATE	1	TRUE	NA	0.634595368800741	5		545	729	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166234	32166234	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	262	858	0	ENST00000375023.3:c.4720G>C	p.Glu1574Gln	p.E1574Q	ENST00000375023	NM_004557.3	1574	Gag/Cag	26/30	0.597529900593646	4	FACETS	1	0.98	1	0.372	0.347	0.396	CLONAL	1	TRUE	1	0.634595368800741	4		858	1211	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342761	87342761	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	155	580	0	ENST00000277120.3:c.1046A>G	p.Asp349Gly	p.D349G	ENST00000277120		349	gAt/gGt	9/19	0.115809709852261	5	FACETS	0.809	0.744	0.877	0.405	0.372	0.439	INDETERMINATE	2	TRUE	1	0.634595368800741	5		580	589	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0052983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	39	330	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.2785577065569	5	FACETS	0.778	0.645	0.928	0.195	0.161	0.232	CLONAL	1	FALSE	1	0.2785577065569	5		330	510	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258109	16258109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs537211881	NA	P-0052983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	65	573	0	ENST00000375759.3:c.5374G>A	p.Glu1792Lys	p.E1792K	ENST00000375759	NM_015001.2	1792	Gaa/Aaa	11/15	0.189933493853757	3	FACETS	0.781	0.676	0.894	0.39	0.338	0.447	SUBCLONAL	1	FALSE	1	0.2785577065569	3		573	681	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351466	89351466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243371355	NA	P-0052983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	82	689	0	ENST00000301030.4:c.1484C>T	p.Ser495Phe	p.S495F	ENST00000301030	NM_001256183.1	495	tCt/tTt	9/13	1	2	FACETS	0.768	0.676	0.866	0.768	0.676	0.866	SUBCLONAL	1	FALSE	1	0.2785577065569	2		689	767	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056210	26056210	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	77	564	0	ENST00000343677.2:c.447G>C	p.Lys149Asn	p.K149N	ENST00000343677	NM_005319.3	149	aaG/aaC	1/1	0.2785577065569	5	FACETS	0.955	0.837	1	0.318	0.279	0.361	CLONAL	1	FALSE	2	0.2785577065569	5		564	821	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054656	13054656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	71	604	1	ENST00000316448.5:c.1183G>A	p.Glu395Lys	p.E395K	ENST00000316448	NM_004343.3	395	Gag/Aag	9/9	1	2	FACETS	0.643	0.56	0.732	0.643	0.56	0.732	SUBCLONAL	1	FALSE	1	0.2785577065569	2		605	793	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11019805	11019805	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	89	694	0	ENST00000327064.4:c.480G>C	p.Gln160His	p.Q160H	ENST00000327064	NM_199141.1	160	caG/caC	4/16	1	2	FACETS	0.787	0.697	0.883	0.787	0.697	0.883	SUBCLONAL	1	FALSE	1	0.2785577065569	2		694	812	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262543	16262543	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	83	532	0	ENST00000375759.3:c.9808C>G	p.Leu3270Val	p.L3270V	ENST00000375759	NM_015001.2	3270	Ctc/Gtc	11/15	0.189933493853757	3	FACETS	1	0.956	1	0.586	0.518	0.659	CLONAL	1	FALSE	1	0.2785577065569	3		532	579	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262645	16262645	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	80	580	0	ENST00000375759.3:c.9910C>G	p.Gln3304Glu	p.Q3304E	ENST00000375759	NM_015001.2	3304	Caa/Gaa	11/15	0.189933493853757	3	FACETS	0.95	0.836	1	0.475	0.418	0.536	CLONAL	1	FALSE	1	0.2785577065569	3		580	689	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46738442	46738442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746819393	NA	P-0052983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	76	619	0	ENST00000371975.4:c.1343C>T	p.Ser448Phe	p.S448F	ENST00000371975	NM_003579.3	448	tCt/tTt	12/18	1	2	FACETS	0.784	0.687	0.888	0.784	0.687	0.888	SUBCLONAL	1	FALSE	1	0.2785577065569	2		619	696	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066806	77066806	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	56	476	0	ENST00000356341.3:c.679A>T	p.Asn227Tyr	p.N227Y	ENST00000356341	NM_002576.4	227	Aat/Tat	7/15	1	2	FACETS	0.699	0.599	0.809	0.699	0.599	0.809	SUBCLONAL	1	FALSE	1	0.2785577065569	2		476	575	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281973	49281973	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	65	631	1	ENST00000282018.3:c.1020G>C	p.Leu340Phe	p.L340F	ENST00000282018	NM_020377.2	340	ttG/ttC	1/1	0.2785577065569	1	FACETS	0.696	0.604	0.796	0.696	0.604	0.796	SUBCLONAL	1	FALSE	0	0.2785577065569	1		632	577	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65569045	65569045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	79	517	0	ENST00000358664.4:c.13G>A	p.Asp5Asn	p.D5N	ENST00000358664	NM_002382.4	5	Gat/Aat	1/5	1	2	FACETS	0.754	0.663	0.853	0.754	0.663	0.853	SUBCLONAL	1	FALSE	1	0.2785577065569	2		517	752	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346619	89346619	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	62	732	0	ENST00000301030.4:c.6331C>T	p.His2111Tyr	p.H2111Y	ENST00000301030	NM_001256183.1	2111	Cac/Tac	9/13	1	2	FACETS	0.54	0.465	0.622	0.54	0.465	0.622	SUBCLONAL	1	FALSE	1	0.2785577065569	2		732	824	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765708	41765708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1207505418	NA	P-0052983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	96	747	0	ENST00000301178.4:c.2584C>T	p.Pro862Ser	p.P862S	ENST00000301178	NM_021913.4	862	Cct/Tct	20/20	1	2	FACETS	0.824	0.734	0.921	0.824	0.734	0.921	CLONAL	1	FALSE	1	0.2785577065569	2		747	836	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012750	36012750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	26	163	0	ENST00000358208.4:c.194G>A	p.Gly65Glu	p.G65E	ENST00000358208		65	gGa/gAa	2/12	1	2	FACETS	0.765	0.608	0.943	0.765	0.608	0.943	CLONAL	1	FALSE	1	0.2785577065569	2		163	244	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531876	41531876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	72	532	1	ENST00000263253.7:c.1588G>A	p.Asp530Asn	p.D530N	ENST00000263253	NM_001429.3	530	Gac/Aac	7/31	1	2	FACETS	0.942	0.824	1	0.942	0.824	1	CLONAL	1	FALSE	1	0.2785577065569	2		533	549	SUCCESS
APC	324	MSKCC	GRCh37	5	112177514	112177514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754004343	NA	P-0052983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	39	381	0	ENST00000257430.4:c.6223G>A	p.Asp2075Asn	p.D2075N	ENST00000257430	NM_000038.5	2075	Gat/Aat	16/16	1	2	FACETS	0.615	0.51	0.733	0.615	0.51	0.733	SUBCLONAL	1	FALSE	1	0.2785577065569	2		381	455	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606225	93606225	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1449828824	NA	P-0052983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	103	762	0	ENST00000375746.1:c.45C>G	p.Phe15Leu	p.F15L	ENST00000375746	NM_001174167.1	15	ttC/ttG	2/14	1	2	FACETS	0.855	0.764	0.951	0.855	0.764	0.951	CLONAL	1	FALSE	1	0.2785577065569	2		762	865	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258541	16258541	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	88	792	0	ENST00000375759.3:c.5806C>T	p.Arg1936Ter	p.R1936*	ENST00000375759	NM_015001.2	1936	Cga/Tga	11/15	1	2	FACETS	0.309	0.274	0.347	0.309	0.274	0.347	SUBCLONAL	1	TRUE	1	0.880357105634164	2		792	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0052988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	346	857	0	ENST00000269305.4:c.838A>T	p.Arg280Ter	p.R280*	ENST00000269305	NM_001126112.2	280	Aga/Tga	8/11	0.423627011503585	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.423627011503585	2		857	737	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0052990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	94	833	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.17	2		837	970	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0052990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	42	322	1	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.17	2		323	422	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247246	153247246	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	84	461	0	ENST00000281708.4:c.1556A>G	p.Tyr519Cys	p.Y519C	ENST00000281708	NM_033632.3	519	tAt/tGt	10/12	1	2	FACETS	0.887	0.785	0.996	1	0.983	1	CLONAL	2	TRUE	1	0.17	2		461	557	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963019	38963019	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	29	325	1	ENST00000357387.3:c.1525G>C	p.Asp509His	p.D509H	ENST00000357387	NM_152756.3	509	Gat/Cat	17/38	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.17	2		326	305	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560464	95560464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	85	600	1	ENST00000393063.1:c.5125G>A	p.Asp1709Asn	p.D1709N	ENST00000393063	NM_030621.3	1709	Gat/Aat	25/28	1	2	FACETS	0.803	0.711	0.9	1	0.98	1	CLONAL	2	TRUE	1	0.191880186146468	2		601	552	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952076	178952076	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	74	464	0	ENST00000263967.3:c.3131A>C	p.Asn1044Thr	p.N1044T	ENST00000263967	NM_006218.2	1044	aAt/aCt	21/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.191880186146468	2		464	515	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0052992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	36	305	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.906	0.746	1	0.906	0.746	1	CLONAL	1	TRUE	1	0.211274065462058	2		305	376	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0052992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	25	388	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.792	0.625	0.983	0.792	0.625	0.983	CLONAL	1	TRUE	1	0.211274065462058	2		388	299	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587118	189587118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761885185	NA	P-0052992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	31	524	0	ENST00000264731.3:c.1135C>T	p.Arg379Cys	p.R379C	ENST00000264731	NM_003722.4	379	Cgt/Tgt	9/14	1	2	FACETS	0.791	0.64	0.961	0.791	0.64	0.961	CLONAL	1	TRUE	1	0.211274065462058	2		524	371	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982036	93982036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1165179670	NA	P-0052992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	27	522	0	ENST00000369303.4:c.1429G>A	p.Glu477Lys	p.E477K	ENST00000369303	NM_004440.3	477	Gaa/Aaa	6/17	1	2	FACETS	0.58	0.46	0.716	0.58	0.46	0.716	SUBCLONAL	1	TRUE	1	0.211274065462058	2		522	441	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410618	32410618	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866837692	NA	P-0052992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	46	783	0	ENST00000332351.3:c.1540C>T	p.Gln514Ter	p.Q514*	ENST00000332351	NM_024426.4	514	Cag/Tag	10/10	1	2	FACETS	0.627	0.527	0.739	0.627	0.527	0.739	SUBCLONAL	1	TRUE	1	0.211274065462058	2		783	694	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962855	2962855	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	56	1032	0	ENST00000396946.4:c.2053G>A	p.Gly685Ser	p.G685S	ENST00000396946	NM_032415.4	685	Ggc/Agc	16/25	1	2	FACETS	0.633	0.541	0.735	0.633	0.541	0.735	SUBCLONAL	1	TRUE	1	0.211274065462058	2		1032	837	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380231	25380232	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCCCAGTCCTCATGTACTGGTCCCTCATTG	novel	NA	P-0052992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	59	610	0	ENST00000311936.3:c.197_226dup	p.Ala66_Gly75dup	p.A66_G75dup	ENST00000311936	NM_004985.3	66	gag/gCAATGAGGGACCAGTACATGAGGACTGGGGag	3/5	0.211274065462058	1	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	0	0.211274065462058	1		610	491	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444091	49444091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1053550290	NA	P-0052992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	119	1045	0	ENST00000301067.7:c.3280C>T	p.Leu1094Phe	p.L1094F	ENST00000301067	NM_003482.3	1094	Ctc/Ttc	11/54	0.155571494756095	2	FACETS	1	0.983	1	0.715	0.645	0.788	CLONAL	1	TRUE	0	0.211274065462058	2		1045	788	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961832	55961832	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	30	497	0	ENST00000263923.4:c.2729G>A	p.Gly910Glu	p.G910E	ENST00000263923	NM_002253.2	910	gGg/gAg	20/30	1	2	FACETS	0.789	0.636	0.962	0.789	0.636	0.962	CLONAL	1	TRUE	1	0.211274065462058	2		497	360	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509969	187509969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	46	648	0	ENST00000441802.2:c.13544C>T	p.Pro4515Leu	p.P4515L	ENST00000441802	NM_005245.3	4515	cCc/cTc	27/27	1	2	FACETS	0.798	0.671	0.937	0.798	0.671	0.937	CLONAL	1	TRUE	1	0.211274065462058	2		648	546	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180049761	180049761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	50	893	0	ENST00000261937.6:c.1627G>A	p.Asp543Asn	p.D543N	ENST00000261937	NM_182925.4	543	Gat/Aat	12/30	1	2	FACETS	0.629	0.533	0.736	0.629	0.533	0.736	SUBCLONAL	1	TRUE	1	0.211274065462058	2		893	752	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111995755	111995755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	56	611	0	ENST00000368678.4:c.1343C>T	p.Ser448Phe	p.S448F	ENST00000368678		448	tCt/tTt	12/13	1	2	FACETS	0.912	0.782	1	0.912	0.782	1	CLONAL	1	TRUE	1	0.211274065462058	2		611	581	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37006487	37006488	+	missense_variant	Missense_Mutation	DNP	GC	GC	CT	novel	NA	P-0052992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	27	477	0	ENST00000358127.4:c.457_458delinsAG	p.Ala153Ser	p.A153S	ENST00000358127	NM_001280556.1	153	GCt/AGt	4/10	0.211274065462058	1	FACETS	0.619	0.493	0.764	0.619	0.493	0.764	SUBCLONAL	1	TRUE	0	0.211274065462058	1		477	369	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904940	101904940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	29	561	0	ENST00000374994.4:c.928G>A	p.Ala310Thr	p.A310T	ENST00000374994	NM_004612.2	310	Gcg/Acg	5/9	0.211274065462058	1	FACETS	0.646	0.519	0.791	0.646	0.519	0.791	SUBCLONAL	1	TRUE	0	0.211274065462058	1		561	380	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266624	115267646	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTACAAAACAAAGGCAGGTACATCTTTCAATTTTATTTCATCTCTACTACATAGAAAGACAAGTAAGCAAAAAATAACAGCACAAATGTTAACAGGGTAGGTTGGCTGGCTGCTATTGAAATGGGGTAGGGAACCTGAAGCCAAGTTCTATTTTTAGAACAGCTGCTGGACTTTAAATACTTCTAAACTACCAAAATGCCTGCTTTTCCTAAATAGAATTGTTTAAATAAAATTGTTTAAGGAATTAATAAGTATTCATAAATAAAACATGCCTTGATCTCTTACTTTTTCCAGGTGACCATATGTCATTTTTTAAGAAGCCTTTCCTGGTCTCTAAAATGTAAATCACAATACTTACATACTGTCCTGATTCATCTTTATTACATGTATTGTTGTCTTTCTAAACATCATATACAGTATTTTACTCCTCTAGTCTGCCCCATATTTTCCACCAAAAAATAAGGTCAATGAATACAGGGATGTATCTGATTTCTTCACTGCTGTATCCCCAGTGTCTAAAACATAACACACACTTAAGAGTTCAGATGAGAGCCAAAAATAAGTTGCAGGTCTTTTAAAGTCAGAGATCCAAGATCCTAAATTACAATTAATTTTTTTAACTTCCCATTATTTTTCACATTTAGATTCATTCTTCTTCAAAACAATCTTCTAGGGAAATGCCTCTCTTCCCTACTCCATGGTGATGTATACATATCTTGGGGTTATTTTTGTTTTTTTCAGACAGTCTTGCTCTGTCACCCAGGTTGGAGTGCAGTGGTAGGATCATCATGGCTCACTGCAGTCTCAACCTACCAGCACAAGCGGCCCTCCCACCTCAGCCTCCCAAGTAACTGTGACTACAGGCATCCACTACCACAGCTGGCTATCCTGGGTTTATTTTTCAAAAGAAGACAATGAATTGAAAATATAAAGCAAATTTCCTAAAATATCTAGGCCAATCCTTCTCAAACTTCAGTGTATACCAGAATCACCTAAAGGATTTATTAAAAAAGAATGCCCACT	CTACAAAACAAAGGCAGGTACATCTTTCAATTTTATTTCATCTCTACTACATAGAAAGACAAGTAAGCAAAAAATAACAGCACAAATGTTAACAGGGTAGGTTGGCTGGCTGCTATTGAAATGGGGTAGGGAACCTGAAGCCAAGTTCTATTTTTAGAACAGCTGCTGGACTTTAAATACTTCTAAACTACCAAAATGCCTGCTTTTCCTAAATAGAATTGTTTAAATAAAATTGTTTAAGGAATTAATAAGTATTCATAAATAAAACATGCCTTGATCTCTTACTTTTTCCAGGTGACCATATGTCATTTTTTAAGAAGCCTTTCCTGGTCTCTAAAATGTAAATCACAATACTTACATACTGTCCTGATTCATCTTTATTACATGTATTGTTGTCTTTCTAAACATCATATACAGTATTTTACTCCTCTAGTCTGCCCCATATTTTCCACCAAAAAATAAGGTCAATGAATACAGGGATGTATCTGATTTCTTCACTGCTGTATCCCCAGTGTCTAAAACATAACACACACTTAAGAGTTCAGATGAGAGCCAAAAATAAGTTGCAGGTCTTTTAAAGTCAGAGATCCAAGATCCTAAATTACAATTAATTTTTTTAACTTCCCATTATTTTTCACATTTAGATTCATTCTTCTTCAAAACAATCTTCTAGGGAAATGCCTCTCTTCCCTACTCCATGGTGATGTATACATATCTTGGGGTTATTTTTGTTTTTTTCAGACAGTCTTGCTCTGTCACCCAGGTTGGAGTGCAGTGGTAGGATCATCATGGCTCACTGCAGTCTCAACCTACCAGCACAAGCGGCCCTCCCACCTCAGCCTCCCAAGTAACTGTGACTACAGGCATCCACTACCACAGCTGGCTATCCTGGGTTTATTTTTCAAAAGAAGACAATGAATTGAAAATATAAAGCAAATTTCCTAAAATATCTAGGCCAATCCTTCTCAAACTTCAGTGTATACCAGAATCACCTAAAGGATTTATTAAAAAAGAATGCCCACT	-	novel	NA	P-0052993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	162	521	1	ENST00000438362.2:c.1891+196_1892-1del		p.X631_splice	ENST00000438362	NM_001242891.1	631			0.3095943908652	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.3095943908652	1		522	778	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115267955	115268831	+	splice_acceptor_variant,splice_donor_variant,intron_variant	Splice_Site	DEL	CTAAGGAGAAAGGAAATGACATTTAACTAAACATTACCATAAACATCAACAGTAACAGGCAGTCTTTATTTTACAGTAACAGTCATGGCATGGCATGCTTATTTACATTAGACACCATTTTAAGTAATTTCTATGTATTGACTCATTTAATCCTCAAGAATGCCCCATGAAGAGGTAACATTATCCCTAACTTCAGGATAATGAAACTAAGATACCAAGAAGTTATTTGGTAAAAATTACACAGGTATAAAGTGGCAGGGCCTGGATTCAAAAACTGAACTGTCTGGTTCTAAGAACCCTTACTTTCTATTTTTTTTTTTGAGACAGAGTCTCACTCTGTTGGCTAGGCTGGAGTACAGTGGTGCGATCTCAGCTTACTGCAACCTCTGCCTCCCAGGATCAAGTGGTCCTCCCACATCAGCCTCCTGAGTTGGTGAGACTACAGGTATGCACCACCATGTCAGGCTAATTTTGGTAATTTTTGTGGAGATGGAGTTTCACCGTGTTGCTCAGGCTGGCCTCGAACTCCTGGGCTCAAGGGATCCACCTGCCTCAGCCCCCAAAGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCAGACCCCTTACTCTTACACTACATTATACACCAAATGGCCAACTCTATGGTACCAACACAAAAAATAAGGTGGCACAGGCCTTTCTATTTCTTTTGGCCACAGGCTCTGTATATAGTAAGATCAGTGATTAACTTCAGTTTATATCTTGCCATAATTCTACCAATATGAAATCTGAACCTCAACAAGTATAATCAATCAATACTAAATGTTTTTTATTCCAACACCAAAGAATGGATGGTAAGTTAGCTGTAAAGTTCCTGAAAGTCACGCCTTAC	CTAAGGAGAAAGGAAATGACATTTAACTAAACATTACCATAAACATCAACAGTAACAGGCAGTCTTTATTTTACAGTAACAGTCATGGCATGGCATGCTTATTTACATTAGACACCATTTTAAGTAATTTCTATGTATTGACTCATTTAATCCTCAAGAATGCCCCATGAAGAGGTAACATTATCCCTAACTTCAGGATAATGAAACTAAGATACCAAGAAGTTATTTGGTAAAAATTACACAGGTATAAAGTGGCAGGGCCTGGATTCAAAAACTGAACTGTCTGGTTCTAAGAACCCTTACTTTCTATTTTTTTTTTTGAGACAGAGTCTCACTCTGTTGGCTAGGCTGGAGTACAGTGGTGCGATCTCAGCTTACTGCAACCTCTGCCTCCCAGGATCAAGTGGTCCTCCCACATCAGCCTCCTGAGTTGGTGAGACTACAGGTATGCACCACCATGTCAGGCTAATTTTGGTAATTTTTGTGGAGATGGAGTTTCACCGTGTTGCTCAGGCTGGCCTCGAACTCCTGGGCTCAAGGGATCCACCTGCCTCAGCCCCCAAAGTGCTGGGATTATAGGCATGAGCCACCACACCCAGTCAGACCCCTTACTCTTACACTACATTATACACCAAATGGCCAACTCTATGGTACCAACACAAAAAATAAGGTGGCACAGGCCTTTCTATTTCTTTTGGCCACAGGCTCTGTATATAGTAAGATCAGTGATTAACTTCAGTTTATATCTTGCCATAATTCTACCAATATGAAATCTGAACCTCAACAAGTATAATCAATCAATACTAAATGTTTTTTATTCCAACACCAAAGAATGGATGGTAAGTTAGCTGTAAAGTTCCTGAAAGTCACGCCTTAC	-	novel	NA	P-0052993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	151	448	0	ENST00000438362.2:c.1778+1_1779-1del		p.X593_splice	ENST00000438362	NM_001242891.1	593			0.3095943908652	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.3095943908652	1		448	621	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115269007	115269602	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTGTGAAAATTAAGGATGCTCATTAACACCATATCACTTCCACACCAATCTCCTTAACTCAGAAAACAAGACCTATAACTCCCCCAGCGCATGCTTTTCATTCCAAATATCCTTTGTTATTACTTCAATGAAATTGATTTTCACCAAAACATTTATGTCTCATCCCACTTTTCACAAAGGATCAAACTTTTATCTTTCAGTCTGTATTCCTTATAGATTCTGAATTTCTCTAGAGGGCTATCCAAAAACCAAACATATTAAGTATGAGAAAAAATGAACAACAACGTAAAATCTTTGGTGTGCTTTTACTTTGATAATGTTTCAGTAGTAACTGTTTTAACTTTCTTACCAATAACGATTTTATTAAGCATGTTTTATCTAACGTTTAAACAGCTAGATTAACAAGGCTTTGATTAACAAAGAGCTTGACAGACACTTTTAATAAGCTGCTTTCAAATACAAGATATTCATGTATTTCTCTTAAACACAAAATATATTTCAGCAAAACTTGATAAAATTTGAAGAACCCATCCTGCAGGATTTATGATTAAGATGACAACTCTTAACCCTCTCTCGAATGAGCAGAATTATCTTG	CCTGTGAAAATTAAGGATGCTCATTAACACCATATCACTTCCACACCAATCTCCTTAACTCAGAAAACAAGACCTATAACTCCCCCAGCGCATGCTTTTCATTCCAAATATCCTTTGTTATTACTTCAATGAAATTGATTTTCACCAAAACATTTATGTCTCATCCCACTTTTCACAAAGGATCAAACTTTTATCTTTCAGTCTGTATTCCTTATAGATTCTGAATTTCTCTAGAGGGCTATCCAAAAACCAAACATATTAAGTATGAGAAAAAATGAACAACAACGTAAAATCTTTGGTGTGCTTTTACTTTGATAATGTTTCAGTAGTAACTGTTTTAACTTTCTTACCAATAACGATTTTATTAAGCATGTTTTATCTAACGTTTAAACAGCTAGATTAACAAGGCTTTGATTAACAAAGAGCTTGACAGACACTTTTAATAAGCTGCTTTCAAATACAAGATATTCATGTATTTCTCTTAAACACAAAATATATTTCAGCAAAACTTGATAAAATTTGAAGAACCCATCCTGCAGGATTTATGATTAAGATGACAACTCTTAACCCTCTCTCGAATGAGCAGAATTATCTTG	-	novel	NA	P-0052993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	120	352	0	ENST00000438362.2:c.1602+2_1603del		p.X534_splice	ENST00000438362	NM_001242891.1	534		14/20	0.3095943908652	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.3095943908652	1		352	522	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419965	152419965	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200128829	NA	P-0052993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	171	714	1	ENST00000206249.3:c.1652C>T	p.Ala551Val	p.A551V	ENST00000206249	NM_000125.3	551	gCg/gTg	8/8	0.3095943908652	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.3095943908652	1		715	894	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273043	115273127	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTAAAAATGATAAAACAAAATTAACTTTCAATTGAAAAAGAAAGCATCAAGAAACACCTCCCAACTTTTCTCAGAAACAACTCA	CCTAAAAATGATAAAACAAAATTAACTTTCAATTGAAAAAGAAAGCATCAAGAAACACCTCCCAACTTTTCTCAGAAACAACTCA	-	novel	NA	P-0052993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	124	438	0	ENST00000438362.2:c.1329+2_1330del		p.X443_splice	ENST00000438362	NM_001242891.1	443		12/20	0.3095943908652	1	FACETS	0.916	0.83	1	0.916	0.83	1	CLONAL	1	TRUE	0	0.3095943908652	1		438	739	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578668	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAAGCAACTGGAAGACGGCAGCAAAGAAACAAACATGCGTAAGCACCTCCTGCAACCCACT	ATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGAAGGAGACAGAGTTGAAAGTCAGGGCACAAGTGAACAGATAAAGCAACTGGAAGACGGCAGCAAAGAAACAAACATGCGTAAGCACCTCCTGCAACCCACT	-	novel	NA	P-0052993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	112	882	0	ENST00000269305.4:c.376-114_398del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	0.300118611569199	1	FACETS	0.638	0.573	0.707	0.638	0.573	0.707	SUBCLONAL	1	TRUE	0	0.3095943908652	1		882	959	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299078	15299078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765979836	NA	P-0052993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	75	671	0	ENST00000263388.2:c.1460G>A	p.Arg487Gln	p.R487Q	ENST00000263388	NM_000435.2	487	cGa/cAa	9/33	1	2	FACETS	0.469	0.409	0.533	0.469	0.409	0.533	SUBCLONAL	1	TRUE	1	0.3095943908652	2		671	1034	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606657	29606657	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	146	641	0	ENST00000389048.3:c.1223C>A	p.Ser408Tyr	p.S408Y	ENST00000389048	NM_004304.4	408	tCc/tAc	5/29	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.3095943908652	2		641	900	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs11575997	NA	P-0052994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	98	726	0	ENST00000269305.4:c.993+1G>T		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.179851311483066	2	FACETS	0.78	0.697	0.869	0.78	0.697	0.869	SUBCLONAL	2	TRUE	0	0.19	2		726	661	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717605	89717626	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGCAGATCCTCAGTTTGTGGTC	TGCAGATCCTCAGTTTGTGGTC	-	novel	NA	P-0052994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	23	448	0	ENST00000371953.3:c.635-2_654del		p.X212_splice	ENST00000371953	NM_000314.4	212		7/9	1	2	FACETS	0.608	0.474	0.765	0.608	0.474	0.765	SUBCLONAL	1	TRUE	1	0.19	2		448	398	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588095	69588095	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	57	698	1	ENST00000168712.1:c.603C>A	p.His201Gln	p.H201Q	ENST00000168712	NM_002007.2	201	caC/caA	3/3	0.26152807846849	4	FACETS	0.888	0.76	1	0.444	0.38	0.514	CLONAL	1	TRUE	2	0.19	4		699	804	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996826	100996826	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0052994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	47	618	0	ENST00000325455.5:c.1701T>A	p.Cys567Ter	p.C567*	ENST00000325455	NM_001202474.3	567	tgT/tgA	2/8	0.26152807846849	4	FACETS	0.929	0.782	1	0.464	0.391	0.545	CLONAL	1	TRUE	2	0.19	4		618	634	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428078	49428078	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	111	807	1	ENST00000301067.7:c.10512A>C	p.Glu3504Asp	p.E3504D	ENST00000301067	NM_003482.3	3504	gaA/gaC	38/54	0.3	3	FACETS	0.805	0.723	0.891	0.805	0.723	0.891	CLONAL	2	TRUE	1	0.19	3		808	795	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931822	28931822	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	55	392	1	ENST00000282397.4:c.2117G>T	p.Gly706Val	p.G706V	ENST00000282397	NM_002019.4	706	gGa/gTa	15/30	0.160541568877242	2	FACETS	0.787	0.676	0.907	0.787	0.676	0.907	CLONAL	2	TRUE	0	0.19	2		393	368	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051183	13051183	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	103	712	0	ENST00000316448.5:c.619A>G	p.Lys207Glu	p.K207E	ENST00000316448	NM_004343.3	207	Aag/Gag	5/9	0.142999393449623	4	FACETS	0.764	0.683	0.851	0.764	0.683	0.851	SUBCLONAL	2	TRUE	2	0.19	4		712	844	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960129	151960129	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	53	544	0	ENST00000262189.6:c.1271C>A	p.Ser424Ter	p.S424*	ENST00000262189	NM_170606.2	424	tCa/tAa	9/59	0.21719378916363	4	FACETS	1	0.957	1			1	CLONAL	1	TRUE	NA	0.19	4		544	491	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345715	152345859	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	TTATGATGTATATCAACAAAATTCAACCCCACTTTCTCCAATAATAAAAAAATGTTTTTTTAAACTGTTACTTTTTAAACAACGTGAAACTAATGAAAATTGGTTGCTGCTTTGAGAATCATCTTGTTTGGAGAAAAACATCCTG	TTATGATGTATATCAACAAAATTCAACCCCACTTTCTCCAATAATAAAAAAATGTTTTTTTAAACTGTTACTTTTTAAACAACGTGAAACTAATGAAAATTGGTTGCTGCTTTGAGAATCATCTTGTTTGGAGAAAAACATCCTG	-	novel	NA	P-0052994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	74	219	0	ENST00000359321.1:c.711_*12del		p.*237*	ENST00000359321	NM_005431.1	237		3/3	0.140757729507071	3	FACETS	0.969	0.863	1			1	CLONAL	4	TRUE	NA	0.19	3		219	220	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738299	145738299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762644049	NA	P-0052994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	206	1024	0	ENST00000428558.2:c.2686G>A	p.Val896Ile	p.V896I	ENST00000428558	NM_004260.3	896	Gtc/Atc	16/22	0.3	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.19	3		1024	1071	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534995	5534995	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	32	524	0	ENST00000397747.3:c.306C>A	p.Cys102Ter	p.C102*	ENST00000397747	NM_025239.3	102	tgC/tgA	3/7	0.20801267886898	3	FACETS	0.588	0.476	0.716	0.196	0.158	0.239	SUBCLONAL	1	TRUE	0	0.19	3		524	627	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	35	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.804	0.677	0.938	0.804	0.677	0.938	CLONAL	1	TRUE	1	0.82901919124993	2		429	105	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42861441	42861441	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	144	426	0	ENST00000398585.3:c.429G>A	p.Trp143Ter	p.W143*	ENST00000398585	NM_001135099.1	143	tgG/tgA	4/14	0.187859276260432	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.82901919124993	0		426	334	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164159	32164159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	249	618	0	ENST00000375023.3:c.5240C>T	p.Ala1747Val	p.A1747V	ENST00000375023	NM_004557.3	1747	gCc/gTc	29/30	1	2	FACETS	0.99	0.933	1	0.99	0.933	1	CLONAL	1	TRUE	1	0.82901919124993	2		618	607	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949086	44949088	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	novel	NA	P-0052997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	109	264	0	ENST00000377967.4:c.3647_3649del	p.Asp1216_Leu1217delinsVal	p.D1216_L1217delinsV	ENST00000377967	NM_021140.2	1216	gATTtg/gtg	25/29	NA	2	FACETS	1	0.949	1			1	INDETERMINATE	2	FALSE	NA	0.303098813261533	2		264	337	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371708	225371708	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	69	496	0	ENST00000264414.4:c.896T>G	p.Met299Arg	p.M299R	ENST00000264414	NM_003590.4	299	aTg/aGg	7/16	1	2	FACETS	0.657	0.573	0.748	0.657	0.573	0.748	SUBCLONAL	1	TRUE	1	0.4	2		496	525	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540662	187540663	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	64	475	1	ENST00000441802.2:c.7077dup	p.Val2360CysfsTer5	p.V2360Cfs*5	ENST00000441802	NM_005245.3	2359	-/T	10/27	1	2	FACETS	0.649	0.563	0.742	0.649	0.563	0.742	SUBCLONAL	1	TRUE	1	0.4	2		476	493	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026436	6026436	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	23	118	0	ENST00000265849.7:c.1960C>A	p.Pro654Thr	p.P654T	ENST00000265849	NM_000535.5	654	Cct/Act	11/15	1	2	FACETS	0.558	0.437	0.697	0.558	0.437	0.697	SUBCLONAL	1	TRUE	1	0.4	2		118	206	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880196	151880196	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	57	495	0	ENST00000262189.6:c.5128C>T	p.Gln1710Ter	p.Q1710*	ENST00000262189	NM_170606.2	1710	Cag/Tag	35/59	0.251039380275385	3	FACETS	0.554	0.475	0.641	0.277	0.237	0.321	SUBCLONAL	1	TRUE	1	0.4	3		495	617	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118784	115118784	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	87	592	0	ENST00000257566.3:c.557T>G	p.Ile186Ser	p.I186S	ENST00000257566	NM_016569.3	186	aTt/aGt	2/8	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		592	601	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	88	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.892	0.795	0.996	0.892	0.795	0.996	CLONAL	1	TRUE	1	0.451278240944552	2		429	437	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	228	411	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.451278240944552	2	FACETS	0.851	0.798	0.903	0.851	0.798	0.903	CLONAL	2	TRUE	0	0.451278240944552	2		411	594	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057835	27057835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	259	808	0	ENST00000324856.7:c.1543C>T	p.Gln515Ter	p.Q515*	ENST00000324856	NM_006015.4	515	Cag/Tag	3/20	1	2	FACETS	0.979	0.917	1	0.979	0.917	1	CLONAL	1	TRUE	1	0.451278240944552	2		808	1172	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510835	157510835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	238	634	0	ENST00000346085.5:c.3610G>A	p.Ala1204Thr	p.A1204T	ENST00000346085	NM_020732.3	1204	Gca/Aca	14/20	0.451278240944552	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.451278240944552	1		634	799	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154432	2154432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376878619	NA	P-0053001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	114	781	0	ENST00000434045.2:c.496G>A	p.Val166Met	p.V166M	ENST00000434045	NM_001127598.1	166	Gtg/Atg	5/5	0.262829786119066	1	FACETS	0.43	0.387	0.477	0.43	0.387	0.477	INDETERMINATE	1	TRUE	0	0.451278240944552	1		781	909	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907522	32907522	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs431825288	NA	P-0053001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	60	264	0	ENST00000380152.3:c.1907C>T	p.Ser636Leu	p.S636L	ENST00000380152		636	tCa/tTa	10/27	1	2	FACETS	0.917	0.797	1	0.917	0.797	1	CLONAL	1	TRUE	1	0.451278240944552	2		264	290	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519912	NA	P-0053002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	20	382	0	ENST00000374080.3:c.3670C>G	p.Leu1224Val	p.L1224V	ENST00000374080		1224	Ctc/Gtc	26/45	NA	2	FACETS	0.359	0.274	0.459			1	INDETERMINATE	1	FALSE	NA	0.3	2		382	371	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936830	32936830	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs80359027	NA	P-0053003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	55	332	0	ENST00000380152.3:c.7976G>A	p.Arg2659Lys	p.R2659K	ENST00000380152		2659	aGa/aAa	17/27	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.32	2		332	292	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0053004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	713	723	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	0.71320825811896	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.742999138945657	2		723	899	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033934	49033934	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	200	437	0	ENST00000267163.4:c.2071G>T	p.Glu691Ter	p.E691*	ENST00000267163	NM_000321.2	691	Gag/Tag	20/27	0.717327915197182	1	FACETS	0.995	0.941	1	0.995	0.941	1	CLONAL	1	TRUE	0	0.742999138945657	1		437	340	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166235	118166235	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	182	434	0	ENST00000369448.3:c.745A>G	p.Asn249Asp	p.N249D	ENST00000369448	NM_017709.3	249	Aac/Gac	2/2	0.742999138945657	3	FACETS	0.963	0.891	1	0.481	0.445	0.518	CLONAL	1	TRUE	1	0.742999138945657	3		434	698	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458992	120458992	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	287	676	0	ENST00000256646.2:c.6353A>C	p.Asn2118Thr	p.N2118T	ENST00000256646	NM_024408.3	2118	aAc/aCc	34/34	0.742999138945657	3	FACETS	0.956	0.899	1	0.478	0.449	0.508	CLONAL	1	TRUE	1	0.742999138945657	3		676	1108	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427585	72427585	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	223	379	0	ENST00000477973.2:c.905C>G	p.Ser302Cys	p.S302C	ENST00000477973	NM_012234.5	302	tCc/tGc	4/4	0.742999138945657	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.742999138945657	1		379	330	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220444	98220444	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	684	608	0	ENST00000331920.6:c.3019T>C	p.Ser1007Pro	p.S1007P	ENST00000331920	NM_000264.3	1007	Tcc/Ccc	18/24	0.599333411629284	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	2	0.742999138945657	4		608	1451	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0053005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	53	353	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.275776918959853	1	FACETS	0.833	0.712	0.964	0.833	0.712	0.964	CLONAL	1	FALSE	0	0.275776918959853	1		353	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0053005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	103	855	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.275776918959853	1	FACETS	0.98	0.878	1	0.98	0.878	1	CLONAL	1	FALSE	0	0.275776918959853	1		855	657	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188196	32188196	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs752469207	NA	P-0053005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	42	715	0	ENST00000375023.3:c.1145C>A	p.Pro382Gln	p.P382Q	ENST00000375023	NM_004557.3	382	cCa/cAa	6/30	0.178318746968624	3	FACETS	0.564	0.47	0.668	0.188	0.156	0.223	SUBCLONAL	1	FALSE	0	0.275776918959853	3		715	615	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115269712	115269712	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0053005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	35	333	0	ENST00000438362.2:c.1495-1G>C		p.X499_splice	ENST00000438362	NM_001242891.1	499			1	2	FACETS	0.811	0.667	0.972	0.811	0.667	0.972	CLONAL	1	FALSE	1	0.275776918959853	2		333	313	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729596	162729596	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	65	449	0	ENST00000367921.3:c.682G>T	p.Gly228Trp	p.G228W	ENST00000367921	NM_006182.2	228	Ggg/Tgg	8/18	0.214677265678355	4	FACETS	1	0.93	1	0.371	0.321	0.424	CLONAL	1	FALSE	1	0.275776918959853	4		449	541	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708614	43708614	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	33	429	0	ENST00000382044.4:c.4682G>T	p.Gly1561Val	p.G1561V	ENST00000382044	NM_001141980.1	1561	gGa/gTa	22/28	0.128986354006872	0	FACETS	0.423	0.344	0.511			1	INDETERMINATE	1	FALSE	0	0.275776918959853	0		429	410	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819628	81819628	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	84	656	1	ENST00000359376.3:c.34G>T	p.Glu12Ter	p.E12*	ENST00000359376	NM_002661.3	12	Gaa/Taa	2/33	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.275776918959853	2		657	533	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231734	66231734	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	49	491	0	ENST00000273854.3:c.1966T>A	p.Tyr656Asn	p.Y656N	ENST00000273854	NM_004439.5	656	Tat/Aat	11/18	0.128986354006872	0	FACETS	0.688	0.585	0.801			1	INDETERMINATE	1	FALSE	0	0.275776918959853	0		491	374	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178125	56178125	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	67	427	0	ENST00000399503.3:c.3098G>C	p.Cys1033Ser	p.C1033S	ENST00000399503	NM_005921.1	1033	tGt/tCt	14/20	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	FALSE	1	0.275776918959853	2		427	450	SUCCESS
AR	367	MSKCC	GRCh37	X	66765547	66765547	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	52	794	3	ENST00000374690.3:c.559G>T	p.Glu187Ter	p.E187*	ENST00000374690	NM_000044.3	187	Gag/Tag	1/8	0.264660832367102	0	FACETS	0.594	0.506	0.69			1	SUBCLONAL	1	FALSE	0	0.275776918959853	0		797	460	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602746	10602746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	80	548	0	ENST00000171111.5:c.832C>T	p.Pro278Ser	p.P278S	ENST00000171111	NM_203500.1	278	Ccg/Tcg	3/6	1	2	FACETS	0.614	0.539	0.695	0.614	0.539	0.695	SUBCLONAL	1	TRUE	1	0.26988686548828	2		548	965	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102033194	102033194	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	34	332	0	ENST00000282441.5:c.580del	p.Asp194IlefsTer17	p.D194Ifs*17	ENST00000282441	NM_001130145.2	194	Gat/at	3/9	1	2	FACETS	0.485	0.396	0.586	0.485	0.396	0.586	SUBCLONAL	1	TRUE	1	0.26988686548828	2		332	519	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807853	3807853	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	44	330	0	ENST00000262367.5:c.3566T>G	p.Ile1189Ser	p.I1189S	ENST00000262367	NM_004380.2	1189	aTt/aGt	18/31	1	2	FACETS	0.589	0.493	0.694	0.589	0.493	0.694	SUBCLONAL	1	TRUE	1	0.26988686548828	2		330	554	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978648	70978648	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	52	417	0	ENST00000276594.2:c.1005G>T	p.Lys335Asn	p.K335N	ENST00000276594	NM_024504.3	335	aaG/aaT	5/8	1	2	FACETS	0.497	0.422	0.579	0.497	0.422	0.579	SUBCLONAL	1	TRUE	1	0.26988686548828	2		417	776	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0053008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	183	485	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.194582332041945	3	FACETS	1	0.961	1	0.705	0.653	0.76	CLONAL	2	TRUE	0	0.271309595665835	3		486	724	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038526	47038526	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	135	279	0	ENST00000377604.3:c.688C>T	p.Arg230Ter	p.R230*	ENST00000377604	NM_001204468.1	230	Cga/Tga	8/24	1	1	FACETS	0.973	0.892	1	1	0.991	1	CLONAL	2	TRUE	0	0.271309595665835	1		279	442	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828824	26828824	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	28	300	0	ENST00000381527.3:c.46G>C	p.Val16Leu	p.V16L	ENST00000381527	NM_001260.1	16	Gtc/Ctc	1/13	0.205594714137588	4	FACETS	0.62	0.495	0.763	0.207	0.165	0.255	SUBCLONAL	1	TRUE	1	0.271309595665835	4		300	423	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575108	48575108	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs377767323	NA	P-0053008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	39	297	0	ENST00000342988.3:c.302G>A	p.Trp101Ter	p.W101*	ENST00000342988	NM_005359.5	101	tGg/tAg	3/12	0.271309595665835	1	FACETS	0.767	0.638	0.91	0.767	0.638	0.91	CLONAL	1	TRUE	0	0.271309595665835	1		297	324	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690848	89690848	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0053009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	25	259	0	ENST00000371953.3:c.253+2T>G		p.X85_splice	ENST00000371953	NM_000314.4	85			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		259	163	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0053010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	302	743	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.449796406351226	3	FACETS	1	0.981	1			1	CLONAL	3	TRUE	NA	0.578611935113066	3		745	434	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18496270	18496270	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	57	130	0	ENST00000266497.5:c.1405C>G	p.Gln469Glu	p.Q469E	ENST00000266497		469	Caa/Gaa	9/31	0.403063365228009	3	FACETS	0.87	0.752	0.996			1	CLONAL	1	TRUE	NA	0.578611935113066	3		130	292	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914513	32914516	+	frameshift_variant	Frame_Shift_Del	DEL	CAAG	CAAG	-	novel	NA	P-0053010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	149	418	0	ENST00000380152.3:c.6025_6028del	p.Gln2009SerfsTer30	p.Q2009Sfs*30	ENST00000380152		2007	acCAAG/ac	11/27	0.578611935113066	2	FACETS	0.873	0.813	0.933	0.873	0.813	0.933	CLONAL	2	TRUE	0	0.578611935113066	2		418	295	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39347476	39347476	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0053010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	107	422	2	ENST00000402219.2:c.87+1G>T		p.X29_splice	ENST00000402219	NM_005633.3	29			0.501604998837312	4	FACETS	0.993	0.904	1	0.993	0.904	1	CLONAL	2	TRUE	2	0.578611935113066	4		424	294	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595557	55595557	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1462960552	NA	P-0053010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	50	340	0	ENST00000288135.5:c.2047A>G	p.Arg683Gly	p.R683G	ENST00000288135	NM_000222.2	683	Aga/Gga	14/21	0.510476819856604	3	FACETS	0.75	0.641	0.869	0.375	0.32	0.435	SUBCLONAL	1	TRUE	1	0.578611935113066	3		340	297	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217197	66217197	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	100	436	0	ENST00000273854.3:c.2418C>G	p.Ile806Met	p.I806M	ENST00000273854	NM_004439.5	806	atC/atG	14/18	0.510476819856604	3	FACETS	1	0.974	1	0.626	0.564	0.69	CLONAL	1	TRUE	1	0.578611935113066	3		436	356	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250143	110250143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750512051	NA	P-0053010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	114	798	1	ENST00000374672.4:c.532G>A	p.Ala178Thr	p.A178T	ENST00000374672	NM_004235.4	178	Gct/Act	3/5	0.403063365228009	3	FACETS	1	0.961	1			1	CLONAL	1	TRUE	NA	0.578611935113066	3		799	456	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	24	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.712	0.562	0.881	0.712	0.562	0.881	SUBCLONAL	1	FALSE	1	0.385489765114134	2		429	175	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	92	372	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.268398363685984	3	FACETS	1	0.934	1	0.533	0.475	0.595	CLONAL	1	FALSE	1	0.385489765114134	3		372	534	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248617	212248617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765120252	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	233	378	0	ENST00000342788.4:c.3650G>A	p.Gly1217Glu	p.G1217E	ENST00000342788	NM_005235.2	1217	gGa/gAa	28/28	0.385489765114134	3	FACETS	0.907	0.854	0.96	0.907	0.854	0.96	CLONAL	3	FALSE	0	0.385489765114134	3		378	530	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	153	311	1	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.385489765114134	3	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	FALSE	1	0.385489765114134	3		312	468	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750440	41750440	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	92	454	0	ENST00000226382.2:c.188G>A	p.Gly63Glu	p.G63E	ENST00000226382	NM_003924.3	63	gGa/gAa	1/3	0.168224317376605	0	FACETS	0.774	0.693	0.859			1	INDETERMINATE	1	FALSE	0	0.385489765114134	0		454	379	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259262	89259262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770780950	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	65	308	1	ENST00000336596.2:c.406C>T	p.Arg136Ter	p.R136*	ENST00000336596	NM_005233.5	136	Cga/Tga	3/17	NA	2	FACETS	0.98	0.855	1			1	INDETERMINATE	1	FALSE	NA	0.385489765114134	2		309	344	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546769	9546769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	53	355	0	ENST00000353224.5:c.1253C>T	p.Ser418Phe	p.S418F	ENST00000353224	NM_177990.2	418	tCc/tTc	5/10	0.241261285800245	0	FACETS	0.748	0.645	0.857			1	SUBCLONAL	1	FALSE	0	0.385489765114134	0		355	226	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858007	9858007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	58	375	0	ENST00000330684.3:c.3394C>T	p.Pro1132Ser	p.P1132S	ENST00000330684	NM_001134407.1	1132	Cca/Tca	13/13	0.385489765114134	1	FACETS	0.903	0.783	1	0.903	0.783	1	CLONAL	1	FALSE	0	0.385489765114134	1		375	269	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1039289	1039289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11571421	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	73	376	1	ENST00000358495.3:c.208C>T	p.Arg70Trp	p.R70W	ENST00000358495	NM_134424.2	70	Cgg/Tgg	4/12	NA	2	FACETS	0.765	0.671	0.866			1	INDETERMINATE	1	FALSE	NA	0.385489765114134	2		377	495	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619437	1619437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	58	500	0	ENST00000344749.5:c.1204C>T	p.His402Tyr	p.H402Y	ENST00000344749	NM_001136139.2	402	Cac/Tac	15/19	1	2	FACETS	0.604	0.52	0.696	0.604	0.52	0.696	SUBCLONAL	1	FALSE	1	0.385489765114134	2		500	498	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972912	55972912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1415977038	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	75	359	0	ENST00000263923.4:c.1478G>A	p.Gly493Glu	p.G493E	ENST00000263923	NM_002253.2	493	gGa/gAa	11/30	0.168224317376605	0	FACETS	0.668	0.589	0.751			1	INDETERMINATE	1	FALSE	0	0.385489765114134	0		359	358	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765576	41765576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763066660	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	61	487	0	ENST00000301178.4:c.2452G>A	p.Glu818Lys	p.E818K	ENST00000301178	NM_021913.4	818	Gaa/Aaa	20/20	1	2	FACETS	0.617	0.533	0.708	0.617	0.533	0.708	SUBCLONAL	1	FALSE	1	0.385489765114134	2		487	513	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331729	68331729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	37	145	0	ENST00000487270.1:c.325C>T	p.Pro109Ser	p.P109S	ENST00000487270	NM_133509.3	109	Cca/Tca	5/11	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	FALSE	1	0.385489765114134	2		145	161	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244913	123244913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1224606327	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	86	540	0	ENST00000358487.5:c.2191G>A	p.Glu731Lys	p.E731K	ENST00000358487	NM_000141.4	731	Gaa/Aaa	16/18	0.385489765114134	0	FACETS	0.814	0.726	0.905			1	CLONAL	1	FALSE	0	0.385489765114134	0		540	337	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608325	100608325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	83	371	0	ENST00000308731.7:c.1765G>A	p.Glu589Lys	p.E589K	ENST00000308731	NM_000061.2	589	Gaa/Aaa	18/19	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	FALSE	1	0.385489765114134	2		371	425	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472522	88472522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55890138	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	169	556	0	ENST00000360948.2:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000360948	NM_001012338.2	678	cGa/cAa	16/19	0.355929300394042	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	0	0.385489765114134	1		556	529	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561090	9561090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	41	305	0	ENST00000353224.5:c.692C>T	p.Ser231Leu	p.S231L	ENST00000353224	NM_177990.2	231	tCa/tTa	4/10	0.241261285800245	0	FACETS	0.542	0.455	0.638			1	SUBCLONAL	1	FALSE	0	0.385489765114134	0		305	241	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692991	89692991	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786202688	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	67	301	0	ENST00000371953.3:c.475A>G	p.Arg159Gly	p.R159G	ENST00000371953	NM_000314.4	159	Agg/Ggg	5/9	0.360325335466203	1	FACETS	0.82	0.718	0.93	0.82	0.718	0.93	CLONAL	1	FALSE	0	0.385489765114134	1		301	342	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466972	18466972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	80	274	0	ENST00000266497.5:c.1111G>A	p.Glu371Lys	p.E371K	ENST00000266497		371	Gaa/Aaa	5/31	0.272691608878345	1	FACETS	0.946	0.839	1	0.946	0.839	1	CLONAL	1	FALSE	0	0.385489765114134	1		274	354	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066570	94066570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	167	354	0	ENST00000369303.4:c.1189G>A	p.Asp397Asn	p.D397N	ENST00000369303	NM_004440.3	397	Gat/Aat	5/17	0.291388484626706	3	FACETS	1	0.984	1	0.809	0.751	0.867	CLONAL	2	FALSE	0	0.385489765114134	3		354	426	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033167	69033167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	84	362	0	ENST00000288368.4:c.3607G>A	p.Glu1203Lys	p.E1203K	ENST00000288368	NM_024870.2	1203	Gaa/Aaa	30/40	0.129014481340026	0	FACETS	0.685	0.609	0.765			1	INDETERMINATE	1	FALSE	0	0.385489765114134	0		362	391	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046410	69046410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868582467	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	145	479	0	ENST00000288368.4:c.3883G>A	p.Glu1295Lys	p.E1295K	ENST00000288368	NM_024870.2	1295	Gaa/Aaa	32/40	0.129014481340026	0	FACETS	0.83	0.761	0.901			1	INDETERMINATE	1	FALSE	0	0.385489765114134	0		479	557	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389318	8389318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	70	378	2	ENST00000356435.5:c.4300G>A	p.Glu1434Lys	p.E1434K	ENST00000356435		1434	Gaa/Aaa	26/35	0.362581994267146	0	FACETS	0.789	0.695	0.888			1	SUBCLONAL	1	FALSE	0	0.385489765114134	0		380	283	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458428	12458428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	93	479	0	ENST00000287820.6:c.1045G>A	p.Gly349Arg	p.G349R	ENST00000287820	NM_015869.4	349	Gga/Aga	6/7	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	FALSE	1	0.385489765114134	2		479	462	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858732	9858732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	55	277	0	ENST00000330684.3:c.2669C>T	p.Ser890Phe	p.S890F	ENST00000330684	NM_001134407.1	890	tCc/tTc	13/13	0.385489765114134	1	FACETS	0.984	0.852	1	0.984	0.852	1	CLONAL	1	FALSE	0	0.385489765114134	1		277	234	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344458	118344458	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	54	215	0	ENST00000534358.1:c.2584C>T	p.Arg862Ter	p.R862*	ENST00000534358	NM_005933.3	862	Cga/Tga	3/36	0.151793664505031	3	FACETS	1	0.947	1	0.61	0.525	0.701	INDETERMINATE	1	FALSE	1	0.385489765114134	3		215	274	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27183486	27183486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	70	347	0	ENST00000380036.4:c.1060G>A	p.Asp354Asn	p.D354N	ENST00000380036	NM_000459.3	354	Gat/Aat	8/23	0.148824586102567	3	FACETS	1	0.917	1	0.354	0.31	0.401	INDETERMINATE	1	FALSE	0	0.385489765114134	3		347	408	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223703	36223703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	102	747	0	ENST00000222270.7:c.6253C>T	p.Pro2085Ser	p.P2085S	ENST00000222270	NM_014727.1	2085	Cct/Tct	28/37	1	2	FACETS	0.771	0.69	0.857	0.771	0.69	0.857	SUBCLONAL	1	FALSE	1	0.385489765114134	2		747	686	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443615	29443615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	104	470	1	ENST00000389048.3:c.3602G>A	p.Gly1201Glu	p.G1201E	ENST00000389048	NM_004304.4	1201	gGg/gAg	23/29	0.272691608878345	1	FACETS	0.804	0.722	0.89	0.804	0.722	0.89	CLONAL	1	FALSE	0	0.385489765114134	1		471	542	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858448	9858448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	62	405	0	ENST00000330684.3:c.2953C>T	p.Pro985Ser	p.P985S	ENST00000330684	NM_001134407.1	985	Cct/Tct	13/13	0.385489765114134	1	FACETS	0.866	0.754	0.985	0.866	0.754	0.985	CLONAL	1	FALSE	0	0.385489765114134	1		405	300	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609417	81609417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150821978	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	92	363	0	ENST00000298171.2:c.1015G>A	p.Glu339Lys	p.E339K	ENST00000298171	NM_000369.2	339	Gaa/Aaa	10/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.385489765114134	2		363	427	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627355	37627355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs910521882	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	96	750	2	ENST00000249071.6:c.364G>A	p.Asp122Asn	p.D122N	ENST00000249071	NM_002872.4	122	Gac/Aac	5/7	0.268398363685984	3	FACETS	0.61	0.542	0.682	0.305	0.271	0.341	SUBCLONAL	1	FALSE	1	0.385489765114134	3		752	974	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867608	78867608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	154	576	1	ENST00000306801.3:c.2344G>A	p.Glu782Lys	p.E782K	ENST00000306801	NM_020761.2	782	Gag/Aag	20/34	0.268398363685984	3	FACETS	1	0.988	1	0.74	0.679	0.803	CLONAL	1	FALSE	1	0.385489765114134	3		577	644	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528015	103528015	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	105	279	0	ENST00000355739.4:c.3323C>T	p.Ser1108Leu	p.S1108L	ENST00000355739	NM_000123.3	1108	tCa/tTa	15/15	0.385489765114134	3	FACETS	0.808	0.73	0.89	0.808	0.73	0.89	CLONAL	2	FALSE	1	0.385489765114134	3		279	402	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256559	133256559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	76	387	0	ENST00000320574.5:c.404C>T	p.Pro135Leu	p.P135L	ENST00000320574	NM_006231.2	135	cCc/cTc	5/49	0.168224317376605	0	FACETS	0.528	0.464	0.596			1	INDETERMINATE	1	FALSE	0	0.385489765114134	0		387	459	SUCCESS
AR	367	MSKCC	GRCh37	X	66765485	66765485	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	82	599	0	ENST00000374690.3:c.497T>C	p.Leu166Pro	p.L166P	ENST00000374690	NM_000044.3	166	cTg/cCg	1/8	0.360325335466203	1	FACETS	0.965	0.857	1	0.965	0.857	1	CLONAL	1	FALSE	0	0.385489765114134	1		599	356	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421005	49421005	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1205058693	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	50	251	0	ENST00000301067.7:c.14744C>T	p.Ser4915Phe	p.S4915F	ENST00000301067	NM_003482.3	4915	tCc/tTc	48/54	0.151793664505031	3	FACETS	1	0.917	1	0.554	0.474	0.642	INDETERMINATE	1	FALSE	1	0.385489765114134	3		251	279	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807507	36807507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1389904784	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	109	622	0	ENST00000373129.3:c.1157C>T	p.Ala386Val	p.A386V	ENST00000373129	NM_032017.1	386	gCc/gTc	12/12	1	2	FACETS	0.871	0.784	0.964	0.871	0.784	0.964	CLONAL	1	FALSE	1	0.385489765114134	2		622	649	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458186	120458186	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1193431892	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	99	558	0	ENST00000256646.2:c.7159C>T	p.Pro2387Ser	p.P2387S	ENST00000256646	NM_024408.3	2387	Cct/Tct	34/34	1	2	FACETS	0.975	0.873	1	0.975	0.873	1	CLONAL	1	FALSE	1	0.385489765114134	2		558	527	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094325	193094325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	68	229	0	ENST00000367435.3:c.215C>T	p.Pro72Leu	p.P72L	ENST00000367435	NM_024529.4	72	cCt/cTt	2/17	1	2	FACETS	0.754	0.658	0.857	0.754	0.658	0.857	SUBCLONAL	1	FALSE	1	0.385489765114134	2		229	468	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243668631	243668631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	57	272	0	ENST00000263826.5:c.1360G>A	p.Glu454Lys	p.E454K	ENST00000263826	NM_005465.4	454	Gag/Aag	13/13	1	2	FACETS	0.797	0.687	0.916	0.797	0.687	0.916	CLONAL	1	FALSE	1	0.385489765114134	2		272	371	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195686	102195686	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	73	323	0	ENST00000263464.3:c.446G>C	p.Arg149Thr	p.R149T	ENST00000263464	NM_001165.4	149	aGa/aCa	2/9	0.151793664505031	3	FACETS	0.916	0.803	1	0.458	0.401	0.519	INDETERMINATE	1	FALSE	1	0.385489765114134	3		323	493	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435193	18435193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	75	271	0	ENST00000266497.5:c.178G>A	p.Glu60Lys	p.E60K	ENST00000266497		60	Gaa/Aaa	1/31	0.272691608878345	1	FACETS	0.955	0.843	1	0.955	0.843	1	CLONAL	1	FALSE	0	0.385489765114134	1		271	329	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244739	46244739	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	80	393	0	ENST00000334344.6:c.2833C>T	p.Gln945Ter	p.Q945*	ENST00000334344	NM_152641.2	945	Caa/Taa	15/21	0.151793664505031	3	FACETS	1	0.911	1	0.519	0.458	0.584	INDETERMINATE	1	FALSE	1	0.385489765114134	3		393	477	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482416	56482416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770284356	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	64	414	0	ENST00000267101.3:c.964C>T	p.Pro322Ser	p.P322S	ENST00000267101	NM_001982.3	322	Cct/Tct	8/28	0.151793664505031	3	FACETS	0.85	0.738	0.971	0.425	0.369	0.486	INDETERMINATE	1	FALSE	1	0.385489765114134	3		414	466	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858570	57858570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	90	521	0	ENST00000228682.2:c.308C>T	p.Pro103Leu	p.P103L	ENST00000228682	NM_005269.2	103	cCc/cTc	4/12	0.151793664505031	3	FACETS	0.764	0.678	0.856	0.382	0.339	0.428	INDETERMINATE	1	FALSE	1	0.385489765114134	3		521	729	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856449	111856449	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	41	161	0	ENST00000341259.2:c.500G>A	p.Gly167Glu	p.G167E	ENST00000341259	NM_005475.2	167	gGa/gAa	2/8	0.151793664505031	3	FACETS	0.9	0.754	1	0.45	0.377	0.53	INDETERMINATE	1	FALSE	1	0.385489765114134	3		161	282	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023291	33023291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1202298191	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	260	494	1	ENST00000300177.4:c.400G>A	p.Glu134Lys	p.E134K	ENST00000300177	NM_001191322.1	134	Gag/Aag	2/2	0.268398363685984	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	FALSE	1	0.385489765114134	3		495	670	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643794	38643794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	236	507	0	ENST00000299084.4:c.1264C>T	p.Pro422Ser	p.P422S	ENST00000299084	NM_152594.2	422	Cct/Tct	7/7	0.268398363685984	3	FACETS	0.984	0.922	1	0.984	0.922	1	CLONAL	2	FALSE	1	0.385489765114134	3		507	742	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724561	43724562	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	219	577	0	ENST00000382044.4:c.3505_3506delinsTT	p.Pro1169Leu	p.P1169L	ENST00000382044	NM_001141980.1	1169	CCa/TTa	17/28	0.268398363685984	3	FACETS	0.897	0.838	0.959	0.897	0.838	0.959	CLONAL	2	FALSE	1	0.385489765114134	3		577	755	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032228	10032228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1200624532	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	83	551	0	ENST00000330684.3:c.595G>A	p.Asp199Asn	p.D199N	ENST00000330684	NM_001134407.1	199	Gac/Aac	3/13	0.385489765114134	1	FACETS	0.885	0.785	0.989	0.885	0.785	0.989	CLONAL	1	FALSE	0	0.385489765114134	1		551	393	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732364	74732364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	128	331	0	ENST00000359995.5:c.545G>A	p.Arg182Gln	p.R182Q	ENST00000359995	NM_001195427.1	182	cGg/cAg	2/3	0.268398363685984	3	FACETS	1	0.983	1	0.677	0.616	0.741	CLONAL	1	FALSE	1	0.385489765114134	3		331	585	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211193	2211193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1452632751	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	81	632	1	ENST00000398665.3:c.1447G>A	p.Ala483Thr	p.A483T	ENST00000398665	NM_032482.2	483	Gcg/Acg	15/28	1	2	FACETS	0.802	0.708	0.902	0.802	0.708	0.902	CLONAL	1	FALSE	1	0.385489765114134	2		633	524	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216167	36216167	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	68	606	0	ENST00000222270.7:c.3575T>G	p.Val1192Gly	p.V1192G	ENST00000222270	NM_014727.1	1192	gTg/gGg	11/37	1	2	FACETS	0.622	0.542	0.709	0.622	0.542	0.709	SUBCLONAL	1	FALSE	1	0.385489765114134	2		606	567	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149051	61149051	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	88	328	0	ENST00000295025.8:c.1241C>T	p.Ser414Leu	p.S414L	ENST00000295025	NM_002908.2	414	tCa/tTa	11/11	0.151793664505031	3	FACETS	1	0.922	1	0.524	0.465	0.586	INDETERMINATE	1	FALSE	1	0.385489765114134	3		328	520	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021341	31021341	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	76	417	0	ENST00000375687.4:c.1340C>T	p.Pro447Leu	p.P447L	ENST00000375687	NM_015338.5	447	cCc/cTc	12/13	0.268398363685984	3	FACETS	0.846	0.743	0.956	0.423	0.371	0.478	CLONAL	1	FALSE	1	0.385489765114134	3		417	556	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125334	47125335	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	65	330	1	ENST00000409792.3:c.5935_5936delinsTT	p.Pro1979Leu	p.P1979L	ENST00000409792	NM_014159.6	1979	CCa/TTa	12/21	1	2	FACETS	0.807	0.702	0.919	0.807	0.702	0.919	CLONAL	1	FALSE	1	0.385489765114134	2		331	418	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643462	52643462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	62	371	0	ENST00000394830.3:c.2434C>T	p.Pro812Ser	p.P812S	ENST00000394830	NM_018313.4	812	Ccc/Tcc	17/30	1	2	FACETS	0.804	0.697	0.919	0.804	0.697	0.919	CLONAL	1	FALSE	1	0.385489765114134	2		371	400	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169999740	169999740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	61	235	0	ENST00000295797.4:c.1051C>T	p.Pro351Ser	p.P351S	ENST00000295797	NM_002740.5	351	Cct/Tct	11/18	1	2	FACETS	0.867	0.752	0.991	0.867	0.752	0.991	CLONAL	1	FALSE	1	0.385489765114134	2		235	365	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586455	189586455	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	66	338	0	ENST00000264731.3:c.1079G>A	p.Arg360Lys	p.R360K	ENST00000264731	NM_003722.4	360	aGa/aAa	8/14	1	2	FACETS	0.976	0.852	1	0.976	0.852	1	CLONAL	1	FALSE	1	0.385489765114134	2		338	351	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808048	1808048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	97	698	1	ENST00000260795.2:c.2024G>A	p.Ser675Asn	p.S675N	ENST00000260795		675	aGt/aAt	14/17	0.168224317376605	0	FACETS	0.544	0.486	0.606			1	INDETERMINATE	1	FALSE	0	0.385489765114134	0		699	568	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981498	55981498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	72	337	0	ENST00000263923.4:c.439G>A	p.Val147Met	p.V147M	ENST00000263923	NM_002253.2	147	Gtg/Atg	4/30	0.168224317376605	0	FACETS	0.581	0.51	0.657			1	INDETERMINATE	1	FALSE	0	0.385489765114134	0		337	395	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984957	55984958	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	75	299	0	ENST00000263923.4:c.171_172delinsAA	p.Asp58Asn	p.D58N	ENST00000263923	NM_002253.2	57	agGGac/agAAac	3/30	0.168224317376605	0	FACETS	0.757	0.669	0.849			1	INDETERMINATE	1	FALSE	0	0.385489765114134	0		299	316	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231673	66231673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	98	321	0	ENST00000273854.3:c.2027C>T	p.Thr676Ile	p.T676I	ENST00000273854	NM_004439.5	676	aCc/aTc	11/18	0.168224317376605	0	FACETS	0.773	0.695	0.856			1	INDETERMINATE	1	FALSE	0	0.385489765114134	0		321	404	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433682	149433682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	106	543	0	ENST00000286301.3:c.2869G>A	p.Gly957Arg	p.G957R	ENST00000286301	NM_005211.3	957	Ggg/Agg	22/22	0.241261285800245	0	FACETS	0.676	0.609	0.747			1	SUBCLONAL	1	FALSE	0	0.385489765114134	0		543	500	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502614	149502614	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	59	342	0	ENST00000261799.4:c.2174C>T	p.Pro725Leu	p.P725L	ENST00000261799	NM_002609.3	725	cCc/cTc	15/23	0.241261285800245	0	FACETS	0.721	0.626	0.821			1	SUBCLONAL	1	FALSE	0	0.385489765114134	0		342	261	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048877	180048877	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	53	660	0	ENST00000261937.6:c.1685C>T	p.Ser562Phe	p.S562F	ENST00000261937	NM_182925.4	562	tCc/tTc	13/30	0.385489765114134	1	FACETS	0.516	0.441	0.598	0.516	0.441	0.598	SUBCLONAL	1	FALSE	0	0.385489765114134	1		660	430	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686794	117686794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	144	305	0	ENST00000368508.3:c.2923G>A	p.Val975Ile	p.V975I	ENST00000368508	NM_002944.2	975	Gta/Ata	19/43	0.272691608878345	1	FACETS	0.917	0.849	0.985	1	0.991	1	CLONAL	2	FALSE	0	0.385489765114134	1		305	329	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397729	116397729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	199	378	0	ENST00000397752.3:c.2003C>T	p.Pro668Leu	p.P668L	ENST00000397752	NM_000245.2	668	cCt/cTt	8/21	0.385489765114134	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	FALSE	1	0.385489765114134	3		378	539	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534966	5534966	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	74	379	0	ENST00000397747.3:c.277C>T	p.Gln93Ter	p.Q93*	ENST00000397747	NM_025239.3	93	Caa/Taa	3/7	0.272691608878345	1	FACETS	0.672	0.59	0.76	0.672	0.59	0.76	SUBCLONAL	1	FALSE	0	0.385489765114134	1		379	461	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376606	8376606	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1356752980	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	77	267	0	ENST00000356435.5:c.4506+1G>A		p.X1502_splice	ENST00000356435		1502			0.362581994267146	0	FACETS	0.944	0.84	1			1	CLONAL	1	FALSE	0	0.385489765114134	0		267	260	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342599	87342599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	104	328	0	ENST00000277120.3:c.884C>T	p.Pro295Leu	p.P295L	ENST00000277120		295	cCa/cTa	9/19	0.355929300394042	1	FACETS	0.778	0.707	0.85	1	0.986	1	SUBCLONAL	2	FALSE	0	0.385489765114134	1		328	280	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118709	115118709	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs756408358	NA	P-0053012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	220	404	0	ENST00000257566.3:c.632A>C	p.Asn211Thr	p.N211T	ENST00000257566	NM_016569.3	211	aAc/aCc	2/8	0.391145395420988	3	FACETS	0.902	0.848	0.956	0.902	0.848	0.956	CLONAL	3	TRUE	0	0.391145395420988	3		404	497	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463524	25463524	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1197133406	NA	P-0053012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	193	613	1	ENST00000264709.3:c.2158C>T	p.Arg720Cys	p.R720C	ENST00000264709	NM_175629.2	720	Cgc/Tgc	18/23	0.372146481240278	3	FACETS	0.814	0.755	0.874	0.814	0.755	0.874	CLONAL	2	TRUE	1	0.391145395420988	3		614	725	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926249	112926249	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs397509344	NA	P-0053012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	216	447	0	ENST00000351677.2:c.1382C>G	p.Ala461Gly	p.A461G	ENST00000351677	NM_002834.3	461	gCt/gGt	12/16	0.391145395420988	3	FACETS	0.927	0.872	0.982	0.927	0.872	0.982	CLONAL	3	TRUE	0	0.391145395420988	3		447	475	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023831	27023831	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	66	266	0	ENST00000324856.7:c.937G>T	p.Gly313Trp	p.G313W	ENST00000324856	NM_006015.4	313	Ggg/Tgg	1/20	0.391145395420988	3	FACETS	1	0.922	1	0.539	0.47	0.613	CLONAL	1	TRUE	1	0.391145395420988	3		266	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	83	706	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.452288827075178	3	FACETS	0.848	0.751	0.952	0.424	0.375	0.476	CLONAL	1	TRUE	1	0.485326074641459	3		706	501	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578463	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371524413	NA	P-0053013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	263	848	0	ENST00000269305.4:c.467G>C	p.Arg156Pro	p.R156P	ENST00000269305	NM_001126112.2	156	cGc/cCc	5/11	0.452288827075178	3	FACETS	0.934	0.88	0.989	0.934	0.88	0.989	CLONAL	2	TRUE	1	0.485326074641459	3		848	721	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033959	49033977	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTTGGACCAAGTAAGAAA	ATTTGGACCAAGTAAGAAA	-	novel	NA	P-0053013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	60	476	0	ENST00000267163.4:c.2098_2106+10del		p.X700_splice	ENST00000267163	NM_000321.2	700		20/27	0.4854144226132	1	FACETS	0.777	0.677	0.883	0.777	0.677	0.883	SUBCLONAL	1	TRUE	0	0.485326074641459	1		476	241	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942446	17942529	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTGAATCCCCACAAGTCCCGGGGCGCCCCCTCGCACCTTGCAGATCTGCGAGGAATAGAGAAGGAGGCGGCTGGCATCGAGGC	GCTGAATCCCCACAAGTCCCGGGGCGCCCCCTCGCACCTTGCAGATCTGCGAGGAATAGAGAAGGAGGCGGCTGGCATCGAGGC	-	novel	NA	P-0053013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	29	625	0	ENST00000458235.1:c.2759_2805+37del		p.X920_splice	ENST00000458235	NM_000215.3	920		20/24	1	2	FACETS	0.258	0.206	0.316	0.258	0.206	0.316	SUBCLONAL	1	TRUE	1	0.485326074641459	2		625	464	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561126	9561126	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	70	459	0	ENST00000353224.5:c.656A>C	p.Tyr219Ser	p.Y219S	ENST00000353224	NM_177990.2	219	tAt/tCt	4/10	0.264447992208963	3	FACETS	0.783	0.684	0.888	0.391	0.342	0.444	INDETERMINATE	1	TRUE	1	0.485326074641459	3		459	458	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46266391	46266391	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0053013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	86	373	0	ENST00000371998.3:c.2377-1G>A		p.X793_splice	ENST00000371998		793			0.264447992208963	3	FACETS	0.979	0.882	1	0.979	0.882	1	INDETERMINATE	2	TRUE	1	0.485326074641459	3		373	225	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579400	7579400	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	107	795	0	ENST00000269305.4:c.287del	p.Ser96LeufsTer27	p.S96Lfs*27	ENST00000269305	NM_001126112.2	96	tCt/tt	4/11	0.281043551298367	1	FACETS	0.629	0.563	0.698	0.629	0.563	0.698	SUBCLONAL	1	TRUE	0	0.333061310346654	1		795	852	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717661	89717661	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0053013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	68	553	0	ENST00000371953.3:c.686C>G	p.Ser229Ter	p.S229*	ENST00000371953	NM_000314.4	229	tCa/tGa	7/9	0.333061310346654	1	FACETS	0.699	0.609	0.795	0.699	0.609	0.795	SUBCLONAL	1	TRUE	0	0.333061310346654	1		553	487	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426580	49426580	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	121	799	0	ENST00000301067.7:c.11908C>T	p.Gln3970Ter	p.Q3970*	ENST00000301067	NM_003482.3	3970	Cag/Tag	39/54	0.140424577805988	3	FACETS	0.822	0.741	0.908	0.411	0.37	0.454	INDETERMINATE	1	TRUE	1	0.333061310346654	3		799	1031	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882954	89882954	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	33	209	0	ENST00000389301.3:c.70G>T	p.Glu24Ter	p.E24*	ENST00000389301	NM_000135.2	24	Gag/Tag	1/43	1	2	FACETS	0.708	0.579	0.852	0.708	0.579	0.852	SUBCLONAL	1	TRUE	1	0.333061310346654	2		209	280	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0053031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	125	715	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.199585333000095	4	FACETS	0.899	0.814	0.989	0.899	0.814	0.989	CLONAL	2	TRUE	2	0.216194102756111	4		715	782	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574000	7574000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	114	819	1	ENST00000269305.4:c.1027G>T	p.Glu343Ter	p.E343*	ENST00000269305	NM_001126112.2	343	Gag/Tag	10/11	0.199585333000095	4	FACETS	1	0.983	1	0.733	0.659	0.811	CLONAL	1	TRUE	2	0.216194102756111	4		820	875	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696229	52696229	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	45	620	0	ENST00000394830.3:c.448G>C	p.Glu150Gln	p.E150Q	ENST00000394830	NM_018313.4	150	Gag/Cag	5/30	1	2	FACETS	0.737	0.619	0.868	0.737	0.619	0.868	SUBCLONAL	1	TRUE	1	0.216194102756111	2		620	565	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098800	178098800	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	144	657	0	ENST00000397062.3:c.245A>G	p.Glu82Gly	p.E82G	ENST00000397062	NM_006164.4	82	gAa/gGa	2/5	0.216194102756111	3	FACETS	1	0.97	1	0.756	0.691	0.823	CLONAL	2	TRUE	0	0.216194102756111	3		657	651	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44515577	44515577	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	68	767	0	ENST00000291552.4:c.319G>C	p.Asp107His	p.D107H	ENST00000291552	NM_006758.2	107	Gac/Cac	5/8	0.210553207509021	3	FACETS	0.941	0.817	1	0.47	0.408	0.537	CLONAL	1	TRUE	1	0.216194102756111	3		767	741	SUCCESS
APC	324	MSKCC	GRCh37	5	112176555	112176555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771967537	NA	P-0053031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	24	347	0	ENST00000257430.4:c.5264C>T	p.Ala1755Val	p.A1755V	ENST00000257430	NM_000038.5	1755	gCg/gTg	16/16	1	2	FACETS	0.645	0.506	0.806	0.645	0.506	0.806	SUBCLONAL	1	TRUE	1	0.216194102756111	2		347	344	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877338	89877338	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	41	603	0	ENST00000389301.3:c.425G>A	p.Arg142Lys	p.R142K	ENST00000389301	NM_000135.2	142	aGa/aAa	4/43	0.216314166268465	3	FACETS	0.593	0.492	0.705	0.296	0.246	0.353	SUBCLONAL	1	TRUE	1	0.216194102756111	3		603	709	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252376	133252376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759414746	NA	P-0053031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	104	461	0	ENST00000320574.5:c.1051G>A	p.Val351Ile	p.V351I	ENST00000320574	NM_006231.2	351	Gtc/Atc	11/49	0.205469595030828	2	FACETS	0.996	0.896	1	0.996	0.896	1	CLONAL	2	TRUE	0	0.216194102756111	2		461	483	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882351	89882351	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	61	685	0	ENST00000389301.3:c.123G>C	p.Gln41His	p.Q41H	ENST00000389301	NM_000135.2	41	caG/caC	2/43	0.216314166268465	3	FACETS	0.781	0.672	0.899	0.39	0.336	0.45	SUBCLONAL	1	TRUE	1	0.216194102756111	3		685	801	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0053033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	143	415	0	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	0.289748135737491	2	FACETS	0.857	0.79	0.925			1	CLONAL	3	FALSE	NA	0.289748135737491	2		415	384	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16097825	16097825	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs73281920	NA	P-0053033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	10	557	0	ENST00000268712.3:c.59A>C	p.Tyr20Ser	p.Y20S	ENST00000268712	NM_006311.3	20	tAt/tCt	2/46	1	2	FACETS	0.451	0.306	0.632	0.451	0.306	0.632	SUBCLONAL	1	FALSE	1	0.289748135737491	2		557	153	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419049	419049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	12	577	1	ENST00000399788.2:c.3298G>A	p.Glu1100Lys	p.E1100K	ENST00000399788	NM_001042603.1	1100	Gaa/Aaa	22/28	0.279725358115059	4	FACETS	0.542	0.381	0.74	0.271	0.19	0.37	SUBCLONAL	1	FALSE	2	0.289748135737491	4		578	197	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143272	108143272	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	19	411	1	ENST00000278616.4:c.3091G>T	p.Glu1031Ter	p.E1031*	ENST00000278616	NM_000051.3	1031	Gag/Tag	21/63	0.215478703775986	3	FACETS	0.975	0.759	1	0.975	0.759	1	CLONAL	2	FALSE	1	0.289748135737491	3		412	77	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143448	108143448	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0053033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	12	501	0	ENST00000278616.4:c.3154-1G>C		p.X1052_splice	ENST00000278616	NM_000051.3	1052			0.215478703775986	3	FACETS	0.818	0.589	1	0.818	0.589	1	CLONAL	2	FALSE	1	0.289748135737491	3		501	58	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0053034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	33	393	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	1	0.21	2		393	302	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692849	89692849	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554898097	NA	P-0053034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	11	146	0	ENST00000371953.3:c.333G>A	p.Trp111Ter	p.W111*	ENST00000371953	NM_000314.4	111	tgG/tgA	5/9	1	2	FACETS	0.979	0.682	1	0.979	0.682	1	CLONAL	1	TRUE	1	0.21	2		146	107	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0053034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	21	398	0	ENST00000349496.5:c.101G>A	p.Gly34Glu	p.G34E	ENST00000349496	NM_001904.3	34	gGa/gAa	3/15	1	2	FACETS	0.606	0.466	0.769	0.606	0.466	0.769	SUBCLONAL	1	TRUE	1	0.21	2		398	330	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591069	67591092	+	inframe_deletion	In_Frame_Del	DEL	TGAGTATCGAGAAATTGACAAACG	TGAGTATCGAGAAATTGACAAACG	-	novel	NA	P-0053034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	14	293	0	ENST00000274335.5:c.1663_1686del	p.Glu555_Arg562del	p.E555_R562del	ENST00000274335		554	gcTGAGTATCGAGAAATTGACAAACGt/gct	12/15	1	2	FACETS	0.59	0.427	0.787	0.59	0.427	0.787	SUBCLONAL	1	TRUE	1	0.21	2		293	226	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339729	70339729	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0053034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	51	569	0	ENST00000374080.3:c.396+2T>A		p.X132_splice	ENST00000374080		132			1	2	FACETS	0.971	0.826	1	0.971	0.826	1	CLONAL	1	TRUE	1	0.21	2		569	500	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696432	47696432	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519968	NA	P-0053035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	109	478	0	ENST00000347630.2:c.391T>G	p.Trp131Gly	p.W131G	ENST00000347630	NM_001007230.1	131	Tgg/Ggg	6/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.3	2		478	513	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828302	72828302	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	143	617	0	ENST00000268489.5:c.8279del	p.Met2760ArgfsTer29	p.M2760Rfs*29	ENST00000268489	NM_006885.3	2760	aTg/ag	9/10	0.037162746641934	3	FACETS	0.958	0.878	1			1	INDETERMINATE	2	FALSE	NA	0.3	3		617	572	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61197650	61197650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148425779	NA	P-0053037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	80	509	0	ENST00000301761.2:c.32C>T	p.Ser11Leu	p.S11L	ENST00000301761	NM_017841.2	11	tCg/tTg	1/4	1	2	FACETS	0.732	0.645	0.825	0.732	0.645	0.825	SUBCLONAL	1	TRUE	1	0.36198821329521	2		509	604	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244651	41244651	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs879254045	NA	P-0053037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	61	693	0	ENST00000357654.3:c.2897T>C	p.Ile966Thr	p.I966T	ENST00000357654	NM_007294.3	966	aTt/aCt	10/23	1	2	FACETS	0.746	0.645	0.855	0.746	0.645	0.855	SUBCLONAL	1	TRUE	1	0.36198821329521	2		693	452	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52649460	52649460	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	54	489	0	ENST00000394830.3:c.1831G>C	p.Ala611Pro	p.A611P	ENST00000394830	NM_018313.4	611	Gca/Cca	16/30	0.36198821329521	1	FACETS	0.873	0.751	1	0.873	0.751	1	CLONAL	1	TRUE	0	0.36198821329521	1		489	280	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226217	53226217	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	111	389	0	ENST00000375401.3:c.2632del	p.Glu878AsnfsTer57	p.E878Nfs*57	ENST00000375401	NM_004187.3	878	Gaa/aa	19/26	1	1	FACETS	0.818	0.746	0.892	1	0.987	1	CLONAL	2	TRUE	0	0.36198821329521	1		389	307	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191483	10191483	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	TTC	novel	NA	P-0053037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	87	476	0	ENST00000256474.2:c.476delinsTTC	p.Lys159IlefsTer12	p.K159Ifs*12	ENST00000256474	NM_000551.3	159	aAa/aTTCa	3/3	0.36198821329521	1	FACETS	0.903	0.803	1	0.903	0.803	1	CLONAL	1	TRUE	0	0.36198821329521	1		476	436	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	25	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.834	1	1	0.834	1	CLONAL	1	TRUE	1	0.2	2		429	235	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0053038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	53	315	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.793	0.676	0.923	0.793	0.676	0.923	CLONAL	1	TRUE	1	0.2	2		315	668	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246590	46246590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	26	304	0	ENST00000334344.6:c.4684C>T	p.Pro1562Ser	p.P1562S	ENST00000334344	NM_152641.2	1562	Cca/Tca	15/21	1	2	FACETS	0.807	0.64	0.999	0.807	0.64	0.999	CLONAL	1	TRUE	1	0.2	2		304	322	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55130041	55130041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	76	669	0	ENST00000257290.5:c.575C>T	p.Thr192Ile	p.T192I	ENST00000257290	NM_006206.4	192	aCc/aTc	4/23	1	2	FACETS	0.99	0.867	1	0.99	0.867	1	CLONAL	1	TRUE	1	0.2	2		669	768	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216482	2216482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372258317	NA	P-0053040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	212	1063	2	ENST00000398665.3:c.2126C>T	p.Pro709Leu	p.P709L	ENST00000398665	NM_032482.2	709	cCg/cTg	20/28	0.300092628613982	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	FALSE	1	0.314076700013186	3		1065	657	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226573252	226573252	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs769550581	NA	P-0053040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	157	824	0	ENST00000366794.5:c.964A>G	p.Met322Val	p.M322V	ENST00000366794	NM_001618.3	322	Atg/Gtg	7/23	0.152487867404884	5	FACETS	1	0.934	1	0.68	0.624	0.738	INDETERMINATE	2	FALSE	2	0.314076700013186	5		824	721	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033970	49033970	+	splice_donor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0053040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	111	430	0	ENST00000267163.4:c.2106+1del		p.X702_splice	ENST00000267163	NM_000321.2	702			0.27704566430349	3	FACETS	1	0.919	1	0.676	0.613	0.743	CLONAL	2	FALSE	0	0.314076700013186	3		430	403	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022420	31022420	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	42	470	0	ENST00000375687.4:c.1905G>C	p.Glu635Asp	p.E635D	ENST00000375687	NM_015338.5	635	gaG/gaC	13/13	0.300092628613982	3	FACETS	1	0.886	1	0.535	0.449	0.63	CLONAL	1	FALSE	1	0.314076700013186	3		470	289	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0053044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	59	1171	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.891	0.765	1	0.891	0.765	1	CLONAL	1	TRUE	1	0.16	2		1171	828	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177467	56177467	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	56	336	0	ENST00000399503.3:c.2440A>G	p.Lys814Glu	p.K814E	ENST00000399503	NM_005921.1	814	Aaa/Gaa	14/20	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.16	2		336	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0053044-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	291	1171	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.752741908003099	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.752741908003099	1		1171	477	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177467	56177467	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053044-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	205	336	0	ENST00000399503.3:c.2440A>G	p.Lys814Glu	p.K814E	ENST00000399503	NM_005921.1	814	Aaa/Gaa	14/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.752741908003099	2		336	477	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172118	99172118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775573311	NA	P-0053044-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	192	443	1	ENST00000074304.5:c.1684G>A	p.Val562Ile	p.V562I	ENST00000074304	NM_001134224.1	562	Gtc/Atc	17/26	1	2	FACETS	0.922	0.859	0.987	0.922	0.859	0.987	CLONAL	1	TRUE	1	0.752741908003099	2		444	553	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086016	16086016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057517770	NA	P-0053047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	152	524	0	ENST00000281043.3:c.1192C>T	p.Arg398Trp	p.R398W	ENST00000281043	NM_005378.4	398	Cgg/Tgg	3/3	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.533077121968317	2		524	523	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717712	89717712	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	223	364	0	ENST00000371953.3:c.737C>G	p.Pro246Arg	p.P246R	ENST00000371953	NM_000314.4	246	cCg/cGg	7/9	0.533077121968317	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.533077121968317	2		364	403	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456502	29456502	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	157	566	1	ENST00000389048.3:c.2416C>A	p.Arg806Ser	p.R806S	ENST00000389048	NM_004304.4	806	Cgt/Agt	14/29	1	2	FACETS	0.962	0.885	1	0.962	0.885	1	CLONAL	1	TRUE	1	0.533077121968317	2		567	612	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967210	134967211	+	missense_variant	Missense_Mutation	DNP	CA	CA	AT	novel	NA	P-0053047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	216	566	1	ENST00000398015.3:c.2549_2550delinsAT	p.Pro850His	p.P850H	ENST00000398015	NM_004441.4	850	cCA/cAT	14/16	0.533077121968317	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	1	0.533077121968317	3		567	505	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591144	67591153	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ATACTTGATG	ATACTTGATG	-	novel	NA	P-0053047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	79	277	0	ENST00000274335.5:c.1737_1745+1del		p.X579_splice	ENST00000274335		579		12/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.533077121968317	2		277	248	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410347	63410347	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	161	793	0	ENST00000330258.3:c.2820G>A	p.Trp940Ter	p.W940*	ENST00000330258	NM_152424.3	940	tgG/tgA	2/2	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.533077121968317	2		793	573	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0053048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	191	315	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.885489821610632	2		315	418	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0053048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	94	305	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.956	0.869	1	0.956	0.869	1	CLONAL	1	TRUE	1	0.885489821610632	2		305	222	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777894	NA	P-0053048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	50	446	0	ENST00000361445.4:c.6644C>T	p.Ser2215Phe	p.S2215F	ENST00000361445	NM_004958.3	2215	tCt/tTt	47/58	0.885489821610632	1	FACETS	0.163	0.139	0.19	0.163	0.139	0.19	SUBCLONAL	1	TRUE	0	0.885489821610632	1		446	385	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256772	19256772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	283	529	1	ENST00000162023.5:c.941C>T	p.Pro314Leu	p.P314L	ENST00000162023		314	cCc/cTc	13/13	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.885489821610632	2		530	595	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275430	115275447	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGTCATTCTGATGAGAA	GGGTCATTCTGATGAGAA	-	novel	NA	P-0053049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	34	329	0	ENST00000438362.2:c.976-10_983del		p.X326_splice	ENST00000438362	NM_001242891.1	326		10/20	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		329	474	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879885	37879885	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2159	144	702	0	ENST00000269571.5:c.2180G>C	p.Gly727Ala	p.G727A	ENST00000269571		727	gGa/gCa	18/27	0.500488703102632	12	FACETS	0.875	0.794	0.961			1	CLONAL	1	TRUE	NA	0.500488703102632	12		702	2303	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209110083	209110083	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	149	525	0	ENST00000345146.2:c.480C>G	p.Asp160Glu	p.D160E	ENST00000345146	NM_005896.2	160	gaC/gaG	5/10	0.500488703102632	3	FACETS	0.918	0.839	1	0.459	0.419	0.5	CLONAL	1	TRUE	1	0.500488703102632	3		525	811	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056500	26056500	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs372319415	NA	P-0053050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	51	354	0	ENST00000343677.2:c.157G>C	p.Glu53Gln	p.E53Q	ENST00000343677	NM_005319.3	53	Gag/Cag	1/1	0.500488703102632	12	FACETS	0.702	0.594	0.821			1	SUBCLONAL	1	TRUE	NA	0.500488703102632	12		354	1017	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56882350	56882350	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	123	558	0	ENST00000519728.1:c.1048C>T	p.Gln350Ter	p.Q350*	ENST00000519728	NM_002350.3	350	Cag/Tag	10/13	0.474286938840041	3	FACETS	0.933	0.845	1	0.466	0.422	0.512	CLONAL	1	TRUE	1	0.500488703102632	3		558	659	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060778	38060779	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0053050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	229	795	0	ENST00000250448.2:c.1210_1211insTT	p.Asn404IlefsTer37	p.N404Ifs*37	ENST00000250448	NM_004496.3	404	aac/aTTac	2/2	0.48272930432975	3	FACETS	1	0.985	1	0.592	0.552	0.633	CLONAL	1	TRUE	1	0.500488703102632	3		795	967	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2224295	2224295	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	109	798	1	ENST00000326181.6:c.1307A>T	p.Glu436Val	p.E436V	ENST00000326181	NM_032271.2	436	gAg/gTg	14/21	0.204917175725189	2	FACETS	0.759	0.683	0.838	0.379	0.341	0.419	INDETERMINATE	1	TRUE	0	0.500488703102632	2		799	574	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325952	30325953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	91	287	0	ENST00000322652.5:c.2154dup	p.Glu719ArgfsTer8	p.E719Rfs*8	ENST00000322652	NM_015355.2	717	tca/tcAa	16/16	NA	2	FACETS	0.88	0.787	0.979			1	INDETERMINATE	1	TRUE	NA	0.500488703102632	2		287	413	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144859	11144859	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	161	679	0	ENST00000358026.2:c.3934G>C	p.Glu1312Gln	p.E1312Q	ENST00000358026	NM_001128849.1	1312	Gag/Cag	28/36	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.500488703102632	2		679	511	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518840	187518840	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	96	398	0	ENST00000441802.2:c.12364G>A	p.Glu4122Lys	p.E4122K	ENST00000441802	NM_005245.3	4122	Gaa/Aaa	24/27	0.48272930432975	3	FACETS	0.924	0.826	1	0.462	0.413	0.514	CLONAL	1	TRUE	1	0.500488703102632	3		398	519	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873413	151873413	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	55	452	0	ENST00000262189.6:c.9125G>C	p.Arg3042Thr	p.R3042T	ENST00000262189	NM_170606.2	3042	aGa/aCa	38/59	0.46313307039609	4	FACETS	0.589	0.504	0.682	0.294	0.252	0.341	SUBCLONAL	1	TRUE	2	0.500488703102632	4		452	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0053051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	161	656	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.173007161366415	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.241869382647311	2		656	599	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695932	117695932	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	38	560	0	ENST00000369458.3:c.505G>C	p.Glu169Gln	p.E169Q	ENST00000369458	NM_024626.3	169	Gag/Cag	4/6	0.185746626814993	3	FACETS	0.562	0.463	0.672			1	SUBCLONAL	1	TRUE	NA	0.241869382647311	3		560	627	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636418	21636418	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	53	587	0	ENST00000421138.2:c.592A>G	p.Lys198Glu	p.K198E	ENST00000421138		198	Aaa/Gaa	7/16	0.199333422914651	3	FACETS	0.915	0.78	1	0.305	0.26	0.354	CLONAL	1	TRUE	0	0.241869382647311	3		587	537	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785554	50785554	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	55	596	0	ENST00000398568.2:c.544C>G	p.Gln182Glu	p.Q182E	ENST00000398568	NM_001042412.1	182	Caa/Gaa	4/18	0.241869382647311	2	FACETS	0.699	0.597	0.81	0.349	0.298	0.405	SUBCLONAL	1	TRUE	0	0.241869382647311	2		596	651	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794436	242794436	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	48	758	0	ENST00000334409.5:c.506T>C	p.Leu169Pro	p.L169P	ENST00000334409	NM_005018.2	169	cTg/cCg	3/5	0.0758923403131644	3	FACETS	0.585	0.494	0.687			1	INDETERMINATE	1	TRUE	NA	0.241869382647311	3		758	760	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683563	162683563	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	64	508	0	ENST00000366898.1:c.406A>T	p.Ser136Cys	p.S136C	ENST00000366898	NM_004562.2	136	Agt/Tgt	3/12	0.173007161366415	2	FACETS	1	0.884	1	0.511	0.443	0.584	CLONAL	1	TRUE	0	0.241869382647311	2		508	518	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0053052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	66	353	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.279726449551062	2		353	449	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426710	47426710	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1164055186	NA	P-0053052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	72	765	0	ENST00000377045.4:c.955G>T	p.Gly319Cys	p.G319C	ENST00000377045	NM_001654.4	319	Ggc/Tgc	10/16	1	2	FACETS	0.832	0.727	0.945	0.832	0.727	0.945	CLONAL	1	TRUE	1	0.279726449551062	2		765	619	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274043	10274043	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1236030143	NA	P-0053052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	64	880	0	ENST00000330684.3:c.226C>T	p.Arg76Cys	p.R76C	ENST00000330684	NM_001134407.1	76	Cgc/Tgc	2/13	1	2	FACETS	0.705	0.61	0.808	0.705	0.61	0.808	SUBCLONAL	1	TRUE	1	0.279726449551062	2		880	649	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610369	10610369	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	127	905	0	ENST00000171111.5:c.341G>T	p.Gly114Val	p.G114V	ENST00000171111	NM_203500.1	114	gGg/gTg	2/6	0.279726449551062	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.279726449551062	1		905	617	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420273	88420273	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	77	557	0	ENST00000360948.2:c.2413G>T	p.Gly805Trp	p.G805W	ENST00000360948	NM_001012338.2	805	Ggg/Tgg	19/19	0.279726449551062	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.279726449551062	1		557	380	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820941	3820941	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	45	656	0	ENST00000262367.5:c.2510G>T	p.Gly837Val	p.G837V	ENST00000262367	NM_004380.2	837	gGg/gTg	14/31	1	2	FACETS	0.575	0.482	0.677	0.575	0.482	0.677	SUBCLONAL	1	TRUE	1	0.279726449551062	2		656	560	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923403	9923403	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	87	652	0	ENST00000330684.3:c.1884G>T	p.Lys628Asn	p.K628N	ENST00000330684	NM_001134407.1	628	aaG/aaT	9/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.279726449551062	2		652	508	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243499	41243499	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1433564897	NA	P-0053052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	48	620	0	ENST00000357654.3:c.4049G>T	p.Gly1350Val	p.G1350V	ENST00000357654	NM_007294.3	1350	gGc/gTc	10/23	1	2	FACETS	0.614	0.519	0.719	0.614	0.519	0.719	SUBCLONAL	1	TRUE	1	0.279726449551062	2		620	559	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31464347	31464347	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	98	575	0	ENST00000344624.3:c.2570G>T	p.Cys857Phe	p.C857F	ENST00000344624		857	tGt/tTt	17/33	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.279726449551062	2		575	602	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524527	176524527	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0053052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	47	870	0	ENST00000292408.4:c.2260-1G>T		p.X754_splice	ENST00000292408	NM_213647.1	754			1	2	FACETS	0.58	0.489	0.681	0.58	0.489	0.681	SUBCLONAL	1	TRUE	1	0.279726449551062	2		870	579	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22008859	22008859	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	68	664	0	ENST00000276925.6:c.94C>G	p.Gln32Glu	p.Q32E	ENST00000276925	NM_004936.3	32	Cag/Gag	1/2	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.279726449551062	2		664	409	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323354	31323354	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	17	410	0	ENST00000412585.2:c.635A>C	p.His212Pro	p.H212P	ENST00000412585	NM_005514.6	212	cAc/cCc	4/8	1	2	FACETS	0.413	0.308	0.539	0.413	0.308	0.539	SUBCLONAL	1	TRUE	1	0.279726449551062	2		410	294	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	215	388	2	ENST00000347630.2:c.399C>A	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttA	6/11	1	2	FACETS	0.749	0.698	0.801	0.749	0.698	0.801	SUBCLONAL	1	TRUE	1	0.744685282868591	2		390	771	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782620	NA	P-0053056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	364	795	0	ENST00000269305.4:c.427G>A	p.Val143Met	p.V143M	ENST00000269305	NM_001126112.2	143	Gtg/Atg	5/11	0.660705932082487	1	FACETS	0.821	0.785	0.858	0.821	0.785	0.858	CLONAL	1	TRUE	0	0.744685282868591	1		795	747	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993872	72993872	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs371765071	NA	P-0053056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	182	486	0	ENST00000268489.5:c.173A>G	p.Asn58Ser	p.N58S	ENST00000268489	NM_006885.3	58	aAt/aGt	2/10	1	2	FACETS	0.909	0.844	0.974	0.909	0.844	0.974	CLONAL	1	TRUE	1	0.744685282868591	2		486	538	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0053057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	129	300	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	0.999	0.919	1	0.999	0.919	1	CLONAL	1	TRUE	1	0.815073629820878	2		300	317	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0053057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	114	329	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	0.995	0.911	1	0.995	0.911	1	CLONAL	1	TRUE	1	0.815073629820878	2		329	281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0053059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	738	656	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA	2	FACETS	0.975	0.958	0.992			1	INDETERMINATE	4	FALSE	NA	0.433835087778879	2		656	872	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0053059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	162	284	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.945	0.878	1	1	0.992	1	CLONAL	2	FALSE	1	0.433835087778879	2		284	395	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829789	76829790	+	inframe_insertion	In_Frame_Ins	INS	-	-	TAA	novel	NA	P-0053059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	255	234	0	ENST00000373344.5:c.6249_6251dup	p.Tyr2084dup	p.Y2084dup	ENST00000373344	NM_000489.3	2084	tac/taTTAc	28/35	1	1	FACETS	0.834	0.799	0.868	1	0.996	1	CLONAL	3	FALSE	0	0.433835087778879	1		234	368	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76949326	76949327	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0053059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	239	138	0	ENST00000373344.5:c.470_471del	p.Leu157GlnfsTer31	p.L157Qfs*31	ENST00000373344	NM_000489.3	157	cTC/c	6/35	1	1	FACETS	0.975	0.941	1	1	0.996	1	CLONAL	3	FALSE	0	0.433835087778879	1		138	295	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0053060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	67	587	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.735	0.639	0.838	0.735	0.639	0.838	SUBCLONAL	1	TRUE	1	0.332272896594694	2		587	549	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0053060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	46	274	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.817	0.69	0.955	0.817	0.69	0.955	CLONAL	1	TRUE	1	0.332272896594694	2		274	339	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0053060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	54	491	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.722	0.618	0.836	0.722	0.618	0.836	SUBCLONAL	1	TRUE	1	0.332272896594694	2		491	450	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	42	270	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	1	2	FACETS	0.913	0.767	1	0.913	0.767	1	CLONAL	1	TRUE	1	0.332272896594694	2		270	277	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692790	89692790	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554898067	NA	P-0053060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	103	263	0	ENST00000371953.3:c.274G>T	p.Asp92Tyr	p.D92Y	ENST00000371953	NM_000314.4	92	Gac/Tac	5/9	0.305793461671569	3	FACETS	1	0.97	1	0.782	0.709	0.858	CLONAL	2	TRUE	0	0.332272896594694	3		263	308	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	67	379	0	ENST00000263967.3:c.3012G>T	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atT	21/21	1	2	FACETS	0.951	0.83	1	0.951	0.83	1	CLONAL	1	TRUE	1	0.332272896594694	2		379	424	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023471	27023471	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	64	297	0	ENST00000324856.7:c.577G>T	p.Glu193Ter	p.E193*	ENST00000324856	NM_006015.4	193	Gag/Tag	1/20	1	2	FACETS	0.928	0.807	1	0.928	0.807	1	CLONAL	1	TRUE	1	0.332272896594694	2		297	415	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821653	72821653	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760410635	NA	P-0053060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	12	97	0	ENST00000268489.5:c.10522G>A	p.Gly3508Ser	p.G3508S	ENST00000268489	NM_006885.3	3508	Ggc/Agc	10/10	1	2	FACETS	0.663	0.47	0.895	0.663	0.47	0.895	SUBCLONAL	1	TRUE	1	0.332272896594694	2		97	109	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654679	67654680	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGACACAT	novel	NA	P-0053060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	38	408	0	ENST00000264010.4:c.1167_1174dup	p.Tyr392TrpfsTer6	p.Y392Wfs*6	ENST00000264010	NM_006565.3	389	agg/agGGACACATg	6/12	1	2	FACETS	0.497	0.411	0.594	0.497	0.411	0.594	SUBCLONAL	1	TRUE	1	0.332272896594694	2		408	460	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981738	70981738	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	122	635	0	ENST00000276594.2:c.358G>A	p.Glu120Lys	p.E120K	ENST00000276594	NM_024504.3	120	Gag/Aag	2/8	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.332272896594694	2		635	670	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	38	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.961	0.82	1	0.961	0.82	1	CLONAL	1	TRUE	1	0.815692060897764	2		429	97	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0053061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	143	330	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.904	0.833	0.976	0.904	0.833	0.976	CLONAL	1	TRUE	1	0.815692060897764	2		330	388	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0053061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	148	658	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.952	0.881	1	0.952	0.881	1	CLONAL	1	TRUE	1	0.815692060897764	2		658	381	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910507	32910507	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	158	317	0	ENST00000380152.3:c.2015G>C	p.Arg672Thr	p.R672T	ENST00000380152		672	aGa/aCa	11/27	0.815692060897764	3	FACETS	0.988	0.911	1	0.494	0.455	0.534	CLONAL	1	TRUE	1	0.815692060897764	3		317	552	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772092	135772092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	243	446	0	ENST00000298552.3:c.3025G>A	p.Glu1009Lys	p.E1009K	ENST00000298552	NM_001162426.1	1009	Gaa/Aaa	23/23	0.815692060897764	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.815692060897764	1		446	339	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099397	27099397	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	215	456	1	ENST00000324856.7:c.3634C>T	p.Gln1212Ter	p.Q1212*	ENST00000324856	NM_006015.4	1212	Cag/Tag	14/20	0.549116807828919	1	FACETS	0.705	0.664	0.746	0.705	0.664	0.746	SUBCLONAL	1	TRUE	0	0.815692060897764	1		457	443	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870260	44870260	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	149	370	0	ENST00000377967.4:c.439C>T	p.Gln147Ter	p.Q147*	ENST00000377967	NM_021140.2	147	Cag/Tag	5/29	1	2	FACETS	0.923	0.853	0.994	0.923	0.853	0.994	CLONAL	1	TRUE	1	0.815692060897764	2		370	396	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948640	71948640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	357	793	1	ENST00000298229.2:c.3352G>A	p.Asp1118Asn	p.D1118N	ENST00000298229	NM_001567.3	1118	Gac/Aac	26/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.815692060897764	2		794	832	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434094	121434094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1206311303	NA	P-0053061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	237	512	0	ENST00000257555.6:c.985G>A	p.Glu329Lys	p.E329K	ENST00000257555		329	Gag/Aag	5/10	1	2	FACETS	0.942	0.885	0.999	0.942	0.885	0.999	CLONAL	1	TRUE	1	0.815692060897764	2		512	617	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36024580	36024580	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0053061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	258	559	0	ENST00000358208.4:c.569C>G	p.Ser190Ter	p.S190*	ENST00000358208		190	tCa/tGa	6/12	1	2	FACETS	0.909	0.856	0.963	0.909	0.856	0.963	CLONAL	1	TRUE	1	0.815692060897764	2		559	696	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940307	49940307	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs766382259	NA	P-0053061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	117	658	0	ENST00000296474.3:c.736A>G	p.Ser246Gly	p.S246G	ENST00000296474	NM_002447.2	246	Agt/Ggt	1/20	1	2	FACETS	0.367	0.331	0.405	0.367	0.331	0.405	SUBCLONAL	1	TRUE	1	0.815692060897764	2		658	782	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875639	35875639	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	169	351	0	ENST00000303115.3:c.826C>G	p.Leu276Val	p.L276V	ENST00000303115	NM_002185.3	276	Ctc/Gtc	7/8	1	2	FACETS	0.946	0.879	1	0.946	0.879	1	CLONAL	1	TRUE	1	0.815692060897764	2		351	438	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942017	44942018	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0053061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	145	272	0	ENST00000377967.4:c.3268_3269dup	p.Ser1091TyrfsTer14	p.S1091Yfs*14	ENST00000377967	NM_021140.2	1089	-/CT	22/29	1	2	FACETS	0.921	0.85	0.993	0.921	0.85	0.993	CLONAL	1	TRUE	1	0.815692060897764	2		272	386	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0053062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	415	682	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.481768947327961	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.491592853569191	2		682	779	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941651	48941651	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	83	169	0	ENST00000267163.4:c.961T>C	p.Tyr321His	p.Y321H	ENST00000267163	NM_000321.2	321	Tac/Cac	10/27	0.474426530163314	2	FACETS	1	0.977	1	0.684	0.612	0.757	CLONAL	1	TRUE	0	0.491592853569191	2		169	247	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0053064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	264	656	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.385779240904811	3	FACETS	0.843	0.798	0.888	0.843	0.798	0.888	CLONAL	3	FALSE	0	0.456318230177368	3		656	562	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	75	265	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.395633038033255	3	FACETS	1	0.966	1	0.792	0.711	0.873	CLONAL	2	FALSE	0	0.456318230177368	3		265	170	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265348	16265348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746234410	NA	P-0053064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	61	547	0	ENST00000375759.3:c.10840G>A	p.Val3614Ile	p.V3614I	ENST00000375759	NM_015001.2	3614	Gtt/Att	14/15	0.456318230177368	5	FACETS	0.514	0.442	0.592	0.171	0.147	0.198	SUBCLONAL	1	FALSE	2	0.456318230177368	5		547	877	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0053064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	40	205	2	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	0.382972857955868	3	FACETS	0.953	0.813	1	0.635	0.542	0.733	CLONAL	2	FALSE	0	0.456318230177368	3		207	113	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40491424	40491424	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	260	438	0	ENST00000264657.5:c.376G>A	p.Gly126Arg	p.G126R	ENST00000264657	NM_139276.2	126	Ggg/Agg	5/24	0.284042079680264	6	FACETS	1	0.987	1	0.861	0.812	0.91	CLONAL	3	FALSE	2	0.456318230177368	6		438	633	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437617	52437618	+	missense_variant	Missense_Mutation	DNP	TT	TT	GG	novel	NA	P-0053064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	34	582	1	ENST00000460680.1:c.1543_1544delinsCC	p.Asn515Pro	p.N515P	ENST00000460680	NM_004656.3	515	AAc/CCc	13/17	0.456318230177368	3	FACETS	0.349	0.285	0.422	0.175	0.142	0.211	SUBCLONAL	1	FALSE	1	0.456318230177368	3		583	524	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710578	114710578	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	292	322	0	ENST00000543371.1:c.63C>G	p.Phe21Leu	p.F21L	ENST00000543371	NM_001198531.1	21	ttC/ttG	1/14	0.456318230177368	6	FACETS	1	0.967	1			1	CLONAL	4	FALSE	NA	0.456318230177368	6		322	598	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426900	6426900	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	74	341	0	ENST00000356142.4:c.93A>T	p.Glu31Asp	p.E31D	ENST00000356142	NM_018890.3	31	gaA/gaT	2/7	0.318830829391738	6	FACETS	1	0.966	1	0.83	0.737	0.928	CLONAL	2	FALSE	3	0.456318230177368	6		341	249	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0053065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	215	1171	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.415110573397734	1	FACETS	0.896	0.834	0.961	0.896	0.834	0.961	CLONAL	1	TRUE	0	0.415110573397734	1		1171	916	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435467	121435467	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	128	872	0	ENST00000257555.6:c.1500C>A	p.His500Gln	p.H500Q	ENST00000257555		500	caC/caA	7/10	0.415110573397734	1	FACETS	0.461	0.416	0.507	0.461	0.416	0.507	SUBCLONAL	1	TRUE	0	0.415110573397734	1		872	1061	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0053066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	189	434	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.614358761635262	1	FACETS	0.949	0.887	1	0.949	0.887	1	CLONAL	1	TRUE	0	0.614358761635262	1		434	449	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845353	42845353	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	231	702	0	ENST00000398585.3:c.909del	p.Trp304GlyfsTer26	p.W304Gfs*26	ENST00000398585	NM_001135099.1	303	gcC/gc	9/14	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.614358761635262	2		702	736	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0053067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	898	833	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.823393086621662	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.823393086621662	3		837	986	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951919	178951919	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	94	262	0	ENST00000263967.3:c.2974C>T	p.Arg992Ter	p.R992*	ENST00000263967	NM_006218.2	992	Cga/Tga	21/21	0.671167899320986	4	FACETS	0.917	0.82	1	0.459	0.41	0.51	CLONAL	1	TRUE	2	0.823393086621662	4		262	454	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45396897	45396897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs984513669	NA	P-0053067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	103	286	0	ENST00000262160.6:c.275C>T	p.Thr92Met	p.T92M	ENST00000262160	NM_005901.5	92	aCg/aTg	3/11	0.527875510186315	4	FACETS	1	0.925	1	0.516	0.464	0.57	CLONAL	1	TRUE	2	0.823393086621662	4		286	442	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864193	57864193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746398371	NA	P-0053067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	452	481	10	ENST00000228682.2:c.1670G>A	p.Arg557His	p.R557H	ENST00000228682	NM_005269.2	557	cGc/cAc	12/12	0.765312238553459	3	FACETS	0.98	0.944	1	0.98	0.944	1	CLONAL	2	TRUE	1	0.823393086621662	3		491	791	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962590	100962590	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	319	283	1	ENST00000325455.5:c.1807T>C	p.Cys603Arg	p.C603R	ENST00000325455	NM_001202474.3	603	Tgt/Cgt	3/8	0.820234465529619	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.823393086621662	2		284	376	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	205	411	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.963	0.895	1	0.963	0.895	1	CLONAL	1	TRUE	1	0.545169484628673	2		411	781	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106327	27106328	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0053068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	295	381	2	ENST00000324856.7:c.5939dup	p.Cys1981LeufsTer18	p.C1981Lfs*18	ENST00000324856	NM_006015.4	1980	cgc/cGgc	20/20	0.545169484628673	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.545169484628673	1		383	768	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915234	32915234	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	256	366	1	ENST00000380152.3:c.6742C>T	p.His2248Tyr	p.H2248Y	ENST00000380152		2248	Cat/Tat	11/27	0.545169484628673	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.545169484628673	1		367	610	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040663	47040664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0053068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	274	267	0	ENST00000377604.3:c.1298_1299insG	p.Asp434ArgfsTer9	p.D434Rfs*9	ENST00000377604	NM_001204468.1	433	gtc/gtGc	13/24	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.545169484628673	1		267	518	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	128	305	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.904922531607374	2		305	230	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504401	8504401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757922864	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	205	348	0	ENST00000356435.5:c.1682G>A	p.Arg561Gln	p.R561Q	ENST00000356435		561	cGa/cAa	12/35	1	2	FACETS	0.972	0.912	1	0.972	0.912	1	CLONAL	1	TRUE	1	0.904922531607374	2		348	466	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037146	71037146	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	216	353	0	ENST00000318789.4:c.1145C>T	p.Pro382Leu	p.P382L	ENST00000318789	NM_032682.5	382	cCc/cTc	14/21	1	2	FACETS	0.94	0.883	0.998	0.94	0.883	0.998	CLONAL	1	TRUE	1	0.904922531607374	2		353	508	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156084	99156084	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	496	533	0	ENST00000074304.5:c.764C>T	p.Ser255Phe	p.S255F	ENST00000074304	NM_001134224.1	255	tCc/tTc	10/26	0.435193151546291	2	FACETS	0.771	0.748	0.794	0.771	0.748	0.794	INDETERMINATE	2	TRUE	0	0.904922531607374	2		533	711	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244952	123244952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	165	473	0	ENST00000358487.5:c.2152G>A	p.Glu718Lys	p.E718K	ENST00000358487	NM_000141.4	718	Gaa/Aaa	16/18	0.601654470743187	1	FACETS	0.364	0.336	0.393	0.364	0.336	0.393	SUBCLONAL	1	TRUE	0	0.904922531607374	1		473	548	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161310	185161310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764242255	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	258	419	0	ENST00000265026.3:c.737G>A	p.Arg246Gln	p.R246Q	ENST00000265026	NM_004721.4	246	cGa/cAa	4/14	1	2	FACETS	0.97	0.916	1	0.97	0.916	1	CLONAL	1	TRUE	1	0.904922531607374	2		419	588	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956958	2956958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1347465052	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	492	565	0	ENST00000396946.4:c.2669C>T	p.Ser890Leu	p.S890L	ENST00000396946	NM_032415.4	890	tCg/tTg	20/25	0.441561624349535	3	FACETS	0.9	0.868	0.933	0.9	0.868	0.933	INDETERMINATE	2	TRUE	1	0.904922531607374	3		565	877	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484293	8484293	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	252	382	0	ENST00000356435.5:c.3239C>T	p.Ser1080Leu	p.S1080L	ENST00000356435		1080	tCa/tTa	19/35	1	2	FACETS	0.894	0.843	0.946	0.894	0.843	0.946	CLONAL	1	TRUE	1	0.904922531607374	2		382	623	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793483	18793483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603405	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	171	254	0	ENST00000266497.5:c.4180G>A	p.Glu1394Lys	p.E1394K	ENST00000266497		1394	Gaa/Aaa	30/31	0.904922531607374	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.904922531607374	1		254	192	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247204	153247204	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	286	302	0	ENST00000281708.4:c.1598G>T	p.Cys533Phe	p.C533F	ENST00000281708	NM_033632.3	533	tGt/tTt	10/12	0.412844330017496	2	FACETS	0.752	0.722	0.782	0.752	0.722	0.782	INDETERMINATE	2	TRUE	0	0.904922531607374	2		302	420	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499405	89499405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	321	399	0	ENST00000336596.2:c.2575G>A	p.Asp859Asn	p.D859N	ENST00000336596	NM_005233.5	859	Gac/Aac	15/17	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.904922531607374	2		399	678	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934906	9934906	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866473134	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	112	335	0	ENST00000330684.3:c.1384G>A	p.Asp462Asn	p.D462N	ENST00000330684	NM_001134407.1	462	Gat/Aat	6/13	0.601654470743187	1	FACETS	0.379	0.344	0.415	0.379	0.344	0.415	SUBCLONAL	1	TRUE	0	0.904922531607374	1		335	358	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729961	41729961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867739441	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	372	552	0	ENST00000242208.4:c.568G>A	p.Glu190Lys	p.E190K	ENST00000242208	NM_002192.2	190	Gaa/Aaa	3/3	0.441561624349535	3	FACETS	1	0.994	1	0.651	0.62	0.682	INDETERMINATE	1	TRUE	1	0.904922531607374	3		552	917	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538897	23538897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1200957711	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	289	467	0	ENST00000380871.4:c.542G>A	p.Arg181Gln	p.R181Q	ENST00000380871	NM_006167.3	181	cGa/cAa	2/2	0.663825569119363	1	FACETS	0.712	0.68	0.744	0.712	0.68	0.744	SUBCLONAL	1	TRUE	0	0.904922531607374	1		467	491	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631443	117631443	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	231	290	0	ENST00000368508.3:c.6235G>A	p.Asp2079Asn	p.D2079N	ENST00000368508	NM_002944.2	2079	Gat/Aat	40/43	0.113881618393768	4	FACETS	0.851	0.809	0.892	0.638	0.606	0.669	INDETERMINATE	3	TRUE	0	0.904922531607374	4		290	381	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858585	9858585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	229	468	0	ENST00000330684.3:c.2816G>A	p.Gly939Glu	p.G939E	ENST00000330684	NM_001134407.1	939	gGg/gAg	13/13	0.601654470743187	1	FACETS	0.709	0.673	0.744	0.709	0.673	0.744	SUBCLONAL	1	TRUE	0	0.904922531607374	1		468	391	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849018	156849018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	536	575	0	ENST00000524377.1:c.1910G>A	p.Gly637Glu	p.G637E	ENST00000524377	NM_002529.3	637	gGg/gAg	15/17	0.429113026238344	3	FACETS	0.873	0.842	0.903	0.873	0.842	0.903	INDETERMINATE	2	TRUE	1	0.904922531607374	3		575	986	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420285	88420285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199690201	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	251	393	0	ENST00000360948.2:c.2401G>A	p.Asp801Asn	p.D801N	ENST00000360948	NM_001012338.2	801	Gat/Aat	19/19	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.904922531607374	2		393	541	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372151	55372151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	191	175	0	ENST00000297316.4:c.841C>T	p.Pro281Ser	p.P281S	ENST00000297316	NM_022454.3	281	Ccc/Tcc	2/2	0.663825569119363	1	FACETS	0.725	0.685	0.764	0.725	0.685	0.764	SUBCLONAL	1	TRUE	0	0.904922531607374	1		175	319	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420191	88420191	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	231	384	1	ENST00000360948.2:c.2495C>A	p.Pro832Gln	p.P832Q	ENST00000360948	NM_001012338.2	832	cCa/cAa	19/19	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.904922531607374	2		385	500	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981578	70981578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	428	672	0	ENST00000276594.2:c.518C>T	p.Ser173Leu	p.S173L	ENST00000276594	NM_024504.3	173	tCa/tTa	2/8	0.663825569119363	1	FACETS	0.706	0.679	0.732	0.706	0.679	0.732	SUBCLONAL	1	TRUE	0	0.904922531607374	1		672	734	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223272	5223272	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	526	445	1	ENST00000357368.4:c.2531C>T	p.Pro844Leu	p.P844L	ENST00000357368	NM_002850.3	844	cCc/cTc	18/38	0.38875246179694	3	FACETS	0.891	0.859	0.921	0.891	0.859	0.921	INDETERMINATE	2	TRUE	1	0.904922531607374	3		446	948	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074200	30074200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	222	382	0	ENST00000338641.4:c.1462C>T	p.Pro488Ser	p.P488S	ENST00000338641	NM_000268.3	488	Cca/Tca	14/16	1	2	FACETS	0.938	0.882	0.995	0.938	0.882	0.995	CLONAL	1	TRUE	1	0.904922531607374	2		382	523	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979457	2979457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769402864	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	446	504	0	ENST00000396946.4:c.790G>A	p.Glu264Lys	p.E264K	ENST00000396946	NM_032415.4	264	Gag/Aag	6/25	0.441561624349535	3	FACETS	0.915	0.881	0.949	0.915	0.881	0.949	INDETERMINATE	2	TRUE	1	0.904922531607374	3		504	782	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778894	3778894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1421133831	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	172	527	0	ENST00000262367.5:c.6154C>T	p.Arg2052Trp	p.R2052W	ENST00000262367	NM_004380.2	2052	Cgg/Tgg	31/31	0.601654470743187	1	FACETS	0.387	0.358	0.416	0.387	0.358	0.416	SUBCLONAL	1	TRUE	0	0.904922531607374	1		527	538	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323193	31323193	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	496	556	0	ENST00000412585.2:c.796C>T	p.Gln266Ter	p.Q266*	ENST00000412585	NM_005514.6	266	Cag/Tag	4/8	0.113881618393768	4	FACETS	1	0.995	1	0.61	0.588	0.631	INDETERMINATE	2	TRUE	0	0.904922531607374	4		556	856	SUCCESS
AR	367	MSKCC	GRCh37	X	66905968	66905968	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1421832550	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	100	314	0	ENST00000374690.3:c.1885G>A	p.Ala629Thr	p.A629T	ENST00000374690	NM_000044.3	629	Gcc/Acc	3/8	0.709119436881773	0	FACETS		NA	1			1	NA	1	TRUE	0	0.904922531607374	0		314	127	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514997	103514997	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137877463	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	110	282	2	ENST00000355739.4:c.1498C>T	p.Arg500Trp	p.R500W	ENST00000355739	NM_000123.3	500	Cgg/Tgg	8/15	0.435193151546291	2	FACETS	0.668	0.606	0.732	0.334	0.303	0.366	INDETERMINATE	1	TRUE	0	0.904922531607374	2		284	364	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27203085	27203085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1367866328	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	322	456	0	ENST00000380036.4:c.2177C>T	p.Ser726Phe	p.S726F	ENST00000380036	NM_000459.3	726	tCt/tTt	13/23	0.231859377410951	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.904922531607374	0		456	641	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198260870	198260870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	110	400	0	ENST00000335508.6:c.3449C>T	p.Ser1150Leu	p.S1150L	ENST00000335508	NM_012433.2	1150	tCg/tTg	23/25	0.435193151546291	2	FACETS	0.522	0.471	0.575	0.261	0.235	0.288	INDETERMINATE	1	TRUE	0	0.904922531607374	2		400	466	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873161	136873161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	258	359	0	ENST00000241393.3:c.337C>T	p.His113Tyr	p.H113Y	ENST00000241393	NM_003467.2	113	Cat/Tat	2/2	0.435193151546291	2	FACETS	1	0.995	1	0.735	0.703	0.766	INDETERMINATE	1	TRUE	0	0.904922531607374	2		359	388	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400130	41400130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	306	500	0	ENST00000373198.4:c.629C>T	p.Thr210Ile	p.T210I	ENST00000373198	NM_133170.3	210	aCa/aTa	5/32	0.441561624349535	3	FACETS	1	0.988	1	0.575	0.544	0.607	INDETERMINATE	1	TRUE	1	0.904922531607374	3		500	854	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405927	49405927	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	334	464	0	ENST00000418115.1:c.211C>T	p.Pro71Ser	p.P71S	ENST00000418115	NM_001664.2	71	Ccc/Tcc	3/5	1	2	FACETS	0.95	0.904	0.997	0.95	0.904	0.997	CLONAL	1	TRUE	1	0.904922531607374	2		464	777	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200689	67200689	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	312	561	0	ENST00000312629.5:c.798+2C>G		p.X266_splice	ENST00000312629	NM_003952.2	266			0.663825569119363	1	FACETS	0.675	0.645	0.706	0.675	0.645	0.706	SUBCLONAL	1	TRUE	0	0.904922531607374	1		561	559	SUCCESS
ATM	472	MSKCC	GRCh37	11	108168025	108168025	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	218	248	0	ENST00000278616.4:c.4921G>A	p.Asp1641Asn	p.D1641N	ENST00000278616	NM_000051.3	1641	Gat/Aat	33/63	0.904922531607374	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.904922531607374	1		248	241	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023663	1023663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	305	466	0	ENST00000358495.3:c.901C>T	p.Pro301Ser	p.P301S	ENST00000358495	NM_134424.2	301	Cct/Tct	10/12	0.140197441855699	3	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.904922531607374	3		466	851	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425424	49425425	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	336	669	1	ENST00000301067.7:c.13063_13064delinsTT	p.Pro4355Phe	p.P4355F	ENST00000301067	NM_003482.3	4355	CCt/TTt	39/54	1	2	FACETS	0.909	0.864	0.954	0.909	0.864	0.954	CLONAL	1	TRUE	1	0.904922531607374	2		670	817	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433235	49433235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1257307993	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	414	649	1	ENST00000301067.7:c.8212C>T	p.Pro2738Ser	p.P2738S	ENST00000301067	NM_003482.3	2738	Ccc/Tcc	32/54	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.904922531607374	2		650	889	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256083	133256083	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	242	335	0	ENST00000320574.5:c.578G>A	p.Ser193Asn	p.S193N	ENST00000320574	NM_006231.2	193	aGt/aAt	6/49	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.904922531607374	2		335	535	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355081	73355081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1566255111	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	301	396	0	ENST00000377767.4:c.289G>A	p.Glu97Lys	p.E97K	ENST00000377767	NM_014953.3	97	Gaa/Aaa	2/21	0.435193151546291	2	FACETS	1	0.995	1	0.706	0.677	0.735	INDETERMINATE	1	TRUE	0	0.904922531607374	2		396	471	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126068	2126068	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	182	535	0	ENST00000219476.3:c.2640-1G>C		p.X880_splice	ENST00000219476	NM_000548.3	880			0.601654470743187	1	FACETS	0.376	0.349	0.405	0.376	0.349	0.405	SUBCLONAL	1	TRUE	0	0.904922531607374	1		535	585	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633145	3633146	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	353	620	1	ENST00000294008.3:c.5105_5106delinsTT	p.Ser1702Phe	p.S1702F	ENST00000294008	NM_032444.2	1702	tCC/tTT	14/15	0.601654470743187	1	FACETS	0.701	0.672	0.73	0.701	0.672	0.73	SUBCLONAL	1	TRUE	0	0.904922531607374	1		621	609	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821964	72821964	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1284146036	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	311	361	0	ENST00000268489.5:c.10211C>T	p.Pro3404Leu	p.P3404L	ENST00000268489	NM_006885.3	3404	cCc/cTc	10/10	0.904922531607374	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.904922531607374	1		361	344	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496907	29496907	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	208	171	0	ENST00000356175.3:c.480-2A>C		p.X160_splice	ENST00000356175	NM_000267.3	160			0.904922531607374	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.904922531607374	2		171	222	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276783	15276783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	503	660	0	ENST00000263388.2:c.5482G>A	p.Gly1828Arg	p.G1828R	ENST00000263388	NM_000435.2	1828	Ggg/Agg	30/33	0.38875246179694	3	FACETS	0.84	0.809	0.871	0.84	0.809	0.871	INDETERMINATE	2	TRUE	1	0.904922531607374	3		660	961	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291906	15291907	+	missense_variant	Missense_Mutation	DNP	AG	AG	TC	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	573	843	1	ENST00000263388.2:c.2859_2860delinsGA	p.Tyr954Asn	p.Y954N	ENST00000263388	NM_000435.2	953	ggCTac/ggGAac	18/33	0.38875246179694	3	FACETS	0.884	0.855	0.914	0.884	0.855	0.914	INDETERMINATE	2	TRUE	1	0.904922531607374	3		844	1040	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367783	15367783	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	335	572	0	ENST00000263377.2:c.1543C>T	p.Gln515Ter	p.Q515*	ENST00000263377	NM_058243.2	515	Cag/Tag	8/20	0.38875246179694	3	FACETS	1	0.992	1	0.617	0.586	0.649	INDETERMINATE	1	TRUE	1	0.904922531607374	3		572	871	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961607	18961607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	474	592	0	ENST00000262803.5:c.740C>T	p.Ser247Phe	p.S247F	ENST00000262803	NM_002911.3	247	tCc/tTc	5/24	0.38875246179694	3	FACETS	0.838	0.806	0.87	0.838	0.806	0.87	INDETERMINATE	2	TRUE	1	0.904922531607374	3		592	908	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257142	19257142	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	232	529	0	ENST00000162023.5:c.821C>T	p.Thr274Ile	p.T274I	ENST00000162023		274	aCc/aTc	12/13	0.38875246179694	3	FACETS	1	0.953	1	0.511	0.478	0.544	INDETERMINATE	1	TRUE	1	0.904922531607374	3		529	729	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39237753	39237753	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	97	267	0	ENST00000402219.2:c.2482A>T	p.Thr828Ser	p.T828S	ENST00000402219	NM_005633.3	828	Acc/Tcc	15/23	0.435193151546291	2	FACETS	0.518	0.465	0.574	0.259	0.232	0.287	INDETERMINATE	1	TRUE	0	0.904922531607374	2		267	414	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103861	209103861	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	252	360	0	ENST00000345146.2:c.1088C>T	p.Ser363Phe	p.S363F	ENST00000345146	NM_005896.2	363	tCt/tTt	9/10	0.435193151546291	2	FACETS	1	0.994	1	0.696	0.664	0.728	INDETERMINATE	1	TRUE	0	0.904922531607374	2		360	400	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610550	215610550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	105	357	0	ENST00000260947.4:c.1706C>T	p.Pro569Leu	p.P569L	ENST00000260947	NM_000465.2	569	cCt/cTt	8/11	0.435193151546291	2	FACETS	0.451	0.406	0.499	0.226	0.203	0.25	INDETERMINATE	1	TRUE	0	0.904922531607374	2		357	514	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440156	220440156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	185	611	0	ENST00000243786.2:c.1009C>T	p.Pro337Ser	p.P337S	ENST00000243786	NM_002191.3	337	Ccc/Tcc	2/2	0.435193151546291	2	FACETS	0.505	0.467	0.544	0.252	0.233	0.272	INDETERMINATE	1	TRUE	0	0.904922531607374	2		611	810	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663322	227663322	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	415	513	1	ENST00000305123.5:c.133G>T	p.Glu45Ter	p.E45*	ENST00000305123	NM_005544.2	45	Gag/Tag	1/2	0.435193151546291	2	FACETS	0.771	0.745	0.795	0.771	0.745	0.795	INDETERMINATE	2	TRUE	0	0.904922531607374	2		514	595	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924788	49924789	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	379	723	1	ENST00000296474.3:c.4154_4155delinsAA	p.Gly1385Glu	p.G1385E	ENST00000296474	NM_002447.2	1385	gGG/gAA	20/20	1	2	FACETS	0.902	0.859	0.944	0.902	0.859	0.944	CLONAL	1	TRUE	1	0.904922531607374	2		724	929	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940928	49940928	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	414	687	0	ENST00000296474.3:c.115G>C	p.Asp39His	p.D39H	ENST00000296474	NM_002447.2	39	Gac/Cac	1/20	1	2	FACETS	0.983	0.94	1	0.983	0.94	1	CLONAL	1	TRUE	1	0.904922531607374	2		687	931	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196661	106196661	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	122	416	0	ENST00000380013.4:c.4994A>G	p.Asp1665Gly	p.D1665G	ENST00000380013	NM_001127208.2	1665	gAc/gGc	11/11	0.412844330017496	2	FACETS	0.482	0.437	0.529	0.241	0.218	0.265	INDETERMINATE	1	TRUE	0	0.904922531607374	2		416	559	SUCCESS
APC	324	MSKCC	GRCh37	5	112179729	112179729	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	190	262	0	ENST00000257430.4:c.8438del	p.Thr2813LysfsTer28	p.T2813Kfs*28	ENST00000257430	NM_000038.5	2813	aCa/aa	16/16	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.904922531607374	2		262	389	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940567	131940567	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	159	261	0	ENST00000265335.6:c.2594G>A	p.Ser865Asn	p.S865N	ENST00000265335		865	aGt/aAt	16/25	1	2	FACETS	0.903	0.839	0.969	0.903	0.839	0.969	CLONAL	1	TRUE	1	0.904922531607374	2		261	389	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31946717	31946717	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	304	474	0	ENST00000375333.2:c.605A>G	p.Gln202Arg	p.Q202R	ENST00000375333	NM_032454.1	202	cAg/cGg	4/8	0.113881618393768	4	FACETS	0.776	0.734	0.818	0.388	0.367	0.409	INDETERMINATE	2	TRUE	0	0.904922531607374	4		474	825	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798399	32798399	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	268	486	0	ENST00000374899.4:c.1457T>C	p.Leu486Pro	p.L486P	ENST00000374899	NM_018833.2	486	cTc/cCc	8/12	0.113881618393768	4	FACETS	1	0.993	1	0.37	0.348	0.392	INDETERMINATE	1	TRUE	0	0.904922531607374	4		486	763	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266458	55266458	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	248	497	0	ENST00000275493.2:c.2750G>A	p.Gly917Glu	p.G917E	ENST00000275493	NM_005228.3	917	gGa/gAa	23/28	0.441561624349535	3	FACETS	1	0.984	1	0.567	0.533	0.602	INDETERMINATE	1	TRUE	1	0.904922531607374	3		497	702	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205070	38205070	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	177	379	0	ENST00000317025.8:c.620G>A	p.Arg207Lys	p.R207K	ENST00000317025	NM_023034.1	207	aGa/aAa	2/24	0.663825569119363	1	FACETS	0.407	0.378	0.437	0.407	0.378	0.437	SUBCLONAL	1	TRUE	0	0.904922531607374	1		379	526	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606541	93606541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	374	635	0	ENST00000375746.1:c.361G>A	p.Glu121Lys	p.E121K	ENST00000375746	NM_001174167.1	121	Gag/Aag	2/14	0.663825569119363	1	FACETS	0.72	0.691	0.748	0.72	0.691	0.748	SUBCLONAL	1	TRUE	0	0.904922531607374	1		635	629	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139440181	139440181	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	35	72	0	ENST00000277541.6:c.58C>T	p.Arg20Ter	p.R20*	ENST00000277541	NM_017617.3	20	Cga/Tga	1/34	0.663825569119363	1	FACETS	0.362	0.303	0.425	0.362	0.303	0.425	SUBCLONAL	1	TRUE	0	0.904922531607374	1		72	117	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191814	123191814	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	78	256	0	ENST00000218089.9:c.1403T>C	p.Phe468Ser	p.F468S	ENST00000218089	NM_001042749.1	468	tTt/tCt	15/35	0.709119436881773	0	FACETS		NA	1			1	NA	1	TRUE	0	0.904922531607374	0		256	97	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0053070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	132	330	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.882	0.807	0.959	0.882	0.807	0.959	CLONAL	1	TRUE	1	0.7010924545716	2		330	427	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0053070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	166	561	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.87	0.805	0.938	0.87	0.805	0.938	CLONAL	1	TRUE	1	0.7010924545716	2		561	544	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023076	150023076	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs187759014	NA	P-0053070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	247	529	1	ENST00000253339.5:c.187C>T	p.Arg63Ter	p.R63*	ENST00000253339		63	Cga/Tga	1/7	0.7010924545716	1	FACETS	0.984	0.933	1	0.984	0.933	1	CLONAL	1	TRUE	0	0.7010924545716	1		530	465	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805077	89805077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374984587	NA	P-0053070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	274	586	0	ENST00000389301.3:c.4300G>A	p.Ala1434Thr	p.A1434T	ENST00000389301	NM_000135.2	1434	Gcc/Acc	43/43	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.7010924545716	2		586	744	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240271	5240271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145504993	NA	P-0053070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	289	739	0	ENST00000357368.4:c.1643C>T	p.Pro548Leu	p.P548L	ENST00000357368	NM_002850.3	548	cCg/cTg	12/38	0.675414286039532	2	FACETS	1	0.982	1	0.545	0.515	0.576	CLONAL	1	TRUE	0	0.7010924545716	2		739	756	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027160	49027160	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0053070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	138	363	0	ENST00000267163.4:c.1727C>G	p.Ser576Ter	p.S576*	ENST00000267163	NM_000321.2	576	tCa/tGa	18/27	1	2	FACETS	0.895	0.821	0.971	0.895	0.821	0.971	CLONAL	1	TRUE	1	0.7010924545716	2		363	440	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934194	48934194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	133	337	0	ENST00000267163.4:c.649C>T	p.Gln217Ter	p.Q217*	ENST00000267163	NM_000321.2	217	Cag/Tag	7/27	1	2	FACETS	0.901	0.826	0.979	0.901	0.826	0.979	CLONAL	1	TRUE	1	0.7010924545716	2		337	421	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564633	86564633	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	226	613	0	ENST00000274376.6:c.365C>A	p.Ser122Ter	p.S122*	ENST00000274376	NM_002890.2	122	tCg/tAg	1/25	0.69478833883769	1	FACETS	0.855	0.805	0.904	0.855	0.805	0.904	CLONAL	1	TRUE	0	0.7010924545716	1		613	490	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28595728	28595728	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769967309	NA	P-0053070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	263	714	0	ENST00000253063.3:c.125G>A	p.Arg42Gln	p.R42Q	ENST00000253063	NM_031459.4	42	cGa/cAa	2/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.7010924545716	2		714	733	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657560	37657560	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	161	422	0	ENST00000447079.4:c.2477C>G	p.Ser826Cys	p.S826C	ENST00000447079	NM_015083.1	826	tCt/tGt	6/14	1	2	FACETS	0.775	0.714	0.837	0.775	0.714	0.837	SUBCLONAL	1	TRUE	1	0.7010924545716	2		422	593	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528157	29528157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	173	453	0	ENST00000356175.3:c.1165C>T	p.His389Tyr	p.H389Y	ENST00000356175	NM_000267.3	389	Cac/Tac	10/57	1	2	FACETS	0.841	0.778	0.905	0.841	0.778	0.905	CLONAL	1	TRUE	1	0.7010924545716	2		453	587	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650610	48650610	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	172	621	0	ENST00000376670.3:c.580C>T	p.Leu194Phe	p.L194F	ENST00000376670	NM_002049.3	194	Ctc/Ttc	3/6	1	2	FACETS	0.879	0.814	0.946	0.879	0.814	0.946	CLONAL	1	TRUE	1	0.7010924545716	2		621	558	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138575	55138575	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	194	430	0	ENST00000257290.5:c.1252C>G	p.Leu418Val	p.L418V	ENST00000257290	NM_006206.4	418	Ctg/Gtg	9/23	1	2	FACETS	0.951	0.886	1	0.951	0.886	1	CLONAL	1	TRUE	1	0.7010924545716	2		430	582	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910371	29910371	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs2230954	NA	P-0053070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	38	639	2	ENST00000376809.5:c.41C>A	p.Ser14Ter	p.S14*	ENST00000376809	NM_002116.7	14	tCg/tAg	1/8	0.7010924545716	1	FACETS	0.122	0.1	0.146	0.122	0.1	0.146	SUBCLONAL	1	TRUE	0	0.7010924545716	1		641	578	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38545389	38545389	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs1324903101	NA	P-0053070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	192	356	0	ENST00000299084.4:c.3G>A	p.Met1?	p.M1?	ENST00000299084	NM_152594.2	1	atG/atA	1/7	1	2	FACETS	0.992	0.924	1	0.992	0.924	1	CLONAL	1	TRUE	1	0.7010924545716	2		356	552	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591070	67591070	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	137	266	1	ENST00000274335.5:c.1663G>T	p.Glu555Ter	p.E555*	ENST00000274335		555	Gag/Tag	12/15	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.7010924545716	2		267	381	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526760	31526760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1478024603	NA	P-0053070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	180	382	0	ENST00000344624.3:c.280C>T	p.Pro94Ser	p.P94S	ENST00000344624		94	Ccc/Tcc	2/33	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.7010924545716	2		382	482	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287412	46287412	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0053070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	118	319	0	ENST00000334344.6:c.5272-1G>A		p.X1758_splice	ENST00000334344	NM_152641.2	1758			1	2	FACETS	0.935	0.853	1	0.935	0.853	1	CLONAL	1	TRUE	1	0.7010924545716	2		319	360	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644476	21644476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	161	408	0	ENST00000421138.2:c.191C>T	p.Ser64Leu	p.S64L	ENST00000421138		64	tCa/tTa	4/16	1	2	FACETS	0.986	0.912	1	0.986	0.912	1	CLONAL	1	TRUE	1	0.7010924545716	2		408	466	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527590	29527590	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	109	375	0	ENST00000356175.3:c.1039C>G	p.Gln347Glu	p.Q347E	ENST00000356175	NM_000267.3	347	Cag/Gag	9/57	1	2	FACETS	0.783	0.709	0.86	0.783	0.709	0.86	SUBCLONAL	1	TRUE	1	0.7010924545716	2		375	397	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33430494	33430494	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	201	579	0	ENST00000345365.6:c.646C>A	p.Leu216Met	p.L216M	ENST00000345365	NM_002878.3	216	Ctg/Atg	7/10	1	2	FACETS	0.89	0.829	0.953	0.89	0.829	0.953	CLONAL	1	TRUE	1	0.7010924545716	2		579	644	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157197	106157197	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1221306241	NA	P-0053070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	181	345	1	ENST00000380013.4:c.2098A>T	p.Lys700Ter	p.K700*	ENST00000380013	NM_001127208.2	700	Aaa/Taa	3/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.7010924545716	2		346	472	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910350	29910350	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	33	620	0	ENST00000376809.5:c.20G>T	p.Arg7Leu	p.R7L	ENST00000376809	NM_002116.7	7	cGa/cTa	1/8	0.7010924545716	1	FACETS	0.105	0.085	0.128	0.105	0.085	0.128	SUBCLONAL	1	TRUE	0	0.7010924545716	1		620	583	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818909	32818909	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	157	349	0	ENST00000354258.4:c.1042del	p.Val348Ter	p.V348*	ENST00000354258	NM_000593.5	348	Gta/ta	4/11	0.7010924545716	1	FACETS	0.903	0.842	0.965	0.903	0.842	0.965	CLONAL	1	TRUE	0	0.7010924545716	1		349	322	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877818	151877818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749660959	NA	P-0053070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	121	324	0	ENST00000262189.6:c.7127C>T	p.Ala2376Val	p.A2376V	ENST00000262189	NM_170606.2	2376	gCa/gTa	36/59	1	2	FACETS	0.948	0.866	1	0.948	0.866	1	CLONAL	1	TRUE	1	0.7010924545716	2		324	364	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123018	5123018	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	157	300	0	ENST00000381652.3:c.3074C>A	p.Ser1025Ter	p.S1025*	ENST00000381652	NM_004972.3	1025	tCa/tAa	23/25	0.7010924545716	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.7010924545716	1		300	269	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247466	53247466	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	217	440	0	ENST00000375401.3:c.343C>G	p.Leu115Val	p.L115V	ENST00000375401	NM_004187.3	115	Ctc/Gtc	3/26	1	2	FACETS	0.795	0.741	0.85	0.795	0.741	0.85	SUBCLONAL	1	TRUE	1	0.7010924545716	2		440	779	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	101	411	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.336551629886577	2		411	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578233	7578234	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0053071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	122	551	0	ENST00000269305.4:c.614_615dup	p.Leu206IlefsTer42	p.L206Ifs*42	ENST00000269305	NM_001126112.2	205	-/AT	6/11	0.336551629886577	1	FACETS	0.968	0.877	1	0.968	0.877	1	CLONAL	1	TRUE	0	0.336551629886577	1		551	623	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971155	21971155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501260	NA	P-0053071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	90	304	0	ENST00000304494.5:c.203C>T	p.Ala68Val	p.A68V	ENST00000304494	NM_000077.4	68	gCg/gTg	2/3	0.336551629886577	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.336551629886577	1		304	339	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2488137	2488137	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	204	508	0	ENST00000355716.4:c.34T>C	p.Trp12Arg	p.W12R	ENST00000355716	NM_003820.2	12	Tgg/Cgg	1/8	0.643190172392841	3	FACETS	0.986	0.916	1	0.493	0.458	0.529	CLONAL	1	TRUE	1	0.652671974378267	3		508	841	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579369	7579389	+	inframe_deletion	In_Frame_Del	DEL	GCTGCCCTGGTAGGTTTTCTG	GCTGCCCTGGTAGGTTTTCTG	-	novel	NA	P-0053073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	525	607	0	ENST00000269305.4:c.298_318del	p.Gln100_Ser106del	p.Q100_S106del	ENST00000269305	NM_001126112.2	100	CAGAAAACCTACCAGGGCAGC/-	4/11	0.295840952013892	5	FACETS	1	0.986	1			1	INDETERMINATE	4	TRUE	NA	0.652671974378267	5		607	774	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	106	429	0				ENST00000310581	NM_198253.2	-/1132			0.298358248834604	5	FACETS	0.888	0.803	0.977	0.666	0.602	0.733	CLONAL	3	TRUE	1	0.298358248834604	5		429	386	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880257	37880257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	165	361	0	ENST00000269571.5:c.2301C>G	p.Ile767Met	p.I767M	ENST00000269571		767	atC/atG	19/27	0.131661542869132	5	FACETS	0.917	0.842	0.995	0.611	0.561	0.663	INDETERMINATE	2	TRUE	2	0.298358248834604	5		361	873	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57569902	57569902	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	100	264	0	ENST00000316660.6:c.82C>T	p.Gln28Ter	p.Q28*	ENST00000316660	NM_021127.2	28	Caa/Taa	2/2	0.255261556791573	3	FACETS	0.879	0.79	0.973	0.586	0.527	0.649	CLONAL	2	TRUE	0	0.298358248834604	3		264	438	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97873861	97873861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	123	548	1	ENST00000289081.3:c.1213G>A	p.Glu405Lys	p.E405K	ENST00000289081	NM_000136.2	405	Gag/Aag	13/15	0.269384824640279	2	FACETS	0.829	0.749	0.915	0.415	0.374	0.458	CLONAL	1	TRUE	0	0.298358248834604	2		549	994	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100467	102100467	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	95	354	1	ENST00000282441.5:c.1311G>T	p.Gln437His	p.Q437H	ENST00000282441	NM_001130145.2	437	caG/caT	9/9	0.283013805198338	4	FACETS	1	0.956	1	0.382	0.34	0.427	CLONAL	1	TRUE	1	0.298358248834604	4		355	721	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374590	118374590	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs142807735	NA	P-0053074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	73	301	0	ENST00000534358.1:c.7983G>C	p.Lys2661Asn	p.K2661N	ENST00000534358	NM_005933.3	2661	aaG/aaC	27/36	0.283013805198338	4	FACETS	0.999	0.874	1	0.333	0.291	0.378	CLONAL	1	TRUE	1	0.298358248834604	4		301	636	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434456	121434456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	335	639	0	ENST00000257555.6:c.1220C>T	p.Ser407Leu	p.S407L	ENST00000257555		407	tCa/tTa	6/10	0.298358248834604	2	FACETS	0.958	0.906	1	0.958	0.906	1	CLONAL	2	TRUE	0	0.298358248834604	2		639	1172	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661918	29661918	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	80	372	0	ENST00000356175.3:c.5812T>G	p.Phe1938Val	p.F1938V	ENST00000356175	NM_000267.3	1938	Ttt/Gtt	39/57	0.131661542869132	5	FACETS	0.854	0.759	0.953	0.854	0.759	0.953	INDETERMINATE	3	TRUE	2	0.298358248834604	5		372	303	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804230	46804230	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	63	523	0	ENST00000290295.7:c.777G>C	p.Gln259His	p.Q259H	ENST00000290295	NM_006361.5	259	caG/caC	2/2	0.131661542869132	5	FACETS	0.495	0.426	0.57	0.165	0.142	0.19	INDETERMINATE	1	TRUE	2	0.298358248834604	5		523	1235	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637874	176637874	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	69	423	0	ENST00000439151.2:c.2474C>A	p.Ala825Asp	p.A825D	ENST00000439151	NM_022455.4	825	gCc/gAc	5/23	0.190498507066107	3	FACETS	0.953	0.83	1	0.476	0.415	0.542	CLONAL	1	TRUE	1	0.298358248834604	3		423	558	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675202	30675202	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	86	519	0	ENST00000376406.3:c.3043G>C	p.Glu1015Gln	p.E1015Q	ENST00000376406	NM_014641.2	1015	Gag/Cag	9/15	0.298358248834604	5	FACETS	0.688	0.606	0.776	0.229	0.202	0.259	SUBCLONAL	1	TRUE	2	0.298358248834604	5		519	1213	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184818	32184818	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	252	466	0	ENST00000375023.3:c.1765G>C	p.Glu589Gln	p.E589Q	ENST00000375023	NM_004557.3	589	Gag/Cag	11/30	0.298358248834604	5	FACETS	1	0.988	1	0.809	0.758	0.863	CLONAL	2	TRUE	2	0.298358248834604	5		466	1007	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856070	151856070	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	116	367	0	ENST00000262189.6:c.11548C>G	p.Arg3850Gly	p.R3850G	ENST00000262189	NM_170606.2	3850	Cga/Gga	44/59	0.296048012601771	3	FACETS	1	0.983	1	0.717	0.648	0.79	CLONAL	1	TRUE	1	0.298358248834604	3		367	623	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	161	429	0				ENST00000310581	NM_198253.2	-/1132			0.714205324351434	5	FACETS	0.908	0.856	0.96	1	0.988	1	CLONAL	4	TRUE	2	0.714205324351434	5		429	257	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555526101	NA	P-0053075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	544	667	0	ENST00000269305.4:c.497C>G	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tGa	5/11	0.714205324351434	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.714205324351434	2		667	682	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	685	622	0	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	0.605394164850991	5	FACETS	1	0.994	1			1	CLONAL	3	TRUE	NA	0.714205324351434	5		622	1210	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056277	27056277	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	198	534	0	ENST00000324856.7:c.1273C>T	p.Gln425Ter	p.Q425*	ENST00000324856	NM_006015.4	425	Cag/Tag	2/20	0.710913964923285	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.714205324351434	1		534	291	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037866	49037866	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs587778860	NA	P-0053075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	177	233	0	ENST00000267163.4:c.2107-1G>A		p.X703_splice	ENST00000267163	NM_000321.2	703			NA	2	FACETS	1	0.981	1			1	INDETERMINATE	2	TRUE	NA	0.714205324351434	2		233	235	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045954	26045954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	194	586	0	ENST00000540144.1:c.316G>A	p.Glu106Lys	p.E106K	ENST00000540144	NM_003531.2	106	Gaa/Aaa	1/1	0.714205324351434	4	FACETS	0.96	0.888	1	0.32	0.296	0.345	CLONAL	1	TRUE	1	0.714205324351434	4		586	970	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790072	40790072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753667	NA	P-0053075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	336	553	2	ENST00000373198.4:c.2659G>A	p.Ala887Thr	p.A887T	ENST00000373198	NM_133170.3	887	Gcc/Acc	18/32	0.321283051044982	5	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.714205324351434	5		555	818	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248391	59248391	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	296	422	0	ENST00000371222.2:c.352C>A	p.Leu118Met	p.L118M	ENST00000371222	NM_002228.3	118	Ctg/Atg	1/1	0.714205324351434	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.714205324351434	3		422	507	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726618	41726618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1787	422	639	0	ENST00000301178.4:c.163C>T	p.Arg55Trp	p.R55W	ENST00000301178	NM_021913.4	55	Cgg/Tgg	2/20	0.714205324351434	9	FACETS	0.936	0.888	0.985			1	CLONAL	2	TRUE	NA	0.714205324351434	9		639	2209	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692975	89692975	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	251	420	0	ENST00000371953.3:c.459T>A	p.Asp153Glu	p.D153E	ENST00000371953	NM_000314.4	153	gaT/gaA	5/9	0.657903494443856	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	1	0.714205324351434	3		420	471	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805531	46805541	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGCCATAGG	CTGGCCATAGG	-	novel	NA	P-0053075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	404	687	0	ENST00000290295.7:c.415_425del	p.Pro139LeufsTer19	p.P139Lfs*19	ENST00000290295	NM_006361.5	139	CCTATGGCCAGt/t	1/2	0.714205324351434	3	FACETS	0.95	0.91	0.99	0.95	0.91	0.99	CLONAL	2	TRUE	1	0.714205324351434	3		687	808	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047026	128047026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	300	458	0	ENST00000285398.2:c.709G>A	p.Asp237Asn	p.D237N	ENST00000285398	NM_000122.1	237	Gat/Aat	6/15	0.714205324351434	3	FACETS	0.96	0.913	1	0.96	0.913	1	CLONAL	2	TRUE	1	0.714205324351434	3		458	594	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488375	20488375	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	248	393	0	ENST00000346618.3:c.1031G>A	p.Gly344Glu	p.G344E	ENST00000346618	NM_001949.4	344	gGg/gAg	6/7	0.714205324351434	4	FACETS	1	0.992	1	0.472	0.443	0.503	CLONAL	1	TRUE	1	0.714205324351434	4		393	840	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488383	20488383	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	248	388	0	ENST00000346618.3:c.1039G>A	p.Glu347Lys	p.E347K	ENST00000346618	NM_001949.4	347	Gag/Aag	6/7	0.714205324351434	4	FACETS	1	0.992	1	0.467	0.438	0.498	CLONAL	1	TRUE	1	0.714205324351434	4		388	849	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403480	139403480	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	724	726	0	ENST00000277541.6:c.3013T>C	p.Phe1005Leu	p.F1005L	ENST00000277541	NM_017617.3	1005	Ttc/Ctc	19/34	0.439486498483245	5	FACETS	0.921	0.896	0.946			1	CLONAL	4	TRUE	NA	0.714205324351434	5		726	1140	SUCCESS
AR	367	MSKCC	GRCh37	X	66943555	66943555	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	108	229	0	ENST00000374690.3:c.2635T>G	p.Phe879Val	p.F879V	ENST00000374690	NM_000044.3	879	Ttt/Gtt	8/8	0.624632019851177	2	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.714205324351434	2		229	254	SUCCESS
AR	367	MSKCC	GRCh37	X	66943565	66943565	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	115	238	0	ENST00000374690.3:c.2645T>C	p.Leu882Pro	p.L882P	ENST00000374690	NM_000044.3	882	cTa/cCa	8/8	0.624632019851177	2	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.714205324351434	2		238	275	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0053076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	99	430	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.200313380625783	2	FACETS	0.875	0.784	0.97	0.875	0.784	0.97	CLONAL	2	TRUE	0	0.226795611217093	2		430	499	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593464	48593465	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0053076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	26	273	0	ENST00000342988.3:c.1217_1218del	p.Ala406GlyfsTer22	p.A406Gfs*22	ENST00000342988	NM_005359.5	405	caCGcg/cacg	10/12	0.226795611217093	1	FACETS	0.574	0.455	0.711	0.574	0.455	0.711	SUBCLONAL	1	TRUE	0	0.226795611217093	1		273	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577549	7577550	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0053076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	126	508	0	ENST00000269305.4:c.730_731dup	p.Gly245AlafsTer3	p.G245Afs*3	ENST00000269305	NM_001126112.2	244	ggc/ggGGc	7/11	0.195442594985273	2	FACETS	0.875	0.794	0.959	0.875	0.794	0.959	CLONAL	2	TRUE	0	0.226795611217093	2		508	635	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1918700	1918700	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	126	327	0	ENST00000382891.5:c.863G>C	p.Gly288Ala	p.G288A	ENST00000382891	NM_133335.3	288	gGa/gCa	4/22	0.400164457885497	2	FACETS	0.757	0.692	0.824			1	SUBCLONAL	2	TRUE	NA	0.43	2		327	387	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541477	187541477	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	70	313	0	ENST00000441802.2:c.6263C>A	p.Ala2088Asp	p.A2088D	ENST00000441802	NM_005245.3	2088	gCc/gAc	10/27	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.43	2		313	225	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968601	55968608	+	protein_altering_variant	In_Frame_Del	DEL	ATGAGACT	ATGAGACT	TC	novel	NA	P-0053077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	237	465	1	ENST00000263923.4:c.2055_2062delinsGA	p.Val686_Cys688delinsSer	p.V686_C688delinsS	ENST00000263923	NM_002253.2	685	gaAGTCTCATgc/gaGAgc	14/30	0.400164457885497	5	FACETS	0.98	0.921	1			1	CLONAL	3	TRUE	NA	0.43	5		466	617	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577093	7577093	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882008	NA	P-0053109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	112	523	0	ENST00000269305.4:c.845G>C	p.Arg282Pro	p.R282P	ENST00000269305	NM_001126112.2	282	cGg/cCg	8/11	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	2	FALSE	NA	0.737846890697375	2		523	131	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576033	29576033	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	156	419	1	ENST00000356175.3:c.4006C>T	p.Gln1336Ter	p.Q1336*	ENST00000356175	NM_000267.3	1336	Cag/Tag	30/57	0.737846890697375	10	FACETS	0.981	0.931	1	1	0.986	1	CLONAL	8	FALSE	3	0.737846890697375	10		420	213	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493661	56493661	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	69	402	0	ENST00000267101.3:c.2977C>T	p.His993Tyr	p.H993Y	ENST00000267101	NM_001982.3	993	Cat/Tat	25/28	0.737846890697375	7	FACETS	0.887	0.787	0.991			1	CLONAL	3	FALSE	NA	0.737846890697375	7		402	200	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367239	50367239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1045233686	NA	P-0053109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	61	298	0	ENST00000331340.3:c.46G>A	p.Glu16Lys	p.E16K	ENST00000331340	NM_006060.4	16	Gaa/Aaa	3/8	0.737846890697375	4	FACETS	0.848	0.76	0.934	1	0.971	1	CLONAL	3	FALSE	2	0.737846890697375	4		298	113	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414251	32414251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121907910	NA	P-0053109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	41	396	0	ENST00000332351.3:c.1300C>T	p.Arg434Cys	p.R434C	ENST00000332351	NM_024426.4	434	Cgt/Tgt	8/10	0.52334899463191	4	FACETS	0.882	0.773	0.988	0.882	0.773	0.988	CLONAL	3	FALSE	1	0.737846890697375	4		396	73	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750975	128750975	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs990645227	NA	P-0053109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	31	377	0	ENST00000377970.2:c.512G>T	p.Arg171Leu	p.R171L	ENST00000377970	NM_002467.4	171	cGc/cTc	2/3	0.737846890697375	6	FACETS	0.937	0.788	1	0.937	0.788	1	CLONAL	3	FALSE	3	0.737846890697375	6		377	74	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719923	18719923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	52	451	0	ENST00000266497.5:c.3820C>T	p.His1274Tyr	p.H1274Y	ENST00000266497		1274	Cac/Tac	27/31	0.637049153581491	5	FACETS	1	0.904	1	1	0.904	1	CLONAL	3	FALSE	2	0.737846890697375	5		451	97	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458329	12458329	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1364613522	NA	P-0053109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	67	508	0	ENST00000287820.6:c.946C>T	p.Arg316Cys	p.R316C	ENST00000287820	NM_015869.4	316	Cgc/Tgc	6/7	0.737846890697375	6	FACETS	0.876	0.779	0.976	0.876	0.779	0.976	CLONAL	3	FALSE	3	0.737846890697375	6		508	171	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067873	30067873	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	54	515	2	ENST00000338641.4:c.1058G>T	p.Arg353Met	p.R353M	ENST00000338641	NM_000268.3	353	aGg/aTg	11/16	0.522393101058381	5	FACETS	1	0.959	1	0.822	0.724	0.923	CLONAL	2	FALSE	2	0.737846890697375	5		517	125	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197082	26197082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763703948	NA	P-0053109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	190	450	0	ENST00000356476.2:c.397G>A	p.Gly133Arg	p.G133R	ENST00000356476		133	Ggg/Agg	1/1	0.737846890697375	8	FACETS	1	0.966	1	1	0.966	1	CLONAL	6	FALSE	2	0.737846890697375	8		450	271	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138870	64138870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	19	188	0	ENST00000334205.4:c.2237C>T	p.Pro746Leu	p.P746L	ENST00000334205	NM_003942.2	746	cCt/cTt	17/17	0.52334899463191	4	FACETS	1	0.909	1	0.459	0.359	0.568	CLONAL	1	FALSE	1	0.737846890697375	4		188	65	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831123	72831123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs546063296	NA	P-0053109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	34	442	0	ENST00000268489.5:c.5458G>A	p.Gly1820Arg	p.G1820R	ENST00000268489	NM_006885.3	1820	Ggg/Agg	9/10	0.229164676270482	2	FACETS	0.781	0.677	0.882	0.781	0.677	0.882	INDETERMINATE	2	FALSE	0	0.737846890697375	2		442	59	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560179	29560179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	55	309	1	ENST00000356175.3:c.3656G>A	p.Gly1219Glu	p.G1219E	ENST00000356175	NM_000267.3	1219	gGa/gAa	27/57	0.737846890697375	10	FACETS	0.972	0.844	1	0.417	0.361	0.475	CLONAL	3	FALSE	3	0.737846890697375	10		310	202	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10283834	10283834	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	33	413	0	ENST00000340748.4:c.652C>T	p.Pro218Ser	p.P218S	ENST00000340748		218	Cct/Tct	8/40	0.609459253785059	3	FACETS	0.98	0.814	1	0.49	0.407	0.579	CLONAL	1	FALSE	1	0.737846890697375	3		413	125	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097613	11097613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	26	659	0	ENST00000358026.2:c.793C>T	p.Pro265Ser	p.P265S	ENST00000358026	NM_001128849.1	265	Ccc/Tcc	5/36	0.609459253785059	3	FACETS	0.946	0.766	1	0.473	0.383	0.572	CLONAL	1	FALSE	1	0.737846890697375	3		659	102	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299124	15299124	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	24	538	0	ENST00000263388.2:c.1414G>T	p.Glu472Ter	p.E472*	ENST00000263388	NM_000435.2	472	Gag/Tag	9/33	0.609459253785059	3	FACETS	1	0.813	1	0.506	0.407	0.614	CLONAL	1	FALSE	1	0.737846890697375	3		538	88	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945925	17945925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	23	584	0	ENST00000458235.1:c.2014C>T	p.Pro672Ser	p.P672S	ENST00000458235	NM_000215.3	672	Cct/Tct	15/24	0.609459253785059	3	FACETS	0.742	0.588	0.914	0.371	0.294	0.457	CLONAL	1	FALSE	1	0.737846890697375	3		584	115	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764348	39764348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4	56	450	3	ENST00000288319.7:c.764C>T	p.Pro255Leu	p.P255L	ENST00000288319	NM_182918.3	255	cCc/cTc	7/10	0.727735417690661	2	FACETS		NA	1	1	0.984	1	NA	3	FALSE	0	0.737846890697375	2		453	60	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52692324	52692324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754615251	NA	P-0053109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	57	393	0	ENST00000394830.3:c.536C>T	p.Pro179Leu	p.P179L	ENST00000394830	NM_018313.4	179	cCa/cTa	6/30	0.737846890697375	6	FACETS	1	0.952	1	0.792	0.694	0.893	CLONAL	2	FALSE	3	0.737846890697375	6		393	161	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990385	69990385	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0053109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	218	267	0	ENST00000394351.3:c.346-2A>G		p.X116_splice	ENST00000394351	NM_000248.3	116			0.737846890697375	13	FACETS	1	0.955	1			1	CLONAL	9	FALSE	NA	0.737846890697375	13		267	331	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138593	55138593	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	43	496	0	ENST00000257290.5:c.1270C>T	p.His424Tyr	p.H424Y	ENST00000257290	NM_006206.4	424	Cac/Tac	9/23	0.474060793717059	4	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	FALSE	2	0.737846890697375	4		496	88	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910395	29910395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	25	560	1	ENST00000376809.5:c.65C>T	p.Thr22Ile	p.T22I	ENST00000376809	NM_002116.7	22	aCc/aTc	1/8	0.737846890697375	8	FACETS	0.789	0.63	0.967	0.263	0.21	0.323	CLONAL	2	FALSE	2	0.737846890697375	8		561	138	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815337	32815337	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	100	587	0	ENST00000354258.4:c.2036C>T	p.Ser679Phe	p.S679F	ENST00000354258	NM_000593.5	679	tCt/tTt	9/11	0.737846890697375	6	FACETS	1	0.954	1	0.834	0.772	0.893	CLONAL	4	FALSE	1	0.737846890697375	6		587	161	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942829	68942829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	53	493	0	ENST00000288368.4:c.641C>T	p.Ala214Val	p.A214V	ENST00000288368	NM_024870.2	214	gCc/gTc	6/40	0.615331101416566	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	FALSE	1	0.737846890697375	3		493	89	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982044	70982044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	51	471	0	ENST00000276594.2:c.52C>T	p.Pro18Ser	p.P18S	ENST00000276594	NM_024504.3	18	Ccg/Tcg	2/8	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.737846890697375	NA		471	105	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651592	48651592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781928506	NA	P-0053109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	56	430	0	ENST00000376670.3:c.758G>A	p.Arg253Gln	p.R253Q	ENST00000376670	NM_002049.3	253	cGg/cAg	5/6	0.607785462773026	3	FACETS	0.845	0.767	0.917	1	0.974	1	CLONAL	3	FALSE	1	0.737846890697375	3		430	82	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411876	63411876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395933177	NA	P-0053109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	25	628	2	ENST00000330258.3:c.1291C>T	p.Pro431Ser	p.P431S	ENST00000330258	NM_152424.3	431	Cca/Tca	2/2	0.607785462773026	3	FACETS	1	0.932	1	0.682	0.558	0.813	CLONAL	1	FALSE	1	0.737846890697375	3		630	68	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938317	76938317	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1	35	525	0	ENST00000373344.5:c.2431C>T	p.Gln811Ter	p.Q811*	ENST00000373344	NM_000489.3	811	Cag/Tag	9/35	0.737846890697375	1	FACETS		NA	1	1	0.979	1	NA	2	FALSE	0	0.737846890697375	1		525	36	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0053110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	96	285	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.974	0.875	1	0.974	0.875	1	CLONAL	1	TRUE	1	0.543261043166327	2		285	363	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416698	29416698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56181542	NA	P-0053110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	144	568	0	ENST00000389048.3:c.4255G>A	p.Glu1419Lys	p.E1419K	ENST00000389048	NM_004304.4	1419	Gag/Aag	29/29	1	2	FACETS	0.92	0.843	1	0.92	0.843	1	CLONAL	1	TRUE	1	0.543261043166327	2		568	576	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279562	123279562	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121918499	NA	P-0053110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	205	717	1	ENST00000358487.5:c.870G>C	p.Trp290Cys	p.W290C	ENST00000358487	NM_000141.4	290	tgG/tgC	7/18	1	2	FACETS	0.879	0.816	0.943	0.879	0.816	0.943	CLONAL	1	TRUE	1	0.543261043166327	2		718	859	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410987	31410987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1236254462	NA	P-0053110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	161	500	3	ENST00000344624.3:c.3533G>A	p.Arg1178Gln	p.R1178Q	ENST00000344624		1178	cGa/cAa	28/33	1	2	FACETS	0.958	0.882	1	0.958	0.882	1	CLONAL	1	TRUE	1	0.543261043166327	2		503	619	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821545	32821545	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	189	499	1	ENST00000354258.4:c.49C>G	p.Pro17Ala	p.P17A	ENST00000354258	NM_000593.5	17	Ccg/Gcg	1/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.543261043166327	2		500	646	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857232	9857232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377337296	NA	P-0053110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	152	511	0	ENST00000330684.3:c.4169C>T	p.Ser1390Leu	p.S1390L	ENST00000330684	NM_001134407.1	1390	tCg/tTg	13/13	1	2	FACETS	0.91	0.835	0.987	0.91	0.835	0.987	CLONAL	1	TRUE	1	0.543261043166327	2		511	615	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369186	40369186	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	185	476	0	ENST00000293328.3:c.1372C>G	p.Gln458Glu	p.Q458E	ENST00000293328	NM_012448.3	458	Caa/Gaa	11/19	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.543261043166327	2		476	657	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092737	27092737	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs387906845	NA	P-0053110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	161	468	0	ENST00000324856.7:c.2758C>T	p.Gln920Ter	p.Q920*	ENST00000324856	NM_006015.4	920	Caa/Taa	9/20	0.512235298151492	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.543261043166327	1		468	400	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153536	108153536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	145	428	0	ENST00000278616.4:c.3676G>A	p.Asp1226Asn	p.D1226N	ENST00000278616	NM_000051.3	1226	Gat/Aat	25/63	1	2	FACETS	0.952	0.872	1	0.952	0.872	1	CLONAL	1	TRUE	1	0.543261043166327	2		428	561	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117703	115117718	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGAACCCTAGCCTACC	TGAACCCTAGCCTACC	-	novel	NA	P-0053110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	216	442	0	ENST00000257566.3:c.717_717+15del		p.X239_splice	ENST00000257566	NM_016569.3	239		3/8	0.530893959618846	2	FACETS	0.882	0.83	0.933	0.882	0.83	0.933	CLONAL	2	TRUE	0	0.543261043166327	2		442	451	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262125	10262125	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	190	599	0	ENST00000340748.4:c.2166G>T	p.Lys722Asn	p.K722N	ENST00000340748		722	aaG/aaT	23/40	1	2	FACETS	0.954	0.885	1	0.954	0.885	1	CLONAL	1	TRUE	1	0.543261043166327	2		599	733	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457159	5457159	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	128	344	0	ENST00000381577.3:c.133G>T	p.Glu45Ter	p.E45*	ENST00000381577	NM_014143.3	45	Gaa/Taa	3/7	0.543261043166327	1	FACETS	0.998	0.916	1	0.998	0.916	1	CLONAL	1	TRUE	0	0.543261043166327	1		344	344	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0053111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	156	430	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.308899620087277	3	FACETS	0.777	0.713	0.844	0.777	0.713	0.844	SUBCLONAL	2	TRUE	1	0.308899620087277	3		430	750	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0053113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	90	574	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	1	2	FACETS	0.947	0.839	1	0.947	0.839	1	CLONAL	1	TRUE	1	0.22	2		574	864	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844088	68844115	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGTTCTTTCAGCTCTTCTCTCACGCTG	TGGTTCTTTCAGCTCTTCTCTCACGCTG	-	novel	NA	P-0053113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	63	309	0	ENST00000261769.5:c.688-10_705del		p.X230_splice	ENST00000261769	NM_004360.3	230		6/16	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.22	2		309	523	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829066	128829066	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs41304185	NA	P-0053114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	28	8	0	ENST00000249373.3:c.74A>G	p.Asp25Gly	p.D25G	ENST00000249373	NM_005631.4	25	gAc/gGc	1/12	0.622447220862804	3	FACETS	0.804	0.669	0.945	0.804	0.669	0.945	CLONAL	2	TRUE	1	0.661861285217545	3		8	70	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191492	10191497	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	GCCTCC	GCCTCC	-	novel	NA	P-0053114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	181	421	0	ENST00000256474.2:c.485_490del	p.Cys162_Gln164delinsTer	p.C162_Q164delins*	ENST00000256474	NM_000551.3	162	tGCCTCCag/tag	3/3	0.613362922111691	1	FACETS	0.875	0.818	0.934	0.875	0.818	0.934	CLONAL	1	TRUE	0	0.661861285217545	1		421	418	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535394	187535394	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	200	452	0	ENST00000441802.2:c.9180C>A	p.Tyr3060Ter	p.Y3060*	ENST00000441802	NM_005245.3	3060	taC/taA	12/27	0.27001681613799	1	FACETS	0.734	0.685	0.784	0.734	0.685	0.784	INDETERMINATE	1	TRUE	0	0.661861285217545	1		452	551	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	99	429	0				ENST00000310581	NM_198253.2	-/1132			0.355153865549584	1	FACETS	0.879	0.806	0.951	0.879	0.806	0.951	INDETERMINATE	1	TRUE	0	0.742048023922912	1		429	191	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0053116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	304	372	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.480651425485985	3	FACETS	1	0.993	1	0.655	0.619	0.691	CLONAL	1	TRUE	1	0.742048023922912	3		372	858	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0053116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	177	311	1	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.480651425485985	3	FACETS	0.965	0.892	1	0.482	0.446	0.52	CLONAL	1	TRUE	1	0.742048023922912	3		312	678	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912061	127912061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1481246558	NA	P-0053116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	516	269	0	ENST00000373547.4:c.809C>T	p.Ser270Leu	p.S270L	ENST00000373547	NM_002721.4	270	tCg/tTg	7/7	0.693512325715693	3	FACETS	0.992	0.968	1	0.992	0.968	1	CLONAL	3	TRUE	0	0.742048023922912	3		269	641	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713470	40713470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318044562	NA	P-0053116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	415	549	0	ENST00000373198.4:c.4045C>T	p.Arg1349Cys	p.R1349C	ENST00000373198	NM_133170.3	1349	Cgt/Tgt	30/32	0.388287747863443	2	FACETS	1	0.996	1	0.722	0.693	0.75	INDETERMINATE	1	TRUE	0	0.742048023922912	2		549	775	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624918	9624918	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	343	399	0	ENST00000353224.5:c.59G>A	p.Arg20Lys	p.R20K	ENST00000353224	NM_177990.2	20	aGg/aAg	3/10	NA	2	FACETS	0.773	0.74	0.805			1	INDETERMINATE	2	TRUE	NA	0.742048023922912	2		399	598	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0053116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	82	137	0				ENST00000310581	NM_198253.2	-/1132			0.355153865549584	1	FACETS	0.717	0.646	0.788	0.717	0.646	0.788	INDETERMINATE	1	TRUE	0	0.742048023922912	1		137	194	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619163	43619163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	295	499	1	ENST00000355710.3:c.2846G>A	p.Gly949Glu	p.G949E	ENST00000355710	NM_020975.4	949	gGa/gAa	17/20	0.355153865549584	1	FACETS	0.769	0.73	0.809	0.769	0.73	0.809	INDETERMINATE	1	TRUE	0	0.742048023922912	1		500	650	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420991	49420991	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	266	409	0	ENST00000301067.7:c.14758C>T	p.Pro4920Ser	p.P4920S	ENST00000301067	NM_003482.3	4920	Ccc/Tcc	48/54	0.355153865549584	1	FACETS	0.775	0.733	0.817	0.775	0.733	0.817	INDETERMINATE	1	TRUE	0	0.742048023922912	1		409	582	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222614	69222614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	128	423	1	ENST00000462284.1:c.587C>T	p.Ser196Phe	p.S196F	ENST00000462284	NM_002392.5	196	tCc/tTc	8/11	0.355153865549584	1	FACETS	0.348	0.316	0.381	0.348	0.316	0.381	INDETERMINATE	1	TRUE	0	0.742048023922912	1		424	624	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784077	120784077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1210006090	NA	P-0053116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	310	608	2	ENST00000257552.2:c.908G>A	p.Arg303His	p.R303H	ENST00000257552	NM_002442.3	303	cGc/cAc	13/15	0.355153865549584	1	FACETS	0.696	0.66	0.732	0.696	0.66	0.732	INDETERMINATE	1	TRUE	0	0.742048023922912	1		610	755	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863449	57863449	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781683841	NA	P-0053116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	281	420	2	ENST00000228682.2:c.1544G>A	p.Arg515Gln	p.R515Q	ENST00000228682	NM_005269.2	515	cGg/cAg	11/12	0.355153865549584	1	FACETS	0.776	0.735	0.817	0.776	0.735	0.817	INDETERMINATE	1	TRUE	0	0.742048023922912	1		422	614	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321667	30321667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1213455983	NA	P-0053116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	265	442	0	ENST00000322652.5:c.1522C>T	p.Arg508Cys	p.R508C	ENST00000322652	NM_015355.2	508	Cgc/Tgc	13/16	1	2	FACETS	0.97	0.914	1	0.97	0.914	1	CLONAL	1	TRUE	1	0.742048023922912	2		442	736	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201137	108201137	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	117	322	0	ENST00000278616.4:c.7504G>T	p.Gly2502Cys	p.G2502C	ENST00000278616	NM_000051.3	2502	Ggc/Tgc	50/63	0.355153865549584	1	FACETS	0.418	0.378	0.458	0.418	0.378	0.458	INDETERMINATE	1	TRUE	0	0.742048023922912	1		322	475	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134703	2134703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	479	561	0	ENST00000219476.3:c.4480G>A	p.Gly1494Ser	p.G1494S	ENST00000219476	NM_000548.3	1494	Ggc/Agc	34/42	0.480651425485985	3	FACETS	0.902	0.867	0.937	0.902	0.867	0.937	CLONAL	2	TRUE	1	0.742048023922912	3		561	981	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826577	50826578	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0053116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	88	248	0	ENST00000398568.2:c.2302_2303delinsTT	p.Pro768Phe	p.P768F	ENST00000398568	NM_001042412.1	768	CCt/TTt	15/18	NA	2	FACETS	0.581	0.518	0.648			1	INDETERMINATE	1	TRUE	NA	0.742048023922912	2		248	408	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346774	89346774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs117997391	NA	P-0053116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	154	326	0	ENST00000301030.4:c.6176C>T	p.Pro2059Leu	p.P2059L	ENST00000301030	NM_001256183.1	2059	cCc/cTc	9/13	0.355153865549584	1	FACETS	0.646	0.598	0.695	0.646	0.598	0.695	INDETERMINATE	1	TRUE	0	0.742048023922912	1		326	404	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25990554	25990554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1392360941	NA	P-0053116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	256	405	0	ENST00000435504.4:c.673C>T	p.Pro225Ser	p.P225S	ENST00000435504		225	Cct/Tct	8/13	1	2	FACETS	0.914	0.859	0.97	0.914	0.859	0.97	CLONAL	1	TRUE	1	0.742048023922912	2		405	755	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47643499	47643499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	276	453	0	ENST00000233146.2:c.1007C>T	p.Pro336Leu	p.P336L	ENST00000233146	NM_000251.2	336	cCt/cTt	6/16	1	2	FACETS	0.943	0.889	0.998	0.943	0.889	0.998	CLONAL	1	TRUE	1	0.742048023922912	2		453	789	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236703	236703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	87	145	0	ENST00000264932.6:c.1421C>T	p.Ser474Leu	p.S474L	ENST00000264932	NM_004168.2	474	tCa/tTa	10/15	0.355153865549584	1	FACETS	0.737	0.668	0.808	0.737	0.668	0.808	INDETERMINATE	1	TRUE	0	0.742048023922912	1		145	200	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967530	90967530	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	177	311	0	ENST00000265433.3:c.1378C>T	p.Gln460Ter	p.Q460*	ENST00000265433	NM_002485.4	460	Cag/Tag	10/16	1	2	FACETS	0.952	0.885	1	0.952	0.885	1	CLONAL	1	TRUE	1	0.742048023922912	2		311	501	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs786203436	NA	P-0053118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	56	493	0	ENST00000269305.4:c.487T>A	p.Tyr163Asn	p.Y163N	ENST00000269305	NM_001126112.2	163	Tac/Aac	5/11	0.194603676147601	4	FACETS	0.898	0.772	1	0.598	0.514	0.689	CLONAL	2	FALSE	1	0.194603676147601	4		493	383	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834548	156834548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763164402	NA	P-0053118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	36	551	0	ENST00000524377.1:c.316G>A	p.Val106Met	p.V106M	ENST00000524377	NM_002529.3	106	Gtg/Atg	3/17	0.194603676147601	4	FACETS	0.752	0.62	0.898	0.752	0.62	0.898	SUBCLONAL	2	FALSE	2	0.194603676147601	4		551	294	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106826	27106830	+	frameshift_variant	Frame_Shift_Del	DEL	AGTTG	AGTTG	-	novel	NA	P-0053118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	77	497	0	ENST00000324856.7:c.6437_6441del	p.Lys2146IlefsTer2	p.K2146Ifs*2	ENST00000324856	NM_006015.4	2146	aAGTTG/a	20/20	0.194603676147601	12	FACETS	1	0.925	1			1	CLONAL	3	FALSE	NA	0.194603676147601	12		497	487	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123905	46123906	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0053118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	63	189	0	ENST00000334344.6:c.173dup	p.Gly59ArgfsTer7	p.G59Rfs*7	ENST00000334344	NM_152641.2	57	-/G	2/21	0.194603676147601	10	FACETS	0.957	0.831	1	0.574	0.499	0.656	CLONAL	3	FALSE	5	0.194603676147601	10		189	401	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244985	46244985	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	53	416	0	ENST00000334344.6:c.3079C>T	p.Gln1027Ter	p.Q1027*	ENST00000334344	NM_152641.2	1027	Caa/Taa	15/21	0.194603676147601	10	FACETS	0.955	0.819	1	0.573	0.491	0.662	CLONAL	3	FALSE	5	0.194603676147601	10		416	338	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058739	180058739	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	13	524	0	ENST00000261937.6:c.98del	p.Asn33ThrfsTer100	p.N33Tfs*100	ENST00000261937	NM_182925.4	33	aAc/ac	2/30	0.194603676147601	0	FACETS	0.468	0.334	0.632			1	SUBCLONAL	1	FALSE	0	0.194603676147601	0		524	230	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002743	37002743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	35	318	0	ENST00000358127.4:c.506C>T	p.Ser169Leu	p.S169L	ENST00000358127	NM_001280556.1	169	tCg/tTg	5/10	0.194603676147601	0	FACETS	0.787	0.652	0.935			1	CLONAL	2	FALSE	0	0.194603676147601	0		318	184	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0053122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	71	377	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.871	0.763	0.986	1	0.979	1	CLONAL	2	TRUE	1	0.19	2		377	429	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0053122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	47	386	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	1	2	FACETS	0.997	0.842	1	0.997	0.842	1	CLONAL	1	TRUE	1	0.19	2		386	496	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107088	27107095	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTGCCC	GGCTGCCC	-	novel	NA	P-0053122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	41	521	0	ENST00000324856.7:c.6700_6707del	p.Ala2234ArgfsTer41	p.A2234Rfs*41	ENST00000324856	NM_006015.4	2233	cgGGCTGCCCgc/cggc	20/20	1	2	FACETS	0.742	0.617	0.881	0.742	0.617	0.881	SUBCLONAL	1	TRUE	1	0.19	2		521	582	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711910	89711910	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs1057522285	NA	P-0053122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	46	525	0	ENST00000371953.3:c.528T>G	p.Tyr176Ter	p.Y176*	ENST00000371953	NM_000314.4	176	taT/taG	6/9	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.19	2		525	323	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959449	26959449	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	19	392	0	ENST00000381527.3:c.616C>A	p.Leu206Ile	p.L206I	ENST00000381527	NM_001260.1	206	Ctt/Att	6/13	1	2	FACETS	0.647	0.491	0.831	0.647	0.491	0.831	SUBCLONAL	1	TRUE	1	0.19	2		392	309	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878960	117878960	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0053122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	20	293	0	ENST00000297338.2:c.9C>G	p.Tyr3Ter	p.Y3*	ENST00000297338	NM_006265.2	3	taC/taG	2/14	1	2	FACETS	0.763	0.584	0.972	0.763	0.584	0.972	CLONAL	1	TRUE	1	0.19	2		293	276	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0053124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	40	286	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.999	0.829	1	0.999	0.829	1	CLONAL	1	TRUE	1	0.15	2		286	534	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0053124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	22	250	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	1	2	FACETS	0.562	0.434	0.711	0.562	0.434	0.711	SUBCLONAL	1	TRUE	1	0.15	2		250	522	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023715	27023716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0053124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	24	371	0	ENST00000324856.7:c.827dup	p.Gly277ArgfsTer123	p.G277Rfs*123	ENST00000324856	NM_006015.4	274	atg/atGg	1/20	1	2	FACETS	0.825	0.646	1	0.825	0.646	1	CLONAL	1	TRUE	1	0.15	2		371	388	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585470	29585470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	30	388	1	ENST00000356175.3:c.4219G>A	p.Asp1407Asn	p.D1407N	ENST00000356175	NM_000267.3	1407	Gat/Aat	31/57	1	2	FACETS	0.821	0.661	1	0.821	0.661	1	CLONAL	1	TRUE	1	0.15	2		389	487	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575677	48575677	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs377767329	NA	P-0053124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	30	555	0	ENST00000342988.3:c.437T>A	p.Leu146Ter	p.L146*	ENST00000342988	NM_005359.5	146	tTa/tAa	4/12	1	2	FACETS	0.759	0.61	0.928	0.759	0.61	0.928	CLONAL	1	TRUE	1	0.15	2		555	527	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545740	106545740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	59	614	0	ENST00000359195.3:c.3217G>A	p.Glu1073Lys	p.E1073K	ENST00000359195	NM_002649.2	1073	Gaa/Aaa	11/11	1	2	FACETS	0.616	0.53	0.71	0.616	0.53	0.71	SUBCLONAL	1	TRUE	1	0.34	2		614	563	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717769	89717770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	55	319	0	ENST00000371953.3:c.800dup	p.Asp268GlyfsTer30	p.D268Gfs*30	ENST00000371953	NM_000314.4	265	cta/ctAa	7/9	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.34	2		319	306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	139	872	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.34	2		873	653	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	8	322	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.194	0.124	0.284	0.194	0.124	0.284	SUBCLONAL	1	TRUE	1	0.34	2		322	243	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	15	519	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.221	0.161	0.294	0.221	0.161	0.294	SUBCLONAL	1	TRUE	1	0.34	2		519	399	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182094	11182094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	127	645	0	ENST00000361445.4:c.6752G>A	p.Arg2251Gln	p.R2251Q	ENST00000361445	NM_004958.3	2251	cGg/cAg	48/58	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.34	2		645	659	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690383	117690383	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	65	483	0	ENST00000369458.3:c.746G>T	p.Ser249Ile	p.S249I	ENST00000369458	NM_024626.3	249	aGt/aTt	5/6	1	2	FACETS	0.67	0.581	0.766	0.67	0.581	0.766	SUBCLONAL	1	TRUE	1	0.34	2		483	571	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844404	156844404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199826686	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	116	749	1	ENST00000524377.1:c.1237G>A	p.Glu413Lys	p.E413K	ENST00000524377	NM_002529.3	413	Gaa/Aaa	10/17	1	2	FACETS	0.885	0.798	0.977	0.885	0.798	0.977	CLONAL	1	TRUE	1	0.34	2		750	771	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724447	162724447	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	76	520	1	ENST00000367921.3:c.219C>A	p.Cys73Ter	p.C73*	ENST00000367921	NM_006182.2	73	tgC/tgA	5/18	1	2	FACETS	0.901	0.793	1	0.901	0.793	1	CLONAL	1	TRUE	1	0.34	2		521	496	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104558	193104558	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	31	467	0	ENST00000367435.3:c.345A>C	p.Glu115Asp	p.E115D	ENST00000367435	NM_024529.4	115	gaA/gaC	4/17	1	2	FACETS	0.412	0.332	0.501	0.412	0.332	0.501	SUBCLONAL	1	TRUE	1	0.34	2		467	443	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218892	193218892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1225502334	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	27	276	1	ENST00000367435.3:c.1450C>T	p.Arg484Cys	p.R484C	ENST00000367435	NM_024529.4	484	Cgt/Tgt	16/17	1	2	FACETS	0.613	0.49	0.753	0.613	0.49	0.753	SUBCLONAL	1	TRUE	1	0.34	2		277	259	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828129	243828129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	26	458	1	ENST00000263826.5:c.229C>T	p.Leu77Phe	p.L77F	ENST00000263826	NM_005465.4	77	Ctc/Ttc	3/13	1	2	FACETS	0.3	0.237	0.373	0.3	0.237	0.373	SUBCLONAL	1	TRUE	1	0.34	2		459	509	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70411621	70411621	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	47	447	0	ENST00000373644.4:c.4295A>G	p.Asp1432Gly	p.D1432G	ENST00000373644	NM_030625.2	1432	gAc/gGc	5/12	1	2	FACETS	0.705	0.596	0.825	0.705	0.596	0.825	SUBCLONAL	1	TRUE	1	0.34	2		447	392	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	60	443	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.912	0.789	1	0.912	0.789	1	CLONAL	1	TRUE	1	0.34	2		443	387	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	9	548	1	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	0.119	0.078	0.171	0.119	0.078	0.171	SUBCLONAL	1	TRUE	1	0.34	2		549	446	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769582	112769582	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	96	587	0	ENST00000369452.4:c.1534G>T	p.Glu512Ter	p.E512*	ENST00000369452	NM_007373.3	512	Gaa/Taa	8/9	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.34	2		587	460	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212905	94212905	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876659042	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	34	342	0	ENST00000323929.3:c.337G>A	p.Asp113Asn	p.D113N	ENST00000323929	NM_005591.3	113	Gat/Aat	5/20	1	2	FACETS	0.581	0.476	0.7	0.581	0.476	0.7	SUBCLONAL	1	TRUE	1	0.34	2		342	344	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912693	100912693	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	23	385	0	ENST00000325455.5:c.2629C>A	p.Leu877Ile	p.L877I	ENST00000325455	NM_001202474.3	877	Ctt/Att	7/8	1	2	FACETS	0.322	0.25	0.405	0.322	0.25	0.405	SUBCLONAL	1	TRUE	1	0.34	2		385	420	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996801	100996801	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	67	591	0	ENST00000325455.5:c.1726G>A	p.Gly576Ser	p.G576S	ENST00000325455	NM_001202474.3	576	Ggc/Agc	2/8	1	2	FACETS	0.681	0.592	0.777	0.681	0.592	0.777	SUBCLONAL	1	TRUE	1	0.34	2		591	579	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098419	108098419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587779858	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	44	419	2	ENST00000278616.4:c.68G>A	p.Arg23Gln	p.R23Q	ENST00000278616	NM_000051.3	23	cGa/cAa	2/63	1	2	FACETS	0.657	0.552	0.773	0.657	0.552	0.773	SUBCLONAL	1	TRUE	1	0.34	2		421	394	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	43	430	1	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.607	0.508	0.715	0.607	0.508	0.715	SUBCLONAL	1	TRUE	1	0.34	2		431	417	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119793	108119793	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	44	363	0	ENST00000278616.4:c.1199T>G	p.Leu400Arg	p.L400R	ENST00000278616	NM_000051.3	400	cTt/cGt	9/63	1	2	FACETS	0.644	0.541	0.757	0.644	0.541	0.757	SUBCLONAL	1	TRUE	1	0.34	2		363	402	SUCCESS
ATM	472	MSKCC	GRCh37	11	108181001	108181001	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	41	371	0	ENST00000278616.4:c.5877A>C	p.Glu1959Asp	p.E1959D	ENST00000278616	NM_000051.3	1959	gaA/gaC	39/63	1	2	FACETS	0.676	0.564	0.799	0.676	0.564	0.799	SUBCLONAL	1	TRUE	1	0.34	2		371	357	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111958593	111958593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555186772	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	29	474	0	ENST00000375549.3:c.65G>A	p.Arg22Gln	p.R22Q	ENST00000375549	NM_003002.3	22	cGa/cAa	2/4	1	2	FACETS	0.332	0.266	0.408	0.332	0.266	0.408	SUBCLONAL	1	TRUE	1	0.34	2		474	514	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343871	118343871	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs782290578	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	108	561	0	ENST00000534358.1:c.1997G>T	p.Gly666Val	p.G666V	ENST00000534358	NM_005933.3	666	gGt/gTt	3/36	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.34	2		561	586	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394635	394635	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	89	533	0	ENST00000399788.2:c.5060A>C	p.Lys1687Thr	p.K1687T	ENST00000399788	NM_001042603.1	1687	aAa/aCa	28/28	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.34	2		533	504	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398035	4398035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	81	581	0	ENST00000261254.3:c.599C>T	p.Ser200Leu	p.S200L	ENST00000261254	NM_001759.3	200	tCg/tTg	4/5	1	2	FACETS	0.77	0.679	0.867	0.77	0.679	0.867	SUBCLONAL	1	TRUE	1	0.34	2		581	619	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905439	11905439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764237239	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	83	404	1	ENST00000396373.4:c.89C>T	p.Ser30Leu	p.S30L	ENST00000396373	NM_001987.4	30	tCg/tTg	2/8	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.34	2		405	484	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573888	18573888	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	20	481	3	ENST00000266497.5:c.2206G>T	p.Glu736Ter	p.E736*	ENST00000266497		736	Gaa/Taa	15/31	1	2	FACETS	0.31	0.236	0.396	0.31	0.236	0.396	SUBCLONAL	1	TRUE	1	0.34	2		484	380	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793412	18793412	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	36	475	0	ENST00000266497.5:c.4109T>G	p.Leu1370Ter	p.L1370*	ENST00000266497		1370	tTa/tGa	30/31	1	2	FACETS	0.52	0.428	0.624	0.52	0.428	0.624	SUBCLONAL	1	TRUE	1	0.34	2		475	407	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793484	18793484	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	42	323	0	ENST00000266497.5:c.4181A>C	p.Glu1394Ala	p.E1394A	ENST00000266497		1394	gAa/gCa	30/31	1	2	FACETS	0.753	0.631	0.888	0.753	0.631	0.888	SUBCLONAL	1	TRUE	1	0.34	2		323	328	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285621	46285621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	37	476	0	ENST00000334344.6:c.4981G>A	p.Asp1661Asn	p.D1661N	ENST00000334344	NM_152641.2	1661	Gat/Aat	17/21	1	2	FACETS	0.446	0.367	0.534	0.446	0.367	0.534	SUBCLONAL	1	TRUE	1	0.34	2		476	488	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416114	49416114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	83	450	0	ENST00000301067.7:c.16361G>A	p.Arg5454Gln	p.R5454Q	ENST00000301067	NM_003482.3	5454	cGa/cAa	52/54	1	2	FACETS	0.926	0.82	1	0.926	0.82	1	CLONAL	1	TRUE	1	0.34	2		450	527	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446069	49446069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs952760497	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	136	790	1	ENST00000301067.7:c.1397G>A	p.Arg466His	p.R466H	ENST00000301067	NM_003482.3	466	cGc/cAc	10/54	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.34	2		791	717	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	168	714	1	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.34	2		715	772	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487629	56487629	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779911233	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	137	555	0	ENST00000267101.3:c.1562G>A	p.Arg521Gln	p.R521Q	ENST00000267101	NM_001982.3	521	cGa/cAa	13/28	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.34	2		555	668	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212500	133212500	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	114	533	6	ENST00000320574.5:c.5789C>A	p.Ser1930Ter	p.S1930*	ENST00000320574	NM_006231.2	1930	tCa/tAa	42/49	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.34	2		539	537	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	113	532	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.34	2		532	567	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967566	26967566	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs369889152	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	104	452	1	ENST00000381527.3:c.709C>T	p.Arg237Ter	p.R237*	ENST00000381527	NM_001260.1	237	Cga/Tga	7/13	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.34	2		453	466	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012441	29012441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55974987	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	46	563	0	ENST00000282397.4:c.430G>A	p.Glu144Lys	p.E144K	ENST00000282397	NM_002019.4	144	Gaa/Aaa	4/30	1	2	FACETS	0.519	0.437	0.61	0.519	0.437	0.61	SUBCLONAL	1	TRUE	1	0.34	2		563	521	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912858	32912858	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs876659847	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	71	452	1	ENST00000380152.3:c.4366G>T	p.Glu1456Ter	p.E1456*	ENST00000380152		1456	Gaa/Taa	11/27	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.34	2		453	349	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937356	32937356	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	29	453	0	ENST00000380152.3:c.8017A>C	p.Lys2673Gln	p.K2673Q	ENST00000380152		2673	Aaa/Caa	18/27	1	2	FACETS	0.44	0.353	0.539	0.44	0.353	0.539	SUBCLONAL	1	TRUE	1	0.34	2		453	388	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239835	41239835	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1566089396	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	90	455	0	ENST00000379561.5:c.515C>T	p.Ala172Val	p.A172V	ENST00000379561	NM_002015.3	172	gCc/gTc	1/3	1	2	FACETS	0.957	0.851	1	0.957	0.851	1	CLONAL	1	TRUE	1	0.34	2		455	553	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934254	48934254	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1131690904	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	45	475	2	ENST00000267163.4:c.709G>T	p.Glu237Ter	p.E237*	ENST00000267163	NM_000321.2	237	Gaa/Taa	7/27	1	2	FACETS	0.639	0.538	0.751	0.639	0.538	0.751	SUBCLONAL	1	TRUE	1	0.34	2		477	414	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954213	48954213	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	39	273	0	ENST00000267163.4:c.1414A>C	p.Asn472His	p.N472H	ENST00000267163	NM_000321.2	472	Aat/Cat	15/27	1	2	FACETS	0.65	0.54	0.772	0.65	0.54	0.772	SUBCLONAL	1	TRUE	1	0.34	2		273	353	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349440	73349440	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	76	548	0	ENST00000377767.4:c.896A>C	p.Lys299Thr	p.K299T	ENST00000377767	NM_014953.3	299	aAg/aCg	6/21	1	2	FACETS	0.92	0.809	1	0.92	0.809	1	CLONAL	1	TRUE	1	0.34	2		548	486	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103513972	103513972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61749896	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	41	485	0	ENST00000355739.4:c.788G>A	p.Arg263Gln	p.R263Q	ENST00000355739	NM_000123.3	263	cGa/cAa	7/15	1	2	FACETS	0.59	0.492	0.698	0.59	0.492	0.698	SUBCLONAL	1	TRUE	1	0.34	2		485	409	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95595877	95595877	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	93	479	0	ENST00000393063.1:c.666G>T	p.Lys222Asn	p.K222N	ENST00000393063	NM_030621.3	222	aaG/aaT	7/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.34	2		479	426	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749004	43749004	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs558975655	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	154	824	0	ENST00000382044.4:c.1802A>G	p.Asp601Gly	p.D601G	ENST00000382044	NM_001141980.1	601	gAc/gGc	12/28	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.34	2		824	849	SUCCESS
BLM	641	MSKCC	GRCh37	15	91341563	91341563	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1351493073	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	90	513	1	ENST00000355112.3:c.3354C>A	p.Phe1118Leu	p.F1118L	ENST00000355112	NM_000057.2	1118	ttC/ttA	17/22	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.34	2		514	481	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273878	10273878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	86	655	2	ENST00000330684.3:c.391G>A	p.Ala131Thr	p.A131T	ENST00000330684	NM_001134407.1	131	Gca/Aca	2/13	1	2	FACETS	0.807	0.714	0.906	0.807	0.714	0.906	CLONAL	1	TRUE	1	0.34	2		657	627	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041557	14041557	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180030515	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	26	501	0	ENST00000311895.7:c.2104C>T	p.Arg702Trp	p.R702W	ENST00000311895	NM_005236.2	702	Cgg/Tgg	11/11	1	2	FACETS	0.313	0.247	0.389	0.313	0.247	0.389	SUBCLONAL	1	TRUE	1	0.34	2		501	488	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50816350	50816350	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	43	444	0	ENST00000398568.2:c.1790C>A	p.Ser597Tyr	p.S597Y	ENST00000398568	NM_001042412.1	597	tCt/tAt	10/18	1	2	FACETS	0.628	0.526	0.74	0.628	0.526	0.74	SUBCLONAL	1	TRUE	1	0.34	2		444	403	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828552	72828552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	135	699	1	ENST00000268489.5:c.8029G>A	p.Glu2677Lys	p.E2677K	ENST00000268489	NM_006885.3	2677	Gag/Aag	9/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.34	2		700	734	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828699	72828699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762362472	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	34	596	1	ENST00000268489.5:c.7882G>A	p.Glu2628Lys	p.E2628K	ENST00000268489	NM_006885.3	2628	Gaa/Aaa	9/10	1	2	FACETS	0.329	0.268	0.398	0.329	0.268	0.398	SUBCLONAL	1	TRUE	1	0.34	2		597	608	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831352	72831352	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	56	408	0	ENST00000268489.5:c.5229A>C	p.Gln1743His	p.Q1743H	ENST00000268489	NM_006885.3	1743	caA/caC	9/10	1	2	FACETS	0.905	0.779	1	0.905	0.779	1	CLONAL	1	TRUE	1	0.34	2		408	364	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942912	15942912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	109	549	0	ENST00000268712.3:c.6790G>A	p.Glu2264Lys	p.E2264K	ENST00000268712	NM_006311.3	2264	Gaa/Aaa	44/46	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.34	2		549	438	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089913	16089913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	73	493	1	ENST00000268712.3:c.197G>A	p.Arg66Gln	p.R66Q	ENST00000268712	NM_006311.3	66	cGa/cAa	3/46	1	2	FACETS	0.734	0.642	0.833	0.734	0.642	0.833	SUBCLONAL	1	TRUE	1	0.34	2		494	585	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131418	17131418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751171641	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	127	620	2	ENST00000285071.4:c.34G>A	p.Glu12Lys	p.E12K	ENST00000285071	NM_144997.5	12	Gag/Aag	4/14	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.34	2		622	648	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541572	29541572	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1555612288	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	77	369	0	ENST00000356175.3:c.1496T>G	p.Leu499Arg	p.L499R	ENST00000356175	NM_000267.3	499	cTa/cGa	13/57	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.34	2		369	311	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650789	37650789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	114	561	0	ENST00000447079.4:c.2261C>T	p.Ala754Val	p.A754V	ENST00000447079	NM_015083.1	754	gCt/gTt	5/14	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.34	2		561	521	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743056	743056	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	79	578	0	ENST00000314574.4:c.922A>C	p.Lys308Gln	p.K308Q	ENST00000314574	NM_005433.3	308	Aaa/Caa	8/12	1	2	FACETS	0.735	0.647	0.83	0.735	0.647	0.83	SUBCLONAL	1	TRUE	1	0.34	2		578	632	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244379	5244379	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1343205425	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	35	604	0	ENST00000357368.4:c.1103A>C	p.Lys368Thr	p.K368T	ENST00000357368	NM_002850.3	368	aAa/aCa	11/38	1	2	FACETS	0.382	0.312	0.46	0.382	0.312	0.46	SUBCLONAL	1	TRUE	1	0.34	2		604	539	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129655	11129655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	72	622	1	ENST00000358026.2:c.2461G>A	p.Glu821Lys	p.E821K	ENST00000358026	NM_001128849.1	821	Gag/Aag	17/36	1	2	FACETS	0.614	0.536	0.698	0.614	0.536	0.698	SUBCLONAL	1	TRUE	1	0.34	2		623	690	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754512	42754512	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	34	750	0	ENST00000222329.4:c.228G>T	p.Met76Ile	p.M76I	ENST00000222329	NM_006494.2	76	atG/atT	2/4	1	2	FACETS	0.305	0.248	0.37	0.305	0.248	0.37	SUBCLONAL	1	TRUE	1	0.34	2		750	655	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871986	45871986	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs748842373	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	95	527	0	ENST00000391945.4:c.262C>T	p.Arg88Ter	p.R88*	ENST00000391945	NM_000400.3	88	Cga/Tga	5/23	1	2	FACETS	0.898	0.801	1	0.898	0.801	1	CLONAL	1	TRUE	1	0.34	2		527	622	SUCCESS
ALK	238	MSKCC	GRCh37	2	29419712	29419712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1281050927	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	21	452	0	ENST00000389048.3:c.4088C>T	p.Thr1363Ile	p.T1363I	ENST00000389048	NM_004304.4	1363	aCt/aTt	28/29	1	2	FACETS	0.295	0.226	0.375	0.295	0.226	0.375	SUBCLONAL	1	TRUE	1	0.34	2		452	419	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39240630	39240630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352826	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	40	418	1	ENST00000402219.2:c.2138G>A	p.Arg713Gln	p.R713Q	ENST00000402219	NM_005633.3	713	cGa/cAa	13/23	1	2	FACETS	0.622	0.518	0.738	0.622	0.518	0.738	SUBCLONAL	1	TRUE	1	0.34	2		419	378	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641447	47641447	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	58	471	2	ENST00000233146.2:c.832G>T	p.Glu278Ter	p.E278*	ENST00000233146	NM_000251.2	278	Gaa/Taa	5/16	1	2	FACETS	0.627	0.539	0.723	0.627	0.539	0.723	SUBCLONAL	1	TRUE	1	0.34	2		473	544	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693857	47693857	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63751207	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	24	422	0	ENST00000233146.2:c.1571G>A	p.Arg524His	p.R524H	ENST00000233146	NM_000251.2	524	cGt/cAt	10/16	1	2	FACETS	0.338	0.264	0.423	0.338	0.264	0.423	SUBCLONAL	1	TRUE	1	0.34	2		422	418	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026822	48026822	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	56	456	0	ENST00000234420.5:c.1700A>C	p.Lys567Thr	p.K567T	ENST00000234420	NM_000179.2	567	aAg/aCg	4/10	1	2	FACETS	0.652	0.559	0.754	0.652	0.559	0.754	SUBCLONAL	1	TRUE	1	0.34	2		456	505	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027147	48027147	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	86	495	3	ENST00000234420.5:c.2025G>T	p.Glu675Asp	p.E675D	ENST00000234420	NM_000179.2	675	gaG/gaT	4/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.34	2		498	443	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030756	48030756	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1443258363	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	36	337	0	ENST00000234420.5:c.3370A>C	p.Asn1124His	p.N1124H	ENST00000234420	NM_000179.2	1124	Aat/Cat	5/10	1	2	FACETS	0.559	0.46	0.669	0.559	0.46	0.669	SUBCLONAL	1	TRUE	1	0.34	2		337	379	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033781	48033781	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs184131049	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	24	353	0	ENST00000234420.5:c.3992G>A	p.Arg1331Gln	p.R1331Q	ENST00000234420	NM_000179.2	1331	cGa/cAa	9/10	1	2	FACETS	0.545	0.428	0.679	0.545	0.428	0.679	SUBCLONAL	1	TRUE	1	0.34	2		353	259	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265007	198265007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773349667	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	27	373	0	ENST00000335508.6:c.2870G>A	p.Arg957Gln	p.R957Q	ENST00000335508	NM_012433.2	957	cGa/cAa	19/25	1	2	FACETS	0.37	0.294	0.457	0.37	0.294	0.457	SUBCLONAL	1	TRUE	1	0.34	2		373	429	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285851	198285851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1360783408	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	44	467	0	ENST00000335508.6:c.202G>A	p.Asp68Asn	p.D68N	ENST00000335508	NM_012433.2	68	Gat/Aat	3/25	1	2	FACETS	0.678	0.569	0.797	0.678	0.569	0.797	SUBCLONAL	1	TRUE	1	0.34	2		467	382	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131412	202131412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339962485	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	72	547	1	ENST00000358485.4:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000358485	NM_001080125.1	127	cGa/cAa	2/9	1	2	FACETS	0.83	0.727	0.942	0.83	0.727	0.942	CLONAL	1	TRUE	1	0.34	2		548	510	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149880	202149880	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	38	560	0	ENST00000358485.4:c.1321G>T	p.Glu441Ter	p.E441*	ENST00000358485	NM_001080125.1	441	Gaa/Taa	8/9	1	2	FACETS	0.414	0.342	0.495	0.414	0.342	0.495	SUBCLONAL	1	TRUE	1	0.34	2		560	540	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812272	212812272	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	72	388	0	ENST00000342788.4:c.304T>G	p.Leu102Val	p.L102V	ENST00000342788	NM_005235.2	102	Tta/Gta	3/28	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.34	2		388	375	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215609803	215609803	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	39	410	3	ENST00000260947.4:c.1891C>A	p.Leu631Ile	p.L631I	ENST00000260947	NM_000465.2	631	Cta/Ata	9/11	1	2	FACETS	0.544	0.451	0.647	0.544	0.451	0.647	SUBCLONAL	1	TRUE	1	0.34	2		413	422	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264067	46264067	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	42	310	2	ENST00000371998.3:c.1114G>T	p.Glu372Ter	p.E372*	ENST00000371998		372	Gaa/Taa	11/23	1	2	FACETS	0.749	0.627	0.882	0.749	0.627	0.882	SUBCLONAL	1	TRUE	1	0.34	2		312	330	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62305308	62305308	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	84	736	0	ENST00000360203.5:c.781G>A	p.Glu261Lys	p.E261K	ENST00000360203	NM_001283009.1	261	Gaa/Aaa	10/35	1	2	FACETS	0.694	0.613	0.781	0.694	0.613	0.781	SUBCLONAL	1	TRUE	1	0.34	2		736	712	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326695	62326695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140411308	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	84	689	1	ENST00000360203.5:c.3514G>A	p.Glu1172Lys	p.E1172K	ENST00000360203	NM_001283009.1	1172	Gag/Aag	34/35	1	2	FACETS	0.71	0.627	0.799	0.71	0.627	0.799	SUBCLONAL	1	TRUE	1	0.34	2		690	696	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41558734	41558734	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	31	440	0	ENST00000263253.7:c.3679A>C	p.Asn1227His	p.N1227H	ENST00000263253	NM_001429.3	1227	Aat/Cat	21/31	1	2	FACETS	0.509	0.412	0.619	0.509	0.412	0.619	SUBCLONAL	1	TRUE	1	0.34	2		440	358	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164577	47164577	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	33	426	1	ENST00000409792.3:c.1549G>T	p.Glu517Ter	p.E517*	ENST00000409792	NM_014159.6	517	Gaa/Taa	3/21	1	2	FACETS	0.495	0.403	0.599	0.495	0.403	0.599	SUBCLONAL	1	TRUE	1	0.34	2		427	392	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799443	72799443	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1221352417	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	127	579	0	ENST00000325599.8:c.1726A>C	p.Asn576His	p.N576H	ENST00000325599	NM_018130.2	576	Aat/Cat	11/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.34	2		579	617	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89176374	89176374	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	18	335	0	ENST00000336596.2:c.104C>A	p.Ser35Ter	p.S35*	ENST00000336596	NM_005233.5	35	tCa/tAa	2/17	1	2	FACETS	0.316	0.237	0.409	0.316	0.237	0.409	SUBCLONAL	1	TRUE	1	0.34	2		335	335	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445012	89445012	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1348993609	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	57	444	1	ENST00000336596.2:c.1332G>T	p.Lys444Asn	p.K444N	ENST00000336596	NM_005233.5	444	aaG/aaT	6/17	1	2	FACETS	0.709	0.609	0.817	0.709	0.609	0.817	SUBCLONAL	1	TRUE	1	0.34	2		445	473	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468407	89468407	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs201062946	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	34	319	0	ENST00000336596.2:c.1941G>T	p.Glu647Asp	p.E647D	ENST00000336596	NM_005233.5	647	gaG/gaT	11/17	1	2	FACETS	0.694	0.57	0.834	0.694	0.57	0.834	SUBCLONAL	1	TRUE	1	0.34	2		319	288	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967173	134967173	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370164002	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	87	382	0	ENST00000398015.3:c.2512G>A	p.Glu838Lys	p.E838K	ENST00000398015	NM_004441.4	838	Gag/Aag	14/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.34	2		382	411	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453486	138453486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451809865	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	34	434	0	ENST00000289153.2:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000289153	NM_006219.2	321	cGa/cAa	5/22	1	2	FACETS	0.51	0.417	0.615	0.51	0.417	0.615	SUBCLONAL	1	TRUE	1	0.34	2		434	392	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188288	142188288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1470834016	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	21	455	0	ENST00000350721.4:c.6443G>A	p.Arg2148Gln	p.R2148Q	ENST00000350721	NM_001184.3	2148	cGa/cAa	38/47	1	2	FACETS	0.3	0.23	0.381	0.3	0.23	0.381	SUBCLONAL	1	TRUE	1	0.34	2		455	412	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226809	142226809	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1553761113	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	51	385	0	ENST00000350721.4:c.4995G>T	p.Lys1665Asn	p.K1665N	ENST00000350721	NM_001184.3	1665	aaG/aaT	28/47	1	2	FACETS	0.701	0.597	0.815	0.701	0.597	0.815	SUBCLONAL	1	TRUE	1	0.34	2		385	428	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921533	178921533	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1428379257	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	47	424	0	ENST00000263967.3:c.1015C>A	p.Leu339Ile	p.L339I	ENST00000263967	NM_006218.2	339	Ctt/Att	5/21	1	2	FACETS	0.853	0.723	0.995	0.853	0.723	0.995	CLONAL	1	TRUE	1	0.34	2		424	324	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937008	178937008	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs758050864	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	27	546	0	ENST00000263967.3:c.1689A>C	p.Glu563Asp	p.E563D	ENST00000263967	NM_006218.2	563	gaA/gaC	11/21	1	2	FACETS	0.33	0.261	0.408	0.33	0.261	0.408	SUBCLONAL	1	TRUE	1	0.34	2		546	482	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952013	178952013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	69	476	1	ENST00000263967.3:c.3068G>A	p.Arg1023Gln	p.R1023Q	ENST00000263967	NM_006218.2	1023	cGa/cAa	21/21	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.34	2		477	396	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	37	444	0	ENST00000263967.3:c.3132T>G	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaG	21/21	1	2	FACETS	0.603	0.498	0.72	0.603	0.498	0.72	SUBCLONAL	1	TRUE	1	0.34	2		444	361	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181425	185181425	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1435276633	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	101	447	0	ENST00000265026.3:c.1366C>T	p.Arg456Ter	p.R456*	ENST00000265026	NM_004721.4	456	Cga/Tga	8/14	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.34	2		447	440	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443345	187443345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	65	457	0	ENST00000232014.4:c.1781G>A	p.Arg594Gln	p.R594Q	ENST00000232014	NM_001130845.1	594	cGa/cAa	8/10	1	2	FACETS	0.774	0.672	0.884	0.774	0.672	0.884	SUBCLONAL	1	TRUE	1	0.34	2		457	494	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594076	55594076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	72	443	0	ENST00000288135.5:c.1862C>T	p.Ala621Val	p.A621V	ENST00000288135	NM_000222.2	621	gCt/gTt	12/21	1	2	FACETS	0.868	0.76	0.983	0.868	0.76	0.983	CLONAL	1	TRUE	1	0.34	2		443	488	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946108	55946108	+	stop_lost	Nonstop_Mutation	SNP	T	T	G	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	47	291	0	ENST00000263923.4:c.4071A>C	p.Ter1357TyrextTer52	p.*1357Yext*52	ENST00000263923	NM_002253.2	1357	taA/taC	30/30	1	2	FACETS	0.864	0.732	1	0.864	0.732	1	CLONAL	1	TRUE	1	0.34	2		291	320	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953780	55953780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	100	527	0	ENST00000263923.4:c.3656G>A	p.Gly1219Glu	p.G1219E	ENST00000263923	NM_002253.2	1219	gGa/gAa	27/30	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.34	2		527	463	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981193	55981193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	57	442	0	ENST00000263923.4:c.506G>A	p.Arg169Lys	p.R169K	ENST00000263923	NM_002253.2	169	aGa/aAa	5/30	1	2	FACETS	0.998	0.861	1	0.998	0.861	1	CLONAL	1	TRUE	1	0.34	2		442	336	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467968	66467968	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	42	397	0	ENST00000273854.3:c.301G>T	p.Val101Leu	p.V101L	ENST00000273854	NM_004439.5	101	Gta/Tta	3/18	1	2	FACETS	0.668	0.559	0.788	0.668	0.559	0.788	SUBCLONAL	1	TRUE	1	0.34	2		397	370	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130180	143130180	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	37	381	1	ENST00000262992.4:c.837-1G>T		p.X279_splice	ENST00000262992	NM_001101669.1	279			1	2	FACETS	0.682	0.564	0.813	0.682	0.564	0.813	SUBCLONAL	1	TRUE	1	0.34	2		382	319	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	123	457	1	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.34	2		458	551	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522578	187522578	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	41	372	0	ENST00000441802.2:c.11485A>G	p.Ser3829Gly	p.S3829G	ENST00000441802	NM_005245.3	3829	Agt/Ggt	21/27	1	2	FACETS	0.631	0.527	0.747	0.631	0.527	0.747	SUBCLONAL	1	TRUE	1	0.34	2		372	382	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534356	187534356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770029391	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	126	615	3	ENST00000441802.2:c.9370G>A	p.Glu3124Lys	p.E3124K	ENST00000441802	NM_005245.3	3124	Gaa/Aaa	13/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.34	2		618	592	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542914	187542914	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	17	298	2	ENST00000441802.2:c.4826C>A	p.Ser1609Tyr	p.S1609Y	ENST00000441802	NM_005245.3	1609	tCt/tAt	10/27	1	2	FACETS	0.308	0.229	0.401	0.308	0.229	0.401	SUBCLONAL	1	TRUE	1	0.34	2		300	325	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867477	35867477	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	23	363	1	ENST00000303115.3:c.291G>T	p.Lys97Asn	p.K97N	ENST00000303115	NM_002185.3	97	aaG/aaT	3/8	1	2	FACETS	0.394	0.307	0.495	0.394	0.307	0.495	SUBCLONAL	1	TRUE	1	0.34	2		364	343	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871163	35871163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756821231	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	20	307	0	ENST00000303115.3:c.385C>T	p.Pro129Ser	p.P129S	ENST00000303115	NM_002185.3	129	Cct/Tct	4/8	1	2	FACETS	0.372	0.284	0.475	0.372	0.284	0.475	SUBCLONAL	1	TRUE	1	0.34	2		307	316	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155720	56155720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	63	430	1	ENST00000399503.3:c.812G>A	p.Arg271Lys	p.R271K	ENST00000399503	NM_005921.1	271	aGa/aAa	3/20	1	2	FACETS	0.814	0.706	0.931	0.814	0.706	0.931	CLONAL	1	TRUE	1	0.34	2		431	455	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177446	56177446	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	61	454	0	ENST00000399503.3:c.2419A>C	p.Asn807His	p.N807H	ENST00000399503	NM_005921.1	807	Aat/Cat	14/20	1	2	FACETS	0.952	0.825	1	0.952	0.825	1	CLONAL	1	TRUE	1	0.34	2		454	377	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79952289	79952289	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	33	440	3	ENST00000265081.6:c.297G>T	p.Lys99Asn	p.K99N	ENST00000265081	NM_002439.4	99	aaG/aaT	2/24	1	2	FACETS	0.423	0.344	0.512	0.423	0.344	0.512	SUBCLONAL	1	TRUE	1	0.34	2		443	459	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80063784	80063784	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	48	515	0	ENST00000265081.6:c.1929A>C	p.Lys643Asn	p.K643N	ENST00000265081	NM_002439.4	643	aaA/aaC	14/24	1	2	FACETS	0.682	0.578	0.796	0.682	0.578	0.796	SUBCLONAL	1	TRUE	1	0.34	2		515	414	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86658374	86658374	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	18	167	0	ENST00000274376.6:c.1339G>T	p.Glu447Ter	p.E447*	ENST00000274376	NM_002890.2	447	Gaa/Taa	10/25	1	2	FACETS	0.679	0.515	0.87	0.679	0.515	0.87	SUBCLONAL	1	TRUE	1	0.34	2		167	156	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672842	86672842	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	66	282	0	ENST00000274376.6:c.2329G>T	p.Glu777Ter	p.E777*	ENST00000274376	NM_002890.2	777	Gaa/Taa	17/25	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.34	2		282	272	SUCCESS
APC	324	MSKCC	GRCh37	5	112111331	112111331	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	15	231	1	ENST00000257430.4:c.428T>C	p.Leu143Ser	p.L143S	ENST00000257430	NM_000038.5	143	tTg/tCg	5/16	1	2	FACETS	0.418	0.306	0.552	0.418	0.306	0.552	SUBCLONAL	1	TRUE	1	0.34	2		232	211	SUCCESS
APC	324	MSKCC	GRCh37	5	112177793	112177793	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	51	363	0	ENST00000257430.4:c.6502C>A	p.Leu2168Ile	p.L2168I	ENST00000257430	NM_000038.5	2168	Cta/Ata	16/16	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.34	2		363	297	SUCCESS
APC	324	MSKCC	GRCh37	5	112177901	112177901	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs752654519	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	85	414	0	ENST00000257430.4:c.6610C>T	p.Arg2204Ter	p.R2204*	ENST00000257430	NM_000038.5	2204	Cga/Tga	16/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.34	2		414	424	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053020	180053020	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	57	692	0	ENST00000261937.6:c.1270A>G	p.Ile424Val	p.I424V	ENST00000261937	NM_182925.4	424	Ata/Gta	10/30	1	2	FACETS	0.656	0.563	0.757	0.656	0.563	0.757	SUBCLONAL	1	TRUE	1	0.34	2		692	511	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748479	43748479	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45533131	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	46	302	0	ENST00000523873.1:c.433C>T	p.Arg145Ter	p.R145*	ENST00000523873		145	Cga/Tga	6/8	1	2	FACETS	0.905	0.766	1	0.905	0.766	1	CLONAL	1	TRUE	1	0.34	2		302	299	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547174	106547174	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	60	298	0	ENST00000369096.4:c.412-1G>A		p.X138_splice	ENST00000369096	NM_001198.3	138			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.34	2		298	257	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109311957	109311957	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	77	602	1	ENST00000436639.2:c.1315C>A	p.His439Asn	p.H439N	ENST00000436639	NM_014454.2	439	Cac/Aac	8/10	1	2	FACETS	0.785	0.69	0.887	0.785	0.69	0.887	SUBCLONAL	1	TRUE	1	0.34	2		603	577	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609786	117609786	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs141670885	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	26	558	0	ENST00000368508.3:c.6913G>T	p.Glu2305Ter	p.E2305*	ENST00000368508	NM_002944.2	2305	Gaa/Taa	43/43	1	2	FACETS	0.321	0.254	0.399	0.321	0.254	0.399	SUBCLONAL	1	TRUE	1	0.34	2		558	476	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683967	117683967	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	44	543	1	ENST00000368508.3:c.3180G>T	p.Lys1060Asn	p.K1060N	ENST00000368508	NM_002944.2	1060	aaG/aaT	21/43	1	2	FACETS	0.558	0.468	0.657	0.558	0.468	0.657	SUBCLONAL	1	TRUE	1	0.34	2		544	464	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525533	137525533	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	45	579	0	ENST00000367739.4:c.482A>T	p.Tyr161Phe	p.Y161F	ENST00000367739	NM_000416.2	161	tAt/tTt	4/7	1	2	FACETS	0.609	0.512	0.715	0.609	0.512	0.715	SUBCLONAL	1	TRUE	1	0.34	2		579	435	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200479	138200479	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	67	431	2	ENST00000237289.4:c.1897G>T	p.Glu633Ter	p.E633*	ENST00000237289	NM_001270507.1	633	Gaa/Taa	7/9	1	2	FACETS	0.861	0.75	0.98	0.861	0.75	0.98	CLONAL	1	TRUE	1	0.34	2		433	458	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997751	149997751	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	66	534	1	ENST00000253339.5:c.2716C>A	p.Leu906Ile	p.L906I	ENST00000253339		906	Cta/Ata	5/7	1	2	FACETS	0.679	0.589	0.775	0.679	0.589	0.775	SUBCLONAL	1	TRUE	1	0.34	2		535	572	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157192770	157192770	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	66	525	0	ENST00000346085.5:c.1760A>C	p.Lys587Thr	p.K587T	ENST00000346085	NM_020732.3	587	aAa/aCa	3/20	1	2	FACETS	0.726	0.631	0.828	0.726	0.631	0.828	SUBCLONAL	1	TRUE	1	0.34	2		525	535	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206912	162206912	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	97	396	0	ENST00000366898.1:c.763T>A	p.Ser255Thr	p.S255T	ENST00000366898	NM_004562.2	255	Tcc/Acc	7/12	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.34	2		396	458	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13949261	13949261	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs765227604	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	27	271	1	ENST00000405192.2:c.867C>A	p.Phe289Leu	p.F289L	ENST00000405192	NM_001163147.1	289	ttC/ttA	9/12	1	2	FACETS	0.516	0.411	0.635	0.516	0.411	0.635	SUBCLONAL	1	TRUE	1	0.34	2		272	308	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367281	50367281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	81	392	0	ENST00000331340.3:c.88C>T	p.Pro30Ser	p.P30S	ENST00000331340	NM_006060.4	30	Ccc/Tcc	3/8	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.34	2		392	422	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350062	81350062	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs759145490	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	67	392	0	ENST00000222390.5:c.1270C>T	p.Arg424Cys	p.R424C	ENST00000222390	NM_000601.4	424	Cgt/Tgt	10/18	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.34	2		392	355	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381528	81381528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776090604	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	46	343	1	ENST00000222390.5:c.533G>A	p.Arg178Gln	p.R178Q	ENST00000222390	NM_000601.4	178	cGa/cAa	5/18	1	2	FACETS	0.676	0.571	0.793	0.676	0.571	0.793	SUBCLONAL	1	TRUE	1	0.34	2		344	400	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513022	106513022	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	23	329	0	ENST00000359195.3:c.2036G>T	p.Arg679Ile	p.R679I	ENST00000359195	NM_002649.2	679	aGa/aTa	3/11	1	2	FACETS	0.412	0.321	0.518	0.412	0.321	0.518	SUBCLONAL	1	TRUE	1	0.34	2		329	328	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412056	116412056	+	intron_variant	Intron	SNP	T	T	G	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	96	714	0	ENST00000397752.3:c.3028+13T>G		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.737	0.657	0.823	0.737	0.657	0.823	SUBCLONAL	1	TRUE	1	0.34	2		714	766	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453185	140453185	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	24	312	2	ENST00000288602.6:c.1750C>A	p.Leu584Ile	p.L584I	ENST00000288602	NM_004333.4	584	Ctt/Att	15/18	1	2	FACETS	0.48	0.377	0.599	0.48	0.377	0.599	SUBCLONAL	1	TRUE	1	0.34	2		314	294	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185613	27185613	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	141	561	0	ENST00000380036.4:c.1313A>C	p.Asn438Thr	p.N438T	ENST00000380036	NM_000459.3	438	aAc/aCc	9/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.34	2		561	669	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317286	87317286	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	38	581	0	ENST00000277120.3:c.311A>C	p.Lys104Thr	p.K104T	ENST00000277120		104	aAa/aCa	4/19	1	2	FACETS	0.434	0.358	0.519	0.434	0.358	0.519	SUBCLONAL	1	TRUE	1	0.34	2		581	515	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864002	97864002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369636116	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	139	502	2	ENST00000289081.3:c.1664G>A	p.Arg555Gln	p.R555Q	ENST00000289081	NM_000136.2	555	cGa/cAa	15/15	1	2	FACETS	0.757	0.693	0.824	1	0.988	1	SUBCLONAL	2	TRUE	1	0.34	2		504	540	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912234	97912234	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	87	526	0	ENST00000289081.3:c.657C>A	p.Phe219Leu	p.F219L	ENST00000289081	NM_000136.2	219	ttC/ttA	7/15	1	2	FACETS	0.819	0.726	0.918	0.819	0.726	0.918	CLONAL	1	TRUE	1	0.34	2		526	625	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133729585	133729585	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	144	544	0	ENST00000318560.5:c.214T>G	p.Phe72Val	p.F72V	ENST00000318560	NM_005157.4	72	Ttt/Gtt	2/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.34	2		544	662	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787757	135787757	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	rs118203454	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	49	557	0	ENST00000298552.3:c.825T>G	p.Tyr275Ter	p.Y275*	ENST00000298552	NM_001162426.1	275	taT/taG	9/23	1	2	FACETS	0.494	0.417	0.577	0.494	0.417	0.577	SUBCLONAL	1	TRUE	1	0.34	2		557	584	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931705	39931705	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	71	675	1	ENST00000378444.4:c.2894G>T	p.Arg965Ile	p.R965I	ENST00000378444	NM_001123385.1	965	aGa/aTa	4/15	1	2	FACETS	0.621	0.542	0.707	0.621	0.542	0.707	SUBCLONAL	1	TRUE	1	0.34	2		676	672	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932255	39932255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1452619451	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	120	756	0	ENST00000378444.4:c.2344G>A	p.Asp782Asn	p.D782N	ENST00000378444	NM_001123385.1	782	Gac/Aac	4/15	1	2	FACETS	0.911	0.823	1	0.911	0.823	1	CLONAL	1	TRUE	1	0.34	2		756	775	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230825	53230825	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	125	756	1	ENST00000375401.3:c.1968G>T	p.Glu656Asp	p.E656D	ENST00000375401	NM_004187.3	656	gaG/gaT	14/26	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.34	2		757	733	SUCCESS
AR	367	MSKCC	GRCh37	X	66765439	66765439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1460789201	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	132	622	2	ENST00000374690.3:c.451G>A	p.Ala151Thr	p.A151T	ENST00000374690	NM_000044.3	151	Gca/Aca	1/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.34	2		624	544	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938995	76938995	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs886044898	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	67	666	0	ENST00000373344.5:c.1753G>T	p.Glu585Ter	p.E585*	ENST00000373344	NM_000489.3	585	Gaa/Taa	9/35	1	2	FACETS	0.657	0.571	0.75	0.657	0.571	0.75	SUBCLONAL	1	TRUE	1	0.34	2		666	600	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611774	100611774	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	23	493	0	ENST00000308731.7:c.1347G>T	p.Met449Ile	p.M449I	ENST00000308731	NM_000061.2	449	atG/atT	14/19	1	2	FACETS	0.307	0.239	0.387	0.307	0.239	0.387	SUBCLONAL	1	TRUE	1	0.34	2		493	440	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615613	100615613	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	55	620	0	ENST00000308731.7:c.719A>G	p.Glu240Gly	p.E240G	ENST00000308731	NM_000061.2	240	gAa/gGa	8/19	1	2	FACETS	0.612	0.523	0.708	0.612	0.523	0.708	SUBCLONAL	1	TRUE	1	0.34	2		620	529	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020059	123020059	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	58	663	0	ENST00000355640.3:c.547G>T	p.Glu183Ter	p.E183*	ENST00000355640		183	Gag/Tag	2/7	1	2	FACETS	0.511	0.438	0.59	0.511	0.438	0.59	SUBCLONAL	1	TRUE	1	0.34	2		663	668	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184977	123184977	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	24	161	0	ENST00000218089.9:c.1024G>A	p.Glu342Lys	p.E342K	ENST00000218089	NM_001042749.1	342	Gaa/Aaa	12/35	1	2	FACETS	0.96	0.761	1	0.96	0.761	1	CLONAL	1	TRUE	1	0.34	2		161	147	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224539	123224539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	35	628	3	ENST00000218089.9:c.3392G>T	p.Arg1131Ile	p.R1131I	ENST00000218089	NM_001042749.1	1131	aGa/aTa	31/35	1	2	FACETS	0.354	0.29	0.427	0.354	0.29	0.427	SUBCLONAL	1	TRUE	1	0.34	2		631	581	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224604	123224604	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	53	544	0	ENST00000218089.9:c.3457C>A	p.Leu1153Ile	p.L1153I	ENST00000218089	NM_001042749.1	1153	Ctt/Att	31/35	1	2	FACETS	0.665	0.567	0.771	0.665	0.567	0.771	SUBCLONAL	1	TRUE	1	0.34	2		544	469	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827580	72827580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	69	597	0	ENST00000268489.5:c.9001G>A	p.Glu3001Lys	p.E3001K	ENST00000268489	NM_006885.3	3001	Gaa/Aaa	9/10	1	2	FACETS	0.636	0.554	0.725	0.636	0.554	0.725	SUBCLONAL	1	TRUE	1	0.34	2		597	638	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832614	72832614	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0053125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	10	202	1	ENST00000268489.5:c.3968-1G>T		p.X1323_splice	ENST00000268489	NM_006885.3	1323			1	2	FACETS	0.308	0.208	0.433	0.308	0.208	0.433	SUBCLONAL	1	TRUE	1	0.34	2		203	191	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0053126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	450	350	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.326102985417155	7	FACETS	0.995	0.957	1	0.995	0.957	1	CLONAL	6	TRUE	1	0.326102985417155	7		350	839	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0053126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	113	743	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.325118534821294	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.326102985417155	1		745	555	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	85	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.778	0.695	0.866	0.778	0.695	0.866	SUBCLONAL	1	TRUE	1	0.7	2		429	312	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0053127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	32	79	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.7	2		79	83	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0053127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	38	377	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	1	2	FACETS	0.218	0.179	0.26	0.218	0.179	0.26	SUBCLONAL	1	TRUE	1	0.7	2		377	499	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926269	112926269	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	238	475	0	ENST00000351677.2:c.1402A>G	p.Thr468Ala	p.T468A	ENST00000351677	NM_002834.3	468	Acg/Gcg	12/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.7	2		475	673	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665806	29665806	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057518807	NA	P-0053127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	172	235	0	ENST00000356175.3:c.6841C>T	p.Gln2281Ter	p.Q2281*	ENST00000356175	NM_000267.3	2281	Cag/Tag	45/57	0.715192645256331	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.7	2		235	230	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	89	429	0				ENST00000310581	NM_198253.2	-/1132			0.568121614405384	4	FACETS	0.985	0.876	1	0.328	0.292	0.367	CLONAL	1	TRUE	1	0.568121614405384	4		429	499	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878094	48878105	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGCCGCGGAA	GCCGCCGCGGAA	C	novel	NA	P-0053128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	65	96	0	ENST00000267163.4:c.46_57delinsC	p.Ala16ProfsTer11	p.A16Pfs*11	ENST00000267163	NM_000321.2	16	GCCGCCGCGGAA/C	1/27	0.561741946056799	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.568121614405384	1		96	122	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992378	72992378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	259	728	0	ENST00000268489.5:c.1667C>T	p.Ser556Phe	p.S556F	ENST00000268489	NM_006885.3	556	tCt/tTt	2/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.568121614405384	2		728	817	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577154	7577154	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs200579969	NA	P-0053128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	196	482	0	ENST00000269305.4:c.784G>A	p.Gly262Ser	p.G262S	ENST00000269305	NM_001126112.2	262	Ggt/Agt	8/11	0.568121614405384	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.568121614405384	1		482	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0053128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	18	564	0	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.568121614405384	1	FACETS	0.113	0.084	0.147	0.113	0.084	0.147	SUBCLONAL	1	TRUE	0	0.568121614405384	1		564	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781845	NA	P-0053128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	240	624	0	ENST00000269305.4:c.511G>A	p.Glu171Lys	p.E171K	ENST00000269305	NM_001126112.2	171	Gag/Aag	5/11	0.568121614405384	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.568121614405384	1		624	477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578423	7578423	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	239	624	0	ENST00000269305.4:c.507G>T	p.Met169Ile	p.M169I	ENST00000269305	NM_001126112.2	169	atG/atT	5/11	0.568121614405384	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.568121614405384	1		624	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578429	7578429	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	244	628	0	ENST00000269305.4:c.501G>C	p.Gln167His	p.Q167H	ENST00000269305	NM_001126112.2	167	caG/caC	5/11	0.568121614405384	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.568121614405384	1		628	498	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370320	40370320	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs760876362	NA	P-0053128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	265	778	0	ENST00000293328.3:c.1018C>G	p.Gln340Glu	p.Q340E	ENST00000293328	NM_012448.3	340	Cag/Gag	9/19	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.568121614405384	2		778	813	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602375	10602376	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTGGTCATGGGGTTG	novel	NA	P-0053128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	71	718	0	ENST00000171111.5:c.1188_1202dup	p.Asn397_Asn401dup	p.N397_N401dup	ENST00000171111	NM_203500.1	397	aat/aaCAACCCCATGACCAAt	3/6	0.568121614405384	1	FACETS	0.312	0.272	0.355	0.312	0.272	0.355	SUBCLONAL	1	TRUE	0	0.568121614405384	1		718	574	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872213	45872213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	254	687	0	ENST00000391945.4:c.221C>T	p.Ser74Leu	p.S74L	ENST00000391945	NM_000400.3	74	tCa/tTa	4/23	0.568121614405384	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.568121614405384	1		687	485	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342956	225342956	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	229	526	0	ENST00000264414.4:c.2136A>C	p.Lys712Asn	p.K712N	ENST00000264414	NM_003590.4	712	aaA/aaC	15/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.568121614405384	2		526	710	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171760	36171760	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0053128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	183	340	0	ENST00000300305.3:c.806-1G>C		p.X269_splice	ENST00000300305		269			0.521133311657779	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.568121614405384	1		340	379	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747919	41747919	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	17	315	0	ENST00000226382.2:c.850C>T	p.Pro284Ser	p.P284S	ENST00000226382	NM_003924.3	284	Ccg/Tcg	3/3	0.568121614405384	1	FACETS	0.159	0.118	0.207	0.159	0.118	0.207	SUBCLONAL	1	TRUE	0	0.568121614405384	1		315	270	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127407	55127407	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	32	700	0	ENST00000257290.5:c.195G>C	p.Glu65Asp	p.E65D	ENST00000257290	NM_006206.4	65	gaG/gaC	3/23	0.568121614405384	1	FACETS	0.15	0.121	0.183	0.15	0.121	0.183	SUBCLONAL	1	TRUE	0	0.568121614405384	1		700	538	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0053128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	173	374	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.564123568264243	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.568121614405384	1		374	347	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833928	44833929	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0053128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	237	258	0	ENST00000377967.4:c.354dup	p.Tyr119ValfsTer7	p.Y119Vfs*7	ENST00000377967	NM_021140.2	118	agg/aGgg	4/29	1	1	FACETS	0.796	0.759	0.833	1	0.995	1	SUBCLONAL	2	TRUE	0	0.568121614405384	1		258	375	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0053130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	33	425	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.382	0.312	0.462	0.382	0.312	0.462	SUBCLONAL	1	TRUE	1	0.494544406989133	2		426	349	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584593	48584593	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	93	439	0	ENST00000342988.3:c.766C>T	p.Gln256Ter	p.Q256*	ENST00000342988	NM_005359.5	256	Cag/Tag	6/12	0.47749066680158	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.494544406989133	1		439	267	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382166	152382166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752526411	NA	P-0053130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	48	407	0	ENST00000206249.3:c.1276G>A	p.Asp426Asn	p.D426N	ENST00000206249	NM_000125.3	426	Gac/Aac	6/8	1	2	FACETS	0.708	0.603	0.823	0.708	0.603	0.823	SUBCLONAL	1	TRUE	1	0.494544406989133	2		407	274	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	118	429	0				ENST00000310581	NM_198253.2	-/1132			0.559988292935794	3	FACETS	0.981	0.901	1	0.981	0.901	1	CLONAL	2	TRUE	1	0.559988292935794	3		429	275	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0053131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	159	364	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.353729601690105	4	FACETS	1	0.989	1	0.738	0.68	0.799	CLONAL	1	TRUE	2	0.559988292935794	4		364	600	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0053131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	135	503	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	1	2	FACETS	0.986	0.902	1	0.986	0.902	1	CLONAL	1	TRUE	1	0.559988292935794	2		503	489	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0053131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	364	920	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	0.554824210818753	2	FACETS	0.995	0.954	1	0.995	0.954	1	CLONAL	2	TRUE	0	0.559988292935794	2		920	653	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955578	48955578	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0053131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	288	418	0	ENST00000267163.4:c.1694C>G	p.Ser565Ter	p.S565*	ENST00000267163	NM_000321.2	565	tCa/tGa	17/27	0.487394824900417	3	FACETS	0.838	0.798	0.877	0.838	0.798	0.877	CLONAL	3	TRUE	0	0.559988292935794	3		418	524	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082313	16082314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs780080562	NA	P-0053131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	117	773	0	ENST00000281043.3:c.134dup	p.Glu47GlyfsTer8	p.E47Gfs*8	ENST00000281043	NM_005378.4	43	acc/aCcc	2/3	0.492431891455546	4	FACETS	0.789	0.711	0.871	0.263	0.237	0.291	SUBCLONAL	1	TRUE	1	0.559988292935794	4		773	826	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048638	6048638	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs372539944	NA	P-0053131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	132	636	0	ENST00000265849.7:c.13G>C	p.Glu5Gln	p.E5Q	ENST00000265849	NM_000535.5	5	Gag/Cag	1/15	0.55877609206024	4	FACETS	0.891	0.809	0.978	0.297	0.269	0.326	CLONAL	1	TRUE	1	0.559988292935794	4		636	825	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119086	70119086	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	116	493	1	ENST00000245479.2:c.658G>A	p.Glu220Lys	p.E220K	ENST00000245479	NM_000346.3	220	Gag/Aag	2/3	0.54519017758501	4	FACETS	1	0.974	1	0.61	0.552	0.67	CLONAL	1	TRUE	2	0.559988292935794	4		494	530	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445359	49445359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1363389206	NA	P-0053131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	142	891	0	ENST00000301067.7:c.2107G>A	p.Glu703Lys	p.E703K	ENST00000301067	NM_003482.3	703	Gag/Aag	10/54	0.559988292935794	3	FACETS	0.753	0.686	0.823	0.377	0.343	0.412	SUBCLONAL	1	TRUE	1	0.559988292935794	3		891	862	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261655	16261655	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	159	609	0	ENST00000375759.3:c.8920C>T	p.Gln2974Ter	p.Q2974*	ENST00000375759	NM_015001.2	2974	Cag/Tag	11/15	1	2	FACETS	0.969	0.893	1	0.969	0.893	1	CLONAL	1	TRUE	1	0.559988292935794	2		609	586	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262678	16262678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	107	415	0	ENST00000375759.3:c.9943C>T	p.His3315Tyr	p.H3315Y	ENST00000375759	NM_015001.2	3315	Cac/Tac	11/15	1	2	FACETS	0.879	0.793	0.968	0.879	0.793	0.968	CLONAL	1	TRUE	1	0.559988292935794	2		415	435	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598946	28598946	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1003343893	NA	P-0053131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	221	754	1	ENST00000253063.3:c.506G>T	p.Arg169Leu	p.R169L	ENST00000253063	NM_031459.4	169	cGg/cTg	4/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.559988292935794	2		755	680	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427609	427609	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	80	386	1	ENST00000399788.2:c.2560G>T	p.Glu854Ter	p.E854*	ENST00000399788	NM_001042603.1	854	Gaa/Taa	19/28	0.559988292935794	3	FACETS	0.628	0.554	0.708	0.314	0.277	0.354	SUBCLONAL	1	TRUE	1	0.559988292935794	3		387	582	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298746	46298746	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	144	490	0	ENST00000334344.6:c.5393C>T	p.Ser1798Leu	p.S1798L	ENST00000334344	NM_152641.2	1798	tCa/tTa	21/21	0.559988292935794	3	FACETS	1	0.948	1	0.524	0.479	0.571	CLONAL	1	TRUE	1	0.559988292935794	3		490	628	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134538	41134538	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	173	599	0	ENST00000379561.5:c.1090G>C	p.Glu364Gln	p.E364Q	ENST00000379561	NM_002015.3	364	Gag/Cag	2/3	0.487394824900417	3	FACETS	1	0.978	1	0.385	0.356	0.416	CLONAL	1	TRUE	0	0.559988292935794	3		599	684	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293279	91293279	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	100	409	0	ENST00000355112.3:c.781C>G	p.His261Asp	p.H261D	ENST00000355112	NM_000057.2	261	Cat/Gat	3/22	1	2	FACETS	0.782	0.702	0.865	0.782	0.702	0.865	SUBCLONAL	1	TRUE	1	0.559988292935794	2		409	457	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120271	70120271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	348	765	1	ENST00000245479.2:c.1273C>T	p.Leu425Phe	p.L425F	ENST00000245479	NM_000346.3	425	Ctc/Ttc	3/3	0.54519017758501	4	FACETS	0.929	0.882	0.978	0.929	0.882	0.978	CLONAL	2	TRUE	2	0.559988292935794	4		766	1043	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224003	36224003	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	252	801	0	ENST00000222270.7:c.6553A>G	p.Lys2185Glu	p.K2185E	ENST00000222270	NM_014727.1	2185	Aaa/Gaa	28/37	0.420866080809839	5	FACETS	0.821	0.769	0.875	0.548	0.512	0.584	CLONAL	2	TRUE	2	0.559988292935794	5		801	1008	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794029	42794029	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	255	745	0	ENST00000575354.2:c.1390G>C	p.Asp464His	p.D464H	ENST00000575354	NM_015125.3	464	Gat/Cat	9/20	0.420866080809839	5	FACETS	0.83	0.778	0.885	0.554	0.518	0.59	CLONAL	2	TRUE	2	0.559988292935794	5		745	1009	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564473	41564473	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	124	467	0	ENST00000263253.7:c.3895G>A	p.Gly1299Ser	p.G1299S	ENST00000263253	NM_001429.3	1299	Ggc/Agc	24/31	1	2	FACETS	0.971	0.885	1	0.971	0.885	1	CLONAL	1	TRUE	1	0.559988292935794	2		467	456	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564500	41564500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	160	576	0	ENST00000263253.7:c.3922G>A	p.Asp1308Asn	p.D1308N	ENST00000263253	NM_001429.3	1308	Gac/Aac	24/31	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.559988292935794	2		576	560	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335043	81335043	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	148	460	0	ENST00000222390.5:c.1784G>C	p.Ser595Thr	p.S595T	ENST00000222390	NM_000601.4	595	aGt/aCt	16/18	1	2	FACETS	0.931	0.854	1	0.931	0.854	1	CLONAL	1	TRUE	1	0.559988292935794	2		460	568	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866415	56866415	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	150	559	0	ENST00000519728.1:c.662G>C	p.Arg221Thr	p.R221T	ENST00000519728	NM_002350.3	221	aGa/aCa	8/13	0.503335894074674	4	FACETS	0.966	0.883	1	0.483	0.441	0.527	CLONAL	1	TRUE	2	0.559988292935794	4		559	865	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866420	56866420	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	149	570	1	ENST00000519728.1:c.667G>T	p.Glu223Ter	p.E223*	ENST00000519728	NM_002350.3	223	Gag/Tag	8/13	0.503335894074674	4	FACETS	0.915	0.836	0.998	0.458	0.418	0.499	CLONAL	1	TRUE	2	0.559988292935794	4		571	907	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0053133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	951	655	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.264609676251421	12	FACETS	0.966	0.942	0.99			1	CLONAL	11	TRUE	NA	0.264609676251421	12		655	1571	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031997	26031997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	50	529	0	ENST00000244661.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000244661	NM_003537.3	98	Gag/Aag	1/1	0.180201010305044	3	FACETS	0.772	0.655	0.901	0.386	0.327	0.451	CLONAL	1	TRUE	1	0.264609676251421	3		529	554	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325870	65325870	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	43	510	0	ENST00000342505.4:c.1252G>C	p.Asp418His	p.D418H	ENST00000342505	NM_002227.2	418	Gat/Cat	9/25	0.209339314265749	3	FACETS	0.646	0.54	0.763	0.215	0.18	0.255	SUBCLONAL	1	TRUE	0	0.264609676251421	3		510	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576899	7576903	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGA	GGAGA	-	novel	NA	P-0053133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	127	681	0	ENST00000269305.4:c.943_947del	p.Ser315ProfsTer20	p.S315Pfs*20	ENST00000269305	NM_001126112.2	315	TCTCCc/c	9/11	0.1858406734071	2	FACETS	1	0.984	1	0.707	0.641	0.776	CLONAL	1	TRUE	0	0.264609676251421	2		681	679	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0053140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	236	503	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	0.663920775693369	3	FACETS	1	0.978	1	0.709	0.671	0.747	CLONAL	2	TRUE	0	0.663920775693369	3		503	445	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645983	215645984	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1559425604	NA	P-0053140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	270	457	0	ENST00000260947.4:c.614dup	p.Gln206AlafsTer8	p.Q206Afs*8	ENST00000260947	NM_000465.2	205	aag/aaAg	4/11	0.663920775693369	4	FACETS	0.87	0.819	0.921	0.58	0.546	0.614	CLONAL	2	TRUE	1	0.663920775693369	4		457	778	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245923	16245923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	135	321	0	ENST00000375759.3:c.1546A>G	p.Thr516Ala	p.T516A	ENST00000375759	NM_015001.2	516	Aca/Gca	8/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.663920775693369	2		321	349	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248442	59248442	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0053140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	191	535	0	ENST00000371222.2:c.301A>T	p.Lys101Ter	p.K101*	ENST00000371222	NM_002228.3	101	Aag/Tag	1/1	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.663920775693369	2		535	558	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138830	64138830	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	216	482	0	ENST00000334205.4:c.2197C>T	p.Gln733Ter	p.Q733*	ENST00000334205	NM_003942.2	733	Cag/Tag	17/17	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.663920775693369	2		482	611	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033926	49033946	+	inframe_deletion	In_Frame_Del	DEL	TGCAGAATGAGTATGAACTCA	TGCAGAATGAGTATGAACTCA	-	novel	NA	P-0053140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	139	346	1	ENST00000267163.4:c.2065_2085del	p.Gln689_Met695del	p.Q689_M695del	ENST00000267163	NM_000321.2	688	cTGCAGAATGAGTATGAACTCAtg/ctg	20/27	0.663920775693369	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.663920775693369	1		347	267	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396459	30396459	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	281	253	0	ENST00000331968.5:c.260A>T	p.Gln87Leu	p.Q87L	ENST00000331968	NM_002742.2	87	cAg/cTg	1/18	0.663920775693369	4	FACETS	0.98	0.935	1	0.98	0.935	1	CLONAL	3	TRUE	1	0.663920775693369	4		253	479	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420210	88420210	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764757272	NA	P-0053140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	159	423	0	ENST00000360948.2:c.2476G>T	p.Ala826Ser	p.A826S	ENST00000360948	NM_001012338.2	826	Gct/Tct	19/19	0.663920775693369	2	FACETS	1	0.973	1	0.554	0.513	0.596	CLONAL	1	TRUE	0	0.663920775693369	2		423	432	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857746	78857746	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	234	678	0	ENST00000306801.3:c.1816A>T	p.Ser606Cys	p.S606C	ENST00000306801	NM_020761.2	606	Agc/Tgc	16/34	0.663920775693369	3	FACETS	1	0.936	1	0.501	0.468	0.535	CLONAL	1	TRUE	1	0.663920775693369	3		678	937	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210740	36210740	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1319210024	NA	P-0053140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	480	760	0	ENST00000222270.7:c.491C>T	p.Pro164Leu	p.P164L	ENST00000222270	NM_014727.1	164	cCt/cTt	3/37	0.663920775693369	3	FACETS	0.97	0.932	1	0.97	0.932	1	CLONAL	2	TRUE	1	0.663920775693369	3		760	993	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143180	30143180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	167	349	0	ENST00000389048.3:c.346G>A	p.Ala116Thr	p.A116T	ENST00000389048	NM_004304.4	116	Gcc/Acc	1/29	0.663920775693369	3	FACETS	1	0.98	1	0.59	0.545	0.636	CLONAL	1	TRUE	1	0.663920775693369	3		349	568	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286817	212286817	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	121	329	0	ENST00000342788.4:c.2879A>C	p.Asp960Ala	p.D960A	ENST00000342788	NM_005235.2	960	gAt/gCt	24/28	0.663920775693369	4	FACETS	1	0.944	1	0.352	0.319	0.387	CLONAL	1	TRUE	1	0.663920775693369	4		329	574	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225360653	225360653	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	72	294	0	ENST00000264414.4:c.1738G>C	p.Ala580Pro	p.A580P	ENST00000264414	NM_003590.4	580	Gca/Cca	13/16	0.585478592694153	3	FACETS	0.735	0.645	0.831			1	SUBCLONAL	1	TRUE	NA	0.663920775693369	3		294	393	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138382815	138382815	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	315	403	0	ENST00000289153.2:c.2729T>G	p.Val910Gly	p.V910G	ENST00000289153	NM_006219.2	910	gTa/gGa	19/22	0.663920775693369	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.663920775693369	2		403	457	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964965	55964965	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	91	241	0	ENST00000263923.4:c.2272C>T	p.Gln758Ter	p.Q758*	ENST00000263923	NM_002253.2	758	Cag/Tag	16/30	1	2	FACETS	0.908	0.815	1	0.908	0.815	1	CLONAL	1	TRUE	1	0.663920775693369	2		241	302	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519385	137519385	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	96	264	0	ENST00000367739.4:c.1253G>T	p.Cys418Phe	p.C418F	ENST00000367739	NM_000416.2	418	tGt/tTt	7/7	0.421557549767527	3	FACETS	1	0.967	1	0.589	0.53	0.65	CLONAL	1	TRUE	1	0.663920775693369	3		264	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0053141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	437	650	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	0.686108440060875	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.686108440060875	2		650	615	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518000	8518000	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	257	414	0	ENST00000356435.5:c.1391A>G	p.Asn464Ser	p.N464S	ENST00000356435		464	aAc/aGc	10/35	0.686108440060875	4	FACETS	0.923	0.87	0.978	0.923	0.87	0.978	CLONAL	2	TRUE	2	0.686108440060875	4		414	684	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937964	36937964	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	461	880	0	ENST00000361632.4:c.872A>G	p.Gln291Arg	p.Q291R	ENST00000361632		291	cAg/cGg	7/16	0.686108440060875	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.686108440060875	3		880	901	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466501	120466501	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	209	547	0	ENST00000256646.2:c.4618G>T	p.Glu1540Ter	p.E1540*	ENST00000256646	NM_024408.3	1540	Gag/Tag	26/34	0.686108440060875	3	FACETS	1	0.97	1	0.538	0.5	0.576	CLONAL	1	TRUE	1	0.686108440060875	3		547	761	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039462	49039462	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	237	389	0	ENST00000267163.4:c.2447C>A	p.Ser816Ter	p.S816*	ENST00000267163	NM_000321.2	816	tCa/tAa	23/27	0.686108440060875	2	FACETS	0.931	0.887	0.974	0.931	0.887	0.974	CLONAL	2	TRUE	0	0.686108440060875	2		389	371	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216749	2216749	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	399	783	0	ENST00000398665.3:c.2393G>T	p.Ser798Ile	p.S798I	ENST00000398665	NM_032482.2	798	aGt/aTt	20/28	0.563781159253388	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.686108440060875	4		783	957	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224102	36224102	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	363	624	0	ENST00000222270.7:c.6652C>G	p.Pro2218Ala	p.P2218A	ENST00000222270	NM_014727.1	2218	Cca/Gca	28/37	0.563781159253388	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.686108440060875	4		624	835	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155188	55155188	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	149	447	0	ENST00000257290.5:c.2787G>T	p.Met929Ile	p.M929I	ENST00000257290	NM_006206.4	929	atG/atT	21/23	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.686108440060875	2		447	432	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439318	149439318	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	364	688	0	ENST00000286301.3:c.2077C>A	p.Pro693Thr	p.P693T	ENST00000286301	NM_005211.3	693	Ccc/Acc	15/22	0.626574549762102	4	FACETS	0.972	0.925	1	0.972	0.925	1	CLONAL	2	TRUE	2	0.686108440060875	4		688	920	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323349	31323349	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	34	625	0	ENST00000412585.2:c.640A>G	p.Thr214Ala	p.T214A	ENST00000412585	NM_005514.6	214	Acc/Gcc	4/8	0.621836831357713	2	FACETS	0.166	0.135	0.201	0.083	0.067	0.101	SUBCLONAL	1	TRUE	0	0.686108440060875	2		625	597	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194715	29194715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	427	861	0	ENST00000240100.2:c.1013C>T	p.Ser338Phe	p.S338F	ENST00000240100	NM_001394.6	338	tCc/tTc	4/4	0.686108440060875	3	FACETS	0.963	0.923	1	0.963	0.923	1	CLONAL	2	TRUE	1	0.686108440060875	3		861	868	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937851	76937851	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	311	452	0	ENST00000373344.5:c.2897A>G	p.Glu966Gly	p.E966G	ENST00000373344	NM_000489.3	966	gAg/gGg	9/35	0.626574549762102	4	FACETS	0.961	0.911	1	0.961	0.911	1	CLONAL	2	TRUE	2	0.686108440060875	4		452	795	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0053142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	126	519	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.825	0.753	0.901	1	0.988	1	CLONAL	2	FALSE	1	0.334074493069938	2		519	457	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407575	407575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748516736	NA	P-0053142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	105	272	0	ENST00000380956.4:c.1333C>T	p.Arg445Cys	p.R445C	ENST00000380956	NM_001195286.1	445	Cgc/Tgc	9/9	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.334074493069938	2		272	464	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553602	106553602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1562174876	NA	P-0053142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	121	394	1	ENST00000369096.4:c.1567G>A	p.Ala523Thr	p.A523T	ENST00000369096	NM_001198.3	523	Gcc/Acc	5/7	1	2	FACETS	0.753	0.684	0.825	1	0.986	1	SUBCLONAL	2	FALSE	1	0.334074493069938	2		395	481	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061215	38061238	+	inframe_deletion	In_Frame_Del	DEL	GCAGCCGTTCTCGAACATGTTGCC	GCAGCCGTTCTCGAACATGTTGCC	-	novel	NA	P-0053142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	90	587	0	ENST00000250448.2:c.751_774del	p.Gly251_Cys258del	p.G251_C258del	ENST00000250448	NM_004496.3	251	GGCAACATGTTCGAGAACGGCTGC/-	2/2	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	1	0.334074493069938	2		587	477	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699430	47699430	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0053142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	87	212	0	ENST00000347630.2:c.79-1G>A		p.X27_splice	ENST00000347630	NM_001007230.1	27			1	2	FACETS	0.874	0.783	0.969	1	0.984	1	CLONAL	2	FALSE	1	0.334074493069938	2		212	298	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114677	108114678	+	splice_acceptor_variant,intron_variant	Splice_Site	DNP	AA	AA	TT	novel	NA	P-0053143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	105	242	1	ENST00000278616.4:c.497-3_497-2inv		p.X166_splice	ENST00000278616	NM_000051.3	166			0.517870470162918	3	FACETS	1	0.932	1	0.683	0.624	0.744	CLONAL	2	TRUE	0	0.517870470162918	3		243	249	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114722	108114722	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs730881334	NA	P-0053143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	203	397	2	ENST00000278616.4:c.539A>G	p.Gln180Arg	p.Q180R	ENST00000278616	NM_000051.3	180	cAa/cGa	6/63	0.517870470162918	3	FACETS	0.837	0.789	0.886	0.837	0.789	0.886	CLONAL	3	TRUE	0	0.517870470162918	3		399	393	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352724	118352724	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	85	483	0	ENST00000534358.1:c.3929C>G	p.Pro1310Arg	p.P1310R	ENST00000534358	NM_005933.3	1310	cCt/cGt	7/36	0.517870470162918	3	FACETS	0.772	0.684	0.866	0.257	0.228	0.289	SUBCLONAL	1	TRUE	0	0.517870470162918	3		483	535	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38978685	38978685	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs775936788	NA	P-0053143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	75	319	1	ENST00000357387.3:c.821A>C	p.Lys274Thr	p.K274T	ENST00000357387	NM_152756.3	274	aAa/aCa	9/38	0.517870470162918	5	FACETS	0.9	0.789	1	0.3	0.263	0.34	CLONAL	1	TRUE	2	0.517870470162918	5		320	572	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939650	76939650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	132	556	0	ENST00000373344.5:c.1098G>A	p.Met366Ile	p.M366I	ENST00000373344	NM_000489.3	366	atG/atA	9/35	0.453106644871835	2	FACETS	1	0.967	1	0.558	0.51	0.607	CLONAL	1	TRUE	0	0.517870470162918	2		556	457	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0053144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	77	430	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.250139061190116	2		430	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0053144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	126	871	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.250139061190116	2		871	745	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971203	21971204	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	53	409	0	ENST00000304494.5:c.154dup	p.Met52AsnfsTer68	p.M52Nfs*68	ENST00000304494	NM_000077.4	52	atg/aAtg	2/3	0.250139061190116	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	0	0.250139061190116	1		409	341	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138382833	138382833	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	29	352	0	ENST00000289153.2:c.2711C>T	p.Ser904Phe	p.S904F	ENST00000289153	NM_006219.2	904	tCc/tTc	19/22	1	2	FACETS	0.15	0.12	0.184	0.15	0.12	0.184	SUBCLONAL	1	TRUE	1	0.909871712015609	2		352	425	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0053148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	72	520	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.155425226422282	3	FACETS	1	0.957	1	0.601	0.528	0.677	INDETERMINATE	1	TRUE	1	0.426490829175204	3		520	341	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913396	NA	P-0053148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	19	386	0	ENST00000349496.5:c.95A>G	p.Asp32Gly	p.D32G	ENST00000349496	NM_001904.3	32	gAc/gGc	3/15	0.173105629737242	3	FACETS	0.351	0.266	0.451			1	INDETERMINATE	1	TRUE	NA	0.426490829175204	3		386	308	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987215	2987215	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	18	492	0	ENST00000396946.4:c.214C>T	p.Arg72Ter	p.R72*	ENST00000396946	NM_032415.4	72	Cga/Tga	3/25	NA	2	FACETS	0.264	0.198	0.341			1	INDETERMINATE	1	TRUE	NA	0.426490829175204	2		492	320	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774738	73774738	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	33	245	0	ENST00000254810.4:c.349A>G	p.Arg117Gly	p.R117G	ENST00000254810	NM_005324.3	117	Aga/Gga	4/4	0.155425226422282	3	FACETS	1	0.851	1	0.519	0.427	0.62	INDETERMINATE	1	TRUE	1	0.426490829175204	3		245	181	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	151	411	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.522613221163436	2	FACETS	0.887	0.827	0.948	0.887	0.827	0.948	CLONAL	2	TRUE	0	0.565437639415803	2		411	301	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593405	48593405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519962	NA	P-0053156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	129	192	0	ENST00000342988.3:c.1156G>A	p.Gly386Ser	p.G386S	ENST00000342988	NM_005359.5	386	Ggt/Agt	10/12	0.565437639415803	2	FACETS	0.931	0.864	0.998	0.931	0.864	0.998	CLONAL	2	TRUE	0	0.565437639415803	2		192	245	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729363	41729363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	74	383	0	ENST00000242208.4:c.1166C>T	p.Ser389Leu	p.S389L	ENST00000242208	NM_002192.2	389	tCg/tTg	3/3	0.565437639415803	3	FACETS	0.817	0.718	0.922	0.408	0.359	0.461	CLONAL	1	TRUE	1	0.565437639415803	3		383	411	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713720	30713720	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	190	345	0	ENST00000295754.5:c.1045A>G	p.Lys349Glu	p.K349E	ENST00000295754	NM_003242.5	349	Aag/Gag	4/7	0.565437639415803	3	FACETS	0.973	0.91	1	0.973	0.91	1	CLONAL	2	TRUE	1	0.565437639415803	3		345	443	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0053159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	28	430	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.867	0.695	1	0.867	0.695	1	CLONAL	1	TRUE	1	0.22739004914401	2		430	284	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0053159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	30	333	1	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	0.919	0.743	1	0.919	0.743	1	CLONAL	1	TRUE	1	0.22739004914401	2		334	287	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457264	67457264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750707381	NA	P-0053159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	69	672	1	ENST00000327367.4:c.238C>T	p.Arg80Trp	p.R80W	ENST00000327367	NM_005902.3	80	Cgg/Tgg	2/9	0.22739004914401	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.22739004914401	1		673	445	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	29	356	1	ENST00000304494.5:c.143C>T	p.Pro48Leu	p.P48L	ENST00000304494	NM_000077.4	48	cCg/cTg	1/3	1	2	FACETS	0.921	0.741	1	0.921	0.741	1	CLONAL	1	TRUE	1	0.22739004914401	2		357	277	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578412	7578412	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519747	NA	P-0053159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	55	689	0	ENST00000269305.4:c.518T>G	p.Val173Gly	p.V173G	ENST00000269305	NM_001126112.2	173	gTg/gGg	5/11	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.22739004914401	2		689	420	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022721	12022722	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0053159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	17	447	0	ENST00000396373.4:c.829_830del	p.Leu277AspfsTer22	p.L277Dfs*22	ENST00000396373	NM_001987.4	276	cCT/c	5/8	0.17996501280911	4	FACETS	0.624	0.466	0.813			1	SUBCLONAL	1	TRUE	NA	0.22739004914401	4		447	294	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	54	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.853	0.742	0.969	0.853	0.742	0.969	CLONAL	1	TRUE	1	0.740398039026761	2		429	171	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692953	89692953	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs786204933	NA	P-0053160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	50	388	0	ENST00000371953.3:c.437T>A	p.Leu146Ter	p.L146*	ENST00000371953	NM_000314.4	146	tTa/tAa	5/9	0.740398039026761	1	FACETS	0.31	0.265	0.359	0.31	0.265	0.359	SUBCLONAL	1	TRUE	0	0.740398039026761	1		388	274	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711894	89711894	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs786204865	NA	P-0053160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	36	308	0	ENST00000371953.3:c.512A>C	p.Gln171Pro	p.Q171P	ENST00000371953	NM_000314.4	171	cAg/cCg	6/9	0.740398039026761	1	FACETS	0.252	0.208	0.3	0.252	0.208	0.3	SUBCLONAL	1	TRUE	0	0.740398039026761	1		308	243	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43773192	43773192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	124	314	0	ENST00000382044.4:c.400C>T	p.Pro134Ser	p.P134S	ENST00000382044	NM_001141980.1	134	Cct/Tct	5/28	1	2	FACETS	0.884	0.808	0.962	0.884	0.808	0.962	CLONAL	1	TRUE	1	0.740398039026761	2		314	379	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50143246	50143246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	162	353	0	ENST00000246792.3:c.110G>A	p.Gly37Asp	p.G37D	ENST00000246792	NM_006270.3	37	gGc/gAc	1/6	0.735498947478706	2	FACETS	1	0.98	1	0.573	0.532	0.614	CLONAL	1	TRUE	0	0.740398039026761	2		353	382	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	21	411	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.919	0.714	1	0.919	0.714	1	CLONAL	1	TRUE	1	0.28738855859738	2		411	159	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0053161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	76	1094	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.28738855859738	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.28738855859738	1		1094	352	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351175	89351175	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	35	511	0	ENST00000301030.4:c.1775T>C	p.Val592Ala	p.V592A	ENST00000301030	NM_001256183.1	592	gTg/gCg	9/13	1	2	FACETS	0.883	0.727	1	0.883	0.727	1	CLONAL	1	TRUE	1	0.28738855859738	2		511	276	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0053162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	10	430	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.21	0.141	0.296	0.21	0.141	0.296	SUBCLONAL	1	TRUE	1	0.33	2		430	289	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	29	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.33	2		429	161	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	35	411	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.734	0.604	0.879	0.734	0.604	0.879	SUBCLONAL	1	TRUE	1	0.33	2		411	289	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0053162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	20	316	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.444	0.34	0.566	0.444	0.34	0.566	SUBCLONAL	1	TRUE	1	0.33	2		316	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0053162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	73	426	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.3	1	FACETS	0.877	0.771	0.991	0.877	0.771	0.991	CLONAL	1	TRUE	0	0.33	1		426	421	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948674	71948674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776092159	NA	P-0053162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	120	689	0	ENST00000298229.2:c.3386C>T	p.Thr1129Met	p.T1129M	ENST00000298229	NM_001567.3	1129	aCg/aTg	26/28	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.33	2		689	676	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933334	100933334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	36	408	0	ENST00000325455.5:c.2056C>T	p.Pro686Ser	p.P686S	ENST00000325455	NM_001202474.3	686	Cca/Tca	4/8	1	2	FACETS	0.482	0.396	0.578	0.482	0.396	0.578	SUBCLONAL	1	TRUE	1	0.33	2		408	453	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857476	9857476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145602289	NA	P-0053162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	50	362	0	ENST00000330684.3:c.3925C>T	p.Arg1309Trp	p.R1309W	ENST00000330684	NM_001134407.1	1309	Cgg/Tgg	13/13	1	2	FACETS	0.907	0.773	1	0.907	0.773	1	CLONAL	1	TRUE	1	0.33	2		362	334	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593504	48593504	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	35	207	0	ENST00000342988.3:c.1255G>C	p.Gly419Arg	p.G419R	ENST00000342988	NM_005359.5	419	Ggg/Cgg	10/12	0.288409946877506	1	FACETS	0.847	0.701	1	0.847	0.701	1	CLONAL	1	TRUE	0	0.33	1		207	209	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211862	36211862	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	110	601	0	ENST00000222270.7:c.1613G>A	p.Arg538His	p.R538H	ENST00000222270	NM_014727.1	538	cGt/cAt	3/37	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.33	2		601	652	SUCCESS
APC	324	MSKCC	GRCh37	5	112174378	112174379	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554084685	NA	P-0053162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	18	221	0	ENST00000257430.4:c.3090dup	p.Tyr1031IlefsTer4	p.Y1031Ifs*4	ENST00000257430	NM_000038.5	1029	-/A	16/16	1	2	FACETS	0.537	0.406	0.692	0.537	0.406	0.692	SUBCLONAL	1	TRUE	1	0.33	2		221	203	SUCCESS
APC	324	MSKCC	GRCh37	5	112175525	112175525	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	39	245	0	ENST00000257430.4:c.4235del	p.Gly1412GlufsTer3	p.G1412Efs*3	ENST00000257430	NM_000038.5	1412	Gga/ga	16/16	1	2	FACETS	0.923	0.77	1	0.923	0.77	1	CLONAL	1	TRUE	1	0.33	2		245	256	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0053162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	13	290	1	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.311	0.222	0.421	0.311	0.222	0.421	SUBCLONAL	1	TRUE	1	0.33	2		291	253	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	30	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.857	0.701	1	0.857	0.701	1	CLONAL	1	TRUE	1	0.507586984246223	2		429	138	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947827	178947827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	36	230	0	ENST00000263967.3:c.2702G>T	p.Cys901Phe	p.C901F	ENST00000263967	NM_006218.2	901	tGt/tTt	19/21	1	2	FACETS	0.839	0.699	0.992	0.839	0.699	0.992	CLONAL	1	TRUE	1	0.507586984246223	2		230	169	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601351	28601351	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	61	266	0	ENST00000241453.7:c.2081G>C	p.Cys694Ser	p.C694S	ENST00000241453	NM_004119.2	694	tGt/tCt	17/24	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.507586984246223	2		266	231	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562965	29562965	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	78	327	0	ENST00000356175.3:c.3901del	p.Leu1301TrpfsTer8	p.L1301Wfs*8	ENST00000356175	NM_000267.3	1300	ctC/ct	29/57	0.507586984246223	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.507586984246223	1		327	207	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631440	117631440	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	45	267	0	ENST00000368508.3:c.6238C>A	p.Leu2080Met	p.L2080M	ENST00000368508	NM_002944.2	2080	Ctg/Atg	40/43	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.507586984246223	2		267	175	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589146	67589152	+	frameshift_variant	Frame_Shift_Del	DEL	CAAATTA	CAAATTA	TTT	novel	NA	P-0053163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	41	202	1	ENST00000274335.5:c.1134_1140delinsTTT	p.Lys379LeufsTer17	p.K379Lfs*17	ENST00000274335		378	aaCAAATTA/aaTTT	9/15	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.507586984246223	2		203	145	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218052	108218052	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1064794840	NA	P-0053166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	55	407	0	ENST00000278616.4:c.8631G>C	p.Leu2877Phe	p.L2877F	ENST00000278616	NM_000051.3	2877	ttG/ttC	59/63	0.546164444458738	1	FACETS	0.963	0.843	1	0.963	0.843	1	CLONAL	1	TRUE	0	0.546164444458738	1		407	152	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156729	20156729	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs757280897	NA	P-0053166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	108	390	0	ENST00000379607.5:c.28A>G	p.Lys10Glu	p.K10E	ENST00000379607	NM_001412.3	10	Aaa/Gaa	2/7	0.546164444458738	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.546164444458738	1		390	230	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892263	9892263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	103	520	0	ENST00000330684.3:c.2227G>A	p.Glu743Lys	p.E743K	ENST00000330684	NM_001134407.1	743	Gaa/Aaa	11/13	1	2	FACETS	0.987	0.891	1	0.987	0.891	1	CLONAL	1	TRUE	1	0.546164444458738	2		520	382	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0053166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	59	711	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	0.887	0.765	1	0.887	0.765	1	CLONAL	1	TRUE	1	0.273648684875588	2		711	486	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115725	8115728	+	frameshift_variant	Frame_Shift_Del	DEL	GAAG	GAAG	-	novel	NA	P-0053166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	45	349	0	ENST00000346208.3:c.1076_1079del	p.Glu359AlafsTer44	p.E359Afs*44	ENST00000346208		357	aaGAAG/aa	6/6	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.273648684875588	2		349	315	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100613	67100613	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	49	519	0	ENST00000412916.2:c.311A>G	p.Asn104Ser	p.N104S	ENST00000412916		104	aAt/aGt	4/6	0.273648684875588	1	FACETS	0.662	0.561	0.773	0.662	0.561	0.773	SUBCLONAL	1	TRUE	0	0.273648684875588	1		519	467	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061186	38061186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	31	367	0	ENST00000250448.2:c.803G>A	p.Cys268Tyr	p.C268Y	ENST00000250448	NM_004496.3	268	tGc/tAc	2/2	1	2	FACETS	0.706	0.572	0.857	0.706	0.572	0.857	SUBCLONAL	1	TRUE	1	0.273648684875588	2		367	321	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117430	115117430	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	43	388	0	ENST00000257566.3:c.744C>A	p.Tyr248Ter	p.Y248*	ENST00000257566	NM_016569.3	248	taC/taA	4/8	1	2	FACETS	0.714	0.598	0.843	0.714	0.598	0.843	SUBCLONAL	1	TRUE	1	0.273648684875588	2		388	440	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662375	67662375	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	59	692	0	ENST00000264010.4:c.1621C>G	p.His541Asp	p.H541D	ENST00000264010	NM_006565.3	541	Cac/Gac	9/12	0.273648684875588	1	FACETS	0.728	0.627	0.838	0.728	0.627	0.838	SUBCLONAL	1	TRUE	0	0.273648684875588	1		692	511	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860352	151860356	+	frameshift_variant	Frame_Shift_Del	DEL	ACCAT	ACCAT	-	novel	NA	P-0053166-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	46	493	0	ENST00000262189.6:c.10306_10310del	p.Met3436GlyfsTer3	p.M3436Gfs*3	ENST00000262189	NM_170606.2	3436	ATGGTg/g	43/59	1	2	FACETS	0.645	0.543	0.758	0.645	0.543	0.758	SUBCLONAL	1	TRUE	1	0.273648684875588	2		493	521	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0053167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	489	430	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.830019139621999	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.830019139621999	2		430	543	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0053167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	198	622	2	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.830019139621999	2		624	427	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248126	59248126	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs763958620	NA	P-0053167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	49	200	0	ENST00000371222.2:c.617A>C	p.Gln206Pro	p.Q206P	ENST00000371222	NM_002228.3	206	cAg/cCg	1/1	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.830019139621999	2		200	109	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624263	89624301	+	inframe_deletion	In_Frame_Del	DEL	AAAAGGAGATATCAAGAGGATGGATTCGACTTAGACTTG	AAAAGGAGATATCAAGAGGATGGATTCGACTTAGACTTG	-	novel	NA	P-0053167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	279	276	0	ENST00000371953.3:c.38_76del	p.Lys13_Leu25del	p.K13_L25del	ENST00000371953	NM_000314.4	13	AAAAGGAGATATCAAGAGGATGGATTCGACTTAGACTTG/-	1/9	0.830019139621999	4	FACETS	0.986	0.961	1	0.986	0.961	1	CLONAL	4	TRUE	0	0.830019139621999	4		276	312	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644826	67644826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	244	527	1	ENST00000264010.4:c.91G>A	p.Gly31Arg	p.G31R	ENST00000264010	NM_006565.3	31	Ggg/Agg	3/12	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.830019139621999	2		528	544	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134872996	134872996	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	191	562	3	ENST00000398015.3:c.1300C>T	p.Pro434Ser	p.P434S	ENST00000398015	NM_004441.4	434	Ccc/Tcc	6/16	0.830019139621999	3	FACETS	1	0.974	1	0.549	0.511	0.589	CLONAL	1	TRUE	1	0.830019139621999	3		565	593	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412167	63412167	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	255	857	3	ENST00000330258.3:c.1000G>T	p.Glu334Ter	p.E334*	ENST00000330258	NM_152424.3	334	Gaa/Taa	2/2	0.830019139621999	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.830019139621999	1		860	329	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	49	429	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		429	245	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0053169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	35	330	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.851	0.696	1	0.851	0.696	1	CLONAL	1	TRUE	1	0.13	2		330	633	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0053169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	36	562	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.908	0.745	1	0.908	0.745	1	CLONAL	1	TRUE	1	0.13	2		562	610	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005513	42005517	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAA	GAAAA	-	novel	NA	P-0053169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	41	484	0	ENST00000219905.7:c.3255_3259del	p.Arg1085SerfsTer5	p.R1085Sfs*5	ENST00000219905	NM_001164273.1	1083	ttGAAAAga/ttga	9/24	1	2	FACETS	0.859	0.714	1	0.859	0.714	1	CLONAL	1	TRUE	1	0.13	2		484	734	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374828	149374828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	13	228	0	ENST00000360632.3:c.266C>T	p.Ser89Leu	p.S89L	ENST00000360632	NM_015472.4	89	tCg/tTg	2/7	1	2	FACETS	0.893	0.637	1	0.893	0.637	1	CLONAL	1	TRUE	1	0.13	2		228	224	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107086	27107087	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGGG	novel	NA	P-0053169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	28	431	0	ENST00000324856.7:c.6700_6701insGGGG	p.Ala2234GlyfsTer45	p.A2234Gfs*45	ENST00000324856	NM_006015.4	2233	cgg/cGGGGgg	20/20	1	2	FACETS	0.838	0.668	1	0.838	0.668	1	CLONAL	1	TRUE	1	0.13	2		431	514	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720824	89720825	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0053169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	64	290	0	ENST00000371953.3:c.976dup	p.Asp326GlyfsTer5	p.D326Gfs*5	ENST00000371953	NM_000314.4	325	-/G	8/9	1	2	FACETS	0.963	0.836	1	1	0.979	1	CLONAL	2	TRUE	1	0.13	2		290	511	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0053170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	150	453	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	0.293542874398865	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	FALSE	0	0.293542874398865	2		453	441	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133269	30133269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778826879	NA	P-0053170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	58	730	1	ENST00000263025.4:c.229G>A	p.Glu77Lys	p.E77K	ENST00000263025	NM_002746.2	77	Gaa/Aaa	2/9	0.270544115249167	3	FACETS	0.612	0.524	0.707	0.306	0.262	0.354	SUBCLONAL	1	FALSE	1	0.293542874398865	3		731	741	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164863	36164863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	113	860	1	ENST00000300305.3:c.1012G>A	p.Ala338Thr	p.A338T	ENST00000300305		338	Gcg/Acg	8/8	0.293542874398865	5	FACETS	1	0.97	1	0.302	0.271	0.335	CLONAL	1	FALSE	1	0.293542874398865	5		861	917	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939479	68939479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778971988	NA	P-0053170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	25	400	1	ENST00000288368.4:c.464G>A	p.Arg155Gln	p.R155Q	ENST00000288368	NM_024870.2	155	cGg/cAg	5/40	0.293542874398865	3	FACETS	0.518	0.408	0.645			1	SUBCLONAL	1	FALSE	NA	0.293542874398865	3		401	377	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856541	111856541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	28	230	0	ENST00000341259.2:c.592G>A	p.Glu198Lys	p.E198K	ENST00000341259	NM_005475.2	198	Gag/Aag	2/8	1	2	FACETS	0.815	0.655	0.996	0.815	0.655	0.996	CLONAL	1	FALSE	1	0.293542874398865	2		230	234	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40451798	40451798	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1314655783	NA	P-0053170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	182	878	0	ENST00000345506.4:c.580C>A	p.Pro194Thr	p.P194T	ENST00000345506	NM_003152.3	194	Ccc/Acc	7/20	NA	2	FACETS	1	0.958	1			1	INDETERMINATE	2	FALSE	NA	0.293542874398865	2		878	593	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	28	411	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.24724112180125	4	FACETS	0.954	0.773	1	0.954	0.773	1	CLONAL	2	TRUE	2	0.24724112180125	4		411	148	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214591	5214591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770889503	NA	P-0053171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	67	692	1	ENST00000357368.4:c.4475G>A	p.Arg1492Gln	p.R1492Q	ENST00000357368	NM_002850.3	1492	cGg/cAg	29/38	0.134046105595309	3	FACETS	0.914	0.8	1	0.914	0.8	1	INDETERMINATE	2	TRUE	1	0.24724112180125	3		693	333	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604712	48604713	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0053171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	26	383	0	ENST00000342988.3:c.1534_1535delinsAT	p.Asp512Ile	p.D512I	ENST00000342988	NM_005359.5	512	GAt/ATt	12/12	0.134046105595309	3	FACETS	0.809	0.649	0.988	0.809	0.649	0.988	INDETERMINATE	2	TRUE	1	0.24724112180125	3		383	146	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0053172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	467	856	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	0.530118268386771	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.58551392700888	2		856	783	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664804	138664804	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	84	199	0	ENST00000330315.3:c.761C>T	p.Ser254Leu	p.S254L	ENST00000330315	NM_023067.3	254	tCg/tTg	1/1	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.58551392700888	2		199	237	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742515	17742515	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768652299	NA	P-0053172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	198	641	0	ENST00000250003.3:c.697G>A	p.Glu233Lys	p.E233K	ENST00000250003	NM_002478.4	233	Gag/Aag	2/3	0.58551392700888	1	FACETS	0.964	0.902	1	0.964	0.902	1	CLONAL	1	TRUE	0	0.58551392700888	1		641	496	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586455	189586455	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	121	330	0	ENST00000264731.3:c.1079G>C	p.Arg360Thr	p.R360T	ENST00000264731	NM_003722.4	360	aGa/aCa	8/14	0.58551392700888	5	FACETS	1	0.912	1			1	CLONAL	1	TRUE	NA	0.58551392700888	5		330	769	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416417	49416417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565753611	NA	P-0053172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	147	511	0	ENST00000301067.7:c.16294C>T	p.Arg5432Trp	p.R5432W	ENST00000301067	NM_003482.3	5432	Cgg/Tgg	51/54	0.296305111154329	1	FACETS	0.703	0.646	0.762	0.703	0.646	0.762	INDETERMINATE	1	TRUE	0	0.58551392700888	1		511	505	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665655	86665655	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	49	171	0	ENST00000274376.6:c.1636C>T	p.Gln546Ter	p.Q546*	ENST00000274376	NM_002890.2	546	Cag/Tag	12/25	0.58551392700888	1	FACETS	0.97	0.846	1	0.97	0.846	1	CLONAL	1	TRUE	0	0.58551392700888	1		171	122	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129227	152129227	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0053172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	199	683	0	ENST00000206249.3:c.180C>G	p.Tyr60Ter	p.Y60*	ENST00000206249	NM_000125.3	60	taC/taG	1/8	0.305980704296337	1	FACETS	0.83	0.774	0.888	0.83	0.774	0.888	INDETERMINATE	1	TRUE	0	0.58551392700888	1		683	579	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916660	178916660	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	104	329	0	ENST00000263967.3:c.47T>C	p.Met16Thr	p.M16T	ENST00000263967	NM_006218.2	16	aTg/aCg	2/21	0.58551392700888	3	FACETS	1	0.96	1			1	CLONAL	1	TRUE	NA	0.58551392700888	3		329	409	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808562	1808562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377402598	NA	P-0053172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	235	935	0	ENST00000260795.2:c.2175G>A	p.Met725Ile	p.M725I	ENST00000260795		725	atG/atA	16/17	0.259446362330642	5	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.58551392700888	5		935	1144	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64289237	64289961	+	splice_acceptor_variant,splice_donor_variant,intron_variant	Splice_Site	DEL	GTAAGTAATGGATTCTCTTTTCATTTGTACTCTCTTTCATTTCCTTGTTGAGTGTCAGTGAGTTTAATAGTCTAATAGCCCATTTAATCATTATGATTATTTTTTGAGATAGTATTAAAACCAGGAAATCAAGATCTTACATTCTTTTTTGCATTTCATGCAGTTGCTCATATTACTAAGATTCTAATCCAACAAGAGTTTTTGAATTATTGTTTTGCTTTAAATACTTGATTGAATATGTTGGTTATTTTGTATTTTTATTGAGGTATAATTAAGATACATTTAAAGATACAATAAAATGCACAGGTCTCCAAAGGAGACCAGTTGACAATAACAGCCAAATTAACCATCCAATACAACACATAGAATATTTTGAGTGCTGTAGAACATGCCTTTGTGGCTTTTGTAGTCATCTTCCCTGCTACCAGAGGCAACTTCTGACTTCACTATAAATTAGTTTTGTCTTTTCGTGGACTTACGTGTAAATGGATTTGTGAGTCGACTGTTGTAACCAATACTCAAACGAAGATATAAAGAAAATTAACTTTTTATGATTTTTTCCATTTACACTGATGTGCCTGTTCATATTCCTTTCTGCATCAGGTCACAGCCTAATTAATCAAAAGATAAATTGCCACAAGAGAGGTGATGGTTGTCTATAAGACACTAAATATTACTGTAGGGGGCTTTTGCCTTGTTTCATTTTTTTTTTTTTTTCCTCCCAG	GTAAGTAATGGATTCTCTTTTCATTTGTACTCTCTTTCATTTCCTTGTTGAGTGTCAGTGAGTTTAATAGTCTAATAGCCCATTTAATCATTATGATTATTTTTTGAGATAGTATTAAAACCAGGAAATCAAGATCTTACATTCTTTTTTGCATTTCATGCAGTTGCTCATATTACTAAGATTCTAATCCAACAAGAGTTTTTGAATTATTGTTTTGCTTTAAATACTTGATTGAATATGTTGGTTATTTTGTATTTTTATTGAGGTATAATTAAGATACATTTAAAGATACAATAAAATGCACAGGTCTCCAAAGGAGACCAGTTGACAATAACAGCCAAATTAACCATCCAATACAACACATAGAATATTTTGAGTGCTGTAGAACATGCCTTTGTGGCTTTTGTAGTCATCTTCCCTGCTACCAGAGGCAACTTCTGACTTCACTATAAATTAGTTTTGTCTTTTCGTGGACTTACGTGTAAATGGATTTGTGAGTCGACTGTTGTAACCAATACTCAAACGAAGATATAAAGAAAATTAACTTTTTATGATTTTTTCCATTTACACTGATGTGCCTGTTCATATTCCTTTCTGCATCAGGTCACAGCCTAATTAATCAAAAGATAAATTGCCACAAGAGAGGTGATGGTTGTCTATAAGACACTAAATATTACTGTAGGGGGCTTTTGCCTTGTTTCATTTTTTTTTTTTTTTCCTCCCAG	-	novel	NA	P-0053172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	78	235	0	ENST00000370651.3:c.404+1_405-1del		p.X135_splice	ENST00000370651	NM_003463.4	135			0.305980704296337	1	FACETS	0.65	0.577	0.726	0.65	0.577	0.726	INDETERMINATE	1	TRUE	0	0.58551392700888	1		235	290	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233261	46233261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1318427003	NA	P-0053172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	79	306	0	ENST00000334344.6:c.1480C>T	p.His494Tyr	p.H494Y	ENST00000334344	NM_152641.2	494	Cat/Tat	11/21	0.296305111154329	1	FACETS	0.773	0.689	0.859	0.773	0.689	0.859	INDETERMINATE	1	TRUE	0	0.58551392700888	1		306	247	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914417	32914417	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs80358825	NA	P-0053172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	57	410	0	ENST00000380152.3:c.5925T>A	p.Cys1975Ter	p.C1975*	ENST00000380152		1975	tgT/tgA	11/27	0.305980704296337	1	FACETS	0.425	0.367	0.488	0.425	0.367	0.488	INDETERMINATE	1	TRUE	0	0.58551392700888	1		410	324	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799626	3799626	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0053172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	82	300	0	ENST00000262367.5:c.3836+2T>A		p.X1279_splice	ENST00000262367	NM_004380.2	1279			1	2	FACETS	0.983	0.877	1	0.983	0.877	1	CLONAL	1	TRUE	1	0.58551392700888	2		300	285	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828669	72828669	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	84	638	0	ENST00000268489.5:c.7912C>G	p.Pro2638Ala	p.P2638A	ENST00000268489	NM_006885.3	2638	Cct/Gct	9/10	1	2	FACETS	0.534	0.473	0.6	0.534	0.473	0.6	SUBCLONAL	1	TRUE	1	0.58551392700888	2		638	537	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559146	29559146	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	61	298	0	ENST00000356175.3:c.3253C>G	p.Leu1085Val	p.L1085V	ENST00000356175	NM_000267.3	1085	Ctg/Gtg	25/57	NA	2	FACETS	0.734	0.638	0.835			1	INDETERMINATE	1	TRUE	NA	0.58551392700888	2		298	284	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740780	58740780	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	69	487	0	ENST00000305921.3:c.1685A>C	p.Gln562Pro	p.Q562P	ENST00000305921	NM_003620.3	562	cAg/cCg	6/6	0.305980704296337	1	FACETS	0.396	0.346	0.45	0.396	0.346	0.45	INDETERMINATE	1	TRUE	0	0.58551392700888	1		487	421	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2202748	2202748	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	97	616	0	ENST00000398665.3:c.757C>G	p.Leu253Val	p.L253V	ENST00000398665	NM_032482.2	253	Ctg/Gtg	9/28	0.305980704296337	1	FACETS	0.411	0.367	0.458	0.411	0.367	0.458	INDETERMINATE	1	TRUE	0	0.58551392700888	1		616	570	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10257099	10257099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	200	671	0	ENST00000340748.4:c.2774C>T	p.Ser925Leu	p.S925L	ENST00000340748		925	tCa/tTa	27/40	0.305980704296337	1	FACETS	0.795	0.741	0.85	0.795	0.741	0.85	INDETERMINATE	1	TRUE	0	0.58551392700888	1		671	608	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311617	30311617	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	77	238	0	ENST00000262643.3:c.471A>T	p.Glu157Asp	p.E157D	ENST00000262643	NM_001238.2	157	gaA/gaT	7/12	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.58551392700888	2		238	242	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204756	128204756	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	238	828	1	ENST00000341105.2:c.685C>A	p.Leu229Met	p.L229M	ENST00000341105	NM_032638.4	229	Ctg/Atg	3/6	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.58551392700888	2		829	787	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928031	178928031	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	76	319	0	ENST00000263967.3:c.1309G>T	p.Val437Leu	p.V437L	ENST00000263967	NM_006218.2	437	Gta/Tta	8/21	0.58551392700888	3	FACETS	0.962	0.85	1			1	CLONAL	1	TRUE	NA	0.58551392700888	3		319	349	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080234	5080234	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	55	174	0	ENST00000381652.3:c.2137C>T	p.Gln713Ter	p.Q713*	ENST00000381652	NM_004972.3	713	Cag/Tag	17/25	0.58551392700888	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.58551392700888	1		174	124	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484163	8484163	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	115	489	0	ENST00000356435.5:c.3369G>C	p.Met1123Ile	p.M1123I	ENST00000356435		1123	atG/atC	19/35	0.58551392700888	1	FACETS	0.951	0.871	1	0.951	0.871	1	CLONAL	1	TRUE	0	0.58551392700888	1		489	292	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486288	8486289	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0053172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	83	294	0	ENST00000356435.5:c.2528_2529delinsAT	p.Trp843Tyr	p.W843Y	ENST00000356435		843	tGG/tAT	17/35	0.58551392700888	1	FACETS	0.998	0.899	1	0.998	0.899	1	CLONAL	1	TRUE	0	0.58551392700888	1		294	201	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411379	63411379	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	76	760	0	ENST00000330258.3:c.1788G>T	p.Arg596Ser	p.R596S	ENST00000330258	NM_152424.3	596	agG/agT	2/2	0.411440550812856	1	FACETS	0.315	0.276	0.356	0.315	0.276	0.356	SUBCLONAL	1	TRUE	0	0.58551392700888	1		760	583	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0053173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	309	569	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.370616358468526	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.425283766535647	2		569	722	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984515	72984515	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	150	780	1	ENST00000268489.5:c.3069G>T	p.Lys1023Asn	p.K1023N	ENST00000268489	NM_006885.3	1023	aaG/aaT	3/10	1	2	FACETS	0.829	0.758	0.903	0.829	0.758	0.903	CLONAL	1	TRUE	1	0.425283766535647	2		781	851	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984820	72984820	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	37	567	0	ENST00000268489.5:c.2764C>A	p.Leu922Met	p.L922M	ENST00000268489	NM_006885.3	922	Ctg/Atg	3/10	1	2	FACETS	0.259	0.213	0.312	0.259	0.213	0.312	SUBCLONAL	1	TRUE	1	0.425283766535647	2		567	671	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104599	69104599	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	151	653	0	ENST00000288368.4:c.4443A>C	p.Glu1481Asp	p.E1481D	ENST00000288368	NM_024870.2	1481	gaA/gaC	37/40	0.345211751115387	4	FACETS	0.979	0.894	1	0.489	0.447	0.534	CLONAL	1	TRUE	2	0.425283766535647	4		653	1034	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106329	27106348	+	protein_altering_variant	In_Frame_Del	DEL	CTGCGTCTGTGTGTCCAATA	CTGCGTCTGTGTGTCCAATA	AC	novel	NA	P-0053173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	181	576	1	ENST00000324856.7:c.5940_5959delinsAC	p.Cys1981_Thr1987delinsPro	p.C1981_T1987delinsP	ENST00000324856	NM_006015.4	1980	cgCTGCGTCTGTGTGTCCAATAcc/cgACcc	20/20	0.311066018546958	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.425283766535647	1		577	639	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0053174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	9	432	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.202315776883836	2	FACETS	0.225	0.148	0.324	0.112	0.074	0.162	SUBCLONAL	1	FALSE	0	0.202315776883836	2		432	396	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0053174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	45	1003	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.716	0.601	0.844	0.716	0.601	0.844	SUBCLONAL	1	FALSE	1	0.202315776883836	2		1007	621	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0053174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	68	393	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.907	0.799	1	1	0.985	1	CLONAL	3	FALSE	1	0.202315776883836	2		393	247	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0053174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	121	552	2	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	1	0.924	1	1	0.99	1	CLONAL	2	FALSE	1	0.202315776883836	2		554	585	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0053174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	35	316	1	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	1	2	FACETS	0.84	0.694	1	1	0.958	1	CLONAL	2	FALSE	1	0.202315776883836	2		317	206	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0053174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	20	311	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	1	2	FACETS	0.675	0.516	0.86	0.675	0.516	0.86	SUBCLONAL	1	FALSE	1	0.202315776883836	2		311	293	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0053174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	157	562	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.889	0.818	0.962	1	0.993	1	CLONAL	3	FALSE	1	0.202315776883836	2		562	582	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	66	780	1	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	FALSE	1	0.202315776883836	2		781	631	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0053174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	137	460	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.202315776883836	2	FACETS	1	0.977	1	1	0.99	1	CLONAL	3	FALSE	0	0.202315776883836	2		460	387	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0053174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	23	288	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	1	0.797	1	1	0.948	1	CLONAL	2	FALSE	1	0.202315776883836	2		288	113	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339111	65339111	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	34	555	1	ENST00000342505.4:c.425del	p.Lys142ArgfsTer26	p.K142Rfs*26	ENST00000342505	NM_002227.2	142	aAg/ag	5/25	1	2	FACETS	0.724	0.591	0.874	0.724	0.591	0.874	SUBCLONAL	1	FALSE	1	0.202315776883836	2		556	464	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636182	28636182	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376895552	NA	P-0053174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	42	512	0	ENST00000241453.7:c.190G>A	p.Gly64Arg	p.G64R	ENST00000241453	NM_004119.2	64	Ggg/Agg	3/24	1	2	FACETS	0.825	0.689	0.977	0.825	0.689	0.977	CLONAL	1	FALSE	1	0.202315776883836	2		512	503	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	97	573	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	1	0.936	1	1	0.987	1	CLONAL	2	FALSE	1	0.202315776883836	2		573	452	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	24	333	2	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.663	0.519	0.828	0.663	0.519	0.828	SUBCLONAL	1	FALSE	1	0.202315776883836	2		335	358	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913255	NA	P-0053174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	9	612	0	ENST00000369535.4:c.183A>C	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caC	3/7	1	2	FACETS	0.226	0.148	0.325	0.226	0.148	0.325	SUBCLONAL	1	FALSE	1	0.202315776883836	2		612	394	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219487	133219487	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	64	903	2	ENST00000320574.5:c.4647del	p.Lys1550AsnfsTer12	p.K1550Nfs*12	ENST00000320574	NM_006231.2	1549	ccC/cc	36/49	1	2	FACETS	0.95	0.822	1	0.95	0.822	1	CLONAL	1	FALSE	1	0.202315776883836	2		905	666	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099396	27099396	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0053174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	93	634	0	ENST00000324856.7:c.3633T>G	p.Tyr1211Ter	p.Y1211*	ENST00000324856	NM_006015.4	1211	taT/taG	14/20	1	2	FACETS	1	0.951	1	1	0.987	1	CLONAL	2	FALSE	1	0.202315776883836	2		634	415	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599219	28599219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	200	994	0	ENST00000253063.3:c.665C>T	p.Ala222Val	p.A222V	ENST00000253063	NM_031459.4	222	gCa/gTa	5/10	1	2	FACETS	0.85	0.79	0.913	1	0.994	1	CLONAL	3	FALSE	1	0.202315776883836	2		994	775	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247548	123247548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	52	562	0	ENST00000358487.5:c.1943C>T	p.Ala648Val	p.A648V	ENST00000358487	NM_000141.4	648	gCc/gTc	14/18	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	FALSE	1	0.202315776883836	2		562	430	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103308	119103308	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	20	467	0	ENST00000264033.4:c.346A>G	p.Arg116Gly	p.R116G	ENST00000264033	NM_005188.3	116	Agg/Ggg	2/16	1	2	FACETS	0.791	0.606	1	0.791	0.606	1	CLONAL	1	FALSE	1	0.202315776883836	2		467	250	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506670	103506670	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	46	249	1	ENST00000355739.4:c.413G>T	p.Arg138Leu	p.R138L	ENST00000355739	NM_000123.3	138	cGa/cTa	4/15	1	2	FACETS	1	0.911	1	1	0.975	1	CLONAL	2	FALSE	1	0.202315776883836	2		250	207	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988708	41988709	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0053174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	22	443	0	ENST00000219905.7:c.1501_1502del	p.Met501ValfsTer12	p.M501Vfs*12	ENST00000219905	NM_001164273.1	500	tcTAtg/tctg	3/24	1	2	FACETS	0.856	0.665	1	0.856	0.665	1	CLONAL	1	FALSE	1	0.202315776883836	2		443	254	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864608	37864608	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	61	774	0	ENST00000269571.5:c.260C>G	p.Ala87Gly	p.A87G	ENST00000269571		87	gCt/gGt	3/27	1	2	FACETS	0.938	0.809	1	0.938	0.809	1	CLONAL	1	FALSE	1	0.202315776883836	2		774	643	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688678	47688678	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1313171285	NA	P-0053174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	129	454	2	ENST00000347630.2:c.622G>A	p.Gly208Ser	p.G208S	ENST00000347630	NM_001007230.1	208	Ggc/Agc	7/11	1	2	FACETS	0.928	0.848	1	1	0.992	1	CLONAL	3	FALSE	1	0.202315776883836	2		456	458	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808309	99808309	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	13	289	0	ENST00000280892.6:c.380del	p.Asn127ThrfsTer8	p.N127Tfs*8	ENST00000280892	NM_001130678.1	127	aAc/ac	5/7	1	2	FACETS	0.73	0.522	0.982	0.73	0.522	0.982	CLONAL	1	FALSE	1	0.202315776883836	2		289	176	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589148	67589151	+	frameshift_variant	Frame_Shift_Del	DEL	AATT	AATT	-	novel	NA	P-0053174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	35	204	0	ENST00000274335.5:c.1139_1142del	p.Leu380SerfsTer16	p.L380Sfs*16	ENST00000274335		379	aAATTa/aa	9/15	1	2	FACETS	0.867	0.724	1	1	0.971	1	CLONAL	3	FALSE	1	0.202315776883836	2		204	133	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589604	67589605	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCA	novel	NA	P-0053174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	46	115	0	ENST00000274335.5:c.1368_1370dup	p.Phe456_Gln457insHis	p.F456_Q457insH	ENST00000274335		456	ttt/ttTCAt	10/15	1	2	FACETS	0.972	0.834	1	1	0.979	1	CLONAL	3	FALSE	1	0.202315776883836	2		115	156	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787746	135787746	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	30	534	0	ENST00000298552.3:c.836A>G	p.His279Arg	p.H279R	ENST00000298552	NM_001162426.1	279	cAc/cGc	9/23	1	2	FACETS	0.597	0.48	0.73	0.597	0.48	0.73	SUBCLONAL	1	FALSE	1	0.202315776883836	2		534	497	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15809081	15809083	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0053174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	27	413	0	ENST00000307771.7:c.70_72del	p.Lys24del	p.K24del	ENST00000307771	NM_005089.3	22	ctGAAg/ctg	2/11	1	2	FACETS	0.662	0.527	0.818	0.662	0.527	0.818	SUBCLONAL	1	FALSE	1	0.202315776883836	2		413	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0053175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	237	656	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.546135739100688	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.546137512547445	1		656	571	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849800	156849800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41358549	NA	P-0053175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	92	499	0	ENST00000524377.1:c.2056C>T	p.Arg686Cys	p.R686C	ENST00000524377	NM_002529.3	686	Cgc/Tgc	16/17	0.201054103211486	5	FACETS	0.709	0.629	0.794	0.236	0.209	0.265	INDETERMINATE	1	TRUE	2	0.546137512547445	5		499	865	SUCCESS
CBL	867	MSKCC	GRCh37	11	119167716	119167716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778155	NA	P-0053175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	137	444	0	ENST00000264033.4:c.2125C>T	p.Arg709Trp	p.R709W	ENST00000264033	NM_005188.3	709	Cgg/Tgg	13/16	1	2	FACETS	0.917	0.838	0.999	0.917	0.838	0.999	CLONAL	1	TRUE	1	0.546137512547445	2		444	547	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325367	1325367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750085547	NA	P-0053175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	58	477	1	ENST00000400841.2:c.308C>T	p.Thr103Met	p.T103M	ENST00000400841		103	aCg/aTg	3/6	NA	2	FACETS	0.348	0.299	0.402			1	INDETERMINATE	1	TRUE	NA	0.546137512547445	2		478	610	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292430	15292430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150338460	NA	P-0053175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	111	841	5	ENST00000263388.2:c.2749G>A	p.Gly917Arg	p.G917R	ENST00000263388	NM_000435.2	917	Gga/Aga	17/33	0.546137512547445	1	FACETS	0.412	0.37	0.456	0.412	0.37	0.456	SUBCLONAL	1	TRUE	0	0.546137512547445	1		846	718	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99181227	99181227	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0053175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	176	483	0	ENST00000074304.5:c.2167+1G>A		p.X723_splice	ENST00000074304	NM_001134224.1	723			0.263756003475013	3	FACETS	1	0.986	1	0.427	0.395	0.461	INDETERMINATE	1	TRUE	0	0.546137512547445	3		483	640	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002819	69002819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	249	235	0	ENST00000288368.4:c.2119G>A	p.Val707Met	p.V707M	ENST00000288368	NM_024870.2	707	Gtg/Atg	20/40	0.546137512547445	5	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	2	0.546137512547445	5		235	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0053185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	417	574	3	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.798137453255341	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.798137453255341	1		577	581	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447621	187447621	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778230721	NA	P-0053185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	396	660	2	ENST00000232014.4:c.572C>T	p.Pro191Leu	p.P191L	ENST00000232014	NM_001130845.1	191	cCg/cTg	5/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.798137453255341	2		662	932	SUCCESS
RET	5979	MSKCC	GRCh37	10	43613865	43613865	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	323	721	0	ENST00000355710.3:c.2329A>G	p.Asn777Asp	p.N777D	ENST00000355710	NM_020975.4	777	Aac/Gac	13/20	1	2	FACETS	0.797	0.753	0.841	0.797	0.753	0.841	SUBCLONAL	1	TRUE	1	0.798137453255341	2		721	1016	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467971	66467971	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	82	297	0	ENST00000273854.3:c.298C>A	p.Gln100Lys	p.Q100K	ENST00000273854	NM_004439.5	100	Caa/Aaa	3/18	0.798137453255341	1	FACETS	0.355	0.315	0.397	0.355	0.315	0.397	SUBCLONAL	1	TRUE	0	0.798137453255341	1		297	348	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069657	69069658	+	stop_gained	Nonsense_Mutation	DNP	CA	CA	AC	novel	NA	P-0053185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	248	437	0	ENST00000288368.4:c.4332_4333delinsAC	p.Tyr1444_Asn1445delinsTer	p.Y1444_N1445delins*	ENST00000288368	NM_024870.2	1444	taCAac/taACac	35/40	0.798137453255341	1	FACETS	0.98	0.936	1	0.98	0.936	1	CLONAL	1	TRUE	0	0.798137453255341	1		437	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0053186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	166	500	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.737405376339668	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.741047587193015	1		500	242	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432121	121432121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	204	736	0	ENST00000257555.6:c.868C>T	p.Pro290Ser	p.P290S	ENST00000257555		290	Ccc/Tcc	4/10	0.741047587193015	2	FACETS	1	0.944	1	0.505	0.472	0.539	CLONAL	1	TRUE	0	0.741047587193015	2		736	545	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066482	94066482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542602078	NA	P-0053186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	62	299	0	ENST00000369303.4:c.1277G>A	p.Arg426Gln	p.R426Q	ENST00000369303	NM_004440.3	426	cGa/cAa	5/17	0.741047587193015	3	FACETS	0.799	0.696	0.909	0.4	0.348	0.455	CLONAL	1	TRUE	1	0.741047587193015	3		299	287	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513282	44513293	+	inframe_deletion	In_Frame_Del	DEL	CCACCGCCACCG	CCACCGCCACCG	-	rs745888281	NA	P-0053186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	225	551	0	ENST00000291552.4:c.642_653del	p.Gly220_Gly223del	p.G220_G223del	ENST00000291552	NM_006758.2	214	ggCGGTGGCGGTGGt/ggt	8/8	1	2	FACETS	0.952	0.892	1	0.952	0.892	1	CLONAL	1	TRUE	1	0.741047587193015	2		551	638	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647990	3647990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	201	668	0	ENST00000294008.3:c.1174C>T	p.His392Tyr	p.H392Y	ENST00000294008	NM_032444.2	392	Cac/Tac	6/15	0.741047587193015	3	FACETS	1	0.96	1	0.523	0.486	0.561	CLONAL	1	TRUE	1	0.741047587193015	3		668	711	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188200	10188200	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	134	454	0	ENST00000256474.2:c.343C>A	p.His115Asn	p.H115N	ENST00000256474	NM_000551.3	115	Cac/Aac	2/3	0.601634375424528	1	FACETS	0.983	0.907	1	0.983	0.907	1	CLONAL	1	TRUE	0	0.601634375424528	1		454	317	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174395	11174395	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	197	521	0	ENST00000361445.4:c.7280T>G	p.Leu2427Arg	p.L2427R	ENST00000361445	NM_004958.3	2427	cTg/cGg	53/58	0.601634375424528	1	FACETS	0.993	0.93	1	0.993	0.93	1	CLONAL	1	TRUE	0	0.601634375424528	1		521	461	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458444	120458445	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0053187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	163	577	0	ENST00000256646.2:c.6900dup	p.Pro2302AlafsTer11	p.P2302Afs*11	ENST00000256646	NM_024408.3	2300	-/C	34/34	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.601634375424528	2		577	488	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457970	69457970	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	117	380	0	ENST00000227507.2:c.370C>G	p.Leu124Val	p.L124V	ENST00000227507	NM_053056.2	124	Ctg/Gtg	2/5	1	2	FACETS	0.965	0.878	1	0.965	0.878	1	CLONAL	1	TRUE	1	0.601634375424528	2		380	403	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213957	2213958	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGCGCTC	novel	NA	P-0053187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	218	740	0	ENST00000398665.3:c.1774_1780dup	p.Gly594AlafsTer75	p.G594Afs*75	ENST00000398665	NM_032482.2	590	cgc/cgCGCGCTCc	18/28	1	2	FACETS	0.845	0.787	0.904	0.845	0.787	0.904	CLONAL	1	TRUE	1	0.601634375424528	2		740	858	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021066	26021066	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	150	554	0	ENST00000357647.3:c.349C>G	p.Arg117Gly	p.R117G	ENST00000357647	NM_003529.2	117	Cgc/Ggc	1/1	1	2	FACETS	0.872	0.801	0.945	0.872	0.801	0.945	CLONAL	1	TRUE	1	0.601634375424528	2		554	572	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94129009	94129009	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	144	386	1	ENST00000369303.4:c.51G>A	p.Trp17Ter	p.W17*	ENST00000369303	NM_004440.3	17	tgG/tgA	1/17	1	2	FACETS	0.931	0.855	1	0.931	0.855	1	CLONAL	1	TRUE	1	0.601634375424528	2		387	514	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0053189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	19	236	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.234315749346204	3	FACETS	0.472	0.357	0.607	0.236	0.178	0.304	SUBCLONAL	1	TRUE	1	0.236283313407407	3		236	381	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0053189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	125	525	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.227150761569425	2	FACETS	0.938	0.852	1	0.938	0.852	1	CLONAL	2	TRUE	0	0.236283313407407	2		525	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576873	7576873	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs863224500	NA	P-0053189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	102	603	0	ENST00000269305.4:c.973G>T	p.Gly325Ter	p.G325*	ENST00000269305	NM_001126112.2	325	Gga/Tga	9/11	0.228379898879972	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.236283313407407	1		603	653	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531867	41531867	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	72	359	0	ENST00000263253.7:c.1579C>A	p.Leu527Ile	p.L527I	ENST00000263253	NM_001429.3	527	Ctt/Att	7/31	0.228379898879972	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.236283313407407	1		359	478	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508734	106508735	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0053189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	84	485	0	ENST00000359195.3:c.728_729delinsAA	p.Ala243Glu	p.A243E	ENST00000359195	NM_002649.2	243	gCC/gAA	2/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.236283313407407	2		485	607	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0053190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	73	330	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.862	0.758	0.972	0.862	0.758	0.972	CLONAL	1	TRUE	1	0.457987149899841	2		330	370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0053190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	208	778	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.457987149899841	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.457987149899841	1		779	633	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0053190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	64	290	1	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.457987149899841	1	FACETS	0.832	0.728	0.942	0.832	0.728	0.942	CLONAL	1	TRUE	0	0.457987149899841	1		291	259	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118901	70118902	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0053190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	200	611	0	ENST00000245479.2:c.474_475dup	p.Glu159GlyfsTer25	p.E159Gfs*25	ENST00000245479	NM_000346.3	158	gcg/gcGGg	2/3	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.457987149899841	2		611	818	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412110	63412110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852216	NA	P-0053190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	283	639	1	ENST00000330258.3:c.1057C>T	p.Arg353Ter	p.R353*	ENST00000330258	NM_152424.3	353	Cga/Tga	2/2	0.457987149899841	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.457987149899841	1		640	667	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295773	15295773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1248140755	NA	P-0053190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	133	824	1	ENST00000263388.2:c.2354G>A	p.Arg785His	p.R785H	ENST00000263388	NM_000435.2	785	cGc/cAc	15/33	0.281739578960957	1	FACETS	0.501	0.454	0.55	0.501	0.454	0.55	SUBCLONAL	1	TRUE	0	0.457987149899841	1		825	894	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78921143	78921143	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	146	477	0	ENST00000306801.3:c.3257C>T	p.Thr1086Met	p.T1086M	ENST00000306801	NM_020761.2	1086	aCg/aTg	27/34	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.457987149899841	2		477	613	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508563	106508563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757016725	NA	P-0053190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	48	307	0	ENST00000359195.3:c.557C>T	p.Ala186Val	p.A186V	ENST00000359195	NM_002649.2	186	gCg/gTg	2/11	1	2	FACETS	0.483	0.409	0.564	0.483	0.409	0.564	SUBCLONAL	1	TRUE	1	0.457987149899841	2		307	434	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs121913370	NA	P-0053190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	55	210	0	ENST00000288602.6:c.1742A>C	p.Asn581Thr	p.N581T	ENST00000288602	NM_004333.4	581	aAt/aCt	15/18	1	2	FACETS	0.972	0.84	1	0.972	0.84	1	CLONAL	1	TRUE	1	0.457987149899841	2		210	247	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115277070	115277070	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	124	349	1	ENST00000438362.2:c.713C>G	p.Ala238Gly	p.A238G	ENST00000438362	NM_001242891.1	238	gCc/gGc	7/20	0.281739578960957	1	FACETS	0.982	0.896	1	0.982	0.896	1	CLONAL	1	TRUE	0	0.457987149899841	1		350	425	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831035	72831035	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	125	384	0	ENST00000268489.5:c.5546T>C	p.Ile1849Thr	p.I1849T	ENST00000268489	NM_006885.3	1849	aTc/aCc	9/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.457987149899841	2		384	466	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127403	55127403	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	108	480	0	ENST00000257290.5:c.191A>C	p.Glu64Ala	p.E64A	ENST00000257290	NM_006206.4	64	gAa/gCa	3/23	0.380843848972835	1	FACETS	0.716	0.645	0.79	0.716	0.645	0.79	SUBCLONAL	1	TRUE	0	0.457987149899841	1		480	508	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1977104	1977104	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	91	683	0	ENST00000382891.5:c.3598G>C	p.Gly1200Arg	p.G1200R	ENST00000382891	NM_133335.3	1200	Gga/Cga	20/22	0.325544484650158	3	FACETS	0.742	0.658	0.832	0.371	0.329	0.416	SUBCLONAL	1	TRUE	1	0.343635303606259	3		683	836	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0053192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	37	430	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.18	2		430	386	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0053192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	34	440	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.825	0.674	0.995	0.825	0.674	0.995	CLONAL	1	TRUE	1	0.18	2		440	458	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0053192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	40	356	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.18	2		356	377	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522259	157522259	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554235831	NA	P-0053192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	25	638	1	ENST00000346085.5:c.4531C>T	p.Gln1511Ter	p.Q1511*	ENST00000346085	NM_020732.3	1511	Cag/Tag	18/20	1	2	FACETS	0.605	0.476	0.754	0.605	0.476	0.754	SUBCLONAL	1	TRUE	1	0.18	2		639	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0053194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	24	485	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.353	0.276	0.441	0.353	0.276	0.441	SUBCLONAL	1	FALSE	1	0.356380930027375	2		486	382	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0053194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	18	848	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	0.451	0.34	0.581	0.451	0.34	0.581	SUBCLONAL	1	FALSE	1	0.356380930027375	2		848	224	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660469	67660469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	23	292	0	ENST00000264010.4:c.1369C>T	p.Arg457Ter	p.R457*	ENST00000264010	NM_006565.3	457	Cga/Tga	8/12	1	2	FACETS	0.429	0.334	0.538	0.429	0.334	0.538	SUBCLONAL	1	FALSE	1	0.356380930027375	2		292	301	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483341	120483341	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	29	364	0	ENST00000256646.2:c.3020A>C	p.Asn1007Thr	p.N1007T	ENST00000256646	NM_024408.3	1007	aAc/aCc	19/34	1	2	FACETS	0.565	0.455	0.69	0.565	0.455	0.69	SUBCLONAL	1	FALSE	1	0.356380930027375	2		364	288	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404962	70404962	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	27	463	0	ENST00000373644.4:c.2476C>T	p.Gln826Ter	p.Q826*	ENST00000373644	NM_030625.2	826	Cag/Tag	4/12	1	2	FACETS	0.371	0.295	0.459	0.371	0.295	0.459	SUBCLONAL	1	FALSE	1	0.356380930027375	2		463	408	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438169	56438169	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	53	692	1	ENST00000407977.2:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000407977		275	tGt/tAt	7/10	1	2	FACETS	0.587	0.5	0.681	0.587	0.5	0.681	SUBCLONAL	1	FALSE	1	0.356380930027375	2		693	507	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602430	10602430	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	34	664	0	ENST00000171111.5:c.1148C>A	p.Ser383Ter	p.S383*	ENST00000171111	NM_203500.1	383	tCg/tAg	3/6	1	2	FACETS	0.406	0.331	0.49	0.406	0.331	0.49	SUBCLONAL	1	FALSE	1	0.356380930027375	2		664	470	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106927	11106928	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	111	589	0	ENST00000358026.2:c.1634dup	p.Lys546GlufsTer18	p.K546Efs*18	ENST00000358026	NM_001128849.1	544	-/A	10/36	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.356380930027375	2		589	428	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662475	117662475	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs1322935214	NA	P-0053194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	85	349	0	ENST00000368508.3:c.4903-1G>C		p.X1635_splice	ENST00000368508	NM_002944.2	1635			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.356380930027375	2		349	322	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0053196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	176	330	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.205185631512985	5	FACETS	1	0.979	1	0.868	0.803	0.935	CLONAL	3	TRUE	1	0.205185631512985	5		330	646	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441780	49441780	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555195442	NA	P-0053196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	59	569	0	ENST00000301067.7:c.4204C>T	p.Gln1402Ter	p.Q1402*	ENST00000301067	NM_003482.3	1402	Cag/Tag	14/54	1	2	FACETS	0.789	0.678	0.91	0.789	0.678	0.91	CLONAL	1	TRUE	1	0.205185631512985	2		569	729	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801491	1801491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	63	775	0	ENST00000260795.2:c.397G>A	p.Asp133Asn	p.D133N	ENST00000260795		133	Gat/Aat	3/17	1	2	FACETS	0.772	0.667	0.888	0.772	0.667	0.888	SUBCLONAL	1	TRUE	1	0.205185631512985	2		775	795	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0053218-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	116	305	0				ENST00000310581	NM_198253.2	-/1132			0.930766572902554	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.930766572902554	1		305	121	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0053218-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	211	658	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.843	0.789	0.897	0.843	0.789	0.897	CLONAL	1	TRUE	1	0.930766572902554	2		658	538	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095917	29095917	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780192	NA	P-0053218-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	995	501	1	ENST00000328354.6:c.917G>A	p.Gly306Glu	p.G306E	ENST00000328354	NM_007194.3	306	gGg/gAg	9/15	0.454881315710123	6	FACETS	0.989	0.981	0.996			1	INDETERMINATE	6	TRUE	NA	0.930766572902554	6		502	1031	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031889	26031889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053218-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	447	379	0	ENST00000244661.2:c.400G>A	p.Glu134Lys	p.E134K	ENST00000244661	NM_003537.3	134	Gaa/Aaa	1/1	0.922718389466653	3	FACETS	0.984	0.968	0.997	0.984	0.968	0.997	CLONAL	3	TRUE	0	0.930766572902554	3		379	477	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683487	29683487	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053218-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	164	331	0	ENST00000356175.3:c.7562A>G	p.Lys2521Arg	p.K2521R	ENST00000356175	NM_000267.3	2521	aAa/aGa	51/57	NA	2	FACETS	0.958	0.892	1			1	INDETERMINATE	1	TRUE	NA	0.930766572902554	2		331	368	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743561	46743561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746927114	NA	P-0053218-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	70	693	0	ENST00000371975.4:c.1942G>A	p.Glu648Lys	p.E648K	ENST00000371975	NM_003579.3	648	Gag/Aag	17/18	1	2	FACETS	0.215	0.187	0.246	0.215	0.187	0.246	SUBCLONAL	1	TRUE	1	0.930766572902554	2		693	699	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115272901	115272901	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs767985022	NA	P-0053218-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	272	542	1	ENST00000438362.2:c.1472G>T	p.Ser491Ile	p.S491I	ENST00000438362	NM_001242891.1	491	aGc/aTc	12/20	1	2	FACETS	0.909	0.859	0.959	0.909	0.859	0.959	CLONAL	1	TRUE	1	0.930766572902554	2		543	643	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786818	3786818	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0053218-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	201	351	0	ENST00000262367.5:c.4395-2A>C		p.X1465_splice	ENST00000262367	NM_004380.2	1465			0.930766572902554	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.930766572902554	1		351	228	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029368	14029368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053218-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	220	397	0	ENST00000311895.7:c.1579G>A	p.Glu527Lys	p.E527K	ENST00000311895	NM_005236.2	527	Gaa/Aaa	8/11	1	2	FACETS	0.973	0.915	1	0.973	0.915	1	CLONAL	1	TRUE	1	0.930766572902554	2		397	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0053219-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	121	778	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.927	0.837	1	0.927	0.837	1	CLONAL	1	FALSE	1	0.3	2		779	870	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412336	139412336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502238	NA	P-0053219-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	70	1068	0	ENST00000277541.6:c.1309G>A	p.Glu437Lys	p.E437K	ENST00000277541	NM_017617.3	437	Gag/Aag	8/34	1	2	FACETS	0.468	0.407	0.535	0.468	0.407	0.535	SUBCLONAL	1	FALSE	1	0.3	2		1068	997	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519895	NA	P-0053219-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	8	192	0	ENST00000281708.4:c.1394G>T	p.Arg465Leu	p.R465L	ENST00000281708	NM_033632.3	465	cGt/cTt	9/12	0.3	1	FACETS	0.139	0.089	0.205	0.139	0.089	0.205	SUBCLONAL	1	FALSE	0	0.3	1		192	325	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0053219-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	86	778	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.17	2		779	971	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412336	139412336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502238	NA	P-0053219-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	44	1068	0	ENST00000277541.6:c.1309G>A	p.Glu437Lys	p.E437K	ENST00000277541	NM_017617.3	437	Gag/Aag	8/34	1	2	FACETS	0.432	0.361	0.513	0.432	0.361	0.513	SUBCLONAL	1	TRUE	1	0.17	2		1068	1197	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101301	27101301	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	252	918	0	ENST00000324856.7:c.4583del	p.Arg1528GlnfsTer37	p.R1528Qfs*37	ENST00000324856	NM_006015.4	1528	cGa/ca	18/20	0.282884912433694	3	FACETS	1	0.992	1	0.739	0.691	0.788	CLONAL	1	TRUE	1	0.391432618424754	3		918	1042	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120529651	120529651	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	204	654	0	ENST00000256646.2:c.806G>T	p.Cys269Phe	p.C269F	ENST00000256646	NM_024408.3	269	tGt/tTt	5/34	0.276292245085464	3	FACETS	1	0.987	1	0.646	0.599	0.695	CLONAL	1	TRUE	1	0.391432618424754	3		654	964	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604478	43604478	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0053220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	198	658	0	ENST00000355710.3:c.1064-1G>T		p.X355_splice	ENST00000355710	NM_020975.4	355			0.276292245085464	3	FACETS	1	0.99	1	0.704	0.653	0.757	CLONAL	1	TRUE	1	0.391432618424754	3		658	859	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332806	70332806	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	105	662	0	ENST00000373644.4:c.711T>A	p.Ser237Arg	p.S237R	ENST00000373644	NM_030625.2	237	agT/agA	2/12	1	2	FACETS	0.657	0.588	0.73	0.657	0.588	0.73	SUBCLONAL	1	TRUE	1	0.391432618424754	2		662	817	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405363	70405363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	106	608	0	ENST00000373644.4:c.2878del	p.Glu960LysfsTer66	p.E960Kfs*66	ENST00000373644	NM_030625.2	959	ttG/tt	4/12	1	2	FACETS	0.65	0.582	0.722	0.65	0.582	0.722	SUBCLONAL	1	TRUE	1	0.391432618424754	2		608	833	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006400	12006400	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	261	570	1	ENST00000396373.4:c.368A>T	p.Gln123Leu	p.Q123L	ENST00000396373	NM_001987.4	123	cAg/cTg	4/8	0.27276999791071	3	FACETS	1	0.973	1	0.706	0.664	0.748	CLONAL	2	TRUE	0	0.391432618424754	3		571	753	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0053220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	474	476	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.391432618424754	4	FACETS	0.898	0.863	0.933			1	CLONAL	4	TRUE	NA	0.391432618424754	4		476	938	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061519	38061519	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	67	319	0	ENST00000250448.2:c.470G>T	p.Gly157Val	p.G157V	ENST00000250448	NM_004496.3	157	gGc/gTc	2/2	0.276292245085464	3	FACETS	0.982	0.856	1	0.491	0.428	0.558	CLONAL	1	TRUE	1	0.391432618424754	3		319	417	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019398	42019398	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	182	533	0	ENST00000219905.7:c.3451G>T	p.Glu1151Ter	p.E1151*	ENST00000219905	NM_001164273.1	1151	Gaa/Taa	10/24	0.279754526201097	2	FACETS	1	0.987	1	0.658	0.609	0.708	CLONAL	1	TRUE	0	0.391432618424754	2		533	707	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647447	23647447	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	197	587	0	ENST00000261584.4:c.420G>T	p.Lys140Asn	p.K140N	ENST00000261584	NM_024675.3	140	aaG/aaT	4/13	0.282884912433694	3	FACETS	1	0.99	1	0.71	0.659	0.764	CLONAL	1	TRUE	1	0.391432618424754	3		587	847	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992156	72992157	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	A	novel	NA	P-0053220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	127	926	0	ENST00000268489.5:c.1888_1889delinsT	p.Gly630TrpfsTer30	p.G630Wfs*30	ENST00000268489	NM_006885.3	630	GGg/Tg	2/10	0.282884912433694	3	FACETS	0.786	0.711	0.865	0.393	0.355	0.433	SUBCLONAL	1	TRUE	1	0.391432618424754	3		926	987	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	246	761	1	ENST00000269305.4:c.859G>T	p.Glu287Ter	p.E287*	ENST00000269305	NM_001126112.2	287	Gag/Tag	8/11	0.279754526201097	2	FACETS	1	0.993	1	0.738	0.691	0.785	CLONAL	1	TRUE	0	0.391432618424754	2		762	852	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39537541	39537541	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	92	300	0	ENST00000262039.4:c.75C>G	p.Ser25Arg	p.S25R	ENST00000262039	NM_002647.2	25	agC/agG	2/25	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.391432618424754	2		300	453	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602736	10602736	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	278	956	0	ENST00000171111.5:c.842T>C	p.Leu281Pro	p.L281P	ENST00000171111	NM_203500.1	281	cTg/cCg	3/6	0.284266071913657	2	FACETS	1	0.992	1	0.682	0.641	0.725	CLONAL	1	TRUE	0	0.391432618424754	2		956	1041	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794048	42794048	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs762143212	NA	P-0053220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	235	680	0	ENST00000575354.2:c.1409G>C	p.Arg470Pro	p.R470P	ENST00000575354	NM_015125.3	470	cGg/cCg	9/20	0.284266071913657	2	FACETS	1	0.992	1	0.719	0.672	0.767	CLONAL	1	TRUE	0	0.391432618424754	2		680	835	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716271	52716271	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	273	815	1	ENST00000322088.6:c.715G>T	p.Asp239Tyr	p.D239Y	ENST00000322088	NM_014225.5	239	Gat/Tat	6/15	0.284266071913657	2	FACETS	0.756	0.71	0.802	0.756	0.71	0.802	SUBCLONAL	2	TRUE	0	0.391432618424754	2		816	923	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082812	16082812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	22	52	0	ENST00000281043.3:c.626C>T	p.Pro209Leu	p.P209L	ENST00000281043	NM_005378.4	209	cCg/cTg	2/3	1	2	FACETS	0.907	0.712	1	0.907	0.712	1	CLONAL	1	TRUE	1	0.391432618424754	2		52	124	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793287	242793287	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	123	872	0	ENST00000334409.5:c.790C>A	p.Arg264Ser	p.R264S	ENST00000334409	NM_005018.2	264	Cgc/Agc	5/5	1	2	FACETS	0.599	0.54	0.66	0.599	0.54	0.66	SUBCLONAL	1	TRUE	1	0.391432618424754	2		872	1050	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256427	46256427	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	90	541	0	ENST00000371998.3:c.655C>A	p.Gln219Lys	p.Q219K	ENST00000371998		219	Cag/Aag	7/23	0.276292245085464	3	FACETS	0.735	0.652	0.824	0.368	0.326	0.412	SUBCLONAL	1	TRUE	1	0.391432618424754	3		541	748	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265103	46265103	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	85	551	0	ENST00000371998.3:c.1973G>C	p.Gly658Ala	p.G658A	ENST00000371998		658	gGa/gCa	12/23	0.276292245085464	3	FACETS	0.736	0.65	0.827	0.368	0.325	0.414	SUBCLONAL	1	TRUE	1	0.391432618424754	3		551	706	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467419	66467419	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	69	375	0	ENST00000273854.3:c.850G>T	p.Val284Leu	p.V284L	ENST00000273854	NM_004439.5	284	Gtg/Ttg	3/18	1	2	FACETS	0.686	0.598	0.78	0.686	0.598	0.78	SUBCLONAL	1	TRUE	1	0.391432618424754	2		375	514	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381523	81381523	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	69	392	0	ENST00000222390.5:c.538C>A	p.Pro180Thr	p.P180T	ENST00000222390	NM_000601.4	180	Cct/Act	5/18	1	2	FACETS	0.693	0.604	0.788	0.693	0.604	0.788	SUBCLONAL	1	TRUE	1	0.391432618424754	2		392	509	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38314967	38314967	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	64	741	0	ENST00000425967.3:c.97G>T	p.Gly33Trp	p.G33W	ENST00000425967	NM_001174067.1	33	Ggg/Tgg	3/19	NA	2	FACETS	0.336	0.29	0.386			1	INDETERMINATE	1	TRUE	NA	0.391432618424754	2		741	974	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371971	55371971	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	80	353	0	ENST00000297316.4:c.661A>T	p.Thr221Ser	p.T221S	ENST00000297316	NM_022454.3	221	Acg/Tcg	2/2	0.172168939057087	3	FACETS	0.989	0.874	1	0.495	0.437	0.557	INDETERMINATE	1	TRUE	1	0.391432618424754	3		353	494	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874402	76874402	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0053220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	173	261	0	ENST00000373344.5:c.5320A>T	p.Lys1774Ter	p.K1774*	ENST00000373344	NM_000489.3	1774	Aag/Tag	21/35	0.391432618424754	2	FACETS	1	0.978	1			1	CLONAL	2	TRUE	NA	0.391432618424754	2		261	395	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0053227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	134	768	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.520669931887139	2		768	437	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0053227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	57	394	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.481	0.413	0.555	0.481	0.413	0.555	SUBCLONAL	1	TRUE	1	0.520669931887139	2		394	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576883	7576883	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	159	701	0	ENST00000269305.4:c.963del	p.Lys321AsnfsTer24	p.K321Nfs*24	ENST00000269305	NM_001126112.2	321	aaA/aa	9/11	0.490072638733355	1	FACETS	0.904	0.834	0.975	0.904	0.834	0.975	CLONAL	1	TRUE	0	0.520669931887139	1		701	500	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968251	134968251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373797543	NA	P-0053227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	91	641	1	ENST00000398015.3:c.2764G>A	p.Ala922Thr	p.A922T	ENST00000398015	NM_004441.4	922	Gcc/Acc	15/16	0.36577748775825	0	FACETS	0.439	0.392	0.487			1	SUBCLONAL	1	TRUE	0	0.520669931887139	0		642	382	SUCCESS
APC	324	MSKCC	GRCh37	5	112111364	112111364	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554071529	NA	P-0053227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	61	175	0	ENST00000257430.4:c.465del	p.Asp156ThrfsTer14	p.D156Tfs*14	ENST00000257430	NM_000038.5	154	gAa/ga	5/16	0.105430793651483	4	FACETS	1	0.946	1	0.588	0.511	0.67	INDETERMINATE	1	TRUE	2	0.520669931887139	4		175	303	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007633	45007633	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	68	229	0	ENST00000558401.1:c.81del	p.Gln28ArgfsTer16	p.Q28Rfs*16	ENST00000558401	NM_004048.2	27	aTt/at	2/4	1	2	FACETS	0.794	0.696	0.898	0.794	0.696	0.898	SUBCLONAL	1	TRUE	1	0.520669931887139	2		229	329	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075175	16075176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0053227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	137	387	0	ENST00000268712.3:c.376dup	p.Val126GlyfsTer19	p.V126Gfs*19	ENST00000268712	NM_006311.3	126	gtt/gGtt	4/46	0.490072638733355	1	FACETS	0.914	0.839	0.991	0.914	0.839	0.991	CLONAL	1	TRUE	0	0.520669931887139	1		387	426	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0053228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	373	768	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.354925790084448	5	FACETS	0.927	0.884	0.97			1	CLONAL	4	TRUE	NA	0.354925790084448	5		768	869	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628571	187628571	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs549553973	NA	P-0053228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	102	706	0	ENST00000441802.2:c.2411C>T	p.Ala804Val	p.A804V	ENST00000441802	NM_005245.3	804	gCg/gTg	2/27	0.354925790084448	3	FACETS	0.747	0.667	0.832	0.249	0.222	0.278	SUBCLONAL	1	TRUE	0	0.354925790084448	3		706	906	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557546	21557546	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	109	674	0	ENST00000382592.4:c.2299C>A	p.Leu767Met	p.L767M	ENST00000382592	NM_014572.2	767	Ctg/Atg	5/8	0.342784004203673	3	FACETS	1	0.959	1	0.564	0.507	0.624	CLONAL	1	TRUE	1	0.354925790084448	3		674	641	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162122	22162122	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	80	379	0	ENST00000215832.6:c.133A>C	p.Asn45His	p.N45H	ENST00000215832	NM_002745.4	45	Aat/Cat	2/9	0.346891651396856	3	FACETS	1	0.962	1	0.406	0.359	0.456	CLONAL	1	TRUE	0	0.354925790084448	3		379	436	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	318	1003	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.983	1	1	0.997	1	CLONAL	4	TRUE	1	0.348431672848636	2		1007	442	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	267	848	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	0.923	0.892	0.952	1	0.997	1	CLONAL	5	TRUE	1	0.348431672848636	2		848	332	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	99	489	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.224933879606839	2	FACETS	0.929	0.849	1	1	0.984	1	CLONAL	3	TRUE	0	0.348431672848636	2		494	204	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	158	741	2	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.981	1	1	0.993	1	CLONAL	2	TRUE	1	0.348431672848636	2		743	389	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740279	46740279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150315374	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	43	520	0	ENST00000371975.4:c.1759C>T	p.Arg587Trp	p.R587W	ENST00000371975	NM_003579.3	587	Cgg/Tgg	16/18	1	2	FACETS	0.619	0.518	0.729	0.619	0.518	0.729	SUBCLONAL	1	TRUE	1	0.348431672848636	2		520	399	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979987	7979987	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746723399	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	68	798	0	ENST00000319144.4:c.1350del	p.Leu451SerfsTer16	p.L451Sfs*16	ENST00000319144	NM_001139.2	450	ggG/gg	10/15	1	2	FACETS	0.745	0.649	0.848	0.745	0.649	0.848	SUBCLONAL	1	TRUE	1	0.348431672848636	2		798	524	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	135	690	0	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	1	0.937	1	1	0.991	1	CLONAL	2	TRUE	1	0.348431672848636	2		690	379	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210006	55210006	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375919121	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	133	456	0	ENST00000275493.2:c.116C>T	p.Thr39Met	p.T39M	ENST00000275493	NM_005228.3	39	aCg/aTg	2/28	0.194585135567631	5	FACETS	1	0.968	1	1	0.968	1	INDETERMINATE	3	TRUE	2	0.348431672848636	5		456	352	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923059	39923059	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	221	656	2	ENST00000378444.4:c.3649C>T	p.Arg1217Ter	p.R1217*	ENST00000378444	NM_001123385.1	1217	Cga/Tga	8/15	0.224933879606839	2	FACETS	0.983	0.929	1	1	0.993	1	CLONAL	3	TRUE	0	0.348431672848636	2		658	430	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	146	726	2	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	0.868	0.798	0.94	1	0.99	1	CLONAL	2	TRUE	1	0.348431672848636	2		728	483	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	113	535	7	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	0.348431672848636	1	FACETS	0.967	0.885	1	1	0.99	1	CLONAL	2	TRUE	0	0.348431672848636	1		542	277	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646085	215646085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	86	565	4	ENST00000260947.4:c.513del	p.Asp172MetfsTer40	p.D172Mfs*40	ENST00000260947	NM_000465.2	171	aaA/aa	4/11	0.348431672848636	1	FACETS	1	0.958	1	1	0.988	1	CLONAL	2	TRUE	0	0.348431672848636	1		569	185	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	120	550	7	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	1	0.971	1	1	0.991	1	CLONAL	2	TRUE	1	0.348431672848636	2		557	303	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196880	108196880	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	26	375	0	ENST00000278616.4:c.6908del	p.Lys2303ArgfsTer7	p.K2303Rfs*7	ENST00000278616	NM_000051.3	2301	gcA/gc	47/63	1	2	FACETS	0.574	0.456	0.708	0.574	0.456	0.708	SUBCLONAL	1	TRUE	1	0.348431672848636	2		375	260	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370236	40370236	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs761761205	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	67	868	18	ENST00000293328.3:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000293328	NM_012448.3	368	Cag/ag	9/19	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.348431672848636	2		886	344	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664761	138664761	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs797044528	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	63	316	0	ENST00000330315.3:c.804del	p.Gly269AlafsTer2	p.G269Afs*2	ENST00000330315	NM_023067.3	268	ccC/cc	1/1	1	2	FACETS	0.776	0.68	0.877	1	0.975	1	SUBCLONAL	2	TRUE	1	0.348431672848636	2		316	233	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120115	70120115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	41	119	0	ENST00000245479.2:c.1121del	p.Pro374ArgfsTer9	p.P374Rfs*9	ENST00000245479	NM_000346.3	373	Ccc/cc	3/3	1	2	FACETS	1	0.94	1	1	0.976	1	CLONAL	2	TRUE	1	0.348431672848636	2		119	99	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969983	161969983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	19	660	0	ENST00000366898.1:c.986del	p.Gly329AlafsTer106	p.G329Afs*106	ENST00000366898	NM_004562.2	329	gGc/gc	9/12	1	2	FACETS	0.331	0.251	0.426	0.331	0.251	0.426	SUBCLONAL	1	TRUE	1	0.348431672848636	2		660	329	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512402	38512402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	59	700	5	ENST00000254066.5:c.1319del	p.Pro440ArgfsTer203	p.P440Rfs*203	ENST00000254066	NM_000964.3	438	gCc/gc	9/9	1	2	FACETS	0.806	0.696	0.926	0.806	0.696	0.926	CLONAL	1	TRUE	1	0.348431672848636	2		705	420	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759406	133759406	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1371645607	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	165	722	0	ENST00000318560.5:c.1729C>T	p.Arg577Ter	p.R577*	ENST00000318560	NM_005157.4	577	Cga/Tga	11/11	1	2	FACETS	1	0.985	1	1	0.994	1	CLONAL	2	TRUE	1	0.348431672848636	2		722	385	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099409	157099426	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAA	CAGCAGCAGCAGCAGCAA	-	rs768349133	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	38	349	0	ENST00000346085.5:c.363_380del	p.Gln126_Gln131del	p.Q126_Q131del	ENST00000346085	NM_020732.3	116	CAGCAGCAGCAGCAGCAA/-	1/20	1	2	FACETS	0.852	0.709	1	0.852	0.709	1	CLONAL	1	TRUE	1	0.348431672848636	2		349	256	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	75	499	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	0.75	0.664	0.84	1	0.977	1	SUBCLONAL	2	TRUE	1	0.348431672848636	2		499	287	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953115	81953115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1336595726	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	92	333	0	ENST00000359376.3:c.2081G>A	p.Arg694His	p.R694H	ENST00000359376	NM_002661.3	694	cGc/cAc	20/33	1	2	FACETS	1	0.972	1	1	0.989	1	CLONAL	2	TRUE	1	0.348431672848636	2		333	221	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223175	36223175	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	120	1142	0	ENST00000222270.7:c.5730del	p.Arg1911AspfsTer23	p.R1911Dfs*23	ENST00000222270	NM_014727.1	1909	Ccc/cc	28/37	0.29719949759184	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.348431672848636	1		1142	443	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433388	49433388	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555191598	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	224	864	2	ENST00000301067.7:c.8059C>T	p.Arg2687Ter	p.R2687*	ENST00000301067	NM_003482.3	2687	Cga/Tga	32/54	0.264981587083451	5	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	2	0.348431672848636	5		866	572	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	274	976	1	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.264981587083451	5	FACETS	0.913	0.863	0.963	1	0.99	1	CLONAL	4	TRUE	2	0.348431672848636	5		977	656	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354436	40354436	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	32	1199	2	ENST00000293328.3:c.2159del	p.Gly720AlafsTer46	p.G720Afs*46	ENST00000293328	NM_012448.3	720	gGc/gc	18/19	1	2	FACETS	0.398	0.323	0.484	0.398	0.323	0.484	SUBCLONAL	1	TRUE	1	0.348431672848636	2		1201	461	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15975514	15975514	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	73	458	1	ENST00000268712.3:c.3840del	p.Ser1281ValfsTer16	p.S1281Vfs*16	ENST00000268712	NM_006311.3	1280	ggG/gg	29/46	1	2	FACETS	0.907	0.805	1	1	0.982	1	CLONAL	2	TRUE	1	0.348431672848636	2		459	231	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222828	36222828	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	29	909	1	ENST00000222270.7:c.5462del	p.Pro1821HisfsTer74	p.P1821Hfs*74	ENST00000222270	NM_014727.1	1819	gaC/ga	27/37	0.29719949759184	1	FACETS	0.32	0.256	0.392	0.32	0.256	0.392	SUBCLONAL	1	TRUE	0	0.348431672848636	1		910	430	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606899	43606899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1226167606	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	166	941	1	ENST00000355710.3:c.1508C>T	p.Thr503Ile	p.T503I	ENST00000355710	NM_020975.4	503	aCa/aTa	7/20	1	2	FACETS	1	0.973	1	1	0.993	1	CLONAL	2	TRUE	1	0.348431672848636	2		942	434	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140487359	140487359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs577372072	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	107	495	0	ENST00000288602.6:c.1166G>A	p.Arg389His	p.R389H	ENST00000288602	NM_004333.4	389	cGt/cAt	9/18	0.264981587083451	5	FACETS	1	0.947	1	1	0.985	1	CLONAL	4	TRUE	2	0.348431672848636	5		495	224	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669430	241669430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1044975651	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	72	313	0	ENST00000366560.3:c.777G>A	p.Met259Ile	p.M259I	ENST00000366560	NM_000143.3	259	atG/atA	6/10	1	2	FACETS	1	0.933	1	1	0.985	1	CLONAL	2	TRUE	1	0.348431672848636	2		313	194	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793708	89793709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	54	364	0	ENST00000336032.3:c.782dup	p.Asn261LysfsTer12	p.N261Kfs*12	ENST00000336032	NM_006813.2	259	-/A	2/2	1	2	FACETS	0.876	0.761	0.996	1	0.975	1	CLONAL	2	TRUE	1	0.348431672848636	2		364	177	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877420	89877420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769824282	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	176	673	0	ENST00000389301.3:c.343G>A	p.Gly115Arg	p.G115R	ENST00000389301	NM_000135.2	115	Ggg/Agg	4/43	1	2	FACETS	1	0.984	1	1	0.994	1	CLONAL	2	TRUE	1	0.348431672848636	2		673	426	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37059062	37059062	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63750034	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	72	475	1	ENST00000231790.2:c.860del	p.Asn287ThrfsTer10	p.N287Tfs*10	ENST00000231790	NM_000249.3	286	Aaa/aa	10/19	1	2	FACETS	0.814	0.72	0.912	1	0.979	1	CLONAL	2	TRUE	1	0.348431672848636	2		476	254	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932026	36932026	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	43	861	0	ENST00000361632.4:c.2443C>T	p.Pro815Ser	p.P815S	ENST00000361632		815	Cca/Tca	16/16	1	2	FACETS	0.496	0.414	0.586	0.496	0.414	0.586	SUBCLONAL	1	TRUE	1	0.348431672848636	2		861	498	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231300	46231300	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1482694206	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	15	374	0	ENST00000334344.6:c.1140T>A	p.Asn380Lys	p.N380K	ENST00000334344	NM_152641.2	380	aaT/aaA	10/21	0.264981587083451	5	FACETS	0.917	0.675	1	0.306	0.225	0.401	CLONAL	1	TRUE	2	0.348431672848636	5		374	143	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434309	49434309	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	36	958	1	ENST00000301067.7:c.7244C>A	p.Pro2415His	p.P2415H	ENST00000301067	NM_003482.3	2415	cCt/cAt	31/54	0.264981587083451	5	FACETS	0.461	0.377	0.554	0.154	0.125	0.185	SUBCLONAL	1	TRUE	2	0.348431672848636	5		959	683	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089878	16089878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1351588347	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	76	323	1	ENST00000268712.3:c.232G>A	p.Gly78Ser	p.G78S	ENST00000268712	NM_006311.3	78	Ggt/Agt	3/46	1	2	FACETS	0.913	0.812	1	1	0.983	1	CLONAL	2	TRUE	1	0.348431672848636	2		324	239	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556462	29556463	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	66	390	0	ENST00000356175.3:c.2835dup	p.Asp946Ter	p.D946*	ENST00000356175	NM_000267.3	943	-/T	21/57	1	2	FACETS	1	0.891	1	1	0.983	1	CLONAL	2	TRUE	1	0.348431672848636	2		390	188	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210592	5210592	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	16	728	0	ENST00000357368.4:c.5375A>G	p.Gln1792Arg	p.Q1792R	ENST00000357368	NM_002850.3	1792	cAg/cGg	35/38	0.348431672848636	1	FACETS	0.242	0.178	0.318	0.242	0.178	0.318	SUBCLONAL	1	TRUE	0	0.348431672848636	1		728	314	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289686	15289686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143684274	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	181	1000	0	ENST00000263388.2:c.3785G>A	p.Arg1262His	p.R1262H	ENST00000263388	NM_000435.2	1262	cGt/cAt	23/33	0.29719949759184	1	FACETS	0.984	0.918	1	1	0.993	1	CLONAL	2	TRUE	0	0.348431672848636	1		1000	436	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221448	36221448	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768632549	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	192	895	0	ENST00000222270.7:c.5207G>A	p.Arg1736His	p.R1736H	ENST00000222270	NM_014727.1	1736	cGc/cAc	25/37	0.29719949759184	1	FACETS	1	0.957	1	1	0.994	1	CLONAL	2	TRUE	0	0.348431672848636	1		895	442	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215617231	215617231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	62	370	2	ENST00000260947.4:c.1617G>A	p.Met539Ile	p.M539I	ENST00000260947	NM_000465.2	539	atG/atA	7/11	0.348431672848636	1	FACETS	1	0.946	1	1	0.984	1	CLONAL	2	TRUE	0	0.348431672848636	1		372	133	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053324	37053324	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	35	348	0	ENST00000231790.2:c.560del	p.Asn187MetfsTer15	p.N187Mfs*15	ENST00000231790	NM_000249.3	187	Aat/at	7/19	1	2	FACETS	1	0.864	1	1	0.968	1	CLONAL	2	TRUE	1	0.348431672848636	2		348	98	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204700	128204700	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	159	904	0	ENST00000341105.2:c.741del	p.Thr248ProfsTer78	p.T248Pfs*78	ENST00000341105	NM_032638.4	247	ccC/cc	3/6	1	2	FACETS	0.953	0.88	1	1	0.992	1	CLONAL	2	TRUE	1	0.348431672848636	2		904	479	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588095	67588095	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	52	272	0	ENST00000274335.5:c.926del	p.Pro309LeufsTer9	p.P309Lfs*9	ENST00000274335		309	Cct/ct	7/15	0.348431672848636	3	FACETS	1	0.906	1	1	0.974	1	CLONAL	3	TRUE	1	0.348431672848636	3		272	113	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149450087	149450087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	108	851	0	ENST00000286301.3:c.1130G>A	p.Gly377Asp	p.G377D	ENST00000286301	NM_005211.3	377	gGc/gAc	8/22	0.224933879606839	2	FACETS	1	0.969	1	0.596	0.537	0.658	CLONAL	1	TRUE	0	0.348431672848636	2		851	520	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056211	26056211	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs754239517	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	26	511	0	ENST00000343677.2:c.446A>C	p.Lys149Thr	p.K149T	ENST00000343677	NM_005319.3	149	aAg/aCg	1/1	0.323622004692405	4	FACETS	0.553	0.438	0.685	0.276	0.219	0.343	SUBCLONAL	1	TRUE	2	0.348431672848636	4		511	364	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671630	30671630	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	20	732	0	ENST00000376406.3:c.5330A>G	p.Gln1777Arg	p.Q1777R	ENST00000376406	NM_014641.2	1777	cAg/cGg	10/15	1	2	FACETS	0.294	0.224	0.376	0.294	0.224	0.376	SUBCLONAL	1	TRUE	1	0.348431672848636	2		732	391	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169952	32169952	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs151325272	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	63	1038	1	ENST00000375023.3:c.3656G>T	p.Arg1219Leu	p.R1219L	ENST00000375023	NM_004557.3	1219	cGg/cTg	21/30	1	2	FACETS	0.776	0.673	0.888	0.776	0.673	0.888	SUBCLONAL	1	TRUE	1	0.348431672848636	2		1039	466	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494216	140494216	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	164	708	0	ENST00000288602.6:c.1032G>T	p.Gln344His	p.Q344H	ENST00000288602	NM_004333.4	344	caG/caT	8/18	0.264981587083451	5	FACETS	1	0.984	1	0.829	0.766	0.895	CLONAL	2	TRUE	2	0.348431672848636	5		708	576	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168910	32168910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1220425760	NA	P-0053232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	263	831	4	ENST00000375023.3:c.4123G>A	p.Asp1375Asn	p.D1375N	ENST00000375023	NM_004557.3	1375	Gac/Aac	22/30	0.924335364298456	3	FACETS	1	0.983	1	0.558	0.525	0.591	CLONAL	1	TRUE	1	0.924335364298456	3		835	746	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101212	27101213	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	CT	novel	NA	P-0053232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	230	799	2	ENST00000324856.7:c.4494_4495delinsCT	p.Trp1498_Gln1499delinsCysTer	p.W1498_Q1499delinsC*	ENST00000324856	NM_006015.4	1498	tgGCag/tgCTag	18/20	0.433614002756595	2	FACETS	0.946	0.918	0.971	0.946	0.918	0.971	INDETERMINATE	2	TRUE	0	0.924335364298456	2		801	263	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265532	152265532	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs768809292	NA	P-0053232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	280	654	0	ENST00000206249.3:c.985T>G	p.Ser329Ala	p.S329A	ENST00000206249	NM_000125.3	329	Tcc/Gcc	4/8	0.924335364298456	1	FACETS	0.368	0.346	0.39	0.368	0.346	0.39	SUBCLONAL	1	TRUE	0	0.924335364298456	1		654	885	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231148	53231148	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	54	518	0	ENST00000375401.3:c.1754G>C	p.Arg585Pro	p.R585P	ENST00000375401	NM_004187.3	585	cGc/cCc	13/26	0.80842148507269	1	FACETS	0.274	0.237	0.315	0.274	0.237	0.315	SUBCLONAL	1	TRUE	0	0.924335364298456	1		518	229	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0053238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	263	286	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.547936240142165	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.547936240142165	3		286	564	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692893	89692893	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	120	403	0	ENST00000371953.3:c.377C>A	p.Ala126Asp	p.A126D	ENST00000371953	NM_000314.4	126	gCt/gAt	5/9	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.547936240142165	2		403	427	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977949	134977949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56186270	NA	P-0053238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	119	538	0	ENST00000398015.3:c.2942C>T	p.Thr981Met	p.T981M	ENST00000398015	NM_004441.4	981	aCg/aTg	16/16	0.547936240142165	3	FACETS	0.72	0.65	0.793	0.36	0.325	0.397	SUBCLONAL	1	TRUE	1	0.547936240142165	3		538	769	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685304	89685305	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1060500113	NA	P-0053238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	32	260	0	ENST00000371953.3:c.200dup	p.Tyr68IlefsTer6	p.Y68Ifs*6	ENST00000371953	NM_000314.4	67	ata/aTta	3/9	1	2	FACETS	0.358	0.291	0.434	0.358	0.291	0.434	SUBCLONAL	1	TRUE	1	0.547936240142165	2		260	326	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644661	134644661	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376895227	NA	P-0053238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	254	474	1	ENST00000398015.3:c.62C>T	p.Thr21Met	p.T21M	ENST00000398015	NM_004441.4	21	aCg/aTg	2/16	0.547936240142165	3	FACETS	0.968	0.913	1	0.968	0.913	1	CLONAL	2	TRUE	1	0.547936240142165	3		475	610	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81922843	81922843	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs988595873	NA	P-0053240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	111	596	2	ENST00000359376.3:c.832C>T	p.Arg278Cys	p.R278C	ENST00000359376	NM_002661.3	278	Cgt/Tgt	10/33	0.613465526632016	3	FACETS	0.694	0.625	0.767	0.347	0.312	0.384	SUBCLONAL	1	TRUE	1	0.658411984537481	3		598	646	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0053241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	10	274	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.283420606884172	3	FACETS	0.143	0.096	0.202	0.071	0.048	0.101	SUBCLONAL	1	TRUE	1	0.388122346585434	3		274	431	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0053241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	264	500	2	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.354057563141476	4	FACETS	0.957	0.903	1	0.957	0.903	1	CLONAL	3	TRUE	1	0.388122346585434	4		502	658	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610109	10610109	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	276	872	0	ENST00000171111.5:c.601C>T	p.Gln201Ter	p.Q201*	ENST00000171111	NM_203500.1	201	Cag/Tag	2/6	0.388122346585434	2	FACETS	0.973	0.918	1	0.973	0.918	1	CLONAL	2	TRUE	0	0.388122346585434	2		872	731	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219412	1219413	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	TT	novel	NA	P-0053241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	169	436	1	ENST00000326873.7:c.464_464+1delinsTT		p.X155_splice	ENST00000326873	NM_000455.4	155		3/10	0.388122346585434	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.388122346585434	2		437	422	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0053242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	195	430	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.334626200626427	3	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	1	0.340060766429596	3		430	661	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435895	149435895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397515556	NA	P-0053242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	105	570	1	ENST00000286301.3:c.2329C>T	p.Arg777Trp	p.R777W	ENST00000286301	NM_005211.3	777	Cgg/Tgg	18/22	0.334626200626427	3	FACETS	0.866	0.776	0.963	0.433	0.388	0.482	CLONAL	1	TRUE	1	0.340060766429596	3		571	834	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124204	2124204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45517231	NA	P-0053242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	149	708	0	ENST00000219476.3:c.2359G>A	p.Glu787Lys	p.E787K	ENST00000219476	NM_000548.3	787	Gag/Aag	22/42	0.334626200626427	3	FACETS	1	0.923	1	0.506	0.462	0.553	CLONAL	1	TRUE	1	0.340060766429596	3		708	1013	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259323	36259324	+	missense_variant	Missense_Mutation	DNP	CA	CA	TG	novel	NA	P-0053242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	119	136	99	ENST00000300305.3:c.167_168inv	p.Leu56Ser	p.L56S	ENST00000300305		56	tTG/tCA	3/8	1	2	FACETS	1	0.975	1	1	0.991	1	CLONAL	2	TRUE	1	0.340060766429596	2		235	300	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	37	429	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.957	0.812	1			1	INDETERMINATE	1	TRUE	NA	0.758306902899575	2		429	102	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929157	44929157	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	238	561	0	ENST00000377967.4:c.2257C>T	p.Gln753Ter	p.Q753*	ENST00000377967	NM_021140.2	753	Cag/Tag	17/29	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.758306902899575	2		561	520	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729636	41729636	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	59	637	1	ENST00000242208.4:c.893G>A	p.Arg298Gln	p.R298Q	ENST00000242208	NM_002192.2	298	cGg/cAg	3/3	0.503119089458751	4	FACETS	0.418	0.359	0.482	0.139	0.119	0.161	SUBCLONAL	1	TRUE	1	0.758306902899575	4		638	655	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39647425	39647425	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	69	498	0	ENST00000262039.4:c.2597G>C	p.Ser866Thr	p.S866T	ENST00000262039	NM_002647.2	866	aGt/aCt	24/25	1	2	FACETS	0.364	0.317	0.414	0.364	0.317	0.414	SUBCLONAL	1	TRUE	1	0.758306902899575	2		498	500	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522714	67522715	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAACTTACGA	novel	NA	P-0053243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	98	187	0	ENST00000274335.5:c.220_221insAGAACTTACG	p.Val74GlufsTer35	p.V74Efs*35	ENST00000274335		71	gga/gGAACTTACGAga	1/15	1	2	FACETS	0.99	0.898	1	0.99	0.898	1	CLONAL	1	TRUE	1	0.758306902899575	2		187	261	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100298	157100298	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	92	219	1	ENST00000346085.5:c.1235C>A	p.Pro412Gln	p.P412Q	ENST00000346085	NM_020732.3	412	cCg/cAg	1/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.758306902899575	2		220	190	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	83	429	0				ENST00000310581	NM_198253.2	-/1132			0.758187903576634	3	FACETS	0.896	0.798	0.999	0.448	0.399	0.5	CLONAL	1	TRUE	1	0.758187903576634	3		429	337	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	201	411	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.758187903576634	2		411	524	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489571	56489571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	257	469	0	ENST00000267101.3:c.2036G>A	p.Arg679Gln	p.R679Q	ENST00000267101	NM_001982.3	679	cGa/cAa	17/28	1	2	FACETS	0.966	0.909	1	0.966	0.909	1	CLONAL	1	TRUE	1	0.758187903576634	2		469	702	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054660	5054660	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1466480406	NA	P-0053244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	123	248	0	ENST00000381652.3:c.712C>T	p.Gln238Ter	p.Q238*	ENST00000381652	NM_004972.3	238	Cag/Tag	7/25	0.758187903576634	3	FACETS	0.911	0.829	0.997	0.456	0.414	0.499	CLONAL	1	TRUE	1	0.758187903576634	3		248	491	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102121	27102121	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	298	604	1	ENST00000324856.7:c.5047G>T	p.Glu1683Ter	p.E1683*	ENST00000324856	NM_006015.4	1683	Gag/Tag	19/20	1	2	FACETS	0.988	0.934	1	0.988	0.934	1	CLONAL	1	TRUE	1	0.758187903576634	2		605	796	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118350924	118350924	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	149	310	0	ENST00000534358.1:c.3605C>T	p.Ser1202Phe	p.S1202F	ENST00000534358	NM_005933.3	1202	tCc/tTc	6/36	1	2	FACETS	0.875	0.807	0.946	0.875	0.807	0.946	CLONAL	1	TRUE	1	0.758187903576634	2		310	449	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135250	2135250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567528487	NA	P-0053244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	473	1003	0	ENST00000219476.3:c.4589C>T	p.Ser1530Leu	p.S1530L	ENST00000219476	NM_000548.3	1530	tCg/tTg	36/42	1	2	FACETS	0.938	0.897	0.98	0.938	0.897	0.98	CLONAL	1	TRUE	1	0.758187903576634	2		1003	1330	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796027	78796027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1209272303	NA	P-0053244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	385	806	0	ENST00000306801.3:c.917G>A	p.Arg306Lys	p.R306K	ENST00000306801	NM_020761.2	306	aGg/aAg	8/34	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.758187903576634	2		806	925	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879679	151879679	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	95	162	0	ENST00000262189.6:c.5266C>T	p.Gln1756Ter	p.Q1756*	ENST00000262189	NM_170606.2	1756	Caa/Taa	36/59	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.758187903576634	2		162	249	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930115	68930115	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0053244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	168	330	0	ENST00000288368.4:c.176C>G	p.Ser59Ter	p.S59*	ENST00000288368	NM_024870.2	59	tCa/tGa	2/40	0.758187903576634	4	FACETS	0.862	0.792	0.935	0.287	0.264	0.312	CLONAL	1	TRUE	1	0.758187903576634	4		330	904	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197045	123197045	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1569515797	NA	P-0053244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	143	120	0	ENST00000218089.9:c.1811G>A	p.Arg604Gln	p.R604Q	ENST00000218089	NM_001042749.1	604	cGa/cAa	19/35	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.758187903576634	1		120	194	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333266	70333266	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	34	722	0	ENST00000373644.4:c.1171G>A	p.Glu391Lys	p.E391K	ENST00000373644	NM_030625.2	391	Gag/Aag	2/12	1	2	FACETS	0.73	0.597	0.88	0.73	0.597	0.88	SUBCLONAL	1	TRUE	1	0.23	2		722	405	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61712950	61712950	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	24	559	0	ENST00000401558.2:c.2461C>G	p.Gln821Glu	p.Q821E	ENST00000401558	NM_003400.3	821	Caa/Gaa	20/25	0.0316357217321075	3	FACETS	0.966	0.76	1	0.483	0.38	0.601	INDETERMINATE	1	TRUE	1	0.23	3		559	241	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900245	101900245	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502042	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	34	422	0	ENST00000374994.4:c.679G>A	p.Glu227Lys	p.E227K	ENST00000374994	NM_004612.2	227	Gaa/Aaa	4/9	0.3	1	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	0	0.23	1		422	218	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481859	56481859	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	55	777	1	ENST00000267101.3:c.787C>G	p.Leu263Val	p.L263V	ENST00000267101	NM_001982.3	263	Ctt/Gtt	7/28	0.0316357217321075	3	FACETS	1	0.951	1	0.633	0.543	0.731	INDETERMINATE	1	TRUE	1	0.23	3		778	421	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044719	47044719	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	60	1064	1	ENST00000377604.3:c.2119C>T	p.Gln707Ter	p.Q707*	ENST00000377604	NM_001204468.1	707	Cag/Tag	19/24	0.3	1	FACETS	0.923	0.797	1	0.923	0.797	1	CLONAL	1	TRUE	0	0.23	1		1065	500	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880494	155880494	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778233462	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	35	734	0	ENST00000368323.3:c.59G>A	p.Arg20Gln	p.R20Q	ENST00000368323	NM_006912.5	20	cGg/cAg	2/6	1	2	FACETS	0.564	0.461	0.679	0.564	0.461	0.679	SUBCLONAL	1	TRUE	1	0.23	2		734	540	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510806	157510806	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	41	655	1	ENST00000346085.5:c.3586del	p.Gln1196SerfsTer15	p.Q1196Sfs*15	ENST00000346085	NM_020732.3	1194	aCc/ac	14/20	1	2	FACETS	0.803	0.669	0.952	0.803	0.669	0.952	CLONAL	1	TRUE	1	0.23	2		656	444	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106159	27106159	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	21	598	0	ENST00000324856.7:c.5770G>T	p.Glu1924Ter	p.E1924*	ENST00000324856	NM_006015.4	1924	Gag/Tag	20/20	1	2	FACETS	0.532	0.41	0.676	0.532	0.41	0.676	SUBCLONAL	1	TRUE	1	0.23	2		598	343	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636758	8636758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	31	547	0	ENST00000356435.5:c.151C>T	p.Pro51Ser	p.P51S	ENST00000356435		51	Cca/Tca	2/35	0.3	1	FACETS	0.803	0.652	0.974	0.803	0.652	0.974	CLONAL	1	TRUE	0	0.23	1		547	297	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399799	139399799	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554727954	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	28	918	2	ENST00000277541.6:c.4549G>A	p.Asp1517Asn	p.D1517N	ENST00000277541	NM_017617.3	1517	Gac/Aac	25/34	0.3	1	FACETS	0.423	0.337	0.521	0.423	0.337	0.521	SUBCLONAL	1	TRUE	0	0.23	1		920	510	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	52	647	1	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.23	2		648	323	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411197	63411197	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	52	783	0	ENST00000330258.3:c.1970G>T	p.Arg657Met	p.R657M	ENST00000330258	NM_152424.3	657	aGg/aTg	2/2	0.3	1	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	0	0.23	1		783	391	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949089	71949089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	93	972	1	ENST00000298229.2:c.3556C>T	p.Pro1186Ser	p.P1186S	ENST00000298229	NM_001567.3	1186	Ccg/Tcg	27/28	1	2	FACETS	0.839	0.749	0.934	1	0.983	1	CLONAL	2	TRUE	1	0.23	2		973	482	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858288	9858288	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	15	506	0	ENST00000330684.3:c.3113C>G	p.Thr1038Arg	p.T1038R	ENST00000330684	NM_001134407.1	1038	aCa/aGa	13/13	0.3	1	FACETS	0.545	0.399	0.719	0.545	0.399	0.719	SUBCLONAL	1	TRUE	0	0.23	1		506	212	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473672	67473672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	58	740	0	ENST00000327367.4:c.752C>T	p.Ser251Leu	p.S251L	ENST00000327367	NM_005902.3	251	tCg/tTg	6/9	0.3	1	FACETS	0.868	0.747	1	0.868	0.747	1	CLONAL	1	TRUE	0	0.23	1		740	514	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566418	139566418	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	81	956	0	ENST00000308874.7:c.677C>A	p.Ser226Ter	p.S226*	ENST00000308874		226	tCg/tAg	9/10	0.3	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.23	1		956	499	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789696	3789696	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs761058155	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	14	555	0	ENST00000262367.5:c.4163C>G	p.Ser1388Cys	p.S1388C	ENST00000262367	NM_004380.2	1388	tCt/tGt	25/31	0.3	1	FACETS	0.418	0.301	0.558	0.418	0.301	0.558	SUBCLONAL	1	TRUE	0	0.23	1		555	258	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600335	10600335	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1339695646	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	75	745	0	ENST00000171111.5:c.1520G>A	p.Arg507Gln	p.R507Q	ENST00000171111	NM_203500.1	507	cGa/cAa	4/6	0.3	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.23	1		745	430	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028004	48028004	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	10	372	0	ENST00000234420.5:c.2882G>A	p.Arg961Lys	p.R961K	ENST00000234420	NM_000179.2	961	aGa/aAa	4/10	0.0316357217321075	3	FACETS	0.487	0.33	0.685	0.244	0.165	0.343	INDETERMINATE	1	TRUE	1	0.23	3		372	199	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81979789	81979789	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781497956	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	18	514	0	ENST00000359376.3:c.3491C>T	p.Ser1164Phe	p.S1164F	ENST00000359376	NM_002661.3	1164	tCc/tTc	31/33	0.3	1	FACETS	0.425	0.319	0.55	0.425	0.319	0.55	SUBCLONAL	1	TRUE	0	0.23	1		514	326	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046245	128046245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	24	444	0	ENST00000285398.2:c.1018C>T	p.Leu340Phe	p.L340F	ENST00000285398	NM_000122.1	340	Ctt/Ttt	7/15	0.0316357217321075	3	FACETS	0.695	0.545	0.867	0.347	0.272	0.434	INDETERMINATE	1	TRUE	1	0.23	3		444	335	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225554	133225554	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	38	930	0	ENST00000320574.5:c.4110G>T	p.Gln1370His	p.Q1370H	ENST00000320574	NM_006231.2	1370	caG/caT	32/49	0.3	1	FACETS	0.569	0.47	0.68	0.569	0.47	0.68	SUBCLONAL	1	TRUE	0	0.23	1		930	514	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864552	57864552	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	42	962	0	ENST00000228682.2:c.2029G>C	p.Asp677His	p.D677H	ENST00000228682	NM_005269.2	677	Gat/Cat	12/12	0.0316357217321075	3	FACETS	0.8	0.668	0.947	0.4	0.334	0.474	INDETERMINATE	1	TRUE	1	0.23	3		962	509	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953288	17953288	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	61	1176	1	ENST00000458235.1:c.698C>T	p.Ser233Leu	p.S233L	ENST00000458235	NM_000215.3	233	tCg/tTg	6/24	0.3	1	FACETS	0.891	0.769	1	0.891	0.769	1	CLONAL	1	TRUE	0	0.23	1		1177	527	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094325	27094325	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1553152590	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	29	485	0	ENST00000324856.7:c.3033G>T	p.Leu1011Phe	p.L1011F	ENST00000324856	NM_006015.4	1011	ttG/ttT	11/20	1	2	FACETS	0.733	0.589	0.897	0.733	0.589	0.897	SUBCLONAL	1	TRUE	1	0.23	2		485	344	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36824360	36824360	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	55	683	0	ENST00000373129.3:c.176C>A	p.Thr59Lys	p.T59K	ENST00000373129	NM_032017.1	59	aCg/aAg	4/12	1	2	FACETS	0.98	0.839	1	0.98	0.839	1	CLONAL	1	TRUE	1	0.23	2		683	488	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937141	36937141	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	71	1024	0	ENST00000361632.4:c.1178T>A	p.Leu393His	p.L393H	ENST00000361632		393	cTc/cAc	9/16	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.23	2		1024	546	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166191	118166191	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	28	447	0	ENST00000369448.3:c.701A>T	p.Lys234Met	p.K234M	ENST00000369448	NM_017709.3	234	aAg/aTg	2/2	1	2	FACETS	0.727	0.581	0.892	0.727	0.581	0.892	SUBCLONAL	1	TRUE	1	0.23	2		447	335	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841548	156841548	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	71	925	2	ENST00000524377.1:c.850+1G>T		p.X284_splice	ENST00000524377	NM_002529.3	284			1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.23	2		927	507	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845892	156845892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200575096	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	70	1009	2	ENST00000524377.1:c.1522C>T	p.Arg508Trp	p.R508W	ENST00000524377	NM_002529.3	508	Cgg/Tgg	13/17	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.23	2		1011	608	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156620	2156620	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	65	830	0	ENST00000434045.2:c.302G>T	p.Cys101Phe	p.C101F	ENST00000434045	NM_001127598.1	101	tGt/tTt	3/5	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.23	2		830	421	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21630864	21630864	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	49	614	0	ENST00000421138.2:c.740A>C	p.Asn247Thr	p.N247T	ENST00000421138		247	aAc/aCc	8/16	0.0316357217321075	3	FACETS	1	0.962	1	0.738	0.628	0.857	INDETERMINATE	1	TRUE	1	0.23	3		614	322	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913071	32913071	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	24	554	0	ENST00000380152.3:c.4579G>C	p.Ala1527Pro	p.A1527P	ENST00000380152		1527	Gct/Cct	11/27	0.283401424457682	3	FACETS	0.92	0.723	1	0.46	0.361	0.573	CLONAL	1	TRUE	1	0.23	3		554	253	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435657	110435657	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	54	692	0	ENST00000375856.3:c.2744G>C	p.Ser915Thr	p.S915T	ENST00000375856	NM_003749.2	915	aGc/aCc	1/2	0.283401424457682	3	FACETS	1	0.914	1	0.55	0.47	0.637	CLONAL	1	TRUE	1	0.23	3		692	476	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669568	88669568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	25	504	1	ENST00000360948.2:c.1330G>A	p.Val444Ile	p.V444I	ENST00000360948	NM_001012338.2	444	Gtc/Atc	12/19	0.3	1	FACETS	0.776	0.614	0.961	0.776	0.614	0.961	CLONAL	1	TRUE	0	0.23	1		505	248	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633447	3633447	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	77	1000	1	ENST00000294008.3:c.4804A>T	p.Thr1602Ser	p.T1602S	ENST00000294008	NM_032444.2	1602	Act/Tct	14/15	0.3	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.23	1		1001	544	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614908	23614908	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs180177137	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	33	514	1	ENST00000261584.4:c.3433G>T	p.Gly1145Cys	p.G1145C	ENST00000261584	NM_024675.3	1145	Ggt/Tgt	13/13	0.3	1	FACETS	0.804	0.656	0.969	0.804	0.656	0.969	CLONAL	1	TRUE	0	0.23	1		515	316	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870637	40870637	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	62	553	0	ENST00000428826.2:c.768-2A>G		p.X256_splice	ENST00000428826		256			1	2	FACETS	0.89	0.775	1	1	0.977	1	CLONAL	2	TRUE	1	0.23	2		553	303	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857639	59857639	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	31	310	0	ENST00000259008.2:c.1918A>T	p.Ile640Phe	p.I640F	ENST00000259008	NM_032043.2	640	Atc/Ttc	13/20	1	2	FACETS	0.853	0.699	1	1	0.954	1	CLONAL	2	TRUE	1	0.23	2		310	158	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39535261	39535261	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	17	335	0	ENST00000262039.4:c.5G>T	p.Gly2Val	p.G2V	ENST00000262039	NM_002647.2	2	gGg/gTg	1/25	1	2	FACETS	0.621	0.464	0.807	0.621	0.464	0.807	SUBCLONAL	1	TRUE	1	0.23	2		335	238	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273588	5273588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	47	518	0	ENST00000357368.4:c.244G>A	p.Glu82Lys	p.E82K	ENST00000357368	NM_002850.3	82	Gag/Aag	4/38	0.3	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.23	1		518	295	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31393148	31393148	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139777286	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	73	467	0	ENST00000328111.2:c.2236G>A	p.Val746Met	p.V746M	ENST00000328111	NM_006892.3	746	Gtg/Atg	21/23	1	2	FACETS	1	0.906	1	1	0.983	1	CLONAL	2	TRUE	1	0.23	2		467	308	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275028	41275028	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	14	390	0	ENST00000349496.5:c.1194G>T	p.Met398Ile	p.M398I	ENST00000349496	NM_001904.3	398	atG/atT	9/15	1	2	FACETS	0.658	0.477	0.876	0.658	0.477	0.876	SUBCLONAL	1	TRUE	1	0.23	2		390	185	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436323	52436323	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	65	885	0	ENST00000460680.1:c.2171A>T	p.Tyr724Phe	p.Y724F	ENST00000460680	NM_004656.3	724	tAc/tTc	17/17	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.23	2		885	408	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799628	72799628	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	46	616	0	ENST00000325599.8:c.1541C>A	p.Ala514Asp	p.A514D	ENST00000325599	NM_018130.2	514	gCc/gAc	11/11	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.23	2		616	363	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430462	181430462	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	68	970	0	ENST00000325404.1:c.314A>T	p.His105Leu	p.H105L	ENST00000325404	NM_003106.3	105	cAc/cTc	1/1	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.23	2		970	544	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1932356	1932356	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	15	488	0	ENST00000382891.5:c.1414G>T	p.Val472Leu	p.V472L	ENST00000382891	NM_133335.3	472	Gta/Tta	6/22	0.3	0	FACETS	0.361	0.264	0.479			1	SUBCLONAL	1	TRUE	0	0.23	0		488	278	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152036	55152036	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	21	652	0	ENST00000257290.5:c.2468A>T	p.Asn823Ile	p.N823I	ENST00000257290	NM_006206.4	823	aAc/aTc	18/23	0.3	1	FACETS	0.412	0.317	0.524	0.412	0.317	0.524	SUBCLONAL	1	TRUE	0	0.23	1		652	392	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753402	57753402	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	13	444	0	ENST00000274289.3:c.722G>C	p.Cys241Ser	p.C241S	ENST00000274289	NM_006622.3	241	tGt/tCt	6/14	1	2	FACETS	0.744	0.533	0.998	0.744	0.533	0.998	CLONAL	1	TRUE	1	0.23	2		444	152	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520462	176520462	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	41	1025	0	ENST00000292408.4:c.1307T>A	p.Val436Glu	p.V436E	ENST00000292408	NM_213647.1	436	gTg/gAg	10/18	0.3	1	FACETS	0.611	0.509	0.726	0.611	0.509	0.726	SUBCLONAL	1	TRUE	0	0.23	1		1025	516	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170124	32170124	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	64	1087	0	ENST00000375023.3:c.3484C>A	p.Pro1162Thr	p.P1162T	ENST00000375023	NM_004557.3	1162	Cct/Act	21/30	0.283401424457682	3	FACETS	0.947	0.82	1	0.474	0.41	0.543	CLONAL	1	TRUE	1	0.23	3		1087	655	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171991	32171991	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	59	719	2	ENST00000375023.3:c.3041C>A	p.Pro1014His	p.P1014H	ENST00000375023	NM_004557.3	1014	cCc/cAc	19/30	0.283401424457682	3	FACETS	1	0.912	1	0.541	0.465	0.623	CLONAL	1	TRUE	1	0.23	3		721	529	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394450	162394450	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	10	360	0	ENST00000366898.1:c.619-1G>T		p.X207_splice	ENST00000366898	NM_004562.2	207			1	2	FACETS	0.527	0.357	0.739	0.527	0.357	0.739	SUBCLONAL	1	TRUE	1	0.23	2		360	165	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846404	128846404	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	50	743	0	ENST00000249373.3:c.1240G>C	p.Val414Leu	p.V414L	ENST00000249373	NM_005631.4	414	Gtg/Ctg	6/12	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.23	2		743	391	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270511	98270511	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	56	534	0	ENST00000331920.6:c.133C>G	p.Pro45Ala	p.P45A	ENST00000331920	NM_000264.3	45	Ccg/Gcg	1/24	0.3	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.23	1		534	364	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933706	39933706	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	31	780	0	ENST00000378444.4:c.893C>T	p.Pro298Leu	p.P298L	ENST00000378444	NM_001123385.1	298	cCt/cTt	4/15	0.3	1	FACETS	0.605	0.49	0.737	0.605	0.49	0.737	SUBCLONAL	1	TRUE	0	0.23	1		780	394	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411079	63411079	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	53	793	0	ENST00000330258.3:c.2088G>T	p.Arg696Ser	p.R696S	ENST00000330258	NM_152424.3	696	agG/agT	2/2	0.3	1	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	0	0.23	1		793	382	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163615	32163615	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1435864899	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	75	332	1	ENST00000375023.3:c.5611C>T	p.Arg1871Cys	p.R1871C	ENST00000375023	NM_004557.3	1871	Cgt/Tgt	30/30	0.283401424457682	3	FACETS	1	0.957	1	0.605	0.53	0.685	CLONAL	1	TRUE	1	0.23	3		333	601	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491335	2491335	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	48	1137	0	ENST00000355716.4:c.378C>G	p.Phe126Leu	p.F126L	ENST00000355716	NM_003820.2	126	ttC/ttG	4/8	1	2	FACETS	0.682	0.576	0.799	0.682	0.576	0.799	SUBCLONAL	1	TRUE	1	0.23	2		1137	612	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119499	193119499	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	19	348	0	ENST00000367435.3:c.894C>G	p.Phe298Leu	p.F298L	ENST00000367435	NM_024529.4	298	ttC/ttG	9/17	1	2	FACETS	0.674	0.513	0.864	0.674	0.513	0.864	SUBCLONAL	1	TRUE	1	0.23	2		348	245	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650036	206650036	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	61	586	0	ENST00000367120.3:c.556G>C	p.Glu186Gln	p.E186Q	ENST00000367120	NM_014002.3	186	Gag/Cag	7/22	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.23	2		586	423	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567716	226567716	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	39	756	0	ENST00000366794.5:c.1450G>C	p.Glu484Gln	p.E484Q	ENST00000366794	NM_001618.3	484	Gag/Cag	10/23	1	2	FACETS	0.63	0.522	0.752	0.63	0.522	0.752	SUBCLONAL	1	TRUE	1	0.23	2		756	538	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690822	89690822	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1554897867	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	12	412	0	ENST00000371953.3:c.229G>C	p.Asp77His	p.D77H	ENST00000371953	NM_000314.4	77	Gac/Cac	4/9	1	2	FACETS	0.629	0.443	0.856	0.629	0.443	0.856	SUBCLONAL	1	TRUE	1	0.23	2		412	166	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443845	49443845	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	45	996	0	ENST00000301067.7:c.3526G>T	p.Ala1176Ser	p.A1176S	ENST00000301067	NM_003482.3	1176	Gca/Tca	11/54	0.0316357217321075	3	FACETS	0.792	0.665	0.932	0.396	0.332	0.466	INDETERMINATE	1	TRUE	1	0.23	3		996	551	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109706	115109706	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	33	1057	1	ENST00000257566.3:c.2172C>G	p.Ile724Met	p.I724M	ENST00000257566	NM_016569.3	724	atC/atG	8/8	0.3	1	FACETS	0.436	0.354	0.529	0.436	0.354	0.529	SUBCLONAL	1	TRUE	0	0.23	1		1058	582	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557875	21557875	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	42	637	0	ENST00000382592.4:c.1970G>T	p.Arg657Met	p.R657M	ENST00000382592	NM_014572.2	657	aGg/aTg	5/8	0.3	1	FACETS	0.923	0.773	1	0.923	0.773	1	CLONAL	1	TRUE	0	0.23	1		637	350	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913539	32913539	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	24	546	0	ENST00000380152.3:c.5047C>G	p.Gln1683Glu	p.Q1683E	ENST00000380152		1683	Cag/Gag	11/27	0.283401424457682	3	FACETS	1	0.843	1	0.544	0.428	0.675	CLONAL	1	TRUE	1	0.23	3		546	214	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042136	42042136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	18	572	0	ENST00000219905.7:c.6331G>A	p.Asp2111Asn	p.D2111N	ENST00000219905	NM_001164273.1	2111	Gat/Aat	17/24	0.3	1	FACETS	0.6	0.452	0.773	0.6	0.452	0.773	SUBCLONAL	1	TRUE	0	0.23	1		572	231	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042313	42042313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1264798673	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	26	522	0	ENST00000219905.7:c.6508G>A	p.Asp2170Asn	p.D2170N	ENST00000219905	NM_001164273.1	2170	Gac/Aac	17/24	0.3	1	FACETS	0.794	0.631	0.979	0.794	0.631	0.979	CLONAL	1	TRUE	0	0.23	1		522	252	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042327	42042327	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	25	560	0	ENST00000219905.7:c.6522G>A	p.Trp2174Ter	p.W2174*	ENST00000219905	NM_001164273.1	2174	tgG/tgA	17/24	0.3	1	FACETS	0.743	0.587	0.921	0.743	0.587	0.921	CLONAL	1	TRUE	0	0.23	1		560	259	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628235	90628235	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	32	982	0	ENST00000330062.3:c.1176C>G	p.Ile392Met	p.I392M	ENST00000330062	NM_002168.2	392	atC/atG	9/11	0.3	1	FACETS	0.494	0.4	0.6	0.494	0.4	0.6	SUBCLONAL	1	TRUE	0	0.23	1		982	499	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89828373	89828373	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	16	547	0	ENST00000389301.3:c.2836C>G	p.Leu946Val	p.L946V	ENST00000389301	NM_000135.2	946	Ctt/Gtt	29/43	0.3	1	FACETS	0.441	0.326	0.579	0.441	0.326	0.579	SUBCLONAL	1	TRUE	0	0.23	1		547	279	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554337	63554337	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	53	748	0	ENST00000307078.5:c.402C>G	p.Ile134Met	p.I134M	ENST00000307078	NM_004655.3	134	atC/atG	2/11	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.23	2		748	402	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118996	70118996	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs61740803	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	38	906	0	ENST00000245479.2:c.568G>C	p.Glu190Gln	p.E190Q	ENST00000245479	NM_000346.3	190	Gag/Cag	2/3	1	2	FACETS	0.633	0.523	0.757	0.633	0.523	0.757	SUBCLONAL	1	TRUE	1	0.23	2		906	522	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632399	1632399	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	51	900	0	ENST00000344749.5:c.151G>C	p.Glu51Gln	p.E51Q	ENST00000344749	NM_001136139.2	51	Gag/Cag	4/19	0.3	1	FACETS	0.921	0.785	1	0.921	0.785	1	CLONAL	1	TRUE	0	0.23	1		900	426	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030327	11030327	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	19	769	0	ENST00000327064.4:c.1077C>G	p.Phe359Leu	p.F359L	ENST00000327064	NM_199141.1	359	ttC/ttG	9/16	0.3	1	FACETS	0.429	0.325	0.551	0.429	0.325	0.551	SUBCLONAL	1	TRUE	0	0.23	1		769	341	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288529	15288529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	11	300	0	ENST00000263388.2:c.4210G>A	p.Glu1404Lys	p.E1404K	ENST00000263388	NM_000435.2	1404	Gag/Aag	24/33	0.3	1	FACETS	0.584	0.405	0.804	0.584	0.405	0.804	SUBCLONAL	1	TRUE	0	0.23	1		300	145	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711155	61711155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	22	554	0	ENST00000401558.2:c.2594C>T	p.Ala865Val	p.A865V	ENST00000401558	NM_003400.3	865	gCt/gTt	21/25	0.0316357217321075	3	FACETS	0.889	0.691	1	0.444	0.345	0.559	INDETERMINATE	1	TRUE	1	0.23	3		554	240	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136261	202136261	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	35	563	0	ENST00000358485.4:c.505G>A	p.Glu169Lys	p.E169K	ENST00000358485	NM_001080125.1	169	Gaa/Aaa	3/9	0.0316357217321075	3	FACETS	1	0.895	1	0.566	0.465	0.678	INDETERMINATE	1	TRUE	1	0.23	3		563	300	SUCCESS
ATR	545	MSKCC	GRCh37	3	142232399	142232399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	22	489	0	ENST00000350721.4:c.4585C>T	p.Leu1529Phe	p.L1529F	ENST00000350721	NM_001184.3	1529	Ctt/Ttt	26/47	1	2	FACETS	0.722	0.56	0.909	0.722	0.56	0.909	CLONAL	1	TRUE	1	0.23	2		489	265	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268460	142268460	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	12	481	0	ENST00000350721.4:c.3032C>T	p.Ser1011Phe	p.S1011F	ENST00000350721	NM_001184.3	1011	tCt/tTt	15/47	1	2	FACETS	0.472	0.332	0.645	0.472	0.332	0.645	SUBCLONAL	1	TRUE	1	0.23	2		481	221	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444644	187444644	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	34	605	0	ENST00000232014.4:c.1583C>A	p.Ser528Tyr	p.S528Y	ENST00000232014	NM_001130845.1	528	tCt/tAt	7/10	1	2	FACETS	0.663	0.541	0.8	0.663	0.541	0.8	SUBCLONAL	1	TRUE	1	0.23	2		605	446	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946290	55946290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	30	416	0	ENST00000263923.4:c.3889G>A	p.Glu1297Lys	p.E1297K	ENST00000263923	NM_002253.2	1297	Gaa/Aaa	30/30	0.3	1	FACETS	0.84	0.679	1	0.84	0.679	1	CLONAL	1	TRUE	0	0.23	1		416	275	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467552	66467552	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	15	404	0	ENST00000273854.3:c.717C>G	p.His239Gln	p.H239Q	ENST00000273854	NM_004439.5	239	caC/caG	3/18	0.3	1	FACETS	0.506	0.37	0.669	0.506	0.37	0.669	SUBCLONAL	1	TRUE	0	0.23	1		404	228	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143324164	143324164	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	12	318	1	ENST00000262992.4:c.299C>A	p.Ser100Tyr	p.S100Y	ENST00000262992	NM_001101669.1	100	tCt/tAt	5/24	0.0316357217321075	3	FACETS	0.526	0.37	0.719	0.263	0.185	0.36	INDETERMINATE	1	TRUE	1	0.23	3		319	221	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861028	35861028	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	30	485	0	ENST00000303115.3:c.157C>A	p.His53Asn	p.H53N	ENST00000303115	NM_002185.3	53	Cac/Aac	2/8	1	2	FACETS	0.783	0.632	0.954	0.783	0.632	0.954	CLONAL	1	TRUE	1	0.23	2		485	333	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930625	131930625	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	14	423	0	ENST00000265335.6:c.1858G>C	p.Glu620Gln	p.E620Q	ENST00000265335		620	Gag/Cag	12/25	0.0316357217321075	3	FACETS	0.617	0.446	0.823	0.308	0.223	0.412	INDETERMINATE	1	TRUE	1	0.23	3		423	220	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197328	26197328	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	61	869	0	ENST00000356476.2:c.151G>C	p.Glu51Gln	p.E51Q	ENST00000356476		51	Gag/Cag	1/1	0.283401424457682	3	FACETS	0.914	0.788	1	0.457	0.394	0.526	CLONAL	1	TRUE	1	0.23	3		869	647	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675925	30675925	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	31	834	2	ENST00000376406.3:c.2431G>C	p.Asp811His	p.D811H	ENST00000376406	NM_014641.2	811	Gat/Cat	8/15	0.283401424457682	3	FACETS	0.555	0.447	0.676	0.277	0.223	0.338	SUBCLONAL	1	TRUE	1	0.23	3		836	542	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201873	152201873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	29	449	0	ENST00000206249.3:c.727C>A	p.Arg243Ser	p.R243S	ENST00000206249	NM_000125.3	243	Cgt/Agt	3/8	1	2	FACETS	0.723	0.58	0.884	0.723	0.58	0.884	SUBCLONAL	1	TRUE	1	0.23	2		449	349	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683674	162683674	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	33	654	0	ENST00000366898.1:c.295C>T	p.Pro99Ser	p.P99S	ENST00000366898	NM_004562.2	99	Ccc/Tcc	3/12	1	2	FACETS	0.595	0.484	0.721	0.595	0.484	0.721	SUBCLONAL	1	TRUE	1	0.23	2		654	482	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336653	81336653	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	17	393	0	ENST00000222390.5:c.1569G>C	p.Leu523Phe	p.L523F	ENST00000222390	NM_000601.4	523	ttG/ttC	14/18	1	2	FACETS	1	0.799	1	1	0.799	1	CLONAL	1	TRUE	1	0.23	2		393	138	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989635	68989635	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	18	480	0	ENST00000288368.4:c.1573G>C	p.Asp525His	p.D525H	ENST00000288368	NM_024870.2	525	Gat/Cat	15/40	1	2	FACETS	0.513	0.386	0.664	0.513	0.386	0.664	SUBCLONAL	1	TRUE	1	0.23	2		480	305	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750872	128750872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	38	745	0	ENST00000377970.2:c.409G>A	p.Glu137Lys	p.E137K	ENST00000377970	NM_002467.4	137	Gag/Aag	2/3	1	2	FACETS	0.725	0.599	0.865	0.725	0.599	0.865	SUBCLONAL	1	TRUE	1	0.23	2		745	456	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141567256	141567256	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	52	803	0	ENST00000220592.5:c.958C>G	p.Leu320Val	p.L320V	ENST00000220592	NM_012154.3	320	Ctg/Gtg	8/19	1	2	FACETS	0.908	0.774	1	0.908	0.774	1	CLONAL	1	TRUE	1	0.23	2		803	498	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045709	47045709	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053245-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	51	1236	0	ENST00000377604.3:c.2590C>G	p.Arg864Gly	p.R864G	ENST00000377604	NM_001204468.1	864	Cgg/Ggg	23/24	0.3	1	FACETS	0.774	0.658	0.901	0.774	0.658	0.901	CLONAL	1	TRUE	0	0.23	1		1236	507	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0053246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	80	280	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.35	2		280	420	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249510	153249510	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1157879635	NA	P-0053246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	114	449	1	ENST00000281708.4:c.1268G>T	p.Gly423Val	p.G423V	ENST00000281708	NM_033632.3	423	gGa/gTa	9/12	1	2	FACETS	0.933	0.841	1	0.933	0.841	1	CLONAL	1	TRUE	1	0.35	2		450	698	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905514	11905514	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0053246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	49	296	0	ENST00000396373.4:c.163+1G>A		p.X55_splice	ENST00000396373	NM_001987.4	55			1	2	FACETS	0.615	0.522	0.718	0.615	0.522	0.718	SUBCLONAL	1	TRUE	1	0.35	2		296	455	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11270924	11270924	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	97	392	0	ENST00000361445.4:c.3601C>T	p.Arg1201Ter	p.R1201*	ENST00000361445	NM_004958.3	1201	Cga/Tga	24/58	0.224933955500184	2	FACETS	0.952	0.851	1	0.476	0.425	0.53	CLONAL	1	TRUE	0	0.35	2		392	582	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	63	279	0	ENST00000256196.4:c.68G>T	p.Gly23Val	p.G23V	ENST00000256196		23	gGc/gTc	1/6	1	2	FACETS	0.94	0.817	1	0.94	0.817	1	CLONAL	1	TRUE	1	0.35	2		279	383	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268418	142268418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771309709	NA	P-0053246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	77	370	2	ENST00000350721.4:c.3074G>A	p.Arg1025His	p.R1025H	ENST00000350721	NM_001184.3	1025	cGt/cAt	15/47	1	2	FACETS	0.928	0.818	1	0.928	0.818	1	CLONAL	1	TRUE	1	0.35	2		372	474	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106316	27106411	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTTGCCAAGCGCTGCGTCTGTGTGTCCAATACCATTCGAAGCCTGTCATTTGTGCCAGGCAATGACTTTGAGATGTCCAAACACCCAGGGCTGC	CTCTTGCCAAGCGCTGCGTCTGTGTGTCCAATACCATTCGAAGCCTGTCATTTGTGCCAGGCAATGACTTTGAGATGTCCAAACACCCAGGGCTGC	GGGGTGT	novel	NA	P-0053246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	275	637	2	ENST00000324856.7:c.5927_6022delinsGGGGTGT	p.Ser1976TrpfsTer27	p.S1976Wfs*27	ENST00000324856	NM_006015.4	1976	tCTCTTGCCAAGCGCTGCGTCTGTGTGTCCAATACCATTCGAAGCCTGTCATTTGTGCCAGGCAATGACTTTGAGATGTCCAAACACCCAGGGCTGCtg/tGGGGTGTtg	20/20	0.224933955500184	2	FACETS	0.89	0.837	0.943	0.89	0.837	0.943	CLONAL	2	TRUE	0	0.35	2		639	883	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717718	89717719	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0053246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	206	407	0	ENST00000371953.3:c.743_744del	p.Pro248ArgfsTer4	p.P248Rfs*4	ENST00000371953	NM_000314.4	248	cCT/c	7/9	0.3	2	FACETS	0.959	0.895	1	0.959	0.895	1	CLONAL	2	TRUE	0	0.35	2		407	614	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86658446	86658446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	25	177	0	ENST00000274376.6:c.1414del	p.Tyr472IlefsTer11	p.Y472Ifs*11	ENST00000274376	NM_002890.2	471	Ttt/tt	10/25	1	2	FACETS	0.794	0.63	0.978	0.794	0.63	0.978	CLONAL	1	TRUE	1	0.35	2		177	180	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675624	86675624	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	60	308	0	ENST00000274376.6:c.2560G>T	p.Glu854Ter	p.E854*	ENST00000274376	NM_002890.2	854	Gag/Tag	19/25	1	2	FACETS	0.812	0.702	0.932	0.812	0.702	0.932	CLONAL	1	TRUE	1	0.35	2		308	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0053247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	390	1171	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.633374851446423	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	2	0.813322938676476	4		1171	868	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0053247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	274	286	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.551417955990834	5	FACETS	0.875	0.829	0.92	0.875	0.829	0.92	CLONAL	3	TRUE	2	0.813322938676476	5		286	570	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0053247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	287	727	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.310161669976016	4	FACETS	1	0.956	1	1	0.956	1	INDETERMINATE	2	TRUE	2	0.813322938676476	4		727	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0053247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	321	641	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.633374851446423	4	FACETS	0.95	0.903	0.998	0.95	0.903	0.998	CLONAL	2	TRUE	2	0.813322938676476	4		641	753	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373736	118373736	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	117	380	0	ENST00000534358.1:c.7129G>C	p.Gly2377Arg	p.G2377R	ENST00000534358	NM_005933.3	2377	Ggg/Cgg	27/36	0.71821039622215	3	FACETS	1	0.913	1	0.502	0.456	0.549	CLONAL	1	TRUE	1	0.813322938676476	3		380	403	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29107974	29107974	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121908702	NA	P-0053247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	126	437	0	ENST00000328354.6:c.715G>C	p.Glu239Gln	p.E239Q	ENST00000328354	NM_007194.3	239	Gag/Cag	6/15	0.813322938676476	3	FACETS	0.812	0.738	0.888			1	CLONAL	1	TRUE	NA	0.813322938676476	3		437	537	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536222	106536222	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	136	491	0	ENST00000369096.4:c.189del	p.Asn63LysfsTer39	p.N63Kfs*39	ENST00000369096	NM_001198.3	63	aaC/aa	2/7	0.813322938676476	3	FACETS	0.986	0.903	1	0.493	0.451	0.536	CLONAL	1	TRUE	1	0.813322938676476	3		491	477	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971130	13971130	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	116	300	0	ENST00000405192.2:c.799T>C	p.Ser267Pro	p.S267P	ENST00000405192	NM_001163147.1	267	Tca/Cca	8/12	0.310161669976016	4	FACETS	0.811	0.74	0.883	0.811	0.74	0.883	INDETERMINATE	2	TRUE	2	0.813322938676476	4		300	319	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462475	92462475	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	315	652	0	ENST00000265734.4:c.163C>G	p.Pro55Ala	p.P55A	ENST00000265734	NM_001259.6	55	Ccg/Gcg	2/8	0.813322938676476	2	FACETS	0.988	0.958	1	0.988	0.958	1	CLONAL	2	TRUE	0	0.813322938676476	2		652	392	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0053248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	46	430	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.144306746005722	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		430	519	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577544	7577544	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587780074	NA	P-0053248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	42	684	0	ENST00000269305.4:c.737T>A	p.Met246Lys	p.M246K	ENST00000269305	NM_001126112.2	246	aTg/aAg	7/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		684	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0053249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	186	656	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.429270755917412	1	FACETS	0.94	0.871	1	0.94	0.871	1	CLONAL	1	TRUE	0	0.429270755917412	1		656	724	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683688	162683688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	156	532	0	ENST00000366898.1:c.281G>A	p.Gly94Asp	p.G94D	ENST00000366898	NM_004562.2	94	gGc/gAc	3/12	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.429270755917412	2		532	727	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010375	48010375	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs876660095	NA	P-0053249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	146	619	0	ENST00000234420.5:c.3G>A	p.Met1?	p.M1?	ENST00000234420	NM_000179.2	1	atG/atA	1/10	0.429270755917412	3	FACETS	0.979	0.894	1	0.489	0.447	0.534	CLONAL	1	TRUE	1	0.429270755917412	3		619	844	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666438	206666438	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553391067	NA	P-0053251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	369	656	0	ENST00000367120.3:c.1918G>A	p.Glu640Lys	p.E640K	ENST00000367120	NM_014002.3	640	Gag/Aag	19/22	1	2	FACETS	0.935	0.888	0.982	0.935	0.888	0.982	CLONAL	1	TRUE	1	0.718566819339662	2		656	1099	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720733	89720734	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	rs1564568350	NA	P-0053251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	37	188	0	ENST00000371953.3:c.885_886del	p.Cys296Ter	p.C296*	ENST00000371953	NM_000314.4	295	cTA/c	8/9	0.718566819339662	1	FACETS	0.446	0.374	0.524	0.446	0.374	0.524	SUBCLONAL	1	TRUE	0	0.718566819339662	1		188	148	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243541	46243541	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	169	270	0	ENST00000334344.6:c.1894C>G	p.Pro632Ala	p.P632A	ENST00000334344	NM_152641.2	632	Cct/Gct	14/21	1	2	FACETS	0.943	0.874	1	0.943	0.874	1	CLONAL	1	TRUE	1	0.718566819339662	2		270	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934571	NA	P-0053251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	378	688	0	ENST00000269305.4:c.747G>C	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agC	7/11	0.675307316251632	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.718566819339662	1		688	672	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220700	1220701	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CG	novel	NA	P-0053251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	396	729	2	ENST00000326873.7:c.719_720dup	p.Ala241ArgfsTer47	p.A241Rfs*47	ENST00000326873	NM_000455.4	240	tcg/tCGcg	5/10	0.718566819339662	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.718566819339662	1		731	702	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502363	186502373	+	frameshift_variant	Frame_Shift_Del	DEL	ATGAGATTGTT	ATGAGATTGTT	-	novel	NA	P-0053251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	375	319	0	ENST00000323963.5:c.86_96del	p.Asn29ArgfsTer2	p.N29Rfs*2	ENST00000323963		29	aATGAGATTGTT/a	3/11	0.695968501875651	3	FACETS	0.98	0.938	1	0.653	0.625	0.681	CLONAL	2	TRUE	0	0.718566819339662	3		319	724	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878886	117879908	+	splice_acceptor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	GTTAGCTTCTTATCCCAATGGGCCGCTAGCCAAATTTTGGCCAGAGGCCCTCTTTTACTGAGAACAAAATGTGCGTAGAACATTGTTCTGGCTGGCTATGAAAACAGAAGAAAACCTAAGAGGGGAAAAAAAAGTTAATGTAAACATCATCTGACAATTTAAATACTTATCAAGACATAAGAAATTTAAAATTTTTCTTCTCTCTTTAATATGAAAACTATAAAATGCTTGAGTAAATGTTTAATATGTATTTTAAAAACAACAGATTTAAAACAAATCTATTGTTTTAATTTTGAGAGAGGAAAAAAAAATAGACCCCAAAATACTAAGAGCTGAAAGTAAAAGGGACAAGAGTCAAATTGCTTTCATGCCTTGTTTCATTTCTATCTTGATTGACAGTAGAAATAGTCTGTTTACTGGCCAAGAGCTAGAGAATATATTTTTCATGGCAAGAAAAGAAAATCTATGAAGAAAGATACTCAGGCACAGATAAAAATCTGTGGAAATTTCCATTTTTAGAATGCCATTAAAAATCGCGATTCTGGGATAAATTATCTGTAAAATTGCTACTACACGAAAAGTACTGTACTAAGCATTTCATATTCCACCAAGCAAAGCTAAGCAGATGGGCTGGCCCCATTTTACAGGTGGGTAGTTTAGAAAAATCGAAGTTCAAAAAAGGTAAAGAATTATATATATAGTTTTCTTAACTTAAGAACTTACAAAGCATTTATCTACTTATAATTTAAATATTAAATCAGGGACAATGGTACAGCAGATTTATCTTATGACTGAAAGTCTTGGAATCACAAATATGTTACTGACATTCTACTTTCCTTCAGCACTCTAATGTATTAAGAAAGGCCGCTTGAAAACCCCAGTTCAGAAGAGTACATTAACTGCAGGATATTTCCTTTATATCATTTAATTCCCCTCTTTCACGGATTTAAAAGAAATCTACTTCAGAGAATGAATTTCCAGATTTAAAACAAATCTATTGTTCTGATTTTTTTCTAAAATGTC	GTTAGCTTCTTATCCCAATGGGCCGCTAGCCAAATTTTGGCCAGAGGCCCTCTTTTACTGAGAACAAAATGTGCGTAGAACATTGTTCTGGCTGGCTATGAAAACAGAAGAAAACCTAAGAGGGGAAAAAAAAGTTAATGTAAACATCATCTGACAATTTAAATACTTATCAAGACATAAGAAATTTAAAATTTTTCTTCTCTCTTTAATATGAAAACTATAAAATGCTTGAGTAAATGTTTAATATGTATTTTAAAAACAACAGATTTAAAACAAATCTATTGTTTTAATTTTGAGAGAGGAAAAAAAAATAGACCCCAAAATACTAAGAGCTGAAAGTAAAAGGGACAAGAGTCAAATTGCTTTCATGCCTTGTTTCATTTCTATCTTGATTGACAGTAGAAATAGTCTGTTTACTGGCCAAGAGCTAGAGAATATATTTTTCATGGCAAGAAAAGAAAATCTATGAAGAAAGATACTCAGGCACAGATAAAAATCTGTGGAAATTTCCATTTTTAGAATGCCATTAAAAATCGCGATTCTGGGATAAATTATCTGTAAAATTGCTACTACACGAAAAGTACTGTACTAAGCATTTCATATTCCACCAAGCAAAGCTAAGCAGATGGGCTGGCCCCATTTTACAGGTGGGTAGTTTAGAAAAATCGAAGTTCAAAAAAGGTAAAGAATTATATATATAGTTTTCTTAACTTAAGAACTTACAAAGCATTTATCTACTTATAATTTAAATATTAAATCAGGGACAATGGTACAGCAGATTTATCTTATGACTGAAAGTCTTGGAATCACAAATATGTTACTGACATTCTACTTTCCTTCAGCACTCTAATGTATTAAGAAAGGCCGCTTGAAAACCCCAGTTCAGAAGAGTACATTAACTGCAGGATATTTCCTTTATATCATTTAATTCCCCTCTTTCACGGATTTAAAAGAAATCTACTTCAGAGAATGAATTTCCAGATTTAAAACAAATCTATTGTTCTGATTTTTTTCTAAAATGTC	-	novel	NA	P-0053251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	93	394	0	ENST00000297338.2:c.-32-908_83del		p.X11_splice	ENST00000297338	NM_006265.2	11		2/14	0.26466966809496	5	FACETS	0.747	0.664	0.835			1	INDETERMINATE	1	TRUE	NA	0.718566819339662	5		394	720	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197834	123197834	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0053251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	257	219	0	ENST00000218089.9:c.1958C>G	p.Ser653Ter	p.S653*	ENST00000218089	NM_001042749.1	653	tCa/tGa	20/35	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.718566819339662	1		219	384	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788617	3788617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519884	NA	P-0053251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	29	419	3	ENST00000262367.5:c.4337G>A	p.Arg1446His	p.R1446H	ENST00000262367	NM_004380.2	1446	cGc/cAc	26/31	1	2	FACETS	0.097	0.077	0.12	0.097	0.077	0.12	SUBCLONAL	1	TRUE	1	0.718566819339662	2		422	832	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577466	64577470	+	frameshift_variant	Frame_Shift_Del	DEL	AAGGA	AAGGA	-	novel	NA	P-0053266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	93	378	0	ENST00000312049.6:c.112_116del	p.Ser38GlyfsTer77	p.S38Gfs*77	ENST00000312049	NM_130799.2	38	TCCTTg/g	2/10	0.613384465326264	1	FACETS	0.659	0.592	0.729	0.659	0.592	0.729	SUBCLONAL	1	TRUE	0	0.613384465326264	1		378	319	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480537	50480537	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0053266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	166	287	0	ENST00000394963.4:c.409-2A>C		p.X137_splice	ENST00000394963	NM_003076.4	137			0.613384465326264	1	FACETS	0.952	0.886	1	0.952	0.886	1	CLONAL	1	TRUE	0	0.613384465326264	1		287	394	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346282	89346282	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs537338393	NA	P-0053266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	129	238	0	ENST00000301030.4:c.6668C>T	p.Ala2223Val	p.A2223V	ENST00000301030	NM_001256183.1	2223	gCg/gTg	9/13	0.613384465326264	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.613384465326264	1		238	244	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983402	90983402	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	353	188	0	ENST00000265433.3:c.701del	p.Gln234ArgfsTer5	p.Q234Rfs*5	ENST00000265433	NM_002485.4	234	cAg/cg	6/16	0.613384465326264	3	FACETS	0.983	0.948	1	0.983	0.948	1	CLONAL	3	TRUE	0	0.613384465326264	3		188	510	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	34	252	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	0.221792792756381	1	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	0	0.334302168953974	1		252	150	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0053267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	84	508	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.334302168953974	1	FACETS	0.902	0.81	0.996	1	0.985	1	CLONAL	2	TRUE	0	0.334302168953974	1		508	232	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540161	187540161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373112377	NA	P-0053267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	14	351	0	ENST00000441802.2:c.7579G>A	p.Val2527Ile	p.V2527I	ENST00000441802	NM_005245.3	2527	Gtt/Att	10/27	0.221792792756381	1	FACETS	0.513	0.373	0.68	0.513	0.373	0.68	SUBCLONAL	1	TRUE	0	0.334302168953974	1		351	136	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216596	108216596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778080	NA	P-0053267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	15	290	0	ENST00000278616.4:c.8545C>T	p.Arg2849Ter	p.R2849*	ENST00000278616	NM_000051.3	2849	Cga/Tga	58/63	0.28953484787113	4	FACETS	0.596	0.437	0.786	0.298	0.218	0.393	SUBCLONAL	1	TRUE	2	0.334302168953974	4		290	201	SUCCESS
APC	324	MSKCC	GRCh37	5	112175253	112175254	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0053267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	24	199	0	ENST00000257430.4:c.3963dup	p.Glu1322ArgfsTer10	p.E1322Rfs*10	ENST00000257430	NM_000038.5	1321	agc/agCc	16/16	0.334302168953974	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.334302168953974	1		199	82	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520087	106520087	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774448553	NA	P-0053267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	17	181	1	ENST00000359195.3:c.2515C>T	p.Arg839Cys	p.R839C	ENST00000359195	NM_002649.2	839	Cgc/Tgc	6/11	0.334302168953974	4	FACETS	1	0.812	1	0.547	0.412	0.703	CLONAL	1	TRUE	2	0.334302168953974	4		182	124	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250823	153250823	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1159697496	NA	P-0053267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	12	278	0	ENST00000281708.4:c.1236+1G>A		p.X412_splice	ENST00000281708	NM_033632.3	412			0.221792792756381	1	FACETS	0.348	0.245	0.474	0.348	0.245	0.474	SUBCLONAL	1	TRUE	0	0.334302168953974	1		278	172	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981808	201981808	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	167	584	0	ENST00000359651.3:c.519del	p.Gln174SerfsTer80	p.Q174Sfs*80	ENST00000359651		173	ggT/gg	4/8	1	2	FACETS	1	0.976	1	1	0.993	1	CLONAL	2	TRUE	1	0.334302168953974	2		584	446	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899045	40899045	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	50	499	0	ENST00000373198.4:c.2225T>A	p.Leu742His	p.L742H	ENST00000373198	NM_133170.3	742	cTc/cAc	14/32	1	2	FACETS	0.875	0.755	1	1	0.973	1	CLONAL	2	TRUE	1	0.334302168953974	2		499	171	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578175	7578175	+	splice_donor_variant	Splice_Site	SNP	A	A	T	rs1555525703	NA	P-0053269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	209	535	0	ENST00000269305.4:c.672+2T>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.775293149090159	1	FACETS	0.999	0.949	1	0.999	0.949	1	CLONAL	1	TRUE	0	0.777538080788269	1		535	329	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426235	49426235	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	111	637	0	ENST00000301067.7:c.12253C>T	p.Gln4085Ter	p.Q4085*	ENST00000301067	NM_003482.3	4085	Cag/Tag	39/54	NA	2	FACETS	0.698	0.632	0.766			1	INDETERMINATE	1	TRUE	NA	0.777538080788269	2		637	409	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439623	51439635	+	frameshift_variant	Frame_Shift_Del	DEL	CCGATTTGAAAGA	CCGATTTGAAAGA	-	novel	NA	P-0053269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	118	313	0	ENST00000262662.1:c.192_204del	p.Asp64GlufsTer56	p.D64Efs*56	ENST00000262662		63	cCCGATTTGAAAGAc/cc	4/4	0.45729257285355	1	FACETS	0.665	0.61	0.721	0.665	0.61	0.721	INDETERMINATE	1	TRUE	0	0.777538080788269	1		313	279	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424062	49424062	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0053269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	194	618	0	ENST00000301067.7:c.13999+1del		p.X4667_splice	ENST00000301067	NM_003482.3	4667			NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.777538080788269	2		618	446	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	44	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.915	0.781	1	0.915	0.781	1	CLONAL	1	TRUE	1	0.608406562617911	2		429	158	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0053270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	100	388	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.608406562617911	2		388	285	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0053270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	332	311	1	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.608406562617911	4	FACETS	0.978	0.936	1	0.978	0.936	1	CLONAL	3	TRUE	1	0.608406562617911	4		312	598	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248423	212248423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771634130	NA	P-0053270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	91	157	0	ENST00000342788.4:c.3844C>T	p.Pro1282Ser	p.P1282S	ENST00000342788	NM_005235.2	1282	Cct/Tct	28/28	1	2	FACETS	0.92	0.826	1	0.92	0.826	1	CLONAL	1	TRUE	1	0.608406562617911	2		157	325	SUCCESS
APC	324	MSKCC	GRCh37	5	112175991	112175991	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	76	116	0	ENST00000257430.4:c.4700C>A	p.Ser1567Ter	p.S1567*	ENST00000257430	NM_000038.5	1567	tCa/tAa	16/16	0.608406562617911	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.608406562617911	1		116	159	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	41	411	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.623	0.519	0.738	0.623	0.519	0.738	SUBCLONAL	1	FALSE	1	0.309769734915732	2		411	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0053271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	65	485	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.309769734915732	1	FACETS	0.627	0.543	0.717	0.627	0.543	0.717	SUBCLONAL	1	FALSE	0	0.309769734915732	1		486	566	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988073	85988073	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs774560012	NA	P-0053271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	15	271	0	ENST00000263360.6:c.1018A>G	p.Ile340Val	p.I340V	ENST00000263360	NM_003797.3	340	Ata/Gta	10/12	1	2	FACETS	0.329	0.24	0.437	0.329	0.24	0.437	SUBCLONAL	1	FALSE	1	0.309769734915732	2		271	294	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436175	56436176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	31	400	0	ENST00000407977.2:c.961dup	p.Ser321PhefsTer122	p.S321Ffs*122	ENST00000407977		321	tca/tTca	9/10	0.309769734915732	1	FACETS	0.438	0.354	0.533	0.438	0.354	0.533	SUBCLONAL	1	FALSE	0	0.309769734915732	1		400	386	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604655	48604683	+	frameshift_variant	Frame_Shift_Del	DEL	GATGACCTTCGTCGCTTATGCATACTCAG	GATGACCTTCGTCGCTTATGCATACTCAG	-	novel	NA	P-0053271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	29	243	0	ENST00000342988.3:c.1482_1510del	p.Asp494GlufsTer23	p.D494Efs*23	ENST00000342988	NM_005359.5	493	GATGACCTTCGTCGCTTATGCATACTCAGg/g	12/12	1	2	FACETS	0.554	0.445	0.678	0.554	0.445	0.678	SUBCLONAL	1	FALSE	1	0.309769734915732	2		243	338	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538356	9538356	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	35	369	0	ENST00000353224.5:c.1642G>C	p.Val548Leu	p.V548L	ENST00000353224	NM_177990.2	548	Gtc/Ctc	7/10	1	2	FACETS	0.519	0.426	0.625	0.519	0.426	0.625	SUBCLONAL	1	FALSE	1	0.309769734915732	2		369	435	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415663	152415663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	92	463	0	ENST00000206249.3:c.1513G>A	p.Ala505Thr	p.A505T	ENST00000206249	NM_000125.3	505	Gcc/Acc	7/8	1	2	FACETS	0.982	0.874	1	0.982	0.874	1	CLONAL	1	FALSE	1	0.309769734915732	2		463	605	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729429	41729429	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	48	487	0	ENST00000242208.4:c.1100C>G	p.Ser367Cys	p.S367C	ENST00000242208	NM_002192.2	367	tCc/tGc	3/3	1	2	FACETS	0.494	0.417	0.58	0.494	0.417	0.58	SUBCLONAL	1	FALSE	1	0.309769734915732	2		487	627	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738317	145738317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750381540	NA	P-0053271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	70	607	0	ENST00000428558.2:c.2668G>A	p.Ala890Thr	p.A890T	ENST00000428558	NM_004260.3	890	Gcc/Acc	16/22	1	2	FACETS	0.624	0.544	0.712	0.624	0.544	0.712	SUBCLONAL	1	FALSE	1	0.309769734915732	2		607	724	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477153	67477174	+	frameshift_variant	Frame_Shift_Del	DEL	TAACCAGCGCTATGGCTGGCAC	TAACCAGCGCTATGGCTGGCAC	GCACCCAA	novel	NA	P-0053271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	72	499	2	ENST00000327367.4:c.960_981delinsGCACCCAA	p.Cys320TrpfsTer37	p.C320Wfs*37	ENST00000327367	NM_005902.3	320	tgTAACCAGCGCTATGGCTGGCAC/tgGCACCCAA	7/9	1	2	FACETS	0.791	0.691	0.898	0.791	0.691	0.898	SUBCLONAL	1	FALSE	1	0.309769734915732	2		501	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579361	7579362	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0053272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	567	559	0	ENST00000269305.4:c.325_326del	p.Phe109ProfsTer39	p.F109Pfs*39	ENST00000269305	NM_001126112.2	109	TTc/c	4/11	0.591105969185167	3	FACETS	0.909	0.881	0.937	0.909	0.881	0.937	CLONAL	3	TRUE	0	0.591105969185167	3		559	911	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56413025	56413025	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0053272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	170	215	2	ENST00000348428.3:c.2037+2T>C		p.X679_splice	ENST00000348428	NM_006785.3	679			0.453733648715496	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	1	0.591105969185167	3		217	366	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873406	151873407	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0053272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	168	267	0	ENST00000262189.6:c.9130_9131dup	p.Pro3045GlyfsTer5	p.P3045Gfs*5	ENST00000262189	NM_170606.2	3044	agg/agAGg	38/59	0.453733648715496	3	FACETS	0.792	0.735	0.85	0.792	0.735	0.85	SUBCLONAL	2	TRUE	1	0.591105969185167	3		267	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0053273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	434	424	0	ENST00000269305.4:c.672+1G>C		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.514190879846727	3	FACETS	0.966	0.932	1	0.966	0.932	1	CLONAL	3	TRUE	0	0.548319758257075	3		424	696	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367975	15367975	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1858	106	394	0	ENST00000263377.2:c.1351G>A	p.Glu451Lys	p.E451K	ENST00000263377	NM_058243.2	451	Gaa/Aaa	8/20	0.548319758257075	12	FACETS	0.737	0.657	0.822			1	SUBCLONAL	1	TRUE	NA	0.548319758257075	12		394	1964	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138313	2138313	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	119	462	0	ENST00000219476.3:c.5246G>C	p.Arg1749Pro	p.R1749P	ENST00000219476	NM_000548.3	1749	cGg/cCg	41/42	0.548319758257075	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.548319758257075	1		462	315	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367924	15367924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201081104	NA	P-0053273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2217	118	516	1	ENST00000263377.2:c.1402G>A	p.Val468Met	p.V468M	ENST00000263377	NM_058243.2	468	Gtg/Atg	8/20	0.548319758257075	12	FACETS	0.69	0.619	0.765			1	SUBCLONAL	1	TRUE	NA	0.548319758257075	12		517	2335	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815620	139815620	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	103	418	1	ENST00000247668.2:c.1091A>G	p.Lys364Arg	p.K364R	ENST00000247668	NM_021138.3	364	aAg/aGg	9/11	1	2	FACETS	0.808	0.727	0.893	0.808	0.727	0.893	CLONAL	1	TRUE	1	0.548319758257075	2		419	465	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164509	36164509	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	16	290	0	ENST00000300305.3:c.1366G>A	p.Glu456Lys	p.E456K	ENST00000300305		456	Gag/Aag	8/8	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		290	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0053275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	321	431	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.678431490116204	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.678431490116204	2		431	441	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575374	64575374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs794728621	NA	P-0053275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	443	507	0	ENST00000312049.6:c.643G>A	p.Val215Met	p.V215M	ENST00000312049	NM_130799.2	215	Gtg/Atg	3/10	0.626138343567105	5	FACETS	1	0.965	1	1	0.965	1	CLONAL	3	TRUE	2	0.678431490116204	5		507	874	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724552	43724552	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	71	686	0	ENST00000382044.4:c.3515T>C	p.Val1172Ala	p.V1172A	ENST00000382044	NM_001141980.1	1172	gTt/gCt	17/28	1	2	FACETS	0.319	0.278	0.363	0.319	0.278	0.363	SUBCLONAL	1	TRUE	1	0.678431490116204	2		686	656	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201756	66201756	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	244	405	0	ENST00000273854.3:c.2746C>T	p.Gln916Ter	p.Q916*	ENST00000273854	NM_004439.5	916	Cag/Tag	16/18	0.678431490116204	3	FACETS	0.979	0.926	1	0.979	0.926	1	CLONAL	2	TRUE	1	0.678431490116204	3		405	492	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920413	114920413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767830105	NA	P-0053276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	105	391	0	ENST00000543371.1:c.1354G>A	p.Gly452Arg	p.G452R	ENST00000543371	NM_001198531.1	452	Ggg/Agg	13/14	0.615798607690244	1	FACETS	0.595	0.537	0.655	0.595	0.537	0.655	SUBCLONAL	1	TRUE	0	0.615798607690244	1		391	397	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987340	2987340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554276653	NA	P-0053276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	211	531	0	ENST00000396946.4:c.89G>A	p.Arg30Gln	p.R30Q	ENST00000396946	NM_032415.4	30	cGg/cAg	3/25	0.615798607690244	1	FACETS	0.956	0.897	1	0.956	0.897	1	CLONAL	1	TRUE	0	0.615798607690244	1		531	496	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255418	16255418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	84	379	0	ENST00000375759.3:c.2683C>T	p.Pro895Ser	p.P895S	ENST00000375759	NM_015001.2	895	Cct/Tct	11/15	NA	2	FACETS	0.439	0.387	0.493			1	INDETERMINATE	1	TRUE	NA	0.615798607690244	2		379	622	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99452048	99452048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs187980012	NA	P-0053276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	58	321	0	ENST00000268035.6:c.1382G>A	p.Arg461His	p.R461H	ENST00000268035	NM_000875.3	461	cGc/cAc	6/21	0.312444008088588	1	FACETS	0.341	0.294	0.392	0.341	0.294	0.392	INDETERMINATE	1	TRUE	0	0.615798607690244	1		321	382	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0053305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	31	441	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.174803773244902	3	FACETS	1	0.913	1	0.618	0.501	0.749	CLONAL	1	TRUE	1	0.19	3		441	289	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441468	40441468	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	30	1051	0	ENST00000345506.4:c.39C>A	p.Asp13Glu	p.D13E	ENST00000345506	NM_003152.3	13	gaC/gaA	3/20	0.174803773244902	1	FACETS	0.668	0.538	0.816	0.668	0.538	0.816	SUBCLONAL	1	TRUE	0	0.19	1		1051	428	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	190	411	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.502546765716784	3	FACETS	0.864	0.805	0.925	0.864	0.805	0.925	CLONAL	2	TRUE	1	0.512256225756994	3		411	539	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0053306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	91	274	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.902	0.806	1	0.902	0.806	1	CLONAL	1	TRUE	1	0.512256225756994	2		274	394	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846166	151846166	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	119	690	0	ENST00000262189.6:c.12846C>A	p.Asn4282Lys	p.N4282K	ENST00000262189	NM_170606.2	4282	aaC/aaA	52/59	0.502546765716784	3	FACETS	0.863	0.78	0.951	0.432	0.39	0.476	CLONAL	1	TRUE	1	0.512256225756994	3		690	676	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443910	18443910	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	53	389	0	ENST00000266497.5:c.883G>C	p.Asp295His	p.D295H	ENST00000266497		295	Gat/Cat	3/31	0.330615596306916	5	FACETS	1	0.929	1	0.38	0.326	0.439	CLONAL	1	TRUE	2	0.526250425319896	5		389	316	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87322800	87322800	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	71	451	0	ENST00000277120.3:c.401A>G	p.His134Arg	p.H134R	ENST00000277120		134	cAt/cGt	5/19	0.526250425319896	2	FACETS	1	0.916	1	0.523	0.462	0.587	CLONAL	1	TRUE	0	0.526250425319896	2		451	258	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413108	139413108	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	187	1105	0	ENST00000277541.6:c.1034T>G	p.Phe345Cys	p.F345C	ENST00000277541	NM_017617.3	345	tTc/tGc	6/34	0.526250425319896	2	FACETS	0.869	0.813	0.925	0.869	0.813	0.925	CLONAL	2	TRUE	0	0.526250425319896	2		1105	409	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0053308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	111	305	0				ENST00000310581	NM_198253.2	-/1132			0.145918017854914	0	FACETS	0.655	0.601	0.708			1	INDETERMINATE	1	TRUE	0	0.591683967681401	0		305	234	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125797	47125797	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	115	343	0	ENST00000409792.3:c.5473C>T	p.Gln1825Ter	p.Q1825*	ENST00000409792	NM_014159.6	1825	Caa/Taa	12/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.591683967681401	2		343	362	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27217702	27217702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773518368	NA	P-0053308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	206	607	0	ENST00000380036.4:c.3008G>A	p.Arg1003His	p.R1003H	ENST00000380036	NM_000459.3	1003	cGc/cAc	19/23	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.591683967681401	2		607	586	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241896	72241896	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	24	367	0	ENST00000357731.5:c.494A>C	p.Lys165Thr	p.K165T	ENST00000357731	NM_173808.2	165	aAa/aCa	3/7	1	2	FACETS	0.171	0.133	0.214	0.171	0.133	0.214	SUBCLONAL	1	TRUE	1	0.591683967681401	2		367	475	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221825	55221825	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1832	13499	885	0	ENST00000275493.2:c.869C>A	p.Thr290Asn	p.T290N	ENST00000275493	NM_005228.3	290	aCc/aAc	7/28	0.591683967681401	50	FACETS	1	0.998	1			1	CLONAL	45	TRUE	NA	0.591683967681401	50		885	15331	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55238897	55238897	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12636	825	576	0	ENST00000275493.2:c.1910C>G	p.Pro637Arg	p.P637R	ENST00000275493	NM_005228.3	637	cCa/cGa	16/28	0.591683967681401	50	FACETS	1	0.985	1			1	CLONAL	3	TRUE	NA	0.591683967681401	50		576	13461	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74859043	74859043	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	140	414	0	ENST00000284811.8:c.161A>G	p.Glu54Gly	p.E54G	ENST00000284811		54	gAg/gGg	4/4	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.591683967681401	2		414	447	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0053309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	43	350	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.779	0.651	0.921	0.779	0.651	0.921	CLONAL	1	TRUE	1	0.19	2		350	581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0053309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	40	633	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.55	0.456	0.656	0.55	0.456	0.656	SUBCLONAL	1	TRUE	1	0.19	2		633	765	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	75	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.794	0.699	0.894	0.794	0.699	0.894	SUBCLONAL	1	TRUE	1	0.497426898732012	2		429	380	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0053310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	132	330	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.143054792626754	3	FACETS	0.638	0.578	0.701	0.319	0.289	0.351	INDETERMINATE	1	TRUE	1	0.497426898732012	3		330	1039	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0053310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	204	658	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.81	0.751	0.872	0.81	0.751	0.872	CLONAL	1	TRUE	1	0.497426898732012	2		658	1012	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397743	49397743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	241	556	0	ENST00000418115.1:c.481G>A	p.Ala161Thr	p.A161T	ENST00000418115	NM_001664.2	161	Gca/Aca	5/5	0.143054792626754	3	FACETS	1	0.982	1	0.571	0.533	0.61	INDETERMINATE	1	TRUE	1	0.497426898732012	3		556	1060	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265465	198265465	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	196	556	0	ENST00000335508.6:c.2692T>C	p.Tyr898His	p.Y898H	ENST00000335508	NM_012433.2	898	Tat/Cat	18/25	1	2	FACETS	0.984	0.913	1	0.984	0.913	1	CLONAL	1	TRUE	1	0.497426898732012	2		556	801	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803622	1803622	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	251	947	0	ENST00000260795.2:c.800T>C	p.Leu267Pro	p.L267P	ENST00000260795		267	cTg/cCg	6/17	1	2	FACETS	0.87	0.813	0.929	0.87	0.813	0.929	CLONAL	1	TRUE	1	0.497426898732012	2		947	1160	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112760193	112760193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	28	476	2	ENST00000369452.4:c.862C>T	p.Arg288Cys	p.R288C	ENST00000369452	NM_007373.3	288	Cgt/Tgt	4/9	1	2	FACETS	0.773	0.62	0.946	0.773	0.62	0.946	CLONAL	1	TRUE	1	0.281807418434339	2		478	257	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793214	42793214	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	62	1116	1	ENST00000575354.2:c.1106A>T	p.Asp369Val	p.D369V	ENST00000575354	NM_015125.3	369	gAc/gTc	7/20	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.281807418434339	2		1117	411	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0053315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	175	284	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.988	0.923	1	0.988	0.923	1	CLONAL	1	TRUE	1	0.930000263479773	2		284	381	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0053315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	98	305	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.930000263479773	2		305	169	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793378	42793378	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	361	672	0	ENST00000575354.2:c.1180C>T	p.Gln394Ter	p.Q394*	ENST00000575354	NM_015125.3	394	Cag/Tag	8/20	0.930000263479773	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.930000263479773	1		672	380	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414841	78414841	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	208	320	0	ENST00000370768.2:c.1925A>G	p.Gln642Arg	p.Q642R	ENST00000370768	NM_003902.3	642	cAg/cGg	19/20	0.930000263479773	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.930000263479773	1		320	224	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380340	14380340	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	19	166	0	ENST00000256196.4:c.77G>A	p.Gly26Asp	p.G26D	ENST00000256196		26	gGc/gAc	1/6	1	2	FACETS	0.172	0.131	0.221	0.172	0.131	0.221	SUBCLONAL	1	TRUE	1	0.930000263479773	2		166	237	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098981	47098981	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0053315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	284	376	0	ENST00000409792.3:c.6294-1G>A		p.X2098_splice	ENST00000409792	NM_014159.6	2098			0.930000263479773	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.930000263479773	1		376	292	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0053316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	178	833	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.342198301581125	1	FACETS	0.881	0.811	0.953	0.881	0.811	0.953	CLONAL	1	TRUE	0	0.342198301581125	1		837	979	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259247	36259248	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0053316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	166	238	0	ENST00000300305.3:c.242_243dup	p.Leu82CysfsTer41	p.L82Cfs*41	ENST00000300305		81	-/TG	3/8	0.266696519108022	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.342198301581125	2		238	470	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829066	128829066	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs41304185	NA	P-0053316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	14	8	0	ENST00000249373.3:c.74A>G	p.Asp25Gly	p.D25G	ENST00000249373	NM_005631.4	25	gAc/gGc	1/12	1	2	FACETS	0.787	0.588	1	1	0.9	1	CLONAL	2	TRUE	1	0.342198301581125	2		8	52	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797309	135797310	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTGC	novel	NA	P-0053316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	85	321	0	ENST00000298552.3:c.556_559dup	p.Leu187ArgfsTer32	p.L187Rfs*32	ENST00000298552	NM_001162426.1	187	ctc/cGCACtc	7/23	0.342198301581125	1	FACETS	0.921	0.818	1	0.921	0.818	1	CLONAL	1	TRUE	0	0.342198301581125	1		321	447	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62009557	62009557	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0053316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	65	646	0	ENST00000392795.3:c.65C>G	p.Ser22Ter	p.S22*	ENST00000392795	NM_001039933.1	22	tCa/tGa	1/6	0.30197851835599	1	FACETS	0.273	0.235	0.314	0.273	0.235	0.314	SUBCLONAL	1	TRUE	0	0.342198301581125	1		646	1155	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055674	152055675	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	103	527	0	ENST00000262189.6:c.247dup	p.Thr83AsnfsTer13	p.T83Nfs*13	ENST00000262189	NM_170606.2	83	aca/aAca	2/59	1	2	FACETS	0.912	0.817	1	0.912	0.817	1	CLONAL	1	TRUE	1	0.342198301581125	2		527	660	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175836	24175837	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555881563	NA	P-0053318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	42	755	0	ENST00000263121.7:c.1066_1067del	p.Leu356AspfsTer4	p.L356Dfs*4	ENST00000263121	NM_003073.3	355	aCT/a	8/9	0.353901810434777	1	FACETS	0.588	0.493	0.694	0.588	0.493	0.694	SUBCLONAL	1	TRUE	0	0.353901810434777	1		755	332	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518100	69518100	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	37	822	1	ENST00000294312.3:c.265A>T	p.Thr89Ser	p.T89S	ENST00000294312	NM_005117.2	89	Acc/Tcc	2/3	0.353901810434777	1	FACETS	0.6	0.496	0.714	0.6	0.496	0.714	SUBCLONAL	1	TRUE	0	0.353901810434777	1		823	287	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163374	108163381	+	frameshift_variant	Frame_Shift_Del	DEL	CGTAGCTT	CGTAGCTT	-	novel	NA	P-0053318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	74	287	0	ENST00000278616.4:c.4466_4473del	p.Arg1489LeufsTer5	p.R1489Lfs*5	ENST00000278616	NM_000051.3	1489	CGTAGCTTc/c	30/63	1	2	FACETS	0.843	0.74	0.954	0.843	0.74	0.954	CLONAL	1	TRUE	1	0.353901810434777	2		287	496	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003344	42003344	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	56	632	0	ENST00000219905.7:c.2881G>T	p.Glu961Ter	p.E961*	ENST00000219905	NM_001164273.1	961	Gaa/Taa	8/24	1	2	FACETS	0.673	0.578	0.777	0.673	0.578	0.777	SUBCLONAL	1	TRUE	1	0.353901810434777	2		632	470	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191470	10191470	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs5030817	NA	P-0053318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	58	476	0	ENST00000256474.2:c.464-1G>A		p.X155_splice	ENST00000256474	NM_000551.3	155			0.353901810434777	1	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	0	0.353901810434777	1		476	261	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539200	187539201	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0053318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	40	482	0	ENST00000441802.2:c.8538_8539dup	p.Ser2847IlefsTer27	p.S2847Ifs*27	ENST00000441802	NM_005245.3	2847	agc/aTAgc	10/27	1	2	FACETS	0.517	0.43	0.614	0.517	0.43	0.614	SUBCLONAL	1	TRUE	1	0.353901810434777	2		482	437	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499817	8499817	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	103	549	1	ENST00000356435.5:c.2152G>T	p.Val718Phe	p.V718F	ENST00000356435		718	Gtc/Ttc	14/35	0.353901810434777	1	FACETS	0.934	0.839	1	0.934	0.839	1	CLONAL	1	TRUE	0	0.353901810434777	1		550	513	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0053319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	260	430	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.240613780994016	3	FACETS	0.987	0.927	1			1	CLONAL	3	TRUE	NA	0.240613780994016	3		430	818	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0053319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	168	833	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.240613780994016	2		837	1021	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900171	101900171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564161322	NA	P-0053319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	67	345	0	ENST00000374994.4:c.605C>T	p.Ala202Val	p.A202V	ENST00000374994	NM_004612.2	202	gCg/gTg	4/9	0.240613780994016	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.240613780994016	1		345	371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28934873	NA	P-0053319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	178	932	0	ENST00000269305.4:c.398T>C	p.Met133Thr	p.M133T	ENST00000269305	NM_001126112.2	133	aTg/aCg	5/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.240613780994016	2		932	1175	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949124	44949124	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	123	225	0	ENST00000377967.4:c.3685C>T	p.Gln1229Ter	p.Q1229*	ENST00000377967	NM_021140.2	1229	Cag/Tag	25/29	1	1	FACETS	1	0.966	1	1	0.991	1	CLONAL	2	TRUE	0	0.240613780994016	1		225	402	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106356	27106356	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	119	699	0	ENST00000324856.7:c.5968del	p.Ser1990AlafsTer25	p.S1990Afs*25	ENST00000324856	NM_006015.4	1989	cgA/cg	20/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.240613780994016	2		699	835	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520302	176520302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	91	485	0	ENST00000292408.4:c.1221G>T	p.Gln407His	p.Q407H	ENST00000292408	NM_213647.1	407	caG/caT	9/18	0.240613780994016	3	FACETS	1	0.976	1	0.692	0.615	0.774	CLONAL	1	TRUE	1	0.240613780994016	3		485	612	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	45	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.786	0.678	0.899	0.786	0.678	0.899	SUBCLONAL	1	TRUE	1	0.908480228141572	2		429	126	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0053320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	271	496	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.908480228141572	2		496	513	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970834	55970834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747693621	NA	P-0053320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	264	546	0	ENST00000263923.4:c.1963G>A	p.Val655Met	p.V655M	ENST00000263923	NM_002253.2	655	Gtg/Atg	13/30	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.908480228141572	2		546	558	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363886	118363886	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	286	476	0	ENST00000534358.1:c.5119C>T	p.Gln1707Ter	p.Q1707*	ENST00000534358	NM_005933.3	1707	Cag/Tag	16/36	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.908480228141572	2		476	616	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	58	429	0				ENST00000310581	NM_198253.2	-/1132			0.385293774546703	3	FACETS	1	0.925	1	1	0.925	1	CLONAL	2	TRUE	1	0.440352688037268	3		429	150	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579349	7579349	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1567555667	NA	P-0053321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	224	703	0	ENST00000269305.4:c.338T>G	p.Phe113Cys	p.F113C	ENST00000269305	NM_001126112.2	113	tTc/tGc	4/11	0.440352688037268	2	FACETS	0.904	0.848	0.96	0.904	0.848	0.96	CLONAL	2	TRUE	0	0.440352688037268	2		703	563	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589581	67589583	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	novel	NA	P-0053321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	160	218	0	ENST00000274335.5:c.1345_1347del	p.Leu449del	p.L449del	ENST00000274335		448	aaATTa/aaa	10/15	0.440352688037268	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.440352688037268	3		218	414	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188296	10188297	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs869025653	NA	P-0053321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	83	474	0	ENST00000256474.2:c.444dup	p.Ala149CysfsTer25	p.A149Cfs*25	ENST00000256474	NM_000551.3	147	att/aTtt	2/3	0.440352688037268	1	FACETS	0.75	0.666	0.839	0.75	0.666	0.839	SUBCLONAL	1	TRUE	0	0.440352688037268	1		474	392	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52621438	52621438	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	99	427	0	ENST00000394830.3:c.2979del	p.Phe993LeufsTer15	p.F993Lfs*15	ENST00000394830	NM_018313.4	993	ttT/tt	20/30	0.440352688037268	1	FACETS	0.991	0.893	1	0.991	0.893	1	CLONAL	1	TRUE	0	0.440352688037268	1		427	354	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	25	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	FALSE	1	0.315552153128894	2		429	143	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	281	706	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.300491685802337	2	FACETS	0.932	0.878	0.989	0.932	0.878	0.989	CLONAL	2	FALSE	0	0.315552153128894	2		706	955	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0053322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	83	335	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.987	0.873	1	0.987	0.873	1	CLONAL	1	FALSE	1	0.315552153128894	2		335	533	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533701	63533701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	166	559	0	ENST00000307078.5:c.1453G>A	p.Gly485Ser	p.G485S	ENST00000307078	NM_004655.3	485	Ggc/Agc	6/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.315552153128894	2		559	863	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0053322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	50	263	0	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	0.139307331148903	1	FACETS	0.776	0.661	0.901	0.776	0.661	0.901	INDETERMINATE	1	FALSE	0	0.315552153128894	1		263	344	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045656	47045656	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0053322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	210	472	0	ENST00000377604.3:c.2538-1G>A		p.X846_splice	ENST00000377604	NM_001204468.1	846			1	1	FACETS	0.837	0.78	0.894	1	0.993	1	CLONAL	2	FALSE	0	0.315552153128894	1		472	670	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196936	106196936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	53	371	0	ENST00000380013.4:c.5269C>T	p.His1757Tyr	p.H1757Y	ENST00000380013	NM_001127208.2	1757	Cat/Tat	11/11	1	2	FACETS	0.556	0.474	0.647	0.556	0.474	0.647	SUBCLONAL	1	FALSE	1	0.315552153128894	2		371	604	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480346	89480346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748206093	NA	P-0053322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	30	341	0	ENST00000336596.2:c.2183G>A	p.Arg728Gln	p.R728Q	ENST00000336596	NM_005233.5	728	cGa/cAa	13/17	1	2	FACETS	0.376	0.302	0.46	0.376	0.302	0.46	SUBCLONAL	1	FALSE	1	0.315552153128894	2		341	506	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337717	73337718	+	missense_variant	Missense_Mutation	DNP	TA	TA	AT	novel	NA	P-0053322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	72	233	0	ENST00000377767.4:c.1998_1999delinsAT	p.Phe666_Met667delinsLeuLeu	p.F666_M667delinsLL	ENST00000377767	NM_014953.3	666	ttTAtg/ttATtg	16/21	1	2	FACETS	0.949	0.831	1	0.949	0.831	1	CLONAL	1	FALSE	1	0.315552153128894	2		233	481	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642845	3642845	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	159	689	0	ENST00000294008.3:c.2182G>C	p.Ala728Pro	p.A728P	ENST00000294008	NM_032444.2	728	Gct/Cct	11/15	0.139307331148903	1	FACETS	0.9	0.825	0.979	0.9	0.825	0.979	INDETERMINATE	1	FALSE	0	0.315552153128894	1		689	943	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41199721	41199721	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0053322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	64	637	1	ENST00000357654.3:c.5407-1G>T		p.X1803_splice	ENST00000357654	NM_007294.3	1803			1	2	FACETS	0.45	0.389	0.517	0.45	0.389	0.517	SUBCLONAL	1	FALSE	1	0.315552153128894	2		638	901	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39772499	39772499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	120	558	0	ENST00000288319.7:c.742C>T	p.Pro248Ser	p.P248S	ENST00000288319	NM_182918.3	248	Cca/Tca	6/10	1	2	FACETS	0.894	0.807	0.986	0.894	0.807	0.986	CLONAL	1	FALSE	1	0.315552153128894	2		558	851	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652125	36652132	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCGAGG	CGGCGAGG	-	novel	NA	P-0053322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	232	869	0	ENST00000244741.5:c.248_255del	p.Arg83ProfsTer3	p.R83Pfs*3	ENST00000244741	NM_000389.4	83	CGGCGAGGc/c	2/3	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.315552153128894	2		869	1408	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878307	151878307	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	160	604	0	ENST00000262189.6:c.6638G>A	p.Gly2213Glu	p.G2213E	ENST00000262189	NM_170606.2	2213	gGa/gAa	36/59	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.315552153128894	2		604	935	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	24	429	0				ENST00000310581	NM_198253.2	-/1132			0.32566676439542	1	FACETS	0.914	0.726	1	0.914	0.726	1	CLONAL	1	TRUE	0	0.32566676439542	1		429	135	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0053324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	264	778	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.313046521596625	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	0	0.32566676439542	2		779	809	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443642	29443642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113994089	NA	P-0053324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	133	641	0	ENST00000389048.3:c.3575G>A	p.Arg1192Gln	p.R1192Q	ENST00000389048	NM_004304.4	1192	cGg/cAg	23/29	1	2	FACETS	0.935	0.848	1	0.935	0.848	1	CLONAL	1	TRUE	1	0.32566676439542	2		641	874	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797891	45797891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199840380	NA	P-0053324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	147	800	0	ENST00000450313.1:c.880C>T	p.Arg294Cys	p.R294C	ENST00000450313	NM_012222.2	294	Cgc/Tgc	10/16	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.32566676439542	2		800	840	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838114	89838114	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	69	490	0	ENST00000389301.3:c.2123C>A	p.Thr708Lys	p.T708K	ENST00000389301	NM_000135.2	708	aCg/aAg	23/43	1	2	FACETS	0.611	0.532	0.697	0.611	0.532	0.697	SUBCLONAL	1	TRUE	1	0.32566676439542	2		490	693	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164836	36164837	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCGGGGGTCGGAGATGGAGGGCAGC	novel	NA	P-0053324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	88	723	0	ENST00000300305.3:c.1014_1038dup	p.Met347AlafsTer261	p.M347Afs*261	ENST00000300305		346	-/GCTGCCCTCCATCTCCGACCCCCGC	8/8	1	2	FACETS	0.6	0.531	0.675	0.6	0.531	0.675	SUBCLONAL	1	TRUE	1	0.32566676439542	2		723	900	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400232	139400232	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	179	588	0	ENST00000277541.6:c.4116C>A	p.Cys1372Ter	p.C1372*	ENST00000277541	NM_017617.3	1372	tgC/tgA	25/34	0.32566676439542	1	FACETS	0.826	0.767	0.887	1	0.992	1	CLONAL	2	TRUE	0	0.32566676439542	1		588	557	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022643	31022643	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs772303842	NA	P-0053331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	87	635	0	ENST00000375687.4:c.2129del	p.Gly710GlufsTer15	p.G710Efs*15	ENST00000375687	NM_015338.5	710	Gga/ga	13/13	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.391221187507129	2		635	440	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427465	427466	+	missense_variant	Missense_Mutation	DNP	GA	GA	AG	novel	NA	P-0053331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	75	535	2	ENST00000399788.2:c.2703_2704delinsCT	p.Arg902Trp	p.R902W	ENST00000399788	NM_001042603.1	901	gcTCgg/gcCTgg	19/28	0.28617202879586	1	FACETS	0.783	0.69	0.882	0.783	0.69	0.882	SUBCLONAL	1	TRUE	0	0.391221187507129	1		537	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577115	7577115	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519983	NA	P-0053333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	40	748	0	ENST00000269305.4:c.823T>C	p.Cys275Arg	p.C275R	ENST00000269305	NM_001126112.2	275	Tgt/Cgt	8/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		748	1078	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240285	41240285	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	15	308	0	ENST00000379561.5:c.65C>G	p.Ser22Trp	p.S22W	ENST00000379561	NM_002015.3	22	tCg/tGg	1/3	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		308	603	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922785	44922786	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	28	302	0	ENST00000377967.4:c.1647dup	p.Val550SerfsTer3	p.V550Sfs*3	ENST00000377967	NM_021140.2	549	aga/agAa	16/29	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	0	NA	2		302	402	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	11	429	0				ENST00000310581	NM_198253.2	-/1132			0.183378103843999	3	FACETS	0.673	0.466	0.929	0.337	0.233	0.465	SUBCLONAL	1	TRUE	1	0.21	3		429	172	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652054	36652055	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0053334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	73	1012	0	ENST00000244741.5:c.178dup	p.Glu60GlyfsTer3	p.E60Gfs*3	ENST00000244741	NM_000389.4	59	ctg/ctGg	2/3	1	2	FACETS	0.8	0.698	0.91	0.8	0.698	0.91	CLONAL	1	TRUE	1	0.21	2		1012	869	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221267	36221267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	40	877	0	ENST00000222270.7:c.5101G>A	p.Asp1701Asn	p.D1701N	ENST00000222270	NM_014727.1	1701	Gat/Aat	24/37	1	2	FACETS	0.527	0.436	0.628	0.527	0.436	0.628	SUBCLONAL	1	TRUE	1	0.21	2		877	723	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488249	56488249	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	75	703	0	ENST00000267101.3:c.1768C>G	p.Pro590Ala	p.P590A	ENST00000267101	NM_001982.3	590	Ccc/Gcc	15/28	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.21	2		703	593	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504261	8504261	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0053334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	42	488	0	ENST00000356435.5:c.1822A>T	p.Lys608Ter	p.K608*	ENST00000356435		608	Aag/Tag	12/35	1	2	FACETS	0.995	0.832	1	0.995	0.832	1	CLONAL	1	TRUE	1	0.21	2		488	402	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503093	125503093	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	18	394	0	ENST00000428830.2:c.460G>A	p.Val154Ile	p.V154I	ENST00000428830	NM_001114121.2	154	Gta/Ata	6/14	1	2	FACETS	0.512	0.385	0.662	0.512	0.385	0.662	SUBCLONAL	1	TRUE	1	0.21	2		394	335	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929491	81929491	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	91	621	0	ENST00000359376.3:c.1152C>A	p.Asp384Glu	p.D384E	ENST00000359376	NM_002661.3	384	gaC/gaA	13/33	0.183378103843999	3	FACETS	0.777	0.691	0.869	0.777	0.691	0.869	SUBCLONAL	2	TRUE	1	0.21	3		621	616	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160339	99160339	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0053334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	52	544	0	ENST00000074304.5:c.819-1G>A		p.X273_splice	ENST00000074304	NM_001134224.1	273			1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.21	2		544	393	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39708813	39708813	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	41	364	0	ENST00000361337.2:c.424G>A	p.Glu142Lys	p.E142K	ENST00000361337	NM_003286.2	142	Gag/Aag	6/21	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.21	2		364	277	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259149	36259149	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	33	505	0	ENST00000300305.3:c.342C>G	p.Ile114Met	p.I114M	ENST00000300305		114	atC/atG	3/8	1	2	FACETS	0.672	0.546	0.813	0.672	0.546	0.813	SUBCLONAL	1	TRUE	1	0.21	2		505	468	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680713	30680713	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	28	684	0	ENST00000376406.3:c.1006G>C	p.Glu336Gln	p.E336Q	ENST00000376406	NM_014641.2	336	Gag/Cag	5/15	1	2	FACETS	0.55	0.439	0.677	0.55	0.439	0.677	SUBCLONAL	1	TRUE	1	0.21	2		684	485	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400138	139400138	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	66	887	0	ENST00000277541.6:c.4210G>T	p.Glu1404Ter	p.E1404*	ENST00000277541	NM_017617.3	1404	Gag/Tag	25/34	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.21	2		887	598	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0053336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	15	330	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.522	0.385	0.682	0.522	0.385	0.682	SUBCLONAL	1	TRUE	1	0.487095438275762	2		330	118	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0053336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	101	205	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.947	0.851	1	0.947	0.851	1	CLONAL	1	TRUE	1	0.487095438275762	2		205	438	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	40	439	1	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	0.487095438275762	1	FACETS	0.971	0.825	1	0.971	0.825	1	CLONAL	1	TRUE	0	0.487095438275762	1		440	128	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579533	7579533	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	496	803	0	ENST00000269305.4:c.154C>T	p.Gln52Ter	p.Q52*	ENST00000269305	NM_001126112.2	52	Caa/Taa	4/11	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.487095438275762	2		803	920	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412958	49412958	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	217	696	0	ENST00000418115.1:c.65T>G	p.Leu22Arg	p.L22R	ENST00000418115	NM_001664.2	22	cTc/cGc	2/5	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.487095438275762	2		696	757	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435381	18435381	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	63	365	0	ENST00000266497.5:c.366A>C	p.Lys122Asn	p.K122N	ENST00000266497		122	aaA/aaC	1/31	1	2	FACETS	0.901	0.787	1	0.901	0.787	1	CLONAL	1	TRUE	1	0.487095438275762	2		365	287	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644521	21644521	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	91	611	0	ENST00000421138.2:c.146G>C	p.Cys49Ser	p.C49S	ENST00000421138		49	tGt/tCt	4/16	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.487095438275762	2		611	371	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599042	28599042	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	61	604	0	ENST00000241453.7:c.2246C>G	p.Ser749Trp	p.S749W	ENST00000241453	NM_004119.2	749	tCg/tGg	18/24	0.465544544937415	3	FACETS	1	0.879	1	0.506	0.439	0.577	CLONAL	1	TRUE	1	0.487095438275762	3		604	308	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435391	110435391	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1376455593	NA	P-0053336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	149	530	2	ENST00000375856.3:c.3010G>A	p.Gly1004Ser	p.G1004S	ENST00000375856	NM_003749.2	1004	Ggc/Agc	1/2	0.244908427942705	1	FACETS	0.748	0.686	0.812	0.748	0.686	0.812	INDETERMINATE	1	TRUE	0	0.487095438275762	1		532	619	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99491816	99491816	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556493537	NA	P-0053336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	138	478	0	ENST00000268035.6:c.3601G>A	p.Val1201Ile	p.V1201I	ENST00000268035	NM_000875.3	1201	Gtc/Atc	20/21	1	2	FACETS	0.996	0.91	1	0.996	0.91	1	CLONAL	1	TRUE	1	0.487095438275762	2		478	569	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819721	81819721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370352962	NA	P-0053336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	193	645	0	ENST00000359376.3:c.127G>A	p.Val43Ile	p.V43I	ENST00000359376	NM_002661.3	43	Gtc/Atc	2/33	0.487095438275762	1	FACETS	0.968	0.901	1	0.968	0.901	1	CLONAL	1	TRUE	0	0.487095438275762	1		645	619	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119961	70120012	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCAGCACCGCGGCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAG	CAGCAGCACCGCGGCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAG	-	novel	NA	P-0053336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	137	299	0	ENST00000245479.2:c.969_1020del	p.Ser323ArgfsTer43	p.S323Rfs*43	ENST00000245479	NM_000346.3	321	atCAGCAGCACCGCGGCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAG/at	3/3	0.487095438275762	2	FACETS	0.756	0.696	0.818	0.756	0.696	0.818	SUBCLONAL	2	TRUE	0	0.487095438275762	2		299	372	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11022941	11022941	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	183	688	0	ENST00000327064.4:c.640G>C	p.Glu214Gln	p.E214Q	ENST00000327064	NM_199141.1	214	Gag/Cag	5/16	0.465544544937415	3	FACETS	0.82	0.756	0.888	0.41	0.378	0.444	CLONAL	1	TRUE	1	0.487095438275762	3		688	1139	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390140	89390140	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	101	387	1	ENST00000336596.2:c.889C>T	p.Gln297Ter	p.Q297*	ENST00000336596	NM_005233.5	297	Cag/Tag	4/17	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.487095438275762	2		388	369	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855964	76855964	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0053336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	45	600	0	ENST00000373344.5:c.5636T>G	p.Leu1879Ter	p.L1879*	ENST00000373344	NM_000489.3	1879	tTa/tGa	23/35	1	2	FACETS	0.915	0.778	1	0.915	0.778	1	CLONAL	1	TRUE	1	0.487095438275762	2		600	202	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0053341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	139	432	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	NA	2	FACETS	1	0.954	1			1	INDETERMINATE	1	TRUE	NA	0.58003373759663	2		432	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0053341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	359	1171	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.58003373759663	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.58003373759663	1		1171	759	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	322	302	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	0.58003373759663	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	0	0.58003373759663	3		302	472	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56787260	56787260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881925	NA	P-0053341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	44	622	1	ENST00000337432.4:c.746G>A	p.Arg249His	p.R249H	ENST00000337432	NM_058216.2	249	cGt/cAt	5/9	1	2	FACETS	0.228	0.19	0.269	0.228	0.19	0.269	SUBCLONAL	1	TRUE	1	0.58003373759663	2		623	666	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437542	110437542	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	245	704	0	ENST00000375856.3:c.859A>T	p.Ile287Phe	p.I287F	ENST00000375856	NM_003749.2	287	Atc/Ttc	1/2	0.576049422777584	4	FACETS	0.949	0.885	1	0.316	0.295	0.339	CLONAL	1	TRUE	1	0.58003373759663	4		704	1406	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459435	50459435	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1222867974	NA	P-0053341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	79	326	0	ENST00000331340.3:c.724G>C	p.Glu242Gln	p.E242Q	ENST00000331340	NM_006060.4	242	Gaa/Caa	7/8	1	2	FACETS	0.691	0.611	0.776	0.691	0.611	0.776	SUBCLONAL	1	TRUE	1	0.58003373759663	2		326	394	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0053342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	102	353	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.468547175509363	2		353	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0053342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	215	633	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.468547175509363	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.468547175509363	1		633	667	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0053342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	78	376	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.968	0.857	1	0.968	0.857	1	CLONAL	1	TRUE	1	0.468547175509363	2		376	344	SUCCESS
APC	324	MSKCC	GRCh37	5	112176027	112176030	+	frameshift_variant	Frame_Shift_Del	DEL	TTAT	TTAT	-	novel	NA	P-0053342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	78	346	0	ENST00000257430.4:c.4738_4741del	p.Ile1580LeufsTer69	p.I1580Lfs*69	ENST00000257430	NM_000038.5	1579	aTTATt/at	16/16	1	2	FACETS	0.839	0.741	0.942	0.839	0.741	0.942	CLONAL	1	TRUE	1	0.468547175509363	2		346	397	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962960	2962960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745349548	NA	P-0053342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	199	907	0	ENST00000396946.4:c.1948C>T	p.Arg650Trp	p.R650W	ENST00000396946	NM_032415.4	650	Cgg/Tgg	16/25	0.469035238785441	3	FACETS	1	0.967	1	0.538	0.498	0.58	CLONAL	1	TRUE	1	0.468547175509363	3		907	974	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015056	37015056	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	152	711	0	ENST00000358127.4:c.348C>A	p.Asp116Glu	p.D116E	ENST00000358127	NM_001280556.1	116	gaC/gaA	3/10	1	2	FACETS	0.932	0.855	1	0.932	0.855	1	CLONAL	1	TRUE	1	0.468547175509363	2		711	696	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44910953	44910953	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0053342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	84	155	0	ENST00000377967.4:c.655-1G>A		p.X219_splice	ENST00000377967	NM_021140.2	219			1	1	FACETS	0.853	0.776	0.929	1	0.986	1	CLONAL	2	TRUE	0	0.468547175509363	1		155	161	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023810	27023810	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	39	238	0	ENST00000324856.7:c.916C>G	p.Arg306Gly	p.R306G	ENST00000324856	NM_006015.4	306	Cgg/Ggg	1/20	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	FALSE	1	0.2462207578727	2		238	282	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873248	71873248	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	46	381	1	ENST00000357731.5:c.946A>T	p.Ser316Cys	p.S316C	ENST00000357731	NM_173808.2	316	Agt/Tgt	7/7	1	2	FACETS	0.671	0.564	0.788	0.671	0.564	0.788	SUBCLONAL	1	FALSE	1	0.2462207578727	2		382	557	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981855	201981855	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771105129	NA	P-0053343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	381	862	1	ENST00000359651.3:c.566C>T	p.Pro189Leu	p.P189L	ENST00000359651		189	cCc/cTc	4/8	0.2462207578727	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	FALSE	1	0.2462207578727	3		863	1470	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226579937	226579937	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1481258529	NA	P-0053343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	124	611	1	ENST00000366794.5:c.365G>A	p.Arg122Lys	p.R122K	ENST00000366794	NM_001618.3	122	aGa/aAa	3/23	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	1	0.2462207578727	2		612	946	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404563	70404563	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	39	441	0	ENST00000373644.4:c.2077G>T	p.Glu693Ter	p.E693*	ENST00000373644	NM_030625.2	693	Gaa/Taa	4/12	0.102580229250775	0	FACETS	0.348	0.287	0.416			1	INDETERMINATE	1	FALSE	0	0.2462207578727	0		441	686	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449502	32449502	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	118	775	2	ENST00000332351.3:c.872G>A	p.Ser291Asn	p.S291N	ENST00000332351	NM_024426.4	291	aGt/aAt	3/10	1	2	FACETS	0.8	0.72	0.885	0.8	0.72	0.885	SUBCLONAL	1	FALSE	1	0.2462207578727	2		777	1198	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631086	69631086	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1554981074	NA	P-0053343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	49	546	0	ENST00000334134.2:c.324+2T>C		p.X108_splice	ENST00000334134	NM_005247.2	108			1	2	FACETS	0.497	0.42	0.583	0.497	0.42	0.583	SUBCLONAL	1	FALSE	1	0.2462207578727	2		546	801	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869552	102869552	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	178	562	0	ENST00000307046.8:c.89C>A	p.Ser30Ter	p.S30*	ENST00000307046	NM_001111285.1	30	tCg/tAg	2/4	1	2	FACETS	0.767	0.707	0.83	1	0.99	1	SUBCLONAL	2	FALSE	1	0.2462207578727	2		562	942	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112128	115112128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	163	510	0	ENST00000257566.3:c.1612G>A	p.Gly538Ser	p.G538S	ENST00000257566	NM_016569.3	538	Ggc/Agc	7/8	1	2	FACETS	0.84	0.772	0.911	1	0.99	1	CLONAL	2	FALSE	1	0.2462207578727	2		510	788	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257865	133257865	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	105	385	0	ENST00000320574.5:c.63G>T	p.Arg21Ser	p.R21S	ENST00000320574	NM_006231.2	21	agG/agT	2/49	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.2462207578727	2		385	667	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614513	38614513	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	112	509	0	ENST00000299084.4:c.279G>T	p.Lys93Asn	p.K93N	ENST00000299084	NM_152594.2	93	aaG/aaT	3/7	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.2462207578727	2		509	711	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813807	50813812	+	frameshift_variant	Frame_Shift_Del	DEL	GTCCAC	GTCCAC	TTCTT	novel	NA	P-0053343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	111	733	3	ENST00000398568.2:c.1361_1366delinsTTCTT	p.Ser454IlefsTer14	p.S454Ifs*14	ENST00000398568	NM_001042412.1	454	aGTCCACcc/aTTCTTcc	8/18	1	2	FACETS	0.885	0.794	0.982	0.885	0.794	0.982	CLONAL	1	FALSE	1	0.2462207578727	2		736	1019	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0053343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	143	682	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.172880480963763	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	0	0.2462207578727	1		682	940	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267400	7267400	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	202	533	0	ENST00000302850.5:c.608G>T	p.Gly203Val	p.G203V	ENST00000302850	NM_000208.2	203	gGg/gTg	2/22	0.20266664793746	2	FACETS	0.919	0.852	0.987	0.919	0.852	0.987	CLONAL	2	FALSE	0	0.2462207578727	2		533	893	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169040	11169040	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0053343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	228	637	0	ENST00000358026.2:c.4629+1G>C		p.X1543_splice	ENST00000358026	NM_001128849.1	1543			0.20266664793746	2	FACETS	0.898	0.837	0.961	0.898	0.837	0.961	CLONAL	2	FALSE	0	0.2462207578727	2		637	1031	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366207	15366207	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	186	639	0	ENST00000263377.2:c.1948G>T	p.Asp650Tyr	p.D650Y	ENST00000263377	NM_058243.2	650	Gac/Tac	10/20	0.20266664793746	2	FACETS	1	0.989	1	0.736	0.679	0.795	CLONAL	1	FALSE	0	0.2462207578727	2		639	1027	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010508	48010508	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	19	191	0	ENST00000234420.5:c.136G>T	p.Gly46Trp	p.G46W	ENST00000234420	NM_000179.2	46	Ggg/Tgg	1/10	0.102580229250775	0	FACETS	0.392	0.297	0.503			1	INDETERMINATE	1	FALSE	0	0.2462207578727	0		191	297	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584563	189584563	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	33	385	0	ENST00000264731.3:c.859C>A	p.Leu287Met	p.L287M	ENST00000264731	NM_003722.4	287	Ctg/Atg	6/14	0.20266664793746	2	FACETS	0.449	0.365	0.545	0.224	0.182	0.273	SUBCLONAL	1	FALSE	0	0.2462207578727	2		385	597	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587118	189587118	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	72	377	0	ENST00000264731.3:c.1135C>A	p.Arg379Ser	p.R379S	ENST00000264731	NM_003722.4	379	Cgt/Agt	9/14	0.20266664793746	2	FACETS	1	0.927	1	0.543	0.475	0.616	CLONAL	1	FALSE	0	0.2462207578727	2		377	539	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249505	153249505	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	121	452	1	ENST00000281708.4:c.1273T>A	p.Trp425Arg	p.W425R	ENST00000281708	NM_033632.3	425	Tgg/Agg	9/12	0.2462207578727	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	0	0.2462207578727	1		453	735	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683610	162683610	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	48	557	0	ENST00000366898.1:c.359C>A	p.Ala120Asp	p.A120D	ENST00000366898	NM_004562.2	120	gCt/gAt	3/12	0.2462207578727	1	FACETS	0.441	0.371	0.517	0.441	0.371	0.517	SUBCLONAL	1	FALSE	0	0.2462207578727	1		557	776	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220286	55220286	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0053343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1299	132	717	0	ENST00000275493.2:c.676A>T	p.Lys226Ter	p.K226*	ENST00000275493	NM_005228.3	226	Aag/Tag	6/28	0.2462207578727	4	FACETS	0.934	0.845	1	0.311	0.281	0.343	CLONAL	1	FALSE	1	0.2462207578727	4		717	1431	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372734	81372734	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs771889279	NA	P-0053343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	36	408	0	ENST00000222390.5:c.800C>A	p.Pro267Gln	p.P267Q	ENST00000222390	NM_000601.4	267	cCg/cAg	7/18	0.2462207578727	3	FACETS	0.47	0.385	0.566	0.235	0.192	0.283	SUBCLONAL	1	FALSE	1	0.2462207578727	3		408	699	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877938	151877938	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	78	405	0	ENST00000262189.6:c.7007C>A	p.Ala2336Glu	p.A2336E	ENST00000262189	NM_170606.2	2336	gCa/gAa	36/59	0.2462207578727	3	FACETS	0.877	0.77	0.993	0.439	0.385	0.497	CLONAL	1	FALSE	1	0.2462207578727	3		405	811	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989645	68989645	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	42	529	0	ENST00000288368.4:c.1583C>A	p.Thr528Asn	p.T528N	ENST00000288368	NM_024870.2	528	aCc/aAc	15/40	1	2	FACETS	0.493	0.41	0.585	0.493	0.41	0.585	SUBCLONAL	1	FALSE	1	0.2462207578727	2		529	692	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992992	68992992	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	54	345	0	ENST00000288368.4:c.1797T>A	p.Asn599Lys	p.N599K	ENST00000288368	NM_024870.2	599	aaT/aaA	17/40	1	2	FACETS	0.737	0.629	0.855	0.737	0.629	0.855	SUBCLONAL	1	FALSE	1	0.2462207578727	2		345	595	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031713	69031713	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	72	523	0	ENST00000288368.4:c.3468C>G	p.Asp1156Glu	p.D1156E	ENST00000288368	NM_024870.2	1156	gaC/gaG	28/40	1	2	FACETS	0.861	0.752	0.979	0.861	0.752	0.979	CLONAL	1	FALSE	1	0.2462207578727	2		523	679	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5456129	5456129	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	40	243	0	ENST00000381577.3:c.16G>C	p.Val6Leu	p.V6L	ENST00000381577	NM_014143.3	6	Gtc/Ctc	2/7	0.2462207578727	1	FACETS	0.729	0.606	0.864	0.729	0.606	0.864	SUBCLONAL	1	FALSE	0	0.2462207578727	1		243	391	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	28	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.921	0.757	1	0.921	0.757	1	CLONAL	1	TRUE	1	0.668018269611731	2		429	91	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0053344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	310	315	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.668018269611731	4	FACETS	0.953	0.903	1	0.953	0.903	1	CLONAL	2	TRUE	2	0.668018269611731	4		315	812	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163615	32163615	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1435864899	NA	P-0053344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	146	332	1	ENST00000375023.3:c.5611C>T	p.Arg1871Cys	p.R1871C	ENST00000375023	NM_004557.3	1871	Cgt/Tgt	30/30	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.668018269611731	2		333	385	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865773	57865773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	284	767	4	ENST00000228682.2:c.3250G>A	p.Ala1084Thr	p.A1084T	ENST00000228682	NM_005269.2	1084	Gct/Act	12/12	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.668018269611731	2		771	774	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946809	17946809	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257320432	NA	P-0053344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	257	868	1	ENST00000458235.1:c.1838G>A	p.Arg613Gln	p.R613Q	ENST00000458235	NM_000215.3	613	cGa/cAa	14/24	1	2	FACETS	0.997	0.937	1	0.997	0.937	1	CLONAL	1	TRUE	1	0.668018269611731	2		869	772	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80024721	80024721	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	191	462	0	ENST00000265081.6:c.1505C>T	p.Ser502Phe	p.S502F	ENST00000265081	NM_002439.4	502	tCt/tTt	10/24	1	2	FACETS	0.921	0.856	0.987	0.921	0.856	0.987	CLONAL	1	TRUE	1	0.668018269611731	2		462	621	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930617	131930617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	162	347	0	ENST00000265335.6:c.1850G>A	p.Arg617Lys	p.R617K	ENST00000265335		617	aGa/aAa	12/25	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.668018269611731	2		347	439	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381559	81381559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777026877	NA	P-0053344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	137	322	0	ENST00000222390.5:c.502C>T	p.Arg168Trp	p.R168W	ENST00000222390	NM_000601.4	168	Cgg/Tgg	5/18	1	2	FACETS	0.924	0.847	1	0.924	0.847	1	CLONAL	1	TRUE	1	0.668018269611731	2		322	444	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956771	68956771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774302685	NA	P-0053344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	296	645	1	ENST00000288368.4:c.889C>T	p.Arg297Cys	p.R297C	ENST00000288368	NM_024870.2	297	Cgt/Tgt	8/40	0.296510438557695	6	FACETS	0.874	0.823	0.927	0.437	0.411	0.464	INDETERMINATE	2	TRUE	2	0.668018269611731	6		646	1184	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410558	63410558	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	276	768	0	ENST00000330258.3:c.2609C>T	p.Pro870Leu	p.P870L	ENST00000330258	NM_152424.3	870	cCt/cTt	2/2	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.668018269611731	2		768	824	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	161	411	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.486942312002079	3	FACETS	0.782	0.722	0.843	0.782	0.722	0.843	SUBCLONAL	2	TRUE	1	0.486942312002079	3		411	526	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222982	1222982	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	rs727504172	NA	P-0053347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	160	628	0	ENST00000326873.7:c.921-2A>C		p.X307_splice	ENST00000326873	NM_000455.4	307			0.486942312002079	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.486942312002079	1		628	449	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715613	30715613	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs878854610	NA	P-0053347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	64	296	0	ENST00000295754.5:c.1271A>T	p.Tyr424Phe	p.Y424F	ENST00000295754	NM_003242.5	424	tAc/tTc	5/7	0.455281696357674	1	FACETS	0.739	0.647	0.837	0.739	0.647	0.837	SUBCLONAL	1	TRUE	0	0.486942312002079	1		296	269	SUCCESS
APC	324	MSKCC	GRCh37	5	112179409	112179416	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTAATG	GGGTAATG	-	novel	NA	P-0053348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	25	519	0	ENST00000257430.4:c.8119_8126del	p.Gly2707GlnfsTer23	p.G2707Qfs*23	ENST00000257430	NM_000038.5	2706	gtGGGTAATGgc/gtgc	16/16	1	2	FACETS	0.138	0.108	0.173	0.138	0.108	0.173	SUBCLONAL	1	TRUE	1	0.757332407516991	2		519	477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0053349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	188	778	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.342014789525372	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.342014789525372	2		779	473	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646264	3646264	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	59	616	0	ENST00000294008.3:c.1814G>T	p.Ser605Ile	p.S605I	ENST00000294008	NM_032444.2	605	aGc/aTc	8/15	0.342014789525372	3	FACETS	0.995	0.859	1	0.498	0.429	0.571	CLONAL	1	TRUE	1	0.342014789525372	3		616	406	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	34	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.796	0.667	0.934	0.796	0.667	0.934	CLONAL	1	TRUE	1	0.776179682902524	2		429	110	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0053350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	142	284	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.963	0.888	1	0.963	0.888	1	CLONAL	1	TRUE	1	0.776179682902524	2		284	380	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412381	139412381	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	45	741	0	ENST00000277541.6:c.1264C>T	p.Pro422Ser	p.P422S	ENST00000277541	NM_017617.3	422	Ccc/Tcc	8/34	1	2	FACETS	0.172	0.144	0.204	0.172	0.144	0.204	SUBCLONAL	1	TRUE	1	0.776179682902524	2		741	673	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795757	42795757	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	24	905	0	ENST00000575354.2:c.2746C>T	p.Gln916Ter	p.Q916*	ENST00000575354	NM_015125.3	916	Cag/Tag	11/20	0.776179682902524	1	FACETS	0.082	0.064	0.104	0.082	0.064	0.104	SUBCLONAL	1	TRUE	0	0.776179682902524	1		905	459	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429338	78429338	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	172	492	1	ENST00000370768.2:c.1104G>A	p.Trp368Ter	p.W368*	ENST00000370768	NM_003902.3	368	tgG/tgA	13/20	0.776179682902524	1	FACETS	0.716	0.668	0.764	0.716	0.668	0.764	SUBCLONAL	1	TRUE	0	0.776179682902524	1		493	379	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794830	42794831	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGAGGAGCAAGAG	novel	NA	P-0053350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	21	747	0	ENST00000575354.2:c.1913_1925dup	p.Gly644AlafsTer50	p.G644Afs*50	ENST00000575354	NM_015125.3	637	aag/aaGGAGGAGCAAGAGg	10/20	0.776179682902524	1	FACETS	0.102	0.078	0.13	0.102	0.078	0.13	SUBCLONAL	1	TRUE	0	0.776179682902524	1		747	325	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797959	42797963	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGA	CCTGA	-	novel	NA	P-0053350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	49	841	1	ENST00000575354.2:c.4011_4015del	p.Leu1338GlufsTer4	p.L1338Efs*4	ENST00000575354	NM_015125.3	1337	ccCCTGAag/ccag	16/20	0.776179682902524	1	FACETS	0.191	0.162	0.223	0.191	0.162	0.223	SUBCLONAL	1	TRUE	0	0.776179682902524	1		842	405	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0053355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	95	430	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.322738711611099	2		430	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519980	NA	P-0053355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	326	730	0	ENST00000269305.4:c.528C>G	p.Cys176Trp	p.C176W	ENST00000269305	NM_001126112.2	176	tgC/tgG	5/11	0.286443794831911	2	FACETS	0.804	0.759	0.85	0.804	0.759	0.85	CLONAL	2	TRUE	0	0.322738711611099	2		730	1256	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492890	56492906	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGCCAGGGCCAGAGG	GCAGCCAGGGCCAGAGG	-	novel	NA	P-0053355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	105	428	0	ENST00000407977.2:c.33_49del	p.Leu12AspfsTer22	p.L12Dfs*22	ENST00000407977		11	gcCCTCTGGCCCTGGCTGCtg/gctg	2/10	0.322738711611099	1	FACETS	0.954	0.857	1	0.954	0.857	1	CLONAL	1	TRUE	0	0.322738711611099	1		428	572	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215936	142215936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1031921536	NA	P-0053355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	93	455	0	ENST00000350721.4:c.5657G>A	p.Arg1886Gln	p.R1886Q	ENST00000350721	NM_001184.3	1886	cGa/cAa	33/47	1	2	FACETS	0.888	0.79	0.992	0.888	0.79	0.992	CLONAL	1	TRUE	1	0.322738711611099	2		455	649	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0053356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	47	743	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.988	0.834	1	0.988	0.834	1	CLONAL	1	TRUE	1	0.181506114007313	2		745	524	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0053356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	41	305	0				ENST00000310581	NM_198253.2	-/1132			0.151594305949714	0	FACETS	0.708	0.594	0.834			1	SUBCLONAL	2	TRUE	0	0.181506114007313	0		305	261	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0053356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	149	372	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.181506114007313	5	FACETS	0.903	0.829	0.98	0.903	0.829	0.98	CLONAL	4	TRUE	1	0.181506114007313	5		372	578	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971116	21971116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552823	NA	P-0053356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	49	614	0	ENST00000304494.5:c.242C>T	p.Pro81Leu	p.P81L	ENST00000304494	NM_000077.4	81	cCc/cTc	2/3	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.181506114007313	2		614	467	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645693	12645693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397516827	NA	P-0053356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	27	348	0	ENST00000251849.4:c.776C>T	p.Ser259Phe	p.S259F	ENST00000251849	NM_002880.3	259	tCc/tTc	7/17	0.181506114007313	1	FACETS	0.956	0.763	1	0.956	0.763	1	CLONAL	1	TRUE	0	0.181506114007313	1		348	283	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218086	108218086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781814	NA	P-0053356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	21	377	0	ENST00000278616.4:c.8665G>A	p.Asp2889Asn	p.D2889N	ENST00000278616	NM_000051.3	2889	Gat/Aat	59/63	1	2	FACETS	0.746	0.575	0.946	0.746	0.575	0.946	CLONAL	1	TRUE	1	0.181506114007313	2		377	310	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971018	21971018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104894104	NA	P-0053356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	34	662	3	ENST00000304494.5:c.340C>T	p.Pro114Ser	p.P114S	ENST00000304494	NM_000077.4	114	Ccc/Tcc	2/3	1	2	FACETS	0.901	0.736	1	0.901	0.736	1	CLONAL	1	TRUE	1	0.181506114007313	2		665	416	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248617	212248617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765120252	NA	P-0053356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	46	378	0	ENST00000342788.4:c.3650G>A	p.Gly1217Glu	p.G1217E	ENST00000342788	NM_005235.2	1217	gGa/gAa	28/28	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.181506114007313	2		378	447	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0053356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	88	813	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.181506114007313	2		813	693	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578400	7578400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751477326	NA	P-0053356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	66	846	0	ENST00000269305.4:c.530C>T	p.Pro177Leu	p.P177L	ENST00000269305	NM_001126112.2	177	cCc/cTc	5/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.181506114007313	2		846	549	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602518	10602518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	56	964	0	ENST00000171111.5:c.1060C>T	p.Arg354Trp	p.R354W	ENST00000171111	NM_203500.1	354	Cgg/Tgg	3/6	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.181506114007313	2		964	574	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499520	89499520	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	38	428	0	ENST00000336596.2:c.2690G>A	p.Arg897Lys	p.R897K	ENST00000336596	NM_005233.5	897	aGg/aAg	15/17	0.181506114007313	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.181506114007313	1		428	285	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888069	81888069	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	48	415	0	ENST00000359376.3:c.214G>A	p.Glu72Lys	p.E72K	ENST00000359376	NM_002661.3	72	Gaa/Aaa	3/33	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.181506114007313	2		415	367	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100221	30100221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	21	445	1	ENST00000331968.5:c.1399C>T	p.Pro467Ser	p.P467S	ENST00000331968	NM_002742.2	467	Cct/Tct	10/18	1	2	FACETS	0.754	0.581	0.956	0.754	0.581	0.956	CLONAL	1	TRUE	1	0.181506114007313	2		446	307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0053356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	49	786	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	1	2	FACETS	0.961	0.813	1	0.961	0.813	1	CLONAL	1	TRUE	1	0.181506114007313	2		786	562	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136900	55136900	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	38	443	0	ENST00000257290.5:c.1222G>T	p.Glu408Ter	p.E408*	ENST00000257290	NM_006206.4	408	Gaa/Taa	8/23	0.181506114007313	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.181506114007313	1		443	322	SUCCESS
APC	324	MSKCC	GRCh37	5	112175246	112175246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	32	250	0	ENST00000257430.4:c.3955C>T	p.Pro1319Ser	p.P1319S	ENST00000257430	NM_000038.5	1319	Cct/Tct	16/16	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.181506114007313	2		250	297	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066952	30066952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	21	402	0	ENST00000331968.5:c.2179G>A	p.Asp727Asn	p.D727N	ENST00000331968	NM_002742.2	727	Gat/Aat	16/18	1	2	FACETS	0.725	0.559	0.92	0.725	0.559	0.92	CLONAL	1	TRUE	1	0.181506114007313	2		402	319	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	465639	465639	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	41	744	2	ENST00000399788.2:c.737C>T	p.Pro246Leu	p.P246L	ENST00000399788	NM_001042603.1	246	cCc/cTc	6/28	1	2	FACETS	0.874	0.727	1	0.874	0.727	1	CLONAL	1	TRUE	1	0.181506114007313	2		746	517	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436021	49436022	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	52	775	0	ENST00000301067.7:c.5959_5960delinsTT	p.Pro1987Phe	p.P1987F	ENST00000301067	NM_003482.3	1987	CCc/TTc	28/54	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.181506114007313	2		775	520	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242049	105242050	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	54	949	2	ENST00000349310.3:c.374_375delinsTT	p.Pro125Leu	p.P125L	ENST00000349310	NM_001014432.1	125	cCC/cTT	6/15	1	2	FACETS	0.975	0.833	1	0.975	0.833	1	CLONAL	1	TRUE	1	0.181506114007313	2		951	610	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761449	59761450	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	28	437	1	ENST00000259008.2:c.2957_2958delinsTT	p.Ser986Phe	p.S986F	ENST00000259008	NM_032043.2	986	tCC/tTT	20/20	1	2	FACETS	0.859	0.687	1	0.859	0.687	1	CLONAL	1	TRUE	1	0.181506114007313	2		438	359	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39600643	39600643	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	34	311	0	ENST00000262039.4:c.1458C>G	p.Asn486Lys	p.N486K	ENST00000262039	NM_002647.2	486	aaC/aaG	13/25	1	2	FACETS	0.781	0.642	0.934	1	0.951	1	CLONAL	2	TRUE	1	0.181506114007313	2		311	240	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763461	41763461	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	37	712	0	ENST00000301178.4:c.2260G>A	p.Glu754Lys	p.E754K	ENST00000301178	NM_021913.4	754	Gag/Aag	19/20	1	2	FACETS	0.737	0.607	0.884	0.737	0.607	0.884	SUBCLONAL	1	TRUE	1	0.181506114007313	2		712	553	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150034	202150035	+	stop_gained	Nonsense_Mutation	DNP	GT	GT	AA	novel	NA	P-0053356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	42	527	0	ENST00000358485.4:c.1475_1476delinsAA	p.Cys492Ter	p.C492*	ENST00000358485	NM_001080125.1	492	tGT/tAA	8/9	1	2	FACETS	0.954	0.797	1	0.954	0.797	1	CLONAL	1	TRUE	1	0.181506114007313	2		527	485	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920212	1920212	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	66	707	1	ENST00000382891.5:c.1272A>T	p.Gln424His	p.Q424H	ENST00000382891	NM_133335.3	424	caA/caT	5/22	NA	2	FACETS	1	0.962	1			1	INDETERMINATE	1	TRUE	NA	0.181506114007313	2		708	555	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541772	187541772	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	41	439	0	ENST00000441802.2:c.5968G>A	p.Glu1990Lys	p.E1990K	ENST00000441802	NM_005245.3	1990	Gag/Aag	10/27	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.181506114007313	2		439	364	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169044	32169044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	46	911	1	ENST00000375023.3:c.3989G>A	p.Arg1330Lys	p.R1330K	ENST00000375023	NM_004557.3	1330	aGg/aAg	22/30	0.181506114007313	1	FACETS	0.759	0.638	0.893	0.759	0.638	0.893	SUBCLONAL	1	TRUE	0	0.181506114007313	1		912	607	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859482	151859482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755711561	NA	P-0053356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	36	558	2	ENST00000262189.6:c.11180C>T	p.Ser3727Phe	p.S3727F	ENST00000262189	NM_170606.2	3727	tCc/tTc	43/59	1	2	FACETS	0.893	0.734	1	0.893	0.734	1	CLONAL	1	TRUE	1	0.181506114007313	2		560	444	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139563100	139563101	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	45	807	2	ENST00000308874.7:c.172_173delinsAA	p.Gly58Lys	p.G58K	ENST00000308874		58	GGg/AAg	4/10	1	2	FACETS	0.934	0.784	1	0.934	0.784	1	CLONAL	1	TRUE	1	0.181506114007313	2		809	531	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934316	39934316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1423559369	NA	P-0053356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	49	335	0	ENST00000378444.4:c.283G>A	p.Gly95Arg	p.G95R	ENST00000378444	NM_001123385.1	95	Gga/Aga	4/15	1	1	FACETS	0.858	0.732	0.995	1	0.97	1	CLONAL	2	TRUE	0	0.181506114007313	1		335	286	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038782	47038783	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	63	467	2	ENST00000377604.3:c.789_790delinsAA	p.Glu264Lys	p.E264K	ENST00000377604	NM_001204468.1	263	cgGGag/cgAAag	9/24	1	1	FACETS	1	0.889	1	1	0.98	1	CLONAL	2	TRUE	0	0.181506114007313	1		469	309	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0053357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	32	572	1	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.308420325018324	3	FACETS	0.316	0.256	0.385	0.158	0.128	0.193	SUBCLONAL	1	TRUE	1	0.394439474846811	3		573	614	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061011	38061011	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	8	445	1	ENST00000250448.2:c.978del	p.Ala329ProfsTer21	p.A329Pfs*21	ENST00000250448	NM_004496.3	326	ccC/cc	2/2	0.320636650595793	3	FACETS	0.125	0.079	0.183	0.062	0.039	0.092	SUBCLONAL	1	TRUE	1	0.394439474846811	3		446	390	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197854	123197854	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	107	285	0	ENST00000218089.9:c.1978G>T	p.Glu660Ter	p.E660*	ENST00000218089	NM_001042749.1	660	Gaa/Taa	20/35	0.394439474846811	2	FACETS	0.864	0.785	0.945			1	CLONAL	2	TRUE	NA	0.394439474846811	2		285	314	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30059989	30061011	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTACTATAGTCCATTTTTTCCCCATTTGATTCTATTAACAGCTTTTACCAAATTATTCCCATGTTCAGAAACCTGTGGTGAGCTCAGGTATCCTGTCACATCAAACCTAAACCCTTCTTTTTTTTGAGATAGGGGTCTGCTCTGTTGCCCAGCCTGGAGTGCAGTTGTGCAATTACAGCTCACTGCAGCCTCAAACTCTTGGCCTCAAGCGATCCTCCTGCTTTGGCCTTCCAAAGTGTTGGGATTACGGGTGTGAGCCACCATATCTGGCCGCCTCTGACTTTTATTCTCACTGCCAGCCCCTACACCCACCCCTTCCTCCCTCTCAGGCTAAACCTATTATATCATCTTAGTCACCAAAAAGCTAATACCACACACACACACACACACACACACACACACACACAGCTCATTTCCCTGTCTCTACCTTATTTCTGGTTTTGCCCTGTGCAGAATGCCCCTTCACCTGCCTTTTAGCTACCCTGTTGGATTGTTCTTCTAAGATCAGCTTCACTCTCTCTTGCTTATGGTGGATCTACTCTGAACCTCCACATATTTGTGATTTGTACCACCCAGTGAAGCACTAATATTTGATGTGATTTCTTGAGTAATTGGCTGTTGTTAGCCTAGTTCCAACTAGATGGTGAGCTTCATGAAGGTGGGCCCATGCCCTCGACTACAGTAGCCCTCCAGTGTTGGCCTCAGGGTTGGGCCCATTAAGGATGCTTATTTTAGGTTGTCAAGAATCCCTTCCCACACTCATGCCTAAGATGGTCTAGAGAGCGTACCTTTAGGGTCCTGAGCTTCCACAGCCCGAGACTTGGTGCTCCTAATTCCCTGAGGTTTAGTGCCTGGATACTGGGAAGCCAGGACAAGGCATAACTTCATGCTGGTCTGTGGCCAGTGTGGTTGCGCATTTGTGGAATTTCCAATTGCTGGTAACATTCCAGGCTGTCGGACTGAAACTGTGTTCTGCTTCATTCTTCCAGTTTACTATTAAACCACTGGATAAGAAAATTGAT	TCTACTATAGTCCATTTTTTCCCCATTTGATTCTATTAACAGCTTTTACCAAATTATTCCCATGTTCAGAAACCTGTGGTGAGCTCAGGTATCCTGTCACATCAAACCTAAACCCTTCTTTTTTTTGAGATAGGGGTCTGCTCTGTTGCCCAGCCTGGAGTGCAGTTGTGCAATTACAGCTCACTGCAGCCTCAAACTCTTGGCCTCAAGCGATCCTCCTGCTTTGGCCTTCCAAAGTGTTGGGATTACGGGTGTGAGCCACCATATCTGGCCGCCTCTGACTTTTATTCTCACTGCCAGCCCCTACACCCACCCCTTCCTCCCTCTCAGGCTAAACCTATTATATCATCTTAGTCACCAAAAAGCTAATACCACACACACACACACACACACACACACACACACACAGCTCATTTCCCTGTCTCTACCTTATTTCTGGTTTTGCCCTGTGCAGAATGCCCCTTCACCTGCCTTTTAGCTACCCTGTTGGATTGTTCTTCTAAGATCAGCTTCACTCTCTCTTGCTTATGGTGGATCTACTCTGAACCTCCACATATTTGTGATTTGTACCACCCAGTGAAGCACTAATATTTGATGTGATTTCTTGAGTAATTGGCTGTTGTTAGCCTAGTTCCAACTAGATGGTGAGCTTCATGAAGGTGGGCCCATGCCCTCGACTACAGTAGCCCTCCAGTGTTGGCCTCAGGGTTGGGCCCATTAAGGATGCTTATTTTAGGTTGTCAAGAATCCCTTCCCACACTCATGCCTAAGATGGTCTAGAGAGCGTACCTTTAGGGTCCTGAGCTTCCACAGCCCGAGACTTGGTGCTCCTAATTCCCTGAGGTTTAGTGCCTGGATACTGGGAAGCCAGGACAAGGCATAACTTCATGCTGGTCTGTGGCCAGTGTGGTTGCGCATTTGTGGAATTTCCAATTGCTGGTAACATTCCAGGCTGTCGGACTGAAACTGTGTTCTGCTTCATTCTTCCAGTTTACTATTAAACCACTGGATAAGAAAATTGAT	-	novel	NA	P-0053357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	.	64	0	0	ENST00000338641.4:c.811-990_843del		p.X271_splice	ENST00000338641	NM_000268.3	271		9/16	0.394439474846811	1	FACETS		NA	1			1	NA	NA	TRUE	0	0.394439474846811	1		0	64	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595798	52595798	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0053357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	208	535	0	ENST00000394830.3:c.4117A>T	p.Lys1373Ter	p.K1373*	ENST00000394830	NM_018313.4	1373	Aaa/Taa	26/30	0.270044301762311	3	FACETS	1	0.98	1	0.745	0.697	0.794	CLONAL	2	TRUE	0	0.394439474846811	3		535	565	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528015	157528015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs530153456	NA	P-0053357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	158	648	2	ENST00000346085.5:c.5740C>T	p.Arg1914Trp	p.R1914W	ENST00000346085	NM_020732.3	1914	Cgg/Tgg	20/20	0.308420325018324	3	FACETS	0.833	0.767	0.901	0.833	0.767	0.901	CLONAL	2	TRUE	1	0.394439474846811	3		650	576	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225138	53225139	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	A	novel	NA	P-0053357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	180	452	0	ENST00000375401.3:c.3079_3080delinsT	p.Ala1027LeufsTer28	p.A1027Lfs*28	ENST00000375401	NM_004187.3	1027	GCt/Tt	20/26	0.394439474846811	2	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.394439474846811	2		452	398	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188194	10188196	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	ATA	ATA	CT	novel	NA	P-0053357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	249	547	3	ENST00000256474.2:c.341-4_341-2delinsCT		p.X114_splice	ENST00000256474	NM_000551.3	114			0.363895252024529	3	FACETS	1	0.99	1	0.831	0.784	0.88	CLONAL	2	TRUE	0	0.394439474846811	3		550	606	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038895	47038895	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0053358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	190	747	0	ENST00000377604.3:c.901+1G>A		p.X301_splice	ENST00000377604	NM_001204468.1	301			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.472411766014649	2		747	723	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653026	29653027	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGCAGT	novel	NA	P-0053358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	113	430	0	ENST00000356175.3:c.4963_4968dup	p.Ala1655_Val1656dup	p.A1655_V1656dup	ENST00000356175	NM_000267.3	1655	tcc/tcCGCAGTc	36/57	0.472411766014649	3	FACETS	0.82	0.739	0.906	0.41	0.369	0.453	CLONAL	1	TRUE	1	0.472411766014649	3		430	721	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653034	29653034	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	122	421	0	ENST00000356175.3:c.4969T>G	p.Tyr1657Asp	p.Y1657D	ENST00000356175	NM_000267.3	1657	Tat/Gat	36/57	0.472411766014649	3	FACETS	0.95	0.86	1	0.475	0.43	0.523	CLONAL	1	TRUE	1	0.472411766014649	3		421	672	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66518990	66518990	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	43	455	0	ENST00000358598.2:c.271G>C	p.Val91Leu	p.V91L	ENST00000358598	NM_212471.2	91	Gtt/Ctt	3/11	0.472411766014649	3	FACETS	0.271	0.226	0.321	0.135	0.113	0.161	SUBCLONAL	1	TRUE	1	0.472411766014649	3		455	831	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982442	10982442	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	12	37	0	ENST00000327064.4:c.64G>T	p.Gly22Cys	p.G22C	ENST00000327064	NM_199141.1	22	Ggc/Tgc	1/16	1	2	FACETS	0.794	0.59	1	1	0.894	1	CLONAL	2	TRUE	1	0.472411766014649	2		37	32	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0053359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	68	330	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.396	0.344	0.452	0.396	0.344	0.452	SUBCLONAL	1	TRUE	1	0.588230060126098	2		330	584	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420777	49420777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761108868	NA	P-0053359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	82	643	0	ENST00000301067.7:c.14972G>A	p.Arg4991Gln	p.R4991Q	ENST00000301067	NM_003482.3	4991	cGg/cAg	48/54	1	2	FACETS	0.335	0.294	0.378	0.335	0.294	0.378	SUBCLONAL	1	TRUE	1	0.588230060126098	2		643	833	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442071	52442072	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	A	novel	NA	P-0053359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	198	554	0	ENST00000460680.1:c.277_278delinsT	p.Thr93PhefsTer5	p.T93Ffs*5	ENST00000460680	NM_004656.3	93	ACt/Tt	5/17	0.588230060126098	1	FACETS	0.869	0.811	0.928	0.869	0.811	0.928	CLONAL	1	TRUE	0	0.588230060126098	1		554	547	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	71	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.797	0.698	0.903	0.797	0.698	0.903	CLONAL	1	TRUE	1	0.393265242390442	2		429	453	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0053360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	205	658	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.85	0.787	0.915	0.85	0.787	0.915	CLONAL	1	TRUE	1	0.393265242390442	2		658	1227	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031973	26031973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	59	529	0	ENST00000244661.2:c.316G>C	p.Glu106Gln	p.E106Q	ENST00000244661	NM_003537.3	106	Gag/Cag	1/1	0.154279204924874	1	FACETS	0.254	0.218	0.294	0.254	0.218	0.294	INDETERMINATE	1	TRUE	0	0.393265242390442	1		529	948	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	204	588	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.393265242390442	2		588	998	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871186	12871186	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	93	288	0	ENST00000228872.4:c.413C>A	p.Ser138Ter	p.S138*	ENST00000228872	NM_004064.3	138	tCg/tAg	1/3	1	2	FACETS	0.865	0.771	0.964	0.865	0.771	0.964	CLONAL	1	TRUE	1	0.393265242390442	2		288	547	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	184	213	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	1	2	FACETS	0.998	0.921	1	0.998	0.921	1	CLONAL	1	TRUE	1	0.393265242390442	2		213	938	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164342	47164342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	44	302	1	ENST00000409792.3:c.1784C>T	p.Ser595Leu	p.S595L	ENST00000409792	NM_014159.6	595	tCa/tTa	3/21	1	2	FACETS	0.796	0.672	0.932	0.796	0.672	0.932	CLONAL	1	TRUE	1	0.393265242390442	2		303	281	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937175	39937175	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	255	850	1	ENST00000378444.4:c.8C>T	p.Ser3Leu	p.S3L	ENST00000378444	NM_001123385.1	3	tCa/tTa	2/15	1	2	FACETS	0.94	0.878	1	0.94	0.878	1	CLONAL	1	TRUE	1	0.393265242390442	2		851	1379	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291782	15291782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs940948912	NA	P-0053360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1400	317	1006	0	ENST00000263388.2:c.2984C>T	p.Pro995Leu	p.P995L	ENST00000263388	NM_000435.2	995	cCg/cTg	18/33	1	2	FACETS	0.939	0.883	0.996	0.939	0.883	0.996	CLONAL	1	TRUE	1	0.393265242390442	2		1006	1717	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860254	151860254	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	133	524	0	ENST00000262189.6:c.10408C>T	p.Gln3470Ter	p.Q3470*	ENST00000262189	NM_170606.2	3470	Cag/Tag	43/59	1	2	FACETS	0.889	0.808	0.974	0.889	0.808	0.974	CLONAL	1	TRUE	1	0.393265242390442	2		524	761	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041576	47041576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	220	776	0	ENST00000377604.3:c.1801C>T	p.Gln601Ter	p.Q601*	ENST00000377604	NM_001204468.1	601	Cag/Tag	17/24	1	2	FACETS	0.879	0.816	0.944	0.879	0.816	0.944	CLONAL	1	TRUE	1	0.393265242390442	2		776	1273	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424997	49424997	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	225	774	1	ENST00000301067.7:c.13491del	p.Leu4498TrpfsTer21	p.L4498Wfs*21	ENST00000301067	NM_003482.3	4497	ggG/gg	39/54	1	2	FACETS	0.83	0.771	0.891	0.83	0.771	0.891	CLONAL	1	TRUE	1	0.393265242390442	2		775	1379	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68934926	68934926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	106	462	1	ENST00000487270.1:c.995C>T	p.Ser332Leu	p.S332L	ENST00000487270	NM_133509.3	332	tCa/tTa	10/11	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.393265242390442	2		463	520	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1258758	1258758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1223394183	NA	P-0053360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	101	613	1	ENST00000310581.5:c.2987C>T	p.Thr996Met	p.T996M	ENST00000310581	NM_198253.2	996	aCg/aTg	13/16	1	2	FACETS	0.435	0.387	0.486	0.435	0.387	0.486	SUBCLONAL	1	TRUE	1	0.393265242390442	2		614	1181	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983116	149983117	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0053360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	102	551	0	ENST00000253339.5:c.3141_3142del	p.Trp1048GlufsTer2	p.W1048Efs*2	ENST00000253339		1047	ttATgg/ttgg	7/7	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.393265242390442	2		551	460	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978581	70978581	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	180	627	0	ENST00000276594.2:c.1072C>T	p.Gln358Ter	p.Q358*	ENST00000276594	NM_024504.3	358	Cag/Tag	5/8	1	2	FACETS	0.918	0.846	0.993	0.918	0.846	0.993	CLONAL	1	TRUE	1	0.393265242390442	2		627	997	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945118	44945118	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	54	373	0	ENST00000377967.4:c.3442G>A	p.Glu1148Lys	p.E1148K	ENST00000377967	NM_021140.2	1148	Gaa/Aaa	24/29	1	2	FACETS	0.75	0.643	0.866	0.75	0.643	0.866	SUBCLONAL	1	TRUE	1	0.393265242390442	2		373	366	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028793	47028793	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782092488	NA	P-0053360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	307	913	0	ENST00000377604.3:c.97G>A	p.Asp33Asn	p.D33N	ENST00000377604	NM_001204468.1	33	Gac/Aac	3/24	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.393265242390442	2		913	1477	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352327	70352327	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	206	690	0	ENST00000374080.3:c.4354G>C	p.Glu1452Gln	p.E1452Q	ENST00000374080		1452	Gag/Cag	31/45	1	2	FACETS	0.954	0.884	1	0.954	0.884	1	CLONAL	1	TRUE	1	0.393265242390442	2		690	1098	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577137	7577137	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	314	802	0	ENST00000269305.4:c.801del	p.Asn268ThrfsTer77	p.N268Tfs*77	ENST00000269305	NM_001126112.2	267	cgG/cg	8/11	0.498018149630282	2	FACETS	0.904	0.859	0.949	0.904	0.859	0.949	CLONAL	2	TRUE	0	0.501293273541762	2		802	693	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258036	123258036	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	135	677	0	ENST00000358487.5:c.1645A>G	p.Asn549Asp	p.N549D	ENST00000358487	NM_000141.4	549	Aat/Gat	12/18	0.498018149630282	2	FACETS	0.919	0.839	1	0.46	0.419	0.502	CLONAL	1	TRUE	0	0.501293273541762	2		677	586	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404360	139404360	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758642073	NA	P-0053361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	251	1172	1	ENST00000277541.6:c.2794G>A	p.Asp932Asn	p.D932N	ENST00000277541	NM_017617.3	932	Gac/Aac	18/34	0.498018149630282	2	FACETS	0.997	0.934	1	0.499	0.467	0.532	CLONAL	1	TRUE	0	0.501293273541762	2		1173	1004	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0053363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1314	102	855	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	1	2	FACETS	0.758	0.676	0.847	0.758	0.676	0.847	SUBCLONAL	1	TRUE	1	0.19	2		855	1416	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0053363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	23	236	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.634	0.494	0.796	0.634	0.494	0.796	SUBCLONAL	1	TRUE	1	0.19	2		236	382	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198299711	198299711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	79	455	0	ENST00000335508.6:c.13G>A	p.Ala5Thr	p.A5T	ENST00000335508	NM_012433.2	5	Gcc/Acc	1/25	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.19	2		455	794	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499483	89499483	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	49	433	0	ENST00000336596.2:c.2655del	p.Gly886AlafsTer3	p.G886Afs*3	ENST00000336596	NM_005233.5	885	Ccc/cc	15/17	1	2	FACETS	0.709	0.599	0.831	0.709	0.599	0.831	SUBCLONAL	1	TRUE	1	0.19	2		433	727	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564689	86564704	+	frameshift_variant	Frame_Shift_Del	DEL	CCTTACCTGCCCCCTT	CCTTACCTGCCCCCTT	-	novel	NA	P-0053363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	111	926	0	ENST00000274376.6:c.421_436del	p.Pro141TrpfsTer28	p.P141Wfs*28	ENST00000274376	NM_002890.2	141	CCTTACCTGCCCCCTTtg/tg	1/25	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.19	2		926	1169	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908843	101908854	+	inframe_deletion	In_Frame_Del	DEL	GCAATGGGCTTA	GCAATGGGCTTA	-	novel	NA	P-0053363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	42	554	0	ENST00000374994.4:c.1208_1219del	p.Ala403_Leu406del	p.A403_L406del	ENST00000374994	NM_004612.2	403	GCAATGGGCTTA/-	7/9	0.153078466375012	1	FACETS	0.657	0.548	0.779	0.657	0.548	0.779	SUBCLONAL	1	TRUE	0	0.19	1		554	609	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0053364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	56	430	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.197952579587659	3	FACETS	1	0.917	1	0.548	0.471	0.632	CLONAL	1	TRUE	1	0.277621055966234	3		430	419	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0053364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	50	286	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.277621055966234	2		286	324	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347891	89347892	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	44	886	0	ENST00000301030.4:c.5058dup	p.Glu1687ArgfsTer10	p.E1687Rfs*10	ENST00000301030	NM_001256183.1	1686	-/A	9/13	1	2	FACETS	0.574	0.481	0.678	0.574	0.481	0.678	SUBCLONAL	1	TRUE	1	0.277621055966234	2		886	552	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0053365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	52	353	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.23	2		353	450	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	39	560	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	1	2	FACETS	0.536	0.443	0.64	0.536	0.443	0.64	SUBCLONAL	1	TRUE	1	0.23	2		560	633	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0053366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	139	432	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.906	0.829	0.986	0.906	0.829	0.986	CLONAL	1	TRUE	1	0.565245999541081	2		432	543	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0053366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	231	316	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.565245999541081	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.565245999541081	2		316	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs967461896	NA	P-0053366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	469	805	0	ENST00000269305.4:c.526T>C	p.Cys176Arg	p.C176R	ENST00000269305	NM_001126112.2	176	Tgc/Cgc	5/11	0.565245999541081	2	FACETS	0.967	0.931	1	0.967	0.931	1	CLONAL	2	TRUE	0	0.565245999541081	2		805	858	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928067	178928067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	170	487	0	ENST00000263967.3:c.1345C>T	p.Pro449Ser	p.P449S	ENST00000263967	NM_006218.2	449	Cct/Tct	8/21	0.565245999541081	2	FACETS	0.98	0.905	1	0.49	0.452	0.529	CLONAL	1	TRUE	0	0.565245999541081	2		487	614	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808345	1808345	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	149	1097	0	ENST00000260795.2:c.2103G>T	p.Glu701Asp	p.E701D	ENST00000260795		701	gaG/gaT	15/17	1	2	FACETS	0.573	0.524	0.623	0.573	0.524	0.623	SUBCLONAL	1	TRUE	1	0.745214369087245	2		1097	698	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	93	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.948	0.854	1	0.948	0.854	1	CLONAL	1	TRUE	1	0.683832013739657	2		429	287	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690802	89690802	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1114167621	NA	P-0053370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	104	345	0	ENST00000371953.3:c.210-1G>A		p.X70_splice	ENST00000371953	NM_000314.4	70			0.683832013739657	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.683832013739657	1		345	163	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045548	47045548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556782397	NA	P-0053370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	282	754	0	ENST00000377604.3:c.2515G>A	p.Gly839Ser	p.G839S	ENST00000377604	NM_001204468.1	839	Ggc/Agc	22/24	1	2	FACETS	0.973	0.917	1	0.973	0.917	1	CLONAL	1	TRUE	1	0.683832013739657	2		754	848	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781939	3781939	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0053370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	158	401	0	ENST00000262367.5:c.4729-1G>A		p.X1577_splice	ENST00000262367	NM_004380.2	1577			1	2	FACETS	0.998	0.923	1	0.998	0.923	1	CLONAL	1	TRUE	1	0.683832013739657	2		401	463	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911523	134911523	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749562219	NA	P-0053371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	162	565	1	ENST00000398015.3:c.1988G>A	p.Arg663Gln	p.R663Q	ENST00000398015	NM_004441.4	663	cGg/cAg	11/16	0.536253518346701	3	FACETS	1	0.982	1	0.612	0.564	0.662	CLONAL	1	TRUE	1	0.536253518346701	3		566	626	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001395	150001395	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	243	402	2	ENST00000253339.5:c.2209C>T	p.Arg737Ter	p.R737*	ENST00000253339		737	Cga/Tga	4/7	0.524682999060123	2	FACETS	0.964	0.913	1	0.964	0.913	1	CLONAL	2	TRUE	0	0.536253518346701	2		404	470	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187560905	187560905	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1302189943	NA	P-0053371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	98	298	0	ENST00000441802.2:c.3613C>T	p.Arg1205Ter	p.R1205*	ENST00000441802	NM_005245.3	1205	Cga/Tga	4/27	0.536253518346701	3	FACETS	1	0.922	1	0.516	0.463	0.572	CLONAL	1	TRUE	1	0.536253518346701	3		298	449	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681514	117681514	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	75	239	0	ENST00000368508.3:c.3436A>G	p.Thr1146Ala	p.T1146A	ENST00000368508	NM_002944.2	1146	Aca/Gca	22/43	0.524682999060123	2	FACETS	0.897	0.793	1	0.448	0.396	0.503	CLONAL	1	TRUE	0	0.536253518346701	2		239	312	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	132	411	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.18385190821751	6	FACETS	0.963	0.882	1	0.963	0.882	1	INDETERMINATE	3	FALSE	3	0.386849085841544	6		411	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0053372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	277	778	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.386849085841544	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	FALSE	0	0.386849085841544	2		779	670	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525914	41525914	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs773503228	NA	P-0053372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	103	411	0	ENST00000263253.7:c.1189C>T	p.Arg397Ter	p.R397*	ENST00000263253	NM_001429.3	397	Cga/Tga	5/31	0.152941365769043	4	FACETS	1	0.937	1	1	0.937	1	INDETERMINATE	2	FALSE	2	0.386849085841544	4		411	352	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0053372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	330	459	0	ENST00000304494.5:c.151-1G>A		p.X51_splice	ENST00000304494	NM_000077.4	51			0.386849085841544	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	4	FALSE	0	0.386849085841544	4		459	567	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630461	187630461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770823750	NA	P-0053372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	210	717	0	ENST00000441802.2:c.521C>T	p.Thr174Met	p.T174M	ENST00000441802	NM_005245.3	174	aCg/aTg	2/27	0.341366700031397	3	FACETS	0.977	0.912	1	0.977	0.912	1	CLONAL	2	FALSE	1	0.386849085841544	3		717	663	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0053373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	67	430	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.905	0.786	1	0.905	0.786	1	CLONAL	1	TRUE	1	0.2	2		430	740	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0053373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	203	871	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	1	2	FACETS	0.778	0.719	0.839	1	0.991	1	SUBCLONAL	2	TRUE	1	0.2	2		871	1305	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602340	10602340	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1181	111	1395	1	ENST00000171111.5:c.1238G>T	p.Arg413Leu	p.R413L	ENST00000171111	NM_203500.1	413	cGt/cTt	3/6	1	2	FACETS	0.859	0.77	0.954	0.859	0.77	0.954	CLONAL	1	TRUE	1	0.2	2		1396	1292	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109809	115109809	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	64	951	0	ENST00000257566.3:c.2069C>G	p.Ser690Cys	p.S690C	ENST00000257566	NM_016569.3	690	tCt/tGt	8/8	1	2	FACETS	0.783	0.677	0.899	0.783	0.677	0.899	SUBCLONAL	1	TRUE	1	0.2	2		951	817	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615705	1615705	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	104	1234	0	ENST00000344749.5:c.1566G>C	p.Lys522Asn	p.K522N	ENST00000344749	NM_001136139.2	522	aaG/aaC	17/19	1	2	FACETS	0.852	0.76	0.949	0.852	0.76	0.949	CLONAL	1	TRUE	1	0.2	2		1234	1221	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622447	158622447	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	41	365	0	ENST00000263640.3:c.1052G>C	p.Cys351Ser	p.C351S	ENST00000263640	NM_001105.4	351	tGc/tCc	8/11	1	2	FACETS	0.733	0.61	0.871	0.733	0.61	0.871	SUBCLONAL	1	TRUE	1	0.2	2		365	559	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165126	47165126	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	54	231	0	ENST00000409792.3:c.1000C>T	p.Gln334Ter	p.Q334*	ENST00000409792	NM_014159.6	334	Caa/Taa	3/21	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.2	2		231	454	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587141	189587141	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	50	429	0	ENST00000264731.3:c.1158G>C	p.Gln386His	p.Q386H	ENST00000264731	NM_003722.4	386	caG/caC	9/14	1	2	FACETS	0.712	0.603	0.833	0.712	0.603	0.833	SUBCLONAL	1	TRUE	1	0.2	2		429	702	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553188	106553188	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	78	839	0	ENST00000369096.4:c.1153G>T	p.Gly385Cys	p.G385C	ENST00000369096	NM_001198.3	385	Ggt/Tgt	5/7	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.2	2		839	780	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482954	140482954	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	66	639	0	ENST00000288602.6:c.1181C>A	p.Ser394Ter	p.S394*	ENST00000288602	NM_004333.4	394	tCa/tAa	10/18	1	2	FACETS	0.739	0.64	0.847	0.739	0.64	0.847	SUBCLONAL	1	TRUE	1	0.2	2		639	893	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845597	151845597	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1459903795	NA	P-0053373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	67	881	0	ENST00000262189.6:c.13415G>C	p.Ser4472Thr	p.S4472T	ENST00000262189	NM_170606.2	4472	aGt/aCt	52/59	1	2	FACETS	0.76	0.659	0.871	0.76	0.659	0.871	SUBCLONAL	1	TRUE	1	0.2	2		881	881	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	86	552	2	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.281068889978194	2		554	586	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	35	313	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.841	0.692	1	0.841	0.692	1	CLONAL	1	TRUE	1	0.281068889978194	2		313	296	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	141	431	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.281068889978194	2		431	786	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	24	339	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.727	0.572	0.904	0.727	0.572	0.904	CLONAL	1	TRUE	1	0.281068889978194	2		339	235	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684089	29684089	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375990655	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	39	510	0	ENST00000356175.3:c.7787C>T	p.Ala2596Val	p.A2596V	ENST00000356175	NM_000267.3	2596	gCg/gTg	52/57	1	2	FACETS	0.821	0.682	0.975	0.821	0.682	0.975	CLONAL	1	TRUE	1	0.281068889978194	2		510	338	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121791	2121792	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs137854144	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	112	1013	0	ENST00000219476.3:c.1959_1960del	p.Gly654LeufsTer2	p.G654Lfs*2	ENST00000219476	NM_000548.3	651	ccAGag/ccag	19/42	1	2	FACETS	0.928	0.834	1	0.928	0.834	1	CLONAL	1	TRUE	1	0.281068889978194	2		1013	859	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	38	316	1	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	1	2	FACETS	0.945	0.785	1	0.945	0.785	1	CLONAL	1	TRUE	1	0.281068889978194	2		317	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	75	786	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	1	2	FACETS	0.65	0.569	0.738	0.65	0.569	0.738	SUBCLONAL	1	TRUE	1	0.281068889978194	2		786	821	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692981	89692982	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	36	527	0	ENST00000371953.3:c.469dup	p.Glu157GlyfsTer23	p.E157Gfs*23	ENST00000371953	NM_000314.4	155	-/G	5/9	1	2	FACETS	0.854	0.705	1	0.854	0.705	1	CLONAL	1	TRUE	1	0.281068889978194	2		527	300	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088788	27088788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	76	630	2	ENST00000324856.7:c.2402del	p.Gly801ValfsTer32	p.G801Vfs*32	ENST00000324856	NM_006015.4	799	caG/ca	7/20	1	2	FACETS	0.854	0.75	0.967	0.854	0.75	0.967	CLONAL	1	TRUE	1	0.281068889978194	2		632	633	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	83	725	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.963	0.851	1	0.963	0.851	1	CLONAL	1	TRUE	1	0.281068889978194	2		725	613	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144049	11144051	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	136	881	1	ENST00000358026.2:c.3634_3636del	p.Glu1212del	p.E1212del	ENST00000358026	NM_001128849.1	1210	gtGGAg/gtg	26/36	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.281068889978194	2		882	824	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270726	10270726	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	62	605	0	ENST00000340748.4:c.1009del	p.Met337TrpfsTer8	p.M337Wfs*8	ENST00000340748		337	Atg/tg	14/40	1	2	FACETS	0.904	0.782	1	0.904	0.782	1	CLONAL	1	TRUE	1	0.281068889978194	2		605	488	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	191	1072	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.84	0.778	0.904	1	0.992	1	CLONAL	2	TRUE	1	0.281068889978194	2		1073	809	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	119	934	3	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	0.251477327223706	3	FACETS	0.934	0.841	1	0.467	0.42	0.516	CLONAL	1	TRUE	1	0.281068889978194	3		937	1034	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614463	38614463	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	41	378	1	ENST00000299084.4:c.234del	p.Asp79ThrfsTer42	p.D79Tfs*42	ENST00000299084	NM_152594.2	77	Aaa/aa	3/7	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.281068889978194	2		379	268	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222762	5222762	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1391073074	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	92	993	3	ENST00000357368.4:c.3041C>T	p.Thr1014Met	p.T1014M	ENST00000357368	NM_002850.3	1014	aCg/aTg	18/38	1	2	FACETS	0.856	0.76	0.958	0.856	0.76	0.958	CLONAL	1	TRUE	1	0.281068889978194	2		996	765	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371649	89371649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750217123	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	119	771	0	ENST00000301030.4:c.191C>T	p.Ala64Val	p.A64V	ENST00000301030	NM_001256183.1	64	gCg/gTg	4/13	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.281068889978194	2		771	793	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322976	31322976	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	206	960	0	ENST00000412585.2:c.920C>A	p.Pro307His	p.P307H	ENST00000412585	NM_005514.6	307	cCc/cAc	5/8	0.281068889978194	2	FACETS	0.831	0.772	0.892	0.831	0.772	0.892	CLONAL	2	TRUE	0	0.281068889978194	2		960	882	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509346	149509346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753978428	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	82	616	0	ENST00000261799.4:c.1553C>T	p.Thr518Met	p.T518M	ENST00000261799	NM_002609.3	518	aCg/aTg	10/23	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.281068889978194	2		616	580	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264751	11264751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1384864432	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	72	708	0	ENST00000361445.4:c.3811G>A	p.Ala1271Thr	p.A1271T	ENST00000361445	NM_004958.3	1271	Gct/Act	26/58	1	2	FACETS	0.722	0.63	0.821	0.722	0.63	0.821	SUBCLONAL	1	TRUE	1	0.281068889978194	2		708	710	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445472	49445472	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780891095	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	111	960	1	ENST00000301067.7:c.1994C>T	p.Pro665Leu	p.P665L	ENST00000301067	NM_003482.3	665	cCg/cTg	10/54	0.240978858841917	3	FACETS	0.994	0.893	1	0.497	0.446	0.551	CLONAL	1	TRUE	1	0.281068889978194	3		961	906	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219204	133219204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	101	792	0	ENST00000320574.5:c.4840G>A	p.Ala1614Thr	p.A1614T	ENST00000320574	NM_006231.2	1614	Gct/Act	37/49	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.281068889978194	2		792	697	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222368	2222368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768623972	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	84	885	0	ENST00000326181.6:c.652G>A	p.Ala218Thr	p.A218T	ENST00000326181	NM_032271.2	218	Gcc/Acc	8/21	1	2	FACETS	0.844	0.745	0.95	0.844	0.745	0.95	CLONAL	1	TRUE	1	0.281068889978194	2		885	708	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101318	27101319	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	91	908	0	ENST00000324856.7:c.4604_4605del	p.Thr1535ArgfsTer36	p.T1535Rfs*36	ENST00000324856	NM_006015.4	1534	CAc/c	18/20	1	2	FACETS	0.728	0.645	0.816	0.728	0.645	0.816	SUBCLONAL	1	TRUE	1	0.281068889978194	2		908	890	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105745	27105747	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	36	394	0	ENST00000324856.7:c.5359_5361del	p.Glu1787del	p.E1787del	ENST00000324856	NM_006015.4	1786	GAG/-	20/20	1	2	FACETS	0.974	0.805	1	0.974	0.805	1	CLONAL	1	TRUE	1	0.281068889978194	2		394	263	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46727008	46727008	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	87	517	0	ENST00000371975.4:c.842A>G	p.His281Arg	p.H281R	ENST00000371975	NM_003579.3	281	cAt/cGt	8/18	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.281068889978194	2		517	513	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492557	50492557	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	122	764	0	ENST00000394963.4:c.1453C>T	p.Pro485Ser	p.P485S	ENST00000394963	NM_003076.4	485	Ccc/Tcc	12/13	0.240978858841917	3	FACETS	1	0.975	1	0.618	0.559	0.681	CLONAL	1	TRUE	1	0.281068889978194	3		764	801	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473791	67473791	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs730880215	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	89	543	1	ENST00000327367.4:c.871G>A	p.Gly291Arg	p.G291R	ENST00000327367	NM_005902.3	291	Gga/Aga	6/9	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.281068889978194	2		544	556	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858957	89858957	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	95	468	0	ENST00000389301.3:c.1007-2A>G		p.X336_splice	ENST00000389301	NM_000135.2	336			1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.281068889978194	2		468	615	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585473	29585473	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	59	372	0	ENST00000356175.3:c.4226del	p.Lys1409SerfsTer10	p.K1409Sfs*10	ENST00000356175	NM_000267.3	1408	Aaa/aa	31/57	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.281068889978194	2		372	314	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118912	70118912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	123	858	0	ENST00000245479.2:c.484C>T	p.Arg162Cys	p.R162C	ENST00000245479	NM_000346.3	162	Cgc/Tgc	2/3	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.281068889978194	2		858	863	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284904	15284904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	155	1002	1	ENST00000263388.2:c.4711C>T	p.Arg1571Trp	p.R1571W	ENST00000263388	NM_000435.2	1571	Cgg/Tgg	25/33	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.281068889978194	2		1003	911	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46602908	46602908	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	85	804	0	ENST00000263734.3:c.969del	p.Thr324ArgfsTer21	p.T324Rfs*21	ENST00000263734	NM_001430.4	322	caG/ca	8/16	1	2	FACETS	0.785	0.694	0.884	0.785	0.694	0.884	SUBCLONAL	1	TRUE	1	0.281068889978194	2		804	770	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259162	36259203	+	inframe_deletion	In_Frame_Del	DEL	TTGTTGCAGCGCCAGTGCGTAGGCAGCACGGAGCAGAGGAAG	TTGTTGCAGCGCCAGTGCGTAGGCAGCACGGAGCAGAGGAAG	-	novel	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	79	835	0	ENST00000300305.3:c.288_329del	p.Asn96_Asn109del	p.N96_N109del	ENST00000300305		96	aaCTTCCTCTGCTCCGTGCTGCCTACGCACTGGCGCTGCAACAAg/aag	3/8	1	2	FACETS	0.658	0.578	0.745	0.658	0.578	0.745	SUBCLONAL	1	TRUE	1	0.281068889978194	2		835	854	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341691	8341691	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0053381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	45	472	0	ENST00000356435.5:c.4947+2T>C		p.X1649_splice	ENST00000356435		1649			1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.281068889978194	2		472	258	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0053382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	94	678	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	1	2	FACETS	0.937	0.833	1	0.937	0.833	1	CLONAL	1	TRUE	1	0.23	2		678	872	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0053382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	50	311	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.23	2		311	405	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928346	69928346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	27	674	0	ENST00000352241.4:c.166C>T	p.Arg56Cys	p.R56C	ENST00000352241	NM_198159.2	56	Cgc/Tgc	2/10	1	2	FACETS	0.436	0.346	0.54	0.436	0.346	0.54	SUBCLONAL	1	TRUE	1	0.23	2		674	538	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275051	41275051	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	53	393	0	ENST00000349496.5:c.1217T>A	p.Val406Asp	p.V406D	ENST00000349496	NM_001904.3	406	gTt/gAt	9/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		393	348	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0053384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	187	393	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.737654756536507	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.737654756536507	1		393	319	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955550	48955550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913304	NA	P-0053384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	188	350	1	ENST00000267163.4:c.1666C>T	p.Arg556Ter	p.R556*	ENST00000267163	NM_000321.2	556	Cga/Tga	17/27	0.735712814438544	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.737654756536507	1		351	296	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121018	29121018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853009	NA	P-0053384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	262	596	0	ENST00000328354.6:c.539G>A	p.Arg180His	p.R180H	ENST00000328354	NM_007194.3	180	cGc/cAc	4/15	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.737654756536507	2		596	696	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69203049	69203049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	236	445	0	ENST00000462284.1:c.76C>T	p.Pro26Ser	p.P26S	ENST00000462284	NM_002392.5	26	Cca/Tca	2/11	1	2	FACETS	0.984	0.924	1	0.984	0.924	1	CLONAL	1	TRUE	1	0.737654756536507	2		445	650	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137313646	137313646	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1202924007	NA	P-0053384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	208	801	0	ENST00000481739.1:c.905G>A	p.Arg302Gln	p.R302Q	ENST00000481739	NM_002957.4	302	cGg/cAg	6/10	0.737654756536507	1	FACETS	0.989	0.936	1	0.989	0.936	1	CLONAL	1	TRUE	0	0.737654756536507	1		801	360	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844097	68844097	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0053386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	49	574	0	ENST00000261769.5:c.688-3C>T		p.X230_splice	ENST00000261769	NM_004360.3	230			0.204941359685259	3	FACETS	0.574	0.485	0.673	0.287	0.242	0.337	SUBCLONAL	1	TRUE	1	0.265462189403406	3		574	728	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375806	118375806	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	66	642	1	ENST00000534358.1:c.9199G>A	p.Val3067Ile	p.V3067I	ENST00000534358	NM_005933.3	3067	Gtc/Atc	27/36	0.265462189403406	2	FACETS	0.738	0.64	0.844	0.369	0.32	0.422	SUBCLONAL	1	TRUE	0	0.265462189403406	2		643	674	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229530	98229530	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	102	558	0	ENST00000331920.6:c.2428G>T	p.Ala810Ser	p.A810S	ENST00000331920	NM_000264.3	810	Gca/Tca	15/24	0.265462189403406	2	FACETS	1	0.936	1	0.531	0.475	0.591	CLONAL	1	TRUE	0	0.265462189403406	2		558	723	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0053387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	80	313	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.450707132579466	3	FACETS	1	0.89	1	0.503	0.445	0.566	CLONAL	1	TRUE	1	0.450707132579466	3		313	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0053387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	255	426	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.450707132579466	2	FACETS	0.926	0.874	0.979	0.926	0.874	0.979	CLONAL	2	TRUE	0	0.450707132579466	2		426	611	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952086	178952086	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	257	317	0	ENST00000263967.3:c.3141T>A	p.His1047Gln	p.H1047Q	ENST00000263967	NM_006218.2	1047	caT/caA	21/21	0.450707132579466	5	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	2	0.450707132579466	5		317	570	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439733	49439733	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	249	630	0	ENST00000301067.7:c.4711G>T	p.Glu1571Ter	p.E1571*	ENST00000301067	NM_003482.3	1571	Gag/Tag	18/54	0.351276112837696	5	FACETS	1	0.964	1	0.694	0.651	0.739	CLONAL	2	TRUE	2	0.450707132579466	5		630	889	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158464	26158464	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	316	663	0	ENST00000289316.2:c.67C>G	p.Gln23Glu	p.Q23E	ENST00000289316	NM_138720.2	23	Cag/Gag	1/2	0.450707132579466	3	FACETS	0.978	0.927	1	0.978	0.927	1	CLONAL	2	TRUE	1	0.450707132579466	3		663	878	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0053388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	218	778	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.952	0.885	1	0.952	0.885	1	CLONAL	1	TRUE	1	0.435232072077851	2		779	1052	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0053388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	218	872	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.937	0.871	1	0.937	0.871	1	CLONAL	1	TRUE	1	0.435232072077851	2		873	1069	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0053388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	99	239	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.435232072077851	2	FACETS	0.872	0.791	0.954	0.872	0.791	0.954	CLONAL	2	TRUE	0	0.435232072077851	2		239	261	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325733	30325733	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	69	246	0	ENST00000322652.5:c.1931G>T	p.Gly644Val	p.G644V	ENST00000322652	NM_015355.2	644	gGa/gTa	16/16	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.435232072077851	2		246	298	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591057	67591058	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAGCAGGCAGCTGAGTATCGAGAAATTGACAAACGTATGAAC	novel	NA	P-0053388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	81	282	0	ENST00000274335.5:c.1652_1693dup	p.Lys551_Asn564dup	p.K551_N564dup	ENST00000274335		551	-/AAGCAGGCAGCTGAGTATCGAGAAATTGACAAACGTATGAAC	12/15	0.435232072077851	2	FACETS	0.98	0.869	1	0.49	0.434	0.549	CLONAL	1	TRUE	0	0.435232072077851	2		282	380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0053390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	21	872	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.714039104767188	1	FACETS	0.059	0.045	0.075	0.059	0.045	0.075	SUBCLONAL	1	TRUE	0	0.714039104767188	1		873	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0053390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	17	603	2	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	0.714039104767188	1	FACETS	0.045	0.033	0.059	0.045	0.033	0.059	SUBCLONAL	1	TRUE	0	0.714039104767188	1		605	682	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576875	7576884	+	frameshift_variant	Frame_Shift_Del	DEL	TCCAGTGGTT	TCCAGTGGTT	-	novel	NA	P-0053392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	189	757	0	ENST00000269305.4:c.962_971del	p.Lys321MetfsTer21	p.K321Mfs*21	ENST00000269305	NM_001126112.2	321	aAACCACTGGAt/at	9/11	0.546962643037166	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.546962643037166	1		757	461	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291889	15291889	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	39	1180	0	ENST00000263388.2:c.2877C>G	p.Cys959Trp	p.C959W	ENST00000263388	NM_000435.2	959	tgC/tgG	18/33	0.51446638155461	1	FACETS	0.233	0.193	0.278	0.233	0.193	0.278	SUBCLONAL	1	TRUE	0	0.546962643037166	1		1180	445	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061116	38061139	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGCCGCCCTTGGCGCCGCTGCC	AGGGCCGCCCTTGGCGCCGCTGCC	GGGGCAGCGG	novel	NA	P-0053392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	15	265	0	ENST00000250448.2:c.850_873delinsCCGCTGCCCC	p.Gly284ProfsTer14	p.G284Pfs*14	ENST00000250448	NM_004496.3	284	GGCAGCGGCGCCAAGGGCGGCCCT/CCGCTGCCCC	2/2	1	2	FACETS	0.116	0.084	0.154	0.116	0.084	0.154	SUBCLONAL	1	TRUE	1	0.546962643037166	2		265	474	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	506	411	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.592724269609259	5	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	TRUE	2	0.592724269609259	5		411	1061	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0053393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	732	485	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.478076335525627	3	FACETS	1	0.979	1			1	CLONAL	3	TRUE	NA	0.592724269609259	3		486	1063	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267489	198267489	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1039242157	NA	P-0053393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	133	446	0	ENST00000335508.6:c.1868A>G	p.Tyr623Cys	p.Y623C	ENST00000335508	NM_012433.2	623	tAt/tGt	14/25	0.577293066454415	3	FACETS	0.949	0.865	1	0.475	0.432	0.519	CLONAL	1	TRUE	1	0.592724269609259	3		446	613	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511690	46511690	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs202055317	NA	P-0053393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	162	595	0	ENST00000262741.5:c.1087A>G	p.Ile363Val	p.I363V	ENST00000262741	NM_003629.3	363	Atc/Gtc	9/10	0.507834555982456	3	FACETS	0.866	0.796	0.94	0.433	0.398	0.47	CLONAL	1	TRUE	1	0.592724269609259	3		595	818	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870876	12870876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	347	330	0	ENST00000228872.4:c.103C>T	p.Pro35Ser	p.P35S	ENST00000228872	NM_004064.3	35	Ccg/Tcg	1/3	0.592724269609259	5	FACETS	0.98	0.935	1	0.98	0.935	1	CLONAL	3	TRUE	2	0.592724269609259	5		330	752	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589542	67589583	+	inframe_deletion	In_Frame_Del	DEL	AGTTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATT	AGTTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATT	-	novel	NA	P-0053393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	110	174	0	ENST00000274335.5:c.1306_1347del	p.Val436_Leu449del	p.V436_L449del	ENST00000274335		435	caAGTTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATTa/caa	10/15	0.541917800165959	2	FACETS	0.919	0.848	0.988	0.919	0.848	0.988	CLONAL	2	TRUE	0	0.592724269609259	2		174	202	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971140	21971154	+	inframe_deletion	In_Frame_Del	DEL	GCGCAGTTGGGCTCC	GCGCAGTTGGGCTCC	-	novel	NA	P-0053393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	373	602	0	ENST00000304494.5:c.204_218del	p.Glu69_Ala73del	p.E69_A73del	ENST00000304494	NM_000077.4	68	gcGGAGCCCAACTGCGCc/gcc	2/3	0.592724269609259	2	FACETS	0.883	0.845	0.92	0.883	0.845	0.92	CLONAL	2	TRUE	0	0.592724269609259	2		602	713	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141570566	141570566	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1279943789	NA	P-0053394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	239	846	0	ENST00000220592.5:c.562T>C	p.Cys188Arg	p.C188R	ENST00000220592	NM_012154.3	188	Tgc/Cgc	5/19	0.488297718607237	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	FALSE	2	0.488297718607237	4		846	650	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0053395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	122	836	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.31962526946629	2		836	727	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244091	153244091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	118	642	1	ENST00000281708.4:c.2066G>A	p.Arg689Gln	p.R689Q	ENST00000281708	NM_033632.3	689	cGg/cAg	12/12	0.31962526946629	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.31962526946629	1		643	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578217	7578217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	271	869	0	ENST00000269305.4:c.632C>T	p.Thr211Ile	p.T211I	ENST00000269305	NM_001126112.2	211	aCt/aTt	6/11	0.31962526946629	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.31962526946629	2		869	845	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207092	1207092	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555735008	NA	P-0053395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	122	1067	0	ENST00000326873.7:c.180del	p.Tyr60Ter	p.Y60*	ENST00000326873	NM_000455.4	60	taC/ta	1/10	0.31962526946629	1	FACETS	0.969	0.877	1	0.969	0.877	1	CLONAL	1	TRUE	0	0.31962526946629	1		1067	662	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038879	12038879	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	82	417	0	ENST00000396373.4:c.1172A>G	p.Tyr391Cys	p.Y391C	ENST00000396373	NM_001987.4	391	tAt/tGt	7/8	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.31962526946629	2		417	436	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784254	43784254	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	149	763	1	ENST00000382044.4:c.232C>T	p.Arg78Ter	p.R78*	ENST00000382044	NM_001141980.1	78	Cga/Tga	3/28	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.31962526946629	2		764	890	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21643205	21643205	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	120	760	0	ENST00000421138.2:c.322G>C	p.Glu108Gln	p.E108Q	ENST00000421138		108	Gag/Cag	5/16	1	2	FACETS	0.855	0.772	0.943	0.855	0.772	0.943	CLONAL	1	TRUE	1	0.31962526946629	2		760	878	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906408	32906408	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0053395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	33	280	0	ENST00000380152.3:c.794-1G>T		p.X265_splice	ENST00000380152		265			0.31962526946629	2	FACETS	0.578	0.472	0.698	0.289	0.236	0.349	SUBCLONAL	1	TRUE	0	0.31962526946629	2		280	357	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645261	67645261	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	47	783	0	ENST00000264010.4:c.526G>T	p.Glu176Ter	p.E176*	ENST00000264010	NM_006565.3	176	Gag/Tag	3/12	1	2	FACETS	0.457	0.385	0.537	0.457	0.385	0.537	SUBCLONAL	1	TRUE	1	0.31962526946629	2		783	643	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40854940	40854940	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	112	710	0	ENST00000428826.2:c.2138C>A	p.Ala713Asp	p.A713D	ENST00000428826		713	gCc/gAc	20/21	1	2	FACETS	0.96	0.864	1	0.96	0.864	1	CLONAL	1	TRUE	1	0.31962526946629	2		710	730	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021085	31021085	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0053395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	90	615	2	ENST00000375687.4:c.1086-2A>G		p.X362_splice	ENST00000375687	NM_015338.5	362			1	2	FACETS	0.922	0.819	1	0.922	0.819	1	CLONAL	1	TRUE	1	0.31962526946629	2		617	611	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127696	47127696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	172	516	0	ENST00000409792.3:c.5386C>T	p.Leu1796Phe	p.L1796F	ENST00000409792	NM_014159.6	1796	Ctt/Ttt	11/21	0.31962526946629	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.31962526946629	2		516	527	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643328	52643328	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0053395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	137	417	0	ENST00000394830.3:c.2567+1G>A		p.X856_splice	ENST00000394830	NM_018313.4	856			0.31962526946629	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.31962526946629	2		417	400	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169991094	169991094	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	50	502	0	ENST00000295797.4:c.612T>A	p.Asp204Glu	p.D204E	ENST00000295797	NM_002740.5	204	gaT/gaA	7/18	0.215183955702337	3	FACETS	0.573	0.486	0.67	0.287	0.243	0.335	SUBCLONAL	1	TRUE	1	0.31962526946629	3		502	633	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672861	30672861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	156	879	0	ENST00000376406.3:c.4099G>A	p.Val1367Ile	p.V1367I	ENST00000376406	NM_014641.2	1367	Gtc/Atc	10/15	0.31962526946629	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.31962526946629	1		879	658	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510899	157510899	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	186	645	0	ENST00000346085.5:c.3674C>G	p.Pro1225Arg	p.P1225R	ENST00000346085	NM_020732.3	1225	cCa/cGa	14/20	0.31962526946629	2	FACETS	0.94	0.873	1	0.94	0.873	1	CLONAL	2	TRUE	0	0.31962526946629	2		645	619	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273396	38273410	+	inframe_deletion	In_Frame_Del	DEL	AGGCCAGATACTCCA	AGGCCAGATACTCCA	-	novel	NA	P-0053395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	95	1169	0	ENST00000425967.3:c.1925_1939del	p.Met642_Ser647delinsThr	p.M642_S647delinsT	ENST00000425967	NM_001174067.1	642	aTGGAGTATCTGGCCTcc/acc	14/19	1	2	FACETS	0.66	0.586	0.738	0.66	0.586	0.738	SUBCLONAL	1	TRUE	1	0.31962526946629	2		1169	901	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137218500	137218500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1175967955	NA	P-0053395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	20	137	0	ENST00000481739.1:c.23C>T	p.Pro8Leu	p.P8L	ENST00000481739	NM_002957.4	8	cCg/cTg	1/10	1	2	FACETS	0.907	0.701	1	0.907	0.701	1	CLONAL	1	TRUE	1	0.31962526946629	2		137	138	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0053396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	34	285	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.672	0.548	0.811	0.672	0.548	0.811	SUBCLONAL	1	TRUE	1	0.21	2		285	482	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0053396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	82	575	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.671	0.59	0.759	0.671	0.59	0.759	SUBCLONAL	1	TRUE	1	0.21	2		576	1164	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0053397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	333	767	0	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	0.545965724740717	1	FACETS	0.98	0.93	1	0.98	0.93	1	CLONAL	1	TRUE	0	0.545965724740717	1		767	905	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44921908	44921908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778421870	NA	P-0053397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	98	481	1	ENST00000377967.4:c.1442G>A	p.Arg481His	p.R481H	ENST00000377967	NM_021140.2	481	cGc/cAc	15/29	0.493928439719198	3	FACETS	0.441	0.392	0.493	0.221	0.196	0.247	SUBCLONAL	1	TRUE	1	0.545965724740717	3		482	1036	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641507	18641507	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	316	405	0	ENST00000266497.5:c.2509del	p.Ile837PhefsTer21	p.I837Ffs*21	ENST00000266497		836	Aaa/aa	17/31	0.490896563874617	2	FACETS	0.832	0.791	0.873	0.832	0.791	0.873	CLONAL	2	TRUE	0	0.545965724740717	2		405	696	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953787	48953787	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1060503087	NA	P-0053397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	188	190	0	ENST00000267163.4:c.1389+1G>T		p.X463_splice	ENST00000267163	NM_000321.2	463			0.545965724740717	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.545965724740717	2		190	343	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342177	70342177	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	154	673	0	ENST00000374080.3:c.1229A>G	p.Asn410Ser	p.N410S	ENST00000374080		410	aAc/aGc	8/45	0.24405428487257	3	FACETS	0.569	0.519	0.621	0.19	0.173	0.207	INDETERMINATE	1	TRUE	0	0.545965724740717	3		673	1263	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	104	429	0				ENST00000310581	NM_198253.2	-/1132			0.431964867509155	4	FACETS	0.917	0.845	0.988	1	0.98	1	CLONAL	4	TRUE	1	0.431964867509155	4		429	188	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0053398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1519	138	575	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.431964867509155	5	FACETS	0.635	0.576	0.699			1	SUBCLONAL	1	TRUE	NA	0.431964867509155	5		576	1657	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916836	178916836	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	101	689	0	ENST00000263967.3:c.223C>G	p.Gln75Glu	p.Q75E	ENST00000263967	NM_006218.2	75	Caa/Gaa	2/21	0.189830415029638	4	FACETS	0.613	0.547	0.684	0.307	0.273	0.342	INDETERMINATE	1	TRUE	2	0.431964867509155	4		689	1092	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0053398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	27	587	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.189830415029638	4	FACETS	0.154	0.122	0.192	0.077	0.061	0.096	INDETERMINATE	1	TRUE	2	0.431964867509155	4		587	1159	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0053398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	173	857	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.121968118291228	0	FACETS	0.507	0.466	0.549			1	INDETERMINATE	1	TRUE	0	0.431964867509155	0		857	898	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577543	7577543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1019340046	NA	P-0053398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	28	832	0	ENST00000269305.4:c.738G>A	p.Met246Ile	p.M246I	ENST00000269305	NM_001126112.2	246	atG/atA	7/11	0.121968118291228	0	FACETS	0.091	0.072	0.113			1	INDETERMINATE	1	TRUE	0	0.431964867509155	0		832	806	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030368	49030368	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0053398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	17	465	0	ENST00000267163.4:c.1843A>T	p.Lys615Ter	p.K615*	ENST00000267163	NM_000321.2	615	Aaa/Taa	19/27	0.423440697389798	0	FACETS	0.136	0.101	0.178			1	SUBCLONAL	1	TRUE	0	0.431964867509155	0		465	329	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6037030	6037030	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1562671039	NA	P-0053398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	64	454	0	ENST00000265849.7:c.730C>T	p.Gln244Ter	p.Q244*	ENST00000265849	NM_000535.5	244	Cag/Tag	7/15	0.431964867509155	3	FACETS	0.542	0.469	0.621	0.271	0.234	0.311	SUBCLONAL	1	TRUE	1	0.431964867509155	3		454	665	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52709296	52709296	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	71	809	0	ENST00000322088.6:c.250G>C	p.Glu84Gln	p.E84Q	ENST00000322088	NM_014225.5	84	Gag/Cag	3/15	NA	2	FACETS	0.442	0.385	0.504			1	INDETERMINATE	1	TRUE	NA	0.431964867509155	2		809	743	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533526	533526	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	45	862	1	ENST00000451590.1:c.377A>T	p.Glu126Val	p.E126V	ENST00000451590	NM_001130442.1	126	gAa/gTa	4/5	0.431964867509155	1	FACETS	0.205	0.171	0.242	0.205	0.171	0.242	SUBCLONAL	1	TRUE	0	0.431964867509155	1		863	798	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206952	102206952	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0053398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	23	300	0	ENST00000263464.3:c.1579+1G>C		p.X527_splice	ENST00000263464	NM_001165.4	527			0.425646640336705	1	FACETS	0.252	0.196	0.317	0.252	0.196	0.317	SUBCLONAL	1	TRUE	0	0.431964867509155	1		300	331	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43772180	43772180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747372898	NA	P-0053398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	220	741	0	ENST00000382044.4:c.535G>A	p.Glu179Lys	p.E179K	ENST00000382044	NM_001141980.1	179	Gaa/Aaa	6/28	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.431964867509155	2		741	858	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655488	67655488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	169	573	0	ENST00000264010.4:c.1351G>A	p.Asp451Asn	p.D451N	ENST00000264010	NM_006565.3	451	Gat/Aat	7/12	0.344010897860501	3	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.431964867509155	3		573	790	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577567	7577618	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACACATGTAGTTGTAGTGGATGGTGGTACAGTCAGAGCCAACCTAGGAGATA	ACACATGTAGTTGTAGTGGATGGTGGTACAGTCAGAGCCAACCTAGGAGATA	-	novel	NA	P-0053398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	66	751	0	ENST00000269305.4:c.673-10_714del		p.X225_splice	ENST00000269305	NM_001126112.2	225		7/11	0.121968118291228	0	FACETS	0.227	0.197	0.261			1	INDETERMINATE	1	TRUE	0	0.431964867509155	0		751	763	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004851	16004873	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCTGATCTACATCCATCTGCT	CTGCTGATCTACATCCATCTGCT	-	novel	NA	P-0053398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	43	741	0	ENST00000268712.3:c.2381_2403del	p.Glu794GlyfsTer5	p.E794Gfs*5	ENST00000268712	NM_006311.3	794	gAGCAGATGGATGTAGATCAGCAG/g	20/46	0.121968118291228	0	FACETS	0.145	0.12	0.172			1	INDETERMINATE	1	TRUE	0	0.431964867509155	0		741	782	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033609	48033609	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587779294	NA	P-0053398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	100	577	0	ENST00000234420.5:c.3820G>C	p.Glu1274Gln	p.E1274Q	ENST00000234420	NM_000179.2	1274	Gaa/Caa	9/10	1	2	FACETS	0.663	0.593	0.738	0.663	0.593	0.738	SUBCLONAL	1	TRUE	1	0.431964867509155	2		577	698	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22153387	22153387	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	273	575	0	ENST00000215832.6:c.523G>C	p.Asp175His	p.D175H	ENST00000215832	NM_002745.4	175	Gat/Cat	4/9	1	2	FACETS	0.795	0.749	0.842	1	0.994	1	SUBCLONAL	2	TRUE	1	0.431964867509155	2		575	795	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178941898	178941898	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1408408816	NA	P-0053398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	56	476	0	ENST00000263967.3:c.2217G>T	p.Met739Ile	p.M739I	ENST00000263967	NM_006218.2	739	atG/atT	15/21	0.189830415029638	4	FACETS	0.471	0.402	0.546	0.235	0.201	0.273	INDETERMINATE	1	TRUE	2	0.431964867509155	4		476	789	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520508	176520508	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	196	1009	1	ENST00000292408.4:c.1353T>A	p.Ser451Arg	p.S451R	ENST00000292408	NM_213647.1	451	agT/agA	10/18	1	2	FACETS	0.926	0.857	0.997	0.926	0.857	0.997	CLONAL	1	TRUE	1	0.431964867509155	2		1010	980	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928846	44928846	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	28	214	0	ENST00000377967.4:c.1946C>A	p.Ser649Ter	p.S649*	ENST00000377967	NM_021140.2	649	tCa/tAa	17/29	1	1	FACETS	0.334	0.267	0.41	0.334	0.267	0.41	SUBCLONAL	1	TRUE	0	0.431964867509155	1		214	304	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502864	186502865	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	A	novel	NA	P-0053398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	80	626	0	ENST00000323963.5:c.322_323delinsA	p.Ala108ThrfsTer13	p.A108Tfs*13	ENST00000323963		108	GCc/Ac	4/11	0.189830415029638	4	FACETS	0.593	0.521	0.671	0.297	0.26	0.336	INDETERMINATE	1	TRUE	2	0.431964867509155	4		626	894	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0053399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	145	432	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.276035401258462	4	FACETS	1	0.983	1	0.665	0.607	0.726	CLONAL	1	TRUE	2	0.393503383811031	4		432	772	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39311610	39311610	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0053399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	77	552	1	ENST00000373001.3:c.1048+1G>A		p.X350_splice	ENST00000373001	NM_022157.3	350			1	2	FACETS	0.998	0.881	1	0.998	0.881	1	CLONAL	1	TRUE	1	0.393503383811031	2		553	392	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913376	28913376	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	215	788	0	ENST00000282397.4:c.2417T>C	p.Leu806Ser	p.L806S	ENST00000282397	NM_002019.4	806	tTg/tCg	17/30	0.393503383811031	5	FACETS	0.982	0.914	1	0.982	0.914	1	CLONAL	2	TRUE	3	0.393503383811031	5		788	885	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782664	NA	P-0053399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	84	828	0	ENST00000269305.4:c.711G>C	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atC	7/11	0.358771554968855	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.393503383811031	1		828	327	SUCCESS
APC	324	MSKCC	GRCh37	5	112173495	112173496	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0053399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	77	491	0	ENST00000257430.4:c.2205dup	p.Lys736GlufsTer20	p.K736Efs*20	ENST00000257430	NM_000038.5	735	gcg/gcGg	16/16	0.231770534394822	4	FACETS	1	0.958	1	0.599	0.528	0.675	INDETERMINATE	1	TRUE	2	0.393503383811031	4		491	455	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0053399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	68	473	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.231770534394822	4	FACETS	0.932	0.812	1	0.466	0.406	0.531	INDETERMINATE	1	TRUE	2	0.393503383811031	4		473	517	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971292	13971292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772105404	NA	P-0053399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	116	665	0	ENST00000405192.2:c.637C>T	p.Arg213Cys	p.R213C	ENST00000405192	NM_001163147.1	213	Cgc/Tgc	8/12	0.393503383811031	5	FACETS	1	0.973	1	0.41	0.369	0.452	CLONAL	1	TRUE	2	0.393503383811031	5		665	763	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	39	258	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.839	0.701	0.99	1	0.962	1	CLONAL	2	FALSE	1	0.205616999332426	2		258	226	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	82	432	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.205616999332426	2		432	540	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	38	561	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.703	0.58	0.84	0.703	0.58	0.84	SUBCLONAL	1	FALSE	1	0.205616999332426	2		561	526	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553478	29553478	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781807	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	69	818	4	ENST00000356175.3:c.2033del	p.Pro678ArgfsTer10	p.P678Rfs*10	ENST00000356175	NM_000267.3	676	aCc/ac	18/57	1	2	FACETS	0.905	0.787	1	0.905	0.787	1	CLONAL	1	FALSE	1	0.205616999332426	2		822	742	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935322	36935323	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs747437399	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	63	1143	5	ENST00000361632.4:c.1404dup	p.Ser469GlnfsTer5	p.S469Qfs*5	ENST00000361632		468	-/C	10/16	1	2	FACETS	0.97	0.838	1	0.97	0.838	1	CLONAL	1	FALSE	1	0.205616999332426	2		1148	632	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	28	286	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.615	0.491	0.757	0.615	0.491	0.757	SUBCLONAL	1	FALSE	1	0.205616999332426	2		286	443	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	46	756	1	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	0.62	0.521	0.73	0.62	0.521	0.73	SUBCLONAL	1	FALSE	1	0.205616999332426	2		757	722	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	61	493	4	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.205616999332426	2		497	419	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	119	942	4	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.784	0.708	0.864	1	0.985	1	SUBCLONAL	2	FALSE	1	0.205616999332426	2		946	738	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	26	315	3	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	0.165680090786737	1	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	FALSE	0	0.205616999332426	1		318	201	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216477	108216477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587782558	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	13	330	0	ENST00000278616.4:c.8432del	p.Lys2811SerfsTer46	p.K2811Sfs*46	ENST00000278616	NM_000051.3	2809	cAa/ca	58/63	1	2	FACETS	0.602	0.43	0.812	0.602	0.43	0.812	SUBCLONAL	1	FALSE	1	0.205616999332426	2		330	210	SUCCESS
APC	324	MSKCC	GRCh37	5	112174112	112174112	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	47	504	1	ENST00000257430.4:c.2821G>T	p.Glu941Ter	p.E941*	ENST00000257430	NM_000038.5	941	Gaa/Taa	16/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.205616999332426	2		505	311	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	71	757	1	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.205616999332426	2		758	574	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879604	37879604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196929947	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	115	1050	3	ENST00000269571.5:c.1979G>A	p.Gly660Asp	p.G660D	ENST00000269571		660	gGc/gAc	17/27	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.205616999332426	2		1053	879	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910638	29910638	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	67	1432	1	ENST00000376809.5:c.178T>G	p.Phe60Val	p.F60V	ENST00000376809	NM_002116.7	60	Ttc/Gtc	2/8	1	2	FACETS	0.754	0.654	0.863	0.754	0.654	0.863	SUBCLONAL	1	FALSE	1	0.205616999332426	2		1433	864	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495736	56495736	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747453114	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	46	752	0	ENST00000267101.3:c.3926G>A	p.Arg1309His	p.R1309H	ENST00000267101	NM_001982.3	1309	cGc/cAc	28/28	1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	FALSE	1	0.205616999332426	2		752	447	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682810	190682810	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	50	526	2	ENST00000441310.2:c.492del	p.Lys164AsnfsTer6	p.K164Nfs*6	ENST00000441310	NM_000534.4	162	gcA/gc	5/13	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	1	0.205616999332426	2		528	420	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	125	489	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.945	1	1	0.99	1	CLONAL	2	FALSE	1	0.205616999332426	2		494	576	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569792	95569792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	23	495	0	ENST00000393063.1:c.3941G>A	p.Arg1314Gln	p.R1314Q	ENST00000393063	NM_030621.3	1314	cGg/cAg	22/28	1	2	FACETS	0.598	0.466	0.752	0.598	0.466	0.752	SUBCLONAL	1	FALSE	1	0.205616999332426	2		495	374	SUCCESS
AR	367	MSKCC	GRCh37	X	66765277	66765277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329298379	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	58	412	1	ENST00000374690.3:c.289C>T	p.Pro97Ser	p.P97S	ENST00000374690	NM_000044.3	97	Ccc/Tcc	1/8	0.205616999332426	2	FACETS	0.859	0.748	0.976			1	CLONAL	3	FALSE	NA	0.205616999332426	2		413	219	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741719	145741719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781314533	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	46	1216	1	ENST00000428558.2:c.784C>T	p.Arg262Trp	p.R262W	ENST00000428558	NM_004260.3	262	Cgg/Tgg	5/22	1	2	FACETS	0.717	0.603	0.843	0.717	0.603	0.843	SUBCLONAL	1	FALSE	1	0.205616999332426	2		1217	624	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	72	1034	1	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	1	2	FACETS	0.971	0.848	1	0.971	0.848	1	CLONAL	1	FALSE	1	0.205616999332426	2		1035	721	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857386	9857386	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754686222	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	41	705	0	ENST00000330684.3:c.4015A>G	p.Lys1339Glu	p.K1339E	ENST00000330684	NM_001134407.1	1339	Aaa/Gaa	13/13	1	2	FACETS	0.945	0.788	1	0.945	0.788	1	CLONAL	1	FALSE	1	0.205616999332426	2		705	422	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222519	39222520	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	45	596	1	ENST00000402219.2:c.3090dup	p.Tyr1031IlefsTer2	p.Y1031Ifs*2	ENST00000402219	NM_005633.3	1030	-/A	20/23	1	2	FACETS	0.884	0.743	1	0.884	0.743	1	CLONAL	1	FALSE	1	0.205616999332426	2		597	495	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420493	49420493	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs727503979	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	124	1019	2	ENST00000301067.7:c.15256C>T	p.Arg5086Ter	p.R5086*	ENST00000301067	NM_003482.3	5086	Cga/Tga	48/54	1	2	FACETS	0.819	0.742	0.901	1	0.987	1	CLONAL	2	FALSE	1	0.205616999332426	2		1021	736	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354506	91354506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779179608	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	59	646	0	ENST00000355112.3:c.3946G>A	p.Asp1316Asn	p.D1316N	ENST00000355112	NM_000057.2	1316	Gac/Aac	21/22	1	2	FACETS	0.983	0.846	1	0.983	0.846	1	CLONAL	1	FALSE	1	0.205616999332426	2		646	584	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845649	68845649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	77	842	0	ENST00000261769.5:c.895G>A	p.Ala299Thr	p.A299T	ENST00000261769	NM_004360.3	299	Gcc/Acc	7/16	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	FALSE	1	0.205616999332426	2		842	711	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991395	72991395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148618101	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	71	999	1	ENST00000268489.5:c.2650G>A	p.Ala884Thr	p.A884T	ENST00000268489	NM_006885.3	884	Gcc/Acc	2/10	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	FALSE	1	0.205616999332426	2		1000	654	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685584	29685585	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1060500387	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	37	756	0	ENST00000356175.3:c.7996_7997del	p.Ser2666CysfsTer5	p.S2666Cfs*5	ENST00000356175	NM_000267.3	2665	cAG/c	54/57	1	2	FACETS	0.631	0.52	0.757	0.631	0.52	0.757	SUBCLONAL	1	FALSE	1	0.205616999332426	2		756	570	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426730	49426735	+	inframe_deletion	In_Frame_Del	DEL	GCTGCT	GCTGCT	-	rs576788910	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	21	550	0	ENST00000301067.7:c.11753_11758del	p.Gln3918_Gln3919del	p.Q3918_Q3919del	ENST00000301067	NM_003482.3	3918	cAGCAGCta/cta	39/54	1	2	FACETS	0.737	0.568	0.934	0.737	0.568	0.934	CLONAL	1	FALSE	1	0.205616999332426	2		550	277	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149819	202149819	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	35	878	0	ENST00000358485.4:c.1264del	p.Asp422IlefsTer19	p.D422Ifs*19	ENST00000358485	NM_001080125.1	420	caG/ca	8/9	1	2	FACETS	0.644	0.527	0.775	0.644	0.527	0.775	SUBCLONAL	1	FALSE	1	0.205616999332426	2		878	529	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246027124	246027125	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	110	819	1	ENST00000388985.4:c.877dup	p.Ile293AsnfsTer2	p.I293Nfs*2	ENST00000388985		293	att/aAtt	9/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.205616999332426	2		820	731	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262313	16262313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1462385531	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	56	569	0	ENST00000375759.3:c.9578G>A	p.Arg3193Gln	p.R3193Q	ENST00000375759	NM_015001.2	3193	cGg/cAg	11/15	1	2	FACETS	0.876	0.755	1	1	0.974	1	CLONAL	2	FALSE	1	0.205616999332426	2		569	311	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981100	201981101	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	123	961	0	ENST00000359651.3:c.184dup	p.Glu62GlyfsTer30	p.E62Gfs*30	ENST00000359651		60	ttg/ttGg	2/8	1	2	FACETS	0.85	0.769	0.934	1	0.987	1	CLONAL	2	FALSE	1	0.205616999332426	2		961	704	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977207	85977207	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	28	570	0	ENST00000263360.6:c.809T>C	p.Met270Thr	p.M270T	ENST00000263360	NM_003797.3	270	aTg/aCg	8/12	1	2	FACETS	0.719	0.574	0.883	0.719	0.574	0.883	SUBCLONAL	1	FALSE	1	0.205616999332426	2		570	379	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025594	1025594	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1212754456	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	50	1032	1	ENST00000358495.3:c.781C>T	p.Gln261Ter	p.Q261*	ENST00000358495	NM_134424.2	261	Cag/Tag	9/12	0.165680090786737	1	FACETS	0.631	0.534	0.737	0.631	0.534	0.737	SUBCLONAL	1	FALSE	0	0.205616999332426	1		1033	692	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205224	46205224	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	52	598	0	ENST00000334344.6:c.308T>A	p.Val103Asp	p.V103D	ENST00000334344	NM_152641.2	103	gTt/gAt	4/21	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	FALSE	1	0.205616999332426	2		598	481	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465492	99465492	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	80	677	0	ENST00000268035.6:c.2317A>C	p.Thr773Pro	p.T773P	ENST00000268035	NM_000875.3	773	Aca/Cca	11/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.205616999332426	2		677	625	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862111	68862112	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	72	776	0	ENST00000261769.5:c.2202_2203del	p.Arg734SerfsTer13	p.R734Sfs*13	ENST00000261769	NM_004360.3	733	agGAga/agga	14/16	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	FALSE	1	0.205616999332426	2		776	658	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684343	29684344	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	70	779	0	ENST00000356175.3:c.7865dup	p.Leu2622PhefsTer17	p.L2622Ffs*17	ENST00000356175	NM_000267.3	2621	-/T	53/57	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	FALSE	1	0.205616999332426	2		779	583	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117891	70117891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	64	705	0	ENST00000245479.2:c.359G>A	p.Arg120His	p.R120H	ENST00000245479	NM_000346.3	120	cGc/cAc	1/3	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.205616999332426	2		705	443	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213966	2213966	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370589055	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	109	1082	3	ENST00000398665.3:c.1778G>A	p.Arg593His	p.R593H	ENST00000398665	NM_032482.2	593	cGc/cAc	18/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.205616999332426	2		1085	763	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145594	61145594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	40	651	0	ENST00000295025.8:c.706G>A	p.Val236Ile	p.V236I	ENST00000295025	NM_002908.2	236	Gta/Ata	7/11	1	2	FACETS	0.67	0.556	0.797	0.67	0.556	0.797	SUBCLONAL	1	FALSE	1	0.205616999332426	2		651	581	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281539	198281539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	81	744	0	ENST00000335508.6:c.592C>T	p.Arg198Trp	p.R198W	ENST00000335508	NM_012433.2	198	Cgg/Tgg	6/25	1	2	FACETS	0.894	0.786	1	0.894	0.786	1	CLONAL	1	FALSE	1	0.205616999332426	2		744	881	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141605	202141605	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	43	579	0	ENST00000358485.4:c.893T>C	p.Ile298Thr	p.I298T	ENST00000358485	NM_001080125.1	298	aTc/aCc	7/9	1	2	FACETS	0.688	0.575	0.814	0.688	0.575	0.814	SUBCLONAL	1	FALSE	1	0.205616999332426	2		579	608	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661711	227661711	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	94	953	0	ENST00000305123.5:c.1744T>C	p.Tyr582His	p.Y582H	ENST00000305123	NM_005544.2	582	Tac/Cac	1/2	1	2	FACETS	0.833	0.743	0.928	1	0.983	1	CLONAL	2	FALSE	1	0.205616999332426	2		953	549	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662272	227662272	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	67	933	0	ENST00000305123.5:c.1183A>G	p.Ser395Gly	p.S395G	ENST00000305123	NM_005544.2	395	Agt/Ggt	1/2	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	FALSE	1	0.205616999332426	2		933	628	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163805	47163805	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	32	691	0	ENST00000409792.3:c.2321T>C	p.Val774Ala	p.V774A	ENST00000409792	NM_014159.6	774	gTa/gCa	3/21	1	2	FACETS	0.648	0.526	0.787	0.648	0.526	0.787	SUBCLONAL	1	FALSE	1	0.205616999332426	2		691	480	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799482	72799482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571050907	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	70	846	0	ENST00000325599.8:c.1687C>T	p.Arg563Cys	p.R563C	ENST00000325599	NM_018130.2	563	Cgc/Tgc	11/11	1	2	FACETS	0.847	0.737	0.966	0.847	0.737	0.966	CLONAL	1	FALSE	1	0.205616999332426	2		846	804	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478082	138478082	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	109	706	2	ENST00000289153.2:c.104T>C	p.Leu35Pro	p.L35P	ENST00000289153	NM_006219.2	35	cTt/cCt	1/22	1	2	FACETS	1	0.945	1	1	0.989	1	CLONAL	2	FALSE	1	0.205616999332426	2		708	496	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204081	142204082	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	35	715	0	ENST00000350721.4:c.6121dup	p.Tyr2041LeufsTer7	p.Y2041Lfs*7	ENST00000350721	NM_001184.3	2041	tac/tTac	36/47	1	2	FACETS	0.56	0.458	0.675	0.56	0.458	0.675	SUBCLONAL	1	FALSE	1	0.205616999332426	2		715	608	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592117	67592117	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	82	462	0	ENST00000274335.5:c.1933A>G	p.Thr645Ala	p.T645A	ENST00000274335		645	Act/Gct	14/15	1	2	FACETS	0.854	0.756	0.958	1	0.982	1	CLONAL	2	FALSE	1	0.205616999332426	2		462	467	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80021297	80021298	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	59	559	0	ENST00000265081.6:c.1369dup	p.Arg457LysfsTer4	p.R457Kfs*4	ENST00000265081	NM_002439.4	456	gaa/gAaa	9/24	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	FALSE	1	0.205616999332426	2		559	571	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149498329	149498329	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	89	880	0	ENST00000261799.4:c.2885T>C	p.Leu962Ser	p.L962S	ENST00000261799	NM_002609.3	962	tTg/tCg	21/23	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	FALSE	1	0.205616999332426	2		880	774	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158607	26158608	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	57	524	0	ENST00000289316.2:c.212dup	p.Glu72ArgfsTer72	p.E72Rfs*72	ENST00000289316	NM_138720.2	70	-/T	1/2	1	2	FACETS	0.877	0.758	1	1	0.975	1	CLONAL	2	FALSE	1	0.205616999332426	2		524	316	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910735	29910735	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	54	966	0	ENST00000376809.5:c.275A>C	p.Lys92Thr	p.K92T	ENST00000376809	NM_002116.7	92	aAg/aCg	2/8	1	2	FACETS	0.974	0.833	1	0.974	0.833	1	CLONAL	1	FALSE	1	0.205616999332426	2		966	539	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324513	31324513	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs41541213	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	35	766	0	ENST00000412585.2:c.295C>T	p.Arg99Ter	p.R99*	ENST00000412585	NM_005514.6	99	Cga/Tga	2/8	1	2	FACETS	0.596	0.488	0.719	0.596	0.488	0.719	SUBCLONAL	1	FALSE	1	0.205616999332426	2		766	571	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271165	38271165	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	72	792	0	ENST00000425967.3:c.2543G>T	p.Gly848Val	p.G848V	ENST00000425967	NM_001174067.1	848	gGc/gTc	19/19	1	2	FACETS	0.929	0.816	1	1	0.981	1	CLONAL	2	FALSE	1	0.205616999332426	2		792	377	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499726	8499726	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	75	829	1	ENST00000356435.5:c.2243A>G	p.Gln748Arg	p.Q748R	ENST00000356435		748	cAg/cGg	14/35	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	1	0.205616999332426	2		830	628	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27168526	27168526	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	56	721	0	ENST00000380036.4:c.398T>C	p.Val133Ala	p.V133A	ENST00000380036	NM_000459.3	133	gTg/gCg	3/23	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	1	0.205616999332426	2		721	487	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772052	135772052	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	36	771	0	ENST00000298552.3:c.3065G>A	p.Arg1022Lys	p.R1022K	ENST00000298552	NM_001162426.1	1022	aGg/aAg	23/23	1	2	FACETS	0.634	0.521	0.762	0.634	0.521	0.762	SUBCLONAL	1	FALSE	1	0.205616999332426	2		771	552	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776179	135776179	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1371334608	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	86	765	0	ENST00000298552.3:c.2548A>G	p.Arg850Gly	p.R850G	ENST00000298552	NM_001162426.1	850	Agg/Ggg	20/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.205616999332426	2		765	625	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933616	39933617	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	91	488	0	ENST00000378444.4:c.982dup	p.Asp328GlyfsTer53	p.D328Gfs*53	ENST00000378444	NM_001123385.1	328	gac/gGac	4/15	0.205616999332426	2	FACETS	1	0.959	1			1	CLONAL	3	FALSE	NA	0.205616999332426	2		488	262	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424478	47424478	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	71	473	0	ENST00000377045.4:c.398A>G	p.His133Arg	p.H133R	ENST00000377045	NM_001654.4	133	cAc/cGc	5/16	0.205616999332426	2	FACETS	1	0.885	1			1	CLONAL	2	FALSE	NA	0.205616999332426	2		473	343	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228264	53228264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794733	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	71	510	0	ENST00000375401.3:c.2138C>T	p.Thr713Met	p.T713M	ENST00000375401	NM_004187.3	713	aCg/aTg	15/26	0.205616999332426	2	FACETS	0.892	0.783	1			1	CLONAL	2	FALSE	NA	0.205616999332426	2		510	387	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349943	70349943	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	37	532	0	ENST00000374080.3:c.3926A>C	p.Asp1309Ala	p.D1309A	ENST00000374080		1309	gAc/gCc	28/45	0.205616999332426	2	FACETS	0.843	0.695	1			1	CLONAL	1	FALSE	NA	0.205616999332426	2		532	427	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0053401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	197	330	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.587660531490481	2		330	616	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619109	37619109	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs781029595	NA	P-0053401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	217	660	0	ENST00000447079.4:c.785A>G	p.Tyr262Cys	p.Y262C	ENST00000447079	NM_015083.1	262	tAc/tGc	1/14	0.587660531490481	3	FACETS	0.886	0.824	0.951	0.443	0.412	0.476	CLONAL	1	TRUE	1	0.587660531490481	3		660	1078	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577061	7577062	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	283	956	0	ENST00000269305.4:c.876dup	p.Gly293ArgfsTer13	p.G293Rfs*13	ENST00000269305	NM_001126112.2	292	-/A	8/11	0.480064298637922	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.480064298637922	1		956	884	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263847	16263847	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	255	911	0	ENST00000375759.3:c.10216G>C	p.Ala3406Pro	p.A3406P	ENST00000375759	NM_015001.2	3406	Gct/Cct	12/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.480064298637922	2		911	1000	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243607	41243607	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	291	811	0	ENST00000357654.3:c.3941del	p.Asp1314ValfsTer4	p.D1314Vfs*4	ENST00000357654	NM_007294.3	1314	gAt/gt	10/23	0.480064298637922	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.480064298637922	1		811	825	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191068	185191068	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1401	234	876	0	ENST00000265026.3:c.1949A>G	p.Gln650Arg	p.Q650R	ENST00000265026	NM_004721.4	650	cAg/cGg	11/14	0.323557303450608	5	FACETS	1	0.949	1	0.342	0.317	0.367	CLONAL	1	TRUE	2	0.480064298637922	5		876	1635	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0053403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	30	322	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.293	0.236	0.358	0.293	0.236	0.358	SUBCLONAL	1	TRUE	1	0.584238721992444	2		322	350	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0053403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	150	495	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.976	0.898	1	0.976	0.898	1	CLONAL	1	TRUE	1	0.584238721992444	2		495	526	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0053403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	167	710	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	0.915	0.844	0.988	0.915	0.844	0.988	CLONAL	1	TRUE	1	0.584238721992444	2		710	625	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0053404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	124	430	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.191057827856695	3	FACETS	0.848	0.767	0.932	0.848	0.767	0.932	CLONAL	2	TRUE	1	0.210561979390296	3		430	768	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0053404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	110	848	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.168056814559083	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.210561979390296	2		848	479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579374	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1060501195	NA	P-0053404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	117	853	0	ENST00000269305.4:c.313G>C	p.Gly105Arg	p.G105R	ENST00000269305	NM_001126112.2	105	Ggc/Cgc	4/11	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.210561979390296	2		853	1066	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443757	52443757	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	212	903	0	ENST00000460680.1:c.40del	p.Leu14SerfsTer58	p.L14Sfs*58	ENST00000460680	NM_004656.3	14	Ctc/tc	2/17	0.469616142738923	1	FACETS	0.666	0.619	0.716	0.666	0.619	0.716	SUBCLONAL	1	TRUE	0	0.469616142738923	1		903	1037	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0053406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	234	956	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.200042944841443	1	FACETS	0.984	0.925	1	0.984	0.925	1	INDETERMINATE	1	TRUE	0	0.580234727920576	1		956	582	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6439797	6439797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	100	580	0	ENST00000356142.4:c.323C>T	p.Ser108Leu	p.S108L	ENST00000356142	NM_018890.3	108	tCa/tTa	5/7	1	2	FACETS	0.874	0.781	0.971	0.874	0.781	0.971	CLONAL	1	TRUE	1	0.354943752353087	2		580	645	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566508	41566508	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1263559023	NA	P-0053407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	102	467	0	ENST00000263253.7:c.4385G>A	p.Arg1462Gln	p.R1462Q	ENST00000263253	NM_001429.3	1462	cGa/cAa	27/31	NA	2	FACETS	0.734	0.656	0.817			1	INDETERMINATE	1	TRUE	NA	0.354943752353087	2		467	783	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0053408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	79	658	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.381	0.335	0.429	0.381	0.335	0.429	SUBCLONAL	1	TRUE	1	0.792420022770855	2		658	524	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200024	123200024	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0053408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	44	114	0	ENST00000218089.9:c.2097-1G>A		p.X699_splice	ENST00000218089	NM_001042749.1	699			0.792420022770855	3	FACETS	0.396	0.332	0.465	0.198	0.166	0.233	SUBCLONAL	1	TRUE	1	0.792420022770855	3		114	392	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44910975	44910975	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	67	167	1	ENST00000377967.4:c.676G>T	p.Glu226Ter	p.E226*	ENST00000377967	NM_021140.2	226	Gaa/Taa	9/29	0.792420022770855	3	FACETS	0.332	0.288	0.379	0.166	0.144	0.19	SUBCLONAL	1	TRUE	1	0.792420022770855	3		168	712	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788605	3788605	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	63	626	0	ENST00000262367.5:c.4349A>G	p.Tyr1450Cys	p.Y1450C	ENST00000262367	NM_004380.2	1450	tAc/tGc	26/31	1	2	FACETS	0.194	0.167	0.223	0.194	0.167	0.223	SUBCLONAL	1	TRUE	1	0.792420022770855	2		626	821	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992792	68992792	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	45	342	0	ENST00000288368.4:c.1757T>G	p.Val586Gly	p.V586G	ENST00000288368	NM_024870.2	586	gTg/gGg	16/40	1	2	FACETS	0.137	0.115	0.162	0.137	0.115	0.162	SUBCLONAL	1	TRUE	1	0.792420022770855	2		342	828	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579362	7579362	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057523496	NA	P-0053431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	86	953	0	ENST00000269305.4:c.325T>G	p.Phe109Val	p.F109V	ENST00000269305	NM_001126112.2	109	Ttc/Gtc	4/11	1	2	FACETS	0.873	0.77	0.985	0.873	0.77	0.985	CLONAL	1	TRUE	1	0.163566274293877	2		953	1204	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574121	41574121	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs372874467	NA	P-0053431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	100	771	0	ENST00000263253.7:c.6406A>G	p.Met2136Val	p.M2136V	ENST00000263253	NM_001429.3	2136	Atg/Gtg	31/31	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.163566274293877	2		771	1075	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0053432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	89	889	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.260729670432705	1	FACETS	0.704	0.624	0.791	0.704	0.624	0.791	SUBCLONAL	1	TRUE	0	0.260729670432705	1		889	843	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0053432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	148	297	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.260729670432705	2		297	915	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223334	2223334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757410464	NA	P-0053432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	67	920	0	ENST00000326181.6:c.946C>T	p.Arg316Cys	p.R316C	ENST00000326181	NM_032271.2	316	Cgc/Tgc	10/21	0.161730260688363	0	FACETS	0.495	0.43	0.567			1	SUBCLONAL	1	TRUE	0	0.260729670432705	0		920	767	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871913	45871913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913020	NA	P-0053432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	186	750	3	ENST00000391945.4:c.335G>A	p.Arg112His	p.R112H	ENST00000391945	NM_000400.3	112	cGc/cAc	5/23	1	2	FACETS	0.767	0.709	0.828	1	0.99	1	SUBCLONAL	2	TRUE	1	0.260729670432705	2		753	930	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711988	89711988	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	53	414	0	ENST00000371953.3:c.606del	p.Ile203PhefsTer18	p.I203Ffs*18	ENST00000371953	NM_000314.4	202	acT/ac	6/9	0.260729670432705	1	FACETS	0.734	0.626	0.851	0.734	0.626	0.851	SUBCLONAL	1	TRUE	0	0.260729670432705	1		414	482	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045729	26045729	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	53	597	1	ENST00000540144.1:c.91C>A	p.Pro31Thr	p.P31T	ENST00000540144	NM_003531.2	31	Ccg/Acg	1/1	1	2	FACETS	0.609	0.518	0.708	0.609	0.518	0.708	SUBCLONAL	1	TRUE	1	0.260729670432705	2		598	668	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482949	140482949	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	92	645	0	ENST00000288602.6:c.1186A>T	p.Thr396Ser	p.T396S	ENST00000288602	NM_004333.4	396	Aca/Tca	10/18	1	2	FACETS	0.807	0.716	0.904	0.807	0.716	0.904	CLONAL	1	TRUE	1	0.260729670432705	2		645	875	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840603	36840603	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs966082163	NA	P-0053433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	139	1155	2	ENST00000358127.4:c.1130G>A	p.Arg377Gln	p.R377Q	ENST00000358127	NM_001280556.1	377	cGa/cAa	10/10	1	2	FACETS	0.833	0.757	0.912	0.833	0.757	0.912	CLONAL	1	FALSE	1	0.341042165083812	2		1157	979	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044941	47044941	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	205	712	0	ENST00000377604.3:c.2268del	p.Trp756CysfsTer46	p.W756Cfs*46	ENST00000377604	NM_001204468.1	756	tGg/tg	20/24	0.0125412395463451	2	FACETS	0.965	0.9	1			1	INDETERMINATE	2	FALSE	NA	0.341042165083812	2		712	623	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123635	108123635	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1041333479	NA	P-0053433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	77	282	0	ENST00000278616.4:c.1894G>T	p.Glu632Ter	p.E632*	ENST00000278616	NM_000051.3	632	Gaa/Taa	12/63	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.341042165083812	2		282	373	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134628	41134628	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	84	596	0	ENST00000379561.5:c.1000G>T	p.Glu334Ter	p.E334*	ENST00000379561	NM_002015.3	334	Gaa/Taa	2/3	0.0983788105406223	3	FACETS	0.914	0.808	1	0.457	0.404	0.514	INDETERMINATE	1	FALSE	1	0.341042165083812	3		596	631	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556460	29556479	+	frameshift_variant	Frame_Shift_Del	DEL	AAGTTTTTTGACTCCCAAGG	AAGTTTTTTGACTCCCAAGG	-	novel	NA	P-0053433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	60	345	0	ENST00000356175.3:c.2828_2847del	p.Lys943ThrfsTer6	p.K943Tfs*6	ENST00000356175	NM_000267.3	943	AAGTTTTTTGACTCCCAAGGa/a	21/57	1	2	FACETS	0.693	0.597	0.796	0.693	0.597	0.796	SUBCLONAL	1	FALSE	1	0.341042165083812	2		345	508	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723457	52723457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	105	766	0	ENST00000322088.6:c.1318G>A	p.Asp440Asn	p.D440N	ENST00000322088	NM_014225.5	440	Gat/Aat	11/15	1	2	FACETS	0.754	0.675	0.837	0.754	0.675	0.837	SUBCLONAL	1	FALSE	1	0.341042165083812	2		766	817	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966955	25966955	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	185	1049	0	ENST00000435504.4:c.2251C>A	p.Gln751Lys	p.Q751K	ENST00000435504		751	Cag/Aag	13/13	1	2	FACETS	0.989	0.912	1	0.989	0.912	1	CLONAL	1	FALSE	1	0.341042165083812	2		1049	1097	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47710041	47710041	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	46	205	0	ENST00000233146.2:c.2758A>C	p.Asn920His	p.N920H	ENST00000233146	NM_000251.2	920	Aat/Cat	16/16	1	2	FACETS	0.703	0.593	0.823	0.703	0.593	0.823	SUBCLONAL	1	FALSE	1	0.341042165083812	2		205	384	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96931081	96931094	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCCCGCCGGGCA	GCGCCCGCCGGGCA	-	novel	NA	P-0053433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	26	140	0	ENST00000258439.3:c.26_39del	p.Leu9ProfsTer17	p.L9Pfs*17	ENST00000258439	NM_001193304.2	9	cTGCCCGGCGGGCGC/c	2/4	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	FALSE	1	0.341042165083812	2		140	122	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790062	40790062	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	180	1065	0	ENST00000373198.4:c.2669T>A	p.Val890Glu	p.V890E	ENST00000373198	NM_133170.3	890	gTg/gAg	18/32	1	2	FACETS	0.928	0.854	1	0.928	0.854	1	CLONAL	1	FALSE	1	0.341042165083812	2		1065	1138	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306638	41306638	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762711002	NA	P-0053433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	153	1170	0	ENST00000373198.4:c.1021G>T	p.Asp341Tyr	p.D341Y	ENST00000373198	NM_133170.3	341	Gac/Tac	7/32	1	2	FACETS	0.897	0.82	0.978	0.897	0.82	0.978	CLONAL	1	FALSE	1	0.341042165083812	2		1170	1000	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946137	55946137	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	101	519	2	ENST00000263923.4:c.4042G>T	p.Gly1348Trp	p.G1348W	ENST00000263923	NM_002253.2	1348	Ggg/Tgg	30/30	1	2	FACETS	0.918	0.822	1	0.918	0.822	1	CLONAL	1	FALSE	1	0.341042165083812	2		521	645	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159063	143159063	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1554013640	NA	P-0053433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	63	278	0	ENST00000262992.4:c.790A>G	p.Ile264Val	p.I264V	ENST00000262992	NM_001101669.1	264	Att/Gtt	10/24	1	2	FACETS	0.897	0.778	1	0.897	0.778	1	CLONAL	1	FALSE	1	0.341042165083812	2		278	412	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920158	76920158	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	110	268	0	ENST00000373344.5:c.3919A>G	p.Asn1307Asp	p.N1307D	ENST00000373344	NM_000489.3	1307	Aat/Gat	11/35	0.0125412395463451	2	FACETS	0.849	0.77	0.931			1	INDETERMINATE	2	FALSE	NA	0.341042165083812	2		268	380	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982309	201982309	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0053435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	434	993	0	ENST00000359651.3:c.689-1G>A		p.X230_splice	ENST00000359651		230			0.505212785697813	3	FACETS	0.993	0.949	1	0.993	0.949	1	CLONAL	2	TRUE	1	0.505212785697813	3		993	1084	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653843	89653843	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	103	520	0	ENST00000371953.3:c.141G>T	p.Arg47Ser	p.R47S	ENST00000371953	NM_000314.4	47	agG/agT	2/9	0.505212785697813	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.505212785697813	2		520	194	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039615	47039615	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556778322	NA	P-0053435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	417	499	0	ENST00000377604.3:c.1067C>T	p.Ala356Val	p.A356V	ENST00000377604	NM_001204468.1	356	gCa/gTa	11/24	0.306619959577728	3	FACETS	0.901	0.873	0.928			1	CLONAL	4	TRUE	NA	0.505212785697813	3		499	574	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508251	38508251	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	426	989	1	ENST00000254066.5:c.559C>T	p.Leu187Phe	p.L187F	ENST00000254066	NM_000964.3	187	Ctc/Ttc	5/9	0.452312687034407	4	FACETS	0.933	0.888	0.978	0.933	0.888	0.978	CLONAL	2	TRUE	2	0.505212785697813	4		990	1361	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146828	185146828	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	149	689	2	ENST00000265026.3:c.459C>A	p.Tyr153Ter	p.Y153*	ENST00000265026	NM_004721.4	153	taC/taA	2/14	0.452312687034407	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.505212785697813	4		691	411	SUCCESS
APC	324	MSKCC	GRCh37	5	112111412	112111416	+	frameshift_variant	Frame_Shift_Del	DEL	ATAGT	ATAGT	-	novel	NA	P-0053435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	48	348	0	ENST00000257430.4:c.509_513del	p.Asp170AlafsTer5	p.D170Afs*5	ENST00000257430	NM_000038.5	170	gATAGT/g	5/16	0.50288890455335	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	2	TRUE	0	0.505212785697813	2		348	95	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236616	236616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1296066077	NA	P-0053436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	21	584	1	ENST00000264932.6:c.1334C>T	p.Ser445Leu	p.S445L	ENST00000264932	NM_004168.2	445	tCg/tTg	10/15	0.173121080887552	3	FACETS	0.227	0.174	0.29	0.114	0.087	0.145	SUBCLONAL	1	TRUE	1	0.256595320214576	3		585	812	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127177	22127177	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0053436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	50	731	0	ENST00000215832.6:c.951C>G	p.Tyr317Ter	p.Y317*	ENST00000215832	NM_002745.4	317	taC/taG	7/9	1	2	FACETS	0.432	0.365	0.506	0.432	0.365	0.506	SUBCLONAL	1	TRUE	1	0.256595320214576	2		731	902	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636860	176636860	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	91	736	0	ENST00000439151.2:c.1460C>A	p.Ala487Glu	p.A487E	ENST00000439151	NM_022455.4	487	gCa/gAa	5/23	1	2	FACETS	0.871	0.773	0.977	0.871	0.773	0.977	CLONAL	1	TRUE	1	0.256595320214576	2		736	814	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411875	116411887	+	intron_variant	Intron	DEL	CAAGCTCTTTCTT	CAAGCTCTTTCTT	-	novel	NA	P-0053436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	227	1050	0	ENST00000397752.3:c.2888-28_2888-16del		p.*963*	ENST00000397752	NM_000245.2	-/1390			0.212861748815725	2	FACETS	1	0.991	1	0.736	0.685	0.789	CLONAL	1	TRUE	0	0.256595320214576	2		1050	1202	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	443	411	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.610771645864497	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.632352037126662	2		411	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0053437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	942	1171	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.597922323653782	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.632352037126662	2		1171	1481	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0053437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	87	441	1	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.265539770286569	3	FACETS	0.642	0.569	0.72	0.214	0.189	0.24	INDETERMINATE	1	TRUE	0	0.632352037126662	3		442	564	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0053437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	408	484	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.265539770286569	3	FACETS	1	0.992	1	0.752	0.722	0.782	INDETERMINATE	2	TRUE	0	0.632352037126662	3		484	753	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903753	114903754	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	571	697	2	ENST00000543371.1:c.758dup	p.His255ProfsTer73	p.H255Pfs*73	ENST00000543371	NM_001198531.1	253	atc/aTtc	7/14	0.208173992955754	3	FACETS	1	0.981	1	0.684	0.659	0.708	INDETERMINATE	2	TRUE	0	0.632352037126662	3		699	1159	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952155	76952155	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	210	660	0	ENST00000373344.5:c.280G>T	p.Asp94Tyr	p.D94Y	ENST00000373344	NM_000489.3	94	Gat/Tat	5/35	0.450164831472017	4	FACETS	1	0.975	1	0.555	0.515	0.596	CLONAL	1	TRUE	2	0.632352037126662	4		660	977	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	114	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.999	0.907	1	0.999	0.907	1	CLONAL	1	TRUE	1	0.560865715350219	2		429	407	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	323	848	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.561280239076013	4	FACETS	1	0.993	1	0.46	0.433	0.487	CLONAL	1	TRUE	1	0.560865715350219	4		848	1304	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	287	808	10	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.849	0.798	0.902	0.849	0.798	0.902	CLONAL	1	TRUE	1	0.560865715350219	2		818	1205	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323362	31323363	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748204482	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	131	705	0	ENST00000412585.2:c.626dup	p.Thr211AspfsTer10	p.T211Dfs*10	ENST00000412585	NM_005514.6	209	cca/ccCa	4/8	1	2	FACETS	0.563	0.511	0.618	0.563	0.511	0.618	SUBCLONAL	1	TRUE	1	0.560865715350219	2		705	830	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779211	3779211	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783507	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	179	675	3	ENST00000262367.5:c.5837del	p.Pro1946HisfsTer30	p.P1946Hfs*30	ENST00000262367	NM_004380.2	1946	cCa/ca	31/31	0.559458583335698	3	FACETS	0.656	0.604	0.712	0.328	0.302	0.356	SUBCLONAL	1	TRUE	1	0.560865715350219	3		678	1245	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791372	42791373	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	398	1104	0	ENST00000575354.2:c.436_437del	p.Ser146Ter	p.S146*	ENST00000575354	NM_015125.3	144	acAGag/acag	3/20	1	2	FACETS	0.902	0.856	0.949	0.902	0.856	0.949	CLONAL	1	TRUE	1	0.560865715350219	2		1104	1574	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	425	1246	0	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.929	0.883	0.975	0.929	0.883	0.975	CLONAL	1	TRUE	1	0.560865715350219	2		1246	1632	SUCCESS
ATR	545	MSKCC	GRCh37	3	142255005	142255005	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	196	391	0	ENST00000350721.4:c.3764del	p.Leu1255TyrfsTer7	p.L1255Yfs*7	ENST00000350721	NM_001184.3	1255	tTa/ta	20/47	0.560865715350219	2	FACETS	1	0.939	1	0.506	0.47	0.543	CLONAL	1	TRUE	0	0.560865715350219	2		391	691	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116168	67116168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1467426352	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	570	696	2	ENST00000412916.2:c.452G>A	p.Arg151His	p.R151H	ENST00000412916		151	cGc/cAc	5/6	0.559458583335698	3	FACETS	0.935	0.899	0.971	0.935	0.899	0.971	CLONAL	2	TRUE	1	0.560865715350219	3		698	1392	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532528	63532528	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138287857	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	443	1347	4	ENST00000307078.5:c.2051C>T	p.Ala684Val	p.A684V	ENST00000307078	NM_004655.3	684	gCg/gTg	8/11	0.560865715350219	2	FACETS	0.956	0.91	1	0.478	0.455	0.502	CLONAL	1	TRUE	0	0.560865715350219	2		1351	1652	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039182	49039182	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587778642	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	242	627	0	ENST00000267163.4:c.2260G>C	p.Val754Leu	p.V754L	ENST00000267163	NM_000321.2	754	Gta/Cta	22/27	1	2	FACETS	0.889	0.831	0.948	0.889	0.831	0.948	CLONAL	1	TRUE	1	0.560865715350219	2		627	971	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354152	15354152	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs868796773	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	240	864	0	ENST00000263377.2:c.2728del	p.Gln910LysfsTer39	p.Q910Kfs*39	ENST00000263377	NM_058243.2	910	Caa/aa	14/20	1	2	FACETS	0.724	0.675	0.774	0.724	0.675	0.774	SUBCLONAL	1	TRUE	1	0.560865715350219	2		864	1182	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954273	32954273	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359752	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	195	710	0	ENST00000380152.3:c.9253del	p.Thr3085GlnfsTer19	p.T3085Qfs*19	ENST00000380152		3083	Aaa/aa	24/27	1	2	FACETS	0.785	0.727	0.845	0.785	0.727	0.845	SUBCLONAL	1	TRUE	1	0.560865715350219	2		710	886	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434682	110434682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	364	902	0	ENST00000375856.3:c.3719G>A	p.Arg1240His	p.R1240H	ENST00000375856	NM_003749.2	1240	cGc/cAc	1/2	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.560865715350219	2		902	1250	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431874	49431874	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	371	1060	3	ENST00000301067.7:c.9265del	p.Val3089TrpfsTer30	p.V3089Wfs*30	ENST00000301067	NM_003482.3	3089	Gtg/tg	34/54	1	2	FACETS	0.934	0.885	0.984	0.934	0.885	0.984	CLONAL	1	TRUE	1	0.560865715350219	2		1063	1417	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562876	176562876	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1268581071	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	364	814	0	ENST00000439151.2:c.772T>C	p.Phe258Leu	p.F258L	ENST00000439151	NM_022455.4	258	Ttt/Ctt	2/23	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.560865715350219	2		814	1271	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069292	30069292	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1161410708	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	399	1056	1	ENST00000338641.4:c.1160del	p.Lys387ArgfsTer39	p.K387Rfs*39	ENST00000338641	NM_000268.3	386	gAa/ga	12/16	1	2	FACETS	0.998	0.949	1	0.998	0.949	1	CLONAL	1	TRUE	1	0.560865715350219	2		1057	1425	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639398	3639398	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748691881	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1228	785	1173	0	ENST00000294008.3:c.4241del	p.Pro1414HisfsTer36	p.P1414Hfs*36	ENST00000294008	NM_032444.2	1414	cCa/ca	12/15	0.559458583335698	3	FACETS	0.89	0.861	0.92	0.89	0.861	0.92	CLONAL	2	TRUE	1	0.560865715350219	3		1173	2013	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395221	139395221	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756056361	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1750	529	1366	0	ENST00000277541.6:c.5717C>T	p.Ala1906Val	p.A1906V	ENST00000277541	NM_017617.3	1906	gCg/gTg	31/34	0.561280239076013	3	FACETS	1	0.984	1	0.53	0.506	0.554	CLONAL	1	TRUE	1	0.560865715350219	3		1366	2279	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753545	42753545	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1254035180	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1295	478	1388	0	ENST00000222329.4:c.719del	p.Gly240ValfsTer31	p.G240Vfs*31	ENST00000222329	NM_006494.2	240	gGt/gt	4/4	1	2	FACETS	0.961	0.917	1	0.961	0.917	1	CLONAL	1	TRUE	1	0.560865715350219	2		1388	1773	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517925	8517925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	251	596	1	ENST00000356435.5:c.1466C>T	p.Ser489Phe	p.S489F	ENST00000356435		489	tCt/tTt	10/35	0.561280239076013	4	FACETS	1	0.963	1	0.348	0.325	0.373	CLONAL	1	TRUE	1	0.560865715350219	4		597	1337	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829303	128829303	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	371	1006	0	ENST00000249373.3:c.311G>A	p.Gly104Asp	p.G104D	ENST00000249373	NM_005631.4	104	gGc/gAc	1/12	1	2	FACETS	0.987	0.935	1	0.987	0.935	1	CLONAL	1	TRUE	1	0.560865715350219	2		1006	1341	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015387	176015387	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	198	643	0	ENST00000367669.3:c.1351G>C	p.Asp451His	p.D451H	ENST00000367669	NM_022457.5	451	Gac/Cac	12/20	1	2	FACETS	0.936	0.87	1	0.936	0.87	1	CLONAL	1	TRUE	1	0.560865715350219	2		643	754	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566523	41566523	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	231	650	0	ENST00000263253.7:c.4400A>G	p.Tyr1467Cys	p.Y1467C	ENST00000263253	NM_001429.3	1467	tAc/tGc	27/31	1	2	FACETS	0.857	0.8	0.916	0.857	0.8	0.916	CLONAL	1	TRUE	1	0.560865715350219	2		650	961	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104353480	104353480	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	367	1083	0	ENST00000369902.3:c.683+2T>C		p.X228_splice	ENST00000369902	NM_016169.3	228			1	2	FACETS	0.894	0.846	0.943	0.894	0.846	0.943	CLONAL	1	TRUE	1	0.560865715350219	2		1083	1464	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431160	49431160	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1225	406	1192	0	ENST00000301067.7:c.9979del	p.Gln3327SerfsTer3	p.Q3327Sfs*3	ENST00000301067	NM_003482.3	3327	Cag/ag	34/54	1	2	FACETS	0.888	0.843	0.934	0.888	0.843	0.934	CLONAL	1	TRUE	1	0.560865715350219	2		1192	1631	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794747	120794747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1191	497	1233	0	ENST00000257552.2:c.610C>T	p.Pro204Ser	p.P204S	ENST00000257552	NM_002442.3	204	Ccc/Tcc	9/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.560865715350219	2		1233	1688	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32971074	32971074	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	265	654	0	ENST00000380152.3:c.9541A>G	p.Met3181Val	p.M3181V	ENST00000380152		3181	Atg/Gtg	26/27	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.560865715350219	2		654	899	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331852	68331852	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	221	597	0	ENST00000487270.1:c.448G>C	p.Glu150Gln	p.E150Q	ENST00000487270	NM_133509.3	150	Gaa/Caa	5/11	0.559458583335698	3	FACETS	0.897	0.834	0.962	0.448	0.417	0.481	CLONAL	1	TRUE	1	0.560865715350219	3		597	1125	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17125879	17125879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs78683075	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	442	1107	0	ENST00000285071.4:c.715C>T	p.Arg239Cys	p.R239C	ENST00000285071	NM_144997.5	239	Cgc/Tgc	7/14	0.269442708937562	2	FACETS	0.986	0.939	1	0.493	0.469	0.517	INDETERMINATE	1	TRUE	0	0.560865715350219	2		1107	1599	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40468879	40468879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293678815	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	124	636	1	ENST00000264657.5:c.2185C>T	p.Arg729Cys	p.R729C	ENST00000264657	NM_139276.2	729	Cgc/Tgc	23/24	0.560865715350219	2	FACETS	0.44	0.397	0.485	0.22	0.198	0.243	SUBCLONAL	1	TRUE	0	0.560865715350219	2		637	1006	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475126	40475126	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	393	895	1	ENST00000264657.5:c.1784G>T	p.Arg595Leu	p.R595L	ENST00000264657	NM_139276.2	595	cGg/cTg	20/24	0.560865715350219	2	FACETS	1	0.968	1	0.513	0.487	0.539	CLONAL	1	TRUE	0	0.560865715350219	2		896	1366	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119815	70119815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	376	960	0	ENST00000245479.2:c.817G>A	p.Val273Met	p.V273M	ENST00000245479	NM_000346.3	273	Gtg/Atg	3/3	0.560865715350219	2	FACETS	1	0.96	1	0.507	0.481	0.534	CLONAL	1	TRUE	0	0.560865715350219	2		960	1322	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912104	50912104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1226	442	1221	1	ENST00000440232.2:c.1838C>T	p.Ala613Val	p.A613V	ENST00000440232	NM_002691.3	613	gCc/gTc	15/27	1	2	FACETS	0.945	0.9	0.991	0.945	0.9	0.991	CLONAL	1	TRUE	1	0.560865715350219	2		1222	1668	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719045	52719046	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	275	894	0	ENST00000322088.6:c.825dup	p.Pro276AlafsTer2	p.P276Afs*2	ENST00000322088	NM_014225.5	274	gtg/gtGg	7/15	1	2	FACETS	0.847	0.795	0.901	0.847	0.795	0.901	CLONAL	1	TRUE	1	0.560865715350219	2		894	1158	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972921	25972921	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	261	648	0	ENST00000435504.4:c.1504G>T	p.Glu502Ter	p.E502*	ENST00000435504		502	Gag/Tag	12/13	1	2	FACETS	0.995	0.934	1	0.995	0.934	1	CLONAL	1	TRUE	1	0.560865715350219	2		648	935	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067458	37067458	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	694	848	2	ENST00000231790.2:c.1369G>T	p.Glu457Ter	p.E457*	ENST00000231790	NM_000249.3	457	Gaa/Taa	12/19	0.560865715350219	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.560865715350219	2		850	1237	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217517	142217517	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	578	738	0	ENST00000350721.4:c.5480G>C	p.Arg1827Thr	p.R1827T	ENST00000350721	NM_001184.3	1827	aGa/aCa	32/47	0.560865715350219	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.560865715350219	2		738	958	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169988330	169988330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	412	603	0	ENST00000295797.4:c.572G>A	p.Gly191Glu	p.G191E	ENST00000295797	NM_002740.5	191	gGg/gAg	6/18	0.561280239076013	3	FACETS	0.891	0.85	0.932	0.891	0.85	0.932	CLONAL	2	TRUE	1	0.560865715350219	3		603	1056	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747922	41747922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	239	583	0	ENST00000226382.2:c.847A>T	p.Ile283Phe	p.I283F	ENST00000226382	NM_003924.3	283	Atc/Ttc	3/3	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.560865715350219	2		583	774	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532905	187532905	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	224	568	0	ENST00000441802.2:c.9488C>G	p.Ser3163Ter	p.S3163*	ENST00000441802	NM_005245.3	3163	tCa/tGa	14/27	0.561280239076013	1	FACETS	0.944	0.885	1	0.944	0.885	1	CLONAL	1	TRUE	0	0.560865715350219	1		568	609	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235324	235324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	356	934	3	ENST00000264932.6:c.1130C>T	p.Ala377Val	p.A377V	ENST00000264932	NM_004168.2	377	gCc/gTc	9/15	1	2	FACETS	0.98	0.928	1	0.98	0.928	1	CLONAL	1	TRUE	1	0.560865715350219	2		937	1295	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527307	157527307	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	186	506	0	ENST00000346085.5:c.5032G>C	p.Gly1678Arg	p.G1678R	ENST00000346085	NM_020732.3	1678	Gga/Cga	20/20	1	2	FACETS	0.933	0.864	1	0.933	0.864	1	CLONAL	1	TRUE	1	0.560865715350219	2		506	711	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879213	151879213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	285	762	0	ENST00000262189.6:c.5732G>A	p.Gly1911Asp	p.G1911D	ENST00000262189	NM_170606.2	1911	gGc/gAc	36/59	1	2	FACETS	0.996	0.938	1	0.996	0.938	1	CLONAL	1	TRUE	1	0.560865715350219	2		762	1020	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38194825	38194825	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	264	703	0	ENST00000317025.8:c.908G>A	p.Arg303Lys	p.R303K	ENST00000317025	NM_023034.1	303	aGa/aAa	4/24	NA	2	FACETS	1	0.948	1			1	INDETERMINATE	1	TRUE	NA	0.560865715350219	2		703	931	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133729604	133729604	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	362	764	0	ENST00000318560.5:c.233A>G	p.Asn78Ser	p.N78S	ENST00000318560	NM_005157.4	78	aAc/aGc	2/11	0.561280239076013	3	FACETS	1	0.984	1	0.548	0.518	0.578	CLONAL	1	TRUE	1	0.560865715350219	3		764	1508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0053439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1274	414	833	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.225773323530222	2	FACETS	0.928	0.882	0.976	0.928	0.882	0.976	CLONAL	2	TRUE	0	0.264197602231014	2		837	1688	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106484	27106506	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAGGAGGAGGAACAGGACCAA	AAAAGGAGGAGGAACAGGACCAA	-	novel	NA	P-0053439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	368	950	0	ENST00000324856.7:c.6095_6117del	p.Glu2032GlyfsTer59	p.E2032Gfs*59	ENST00000324856	NM_006015.4	2032	gAAAAGGAGGAGGAACAGGACCAA/g	20/20	0.225773323530222	2	FACETS	0.942	0.892	0.993	0.942	0.892	0.993	CLONAL	2	TRUE	0	0.264197602231014	2		950	1479	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0053454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	14	364	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.199	0.143	0.267	0.199	0.143	0.267	SUBCLONAL	1	TRUE	1	0.399673613119676	2		364	352	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175793	24175793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772804160	NA	P-0053454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	147	739	0	ENST00000263121.7:c.1021C>T	p.Arg341Trp	p.R341W	ENST00000263121	NM_003073.3	341	Cgg/Tgg	8/9	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.399673613119676	2		739	725	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130612	29130612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	114	632	0	ENST00000328354.6:c.98C>T	p.Ser33Leu	p.S33L	ENST00000328354	NM_007194.3	33	tCa/tTa	2/15	1	2	FACETS	0.822	0.741	0.908	0.822	0.741	0.908	CLONAL	1	TRUE	1	0.399673613119676	2		632	694	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967964	93967964	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs768474651	NA	P-0053454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	108	446	0	ENST00000369303.4:c.1963C>G	p.Pro655Ala	p.P655A	ENST00000369303	NM_004440.3	655	Cca/Gca	11/17	0.399673613119676	1	FACETS	0.946	0.854	1	0.946	0.854	1	CLONAL	1	TRUE	0	0.399673613119676	1		446	457	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0053455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	63	258	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.407676661563913	2		258	237	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0053455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	93	432	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.407676661563913	2		432	385	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0053455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	103	550	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.92	0.826	1	0.92	0.826	1	CLONAL	1	TRUE	1	0.407676661563913	2		550	549	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0053455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	95	316	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.407676661563913	2		316	322	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0053455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	218	942	4	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.407676661563913	2		946	756	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217302	11217302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	133	711	0	ENST00000361445.4:c.4376C>A	p.Ala1459Asp	p.A1459D	ENST00000361445	NM_004958.3	1459	gCc/gAc	30/58	0.407676661563913	1	FACETS	0.885	0.807	0.967	0.885	0.807	0.967	CLONAL	1	TRUE	0	0.407676661563913	1		711	587	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453149	140453149	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913361	NA	P-0053455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	192	404	0	ENST00000288602.6:c.1786G>C	p.Gly596Arg	p.G596R	ENST00000288602	NM_004333.4	596	Ggt/Cgt	15/18	0.397563887065766	4	FACETS	0.906	0.846	0.967	0.906	0.846	0.967	CLONAL	3	TRUE	1	0.407676661563913	4		404	488	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497299	149497299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142762235	NA	P-0053455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	138	723	2	ENST00000261799.4:c.3019G>A	p.Val1007Ile	p.V1007I	ENST00000261799	NM_002609.3	1007	Gtc/Atc	22/23	1	2	FACETS	0.964	0.879	1	0.964	0.879	1	CLONAL	1	TRUE	1	0.407676661563913	2		725	702	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056545	26056545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756017745	NA	P-0053455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	26	438	0	ENST00000343677.2:c.112C>T	p.Pro38Ser	p.P38S	ENST00000343677	NM_005319.3	38	Ccc/Tcc	1/1	0.379198860878471	2	FACETS	0.321	0.254	0.398	0.161	0.127	0.199	SUBCLONAL	1	TRUE	0	0.407676661563913	2		438	397	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632671	3632671	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752633436	NA	P-0053455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	226	787	1	ENST00000294008.3:c.5177C>T	p.Ala1726Val	p.A1726V	ENST00000294008	NM_032444.2	1726	gCg/gTg	15/15	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.407676661563913	2		788	761	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566874	212566874	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	148	287	0	ENST00000342788.4:c.1307T>A	p.Ile436Asn	p.I436N	ENST00000342788	NM_005235.2	436	aTc/aAc	12/28	0.36620191141467	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.407676661563913	3		287	359	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158423	26158423	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs116484757	NA	P-0053455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	286	699	0	ENST00000289316.2:c.26C>T	p.Pro9Leu	p.P9L	ENST00000289316	NM_138720.2	9	cCt/cTt	1/2	0.379198860878471	2	FACETS	0.88	0.831	0.93	0.88	0.831	0.93	CLONAL	2	TRUE	0	0.407676661563913	2		699	797	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412489	63412490	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	317	397	0	ENST00000330258.3:c.677dup	p.Glu227GlyfsTer4	p.E227Gfs*4	ENST00000330258	NM_152424.3	226	aag/aaAg	2/2	0.164894077491131	3	FACETS	0.944	0.905	0.981			1	INDETERMINATE	4	TRUE	NA	0.407676661563913	3		397	496	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0053456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	35	305	0				ENST00000310581	NM_198253.2	-/1132			0.39217890482081	1	FACETS	0.533	0.439	0.638	0.533	0.439	0.638	SUBCLONAL	1	TRUE	0	0.399516996232804	1		305	263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0053456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	197	813	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.333667182222079	1	FACETS	0.945	0.877	1	0.945	0.877	1	CLONAL	1	TRUE	0	0.399516996232804	1		813	835	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371801	55371801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746536924	NA	P-0053456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	11	137	1	ENST00000297316.4:c.491C>T	p.Ala164Val	p.A164V	ENST00000297316	NM_022454.3	164	gCg/gTg	2/2	0.399516996232804	3	FACETS	0.398	0.275	0.55	0.199	0.137	0.275	SUBCLONAL	1	TRUE	1	0.399516996232804	3		138	166	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557362	187557362	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1223493108	NA	P-0053456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	62	520	0	ENST00000441802.2:c.4000C>T	p.Gln1334Ter	p.Q1334*	ENST00000441802	NM_005245.3	1334	Caa/Taa	6/27	0.333667182222079	1	FACETS	0.497	0.43	0.57	0.497	0.43	0.57	SUBCLONAL	1	TRUE	0	0.399516996232804	1		520	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578289	7578289	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	62	727	0	ENST00000269305.4:c.560del	p.Gly187ValfsTer60	p.G187Vfs*60	ENST00000269305	NM_001126112.2	187	gGt/gt	6/11	0.333667182222079	1	FACETS	0.355	0.306	0.409	0.355	0.306	0.409	SUBCLONAL	1	TRUE	0	0.399516996232804	1		727	699	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41521902	41521902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767063384	NA	P-0053456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	66	579	1	ENST00000263253.7:c.764C>T	p.Ser255Leu	p.S255L	ENST00000263253	NM_001429.3	255	tCa/tTa	3/31	0.333667182222079	1	FACETS	0.375	0.325	0.429	0.375	0.325	0.429	SUBCLONAL	1	TRUE	0	0.399516996232804	1		580	705	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164458	36164458	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	74	287	0	ENST00000300305.3:c.1417G>A	p.Glu473Lys	p.E473K	ENST00000300305		473	Gag/Aag	8/8	1	2	FACETS	0.926	0.815	1	0.926	0.815	1	CLONAL	1	TRUE	1	0.399516996232804	2		287	400	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268787	41268787	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	108	491	0	ENST00000349496.5:c.1025G>C	p.Arg342Thr	p.R342T	ENST00000349496	NM_001904.3	342	aGa/aCa	7/15	1	2	FACETS	0.91	0.819	1	0.91	0.819	1	CLONAL	1	TRUE	1	0.399516996232804	2		491	594	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495711	56495711	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	124	491	1	ENST00000267101.3:c.3901C>T	p.Gln1301Ter	p.Q1301*	ENST00000267101	NM_001982.3	1301	Cag/Tag	28/28	1	2	FACETS	0.967	0.877	1	0.967	0.877	1	CLONAL	1	TRUE	1	0.399516996232804	2		492	642	SUCCESS
CBL	867	MSKCC	GRCh37	11	119158592	119158592	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1565874960	NA	P-0053456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	145	471	0	ENST00000264033.4:c.1972G>C	p.Glu658Gln	p.E658Q	ENST00000264033	NM_005188.3	658	Gag/Cag	12/16	0.204669683793027	3	FACETS	0.958	0.874	1	0.479	0.437	0.523	INDETERMINATE	1	TRUE	1	0.399516996232804	3		471	909	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240171	41240171	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	37	81	0	ENST00000379561.5:c.179C>A	p.Ser60Ter	p.S60*	ENST00000379561	NM_002015.3	60	tCg/tAg	1/3	0.204669683793027	3	FACETS	0.817	0.687	0.957	0.817	0.687	0.957	INDETERMINATE	2	TRUE	1	0.399516996232804	3		81	136	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375442	40375442	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	110	764	0	ENST00000293328.3:c.508G>C	p.Glu170Gln	p.E170Q	ENST00000293328	NM_012448.3	170	Gag/Cag	5/19	0.333667182222079	1	FACETS	0.451	0.404	0.501	0.451	0.404	0.501	SUBCLONAL	1	TRUE	0	0.399516996232804	1		764	977	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918293	44918293	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	81	387	0	ENST00000377967.4:c.919del	p.Tyr307ThrfsTer18	p.Y307Tfs*18	ENST00000377967	NM_021140.2	306	tcT/tc	11/29	0.399516996232804	1	FACETS	0.877	0.778	0.982	0.877	0.778	0.982	CLONAL	1	TRUE	0	0.399516996232804	1		387	370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0053457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	279	426	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.799683018722303	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.826341650969871	1		426	384	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10271093	10271093	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	111	503	0	ENST00000340748.4:c.962A>T	p.Glu321Val	p.E321V	ENST00000340748		321	gAg/gTg	13/40	0.361183798250816	3	FACETS	0.788	0.712	0.867	0.394	0.356	0.434	INDETERMINATE	1	TRUE	1	0.826341650969871	3		503	482	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0053458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	91	305	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.687694859192811	2		305	250	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606436	93606436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201455170	NA	P-0053458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	302	821	3	ENST00000375746.1:c.256G>A	p.Ala86Thr	p.A86T	ENST00000375746	NM_001174167.1	86	Gcc/Acc	2/14	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.687694859192811	2		824	856	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223582	55223582	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7376	2168	625	0	ENST00000275493.2:c.949G>C	p.Glu317Gln	p.E317Q	ENST00000275493	NM_005228.3	317	Gag/Cag	8/28	0.687694859192811	20	FACETS	0.95	0.928	0.972			1	CLONAL	5	TRUE	NA	0.687694859192811	20		625	9544	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923375	9923375	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	57	626	0	ENST00000330684.3:c.1912G>A	p.Ala638Thr	p.A638T	ENST00000330684	NM_001134407.1	638	Gct/Act	9/13	1	2	FACETS	0.653	0.559	0.756	0.653	0.559	0.756	SUBCLONAL	1	FALSE	1	0.233933195095299	2		626	746	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212484001	212484001	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0053459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	43	310	0	ENST00000342788.4:c.2203-1G>T		p.X735_splice	ENST00000342788	NM_005235.2	735			0.233933195095299	1	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	FALSE	0	0.233933195095299	1		310	308	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561022	9561022	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0053459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	39	475	0	ENST00000353224.5:c.760G>T	p.Glu254Ter	p.E254*	ENST00000353224	NM_177990.2	254	Gaa/Taa	4/10	0.134328324686566	3	FACETS	0.556	0.459	0.664	0.278	0.229	0.332	INDETERMINATE	1	FALSE	1	0.233933195095299	3		475	670	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372479	55372479	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	98	921	0	ENST00000297316.4:c.1169A>G	p.Asp390Gly	p.D390G	ENST00000297316	NM_022454.3	390	gAc/gGc	2/2	1	2	FACETS	0.721	0.641	0.806	0.721	0.641	0.806	SUBCLONAL	1	FALSE	1	0.233933195095299	2		921	1162	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76812999	76812999	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	75	242	0	ENST00000373344.5:c.6622del	p.Tyr2208IlefsTer8	p.Y2208Ifs*8	ENST00000373344	NM_000489.3	2208	Tat/at	30/35	1	1	FACETS	0.89	0.787	0.999	1	0.982	1	CLONAL	2	FALSE	0	0.233933195095299	1		242	318	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	65	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.543505928148591	2		429	193	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0053460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	21	682	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.299053805375427	1	FACETS	0.063	0.048	0.081	0.063	0.048	0.081	INDETERMINATE	1	TRUE	0	0.543505928148591	1		682	892	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0053460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	311	833	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.299053805375427	1	FACETS	0.862	0.814	0.91	0.862	0.814	0.91	INDETERMINATE	1	TRUE	0	0.543505928148591	1		837	967	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881462	48881462	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	140	301	0	ENST00000267163.4:c.184C>T	p.Gln62Ter	p.Q62*	ENST00000267163	NM_000321.2	62	Cag/Tag	2/27	0.543505928148591	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.543505928148591	1		301	285	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720876	89720876	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs786201041	NA	P-0053460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	152	319	0	ENST00000371953.3:c.1026+1G>A		p.X342_splice	ENST00000371953	NM_000314.4	342			0.543505928148591	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.543505928148591	1		319	355	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0053460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	24	548	0	ENST00000269305.4:c.375+1G>T		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.299053805375427	1	FACETS	0.082	0.063	0.103	0.082	0.063	0.103	INDETERMINATE	1	TRUE	0	0.543505928148591	1		548	789	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579533	7579533	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	73	817	0	ENST00000269305.4:c.154del	p.Gln52AsnfsTer71	p.Q52Nfs*71	ENST00000269305	NM_001126112.2	52	Caa/aa	4/11	0.299053805375427	1	FACETS	0.198	0.172	0.225	0.198	0.172	0.225	INDETERMINATE	1	TRUE	0	0.543505928148591	1		817	990	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	178	411	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.893	0.83	0.957	1	0.992	1	CLONAL	2	TRUE	1	0.403603540935833	2		411	494	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0053462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	194	353	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.256161389090727	3	FACETS	0.858	0.798	0.919	0.858	0.798	0.919	CLONAL	3	TRUE	0	0.286872159877787	3		353	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0053462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	351	678	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.286872159877787	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	0	0.286872159877787	3		678	880	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78704418	78704418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	92	511	0	ENST00000306801.3:c.566C>T	p.Pro189Leu	p.P189L	ENST00000306801	NM_020761.2	189	cCg/cTg	5/34	0.260268883962041	3	FACETS	1	0.937	1	0.539	0.479	0.603	CLONAL	1	TRUE	1	0.286872159877787	3		511	680	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641445	47641445	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	79	545	0	ENST00000233146.2:c.830T>C	p.Leu277Ser	p.L277S	ENST00000233146	NM_000251.2	277	tTa/tCa	5/16	0.286872159877787	3	FACETS	1	0.969	1	0.657	0.58	0.74	CLONAL	1	TRUE	1	0.286872159877787	3		545	479	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104740	69104740	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	93	586	3	ENST00000288368.4:c.4584G>T	p.Met1528Ile	p.M1528I	ENST00000288368	NM_024870.2	1528	atG/atT	37/40	0.286872159877787	4	FACETS	0.947	0.841	1	0.316	0.28	0.354	CLONAL	1	TRUE	1	0.286872159877787	4		589	881	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948635	71948635	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	203	933	0	ENST00000298229.2:c.3347G>T	p.Gly1116Val	p.G1116V	ENST00000298229	NM_001567.3	1116	gGg/gTg	26/28	0.260268883962041	3	FACETS	1	0.987	1	0.655	0.606	0.706	CLONAL	1	TRUE	1	0.286872159877787	3		933	1236	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420799	49420799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	89	681	0	ENST00000301067.7:c.14950G>A	p.Gly4984Arg	p.G4984R	ENST00000301067	NM_003482.3	4984	Gga/Aga	48/54	0.230295502002353	4	FACETS	0.851	0.753	0.956	0.426	0.376	0.478	CLONAL	1	TRUE	2	0.286872159877787	4		681	938	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861858	57861858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	234	723	1	ENST00000228682.2:c.1159C>T	p.His387Tyr	p.H387Y	ENST00000228682	NM_005269.2	387	Cat/Tat	10/12	0.230295502002353	4	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	2	0.286872159877787	4		724	1030	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133627	55133627	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	153	454	0	ENST00000257290.5:c.931G>T	p.Glu311Ter	p.E311*	ENST00000257290	NM_006206.4	311	Gag/Tag	6/23	0.286872159877787	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.286872159877787	3		454	553	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973977	55973977	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	172	638	0	ENST00000263923.4:c.1339G>T	p.Val447Phe	p.V447F	ENST00000263923	NM_002253.2	447	Gtc/Ttc	10/30	0.286872159877787	3	FACETS	0.913	0.842	0.987	0.913	0.842	0.987	CLONAL	2	TRUE	1	0.286872159877787	3		638	751	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979513	55979513	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	84	592	0	ENST00000263923.4:c.934G>T	p.Gly312Trp	p.G312W	ENST00000263923	NM_002253.2	312	Ggg/Tgg	7/30	0.286872159877787	3	FACETS	0.944	0.834	1	0.472	0.417	0.532	CLONAL	1	TRUE	1	0.286872159877787	3		592	709	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974785	21974826	+	start_lost,inframe_deletion	Translation_Start_Site	DEL	GTCAGCCGAAGGCTCCATGCTGCTCCCCGCCGCCGGCTCCAT	GTCAGCCGAAGGCTCCATGCTGCTCCCCGCCGCCGGCTCCAT	-	novel	NA	P-0053462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	9	178	0	ENST00000304494.5:c.1_42del	p.MetGluProAlaAlaGlySerSerMetGluProSerAlaAsp1_?14	p.MEPAAGSSMEPSAD1_?14	ENST00000304494	NM_000077.4	1	ATGGAGCCGGCGGCGGGGAGCAGCATGGAGCCTTCGGCTGAC/-	1/3	0.286872159877787	1	FACETS	0.354	0.234	0.505	0.354	0.234	0.505	SUBCLONAL	1	TRUE	0	0.286872159877787	1		178	152	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs878854073	NA	P-0053473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	188	537	0	ENST00000269305.4:c.673-1G>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.418327488563692	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.418327488563692	1		537	696	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195452	102195452	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	159	411	1	ENST00000263464.3:c.212T>C	p.Leu71Pro	p.L71P	ENST00000263464	NM_001165.4	71	cTg/cCg	2/9	0.204203067173857	1	FACETS	0.915	0.842	0.991	0.915	0.842	0.991	INDETERMINATE	1	TRUE	0	0.418327488563692	1		412	657	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0053474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	85	885	2	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.633350352215367	1	FACETS	0.849	0.796	0.897	1	0.989	1	CLONAL	2	TRUE	0	0.633350352215367	1		887	108	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553478	29553478	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781807	NA	P-0053474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	65	818	4	ENST00000356175.3:c.2033del	p.Pro678ArgfsTer10	p.P678Rfs*10	ENST00000356175	NM_000267.3	676	aCc/ac	18/57	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.633350352215367	2		822	185	SUCCESS
AR	367	MSKCC	GRCh37	X	66766261	66766261	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	58	423	0	ENST00000374690.3:c.1273G>T	p.Gly425Trp	p.G425W	ENST00000374690	NM_000044.3	425	Ggg/Tgg	1/8	0.173391262518364	0	FACETS	0.517	0.457	0.577			1	INDETERMINATE	1	TRUE	0	0.633350352215367	0		423	130	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878185	48878185	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	29	159	0	ENST00000267163.4:c.137G>A	p.Arg46Lys	p.R46K	ENST00000267163	NM_000321.2	46	aGg/aAg	1/27	0.633350352215367	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.633350352215367	1		159	46	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860257	151860257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	94	497	0	ENST00000262189.6:c.10405C>T	p.Leu3469Phe	p.L3469F	ENST00000262189	NM_170606.2	3469	Ctt/Ttt	43/59	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.633350352215367	2		497	202	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845374	156845374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	244	935	0	ENST00000524377.1:c.1417G>A	p.Gly473Ser	p.G473S	ENST00000524377	NM_002529.3	473	Ggc/Agc	12/17	0.633350352215367	3	FACETS	0.979	0.959	0.996	1	0.996	1	CLONAL	4	TRUE	0	0.633350352215367	3		935	259	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132972	30132972	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	91	597	0	ENST00000331968.5:c.629C>G	p.Thr210Ser	p.T210S	ENST00000331968	NM_002742.2	210	aCt/aGt	4/18	0.126151336823557	4	FACETS	1	0.973	1	1	0.973	1	INDETERMINATE	2	TRUE	2	0.633350352215367	4		597	196	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829353	72829353	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	76	723	0	ENST00000268489.5:c.7228A>G	p.Thr2410Ala	p.T2410A	ENST00000268489	NM_006885.3	2410	Aca/Gca	9/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.633350352215367	2		723	177	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942064	81942064	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	97	636	0	ENST00000359376.3:c.1601A>T	p.His534Leu	p.H534L	ENST00000359376	NM_002661.3	534	cAc/cTc	17/33	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.633350352215367	2		636	208	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677300	29677300	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	51	393	0	ENST00000356175.3:c.7358del	p.Asp2453ValfsTer15	p.D2453Vfs*15	ENST00000356175	NM_000267.3	2453	gAt/gt	49/57	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.633350352215367	2		393	112	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495270	212495270	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	15	545	0	ENST00000342788.4:c.1996A>T	p.Ile666Phe	p.I666F	ENST00000342788	NM_005235.2	666	Att/Ttt	17/28	0.633350352215367	1	FACETS	0.3	0.221	0.391	0.3	0.221	0.391	SUBCLONAL	1	TRUE	0	0.633350352215367	1		545	108	SUCCESS
ATR	545	MSKCC	GRCh37	3	142211974	142211974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	44	377	0	ENST00000350721.4:c.6078G>T	p.Lys2026Asn	p.K2026N	ENST00000350721	NM_001184.3	2026	aaG/aaT	35/47	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.633350352215367	2		377	131	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519186	187519186	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780242823	NA	P-0053474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	78	553	0	ENST00000441802.2:c.12197C>T	p.Thr4066Met	p.T4066M	ENST00000441802	NM_005245.3	4066	aCg/aTg	23/27	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.633350352215367	2		553	212	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471087	8471087	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0053474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	33	290	1	ENST00000356435.5:c.3414-2A>T		p.X1138_splice	ENST00000356435		1138			1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.633350352215367	2		291	100	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045521	47045521	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	79	774	0	ENST00000377604.3:c.2489del	p.Pro830ArgfsTer17	p.P830Rfs*17	ENST00000377604	NM_001204468.1	830	Ccg/cg	22/24	0.173391262518364	0	FACETS	0.554	0.501	0.608			1	INDETERMINATE	1	TRUE	0	0.633350352215367	0		774	165	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0053475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	150	608	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.277312009405598	3	FACETS	1	0.969	1	0.734	0.677	0.793	CLONAL	2	TRUE	0	0.353065343650814	3		608	454	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220400	1220400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	80	873	0	ENST00000326873.7:c.493G>A	p.Glu165Lys	p.E165K	ENST00000326873	NM_000455.4	165	Gag/Aag	4/10	NA	2	FACETS	1	0.886	1			1	INDETERMINATE	1	TRUE	NA	0.353065343650814	2		873	452	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591126	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAGAAAGAC	GAGAAAGAC	-	novel	NA	P-0053475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	30	125	0	ENST00000274335.5:c.1723_1731del	p.Lys575_Arg577del	p.K575_R577del	ENST00000274335		573	ctGAGAAAGACg/ctg	12/15	0.353065343650814	3	FACETS	0.934	0.758	1	0.311	0.252	0.377	CLONAL	1	TRUE	0	0.353065343650814	3		125	214	SUCCESS
AR	367	MSKCC	GRCh37	X	66931256	66931256	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	112	192	0	ENST00000374690.3:c.1898A>C	p.Lys633Thr	p.K633T	ENST00000374690	NM_000044.3	633	aAg/aCg	4/8	0.352194760740185	2	FACETS	0.961	0.886	1			1	CLONAL	3	TRUE	NA	0.353065343650814	2		192	220	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92247496	92247496	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	30	231	1	ENST00000265734.4:c.724G>T	p.Asp242Tyr	p.D242Y	ENST00000265734	NM_001259.6	242	Gac/Tac	7/8	0.353065343650814	3	FACETS	0.769	0.622	0.934	0.385	0.311	0.467	CLONAL	1	TRUE	1	0.353065343650814	3		232	260	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680747	88680747	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	95	830	0	ENST00000360948.2:c.510G>A	p.Trp170Ter	p.W170*	ENST00000360948	NM_001012338.2	170	tgG/tgA	6/19	0.353065343650814	5	FACETS	1	0.975	1	0.334	0.297	0.372	CLONAL	1	TRUE	1	0.353065343650814	5		830	617	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566520	41566520	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	43	288	0	ENST00000263253.7:c.4397G>T	p.Trp1466Leu	p.W1466L	ENST00000263253	NM_001429.3	1466	tGg/tTg	27/31	1	2	FACETS	0.729	0.612	0.858	0.729	0.612	0.858	SUBCLONAL	1	TRUE	1	0.353065343650814	2		288	334	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510205	120510205	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	62	363	0	ENST00000256646.2:c.1304A>G	p.Asn435Ser	p.N435S	ENST00000256646	NM_024408.3	435	aAc/aGc	8/34	0.353065343650814	3	FACETS	0.993	0.861	1	0.497	0.43	0.568	CLONAL	1	TRUE	1	0.353065343650814	3		363	416	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435116	18435116	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	28	146	1	ENST00000266497.5:c.101G>T	p.Ser34Ile	p.S34I	ENST00000266497		34	aGc/aTc	1/31	1	2	FACETS	0.666	0.535	0.815	0.666	0.535	0.815	SUBCLONAL	1	TRUE	1	0.353065343650814	2		147	238	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424743	49424743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	93	922	1	ENST00000301067.7:c.13604C>T	p.Ser4535Phe	p.S4535F	ENST00000301067	NM_003482.3	4535	tCc/tTc	40/54	0.353065343650814	3	FACETS	1	0.949	1	0.556	0.496	0.621	CLONAL	1	TRUE	1	0.353065343650814	3		923	557	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435631	110435631	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	46	444	0	ENST00000375856.3:c.2770T>A	p.Phe924Ile	p.F924I	ENST00000375856	NM_003749.2	924	Ttt/Att	1/2	NA	2	FACETS	0.954	0.809	1			1	INDETERMINATE	1	TRUE	NA	0.353065343650814	2		444	273	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251028	99251028	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	261	618	0	ENST00000268035.6:c.332T>C	p.Leu111Pro	p.L111P	ENST00000268035	NM_000875.3	111	cTc/cCc	2/21	0.353065343650814	5	FACETS	0.93	0.878	0.982	0.93	0.878	0.982	CLONAL	4	TRUE	1	0.353065343650814	5		618	608	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029139	14029139	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1411517457	NA	P-0053475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	56	155	0	ENST00000311895.7:c.1350G>A	p.Trp450Ter	p.W450*	ENST00000311895	NM_005236.2	450	tgG/tgA	8/11	0.353065343650814	6	FACETS	0.94	0.811	1			1	CLONAL	2	TRUE	NA	0.353065343650814	6		155	288	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350873	89350873	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	53	378	0	ENST00000301030.4:c.2077C>G	p.His693Asp	p.H693D	ENST00000301030	NM_001256183.1	693	Cac/Gac	9/13	1	2	FACETS	0.832	0.712	0.961	0.832	0.712	0.961	CLONAL	1	TRUE	1	0.353065343650814	2		378	361	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89866027	89866027	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs762721928	NA	P-0053475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	47	359	0	ENST00000389301.3:c.812A>C	p.Gln271Pro	p.Q271P	ENST00000389301	NM_000135.2	271	cAg/cCg	9/43	1	2	FACETS	0.837	0.71	0.976	0.837	0.71	0.976	CLONAL	1	TRUE	1	0.353065343650814	2		359	318	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618863	37618873	+	frameshift_variant	Frame_Shift_Del	DEL	ACAAGGAGAAG	ACAAGGAGAAG	-	novel	NA	P-0053475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	168	533	0	ENST00000447079.4:c.541_551del	p.Lys181GlnfsTer15	p.K181Qfs*15	ENST00000447079	NM_015083.1	180	cACAAGGAGAAG/c	1/14	0.353065343650814	5	FACETS	0.909	0.841	0.978			1	CLONAL	3	TRUE	NA	0.353065343650814	5		533	534	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554720	63554720	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs878854723	NA	P-0053475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	71	614	0	ENST00000307078.5:c.19G>T	p.Val7Leu	p.V7L	ENST00000307078	NM_004655.3	7	Gtg/Ttg	2/11	0.350018673616232	2	FACETS	1	0.908	1	0.521	0.457	0.589	CLONAL	1	TRUE	0	0.353065343650814	2		614	386	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436691	8436691	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0053475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	35	129	0	ENST00000356435.5:c.3989-2A>G		p.X1330_splice	ENST00000356435		1330			0.227617811031021	3	FACETS	0.997	0.823	1	0.498	0.411	0.595	CLONAL	1	TRUE	1	0.353065343650814	3		129	234	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937643	76937672	+	inframe_deletion	In_Frame_Del	DEL	AATTTGTTTTATGCCCTTAGGAAAATGACA	AATTTGTTTTATGCCCTTAGGAAAATGACA	-	novel	NA	P-0053475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	36	63	0	ENST00000373344.5:c.3076_3105del	p.Cys1026_Ile1035del	p.C1026_I1035del	ENST00000373344	NM_000489.3	1026	TGTCATTTTCCTAAGGGCATAAAACAAATT/-	9/35	0.352194760740185	2	FACETS	1	0.925	1			1	CLONAL	1	TRUE	NA	0.353065343650814	2		63	168	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023512	27023517	+	frameshift_variant	Frame_Shift_Del	DEL	CTTCCC	CTTCCC	TA	novel	NA	P-0053475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	48	462	2	ENST00000324856.7:c.618_623delinsTA	p.Phe207ThrfsTer24	p.F207Tfs*24	ENST00000324856	NM_006015.4	206	ggCTTCCCc/ggTAc	1/20	0.297165734851183	2	FACETS	0.968	0.824	1	0.484	0.412	0.562	CLONAL	1	TRUE	0	0.353065343650814	2		464	281	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631839	90631839	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519906	NA	P-0053477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	13	749	0	ENST00000330062.3:c.514A>T	p.Arg172Trp	p.R172W	ENST00000330062	NM_002168.2	172	Agg/Tgg	4/11	1	2	FACETS	1	0.814	1	1	0.814	1	CLONAL	1	TRUE	1	0.257447604751553	2		749	86	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242511	55242511	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs121913418	NA	P-0053477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	8	420	1	ENST00000275493.2:c.2281G>A	p.Asp761Asn	p.D761N	ENST00000275493	NM_005228.3	761	Gat/Aat	19/28	0.222601844290114	0	FACETS	0.563	0.366	0.812			1	SUBCLONAL	1	TRUE	0	0.257447604751553	0		421	82	SUCCESS
ATM	472	MSKCC	GRCh37	11	108126975	108126975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs565622131	NA	P-0053477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	10	606	1	ENST00000278616.4:c.2158C>T	p.Arg720Cys	p.R720C	ENST00000278616	NM_000051.3	720	Cgt/Tgt	14/63	1	2	FACETS	0.844	0.589	1	1	0.872	1	CLONAL	2	TRUE	1	0.257447604751553	2		607	46	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0053478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	678	656	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.798524806473088	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.798524806473088	2		656	798	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0053478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	139	284	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.989	0.912	1	0.989	0.912	1	CLONAL	1	TRUE	1	0.798524806473088	2		284	352	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939600	76939601	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	298	295	0	ENST00000373344.5:c.1147dup	p.Ile383AsnfsTer11	p.I383Nfs*11	ENST00000373344	NM_000489.3	383	atc/aAtc	9/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.798524806473088	1		295	381	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4388006	4388006	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	213	570	0	ENST00000261254.3:c.492G>C	p.Leu164Phe	p.L164F	ENST00000261254	NM_001759.3	164	ttG/ttC	3/5	0.798524806473088	3	FACETS	0.909	0.847	0.974	0.455	0.423	0.487	CLONAL	1	TRUE	1	0.798524806473088	3		570	821	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0053480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	80	350	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.247143579673801	2		350	598	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602413	10602413	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	114	865	1	ENST00000171111.5:c.1165G>T	p.Asp389Tyr	p.D389Y	ENST00000171111	NM_203500.1	389	Gac/Tac	3/6	0.247143579673801	1	FACETS	0.889	0.799	0.983	0.889	0.799	0.983	CLONAL	1	TRUE	0	0.247143579673801	1		866	910	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303689	65303689	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	115	465	1	ENST00000342505.4:c.3066del	p.Phe1022LeufsTer3	p.F1022Lfs*3	ENST00000342505	NM_002227.2	1022	ttC/tt	22/25	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.247143579673801	2		466	902	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843797	151843797	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	74	348	0	ENST00000262189.6:c.13918C>A	p.Pro4640Thr	p.P4640T	ENST00000262189	NM_170606.2	4640	Cct/Act	53/59	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.247143579673801	2		348	505	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220416	1220417	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0053480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	90	736	0	ENST00000326873.7:c.509_510insC	p.Gln170HisfsTer96	p.Q170Hfs*96	ENST00000326873	NM_000455.4	170	cag/caCg	4/10	0.247143579673801	1	FACETS	0.8	0.709	0.897	0.8	0.709	0.897	SUBCLONAL	1	TRUE	0	0.247143579673801	1		736	798	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0053481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	422	1003	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.338437088033386	3	FACETS	0.9	0.86	0.94	0.9	0.86	0.94	CLONAL	3	TRUE	0	0.351840946404693	3		1007	1045	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0053481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	446	485	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.338437088033386	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.351840946404693	3		486	923	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0053481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	85	375	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.351840946404693	1	FACETS	0.897	0.796	1	0.897	0.796	1	CLONAL	1	TRUE	0	0.351840946404693	1		375	444	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0053481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	192	299	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	0.338437088033386	3	FACETS	0.972	0.91	1	0.972	0.91	1	CLONAL	3	TRUE	0	0.351840946404693	3		299	440	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961400	41961400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	194	385	1	ENST00000219905.7:c.308G>A	p.Arg103His	p.R103H	ENST00000219905	NM_001164273.1	103	cGc/cAc	2/24	0.32426979211148	4	FACETS	0.911	0.845	0.98	0.911	0.845	0.98	CLONAL	2	TRUE	2	0.351840946404693	4		386	818	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034923	42034923	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	265	547	0	ENST00000219905.7:c.4765G>T	p.Val1589Leu	p.V1589L	ENST00000219905	NM_001164273.1	1589	Gtg/Ttg	15/24	0.32426979211148	4	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	2	0.351840946404693	4		547	1012	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664849	29664849	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	291	332	0	ENST00000356175.3:c.6592G>C	p.Asp2198His	p.D2198H	ENST00000356175	NM_000267.3	2198	Gat/Cat	43/57	0.351840946404693	5	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	2	0.351840946404693	5		332	812	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677993	58677993	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	108	195	0	ENST00000305921.3:c.218G>C	p.Arg73Pro	p.R73P	ENST00000305921	NM_003620.3	73	cGa/cCa	1/6	0.338437088033386	3	FACETS	0.915	0.836	0.996	0.915	0.836	0.996	CLONAL	3	TRUE	0	0.351840946404693	3		195	263	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	128	411	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.388741365366976	2		411	581	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0053482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	373	848	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.388741365366976	2	FACETS	0.939	0.9	0.978	1	0.996	1	CLONAL	3	TRUE	0	0.388741365366976	2		848	681	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450244	50450244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	87	416	0	ENST00000331340.3:c.428G>A	p.Arg143Gln	p.R143Q	ENST00000331340	NM_006060.4	143	cGg/cAg	5/8	1	2	FACETS	0.853	0.757	0.954	0.853	0.757	0.954	CLONAL	1	TRUE	1	0.388741365366976	2		416	525	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575231	48575231	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0053482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	86	187	0	ENST00000342988.3:c.424+1G>T		p.X142_splice	ENST00000342988	NM_005359.5	142			0.324415888169667	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.388741365366976	1		187	296	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039297	47039297	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	203	368	0	ENST00000377604.3:c.920T>G	p.Leu307Arg	p.L307R	ENST00000377604	NM_001204468.1	307	cTg/cGg	10/24	1	1	FACETS	0.941	0.883	0.999	1	0.994	1	CLONAL	2	TRUE	0	0.388741365366976	1		368	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578246	7578247	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	215	624	0	ENST00000269305.4:c.602dup	p.Leu201PhefsTer8	p.L201Ffs*8	ENST00000269305	NM_001126112.2	201	ttg/ttTg	6/11	0.388741365366976	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.388741365366976	1		624	598	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922719	44922720	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0053482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	139	182	0	ENST00000377967.4:c.1580_1581del	p.Pro527HisfsTer3	p.P527Hfs*3	ENST00000377967	NM_021140.2	527	cCA/c	16/29	1	1	FACETS	0.941	0.872	1	1	0.991	1	CLONAL	2	TRUE	0	0.388741365366976	1		182	306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	360	743	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.819783940108736	2		745	873	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546317	46546317	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	143	304	0	ENST00000262741.5:c.212C>T	p.Ser71Leu	p.S71L	ENST00000262741	NM_003629.3	71	tCa/tTa	2/10	0.680272052107738	4	FACETS	0.935	0.854	1	0.468	0.427	0.51	CLONAL	1	TRUE	2	0.819783940108736	4		304	679	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533586	533586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730880462	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	472	809	2	ENST00000451590.1:c.317C>T	p.Ser106Leu	p.S106L	ENST00000451590	NM_001130442.1	106	tCg/tTg	4/5	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.819783940108736	2		811	1082	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122566	108122566	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	48	285	0	ENST00000278616.4:c.1610C>T	p.Pro537Leu	p.P537L	ENST00000278616	NM_000051.3	537	cCt/cTt	11/63	0.477986776873946	1	FACETS	0.362	0.31	0.417	0.362	0.31	0.417	INDETERMINATE	1	TRUE	0	0.819783940108736	1		285	191	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644464	21644464	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	110	352	0	ENST00000421138.2:c.203G>A	p.Trp68Ter	p.W68*	ENST00000421138		68	tGg/tAg	4/16	0.819783940108736	3	FACETS	0.726	0.655	0.801	0.363	0.327	0.401	SUBCLONAL	1	TRUE	1	0.819783940108736	3		352	521	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489040	56489041	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	445	455	0	ENST00000267101.3:c.1860-1_1860delinsAA		p.X620_splice	ENST00000267101	NM_001982.3	620		16/28	0.228175209427985	5	FACETS	1	0.993	1	0.671	0.647	0.694	INDETERMINATE	3	TRUE	0	0.819783940108736	5		455	722	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947560	48947560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690846	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	303	213	0	ENST00000267163.4:c.1147C>T	p.Gln383Ter	p.Q383*	ENST00000267163	NM_000321.2	383	Caa/Taa	12/27	0.819783940108736	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.819783940108736	2		213	350	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066721	30066721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1263767545	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	147	342	0	ENST00000331968.5:c.2410C>T	p.Pro804Ser	p.P804S	ENST00000331968	NM_002742.2	804	Ccc/Tcc	16/18	NA	2	FACETS	0.908	0.838	0.979			1	INDETERMINATE	1	TRUE	NA	0.819783940108736	2		342	395	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675047	40675047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	309	667	1	ENST00000249776.8:c.11C>T	p.Pro4Leu	p.P4L	ENST00000249776	NM_033286.3	4	cCc/cTc	1/9	0.323667290064509	1	FACETS	0.472	0.446	0.498	0.472	0.446	0.498	INDETERMINATE	1	TRUE	0	0.819783940108736	1		668	943	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41021737	41021737	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	239	474	0	ENST00000267868.3:c.679C>T	p.Leu227Phe	p.L227F	ENST00000267868	NM_002875.4	227	Ctt/Ttt	8/10	0.323667290064509	1	FACETS	0.563	0.529	0.597	0.563	0.529	0.597	INDETERMINATE	1	TRUE	0	0.819783940108736	1		474	611	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129560	2129560	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs140772300	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	426	877	4	ENST00000219476.3:c.3287C>T	p.Ser1096Phe	p.S1096F	ENST00000219476	NM_000548.3	1096	tCc/tTc	29/42	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.819783940108736	2		881	973	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640992	3640992	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	414	891	0	ENST00000294008.3:c.2647G>A	p.Gly883Ser	p.G883S	ENST00000294008	NM_032444.2	883	Ggc/Agc	12/15	1	2	FACETS	0.988	0.944	1	0.988	0.944	1	CLONAL	1	TRUE	1	0.819783940108736	2		891	1022	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991712	72991723	+	inframe_deletion	In_Frame_Del	DEL	GCCACCGCCGCC	GCCACCGCCGCC	-	rs779341897	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	32	247	0	ENST00000268489.5:c.2322_2333del	p.Val777_Ala780del	p.V777_A780del	ENST00000268489	NM_006885.3	774	gcGGCGGCGGTGGCt/gct	2/10	0.819783940108736	1	FACETS	0.284	0.233	0.34	0.284	0.233	0.34	SUBCLONAL	1	TRUE	0	0.819783940108736	1		247	162	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	412	742	0	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.819783940108736	2		742	981	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857671	78857671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	778	854	1	ENST00000306801.3:c.1741C>T	p.Leu581Phe	p.L581F	ENST00000306801	NM_020761.2	581	Ctc/Ttc	16/34	0.610778937788949	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.819783940108736	4		855	1697	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291043	10291043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	620	557	0	ENST00000340748.4:c.428C>T	p.Ser143Phe	p.S143F	ENST00000340748		143	tCc/tTc	4/40	0.819783940108736	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.819783940108736	3		557	1007	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050365	13050365	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	925	686	0	ENST00000316448.5:c.317G>A	p.Gly106Glu	p.G106E	ENST00000316448	NM_004343.3	106	gGg/gAg	3/9	0.819783940108736	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.819783940108736	3		686	1577	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350271	15350271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	420	820	0	ENST00000263377.2:c.3508C>T	p.Pro1170Ser	p.P1170S	ENST00000263377	NM_058243.2	1170	Ccg/Tcg	17/20	0.819783940108736	3	FACETS	1	0.971	1	0.513	0.488	0.539	CLONAL	1	TRUE	1	0.819783940108736	3		820	1407	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375526	15375526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	1083	925	0	ENST00000263377.2:c.901G>A	p.Asp301Asn	p.D301N	ENST00000263377	NM_058243.2	301	Gac/Aac	6/20	0.819783940108736	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	1	0.819783940108736	3		925	1728	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752860	42752861	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	464	956	2	ENST00000222329.4:c.1403_1404delinsTT	p.Pro468Leu	p.P468L	ENST00000222329	NM_006494.2	468	cCC/cTT	4/4	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.819783940108736	2		958	1113	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719332	190719332	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	63	190	0	ENST00000441310.2:c.1334C>T	p.Ser445Leu	p.S445L	ENST00000441310	NM_000534.4	445	tCa/tTa	9/13	1	2	FACETS	0.776	0.683	0.874	0.776	0.683	0.874	SUBCLONAL	1	TRUE	1	0.819783940108736	2		190	198	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014208	70014208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	352	689	1	ENST00000394351.3:c.1069G>A	p.Gly357Arg	p.G357R	ENST00000394351	NM_000248.3	357	Ggg/Agg	9/9	0.819783940108736	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.819783940108736	1		690	438	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480299	89480299	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	105	207	0	ENST00000336596.2:c.2137-1G>A		p.X713_splice	ENST00000336596	NM_005233.5	713			0.819783940108736	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.819783940108736	1		207	127	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919311	178919311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758142827	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	94	146	0	ENST00000263967.3:c.796C>T	p.Pro266Ser	p.P266S	ENST00000263967	NM_006218.2	266	Cct/Tct	4/21	0.337392516735453	3	FACETS	1	0.96	1	0.563	0.508	0.621	INDETERMINATE	1	TRUE	1	0.819783940108736	3		146	287	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	235	364	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.337392516735453	3	FACETS	0.902	0.854	0.95	0.902	0.854	0.95	INDETERMINATE	2	TRUE	1	0.819783940108736	3		364	448	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191527	185191527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754424536	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	129	561	1	ENST00000265026.3:c.2408G>A	p.Arg803Gln	p.R803Q	ENST00000265026	NM_004721.4	803	cGa/cAa	11/14	0.337392516735453	3	FACETS	0.483	0.437	0.531	0.241	0.218	0.266	INDETERMINATE	1	TRUE	1	0.819783940108736	3		562	919	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141023	55141023	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	149	337	0	ENST00000257290.5:c.1669A>G	p.Ile557Val	p.I557V	ENST00000257290	NM_006206.4	557	Att/Gtt	12/23	0.323667290064509	1	FACETS	0.589	0.545	0.634	0.589	0.545	0.634	INDETERMINATE	1	TRUE	0	0.819783940108736	1		337	364	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156696	55156696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	241	523	0	ENST00000257290.5:c.3097G>A	p.Asp1033Asn	p.D1033N	ENST00000257290	NM_006206.4	1033	Gac/Aac	22/23	0.323667290064509	1	FACETS	0.61	0.574	0.646	0.61	0.574	0.646	INDETERMINATE	1	TRUE	0	0.819783940108736	1		523	569	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467824	66467824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	142	287	0	ENST00000273854.3:c.445G>A	p.Glu149Lys	p.E149K	ENST00000273854	NM_004439.5	149	Gaa/Aaa	3/18	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.819783940108736	2		287	325	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526378	31526378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	481	1011	0	ENST00000344624.3:c.662C>T	p.Ser221Phe	p.S221F	ENST00000344624		221	tCc/tTc	2/33	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.819783940108736	2		1011	1067	SUCCESS
APC	324	MSKCC	GRCh37	5	112178531	112178531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	134	274	0	ENST00000257430.4:c.7240G>A	p.Val2414Ile	p.V2414I	ENST00000257430	NM_000038.5	2414	Gta/Ata	16/16	0.198531088511009	3	FACETS	0.792	0.733	0.852	0.792	0.733	0.852	INDETERMINATE	2	TRUE	1	0.819783940108736	3		274	291	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637792	176637793	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	229	532	1	ENST00000439151.2:c.2392_2393delinsTT	p.Pro798Leu	p.P798L	ENST00000439151	NM_022455.4	798	CCa/TTa	5/23	NA	2	FACETS	0.989	0.929	1			1	INDETERMINATE	1	TRUE	NA	0.819783940108736	2		533	565	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673706	30673706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	324	690	0	ENST00000376406.3:c.3254G>A	p.Gly1085Glu	p.G1085E	ENST00000376406	NM_014641.2	1085	gGg/gAg	10/15	1	2	FACETS	0.948	0.899	0.997	0.948	0.899	0.997	CLONAL	1	TRUE	1	0.819783940108736	2		690	834	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969132	93969132	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	143	392	0	ENST00000369303.4:c.1864C>T	p.His622Tyr	p.H622Y	ENST00000369303	NM_004440.3	622	Cat/Tat	10/17	0.819783940108736	3	FACETS	0.99	0.908	1	0.495	0.454	0.537	CLONAL	1	TRUE	1	0.819783940108736	3		392	497	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120690	94120690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	344	440	0	ENST00000369303.4:c.361G>A	p.Glu121Lys	p.E121K	ENST00000369303	NM_004440.3	121	Gaa/Aaa	3/17	0.819783940108736	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.819783940108736	3		440	590	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935537	13935537	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs980825182	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	266	411	0	ENST00000405192.2:c.1319G>A	p.Gly440Glu	p.G440E	ENST00000405192	NM_001163147.1	440	gGg/gAg	12/12	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.819783940108736	2		411	553	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128849154	128849154	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	427	739	0	ENST00000249373.3:c.1382G>T	p.Gly461Val	p.G461V	ENST00000249373	NM_005631.4	461	gGc/gTc	8/12	0.218814729335416	3	FACETS	0.803	0.769	0.837	0.803	0.769	0.837	INDETERMINATE	2	TRUE	1	0.819783940108736	3		739	915	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494121	140494121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	280	574	0	ENST00000288602.6:c.1127C>T	p.Pro376Leu	p.P376L	ENST00000288602	NM_004333.4	376	cCt/cTt	8/18	0.218814729335416	3	FACETS	1	0.993	1	0.703	0.665	0.742	INDETERMINATE	1	TRUE	1	0.819783940108736	3		574	685	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38314972	38314972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1175350192	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	391	774	0	ENST00000425967.3:c.92G>A	p.Arg31Lys	p.R31K	ENST00000425967	NM_001174067.1	31	aGa/aAa	3/19	0.341343890512539	1	FACETS	0.649	0.62	0.678	0.649	0.62	0.678	INDETERMINATE	1	TRUE	0	0.819783940108736	1		774	867	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971027	21971028	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	GT	novel	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	583	445	1	ENST00000304494.5:c.330_331delinsAC	p.Trp110_Gly111delinsTer	p.W110_G111delins*	ENST00000304494	NM_000077.4	110	tgGGgc/tgACgc	2/3	0.806233218298808	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.819783940108736	2		446	641	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397653	139397653	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	650	832	0	ENST00000277541.6:c.5148C>G	p.Tyr1716Ter	p.Y1716*	ENST00000277541	NM_017617.3	1716	taC/taG	27/34	0.819783940108736	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.819783940108736	1		832	774	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649557	48649557	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1478971085	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	500	953	0	ENST00000376670.3:c.41C>T	p.Pro14Leu	p.P14L	ENST00000376670	NM_002049.3	14	cCc/cTc	2/6	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.819783940108736	2		953	1042	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228269	53228269	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	359	754	0	ENST00000375401.3:c.2133G>T	p.Lys711Asn	p.K711N	ENST00000375401	NM_004187.3	711	aaG/aaT	15/26	NA	2	FACETS	0.937	0.891	0.983			1	INDETERMINATE	1	TRUE	NA	0.819783940108736	2		754	935	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412411	63412411	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	175	956	0	ENST00000330258.3:c.756A>T	p.Lys252Asn	p.K252N	ENST00000330258	NM_152424.3	252	aaA/aaT	2/2	0.731745365389664	1	FACETS	0.365	0.337	0.394	0.365	0.337	0.394	SUBCLONAL	1	TRUE	0	0.819783940108736	1		956	690	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	160	315	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.173227547275892	3	FACETS	0.992	0.914	1	0.992	0.914	1	INDETERMINATE	2	TRUE	1	0.31713599311027	3		315	589	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	411	1003	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.986	1	1	0.997	1	CLONAL	3	TRUE	1	0.31713599311027	2		1007	813	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	175	328	0	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.815	0.753	0.879	1	0.991	1	CLONAL	2	TRUE	1	0.31713599311027	2		328	677	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024721	14024721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1340754747	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	60	326	0	ENST00000311895.7:c.947C>T	p.Thr316Met	p.T316M	ENST00000311895	NM_005236.2	316	aCg/aTg	5/11	1	2	FACETS	0.677	0.583	0.779	0.677	0.583	0.779	SUBCLONAL	1	TRUE	1	0.31713599311027	2		326	559	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738411	145738416	+	inframe_deletion	In_Frame_Del	DEL	GGTGCA	GGTGCA	-	rs548804317	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	150	728	0	ENST00000428558.2:c.2569_2574del	p.Cys857_Thr858del	p.C857_T858del	ENST00000428558	NM_004260.3	857	TGCACC/-	16/22	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.31713599311027	2		728	841	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1232964733	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	34	113	0	ENST00000324856.7:c.1015del	p.Ala339LeufsTer24	p.A339Lfs*24	ENST00000324856	NM_006015.4	337	tGg/tg	1/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.31713599311027	2		113	143	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	70	354	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.31713599311027	2		354	354	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	60	552	2	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.558	0.48	0.643	0.558	0.48	0.643	SUBCLONAL	1	TRUE	1	0.31713599311027	2		554	678	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692849	89692849	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554898097	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	62	146	0	ENST00000371953.3:c.333G>A	p.Trp111Ter	p.W111*	ENST00000371953	NM_000314.4	111	tgG/tgA	5/9	1	2	FACETS	0.877	0.768	0.991	1	0.978	1	CLONAL	2	TRUE	1	0.31713599311027	2		146	223	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	226	419	1	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	1	2	FACETS	0.911	0.851	0.973	1	0.994	1	CLONAL	2	TRUE	1	0.31713599311027	2		420	782	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522033	157522033	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	69	497	0	ENST00000346085.5:c.4308del	p.Gln1437ArgfsTer11	p.Q1437Rfs*11	ENST00000346085	NM_020732.3	1435	ccG/cc	18/20	1	2	FACETS	0.812	0.708	0.924	0.812	0.708	0.924	CLONAL	1	TRUE	1	0.31713599311027	2		497	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519999	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	207	482	1	ENST00000269305.4:c.716A>G	p.Asn239Ser	p.N239S	ENST00000269305	NM_001126112.2	239	aAc/aGc	7/11	1	2	FACETS	0.91	0.848	0.975	1	0.993	1	CLONAL	2	TRUE	1	0.31713599311027	2		483	717	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743930	41743930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141302305	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	195	678	0	ENST00000301178.4:c.865G>A	p.Val289Met	p.V289M	ENST00000301178	NM_021913.4	289	Gtg/Atg	7/20	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.31713599311027	2		678	824	SUCCESS
AR	367	MSKCC	GRCh37	X	66905930	66905930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754201976	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	95	328	0	ENST00000374690.3:c.1847G>A	p.Arg616His	p.R616H	ENST00000374690	NM_000044.3	616	cGt/cAt	3/8	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.31713599311027	2		328	506	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432041	121432041	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057520504	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	234	721	0	ENST00000257555.6:c.788G>A	p.Arg263His	p.R263H	ENST00000257555		263	cGt/cAt	4/10	1	2	FACETS	0.805	0.751	0.859	1	0.993	1	CLONAL	2	TRUE	1	0.31713599311027	2		721	917	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	127	280	3	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.817	0.745	0.893	1	0.988	1	CLONAL	2	TRUE	1	0.31713599311027	2		283	490	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	149	343	0	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.31713599311027	2		343	655	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651438	52651438	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	111	438	0	ENST00000394830.3:c.1658del	p.Lys553ArgfsTer16	p.K553Rfs*16	ENST00000394830	NM_018313.4	553	aAg/ag	15/30	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.31713599311027	2		438	635	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220390	98220390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	185	445	0	ENST00000331920.6:c.3073C>T	p.Arg1025Cys	p.R1025C	ENST00000331920	NM_000264.3	1025	Cgc/Tgc	18/24	1	2	FACETS	0.833	0.772	0.897	1	0.992	1	CLONAL	2	TRUE	1	0.31713599311027	2		445	700	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	145	360	4	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	0.762	0.698	0.829	1	0.988	1	SUBCLONAL	2	TRUE	1	0.31713599311027	2		364	600	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513282	44513287	+	inframe_deletion	In_Frame_Del	DEL	CCACCG	CCACCG	-	rs745888281	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	104	436	4	ENST00000291552.4:c.648_653del	p.Gly222_Gly223del	p.G222_G223del	ENST00000291552	NM_006758.2	216	ggCGGTGGt/ggt	8/8	1	2	FACETS	0.758	0.678	0.843	0.758	0.678	0.843	SUBCLONAL	1	TRUE	1	0.31713599311027	2		440	865	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142913	7142913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1283504748	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	226	573	2	ENST00000302850.5:c.2456G>A	p.Arg819His	p.R819H	ENST00000302850	NM_000208.2	819	cGc/cAc	12/22	1	2	FACETS	0.872	0.814	0.932	1	0.993	1	CLONAL	2	TRUE	1	0.31713599311027	2		575	817	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007689	45007690	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	41	335	0	ENST00000558401.1:c.137_138del	p.Tyr46CysfsTer10	p.Y46Cfs*10	ENST00000558401	NM_004048.2	46	TAt/t	2/4	1	2	FACETS	0.519	0.432	0.616	0.519	0.432	0.616	SUBCLONAL	1	TRUE	1	0.31713599311027	2		335	498	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799131	42799131	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	194	680	0	ENST00000575354.2:c.4620del	p.Thr1541LeufsTer79	p.T1541Lfs*79	ENST00000575354	NM_015125.3	1539	Ccc/cc	20/20	1	2	FACETS	0.77	0.714	0.828	1	0.991	1	SUBCLONAL	2	TRUE	1	0.31713599311027	2		680	794	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249361	153249361	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	89	291	1	ENST00000281708.4:c.1417del	p.Arg473GlufsTer25	p.R473Efs*25	ENST00000281708	NM_033632.3	473	Aga/ga	9/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.31713599311027	2		292	455	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935322	36935323	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs747437399	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	155	1143	5	ENST00000361632.4:c.1404dup	p.Ser469GlnfsTer5	p.S469Qfs*5	ENST00000361632		468	-/C	10/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.31713599311027	2		1148	812	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403254	213403254	+	frameshift_variant,start_lost,start_retained_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	178	363	0	ENST00000342788.4:c.1del	p.Met1?	p.M1?	ENST00000342788	NM_005235.2	1	Atg/tg	1/28	0.31713599311027	3	FACETS	1	0.971	1	0.729	0.675	0.784	CLONAL	2	TRUE	0	0.31713599311027	3		363	595	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115753	108115753	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	32	147	0	ENST00000278616.4:c.901G>T	p.Gly301Cys	p.G301C	ENST00000278616	NM_000051.3	301	Ggt/Tgt	7/63	1	2	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	TRUE	1	0.31713599311027	2		147	195	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829075	128829075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1247591045	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	25	29	0	ENST00000249373.3:c.88del	p.Ala30ArgfsTer25	p.A30Rfs*25	ENST00000249373	NM_005631.4	28	cGg/cg	1/12	0.173227547275892	3	FACETS	1	0.905	1	1	0.905	1	INDETERMINATE	2	TRUE	1	0.31713599311027	3		29	76	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	141	808	10	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.31713599311027	2		818	691	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741838	17741838	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	47	192	0	ENST00000250003.3:c.509C>T	p.Ala170Val	p.A170V	ENST00000250003	NM_002478.4	170	gCg/gTg	1/3	1	2	FACETS	0.756	0.646	0.874	1	0.965	1	SUBCLONAL	2	TRUE	1	0.31713599311027	2		192	196	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445500	49445500	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs886042284	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	222	466	2	ENST00000301067.7:c.1966del	p.Leu656CysfsTer274	p.L656Cfs*274	ENST00000301067	NM_003482.3	656	Ctg/tg	10/54	1	2	FACETS	0.782	0.729	0.837	1	0.992	1	SUBCLONAL	2	TRUE	1	0.31713599311027	2		468	895	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	154	461	0	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.31713599311027	2		461	826	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445173	49445173	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs560581125	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	83	700	0	ENST00000301067.7:c.2293G>C	p.Ala765Pro	p.A765P	ENST00000301067	NM_003482.3	765	Gct/Cct	10/54	1	2	FACETS	0.711	0.627	0.801	0.711	0.627	0.801	SUBCLONAL	1	TRUE	1	0.31713599311027	2		700	736	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101068	27101068	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	72	594	1	ENST00000324856.7:c.4354del	p.Gln1452ArgfsTer29	p.Q1452Rfs*29	ENST00000324856	NM_006015.4	1450	ggC/gg	18/20	1	2	FACETS	0.593	0.517	0.675	0.593	0.517	0.675	SUBCLONAL	1	TRUE	1	0.31713599311027	2		595	766	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323362	31323363	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748204482	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	237	705	0	ENST00000412585.2:c.626dup	p.Thr211AspfsTer10	p.T211Dfs*10	ENST00000412585	NM_005514.6	209	cca/ccCa	4/8	1	2	FACETS	1	0.981	1	1	0.996	1	CLONAL	3	TRUE	1	0.31713599311027	2		705	461	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218451	36218451	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs34078597	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	152	598	0	ENST00000222270.7:c.4235del	p.Gly1412AlafsTer10	p.G1412Afs*10	ENST00000222270	NM_014727.1	1410	caG/ca	16/37	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.31713599311027	2		598	739	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387698	17387698	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199960321	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	170	458	0	ENST00000359435.4:c.766G>A	p.Glu256Lys	p.E256K	ENST00000359435	NM_001033549.1	256	Gag/Aag	8/9	1	2	FACETS	0.794	0.733	0.858	1	0.99	1	SUBCLONAL	2	TRUE	1	0.31713599311027	2		458	675	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118890	70118890	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs137853129	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	217	566	0	ENST00000245479.2:c.462C>G	p.Phe154Leu	p.F154L	ENST00000245479	NM_000346.3	154	ttC/ttG	2/3	1	2	FACETS	1	0.961	1	1	0.994	1	CLONAL	2	TRUE	1	0.31713599311027	2		566	659	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820938	3820938	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	86	526	0	ENST00000262367.5:c.2513C>A	p.Pro838His	p.P838H	ENST00000262367	NM_004380.2	838	cCt/cAt	14/31	1	2	FACETS	0.628	0.555	0.707	0.628	0.555	0.707	SUBCLONAL	1	TRUE	1	0.31713599311027	2		526	863	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205092	38205092	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	136	475	1	ENST00000317025.8:c.598del	p.Ser200AlafsTer20	p.S200Afs*20	ENST00000317025	NM_023034.1	200	Agc/gc	2/24	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.31713599311027	2		476	771	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379841	17379841	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	235	729	0	ENST00000359435.4:c.230del	p.Pro77ArgfsTer19	p.P77Rfs*19	ENST00000359435	NM_001033549.1	76	Ccc/cc	2/9	1	2	FACETS	0.772	0.721	0.825	1	0.993	1	SUBCLONAL	2	TRUE	1	0.31713599311027	2		729	960	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012710	36012710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1228673150	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	46	73	0	ENST00000358208.4:c.154G>A	p.Ala52Thr	p.A52T	ENST00000358208		52	Gcg/Acg	2/12	1	2	FACETS	1	0.947	1	1	0.978	1	CLONAL	2	TRUE	1	0.31713599311027	2		73	120	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597990	43597990	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs76449634	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	216	674	0	ENST00000355710.3:c.538C>T	p.Arg180Ter	p.R180*	ENST00000355710	NM_020975.4	180	Cga/Tga	3/20	1	2	FACETS	0.786	0.731	0.841	1	0.992	1	SUBCLONAL	2	TRUE	1	0.31713599311027	2		674	867	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224316	36224316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749880112	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	220	619	0	ENST00000222270.7:c.6866C>T	p.Pro2289Leu	p.P2289L	ENST00000222270	NM_014727.1	2289	cCg/cTg	28/37	1	2	FACETS	0.813	0.758	0.87	1	0.993	1	CLONAL	2	TRUE	1	0.31713599311027	2		619	853	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89825093	89825093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1374262828	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	42	411	1	ENST00000389301.3:c.2873C>T	p.Ala958Val	p.A958V	ENST00000389301	NM_000135.2	958	gCg/gTg	30/43	1	2	FACETS	0.368	0.306	0.437	0.368	0.306	0.437	SUBCLONAL	1	TRUE	1	0.31713599311027	2		412	720	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842662	68842662	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	123	567	0	ENST00000261769.5:c.602del	p.Pro201LeufsTer14	p.P201Lfs*14	ENST00000261769	NM_004360.3	200	Ccc/cc	5/16	1	2	FACETS	0.804	0.726	0.886	0.804	0.726	0.886	CLONAL	1	TRUE	1	0.31713599311027	2		567	965	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985768	60985768	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	142	242	1	ENST00000333681.4:c.132del	p.Ala45HisfsTer51	p.A45Hfs*51	ENST00000333681		44	ccC/cc	2/3	0.190051640755341	3	FACETS	0.862	0.794	0.932	1	0.984	1	INDETERMINATE	3	TRUE	1	0.31713599311027	3		243	401	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445094	89445094	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	52	319	0	ENST00000336596.2:c.1414G>T	p.Val472Phe	p.V472F	ENST00000336596	NM_005233.5	472	Gtc/Ttc	6/17	1	2	FACETS	0.683	0.582	0.794	0.683	0.582	0.794	SUBCLONAL	1	TRUE	1	0.31713599311027	2		319	480	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65351940	65351940	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs753624838	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	89	307	0	ENST00000342505.4:c.6+2T>C		p.X2_splice	ENST00000342505	NM_002227.2	2			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.31713599311027	2		307	421	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275305	115275305	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	171	529	0	ENST00000438362.2:c.1108C>T	p.Arg370Ter	p.R370*	ENST00000438362	NM_001242891.1	370	Cga/Tga	10/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.31713599311027	2		529	772	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471755	120471756	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	150	420	0	ENST00000256646.2:c.3735dup	p.Gly1246TrpfsTer17	p.G1246Wfs*17	ENST00000256646	NM_024408.3	1245	-/T	23/34	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.31713599311027	2		420	637	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608321	43608321	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	219	710	0	ENST00000355710.3:c.1669A>G	p.Thr557Ala	p.T557A	ENST00000355710	NM_020975.4	557	Acc/Gcc	9/20	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.31713599311027	2		710	943	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332889	70332889	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1241334779	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	66	466	1	ENST00000373644.4:c.794A>T	p.Asn265Ile	p.N265I	ENST00000373644	NM_030625.2	265	aAc/aTc	2/12	1	2	FACETS	0.556	0.482	0.636	0.556	0.482	0.636	SUBCLONAL	1	TRUE	1	0.31713599311027	2		467	749	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138867	64138867	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	153	511	0	ENST00000334205.4:c.2237del	p.Pro746LeufsTer38	p.P746Lfs*38	ENST00000334205	NM_003942.2	745	tCc/tc	17/17	1	2	FACETS	0.866	0.797	0.938	1	0.991	1	CLONAL	2	TRUE	1	0.31713599311027	2		511	557	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589782	69589782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs906608234	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	37	42	1	ENST00000168712.1:c.71C>T	p.Ala24Val	p.A24V	ENST00000168712	NM_002007.2	24	gCg/gTg	1/3	1	2	FACETS	0.897	0.755	1	1	0.965	1	CLONAL	2	TRUE	1	0.31713599311027	2		43	130	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240154	41240154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	16	76	2	ENST00000379561.5:c.196G>A	p.Val66Ile	p.V66I	ENST00000379561	NM_002015.3	66	Gtc/Atc	1/3	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.31713599311027	2		78	77	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281659	49281659	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	251	537	0	ENST00000282018.3:c.706T>C	p.Ser236Pro	p.S236P	ENST00000282018	NM_020377.2	236	Tcg/Ccg	1/1	0.31713599311027	3	FACETS	0.853	0.798	0.91	0.853	0.798	0.91	CLONAL	2	TRUE	1	0.31713599311027	3		537	1075	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007803	45007803	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	38	318	0	ENST00000558401.1:c.250C>A	p.Leu84Ile	p.L84I	ENST00000558401	NM_004048.2	84	Ctc/Atc	2/4	1	2	FACETS	0.422	0.348	0.505	0.422	0.348	0.505	SUBCLONAL	1	TRUE	1	0.31713599311027	2		318	568	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856104	68856104	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	107	394	0	ENST00000261769.5:c.1912T>C	p.Trp638Arg	p.W638R	ENST00000261769	NM_004360.3	638	Tgg/Cgg	12/16	1	2	FACETS	0.877	0.787	0.973	0.877	0.787	0.973	CLONAL	1	TRUE	1	0.31713599311027	2		394	769	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347881	89347881	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	94	528	0	ENST00000301030.4:c.5069C>A	p.Pro1690His	p.P1690H	ENST00000301030	NM_001256183.1	1690	cCt/cAt	9/13	1	2	FACETS	0.835	0.743	0.933	0.835	0.743	0.933	CLONAL	1	TRUE	1	0.31713599311027	2		528	710	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585499	29585499	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	22	171	0	ENST00000356175.3:c.4248G>T	p.Arg1416Ser	p.R1416S	ENST00000356175	NM_000267.3	1416	agG/agT	31/57	1	2	FACETS	0.489	0.379	0.615	0.489	0.379	0.615	SUBCLONAL	1	TRUE	1	0.31713599311027	2		171	284	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619419	1619419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760988552	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	159	518	0	ENST00000344749.5:c.1222G>A	p.Ala408Thr	p.A408T	ENST00000344749	NM_001136139.2	408	Gcc/Acc	15/19	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.31713599311027	2		518	673	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416400	29416400	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	87	486	0	ENST00000389048.3:c.4553del	p.Lys1518ArgfsTer5	p.K1518Rfs*5	ENST00000389048	NM_004304.4	1518	aAg/ag	29/29	0.190051640755341	3	FACETS	0.674	0.595	0.759	0.337	0.297	0.38	INDETERMINATE	1	TRUE	1	0.31713599311027	3		486	943	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743935	40743935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	192	379	0	ENST00000373198.4:c.3060G>T	p.Trp1020Cys	p.W1020C	ENST00000373198	NM_133170.3	1020	tgG/tgT	23/32	0.218369562377773	0	FACETS	1	0.979	1			1	CLONAL	1	TRUE	0	0.31713599311027	0		379	721	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958123	54958123	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	164	356	1	ENST00000312783.6:c.484A>G	p.Lys162Glu	p.K162E	ENST00000312783	NM_198436.1	162	Aaa/Gaa	6/10	0.173227547275892	3	FACETS	0.941	0.867	1	0.941	0.867	1	INDETERMINATE	2	TRUE	1	0.31713599311027	3		357	637	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691916	30691916	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	131	320	0	ENST00000295754.5:c.418T>C	p.Ser140Pro	p.S140P	ENST00000295754	NM_003242.5	140	Tct/Cct	3/7	1	2	FACETS	0.808	0.738	0.882	1	0.988	1	CLONAL	2	TRUE	1	0.31713599311027	2		320	511	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163857	32163857	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	137	485	1	ENST00000375023.3:c.5369G>T	p.Gly1790Val	p.G1790V	ENST00000375023	NM_004557.3	1790	gGg/gTg	30/30	1	2	FACETS	0.836	0.764	0.909	1	0.989	1	CLONAL	2	TRUE	1	0.31713599311027	2		486	517	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187986	32187987	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	202	672	0	ENST00000375023.3:c.1234dup	p.Leu412ProfsTer36	p.L412Pfs*36	ENST00000375023	NM_004557.3	412	ctc/cCtc	7/30	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.31713599311027	2		672	850	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358948	81358948	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	38	378	0	ENST00000222390.5:c.1013A>G	p.Asp338Gly	p.D338G	ENST00000222390	NM_000601.4	338	gAc/gGc	8/18	0.173227547275892	3	FACETS	0.428	0.353	0.512	0.214	0.176	0.256	INDETERMINATE	1	TRUE	1	0.31713599311027	3		378	649	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146253	38146253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748817925	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	188	464	0	ENST00000317025.8:c.3253G>A	p.Val1085Met	p.V1085M	ENST00000317025	NM_023034.1	1085	Gtg/Atg	19/24	1	2	FACETS	0.797	0.738	0.857	1	0.991	1	SUBCLONAL	2	TRUE	1	0.31713599311027	2		464	744	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499798	8499798	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	170	441	0	ENST00000356435.5:c.2171A>C	p.Asn724Thr	p.N724T	ENST00000356435		724	aAc/aCc	14/35	1	2	FACETS	0.797	0.735	0.86	1	0.99	1	SUBCLONAL	2	TRUE	1	0.31713599311027	2		441	673	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244439	98244439	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs776773031	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	125	409	0	ENST00000331920.6:c.631A>G	p.Thr211Ala	p.T211A	ENST00000331920	NM_000264.3	211	Aca/Gca	4/24	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.31713599311027	2		409	605	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400302	139400302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752951296	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	57	666	0	ENST00000277541.6:c.4046C>T	p.Ala1349Val	p.A1349V	ENST00000277541	NM_017617.3	1349	gCt/gTt	25/34	1	2	FACETS	0.496	0.424	0.574	0.496	0.424	0.574	SUBCLONAL	1	TRUE	1	0.31713599311027	2		666	725	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564407	139564407	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	104	721	0	ENST00000308874.7:c.355C>A	p.Gln119Lys	p.Q119K	ENST00000308874		119	Cag/Aag	6/10	1	2	FACETS	0.82	0.734	0.911	0.82	0.734	0.911	CLONAL	1	TRUE	1	0.31713599311027	2		721	800	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815543	139815543	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	188	683	0	ENST00000247668.2:c.1014G>T	p.Leu338Phe	p.L338F	ENST00000247668	NM_021138.3	338	ttG/ttT	9/11	1	2	FACETS	0.753	0.697	0.811	1	0.99	1	SUBCLONAL	2	TRUE	1	0.31713599311027	2		683	787	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412462	63412463	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	47	695	0	ENST00000330258.3:c.704_705insA	p.Gly236TrpfsTer16	p.G236Wfs*16	ENST00000330258	NM_152424.3	235	cct/ccAt	2/2	1	2	FACETS	0.343	0.288	0.404	0.343	0.288	0.404	SUBCLONAL	1	TRUE	1	0.31713599311027	2		695	864	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190080	123190081	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	94	296	0	ENST00000218089.9:c.1304dup	p.Leu436AlafsTer5	p.L436Afs*5	ENST00000218089	NM_001042749.1	433	-/A	14/35	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.31713599311027	2		296	518	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	224	411	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.364750211744383	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.364750211744383	3		411	704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs747342068	NA	P-0053490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	315	880	0	ENST00000269305.4:c.394A>C	p.Lys132Gln	p.K132Q	ENST00000269305	NM_001126112.2	132	Aag/Cag	5/11	0.364750211744383	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.364750211744383	1		880	1344	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	52	252	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.364750211744383	2		252	258	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288246	21288246	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200712124	NA	P-0053490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	212	545	0	ENST00000354336.3:c.491G>A	p.Arg164Gln	p.R164Q	ENST00000354336	NM_005207.3	164	cGg/cAg	2/3	0.364750211744383	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.364750211744383	1		545	886	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0053492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	254	353	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.572606375486663	3	FACETS	0.934	0.881	0.986	0.934	0.881	0.986	CLONAL	2	TRUE	1	0.594117414155642	3		353	594	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0053493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	529	350	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.564921603243978	5	FACETS	1	0.978	1			1	CLONAL	4	TRUE	NA	0.564921603243978	5		350	853	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40742257	40742257	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1680	727	777	0	ENST00000392038.2:c.867C>G	p.Ile289Met	p.I289M	ENST00000392038	NM_001626.4	289	atC/atG	10/14	0.564921603243978	7	FACETS	0.86	0.828	0.892			1	CLONAL	3	TRUE	NA	0.564921603243978	7		777	2407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578410	7578410	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	550	826	0	ENST00000269305.4:c.520A>T	p.Arg174Trp	p.R174W	ENST00000269305	NM_001126112.2	174	Agg/Tgg	5/11	0.563348256522576	2	FACETS	0.946	0.913	0.979	0.946	0.913	0.979	CLONAL	2	TRUE	0	0.564921603243978	2		826	1029	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741849	17741849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750173588	NA	P-0053493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	71	192	1	ENST00000250003.3:c.520G>A	p.Ala174Thr	p.A174T	ENST00000250003	NM_002478.4	174	Gcc/Acc	1/3	0.554767804185888	3	FACETS	1	0.937	1	0.55	0.485	0.619	CLONAL	1	TRUE	1	0.564921603243978	3		193	293	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581225	48581226	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATTCA	novel	NA	P-0053493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	155	526	0	ENST00000342988.3:c.536_540dup	p.Thr181PhefsTer23	p.T181Ffs*23	ENST00000342988	NM_005359.5	177	cat/cATTCAat	5/12	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.564921603243978	2		526	454	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974708	21974708	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	333	432	0	ENST00000304494.5:c.119del	p.Ala40AspfsTer13	p.A40Dfs*13	ENST00000304494	NM_000077.4	40	gCa/ga	1/3	0.563348256522576	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.564921603243978	2		432	571	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0053494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	15	377	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.347483766964843	2	FACETS	0.189	0.137	0.251	0.094	0.068	0.126	SUBCLONAL	1	TRUE	0	0.347483766964843	2		377	458	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630626	158630626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912678	NA	P-0053494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	39	186	0	ENST00000263640.3:c.617G>A	p.Arg206His	p.R206H	ENST00000263640	NM_001105.4	206	cGc/cAc	6/11	1	2	FACETS	0.651	0.541	0.773	0.651	0.541	0.773	SUBCLONAL	1	TRUE	1	0.347483766964843	2		186	345	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155399	99155399	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1559033620	NA	P-0053494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	106	329	0	ENST00000074304.5:c.625C>T	p.Arg209Ter	p.R209*	ENST00000074304	NM_001134224.1	209	Cga/Tga	9/26	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.347483766964843	2		329	541	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0053494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	74	305	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.347483766964843	2		305	299	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692887	89692887	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	95	236	0	ENST00000371953.3:c.371G>T	p.Cys124Phe	p.C124F	ENST00000371953	NM_000314.4	124	tGt/tTt	5/9	0.347483766964843	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.347483766964843	2		236	253	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274746	123274746	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs387906677	NA	P-0053494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	46	426	0	ENST00000358487.5:c.1172T>G	p.Met391Arg	p.M391R	ENST00000358487	NM_000141.4	391	aTg/aGg	9/18	0.347483766964843	2	FACETS	0.444	0.373	0.523	0.222	0.186	0.262	SUBCLONAL	1	TRUE	0	0.347483766964843	2		426	596	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193554	99193554	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	123	521	0	ENST00000074304.5:c.2749G>T	p.Glu917Ter	p.E917*	ENST00000074304	NM_001134224.1	917	Gag/Tag	25/26	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.347483766964843	2		521	660	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372518	55372519	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0053494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	30	612	2	ENST00000297316.4:c.1208_1209delinsTT	p.Ser403Ile	p.S403I	ENST00000297316	NM_022454.3	403	aGC/aTT	2/2	1	2	FACETS	0.2	0.16	0.246	0.2	0.16	0.246	SUBCLONAL	1	TRUE	1	0.347483766964843	2		614	863	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466018	69466018	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	121	751	0	ENST00000227507.2:c.856A>C	p.Thr286Pro	p.T286P	ENST00000227507	NM_053056.2	286	Aca/Cca	5/5	1	2	FACETS	0.901	0.814	0.992	0.901	0.814	0.992	CLONAL	1	TRUE	1	0.347483766964843	2		751	773	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100840	27100854	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCACATATGGCCC	TGGCACATATGGCCC	GGGCA	novel	NA	P-0053494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	177	399	1	ENST00000324856.7:c.4122_4136delinsGGGCA	p.Asp1374GlufsTer104	p.D1374Efs*104	ENST00000324856	NM_006015.4	1374	gaTGGCACATATGGCCCt/gaGGGCAt	18/20	0.347483766964843	2	FACETS	0.983	0.913	1	0.983	0.913	1	CLONAL	2	TRUE	0	0.347483766964843	2		400	518	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573209	64573209	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	153	531	0	ENST00000312049.6:c.1083C>A	p.Tyr361Ter	p.Y361*	ENST00000312049	NM_130799.2	361	taC/taA	8/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.347483766964843	2		531	702	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644796	67644799	+	frameshift_variant	Frame_Shift_Del	DEL	GAGA	GAGA	-	novel	NA	P-0053494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	110	316	0	ENST00000264010.4:c.63_66del	p.Lys23LeufsTer38	p.K23Lfs*38	ENST00000264010	NM_006565.3	21	GAGAga/ga	3/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.347483766964843	2		316	538	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10257045	10257045	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	57	436	0	ENST00000340748.4:c.2828C>T	p.Pro943Leu	p.P943L	ENST00000340748		943	cCt/cTt	27/40	1	2	FACETS	0.565	0.484	0.652	0.565	0.484	0.652	SUBCLONAL	1	TRUE	1	0.347483766964843	2		436	581	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155690	106155690	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0053494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	73	273	0	ENST00000380013.4:c.591T>G	p.Ile197Met	p.I197M	ENST00000380013	NM_001127208.2	197	atT/atG	3/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.347483766964843	2		273	372	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178148	56178149	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0053494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	60	256	0	ENST00000399503.3:c.3121_3122insCT	p.Lys1041ThrfsTer42	p.K1041Tfs*42	ENST00000399503	NM_005921.1	1041	aaa/aCTaa	14/20	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.347483766964843	2		256	320	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370712	55370712	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	53	359	0	ENST00000297316.4:c.14A>T	p.Asp5Val	p.D5V	ENST00000297316	NM_022454.3	5	gAt/gTt	1/2	1	2	FACETS	0.784	0.671	0.907	0.784	0.671	0.907	CLONAL	1	TRUE	1	0.347483766964843	2		359	389	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833910	44833910	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0053494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	39	288	0	ENST00000377967.4:c.335-1G>T		p.X112_splice	ENST00000377967	NM_021140.2	112			1	2	FACETS	0.753	0.627	0.893	0.753	0.627	0.893	SUBCLONAL	1	TRUE	1	0.347483766964843	2		288	298	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200218	123200218	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	67	330	0	ENST00000218089.9:c.2197del	p.Ala733HisfsTer8	p.A733Hfs*8	ENST00000218089	NM_001042749.1	733	Gca/ca	23/35	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.347483766964843	2		330	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0053495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	431	618	1	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.605821868375749	2		619	677	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652207	3652207	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	214	719	0	ENST00000294008.3:c.862C>G	p.Leu288Val	p.L288V	ENST00000294008	NM_032444.2	288	Ctg/Gtg	4/15	0.605821868375749	2	FACETS	1	0.983	1	0.574	0.537	0.613	CLONAL	1	TRUE	0	0.605821868375749	2		719	615	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832779	3832779	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	167	613	0	ENST00000262367.5:c.1479G>A	p.Met493Ile	p.M493I	ENST00000262367	NM_004380.2	493	atG/atA	6/31	0.517745039616378	1	FACETS	0.724	0.669	0.78	0.724	0.669	0.78	SUBCLONAL	1	TRUE	0	0.605821868375749	1		613	531	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421343	12421343	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs201978569	NA	P-0053495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	198	605	0	ENST00000287820.6:c.223A>G	p.Thr75Ala	p.T75A	ENST00000287820	NM_015869.4	75	Act/Gct	2/7	1	2	FACETS	0.866	0.804	0.929	0.866	0.804	0.929	CLONAL	1	TRUE	1	0.605821868375749	2		605	755	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913517	NA	P-0053496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	16	390	0	ENST00000288135.5:c.1676T>G	p.Val559Gly	p.V559G	ENST00000288135	NM_000222.2	559	gTt/gGt	11/21	1	2	FACETS	0.616	0.469	0.779	0.616	0.469	0.779	SUBCLONAL	1	FALSE	1	0.852088612025735	2		390	61	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0053497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	347	768	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.57707014621333	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.57707014621333	2		768	590	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175942	176175942	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	54	81	1	ENST00000367669.3:c.173C>A	p.Ser58Ter	p.S58*	ENST00000367669	NM_022457.5	58	tCg/tAg	1/20	0.57707014621333	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.57707014621333	2		82	76	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144584	119144584	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	157	373	0	ENST00000264033.4:c.597A>G	p.Ile199Met	p.I199M	ENST00000264033	NM_005188.3	199	atA/atG	4/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.57707014621333	2		373	449	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432470	49432470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1348233264	NA	P-0053497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	224	833	0	ENST00000301067.7:c.8669C>T	p.Pro2890Leu	p.P2890L	ENST00000301067	NM_003482.3	2890	cCt/cTt	34/54	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.57707014621333	2		833	740	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434538	49434538	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	221	923	0	ENST00000301067.7:c.7015G>A	p.Glu2339Lys	p.E2339K	ENST00000301067	NM_003482.3	2339	Gag/Aag	31/54	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.57707014621333	2		923	713	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431985	121431986	+	missense_variant	Missense_Mutation	DNP	AG	AG	GA	novel	NA	P-0053497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	187	896	2	ENST00000257555.6:c.732_733delinsGA	p.Gly245Arg	p.G245R	ENST00000257555		244	agAGgg/agGAgg	4/10	1	2	FACETS	0.921	0.853	0.99	0.921	0.853	0.99	CLONAL	1	TRUE	1	0.57707014621333	2		898	704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0053497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	196	713	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.555290126885464	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.57707014621333	1		713	456	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637978	39637978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1406322792	NA	P-0053497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	156	633	0	ENST00000262039.4:c.2395C>T	p.Arg799Cys	p.R799C	ENST00000262039	NM_002647.2	799	Cgt/Tgt	22/25	1	2	FACETS	0.797	0.732	0.865	0.797	0.732	0.865	SUBCLONAL	1	TRUE	1	0.57707014621333	2		633	678	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260254	10260254	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	208	630	0	ENST00000340748.4:c.2413C>T	p.Leu805Phe	p.L805F	ENST00000340748		805	Ctc/Ttc	25/40	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.57707014621333	2		630	712	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132522	11132522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778175819	NA	P-0053497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	245	833	0	ENST00000358026.2:c.2738C>T	p.Pro913Leu	p.P913L	ENST00000358026	NM_001128849.1	913	cCg/cTg	19/36	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.57707014621333	2		833	770	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223344	36223344	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	255	1071	1	ENST00000222270.7:c.5894C>T	p.Pro1965Leu	p.P1965L	ENST00000222270	NM_014727.1	1965	cCa/cTa	28/37	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.57707014621333	2		1072	881	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223703	36223704	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0053497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	230	1099	1	ENST00000222270.7:c.6253_6254delinsTT	p.Pro2085Phe	p.P2085F	ENST00000222270	NM_014727.1	2085	CCt/TTt	28/37	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.57707014621333	2		1100	776	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754650	41754650	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	207	748	0	ENST00000301178.4:c.1636G>A	p.Glu546Lys	p.E546K	ENST00000301178	NM_021913.4	546	Gag/Aag	14/20	1	2	FACETS	0.967	0.9	1	0.967	0.9	1	CLONAL	1	TRUE	1	0.57707014621333	2		748	742	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797282	42797282	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	199	912	0	ENST00000575354.2:c.3644A>G	p.Glu1215Gly	p.E1215G	ENST00000575354	NM_015125.3	1215	gAg/gGg	15/20	1	2	FACETS	0.965	0.897	1	0.965	0.897	1	CLONAL	1	TRUE	1	0.57707014621333	2		912	715	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523297	9523297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1229227713	NA	P-0053497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	166	579	0	ENST00000353224.5:c.1940C>T	p.Pro647Leu	p.P647L	ENST00000353224	NM_177990.2	647	cCt/cTt	9/10	0.57707014621333	3	FACETS	0.981	0.902	1	0.49	0.451	0.531	CLONAL	1	TRUE	1	0.57707014621333	3		579	756	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275705	41275705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	131	508	0	ENST00000349496.5:c.1600C>T	p.Pro534Ser	p.P534S	ENST00000349496	NM_001904.3	534	Cca/Tca	10/15	0.57707014621333	3	FACETS	0.841	0.764	0.921	0.42	0.382	0.461	CLONAL	1	TRUE	1	0.57707014621333	3		508	696	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725190	49725190	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	113	351	0	ENST00000449682.2:c.235G>A	p.Asp79Asn	p.D79N	ENST00000449682	NM_020998.3	79	Gac/Aac	2/18	0.57707014621333	3	FACETS	1	0.976	1	0.62	0.562	0.68	CLONAL	1	TRUE	1	0.57707014621333	3		351	407	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0053497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	69	151	0				ENST00000310581	NM_198253.2	-/1132			0.57707014621333	3	FACETS	0.984	0.865	1	0.492	0.432	0.556	CLONAL	1	TRUE	1	0.57707014621333	3		151	313	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805917	32805917	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	471	834	0	ENST00000374899.4:c.94C>T	p.Pro32Ser	p.P32S	ENST00000374899	NM_018833.2	32	Cct/Tct	2/12	0.57707014621333	2	FACETS	0.998	0.962	1	0.998	0.962	1	CLONAL	2	TRUE	0	0.57707014621333	2		834	818	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289262	33289262	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763431811	NA	P-0053497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	314	550	1	ENST00000374542.5:c.290C>T	p.Ser97Phe	p.S97F	ENST00000374542	NM_001141970.1	97	tCt/tTt	3/8	0.57707014621333	2	FACETS	0.932	0.889	0.974	0.932	0.889	0.974	CLONAL	2	TRUE	0	0.57707014621333	2		551	584	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647515	117647515	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1256569613	NA	P-0053497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	294	465	0	ENST00000368508.3:c.5429C>T	p.Ser1810Phe	p.S1810F	ENST00000368508	NM_002944.2	1810	tCc/tTc	33/43	0.57707014621333	2	FACETS	0.987	0.942	1	0.987	0.942	1	CLONAL	2	TRUE	0	0.57707014621333	2		465	516	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0053497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	133	386	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.57707014621333	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.57707014621333	1		386	327	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0053498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	806	353	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.719818826979523	8	FACETS	0.971	0.956	0.985	0.971	0.956	0.985	CLONAL	8	TRUE	0	0.719818826979523	8		353	911	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61213412	61213412	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1419393959	NA	P-0053498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	150	312	0	ENST00000301761.2:c.371-1G>A		p.X124_splice	ENST00000301761	NM_017841.2	124			0.347362402909227	3	FACETS	1	0.964	1	0.697	0.652	0.742	INDETERMINATE	2	TRUE	0	0.719818826979523	3		312	271	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610227	81610227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs763679435	NA	P-0053498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	85	424	0	ENST00000298171.2:c.1825C>T	p.Arg609Ter	p.R609*	ENST00000298171	NM_000369.2	609	Cga/Tga	10/10	0.346061156905211	4	FACETS	1	0.963	1			1	INDETERMINATE	1	TRUE	NA	0.719818826979523	4		424	342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0053498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	303	775	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.607870701640601	3	FACETS	0.844	0.811	0.877	0.844	0.811	0.877	CLONAL	3	TRUE	0	0.719818826979523	3		775	452	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557291	29557291	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	142	182	0	ENST00000356175.3:c.3004C>A	p.Leu1002Ile	p.L1002I	ENST00000356175	NM_000267.3	1002	Ctt/Att	23/57	0.575791971781142	5	FACETS	1	0.936	1	1	0.936	1	CLONAL	3	TRUE	2	0.719818826979523	5		182	272	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40379681	40379681	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	31	583	0	ENST00000293328.3:c.151C>G	p.Pro51Ala	p.P51A	ENST00000293328	NM_012448.3	51	Cca/Gca	3/19	0.616601951532808	4	FACETS	0.265	0.214	0.323			1	SUBCLONAL	1	TRUE	NA	0.719818826979523	4		583	559	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870504	40870504	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	160	476	1	ENST00000428826.2:c.899G>A	p.Arg300Gln	p.R300Q	ENST00000428826		300	cGg/cAg	9/21	0.616601951532808	4	FACETS	0.791	0.732	0.853			1	SUBCLONAL	2	TRUE	NA	0.719818826979523	4		477	483	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386571	81386571	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs969488858	NA	P-0053498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	213	366	0	ENST00000222390.5:c.416C>T	p.Thr139Ile	p.T139I	ENST00000222390	NM_000601.4	139	aCa/aTa	4/18	0.719818826979523	6	FACETS	1	0.987	1	0.814	0.762	0.868	CLONAL	2	TRUE	3	0.719818826979523	6		366	591	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524643	106524643	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1035403350	NA	P-0053498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	166	227	0	ENST00000359195.3:c.2804A>G	p.Tyr935Cys	p.Y935C	ENST00000359195	NM_002649.2	935	tAc/tGc	9/11	0.719818826979523	6	FACETS	0.868	0.806	0.932	0.868	0.806	0.932	CLONAL	3	TRUE	3	0.719818826979523	6		227	432	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968205	68968205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	118	491	0	ENST00000288368.4:c.1234G>A	p.Gly412Arg	p.G412R	ENST00000288368	NM_024870.2	412	Gga/Aga	10/40	0.680332176676193	4	FACETS	0.927	0.839	1	0.309	0.279	0.34	CLONAL	1	TRUE	1	0.719818826979523	4		491	608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579575	7579575	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555526795	NA	P-0053499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	362	566	0	ENST00000269305.4:c.112del	p.Gln38LysfsTer6	p.Q38Kfs*6	ENST00000269305	NM_001126112.2	38	Caa/aa	4/11	0.325450951190276	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.328650136176688	2		566	1062	SUCCESS
APC	324	MSKCC	GRCh37	5	112174094	112174095	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs863225332	NA	P-0053499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	56	278	0	ENST00000257430.4:c.2804dup	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	tac/tAac	16/16	1	2	FACETS	0.955	0.822	1	0.955	0.822	1	CLONAL	1	TRUE	1	0.328650136176688	2		278	357	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281668	49281668	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201815757	NA	P-0053499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1444	155	524	0	ENST00000282018.3:c.715C>T	p.Arg239Trp	p.R239W	ENST00000282018	NM_020377.2	239	Cgg/Tgg	1/1	0.328650136176688	4	FACETS	0.784	0.715	0.857	0.392	0.357	0.429	SUBCLONAL	1	TRUE	2	0.328650136176688	4		524	1599	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869550	102869550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	106	431	0	ENST00000307046.8:c.91C>T	p.His31Tyr	p.H31Y	ENST00000307046	NM_001111285.1	31	Cat/Tat	2/4	0.328650136176688	3	FACETS	0.797	0.714	0.886	0.399	0.357	0.443	SUBCLONAL	1	TRUE	1	0.328650136176688	3		431	942	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984671	11984674	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGAG	AGAG	-	novel	NA	P-0053499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	33	222	0	ENST00000353533.5:c.222_225del		p.X74_splice	ENST00000353533	NM_003010.3	74		3/11	0.325450951190276	2	FACETS	0.747	0.611	0.898	0.373	0.305	0.449	SUBCLONAL	1	TRUE	0	0.328650136176688	2		222	269	SUCCESS
APC	324	MSKCC	GRCh37	5	112175147	112175148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	39	147	0	ENST00000257430.4:c.3859dup	p.Ile1287AsnfsTer4	p.I1287Nfs*4	ENST00000257430	NM_000038.5	1286	gaa/gAaa	16/16	1	2	FACETS	0.821	0.684	0.973	0.821	0.684	0.973	CLONAL	1	TRUE	1	0.328650136176688	2		147	289	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0053515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	744	833	4	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.559362406315048	3	FACETS	0.966	0.941	0.991	0.966	0.941	0.991	CLONAL	3	TRUE	0	0.571436686703157	3		837	1155	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913255	NA	P-0053515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	602	627	0	ENST00000369535.4:c.183A>T	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caT	3/7	0.533259972288698	4	FACETS	0.985	0.952	1	0.985	0.952	1	CLONAL	3	TRUE	1	0.571436686703157	4		627	1121	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027541	48027541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587779923	NA	P-0053515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	285	338	0	ENST00000234420.5:c.2419G>A	p.Glu807Lys	p.E807K	ENST00000234420	NM_000179.2	807	Gaa/Aaa	4/10	0.558765504142925	4	FACETS	0.918	0.873	0.964	0.689	0.654	0.723	CLONAL	3	TRUE	0	0.571436686703157	4		338	569	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0053515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	271	550	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	0.571436686703157	3	FACETS	0.931	0.88	0.983	0.931	0.88	0.983	CLONAL	2	TRUE	1	0.571436686703157	3		550	655	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0053515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	161	194	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.550219883592527	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.571436686703157	2		194	264	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7978933	7978933	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0053515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	167	612	0	ENST00000319144.4:c.1634T>G	p.Leu545Arg	p.L545R	ENST00000319144	NM_001139.2	545	cTc/cGc	12/15	0.559362406315048	3	FACETS	0.973	0.896	1	0.324	0.298	0.352	CLONAL	1	TRUE	0	0.571436686703157	3		612	772	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0053529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	272	592	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.778878565751635	2		592	685	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0053529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	223	851	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	1	2	FACETS	0.719	0.671	0.769	0.719	0.671	0.769	SUBCLONAL	1	TRUE	1	0.778878565751635	2		851	796	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159752	20159752	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	203	538	0	ENST00000379607.5:c.7A>G	p.Lys3Glu	p.K3E	ENST00000379607	NM_001412.3	3	Aag/Gag	1/7	0.778878565751635	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.778878565751635	1		538	318	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435213	110435213	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780007007	NA	P-0053529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	220	499	0	ENST00000375856.3:c.3188C>T	p.Ser1063Phe	p.S1063F	ENST00000375856	NM_003749.2	1063	tCc/tTc	1/2	1	2	FACETS	0.928	0.869	0.987	0.928	0.869	0.987	CLONAL	1	TRUE	1	0.778878565751635	2		499	609	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503914	149503914	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56339845	NA	P-0053529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	248	689	0	ENST00000261799.4:c.1922G>A	p.Arg641His	p.R641H	ENST00000261799	NM_002609.3	641	cGc/cAc	14/23	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.778878565751635	2		689	584	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022324	36022324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760138531	NA	P-0053529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	234	814	0	ENST00000358208.4:c.377C>T	p.Ser126Leu	p.S126L	ENST00000358208		126	tCg/tTg	4/12	1	2	FACETS	0.933	0.876	0.991	0.933	0.876	0.991	CLONAL	1	TRUE	1	0.778878565751635	2		814	644	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421621	49421621	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0053529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	297	743	0	ENST00000301067.7:c.14608A>T	p.Lys4870Ter	p.K4870*	ENST00000301067	NM_003482.3	4870	Aag/Tag	47/54	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.778878565751635	2		743	744	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434368	121434368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	234	802	2	ENST00000257555.6:c.1132C>T	p.Pro378Ser	p.P378S	ENST00000257555		378	Ccc/Tcc	6/10	1	2	FACETS	0.849	0.795	0.903	0.849	0.795	0.903	CLONAL	1	TRUE	1	0.778878565751635	2		804	708	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295786	212295786	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	271	577	0	ENST00000342788.4:c.2527G>T	p.Asp843Tyr	p.D843Y	ENST00000342788	NM_005235.2	843	Gat/Tat	21/28	1	2	FACETS	0.998	0.942	1	0.998	0.942	1	CLONAL	1	TRUE	1	0.778878565751635	2		577	697	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845165	128845165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200359079	NA	P-0053529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	336	920	0	ENST00000249373.3:c.659C>T	p.Pro220Leu	p.P220L	ENST00000249373	NM_005631.4	220	cCg/cTg	3/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.778878565751635	2		920	842	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751044	128751044	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs775690959	NA	P-0053529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	237	608	0	ENST00000377970.2:c.581A>G	p.Gln194Arg	p.Q194R	ENST00000377970	NM_002467.4	194	cAg/cGg	2/3	0.738247287322298	4	FACETS	1	0.976	1	0.365	0.341	0.39	CLONAL	1	TRUE	1	0.778878565751635	4		608	988	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0053532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	310	430	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.567541113737486	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.567541113737486	2		430	522	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0053532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	354	285	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.567541113737486	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	4	TRUE	0	0.567541113737486	4		285	483	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0053532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	146	258	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.479727654833709	4	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	2	0.567541113737486	4		258	399	SUCCESS
APC	324	MSKCC	GRCh37	5	112170647	112170647	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0053532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	211	332	0	ENST00000257430.4:c.1744-1G>A		p.X582_splice	ENST00000257430	NM_000038.5	582			0.479727654833709	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.567541113737486	4		332	564	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106096	27106111	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGAAAAACGGATCA	CCAGAAAAACGGATCA	-	novel	NA	P-0053532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	254	594	0	ENST00000324856.7:c.5708_5723del	p.Pro1903GlnfsTer15	p.P1903Qfs*15	ENST00000324856	NM_006015.4	1903	CCAGAAAAACGGATCAca/ca	20/20	0.567541113737486	2	FACETS	0.952	0.904	1	0.952	0.904	1	CLONAL	2	TRUE	0	0.567541113737486	2		594	470	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392066	81392066	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	241	423	0	ENST00000222390.5:c.211G>C	p.Ala71Pro	p.A71P	ENST00000222390	NM_000601.4	71	Gct/Cct	2/18	0.479727654833709	4	FACETS	0.876	0.821	0.932	0.876	0.821	0.932	CLONAL	2	TRUE	2	0.567541113737486	4		423	760	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0053533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	69	446	0	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	0.612358337672539	4	FACETS	0.581	0.506	0.661	0.29	0.253	0.331	SUBCLONAL	1	TRUE	2	0.663356018779463	4		446	596	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0053533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	251	432	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.663356018779463	3	FACETS	0.947	0.896	0.999	0.947	0.896	0.999	CLONAL	2	TRUE	1	0.663356018779463	3		432	532	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098949	47098949	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	132	543	1	ENST00000409792.3:c.6325C>T	p.Arg2109Ter	p.R2109*	ENST00000409792	NM_014159.6	2109	Cga/Tga	15/21	0.663356018779463	3	FACETS	0.756	0.687	0.828	0.378	0.343	0.414	SUBCLONAL	1	TRUE	1	0.663356018779463	3		544	701	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439889	51439889	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	102	436	1	ENST00000262662.1:c.454G>T	p.Val152Phe	p.V152F	ENST00000262662		152	Gtt/Ttt	4/4	0.663356018779463	3	FACETS	0.746	0.669	0.827	0.249	0.223	0.276	SUBCLONAL	1	TRUE	0	0.663356018779463	3		437	549	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599868	10599868	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	481	928	1	ENST00000171111.5:c.1708G>C	p.Gly570Arg	p.G570R	ENST00000171111	NM_203500.1	570	Gga/Cga	5/6	0.57782066535916	2	FACETS	0.869	0.838	0.9	0.869	0.838	0.9	CLONAL	2	TRUE	0	0.663356018779463	2		929	834	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0053542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	139	430	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.373597171062096	3	FACETS	0.894	0.819	0.971	0.894	0.819	0.971	CLONAL	2	TRUE	1	0.373597171062096	3		430	494	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313211	30313211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1449890888	NA	P-0053542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	99	593	0	ENST00000262643.3:c.905C>T	p.Ser302Leu	p.S302L	ENST00000262643	NM_001238.2	302	tCg/tTg	10/12	1	2	FACETS	0.856	0.766	0.952	0.856	0.766	0.952	CLONAL	1	TRUE	1	0.373597171062096	2		593	619	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266064	41266656	+	splice_donor_variant,splice_acceptor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	GCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCAAGATGATGCAGAACTTGCCACACGT	GCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCAAGATGATGCAGAACTTGCCACACGT	-	novel	NA	P-0053542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	105	309	0	ENST00000349496.5:c.63_455del		p.X21_splice	ENST00000349496	NM_001904.3	21	GCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCAAGATGATGCAGAACTTGCCACACGT/-	3-4/15	0.373597171062096	2	FACETS	1	0.98	1	0.685	0.619	0.755	CLONAL	1	TRUE	0	0.373597171062096	2		309	410	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952063	178952063	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	77	421	0	ENST00000263967.3:c.3118A>T	p.Met1040Leu	p.M1040L	ENST00000263967	NM_006218.2	1040	Atg/Ttg	21/21	1	2	FACETS	0.945	0.834	1	0.945	0.834	1	CLONAL	1	TRUE	1	0.373597171062096	2		421	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057519990	NA	P-0053543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	72	516	1	ENST00000269305.4:c.796G>T	p.Gly266Ter	p.G266*	ENST00000269305	NM_001126112.2	266	Gga/Tga	8/11	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.14	2		517	929	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602799	10602799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1419	55	862	0	ENST00000171111.5:c.779G>T	p.Arg260Leu	p.R260L	ENST00000171111	NM_203500.1	260	cGa/cTa	3/6	1	2	FACETS	0.533	0.454	0.621	0.533	0.454	0.621	SUBCLONAL	1	TRUE	1	0.14	2		862	1474	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461038	120461038	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	73	392	0	ENST00000256646.2:c.5920G>T	p.Asp1974Tyr	p.D1974Y	ENST00000256646	NM_024408.3	1974	Gat/Tat	32/34	1	2	FACETS	0.762	0.666	0.866	1	0.975	1	SUBCLONAL	2	TRUE	1	0.14	2		392	684	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090424	77090424	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	51	317	0	ENST00000356341.3:c.301G>C	p.Glu101Gln	p.E101Q	ENST00000356341	NM_002576.4	101	Gag/Cag	4/15	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.14	2		317	586	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856234	111856237	+	frameshift_variant	Frame_Shift_Del	DEL	GCCC	GCCC	ACA	novel	NA	P-0053543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	21	161	1	ENST00000341259.2:c.285_288delinsACA	p.Pro96HisfsTer101	p.P96Hfs*101	ENST00000341259	NM_005475.2	95	ggGCCC/ggACA	2/8	1	2	FACETS	0.804	0.619	1	0.804	0.619	1	CLONAL	1	TRUE	1	0.14	2		162	373	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533618	63533618	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1247	91	757	0	ENST00000307078.5:c.1536G>C	p.Lys512Asn	p.K512N	ENST00000307078	NM_004655.3	512	aaG/aaC	6/11	1	2	FACETS	0.972	0.86	1	0.972	0.86	1	CLONAL	1	TRUE	1	0.14	2		757	1338	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0053544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	212	550	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.904	0.843	0.966	0.904	0.843	0.966	CLONAL	1	TRUE	1	0.69	2		550	680	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352259	70352259	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	311	763	2	ENST00000374080.3:c.4291del	p.Leu1431SerfsTer14	p.L1431Sfs*14	ENST00000374080		1429	gCc/gc	31/45	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.69	2		765	799	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	124	429	0				ENST00000310581	NM_198253.2	-/1132			0.364528307565529	5	FACETS	1	0.93	1	1	0.93	1	INDETERMINATE	3	TRUE	2	0.889658236717654	5		429	217	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545740	106545740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	68	614	0	ENST00000359195.3:c.3217G>A	p.Glu1073Lys	p.E1073K	ENST00000359195	NM_002649.2	1073	Gaa/Aaa	11/11	0.697956171615079	6	FACETS	0.624	0.542	0.712	0.156	0.135	0.178	SUBCLONAL	1	TRUE	2	0.889658236717654	6		614	681	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856607	111856607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs982851788	NA	P-0053545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	126	195	0	ENST00000341259.2:c.658G>A	p.Gly220Arg	p.G220R	ENST00000341259	NM_005475.2	220	Ggg/Agg	2/8	0.742288500443214	3	FACETS	0.901	0.838	0.965	0.901	0.838	0.965	CLONAL	2	TRUE	1	0.889658236717654	3		195	227	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571819	64571819	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	193	856	0	ENST00000312049.6:c.1820G>A	p.Arg607His	p.R607H	ENST00000312049	NM_130799.2	607	cGc/cAc	10/10	0.1465483912263	5	FACETS	0.906	0.844	0.969	0.453	0.422	0.485	INDETERMINATE	2	TRUE	1	0.889658236717654	5		856	559	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0053546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	118	350	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.391860797414854	2		350	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0053546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	192	649	1	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.391860797414854	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.391860797414854	1		650	662	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405942	49405942	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	123	575	0	ENST00000418115.1:c.196T>A	p.Tyr66Asn	p.Y66N	ENST00000418115	NM_001664.2	66	Tat/Aat	3/5	0.220072614806068	1	FACETS	0.654	0.591	0.72	0.654	0.591	0.72	INDETERMINATE	1	TRUE	0	0.391860797414854	1		575	772	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435462	49435462	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	231	741	0	ENST00000301067.7:c.6210del	p.His2071ThrfsTer23	p.H2071Tfs*23	ENST00000301067	NM_003482.3	2070	gcT/gc	30/54	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.391860797414854	2		741	997	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106577	27106615	+	frameshift_variant	Frame_Shift_Del	DEL	CACTCGCCAACATCTCGGGGCAGTTGGACCTATCTCCAT	CACTCGCCAACATCTCGGGGCAGTTGGACCTATCTCCAT	A	novel	NA	P-0053546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	205	729	0	ENST00000324856.7:c.6188_6226delinsA	p.Thr2063LysfsTer23	p.T2063Kfs*23	ENST00000324856	NM_006015.4	2063	aCACTCGCCAACATCTCGGGGCAGTTGGACCTATCTCCATac/aAac	20/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.391860797414854	2		729	964	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0053547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	242	889	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.46002771660152	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.477360317763961	1		889	738	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955394	48955394	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886043247	NA	P-0053547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	59	219	0	ENST00000267163.4:c.1510C>T	p.Gln504Ter	p.Q504*	ENST00000267163	NM_000321.2	504	Cag/Tag	17/27	0.477360317763961	3	FACETS	0.837	0.744	0.929	0.837	0.744	0.929	CLONAL	3	TRUE	0	0.477360317763961	3		219	122	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212090	142212090	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	87	529	0	ENST00000350721.4:c.5962G>C	p.Glu1988Gln	p.E1988Q	ENST00000350721	NM_001184.3	1988	Gaa/Caa	35/47	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.477360317763961	2		529	340	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	131	411	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.154482735530304	4	FACETS	0.956	0.872	1	0.956	0.872	1	INDETERMINATE	2	TRUE	2	0.34975686917657	4		411	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555526101	NA	P-0053548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	375	667	0	ENST00000269305.4:c.497C>G	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tGa	5/11	0.34975686917657	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.34975686917657	2		667	1031	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575080	48575080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	93	295	0	ENST00000342988.3:c.274C>T	p.His92Tyr	p.H92Y	ENST00000342988	NM_005359.5	92	Cat/Tat	3/12	0.34975686917657	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.34975686917657	1		295	327	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299824	15299824	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	204	816	0	ENST00000263388.2:c.1354C>A	p.Gln452Lys	p.Q452K	ENST00000263388	NM_000435.2	452	Cag/Aag	8/33	0.312478857760389	3	FACETS	1	0.979	1	0.576	0.533	0.621	CLONAL	1	TRUE	1	0.34975686917657	3		816	1189	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97876969	97876969	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0053548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	65	518	0	ENST00000289081.3:c.1096C>T	p.Gln366Ter	p.Q366*	ENST00000289081	NM_000136.2	366	Cag/Tag	12/15	1	2	FACETS	0.47	0.407	0.54	0.47	0.407	0.54	SUBCLONAL	1	TRUE	1	0.34975686917657	2		518	790	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97887448	97887448	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	125	511	0	ENST00000289081.3:c.916G>C	p.Asp306His	p.D306H	ENST00000289081	NM_000136.2	306	Gat/Cat	10/15	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.34975686917657	2		511	663	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570287	87570287	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	17	674	1	ENST00000277120.3:c.2027T>A	p.Ile676Asn	p.I676N	ENST00000277120		676	aTc/aAc	17/19	1	2	FACETS	0.759	0.567	0.986	0.759	0.567	0.986	CLONAL	1	TRUE	1	0.187483610300682	2		675	239	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	70	429	0				ENST00000310581	NM_198253.2	-/1132			0.277033809142248	4	FACETS	1	0.951	1	0.749	0.668	0.832	INDETERMINATE	2	TRUE	1	0.55325191734491	4		429	175	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	268	330	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.55325191734491	4	FACETS	0.902	0.855	0.949	0.902	0.855	0.949	CLONAL	3	TRUE	1	0.55325191734491	4		330	556	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1022604	1022604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	134	436	0	ENST00000358495.3:c.1210C>T	p.His404Tyr	p.H404Y	ENST00000358495	NM_134424.2	404	Cat/Tat	12/12	0.359668542309518	4	FACETS	0.844	0.772	0.917			1	CLONAL	2	TRUE	NA	0.55325191734491	4		436	446	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918502	44918502	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	112	211	0	ENST00000377967.4:c.985C>T	p.Gln329Ter	p.Q329*	ENST00000377967	NM_021140.2	329	Cag/Tag	12/29	0.480433651195024	2	FACETS	1	0.98	1			1	CLONAL	2	TRUE	NA	0.55325191734491	2		211	176	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280028	66280028	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	49	239	0	ENST00000273854.3:c.1661G>A	p.Arg554Lys	p.R554K	ENST00000273854	NM_004439.5	554	aGa/aAa	7/18	1	2	FACETS	0.968	0.833	1	0.968	0.833	1	CLONAL	1	TRUE	1	0.55325191734491	2		239	183	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998472	100998472	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11571150	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	63	565	0	ENST00000325455.5:c.1330G>T	p.Ala444Ser	p.A444S	ENST00000325455	NM_001202474.3	444	Gcc/Tcc	1/8	1	2	FACETS	0.977	0.857	1	0.977	0.857	1	CLONAL	1	TRUE	1	0.55325191734491	2		565	233	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457304	67457304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223765	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	108	829	2	ENST00000327367.4:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000327367	NM_005902.3	93	cGa/cAa	2/9	0.541586602980224	3	FACETS	0.948	0.854	1	0.474	0.427	0.523	CLONAL	1	TRUE	1	0.55325191734491	3		831	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577519	7577527	+	inframe_deletion	In_Frame_Del	DEL	GATGGTGAG	GATGGTGAG	-	novel	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	194	709	0	ENST00000269305.4:c.754_762del	p.Leu252_Ile254del	p.L252_I254del	ENST00000269305	NM_001126112.2	252	CTCACCATC/-	7/11	0.465628251011008	2	FACETS	0.819	0.768	0.871	0.819	0.768	0.871	CLONAL	2	TRUE	0	0.55325191734491	2		709	428	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	184	784	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.519605820194257	2	FACETS	0.809	0.757	0.862	0.809	0.757	0.862	CLONAL	2	TRUE	0	0.55325191734491	2		784	411	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981851	201981852	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	119	920	0	ENST00000359651.3:c.567dup	p.Ser190LeufsTer6	p.S190Lfs*6	ENST00000359651		188	gcc/gCcc	4/8	0.541586602980224	3	FACETS	0.825	0.746	0.908	0.412	0.373	0.454	CLONAL	1	TRUE	1	0.55325191734491	3		920	666	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716304	52716304	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	110	807	0	ENST00000322088.6:c.748C>T	p.Gln250Ter	p.Q250*	ENST00000322088	NM_014225.5	250	Cag/Tag	6/15	0.477335009720135	3	FACETS	1	0.92	1	0.511	0.461	0.563	CLONAL	1	TRUE	1	0.55325191734491	3		807	497	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035986	47035986	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	244	403	0	ENST00000377604.3:c.663+1G>T		p.X221_splice	ENST00000377604	NM_001204468.1	221			0.480433651195024	2	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.55325191734491	2		403	356	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368229	45368229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	66	408	0	ENST00000262160.6:c.1373C>T	p.Ser458Phe	p.S458F	ENST00000262160	NM_005901.5	458	tCc/tTc	11/11	0.541586602980224	3	FACETS	0.946	0.827	1	0.473	0.413	0.536	CLONAL	1	TRUE	1	0.55325191734491	3		408	322	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189388	99189388	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	144	569	0	ENST00000074304.5:c.2644G>A	p.Glu882Lys	p.E882K	ENST00000074304	NM_001134224.1	882	Gag/Aag	24/26	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.55325191734491	2		569	409	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117870648	117870648	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	68	379	0	ENST00000297338.2:c.424G>C	p.Glu142Gln	p.E142Q	ENST00000297338	NM_006265.2	142	Gag/Cag	5/14	0.541586602980224	3	FACETS	0.805	0.703	0.913	0.402	0.351	0.457	CLONAL	1	TRUE	1	0.55325191734491	3		379	390	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309797	65309797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	103	585	0	ENST00000342505.4:c.2353G>A	p.Glu785Lys	p.E785K	ENST00000342505	NM_002227.2	785	Gaa/Aaa	17/25	0.541586602980224	3	FACETS	1	0.907	1	0.505	0.454	0.558	CLONAL	1	TRUE	1	0.55325191734491	3		585	471	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343259	118343259	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	59	351	0	ENST00000534358.1:c.1385C>G	p.Ser462Ter	p.S462*	ENST00000534358	NM_005933.3	462	tCa/tGa	3/36	1	2	FACETS	0.961	0.838	1	0.961	0.838	1	CLONAL	1	TRUE	1	0.55325191734491	2		351	222	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352717	118352717	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	88	546	0	ENST00000534358.1:c.3922C>T	p.Gln1308Ter	p.Q1308*	ENST00000534358	NM_005933.3	1308	Cag/Tag	7/36	1	2	FACETS	0.828	0.739	0.923	0.828	0.739	0.923	CLONAL	1	TRUE	1	0.55325191734491	2		546	384	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434618	49434618	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	206	1011	0	ENST00000301067.7:c.6935C>G	p.Ser2312Ter	p.S2312*	ENST00000301067	NM_003482.3	2312	tCa/tGa	31/54	0.534997445654828	5	FACETS	1	0.946	1	0.678	0.632	0.725	CLONAL	2	TRUE	2	0.55325191734491	5		1011	670	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801807	3801807	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	171	522	0	ENST00000262367.5:c.3699G>T	p.Arg1233Ser	p.R1233S	ENST00000262367	NM_004380.2	1233	agG/agT	20/31	0.477335009720135	3	FACETS	0.977	0.91	1	0.977	0.91	1	CLONAL	2	TRUE	1	0.55325191734491	3		522	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579356	7579356	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	254	809	0	ENST00000269305.4:c.331C>G	p.Leu111Val	p.L111V	ENST00000269305	NM_001126112.2	111	Ctg/Gtg	4/11	0.465628251011008	2	FACETS	0.904	0.856	0.951	0.904	0.856	0.951	CLONAL	2	TRUE	0	0.55325191734491	2		809	508	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16021242	16021242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	123	320	0	ENST00000268712.3:c.2015G>A	p.Arg672Gln	p.R672Q	ENST00000268712	NM_006311.3	672	cGa/cAa	18/46	0.465628251011008	2	FACETS	0.896	0.829	0.964	0.896	0.829	0.964	CLONAL	2	TRUE	0	0.55325191734491	2		320	248	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47684617	47684617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	78	417	1	ENST00000347630.2:c.832G>A	p.Asp278Asn	p.D278N	ENST00000347630	NM_001007230.1	278	Gac/Aac	9/11	0.406081147809456	4	FACETS	0.878	0.773	0.989	0.439	0.386	0.495	CLONAL	1	TRUE	2	0.55325191734491	4		418	499	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621952	1621952	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	105	1008	0	ENST00000344749.5:c.840del	p.Ala281GlnfsTer3	p.A281Qfs*3	ENST00000344749	NM_001136139.2	280	ggA/gg	11/19	1	2	FACETS	0.796	0.717	0.879	0.796	0.717	0.879	SUBCLONAL	1	TRUE	1	0.55325191734491	2		1008	477	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919777	96919777	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	88	586	0	ENST00000258439.3:c.486G>C	p.Lys162Asn	p.K162N	ENST00000258439	NM_001193304.2	162	aaG/aaC	4/4	1	2	FACETS	0.673	0.598	0.751	0.673	0.598	0.751	SUBCLONAL	1	TRUE	1	0.55325191734491	2		586	473	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104719	209104719	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	51	343	1	ENST00000345146.2:c.859T>C	p.Ser287Pro	p.S287P	ENST00000345146	NM_005896.2	287	Tct/Cct	8/10	1	2	FACETS	0.931	0.803	1	0.931	0.803	1	CLONAL	1	TRUE	1	0.55325191734491	2		344	198	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248429	212248429	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	51	348	0	ENST00000342788.4:c.3838G>C	p.Glu1280Gln	p.E1280Q	ENST00000342788	NM_005235.2	1280	Gag/Cag	28/28	1	2	FACETS	0.955	0.824	1	0.955	0.824	1	CLONAL	1	TRUE	1	0.55325191734491	2		348	193	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138400888	138400888	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	238	395	1	ENST00000289153.2:c.2426-1G>C		p.X809_splice	ENST00000289153	NM_006219.2	809			0.465628251011008	2	FACETS	0.945	0.895	0.996	0.945	0.895	0.996	CLONAL	2	TRUE	0	0.55325191734491	2		396	455	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413749	138413749	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	211	322	2	ENST00000289153.2:c.1771C>T	p.Leu591Phe	p.L591F	ENST00000289153	NM_006219.2	591	Ctt/Ttt	12/22	0.465628251011008	2	FACETS	0.961	0.907	1	0.961	0.907	1	CLONAL	2	TRUE	0	0.55325191734491	2		324	397	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504384	186504384	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	36	345	0	ENST00000323963.5:c.721G>C	p.Glu241Gln	p.E241Q	ENST00000323963		241	Gaa/Caa	7/11	0.55325191734491	4	FACETS	0.536	0.441	0.642	0.179	0.147	0.214	SUBCLONAL	1	TRUE	1	0.55325191734491	4		345	377	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524066	187524066	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	80	591	0	ENST00000441802.2:c.11473C>G	p.Gln3825Glu	p.Q3825E	ENST00000441802	NM_005245.3	3825	Cag/Gag	20/27	0.55325191734491	3	FACETS	0.881	0.78	0.989			1	CLONAL	1	TRUE	NA	0.55325191734491	3		591	419	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117739630	117739630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	94	305	0	ENST00000368508.3:c.163G>A	p.Glu55Lys	p.E55K	ENST00000368508	NM_002944.2	55	Gaa/Aaa	2/43	0.477335009720135	3	FACETS	1	0.98	1	0.709	0.638	0.782	CLONAL	1	TRUE	1	0.55325191734491	3		305	306	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099403	157099423	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAG	CAGCAGCAGCAGCAGCAGCAG	-	rs587779743	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	48	367	0	ENST00000346085.5:c.342_362del	p.Gln125_Gln131del	p.Q125_Q131del	ENST00000346085	NM_020732.3	114	CAGCAGCAGCAGCAGCAGCAG/-	1/20	0.10992733265804	0	FACETS	0.396	0.339	0.456			1	INDETERMINATE	1	TRUE	0	0.55325191734491	0		367	196	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346361	152346361	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs779794261	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	135	525	0	ENST00000359321.1:c.209C>G	p.Ser70Ter	p.S70*	ENST00000359321	NM_005431.1	70	tCa/tGa	3/3	0.512566240186482	4	FACETS	0.92	0.844	0.998	0.92	0.844	0.998	CLONAL	2	TRUE	2	0.55325191734491	4		525	412	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93629450	93629450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868127003	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	138	327	1	ENST00000375746.1:c.884C>T	p.Ser295Leu	p.S295L	ENST00000375746	NM_001174167.1	295	tCa/tTa	7/14	0.519605820194257	2	FACETS	0.945	0.879	1	0.945	0.879	1	CLONAL	2	TRUE	0	0.55325191734491	2		328	264	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021631	31021638	+	frameshift_variant	Frame_Shift_Del	DEL	GATCGTCA	GATCGTCA	TTGT	novel	NA	P-0053564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	164	521	1	ENST00000375687.4:c.1630_1637delinsTTGT	p.Asp544LeufsTer158	p.D544Lfs*158	ENST00000375687	NM_015338.5	544	GATCGTCAg/TTGTg	12/13	0.277033809142248	4	FACETS	0.856	0.791	0.923	0.571	0.527	0.615	INDETERMINATE	2	TRUE	1	0.55325191734491	4		522	538	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	40	315	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.568	0.473	0.674	0.568	0.473	0.674	SUBCLONAL	1	TRUE	1	0.381554300101409	2		315	369	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	31	179	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.677	0.551	0.819	0.677	0.551	0.819	SUBCLONAL	1	TRUE	1	0.381554300101409	2		179	240	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799299	42799300	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1158987717	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	40	425	1	ENST00000575354.2:c.4790dup	p.Pro1598ThrfsTer16	p.P1598Tfs*16	ENST00000575354	NM_015125.3	1595	tcc/tCcc	20/20	1	2	FACETS	0.779	0.651	0.92	0.779	0.651	0.92	CLONAL	1	TRUE	1	0.381554300101409	2		426	269	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	212	1003	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.803	0.749	0.858	1	0.993	1	CLONAL	2	TRUE	1	0.381554300101409	2		1007	692	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	40	561	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.589	0.49	0.698	0.589	0.49	0.698	SUBCLONAL	1	TRUE	1	0.381554300101409	2		561	356	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	40	221	0	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	1	2	FACETS	0.67	0.559	0.793	0.67	0.559	0.793	SUBCLONAL	1	TRUE	1	0.381554300101409	2		221	313	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298740	15298740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	92	981	4	ENST00000263388.2:c.1558G>A	p.Ala520Thr	p.A520T	ENST00000263388	NM_000435.2	520	Gcc/Acc	10/33	1	2	FACETS	0.617	0.547	0.691	0.617	0.547	0.691	SUBCLONAL	1	TRUE	1	0.381554300101409	2		985	782	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260241	10260241	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555690467	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	116	724	1	ENST00000340748.4:c.2426C>T	p.Ser809Leu	p.S809L	ENST00000340748		809	tCg/tTg	25/40	1	2	FACETS	0.905	0.817	0.998	0.905	0.817	0.998	CLONAL	1	TRUE	1	0.381554300101409	2		725	672	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241722	55241722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1051753269	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	89	596	0	ENST00000275493.2:c.2170G>A	p.Gly724Ser	p.G724S	ENST00000275493	NM_005228.3	724	Ggc/Agc	18/28	1	2	FACETS	0.81	0.719	0.906	0.81	0.719	0.906	CLONAL	1	TRUE	1	0.381554300101409	2		596	576	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857524	9857524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778230379	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	38	436	0	ENST00000330684.3:c.3877G>A	p.Asp1293Asn	p.D1293N	ENST00000330684	NM_001134407.1	1293	Gat/Aat	13/13	1	2	FACETS	0.577	0.478	0.687	0.577	0.478	0.687	SUBCLONAL	1	TRUE	1	0.381554300101409	2		436	345	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807829	1807829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1336255288	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	125	1146	1	ENST00000260795.2:c.1888G>A	p.Val630Met	p.V630M	ENST00000260795		630	Gtg/Atg	13/17	1	2	FACETS	0.863	0.782	0.949	0.863	0.782	0.949	CLONAL	1	TRUE	1	0.381554300101409	2		1147	759	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882050	36882050	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs780753361	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	102	965	3	ENST00000358127.4:c.963del	p.Ala322LeufsTer11	p.A322Lfs*11	ENST00000358127	NM_001280556.1	321	ccC/cc	8/10	1	2	FACETS	0.709	0.634	0.789	0.709	0.634	0.789	SUBCLONAL	1	TRUE	1	0.381554300101409	2		968	754	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933744	49933744	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs750582514	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	98	844	2	ENST00000296474.3:c.2533C>T	p.Arg845Ter	p.R845*	ENST00000296474	NM_002447.2	845	Cga/Tga	10/20	1	2	FACETS	0.801	0.716	0.892	0.801	0.716	0.892	CLONAL	1	TRUE	1	0.381554300101409	2		846	641	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	61	442	4	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.788	0.682	0.902	0.788	0.682	0.902	CLONAL	1	TRUE	1	0.381554300101409	2		446	406	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411530	63411530	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	110	442	1	ENST00000330258.3:c.1637del	p.Leu546CysfsTer16	p.L546Cfs*16	ENST00000330258	NM_152424.3	546	tTg/tg	2/2	1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.381554300101409	1		443	358	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	75	405	1	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	0.855	0.751	0.965	0.855	0.751	0.965	CLONAL	1	TRUE	1	0.381554300101409	2		406	460	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919935	50919935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1044937882	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	118	1096	1	ENST00000440232.2:c.3022C>T	p.Arg1008Cys	p.R1008C	ENST00000440232	NM_002691.3	1008	Cgc/Tgc	24/27	1	2	FACETS	0.812	0.733	0.895	0.812	0.733	0.895	CLONAL	1	TRUE	1	0.381554300101409	2		1097	762	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920452	114920452	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	84	370	0	ENST00000543371.1:c.1391+2T>C		p.X464_splice	ENST00000543371	NM_001198531.1	464			1	2	FACETS	0.931	0.825	1	0.931	0.825	1	CLONAL	1	TRUE	1	0.381554300101409	2		370	473	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383793	15383793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768982122	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	112	804	1	ENST00000263377.2:c.118G>A	p.Ala40Thr	p.A40T	ENST00000263377	NM_058243.2	40	Gca/Aca	2/20	1	2	FACETS	0.806	0.726	0.892	0.806	0.726	0.892	CLONAL	1	TRUE	1	0.381554300101409	2		805	728	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240271	5240271	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	112	983	1	ENST00000357368.4:c.1643del	p.Pro548ArgfsTer37	p.P548Rfs*37	ENST00000357368	NM_002850.3	548	cCg/cg	12/38	1	2	FACETS	0.91	0.82	1	0.91	0.82	1	CLONAL	1	TRUE	1	0.381554300101409	2		984	645	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618930	37618930	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	84	542	1	ENST00000447079.4:c.610del	p.Arg204GlyfsTer134	p.R204Gfs*134	ENST00000447079	NM_015083.1	202	cgA/cg	1/14	1	2	FACETS	0.832	0.737	0.934	0.832	0.737	0.934	CLONAL	1	TRUE	1	0.381554300101409	2		543	529	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922363	178922363	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	49	263	0	ENST00000263967.3:c.1132T>C	p.Cys378Arg	p.C378R	ENST00000263967	NM_006218.2	378	Tgt/Cgt	6/21	1	2	FACETS	0.865	0.737	1	0.865	0.737	1	CLONAL	1	TRUE	1	0.381554300101409	2		263	297	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107749	30107749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760459161	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	61	396	0	ENST00000331968.5:c.931C>T	p.Arg311Cys	p.R311C	ENST00000331968	NM_002742.2	311	Cgt/Tgt	6/18	1	2	FACETS	0.574	0.495	0.66	0.574	0.495	0.66	SUBCLONAL	1	TRUE	1	0.381554300101409	2		396	557	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372092	55372092	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	63	627	0	ENST00000297316.4:c.782G>C	p.Gly261Ala	p.G261A	ENST00000297316	NM_022454.3	261	gGc/gCc	2/2	1	2	FACETS	0.723	0.626	0.826	0.723	0.626	0.826	SUBCLONAL	1	TRUE	1	0.381554300101409	2		627	457	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209593	98209593	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	85	826	1	ENST00000331920.6:c.3945del	p.Tyr1316ThrfsTer56	p.Y1316Tfs*56	ENST00000331920	NM_000264.3	1315	ccC/cc	23/24	1	2	FACETS	0.679	0.601	0.763	0.679	0.601	0.763	SUBCLONAL	1	TRUE	1	0.381554300101409	2		827	656	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437223	220437223	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	106	1166	3	ENST00000243786.2:c.132del	p.Ala45ArgfsTer2	p.A45Rfs*2	ENST00000243786	NM_002191.3	43	Ccc/cc	1/2	1	2	FACETS	0.723	0.648	0.803	0.723	0.648	0.803	SUBCLONAL	1	TRUE	1	0.381554300101409	2		1169	768	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562181	21562181	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769047956	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	169	1047	1	ENST00000382592.4:c.1738G>T	p.Val580Phe	p.V580F	ENST00000382592	NM_014572.2	580	Gtc/Ttc	4/8	1	2	FACETS	0.92	0.845	0.998	0.92	0.845	0.998	CLONAL	1	TRUE	1	0.381554300101409	2		1048	963	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456447	32456447	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	89	672	0	ENST00000332351.3:c.445G>A	p.Ala149Thr	p.A149T	ENST00000332351	NM_024426.4	149	Gcg/Acg	1/10	1	2	FACETS	0.889	0.79	0.993	0.889	0.79	0.993	CLONAL	1	TRUE	1	0.381554300101409	2		672	525	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651316	45651316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756890702	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	90	595	0	ENST00000407780.3:c.709G>A	p.Gly237Arg	p.G237R	ENST00000407780	NM_001283052.1	237	Gga/Aga	5/7	1	2	FACETS	0.77	0.684	0.861	0.77	0.684	0.861	SUBCLONAL	1	TRUE	1	0.381554300101409	2		595	613	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951811	2951811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146334064	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	88	662	0	ENST00000396946.4:c.3139G>A	p.Ala1047Thr	p.A1047T	ENST00000396946	NM_032415.4	1047	Gcc/Acc	23/25	1	2	FACETS	0.79	0.701	0.885	0.79	0.701	0.885	SUBCLONAL	1	TRUE	1	0.381554300101409	2		662	584	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627983	37627983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375471633	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	119	903	1	ENST00000249071.6:c.277G>A	p.Val93Ile	p.V93I	ENST00000249071	NM_002872.4	93	Gtc/Atc	4/7	1	2	FACETS	0.89	0.804	0.98	0.89	0.804	0.98	CLONAL	1	TRUE	1	0.381554300101409	2		904	701	SUCCESS
MET	4233	MSKCC	GRCh37	7	116422111	116422111	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	57	331	0	ENST00000397752.3:c.3596del	p.Lys1199SerfsTer49	p.K1199Sfs*49	ENST00000397752	NM_000245.2	1198	Aaa/aa	18/21	1	2	FACETS	0.695	0.598	0.8	0.695	0.598	0.8	SUBCLONAL	1	TRUE	1	0.381554300101409	2		331	430	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685314	89685314	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	28	86	0	ENST00000371953.3:c.209T>A	p.Leu70His	p.L70H	ENST00000371953	NM_000314.4	70	cTt/cAt	3/9	1	2	FACETS	0.768	0.619	0.936	0.768	0.619	0.936	CLONAL	1	TRUE	1	0.381554300101409	2		86	191	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520552	176520552	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	117	968	1	ENST00000292408.4:c.1397G>T	p.Arg466Met	p.R466M	ENST00000292408	NM_213647.1	466	aGg/aTg	10/18	1	2	FACETS	0.837	0.755	0.923	0.837	0.755	0.923	CLONAL	1	TRUE	1	0.381554300101409	2		969	733	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187203	11187203	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	52	528	0	ENST00000361445.4:c.6217-2A>G		p.X2073_splice	ENST00000361445	NM_004958.3	2073			1	2	FACETS	0.695	0.594	0.806	0.695	0.594	0.806	SUBCLONAL	1	TRUE	1	0.381554300101409	2		528	392	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17371343	17371344	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	68	472	0	ENST00000375499.3:c.112dup	p.Arg38ProfsTer25	p.R38Pfs*25	ENST00000375499	NM_003000.2	38	cgt/cCgt	2/8	1	2	FACETS	0.684	0.596	0.779	0.684	0.596	0.779	SUBCLONAL	1	TRUE	1	0.381554300101409	2		472	521	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256520	115256520	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	101	491	0	ENST00000369535.4:c.191A>G	p.Tyr64Cys	p.Y64C	ENST00000369535	NM_002524.4	64	tAc/tGc	3/7	1	2	FACETS	0.968	0.868	1	0.968	0.868	1	CLONAL	1	TRUE	1	0.381554300101409	2		491	547	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262200	115262200	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	63	310	1	ENST00000438362.2:c.2354G>A	p.Cys785Tyr	p.C785Y	ENST00000438362	NM_001242891.1	785	tGt/tAt	18/20	1	2	FACETS	0.739	0.641	0.845	0.739	0.641	0.845	SUBCLONAL	1	TRUE	1	0.381554300101409	2		311	447	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851540	63851540	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	82	598	0	ENST00000279873.7:c.2318T>C	p.Phe773Ser	p.F773S	ENST00000279873	NM_032199.2	773	tTt/tCt	10/10	1	2	FACETS	0.867	0.766	0.973	0.867	0.766	0.973	CLONAL	1	TRUE	1	0.381554300101409	2		598	496	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977260	85977260	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	29	79	0	ENST00000263360.6:c.860+2T>C		p.X287_splice	ENST00000263360	NM_003797.3	287			1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.381554300101409	2		79	146	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343330	118343330	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	57	350	0	ENST00000534358.1:c.1456A>G	p.Thr486Ala	p.T486A	ENST00000534358	NM_005933.3	486	Acc/Gcc	3/36	1	2	FACETS	0.876	0.756	1	0.876	0.756	1	CLONAL	1	TRUE	1	0.381554300101409	2		350	341	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466910	18466910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	41	288	0	ENST00000266497.5:c.1049G>A	p.Gly350Glu	p.G350E	ENST00000266497		350	gGg/gAg	5/31	1	2	FACETS	0.702	0.587	0.829	0.702	0.587	0.829	SUBCLONAL	1	TRUE	1	0.381554300101409	2		288	306	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800870	18800870	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	19	320	0	ENST00000266497.5:c.4249del	p.Thr1417LeufsTer24	p.T1417Lfs*24	ENST00000266497		1416	Aaa/aa	31/31	1	2	FACETS	0.305	0.231	0.391	0.305	0.231	0.391	SUBCLONAL	1	TRUE	1	0.381554300101409	2		320	327	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123712	46123712	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	43	304	1	ENST00000334344.6:c.92+1G>A		p.X31_splice	ENST00000334344	NM_152641.2	31			1	2	FACETS	0.972	0.82	1	0.972	0.82	1	CLONAL	1	TRUE	1	0.381554300101409	2		305	232	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434607	49434607	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	41	1084	0	ENST00000301067.7:c.6946C>A	p.Leu2316Met	p.L2316M	ENST00000301067	NM_003482.3	2316	Ctg/Atg	31/54	1	2	FACETS	0.273	0.227	0.326	0.273	0.227	0.326	SUBCLONAL	1	TRUE	1	0.381554300101409	2		1084	786	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110066	115110066	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	77	902	1	ENST00000257566.3:c.1812del	p.Tyr605ThrfsTer27	p.Y605Tfs*27	ENST00000257566	NM_016569.3	604	ccC/cc	8/8	1	2	FACETS	0.612	0.538	0.693	0.612	0.538	0.693	SUBCLONAL	1	TRUE	1	0.381554300101409	2		903	659	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592612	28592612	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	75	362	0	ENST00000241453.7:c.2533A>G	p.Arg845Gly	p.R845G	ENST00000241453	NM_004119.2	845	Agg/Ggg	20/24	1	2	FACETS	0.98	0.864	1	0.98	0.864	1	CLONAL	1	TRUE	1	0.381554300101409	2		362	401	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89383424	89383424	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	110	732	0	ENST00000301030.4:c.4C>T	p.Pro2Ser	p.P2S	ENST00000301030	NM_001256183.1	2	Ccc/Tcc	3/13	1	2	FACETS	0.89	0.801	0.984	0.89	0.801	0.984	CLONAL	1	TRUE	1	0.381554300101409	2		732	648	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89865616	89865616	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	90	583	1	ENST00000389301.3:c.851G>T	p.Gly284Val	p.G284V	ENST00000389301	NM_000135.2	284	gGa/gTa	10/43	1	2	FACETS	0.899	0.8	1	0.899	0.8	1	CLONAL	1	TRUE	1	0.381554300101409	2		584	525	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667816	37667816	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	71	397	0	ENST00000447079.4:c.2701T>C	p.Tyr901His	p.Y901H	ENST00000447079	NM_015083.1	901	Tac/Cac	8/14	1	2	FACETS	0.698	0.61	0.793	0.698	0.61	0.793	SUBCLONAL	1	TRUE	1	0.381554300101409	2		397	533	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226439	2226439	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	155	1129	0	ENST00000398665.3:c.3919A>G	p.Ser1307Gly	p.S1307G	ENST00000398665	NM_032482.2	1307	Agc/Ggc	27/28	1	2	FACETS	0.924	0.846	1	0.924	0.846	1	CLONAL	1	TRUE	1	0.381554300101409	2		1129	879	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144458	11144458	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	116	848	1	ENST00000358026.2:c.3790A>G	p.Thr1264Ala	p.T1264A	ENST00000358026	NM_001128849.1	1264	Acg/Gcg	27/36	1	2	FACETS	0.762	0.687	0.842	0.762	0.687	0.842	SUBCLONAL	1	TRUE	1	0.381554300101409	2		849	798	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285142	15285142	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	129	1038	0	ENST00000263388.2:c.4473G>T	p.Glu1491Asp	p.E1491D	ENST00000263388	NM_000435.2	1491	gaG/gaT	25/33	1	2	FACETS	0.839	0.761	0.921	0.839	0.761	0.921	CLONAL	1	TRUE	1	0.381554300101409	2		1038	806	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311618	15311619	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGC	rs746497955	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	33	213	0	ENST00000263388.2:c.96_98dup	p.Leu33dup	p.L33dup	ENST00000263388	NM_000435.2	33	cta/ctGCTa	1/33	1	2	FACETS	0.94	0.774	1	0.94	0.774	1	CLONAL	1	TRUE	1	0.381554300101409	2		213	184	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273102	18273102	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	103	944	0	ENST00000222254.8:c.992A>G	p.Tyr331Cys	p.Y331C	ENST00000222254	NM_005027.3	331	tAc/tGc	8/16	1	2	FACETS	0.724	0.648	0.805	0.724	0.648	0.805	SUBCLONAL	1	TRUE	1	0.381554300101409	2		944	746	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974423	18974423	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	47	490	0	ENST00000262803.5:c.2775+2T>G		p.X925_splice	ENST00000262803	NM_002911.3	925			1	2	FACETS	0.617	0.522	0.722	0.617	0.522	0.722	SUBCLONAL	1	TRUE	1	0.381554300101409	2		490	399	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797310	42797310	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	93	1046	0	ENST00000575354.2:c.3675del	p.Gln1226SerfsTer76	p.Q1226Sfs*76	ENST00000575354	NM_015125.3	1224	gaG/ga	15/20	1	2	FACETS	0.731	0.65	0.817	0.731	0.65	0.817	SUBCLONAL	1	TRUE	1	0.381554300101409	2		1046	667	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145343	61145343	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	35	189	0	ENST00000295025.8:c.553G>T	p.Glu185Ter	p.E185*	ENST00000295025	NM_002908.2	185	Gaa/Taa	6/11	1	2	FACETS	0.731	0.603	0.873	0.731	0.603	0.873	SUBCLONAL	1	TRUE	1	0.381554300101409	2		189	251	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668648	52668648	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	54	363	0	ENST00000394830.3:c.1271T>A	p.Ile424Asn	p.I424N	ENST00000394830	NM_018313.4	424	aTt/aAt	12/30	1	2	FACETS	0.711	0.609	0.822	0.711	0.609	0.822	SUBCLONAL	1	TRUE	1	0.381554300101409	2		363	398	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178490	56178490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	31	240	0	ENST00000399503.3:c.3463G>A	p.Val1155Ile	p.V1155I	ENST00000399503	NM_005921.1	1155	Gtc/Atc	14/20	1	2	FACETS	0.713	0.58	0.861	0.713	0.58	0.861	SUBCLONAL	1	TRUE	1	0.381554300101409	2		240	228	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750776	57750776	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	59	414	0	ENST00000274289.3:c.1828A>G	p.Lys610Glu	p.K610E	ENST00000274289	NM_006622.3	610	Aag/Gag	13/14	1	2	FACETS	0.767	0.663	0.881	0.767	0.663	0.881	SUBCLONAL	1	TRUE	1	0.381554300101409	2		414	403	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858180	27858180	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	70	608	0	ENST00000359303.2:c.391A>G	p.Ile131Val	p.I131V	ENST00000359303	NM_003535.2	131	Atc/Gtc	1/1	1	2	FACETS	0.774	0.677	0.879	0.774	0.677	0.879	SUBCLONAL	1	TRUE	1	0.381554300101409	2		608	474	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139048	37139048	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	91	794	0	ENST00000373509.5:c.388T>C	p.Phe130Leu	p.F130L	ENST00000373509	NM_002648.3	130	Ttc/Ctc	4/6	1	2	FACETS	0.732	0.65	0.819	0.732	0.65	0.819	SUBCLONAL	1	TRUE	1	0.381554300101409	2		794	652	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609872	117609872	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	77	527	0	ENST00000368508.3:c.6827T>C	p.Val2276Ala	p.V2276A	ENST00000368508	NM_002944.2	2276	gTa/gCa	43/43	1	2	FACETS	0.79	0.695	0.891	0.79	0.695	0.891	SUBCLONAL	1	TRUE	1	0.381554300101409	2		527	511	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879058	151879059	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	87	538	0	ENST00000262189.6:c.5886dup	p.Tyr1963LeufsTer9	p.Y1963Lfs*9	ENST00000262189	NM_170606.2	1962	-/C	36/59	1	2	FACETS	0.875	0.777	0.98	0.875	0.777	0.98	CLONAL	1	TRUE	1	0.381554300101409	2		538	521	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641128	93641128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	91	564	0	ENST00000375746.1:c.1474C>T	p.His492Tyr	p.H492Y	ENST00000375746	NM_001174167.1	492	Cac/Tac	11/14	1	2	FACETS	0.798	0.709	0.892	0.798	0.709	0.892	SUBCLONAL	1	TRUE	1	0.381554300101409	2		564	598	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338606	70338606	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0053566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	85	337	0	ENST00000374080.3:c.2T>C	p.Met1?	p.M1?	ENST00000374080		1	aTg/aCg	1/45	1	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.381554300101409	1		337	295	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15808623	15808623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	100	603	0	ENST00000307771.7:c.5C>T	p.Ala2Val	p.A2V	ENST00000307771	NM_005089.3	2	gCt/gTt	1/11	0.251220931630961	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.251220931630961	1		603	491	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118361924	118361929	+	inframe_deletion	In_Frame_Del	DEL	TCTCTG	TCTCTG	-	novel	NA	P-0053567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	27	244	0	ENST00000534358.1:c.4711_4716del	p.Leu1571_Cys1572del	p.L1571_C1572del	ENST00000534358	NM_005933.3	1570	ccTCTCTGt/cct	14/36	0.251220931630961	1	FACETS	0.671	0.535	0.826	0.671	0.535	0.826	SUBCLONAL	1	TRUE	0	0.251220931630961	1		244	280	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578536	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0053567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	361	843	0	ENST00000269305.4:c.394_395del	p.Lys132AspfsTer16	p.K132Dfs*16	ENST00000269305	NM_001126112.2	132	AAg/g	5/11	0.251220931630961	4	FACETS	0.935	0.889	0.981	1	0.993	1	CLONAL	4	TRUE	1	0.251220931630961	4		843	962	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326471	62326472	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0053567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	69	1090	0	ENST00000360203.5:c.3398_3399del	p.Thr1133ArgfsTer53	p.T1133Rfs*53	ENST00000360203	NM_001283009.1	1132	tgCAca/tgca	33/35	0.251220931630961	0	FACETS	0.723	0.63	0.823			1	SUBCLONAL	1	TRUE	0	0.251220931630961	0		1090	569	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194638	29194638	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	71	877	0	ENST00000240100.2:c.1090T>C	p.Phe364Leu	p.F364L	ENST00000240100	NM_001394.6	364	Ttc/Ctc	4/4	0.144210566806976	2	FACETS	0.763	0.665	0.869	0.381	0.332	0.435	INDETERMINATE	1	TRUE	0	0.251220931630961	2		877	741	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383232	31383232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35846833	NA	P-0053568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	76	431	1	ENST00000328111.2:c.1144C>T	p.Arg382Cys	p.R382C	ENST00000328111	NM_006892.3	382	Cgc/Tgc	11/23	1	2	FACETS	0.834	0.732	0.943	0.834	0.732	0.943	CLONAL	1	TRUE	1	0.31	2		432	588	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0053568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	61	393	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.0246215112757446	3	FACETS	1	0.957	1	0.635	0.55	0.726	INDETERMINATE	1	TRUE	1	0.31	3		393	358	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717769	89717770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	48	319	0	ENST00000371953.3:c.800dup	p.Asp268GlyfsTer30	p.D268Gfs*30	ENST00000371953	NM_000314.4	265	cta/ctAa	7/9	0.0246215112757446	3	FACETS	1	0.941	1	0.612	0.521	0.712	INDETERMINATE	1	TRUE	1	0.31	3		319	292	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0053568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	59	205	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.942	0.814	1	0.942	0.814	1	CLONAL	1	TRUE	1	0.31	2		205	404	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589019	67589020	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	12	218	0	ENST00000274335.5:c.1111dup	p.Thr371AsnfsTer8	p.T371Nfs*8	ENST00000274335		370	-/A	8/15	1	2	FACETS	0.41	0.288	0.559	0.41	0.288	0.559	SUBCLONAL	1	TRUE	1	0.31	2		218	189	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592097	67592097	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0053568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	64	263	0	ENST00000274335.5:c.1913T>C	p.Leu638Ser	p.L638S	ENST00000274335		638	tTg/tCg	14/15	1	2	FACETS	0.974	0.846	1	0.974	0.846	1	CLONAL	1	TRUE	1	0.31	2		263	424	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81971362	81971362	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0053568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	63	431	0	ENST00000359376.3:c.3053-1G>T		p.X1018_splice	ENST00000359376	NM_002661.3	1018			1	2	FACETS	0.865	0.75	0.989	0.865	0.75	0.989	CLONAL	1	TRUE	1	0.31	2		431	470	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589017	67589018	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0053568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	17	211	0	ENST00000274335.5:c.1110dup	p.Thr371TyrfsTer8	p.T371Yfs*8	ENST00000274335		370	ctt/cTtt	8/15	1	2	FACETS	0.571	0.428	0.74	0.571	0.428	0.74	SUBCLONAL	1	TRUE	1	0.31	2		211	192	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589102	67589147	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATACCTTTATTTTTATATTGTTTTTACAGGAAAGGGGGAAATAACA	ATACCTTTATTTTTATATTGTTTTTACAGGAAAGGGGGAAATAACA	TTTCCCCCT	novel	NA	P-0053568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	21	242	1	ENST00000274335.5:c.1119-29_1135delinsTTTCCCCCT		p.X373_splice	ENST00000274335		373		9/15	1	2	FACETS	0.783	0.607	0.985	0.783	0.607	0.985	CLONAL	1	TRUE	1	0.31	2		243	173	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0053570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	123	310	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		310	305	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0053571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	65	315	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.871	0.757	0.994	0.871	0.757	0.994	CLONAL	1	TRUE	1	0.324491419320043	2		315	460	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0053572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	49	429	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.986	0.838	1	0.986	0.838	1	CLONAL	1	TRUE	1	0.263598484072973	2		429	377	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0053572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	64	411	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.263598484072973	2		411	478	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0053572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	116	743	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.263598484072973	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.263598484072973	1		745	658	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0053572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	42	316	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.797	0.666	0.941	0.797	0.666	0.941	CLONAL	1	TRUE	1	0.263598484072973	2		316	400	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435645	149435645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780804532	NA	P-0053572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	62	664	0	ENST00000286301.3:c.2498C>T	p.Thr833Met	p.T833M	ENST00000286301	NM_005211.3	833	aCg/aTg	19/22	1	2	FACETS	0.653	0.563	0.751	0.653	0.563	0.751	SUBCLONAL	1	TRUE	1	0.263598484072973	2		664	720	SUCCESS
APC	324	MSKCC	GRCh37	5	112175770	112175770	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	43	296	0	ENST00000257430.4:c.4480del	p.Glu1494LysfsTer13	p.E1494Kfs*13	ENST00000257430	NM_000038.5	1493	acG/ac	16/16	1	2	FACETS	0.909	0.763	1	0.909	0.763	1	CLONAL	1	TRUE	1	0.263598484072973	2		296	359	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546832	9546832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1018346655	NA	P-0053572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	73	447	1	ENST00000353224.5:c.1190C>T	p.Thr397Met	p.T397M	ENST00000353224	NM_177990.2	397	aCg/aTg	5/10	0.263598484072973	3	FACETS	1	0.894	1	0.512	0.448	0.581	CLONAL	1	TRUE	1	0.263598484072973	3		448	612	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662789	227662791	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs755451703	NA	P-0053572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	80	737	0	ENST00000305123.5:c.664_666del	p.Phe222del	p.F222del	ENST00000305123	NM_005544.2	222	TTC/-	1/2	1	2	FACETS	0.818	0.72	0.924	0.818	0.72	0.924	CLONAL	1	TRUE	1	0.263598484072973	2		737	742	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300359	11300359	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0053572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	81	406	0	ENST00000361445.4:c.1786+1G>A		p.X596_splice	ENST00000361445	NM_004958.3	596			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.263598484072973	2		406	472	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406076	70406076	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	40	535	0	ENST00000373644.4:c.3590A>G	p.Asn1197Ser	p.N1197S	ENST00000373644	NM_030625.2	1197	aAt/aGt	4/12	1	2	FACETS	0.458	0.379	0.546	0.458	0.379	0.546	SUBCLONAL	1	TRUE	1	0.263598484072973	2		535	663	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280068	66280068	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	46	317	0	ENST00000273854.3:c.1621C>G	p.Arg541Gly	p.R541G	ENST00000273854	NM_004439.5	541	Cga/Gga	7/18	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.263598484072973	2		317	339	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505016	149505016	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0053572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	37	373	1	ENST00000261799.4:c.1799T>C	p.Leu600Pro	p.L600P	ENST00000261799	NM_002609.3	600	cTt/cCt	12/23	1	2	FACETS	0.61	0.503	0.73	0.61	0.503	0.73	SUBCLONAL	1	TRUE	1	0.263598484072973	2		374	460	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395027	139395027	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	99	667	2	ENST00000277541.6:c.5911G>A	p.Ala1971Thr	p.A1971T	ENST00000277541	NM_017617.3	1971	Gcc/Acc	31/34	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.263598484072973	2		669	696	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0053573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	50	455	3	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.339	0.287	0.397	0.339	0.287	0.397	SUBCLONAL	1	TRUE	1	0.469957428085693	2		458	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0053573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	204	1171	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.125714983107313	3	FACETS	1	0.946	1	0.512	0.474	0.551	INDETERMINATE	1	TRUE	1	0.469957428085693	3		1171	1047	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0053573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	164	482	1	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.339054108670457	2	FACETS	1	0.988	1	0.683	0.631	0.736	CLONAL	1	TRUE	0	0.469957428085693	2		483	511	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244664	41244664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80356955	NA	P-0053573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	44	572	0	ENST00000357654.3:c.2884G>A	p.Glu962Lys	p.E962K	ENST00000357654	NM_007294.3	962	Gaa/Aaa	10/23	1	2	FACETS	0.243	0.203	0.287	0.243	0.203	0.287	SUBCLONAL	1	TRUE	1	0.469957428085693	2		572	771	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524687	187524687	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs928653182	NA	P-0053573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	265	587	2	ENST00000441802.2:c.10993C>T	p.Arg3665Ter	p.R3665*	ENST00000441802	NM_005245.3	3665	Cga/Tga	19/27	0.334803721922458	2	FACETS	1	0.993	1	0.732	0.689	0.776	CLONAL	1	TRUE	0	0.469957428085693	2		589	770	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430992	181430992	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0053573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	104	731	0	ENST00000325404.1:c.844G>C	p.Glu282Gln	p.E282Q	ENST00000325404	NM_003106.3	282	Gag/Cag	1/1	0.469957428085693	3	FACETS	0.504	0.45	0.562	0.168	0.15	0.188	SUBCLONAL	1	TRUE	0	0.469957428085693	3		731	1084	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856409	111856443	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCCAGCGGCCCACACCGCTGCCGCCCCCGGGAC	CTGCCAGCGGCCCACACCGCTGCCGCCCCCGGGAC	-	novel	NA	P-0053573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	16	167	0	ENST00000341259.2:c.461_495del	p.Leu154ProfsTer6	p.L154Pfs*6	ENST00000341259	NM_005475.2	154	CTGCCAGCGGCCCACACCGCTGCCGCCCCCGGGACc/c	2/8	0.246249427898625	1	FACETS	0.293	0.217	0.382	0.293	0.217	0.382	INDETERMINATE	1	TRUE	0	0.469957428085693	1		167	178	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093435	30093435	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs759932872	NA	P-0053573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	37	363	0	ENST00000331968.5:c.1828G>C	p.Ala610Pro	p.A610P	ENST00000331968	NM_002742.2	610	Gct/Cct	13/18	0.125714983107313	3	FACETS	0.418	0.344	0.501	0.209	0.172	0.251	INDETERMINATE	1	TRUE	1	0.469957428085693	3		363	465	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346340	89346340	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	58	543	1	ENST00000301030.4:c.6610G>A	p.Glu2204Lys	p.E2204K	ENST00000301030	NM_001256183.1	2204	Gag/Aag	9/13	1	2	FACETS	0.42	0.361	0.485	0.42	0.361	0.485	SUBCLONAL	1	TRUE	1	0.469957428085693	2		544	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578276	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0053573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	183	620	0	ENST00000269305.4:c.573dup	p.Gln192SerfsTer17	p.Q192Sfs*17	ENST00000269305	NM_001126112.2	191	-/T	6/11	0.125714983107313	3	FACETS	1	0.982	1	0.6	0.555	0.648	INDETERMINATE	1	TRUE	1	0.469957428085693	3		620	801	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302258	15302258	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0053573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	139	682	0	ENST00000263388.2:c.1013G>A	p.Cys338Tyr	p.C338Y	ENST00000263388	NM_000435.2	338	tGt/tAt	6/33	1	2	FACETS	0.707	0.643	0.773	0.707	0.643	0.773	SUBCLONAL	1	TRUE	1	0.469957428085693	2		682	837	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0053574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	208	634	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.432913604232268	2	FACETS	0.951	0.892	1	0.951	0.892	1	CLONAL	2	FALSE	0	0.432913604232268	2		634	505	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223071	1223072	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0053574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	277	740	0	ENST00000326873.7:c.1010_1011del	p.Val337GlyfsTer22	p.V337Gfs*22	ENST00000326873	NM_000455.4	336	acTGtg/actg	8/10	0.432913604232268	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	FALSE	0	0.432913604232268	2		740	588	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000572-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	66	460	0				ENST00000310581	NM_198253.2	-/1132			0.228003993885595	5	FACETS	0.916	0.809	1			1	INDETERMINATE	2	TRUE	NA	0.783785849137394	5		460	200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0000572-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	506	827	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	2	TRUE	NA	0.783785849137394	2		827	644	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145736819	145736819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41555416	NA	P-0000572-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	123	222	0	ENST00000428558.2:c.3622C>T	p.Arg1208Cys	p.R1208C	ENST00000428558	NM_004260.3	1208	Cgc/Tgc	22/22	0.711116294511369	4	FACETS	0.821	0.744	0.902	0.41	0.372	0.451	CLONAL	1	TRUE	2	0.783785849137394	4		222	682	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984885	9984885	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000572-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	164	461	0	ENST00000330684.3:c.1080G>C	p.Arg360Ser	p.R360S	ENST00000330684	NM_001134407.1	360	agG/agC	4/13	0.783785849137394	3	FACETS	0.578	0.53	0.629	0.289	0.265	0.315	SUBCLONAL	1	TRUE	1	0.783785849137394	3		461	1007	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726666	41726666	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778883675	NA	P-0000572-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	150	362	0	ENST00000301178.4:c.211C>T	p.Arg71Trp	p.R71W	ENST00000301178	NM_021913.4	71	Cgg/Tgg	2/20	0.529071116512959	4	FACETS	0.791	0.723	0.862	0.396	0.361	0.431	SUBCLONAL	1	TRUE	2	0.783785849137394	4		362	863	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099042	27099042	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000572-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	225	229	0	ENST00000324856.7:c.3459del	p.Met1154TrpfsTer7	p.M1154Wfs*7	ENST00000324856	NM_006015.4	1153	tCc/tc	13/20	0.529071116512959	4	FACETS	0.852	0.799	0.906	0.852	0.799	0.906	CLONAL	2	TRUE	2	0.783785849137394	4		229	601	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106336	27106337	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0000572-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	274	214	0	ENST00000324856.7:c.5952_5953del	p.Ser1985GlnfsTer13	p.S1985Qfs*13	ENST00000324856	NM_006015.4	1983	TGt/t	20/20	0.529071116512959	4	FACETS	0.958	0.906	1	0.958	0.906	1	CLONAL	2	TRUE	2	0.783785849137394	4		214	651	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185244	123185247	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTA	AGTA	-	novel	NA	P-0000572-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	540	224	0	ENST00000218089.9:c.1196+4_1196+7del		p.X399_splice	ENST00000218089	NM_001042749.1	399		13/35	0.680558666568918	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.783785849137394	2		224	652	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0001412-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	61	537	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.553699079945213	2		537	148	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0001412-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	94	379	3	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.954	0.856	1	0.954	0.856	1	CLONAL	1	TRUE	1	0.553699079945213	2		382	356	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983146	149983146	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001412-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	122	485	0	ENST00000253339.5:c.3112A>G	p.Asn1038Asp	p.N1038D	ENST00000253339		1038	Aat/Gat	7/7	1	2	FACETS	0.866	0.787	0.948	0.866	0.787	0.948	CLONAL	1	TRUE	1	0.553699079945213	2		485	509	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144113	11144113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001412-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	202	703	1	ENST00000358026.2:c.3694G>A	p.Gly1232Ser	p.G1232S	ENST00000358026	NM_001128849.1	1232	Ggc/Agc	26/36	1	2	FACETS	0.969	0.901	1	0.969	0.901	1	CLONAL	1	TRUE	1	0.553699079945213	2		704	753	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0001412-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	95	639	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.741	0.663	0.824	0.741	0.663	0.824	SUBCLONAL	1	TRUE	1	0.553699079945213	2		640	463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579395	7579395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001412-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	191	776	0	ENST00000269305.4:c.292C>T	p.Pro98Ser	p.P98S	ENST00000269305	NM_001126112.2	98	Cct/Tct	4/11	1	2	FACETS	0.858	0.795	0.923	0.858	0.795	0.923	CLONAL	1	TRUE	1	0.553699079945213	2		776	804	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680869	30680869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001412-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	143	527	0	ENST00000376406.3:c.850C>T	p.Pro284Ser	p.P284S	ENST00000376406	NM_014641.2	284	Cca/Tca	5/15	1	2	FACETS	0.752	0.687	0.82	0.752	0.687	0.82	SUBCLONAL	1	TRUE	1	0.553699079945213	2		527	687	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639858	3639858	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141860134	NA	P-0001412-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	136	695	0	ENST00000294008.3:c.3781C>T	p.Pro1261Ser	p.P1261S	ENST00000294008	NM_032444.2	1261	Ccg/Tcg	12/15	1	2	FACETS	0.743	0.677	0.812	0.743	0.677	0.812	SUBCLONAL	1	TRUE	1	0.553699079945213	2		695	661	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8252052	8252052	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0001412-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	128	610	0	ENST00000335790.3:c.26-1G>A		p.X9_splice	ENST00000335790	NM_002315.2	9			0.501649206219261	3	FACETS	0.686	0.622	0.755	0.343	0.311	0.378	SUBCLONAL	1	TRUE	1	0.553699079945213	3		610	860	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740768	58740768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001412-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	108	500	0	ENST00000305921.3:c.1673G>A	p.Ser558Asn	p.S558N	ENST00000305921	NM_003620.3	558	aGt/aAt	6/6	1	2	FACETS	0.547	0.491	0.606	0.547	0.491	0.606	SUBCLONAL	1	TRUE	1	0.553699079945213	2		500	713	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302577	15302577	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001412-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	166	727	0	ENST00000263388.2:c.781C>T	p.Gln261Ter	p.Q261*	ENST00000263388	NM_000435.2	261	Cag/Tag	5/33	1	2	FACETS	0.827	0.761	0.895	0.827	0.761	0.895	CLONAL	1	TRUE	1	0.553699079945213	2		727	725	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383865	15383865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001412-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	171	550	0	ENST00000263377.2:c.46G>A	p.Val16Ile	p.V16I	ENST00000263377	NM_058243.2	16	Gta/Ata	2/20	1	2	FACETS	0.879	0.811	0.949	0.879	0.811	0.949	CLONAL	1	TRUE	1	0.553699079945213	2		550	703	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47643505	47643505	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587779065	NA	P-0001412-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	136	517	0	ENST00000233146.2:c.1013G>A	p.Gly338Glu	p.G338E	ENST00000233146	NM_000251.2	338	gGa/gAa	6/16	1	2	FACETS	0.804	0.733	0.878	0.804	0.733	0.878	CLONAL	1	TRUE	1	0.553699079945213	2		517	611	SUCCESS
ATR	545	MSKCC	GRCh37	3	142285017	142285017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763821441	NA	P-0001412-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	40	394	0	ENST00000350721.4:c.238C>T	p.Pro80Ser	p.P80S	ENST00000350721	NM_001184.3	80	Cca/Tca	3/47	1	2	FACETS	0.278	0.23	0.331	0.278	0.23	0.331	SUBCLONAL	1	TRUE	1	0.553699079945213	2		394	520	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430689	181430689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369111881	NA	P-0001412-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	138	535	0	ENST00000325404.1:c.541C>T	p.Pro181Ser	p.P181S	ENST00000325404	NM_003106.3	181	Ccg/Tcg	1/1	1	2	FACETS	0.69	0.629	0.755	0.69	0.629	0.755	SUBCLONAL	1	TRUE	1	0.553699079945213	2		535	722	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952297	38952297	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0001412-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	26	208	0	ENST00000357387.3:c.3127+1G>A		p.X1043_splice	ENST00000357387	NM_152756.3	1043			1	2	FACETS	0.33	0.261	0.407	0.33	0.261	0.407	SUBCLONAL	1	TRUE	1	0.553699079945213	2		208	285	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564659	86564659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001412-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	162	673	0	ENST00000274376.6:c.392del	p.Gly131AlafsTer43	p.G131Afs*43	ENST00000274376	NM_002890.2	131	Ggc/gc	1/25	1	2	FACETS	0.767	0.705	0.832	0.767	0.705	0.832	SUBCLONAL	1	TRUE	1	0.553699079945213	2		673	763	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149437154	149437154	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001412-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	130	540	0	ENST00000286301.3:c.2134G>A	p.Asp712Asn	p.D712N	ENST00000286301	NM_005211.3	712	Gac/Aac	16/22	1	2	FACETS	0.848	0.772	0.926	0.848	0.772	0.926	CLONAL	1	TRUE	1	0.553699079945213	2		540	554	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681479	30681479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001412-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	98	329	0	ENST00000376406.3:c.533G>A	p.Arg178Lys	p.R178K	ENST00000376406	NM_014641.2	178	aGg/aAg	4/15	1	2	FACETS	0.837	0.751	0.927	0.837	0.751	0.927	CLONAL	1	TRUE	1	0.553699079945213	2		329	423	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509205	106509205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001412-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	159	567	0	ENST00000359195.3:c.1199G>A	p.Ser400Asn	p.S400N	ENST00000359195	NM_002649.2	400	aGc/aAc	2/11	1	2	FACETS	0.746	0.685	0.81	0.746	0.685	0.81	SUBCLONAL	1	TRUE	1	0.553699079945213	2		567	770	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534531	140534531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001412-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	97	406	1	ENST00000288602.6:c.382C>T	p.Leu128Phe	p.L128F	ENST00000288602	NM_004333.4	128	Ctt/Ttt	3/18	1	2	FACETS	0.646	0.578	0.719	0.646	0.578	0.719	SUBCLONAL	1	TRUE	1	0.553699079945213	2		407	542	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27183470	27183470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001412-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	44	414	0	ENST00000380036.4:c.1044G>A	p.Met348Ile	p.M348I	ENST00000380036	NM_000459.3	348	atG/atA	8/23	0.553699079945213	1	FACETS	0.347	0.292	0.408	0.347	0.292	0.408	SUBCLONAL	1	TRUE	0	0.553699079945213	1		414	331	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772909	135772909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001412-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	169	457	1	ENST00000298552.3:c.2714C>T	p.Ser905Phe	p.S905F	ENST00000298552	NM_001162426.1	905	tCc/tTc	21/23	1	2	FACETS	0.857	0.79	0.927	0.857	0.79	0.927	CLONAL	1	TRUE	1	0.553699079945213	2		458	712	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591895	48591895	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs377767346	NA	P-0001684-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	299	506	0	ENST00000342988.3:c.1058A>G	p.Tyr353Cys	p.Y353C	ENST00000342988	NM_005359.5	353	tAc/tGc	9/12	0.901892726501219	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.901892726501219	1		506	344	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259479	16259480	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0001684-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	265	588	1	ENST00000375759.3:c.6750dup	p.Ala2251ArgfsTer10	p.A2251Rfs*10	ENST00000375759	NM_015001.2	2248	-/C	11/15	1	2	FACETS	0.897	0.847	0.948	0.897	0.847	0.948	CLONAL	1	TRUE	1	0.901892726501219	2		589	655	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574065	46574065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001684-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	409	804	0	ENST00000263734.3:c.80G>A	p.Arg27Gln	p.R27Q	ENST00000263734	NM_001430.4	27	cGg/cAg	2/16	1	2	FACETS	0.984	0.941	1	0.984	0.941	1	CLONAL	1	TRUE	1	0.901892726501219	2		804	922	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0001800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	115	432	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.961	0.875	1	0.961	0.875	1	CLONAL	1	TRUE	1	0.68	2		432	352	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148727	20148727	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0001800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	88	334	0	ENST00000379607.5:c.338-2A>T		p.X113_splice	ENST00000379607	NM_001412.3	113			0.0996454550168916	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.68	0		334	216	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032533	47032533	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	113	577	0	ENST00000377604.3:c.440del	p.Gly147AlafsTer15	p.G147Afs*15	ENST00000377604	NM_001204468.1	147	Ggc/gc	5/24	0.0996454550168916	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.68	0		577	342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0003119-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	20	706	1	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	1	2	FACETS	0.361	0.275	0.464	0.361	0.275	0.464	SUBCLONAL	1	TRUE	1	0.11	2		707	1006	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665210	138665210	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003119-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	22	0	0	ENST00000330315.3:c.355G>T	p.Gly119Cys	p.G119C	ENST00000330315	NM_023067.3	119	Ggc/Tgc	1/1	1	2	FACETS	0.373	0.287	0.474	0.373	0.287	0.474	SUBCLONAL	1	TRUE	1	0.11	2		0	1073	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55143565	55143565	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003119-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	22	0	0	ENST00000257290.5:c.1797G>T	p.Leu599Phe	p.L599F	ENST00000257290	NM_006206.4	599	ttG/ttT	13/23	1	2	FACETS	0.658	0.508	0.833	0.658	0.508	0.833	SUBCLONAL	1	TRUE	1	0.11	2		0	608	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600392	10600392	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003119-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	50	0	0	ENST00000171111.5:c.1463A>T	p.Glu488Val	p.E488V	ENST00000171111	NM_203500.1	488	gAg/gTg	4/6	1	2	FACETS	0.774	0.654	0.908	0.774	0.654	0.908	CLONAL	1	TRUE	1	0.11	2		0	1174	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003370-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	53	460	0				ENST00000310581	NM_198253.2	-/1132			0.184119226430352	0	FACETS	0.422	0.361	0.488			1	INDETERMINATE	1	FALSE	0	0.419302306424551	0		460	348	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0003370-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	41	1087	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.130534754744659	0	FACETS	0.138	0.114	0.165			1	INDETERMINATE	1	FALSE	0	0.419302306424551	0		1087	821	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003370-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	10	455	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.097	0.065	0.137	0.097	0.065	0.137	SUBCLONAL	1	FALSE	1	0.419302306424551	2		455	494	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982463	25982463	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003370-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	45	425	0	ENST00000435504.4:c.827C>G	p.Ser276Cys	p.S276C	ENST00000435504		276	tCc/tGc	9/13	1	2	FACETS	0.282	0.236	0.333	0.282	0.236	0.333	SUBCLONAL	1	FALSE	1	0.419302306424551	2		425	762	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41197781	41197781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80356942	NA	P-0003370-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	80	667	0	ENST00000357654.3:c.5506G>A	p.Glu1836Lys	p.E1836K	ENST00000357654	NM_007294.3	1836	Gag/Aag	23/23	1	2	FACETS	0.392	0.344	0.444	0.392	0.344	0.444	SUBCLONAL	1	FALSE	1	0.419302306424551	2		667	974	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56376666	56376666	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003370-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	49	588	0	ENST00000348428.3:c.706C>T	p.Gln236Ter	p.Q236*	ENST00000348428	NM_006785.3	236	Caa/Taa	5/17	1	2	FACETS	0.277	0.233	0.325	0.277	0.233	0.325	SUBCLONAL	1	FALSE	1	0.419302306424551	2		588	845	SUCCESS
ATM	472	MSKCC	GRCh37	11	108127026	108127029	+	frameshift_variant	Frame_Shift_Ins	INS	GAAG	GAAG	AAAAA	novel	NA	P-0003370-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	51	513	0	ENST00000278616.4:c.2209_2212delinsAAAAA	p.Glu737LysfsTer6	p.E737Kfs*6	ENST00000278616	NM_000051.3	737	GAAGag/AAAAAag	14/63	1	2	FACETS	0.358	0.303	0.418	0.358	0.303	0.418	SUBCLONAL	1	FALSE	1	0.419302306424551	2		513	680	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163848	32163848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1210630301	NA	P-0003370-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	81	751	0	ENST00000375023.3:c.5378G>A	p.Arg1793Gln	p.R1793Q	ENST00000375023	NM_004557.3	1793	cGa/cAa	30/30	0.0905321411954925	4	FACETS	0.49	0.43	0.555	0.245	0.215	0.278	INDETERMINATE	1	FALSE	2	0.419302306424551	4		751	1119	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53254021	53254021	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003370-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	80	374	0	ENST00000375401.3:c.51C>G	p.Phe17Leu	p.F17L	ENST00000375401	NM_004187.3	17	ttC/ttG	1/26	1	1	FACETS	0.561	0.494	0.631	0.561	0.494	0.631	SUBCLONAL	1	FALSE	0	0.419302306424551	1		374	538	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430824	78430824	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003370-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	58	641	0	ENST00000370768.2:c.565G>C	p.Glu189Gln	p.E189Q	ENST00000370768	NM_003902.3	189	Gaa/Caa	8/20	1	2	FACETS	0.279	0.239	0.324	0.279	0.239	0.324	SUBCLONAL	1	FALSE	1	0.419302306424551	2		641	991	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800928	120800928	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003370-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	63	620	0	ENST00000257552.2:c.320G>C	p.Arg107Pro	p.R107P	ENST00000257552	NM_002442.3	107	cGa/cCa	6/15	1	2	FACETS	0.397	0.343	0.456	0.397	0.343	0.456	SUBCLONAL	1	FALSE	1	0.419302306424551	2		620	757	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	81	856	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.883	0.778	0.995	0.883	0.778	0.995	CLONAL	1	TRUE	1	0.283564277593614	2		856	647	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	62	1140	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.917	0.793	1	0.917	0.793	1	CLONAL	1	TRUE	1	0.283564277593614	2		1144	477	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	44	499	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.283564277593614	2		500	250	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	25	504	3	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	0.283564277593614	2	FACETS	0.432	0.34	0.538	0.216	0.17	0.269	SUBCLONAL	1	TRUE	0	0.283564277593614	2		507	408	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	71	572	6	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	0.194312810654723	4	FACETS	0.814	0.714	0.92	0.814	0.714	0.92	CLONAL	2	TRUE	2	0.283564277593614	4		578	395	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029457	16029457	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	48	455	0	ENST00000268712.3:c.1573del	p.Thr525GlnfsTer30	p.T525Qfs*30	ENST00000268712	NM_006311.3	525	Aca/ca	15/46	1	2	FACETS	0.928	0.787	1	0.928	0.787	1	CLONAL	1	TRUE	1	0.283564277593614	2		455	365	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	47	539	1	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	0.283564277593614	6	FACETS	1	0.946	1			1	CLONAL	1	TRUE	NA	0.283564277593614	6		540	404	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	144	1049	1	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	0.27887561578027	4	FACETS	0.946	0.865	1	0.946	0.865	1	CLONAL	2	TRUE	2	0.283564277593614	4		1050	689	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217234	11217234	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1031980569	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	53	727	0	ENST00000361445.4:c.4444C>T	p.Arg1482Cys	p.R1482C	ENST00000361445	NM_004958.3	1482	Cgc/Tgc	30/58	1	2	FACETS	0.73	0.623	0.847	0.73	0.623	0.847	SUBCLONAL	1	TRUE	1	0.283564277593614	2		727	512	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317099	11317099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201093943	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	52	855	1	ENST00000361445.4:c.395G>A	p.Arg132His	p.R132H	ENST00000361445	NM_004958.3	132	cGt/cAt	4/58	1	2	FACETS	0.711	0.605	0.826	0.711	0.605	0.826	SUBCLONAL	1	TRUE	1	0.283564277593614	2		856	516	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023384	27023384	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1229573624	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	109	276	0	ENST00000324856.7:c.490G>A	p.Ala164Thr	p.A164T	ENST00000324856	NM_006015.4	164	Gcc/Acc	1/20	1	2	FACETS	0.886	0.801	0.974	1	0.987	1	CLONAL	2	TRUE	1	0.283564277593614	2		276	434	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	50	696	1	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.283564277593614	2		697	347	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430775	78430775	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	51	609	0	ENST00000370768.2:c.614del	p.Gly205GlufsTer17	p.G205Efs*17	ENST00000370768	NM_003902.3	205	gGa/ga	8/20	1	2	FACETS	0.848	0.723	0.986	0.848	0.723	0.986	CLONAL	1	TRUE	1	0.283564277593614	2		609	424	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120496279	120496279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	27	510	0	ENST00000256646.2:c.2252G>A	p.Gly751Asp	p.G751D	ENST00000256646	NM_024408.3	751	gGc/gAc	14/34	1	2	FACETS	0.777	0.621	0.954	0.777	0.621	0.954	CLONAL	1	TRUE	1	0.283564277593614	2		510	245	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204515939	204515939	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	25	414	0	ENST00000367182.3:c.842del	p.Asn281MetfsTer10	p.N281Mfs*10	ENST00000367182	NM_001278516.1	279	ggA/gg	10/11	1	2	FACETS	0.741	0.586	0.917	0.741	0.586	0.917	CLONAL	1	TRUE	1	0.283564277593614	2		414	238	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115780	8115780	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	93	587	4	ENST00000346208.3:c.1131del	p.Val378CysfsTer26	p.V378Cfs*26	ENST00000346208		376	Aaa/aa	6/6	0.27887561578027	4	FACETS	0.847	0.756	0.943	0.847	0.756	0.943	CLONAL	2	TRUE	2	0.283564277593614	4		591	497	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619159	43619159	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs794728689	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	55	816	0	ENST00000355710.3:c.2846del	p.Gly949GlufsTer16	p.G949Efs*16	ENST00000355710	NM_020975.4	948	Ggg/gg	17/20	0.27887561578027	4	FACETS	1	0.9	1	0.532	0.456	0.615	CLONAL	1	TRUE	2	0.283564277593614	4		816	468	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759976	63759977	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	30	426	0	ENST00000279873.7:c.635dup	p.Ile213HisfsTer18	p.I213Hfs*18	ENST00000279873	NM_032199.2	210	ctg/ctGg	4/10	0.27887561578027	4	FACETS	0.813	0.656	0.991	0.407	0.328	0.496	CLONAL	1	TRUE	2	0.283564277593614	4		426	334	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852118	63852118	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	25	610	0	ENST00000279873.7:c.2901del	p.Lys967AsnfsTer15	p.K967Nfs*15	ENST00000279873	NM_032199.2	966	Aaa/aa	10/10	0.27887561578027	4	FACETS	0.517	0.406	0.644	0.258	0.203	0.322	SUBCLONAL	1	TRUE	2	0.283564277593614	4		610	438	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344476	118344476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782640926	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	24	343	0	ENST00000534358.1:c.2602G>A	p.Val868Met	p.V868M	ENST00000534358	NM_005933.3	868	Gtg/Atg	3/36	1	2	FACETS	0.905	0.715	1	0.905	0.715	1	CLONAL	1	TRUE	1	0.283564277593614	2		343	187	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431595	431595	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	37	428	0	ENST00000399788.2:c.2414del	p.Lys805SerfsTer17	p.K805Sfs*17	ENST00000399788	NM_001042603.1	805	aAg/ag	17/28	0.194312810654723	4	FACETS	1	0.908	1	0.578	0.478	0.688	CLONAL	1	TRUE	2	0.283564277593614	4		428	290	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398080	4398080	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	50	647	0	ENST00000261254.3:c.644A>G	p.Gln215Arg	p.Q215R	ENST00000261254	NM_001759.3	215	cAg/cGg	4/5	0.194312810654723	4	FACETS	0.92	0.781	1	0.46	0.39	0.536	CLONAL	1	TRUE	2	0.283564277593614	4		647	492	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425038	49425038	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783690	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	74	1007	2	ENST00000301067.7:c.13450C>T	p.Arg4484Ter	p.R4484*	ENST00000301067	NM_003482.3	4484	Cga/Tga	39/54	0.194312810654723	4	FACETS	1	0.945	1	0.572	0.501	0.648	CLONAL	1	TRUE	2	0.283564277593614	4		1009	586	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437701	49437701	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555194045	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	98	950	1	ENST00000301067.7:c.5269C>T	p.Arg1757Ter	p.R1757*	ENST00000301067	NM_003482.3	1757	Cga/Tga	22/54	0.194312810654723	4	FACETS	0.754	0.674	0.839	0.754	0.674	0.839	SUBCLONAL	2	TRUE	2	0.283564277593614	4		951	588	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446066	49446066	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	94	1073	0	ENST00000301067.7:c.1400T>G	p.Leu467Arg	p.L467R	ENST00000301067	NM_003482.3	467	cTg/cGg	10/54	0.194312810654723	4	FACETS	1	0.966	1	0.608	0.541	0.679	CLONAL	1	TRUE	2	0.283564277593614	4		1073	700	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858476	57858476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199685332	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	65	649	1	ENST00000228682.2:c.214C>T	p.Arg72Trp	p.R72W	ENST00000228682	NM_005269.2	72	Cgg/Tgg	4/12	0.194312810654723	4	FACETS	1	0.932	1	0.559	0.485	0.639	CLONAL	1	TRUE	2	0.283564277593614	4		650	526	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201338	133201338	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	67	1009	0	ENST00000320574.5:c.6806A>G	p.Tyr2269Cys	p.Y2269C	ENST00000320574	NM_006231.2	2269	tAc/tGc	49/49	0.194312810654723	4	FACETS	1	0.941	1	0.572	0.498	0.653	CLONAL	1	TRUE	2	0.283564277593614	4		1009	530	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219278	133219278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	51	875	0	ENST00000320574.5:c.4766C>T	p.Ser1589Phe	p.S1589F	ENST00000320574	NM_006231.2	1589	tCc/tTc	37/49	0.194312810654723	4	FACETS	0.956	0.813	1	0.478	0.406	0.556	CLONAL	1	TRUE	2	0.283564277593614	4		875	483	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219579	133219579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542430685	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	40	794	0	ENST00000320574.5:c.4555C>T	p.Arg1519Cys	p.R1519C	ENST00000320574	NM_006231.2	1519	Cgc/Tgc	36/49	0.194312810654723	4	FACETS	1	0.892	1	0.547	0.456	0.648	CLONAL	1	TRUE	2	0.283564277593614	4		794	331	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563252	21563252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	74	1090	1	ENST00000382592.4:c.667G>A	p.Gly223Arg	p.G223R	ENST00000382592	NM_014572.2	223	Ggg/Agg	4/8	0.108376121981389	0	FACETS	0.571	0.5	0.648			1	INDETERMINATE	1	TRUE	0	0.283564277593614	0		1091	655	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068276	30068276	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	46	444	0	ENST00000331968.5:c.2123A>G	p.Lys708Arg	p.K708R	ENST00000331968	NM_002742.2	708	aAa/aGa	15/18	0.135171792003881	4	FACETS	1	0.939	1	0.618	0.522	0.722	INDETERMINATE	1	TRUE	2	0.283564277593614	4		444	337	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640332	3640332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200708159	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	61	1042	2	ENST00000294008.3:c.3307C>T	p.Arg1103Cys	p.R1103C	ENST00000294008	NM_032444.2	1103	Cgt/Tgt	12/15	1	2	FACETS	0.506	0.435	0.583	0.506	0.435	0.583	SUBCLONAL	1	TRUE	1	0.283564277593614	2		1044	851	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778603	3778603	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147448293	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	62	952	2	ENST00000262367.5:c.6445G>A	p.Val2149Met	p.V2149M	ENST00000262367	NM_004380.2	2149	Gtg/Atg	31/31	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.283564277593614	2		954	420	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781417	3781417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776549587	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	65	857	1	ENST00000262367.5:c.4948G>A	p.Val1650Ile	p.V1650I	ENST00000262367	NM_004380.2	1650	Gtc/Atc	30/31	1	2	FACETS	0.921	0.8	1	0.921	0.8	1	CLONAL	1	TRUE	1	0.283564277593614	2		858	498	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826565	50826565	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	44	420	0	ENST00000398568.2:c.2296del	p.Ile766PhefsTer7	p.I766Ffs*7	ENST00000398568	NM_001042412.1	764	Aaa/aa	15/18	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.283564277593614	2		420	285	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56852600	56852600	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	69	648	6	ENST00000308159.5:c.518del	p.Pro173LeufsTer25	p.P173Lfs*25	ENST00000308159	NM_014669.4	172	Ccc/cc	6/22	1	2	FACETS	0.966	0.843	1	0.966	0.843	1	CLONAL	1	TRUE	1	0.283564277593614	2		654	504	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671655	67671655	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1400980130	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	50	538	5	ENST00000264010.4:c.2070del	p.Glu691SerfsTer30	p.E691Sfs*30	ENST00000264010	NM_006565.3	688	gtA/gt	12/12	1	2	FACETS	0.943	0.803	1	0.943	0.803	1	CLONAL	1	TRUE	1	0.283564277593614	2		543	374	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845830	72845830	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	50	695	1	ENST00000268489.5:c.3637del	p.Thr1213GlnfsTer31	p.T1213Qfs*31	ENST00000268489	NM_006885.3	1213	Aca/ca	6/10	0.283564277593614	6	FACETS	1	0.886	1			1	CLONAL	1	TRUE	NA	0.283564277593614	6		696	525	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117573	70117573	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	76	778	0	ENST00000245479.2:c.41A>G	p.Gln14Arg	p.Q14R	ENST00000245479	NM_000346.3	14	cAg/cGg	1/3	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.283564277593614	2		778	470	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897438	78897438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	87	998	0	ENST00000306801.3:c.2773C>T	p.Arg925Trp	p.R925W	ENST00000306801	NM_020761.2	925	Cgg/Tgg	23/34	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.283564277593614	2		998	493	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7174633	7174633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs72549237	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	83	769	1	ENST00000302850.5:c.1084G>A	p.Val362Ile	p.V362I	ENST00000302850	NM_000208.2	362	Gtc/Atc	4/22	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.283564277593614	2		770	546	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105645	11105645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	75	780	0	ENST00000358026.2:c.1561C>T	p.Arg521Trp	p.R521W	ENST00000358026	NM_001128849.1	521	Cgg/Tgg	9/36	1	2	FACETS	0.994	0.873	1	0.994	0.873	1	CLONAL	1	TRUE	1	0.283564277593614	2		780	532	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276788	15276788	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	85	965	0	ENST00000263388.2:c.5477G>A	p.Cys1826Tyr	p.C1826Y	ENST00000263388	NM_000435.2	1826	tGc/tAc	30/33	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.283564277593614	2		965	565	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281554	15281554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	58	757	1	ENST00000263388.2:c.4819G>A	p.Ala1607Thr	p.A1607T	ENST00000263388	NM_000435.2	1607	Gcc/Acc	26/33	1	2	FACETS	0.723	0.621	0.834	0.723	0.621	0.834	SUBCLONAL	1	TRUE	1	0.283564277593614	2		758	566	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	92	1222	2	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.935	0.831	1	0.935	0.831	1	CLONAL	1	TRUE	1	0.283564277593614	2		1224	694	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919079	50919079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064795958	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	55	865	0	ENST00000440232.2:c.2816C>T	p.Ser939Leu	p.S939L	ENST00000440232	NM_002691.3	939	tCg/tTg	22/27	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.283564277593614	2		865	374	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222520	39222520	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	38	542	1	ENST00000402219.2:c.3090del	p.Lys1030AsnfsTer6	p.K1030Nfs*6	ENST00000402219	NM_005633.3	1030	aaA/aa	20/23	0.283564277593614	2	FACETS	0.728	0.603	0.868	0.364	0.301	0.434	SUBCLONAL	1	TRUE	0	0.283564277593614	2		543	368	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010590	48010590	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	183	555	0	ENST00000234420.5:c.218A>G	p.Asn73Ser	p.N73S	ENST00000234420	NM_000179.2	73	aAc/aGc	1/10	0.283564277593614	2	FACETS	0.858	0.794	0.925	0.858	0.794	0.925	CLONAL	2	TRUE	0	0.283564277593614	2		555	752	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145601	61145601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1352140789	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	37	503	0	ENST00000295025.8:c.713G>A	p.Arg238His	p.R238H	ENST00000295025	NM_002908.2	238	cGt/cAt	7/11	0.283564277593614	2	FACETS	0.743	0.614	0.887	0.372	0.307	0.444	SUBCLONAL	1	TRUE	0	0.283564277593614	2		503	351	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032747	30032747	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555986860	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	40	373	0	ENST00000338641.4:c.122G>A	p.Trp41Ter	p.W41*	ENST00000338641	NM_000268.3	41	tGg/tAg	2/16	1	2	FACETS	0.901	0.752	1	0.901	0.752	1	CLONAL	1	TRUE	1	0.283564277593614	2		373	313	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627983	37627983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375471633	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	52	956	2	ENST00000249071.6:c.277G>A	p.Val93Ile	p.V93I	ENST00000249071	NM_002872.4	93	Gtc/Atc	4/7	1	2	FACETS	0.523	0.444	0.61	0.523	0.444	0.61	SUBCLONAL	1	TRUE	1	0.283564277593614	2		958	701	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280754	41280754	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	65	613	0	ENST00000349496.5:c.2267T>C	p.Leu756Pro	p.L756P	ENST00000349496	NM_001904.3	756	cTg/cCg	15/15	0.135171792003881	4	FACETS	0.815	0.711	0.927	0.815	0.711	0.927	INDETERMINATE	2	TRUE	2	0.283564277593614	4		613	361	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725205	49725205	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	16	244	0	ENST00000449682.2:c.220T>C	p.Cys74Arg	p.C74R	ENST00000449682	NM_020998.3	74	Tgt/Cgt	2/18	0.135171792003881	4	FACETS	0.929	0.69	1	0.464	0.345	0.605	INDETERMINATE	1	TRUE	2	0.283564277593614	4		244	156	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71019947	71019950	+	frameshift_variant	Frame_Shift_Del	DEL	GGAA	GGAA	-	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	31	200	0	ENST00000318789.4:c.1659_1662del	p.Ser554LeufsTer44	p.S554Lfs*44	ENST00000318789	NM_032682.5	553	ccTTCC/cc	19/21	0.135171792003881	4	FACETS	1	0.936	1	0.695	0.566	0.837	INDETERMINATE	1	TRUE	2	0.283564277593614	4		200	202	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55991458	55991458	+	start_lost	Translation_Start_Site	SNP	C	C	T	rs773557368	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	60	806	0	ENST00000263923.4:c.3G>A	p.Met1?	p.M1?	ENST00000263923	NM_002253.2	1	atG/atA	1/30	0.27887561578027	4	FACETS	0.941	0.811	1	0.471	0.405	0.542	CLONAL	1	TRUE	2	0.283564277593614	4		806	577	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197563	106197563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745668941	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	37	418	0	ENST00000380013.4:c.5896C>T	p.Arg1966Cys	p.R1966C	ENST00000380013	NM_001127208.2	1966	Cgt/Tgt	11/11	0.27887561578027	4	FACETS	1	0.869	1	0.53	0.438	0.632	CLONAL	1	TRUE	2	0.283564277593614	4		418	316	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542188	187542188	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	48	540	0	ENST00000441802.2:c.5552A>C	p.Asp1851Ala	p.D1851A	ENST00000441802	NM_005245.3	1851	gAc/gCc	10/27	0.27887561578027	4	FACETS	1	0.961	1	0.732	0.622	0.851	CLONAL	1	TRUE	2	0.283564277593614	4		540	297	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952435	38952435	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138880117	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	17	372	0	ENST00000357387.3:c.2990G>A	p.Arg997His	p.R997H	ENST00000357387	NM_152756.3	997	cGc/cAc	30/38	0.135171792003881	4	FACETS	0.506	0.377	0.66	0.253	0.188	0.33	INDETERMINATE	1	TRUE	2	0.283564277593614	4		372	304	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675571	86675571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1561325048	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	20	336	0	ENST00000274376.6:c.2513del	p.Asn838MetfsTer4	p.N838Mfs*4	ENST00000274376	NM_002890.2	836	gAa/ga	19/25	0.135171792003881	4	FACETS	0.831	0.637	1	0.415	0.318	0.528	INDETERMINATE	1	TRUE	2	0.283564277593614	4		336	218	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502729	149502729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777708927	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	63	765	0	ENST00000261799.4:c.2059G>A	p.Gly687Arg	p.G687R	ENST00000261799	NM_002609.3	687	Gga/Aga	15/23	0.135171792003881	4	FACETS	1	0.949	1	0.6	0.52	0.687	INDETERMINATE	1	TRUE	2	0.283564277593614	4		765	475	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180979	32180981	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	54	885	0	ENST00000375023.3:c.2369_2371del	p.Ser790del	p.S790del	ENST00000375023	NM_004557.3	790	tCCTgc/tgc	15/30	0.27887561578027	4	FACETS	0.912	0.779	1	0.456	0.389	0.529	CLONAL	1	TRUE	2	0.283564277593614	4		885	536	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181929	32181929	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	47	865	0	ENST00000375023.3:c.2125del	p.Gln709SerfsTer22	p.Q709Sfs*22	ENST00000375023	NM_004557.3	709	Cag/ag	13/30	0.27887561578027	4	FACETS	0.801	0.676	0.94	0.401	0.338	0.47	CLONAL	1	TRUE	2	0.283564277593614	4		865	531	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797232	32797232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1247287824	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	94	1047	1	ENST00000374899.4:c.1877G>A	p.Arg626Gln	p.R626Q	ENST00000374899	NM_018833.2	626	cGg/cAg	11/12	0.27887561578027	4	FACETS	1	0.978	1	0.708	0.631	0.79	CLONAL	1	TRUE	2	0.283564277593614	4		1048	601	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43749782	43749782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369593555	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	74	551	1	ENST00000523873.1:c.635G>A	p.Arg212His	p.R212H	ENST00000523873		212	cGt/cAt	7/8	0.27887561578027	4	FACETS	1	0.965	1	0.643	0.564	0.728	CLONAL	1	TRUE	2	0.283564277593614	4		552	521	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553578	106553578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1020395697	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	48	540	0	ENST00000369096.4:c.1543G>A	p.Gly515Arg	p.G515R	ENST00000369096	NM_001198.3	515	Ggg/Agg	5/7	0.27887561578027	4	FACETS	1	0.959	1	0.715	0.608	0.831	CLONAL	1	TRUE	2	0.283564277593614	4		540	304	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322675	109322675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1375852932	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	44	503	0	ENST00000436639.2:c.362G>A	p.Ser121Asn	p.S121N	ENST00000436639	NM_014454.2	121	aGt/aAt	3/10	0.27887561578027	4	FACETS	1	0.935	1	0.613	0.516	0.719	CLONAL	1	TRUE	2	0.283564277593614	4		503	325	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200087	138200087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150513567	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	42	565	2	ENST00000237289.4:c.1505G>A	p.Arg502Gln	p.R502Q	ENST00000237289	NM_001270507.1	502	cGg/cAg	7/9	0.27887561578027	4	FACETS	0.836	0.698	0.988	0.418	0.349	0.494	CLONAL	1	TRUE	2	0.283564277593614	4		567	455	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005408	150005409	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	58	663	0	ENST00000253339.5:c.816_817del	p.Gln273AsnfsTer41	p.Q273Nfs*41	ENST00000253339		272	tcTCaa/tcaa	3/7	0.27887561578027	4	FACETS	1	0.923	1	0.555	0.478	0.639	CLONAL	1	TRUE	2	0.283564277593614	4		663	473	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129329	152129329	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	47	781	0	ENST00000206249.3:c.287del	p.Gly96ValfsTer13	p.G96Vfs*13	ENST00000206249	NM_000125.3	94	ctG/ct	1/8	0.27887561578027	4	FACETS	0.996	0.842	1	0.498	0.421	0.583	CLONAL	1	TRUE	2	0.283564277593614	4		781	427	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522283	157522283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285642669	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	82	829	1	ENST00000346085.5:c.4555C>T	p.Arg1519Cys	p.R1519C	ENST00000346085	NM_020732.3	1519	Cgt/Tgt	18/20	0.27887561578027	4	FACETS	1	0.973	1	0.69	0.61	0.776	CLONAL	1	TRUE	2	0.283564277593614	4		830	538	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	107	577	2	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	0.237221311993083	5	FACETS	0.964	0.867	1	0.643	0.578	0.711	CLONAL	2	TRUE	2	0.283564277593614	5		579	558	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395560	116395560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753407699	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	75	445	0	ENST00000397752.3:c.1853C>T	p.Thr618Met	p.T618M	ENST00000397752	NM_000245.2	618	aCg/aTg	6/21	0.237221311993083	5	FACETS	1	0.94	1	0.737	0.651	0.828	CLONAL	2	TRUE	2	0.283564277593614	5		445	341	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752783	128752783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	52	336	0	ENST00000377970.2:c.944G>A	p.Cys315Tyr	p.C315Y	ENST00000377970	NM_002467.4	315	tGc/tAc	3/3	0.135171792003881	4	FACETS	0.853	0.732	0.983	0.853	0.732	0.983	INDETERMINATE	2	TRUE	2	0.283564277593614	4		336	276	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145736822	145736822	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	74	786	0	ENST00000428558.2:c.3619G>A	p.Ala1207Thr	p.A1207T	ENST00000428558	NM_004260.3	1207	Gcc/Acc	22/22	0.135171792003881	4	FACETS	1	0.973	1	0.72	0.633	0.814	INDETERMINATE	1	TRUE	2	0.283564277593614	4		786	465	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319901	8319901	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	24	453	0	ENST00000356435.5:c.5600A>G	p.Glu1867Gly	p.E1867G	ENST00000356435		1867	gAa/gGa	34/35	1	2	FACETS	0.534	0.419	0.667	0.534	0.419	0.667	SUBCLONAL	1	TRUE	1	0.283564277593614	2		453	317	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376675	8376675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs571411218	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	55	591	2	ENST00000356435.5:c.4438G>A	p.Val1480Ile	p.V1480I	ENST00000356435		1480	Gtt/Att	27/35	1	2	FACETS	0.806	0.691	0.933	0.806	0.691	0.933	CLONAL	1	TRUE	1	0.283564277593614	2		593	481	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27172637	27172637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1320313686	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	46	648	1	ENST00000380036.4:c.652C>T	p.Pro218Ser	p.P218S	ENST00000380036	NM_000459.3	218	Cct/Tct	5/23	1	2	FACETS	0.793	0.669	0.93	0.793	0.669	0.93	CLONAL	1	TRUE	1	0.283564277593614	2		649	409	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211514	98211514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200029534	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	68	868	1	ENST00000331920.6:c.3641C>T	p.Thr1214Met	p.T1214M	ENST00000331920	NM_000264.3	1214	aCg/aTg	22/24	1	2	FACETS	0.926	0.807	1	0.926	0.807	1	CLONAL	1	TRUE	1	0.283564277593614	2		869	518	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753910	133753910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149852028	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	66	713	1	ENST00000318560.5:c.1379G>A	p.Arg460His	p.R460H	ENST00000318560	NM_005157.4	460	cGc/cAc	8/11	1	2	FACETS	0.92	0.8	1	0.92	0.8	1	CLONAL	1	TRUE	1	0.283564277593614	2		714	506	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760264	133760264	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	48	792	0	ENST00000318560.5:c.2591del	p.Gly864AlafsTer12	p.G864Afs*12	ENST00000318560	NM_005157.4	863	Ggg/gg	11/11	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.283564277593614	2		792	323	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397706	139397706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	93	965	1	ENST00000277541.6:c.5095G>A	p.Val1699Met	p.V1699M	ENST00000277541	NM_017617.3	1699	Gtg/Atg	27/34	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.283564277593614	2		966	632	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404348	139404348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773847667	NA	P-0003555-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	101	1105	0	ENST00000277541.6:c.2806G>A	p.Gly936Ser	p.G936S	ENST00000277541	NM_017617.3	936	Ggc/Agc	18/34	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.283564277593614	2		1105	681	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0003832-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	339	471	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	1	0.982	1	1	0.997	1	CLONAL	7	FALSE	1	0.199431087312808	2		472	473	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565564	41565564	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003832-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	215	567	0	ENST00000263253.7:c.4230G>T	p.Arg1410Ser	p.R1410S	ENST00000263253	NM_001429.3	1410	agG/agT	26/31	1	2	FACETS	1	0.969	1	1	0.996	1	CLONAL	4	FALSE	1	0.199431087312808	2		567	513	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023685	27023685	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003832-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	182	404	0	ENST00000324856.7:c.791C>A	p.Ser264Ter	p.S264*	ENST00000324856	NM_006015.4	264	tCg/tAg	1/20	1	2	FACETS	1	0.973	1	1	0.995	1	CLONAL	4	FALSE	1	0.199431087312808	2		404	423	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860601	151860601	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003832-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	231	915	0	ENST00000262189.6:c.10061del	p.Pro3354GlnfsTer7	p.P3354Qfs*7	ENST00000262189	NM_170606.2	3354	cCa/ca	43/59	1	2	FACETS	1	0.957	1	1	0.996	1	CLONAL	4	FALSE	1	0.199431087312808	2		915	567	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981316	68981316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756231722	NA	P-0003832-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	131	549	0	ENST00000288368.4:c.1388G>A	p.Arg463His	p.R463H	ENST00000288368	NM_024870.2	463	cGc/cAc	12/40	1	2	FACETS	0.92	0.845	0.997	1	0.993	1	CLONAL	4	FALSE	1	0.199431087312808	2		549	357	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056100	26056100	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1235205455	NA	P-0004381-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	81	406	0	ENST00000343677.2:c.557C>T	p.Ala186Val	p.A186V	ENST00000343677	NM_005319.3	186	gCc/gTc	1/1	0.76182637660152	4	FACETS	0.925	0.82	1	0.463	0.41	0.519	CLONAL	1	TRUE	2	0.761430904604368	4		406	405	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23625374	23625374	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760373091	NA	P-0004381-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	212	517	0	ENST00000261584.4:c.3152T>C	p.Ile1051Thr	p.I1051T	ENST00000261584	NM_024675.3	1051	aTt/aCt	11/13	0.761430904604368	6	FACETS	1	0.984	1			1	CLONAL	2	TRUE	NA	0.761430904604368	6		517	604	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231375	5231375	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs757257991	NA	P-0004381-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	137	707	0	ENST00000357368.4:c.2101G>C	p.Glu701Gln	p.E701Q	ENST00000357368	NM_002850.3	701	Gag/Cag	14/38	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.761430904604368	2		707	345	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612958	228612958	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004381-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	140	629	0	ENST00000366696.1:c.69del	p.Lys24ArgfsTer13	p.K24Rfs*13	ENST00000366696	NM_003493.2	23	acC/ac	1/1	0.761430904604368	7	FACETS	1	0.981	1	0.184	0.167	0.201	CLONAL	1	TRUE	0	0.761430904604368	7		629	831	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402318	402318	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004381-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	85	390	0	ENST00000399788.2:c.4473G>C	p.Glu1491Asp	p.E1491D	ENST00000399788	NM_001042603.1	1491	gaG/gaC	27/28	0.752154441848358	4	FACETS	1	0.929	1	0.529	0.47	0.59	CLONAL	1	TRUE	2	0.761430904604368	4		390	372	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453321	40453321	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004381-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	234	814	0	ENST00000345506.4:c.1018C>A	p.Gln340Lys	p.Q340K	ENST00000345506	NM_003152.3	340	Cag/Aag	10/20	0.673952667627539	4	FACETS	0.986	0.928	1			1	CLONAL	2	TRUE	NA	0.761430904604368	4		814	549	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0005198-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	14	455	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.203	0.146	0.273	0.203	0.146	0.273	SUBCLONAL	1	TRUE	1	0.366354701869634	2		455	376	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519886	NA	P-0005198-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	77	308	0	ENST00000349496.5:c.97T>C	p.Ser33Pro	p.S33P	ENST00000349496	NM_001904.3	33	Tct/Cct	3/15	1	2	FACETS	0.998	0.881	1	0.998	0.881	1	CLONAL	1	TRUE	1	0.366354701869634	2		308	421	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040945	47040945	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005198-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	131	797	0	ENST00000377604.3:c.1475C>A	p.Ser492Ter	p.S492*	ENST00000377604	NM_001204468.1	492	tCg/tAg	14/24	1	2	FACETS	0.923	0.838	1	0.923	0.838	1	CLONAL	1	TRUE	1	0.366354701869634	2		797	775	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242486	55242486	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005198-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	85	577	0	ENST00000275493.2:c.2256del	p.Pro753ArgfsTer13	p.P753Rfs*13	ENST00000275493	NM_005228.3	752	tcT/tc	19/28	1	2	FACETS	0.771	0.682	0.866	0.771	0.682	0.866	SUBCLONAL	1	TRUE	1	0.366354701869634	2		577	602	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357700	70357700	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005198-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	160	786	0	ENST00000374080.3:c.5952del	p.Val1985Ter	p.V1985*	ENST00000374080		1984	cTt/ct	41/45	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.366354701869634	2		786	842	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097135	11097135	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778071122	NA	P-0005198-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	58	758	2	ENST00000358026.2:c.626C>T	p.Pro209Leu	p.P209L	ENST00000358026	NM_001128849.1	209	cCg/cTg	4/36	1	2	FACETS	0.402	0.344	0.465	0.402	0.344	0.465	SUBCLONAL	1	TRUE	1	0.366354701869634	2		760	788	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242486	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATCT	AATTAAGAGAAGCAACATCT	TC	rs121913424	NA	P-0005198-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	85	600	2	ENST00000275493.2:c.2237_2256delinsTC	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCT/gTC	19/28	1	2	FACETS	0.727	0.643	0.817	0.727	0.643	0.817	SUBCLONAL	1	TRUE	1	0.366354701869634	2		602	638	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828914	72828914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147043604	NA	P-0121583-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	400	936	2	ENST00000268489.5:c.7667C>T	p.Ala2556Val	p.A2556V	ENST00000268489	NM_006885.3	2556	gCg/gTg	9/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	NA	1	0.598769589594657	2		938	1281	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075655	8075655	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs772410037	NA	P-0006132-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	37	393	0	ENST00000377482.5:c.25C>T	p.Gln9Ter	p.Q9*	ENST00000377482	NM_018948.3	9	Cag/Tag	2/4	0.26283142034463	1	FACETS	0.539	0.444	0.645	0.539	0.444	0.645	SUBCLONAL	1	TRUE	0	0.26338812742619	1		393	453	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115958	8115959	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0006429-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	62	625	0	ENST00000346208.3:c.1306_1307dup	p.Ser437ProfsTer39	p.S437Pfs*39	ENST00000346208		435	ccc/ccCTc	6/6	1	2	FACETS	0.207	0.178	0.238	0.207	0.178	0.238	SUBCLONAL	1	TRUE	1	0.854455856904005	2		625	701	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0006429-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	44	798	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	0.854455856904005	1	FACETS	0.157	0.132	0.185	0.157	0.132	0.185	SUBCLONAL	1	TRUE	0	0.854455856904005	1		798	375	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153558	108153558	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006429-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	43	545	2	ENST00000278616.4:c.3698C>A	p.Ser1233Tyr	p.S1233Y	ENST00000278616	NM_000051.3	1233	tCt/tAt	25/63	1	2	FACETS	0.204	0.17	0.241	0.204	0.17	0.241	SUBCLONAL	1	TRUE	1	0.854455856904005	2		547	494	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0006429-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	92	1179	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	0.205	0.181	0.23	0.205	0.181	0.23	SUBCLONAL	1	TRUE	1	0.854455856904005	2		1179	1053	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966733	44966733	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006429-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	57	411	0	ENST00000377967.4:c.3957G>A	p.Trp1319Ter	p.W1319*	ENST00000377967	NM_021140.2	1319	tgG/tgA	27/29	1	1	FACETS	0.203	0.175	0.234	0.203	0.175	0.234	SUBCLONAL	1	TRUE	0	0.854455856904005	1		411	376	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034471	47034472	+	stop_gained	Nonsense_Mutation	DNP	CG	CG	TA	novel	NA	P-0006429-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	98	544	2	ENST00000377604.3:c.556_557delinsTA	p.Arg186Ter	p.R186*	ENST00000377604	NM_001204468.1	186	CGa/TAa	6/24	1	1	FACETS	0.251	0.225	0.279	0.251	0.225	0.279	SUBCLONAL	1	TRUE	0	0.854455856904005	1		546	523	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0006851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	72	432	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.198	0.172	0.226	0.198	0.172	0.226	SUBCLONAL	1	TRUE	1	0.656105258309105	2		432	1107	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0007545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	25	449	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.28531630261852	3	FACETS	0.199	0.156	0.248	0.099	0.078	0.124	INDETERMINATE	1	FALSE	1	0.584880324168096	3		449	556	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0007545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	132	359	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.54236522957063	4	FACETS	1	0.944	1	0.525	0.478	0.575	CLONAL	1	FALSE	2	0.584880324168096	4		359	681	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779085	135779085	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763357144	NA	P-0007545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	161	384	0	ENST00000298552.3:c.2161C>T	p.Arg721Cys	p.R721C	ENST00000298552	NM_001162426.1	721	Cgc/Tgc	17/23	0.305014048312418	3	FACETS	1	0.986	1	0.438	0.404	0.473	INDETERMINATE	1	FALSE	0	0.584880324168096	3		384	541	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858225	9858225	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs772497745	NA	P-0008008-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	11	563	0	ENST00000330684.3:c.3176C>A	p.Ser1059Tyr	p.S1059Y	ENST00000330684	NM_001134407.1	1059	tCt/tAt	13/13	0.155008939987267	3	FACETS	0.504	0.348	0.698	0.252	0.174	0.349	SUBCLONAL	1	TRUE	1	0.244716915704701	3		563	200	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274028	10274028	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008008-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	22	921	0	ENST00000330684.3:c.241A>G	p.Ser81Gly	p.S81G	ENST00000330684	NM_001134407.1	81	Agc/Ggc	2/13	0.155008939987267	3	FACETS	0.791	0.615	0.995	0.396	0.307	0.498	CLONAL	1	TRUE	1	0.244716915704701	3		921	255	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782210	135782210	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008008-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	19	450	0	ENST00000298552.3:c.1346G>A	p.Gly449Asp	p.G449D	ENST00000298552	NM_001162426.1	449	gGc/gAc	14/23	1	2	FACETS	0.693	0.528	0.887	0.693	0.528	0.887	SUBCLONAL	1	TRUE	1	0.244716915704701	2		450	224	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201381	133201381	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs73155056	NA	P-0008551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	100	648	0	ENST00000320574.5:c.6763A>G	p.Ile2255Val	p.I2255V	ENST00000320574	NM_006231.2	2255	Atc/Gtc	49/49	0.235352222929156	3	FACETS	0.949	0.846	1	0.474	0.423	0.529	CLONAL	1	TRUE	1	0.26	3		648	916	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001303	29001303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201407326	NA	P-0008551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	116	253	0	ENST00000282397.4:c.1429G>A	p.Glu477Lys	p.E477K	ENST00000282397	NM_002019.4	477	Gaa/Aaa	10/30	0.301538406760551	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.26	3		253	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578518	7578518	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934875	NA	P-0008551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	314	711	0	ENST00000269305.4:c.412G>C	p.Ala138Pro	p.A138P	ENST00000269305	NM_001126112.2	138	Gcc/Ccc	5/11	0.233645356445354	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.26	2		711	1206	SUCCESS
APC	324	MSKCC	GRCh37	5	112175536	112175536	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	94	340	0	ENST00000257430.4:c.4245del	p.Ser1415ArgfsTer4	p.S1415Rfs*4	ENST00000257430	NM_000038.5	1415	agT/ag	16/16	0.233645356445354	2	FACETS	0.816	0.73	0.907	0.816	0.73	0.907	CLONAL	2	TRUE	0	0.26	2		340	443	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5078445	5078445	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0008551-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	31	251	1	ENST00000381652.3:c.2131+1G>A		p.X711_splice	ENST00000381652	NM_004972.3	711			0.25991104215044	1	FACETS	0.84	0.683	1	0.84	0.683	1	CLONAL	1	TRUE	0	0.26	1		252	247	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201381	133201381	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs73155056	NA	P-0008551-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	75	648	0	ENST00000320574.5:c.6763A>G	p.Ile2255Val	p.I2255V	ENST00000320574	NM_006231.2	2255	Atc/Gtc	49/49	0.353237471836229	3	FACETS	0.961	0.844	1	0.481	0.422	0.543	CLONAL	1	TRUE	1	0.374270656062285	3		648	495	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001303	29001303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201407326	NA	P-0008551-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	191	253	0	ENST00000282397.4:c.1429G>A	p.Glu477Lys	p.E477K	ENST00000282397	NM_002019.4	477	Gaa/Aaa	10/30	0.374270656062285	6	FACETS	1	0.976	1	0.868	0.814	0.923	CLONAL	4	TRUE	1	0.374270656062285	6		253	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578518	7578518	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934875	NA	P-0008551-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	230	711	0	ENST00000269305.4:c.412G>C	p.Ala138Pro	p.A138P	ENST00000269305	NM_001126112.2	138	Gcc/Ccc	5/11	0.331126545201787	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.374270656062285	2		711	586	SUCCESS
APC	324	MSKCC	GRCh37	5	112175536	112175536	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008551-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	94	340	0	ENST00000257430.4:c.4245del	p.Ser1415ArgfsTer4	p.S1415Rfs*4	ENST00000257430	NM_000038.5	1415	agT/ag	16/16	0.331126545201787	2	FACETS	0.917	0.827	1	0.917	0.827	1	CLONAL	2	TRUE	0	0.374270656062285	2		340	274	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5078445	5078445	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0008551-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	54	251	1	ENST00000381652.3:c.2131+1G>A		p.X711_splice	ENST00000381652	NM_004972.3	711			0.353237471836229	3	FACETS	1	0.967	1	0.729	0.629	0.835	CLONAL	1	TRUE	1	0.374270656062285	3		252	235	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11270938	11270938	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1263804740	NA	P-0008771-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	117	234	0	ENST00000361445.4:c.3587A>G	p.Asn1196Ser	p.N1196S	ENST00000361445	NM_004958.3	1196	aAt/aGt	24/58	1	2	FACETS	0.937	0.852	1	0.937	0.852	1	CLONAL	1	TRUE	1	0.604512282963354	2		234	413	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005421	42005421	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008771-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	215	545	1	ENST00000219905.7:c.3157C>T	p.Arg1053Ter	p.R1053*	ENST00000219905	NM_001164273.1	1053	Cga/Tga	9/24	1	2	FACETS	0.94	0.876	1	0.94	0.876	1	CLONAL	1	TRUE	1	0.604512282963354	2		546	757	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435296	56435296	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008771-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	230	833	0	ENST00000407977.2:c.1841A>G	p.Gln614Arg	p.Q614R	ENST00000407977		614	cAg/cGg	9/10	NA	2	FACETS	0.905	0.845	0.966			1	INDETERMINATE	1	TRUE	NA	0.604512282963354	2		833	841	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346157	89346158	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs878855327	NA	P-0008771-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	140	606	1	ENST00000301030.4:c.6792dup	p.Ala2265ArgfsTer8	p.A2265Rfs*8	ENST00000301030	NM_001256183.1	2264	-/C	9/13	0.604512282963354	1	FACETS	0.766	0.704	0.829	0.766	0.704	0.829	SUBCLONAL	1	TRUE	0	0.604512282963354	1		607	422	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332682	70332682	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008771-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	189	415	0	ENST00000373644.4:c.587T>G	p.Val196Gly	p.V196G	ENST00000373644	NM_030625.2	196	gTt/gGt	2/12	1	2	FACETS	0.997	0.926	1	0.997	0.926	1	CLONAL	1	TRUE	1	0.604512282963354	2		415	627	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210741	2210741	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008928-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	212	669	0	ENST00000398665.3:c.1238G>A	p.Arg413His	p.R413H	ENST00000398665	NM_032482.2	413	cGc/cAc	14/28	0.210107500714863	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.210107500714863	3		669	1014	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28903831	28903831	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1278121302	NA	P-0008928-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	99	582	2	ENST00000282397.4:c.2628G>A	p.Met876Ile	p.M876I	ENST00000282397	NM_002019.4	876	atG/atA	19/30	0.210107500714863	5	FACETS	1	0.941	1	0.363	0.323	0.406	CLONAL	1	TRUE	2	0.210107500714863	5		584	1139	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661658	227661658	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008928-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	74	614	0	ENST00000305123.5:c.1797C>A	p.His599Gln	p.H599Q	ENST00000305123	NM_005544.2	599	caC/caA	1/2	0.207111442762975	4	FACETS	0.744	0.649	0.848	0.372	0.324	0.424	SUBCLONAL	1	TRUE	2	0.210107500714863	4		614	1145	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911075	29911075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008928-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1575	179	958	0	ENST00000376809.5:c.374G>A	p.Cys125Tyr	p.C125Y	ENST00000376809	NM_002116.7	125	tGc/tAc	3/8	0.210107500714863	5	FACETS	1	0.984	1	0.426	0.391	0.463	CLONAL	1	TRUE	2	0.210107500714863	5		958	1754	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37671998	37671999	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATACACAAAGAT	novel	NA	P-0008928-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	88	391	0	ENST00000447079.4:c.2784_2785insTACACAAAGATA	p.Glu928_Leu929insTyrThrLysIle	p.E928_L929insYTKI	ENST00000447079	NM_015083.1	928	gaa/gaATACACAAAGATa	9/14	0.210107500714863	3	FACETS	0.75	0.665	0.841	0.75	0.665	0.841	SUBCLONAL	2	TRUE	1	0.210107500714863	3		391	617	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956772	68956772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199819614	NA	P-0008928-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	96	562	0	ENST00000288368.4:c.890G>A	p.Arg297His	p.R297H	ENST00000288368	NM_024870.2	297	cGt/cAt	8/40	0.210107500714863	5	FACETS	1	0.955	1	0.382	0.339	0.428	CLONAL	1	TRUE	2	0.210107500714863	5		562	1048	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783730	50783730	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008928-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	72	502	0	ENST00000398568.2:c.121G>C	p.Val41Leu	p.V41L	ENST00000398568	NM_001042412.1	41	Gta/Cta	3/18	0.210107500714863	3	FACETS	0.975	0.85	1	0.487	0.425	0.555	CLONAL	1	TRUE	1	0.210107500714863	3		502	777	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627217	37627217	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008928-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	79	482	0	ENST00000447079.4:c.1132del	p.Arg378AlafsTer58	p.R378Afs*58	ENST00000447079	NM_015083.1	378	Cgc/gc	2/14	0.210107500714863	3	FACETS	1	0.924	1	0.535	0.47	0.605	CLONAL	1	TRUE	1	0.210107500714863	3		482	777	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481593	20481796	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCACCAACGTTCTGGAAGGCATCCACCTCATTAAGAAGAAGTCTAAAAACAACGTCCAATGGATGTGAGTAGGAGTCCTCCCCATGCCCCGGCTCTGAGGGGGTCGTTTCAAACTGCCTGGTTTCTTAGTTCCTCACTTTCACATCCACGCCCACACGTTCTTTTCTTTTCTCTCCTACTGTTTTCTTCTCTCTCATTCTCTCT	TCACCAACGTTCTGGAAGGCATCCACCTCATTAAGAAGAAGTCTAAAAACAACGTCCAATGGATGTGAGTAGGAGTCCTCCCCATGCCCCGGCTCTGAGGGGGTCGTTTCAAACTGCCTGGTTTCTTAGTTCCTCACTTTCACATCCACGCCCACACGTTCTTTTCTTTTCTCTCCTACTGTTTTCTTCTCTCTCATTCTCTCT	-	novel	NA	P-0008928-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	32	304	0	ENST00000346618.3:c.664_725+142del		p.X222_splice	ENST00000346618	NM_001949.4	222		3/7	0.210107500714863	5	FACETS	0.736	0.597	0.895	0.245	0.199	0.299	SUBCLONAL	1	TRUE	2	0.210107500714863	5		304	544	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760463	133760463	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008928-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1343	84	725	0	ENST00000318560.5:c.2786G>A	p.Gly929Asp	p.G929D	ENST00000318560	NM_005157.4	929	gGc/gAc	11/11	0.210107500714863	6	FACETS	0.796	0.7	0.899	0.199	0.175	0.225	SUBCLONAL	1	TRUE	2	0.210107500714863	6		725	1427	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0121446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	879	355	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	0.696548806779271	3	FACETS	0.892	0.872	0.912	1	0.998	1	CLONAL	3	NA	1	0.696548806779271	3		355	1271	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62009594	62009594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0121446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	223	369	1	ENST00000392795.3:c.28C>T	p.Pro10Ser	p.P10S	ENST00000392795	NM_001039933.1	10	Ccc/Tcc	1/6	0.519923973316901	4	FACETS	0.863	0.802	0.926	0.431	0.401	0.463	CLONAL	1	NA	2	0.696548806779271	4		370	1259	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144007	11144007	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	179	283	0	ENST00000358026.2:c.3588G>T	p.Gln1196His	p.Q1196H	ENST00000358026	NM_001128849.1	1196	caG/caT	26/36	0.216593449337541	0	FACETS		NA	1			1	INDETERMINATE	1	NA	0	0.696548806779271	0		283	570	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938761	76938762	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTA	novel	NA	P-0121446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	222	186	0	ENST00000373344.5:c.1983_1986dup	p.Pro663TyrfsTer10	p.P663Yfs*10	ENST00000373344	NM_000489.3	662	-/TACA	9/35	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	NA	0	0.696548806779271	1		186	386	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799221	42799221	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs569706440	NA	P-0121446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	27	61	0	ENST00000575354.2:c.4705G>T	p.Ala1569Ser	p.A1569S	ENST00000575354	NM_015125.3	1569	Gcc/Tcc	20/20	NA	2	FACETS	0.57	0.46	0.692			1	INDETERMINATE	1	NA	NA	0.696548806779271	2		61	136	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0121446-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	1122	355	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	0.53166963249761	6	FACETS	0.994	0.973	1			1	CLONAL	5	NA	NA	0.53166963249761	6		355	1752	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62009594	62009594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0121446-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1411	355	369	1	ENST00000392795.3:c.28C>T	p.Pro10Ser	p.P10S	ENST00000392795	NM_001039933.1	10	Ccc/Tcc	1/6	0.309898789605989	6	FACETS	0.78	0.737	0.825	0.52	0.491	0.55	INDETERMINATE	2	NA	3	0.53166963249761	6		370	1766	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144007	11144007	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121446-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	365	283	0	ENST00000358026.2:c.3588G>T	p.Gln1196His	p.Q1196H	ENST00000358026	NM_001128849.1	1196	caG/caT	26/36	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	NA	1	0.53166963249761	2		283	991	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938761	76938762	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTA	novel	NA	P-0121446-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	434	186	0	ENST00000373344.5:c.1983_1986dup	p.Pro663TyrfsTer10	p.P663Yfs*10	ENST00000373344	NM_000489.3	662	-/TACA	9/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	NA	0	0.53166963249761	1		186	803	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339184	116339184	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0121446-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1184	408	483	0	ENST00000397752.3:c.46T>C	p.Phe16Leu	p.F16L	ENST00000397752	NM_000245.2	16	Ttt/Ctt	2/21	0.53166963249761	3	FACETS	1	0.992	1	0.61	0.579	0.642	CLONAL	1	NA	1	0.53166963249761	3		483	1592	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0121446-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	792	355	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	0.542600226817195	4	FACETS	1	0.991	1			1	CLONAL	3	NA	NA	0.632779630271145	4		355	1310	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62009594	62009594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0121446-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	187	369	1	ENST00000392795.3:c.28C>T	p.Pro10Ser	p.P10S	ENST00000392795	NM_001039933.1	10	Ccc/Tcc	1/6	0.533554072315327	4	FACETS	0.999	0.923	1	0.5	0.461	0.539	CLONAL	1	NA	2	0.632779630271145	4		370	966	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144007	11144007	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121446-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	178	283	0	ENST00000358026.2:c.3588G>T	p.Gln1196His	p.Q1196H	ENST00000358026	NM_001128849.1	1196	caG/caT	26/36	0.285558499585178	1	FACETS	0.703	0.652	0.755	0.703	0.652	0.755	INDETERMINATE	1	NA	0	0.632779630271145	1		283	547	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938761	76938762	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTA	novel	NA	P-0121446-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	267	186	0	ENST00000373344.5:c.1983_1986dup	p.Pro663TyrfsTer10	p.P663Yfs*10	ENST00000373344	NM_000489.3	662	-/TACA	9/35	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	NA	0	0.632779630271145	1		186	485	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276736	115276736	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0121446-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	147	374	0	ENST00000438362.2:c.723G>C	p.Glu241Asp	p.E241D	ENST00000438362	NM_001242891.1	241	gaG/gaC	8/20	1	2	FACETS	0.902	0.829	0.978	0.902	0.829	0.978	CLONAL	1	NA	1	0.632779630271145	2		374	515	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877430	28877430	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0121446-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	136	556	2	ENST00000282397.4:c.3891T>A	p.Cys1297Ter	p.C1297*	ENST00000282397	NM_002019.4	1297	tgT/tgA	30/30	0.334304894340848	3	FACETS	0.696	0.633	0.762			1	INDETERMINATE	1	NA	NA	0.632779630271145	3		558	813	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528426	157528426	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0121446-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	211	578	0	ENST00000346085.5:c.6152del	p.Gly2051AlafsTer48	p.G2051Afs*48	ENST00000346085	NM_020732.3	2051	Ggc/gc	20/20	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	NA	1	0.632779630271145	2		578	654	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683601	162683601	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0121446-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	65	542	0	ENST00000366898.1:c.368T>A	p.Leu123Gln	p.L123Q	ENST00000366898	NM_004562.2	123	cTg/cAg	3/12	1	2	FACETS	0.323	0.279	0.369	0.323	0.279	0.369	SUBCLONAL	1	NA	1	0.632779630271145	2		542	637	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376084	118376084	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121446-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	54	561	1	ENST00000534358.1:c.9477G>T	p.Met3159Ile	p.M3159I	ENST00000534358	NM_005933.3	3159	atG/atT	27/36	0.632779630271145	1	FACETS	0.281	0.24	0.325	0.281	0.24	0.325	SUBCLONAL	1	NA	0	0.632779630271145	1		562	415	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023535	31023535	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121446-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	60	520	0	ENST00000375687.4:c.3020G>T	p.Gly1007Val	p.G1007V	ENST00000375687	NM_015338.5	1007	gGt/gTt	13/13	1	2	FACETS	0.32	0.276	0.369	0.32	0.276	0.369	SUBCLONAL	1	NA	1	0.632779630271145	2		520	592	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852427	42852427	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751523924	NA	P-0121446-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	51	582	1	ENST00000398585.3:c.659C>T	p.Ala220Val	p.A220V	ENST00000398585	NM_001135099.1	220	gCg/gTg	6/14	1	2	FACETS	0.267	0.226	0.311	0.267	0.226	0.311	SUBCLONAL	1	NA	1	0.632779630271145	2		583	604	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0121446-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	891	355	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	0.535452194594038	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	NA	1	0.885327886477452	4		355	1235	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62009594	62009594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0121446-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	250	369	1	ENST00000392795.3:c.28C>T	p.Pro10Ser	p.P10S	ENST00000392795	NM_001039933.1	10	Ccc/Tcc	1/6	0.864615887887508	4	FACETS	1	0.942	1	0.504	0.471	0.537	CLONAL	1	NA	2	0.885327886477452	4		370	1057	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144007	11144007	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121446-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	240	283	0	ENST00000358026.2:c.3588G>T	p.Gln1196His	p.Q1196H	ENST00000358026	NM_001128849.1	1196	caG/caT	26/36	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	NA	1	0.885327886477452	2		283	465	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938761	76938762	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTA	novel	NA	P-0121446-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	325	186	0	ENST00000373344.5:c.1983_1986dup	p.Pro663TyrfsTer10	p.P663Yfs*10	ENST00000373344	NM_000489.3	662	-/TACA	9/35	1	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	NA	0	0.885327886477452	1		186	409	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276736	115276736	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0121446-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	135	374	0	ENST00000438362.2:c.723G>C	p.Glu241Asp	p.E241D	ENST00000438362	NM_001242891.1	241	gaG/gaC	8/20	1	2	FACETS	0.95	0.877	1	0.95	0.877	1	CLONAL	1	NA	1	0.885327886477452	2		374	321	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877430	28877430	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0121446-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	162	556	2	ENST00000282397.4:c.3891T>A	p.Cys1297Ter	p.C1297*	ENST00000282397	NM_002019.4	1297	tgT/tgA	30/30	0.885327886477452	3	FACETS	0.987	0.911	1	0.493	0.455	0.533	CLONAL	1	NA	1	0.885327886477452	3		558	535	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528426	157528426	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0121446-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	242	578	0	ENST00000346085.5:c.6152del	p.Gly2051AlafsTer48	p.G2051Afs*48	ENST00000346085	NM_020732.3	2051	Ggc/gc	20/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	NA	1	0.885327886477452	2		578	509	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683601	162683601	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0121446-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	165	542	0	ENST00000366898.1:c.368T>A	p.Leu123Gln	p.L123Q	ENST00000366898	NM_004562.2	123	cTg/cAg	3/12	1	2	FACETS	0.823	0.763	0.884	0.823	0.763	0.884	CLONAL	1	NA	1	0.885327886477452	2		542	453	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295697	212295697	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0121446-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	32	648	0	ENST00000342788.4:c.2616A>T	p.Glu872Asp	p.E872D	ENST00000342788	NM_005235.2	872	gaA/gaT	21/28	1	2	FACETS	0.136	0.109	0.165	0.136	0.109	0.165	SUBCLONAL	1	NA	1	0.885327886477452	2		648	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0009432-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	375	656	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.656183180191011	1	FACETS	0.958	0.915	1	0.958	0.915	1	CLONAL	1	TRUE	0	0.656183180191011	1		657	802	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17355104	17355104	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009432-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	254	653	0	ENST00000375499.3:c.414T>A	p.Asp138Glu	p.D138E	ENST00000375499	NM_003000.2	138	gaT/gaA	4/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.656183180191011	2		653	763	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115975	8115975	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009432-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	228	582	0	ENST00000346208.3:c.1321del	p.Ala441ProfsTer34	p.A441Pfs*34	ENST00000346208		441	Gcc/cc	6/6	0.612028702375414	3	FACETS	1	0.938	1	0.503	0.469	0.538	CLONAL	1	TRUE	1	0.656183180191011	3		582	918	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0009817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	261	312	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.582212633409813	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.588216262262826	2		312	434	SUCCESS
AR	367	MSKCC	GRCh37	X	66943552	66943552	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137852578	NA	P-0009817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	167	170	0	ENST00000374690.3:c.2632A>G	p.Thr878Ala	p.T878A	ENST00000374690	NM_000044.3	878	Act/Gct	8/8	0.588216262262826	4	FACETS	0.858	0.787	0.932			1	CLONAL	1	TRUE	NA	0.588216262262826	4		170	1051	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696467	47696467	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	295	362	0	ENST00000347630.2:c.356G>A	p.Ser119Asn	p.S119N	ENST00000347630	NM_001007230.1	119	aGt/aAt	6/11	0.588216262262826	3	FACETS	0.992	0.942	1	0.992	0.942	1	CLONAL	2	TRUE	1	0.588216262262826	3		362	654	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913127	44913127	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	191	241	0	ENST00000377967.4:c.802T>A	p.Tyr268Asn	p.Y268N	ENST00000377967	NM_021140.2	268	Tat/Aat	10/29	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.588216262262826	1		241	353	SUCCESS
AR	367	MSKCC	GRCh37	X	66943537	66943557	+	inframe_deletion	In_Frame_Del	DEL	GAGCTGCATCAGTTCACTTTT	GAGCTGCATCAGTTCACTTTT	-	novel	NA	P-0009817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	114	158	0	ENST00000374690.3:c.2619_2639del	p.Glu873_Phe879del	p.E873_F879del	ENST00000374690	NM_000044.3	873	GAGCTGCATCAGTTCACTTTT/-	8/8	0.588216262262826	4	FACETS	0.663	0.596	0.734			1	SUBCLONAL	1	TRUE	NA	0.588216262262826	4		158	929	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609942	43609947	+	inframe_deletion	In_Frame_Del	DEL	GAGCTG	GAGCTG	-	rs121913312	NA	P-0010017-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	18147	638	1	ENST00000355710.3:c.1894_1899del	p.Glu632_Leu633del	p.E632_L633del	ENST00000355710	NM_020975.4	632	GAGCTG/-	11/20	0.662169850826283	19	FACETS	0.981	0.979	0.983			1	CLONAL	20	TRUE	NA	0.662169850826283	19		639	18521	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405827	157405827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373508866	NA	P-0010017-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	105	332	0	ENST00000346085.5:c.2069C>T	p.Thr690Met	p.T690M	ENST00000346085	NM_020732.3	690	aCg/aTg	6/20	0.621384502259387	3	FACETS	0.856	0.771	0.946	0.428	0.385	0.473	CLONAL	1	TRUE	1	0.662169850826283	3		332	493	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	146	749	6	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	0.135904133961486	3	FACETS	0.756	0.692	0.823	0.504	0.461	0.549	INDETERMINATE	2	TRUE	0	0.339546063738551	3		755	665	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0010083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	392	401	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.339546063738551	4	FACETS	0.995	0.948	1			1	CLONAL	3	TRUE	NA	0.339546063738551	4		401	1036	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0010083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	142	393	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.18272465546887	5	FACETS	1	0.986	1	0.492	0.448	0.538	INDETERMINATE	1	TRUE	2	0.339546063738551	5		393	856	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782177	NA	P-0010083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	283	526	0	ENST00000269305.4:c.644G>A	p.Ser215Asn	p.S215N	ENST00000269305	NM_001126112.2	215	aGt/aAt	6/11	0.264613498488453	2	FACETS	1	0.993	1	0.747	0.702	0.793	CLONAL	1	TRUE	0	0.339546063738551	2		526	1116	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416559	29416559	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	98	443	0	ENST00000389048.3:c.4394T>C	p.Val1465Ala	p.V1465A	ENST00000389048	NM_004304.4	1465	gTc/gCc	29/29	0.135904133961486	3	FACETS	0.74	0.659	0.827	0.247	0.219	0.276	INDETERMINATE	1	TRUE	0	0.339546063738551	3		443	912	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202801	128202801	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	46	391	0	ENST00000341105.2:c.919C>T	p.Arg307Trp	p.R307W	ENST00000341105	NM_032638.4	307	Cgg/Tgg	4/6	0.33810063060104	3	FACETS	0.394	0.331	0.465	0.197	0.165	0.233	SUBCLONAL	1	TRUE	1	0.339546063738551	3		391	804	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146538	185146538	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	177	344	0	ENST00000265026.3:c.169A>T	p.Ile57Phe	p.I57F	ENST00000265026	NM_004721.4	57	Atc/Ttc	2/14	0.33810063060104	3	FACETS	1	0.987	1	0.67	0.617	0.725	CLONAL	1	TRUE	1	0.339546063738551	3		344	910	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6045573	6045573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148270248	NA	P-0010083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	70	304	0	ENST00000265849.7:c.113C>T	p.Ala38Val	p.A38V	ENST00000265849	NM_000535.5	38	gCg/gTg	2/15	0.33810063060104	3	FACETS	0.951	0.831	1	0.476	0.415	0.541	CLONAL	1	TRUE	1	0.339546063738551	3		304	507	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995224	15995224	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	49	532	2	ENST00000268712.3:c.2969C>A	p.Ser990Tyr	p.S990Y	ENST00000268712	NM_006311.3	990	tCt/tAt	22/46	0.264613498488453	2	FACETS	0.306	0.258	0.359	0.153	0.129	0.18	SUBCLONAL	1	TRUE	0	0.339546063738551	2		534	943	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39704899	39704900	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0010083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	269	636	1	ENST00000361337.2:c.245_246del	p.Lys82ArgfsTer30	p.K82Rfs*30	ENST00000361337	NM_003286.2	82	AAa/a	4/21	0.135904133961486	3	FACETS	0.765	0.717	0.815	0.51	0.478	0.543	INDETERMINATE	2	TRUE	0	0.339546063738551	3		637	1211	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0010293-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	256	656	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.55234159892322	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.55234159892322	1		657	658	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076794	72076794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145840571	NA	P-0010293-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	166	494	0	ENST00000357731.5:c.703G>A	p.Val235Met	p.V235M	ENST00000357731	NM_173808.2	235	Gtg/Atg	5/7	1	2	FACETS	0.905	0.834	0.979	0.905	0.834	0.979	CLONAL	1	TRUE	1	0.55234159892322	2		494	664	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037876	49037876	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010293-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	140	241	0	ENST00000267163.4:c.2116T>C	p.Cys706Arg	p.C706R	ENST00000267163	NM_000321.2	706	Tgt/Cgt	21/27	0.311132646604602	1	FACETS	1	0.976	1	1	0.976	1	INDETERMINATE	1	TRUE	0	0.55234159892322	1		241	324	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435434	18435434	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010293-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	93	273	0	ENST00000266497.5:c.419G>T	p.Arg140Ile	p.R140I	ENST00000266497		140	aGa/aTa	1/31	1	2	FACETS	0.811	0.726	0.901	0.811	0.726	0.901	CLONAL	1	TRUE	1	0.55234159892322	2		273	415	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100139	30100139	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010293-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	269	590	1	ENST00000331968.5:c.1481T>A	p.Ile494Asn	p.I494N	ENST00000331968	NM_002742.2	494	aTc/aAc	10/18	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.55234159892322	2		591	930	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670716	67670716	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	248	532	0	ENST00000264010.4:c.1961G>C	p.Arg654Pro	p.R654P	ENST00000264010	NM_006565.3	654	cGa/cCa	11/12	0.652619789110875	2	FACETS	0.88	0.836	0.923	0.88	0.836	0.923	CLONAL	2	FALSE	0	0.652619789110875	2		532	432	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774101	56774101	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	95	558	0	ENST00000337432.4:c.452T>G	p.Val151Gly	p.V151G	ENST00000337432	NM_058216.2	151	gTg/gGg	3/9	0.618210526680197	2	FACETS	0.731	0.656	0.811	0.366	0.328	0.406	SUBCLONAL	1	FALSE	0	0.652619789110875	2		558	398	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514567	149514567	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371293050	NA	P-0010323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	110	412	8	ENST00000261799.4:c.377G>A	p.Gly126Asp	p.G126D	ENST00000261799	NM_002609.3	126	gGc/gAc	4/23	0.384981180742843	3	FACETS	1	0.97	1	0.39	0.353	0.428	INDETERMINATE	1	FALSE	0	0.652619789110875	3		420	382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0010475-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	912	825	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.502383600773375	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.502383600773375	2		826	1594	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0010475-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	271	451	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.462301228339227	3	FACETS	0.88	0.829	0.931	0.88	0.829	0.931	CLONAL	2	TRUE	1	0.502383600773375	3		452	767	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0010475-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	730	918	1	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.502383600773375	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.502383600773375	2		919	1415	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0010475-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	98	387	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	0.381835766234597	1	FACETS	0.585	0.524	0.65	0.585	0.524	0.65	SUBCLONAL	1	TRUE	0	0.502383600773375	1		387	499	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380309	25380309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1407509439	NA	P-0010475-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	147	464	0	ENST00000311936.3:c.149C>T	p.Thr50Ile	p.T50I	ENST00000311936	NM_004985.3	50	aCc/aTc	3/5	1	2	FACETS	0.792	0.724	0.863	0.792	0.724	0.863	SUBCLONAL	1	TRUE	1	0.502383600773375	2		464	739	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828578	72828578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1199271359	NA	P-0010475-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	338	771	0	ENST00000268489.5:c.8003G>A	p.Arg2668Gln	p.R2668Q	ENST00000268489	NM_006885.3	2668	cGa/cAa	9/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.502383600773375	2		771	1322	SUCCESS
APC	324	MSKCC	GRCh37	5	112175969	112175969	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010475-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	54	297	0	ENST00000257430.4:c.4678G>T	p.Glu1560Ter	p.E1560*	ENST00000257430	NM_000038.5	1560	Gaa/Taa	16/16	0.381835766234597	1	FACETS	0.393	0.336	0.454	0.393	0.336	0.454	SUBCLONAL	1	TRUE	0	0.502383600773375	1		297	410	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035987	47035987	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0010475-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	329	790	0	ENST00000377604.3:c.663+2T>C		p.X221_splice	ENST00000377604	NM_001204468.1	221			0.502383600773375	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.502383600773375	1		790	948	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195568	102195568	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010475-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	206	540	0	ENST00000263464.3:c.328C>T	p.Gln110Ter	p.Q110*	ENST00000263464	NM_001165.4	110	Cag/Tag	2/9	0.462301228339227	3	FACETS	0.923	0.855	0.993	0.461	0.427	0.497	CLONAL	1	TRUE	1	0.502383600773375	3		540	1112	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715745	18715746	+	missense_variant	Missense_Mutation	DNP	TC	TC	CA	novel	NA	P-0010475-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	125	392	0	ENST00000266497.5:c.3576_3577delinsCA	p.Pro1193Thr	p.P1193T	ENST00000266497		1192	ttTCct/ttCAct	25/31	NA	2	FACETS	0.872	0.792	0.955			1	INDETERMINATE	1	TRUE	NA	0.502383600773375	2		392	571	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99192889	99192889	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010475-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	456	526	0	ENST00000268035.6:c.79C>G	p.Pro27Ala	p.P27A	ENST00000268035	NM_000875.3	27	Ccg/Gcg	1/21	0.25779657226588	3	FACETS	0.977	0.934	1	0.977	0.934	1	INDETERMINATE	2	TRUE	1	0.502383600773375	3		526	1163	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641488	23641488	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs62625277	NA	P-0010475-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	217	634	3	ENST00000261584.4:c.1987C>T	p.Arg663Cys	p.R663C	ENST00000261584	NM_024675.3	663	Cgc/Tgc	5/13	1	2	FACETS	0.896	0.834	0.961	0.896	0.834	0.961	CLONAL	1	TRUE	1	0.502383600773375	2		637	964	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572390	41572390	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010475-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1215	398	918	0	ENST00000263253.7:c.4919A>C	p.Glu1640Ala	p.E1640A	ENST00000263253	NM_001429.3	1640	gAg/gCg	30/31	1	2	FACETS	0.982	0.932	1	0.982	0.932	1	CLONAL	1	TRUE	1	0.502383600773375	2		918	1613	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424388	47424388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010475-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	302	704	0	ENST00000377045.4:c.308G>A	p.Arg103Gln	p.R103Q	ENST00000377045	NM_001654.4	103	cGg/cAg	5/16	0.502383600773375	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.502383600773375	1		704	874	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274181	10274182	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	A	novel	NA	P-0010475-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	310	703	2	ENST00000330684.3:c.87_88delinsT	p.Lys29AsnfsTer6	p.K29Nfs*6	ENST00000330684	NM_001134407.1	29	aaGGgt/aaTgt	2/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.502383600773375	2		705	1161	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057054	180057054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010811-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	370	721	1	ENST00000261937.6:c.565C>T	p.Arg189Trp	p.R189W	ENST00000261937	NM_182925.4	189	Cgg/Tgg	5/30	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.784257977483344	2		722	905	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679810	88679810	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010811-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	238	416	0	ENST00000360948.2:c.653del	p.Asn218ThrfsTer2	p.N218Tfs*2	ENST00000360948	NM_001012338.2	218	aAc/ac	7/19	1	2	FACETS	0.974	0.916	1	0.974	0.916	1	CLONAL	1	TRUE	1	0.784257977483344	2		416	623	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443893	52443893	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1467015377	NA	P-0010811-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	292	539	0	ENST00000460680.1:c.2T>C	p.Met1?	p.M1?	ENST00000460680	NM_004656.3	1	aTg/aCg	1/17	0.784257977483344	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.784257977483344	1		539	452	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954217	48954217	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010811-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	151	267	0	ENST00000267163.4:c.1418T>G	p.Phe473Cys	p.F473C	ENST00000267163	NM_000321.2	473	tTt/tGt	15/27	0.745076653804344	1	FACETS	0.933	0.875	0.989	0.933	0.875	0.989	CLONAL	1	TRUE	0	0.784257977483344	1		267	251	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0012534-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	249	449	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.642293626552778	2	FACETS	0.925	0.881	0.969	0.925	0.881	0.969	CLONAL	2	TRUE	0	0.650165367024125	2		449	414	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855921	68855921	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012534-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	273	495	0	ENST00000261769.5:c.1730del	p.Gly577GlufsTer7	p.G577Efs*7	ENST00000261769	NM_004360.3	577	Gga/ga	12/16	0.650165367024125	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.650165367024125	1		495	551	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850987	63850987	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012534-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	354	619	0	ENST00000279873.7:c.1765G>T	p.Glu589Ter	p.E589*	ENST00000279873	NM_032199.2	589	Gaa/Taa	10/10	1	2	FACETS	0.951	0.902	1	0.951	0.902	1	CLONAL	1	TRUE	1	0.650165367024125	2		619	1145	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426701	121426701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753998395	NA	P-0012534-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	412	816	1	ENST00000257555.6:c.392G>A	p.Arg131Gln	p.R131Q	ENST00000257555		131	cGg/cAg	2/10	1	2	FACETS	0.916	0.871	0.961	0.916	0.871	0.961	CLONAL	1	TRUE	1	0.650165367024125	2		817	1384	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851728	63851728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285691243	NA	P-0012534-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	332	681	0	ENST00000279873.7:c.2506C>T	p.His836Tyr	p.H836Y	ENST00000279873	NM_032199.2	836	Cat/Tat	10/10	1	2	FACETS	0.94	0.889	0.991	0.94	0.889	0.991	CLONAL	1	TRUE	1	0.650165367024125	2		681	1087	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560967	9560967	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012534-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	311	538	0	ENST00000353224.5:c.815A>T	p.Tyr272Phe	p.Y272F	ENST00000353224	NM_177990.2	272	tAc/tTc	4/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.650165367024125	2		538	951	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776294	76776294	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012534-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	121	648	0	ENST00000373344.5:c.7172A>G	p.Tyr2391Cys	p.Y2391C	ENST00000373344	NM_000489.3	2391	tAc/tGc	34/35	0.442343458161464	1	FACETS	0.438	0.397	0.481	0.438	0.397	0.481	SUBCLONAL	1	TRUE	0	0.650165367024125	1		648	574	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961067	79961067	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012534-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	247	604	0	ENST00000265081.6:c.464C>G	p.Ser155Cys	p.S155C	ENST00000265081	NM_002439.4	155	tCt/tGt	3/24	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.650165367024125	2		604	753	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0012534-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	344	589	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.650165367024125	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.650165367024125	1		589	698	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981825	101981825	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1465324347	NA	P-0012534-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	211	698	0	ENST00000282441.5:c.246G>C	p.Gln82His	p.Q82H	ENST00000282441	NM_001130145.2	82	caG/caC	1/9	0.343188179637834	1	FACETS	0.434	0.403	0.466	0.434	0.403	0.466	INDETERMINATE	1	TRUE	0	0.650165367024125	1		698	1010	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588597	28588597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012534-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	101	445	0	ENST00000241453.7:c.2851G>A	p.Glu951Lys	p.E951K	ENST00000241453	NM_004119.2	951	Gaa/Aaa	23/24	0.650165367024125	1	FACETS	0.498	0.448	0.551	0.498	0.448	0.551	SUBCLONAL	1	TRUE	0	0.650165367024125	1		445	421	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965519	25965519	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012534-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	371	653	0	ENST00000435504.4:c.3687G>C	p.Lys1229Asn	p.K1229N	ENST00000435504		1229	aaG/aaC	13/13	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.650165367024125	2		653	1135	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966466	25966466	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012534-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	377	740	0	ENST00000435504.4:c.2740G>C	p.Ala914Pro	p.A914P	ENST00000435504		914	Gct/Cct	13/13	1	2	FACETS	0.969	0.92	1	0.969	0.92	1	CLONAL	1	TRUE	1	0.650165367024125	2		740	1197	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584707	187584707	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs377347450	NA	P-0012534-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	92	510	0	ENST00000441802.2:c.3326T>C	p.Val1109Ala	p.V1109A	ENST00000441802	NM_005245.3	1109	gTc/gCc	3/27	0.650165367024125	1	FACETS	0.368	0.328	0.411	0.368	0.328	0.411	SUBCLONAL	1	TRUE	0	0.650165367024125	1		510	519	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80037300	80037300	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs758191157	NA	P-0012534-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	54	330	0	ENST00000265081.6:c.1586C>G	p.Ser529Ter	p.S529*	ENST00000265081	NM_002439.4	529	tCa/tGa	11/24	1	2	FACETS	0.464	0.398	0.536	0.464	0.398	0.536	SUBCLONAL	1	TRUE	1	0.650165367024125	2		330	358	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000077	30000078	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0013567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	88	524	0	ENST00000338641.4:c.91dup	p.Ala31GlyfsTer18	p.A31Gfs*18	ENST00000338641	NM_000268.3	30	-/G	1/16	0.110892736253433	0	FACETS	0.9	0.816	0.985			1	CLONAL	8	FALSE	0	0.110892736253433	0		524	196	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0014127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	230	516	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.282153016417466	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	0	0.289384496095755	2		516	794	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0014127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	171	443	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.202877479502252	5	FACETS	0.992	0.914	1	0.662	0.609	0.716	CLONAL	2	TRUE	2	0.289384496095755	5		443	854	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971187	21971197	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGCTGCCCA	GGCGCTGCCCA	-	novel	NA	P-0014127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	66	383	0	ENST00000304494.5:c.161_171del	p.Met54ThrfsTer62	p.M54Tfs*62	ENST00000304494	NM_000077.4	54	aTGGGCAGCGCC/a	2/3	0.289384496095755	1	FACETS	0.859	0.748	0.979	0.859	0.748	0.979	CLONAL	1	TRUE	0	0.289384496095755	1		383	454	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73108243	73108243	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	15	121	0	ENST00000356692.5:c.343T>C	p.Tyr115His	p.Y115H	ENST00000356692		115	Tat/Cat	4/9	0.289384496095755	1	FACETS	0.558	0.41	0.733	0.558	0.41	0.733	SUBCLONAL	1	TRUE	0	0.289384496095755	1		121	159	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539410	187539410	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	65	396	0	ENST00000441802.2:c.8330C>A	p.Ser2777Tyr	p.S2777Y	ENST00000441802	NM_005245.3	2777	tCc/tAc	10/27	0.289384496095755	1	FACETS	0.7	0.607	0.8	0.7	0.607	0.8	SUBCLONAL	1	TRUE	0	0.289384496095755	1		396	549	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014244-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	378	803	5	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.792294705477528	1	FACETS	0.952	0.916	0.988	0.952	0.916	0.988	CLONAL	1	TRUE	0	0.792294705477528	1		808	605	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347935	89347935	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0014244-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	458	794	0	ENST00000301030.4:c.5015C>G	p.Ser1672Ter	p.S1672*	ENST00000301030	NM_001256183.1	1672	tCa/tGa	9/13	0.792294705477528	1	FACETS	0.978	0.945	1	0.978	0.945	1	CLONAL	1	TRUE	0	0.792294705477528	1		794	714	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750824	57750824	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014244-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	301	511	0	ENST00000274289.3:c.1780G>T	p.Asp594Tyr	p.D594Y	ENST00000274289	NM_006622.3	594	Gat/Tat	13/14	1	2	FACETS	0.938	0.887	0.989	0.938	0.887	0.989	CLONAL	1	TRUE	1	0.792294705477528	2		511	810	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417896	138417896	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014244-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	331	468	0	ENST00000289153.2:c.1623C>G	p.Ile541Met	p.I541M	ENST00000289153	NM_006219.2	541	atC/atG	11/22	0.710832993121548	3	FACETS	1	0.955	1			1	CLONAL	1	TRUE	NA	0.792294705477528	3		468	1153	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435254	49435254	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199761931	NA	P-0014244-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	410	675	0	ENST00000301067.7:c.6299C>A	p.Pro2100Gln	p.P2100Q	ENST00000301067	NM_003482.3	2100	cCg/cAg	31/54	0.792294705477528	3	FACETS	1	0.967	1	0.511	0.486	0.537	CLONAL	1	TRUE	1	0.792294705477528	3		675	1414	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906434	32906444	+	frameshift_variant	Frame_Shift_Del	DEL	ATTTAAAGTAA	ATTTAAAGTAA	-	novel	NA	P-0014244-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	290	441	0	ENST00000380152.3:c.821_831del	p.Phe274Ter	p.F274*	ENST00000380152		273	tcATTTAAAGTAAat/tcat	10/27	0.792294705477528	1	FACETS	0.98	0.939	1	0.98	0.939	1	CLONAL	1	TRUE	0	0.792294705477528	1		441	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578224	7578224	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1429743956	NA	P-0014640-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	235	591	1	ENST00000269305.4:c.625A>T	p.Arg209Ter	p.R209*	ENST00000269305	NM_001126112.2	209	Aga/Tga	6/11	0.733582349217018	1	FACETS	0.999	0.948	1	0.999	0.948	1	CLONAL	1	TRUE	0	0.734968958182068	1		592	405	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741946	17741946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014640-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	37	255	0	ENST00000250003.3:c.617G>T	p.Cys206Phe	p.C206F	ENST00000250003	NM_002478.4	206	tGc/tTc	1/3	0.412446760594367	1	FACETS	0.36	0.3	0.425	0.36	0.3	0.425	INDETERMINATE	1	TRUE	0	0.734968958182068	1		255	177	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086199	16086199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014640-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	162	510	0	ENST00000281043.3:c.1375G>A	p.Glu459Lys	p.E459K	ENST00000281043	NM_005378.4	459	Gaa/Aaa	3/3	1	2	FACETS	0.875	0.808	0.943	0.875	0.808	0.943	CLONAL	1	TRUE	1	0.734968958182068	2		510	504	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	protein_altering_variant	In_Frame_Ins	INS	-	-	GTT	rs1554350347	NA	P-0014640-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	573	522	0	ENST00000275493.2:c.2308_2309insGTT	p.Asp770delinsGlyTyr	p.D770delinsGY	ENST00000275493	NM_005228.3	770	gac/gGTTac	20/28	0.699712291222716	4	FACETS	0.924	0.894	0.953	0.924	0.894	0.953	CLONAL	3	TRUE	1	0.734968958182068	4		522	976	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0016354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	369	630	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	NA	2	FACETS	0.84	0.8	0.88			1	INDETERMINATE	2	TRUE	NA	0.480823743930187	2		630	914	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244068	5244068	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	164	438	1	ENST00000357368.4:c.1414G>T	p.Val472Leu	p.V472L	ENST00000357368	NM_002850.3	472	Gtg/Ttg	11/38	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.480823743930187	2		439	659	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612226	189612226	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1164945219	NA	P-0016354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	95	380	0	ENST00000264731.3:c.1978G>A	p.Asp660Asn	p.D660N	ENST00000264731	NM_003722.4	660	Gac/Aac	14/14	1	2	FACETS	0.941	0.843	1	0.941	0.843	1	CLONAL	1	TRUE	1	0.480823743930187	2		380	420	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293167	1294189	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGTTCACTGCTCTGGCCTCGGCGCCTGGAAACCGCGTGTCCATCAAAACGTGAAGGTGAACCTCGTAAGTTTATGCAAACTGGACAGGAGGGAGAGCAGAGGCAGAGATCACCGTGTCCACTCGACGTCCTGAGCGAAAAGCCACGTGTGCCCACGTGACGATGGAGACAGGAGGACCAGGGCTCTGCCTGCCCCCTTTTCTGAGCCCCTACTGCATTCAGCTCTGGGGCCTGGGCCCTCGACGGCCACCACCTCCTCACCTGGGCTCCTGCGCAGCCAAGCGCAGTCCCGCACGCTCATCTTCCACGTCAGCTCCTGCAGCGAGAGCTTGGCATGCTTCCCCAGGGAGATGAACTTCTTGGTGTTCCTGAGGAAGCGGCGTTCGTTGTGCCTGGAGCCCCAGAGGCCTGGGGGCACCAGCCGGCGCAGGCAGGCCCGCACGAAGCCGTACACCTGCCAGGGGCTGCTGTGCTGGCGGAGCAGCTGCACCAGGCGACGGGGGTCTGTGTCCTCCTCCTCGGGGGCCGCCACAGAGCCCTGGGGCTTCTCCCGGGCACAGACACCGGCTGCTGGGGTGACCGCAGCTCGCAGCGGGCAGTGCGTCTTGAGGAGCACCCCGTAGGGGCACTGCGCGTGGTTCCCAAGCAGCTCCAGAAACAGGGGCCGCATTTGCCAGTAGCGCTGGGGCAGGCGGGGCAACCTGCGGGGAGTCCCTGGCATCCAGGGCCTGGAACCCAGAAAGATGGTCTCCACGAGCCTCCGAGCGCCAGTCAGGCTGGGCCTCAGAGAGCTGAGTAGGAAGGAGGGCCGCAGCTGCTCCTTGTCGCCTGAGGAGTAGAGGAAGTGCTTGGTCTCGGCGTACACCGGGGGACAAGGCGTGTCCCAGGGACGTGGTGGCCGCGATGTGGATGGGGGGCCCGCGTGGTGCTGGCGGCCCACGGATGGGTGGGAGTGGCGCGTGCCAGAGAGCGCACCCTCCAAAGAGGTGGCTTCTTCGGCGGGTCTGGCAGGTGACACCACAC	CTGTTCACTGCTCTGGCCTCGGCGCCTGGAAACCGCGTGTCCATCAAAACGTGAAGGTGAACCTCGTAAGTTTATGCAAACTGGACAGGAGGGAGAGCAGAGGCAGAGATCACCGTGTCCACTCGACGTCCTGAGCGAAAAGCCACGTGTGCCCACGTGACGATGGAGACAGGAGGACCAGGGCTCTGCCTGCCCCCTTTTCTGAGCCCCTACTGCATTCAGCTCTGGGGCCTGGGCCCTCGACGGCCACCACCTCCTCACCTGGGCTCCTGCGCAGCCAAGCGCAGTCCCGCACGCTCATCTTCCACGTCAGCTCCTGCAGCGAGAGCTTGGCATGCTTCCCCAGGGAGATGAACTTCTTGGTGTTCCTGAGGAAGCGGCGTTCGTTGTGCCTGGAGCCCCAGAGGCCTGGGGGCACCAGCCGGCGCAGGCAGGCCCGCACGAAGCCGTACACCTGCCAGGGGCTGCTGTGCTGGCGGAGCAGCTGCACCAGGCGACGGGGGTCTGTGTCCTCCTCCTCGGGGGCCGCCACAGAGCCCTGGGGCTTCTCCCGGGCACAGACACCGGCTGCTGGGGTGACCGCAGCTCGCAGCGGGCAGTGCGTCTTGAGGAGCACCCCGTAGGGGCACTGCGCGTGGTTCCCAAGCAGCTCCAGAAACAGGGGCCGCATTTGCCAGTAGCGCTGGGGCAGGCGGGGCAACCTGCGGGGAGTCCCTGGCATCCAGGGCCTGGAACCCAGAAAGATGGTCTCCACGAGCCTCCGAGCGCCAGTCAGGCTGGGCCTCAGAGAGCTGAGTAGGAAGGAGGGCCGCAGCTGCTCCTTGTCGCCTGAGGAGTAGAGGAAGTGCTTGGTCTCGGCGTACACCGGGGGACAAGGCGTGTCCCAGGGACGTGGTGGCCGCGATGTGGATGGGGGGCCCGCGTGGTGCTGGCGGCCCACGGATGGGTGGGAGTGGCGCGTGCCAGAGAGCGCACCCTCCAAAGAGGTGGCTTCTTCGGCGGGTCTGGCAGGTGACACCACAC	-	novel	NA	P-0016354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	44	3	0	ENST00000310581.5:c.812_1573+261del		p.X271_splice	ENST00000310581	NM_198253.2	271		2/16	0.480823743930187	11	FACETS	1	0.948	1			1	CLONAL	11	TRUE	NA	0.480823743930187	11		3	51	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115955	8115956	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0016627-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	108	558	0	ENST00000346208.3:c.1305dup	p.Ser436LeufsTer71	p.S436Lfs*71	ENST00000346208		434	cac/caCc	6/6	0.556665745705555	2	FACETS	0.646	0.582	0.714	0.323	0.291	0.357	SUBCLONAL	1	TRUE	0	0.611161186354302	2		558	547	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530077	63530077	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016627-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4437	987	721	0	ENST00000307078.5:c.2358G>C	p.Leu786Phe	p.L786F	ENST00000307078	NM_004655.3	786	ttG/ttC	10/11	0.611161186354302	16	FACETS	1	0.988	1			1	CLONAL	3	TRUE	NA	0.611161186354302	16		721	5424	SUCCESS
BTK	695	MSKCC	GRCh37	X	100612524	100612524	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016627-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	144	624	0	ENST00000308731.7:c.1150G>A	p.Ala384Thr	p.A384T	ENST00000308731	NM_000061.2	384	Gca/Aca	13/19	0.506008332615826	0	FACETS	0.454	0.418	0.49			1	SUBCLONAL	1	TRUE	0	0.611161186354302	0		624	404	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521306	8521306	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs776820755	NA	P-0016627-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	43	476	0	ENST00000356435.5:c.932T>C	p.Ile311Thr	p.I311T	ENST00000356435		311	aTt/aCt	9/35	0.611161186354302	1	FACETS	0.31	0.26	0.365	0.31	0.26	0.365	SUBCLONAL	1	TRUE	0	0.611161186354302	1		476	315	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212002	94212002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016627-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	23	577	0	ENST00000323929.3:c.443G>A	p.Gly148Glu	p.G148E	ENST00000323929	NM_005591.3	148	gGa/gAa	6/20	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.611161186354302	NA		577	391	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0016642-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	32	542	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.29543451629437	4	FACETS	0.56	0.453	0.682	0.187	0.151	0.228	SUBCLONAL	1	TRUE	1	0.19	4		542	716	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471614	120471614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1399178397	NA	P-0016642-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	70	466	0	ENST00000256646.2:c.3877C>T	p.Arg1293Cys	p.R1293C	ENST00000256646	NM_024408.3	1293	Cgt/Tgt	23/34	0.224415865150511	3	FACETS	1	0.965	1	0.666	0.58	0.758	CLONAL	1	TRUE	1	0.19	3		466	606	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190718	108190718	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016642-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	55	466	0	ENST00000278616.4:c.6385T>A	p.Tyr2129Asn	p.Y2129N	ENST00000278616	NM_000051.3	2129	Tac/Aac	44/63	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.19	2		466	550	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343489	118343489	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016642-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	33	482	0	ENST00000534358.1:c.1615G>T	p.Gly539Ter	p.G539*	ENST00000534358	NM_005933.3	539	Gga/Tga	3/36	1	2	FACETS	0.549	0.446	0.666	0.549	0.446	0.666	SUBCLONAL	1	TRUE	1	0.19	2		482	633	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554270	63554270	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs951973598	NA	P-0016642-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	124	729	0	ENST00000307078.5:c.469A>G	p.Ile157Val	p.I157V	ENST00000307078	NM_004655.3	157	Ata/Gta	2/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.19	2		729	993	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221309	1221310	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs587776659	NA	P-0016642-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	185	926	0	ENST00000326873.7:c.834_835del	p.Cys278TrpfsTer6	p.C278Wfs*6	ENST00000326873	NM_000455.4	278	TGt/t	6/10	1	2	FACETS	0.873	0.805	0.944	1	0.992	1	CLONAL	2	TRUE	1	0.19	2		926	1115	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295731	212295731	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016642-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	46	600	0	ENST00000342788.4:c.2582A>G	p.Asp861Gly	p.D861G	ENST00000342788	NM_005235.2	861	gAt/gGt	21/28	1	2	FACETS	0.682	0.573	0.803	0.682	0.573	0.803	SUBCLONAL	1	TRUE	1	0.19	2		600	710	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521667	89521667	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016642-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	87	588	0	ENST00000336596.2:c.2744C>A	p.Thr915Lys	p.T915K	ENST00000336596	NM_005233.5	915	aCa/aAa	16/17	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.19	2		588	754	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535298	66535298	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016642-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	61	839	0	ENST00000273854.3:c.163G>C	p.Ala55Pro	p.A55P	ENST00000273854	NM_004439.5	55	Gcc/Ccc	1/18	1	2	FACETS	0.748	0.643	0.861	0.748	0.643	0.861	SUBCLONAL	1	TRUE	1	0.19	2		839	859	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409851	63409851	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016642-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	95	736	0	ENST00000330258.3:c.3316A>G	p.Ser1106Gly	p.S1106G	ENST00000330258	NM_152424.3	1106	Agc/Ggc	2/2	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.19	2		736	823	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017682-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	254	264	0	ENST00000397062.3:c.92G>A	p.Gly31Glu	p.G31E	ENST00000397062	NM_006164.4	31	gGa/gAa	2/5	0.836567168339705	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.836567168339705	3		264	279	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024001	27024002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0017682-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	75	176	2	ENST00000324856.7:c.1113dup	p.Gln372AlafsTer28	p.Q372Afs*28	ENST00000324856	NM_006015.4	369	-/G	1/20	0.825328213072599	2	FACETS	0.924	0.861	0.981	0.924	0.861	0.981	CLONAL	2	TRUE	0	0.836567168339705	2		178	97	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998898	11998898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017682-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	66	197	0	ENST00000353533.5:c.400C>T	p.Arg134Trp	p.R134W	ENST00000353533	NM_003010.3	134	Cgg/Tgg	4/11	0.281908162756877	3	FACETS	0.772	0.689	0.855	0.772	0.689	0.855	INDETERMINATE	2	TRUE	1	0.836567168339705	3		197	145	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247367	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747241612	NA	P-0017682-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	154	265	0	ENST00000281708.4:c.1435C>G	p.Arg479Gly	p.R479G	ENST00000281708	NM_033632.3	479	Cga/Gga	10/12	0.826908195749879	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.836567168339705	2		265	184	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163297333	163297333	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017682-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	72	427	1	ENST00000271452.3:c.179G>T	p.Arg60Leu	p.R60L	ENST00000271452	NM_145697.2	60	cGa/cTa	3/14	0.529076210714683	6	FACETS	1	0.952	1	0.39	0.342	0.441	CLONAL	1	TRUE	3	0.836567168339705	6		428	393	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211581	46211581	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017682-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	75	267	0	ENST00000334344.6:c.547C>G	p.Leu183Val	p.L183V	ENST00000334344	NM_152641.2	183	Cta/Gta	5/21	0.836567168339705	3	FACETS	0.938	0.832	1	0.469	0.416	0.525	CLONAL	1	TRUE	1	0.836567168339705	3		267	271	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624812	9624812	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017682-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	117	453	0	ENST00000353224.5:c.165C>A	p.Asp55Glu	p.D55E	ENST00000353224	NM_177990.2	55	gaC/gaA	3/10	0.836567168339705	4	FACETS	1	0.959	1	0.551	0.5	0.605	CLONAL	1	TRUE	2	0.836567168339705	4		453	466	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319901	62319901	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017682-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	194	830	0	ENST00000360203.5:c.1743G>C	p.Lys581Asn	p.K581N	ENST00000360203	NM_001283009.1	581	aaG/aaC	21/35	0.836567168339705	4	FACETS	1	0.971	1	0.546	0.506	0.587	CLONAL	1	TRUE	2	0.836567168339705	4		830	780	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272456	21272456	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017682-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	194	784	0	ENST00000354336.3:c.234T>A	p.Phe78Leu	p.F78L	ENST00000354336	NM_005207.3	78	ttT/ttA	1/3	0.836567168339705	3	FACETS	0.995	0.925	1	0.498	0.462	0.534	CLONAL	1	TRUE	1	0.836567168339705	3		784	661	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648406	30648406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017682-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	124	592	1	ENST00000295754.5:c.31C>T	p.Pro11Ser	p.P11S	ENST00000295754	NM_003242.5	11	Ccg/Tcg	1/7	0.825328213072599	2	FACETS	1	0.969	1	0.551	0.508	0.594	CLONAL	1	TRUE	0	0.836567168339705	2		593	269	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967154	25967171	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCTGCAGCAGCTGC	GGCGGCTGCAGCAGCTGC	-	novel	NA	P-0017801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	100	239	0	ENST00000435504.4:c.2035_2052del	p.Ala679_Ala684del	p.A679_A684del	ENST00000435504		679	GCAGCTGCTGCAGCCGCC/-	13/13	1	2	FACETS	0.919	0.831	1	0.919	0.831	1	CLONAL	1	TRUE	1	0.671348547762158	2		239	324	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967154	25967171	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCTGCAGCAGCTGC	GGCGGCTGCAGCAGCTGC	-	novel	NA	P-0017801-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	100	239	0	ENST00000435504.4:c.2035_2052del	p.Ala679_Ala684del	p.A679_A684del	ENST00000435504		679	GCAGCTGCTGCAGCCGCC/-	13/13	1	2	FACETS	0.681	0.61	0.755	0.681	0.61	0.755	SUBCLONAL	1	TRUE	1	0.559617476677659	2		239	525	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0019590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	693	475	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	NA	2	FACETS	1	0.997	1			1	INDETERMINATE	2	TRUE	NA	0.75775819221464	2		476	808	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240266	41240295	+	inframe_deletion	In_Frame_Del	DEL	GGGCAGCGGCCAGGTGCACGAGCGCGGCCG	GGGCAGCGGCCAGGTGCACGAGCGCGGCCG	-	novel	NA	P-0019590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	221	281	0	ENST00000379561.5:c.55_84del	p.Arg21_Pro30del	p.R21_P30del	ENST00000379561	NM_002015.3	19	CGGCCGCGCTCGTGCACCTGGCCGCTGCCC/-	1/3	0.294599109386081	5	FACETS	0.999	0.944	1	0.999	0.944	1	INDETERMINATE	3	TRUE	2	0.75775819221464	5		281	416	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435050	56435050	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	254	870	1	ENST00000407977.2:c.2087C>T	p.Ala696Val	p.A696V	ENST00000407977		696	gCa/gTa	9/10	0.521009079605348	4	FACETS	0.966	0.903	1	0.483	0.451	0.516	CLONAL	1	TRUE	2	0.75775819221464	4		871	1220	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938368	76938368	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0019590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	528	690	0	ENST00000373344.5:c.2380A>T	p.Lys794Ter	p.K794*	ENST00000373344	NM_000489.3	794	Aag/Tag	9/35	0.521009079605348	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	2	0.75775819221464	4		690	1130	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059188	27059194	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTCTC	GGGTCTC	-	novel	NA	P-0021868-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	537	322	1	ENST00000324856.7:c.1825_1831del	p.Gly609ArgfsTer8	p.G609Rfs*8	ENST00000324856	NM_006015.4	609	GGGTCTCag/ag	4/20	0.715507638659103	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.715507638659103	2		323	643	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339171	65339172	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0022637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	63	1107	0	ENST00000342505.4:c.364_365del	p.Asn122Ter	p.N122*	ENST00000342505	NM_002227.2	122	AAt/t	5/25	1	2	FACETS	0.332	0.288	0.379	0.332	0.288	0.379	SUBCLONAL	1	TRUE	1	1.01	2		1107	376	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711888	89711889	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0022637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	54	838	0	ENST00000371953.3:c.507_508dup	p.Ser170ThrfsTer14	p.S170Tfs*14	ENST00000371953	NM_000314.4	169	ccc/ccCAc	6/9	0.3	1	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	1.01	1		838	250	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420285	49420285	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	85	1528	0	ENST00000301067.7:c.15464T>A	p.Val5155Asp	p.V5155D	ENST00000301067	NM_003482.3	5155	gTc/gAc	48/54	1	2	FACETS	0.339	0.3	0.38	0.339	0.3	0.38	SUBCLONAL	1	TRUE	1	1.01	2		1528	497	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061312	38061312	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1329067081	NA	P-0022637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	156	1694	2	ENST00000250448.2:c.677A>G	p.Asp226Gly	p.D226G	ENST00000250448	NM_004496.3	226	gAc/gGc	2/2	0.177289725839775	3	FACETS	0.707	0.649	0.766	0.353	0.324	0.383	INDETERMINATE	1	TRUE	1	1.01	3		1696	658	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40681779	40681789	+	frameshift_variant	Frame_Shift_Del	DEL	CAAGCAGTTGC	CAAGCAGTTGC	GAGTTGT	novel	NA	P-0022637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	55	736	1	ENST00000249776.8:c.558_568delinsGAGTTGT	p.Asn186LysfsTer7	p.N186Kfs*7	ENST00000249776	NM_033286.3	186	aaCAAGCAGTTGCac/aaGAGTTGTac	5/9	1	2	FACETS	0.355	0.305	0.408	0.355	0.305	0.408	SUBCLONAL	1	TRUE	1	1.01	2		737	307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0022691-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	26	856	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.121821658102028	1	FACETS	0.838	0.663	1	0.838	0.663	1	CLONAL	1	TRUE	0	0.12	1		856	486	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0022691-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	22	312	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.935	0.724	1	0.935	0.724	1	CLONAL	1	TRUE	1	0.12	2		312	392	SUCCESS
APC	324	MSKCC	GRCh37	5	112154942	112154942	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779780	NA	P-0022691-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	24	0	0	ENST00000257430.4:c.1213C>T	p.Arg405Ter	p.R405*	ENST00000257430	NM_000038.5	405	Cga/Tga	10/16	1	2	FACETS	0.677	0.529	0.849	0.677	0.529	0.849	SUBCLONAL	1	TRUE	1	0.12	2		0	591	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920435	114920435	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022691-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	9	0	0	ENST00000543371.1:c.1376G>T	p.Trp459Leu	p.W459L	ENST00000543371	NM_001198531.1	459	tGg/tTg	13/14	1	2	FACETS	0.311	0.205	0.448	0.311	0.205	0.448	SUBCLONAL	1	TRUE	1	0.12	2		0	482	SUCCESS
APC	324	MSKCC	GRCh37	5	112177149	112177149	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022691-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	16	0	0	ENST00000257430.4:c.5858A>G	p.Asn1953Ser	p.N1953S	ENST00000257430	NM_000038.5	1953	aAt/aGt	16/16	1	2	FACETS	0.601	0.442	0.791	0.601	0.442	0.791	SUBCLONAL	1	TRUE	1	0.12	2		0	444	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394436	162394436	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022691-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	15	0	0	ENST00000366898.1:c.632A>C	p.Lys211Thr	p.K211T	ENST00000366898	NM_004562.2	211	aAa/aCa	6/12	1	2	FACETS	0.566	0.412	0.752	0.566	0.412	0.752	SUBCLONAL	1	TRUE	1	0.12	2		0	442	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624294	89624294	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0023618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	310	636	0	ENST00000371953.3:c.68T>G	p.Leu23Ter	p.L23*	ENST00000371953	NM_000314.4	23	tTa/tGa	1/9	0.665783960751416	1	FACETS	0.986	0.939	1	0.986	0.939	1	CLONAL	1	TRUE	0	0.665783960751416	1		636	630	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281378	142281378	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	300	665	1	ENST00000350721.4:c.866A>T	p.Lys289Ile	p.K289I	ENST00000350721	NM_001184.3	289	aAa/aTa	4/47	0.665783960751416	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.665783960751416	1		666	600	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624294	89624294	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0023618-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	145	636	0	ENST00000371953.3:c.68T>G	p.Leu23Ter	p.L23*	ENST00000371953	NM_000314.4	23	tTa/tGa	1/9	0.320408629643727	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.320408629643727	1		636	620	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281378	142281378	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023618-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	205	665	1	ENST00000350721.4:c.866A>T	p.Lys289Ile	p.K289I	ENST00000350721	NM_001184.3	289	aAa/aTa	4/47	0.294262279671271	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.320408629643727	1		666	891	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421039	49421039	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123721	NA	P-0024026-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	90	799	0	ENST00000301067.7:c.14710C>T	p.Arg4904Ter	p.R4904*	ENST00000301067	NM_003482.3	4904	Cga/Tga	48/54	0.311049931442916	4	FACETS	0.664	0.587	0.746	0.332	0.293	0.373	SUBCLONAL	1	TRUE	2	0.335161289125682	4		799	1080	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0024026-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	424	733	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.335161289125682	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	0	0.335161289125682	3		733	943	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155921	106155921	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs777145283	NA	P-0024026-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	104	557	0	ENST00000380013.4:c.822del	p.Asn275IlefsTer18	p.N275Ifs*18	ENST00000380013	NM_001127208.2	274	atC/at	3/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.335161289125682	2		557	549	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163305	32163305	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024026-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1452	96	1423	0	ENST00000375023.3:c.5921C>G	p.Pro1974Arg	p.P1974R	ENST00000375023	NM_004557.3	1974	cCg/cGg	30/30	1	2	FACETS	0.37	0.328	0.415	0.37	0.328	0.415	SUBCLONAL	1	TRUE	1	0.335161289125682	2		1423	1548	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349024	89349024	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779550492	NA	P-0024026-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	111	1167	0	ENST00000301030.4:c.3926C>T	p.Thr1309Met	p.T1309M	ENST00000301030	NM_001256183.1	1309	aCg/aTg	9/13	1	2	FACETS	0.569	0.51	0.632	0.569	0.51	0.632	SUBCLONAL	1	TRUE	1	0.335161289125682	2		1167	1164	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65349035	65349035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024026-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	146	848	0	ENST00000342505.4:c.130G>A	p.Asp44Asn	p.D44N	ENST00000342505	NM_002227.2	44	Gac/Aac	3/25	0.335161289125682	4	FACETS	1	0.967	1	0.375	0.341	0.41	CLONAL	1	TRUE	1	0.335161289125682	4		848	1034	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40490751	40490751	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024026-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	154	556	0	ENST00000264657.5:c.548G>C	p.Gly183Ala	p.G183A	ENST00000264657	NM_139276.2	183	gGa/gCa	6/24	0.335161289125682	3	FACETS	1	0.988	1	0.744	0.682	0.808	CLONAL	1	TRUE	1	0.335161289125682	3		556	721	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156204	106156204	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024026-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	89	502	0	ENST00000380013.4:c.1105C>G	p.Arg369Gly	p.R369G	ENST00000380013	NM_001127208.2	369	Cgg/Ggg	3/11	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.335161289125682	2		502	520	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994186	21994187	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0024026-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	541	1004	0	ENST00000579755.1:c.144dup	p.Leu49AlafsTer14	p.L49Afs*14	ENST00000579755		48	-/G	1/3	0.335161289125682		FACETS		0.928	1				CLONAL	3	TRUE	0	0.335161289125682	3		1004	1301	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139818323	139818323	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0024026-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	478	1003	0	ENST00000247668.2:c.1158C>G	p.Tyr386Ter	p.Y386*	ENST00000247668	NM_021138.3	386	taC/taG	10/11	0.335161289125682	3	FACETS	0.982	0.942	1	0.982	0.942	1	CLONAL	3	TRUE	0	0.335161289125682	3		1003	1130	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980426	7980426	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024026-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1206	94	1334	0	ENST00000319144.4:c.1157del	p.Arg386ProfsTer29	p.R386Pfs*29	ENST00000319144	NM_001139.2	386	cGc/cc	9/15	0.335161289125682	3	FACETS	0.504	0.446	0.565	0.252	0.223	0.283	SUBCLONAL	1	TRUE	1	0.335161289125682	3		1334	1300	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341718	8341718	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024026-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	66	697	0	ENST00000356435.5:c.4922T>G	p.Val1641Gly	p.V1641G	ENST00000356435		1641	gTc/gGc	29/35	0.335161289125682	3	FACETS	0.54	0.467	0.619	0.18	0.155	0.207	SUBCLONAL	1	TRUE	0	0.335161289125682	3		697	852	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303220	11303220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778152958	NA	P-0024459-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	57	638	0	ENST00000361445.4:c.1363G>A	p.Val455Met	p.V455M	ENST00000361445	NM_004958.3	455	Gtg/Atg	9/58	1	2	FACETS	0.384	0.328	0.445	0.384	0.328	0.445	SUBCLONAL	1	TRUE	1	0.336379606240132	2		638	883	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982439	25982439	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024459-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	158	355	0	ENST00000435504.4:c.851del	p.Arg284GlnfsTer3	p.R284Qfs*3	ENST00000435504		284	cGa/ca	9/13	1	2	FACETS	0.834	0.769	0.902	1	0.99	1	CLONAL	2	TRUE	1	0.336379606240132	2		355	563	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0025347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	113	537	0				ENST00000310581	NM_198253.2	-/1132			0.540003208939428	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.540003208939428	4		537	260	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330547	65330547	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	249	585	0	ENST00000342505.4:c.1099T>G	p.Ser367Ala	p.S367A	ENST00000342505	NM_002227.2	367	Tct/Gct	8/25	0.540003208939428	4	FACETS	0.941	0.883	0.999	0.941	0.883	0.999	CLONAL	2	TRUE	2	0.540003208939428	4		585	755	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456797	32456797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	235	746	1	ENST00000332351.3:c.95G>A	p.Gly32Glu	p.G32E	ENST00000332351	NM_024426.4	32	gGa/gAa	1/10	0.540003208939428	3	FACETS	0.99	0.932	1	0.99	0.932	1	CLONAL	2	TRUE	1	0.540003208939428	3		747	558	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422712	49422712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777053146	NA	P-0025347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	278	790	0	ENST00000301067.7:c.14281C>T	p.Leu4761Phe	p.L4761F	ENST00000301067	NM_003482.3	4761	Ctt/Ttt	45/54	0.536132818573451	3	FACETS	0.977	0.924	1	0.977	0.924	1	CLONAL	2	TRUE	1	0.540003208939428	3		790	669	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436084	49436084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	171	662	0	ENST00000301067.7:c.5897C>T	p.Pro1966Leu	p.P1966L	ENST00000301067	NM_003482.3	1966	cCc/cTc	28/54	0.536132818573451	3	FACETS	0.908	0.844	0.973	0.908	0.844	0.973	CLONAL	2	TRUE	1	0.540003208939428	3		662	443	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560494	95560494	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0025347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	208	479	0	ENST00000393063.1:c.5096-1G>A		p.X1699_splice	ENST00000393063	NM_030621.3	1699			0.540003208939428	4	FACETS	0.904	0.844	0.966	0.904	0.844	0.966	CLONAL	2	TRUE	2	0.540003208939428	4		479	656	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828381	72828381	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	233	770	0	ENST00000268489.5:c.8200C>T	p.His2734Tyr	p.H2734Y	ENST00000268489	NM_006885.3	2734	Cac/Tac	9/10	0.504977868609866	4	FACETS	0.953	0.893	1	0.953	0.893	1	CLONAL	2	TRUE	2	0.540003208939428	4		770	697	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545699	63545699	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	226	723	0	ENST00000307078.5:c.895G>C	p.Asp299His	p.D299H	ENST00000307078	NM_004655.3	299	Gac/Cac	3/11	0.540003208939428	6	FACETS	0.959	0.894	1	0.479	0.447	0.513	CLONAL	2	TRUE	2	0.540003208939428	6		723	908	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119768	70119768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	199	645	0	ENST00000245479.2:c.770G>A	p.Arg257His	p.R257H	ENST00000245479	NM_000346.3	257	cGc/cAc	3/3	0.540003208939428	6	FACETS	1	0.974	1	0.55	0.511	0.59	CLONAL	2	TRUE	2	0.540003208939428	6		645	697	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584367	39584409	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCAAACAGGCCTTGGAACTTCTGGGAAAATGGAAGCCGATG	GGCCAAACAGGCCTTGGAACTTCTGGGAAAATGGAAGCCGATG	-	novel	NA	P-0025347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	141	439	0	ENST00000262039.4:c.1033_1075del	p.Ala345MetfsTer2	p.A345Mfs*2	ENST00000262039	NM_002647.2	344	gaGGCCAAACAGGCCTTGGAACTTCTGGGAAAATGGAAGCCGATG/ga	10/25	0.380082978413772	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.540003208939428	4		439	378	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274344	5274345	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	novel	NA	P-0025347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	141	587	3	ENST00000357368.4:c.102_103delinsAA	p.Phe35Ile	p.F35I	ENST00000357368	NM_002850.3	34	agGTtt/agAAtt	3/38	0.445220222889519	4	FACETS	0.836	0.767	0.907	0.836	0.767	0.907	CLONAL	2	TRUE	2	0.540003208939428	4		590	481	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210709	36210709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780868475	NA	P-0025347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	293	917	0	ENST00000222270.7:c.460C>T	p.Arg154Cys	p.R154C	ENST00000222270	NM_014727.1	154	Cgc/Tgc	3/37	0.445220222889519	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.540003208939428	4		917	783	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224343	36224344	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	242	955	0	ENST00000222270.7:c.6893_6894delinsTT	p.Pro2298Leu	p.P2298L	ENST00000222270	NM_014727.1	2298	cCC/cTT	28/37	0.445220222889519	4	FACETS	0.861	0.806	0.916	0.861	0.806	0.916	CLONAL	2	TRUE	2	0.540003208939428	4		955	802	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224713	36224713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1280550594	NA	P-0025347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	325	1027	0	ENST00000222270.7:c.7099C>T	p.Pro2367Ser	p.P2367S	ENST00000222270	NM_014727.1	2367	Ccc/Tcc	30/37	0.445220222889519	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.540003208939428	4		1027	905	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994410	25994410	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0025347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	143	346	0	ENST00000435504.4:c.404-1G>A		p.X135_splice	ENST00000435504		135			NA	2	FACETS	0.996	0.928	1			1	INDETERMINATE	2	TRUE	NA	0.540003208939428	2		346	266	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561263	9561263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769939031	NA	P-0025347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	231	566	0	ENST00000353224.5:c.519G>A	p.Met173Ile	p.M173I	ENST00000353224	NM_177990.2	173	atG/atA	4/10	0.540003208939428	4	FACETS	0.997	0.934	1	0.997	0.934	1	CLONAL	2	TRUE	2	0.540003208939428	4		566	661	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447438	12447438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	273	694	1	ENST00000287820.6:c.677C>T	p.Ser226Phe	p.S226F	ENST00000287820	NM_015869.4	226	tCc/tTc	5/7	0.540003208939428	5	FACETS	0.928	0.872	0.985	0.619	0.581	0.657	CLONAL	2	TRUE	2	0.540003208939428	5		695	986	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934849	49934849	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	385	816	0	ENST00000296474.3:c.2047G>A	p.Glu683Lys	p.E683K	ENST00000296474	NM_002447.2	683	Gag/Aag	7/20	0.540003208939428	5	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	2	0.540003208939428	5		816	793	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185169089	185169089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746110965	NA	P-0025347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	726	569	0	ENST00000265026.3:c.1184G>A	p.Arg395Gln	p.R395Q	ENST00000265026	NM_004721.4	395	cGa/cAa	7/14	0.540003208939428	7	FACETS	1	0.993	1			1	CLONAL	5	TRUE	NA	0.540003208939428	7		569	1192	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80074648	80074648	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	257	455	0	ENST00000265081.6:c.2428T>G	p.Phe810Val	p.F810V	ENST00000265081	NM_002439.4	810	Ttt/Gtt	17/24	0.540003208939428	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.540003208939428	4		455	706	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517785	176517785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	293	843	0	ENST00000292408.4:c.395C>T	p.Ser132Phe	p.S132F	ENST00000292408	NM_213647.1	132	tCc/tTc	4/18	0.504977868609866	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.540003208939428	4		843	717	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673130	30673130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	109	615	0	ENST00000376406.3:c.3830C>T	p.Ser1277Phe	p.S1277F	ENST00000376406	NM_014641.2	1277	tCt/tTt	10/15	0.540003208939428	5	FACETS	0.981	0.881	1	0.327	0.293	0.362	CLONAL	1	TRUE	2	0.540003208939428	5		615	745	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547265	106547265	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	197	481	0	ENST00000369096.4:c.502C>T	p.Pro168Ser	p.P168S	ENST00000369096	NM_001198.3	168	Ccc/Tcc	4/7	0.540003208939428	3	FACETS	0.957	0.895	1			1	CLONAL	2	TRUE	NA	0.540003208939428	3		481	484	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952956	2952956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1338162870	NA	P-0025347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	228	949	0	ENST00000396946.4:c.2984C>T	p.Ser995Leu	p.S995L	ENST00000396946	NM_032415.4	995	tCg/tTg	22/25	0.540003208939428	4	FACETS	0.933	0.873	0.994	0.933	0.873	0.994	CLONAL	2	TRUE	2	0.540003208939428	4		949	697	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266443	55266443	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	200	623	0	ENST00000275493.2:c.2735C>T	p.Ser912Phe	p.S912F	ENST00000275493	NM_005228.3	912	tCc/tTc	23/28	0.540003208939428	4	FACETS	0.93	0.867	0.995	0.93	0.867	0.995	CLONAL	2	TRUE	2	0.540003208939428	4		623	613	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453132	140453132	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913365	NA	P-0025347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	273	496	0	ENST00000288602.6:c.1803A>C	p.Lys601Asn	p.K601N	ENST00000288602	NM_004333.4	601	aaA/aaC	15/18	0.540003208939428	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.540003208939428	4		496	725	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231109	98231109	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	238	707	0	ENST00000331920.6:c.2174C>T	p.Pro725Leu	p.P725L	ENST00000331920	NM_000264.3	725	cCc/cTc	14/24	0.540003208939428	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.540003208939428	2		707	436	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391172	139391172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1254082910	NA	P-0025347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	439	1204	0	ENST00000277541.6:c.7019C>T	p.Pro2340Leu	p.P2340L	ENST00000277541	NM_017617.3	2340	cCc/cTc	34/34	0.540003208939428	3	FACETS	0.986	0.952	1	0.986	0.952	1	CLONAL	3	TRUE	0	0.540003208939428	3		1204	698	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0025465-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	57	660	0	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			1	2	FACETS	0.671	0.574	0.777	0.671	0.574	0.777	SUBCLONAL	1	TRUE	1	0.183962049606911	2		660	924	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348214	348214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025465-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1305	153	959	0	ENST00000262320.3:c.1292C>T	p.Pro431Leu	p.P431L	ENST00000262320	NM_003502.3	431	cCc/cTc	6/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.183962049606911	2		959	1458	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589519	69589519	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs779390973	NA	P-0025465-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	60	198	0	ENST00000168712.1:c.334C>G	p.Arg112Gly	p.R112G	ENST00000168712	NM_002007.2	112	Cgc/Ggc	1/3	0.183962049606911	3	FACETS	1	0.895	1			1	CLONAL	2	TRUE	NA	0.183962049606911	3		198	343	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856550	111856550	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025465-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	42	423	0	ENST00000341259.2:c.601C>G	p.Leu201Val	p.L201V	ENST00000341259	NM_005475.2	201	Ctg/Gtg	2/8	1	2	FACETS	0.674	0.562	0.8	0.674	0.562	0.8	SUBCLONAL	1	TRUE	1	0.183962049606911	2		423	677	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554565	29554565	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025465-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	35	280	0	ENST00000356175.3:c.2350T>A	p.Trp784Arg	p.W784R	ENST00000356175	NM_000267.3	784	Tgg/Agg	20/57	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.183962049606911	2		280	357	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966679	25966679	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025465-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	53	718	0	ENST00000435504.4:c.2527G>T	p.Gly843Cys	p.G843C	ENST00000435504		843	Ggt/Tgt	13/13	1	2	FACETS	0.59	0.502	0.688	0.59	0.502	0.688	SUBCLONAL	1	TRUE	1	0.183962049606911	2		718	976	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039342	47039342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	166	673	0	ENST00000377604.3:c.965C>T	p.Pro322Leu	p.P322L	ENST00000377604	NM_001204468.1	322	cCc/cTc	10/24	0.228748818432686	0	FACETS	0.716	0.664	0.769			1	INDETERMINATE	1	TRUE	0	0.507403651856395	0		673	450	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118354899	118354900	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AA	AA	C	novel	NA	P-0025825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	94	449	0	ENST00000534358.1:c.4088_4089delinsC	p.Glu1363AlafsTer15	p.E1363Afs*15	ENST00000534358	NM_005933.3	1363	gAA/gC	9/36	NA	2	FACETS	0.782	0.699	0.869			1	INDETERMINATE	1	TRUE	NA	0.507403651856395	2		449	474	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218086	108218086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781814	NA	P-0026429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	236	514	1	ENST00000278616.4:c.8665G>A	p.Asp2889Asn	p.D2889N	ENST00000278616	NM_000051.3	2889	Gat/Aat	59/63	0.705141065050063	1	FACETS	0.936	0.885	0.987	0.936	0.885	0.987	CLONAL	1	TRUE	0	0.705141065050063	1		515	463	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064748	80064748	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs376667075	NA	P-0026429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	174	694	0	ENST00000265081.6:c.2179C>T	p.Arg727Ter	p.R727*	ENST00000265081	NM_002439.4	727	Cga/Tga	15/24	0.368449121505076	1	FACETS	0.376	0.346	0.407	0.376	0.346	0.407	INDETERMINATE	1	TRUE	0	0.705141065050063	1		694	850	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578518	7578518	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	529	804	0	ENST00000269305.4:c.412del	p.Ala138ProfsTer32	p.A138Pfs*32	ENST00000269305	NM_001126112.2	138	Gcc/cc	5/11	0.385848657188145	3	FACETS	0.929	0.896	0.962	0.929	0.896	0.962	CLONAL	3	TRUE	0	0.476861160546778	3		804	986	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119004	3119004	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1309810840	NA	P-0026793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	41	769	1	ENST00000078429.4:c.688G>A	p.Val230Ile	p.V230I	ENST00000078429	NM_002067.2	230	Gtc/Atc	5/7	1	2	FACETS	0.248	0.206	0.295	0.248	0.206	0.295	SUBCLONAL	1	TRUE	1	0.476861160546778	2		770	693	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732967	30732967	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs727503476	NA	P-0026793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	180	434	0	ENST00000295754.5:c.1580C>T	p.Ala527Val	p.A527V	ENST00000295754	NM_003242.5	527	gCc/gTc	7/7	0.476861160546778	2	FACETS	0.87	0.811	0.929	0.87	0.811	0.929	CLONAL	2	TRUE	0	0.476861160546778	2		434	434	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026839-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	17	460	0				ENST00000310581	NM_198253.2	-/1132			0.179985825098759	1	FACETS	0.63	0.476	0.808	0.63	0.476	0.808	INDETERMINATE	1	TRUE	0	0.385582348740049	1		460	113	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652147	36652148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026839-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	45	654	0	ENST00000244741.5:c.270dup	p.Gly91ArgfsTer38	p.G91Rfs*38	ENST00000244741	NM_000389.4	90	gga/ggAa	2/3	1	2	FACETS	0.705	0.595	0.826	0.705	0.595	0.826	SUBCLONAL	1	TRUE	1	0.385582348740049	2		654	331	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651893	36651894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026839-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	40	594	0	ENST00000244741.5:c.19dup	p.Asp7GlyfsTer29	p.D7Gfs*29	ENST00000244741	NM_000389.4	5	-/G	2/3	1	2	FACETS	0.725	0.606	0.857	0.725	0.606	0.857	SUBCLONAL	1	TRUE	1	0.385582348740049	2		594	286	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281768	49281768	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148425155	NA	P-0026839-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	44	698	0	ENST00000282018.3:c.815C>T	p.Thr272Met	p.T272M	ENST00000282018	NM_020377.2	272	aCg/aTg	1/1	1	2	FACETS	0.667	0.562	0.784	0.667	0.562	0.784	SUBCLONAL	1	TRUE	1	0.385582348740049	2		698	342	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050349	176050349	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	144	574	1	ENST00000367669.3:c.1216C>T	p.Arg406Ter	p.R406*	ENST00000367669	NM_022457.5	406	Cga/Tga	11/20	0.76451186747167	1	FACETS	0.927	0.867	0.987	0.927	0.867	0.987	CLONAL	1	TRUE	0	0.76451186747167	1		575	251	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111025	193111025	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	63	278	0	ENST00000367435.3:c.558A>T	p.Lys186Asn	p.K186N	ENST00000367435	NM_024529.4	186	aaA/aaT	7/17	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.76451186747167	2		278	130	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934639	9934639	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	136	368	0	ENST00000330684.3:c.1516G>T	p.Val506Phe	p.V506F	ENST00000330684	NM_001134407.1	506	Gtc/Ttc	7/13	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.76451186747167	2		368	355	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807600	1807600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	226	955	1	ENST00000260795.2:c.1769C>T	p.Thr590Ile	p.T590I	ENST00000260795		590	aCc/aTc	12/17	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.76451186747167	2		956	572	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463580	25463580	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	352	785	0	ENST00000264709.3:c.2102T>G	p.Phe701Cys	p.F701C	ENST00000264709	NM_175629.2	701	tTc/tGc	18/23	0.624819041138771	3	FACETS	0.802	0.762	0.842	0.802	0.762	0.842	CLONAL	2	TRUE	1	0.624819041138771	3		785	922	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250823	153250823	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0028098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	266	451	0	ENST00000281708.4:c.1236+1G>C		p.X412_splice	ENST00000281708	NM_033632.3	412			0.546923447319344	2	FACETS	0.848	0.806	0.89	0.848	0.806	0.89	CLONAL	2	TRUE	0	0.624819041138771	2		451	502	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299069	15299069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1192	175	741	0	ENST00000263388.2:c.1469G>A	p.Gly490Asp	p.G490D	ENST00000263388	NM_000435.2	490	gGc/gAc	9/33	0.582443883764061	5	FACETS	0.794	0.729	0.862	0.265	0.243	0.288	SUBCLONAL	1	TRUE	2	0.624819041138771	5		741	1367	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877824	151877824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	119	478	1	ENST00000262189.6:c.7121C>T	p.Ala2374Val	p.A2374V	ENST00000262189	NM_170606.2	2374	gCc/gTc	36/59	0.593970949613502	4	FACETS	0.826	0.746	0.911	0.413	0.373	0.456	CLONAL	1	TRUE	2	0.624819041138771	4		479	749	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737630	145737630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35348691	NA	P-0028098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	231	1006	0	ENST00000428558.2:c.3133G>A	p.Ala1045Thr	p.A1045T	ENST00000428558	NM_004260.3	1045	Gct/Act	19/22	0.624819041138771	4	FACETS	0.869	0.809	0.932	0.29	0.269	0.311	CLONAL	1	TRUE	1	0.624819041138771	4		1006	1382	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021635	31021635	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028508-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	245	549	1	ENST00000375687.4:c.1634G>T	p.Arg545Leu	p.R545L	ENST00000375687	NM_015338.5	545	cGt/cTt	12/13	0.844845073535002	4	FACETS	0.957	0.894	1	0.319	0.298	0.341	CLONAL	1	TRUE	1	0.844845073535002	4		550	1118	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	151	460	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.577624077368303	2		460	422	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0028679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	201	1087	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.577624077368303	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.577624077368303	1		1087	490	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119789	70119789	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	284	773	0	ENST00000245479.2:c.791G>C	p.Arg264Thr	p.R264T	ENST00000245479	NM_000346.3	264	aGa/aCa	3/3	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.577624077368303	2		773	842	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628335	187628335	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	272	748	0	ENST00000441802.2:c.2647C>A	p.Leu883Met	p.L883M	ENST00000441802	NM_005245.3	883	Ctg/Atg	2/27	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.577624077368303	2		748	891	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373293	118373293	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	179	575	0	ENST00000534358.1:c.6686C>A	p.Ser2229Ter	p.S2229*	ENST00000534358	NM_005933.3	2229	tCa/tAa	27/36	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.577624077368303	2		575	576	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665463	176665463	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	199	621	0	ENST00000439151.2:c.4147C>G	p.Pro1383Ala	p.P1383A	ENST00000439151	NM_022455.4	1383	Cca/Gca	7/23	0.577624077368303	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.577624077368303	1		621	480	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884510	151884510	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	119	417	0	ENST00000262189.6:c.4845G>C	p.Trp1615Cys	p.W1615C	ENST00000262189	NM_170606.2	1615	tgG/tgC	33/59	NA	2	FACETS	0.941	0.855	1			1	INDETERMINATE	1	TRUE	NA	0.577624077368303	2		417	438	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874118	151874118	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	141	696	0	ENST00000262189.6:c.8420C>G	p.Ser2807Cys	p.S2807C	ENST00000262189	NM_170606.2	2807	tCt/tGt	38/59	NA	2	FACETS	0.978	0.897	1			1	INDETERMINATE	1	TRUE	NA	0.577624077368303	2		696	499	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288330	33288330	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138962926	NA	P-0028679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	256	640	1	ENST00000374542.5:c.1078C>T	p.Arg360Cys	p.R360C	ENST00000374542	NM_001141970.1	360	Cgc/Tgc	4/8	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.577624077368303	2		641	822	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874091	151874091	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	143	716	0	ENST00000262189.6:c.8447C>G	p.Ser2816Cys	p.S2816C	ENST00000262189	NM_170606.2	2816	tCc/tGc	38/59	NA	2	FACETS	0.967	0.887	1			1	INDETERMINATE	1	TRUE	NA	0.577624077368303	2		716	512	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217409	7217417	+	missense_variant	Missense_Mutation	ONP	GAGGAGATG	GAGGAGATG	CAGGAAATA	novel	NA	P-0028679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	244	734	0	ENST00000380728.2:c.379_387delinsTATTTCCTG	p.His127_Leu128delinsTyrPhe	p.H127_L128delinsYF	ENST00000380728		127	CATCTCCTC/TATTTCCTG	5/11	1	2	FACETS	0.912	0.854	0.973	0.912	0.854	0.973	CLONAL	1	TRUE	1	0.577624077368303	2		734	926	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438210	56438210	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029636-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	49	463	0	ENST00000407977.2:c.783C>G	p.Asp261Glu	p.D261E	ENST00000407977		261	gaC/gaG	7/10	0.270754719880261	3	FACETS	0.765	0.648	0.893	0.383	0.324	0.447	SUBCLONAL	1	FALSE	1	0.3	3		463	491	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356282	70356282	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030044-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	432	356	0	ENST00000374080.3:c.5177A>G	p.Tyr1726Cys	p.Y1726C	ENST00000374080		1726	tAc/tGc	37/45	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.9	1		356	460	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0030394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	105	1087	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.414881652440559	2		1087	408	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0030394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	104	455	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.414881652440559	2		455	358	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0030394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	237	537	0				ENST00000310581	NM_198253.2	-/1132			0.257539467341348	5	FACETS	1	0.975	1	1	0.975	1	CLONAL	5	TRUE	0	0.414881652440559	5		537	359	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094386	27094386	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	166	811	0	ENST00000324856.7:c.3094G>T	p.Glu1032Ter	p.E1032*	ENST00000324856	NM_006015.4	1032	Gag/Tag	11/20	1	2	FACETS	0.827	0.766	0.889	1	0.991	1	CLONAL	2	TRUE	1	0.414881652440559	2		811	484	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981550	201981551	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0030394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	153	963	0	ENST00000359651.3:c.467dup	p.Gly157ArgfsTer4	p.G157Rfs*4	ENST00000359651		155	gac/gaCc	3/8	1	2	FACETS	0.821	0.758	0.886	1	0.99	1	CLONAL	2	TRUE	1	0.414881652440559	2		963	449	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376973	118376973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	93	567	0	ENST00000534358.1:c.10366C>T	p.Gln3456Ter	p.Q3456*	ENST00000534358	NM_005933.3	3456	Cag/Tag	27/36	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.414881652440559	2		567	402	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18439817	18439817	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	102	442	0	ENST00000266497.5:c.715C>G	p.Gln239Glu	p.Q239E	ENST00000266497		239	Caa/Gaa	2/31	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.414881652440559	2		442	369	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478935	56478935	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	168	886	0	ENST00000267101.3:c.391C>G	p.Leu131Val	p.L131V	ENST00000267101	NM_001982.3	131	Ctg/Gtg	3/28	0.284693198591215	3	FACETS	0.785	0.724	0.847	0.785	0.724	0.847	SUBCLONAL	2	TRUE	1	0.414881652440559	3		886	623	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487641	56487641	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771536549	NA	P-0030394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	145	842	0	ENST00000267101.3:c.1574G>A	p.Arg525Gln	p.R525Q	ENST00000267101	NM_001982.3	525	cGa/cAa	13/28	0.284693198591215	3	FACETS	0.801	0.735	0.869	0.801	0.735	0.869	CLONAL	2	TRUE	1	0.414881652440559	3		842	527	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807863	3807863	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	121	670	0	ENST00000262367.5:c.3556G>C	p.Glu1186Gln	p.E1186Q	ENST00000262367	NM_004380.2	1186	Gag/Cag	18/31	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.414881652440559	2		670	474	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645327	67645327	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	27	653	0	ENST00000264010.4:c.592C>T	p.Gln198Ter	p.Q198*	ENST00000264010	NM_006565.3	198	Cag/Tag	3/12	1	2	FACETS	0.287	0.227	0.355	0.287	0.227	0.355	SUBCLONAL	1	TRUE	1	0.414881652440559	2		653	454	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602694	10602694	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	144	1238	0	ENST00000171111.5:c.884C>G	p.Ser295Cys	p.S295C	ENST00000171111	NM_203500.1	295	tCc/tGc	3/6	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.414881652440559	2		1238	614	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219930	36219930	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	32	1028	0	ENST00000222270.7:c.4732C>G	p.Pro1578Ala	p.P1578A	ENST00000222270	NM_014727.1	1578	Ccc/Gcc	21/37	1	2	FACETS	0.299	0.242	0.364	0.299	0.242	0.364	SUBCLONAL	1	TRUE	1	0.414881652440559	2		1028	516	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796985	42796985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758868794	NA	P-0030394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	165	1318	3	ENST00000575354.2:c.3443C>T	p.Pro1148Leu	p.P1148L	ENST00000575354	NM_015125.3	1148	cCg/cTg	14/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.414881652440559	2		1321	560	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175861	24175861	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1568963037	NA	P-0030394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	134	859	2	ENST00000263121.7:c.1089G>T	p.Lys363Asn	p.K363N	ENST00000263121	NM_003073.3	363	aaG/aaT	8/9	1	2	FACETS	0.771	0.707	0.837	1	0.988	1	SUBCLONAL	2	TRUE	1	0.414881652440559	2		861	419	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569659	41569659	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	87	326	1	ENST00000263253.7:c.4650G>T	p.Lys1550Asn	p.K1550N	ENST00000263253	NM_001429.3	1550	aaG/aaT	29/31	1	2	FACETS	0.826	0.742	0.912	1	0.984	1	CLONAL	2	TRUE	1	0.414881652440559	2		327	254	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569713	41569716	+	frameshift_variant	Frame_Shift_Del	DEL	GAAG	GAAG	AAA	novel	NA	P-0030394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	108	440	4	ENST00000263253.7:c.4704_4707delinsAAA	p.Lys1570AsnfsTer28	p.K1570Nfs*28	ENST00000263253	NM_001429.3	1568	aaGAAG/aaAAA	29/31	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.414881652440559	2		444	355	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569773	41569773	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	87	366	0	ENST00000263253.7:c.4764G>T	p.Met1588Ile	p.M1588I	ENST00000263253	NM_001429.3	1588	atG/atT	29/31	1	2	FACETS	0.78	0.7	0.862	1	0.982	1	SUBCLONAL	2	TRUE	1	0.414881652440559	2		366	269	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572904	41572904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	31	1043	0	ENST00000263253.7:c.5189C>T	p.Ser1730Phe	p.S1730F	ENST00000263253	NM_001429.3	1730	tCt/tTt	31/31	1	2	FACETS	0.244	0.197	0.298	0.244	0.197	0.298	SUBCLONAL	1	TRUE	1	0.414881652440559	2		1043	612	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573438	41573438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1284977519	NA	P-0030394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	156	1109	0	ENST00000263253.7:c.5723C>T	p.Pro1908Leu	p.P1908L	ENST00000263253	NM_001429.3	1908	cCa/cTa	31/31	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.414881652440559	2		1109	531	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573636	41573636	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	166	1004	0	ENST00000263253.7:c.5921G>C	p.Arg1974Thr	p.R1974T	ENST00000263253	NM_001429.3	1974	aGa/aCa	31/31	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.414881652440559	2		1004	542	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574326	41574326	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	162	955	0	ENST00000263253.7:c.6611G>T	p.Gly2204Val	p.G2204V	ENST00000263253	NM_001429.3	2204	gGa/gTa	31/31	1	2	FACETS	0.76	0.702	0.819	1	0.99	1	SUBCLONAL	2	TRUE	1	0.414881652440559	2		955	514	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564578	55564578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	169	804	0	ENST00000288135.5:c.466C>T	p.Leu156Phe	p.L156F	ENST00000288135	NM_000222.2	156	Ctt/Ttt	3/21	1	2	FACETS	0.836	0.775	0.899	1	0.991	1	CLONAL	2	TRUE	1	0.414881652440559	2		804	487	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629939	187629939	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	110	915	0	ENST00000441802.2:c.1043C>G	p.Ser348Cys	p.S348C	ENST00000441802	NM_005245.3	348	tCt/tGt	2/27	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.414881652440559	2		915	483	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651963	36651963	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	405	1077	1	ENST00000244741.5:c.85C>T	p.Gln29Ter	p.Q29*	ENST00000244741	NM_000389.4	29	Cag/Tag	2/3	0.414881652440559	4	FACETS	1	0.986	1			1	CLONAL	4	TRUE	NA	0.414881652440559	4		1078	658	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553193	106553193	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	36	930	0	ENST00000369096.4:c.1158G>C	p.Leu386Phe	p.L386F	ENST00000369096	NM_001198.3	386	ttG/ttC	5/7	0.284693198591215	3	FACETS	0.359	0.295	0.432	0.18	0.147	0.216	SUBCLONAL	1	TRUE	1	0.414881652440559	3		930	583	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045016	47045016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556782040	NA	P-0030394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	134	564	0	ENST00000377604.3:c.2342C>T	p.Ser781Leu	p.S781L	ENST00000377604	NM_001204468.1	781	tCa/tTa	20/24	1	1	FACETS	0.81	0.748	0.873	1	0.99	1	CLONAL	2	TRUE	0	0.414881652440559	1		564	316	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889176	76889176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030394-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	123	231	0	ENST00000373344.5:c.4834C>T	p.Leu1612Phe	p.L1612F	ENST00000373344	NM_000489.3	1612	Ctt/Ttt	18/35	1	1	FACETS	1	0.973	1	1	0.992	1	CLONAL	2	TRUE	0	0.414881652440559	1		231	214	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0030858-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	437	536	1	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.183384805124392	2	FACETS	1	0.995	1	0.641	0.616	0.665	INDETERMINATE	1	TRUE	0	0.86872041696569	2		537	785	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0030858-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	90	568	0	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	0.856192555383535	1	FACETS	0.273	0.243	0.304	0.273	0.243	0.304	SUBCLONAL	1	TRUE	0	0.86872041696569	1		568	430	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404549	70404549	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030858-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	214	550	0	ENST00000373644.4:c.2063A>G	p.Asn688Ser	p.N688S	ENST00000373644	NM_030625.2	688	aAc/aGc	4/12	1	2	FACETS	0.691	0.645	0.739	0.691	0.645	0.739	SUBCLONAL	1	TRUE	1	0.86872041696569	2		550	713	SUCCESS
ALK	238	MSKCC	GRCh37	2	29448327	29448327	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030858-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	437	784	0	ENST00000389048.3:c.3172G>T	p.Val1058Leu	p.V1058L	ENST00000389048	NM_004304.4	1058	Gtg/Ttg	19/29	0.86872041696569	3	FACETS	0.993	0.946	1	0.497	0.473	0.521	CLONAL	1	TRUE	1	0.86872041696569	3		784	1453	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198269823	198269823	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030858-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	90	509	1	ENST00000335508.6:c.1516A>G	p.Asn506Asp	p.N506D	ENST00000335508	NM_012433.2	506	Aat/Gat	11/25	0.86872041696569	3	FACETS	0.274	0.242	0.308	0.137	0.121	0.154	SUBCLONAL	1	TRUE	1	0.86872041696569	3		510	1084	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275229	142275229	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030858-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	202	416	0	ENST00000350721.4:c.2074C>A	p.Leu692Ile	p.L692I	ENST00000350721	NM_001184.3	692	Ctt/Att	9/47	1	2	FACETS	0.901	0.843	0.96	0.901	0.843	0.96	CLONAL	1	TRUE	1	0.86872041696569	2		416	516	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145582	24145582	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555877286	NA	P-0031095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	503	598	2	ENST00000263121.7:c.601C>T	p.Arg201Ter	p.R201*	ENST00000263121	NM_003073.3	201	Cga/Tga	5/9	0.393029966483674	2	FACETS	0.901	0.875	0.927	1	0.998	1	CLONAL	4	TRUE	0	0.393029966483674	2		600	710	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255563	16255564	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	223	462	0	ENST00000375759.3:c.2832dup	p.Leu945AlafsTer6	p.L945Afs*6	ENST00000375759	NM_015001.2	943	aag/aaGg	11/15	1	2	FACETS	0.93	0.872	0.99	1	0.994	1	CLONAL	2	TRUE	1	0.393029966483674	2		462	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	841	656	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.997	1	1	0.999	1	CLONAL	2	TRUE	1	0.821709581301968	2		657	956	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	264	504	3	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.914	0.862	0.967	0.914	0.862	0.967	CLONAL	1	TRUE	1	0.821709581301968	2		507	703	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	31	639	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.087	0.07	0.107	0.087	0.07	0.107	SUBCLONAL	1	TRUE	1	0.821709581301968	2		640	866	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573032	41573032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238889159	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	465	866	1	ENST00000263253.7:c.5317C>T	p.Arg1773Trp	p.R1773W	ENST00000263253	NM_001429.3	1773	Cgg/Tgg	31/31	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.821709581301968	2		867	1056	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909629	76909629	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs919106518	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	279	571	0	ENST00000373344.5:c.4276C>T	p.Arg1426Ter	p.R1426*	ENST00000373344	NM_000489.3	1426	Cga/Tga	14/35	0.821709581301968	1	FACETS	0.939	0.899	0.978	0.939	0.899	0.978	CLONAL	1	TRUE	0	0.821709581301968	1		571	426	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952435	38952435	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138880117	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	220	372	0	ENST00000357387.3:c.2990G>A	p.Arg997His	p.R997H	ENST00000357387	NM_152756.3	997	cGc/cAc	30/38	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.821709581301968	2		372	534	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191118	185191118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564401067	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	60	585	0	ENST00000265026.3:c.1999G>A	p.Ala667Thr	p.A667T	ENST00000265026	NM_004721.4	667	Gcc/Acc	11/14	1	2	FACETS	0.208	0.179	0.24	0.208	0.179	0.24	SUBCLONAL	1	TRUE	1	0.821709581301968	2		585	701	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512401	38512402	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs745553450	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	46	652	2	ENST00000254066.5:c.1319dup	p.Pro441AlafsTer5	p.P441Afs*5	ENST00000254066	NM_000964.3	438	gcc/gCcc	9/9	1	2	FACETS	0.154	0.129	0.181	0.154	0.129	0.181	SUBCLONAL	1	TRUE	1	0.821709581301968	2		654	729	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143994	11143994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	275	564	1	ENST00000358026.2:c.3575G>A	p.Arg1192His	p.R1192H	ENST00000358026	NM_001128849.1	1192	cGc/cAc	26/36	1	2	FACETS	0.883	0.833	0.934	0.883	0.833	0.934	CLONAL	1	TRUE	1	0.821709581301968	2		565	758	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656879	45656879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370218763	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	266	580	0	ENST00000407780.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000407780	NM_001283052.1	93	Cgg/Tgg	3/7	1	2	FACETS	0.898	0.846	0.95	0.898	0.846	0.95	CLONAL	1	TRUE	1	0.821709581301968	2		580	721	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681708	78681708	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767783333	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	69	607	1	ENST00000306801.3:c.416G>A	p.Arg139His	p.R139H	ENST00000306801	NM_020761.2	139	cGc/cAc	4/34	1	2	FACETS	0.21	0.182	0.24	0.21	0.182	0.24	SUBCLONAL	1	TRUE	1	0.821709581301968	2		608	800	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479811	67479811	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500766	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	304	592	0	ENST00000327367.4:c.1118G>A	p.Arg373His	p.R373H	ENST00000327367	NM_005902.3	373	cGc/cAc	8/9	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.821709581301968	2		592	729	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114337	143114337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747045725	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	247	495	0	ENST00000262992.4:c.1084G>A	p.Asp362Asn	p.D362N	ENST00000262992	NM_001101669.1	362	Gat/Aat	13/24	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.821709581301968	2		495	587	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156720	20156720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	47	531	0	ENST00000379607.5:c.37C>T	p.Arg13Cys	p.R13C	ENST00000379607	NM_001412.3	13	Cgc/Tgc	2/7	0.821709581301968	1	FACETS	0.131	0.11	0.154	0.131	0.11	0.154	SUBCLONAL	1	TRUE	0	0.821709581301968	1		531	514	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518690	176518690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770565518	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	292	565	0	ENST00000292408.4:c.608G>A	p.Arg203His	p.R203H	ENST00000292408	NM_213647.1	203	cGc/cAc	6/18	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.821709581301968	2		565	691	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578341	212578341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1216559792	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	238	426	1	ENST00000342788.4:c.916C>T	p.Arg306Cys	p.R306C	ENST00000342788	NM_005235.2	306	Cgt/Tgt	8/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.821709581301968	2		427	529	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004256	150004256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	226	423	0	ENST00000253339.5:c.1969C>T	p.Arg657Cys	p.R657C	ENST00000253339		657	Cgt/Tgt	3/7	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.821709581301968	2		423	543	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026664	6026664	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750534	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1182	155	950	0	ENST00000265849.7:c.1732C>T	p.Arg578Cys	p.R578C	ENST00000265849	NM_000535.5	578	Cgt/Tgt	11/15	1	2	FACETS	0.282	0.257	0.308	0.282	0.257	0.308	SUBCLONAL	1	TRUE	1	0.821709581301968	2		950	1337	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984241	7984241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	406	616	0	ENST00000319144.4:c.488G>A	p.Arg163His	p.R163H	ENST00000319144	NM_001139.2	163	cGc/cAc	4/15	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.821709581301968	2		616	822	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795016	42795016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150818299	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	438	773	0	ENST00000575354.2:c.2096C>T	p.Ala699Val	p.A699V	ENST00000575354	NM_015125.3	699	gCg/gTg	10/20	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.821709581301968	2		773	922	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918577	44918577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	277	583	1	ENST00000377967.4:c.1060G>A	p.Ala354Thr	p.A354T	ENST00000377967	NM_021140.2	354	Gcc/Acc	12/29	0.821709581301968	1	FACETS	0.953	0.912	0.992	0.953	0.912	0.992	CLONAL	1	TRUE	0	0.821709581301968	1		584	417	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553257	106553257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	327	583	1	ENST00000369096.4:c.1222G>A	p.Ala408Thr	p.A408T	ENST00000369096	NM_001198.3	408	Gct/Act	5/7	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.821709581301968	2		584	709	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417422	139417422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745817995	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	72	723	0	ENST00000277541.6:c.622G>A	p.Ala208Thr	p.A208T	ENST00000277541	NM_017617.3	208	Gcc/Acc	4/34	1	2	FACETS	0.191	0.166	0.218	0.191	0.166	0.218	SUBCLONAL	1	TRUE	1	0.821709581301968	2		723	919	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404381	139404381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775047070	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	475	784	1	ENST00000277541.6:c.2773G>A	p.Gly925Ser	p.G925S	ENST00000277541	NM_017617.3	925	Ggc/Agc	18/34	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.821709581301968	2		785	1040	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517609	176517609	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs755455944	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	447	855	0	ENST00000292408.4:c.310C>T	p.Arg104Ter	p.R104*	ENST00000292408	NM_213647.1	104	Cga/Tga	3/18	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.821709581301968	2		855	989	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562694	29562694	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	340	576	0	ENST00000356175.3:c.3774G>A	p.Trp1258Ter	p.W1258*	ENST00000356175	NM_000267.3	1258	tgG/tgA	28/57	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.821709581301968	2		576	724	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	28	492	0	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	1	2	FACETS	0.096	0.076	0.119	0.096	0.076	0.119	SUBCLONAL	1	TRUE	1	0.821709581301968	2		492	711	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383999	84383999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150371881	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	49	634	0	ENST00000321945.7:c.853C>T	p.Arg285Trp	p.R285W	ENST00000321945	NM_139076.2	285	Cgg/Tgg	9/9	1	2	FACETS	0.14	0.118	0.165	0.14	0.118	0.165	SUBCLONAL	1	TRUE	1	0.821709581301968	2		634	850	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182252	38182252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1559484916	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	197	495	0	ENST00000396334.3:c.688C>T	p.Arg230Cys	p.R230C	ENST00000396334	NM_002468.4	230	Cgc/Tgc	4/5	1	2	FACETS	0.798	0.743	0.854	0.798	0.743	0.854	SUBCLONAL	1	TRUE	1	0.821709581301968	2		495	601	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638456	176638456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750354456	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	454	737	0	ENST00000439151.2:c.3056G>A	p.Arg1019His	p.R1019H	ENST00000439151	NM_022455.4	1019	cGc/cAc	5/23	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.821709581301968	2		737	1018	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042235	6042235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752284380	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	262	495	1	ENST00000265849.7:c.386C>T	p.Ala129Val	p.A129V	ENST00000265849	NM_000535.5	129	gCg/gTg	5/15	1	2	FACETS	0.981	0.926	1	0.981	0.926	1	CLONAL	1	TRUE	1	0.821709581301968	2		496	650	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149324	61149324	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	212	468	0	ENST00000295025.8:c.1514G>A	p.Ser505Asn	p.S505N	ENST00000295025	NM_002908.2	505	aGc/aAc	11/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.821709581301968	2		468	471	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042160	42042160	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	413	722	0	ENST00000219905.7:c.6355G>T	p.Gly2119Ter	p.G2119*	ENST00000219905	NM_001164273.1	2119	Gga/Tga	17/24	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.821709581301968	2		722	934	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347854	89347854	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1338087158	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	265	529	0	ENST00000301030.4:c.5096G>A	p.Arg1699Gln	p.R1699Q	ENST00000301030	NM_001256183.1	1699	cGg/cAg	9/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.821709581301968	2		529	614	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022592	31022592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs373221034	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	329	589	1	ENST00000375687.4:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000375687	NM_015338.5	693	Cga/Tga	13/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.821709581301968	2		590	758	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485014	57485014	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	190	371	0	ENST00000371085.3:c.848G>A	p.Arg283His	p.R283H	ENST00000371085	NM_000516.4	283	cGc/cAc	11/13	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.821709581301968	2		371	418	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346338	73346338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	203	470	0	ENST00000377767.4:c.1462G>A	p.Asp488Asn	p.D488N	ENST00000377767	NM_014953.3	488	Gat/Aat	10/21	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.821709581301968	2		470	487	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	34	337	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	1	2	FACETS	0.159	0.129	0.192	0.159	0.129	0.192	SUBCLONAL	1	TRUE	1	0.821709581301968	2		337	521	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182538	99182538	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767204088	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	316	617	0	ENST00000074304.5:c.2341G>A	p.Ala781Thr	p.A781T	ENST00000074304	NM_001134224.1	781	Gcc/Acc	22/26	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.821709581301968	2		617	722	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93657854	93657854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	61	485	0	ENST00000375746.1:c.1880G>A	p.Arg627His	p.R627H	ENST00000375746	NM_001174167.1	627	cGc/cAc	14/14	1	2	FACETS	0.226	0.194	0.26	0.226	0.194	0.26	SUBCLONAL	1	TRUE	1	0.821709581301968	2		485	657	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852526	42852526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779200981	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	386	716	0	ENST00000398585.3:c.560G>A	p.Arg187His	p.R187H	ENST00000398585	NM_001135099.1	187	cGc/cAc	6/14	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.821709581301968	2		716	876	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969933	81969933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752209691	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	259	546	0	ENST00000359376.3:c.3002G>A	p.Arg1001His	p.R1001H	ENST00000359376	NM_002661.3	1001	cGc/cAc	27/33	1	2	FACETS	0.895	0.843	0.948	0.895	0.843	0.948	CLONAL	1	TRUE	1	0.821709581301968	2		546	704	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227982	53227982	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1556840029	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	35	699	0	ENST00000375401.3:c.2332C>T	p.Arg778Ter	p.R778*	ENST00000375401	NM_004187.3	778	Cga/Tga	16/26	0.821709581301968	1	FACETS	0.081	0.066	0.099	0.081	0.066	0.099	SUBCLONAL	1	TRUE	0	0.821709581301968	1		699	616	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872498	136872498	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs104893624	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	201	350	1	ENST00000241393.3:c.1000C>T	p.Arg334Ter	p.R334*	ENST00000241393	NM_003467.2	334	Cga/Tga	2/2	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.821709581301968	2		351	473	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244137	153244137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140856583	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	341	457	0	ENST00000281708.4:c.2020C>T	p.Arg674Trp	p.R674W	ENST00000281708	NM_033632.3	674	Cgg/Tgg	12/12	0.821709581301968	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.821709581301968	1		457	446	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439724	220439724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201577506	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	397	664	2	ENST00000243786.2:c.577G>A	p.Val193Ile	p.V193I	ENST00000243786	NM_002191.3	193	Gtc/Atc	2/2	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.821709581301968	2		666	866	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733280	40733280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370508724	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	296	601	1	ENST00000373198.4:c.3526C>T	p.Arg1176Cys	p.R1176C	ENST00000373198	NM_133170.3	1176	Cgt/Tgt	26/32	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.821709581301968	2		602	703	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211752	2211752	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	334	672	0	ENST00000398665.3:c.1468T>C	p.Ser490Pro	p.S490P	ENST00000398665	NM_032482.2	490	Tcc/Ccc	16/28	1	2	FACETS	0.897	0.851	0.944	0.897	0.851	0.944	CLONAL	1	TRUE	1	0.821709581301968	2		672	906	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849069	156849069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750168062	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	370	758	0	ENST00000524377.1:c.1961G>A	p.Arg654His	p.R654H	ENST00000524377	NM_002529.3	654	cGc/cAc	15/17	1	2	FACETS	0.948	0.902	0.994	0.948	0.902	0.994	CLONAL	1	TRUE	1	0.821709581301968	2		758	950	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163277	47163277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149265978	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	285	476	0	ENST00000409792.3:c.2849G>A	p.Arg950His	p.R950H	ENST00000409792	NM_014159.6	950	cGt/cAt	3/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.821709581301968	2		476	657	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612810	228612810	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148579172	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	321	597	1	ENST00000366696.1:c.217C>T	p.Arg73Cys	p.R73C	ENST00000366696	NM_003493.2	73	Cgc/Tgc	1/1	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.821709581301968	2		598	741	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274877	41274877	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	276	522	0	ENST00000349496.5:c.1127G>A	p.Arg376His	p.R376H	ENST00000349496	NM_001904.3	376	cGt/cAt	8/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.821709581301968	2		522	651	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633320	8633320	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866980874	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	33	561	0	ENST00000356435.5:c.349C>T	p.Arg117Trp	p.R117W	ENST00000356435		117	Cgg/Tgg	3/35	0.821709581301968	1	FACETS	0.099	0.08	0.12	0.099	0.08	0.12	SUBCLONAL	1	TRUE	0	0.821709581301968	1		561	479	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670957	30670957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868678495	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	388	706	0	ENST00000376406.3:c.5789G>A	p.Arg1930His	p.R1930H	ENST00000376406	NM_014641.2	1930	cGc/cAc	12/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.821709581301968	2		706	935	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556079	29556079	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886041347	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	114	279	2	ENST00000356175.3:c.2446C>T	p.Arg816Ter	p.R816*	ENST00000356175	NM_000267.3	816	Cga/Tga	21/57	1	2	FACETS	0.8	0.728	0.873	0.8	0.728	0.873	SUBCLONAL	1	TRUE	1	0.821709581301968	2		281	347	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801241	1801241	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199740841	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	350	637	0	ENST00000260795.2:c.370C>T	p.Arg124Trp	p.R124W	ENST00000260795		124	Cgg/Tgg	2/17	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.821709581301968	2		637	799	SUCCESS
BLM	641	MSKCC	GRCh37	15	91290665	91290665	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148545569	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	335	560	2	ENST00000355112.3:c.43C>T	p.Arg15Cys	p.R15C	ENST00000355112	NM_000057.2	15	Cgt/Tgt	2/22	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.821709581301968	2		562	796	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508082	106508082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	25	272	0	ENST00000359195.3:c.76C>T	p.Arg26Cys	p.R26C	ENST00000359195	NM_002649.2	26	Cgc/Tgc	2/11	1	2	FACETS	0.217	0.171	0.269	0.217	0.171	0.269	SUBCLONAL	1	TRUE	1	0.821709581301968	2		272	281	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127817	64127817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	57	675	0	ENST00000334205.4:c.310G>A	p.Ala104Thr	p.A104T	ENST00000334205	NM_003942.2	104	Gct/Act	3/17	1	2	FACETS	0.168	0.144	0.195	0.168	0.144	0.195	SUBCLONAL	1	TRUE	1	0.821709581301968	2		675	824	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294277	1294277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	274	589	0	ENST00000310581.5:c.724G>A	p.Ala242Thr	p.A242T	ENST00000310581	NM_198253.2	242	Gct/Act	2/16	1	2	FACETS	0.998	0.944	1	0.998	0.944	1	CLONAL	1	TRUE	1	0.821709581301968	2		589	668	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068121	94068121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149408123	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	202	315	0	ENST00000369303.4:c.841C>T	p.Arg281Cys	p.R281C	ENST00000369303	NM_004440.3	281	Cgt/Tgt	4/17	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.821709581301968	2		315	429	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798822	42798822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	403	700	1	ENST00000575354.2:c.4394G>A	p.Arg1465His	p.R1465H	ENST00000575354	NM_015125.3	1465	cGc/cAc	19/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.821709581301968	2		701	928	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264412	46264412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746670862	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	334	520	0	ENST00000371998.3:c.1459C>T	p.Arg487Cys	p.R487C	ENST00000371998		487	Cgt/Tgt	11/23	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.821709581301968	2		520	756	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991757	72991758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760959844	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	184	468	0	ENST00000268489.5:c.2287dup	p.Glu763GlyfsTer26	p.E763Gfs*26	ENST00000268489	NM_006885.3	763	gag/gGag	2/10	1	2	FACETS	0.724	0.671	0.777	0.724	0.671	0.777	SUBCLONAL	1	TRUE	1	0.821709581301968	2		468	619	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724361	52724361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	49	445	0	ENST00000322088.6:c.1493G>A	p.Arg498His	p.R498H	ENST00000322088	NM_014225.5	498	cGc/cAc	12/15	1	2	FACETS	0.19	0.16	0.223	0.19	0.16	0.223	SUBCLONAL	1	TRUE	1	0.821709581301968	2		445	628	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309887	65309887	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1304838920	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	222	459	2	ENST00000342505.4:c.2263C>T	p.Arg755Ter	p.R755*	ENST00000342505	NM_002227.2	755	Cga/Tga	17/25	1	2	FACETS	0.896	0.84	0.953	0.896	0.84	0.953	CLONAL	1	TRUE	1	0.821709581301968	2		461	603	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856305	111856305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777034332	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	73	42	0	ENST00000341259.2:c.356G>A	p.Arg119His	p.R119H	ENST00000341259	NM_005475.2	119	cGc/cAc	2/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.821709581301968	2		42	132	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526170	189526170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1225645471	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	372	675	2	ENST00000264731.3:c.434C>T	p.Ala145Val	p.A145V	ENST00000264731	NM_003722.4	145	gCg/gTg	4/14	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.821709581301968	2		677	813	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066648	94066648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371089003	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	283	524	1	ENST00000369303.4:c.1111C>T	p.Arg371Trp	p.R371W	ENST00000369303	NM_004440.3	371	Cgg/Tgg	5/17	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.821709581301968	2		525	686	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923738	72923738	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	334	555	2	ENST00000268489.5:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000268489	NM_006885.3	1114	Cga/Tga	4/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.821709581301968	2		557	729	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593573	215593573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554708247	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	244	376	0	ENST00000260947.4:c.2161G>A	p.Ala721Thr	p.A721T	ENST00000260947	NM_000465.2	721	Gca/Aca	11/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.821709581301968	2		376	541	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269072	142269072	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	311	614	1	ENST00000350721.4:c.2878C>T	p.Arg960Ter	p.R960*	ENST00000350721	NM_001184.3	960	Cga/Tga	14/47	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.821709581301968	2		615	726	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426784	121426784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765432081	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	294	677	0	ENST00000257555.6:c.475C>T	p.Arg159Trp	p.R159W	ENST00000257555		159	Cgg/Tgg	2/10	1	2	FACETS	0.841	0.794	0.888	0.841	0.794	0.888	CLONAL	1	TRUE	1	0.821709581301968	2		677	851	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737081	145737081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747815189	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	65	630	1	ENST00000428558.2:c.3485G>A	p.Arg1162His	p.R1162H	ENST00000428558	NM_004260.3	1162	cGc/cAc	21/22	1	2	FACETS	0.34	0.295	0.389	0.34	0.295	0.389	SUBCLONAL	1	TRUE	1	0.821709581301968	2		631	465	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246078900	246078900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1367184255	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	375	586	1	ENST00000388985.4:c.745C>T	p.Arg249Cys	p.R249C	ENST00000388985		249	Cgc/Tgc	8/12	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.821709581301968	2		587	806	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158132	27158132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773256013	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	255	497	0	ENST00000380036.4:c.356G>A	p.Arg119His	p.R119H	ENST00000380036	NM_000459.3	119	cGt/cAt	2/23	0.821709581301968	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.821709581301968	1		497	363	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223424	53223424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs971564188	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	389	720	0	ENST00000375401.3:c.3935G>A	p.Arg1312His	p.R1312H	ENST00000375401	NM_004187.3	1312	cGc/cAc	23/26	0.821709581301968	1	FACETS	0.996	0.962	1	0.996	0.962	1	CLONAL	1	TRUE	0	0.821709581301968	1		720	560	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856283	111856283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1420086510	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	38	27	0	ENST00000341259.2:c.334G>A	p.Ala112Thr	p.A112T	ENST00000341259	NM_005475.2	112	Gcc/Acc	2/8	1	2	FACETS	0.944	0.805	1	0.944	0.805	1	CLONAL	1	TRUE	1	0.821709581301968	2		27	98	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557912	21557912	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757472527	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	274	492	0	ENST00000382592.4:c.1933C>T	p.Arg645Trp	p.R645W	ENST00000382592	NM_014572.2	645	Cgg/Tgg	5/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.821709581301968	2		492	619	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399315	139399315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369467132	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	103	842	0	ENST00000277541.6:c.4828G>A	p.Ala1610Thr	p.A1610T	ENST00000277541	NM_017617.3	1610	Gca/Aca	26/34	1	2	FACETS	0.236	0.21	0.263	0.236	0.21	0.263	SUBCLONAL	1	TRUE	1	0.821709581301968	2		842	1062	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274172	10274172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567354612	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	48	490	2	ENST00000330684.3:c.97G>A	p.Ala33Thr	p.A33T	ENST00000330684	NM_001134407.1	33	Gcg/Acg	2/13	1	2	FACETS	0.224	0.189	0.263	0.224	0.189	0.263	SUBCLONAL	1	TRUE	1	0.821709581301968	2		492	521	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274645	123274645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	256	363	0	ENST00000358487.5:c.1273C>T	p.Arg425Trp	p.R425W	ENST00000358487	NM_000141.4	425	Cgg/Tgg	9/18	0.821709581301968	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.821709581301968	1		363	311	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407576	407576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756602021	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	260	481	0	ENST00000380956.4:c.1334G>A	p.Arg445His	p.R445H	ENST00000380956	NM_001195286.1	445	cGc/cAc	9/9	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.821709581301968	2		481	632	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899231	78899231	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200514795	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	57	494	0	ENST00000306801.3:c.2870C>T	p.Thr957Met	p.T957M	ENST00000306801	NM_020761.2	957	aCg/aTg	24/34	1	2	FACETS	0.187	0.16	0.217	0.187	0.16	0.217	SUBCLONAL	1	TRUE	1	0.821709581301968	2		494	742	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125398	47125398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377115716	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	231	474	0	ENST00000409792.3:c.5872G>A	p.Ala1958Thr	p.A1958T	ENST00000409792	NM_014159.6	1958	Gct/Act	12/21	1	2	FACETS	0.883	0.828	0.938	0.883	0.828	0.938	CLONAL	1	TRUE	1	0.821709581301968	2		474	637	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705201	52705201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1372727039	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	233	410	0	ENST00000322088.6:c.83G>A	p.Arg28His	p.R28H	ENST00000322088	NM_014225.5	28	cGc/cAc	2/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.821709581301968	2		410	524	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278407	39278407	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	245	652	1	ENST00000402219.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000402219	NM_005633.3	248	Cgc/Tgc	6/23	1	2	FACETS	0.858	0.806	0.911	0.858	0.806	0.911	CLONAL	1	TRUE	1	0.821709581301968	2		653	695	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811624	102811624	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs6213	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	336	621	0	ENST00000307046.8:c.560C>A	p.Ala187Asp	p.A187D	ENST00000307046	NM_001111285.1	187	gCt/gAt	4/4	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.821709581301968	2		621	775	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273432	38273432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1412996644	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	424	840	0	ENST00000425967.3:c.1903G>A	p.Ala635Thr	p.A635T	ENST00000425967	NM_001174067.1	635	Gcc/Acc	14/19	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.821709581301968	2		840	1026	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3114967	3114967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	289	669	1	ENST00000078429.4:c.502G>A	p.Ala168Thr	p.A168T	ENST00000078429	NM_002067.2	168	Gcc/Acc	4/7	1	2	FACETS	0.842	0.795	0.89	0.842	0.795	0.89	CLONAL	1	TRUE	1	0.821709581301968	2		670	835	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399216	139399216	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566680728	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	41	689	1	ENST00000277541.6:c.4927G>A	p.Ala1643Thr	p.A1643T	ENST00000277541	NM_017617.3	1643	Gcc/Acc	26/34	1	2	FACETS	0.126	0.104	0.15	0.126	0.104	0.15	SUBCLONAL	1	TRUE	1	0.821709581301968	2		690	793	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339110	65339111	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	279	529	3	ENST00000342505.4:c.425dup	p.Ile143AspfsTer9	p.I143Dfs*9	ENST00000342505	NM_002227.2	142	aag/aaAg	5/25	1	2	FACETS	0.861	0.812	0.91	0.861	0.812	0.91	CLONAL	1	TRUE	1	0.821709581301968	2		532	789	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395677	31395677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1267164985	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	263	497	1	ENST00000328111.2:c.2530G>A	p.Ala844Thr	p.A844T	ENST00000328111	NM_006892.3	844	Gcc/Acc	23/23	1	2	FACETS	0.985	0.93	1	0.985	0.93	1	CLONAL	1	TRUE	1	0.821709581301968	2		498	650	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039374	47039374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	55	732	1	ENST00000377604.3:c.997G>A	p.Val333Ile	p.V333I	ENST00000377604	NM_001204468.1	333	Gtc/Atc	10/24	0.821709581301968	1	FACETS	0.148	0.126	0.172	0.148	0.126	0.172	SUBCLONAL	1	TRUE	0	0.821709581301968	1		733	532	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94211916	94211916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142996063	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	44	536	0	ENST00000323929.3:c.529G>A	p.Ala177Thr	p.A177T	ENST00000323929	NM_005591.3	177	Gcg/Acg	6/20	0.821709581301968	1	FACETS	0.151	0.127	0.178	0.151	0.127	0.178	SUBCLONAL	1	TRUE	0	0.821709581301968	1		536	417	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465600	8465600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1427192894	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	45	624	2	ENST00000356435.5:c.3580G>A	p.Ala1194Thr	p.A1194T	ENST00000356435		1194	Gct/Act	21/35	0.821709581301968	1	FACETS	0.147	0.123	0.173	0.147	0.123	0.173	SUBCLONAL	1	TRUE	0	0.821709581301968	1		626	440	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088712	27088712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754046530	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	369	716	0	ENST00000324856.7:c.2321G>A	p.Arg774His	p.R774H	ENST00000324856	NM_006015.4	774	cGt/cAt	7/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.821709581301968	2		716	868	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21643223	21643223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1065751	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	65	798	2	ENST00000421138.2:c.304G>A	p.Val102Ile	p.V102I	ENST00000421138		102	Gta/Ata	5/16	1	2	FACETS	0.149	0.128	0.171	0.149	0.128	0.171	SUBCLONAL	1	TRUE	1	0.821709581301968	2		800	1062	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131727	2131727	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	72	770	0	ENST00000219476.3:c.3742G>A	p.Ala1248Thr	p.A1248T	ENST00000219476	NM_000548.3	1248	Gcc/Acc	31/42	1	2	FACETS	0.173	0.15	0.198	0.173	0.15	0.198	SUBCLONAL	1	TRUE	1	0.821709581301968	2		770	1012	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828866	26828866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	52	427	0	ENST00000381527.3:c.88G>A	p.Gly30Ser	p.G30S	ENST00000381527	NM_001260.1	30	Ggc/Agc	1/13	1	2	FACETS	0.206	0.175	0.24	0.206	0.175	0.24	SUBCLONAL	1	TRUE	1	0.821709581301968	2		427	615	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138594	11138594	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755069412	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	338	657	0	ENST00000358026.2:c.3350C>T	p.Ala1117Val	p.A1117V	ENST00000358026	NM_001128849.1	1117	gCg/gTg	24/36	1	2	FACETS	0.976	0.927	1	0.976	0.927	1	CLONAL	1	TRUE	1	0.821709581301968	2		657	843	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730008	41730008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537531066	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	232	572	2	ENST00000242208.4:c.521G>A	p.Arg174His	p.R174H	ENST00000242208	NM_002192.2	174	cGc/cAc	3/3	1	2	FACETS	0.785	0.735	0.836	0.785	0.735	0.836	SUBCLONAL	1	TRUE	1	0.821709581301968	2		574	719	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325126	123325126	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374996878	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	363	585	0	ENST00000358487.5:c.202G>A	p.Ala68Thr	p.A68T	ENST00000358487	NM_000141.4	68	Gcc/Acc	3/18	0.821709581301968	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.821709581301968	1		585	463	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495603	56495603	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369300309	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	311	580	2	ENST00000267101.3:c.3793C>T	p.Arg1265Trp	p.R1265W	ENST00000267101	NM_001982.3	1265	Cgg/Tgg	28/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.821709581301968	2		582	705	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732626	190732626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139826569	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	302	497	0	ENST00000441310.2:c.2444C>T	p.Ala815Val	p.A815V	ENST00000441310	NM_000534.4	815	gCg/gTg	11/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.821709581301968	2		497	696	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193150	11193150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764395301	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	295	554	1	ENST00000361445.4:c.5351G>A	p.Arg1784His	p.R1784H	ENST00000361445	NM_004958.3	1784	cGc/cAc	38/58	1	2	FACETS	0.992	0.939	1	0.992	0.939	1	CLONAL	1	TRUE	1	0.821709581301968	2		555	724	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3645613	3645613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200807331	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	64	583	1	ENST00000294008.3:c.2006G>A	p.Arg669His	p.R669H	ENST00000294008	NM_032444.2	669	cGc/cAc	9/15	1	2	FACETS	0.203	0.175	0.233	0.203	0.175	0.233	SUBCLONAL	1	TRUE	1	0.821709581301968	2		584	767	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965830	18965830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	76	647	4	ENST00000262803.5:c.1408G>A	p.Asp470Asn	p.D470N	ENST00000262803	NM_002911.3	470	Gac/Aac	10/24	1	2	FACETS	0.245	0.214	0.278	0.245	0.214	0.278	SUBCLONAL	1	TRUE	1	0.821709581301968	2		651	756	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336100	73336100	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs117383606	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	182	384	1	ENST00000377767.4:c.2303C>T	p.Ala768Val	p.A768V	ENST00000377767	NM_014953.3	768	gCg/gTg	17/21	1	2	FACETS	0.959	0.894	1	0.959	0.894	1	CLONAL	1	TRUE	1	0.821709581301968	2		385	462	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434890	110434890	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	484	806	0	ENST00000375856.3:c.3511C>T	p.Arg1171Cys	p.R1171C	ENST00000375856	NM_003749.2	1171	Cgc/Tgc	1/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.821709581301968	2		806	1133	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803455	32803455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148976382	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	300	734	0	ENST00000374899.4:c.704G>A	p.Arg235His	p.R235H	ENST00000374899	NM_018833.2	235	cGc/cAc	4/12	1	2	FACETS	0.784	0.74	0.829	0.784	0.74	0.829	SUBCLONAL	1	TRUE	1	0.821709581301968	2		734	931	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210907	36210907	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770426704	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	370	669	1	ENST00000222270.7:c.658C>T	p.Arg220Trp	p.R220W	ENST00000222270	NM_014727.1	220	Cgg/Tgg	3/37	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.821709581301968	2		670	870	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367969	15367969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759001252	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	362	664	1	ENST00000263377.2:c.1357C>T	p.Arg453Cys	p.R453C	ENST00000263377	NM_058243.2	453	Cgc/Tgc	8/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.821709581301968	2		665	809	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310895	123310895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141796960	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	299	455	0	ENST00000358487.5:c.533G>A	p.Arg178His	p.R178H	ENST00000358487	NM_000141.4	178	cGc/cAc	5/18	0.821709581301968	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.821709581301968	1		455	373	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352037	89352037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138353708	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	388	698	1	ENST00000301030.4:c.913G>A	p.Ala305Thr	p.A305T	ENST00000301030	NM_001256183.1	305	Gca/Aca	9/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.821709581301968	2		699	886	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096156	71096156	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	208	374	1	ENST00000318789.4:c.601C>T	p.Arg201Cys	p.R201C	ENST00000318789	NM_032682.5	201	Cgc/Tgc	10/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.821709581301968	2		375	478	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435889	110435889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1329734454	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	235	533	0	ENST00000375856.3:c.2512C>T	p.Arg838Cys	p.R838C	ENST00000375856	NM_003749.2	838	Cgt/Tgt	1/2	1	2	FACETS	0.839	0.787	0.892	0.839	0.787	0.892	CLONAL	1	TRUE	1	0.821709581301968	2		533	682	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152049	11152049	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558017726	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	357	593	0	ENST00000358026.2:c.4333C>T	p.Arg1445Cys	p.R1445C	ENST00000358026	NM_001128849.1	1445	Cgc/Tgc	31/36	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.821709581301968	2		593	804	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447543	12447543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	368	664	0	ENST00000287820.6:c.782C>T	p.Ala261Val	p.A261V	ENST00000287820	NM_015869.4	261	gCg/gTg	5/7	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.821709581301968	2		664	804	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347168	347168	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375543956	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	419	727	1	ENST00000262320.3:c.1843G>A	p.Ala615Thr	p.A615T	ENST00000262320	NM_003502.3	615	Gcc/Acc	7/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.821709581301968	2		728	950	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845190	151845190	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764910946	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	64	586	2	ENST00000262189.6:c.13822C>T	p.Arg4608Cys	p.R4608C	ENST00000262189	NM_170606.2	4608	Cgc/Tgc	52/59	1	2	FACETS	0.189	0.163	0.217	0.189	0.163	0.217	SUBCLONAL	1	TRUE	1	0.821709581301968	2		588	825	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223634	55223634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771929085	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	267	450	0	ENST00000275493.2:c.1001G>A	p.Arg334His	p.R334H	ENST00000275493	NM_005228.3	334	cGc/cAc	8/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.821709581301968	2		450	617	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815530	139815530	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528114067	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	406	683	0	ENST00000247668.2:c.1001C>T	p.Ala334Val	p.A334V	ENST00000247668	NM_021138.3	334	gCg/gTg	9/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.821709581301968	2		683	896	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440867	52440867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	310	550	0	ENST00000460680.1:c.637C>T	p.Arg213Cys	p.R213C	ENST00000460680	NM_004656.3	213	Cgt/Tgt	8/17	1	2	FACETS	0.988	0.936	1	0.988	0.936	1	CLONAL	1	TRUE	1	0.821709581301968	2		550	764	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292520	15292520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	351	754	0	ENST00000263388.2:c.2659G>A	p.Asp887Asn	p.D887N	ENST00000263388	NM_000435.2	887	Gat/Aat	17/33	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.821709581301968	2		754	850	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781260	3781260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1275659601	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	466	832	1	ENST00000262367.5:c.5105G>A	p.Arg1702His	p.R1702H	ENST00000262367	NM_004380.2	1702	cGc/cAc	30/31	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.821709581301968	2		833	1079	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777159	9777159	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749687214	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	369	642	0	ENST00000377346.4:c.923C>T	p.Ala308Val	p.A308V	ENST00000377346	NM_005026.3	308	gCg/gTg	7/24	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.821709581301968	2		642	887	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300377	11300377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	197	473	0	ENST00000361445.4:c.1769G>A	p.Gly590Asp	p.G590D	ENST00000361445	NM_004958.3	590	gGc/gAc	11/58	1	2	FACETS	0.82	0.764	0.877	0.82	0.764	0.877	CLONAL	1	TRUE	1	0.821709581301968	2		473	585	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256481	16256481	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757806135	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	410	721	1	ENST00000375759.3:c.3746G>A	p.Arg1249His	p.R1249H	ENST00000375759	NM_015001.2	1249	cGc/cAc	11/15	1	2	FACETS	0.989	0.944	1	0.989	0.944	1	CLONAL	1	TRUE	1	0.821709581301968	2		722	1009	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094450	27094450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779484265	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	310	553	0	ENST00000324856.7:c.3158G>A	p.Arg1053His	p.R1053H	ENST00000324856	NM_006015.4	1053	cGc/cAc	11/20	1	2	FACETS	0.99	0.939	1	0.99	0.939	1	CLONAL	1	TRUE	1	0.821709581301968	2		553	762	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099374	27099374	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	327	615	1	ENST00000324856.7:c.3611C>T	p.Ser1204Phe	p.S1204F	ENST00000324856	NM_006015.4	1204	tCc/tTc	14/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.821709581301968	2		616	779	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107086	27107086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	232	496	0	ENST00000324856.7:c.6697C>T	p.Arg2233Trp	p.R2233W	ENST00000324856	NM_006015.4	2233	Cgg/Tgg	20/20	1	2	FACETS	0.936	0.88	0.994	0.936	0.88	0.994	CLONAL	1	TRUE	1	0.821709581301968	2		496	603	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809513	36809513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1200783623	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	454	722	1	ENST00000373129.3:c.952C>T	p.Arg318Cys	p.R318C	ENST00000373129	NM_032017.1	318	Cgc/Tgc	10/12	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.821709581301968	2		723	977	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809754	36809754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs188394458	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	323	538	1	ENST00000373129.3:c.851G>A	p.Arg284His	p.R284H	ENST00000373129	NM_032017.1	284	cGc/cAc	9/12	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.821709581301968	2		539	687	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321323	65321323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201595595	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	90	630	1	ENST00000342505.4:c.1517G>A	p.Arg506His	p.R506H	ENST00000342505	NM_002227.2	506	cGc/cAc	11/25	1	2	FACETS	0.245	0.217	0.275	0.245	0.217	0.275	SUBCLONAL	1	TRUE	1	0.821709581301968	2		631	894	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332691	65332691	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	282	462	0	ENST00000342505.4:c.848C>A	p.Ala283Asp	p.A283D	ENST00000342505	NM_002227.2	283	gCt/gAt	7/25	1	2	FACETS	0.993	0.94	1	0.993	0.94	1	CLONAL	1	TRUE	1	0.821709581301968	2		462	691	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344759	65344759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	262	386	0	ENST00000342505.4:c.278G>A	p.Arg93His	p.R93H	ENST00000342505	NM_002227.2	93	cGc/cAc	4/25	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.821709581301968	2		386	584	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400933	72400934	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	243	495	0	ENST00000357731.5:c.237dup	p.Ala80CysfsTer4	p.A80Cfs*4	ENST00000357731	NM_173808.2	79	-/T	2/7	1	2	FACETS	0.989	0.931	1	0.989	0.931	1	CLONAL	1	TRUE	1	0.821709581301968	2		495	598	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465048	120465048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372916164	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	199	487	1	ENST00000256646.2:c.5024G>A	p.Arg1675His	p.R1675H	ENST00000256646	NM_024408.3	1675	cGc/cAc	28/34	1	2	FACETS	0.789	0.735	0.844	0.789	0.735	0.844	SUBCLONAL	1	TRUE	1	0.821709581301968	2		488	614	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117087	193117087	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	231	424	0	ENST00000367435.3:c.820G>T	p.Ala274Ser	p.A274S	ENST00000367435	NM_024529.4	274	Gca/Tca	8/17	1	2	FACETS	0.958	0.9	1	0.958	0.9	1	CLONAL	1	TRUE	1	0.821709581301968	2		424	587	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204506586	204506586	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	303	560	1	ENST00000367182.3:c.372G>T	p.Gln124His	p.Q124H	ENST00000367182	NM_001278516.1	124	caG/caT	6/11	1	2	FACETS	0.943	0.893	0.994	0.943	0.893	0.994	CLONAL	1	TRUE	1	0.821709581301968	2		561	782	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552740	226552740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	318	490	1	ENST00000366794.5:c.2621C>T	p.Ser874Phe	p.S874F	ENST00000366794	NM_001618.3	874	tCc/tTc	19/23	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.821709581301968	2		491	699	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683184	88683184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	261	398	1	ENST00000372037.3:c.1394C>T	p.Pro465Leu	p.P465L	ENST00000372037	NM_004329.2	465	cCg/cTg	12/13	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.821709581301968	2		399	502	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572273	64572273	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765306552	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	380	608	0	ENST00000312049.6:c.1366C>T	p.Arg456Cys	p.R456C	ENST00000312049	NM_130799.2	456	Cgc/Tgc	10/10	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.821709581301968	2		608	783	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200616	67200616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201207505	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	374	641	0	ENST00000312629.5:c.727C>T	p.Arg243Cys	p.R243C	ENST00000312629	NM_003952.2	243	Cgc/Tgc	9/15	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.821709581301968	2		641	800	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946382	71946382	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1299556537	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	410	739	0	ENST00000298229.2:c.2546C>T	p.Ala849Val	p.A849V	ENST00000298229	NM_001567.3	849	gCc/gTc	23/28	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.821709581301968	2		739	934	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122736	108122736	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	240	539	0	ENST00000278616.4:c.1780G>A	p.Glu594Lys	p.E594K	ENST00000278616	NM_000051.3	594	Gaa/Aaa	11/63	0.821709581301968	1	FACETS	0.969	0.926	1	0.969	0.926	1	CLONAL	1	TRUE	0	0.821709581301968	1		539	355	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342932	118342932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	251	495	0	ENST00000534358.1:c.1058G>A	p.Arg353Gln	p.R353Q	ENST00000534358	NM_005933.3	353	cGa/cAa	3/36	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.821709581301968	2		495	581	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644546	21644547	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs745659712	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	274	599	16	ENST00000421138.2:c.120dup	p.Val41SerfsTer14	p.V41Sfs*14	ENST00000421138		40	-/A	4/16	1	2	FACETS	0.883	0.833	0.934	0.883	0.833	0.934	CLONAL	1	TRUE	1	0.821709581301968	2		615	755	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427032	49427032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs527356550	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	251	540	0	ENST00000301067.7:c.11456G>A	p.Gly3819Asp	p.G3819D	ENST00000301067	NM_003482.3	3819	gGc/gAc	39/54	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.821709581301968	2		540	562	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431219	49431219	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	57	564	0	ENST00000301067.7:c.9920C>A	p.Ala3307Asp	p.A3307D	ENST00000301067	NM_003482.3	3307	gCt/gAt	34/54	1	2	FACETS	0.172	0.147	0.199	0.172	0.147	0.199	SUBCLONAL	1	TRUE	1	0.821709581301968	2		564	807	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433763	49433763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	447	826	0	ENST00000301067.7:c.7790G>A	p.Ser2597Asn	p.S2597N	ENST00000301067	NM_003482.3	2597	aGc/aAc	31/54	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.821709581301968	2		826	967	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860074	57860075	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs759448855	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	73	786	6	ENST00000228682.2:c.821dup	p.Cys275LeufsTer32	p.C275Lfs*32	ENST00000228682	NM_005269.2	272	tgg/tGgg	8/12	1	2	FACETS	0.19	0.165	0.216	0.19	0.165	0.216	SUBCLONAL	1	TRUE	1	0.821709581301968	2		792	937	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811681	102811681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	377	722	1	ENST00000307046.8:c.503G>A	p.Ser168Asn	p.S168N	ENST00000307046	NM_001111285.1	168	aGt/aAt	4/4	1	2	FACETS	0.973	0.927	1	0.973	0.927	1	CLONAL	1	TRUE	1	0.821709581301968	2		723	943	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118801	115118801	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	362	551	0	ENST00000257566.3:c.540G>A	p.Met180Ile	p.M180I	ENST00000257566	NM_016569.3	180	atG/atA	2/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.821709581301968	2		551	802	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249355	133249355	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	380	662	0	ENST00000320574.5:c.1544T>G	p.Ile515Ser	p.I515S	ENST00000320574	NM_006231.2	515	aTc/aGc	15/49	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.821709581301968	2		662	895	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252729	133252729	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	384	647	0	ENST00000320574.5:c.971C>T	p.Pro324Leu	p.P324L	ENST00000320574	NM_006231.2	324	cCc/cTc	10/49	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.821709581301968	2		647	810	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26956990	26956990	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1318765332	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	232	394	0	ENST00000381527.3:c.496C>T	p.Arg166Ter	p.R166*	ENST00000381527	NM_001260.1	166	Cga/Tga	5/13	1	2	FACETS	0.97	0.912	1	0.97	0.912	1	CLONAL	1	TRUE	1	0.821709581301968	2		394	582	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912295	32912295	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	306	544	0	ENST00000380152.3:c.3803C>A	p.Ser1268Tyr	p.S1268Y	ENST00000380152		1268	tCt/tAt	11/27	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.821709581301968	2		544	741	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434971	110434971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	367	711	0	ENST00000375856.3:c.3430C>T	p.Arg1144Cys	p.R1144C	ENST00000375856	NM_003749.2	1144	Cgc/Tgc	1/2	1	2	FACETS	0.892	0.849	0.937	0.892	0.849	0.937	CLONAL	1	TRUE	1	0.821709581301968	2		711	1001	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435844	110435844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	311	403	0	ENST00000375856.3:c.2557G>A	p.Ala853Thr	p.A853T	ENST00000375856	NM_003749.2	853	Gcc/Acc	1/2	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.821709581301968	2		403	591	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437970	110437970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	10	124	1	ENST00000375856.3:c.431G>A	p.Ser144Asn	p.S144N	ENST00000375856	NM_003749.2	144	aGc/aAc	1/2	1	2	FACETS	0.126	0.085	0.178	0.126	0.085	0.178	SUBCLONAL	1	TRUE	1	0.821709581301968	2		125	193	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610659	81610659	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	38	477	0	ENST00000298171.2:c.2257G>T	p.Gly753Cys	p.G753C	ENST00000298171	NM_000369.2	753	Ggc/Tgc	10/10	1	2	FACETS	0.147	0.12	0.176	0.147	0.12	0.176	SUBCLONAL	1	TRUE	1	0.821709581301968	2		477	631	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570237	95570237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368588781	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	236	436	0	ENST00000393063.1:c.3496G>A	p.Val1166Ile	p.V1166I	ENST00000393063	NM_030621.3	1166	Gtt/Att	22/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.821709581301968	2		436	549	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571498	95571498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	315	504	0	ENST00000393063.1:c.3179G>A	p.Arg1060His	p.R1060H	ENST00000393063	NM_030621.3	1060	cGc/cAc	21/28	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.821709581301968	2		504	679	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95573960	95573960	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	159	360	0	ENST00000393063.1:c.2789C>T	p.Ala930Val	p.A930V	ENST00000393063	NM_030621.3	930	gCc/gTc	18/28	1	2	FACETS	0.787	0.727	0.848	0.787	0.727	0.848	SUBCLONAL	1	TRUE	1	0.821709581301968	2		360	492	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95577656	95577656	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	222	396	0	ENST00000393063.1:c.2254G>A	p.Ala752Thr	p.A752T	ENST00000393063	NM_030621.3	752	Gca/Aca	15/28	1	2	FACETS	0.941	0.883	1	0.941	0.883	1	CLONAL	1	TRUE	1	0.821709581301968	2		396	574	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000376	42000376	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	328	491	0	ENST00000219905.7:c.2395T>A	p.Phe799Ile	p.F799I	ENST00000219905	NM_001164273.1	799	Ttt/Att	7/24	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.821709581301968	2		491	728	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799259	88799259	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	258	538	0	ENST00000360948.2:c.126G>T	p.Glu42Asp	p.E42D	ENST00000360948	NM_001012338.2	42	gaG/gaT	2/19	1	2	FACETS	0.842	0.792	0.893	0.842	0.792	0.893	CLONAL	1	TRUE	1	0.821709581301968	2		538	746	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251090	99251090	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	48	631	0	ENST00000268035.6:c.394A>G	p.Asn132Asp	p.N132D	ENST00000268035	NM_000875.3	132	Aac/Gac	2/21	1	2	FACETS	0.163	0.137	0.192	0.163	0.137	0.192	SUBCLONAL	1	TRUE	1	0.821709581301968	2		631	717	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456422	99456422	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	294	558	0	ENST00000268035.6:c.1739A>G	p.Tyr580Cys	p.Y580C	ENST00000268035	NM_000875.3	580	tAc/tGc	8/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.821709581301968	2		558	696	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	364610	364610	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	480	757	1	ENST00000262320.3:c.952G>A	p.Ala318Thr	p.A318T	ENST00000262320	NM_003502.3	318	Gcc/Acc	3/11	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.821709581301968	2		758	1001	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639911	3639911	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	357	611	0	ENST00000294008.3:c.3728G>T	p.Ser1243Ile	p.S1243I	ENST00000294008	NM_032444.2	1243	aGc/aTc	12/15	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.821709581301968	2		611	764	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823928	3823928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768288810	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	339	649	0	ENST00000262367.5:c.2287G>A	p.Ala763Thr	p.A763T	ENST00000262367	NM_004380.2	763	Gcc/Acc	13/31	1	2	FACETS	0.994	0.945	1	0.994	0.945	1	CLONAL	1	TRUE	1	0.821709581301968	2		649	830	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81927372	81927372	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	412	642	0	ENST00000359376.3:c.1045C>A	p.Leu349Met	p.L349M	ENST00000359376	NM_002661.3	349	Ctg/Atg	12/33	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.821709581301968	2		642	895	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934275	81934275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867891510	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	265	693	0	ENST00000359376.3:c.1252G>A	p.Ala418Thr	p.A418T	ENST00000359376	NM_002661.3	418	Gcc/Acc	14/33	1	2	FACETS	0.812	0.764	0.861	0.812	0.764	0.861	CLONAL	1	TRUE	1	0.821709581301968	2		693	794	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972511	81972511	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	225	486	0	ENST00000359376.3:c.3304A>G	p.Thr1102Ala	p.T1102A	ENST00000359376	NM_002661.3	1102	Acg/Gcg	29/33	1	2	FACETS	0.778	0.728	0.829	0.778	0.728	0.829	SUBCLONAL	1	TRUE	1	0.821709581301968	2		486	704	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350350	89350350	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	264	731	0	ENST00000301030.4:c.2600A>G	p.Asp867Gly	p.D867G	ENST00000301030	NM_001256183.1	867	gAc/gGc	9/13	1	2	FACETS	0.641	0.601	0.682	0.641	0.601	0.682	SUBCLONAL	1	TRUE	1	0.821709581301968	2		731	1003	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89837023	89837023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777032467	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	405	637	1	ENST00000389301.3:c.2171C>T	p.Thr724Met	p.T724M	ENST00000389301	NM_000135.2	724	aCg/aTg	24/43	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.821709581301968	2		638	906	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89871793	89871793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779131886	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	365	631	0	ENST00000389301.3:c.604G>A	p.Asp202Asn	p.D202N	ENST00000389301	NM_000135.2	202	Gac/Aac	7/43	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.821709581301968	2		631	848	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15952271	15952271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150237987	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	325	575	0	ENST00000268712.3:c.6424G>A	p.Val2142Ile	p.V2142I	ENST00000268712	NM_006311.3	2142	Gtc/Atc	41/46	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.821709581301968	2		575	791	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995241	15995241	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	65	552	0	ENST00000268712.3:c.2952T>A	p.Asp984Glu	p.D984E	ENST00000268712	NM_006311.3	984	gaT/gaA	22/46	1	2	FACETS	0.193	0.167	0.222	0.193	0.167	0.222	SUBCLONAL	1	TRUE	1	0.821709581301968	2		552	819	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533275	29533275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1131691085	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	33	340	1	ENST00000356175.3:c.1278G>A	p.Trp426Ter	p.W426*	ENST00000356175	NM_000267.3	426	tgG/tgA	12/57	1	2	FACETS	0.156	0.126	0.189	0.156	0.126	0.189	SUBCLONAL	1	TRUE	1	0.821709581301968	2		341	516	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679390	29679390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	284	454	0	ENST00000356175.3:c.7510G>A	p.Asp2504Asn	p.D2504N	ENST00000356175	NM_000267.3	2504	Gac/Aac	50/57	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.821709581301968	2		454	690	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362305	40362305	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	62	561	0	ENST00000293328.3:c.1790T>C	p.Phe597Ser	p.F597S	ENST00000293328	NM_012448.3	597	tTt/tCt	15/19	1	2	FACETS	0.205	0.177	0.236	0.205	0.177	0.236	SUBCLONAL	1	TRUE	1	0.821709581301968	2		561	735	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489786	40489786	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	313	559	0	ENST00000264657.5:c.640C>T	p.Arg214Trp	p.R214W	ENST00000264657	NM_139276.2	214	Cgg/Tgg	7/24	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.821709581301968	2		559	751	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244703	41244703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1324818767	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	409	737	0	ENST00000357654.3:c.2845G>A	p.Gly949Ser	p.G949S	ENST00000357654	NM_007294.3	949	Ggc/Agc	10/23	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.821709581301968	2		737	913	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780626	56780626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760911964	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	413	636	0	ENST00000337432.4:c.641G>A	p.Arg214His	p.R214H	ENST00000337432	NM_058216.2	214	cGt/cAt	4/9	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.821709581301968	2		636	913	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724469	724469	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	337	671	0	ENST00000314574.4:c.1587C>A	p.Tyr529Ter	p.Y529*	ENST00000314574	NM_005433.3	529	taC/taA	12/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.821709581301968	2		671	795	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7163133	7163133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	458	744	0	ENST00000302850.5:c.1939G>A	p.Asp647Asn	p.D647N	ENST00000302850	NM_000208.2	647	Gac/Aac	9/22	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.821709581301968	2		744	1050	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170578	7170578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	257	512	0	ENST00000302850.5:c.1453G>A	p.Ala485Thr	p.A485T	ENST00000302850	NM_000208.2	485	Gcc/Acc	6/22	1	2	FACETS	0.985	0.929	1	0.985	0.929	1	CLONAL	1	TRUE	1	0.821709581301968	2		512	635	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267416	7267416	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	248	513	0	ENST00000302850.5:c.592G>A	p.Ala198Thr	p.A198T	ENST00000302850	NM_000208.2	198	Gcc/Acc	2/22	1	2	FACETS	0.879	0.826	0.932	0.879	0.826	0.932	CLONAL	1	TRUE	1	0.821709581301968	2		513	687	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249281	10249281	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	178	410	0	ENST00000340748.4:c.3901G>A	p.Ala1301Thr	p.A1301T	ENST00000340748		1301	Gcc/Acc	34/40	1	2	FACETS	0.843	0.783	0.904	0.843	0.783	0.904	CLONAL	1	TRUE	1	0.821709581301968	2		410	514	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291155	10291155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759600542	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	416	757	0	ENST00000340748.4:c.316C>T	p.Arg106Cys	p.R106C	ENST00000340748		106	Cgt/Tgt	4/40	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.821709581301968	2		757	949	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169500	11169500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	409	727	0	ENST00000358026.2:c.4666G>A	p.Asp1556Asn	p.D1556N	ENST00000358026	NM_001128849.1	1556	Gac/Aac	33/36	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.821709581301968	2		727	936	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945764	17945764	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201784993	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	369	695	0	ENST00000458235.1:c.2096C>T	p.Ala699Val	p.A699V	ENST00000458235	NM_000215.3	699	gCg/gTg	16/24	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.821709581301968	2		695	827	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278091	18278091	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1165324884	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	464	702	0	ENST00000222254.8:c.1711C>T	p.Arg571Cys	p.R571C	ENST00000222254	NM_005027.3	571	Cgc/Tgc	13/16	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.821709581301968	2		702	1000	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210854	36210854	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777039998	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	431	656	0	ENST00000222270.7:c.605C>T	p.Ala202Val	p.A202V	ENST00000222270	NM_014727.1	202	gCa/gTa	3/37	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.821709581301968	2		656	992	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213515	36213515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746928288	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	467	867	0	ENST00000222270.7:c.2617C>T	p.Arg873Cys	p.R873C	ENST00000222270	NM_014727.1	873	Cgt/Tgt	5/37	1	2	FACETS	0.954	0.914	0.996	0.954	0.914	0.996	CLONAL	1	TRUE	1	0.821709581301968	2		867	1191	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216697	36216697	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	272	572	0	ENST00000222270.7:c.3863C>T	p.Ala1288Val	p.A1288V	ENST00000222270	NM_014727.1	1288	gCc/gTc	13/37	1	2	FACETS	0.948	0.895	1	0.948	0.895	1	CLONAL	1	TRUE	1	0.821709581301968	2		572	698	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218461	36218461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775217613	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	336	580	0	ENST00000222270.7:c.4240C>T	p.Arg1414Cys	p.R1414C	ENST00000222270	NM_014727.1	1414	Cgc/Tgc	16/37	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.821709581301968	2		580	733	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229354	36229354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190330467	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	323	572	0	ENST00000222270.7:c.8044C>T	p.Arg2682Cys	p.R2682C	ENST00000222270	NM_014727.1	2682	Cgt/Tgt	37/37	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.821709581301968	2		572	748	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748866	41748866	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs777982238	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	391	615	0	ENST00000301178.4:c.1391T>C	p.Val464Ala	p.V464A	ENST00000301178	NM_021913.4	464	gTc/gCc	11/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.821709581301968	2		615	865	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793516	42793516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	467	717	2	ENST00000575354.2:c.1318C>T	p.Arg440Cys	p.R440C	ENST00000575354	NM_015125.3	440	Cgc/Tgc	8/20	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.821709581301968	2		719	978	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905987	50905987	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	285	603	0	ENST00000440232.2:c.959C>T	p.Ala320Val	p.A320V	ENST00000440232	NM_002691.3	320	gCc/gTc	8/27	1	2	FACETS	0.981	0.928	1	0.981	0.928	1	CLONAL	1	TRUE	1	0.821709581301968	2		603	707	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466773	25466773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1431156021	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	303	526	0	ENST00000264709.3:c.1930G>A	p.Ala644Thr	p.A644T	ENST00000264709	NM_175629.2	644	Gct/Act	16/23	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.821709581301968	2		526	725	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467072	25467072	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs767692203	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	353	706	2	ENST00000264709.3:c.1803G>A	p.Trp601Ter	p.W601*	ENST00000264709	NM_175629.2	601	tgG/tgA	15/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.821709581301968	2		708	814	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965968	25965968	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	112	729	0	ENST00000435504.4:c.3238C>A	p.Leu1080Ile	p.L1080I	ENST00000435504		1080	Ctc/Atc	13/13	1	2	FACETS	0.299	0.268	0.331	0.299	0.268	0.331	SUBCLONAL	1	TRUE	1	0.821709581301968	2		729	913	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443582	29443582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143790259	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	51	694	0	ENST00000389048.3:c.3635G>A	p.Arg1212His	p.R1212H	ENST00000389048	NM_004304.4	1212	cGc/cAc	23/29	1	2	FACETS	0.143	0.121	0.168	0.143	0.121	0.168	SUBCLONAL	1	TRUE	1	0.821709581301968	2		694	868	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551323	29551323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1430324218	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	317	635	0	ENST00000389048.3:c.1307C>T	p.Ala436Val	p.A436V	ENST00000389048	NM_004304.4	436	gCc/gTc	6/29	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.821709581301968	2		635	754	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61709657	61709657	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	174	280	0	ENST00000401558.2:c.2830T>A	p.Ser944Thr	p.S944T	ENST00000401558	NM_003400.3	944	Tca/Aca	23/25	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.821709581301968	2		280	405	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152614	99152614	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61757084	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	292	474	0	ENST00000074304.5:c.410C>T	p.Thr137Met	p.T137M	ENST00000074304	NM_001134224.1	137	aCg/aTg	7/26	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.821709581301968	2		474	657	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99181160	99181160	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777200638	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	321	573	1	ENST00000074304.5:c.2101G>A	p.Gly701Ser	p.G701S	ENST00000074304	NM_001134224.1	701	Ggc/Agc	20/26	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.821709581301968	2		574	759	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660834	227660834	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	50	541	0	ENST00000305123.5:c.2621C>T	p.Ala874Val	p.A874V	ENST00000305123	NM_005544.2	874	gCc/gTc	1/2	1	2	FACETS	0.196	0.165	0.229	0.196	0.165	0.229	SUBCLONAL	1	TRUE	1	0.821709581301968	2		541	622	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019136	31019136	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139716375	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	40	582	0	ENST00000375687.4:c.731G>A	p.Arg244His	p.R244H	ENST00000375687	NM_015338.5	244	cGc/cAc	9/13	1	2	FACETS	0.125	0.103	0.149	0.125	0.103	0.149	SUBCLONAL	1	TRUE	1	0.821709581301968	2		582	781	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019217	31019217	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs576447224	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	79	554	0	ENST00000375687.4:c.812G>A	p.Arg271Gln	p.R271Q	ENST00000375687	NM_015338.5	271	cGg/cAg	9/13	1	2	FACETS	0.238	0.208	0.269	0.238	0.208	0.269	SUBCLONAL	1	TRUE	1	0.821709581301968	2		554	809	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019393	31019393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373599045	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	267	455	0	ENST00000375687.4:c.890C>T	p.Thr297Met	p.T297M	ENST00000375687	NM_015338.5	297	aCg/aTg	10/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.821709581301968	2		455	585	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39725942	39725942	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	60	486	0	ENST00000361337.2:c.813G>T	p.Lys271Asn	p.K271N	ENST00000361337	NM_003286.2	271	aaG/aaT	10/21	1	2	FACETS	0.217	0.187	0.251	0.217	0.187	0.251	SUBCLONAL	1	TRUE	1	0.821709581301968	2		486	672	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945592	54945592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	215	554	0	ENST00000312783.6:c.978G>T	p.Lys326Asn	p.K326N	ENST00000312783	NM_198436.1	326	aaG/aaT	9/10	1	2	FACETS	0.796	0.744	0.85	0.796	0.744	0.85	SUBCLONAL	1	TRUE	1	0.821709581301968	2		554	657	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62303918	62303918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1023502136	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	363	567	0	ENST00000360203.5:c.709G>A	p.Ala237Thr	p.A237T	ENST00000360203	NM_001283009.1	237	Gca/Aca	9/35	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.821709581301968	2		567	784	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326190	62326190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	339	711	0	ENST00000360203.5:c.3206G>A	p.Arg1069Lys	p.R1069K	ENST00000360203	NM_001283009.1	1069	aGg/aAg	32/35	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.821709581301968	2		711	769	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817462	39817462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	280	524	3	ENST00000288319.7:c.101C>T	p.Thr34Ile	p.T34I	ENST00000288319	NM_182918.3	34	aCc/aTc	2/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.821709581301968	2		527	662	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22142672	22142672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	174	292	0	ENST00000215832.6:c.730C>T	p.Leu244Phe	p.L244F	ENST00000215832	NM_002745.4	244	Ctt/Ttt	6/9	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.821709581301968	2		292	386	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458366	12458366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	309	656	2	ENST00000287820.6:c.983C>T	p.Ala328Val	p.A328V	ENST00000287820	NM_015869.4	328	gCc/gTc	6/7	1	2	FACETS	0.826	0.781	0.871	0.826	0.781	0.871	CLONAL	1	TRUE	1	0.821709581301968	2		658	911	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090489	37090489	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63749995	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	177	453	0	ENST00000231790.2:c.2084C>T	p.Ser695Leu	p.S695L	ENST00000231790	NM_000249.3	695	tCg/tTg	18/19	1	2	FACETS	0.736	0.682	0.792	0.736	0.682	0.792	SUBCLONAL	1	TRUE	1	0.821709581301968	2		453	585	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280681	41280681	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	306	569	0	ENST00000349496.5:c.2194G>A	p.Asp732Asn	p.D732N	ENST00000349496	NM_001904.3	732	Gac/Aac	15/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.821709581301968	2		569	704	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927965	49927965	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	395	668	1	ENST00000296474.3:c.3763G>A	p.Ala1255Thr	p.A1255T	ENST00000296474	NM_002447.2	1255	Gcg/Acg	18/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.821709581301968	2		669	877	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008511	71008511	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs541340602	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	31	332	0	ENST00000318789.4:c.1921G>A	p.Asp641Asn	p.D641N	ENST00000318789	NM_032682.5	641	Gat/Aat	21/21	1	2	FACETS	0.161	0.129	0.196	0.161	0.129	0.196	SUBCLONAL	1	TRUE	1	0.821709581301968	2		332	470	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021722	71021722	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	228	437	0	ENST00000318789.4:c.1636C>A	p.Pro546Thr	p.P546T	ENST00000318789	NM_032682.5	546	Cca/Aca	18/21	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.821709581301968	2		437	549	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72881557	72881557	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	323	487	1	ENST00000325599.8:c.562G>A	p.Ala188Thr	p.A188T	ENST00000325599	NM_018130.2	188	Gcc/Acc	5/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.821709581301968	2		488	691	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670483	134670483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	295	607	0	ENST00000398015.3:c.394G>A	p.Ala132Thr	p.A132T	ENST00000398015	NM_004441.4	132	Gcc/Acc	3/16	1	2	FACETS	0.941	0.89	0.992	0.941	0.89	0.992	CLONAL	1	TRUE	1	0.821709581301968	2		607	763	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165677	185165677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753496412	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	296	489	2	ENST00000265026.3:c.952G>A	p.Ala318Thr	p.A318T	ENST00000265026	NM_004721.4	318	Gca/Aca	5/14	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.821709581301968	2		491	672	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808943	1808943	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	281	649	0	ENST00000260795.2:c.2375A>G	p.Asp792Gly	p.D792G	ENST00000260795		792	gAc/gGc	17/17	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.821709581301968	2		649	671	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1919964	1919964	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	323	655	0	ENST00000382891.5:c.1024G>T	p.Ala342Ser	p.A342S	ENST00000382891	NM_133335.3	342	Gcc/Tcc	5/22	1	2	FACETS	0.842	0.797	0.887	0.842	0.797	0.887	CLONAL	1	TRUE	1	0.821709581301968	2		655	934	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1977024	1977024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201530243	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	364	644	0	ENST00000382891.5:c.3518C>T	p.Thr1173Met	p.T1173M	ENST00000382891	NM_133335.3	1173	aCg/aTg	20/22	1	2	FACETS	0.982	0.935	1	0.982	0.935	1	CLONAL	1	TRUE	1	0.821709581301968	2		644	902	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99812464	99812465	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	222	434	0	ENST00000280892.6:c.204dup	p.Lys69Ter	p.K69*	ENST00000280892	NM_001130678.1	68	-/T	3/7	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.821709581301968	2		434	514	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156429	106156429	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	285	548	0	ENST00000380013.4:c.1330A>C	p.Thr444Pro	p.T444P	ENST00000380013	NM_001127208.2	444	Aca/Cca	3/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.821709581301968	2		548	639	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164734	106164734	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs902035179	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	26	370	0	ENST00000380013.4:c.3602G>A	p.Arg1201His	p.R1201H	ENST00000380013	NM_001127208.2	1201	cGc/cAc	6/11	1	2	FACETS	0.137	0.108	0.17	0.137	0.108	0.17	SUBCLONAL	1	TRUE	1	0.821709581301968	2		370	463	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751937	57751937	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs552180691	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	302	538	0	ENST00000274289.3:c.1300G>A	p.Ala434Thr	p.A434T	ENST00000274289	NM_006622.3	434	Gca/Aca	10/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.821709581301968	2		538	692	SUCCESS
APC	324	MSKCC	GRCh37	5	112178550	112178550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	244	434	0	ENST00000257430.4:c.7259C>T	p.Ser2420Phe	p.S2420F	ENST00000257430	NM_000038.5	2420	tCt/tTt	16/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.821709581301968	2		434	583	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515246	149515246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	390	644	0	ENST00000261799.4:c.236G>A	p.Gly79Asp	p.G79D	ENST00000261799	NM_002609.3	79	gGc/gAc	3/23	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.821709581301968	2		644	806	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721993	176721993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	293	512	0	ENST00000439151.2:c.7624C>T	p.Pro2542Ser	p.P2542S	ENST00000439151	NM_022455.4	2542	Cct/Tct	23/23	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.821709581301968	2		512	628	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816535	32816535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373556147	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	498	773	3	ENST00000354258.4:c.1640G>A	p.Arg547His	p.R547H	ENST00000354258	NM_000593.5	547	cGc/cAc	7/11	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.821709581301968	2		776	1101	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821590	32821590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	76	662	0	ENST00000354258.4:c.4G>A	p.Ala2Thr	p.A2T	ENST00000354258	NM_000593.5	2	Gct/Act	1/11	1	2	FACETS	0.209	0.183	0.238	0.209	0.183	0.238	SUBCLONAL	1	TRUE	1	0.821709581301968	2		662	885	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745232	43745232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1208889729	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	396	616	0	ENST00000523873.1:c.145C>T	p.Arg49Cys	p.R49C	ENST00000523873		49	Cgc/Tgc	3/8	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.821709581301968	2		616	877	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683754	162683754	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	298	487	0	ENST00000366898.1:c.215G>T	p.Arg72Ile	p.R72I	ENST00000366898	NM_004562.2	72	aGa/aTa	3/12	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.821709581301968	2		487	664	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977555	2977555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349696922	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	239	527	0	ENST00000396946.4:c.1129C>T	p.Arg377Trp	p.R377W	ENST00000396946	NM_032415.4	377	Cgg/Tgg	8/25	1	2	FACETS	0.838	0.787	0.891	0.838	0.787	0.891	CLONAL	1	TRUE	1	0.821709581301968	2		527	694	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233081	55233081	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201061916	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	270	612	3	ENST00000275493.2:c.1831G>A	p.Ala611Thr	p.A611T	ENST00000275493	NM_005228.3	611	Gca/Aca	15/28	1	2	FACETS	0.797	0.75	0.844	0.797	0.75	0.844	SUBCLONAL	1	TRUE	1	0.821709581301968	2		615	825	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374356	81374356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	256	445	0	ENST00000222390.5:c.706G>A	p.Asp236Asn	p.D236N	ENST00000222390	NM_000601.4	236	Gat/Aat	6/18	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.821709581301968	2		445	598	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371756	116371756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371463233	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	184	407	0	ENST00000397752.3:c.1235G>A	p.Arg412His	p.R412H	ENST00000397752	NM_000245.2	412	cGc/cAc	3/21	1	2	FACETS	0.845	0.786	0.905	0.845	0.786	0.905	CLONAL	1	TRUE	1	0.821709581301968	2		407	530	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133239	38133239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	314	587	0	ENST00000317025.8:c.4234G>A	p.Ala1412Thr	p.A1412T	ENST00000317025	NM_023034.1	1412	Gct/Act	24/24	1	2	FACETS	0.867	0.82	0.914	0.867	0.82	0.914	CLONAL	1	TRUE	1	0.821709581301968	2		587	882	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68973016	68973016	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	200	371	1	ENST00000288368.4:c.1339+2T>C		p.X447_splice	ENST00000288368	NM_024870.2	447			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.821709581301968	2		372	445	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981420	70981420	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	385	753	0	ENST00000276594.2:c.676C>A	p.Leu226Ile	p.L226I	ENST00000276594	NM_024504.3	226	Ctc/Atc	2/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.821709581301968	2		753	916	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864285	117864285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	271	426	0	ENST00000297338.2:c.1372G>A	p.Ala458Thr	p.A458T	ENST00000297338	NM_006265.2	458	Gcc/Acc	11/14	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.821709581301968	2		426	589	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752816	128752816	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	213	377	1	ENST00000377970.2:c.977C>T	p.Ala326Val	p.A326V	ENST00000377970	NM_002467.4	326	gCg/gTg	3/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.821709581301968	2		378	454	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566045	141566045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	341	610	0	ENST00000220592.5:c.1219G>A	p.Asp407Asn	p.D407N	ENST00000220592	NM_012154.3	407	Gac/Aac	10/19	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.821709581301968	2		610	752	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738239	145738239	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	307	732	0	ENST00000428558.2:c.2746C>T	p.Pro916Ser	p.P916S	ENST00000428558	NM_004260.3	916	Ccg/Tcg	16/22	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.821709581301968	2		732	580	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741899	145741899	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	90	703	0	ENST00000428558.2:c.604C>A	p.Leu202Met	p.L202M	ENST00000428558	NM_004260.3	202	Ctg/Atg	5/22	1	2	FACETS	0.349	0.31	0.391	0.349	0.31	0.391	SUBCLONAL	1	TRUE	1	0.821709581301968	2		703	628	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044450	5044450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376070326	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	66	582	0	ENST00000381652.3:c.398G>A	p.Arg133Gln	p.R133Q	ENST00000381652	NM_004972.3	133	cGg/cAg	5/25	0.821709581301968	1	FACETS	0.2	0.174	0.228	0.2	0.174	0.228	SUBCLONAL	1	TRUE	0	0.821709581301968	1		582	473	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484167	8484167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	46	545	0	ENST00000356435.5:c.3365G>A	p.Gly1122Asp	p.G1122D	ENST00000356435		1122	gGc/gAc	19/35	0.821709581301968	1	FACETS	0.16	0.135	0.188	0.16	0.135	0.188	SUBCLONAL	1	TRUE	0	0.821709581301968	1		545	411	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624559	93624559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	346	596	0	ENST00000375746.1:c.650G>A	p.Arg217His	p.R217H	ENST00000375746	NM_001174167.1	217	cGc/cAc	4/14	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.821709581301968	2		596	815	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220525	98220525	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778337760	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	289	566	1	ENST00000331920.6:c.2938G>A	p.Gly980Ser	p.G980S	ENST00000331920	NM_000264.3	980	Ggc/Agc	18/24	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.821709581301968	2		567	692	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239981	98239981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142791675	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	31	428	0	ENST00000331920.6:c.1351G>A	p.Ala451Thr	p.A451T	ENST00000331920	NM_000264.3	451	Gcc/Acc	10/24	1	2	FACETS	0.125	0.1	0.153	0.125	0.1	0.153	SUBCLONAL	1	TRUE	1	0.821709581301968	2		428	604	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907143	101907143	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	168	501	0	ENST00000374994.4:c.1103C>T	p.Ala368Val	p.A368V	ENST00000374994	NM_004612.2	368	gCt/gTt	6/9	1	2	FACETS	0.652	0.602	0.704	0.652	0.602	0.704	SUBCLONAL	1	TRUE	1	0.821709581301968	2		501	627	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772731	135772731	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	117	494	0	ENST00000298552.3:c.2815G>T	p.Gly939Ter	p.G939*	ENST00000298552	NM_001162426.1	939	Gga/Tga	22/23	1	2	FACETS	0.361	0.326	0.399	0.361	0.326	0.399	SUBCLONAL	1	TRUE	1	0.821709581301968	2		494	788	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932981	39932981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	61	680	0	ENST00000378444.4:c.1618C>T	p.Arg540Trp	p.R540W	ENST00000378444	NM_001123385.1	540	Cgg/Tgg	4/15	0.821709581301968	1	FACETS	0.156	0.135	0.18	0.156	0.135	0.18	SUBCLONAL	1	TRUE	0	0.821709581301968	1		680	559	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928971	44928971	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	82	587	0	ENST00000377967.4:c.2071A>T	p.Thr691Ser	p.T691S	ENST00000377967	NM_021140.2	691	Aca/Tca	17/29	0.821709581301968	1	FACETS	0.231	0.203	0.259	0.231	0.203	0.259	SUBCLONAL	1	TRUE	0	0.821709581301968	1		587	510	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044904	47044904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	405	815	0	ENST00000377604.3:c.2230C>T	p.Arg744Cys	p.R744C	ENST00000377604	NM_001204468.1	744	Cgt/Tgt	20/24	0.821709581301968	1	FACETS	0.983	0.95	1	0.983	0.95	1	CLONAL	1	TRUE	0	0.821709581301968	1		815	591	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428239	47428239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764255925	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	65	663	1	ENST00000377045.4:c.1199G>A	p.Arg400His	p.R400H	ENST00000377045	NM_001654.4	400	cGc/cAc	11/16	0.821709581301968	1	FACETS	0.163	0.141	0.187	0.163	0.141	0.187	SUBCLONAL	1	TRUE	0	0.821709581301968	1		664	572	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223440	53223440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782631044	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	41	724	2	ENST00000375401.3:c.3919C>T	p.Arg1307Trp	p.R1307W	ENST00000375401	NM_004187.3	1307	Cgg/Tgg	23/26	0.821709581301968	1	FACETS	0.109	0.091	0.13	0.109	0.091	0.13	SUBCLONAL	1	TRUE	0	0.821709581301968	1		726	538	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246389	53246389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1569279367	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	82	708	1	ENST00000375401.3:c.593G>A	p.Arg198Gln	p.R198Q	ENST00000375401	NM_004187.3	198	cGa/cAa	5/26	0.821709581301968	1	FACETS	0.184	0.162	0.208	0.184	0.162	0.208	SUBCLONAL	1	TRUE	0	0.821709581301968	1		709	638	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412151	63412151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	306	915	0	ENST00000330258.3:c.1016G>A	p.Ser339Asn	p.S339N	ENST00000330258	NM_152424.3	339	aGt/aAt	2/2	0.821709581301968	1	FACETS	0.474	0.448	0.501	0.474	0.448	0.501	SUBCLONAL	1	TRUE	0	0.821709581301968	1		915	925	SUCCESS
AR	367	MSKCC	GRCh37	X	66937323	66937323	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	18	478	0	ENST00000374690.3:c.2177T>C	p.Phe726Ser	p.F726S	ENST00000374690	NM_000044.3	726	tTc/tCc	5/8	0.821709581301968	1	FACETS	0.076	0.057	0.099	0.076	0.057	0.099	SUBCLONAL	1	TRUE	0	0.821709581301968	1		478	340	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342180	70342180	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	61	572	0	ENST00000374080.3:c.1232G>A	p.Ser411Asn	p.S411N	ENST00000374080		411	aGt/aAt	8/45	0.821709581301968	1	FACETS	0.186	0.16	0.214	0.186	0.16	0.214	SUBCLONAL	1	TRUE	0	0.821709581301968	1		572	470	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344633	70344633	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	334	602	1	ENST00000374080.3:c.1994C>A	p.Ser665Tyr	p.S665Y	ENST00000374080		665	tCt/tAt	14/45	0.821709581301968	1	FACETS	0.96	0.923	0.995	0.96	0.923	0.995	CLONAL	1	TRUE	0	0.821709581301968	1		603	499	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344959	70344959	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	455	707	0	ENST00000374080.3:c.2189G>A	p.Arg730Gln	p.R730Q	ENST00000374080		730	cGa/cAa	15/45	0.821709581301968	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.821709581301968	1		707	608	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123499634	123499634	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031289-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	71	613	0	ENST00000371139.4:c.161A>G	p.Tyr54Cys	p.Y54C	ENST00000371139	NM_001114937.2	54	tAc/tGc	2/4	0.821709581301968	1	FACETS	0.214	0.187	0.243	0.214	0.187	0.243	SUBCLONAL	1	TRUE	0	0.821709581301968	1		613	475	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0032252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	283	485	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	1	2	FACETS	0.937	0.888	0.987	0.937	0.888	0.987	CLONAL	1	TRUE	1	0.951123631317857	2		485	635	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466000	69466000	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30956	3373	1113	0	ENST00000227507.2:c.838G>A	p.Glu280Lys	p.E280K	ENST00000227507	NM_053056.2	280	Gag/Aag	5/5	0.951123631317857	29	FACETS	0.953	0.934	0.972			1	CLONAL	3	TRUE	NA	0.951123631317857	29		1113	34329	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965011	15965011	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	260	811	0	ENST00000268712.3:c.5585A>G	p.Glu1862Gly	p.E1862G	ENST00000268712	NM_006311.3	1862	gAa/gGa	37/46	0.579319558629301	1	FACETS	0.373	0.35	0.396	0.373	0.35	0.396	SUBCLONAL	1	TRUE	0	0.951123631317857	1		811	769	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278114	41278114	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	210	641	0	ENST00000349496.5:c.1990G>A	p.Glu664Lys	p.E664K	ENST00000349496	NM_001904.3	664	Gag/Aag	13/15	1	2	FACETS	0.603	0.562	0.646	0.603	0.562	0.646	SUBCLONAL	1	TRUE	1	0.951123631317857	2		641	732	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162609	47162609	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	275	584	0	ENST00000409792.3:c.3517C>T	p.His1173Tyr	p.H1173Y	ENST00000409792	NM_014159.6	1173	Cat/Tat	3/21	1	2	FACETS	0.908	0.859	0.957	0.908	0.859	0.957	CLONAL	1	TRUE	1	0.951123631317857	2		584	637	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71019939	71019942	+	frameshift_variant	Frame_Shift_Del	DEL	TTAA	TTAA	-	novel	NA	P-0032252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	170	317	0	ENST00000318789.4:c.1667_1670del	p.Ile556LysfsTer42	p.I556Kfs*42	ENST00000318789	NM_032682.5	556	aTTAAa/aa	19/21	1	2	FACETS	0.9	0.839	0.963	0.9	0.839	0.963	CLONAL	1	TRUE	1	0.951123631317857	2		317	397	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938406	44938406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	325	250	0	ENST00000377967.4:c.2954C>T	p.Ser985Phe	p.S985F	ENST00000377967	NM_021140.2	985	tCt/tTt	20/29	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.951123631317857	1		250	338	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627415	37627415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415916204	NA	P-0032252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	232	952	1	ENST00000249071.6:c.304C>T	p.Arg102Trp	p.R102W	ENST00000249071	NM_002872.4	102	Cgg/Tgg	5/7	1	2	FACETS	0.478	0.445	0.511	0.478	0.445	0.511	SUBCLONAL	1	TRUE	1	0.951123631317857	2		953	1021	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465885	69465885	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0032252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26986	2743	797	0	ENST00000227507.2:c.724-1G>T		p.X242_splice	ENST00000227507	NM_053056.2	242			0.951123631317857	29	FACETS	0.895	0.876	0.915			1	CLONAL	3	TRUE	NA	0.951123631317857	29		797	29729	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889068	76889068	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	20	242	0	ENST00000373344.5:c.4942G>C	p.Asp1648His	p.D1648H	ENST00000373344	NM_000489.3	1648	Gat/Cat	18/35	1	1	FACETS	0.093	0.071	0.119	0.093	0.071	0.119	SUBCLONAL	1	TRUE	0	0.951123631317857	1		242	237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577098	7577098	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	501	604	0	ENST00000269305.4:c.840A>T	p.Arg280Ser	p.R280S	ENST00000269305	NM_001126112.2	280	agA/agT	8/11	NA	2	FACETS	0.994	0.971	1			1	INDETERMINATE	2	TRUE	NA	0.823328791315216	2		604	612	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186757	108186757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs864622251	NA	P-0032963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	102	406	0	ENST00000278616.4:c.6115G>A	p.Glu2039Lys	p.E2039K	ENST00000278616	NM_000051.3	2039	Gaa/Aaa	42/63	0.889381795067363	2	FACETS	0.834	0.759	0.911	0.417	0.379	0.456	CLONAL	1	TRUE	0	0.94769239686016	2		406	258	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085893	16085893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1324334894	NA	P-0032963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	151	424	0	ENST00000281043.3:c.1069C>T	p.Arg357Cys	p.R357C	ENST00000281043	NM_005378.4	357	Cgt/Tgt	3/3	0.856590022052802	4	FACETS	1	0.963	1	0.542	0.497	0.587	CLONAL	1	TRUE	2	0.94769239686016	4		424	573	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0033463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	245	449	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.730787740662708	3	FACETS	0.982	0.931	1	0.982	0.931	1	CLONAL	2	TRUE	1	0.730787740662708	3		449	466	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984428	201984428	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	239	671	1	ENST00000359651.3:c.1093G>T	p.Glu365Ter	p.E365*	ENST00000359651		365	Gag/Tag	8/8	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.730787740662708	2		672	583	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441780	49441780	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555195442	NA	P-0033463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	209	502	0	ENST00000301067.7:c.4204C>T	p.Gln1402Ter	p.Q1402*	ENST00000301067	NM_003482.3	1402	Cag/Tag	14/54	0.730787740662708	1	FACETS	0.943	0.89	0.995	0.943	0.89	0.995	CLONAL	1	TRUE	0	0.730787740662708	1		502	385	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727523	88727523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	146	549	0	ENST00000360948.2:c.256G>A	p.Glu86Lys	p.E86K	ENST00000360948	NM_001012338.2	86	Gag/Aag	3/19	0.730787740662708	1	FACETS	0.987	0.923	1	0.987	0.923	1	CLONAL	1	TRUE	0	0.730787740662708	1		549	257	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240343	41240343	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	160	355	0	ENST00000379561.5:c.7G>A	p.Glu3Lys	p.E3K	ENST00000379561	NM_002015.3	3	Gag/Aag	1/3	0.721663703715693	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.730787740662708	1		355	262	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982122	201982122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	243	775	0	ENST00000359651.3:c.646G>A	p.Asp216Asn	p.D216N	ENST00000359651		216	Gac/Aac	5/8	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.730787740662708	2		775	650	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861689	59861689	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	222	624	0	ENST00000259008.2:c.1570C>T	p.Gln524Ter	p.Q524*	ENST00000259008	NM_032043.2	524	Caa/Taa	11/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.730787740662708	2		624	563	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541229	187541229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	162	516	0	ENST00000441802.2:c.6511C>T	p.Pro2171Ser	p.P2171S	ENST00000441802	NM_005245.3	2171	Ccg/Tcg	10/27	0.13652869311749	1	FACETS	0.638	0.591	0.686	0.638	0.591	0.686	INDETERMINATE	1	TRUE	0	0.730787740662708	1		516	441	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542656	187542656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	169	613	0	ENST00000441802.2:c.5084C>T	p.Ser1695Leu	p.S1695L	ENST00000441802	NM_005245.3	1695	tCa/tTa	10/27	0.13652869311749	1	FACETS	0.63	0.584	0.676	0.63	0.584	0.676	INDETERMINATE	1	TRUE	0	0.730787740662708	1		613	466	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860374	151860374	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	195	608	0	ENST00000262189.6:c.10288G>T	p.Glu3430Ter	p.E3430*	ENST00000262189	NM_170606.2	3430	Gaa/Taa	43/59	1	2	FACETS	0.936	0.872	1	0.936	0.872	1	CLONAL	1	TRUE	1	0.730787740662708	2		608	570	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38184277	38184277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1420471815	NA	P-0033463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	211	630	0	ENST00000317025.8:c.1679C>T	p.Ser560Leu	p.S560L	ENST00000317025	NM_023034.1	560	tCa/tTa	7/24	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.730787740662708	2		630	574	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49399991	49399991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	224	704	0	ENST00000418115.1:c.346G>A	p.Gly116Arg	p.G116R	ENST00000418115	NM_001664.2	116	Ggg/Agg	4/5	0.730787740662708	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.730787740662708	1		704	364	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21630790	21630790	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	177	596	0	ENST00000421138.2:c.814G>C	p.Glu272Gln	p.E272Q	ENST00000421138		272	Gaa/Caa	8/16	0.730787740662708	1	FACETS	0.943	0.886	1	0.943	0.886	1	CLONAL	1	TRUE	0	0.730787740662708	1		596	326	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222460	39222460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1194032302	NA	P-0033463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	226	748	0	ENST00000402219.2:c.3150G>A	p.Met1050Ile	p.M1050I	ENST00000402219	NM_005633.3	1050	atG/atA	20/23	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.730787740662708	2		748	615	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397679	49397679	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	235	567	0	ENST00000418115.1:c.545G>C	p.Arg182Thr	p.R182T	ENST00000418115	NM_001664.2	182	aGa/aCa	5/5	0.730787740662708	1	FACETS	0.96	0.91	1	0.96	0.91	1	CLONAL	1	TRUE	0	0.730787740662708	1		567	425	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49399983	49399983	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	217	700	1	ENST00000418115.1:c.354G>T	p.Lys118Asn	p.K118N	ENST00000418115	NM_001664.2	118	aaG/aaT	4/5	0.730787740662708	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.730787740662708	1		701	357	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525603	137525603	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	148	674	0	ENST00000367739.4:c.412G>T	p.Glu138Ter	p.E138*	ENST00000367739	NM_000416.2	138	Gag/Tag	4/7	0.721663703715693	1	FACETS	0.989	0.925	1	0.989	0.925	1	CLONAL	1	TRUE	0	0.730787740662708	1		674	260	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146976	38146976	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033463-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	222	793	0	ENST00000317025.8:c.3166G>A	p.Glu1056Lys	p.E1056K	ENST00000317025	NM_023034.1	1056	Gaa/Aaa	18/24	1	2	FACETS	0.972	0.911	1	0.972	0.911	1	CLONAL	1	TRUE	1	0.730787740662708	2		793	625	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0033463-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	49	449	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.332121175093486	3	FACETS	0.788	0.676	0.909	0.788	0.676	0.909	CLONAL	2	TRUE	1	0.345510121931748	3		449	211	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984428	201984428	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033463-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	178	671	1	ENST00000359651.3:c.1093G>T	p.Glu365Ter	p.E365*	ENST00000359651		365	Gag/Tag	8/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.345510121931748	2		672	985	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441780	49441780	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555195442	NA	P-0033463-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	179	502	0	ENST00000301067.7:c.4204C>T	p.Gln1402Ter	p.Q1402*	ENST00000301067	NM_003482.3	1402	Cag/Tag	14/54	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.345510121931748	2		502	810	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727523	88727523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033463-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	93	549	0	ENST00000360948.2:c.256G>A	p.Glu86Lys	p.E86K	ENST00000360948	NM_001012338.2	86	Gag/Aag	3/19	0.345510121931748	1	FACETS	0.759	0.676	0.847	0.759	0.676	0.847	SUBCLONAL	1	TRUE	0	0.345510121931748	1		549	587	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240343	41240343	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033463-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	105	355	0	ENST00000379561.5:c.7G>A	p.Glu3Lys	p.E3K	ENST00000379561	NM_002015.3	3	Gag/Aag	1/3	0.345510121931748	1	FACETS	0.874	0.786	0.968	0.874	0.786	0.968	CLONAL	1	TRUE	0	0.345510121931748	1		355	575	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982122	201982122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033463-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	207	775	0	ENST00000359651.3:c.646G>A	p.Asp216Asn	p.D216N	ENST00000359651		216	Gac/Aac	5/8	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.345510121931748	2		775	1116	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861689	59861689	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033463-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	25	624	0	ENST00000259008.2:c.1570C>T	p.Gln524Ter	p.Q524*	ENST00000259008	NM_032043.2	524	Caa/Taa	11/20	1	2	FACETS	0.679	0.538	0.84	0.679	0.538	0.84	SUBCLONAL	1	TRUE	1	0.345510121931748	2		624	213	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541229	187541229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033463-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	61	516	0	ENST00000441802.2:c.6511C>T	p.Pro2171Ser	p.P2171S	ENST00000441802	NM_005245.3	2171	Ccg/Tcg	10/27	1	2	FACETS	0.952	0.825	1	0.952	0.825	1	CLONAL	1	TRUE	1	0.345510121931748	2		516	371	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542656	187542656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033463-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	55	613	0	ENST00000441802.2:c.5084C>T	p.Ser1695Leu	p.S1695L	ENST00000441802	NM_005245.3	1695	tCa/tTa	10/27	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.345510121931748	2		613	263	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860374	151860374	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033463-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	81	608	0	ENST00000262189.6:c.10288G>T	p.Glu3430Ter	p.E3430*	ENST00000262189	NM_170606.2	3430	Gaa/Taa	43/59	1	2	FACETS	0.767	0.677	0.865	0.767	0.677	0.865	SUBCLONAL	1	TRUE	1	0.345510121931748	2		608	611	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38184277	38184277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1420471815	NA	P-0033463-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	60	630	0	ENST00000317025.8:c.1679C>T	p.Ser560Leu	p.S560L	ENST00000317025	NM_023034.1	560	tCa/tTa	7/24	1	2	FACETS	0.855	0.74	0.981	0.855	0.74	0.981	CLONAL	1	TRUE	1	0.345510121931748	2		630	406	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876392	35876392	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033463-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	41	691	0	ENST00000303115.3:c.1184A>T	p.Lys395Met	p.K395M	ENST00000303115	NM_002185.3	395	aAg/aTg	8/8	0.319055020640242	4	FACETS	0.322	0.267	0.384	0.107	0.089	0.128	SUBCLONAL	1	TRUE	1	0.345510121931748	4		691	992	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0033466-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	309	825	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.464432453589933	2	FACETS	0.925	0.88	0.97	0.925	0.88	0.97	CLONAL	2	TRUE	0	0.513211326078461	2		826	651	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148993	119150015	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTACATCCTGGCAGGTACGGATCTAAACAGCGACTTTTTTCAGCTATGTAATAACCTTGGAAAATTCGGTATTATATAGCCTTTACTGATACAAGGGGTGGCCTGGCTTTTGGGGTTAGGTTTAAACTTTTACTTTTTTTTGATCTCTAGGAAATGTATTTTCTAGTAGATTAATATTTTAAGTATTTTCAGATGCATCTGTTACTATCTTTTGCTTCTTCTGCAGGAATCAGAAGGTCAGGGCTGTCCTTTCTGCCGATGTGAAATTAAAGGTACTGAACCCATCGTGGTAGATCCGTTTGATCCTAGAGGGAGTGGCAGCCTGTTGAGGCAAGGAGCAGAGGGAGCTCCCTCCCCAAATTATGATGATGATGATGATGAACGAGCTGATGATACTCTCTTCATGATGAAGGAATTGGCTGGTGCCAAGGTAAGATGGCAGTTTAGGAGACTGGCAAAATCCATTGTGAGTTGTCTTCTAAAGCCGTAAAACACTTAACGATATCCAAACTACAATGATAGGTAGTATTAATAGCTAATATTTATTGAGCATTTACTATATGACAGATATTGTGTTAAGCACTTTACTTGTTTTTTACTCAATCTTTACTACAGCCCTATGAGTACATACTACTATTATCCTTATTTAACAGATGAAGAAACTGAGGCACAAAGAGGTTAAGGAATTTGCCGAAGACCACACAGCTAGTAGGTTGAAGCATCTGTGAGCTGCATCTATGACCAGGCATTCCAGCTTAAGGCCCATGTTCTTACTGTCTGTATTTTTTAGGACTAAGACTTTATTCATATCTGTTGGTGGAGAATATGAGGGAGAAATAAAAGAACTGGACCCTCTTTTGCTAATGCAACTAGAATAAGTTCTGTTCCCTTTTTTTTTTTTTATTTTAATGGAGTCTTGGCATTAGAAGGTTGGGGCTGGGCATGCCCATAGCTCATGCCTATAATCCCAGTACTTTGGGACGTTGAGGCTGGAGGATCAGTTGAGCCCAGTTTGAGGCCAG	CTTACATCCTGGCAGGTACGGATCTAAACAGCGACTTTTTTCAGCTATGTAATAACCTTGGAAAATTCGGTATTATATAGCCTTTACTGATACAAGGGGTGGCCTGGCTTTTGGGGTTAGGTTTAAACTTTTACTTTTTTTTGATCTCTAGGAAATGTATTTTCTAGTAGATTAATATTTTAAGTATTTTCAGATGCATCTGTTACTATCTTTTGCTTCTTCTGCAGGAATCAGAAGGTCAGGGCTGTCCTTTCTGCCGATGTGAAATTAAAGGTACTGAACCCATCGTGGTAGATCCGTTTGATCCTAGAGGGAGTGGCAGCCTGTTGAGGCAAGGAGCAGAGGGAGCTCCCTCCCCAAATTATGATGATGATGATGATGAACGAGCTGATGATACTCTCTTCATGATGAAGGAATTGGCTGGTGCCAAGGTAAGATGGCAGTTTAGGAGACTGGCAAAATCCATTGTGAGTTGTCTTCTAAAGCCGTAAAACACTTAACGATATCCAAACTACAATGATAGGTAGTATTAATAGCTAATATTTATTGAGCATTTACTATATGACAGATATTGTGTTAAGCACTTTACTTGTTTTTTACTCAATCTTTACTACAGCCCTATGAGTACATACTACTATTATCCTTATTTAACAGATGAAGAAACTGAGGCACAAAGAGGTTAAGGAATTTGCCGAAGACCACACAGCTAGTAGGTTGAAGCATCTGTGAGCTGCATCTATGACCAGGCATTCCAGCTTAAGGCCCATGTTCTTACTGTCTGTATTTTTTAGGACTAAGACTTTATTCATATCTGTTGGTGGAGAATATGAGGGAGAAATAAAAGAACTGGACCCTCTTTTGCTAATGCAACTAGAATAAGTTCTGTTCCCTTTTTTTTTTTTTATTTTAATGGAGTCTTGGCATTAGAAGGTTGGGGCTGGGCATGCCCATAGCTCATGCCTATAATCCCAGTACTTTGGGACGTTGAGGCTGGAGGATCAGTTGAGCCCAGTTTGAGGCCAG	-	novel	NA	P-0033466-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	69	440	0	ENST00000264033.4:c.1214_1431+593del		p.X405_splice	ENST00000264033	NM_005188.3	405		8-9/16	NA	2	FACETS	0.576	0.503	0.654			1	INDETERMINATE	1	TRUE	NA	0.513211326078461	2		440	467	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89881018	89881018	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033466-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	181	372	0	ENST00000389301.3:c.193G>C	p.Glu65Gln	p.E65Q	ENST00000389301	NM_000135.2	65	Gaa/Caa	3/43	0.509591478203942	3	FACETS	0.847	0.788	0.908	0.847	0.788	0.908	CLONAL	2	TRUE	1	0.513211326078461	3		372	523	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222777	5222777	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033466-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	306	892	0	ENST00000357368.4:c.3026A>C	p.Gln1009Pro	p.Q1009P	ENST00000357368	NM_002850.3	1009	cAa/cCa	18/38	0.509591478203942	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.513211326078461	3		892	729	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379803	17379804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0033466-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	335	869	0	ENST00000359435.4:c.189dup	p.Asn64GlnfsTer8	p.N64Qfs*8	ENST00000359435	NM_001033549.1	63	ctc/ctCc	2/9	0.509591478203942	3	FACETS	0.859	0.814	0.904	0.859	0.814	0.904	CLONAL	2	TRUE	1	0.513211326078461	3		869	955	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31015950	31015950	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033466-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	209	399	1	ENST00000375687.4:c.272C>A	p.Ser91Tyr	p.S91Y	ENST00000375687	NM_015338.5	91	tCt/tAt	5/13	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	2	TRUE	NA	0.513211326078461	2		400	396	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720924	119720924	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033466-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	258	389	1	ENST00000316626.5:c.251T>A	p.Ile84Asn	p.I84N	ENST00000316626		84	aTc/aAc	2/12	0.443827850860264	4	FACETS	0.958	0.901	1			1	CLONAL	2	TRUE	NA	0.513211326078461	4		390	794	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459223	99459257	+	frameshift_variant	Frame_Shift_Del	DEL	CATCGAACTCCTCTTCTCAGTTAATCGTGAAGTGG	CATCGAACTCCTCTTCTCAGTTAATCGTGAAGTGG	T	novel	NA	P-0033466-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	152	593	0	ENST00000268035.6:c.1859_1893delinsT	p.Ala620ValfsTer11	p.A620Vfs*11	ENST00000268035	NM_000875.3	620	gCATCGAACTCCTCTTCTCAGTTAATCGTGAAGTGG/gT	9/21	0.412378939908119	4	FACETS	1	0.978	1	0.598	0.548	0.651	CLONAL	1	TRUE	2	0.513211326078461	4		593	749	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993108	72993108	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0033466-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	169	707	0	ENST00000268489.5:c.937G>T	p.Glu313Ter	p.E313*	ENST00000268489	NM_006885.3	313	Gag/Tag	2/10	0.509591478203942	3	FACETS	0.997	0.918	1	0.499	0.459	0.54	CLONAL	1	TRUE	1	0.513211326078461	3		707	830	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119642231	119642231	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033466-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	102	361	2	ENST00000316626.5:c.466A>T	p.Ile156Phe	p.I156F	ENST00000316626		156	Att/Ttt	4/12	0.443827850860264	4	FACETS	0.91	0.815	1			1	CLONAL	1	TRUE	NA	0.513211326078461	4		363	661	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954198	48954233	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGATTATCCATTCAAAATTTTAGGTAAATTTTTTAC	CGATTATCCATTCAAAATTTTAGGTAAATTTTTTAC	TT	novel	NA	P-0033466-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	38	180	2	ENST00000267163.4:c.1399_1421+13delinsTT		p.X467_splice	ENST00000267163	NM_000321.2	467		15/27	0.464432453589933	2	FACETS	0.695	0.58	0.821	0.348	0.29	0.411	SUBCLONAL	1	TRUE	0	0.513211326078461	2		182	213	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880251	155880345	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCATGATCTTCTGGGAATCGGTGGCTGATGAACTGCATGGTCATGGCTTCAAAAGAAGAAATAAAAGTCAAATCCTCACAAAGGTGACCCACAG	ATCATGATCTTCTGGGAATCGGTGGCTGATGAACTGCATGGTCATGGCTTCAAAAGAAGAAATAAAAGTCAAATCCTCACAAAGGTGACCCACAG	TAAGCA	novel	NA	P-0033466-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	60	466	2	ENST00000368323.3:c.107-48_153delinsTGCTTA		p.X36_splice	ENST00000368323	NM_006912.5	36		3/6	0.505100628726401	4	FACETS	0.485	0.417	0.56	0.162	0.139	0.187	SUBCLONAL	1	TRUE	1	0.513211326078461	4		468	729	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363243	40363243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033799-T10-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	229	672	1	ENST00000397332.2:c.986C>T	p.Ser329Leu	p.S329L	ENST00000397332	NM_001033082.2	329	tCg/tTg	3/3	0.421990250760914	1	FACETS	0.398	0.371	0.425	0.398	0.371	0.425	INDETERMINATE	1	TRUE	0	0.828004332748842	1		673	815	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397742	49397742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552757	NA	P-0033799-T10-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	448	698	0	ENST00000418115.1:c.482C>T	p.Ala161Val	p.A161V	ENST00000418115	NM_001664.2	161	gCa/gTa	5/5	0.419843250491009	1	FACETS	0.734	0.705	0.763	0.734	0.705	0.763	INDETERMINATE	1	TRUE	0	0.828004332748842	1		698	864	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521253	187521253	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033799-T10-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	465	823	0	ENST00000441802.2:c.11902C>T	p.Gln3968Ter	p.Q3968*	ENST00000441802	NM_005245.3	3968	Caa/Taa	22/27	0.785555392331275	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.828004332748842	1		823	617	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216899	7216899	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033799-T10-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	204	658	0	ENST00000380728.2:c.622C>T	p.Gln208Ter	p.Q208*	ENST00000380728		208	Cag/Tag	7/11	0.421990250760914	1	FACETS	0.372	0.346	0.399	0.372	0.346	0.399	INDETERMINATE	1	TRUE	0	0.828004332748842	1		658	776	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056181	27056181	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033799-T10-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	416	649	0	ENST00000324856.7:c.1177C>T	p.Gln393Ter	p.Q393*	ENST00000324856	NM_006015.4	393	Cag/Tag	2/20	0.421990250760914	1	FACETS	0.747	0.717	0.777	0.747	0.717	0.777	INDETERMINATE	1	TRUE	0	0.828004332748842	1		649	788	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797891	45797891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199840380	NA	P-0033799-T10-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	261	828	0	ENST00000450313.1:c.880C>T	p.Arg294Cys	p.R294C	ENST00000450313	NM_012222.2	294	Cgc/Tgc	10/16	0.421990250760914	1	FACETS	0.36	0.337	0.384	0.36	0.337	0.384	INDETERMINATE	1	TRUE	0	0.828004332748842	1		828	1026	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118354897	118354897	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0033799-T10-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	301	439	0	ENST00000534358.1:c.4087-1G>A		p.X1363_splice	ENST00000534358	NM_005933.3	1363			1	2	FACETS	0.955	0.905	1	0.955	0.905	1	CLONAL	1	TRUE	1	0.828004332748842	2		439	761	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807967	3807967	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033799-T10-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	208	595	0	ENST00000262367.5:c.3452G>A	p.Trp1151Ter	p.W1151*	ENST00000262367	NM_004380.2	1151	tGg/tAg	18/31	0.421990250760914	1	FACETS	0.358	0.333	0.384	0.358	0.333	0.384	INDETERMINATE	1	TRUE	0	0.828004332748842	1		595	822	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56401603	56401603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033799-T10-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	132	460	0	ENST00000348428.3:c.1465G>A	p.Gly489Arg	p.G489R	ENST00000348428	NM_006785.3	489	Gga/Aga	12/17	0.421990250760914	1	FACETS	0.354	0.323	0.386	0.354	0.323	0.386	INDETERMINATE	1	TRUE	0	0.828004332748842	1		460	528	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56402522	56402522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033799-T10-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	58	267	0	ENST00000348428.3:c.1564G>A	p.Asp522Asn	p.D522N	ENST00000348428	NM_006785.3	522	Gat/Aat	13/17	0.421990250760914	1	FACETS	0.253	0.218	0.29	0.253	0.218	0.29	INDETERMINATE	1	TRUE	0	0.828004332748842	1		267	325	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513814	41513814	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033799-T10-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	461	588	0	ENST00000263253.7:c.718C>T	p.Gln240Ter	p.Q240*	ENST00000263253	NM_001429.3	240	Cag/Tag	2/31	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.828004332748842	2		588	1104	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659164	86659164	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0033799-T10-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	95	152	0	ENST00000274376.6:c.1454-1G>A		p.X485_splice	ENST00000274376	NM_002890.2	485			0.419843250491009	1	FACETS	0.768	0.705	0.831	0.768	0.705	0.831	INDETERMINATE	1	TRUE	0	0.828004332748842	1		152	175	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138913	37138913	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033799-T10-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	514	763	0	ENST00000373509.5:c.253C>T	p.Arg85Ter	p.R85*	ENST00000373509	NM_002648.3	85	Cga/Tga	4/6	1	2	FACETS	0.988	0.948	1	0.988	0.948	1	CLONAL	1	TRUE	1	0.828004332748842	2		763	1257	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918645	44918646	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AATGC	novel	NA	P-0033799-T10-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	391	269	0	ENST00000377967.4:c.1131_1135dup	p.Thr379MetfsTer62	p.T379Mfs*62	ENST00000377967	NM_021140.2	376	-/AATGC	12/29	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.828004332748842	1		269	533	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940441	13940441	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033799-T10-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	112	385	0	ENST00000405192.2:c.1065G>C	p.Gln355His	p.Q355H	ENST00000405192	NM_001163147.1	355	caG/caC	11/12	0.514230139160601	3	FACETS	0.509	0.458	0.564	0.255	0.229	0.282	SUBCLONAL	1	TRUE	1	0.828004332748842	3		385	751	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484252	8484252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033799-T10-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	188	620	0	ENST00000356435.5:c.3280G>A	p.Gly1094Arg	p.G1094R	ENST00000356435		1094	Ggg/Agg	19/35	NA	2	FACETS	0.503	0.465	0.543			1	INDETERMINATE	1	TRUE	NA	0.828004332748842	2		620	903	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484303	8484303	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033799-T10-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	153	563	2	ENST00000356435.5:c.3229C>A	p.Pro1077Thr	p.P1077T	ENST00000356435		1077	Cct/Act	19/35	NA	2	FACETS	0.452	0.413	0.492			1	INDETERMINATE	1	TRUE	NA	0.828004332748842	2		565	818	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39751865	39751865	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	103	503	0	ENST00000361337.2:c.2226G>T	p.Lys742Asn	p.K742N	ENST00000361337	NM_003286.2	742	aaG/aaT	21/21	1	2	FACETS	0.384	0.344	0.426	0.384	0.344	0.426	SUBCLONAL	1	NA	1	0.857834878558627	2		503	626	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0034568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	16	516	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	1	2	FACETS	0.472	0.348	0.621	0.472	0.348	0.621	SUBCLONAL	1	TRUE	1	0.2	2		516	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203436	NA	P-0034568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	13	589	0	ENST00000269305.4:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269305	NM_001126112.2	163	Tac/Cac	5/11	1	2	FACETS	0.357	0.254	0.484	0.357	0.254	0.484	SUBCLONAL	1	TRUE	1	0.2	2		589	364	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425106	49425106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	34	662	1	ENST00000301067.7:c.13382T>C	p.Leu4461Pro	p.L4461P	ENST00000301067	NM_003482.3	4461	cTg/cCg	39/54	NA	2	FACETS	0.885	0.724	1			1	INDETERMINATE	1	TRUE	NA	0.2	2		663	384	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431721	49431722	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0034568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	23	547	0	ENST00000301067.7:c.9417dup	p.Lys3140GlnfsTer36	p.K3140Qfs*36	ENST00000301067	NM_003482.3	3139	-/C	34/54	NA	2	FACETS	0.807	0.63	1			1	INDETERMINATE	1	TRUE	NA	0.2	2		547	285	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81979830	81979830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772932697	NA	P-0034568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	22	407	0	ENST00000359376.3:c.3532G>A	p.Ala1178Thr	p.A1178T	ENST00000359376	NM_002661.3	1178	Gct/Act	31/33	0.3	1	FACETS	0.484	0.374	0.612	0.484	0.374	0.612	SUBCLONAL	1	TRUE	0	0.2	1		407	409	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034906-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	95	460	0				ENST00000310581	NM_198253.2	-/1132			0.607239326246059	7	FACETS	1	0.913	1	0.172	0.152	0.192	CLONAL	1	TRUE	1	0.607239326246059	7		460	765	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0034906-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	312	693	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.607239326246059	1	FACETS	0.997	0.946	1	0.997	0.946	1	CLONAL	1	TRUE	0	0.607239326246059	1		693	718	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013691	12013691	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0034906-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	183	354	0	ENST00000353533.5:c.634-1G>C		p.X212_splice	ENST00000353533	NM_003010.3	212			0.607239326246059	1	FACETS	0.927	0.864	0.99	0.927	0.864	0.99	CLONAL	1	TRUE	0	0.607239326246059	1		354	453	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170531	11170531	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034906-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	312	727	0	ENST00000358026.2:c.4834G>C	p.Glu1612Gln	p.E1612Q	ENST00000358026	NM_001128849.1	1612	Gag/Cag	34/36	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.607239326246059	2		727	977	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785992	135785992	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0034906-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	323	727	0	ENST00000298552.3:c.1229C>G	p.Ser410Ter	p.S410*	ENST00000298552	NM_001162426.1	410	tCa/tGa	12/23	0.607239326246059	1	FACETS	0.938	0.89	0.986	0.938	0.89	0.986	CLONAL	1	TRUE	0	0.607239326246059	1		727	790	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606412	93606412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773659676	NA	P-0034906-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	328	683	0	ENST00000375746.1:c.232G>A	p.Gly78Ser	p.G78S	ENST00000375746	NM_001174167.1	78	Ggt/Agt	2/14	0.607239326246059	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.607239326246059	1		683	713	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983140	201983141	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034906-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	258	712	0	ENST00000359651.3:c.991dup	p.Arg331ProfsTer140	p.R331Pfs*140	ENST00000359651		330	agc/agCc	7/8	1	2	FACETS	0.893	0.837	0.95	0.893	0.837	0.95	CLONAL	1	TRUE	1	0.607239326246059	2		712	952	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264275	30264275	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034906-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	22	54	0	ENST00000322652.5:c.10C>G	p.Gln4Glu	p.Q4E	ENST00000322652	NM_015355.2	4	Cag/Gag	1/16	0.599541643188842	3	FACETS	0.794	0.624	0.984	0.397	0.312	0.492	CLONAL	1	TRUE	1	0.607239326246059	3		54	119	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288499	15288499	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393495970	NA	P-0034906-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	93	103	0	ENST00000263388.2:c.4240G>A	p.Gly1414Ser	p.G1414S	ENST00000263388	NM_000435.2	1414	Ggc/Agc	24/33	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.607239326246059	2		103	268	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983111	201983111	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034906-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	344	714	0	ENST00000359651.3:c.960del	p.Asn321ThrfsTer4	p.N321Tfs*4	ENST00000359651		320	aaG/aa	7/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.607239326246059	2		714	1030	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366206	15366206	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034906-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	295	740	0	ENST00000263377.2:c.1949A>G	p.Asp650Gly	p.D650G	ENST00000263377	NM_058243.2	650	gAc/gGc	10/20	1	2	FACETS	0.904	0.851	0.958	0.904	0.851	0.958	CLONAL	1	TRUE	1	0.607239326246059	2		740	1075	SUCCESS
ATR	545	MSKCC	GRCh37	3	142180806	142180806	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034906-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	65	399	0	ENST00000350721.4:c.7168C>G	p.Leu2390Val	p.L2390V	ENST00000350721	NM_001184.3	2390	Ctg/Gtg	42/47	1	2	FACETS	0.281	0.243	0.322	0.281	0.243	0.322	SUBCLONAL	1	TRUE	1	0.607239326246059	2		399	762	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798190	32798190	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034906-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	238	645	1	ENST00000374899.4:c.1489G>T	p.Glu497Ter	p.E497*	ENST00000374899	NM_018833.2	497	Gag/Tag	9/12	0.607239326246059	1	FACETS	0.871	0.818	0.924	0.871	0.818	0.924	CLONAL	1	TRUE	0	0.607239326246059	1		646	627	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137540382	137540382	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	rs1468647789	NA	P-0034906-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	201	493	0	ENST00000367739.4:c.83C>G	p.Ser28Ter	p.S28*	ENST00000367739	NM_000416.2	28	tCa/tGa	1/7	0.599934726923462	1	FACETS	0.933	0.873	0.994	0.933	0.873	0.994	CLONAL	1	TRUE	0	0.607239326246059	1		493	494	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0034947-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	116	1087	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.18225166973471	3	FACETS	0.842	0.768	0.918	1	0.98	1	INDETERMINATE	3	TRUE	1	0.32	3		1087	333	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0034947-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	90	471	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	0.18225166973471	3	FACETS	1	0.919	1	1	0.919	1	INDETERMINATE	2	TRUE	1	0.32	3		472	317	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0034947-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	94	480	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.18225166973471	3	FACETS	0.841	0.76	0.926	1	0.975	1	INDETERMINATE	3	TRUE	1	0.32	3		480	270	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942739	44942739	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034947-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	216	313	0	ENST00000377967.4:c.3320del	p.Pro1107LeufsTer13	p.P1107Lfs*13	ENST00000377967	NM_021140.2	1107	Cct/ct	23/29	0.3	2	FACETS	1	0.985	1			1	CLONAL	5	TRUE	NA	0.32	2		313	260	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199896	108199896	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034947-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	108	367	0	ENST00000278616.4:c.7238A>G	p.Lys2413Arg	p.K2413R	ENST00000278616	NM_000051.3	2413	aAg/aGg	49/63	0.18225166973471	3	FACETS	1	0.933	1	1	0.986	1	INDETERMINATE	3	TRUE	1	0.32	3		367	255	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459148	120459148	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs758985315	NA	P-0034947-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	179	847	0	ENST00000256646.2:c.6197A>G	p.Asn2066Ser	p.N2066S	ENST00000256646	NM_024408.3	2066	aAt/aGt	34/34	1	2	FACETS	0.919	0.858	0.98	1	0.994	1	CLONAL	3	TRUE	1	0.32	2		847	406	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555974	226555974	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034947-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	113	643	1	ENST00000366794.5:c.2203C>A	p.Arg735Ser	p.R735S	ENST00000366794	NM_001618.3	735	Cgc/Agc	16/23	1	2	FACETS	1	0.918	1	1	0.989	1	CLONAL	2	TRUE	1	0.32	2		644	350	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201059	108201062	+	frameshift_variant	Frame_Shift_Del	DEL	AGTG	AGTG	-	novel	NA	P-0034947-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	104	541	0	ENST00000278616.4:c.7426_7429del	p.Ser2476GlufsTer27	p.S2476Efs*27	ENST00000278616	NM_000051.3	2476	AGTGga/ga	50/63	0.18225166973471	3	FACETS	0.879	0.799	0.961	1	0.98	1	INDETERMINATE	3	TRUE	1	0.32	3		541	286	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190031	123190032	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0034947-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	198	380	0	ENST00000218089.9:c.1251_1252del	p.Tyr418PhefsTer22	p.Y418Ffs*22	ENST00000218089	NM_001042749.1	417	gTT/g	14/35	0.3	2	FACETS	1	0.988	1			1	CLONAL	4	TRUE	NA	0.32	2		380	276	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023650	27023651	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034947-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	96	257	0	ENST00000324856.7:c.759dup	p.Ser254LeufsTer146	p.S254Lfs*146	ENST00000324856	NM_006015.4	252	-/C	1/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.32	2		257	422	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532463	63532463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121908567	NA	P-0034947-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	212	1021	1	ENST00000307078.5:c.2116G>A	p.Glu706Lys	p.E706K	ENST00000307078	NM_004655.3	706	Gag/Aag	8/11	1	2	FACETS	1	0.982	1	1	0.995	1	CLONAL	2	TRUE	1	0.32	2		1022	585	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931472	131931472	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28903092	NA	P-0034979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	125	484	0	ENST00000265335.6:c.2177G>A	p.Arg726His	p.R726H	ENST00000265335		726	cGt/cAt	13/25	1	2	FACETS	0.852	0.781	0.925	0.852	0.781	0.925	CLONAL	1	TRUE	1	0.845723877055781	2		484	347	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944546	38944547	+	splice_donor_variant	Splice_Site	DNP	AC	AC	TA	novel	NA	P-0034979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	63	444	0	ENST00000357387.3:c.4913+1_4913+2delinsTA		p.X1638_splice	ENST00000357387	NM_152756.3	1638			0.833506092026434	3	FACETS	0.726	0.633	0.825	0.363	0.316	0.413	SUBCLONAL	1	TRUE	1	0.845723877055781	3		444	292	SUCCESS
APC	324	MSKCC	GRCh37	5	112178000	112178000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768922431	NA	P-0034990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	192	346	0	ENST00000257430.4:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000257430	NM_000038.5	2237	Cga/Tga	16/16	0.767456613654822	1	FACETS	0.979	0.926	1	0.979	0.926	1	CLONAL	1	TRUE	0	0.767456613654822	1		346	315	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211138	36211138	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1698	137	873	0	ENST00000222270.7:c.889C>T	p.Arg297Ter	p.R297*	ENST00000222270	NM_014727.1	297	Cga/Tga	3/37	0.73858386762423	3	FACETS	0.269	0.243	0.297	0.135	0.121	0.149	SUBCLONAL	1	TRUE	1	0.767456613654822	3		873	1835	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117755	108117755	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	98	308	0	ENST00000278616.4:c.966G>C	p.Glu322Asp	p.E322D	ENST00000278616	NM_000051.3	322	gaG/gaC	8/63	1	2	FACETS	0.457	0.408	0.508	0.457	0.408	0.508	SUBCLONAL	1	TRUE	1	0.767456613654822	2		308	559	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265185	46265185	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	97	305	0	ENST00000371998.3:c.2055G>T	p.Leu685Phe	p.L685F	ENST00000371998		685	ttG/ttT	12/23	1	2	FACETS	0.528	0.472	0.586	0.528	0.472	0.586	SUBCLONAL	1	TRUE	1	0.767456613654822	2		305	479	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779603	3779604	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0035153-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	529	1386	0	ENST00000262367.5:c.5444dup	p.Cys1816LeufsTer150	p.C1816Lfs*150	ENST00000262367	NM_004380.2	1815	ggc/ggGc	31/31	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		1386	1359	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0035998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	136	451	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.232501531357872	3	FACETS	0.934	0.853	1	0.934	0.853	1	CLONAL	2	TRUE	1	0.290049524920549	3		452	575	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0035998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	58	518	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.28295501797594	1	FACETS	0.834	0.719	0.959	0.834	0.719	0.959	CLONAL	1	TRUE	0	0.290049524920549	1		518	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0035998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	206	679	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	NA	2	FACETS	0.998	0.929	1			1	INDETERMINATE	2	TRUE	NA	0.290049524920549	2		679	712	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933754	36933754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1164628469	NA	P-0035998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	133	979	0	ENST00000361632.4:c.1645C>T	p.Pro549Ser	p.P549S	ENST00000361632		549	Cct/Tct	12/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.290049524920549	2		979	839	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180641	56180641	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	61	406	0	ENST00000399503.3:c.3970G>A	p.Glu1324Lys	p.E1324K	ENST00000399503	NM_005921.1	1324	Gaa/Aaa	16/20	0.232501531357872	3	FACETS	0.983	0.849	1	0.491	0.424	0.564	CLONAL	1	TRUE	1	0.290049524920549	3		406	490	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295192	1295193	+	upstream_gene_variant	5'Flank	INS	-	-	GCGGAAAGGAAGGGGAGGGGCTA	novel	NA	P-0035998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	49	313	0				ENST00000310581	NM_198253.2	-/1132			0.232501531357872	3	FACETS	1	0.868	1	0.512	0.435	0.596	CLONAL	1	TRUE	1	0.290049524920549	3		313	378	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155250	106155250	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	68	427	0	ENST00000380013.4:c.151G>C	p.Asp51His	p.D51H	ENST00000380013	NM_001127208.2	51	Gac/Cac	3/11	0.232501531357872	3	FACETS	1	0.963	1	0.647	0.565	0.735	CLONAL	1	TRUE	1	0.290049524920549	3		427	415	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681655	30681655	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	68	610	0	ENST00000376406.3:c.442G>C	p.Glu148Gln	p.E148Q	ENST00000376406	NM_014641.2	148	Gaa/Caa	3/15	NA	2	FACETS	0.659	0.572	0.752			1	INDETERMINATE	1	TRUE	NA	0.290049524920549	2		610	712	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072553	5072553	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	56	466	0	ENST00000381652.3:c.1703G>C	p.Gly568Ala	p.G568A	ENST00000381652	NM_004972.3	568	gGa/gCa	13/25	0.28295501797594	1	FACETS	0.749	0.643	0.864	0.749	0.643	0.864	SUBCLONAL	1	TRUE	0	0.290049524920549	1		466	441	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072579	5072579	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	55	450	0	ENST00000381652.3:c.1729G>C	p.Glu577Gln	p.E577Q	ENST00000381652	NM_004972.3	577	Gaa/Caa	13/25	0.28295501797594	1	FACETS	0.734	0.629	0.848	0.734	0.629	0.848	SUBCLONAL	1	TRUE	0	0.290049524920549	1		450	442	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032756	30032758	+	frameshift_variant	Frame_Shift_Del	DEL	AGG	AGG	CC	novel	NA	P-0035998-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	53	390	0	ENST00000338641.4:c.131_133delinsCC	p.Lys44ThrfsTer79	p.K44Tfs*79	ENST00000338641	NM_000268.3	44	aAGGac/aCCac	2/16	0.28295501797594	1	FACETS	0.84	0.719	0.971	0.84	0.719	0.971	CLONAL	1	TRUE	0	0.290049524920549	1		390	372	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0036000-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	48	537	0				ENST00000310581	NM_198253.2	-/1132			0.454873965339252	3	FACETS	1	0.871	1	0.512	0.436	0.594	CLONAL	1	TRUE	1	0.454873965339252	3		537	253	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036000-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	326	1118	2	ENST00000269305.4:c.383del	p.Pro128LeufsTer42	p.P128Lfs*42	ENST00000269305	NM_001126112.2	128	cCt/ct	5/11	0.454873965339252	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.454873965339252	2		1120	713	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207468	29207468	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036000-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	103	706	0	ENST00000240100.2:c.328G>C	p.Glu110Gln	p.E110Q	ENST00000240100	NM_001394.6	110	Gag/Cag	1/4	0.454873965339252	3	FACETS	1	0.96	1	0.567	0.51	0.628	CLONAL	1	TRUE	1	0.454873965339252	3		706	490	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107018	11107018	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036000-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	231	855	0	ENST00000358026.2:c.1723C>T	p.Gln575Ter	p.Q575*	ENST00000358026	NM_001128849.1	575	Cag/Tag	10/36	0.454873965339252	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.454873965339252	2		855	466	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600006	10600006	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036000-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	348	1065	0	ENST00000171111.5:c.1570G>T	p.Gly524Cys	p.G524C	ENST00000171111	NM_203500.1	524	Ggc/Tgc	5/6	0.454873965339252	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.454873965339252	2		1065	734	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221327	1221327	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036000-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	249	931	0	ENST00000326873.7:c.850G>C	p.Asp284His	p.D284H	ENST00000326873	NM_000455.4	284	Gac/Cac	6/10	0.454873965339252	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.454873965339252	2		931	539	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222152	2222152	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036000-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	311	1084	0	ENST00000398665.3:c.2984G>T	p.Arg995Leu	p.R995L	ENST00000398665	NM_032482.2	995	cGg/cTg	24/28	0.454873965339252	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.454873965339252	2		1084	658	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950291	17950291	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1346219310	NA	P-0036000-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	309	969	1	ENST00000458235.1:c.1436C>A	p.Pro479His	p.P479H	ENST00000458235	NM_000215.3	479	cCc/cAc	10/24	0.454873965339252	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.454873965339252	2		970	630	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952244	17952244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036000-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	318	1026	1	ENST00000458235.1:c.1096C>T	p.Pro366Ser	p.P366S	ENST00000458235	NM_000215.3	366	Ccg/Tcg	8/24	0.454873965339252	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.454873965339252	2		1027	611	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211130	36211130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036000-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	365	1298	0	ENST00000222270.7:c.881G>T	p.Gly294Val	p.G294V	ENST00000222270	NM_014727.1	294	gGc/gTc	3/37	0.428759513660656	4	FACETS	0.955	0.905	1	0.955	0.905	1	CLONAL	2	TRUE	2	0.454873965339252	4		1298	1223	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795499	42795499	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036000-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	269	1046	0	ENST00000575354.2:c.2579C>G	p.Thr860Ser	p.T860S	ENST00000575354	NM_015125.3	860	aCc/aGc	10/20	0.428759513660656	4	FACETS	0.972	0.914	1	0.972	0.914	1	CLONAL	2	TRUE	2	0.454873965339252	4		1046	885	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81399266	81399266	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036000-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	257	914	0	ENST00000222390.5:c.22C>A	p.Pro8Thr	p.P8T	ENST00000222390	NM_000601.4	8	Cca/Aca	1/18	0.428759513660656	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.454873965339252	4		914	750	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038524	47038524	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036000-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	128	938	0	ENST00000377604.3:c.686G>T	p.Arg229Leu	p.R229L	ENST00000377604	NM_001204468.1	229	cGc/cTc	8/24	0.177567900635072	3	FACETS	0.919	0.833	1	0.306	0.277	0.336	INDETERMINATE	1	TRUE	0	0.454873965339252	3		938	752	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9928033	9928033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036000-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	65	418	0	ENST00000330684.3:c.1706C>T	p.Ser569Phe	p.S569F	ENST00000330684	NM_001134407.1	569	tCt/tTt	8/13	0.454873965339252	3	FACETS	0.771	0.67	0.88	0.385	0.335	0.44	SUBCLONAL	1	TRUE	1	0.454873965339252	3		418	455	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214798	36214798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036000-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	135	983	0	ENST00000222270.7:c.3224C>T	p.Ser1075Leu	p.S1075L	ENST00000222270	NM_014727.1	1075	tCa/tTa	8/37	0.428759513660656	4	FACETS	1	0.97	1	0.576	0.524	0.63	CLONAL	1	TRUE	2	0.454873965339252	4		983	750	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461492	138461492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758175087	NA	P-0036000-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	148	688	1	ENST00000289153.2:c.529C>T	p.Pro177Ser	p.P177S	ENST00000289153	NM_006219.2	177	Cca/Tca	3/22	0.454873965339252	3	FACETS	1	0.974	1	0.578	0.529	0.629	CLONAL	1	TRUE	1	0.454873965339252	3		689	691	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970818	79970818	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs766534747	NA	P-0036000-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	88	448	0	ENST00000265081.6:c.1044C>G	p.Ile348Met	p.I348M	ENST00000265081	NM_002439.4	348	atC/atG	7/24	0.159582445835044	3	FACETS	1	0.976	1	0.68	0.608	0.756	INDETERMINATE	1	TRUE	1	0.454873965339252	3		448	349	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722069	176722069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036000-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	92	597	0	ENST00000439151.2:c.7700C>T	p.Pro2567Leu	p.P2567L	ENST00000439151	NM_022455.4	2567	cCa/cTa	23/23	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.454873965339252	2		597	372	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030523	47030523	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036000-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	123	1072	0	ENST00000377604.3:c.298G>T	p.Gly100Cys	p.G100C	ENST00000377604	NM_001204468.1	100	Ggc/Tgc	4/24	0.177567900635072	3	FACETS	0.934	0.845	1	0.311	0.281	0.343	INDETERMINATE	1	TRUE	0	0.454873965339252	3		1072	711	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907636	76907636	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036000-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	126	756	0	ENST00000373344.5:c.4525G>C	p.Glu1509Gln	p.E1509Q	ENST00000373344	NM_000489.3	1509	Gag/Cag	15/35	0.177567900635072	3	FACETS	0.981	0.89	1	0.327	0.296	0.359	INDETERMINATE	1	TRUE	0	0.454873965339252	3		756	693	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436859	29436859	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs863225283	NA	P-0121549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	37	524	0	ENST00000389048.3:c.3734T>G	p.Phe1245Cys	p.F1245C	ENST00000389048	NM_004304.4	1245	tTc/tGc	24/29	1	2	FACETS	0.137	0.113	0.165	0.137	0.113	0.165	SUBCLONAL	1	NA	1	0.812229580472696	2		524	663	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933151	39933151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778096	NA	P-0036482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	164	962	2	ENST00000378444.4:c.1448C>T	p.Pro483Leu	p.P483L	ENST00000378444	NM_001123385.1	483	cCg/cTg	4/15	1	2	FACETS	0.951	0.876	1	0.951	0.876	1	CLONAL	1	TRUE	1	0.518016550992682	2		964	666	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440372	52440372	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	146	823	0	ENST00000460680.1:c.680G>C	p.Arg227Pro	p.R227P	ENST00000460680	NM_004656.3	227	cGc/cCc	9/17	1	2	FACETS	0.886	0.812	0.964	0.886	0.812	0.964	CLONAL	1	TRUE	1	0.518016550992682	2		823	636	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949152	44949153	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTG	novel	NA	P-0036482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	145	577	0	ENST00000377967.4:c.3714_3716dup	p.Ala1238_Trp1239insCys	p.A1238_W1239insC	ENST00000377967	NM_021140.2	1238	gct/gcTTGt	25/29	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.518016550992682	2		577	532	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274592	198274592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	166	738	0	ENST00000335508.6:c.806G>T	p.Gly269Val	p.G269V	ENST00000335508	NM_012433.2	269	gGa/gTa	7/25	1	2	FACETS	0.876	0.806	0.948	0.876	0.806	0.948	CLONAL	1	TRUE	1	0.518016550992682	2		738	732	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436691	52436691	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1553644634	NA	P-0036482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	112	867	1	ENST00000460680.1:c.1984-1G>A		p.X662_splice	ENST00000460680	NM_004656.3	662			1	2	FACETS	0.819	0.74	0.902	0.819	0.74	0.902	CLONAL	1	TRUE	1	0.518016550992682	2		868	528	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436810	52436810	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	151	862	0	ENST00000460680.1:c.1968G>C	p.Lys656Asn	p.K656N	ENST00000460680	NM_004656.3	656	aaG/aaC	15/17	1	2	FACETS	0.931	0.855	1	0.931	0.855	1	CLONAL	1	TRUE	1	0.518016550992682	2		862	626	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437169	52437169	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	135	780	0	ENST00000460680.1:c.1875G>C	p.Glu625Asp	p.E625D	ENST00000460680	NM_004656.3	625	gaG/gaC	14/17	1	2	FACETS	0.958	0.875	1	0.958	0.875	1	CLONAL	1	TRUE	1	0.518016550992682	2		780	544	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437246	52437246	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036482-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	159	971	0	ENST00000460680.1:c.1798G>C	p.Glu600Gln	p.E600Q	ENST00000460680	NM_004656.3	600	Gag/Cag	14/17	1	2	FACETS	0.925	0.85	1	0.925	0.85	1	CLONAL	1	TRUE	1	0.518016550992682	2		971	664	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0036642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	385	451	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.330407056570739	4	FACETS	0.916	0.879	0.952	1	0.996	1	CLONAL	5	TRUE	1	0.330407056570739	4		452	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782177	NA	P-0037413-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	153	526	0	ENST00000269305.4:c.644G>A	p.Ser215Asn	p.S215N	ENST00000269305	NM_001126112.2	215	aGt/aAt	6/11	0.188592398027058	2	FACETS	1	0.985	1	0.67	0.614	0.729	INDETERMINATE	1	TRUE	0	0.319660144230597	2		526	714	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0037413-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1383	237	458	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.319660144230597	11	FACETS	1	0.977	1	0.279	0.259	0.3	CLONAL	2	TRUE	3	0.319660144230597	11		458	1620	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959897	38959898	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0037413-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	26	217	0	ENST00000357387.3:c.2034dup	p.Cys679MetfsTer9	p.C679Mfs*9	ENST00000357387	NM_152756.3	678	-/A	21/38	0.227986840003094	4	FACETS	0.686	0.544	0.848	0.343	0.272	0.424	SUBCLONAL	1	TRUE	2	0.319660144230597	4		217	313	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020294	123020301	+	frameshift_variant	Frame_Shift_Del	DEL	CCATGGCA	CCATGGCA	-	novel	NA	P-0037413-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	114	461	0	ENST00000355640.3:c.782_789del	p.Ser261Ter	p.S261*	ENST00000355640		261	tCCATGGCA/t	2/7	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.319660144230597	2		461	615	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406327	70406327	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037413-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	49	479	0	ENST00000373644.4:c.3841G>C	p.Ala1281Pro	p.A1281P	ENST00000373644	NM_030625.2	1281	Gct/Cct	4/12	0.327826615787612	3	FACETS	0.492	0.416	0.577	0.246	0.208	0.289	SUBCLONAL	1	TRUE	1	0.319660144230597	3		479	722	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037465-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	263	460	0				ENST00000310581	NM_198253.2	-/1132			0.408496498342345	5	FACETS	1	0.988	1	0.798	0.75	0.848	CLONAL	2	TRUE	2	0.408496498342345	5		460	867	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0037465-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	327	681	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.311397298236954	2	FACETS	1	0.994	1	0.742	0.701	0.783	CLONAL	1	TRUE	0	0.408496498342345	2		681	1079	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477837	140477851	+	inframe_deletion	In_Frame_Del	DEL	TAGGTGCTGTCACAT	TAGGTGCTGTCACAT	-	novel	NA	P-0037465-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	337	693	0	ENST00000288602.6:c.1457_1471del	p.Asn486_Pro490del	p.N486_P490del	ENST00000288602	NM_004333.4	486	aATGTGACAGCACCTAca/aca	12/18	0.408496498342345	3	FACETS	0.848	0.802	0.895	0.848	0.802	0.895	CLONAL	2	TRUE	1	0.408496498342345	3		693	1171	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256243	16256243	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037465-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	140	666	0	ENST00000375759.3:c.3508C>G	p.Arg1170Gly	p.R1170G	ENST00000375759	NM_015001.2	1170	Cga/Gga	11/15	1	2	FACETS	0.773	0.703	0.846	0.773	0.703	0.846	SUBCLONAL	1	TRUE	1	0.408496498342345	2		666	887	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982329	201982330	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0037465-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	221	1080	0	ENST00000359651.3:c.710dup	p.Asp239GlyfsTer62	p.D239Gfs*62	ENST00000359651		236	-/A	6/8	1	2	FACETS	0.778	0.722	0.836	0.778	0.722	0.836	SUBCLONAL	1	TRUE	1	0.408496498342345	2		1080	1391	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405688	139405688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377353441	NA	P-0037465-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1549	378	1234	1	ENST00000277541.6:c.2503C>T	p.Pro835Ser	p.P835S	ENST00000277541	NM_017617.3	835	Ccc/Tcc	16/34	0.393763970270411	3	FACETS	1	0.989	1	0.386	0.364	0.407	CLONAL	1	TRUE	0	0.408496498342345	3		1235	1927	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436315	110436315	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0121424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	121	298	5	ENST00000375856.3:c.2086G>A	p.Ala696Thr	p.A696T	ENST00000375856	NM_003749.2	696	Gcc/Acc	1/2	0.459531994342458	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	NA	2	0.459531994342458	4		303	321	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0037761-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	263	449	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.348433653369872	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.350434006257775	4		449	886	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0037761-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	107	446	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.350434006257775	1	FACETS	0.936	0.843	1	0.936	0.843	1	CLONAL	1	TRUE	0	0.350434006257775	1		446	538	SUCCESS
APC	324	MSKCC	GRCh37	5	112173572	112173572	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037761-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	73	532	0	ENST00000257430.4:c.2281G>T	p.Glu761Ter	p.E761*	ENST00000257430	NM_000038.5	761	Gaa/Taa	16/16	0.350434006257775	2	FACETS	0.797	0.698	0.903	0.398	0.349	0.452	CLONAL	1	TRUE	0	0.350434006257775	2		532	523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0037761-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	354	983	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	NA	2	FACETS	0.928	0.88	0.976			1	INDETERMINATE	2	TRUE	NA	0.350434006257775	2		983	1089	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986533	36986534	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGAG	novel	NA	P-0037761-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	251	848	0	ENST00000354822.5:c.1152_1155dup	p.Asp386LeufsTer54	p.D386Lfs*54	ENST00000354822	NM_001079668.2	385	-/CTCG	3/3	0.34914924175026	2	FACETS	0.783	0.733	0.833	0.783	0.733	0.833	SUBCLONAL	2	TRUE	0	0.350434006257775	2		848	915	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	25	460	0				ENST00000310581	NM_198253.2	-/1132			0.442848985745273	1	FACETS	0.916	0.738	1	0.916	0.738	1	CLONAL	1	FALSE	0	0.442848985745273	1		460	96	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0038879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	127	487	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	0.240892327970581	3	FACETS	0.83	0.758	0.904	0.83	0.758	0.904	INDETERMINATE	2	FALSE	1	0.442848985745273	3		487	422	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050363	176050363	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1301409514	NA	P-0038879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	59	660	0	ENST00000367669.3:c.1202G>A	p.Arg401Gln	p.R401Q	ENST00000367669	NM_022457.5	401	cGa/cAa	11/20	0.167583694962327	5	FACETS	1	0.911	1	0.358	0.309	0.411	INDETERMINATE	1	FALSE	2	0.442848985745273	5		660	413	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0038879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	162	1118	1	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.240892327970581	3	FACETS	0.823	0.76	0.888	0.823	0.76	0.888	INDETERMINATE	2	FALSE	1	0.442848985745273	3		1119	543	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692794	89692794	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121909238	NA	P-0038879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	100	456	0	ENST00000371953.3:c.278A>G	p.His93Arg	p.H93R	ENST00000371953	NM_000314.4	93	cAt/cGt	5/9	0.442848985745273	1	FACETS	0.768	0.7	0.836	1	0.986	1	SUBCLONAL	2	FALSE	0	0.442848985745273	1		456	229	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143293	30143293	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs748978993	NA	P-0038879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	113	689	0	ENST00000389048.3:c.233C>G	p.Ser78Trp	p.S78W	ENST00000389048	NM_004304.4	78	tCg/tGg	1/29	0.215466887992068	4	FACETS	1	0.919	1	1	0.919	1	INDETERMINATE	2	FALSE	2	0.442848985745273	4		689	364	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158629	26158629	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	61	327	2	ENST00000289316.2:c.232G>A	p.Ala78Thr	p.A78T	ENST00000289316	NM_138720.2	78	Gct/Act	1/2	0.442848985745273	6	FACETS	0.86	0.748	0.98	0.43	0.374	0.49	CLONAL	2	FALSE	2	0.442848985745273	6		329	302	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309890	65309890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	35	616	0	ENST00000342505.4:c.2260G>A	p.Glu754Lys	p.E754K	ENST00000342505	NM_002227.2	754	Gaa/Aaa	17/25	0.413655693751317	4	FACETS	0.755	0.621	0.905	0.378	0.31	0.453	CLONAL	1	FALSE	2	0.442848985745273	4		616	302	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829847	72829847	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750842718	NA	P-0038879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	66	958	1	ENST00000268489.5:c.6734C>T	p.Ser2245Leu	p.S2245L	ENST00000268489	NM_006885.3	2245	tCa/tTa	9/10	NA	2	FACETS	0.828	0.723	0.941			1	INDETERMINATE	1	FALSE	NA	0.442848985745273	2		959	360	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107122	27107122	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	160	726	0	ENST00000324856.7:c.6733G>T	p.Asp2245Tyr	p.D2245Y	ENST00000324856	NM_006015.4	2245	Gac/Tac	20/20	0.442848985745273	3	FACETS	0.972	0.9	1			1	CLONAL	2	FALSE	NA	0.442848985745273	3		726	454	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447000	49447000	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	123	681	0	ENST00000301067.7:c.944G>C	p.Trp315Ser	p.W315S	ENST00000301067	NM_003482.3	315	tGg/tCg	7/54	0.167583694962327	5	FACETS	0.854	0.781	0.929	0.854	0.781	0.929	INDETERMINATE	3	FALSE	2	0.442848985745273	5		681	361	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032558	12032558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1355543573	NA	P-0038879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	83	522	0	ENST00000353533.5:c.994G>A	p.Glu332Lys	p.E332K	ENST00000353533	NM_003010.3	332	Gag/Aag	9/11	0.240892327970581	3	FACETS	1	0.979	1	0.736	0.656	0.82	INDETERMINATE	1	FALSE	1	0.442848985745273	3		522	311	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023595	31023595	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	43	754	0	ENST00000375687.4:c.3080C>G	p.Ser1027Cys	p.S1027C	ENST00000375687	NM_015338.5	1027	tCt/tGt	13/13	0.401923783055651	3	FACETS	0.487	0.407	0.575	0.244	0.203	0.288	SUBCLONAL	1	FALSE	1	0.442848985745273	3		754	487	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024183	31024183	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	53	826	0	ENST00000375687.4:c.3668C>G	p.Ser1223Cys	p.S1223C	ENST00000375687	NM_015338.5	1223	tCt/tGt	13/13	0.401923783055651	3	FACETS	0.637	0.544	0.739	0.318	0.272	0.37	SUBCLONAL	1	FALSE	1	0.442848985745273	3		826	459	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547861	41547861	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	104	577	0	ENST00000263253.7:c.2842G>C	p.Glu948Gln	p.E948Q	ENST00000263253	NM_001429.3	948	Gaa/Caa	15/31	0.442848985745273	1	FACETS	0.781	0.714	0.849	1	0.986	1	SUBCLONAL	2	FALSE	0	0.442848985745273	1		577	234	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934729	49934729	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	57	860	0	ENST00000296474.3:c.2167G>C	p.Glu723Gln	p.E723Q	ENST00000296474	NM_002447.2	723	Gag/Cag	7/20	0.240892327970581	3	FACETS	0.947	0.817	1	0.474	0.408	0.544	INDETERMINATE	1	FALSE	1	0.442848985745273	3		860	332	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259063	89259063	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	59	380	0	ENST00000336596.2:c.207G>T	p.Gln69His	p.Q69H	ENST00000336596	NM_005233.5	69	caG/caT	3/17	0.363141880222209	4	FACETS	0.801	0.697	0.911	0.801	0.697	0.911	CLONAL	2	FALSE	2	0.442848985745273	4		380	240	SUCCESS
ATR	545	MSKCC	GRCh37	3	142185372	142185372	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	22	415	0	ENST00000350721.4:c.6691G>C	p.Asp2231His	p.D2231H	ENST00000350721	NM_001184.3	2231	Gat/Cat	40/47	0.363141880222209	4	FACETS	0.573	0.445	0.721	0.287	0.222	0.361	SUBCLONAL	1	FALSE	2	0.442848985745273	4		415	250	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998990	169998990	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	69	482	0	ENST00000295797.4:c.919G>C	p.Glu307Gln	p.E307Q	ENST00000295797	NM_002740.5	307	Gag/Cag	10/18	0.363141880222209	4	FACETS	1	0.957	1	0.609	0.533	0.69	CLONAL	1	FALSE	2	0.442848985745273	4		482	369	SUCCESS
APC	324	MSKCC	GRCh37	5	112178697	112178697	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1561615265	NA	P-0038879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	51	495	0	ENST00000257430.4:c.7406C>G	p.Ser2469Cys	p.S2469C	ENST00000257430	NM_000038.5	2469	tCt/tGt	16/16	0.413655693751317	4	FACETS	0.817	0.696	0.948	0.408	0.348	0.474	CLONAL	1	FALSE	2	0.442848985745273	4		495	407	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652094	36652101	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGCCCA	CCTGCCCA	-	novel	NA	P-0038879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	69	1105	0	ENST00000244741.5:c.216_223del	p.Leu73AlafsTer13	p.L73Afs*13	ENST00000244741	NM_000389.4	72	ggCCTGCCCAag/ggag	2/3	0.306035345645944	3	FACETS	0.877	0.767	0.995	0.439	0.383	0.498	CLONAL	1	FALSE	1	0.442848985745273	3		1105	434	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415150	116415150	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	138	711	0	ENST00000397752.3:c.3244G>A	p.Glu1082Lys	p.E1082K	ENST00000397752	NM_000245.2	1082	Gaa/Aaa	15/21	0.363141880222209	4	FACETS	0.949	0.869	1	0.949	0.869	1	CLONAL	2	FALSE	2	0.442848985745273	4		711	474	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87322782	87322782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201256653	NA	P-0038879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	133	518	0	ENST00000277120.3:c.383C>T	p.Thr128Met	p.T128M	ENST00000277120		128	aCg/aTg	5/19	0.240892327970581	3	FACETS	0.841	0.77	0.915	0.841	0.77	0.915	INDETERMINATE	2	FALSE	1	0.442848985745273	3		518	436	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0121507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	264	536	1	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	0.986	0.931	1	0.986	0.931	1	CLONAL	1	NA	1	0.838415222669628	2		537	639	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004577	16004577	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs111428551	NA	P-0121507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	157	330	1	ENST00000268712.3:c.2677C>T	p.Pro893Ser	p.P893S	ENST00000268712	NM_006311.3	893	Cca/Tca	20/46	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	NA	1	0.838415222669628	2		331	349	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0121507-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	228	536	1	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	NA	1	0.91364908550556	2		537	495	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004577	16004577	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs111428551	NA	P-0121507-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	211	330	1	ENST00000268712.3:c.2677C>T	p.Pro893Ser	p.P893S	ENST00000268712	NM_006311.3	893	Cca/Tca	20/46	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	NA	1	0.91364908550556	2		331	435	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608577	189608577	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0121507-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	31	388	0	ENST00000264731.3:c.1653-1G>T		p.X551_splice	ENST00000264731	NM_003722.4	551			1	2	FACETS	0.111	0.089	0.136	0.111	0.089	0.136	SUBCLONAL	1	NA	1	0.91364908550556	2		388	609	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0039586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	91	858	2	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	0.201493759064039	1	FACETS	0.873	0.775	0.979	0.873	0.775	0.979	CLONAL	1	TRUE	0	0.223548515627798	1		860	828	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138376590	138376590	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	89	541	0	ENST00000289153.2:c.2884T>A	p.Tyr962Asn	p.Y962N	ENST00000289153	NM_006219.2	962	Tat/Aat	20/22	0.223555119832701	3	FACETS	1	0.974	1	0.675	0.599	0.756	CLONAL	1	TRUE	1	0.223548515627798	3		541	656	SUCCESS
APC	324	MSKCC	GRCh37	5	112178864	112178864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774952444	NA	P-0039586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	23	384	0	ENST00000257430.4:c.7573C>T	p.Arg2525Cys	p.R2525C	ENST00000257430	NM_000038.5	2525	Cgc/Tgc	16/16	0.223555119832701	3	FACETS	0.541	0.421	0.68	0.27	0.21	0.34	SUBCLONAL	1	TRUE	1	0.223548515627798	3		384	423	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281645	49281645	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	144	833	0	ENST00000282018.3:c.692T>C	p.Val231Ala	p.V231A	ENST00000282018	NM_020377.2	231	gTg/gCg	1/1	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.223548515627798	2		833	998	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639605	3639605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757202686	NA	P-0039586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	61	1047	3	ENST00000294008.3:c.4034G>A	p.Arg1345His	p.R1345H	ENST00000294008	NM_032444.2	1345	cGt/cAt	12/15	0.201493759064039	1	FACETS	0.462	0.397	0.533	0.462	0.397	0.533	SUBCLONAL	1	TRUE	0	0.223548515627798	1		1050	1049	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0039653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	62	322	0	ENST00000349496.5:c.101G>A	p.Gly34Glu	p.G34E	ENST00000349496	NM_001904.3	34	gGa/gAa	3/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		322	491	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023168	27023184	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGGCCCGGCGCGGA	GGCGGGCCCGGCGCGGA	-	novel	NA	P-0039653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	59	77	0	ENST00000324856.7:c.275_291del	p.Gly92AlafsTer13	p.G92Afs*13	ENST00000324856	NM_006015.4	92	GGCGGGCCCGGCGCGGAg/g	1/20	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		77	137	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0039872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	32	825	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.101	0.081	0.124	0.101	0.081	0.124	SUBCLONAL	1	TRUE	1	0.53	2		826	1196	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0039872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	324	656	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.999	0.943	1	0.999	0.943	1	CLONAL	1	TRUE	1	0.53	2		657	1224	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0039872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	229	349	9	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	0.809	0.761	0.857	1	0.994	1	CLONAL	2	TRUE	1	0.53	2		358	534	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469548	25469548	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	270	906	0	ENST00000264709.3:c.1220T>G	p.Ile407Ser	p.I407S	ENST00000264709	NM_175629.2	407	aTt/aGt	10/23	1	2	FACETS	0.721	0.675	0.769	0.721	0.675	0.769	SUBCLONAL	1	TRUE	1	0.53	2		906	1413	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872828	136872828	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	36	467	0	ENST00000241393.3:c.670T>C	p.Ser224Pro	p.S224P	ENST00000241393	NM_003467.2	224	Tcc/Ccc	2/2	1	2	FACETS	0.221	0.181	0.266	0.221	0.181	0.266	SUBCLONAL	1	TRUE	1	0.53	2		467	616	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163436	47163436	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	120	376	0	ENST00000409792.3:c.2690del	p.Leu897ProfsTer2	p.L897Pfs*2	ENST00000409792	NM_014159.6	897	cTc/cc	3/21	1	2	FACETS	0.922	0.837	1	0.922	0.837	1	CLONAL	1	TRUE	1	0.53	2		376	491	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553090	106553090	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	58	540	0	ENST00000369096.4:c.1055C>T	p.Pro352Leu	p.P352L	ENST00000369096	NM_001198.3	352	cCt/cTt	5/7	1	2	FACETS	0.507	0.434	0.587	0.507	0.434	0.587	SUBCLONAL	1	TRUE	1	0.246851536185302	2		540	927	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658506	3658506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141639275	NA	P-0040092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	59	587	1	ENST00000294008.3:c.460C>T	p.Arg154Trp	p.R154W	ENST00000294008	NM_032444.2	154	Cgg/Tgg	2/15	1	2	FACETS	0.456	0.39	0.527	0.456	0.39	0.527	SUBCLONAL	1	TRUE	1	0.246851536185302	2		588	1049	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145588	24145588	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	112	629	1	ENST00000263121.7:c.607del	p.Ala203ProfsTer6	p.A203Pfs*6	ENST00000263121	NM_003073.3	203	Gcc/cc	5/9	1	2	FACETS	0.959	0.862	1	0.959	0.862	1	CLONAL	1	TRUE	1	0.246851536185302	2		630	946	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0041584-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	624	1142	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.733336991470571	4	FACETS	1	0.984	1			1	CLONAL	2	TRUE	NA	0.736618414340288	4		1142	1423	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636999	158636999	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772534199	NA	P-0041584-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	475	817	3	ENST00000263640.3:c.181G>A	p.Asp61Asn	p.D61N	ENST00000263640	NM_001105.4	61	Gat/Aat	4/11	0.736618414340288	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.736618414340288	4		820	1064	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456254	32456254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756414084	NA	P-0041584-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	525	1254	5	ENST00000332351.3:c.638G>A	p.Arg213His	p.R213H	ENST00000332351	NM_024426.4	213	cGc/cAc	1/10	0.736618414340288	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.736618414340288	4		1259	1199	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42843797	42843798	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0041584-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	437	881	0	ENST00000398585.3:c.1121_1122del	p.Tyr374Ter	p.Y374*	ENST00000398585	NM_001135099.1	374	tAT/t	10/14	0.736618414340288	4	FACETS	1	0.971	1			1	CLONAL	2	TRUE	NA	0.736618414340288	4		881	1012	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021727	71021727	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041584-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	323	599	0	ENST00000318789.4:c.1631G>T	p.Arg544Leu	p.R544L	ENST00000318789	NM_032682.5	544	cGa/cTa	18/21	0.736618414340288	4	FACETS	0.997	0.947	1	0.997	0.947	1	CLONAL	2	TRUE	2	0.736618414340288	4		599	764	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522551	176522551	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774571806	NA	P-0042571-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	81	943	0	ENST00000292408.4:c.1648G>A	p.Val550Met	p.V550M	ENST00000292408	NM_213647.1	550	Gtg/Atg	13/18	0.180850905421901	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		943	761	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419025	419025	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042571-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	45	633	1	ENST00000399788.2:c.3322G>T	p.Glu1108Ter	p.E1108*	ENST00000399788	NM_001042603.1	1108	Gag/Tag	22/28	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		634	780	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41560070	41560071	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGAGTG	novel	NA	P-0042571-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	31	319	0	ENST00000263253.7:c.3744_3750dup	p.Gly1251ArgfsTer15	p.G1251Rfs*15	ENST00000263253	NM_001429.3	1248	aca/aCAGAGTGca	22/31	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		319	403	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0042657-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	229	542	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.681301702309031	3	FACETS	0.802	0.754	0.851	0.802	0.754	0.851	CLONAL	2	TRUE	1	0.681301702309031	3		542	562	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472554	88472554	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042657-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	257	587	0	ENST00000360948.2:c.2001G>T	p.Met667Ile	p.M667I	ENST00000360948	NM_001012338.2	667	atG/atT	16/19	0.569486089281415	2	FACETS	0.865	0.824	0.906	0.865	0.824	0.906	CLONAL	2	TRUE	0	0.681301702309031	2		587	436	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220640	1220640	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690940	NA	P-0042657-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	453	733	2	ENST00000326873.7:c.658C>T	p.Gln220Ter	p.Q220*	ENST00000326873	NM_000455.4	220	Cag/Tag	5/10	0.442676100822702	3	FACETS	0.902	0.873	0.93			1	CLONAL	3	TRUE	NA	0.681301702309031	3		735	659	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11269480	11269480	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042657-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	93	419	0	ENST00000361445.4:c.3690G>T	p.Leu1230Phe	p.L1230F	ENST00000361445	NM_004958.3	1230	ttG/ttT	25/58	NA	2	FACETS	0.892	0.803	0.985			1	INDETERMINATE	1	TRUE	NA	0.681301702309031	2		419	306	SUCCESS
ATM	472	MSKCC	GRCh37	11	108138042	108138042	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042657-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	307	336	0	ENST00000278616.4:c.2611G>T	p.Glu871Ter	p.E871*	ENST00000278616	NM_000051.3	871	Gaa/Taa	17/63	0.62372132055291	4	FACETS	0.91	0.869	0.951	0.91	0.869	0.951	CLONAL	3	TRUE	1	0.681301702309031	4		336	555	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154395	2154395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042657-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	90	706	0	ENST00000434045.2:c.533C>T	p.Ser178Phe	p.S178F	ENST00000434045	NM_001127598.1	178	tCc/tTc	5/5	1	2	FACETS	0.686	0.613	0.763	0.686	0.613	0.763	SUBCLONAL	1	TRUE	1	0.681301702309031	2		706	385	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413581	32413581	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042657-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	372	406	0	ENST00000332351.3:c.1369C>A	p.Gln457Lys	p.Q457K	ENST00000332351	NM_024426.4	457	Cag/Aag	9/10	0.681301702309031	4	FACETS	0.908	0.87	0.945	0.908	0.87	0.945	CLONAL	3	TRUE	1	0.681301702309031	4		406	674	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236234	108236234	+	stop_lost	Nonstop_Mutation	SNP	G	G	T	novel	NA	P-0042657-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	106	423	0	ENST00000278616.4:c.9170G>T	p.Ter3057LeuextTer29	p.*3057Lext*29	ENST00000278616	NM_000051.3	3057	tGa/tTa	63/63	0.62372132055291	4	FACETS	0.798	0.716	0.884	0.266	0.238	0.295	SUBCLONAL	1	TRUE	1	0.681301702309031	4		423	656	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427266	49427274	+	inframe_deletion	In_Frame_Del	DEL	TGCTGCTGC	TGCTGCTGC	-	rs398123707	NA	P-0042657-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	107	620	1	ENST00000301067.7:c.11214_11222del	p.Gln3743_Gln3745del	p.Q3743_Q3745del	ENST00000301067	NM_003482.3	3738	caGCAGCAGCAa/caa	39/54	0.681301702309031	3	FACETS	0.781	0.703	0.863	0.391	0.351	0.432	SUBCLONAL	1	TRUE	1	0.681301702309031	3		621	539	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687337	37687337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778522020	NA	P-0042657-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	129	508	1	ENST00000447079.4:c.4241C>T	p.Pro1414Leu	p.P1414L	ENST00000447079	NM_015083.1	1414	cCg/cTg	14/14	0.442676100822702	3	FACETS	0.91	0.828	0.995			1	CLONAL	1	TRUE	NA	0.681301702309031	3		509	558	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954223	17954223	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042657-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	253	561	0	ENST00000458235.1:c.386T>C	p.Leu129Pro	p.L129P	ENST00000458235	NM_000215.3	129	cTt/cCt	4/24	0.571628183658426	3	FACETS	0.878	0.829	0.927	0.878	0.829	0.927	CLONAL	2	TRUE	1	0.681301702309031	3		561	567	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505581	25505581	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0042657-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	146	591	0	ENST00000264709.3:c.178-1G>C		p.X60_splice	ENST00000264709	NM_175629.2	60			0.681301702309031	3	FACETS	0.887	0.812	0.965	0.443	0.406	0.483	CLONAL	1	TRUE	1	0.681301702309031	3		591	648	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142949975	142949975	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042657-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	236	456	0	ENST00000262992.4:c.2735A>T	p.Tyr912Phe	p.Y912F	ENST00000262992	NM_001101669.1	912	tAc/tTc	24/24	0.681301702309031	3	FACETS	0.87	0.82	0.92	0.87	0.82	0.92	CLONAL	2	TRUE	1	0.681301702309031	3		456	534	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045913	143045913	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042657-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	166	317	1	ENST00000262992.4:c.1721A>T	p.Glu574Val	p.E574V	ENST00000262992	NM_001101669.1	574	gAg/gTg	17/24	0.681301702309031	3	FACETS	0.964	0.9	1	0.964	0.9	1	CLONAL	2	TRUE	1	0.681301702309031	3		318	339	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635120	87635120	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0042657-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	88	329	0	ENST00000277120.3:c.2173-1G>T		p.X725_splice	ENST00000277120		725			0.608750644430798	3	FACETS	0.978	0.874	1	0.489	0.437	0.544	CLONAL	1	TRUE	1	0.681301702309031	3		329	354	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0042797-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	234	578	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.642115888788616	2		578	716	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042797-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	161	417	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	1	2	FACETS	0.92	0.849	0.993	0.92	0.849	0.993	CLONAL	1	TRUE	1	0.642115888788616	2		417	545	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056053	26056067	+	inframe_deletion	In_Frame_Del	DEL	CCTTGGGCTTAGCGG	CCTTGGGCTTAGCGG	-	rs756916945	NA	P-0042797-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	130	624	0	ENST00000343677.2:c.590_604del	p.Ala197_Lys201del	p.A197_K201del	ENST00000343677	NM_005319.3	197	gCCGCTAAGCCCAAGGtt/gtt	1/1	0.404906210363907	3	FACETS	1	0.971	1	0.574	0.524	0.626	CLONAL	1	TRUE	1	0.642115888788616	3		624	466	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481412	140481412	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913353	NA	P-0042797-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	167	633	0	ENST00000288602.6:c.1396G>C	p.Gly466Arg	p.G466R	ENST00000288602	NM_004333.4	466	Gga/Cga	11/18	0.623929236807172	1	FACETS	0.91	0.848	0.974	0.91	0.848	0.974	CLONAL	1	TRUE	0	0.642115888788616	1		633	388	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595346	141595358	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTCTAGGTGGA	GGGTCTAGGTGGA	-	novel	NA	P-0042797-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	230	1082	0	ENST00000220592.5:c.75_87del	p.Pro26ThrfsTer109	p.P26Tfs*109	ENST00000220592	NM_012154.3	25	ccTCCACCTAGACCC/cc	2/19	0.642115888788616	4	FACETS	0.855	0.795	0.917	0.285	0.265	0.306	CLONAL	1	TRUE	1	0.642115888788616	4		1082	1376	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560464	95560464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	157	622	1	ENST00000393063.1:c.5125G>A	p.Asp1709Asn	p.D1709N	ENST00000393063	NM_030621.3	1709	Gat/Aat	25/28	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.512296390204314	2		623	613	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436047	51436047	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043562-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	55	496	0	ENST00000262662.1:c.7G>T	p.Glu3Ter	p.E3*	ENST00000262662		3	Gag/Tag	3/4	1	2	FACETS	0.765	0.655	0.884	0.765	0.655	0.884	SUBCLONAL	1	TRUE	1	0.31	2		496	464	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99472841	99472841	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043562-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	52	739	0	ENST00000268035.6:c.2837T>G	p.Leu946Trp	p.L946W	ENST00000268035	NM_000875.3	946	tTg/tGg	14/21	0.20626311065508	0	FACETS	0.316	0.268	0.368			1	SUBCLONAL	1	TRUE	0	0.31	0		739	733	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411902	116411902	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0043562-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	240	1021	0	ENST00000397752.3:c.2888-1G>C		p.X963_splice	ENST00000397752	NM_000245.2	963			0.300042496219863	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.31	1		1021	886	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0044602-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	101	379	3	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.894	0.814	0.975	1	0.991	1	CLONAL	4	FALSE	1	0.228736028247527	2		382	247	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0044602-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	376	668	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.228736028247527	10	FACETS	1	0.969	1			1	CLONAL	8	FALSE	NA	0.228736028247527	10		669	774	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579310	7579310	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1555526469	NA	P-0044602-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	222	492	0	ENST00000269305.4:c.375+2T>C		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.228736028247527	10	FACETS	1	0.951	1			1	CLONAL	7	FALSE	NA	0.228736028247527	10		492	524	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447395	12447395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044602-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	126	477	0	ENST00000287820.6:c.634C>T	p.Arg212Trp	p.R212W	ENST00000287820	NM_015869.4	212	Cgg/Tgg	5/7	0.151436896065393	3	FACETS	1	0.919	1	1	0.991	1	CLONAL	4	FALSE	1	0.228736028247527	3		477	307	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918978	76918981	+	frameshift_variant	Frame_Shift_Del	DEL	TGTC	TGTC	-	novel	NA	P-0044602-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	164	399	0	ENST00000373344.5:c.4010_4013del	p.Arg1337IlefsTer8	p.R1337Ifs*8	ENST00000373344	NM_000489.3	1337	aGACAt/at	12/35	0.228736028247527	0	FACETS	0.97	0.911	1			1	CLONAL	4	FALSE	0	0.228736028247527	0		399	285	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638929	176638929	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044602-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	34	479	0	ENST00000439151.2:c.3529T>C	p.Phe1177Leu	p.F1177L	ENST00000439151	NM_022455.4	1177	Ttt/Ctt	5/23	0.228736028247527	2	FACETS	0.53	0.432	0.64	0.265	0.216	0.32	SUBCLONAL	1	FALSE	0	0.228736028247527	2		479	561	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044969-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	163	380	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.225264554251729	5	FACETS	1	0.968	1	1	0.968	1	CLONAL	4	TRUE	1	0.225264554251729	5		380	448	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347494	89347494	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044969-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	74	582	0	ENST00000301030.4:c.5456C>G	p.Ser1819Cys	p.S1819C	ENST00000301030	NM_001256183.1	1819	tCc/tGc	9/13	0.225264554251729	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.225264554251729	1		582	452	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41022160	41022160	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044969-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	33	398	0	ENST00000267868.3:c.884C>A	p.Ala295Glu	p.A295E	ENST00000267868	NM_002875.4	295	gCa/gAa	9/10	1	2	FACETS	0.847	0.691	1	0.847	0.691	1	CLONAL	1	TRUE	1	0.225264554251729	2		398	346	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122748	7122748	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044969-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	74	590	0	ENST00000302850.5:c.3406A>G	p.Met1136Val	p.M1136V	ENST00000302850	NM_000208.2	1136	Atg/Gtg	19/22	0.225264554251729	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.225264554251729	1		590	476	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488717	212488717	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044969-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	51	428	0	ENST00000342788.4:c.2132G>T	p.Arg711Leu	p.R711L	ENST00000342788	NM_005235.2	711	cGt/cTt	18/28	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.225264554251729	2		428	363	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979334	40979334	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0044969-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	25	485	0	ENST00000373198.4:c.1799T>A	p.Leu600Ter	p.L600*	ENST00000373198	NM_133170.3	600	tTg/tAg	11/32	0.225264554251729	4	FACETS	0.628	0.494	0.782	0.314	0.247	0.391	SUBCLONAL	1	TRUE	2	0.225264554251729	4		485	433	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31493360	31493360	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1364018217	NA	P-0044969-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	28	329	0	ENST00000344624.3:c.1796A>G	p.Tyr599Cys	p.Y599C	ENST00000344624		599	tAt/tGt	10/33	0.225264554251729	4	FACETS	0.745	0.595	0.916	0.372	0.297	0.458	CLONAL	1	TRUE	2	0.225264554251729	4		329	409	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0044972-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	46	464	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.95	0.799	1	0.95	0.799	1	CLONAL	1	TRUE	1	0.168202374774827	2		464	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0044972-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	67	740	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.168202374774827	2		740	635	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183725	10183725	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs5030826	NA	P-0045457-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	16	663	0	ENST00000256474.2:c.194C>G	p.Ser65Trp	p.S65W	ENST00000256474	NM_000551.3	65	tCg/tGg	1/3	0.261026152239707	4	FACETS	0.946	0.712	1	0.473	0.356	0.608	INDETERMINATE	1	TRUE	2	0.624253775288704	4		663	88	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998985	11998985	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045912-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	58	295	0	ENST00000353533.5:c.487C>T	p.Gln163Ter	p.Q163*	ENST00000353533	NM_003010.3	163	Cag/Tag	4/11	0.214595455781822	1	FACETS	0.952	0.819	1	0.952	0.819	1	CLONAL	1	TRUE	0	0.214595455781822	1		295	507	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421039	49421039	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123721	NA	P-0045912-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	169	799	0	ENST00000301067.7:c.14710C>T	p.Arg4904Ter	p.R4904*	ENST00000301067	NM_003482.3	4904	Cga/Tga	48/54	1	2	FACETS	0.841	0.773	0.912	1	0.991	1	CLONAL	2	TRUE	1	0.214595455781822	2		799	936	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005347	42005347	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0045915-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	131	368	0	ENST00000219905.7:c.3085-2A>C		p.X1029_splice	ENST00000219905	NM_001164273.1	1029			0.364148771427431	1	FACETS	0.85	0.773	0.93	0.85	0.773	0.93	CLONAL	1	TRUE	0	0.391135251747278	1		368	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579445	7579446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TAGGAGC	novel	NA	P-0045915-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	268	949	1	ENST00000269305.4:c.235_241dup	p.Thr81SerfsTer70	p.T81Sfs*70	ENST00000269305	NM_001126112.2	81	aca/aGCTCCTAca	4/11	0.364148771427431	1	FACETS	0.812	0.76	0.866	0.812	0.76	0.866	CLONAL	1	TRUE	0	0.391135251747278	1		950	1357	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096273	178096273	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs759117836	NA	P-0045915-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	60	573	0	ENST00000397062.3:c.1058G>C	p.Ser353Thr	p.S353T	ENST00000397062	NM_006164.4	353	aGt/aCt	5/5	1	2	FACETS	0.279	0.239	0.322	0.279	0.239	0.322	SUBCLONAL	1	TRUE	1	0.391135251747278	2		573	1101	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43752295	43752295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374253522	NA	P-0045915-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	228	578	2	ENST00000523873.1:c.695G>A	p.Arg232Gln	p.R232Q	ENST00000523873		232	cGg/cAg	8/8	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.391135251747278	2		580	1121	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50358685	50358685	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045915-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	98	270	0	ENST00000331340.3:c.28T>C	p.Ser10Pro	p.S10P	ENST00000331340	NM_006060.4	10	Tcc/Ccc	2/8	1	2	FACETS	0.828	0.74	0.922	0.828	0.74	0.922	CLONAL	1	TRUE	1	0.391135251747278	2		270	605	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873654	151873654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045915-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	226	536	0	ENST00000262189.6:c.8884G>A	p.Gly2962Ser	p.G2962S	ENST00000262189	NM_170606.2	2962	Ggc/Agc	38/59	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.391135251747278	2		536	1099	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949673	151949673	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045915-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	154	472	0	ENST00000262189.6:c.1427C>G	p.Pro476Arg	p.P476R	ENST00000262189	NM_170606.2	476	cCa/cGa	10/59	1	2	FACETS	0.824	0.753	0.897	0.824	0.753	0.897	CLONAL	1	TRUE	1	0.391135251747278	2		472	956	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521632	46521632	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs890946693	NA	P-0045962-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	54	402	0	ENST00000262741.5:c.776A>G	p.Asn259Ser	p.N259S	ENST00000262741	NM_003629.3	259	aAt/aGt	7/10	0.276130953944483	2	FACETS	0.532	0.455	0.617	0.266	0.227	0.309	SUBCLONAL	1	TRUE	0	0.420901888653215	2		402	482	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128020	64128020	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs746032255	NA	P-0045962-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	72	825	0	ENST00000334205.4:c.418G>C	p.Val140Leu	p.V140L	ENST00000334205	NM_003942.2	140	Gtg/Ctg	4/17	0.274463634615783	2	FACETS	0.592	0.517	0.672	0.296	0.258	0.336	SUBCLONAL	1	TRUE	0	0.420901888653215	2		825	578	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589571	69589571	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045962-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	126	237	1	ENST00000168712.1:c.282C>A	p.Phe94Leu	p.F94L	ENST00000168712	NM_002007.2	94	ttC/ttA	1/3	0.0983897081661547	6	FACETS	1	0.975	1			1	INDETERMINATE	3	TRUE	NA	0.420901888653215	6		238	318	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432552	49432552	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045962-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	73	737	0	ENST00000301067.7:c.8587G>T	p.Gly2863Cys	p.G2863C	ENST00000301067	NM_003482.3	2863	Ggc/Tgc	34/54	0.265576186008635	2	FACETS	0.517	0.452	0.587	0.258	0.226	0.294	SUBCLONAL	1	TRUE	0	0.420901888653215	2		737	671	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244942	133244943	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0045962-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	67	835	0	ENST00000320574.5:c.2172_2173delinsTT	p.Asp725Tyr	p.D725Y	ENST00000320574	NM_006231.2	724	gcGGat/gcTTat	19/49	0.265576186008635	2	FACETS	0.474	0.412	0.542	0.237	0.206	0.271	SUBCLONAL	1	TRUE	0	0.420901888653215	2		835	671	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643214	38643214	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs76128643	NA	P-0045962-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	52	347	0	ENST00000299084.4:c.685-1G>T		p.X229_splice	ENST00000299084	NM_152594.2	229			1	2	FACETS	0.725	0.62	0.838	0.725	0.62	0.838	SUBCLONAL	1	TRUE	1	0.420901888653215	2		347	341	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576101	88576101	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045962-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	108	748	1	ENST00000360948.2:c.1572C>A	p.His524Gln	p.H524Q	ENST00000360948	NM_001012338.2	524	caC/caA	13/19	1	2	FACETS	0.915	0.824	1	0.915	0.824	1	CLONAL	1	TRUE	1	0.420901888653215	2		749	561	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969899	81969899	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045962-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	113	598	1	ENST00000359376.3:c.2968C>A	p.Gln990Lys	p.Q990K	ENST00000359376	NM_002661.3	990	Caa/Aaa	27/33	0.420901888653215	1	FACETS	0.977	0.885	1	0.977	0.885	1	CLONAL	1	TRUE	0	0.420901888653215	1		599	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577535	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0045962-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	245	707	0	ENST00000269305.4:c.746_747delinsAT	p.Arg249Asn	p.R249N	ENST00000269305	NM_001126112.2	249	aGG/aAT	7/11	0.369867783321641	2	FACETS	0.975	0.919	1	0.975	0.919	1	CLONAL	2	TRUE	0	0.420901888653215	2		707	597	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222986	1222986	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs864622488	NA	P-0045962-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	165	587	0	ENST00000326873.7:c.923G>T	p.Trp308Leu	p.W308L	ENST00000326873	NM_000455.4	308	tGg/tTg	8/10	0.420901888653215	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.420901888653215	1		587	444	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739027	40739027	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045962-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	149	637	0	ENST00000373198.4:c.3257G>T	p.Arg1086Leu	p.R1086L	ENST00000373198	NM_133170.3	1086	cGc/cTc	24/32	0.194650950496085	3	FACETS	1	0.985	1	0.68	0.623	0.739	INDETERMINATE	1	TRUE	1	0.420901888653215	3		637	630	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890242	72890242	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045962-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	121	507	0	ENST00000325599.8:c.440A>G	p.His147Arg	p.H147R	ENST00000325599	NM_018130.2	147	cAc/cGc	4/11	0.420901888653215	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.420901888653215	1		507	448	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31485060	31485060	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1291264597	NA	P-0045962-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	282	270	1	ENST00000344624.3:c.1924G>T	p.Val642Leu	p.V642L	ENST00000344624		642	Gtg/Ttg	12/33	0.420901888653215	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	1	0.420901888653215	4		271	583	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31493397	31493397	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045962-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	41	360	0	ENST00000344624.3:c.1759G>C	p.Asp587His	p.D587H	ENST00000344624		587	Gac/Cac	10/33	0.420901888653215	4	FACETS	0.397	0.33	0.472	0.132	0.11	0.158	SUBCLONAL	1	TRUE	1	0.420901888653215	4		360	697	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045702	26045702	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs781070029	NA	P-0045962-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	50	464	0	ENST00000540144.1:c.64G>C	p.Ala22Pro	p.A22P	ENST00000540144	NM_003531.2	22	Gct/Cct	1/1	0.265576186008635	2	FACETS	0.504	0.428	0.588	0.252	0.214	0.294	SUBCLONAL	1	TRUE	0	0.420901888653215	2		464	471	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864439	162864439	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045962-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	55	479	0	ENST00000366898.1:c.74A>G	p.Gln25Arg	p.Q25R	ENST00000366898	NM_004562.2	25	cAg/cGg	2/12	0.302438879341926	1	FACETS	0.423	0.362	0.489	0.423	0.362	0.489	SUBCLONAL	1	TRUE	0	0.420901888653215	1		479	488	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508919	106508919	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045962-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	115	497	0	ENST00000359195.3:c.913G>T	p.Val305Leu	p.V305L	ENST00000359195	NM_002649.2	305	Gtg/Ttg	2/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.420901888653215	2		497	477	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285530	38285530	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045962-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	113	625	0	ENST00000425967.3:c.623A>T	p.Lys208Ile	p.K208I	ENST00000425967	NM_001174067.1	208	aAa/aTa	6/19	0.264912320231626	1	FACETS	0.726	0.655	0.8	0.726	0.655	0.8	SUBCLONAL	1	TRUE	0	0.420901888653215	1		625	584	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372098	55372098	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045962-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	79	456	0	ENST00000297316.4:c.788C>A	p.Pro263Gln	p.P263Q	ENST00000297316	NM_022454.3	263	cCg/cAg	2/2	0.410132911403693	4	FACETS	1	0.946	1	0.376	0.331	0.423	CLONAL	1	TRUE	1	0.420901888653215	4		456	473	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518357	8518357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045962-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	33	285	0	ENST00000356435.5:c.1034C>T	p.Ser345Phe	p.S345F	ENST00000356435		345	tCt/tTt	10/35	0.193636877845795	2	FACETS	0.498	0.406	0.6	0.249	0.203	0.3	INDETERMINATE	1	TRUE	0	0.420901888653215	2		285	315	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393563	139393563	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0045962-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	143	857	0	ENST00000277541.6:c.6082+1G>T		p.X2028_splice	ENST00000277541	NM_017617.3	2028			0.327750366261584	1	FACETS	0.897	0.821	0.976	0.897	0.821	0.976	CLONAL	1	TRUE	0	0.420901888653215	1		857	598	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923601	39923601	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045962-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	136	768	1	ENST00000378444.4:c.3490C>T	p.Arg1164Ter	p.R1164*	ENST00000378444	NM_001123385.1	1164	Cga/Tga	7/15	NA	2	FACETS	0.862	0.784	0.943			1	INDETERMINATE	1	TRUE	NA	0.420901888653215	2		769	750	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966734	18966737	+	frameshift_variant	Frame_Shift_Del	DEL	GCCG	GCCG	CCC	novel	NA	P-0045962-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	51	715	0	ENST00000262803.5:c.1545_1548delinsCCC	p.Val517CysfsTer14	p.V517Cfs*14	ENST00000262803	NM_002911.3	515	ggGCCG/ggCCC	12/24	0.420901888653215	1	FACETS	0.386	0.328	0.449	0.386	0.328	0.449	SUBCLONAL	1	TRUE	0	0.420901888653215	1		715	496	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046153-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	66	528	0	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	1	2	FACETS	0.421	0.364	0.483	0.421	0.364	0.483	SUBCLONAL	1	TRUE	1	0.35	2		528	896	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0046153-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	71	508	2	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	0.154444244480319	4	FACETS	0.714	0.622	0.813	0.357	0.311	0.407	INDETERMINATE	1	TRUE	2	0.35	4		510	767	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113304	209113304	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046153-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	53	459	0	ENST00000345146.2:c.203A>G	p.Asn68Ser	p.N68S	ENST00000345146	NM_005896.2	68	aAt/aGt	4/10	1	2	FACETS	0.499	0.425	0.58	0.499	0.425	0.58	SUBCLONAL	1	TRUE	1	0.35	2		459	607	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0046603-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	120	449	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.445309484228325	1	FACETS	0.817	0.741	0.896	0.817	0.741	0.896	CLONAL	1	TRUE	0	0.445309484228325	1		449	513	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0046603-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	97	443	2	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.43862654746754	1	FACETS	0.706	0.632	0.783	0.706	0.632	0.783	SUBCLONAL	1	TRUE	0	0.445309484228325	1		445	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0046603-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	141	685	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.445309484228325	1	FACETS	0.509	0.463	0.557	0.509	0.463	0.557	SUBCLONAL	1	TRUE	0	0.445309484228325	1		685	968	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007689	45007690	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0046603-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	67	415	0	ENST00000558401.1:c.137_138del	p.Tyr46CysfsTer10	p.Y46Cfs*10	ENST00000558401	NM_004048.2	46	TAt/t	2/4	0.445309484228325	1	FACETS	0.338	0.293	0.386	0.338	0.293	0.386	SUBCLONAL	1	TRUE	0	0.445309484228325	1		415	693	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604625	48604625	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0046603-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	27	198	0	ENST00000342988.3:c.1448-1G>A		p.X483_splice	ENST00000342988	NM_005359.5	483			0.43862654746754	1	FACETS	0.27	0.215	0.333	0.27	0.215	0.333	SUBCLONAL	1	TRUE	0	0.445309484228325	1		198	349	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994354	25994355	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0046603-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	184	421	0	ENST00000435504.4:c.458_459del	p.Lys153SerfsTer51	p.K153Sfs*51	ENST00000435504		153	aAA/a	6/13	0.445309484228325	1	FACETS	0.891	0.825	0.959	0.891	0.825	0.959	CLONAL	1	TRUE	0	0.445309484228325	1		421	721	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217855	7217858	+	frameshift_variant	Frame_Shift_Del	DEL	CTTC	CTTC	-	novel	NA	P-0046603-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	200	633	0	ENST00000380728.2:c.153_156del	p.Lys53ArgfsTer9	p.K53Rfs*9	ENST00000380728		51	agGAAG/ag	3/11	0.445309484228325	1	FACETS	0.828	0.769	0.89	0.828	0.769	0.89	CLONAL	1	TRUE	0	0.445309484228325	1		633	843	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051644	30051651	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAGCAC	CAGAGCAC	-	novel	NA	P-0046603-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	70	365	0	ENST00000338641.4:c.579_586del	p.Glu194ArgfsTer6	p.E194Rfs*6	ENST00000338641	NM_000268.3	193	gCAGAGCAC/g	6/16	0.445309484228325	1	FACETS	0.466	0.406	0.529	0.466	0.406	0.529	SUBCLONAL	1	TRUE	0	0.445309484228325	1		365	525	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0121545-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	151	460	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.907	0.835	0.981	0.907	0.835	0.981	CLONAL	1	NA	1	0.658296459180713	2		460	506	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201693	66201693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142359231	NA	P-0121545-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	81	622	3	ENST00000273854.3:c.2809C>T	p.Arg937Cys	p.R937C	ENST00000273854	NM_004439.5	937	Cgt/Tgt	16/18	1	2	FACETS	0.256	0.225	0.29	0.256	0.225	0.29	SUBCLONAL	1	NA	1	0.658296459180713	2		625	961	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665755	29665756	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs876657715	NA	P-0121545-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	283	351	2	ENST00000356175.3:c.6791dup	p.Tyr2264Ter	p.Y2264*	ENST00000356175	NM_000267.3	2264	tac/tAac	45/57	0.658296459180713	2	FACETS	0.993	0.951	1	0.993	0.951	1	CLONAL	2	NA	0	0.658296459180713	2		353	433	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945144	32945144	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0121545-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	180	452	2	ENST00000380152.3:c.8539G>T	p.Glu2847Ter	p.E2847*	ENST00000380152		2847	Gaa/Taa	20/27	1	2	FACETS	0.888	0.823	0.955	0.888	0.823	0.955	CLONAL	1	NA	1	0.658296459180713	2		454	616	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821904	59821904	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060501745	NA	P-0121545-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	470	542	2	ENST00000259008.2:c.2146A>G	p.Asn716Asp	p.N716D	ENST00000259008	NM_032043.2	716	Aat/Gat	15/20	0.658296459180713	3	FACETS	0.99	0.951	1	0.99	0.951	1	CLONAL	2	NA	1	0.658296459180713	3		544	959	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097098	11097098	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0121545-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	414	1201	3	ENST00000358026.2:c.589C>G	p.Pro197Ala	p.P197A	ENST00000358026	NM_001128849.1	197	Ccc/Gcc	4/36	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	NA	1	0.658296459180713	2		1204	1212	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	143	460	0				ENST00000310581	NM_198253.2	-/1132			0.431085856452045	3	FACETS	0.896	0.824	0.97	0.896	0.824	0.97	CLONAL	2	TRUE	1	0.431085856452045	3		460	450	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0048009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	180	455	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.363480039455244	4	FACETS	1	0.958	1	1	0.992	1	CLONAL	3	TRUE	2	0.431085856452045	4		455	386	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0048009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	113	853	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.228656354088905	3	FACETS	0.782	0.703	0.865	0.391	0.351	0.433	INDETERMINATE	1	TRUE	1	0.431085856452045	3		853	815	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0048009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	261	693	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.228656354088905	3	FACETS	1	0.986	1	1	0.986	1	INDETERMINATE	2	TRUE	1	0.431085856452045	3		693	647	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478922	56478922	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	432	675	0	ENST00000267101.3:c.378C>A	p.Asn126Lys	p.N126K	ENST00000267101	NM_001982.3	126	aaC/aaA	3/28	0.310224029338204	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.431085856452045	3		675	765	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936983	48936983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690863	NA	P-0048009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	123	351	0	ENST00000267163.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000267163	NM_000321.2	251	Cga/Tga	8/27	0.364153065914804	0	FACETS	0.629	0.581	0.678			1	SUBCLONAL	2	TRUE	0	0.431085856452045	0		351	258	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061327	38061327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	161	708	0	ENST00000250448.2:c.662C>T	p.Ser221Leu	p.S221L	ENST00000250448	NM_004496.3	221	tCg/tTg	2/2	0.224177072936983	2	FACETS	1	0.978	1	0.585	0.539	0.634	INDETERMINATE	1	TRUE	0	0.431085856452045	2		708	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28934873	NA	P-0048009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	359	835	0	ENST00000269305.4:c.398T>C	p.Met133Thr	p.M133T	ENST00000269305	NM_001126112.2	133	aTg/aCg	5/11	0.228656354088905	3	FACETS	0.995	0.945	1	0.995	0.945	1	INDETERMINATE	2	TRUE	1	0.431085856452045	3		835	1017	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677876	47677876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	117	440	1	ENST00000347630.2:c.989C>T	p.Ser330Leu	p.S330L	ENST00000347630	NM_001007230.1	330	tCg/tTg	11/11	0.228656354088905	3	FACETS	1	0.94	1	0.527	0.476	0.581	INDETERMINATE	1	TRUE	1	0.431085856452045	3		441	626	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40490803	40490803	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	33	251	0	ENST00000264657.5:c.496G>C	p.Glu166Gln	p.E166Q	ENST00000264657	NM_139276.2	166	Gag/Cag	6/24	0.228656354088905	3	FACETS	0.554	0.452	0.668	0.277	0.226	0.334	INDETERMINATE	1	TRUE	1	0.431085856452045	3		251	336	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722764	49722764	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750737005	NA	P-0048009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	18	69	0	ENST00000449682.2:c.1475G>A	p.Arg492Gln	p.R492Q	ENST00000449682	NM_020998.3	492	cGg/cAg	13/18	0.431085856452045	4	FACETS	0.842	0.651	1	0.842	0.651	1	CLONAL	2	TRUE	2	0.431085856452045	4		69	71	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821455	72821455	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	73	564	0	ENST00000268489.5:c.10720C>T	p.His3574Tyr	p.H3574Y	ENST00000268489	NM_006885.3	3574	Cac/Tac	10/10	1	2	FACETS	0.542	0.474	0.615	0.542	0.474	0.615	SUBCLONAL	1	TRUE	1	0.431085856452045	2		564	625	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433858	78433858	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	51	156	0	ENST00000370768.2:c.241C>T	p.Gln81Ter	p.Q81*	ENST00000370768	NM_003902.3	81	Caa/Taa	3/20	0.431085856452045	5	FACETS	1	0.939	1	0.398	0.34	0.462	CLONAL	1	TRUE	2	0.431085856452045	5		156	326	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245954	16245954	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	68	341	0	ENST00000375759.3:c.1577C>T	p.Ser526Leu	p.S526L	ENST00000375759	NM_015001.2	526	tCg/tTg	8/15	0.431085856452045	5	FACETS	0.827	0.72	0.944	0.276	0.24	0.315	CLONAL	1	TRUE	2	0.431085856452045	5		341	628	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872197	45872197	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	292	682	0	ENST00000391945.4:c.237G>C	p.Glu79Asp	p.E79D	ENST00000391945	NM_000400.3	79	gaG/gaC	4/23	0.224177072936983	2	FACETS	1	0.971	1	1	0.971	1	INDETERMINATE	2	TRUE	0	0.431085856452045	2		682	654	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371824	118371824	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	124	417	0	ENST00000534358.1:c.6284del	p.Asn2095ThrfsTer26	p.N2095Tfs*26	ENST00000534358	NM_005933.3	2094	gAa/ga	25/36	0.3044734638845	6	FACETS	0.769	0.696	0.844	0.256	0.232	0.282	SUBCLONAL	2	TRUE	0	0.431085856452045	6		417	697	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380680	118380699	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGAGGAAAGTAATTTCAG	GAAGAGGAAAGTAATTTCAG	-	novel	NA	P-0048009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	269	329	0	ENST00000534358.1:c.10918_10937del	p.Glu3640LeufsTer19	p.E3640Lfs*19	ENST00000534358	NM_005933.3	3640	GAAGAGGAAAGTAATTTCAGc/c	30/36	0.3044734638845	6	FACETS	1	0.987	1	0.909	0.869	0.949	CLONAL	5	TRUE	0	0.431085856452045	6		329	426	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106253	27106280	+	frameshift_variant	Frame_Shift_Del	DEL	TAGAGGACGAACCCCACAGTAAGGATGA	TAGAGGACGAACCCCACAGTAAGGATGA	-	novel	NA	P-0048009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	410	636	0	ENST00000324856.7:c.5864_5891del	p.Leu1955ArgfsTer51	p.L1955Rfs*51	ENST00000324856	NM_006015.4	1955	cTAGAGGACGAACCCCACAGTAAGGATGAg/cg	20/20	0.431085856452045	5	FACETS	0.955	0.915	0.995	1	0.995	1	CLONAL	4	TRUE	2	0.431085856452045	5		636	820	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318829	163318829	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	35	177	0	ENST00000271452.3:c.1219C>G	p.Gln407Glu	p.Q407E	ENST00000271452	NM_145697.2	407	Caa/Gaa	13/14	0.339384276471126	5	FACETS	0.874	0.719	1	0.291	0.239	0.349	CLONAL	1	TRUE	2	0.431085856452045	5		177	306	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436315	110436315	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1444427299	NA	P-0048009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	135	316	0	ENST00000375856.3:c.2086G>T	p.Ala696Ser	p.A696S	ENST00000375856	NM_003749.2	696	Gcc/Tcc	1/2	0.23678899081528	4	FACETS	1	0.945	1	1	0.945	1	INDETERMINATE	2	TRUE	2	0.431085856452045	4		316	431	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675069	40675069	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	126	672	0	ENST00000249776.8:c.33A>C	p.Arg11Ser	p.R11S	ENST00000249776	NM_033286.3	11	agA/agC	1/9	0.379999964863172	1	FACETS	0.752	0.683	0.824	0.752	0.683	0.824	SUBCLONAL	1	TRUE	0	0.431085856452045	1		672	610	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627114	37627131	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	GGCTTTTTATTTTTCCAG	GGCTTTTTATTTTTCCAG	-	novel	NA	P-0048009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	32	204	0	ENST00000447079.4:c.1047-18_1047-1del		p.X349_splice	ENST00000447079	NM_015083.1	349			0.228656354088905	3	FACETS	0.785	0.641	0.945	0.392	0.32	0.473	INDETERMINATE	1	TRUE	1	0.431085856452045	3		204	230	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657022	45657022	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	100	518	0	ENST00000407780.3:c.134T>G	p.Phe45Cys	p.F45C	ENST00000407780	NM_001283052.1	45	tTt/tGt	3/7	0.395487901881463	5	FACETS	0.82	0.731	0.914			1	CLONAL	1	TRUE	NA	0.431085856452045	5		518	932	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447190	187447190	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	152	639	0	ENST00000232014.4:c.1003C>T	p.Gln335Ter	p.Q335*	ENST00000232014	NM_001130845.1	335	Cag/Tag	5/10	0.363480039455244	4	FACETS	1	0.978	1	0.604	0.552	0.657	CLONAL	1	TRUE	2	0.431085856452045	4		639	836	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542348	187542348	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	72	377	0	ENST00000441802.2:c.5392G>A	p.Asp1798Asn	p.D1798N	ENST00000441802	NM_005245.3	1798	Gat/Aat	10/27	0.431085856452045	5	FACETS	1	0.969	1	0.338	0.296	0.382	CLONAL	1	TRUE	1	0.431085856452045	5		377	407	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92247486	92247486	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	60	298	0	ENST00000265734.4:c.734G>C	p.Arg245Thr	p.R245T	ENST00000265734	NM_001259.6	245	aGa/aCa	7/8	0.279180364808961	4	FACETS	0.967	0.836	1	0.483	0.418	0.554	CLONAL	1	TRUE	2	0.431085856452045	4		298	412	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403202	116403202	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	92	412	0	ENST00000397752.3:c.2463C>G	p.Phe821Leu	p.F821L	ENST00000397752	NM_000245.2	821	ttC/ttG	11/21	0.279180364808961	4	FACETS	1	0.964	1	0.597	0.532	0.665	CLONAL	1	TRUE	2	0.431085856452045	4		412	512	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38184260	38184260	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	91	411	0	ENST00000317025.8:c.1696T>C	p.Ser566Pro	p.S566P	ENST00000317025	NM_023034.1	566	Tct/Cct	7/24	0.220027941268871	2	FACETS	1	0.916	1	0.515	0.46	0.573	INDETERMINATE	1	TRUE	0	0.431085856452045	2		411	410	SUCCESS
AR	367	MSKCC	GRCh37	X	66765955	66765955	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048009-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	168	416	0	ENST00000374690.3:c.967G>T	p.Glu323Ter	p.E323*	ENST00000374690	NM_000044.3	323	Gag/Tag	1/8	0.431085856452045	4	FACETS	0.751	0.691	0.812			1	SUBCLONAL	2	TRUE	NA	0.431085856452045	4		416	743	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0048056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	397	380	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.46106738441803	5	FACETS	0.923	0.88	0.967	0.923	0.88	0.967	CLONAL	3	TRUE	2	0.46106738441803	5		380	1052	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224163	98224163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138154222	NA	P-0048056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	205	373	1	ENST00000331920.6:c.2678G>A	p.Arg893His	p.R893H	ENST00000331920	NM_000264.3	893	cGc/cAc	16/24	NA	2	FACETS	0.934	0.876	0.993			1	INDETERMINATE	2	TRUE	NA	0.46106738441803	2		374	476	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908873	101908873	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200595614	NA	P-0048056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	303	526	1	ENST00000374994.4:c.1237C>T	p.Arg413Ter	p.R413*	ENST00000374994	NM_004612.2	413	Cga/Tga	7/9	NA	2	FACETS	0.89	0.844	0.937			1	INDETERMINATE	2	TRUE	NA	0.46106738441803	2		527	738	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106532	27106532	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	233	843	0	ENST00000324856.7:c.6143G>A	p.Trp2048Ter	p.W2048*	ENST00000324856	NM_006015.4	2048	tGg/tAg	20/20	0.405383255989727	1	FACETS	0.988	0.925	1	0.988	0.925	1	CLONAL	1	TRUE	0	0.46106738441803	1		843	787	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781494	135781494	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	265	568	0	ENST00000298552.3:c.1471A>G	p.Thr491Ala	p.T491A	ENST00000298552	NM_001162426.1	491	Aca/Gca	15/23	0.326738454675471	5	FACETS	1	0.973	1	0.709	0.666	0.753	CLONAL	2	TRUE	2	0.46106738441803	5		568	914	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422317	422317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763626820	NA	P-0048056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	314	484	0	ENST00000399788.2:c.2941G>A	p.Ala981Thr	p.A981T	ENST00000399788	NM_001042603.1	981	Gcc/Acc	20/28	0.423133449206924	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.46106738441803	2		484	645	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679265	88679265	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	153	599	0	ENST00000360948.2:c.772C>A	p.Leu258Met	p.L258M	ENST00000360948	NM_001012338.2	258	Ctg/Atg	8/19	1	2	FACETS	0.856	0.784	0.931	0.856	0.784	0.931	CLONAL	1	TRUE	1	0.46106738441803	2		599	775	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579454	7579457	+	frameshift_variant	Frame_Shift_Del	DEL	GCTG	GCTG	-	novel	NA	P-0048056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	466	931	0	ENST00000269305.4:c.230_233del	p.Pro77GlnfsTer45	p.P77Qfs*45	ENST00000269305	NM_001126112.2	77	cCAGCa/ca	4/11	0.46106738441803	2	FACETS	0.953	0.914	0.993	0.953	0.914	0.993	CLONAL	2	TRUE	0	0.46106738441803	2		931	1060	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778056	27778056	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	426	928	0	ENST00000369163.2:c.205C>T	p.Gln69Ter	p.Q69*	ENST00000369163	NM_003536.2	69	Cag/Tag	1/1	NA	2	FACETS	0.95	0.909	0.991			1	INDETERMINATE	2	TRUE	NA	0.46106738441803	2		928	973	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771508	112771508	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	192	574	0	ENST00000369452.4:c.1681G>T	p.Val561Phe	p.V561F	ENST00000369452	NM_007373.3	561	Gtt/Ttt	9/9	0.326738454675471	5	FACETS	1	0.986	1	0.435	0.402	0.47	CLONAL	1	TRUE	2	0.46106738441803	5		574	1080	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993012	72993014	+	frameshift_variant	Frame_Shift_Del	DEL	TGT	TGT	GG	novel	NA	P-0048056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	474	883	1	ENST00000268489.5:c.1031_1033delinsCC	p.Asn344ThrfsTer8	p.N344Tfs*8	ENST00000268489	NM_006885.3	344	aACAaa/aCCaa	2/10	0.420543080215867	3	FACETS	0.928	0.887	0.969	0.928	0.887	0.969	CLONAL	2	TRUE	1	0.46106738441803	3		884	1363	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0048300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	95	699	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.190172232641601	1	FACETS	0.269	0.24	0.301	0.269	0.24	0.301	INDETERMINATE	1	FALSE	0	0.744870310922372	1		699	594	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0048300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	77	706	1	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.200419256506806	5	FACETS	1	0.974	1	0.459	0.406	0.514	INDETERMINATE	1	FALSE	2	0.744870310922372	5		707	318	SUCCESS
APC	324	MSKCC	GRCh37	5	112116485	112116485	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs752152148	NA	P-0048300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	33	369	0	ENST00000257430.4:c.532-2A>T		p.X178_splice	ENST00000257430	NM_000038.5	178			0.200419256506806	5	FACETS	1	0.861	1	0.351	0.289	0.42	INDETERMINATE	1	FALSE	2	0.744870310922372	5		369	178	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812259	212812259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs991337964	NA	P-0048300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	29	546	0	ENST00000342788.4:c.317G>A	p.Arg106His	p.R106H	ENST00000342788	NM_005235.2	106	cGt/cAt	3/28	0.676426597104197	1	FACETS	0.234	0.189	0.284	0.234	0.189	0.284	SUBCLONAL	1	FALSE	0	0.744870310922372	1		546	209	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748191	43748191	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	137	910	2	ENST00000382044.4:c.2615C>A	p.Ser872Ter	p.S872*	ENST00000382044	NM_001141980.1	872	tCa/tAa	12/28	0.463096428060949	4	FACETS	1	0.977	1	0.598	0.546	0.651	CLONAL	1	FALSE	2	0.744870310922372	4		912	537	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557629	95557629	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048329-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	257	242	0	ENST00000393063.1:c.5438A>G	p.Glu1813Gly	p.E1813G	ENST00000393063	NM_030621.3	1813	gAg/gGg	26/28	1	2	FACETS	0.853	0.804	0.903	0.853	0.804	0.903	CLONAL	1	TRUE	1	0.89665037593477	2		242	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577586	7577586	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048329-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	402	431	0	ENST00000269305.4:c.695T>A	p.Ile232Asn	p.I232N	ENST00000269305	NM_001126112.2	232	aTc/aAc	7/11	0.89665037593477	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.89665037593477	1		431	483	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557629	95557629	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048329-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	340	242	0	ENST00000393063.1:c.5438A>G	p.Glu1813Gly	p.E1813G	ENST00000393063	NM_030621.3	1813	gAg/gGg	26/28	0.572651850955143	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	FALSE	1	0.572651850955143	3		242	663	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577586	7577586	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048329-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	426	431	0	ENST00000269305.4:c.695T>A	p.Ile232Asn	p.I232N	ENST00000269305	NM_001126112.2	232	aTc/aAc	7/11	0.572651850955143	2	FACETS	0.838	0.812	0.863	1	0.996	1	CLONAL	3	FALSE	0	0.572651850955143	2		431	592	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	67	460	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.787	0.687	0.896	0.787	0.687	0.896	SUBCLONAL	1	TRUE	1	0.39667986280187	2		460	429	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191385	185191385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	140	842	1	ENST00000265026.3:c.2266G>A	p.Asp756Asn	p.D756N	ENST00000265026	NM_004721.4	756	Gac/Aac	11/14	1	2	FACETS	0.86	0.783	0.94	0.86	0.783	0.94	CLONAL	1	TRUE	1	0.39667986280187	2		843	821	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106732	27106732	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	152	785	0	ENST00000324856.7:c.6343C>T	p.Gln2115Ter	p.Q2115*	ENST00000324856	NM_006015.4	2115	Cag/Tag	20/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.39667986280187	2		785	741	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130576	29130576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs558321010	NA	P-0048532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	57	754	0	ENST00000328354.6:c.134C>T	p.Thr45Met	p.T45M	ENST00000328354	NM_007194.3	45	aCg/aTg	2/15	1	2	FACETS	0.374	0.32	0.433	0.374	0.32	0.433	SUBCLONAL	1	TRUE	1	0.39667986280187	2		754	769	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981140	201981141	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0048532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	170	878	0	ENST00000359651.3:c.219_220del	p.Asp74LeufsTer17	p.D74Lfs*17	ENST00000359651		73	ctGGac/ctac	2/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.39667986280187	2		878	712	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204852	94204852	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	63	488	0	ENST00000323929.3:c.733C>T	p.His245Tyr	p.H245Y	ENST00000323929	NM_005591.3	245	Cat/Tat	8/20	0.15758569128821	3	FACETS	0.931	0.808	1	0.465	0.404	0.532	INDETERMINATE	1	TRUE	1	0.39667986280187	3		488	409	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611750	1611750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	260	847	0	ENST00000344749.5:c.1912C>T	p.His638Tyr	p.H638Y	ENST00000344749	NM_001136139.2	638	Cac/Tac	19/19	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.39667986280187	2		847	941	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2202733	2202733	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	163	762	0	ENST00000398665.3:c.742G>C	p.Glu248Gln	p.E248Q	ENST00000398665	NM_032482.2	248	Gag/Cag	9/28	1	2	FACETS	0.947	0.869	1	0.947	0.869	1	CLONAL	1	TRUE	1	0.39667986280187	2		762	868	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191103	185191103	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	145	878	0	ENST00000265026.3:c.1984G>C	p.Asp662His	p.D662H	ENST00000265026	NM_004721.4	662	Gac/Cac	11/14	1	2	FACETS	0.996	0.91	1	0.996	0.91	1	CLONAL	1	TRUE	1	0.39667986280187	2		878	734	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191349	185191349	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	155	814	1	ENST00000265026.3:c.2230G>A	p.Asp744Asn	p.D744N	ENST00000265026	NM_004721.4	744	Gac/Aac	11/14	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.39667986280187	2		815	739	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405706	139405706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	356	1023	2	ENST00000277541.6:c.2485G>A	p.Val829Met	p.V829M	ENST00000277541	NM_017617.3	829	Gtg/Atg	16/34	0.39667986280187	1	FACETS	0.769	0.731	0.807	1	0.995	1	SUBCLONAL	2	TRUE	0	0.39667986280187	1		1025	936	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211614	46211614	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	25	412	0	ENST00000334344.6:c.580G>A	p.Glu194Lys	p.E194K	ENST00000334344	NM_152641.2	194	Gaa/Aaa	5/21	0.15758569128821	3	FACETS	0.412	0.324	0.512	0.206	0.162	0.256	INDETERMINATE	1	TRUE	1	0.39667986280187	3		412	367	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752392	55752392	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766409125	NA	P-0048532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	163	1060	0	ENST00000284073.2:c.850G>A	p.Asp284Asn	p.D284N	ENST00000284073	NM_138962.2	284	Gat/Aat	12/14	0.15758569128821	3	FACETS	0.869	0.796	0.946	0.435	0.398	0.473	INDETERMINATE	1	TRUE	1	0.39667986280187	3		1060	1133	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038832	47038857	+	frameshift_variant	Frame_Shift_Del	DEL	GAGTCCTGGCCTCCCAAGCCCTGTCA	GAGTCCTGGCCTCCCAAGCCCTGTCA	ACT	novel	NA	P-0048532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	219	525	0	ENST00000377604.3:c.839_864delinsACT	p.Gly280AspfsTer13	p.G280Dfs*13	ENST00000377604	NM_001204468.1	280	gGAGTCCTGGCCTCCCAAGCCCTGTCA/gACT	9/24	0.304711398925422	2	FACETS	0.998	0.937	1			1	CLONAL	2	TRUE	NA	0.39667986280187	2		525	553	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0048716-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	163	918	1	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.564604717062291	3	FACETS	0.941	0.865	1	0.47	0.432	0.51	CLONAL	1	TRUE	1	0.564604717062291	3		919	787	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048716-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	50	460	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.798	0.685	0.919	0.798	0.685	0.919	CLONAL	1	TRUE	1	0.564604717062291	2		460	222	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151863	108151863	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs377349886	NA	P-0048716-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	35	510	0	ENST00000278616.4:c.3544G>C	p.Glu1182Gln	p.E1182Q	ENST00000278616	NM_000051.3	1182	Gag/Cag	24/63	1	2	FACETS	0.588	0.486	0.7	0.588	0.486	0.7	SUBCLONAL	1	TRUE	1	0.564604717062291	2		510	211	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830754	3830754	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048716-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	64	532	0	ENST00000262367.5:c.1802G>C	p.Arg601Pro	p.R601P	ENST00000262367	NM_004380.2	601	cGg/cCg	8/31	1	2	FACETS	0.727	0.634	0.825	0.727	0.634	0.825	SUBCLONAL	1	TRUE	1	0.564604717062291	2		532	312	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807891	1807891	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28928868	NA	P-0048716-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	1087	1094	0	ENST00000260795.2:c.1950G>C	p.Lys650Asn	p.K650N	ENST00000260795		650	aaG/aaC	13/17	0.564604717062291	9	FACETS	1	0.99	1			1	CLONAL	8	TRUE	NA	0.564604717062291	9		1094	1416	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971091	21971100	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCTCCCGG	GCCCTCCCGG	-	novel	NA	P-0048716-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	124	732	0	ENST00000304494.5:c.258_267del	p.Arg87SerfsTer56	p.R87Sfs*56	ENST00000304494	NM_000077.4	86	gcCCGGGAGGGC/gc	2/3	0.564604717062291	1	FACETS	0.841	0.769	0.915	0.841	0.769	0.915	CLONAL	1	TRUE	0	0.564604717062291	1		732	375	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891190	101891190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048716-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	6	0	0	ENST00000374994.4:c.151G>A	p.Asp51Asn	p.D51N	ENST00000374994	NM_004612.2	51	Gat/Aat	2/9	0.564604717062291	1	FACETS	0.094	0.055	0.145	0.094	0.055	0.145	SUBCLONAL	1	TRUE	0	0.564604717062291	1		0	163	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0048834-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	114	742	0	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	1	2	FACETS	0.979	0.88	1	0.979	0.88	1	CLONAL	1	TRUE	1	0.256830699056752	2		742	907	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0048834-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	36	240	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	NA	2	FACETS	0.609	0.501	0.731			1	INDETERMINATE	1	TRUE	NA	0.256830699056752	2		240	460	SUCCESS
APC	324	MSKCC	GRCh37	5	112175322	112175322	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1114167578	NA	P-0048834-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	22	339	0	ENST00000257430.4:c.4031C>G	p.Ser1344Ter	p.S1344*	ENST00000257430	NM_000038.5	1344	tCa/tGa	16/16	NA	2	FACETS	0.426	0.33	0.539			1	INDETERMINATE	1	TRUE	NA	0.256830699056752	2		339	402	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268762	41268762	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1245266458	NA	P-0048834-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	42	550	0	ENST00000349496.5:c.1000G>A	p.Glu334Lys	p.E334K	ENST00000349496	NM_001904.3	334	Gaa/Aaa	7/15	1	2	FACETS	0.558	0.465	0.662	0.558	0.465	0.662	SUBCLONAL	1	TRUE	1	0.256830699056752	2		550	586	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965472	68965472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200682883	NA	P-0048834-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	166	605	1	ENST00000288368.4:c.1084C>T	p.Arg362Trp	p.R362W	ENST00000288368	NM_024870.2	362	Cgg/Tgg	9/40	0.248104442625259	4	FACETS	0.831	0.763	0.903	0.831	0.763	0.903	CLONAL	2	TRUE	2	0.256830699056752	4		606	977	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0049930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	193	856	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.225029055563231	3	FACETS	0.866	0.807	0.926	0.866	0.807	0.926	CLONAL	3	FALSE	0	0.320492816862591	3		856	538	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971035	21971035	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	56	532	0	ENST00000304494.5:c.323A>G	p.Asp108Gly	p.D108G	ENST00000304494	NM_000077.4	108	gAt/gGt	2/3	0.144310365034901	0	FACETS	0.703	0.605	0.808			1	INDETERMINATE	1	FALSE	0	0.320492816862591	0		532	338	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627549	14627550	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1251025883	NA	P-0049930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	29	576	0	ENST00000254322.2:c.520dup	p.Glu174GlyfsTer61	p.E174Gfs*61	ENST00000254322	NM_006145.1	174	gag/gGag	2/3	0.258739812479203	1	FACETS	0.401	0.322	0.491	0.401	0.322	0.491	SUBCLONAL	1	FALSE	0	0.320492816862591	1		576	379	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965421	68965421	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs777847032	NA	P-0049930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	28	656	0	ENST00000288368.4:c.1033A>T	p.Thr345Ser	p.T345S	ENST00000288368	NM_024870.2	345	Aca/Tca	9/40	0.320066110599656	4	FACETS	0.528	0.421	0.65	0.264	0.21	0.325	SUBCLONAL	1	FALSE	2	0.320492816862591	4		656	437	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0049968-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	26	486	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.202422549690647	4	FACETS	1	0.908	1	1	0.908	1	CLONAL	2	TRUE	2	0.221060601573006	4		486	116	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164531	47164531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049968-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	11	357	0	ENST00000409792.3:c.1595C>T	p.Ser532Phe	p.S532F	ENST00000409792	NM_014159.6	532	tCt/tTt	3/21	0.202422549690647	4	FACETS	1	0.785	1	0.584	0.407	0.8	CLONAL	1	TRUE	2	0.221060601573006	4		357	104	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0050023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	63	1042	1	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	0.140682798814405	1	FACETS	0.883	0.764	1	0.883	0.764	1	CLONAL	1	FALSE	0	0.222475137410903	1		1043	570	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244664	46244664	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555155026	NA	P-0050023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	20	750	0	ENST00000334344.6:c.2758C>T	p.Gln920Ter	p.Q920*	ENST00000334344	NM_152641.2	920	Cag/Tag	15/21	0.160451532536431	3	FACETS	0.609	0.465	0.777	0.305	0.232	0.389	SUBCLONAL	1	FALSE	1	0.222475137410903	3		750	328	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599874	10599874	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	45	1103	0	ENST00000171111.5:c.1702G>T	p.Val568Phe	p.V568F	ENST00000171111	NM_203500.1	568	Gtc/Ttc	5/6	0.140682798814405	1	FACETS	0.658	0.553	0.775	0.658	0.553	0.775	SUBCLONAL	1	FALSE	0	0.222475137410903	1		1103	546	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260837	16260837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	26	935	1	ENST00000375759.3:c.8102C>T	p.Thr2701Met	p.T2701M	ENST00000375759	NM_015001.2	2701	aCg/aTg	11/15	1	2	FACETS	0.476	0.376	0.591	0.476	0.376	0.591	SUBCLONAL	1	FALSE	1	0.222475137410903	2		936	491	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874031	123874031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1447464550	NA	P-0050023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	16	45	0	ENST00000330479.4:c.62C>T	p.Ala21Val	p.A21V	ENST00000330479	NM_020382.3	21	gCg/gTg	2/9	0.160451532536431	3	FACETS	1	0.89	1	0.714	0.534	0.923	CLONAL	1	FALSE	1	0.222475137410903	3		45	112	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436084	51436084	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	32	559	0	ENST00000262662.1:c.44G>T	p.Arg15Met	p.R15M	ENST00000262662		15	aGg/aTg	3/4	1	2	FACETS	0.856	0.696	1	0.856	0.696	1	CLONAL	1	FALSE	1	0.222475137410903	2		559	336	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436923	29436923	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	30	872	0	ENST00000389048.3:c.3670C>A	p.Leu1224Met	p.L1224M	ENST00000389048	NM_004304.4	1224	Ctg/Atg	24/29	0.140682798814405	1	FACETS	0.52	0.418	0.636	0.52	0.418	0.636	SUBCLONAL	1	FALSE	0	0.222475137410903	1		872	461	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163310199	163310199	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	12	622	1	ENST00000271452.3:c.652G>T	p.Glu218Ter	p.E218*	ENST00000271452	NM_145697.2	218	Gag/Tag	9/14	1	2	FACETS	0.506	0.356	0.692	0.506	0.356	0.692	SUBCLONAL	1	FALSE	1	0.222475137410903	2		623	213	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091340	193091340	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	31	432	0	ENST00000367435.3:c.10G>A	p.Val4Met	p.V4M	ENST00000367435	NM_024529.4	4	Gtg/Atg	1/17	1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	FALSE	1	0.222475137410903	2		432	262	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920771	100920771	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	22	556	0	ENST00000325455.5:c.2377T>A	p.Ser793Thr	p.S793T	ENST00000325455	NM_001202474.3	793	Tca/Aca	6/8	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	FALSE	1	0.222475137410903	2		556	175	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373892	118373892	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	13	434	1	ENST00000534358.1:c.7285A>G	p.Arg2429Gly	p.R2429G	ENST00000534358	NM_005933.3	2429	Aga/Gga	27/36	1	2	FACETS	1	0.731	1	1	0.731	1	CLONAL	1	FALSE	1	0.222475137410903	2		435	115	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109958	115109958	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	103	1039	0	ENST00000257566.3:c.1920C>A	p.Tyr640Ter	p.Y640*	ENST00000257566	NM_016569.3	640	taC/taA	8/8	0.160451532536431	3	FACETS	0.903	0.81	1	0.903	0.81	1	CLONAL	2	FALSE	1	0.222475137410903	3		1039	570	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335921	73335921	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	23	530	0	ENST00000377767.4:c.2374G>C	p.Ala792Pro	p.A792P	ENST00000377767	NM_014953.3	792	Gct/Cct	18/21	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	FALSE	1	0.222475137410903	2		530	178	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73343030	73343030	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	12	414	1	ENST00000377767.4:c.1776A>T	p.Glu592Asp	p.E592D	ENST00000377767	NM_014953.3	592	gaA/gaT	14/21	1	2	FACETS	0.93	0.659	1	0.93	0.659	1	CLONAL	1	FALSE	1	0.222475137410903	2		415	116	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655480	67655480	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	18	595	0	ENST00000264010.4:c.1343G>T	p.Arg448Leu	p.R448L	ENST00000264010	NM_006565.3	448	cGa/cTa	7/12	1	2	FACETS	0.843	0.637	1	0.843	0.637	1	CLONAL	1	FALSE	1	0.222475137410903	2		595	192	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805398	46805399	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0050023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	38	1330	0	ENST00000290295.7:c.557dup	p.Glu187ArgfsTer23	p.E187Rfs*23	ENST00000290295	NM_006361.5	186	gga/ggGa	1/2	0.140682798814405	1	FACETS	0.606	0.5	0.724	0.606	0.5	0.724	SUBCLONAL	1	FALSE	0	0.222475137410903	1		1330	501	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291542	15291542	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1242208956	NA	P-0050023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	53	1259	0	ENST00000263388.2:c.3092G>T	p.Arg1031Leu	p.R1031L	ENST00000263388	NM_000435.2	1031	cGc/cTc	19/33	0.140682798814405	1	FACETS	0.796	0.679	0.924	0.796	0.679	0.924	CLONAL	1	FALSE	0	0.222475137410903	1		1259	532	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860887	45860887	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0050023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	78	1190	0	ENST00000391945.4:c.1307+1G>A		p.X436_splice	ENST00000391945	NM_000400.3	436			0.140682798814405	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	FALSE	0	0.222475137410903	1		1190	567	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281745	46281745	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	48	952	0	ENST00000371998.3:c.4192A>G	p.Ser1398Gly	p.S1398G	ENST00000371998		1398	Agc/Ggc	22/23	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	FALSE	1	0.222475137410903	2		952	407	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162176	47162176	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	26	649	0	ENST00000409792.3:c.3950G>T	p.Gly1317Val	p.G1317V	ENST00000409792	NM_014159.6	1317	gGg/gTg	3/21	1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	FALSE	1	0.222475137410903	2		649	216	SUCCESS
ATR	545	MSKCC	GRCh37	3	142172026	142172026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	26	678	0	ENST00000350721.4:c.7705G>A	p.Val2569Met	p.V2569M	ENST00000350721	NM_001184.3	2569	Gtg/Atg	46/47	1	2	FACETS	0.892	0.709	1	0.892	0.709	1	CLONAL	1	FALSE	1	0.222475137410903	2		678	262	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715464	117715464	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	10	574	2	ENST00000368508.3:c.1025G>T	p.Gly342Val	p.G342V	ENST00000368508	NM_002944.2	342	gGa/gTa	10/43	1	2	FACETS	0.642	0.436	0.898	0.642	0.436	0.898	SUBCLONAL	1	FALSE	1	0.222475137410903	2		576	140	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0050086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	262	827	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.220274268184022	3	FACETS	0.911	0.854	0.968			1	CLONAL	2	TRUE	NA	0.347473859939192	3		827	972	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099878	27099890	+	frameshift_variant	Frame_Shift_Del	DEL	AACGGCGGGATGG	AACGGCGGGATGG	-	novel	NA	P-0050086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	120	676	0	ENST00000324856.7:c.3757_3769del	p.Asn1253ValfsTer12	p.N1253Vfs*12	ENST00000324856	NM_006015.4	1253	AACGGCGGGATGGgt/gt	15/20	0.223130503503056	3	FACETS	0.875	0.79	0.966	0.438	0.395	0.483	CLONAL	1	TRUE	1	0.347473859939192	3		676	926	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133800	55133800	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	57	554	0	ENST00000257290.5:c.1013A>C	p.Glu338Ala	p.E338A	ENST00000257290	NM_006206.4	338	gAg/gCg	7/23	0.225254278632732	1	FACETS	0.426	0.365	0.492	0.426	0.365	0.492	SUBCLONAL	1	TRUE	0	0.347473859939192	1		554	637	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559113	29559113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781567020	NA	P-0050093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	10	249	0	ENST00000356175.3:c.3220G>A	p.Glu1074Lys	p.E1074K	ENST00000356175	NM_000267.3	1074	Gaa/Aaa	25/57	1	2	FACETS	0.352	0.239	0.492	0.352	0.239	0.492	SUBCLONAL	1	FALSE	1	0.427147865922144	2		249	133	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188258	10188258	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs869025646	NA	P-0050093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	66	678	0	ENST00000256474.2:c.402del	p.Glu134AspfsTer25	p.E134Dfs*25	ENST00000256474	NM_000551.3	134	gAa/ga	2/3	0.427147865922144	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	0	0.427147865922144	1		678	207	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933240	49933240	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143096514	NA	P-0050232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	114	1060	1	ENST00000296474.3:c.2870C>T	p.Thr957Met	p.T957M	ENST00000296474	NM_002447.2	957	aCg/aTg	12/20	0.218295264394068	5	FACETS	1	0.972	1	0.769	0.702	0.836	INDETERMINATE	2	TRUE	2	0.669593847558227	5		1061	296	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030952	36030952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	110	1005	2	ENST00000358208.4:c.1231G>A	p.Ala411Thr	p.A411T	ENST00000358208		411	Gct/Act	10/12	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.669593847558227	2		1007	244	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0050451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	121	449	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.29701943619189	6	FACETS	1	0.965	1	0.75	0.681	0.822	CLONAL	2	TRUE	3	0.38	6		449	498	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	111	460	0				ENST00000310581	NM_198253.2	-/1132			0.29701943619189	5	FACETS	1	0.976	1	0.822	0.746	0.901	CLONAL	2	TRUE	2	0.38	5		460	372	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0050451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	173	699	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.291883551870813	4	FACETS	0.836	0.776	0.898	0.836	0.776	0.898	CLONAL	3	TRUE	1	0.38	4		699	501	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736346	85736346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	47	343	0	ENST00000370580.1:c.301G>A	p.Asp101Asn	p.D101N	ENST00000370580	NM_003921.4	101	Gat/Aat	2/3	0.279833842759561	3	FACETS	0.827	0.7	0.966	0.413	0.35	0.483	CLONAL	1	TRUE	1	0.38	3		343	356	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051596	30051596	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	176	353	0	ENST00000338641.4:c.530A>G	p.Tyr177Cys	p.Y177C	ENST00000338641	NM_000268.3	177	tAt/tGt	6/16	0.29701943619189	3	FACETS	0.843	0.785	0.901	0.843	0.785	0.901	CLONAL	3	TRUE	0	0.38	3		353	436	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922884	44922884	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	142	271	0	ENST00000377967.4:c.1745del	p.Ser582Ter	p.S582*	ENST00000377967	NM_021140.2	582	tCa/ta	16/29	0.29701943619189	2	FACETS	1	0.98	1			1	CLONAL	2	TRUE	NA	0.38	2		271	319	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259995	16259995	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	71	636	0	ENST00000375759.3:c.7260G>C	p.Arg2420Ser	p.R2420S	ENST00000375759	NM_015001.2	2420	agG/agC	11/15	0.279833842759561	3	FACETS	0.718	0.627	0.817	0.359	0.313	0.409	SUBCLONAL	1	TRUE	1	0.38	3		636	619	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961418	54961418	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	45	328	0	ENST00000312783.6:c.214C>G	p.Gln72Glu	p.Q72E	ENST00000312783	NM_198436.1	72	Cag/Gag	4/10	0.207094039283735	4	FACETS	0.984	0.831	1	0.492	0.415	0.577	INDETERMINATE	1	TRUE	2	0.38	4		328	332	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631640	119631640	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1371764974	NA	P-0050451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	82	302	0	ENST00000316626.5:c.626G>A	p.Arg209Gln	p.R209Q	ENST00000316626		209	cGa/cAa	6/12	0.29701943619189	6	FACETS	0.984	0.873	1	0.656	0.582	0.734	CLONAL	2	TRUE	3	0.38	6		302	386	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736487	85736490	+	missense_variant	Missense_Mutation	ONP	CTTC	CTTC	TTTT	novel	NA	P-0050451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	41	379	0	ENST00000370580.1:c.157_160delinsAAAA	p.Glu53_Glu54delinsLysLys	p.E53_E54delinsKK	ENST00000370580	NM_003921.4	53	GAAGaa/AAAAaa	2/3	0.279833842759561	3	FACETS	0.7	0.584	0.828	0.35	0.292	0.414	SUBCLONAL	1	TRUE	1	0.38	3		379	367	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0050471-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	130	641	1	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.226261825624258	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.226261825624258	1		642	910	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0050471-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	164	681	0	ENST00000269305.4:c.560-1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.188256499120161	2	FACETS	0.815	0.749	0.885	0.815	0.749	0.885	CLONAL	2	TRUE	0	0.226261825624258	2		681	889	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667552	29667552	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050471-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	91	568	0	ENST00000356175.3:c.6888G>A	p.Trp2296Ter	p.W2296*	ENST00000356175	NM_000267.3	2296	tgG/tgA	46/57	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.226261825624258	2		568	792	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750842	57750842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050471-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	47	408	0	ENST00000274289.3:c.1762G>T	p.Asp588Tyr	p.D588Y	ENST00000274289	NM_006622.3	588	Gat/Tat	13/14	1	2	FACETS	0.755	0.637	0.886	0.755	0.637	0.886	SUBCLONAL	1	TRUE	1	0.226261825624258	2		408	550	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597400	10597401	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0050471-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	127	787	1	ENST00000171111.5:c.1802_1803delinsTT	p.Arg601Leu	p.R601L	ENST00000171111	NM_203500.1	601	cGG/cTT	6/6	0.226261825624258	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.226261825624258	1		788	952	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935703	13935703	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050471-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	63	463	0	ENST00000405192.2:c.1153G>T	p.Glu385Ter	p.E385*	ENST00000405192	NM_001163147.1	385	Gag/Tag	12/12	1	2	FACETS	0.963	0.834	1	0.963	0.834	1	CLONAL	1	TRUE	1	0.226261825624258	2		463	578	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100186	27100186	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050471-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	113	572	0	ENST00000324856.7:c.3982C>T	p.Gln1328Ter	p.Q1328*	ENST00000324856	NM_006015.4	1328	Cag/Tag	16/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.226261825624258	2		572	832	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579355	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519997	NA	P-0050488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	99	680	0	ENST00000269305.4:c.332T>A	p.Leu111Gln	p.L111Q	ENST00000269305	NM_001126112.2	111	cTg/cAg	4/11	1	2	FACETS	0.659	0.588	0.735	0.659	0.588	0.735	SUBCLONAL	1	FALSE	1	0.377733497511787	2		680	795	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372007	55372007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	39	426	0	ENST00000297316.4:c.697G>A	p.Asp233Asn	p.D233N	ENST00000297316	NM_022454.3	233	Gac/Aac	2/2	0.377733497511787	3	FACETS	0.363	0.3	0.433	0.181	0.15	0.217	SUBCLONAL	1	FALSE	1	0.377733497511787	3		426	677	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983995	2983995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	45	684	1	ENST00000396946.4:c.535C>T	p.Arg179Trp	p.R179W	ENST00000396946	NM_032415.4	179	Cgg/Tgg	5/25	1	2	FACETS	0.307	0.257	0.363	0.307	0.257	0.363	SUBCLONAL	1	FALSE	1	0.377733497511787	2		685	776	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338650	70338650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	59	570	1	ENST00000374080.3:c.46C>T	p.Arg16Trp	p.R16W	ENST00000374080		16	Cgg/Tgg	1/45	1	2	FACETS	0.508	0.437	0.586	0.508	0.437	0.586	SUBCLONAL	1	FALSE	1	0.377733497511787	2		571	615	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178129262	178129262	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	29	365	0	ENST00000397062.3:c.43C>G	p.Gln15Glu	p.Q15E	ENST00000397062	NM_006164.4	15	Cag/Gag	1/5	1	2	FACETS	0.442	0.355	0.541	0.442	0.355	0.541	SUBCLONAL	1	FALSE	1	0.377733497511787	2		365	347	SUCCESS
APC	324	MSKCC	GRCh37	5	112174770	112174771	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	18	294	0	ENST00000257430.4:c.3482dup	p.Asn1161LysfsTer3	p.N1161Kfs*3	ENST00000257430	NM_000038.5	1160	aca/acAa	16/16	1	2	FACETS	0.311	0.234	0.403	0.311	0.234	0.403	SUBCLONAL	1	FALSE	1	0.377733497511787	2		294	306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0050581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	752	972	1	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.521978547405499	2		973	1340	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610505	10610505	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	620	900	0	ENST00000171111.5:c.205G>T	p.Glu69Ter	p.E69*	ENST00000171111	NM_203500.1	69	Gag/Tag	2/6	0.521978547405499	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.521978547405499	2		900	1161	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233137	66233137	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	117	453	0	ENST00000273854.3:c.1862G>T	p.Cys621Phe	p.C621F	ENST00000273854	NM_004439.5	621	tGt/tTt	10/18	0.510802081934378	4	FACETS	0.817	0.736	0.902			1	CLONAL	1	TRUE	NA	0.521978547405499	4		453	835	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247576	123247576	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	101	625	0	ENST00000358487.5:c.1915G>T	p.Val639Leu	p.V639L	ENST00000358487	NM_000141.4	639	Gtg/Ttg	14/18	0.283274596132019	1	FACETS	0.445	0.398	0.495	0.445	0.398	0.495	INDETERMINATE	1	TRUE	0	0.521978547405499	1		625	642	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199465	16199465	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	76	463	1	ENST00000375759.3:c.238G>A	p.Glu80Lys	p.E80K	ENST00000375759	NM_015001.2	80	Gaa/Aaa	2/15	0.227714442091318	1	FACETS	0.385	0.338	0.435	0.385	0.338	0.435	INDETERMINATE	1	TRUE	0	0.521978547405499	1		464	559	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154365	2154365	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	169	1115	0	ENST00000434045.2:c.563C>A	p.Ala188Asp	p.A188D	ENST00000434045	NM_001127598.1	188	gCc/gAc	5/5	0.250296504496489	2	FACETS	0.491	0.45	0.534	0.245	0.225	0.267	INDETERMINATE	1	TRUE	0	0.521978547405499	2		1115	1319	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456396	32456396	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	139	808	0	ENST00000332351.3:c.496G>T	p.Gly166Cys	p.G166C	ENST00000332351	NM_024426.4	166	Ggc/Tgc	1/10	0.250296504496489	2	FACETS	0.55	0.5	0.603	0.275	0.25	0.302	INDETERMINATE	1	TRUE	0	0.521978547405499	2		808	968	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492796	56492824	+	frameshift_variant	Frame_Shift_Del	DEL	ATAATAGCTTTCTGTTCTGCTGATCTTTC	ATAATAGCTTTCTGTTCTGCTGATCTTTC	-	novel	NA	P-0050581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	113	659	0	ENST00000407977.2:c.115_143del	p.Glu39GlnfsTer26	p.E39Qfs*26	ENST00000407977		39	GAAAGATCAGCAGAACAGAAAGCTATTATc/c	2/10	0.521978547405499	3	FACETS	0.509	0.457	0.564	0.254	0.228	0.282	SUBCLONAL	1	TRUE	1	0.521978547405499	3		659	1073	SUCCESS
REL	5966	MSKCC	GRCh37	2	61128213	61128213	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	162	205	1	ENST00000295025.8:c.389T>A	p.Phe130Tyr	p.F130Y	ENST00000295025	NM_002908.2	130	tTc/tAc	4/11	0.420383115851163	4	FACETS	0.845	0.78	0.912	0.845	0.78	0.912	CLONAL	2	TRUE	2	0.521978547405499	4		206	559	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0050660-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	24	1087	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		1087	599	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	168	460	0				ENST00000310581	NM_198253.2	-/1132			0.157233562210974	3	FACETS	0.766	0.715	0.817	0.766	0.715	0.817	INDETERMINATE	2	TRUE	1	0.86595377618645	3		460	363	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0050768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	245	1087	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.175207408526132	2	FACETS	1	0.986	1	0.561	0.531	0.592	INDETERMINATE	1	TRUE	0	0.86595377618645	2		1087	504	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179165	123179166	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGGATT	novel	NA	P-0050768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	69	243	0	ENST00000218089.9:c.615_620dup	p.Gly206_Leu207dup	p.G206_L207dup	ENST00000218089	NM_001042749.1	206	aca/acAGGATTa	8/35	1	1	FACETS	0.326	0.287	0.368	0.326	0.287	0.368	SUBCLONAL	1	TRUE	0	0.86595377618645	1		243	277	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	81	380	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.114658053227	4	FACETS	0.872	0.771	0.98	0.872	0.771	0.98	INDETERMINATE	2	TRUE	2	0.241686329633485	4		380	477	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	84	446	0	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	0.221138687210536	3	FACETS	1	0.965	1	0.623	0.551	0.701	CLONAL	1	TRUE	1	0.241686329633485	3		446	625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587781525	NA	P-0050804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	169	549	0	ENST00000269305.4:c.842A>G	p.Asp281Gly	p.D281G	ENST00000269305	NM_001126112.2	281	gAc/gGc	8/11	0.16983331154103	2	FACETS	0.93	0.857	1	0.93	0.857	1	CLONAL	2	TRUE	0	0.241686329633485	2		549	752	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245372	153245372	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	43	393	0	ENST00000281708.4:c.1819del	p.Asp607IlefsTer21	p.D607Ifs*21	ENST00000281708	NM_033632.3	607	Gat/at	11/12	0.221138687210536	3	FACETS	0.75	0.627	0.886	0.375	0.313	0.443	SUBCLONAL	1	TRUE	1	0.241686329633485	3		393	532	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0050804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	83	193	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.241686329633485	3	FACETS	1	0.936	1	1	0.936	1	CLONAL	3	TRUE	0	0.241686329633485	3		193	242	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317907	8317907	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	38	296	0	ENST00000356435.5:c.5706G>T	p.Glu1902Asp	p.E1902D	ENST00000356435		1902	gaG/gaT	35/35	0.196689751021801	2	FACETS	0.883	0.732	1	0.442	0.366	0.526	CLONAL	1	TRUE	0	0.241686329633485	2		296	356	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674313	117674313	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	117	418	0	ENST00000368508.3:c.4161C>A	p.Ser1387Arg	p.S1387R	ENST00000368508	NM_002944.2	1387	agC/agA	26/43	1	2	FACETS	0.965	0.883	1	0.965	0.883	1	CLONAL	1	TRUE	1	0.797732885115117	2		418	304	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131411	202131411	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs777784105	NA	P-0050862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	40	526	0	ENST00000358485.4:c.379C>T	p.Arg127Ter	p.R127*	ENST00000358485	NM_001080125.1	127	Cga/Tga	2/9	0.414953490162674	1	FACETS	0.372	0.309	0.441	0.372	0.309	0.441	SUBCLONAL	1	TRUE	0	0.414953490162674	1		526	411	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861563	152861563	+	synonymous_variant	Silent	SNP	G	G	A	rs139660436	NA	P-0050862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	155	870	0	ENST00000406277.2:c.189C>T	p.Asp63=	p.D63=	ENST00000406277	NM_152274.4	63	gaC/gaT	4/7	0.414953490162674		FACETS		0.774	0.916				CLONAL	1	TRUE	0	0.414953490162674	1		870	702	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919710	50919710	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs761160001	NA	P-0050862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	234	1000	0	ENST00000440232.2:c.2878C>A	p.Gln960Lys	p.Q960K	ENST00000440232	NM_002691.3	960	Cag/Aag	23/27	0.414953490162674	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.414953490162674	1		1000	811	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157711	106157711	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	44	268	0	ENST00000380013.4:c.2612A>C	p.Asn871Thr	p.N871T	ENST00000380013	NM_001127208.2	871	aAt/aCt	3/11	1	2	FACETS	0.744	0.628	0.871	0.744	0.628	0.871	SUBCLONAL	1	TRUE	1	0.414953490162674	2		268	285	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93636954	93636955	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0050862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	75	342	0	ENST00000375746.1:c.1009dup	p.Gln337ProfsTer45	p.Q337Pfs*45	ENST00000375746	NM_001174167.1	335	ggc/ggCc	9/14	1	2	FACETS	0.803	0.706	0.907	0.803	0.706	0.907	CLONAL	1	TRUE	1	0.414953490162674	2		342	450	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649631	48649631	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs782474159	NA	P-0050866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	76	593	0	ENST00000376670.3:c.115G>C	p.Glu39Gln	p.E39Q	ENST00000376670	NM_002049.3	39	Gag/Cag	2/6	0.105491284417069	3	FACETS	0.57	0.498	0.647	0.285	0.249	0.324	INDETERMINATE	1	TRUE	1	0.306000556791877	3		593	1005	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399237	139399237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764006572	NA	P-0050866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	81	552	1	ENST00000277541.6:c.4906G>A	p.Glu1636Lys	p.E1636K	ENST00000277541	NM_017617.3	1636	Gag/Aag	26/34	1	2	FACETS	0.663	0.583	0.748	0.663	0.583	0.748	SUBCLONAL	1	TRUE	1	0.306000556791877	2		553	799	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324058	123324058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs938460066	NA	P-0050866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	78	435	0	ENST00000358487.5:c.412G>A	p.Asp138Asn	p.D138N	ENST00000358487	NM_000141.4	138	Gat/Aat	4/18	0.245759012366559	2	FACETS	0.744	0.654	0.842	0.372	0.327	0.421	SUBCLONAL	1	TRUE	0	0.306000556791877	2		435	685	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917021	50917021	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	79	527	0	ENST00000440232.2:c.2273C>G	p.Ser758Cys	p.S758C	ENST00000440232	NM_002691.3	758	tCc/tGc	19/27	0.243692234440801	3	FACETS	0.719	0.631	0.813	0.36	0.315	0.407	SUBCLONAL	1	TRUE	1	0.306000556791877	3		527	828	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0050928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	285	706	1	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.387054525225636	2	FACETS	0.901	0.854	0.949	0.901	0.854	0.949	CLONAL	2	TRUE	0	0.487164034993005	2		707	649	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0050928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	207	464	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.487164034993005	4	FACETS	0.922	0.866	0.978			1	CLONAL	3	TRUE	NA	0.487164034993005	4		464	457	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974695	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691187	NA	P-0050928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	193	546	0	ENST00000304494.5:c.132del	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	taC/ta	1/3	0.477526162655198	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.487164034993005	1		546	508	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144847	47144847	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	74	505	0	ENST00000409792.3:c.4906G>T	p.Glu1636Ter	p.E1636*	ENST00000409792	NM_014159.6	1636	Gaa/Taa	7/21	0.487164034993005	3	FACETS	0.843	0.741	0.953	0.422	0.37	0.477	CLONAL	1	TRUE	1	0.487164034993005	3		505	448	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045710	47045710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782812073	NA	P-0050928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	230	1183	0	ENST00000377604.3:c.2591G>A	p.Arg864Gln	p.R864Q	ENST00000377604	NM_001204468.1	864	cGg/cAg	23/24	1	2	FACETS	0.974	0.909	1	0.974	0.909	1	CLONAL	1	TRUE	1	0.487164034993005	2		1183	969	SUCCESS
BTK	695	MSKCC	GRCh37	X	100614287	100614287	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	131	561	0	ENST00000308731.7:c.888G>T	p.Lys296Asn	p.K296N	ENST00000308731	NM_000061.2	296	aaG/aaT	10/19	1	2	FACETS	0.992	0.905	1	0.992	0.905	1	CLONAL	1	TRUE	1	0.487164034993005	2		561	542	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0050950-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	64	640	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.290554986754561	1	FACETS	0.75	0.653	0.855	0.75	0.653	0.855	SUBCLONAL	1	TRUE	0	0.360422912080321	1		640	388	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0050950-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	88	405	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	0.360422912080321	3	FACETS	1	0.98	1	0.748	0.668	0.834	CLONAL	1	TRUE	1	0.360422912080321	3		405	385	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	89	460	0				ENST00000310581	NM_198253.2	-/1132			0.634079837655218	3	FACETS	0.931	0.831	1	0.466	0.415	0.519	CLONAL	1	TRUE	1	0.636122435926677	3		460	396	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0050955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	345	1049	1	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.636122435926677	2		1050	1013	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937104	39937104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	98	830	3	ENST00000378444.4:c.79G>A	p.Glu27Lys	p.E27K	ENST00000378444	NM_001123385.1	27	Gaa/Aaa	2/15	0.398769217556624	1	FACETS	0.271	0.241	0.303	0.271	0.241	0.303	SUBCLONAL	1	TRUE	0	0.636122435926677	1		833	775	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481418	140481418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913349	NA	P-0050955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	145	276	0	ENST00000288602.6:c.1390G>A	p.Gly464Arg	p.G464R	ENST00000288602	NM_004333.4	464	Gga/Aga	11/18	1	2	FACETS	0.923	0.848	1	0.923	0.848	1	CLONAL	1	TRUE	1	0.636122435926677	2		276	494	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106917	27106917	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	252	672	1	ENST00000324856.7:c.6532del	p.Asp2178ThrfsTer22	p.D2178Tfs*22	ENST00000324856	NM_006015.4	2176	caG/ca	20/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.636122435926677	2		673	770	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010560	48010560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	212	594	1	ENST00000234420.5:c.188C>T	p.Ser63Phe	p.S63F	ENST00000234420	NM_000179.2	63	tCc/tTc	1/10	0.634079837655218	3	FACETS	1	0.983	1	0.581	0.541	0.622	CLONAL	1	TRUE	1	0.636122435926677	3		595	756	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325403	1325403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1398846596	NA	P-0050955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	199	634	0	ENST00000400841.2:c.272G>A	p.Arg91Gln	p.R91Q	ENST00000400841		91	cGa/cAa	3/6	0.398769217556624	1	FACETS	0.776	0.724	0.828	0.776	0.724	0.828	SUBCLONAL	1	TRUE	0	0.636122435926677	1		634	550	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265455	198265455	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	142	168	0	ENST00000335508.6:c.2702A>G	p.Gln901Arg	p.Q901R	ENST00000335508	NM_012433.2	901	cAa/cGa	18/25	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.636122435926677	2		168	444	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375647	118375660	+	frameshift_variant	Frame_Shift_Del	DEL	TCAGTAGAGCAAGG	TCAGTAGAGCAAGG	-	novel	NA	P-0050955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	185	467	0	ENST00000534358.1:c.9043_9056del	p.Val3015TrpfsTer8	p.V3015Wfs*8	ENST00000534358	NM_005933.3	3014	TCAGTAGAGCAAGGt/t	27/36	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.636122435926677	2		467	557	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336266	73336266	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	92	122	0	ENST00000377767.4:c.2137A>T	p.Ile713Phe	p.I713F	ENST00000377767	NM_014953.3	713	Att/Ttt	17/21	1	2	FACETS	0.997	0.898	1	0.997	0.898	1	CLONAL	1	TRUE	1	0.636122435926677	2		122	290	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988654	41988654	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	194	372	0	ENST00000219905.7:c.1446G>C	p.Lys482Asn	p.K482N	ENST00000219905	NM_001164273.1	482	aaG/aaC	3/24	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.636122435926677	2		372	601	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124204	2124204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45517231	NA	P-0050955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	238	860	0	ENST00000219476.3:c.2359G>A	p.Glu787Lys	p.E787K	ENST00000219476	NM_000548.3	787	Gag/Aag	22/42	NA	2	FACETS	0.896	0.839	0.955			1	INDETERMINATE	1	TRUE	NA	0.636122435926677	2		860	835	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662456	67662456	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0050955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	258	639	0	ENST00000264010.4:c.1701+1G>T		p.X567_splice	ENST00000264010	NM_006565.3	567			1	2	FACETS	0.978	0.919	1	0.978	0.919	1	CLONAL	1	TRUE	1	0.636122435926677	2		639	829	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448381	56448381	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	53	920	0	ENST00000407977.2:c.266del	p.Tyr89SerfsTer69	p.Y89Sfs*69	ENST00000407977		89	tAc/tc	3/10	1	2	FACETS	0.16	0.135	0.187	0.16	0.135	0.187	SUBCLONAL	1	TRUE	1	0.636122435926677	2		920	1044	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856355	45856355	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	289	967	0	ENST00000391945.4:c.1817A>C	p.Glu606Ala	p.E606A	ENST00000391945	NM_000400.3	606	gAg/gCg	19/23	1	2	FACETS	0.943	0.888	0.998	0.943	0.888	0.998	CLONAL	1	TRUE	1	0.636122435926677	2		967	964	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569760	41569760	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	115	268	0	ENST00000263253.7:c.4751T>C	p.Leu1584Pro	p.L1584P	ENST00000263253	NM_001429.3	1584	cTa/cCa	29/31	1	2	FACETS	0.949	0.863	1	0.949	0.863	1	CLONAL	1	TRUE	1	0.636122435926677	2		268	381	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162104	47162104	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	132	324	1	ENST00000409792.3:c.4022G>A	p.Trp1341Ter	p.W1341*	ENST00000409792	NM_014159.6	1341	tGg/tAg	3/21	1	2	FACETS	0.893	0.816	0.972	0.893	0.816	0.972	CLONAL	1	TRUE	1	0.636122435926677	2		325	465	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504024	186504024	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	134	158	0	ENST00000323963.5:c.589A>T	p.Ile197Phe	p.I197F	ENST00000323963		197	Atc/Ttc	6/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.636122435926677	2		158	374	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247197	153247205	+	inframe_deletion	In_Frame_Del	DEL	GTGTAGACA	GTGTAGACA	-	novel	NA	P-0050955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	196	294	0	ENST00000281708.4:c.1597_1605del	p.Cys533_His535del	p.C533_H535del	ENST00000281708	NM_033632.3	533	TGTCTACAC/-	10/12	0.124330308112154	4	FACETS	0.888	0.827	0.949	0.888	0.827	0.949	INDETERMINATE	2	TRUE	2	0.636122435926677	4		294	568	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247241	153247256	+	frameshift_variant	Frame_Shift_Del	DEL	AATCATATGCTCCACT	AATCATATGCTCCACT	-	novel	NA	P-0050955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	146	346	0	ENST00000281708.4:c.1546_1561del	p.Ser516LeufsTer3	p.S516Lfs*3	ENST00000281708	NM_033632.3	516	AGTGGAGCATATGATTtt/tt	10/12	0.124330308112154	4	FACETS	1	0.975	1	0.582	0.533	0.634	INDETERMINATE	1	TRUE	2	0.636122435926677	4		346	645	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624394	140624395	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0050955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	73	246	1	ENST00000288602.6:c.109_110delinsAT	p.Ser37Met	p.S37M	ENST00000288602	NM_004333.4	37	TCg/ATg	1/18	1	2	FACETS	0.937	0.831	1	0.937	0.831	1	CLONAL	1	TRUE	1	0.636122435926677	2		247	245	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970951	21970969	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCCCGCAGCCGCGCGCA	CCCCCCGCAGCCGCGCGCA	-	novel	NA	P-0050955-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	350	845	0	ENST00000304494.5:c.389_407del	p.Leu130ProfsTer10	p.L130Pfs*10	ENST00000304494	NM_000077.4	130	cTGCGCGCGGCTGCGGGGGGc/cc	2/3	0.636122435926677	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.636122435926677	1		845	681	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0051012-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	19	414	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.17395305101937	4	FACETS	0.87	0.665	1	0.435	0.332	0.554	INDETERMINATE	1	TRUE	2	0.359839011924177	4		414	165	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828483	72828483	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051012-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	21	741	0	ENST00000268489.5:c.8098C>A	p.Gln2700Lys	p.Q2700K	ENST00000268489	NM_006885.3	2700	Cag/Aag	9/10	0.359839011924177	1	FACETS	0.474	0.366	0.598	0.474	0.366	0.598	SUBCLONAL	1	TRUE	0	0.359839011924177	1		741	202	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0051046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	20	322	0	ENST00000349496.5:c.101G>A	p.Gly34Glu	p.G34E	ENST00000349496	NM_001904.3	34	gGa/gAa	3/15	0.688729237344877	4	FACETS	0.766	0.606	0.94	0.766	0.606	0.94	CLONAL	2	TRUE	2	0.688729237344877	4		322	64	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0051055-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	196	512	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.174688090855124	4	FACETS	0.926	0.86	0.994	0.926	0.86	0.994	INDETERMINATE	2	TRUE	2	0.398508180118899	4		512	743	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051055-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	136	740	2	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.398508180118899	1	FACETS	0.798	0.727	0.872	0.798	0.727	0.872	SUBCLONAL	1	TRUE	0	0.398508180118899	1		742	685	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0051055-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	40	368	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.407	0.338	0.484	0.407	0.338	0.484	SUBCLONAL	1	TRUE	1	0.398508180118899	2		368	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0051055-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	48	558	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.398508180118899	1	FACETS	0.253	0.213	0.297	0.253	0.213	0.297	SUBCLONAL	1	TRUE	0	0.398508180118899	1		558	763	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191118	185191118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564401067	NA	P-0051055-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	166	585	0	ENST00000265026.3:c.1999G>A	p.Ala667Thr	p.A667T	ENST00000265026	NM_004721.4	667	Gcc/Acc	11/14	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.398508180118899	2		585	788	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336064	73336064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051055-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	65	254	0	ENST00000377767.4:c.2339G>A	p.Arg780Lys	p.R780K	ENST00000377767	NM_014953.3	780	aGa/aAa	17/21	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.398508180118899	2		254	308	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868268	37868268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768206712	NA	P-0051055-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	72	825	1	ENST00000269571.5:c.989G>A	p.Arg330Gln	p.R330Q	ENST00000269571		330	cGg/cAg	8/27	0.174688090855124	4	FACETS	0.407	0.354	0.464	0.203	0.177	0.233	INDETERMINATE	1	TRUE	2	0.398508180118899	4		826	1242	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577265	64577266	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0051055-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	319	841	0	ENST00000312049.6:c.315_316dup	p.Tyr106SerfsTer14	p.Y106Sfs*14	ENST00000312049	NM_130799.2	106	tat/tCTat	2/10	NA	2	FACETS	0.838	0.793	0.884			1	INDETERMINATE	2	TRUE	NA	0.398508180118899	2		841	955	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0051096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	388	825	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.219235708165512	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	4	TRUE	0	0.219235708165512	4		826	1014	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749206	43749206	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	57	215	0	ENST00000382044.4:c.1600G>T	p.Glu534Ter	p.E534*	ENST00000382044	NM_001141980.1	534	Gag/Tag	12/28	0.219235708165512	3	FACETS	0.804	0.688	0.93	0.402	0.344	0.465	CLONAL	1	TRUE	1	0.219235708165512	3		215	718	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637598	52637601	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	novel	NA	P-0051127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	68	413	0	ENST00000394830.3:c.2715_2718del	p.Glu908AsnfsTer6	p.E908Nfs*6	ENST00000394830	NM_018313.4	905	gaGAGA/ga	18/30	0.3993248761426	2	FACETS	0.873	0.774	0.976	0.873	0.774	0.976	CLONAL	2	FALSE	0	0.3993248761426	2		413	195	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436489	110436489	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774109455	NA	P-0051127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	62	780	1	ENST00000375856.3:c.1912G>A	p.Gly638Ser	p.G638S	ENST00000375856	NM_003749.2	638	Ggc/Agc	1/2	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	1	0.3993248761426	2		781	263	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988320	41988320	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0051127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	56	504	0	ENST00000219905.7:c.1112T>G	p.Leu371Ter	p.L371*	ENST00000219905	NM_001164273.1	371	tTa/tGa	3/24	0.126598273675009	0	FACETS	0.688	0.595	0.786			1	INDETERMINATE	1	FALSE	0	0.3993248761426	0		504	245	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143008	47143008	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	77	463	0	ENST00000409792.3:c.4955C>T	p.Thr1652Ile	p.T1652I	ENST00000409792	NM_014159.6	1652	aCc/aTc	8/21	0.3993248761426	2	FACETS	0.901	0.805	1	0.901	0.805	1	CLONAL	2	FALSE	0	0.3993248761426	2		463	214	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391112	89391112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1211409809	NA	P-0051127-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	65	564	0	ENST00000336596.2:c.1178C>T	p.Thr393Met	p.T393M	ENST00000336596	NM_005233.5	393	aCg/aTg	5/17	0.3993248761426	2	FACETS	0.987	0.861	1	0.493	0.43	0.56	CLONAL	1	FALSE	0	0.3993248761426	2		564	330	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051166	13051166	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051171-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	157	435	1	ENST00000316448.5:c.602A>G	p.Asp201Gly	p.D201G	ENST00000316448	NM_004343.3	201	gAc/gGc	5/9	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.565417565102634	2		436	552	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069420	30069420	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0051171-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	178	508	1	ENST00000338641.4:c.1285A>T	p.Lys429Ter	p.K429*	ENST00000338641	NM_000268.3	429	Aag/Tag	12/16	0.565417565102634	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.565417565102634	1		509	362	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441984	52441984	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051171-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	112	352	0	ENST00000460680.1:c.365del	p.Phe122SerfsTer65	p.F122Sfs*65	ENST00000460680	NM_004656.3	122	tTc/tc	5/17	0.565417565102634	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.565417565102634	1		352	265	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549150	21549150	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051171-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	49	538	0	ENST00000382592.4:c.3126C>A	p.Phe1042Leu	p.F1042L	ENST00000382592	NM_014572.2	1042	ttC/ttA	8/8	0.565417565102634	1	FACETS	0.256	0.216	0.299	0.256	0.216	0.299	SUBCLONAL	1	TRUE	0	0.565417565102634	1		538	486	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428159	47428159	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051171-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	70	781	0	ENST00000377045.4:c.1119G>C	p.Met373Ile	p.M373I	ENST00000377045	NM_001654.4	373	atG/atC	11/16	0.167844456572678	0	FACETS	0.267	0.232	0.305			1	INDETERMINATE	1	TRUE	0	0.324009230043949	0		781	1094	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339201	65339201	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747503301	NA	P-0051171-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	37	411	0	ENST00000342505.4:c.335A>G	p.Tyr112Cys	p.Y112C	ENST00000342505	NM_002227.2	112	tAt/tGt	5/25	0.324009230043949	1	FACETS	0.369	0.304	0.443	0.369	0.304	0.443	SUBCLONAL	1	TRUE	0	0.324009230043949	1		411	518	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051166	13051166	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051171-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	156	435	1	ENST00000316448.5:c.602A>G	p.Asp201Gly	p.D201G	ENST00000316448	NM_004343.3	201	gAc/gGc	5/9	1	2	FACETS	0.929	0.85	1	0.929	0.85	1	CLONAL	1	TRUE	1	0.324009230043949	2		436	1036	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069420	30069420	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0051171-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	186	508	1	ENST00000338641.4:c.1285A>T	p.Lys429Ter	p.K429*	ENST00000338641	NM_000268.3	429	Aag/Tag	12/16	0.324009230043949	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.324009230043949	1		509	850	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441984	52441984	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051171-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	136	352	0	ENST00000460680.1:c.365del	p.Phe122SerfsTer65	p.F122Sfs*65	ENST00000460680	NM_004656.3	122	tTc/tc	5/17	0.321903691084306	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.324009230043949	1		352	657	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637690	52637690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239654517	NA	P-0051252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	14	459	0	ENST00000394830.3:c.2626C>T	p.Arg876Cys	p.R876C	ENST00000394830	NM_018313.4	876	Cgt/Tgt	18/30	0.194640520606895	1	FACETS	0.642	0.465	0.854	0.642	0.465	0.854	SUBCLONAL	1	TRUE	0	0.218376502190398	1		459	178	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17947999	17947999	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	52	861	0	ENST00000458235.1:c.1725G>C	p.Leu575Phe	p.L575F	ENST00000458235	NM_000215.3	575	ttG/ttC	13/24	1	2	FACETS	0.909	0.774	1	0.909	0.774	1	CLONAL	1	TRUE	1	0.218376502190398	2		861	524	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183746	10183746	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	44	919	0	ENST00000256474.2:c.217del	p.Gln73ArgfsTer86	p.Q73Rfs*86	ENST00000256474	NM_000551.3	72	tCc/tc	1/3	0.194640520606895	1	FACETS	0.923	0.776	1	0.923	0.776	1	CLONAL	1	TRUE	0	0.218376502190398	1		919	389	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442591	52442591	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	54	450	0	ENST00000460680.1:c.154T>G	p.Trp52Gly	p.W52G	ENST00000460680	NM_004656.3	52	Tgg/Ggg	4/17	0.194640520606895	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.218376502190398	1		450	365	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133471	55133472	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	novel	NA	P-0051252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	27	471	0	ENST00000257290.5:c.775_776delinsTT	p.Thr259Leu	p.T259L	ENST00000257290	NM_006206.4	259	ACa/TTa	6/23	1	2	FACETS	0.727	0.579	0.896	0.727	0.579	0.896	SUBCLONAL	1	TRUE	1	0.218376502190398	2		471	340	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858168	27858168	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	29	491	0	ENST00000359303.2:c.403del	p.Arg135GlufsTer?	p.R135Efs*?	ENST00000359303	NM_003535.2	135	Cga/ga	1/1	0.215450659093722	5	FACETS	0.966	0.776	1	0.322	0.258	0.394	CLONAL	1	TRUE	2	0.218376502190398	5		491	365	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188081	151188081	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	30	383	0	ENST00000262187.5:c.72T>G	p.Ile24Met	p.I24M	ENST00000262187	NM_005614.3	24	atT/atG	2/8	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.218376502190398	2		383	232	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231142	53231142	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	44	259	0	ENST00000375401.3:c.1760del	p.Asn587ThrfsTer72	p.N587Tfs*72	ENST00000375401	NM_004187.3	587	aAc/ac	13/26	1	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.218376502190398	1		259	249	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11293533	11293556	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAAAATTAATGCCTAGAGAAAGAA	CAAAATTAATGCCTAGAGAAAGAA	-	novel	NA	P-0051252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	11	428	0	ENST00000361445.4:c.2332-12_2343del		p.X778_splice	ENST00000361445	NM_004958.3	778		15/58	1	2	FACETS	0.466	0.322	0.646	0.466	0.322	0.646	SUBCLONAL	1	TRUE	1	0.218376502190398	2		428	216	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051301-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	74	460	0				ENST00000310581	NM_198253.2	-/1132			0.31015999237161	1	FACETS	0.983	0.877	1	1	0.984	1	CLONAL	2	FALSE	0	0.31015999237161	1		460	205	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0051301-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	171	920	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	0.31015999237161	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	0	0.31015999237161	1		920	627	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	35	380	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.497	0.409	0.596	0.497	0.409	0.596	SUBCLONAL	1	TRUE	1	0.456927121416507	2		380	308	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	40	1142	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.276	0.229	0.329	0.276	0.229	0.329	SUBCLONAL	1	TRUE	1	0.456927121416507	2		1146	634	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258978	16258978	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	42	416	0	ENST00000375759.3:c.6245del	p.Asn2082ThrfsTer4	p.N2082Tfs*4	ENST00000375759	NM_015001.2	2081	cgA/cg	11/15	1	2	FACETS	0.294	0.244	0.349	0.294	0.244	0.349	SUBCLONAL	1	TRUE	1	0.456927121416507	2		416	626	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100989	27100989	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs868656622	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	29	489	0	ENST00000324856.7:c.4271A>G	p.Gln1424Arg	p.Q1424R	ENST00000324856	NM_006015.4	1424	cAg/cGg	18/20	1	2	FACETS	0.242	0.193	0.297	0.242	0.193	0.297	SUBCLONAL	1	TRUE	1	0.456927121416507	2		489	525	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	79	540	1	ENST00000324856.7:c.4555del	p.Gln1519ArgfsTer8	p.Q1519Rfs*8	ENST00000324856	NM_006015.4	1517	gCc/gc	18/20	1	2	FACETS	0.547	0.481	0.618	0.547	0.481	0.618	SUBCLONAL	1	TRUE	1	0.456927121416507	2		541	632	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105892	27105892	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	51	397	0	ENST00000324856.7:c.5503C>T	p.Gln1835Ter	p.Q1835*	ENST00000324856	NM_006015.4	1835	Cag/Tag	20/20	1	2	FACETS	0.371	0.315	0.433	0.371	0.315	0.433	SUBCLONAL	1	TRUE	1	0.456927121416507	2		397	601	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938219	36938219	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	53	652	0	ENST00000361632.4:c.742T>A	p.Cys248Ser	p.C248S	ENST00000361632		248	Tgc/Agc	6/16	1	2	FACETS	0.332	0.282	0.386	0.332	0.282	0.386	SUBCLONAL	1	TRUE	1	0.456927121416507	2		652	699	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330549	65330549	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	31	333	0	ENST00000342505.4:c.1097T>G	p.Phe366Cys	p.F366C	ENST00000342505	NM_002227.2	366	tTt/tGt	8/25	1	2	FACETS	0.322	0.26	0.392	0.322	0.26	0.392	SUBCLONAL	1	TRUE	1	0.456927121416507	2		333	422	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483203	120483204	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	28	395	0	ENST00000256646.2:c.3157dup	p.Leu1053ProfsTer21	p.L1053Pfs*21	ENST00000256646	NM_024408.3	1053	ctg/cCtg	19/34	1	2	FACETS	0.233	0.186	0.288	0.233	0.186	0.288	SUBCLONAL	1	TRUE	1	0.456927121416507	2		395	525	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484269	120484269	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	29	409	0	ENST00000256646.2:c.2861T>C	p.Leu954Pro	p.L954P	ENST00000256646	NM_024408.3	954	cTg/cCg	18/34	1	2	FACETS	0.238	0.19	0.293	0.238	0.19	0.293	SUBCLONAL	1	TRUE	1	0.456927121416507	2		409	533	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176104223	176104223	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	17	229	0	ENST00000367669.3:c.892-1G>A		p.X298_splice	ENST00000367669	NM_022457.5	298			0.456927121416507	3	FACETS	0.367	0.274	0.477	0.184	0.137	0.239	SUBCLONAL	1	TRUE	1	0.456927121416507	3		229	249	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099341	193099341	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	24	206	0	ENST00000367435.3:c.275A>C	p.Lys92Thr	p.K92T	ENST00000367435	NM_024529.4	92	aAa/aCa	3/17	0.456927121416507	3	FACETS	0.365	0.285	0.456	0.182	0.142	0.228	SUBCLONAL	1	TRUE	1	0.456927121416507	3		206	354	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100301	8100301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	45	659	0	ENST00000346208.3:c.275G>A	p.Gly92Glu	p.G92E	ENST00000346208		92	gGa/gAa	3/6	0.428081934100145	3	FACETS	0.278	0.233	0.329	0.139	0.116	0.165	SUBCLONAL	1	TRUE	1	0.456927121416507	3		659	869	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610030	43610030	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	46	565	0	ENST00000355710.3:c.1982A>G	p.His661Arg	p.H661R	ENST00000355710	NM_020975.4	661	cAc/cGc	11/20	0.428081934100145	3	FACETS	0.286	0.24	0.337	0.143	0.12	0.169	SUBCLONAL	1	TRUE	1	0.456927121416507	3		565	865	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333413	70333413	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs778059839	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	39	422	0	ENST00000373644.4:c.1318A>T	p.Ile440Phe	p.I440F	ENST00000373644	NM_030625.2	440	Att/Ttt	2/12	0.428081934100145	3	FACETS	0.291	0.24	0.348	0.145	0.12	0.174	SUBCLONAL	1	TRUE	1	0.456927121416507	3		422	721	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404564	70404564	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	21	314	0	ENST00000373644.4:c.2081del	p.Asn694MetfsTer2	p.N694Mfs*2	ENST00000373644	NM_030625.2	693	gAa/ga	4/12	0.428081934100145	3	FACETS	0.301	0.231	0.383	0.151	0.115	0.192	SUBCLONAL	1	TRUE	1	0.456927121416507	3		314	375	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692961	89692961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060500122	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	133	337	0	ENST00000371953.3:c.445C>T	p.Gln149Ter	p.Q149*	ENST00000371953	NM_000314.4	149	Caa/Taa	5/9	0.428081934100145	3	FACETS	0.889	0.816	0.965	0.889	0.816	0.965	CLONAL	2	TRUE	1	0.456927121416507	3		337	402	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132834	64132834	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752611628	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	43	523	2	ENST00000334205.4:c.968G>A	p.Arg323His	p.R323H	ENST00000334205	NM_003942.2	323	cGc/cAc	9/17	1	2	FACETS	0.276	0.23	0.327	0.276	0.23	0.327	SUBCLONAL	1	TRUE	1	0.456927121416507	2		525	683	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940153	71940153	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs780137670	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	37	561	0	ENST00000298229.2:c.538A>G	p.Thr180Ala	p.T180A	ENST00000298229	NM_001567.3	180	Acc/Gcc	5/28	1	2	FACETS	0.223	0.183	0.269	0.223	0.183	0.269	SUBCLONAL	1	TRUE	1	0.456927121416507	2		561	725	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941164	71941164	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	60	557	0	ENST00000298229.2:c.940-1G>T		p.X314_splice	ENST00000298229	NM_001567.3	314			1	2	FACETS	0.406	0.349	0.468	0.406	0.349	0.468	SUBCLONAL	1	TRUE	1	0.456927121416507	2		557	647	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941316	71941316	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	48	553	0	ENST00000298229.2:c.1090+1G>T		p.X364_splice	ENST00000298229	NM_001567.3	364			1	2	FACETS	0.333	0.281	0.391	0.333	0.281	0.391	SUBCLONAL	1	TRUE	1	0.456927121416507	2		553	631	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204759	94204759	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	15	239	0	ENST00000323929.3:c.826C>A	p.Pro276Thr	p.P276T	ENST00000323929	NM_005591.3	276	Cca/Aca	8/20	1	2	FACETS	0.277	0.202	0.367	0.277	0.202	0.367	SUBCLONAL	1	TRUE	1	0.456927121416507	2		239	237	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216566	108216566	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs876658958	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	13	218	0	ENST00000278616.4:c.8515T>A	p.Phe2839Ile	p.F2839I	ENST00000278616	NM_000051.3	2839	Ttc/Atc	58/63	1	2	FACETS	0.236	0.168	0.319	0.236	0.168	0.319	SUBCLONAL	1	TRUE	1	0.456927121416507	2		218	241	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375659	118375659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	21	348	0	ENST00000534358.1:c.9052G>A	p.Gly3018Ser	p.G3018S	ENST00000534358	NM_005933.3	3018	Ggt/Agt	27/36	1	2	FACETS	0.222	0.17	0.283	0.222	0.17	0.283	SUBCLONAL	1	TRUE	1	0.456927121416507	2		348	414	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376961	118376961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	21	320	0	ENST00000534358.1:c.10354C>T	p.His3452Tyr	p.H3452Y	ENST00000534358	NM_005933.3	3452	Cac/Tac	27/36	1	2	FACETS	0.219	0.168	0.279	0.219	0.168	0.279	SUBCLONAL	1	TRUE	1	0.456927121416507	2		320	420	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416792	416792	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	24	336	0	ENST00000399788.2:c.3758C>A	p.Ala1253Asp	p.A1253D	ENST00000399788	NM_001042603.1	1253	gCt/gAt	23/28	1	2	FACETS	0.224	0.175	0.28	0.224	0.175	0.28	SUBCLONAL	1	TRUE	1	0.456927121416507	2		336	470	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644461	18644461	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	17	312	0	ENST00000266497.5:c.2639C>A	p.Pro880His	p.P880H	ENST00000266497		880	cCt/cAt	18/31	1	2	FACETS	0.351	0.262	0.456	0.351	0.262	0.456	SUBCLONAL	1	TRUE	1	0.456927121416507	2		312	212	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444933	49444933	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767415197	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	50	443	2	ENST00000301067.7:c.2533del	p.Arg845GlyfsTer85	p.R845Gfs*85	ENST00000301067	NM_003482.3	845	Cgg/gg	10/54	1	2	FACETS	0.353	0.299	0.413	0.353	0.299	0.413	SUBCLONAL	1	TRUE	1	0.456927121416507	2		445	620	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864459	57864459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	37	545	1	ENST00000228682.2:c.1936G>A	p.Ala646Thr	p.A646T	ENST00000228682	NM_005269.2	646	Gct/Act	12/12	1	2	FACETS	0.251	0.206	0.302	0.251	0.206	0.302	SUBCLONAL	1	TRUE	1	0.456927121416507	2		546	645	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434343	121434343	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	31	528	0	ENST00000257555.6:c.1108-1G>T		p.X370_splice	ENST00000257555		370			1	2	FACETS	0.232	0.186	0.283	0.232	0.186	0.283	SUBCLONAL	1	TRUE	1	0.456927121416507	2		528	586	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209294	133209294	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1284062861	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	56	550	0	ENST00000320574.5:c.6092G>T	p.Ser2031Ile	p.S2031I	ENST00000320574	NM_006231.2	2031	aGc/aTc	44/49	1	2	FACETS	0.344	0.294	0.399	0.344	0.294	0.399	SUBCLONAL	1	TRUE	1	0.456927121416507	2		550	712	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880834	28880834	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	31	420	0	ENST00000282397.4:c.3796A>G	p.Lys1266Glu	p.K1266E	ENST00000282397	NM_002019.4	1266	Aag/Gag	29/30	1	2	FACETS	0.232	0.187	0.284	0.232	0.187	0.284	SUBCLONAL	1	TRUE	1	0.456927121416507	2		420	584	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906602	32906602	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	17	227	0	ENST00000380152.3:c.987G>T	p.Arg329Ser	p.R329S	ENST00000380152		329	agG/agT	10/27	1	2	FACETS	0.457	0.342	0.59	0.457	0.342	0.59	SUBCLONAL	1	TRUE	1	0.456927121416507	2		227	163	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912531	32912531	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358653	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	12	267	0	ENST00000380152.3:c.4039G>A	p.Val1347Ile	p.V1347I	ENST00000380152		1347	Gtt/Att	11/27	1	2	FACETS	0.245	0.172	0.335	0.245	0.172	0.335	SUBCLONAL	1	TRUE	1	0.456927121416507	2		267	214	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913236	32913236	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	27	350	0	ENST00000380152.3:c.4744A>G	p.Thr1582Ala	p.T1582A	ENST00000380152		1582	Acc/Gcc	11/27	1	2	FACETS	0.291	0.231	0.36	0.291	0.231	0.36	SUBCLONAL	1	TRUE	1	0.456927121416507	2		350	406	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953632	32953633	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359732	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	19	259	0	ENST00000380152.3:c.8940dup	p.Glu2981ArgfsTer37	p.E2981Rfs*37	ENST00000380152		2978	tca/tcAa	22/27	1	2	FACETS	0.355	0.27	0.455	0.355	0.27	0.455	SUBCLONAL	1	TRUE	1	0.456927121416507	2		259	234	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916849	48916849	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs775559506	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	14	194	0	ENST00000267163.4:c.379A>G	p.Ser127Gly	p.S127G	ENST00000267163	NM_000321.2	127	Agt/Ggt	3/27	1	2	FACETS	0.328	0.237	0.437	0.328	0.237	0.437	SUBCLONAL	1	TRUE	1	0.456927121416507	2		194	187	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504617	103504617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	13	186	0	ENST00000355739.4:c.238G>A	p.Ala80Thr	p.A80T	ENST00000355739	NM_000123.3	80	Gct/Act	2/15	1	2	FACETS	0.257	0.183	0.348	0.257	0.183	0.348	SUBCLONAL	1	TRUE	1	0.456927121416507	2		186	221	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527918	103527918	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	20	260	0	ENST00000355739.4:c.3226T>C	p.Ser1076Pro	p.S1076P	ENST00000355739	NM_000123.3	1076	Tca/Cca	15/15	1	2	FACETS	0.274	0.209	0.35	0.274	0.209	0.35	SUBCLONAL	1	TRUE	1	0.456927121416507	2		260	319	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40684200	40684201	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	22	309	0	ENST00000249776.8:c.803dup	p.Gln269AlafsTer29	p.Q269Afs*29	ENST00000249776	NM_033286.3	266	-/A	8/9	1	2	FACETS	0.249	0.193	0.315	0.249	0.193	0.315	SUBCLONAL	1	TRUE	1	0.456927121416507	2		309	386	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74000682	74000682	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	35	486	0	ENST00000318443.5:c.1372C>T	p.Gln458Ter	p.Q458*	ENST00000318443	NM_001024736.1	458	Cag/Tag	7/10	1	2	FACETS	0.25	0.204	0.302	0.25	0.204	0.302	SUBCLONAL	1	TRUE	1	0.456927121416507	2		486	612	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669529	88669529	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	26	335	0	ENST00000360948.2:c.1369G>T	p.Gly457Cys	p.G457C	ENST00000360948	NM_001012338.2	457	Ggt/Tgt	12/19	1	2	FACETS	0.231	0.182	0.287	0.231	0.182	0.287	SUBCLONAL	1	TRUE	1	0.456927121416507	2		335	493	SUCCESS
BLM	641	MSKCC	GRCh37	15	91328288	91328288	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	29	361	0	ENST00000355112.3:c.2800T>C	p.Trp934Arg	p.W934R	ENST00000355112	NM_000057.2	934	Tgg/Cgg	14/22	1	2	FACETS	0.246	0.197	0.303	0.246	0.197	0.303	SUBCLONAL	1	TRUE	1	0.456927121416507	2		361	515	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396354	396354	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	41	589	1	ENST00000262320.3:c.672G>T	p.Gln224His	p.Q224H	ENST00000262320	NM_003502.3	224	caG/caT	2/11	1	2	FACETS	0.27	0.224	0.322	0.27	0.224	0.322	SUBCLONAL	1	TRUE	1	0.456927121416507	2		590	664	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900938	3900938	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	31	437	0	ENST00000262367.5:c.158T>C	p.Leu53Pro	p.L53P	ENST00000262367	NM_004380.2	53	cTt/cCt	2/31	1	2	FACETS	0.225	0.181	0.274	0.225	0.181	0.274	SUBCLONAL	1	TRUE	1	0.456927121416507	2		437	604	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024631	14024631	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	17	330	0	ENST00000311895.7:c.857A>G	p.Gln286Arg	p.Q286R	ENST00000311895	NM_005236.2	286	cAg/cGg	5/11	1	2	FACETS	0.242	0.18	0.315	0.242	0.18	0.315	SUBCLONAL	1	TRUE	1	0.456927121416507	2		330	308	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56872862	56872862	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	23	249	0	ENST00000308159.5:c.2019-2A>C		p.X673_splice	ENST00000308159	NM_014669.4	673			NA	2	FACETS	0.299	0.233	0.375			1	INDETERMINATE	1	TRUE	NA	0.456927121416507	2		249	337	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662285	67662286	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	89	334	0	ENST00000264010.4:c.1532dup	p.Met512HisfsTer19	p.M512Hfs*19	ENST00000264010	NM_006565.3	511	atc/aTtc	9/12	NA	2	FACETS	0.854	0.761	0.953			1	INDETERMINATE	1	TRUE	NA	0.456927121416507	2		334	456	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847261	68847261	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs201135424	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	32	391	0	ENST00000261769.5:c.1183A>G	p.Thr395Ala	p.T395A	ENST00000261769	NM_004360.3	395	Aca/Gca	9/16	NA	2	FACETS	0.236	0.191	0.287			1	INDETERMINATE	1	TRUE	NA	0.456927121416507	2		391	594	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849545	68849545	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	43	514	0	ENST00000261769.5:c.1452del	p.Ile485SerfsTer37	p.I485Sfs*37	ENST00000261769	NM_004360.3	483	gCc/gc	10/16	NA	2	FACETS	0.232	0.193	0.275			1	INDETERMINATE	1	TRUE	NA	0.456927121416507	2		514	813	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822586	72822586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	55	451	1	ENST00000268489.5:c.9589del	p.Gln3197SerfsTer44	p.Q3197Sfs*44	ENST00000268489	NM_006885.3	3197	Cag/ag	10/10	NA	2	FACETS	0.378	0.323	0.438			1	INDETERMINATE	1	TRUE	NA	0.456927121416507	2		452	637	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348325	89348325	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1383324924	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	46	527	0	ENST00000301030.4:c.4625A>G	p.Lys1542Arg	p.K1542R	ENST00000301030	NM_001256183.1	1542	aAg/aGg	9/13	1	2	FACETS	0.259	0.217	0.306	0.259	0.217	0.306	SUBCLONAL	1	TRUE	1	0.456927121416507	2		527	777	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349519	89349519	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs137894790	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	43	502	1	ENST00000301030.4:c.3431C>A	p.Pro1144Gln	p.P1144Q	ENST00000301030	NM_001256183.1	1144	cCg/cAg	9/13	1	2	FACETS	0.275	0.229	0.326	0.275	0.229	0.326	SUBCLONAL	1	TRUE	1	0.456927121416507	2		503	685	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349894	89349894	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	54	569	0	ENST00000301030.4:c.3056G>T	p.Arg1019Met	p.R1019M	ENST00000301030	NM_001256183.1	1019	aGg/aTg	9/13	1	2	FACETS	0.302	0.257	0.351	0.302	0.257	0.351	SUBCLONAL	1	TRUE	1	0.456927121416507	2		569	783	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	154	646	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.957	0.878	1	0.957	0.878	1	CLONAL	1	TRUE	1	0.456927121416507	2		646	704	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989483	7989483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769533529	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	59	527	0	ENST00000319144.4:c.203G>A	p.Arg68His	p.R68H	ENST00000319144	NM_001139.2	68	cGc/cAc	2/15	1	2	FACETS	0.434	0.373	0.5	0.434	0.373	0.5	SUBCLONAL	1	TRUE	1	0.456927121416507	2		527	595	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652995	29652996	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1135402867	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	25	294	0	ENST00000356175.3:c.4935dup	p.Pro1646SerfsTer15	p.P1646Sfs*15	ENST00000356175	NM_000267.3	1644	gtt/gTtt	36/57	1	2	FACETS	0.249	0.196	0.311	0.249	0.196	0.311	SUBCLONAL	1	TRUE	1	0.456927121416507	2		294	439	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618343	37618343	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1477267149	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	81	276	0	ENST00000447079.4:c.19C>G	p.His7Asp	p.H7D	ENST00000447079	NM_015083.1	7	Cat/Gat	1/14	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.456927121416507	2		276	299	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650902	37650902	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	29	370	0	ENST00000447079.4:c.2374A>G	p.Ile792Val	p.I792V	ENST00000447079	NM_015083.1	792	Att/Gtt	5/14	1	2	FACETS	0.246	0.197	0.303	0.246	0.197	0.303	SUBCLONAL	1	TRUE	1	0.456927121416507	2		370	515	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37865696	37865696	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	37	372	0	ENST00000269571.5:c.565T>C	p.Ser189Pro	p.S189P	ENST00000269571		189	Tct/Cct	4/27	1	2	FACETS	0.282	0.232	0.339	0.282	0.232	0.339	SUBCLONAL	1	TRUE	1	0.456927121416507	2		372	574	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244600	41244600	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	22	368	1	ENST00000357654.3:c.2948T>C	p.Leu983Pro	p.L983P	ENST00000357654	NM_007294.3	983	cTt/cCt	10/23	1	2	FACETS	0.31	0.24	0.391	0.31	0.24	0.391	SUBCLONAL	1	TRUE	1	0.456927121416507	2		369	311	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245282	41245282	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1064795091	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	57	465	0	ENST00000357654.3:c.2266A>G	p.Arg756Gly	p.R756G	ENST00000357654	NM_007294.3	756	Agg/Ggg	10/23	1	2	FACETS	0.537	0.461	0.619	0.537	0.461	0.619	SUBCLONAL	1	TRUE	1	0.456927121416507	2		465	465	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55334876	55334876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	24	309	0	ENST00000284073.2:c.153G>A	p.Met51Ile	p.M51I	ENST00000284073	NM_138962.2	51	atG/atA	3/14	1	2	FACETS	0.25	0.195	0.313	0.25	0.195	0.313	SUBCLONAL	1	TRUE	1	0.456927121416507	2		309	420	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760967	59760967	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	21	347	2	ENST00000259008.2:c.3440del	p.Asn1147MetfsTer3	p.N1147Mfs*3	ENST00000259008	NM_032043.2	1147	aAt/at	20/20	1	2	FACETS	0.351	0.27	0.444	0.351	0.27	0.444	SUBCLONAL	1	TRUE	1	0.456927121416507	2		349	262	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533592	63533592	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	65	616	0	ENST00000307078.5:c.1562A>G	p.His521Arg	p.H521R	ENST00000307078	NM_004655.3	521	cAc/cGc	6/11	1	2	FACETS	0.434	0.376	0.498	0.434	0.376	0.498	SUBCLONAL	1	TRUE	1	0.456927121416507	2		616	655	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119780	70119780	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	31	425	0	ENST00000245479.2:c.782A>G	p.Glu261Gly	p.E261G	ENST00000245479	NM_000346.3	261	gAg/gGg	3/3	1	2	FACETS	0.262	0.211	0.32	0.262	0.211	0.32	SUBCLONAL	1	TRUE	1	0.456927121416507	2		425	518	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858937	78858937	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	32	397	0	ENST00000306801.3:c.1972A>G	p.Met658Val	p.M658V	ENST00000306801	NM_020761.2	658	Atg/Gtg	17/34	1	2	FACETS	0.268	0.217	0.326	0.268	0.217	0.326	SUBCLONAL	1	TRUE	1	0.456927121416507	2		397	523	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60795926	60795926	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	45	416	0	ENST00000333681.4:c.652A>G	p.Lys218Glu	p.K218E	ENST00000333681		218	Aag/Gag	3/3	1	2	FACETS	0.306	0.256	0.361	0.306	0.256	0.361	SUBCLONAL	1	TRUE	1	0.456927121416507	2		416	644	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250740	10250740	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	39	524	0	ENST00000340748.4:c.3740T>C	p.Leu1247Pro	p.L1247P	ENST00000340748		1247	cTg/cCg	32/40	1	2	FACETS	0.229	0.189	0.274	0.229	0.189	0.274	SUBCLONAL	1	TRUE	1	0.456927121416507	2		524	746	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610271	10610271	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	44	630	1	ENST00000171111.5:c.439A>G	p.Met147Val	p.M147V	ENST00000171111	NM_203500.1	147	Atg/Gtg	2/6	1	2	FACETS	0.266	0.222	0.315	0.266	0.222	0.315	SUBCLONAL	1	TRUE	1	0.456927121416507	2		631	723	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610600	10610600	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1465714155	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	38	566	0	ENST00000171111.5:c.110A>G	p.Glu37Gly	p.E37G	ENST00000171111	NM_203500.1	37	gAg/gGg	2/6	1	2	FACETS	0.255	0.21	0.306	0.255	0.21	0.306	SUBCLONAL	1	TRUE	1	0.456927121416507	2		566	652	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953310	17953310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs918213968	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	54	577	2	ENST00000458235.1:c.676G>A	p.Ala226Thr	p.A226T	ENST00000458235	NM_000215.3	226	Gcc/Acc	6/24	1	2	FACETS	0.39	0.333	0.453	0.39	0.333	0.453	SUBCLONAL	1	TRUE	1	0.456927121416507	2		579	606	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271894	18271894	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1442806847	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	33	478	0	ENST00000222254.8:c.497A>T	p.Asp166Val	p.D166V	ENST00000222254	NM_005027.3	166	gAc/gTc	5/16	1	2	FACETS	0.245	0.199	0.298	0.245	0.199	0.298	SUBCLONAL	1	TRUE	1	0.456927121416507	2		478	589	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219683	36219683	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	36	536	0	ENST00000222270.7:c.4581del	p.Asn1529MetfsTer117	p.N1529Mfs*117	ENST00000222270	NM_014727.1	1527	cTt/ct	20/37	1	2	FACETS	0.255	0.209	0.307	0.255	0.209	0.307	SUBCLONAL	1	TRUE	1	0.456927121416507	2		536	618	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	36	571	0	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	0.227	0.186	0.274	0.227	0.186	0.274	SUBCLONAL	1	TRUE	1	0.456927121416507	2		571	694	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753518	42753518	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	67	663	0	ENST00000222329.4:c.746C>A	p.Pro249His	p.P249H	ENST00000222329	NM_006494.2	249	cCt/cAt	4/4	1	2	FACETS	0.417	0.362	0.477	0.417	0.362	0.477	SUBCLONAL	1	TRUE	1	0.456927121416507	2		663	703	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139954	50139954	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs774660560	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	61	626	0	ENST00000246792.3:c.375G>T	p.Gln125His	p.Q125H	ENST00000246792	NM_006270.3	125	caG/caT	4/6	1	2	FACETS	0.361	0.31	0.416	0.361	0.31	0.416	SUBCLONAL	1	TRUE	1	0.456927121416507	2		626	740	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905981	50905981	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555790304	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	68	624	0	ENST00000440232.2:c.953A>G	p.Glu318Gly	p.E318G	ENST00000440232	NM_002691.3	318	gAg/gGg	8/27	1	2	FACETS	0.43	0.374	0.491	0.43	0.374	0.491	SUBCLONAL	1	TRUE	1	0.456927121416507	2		624	692	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085999	16085999	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	41	397	0	ENST00000281043.3:c.1175A>G	p.Gln392Arg	p.Q392R	ENST00000281043	NM_005378.4	392	cAg/cGg	3/3	0.456927121416507	2	FACETS	0.276	0.229	0.328	0.138	0.114	0.164	SUBCLONAL	1	TRUE	0	0.456927121416507	2		397	650	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086118	16086118	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	33	417	0	ENST00000281043.3:c.1294T>C	p.Ser432Pro	p.S432P	ENST00000281043	NM_005378.4	432	Tcc/Ccc	3/3	0.456927121416507	2	FACETS	0.227	0.184	0.276	0.114	0.092	0.138	SUBCLONAL	1	TRUE	0	0.456927121416507	2		417	636	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966042	25966042	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	32	486	0	ENST00000435504.4:c.3164A>G	p.His1055Arg	p.H1055R	ENST00000435504		1055	cAc/cGc	13/13	0.456927121416507	2	FACETS	0.223	0.18	0.272	0.112	0.09	0.136	SUBCLONAL	1	TRUE	0	0.456927121416507	2		486	627	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456438	29456438	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs753584062	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	40	459	0	ENST00000389048.3:c.2480T>C	p.Val827Ala	p.V827A	ENST00000389048	NM_004304.4	827	gTa/gCa	14/29	0.456927121416507	2	FACETS	0.282	0.233	0.336	0.141	0.116	0.168	SUBCLONAL	1	TRUE	0	0.456927121416507	2		459	621	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224473	39224473	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	21	322	0	ENST00000402219.2:c.2885G>T	p.Arg962Met	p.R962M	ENST00000402219	NM_005633.3	962	aGg/aTg	18/23	0.456927121416507	2	FACETS	0.236	0.181	0.301	0.118	0.09	0.151	SUBCLONAL	1	TRUE	0	0.456927121416507	2		322	389	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030615	48030615	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	30	391	0	ENST00000234420.5:c.3229C>A	p.Pro1077Thr	p.P1077T	ENST00000234420	NM_000179.2	1077	Cca/Aca	5/10	0.456927121416507	2	FACETS	0.234	0.187	0.286	0.117	0.093	0.143	SUBCLONAL	1	TRUE	0	0.456927121416507	2		391	562	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711100	61711100	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	21	308	0	ENST00000401558.2:c.2649A>T	p.Lys883Asn	p.K883N	ENST00000401558	NM_003400.3	883	aaA/aaT	21/25	0.456927121416507	2	FACETS	0.304	0.234	0.386	0.152	0.117	0.193	SUBCLONAL	1	TRUE	0	0.456927121416507	2		308	302	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095902	178095902	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	36	337	0	ENST00000397062.3:c.1429C>A	p.Pro477Thr	p.P477T	ENST00000397062	NM_006164.4	477	Cct/Act	5/5	0.456927121416507	2	FACETS	0.452	0.372	0.54	0.226	0.186	0.27	SUBCLONAL	1	TRUE	0	0.456927121416507	2		337	349	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251805	212251805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	21	307	0	ENST00000342788.4:c.3254C>T	p.Thr1085Ile	p.T1085I	ENST00000342788	NM_005235.2	1085	aCt/aTt	27/28	0.456927121416507	2	FACETS	0.247	0.19	0.314	0.124	0.095	0.157	SUBCLONAL	1	TRUE	0	0.456927121416507	2		307	372	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212522482	212522482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	17	269	0	ENST00000342788.4:c.1943C>T	p.Ala648Val	p.A648V	ENST00000342788	NM_005235.2	648	gCt/gTt	16/28	0.456927121416507	2	FACETS	0.251	0.187	0.327	0.125	0.093	0.164	SUBCLONAL	1	TRUE	0	0.456927121416507	2		269	297	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794820	242794820	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	35	446	0	ENST00000334409.5:c.389C>A	p.Pro130His	p.P130H	ENST00000334409	NM_005018.2	130	cCc/cAc	2/5	0.456927121416507	2	FACETS	0.276	0.225	0.332	0.138	0.112	0.166	SUBCLONAL	1	TRUE	0	0.456927121416507	2		446	556	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714387	40714387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1441976520	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	38	408	0	ENST00000373198.4:c.4010G>A	p.Arg1337His	p.R1337H	ENST00000373198	NM_133170.3	1337	cGc/cAc	29/32	1	2	FACETS	0.337	0.278	0.402	0.337	0.278	0.402	SUBCLONAL	1	TRUE	1	0.456927121416507	2		408	494	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326304	62326304	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	42	650	0	ENST00000360203.5:c.3320C>A	p.Pro1107Gln	p.P1107Q	ENST00000360203	NM_001283009.1	1107	cCa/cAa	32/35	1	2	FACETS	0.241	0.2	0.287	0.241	0.2	0.287	SUBCLONAL	1	TRUE	1	0.456927121416507	2		650	762	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231877	36231877	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	28	341	0	ENST00000300305.3:c.509-2A>G		p.X170_splice	ENST00000300305		170			1	2	FACETS	0.283	0.226	0.349	0.283	0.226	0.349	SUBCLONAL	1	TRUE	1	0.456927121416507	2		341	433	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130435	29130435	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779269031	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	33	515	2	ENST00000328354.6:c.275C>A	p.Pro92His	p.P92H	ENST00000328354	NM_007194.3	92	cCc/cAc	2/15	1	2	FACETS	0.228	0.185	0.277	0.228	0.185	0.277	SUBCLONAL	1	TRUE	1	0.456927121416507	2		517	634	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551064	41551064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	38	418	0	ENST00000263253.7:c.3208C>T	p.Pro1070Ser	p.P1070S	ENST00000263253	NM_001429.3	1070	Cca/Tca	17/31	1	2	FACETS	0.25	0.206	0.299	0.25	0.206	0.299	SUBCLONAL	1	TRUE	1	0.456927121416507	2		418	666	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573890	41573890	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1295897899	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	54	529	0	ENST00000263253.7:c.6175A>G	p.Arg2059Gly	p.R2059G	ENST00000263253	NM_001429.3	2059	Agg/Ggg	31/31	1	2	FACETS	0.313	0.267	0.365	0.313	0.267	0.365	SUBCLONAL	1	TRUE	1	0.456927121416507	2		529	754	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52677307	52677307	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	46	442	0	ENST00000394830.3:c.952G>T	p.Gly318Cys	p.G318C	ENST00000394830	NM_018313.4	318	Ggc/Tgc	10/30	0.428081934100145	3	FACETS	0.315	0.264	0.371	0.157	0.132	0.186	SUBCLONAL	1	TRUE	1	0.456927121416507	3		442	786	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911661	134911661	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	25	239	0	ENST00000398015.3:c.2126T>A	p.Leu709His	p.L709H	ENST00000398015	NM_004441.4	709	cTc/cAc	11/16	0.428081934100145	3	FACETS	0.354	0.278	0.44	0.177	0.139	0.22	SUBCLONAL	1	TRUE	1	0.456927121416507	3		239	380	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279172	142279172	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	21	297	0	ENST00000350721.4:c.1474G>T	p.Gly492Ter	p.G492*	ENST00000350721	NM_001184.3	492	Gga/Tga	6/47	0.428081934100145	3	FACETS	0.276	0.212	0.351	0.138	0.106	0.176	SUBCLONAL	1	TRUE	1	0.456927121416507	3		297	409	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149243894	149243894	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	47	402	0	ENST00000360632.3:c.924G>T	p.Arg308Ser	p.R308S	ENST00000360632	NM_015472.4	308	agG/agT	6/7	0.428081934100145	3	FACETS	0.362	0.304	0.425	0.181	0.152	0.213	SUBCLONAL	1	TRUE	1	0.456927121416507	3		402	699	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170002298	170002298	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	10	105	0	ENST00000295797.4:c.1117G>T	p.Gly373Trp	p.G373W	ENST00000295797	NM_002740.5	373	Ggg/Tgg	12/18	0.428081934100145	3	FACETS	0.489	0.333	0.681	0.244	0.166	0.341	SUBCLONAL	1	TRUE	1	0.456927121416507	3		105	110	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013707	170013708	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	32	286	0	ENST00000295797.4:c.1431dup	p.Gln478ThrfsTer21	p.Q478Tfs*21	ENST00000295797	NM_002740.5	476	gaa/gAaa	15/18	0.428081934100145	3	FACETS	0.46	0.374	0.558	0.23	0.187	0.279	SUBCLONAL	1	TRUE	1	0.456927121416507	3		286	374	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936096	178936096	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519940	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	16	338	1	ENST00000263967.3:c.1638G>T	p.Gln546His	p.Q546H	ENST00000263967	NM_006218.2	546	caG/caT	10/21	0.428081934100145	3	FACETS	0.26	0.191	0.342	0.13	0.095	0.171	SUBCLONAL	1	TRUE	1	0.456927121416507	3		339	331	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612243	189612243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	42	335	1	ENST00000264731.3:c.1995G>A	p.Met665Ile	p.M665I	ENST00000264731	NM_003722.4	665	atG/atA	14/14	0.428081934100145	3	FACETS	0.391	0.326	0.464	0.196	0.163	0.232	SUBCLONAL	1	TRUE	1	0.456927121416507	3		336	577	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197702	66197702	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	24	278	0	ENST00000273854.3:c.2997G>T	p.Gln999His	p.Q999H	ENST00000273854	NM_004439.5	999	caG/caT	17/18	1	2	FACETS	0.323	0.253	0.404	0.323	0.253	0.404	SUBCLONAL	1	TRUE	1	0.456927121416507	2		278	325	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264684	1264684	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	54	608	0	ENST00000310581.5:c.2678A>C	p.Glu893Ala	p.E893A	ENST00000310581	NM_198253.2	893	gAg/gCg	11/16	1	2	FACETS	0.375	0.319	0.435	0.375	0.319	0.435	SUBCLONAL	1	TRUE	1	0.456927121416507	2		608	631	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522700	67522700	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	16	233	0	ENST00000274335.5:c.202del	p.Asp68ThrfsTer7	p.D68Tfs*7	ENST00000274335		66	aGg/ag	1/15	1	2	FACETS	0.237	0.174	0.311	0.237	0.174	0.311	SUBCLONAL	1	TRUE	1	0.456927121416507	2		233	296	SUCCESS
APC	324	MSKCC	GRCh37	5	112178912	112178912	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587778033	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	16	261	0	ENST00000257430.4:c.7621A>G	p.Ile2541Val	p.I2541V	ENST00000257430	NM_000038.5	2541	Atc/Gtc	16/16	1	2	FACETS	0.255	0.188	0.334	0.255	0.188	0.334	SUBCLONAL	1	TRUE	1	0.456927121416507	2		261	275	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522696	176522696	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369266328	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	43	595	0	ENST00000292408.4:c.1793G>A	p.Arg598Gln	p.R598Q	ENST00000292408	NM_213647.1	598	cGa/cAa	13/18	1	2	FACETS	0.264	0.22	0.313	0.264	0.22	0.313	SUBCLONAL	1	TRUE	1	0.456927121416507	2		595	713	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673241	30673241	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	26	271	0	ENST00000376406.3:c.3719del	p.Pro1240LeufsTer121	p.P1240Lfs*121	ENST00000376406	NM_014641.2	1240	cCt/ct	10/15	1	2	FACETS	0.262	0.207	0.326	0.262	0.207	0.326	SUBCLONAL	1	TRUE	1	0.456927121416507	2		271	434	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120314	94120314	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	18	259	0	ENST00000369303.4:c.737C>A	p.Pro246His	p.P246H	ENST00000369303	NM_004440.3	246	cCc/cAc	3/17	1	2	FACETS	0.22	0.165	0.285	0.22	0.165	0.285	SUBCLONAL	1	TRUE	1	0.456927121416507	2		259	358	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120579	94120579	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	31	337	0	ENST00000369303.4:c.472G>T	p.Gly158Cys	p.G158C	ENST00000369303	NM_004440.3	158	Ggt/Tgt	3/17	1	2	FACETS	0.438	0.355	0.531	0.438	0.355	0.531	SUBCLONAL	1	TRUE	1	0.456927121416507	2		337	310	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149982908	149982908	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	31	339	0	ENST00000253339.5:c.3350del	p.Asn1117ThrfsTer11	p.N1117Tfs*11	ENST00000253339		1117	aAc/ac	7/7	1	2	FACETS	0.425	0.345	0.516	0.425	0.345	0.516	SUBCLONAL	1	TRUE	1	0.456927121416507	2		339	319	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001515	150001515	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs869300430	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	15	270	0	ENST00000253339.5:c.2089del	p.Arg697GlyfsTer10	p.R697Gfs*10	ENST00000253339		697	Agg/gg	4/7	1	2	FACETS	0.231	0.169	0.307	0.231	0.169	0.307	SUBCLONAL	1	TRUE	1	0.456927121416507	2		270	284	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528227	157528227	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	47	355	0	ENST00000346085.5:c.5952G>T	p.Glu1984Asp	p.E1984D	ENST00000346085	NM_020732.3	1984	gaG/gaT	20/20	1	2	FACETS	0.383	0.323	0.45	0.383	0.323	0.45	SUBCLONAL	1	TRUE	1	0.456927121416507	2		355	537	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976817	2976817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	42	525	0	ENST00000396946.4:c.1195G>A	p.Glu399Lys	p.E399K	ENST00000396946	NM_032415.4	399	Gaa/Aaa	9/25	1	2	FACETS	0.243	0.202	0.289	0.243	0.202	0.289	SUBCLONAL	1	TRUE	1	0.456927121416507	2		525	756	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739661	41739661	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	53	394	0	ENST00000242208.4:c.312G>T	p.Glu104Asp	p.E104D	ENST00000242208	NM_002192.2	104	gaG/gaT	2/3	1	2	FACETS	0.437	0.372	0.507	0.437	0.372	0.507	SUBCLONAL	1	TRUE	1	0.456927121416507	2		394	531	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462420	92462420	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	30	425	0	ENST00000265734.4:c.218A>G	p.His73Arg	p.H73R	ENST00000265734	NM_001259.6	73	cAc/cGc	2/8	1	2	FACETS	0.265	0.213	0.325	0.265	0.213	0.325	SUBCLONAL	1	TRUE	1	0.456927121416507	2		425	495	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514397	148514397	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	19	361	0	ENST00000320356.2:c.1327T>C	p.Ser443Pro	p.S443P	ENST00000320356	NM_004456.4	443	Tca/Cca	11/20	1	2	FACETS	0.252	0.191	0.324	0.252	0.191	0.324	SUBCLONAL	1	TRUE	1	0.456927121416507	2		361	330	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845989	151845989	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	30	448	0	ENST00000262189.6:c.13023del	p.Phe4342LeufsTer14	p.F4342Lfs*14	ENST00000262189	NM_170606.2	4341	ggG/gg	52/59	1	2	FACETS	0.238	0.191	0.292	0.238	0.191	0.292	SUBCLONAL	1	TRUE	1	0.456927121416507	2		448	551	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554341	141554341	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	47	569	0	ENST00000220592.5:c.1810G>T	p.Gly604Trp	p.G604W	ENST00000220592	NM_012154.3	604	Ggg/Tgg	14/19	1	2	FACETS	0.258	0.217	0.304	0.258	0.217	0.304	SUBCLONAL	1	TRUE	1	0.456927121416507	2		569	797	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742883	145742883	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	22	230	0	ENST00000428558.2:c.128G>T	p.Arg43Leu	p.R43L	ENST00000428558	NM_004260.3	43	cGg/cTg	3/22	1	2	FACETS	0.289	0.224	0.365	0.289	0.224	0.365	SUBCLONAL	1	TRUE	1	0.456927121416507	2		230	333	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341712	8341712	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	26	401	1	ENST00000356435.5:c.4928G>A	p.Gly1643Glu	p.G1643E	ENST00000356435		1643	gGa/gAa	29/35	1	2	FACETS	0.263	0.208	0.326	0.263	0.208	0.326	SUBCLONAL	1	TRUE	1	0.456927121416507	2		402	433	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006006	22006006	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749530069	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	51	557	1	ENST00000276925.6:c.397C>T	p.Arg133Cys	p.R133C	ENST00000276925	NM_004936.3	133	Cgc/Tgc	2/2	1	2	FACETS	0.279	0.237	0.327	0.279	0.237	0.327	SUBCLONAL	1	TRUE	1	0.456927121416507	2		558	799	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882061	36882061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	46	599	0	ENST00000358127.4:c.952C>T	p.His318Tyr	p.H318Y	ENST00000358127	NM_001280556.1	318	Cac/Tac	8/10	1	2	FACETS	0.264	0.222	0.312	0.264	0.222	0.312	SUBCLONAL	1	TRUE	1	0.456927121416507	2		599	762	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250533	110250533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	25	443	0	ENST00000374672.4:c.142C>T	p.Leu48Phe	p.L48F	ENST00000374672	NM_004235.4	48	Ctc/Ttc	3/5	1	2	FACETS	0.227	0.178	0.283	0.227	0.178	0.283	SUBCLONAL	1	TRUE	1	0.456927121416507	2		443	482	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932036	39932036	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	43	501	0	ENST00000378444.4:c.2563C>A	p.Leu855Met	p.L855M	ENST00000378444	NM_001123385.1	855	Ctg/Atg	4/15	1	2	FACETS	0.268	0.224	0.318	0.268	0.224	0.318	SUBCLONAL	1	TRUE	1	0.456927121416507	2		501	701	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932923	39932923	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	51	507	0	ENST00000378444.4:c.1676G>T	p.Gly559Val	p.G559V	ENST00000378444	NM_001123385.1	559	gGg/gTg	4/15	1	2	FACETS	0.376	0.319	0.438	0.376	0.319	0.438	SUBCLONAL	1	TRUE	1	0.456927121416507	2		507	594	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041200	47041200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	48	613	1	ENST00000377604.3:c.1628C>T	p.Thr543Ile	p.T543I	ENST00000377604	NM_001204468.1	543	aCc/aTc	15/24	1	2	FACETS	0.264	0.222	0.311	0.264	0.222	0.311	SUBCLONAL	1	TRUE	1	0.456927121416507	2		614	795	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649610	48649610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782698349	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	73	604	0	ENST00000376670.3:c.94G>A	p.Val32Ile	p.V32I	ENST00000376670	NM_002049.3	32	Gtt/Att	2/6	1	2	FACETS	0.453	0.395	0.514	0.453	0.395	0.514	SUBCLONAL	1	TRUE	1	0.456927121416507	2		604	706	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411338	63411338	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1233790837	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	47	573	1	ENST00000330258.3:c.1829C>T	p.Ala610Val	p.A610V	ENST00000330258	NM_152424.3	610	gCc/gTc	2/2	1	2	FACETS	0.293	0.246	0.344	0.293	0.246	0.344	SUBCLONAL	1	TRUE	1	0.456927121416507	2		574	703	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343498	70343498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	38	476	0	ENST00000374080.3:c.1672C>T	p.Leu558Phe	p.L558F	ENST00000374080		558	Ctt/Ttt	12/45	1	2	FACETS	0.245	0.201	0.293	0.245	0.201	0.293	SUBCLONAL	1	TRUE	1	0.456927121416507	2		476	680	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890105	76890105	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	24	310	0	ENST00000373344.5:c.4789G>T	p.Gly1597Cys	p.G1597C	ENST00000373344	NM_000489.3	1597	Ggc/Tgc	17/35	1	2	FACETS	0.301	0.236	0.376	0.301	0.236	0.376	SUBCLONAL	1	TRUE	1	0.456927121416507	2		310	349	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019514	123019514	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0051326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	29	260	0	ENST00000355640.3:c.2T>C	p.Met1?	p.M1?	ENST00000355640		1	aTg/aCg	2/7	1	2	FACETS	0.518	0.418	0.631	0.518	0.418	0.631	SUBCLONAL	1	TRUE	1	0.456927121416507	2		260	245	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0051369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	75	537	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.989	0.875	1	0.989	0.875	1	CLONAL	1	TRUE	1	0.516015129750756	2		537	294	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412884	49412884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	151	940	0	ENST00000418115.1:c.139G>A	p.Glu47Lys	p.E47K	ENST00000418115	NM_001664.2	47	Gag/Aag	2/5	0.224514310307502	3	FACETS	1	0.969	1	0.559	0.513	0.608	INDETERMINATE	1	TRUE	1	0.516015129750756	3		940	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	358	1097	1	ENST00000269305.4:c.313G>T	p.Gly105Cys	p.G105C	ENST00000269305	NM_001126112.2	105	Ggc/Tgc	4/11	0.43129267755462	2	FACETS	0.954	0.912	0.997	0.954	0.912	0.997	CLONAL	2	TRUE	0	0.516015129750756	2		1098	727	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792453	33792453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	36	690	0	ENST00000498907.2:c.868G>A	p.Glu290Lys	p.E290K	ENST00000498907	NM_004364.3	290	Gag/Aag	1/1	0.404584476431239	3	FACETS	0.296	0.243	0.356	0.148	0.121	0.178	SUBCLONAL	1	TRUE	1	0.516015129750756	3		690	593	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967269	134967269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749666684	NA	P-0051369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	127	854	0	ENST00000398015.3:c.2608C>T	p.Arg870Trp	p.R870W	ENST00000398015	NM_004441.4	870	Cgg/Tgg	14/16	0.181782451937915	0	FACETS	0.515	0.469	0.562			1	INDETERMINATE	1	TRUE	0	0.516015129750756	0		854	463	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923421	36923421	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	54	928	0	ENST00000358127.4:c.841C>G	p.Leu281Val	p.L281V	ENST00000358127	NM_001280556.1	281	Ctg/Gtg	7/10	0.206831005652217	0	FACETS	0.174	0.148	0.202			1	INDETERMINATE	1	TRUE	0	0.516015129750756	0		928	583	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444684	49444684	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	83	1151	0	ENST00000301067.7:c.2782C>T	p.Gln928Ter	p.Q928*	ENST00000301067	NM_003482.3	928	Cag/Tag	10/54	0.489750644600332	4	FACETS	0.531	0.468	0.6	0.266	0.234	0.3	SUBCLONAL	1	TRUE	2	0.516015129750756	4		1151	918	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448439	49448439	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	225	938	0	ENST00000301067.7:c.272G>A	p.Trp91Ter	p.W91*	ENST00000301067	NM_003482.3	91	tGg/tAg	3/54	0.489750644600332	4	FACETS	0.805	0.752	0.86	0.805	0.752	0.86	CLONAL	2	TRUE	2	0.516015129750756	4		938	821	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38942465	38942465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	47	585	0	ENST00000357387.3:c.5068G>A	p.Glu1690Lys	p.E1690K	ENST00000357387	NM_152756.3	1690	Gag/Aag	38/38	0.280410351592119	5	FACETS	0.562	0.474	0.66	0.187	0.158	0.22	INDETERMINATE	1	TRUE	2	0.516015129750756	5		585	575	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223254	5223254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1407721470	NA	P-0051369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	217	938	0	ENST00000357368.4:c.2549C>T	p.Ala850Val	p.A850V	ENST00000357368	NM_002850.3	850	gCa/gTa	18/38	0.350574369768641	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.516015129750756	1		938	599	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820720	3820720	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	224	1087	0	ENST00000262367.5:c.2731C>T	p.Gln911Ter	p.Q911*	ENST00000262367	NM_004380.2	911	Caa/Taa	14/31	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.516015129750756	2		1087	864	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805061	89805061	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587778322	NA	P-0051369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	329	934	0	ENST00000389301.3:c.4316G>C	p.Arg1439Thr	p.R1439T	ENST00000389301	NM_000135.2	1439	aGa/aCa	43/43	0.228243466607783	3	FACETS	0.946	0.898	0.995	0.631	0.598	0.663	INDETERMINATE	2	TRUE	0	0.516015129750756	3		934	848	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7168032	7168032	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	134	786	0	ENST00000302850.5:c.1557C>A	p.Tyr519Ter	p.Y519*	ENST00000302850	NM_000208.2	519	taC/taA	7/22	0.350574369768641	1	FACETS	0.653	0.596	0.713	0.653	0.596	0.713	SUBCLONAL	1	TRUE	0	0.516015129750756	1		786	590	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254594	10254594	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	207	758	0	ENST00000340748.4:c.2916C>G	p.His972Gln	p.H972Q	ENST00000340748		972	caC/caG	28/40	0.404584476431239	3	FACETS	0.797	0.744	0.852	0.797	0.744	0.852	SUBCLONAL	2	TRUE	1	0.516015129750756	3		758	633	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513680	41513680	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0051369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	340	900	0	ENST00000263253.7:c.584C>G	p.Ser195Ter	p.S195*	ENST00000263253	NM_001429.3	195	tCa/tGa	2/31	NA	2	FACETS	0.904	0.861	0.947			1	INDETERMINATE	2	TRUE	NA	0.516015129750756	2		900	729	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412903	49412903	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	166	992	0	ENST00000418115.1:c.120G>C	p.Glu40Asp	p.E40D	ENST00000418115	NM_001664.2	40	gaG/gaC	2/5	0.224514310307502	3	FACETS	1	0.976	1	0.574	0.529	0.621	INDETERMINATE	1	TRUE	1	0.516015129750756	3		992	705	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873066	134873066	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	125	874	0	ENST00000398015.3:c.1370C>A	p.Pro457Gln	p.P457Q	ENST00000398015	NM_004441.4	457	cCg/cAg	6/16	0.181782451937915	0	FACETS	0.464	0.422	0.508			1	INDETERMINATE	1	TRUE	0	0.516015129750756	0		874	505	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556674	41556674	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	50	680	0	ENST00000263253.7:c.3619G>C	p.Glu1207Gln	p.E1207Q	ENST00000263253	NM_001429.3	1207	Gag/Cag	20/31	NA	2	FACETS	0.282	0.239	0.331			1	INDETERMINATE	1	TRUE	NA	0.516015129750756	2		680	686	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946457	2946457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051369-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	92	859	0	ENST00000396946.4:c.3280G>A	p.Glu1094Lys	p.E1094K	ENST00000396946	NM_032415.4	1094	Gag/Aag	25/25	0.224514310307502	3	FACETS	0.759	0.676	0.848	0.38	0.338	0.424	INDETERMINATE	1	TRUE	1	0.516015129750756	3		859	591	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459531	50459531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051400-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	54	275	0	ENST00000331340.3:c.820C>T	p.Arg274Cys	p.R274C	ENST00000331340	NM_006060.4	274	Cgt/Tgt	7/8	1	2	FACETS	0.813	0.697	0.938	0.813	0.697	0.938	CLONAL	1	TRUE	1	0.370107564857923	2		275	359	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217650	7217653	+	frameshift_variant	Frame_Shift_Del	DEL	CTTT	CTTT	-	novel	NA	P-0051400-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	60	425	0	ENST00000380728.2:c.274_277del	p.Lys92PhefsTer16	p.K92Ffs*16	ENST00000380728		92	AAAGtt/tt	4/11	0.370107564857923	1	FACETS	0.881	0.765	1	0.881	0.765	1	CLONAL	1	TRUE	0	0.370107564857923	1		425	300	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230549	46230549	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051462-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	61	353	0	ENST00000334344.6:c.798G>A	p.Trp266Ter	p.W266*	ENST00000334344	NM_152641.2	266	tgG/tgA	8/21	0.157821364494576	4	FACETS	0.853	0.75	0.961	1	0.964	1	INDETERMINATE	3	TRUE	2	0.344547143994591	4		353	186	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0051473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	45	642	0	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	0.3	3	FACETS	0.625	0.524	0.736	0.312	0.262	0.368	SUBCLONAL	1	TRUE	1	0.29	3		642	569	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056209	26056211	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs779842031	NA	P-0051473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	82	599	0	ENST00000343677.2:c.446_448del	p.Lys149del	p.K149del	ENST00000343677	NM_005319.3	149	aAGAgc/agc	1/1	0.3	3	FACETS	0.851	0.75	0.96	0.425	0.375	0.48	CLONAL	1	TRUE	1	0.29	3		599	761	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480495	57480495	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1422801076	NA	P-0051473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	35	386	0	ENST00000371085.3:c.490G>A	p.Glu164Lys	p.E164K	ENST00000371085	NM_000516.4	164	Gaa/Aaa	6/13	1	2	FACETS	0.444	0.363	0.535	0.444	0.363	0.535	SUBCLONAL	1	TRUE	1	0.29	2		386	544	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656625	3656625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs79842542	NA	P-0051473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	100	945	0	ENST00000294008.3:c.610C>T	p.Arg204Cys	p.R204C	ENST00000294008	NM_032444.2	204	Cgc/Tgc	3/15	0.115130336416937	3	FACETS	0.925	0.825	1	0.308	0.275	0.344	INDETERMINATE	1	TRUE	0	0.29	3		945	854	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100387	27100387	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	118	654	0	ENST00000324856.7:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000324856	NM_006015.4	1367	Cag/Tag	17/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.29	2		654	573	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696462	47696462	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	133	502	0	ENST00000347630.2:c.361C>G	p.Arg121Gly	p.R121G	ENST00000347630	NM_001007230.1	121	Cgg/Ggg	6/11	0.272658587546847	2	FACETS	0.831	0.758	0.907	0.831	0.758	0.907	CLONAL	2	TRUE	0	0.29	2		502	552	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210583	5210583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253335014	NA	P-0051473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	44	799	3	ENST00000357368.4:c.5384C>T	p.Pro1795Leu	p.P1795L	ENST00000357368	NM_002850.3	1795	cCg/cTg	35/38	1	2	FACETS	0.512	0.428	0.604	0.512	0.428	0.604	SUBCLONAL	1	TRUE	1	0.29	2		802	593	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714543	52714543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	87	799	0	ENST00000322088.6:c.301G>A	p.Glu101Lys	p.E101K	ENST00000322088	NM_014225.5	101	Gag/Aag	4/15	1	2	FACETS	0.998	0.885	1	0.998	0.885	1	CLONAL	1	TRUE	1	0.29	2		799	601	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164139	32164139	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	53	890	0	ENST00000375023.3:c.5260C>T	p.Leu1754Phe	p.L1754F	ENST00000375023	NM_004557.3	1754	Ctc/Ttc	29/30	0.3	3	FACETS	0.453	0.385	0.529	0.227	0.192	0.265	SUBCLONAL	1	TRUE	1	0.29	3		890	923	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0051497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	147	740	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.285796556118896	1	FACETS	0.959	0.876	1	0.959	0.876	1	CLONAL	1	TRUE	0	0.285796556118896	1		740	919	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964419	70964419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1254551312	NA	P-0051497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	105	714	1	ENST00000276594.2:c.1609C>T	p.Arg537Trp	p.R537W	ENST00000276594	NM_024504.3	537	Cgg/Tgg	8/8	1	2	FACETS	0.941	0.843	1	0.941	0.843	1	CLONAL	1	TRUE	1	0.285796556118896	2		715	781	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880881	134880881	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	166	673	1	ENST00000398015.3:c.1444T>A	p.Ser482Thr	p.S482T	ENST00000398015	NM_004441.4	482	Tcc/Acc	7/16	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.285796556118896	2		674	836	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599333	55599333	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913682	NA	P-0051524-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	130	365	0	ENST00000288135.5:c.2459A>G	p.Asp820Gly	p.D820G	ENST00000288135	NM_000222.2	820	gAt/gGt	17/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.561072953653978	2		365	421	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051524-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	76	249	0	ENST00000256196.4:c.68G>A	p.Gly23Asp	p.G23D	ENST00000256196		23	gGc/gAc	1/6	1	2	FACETS	0.957	0.849	1	0.957	0.849	1	CLONAL	1	TRUE	1	0.561072953653978	2		249	283	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051524-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	94	378	0	ENST00000256196.4:c.68G>T	p.Gly23Val	p.G23V	ENST00000256196		23	gGc/gTc	1/6	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.561072953653978	2		378	283	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712658	43712658	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051524-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	175	723	0	ENST00000382044.4:c.4526G>A	p.Gly1509Glu	p.G1509E	ENST00000382044	NM_001141980.1	1509	gGg/gAg	21/28	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.561072953653978	2		723	583	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727447	66727449	+	inframe_deletion	In_Frame_Del	DEL	ACC	ACC	-	novel	NA	P-0051524-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	108	458	1	ENST00000307102.5:c.163_165del	p.Thr55del	p.T55del	ENST00000307102	NM_002755.3	55	ACC/-	2/11	1	2	FACETS	0.897	0.811	0.988	0.897	0.811	0.988	CLONAL	1	TRUE	1	0.561072953653978	2		459	429	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923726	39923726	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051524-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	170	337	0	ENST00000378444.4:c.3365C>A	p.Ser1122Ter	p.S1122*	ENST00000378444	NM_001123385.1	1122	tCg/tAg	7/15	1	1	FACETS	0.768	0.723	0.812	1	0.992	1	SUBCLONAL	2	TRUE	0	0.561072953653978	1		337	284	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0051557-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	120	401	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.163192048735395	5	FACETS	0.887	0.807	0.97			1	INDETERMINATE	2	FALSE	NA	0.58087412629282	5		401	436	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0051557-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	121	393	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.177765637502971	4	FACETS	0.777	0.707	0.849	0.777	0.707	0.849	INDETERMINATE	2	FALSE	2	0.58087412629282	4		393	424	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900873	3900873	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051557-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	157	703	0	ENST00000262367.5:c.223C>T	p.Arg75Ter	p.R75*	ENST00000262367	NM_004380.2	75	Cga/Tga	2/31	1	2	FACETS	0.929	0.855	1	0.929	0.855	1	CLONAL	1	FALSE	1	0.58087412629282	2		703	582	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0051557-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	243	627	0	ENST00000269305.4:c.375+1G>C		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.54727189648885	2	FACETS	0.877	0.83	0.924	0.877	0.83	0.924	CLONAL	2	FALSE	0	0.58087412629282	2		627	477	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288798	33288798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051557-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	121	561	0	ENST00000374542.5:c.754G>A	p.Val252Ile	p.V252I	ENST00000374542	NM_001141970.1	252	Gtc/Atc	3/8	0.58087412629282	3	FACETS	0.914	0.829	1	0.457	0.414	0.502	CLONAL	1	FALSE	1	0.58087412629282	3		561	588	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490980	56490980	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs931676601	NA	P-0051616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	352	704	0	ENST00000267101.3:c.2426A>G	p.Gln809Arg	p.Q809R	ENST00000267101	NM_001982.3	809	cAg/cGg	20/28	0.268899875655618	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.268899875655618	3		704	924	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0051616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	85	864	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	0.243824379478641	2	FACETS	0.664	0.586	0.748	0.332	0.293	0.374	SUBCLONAL	1	TRUE	0	0.268899875655618	2		864	952	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158417	26158417	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs368384735	NA	P-0051616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1666	113	1048	0	ENST00000289316.2:c.20C>G	p.Ser7Cys	p.S7C	ENST00000289316	NM_138720.2	7	tCt/tGt	1/2	0.268899875655618	6	FACETS	0.727	0.651	0.807	0.182	0.162	0.202	SUBCLONAL	1	TRUE	2	0.268899875655618	6		1048	1779	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562657	29562660	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs1064794276	NA	P-0051616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	161	563	0	ENST00000356175.3:c.3739_3742del	p.Phe1247IlefsTer18	p.F1247Ifs*18	ENST00000356175	NM_000267.3	1246	cTGTTt/ct	28/57	0.243824379478641	2	FACETS	0.983	0.906	1	0.983	0.906	1	CLONAL	2	TRUE	0	0.268899875655618	2		563	609	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437328	121437328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	126	1047	0	ENST00000257555.6:c.1666C>T	p.His556Tyr	p.H556Y	ENST00000257555		556	Cac/Tac	9/10	0.268899875655618	2	FACETS	0.836	0.755	0.921	0.418	0.377	0.461	CLONAL	1	TRUE	0	0.268899875655618	2		1047	1121	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553102	106553102	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs137921759	NA	P-0051616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	93	844	0	ENST00000369096.4:c.1067C>G	p.Pro356Arg	p.P356R	ENST00000369096	NM_001198.3	356	cCt/cGt	5/7	0.235634514006171	2	FACETS	0.822	0.73	0.92	0.411	0.365	0.46	CLONAL	1	TRUE	0	0.268899875655618	2		844	842	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875906	76875906	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	75	747	0	ENST00000373344.5:c.5229G>T	p.Arg1743Ser	p.R1743S	ENST00000373344	NM_000489.3	1743	agG/agT	20/35	0.129116896223987	4	FACETS	1	0.91	1	0.524	0.458	0.594	INDETERMINATE	1	TRUE	2	0.268899875655618	4		747	676	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11318641	11318641	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	52	570	0	ENST00000361445.4:c.172G>C	p.Glu58Gln	p.E58Q	ENST00000361445	NM_004958.3	58	Gag/Cag	3/58	0.243750814104214	3	FACETS	0.636	0.54	0.741	0.318	0.27	0.371	SUBCLONAL	1	TRUE	1	0.268899875655618	3		570	690	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46724393	46724393	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1176799900	NA	P-0051616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	74	732	0	ENST00000371975.4:c.246C>G	p.Phe82Leu	p.F82L	ENST00000371975	NM_003579.3	82	ttC/ttG	4/18	0.243750814104214	3	FACETS	0.745	0.651	0.847	0.373	0.325	0.424	SUBCLONAL	1	TRUE	1	0.268899875655618	3		732	838	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115575	108115575	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	57	603	0	ENST00000278616.4:c.723G>C	p.Lys241Asn	p.K241N	ENST00000278616	NM_000051.3	241	aaG/aaC	7/63	0.256263218071833	4	FACETS	0.868	0.744	1	0.217	0.186	0.251	CLONAL	1	TRUE	0	0.268899875655618	4		603	620	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019488	42019488	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	78	743	0	ENST00000219905.7:c.3541G>C	p.Glu1181Gln	p.E1181Q	ENST00000219905	NM_001164273.1	1181	Gag/Cag	10/24	1	2	FACETS	0.814	0.715	0.92	0.814	0.715	0.92	CLONAL	1	TRUE	1	0.268899875655618	2		743	713	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134376	2134376	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	220	1026	0	ENST00000219476.3:c.4153T>A	p.Ser1385Thr	p.S1385T	ENST00000219476	NM_000548.3	1385	Tcc/Acc	34/42	0.244394954021247	5	FACETS	0.865	0.803	0.929	0.576	0.535	0.619	CLONAL	2	TRUE	2	0.268899875655618	5		1026	1328	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56870557	56870557	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	79	611	2	ENST00000308159.5:c.1827C>G	p.Ile609Met	p.I609M	ENST00000308159	NM_014669.4	609	atC/atG	17/22	0.244394954021247	5	FACETS	0.906	0.795	1	0.302	0.265	0.342	CLONAL	1	TRUE	2	0.268899875655618	5		613	910	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518732	176518732	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	142	999	0	ENST00000292408.4:c.650C>A	p.Ser217Ter	p.S217*	ENST00000292408	NM_213647.1	217	tCg/tAg	6/18	0.268899875655618	3	FACETS	1	0.948	1	0.53	0.482	0.581	CLONAL	1	TRUE	1	0.268899875655618	3		999	1130	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228000	53228000	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	92	1049	0	ENST00000375401.3:c.2314A>T	p.Thr772Ser	p.T772S	ENST00000375401	NM_004187.3	772	Acc/Tcc	16/26	0.129116896223987	4	FACETS	0.73	0.646	0.819	0.365	0.323	0.41	INDETERMINATE	1	TRUE	2	0.268899875655618	4		1049	1190	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0051671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	149	374	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	1	2	FACETS	0.951	0.875	1	0.951	0.875	1	CLONAL	1	TRUE	1	0.637952613377886	2		374	491	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303204	11303204	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	230	518	0	ENST00000361445.4:c.1379G>T	p.Arg460Leu	p.R460L	ENST00000361445	NM_004958.3	460	cGa/cTa	9/58	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.637952613377886	2		518	720	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77060297	77060297	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	22	204	0	ENST00000356341.3:c.872C>T	p.Ala291Val	p.A291V	ENST00000356341	NM_002576.4	291	gCc/gTc	9/15	1	2	FACETS	0.198	0.153	0.25	0.198	0.153	0.25	SUBCLONAL	1	TRUE	1	0.637952613377886	2		204	348	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47679260	47679260	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	188	434	0	ENST00000347630.2:c.947A>T	p.Gln316Leu	p.Q316L	ENST00000347630	NM_001007230.1	316	cAg/cTg	10/11	1	2	FACETS	0.994	0.924	1	0.994	0.924	1	CLONAL	1	TRUE	1	0.637952613377886	2		434	593	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050657	30050657	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	172	330	0	ENST00000338641.4:c.459del	p.Tyr153Ter	p.Y153*	ENST00000338641	NM_000268.3	153	taC/ta	5/16	0.637952613377886	1	FACETS	0.971	0.907	1	0.971	0.907	1	CLONAL	1	TRUE	0	0.637952613377886	1		330	378	SUCCESS
AR	367	MSKCC	GRCh37	X	66931244	66931244	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	153	195	0	ENST00000374690.3:c.1886C>A	p.Ala629Asp	p.A629D	ENST00000374690	NM_000044.3	629	gCc/gAc	4/8	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.637952613377886	1		195	256	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315349	30315349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	51	366	0	ENST00000322652.5:c.1034C>T	p.Pro345Leu	p.P345L	ENST00000322652	NM_015355.2	345	cCa/cTa	10/16	0.205328678665155	3	FACETS	1	0.903	1	0.542	0.461	0.631	CLONAL	1	FALSE	1	0.214475739400397	3		366	486	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0051760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	104	414	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.618444744885599	2		414	325	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526594	31526594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	303	433	0	ENST00000344624.3:c.446C>T	p.Pro149Leu	p.P149L	ENST00000344624		149	cCc/cTc	2/33	0.618444744885599	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.618444744885599	2		433	435	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945118	151945118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774935898	NA	P-0051760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	44	477	0	ENST00000262189.6:c.2401C>T	p.Pro801Ser	p.P801S	ENST00000262189	NM_170606.2	801	Cct/Tct	14/59	1	2	FACETS	0.316	0.265	0.373	0.316	0.265	0.373	SUBCLONAL	1	TRUE	1	0.618444744885599	2		477	450	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524343	148524343	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs973062748	NA	P-0051760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	118	404	0	ENST00000320356.2:c.641C>T	p.Pro214Leu	p.P214L	ENST00000320356	NM_004456.4	214	cCa/cTa	7/20	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.618444744885599	2		404	373	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797201	45797201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529008617	NA	P-0051760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	216	924	1	ENST00000450313.1:c.1214C>T	p.Pro405Leu	p.P405L	ENST00000450313	NM_012222.2	405	cCg/cTg	13/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.618444744885599	2		925	672	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136341	2136341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771289256	NA	P-0051760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	240	846	0	ENST00000219476.3:c.4810G>A	p.Gly1604Ser	p.G1604S	ENST00000219476	NM_000548.3	1604	Ggc/Agc	37/42	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.618444744885599	2		846	725	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830226	72830226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	147	520	0	ENST00000268489.5:c.6355G>A	p.Gly2119Arg	p.G2119R	ENST00000268489	NM_006885.3	2119	Gga/Aga	9/10	0.618444744885599	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.618444744885599	1		520	313	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434903	56434903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370703233	NA	P-0051760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	242	758	0	ENST00000407977.2:c.2234C>T	p.Ser745Phe	p.S745F	ENST00000407977		745	tCt/tTt	9/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.618444744885599	2		758	727	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78617545	78617545	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	92	420	0	ENST00000306801.3:c.283C>T	p.Pro95Ser	p.P95S	ENST00000306801	NM_020761.2	95	Cct/Tct	3/34	1	2	FACETS	0.712	0.636	0.791	0.712	0.636	0.791	SUBCLONAL	1	TRUE	1	0.618444744885599	2		420	418	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78882674	78882674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	230	720	0	ENST00000306801.3:c.2465C>T	p.Pro822Leu	p.P822L	ENST00000306801	NM_020761.2	822	cCc/cTc	21/34	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.618444744885599	2		720	741	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212035	5212036	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0051760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	217	887	1	ENST00000357368.4:c.4995_4996delinsTT	p.Gln1666Ter	p.Q1666*	ENST00000357368	NM_002850.3	1665	atCCag/atTTag	32/38	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.618444744885599	2		888	695	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47604166	47604166	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	187	417	0	ENST00000263735.4:c.505G>A	p.Glu169Lys	p.E169K	ENST00000263735	NM_002354.2	169	Gag/Aag	5/9	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.618444744885599	2		417	555	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180375	38180375	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	205	874	0	ENST00000396334.3:c.223C>T	p.Arg75Trp	p.R75W	ENST00000396334	NM_002468.4	75	Cgg/Tgg	1/5	0.618444744885599	3	FACETS	0.893	0.828	0.96	0.446	0.414	0.48	CLONAL	1	TRUE	1	0.618444744885599	3		874	972	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106194018	106194018	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051760-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	86	301	0	ENST00000380013.4:c.4480T>A	p.Ser1494Thr	p.S1494T	ENST00000380013	NM_001127208.2	1494	Tca/Aca	10/11	1	2	FACETS	0.858	0.767	0.954	0.858	0.767	0.954	CLONAL	1	TRUE	1	0.618444744885599	2		301	324	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	298	417	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	0.560568800334272	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	2	0.560568800334272	4		417	678	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0051797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	468	603	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.560568800334272	2	FACETS	0.901	0.876	0.925	1	0.997	1	CLONAL	3	TRUE	0	0.560568800334272	2		603	618	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074178	8074179	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0051797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	760	440	0	ENST00000377482.5:c.480_481insCA	p.Ala161GlnfsTer15	p.A161Qfs*15	ENST00000377482	NM_018948.3	160	-/CA	4/4	0.560568800334272	7	FACETS	1	0.986	1	1	0.986	1	CLONAL	6	TRUE	1	0.560568800334272	7		440	1071	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106645	2106645	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	56	700	0	ENST00000219476.3:c.649G>A	p.Val217Ile	p.V217I	ENST00000219476	NM_000548.3	217	Gtc/Atc	8/42	0.560568800334272	4	FACETS	0.29	0.247	0.337	0.145	0.123	0.169	SUBCLONAL	1	TRUE	2	0.560568800334272	4		700	1076	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106767	2106767	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	70	693	0	ENST00000219476.3:c.771G>T	p.Trp257Cys	p.W257C	ENST00000219476	NM_000548.3	257	tgG/tgT	8/42	0.560568800334272	4	FACETS	0.333	0.289	0.381	0.167	0.144	0.191	SUBCLONAL	1	TRUE	2	0.560568800334272	4		693	1169	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721696	176721696	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	35	490	0	ENST00000439151.2:c.7327G>T	p.Asp2443Tyr	p.D2443Y	ENST00000439151	NM_022455.4	2443	Gac/Tac	23/23	0.560568800334272	3	FACETS	0.247	0.201	0.298	0.123	0.1	0.149	SUBCLONAL	1	TRUE	1	0.560568800334272	3		490	648	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38173064	38173064	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0051797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	24	302	0	ENST00000317025.8:c.1987-2A>T		p.X663_splice	ENST00000317025	NM_023034.1	663			0.560568800334272	1	FACETS	0.241	0.189	0.3	0.241	0.189	0.3	SUBCLONAL	1	TRUE	0	0.560568800334272	1		302	256	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0051815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	75	567	1	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	0.261997340420877	2	FACETS	0.984	0.88	1	1	0.979	1	CLONAL	3	TRUE	0	0.261997340420877	2		568	194	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249020	55249022	+	missense_variant	Missense_Mutation	TNP	ACG	ACG	TCA	novel	NA	P-0051815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	95	529	0	ENST00000275493.2:c.2318_2320delinsTCA	p.His773_Val774delinsLeuMet	p.H773_V774delinsLM	ENST00000275493	NM_005228.3	773	cACGtg/cTCAtg	20/28	0.261997340420877	5	FACETS	1	0.957	1	1	0.957	1	CLONAL	4	TRUE	1	0.261997340420877	5		529	231	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342833	118342833	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	53	294	0	ENST00000534358.1:c.959T>A	p.Ile320Asn	p.I320N	ENST00000534358	NM_005933.3	320	aTt/aAt	3/36	0.261997340420877	3	FACETS	0.887	0.77	1	1	0.962	1	CLONAL	3	TRUE	1	0.261997340420877	3		294	172	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934843	9934843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	41	441	0	ENST00000330684.3:c.1447G>A	p.Gly483Arg	p.G483R	ENST00000330684	NM_001134407.1	483	Ggg/Agg	6/13	0.261997340420877	5	FACETS	0.932	0.782	1	0.466	0.391	0.547	CLONAL	2	TRUE	1	0.261997340420877	5		441	234	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257860	19257860	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0051815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	50	712	0	ENST00000162023.5:c.526A>T	p.Lys176Ter	p.K176*	ENST00000162023		176	Aaa/Taa	9/13	1	2	FACETS	0.823	0.705	0.949	1	0.97	1	CLONAL	2	TRUE	1	0.261997340420877	2		712	232	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966787	25966787	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	22	588	0	ENST00000435504.4:c.2419A>G	p.Asn807Asp	p.N807D	ENST00000435504		807	Aac/Gac	13/13	0.117954624905348	3	FACETS	0.801	0.623	1	0.401	0.311	0.504	INDETERMINATE	1	TRUE	1	0.261997340420877	3		588	237	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243859016	243859016	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs397514606	NA	P-0051876-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	108	465	0	ENST00000263826.5:c.49G>A	p.Glu17Lys	p.E17K	ENST00000263826	NM_005465.4	17	Gaa/Aaa	2/13	0.466953077841842	3	FACETS	0.954	0.868	1	0.954	0.868	1	CLONAL	2	TRUE	1	0.466953077841842	3		465	299	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411767	63411767	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051876-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	216	640	0	ENST00000330258.3:c.1400G>C	p.Ser467Thr	p.S467T	ENST00000330258	NM_152424.3	467	aGt/aCt	2/2	1	1	FACETS	0.767	0.722	0.813	1	0.993	1	SUBCLONAL	2	TRUE	0	0.466953077841842	1		640	462	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0051881-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	57	449	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.412332344040796	3	FACETS	0.992	0.869	1	0.992	0.869	1	CLONAL	2	TRUE	1	0.424995167706292	3		449	164	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0051881-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	181	401	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.413617427144596	3	FACETS	0.867	0.811	0.924			1	CLONAL	3	TRUE	NA	0.424995167706292	3		401	397	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428257	33428257	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051881-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	86	693	0	ENST00000345365.6:c.866G>T	p.Gly289Val	p.G289V	ENST00000345365	NM_002878.3	289	gGc/gTc	9/10	1	2	FACETS	0.98	0.872	1	0.98	0.872	1	CLONAL	1	TRUE	1	0.424995167706292	2		693	413	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829040	128829042	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	rs570242755	NA	P-0051881-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	10	105	2	ENST00000249373.3:c.67_69del	p.Leu23del	p.L23del	ENST00000249373	NM_005631.4	16	ggGCTg/ggg	1/12	0.412332344040796	3	FACETS	0.601	0.411	0.834	0.3	0.205	0.417	SUBCLONAL	1	TRUE	1	0.424995167706292	3		107	95	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282315	115282315	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051881-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	57	384	0	ENST00000438362.2:c.335G>T	p.Gly112Val	p.G112V	ENST00000438362	NM_001242891.1	112	gGa/gTa	3/20	1	2	FACETS	0.798	0.699	0.902	1	0.975	1	CLONAL	2	TRUE	1	0.424995167706292	2		384	168	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281369	49281369	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051881-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	120	889	0	ENST00000282018.3:c.416C>A	p.Ala139Glu	p.A139E	ENST00000282018	NM_020377.2	139	gCa/gAa	1/1	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.424995167706292	2		889	467	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222217	2222217	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051881-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	111	964	0	ENST00000398665.3:c.3049C>T	p.Gln1017Ter	p.Q1017*	ENST00000398665	NM_032482.2	1017	Cag/Tag	24/28	1	2	FACETS	0.969	0.875	1	0.969	0.875	1	CLONAL	1	TRUE	1	0.424995167706292	2		964	539	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354206	15354206	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051881-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	108	972	0	ENST00000263377.2:c.2674C>A	p.Pro892Thr	p.P892T	ENST00000263377	NM_058243.2	892	Cca/Aca	14/20	1	2	FACETS	0.86	0.774	0.951	0.86	0.774	0.951	CLONAL	1	TRUE	1	0.424995167706292	2		972	591	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436656	52436661	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	TCATCG	TCATCG	-	novel	NA	P-0051881-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	186	806	0	ENST00000460680.1:c.2013_2018del	p.Tyr671_Glu673delinsTer	p.Y671_E673delins*	ENST00000460680	NM_004656.3	671	taCGATGAg/tag	16/17	0.41361634755972	2	FACETS	0.906	0.845	0.968	0.906	0.845	0.968	CLONAL	2	TRUE	0	0.424995167706292	2		806	483	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0051884-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	203	495	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.590982513956072	4	FACETS	1	0.984	1	0.81	0.771	0.847	CLONAL	3	TRUE	0	0.73027943781992	4		495	297	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051884-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	153	803	5	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.617964037381839	4	FACETS	1	0.986	1	0.683	0.628	0.739	CLONAL	1	TRUE	2	0.73027943781992	4		808	531	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051884-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	359	1065	4	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.633821213046062	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.73027943781992	2		1069	438	SUCCESS
BTK	695	MSKCC	GRCh37	X	100625009	100625009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782731222	NA	P-0051884-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	99	769	3	ENST00000308731.7:c.368G>A	p.Arg123Gln	p.R123Q	ENST00000308731	NM_000061.2	123	cGg/cAg	5/19	0.448743779305298	2	FACETS	0.829	0.748	0.913	0.415	0.374	0.457	CLONAL	1	TRUE	0	0.73027943781992	2		772	327	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40681804	40681804	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051884-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	54	351	1	ENST00000249776.8:c.583G>A	p.Glu195Lys	p.E195K	ENST00000249776	NM_033286.3	195	Gaa/Aaa	5/9	1	2	FACETS	0.808	0.702	0.92	0.808	0.702	0.92	CLONAL	1	TRUE	1	0.73027943781992	2		352	183	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116114	67116114	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0051884-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	141	444	2	ENST00000412916.2:c.400-2A>T		p.X134_splice	ENST00000412916		134			0.633821213046062	2	FACETS	0.961	0.907	1	0.961	0.907	1	CLONAL	2	TRUE	0	0.73027943781992	2		446	201	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410451	63410451	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051884-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	19	962	4	ENST00000330258.3:c.2716C>G	p.Leu906Val	p.L906V	ENST00000330258	NM_152424.3	906	Ctc/Gtc	2/2	0.654836928323211	2	FACETS	0.238	0.181	0.304	0.119	0.09	0.152	SUBCLONAL	1	TRUE	0	0.73027943781992	2		966	219	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871103	12871146	+	frameshift_variant	Frame_Shift_Del	DEL	CGGGAGCCGCCCGGCGGCGCCTTTAATTGGGGCTCCGGCTAACT	CGGGAGCCGCCCGGCGGCGCCTTTAATTGGGGCTCCGGCTAACT	-	novel	NA	P-0051884-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	286	484	2	ENST00000228872.4:c.331_374del	p.Gly111Ter	p.G111*	ENST00000228872	NM_004064.3	110	agCGGGAGCCGCCCGGCGGCGCCTTTAATTGGGGCTCCGGCTAACTct/agct	1/3	0.73027943781992	7	FACETS	1	0.987	1	0.877	0.836	0.917	CLONAL	4	TRUE	2	0.73027943781992	7		486	505	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0051899-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	75	542	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.160377158597257	3	FACETS	1	0.954	1	0.583	0.514	0.657	INDETERMINATE	1	TRUE	1	0.423256430171762	3		542	368	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160488	108160488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730881369	NA	P-0051899-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	71	621	0	ENST00000278616.4:c.4396C>T	p.Arg1466Ter	p.R1466*	ENST00000278616	NM_000051.3	1466	Cga/Tga	29/63	1	2	FACETS	0.927	0.814	1	0.927	0.814	1	CLONAL	1	TRUE	1	0.423256430171762	2		621	362	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207081	1207081	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs137854584	NA	P-0051899-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	284	849	0	ENST00000326873.7:c.169G>T	p.Glu57Ter	p.E57*	ENST00000326873	NM_000455.4	57	Gaa/Taa	1/10	0.423256430171762	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.423256430171762	1		849	891	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214064	108214064	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051899-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	46	432	0	ENST00000278616.4:c.8384A>T	p.Asp2795Val	p.D2795V	ENST00000278616	NM_000051.3	2795	gAt/gTt	57/63	1	2	FACETS	0.817	0.693	0.952	0.817	0.693	0.952	CLONAL	1	TRUE	1	0.423256430171762	2		432	266	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376007	118376007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138969270	NA	P-0051899-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	101	613	0	ENST00000534358.1:c.9400C>T	p.Leu3134Phe	p.L3134F	ENST00000534358	NM_005933.3	3134	Ctt/Ttt	27/36	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.423256430171762	2		613	463	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602477	10602502	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGGCCAGGCCGCTCCGCGGCACCT	GCCGGCCAGGCCGCTCCGCGGCACCT	-	novel	NA	P-0051899-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	299	939	0	ENST00000171111.5:c.1076_1101del	p.Gln359LeufsTer47	p.Q359Lfs*47	ENST00000171111	NM_203500.1	359	cAGGTGCCGCGGAGCGGCCTGGCCGGC/c	3/6	0.423256430171762	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.423256430171762	1		939	894	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61710200	61710200	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051899-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	82	438	0	ENST00000401558.2:c.2704C>A	p.Gln902Lys	p.Q902K	ENST00000401558	NM_003400.3	902	Caa/Aaa	22/25	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.423256430171762	2		438	370	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056320	26056320	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051899-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	185	547	1	ENST00000343677.2:c.337T>A	p.Ser113Thr	p.S113T	ENST00000343677	NM_005319.3	113	Tcc/Acc	1/1	0.365165376519172	4	FACETS	1	0.989	1	0.702	0.649	0.758	CLONAL	1	TRUE	2	0.423256430171762	4		548	886	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256718	16256718	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs774004188	NA	P-0051912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	90	501	0	ENST00000375759.3:c.3983T>C	p.Leu1328Pro	p.L1328P	ENST00000375759	NM_015001.2	1328	cTa/cCa	11/15	0.3	4	FACETS	0.89	0.794	0.992			1	CLONAL	2	FALSE	NA	0.3	4		501	438	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	61	460	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.995	0.861	1	0.995	0.861	1	CLONAL	1	TRUE	1	0.28	2		460	438	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058033	27058033	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	276	473	1	ENST00000324856.7:c.1741C>T	p.Gln581Ter	p.Q581*	ENST00000324856	NM_006015.4	581	Cag/Tag	3/20	0.106646977537297	5	FACETS	0.967	0.913	1			1	INDETERMINATE	4	TRUE	NA	0.28	5		474	724	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591070	67591070	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	27	232	0	ENST00000274335.5:c.1663G>C	p.Glu555Gln	p.E555Q	ENST00000274335		555	Gag/Cag	12/15	1	2	FACETS	0.814	0.65	0.998	0.814	0.65	0.998	CLONAL	1	TRUE	1	0.28	2		232	237	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573032	41573032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238889159	NA	P-0052003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	65	866	1	ENST00000263253.7:c.5317C>T	p.Arg1773Trp	p.R1773W	ENST00000263253	NM_001429.3	1773	Cgg/Tgg	31/31	1	2	FACETS	0.48	0.414	0.551	0.48	0.414	0.551	SUBCLONAL	1	TRUE	1	0.28	2		867	968	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561372	9561372	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	57	474	0	ENST00000353224.5:c.410C>A	p.Thr137Asn	p.T137N	ENST00000353224	NM_177990.2	137	aCt/aAt	4/10	0.115992458567733	3	FACETS	0.791	0.678	0.914	0.395	0.339	0.457	INDETERMINATE	1	TRUE	1	0.28	3		474	587	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964191	28964191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	17	319	0	ENST00000282397.4:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000282397	NM_002019.4	571	Gag/Aag	13/30	1	2	FACETS	0.425	0.317	0.553	0.425	0.317	0.553	SUBCLONAL	1	TRUE	1	0.28	2		319	286	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	77	460	0				ENST00000310581	NM_198253.2	-/1132			0.164603777789595	5	FACETS	1	0.89	1	0.67	0.594	0.751	INDETERMINATE	2	TRUE	2	0.377136138149687	5		460	318	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0052007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1442	137	853	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.377136138149687	9	FACETS	1	0.948	1			1	CLONAL	1	TRUE	NA	0.377136138149687	9		853	1579	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0052007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	228	803	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.377136138149687	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.377136138149687	2		803	576	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463227	25463227	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	55	800	0	ENST00000264709.3:c.2266G>C	p.Glu756Gln	p.E756Q	ENST00000264709	NM_175629.2	756	Gag/Cag	19/23	0.354769260923305	3	FACETS	0.533	0.455	0.618	0.266	0.227	0.309	SUBCLONAL	1	TRUE	1	0.377136138149687	3		800	651	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100934	27100934	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	186	757	2	ENST00000324856.7:c.4220del	p.Pro1407GlnfsTer74	p.P1407Qfs*74	ENST00000324856	NM_006015.4	1406	Ccc/cc	18/20	0.354769260923305	3	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	1	0.377136138149687	3		759	579	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306554	41306554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1785	233	673	1	ENST00000373198.4:c.1105G>A	p.Gly369Ser	p.G369S	ENST00000373198	NM_133170.3	369	Ggt/Agt	7/32	0.377136138149687	14	FACETS	0.999	0.927	1			1	CLONAL	2	TRUE	NA	0.377136138149687	14		674	2018	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548276	41548276	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	76	394	0	ENST00000263253.7:c.3064G>A	p.Glu1022Lys	p.E1022K	ENST00000263253	NM_001429.3	1022	Gaa/Aaa	16/31	NA	2	FACETS	0.892	0.785	1			1	INDETERMINATE	1	TRUE	NA	0.377136138149687	2		394	452	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600417	10600417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	60	980	0	ENST00000171111.5:c.1438G>A	p.Gly480Arg	p.G480R	ENST00000171111	NM_203500.1	480	Ggg/Agg	4/6	1	2	FACETS	0.426	0.366	0.491	0.426	0.366	0.491	SUBCLONAL	1	TRUE	1	0.377136138149687	2		980	747	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981084	201981084	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0052007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	57	696	0	ENST00000359651.3:c.164-1G>C		p.X55_splice	ENST00000359651		55			0.164603777789595	5	FACETS	0.689	0.59	0.797	0.23	0.196	0.266	INDETERMINATE	1	TRUE	2	0.377136138149687	5		696	687	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946210	13946210	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	46	500	0	ENST00000405192.2:c.886G>C	p.Glu296Gln	p.E296Q	ENST00000405192	NM_001163147.1	296	Gag/Cag	10/12	0.164603777789595	5	FACETS	0.581	0.489	0.684	0.194	0.163	0.228	INDETERMINATE	1	TRUE	2	0.377136138149687	5		500	657	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244280	153244280	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	197	371	0	ENST00000281708.4:c.1877C>G	p.Ala626Gly	p.A626G	ENST00000281708	NM_033632.3	626	gCt/gGt	12/12	0.377136138149687	4	FACETS	1	0.937	1	1	0.937	1	CLONAL	3	TRUE	1	0.377136138149687	4		371	479	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878111	48878119	+	frameshift_variant	Frame_Shift_Del	DEL	GGCACCGCC	GGCACCGCC	T	novel	NA	P-0052007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	160	105	0	ENST00000267163.4:c.63_71delinsT	p.Pro23AlafsTer5	p.P23Afs*5	ENST00000267163	NM_000321.2	21	ccGGCACCGCCg/ccTg	1/27	0.34910480586804	4	FACETS	0.966	0.912	1	1	0.988	1	CLONAL	5	TRUE	0	0.377136138149687	4		105	242	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007146	152007146	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	46	485	0	ENST00000262189.6:c.754C>G	p.His252Asp	p.H252D	ENST00000262189	NM_170606.2	252	Cat/Gat	6/59	0.164603777789595	5	FACETS	0.546	0.458	0.642	0.182	0.152	0.214	INDETERMINATE	1	TRUE	2	0.377136138149687	5		485	700	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740408	145740408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501361	NA	P-0052007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	73	1101	1	ENST00000428558.2:c.1532G>A	p.Cys511Tyr	p.C511Y	ENST00000428558	NM_004260.3	511	tGc/tAc	9/22	0.28187822701133	4	FACETS	0.616	0.538	0.701	0.308	0.269	0.351	SUBCLONAL	1	TRUE	2	0.377136138149687	4		1102	865	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937710	76937710	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	24	263	0	ENST00000373344.5:c.3038C>G	p.Ser1013Cys	p.S1013C	ENST00000373344	NM_000489.3	1013	tCt/tGt	9/35	0.228074637714148	2	FACETS	0.277	0.216	0.347			1	SUBCLONAL	1	TRUE	NA	0.377136138149687	2		263	460	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974748	21974748	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1554656411	NA	P-0052013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	55	363	0	ENST00000304494.5:c.79G>T	p.Glu27Ter	p.E27*	ENST00000304494	NM_000077.4	27	Gag/Tag	1/3	1	2	FACETS	1	0.86	1	1	0.977	1	CLONAL	2	TRUE	1	0.14	2		363	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577548	+	missense_variant	Missense_Mutation	ONP	TGCC	TGCC	GGCA	novel	NA	P-0052013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	66	647	0	ENST00000269305.4:c.733_736inv	p.Gly245_Met246delinsCysLeu	p.G245_M246delinsCL	ENST00000269305	NM_001126112.2	245	GGCAtg/TGCCtg	7/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.14	2		647	764	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944877	31944877	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs886286883	NA	P-0052013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	64	395	0	ENST00000340398.3:c.224C>G	p.Ala75Gly	p.A75G	ENST00000340398	NM_001013699.2	75	gCg/gGg	1/1	1	2	FACETS	0.891	0.773	1	1	0.977	1	CLONAL	2	TRUE	1	0.14	2		395	513	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872823	136872824	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	34	415	0	ENST00000241393.3:c.674dup	p.Leu226AlafsTer50	p.L226Afs*50	ENST00000241393	NM_003467.2	225	aag/aaAg	2/2	1	2	FACETS	0.888	0.724	1	0.888	0.724	1	CLONAL	1	TRUE	1	0.14	2		415	547	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466852	57466852	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	52	343	0	ENST00000371085.3:c.71A>C	p.Lys24Thr	p.K24T	ENST00000371085	NM_000516.4	24	aAa/aCa	1/13	1	2	FACETS	0.806	0.687	0.936	1	0.968	1	CLONAL	2	TRUE	1	0.14	2		343	461	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670822	134670822	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	31	544	0	ENST00000398015.3:c.733G>T	p.Glu245Ter	p.E245*	ENST00000398015	NM_004441.4	245	Gaa/Taa	3/16	1	2	FACETS	0.758	0.612	0.925	0.758	0.612	0.925	CLONAL	1	TRUE	1	0.14	2		544	584	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557917	187557917	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	48	454	0	ENST00000441802.2:c.3794del	p.Asn1265MetfsTer11	p.N1265Mfs*11	ENST00000441802	NM_005245.3	1265	aAt/at	5/27	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.14	2		454	622	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051051	180051053	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	novel	NA	P-0052013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	45	605	0	ENST00000261937.6:c.1430_1432del	p.Arg477del	p.R477del	ENST00000261937	NM_182925.4	477	cGGCag/cag	11/30	1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.14	2		605	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0052075-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	635	740	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.89339935476813	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.885182730498724	2		740	660	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341794	8341794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052075-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	313	683	0	ENST00000356435.5:c.4846G>A	p.Gly1616Arg	p.G1616R	ENST00000356435		1616	Gga/Aga	29/35	0.515213376504022	6	FACETS	1	0.993	1	0.479	0.451	0.508	INDETERMINATE	1	TRUE	3	0.885182730498724	6		683	1363	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449602	32449602	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052075-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	314	926	1	ENST00000332351.3:c.772G>T	p.Glu258Ter	p.E258*	ENST00000332351	NM_024426.4	258	Gag/Tag	3/10	0.554364194530325	3	FACETS	1	0.987	1	0.379	0.359	0.4	CLONAL	1	TRUE	0	0.885182730498724	3		927	899	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180958	108180959	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0052101-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	264	381	3	ENST00000278616.4:c.5835_5836del	p.Gln1946ValfsTer18	p.Q1946Vfs*18	ENST00000278616	NM_000051.3	1945	gCT/g	39/63	0.726864070207662	1	FACETS	0.896	0.85	0.942	0.896	0.85	0.942	CLONAL	1	TRUE	0	0.726864070207662	1		384	516	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71019958	71019958	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0052131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	45	223	0	ENST00000318789.4:c.1653-2A>G		p.X551_splice	ENST00000318789	NM_032682.5	551			1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.310387430798412	2		223	234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579592	7579592	+	splice_acceptor_variant	Splice_Site	DEL	T	T	-	rs1567557258	NA	P-0052131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	87	525	0	ENST00000269305.4:c.97-2del		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.235996229160991	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.310387430798412	1		525	356	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249896	39249896	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs201624023	NA	P-0052131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	52	678	1	ENST00000402219.2:c.1673T>C	p.Met558Thr	p.M558T	ENST00000402219	NM_005633.3	558	aTg/aCg	10/23	1	2	FACETS	0.831	0.71	0.964	0.831	0.71	0.964	CLONAL	1	TRUE	1	0.310387430798412	2		679	403	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717661	89717661	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0052141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	308	515	0	ENST00000371953.3:c.686C>G	p.Ser229Ter	p.S229*	ENST00000371953	NM_000314.4	229	tCa/tGa	7/9	0.735021648590684	2	FACETS	0.976	0.941	1	0.976	0.941	1	CLONAL	2	TRUE	0	0.753410020460192	2		515	419	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672669	30672669	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	415	675	0	ENST00000376406.3:c.4291C>G	p.Gln1431Glu	p.Q1431E	ENST00000376406	NM_014641.2	1431	Cag/Gag	10/15	0.741942390272944	2	FACETS	0.984	0.954	1	0.984	0.954	1	CLONAL	2	TRUE	0	0.753410020460192	2		675	560	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3094752	3094752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	215	312	0	ENST00000078429.4:c.103G>A	p.Asp35Asn	p.D35N	ENST00000078429	NM_002067.2	35	Gac/Aac	1/7	0.735021648590684	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.753410020460192	2		312	279	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0052141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	452	615	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.741171874250073	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.753410020460192	2		615	575	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890256	72890256	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	361	507	0	ENST00000325599.8:c.426G>C	p.Leu142Phe	p.L142F	ENST00000325599	NM_018130.2	142	ttG/ttC	4/11	0.735021648590684	2	FACETS	0.945	0.913	0.976	0.945	0.913	0.976	CLONAL	2	TRUE	0	0.753410020460192	2		507	507	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939053	48939053	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	197	302	0	ENST00000267163.4:c.888del	p.Phe296LeufsTer5	p.F296Lfs*5	ENST00000267163	NM_000321.2	295	aaT/aa	9/27	0.741942390272944	2	FACETS	0.965	0.921	1	0.965	0.921	1	CLONAL	2	TRUE	0	0.753410020460192	2		302	271	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922727	44922727	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	310	268	0	ENST00000377967.4:c.1588G>T	p.Asp530Tyr	p.D530Y	ENST00000377967	NM_021140.2	530	Gac/Tac	16/29	0.664716828899955	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.753410020460192	2		268	357	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11313995	11313995	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	201	599	0	ENST00000361445.4:c.741G>C	p.Glu247Asp	p.E247D	ENST00000361445	NM_004958.3	247	gaG/gaC	6/58	0.719938753010736	3	FACETS	1	0.932	1	0.501	0.466	0.538	CLONAL	1	TRUE	1	0.753410020460192	3		599	733	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315414	30315414	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	371	533	0	ENST00000322652.5:c.1099G>A	p.Asp367Asn	p.D367N	ENST00000322652	NM_015355.2	367	Gat/Aat	10/16	0.735021648590684	2	FACETS	0.958	0.926	0.989	0.958	0.926	0.989	CLONAL	2	TRUE	0	0.753410020460192	2		533	514	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280789	41280789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	267	456	0	ENST00000349496.5:c.2302C>T	p.Pro768Ser	p.P768S	ENST00000349496	NM_001904.3	768	Cca/Tca	15/15	0.735021648590684	2	FACETS	0.955	0.918	0.991	0.955	0.918	0.991	CLONAL	2	TRUE	0	0.753410020460192	2		456	371	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890300	72890300	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768014308	NA	P-0052141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	315	483	0	ENST00000325599.8:c.382G>A	p.Glu128Lys	p.E128K	ENST00000325599	NM_018130.2	128	Gaa/Aaa	4/11	0.735021648590684	2	FACETS	0.931	0.896	0.965	0.931	0.896	0.965	CLONAL	2	TRUE	0	0.753410020460192	2		483	449	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151948040	151948040	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	241	442	0	ENST00000262189.6:c.1633G>C	p.Glu545Gln	p.E545Q	ENST00000262189	NM_170606.2	545	Gaa/Caa	12/59	0.719938753010736	3	FACETS	0.953	0.903	1	0.953	0.903	1	CLONAL	2	TRUE	1	0.753410020460192	3		442	462	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194929	29194929	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0052141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	430	589	0	ENST00000240100.2:c.800-1G>C		p.X267_splice	ENST00000240100	NM_001394.6	267			0.753410020460192	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.753410020460192	2		589	553	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434770	128434770	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	371	632	0	ENST00000265960.3:c.84G>C	p.Glu28Asp	p.E28D	ENST00000265960	NM_001006617.1	28	gaG/gaC	2/12	0.735021648590684	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.753410020460192	2		632	487	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0052142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	221	380	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.971	0.906	1	0.971	0.906	1	CLONAL	1	TRUE	1	0.601489396968806	2		380	757	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635202	87635202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1170229422	NA	P-0052142-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	295	447	1	ENST00000277120.3:c.2254G>A	p.Val752Ile	p.V752I	ENST00000277120		752	Gtc/Atc	18/19	0.601489396968806	1	FACETS	0.967	0.917	1	0.967	0.917	1	CLONAL	1	TRUE	0	0.601489396968806	1		448	709	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0052144-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	152	706	1	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.229941277113342	5	FACETS	1	0.942	1	0.688	0.631	0.747	CLONAL	2	FALSE	2	0.343872450149729	5		707	649	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0052144-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	220	542	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.343872450149729	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	FALSE	1	0.343872450149729	4		542	513	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180982	108180982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781963	NA	P-0052144-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	90	458	0	ENST00000278616.4:c.5858C>T	p.Thr1953Ile	p.T1953I	ENST00000278616	NM_000051.3	1953	aCa/aTa	39/63	0.343872450149729	2	FACETS	0.896	0.805	0.991	0.896	0.805	0.991	CLONAL	2	FALSE	0	0.343872450149729	2		458	292	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023735	31023735	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052144-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	247	656	0	ENST00000375687.4:c.3220C>T	p.Gln1074Ter	p.Q1074*	ENST00000375687	NM_015338.5	1074	Caa/Taa	13/13	0.343872450149729	6	FACETS	0.859	0.804	0.915	0.859	0.804	0.915	CLONAL	3	FALSE	3	0.343872450149729	6		656	941	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937104	36937104	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052144-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	59	636	0	ENST00000361632.4:c.1215G>T	p.Glu405Asp	p.E405D	ENST00000361632		405	gaG/gaT	9/16	1	2	FACETS	0.528	0.454	0.609	0.528	0.454	0.609	SUBCLONAL	1	FALSE	1	0.343872450149729	2		636	650	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433321	78433321	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052144-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	46	527	0	ENST00000370768.2:c.280C>T	p.Gln94Ter	p.Q94*	ENST00000370768	NM_003902.3	94	Cag/Tag	4/20	1	2	FACETS	0.741	0.626	0.867	0.741	0.626	0.867	SUBCLONAL	1	FALSE	1	0.343872450149729	2		527	361	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948310	71948310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052144-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	197	840	0	ENST00000298229.2:c.3022C>T	p.Pro1008Ser	p.P1008S	ENST00000298229	NM_001567.3	1008	Cct/Tct	26/28	0.229941277113342	5	FACETS	0.96	0.889	1	0.64	0.593	0.688	CLONAL	2	FALSE	2	0.343872450149729	5		840	905	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359387	118359387	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052144-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	35	493	0	ENST00000534358.1:c.4391A>C	p.Glu1464Ala	p.E1464A	ENST00000534358	NM_005933.3	1464	gAg/gCg	11/36	0.343872450149729	2	FACETS	0.53	0.435	0.637	0.265	0.217	0.319	SUBCLONAL	1	FALSE	0	0.343872450149729	2		493	384	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112014	115112014	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052144-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	226	710	0	ENST00000257566.3:c.1726G>C	p.Ala576Pro	p.A576P	ENST00000257566	NM_016569.3	576	Gcc/Ccc	7/8	0.343872450149729	3	FACETS	1	0.976	1			1	CLONAL	2	FALSE	NA	0.343872450149729	3		710	707	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991357	41991357	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052144-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	91	527	0	ENST00000219905.7:c.2188+1del		p.V730fs	ENST00000219905	NM_001164273.1	730	Gtg/tg	5/24	0.239072893467634	3	FACETS	0.76	0.679	0.845	0.76	0.679	0.845	SUBCLONAL	2	FALSE	1	0.343872450149729	3		527	408	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042379	42042379	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052144-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	80	708	0	ENST00000219905.7:c.6574G>T	p.Glu2192Ter	p.E2192*	ENST00000219905	NM_001164273.1	2192	Gaa/Taa	17/24	0.239072893467634	3	FACETS	1	0.934	1	0.543	0.479	0.611	CLONAL	1	FALSE	1	0.343872450149729	3		708	502	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268461	198268461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052144-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	152	529	0	ENST00000335508.6:c.1567G>A	p.Ala523Thr	p.A523T	ENST00000335508	NM_012433.2	523	Gct/Act	12/25	0.343872450149729	4	FACETS	0.839	0.773	0.906	0.839	0.773	0.906	CLONAL	3	FALSE	1	0.343872450149729	4		529	472	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31390197	31390197	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052144-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	77	540	0	ENST00000328111.2:c.2152C>T	p.Pro718Ser	p.P718S	ENST00000328111	NM_006892.3	718	Cca/Tca	20/23	0.343872450149729	6	FACETS	1	0.885	1	0.336	0.295	0.381	CLONAL	1	FALSE	3	0.343872450149729	6		540	749	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041658	47041658	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052144-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	88	705	0	ENST00000377604.3:c.1883del	p.Glu628GlyfsTer76	p.E628Gfs*76	ENST00000377604	NM_001204468.1	628	gAg/gg	17/24	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	FALSE	1	0.343872450149729	2		705	512	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410963	63410963	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052144-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	104	729	0	ENST00000330258.3:c.2204C>A	p.Ala735Glu	p.A735E	ENST00000330258	NM_152424.3	735	gCa/gAa	2/2	0.239072893467634	3	FACETS	1	0.912	1	0.51	0.457	0.566	CLONAL	1	FALSE	1	0.343872450149729	3		729	695	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0052145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	241	521	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.217971100642184	5	FACETS	0.927	0.869	0.987	0.927	0.869	0.987	CLONAL	4	TRUE	1	0.217971100642184	5		521	791	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574035	7574035	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0052145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	112	534	0	ENST00000269305.4:c.994-2A>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.173734719377069	2	FACETS	0.897	0.809	0.989	0.897	0.809	0.989	CLONAL	2	TRUE	0	0.217971100642184	2		534	573	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458417	12458417	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052145-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	89	743	0	ENST00000287820.6:c.1034T>A	p.Leu345His	p.L345H	ENST00000287820	NM_015869.4	345	cTc/cAc	6/7	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.217971100642184	2		743	664	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0052146-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	19	754	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.386	0.291	0.498	0.386	0.291	0.498	SUBCLONAL	1	TRUE	1	0.11	2		754	896	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155692	119155692	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052146-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	44	613	1	ENST00000264033.4:c.1445C>T	p.Pro482Leu	p.P482L	ENST00000264033	NM_005188.3	482	cCt/cTt	10/16	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.11	2		614	735	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880257	37880257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	174	641	1	ENST00000269571.5:c.2301C>G	p.Ile767Met	p.I767M	ENST00000269571		767	atC/atG	19/27	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.388228451424637	2		642	724	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951925	2951925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147381531	NA	P-0052155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	156	790	2	ENST00000396946.4:c.3025G>A	p.Val1009Ile	p.V1009I	ENST00000396946	NM_032415.4	1009	Gtc/Atc	23/25	1	2	FACETS	0.972	0.891	1	0.972	0.891	1	CLONAL	1	TRUE	1	0.388228451424637	2		792	827	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420158	420158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	181	599	0	ENST00000399788.2:c.3109C>T	p.Leu1037Phe	p.L1037F	ENST00000399788	NM_001042603.1	1037	Ctt/Ttt	21/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.388228451424637	2		599	785	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691039	NA	P-0052155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	211	956	4	ENST00000269305.4:c.919+1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.388228451424637	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.388228451424637	1		960	863	SUCCESS
APC	324	MSKCC	GRCh37	5	112174391	112174391	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	86	350	0	ENST00000257430.4:c.3100G>T	p.Glu1034Ter	p.E1034*	ENST00000257430	NM_000038.5	1034	Gag/Tag	16/16	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.388228451424637	2		350	396	SUCCESS
APC	324	MSKCC	GRCh37	5	112175944	112175945	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0052155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	62	353	0	ENST00000257430.4:c.4655_4656del	p.Glu1552GlyfsTer6	p.E1552Gfs*6	ENST00000257430	NM_000038.5	1551	aaAGag/aaag	16/16	1	2	FACETS	0.791	0.685	0.904	0.791	0.685	0.904	CLONAL	1	TRUE	1	0.388228451424637	2		353	404	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437265	220437265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1224525818	NA	P-0052155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	226	1351	2	ENST00000243786.2:c.169C>T	p.Arg57Trp	p.R57W	ENST00000243786	NM_002191.3	57	Cgg/Tgg	1/2	0.185106408460313	0	FACETS	0.576	0.535	0.618			1	INDETERMINATE	1	TRUE	0	0.388228451424637	0		1353	1237	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243560	46243560	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0052155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	76	311	0	ENST00000334344.6:c.1912+1G>C		p.X638_splice	ENST00000334344	NM_152641.2	638			1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.388228451424637	2		311	371	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245627	46245633	+	frameshift_variant	Frame_Shift_Del	DEL	AAAATAA	AAAATAA	-	novel	NA	P-0052155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	97	487	0	ENST00000334344.6:c.3721_3727del	p.Lys1241PhefsTer52	p.K1241Ffs*52	ENST00000334344	NM_152641.2	1241	AAAATAAtt/tt	15/21	1	2	FACETS	0.907	0.811	1	0.907	0.811	1	CLONAL	1	TRUE	1	0.388228451424637	2		487	551	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436864	29436864	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	144	755	2	ENST00000389048.3:c.3729C>A	p.Asn1243Lys	p.N1243K	ENST00000389048	NM_004304.4	1243	aaC/aaA	24/29	1	2	FACETS	0.917	0.837	1	0.917	0.837	1	CLONAL	1	TRUE	1	0.388228451424637	2		757	809	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952516	38952516	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	75	332	0	ENST00000357387.3:c.2909A>G	p.Tyr970Cys	p.Y970C	ENST00000357387	NM_152756.3	970	tAt/tGt	30/38	1	2	FACETS	0.847	0.745	0.957	0.847	0.745	0.957	CLONAL	1	TRUE	1	0.388228451424637	2		332	456	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240002	53240002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057518697	NA	P-0052155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	228	483	0	ENST00000375401.3:c.1439C>T	p.Pro480Leu	p.P480L	ENST00000375401	NM_004187.3	480	cCg/cTg	11/26	1	1	FACETS	0.782	0.734	0.831	1	0.993	1	SUBCLONAL	2	TRUE	0	0.388228451424637	1		483	605	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575189	48575210	+	frameshift_variant	Frame_Shift_Del	DEL	TGAATCCATATCACTACGAACG	TGAATCCATATCACTACGAACG	AT	novel	NA	P-0052155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	69	415	1	ENST00000342988.3:c.383_404delinsAT	p.Val128AspfsTer8	p.V128Dfs*8	ENST00000342988	NM_005359.5	128	gTGAATCCATATCACTACGAACGa/gATa	3/12	0.388228451424637	1	FACETS	0.679	0.593	0.77	0.679	0.593	0.77	SUBCLONAL	1	TRUE	0	0.388228451424637	1		416	422	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0052156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	191	537	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.891886647387693	2		537	391	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210075	55210075	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18338	3118	662	0	ENST00000275493.2:c.185T>G	p.Leu62Arg	p.L62R	ENST00000275493	NM_005228.3	62	cTt/cGt	2/28	0.891886647387693	36	FACETS	1	0.996	1	0.15	0.147	0.154	CLONAL	5	TRUE	1	0.891886647387693	36		662	21456	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1255456	1255456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374968697	NA	P-0052156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	474	875	1	ENST00000310581.5:c.3103G>A	p.Val1035Ile	p.V1035I	ENST00000310581	NM_198253.2	1035	Gtc/Atc	14/16	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.891886647387693	2		876	1009	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0052158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	82	378	0	ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	4/10	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.372725412761038	2		378	408	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426127	47426127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	176	1097	0	ENST00000377045.4:c.647C>G	p.Pro216Arg	p.P216R	ENST00000377045	NM_001654.4	216	cCc/cGc	7/16	1	2	FACETS	0.924	0.851	1	0.924	0.851	1	CLONAL	1	TRUE	1	0.372725412761038	2		1097	1022	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064328	30064328	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	78	423	0	ENST00000338641.4:c.892C>T	p.Gln298Ter	p.Q298*	ENST00000338641	NM_000268.3	298	Cag/Tag	10/16	0.372725412761038	1	FACETS	0.938	0.83	1	0.938	0.83	1	CLONAL	1	TRUE	0	0.372725412761038	1		423	363	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589592	67589594	+	inframe_deletion	In_Frame_Del	DEL	ATA	ATA	-	novel	NA	P-0052159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	51	301	0	ENST00000274335.5:c.1356_1358del	p.Asn453del	p.N453del	ENST00000274335		452	tATAac/tac	10/15	0.107439661621159	3	FACETS	0.853	0.725	0.992	0.426	0.362	0.497	INDETERMINATE	1	TRUE	1	0.279303377598731	3		301	488	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831069	72831069	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	71	531	1	ENST00000268489.5:c.5512C>T	p.Gln1838Ter	p.Q1838*	ENST00000268489	NM_006885.3	1838	Cag/Tag	9/10	0.157124428912373	3	FACETS	1	0.946	1			1	INDETERMINATE	1	TRUE	NA	0.279303377598731	3		532	503	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619236	23619236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	98	677	0	ENST00000261584.4:c.3299C>T	p.Thr1100Ile	p.T1100I	ENST00000261584	NM_024675.3	1100	aCt/aTt	12/13	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.279303377598731	2		677	695	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548297	41548297	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	67	331	0	ENST00000263253.7:c.3085C>G	p.Gln1029Glu	p.Q1029E	ENST00000263253	NM_001429.3	1029	Cag/Gag	16/31	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.279303377598731	2		331	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0052160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	370	646	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.591032837240182	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.591032837240182	1		646	743	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520328	176520328	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200070761	NA	P-0052160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	225	732	0	ENST00000292408.4:c.1247G>A	p.Arg416Gln	p.R416Q	ENST00000292408	NM_213647.1	416	cGa/cAa	9/18	0.591032837240182	2	FACETS	1	0.978	1	0.549	0.513	0.585	CLONAL	1	TRUE	0	0.591032837240182	2		732	694	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883623	37883623	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1038581447	NA	P-0052160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	290	1184	2	ENST00000269571.5:c.3235G>A	p.Glu1079Lys	p.E1079K	ENST00000269571		1079	Gaa/Aaa	26/27	1	2	FACETS	0.935	0.881	0.992	0.935	0.881	0.992	CLONAL	1	TRUE	1	0.591032837240182	2		1186	1049	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0052161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	245	495	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.601612826388101	3	FACETS	0.934	0.881	0.988	0.934	0.881	0.988	CLONAL	2	TRUE	1	0.601612826388101	3		495	567	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835581	68835581	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	291	573	0	ENST00000261769.5:c.172G>T	p.Glu58Ter	p.E58*	ENST00000261769	NM_004360.3	58	Gaa/Taa	3/16	0.601612826388101	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.601612826388101	2		573	459	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115725	8115725	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	205	408	0	ENST00000346208.3:c.1071G>C	p.Lys357Asn	p.K357N	ENST00000346208		357	aaG/aaC	6/6	0.497218244362467	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	FALSE	0	0.497448323866838	2		408	391	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972306	32972308	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0052162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	50	400	0	ENST00000380152.3:c.9658_9660del	p.Pro3220del	p.P3220del	ENST00000380152		3219	tCTCct/tct	27/27	0.20210015259833	5	FACETS	0.586	0.497	0.684	0.195	0.165	0.228	INDETERMINATE	1	FALSE	2	0.497448323866838	5		400	599	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041867	42041870	+	frameshift_variant	Frame_Shift_Del	DEL	TGAA	TGAA	-	novel	NA	P-0052162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	40	557	0	ENST00000219905.7:c.6065_6068del	p.Asn2022IlefsTer79	p.N2022Ifs*79	ENST00000219905	NM_001164273.1	2021	cTGAAt/ct	17/24	0.26661997555981	5	FACETS	0.351	0.29	0.419	0.117	0.096	0.14	INDETERMINATE	1	FALSE	2	0.497448323866838	5		557	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0052163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	165	812	2	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	0.123799764600134	3	FACETS	1	0.964	1	0.72	0.663	0.78	INDETERMINATE	2	TRUE	0	0.240961528440251	3		814	710	SUCCESS
APC	324	MSKCC	GRCh37	5	112175513	112175513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	32	406	0	ENST00000257430.4:c.4222G>T	p.Glu1408Ter	p.E1408*	ENST00000257430	NM_000038.5	1408	Gaa/Taa	16/16	0.240961528440251	3	FACETS	0.807	0.655	0.977	0.403	0.327	0.489	CLONAL	1	TRUE	1	0.240961528440251	3		406	369	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048698	180048698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771458044	NA	P-0052163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	44	946	0	ENST00000261937.6:c.1864G>A	p.Ala622Thr	p.A622T	ENST00000261937	NM_182925.4	622	Gcc/Acc	13/30	0.240961528440251	3	FACETS	0.614	0.514	0.726	0.307	0.257	0.363	SUBCLONAL	1	TRUE	1	0.240961528440251	3		946	666	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539467	187539467	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	46	481	2	ENST00000441802.2:c.8273G>A	p.Gly2758Glu	p.G2758E	ENST00000441802	NM_005245.3	2758	gGg/gAg	10/27	0.13895295385356	4	FACETS	1	0.906	1	0.369	0.311	0.433	INDETERMINATE	1	TRUE	1	0.240961528440251	4		483	428	SUCCESS
APC	324	MSKCC	GRCh37	5	112173854	112173854	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	71	365	0	ENST00000257430.4:c.2563G>T	p.Glu855Ter	p.E855*	ENST00000257430	NM_000038.5	855	Gaa/Taa	16/16	0.240961528440251	3	FACETS	0.977	0.859	1	0.977	0.859	1	CLONAL	2	TRUE	1	0.240961528440251	3		365	338	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421005	49421006	+	frameshift_variant	Frame_Shift_Ins	INS	GA	GA	AAG	novel	NA	P-0052163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	17	385	1	ENST00000301067.7:c.14743_14744delinsCTT	p.Ser4915LeufsTer17	p.S4915Lfs*17	ENST00000301067	NM_003482.3	4915	TCc/CTTc	48/54	0.240961528440251	3	FACETS	0.518	0.386	0.675	0.259	0.193	0.338	SUBCLONAL	1	TRUE	1	0.240961528440251	3		386	305	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0052164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	186	449	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.583841542483944	2	FACETS	0.878	0.814	0.945	0.439	0.407	0.473	CLONAL	1	TRUE	0	0.603418670383197	2		449	702	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0052164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	272	448	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.505367313278648	3	FACETS	1	0.99	1	0.77	0.732	0.808	CLONAL	2	TRUE	0	0.603418670383197	3		448	508	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220578	1220578	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1131690934	NA	P-0052164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	350	830	1	ENST00000326873.7:c.598-2A>G		p.X200_splice	ENST00000326873	NM_000455.4	200			0.603418670383197	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.603418670383197	2		831	567	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098566	11098566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776534924	NA	P-0052164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	408	766	0	ENST00000358026.2:c.1084G>A	p.Asp362Asn	p.D362N	ENST00000358026	NM_001128849.1	362	Gac/Aac	6/36	0.603418670383197	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.603418670383197	2		766	613	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2097724	2097724	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388213392	NA	P-0052164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	139	640	0	ENST00000219066.1:c.125G>A	p.Arg42Lys	p.R42K	ENST00000219066	NM_002528.5	42	aGa/aAa	1/6	0.603418670383197	3	FACETS	0.978	0.894	1	0.489	0.447	0.533	CLONAL	1	TRUE	1	0.603418670383197	3		640	613	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233081	66233081	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	343	362	0	ENST00000273854.3:c.1918G>T	p.Gly640Trp	p.G640W	ENST00000273854	NM_004439.5	640	Ggg/Tgg	10/18	0.583841542483944	2	FACETS	0.992	0.951	1	0.992	0.951	1	CLONAL	2	TRUE	0	0.603418670383197	2		362	573	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196621	106196621	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	280	535	0	ENST00000380013.4:c.4954C>T	p.Gln1652Ter	p.Q1652*	ENST00000380013	NM_001127208.2	1652	Cag/Tag	11/11	0.583841542483944	2	FACETS	0.932	0.888	0.975	0.932	0.888	0.975	CLONAL	2	TRUE	0	0.603418670383197	2		535	498	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156180	106156180	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	127	382	0	ENST00000380013.4:c.1081C>T	p.Gln361Ter	p.Q361*	ENST00000380013	NM_001127208.2	361	Caa/Taa	3/11	0.583841542483944	2	FACETS	1	0.945	1	0.522	0.477	0.569	CLONAL	1	TRUE	0	0.603418670383197	2		382	403	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857980	9857980	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	274	604	0	ENST00000330684.3:c.3421C>A	p.Leu1141Met	p.L1141M	ENST00000330684	NM_001134407.1	1141	Ctg/Atg	13/13	0.603418670383197	3	FACETS	0.966	0.914	1	0.966	0.914	1	CLONAL	2	TRUE	1	0.603418670383197	3		604	612	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518700	204518700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	91	347	0	ENST00000367182.3:c.1363G>A	p.Gly455Ser	p.G455S	ENST00000367182	NM_001278516.1	455	Ggc/Agc	11/11	0.50600348719954	4	FACETS	0.835	0.743	0.933	0.418	0.371	0.467	CLONAL	1	TRUE	2	0.603418670383197	4		347	579	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589702	69589702	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	34	60	0	ENST00000168712.1:c.151G>T	p.Val51Leu	p.V51L	ENST00000168712	NM_002007.2	51	Gtg/Ttg	1/3	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.603418670383197	2		60	90	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455298	29455298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	253	581	0	ENST00000389048.3:c.2504del	p.Pro835ArgfsTer4	p.P835Rfs*4	ENST00000389048	NM_004304.4	835	cCg/cg	15/29	0.594093692235118	3	FACETS	0.913	0.861	0.965	0.913	0.861	0.965	CLONAL	2	TRUE	1	0.603418670383197	3		581	598	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021746	71021746	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199658468	NA	P-0052164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	129	388	1	ENST00000318789.4:c.1612G>A	p.Glu538Lys	p.E538K	ENST00000318789	NM_032682.5	538	Gaa/Aaa	18/21	0.583841542483944	2	FACETS	0.852	0.777	0.93	0.426	0.388	0.465	CLONAL	1	TRUE	0	0.603418670383197	2		389	502	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433953	149433953	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	236	984	0	ENST00000286301.3:c.2695C>A	p.His899Asn	p.H899N	ENST00000286301	NM_005211.3	899	Cac/Aac	21/22	1	2	FACETS	0.98	0.917	1	0.98	0.917	1	CLONAL	1	TRUE	1	0.603418670383197	2		984	798	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521912	157521912	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	257	587	0	ENST00000346085.5:c.4184A>T	p.Gln1395Leu	p.Q1395L	ENST00000346085	NM_020732.3	1395	cAg/cTg	18/20	0.583841542483944	2	FACETS	0.926	0.88	0.971	0.926	0.88	0.971	CLONAL	2	TRUE	0	0.603418670383197	2		587	460	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339524	81339524	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	354	465	0	ENST00000222390.5:c.1480C>G	p.Arg494Gly	p.R494G	ENST00000222390	NM_000601.4	494	Cga/Gga	13/18	0.603418670383197	3	FACETS	0.898	0.855	0.942	0.898	0.855	0.942	CLONAL	2	TRUE	1	0.603418670383197	3		465	850	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407915	139407915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	464	881	0	ENST00000277541.6:c.2282C>T	p.Pro761Leu	p.P761L	ENST00000277541	NM_017617.3	761	cCt/cTt	14/34	0.594093692235118	3	FACETS	0.986	0.946	1	0.986	0.946	1	CLONAL	2	TRUE	1	0.603418670383197	3		881	1015	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613606	100613606	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	151	693	0	ENST00000308731.7:c.973G>T	p.Gly325Trp	p.G325W	ENST00000308731	NM_000061.2	325	Ggg/Tgg	11/19	1	2	FACETS	0.887	0.815	0.962	0.887	0.815	0.962	CLONAL	1	TRUE	1	0.603418670383197	2		693	564	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220512	123220512	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	184	676	0	ENST00000218089.9:c.3169A>C	p.Met1057Leu	p.M1057L	ENST00000218089	NM_001042749.1	1057	Atg/Ctg	30/35	1	2	FACETS	0.848	0.785	0.913	0.848	0.785	0.913	CLONAL	1	TRUE	1	0.603418670383197	2		676	719	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58142400	58142400	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2153	544	573	0	ENST00000257904.6:c.820G>A	p.Glu274Lys	p.E274K	ENST00000257904	NM_000075.3	274	Gaa/Aaa	8/8	0.3	21	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	21		573	2697	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0052172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	71	449	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.2	2		449	652	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070572	67070572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	29	313	0	ENST00000412916.2:c.196C>T	p.Leu66Phe	p.L66F	ENST00000412916		66	Ctc/Ttc	3/6	0.239556083938859	1	FACETS	0.816	0.656	0.997	0.816	0.656	0.997	CLONAL	1	TRUE	0	0.2	1		313	320	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028103	48028103	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	36	443	0	ENST00000234420.5:c.2981A>C	p.Tyr994Ser	p.Y994S	ENST00000234420	NM_000179.2	994	tAc/tCc	4/10	1	2	FACETS	0.896	0.737	1	0.896	0.737	1	CLONAL	1	TRUE	1	0.2	2		443	402	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	23	460	0				ENST00000310581	NM_198253.2	-/1132			0.259328970330809	0	FACETS	0.664	0.528	0.814			1	SUBCLONAL	2	FALSE	0	0.259318504585391	0		460	99	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0052173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	174	486	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.19638779369608	2	FACETS	0.859	0.796	0.922	1	0.987	1	CLONAL	3	FALSE	0	0.259318504585391	2		486	521	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880962	134880962	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290751781	NA	P-0052173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	33	830	2	ENST00000398015.3:c.1525C>T	p.Arg509Cys	p.R509C	ENST00000398015	NM_004441.4	509	Cgc/Tgc	7/16	0.259328970330809	0	FACETS	0.641	0.53	0.762			1	SUBCLONAL	2	FALSE	0	0.259318504585391	0		832	147	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212731	27212731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	61	995	2	ENST00000380036.4:c.2713G>A	p.Ala905Thr	p.A905T	ENST00000380036	NM_000459.3	905	Gcg/Acg	17/23	0.259318504585391	0	FACETS	1	0.953	1			1	CLONAL	1	FALSE	0	0.259318504585391	0		997	286	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46725704	46725704	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	113	741	0	ENST00000371975.4:c.340G>T	p.Glu114Ter	p.E114*	ENST00000371975	NM_003579.3	114	Gaa/Taa	5/18	0.259328970330809	4	FACETS	1	0.975	1			1	CLONAL	2	FALSE	NA	0.259318504585391	4		741	444	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398242	25398242	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	185	598	0	ENST00000311936.3:c.77A>G	p.Asn26Ser	p.N26S	ENST00000311936	NM_004985.3	26	aAt/aGt	2/5	0.19638779369608	2	FACETS	0.849	0.789	0.911	1	0.987	1	CLONAL	3	FALSE	0	0.259318504585391	2		598	560	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807379	3807379	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0052173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	107	449	0	ENST00000262367.5:c.3610-2A>G		p.X1204_splice	ENST00000262367	NM_004380.2	1204			0.2589220373509	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	FALSE	1	0.259318504585391	3		449	376	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056259	180056259	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	37	982	0	ENST00000261937.6:c.985G>A	p.Glu329Lys	p.E329K	ENST00000261937	NM_182925.4	329	Gaa/Aaa	7/30	0.259328970330809	0	FACETS	1	0.905	1			1	CLONAL	1	FALSE	0	0.259318504585391	0		982	187	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907101	101907101	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	17	499	0	ENST00000374994.4:c.1061del	p.Leu354ArgfsTer3	p.L354Rfs*3	ENST00000374994	NM_004612.2	354	cTg/cg	6/9	0.259328970330809	0	FACETS	0.483	0.362	0.627			1	SUBCLONAL	1	FALSE	0	0.259318504585391	0		499	201	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820188	139820188	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	189	935	0	ENST00000247668.2:c.1341C>G	p.Phe447Leu	p.F447L	ENST00000247668	NM_021138.3	447	ttC/ttG	11/11	1	2	FACETS	1	0.969	1	1	0.994	1	CLONAL	2	FALSE	1	0.259318504585391	2		935	676	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610576	10610576	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	45	1041	0	ENST00000171111.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000171111	NM_203500.1	45	tCc/tTc	2/6	0.125989747920201	0	FACETS	0.483	0.404	0.57			1	SUBCLONAL	1	TRUE	0	0.2	0		1041	746	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909972	100909972	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	40	425	0	ENST00000325455.5:c.2677A>C	p.Asn893His	p.N893H	ENST00000325455	NM_001202474.3	893	Aat/Cat	8/8	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.2	2		425	369	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190767	108190767	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1255710647	NA	P-0052175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	32	405	0	ENST00000278616.4:c.6434A>T	p.Glu2145Val	p.E2145V	ENST00000278616	NM_000051.3	2145	gAa/gTa	44/63	1	2	FACETS	0.936	0.761	1	0.936	0.761	1	CLONAL	1	TRUE	1	0.2	2		405	342	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0052176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	338	724	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.537776932262326	4	FACETS	0.946	0.903	0.99	0.946	0.903	0.99	CLONAL	3	TRUE	1	0.537776932262326	4		724	681	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100111	27100111	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	130	983	0	ENST00000324856.7:c.3910del	p.Ala1304ProfsTer177	p.A1304Pfs*177	ENST00000324856	NM_006015.4	1303	Ggg/gg	16/20	0.537776932262326	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.537776932262326	1		983	332	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398873	398873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	105	833	0	ENST00000380956.4:c.683C>A	p.Ser228Tyr	p.S228Y	ENST00000380956	NM_001195286.1	228	tCc/tAc	6/9	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.537776932262326	2		833	389	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100119	27100121	+	missense_variant	Missense_Mutation	TNP	ACA	ACA	CCC	novel	NA	P-0052176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	124	935	0	ENST00000324856.7:c.3915_3917delinsCCC	p.Gln1306Pro	p.Q1306P	ENST00000324856	NM_006015.4	1305	ccACAg/ccCCCg	16/20	0.537776932262326	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.537776932262326	1		935	315	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0052177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	258	455	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.112864400753882	5	FACETS	1	0.99	1	0.822	0.774	0.872	INDETERMINATE	2	FALSE	2	0.503600720383044	5		455	729	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112401	115112401	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs888338239	NA	P-0052177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	115	652	0	ENST00000257566.3:c.1339C>T	p.Arg447Cys	p.R447C	ENST00000257566	NM_016569.3	447	Cgc/Tgc	7/8	1	2	FACETS	0.663	0.598	0.732	0.663	0.598	0.732	SUBCLONAL	1	FALSE	1	0.503600720383044	2		652	689	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165874	118165874	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	126	482	0	ENST00000369448.3:c.384A>C	p.Lys128Asn	p.K128N	ENST00000369448	NM_017709.3	128	aaA/aaC	2/2	0.503600720383044	3	FACETS	0.831	0.753	0.913	0.415	0.376	0.457	CLONAL	1	FALSE	1	0.503600720383044	3		482	754	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316391	14316391	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	261	590	0	ENST00000256196.4:c.214C>G	p.Gln72Glu	p.Q72E	ENST00000256196		72	Caa/Gaa	3/6	0.196653766271802	2	FACETS	1	0.993	1	0.725	0.683	0.768	INDETERMINATE	1	FALSE	0	0.503600720383044	2		590	715	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143335	108143335	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0052177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	182	505	0	ENST00000278616.4:c.3153+1G>A		p.X1051_splice	ENST00000278616	NM_000051.3	1051			0.196653766271802	2	FACETS	1	0.988	1	0.655	0.608	0.703	INDETERMINATE	1	FALSE	0	0.503600720383044	2		505	552	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961417	1961418	+	missense_variant	Missense_Mutation	DNP	AA	AA	TT	novel	NA	P-0052177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	51	728	0	ENST00000382891.5:c.3205_3206inv	p.Lys1069Leu	p.K1069L	ENST00000382891	NM_133335.3	1069	AAg/TTg	17/22	0.262029876737604	1	FACETS	0.21	0.178	0.246	0.21	0.178	0.246	INDETERMINATE	1	FALSE	0	0.503600720383044	1		728	721	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469982	157469982	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057517704	NA	P-0052177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	266	731	0	ENST00000346085.5:c.2776C>T	p.Gln926Ter	p.Q926*	ENST00000346085	NM_020732.3	926	Cag/Tag	9/20	0.196653766271802	2	FACETS	0.815	0.77	0.861	0.815	0.77	0.861	INDETERMINATE	2	FALSE	0	0.503600720383044	2		731	648	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023714	27023715	+	frameshift_variant	Frame_Shift_Ins	INS	AT	AT	CCAG	novel	NA	P-0052177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	174	450	0	ENST00000324856.7:c.820_821delinsCCAG	p.Met274ProfsTer90	p.M274Pfs*90	ENST00000324856	NM_006015.4	274	ATg/CCAGg	1/20	0.196653766271802	2	FACETS	1	0.988	1	0.674	0.625	0.723	INDETERMINATE	1	FALSE	0	0.503600720383044	2		450	513	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0052193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	144	827	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.232512664355502	2	FACETS	1	0.986	1	0.733	0.668	0.8	CLONAL	1	FALSE	0	0.232512664355502	2		827	845	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980402	55980402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1357848255	NA	P-0052194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	55	396	0	ENST00000263923.4:c.689C>T	p.Pro230Leu	p.P230L	ENST00000263923	NM_002253.2	230	cCg/cTg	6/30	1	2	FACETS	0.871	0.746	1	0.871	0.746	1	CLONAL	1	TRUE	1	0.26	2		396	486	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89851314	89851314	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	89	692	2	ENST00000389301.3:c.1418T>A	p.Leu473Gln	p.L473Q	ENST00000389301	NM_000135.2	473	cTg/cAg	15/43	1	2	FACETS	0.933	0.827	1	0.933	0.827	1	CLONAL	1	TRUE	1	0.26	2		694	734	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451797	29451797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs79530637	NA	P-0052196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	36	505	1	ENST00000389048.3:c.2768G>A	p.Gly923Glu	p.G923E	ENST00000389048	NM_004304.4	923	gGg/gAg	16/29	0.835807958433675	3	FACETS	0.269	0.221	0.323	0.135	0.11	0.162	SUBCLONAL	1	TRUE	1	0.855878542184346	3		506	446	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708597	43708597	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	116	590	0	ENST00000382044.4:c.4699A>T	p.Arg1567Trp	p.R1567W	ENST00000382044	NM_001141980.1	1567	Agg/Tgg	22/28	1	2	FACETS	0.513	0.464	0.565	0.513	0.464	0.565	SUBCLONAL	1	TRUE	1	0.855878542184346	2		590	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0052198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	403	534	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	0.440696888529309	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.485559148816429	2		534	811	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	342	459	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.485559148816429	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.485559148816429	3		459	836	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539128	187539128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756707942	NA	P-0052198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	71	390	0	ENST00000441802.2:c.8612C>T	p.Thr2871Ile	p.T2871I	ENST00000441802	NM_005245.3	2871	aCt/aTt	10/27	0.265767517275878	3	FACETS	0.913	0.801	1	0.457	0.4	0.517	INDETERMINATE	1	TRUE	1	0.485559148816429	3		390	398	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909655	76909655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557118749	NA	P-0052199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	90	400	0	ENST00000373344.5:c.4250G>A	p.Arg1417Gln	p.R1417Q	ENST00000373344	NM_000489.3	1417	cGg/cAg	14/35	0.211886601223467	0	FACETS	0.94	0.837	1			1	CLONAL	1	FALSE	0	0.282187873824172	0		400	487	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287454	46287455	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	novel	NA	P-0052199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	182	390	0	ENST00000334344.6:c.5316_5318dup	p.Ala1773dup	p.A1773dup	ENST00000334344	NM_152641.2	1773	-/GCT	20/21	0.279459263011832	4	FACETS	0.884	0.819	0.95	1	0.988	1	CLONAL	3	FALSE	2	0.282187873824172	4		390	624	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0052200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	133	518	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.411803156152557	1	FACETS	0.809	0.737	0.885	0.809	0.737	0.885	CLONAL	1	TRUE	0	0.411803156152557	1		518	634	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0052200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	134	464	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.157644283135533	2	FACETS	0.83	0.762	0.9	0.83	0.762	0.9	INDETERMINATE	2	TRUE	0	0.411803156152557	2		464	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0052200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	154	681	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.350152099264287	1	FACETS	0.904	0.83	0.981	0.904	0.83	0.981	CLONAL	1	TRUE	0	0.411803156152557	1		681	657	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	213	1140	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.432325015183213	2		1144	784	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	193	1142	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.432325015183213	2		1146	846	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	107	540	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.927	0.835	1	0.927	0.835	1	CLONAL	1	FALSE	1	0.432325015183213	2		540	534	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	205	944	4	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.432325015183213	2		948	762	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552144	29552144	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	79	294	0	ENST00000356175.3:c.1882del	p.Tyr628ThrfsTer3	p.Y628Tfs*3	ENST00000356175	NM_000267.3	626	cTt/ct	17/57	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.432325015183213	2		294	246	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560514	65560514	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	176	558	0	ENST00000358664.4:c.83A>G	p.His28Arg	p.H28R	ENST00000358664	NM_002382.4	28	cAt/cGt	3/5	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.432325015183213	2		558	608	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	34	491	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.382	0.312	0.46	0.382	0.312	0.46	SUBCLONAL	1	FALSE	1	0.432325015183213	2		491	412	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	108	461	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.432325015183213	2		461	392	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422384	47422384	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	172	611	1	ENST00000377045.4:c.23del	p.Pro8LeufsTer26	p.P8Lfs*26	ENST00000377045	NM_001654.4	6	ggC/gg	2/16	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.432325015183213	2		612	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs267605076	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	19	777	0	ENST00000269305.4:c.672G>T	p.Glu224Asp	p.E224D	ENST00000269305	NM_001126112.2	224	gaG/gaT	6/11	1	2	FACETS	0.098	0.073	0.127	0.098	0.073	0.127	SUBCLONAL	1	FALSE	1	0.432325015183213	2		777	898	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685303	89685304	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	50	353	0	ENST00000371953.3:c.202_203dup	p.Asn69ThrfsTer31	p.N69Tfs*31	ENST00000371953	NM_000314.4	66	-/AT	3/9	1	2	FACETS	0.929	0.795	1	0.929	0.795	1	CLONAL	1	FALSE	1	0.432325015183213	2		353	249	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576097	29576098	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	156	524	0	ENST00000356175.3:c.4076dup	p.Gln1360SerfsTer14	p.Q1360Sfs*14	ENST00000356175	NM_000267.3	1357	ttc/ttCc	30/57	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.432325015183213	2		524	627	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939998	49939998	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	227	962	0	ENST00000296474.3:c.1045G>A	p.Val349Ile	p.V349I	ENST00000296474	NM_002447.2	349	Gtc/Atc	1/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.432325015183213	2		962	922	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790819	89790819	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	66	849	6	ENST00000336032.3:c.211del	p.Gln71SerfsTer112	p.Q71Sfs*112	ENST00000336032	NM_006813.2	69	aCc/ac	1/2	1	2	FACETS	0.341	0.295	0.391	0.341	0.295	0.391	SUBCLONAL	1	FALSE	1	0.432325015183213	2		855	896	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49929253	49929253	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1458622585	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	75	660	0	ENST00000296474.3:c.3290A>G	p.Tyr1097Cys	p.Y1097C	ENST00000296474	NM_002447.2	1097	tAc/tGc	15/20	1	2	FACETS	0.464	0.406	0.527	0.464	0.406	0.527	SUBCLONAL	1	FALSE	1	0.432325015183213	2		660	747	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692805	89692805	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204928	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	73	330	0	ENST00000371953.3:c.289C>T	p.Gln97Ter	p.Q97*	ENST00000371953	NM_000314.4	97	Cag/Tag	5/9	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	1	0.432325015183213	2		330	315	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656840	45656840	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	81	697	2	ENST00000407780.3:c.316del	p.Gln106ArgfsTer11	p.Q106Rfs*11	ENST00000407780	NM_001283052.1	106	Cag/ag	3/7	1	2	FACETS	0.51	0.449	0.575	0.51	0.449	0.575	SUBCLONAL	1	FALSE	1	0.432325015183213	2		699	735	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259251	89259251	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	88	504	1	ENST00000336596.2:c.395G>T	p.Gly132Val	p.G132V	ENST00000336596	NM_005233.5	132	gGg/gTg	3/17	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	1	0.432325015183213	2		505	376	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	83	393	0	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	1	0.432325015183213	2		393	339	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101068	27101068	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	239	859	0	ENST00000324856.7:c.4354del	p.Gln1452ArgfsTer29	p.Q1452Rfs*29	ENST00000324856	NM_006015.4	1450	ggC/gg	18/20	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.432325015183213	2		859	805	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712647	43712647	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1305746795	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	94	906	0	ENST00000382044.4:c.4537C>T	p.Arg1513Ter	p.R1513*	ENST00000382044	NM_001141980.1	1513	Cga/Tga	21/28	1	2	FACETS	0.469	0.416	0.525	0.469	0.416	0.525	SUBCLONAL	1	FALSE	1	0.432325015183213	2		906	928	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861577	152861577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149734965	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	54	885	1	ENST00000406277.2:c.175G>A	p.Glu59Lys	p.E59K	ENST00000406277	NM_152274.4	59	Gag/Aag	4/7	0.432325015183213		FACETS		0.37	0.506				SUBCLONAL	1	FALSE	0	0.432325015183213	4		886	823	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867626	78867626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781190662	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	276	854	3	ENST00000306801.3:c.2362C>T	p.Arg788Cys	p.R788C	ENST00000306801	NM_020761.2	788	Cgc/Tgc	20/34	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	1	0.432325015183213	2		857	966	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152098	11152098	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1290442223	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	58	617	0	ENST00000358026.2:c.4382G>A	p.Arg1461His	p.R1461H	ENST00000358026	NM_001128849.1	1461	cGc/cAc	31/36	1	2	FACETS	0.399	0.342	0.461	0.399	0.342	0.461	SUBCLONAL	1	FALSE	1	0.432325015183213	2		617	672	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778953	9778955	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs1259321686	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	173	782	0	ENST00000377346.4:c.1228_1230del	p.Lys410del	p.K410del	ENST00000377346	NM_005026.3	408	AAG/-	9/24	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.432325015183213	2		782	675	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885994	59885994	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780834054	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	43	617	1	ENST00000259008.2:c.752G>A	p.Arg251His	p.R251H	ENST00000259008	NM_032043.2	251	cGc/cAc	7/20	1	2	FACETS	0.302	0.252	0.358	0.302	0.252	0.358	SUBCLONAL	1	FALSE	1	0.432325015183213	2		618	659	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645270	67645270	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	226	700	1	ENST00000264010.4:c.535G>T	p.Glu179Ter	p.E179*	ENST00000264010	NM_006565.3	179	Gaa/Taa	3/12	1	2	FACETS	0.752	0.704	0.802	1	0.992	1	SUBCLONAL	2	FALSE	1	0.432325015183213	2		701	695	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784098	120784098	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	236	1038	0	ENST00000257552.2:c.887del	p.Pro296LeufsTer57	p.P296Lfs*57	ENST00000257552	NM_002442.3	296	cCt/ct	13/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.432325015183213	2		1038	915	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161747	47161747	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	124	362	0	ENST00000409792.3:c.4379G>T	p.Trp1460Leu	p.W1460L	ENST00000409792	NM_014159.6	1460	tGg/tTg	3/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.432325015183213	2		362	403	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087389	27087389	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	228	720	0	ENST00000324856.7:c.1963G>T	p.Gly655Ter	p.G655*	ENST00000324856	NM_006015.4	655	Gga/Tga	5/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.432325015183213	2		720	818	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981101	201981101	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1558273354	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	93	773	3	ENST00000359651.3:c.184del	p.Glu62AsnfsTer93	p.E62Nfs*93	ENST00000359651		60	ttG/tt	2/8	1	2	FACETS	0.555	0.493	0.621	0.555	0.493	0.621	SUBCLONAL	1	FALSE	1	0.432325015183213	2		776	775	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4388037	4388037	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	157	537	0	ENST00000261254.3:c.523T>C	p.Ser175Pro	p.S175P	ENST00000261254	NM_001759.3	175	Tct/Cct	3/5	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.432325015183213	2		537	544	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499770	18499770	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	93	337	2	ENST00000266497.5:c.1625G>T	p.Arg542Met	p.R542M	ENST00000266497		542	aGg/aTg	10/31	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.432325015183213	2		339	353	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49423208	49423208	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	75	796	0	ENST00000301067.7:c.14051del	p.Pro4684LeufsTer113	p.P4684Lfs*113	ENST00000301067	NM_003482.3	4684	cCt/ct	43/54	1	2	FACETS	0.399	0.349	0.453	0.399	0.349	0.453	SUBCLONAL	1	FALSE	1	0.432325015183213	2		796	870	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14031696	14031696	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	61	357	0	ENST00000311895.7:c.1885G>T	p.Ala629Ser	p.A629S	ENST00000311895	NM_005236.2	629	Gct/Tct	9/11	1	2	FACETS	0.78	0.676	0.891	0.78	0.676	0.891	SUBCLONAL	1	FALSE	1	0.432325015183213	2		357	362	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348782	89348782	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs201207422	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	281	967	1	ENST00000301030.4:c.4168G>T	p.Gly1390Cys	p.G1390C	ENST00000301030	NM_001256183.1	1390	Ggc/Tgc	9/13	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.432325015183213	2		968	1013	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110284	3110284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753693838	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	60	863	0	ENST00000078429.4:c.274C>T	p.Arg92Trp	p.R92W	ENST00000078429	NM_002067.2	92	Cgg/Tgg	2/7	1	2	FACETS	0.322	0.277	0.372	0.322	0.277	0.372	SUBCLONAL	1	FALSE	1	0.432325015183213	2		863	861	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221318	36221318	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	264	930	0	ENST00000222270.7:c.5152A>T	p.Lys1718Ter	p.K1718*	ENST00000222270	NM_014727.1	1718	Aag/Tag	24/37	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	1	0.432325015183213	2		930	901	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029189	26029189	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	123	377	1	ENST00000435504.4:c.161C>T	p.Ala54Val	p.A54V	ENST00000435504		54	gCa/gTa	4/13	1	2	FACETS	0.767	0.701	0.835	1	0.987	1	SUBCLONAL	2	FALSE	1	0.432325015183213	2		378	371	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607730	46607730	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	258	925	0	ENST00000263734.3:c.1919C>A	p.Pro640His	p.P640H	ENST00000263734	NM_001430.4	640	cCc/cAc	12/16	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	1	0.432325015183213	2		925	861	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881487	111881487	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	46	667	0	ENST00000393256.3:c.169del	p.His57ThrfsTer27	p.H57Tfs*27	ENST00000393256	NM_006538.4	55	tgC/tg	2/4	1	2	FACETS	0.331	0.278	0.39	0.331	0.278	0.39	SUBCLONAL	1	FALSE	1	0.432325015183213	2		667	643	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157741	106157741	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	79	296	0	ENST00000380013.4:c.2642G>T	p.Arg881Met	p.R881M	ENST00000380013	NM_001127208.2	881	aGg/aTg	3/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.432325015183213	2		296	267	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395908	395908	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	161	612	0	ENST00000380956.4:c.466del	p.Thr156ArgfsTer15	p.T156Rfs*15	ENST00000380956	NM_001195286.1	155	acA/ac	4/9	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.432325015183213	2		612	606	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140913	37140913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	164	609	0	ENST00000373509.5:c.749G>A	p.Arg250Lys	p.R250K	ENST00000373509	NM_002648.3	250	aGg/aAg	5/6	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.432325015183213	2		609	586	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981503	70981503	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	82	997	3	ENST00000276594.2:c.593C>T	p.Thr198Met	p.T198M	ENST00000276594	NM_024504.3	198	aCg/aTg	2/8	1	2	FACETS	0.38	0.334	0.429	0.38	0.334	0.429	SUBCLONAL	1	FALSE	1	0.432325015183213	2		1000	999	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874550	35874550	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0052202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	130	461	0	ENST00000303115.3:c.709del		p.X237_splice	ENST00000303115	NM_002185.3	237			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.432325015183213	2		461	470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs864622237	NA	P-0052203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	197	639	0	ENST00000269305.4:c.700T>C	p.Tyr234His	p.Y234H	ENST00000269305	NM_001126112.2	234	Tac/Cac	7/11	0.51617787838027	1	FACETS	0.974	0.908	1	0.974	0.908	1	CLONAL	1	TRUE	0	0.521119164486861	1		639	574	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117054	193117054	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878855091	NA	P-0052203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	37	448	0	ENST00000367435.3:c.787C>T	p.Arg263Cys	p.R263C	ENST00000367435	NM_024529.4	263	Cgt/Tgt	8/17	0.506089514353864	1	FACETS	0.186	0.152	0.223	0.186	0.152	0.223	SUBCLONAL	1	TRUE	0	0.521119164486861	1		448	566	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404706	70404706	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	196	481	1	ENST00000373644.4:c.2220A>T	p.Glu740Asp	p.E740D	ENST00000373644	NM_030625.2	740	gaA/gaT	4/12	1	2	FACETS	0.964	0.895	1	0.964	0.895	1	CLONAL	1	TRUE	1	0.521119164486861	2		482	780	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47600697	47600697	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	80	505	0	ENST00000263735.4:c.172A>T	p.Ile58Phe	p.I58F	ENST00000263735	NM_002354.2	58	Att/Ttt	2/9	1	2	FACETS	0.432	0.38	0.488	0.432	0.38	0.488	SUBCLONAL	1	TRUE	1	0.521119164486861	2		505	710	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169940462	169940462	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1305218534	NA	P-0052203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	123	563	0	ENST00000295797.4:c.5C>G	p.Pro2Arg	p.P2R	ENST00000295797	NM_002740.5	2	cCg/cGg	1/18	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.521119164486861	2		563	464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	747	656	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.344721416360683	3	FACETS	0.907	0.881	0.933			1	CLONAL	3	TRUE	NA	0.536851809609879	3		657	1297	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	166	460	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.756	0.703	0.81	1	0.991	1	SUBCLONAL	2	TRUE	1	0.536851809609879	2		460	409	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	205	534	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	0.336442604467875	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.536851809609879	3		534	454	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450766	70450766	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	340	706	0	ENST00000373644.4:c.5606C>T	p.Ser1869Leu	p.S1869L	ENST00000373644	NM_030625.2	1869	tCa/tTa	12/12	0.336297709031777	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.536851809609879	1		706	709	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	200	485	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	0.336442604467875	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.536851809609879	3		485	434	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160670	56160670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	85	489	0	ENST00000399503.3:c.944G>A	p.Arg315Lys	p.R315K	ENST00000399503	NM_005921.1	315	aGa/aAa	4/20	1	2	FACETS	0.637	0.565	0.714	0.637	0.565	0.714	SUBCLONAL	1	TRUE	1	0.536851809609879	2		489	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579406	7579406	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1583	177	1083	1	ENST00000269305.4:c.281C>A	p.Ser94Ter	p.S94*	ENST00000269305	NM_001126112.2	94	tCa/tAa	4/11	0.344721416360683	3	FACETS	0.475	0.436	0.517			1	SUBCLONAL	1	TRUE	NA	0.536851809609879	3		1084	1760	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713315	30713315	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764821003	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	89	506	0	ENST00000295754.5:c.640G>A	p.Glu214Lys	p.E214K	ENST00000295754	NM_003242.5	214	Gag/Aag	4/7	0.454987368368678	2	FACETS	0.496	0.439	0.556	0.248	0.219	0.278	SUBCLONAL	1	TRUE	0	0.536851809609879	2		506	669	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120882	94120882	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867992353	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	58	480	0	ENST00000369303.4:c.169G>A	p.Glu57Lys	p.E57K	ENST00000369303	NM_004440.3	57	Gaa/Aaa	3/17	0.210442053512397	1	FACETS	0.377	0.325	0.434	0.377	0.325	0.434	INDETERMINATE	1	TRUE	0	0.536851809609879	1		480	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577563	7577563	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1567549584	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1162	150	772	0	ENST00000269305.4:c.718A>G	p.Ser240Gly	p.S240G	ENST00000269305	NM_001126112.2	240	Agt/Ggt	7/11	0.344721416360683	3	FACETS	0.54	0.492	0.591			1	SUBCLONAL	1	TRUE	NA	0.536851809609879	3		772	1312	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830732	3830732	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	139	413	0	ENST00000262367.5:c.1823+1G>A		p.X608_splice	ENST00000262367	NM_004380.2	608			0.336297709031777	1	FACETS	0.849	0.78	0.921	0.849	0.78	0.921	CLONAL	1	TRUE	0	0.536851809609879	1		413	446	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942143	17942143	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs749741343	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	139	1054	0	ENST00000458235.1:c.2872G>C	p.Glu958Gln	p.E958Q	ENST00000458235	NM_000215.3	958	Gag/Cag	21/24	NA	2	FACETS	0.426	0.386	0.467			1	INDETERMINATE	1	TRUE	NA	0.536851809609879	2		1054	1216	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	110	776	0	ENST00000267101.3:c.273G>C	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atC	3/28	0.268691248326007	2	FACETS	0.383	0.343	0.426	0.192	0.171	0.213	INDETERMINATE	1	TRUE	0	0.536851809609879	2		776	1069	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162735812	162735812	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	101	635	0	ENST00000367921.3:c.1121C>G	p.Ser374Cys	p.S374C	ENST00000367921	NM_006182.2	374	tCt/tGt	10/18	0.195513575110171	2	FACETS	0.472	0.422	0.526	0.236	0.211	0.263	INDETERMINATE	1	TRUE	0	0.536851809609879	2		635	797	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720294	43720294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	106	659	0	ENST00000382044.4:c.3748G>A	p.Glu1250Lys	p.E1250K	ENST00000382044	NM_001141980.1	1250	Gaa/Aaa	18/28	0.235486794738401	0	FACETS	0.262	0.235	0.291			1	INDETERMINATE	1	TRUE	0	0.536851809609879	0		659	697	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105812	27105813	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	213	648	0	ENST00000324856.7:c.5423_5424del	p.Lys1808IlefsTer2	p.K1808Ifs*2	ENST00000324856	NM_006015.4	1808	aAG/a	20/20	0.195513575110171	2	FACETS	1	0.984	1	0.584	0.545	0.624	INDETERMINATE	1	TRUE	0	0.536851809609879	2		648	679	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981535	201981536	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	194	1053	0	ENST00000359651.3:c.449_450insA	p.Phe150LeufsTer11	p.F150Lfs*11	ENST00000359651		150	ttc/ttAc	3/8	0.418154351004638	1	FACETS	0.385	0.355	0.417	0.385	0.355	0.417	SUBCLONAL	1	TRUE	0	0.536851809609879	1		1053	1372	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206667320	206667320	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553391457	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	152	878	1	ENST00000367120.3:c.2113G>A	p.Glu705Lys	p.E705K	ENST00000367120	NM_014002.3	705	Gaa/Aaa	21/22	0.418154351004638	1	FACETS	0.356	0.325	0.389	0.356	0.325	0.389	SUBCLONAL	1	TRUE	0	0.536851809609879	1		879	1164	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226576395	226576395	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	223	570	0	ENST00000366794.5:c.679G>C	p.Glu227Gln	p.E227Q	ENST00000366794	NM_001618.3	227	Gaa/Caa	5/23	0.210121204927787	2	FACETS	1	0.992	1	0.709	0.665	0.754	INDETERMINATE	1	TRUE	0	0.536851809609879	2		570	586	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612908	228612908	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1177161942	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	130	1119	0	ENST00000366696.1:c.119A>G	p.His40Arg	p.H40R	ENST00000366696	NM_003493.2	40	cAc/cGc	1/1	0.210121204927787	2	FACETS	0.388	0.351	0.428	0.194	0.175	0.214	INDETERMINATE	1	TRUE	0	0.536851809609879	2		1119	1248	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450865	70450865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	378	751	0	ENST00000373644.4:c.5705C>T	p.Ser1902Leu	p.S1902L	ENST00000373644	NM_030625.2	1902	tCa/tTa	12/12	0.336297709031777	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.536851809609879	1		751	750	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771502	112771502	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	178	586	0	ENST00000369452.4:c.1675C>G	p.Gln559Glu	p.Q559E	ENST00000369452	NM_007373.3	559	Cag/Gag	9/9	0.536851809609879	1	FACETS	0.789	0.731	0.849	0.789	0.731	0.849	SUBCLONAL	1	TRUE	0	0.536851809609879	1		586	615	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432373	432373	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	23	156	0	ENST00000399788.2:c.2151-1G>A		p.X717_splice	ENST00000399788	NM_001042603.1	717			0.304781372160915	3	FACETS	0.611	0.479	0.76	0.204	0.159	0.254	INDETERMINATE	1	TRUE	0	0.536851809609879	3		156	178	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463298	463298	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	327	564	0	ENST00000399788.2:c.973C>A	p.Pro325Thr	p.P325T	ENST00000399788	NM_001042603.1	325	Cct/Act	8/28	0.304781372160915	3	FACETS	1	0.989	1	0.755	0.719	0.791	INDETERMINATE	2	TRUE	0	0.536851809609879	3		564	682	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239312	105239312	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	495	995	0	ENST00000349310.3:c.1075G>C	p.Glu359Gln	p.E359Q	ENST00000349310	NM_001014432.1	359	Gag/Cag	12/15	0.483583421073572	2	FACETS	0.812	0.779	0.845	0.812	0.779	0.845	CLONAL	2	TRUE	0	0.536851809609879	2		995	1136	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714282	43714282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	134	919	0	ENST00000382044.4:c.3871G>A	p.Glu1291Lys	p.E1291K	ENST00000382044	NM_001141980.1	1291	Gaa/Aaa	19/28	0.235486794738401	0	FACETS	0.283	0.257	0.311			1	INDETERMINATE	1	TRUE	0	0.536851809609879	0		919	816	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842064	3842064	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	108	494	0	ENST00000262367.5:c.1248C>G	p.Ile416Met	p.I416M	ENST00000262367	NM_004380.2	416	atC/atG	5/31	0.336297709031777	1	FACETS	0.68	0.614	0.748	0.68	0.614	0.748	SUBCLONAL	1	TRUE	0	0.536851809609879	1		494	433	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129678	30129678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	222	733	0	ENST00000263025.4:c.535G>A	p.Asp179Asn	p.D179N	ENST00000263025	NM_002746.2	179	Gac/Aac	3/9	NA	2	FACETS	0.871	0.811	0.932			1	INDETERMINATE	1	TRUE	NA	0.536851809609879	2		733	950	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884240	37884240	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	152	937	0	ENST00000269571.5:c.3711C>G	p.Phe1237Leu	p.F1237L	ENST00000269571		1237	ttC/ttG	27/27	0.210121204927787	2	FACETS	0.468	0.427	0.511	0.234	0.213	0.256	INDETERMINATE	1	TRUE	0	0.536851809609879	2		937	1210	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3113467	3113467	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	132	798	0	ENST00000078429.4:c.461C>G	p.Ser154Cys	p.S154C	ENST00000078429	NM_002067.2	154	tCc/tGc	3/7	0.269542171600536	1	FACETS	0.421	0.382	0.462	0.421	0.382	0.462	INDETERMINATE	1	TRUE	0	0.536851809609879	1		798	854	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015029	27015029	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	116	547	0	ENST00000335756.4:c.131G>C	p.Arg44Thr	p.R44T	ENST00000335756	NM_001809.3	44	aGa/aCa	2/5	1	2	FACETS	0.597	0.538	0.659	0.597	0.538	0.659	SUBCLONAL	1	TRUE	1	0.536851809609879	2		547	724	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436824	52436824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	360	924	0	ENST00000460680.1:c.1954G>A	p.Glu652Lys	p.E652K	ENST00000460680	NM_004656.3	652	Gag/Aag	15/17	0.454987368368678	2	FACETS	1	0.994	1	0.652	0.619	0.685	CLONAL	1	TRUE	0	0.536851809609879	2		924	1029	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807997	1807997	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	176	1359	0	ENST00000260795.2:c.1973T>G	p.Val658Gly	p.V658G	ENST00000260795		658	gTg/gGg	14/17	0.269542171600536	1	FACETS	0.357	0.328	0.388	0.357	0.328	0.388	INDETERMINATE	1	TRUE	0	0.536851809609879	1		1359	1343	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981486	55981486	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	138	490	0	ENST00000263923.4:c.451C>G	p.Leu151Val	p.L151V	ENST00000263923	NM_002253.2	151	Ctc/Gtc	4/30	0.269542171600536	1	FACETS	0.977	0.899	1	0.977	0.899	1	INDETERMINATE	1	TRUE	0	0.536851809609879	1		490	385	SUCCESS
APC	324	MSKCC	GRCh37	5	112173572	112173572	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	41	404	0	ENST00000257430.4:c.2281G>C	p.Glu761Gln	p.E761Q	ENST00000257430	NM_000038.5	761	Gaa/Caa	16/16	0.362626613946115	1	FACETS	0.368	0.307	0.434	0.368	0.307	0.434	SUBCLONAL	1	TRUE	0	0.536851809609879	1		404	304	SUCCESS
APC	324	MSKCC	GRCh37	5	112176386	112176386	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	97	382	0	ENST00000257430.4:c.5095G>C	p.Glu1699Gln	p.E1699Q	ENST00000257430	NM_000038.5	1699	Gag/Cag	16/16	0.362626613946115	1	FACETS	0.875	0.79	0.964	0.875	0.79	0.964	CLONAL	1	TRUE	0	0.536851809609879	1		382	302	SUCCESS
APC	324	MSKCC	GRCh37	5	112176956	112176956	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	78	471	0	ENST00000257430.4:c.5665G>C	p.Glu1889Gln	p.E1889Q	ENST00000257430	NM_000038.5	1889	Gaa/Caa	16/16	0.362626613946115	1	FACETS	0.69	0.612	0.772	0.69	0.612	0.772	SUBCLONAL	1	TRUE	0	0.536851809609879	1		471	308	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547355	106547355	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	70	559	0	ENST00000369096.4:c.592G>C	p.Val198Leu	p.V198L	ENST00000369096	NM_001198.3	198	Gtg/Ctg	4/7	0.210442053512397	1	FACETS	0.308	0.268	0.351	0.308	0.268	0.351	INDETERMINATE	1	TRUE	0	0.536851809609879	1		559	620	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6038745	6038745	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	122	793	0	ENST00000265849.7:c.699G>C	p.Gln233His	p.Q233H	ENST00000265849	NM_000535.5	233	caG/caC	6/15	1	2	FACETS	0.436	0.393	0.482	0.436	0.393	0.482	SUBCLONAL	1	TRUE	1	0.536851809609879	2		793	1042	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935698	13935698	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	43	555	1	ENST00000405192.2:c.1158A>T	p.Arg386Ser	p.R386S	ENST00000405192	NM_001163147.1	386	agA/agT	12/12	1	2	FACETS	0.28	0.233	0.331	0.28	0.233	0.331	SUBCLONAL	1	TRUE	1	0.536851809609879	2		556	573	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266511	55266511	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	388	760	0	ENST00000275493.2:c.2803C>T	p.Gln935Ter	p.Q935*	ENST00000275493	NM_005228.3	935	Cag/Tag	23/28	1	2	FACETS	0.766	0.731	0.802	1	0.996	1	SUBCLONAL	2	TRUE	1	0.536851809609879	2		760	943	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132798	152132798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749087296	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	197	729	1	ENST00000262189.6:c.74C>T	p.Pro25Leu	p.P25L	ENST00000262189	NM_170606.2	25	cCg/cTg	1/59	0.297998179449276	3	FACETS	1	0.927	1	0.5	0.463	0.539	INDETERMINATE	1	TRUE	1	0.536851809609879	3		730	930	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372166	55372166	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1381547285	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	332	560	0	ENST00000297316.4:c.856C>A	p.Leu286Ile	p.L286I	ENST00000297316	NM_022454.3	286	Ctc/Atc	2/2	1	2	FACETS	0.812	0.772	0.852	1	0.996	1	CLONAL	2	TRUE	1	0.536851809609879	2		560	762	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8501042	8501042	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs201991300	NA	P-0052217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	47	391	0	ENST00000356435.5:c.1840C>G	p.Gln614Glu	p.Q614E	ENST00000356435		614	Caa/Gaa	13/35	0.536851809609879	4	FACETS	0.433	0.365	0.509	0.144	0.121	0.17	SUBCLONAL	1	TRUE	1	0.536851809609879	4		391	621	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0052218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	117	472	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	0.54787003089519	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.54787003089519	1		472	270	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555525585	NA	P-0052218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	160	732	0	ENST00000269305.4:c.673-2A>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.54787003089519	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.54787003089519	1		732	409	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402540	20402540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	118	675	0	ENST00000346618.3:c.77C>T	p.Ala26Val	p.A26V	ENST00000346618	NM_001949.4	26	gCc/gTc	1/7	1	2	FACETS	0.981	0.892	1	0.981	0.892	1	CLONAL	1	TRUE	1	0.54787003089519	2		675	439	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998873	100998968	+	inframe_deletion	In_Frame_Del	DEL	GGCAGGATAGGCACGTGGATGAAATCCATCACCGTGGTGGCCAGCGGGGAGCGCCCGGGCGCCATCGGCGCGTCCTGCTCCACCAGGGCGACCCTG	GGCAGGATAGGCACGTGGATGAAATCCATCACCGTGGTGGCCAGCGGGGAGCGCCCGGGCGCCATCGGCGCGTCCTGCTCCACCAGGGCGACCCTG	-	novel	NA	P-0052218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	170	1248	0	ENST00000325455.5:c.834_929del	p.Arg279_Pro310del	p.R279_P310del	ENST00000325455	NM_001202474.3	278	ccCAGGGTCGCCCTGGTGGAGCAGGACGCGCCGATGGCGCCCGGGCGCTCCCCGCTGGCCACCACGGTGATGGATTTCATCCACGTGCCTATCCTGCCt/cct	1/8	1	2	FACETS	0.893	0.824	0.965	0.893	0.824	0.965	CLONAL	1	TRUE	1	0.54787003089519	2		1248	695	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119751	70119751	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	282	767	0	ENST00000245479.2:c.754del	p.Leu252Ter	p.L252*	ENST00000245479	NM_000346.3	251	gaC/ga	3/3	0.54787003089519	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	1	0.54787003089519	3		767	655	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41544688	41545044	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATGACCTCATGAAATTGTGATTAACTCTCCTCACTTAACAGAGCATGCAAAGAAAATTACCTGCTATCCTTGTGCTAGGCATATTTGTGTACCAAGAGAATGTGTGTTCCATCCTCTTACTATTTCTTGGAGTAGGCCTAGGTAAACTGTGAGGCTATTTCTCTTTATCTTGGCACAAGAGTCAGTTGTTCTACAACTTTCTTCCTTCTCCTCTTCAGCCCTCTTCACCTATACTCCTGTCTTTGGCTTTTCTCTACTTAATAAGCCTGACGTTAGGAGCATTTGATGATTTTAGTTATAGTAGAATAACTATAATGAAGCAGTTTGGTGATTTGTGTTTTTTTTTTTTTTCAGCCT	ATGACCTCATGAAATTGTGATTAACTCTCCTCACTTAACAGAGCATGCAAAGAAAATTACCTGCTATCCTTGTGCTAGGCATATTTGTGTACCAAGAGAATGTGTGTTCCATCCTCTTACTATTTCTTGGAGTAGGCCTAGGTAAACTGTGAGGCTATTTCTCTTTATCTTGGCACAAGAGTCAGTTGTTCTACAACTTTCTTCCTTCTCCTCTTCAGCCCTCTTCACCTATACTCCTGTCTTTGGCTTTTCTCTACTTAATAAGCCTGACGTTAGGAGCATTTGATGATTTTAGTTATAGTAGAATAACTATAATGAAGCAGTTTGGTGATTTGTGTTTTTTTTTTTTTTCAGCCT	-	novel	NA	P-0052218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3	147	12	1	ENST00000263253.7:c.2242-351_2247del		p.X748_splice	ENST00000263253	NM_001429.3	748		13/31	0.547602839400771	1	FACETS		NA	1	1	0.995	1	NA	3	TRUE	0	0.54787003089519	1		13	150	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243998	53243998	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	249	557	0	ENST00000375401.3:c.995G>A	p.Arg332Gln	p.R332Q	ENST00000375401	NM_004187.3	332	cGa/cAa	8/26	1	1	FACETS	0.778	0.74	0.816	1	0.995	1	SUBCLONAL	2	TRUE	0	0.54787003089519	1		557	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0052219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	246	656	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.84	0.787	0.895	1	0.995	1	CLONAL	3	FALSE	1	0.227692428296416	2		657	857	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0052219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	92	379	3	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.969	1	1	0.988	1	CLONAL	2	FALSE	1	0.227692428296416	2		382	332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579400	7579401	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	250	1183	0	ENST00000269305.4:c.286dup	p.Ser96PhefsTer53	p.S96Ffs*53	ENST00000269305	NM_001126112.2	96	tct/tTct	4/11	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	FALSE	1	0.227692428296416	2		1183	935	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875997	76875997	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	67	258	0	ENST00000373344.5:c.5138del	p.Pro1713LeufsTer12	p.P1713Lfs*12	ENST00000373344	NM_000489.3	1713	cCt/ct	20/35	0.227692428296416	0	FACETS	0.802	0.71	0.896			1	CLONAL	3	FALSE	0	0.227692428296416	0		258	189	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552152	29552152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199474738	NA	P-0052220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	57	384	0	ENST00000356175.3:c.1885G>A	p.Gly629Arg	p.G629R	ENST00000356175	NM_000267.3	629	Ggg/Agg	17/57	0.144805620342112	3	FACETS	1	0.957	1			1	INDETERMINATE	1	TRUE	NA	0.349460522366937	3		384	297	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	50	460	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.349460522366937	2		460	259	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166184	118166184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371434677	NA	P-0052220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	79	461	0	ENST00000369448.3:c.694G>A	p.Ala232Thr	p.A232T	ENST00000369448	NM_017709.3	232	Gcc/Acc	2/2	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.349460522366937	2		461	407	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692910	89692910	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	100	567	0	ENST00000371953.3:c.394G>C	p.Gly132Arg	p.G132R	ENST00000371953	NM_000314.4	132	Ggt/Cgt	5/9	0.349460522366937	1	FACETS	0.91	0.816	1	0.91	0.816	1	CLONAL	1	TRUE	0	0.349460522366937	1		567	519	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845697	151845697	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	202	702	0	ENST00000262189.6:c.13315G>T	p.Val4439Phe	p.V4439F	ENST00000262189	NM_170606.2	4439	Gtc/Ttc	52/59	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		702	954	SUCCESS
APC	324	MSKCC	GRCh37	5	112111412	112111412	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	36	335	0	ENST00000257430.4:c.509A>G	p.Asp170Gly	p.D170G	ENST00000257430	NM_000038.5	170	gAt/gGt	5/16	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		335	196	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057923	27057924	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0052222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	165	774	2	ENST00000324856.7:c.1636dup	p.Gln546ProfsTer77	p.Q546Pfs*77	ENST00000324856	NM_006015.4	544	cac/caCc	3/20	1	2	FACETS	0.831	0.762	0.902	0.831	0.762	0.902	CLONAL	1	TRUE	1	0.398076578914762	2		776	998	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056244	27056245	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GACA	novel	NA	P-0052222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	199	759	8	ENST00000324856.7:c.1241_1244dup	p.His415GlnfsTer209	p.H415Qfs*209	ENST00000324856	NM_006015.4	414	gga/gGACAga	2/20	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.398076578914762	2		767	970	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052624	42052625	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCG	novel	NA	P-0052222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	128	533	4	ENST00000219905.7:c.7305_7307dup	p.Arg2436dup	p.R2436dup	ENST00000219905	NM_001164273.1	2436	gag/gaGCGg	20/24	1	2	FACETS	0.911	0.827	0.999	0.911	0.827	0.999	CLONAL	1	TRUE	1	0.398076578914762	2		537	706	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976403	25976403	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	252	459	8	ENST00000435504.4:c.1142G>A	p.Ser381Asn	p.S381N	ENST00000435504		381	aGt/aAt	11/13	0.398076578914762	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.398076578914762	2		467	629	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163148	47163149	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	120	394	6	ENST00000409792.3:c.2977_2978insA	p.Ser993TyrfsTer2	p.S993Yfs*2	ENST00000409792	NM_014159.6	993	tct/tAct	3/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.398076578914762	2		400	498	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31435971	31435971	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	91	295	4	ENST00000344624.3:c.2943C>G	p.Ser981Arg	p.S981R	ENST00000344624		981	agC/agG	22/33	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.398076578914762	2		299	367	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933236	39933237	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	300	433	27	ENST00000378444.4:c.1362dup	p.Ala455SerfsTer2	p.A455Sfs*2	ENST00000378444	NM_001123385.1	454	-/A	4/15	1	1	FACETS	0.912	0.866	0.958	1	0.996	1	CLONAL	2	TRUE	0	0.398076578914762	1		460	662	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974782	21974783	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CAGT	novel	NA	P-0052225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	64	296	0	ENST00000304494.5:c.41_44dup	p.Trp15Ter	p.W15*	ENST00000304494	NM_000077.4	15	tgg/tgACTGg	1/3	0.674534647812765	1	FACETS	0.892	0.795	0.99	0.892	0.795	0.99	CLONAL	1	TRUE	0	0.674534647812765	1		296	141	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578502	7578502	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	166	1142	0	ENST00000269305.4:c.428T>C	p.Val143Ala	p.V143A	ENST00000269305	NM_001126112.2	143	gTg/gCg	5/11	0.666972295471054	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.674534647812765	1		1142	292	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784045	120784045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763290869	NA	P-0052225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	258	1235	3	ENST00000257552.2:c.940G>A	p.Gly314Ser	p.G314S	ENST00000257552	NM_002442.3	314	Ggc/Agc	13/15	0.604971547810173	3	FACETS	0.945	0.895	0.996	0.945	0.895	0.996	CLONAL	2	TRUE	1	0.674534647812765	3		1238	541	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748117	72748117	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	131	643	0	ENST00000357731.5:c.61C>G	p.Leu21Val	p.L21V	ENST00000357731	NM_173808.2	21	Ctc/Gtc	1/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.674534647812765	2		643	331	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421807	49421807	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	140	1051	1	ENST00000301067.7:c.14500del	p.Glu4834LysfsTer24	p.E4834Kfs*24	ENST00000301067	NM_003482.3	4834	Gaa/aa	46/54	0.674534647812765	1	FACETS	0.976	0.906	1	0.976	0.906	1	CLONAL	1	TRUE	0	0.674534647812765	1		1052	282	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101110	41101110	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	105	841	0	ENST00000373198.4:c.1246C>A	p.Arg416Ser	p.R416S	ENST00000373198	NM_133170.3	416	Cgc/Agc	8/32	1	2	FACETS	0.887	0.803	0.974	0.887	0.803	0.974	CLONAL	1	TRUE	1	0.674534647812765	2		841	351	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520407	176520409	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0052225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	244	1014	0	ENST00000292408.4:c.1253_1255del	p.Phe418del	p.F418del	ENST00000292408	NM_213647.1	418	TTC/-	10/18	0.638958330312226	2	FACETS	0.904	0.861	0.947	0.904	0.861	0.947	CLONAL	2	TRUE	0	0.674534647812765	2		1014	400	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090563	5090564	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	71	441	0	ENST00000381652.3:c.2880dup	p.Cys961MetfsTer31	p.C961Mfs*31	ENST00000381652	NM_004972.3	960	ata/atAa	21/25	0.674534647812765	1	FACETS	0.889	0.797	0.981	0.889	0.797	0.981	CLONAL	1	TRUE	0	0.674534647812765	1		441	157	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913315	NA	P-0052226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	127	926	1	ENST00000326873.7:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000326873	NM_000455.4	194	Gac/Tac	4/10	0.290952054654656	1	FACETS	0.932	0.845	1	0.932	0.845	1	CLONAL	1	FALSE	0	0.290952054654656	1		927	800	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913535	NA	P-0052226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	71	466	0	ENST00000311936.3:c.37G>C	p.Gly13Arg	p.G13R	ENST00000311936	NM_004985.3	13	Ggc/Cgc	2/5	1	2	FACETS	0.837	0.731	0.951	0.837	0.731	0.951	CLONAL	1	FALSE	1	0.290952054654656	2		466	583	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185184	123185184	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	54	490	0	ENST00000218089.9:c.1136C>A	p.Thr379Asn	p.T379N	ENST00000218089	NM_001042749.1	379	aCc/aAc	13/35	1	2	FACETS	0.538	0.459	0.625	0.538	0.459	0.625	SUBCLONAL	1	FALSE	1	0.290952054654656	2		490	690	SUCCESS
APC	324	MSKCC	GRCh37	5	112178282	112178282	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1554087893	NA	P-0052226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	66	460	0	ENST00000257430.4:c.6991C>G	p.Pro2331Ala	p.P2331A	ENST00000257430	NM_000038.5	2331	Cct/Gct	16/16	1	2	FACETS	0.895	0.778	1	0.895	0.778	1	CLONAL	1	FALSE	1	0.290952054654656	2		460	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0052227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	20	685	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	1	2	FACETS	0.09	0.068	0.115	0.09	0.068	0.115	SUBCLONAL	1	TRUE	1	0.574099064750029	2		685	778	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591887	48591889	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0052227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	151	519	0	ENST00000342988.3:c.1052_1054del	p.Asp351del	p.D351del	ENST00000342988	NM_005359.5	350	gtTGAt/gtt	9/12	0.574099064750029	1	FACETS	0.897	0.829	0.967	0.897	0.829	0.967	CLONAL	1	TRUE	0	0.574099064750029	1		519	418	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289345	33289345	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0052227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	122	388	0	ENST00000374542.5:c.208-1G>A		p.X70_splice	ENST00000374542	NM_001141970.1	70			0.574099064750029	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.574099064750029	1		388	298	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	201	460	0				ENST00000310581	NM_198253.2	-/1132			0.622134812573981	3	FACETS	1	0.955	1	0.519	0.482	0.558	CLONAL	1	TRUE	1	0.622134812573981	3		460	816	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912656	NA	P-0052228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	312	807	0	ENST00000269305.4:c.734G>C	p.Gly245Ala	p.G245A	ENST00000269305	NM_001126112.2	245	gGc/gCc	7/11	0.622134812573981	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.622134812573981	1		807	563	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628436	187628437	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0052228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	356	866	0	ENST00000441802.2:c.2545_2546insC	p.Lys849ThrfsTer23	p.K849Tfs*23	ENST00000441802	NM_005245.3	849	aaa/aCaa	2/27	NA	2	FACETS	0.835	0.799	0.872			1	INDETERMINATE	2	TRUE	NA	0.622134812573981	2		866	685	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0052229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	33	542	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.671	0.544	0.814	0.671	0.544	0.814	SUBCLONAL	1	TRUE	1	0.14	2		542	703	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0052229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	25	648	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.53	0.416	0.662	0.53	0.416	0.662	SUBCLONAL	1	TRUE	1	0.14	2		648	674	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221999	1221999	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	79	995	2	ENST00000326873.7:c.914A>C	p.Gln305Pro	p.Q305P	ENST00000326873	NM_000455.4	305	cAg/cCg	7/10	0.17695563755869	1	FACETS	0.871	0.763	0.987	0.871	0.763	0.987	CLONAL	1	TRUE	0	0.14	1		997	1205	SUCCESS
APC	324	MSKCC	GRCh37	5	112175373	112175373	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	TT	novel	NA	P-0052229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	32	316	0	ENST00000257430.4:c.4082delinsTT	p.Pro1361LeufsTer14	p.P1361Lfs*14	ENST00000257430	NM_000038.5	1361	cCc/cTTc	16/16	1	2	FACETS	1	0.829	1	1	0.829	1	CLONAL	1	TRUE	1	0.14	2		316	447	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0052230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	79	380	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.183024769527031	2		380	628	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203492	108203492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs138941496	NA	P-0052230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	82	297	0	ENST00000278616.4:c.7792C>T	p.Arg2598Ter	p.R2598*	ENST00000278616	NM_000051.3	2598	Cga/Tga	53/63	1	2	FACETS	1	0.943	1	1	0.986	1	CLONAL	2	TRUE	1	0.183024769527031	2		297	406	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492821	56492821	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	79	701	0	ENST00000407977.2:c.118del	p.Arg40AspfsTer11	p.R40Dfs*11	ENST00000407977		40	Aga/ga	2/10	1	2	FACETS	0.954	0.837	1	0.954	0.837	1	CLONAL	1	TRUE	1	0.183024769527031	2		701	905	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0052231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	88	537	0				ENST00000310581	NM_198253.2	-/1132			0.301901558521836	1	FACETS	0.977	0.869	1	0.977	0.869	1	CLONAL	1	TRUE	0	0.33	1		537	456	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692995	89692995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554898225	NA	P-0052231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	127	566	0	ENST00000371953.3:c.479C>T	p.Thr160Ile	p.T160I	ENST00000371953	NM_000314.4	160	aCc/aTc	5/9	0.301901558521836	1	FACETS	0.933	0.846	1	0.933	0.846	1	CLONAL	1	TRUE	0	0.33	1		566	689	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467823	50467823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	88	756	2	ENST00000331340.3:c.1058C>T	p.Pro353Leu	p.P353L	ENST00000331340	NM_006060.4	353	cCg/cTg	8/8	0.27427141077961	3	FACETS	0.745	0.659	0.837	0.373	0.329	0.419	SUBCLONAL	1	TRUE	1	0.33	3		758	834	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191804	123191805	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1392503050	NA	P-0052231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	98	416	0	ENST00000218089.9:c.1400dup	p.Phe468LeufsTer5	p.F468Lfs*5	ENST00000218089	NM_001042749.1	465	gtt/gTtt	15/35	1	2	FACETS	0.871	0.777	0.97	0.871	0.777	0.97	CLONAL	1	TRUE	1	0.33	2		416	682	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707856	43707857	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0052231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	161	938	1	ENST00000382044.4:c.5024_5025del	p.Leu1675HisfsTer4	p.L1675Hfs*4	ENST00000382044	NM_001141980.1	1675	cTT/c	23/28	1	2	FACETS	0.875	0.801	0.953	0.875	0.801	0.953	CLONAL	1	TRUE	1	0.33	2		939	1115	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525641	187525641	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs201423674	NA	P-0052231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	100	643	0	ENST00000441802.2:c.10438A>G	p.Ile3480Val	p.I3480V	ENST00000441802	NM_005245.3	3480	Att/Gtt	18/27	1	2	FACETS	0.735	0.656	0.819	0.735	0.656	0.819	SUBCLONAL	1	TRUE	1	0.33	2		643	825	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0052232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	194	825	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.415490832880059	1	FACETS	0.958	0.889	1	0.958	0.889	1	CLONAL	1	TRUE	0	0.441001937517713	1		826	716	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0052232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	98	486	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.903	0.809	1	0.903	0.809	1	CLONAL	1	TRUE	1	0.441001937517713	2		486	492	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936093	178936095	+	missense_variant	Missense_Mutation	TNP	GCA	GCA	CTT	novel	NA	P-0052232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	217	742	1	ENST00000263967.3:c.1635_1637delinsCTT	p.Glu545_Gln546delinsAspLeu	p.E545_Q546delinsDL	ENST00000263967	NM_006218.2	545	gaGCAg/gaCTTg	10/21	0.441001937517713	3	FACETS	0.913	0.853	0.974	0.913	0.853	0.974	CLONAL	2	TRUE	1	0.441001937517713	3		743	658	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294903	1294903	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1038954321	NA	P-0052232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	19	148	0	ENST00000310581.5:c.202G>T	p.Ala68Ser	p.A68S	ENST00000310581	NM_198253.2	68	Gcc/Tcc	1/16	1	2	FACETS	0.712	0.547	0.901	0.712	0.547	0.901	CLONAL	1	TRUE	1	0.441001937517713	2		148	121	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0052233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	418	1333	1	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1334	989	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933358	39933358	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779371249	NA	P-0052233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	179	1335	4	ENST00000378444.4:c.1241C>T	p.Ala414Val	p.A414V	ENST00000378444	NM_001123385.1	414	gCg/gTg	4/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1339	993	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370879	55370879	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	220	1131	1	ENST00000297316.4:c.181C>T	p.Arg61Ter	p.R61*	ENST00000297316	NM_022454.3	61	Cga/Tga	1/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1132	1190	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267268	41267294	+	inframe_deletion	In_Frame_Del	DEL	CTTGCTCAACAAAACAAATGTTAAATT	CTTGCTCAACAAAACAAATGTTAAATT	-	novel	NA	P-0052233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	99	623	0	ENST00000349496.5:c.856_882del	p.Leu286_Leu294del	p.L286_L294del	ENST00000349496	NM_001904.3	284	gcCTTGCTCAACAAAACAAATGTTAAATTc/gcc	6/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		623	294	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	141	460	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.99	0.913	1	0.99	0.913	1	CLONAL	1	TRUE	1	0.753266789515205	2		460	378	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023421	33023421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1190459895	NA	P-0052234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	327	743	1	ENST00000300177.4:c.530G>A	p.Arg177His	p.R177H	ENST00000300177	NM_001191322.1	177	cGt/cAt	2/2	1	2	FACETS	0.997	0.945	1	0.997	0.945	1	CLONAL	1	TRUE	1	0.753266789515205	2		744	871	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578484	7578485	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1064793929	NA	P-0052234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	510	1322	1	ENST00000269305.4:c.445dup	p.Ser149PhefsTer32	p.S149Ffs*32	ENST00000269305	NM_001126112.2	149	tcc/tTcc	5/11	0.753266789515205	1	FACETS	0.946	0.913	0.979	0.946	0.913	0.979	CLONAL	1	TRUE	0	0.753266789515205	1		1323	892	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864656	37864656	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	419	1181	0	ENST00000269571.5:c.308G>T	p.Arg103Leu	p.R103L	ENST00000269571		103	cGa/cTa	3/27	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.753266789515205	2		1181	1089	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0052234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	99	189	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	1	2	FACETS	0.974	0.883	1	0.974	0.883	1	CLONAL	1	TRUE	1	0.753266789515205	2		189	270	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955080	93955080	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	172	346	0	ENST00000369303.4:c.2818T>A	p.Tyr940Asn	p.Y940N	ENST00000369303	NM_004440.3	940	Tat/Aat	16/17	1	2	FACETS	0.991	0.92	1	0.991	0.92	1	CLONAL	1	TRUE	1	0.753266789515205	2		346	461	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519893	NA	P-0052235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	375	1060	0	ENST00000267101.3:c.310G>T	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ttg	3/28	0.234207578727529	3	FACETS	1	0.994	1	0.657	0.623	0.691	INDETERMINATE	1	TRUE	1	0.606867265455668	3		1060	1226	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	373	946	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.606867265455668	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.606867265455668	1		946	715	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433994	49433994	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369965791	NA	P-0052235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	244	1559	0	ENST00000301067.7:c.7559G>A	p.Arg2520Gln	p.R2520Q	ENST00000301067	NM_003482.3	2520	cGg/cAg	31/54	0.234207578727529	3	FACETS	0.993	0.927	1	0.496	0.463	0.53	INDETERMINATE	1	TRUE	1	0.606867265455668	3		1559	1056	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349312	89349312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141743597	NA	P-0052235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	490	1183	0	ENST00000301030.4:c.3638C>T	p.Ser1213Phe	p.S1213F	ENST00000301030	NM_001256183.1	1213	tCc/tTc	9/13	0.606867265455668	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.606867265455668	1		1183	1023	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7163161	7163161	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	49	802	0	ENST00000302850.5:c.1911G>C	p.Gln637His	p.Q637H	ENST00000302850	NM_000208.2	637	caG/caC	9/22	0.423834041139074	1	FACETS	0.143	0.121	0.169	0.143	0.121	0.169	SUBCLONAL	1	TRUE	0	0.606867265455668	1		802	784	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251498	251520	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTGATGCTGTGTGCGCTGCAG	ACCTGATGCTGTGTGCGCTGCAG	-	novel	NA	P-0052235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	31	162	0	ENST00000264932.6:c.1712_1734del	p.Leu571HisfsTer24	p.L571Hfs*24	ENST00000264932	NM_004168.2	570	aACCTGATGCTGTGTGCGCTGCAG/a	13/15	0.540082995150626	5	FACETS	0.651	0.527	0.789	0.163	0.131	0.198	SUBCLONAL	1	TRUE	1	0.606867265455668	5		162	300	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752655	128752655	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	99	317	0	ENST00000377970.2:c.816A>T	p.Glu272Asp	p.E272D	ENST00000377970	NM_002467.4	272	gaA/gaT	3/3	0.606867265455668	3	FACETS	0.933	0.837	1	0.466	0.418	0.517	CLONAL	1	TRUE	1	0.606867265455668	3		317	456	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633443	8633443	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	20	335	0	ENST00000356435.5:c.226G>C	p.Asp76His	p.D76H	ENST00000356435		76	Gat/Cat	3/35	0.606867265455668	1	FACETS	0.159	0.121	0.203	0.159	0.121	0.203	SUBCLONAL	1	TRUE	0	0.606867265455668	1		335	289	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0052236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	295	380	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.450266323359911	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.450266323359911	2		380	621	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0052236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	156	648	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.450266323359911	2		648	633	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0052236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	293	801	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.405133584404335	1	FACETS	0.904	0.851	0.959	0.904	0.851	0.959	CLONAL	1	TRUE	0	0.450266323359911	1		801	1115	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0052236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	129	523	1	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.450266323359911	1	FACETS	0.812	0.739	0.887	0.812	0.739	0.887	CLONAL	1	TRUE	0	0.450266323359911	1		524	547	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0052236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	89	439	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.333545103793021	3	FACETS	0.777	0.69	0.871	0.389	0.345	0.436	SUBCLONAL	1	TRUE	1	0.450266323359911	3		439	623	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	142	388	1	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	1	2	FACETS	0.975	0.891	1	0.975	0.891	1	CLONAL	1	TRUE	1	0.450266323359911	2		389	647	SUCCESS
APC	324	MSKCC	GRCh37	5	112175761	112175761	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	161	336	1	ENST00000257430.4:c.4473del	p.Phe1491LeufsTer16	p.F1491Lfs*16	ENST00000257430	NM_000038.5	1490	caT/ca	16/16	0.333545103793021	3	FACETS	1	0.989	1	0.746	0.688	0.807	CLONAL	1	TRUE	1	0.450266323359911	3		337	587	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977952	131977952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201810	NA	P-0052236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	153	488	1	ENST00000265335.6:c.3835C>T	p.Arg1279Cys	p.R1279C	ENST00000265335		1279	Cgt/Tgt	25/25	0.333545103793021	3	FACETS	1	0.944	1	0.52	0.476	0.566	CLONAL	1	TRUE	1	0.450266323359911	3		489	801	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184785	32184785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11963697	NA	P-0052236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	275	828	3	ENST00000375023.3:c.1798G>A	p.Val600Ile	p.V600I	ENST00000375023	NM_004557.3	600	Gtt/Att	11/30	1	2	FACETS	0.905	0.849	0.964	0.905	0.849	0.964	CLONAL	1	TRUE	1	0.450266323359911	2		831	1349	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620539	52620539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143085435	NA	P-0052236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	217	662	3	ENST00000394830.3:c.3214G>A	p.Val1072Met	p.V1072M	ENST00000394830	NM_018313.4	1072	Gtg/Atg	21/30	0.450266323359911	1	FACETS	0.924	0.862	0.989	0.924	0.862	0.989	CLONAL	1	TRUE	0	0.450266323359911	1		665	808	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966538	25966538	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	262	773	2	ENST00000435504.4:c.2668T>G	p.Leu890Val	p.L890V	ENST00000435504		890	Tta/Gta	13/13	1	2	FACETS	0.967	0.905	1	0.967	0.905	1	CLONAL	1	TRUE	1	0.450266323359911	2		775	1204	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151932969	151932969	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs370313067	NA	P-0052236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	11	14	0	ENST00000262189.6:c.2702T>C	p.Leu901Pro	p.L901P	ENST00000262189	NM_170606.2	901	cTg/cCg	16/59	0.420620513015748	3	FACETS	1	0.717	1	0.507	0.358	0.683	CLONAL	1	TRUE	1	0.450266323359911	3		14	59	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0052237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	322	429	0	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	0.400884592064905	3	FACETS	0.825	0.785	0.865	0.825	0.785	0.865	INDETERMINATE	2	TRUE	1	0.790533356883561	3		429	689	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593605	55593610	+	inframe_deletion	In_Frame_Del	DEL	GAAGGT	GAAGGT	-	novel	NA	P-0052237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	288	411	0	ENST00000288135.5:c.1671_1676del	p.Trp557_Val559delinsCys	p.W557_V559delinsC	ENST00000288135	NM_000222.2	557	tgGAAGGTt/tgt	11/21	0.400884592064905	3	FACETS	0.823	0.78	0.865	0.823	0.78	0.865	INDETERMINATE	2	TRUE	1	0.790533356883561	3		411	618	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021073	26021076	+	frameshift_variant	Frame_Shift_Del	DEL	CTAT	CTAT	-	novel	NA	P-0052237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	493	704	0	ENST00000357647.3:c.357_360del	p.Ile120CysfsTer?	p.I120Cfs*?	ENST00000357647	NM_003529.2	119	aCTATc/ac	1/1	0.417400916062728	3	FACETS	0.819	0.786	0.851	0.819	0.786	0.851	INDETERMINATE	2	TRUE	1	0.790533356883561	3		704	1063	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148967	119148967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	299	558	0	ENST00000264033.4:c.1187G>A	p.Cys396Tyr	p.C396Y	ENST00000264033	NM_005188.3	396	tGt/tAt	8/16	0.543968244755804	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.635894433081369	1		558	606	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196880	108196882	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	novel	NA	P-0052238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	217	433	0	ENST00000278616.4:c.6906_6908del	p.Lys2303del	p.K2303del	ENST00000278616	NM_000051.3	2301	gcAAAa/gca	47/63	0.543968244755804	1	FACETS	0.988	0.93	1	0.988	0.93	1	CLONAL	1	TRUE	0	0.635894433081369	1		433	471	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38616976	38616977	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	237	393	0	ENST00000299084.4:c.395dup	p.Asn132LysfsTer2	p.N132Kfs*2	ENST00000299084	NM_152594.2	130	tca/tcAa	4/7	0.635894433081369	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.635894433081369	1		393	501	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266126	+	inframe_deletion	In_Frame_Del	DEL	ACC	ACC	-	novel	NA	P-0052238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	189	406	0	ENST00000349496.5:c.123_125del	p.Thr42del	p.T42del	ENST00000349496	NM_001904.3	41	ACC/-	3/15	0.635894433081369	1	FACETS	0.928	0.868	0.988	0.928	0.868	0.988	CLONAL	1	TRUE	0	0.635894433081369	1		406	437	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0052239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	105	1140	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.479	0.429	0.532	0.479	0.429	0.532	SUBCLONAL	1	TRUE	1	0.537389941753189	2		1144	816	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0052239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	90	486	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.628	0.559	0.702	0.628	0.559	0.702	SUBCLONAL	1	TRUE	1	0.537389941753189	2		486	533	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0052239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	108	374	3	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	1	2	FACETS	0.98	0.887	1	0.98	0.887	1	CLONAL	1	TRUE	1	0.537389941753189	2		377	410	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097751	27097751	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	73	821	1	ENST00000324856.7:c.3344del	p.Pro1115GlnfsTer46	p.P1115Qfs*46	ENST00000324856	NM_006015.4	1114	Ccc/cc	12/20	1	2	FACETS	0.425	0.372	0.483	0.425	0.372	0.483	SUBCLONAL	1	TRUE	1	0.537389941753189	2		822	639	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725042	89725042	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1085308041	NA	P-0052239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	95	333	1	ENST00000371953.3:c.1027-2A>G		p.X343_splice	ENST00000371953	NM_000314.4	343			0.495617151951725	3	FACETS	1	0.977	1	0.658	0.591	0.727	CLONAL	1	TRUE	1	0.537389941753189	3		334	341	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0052239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	87	752	3	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	1	2	FACETS	0.483	0.427	0.542	0.483	0.427	0.542	SUBCLONAL	1	TRUE	1	0.537389941753189	2		755	671	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0052239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	43	505	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	0.329	0.275	0.388	0.329	0.275	0.388	SUBCLONAL	1	TRUE	1	0.537389941753189	2		505	487	SUCCESS
AR	367	MSKCC	GRCh37	X	66765080	66765080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	110	1081	1	ENST00000374690.3:c.92G>A	p.Arg31His	p.R31H	ENST00000374690	NM_000044.3	31	cGc/cAc	1/8	1	2	FACETS	0.562	0.505	0.623	0.562	0.505	0.623	SUBCLONAL	1	TRUE	1	0.537389941753189	2		1082	728	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	189	1305	1	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.855	0.791	0.921	0.855	0.791	0.921	CLONAL	1	TRUE	1	0.537389941753189	2		1306	823	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78435626	78435627	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	100	618	0	ENST00000370768.2:c.193dup	p.Arg65LysfsTer12	p.R65Kfs*12	ENST00000370768	NM_003902.3	65	aga/aAga	2/20	1	2	FACETS	0.702	0.629	0.779	0.702	0.629	0.779	SUBCLONAL	1	TRUE	1	0.537389941753189	2		618	530	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	111	622	1	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.793	0.716	0.874	0.793	0.716	0.874	SUBCLONAL	1	TRUE	1	0.537389941753189	2		623	521	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938230	76938230	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	66	756	3	ENST00000373344.5:c.2518del	p.Arg840GlufsTer29	p.R840Efs*29	ENST00000373344	NM_000489.3	840	Aga/ga	9/35	1	2	FACETS	0.386	0.334	0.441	0.386	0.334	0.441	SUBCLONAL	1	TRUE	1	0.537389941753189	2		759	637	SUCCESS
AXL	558	MSKCC	GRCh37	19	41725374	41725374	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	169	1191	1	ENST00000301178.4:c.81del	p.Arg28GlyfsTer70	p.R28Gfs*70	ENST00000301178	NM_021913.4	26	gCc/gc	1/20	1	2	FACETS	0.817	0.752	0.884	0.817	0.752	0.884	CLONAL	1	TRUE	1	0.537389941753189	2		1192	770	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504584	103504584	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	78	464	0	ENST00000355739.4:c.205C>T	p.Arg69Ter	p.R69*	ENST00000355739	NM_000123.3	69	Cga/Tga	2/15	1	2	FACETS	0.669	0.59	0.753	0.669	0.59	0.753	SUBCLONAL	1	TRUE	1	0.537389941753189	2		464	434	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626689	28626689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	156	688	0	ENST00000241453.7:c.607G>A	p.Gly203Arg	p.G203R	ENST00000241453	NM_004119.2	203	Ggg/Agg	5/24	1	2	FACETS	0.865	0.795	0.939	0.865	0.795	0.939	CLONAL	1	TRUE	1	0.537389941753189	2		688	671	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436092	116436092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45578433	NA	P-0052239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	140	657	1	ENST00000397752.3:c.4087G>A	p.Ala1363Thr	p.A1363T	ENST00000397752	NM_000245.2	1363	Gct/Act	21/21	1	2	FACETS	0.925	0.847	1	0.925	0.847	1	CLONAL	1	TRUE	1	0.537389941753189	2		658	563	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127397	55127397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	94	929	0	ENST00000257290.5:c.185C>T	p.Ser62Phe	p.S62F	ENST00000257290	NM_006206.4	62	tCt/tTt	3/23	1	2	FACETS	0.487	0.433	0.544	0.487	0.433	0.544	SUBCLONAL	1	TRUE	1	0.537389941753189	2		929	719	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647656	3647657	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs774532876	NA	P-0052239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	47	1261	5	ENST00000294008.3:c.1406dup	p.Leu470IlefsTer8	p.L470Ifs*8	ENST00000294008	NM_032444.2	469	cca/ccCa	7/15	1	2	FACETS	0.187	0.157	0.221	0.187	0.157	0.221	SUBCLONAL	1	TRUE	1	0.537389941753189	2		1266	934	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846240	156846240	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1406253599	NA	P-0052239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	115	1233	1	ENST00000524377.1:c.1681G>A	p.Ala561Thr	p.A561T	ENST00000524377	NM_002529.3	561	Gct/Act	14/17	0.537389941753189	3	FACETS	0.451	0.405	0.5	0.225	0.202	0.25	SUBCLONAL	1	TRUE	1	0.537389941753189	3		1234	1205	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624274	89624274	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	116	554	0	ENST00000371953.3:c.48del	p.Gln17LysfsTer7	p.Q17Kfs*7	ENST00000371953	NM_000314.4	16	taT/ta	1/9	0.495617151951725	3	FACETS	0.872	0.788	0.961	0.436	0.394	0.481	CLONAL	1	TRUE	1	0.537389941753189	3		554	628	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913656	32913656	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	35	357	0	ENST00000380152.3:c.5164A>C	p.Ser1722Arg	p.S1722R	ENST00000380152		1722	Agt/Cgt	11/27	1	2	FACETS	0.414	0.34	0.496	0.414	0.34	0.496	SUBCLONAL	1	TRUE	1	0.537389941753189	2		357	315	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16022769	16022769	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	53	488	1	ENST00000268712.3:c.1883G>A	p.Trp628Ter	p.W628*	ENST00000268712	NM_006311.3	628	tGg/tAg	17/46	1	2	FACETS	0.332	0.283	0.386	0.332	0.283	0.386	SUBCLONAL	1	TRUE	1	0.537389941753189	2		489	594	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511537	38511537	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	153	1096	0	ENST00000254066.5:c.1036del	p.Asp346ThrfsTer14	p.D346Tfs*14	ENST00000254066	NM_000964.3	345	ccG/cc	8/9	1	2	FACETS	0.861	0.79	0.935	0.861	0.79	0.935	CLONAL	1	TRUE	1	0.537389941753189	2		1096	661	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448336	56448336	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	107	1143	1	ENST00000407977.2:c.311T>G	p.Ile104Ser	p.I104S	ENST00000407977		104	aTc/aGc	3/10	1	2	FACETS	0.418	0.374	0.465	0.418	0.374	0.465	SUBCLONAL	1	TRUE	1	0.537389941753189	2		1144	953	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129987	55129987	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1207595829	NA	P-0052239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	80	854	1	ENST00000257290.5:c.521G>A	p.Ser174Asn	p.S174N	ENST00000257290	NM_006206.4	174	aGc/aAc	4/23	1	2	FACETS	0.354	0.311	0.401	0.354	0.311	0.401	SUBCLONAL	1	TRUE	1	0.537389941753189	2		855	841	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142949990	142949990	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781427853	NA	P-0052239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	123	615	0	ENST00000262992.4:c.2720C>T	p.Ala907Val	p.A907V	ENST00000262992	NM_001101669.1	907	gCt/gTt	24/24	1	2	FACETS	0.879	0.798	0.962	0.879	0.798	0.962	CLONAL	1	TRUE	1	0.537389941753189	2		615	521	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591108	67591116	+	inframe_deletion	In_Frame_Del	DEL	ACCAGACCT	ACCAGACCT	-	novel	NA	P-0052239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	54	435	0	ENST00000274335.5:c.1701_1709del	p.Lys567_Leu570delinsAsn	p.K567_L570delinsN	ENST00000274335		567	aaACCAGACCTt/aat	12/15	1	2	FACETS	0.578	0.495	0.666	0.578	0.495	0.666	SUBCLONAL	1	TRUE	1	0.537389941753189	2		435	348	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205596	38205596	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	57	1053	0	ENST00000317025.8:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000317025	NM_023034.1	32	Gat/Tat	2/24	1	2	FACETS	0.237	0.202	0.275	0.237	0.202	0.275	SUBCLONAL	1	TRUE	1	0.537389941753189	2		1053	895	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553452	29553452	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1555613743	NA	P-0052240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	526	851	0	ENST00000356175.3:c.2002-1G>A		p.X668_splice	ENST00000356175	NM_000267.3	668			NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.929122256620919	2		851	557	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435771	110435771	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775002025	NA	P-0052240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	165	516	1	ENST00000375856.3:c.2630C>T	p.Pro877Leu	p.P877L	ENST00000375856	NM_003749.2	877	cCg/cTg	1/2	0.929122256620919	2	FACETS	1	0.99	1	0.655	0.617	0.693	CLONAL	1	TRUE	0	0.929122256620919	2		517	271	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550466	29550466	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	93	254	0	ENST00000356175.3:c.1726C>G	p.Gln576Glu	p.Q576E	ENST00000356175	NM_000267.3	576	Caa/Gaa	16/57	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.929122256620919	2		254	177	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469549	25469549	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	628	1623	0	ENST00000264709.3:c.1219A>T	p.Ile407Phe	p.I407F	ENST00000264709	NM_175629.2	407	Att/Ttt	10/23	0.519663150013984	6	FACETS	1	0.983	1	1	0.983	1	INDETERMINATE	3	TRUE	3	0.929122256620919	6		1623	1254	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0052241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	129	486	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.213930690079413	3	FACETS	0.821	0.744	0.902			1	CLONAL	2	TRUE	NA	0.213930690079413	3		486	813	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0052241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	101	765	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.213930690079413	1	FACETS	0.886	0.79	0.988	0.886	0.79	0.988	CLONAL	1	TRUE	0	0.213930690079413	1		766	952	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974809	21974809	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	71	244	0	ENST00000304494.5:c.18del	p.Ser7AlafsTer19	p.S7Afs*19	ENST00000304494	NM_000077.4	6	ggG/gg	1/3	0.186981042512656	2	FACETS	0.97	0.853	1	0.97	0.853	1	CLONAL	2	TRUE	0	0.213930690079413	2		244	342	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916935	178916935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	59	522	1	ENST00000263967.3:c.322C>T	p.Arg108Cys	p.R108C	ENST00000263967	NM_006218.2	108	Cgt/Tgt	2/21	1	2	FACETS	0.742	0.638	0.857	0.742	0.638	0.857	SUBCLONAL	1	TRUE	1	0.213930690079413	2		523	743	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951075	48951075	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	38	325	0	ENST00000267163.4:c.1237G>T	p.Glu413Ter	p.E413*	ENST00000267163	NM_000321.2	413	Gaa/Taa	13/27	0.213930690079413	1	FACETS	0.755	0.625	0.901	0.755	0.625	0.901	CLONAL	1	TRUE	0	0.213930690079413	1		325	420	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	55	443	2	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.435	0.372	0.503	0.435	0.372	0.503	SUBCLONAL	1	TRUE	1	0.463509226142074	2		445	546	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760024	133760024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	84	1063	3	ENST00000318560.5:c.2352del	p.Arg785GlyfsTer3	p.R785Gfs*3	ENST00000318560	NM_005157.4	783	Ccc/cc	11/11	1	2	FACETS	0.301	0.265	0.34	0.301	0.265	0.34	SUBCLONAL	1	TRUE	1	0.463509226142074	2		1066	1204	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	128	706	4	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	0.252456216578557	3	FACETS	0.677	0.612	0.745	0.338	0.306	0.373	INDETERMINATE	1	TRUE	1	0.463509226142074	3		710	1005	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	131	618	2	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	1	2	FACETS	0.454	0.411	0.5	0.454	0.411	0.5	SUBCLONAL	1	TRUE	1	0.463509226142074	2		620	1244	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263974	104263974	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776579	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	76	395	1	ENST00000369902.3:c.71del	p.Pro24ArgfsTer72	p.P24Rfs*72	ENST00000369902	NM_016169.3	22	gCc/gc	1/12	1	2	FACETS	0.68	0.598	0.768	0.68	0.598	0.768	SUBCLONAL	1	TRUE	1	0.463509226142074	2		396	482	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789591	3789591	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	45	632	0	ENST00000262367.5:c.4268del	p.Pro1423LeufsTer36	p.P1423Lfs*36	ENST00000262367	NM_004380.2	1423	cCt/ct	25/31	1	2	FACETS	0.263	0.22	0.311	0.263	0.22	0.311	SUBCLONAL	1	TRUE	1	0.463509226142074	2		632	738	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	78	478	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.545	0.479	0.615	0.545	0.479	0.615	SUBCLONAL	1	TRUE	1	0.463509226142074	2		478	618	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	74	752	3	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	1	2	FACETS	0.379	0.331	0.431	0.379	0.331	0.431	SUBCLONAL	1	TRUE	1	0.463509226142074	2		755	842	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480582	120480582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368918146	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	143	679	2	ENST00000256646.2:c.3235G>A	p.Val1079Ile	p.V1079I	ENST00000256646	NM_024408.3	1079	Gtt/Att	20/34	1	2	FACETS	0.743	0.677	0.811	0.743	0.677	0.811	SUBCLONAL	1	TRUE	1	0.463509226142074	2		681	831	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	200	1118	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.738	0.683	0.796	0.738	0.683	0.796	SUBCLONAL	1	TRUE	1	0.463509226142074	2		1118	1169	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	78	399	2	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	1	2	FACETS	0.594	0.522	0.67	0.594	0.522	0.67	SUBCLONAL	1	TRUE	1	0.463509226142074	2		401	567	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457303	67457303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768713596	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	157	1143	2	ENST00000327367.4:c.277C>T	p.Arg93Ter	p.R93*	ENST00000327367	NM_005902.3	93	Cga/Tga	2/9	1	2	FACETS	0.596	0.545	0.65	0.596	0.545	0.65	SUBCLONAL	1	TRUE	1	0.463509226142074	2		1145	1137	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211462	46211462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	136	308	0	ENST00000334344.6:c.428G>A	p.Arg143His	p.R143H	ENST00000334344	NM_152641.2	143	cGt/cAt	5/21	0.463509226142074	3	FACETS	0.856	0.786	0.929	0.856	0.786	0.929	CLONAL	2	TRUE	1	0.463509226142074	3		308	422	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456893	149456893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3829986	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	161	887	2	ENST00000286301.3:c.835G>A	p.Val279Met	p.V279M	ENST00000286301	NM_005211.3	279	Gtg/Atg	6/22	1	2	FACETS	0.673	0.617	0.732	0.673	0.617	0.732	SUBCLONAL	1	TRUE	1	0.463509226142074	2		889	1032	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412110	63412110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852216	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	334	1124	1	ENST00000330258.3:c.1057C>T	p.Arg353Ter	p.R353*	ENST00000330258	NM_152424.3	353	Cga/Tga	2/2	0.29923172995586	2	FACETS	1	0.993	1	0.662	0.626	0.698	CLONAL	1	TRUE	0	0.463509226142074	2		1125	1089	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	122	685	4	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	0.625	0.565	0.689	0.625	0.565	0.689	SUBCLONAL	1	TRUE	1	0.463509226142074	2		689	842	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	248	698	7	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.463509226142074	2		705	750	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954320	48954321	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	245	348	0	ENST00000267163.4:c.1446dup	p.His483SerfsTer10	p.H483Sfs*10	ENST00000267163	NM_000321.2	481	att/aTtt	16/27	0.463509226142074	3	FACETS	0.901	0.846	0.957	0.901	0.846	0.957	CLONAL	2	TRUE	1	0.463509226142074	3		348	723	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007619	45007619	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs111482205	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	120	357	0	ENST00000558401.1:c.68-2A>G		p.X23_splice	ENST00000558401	NM_004048.2	23			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.463509226142074	2		357	408	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831026	72831026	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs61737017	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	94	677	0	ENST00000268489.5:c.5555A>C	p.Gln1852Pro	p.Q1852P	ENST00000268489	NM_006885.3	1852	cAg/cCg	9/10	1	2	FACETS	0.559	0.498	0.625	0.559	0.498	0.625	SUBCLONAL	1	TRUE	1	0.463509226142074	2		677	725	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979246	93979246	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	37	460	0	ENST00000369303.4:c.1582C>T	p.Pro528Ser	p.P528S	ENST00000369303	NM_004440.3	528	Ccc/Tcc	7/17	1	2	FACETS	0.292	0.24	0.35	0.292	0.24	0.35	SUBCLONAL	1	TRUE	1	0.463509226142074	2		460	547	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405658	70405658	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	127	653	0	ENST00000373644.4:c.3172T>A	p.Leu1058Met	p.L1058M	ENST00000373644	NM_030625.2	1058	Ttg/Atg	4/12	1	2	FACETS	0.651	0.589	0.716	0.651	0.589	0.716	SUBCLONAL	1	TRUE	1	0.463509226142074	2		653	842	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439906	56439906	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs763974538	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	169	814	0	ENST00000407977.2:c.686C>T	p.Pro229Leu	p.P229L	ENST00000407977		229	cCg/cTg	6/10	1	2	FACETS	0.808	0.743	0.875	0.808	0.743	0.875	CLONAL	1	TRUE	1	0.463509226142074	2		814	903	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643942	52643943	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	45	521	0	ENST00000394830.3:c.1953dup	p.Ser652IlefsTer13	p.S652Ifs*13	ENST00000394830	NM_018313.4	651	-/A	17/30	1	2	FACETS	0.252	0.211	0.298	0.252	0.211	0.298	SUBCLONAL	1	TRUE	1	0.463509226142074	2		521	770	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964748	15964748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	146	701	2	ENST00000268712.3:c.5848C>T	p.Arg1950Cys	p.R1950C	ENST00000268712	NM_006311.3	1950	Cgt/Tgt	37/46	1	2	FACETS	0.735	0.671	0.802	0.735	0.671	0.802	SUBCLONAL	1	TRUE	1	0.463509226142074	2		703	857	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781213	161781213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs571092914	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	147	800	0	ENST00000366898.1:c.1192G>A	p.Ala398Thr	p.A398T	ENST00000366898	NM_004562.2	398	Gcc/Acc	11/12	1	2	FACETS	0.778	0.711	0.849	0.778	0.711	0.849	SUBCLONAL	1	TRUE	1	0.463509226142074	2		800	815	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495016	56495016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776728303	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	155	912	1	ENST00000267101.3:c.3373C>T	p.Arg1125Trp	p.R1125W	ENST00000267101	NM_001982.3	1125	Cgg/Tgg	27/28	0.463509226142074	3	FACETS	0.656	0.599	0.716	0.328	0.299	0.358	SUBCLONAL	1	TRUE	1	0.463509226142074	3		913	1256	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004601	16004601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1406850631	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	116	629	1	ENST00000268712.3:c.2653G>A	p.Ala885Thr	p.A885T	ENST00000268712	NM_006311.3	885	Gct/Act	20/46	1	2	FACETS	0.669	0.603	0.739	0.669	0.603	0.739	SUBCLONAL	1	TRUE	1	0.463509226142074	2		630	748	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992721	68992721	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs764112302	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	125	762	4	ENST00000288368.4:c.1693del	p.Ser565ArgfsTer10	p.S565Rfs*10	ENST00000288368	NM_024870.2	562	cgT/cg	16/40	1	2	FACETS	0.627	0.567	0.69	0.627	0.567	0.69	SUBCLONAL	1	TRUE	1	0.463509226142074	2		766	860	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1250	549	1512	1	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	0.463509226142074	3	FACETS	0.811	0.777	0.846	0.811	0.777	0.846	CLONAL	2	TRUE	1	0.463509226142074	3		1513	1799	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114277	143114277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs76891221	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	70	481	0	ENST00000262992.4:c.1144C>T	p.Arg382Trp	p.R382W	ENST00000262992	NM_001101669.1	382	Cgg/Tgg	13/24	1	2	FACETS	0.556	0.485	0.633	0.556	0.485	0.633	SUBCLONAL	1	TRUE	1	0.463509226142074	2		481	543	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212851	27212851	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760084463	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	208	996	1	ENST00000380036.4:c.2833G>A	p.Ala945Thr	p.A945T	ENST00000380036	NM_000459.3	945	Gct/Act	17/23	1	2	FACETS	0.751	0.696	0.808	0.751	0.696	0.808	SUBCLONAL	1	TRUE	1	0.463509226142074	2		997	1195	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1308	442	1303	8	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	0.463509226142074	3	FACETS	1	0.995	1	0.671	0.639	0.705	CLONAL	1	TRUE	1	0.463509226142074	3		1311	1750	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897444	78897444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746953724	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	202	1284	0	ENST00000306801.3:c.2779C>T	p.Arg927Trp	p.R927W	ENST00000306801	NM_020761.2	927	Cgg/Tgg	23/34	1	2	FACETS	0.702	0.649	0.757	0.702	0.649	0.757	SUBCLONAL	1	TRUE	1	0.463509226142074	2		1284	1242	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409805	139409805	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1182867386	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	287	1350	1	ENST00000277541.6:c.1951G>A	p.Asp651Asn	p.D651N	ENST00000277541	NM_017617.3	651	Gac/Aac	12/34	1	2	FACETS	0.867	0.814	0.922	0.867	0.814	0.922	CLONAL	1	TRUE	1	0.463509226142074	2		1351	1428	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214728	36214728	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	361	1038	4	ENST00000222270.7:c.3159del	p.Arg1055GlyfsTer127	p.R1055Gfs*127	ENST00000222270	NM_014727.1	1052	Ggg/gg	8/37	0.463509226142074	3	FACETS	0.79	0.749	0.832	0.79	0.749	0.832	SUBCLONAL	2	TRUE	1	0.463509226142074	3		1042	1214	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870471	40870471	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	114	639	0	ENST00000428826.2:c.931+1G>A		p.X311_splice	ENST00000428826		311			1	2	FACETS	0.727	0.655	0.802	0.727	0.655	0.802	SUBCLONAL	1	TRUE	1	0.463509226142074	2		639	677	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657008	47657008	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63751412	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	108	450	1	ENST00000233146.2:c.1204C>T	p.Gln402Ter	p.Q402*	ENST00000233146	NM_000251.2	402	Caa/Taa	7/16	1	2	FACETS	0.724	0.65	0.801	0.724	0.65	0.801	SUBCLONAL	1	TRUE	1	0.463509226142074	2		451	644	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139804438	139804438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774024927	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	184	925	0	ENST00000247668.2:c.595C>T	p.Arg199Trp	p.R199W	ENST00000247668	NM_021138.3	199	Cgg/Tgg	6/11	1	2	FACETS	0.705	0.65	0.763	0.705	0.65	0.763	SUBCLONAL	1	TRUE	1	0.463509226142074	2		925	1126	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534307	187534307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375308616	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	120	773	0	ENST00000441802.2:c.9419C>T	p.Pro3140Leu	p.P3140L	ENST00000441802	NM_005245.3	3140	cCg/cTg	13/27	1	2	FACETS	0.602	0.543	0.664	0.602	0.543	0.664	SUBCLONAL	1	TRUE	1	0.463509226142074	2		773	860	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391212	139391212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751007903	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1366	261	1507	3	ENST00000277541.6:c.6979C>T	p.Arg2327Trp	p.R2327W	ENST00000277541	NM_017617.3	2327	Cgg/Tgg	34/34	1	2	FACETS	0.692	0.646	0.74	0.692	0.646	0.74	SUBCLONAL	1	TRUE	1	0.463509226142074	2		1510	1627	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72881575	72881575	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1040831506	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	104	543	1	ENST00000325599.8:c.544C>T	p.Arg182Ter	p.R182*	ENST00000325599	NM_018130.2	182	Cga/Tga	5/11	1	2	FACETS	0.621	0.556	0.689	0.621	0.556	0.689	SUBCLONAL	1	TRUE	1	0.463509226142074	2		544	723	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088668	27088669	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	196	960	0	ENST00000324856.7:c.2281dup	p.Gln761ProfsTer56	p.Q761Pfs*56	ENST00000324856	NM_006015.4	759	-/C	7/20	1	2	FACETS	0.738	0.682	0.796	0.738	0.682	0.796	SUBCLONAL	1	TRUE	1	0.463509226142074	2		960	1146	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440135	49440136	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	373	942	2	ENST00000301067.7:c.4490_4491del	p.His1497LeufsTer30	p.H1497Lfs*30	ENST00000301067	NM_003482.3	1497	cAC/c	16/54	0.463509226142074	3	FACETS	1	0.995	1	0.745	0.707	0.785	CLONAL	1	TRUE	1	0.463509226142074	3		944	1330	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14317322	14317322	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782597266	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	118	619	0	ENST00000256196.4:c.188G>A	p.Arg63Gln	p.R63Q	ENST00000256196		63	cGg/cAg	2/6	1	2	FACETS	0.704	0.636	0.776	0.704	0.636	0.776	SUBCLONAL	1	TRUE	1	0.463509226142074	2		619	723	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779440	3779440	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1411086593	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	208	1294	1	ENST00000262367.5:c.5608G>A	p.Ala1870Thr	p.A1870T	ENST00000262367	NM_004380.2	1870	Gcc/Acc	31/31	1	2	FACETS	0.671	0.621	0.723	0.671	0.621	0.723	SUBCLONAL	1	TRUE	1	0.463509226142074	2		1295	1337	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622171	43622171	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1233945445	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	180	777	1	ENST00000355710.3:c.3187+1G>A		p.X1063_splice	ENST00000355710	NM_020975.4	1063			1	2	FACETS	0.78	0.719	0.844	0.78	0.719	0.844	SUBCLONAL	1	TRUE	1	0.463509226142074	2		778	996	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946469	71946469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778999359	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	173	1021	0	ENST00000298229.2:c.2633G>A	p.Arg878His	p.R878H	ENST00000298229	NM_001567.3	878	cGc/cAc	23/28	1	2	FACETS	0.69	0.634	0.748	0.69	0.634	0.748	SUBCLONAL	1	TRUE	1	0.463509226142074	2		1021	1082	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946468	71946468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	177	1023	1	ENST00000298229.2:c.2632C>T	p.Arg878Cys	p.R878C	ENST00000298229	NM_001567.3	878	Cgc/Tgc	23/28	1	2	FACETS	0.701	0.645	0.76	0.701	0.645	0.76	SUBCLONAL	1	TRUE	1	0.463509226142074	2		1024	1089	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44520604	44520604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	97	437	1	ENST00000291552.4:c.158G>A	p.Arg53His	p.R53H	ENST00000291552	NM_006758.2	53	cGt/cAt	3/8	1	2	FACETS	0.803	0.719	0.893	0.803	0.719	0.893	CLONAL	1	TRUE	1	0.463509226142074	2		438	521	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663346	67663346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771793540	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	92	495	0	ENST00000264010.4:c.1747G>A	p.Val583Ile	p.V583I	ENST00000264010	NM_006565.3	583	Gta/Ata	10/12	1	2	FACETS	0.615	0.547	0.688	0.615	0.547	0.688	SUBCLONAL	1	TRUE	1	0.463509226142074	2		495	645	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046461	30046461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763048984	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	118	757	1	ENST00000331968.5:c.2722C>T	p.Arg908Cys	p.R908C	ENST00000331968	NM_002742.2	908	Cgt/Tgt	18/18	1	2	FACETS	0.625	0.563	0.69	0.625	0.563	0.69	SUBCLONAL	1	TRUE	1	0.463509226142074	2		758	815	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607783	46607783	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766696421	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	194	1191	3	ENST00000263734.3:c.1972C>T	p.Arg658Cys	p.R658C	ENST00000263734	NM_001430.4	658	Cgc/Tgc	12/16	1	2	FACETS	0.637	0.587	0.688	0.637	0.587	0.688	SUBCLONAL	1	TRUE	1	0.463509226142074	2		1194	1315	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288885	11288885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1201340871	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	149	826	3	ENST00000361445.4:c.2870G>A	p.Arg957Gln	p.R957Q	ENST00000361445	NM_004958.3	957	cGg/cAg	19/58	1	2	FACETS	0.697	0.636	0.76	0.697	0.636	0.76	SUBCLONAL	1	TRUE	1	0.463509226142074	2		829	923	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120469231	120469231	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773971657	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	105	579	0	ENST00000256646.2:c.3896G>A	p.Arg1299Gln	p.R1299Q	ENST00000256646	NM_024408.3	1299	cGg/cAg	24/34	1	2	FACETS	0.621	0.557	0.69	0.621	0.557	0.69	SUBCLONAL	1	TRUE	1	0.463509226142074	2		579	729	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193202163	193202163	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	81	423	0	ENST00000367435.3:c.1195C>T	p.Arg399Ter	p.R399*	ENST00000367435	NM_024529.4	399	Cga/Tga	14/17	1	2	FACETS	0.584	0.515	0.658	0.584	0.515	0.658	SUBCLONAL	1	TRUE	1	0.463509226142074	2		423	598	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114905815	114905815	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	164	731	0	ENST00000543371.1:c.837del	p.Tyr280ThrfsTer5	p.Y280Tfs*5	ENST00000543371	NM_001198531.1	278	caC/ca	8/14	1	2	FACETS	0.812	0.745	0.881	0.812	0.745	0.881	CLONAL	1	TRUE	1	0.463509226142074	2		731	872	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374453	118374453	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	117	689	0	ENST00000534358.1:c.7849del	p.Arg2617GlyfsTer24	p.R2617Gfs*24	ENST00000534358	NM_005933.3	2616	Aaa/aa	27/36	1	2	FACETS	0.668	0.602	0.737	0.668	0.602	0.737	SUBCLONAL	1	TRUE	1	0.463509226142074	2		689	756	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416396	49416396	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	137	686	3	ENST00000301067.7:c.16315C>T	p.Arg5439Trp	p.R5439W	ENST00000301067	NM_003482.3	5439	Cgg/Tgg	51/54	0.463509226142074	3	FACETS	0.727	0.661	0.798	0.364	0.33	0.399	SUBCLONAL	1	TRUE	1	0.463509226142074	3		689	1001	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95598957	95598957	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	58	501	0	ENST00000393063.1:c.202T>G	p.Ser68Ala	p.S68A	ENST00000393063	NM_030621.3	68	Tca/Gca	4/28	1	2	FACETS	0.381	0.327	0.44	0.381	0.327	0.44	SUBCLONAL	1	TRUE	1	0.463509226142074	2		501	657	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43766921	43766921	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	67	348	0	ENST00000382044.4:c.1130C>A	p.Ser377Tyr	p.S377Y	ENST00000382044	NM_001141980.1	377	tCt/tAt	10/28	1	2	FACETS	0.674	0.588	0.767	0.674	0.588	0.767	SUBCLONAL	1	TRUE	1	0.463509226142074	2		348	429	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584713	48584713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	135	543	1	ENST00000342988.3:c.791G>A	p.Ser264Asn	p.S264N	ENST00000342988	NM_005359.5	264	aGc/aAc	7/12	1	2	FACETS	0.868	0.791	0.949	0.868	0.791	0.949	CLONAL	1	TRUE	1	0.463509226142074	2		544	671	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18972831	18972831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767124146	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	113	701	0	ENST00000262803.5:c.2470G>A	p.Ala824Thr	p.A824T	ENST00000262803	NM_002911.3	824	Gcc/Acc	18/24	1	2	FACETS	0.639	0.575	0.707	0.639	0.575	0.707	SUBCLONAL	1	TRUE	1	0.463509226142074	2		701	763	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229052	36229052	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1297	175	1132	0	ENST00000222270.7:c.7832C>T	p.Ser2611Leu	p.S2611L	ENST00000222270	NM_014727.1	2611	tCg/tTg	36/37	0.463509226142074	3	FACETS	0.632	0.58	0.686	0.316	0.29	0.343	SUBCLONAL	1	TRUE	1	0.463509226142074	3		1132	1472	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754928	29754928	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1450440625	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	140	825	1	ENST00000389048.3:c.1007C>T	p.Pro336Leu	p.P336L	ENST00000389048	NM_004304.4	336	cCg/cTg	4/29	1	2	FACETS	0.717	0.653	0.784	0.717	0.653	0.784	SUBCLONAL	1	TRUE	1	0.463509226142074	2		826	843	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130456	29130456	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs17883862	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	125	968	0	ENST00000328354.6:c.254C>A	p.Pro85His	p.P85H	ENST00000328354	NM_007194.3	85	cCt/cAt	2/15	1	2	FACETS	0.48	0.433	0.529	0.48	0.433	0.529	SUBCLONAL	1	TRUE	1	0.463509226142074	2		968	1124	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707732	176707732	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1391504793	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	144	642	1	ENST00000439151.2:c.5789G>A	p.Arg1930His	p.R1930H	ENST00000439151	NM_022455.4	1930	cGc/cAc	18/23	1	2	FACETS	0.731	0.667	0.798	0.731	0.667	0.798	SUBCLONAL	1	TRUE	1	0.463509226142074	2		643	850	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720991	176720991	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	145	752	0	ENST00000439151.2:c.6622T>C	p.Cys2208Arg	p.C2208R	ENST00000439151	NM_022455.4	2208	Tgt/Cgt	23/23	1	2	FACETS	0.698	0.637	0.763	0.698	0.637	0.763	SUBCLONAL	1	TRUE	1	0.463509226142074	2		752	896	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287799	33287799	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs778324215	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	188	1110	1	ENST00000374542.5:c.1454A>C	p.Glu485Ala	p.E485A	ENST00000374542	NM_001141970.1	485	gAa/gCa	5/8	1	2	FACETS	0.669	0.617	0.723	0.669	0.617	0.723	SUBCLONAL	1	TRUE	1	0.463509226142074	2		1111	1213	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41905030	41905030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1379330174	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	155	723	0	ENST00000372991.4:c.517G>A	p.Asp173Asn	p.D173N	ENST00000372991	NM_001760.3	173	Gac/Aac	3/5	1	2	FACETS	0.752	0.689	0.819	0.752	0.689	0.819	SUBCLONAL	1	TRUE	1	0.463509226142074	2		723	889	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396541	139396541	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0052242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	84	992	1	ENST00000277541.6:c.5385-1G>T		p.X1795_splice	ENST00000277541	NM_017617.3	1795			1	2	FACETS	0.368	0.324	0.416	0.368	0.324	0.416	SUBCLONAL	1	TRUE	1	0.463509226142074	2		993	984	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061223	38061228	+	inframe_deletion	In_Frame_Del	DEL	TCTCGA	TCTCGA	-	novel	NA	P-0052243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	316	857	1	ENST00000250448.2:c.761_766del	p.Phe254_Asn256delinsTyr	p.F254_N256delinsY	ENST00000250448	NM_004496.3	254	tTCGAGAac/tac	2/2	1	2	FACETS	0.936	0.886	0.988	0.936	0.886	0.988	CLONAL	1	TRUE	1	0.703786645076025	2		858	959	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777867	3777867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	434	1381	1	ENST00000262367.5:c.7181C>T	p.Ser2394Phe	p.S2394F	ENST00000262367	NM_004380.2	2394	tCc/tTc	31/31	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.703786645076025	2		1382	1169	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0052244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	128	333	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.44	2		333	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0052245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	145	651	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.424096658354181	2	FACETS	0.794	0.732	0.856	0.794	0.732	0.856	SUBCLONAL	2	TRUE	0	0.460288974665785	2		651	397	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5258115	5258115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	84	652	0	ENST00000357368.4:c.619G>A	p.Glu207Lys	p.E207K	ENST00000357368	NM_002850.3	207	Gag/Aag	8/38	0.424096658354181	2	FACETS	0.678	0.6	0.762	0.339	0.3	0.381	SUBCLONAL	1	TRUE	0	0.460288974665785	2		652	538	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488714	212488714	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	133	459	0	ENST00000342788.4:c.2135T>G	p.Ile712Ser	p.I712S	ENST00000342788	NM_005235.2	712	aTt/aGt	18/28	0.399374472479742	3	FACETS	0.938	0.861	1	0.938	0.861	1	CLONAL	2	TRUE	1	0.460288974665785	3		459	379	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236697	236697	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs200305419	NA	P-0052245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	15	307	0	ENST00000264932.6:c.1415A>C	p.Glu472Ala	p.E472A	ENST00000264932	NM_004168.2	472	gAa/gCa	10/15	0.440612337326248	2	FACETS	0.339	0.249	0.448	0.17	0.124	0.224	SUBCLONAL	1	TRUE	0	0.460288974665785	2		307	192	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577560	7577560	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520002	NA	P-0052246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	416	587	0	ENST00000269305.4:c.721T>C	p.Ser241Pro	p.S241P	ENST00000269305	NM_001126112.2	241	Tcc/Ccc	7/11	0.624540971236415	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.624540971236415	1		587	715	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0052246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	94	299	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	1	2	FACETS	0.848	0.761	0.939	0.848	0.761	0.939	CLONAL	1	TRUE	1	0.624540971236415	2		299	355	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665800	29665800	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0052246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	90	173	0	ENST00000356175.3:c.6835A>T	p.Lys2279Ter	p.K2279*	ENST00000356175	NM_000267.3	2279	Aaa/Taa	45/57	0.624540971236415	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.624540971236415	1		173	161	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576851	7576851	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0052248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	211	691	0	ENST00000269305.4:c.993+2T>C		p.X331_splice	ENST00000269305	NM_001126112.2	331			1	2	FACETS	0.987	0.917	1	0.987	0.917	1	CLONAL	1	TRUE	1	0.465237430688674	2		691	919	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434289	49434289	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	259	956	0	ENST00000301067.7:c.7264C>T	p.Gln2422Ter	p.Q2422*	ENST00000301067	NM_003482.3	2422	Cag/Tag	31/54	0.357375809922055	1	FACETS	0.817	0.765	0.87	0.817	0.765	0.87	CLONAL	1	TRUE	0	0.465237430688674	1		956	1046	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599916	10599916	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs946921406	NA	P-0052248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	570	803	1	ENST00000171111.5:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000171111	NM_203500.1	554	Cga/Tga	5/6	0.465237430688674	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.465237430688674	2		804	1119	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497683	120497747	+	frameshift_variant	Frame_Shift_Del	DEL	GTTTCCATGGATGCAGGGATTGCTCAGGCATTCGTTCACCTGTGAGTAGCAGCTGGGGTGATGGG	GTTTCCATGGATGCAGGGATTGCTCAGGCATTCGTTCACCTGTGAGTAGCAGCTGGGGTGATGGG	-	novel	NA	P-0052248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	141	431	0	ENST00000256646.2:c.2135_2199del	p.Pro712LeufsTer9	p.P712Lfs*9	ENST00000256646	NM_024408.3	712	cCCCATCACCCCAGCTGCTACTCACAGGTGAACGAATGCCTGAGCAATCCCTGCATCCATGGAAAC/c	13/34	0.465237430688674	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.465237430688674	1		431	451	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204651	108204651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	65	172	0	ENST00000278616.4:c.7966C>T	p.Leu2656Phe	p.L2656F	ENST00000278616	NM_000051.3	2656	Ctt/Ttt	54/63	1	2	FACETS	0.947	0.828	1	0.947	0.828	1	CLONAL	1	TRUE	1	0.465237430688674	2		172	295	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041977	14041977	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	124	432	0	ENST00000311895.7:c.2524G>T	p.Glu842Ter	p.E842*	ENST00000311895	NM_005236.2	842	Gag/Tag	11/11	1	2	FACETS	0.967	0.879	1	0.967	0.879	1	CLONAL	1	TRUE	1	0.465237430688674	2		432	551	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654634	67654634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	154	497	0	ENST00000264010.4:c.1121C>T	p.Thr374Ile	p.T374I	ENST00000264010	NM_006565.3	374	aCt/aTt	6/12	1	2	FACETS	0.906	0.83	0.984	0.906	0.83	0.984	CLONAL	1	TRUE	1	0.465237430688674	2		497	731	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577133	7577146	+	frameshift_variant	Frame_Shift_Del	DEL	TGTTCCGTCCCAGT	TGTTCCGTCCCAGT	-	novel	NA	P-0052248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	196	652	0	ENST00000269305.4:c.792_805del	p.Gly266Ter	p.G266*	ENST00000269305	NM_001126112.2	264	ctACTGGGACGGAACAgc/ctgc	8/11	1	2	FACETS	0.914	0.846	0.984	0.914	0.846	0.984	CLONAL	1	TRUE	1	0.465237430688674	2		652	922	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99850117	99850117	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	185	747	1	ENST00000280892.6:c.7G>T	p.Asp3Tyr	p.D3Y	ENST00000280892	NM_001130678.1	3	Gac/Tac	1/7	0.465237430688674	1	FACETS	0.988	0.916	1	0.988	0.916	1	CLONAL	1	TRUE	0	0.465237430688674	1		748	618	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541408	187541409	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	125	347	0	ENST00000441802.2:c.6331_6332insT	p.Gly2111ValfsTer15	p.G2111Vfs*15	ENST00000441802	NM_005245.3	2111	ggc/gTgc	10/27	0.465237430688674	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.465237430688674	1		347	380	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250524	26250524	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	192	855	0	ENST00000446824.2:c.310C>A	p.Leu104Ile	p.L104I	ENST00000446824	NM_021018.2	104	Ctc/Atc	1/1	0.374834177334376	1	FACETS	0.767	0.71	0.825	0.767	0.71	0.825	SUBCLONAL	1	TRUE	0	0.465237430688674	1		855	826	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519739	137519739	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	58	253	0	ENST00000367739.4:c.899C>T	p.Pro300Leu	p.P300L	ENST00000367739	NM_000416.2	300	cCt/cTt	7/7	0.374834177334376	1	FACETS	0.505	0.435	0.58	0.505	0.435	0.58	SUBCLONAL	1	TRUE	0	0.465237430688674	1		253	379	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799299	42799300	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1158987717	NA	P-0052249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	57	363	2	ENST00000575354.2:c.4790dup	p.Pro1598ThrfsTer16	p.P1598Tfs*16	ENST00000575354	NM_015125.3	1595	tcc/tCcc	20/20	1	2	FACETS	0.604	0.52	0.696	0.604	0.52	0.696	SUBCLONAL	1	TRUE	1	0.437789944356093	2		365	431	SUCCESS
AR	367	MSKCC	GRCh37	X	66937326	66937326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137852593	NA	P-0052249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	34	473	0	ENST00000374690.3:c.2180G>A	p.Arg727His	p.R727H	ENST00000374690	NM_000044.3	727	cGc/cAc	5/8	0.437789944356093	1	FACETS	0.235	0.191	0.284	0.235	0.191	0.284	SUBCLONAL	1	TRUE	0	0.437789944356093	1		473	517	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573156	64573156	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	168	504	1	ENST00000312049.6:c.1136C>A	p.Ala379Glu	p.A379E	ENST00000312049	NM_130799.2	379	gCa/gAa	8/10	1	2	FACETS	0.997	0.918	1	0.997	0.918	1	CLONAL	1	TRUE	1	0.437789944356093	2		505	770	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506913	186506913	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0052249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	27	159	0	ENST00000323963.5:c.1080-1G>C		p.X360_splice	ENST00000323963		360			1	2	FACETS	0.452	0.36	0.556	0.452	0.36	0.556	SUBCLONAL	1	TRUE	1	0.437789944356093	2		159	273	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0052251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	37	537	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.685	0.569	0.814	0.685	0.569	0.814	SUBCLONAL	1	TRUE	1	0.453691652578022	2		537	238	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0052251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	149	756	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.453691652578022	2		756	570	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692892	89692892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554898129	NA	P-0052252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	178	375	0	ENST00000371953.3:c.376G>A	p.Ala126Thr	p.A126T	ENST00000371953	NM_000314.4	126	Gct/Act	5/9	0.477975337966269	2	FACETS	1	0.991	1	0.702	0.657	0.748	CLONAL	1	TRUE	0	0.665392092148394	2		375	381	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670325	134670325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	100	464	0	ENST00000398015.3:c.236G>A	p.Arg79Gln	p.R79Q	ENST00000398015	NM_004441.4	79	cGg/cAg	3/16	1	2	FACETS	0.618	0.555	0.686	0.618	0.555	0.686	SUBCLONAL	1	TRUE	1	0.665392092148394	2		464	486	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881488	48881489	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0052252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	93	249	0	ENST00000267163.4:c.219_220dup	p.Ala74GlufsTer4	p.A74Efs*4	ENST00000267163	NM_000321.2	70	-/AG	2/27	1	2	FACETS	0.702	0.629	0.78	0.702	0.629	0.78	SUBCLONAL	1	TRUE	1	0.665392092148394	2		249	398	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991949	72991949	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs753977275	NA	P-0052252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	146	647	1	ENST00000268489.5:c.2096del	p.Gly699AlafsTer125	p.G699Afs*125	ENST00000268489	NM_006885.3	699	gGc/gc	2/10	1	2	FACETS	0.67	0.613	0.729	0.67	0.613	0.729	SUBCLONAL	1	TRUE	1	0.665392092148394	2		648	655	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	195	869	2	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.655	0.606	0.705	0.655	0.606	0.705	SUBCLONAL	1	TRUE	1	0.665392092148394	2		871	895	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134628	41134628	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759316607	NA	P-0052252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	103	417	0	ENST00000379561.5:c.1000G>A	p.Glu334Lys	p.E334K	ENST00000379561	NM_002015.3	334	Gaa/Aaa	2/3	1	2	FACETS	0.712	0.641	0.786	0.712	0.641	0.786	SUBCLONAL	1	TRUE	1	0.665392092148394	2		417	435	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357070	70357070	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773713291	NA	P-0052252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	194	781	1	ENST00000374080.3:c.5585G>A	p.Arg1862His	p.R1862H	ENST00000374080		1862	cGc/cAc	39/45	1	2	FACETS	0.648	0.6	0.698	0.648	0.6	0.698	SUBCLONAL	1	TRUE	1	0.665392092148394	2		782	900	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665096	138665096	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs758370933	NA	P-0052252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	60	356	0	ENST00000330315.3:c.469C>G	p.Pro157Ala	p.P157A	ENST00000330315	NM_023067.3	157	Ccc/Gcc	1/1	1	2	FACETS	0.509	0.441	0.583	0.509	0.441	0.583	SUBCLONAL	1	TRUE	1	0.665392092148394	2		356	354	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856008	111856008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1222585515	NA	P-0052252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	176	586	3	ENST00000341259.2:c.59C>T	p.Ala20Val	p.A20V	ENST00000341259	NM_005475.2	20	gCg/gTg	2/8	0.463993761881593	3	FACETS	0.78	0.719	0.844	0.39	0.359	0.422	SUBCLONAL	1	TRUE	1	0.665392092148394	3		589	904	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828497	72828497	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	187	746	1	ENST00000268489.5:c.8084G>A	p.Arg2695Gln	p.R2695Q	ENST00000268489	NM_006885.3	2695	cGg/cAg	9/10	1	2	FACETS	0.695	0.643	0.749	0.695	0.643	0.749	SUBCLONAL	1	TRUE	1	0.665392092148394	2		747	809	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212913	94212913	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	98	302	0	ENST00000323929.3:c.329A>T	p.Asn110Ile	p.N110I	ENST00000323929	NM_005591.3	110	aAc/aTc	5/20	1	2	FACETS	0.759	0.682	0.839	0.759	0.682	0.839	SUBCLONAL	1	TRUE	1	0.665392092148394	2		302	388	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937089	48937089	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1131690864	NA	P-0052252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	56	174	0	ENST00000267163.4:c.857A>G	p.Asp286Gly	p.D286G	ENST00000267163	NM_000321.2	286	gAt/gGt	8/27	1	2	FACETS	0.722	0.626	0.825	0.722	0.626	0.825	SUBCLONAL	1	TRUE	1	0.665392092148394	2		174	233	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73995338	73995338	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	59	368	0	ENST00000318443.5:c.644A>T	p.Asn215Ile	p.N215I	ENST00000318443	NM_001024736.1	215	aAt/aTt	4/10	1	2	FACETS	0.517	0.447	0.592	0.517	0.447	0.592	SUBCLONAL	1	TRUE	1	0.665392092148394	2		368	343	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99473513	99473513	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	119	312	0	ENST00000268035.6:c.2935G>T	p.Glu979Ter	p.E979*	ENST00000268035	NM_000875.3	979	Gag/Tag	15/21	1	2	FACETS	0.885	0.806	0.967	0.885	0.806	0.967	CLONAL	1	TRUE	1	0.665392092148394	2		312	404	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591115	67591116	+	protein_altering_variant	In_Frame_Ins	INS	-	-	ATA	novel	NA	P-0052252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	86	270	0	ENST00000274335.5:c.1708_1709insATA	p.Leu570delinsHisIle	p.L570delinsHI	ENST00000274335		570	ctt/cATAtt	12/15	1	2	FACETS	0.637	0.566	0.711	0.637	0.566	0.711	SUBCLONAL	1	TRUE	1	0.665392092148394	2		270	406	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819759	170819759	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	76	251	0	ENST00000296930.5:c.398T>C	p.Val133Ala	p.V133A	ENST00000296930	NM_002520.6	133	gTg/gCg	5/11	1	2	FACETS	0.707	0.626	0.793	0.707	0.626	0.793	SUBCLONAL	1	TRUE	1	0.665392092148394	2		251	323	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803073	32803073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	148	593	4	ENST00000374899.4:c.803C>T	p.Ala268Val	p.A268V	ENST00000374899	NM_018833.2	268	gCc/gTc	5/12	1	2	FACETS	0.627	0.573	0.682	0.627	0.573	0.682	SUBCLONAL	1	TRUE	1	0.665392092148394	2		597	710	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0052253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	307	753	0	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.549368590873621	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.549368590873621	1		753	777	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0052253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	198	240	0	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	0.549368590873621	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.549368590873621	2		240	348	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170046	32170046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768387019	NA	P-0052253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	310	905	0	ENST00000375023.3:c.3562G>A	p.Asp1188Asn	p.D1188N	ENST00000375023	NM_004557.3	1188	Gat/Aat	21/30	1	2	FACETS	0.959	0.904	1	0.959	0.904	1	CLONAL	1	TRUE	1	0.549368590873621	2		905	1177	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68984738	68984738	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	15	79	0	ENST00000288368.4:c.1502A>G	p.Asp501Gly	p.D501G	ENST00000288368	NM_024870.2	501	gAt/gGt	14/40	1	2	FACETS	0.25	0.183	0.331	0.25	0.183	0.331	SUBCLONAL	1	TRUE	1	0.549368590873621	2		79	218	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104696	69104696	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	267	596	0	ENST00000288368.4:c.4540T>A	p.Ser1514Thr	p.S1514T	ENST00000288368	NM_024870.2	1514	Tcc/Acc	37/40	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.549368590873621	2		596	893	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0052254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	41	594	1	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	1	2	FACETS	0.388	0.321	0.462	0.388	0.321	0.462	SUBCLONAL	1	TRUE	1	0.243491297738804	2		595	869	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900288	101900288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111854391	NA	P-0052254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	70	346	1	ENST00000374994.4:c.722C>T	p.Ser241Leu	p.S241L	ENST00000374994	NM_004612.2	241	tCg/tTg	4/9	0.193734783465017	2	FACETS	1	0.96	1	0.626	0.548	0.711	CLONAL	1	TRUE	0	0.243491297738804	2		347	459	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762839	40762839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1407888862	NA	P-0052254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	58	509	0	ENST00000392038.2:c.169G>A	p.Val57Ile	p.V57I	ENST00000392038	NM_001626.4	57	Gta/Ata	3/14	1	2	FACETS	0.656	0.563	0.758	0.656	0.563	0.758	SUBCLONAL	1	TRUE	1	0.243491297738804	2		509	726	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374311	31374311	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	65	489	0	ENST00000328111.2:c.310C>T	p.Arg104Ter	p.R104*	ENST00000328111	NM_006892.3	104	Cga/Tga	5/23	1	2	FACETS	0.871	0.755	0.997	0.871	0.755	0.997	CLONAL	1	TRUE	1	0.243491297738804	2		489	613	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223075	5223075	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1369452734	NA	P-0052254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	95	732	0	ENST00000357368.4:c.2728C>T	p.Arg910Cys	p.R910C	ENST00000357368	NM_002850.3	910	Cgc/Tgc	18/38	1	2	FACETS	0.903	0.803	1	0.903	0.803	1	CLONAL	1	TRUE	1	0.243491297738804	2		732	864	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923272	26923272	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	39	296	0	ENST00000381527.3:c.268G>C	p.Asp90His	p.D90H	ENST00000381527	NM_001260.1	90	Gat/Cat	3/13	1	2	FACETS	0.73	0.605	0.869	0.73	0.605	0.869	SUBCLONAL	1	TRUE	1	0.243491297738804	2		296	439	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414685	56414685	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	65	341	0	ENST00000348428.3:c.2086G>T	p.Glu696Ter	p.E696*	ENST00000348428	NM_006785.3	696	Gaa/Taa	17/17	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.243491297738804	2		341	504	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632117	1632117	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0052254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	74	629	0	ENST00000344749.5:c.220-2A>G		p.X74_splice	ENST00000344749	NM_001136139.2	74			1	2	FACETS	0.798	0.697	0.906	0.798	0.697	0.906	CLONAL	1	TRUE	1	0.243491297738804	2		629	762	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0052255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	435	679	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.74498594209194	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.746770930519258	2		679	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0052257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	113	567	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.427851058604389	1	FACETS	0.991	0.899	1	0.991	0.899	1	CLONAL	1	TRUE	0	0.431063950345653	1		567	415	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	120	508	0	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.431063950345653	2		508	549	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64126894	64126894	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	145	737	1	ENST00000334205.4:c.100G>A	p.Glu34Lys	p.E34K	ENST00000334205	NM_003942.2	34	Gag/Aag	2/17	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.431063950345653	2		738	631	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692800	89693200	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CACCACAGCTAGAACTTATCAAACCCTTTTGTGAAGATCTTGACCAATGGCTAAGTGAAGATGACAATCATGTTGCAGCAATTCACTGTAAAGCTGGAAAGGGACGAACTGGTGTAATGATATGTGCATATTTATTACATCGGGGCAAATTTTTAAAGGCACAAGAGGCCCTAGATTTCTATGGGGAAGTAAGGACCAGAGACAAAAAGGTAAGTTATTTTTTGATGTTTTTCCTTTCCTCTTCCTGGATCTGAGAATTTATTGGAAAACAGATTTTGGGTTTCTTTTTTTCCTTCAGTTTTATTGAGGTGTAATTGACAAGTAAAAATTATATATAAATACAATGTATAATATGATGTTTTGATGTATGTGTATATACATTGTGAAATGATTACTACAGT	CACCACAGCTAGAACTTATCAAACCCTTTTGTGAAGATCTTGACCAATGGCTAAGTGAAGATGACAATCATGTTGCAGCAATTCACTGTAAAGCTGGAAAGGGACGAACTGGTGTAATGATATGTGCATATTTATTACATCGGGGCAAATTTTTAAAGGCACAAGAGGCCCTAGATTTCTATGGGGAAGTAAGGACCAGAGACAAAAAGGTAAGTTATTTTTTGATGTTTTTCCTTTCCTCTTCCTGGATCTGAGAATTTATTGGAAAACAGATTTTGGGTTTCTTTTTTTCCTTCAGTTTTATTGAGGTGTAATTGACAAGTAAAAATTATATATAAATACAATGTATAATATGATGTTTTGATGTATGTGTATATACATTGTGAAATGATTACTACAGT	-	novel	NA	P-0052257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	45	301	0	ENST00000371953.3:c.286_492+194del		p.X96_splice	ENST00000371953	NM_000314.4	96		5/9	0.427851058604389	1	FACETS	0.642	0.544	0.749	0.642	0.544	0.749	SUBCLONAL	1	TRUE	0	0.431063950345653	1		301	255	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037883	49037883	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	97	250	0	ENST00000267163.4:c.2123T>C	p.Met708Thr	p.M708T	ENST00000267163	NM_000321.2	708	aTg/aCg	21/27	0.431063950345653	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.431063950345653	1		250	323	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825563	50825563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	120	403	0	ENST00000398568.2:c.2194G>A	p.Glu732Lys	p.E732K	ENST00000398568	NM_001042412.1	732	Gaa/Aaa	14/18	0.431063950345653	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.431063950345653	1		403	390	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573291	41573291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326145389	NA	P-0052257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	119	823	1	ENST00000263253.7:c.5576C>T	p.Thr1859Ile	p.T1859I	ENST00000263253	NM_001429.3	1859	aCt/aTt	31/31	0.171347171033323	3	FACETS	1	0.919	1			1	INDETERMINATE	1	TRUE	NA	0.431063950345653	3		824	659	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182661	38182661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199631431	NA	P-0052257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	72	424	0	ENST00000396334.3:c.814G>A	p.Ala272Thr	p.A272T	ENST00000396334	NM_002468.4	272	Gca/Aca	5/5	1	2	FACETS	0.852	0.748	0.963	0.852	0.748	0.963	CLONAL	1	TRUE	1	0.431063950345653	2		424	392	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286580	33286773	+	splice_donor_variant,splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTGCAGGGAAGTGAGAGACAAAGAGTCAAAGAGATCTGGAGTACAGGAGAAAAGAAACAGGAGGATTTAGAGGATAAAATGGGTGGGAAAAAGGAAGAGACAGGATGTGGCACGTGGAATATTCAGACAGAGCAGCTGAAACAGCCAATGAAAGAGAACAAATTGTCAGAGGAAACACGCCCTCCCCTTCTTAC	CTGCAGGGAAGTGAGAGACAAAGAGTCAAAGAGATCTGGAGTACAGGAGAAAAGAAACAGGAGGATTTAGAGGATAAAATGGGTGGGAAAAAGGAAGAGACAGGATGTGGCACGTGGAATATTCAGACAGAGCAGCTGAAACAGCCAATGAAAGAGAACAAATTGTCAGAGGAAACACGCCCTCCCCTTCTTAC	-	novel	NA	P-0052257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	99	467	0	ENST00000374542.5:c.2163+1_2164-1del		p.X721_splice	ENST00000374542	NM_001141970.1	721			0.427851058604389	1	FACETS	0.705	0.632	0.783	0.705	0.632	0.783	SUBCLONAL	1	TRUE	0	0.431063950345653	1		467	511	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286997	33287156	+	splice_donor_variant,splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTAGAAACAGAAACATAAATATGTGGAGGGGTACGGGAAGACTGAGGCTGGAGGGGGGCAGTCCAGTCTCTCCCAGCAGACTCAGTTCCCCAGTATTGCTCTCCGAAAGTCCCCTGCAATCCCTCCTTGGCTTCCCTCTTCCTCCTCCTCTTGTTATTAC	CTAGAAACAGAAACATAAATATGTGGAGGGGTACGGGAAGACTGAGGCTGGAGGGGGGCAGTCCAGTCTCTCCCAGCAGACTCAGTTCCCCAGTATTGCTCTCCGAAAGTCCCCTGCAATCCCTCCTTGGCTTCCCTCTTCCTCCTCCTCTTGTTATTAC	-	novel	NA	P-0052257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	127	620	0	ENST00000374542.5:c.1940+1_1941-1del		p.X647_splice	ENST00000374542	NM_001141970.1	647			0.427851058604389	1	FACETS	0.741	0.673	0.812	0.741	0.673	0.812	SUBCLONAL	1	TRUE	0	0.431063950345653	1		620	624	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	61	460	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.779	0.674	0.894	0.779	0.674	0.894	SUBCLONAL	1	FALSE	1	0.324045206676415	2		460	483	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0052258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	119	380	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.121097115285592	3	FACETS	1	0.976	1			1	INDETERMINATE	1	FALSE	NA	0.324045206676415	3		380	681	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456456	89456456	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	74	367	0	ENST00000336596.2:c.1632G>T	p.Met544Ile	p.M544I	ENST00000336596	NM_005233.5	544	atG/atT	8/17	0.324045206676415	1	FACETS	0.773	0.679	0.875	0.773	0.679	0.875	SUBCLONAL	1	FALSE	0	0.324045206676415	1		367	495	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346592	81346592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764869064	NA	P-0052258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	77	378	0	ENST00000222390.5:c.1361C>T	p.Thr454Met	p.T454M	ENST00000222390	NM_000601.4	454	aCg/aTg	11/18	0.168708076208378	3	FACETS	0.886	0.779	1	0.295	0.259	0.334	INDETERMINATE	1	FALSE	0	0.324045206676415	3		378	623	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968199	134968199	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1232280655	NA	P-0052258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	68	611	0	ENST00000398015.3:c.2712C>A	p.Asp904Glu	p.D904E	ENST00000398015	NM_004441.4	904	gaC/gaA	15/16	0.324045206676415	1	FACETS	0.555	0.482	0.633	0.555	0.482	0.633	SUBCLONAL	1	FALSE	0	0.324045206676415	1		611	634	SUCCESS
FH	2271	MSKCC	GRCh37	1	241683021	241683021	+	start_lost	Translation_Start_Site	SNP	A	A	T	rs201261794	NA	P-0052258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	44	599	0	ENST00000366560.3:c.2T>A	p.Met1?	p.M1?	ENST00000366560	NM_000143.3	1	aTg/aAg	1/10	1	2	FACETS	0.342	0.286	0.405	0.342	0.286	0.405	SUBCLONAL	1	FALSE	1	0.324045206676415	2		599	793	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606901	43606901	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	83	895	0	ENST00000355710.3:c.1510G>C	p.Val504Leu	p.V504L	ENST00000355710	NM_020975.4	504	Gtg/Ctg	7/20	0.143587297328922	0	FACETS	0.333	0.293	0.377			1	INDETERMINATE	1	FALSE	0	0.324045206676415	0		895	1039	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456633	32456633	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	39	251	0	ENST00000332351.3:c.259G>T	p.Gly87Cys	p.G87C	ENST00000332351	NM_024426.4	87	Ggt/Tgt	1/10	1	2	FACETS	0.797	0.663	0.945	0.797	0.663	0.945	CLONAL	1	FALSE	1	0.324045206676415	2		251	302	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383273	4383273	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	90	553	0	ENST00000261254.3:c.67G>T	p.Asp23Tyr	p.D23Y	ENST00000261254	NM_001759.3	23	Gac/Tac	1/5	0.324045206676415	3	FACETS	0.738	0.653	0.828	0.369	0.326	0.414	SUBCLONAL	1	FALSE	1	0.324045206676415	3		553	875	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884964	111884964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	99	651	0	ENST00000341259.2:c.962C>T	p.Ser321Leu	p.S321L	ENST00000341259	NM_005475.2	321	tCa/tTa	5/8	1	2	FACETS	0.665	0.593	0.742	0.665	0.593	0.742	SUBCLONAL	1	FALSE	1	0.324045206676415	2		651	919	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945174	32945174	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881565	NA	P-0052258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	48	443	0	ENST00000380152.3:c.8569G>A	p.Ala2857Thr	p.A2857T	ENST00000380152		2857	Gcc/Acc	20/27	1	2	FACETS	0.49	0.414	0.575	0.49	0.414	0.575	SUBCLONAL	1	FALSE	1	0.324045206676415	2		443	604	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281827	49281827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	69	687	0	ENST00000282018.3:c.874G>T	p.Ala292Ser	p.A292S	ENST00000282018	NM_020377.2	292	Gcc/Tcc	1/1	1	2	FACETS	0.625	0.544	0.713	0.625	0.544	0.713	SUBCLONAL	1	FALSE	1	0.324045206676415	2		687	681	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303970	91303970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	99	618	0	ENST00000355112.3:c.1367C>T	p.Ser456Leu	p.S456L	ENST00000355112	NM_000057.2	456	tCa/tTa	7/22	0.121097115285592	3	FACETS	0.863	0.77	0.962			1	INDETERMINATE	1	FALSE	NA	0.324045206676415	3		618	823	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304042	91304042	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	90	679	0	ENST00000355112.3:c.1439C>T	p.Ser480Phe	p.S480F	ENST00000355112	NM_000057.2	480	tCt/tTt	7/22	0.121097115285592	3	FACETS	0.724	0.641	0.812			1	INDETERMINATE	1	FALSE	NA	0.324045206676415	3		679	892	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645081	67645081	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	105	793	0	ENST00000264010.4:c.346G>T	p.Val116Phe	p.V116F	ENST00000264010	NM_006565.3	116	Gtt/Ttt	3/12	0.121097115285592	3	FACETS	0.734	0.656	0.817			1	INDETERMINATE	1	FALSE	NA	0.324045206676415	3		793	1026	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240312	5240312	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	118	833	0	ENST00000357368.4:c.1602G>T	p.Glu534Asp	p.E534D	ENST00000357368	NM_002850.3	534	gaG/gaT	12/38	0.143587297328922	0	FACETS	0.53	0.478	0.586			1	INDETERMINATE	1	FALSE	0	0.324045206676415	0		833	928	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796538	42796538	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	97	916	0	ENST00000575354.2:c.3095A>G	p.Tyr1032Cys	p.Y1032C	ENST00000575354	NM_015125.3	1032	tAc/tGc	13/20	1	2	FACETS	0.562	0.499	0.628	0.562	0.499	0.628	SUBCLONAL	1	FALSE	1	0.324045206676415	2		916	1066	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288699	198288699	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0052258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	76	379	0	ENST00000335508.6:c.29-1G>A		p.X10_splice	ENST00000335508	NM_012433.2	10			0.303711470366868	3	FACETS	0.886	0.778	1			1	CLONAL	1	FALSE	NA	0.324045206676415	3		379	615	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645872	215645872	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	68	662	0	ENST00000260947.4:c.726C>A	p.Phe242Leu	p.F242L	ENST00000260947	NM_000465.2	242	ttC/ttA	4/11	1	2	FACETS	0.527	0.457	0.602	0.527	0.457	0.602	SUBCLONAL	1	FALSE	1	0.324045206676415	2		662	797	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026155	36026155	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	118	828	1	ENST00000358208.4:c.757C>A	p.Pro253Thr	p.P253T	ENST00000358208		253	Ccg/Acg	7/12	1	2	FACETS	0.727	0.655	0.804	0.727	0.655	0.804	SUBCLONAL	1	FALSE	1	0.324045206676415	2		829	1002	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146754	185146754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	85	761	1	ENST00000265026.3:c.385G>A	p.Gly129Arg	p.G129R	ENST00000265026	NM_004721.4	129	Ggg/Agg	2/14	1	2	FACETS	0.614	0.541	0.691	0.614	0.541	0.691	SUBCLONAL	1	FALSE	1	0.324045206676415	2		762	855	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392041	81392042	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0052258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	41	306	1	ENST00000222390.5:c.235_236delinsTT	p.Gly79Leu	p.G79L	ENST00000222390	NM_000601.4	79	GGa/TTa	2/18	0.168708076208378	3	FACETS	0.581	0.484	0.69	0.194	0.161	0.23	INDETERMINATE	1	FALSE	0	0.324045206676415	3		307	506	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852191	128852192	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0052258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	267	853	1	ENST00000249373.3:c.2263_2264delinsAA	p.Pro755Asn	p.P755N	ENST00000249373	NM_005631.4	755	CCc/AAc	12/12	0.303711470366868	3	FACETS	0.833	0.78	0.886			1	CLONAL	2	FALSE	NA	0.324045206676415	3		854	1150	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845366	151845366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	246	614	0	ENST00000262189.6:c.13646G>T	p.Arg4549Leu	p.R4549L	ENST00000262189	NM_170606.2	4549	cGc/cTc	52/59	0.258037729347747	4	FACETS	1	0.963	1	0.694	0.65	0.741	CLONAL	2	FALSE	1	0.324045206676415	4		614	965	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564789	41564792	+	frameshift_variant	Frame_Shift_Del	DEL	GAAG	GAAG	AAA	novel	NA	P-0052258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	85	651	1	ENST00000263253.7:c.4090_4093delinsAAA	p.Glu1364LysfsTer46	p.E1364Kfs*46	ENST00000263253	NM_001429.3	1364	GAAGaa/AAAaa	25/31	0.130439696541797	3	FACETS	0.69	0.608	0.777	0.345	0.304	0.389	INDETERMINATE	1	FALSE	1	0.324045206676415	3		652	884	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0052259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	221	380	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.532321570039079	4	FACETS	0.945	0.884	1	0.945	0.884	1	CLONAL	2	TRUE	2	0.532321570039079	4		380	673	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0052259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	154	220	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.532321570039079	2	FACETS	0.936	0.873	1	0.936	0.873	1	CLONAL	2	TRUE	0	0.532321570039079	2		220	309	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591892	48591892	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	364	426	0	ENST00000342988.3:c.1055G>T	p.Gly352Val	p.G352V	ENST00000342988	NM_005359.5	352	gGa/gTa	9/12	0.243923484284169	4	FACETS	1	0.993	1			1	INDETERMINATE	3	TRUE	NA	0.532321570039079	4		426	606	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784110	120784110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs538550275	NA	P-0052259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	222	660	0	ENST00000257552.2:c.875C>T	p.Thr292Met	p.T292M	ENST00000257552	NM_002442.3	292	aCg/aTg	13/15	0.532321570039079	3	FACETS	1	0.98	1	0.567	0.528	0.607	CLONAL	1	TRUE	1	0.532321570039079	3		660	931	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637008	93637008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201479078	NA	P-0052259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	115	384	0	ENST00000375746.1:c.1058C>T	p.Ala353Val	p.A353V	ENST00000375746	NM_001174167.1	353	gCg/gTg	9/14	0.532321570039079	3	FACETS	1	0.923	1	0.511	0.462	0.563	CLONAL	1	TRUE	1	0.532321570039079	3		384	535	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248146	59248147	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0052259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	56	87	0	ENST00000371222.2:c.596dup	p.Gln200AlafsTer110	p.Q200Afs*110	ENST00000371222	NM_002228.3	199	gcg/gcCg	1/1	0.532321570039079	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.532321570039079	2		87	97	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061677	38061677	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	181	241	0	ENST00000250448.2:c.312G>C	p.Met104Ile	p.M104I	ENST00000250448	NM_004496.3	104	atG/atC	2/2	0.532321570039079	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.532321570039079	3		241	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057520000	NA	P-0052260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	292	723	0	ENST00000269305.4:c.452C>G	p.Pro151Arg	p.P151R	ENST00000269305	NM_001126112.2	151	cCc/cGc	5/11	0.41901259004373	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.536447483352892	1		723	775	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987388	2987388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1192456063	NA	P-0052260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	82	551	0	ENST00000396946.4:c.41C>T	p.Thr14Met	p.T14M	ENST00000396946	NM_032415.4	14	aCg/aTg	3/25	0.458910030881609	3	FACETS	0.491	0.433	0.555	0.164	0.144	0.185	SUBCLONAL	1	TRUE	0	0.536447483352892	3		551	789	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4090610	4090611	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGTGGGTGTGC	novel	NA	P-0052260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	96	463	0	ENST00000262948.5:c.1178_1188dup	p.Arg397AlafsTer33	p.R397Afs*33	ENST00000262948	NM_030662.3	396	-/GCACACCCACG	11/11	1	2	FACETS	0.563	0.502	0.627	0.563	0.502	0.627	SUBCLONAL	1	TRUE	1	0.536447483352892	2		463	636	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934953	49934953	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	240	586	0	ENST00000296474.3:c.2046G>T	p.Met682Ile	p.M682I	ENST00000296474	NM_002447.2	682	atG/atT	6/20	0.535134693089998	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.536447483352892	1		586	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577571	7577571	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs765848205	NA	P-0052261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	11	738	1	ENST00000269305.4:c.710T>A	p.Met237Lys	p.M237K	ENST00000269305	NM_001126112.2	237	aTg/aAg	7/11	0.623413083372731	0	FACETS		NA	1			1	NA	1	TRUE	0	0.768251382099	0		739	127	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597850	43597850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138265837	NA	P-0052261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	224	980	1	ENST00000355710.3:c.398G>A	p.Arg133His	p.R133H	ENST00000355710	NM_020975.4	133	cGt/cAt	3/20	0.185339338860819	4	FACETS	1	0.969	1	1	0.969	1	INDETERMINATE	2	TRUE	2	0.768251382099	4		981	494	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343591	118343591	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	100	511	0	ENST00000534358.1:c.1717C>T	p.Gln573Ter	p.Q573*	ENST00000534358	NM_005933.3	573	Cag/Tag	3/36	0.33075903432468	1	FACETS	0.594	0.539	0.65	0.594	0.539	0.65	INDETERMINATE	1	TRUE	0	0.768251382099	1		511	270	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098718	47098718	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	62	782	0	ENST00000409792.3:c.6556A>G	p.Lys2186Glu	p.K2186E	ENST00000409792	NM_014159.6	2186	Aag/Gag	15/21	0.33075903432468	1	FACETS	0.28	0.243	0.32	0.28	0.243	0.32	INDETERMINATE	1	TRUE	0	0.768251382099	1		782	355	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0052263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	35	495	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.735	0.604	0.881	0.735	0.604	0.881	SUBCLONAL	1	TRUE	1	0.306119064324322	2		495	311	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577560	7577560	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520002	NA	P-0052263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	139	587	0	ENST00000269305.4:c.721T>C	p.Ser241Pro	p.S241P	ENST00000269305	NM_001126112.2	241	Tcc/Ccc	7/11	0.306119064324322	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.306119064324322	1		587	599	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056500	26056500	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs372319415	NA	P-0052263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	50	301	0	ENST00000343677.2:c.157G>C	p.Glu53Gln	p.E53Q	ENST00000343677	NM_005319.3	53	Gag/Cag	1/1	1	2	FACETS	0.947	0.807	1	0.947	0.807	1	CLONAL	1	TRUE	1	0.306119064324322	2		301	345	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714415	40714415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765339833	NA	P-0052263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	72	574	1	ENST00000373198.4:c.3982G>A	p.Asp1328Asn	p.D1328N	ENST00000373198	NM_133170.3	1328	Gac/Aac	29/32	0.306119064324322	5	FACETS	0.736	0.641	0.838	0.245	0.213	0.28	SUBCLONAL	1	TRUE	2	0.306119064324322	5		575	933	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965846	90965846	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	18	390	0	ENST00000265433.3:c.1471G>C	p.Glu491Gln	p.E491Q	ENST00000265433	NM_002485.4	491	Gaa/Caa	11/16	1	2	FACETS	0.425	0.32	0.549	0.425	0.32	0.549	SUBCLONAL	1	TRUE	1	0.306119064324322	2		390	277	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724175	112724175	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	21	399	0	ENST00000369452.4:c.59C>T	p.Ser20Leu	p.S20L	ENST00000369452	NM_007373.3	20	tCa/tTa	2/9	1	2	FACETS	0.395	0.304	0.502	0.395	0.304	0.502	SUBCLONAL	1	TRUE	1	0.306119064324322	2		399	347	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856453	111856453	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	27	262	0	ENST00000341259.2:c.504G>T	p.Glu168Asp	p.E168D	ENST00000341259	NM_005475.2	168	gaG/gaT	2/8	0.306119064324322	1	FACETS	0.453	0.36	0.558	0.453	0.36	0.558	SUBCLONAL	1	TRUE	0	0.306119064324322	1		262	330	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687075	37687075	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	112	583	0	ENST00000447079.4:c.3979G>C	p.Glu1327Gln	p.E1327Q	ENST00000447079	NM_015083.1	1327	Gag/Cag	14/14	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.306119064324322	2		583	616	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722059	176722059	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	41	502	0	ENST00000439151.2:c.7690G>C	p.Glu2564Gln	p.E2564Q	ENST00000439151	NM_022455.4	2564	Gag/Cag	23/23	1	2	FACETS	0.475	0.395	0.564	0.475	0.395	0.564	SUBCLONAL	1	TRUE	1	0.306119064324322	2		502	564	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069124	5069124	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	12	500	0	ENST00000381652.3:c.1429C>G	p.Leu477Val	p.L477V	ENST00000381652	NM_004972.3	477	Ctt/Gtt	11/25	0.241731677221422	0	FACETS	0.228	0.159	0.311			1	SUBCLONAL	1	TRUE	0	0.306119064324322	0		500	239	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422666	47422666	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	84	677	1	ENST00000377045.4:c.138C>A	p.Asp46Glu	p.D46E	ENST00000377045	NM_001654.4	46	gaC/gaA	3/16	1	2	FACETS	0.743	0.655	0.836	0.743	0.655	0.836	SUBCLONAL	1	TRUE	1	0.306119064324322	2		678	739	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0052264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	65	518	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	1	2	FACETS	0.778	0.677	0.885	0.778	0.677	0.885	SUBCLONAL	1	TRUE	1	0.44	2		518	380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579310	7579310	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1555526469	NA	P-0052264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	126	492	0	ENST00000269305.4:c.375+2T>C		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.3	2	FACETS	0.789	0.722	0.857	0.789	0.722	0.857	SUBCLONAL	2	TRUE	0	0.44	2		492	363	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0052264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	129	464	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.102369811685403	5	FACETS	1	0.975	1	0.588	0.538	0.64	INDETERMINATE	2	TRUE	1	0.44	5		464	414	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971189	21971189	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	114	421	0	ENST00000304494.5:c.169del	p.Ala57ProfsTer89	p.A57Pfs*89	ENST00000304494	NM_000077.4	57	Gcc/cc	2/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.44	2		421	422	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0052266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	33	41	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.130220728629082	3	FACETS	1	0.919	1	0.62	0.507	0.747	CLONAL	1	TRUE	1	0.216746604964989	3		41	272	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs1057519842	NA	P-0052266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	20	277	0	ENST00000274335.5:c.1727_1729del	p.Thr576del	p.T576del	ENST00000274335		575	aaGACg/aag	12/15	1	2	FACETS	0.591	0.452	0.755	0.591	0.452	0.755	SUBCLONAL	1	TRUE	1	0.216746604964989	2		277	312	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106910	27106910	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	133	532	0	ENST00000324856.7:c.6521T>C	p.Leu2174Pro	p.L2174P	ENST00000324856	NM_006015.4	2174	cTg/cCg	20/20	0.177230596300091	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	2	TRUE	0	0.216746604964989	2		532	608	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692884	89692884	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	28	329	0	ENST00000371953.3:c.368del	p.His123ProfsTer11	p.H123Pfs*11	ENST00000371953	NM_000314.4	123	cAc/cc	5/9	0.130220728629082	3	FACETS	0.816	0.652	1	0.408	0.326	0.501	CLONAL	1	TRUE	1	0.216746604964989	3		329	351	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371002	55371003	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	57	488	0	ENST00000297316.4:c.305dup	p.Lys104GlnfsTer58	p.K104Qfs*58	ENST00000297316	NM_022454.3	102	ctg/cTtg	1/2	1	2	FACETS	0.983	0.844	1	0.983	0.844	1	CLONAL	1	TRUE	1	0.216746604964989	2		488	535	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411098	63411098	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	62	631	0	ENST00000330258.3:c.2069G>T	p.Ser690Ile	p.S690I	ENST00000330258	NM_152424.3	690	aGc/aTc	2/2	1	2	FACETS	0.815	0.703	0.937	0.815	0.703	0.937	CLONAL	1	TRUE	1	0.216746604964989	2		631	702	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	49	460	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.793	0.674	0.921	1	0.966	1	CLONAL	2	TRUE	1	0.189646425864088	2		460	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0052267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	56	567	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.189646425864088	1	FACETS	0.909	0.779	1	0.909	0.779	1	CLONAL	1	TRUE	0	0.189646425864088	1		567	588	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441780	49441780	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555195442	NA	P-0052267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	61	502	0	ENST00000301067.7:c.4204C>T	p.Gln1402Ter	p.Q1402*	ENST00000301067	NM_003482.3	1402	Cag/Tag	14/54	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.189646425864088	2		502	607	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971157	21971158	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	72	393	0	ENST00000304494.5:c.200_201insT	p.Ala68ArgfsTer52	p.A68Rfs*52	ENST00000304494	NM_000077.4	67	ggc/ggTc	2/3	1	2	FACETS	0.811	0.711	0.919	1	0.977	1	CLONAL	2	TRUE	1	0.189646425864088	2		393	468	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0052268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	291	380	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.290781833762377	4	FACETS	1	0.968	1	1	0.968	1	INDETERMINATE	2	TRUE	2	0.592508754632561	4		380	757	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400051	49400051	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	230	414	0	ENST00000418115.1:c.286C>G	p.Pro96Ala	p.P96A	ENST00000418115	NM_001664.2	96	Cca/Gca	4/5	1	2	FACETS	0.999	0.934	1	0.999	0.934	1	CLONAL	1	TRUE	1	0.592508754632561	2		414	777	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282653	1282653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	278	660	0	ENST00000310581.5:c.1660G>A	p.Val554Ile	p.V554I	ENST00000310581	NM_198253.2	554	Gtc/Atc	3/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.592508754632561	2		660	915	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0052271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	75	446	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	0.937	0.821	1	0.937	0.821	1	CLONAL	1	TRUE	1	0.23	2		446	696	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0052271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	66	380	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.835	0.725	0.956	0.835	0.725	0.956	CLONAL	1	TRUE	1	0.23	2		380	687	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0052271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	96	812	2	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	0.181599720984041	1	FACETS	0.657	0.584	0.736	0.657	0.584	0.736	SUBCLONAL	1	TRUE	0	0.23	1		814	1124	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198108	185198108	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	53	431	0	ENST00000265026.3:c.2590A>T	p.Ser864Cys	p.S864C	ENST00000265026	NM_004721.4	864	Agt/Tgt	13/14	1	2	FACETS	0.61	0.519	0.711	0.61	0.519	0.711	SUBCLONAL	1	TRUE	1	0.23	2		431	755	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441769	49441769	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	87	635	1	ENST00000301067.7:c.4215C>G	p.His1405Gln	p.H1405Q	ENST00000301067	NM_003482.3	1405	caC/caG	14/54	1	2	FACETS	0.45	0.398	0.506	0.45	0.398	0.506	SUBCLONAL	1	TRUE	1	0.479997825633509	2		636	805	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042728	42042728	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	148	285	2	ENST00000219905.7:c.6923A>G	p.Asp2308Gly	p.D2308G	ENST00000219905	NM_001164273.1	2308	gAt/gGt	17/24	0.474937283417275	1	FACETS	0.953	0.876	1	0.953	0.876	1	CLONAL	1	TRUE	0	0.479997825633509	1		287	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578179	7578179	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	274	660	1	ENST00000269305.4:c.670G>T	p.Glu224Ter	p.E224*	ENST00000269305	NM_001126112.2	224	Gag/Tag	6/11	0.479997825633509	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.479997825633509	1		661	740	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278198	41278198	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	126	293	0	ENST00000349496.5:c.2074G>C	p.Glu692Gln	p.E692Q	ENST00000349496	NM_001904.3	692	Gag/Cag	13/15	1	2	FACETS	0.943	0.857	1	0.943	0.857	1	CLONAL	1	TRUE	1	0.479997825633509	2		293	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0052273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	25	825	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.636	0.502	0.79	0.636	0.502	0.79	SUBCLONAL	1	TRUE	1	0.25033354854419	2		826	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0052273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	21	809	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	1	2	FACETS	0.521	0.401	0.661	0.521	0.401	0.661	SUBCLONAL	1	TRUE	1	0.25033354854419	2		809	322	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845583	128845583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764495218	NA	P-0052273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	21	698	0	ENST00000249373.3:c.880G>A	p.Val294Ile	p.V294I	ENST00000249373	NM_005631.4	294	Gtc/Atc	4/12	0.191083347803384	1	FACETS	0.565	0.435	0.714	0.565	0.435	0.714	SUBCLONAL	1	TRUE	0	0.25033354854419	1		698	260	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570763	226570763	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	26	643	0	ENST00000366794.5:c.1133C>G	p.Ala378Gly	p.A378G	ENST00000366794	NM_001618.3	378	gCt/gGt	8/23	1	2	FACETS	0.672	0.533	0.831	0.672	0.533	0.831	SUBCLONAL	1	TRUE	1	0.25033354854419	2		643	309	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0052274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	319	719	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.464558935671381	2	FACETS	0.803	0.764	0.842	0.803	0.764	0.842	CLONAL	2	TRUE	0	0.578514386743575	2		719	687	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549392	21549392	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	126	634	0	ENST00000382592.4:c.2884A>G	p.Asn962Asp	p.N962D	ENST00000382592	NM_014572.2	962	Aat/Gat	8/8	1	2	FACETS	0.766	0.696	0.838	0.766	0.696	0.838	SUBCLONAL	1	TRUE	1	0.578514386743575	2		634	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579350	7579350	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587781642	NA	P-0052277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	544	751	0	ENST00000269305.4:c.337T>G	p.Phe113Val	p.F113V	ENST00000269305	NM_001126112.2	113	Ttc/Gtc	4/11	0.898910987621488	1	FACETS	0.983	0.961	1	0.983	0.961	1	CLONAL	1	TRUE	0	0.910584124991116	1		751	662	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176430	123176441	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGAAATGTTT	GCAGAAATGTTT	A	novel	NA	P-0052277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	181	75	0	ENST00000218089.9:c.397_408delinsA	p.Ala133LysfsTer7	p.A133Kfs*7	ENST00000218089	NM_001042749.1	133	GCAGAAATGTTT/A	7/35	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.910584124991116	1		75	201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0052278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	463	743	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.657954594414798	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.642318292888922	1		743	715	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878061	48878062	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1131690852	NA	P-0052278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	219	261	0	ENST00000267163.4:c.19dup	p.Arg7ProfsTer24	p.R7Pfs*24	ENST00000267163	NM_000321.2	5	acc/aCcc	1/27	0.657954594414798	2	FACETS	0.789	0.745	0.834	0.789	0.745	0.834	SUBCLONAL	2	TRUE	0	0.642318292888922	2		261	432	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561358	9561358	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	219	484	0	ENST00000353224.5:c.424A>G	p.Thr142Ala	p.T142A	ENST00000353224	NM_177990.2	142	Acg/Gcg	4/10	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.642318292888922	2		484	540	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266221	41266221	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	114	355	0	ENST00000349496.5:c.218C>T	p.Ser73Phe	p.S73F	ENST00000349496	NM_001904.3	73	tCc/tTc	3/15	0.657954594414798	1	FACETS	0.732	0.668	0.799	0.732	0.668	0.799	SUBCLONAL	1	TRUE	0	0.642318292888922	1		355	329	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0052280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	107	656	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.938	0.841	1	0.938	0.841	1	CLONAL	1	TRUE	1	0.29	2		657	787	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352765	70352765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759105512	NA	P-0052280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	96	539	0	ENST00000374080.3:c.4486C>T	p.Arg1496Cys	p.R1496C	ENST00000374080		1496	Cgc/Tgc	32/45	1	2	FACETS	0.836	0.744	0.934	0.836	0.744	0.934	CLONAL	1	TRUE	1	0.29	2		539	792	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118632	11118632	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	90	573	0	ENST00000358026.2:c.2056G>T	p.Glu686Ter	p.E686*	ENST00000358026	NM_001128849.1	686	Gag/Tag	14/36	1	2	FACETS	0.94	0.835	1	0.94	0.835	1	CLONAL	1	TRUE	1	0.29	2		573	660	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207088	1207089	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	115	651	0	ENST00000326873.7:c.178dup	p.Tyr60LeufsTer103	p.Y60Lfs*103	ENST00000326873	NM_000455.4	59	tct/tcTt	1/10	1	2	FACETS	0.895	0.806	0.99	0.895	0.806	0.99	CLONAL	1	TRUE	1	0.29	2		651	886	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610611	10610611	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs575186517	NA	P-0052280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	88	571	0	ENST00000171111.5:c.99C>A	p.Tyr33Ter	p.Y33*	ENST00000171111	NM_203500.1	33	taC/taA	2/6	1	2	FACETS	0.817	0.723	0.917	0.817	0.723	0.917	CLONAL	1	TRUE	1	0.29	2		571	743	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216693	36216693	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765981100	NA	P-0052280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	75	522	0	ENST00000222270.7:c.3859C>T	p.Arg1287Trp	p.R1287W	ENST00000222270	NM_014727.1	1287	Cgg/Tgg	13/37	0.23320586987577	3	FACETS	0.685	0.599	0.778	0.342	0.299	0.389	SUBCLONAL	1	TRUE	1	0.29	3		522	865	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553540	106553540	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	30	312	0	ENST00000369096.4:c.1505C>A	p.Ala502Asp	p.A502D	ENST00000369096	NM_001198.3	502	gCc/gAc	5/7	1	2	FACETS	0.48	0.386	0.586	0.48	0.386	0.586	SUBCLONAL	1	TRUE	1	0.29	2		312	431	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0052281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	126	401	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.085611072769407	4	FACETS	0.924	0.839	1	1	0.983	1	INDETERMINATE	3	FALSE	2	0.184088864534112	4		401	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0052281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	73	462	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	1	2	FACETS	0.918	0.806	1	1	0.981	1	CLONAL	2	FALSE	1	0.184088864534112	2		462	432	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971109	21971109	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs34968276	NA	P-0052281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	64	436	0	ENST00000304494.5:c.249C>G	p.His83Gln	p.H83Q	ENST00000304494	NM_000077.4	83	caC/caG	2/3	1	2	FACETS	0.968	0.843	1	1	0.98	1	CLONAL	2	FALSE	1	0.184088864534112	2		436	359	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573537	48573537	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	48	277	0	ENST00000342988.3:c.121G>T	p.Glu41Ter	p.E41*	ENST00000342988	NM_005359.5	41	Gaa/Taa	2/12	0.184088864534112	3	FACETS	1	0.908	1	1	0.908	1	CLONAL	2	FALSE	1	0.184088864534112	3		277	261	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	53	701	11	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.15900302585795	3	FACETS	1	0.936	1	0.58	0.499	0.668	INDETERMINATE	1	TRUE	1	0.4	3		712	274	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	65	618	2	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	0.0910154360402561	0	FACETS	0.474	0.413	0.541			1	INDETERMINATE	1	TRUE	0	0.4	0		620	411	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	57	388	1	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.4	2		389	276	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	83	471	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	0.798	0.714	0.885	1	0.982	1	SUBCLONAL	2	TRUE	1	0.4	2		472	260	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457243	25457243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377577594	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	79	511	2	ENST00000264709.3:c.2644C>T	p.Arg882Cys	p.R882C	ENST00000264709	NM_175629.2	882	Cgc/Tgc	23/23	0.0910154360402561	0	FACETS	0.562	0.496	0.631			1	INDETERMINATE	1	TRUE	0	0.4	0		513	422	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	91	619	0	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	1	2	FACETS	0.956	0.852	1	0.956	0.852	1	CLONAL	1	TRUE	1	0.4	2		619	476	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660469	67660469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	35	357	1	ENST00000264010.4:c.1369C>T	p.Arg457Ter	p.R457*	ENST00000264010	NM_006565.3	457	Cga/Tga	8/12	0.0910154360402561	0	FACETS	0.467	0.385	0.557			1	INDETERMINATE	1	TRUE	0	0.4	0		358	225	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103400	77103400	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs748471279	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	42	251	0	ENST00000356341.3:c.166C>T	p.Arg56Ter	p.R56*	ENST00000356341	NM_002576.4	56	Cga/Tga	2/15	1	2	FACETS	0.991	0.836	1	0.991	0.836	1	CLONAL	1	TRUE	1	0.4	2		251	212	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972893	32972893	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	21	247	0	ENST00000380152.3:c.10248del	p.Lys3416AsnfsTer11	p.K3416Nfs*11	ENST00000380152		3415	Aaa/aa	27/27	0.15900302585795	4	FACETS	1	0.864	1	0.579	0.451	0.723	INDETERMINATE	1	TRUE	2	0.4	4		247	127	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512401	38512402	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs745553450	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	64	652	2	ENST00000254066.5:c.1319dup	p.Pro441AlafsTer5	p.P441Afs*5	ENST00000254066	NM_000964.3	438	gcc/gCcc	9/9	1	2	FACETS	0.976	0.851	1	0.976	0.851	1	CLONAL	1	TRUE	1	0.4	2		654	328	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108184	209108184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778401	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	36	367	0	ENST00000345146.2:c.665G>A	p.Arg222His	p.R222H	ENST00000345146	NM_005896.2	222	cGt/cAt	6/10	1	2	FACETS	0.963	0.8	1	0.963	0.8	1	CLONAL	1	TRUE	1	0.4	2		367	187	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657020	47657020	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63751108	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	36	344	0	ENST00000233146.2:c.1216C>T	p.Arg406Ter	p.R406*	ENST00000233146	NM_000251.2	406	Cga/Tga	7/16	0.0910154360402561	0	FACETS	0.794	0.665	0.933			1	INDETERMINATE	1	TRUE	0	0.4	0		344	136	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431395	121431395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs893256143	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	53	540	0	ENST00000257555.6:c.599G>A	p.Arg200Gln	p.R200Q	ENST00000257555		200	cGg/cAg	3/10	0.15900302585795	0	FACETS	0.494	0.423	0.57			1	INDETERMINATE	1	TRUE	0	0.4	0		540	322	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144026	11144026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	85	569	0	ENST00000358026.2:c.3607C>T	p.Arg1203Cys	p.R1203C	ENST00000358026	NM_001128849.1	1203	Cgc/Tgc	26/36	1	2	FACETS	0.962	0.854	1	0.962	0.854	1	CLONAL	1	TRUE	1	0.4	2		569	442	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122925	2122925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150672640	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	82	611	1	ENST00000219476.3:c.2296G>A	p.Val766Met	p.V766M	ENST00000219476	NM_000548.3	766	Gtg/Atg	21/42	0.0910154360402561	0	FACETS	0.584	0.518	0.655			1	INDETERMINATE	1	TRUE	0	0.4	0		612	421	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420670	49420670	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs797045659	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	59	522	1	ENST00000301067.7:c.15079C>T	p.Arg5027Ter	p.R5027*	ENST00000301067	NM_003482.3	5027	Cga/Tga	48/54	0.305133716407763	4	FACETS	1	0.904	1	0.529	0.457	0.608	CLONAL	1	TRUE	2	0.4	4		523	390	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475550	12475550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479145908	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	80	435	0	ENST00000287820.6:c.1424C>T	p.Thr475Met	p.T475M	ENST00000287820	NM_015869.4	475	aCg/aTg	7/7	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.4	2		435	367	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395001	395001	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1300046652	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	36	356	3	ENST00000380956.4:c.402del	p.Gly135GlufsTer14	p.G135Efs*14	ENST00000380956	NM_001195286.1	133	Aaa/aa	3/9	0.3	2	FACETS	0.793	0.657	0.943			1	CLONAL	1	TRUE	NA	0.4	2		359	227	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589875	212589875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758827443	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	71	474	0	ENST00000342788.4:c.667G>A	p.Gly223Arg	p.G223R	ENST00000342788	NM_005235.2	223	Gga/Aga	6/28	1	2	FACETS	0.853	0.748	0.966	0.853	0.748	0.966	CLONAL	1	TRUE	1	0.4	2		474	416	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438647	49438647	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	80	581	0	ENST00000301067.7:c.4843C>T	p.Arg1615Ter	p.R1615*	ENST00000301067	NM_003482.3	1615	Cga/Tga	19/54	0.305133716407763	4	FACETS	1	0.969	1	0.648	0.573	0.728	CLONAL	1	TRUE	2	0.4	4		581	432	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226674	2226674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377222686	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	57	586	0	ENST00000398665.3:c.4154G>A	p.Arg1385His	p.R1385H	ENST00000398665	NM_032482.2	1385	cGc/cAc	27/28	1	2	FACETS	0.81	0.698	0.93	0.81	0.698	0.93	CLONAL	1	TRUE	1	0.4	2		586	352	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014170	70014170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769488988	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	60	537	1	ENST00000394351.3:c.1031C>T	p.Thr344Met	p.T344M	ENST00000394351	NM_000248.3	344	aCg/aTg	9/9	1	2	FACETS	0.831	0.72	0.951	0.831	0.72	0.951	CLONAL	1	TRUE	1	0.4	2		538	361	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917083	50917083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747996611	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	87	671	1	ENST00000440232.2:c.2335G>A	p.Ala779Thr	p.A779T	ENST00000440232	NM_002691.3	779	Gcg/Acg	19/27	1	2	FACETS	0.975	0.868	1	0.975	0.868	1	CLONAL	1	TRUE	1	0.4	2		672	446	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794787	42794787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747706524	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	61	609	0	ENST00000575354.2:c.1867G>A	p.Gly623Arg	p.G623R	ENST00000575354	NM_015125.3	623	Gga/Aga	10/20	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.4	2		609	305	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80063860	80063860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35045151	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	48	406	0	ENST00000265081.6:c.2005C>T	p.Arg669Trp	p.R669W	ENST00000265081	NM_002439.4	669	Cgg/Tgg	14/24	0.15900302585795	3	FACETS	1	0.923	1	0.567	0.483	0.657	INDETERMINATE	1	TRUE	1	0.4	3		406	254	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568635	41568635	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1569118537	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	49	385	1	ENST00000263253.7:c.4585C>T	p.Arg1529Ter	p.R1529*	ENST00000263253	NM_001429.3	1529	Cga/Tga	28/31	0.0910154360402561	0	FACETS	0.542	0.463	0.629			1	INDETERMINATE	1	TRUE	0	0.4	0		386	271	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434247	49434247	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	96	776	0	ENST00000301067.7:c.7306del	p.Cys2436AlafsTer49	p.C2436Afs*49	ENST00000301067	NM_003482.3	2436	Tgc/gc	31/54	0.305133716407763	4	FACETS	1	0.962	1	0.586	0.523	0.653	CLONAL	1	TRUE	2	0.4	4		776	573	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228801	36228801	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	80	685	0	ENST00000222270.7:c.7700G>A	p.Arg2567His	p.R2567H	ENST00000222270	NM_014727.1	2567	cGt/cAt	35/37	1	2	FACETS	0.766	0.676	0.863	0.766	0.676	0.863	SUBCLONAL	1	TRUE	1	0.4	2		685	522	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673728	30673728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778019975	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	55	518	0	ENST00000376406.3:c.3232G>A	p.Val1078Ile	p.V1078I	ENST00000376406	NM_014641.2	1078	Gtt/Att	10/15	0.15900302585795	3	FACETS	0.862	0.74	0.994	0.431	0.37	0.497	INDETERMINATE	1	TRUE	1	0.4	3		518	383	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306593	41306593	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	31	576	0	ENST00000373198.4:c.1066T>C	p.Tyr356His	p.Y356H	ENST00000373198	NM_133170.3	356	Tat/Cat	7/32	0.15900302585795	0	FACETS	0.338	0.274	0.41			1	INDETERMINATE	1	TRUE	0	0.4	0		576	275	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133685	41133685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1216360372	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	43	333	0	ENST00000379561.5:c.1943C>T	p.Thr648Met	p.T648M	ENST00000379561	NM_002015.3	648	aCg/aTg	2/3	0.15900302585795	4	FACETS	1	0.95	1	0.669	0.565	0.782	INDETERMINATE	1	TRUE	2	0.4	4		333	225	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211602	46211602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766610841	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	39	264	0	ENST00000334344.6:c.568G>A	p.Val190Ile	p.V190I	ENST00000334344	NM_152641.2	190	Gtc/Atc	5/21	0.305133716407763	4	FACETS	0.754	0.633	0.885	0.754	0.633	0.885	SUBCLONAL	2	TRUE	2	0.4	4		264	181	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133234459	133234459	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs139603739	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	26	364	0	ENST00000320574.5:c.3373C>T	p.Arg1125Ter	p.R1125*	ENST00000320574	NM_006231.2	1125	Cga/Tga	27/49	0.15900302585795	0	FACETS	0.348	0.277	0.429			1	INDETERMINATE	1	TRUE	0	0.4	0		364	224	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5258034	5258034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1435990354	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	38	398	1	ENST00000357368.4:c.700G>A	p.Val234Met	p.V234M	ENST00000357368	NM_002850.3	234	Gtg/Atg	8/38	1	2	FACETS	0.927	0.774	1	0.927	0.774	1	CLONAL	1	TRUE	1	0.4	2		399	205	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141801	108141801	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	27	326	0	ENST00000278616.4:c.2852del	p.Leu951Ter	p.L951*	ENST00000278616	NM_000051.3	950	cTt/ct	19/63	1	2	FACETS	0.722	0.579	0.882	0.722	0.579	0.882	SUBCLONAL	1	TRUE	1	0.4	2		326	187	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005461	42005461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778156846	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	106	587	0	ENST00000219905.7:c.3197G>A	p.Arg1066His	p.R1066H	ENST00000219905	NM_001164273.1	1066	cGc/cAc	9/24	0.0910154360402561	0	FACETS	0.571	0.513	0.632			1	INDETERMINATE	1	TRUE	0	0.4	0		587	557	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222294	2222294	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751408271	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	79	653	1	ENST00000326181.6:c.578G>A	p.Arg193Gln	p.R193Q	ENST00000326181	NM_032271.2	193	cGg/cAg	8/21	0.0910154360402561	0	FACETS	0.731	0.649	0.818			1	INDETERMINATE	1	TRUE	0	0.4	0		654	324	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923638	72923638	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142746363	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	51	501	0	ENST00000268489.5:c.3440C>T	p.Thr1147Met	p.T1147M	ENST00000268489	NM_006885.3	1147	aCg/aTg	4/10	0.0910154360402561	0	FACETS	0.515	0.44	0.596			1	INDETERMINATE	1	TRUE	0	0.4	0		501	297	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226428	2226428	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs540044548	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	90	710	0	ENST00000398665.3:c.3908C>A	p.Ala1303Asp	p.A1303D	ENST00000398665	NM_032482.2	1303	gCt/gAt	27/28	1	2	FACETS	0.989	0.882	1	0.989	0.882	1	CLONAL	1	TRUE	1	0.4	2		710	455	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266735	18266735	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80233027	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	108	569	0	ENST00000222254.8:c.46C>T	p.Arg16Cys	p.R16C	ENST00000222254	NM_005027.3	16	Cgc/Tgc	2/16	1	2	FACETS	0.905	0.814	1	0.905	0.814	1	CLONAL	1	TRUE	1	0.4	2		569	597	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224219	36224219	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	51	519	1	ENST00000222270.7:c.6773del	p.Pro2258LeufsTer3	p.P2258Lfs*3	ENST00000222270	NM_014727.1	2257	Ccc/cc	28/37	1	2	FACETS	0.948	0.812	1	0.948	0.812	1	CLONAL	1	TRUE	1	0.4	2		520	269	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162861	47162861	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763434646	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	46	411	0	ENST00000409792.3:c.3265C>T	p.Arg1089Trp	p.R1089W	ENST00000409792	NM_014159.6	1089	Cgg/Tgg	3/21	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.4	2		411	227	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180049739	180049739	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1469512739	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	36	506	0	ENST00000261937.6:c.1649A>G	p.Tyr550Cys	p.Y550C	ENST00000261937	NM_182925.4	550	tAt/tGt	12/30	0.15900302585795	0	FACETS	0.476	0.394	0.566			1	INDETERMINATE	1	TRUE	0	0.4	0		506	227	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032065	26032065	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1325560590	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	129	475	0	ENST00000244661.2:c.224T>C	p.Ile75Thr	p.I75T	ENST00000244661	NM_003537.3	75	aTc/aCc	1/1	0.3	11	FACETS	0.936	0.851	1			1	CLONAL	3	TRUE	NA	0.4	11		475	643	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800232	32800232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1413092570	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	40	344	0	ENST00000374899.4:c.1150C>T	p.His384Tyr	p.H384Y	ENST00000374899	NM_018833.2	384	Cac/Tac	7/12	0.15900302585795	3	FACETS	1	0.901	1	0.553	0.464	0.65	INDETERMINATE	1	TRUE	1	0.4	3		344	217	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967743	90967743	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	22	226	0	ENST00000265433.3:c.1165del	p.Met389TrpfsTer15	p.M389Wfs*15	ENST00000265433	NM_002485.4	389	Atg/tg	10/16	0.0910154360402561	0	FACETS	0.429	0.335	0.535			1	INDETERMINATE	1	TRUE	0	0.4	0		226	154	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426738	47426738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766305105	NA	P-0052282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	33	629	0	ENST00000377045.4:c.983G>A	p.Arg328Gln	p.R328Q	ENST00000377045	NM_001654.4	328	cGg/cAg	10/16	0.235836016029973	0	FACETS	0.264	0.215	0.319			1	INDETERMINATE	1	TRUE	0	0.4	0		629	375	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0052284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	13	540	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.251659858860873	5	FACETS	0.248	0.175	0.336	0.083	0.058	0.112	SUBCLONAL	1	TRUE	2	0.251659858860873	5		540	575	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727451	66727451	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519729	NA	P-0052284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	115	408	0	ENST00000307102.5:c.167A>C	p.Gln56Pro	p.Q56P	ENST00000307102	NM_002755.3	56	cAg/cCg	2/11	0.243353339696893	3	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	1	0.251659858860873	3		408	482	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0052284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	70	377	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	0.909	0.8	1	1	0.981	1	CLONAL	2	TRUE	1	0.251659858860873	2		377	306	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141492	11141492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	164	576	0	ENST00000358026.2:c.3469C>T	p.Arg1157Trp	p.R1157W	ENST00000358026	NM_001128849.1	1157	Cgg/Tgg	25/36	0.243353339696893	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.251659858860873	3		576	588	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77064603	77064603	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767363828	NA	P-0052284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	124	459	1	ENST00000356341.3:c.814C>T	p.Arg272Trp	p.R272W	ENST00000356341	NM_002576.4	272	Cgg/Tgg	8/15	0.214049005902397	4	FACETS	1	0.91	1	1	0.91	1	CLONAL	2	TRUE	2	0.251659858860873	4		460	615	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578260	7578260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204041	NA	P-0052284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	174	554	0	ENST00000269305.4:c.589G>A	p.Val197Met	p.V197M	ENST00000269305	NM_001126112.2	197	Gtg/Atg	6/11	0.251659858860873	2	FACETS	0.916	0.851	0.984	1	0.989	1	CLONAL	3	TRUE	0	0.251659858860873	2		554	503	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434903	49434903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1201197190	NA	P-0052284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	145	562	0	ENST00000301067.7:c.6650G>A	p.Arg2217His	p.R2217H	ENST00000301067	NM_003482.3	2217	cGt/cAt	31/54	0.180490256583056	5	FACETS	0.906	0.83	0.985	0.906	0.83	0.985	CLONAL	3	TRUE	2	0.251659858860873	5		562	584	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998247	100998247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	70	269	0	ENST00000325455.5:c.1555G>A	p.Gly519Arg	p.G519R	ENST00000325455	NM_001202474.3	519	Ggg/Agg	1/8	0.214049005902397	4	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	2	0.251659858860873	4		269	312	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914265	32914265	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs80358806	NA	P-0052284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	65	411	0	ENST00000380152.3:c.5773C>G	p.Gln1925Glu	p.Q1925E	ENST00000380152		1925	Cag/Gag	11/27	0.251659858860873	2	FACETS	1	0.925	1	0.547	0.475	0.625	CLONAL	1	TRUE	0	0.251659858860873	2		411	472	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146680	185146681	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGTGGACG	novel	NA	P-0052284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	80	559	0	ENST00000265026.3:c.313_320dup	p.Glu108TrpfsTer12	p.E108Wfs*12	ENST00000265026	NM_004721.4	104	acg/acGGTGGACGg	2/14	0.25123476678824	3	FACETS	1	0.955	1	0.588	0.518	0.663	CLONAL	1	TRUE	1	0.251659858860873	3		559	609	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000406	42000406	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	124	169	0	ENST00000219905.7:c.2425G>A	p.Gly809Ser	p.G809S	ENST00000219905	NM_001164273.1	809	Ggt/Agt	7/24	0.586252454205202	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.586252454205202	2		169	208	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572568	64572568	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	254	514	0	ENST00000312049.6:c.1288C>G	p.Pro430Ala	p.P430A	ENST00000312049	NM_130799.2	430	Cct/Gct	9/10	0.586252454205202	2	FACETS	0.969	0.922	1	0.969	0.922	1	CLONAL	2	TRUE	0	0.586252454205202	2		514	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0052287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	323	475	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.402071631951103	2	FACETS	0.964	0.915	1	0.964	0.915	1	CLONAL	2	TRUE	0	0.402071631951103	2		476	833	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248746	212248746	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762661533	NA	P-0052287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	137	216	0	ENST00000342788.4:c.3521G>A	p.Arg1174Gln	p.R1174Q	ENST00000342788	NM_005235.2	1174	cGg/cAg	28/28	0.402071631951103	3	FACETS	0.863	0.791	0.938	0.576	0.527	0.626	CLONAL	2	TRUE	0	0.402071631951103	3		216	474	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435793	110435793	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs761634910	NA	P-0052287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	66	201	0	ENST00000375856.3:c.2608G>T	p.Val870Leu	p.V870L	ENST00000375856	NM_003749.2	870	Gtg/Ttg	1/2	0.116643871470617	5	FACETS	1	0.96	1			1	INDETERMINATE	1	TRUE	NA	0.402071631951103	5		201	414	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0052289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	344	449	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.311072074647083	9	FACETS	1	0.968	1	1	0.992	1	CLONAL	7	TRUE	3	0.311072074647083	9		449	650	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0052289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	86	272	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	0.311072074647083	12	FACETS	1	0.914	1			1	CLONAL	2	TRUE	NA	0.311072074647083	12		272	680	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73096464	73096464	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	47	143	0	ENST00000356692.5:c.244G>T	p.Glu82Ter	p.E82*	ENST00000356692		82	Gaa/Taa	3/9	0.311072074647083	3	FACETS	0.831	0.71	0.962	0.554	0.473	0.642	CLONAL	2	TRUE	0	0.311072074647083	3		143	210	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678007	58678025	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCTCCCGGACGCCGGGG	CCTCTCCCGGACGCCGGGG	-	novel	NA	P-0052289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	83	234	0	ENST00000305921.3:c.236_254del	p.Leu79ArgfsTer80	p.L79Rfs*80	ENST00000305921	NM_003620.3	78	CCTCTCCCGGACGCCGGGGcc/cc	1/6	0.311072074647083	6	FACETS	0.984	0.872	1			1	CLONAL	2	TRUE	NA	0.311072074647083	6		234	440	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407476	407476	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	74	311	0	ENST00000380956.4:c.1234C>G	p.Gln412Glu	p.Q412E	ENST00000380956	NM_001195286.1	412	Caa/Gaa	9/9	0.311072074647083	6	FACETS	0.912	0.802	1	0.456	0.401	0.515	CLONAL	2	TRUE	2	0.311072074647083	6		311	423	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021819	69021819	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	1297	486	0	ENST00000288368.4:c.3107C>A	p.Ala1036Glu	p.A1036E	ENST00000288368	NM_024870.2	1036	gCa/gAa	25/40	0.311072074647083	17	FACETS	0.98	0.966	0.994	1	0.998	1	CLONAL	18	TRUE	1	0.311072074647083	17		486	1575	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040962	47040965	+	frameshift_variant	Frame_Shift_Del	DEL	CGCG	CGCG	-	novel	NA	P-0052289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	153	603	0	ENST00000377604.3:c.1493_1496del	p.Arg498ProfsTer205	p.R498Pfs*205	ENST00000377604	NM_001204468.1	498	CGCGcc/cc	14/24	0.311072074647083	3	FACETS	0.756	0.692	0.822	0.504	0.461	0.548	SUBCLONAL	2	TRUE	0	0.311072074647083	3		603	752	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225525	133225525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762090058	NA	P-0052291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	41	604	0	ENST00000320574.5:c.4139C>T	p.Ser1380Leu	p.S1380L	ENST00000320574	NM_006231.2	1380	tCg/tTg	32/49	0.38603706967274	1	FACETS	0.688	0.578	0.81	0.688	0.578	0.81	SUBCLONAL	1	TRUE	0	0.38603706967274	1		604	249	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0052291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	145	655	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.38603706967274	1	FACETS	0.754	0.695	0.814	1	0.989	1	SUBCLONAL	2	TRUE	0	0.38603706967274	1		655	402	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426124	49426124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326879451	NA	P-0052291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	106	657	0	ENST00000301067.7:c.12364G>A	p.Gly4122Arg	p.G4122R	ENST00000301067	NM_003482.3	4122	Gga/Aga	39/54	0.277039876958855	3	FACETS	0.853	0.771	0.938	0.853	0.771	0.938	CLONAL	2	TRUE	1	0.38603706967274	3		657	384	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115413	115115413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	44	587	0	ENST00000257566.3:c.913G>A	p.Asp305Asn	p.D305N	ENST00000257566	NM_016569.3	305	Gac/Aac	5/8	0.38603706967274	1	FACETS	0.493	0.414	0.58	0.493	0.414	0.58	SUBCLONAL	1	TRUE	0	0.38603706967274	1		587	373	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045802	26045802	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	252	647	0	ENST00000540144.1:c.164A>G	p.Tyr55Cys	p.Y55C	ENST00000540144	NM_003531.2	55	tAc/tGc	1/1	1	2	FACETS	0.885	0.833	0.938	0.885	0.833	0.938	CLONAL	1	TRUE	1	0.836042480899964	2		647	681	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939788	71939788	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	226	557	2	ENST00000298229.2:c.419del	p.Pro140ArgfsTer39	p.P140Rfs*39	ENST00000298229	NM_001567.3	139	Ccc/cc	4/28	1	2	FACETS	0.892	0.837	0.948	0.892	0.837	0.948	CLONAL	1	TRUE	1	0.836042480899964	2		559	606	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822378	72822378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369772600	NA	P-0052296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	301	747	0	ENST00000268489.5:c.9797C>T	p.Thr3266Met	p.T3266M	ENST00000268489	NM_006885.3	3266	aCg/aTg	10/10	1	2	FACETS	0.954	0.903	1	0.954	0.903	1	CLONAL	1	TRUE	1	0.836042480899964	2		747	755	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439843	51439843	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	228	368	0	ENST00000262662.1:c.412del	p.Asp138ThrfsTer18	p.D138Tfs*18	ENST00000262662		136	aaG/aa	4/4	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.836042480899964	2		368	478	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061248	38061249	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	novel	NA	P-0052296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	246	499	0	ENST00000250448.2:c.738_740dup	p.Leu246_His247insGln	p.L246_H247insQ	ENST00000250448	NM_004496.3	247	cac/caGCAc	2/2	1	2	FACETS	0.925	0.871	0.981	0.925	0.871	0.981	CLONAL	1	TRUE	1	0.836042480899964	2		499	636	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916128	9916128	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	23	425	0	ENST00000330684.3:c.2161A>G	p.Lys721Glu	p.K721E	ENST00000330684	NM_001134407.1	721	Aaa/Gaa	10/13	1	2	FACETS	0.128	0.099	0.161	0.128	0.099	0.161	SUBCLONAL	1	TRUE	1	0.836042480899964	2		425	430	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266710	198266710	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	161	494	0	ENST00000335508.6:c.2222A>C	p.Lys741Thr	p.K741T	ENST00000335508	NM_012433.2	741	aAg/aCg	15/25	1	2	FACETS	0.717	0.662	0.774	0.717	0.662	0.774	SUBCLONAL	1	TRUE	1	0.836042480899964	2		494	537	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274898	41274898	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	440	474	0	ENST00000349496.5:c.1148G>C	p.Trp383Ser	p.W383S	ENST00000349496	NM_001904.3	383	tGg/tCg	8/15	0.8134837511872	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.836042480899964	2		474	512	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202845	27202845	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052296-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	114	397	0	ENST00000380036.4:c.1937A>C	p.Lys646Thr	p.K646T	ENST00000380036	NM_000459.3	646	aAg/aCg	13/23	1	2	FACETS	0.588	0.532	0.646	0.588	0.532	0.646	SUBCLONAL	1	TRUE	1	0.836042480899964	2		397	464	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696688	47696688	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519971	NA	P-0052320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	19	389	0	ENST00000347630.2:c.260A>C	p.Tyr87Ser	p.Y87S	ENST00000347630	NM_001007230.1	87	tAc/tCc	5/11	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.275745910169826	2		389	116	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0052321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	173	475	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.277258704601704	2	FACETS	0.766	0.707	0.827	0.766	0.707	0.827	SUBCLONAL	2	TRUE	0	0.326452860135048	2		476	692	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0052321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	34	41	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.30524340271388	2	FACETS	0.96	0.791	1	0.48	0.395	0.574	CLONAL	1	TRUE	0	0.326452860135048	2		41	217	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341255	8341255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	37	258	0	ENST00000356435.5:c.4961C>T	p.Ser1654Leu	p.S1654L	ENST00000356435		1654	tCa/tTa	30/35	1	2	FACETS	0.833	0.691	0.991	0.833	0.691	0.991	CLONAL	1	TRUE	1	0.326452860135048	2		258	272	SUCCESS
AR	367	MSKCC	GRCh37	X	66766603	66766603	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs753693014	NA	P-0052321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	81	646	2	ENST00000374690.3:c.1615C>A	p.Arg539Ser	p.R539S	ENST00000374690	NM_000044.3	539	Cgt/Agt	1/8	0.326452860135048	3	FACETS	0.71	0.625	0.802			1	SUBCLONAL	1	TRUE	NA	0.326452860135048	3		648	813	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271447	26271447	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	99	692	0	ENST00000305910.3:c.166C>G	p.Gln56Glu	p.Q56E	ENST00000305910	NM_003534.2	56	Cag/Gag	1/1	0.320621922228721	4	FACETS	0.878	0.783	0.98	0.439	0.391	0.49	CLONAL	1	TRUE	2	0.326452860135048	4		692	916	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193209	11193209	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	58	530	0	ENST00000361445.4:c.5292C>G	p.Ile1764Met	p.I1764M	ENST00000361445	NM_004958.3	1764	atC/atG	38/58	0.326452860135048	3	FACETS	0.534	0.458	0.618	0.267	0.229	0.309	SUBCLONAL	1	TRUE	1	0.326452860135048	3		530	774	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054683	13054683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	46	440	0	ENST00000316448.5:c.1210G>A	p.Asp404Asn	p.D404N	ENST00000316448	NM_004343.3	404	Gat/Aat	9/9	0.326452860135048	4	FACETS	0.533	0.448	0.628	0.267	0.224	0.314	SUBCLONAL	1	TRUE	2	0.326452860135048	4		440	701	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379709	17379709	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	99	745	0	ENST00000359435.4:c.94G>C	p.Glu32Gln	p.E32Q	ENST00000359435	NM_001033549.1	32	Gaa/Caa	2/9	0.326452860135048	4	FACETS	0.785	0.699	0.877	0.392	0.349	0.439	SUBCLONAL	1	TRUE	2	0.326452860135048	4		745	1025	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704672	117704672	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0052321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	47	177	0	ENST00000368508.3:c.2305-1G>C		p.X769_splice	ENST00000368508	NM_002944.2	769			0.320621922228721	4	FACETS	1	0.885	1	0.528	0.446	0.616	CLONAL	1	TRUE	2	0.326452860135048	4		177	362	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859220	151859220	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	45	276	0	ENST00000262189.6:c.11442G>C	p.Gln3814His	p.Q3814H	ENST00000262189	NM_170606.2	3814	caG/caC	43/59	0.326452860135048	4	FACETS	0.743	0.625	0.874	0.372	0.312	0.437	SUBCLONAL	1	TRUE	2	0.326452860135048	4		276	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577578	7577579	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTAGTGGATGGTGGTACAGTCAGAGCC	novel	NA	P-0052322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	37	519	0	ENST00000269305.4:c.676_702dup	p.Gly226_Tyr234dup	p.G226_Y234dup	ENST00000269305	NM_001126112.2	226	-/GGCTCTGACTGTACCACCATCCACTAC	7/11	0.219525855485574	2	FACETS	0.844	0.698	1	0.422	0.349	0.503	CLONAL	1	TRUE	0	0.281018704515235	2		519	312	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971115	21971133	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTCGGGTGAGAGTGGCG	GGGTCGGGTGAGAGTGGCG	-	rs730881674	NA	P-0052322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1234	275	634	0	ENST00000304494.5:c.225_243del	p.Ala76CysfsTer64	p.A76Cfs*64	ENST00000304494	NM_000077.4	75	ccCGCCACTCTCACCCGACCC/cc	2/3	0.281018704515235	15	FACETS	0.917	0.858	0.977			1	CLONAL	4	TRUE	NA	0.281018704515235	15		634	1509	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650553	48650554	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	14	754	0	ENST00000376670.3:c.523_524insA	p.Pro175HisfsTer26	p.P175Hfs*26	ENST00000376670	NM_002049.3	175	ccc/cAcc	3/6	0.248260040401983	3	FACETS	0.748	0.543	0.992	0.374	0.271	0.496	CLONAL	1	TRUE	1	0.281018704515235	3		754	152	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574560	64574560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	241	795	0	ENST00000312049.6:c.835del	p.Ala279ProfsTer2	p.A279Pfs*2	ENST00000312049	NM_130799.2	279	Gcc/cc	6/10	0.770630366120282	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.770630366120282	1		795	379	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	55	460	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.901	0.771	1	0.901	0.771	1	CLONAL	1	TRUE	1	0.250227295321803	2		460	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0052324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	145	754	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.250227295321803	2		754	1076	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678391	88678391	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	57	864	0	ENST00000360948.2:c.1145A>C	p.Asn382Thr	p.N382T	ENST00000360948	NM_001012338.2	382	aAc/aCc	9/19	1	2	FACETS	0.435	0.371	0.504	0.435	0.371	0.504	SUBCLONAL	1	TRUE	1	0.250227295321803	2		864	1048	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023301	27023304	+	frameshift_variant	Frame_Shift_Del	DEL	CTCA	CTCA	-	novel	NA	P-0052324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	27	215	0	ENST00000324856.7:c.411_414del	p.His137GlnfsTer94	p.H137Qfs*94	ENST00000324856	NM_006015.4	136	cCTCAc/cc	1/20	1	2	FACETS	0.698	0.557	0.86	0.698	0.557	0.86	SUBCLONAL	1	TRUE	1	0.250227295321803	2		215	309	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515292	149515292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367993439	NA	P-0052324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	67	699	1	ENST00000261799.4:c.190C>T	p.Arg64Trp	p.R64W	ENST00000261799	NM_002609.3	64	Cgg/Tgg	3/23	1	2	FACETS	0.672	0.583	0.769	0.672	0.583	0.769	SUBCLONAL	1	TRUE	1	0.250227295321803	2		700	797	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20483147	20483147	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	43	310	0	ENST00000346618.3:c.880C>G	p.Gln294Glu	p.Q294E	ENST00000346618	NM_001949.4	294	Caa/Gaa	4/7	1	2	FACETS	0.721	0.603	0.851	0.721	0.603	0.851	SUBCLONAL	1	TRUE	1	0.250227295321803	2		310	477	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182867	123182867	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	11	301	0	ENST00000218089.9:c.832C>T	p.Gln278Ter	p.Q278*	ENST00000218089	NM_001042749.1	278	Caa/Taa	10/35	0.250227295321803	1	FACETS	0.461	0.319	0.636	0.461	0.319	0.636	SUBCLONAL	1	TRUE	0	0.250227295321803	1		301	167	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0052325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	13	446	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	0.323	0.229	0.439	0.323	0.229	0.439	SUBCLONAL	1	TRUE	1	0.15	2		446	537	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0052325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	62	380	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.245779998197661	3	FACETS	1	0.966	1	0.705	0.609	0.81	CLONAL	1	TRUE	1	0.15	3		380	630	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0052325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	50	719	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.88	0.744	1	0.88	0.744	1	CLONAL	1	TRUE	1	0.15	2		719	758	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713341	40713341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1305277749	NA	P-0052325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	50	590	0	ENST00000373198.4:c.4174C>T	p.Arg1392Cys	p.R1392C	ENST00000373198	NM_133170.3	1392	Cgt/Tgt	30/32	1	2	FACETS	0.959	0.812	1	0.959	0.812	1	CLONAL	1	TRUE	1	0.15	2		590	695	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289231	33289231	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	50	489	0	ENST00000374542.5:c.321C>A	p.Asn107Lys	p.N107K	ENST00000374542	NM_001141970.1	107	aaC/aaA	3/8	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.15	2		489	643	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0052326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	478	507	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.620400322419453	2	FACETS	0.904	0.871	0.937	0.904	0.871	0.937	CLONAL	2	TRUE	0	0.620400322419453	2		507	852	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258889	16258889	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	307	658	4	ENST00000375759.3:c.6158del	p.Asn2053ThrfsTer11	p.N2053Tfs*11	ENST00000375759	NM_015001.2	2052	Aaa/aa	11/15	0.598301536281202	1	FACETS	0.849	0.804	0.895	0.849	0.804	0.895	CLONAL	1	TRUE	0	0.620400322419453	1		662	804	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169991111	169991111	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	203	325	0	ENST00000295797.4:c.629C>G	p.Ser210Cys	p.S210C	ENST00000295797	NM_002740.5	210	tCt/tGt	7/18	1	2	FACETS	0.975	0.908	1	0.975	0.908	1	CLONAL	1	TRUE	1	0.620400322419453	2		325	671	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115907	8115910	+	frameshift_variant	Frame_Shift_Del	DEL	CGCC	CGCC	-	novel	NA	P-0052326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	246	566	0	ENST00000346208.3:c.1254_1257del	p.Pro419ArgfsTer55	p.P419Rfs*55	ENST00000346208		418	aCGCCc/ac	6/6	1	2	FACETS	0.922	0.864	0.982	0.922	0.864	0.982	CLONAL	1	TRUE	1	0.620400322419453	2		566	860	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372408	118372408	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	197	337	0	ENST00000534358.1:c.6344del	p.Asn2115ThrfsTer6	p.N2115Tfs*6	ENST00000534358	NM_005933.3	2114	cAa/ca	26/36	0.563221880523699	1	FACETS	0.94	0.88	1	0.94	0.88	1	CLONAL	1	TRUE	0	0.620400322419453	1		337	466	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321526	62321526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2008	374	886	1	ENST00000360203.5:c.2228G>A	p.Arg743Gln	p.R743Q	ENST00000360203	NM_001283009.1	743	cGa/cAa	25/35	0.54585797918653	5	FACETS	0.977	0.923	1	0.244	0.23	0.259	CLONAL	1	TRUE	1	0.620400322419453	5		887	2382	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630516	187630516	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376750393	NA	P-0052326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	353	641	0	ENST00000441802.2:c.466G>A	p.Val156Ile	p.V156I	ENST00000441802	NM_005245.3	156	Gtt/Att	2/27	0.620400322419453	1	FACETS	0.992	0.946	1	0.992	0.946	1	CLONAL	1	TRUE	0	0.620400322419453	1		641	791	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873644	151873645	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0052326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	236	533	0	ENST00000262189.6:c.8893_8894del	p.Leu2965GlyfsTer2	p.L2965Gfs*2	ENST00000262189	NM_170606.2	2965	TTg/g	38/59	1	2	FACETS	0.86	0.804	0.917	0.86	0.804	0.917	CLONAL	1	TRUE	1	0.620400322419453	2		533	885	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0052327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	79	41	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.570575770475012	2	FACETS	1	0.979	1	0.712	0.639	0.786	CLONAL	1	TRUE	0	0.566299959336465	2		41	196	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0052327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	156	703	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.527423292712271	2	FACETS	1	0.983	1	0.616	0.569	0.664	CLONAL	1	TRUE	0	0.566299959336465	2		703	447	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502382	186502384	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1171371205	NA	P-0052327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	118	266	0	ENST00000323963.5:c.109_111del	p.Asp37del	p.D37del	ENST00000323963		35	ttTGAt/ttt	3/11	0.566299959336465	6	FACETS	0.973	0.877	1	0.324	0.292	0.359	CLONAL	1	TRUE	3	0.566299959336465	6		266	913	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80021297	80021297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs963234468	NA	P-0052327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	239	150	0	ENST00000265081.6:c.1366G>A	p.Glu456Lys	p.E456K	ENST00000265081	NM_002439.4	456	Gaa/Aaa	9/24	0.261830673944562	5	FACETS	0.999	0.943	1			1	INDETERMINATE	3	TRUE	NA	0.566299959336465	5		150	521	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355936	73355936	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1395653455	NA	P-0052327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	166	762	1	ENST00000377767.4:c.35G>T	p.Arg12Leu	p.R12L	ENST00000377767	NM_014953.3	12	cGg/cTg	1/21	0.549127737974527	3	FACETS	0.833	0.765	0.904	0.417	0.382	0.452	CLONAL	1	TRUE	1	0.566299959336465	3		763	903	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745632	162745632	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1458	97	419	0	ENST00000367921.3:c.2047A>C	p.Ser683Arg	p.S683R	ENST00000367921	NM_006182.2	683	Agt/Cgt	15/18	0.566299959336465	11	FACETS	0.782	0.694	0.876			1	SUBCLONAL	1	TRUE	NA	0.566299959336465	11		419	1555	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333735	70333735	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	420	548	1	ENST00000373644.4:c.1640A>T	p.Gln547Leu	p.Q547L	ENST00000373644	NM_030625.2	547	cAg/cTg	2/12	0.508095008299016	4	FACETS	1	0.993	1			1	CLONAL	3	TRUE	NA	0.566299959336465	4		549	681	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920730	100920730	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	90	203	0	ENST00000325455.5:c.2418G>C	p.Gln806His	p.Q806H	ENST00000325455	NM_001202474.3	806	caG/caC	6/8	0.570575770475012	4	FACETS	1	0.907	1	0.34	0.303	0.38	CLONAL	1	TRUE	1	0.566299959336465	4		203	488	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43699682	43699682	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	176	662	0	ENST00000382044.4:c.5833C>A	p.Pro1945Thr	p.P1945T	ENST00000382044	NM_001141980.1	1945	Cct/Act	28/28	0.534941061477276	3	FACETS	1	0.975	1	0.565	0.522	0.61	CLONAL	1	TRUE	1	0.566299959336465	3		662	706	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614920	23614920	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1064795975	NA	P-0052327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	118	487	0	ENST00000261584.4:c.3421G>C	p.Asp1141His	p.D1141H	ENST00000261584	NM_024675.3	1141	Gac/Cac	13/13	0.513648215293265	5	FACETS	1	0.928	1			1	CLONAL	1	TRUE	NA	0.566299959336465	5		487	746	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097672	11097672	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs761071237	NA	P-0052327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	201	1011	0	ENST00000358026.2:c.852G>T	p.Trp284Cys	p.W284C	ENST00000358026	NM_001128849.1	284	tgG/tgT	5/36	0.391996905964069	5	FACETS	1	0.953	1	0.347	0.32	0.374	CLONAL	1	TRUE	2	0.566299959336465	5		1011	1262	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793396	42793396	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	171	873	0	ENST00000575354.2:c.1198C>A	p.Pro400Thr	p.P400T	ENST00000575354	NM_015125.3	400	Ccc/Acc	8/20	0.570575770475012	3	FACETS	0.836	0.769	0.906	0.418	0.384	0.453	CLONAL	1	TRUE	1	0.566299959336465	3		873	927	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626112	12626112	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1240899335	NA	P-0052327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	80	462	0	ENST00000251849.4:c.1848C>G	p.Ile616Met	p.I616M	ENST00000251849	NM_002880.3	616	atC/atG	17/17	1	2	FACETS	0.538	0.475	0.606	0.538	0.475	0.606	SUBCLONAL	1	TRUE	1	0.566299959336465	2		462	525	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125386	47125386	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	117	347	0	ENST00000409792.3:c.5884C>G	p.Pro1962Ala	p.P1962A	ENST00000409792	NM_014159.6	1962	Ccc/Gcc	12/21	1	2	FACETS	0.92	0.835	1	0.92	0.835	1	CLONAL	1	TRUE	1	0.566299959336465	2		347	449	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100041	157100049	+	inframe_deletion	In_Frame_Del	DEL	AGGAGGAGC	AGGAGGAGC	-	novel	NA	P-0052327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	12	89	1	ENST00000346085.5:c.983_991del	p.Gly328_Gly330del	p.G328_G330del	ENST00000346085	NM_020732.3	326	ggAGGAGGAGCa/gga	1/20	0.570575770475012	5	FACETS	0.375	0.263	0.512	0.075	0.052	0.103	SUBCLONAL	1	TRUE	0	0.566299959336465	5		90	209	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205106	123205106	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	70	245	0	ENST00000218089.9:c.2466G>C	p.Gln822His	p.Q822H	ENST00000218089	NM_001042749.1	822	caG/caC	25/35	0.566299959336465	5	FACETS	0.71	0.619	0.808			1	SUBCLONAL	1	TRUE	NA	0.566299959336465	5		245	644	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61213469	61213484	+	frameshift_variant	Frame_Shift_Del	DEL	TTTGCTAAAAACAAAA	TTTGCTAAAAACAAAA	AC	novel	NA	P-0052327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	108	432	3	ENST00000301761.2:c.427_442delinsAC	p.Phe143ThrfsTer12	p.F143Tfs*12	ENST00000301761	NM_017841.2	143	TTTGCTAAAAACAAAAac/ACac	4/4	0.391996905964069	5	FACETS	0.783	0.702	0.869	0.261	0.234	0.29	SUBCLONAL	1	TRUE	2	0.566299959336465	5		435	901	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0052328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	194	449	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.551837399108201	5	FACETS	0.962	0.894	1	0.641	0.596	0.688	CLONAL	2	TRUE	2	0.551837399108201	5		449	668	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89839769	89839769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	146	723	0	ENST00000389301.3:c.1924G>A	p.Glu642Lys	p.E642K	ENST00000389301	NM_000135.2	642	Gaa/Aaa	22/43	0.551837399108201	3	FACETS	1	0.97	1	0.562	0.514	0.611	CLONAL	1	TRUE	1	0.551837399108201	3		723	601	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502466	186502468	+	inframe_deletion	In_Frame_Del	DEL	TAT	TAT	-	rs755185062	NA	P-0052328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	83	212	0	ENST00000323963.5:c.193_195del	p.Ile65del	p.I65del	ENST00000323963		63	gcTATt/gct	3/11	0.551837399108201	5	FACETS	1	0.951	1	0.38	0.336	0.427	CLONAL	1	TRUE	2	0.551837399108201	5		212	482	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614463	38614463	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	14	284	0	ENST00000299084.4:c.234del	p.Asp79ThrfsTer42	p.D79Tfs*42	ENST00000299084	NM_152594.2	77	Aaa/aa	3/7	0.457188239107794	0	FACETS	0.105	0.076	0.141			1	SUBCLONAL	1	TRUE	0	0.551837399108201	0		284	216	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956568	93956568	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	78	275	0	ENST00000369303.4:c.2668C>A	p.Leu890Ile	p.L890I	ENST00000369303	NM_004440.3	890	Cta/Ata	15/17	0.522069696503742	3	FACETS	1	0.977	1	0.471	0.42	0.525	CLONAL	1	TRUE	0	0.551837399108201	3		275	255	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828186	72828186	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	70	513	0	ENST00000268489.5:c.8395C>T	p.Leu2799Phe	p.L2799F	ENST00000268489	NM_006885.3	2799	Ctt/Ttt	9/10	0.551837399108201	3	FACETS	1	0.901	1	0.514	0.451	0.58	CLONAL	1	TRUE	1	0.551837399108201	3		513	315	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031928	26031928	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	255	405	0	ENST00000244661.2:c.361A>G	p.Met121Val	p.M121V	ENST00000244661	NM_003537.3	121	Atg/Gtg	1/1	0.522069696503742	3	FACETS	0.84	0.797	0.882	0.84	0.797	0.882	CLONAL	3	TRUE	0	0.551837399108201	3		405	468	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104356924	104356924	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	117	486	0	ENST00000369902.3:c.784G>C	p.Asp262His	p.D262H	ENST00000369902	NM_016169.3	262	Gat/Cat	7/12	1	2	FACETS	0.977	0.887	1	0.977	0.887	1	CLONAL	1	TRUE	1	0.551837399108201	2		486	434	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435375	121435375	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	95	733	0	ENST00000257555.6:c.1408C>T	p.Pro470Ser	p.P470S	ENST00000257555		470	Ccc/Tcc	7/10	0.136677459263262	0	FACETS	0.473	0.426	0.523			1	INDETERMINATE	1	TRUE	0	0.551837399108201	0		733	326	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004303	29004303	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	49	236	0	ENST00000282397.4:c.990T>A	p.Asp330Glu	p.D330E	ENST00000282397	NM_002019.4	330	gaT/gaA	8/30	0.29324154974969	0	FACETS	0.488	0.421	0.559			1	INDETERMINATE	1	TRUE	0	0.551837399108201	0		236	163	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632544	3632544	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555449297	NA	P-0052328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	156	811	0	ENST00000294008.3:c.5304G>C	p.Gln1768His	p.Q1768H	ENST00000294008	NM_032444.2	1768	caG/caC	15/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.551837399108201	2		811	420	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348049	89348049	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	174	720	0	ENST00000301030.4:c.4901G>T	p.Gly1634Val	p.G1634V	ENST00000301030	NM_001256183.1	1634	gGt/gTt	9/13	0.551837399108201	3	FACETS	1	0.984	1	0.616	0.569	0.664	CLONAL	1	TRUE	1	0.551837399108201	3		720	653	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222265	2222265	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369350082	NA	P-0052328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	110	800	0	ENST00000398665.3:c.3097G>A	p.Gly1033Ser	p.G1033S	ENST00000398665	NM_032482.2	1033	Ggc/Agc	24/28	0.363925051469834	0	FACETS	0.354	0.319	0.39			1	SUBCLONAL	1	TRUE	0	0.551837399108201	0		800	505	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170525	11170525	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555795999	NA	P-0052328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	126	731	0	ENST00000358026.2:c.4828G>C	p.Glu1610Gln	p.E1610Q	ENST00000358026	NM_001128849.1	1610	Gag/Cag	34/36	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.551837399108201	2		731	381	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251752	212251753	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	57	309	0	ENST00000342788.4:c.3306dup	p.Asp1103Ter	p.D1103*	ENST00000342788	NM_005235.2	1102	-/T	27/28	1	2	FACETS	0.738	0.638	0.844	0.738	0.638	0.844	SUBCLONAL	1	TRUE	1	0.551837399108201	2		309	280	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022255	31022261	+	frameshift_variant	Frame_Shift_Del	DEL	ACCACCC	ACCACCC	-	novel	NA	P-0052328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	79	305	0	ENST00000375687.4:c.1740_1746del	p.Lys580AsnfsTer121	p.K580Nfs*121	ENST00000375687	NM_015338.5	580	aaACCACCC/aa	13/13	0.282479607029894	2	FACETS	1	0.978	1	0.705	0.633	0.78	INDETERMINATE	1	TRUE	0	0.551837399108201	2		305	203	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41818313	41818313	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	14	29	0	ENST00000373198.4:c.61C>A	p.Pro21Thr	p.P21T	ENST00000373198	NM_133170.3	21	Ccc/Acc	1/32	0.282479607029894	2	FACETS	0.94	0.701	1	0.47	0.35	0.604	INDETERMINATE	1	TRUE	0	0.551837399108201	2		29	54	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430533	181430533	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	72	580	0	ENST00000325404.1:c.385G>T	p.Gly129Cys	p.G129C	ENST00000325404	NM_003106.3	129	Ggc/Tgc	1/1	0.551837399108201	5	FACETS	0.782	0.683	0.888	0.261	0.227	0.296	SUBCLONAL	1	TRUE	2	0.551837399108201	5		580	610	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495453	149495453	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	99	818	0	ENST00000261799.4:c.3194A>T	p.Glu1065Val	p.E1065V	ENST00000261799	NM_002609.3	1065	gAg/gTg	23/23	0.177124580158612	3	FACETS	1	0.927	1	0.52	0.467	0.576	INDETERMINATE	1	TRUE	1	0.551837399108201	3		818	440	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638474	176638474	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	27	641	0	ENST00000439151.2:c.3074A>C	p.Lys1025Thr	p.K1025T	ENST00000439151	NM_022455.4	1025	aAg/aCg	5/23	0.177124580158612	3	FACETS	0.264	0.209	0.327	0.132	0.104	0.164	INDETERMINATE	1	TRUE	1	0.551837399108201	3		641	473	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450240	50450240	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	82	396	0	ENST00000331340.3:c.424G>C	p.Glu142Gln	p.E142Q	ENST00000331340	NM_006060.4	142	Gaa/Caa	5/8	0.257859212995928	0	FACETS	0.514	0.46	0.571			1	INDETERMINATE	1	TRUE	0	0.551837399108201	0		396	259	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482957	140482957	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	102	477	0	ENST00000288602.6:c.1178G>C	p.Gly393Ala	p.G393A	ENST00000288602	NM_004333.4	393	gGa/gCa	10/18	0.188284011109991	4	FACETS	0.788	0.711	0.868	0.788	0.711	0.868	INDETERMINATE	2	TRUE	2	0.551837399108201	4		477	364	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929161	32929161	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	G	G	TA	novel	NA	P-0052328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	39	399	0	ENST00000380152.3:c.7171delinsTA	p.Glu2391Ter	p.E2391*	ENST00000380152		2391	Gaa/TAaa	14/27	0.551837399108201	3	FACETS	0.55	0.457	0.653	0.275	0.228	0.327	SUBCLONAL	1	TRUE	1	0.551837399108201	3		399	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0052329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	264	740	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.636353233259567	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.636353233259567	2		740	412	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686796	117686796	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759586931	NA	P-0052329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	107	315	0	ENST00000368508.3:c.2921C>T	p.Ala974Val	p.A974V	ENST00000368508	NM_002944.2	974	gCg/gTg	19/43	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.636353233259567	2		315	323	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493501	56493501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774326613	NA	P-0052329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	110	467	0	ENST00000267101.3:c.2909G>A	p.Arg970Gln	p.R970Q	ENST00000267101	NM_001982.3	970	cGa/cAa	24/28	0.636353233259567	3	FACETS	0.986	0.891	1	0.329	0.297	0.362	CLONAL	1	TRUE	0	0.636353233259567	3		467	462	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432772	49432772	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	322	632	0	ENST00000301067.7:c.8367del	p.Gln2790AsnfsTer3	p.Q2790Nfs*3	ENST00000301067	NM_003482.3	2789	cgG/cg	34/54	0.636353233259567	3	FACETS	0.965	0.929	0.999	0.965	0.929	0.999	CLONAL	3	TRUE	0	0.636353233259567	3		632	461	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251216	251216	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs376391115	NA	P-0052329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	51	374	0	ENST00000264932.6:c.1661G>A	p.Arg554Gln	p.R554Q	ENST00000264932	NM_004168.2	554	cGg/cAg	12/15	0.285436162880947	5	FACETS	0.916	0.782	1			1	INDETERMINATE	1	TRUE	NA	0.636353233259567	5		374	342	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	439	460	0				ENST00000310581	NM_198253.2	-/1132			0.288441242933747	4	FACETS	0.938	0.902	0.974	0.703	0.676	0.731	INDETERMINATE	3	TRUE	0	0.632902325780479	4		460	805	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0052331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	791	679	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.632902325780479	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.632902325780479	2		679	1230	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	455	1162	0	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	0.206530230337545	2	FACETS	1	0.995	1	0.636	0.609	0.664	INDETERMINATE	1	TRUE	0	0.632902325780479	2		1162	1130	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039385	49039385	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs794727372	NA	P-0052331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	79	847	0	ENST00000267163.4:c.2370C>A	p.Tyr790Ter	p.Y790*	ENST00000267163	NM_000321.2	790	taC/taA	23/27	0.442624642291537	2	FACETS	0.319	0.28	0.361	0.159	0.14	0.181	SUBCLONAL	1	TRUE	0	0.632902325780479	2		847	783	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247174	153247174	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	190	449	0	ENST00000281708.4:c.1628G>C	p.Arg543Thr	p.R543T	ENST00000281708	NM_033632.3	543	aGa/aCa	10/12	0.632902325780479	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.632902325780479	1		449	345	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874923	151874923	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	145	523	1	ENST00000262189.6:c.7615C>T	p.Gln2539Ter	p.Q2539*	ENST00000262189	NM_170606.2	2539	Cag/Tag	38/59	0.632902325780479	3	FACETS	0.824	0.753	0.898	0.412	0.376	0.449	CLONAL	1	TRUE	1	0.632902325780479	3		524	732	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193181558	193181569	+	inframe_deletion	In_Frame_Del	DEL	ACCTCTTTAATA	ACCTCTTTAATA	-	novel	NA	P-0052331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	57	555	0	ENST00000367435.3:c.1108_1119del	p.Ser370_Thr373del	p.S370_T373del	ENST00000367435	NM_024529.4	369	ACCTCTTTAATA/-	13/17	0.453100440734484	1	FACETS	0.805	0.707	0.906	0.805	0.707	0.906	CLONAL	1	TRUE	0	0.632902325780479	1		555	153	SUCCESS
FH	2271	MSKCC	GRCh37	1	241672057	241672057	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs863223965	NA	P-0052331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	65	566	0	ENST00000366560.3:c.584T>C	p.Met195Thr	p.M195T	ENST00000366560	NM_000143.3	195	aTg/aCg	5/10	0.453100440734484	1	FACETS	0.396	0.345	0.45	0.396	0.345	0.45	SUBCLONAL	1	TRUE	0	0.632902325780479	1		566	355	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134823	41134823	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	172	590	0	ENST00000379561.5:c.805C>G	p.Arg269Gly	p.R269G	ENST00000379561	NM_002015.3	269	Cga/Gga	2/3	0.442624642291537	2	FACETS	0.747	0.689	0.807	0.373	0.344	0.404	SUBCLONAL	1	TRUE	0	0.632902325780479	2		590	728	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240114	41240114	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	151	186	0	ENST00000379561.5:c.236A>G	p.Glu79Gly	p.E79G	ENST00000379561	NM_002015.3	79	gAg/gGg	1/3	0.442624642291537	2	FACETS	0.831	0.776	0.886	0.831	0.776	0.886	CLONAL	2	TRUE	0	0.632902325780479	2		186	287	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027128	49027128	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0052331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	90	366	0	ENST00000267163.4:c.1696-1G>C		p.X566_splice	ENST00000267163	NM_000321.2	566			0.442624642291537	2	FACETS	0.841	0.769	0.913	0.841	0.769	0.913	CLONAL	2	TRUE	0	0.632902325780479	2		366	169	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2097757	2097757	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs749963973	NA	P-0052331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	716	1050	2	ENST00000219066.1:c.92G>T	p.Gly31Val	p.G31V	ENST00000219066	NM_002528.5	31	gGg/gTg	1/6	0.381519427156647	3	FACETS	0.908	0.878	0.939	0.908	0.878	0.939	CLONAL	2	TRUE	1	0.632902325780479	3		1052	1640	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828322	50828322	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	214	598	0	ENST00000398568.2:c.2660G>A	p.Ser887Asn	p.S887N	ENST00000398568	NM_001042412.1	887	aGc/aAc	17/18	0.289228822138595	2	FACETS	1	0.98	1	0.558	0.522	0.595	INDETERMINATE	1	TRUE	0	0.632902325780479	2		598	606	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41228544	41228544	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	292	853	0	ENST00000357654.3:c.4445A>G	p.Asp1482Gly	p.D1482G	ENST00000357654	NM_007294.3	1482	gAt/gGt	13/23	0.307098495134862	2	FACETS	0.867	0.826	0.908	0.867	0.826	0.908	INDETERMINATE	2	TRUE	0	0.632902325780479	2		853	532	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250248	39250248	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	94	872	0	ENST00000402219.2:c.1321T>G	p.Cys441Gly	p.C441G	ENST00000402219	NM_005633.3	441	Tgt/Ggt	10/23	0.213634142719677	3	FACETS	0.524	0.466	0.586	0.175	0.155	0.196	INDETERMINATE	1	TRUE	0	0.632902325780479	3		872	746	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183734	10183734	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs869025617	NA	P-0052331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2172	326	1178	0	ENST00000256474.2:c.203C>T	p.Ser68Leu	p.S68L	ENST00000256474	NM_000551.3	68	tCg/tTg	1/3	0.632902325780479	4	FACETS	0.673	0.633	0.716			1	SUBCLONAL	1	TRUE	NA	0.632902325780479	4		1178	2498	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713519	30713519	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	91	693	0	ENST00000295754.5:c.844G>C	p.Glu282Gln	p.E282Q	ENST00000295754	NM_003242.5	282	Gag/Cag	4/7	0.449910401347199	3	FACETS	0.416	0.369	0.467	0.208	0.184	0.234	SUBCLONAL	1	TRUE	1	0.632902325780479	3		693	909	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665237	138665237	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	346	1014	0	ENST00000330315.3:c.328G>T	p.Glu110Ter	p.E110*	ENST00000330315	NM_023067.3	110	Gag/Tag	1/1	1	2	FACETS	0.792	0.749	0.837	0.792	0.749	0.837	SUBCLONAL	1	TRUE	1	0.632902325780479	2		1014	1380	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032152	26032152	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	461	809	1	ENST00000244661.2:c.137C>T	p.Thr46Ile	p.T46I	ENST00000244661	NM_003537.3	46	aCt/aTt	1/1	0.399417148650983	5	FACETS	0.946	0.903	0.99	0.631	0.602	0.66	CLONAL	2	TRUE	2	0.632902325780479	5		810	1501	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651881	36651903	+	frameshift_variant,start_lost	Frame_Shift_Del	DEL	GTCAGAACCGGCTGGGGATGTCC	GTCAGAACCGGCTGGGGATGTCC	-	rs1295208193	NA	P-0052331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	113	900	0	ENST00000244741.5:c.12_34del	p.Ala5_?12	p.A5_?12	ENST00000244741	NM_000389.4	1	atGTCAGAACCGGCTGGGGATGTCCgt/atgt	2/3	0.632902325780479	3	FACETS	0.412	0.37	0.457	0.206	0.185	0.229	SUBCLONAL	1	TRUE	1	0.632902325780479	3		900	1141	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342784	87342784	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	52	625	0	ENST00000277120.3:c.1069G>A	p.Gly357Arg	p.G357R	ENST00000277120		357	Ggg/Agg	9/19	0.107450911638555	3	FACETS	0.316	0.268	0.368	0.105	0.089	0.123	INDETERMINATE	1	TRUE	0	0.632902325780479	3		625	685	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030479	49030479	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0052332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	99	337	0	ENST00000267163.4:c.1954A>T	p.Lys652Ter	p.K652*	ENST00000267163	NM_000321.2	652	Aaa/Taa	19/27	0.653388874991701	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.74592530338418	1		337	162	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576880	7576998	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGTTTCTTCTTTGGCTGGGGAGAGGAGCTGGTGTTGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAAGTGAATCTGAGGCATAACTGCACCCTTGGTCTCCTCCACCGC	TGGTTTCTTCTTTGGCTGGGGAGAGGAGCTGGTGTTGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAAGTGAATCTGAGGCATAACTGCACCCTTGGTCTCCTCCACCGC	-	novel	NA	P-0052332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	778	856	0	ENST00000269305.4:c.919+21_966del		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	0.288212304874946	5	FACETS	0.924	0.906	0.941	0.924	0.906	0.941	INDETERMINATE	5	TRUE	0	0.74592530338418	5		856	957	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0052334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1385	116	1049	1	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	0.313	0.281	0.348	0.313	0.281	0.348	SUBCLONAL	1	TRUE	1	0.493466260648793	2		1050	1501	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982975	201982976	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTGG	novel	NA	P-0052334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	106	866	0	ENST00000359651.3:c.826_829dup	p.Glu277ValfsTer25	p.E277Vfs*25	ENST00000359651		275	ctg/ctGTGGg	7/8	0.258766959796661	1	FACETS	0.265	0.236	0.295	0.265	0.236	0.295	INDETERMINATE	1	TRUE	0	0.493466260648793	1		866	1222	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175471	108175471	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	199	413	0	ENST00000278616.4:c.5566G>T	p.Glu1856Ter	p.E1856*	ENST00000278616	NM_000051.3	1856	Gaa/Taa	37/63	0.493466260648793	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.493466260648793	1		413	587	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99491843	99491843	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	94	643	0	ENST00000268035.6:c.3628G>T	p.Glu1210Ter	p.E1210*	ENST00000268035	NM_000875.3	1210	Gag/Tag	20/21	1	2	FACETS	0.35	0.31	0.392	0.35	0.31	0.392	SUBCLONAL	1	TRUE	1	0.493466260648793	2		643	1089	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632620	3632620	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144057906	NA	P-0052334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1299	108	996	0	ENST00000294008.3:c.5228C>T	p.Ser1743Leu	p.S1743L	ENST00000294008	NM_032444.2	1743	tCg/tTg	15/15	0.142472680556316	1	FACETS	0.234	0.209	0.261	0.234	0.209	0.261	INDETERMINATE	1	TRUE	0	0.493466260648793	1		996	1407	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488383	20488383	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	71	459	0	ENST00000346618.3:c.1039G>T	p.Glu347Ter	p.E347*	ENST00000346618	NM_001949.4	347	Gag/Tag	6/7	1	2	FACETS	0.256	0.223	0.293	0.256	0.223	0.293	SUBCLONAL	1	TRUE	1	0.493466260648793	2		459	1123	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034444	47034444	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	358	463	2	ENST00000377604.3:c.529G>T	p.Glu177Ter	p.E177*	ENST00000377604	NM_001204468.1	177	Gag/Tag	6/24	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.493466260648793	1		465	732	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0052335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	174	379	3	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.963	1	1	0.994	1	CLONAL	3	FALSE	1	0.250313327359498	2		382	440	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0052335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	615	558	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.250313327359498	2	FACETS	0.967	0.942	0.991	1	0.998	1	CLONAL	6	FALSE	0	0.250313327359498	2		558	847	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588123	69588123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751257747	NA	P-0052335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	39	683	0	ENST00000168712.1:c.575G>A	p.Arg192Gln	p.R192Q	ENST00000168712	NM_002007.2	192	cGa/cAa	3/3	1	2	FACETS	0.405	0.335	0.484	0.405	0.335	0.484	SUBCLONAL	1	FALSE	1	0.250313327359498	2		683	769	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890149	76890150	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	225	486	0	ENST00000373344.5:c.4744dup	p.Thr1582AsnfsTer19	p.T1582Nfs*19	ENST00000373344	NM_000489.3	1582	aca/aAca	17/35	0.250313327359498	1	FACETS	1	0.97	1	1	0.995	1	CLONAL	2	FALSE	0	0.250313327359498	1		486	740	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100581	8100581	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	90	949	0	ENST00000346208.3:c.555G>C	p.Lys185Asn	p.K185N	ENST00000346208		185	aaG/aaC	3/6	1	2	FACETS	0.796	0.705	0.894	0.796	0.705	0.894	SUBCLONAL	1	FALSE	1	0.250313327359498	2		949	903	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39704865	39704865	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	18	190	0	ENST00000361337.2:c.210A>C	p.Lys70Asn	p.K70N	ENST00000361337	NM_003286.2	70	aaA/aaC	4/21	1	2	FACETS	0.505	0.38	0.652	0.505	0.38	0.652	SUBCLONAL	1	FALSE	1	0.250313327359498	2		190	285	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0052336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	14	346	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	1	2	FACETS	0.908	0.661	1	0.908	0.661	1	CLONAL	1	TRUE	1	0.24093575491341	2		346	128	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023771	27023774	+	frameshift_variant	Frame_Shift_Del	DEL	CCCA	CCCA	-	novel	NA	P-0052336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	10	599	0	ENST00000324856.7:c.880_883del	p.Thr294SerfsTer68	p.T294Sfs*68	ENST00000324856	NM_006015.4	293	CCCAcc/cc	1/20	0.210020467368112	0	FACETS	0.75	0.514	1			1	CLONAL	1	TRUE	0	0.24093575491341	0		599	84	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843642	156843642	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	19	1157	1	ENST00000524377.1:c.1068C>A	p.Asn356Lys	p.N356K	ENST00000524377	NM_002529.3	356	aaC/aaA	8/17	0.189108964732054	1	FACETS	0.746	0.569	0.951	0.746	0.569	0.951	CLONAL	1	TRUE	0	0.24093575491341	1		1158	186	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0052338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	771	1051	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.491247412744031	3	FACETS	0.891	0.866	0.916	0.891	0.866	0.916	CLONAL	3	TRUE	0	0.555664715384508	3		1051	1327	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670789	134670789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368276671	NA	P-0052338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	107	737	1	ENST00000398015.3:c.700G>A	p.Val234Met	p.V234M	ENST00000398015	NM_004441.4	234	Gtg/Atg	3/16	0.555664715384508	3	FACETS	0.494	0.442	0.549	0.247	0.221	0.275	SUBCLONAL	1	TRUE	1	0.555664715384508	3		738	996	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797981	42797981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1355	169	1115	2	ENST00000575354.2:c.4033G>A	p.Val1345Met	p.V1345M	ENST00000575354	NM_015125.3	1345	Gtg/Atg	16/20	0.511876169886219	3	FACETS	0.51	0.467	0.555	0.255	0.233	0.278	SUBCLONAL	1	TRUE	1	0.555664715384508	3		1117	1524	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613414	100613414	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555978153	NA	P-0052338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	152	673	0	ENST00000308731.7:c.986G>T	p.Gly329Val	p.G329V	ENST00000308731	NM_000061.2	329	gGg/gTg	12/19	0.555664715384508	1	FACETS	0.612	0.561	0.664	0.612	0.561	0.664	SUBCLONAL	1	TRUE	0	0.555664715384508	1		673	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	222	809	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	1	2	FACETS	0.996	0.929	1	0.996	0.929	1	CLONAL	1	TRUE	1	0.54590605804427	2		809	817	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117739669	117739669	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	149	532	0	ENST00000368508.3:c.124G>A	p.Gly42Ser	p.G42S	ENST00000368508	NM_002944.2	42	Ggc/Agc	2/43	1	2	FACETS	0.975	0.895	1	0.975	0.895	1	CLONAL	1	TRUE	1	0.54590605804427	2		532	560	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435604	149435604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	158	851	1	ENST00000286301.3:c.2539G>A	p.Glu847Lys	p.E847K	ENST00000286301	NM_005211.3	847	Gag/Aag	19/22	1	2	FACETS	0.876	0.805	0.949	0.876	0.805	0.949	CLONAL	1	TRUE	1	0.54590605804427	2		852	661	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735503	40735503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763584414	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	273	898	0	ENST00000373198.4:c.3370G>A	p.Glu1124Lys	p.E1124K	ENST00000373198	NM_133170.3	1124	Gag/Aag	25/32	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.54590605804427	2		898	932	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273997	10273997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	64	1220	2	ENST00000330684.3:c.272C>T	p.Ser91Phe	p.S91F	ENST00000330684	NM_001134407.1	91	tCc/tTc	2/13	1	2	FACETS	0.236	0.203	0.271	0.236	0.203	0.271	SUBCLONAL	1	TRUE	1	0.54590605804427	2		1222	995	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082316	16082317	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	261	1257	1	ENST00000281043.3:c.130_131delinsTT	p.Pro44Phe	p.P44F	ENST00000281043	NM_005378.4	44	CCc/TTc	2/3	1	2	FACETS	0.89	0.834	0.948	0.89	0.834	0.948	CLONAL	1	TRUE	1	0.54590605804427	2		1258	1074	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219243	133219243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147467247	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	233	1055	0	ENST00000320574.5:c.4801C>T	p.Pro1601Ser	p.P1601S	ENST00000320574	NM_006231.2	1601	Cct/Tct	37/49	1	2	FACETS	0.966	0.902	1	0.966	0.902	1	CLONAL	1	TRUE	1	0.54590605804427	2		1055	884	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641174	117641174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	273	923	0	ENST00000368508.3:c.5797G>A	p.Glu1933Lys	p.E1933K	ENST00000368508	NM_002944.2	1933	Gag/Aag	36/43	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.54590605804427	2		923	972	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608664	189608664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1464459460	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	126	542	0	ENST00000264731.3:c.1739C>T	p.Ser580Phe	p.S580F	ENST00000264731	NM_003722.4	580	tCc/tTc	13/14	1	2	FACETS	0.737	0.669	0.809	0.737	0.669	0.809	SUBCLONAL	1	TRUE	1	0.54590605804427	2		542	626	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568555	41568555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555911573	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	92	720	2	ENST00000263253.7:c.4505C>T	p.Pro1502Leu	p.P1502L	ENST00000263253	NM_001429.3	1502	cCt/cTt	28/31	1	2	FACETS	0.545	0.485	0.61	0.545	0.485	0.61	SUBCLONAL	1	TRUE	1	0.54590605804427	2		722	618	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120496243	120496243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782306821	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	182	671	1	ENST00000256646.2:c.2288C>T	p.Ser763Leu	p.S763L	ENST00000256646	NM_024408.3	763	tCg/tTg	14/34	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.54590605804427	2		672	653	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353815	15353815	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780028668	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	61	551	3	ENST00000263377.2:c.3065C>T	p.Pro1022Leu	p.P1022L	ENST00000263377	NM_058243.2	1022	cCg/cTg	14/20	1	2	FACETS	0.412	0.355	0.473	0.412	0.355	0.473	SUBCLONAL	1	TRUE	1	0.54590605804427	2		554	543	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912061	127912061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1481246558	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	24	471	1	ENST00000373547.4:c.809C>T	p.Ser270Leu	p.S270L	ENST00000373547	NM_002721.4	270	tCg/tTg	7/7	0.54590605804427	1	FACETS	0.229	0.18	0.286	0.229	0.18	0.286	SUBCLONAL	1	TRUE	0	0.54590605804427	1		472	279	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811643	102811643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	49	914	0	ENST00000307046.8:c.541G>A	p.Glu181Lys	p.E181K	ENST00000307046	NM_001111285.1	181	Gag/Aag	4/4	1	2	FACETS	0.207	0.174	0.243	0.207	0.174	0.243	SUBCLONAL	1	TRUE	1	0.54590605804427	2		914	867	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509236	106509236	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	85	820	1	ENST00000359195.3:c.1230G>A	p.Trp410Ter	p.W410*	ENST00000359195	NM_002649.2	410	tgG/tgA	2/11	0.54590605804427	3	FACETS	0.384	0.338	0.433	0.192	0.169	0.217	SUBCLONAL	1	TRUE	1	0.54590605804427	3		821	1033	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875705	56875705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs572483425	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	195	726	0	ENST00000308159.5:c.2309C>T	p.Ser770Leu	p.S770L	ENST00000308159	NM_014669.4	770	tCg/tTg	21/22	1	2	FACETS	0.916	0.85	0.984	0.916	0.85	0.984	CLONAL	1	TRUE	1	0.54590605804427	2		726	780	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176118155	176118155	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	103	337	0	ENST00000367669.3:c.818G>A	p.Arg273Lys	p.R273K	ENST00000367669	NM_022457.5	273	aGa/aAa	6/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.54590605804427	2		337	326	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622446	28622446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	134	685	0	ENST00000241453.7:c.1171C>T	p.Pro391Ser	p.P391S	ENST00000241453	NM_004119.2	391	Cct/Tct	9/24	1	2	FACETS	0.846	0.772	0.924	0.846	0.772	0.924	CLONAL	1	TRUE	1	0.54590605804427	2		685	580	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265314	152265314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781741770	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	23	465	0	ENST00000206249.3:c.767G>A	p.Arg256Gln	p.R256Q	ENST00000206249	NM_000125.3	256	cGa/cAa	4/8	1	2	FACETS	0.202	0.157	0.254	0.202	0.157	0.254	SUBCLONAL	1	TRUE	1	0.54590605804427	2		465	418	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346891	89346891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	113	677	0	ENST00000301030.4:c.6059C>T	p.Ala2020Val	p.A2020V	ENST00000301030	NM_001256183.1	2020	gCc/gTc	9/13	1	2	FACETS	0.979	0.887	1	0.979	0.887	1	CLONAL	1	TRUE	1	0.54590605804427	2		677	423	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	102	1160	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	1	2	FACETS	0.369	0.329	0.412	0.369	0.329	0.412	SUBCLONAL	1	TRUE	1	0.54590605804427	2		1160	1012	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999777	100999777	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	240	1205	0	ENST00000325455.5:c.25C>T	p.Pro9Ser	p.P9S	ENST00000325455	NM_001202474.3	9	Ccc/Tcc	1/8	1	2	FACETS	0.975	0.912	1	0.975	0.912	1	CLONAL	1	TRUE	1	0.54590605804427	2		1205	902	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771428	112771428	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	216	797	0	ENST00000369452.4:c.1601C>T	p.Pro534Leu	p.P534L	ENST00000369452	NM_007373.3	534	cCc/cTc	9/9	1	2	FACETS	0.955	0.889	1	0.955	0.889	1	CLONAL	1	TRUE	1	0.54590605804427	2		797	829	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162137	47162137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	166	548	0	ENST00000409792.3:c.3989C>T	p.Ser1330Phe	p.S1330F	ENST00000409792	NM_014159.6	1330	tCc/tTc	3/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.54590605804427	2		548	577	SUCCESS
ALK	238	MSKCC	GRCh37	2	29541192	29541192	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	194	692	0	ENST00000389048.3:c.1625C>G	p.Pro542Arg	p.P542R	ENST00000389048	NM_004304.4	542	cCg/cGg	8/29	1	2	FACETS	0.919	0.853	0.988	0.919	0.853	0.988	CLONAL	1	TRUE	1	0.54590605804427	2		692	773	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136368	2136368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	205	1074	0	ENST00000219476.3:c.4837G>A	p.Asp1613Asn	p.D1613N	ENST00000219476	NM_000548.3	1613	Gac/Aac	37/42	1	2	FACETS	0.942	0.876	1	0.942	0.876	1	CLONAL	1	TRUE	1	0.54590605804427	2		1074	797	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287373	33287373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	230	756	1	ENST00000374542.5:c.1724C>T	p.Pro575Leu	p.P575L	ENST00000374542	NM_001141970.1	575	cCc/cTc	6/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.54590605804427	2		757	714	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564686	55564686	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	38	757	0	ENST00000288135.5:c.574G>A	p.Gly192Ser	p.G192S	ENST00000288135	NM_000222.2	192	Ggc/Agc	3/21	1	2	FACETS	0.212	0.174	0.254	0.212	0.174	0.254	SUBCLONAL	1	TRUE	1	0.54590605804427	2		757	658	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696372	47696372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	173	605	0	ENST00000347630.2:c.451C>T	p.Pro151Ser	p.P151S	ENST00000347630	NM_001007230.1	151	Cct/Tct	6/11	1	2	FACETS	0.874	0.807	0.944	0.874	0.807	0.944	CLONAL	1	TRUE	1	0.54590605804427	2		605	725	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21304081	21304081	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	130	712	0	ENST00000354336.3:c.860C>T	p.Pro287Leu	p.P287L	ENST00000354336	NM_005207.3	287	cCc/cTc	3/3	1	2	FACETS	0.521	0.472	0.572	0.521	0.472	0.572	SUBCLONAL	1	TRUE	1	0.54590605804427	2		712	915	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953930	17953930	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	61	1311	0	ENST00000458235.1:c.472G>A	p.Glu158Lys	p.E158K	ENST00000458235	NM_000215.3	158	Gag/Aag	5/24	1	2	FACETS	0.235	0.202	0.272	0.235	0.202	0.272	SUBCLONAL	1	TRUE	1	0.54590605804427	2		1311	949	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674236	117674236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	241	717	0	ENST00000368508.3:c.4238G>A	p.Gly1413Glu	p.G1413E	ENST00000368508	NM_002944.2	1413	gGa/gAa	26/43	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.54590605804427	2		717	817	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61722741	61722742	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	106	470	0	ENST00000401558.2:c.895_896delinsTT	p.Pro299Phe	p.P299F	ENST00000401558	NM_003400.3	299	CCt/TTt	11/25	1	2	FACETS	0.802	0.723	0.886	0.802	0.723	0.886	CLONAL	1	TRUE	1	0.54590605804427	2		470	484	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492952	8492952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	156	662	0	ENST00000356435.5:c.2377G>A	p.Glu793Lys	p.E793K	ENST00000356435		793	Gaa/Aaa	16/35	0.464996859323911	3	FACETS	0.809	0.741	0.881	0.405	0.37	0.441	CLONAL	1	TRUE	1	0.54590605804427	3		662	899	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731445	47731445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	101	208	0	ENST00000449228.1:c.347C>T	p.Pro116Leu	p.P116L	ENST00000449228	NM_001127240.2	116	cCg/cTg	2/4	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.54590605804427	2		208	284	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373689	118373689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782524513	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	49	615	0	ENST00000534358.1:c.7082C>T	p.Ser2361Leu	p.S2361L	ENST00000534358	NM_005933.3	2361	tCg/tTg	27/36	1	2	FACETS	0.27	0.228	0.316	0.27	0.228	0.316	SUBCLONAL	1	TRUE	1	0.54590605804427	2		615	665	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222554	2222554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	56	873	0	ENST00000398665.3:c.3386C>T	p.Ser1129Phe	p.S1129F	ENST00000398665	NM_032482.2	1129	tCc/tTc	24/28	1	2	FACETS	0.245	0.209	0.285	0.245	0.209	0.285	SUBCLONAL	1	TRUE	1	0.54590605804427	2		873	837	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981501	70981501	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200062567	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	72	1265	1	ENST00000276594.2:c.595G>A	p.Glu199Lys	p.E199K	ENST00000276594	NM_024504.3	199	Gag/Aag	2/8	1	2	FACETS	0.241	0.21	0.275	0.241	0.21	0.275	SUBCLONAL	1	TRUE	1	0.54590605804427	2		1266	1094	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994914	73994914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	16	253	0	ENST00000318443.5:c.398C>T	p.Ala133Val	p.A133V	ENST00000318443	NM_001024736.1	133	gCc/gTc	3/10	1	2	FACETS	0.388	0.289	0.505	0.388	0.289	0.505	SUBCLONAL	1	TRUE	1	0.54590605804427	2		253	151	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237652	133237652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138391248	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	249	973	0	ENST00000320574.5:c.2963C>T	p.Ser988Leu	p.S988L	ENST00000320574	NM_006231.2	988	tCg/tTg	25/49	1	2	FACETS	0.949	0.889	1	0.949	0.889	1	CLONAL	1	TRUE	1	0.54590605804427	2		973	961	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166091	118166091	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs745444038	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	149	586	1	ENST00000369448.3:c.601C>A	p.Pro201Thr	p.P201T	ENST00000369448	NM_017709.3	201	Ccc/Acc	2/2	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.54590605804427	2		587	534	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458092	120458092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	100	856	0	ENST00000256646.2:c.7253C>T	p.Ser2418Phe	p.S2418F	ENST00000256646	NM_024408.3	2418	tCc/tTc	34/34	1	2	FACETS	0.438	0.391	0.489	0.438	0.391	0.489	SUBCLONAL	1	TRUE	1	0.54590605804427	2		856	836	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406228	70406228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866149880	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	191	802	0	ENST00000373644.4:c.3742C>T	p.Pro1248Ser	p.P1248S	ENST00000373644	NM_030625.2	1248	Cct/Tct	4/12	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.54590605804427	2		802	656	SUCCESS
ATM	472	MSKCC	GRCh37	11	108137906	108137906	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	94	450	0	ENST00000278616.4:c.2475C>A	p.Phe825Leu	p.F825L	ENST00000278616	NM_000051.3	825	ttC/ttA	17/63	1	2	FACETS	0.954	0.856	1	0.954	0.856	1	CLONAL	1	TRUE	1	0.54590605804427	2		450	361	SUCCESS
ATM	472	MSKCC	GRCh37	11	108159820	108159820	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	28	174	0	ENST00000278616.4:c.4226C>T	p.Ser1409Phe	p.S1409F	ENST00000278616	NM_000051.3	1409	tCc/tTc	28/63	1	2	FACETS	0.855	0.696	1	0.855	0.696	1	CLONAL	1	TRUE	1	0.54590605804427	2		174	120	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245144	46245144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	36	692	0	ENST00000334344.6:c.3238C>T	p.Pro1080Ser	p.P1080S	ENST00000334344	NM_152641.2	1080	Cca/Tca	15/21	1	2	FACETS	0.197	0.161	0.237	0.197	0.161	0.237	SUBCLONAL	1	TRUE	1	0.54590605804427	2		692	670	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233147	69233147	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	119	466	0	ENST00000462284.1:c.1012G>A	p.Glu338Lys	p.E338K	ENST00000462284	NM_002392.5	338	Gaa/Aaa	11/11	0.464996859323911	3	FACETS	0.95	0.86	1	0.475	0.43	0.522	CLONAL	1	TRUE	1	0.54590605804427	3		466	584	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856631	111856632	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TA	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	159	485	2	ENST00000341259.2:c.682_683delinsTA	p.Pro228Ter	p.P228*	ENST00000341259	NM_005475.2	228	CCg/TAg	2/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.54590605804427	2		487	486	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114172	115114172	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	251	890	1	ENST00000257566.3:c.1045T>C	p.Phe349Leu	p.F349L	ENST00000257566	NM_016569.3	349	Ttc/Ctc	6/8	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.54590605804427	2		891	920	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114223	115114223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	55	821	0	ENST00000257566.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000257566	NM_016569.3	332	Gag/Aag	6/8	1	2	FACETS	0.226	0.192	0.263	0.226	0.192	0.263	SUBCLONAL	1	TRUE	1	0.54590605804427	2		821	893	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712554	43712554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	319	986	1	ENST00000382044.4:c.4630C>T	p.Pro1544Ser	p.P1544S	ENST00000382044	NM_001141980.1	1544	Ccg/Tcg	21/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.54590605804427	2		987	1075	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396965	396965	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	269	1095	0	ENST00000262320.3:c.61C>T	p.Pro21Ser	p.P21S	ENST00000262320	NM_003502.3	21	Ccc/Tcc	2/11	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.54590605804427	2		1095	977	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40497615	40497615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	255	885	0	ENST00000264657.5:c.334G>A	p.Glu112Lys	p.E112K	ENST00000264657	NM_139276.2	112	Gaa/Aaa	4/24	1	2	FACETS	0.963	0.902	1	0.963	0.902	1	CLONAL	1	TRUE	1	0.54590605804427	2		885	970	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40500519	40500519	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	186	674	0	ENST00000264657.5:c.16C>T	p.Gln6Ter	p.Q6*	ENST00000264657	NM_139276.2	6	Cag/Tag	2/24	1	2	FACETS	0.923	0.855	0.994	0.923	0.855	0.994	CLONAL	1	TRUE	1	0.54590605804427	2		674	738	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40880881	40880881	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	210	885	0	ENST00000428826.2:c.79C>T	p.Arg27Ter	p.R27*	ENST00000428826		27	Cga/Tga	3/21	1	2	FACETS	0.934	0.869	1	0.934	0.869	1	CLONAL	1	TRUE	1	0.54590605804427	2		885	824	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222874	5222875	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	213	901	1	ENST00000357368.4:c.2928_2929delinsTT	p.Pro977Ser	p.P977S	ENST00000357368	NM_002850.3	976	ggCCct/ggTTct	18/38	1	2	FACETS	0.92	0.857	0.986	0.92	0.857	0.986	CLONAL	1	TRUE	1	0.54590605804427	2		902	848	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610640	10610641	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	51	952	1	ENST00000171111.5:c.69_70delinsTT	p.Pro24Ser	p.P24S	ENST00000171111	NM_203500.1	23	tgCCct/tgTTct	2/6	1	2	FACETS	0.228	0.193	0.267	0.228	0.193	0.267	SUBCLONAL	1	TRUE	1	0.54590605804427	2		953	819	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726562	41726562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536724919	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	194	945	1	ENST00000301178.4:c.107C>T	p.Pro36Leu	p.P36L	ENST00000301178	NM_021913.4	36	cCc/cTc	2/20	1	2	FACETS	0.875	0.811	0.941	0.875	0.811	0.941	CLONAL	1	TRUE	1	0.54590605804427	2		946	812	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794658	42794658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	270	1164	0	ENST00000575354.2:c.1738G>A	p.Gly580Ser	p.G580S	ENST00000575354	NM_015125.3	580	Ggt/Agt	10/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.54590605804427	2		1164	867	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560905	9560905	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	173	679	0	ENST00000353224.5:c.877C>T	p.Gln293Ter	p.Q293*	ENST00000353224	NM_177990.2	293	Cag/Tag	4/10	1	2	FACETS	0.977	0.902	1	0.977	0.902	1	CLONAL	1	TRUE	1	0.54590605804427	2		679	649	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62293925	62293926	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	284	1111	0	ENST00000360203.5:c.422_423delinsAA	p.Arg141Gln	p.R141Q	ENST00000360203	NM_001283009.1	141	cGG/cAA	5/35	1	2	FACETS	0.966	0.908	1	0.966	0.908	1	CLONAL	1	TRUE	1	0.54590605804427	2		1111	1077	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39772537	39772537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	157	569	0	ENST00000288319.7:c.704C>T	p.Ser235Leu	p.S235L	ENST00000288319	NM_182918.3	235	tCa/tTa	6/10	1	2	FACETS	0.977	0.899	1	0.977	0.899	1	CLONAL	1	TRUE	1	0.54590605804427	2		569	589	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574374	41574374	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	192	970	0	ENST00000263253.7:c.6659C>T	p.Pro2220Leu	p.P2220L	ENST00000263253	NM_001429.3	2220	cCa/cTa	31/31	1	2	FACETS	0.942	0.873	1	0.942	0.873	1	CLONAL	1	TRUE	1	0.54590605804427	2		970	747	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162168	47162168	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	45	600	0	ENST00000409792.3:c.3958T>C	p.Tyr1320His	p.Y1320H	ENST00000409792	NM_014159.6	1320	Tat/Cat	3/21	1	2	FACETS	0.26	0.218	0.307	0.26	0.218	0.307	SUBCLONAL	1	TRUE	1	0.54590605804427	2		600	634	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643603	52643603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	169	640	0	ENST00000394830.3:c.2293G>A	p.Gly765Arg	p.G765R	ENST00000394830	NM_018313.4	765	Gga/Aga	17/30	1	2	FACETS	0.986	0.91	1	0.986	0.91	1	CLONAL	1	TRUE	1	0.54590605804427	2		640	628	SUCCESS
ATR	545	MSKCC	GRCh37	3	142232423	142232423	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	96	580	1	ENST00000350721.4:c.4561G>A	p.Asp1521Asn	p.D1521N	ENST00000350721	NM_001184.3	1521	Gat/Aat	26/47	1	2	FACETS	0.778	0.697	0.864	0.778	0.697	0.864	SUBCLONAL	1	TRUE	1	0.54590605804427	2		581	452	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505311	186505311	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	107	490	0	ENST00000323963.5:c.937G>A	p.Asp313Asn	p.D313N	ENST00000323963		313	Gat/Aat	9/11	1	2	FACETS	0.92	0.831	1	0.92	0.831	1	CLONAL	1	TRUE	1	0.54590605804427	2		490	426	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127453	55127453	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	213	776	0	ENST00000257290.5:c.241T>G	p.Phe81Val	p.F81V	ENST00000257290	NM_006206.4	81	Ttt/Gtt	3/23	1	2	FACETS	0.893	0.831	0.957	0.893	0.831	0.957	CLONAL	1	TRUE	1	0.54590605804427	2		776	874	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509115	66509115	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	98	406	0	ENST00000273854.3:c.212G>C	p.Gly71Ala	p.G71A	ENST00000273854	NM_004439.5	71	gGg/gCg	2/18	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.54590605804427	2		406	341	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510030	187510030	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	160	571	0	ENST00000441802.2:c.13483C>T	p.Pro4495Ser	p.P4495S	ENST00000441802	NM_005245.3	4495	Ccc/Tcc	27/27	0.542317764851877	1	FACETS	0.98	0.908	1	0.98	0.908	1	CLONAL	1	TRUE	0	0.54590605804427	1		571	435	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876172	35876172	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	157	700	0	ENST00000303115.3:c.964G>T	p.Gly322Cys	p.G322C	ENST00000303115	NM_002185.3	322	Ggt/Tgt	8/8	1	2	FACETS	0.952	0.876	1	0.952	0.876	1	CLONAL	1	TRUE	1	0.54590605804427	2		700	604	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111422	56111422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868220086	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	114	502	0	ENST00000399503.3:c.22C>T	p.Arg8Cys	p.R8C	ENST00000399503	NM_005921.1	8	Cgc/Tgc	1/20	1	2	FACETS	0.824	0.745	0.906	0.824	0.745	0.906	CLONAL	1	TRUE	1	0.54590605804427	2		502	507	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681028	30681028	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	53	707	0	ENST00000376406.3:c.691G>A	p.Glu231Lys	p.E231K	ENST00000376406	NM_014641.2	231	Gag/Aag	5/15	1	2	FACETS	0.274	0.233	0.319	0.274	0.233	0.319	SUBCLONAL	1	TRUE	1	0.54590605804427	2		707	709	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201836	152201836	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	132	565	0	ENST00000206249.3:c.690T>A	p.Asp230Glu	p.D230E	ENST00000206249	NM_000125.3	230	gaT/gaA	3/8	1	2	FACETS	0.727	0.662	0.796	0.727	0.662	0.796	SUBCLONAL	1	TRUE	1	0.54590605804427	2		565	665	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405829	157405829	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	62	585	0	ENST00000346085.5:c.2071G>A	p.Gly691Arg	p.G691R	ENST00000346085	NM_020732.3	691	Gga/Aga	6/20	1	2	FACETS	0.359	0.31	0.413	0.359	0.31	0.413	SUBCLONAL	1	TRUE	1	0.54590605804427	2		585	632	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956929	2956929	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	232	795	0	ENST00000396946.4:c.2698C>G	p.Leu900Val	p.L900V	ENST00000396946	NM_032415.4	900	Ctt/Gtt	20/25	0.54590605804427	3	FACETS	0.952	0.887	1	0.476	0.443	0.51	CLONAL	1	TRUE	1	0.54590605804427	3		795	1136	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372143	55372143	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	192	781	0	ENST00000297316.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000297316	NM_022454.3	278	cCc/cTc	2/2	1	2	FACETS	0.965	0.895	1	0.965	0.895	1	CLONAL	1	TRUE	1	0.54590605804427	2		781	729	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209334	98209335	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	42	1084	0	ENST00000331920.6:c.4203_4204delinsTT	p.Pro1402Ser	p.P1402S	ENST00000331920	NM_000264.3	1401	taCCct/taTTct	23/24	0.54590605804427	1	FACETS	0.181	0.151	0.215	0.181	0.151	0.215	SUBCLONAL	1	TRUE	0	0.54590605804427	1		1084	617	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239868	98239868	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	208	800	1	ENST00000331920.6:c.1464C>A	p.Cys488Ter	p.C488*	ENST00000331920	NM_000264.3	488	tgC/tgA	10/24	0.54590605804427	1	FACETS	0.908	0.848	0.97	0.908	0.848	0.97	CLONAL	1	TRUE	0	0.54590605804427	1		801	610	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396940	139396941	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0052339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	123	601	1	ENST00000277541.6:c.5168-1_5168delinsAA		p.X1723_splice	ENST00000277541	NM_017617.3	1723		28/34	0.54590605804427	1	FACETS	0.851	0.777	0.927	0.851	0.777	0.927	CLONAL	1	TRUE	0	0.54590605804427	1		602	385	SUCCESS
APC	324	MSKCC	GRCh37	5	112175324	112175324	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1211642532	NA	P-0052340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	71	344	0	ENST00000257430.4:c.4033G>T	p.Glu1345Ter	p.E1345*	ENST00000257430	NM_000038.5	1345	Gaa/Taa	16/16	0.29629396262918	2	FACETS	0.816	0.72	0.918	0.816	0.72	0.918	CLONAL	2	TRUE	0	0.308563786403464	2		344	282	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0052340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	75	489	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.2929432429554	3	FACETS	1	0.92	1	1	0.92	1	CLONAL	2	TRUE	1	0.308563786403464	3		490	268	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436839	110436839	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	149	916	0	ENST00000375856.3:c.1562C>T	p.Pro521Leu	p.P521L	ENST00000375856	NM_003749.2	521	cCc/cTc	1/2	0.308563786403464	3	FACETS	0.814	0.745	0.885	0.814	0.745	0.885	CLONAL	2	TRUE	1	0.308563786403464	3		916	685	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856422	111856422	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	27	267	3	ENST00000341259.2:c.473A>C	p.His158Pro	p.H158P	ENST00000341259	NM_005475.2	158	cAc/cCc	2/8	1	2	FACETS	0.738	0.59	0.906	0.738	0.59	0.906	CLONAL	1	TRUE	1	0.308563786403464	2		270	237	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774975	73775001	+	inframe_deletion	In_Frame_Del	DEL	CAGCTTCCGGATGAGCAGCTCGGTCGA	CAGCTTCCGGATGAGCAGCTCGGTCGA	-	novel	NA	P-0052340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	78	404	0	ENST00000254810.4:c.172_198del	p.Ser58_Leu66del	p.S58_L66del	ENST00000254810	NM_005324.3	58	TCGACCGAGCTGCTCATCCGGAAGCTG/-	3/4	0.29130423703529	4	FACETS	0.813	0.718	0.914	0.813	0.718	0.914	CLONAL	2	TRUE	2	0.308563786403464	4		404	407	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056019	26056021	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs1198017017	NA	P-0052340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	135	306	0	ENST00000343677.2:c.636_638del	p.Lys213del	p.K213del	ENST00000343677	NM_005319.3	212	aaGAAa/aaa	1/1	0.308563786403464	4	FACETS	0.886	0.812	0.961	0.886	0.812	0.961	CLONAL	3	TRUE	1	0.308563786403464	4		306	431	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	145	504	3	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.713	0.651	0.779	0.713	0.651	0.779	SUBCLONAL	1	TRUE	1	0.470560796967114	2		507	864	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	120	495	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.470560796967114	2		495	509	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	140	749	6	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.876	0.8	0.956	0.876	0.8	0.956	CLONAL	1	TRUE	1	0.470560796967114	2		755	679	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	337	701	11	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.909	0.864	0.954	1	0.996	1	CLONAL	2	TRUE	1	0.470560796967114	2		712	788	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	230	1227	2	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.914	0.852	0.979	0.914	0.852	0.979	CLONAL	1	TRUE	1	0.470560796967114	2		1229	1069	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007871	45007872	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	155	522	0	ENST00000558401.1:c.319_320del	p.Leu107ValfsTer7	p.L107Vfs*7	ENST00000558401	NM_004048.2	106	acTTtg/actg	2/4	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.470560796967114	2		522	639	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	178	944	4	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.901	0.831	0.973	0.901	0.831	0.973	CLONAL	1	TRUE	1	0.470560796967114	2		948	840	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523009	25523009	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	229	1038	3	ENST00000264709.3:c.176del	p.Pro59ArgfsTer13	p.P59Rfs*13	ENST00000264709	NM_175629.2	59	cCg/cg	3/23	1	2	FACETS	0.894	0.833	0.957	0.894	0.833	0.957	CLONAL	1	TRUE	1	0.470560796967114	2		1041	1089	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643942	52643943	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	104	521	0	ENST00000394830.3:c.1953dup	p.Ser652IlefsTer13	p.S652Ifs*13	ENST00000394830	NM_018313.4	651	-/A	17/30	1	2	FACETS	0.822	0.738	0.91	0.822	0.738	0.91	CLONAL	1	TRUE	1	0.470560796967114	2		521	538	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	163	425	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.89	0.828	0.954	1	0.992	1	CLONAL	2	TRUE	1	0.470560796967114	2		425	389	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	152	579	1	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	0.470560796967114	2	FACETS	0.936	0.869	1	0.936	0.869	1	CLONAL	2	TRUE	0	0.470560796967114	2		580	345	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920412	134920412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746798014	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	166	765	1	ENST00000398015.3:c.2227C>T	p.Arg743Trp	p.R743W	ENST00000398015	NM_004441.4	743	Cgg/Tgg	12/16	1	2	FACETS	0.966	0.89	1	0.966	0.89	1	CLONAL	1	TRUE	1	0.470560796967114	2		766	730	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440943	56440943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786205215	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	196	819	0	ENST00000407977.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000407977		132	Cga/Tga	4/10	1	2	FACETS	0.979	0.907	1	0.979	0.907	1	CLONAL	1	TRUE	1	0.470560796967114	2		819	851	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100728	8100728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs771019738	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	170	1006	7	ENST00000346208.3:c.708del	p.Ser237AlafsTer28	p.S237Afs*28	ENST00000346208		234	ttC/tt	3/6	1	2	FACETS	0.878	0.808	0.95	0.878	0.808	0.95	CLONAL	1	TRUE	1	0.470560796967114	2		1013	823	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664989	138664989	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	47	364	0	ENST00000330315.3:c.576del	p.Lys193SerfsTer78	p.K193Sfs*78	ENST00000330315	NM_023067.3	192	ccC/cc	1/1	1	2	FACETS	0.732	0.622	0.851	0.732	0.622	0.851	SUBCLONAL	1	TRUE	1	0.470560796967114	2		364	273	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	231	1116	19	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.470560796967114	2		1135	914	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794441	42794441	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	487	1295	1	ENST00000575354.2:c.1526del	p.Pro509HisfsTer14	p.P509Hfs*14	ENST00000575354	NM_015125.3	507	cgC/cg	10/20	0.470560796967114	2	FACETS	0.905	0.868	0.942	0.905	0.868	0.942	CLONAL	2	TRUE	0	0.470560796967114	2		1296	1144	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116263	209116263	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	139	343	1	ENST00000345146.2:c.13del	p.Ile5SerfsTer7	p.I5Sfs*7	ENST00000345146	NM_005896.2	5	Atc/tc	3/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.470560796967114	2		344	466	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905516	50905516	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs993539085	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	499	1370	1	ENST00000440232.2:c.644C>T	p.Ala215Val	p.A215V	ENST00000440232	NM_002691.3	215	gCg/gTg	6/27	0.470560796967114	2	FACETS	0.957	0.919	0.995	0.957	0.919	0.995	CLONAL	2	TRUE	0	0.470560796967114	2		1371	1108	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257144	19257144	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	116	997	0	ENST00000162023.5:c.819del	p.Thr274ProfsTer?	p.T274Pfs*?	ENST00000162023		273	ccC/cc	12/13	1	2	FACETS	0.618	0.557	0.682	0.618	0.557	0.682	SUBCLONAL	1	TRUE	1	0.470560796967114	2		997	798	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945033	31945033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	230	1014	0	ENST00000340398.3:c.68C>T	p.Thr23Met	p.T23M	ENST00000340398	NM_001013699.2	23	aCg/aTg	1/1	1	2	FACETS	0.956	0.891	1	0.956	0.891	1	CLONAL	1	TRUE	1	0.470560796967114	2		1014	1023	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648217	206648217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149591181	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	128	647	1	ENST00000367120.3:c.238C>T	p.Arg80Trp	p.R80W	ENST00000367120	NM_014002.3	80	Cgg/Tgg	5/22	1	2	FACETS	0.982	0.894	1	0.982	0.894	1	CLONAL	1	TRUE	1	0.470560796967114	2		648	554	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736510	85736511	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs387906351	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	97	395	5	ENST00000370580.1:c.136dup	p.Ile46AsnfsTer4	p.I46Nfs*4	ENST00000370580	NM_003921.4	46	ata/aAta	2/3	1	2	FACETS	0.963	0.864	1	0.963	0.864	1	CLONAL	1	TRUE	1	0.470560796967114	2		400	428	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404576	8404576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146844299	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	84	438	1	ENST00000356435.5:c.4171G>A	p.Ala1391Thr	p.A1391T	ENST00000356435		1391	Gca/Aca	25/35	1	2	FACETS	0.858	0.762	0.96	0.858	0.762	0.96	CLONAL	1	TRUE	1	0.470560796967114	2		439	416	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615698	1615698	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	217	1292	6	ENST00000344749.5:c.1573del	p.Arg525GlyfsTer18	p.R525Gfs*18	ENST00000344749	NM_001136139.2	525	Cgg/gg	17/19	1	2	FACETS	0.895	0.832	0.96	0.895	0.832	0.96	CLONAL	1	TRUE	1	0.470560796967114	2		1298	1031	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753011	57753012	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	97	420	3	ENST00000274289.3:c.1004dup	p.Leu335PhefsTer12	p.L335Ffs*12	ENST00000274289	NM_006622.3	335	ttg/ttTg	7/14	1	2	FACETS	0.854	0.764	0.948	0.854	0.764	0.948	CLONAL	1	TRUE	1	0.470560796967114	2		423	483	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566524	41566525	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	133	498	0	ENST00000263253.7:c.4408dup	p.Met1470AsnfsTer3	p.M1470Nfs*3	ENST00000263253	NM_001429.3	1467	-/A	27/31	1	2	FACETS	0.826	0.752	0.904	0.826	0.752	0.904	CLONAL	1	TRUE	1	0.470560796967114	2		498	684	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260644	1260644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1278994586	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	219	949	3	ENST00000310581.5:c.2915G>A	p.Arg972His	p.R972H	ENST00000310581	NM_198253.2	972	cGc/cAc	12/16	0.470560796967114	3	FACETS	0.903	0.838	0.97	0.451	0.419	0.485	CLONAL	1	TRUE	1	0.470560796967114	3		952	1274	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245995	5245996	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	193	1069	0	ENST00000357368.4:c.779dup	p.Asn261GlnfsTer30	p.N261Qfs*30	ENST00000357368	NM_002850.3	260	ggc/ggGc	10/38	1	2	FACETS	0.799	0.738	0.861	0.799	0.738	0.861	SUBCLONAL	1	TRUE	1	0.470560796967114	2		1069	1027	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193850	106193850	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	93	457	1	ENST00000380013.4:c.4317del	p.Lys1439AsnfsTer9	p.K1439Nfs*9	ENST00000380013	NM_001127208.2	1438	Aaa/aa	10/11	1	2	FACETS	0.727	0.648	0.81	0.727	0.648	0.81	SUBCLONAL	1	TRUE	1	0.470560796967114	2		458	544	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913836	32913837	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359507	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	93	530	1	ENST00000380152.3:c.5351dup	p.Asn1784LysfsTer3	p.N1784Kfs*3	ENST00000380152		1782	caa/cAaa	11/27	1	2	FACETS	0.697	0.621	0.778	0.697	0.621	0.778	SUBCLONAL	1	TRUE	1	0.470560796967114	2		531	567	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420661	49420661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555185875	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	176	824	0	ENST00000301067.7:c.15088C>T	p.Arg5030Cys	p.R5030C	ENST00000301067	NM_003482.3	5030	Cgt/Tgt	48/54	1	2	FACETS	0.909	0.838	0.982	0.909	0.838	0.982	CLONAL	1	TRUE	1	0.470560796967114	2		824	823	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204992	128204992	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	149	1133	2	ENST00000341105.2:c.449del	p.Gly150GlufsTer68	p.G150Efs*68	ENST00000341105	NM_032638.4	150	gGa/ga	3/6	1	2	FACETS	0.949	0.87	1	0.949	0.87	1	CLONAL	1	TRUE	1	0.470560796967114	2		1135	667	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250047	53250047	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	58	744	3	ENST00000375401.3:c.202del	p.Arg68GlufsTer5	p.R68Efs*5	ENST00000375401	NM_004187.3	68	Cga/ga	2/26	1	2	FACETS	0.248	0.212	0.287	0.248	0.212	0.287	SUBCLONAL	1	TRUE	1	0.470560796967114	2		747	995	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11022898	11022899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	261	1020	1	ENST00000327064.4:c.603dup	p.Ala202CysfsTer22	p.A202Cfs*22	ENST00000327064	NM_199141.1	199	-/T	5/16	1	2	FACETS	0.905	0.847	0.965	0.905	0.847	0.965	CLONAL	1	TRUE	1	0.470560796967114	2		1021	1226	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120366	94120366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1216099858	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	78	391	0	ENST00000369303.4:c.685G>A	p.Glu229Lys	p.E229K	ENST00000369303	NM_004440.3	229	Gag/Aag	3/17	1	2	FACETS	0.773	0.682	0.869	0.773	0.682	0.869	SUBCLONAL	1	TRUE	1	0.470560796967114	2		391	429	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38955709	38955709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762042928	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	35	404	0	ENST00000357387.3:c.2597G>A	p.Arg866Gln	p.R866Q	ENST00000357387	NM_152756.3	866	cGg/cAg	26/38	0.470560796967114	3	FACETS	0.367	0.3	0.442	0.183	0.15	0.221	SUBCLONAL	1	TRUE	1	0.470560796967114	3		404	501	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438262	49438262	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	196	903	0	ENST00000301067.7:c.5007del	p.Val1670SerfsTer52	p.V1670Sfs*52	ENST00000301067	NM_003482.3	1669	ccC/cc	20/54	1	2	FACETS	0.888	0.822	0.956	0.888	0.822	0.956	CLONAL	1	TRUE	1	0.470560796967114	2		903	938	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs758286312	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	186	895	2	ENST00000407977.2:c.349C>A	p.Arg117Ser	p.R117S	ENST00000407977		117	Cgc/Agc	3/10	1	2	FACETS	0.836	0.772	0.902	0.836	0.772	0.902	CLONAL	1	TRUE	1	0.470560796967114	2		897	946	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448297	56448297	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	185	867	1	ENST00000407977.2:c.350del	p.Arg117ProfsTer41	p.R117Pfs*41	ENST00000407977		117	cGc/cc	3/10	1	2	FACETS	0.835	0.771	0.901	0.835	0.771	0.901	CLONAL	1	TRUE	1	0.470560796967114	2		868	942	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776393	76776393	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	120	483	1	ENST00000373344.5:c.7073G>T	p.Trp2358Leu	p.W2358L	ENST00000373344	NM_000489.3	2358	tGg/tTg	34/35	1	2	FACETS	0.922	0.836	1	0.922	0.836	1	CLONAL	1	TRUE	1	0.470560796967114	2		484	553	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864003	97864003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs370974124	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	147	666	1	ENST00000289081.3:c.1663C>T	p.Arg555Ter	p.R555*	ENST00000289081	NM_000136.2	555	Cga/Tga	15/15	1	2	FACETS	0.886	0.811	0.965	0.886	0.811	0.965	CLONAL	1	TRUE	1	0.470560796967114	2		667	705	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161180	56161180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs995383293	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	110	422	0	ENST00000399503.3:c.1049C>T	p.Ala350Val	p.A350V	ENST00000399503	NM_005921.1	350	gCa/gTa	5/20	1	2	FACETS	0.901	0.813	0.993	0.901	0.813	0.993	CLONAL	1	TRUE	1	0.470560796967114	2		422	519	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164548	36164548	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	124	753	0	ENST00000300305.3:c.1327A>G	p.Asn443Asp	p.N443D	ENST00000300305		443	Aac/Gac	8/8	1	2	FACETS	0.739	0.669	0.812	0.739	0.669	0.812	SUBCLONAL	1	TRUE	1	0.470560796967114	2		753	713	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31464435	31464435	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1471632102	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	208	819	0	ENST00000344624.3:c.2482del	p.Ile828TyrfsTer7	p.I828Yfs*7	ENST00000344624		828	Ata/ta	17/33	0.470560796967114	3	FACETS	0.781	0.723	0.842	0.391	0.361	0.421	SUBCLONAL	1	TRUE	1	0.470560796967114	3		819	1398	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202961	27202961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745978641	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	146	646	0	ENST00000380036.4:c.2053G>A	p.Val685Ile	p.V685I	ENST00000380036	NM_000459.3	685	Gtt/Att	13/23	1	2	FACETS	0.879	0.804	0.957	0.879	0.804	0.957	CLONAL	1	TRUE	1	0.470560796967114	2		646	706	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223605	53223605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	175	1085	0	ENST00000375401.3:c.3754C>T	p.Arg1252Cys	p.R1252C	ENST00000375401	NM_004187.3	1252	Cgc/Tgc	23/26	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.470560796967114	2		1085	735	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670549	30670549	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1262512315	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	51	711	0	ENST00000376406.3:c.5971C>T	p.Arg1991Trp	p.R1991W	ENST00000376406	NM_014641.2	1991	Cgg/Tgg	13/15	1	2	FACETS	0.282	0.238	0.329	0.282	0.238	0.329	SUBCLONAL	1	TRUE	1	0.470560796967114	2		711	770	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097604	11097604	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	224	1234	1	ENST00000358026.2:c.788del	p.Pro263GlnfsTer40	p.P263Qfs*40	ENST00000358026	NM_001128849.1	262	Ccc/cc	5/36	1	2	FACETS	0.879	0.818	0.942	0.879	0.818	0.942	CLONAL	1	TRUE	1	0.470560796967114	2		1235	1083	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909526	50909526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	65	1123	2	ENST00000440232.2:c.1330C>T	p.Arg444Trp	p.R444W	ENST00000440232	NM_002691.3	444	Cgg/Tgg	11/27	0.470560796967114	2	FACETS	0.249	0.214	0.286	0.124	0.107	0.143	SUBCLONAL	1	TRUE	0	0.470560796967114	2		1125	1111	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294642	1294642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	414	880	0	ENST00000310581.5:c.359G>A	p.Arg120His	p.R120H	ENST00000310581	NM_198253.2	120	cGc/cAc	2/16	0.470560796967114	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.470560796967114	3		880	1028	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249347	110249348	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	274	1186	0	ENST00000374672.4:c.1225_1226del	p.Lys409GlufsTer14	p.K409Efs*14	ENST00000374672	NM_004235.4	409	AAg/g	4/5	1	2	FACETS	0.866	0.812	0.923	0.866	0.812	0.923	CLONAL	1	TRUE	1	0.470560796967114	2		1186	1344	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978659	70978659	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	201	813	0	ENST00000276594.2:c.994C>A	p.Arg332Ser	p.R332S	ENST00000276594	NM_024504.3	332	Cgc/Agc	5/8	1	2	FACETS	0.928	0.86	0.997	0.928	0.86	0.997	CLONAL	1	TRUE	1	0.470560796967114	2		813	921	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262373	16262373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372303430	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	83	510	0	ENST00000375759.3:c.9638C>T	p.Ala3213Val	p.A3213V	ENST00000375759	NM_015001.2	3213	gCg/gTg	11/15	1	2	FACETS	0.972	0.864	1	0.972	0.864	1	CLONAL	1	TRUE	1	0.470560796967114	2		510	363	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262478	16262478	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	50	320	0	ENST00000375759.3:c.9747del	p.Val3250SerfsTer34	p.V3250Sfs*34	ENST00000375759	NM_015001.2	3248	gCc/gc	11/15	1	2	FACETS	0.936	0.803	1	0.936	0.803	1	CLONAL	1	TRUE	1	0.470560796967114	2		320	227	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932187	36932187	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	165	977	0	ENST00000361632.4:c.2282G>T	p.Ser761Ile	p.S761I	ENST00000361632		761	aGc/aTc	16/16	1	2	FACETS	0.929	0.855	1	0.929	0.855	1	CLONAL	1	TRUE	1	0.470560796967114	2		977	755	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830841	156830841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	131	801	0	ENST00000524377.1:c.115G>A	p.Ala39Thr	p.A39T	ENST00000524377	NM_002529.3	39	Gcc/Acc	1/17	1	2	FACETS	0.987	0.9	1	0.987	0.9	1	CLONAL	1	TRUE	1	0.470560796967114	2		801	564	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135983	64135983	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	237	1164	0	ENST00000334205.4:c.1244C>A	p.Pro415His	p.P415H	ENST00000334205	NM_003942.2	415	cCt/cAt	11/17	1	2	FACETS	0.928	0.865	0.992	0.928	0.865	0.992	CLONAL	1	TRUE	1	0.470560796967114	2		1164	1086	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992240	11992240	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	122	455	0	ENST00000396373.4:c.328+2T>C		p.X110_splice	ENST00000396373	NM_001987.4	110			1	2	FACETS	0.888	0.805	0.974	0.888	0.805	0.974	CLONAL	1	TRUE	1	0.470560796967114	2		455	584	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281877	49281878	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	164	745	0	ENST00000282018.3:c.928dup	p.Glu310GlyfsTer4	p.E310Gfs*4	ENST00000282018	NM_020377.2	308	-/G	1/1	1	2	FACETS	0.849	0.78	0.921	0.849	0.78	0.921	CLONAL	1	TRUE	1	0.470560796967114	2		745	821	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562572	95562572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	90	514	0	ENST00000393063.1:c.4685G>A	p.Cys1562Tyr	p.C1562Y	ENST00000393063	NM_030621.3	1562	tGt/tAt	24/28	1	2	FACETS	0.826	0.736	0.921	0.826	0.736	0.921	CLONAL	1	TRUE	1	0.470560796967114	2		514	463	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003780	45003781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	119	795	0	ENST00000558401.1:c.43_44dup	p.Ser16PhefsTer29	p.S16Ffs*29	ENST00000558401	NM_004048.2	12	-/CT	1/4	1	2	FACETS	0.728	0.658	0.802	0.728	0.658	0.802	SUBCLONAL	1	TRUE	1	0.470560796967114	2		795	695	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096344	2096344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1210160367	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	252	1046	0	ENST00000219066.1:c.163G>A	p.Val55Met	p.V55M	ENST00000219066	NM_002528.5	55	Gtg/Atg	2/6	1	2	FACETS	0.876	0.819	0.936	0.876	0.819	0.936	CLONAL	1	TRUE	1	0.470560796967114	2		1046	1222	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860695	3860695	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	159	766	0	ENST00000262367.5:c.884C>A	p.Pro295His	p.P295H	ENST00000262367	NM_004380.2	295	cCc/cAc	3/31	1	2	FACETS	0.863	0.792	0.937	0.863	0.792	0.937	CLONAL	1	TRUE	1	0.470560796967114	2		766	783	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041555	14041555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762543560	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	144	603	0	ENST00000311895.7:c.2102G>A	p.Arg701His	p.R701H	ENST00000311895	NM_005236.2	701	cGt/cAt	11/11	1	2	FACETS	0.897	0.82	0.978	0.897	0.82	0.978	CLONAL	1	TRUE	1	0.470560796967114	2		603	682	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17117000	17117000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201056799	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	178	790	1	ENST00000285071.4:c.1709G>A	p.Arg570His	p.R570H	ENST00000285071	NM_144997.5	570	cGc/cAc	14/14	1	2	FACETS	0.958	0.884	1	0.958	0.884	1	CLONAL	1	TRUE	1	0.470560796967114	2		791	790	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414671	56414671	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	109	519	0	ENST00000348428.3:c.2072A>G	p.Gln691Arg	p.Q691R	ENST00000348428	NM_006785.3	691	cAg/cGg	17/17	1	2	FACETS	0.971	0.877	1	0.971	0.877	1	CLONAL	1	TRUE	1	0.470560796967114	2		519	477	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222110	2222110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1013270501	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	228	1243	1	ENST00000398665.3:c.2942G>A	p.Arg981His	p.R981H	ENST00000398665	NM_032482.2	981	cGc/cAc	24/28	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.470560796967114	2		1244	937	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18943157	18943157	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	37	256	0	ENST00000262803.5:c.144del	p.Gly49AlafsTer45	p.G49Afs*45	ENST00000262803	NM_002911.3	47	Ccc/cc	1/24	1	2	FACETS	0.731	0.608	0.867	0.731	0.608	0.867	SUBCLONAL	1	TRUE	1	0.470560796967114	2		256	215	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46611659	46611659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753610303	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	227	1032	0	ENST00000263734.3:c.2473C>T	p.Arg825Trp	p.R825W	ENST00000263734	NM_001430.4	825	Cgg/Tgg	16/16	1	2	FACETS	0.987	0.92	1	0.987	0.92	1	CLONAL	1	TRUE	1	0.470560796967114	2		1032	978	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659880	227659880	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	156	924	0	ENST00000305123.5:c.3575C>A	p.Pro1192His	p.P1192H	ENST00000305123	NM_005544.2	1192	cCt/cAt	1/2	1	2	FACETS	0.942	0.865	1	0.942	0.865	1	CLONAL	1	TRUE	1	0.470560796967114	2		924	704	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573158	41573158	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1432882937	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	185	1047	0	ENST00000263253.7:c.5443C>T	p.Gln1815Ter	p.Q1815*	ENST00000263253	NM_001429.3	1815	Cag/Tag	31/31	1	2	FACETS	0.921	0.851	0.993	0.921	0.851	0.993	CLONAL	1	TRUE	1	0.470560796967114	2		1047	854	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574448	41574449	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	155	897	0	ENST00000263253.7:c.6735dup	p.Pro2246SerfsTer56	p.P2246Sfs*56	ENST00000263253	NM_001429.3	2245	ctt/cTtt	31/31	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.470560796967114	2		897	636	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37059062	37059062	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63750034	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	126	640	0	ENST00000231790.2:c.860del	p.Asn287ThrfsTer10	p.N287Tfs*10	ENST00000231790	NM_000249.3	286	Aaa/aa	10/19	1	2	FACETS	0.736	0.667	0.808	0.736	0.667	0.808	SUBCLONAL	1	TRUE	1	0.470560796967114	2		640	728	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573361	55573362	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	118	660	0	ENST00000288135.5:c.1026dup	p.Pro343ThrfsTer2	p.P343Tfs*2	ENST00000288135	NM_000222.2	341	-/A	6/21	1	2	FACETS	0.754	0.681	0.831	0.754	0.681	0.831	SUBCLONAL	1	TRUE	1	0.470560796967114	2		660	665	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961184	79961184	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	116	529	0	ENST00000265081.6:c.579+2T>C		p.X193_splice	ENST00000265081	NM_002439.4	193			1	2	FACETS	0.88	0.796	0.969	0.88	0.796	0.969	CLONAL	1	TRUE	1	0.470560796967114	2		529	560	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188296	32188297	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	190	1134	1	ENST00000375023.3:c.1044_1045del	p.Gly349HisfsTer4	p.G349Hfs*4	ENST00000375023	NM_004557.3	348	ggCGgc/gggc	6/30	1	2	FACETS	0.832	0.769	0.897	0.832	0.769	0.897	CLONAL	1	TRUE	1	0.470560796967114	2		1135	971	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521896	157521896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753434703	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	124	739	0	ENST00000346085.5:c.4168G>A	p.Asp1390Asn	p.D1390N	ENST00000346085	NM_020732.3	1390	Gac/Aac	18/20	1	2	FACETS	0.87	0.789	0.954	0.87	0.789	0.954	CLONAL	1	TRUE	1	0.470560796967114	2		739	606	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221825	55221825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1020654485	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	200	1062	0	ENST00000275493.2:c.869C>T	p.Thr290Ile	p.T290I	ENST00000275493	NM_005228.3	290	aCc/aTc	7/28	1	2	FACETS	0.846	0.783	0.911	0.846	0.783	0.911	CLONAL	1	TRUE	1	0.470560796967114	2		1062	1005	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404266	139404266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	213	1102	1	ENST00000277541.6:c.2888G>A	p.Cys963Tyr	p.C963Y	ENST00000277541	NM_017617.3	963	tGc/tAc	18/34	1	2	FACETS	0.913	0.848	0.979	0.913	0.848	0.979	CLONAL	1	TRUE	1	0.470560796967114	2		1103	992	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69103959	69103959	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	142	551	0	ENST00000288368.4:c.4349C>A	p.Ala1450Glu	p.A1450E	ENST00000288368	NM_024870.2	1450	gCa/gAa	36/40	1	2	FACETS	0.842	0.773	0.914	0.842	0.773	0.914	CLONAL	1	TRUE	1	0.699724707824256	2		551	482	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245638	46245638	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	233	401	1	ENST00000334344.6:c.3732C>A	p.Cys1244Ter	p.C1244*	ENST00000334344	NM_152641.2	1244	tgC/tgA	15/21	0.699724707824256	1	FACETS	0.966	0.914	1	0.966	0.914	1	CLONAL	1	TRUE	0	0.699724707824256	1		402	448	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424777	49424777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778634045	NA	P-0052343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	295	777	1	ENST00000301067.7:c.13570C>T	p.Arg4524Trp	p.R4524W	ENST00000301067	NM_003482.3	4524	Cgg/Tgg	40/54	1	2	FACETS	0.668	0.628	0.709	0.668	0.628	0.709	SUBCLONAL	1	TRUE	1	0.699724707824256	2		778	1263	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761290	59761290	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1401	303	614	0	ENST00000259008.2:c.3117G>C	p.Glu1039Asp	p.E1039D	ENST00000259008	NM_032043.2	1039	gaG/gaC	20/20	0.584225131041247	5	FACETS	1	0.966	1			1	CLONAL	1	TRUE	NA	0.699724707824256	5		614	1704	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754068	42754068	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	239	648	0	ENST00000222329.4:c.284A>G	p.His95Arg	p.H95R	ENST00000222329	NM_006494.2	95	cAc/cGc	3/4	1	2	FACETS	0.641	0.599	0.686	0.641	0.599	0.686	SUBCLONAL	1	TRUE	1	0.699724707824256	2		648	1065	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973168	25973168	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	100	449	0	ENST00000435504.4:c.1257del	p.Ile420SerfsTer3	p.I420Sfs*3	ENST00000435504		419	ctT/ct	12/13	1	2	FACETS	0.366	0.327	0.408	0.366	0.327	0.408	SUBCLONAL	1	TRUE	1	0.699724707824256	2		449	781	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574198	41574198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	169	614	1	ENST00000263253.7:c.6483G>A	p.Met2161Ile	p.M2161I	ENST00000263253	NM_001429.3	2161	atG/atA	31/31	0.697033995460644	1	FACETS	0.415	0.382	0.45	0.415	0.382	0.45	SUBCLONAL	1	TRUE	0	0.699724707824256	1		615	756	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0052344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	12	449	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.573	0.401	0.786	0.573	0.401	0.786	SUBCLONAL	1	TRUE	1	0.11	2		449	381	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0052344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	30	853	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.923	0.742	1	0.923	0.742	1	CLONAL	1	TRUE	1	0.11	2		853	591	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187560905	187560905	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1302189943	NA	P-0052344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	20	425	0	ENST00000441802.2:c.3613C>T	p.Arg1205Ter	p.R1205*	ENST00000441802	NM_005245.3	1205	Cga/Tga	4/27	0.159201334851905	4	FACETS	1	0.819	1	0.544	0.415	0.695	CLONAL	1	TRUE	2	0.11	4		425	371	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273179	115273179	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	25	582	0	ENST00000438362.2:c.1279G>A	p.Asp427Asn	p.D427N	ENST00000438362	NM_001242891.1	427	Gat/Aat	11/20	1	2	FACETS	1	0.823	1	1	0.823	1	CLONAL	1	TRUE	1	0.11	2		582	432	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273188	115273188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	23	588	2	ENST00000438362.2:c.1270G>A	p.Glu424Lys	p.E424K	ENST00000438362	NM_001242891.1	424	Gaa/Aaa	11/20	1	2	FACETS	0.968	0.753	1	0.968	0.753	1	CLONAL	1	TRUE	1	0.11	2		590	432	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934262	48934263	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	15	476	0	ENST00000267163.4:c.718dup	p.Thr241AsnfsTer7	p.T241Nfs*7	ENST00000267163	NM_000321.2	239	-/A	7/27	1	2	FACETS	0.931	0.68	1	0.931	0.68	1	CLONAL	1	TRUE	1	0.11	2		476	293	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949107	44949107	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	35	654	2	ENST00000377967.4:c.3668G>A	p.Gly1223Asp	p.G1223D	ENST00000377967	NM_021140.2	1223	gGc/gAc	25/29	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.11	2		656	523	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0052345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	520	380	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.635622189433146	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	0	0.635622189433146	3		380	717	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0052345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	166	455	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.938	0.867	1	0.938	0.867	1	CLONAL	1	TRUE	1	0.635622189433146	2		455	557	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063718	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0052345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	306	299	0	ENST00000412916.2:c.165+2dup		p.X55_splice	ENST00000412916		55			0.635622189433146	3	FACETS	0.986	0.949	1	0.986	0.949	1	CLONAL	3	TRUE	0	0.635622189433146	3		299	429	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533256	29533256	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0052346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	14	526	0	ENST00000356175.3:c.1261-2A>T		p.X421_splice	ENST00000356175	NM_000267.3	421			0.20088655700075	1	FACETS	0.586	0.424	0.782	0.586	0.424	0.782	SUBCLONAL	1	FALSE	0	0.20088655700075	1		526	214	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326622	161326622	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764575966	NA	P-0052346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	16	1017	0	ENST00000367975.2:c.397C>T	p.Arg133Ter	p.R133*	ENST00000367975	NM_003001.3	133	Cga/Tga	5/6	1	2	FACETS	0.571	0.422	0.749	0.571	0.422	0.749	SUBCLONAL	1	FALSE	1	0.20088655700075	2		1017	279	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483133	29483134	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	89	559	0	ENST00000356175.3:c.195dup	p.Asn66Ter	p.N66*	ENST00000356175	NM_000267.3	65	gtt/gTtt	2/57	0.144640752328843	0	FACETS	0.843	0.753	0.939			1	INDETERMINATE	1	FALSE	0	0.345399596930879	0		559	400	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0052348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	385	475	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.585761917476988	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.585761917476988	1		476	911	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397516436	NA	P-0052348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	41	963	0	ENST00000269305.4:c.637C>G	p.Arg213Gly	p.R213G	ENST00000269305	NM_001126112.2	213	Cga/Gga	6/11	0.585761917476988	1	FACETS	0.094	0.077	0.112	0.094	0.077	0.112	SUBCLONAL	1	TRUE	0	0.585761917476988	1		963	1056	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129240	152129240	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1172047540	NA	P-0052348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	378	927	1	ENST00000206249.3:c.193G>A	p.Ala65Thr	p.A65T	ENST00000206249	NM_000125.3	65	Gcg/Acg	1/8	1	2	FACETS	0.994	0.943	1	0.994	0.943	1	CLONAL	1	TRUE	1	0.585761917476988	2		928	1299	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974766	21974766	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	298	369	0	ENST00000304494.5:c.61G>C	p.Ala21Pro	p.A21P	ENST00000304494	NM_000077.4	21	Gcc/Ccc	1/3	0.584470584582962	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.585761917476988	2		369	497	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402266	402266	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0052348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	358	968	0	ENST00000399788.2:c.4525A>T	p.Lys1509Ter	p.K1509*	ENST00000399788	NM_001042603.1	1509	Aag/Tag	27/28	0.562923253912714	1	FACETS	0.902	0.858	0.947	0.902	0.858	0.947	CLONAL	1	TRUE	0	0.585761917476988	1		968	958	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	61	460	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.24	2		460	456	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0052349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	1499	432	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.300767617707182	10	FACETS	0.985	0.966	1			1	CLONAL	10	TRUE	NA	0.24	10		432	2485	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0052349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	120	648	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.906	0.816	1	0.906	0.816	1	CLONAL	1	TRUE	1	0.24	2		648	1104	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165692	118165692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771057074	NA	P-0052349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	1455	603	1	ENST00000369448.3:c.202G>A	p.Asp68Asn	p.D68N	ENST00000369448	NM_017709.3	68	Gac/Aac	2/2	0.300767617707182	15	FACETS	1	0.994	1			1	CLONAL	14	TRUE	NA	0.24	15		604	2160	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383309	4383309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565430722	NA	P-0052349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	131	849	0	ENST00000261254.3:c.103G>A	p.Glu35Lys	p.E35K	ENST00000261254	NM_001759.3	35	Gag/Aag	1/5	1	2	FACETS	0.969	0.877	1	0.969	0.877	1	CLONAL	1	TRUE	1	0.24	2		849	1127	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435892	110435892	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	50	765	0	ENST00000375856.3:c.2509G>T	p.Glu837Ter	p.E837*	ENST00000375856	NM_003749.2	837	Gag/Tag	1/2	1	2	FACETS	0.454	0.384	0.532	0.454	0.384	0.532	SUBCLONAL	1	TRUE	1	0.24	2		765	918	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3795277	3795277	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0052349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	86	594	0	ENST00000262367.5:c.3914+1G>A		p.X1305_splice	ENST00000262367	NM_004380.2	1305			1	2	FACETS	0.835	0.738	0.94	0.835	0.738	0.94	CLONAL	1	TRUE	1	0.24	2		594	858	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857076	9857076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	83	558	0	ENST00000330684.3:c.4325C>T	p.Pro1442Leu	p.P1442L	ENST00000330684	NM_001134407.1	1442	cCc/cTc	13/13	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.24	2		558	674	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212054	36212054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1390	135	1182	0	ENST00000222270.7:c.1805C>T	p.Ser602Phe	p.S602F	ENST00000222270	NM_014727.1	602	tCc/tTc	3/37	1	2	FACETS	0.738	0.668	0.812	0.738	0.668	0.812	SUBCLONAL	1	TRUE	1	0.24	2		1182	1525	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546606	9546607	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0052349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	99	845	0	ENST00000353224.5:c.1415_1416delinsAA	p.Gly472Glu	p.G472E	ENST00000353224	NM_177990.2	472	gGG/gAA	5/10	1	2	FACETS	0.793	0.706	0.886	0.793	0.706	0.886	SUBCLONAL	1	TRUE	1	0.24	2		845	1040	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582169	189582169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908836	NA	P-0052349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	107	694	2	ENST00000264731.3:c.728G>A	p.Arg243Gln	p.R243Q	ENST00000264731	NM_003722.4	243	cGg/cAg	5/14	1	2	FACETS	0.902	0.808	1	0.902	0.808	1	CLONAL	1	TRUE	1	0.24	2		696	988	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586422	189586422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866267914	NA	P-0052349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	81	596	0	ENST00000264731.3:c.1046G>A	p.Gly349Glu	p.G349E	ENST00000264731	NM_003722.4	349	gGa/gAa	8/14	1	2	FACETS	0.879	0.774	0.992	0.879	0.774	0.992	CLONAL	1	TRUE	1	0.24	2		596	768	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976852	2976852	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	114	879	6	ENST00000396946.4:c.1160A>C	p.Asp387Ala	p.D387A	ENST00000396946	NM_032415.4	387	gAt/gCt	9/25	1	2	FACETS	0.833	0.748	0.923	0.833	0.748	0.923	CLONAL	1	TRUE	1	0.24	2		885	1141	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465651	8465651	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772237001	NA	P-0052350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	45	646	0	ENST00000356435.5:c.3529C>T	p.Arg1177Cys	p.R1177C	ENST00000356435		1177	Cgc/Tgc	21/35	0.219920542953896	0	FACETS	0.568	0.478	0.667			1	SUBCLONAL	1	TRUE	0	0.29	0		646	388	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223252	5223252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763535247	NA	P-0052350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	96	967	1	ENST00000357368.4:c.2551C>T	p.Arg851Cys	p.R851C	ENST00000357368	NM_002850.3	851	Cgc/Tgc	18/38	0.3	0	FACETS	1	0.925	1			1	CLONAL	1	TRUE	0	0.29	0		968	452	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107077	27107077	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	144	775	0	ENST00000324856.7:c.6688del	p.Met2230Ter	p.M2230*	ENST00000324856	NM_006015.4	2230	Atg/tg	20/20	0.3	2	FACETS	0.908	0.832	0.986	0.908	0.832	0.986	CLONAL	2	TRUE	0	0.29	2		775	547	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578422	7578423	+	inframe_insertion	In_Frame_Ins	INS	-	-	CATGTGCTG	novel	NA	P-0052351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	517	1056	0	ENST00000269305.4:c.499_507dup	p.Gln167_Met169dup	p.Q167_M169dup	ENST00000269305	NM_001126112.2	167	-/CAGCACATG	5/11	0.566191518572087	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.722216829040937	1		1056	885	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246665	41246665	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	413	759	0	ENST00000357654.3:c.883del	p.Asp295ThrfsTer3	p.D295Tfs*3	ENST00000357654	NM_007294.3	295	Gac/ac	10/23	0.722216829040937	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.722216829040937	1		759	597	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050275	13050275	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	247	711	0	ENST00000316448.5:c.227C>A	p.Ala76Asp	p.A76D	ENST00000316448	NM_004343.3	76	gCt/gAt	3/9	0.185951704980518	3	FACETS	1	0.991	1	0.668	0.628	0.709	INDETERMINATE	1	TRUE	1	0.722216829040937	3		711	697	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754482	42754489	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CCGCAGGG	CCGCAGGG	-	novel	NA	P-0052351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	136	882	0	ENST00000222329.4:c.251_257+1del		p.X84_splice	ENST00000222329	NM_006494.2	84		2/4	0.185951704980518	3	FACETS	0.606	0.551	0.664	0.303	0.275	0.332	INDETERMINATE	1	TRUE	1	0.722216829040937	3		882	846	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820536	44820536	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	190	556	0	ENST00000377967.4:c.233G>T	p.Arg78Leu	p.R78L	ENST00000377967	NM_021140.2	78	cGc/cTc	3/29	0.722216829040937	1	FACETS	0.96	0.904	1	0.96	0.904	1	CLONAL	1	TRUE	0	0.722216829040937	1		556	350	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	75	460	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.934	0.83	1	0.934	0.83	1	CLONAL	1	TRUE	1	0.647234181192922	2		460	248	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505595	186505595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	193	486	2	ENST00000323963.5:c.1003C>T	p.Arg335Cys	p.R335C	ENST00000323963		335	Cgc/Tgc	10/11	1	2	FACETS	0.967	0.899	1	0.967	0.899	1	CLONAL	1	TRUE	1	0.647234181192922	2		488	617	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097665	27097665	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0052352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	507	791	0	ENST00000324856.7:c.3254C>G	p.Ser1085Ter	p.S1085*	ENST00000324856	NM_006015.4	1085	tCa/tGa	12/20	0.632674668900198	2	FACETS	0.969	0.938	1	0.969	0.938	1	CLONAL	2	TRUE	0	0.647234181192922	2		791	808	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535316	66535316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	199	706	0	ENST00000273854.3:c.145G>A	p.Ala49Thr	p.A49T	ENST00000273854	NM_004439.5	49	Gca/Aca	1/18	1	2	FACETS	0.961	0.895	1	0.961	0.895	1	CLONAL	1	TRUE	1	0.647234181192922	2		706	640	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983123	201983123	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	708	858	0	ENST00000359651.3:c.972G>A	p.Met324Ile	p.M324I	ENST00000359651		324	atG/atA	7/8	0.645465096020691	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.647234181192922	3		858	913	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46725695	46725695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1322473345	NA	P-0052352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	405	708	0	ENST00000371975.4:c.331G>A	p.Asp111Asn	p.D111N	ENST00000371975	NM_003579.3	111	Gac/Aac	5/18	0.632674668900198	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.647234181192922	2		708	623	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998928	100998928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773960696	NA	P-0052352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	226	845	0	ENST00000325455.5:c.874G>A	p.Gly292Arg	p.G292R	ENST00000325455	NM_001202474.3	292	Ggg/Agg	1/8	0.577276518399627	3	FACETS	1	0.984	1	0.584	0.546	0.624	CLONAL	1	TRUE	1	0.647234181192922	3		845	791	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214009	108214009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	402	574	0	ENST00000278616.4:c.8329G>A	p.Gly2777Ser	p.G2777S	ENST00000278616	NM_000051.3	2777	Ggt/Agt	57/63	0.577276518399627	3	FACETS	0.934	0.893	0.975	0.934	0.893	0.975	CLONAL	2	TRUE	1	0.647234181192922	3		574	880	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210913	133210913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755805420	NA	P-0052352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	257	1043	0	ENST00000320574.5:c.5863G>A	p.Asp1955Asn	p.D1955N	ENST00000320574	NM_006231.2	1955	Gat/Aat	43/49	1	2	FACETS	0.964	0.905	1	0.964	0.905	1	CLONAL	1	TRUE	1	0.647234181192922	2		1043	824	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675211	40675211	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	220	849	0	ENST00000249776.8:c.175G>C	p.Glu59Gln	p.E59Q	ENST00000249776	NM_033286.3	59	Gag/Cag	1/9	1	2	FACETS	0.942	0.88	1	0.942	0.88	1	CLONAL	1	TRUE	1	0.647234181192922	2		849	722	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478099	99478099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1163550820	NA	P-0052352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	232	638	0	ENST00000268035.6:c.3003G>A	p.Met1001Ile	p.M1001I	ENST00000268035	NM_000875.3	1001	atG/atA	16/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.647234181192922	2		638	669	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640197	3640197	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	313	1195	0	ENST00000294008.3:c.3442G>C	p.Glu1148Gln	p.E1148Q	ENST00000294008	NM_032444.2	1148	Gaa/Caa	12/15	1	2	FACETS	0.965	0.912	1	0.965	0.912	1	CLONAL	1	TRUE	1	0.647234181192922	2		1195	1002	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367942	15367942	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	256	1003	0	ENST00000263377.2:c.1384G>C	p.Glu462Gln	p.E462Q	ENST00000263377	NM_058243.2	462	Gag/Cag	8/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.647234181192922	2		1003	775	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443377	187443377	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	181	611	0	ENST00000232014.4:c.1749C>A	p.Phe583Leu	p.F583L	ENST00000232014	NM_001130845.1	583	ttC/ttA	8/10	1	2	FACETS	0.95	0.881	1	0.95	0.881	1	CLONAL	1	TRUE	1	0.647234181192922	2		611	589	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196295	106196295	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	149	453	0	ENST00000380013.4:c.4628G>C	p.Arg1543Thr	p.R1543T	ENST00000380013	NM_001127208.2	1543	aGa/aCa	11/11	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.647234181192922	2		453	458	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531018	187531018	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	160	595	1	ENST00000441802.2:c.10005C>G	p.Phe3335Leu	p.F3335L	ENST00000441802	NM_005245.3	3335	ttC/ttG	15/27	1	2	FACETS	0.745	0.685	0.807	0.745	0.685	0.807	SUBCLONAL	1	TRUE	1	0.647234181192922	2		596	664	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665486	176665487	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0052352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	201	567	0	ENST00000439151.2:c.4171_4172dup	p.Leu1392AsnfsTer3	p.L1392Nfs*3	ENST00000439151	NM_022455.4	1390	-/GA	7/23	0.647234181192922	1	FACETS	0.942	0.884	1	0.942	0.884	1	CLONAL	1	TRUE	0	0.647234181192922	1		567	446	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120534	94120534	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	183	598	0	ENST00000369303.4:c.517G>C	p.Glu173Gln	p.E173Q	ENST00000369303	NM_004440.3	173	Gag/Cag	3/17	1	2	FACETS	0.975	0.905	1	0.975	0.905	1	CLONAL	1	TRUE	1	0.647234181192922	2		598	580	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099792	157099792	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1213064562	NA	P-0052352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	70	374	0	ENST00000346085.5:c.732del	p.Gly245AlafsTer21	p.G245Afs*21	ENST00000346085	NM_020732.3	243	ggC/gg	1/20	1	2	FACETS	0.616	0.541	0.697	0.616	0.541	0.697	SUBCLONAL	1	TRUE	1	0.647234181192922	2		374	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0052353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	651	475	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	2	TRUE	NA	0.81224073503232	2		476	801	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989557	85989557	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	123	583	0	ENST00000263360.6:c.1316G>T	p.Arg439Leu	p.R439L	ENST00000263360	NM_003797.3	439	cGa/cTa	12/12	0.81224073503232	3	FACETS	0.737	0.669	0.808	0.368	0.334	0.404	SUBCLONAL	1	TRUE	1	0.81224073503232	3		583	578	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743892	41743892	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	299	977	0	ENST00000301178.4:c.827C>A	p.Pro276Gln	p.P276Q	ENST00000301178	NM_021913.4	276	cCa/cAa	7/20	0.512651328535633	3	FACETS	1	0.951	1	0.337	0.317	0.357	CLONAL	1	TRUE	0	0.81224073503232	3		977	1025	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902626	50902626	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0052353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	76	834	0	ENST00000440232.2:c.203-2A>T		p.X68_splice	ENST00000440232	NM_002691.3	68			0.512651328535633	3	FACETS	0.347	0.303	0.393	0.116	0.101	0.131	SUBCLONAL	1	TRUE	0	0.81224073503232	3		834	759	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750657	39750657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	119	460	0	ENST00000361337.2:c.2057C>T	p.Ser686Leu	p.S686L	ENST00000361337	NM_003286.2	686	tCa/tTa	20/21	0.81224073503232	4	FACETS	0.584	0.527	0.645	0.195	0.175	0.215	SUBCLONAL	1	TRUE	1	0.81224073503232	4		460	909	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912100	56912100	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	163	710	0	ENST00000519728.1:c.1328C>T	p.Pro443Leu	p.P443L	ENST00000519728	NM_002350.3	443	cCc/cTc	12/13	0.777991561738068	3	FACETS	0.746	0.685	0.808	0.373	0.342	0.404	SUBCLONAL	1	TRUE	1	0.81224073503232	3		710	757	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0052354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	292	668	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.497632038452985	2		669	1099	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0052354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	492	464	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.332904934196415	4	FACETS	0.915	0.879	0.951			1	CLONAL	3	TRUE	NA	0.497632038452985	4		464	1079	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306676	41306676	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754008236	NA	P-0052354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	164	819	0	ENST00000373198.4:c.983G>A	p.Arg328His	p.R328H	ENST00000373198	NM_133170.3	328	cGc/cAc	7/32	0.497632038452985	3	FACETS	0.674	0.617	0.733	0.337	0.308	0.367	SUBCLONAL	1	TRUE	1	0.497632038452985	3		819	1222	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578421	7578421	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	295	993	0	ENST00000269305.4:c.509del	p.Thr170ArgfsTer4	p.T170Rfs*4	ENST00000269305	NM_001126112.2	170	aCg/ag	5/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.497632038452985	2		993	1110	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873128	136873128	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	161	540	0	ENST00000241393.3:c.370del	p.Val124SerfsTer44	p.V124Sfs*44	ENST00000241393	NM_003467.2	124	Gtc/tc	2/2	1	2	FACETS	0.934	0.859	1	0.934	0.859	1	CLONAL	1	TRUE	1	0.497632038452985	2		540	693	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845210	128845210	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142599757	NA	P-0052355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	99	948	0	ENST00000249373.3:c.704C>T	p.Ala235Val	p.A235V	ENST00000249373	NM_005631.4	235	gCg/gTg	3/12	0.266340394852977	1	FACETS	0.724	0.646	0.808	0.724	0.646	0.808	SUBCLONAL	1	TRUE	0	0.29	1		948	806	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195630	102195630	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	137	739	0	ENST00000263464.3:c.390C>A	p.Asn130Lys	p.N130K	ENST00000263464	NM_001165.4	130	aaC/aaA	2/9	0.295430667165717	5	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.29	5		739	1068	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348628	89348628	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs748038681	NA	P-0052355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1471	214	1120	0	ENST00000301030.4:c.4322T>C	p.Ile1441Thr	p.I1441T	ENST00000301030	NM_001256183.1	1441	aTa/aCa	9/13	1	2	FACETS	0.876	0.811	0.944	0.876	0.811	0.944	CLONAL	1	TRUE	1	0.29	2		1120	1685	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857283	78857283	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	119	766	0	ENST00000306801.3:c.1649A>G	p.Gln550Arg	p.Q550R	ENST00000306801	NM_020761.2	550	cAg/cGg	15/34	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.29	2		766	787	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279555	18279555	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	109	712	0	ENST00000222254.8:c.1828G>C	p.Asp610His	p.D610H	ENST00000222254	NM_005027.3	610	Gac/Cac	15/16	0.295430667165717	1	FACETS	0.852	0.766	0.944	0.852	0.766	0.944	CLONAL	1	TRUE	0	0.29	1		712	754	SUCCESS
AXL	558	MSKCC	GRCh37	19	41759598	41759598	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs984694773	NA	P-0052355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	163	1000	2	ENST00000301178.4:c.2021C>T	p.Ala674Val	p.A674V	ENST00000301178	NM_021913.4	674	gCg/gTg	17/20	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.29	2		1002	1123	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535330	66535330	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	103	913	0	ENST00000273854.3:c.131T>G	p.Leu44Arg	p.L44R	ENST00000273854	NM_004439.5	44	cTt/cGt	1/18	1	2	FACETS	0.88	0.787	0.979	0.88	0.787	0.979	CLONAL	1	TRUE	1	0.29	2		913	807	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178564	32178564	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	152	1001	1	ENST00000375023.3:c.2830A>T	p.Thr944Ser	p.T944S	ENST00000375023	NM_004557.3	944	Acc/Tcc	18/30	0.295430667165717	1	FACETS	0.891	0.814	0.972	0.891	0.814	0.972	CLONAL	1	TRUE	0	0.29	1		1002	1006	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647786	206647786	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	121	829	0	ENST00000367120.3:c.200T>A	p.Ile67Asn	p.I67N	ENST00000367120	NM_014002.3	67	aTt/aAt	4/22	1	2	FACETS	0.853	0.77	0.942	0.853	0.77	0.942	CLONAL	1	TRUE	1	0.29	2		829	978	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111502	8111503	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0052357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	159	720	0	ENST00000346208.3:c.990dup	p.Asn331GlufsTer21	p.N331Efs*21	ENST00000346208		330	agg/aGgg	5/6	0.385112189215589	4	FACETS	0.866	0.797	0.938	0.866	0.797	0.938	CLONAL	2	TRUE	2	0.401326632233924	4		720	641	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101392	27101399	+	frameshift_variant	Frame_Shift_Del	DEL	TGCCCCTG	TGCCCCTG	-	novel	NA	P-0052357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	180	627	0	ENST00000324856.7:c.4680_4687del	p.Val1561HisfsTer8	p.V1561Hfs*8	ENST00000324856	NM_006015.4	1558	tcTGCCCCTGtg/tctg	18/20	0.401326632233924	3	FACETS	1	0.985	1	0.8	0.745	0.855	CLONAL	2	TRUE	0	0.401326632233924	3		627	449	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085758	16085758	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	93	671	0	ENST00000281043.3:c.934A>G	p.Arg312Gly	p.R312G	ENST00000281043	NM_005378.4	312	Agg/Ggg	3/3	0.401326632233924	3	FACETS	1	0.964	1	0.593	0.53	0.66	CLONAL	1	TRUE	1	0.401326632233924	3		671	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934574	NA	P-0052358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	460	886	0	ENST00000269305.4:c.844C>G	p.Arg282Gly	p.R282G	ENST00000269305	NM_001126112.2	282	Cgg/Ggg	8/11	0.568373927644511	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.568373927644511	2		886	806	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805940	46805940	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	121	471	0	ENST00000290295.7:c.16T>A	p.Tyr6Asn	p.Y6N	ENST00000290295	NM_006361.5	6	Tat/Aat	1/2	0.568373927644511	2	FACETS	1	0.972	1	0.58	0.53	0.632	CLONAL	1	TRUE	0	0.568373927644511	2		471	367	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256223	41256251	+	frameshift_variant	Frame_Shift_Del	DEL	TTTTAGATGTTCAGGAGAGTTATTTTCCT	TTTTAGATGTTCAGGAGAGTTATTTTCCT	-	novel	NA	P-0052358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	156	632	0	ENST00000357654.3:c.329_357del	p.Lys110ArgfsTer2	p.K110Rfs*2	ENST00000357654	NM_007294.3	110	aAGGAAAATAACTCTCCTGAACATCTAAAA/a	6/23	0.568373927644511	2	FACETS	0.816	0.749	0.885	0.408	0.374	0.443	CLONAL	1	TRUE	0	0.568373927644511	2		632	673	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220499	1220499	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	200	881	0	ENST00000326873.7:c.592G>T	p.Ala198Ser	p.A198S	ENST00000326873	NM_000455.4	198	Gcc/Tcc	4/10	0.568373927644511	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.568373927644511	1		881	469	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10277296	10277296	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	259	925	0	ENST00000340748.4:c.821A>G	p.Glu274Gly	p.E274G	ENST00000340748		274	gAg/gGg	10/40	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.568373927644511	2		925	892	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720732	89720732	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	33	220	0	ENST00000371953.3:c.883C>G	p.Leu295Val	p.L295V	ENST00000371953	NM_000314.4	295	Cta/Gta	8/9	1	2	FACETS	0.884	0.722	1	0.884	0.722	1	CLONAL	1	TRUE	1	0.226187397662473	2		220	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574010	7574013	+	frameshift_variant	Frame_Shift_Del	DEL	CTCG	CTCG	-	novel	NA	P-0052361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	170	764	0	ENST00000269305.4:c.1014_1017del	p.Phe338LeufsTer6	p.F338Lfs*6	ENST00000269305	NM_001126112.2	338	ttCGAG/tt	10/11	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.226187397662473	2		764	1088	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62322267	62322267	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1614	88	969	2	ENST00000360203.5:c.2523C>G	p.Ser841Arg	p.S841R	ENST00000360203	NM_001283009.1	841	agC/agG	27/35	0.226187397662473	5	FACETS	0.612	0.54	0.691			1	SUBCLONAL	1	TRUE	NA	0.226187397662473	5		971	1702	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0052362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	150	594	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.294451216382038	3	FACETS	0.969	0.885	1			1	CLONAL	1	TRUE	NA	0.364919804900204	3		594	1003	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0052362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	46	542	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.316	0.265	0.372	0.316	0.265	0.372	SUBCLONAL	1	TRUE	1	0.364919804900204	2		542	798	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0052362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	281	856	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.364919804900204	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.364919804900204	1		856	965	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604655	48604655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	88	370	0	ENST00000342988.3:c.1477G>A	p.Asp493Asn	p.D493N	ENST00000342988	NM_005359.5	493	Gat/Aat	12/12	0.364919804900204	1	FACETS	0.874	0.778	0.976	0.874	0.778	0.976	CLONAL	1	TRUE	0	0.364919804900204	1		370	451	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158131	47158131	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	137	644	0	ENST00000409792.3:c.4568G>A	p.Arg1523His	p.R1523H	ENST00000409792	NM_014159.6	1523	cGt/cAt	4/21	1	2	FACETS	0.916	0.833	1	0.916	0.833	1	CLONAL	1	TRUE	1	0.364919804900204	2		644	820	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519889	NA	P-0052362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	19	503	1	ENST00000263253.7:c.4195G>T	p.Asp1399Tyr	p.D1399Y	ENST00000263253	NM_001429.3	1399	Gat/Tat	26/31	0.364919804900204	1	FACETS	0.16	0.121	0.207	0.16	0.121	0.207	SUBCLONAL	1	TRUE	0	0.364919804900204	1		504	532	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400015	49400015	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	58	733	0	ENST00000418115.1:c.322C>A	p.Pro108Thr	p.P108T	ENST00000418115	NM_001664.2	108	Ccc/Acc	4/5	1	2	FACETS	0.311	0.266	0.361	0.311	0.266	0.361	SUBCLONAL	1	TRUE	1	0.364919804900204	2		733	1021	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69207346	69207346	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	102	562	0	ENST00000462284.1:c.112C>G	p.Pro38Ala	p.P38A	ENST00000462284	NM_002392.5	38	Cca/Gca	3/11	1	2	FACETS	0.781	0.699	0.868	0.781	0.699	0.868	SUBCLONAL	1	TRUE	1	0.364919804900204	2		562	716	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974782	21974799	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGTCAGCCGAAGGCTC	CCAGTCAGCCGAAGGCTC	GCTGA	novel	NA	P-0052362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	22	243	1	ENST00000304494.5:c.28_45delinsTCAGC	p.Glu10SerfsTer12	p.E10Sfs*12	ENST00000304494	NM_000077.4	10	GAGCCTTCGGCTGACTGG/TCAGC	1/3	0.353931008624582	1	FACETS	0.483	0.376	0.606	0.483	0.376	0.606	SUBCLONAL	1	TRUE	0	0.364919804900204	1		244	204	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367293	50367293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	206	552	0	ENST00000331340.3:c.100C>T	p.Pro34Ser	p.P34S	ENST00000331340	NM_006060.4	34	Ccc/Tcc	3/8	0.329620249103964	5	FACETS	1	0.944	1	1	0.944	1	CLONAL	3	TRUE	2	0.329620249103964	5		552	615	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491397	2491397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194006438	NA	P-0052363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	175	985	0	ENST00000355716.4:c.440G>A	p.Gly147Asp	p.G147D	ENST00000355716	NM_003820.2	147	gGc/gAc	4/8	0.255013192659427	4	FACETS	0.926	0.855	1			1	CLONAL	2	TRUE	NA	0.329620249103964	4		985	762	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0052368-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	157	380	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.933	0.858	1	0.933	0.858	1	CLONAL	1	TRUE	1	0.537791474268608	2		380	626	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008324	29008324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770377283	NA	P-0052368-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	101	405	0	ENST00000282397.4:c.547C>T	p.Arg183Cys	p.R183C	ENST00000282397	NM_002019.4	183	Cgc/Tgc	5/30	1	2	FACETS	0.882	0.793	0.974	0.882	0.793	0.974	CLONAL	1	TRUE	1	0.537791474268608	2		405	426	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181358	185181359	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1560126178	NA	P-0052368-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	116	475	0	ENST00000265026.3:c.1305dup	p.His436ThrfsTer3	p.H436Tfs*3	ENST00000265026	NM_004721.4	433	-/A	8/14	1	2	FACETS	0.926	0.839	1	0.926	0.839	1	CLONAL	1	TRUE	1	0.537791474268608	2		475	466	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266509	198266509	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052368-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	119	420	0	ENST00000335508.6:c.2327A>G	p.Glu776Gly	p.E776G	ENST00000335508	NM_012433.2	776	gAa/gGa	16/25	1	2	FACETS	0.926	0.841	1	0.926	0.841	1	CLONAL	1	TRUE	1	0.537791474268608	2		420	478	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627292	86627292	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052368-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	105	432	0	ENST00000274376.6:c.667C>T	p.Gln223Ter	p.Q223*	ENST00000274376	NM_002890.2	223	Cag/Tag	2/25	1	2	FACETS	0.842	0.758	0.929	0.842	0.758	0.929	CLONAL	1	TRUE	1	0.537791474268608	2		432	464	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	170	460	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.981	0.911	1	0.981	0.911	1	CLONAL	1	TRUE	1	0.746741800431914	2		460	464	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0052374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	315	536	1	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.234505039894973	2	FACETS	1	0.994	1	0.67	0.638	0.701	INDETERMINATE	1	TRUE	0	0.746741800431914	2		537	630	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858549	9858549	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	93	658	0	ENST00000330684.3:c.2852G>A	p.Gly951Glu	p.G951E	ENST00000330684	NM_001134407.1	951	gGg/gAg	13/13	0.234505039894973	2	FACETS	0.618	0.553	0.686	0.309	0.276	0.343	INDETERMINATE	1	TRUE	0	0.746741800431914	2		658	403	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862887	9862887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868222927	NA	P-0052374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	279	765	0	ENST00000330684.3:c.2416G>A	p.Glu806Lys	p.E806K	ENST00000330684	NM_001134407.1	806	Gag/Aag	12/13	0.234505039894973	2	FACETS	1	0.994	1	0.682	0.648	0.716	INDETERMINATE	1	TRUE	0	0.746741800431914	2		765	548	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518073	8518073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1480778931	NA	P-0052374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	171	572	0	ENST00000356435.5:c.1318G>A	p.Glu440Lys	p.E440K	ENST00000356435		440	Gaa/Aaa	10/35	0.746741800431914	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.746741800431914	1		572	268	SUCCESS
ALK	238	MSKCC	GRCh37	2	29541268	29541268	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	111	467	0	ENST00000389048.3:c.1549C>T	p.His517Tyr	p.H517Y	ENST00000389048	NM_004304.4	517	Cat/Tat	8/29	0.419082509648666	1	FACETS	0.393	0.355	0.433	0.393	0.355	0.433	INDETERMINATE	1	TRUE	0	0.746741800431914	1		467	474	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251889	153251889	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	210	515	0	ENST00000281708.4:c.1117C>T	p.Pro373Ser	p.P373S	ENST00000281708	NM_033632.3	373	Cct/Tct	7/12	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.746741800431914	2		515	486	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486193	99486193	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374121578	NA	P-0052374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	144	708	0	ENST00000268035.6:c.3499C>T	p.Arg1167Trp	p.R1167W	ENST00000268035	NM_000875.3	1167	Cgg/Tgg	19/21	0.389510649543836	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.746741800431914	0		708	442	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858331	9858331	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	177	454	0	ENST00000330684.3:c.3070G>A	p.Asp1024Asn	p.D1024N	ENST00000330684	NM_001134407.1	1024	Gat/Aat	13/13	0.234505039894973	2	FACETS	1	0.991	1	0.693	0.65	0.736	INDETERMINATE	1	TRUE	0	0.746741800431914	2		454	342	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805826	46805826	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1298	139	894	0	ENST00000290295.7:c.130C>G	p.Pro44Ala	p.P44A	ENST00000290295	NM_006361.5	44	Cct/Gct	1/2	0.744548717413269	5	FACETS	0.549	0.498	0.603	0.11	0.099	0.121	SUBCLONAL	1	TRUE	0	0.746741800431914	5		894	1437	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226569	2226569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777538090	NA	P-0052374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	582	1185	0	ENST00000398665.3:c.4049C>T	p.Pro1350Leu	p.P1350L	ENST00000398665	NM_032482.2	1350	cCg/cTg	27/28	0.234505039894973	2	FACETS	1	0.995	1	0.612	0.589	0.634	INDETERMINATE	1	TRUE	0	0.746741800431914	2		1185	1274	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566719	212566720	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0052374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	71	441	1	ENST00000342788.4:c.1461_1462delinsTT	p.Arg488Trp	p.R488W	ENST00000342788	NM_005235.2	487	atCCgg/atTTgg	12/28	0.234505039894973	2	FACETS	0.53	0.465	0.599	0.265	0.232	0.3	INDETERMINATE	1	TRUE	0	0.746741800431914	2		442	359	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633234	12633234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	360	691	1	ENST00000251849.4:c.1166C>T	p.Ala389Val	p.A389V	ENST00000251849	NM_002880.3	389	gCc/gTc	11/17	0.190557373779135	4	FACETS	0.878	0.835	0.922	0.878	0.835	0.922	INDETERMINATE	2	TRUE	2	0.746741800431914	4		692	959	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877210	151877210	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs757303272	NA	P-0052374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	90	372	0	ENST00000262189.6:c.7151G>A	p.Arg2384Gln	p.R2384Q	ENST00000262189	NM_170606.2	2384	cGg/cAg	37/59	0.283046584671971	4	FACETS	0.727	0.646	0.813	0.364	0.323	0.407	INDETERMINATE	1	TRUE	2	0.746741800431914	4		372	579	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939496	68939496	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	355	485	0	ENST00000288368.4:c.481C>A	p.Pro161Thr	p.P161T	ENST00000288368	NM_024870.2	161	Ccc/Acc	5/40	0.201521956567634	4	FACETS	0.864	0.827	0.9	0.648	0.62	0.675	INDETERMINATE	3	TRUE	0	0.746741800431914	4		485	641	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974704	21974724	+	inframe_deletion	In_Frame_Del	DEL	CGGTGCGTTGGGCAGCGCCCC	CGGTGCGTTGGGCAGCGCCCC	-	novel	NA	P-0052374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	345	528	0	ENST00000304494.5:c.103_123del	p.Gly35_Pro41del	p.G35_P41del	ENST00000304494	NM_000077.4	35	GGGGCGCTGCCCAACGCACCG/-	1/3	0.746741800431914	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.746741800431914	1		528	521	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	124	460	0				ENST00000310581	NM_198253.2	-/1132			0.199196049521712	3	FACETS	0.873	0.797	0.953	0.873	0.797	0.953	INDETERMINATE	2	TRUE	1	0.39988683404332	3		460	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0052375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	420	571	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.297222442581435	3	FACETS	0.995	0.954	1	0.995	0.954	1	CLONAL	3	TRUE	0	0.39988683404332	3		571	844	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568668	41568668	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0052375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	65	244	0	ENST00000263253.7:c.4617+1G>A		p.X1539_splice	ENST00000263253	NM_001429.3	1539			0.154674433753692	3	FACETS	1	0.943	1	0.574	0.5	0.652	INDETERMINATE	1	TRUE	1	0.39988683404332	3		244	340	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25498371	25498371	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	103	474	0	ENST00000264709.3:c.490G>A	p.Glu164Lys	p.E164K	ENST00000264709	NM_175629.2	164	Gag/Aag	5/23	1	2	FACETS	0.87	0.781	0.965	0.87	0.781	0.965	CLONAL	1	TRUE	1	0.39988683404332	2		474	592	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248367	59248367	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	148	347	0	ENST00000371222.2:c.376A>T	p.Thr126Ser	p.T126S	ENST00000371222	NM_002228.3	126	Acg/Tcg	1/1	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.39988683404332	2		347	523	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200971	108200971	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	21	370	0	ENST00000278616.4:c.7338G>C	p.Glu2446Asp	p.E2446D	ENST00000278616	NM_000051.3	2446	gaG/gaC	50/63	0.39988683404332	1	FACETS	0.221	0.17	0.281	0.221	0.17	0.281	SUBCLONAL	1	TRUE	0	0.39988683404332	1		370	380	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43700242	43700242	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	42	571	0	ENST00000382044.4:c.5645T>C	p.Val1882Ala	p.V1882A	ENST00000382044	NM_001141980.1	1882	gTa/gCa	27/28	0.39988683404332	1	FACETS	0.268	0.223	0.318	0.268	0.223	0.318	SUBCLONAL	1	TRUE	0	0.39988683404332	1		571	628	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831280	3831280	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	94	396	0	ENST00000262367.5:c.1601G>C	p.Gly534Ala	p.G534A	ENST00000262367	NM_004380.2	534	gGa/gCa	7/31	1	2	FACETS	0.846	0.754	0.942	0.846	0.754	0.942	CLONAL	1	TRUE	1	0.39988683404332	2		396	556	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378294	225378294	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	137	293	0	ENST00000264414.4:c.601T>C	p.Tyr201His	p.Y201H	ENST00000264414	NM_003590.4	201	Tat/Cat	5/16	1	2	FACETS	0.791	0.726	0.858	1	0.989	1	SUBCLONAL	2	TRUE	1	0.39988683404332	2		293	433	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458293	12458293	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	158	508	0	ENST00000287820.6:c.910G>C	p.Glu304Gln	p.E304Q	ENST00000287820	NM_015869.4	304	Gag/Cag	6/7	0.154674433753692	3	FACETS	1	0.988	1	0.717	0.659	0.777	INDETERMINATE	1	TRUE	1	0.39988683404332	3		508	661	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971059	21971081	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCGGTGCAGCACCACCAGCGT	GCCCGGTGCAGCACCACCAGCGT	-	novel	NA	P-0052375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	245	486	0	ENST00000304494.5:c.277_299del	p.Thr93ArgfsTer19	p.T93Rfs*19	ENST00000304494	NM_000077.4	93	ACGCTGGTGGTGCTGCACCGGGCc/c	2/3	0.39988683404332	1	FACETS	0.809	0.762	0.857	1	0.994	1	CLONAL	2	TRUE	0	0.39988683404332	1		486	606	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0052378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	95	1087	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.798	0.71	0.892	0.798	0.71	0.892	SUBCLONAL	1	TRUE	1	0.31	2		1087	768	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0052378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	80	537	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.31	2		537	507	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680489	241680489	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200007371	NA	P-0052378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	79	456	0	ENST00000366560.3:c.260G>A	p.Arg87His	p.R87H	ENST00000366560	NM_000143.3	87	cGc/cAc	2/10	1	2	FACETS	0.819	0.721	0.925	0.819	0.721	0.925	CLONAL	1	TRUE	1	0.31	2		456	622	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881573	111881573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	129	815	1	ENST00000393256.3:c.251G>A	p.Arg84Lys	p.R84K	ENST00000393256	NM_006538.4	84	aGa/aAa	2/4	1	2	FACETS	0.849	0.769	0.934	0.849	0.769	0.934	CLONAL	1	TRUE	1	0.31	2		816	980	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44515577	44515577	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	165	928	0	ENST00000291552.4:c.319G>C	p.Asp107His	p.D107H	ENST00000291552	NM_006758.2	107	Gac/Cac	5/8	1	2	FACETS	0.982	0.901	1	0.982	0.901	1	CLONAL	1	TRUE	1	0.31	2		928	1084	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982502	25982502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	56	325	0	ENST00000435504.4:c.788G>A	p.Arg263Lys	p.R263K	ENST00000435504		263	aGa/aAa	9/13	1	2	FACETS	0.834	0.717	0.962	0.834	0.717	0.962	CLONAL	1	TRUE	1	0.31	2		325	433	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059213	27059213	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	95	640	0	ENST00000324856.7:c.1850C>A	p.Ser617Ter	p.S617*	ENST00000324856	NM_006015.4	617	tCa/tAa	4/20	1	2	FACETS	0.755	0.671	0.844	0.755	0.671	0.844	SUBCLONAL	1	TRUE	1	0.31	2		640	812	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982507	25982507	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	52	309	0	ENST00000435504.4:c.783G>T	p.Met261Ile	p.M261I	ENST00000435504		261	atG/atT	9/13	1	2	FACETS	0.832	0.711	0.965	0.832	0.711	0.965	CLONAL	1	TRUE	1	0.31	2		309	403	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80074565	80074565	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	97	588	0	ENST00000265081.6:c.2345C>G	p.Ser782Cys	p.S782C	ENST00000265081	NM_002439.4	782	tCt/tGt	17/24	1	2	FACETS	0.849	0.757	0.947	0.849	0.757	0.947	CLONAL	1	TRUE	1	0.31	2		588	737	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704651	117704651	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	55	331	0	ENST00000368508.3:c.2325G>C	p.Leu775Phe	p.L775F	ENST00000368508	NM_002944.2	775	ttG/ttC	16/43	0.164357566183657	1	FACETS	0.721	0.618	0.832	0.721	0.618	0.832	INDETERMINATE	1	TRUE	0	0.31	1		331	416	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592288	29592288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs185660700	NA	P-0052379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	32	304	0	ENST00000356175.3:c.4703C>T	p.Thr1568Met	p.T1568M	ENST00000356175	NM_000267.3	1568	aCg/aTg	35/57	1	2	FACETS	0.359	0.291	0.435	0.359	0.291	0.435	SUBCLONAL	1	TRUE	1	0.515426349121861	2		304	346	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235912	133235912	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745349336	NA	P-0052379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	168	665	0	ENST00000320574.5:c.3244C>T	p.Arg1082Cys	p.R1082C	ENST00000320574	NM_006231.2	1082	Cgc/Tgc	26/49	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.515426349121861	2		665	594	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875980	76875980	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	88	366	0	ENST00000373344.5:c.5155G>C	p.Asp1719His	p.D1719H	ENST00000373344	NM_000489.3	1719	Gat/Cat	20/35	NA	2	FACETS	0.674	0.598	0.754			1	INDETERMINATE	1	TRUE	NA	0.49116444321672	2		366	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0052381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	404	475	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.728366499228271	1	FACETS	0.995	0.956	1	0.995	0.956	1	CLONAL	1	TRUE	0	0.728366499228271	1		476	709	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844702	156844702	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765681685	NA	P-0052381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2387	504	940	1	ENST00000524377.1:c.1256C>T	p.Ser419Leu	p.S419L	ENST00000524377	NM_002529.3	419	tCg/tTg	11/17	0.647566101139738	5	FACETS	1	0.954	1			1	CLONAL	1	TRUE	NA	0.728366499228271	5		941	2891	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129474	152129474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	194	343	0	ENST00000206249.3:c.427G>A	p.Glu143Lys	p.E143K	ENST00000206249	NM_000125.3	143	Gag/Aag	1/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.728366499228271	2		343	513	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798966	45799003	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCGCCTGTCCAGGTCCATCTCATCTTCTGCCTGTCAA	CCCGCCTGTCCAGGTCCATCTCATCTTCTGCCTGTCAA	-	novel	NA	P-0052381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	311	818	0	ENST00000450313.1:c.349-7_379del		p.X117_splice	ENST00000450313	NM_012222.2	117		4/16	1	2	FACETS	0.655	0.617	0.695	0.655	0.617	0.695	SUBCLONAL	1	TRUE	1	0.728366499228271	2		818	1303	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783753	50783753	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	356	649	0	ENST00000398568.2:c.144G>C	p.Gln48His	p.Q48H	ENST00000398568	NM_001042412.1	48	caG/caC	3/18	1	2	FACETS	0.982	0.933	1	0.982	0.933	1	CLONAL	1	TRUE	1	0.728366499228271	2		649	995	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024453	31024453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	862	773	0	ENST00000375687.4:c.3938C>T	p.Thr1313Ile	p.T1313I	ENST00000375687	NM_015338.5	1313	aCc/aTc	13/13	0.715985973017549	3	FACETS	0.986	0.958	1	0.986	0.958	1	CLONAL	2	TRUE	1	0.728366499228271	3		773	1638	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434500	140434500	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	249	379	0	ENST00000288602.6:c.2198T>G	p.Leu733Trp	p.L733W	ENST00000288602	NM_004333.4	733	tTg/tGg	18/18	0.728366499228271	1	FACETS	0.923	0.875	0.971	0.923	0.875	0.971	CLONAL	1	TRUE	0	0.728366499228271	1		379	471	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0052382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	192	542	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.89	0.825	0.957	0.89	0.825	0.957	CLONAL	1	TRUE	1	0.548298797194656	2		542	787	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0052382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	198	464	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.918	0.852	0.986	0.918	0.852	0.986	CLONAL	1	TRUE	1	0.548298797194656	2		464	787	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669547	88669547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56394626	NA	P-0052382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	217	466	0	ENST00000360948.2:c.1351G>A	p.Val451Ile	p.V451I	ENST00000360948	NM_001012338.2	451	Gtc/Atc	12/19	1	2	FACETS	0.985	0.918	1	0.985	0.918	1	CLONAL	1	TRUE	1	0.548298797194656	2		466	804	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531833	46531833	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	33	298	0	ENST00000262741.5:c.514G>A	p.Asp172Asn	p.D172N	ENST00000262741	NM_003629.3	172	Gat/Aat	5/10	1	2	FACETS	0.212	0.172	0.257	0.212	0.172	0.257	SUBCLONAL	1	TRUE	1	0.548298797194656	2		298	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0052383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	811	646	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.69047250716413	3	FACETS	0.977	0.956	0.997	0.977	0.956	0.997	CLONAL	3	TRUE	0	0.687532865151538	3		646	1082	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0052383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	124	389	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	0.679183062231354	1	FACETS	0.954	0.883	1	0.954	0.883	1	CLONAL	1	TRUE	0	0.687532865151538	1		389	248	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513663	41513663	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	285	720	0	ENST00000263253.7:c.567T>G	p.Asn189Lys	p.N189K	ENST00000263253	NM_001429.3	189	aaT/aaG	2/31	0.69047250716413	3	FACETS	1	0.975	1	0.355	0.333	0.377	CLONAL	1	TRUE	0	0.687532865151538	3		720	1047	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117874123	117874123	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	119	436	0	ENST00000297338.2:c.331C>T	p.Pro111Ser	p.P111S	ENST00000297338	NM_006265.2	111	Cct/Tct	4/14	0.687532865151538	7	FACETS	0.837	0.754	0.926			1	CLONAL	1	TRUE	NA	0.687532865151538	7		436	1124	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191506	10191506	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs5030820	NA	P-0052384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	47	557	0	ENST00000256474.2:c.499C>T	p.Arg167Trp	p.R167W	ENST00000256474	NM_000551.3	167	Cgg/Tgg	3/3	0.155816896740807	1	FACETS	0.7	0.589	0.823	0.7	0.589	0.823	SUBCLONAL	1	TRUE	0	0.16	1		557	772	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437795	52437795	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	119	803	0	ENST00000460680.1:c.1366C>T	p.Gln456Ter	p.Q456*	ENST00000460680	NM_004656.3	456	Cag/Tag	13/17	0.155816896740807	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.16	1		803	1124	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30061019	30061019	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs764034925	NA	P-0052384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	50	444	2	ENST00000338641.4:c.851A>G	p.Lys284Arg	p.K284R	ENST00000338641	NM_000268.3	284	aAg/aGg	9/16	0.3	1	FACETS	0.848	0.718	0.991	0.848	0.718	0.991	CLONAL	1	TRUE	0	0.16	1		446	678	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098424	47098425	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	AG	novel	NA	P-0052384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	59	633	1	ENST00000409792.3:c.6849_6850delinsCT	p.Gln2283_Gln2284delinsHisTer	p.Q2283_Q2284delinsH*	ENST00000409792	NM_014159.6	2283	caGCag/caCTag	15/21	0.155816896740807	1	FACETS	0.784	0.673	0.906	0.784	0.673	0.906	CLONAL	1	TRUE	0	0.16	1		634	865	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539731	187539731	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	32	455	0	ENST00000441802.2:c.8009C>G	p.Thr2670Ser	p.T2670S	ENST00000441802	NM_005245.3	2670	aCt/aGt	10/27	1	2	FACETS	0.645	0.522	0.785	0.645	0.522	0.785	SUBCLONAL	1	TRUE	1	0.16	2		455	620	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0052385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	195	668	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.425407548132233	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.425407548132233	1		669	620	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115267898	115267898	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	248	523	0	ENST00000438362.2:c.1835T>G	p.Leu612Trp	p.L612W	ENST00000438362	NM_001242891.1	612	tTg/tGg	15/20	0.425407548132233	3	FACETS	0.975	0.916	1	0.975	0.916	1	CLONAL	2	TRUE	1	0.425407548132233	3		523	725	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120535105	120535105	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	266	559	0	ENST00000229340.5:c.550C>A	p.Gln184Lys	p.Q184K	ENST00000229340	NM_006861.6	184	Cag/Aag	6/6	0.181525097417313	5	FACETS	1	0.963	1			1	INDETERMINATE	2	TRUE	NA	0.425407548132233	5		559	988	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955484	48955484	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	170	370	0	ENST00000267163.4:c.1600A>T	p.Ser534Cys	p.S534C	ENST00000267163	NM_000321.2	534	Agt/Tgt	17/27	0.425407548132233	2	FACETS	0.912	0.848	0.978	0.912	0.848	0.978	CLONAL	2	TRUE	0	0.425407548132233	2		370	438	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618802	37618802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	118	578	0	ENST00000447079.4:c.478G>A	p.Asp160Asn	p.D160N	ENST00000447079	NM_015083.1	160	Gac/Aac	1/14	0.425407548132233	2	FACETS	0.923	0.835	1	0.462	0.417	0.508	CLONAL	1	TRUE	0	0.425407548132233	2		578	601	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42842610	42842610	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	335	814	0	ENST00000398585.3:c.1247G>C	p.Cys416Ser	p.C416S	ENST00000398585	NM_001135099.1	416	tGc/tCc	11/14	0.425407548132233	2	FACETS	0.97	0.922	1	0.97	0.922	1	CLONAL	2	TRUE	0	0.425407548132233	2		814	812	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045989	180046228	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGCCCGCGGCGCCCCGCAGGCCGCCCGCTCACCGCGCAGGGGCTGAAGGCGTCCCGCTTGGCGCGCAGGAAGTTGGAGAGGTTGCCGTACTTGCAGAACTCCACGATCACCATGAGGGGGCCTGCGGCGGGACCGGGCGGCGGCCGTGCGTTCGGAACCCGGGGCGCGCTGCGGGCGCGCTCCGCGTTTGCACCCGCGCCCCCTCCCGCCCGCGGCGCCCCGCGCCCGGGGTCTCGCCGT	CGCCCGCGGCGCCCCGCAGGCCGCCCGCTCACCGCGCAGGGGCTGAAGGCGTCCCGCTTGGCGCGCAGGAAGTTGGAGAGGTTGCCGTACTTGCAGAACTCCACGATCACCATGAGGGGGCCTGCGGCGGGACCGGGCGGCGGCCGTGCGTTCGGAACCCGGGGCGCGCTGCGGGCGCGCTCCGCGTTTGCACCCGCGCCCCCTCCCGCCCGCGGCGCCCCGCGCCCGGGGTCTCGCCGT	-	novel	NA	P-0052385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	368	169	0	ENST00000261937.6:c.2761+25_2850+32del		p.X921_splice	ENST00000261937	NM_182925.4	921		20/30	0.425407548132233	6	FACETS	0.922	0.887	0.956	1	0.991	1	CLONAL	6	TRUE	1	0.425407548132233	6		169	579	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	245	503	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.764586527224086	2		503	623	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	206	435	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.945	0.884	1	0.945	0.884	1	CLONAL	1	TRUE	1	0.764586527224086	2		435	570	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	72	395	6	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	2	FACETS	0.566	0.498	0.638	0.566	0.498	0.638	SUBCLONAL	1	TRUE	1	0.764586527224086	2		401	333	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	388	1140	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.961	0.915	1	0.961	0.915	1	CLONAL	1	TRUE	1	0.764586527224086	2		1144	1056	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	264	593	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.764586527224086	2		593	612	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	238	499	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.964	0.905	1	0.964	0.905	1	CLONAL	1	TRUE	1	0.764586527224086	2		500	646	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	195	468	0	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	1	2	FACETS	0.987	0.921	1	0.987	0.921	1	CLONAL	1	TRUE	1	0.764586527224086	2		468	517	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142000	108142000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779830	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	287	631	1	ENST00000278616.4:c.2944C>T	p.Arg982Cys	p.R982C	ENST00000278616	NM_000051.3	982	Cgt/Tgt	20/63	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.764586527224086	2		632	658	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	232	349	9	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.764586527224086	2		358	591	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	286	643	14	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.764586527224086	2		657	722	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661664	227661664	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs761880048	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	354	1016	16	ENST00000305123.5:c.1791del	p.His598ThrfsTer38	p.H598Tfs*38	ENST00000305123	NM_005544.2	597	ggG/gg	1/2	1	2	FACETS	0.978	0.929	1	0.978	0.929	1	CLONAL	1	TRUE	1	0.764586527224086	2		1032	947	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785964	135785964	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs118203506	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	329	937	0	ENST00000298552.3:c.1257del	p.Arg420GlyfsTer20	p.R420Gfs*20	ENST00000298552	NM_001162426.1	419	ccC/cc	12/23	1	2	FACETS	0.989	0.938	1	0.989	0.938	1	CLONAL	1	TRUE	1	0.764586527224086	2		937	870	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831357	72831358	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTG	rs34918837	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	122	627	3	ENST00000268489.5:c.5221_5223dup	p.Gln1741dup	p.Q1741dup	ENST00000268489	NM_006885.3	1741	-/CAA	9/10	1	2	FACETS	0.533	0.483	0.585	0.533	0.483	0.585	SUBCLONAL	1	TRUE	1	0.764586527224086	2		630	599	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029445	16029446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	198	418	2	ENST00000268712.3:c.1584dup	p.Glu529ArgfsTer7	p.E529Rfs*7	ENST00000268712	NM_006311.3	528	-/A	15/46	1	2	FACETS	0.86	0.802	0.92	0.86	0.802	0.92	CLONAL	1	TRUE	1	0.764586527224086	2		420	602	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528849	157528849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761204913	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	303	782	1	ENST00000346085.5:c.6574G>A	p.Val2192Ile	p.V2192I	ENST00000346085	NM_020732.3	2192	Gta/Ata	20/20	1	2	FACETS	0.999	0.946	1	0.999	0.946	1	CLONAL	1	TRUE	1	0.764586527224086	2		783	793	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248123	59248123	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs370122841	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	114	259	0	ENST00000371222.2:c.620C>A	p.Pro207Gln	p.P207Q	ENST00000371222	NM_002228.3	207	cCg/cAg	1/1	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.764586527224086	2		259	262	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271271	1271271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199422301	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	270	701	0	ENST00000310581.5:c.2431C>T	p.Arg811Cys	p.R811C	ENST00000310581	NM_198253.2	811	Cgc/Tgc	8/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.764586527224086	2		701	668	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780224	9780224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368722127	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	440	1081	0	ENST00000377346.4:c.1394C>T	p.Thr465Met	p.T465M	ENST00000377346	NM_005026.3	465	aCg/aTg	11/24	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.764586527224086	2		1081	1075	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332152	70332153	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1196853334	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	106	351	1	ENST00000373644.4:c.65dup	p.Lys23GlufsTer37	p.K23Efs*37	ENST00000373644	NM_030625.2	19	-/A	2/12	1	2	FACETS	0.76	0.687	0.835	0.76	0.687	0.835	SUBCLONAL	1	TRUE	1	0.764586527224086	2		352	365	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339002	225339002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	265	603	0	ENST00000264414.4:c.2267G>A	p.Arg756Gln	p.R756Q	ENST00000264414	NM_003590.4	756	cGa/cAa	16/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.764586527224086	2		603	667	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288788	15288789	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	47	145	0	ENST00000263388.2:c.3950dup	p.Gly1318ArgfsTer245	p.G1318Rfs*245	ENST00000263388	NM_000435.2	1317	cca/ccCa	24/33	1	2	FACETS	0.707	0.606	0.814	0.707	0.606	0.814	SUBCLONAL	1	TRUE	1	0.764586527224086	2		145	174	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942053	71942053	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	124	928	0	ENST00000298229.2:c.1322del	p.Asn441ThrfsTer2	p.N441Tfs*2	ENST00000298229	NM_001567.3	439	ccA/cc	12/28	1	2	FACETS	0.324	0.292	0.358	0.324	0.292	0.358	SUBCLONAL	1	TRUE	1	0.764586527224086	2		928	1001	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	895	1142	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.998	0.978	1	1	0.999	1	CLONAL	2	TRUE	1	0.764586527224086	2		1146	1173	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210440	36210440	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	348	883	0	ENST00000222270.7:c.433C>T	p.Arg145Ter	p.R145*	ENST00000222270	NM_014727.1	145	Cga/Tga	2/37	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.764586527224086	2		883	825	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026915	6026915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782602	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	78	133	0	ENST00000265849.7:c.1481C>T	p.Ser494Leu	p.S494L	ENST00000265849	NM_000535.5	494	tCg/tTg	11/15	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.764586527224086	2		133	183	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158026	27158026	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	326	860	1	ENST00000380036.4:c.255del	p.Val86LeufsTer31	p.V86Lfs*31	ENST00000380036	NM_000459.3	84	Aaa/aa	2/23	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.764586527224086	2		861	850	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	456	641	23	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	1	2	FACETS	0.866	0.837	0.894	1	0.997	1	CLONAL	2	TRUE	1	0.764586527224086	2		664	689	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226279	2226281	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	395	1120	0	ENST00000326181.6:c.1895_1897del	p.Asn632del	p.N632del	ENST00000326181	NM_032271.2	631	gACAac/gac	20/21	1	2	FACETS	0.923	0.878	0.967	0.923	0.878	0.967	CLONAL	1	TRUE	1	0.764586527224086	2		1120	1120	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112434	115112434	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs906508818	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	301	774	0	ENST00000257566.3:c.1306C>T	p.Arg436Cys	p.R436C	ENST00000257566	NM_016569.3	436	Cgc/Tgc	7/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.764586527224086	2		774	764	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605204	46605204	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1459319402	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	212	571	7	ENST00000263734.3:c.1421G>C	p.Ser474Thr	p.S474T	ENST00000263734	NM_001430.4	474	aGc/aCc	10/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.764586527224086	2		578	537	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223229	36223229	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749130618	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	220	1299	1	ENST00000222270.7:c.5779C>T	p.Arg1927Trp	p.R1927W	ENST00000222270	NM_014727.1	1927	Cgg/Tgg	28/37	1	2	FACETS	0.475	0.441	0.51	0.475	0.441	0.51	SUBCLONAL	1	TRUE	1	0.764586527224086	2		1300	1212	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424177	49424178	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	58	546	1	ENST00000301067.7:c.13884dup	p.Thr4629HisfsTer18	p.T4629Hfs*18	ENST00000301067	NM_003482.3	4628	-/C	42/54	1	2	FACETS	0.359	0.309	0.413	0.359	0.309	0.413	SUBCLONAL	1	TRUE	1	0.764586527224086	2		547	423	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057831	27057832	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	410	880	0	ENST00000324856.7:c.1542_1543del	p.Gln515AlafsTer107	p.Q515Afs*107	ENST00000324856	NM_006015.4	513	tcCTct/tcct	3/20	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.764586527224086	2		880	945	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653815	89653815	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1064796886	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	226	521	0	ENST00000371953.3:c.113C>G	p.Pro38Arg	p.P38R	ENST00000371953	NM_000314.4	38	cCt/cGt	2/9	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.764586527224086	2		521	557	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849662	68849662	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs863224725	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	274	673	0	ENST00000261769.5:c.1565C>T	p.Thr522Ile	p.T522I	ENST00000261769	NM_004360.3	522	aCa/aTa	10/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.764586527224086	2		673	657	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981492	70981492	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	443	1070	0	ENST00000276594.2:c.604C>A	p.Leu202Met	p.L202M	ENST00000276594	NM_024504.3	202	Ctg/Atg	2/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.764586527224086	2		1070	1082	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93607789	93607789	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	220	599	0	ENST00000375746.1:c.496del	p.Met166CysfsTer18	p.M166Cfs*18	ENST00000375746	NM_001174167.1	164	gAa/ga	3/14	1	2	FACETS	0.883	0.826	0.941	0.883	0.826	0.941	CLONAL	1	TRUE	1	0.764586527224086	2		599	652	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724871	43724872	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	241	495	0	ENST00000382044.4:c.3195dup	p.Asn1066GlufsTer20	p.N1066Efs*20	ENST00000382044	NM_001141980.1	1065	-/G	17/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.764586527224086	2		495	594	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662337	227662337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762739828	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	425	972	3	ENST00000305123.5:c.1118G>A	p.Arg373His	p.R373H	ENST00000305123	NM_005544.2	373	cGc/cAc	1/2	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.764586527224086	2		975	1051	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106295	27106295	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	349	873	0	ENST00000324856.7:c.5908del	p.Leu1970PhefsTer45	p.L1970Ffs*45	ENST00000324856	NM_006015.4	1969	aCc/ac	20/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.764586527224086	2		873	900	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330525	65330525	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	292	615	0	ENST00000342505.4:c.1121A>G	p.His374Arg	p.H374R	ENST00000342505	NM_002227.2	374	cAc/cGc	8/25	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.764586527224086	2		615	694	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120509067	120509067	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	260	611	0	ENST00000256646.2:c.1499G>T	p.Ser500Ile	p.S500I	ENST00000256646	NM_024408.3	500	aGc/aTc	9/34	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.764586527224086	2		611	672	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161298269	161298269	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	201	457	0	ENST00000367975.2:c.161C>A	p.Pro54His	p.P54H	ENST00000367975	NM_003001.3	54	cCc/cAc	3/6	0.764586527224086	4	FACETS	1	0.967	1	0.357	0.331	0.384	CLONAL	1	TRUE	1	0.764586527224086	4		457	867	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749960	162749960	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	264	677	0	ENST00000367921.3:c.2492G>A	p.Cys831Tyr	p.C831Y	ENST00000367921	NM_006182.2	831	tGc/tAc	18/18	0.764586527224086	4	FACETS	0.996	0.932	1	0.332	0.31	0.354	CLONAL	1	TRUE	1	0.764586527224086	4		677	1224	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163298643	163298643	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	276	682	0	ENST00000271452.3:c.287del	p.Leu96CysfsTer6	p.L96Cfs*6	ENST00000271452	NM_145697.2	95	Ttt/tt	5/14	0.764586527224086	4	FACETS	1	0.96	1	0.344	0.322	0.366	CLONAL	1	TRUE	1	0.764586527224086	4		682	1236	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012859	176012859	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	176	480	0	ENST00000367669.3:c.1517C>T	p.Ser506Leu	p.S506L	ENST00000367669	NM_022457.5	506	tCa/tTa	13/20	0.764586527224086	4	FACETS	0.925	0.853	1	0.308	0.284	0.334	CLONAL	1	TRUE	1	0.764586527224086	4		480	878	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097695	8097695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	280	631	1	ENST00000346208.3:c.77C>T	p.Thr26Met	p.T26M	ENST00000346208		26	aCg/aTg	2/6	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.764586527224086	2		632	670	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376815	118376815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs942230098	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	267	620	0	ENST00000534358.1:c.10208C>T	p.Pro3403Leu	p.P3403L	ENST00000534358	NM_005933.3	3403	cCg/cTg	27/36	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.764586527224086	2		620	633	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435473	49435474	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	379	1013	0	ENST00000301067.7:c.6198_6199del	p.Asp2066GlufsTer15	p.D2066Efs*15	ENST00000301067	NM_003482.3	2066	gaTAac/gaac	30/54	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.764586527224086	2		1013	975	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599039	28599039	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	126	674	0	ENST00000241453.7:c.2249A>G	p.Asp750Gly	p.D750G	ENST00000241453	NM_004119.2	750	gAt/gGt	18/24	1	2	FACETS	0.423	0.383	0.465	0.423	0.383	0.465	SUBCLONAL	1	TRUE	1	0.764586527224086	2		674	779	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001928	29001928	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	257	595	0	ENST00000282397.4:c.1237A>G	p.Asn413Asp	p.N413D	ENST00000282397	NM_002019.4	413	Aat/Gat	9/30	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.764586527224086	2		595	656	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570372	95570372	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	210	418	0	ENST00000393063.1:c.3361T>C	p.Tyr1121His	p.Y1121H	ENST00000393063	NM_030621.3	1121	Tac/Cac	22/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.764586527224086	2		418	497	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701149	43701149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756730049	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	310	727	1	ENST00000382044.4:c.5546G>A	p.Arg1849His	p.R1849H	ENST00000382044	NM_001141980.1	1849	cGt/cAt	26/28	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.764586527224086	2		728	797	SUCCESS
BLM	641	MSKCC	GRCh37	15	91308539	91308540	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	236	522	0	ENST00000355112.3:c.2089_2090del	p.Leu697ValfsTer43	p.L697Vfs*43	ENST00000355112	NM_000057.2	696	agTTtg/agtg	9/22	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.764586527224086	2		522	584	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3634841	3634841	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs752736478	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	343	867	0	ENST00000294008.3:c.4668del	p.Val1558CysfsTer3	p.V1558Cfs*3	ENST00000294008	NM_032444.2	1556	ccC/cc	13/15	1	2	FACETS	0.942	0.894	0.991	0.942	0.894	0.991	CLONAL	1	TRUE	1	0.764586527224086	2		867	952	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042034	14042034	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	262	543	0	ENST00000311895.7:c.2585del	p.Asn862ThrfsTer5	p.N862Tfs*5	ENST00000311895	NM_005236.2	861	Aaa/aa	11/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.764586527224086	2		543	618	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108619	8108619	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs750194641	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	134	890	0	ENST00000585124.1:c.776T>C	p.Ile259Thr	p.I259T	ENST00000585124	NM_004217.3	259	aTt/aCt	8/9	1	2	FACETS	0.337	0.305	0.37	0.337	0.305	0.37	SUBCLONAL	1	TRUE	1	0.764586527224086	2		890	1041	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362500	40362500	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219718677	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	295	753	3	ENST00000293328.3:c.1696C>T	p.Arg566Trp	p.R566W	ENST00000293328	NM_012448.3	566	Cgg/Tgg	14/19	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.764586527224086	2		756	717	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40451816	40451816	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1480453414	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	286	782	0	ENST00000345506.4:c.598C>T	p.Arg200Trp	p.R200W	ENST00000345506	NM_003152.3	200	Cgg/Tgg	7/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.764586527224086	2		782	713	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435407	56435408	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	412	1134	0	ENST00000407977.2:c.1729dup	p.Gln577ProfsTer19	p.Q577Pfs*19	ENST00000407977		577	cag/cCag	9/10	1	2	FACETS	0.966	0.921	1	0.966	0.921	1	CLONAL	1	TRUE	1	0.764586527224086	2		1134	1116	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763442	59763442	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	285	744	0	ENST00000259008.2:c.2660del	p.Lys887SerfsTer10	p.K887Sfs*10	ENST00000259008	NM_032043.2	887	aAg/ag	19/20	1	2	FACETS	0.969	0.916	1	0.969	0.916	1	CLONAL	1	TRUE	1	0.764586527224086	2		744	769	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248548	212248548	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	278	758	0	ENST00000342788.4:c.3719C>A	p.Pro1240His	p.P1240H	ENST00000342788	NM_005235.2	1240	cCt/cAt	28/28	1	2	FACETS	0.975	0.92	1	0.975	0.92	1	CLONAL	1	TRUE	1	0.764586527224086	2		758	746	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346767	225346775	+	inframe_deletion	In_Frame_Del	DEL	TCAGGGATA	TCAGGGATA	-	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	169	598	0	ENST00000264414.4:c.1863_1871del	p.Asp621_Pro623del	p.D621_P623del	ENST00000264414	NM_003590.4	621	gaTATCCCTGAa/gaa	14/16	1	2	FACETS	0.753	0.696	0.812	0.753	0.696	0.812	SUBCLONAL	1	TRUE	1	0.764586527224086	2		598	587	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30946592	30946596	+	frameshift_variant	Frame_Shift_Del	DEL	AGAAG	AGAAG	-	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	114	220	1	ENST00000375687.4:c.15_19del	p.Lys6GlufsTer66	p.K6Efs*66	ENST00000375687	NM_015338.5	5	cAGAAG/c	1/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.764586527224086	2		221	258	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57473994	57473994	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs111716808	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	219	492	1	ENST00000371085.3:c.213-2A>G		p.X71_splice	ENST00000371085	NM_000516.4	71			1	2	FACETS	0.956	0.896	1	0.956	0.896	1	CLONAL	1	TRUE	1	0.764586527224086	2		493	599	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147544	47147546	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	197	575	0	ENST00000409792.3:c.4780_4782del	p.Lys1594del	p.K1594del	ENST00000409792	NM_014159.6	1594	AAG/-	6/21	1	2	FACETS	0.93	0.868	0.994	0.93	0.868	0.994	CLONAL	1	TRUE	1	0.764586527224086	2		575	554	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936097	49936097	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	379	1112	0	ENST00000296474.3:c.1573C>A	p.Pro525Thr	p.P525T	ENST00000296474	NM_002447.2	525	Cct/Act	4/20	1	2	FACETS	0.958	0.912	1	0.958	0.912	1	CLONAL	1	TRUE	1	0.764586527224086	2		1112	1035	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247499	71247499	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	154	596	0	ENST00000318789.4:c.34A>G	p.Asn12Asp	p.N12D	ENST00000318789	NM_032682.5	12	Aac/Gac	6/21	1	2	FACETS	0.599	0.55	0.651	0.599	0.55	0.651	SUBCLONAL	1	TRUE	1	0.764586527224086	2		596	672	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409412	31409412	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	235	596	1	ENST00000344624.3:c.3695A>G	p.Lys1232Arg	p.K1232R	ENST00000344624		1232	aAg/aGg	29/33	1	2	FACETS	0.955	0.896	1	0.955	0.896	1	CLONAL	1	TRUE	1	0.764586527224086	2		597	644	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481528	20481529	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	181	463	0	ENST00000346618.3:c.601dup	p.Val201GlyfsTer20	p.V201Gfs*20	ENST00000346618	NM_001949.4	199	-/G	3/7	1	2	FACETS	0.98	0.913	1	0.98	0.913	1	CLONAL	1	TRUE	1	0.764586527224086	2		463	483	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111982947	111982947	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	286	735	1	ENST00000368678.4:c.1600C>A	p.Leu534Met	p.L534M	ENST00000368678		534	Ctg/Atg	13/13	1	2	FACETS	0.977	0.923	1	0.977	0.923	1	CLONAL	1	TRUE	1	0.764586527224086	2		736	766	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843734	151843734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	238	527	0	ENST00000262189.6:c.13981G>A	p.Glu4661Lys	p.E4661K	ENST00000262189	NM_170606.2	4661	Gag/Aag	53/59	1	2	FACETS	0.948	0.89	1	0.948	0.89	1	CLONAL	1	TRUE	1	0.764586527224086	2		527	657	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570361	87570361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	418	1084	1	ENST00000277120.3:c.2101G>A	p.Gly701Arg	p.G701R	ENST00000277120		701	Ggg/Agg	17/19	1	2	FACETS	0.986	0.941	1	0.986	0.941	1	CLONAL	1	TRUE	1	0.764586527224086	2		1085	1109	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227733	53227733	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	386	972	1	ENST00000375401.3:c.2455C>A	p.Leu819Met	p.L819M	ENST00000375401	NM_004187.3	819	Ctg/Atg	17/26	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.764586527224086	2		973	901	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70355057	70355057	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	379	1136	0	ENST00000374080.3:c.4979C>T	p.Thr1660Ile	p.T1660I	ENST00000374080		1660	aCc/aTc	36/45	1	2	FACETS	0.984	0.937	1	0.984	0.937	1	CLONAL	1	TRUE	1	0.764586527224086	2		1136	1007	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591283	67591313	+	protein_altering_variant	In_Frame_Del	DEL	TGAACGAGTGGTTGGGCAATGAAAACACTGA	TGAACGAGTGGTTGGGCAATGAAAACACTGA	CTCGTTC	novel	NA	P-0052390-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	153	467	1	ENST00000274335.5:c.1781_1811delinsCTCGTTC	p.Leu594_Glu604delinsSerArgSer	p.L594_E604delinsSRS	ENST00000274335		594	tTGAACGAGTGGTTGGGCAATGAAAACACTGAa/tCTCGTTCa	13/15	1	2	FACETS	0.823	0.759	0.89	0.823	0.759	0.89	CLONAL	1	TRUE	1	0.764586527224086	2		468	486	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0052408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	400	486	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		486	741	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111521	8111521	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	354	524	0	ENST00000346208.3:c.1007C>A	p.Pro336His	p.P336H	ENST00000346208		336	cCt/cAt	5/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		524	823	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447070	49447070	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	135	515	0	ENST00000301067.7:c.874G>A	p.Glu292Lys	p.E292K	ENST00000301067	NM_003482.3	292	Gag/Aag	7/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		515	692	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120806065	120806065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1339175713	NA	P-0052408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	114	527	0	ENST00000257552.2:c.112G>A	p.Glu38Lys	p.E38K	ENST00000257552	NM_002442.3	38	Gaa/Aaa	3/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		527	1052	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562773	21562773	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	64	493	0	ENST00000382592.4:c.1146G>T	p.Gln382His	p.Q382H	ENST00000382592	NM_014572.2	382	caG/caT	4/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		493	649	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601358	28601358	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	40	325	0	ENST00000241453.7:c.2074G>T	p.Glu692Ter	p.E692*	ENST00000241453	NM_004119.2	692	Gaa/Taa	17/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		325	332	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103376	2103376	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1166291219	NA	P-0052408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1210	181	714	0	ENST00000219476.3:c.259G>A	p.Asp87Asn	p.D87N	ENST00000219476	NM_000548.3	87	Gat/Aat	4/42	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		714	1391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0052408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	446	733	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		733	1053	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37865642	37865642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	85	615	0	ENST00000269571.5:c.511G>A	p.Asp171Asn	p.D171N	ENST00000269571		171	Gac/Aac	4/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		615	1032	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223019	41223019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	167	607	0	ENST00000357654.3:c.4912G>A	p.Glu1638Lys	p.E1638K	ENST00000357654	NM_007294.3	1638	Gaa/Aaa	15/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		607	1018	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218395	36218395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	204	786	0	ENST00000222270.7:c.4174C>T	p.Pro1392Ser	p.P1392S	ENST00000222270	NM_014727.1	1392	Ccg/Tcg	16/37	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		786	1353	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416513	29416513	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	393	652	0	ENST00000389048.3:c.4440C>A	p.Phe1480Leu	p.F1480L	ENST00000389048	NM_004304.4	1480	ttC/ttA	29/29	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		652	1116	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872941	136872941	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	91	383	0	ENST00000241393.3:c.557G>T	p.Cys186Phe	p.C186F	ENST00000241393	NM_003467.2	186	tGt/tTt	2/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		383	592	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	199	267	0	ENST00000397062.3:c.101G>T	p.Arg34Leu	p.R34L	ENST00000397062	NM_006164.4	34	cGa/cTa	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		267	427	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663008	227663008	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs761257723	NA	P-0052408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	73	581	0	ENST00000305123.5:c.447G>C	p.Leu149Phe	p.L149F	ENST00000305123	NM_005544.2	149	ttG/ttC	1/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		581	922	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540494	187540494	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	58	411	0	ENST00000441802.2:c.7246G>A	p.Asp2416Asn	p.D2416N	ENST00000441802	NM_005245.3	2416	Gat/Aat	10/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		411	586	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526240	31526240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1278	182	700	1	ENST00000344624.3:c.800C>T	p.Ser267Phe	p.S267F	ENST00000344624		267	tCt/tTt	2/33	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		701	1460	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038338	180038338	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs755474389	NA	P-0052408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	174	587	0	ENST00000261937.6:c.3679G>T	p.Ala1227Ser	p.A1227S	ENST00000261937	NM_182925.4	1227	Gcc/Tcc	27/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		587	942	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020549	69020549	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	117	415	0	ENST00000288368.4:c.2921A>T	p.Asn974Ile	p.N974I	ENST00000288368	NM_024870.2	974	aAc/aTc	24/40	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		415	672	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376681	8376681	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	237	522	1	ENST00000356435.5:c.4432G>T	p.Gly1478Ter	p.G1478*	ENST00000356435		1478	Gga/Tga	27/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		523	663	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389324	8389324	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	115	434	0	ENST00000356435.5:c.4294C>T	p.Leu1432Phe	p.L1432F	ENST00000356435		1432	Ctc/Ttc	26/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		434	650	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389393	8389393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	64	313	0	ENST00000356435.5:c.4225G>A	p.Asp1409Asn	p.D1409N	ENST00000356435		1409	Gac/Aac	26/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		313	421	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148708	20148708	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	62	124	0	ENST00000379607.5:c.355G>C	p.Asp119His	p.D119H	ENST00000379607	NM_001412.3	119	Gat/Cat	6/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		124	187	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563167	21563167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371775408	NA	P-0052410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	103	726	1	ENST00000382592.4:c.752C>T	p.Ala251Val	p.A251V	ENST00000382592	NM_014572.2	251	gCg/gTg	4/8	0.380792836958232	2	FACETS	0.466	0.415	0.519	0.233	0.207	0.26	SUBCLONAL	1	TRUE	0	0.381490922671469	2		727	1160	SUCCESS
ALK	238	MSKCC	GRCh37	2	29420502	29420502	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	32	410	0	ENST00000389048.3:c.3979T>C	p.Tyr1327His	p.Y1327H	ENST00000389048	NM_004304.4	1327	Tat/Cat	27/29	0.269388725559729	3	FACETS	0.326	0.264	0.397	0.163	0.132	0.199	SUBCLONAL	1	TRUE	1	0.381490922671469	3		410	612	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383458	31383458	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	52	480	0	ENST00000328111.2:c.1255C>A	p.Gln419Lys	p.Q419K	ENST00000328111	NM_006892.3	419	Caa/Aaa	12/23	0.381490922671469	3	FACETS	0.425	0.361	0.496	0.213	0.18	0.248	SUBCLONAL	1	TRUE	1	0.381490922671469	3		480	763	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505112	149505112	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	227	577	0	ENST00000261799.4:c.1703T>G	p.Val568Gly	p.V568G	ENST00000261799	NM_002609.3	568	gTg/gGg	12/23	0.269388725559729	3	FACETS	0.85	0.793	0.907	0.85	0.793	0.907	CLONAL	2	TRUE	1	0.381490922671469	3		577	834	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360550	70360550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	10	601	1	ENST00000374080.3:c.6110G>A	p.Gly2037Asp	p.G2037D	ENST00000374080		2037	gGc/gAc	42/45	0.382839246004238	1	FACETS	0.536	0.386	0.699	0.536	0.386	0.699	INDETERMINATE	1	TRUE	0	0.817105928857288	1		602	27	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576857	7576857	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	46	516	0	ENST00000269305.4:c.989T>A	p.Leu330His	p.L330H	ENST00000269305	NM_001126112.2	330	cTt/cAt	9/11	1	2	FACETS	0.531	0.446	0.625	0.531	0.446	0.625	SUBCLONAL	1	TRUE	1	0.25	2		516	693	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517818	176517818	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	35	563	0	ENST00000292408.4:c.428C>A	p.Pro143His	p.P143H	ENST00000292408	NM_213647.1	143	cCc/cAc	4/18	1	2	FACETS	0.418	0.341	0.504	0.418	0.341	0.504	SUBCLONAL	1	TRUE	1	0.25	2		563	670	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319408	11319408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	322	525	0	ENST00000361445.4:c.59G>A	p.Ser20Asn	p.S20N	ENST00000361445	NM_004958.3	20	aGc/aAc	2/58	1	2	FACETS	0.982	0.931	1	0.982	0.931	1	CLONAL	1	TRUE	1	0.780935743695667	2		525	840	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933510	36933510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754739637	NA	P-0052414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	351	691	0	ENST00000361632.4:c.1777G>A	p.Ala593Thr	p.A593T	ENST00000361632		593	Gcc/Acc	13/16	1	2	FACETS	0.938	0.891	0.986	0.938	0.891	0.986	CLONAL	1	TRUE	1	0.780935743695667	2		691	958	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490557	56490557	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	230	363	0	ENST00000267101.3:c.2201C>T	p.Ser734Leu	p.S734L	ENST00000267101	NM_001982.3	734	tCa/tTa	19/28	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.780935743695667	2		363	584	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211133	36211133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201967801	NA	P-0052414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	325	733	1	ENST00000222270.7:c.884G>A	p.Arg295His	p.R295H	ENST00000222270	NM_014727.1	295	cGc/cAc	3/37	1	2	FACETS	0.856	0.811	0.903	0.856	0.811	0.903	CLONAL	1	TRUE	1	0.780935743695667	2		734	972	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881494	111881494	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753995918	NA	P-0052414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	257	532	0	ENST00000393256.3:c.172G>A	p.Gly58Ser	p.G58S	ENST00000393256	NM_006538.4	58	Ggc/Agc	2/4	1	2	FACETS	0.975	0.919	1	0.975	0.919	1	CLONAL	1	TRUE	1	0.780935743695667	2		532	675	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632293	215632293	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	228	464	0	ENST00000260947.4:c.1481A>T	p.Asn494Ile	p.N494I	ENST00000260947	NM_000465.2	494	aAt/aTt	6/11	1	2	FACETS	0.917	0.859	0.975	0.917	0.859	0.975	CLONAL	1	TRUE	1	0.780935743695667	2		464	637	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0052414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	362	247	1	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	0.754089110208687	2	FACETS	0.922	0.89	0.952	0.922	0.89	0.952	CLONAL	2	TRUE	0	0.780935743695667	2		248	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0052415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	130	851	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	1	2	FACETS	1	0.951	1	1	0.991	1	CLONAL	2	TRUE	1	0.361300503866722	2		851	343	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306959	65306959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358494508	NA	P-0052415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	73	519	1	ENST00000342505.4:c.2618G>A	p.Arg873His	p.R873H	ENST00000342505	NM_002227.2	873	cGc/cAc	19/25	0.361300503866722	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.361300503866722	1		520	291	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685287	89685287	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs398123316	NA	P-0052415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	37	91	0	ENST00000371953.3:c.182A>G	p.His61Arg	p.H61R	ENST00000371953	NM_000314.4	61	cAt/cGt	3/9	0.361300503866722	1	FACETS	0.874	0.744	1	1	0.967	1	CLONAL	2	TRUE	0	0.361300503866722	1		91	96	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060911	38060911	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	73	654	0	ENST00000250448.2:c.1078del	p.Ile360Ter	p.I360*	ENST00000250448	NM_004496.3	360	Ata/ta	2/2	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.361300503866722	2		654	311	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342943	225342943	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	113	494	0	ENST00000264414.4:c.2149A>G	p.Met717Val	p.M717V	ENST00000264414	NM_003590.4	717	Atg/Gtg	15/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.361300503866722	2		494	463	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0052416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	151	401	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.874	0.803	0.948	0.874	0.803	0.948	CLONAL	1	TRUE	1	0.586463917138587	2		401	589	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0052416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	232	765	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.586463917138587	1	FACETS	0.943	0.886	1	0.943	0.886	1	CLONAL	1	TRUE	0	0.586463917138587	1		766	593	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0052416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	130	503	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	1	2	FACETS	0.937	0.856	1	0.937	0.856	1	CLONAL	1	TRUE	1	0.586463917138587	2		503	473	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479810	67479810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863223746	NA	P-0052416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	179	653	0	ENST00000327367.4:c.1117C>T	p.Arg373Cys	p.R373C	ENST00000327367	NM_005902.3	373	Cgc/Tgc	8/9	0.562092062266796	1	FACETS	0.706	0.654	0.76	0.706	0.654	0.76	SUBCLONAL	1	TRUE	0	0.586463917138587	1		653	611	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199451	16199451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	174	474	0	ENST00000375759.3:c.224G>A	p.Arg75His	p.R75H	ENST00000375759	NM_015001.2	75	cGc/cAc	2/15	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.586463917138587	2		474	566	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595967	43595967	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763526874	NA	P-0052416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	257	827	0	ENST00000355710.3:c.134C>T	p.Ala45Val	p.A45V	ENST00000355710	NM_020975.4	45	gCa/gTa	2/20	0.562092062266796	1	FACETS	0.9	0.848	0.954	0.9	0.848	0.954	CLONAL	1	TRUE	0	0.586463917138587	1		827	688	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266130	41266647	+	splice_donor_variant,splice_acceptor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	GCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCAAGATGATGCAGAACTT	GCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCAAGATGATGCAGAACTT	-	novel	NA	P-0052416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	174	403	0	ENST00000349496.5:c.129_446del		p.X43_splice	ENST00000349496	NM_001904.3	43	GCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCAAGATGATGCAGAACTT/-	3-4/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.586463917138587	2		403	559	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983022	149983022	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	130	585	0	ENST00000253339.5:c.3236C>A	p.Thr1079Asn	p.T1079N	ENST00000253339		1079	aCc/aAc	7/7	1	2	FACETS	0.945	0.863	1	0.945	0.863	1	CLONAL	1	TRUE	1	0.586463917138587	2		585	469	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0052419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	64	449	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.25431687867352	2		449	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0052419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	99	801	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.25431687867352	1	FACETS	0.932	0.832	1	0.932	0.832	1	CLONAL	1	TRUE	0	0.25431687867352	1		801	729	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0052419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	174	677	0	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	0.239505092058968	3	FACETS	0.846	0.779	0.915	0.846	0.779	0.915	CLONAL	2	TRUE	1	0.25431687867352	3		677	912	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676201	29676202	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0052419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	46	446	0	ENST00000356175.3:c.7192_7193del	p.Leu2398GlyfsTer2	p.L2398Gfs*2	ENST00000356175	NM_000267.3	2397	aCT/a	48/57	0.25431687867352	1	FACETS	0.996	0.843	1	0.996	0.843	1	CLONAL	1	TRUE	0	0.25431687867352	1		446	317	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631585	119631585	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	42	454	2	ENST00000316626.5:c.681G>T	p.Leu227Phe	p.L227F	ENST00000316626		227	ttG/ttT	6/12	1	2	FACETS	0.888	0.743	1	0.888	0.743	1	CLONAL	1	TRUE	1	0.25431687867352	2		456	372	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248138	110248139	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0052419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	81	627	0	ENST00000374672.4:c.1332_1333dup	p.Arg445ThrfsTer32	p.R445Tfs*32	ENST00000374672	NM_004235.4	445	agg/aCAgg	5/5	1	2	FACETS	0.896	0.789	1	0.896	0.789	1	CLONAL	1	TRUE	1	0.25431687867352	2		627	711	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	106	460	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.804	0.73	0.879	0.804	0.73	0.879	CLONAL	1	TRUE	1	0.879388290488828	2		460	300	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599321	55599321	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913507	NA	P-0052420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	558	592	0	ENST00000288135.5:c.2447A>T	p.Asp816Val	p.D816V	ENST00000288135	NM_000222.2	816	gAc/gTc	17/21	0.749217405546456	3	FACETS	0.964	0.932	0.995			1	CLONAL	2	TRUE	NA	0.879388290488828	3		592	948	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409995	139409995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764942073	NA	P-0052420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	406	1228	2	ENST00000277541.6:c.1843G>A	p.Gly615Arg	p.G615R	ENST00000277541	NM_017617.3	615	Ggg/Agg	11/34	1	2	FACETS	0.952	0.909	0.995	0.952	0.909	0.995	CLONAL	1	TRUE	1	0.879388290488828	2		1230	970	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485286	8485286	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	318	567	0	ENST00000356435.5:c.3094A>G	p.Thr1032Ala	p.T1032A	ENST00000356435		1032	Act/Gct	18/35	0.879388290488828	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.879388290488828	1		567	393	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434835	56434835	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	361	886	0	ENST00000407977.2:c.2302C>T	p.Gln768Ter	p.Q768*	ENST00000407977		768	Cag/Tag	9/10	1	2	FACETS	0.982	0.936	1	0.982	0.936	1	CLONAL	1	TRUE	1	0.879388290488828	2		886	836	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229255	36229255	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	379	1033	0	ENST00000222270.7:c.7945C>T	p.Arg2649Cys	p.R2649C	ENST00000222270	NM_014727.1	2649	Cgc/Tgc	37/37	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.879388290488828	2		1033	835	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727182	40727182	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	188	745	0	ENST00000373198.4:c.3782A>C	p.Gln1261Pro	p.Q1261P	ENST00000373198	NM_133170.3	1261	cAg/cCg	28/32	1	2	FACETS	0.622	0.577	0.669	0.622	0.577	0.669	SUBCLONAL	1	TRUE	1	0.879388290488828	2		745	687	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604325	189604325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	273	575	0	ENST00000264731.3:c.1492G>A	p.Gly498Ser	p.G498S	ENST00000264731	NM_003722.4	498	Ggc/Agc	11/14	1	2	FACETS	0.954	0.902	1	0.954	0.902	1	CLONAL	1	TRUE	1	0.879388290488828	2		575	651	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480075	20480075	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0052420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	206	469	0	ENST00000346618.3:c.394-2A>T		p.X132_splice	ENST00000346618	NM_001949.4	132			0.866681656069016	3	FACETS	0.975	0.908	1	0.487	0.454	0.522	CLONAL	1	TRUE	1	0.879388290488828	3		469	692	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673473	30673473	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	241	610	0	ENST00000376406.3:c.3487C>T	p.Pro1163Ser	p.P1163S	ENST00000376406	NM_014641.2	1163	Ccc/Tcc	10/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.792162536938091	2		610	554	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	232	740	2	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	1	2	FACETS	0.957	0.899	1	0.957	0.899	1	CLONAL	1	TRUE	1	0.792162536938091	2		742	612	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873161	136873161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	136	499	0	ENST00000241393.3:c.337C>T	p.His113Tyr	p.H113Y	ENST00000241393	NM_003467.2	113	Cat/Tat	2/2	1	2	FACETS	0.899	0.826	0.973	0.899	0.826	0.973	CLONAL	1	TRUE	1	0.792162536938091	2		499	382	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953743	48953743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	108	288	0	ENST00000267163.4:c.1346G>A	p.Gly449Glu	p.G449E	ENST00000267163	NM_000321.2	449	gGa/gAa	14/27	0.792162536938091	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.792162536938091	1		288	157	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250809	10250809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	311	942	0	ENST00000340748.4:c.3671C>T	p.Pro1224Leu	p.P1224L	ENST00000340748		1224	cCg/cTg	32/40	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.792162536938091	2		942	721	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259822	16259822	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	220	621	0	ENST00000375759.3:c.7087C>T	p.Gln2363Ter	p.Q2363*	ENST00000375759	NM_015001.2	2363	Caa/Taa	11/15	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.792162536938091	2		621	554	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933176	36933176	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	257	761	1	ENST00000361632.4:c.1941G>A	p.Trp647Ter	p.W647*	ENST00000361632		647	tgG/tgA	14/16	1	2	FACETS	0.968	0.913	1	0.968	0.913	1	CLONAL	1	TRUE	1	0.792162536938091	2		762	670	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731046	162731046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1378895579	NA	P-0052421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	173	552	0	ENST00000367921.3:c.901G>A	p.Glu301Lys	p.E301K	ENST00000367921	NM_006182.2	301	Gag/Aag	9/18	1	2	FACETS	0.85	0.788	0.913	0.85	0.788	0.913	CLONAL	1	TRUE	1	0.792162536938091	2		552	514	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949334	71949335	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0052421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	211	851	2	ENST00000298229.2:c.3714_3715delinsAA	p.Ala1239Thr	p.A1239T	ENST00000298229	NM_001567.3	1238	gaGGct/gaAAct	28/28	1	2	FACETS	0.936	0.876	0.997	0.936	0.876	0.997	CLONAL	1	TRUE	1	0.792162536938091	2		853	569	SUCCESS
EED	8726	MSKCC	GRCh37	11	85968599	85968599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	140	458	0	ENST00000263360.6:c.595C>T	p.His199Tyr	p.H199Y	ENST00000263360	NM_003797.3	199	Cat/Tat	6/12	1	2	FACETS	0.966	0.891	1	0.966	0.891	1	CLONAL	1	TRUE	1	0.792162536938091	2		458	366	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69214130	69214130	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	140	461	0	ENST00000462284.1:c.334A>T	p.Asn112Tyr	p.N112Y	ENST00000462284	NM_002392.5	112	Aac/Tac	5/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.792162536938091	2		461	339	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99192899	99192899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	217	517	0	ENST00000268035.6:c.89G>A	p.Gly30Glu	p.G30E	ENST00000268035	NM_000875.3	30	gGa/gAa	1/21	0.755707152117983	1	FACETS	0.954	0.906	1	0.954	0.906	1	CLONAL	1	TRUE	0	0.792162536938091	1		517	347	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808011	3808012	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0052421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	192	526	0	ENST00000262367.5:c.3407_3408delinsTT	p.Ser1136Phe	p.S1136F	ENST00000262367	NM_004380.2	1136	tCC/tTT	18/31	1	2	FACETS	0.899	0.838	0.962	0.899	0.838	0.962	CLONAL	1	TRUE	1	0.792162536938091	2		526	539	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348637	89348637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	243	813	1	ENST00000301030.4:c.4313C>T	p.Ser1438Phe	p.S1438F	ENST00000301030	NM_001256183.1	1438	tCc/tTc	9/13	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.792162536938091	2		814	589	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15975543	15975543	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0052421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	132	411	0	ENST00000268712.3:c.3812-1G>A		p.X1271_splice	ENST00000268712	NM_006311.3	1271			1	2	FACETS	0.813	0.745	0.883	0.813	0.745	0.883	CLONAL	1	TRUE	1	0.792162536938091	2		411	410	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441954	40441954	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769367905	NA	P-0052421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	283	884	1	ENST00000345506.4:c.199G>A	p.Glu67Lys	p.E67K	ENST00000345506	NM_003152.3	67	Gag/Aag	4/20	1	2	FACETS	0.984	0.93	1	0.984	0.93	1	CLONAL	1	TRUE	1	0.792162536938091	2		885	726	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729842	47729842	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	206	622	0	ENST00000449228.1:c.547C>T	p.Gln183Ter	p.Q183*	ENST00000449228	NM_001127240.2	183	Caa/Taa	3/4	1	2	FACETS	0.976	0.913	1	0.976	0.913	1	CLONAL	1	TRUE	1	0.792162536938091	2		622	533	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912407	50912407	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	235	942	0	ENST00000440232.2:c.1921C>T	p.Pro641Ser	p.P641S	ENST00000440232	NM_002691.3	641	Ccc/Tcc	16/27	1	2	FACETS	0.959	0.901	1	0.959	0.901	1	CLONAL	1	TRUE	1	0.792162536938091	2		942	619	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478778	57478778	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	196	510	0	ENST00000371085.3:c.364C>T	p.Pro122Ser	p.P122S	ENST00000371085	NM_000516.4	122	Ccc/Tcc	5/13	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.792162536938091	2		510	480	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651181	45651181	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	275	696	0	ENST00000407780.3:c.844C>T	p.Leu282Phe	p.L282F	ENST00000407780	NM_001283052.1	282	Ctc/Ttc	5/7	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.792162536938091	2		696	658	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591120	67591121	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0052421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	104	379	0	ENST00000274335.5:c.1713_1714delinsTT	p.Gln572Ter	p.Q572*	ENST00000274335		571	atCCag/atTTag	12/15	0.792162536938091	1	FACETS	0.933	0.864	0.999	0.933	0.864	0.999	CLONAL	1	TRUE	0	0.792162536938091	1		379	170	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672561	30672562	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0052421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	184	677	2	ENST00000376406.3:c.4398_4399delinsTT	p.Pro1467Ser	p.P1467S	ENST00000376406	NM_014641.2	1466	acCCct/acTTct	10/15	1	2	FACETS	0.787	0.731	0.845	0.787	0.731	0.845	SUBCLONAL	1	TRUE	1	0.792162536938091	2		679	590	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022159	5022159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	153	674	1	ENST00000381652.3:c.172C>T	p.Pro58Ser	p.P58S	ENST00000381652	NM_004972.3	58	Cca/Tca	3/25	1	2	FACETS	0.929	0.859	1	0.929	0.859	1	CLONAL	1	TRUE	1	0.792162536938091	2		675	416	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486101	8486102	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0052421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	169	549	2	ENST00000356435.5:c.2715_2716delinsAA	p.Glu906Lys	p.E906K	ENST00000356435		905	gaGGag/gaAAag	17/35	1	2	FACETS	0.896	0.831	0.963	0.896	0.831	0.963	CLONAL	1	TRUE	1	0.792162536938091	2		551	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578277	+	stop_gained	Nonsense_Mutation	TNP	GAG	GAG	AAA	novel	NA	P-0052421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	228	767	0	ENST00000269305.4:c.572_574delinsTTT	p.Pro191_Gln192delinsLeuTer	p.P191_Q192delinsL*	ENST00000269305	NM_001126112.2	191	cCTCag/cTTTag	6/11	1	2	FACETS	0.933	0.875	0.992	0.933	0.875	0.992	CLONAL	1	TRUE	1	0.792162536938091	2		767	617	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	179	1142	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.686634441260597	2		1146	506	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405953	157405954	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1554294674	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	124	629	0	ENST00000346085.5:c.2201dup	p.Ser736IlefsTer27	p.S736Ifs*27	ENST00000346085	NM_020732.3	732	ccg/ccGg	6/20	1	2	FACETS	0.712	0.648	0.78	0.712	0.648	0.78	SUBCLONAL	1	TRUE	1	0.686634441260597	2		629	507	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	173	549	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.938	0.87	1	0.938	0.87	1	CLONAL	1	TRUE	1	0.686634441260597	2		549	537	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	196	577	2	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.686634441260597	2		579	512	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262680	16262680	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	80	471	1	ENST00000375759.3:c.9950del	p.Pro3317ArgfsTer83	p.P3317Rfs*83	ENST00000375759	NM_015001.2	3315	caC/ca	11/15	1	2	FACETS	0.474	0.418	0.533	0.474	0.418	0.533	SUBCLONAL	1	TRUE	1	0.686634441260597	2		472	492	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088717	27088717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	200	625	1	ENST00000324856.7:c.2326C>T	p.Pro776Ser	p.P776S	ENST00000324856	NM_006015.4	776	Cct/Tct	7/20	1	2	FACETS	0.94	0.876	1	0.94	0.876	1	CLONAL	1	TRUE	1	0.686634441260597	2		626	620	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803535	43803535	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	219	694	1	ENST00000372470.3:c.16C>A	p.Leu6Ile	p.L6I	ENST00000372470	NM_005373.2	6	Ctc/Atc	1/12	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.686634441260597	2		695	556	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	135	339	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.686634441260597	2		339	362	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	89	275	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	0.867	0.778	0.96	0.867	0.778	0.96	CLONAL	1	TRUE	1	0.686634441260597	2		275	299	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104357035	104357035	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	31	508	0	ENST00000369902.3:c.895C>T	p.Arg299Ter	p.R299*	ENST00000369902	NM_016169.3	299	Cga/Tga	7/12	1	2	FACETS	0.184	0.148	0.224	0.184	0.148	0.224	SUBCLONAL	1	TRUE	1	0.686634441260597	2		508	491	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573812	64573812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771645621	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	165	665	2	ENST00000312049.6:c.941G>A	p.Arg314Gln	p.R314Q	ENST00000312049	NM_130799.2	314	cGg/cAg	7/10	1	2	FACETS	0.895	0.827	0.965	0.895	0.827	0.965	CLONAL	1	TRUE	1	0.686634441260597	2		667	537	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943290	71943291	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	171	537	2	ENST00000298229.2:c.1627dup	p.Ala543GlyfsTer9	p.A543Gfs*9	ENST00000298229	NM_001567.3	541	aag/aaGg	14/28	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.686634441260597	2		539	474	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434851	49434851	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1460481305	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	206	798	0	ENST00000301067.7:c.6702del	p.Arg2235AspfsTer29	p.R2235Dfs*29	ENST00000301067	NM_003482.3	2234	ccC/cc	31/54	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.686634441260597	2		798	589	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860071	57860071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1412253333	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	243	781	0	ENST00000228682.2:c.811C>T	p.His271Tyr	p.H271Y	ENST00000228682	NM_005269.2	271	Cac/Tac	8/12	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.686634441260597	2		781	576	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426790	121426790	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201095611	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	171	675	2	ENST00000257555.6:c.481G>A	p.Ala161Thr	p.A161T	ENST00000257555		161	Gcc/Acc	2/10	1	2	FACETS	0.914	0.846	0.983	0.914	0.846	0.983	CLONAL	1	TRUE	1	0.686634441260597	2		677	545	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	171	761	9	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.984	0.913	1	0.984	0.913	1	CLONAL	1	TRUE	1	0.686634441260597	2		770	506	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437179	121437179	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372624970	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	227	849	0	ENST00000257555.6:c.1610C>T	p.Thr537Met	p.T537M	ENST00000257555		537	aCg/aTg	8/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.686634441260597	2		849	647	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337684	73337684	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771690280	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	99	263	3	ENST00000377767.4:c.2032del	p.Ile678PhefsTer59	p.I678Ffs*59	ENST00000377767	NM_014953.3	678	Att/tt	16/21	1	2	FACETS	0.936	0.846	1	0.936	0.846	1	CLONAL	1	TRUE	1	0.686634441260597	2		266	308	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986782	36986782	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	80	125	0	ENST00000354822.5:c.907G>T	p.Gly303Cys	p.G303C	ENST00000354822	NM_001079668.2	303	Ggt/Tgt	3/3	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.686634441260597	2		125	189	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40683745	40683745	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	118	586	0	ENST00000249776.8:c.737T>C	p.Met246Thr	p.M246T	ENST00000249776	NM_033286.3	246	aTg/aCg	7/9	1	2	FACETS	0.55	0.497	0.605	0.55	0.497	0.605	SUBCLONAL	1	TRUE	1	0.686634441260597	2		586	625	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054541	42054541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1458609443	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	131	352	0	ENST00000219905.7:c.7731del	p.Asp2578ThrfsTer10	p.D2578Tfs*10	ENST00000219905	NM_001164273.1	2575	agA/ag	22/24	1	2	FACETS	0.971	0.89	1	0.971	0.89	1	CLONAL	1	TRUE	1	0.686634441260597	2		352	393	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748660	43748661	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	252	707	1	ENST00000382044.4:c.2145dup	p.Glu716ArgfsTer9	p.E716Rfs*9	ENST00000382044	NM_001141980.1	715	-/A	12/28	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.686634441260597	2		708	697	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90633818	90633818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371777275	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	64	643	0	ENST00000330062.3:c.266G>A	p.Arg89His	p.R89H	ENST00000330062	NM_002168.2	89	cGt/cAt	3/11	1	2	FACETS	0.299	0.258	0.343	0.299	0.258	0.343	SUBCLONAL	1	TRUE	1	0.686634441260597	2		643	624	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67646012	67646013	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	177	494	4	ENST00000264010.4:c.950_951dup	p.Gly318GlnfsTer16	p.G318Qfs*16	ENST00000264010	NM_006565.3	314	aac/aACac	4/12	1	2	FACETS	0.965	0.896	1	0.965	0.896	1	CLONAL	1	TRUE	1	0.686634441260597	2		498	534	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821381	72821382	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	68	367	1	ENST00000268489.5:c.10793dup	p.Pro3599SerfsTer67	p.P3599Sfs*67	ENST00000268489	NM_006885.3	3598	cct/ccCt	10/10	1	2	FACETS	0.604	0.529	0.683	0.604	0.529	0.683	SUBCLONAL	1	TRUE	1	0.686634441260597	2		368	328	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821457	72821457	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	157	443	1	ENST00000268489.5:c.10718C>A	p.Pro3573His	p.P3573H	ENST00000268489	NM_006885.3	3573	cCt/cAt	10/10	1	2	FACETS	0.911	0.841	0.983	0.911	0.841	0.983	CLONAL	1	TRUE	1	0.686634441260597	2		444	502	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346204	89346204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201043388	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	85	444	0	ENST00000301030.4:c.6746G>A	p.Arg2249His	p.R2249H	ENST00000301030	NM_001256183.1	2249	cGc/cAc	9/13	1	2	FACETS	0.722	0.643	0.804	0.722	0.643	0.804	SUBCLONAL	1	TRUE	1	0.686634441260597	2		444	343	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110130	8110130	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	42	604	0	ENST00000585124.1:c.475del	p.Arg159AlafsTer30	p.R159Afs*30	ENST00000585124	NM_004217.3	159	Cgc/gc	6/9	1	2	FACETS	0.215	0.179	0.255	0.215	0.179	0.255	SUBCLONAL	1	TRUE	1	0.686634441260597	2		604	570	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995291	15995291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	225	538	0	ENST00000268712.3:c.2902C>T	p.His968Tyr	p.H968Y	ENST00000268712	NM_006311.3	968	Cat/Tat	22/46	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.686634441260597	2		538	557	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872805	37872805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	225	698	0	ENST00000269571.5:c.1684C>T	p.Pro562Ser	p.P562S	ENST00000269571		562	Ccg/Tcg	14/27	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.686634441260597	2		698	568	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370236	40370236	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs761761205	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	133	828	10	ENST00000293328.3:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000293328	NM_012448.3	368	Cag/ag	9/19	1	2	FACETS	0.655	0.597	0.716	0.655	0.597	0.716	SUBCLONAL	1	TRUE	1	0.686634441260597	2		838	591	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262108	10262108	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	179	558	0	ENST00000340748.4:c.2183A>T	p.Lys728Met	p.K728M	ENST00000340748		728	aAg/aTg	23/40	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.686634441260597	2		558	488	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050403	13050406	+	frameshift_variant	Frame_Shift_Del	DEL	CAGA	CAGA	-	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	177	535	0	ENST00000316448.5:c.361_364del	p.Asp121CysfsTer35	p.D121Cfs*35	ENST00000316448	NM_004343.3	119	CAGAca/ca	3/9	1	2	FACETS	0.971	0.901	1	0.971	0.901	1	CLONAL	1	TRUE	1	0.686634441260597	2		535	531	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355135	15355135	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	180	738	0	ENST00000263377.2:c.2488C>A	p.Leu830Met	p.L830M	ENST00000263377	NM_058243.2	830	Ctg/Atg	13/20	1	2	FACETS	0.884	0.82	0.95	0.884	0.82	0.95	CLONAL	1	TRUE	1	0.686634441260597	2		738	593	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273216	18273216	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	177	654	0	ENST00000222254.8:c.1011-2A>C		p.X337_splice	ENST00000222254	NM_005027.3	337			1	2	FACETS	0.958	0.889	1	0.958	0.889	1	CLONAL	1	TRUE	1	0.686634441260597	2		654	538	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273255	18273255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	231	648	0	ENST00000222254.8:c.1048G>A	p.Gly350Ser	p.G350S	ENST00000222254	NM_005027.3	350	Ggc/Agc	9/16	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.686634441260597	2		648	544	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961041	18961041	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	174	538	0	ENST00000262803.5:c.619C>G	p.Leu207Val	p.L207V	ENST00000262803	NM_002911.3	207	Ctg/Gtg	4/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.686634441260597	2		538	467	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216627	36216627	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	203	733	0	ENST00000222270.7:c.3793C>A	p.Leu1265Ile	p.L1265I	ENST00000222270	NM_014727.1	1265	Ctc/Atc	13/37	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.686634441260597	2		733	549	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223581	36223581	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	234	847	0	ENST00000222270.7:c.6134del	p.Pro2045LeufsTer46	p.P2045Lfs*46	ENST00000222270	NM_014727.1	2044	gCc/gc	28/37	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.686634441260597	2		847	615	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796883	42796883	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	212	837	0	ENST00000575354.2:c.3347del	p.Pro1116GlnfsTer45	p.P1116Qfs*45	ENST00000575354	NM_015125.3	1114	gCc/gc	14/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.686634441260597	2		837	613	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796976	42796976	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	234	861	0	ENST00000575354.2:c.3437del	p.Pro1146GlnfsTer15	p.P1146Qfs*15	ENST00000575354	NM_015125.3	1145	aCc/ac	14/20	1	2	FACETS	0.982	0.921	1	0.982	0.921	1	CLONAL	1	TRUE	1	0.686634441260597	2		861	694	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523009	25523009	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	251	1038	3	ENST00000264709.3:c.176del	p.Pro59ArgfsTer13	p.P59Rfs*13	ENST00000264709	NM_175629.2	59	cCg/cg	3/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.686634441260597	2		1041	671	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607487	46607487	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	253	757	0	ENST00000263734.3:c.1681del	p.Gln561SerfsTer7	p.Q561Sfs*7	ENST00000263734	NM_001430.4	559	aCc/ac	12/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.686634441260597	2		757	720	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637390	47637391	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs587779164	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	168	608	0	ENST00000233146.2:c.528_529del	p.Cys176Ter	p.C176*	ENST00000233146	NM_000251.2	175	cTG/c	3/16	1	2	FACETS	0.993	0.92	1	0.993	0.92	1	CLONAL	1	TRUE	1	0.686634441260597	2		608	493	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693887	47693887	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	162	387	0	ENST00000233146.2:c.1601del	p.Arg534LeufsTer9	p.R534Lfs*9	ENST00000233146	NM_000251.2	534	cGt/ct	10/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.686634441260597	2		387	434	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546626	9546626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751328296	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	150	481	2	ENST00000353224.5:c.1396G>A	p.Ala466Thr	p.A466T	ENST00000353224	NM_177990.2	466	Gcc/Acc	5/10	1	2	FACETS	0.991	0.914	1	0.991	0.914	1	CLONAL	1	TRUE	1	0.686634441260597	2		483	441	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021497	31021497	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs549287573	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	96	608	0	ENST00000375687.4:c.1496G>A	p.Arg499His	p.R499H	ENST00000375687	NM_015338.5	499	cGt/cAt	12/13	1	2	FACETS	0.505	0.451	0.562	0.505	0.451	0.562	SUBCLONAL	1	TRUE	1	0.686634441260597	2		608	554	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031679	36031679	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1405253806	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	221	734	0	ENST00000358208.4:c.1508G>A	p.Arg503Gln	p.R503Q	ENST00000358208		503	cGg/cAg	12/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.686634441260597	2		734	589	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513557	41513557	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs112711413	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	196	633	0	ENST00000263253.7:c.461T>C	p.Met154Thr	p.M154T	ENST00000263253	NM_001429.3	154	aTg/aCg	2/31	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.686634441260597	2		633	500	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523693	41523693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs983340187	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	257	727	0	ENST00000263253.7:c.1109G>A	p.Arg370His	p.R370H	ENST00000263253	NM_001429.3	370	cGc/cAc	4/31	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.686634441260597	2		727	696	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713498	30713498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	183	584	0	ENST00000295754.5:c.823G>A	p.Ala275Thr	p.A275T	ENST00000295754	NM_003242.5	275	Gca/Aca	4/7	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.686634441260597	2		584	518	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181879	38181879	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	152	402	0	ENST00000396334.3:c.503G>T	p.Gly168Val	p.G168V	ENST00000396334	NM_002468.4	168	gGg/gTg	3/5	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.686634441260597	2		402	390	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103754	47103755	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	rs749901643	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	185	477	0	ENST00000409792.3:c.6190_6191dup	p.Asp2064GlufsTer84	p.D2064Efs*84	ENST00000409792	NM_014159.6	2064	gac/gaGAc	14/21	1	2	FACETS	0.969	0.901	1	0.969	0.901	1	CLONAL	1	TRUE	1	0.686634441260597	2		477	556	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446958	187446958	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	238	738	0	ENST00000232014.4:c.1235C>A	p.Pro412His	p.P412H	ENST00000232014	NM_001130845.1	412	cCt/cAt	5/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.686634441260597	2		738	602	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526780	31526780	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530480889	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	123	476	0	ENST00000344624.3:c.260C>T	p.Pro87Leu	p.P87L	ENST00000344624		87	cCg/cTg	2/33	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.686634441260597	2		476	344	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177901	56177901	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	169	425	1	ENST00000399503.3:c.2877del	p.Gly960AlafsTer8	p.G960Afs*8	ENST00000399503	NM_005921.1	958	acA/ac	14/20	1	2	FACETS	0.992	0.92	1	0.992	0.92	1	CLONAL	1	TRUE	1	0.686634441260597	2		426	496	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752855	57752855	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	124	426	2	ENST00000274289.3:c.1073G>A	p.Ser358Asn	p.S358N	ENST00000274289	NM_006622.3	358	aGc/aAc	8/14	1	2	FACETS	0.856	0.781	0.934	0.856	0.781	0.934	CLONAL	1	TRUE	1	0.686634441260597	2		428	422	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944381	131944382	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs748536322	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	113	231	1	ENST00000265335.6:c.2801dup	p.Asn934LysfsTer10	p.N934Kfs*10	ENST00000265335		931	-/A	17/25	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.686634441260597	2		232	322	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057057	180057057	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372854098	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	216	742	0	ENST00000261937.6:c.562C>T	p.Arg188Trp	p.R188W	ENST00000261937	NM_182925.4	188	Cgg/Tgg	5/30	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.686634441260597	2		742	543	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840018	27840018	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	277	632	0	ENST00000328488.2:c.76G>T	p.Ala26Ser	p.A26S	ENST00000328488	NM_003533.2	26	Gct/Tct	1/1	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.686634441260597	2		632	586	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903745	41903746	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	191	755	1	ENST00000372991.4:c.811dup	p.Arg271ProfsTer53	p.R271Pfs*53	ENST00000372991	NM_001760.3	271	cgg/cCgg	5/5	1	2	FACETS	0.886	0.823	0.95	0.886	0.823	0.95	CLONAL	1	TRUE	1	0.686634441260597	2		756	628	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200293	138200293	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748312513	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	205	512	0	ENST00000237289.4:c.1711G>A	p.Val571Ile	p.V571I	ENST00000237289	NM_001270507.1	571	Gtc/Atc	7/9	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.686634441260597	2		512	536	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528225	157528225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786205584	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	161	589	0	ENST00000346085.5:c.5950G>A	p.Glu1984Lys	p.E1984K	ENST00000346085	NM_020732.3	1984	Gag/Aag	20/20	1	2	FACETS	0.842	0.777	0.909	0.842	0.777	0.909	CLONAL	1	TRUE	1	0.686634441260597	2		589	557	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042170	6042170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758561884	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	196	470	0	ENST00000265849.7:c.451C>T	p.Arg151Cys	p.R151C	ENST00000265849	NM_000535.5	151	Cgc/Tgc	5/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.686634441260597	2		470	482	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367288	50367288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775793261	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	144	445	1	ENST00000331340.3:c.95C>T	p.Pro32Leu	p.P32L	ENST00000331340	NM_006060.4	32	cCg/cTg	3/8	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.686634441260597	2		446	402	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878877	117878877	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	168	400	0	ENST00000297338.2:c.92A>G	p.His31Arg	p.H31R	ENST00000297338	NM_006265.2	31	cAt/cGt	2/14	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.686634441260597	2		400	485	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020769	37020769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	173	508	1	ENST00000358127.4:c.76del	p.Val26PhefsTer3	p.V26Ffs*3	ENST00000358127	NM_001280556.1	26	Gtt/tt	2/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.686634441260597	2		509	471	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796804	135796804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223799508	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	125	349	0	ENST00000298552.3:c.683G>A	p.Arg228Gln	p.R228Q	ENST00000298552	NM_001162426.1	228	cGa/cAa	8/23	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.686634441260597	2		349	345	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222954	53222954	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	176	679	2	ENST00000375401.3:c.4117+1G>A		p.X1373_splice	ENST00000375401	NM_004187.3	1373			1	2	FACETS	0.924	0.856	0.993	0.924	0.856	0.993	CLONAL	1	TRUE	1	0.686634441260597	2		681	555	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412974	63412974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	211	731	0	ENST00000330258.3:c.193G>A	p.Gly65Ser	p.G65S	ENST00000330258	NM_152424.3	65	Ggt/Agt	2/2	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.686634441260597	2		731	596	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0052423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	277	549	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.388494682432547	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.388494682432547	4		549	932	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602446	10602446	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	249	790	0	ENST00000171111.5:c.1132G>T	p.Gly378Cys	p.G378C	ENST00000171111	NM_203500.1	378	Ggc/Tgc	3/6	0.388494682432547	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.388494682432547	1		790	949	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326461	62326461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	260	942	0	ENST00000360203.5:c.3386C>T	p.Ser1129Leu	p.S1129L	ENST00000360203	NM_001283009.1	1129	tCa/tTa	33/35	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.388494682432547	2		942	1211	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776522	9776522	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs751559889	NA	P-0052423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	211	728	0	ENST00000377346.4:c.625A>G	p.Thr209Ala	p.T209A	ENST00000377346	NM_005026.3	209	Acc/Gcc	6/24	0.388494682432547	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.388494682432547	1		728	836	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843688	156843688	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs754611476	NA	P-0052423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	425	782	0	ENST00000524377.1:c.1114G>T	p.Ala372Ser	p.A372S	ENST00000524377	NM_002529.3	372	Gcc/Tcc	8/17	0.388494682432547	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.388494682432547	3		782	1305	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852083	63852083	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	157	614	0	ENST00000279873.7:c.2861C>T	p.Ala954Val	p.A954V	ENST00000279873	NM_032199.2	954	gCc/gTc	10/10	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.388494682432547	2		614	798	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441882	40441882	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1419458682	NA	P-0052423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	180	699	0	ENST00000345506.4:c.129-2A>G		p.X43_splice	ENST00000345506	NM_003152.3	43			1	2	FACETS	0.929	0.856	1	0.929	0.856	1	CLONAL	1	TRUE	1	0.388494682432547	2		699	998	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446848	187446848	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs775834769	NA	P-0052423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	165	576	0	ENST00000232014.4:c.1345A>G	p.Ile449Val	p.I449V	ENST00000232014	NM_001130845.1	449	Atc/Gtc	5/10	0.388494682432547	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.388494682432547	1		576	632	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041261	47041261	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	195	777	0	ENST00000377604.3:c.1689del	p.Gln563HisfsTer141	p.Q563Hfs*141	ENST00000377604	NM_001204468.1	563	caG/ca	15/24	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.388494682432547	2		777	986	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860124	152860124	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	179	568	0	ENST00000406277.2:c.304A>T	p.Ser102Cys	p.S102C	ENST00000406277	NM_152274.4	102	Agc/Tgc	5/7	1		FACETS		0.981	1				CLONAL	1	TRUE	1	0.388494682432547	2		568	772	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965749	93965752	+	missense_variant	Missense_Mutation	ONP	CATG	CATG	TAAT	novel	NA	P-0052423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	53	292	0	ENST00000369303.4:c.2176_2179delinsATTA	p.His726_Asp727delinsIleAsn	p.H726_D727delinsIN	ENST00000369303	NM_004440.3	726	CATGat/ATTAat	13/17	1	2	FACETS	0.847	0.727	0.978	0.847	0.727	0.978	CLONAL	1	TRUE	1	0.388494682432547	2		292	322	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0052424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	197	401	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.572303264848559	2		401	634	SUCCESS
APC	324	MSKCC	GRCh37	5	112175324	112175324	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1211642532	NA	P-0052424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	230	344	0	ENST00000257430.4:c.4033G>T	p.Glu1345Ter	p.E1345*	ENST00000257430	NM_000038.5	1345	Gaa/Taa	16/16	0.572303264848559	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.572303264848559	2		344	384	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008017	29008017	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs767050810	NA	P-0052424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	253	465	2	ENST00000282397.4:c.752A>G	p.Asn251Ser	p.N251S	ENST00000282397	NM_002019.4	251	aAt/aGt	6/30	0.572303264848559	3	FACETS	0.849	0.799	0.899	0.849	0.799	0.899	CLONAL	2	TRUE	1	0.572303264848559	3		467	670	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844722	156844722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs986498490	NA	P-0052424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	281	784	2	ENST00000524377.1:c.1276G>A	p.Val426Ile	p.V426I	ENST00000524377	NM_002529.3	426	Gtc/Atc	11/17	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.572303264848559	2		786	965	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204669	108204669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	94	287	0	ENST00000278616.4:c.7984G>T	p.Val2662Phe	p.V2662F	ENST00000278616	NM_000051.3	2662	Gtt/Ttt	54/63	0.572303264848559	1	FACETS	0.969	0.878	1	0.969	0.878	1	CLONAL	1	TRUE	0	0.572303264848559	1		287	242	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637623	23637657	+	frameshift_variant	Frame_Shift_Del	DEL	TACATCTTCGCAAGCAGTTATGATACATGGCTCTT	TACATCTTCGCAAGCAGTTATGATACATGGCTCTT	-	novel	NA	P-0052424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	196	669	0	ENST00000261584.4:c.2648_2682del	p.Lys883SerfsTer33	p.K883Sfs*33	ENST00000261584	NM_024675.3	883	aAAGAGCCATGTATCATAACTGCTTGCGAAGATGTA/a	7/13	1	2	FACETS	0.846	0.784	0.909	0.846	0.784	0.909	CLONAL	1	TRUE	1	0.572303264848559	2		669	810	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276215	15276215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748889237	NA	P-0052424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	238	697	2	ENST00000263388.2:c.5779G>A	p.Ala1927Thr	p.A1927T	ENST00000263388	NM_000435.2	1927	Gcc/Acc	31/33	1	2	FACETS	0.989	0.925	1	0.989	0.925	1	CLONAL	1	TRUE	1	0.572303264848559	2		699	841	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361136	66361136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	149	431	0	ENST00000273854.3:c.1036G>A	p.Glu346Lys	p.E346K	ENST00000273854	NM_004439.5	346	Gag/Aag	4/18	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.572303264848559	2		431	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912664	NA	P-0052425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	305	687	0	ENST00000269305.4:c.1010G>C	p.Arg337Pro	p.R337P	ENST00000269305	NM_001126112.2	337	cGc/cCc	10/11	0.548964160530859	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.548964160530859	1		687	718	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249011	55249012	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAACCCAGG	novel	NA	P-0052425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	259	665	0	ENST00000275493.2:c.2315_2316insAGGCAACCC	p.Pro772_His773insGlyAsnPro	p.P772_H773insGNP	ENST00000275493	NM_005228.3	770	gac/gaCAACCCAGGc	20/28	0.219328641293324	3	FACETS	1	0.992	1	0.679	0.637	0.721	INDETERMINATE	1	TRUE	1	0.548964160530859	3		665	886	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562657	29562660	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs1064794276	NA	P-0052426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	23	563	0	ENST00000356175.3:c.3739_3742del	p.Phe1247IlefsTer18	p.F1247Ifs*18	ENST00000356175	NM_000267.3	1246	cTGTTt/ct	28/57	1	2	FACETS	0.771	0.6	0.97	0.771	0.6	0.97	CLONAL	1	TRUE	1	0.14	2		563	426	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692892	89692892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554898129	NA	P-0052426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	23	375	0	ENST00000371953.3:c.376G>A	p.Ala126Thr	p.A126T	ENST00000371953	NM_000314.4	126	Gct/Act	5/9	1	2	FACETS	0.933	0.728	1	0.933	0.728	1	CLONAL	1	TRUE	1	0.14	2		375	352	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0052427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	131	765	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.260091099928694	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.260091099928694	1		766	761	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928232	178928233	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGAGTT	novel	NA	P-0052427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	123	481	0	ENST00000263967.3:c.1418_1419insTGAGTT	p.Cys472_Leu473insPheGlu	p.C472_L473insFE	ENST00000263967	NM_006218.2	473	tta/ttTGAGTTa	9/21	0.260091099928694	3	FACETS	0.82	0.743	0.9	0.82	0.743	0.9	CLONAL	2	TRUE	1	0.260091099928694	3		481	652	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0052428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	691	825	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.540712131873384	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.540712131873384	2		826	1164	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266140	198266140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	128	335	1	ENST00000335508.6:c.2480G>A	p.Arg827Lys	p.R827K	ENST00000335508	NM_012433.2	827	aGa/aAa	17/25	0.540712131873384	3	FACETS	1	0.941	1	0.523	0.476	0.573	CLONAL	1	TRUE	1	0.540712131873384	3		336	575	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713427	40713427	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752787425	NA	P-0052428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1901	297	605	2	ENST00000373198.4:c.4088G>A	p.Arg1363Gln	p.R1363Q	ENST00000373198	NM_133170.3	1363	cGg/cAg	30/32	0.540712131873384	6	FACETS	1	0.964	1	0.26	0.243	0.277	CLONAL	1	TRUE	2	0.540712131873384	6		607	2198	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526163	189526163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	541	606	0	ENST00000264731.3:c.427G>A	p.Val143Ile	p.V143I	ENST00000264731	NM_003722.4	143	Gtc/Atc	4/14	0.540712131873384	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.540712131873384	3		606	1236	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225533	26225533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1595	287	684	2	ENST00000360408.1:c.151G>A	p.Glu51Lys	p.E51K	ENST00000360408	NM_003532.2	51	Gag/Aag	1/1	0.540712131873384	5	FACETS	1	0.953	1	0.341	0.319	0.363	CLONAL	1	TRUE	2	0.540712131873384	5		686	1882	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271548	26271548	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs765739684	NA	P-0052428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1370	316	445	0	ENST00000305910.3:c.65C>G	p.Ala22Gly	p.A22G	ENST00000305910	NM_003534.2	22	gCc/gGc	1/1	0.540712131873384	5	FACETS	1	0.991	1	0.419	0.393	0.444	CLONAL	1	TRUE	2	0.540712131873384	5		445	1686	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93626877	93626877	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	137	399	0	ENST00000375746.1:c.724G>T	p.Glu242Ter	p.E242*	ENST00000375746	NM_001174167.1	242	Gag/Tag	5/14	1	2	FACETS	0.732	0.667	0.8	0.732	0.667	0.8	SUBCLONAL	1	TRUE	1	0.540712131873384	2		399	692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577025	7577025	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0052429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	184	729	0	ENST00000269305.4:c.913A>T	p.Lys305Ter	p.K305*	ENST00000269305	NM_001126112.2	305	Aag/Tag	8/11	0.149007034017221	3	FACETS	1	0.984	1	0.824	0.762	0.889	CLONAL	2	TRUE	0	0.21	3		729	783	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784254	43784254	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	59	659	1	ENST00000382044.4:c.232C>T	p.Arg78Ter	p.R78*	ENST00000382044	NM_001141980.1	78	Cga/Tga	3/28	0.159079872123529	4	FACETS	0.913	0.784	1	0.456	0.392	0.527	CLONAL	1	TRUE	2	0.21	4		660	745	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761262	59761262	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	138	655	0	ENST00000259008.2:c.3145T>G	p.Phe1049Val	p.F1049V	ENST00000259008	NM_032043.2	1049	Ttc/Gtc	20/20	0.220965455766092	4	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	2	0.21	4		655	757	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602871	10602871	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	186	861	0	ENST00000171111.5:c.707A>G	p.Asp236Gly	p.D236G	ENST00000171111	NM_203500.1	236	gAc/gGc	3/6	0.19766650444134	2	FACETS	0.866	0.799	0.935	0.866	0.799	0.935	CLONAL	2	TRUE	0	0.21	2		861	1023	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11137022	11137022	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	164	648	0	ENST00000358026.2:c.3215G>T	p.Gly1072Val	p.G1072V	ENST00000358026	NM_001128849.1	1072	gGg/gTg	23/36	0.19766650444134	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.21	2		648	720	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498347	29498347	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1302907379	NA	P-0052429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	34	575	0	ENST00000389048.3:c.1833G>A	p.Met611Ile	p.M611I	ENST00000389048	NM_004304.4	611	atG/atA	10/29	0.159079872123529	4	FACETS	0.62	0.505	0.75	0.31	0.252	0.375	SUBCLONAL	1	TRUE	2	0.21	4		575	632	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417927	138417927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	37	398	0	ENST00000289153.2:c.1592G>A	p.Gly531Glu	p.G531E	ENST00000289153	NM_006219.2	531	gGa/gAa	11/22	0.220965455766092	4	FACETS	0.915	0.754	1	0.457	0.377	0.548	CLONAL	1	TRUE	2	0.21	4		398	466	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665023	138665023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	41	114	0	ENST00000330315.3:c.542C>T	p.Ala181Val	p.A181V	ENST00000330315	NM_023067.3	181	gCc/gTc	1/1	0.220965455766092	4	FACETS	0.88	0.743	1	1	0.947	1	CLONAL	3	TRUE	2	0.21	4		114	179	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540247	187540247	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	58	530	0	ENST00000441802.2:c.7493A>G	p.Glu2498Gly	p.E2498G	ENST00000441802	NM_005245.3	2498	gAa/gGa	10/27	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.21	2		530	503	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541797	187541797	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	71	499	0	ENST00000441802.2:c.5943G>T	p.Gln1981His	p.Q1981H	ENST00000441802	NM_005245.3	1981	caG/caT	10/27	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.21	2		499	498	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35860962	35860962	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	102	419	2	ENST00000303115.3:c.91G>T	p.Glu31Ter	p.E31*	ENST00000303115	NM_002185.3	31	Gaa/Taa	2/8	0.288807014556287	4	FACETS	1	0.968	1			1	CLONAL	2	TRUE	NA	0.21	4		421	492	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622263	117622263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs556427413	NA	P-0052429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	48	507	0	ENST00000368508.3:c.6607G>A	p.Asp2203Asn	p.D2203N	ENST00000368508	NM_002944.2	2203	Gac/Aac	42/43	0.3	1	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	0	0.21	1		507	404	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874638	151874638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	48	526	0	ENST00000262189.6:c.7900G>A	p.Glu2634Lys	p.E2634K	ENST00000262189	NM_170606.2	2634	Gag/Aag	38/59	0.220965455766092	4	FACETS	0.889	0.751	1	0.445	0.375	0.521	CLONAL	1	TRUE	2	0.21	4		526	622	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970976	21970986	+	frameshift_variant	Frame_Shift_Del	DEL	GTGCGACATCG	GTGCGACATCG	-	novel	NA	P-0052429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	111	679	0	ENST00000304494.5:c.372_382del	p.Asp125ValfsTer13	p.D125Vfs*13	ENST00000304494	NM_000077.4	124	cgCGATGTCGCACgg/cggg	2/3	0.3	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.21	1		679	682	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578410	7578410	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	231	886	0	ENST00000269305.4:c.520A>T	p.Arg174Trp	p.R174W	ENST00000269305	NM_001126112.2	174	Agg/Tgg	5/11	0.25901730593305	3	FACETS	1	0.971	1	0.711	0.665	0.758	CLONAL	2	TRUE	0	0.332350372128461	3		886	760	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134266	11134266	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064796254	NA	P-0052430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	268	699	1	ENST00000358026.2:c.2932C>T	p.Arg978Ter	p.R978*	ENST00000358026	NM_001128849.1	978	Cga/Tga	20/36	0.332350372128461	3	FACETS	0.948	0.896	1	0.948	0.896	1	CLONAL	3	TRUE	0	0.332350372128461	3		700	661	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873726	37873726	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1258745095	NA	P-0052430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	181	675	0	ENST00000269571.5:c.1891A>T	p.Thr631Ser	p.T631S	ENST00000269571		631	Acc/Tcc	15/27	0.332350372128461	5	FACETS	1	0.938	1			1	CLONAL	2	TRUE	NA	0.332350372128461	5		675	802	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675162	40675162	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	122	811	0	ENST00000249776.8:c.126C>G	p.Asp42Glu	p.D42E	ENST00000249776	NM_033286.3	42	gaC/gaG	1/9	0.332350372128461	3	FACETS	0.932	0.841	1	0.466	0.42	0.514	CLONAL	1	TRUE	1	0.332350372128461	3		811	919	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670673	67670673	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	89	586	0	ENST00000264010.4:c.1918C>A	p.Pro640Thr	p.P640T	ENST00000264010	NM_006565.3	640	Cct/Act	11/12	0.332350372128461	6	FACETS	1	0.92	1			1	CLONAL	1	TRUE	NA	0.332350372128461	6		586	850	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170016829	170016829	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1458271182	NA	P-0052430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	84	495	0	ENST00000295797.4:c.1634G>T	p.Gly545Val	p.G545V	ENST00000295797	NM_002740.5	545	gGg/gTg	17/18	0.332350372128461	9	FACETS	1	0.936	1	0.137	0.12	0.155	CLONAL	1	TRUE	1	0.332350372128461	9		495	999	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937822	76937822	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	51	568	0	ENST00000373344.5:c.2926G>A	p.Glu976Lys	p.E976K	ENST00000373344	NM_000489.3	976	Gaa/Aaa	9/35	0.307771197439894	3	FACETS	0.519	0.44	0.606	0.173	0.146	0.202	SUBCLONAL	1	TRUE	0	0.332350372128461	3		568	690	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0052432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	23	594	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.242	0.187	0.305	0.242	0.187	0.305	SUBCLONAL	1	TRUE	1	0.33	2		594	577	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161324	55161324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514550	NA	P-0052432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	73	635	0	ENST00000257290.5:c.3155C>T	p.Thr1052Met	p.T1052M	ENST00000257290	NM_006206.4	1052	aCg/aTg	23/23	1	2	FACETS	0.968	0.85	1	0.968	0.85	1	CLONAL	1	TRUE	1	0.33	2		635	457	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942122	71942123	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0052432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	71	972	0	ENST00000298229.2:c.1390dup	p.His464ProfsTer2	p.H464Pfs*2	ENST00000298229	NM_001567.3	462	-/C	12/28	1	2	FACETS	0.8	0.699	0.908	0.8	0.699	0.908	CLONAL	1	TRUE	1	0.33	2		972	538	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949108	71949108	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	81	1031	0	ENST00000298229.2:c.3577del	p.Ala1193ProfsTer9	p.A1193Pfs*9	ENST00000298229	NM_001567.3	1192	cGg/cg	27/28	1	2	FACETS	0.978	0.864	1	0.978	0.864	1	CLONAL	1	TRUE	1	0.33	2		1031	502	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40678575	40678575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs557155424	NA	P-0052432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	88	655	0	ENST00000249776.8:c.317G>A	p.Arg106Gln	p.R106Q	ENST00000249776	NM_033286.3	106	cGg/cAg	3/9	1	2	FACETS	0.857	0.76	0.961	0.857	0.76	0.961	CLONAL	1	TRUE	1	0.33	2		655	622	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715715	30715715	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	70	532	0	ENST00000295754.5:c.1373C>A	p.Thr458Lys	p.T458K	ENST00000295754	NM_003242.5	458	aCa/aAa	5/7	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.33	2		532	381	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0052445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	113	380	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.177012349536041	4	FACETS	0.864	0.778	0.954	0.864	0.778	0.954	CLONAL	2	TRUE	2	0.239914899404252	4		380	676	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0052445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	82	306	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.239914899404252	3	FACETS	0.862	0.764	0.967	0.575	0.509	0.645	CLONAL	2	TRUE	0	0.239914899404252	3		306	444	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0052445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	84	298	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	0.239914899404252	3	FACETS	0.952	0.845	1	0.635	0.563	0.71	CLONAL	2	TRUE	0	0.239914899404252	3		298	412	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100436	8100436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1220437638	NA	P-0052445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	87	881	0	ENST00000346208.3:c.410C>T	p.Ser137Leu	p.S137L	ENST00000346208		137	tCg/tTg	3/6	0.215640812007212	2	FACETS	0.849	0.751	0.955	0.425	0.375	0.478	CLONAL	1	TRUE	0	0.239914899404252	2		881	854	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274223	10274223	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	80	497	0	ENST00000330684.3:c.46C>G	p.Leu16Val	p.L16V	ENST00000330684	NM_001134407.1	16	Ctg/Gtg	2/13	0.239914899404252	4	FACETS	1	0.951	1	0.387	0.34	0.437	CLONAL	1	TRUE	1	0.239914899404252	4		497	713	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964366	70964366	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	29	418	0	ENST00000276594.2:c.1662C>G	p.Ile554Met	p.I554M	ENST00000276594	NM_024504.3	554	atC/atG	8/8	1	2	FACETS	0.487	0.39	0.598	0.487	0.39	0.598	SUBCLONAL	1	TRUE	1	0.239914899404252	2		418	496	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174899	56174900	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	82	459	0	ENST00000399503.3:c.2059dup	p.Ile687AsnfsTer10	p.I687Nfs*10	ENST00000399503	NM_005921.1	686	-/A	11/20	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.239914899404252	2		459	603	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180536	56180537	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	39	390	0	ENST00000399503.3:c.3867dup	p.Ala1290SerfsTer19	p.A1290Sfs*19	ENST00000399503	NM_005921.1	1289	gaa/gAaa	16/20	1	2	FACETS	0.615	0.509	0.733	0.615	0.509	0.733	SUBCLONAL	1	TRUE	1	0.239914899404252	2		390	529	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672333	86672346	+	frameshift_variant	Frame_Shift_Del	DEL	ACTCTATGGAAAAA	ACTCTATGGAAAAA	-	novel	NA	P-0052445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	62	428	0	ENST00000274376.6:c.2136_2149del	p.Ser713HisfsTer8	p.S713Hfs*8	ENST00000274376	NM_002890.2	712	tACTCTATGGAAAAA/t	16/25	1	2	FACETS	0.89	0.769	1	0.89	0.769	1	CLONAL	1	TRUE	1	0.239914899404252	2		428	581	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587388	29587400	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TTTTTCCTTGATA	TTTTTCCTTGATA	-	novel	NA	P-0052446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	27	391	0	ENST00000356175.3:c.4370_4382del	p.Phe1457Ter	p.F1457*	ENST00000356175	NM_000267.3	1457	TTTTTCCTTGATAta/ta	33/57	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		391	279	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0052447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	15	449	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.747	0.545	0.99	0.747	0.545	0.99	CLONAL	1	TRUE	1	0.13	2		449	309	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106648	27106648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553153748	NA	P-0052447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	26	640	0	ENST00000324856.7:c.6259G>A	p.Gly2087Arg	p.G2087R	ENST00000324856	NM_006015.4	2087	Gga/Aga	20/20	1	2	FACETS	0.65	0.513	0.809	0.65	0.513	0.809	SUBCLONAL	1	TRUE	1	0.13	2		640	615	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578460	+	inframe_deletion	In_Frame_Del	DEL	CGCGGA	CGCGGA	-	novel	NA	P-0052447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	52	690	0	ENST00000269305.4:c.470_475del	p.Val157_Arg158del	p.V157_R158del	ENST00000269305	NM_001126112.2	157	gTCCGCGcc/gcc	5/11	1	2	FACETS	0.982	0.834	1	0.982	0.834	1	CLONAL	1	TRUE	1	0.13	2		690	815	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0052447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	33	551	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.883	0.718	1	0.883	0.718	1	CLONAL	1	TRUE	1	0.13	2		551	575	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279674	123279674	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs77543610	NA	P-0052447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	51	441	0	ENST00000358487.5:c.758C>G	p.Pro253Arg	p.P253R	ENST00000358487	NM_000141.4	253	cCt/cGt	7/18	0.136453452266606	3	FACETS	0.967	0.824	1	0.967	0.824	1	CLONAL	2	TRUE	1	0.13	3		441	432	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411216	63411216	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778026	NA	P-0052447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	39	668	0	ENST00000330258.3:c.1951G>A	p.Val651Ile	p.V651I	ENST00000330258	NM_152424.3	651	Gtc/Atc	2/2	1	2	FACETS	0.946	0.783	1	0.946	0.783	1	CLONAL	1	TRUE	1	0.13	2		668	634	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685269	89685269	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs786203847	NA	P-0052447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	27	227	0	ENST00000371953.3:c.165-1G>A		p.X55_splice	ENST00000371953	NM_000314.4	55			0.136453452266606	3	FACETS	1	0.87	1	1	0.87	1	CLONAL	2	TRUE	1	0.13	3		227	198	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098949	178098951	+	inframe_deletion	In_Frame_Del	DEL	TAC	TAC	-	novel	NA	P-0052447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	18	319	0	ENST00000397062.3:c.94_96del	p.Val32del	p.V32del	ENST00000397062	NM_006164.4	32	GTA/-	2/5	1	2	FACETS	0.839	0.631	1	0.839	0.631	1	CLONAL	1	TRUE	1	0.13	2		319	330	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050911	49050911	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	33	463	0	ENST00000267163.4:c.2596del	p.Ser866AlafsTer7	p.S866Afs*7	ENST00000267163	NM_000321.2	865	ggA/gg	25/27	1	2	FACETS	1	0.83	1	1	0.83	1	CLONAL	1	TRUE	1	0.13	2		463	497	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645378	67645379	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0052447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	37	423	0	ENST00000264010.4:c.644_645del	p.Thr215ArgfsTer14	p.T215Rfs*14	ENST00000264010	NM_006565.3	215	ACa/a	3/12	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.13	2		423	469	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0052449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	141	380	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.499412248481592	2		380	556	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0052449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	91	1142	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.597	0.531	0.668	0.597	0.531	0.668	SUBCLONAL	1	TRUE	1	0.499412248481592	2		1146	610	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671655	67671655	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1400980130	NA	P-0052449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	63	538	5	ENST00000264010.4:c.2070del	p.Glu691SerfsTer30	p.E691Sfs*30	ENST00000264010	NM_006565.3	688	gtA/gt	12/12	0.482132649978332	1	FACETS	0.549	0.477	0.625	0.549	0.477	0.625	SUBCLONAL	1	TRUE	0	0.499412248481592	1		543	345	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692893	89692893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1114167656	NA	P-0052449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	119	369	0	ENST00000371953.3:c.377C>T	p.Ala126Val	p.A126V	ENST00000371953	NM_000314.4	126	gCt/gTt	5/9	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.499412248481592	2		369	456	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	88	697	0	ENST00000397062.3:c.246A>T	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaT	2/5	0.499412248481592	3	FACETS	0.507	0.449	0.57	0.254	0.224	0.285	SUBCLONAL	1	TRUE	1	0.499412248481592	3		697	868	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476733	140476733	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1278812236	NA	P-0052449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	42	365	0	ENST00000288602.6:c.1673G>A	p.Arg558Gln	p.R558Q	ENST00000288602	NM_004333.4	558	cGa/cAa	13/18	1	2	FACETS	0.39	0.326	0.462	0.39	0.326	0.462	SUBCLONAL	1	TRUE	1	0.499412248481592	2		365	431	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023861	27023861	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1336228861	NA	P-0052449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	46	260	2	ENST00000324856.7:c.971del	p.Gly324AlafsTer39	p.G324Afs*39	ENST00000324856	NM_006015.4	323	Ggg/gg	1/20	1	2	FACETS	0.804	0.684	0.934	0.804	0.684	0.934	CLONAL	1	TRUE	1	0.499412248481592	2		262	229	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512401	38512401	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1441911200	NA	P-0052449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	44	636	2	ENST00000254066.5:c.1312G>C	p.Ala438Pro	p.A438P	ENST00000254066	NM_000964.3	438	Gcc/Ccc	9/9	1	2	FACETS	0.392	0.328	0.461	0.392	0.328	0.461	SUBCLONAL	1	TRUE	1	0.499412248481592	2		638	450	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852659	63852659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1349220963	NA	P-0052449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	131	634	4	ENST00000279873.7:c.3437C>T	p.Ala1146Val	p.A1146V	ENST00000279873	NM_032199.2	1146	gCg/gTg	10/10	1	2	FACETS	0.877	0.799	0.959	0.877	0.799	0.959	CLONAL	1	TRUE	1	0.499412248481592	2		638	598	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993581	72993581	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	50	809	0	ENST00000268489.5:c.464del	p.Gly155AlafsTer17	p.G155Afs*17	ENST00000268489	NM_006885.3	155	gGc/gc	2/10	0.482132649978332	1	FACETS	0.37	0.314	0.431	0.37	0.314	0.431	SUBCLONAL	1	TRUE	0	0.499412248481592	1		809	406	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591115	67591116	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTA	novel	NA	P-0052449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	105	339	0	ENST00000274335.5:c.1710_1712dup	p.Ile571dup	p.I571dup	ENST00000274335		571	ctt/cTTAtt	12/15	1	2	FACETS	0.916	0.825	1	0.916	0.825	1	CLONAL	1	TRUE	1	0.499412248481592	2		339	459	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206933	162206933	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777074432	NA	P-0052449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	56	369	0	ENST00000366898.1:c.742G>A	p.Val248Ile	p.V248I	ENST00000366898	NM_004562.2	248	Gtc/Atc	7/12	1	2	FACETS	0.614	0.529	0.707	0.614	0.529	0.707	SUBCLONAL	1	TRUE	1	0.499412248481592	2		369	365	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933622	39933622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200141801	NA	P-0052449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	63	679	1	ENST00000378444.4:c.977C>T	p.Pro326Leu	p.P326L	ENST00000378444	NM_001123385.1	326	cCg/cTg	4/15	1	2	FACETS	0.455	0.393	0.521	0.455	0.393	0.521	SUBCLONAL	1	TRUE	1	0.499412248481592	2		680	555	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089769	27089770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	53	604	0	ENST00000324856.7:c.2729dup	p.Asn910LysfsTer26	p.N910Kfs*26	ENST00000324856	NM_006015.4	909	caa/cAaa	8/20	1	2	FACETS	0.405	0.345	0.47	0.405	0.345	0.47	SUBCLONAL	1	TRUE	1	0.499412248481592	2		604	524	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106611	27106611	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	131	703	0	ENST00000324856.7:c.6222del	p.Pro2075HisfsTer60	p.P2075Hfs*60	ENST00000324856	NM_006015.4	2074	tcT/tc	20/20	1	2	FACETS	0.874	0.796	0.956	0.874	0.796	0.956	CLONAL	1	TRUE	1	0.499412248481592	2		703	600	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246091259	246091259	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	62	570	0	ENST00000388985.4:c.676G>C	p.Val226Leu	p.V226L	ENST00000388985		226	Gtc/Ctc	7/12	0.469529459100114	4	FACETS	0.5	0.431	0.575	0.25	0.215	0.288	SUBCLONAL	1	TRUE	2	0.499412248481592	4		570	745	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434261	49434261	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	54	906	1	ENST00000301067.7:c.7292C>T	p.Ser2431Phe	p.S2431F	ENST00000301067	NM_003482.3	2431	tCt/tTt	31/54	1	2	FACETS	0.314	0.267	0.365	0.314	0.267	0.365	SUBCLONAL	1	TRUE	1	0.499412248481592	2		907	689	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348712	11348712	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	36	607	0	ENST00000332029.2:c.624del	p.Phe209SerfsTer14	p.F209Sfs*14	ENST00000332029	NM_003745.1	208	ccC/cc	2/2	1	2	FACETS	0.283	0.232	0.34	0.283	0.232	0.34	SUBCLONAL	1	TRUE	1	0.499412248481592	2		607	509	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660596	67660596	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	72	643	0	ENST00000264010.4:c.1496A>G	p.Gln499Arg	p.Q499R	ENST00000264010	NM_006565.3	499	cAg/cGg	8/12	0.482132649978332	1	FACETS	0.458	0.401	0.519	0.458	0.401	0.519	SUBCLONAL	1	TRUE	0	0.499412248481592	1		643	472	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929492	81929492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777445397	NA	P-0052449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	68	621	0	ENST00000359376.3:c.1153G>A	p.Val385Ile	p.V385I	ENST00000359376	NM_002661.3	385	Gtc/Atc	13/33	1	2	FACETS	0.48	0.418	0.548	0.48	0.418	0.548	SUBCLONAL	1	TRUE	1	0.499412248481592	2		621	567	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735570	204735570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757773669	NA	P-0052449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	36	556	0	ENST00000302823.3:c.371C>T	p.Thr124Met	p.T124M	ENST00000302823	NM_005214.4	124	aCg/aTg	2/4	0.499412248481592	3	FACETS	0.306	0.251	0.369	0.153	0.125	0.185	SUBCLONAL	1	TRUE	1	0.499412248481592	3		556	588	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114562	73114562	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	90	281	0	ENST00000356692.5:c.943T>A	p.Ser315Thr	p.S315T	ENST00000356692		315	Tca/Aca	9/9	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.499412248481592	2		281	359	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	49	307	0	ENST00000274335.5:c.1126G>T	p.Gly376Ter	p.G376*	ENST00000274335		376	Gga/Tga	9/15	1	2	FACETS	0.507	0.43	0.591	0.507	0.43	0.591	SUBCLONAL	1	TRUE	1	0.499412248481592	2		307	387	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977881	131977881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1202026618	NA	P-0052449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	37	416	0	ENST00000265335.6:c.3764G>A	p.Ser1255Asn	p.S1255N	ENST00000265335		1255	aGt/aAt	25/25	1	2	FACETS	0.396	0.327	0.473	0.396	0.327	0.473	SUBCLONAL	1	TRUE	1	0.499412248481592	2		416	374	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910771	29910771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1136690	NA	P-0052449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	78	971	0	ENST00000376809.5:c.311C>T	p.Thr104Ile	p.T104I	ENST00000376809	NM_002116.7	104	aCc/aTc	2/8	1	2	FACETS	0.406	0.356	0.459	0.406	0.356	0.459	SUBCLONAL	1	TRUE	1	0.499412248481592	2		971	770	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066546	94066546	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	43	446	0	ENST00000369303.4:c.1213C>A	p.Leu405Met	p.L405M	ENST00000369303	NM_004440.3	405	Ctg/Atg	5/17	1	2	FACETS	0.385	0.322	0.455	0.385	0.322	0.455	SUBCLONAL	1	TRUE	1	0.499412248481592	2		446	447	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0052466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	93	494	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	1	2	FACETS	0.752	0.671	0.837	1	0.981	1	SUBCLONAL	2	TRUE	1	0.25	2		494	495	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591145	67591145	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	44	348	0	ENST00000274335.5:c.1738T>A	p.Tyr580Asn	p.Y580N	ENST00000274335		580	Tac/Aac	12/15	1	2	FACETS	0.869	0.73	1	0.869	0.73	1	CLONAL	1	TRUE	1	0.25	2		348	405	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692886	89692886	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	37	340	0	ENST00000371953.3:c.370T>A	p.Cys124Ser	p.C124S	ENST00000371953	NM_000314.4	124	Tgt/Agt	5/9	1	2	FACETS	0.908	0.751	1	0.908	0.751	1	CLONAL	1	TRUE	1	0.25	2		340	326	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589605	67589616	+	inframe_deletion	In_Frame_Del	DEL	TCAAGAAAAAAG	TCAAGAAAAAAG	-	novel	NA	P-0052466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	33	217	0	ENST00000274335.5:c.1370_1381del	p.Gln457_Ser460del	p.Q457_S460del	ENST00000274335		456	ttTCAAGAAAAAAGt/ttt	10/15	1	2	FACETS	0.815	0.665	0.983	0.815	0.665	0.983	CLONAL	1	TRUE	1	0.25	2		217	324	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729363	41729363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	115	645	1	ENST00000242208.4:c.1166C>T	p.Ser389Leu	p.S389L	ENST00000242208	NM_002192.2	389	tCg/tTg	3/3	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.25	2		646	807	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725033	89725060	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTTTCTCTAGGTGAAGCTGTACTTCAC	TCTTTCTCTAGGTGAAGCTGTACTTCAC	-	novel	NA	P-0052466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	16	243	0	ENST00000371953.3:c.1027-11_1043del		p.X343_splice	ENST00000371953	NM_000314.4	343		9/9	1	2	FACETS	0.512	0.378	0.671	0.512	0.378	0.671	SUBCLONAL	1	TRUE	1	0.25	2		243	250	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377037	118377037	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	31	460	0	ENST00000534358.1:c.10430C>G	p.Ser3477Cys	p.S3477C	ENST00000534358	NM_005933.3	3477	tCt/tGt	27/36	1	2	FACETS	0.432	0.348	0.527	0.432	0.348	0.527	SUBCLONAL	1	TRUE	1	0.25	2		460	574	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670615	67670616	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GACAATG	novel	NA	P-0052466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	66	405	0	ENST00000264010.4:c.1861_1867dup	p.Glu623GlyfsTer3	p.E623Gfs*3	ENST00000264010	NM_006565.3	620	-/GACAATG	11/12	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.25	2		405	518	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0052467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	59	449	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.226083114145193	2		449	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0052467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	123	928	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.226083114145193	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.226083114145193	1		928	765	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027160	49027160	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0052467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	32	501	0	ENST00000267163.4:c.1727C>G	p.Ser576Ter	p.S576*	ENST00000267163	NM_000321.2	576	tCa/tGa	18/27	1	2	FACETS	0.701	0.569	0.85	0.701	0.569	0.85	SUBCLONAL	1	TRUE	1	0.226083114145193	2		501	404	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057949	27057949	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	54	652	0	ENST00000324856.7:c.1657C>T	p.Gln553Ter	p.Q553*	ENST00000324856	NM_006015.4	553	Cag/Tag	3/20	1	2	FACETS	0.778	0.664	0.903	0.778	0.664	0.903	CLONAL	1	TRUE	1	0.226083114145193	2		652	614	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902287	50902287	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0052467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	41	760	0	ENST00000440232.2:c.179C>G	p.Ser60Ter	p.S60*	ENST00000440232	NM_002691.3	60	tCa/tGa	2/27	0.226083114145193	1	FACETS	0.578	0.48	0.686	0.578	0.48	0.686	SUBCLONAL	1	TRUE	0	0.226083114145193	1		760	557	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838145	89838145	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	91	598	0	ENST00000389301.3:c.2092G>C	p.Glu698Gln	p.E698Q	ENST00000389301	NM_000135.2	698	Gag/Cag	23/43	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.226083114145193	2		598	660	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124542	108124542	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	20	322	0	ENST00000278616.4:c.1900G>C	p.Glu634Gln	p.E634Q	ENST00000278616	NM_000051.3	634	Gaa/Caa	13/63	1	2	FACETS	0.678	0.519	0.863	0.678	0.519	0.863	SUBCLONAL	1	TRUE	1	0.226083114145193	2		322	261	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376088	118376088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	62	579	0	ENST00000534358.1:c.9481C>T	p.His3161Tyr	p.H3161Y	ENST00000534358	NM_005933.3	3161	Cat/Tat	27/36	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.226083114145193	2		579	530	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440445	49440446	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0052467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	99	646	0	ENST00000301067.7:c.4364_4365del	p.Tyr1455LeufsTer35	p.Y1455Lfs*35	ENST00000301067	NM_003482.3	1455	tAC/t	15/54	NA	4	FACETS	1	0.979	1	0.71	0.634	0.791	INDETERMINATE	1	TRUE	2	0.226083114145193	4		646	756	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37882863	37882863	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	41	635	0	ENST00000269571.5:c.2921C>G	p.Ser974Cys	p.S974C	ENST00000269571		974	tCt/tGt	24/27	0.226083114145193	1	FACETS	0.558	0.464	0.662	0.558	0.464	0.662	SUBCLONAL	1	TRUE	0	0.226083114145193	1		635	577	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902200	50902200	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	28	697	0	ENST00000440232.2:c.92C>G	p.Pro31Arg	p.P31R	ENST00000440232	NM_002691.3	31	cCa/cGa	2/27	0.226083114145193	1	FACETS	0.446	0.355	0.549	0.446	0.355	0.549	SUBCLONAL	1	TRUE	0	0.226083114145193	1		697	493	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639190	176639190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	54	481	1	ENST00000439151.2:c.3790G>A	p.Glu1264Lys	p.E1264K	ENST00000439151	NM_022455.4	1264	Gaa/Aaa	5/23	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.226083114145193	2		482	412	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288672	33288672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	36	450	1	ENST00000374542.5:c.880G>A	p.Glu294Lys	p.E294K	ENST00000374542	NM_001141970.1	294	Gag/Aag	3/8	0.193968109800181	4	FACETS	0.71	0.583	0.853	0.237	0.194	0.285	SUBCLONAL	1	TRUE	1	0.226083114145193	4		451	550	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918586	44918586	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	63	285	0	ENST00000377967.4:c.1069G>T	p.Asp357Tyr	p.D357Y	ENST00000377967	NM_021140.2	357	Gac/Tac	12/29	0.0574230404799447	2	FACETS	0.868	0.756	0.988			1	INDETERMINATE	2	TRUE	NA	0.226083114145193	2		285	321	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0052468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	99	542	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.909	0.811	1	0.909	0.811	1	CLONAL	1	TRUE	1	0.288891163994829	2		542	754	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447190	187447190	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	105	639	0	ENST00000232014.4:c.1003C>T	p.Gln335Ter	p.Q335*	ENST00000232014	NM_001130845.1	335	Cag/Tag	5/10	0.288891163994829	1	FACETS	0.913	0.819	1	0.913	0.819	1	CLONAL	1	TRUE	0	0.288891163994829	1		639	681	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599949	10599950	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0052468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	105	595	0	ENST00000171111.5:c.1626_1627del	p.Glu542AspfsTer31	p.E542Dfs*31	ENST00000171111	NM_203500.1	542	gaGAcg/gacg	5/6	0.288891163994829	1	FACETS	0.871	0.781	0.967	0.871	0.781	0.967	CLONAL	1	TRUE	0	0.288891163994829	1		595	714	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023441	31023441	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs776868653	NA	P-0052468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	201	601	0	ENST00000375687.4:c.2926C>T	p.Gln976Ter	p.Q976*	ENST00000375687	NM_015338.5	976	Caa/Taa	13/13	0.261477282811238	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.288891163994829	3		601	767	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679724	88679724	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	95	589	1	ENST00000360948.2:c.739G>T	p.Gly247Trp	p.G247W	ENST00000360948	NM_001012338.2	247	Ggg/Tgg	7/19	1	2	FACETS	0.95	0.847	1	0.95	0.847	1	CLONAL	1	TRUE	1	0.288891163994829	2		590	692	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218473	1218494	+	frameshift_variant	Frame_Shift_Del	DEL	GTTATACAACGAAGAGAAGCAG	GTTATACAACGAAGAGAAGCAG	-	novel	NA	P-0052468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	75	659	1	ENST00000326873.7:c.348_369del	p.Leu117LysfsTer5	p.L117Kfs*5	ENST00000326873	NM_000455.4	116	gtGTTATACAACGAAGAGAAGCAG/gt	2/10	0.288891163994829	1	FACETS	0.747	0.655	0.845	0.747	0.655	0.845	SUBCLONAL	1	TRUE	0	0.288891163994829	1		660	595	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942807	68942807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	110	603	0	ENST00000288368.4:c.619G>T	p.Val207Phe	p.V207F	ENST00000288368	NM_024870.2	207	Gtc/Ttc	6/40	1	2	FACETS	0.882	0.792	0.978	0.882	0.792	0.978	CLONAL	1	TRUE	1	0.288891163994829	2		603	863	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317136	87317136	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	104	508	0	ENST00000277120.3:c.275G>T	p.Gly92Val	p.G92V	ENST00000277120		92	gGa/gTa	3/19	1	2	FACETS	0.908	0.813	1	0.908	0.813	1	CLONAL	1	TRUE	1	0.288891163994829	2		508	793	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0052470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	389	684	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.853496250411772	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.853496250411772	1		684	505	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0052470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	357	724	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.978	0.932	1	0.978	0.932	1	CLONAL	1	TRUE	1	0.853496250411772	2		724	855	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157256609	157256609	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554270802	NA	P-0052470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	222	316	0	ENST00000346085.5:c.1936C>T	p.Gln646Ter	p.Q646*	ENST00000346085	NM_020732.3	646	Cag/Tag	5/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.853496250411772	2		316	514	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0052471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	134	379	3	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.85	0.779	0.922	1	0.989	1	CLONAL	2	TRUE	1	0.38	2		382	415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578232	7578232	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	574	668	0	ENST00000269305.4:c.617del	p.Leu206TrpfsTer41	p.L206Wfs*41	ENST00000269305	NM_001126112.2	206	tTg/tg	6/11	0.3	2	FACETS	0.967	0.942	0.992	1	0.998	1	CLONAL	4	TRUE	0	0.38	2		668	781	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779586	3779586	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	87	902	1	ENST00000262367.5:c.5462A>G	p.Gln1821Arg	p.Q1821R	ENST00000262367	NM_004380.2	1821	cAg/cGg	31/31	1	2	FACETS	0.496	0.438	0.558	0.496	0.438	0.558	SUBCLONAL	1	TRUE	1	0.38	2		903	924	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76764109	76764109	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1569513021	NA	P-0052471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	154	193	0	ENST00000373344.5:c.7201-2A>G		p.X2401_splice	ENST00000373344	NM_000489.3	2401			1	1	FACETS	1	0.984	1	1	0.995	1	CLONAL	3	TRUE	0	0.38	1		193	201	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0052472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	165	432	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.992	0.914	1	0.992	0.914	1	CLONAL	1	TRUE	1	0.459919781229069	2		432	723	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687306	37687306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1172789499	NA	P-0052472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	167	616	0	ENST00000447079.4:c.4210C>T	p.Arg1404Cys	p.R1404C	ENST00000447079	NM_015083.1	1404	Cgt/Tgt	14/14	1	2	FACETS	0.894	0.823	0.969	0.894	0.823	0.969	CLONAL	1	TRUE	1	0.459919781229069	2		616	812	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041375	42041375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764277967	NA	P-0052472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	173	710	0	ENST00000219905.7:c.5570C>T	p.Ser1857Leu	p.S1857L	ENST00000219905	NM_001164273.1	1857	tCg/tTg	17/24	1	2	FACETS	0.944	0.87	1	0.944	0.87	1	CLONAL	1	TRUE	1	0.459919781229069	2		710	797	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259244	89259244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	107	511	0	ENST00000336596.2:c.388G>A	p.Asp130Asn	p.D130N	ENST00000336596	NM_005233.5	130	Gat/Aat	3/17	0.174131253891589	5	FACETS	1	0.972	1			1	INDETERMINATE	1	TRUE	NA	0.459919781229069	5		511	635	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916903	178916903	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	173	635	0	ENST00000263967.3:c.290C>A	p.Pro97His	p.P97H	ENST00000263967	NM_006218.2	97	cCc/cAc	2/21	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.459919781229069	2		635	627	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0052472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	101	367	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.459919781229069	2		367	425	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076945	41076945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767453141	NA	P-0052472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	126	569	1	ENST00000373198.4:c.1475C>T	p.Ser492Phe	p.S492F	ENST00000373198	NM_133170.3	492	tCc/tTc	9/32	1	2	FACETS	0.907	0.824	0.994	0.907	0.824	0.994	CLONAL	1	TRUE	1	0.459919781229069	2		570	604	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545734	106545734	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	172	681	0	ENST00000359195.3:c.3211C>T	p.Gln1071Ter	p.Q1071*	ENST00000359195	NM_002649.2	1071	Cag/Tag	11/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.459919781229069	2		681	708	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595821	52595821	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	353	608	0	ENST00000394830.3:c.4094G>A	p.Trp1365Ter	p.W1365*	ENST00000394830	NM_018313.4	1365	tGg/tAg	26/30	0.459919781229069	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.459919781229069	2		608	750	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631107	69631107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782695249	NA	P-0052472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	196	607	0	ENST00000334134.2:c.305G>A	p.Arg102Lys	p.R102K	ENST00000334134	NM_005247.2	102	aGg/aAg	2/3	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.459919781229069	2		607	765	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106208	27106208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773088565	NA	P-0052472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	167	701	0	ENST00000324856.7:c.5819C>T	p.Pro1940Leu	p.P1940L	ENST00000324856	NM_006015.4	1940	cCa/cTa	20/20	1	2	FACETS	0.92	0.847	0.997	0.92	0.847	0.997	CLONAL	1	TRUE	1	0.459919781229069	2		701	789	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210790	36210790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	180	697	1	ENST00000222270.7:c.541C>T	p.Arg181Trp	p.R181W	ENST00000222270	NM_014727.1	181	Cgg/Tgg	3/37	1	2	FACETS	0.882	0.814	0.953	0.882	0.814	0.953	CLONAL	1	TRUE	1	0.459919781229069	2		698	887	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40684192	40684192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199907924	NA	P-0052472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	126	523	0	ENST00000249776.8:c.790G>A	p.Glu264Lys	p.E264K	ENST00000249776	NM_033286.3	264	Gaa/Aaa	8/9	1	2	FACETS	0.97	0.882	1	0.97	0.882	1	CLONAL	1	TRUE	1	0.459919781229069	2		523	565	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125513777	125513777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1363144435	NA	P-0052472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	123	541	0	ENST00000428830.2:c.905C>T	p.Pro302Leu	p.P302L	ENST00000428830	NM_001114121.2	302	cCa/cTa	9/14	1	2	FACETS	0.937	0.85	1	0.937	0.85	1	CLONAL	1	TRUE	1	0.459919781229069	2		541	571	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437498	49437498	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223905716	NA	P-0052472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	184	646	0	ENST00000301067.7:c.5387G>A	p.Arg1796Gln	p.R1796Q	ENST00000301067	NM_003482.3	1796	cGg/cAg	23/54	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.459919781229069	2		646	793	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748290	43748290	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	217	825	0	ENST00000382044.4:c.2516C>T	p.Ser839Phe	p.S839F	ENST00000382044	NM_001141980.1	839	tCc/tTc	12/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.459919781229069	2		825	873	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66525086	66525086	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	124	441	0	ENST00000358598.2:c.845T>C	p.Ile282Thr	p.I282T	ENST00000358598	NM_212471.2	282	aTt/aCt	9/11	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.459919781229069	2		441	533	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252762	10252762	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	172	689	0	ENST00000340748.4:c.3203T>A	p.Leu1068Gln	p.L1068Q	ENST00000340748		1068	cTg/cAg	29/40	1	2	FACETS	0.882	0.812	0.955	0.882	0.812	0.955	CLONAL	1	TRUE	1	0.459919781229069	2		689	848	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968261	18968261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	185	709	0	ENST00000262803.5:c.2101C>T	p.Gln701Ter	p.Q701*	ENST00000262803	NM_002911.3	701	Cag/Tag	15/24	1	2	FACETS	0.965	0.892	1	0.965	0.892	1	CLONAL	1	TRUE	1	0.459919781229069	2		709	834	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705553	47705553	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553369759	NA	P-0052472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	87	487	0	ENST00000233146.2:c.2353C>T	p.His785Tyr	p.H785Y	ENST00000233146	NM_000251.2	785	Cat/Tat	14/16	1	2	FACETS	0.88	0.783	0.982	0.88	0.783	0.982	CLONAL	1	TRUE	1	0.459919781229069	2		487	430	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770617	40770617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749916516	NA	P-0052472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	111	473	1	ENST00000373198.4:c.2765C>T	p.Ser922Leu	p.S922L	ENST00000373198	NM_133170.3	922	tCg/tTg	19/32	1	2	FACETS	0.914	0.825	1	0.914	0.825	1	CLONAL	1	TRUE	1	0.459919781229069	2		474	528	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775479	39775479	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	200	683	0	ENST00000288319.7:c.541C>T	p.Pro181Ser	p.P181S	ENST00000288319	NM_182918.3	181	Ccc/Tcc	4/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.459919781229069	2		683	812	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589818	55589818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	154	531	0	ENST00000288135.5:c.1300C>T	p.Pro434Ser	p.P434S	ENST00000288135	NM_000222.2	434	Cca/Tca	8/21	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.459919781229069	2		531	668	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249505	153249505	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	126	587	0	ENST00000281708.4:c.1273T>G	p.Trp425Gly	p.W425G	ENST00000281708	NM_033632.3	425	Tgg/Ggg	9/12	1	2	FACETS	0.945	0.859	1	0.945	0.859	1	CLONAL	1	TRUE	1	0.459919781229069	2		587	580	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978432	2978432	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	192	696	3	ENST00000396946.4:c.898G>A	p.Ala300Thr	p.A300T	ENST00000396946	NM_032415.4	300	Gcc/Acc	7/25	1	2	FACETS	0.952	0.881	1	0.952	0.881	1	CLONAL	1	TRUE	1	0.459919781229069	2		699	877	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729382	41729382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	175	622	1	ENST00000242208.4:c.1147C>T	p.Pro383Ser	p.P383S	ENST00000242208	NM_002192.2	383	Ccc/Tcc	3/3	1	2	FACETS	0.962	0.887	1	0.962	0.887	1	CLONAL	1	TRUE	1	0.459919781229069	2		623	791	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250527	110250527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	113	545	0	ENST00000374672.4:c.148C>T	p.His50Tyr	p.H50Y	ENST00000374672	NM_004235.4	50	Cac/Tac	3/5	1	2	FACETS	0.827	0.746	0.912	0.827	0.746	0.912	CLONAL	1	TRUE	1	0.459919781229069	2		545	594	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128246859	128246859	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	168	687	0	ENST00000265960.3:c.1070C>T	p.Ser357Leu	p.S357L	ENST00000265960	NM_001006617.1	357	tCa/tTa	9/12	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.459919781229069	2		687	723	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0052473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	96	537	0				ENST00000310581	NM_198253.2	-/1132			0.17550396339564	1	FACETS	0.594	0.533	0.657	0.594	0.533	0.657	INDETERMINATE	1	TRUE	0	0.60361431294492	1		537	374	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0052473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	94	367	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	0.559706994347488	1	FACETS	0.843	0.762	0.926	0.843	0.762	0.926	CLONAL	1	TRUE	0	0.60361431294492	1		367	258	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525504	137525504	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	108	429	0	ENST00000367739.4:c.511G>C	p.Val171Leu	p.V171L	ENST00000367739	NM_000416.2	171	Gtg/Ctg	4/7	1	2	FACETS	0.937	0.848	1	0.937	0.848	1	CLONAL	1	TRUE	1	0.60361431294492	2		429	382	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	810	542	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.527389817342746	5	FACETS	0.995	0.968	1	0.995	0.968	1	CLONAL	4	TRUE	1	0.527389817342746	5		542	1382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	212	700	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.117550562538455	5	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.527389817342746	5		700	1262	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1023835002	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	91	483	0	ENST00000558401.1:c.1A>G	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Gtg	1/4	1	2	FACETS	0.5	0.444	0.56	0.5	0.444	0.56	SUBCLONAL	1	TRUE	1	0.527389817342746	2		483	690	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140508697	140508697	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	129	467	0	ENST00000288602.6:c.603G>T	p.Gln201His	p.Q201H	ENST00000288602	NM_004333.4	201	caG/caT	4/18	0.527994366302526	3	FACETS	0.766	0.695	0.841	0.383	0.347	0.421	SUBCLONAL	1	TRUE	1	0.527389817342746	3		467	807	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229510	5229510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1303613614	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	38	142	1	ENST00000357368.4:c.2341G>A	p.Asp781Asn	p.D781N	ENST00000357368	NM_002850.3	781	Gat/Aat	15/38	0.484578100146479	2	FACETS	0.779	0.652	0.917	0.389	0.326	0.459	CLONAL	1	TRUE	0	0.527389817342746	2		143	185	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628612	21628612	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs1326657671	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	85	524	0	ENST00000421138.2:c.1096C>T	p.Gln366Ter	p.Q366*	ENST00000421138		366	Cag/Tag	10/16	0.527389817342746	5	FACETS	0.484	0.426	0.547	0.121	0.106	0.137	SUBCLONAL	1	TRUE	1	0.527389817342746	5		524	1192	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865301	57865301	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	223	676	2	ENST00000228682.2:c.2778G>T	p.Gln926His	p.Q926H	ENST00000228682	NM_005269.2	926	caG/caT	12/12	0.527994366302526	3	FACETS	0.963	0.896	1	0.481	0.448	0.516	CLONAL	1	TRUE	1	0.527389817342746	3		678	1110	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089744	5089745	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	33	270	0	ENST00000381652.3:c.2648dup	p.Leu884AlafsTer4	p.L884Afs*4	ENST00000381652	NM_004972.3	881	gta/gtAa	20/25	0.527994366302526	1	FACETS	0.321	0.262	0.387	0.321	0.262	0.387	SUBCLONAL	1	TRUE	0	0.527389817342746	1		270	287	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36826915	36826915	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	98	652	0	ENST00000373129.3:c.19G>C	p.Asp7His	p.D7H	ENST00000373129	NM_032017.1	7	Gac/Cac	3/12	0.172315786835296	3	FACETS	0.488	0.434	0.545	0.244	0.217	0.273	INDETERMINATE	1	TRUE	1	0.527389817342746	3		652	963	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226551651	226551652	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	196	498	0	ENST00000366794.5:c.2778dup	p.Gly927TrpfsTer5	p.G927Wfs*5	ENST00000366794	NM_001618.3	926	-/T	20/23	0.527994366302526	3	FACETS	1	0.958	1	0.525	0.486	0.565	CLONAL	1	TRUE	1	0.527389817342746	3		498	895	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226466	133226466	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	164	404	0	ENST00000320574.5:c.3592G>T	p.Ala1198Ser	p.A1198S	ENST00000320574	NM_006231.2	1198	Gcc/Tcc	30/49	0.527389817342746	2	FACETS	1	0.981	1	0.597	0.552	0.643	CLONAL	1	TRUE	0	0.527389817342746	2		404	521	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609782	28609782	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	110	557	0	ENST00000241453.7:c.1447T>G	p.Trp483Gly	p.W483G	ENST00000241453	NM_004119.2	483	Tgg/Ggg	12/24	0.480471137164906	2	FACETS	0.597	0.537	0.66	0.298	0.268	0.33	SUBCLONAL	1	TRUE	0	0.527389817342746	2		557	699	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724706	43724706	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	73	667	0	ENST00000382044.4:c.3361C>G	p.Gln1121Glu	p.Q1121E	ENST00000382044	NM_001141980.1	1121	Caa/Gaa	17/28	1	2	FACETS	0.343	0.299	0.39	0.343	0.299	0.39	SUBCLONAL	1	TRUE	1	0.527389817342746	2		667	807	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11114074	11114074	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	133	466	0	ENST00000358026.2:c.2001+1G>T		p.X667_splice	ENST00000358026	NM_001128849.1	667			0.527994366302526	1	FACETS	0.597	0.544	0.653	0.597	0.544	0.653	SUBCLONAL	1	TRUE	0	0.527389817342746	1		466	622	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716024	52716024	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	136	693	0	ENST00000322088.6:c.589G>T	p.Glu197Ter	p.E197*	ENST00000322088	NM_014225.5	197	Gag/Tag	5/15	NA	2	FACETS	0.516	0.468	0.566			1	INDETERMINATE	1	TRUE	NA	0.527389817342746	2		693	1000	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964968	25964968	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	58	577	0	ENST00000435504.4:c.4238G>T	p.Cys1413Phe	p.C1413F	ENST00000435504		1413	tGt/tTt	13/13	0.527994366302526	3	FACETS	0.287	0.246	0.333	0.144	0.123	0.167	SUBCLONAL	1	TRUE	1	0.527389817342746	3		577	968	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973208	25973208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	66	459	0	ENST00000435504.4:c.1217C>T	p.Ala406Val	p.A406V	ENST00000435504		406	gCt/gTt	12/13	0.527994366302526	3	FACETS	0.342	0.295	0.392	0.171	0.147	0.196	SUBCLONAL	1	TRUE	1	0.527389817342746	3		459	926	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306614	41306614	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	448	585	0	ENST00000373198.4:c.1045C>A	p.His349Asn	p.H349N	ENST00000373198	NM_133170.3	349	Cat/Aat	7/32	0.257503055734486	3	FACETS	1	0.989	1	0.725	0.695	0.755	INDETERMINATE	2	TRUE	0	0.527389817342746	3		585	987	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47079182	47079182	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	527	587	0	ENST00000409792.3:c.7324C>G	p.Pro2442Ala	p.P2442A	ENST00000409792	NM_014159.6	2442	Cca/Gca	18/21	0.455958272793315	3	FACETS	1	0.995	1	0.818	0.788	0.848	CLONAL	2	TRUE	0	0.527389817342746	3		587	1029	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750537	41750537	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	278	573	0	ENST00000226382.2:c.91G>T	p.Ala31Ser	p.A31S	ENST00000226382	NM_003924.3	31	Gct/Tct	1/3	0.527994366302526	3	FACETS	1	0.991	1	0.66	0.62	0.7	CLONAL	1	TRUE	1	0.527389817342746	3		573	1010	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948761	55948761	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	150	563	0	ENST00000263923.4:c.3704G>C	p.Ser1235Thr	p.S1235T	ENST00000263923	NM_002253.2	1235	aGt/aCt	28/30	0.527994366302526	3	FACETS	0.736	0.672	0.803	0.368	0.336	0.402	SUBCLONAL	1	TRUE	1	0.527389817342746	3		563	977	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518810	176518810	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs775260233	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	139	597	0	ENST00000292408.4:c.727+1G>T		p.X243_splice	ENST00000292408	NM_213647.1	243			0.484578100146479	2	FACETS	0.705	0.642	0.77	0.352	0.321	0.385	SUBCLONAL	1	TRUE	0	0.527389817342746	2		597	748	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058683	180058683	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	194	667	0	ENST00000261937.6:c.154A>T	p.Arg52Trp	p.R52W	ENST00000261937	NM_182925.4	52	Agg/Tgg	2/30	0.484578100146479	2	FACETS	0.968	0.898	1	0.484	0.449	0.52	CLONAL	1	TRUE	0	0.527389817342746	2		667	760	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322917	31322917	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	113	752	0	ENST00000412585.2:c.979G>T	p.Val327Phe	p.V327F	ENST00000412585	NM_005514.6	327	Gtc/Ttc	5/8	0.294193757609274	3	FACETS	0.459	0.412	0.509	0.153	0.137	0.17	INDETERMINATE	1	TRUE	0	0.527389817342746	3		752	1180	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394400	162394400	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	283	430	0	ENST00000366898.1:c.668C>A	p.Ser223Ter	p.S223*	ENST00000366898	NM_004562.2	223	tCa/tAa	6/12	0.484578100146479	2	FACETS	0.805	0.761	0.848	0.805	0.761	0.848	CLONAL	2	TRUE	0	0.527389817342746	2		430	667	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334994	81334994	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	123	484	0	ENST00000222390.5:c.1833T>A	p.Ser611Arg	p.S611R	ENST00000222390	NM_000601.4	611	agT/agA	16/18	0.527994366302526	3	FACETS	0.768	0.694	0.845	0.384	0.347	0.423	SUBCLONAL	1	TRUE	1	0.527389817342746	3		484	768	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523501	106523501	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	106	328	0	ENST00000359195.3:c.2653G>T	p.Ala885Ser	p.A885S	ENST00000359195	NM_002649.2	885	Gcc/Tcc	8/11	0.527994366302526	3	FACETS	0.862	0.775	0.955	0.431	0.387	0.478	CLONAL	1	TRUE	1	0.527389817342746	3		328	589	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453137	140453137	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913378	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	152	467	0	ENST00000288602.6:c.1798G>T	p.Val600Leu	p.V600L	ENST00000288602	NM_004333.4	600	Gtg/Ttg	15/18	0.527994366302526	3	FACETS	0.948	0.869	1	0.474	0.434	0.516	CLONAL	1	TRUE	1	0.527389817342746	3		467	768	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949639	151949639	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	91	411	0	ENST00000262189.6:c.1461G>T	p.Met487Ile	p.M487I	ENST00000262189	NM_170606.2	487	atG/atT	10/59	0.527994366302526	3	FACETS	0.713	0.633	0.797	0.356	0.316	0.399	SUBCLONAL	1	TRUE	1	0.527389817342746	3		411	612	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069210	5069210	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	30	392	0	ENST00000381652.3:c.1513+2T>A		p.X505_splice	ENST00000381652	NM_004972.3	505			0.527994366302526	1	FACETS	0.275	0.221	0.335	0.275	0.221	0.335	SUBCLONAL	1	TRUE	0	0.527389817342746	1		392	305	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932961	39932966	+	inframe_deletion	In_Frame_Del	DEL	GCGCGG	GCGCGG	-	novel	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	92	658	0	ENST00000378444.4:c.1633_1638del	p.Pro545_Arg546del	p.P545_R546del	ENST00000378444	NM_001123385.1	545	CCGCGC/-	4/15	0.213414634879159	2	FACETS	0.434	0.385	0.487	0.217	0.192	0.244	INDETERMINATE	1	TRUE	0	0.527389817342746	2		658	803	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411234	63411235	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	123	668	0	ENST00000330258.3:c.1932_1933delinsTT	p.Gln644_Ala645delinsHisSer	p.Q644_A645delinsHS	ENST00000330258	NM_152424.3	644	caGGcc/caTTcc	2/2	0.213414634879159	2	FACETS	0.525	0.474	0.578	0.262	0.237	0.289	INDETERMINATE	1	TRUE	0	0.527389817342746	2		668	889	SUCCESS
AR	367	MSKCC	GRCh37	X	66937372	66937372	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	138	669	1	ENST00000374690.3:c.2226G>A	p.Trp742Ter	p.W742*	ENST00000374690	NM_000044.3	742	tgG/tgA	5/8	0.213414634879159	2	FACETS	0.595	0.541	0.651	0.297	0.27	0.326	INDETERMINATE	1	TRUE	0	0.527389817342746	2		670	880	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344880	70344880	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	165	658	0	ENST00000374080.3:c.2110C>A	p.Pro704Thr	p.P704T	ENST00000374080		704	Cca/Aca	15/45	0.213414634879159	2	FACETS	0.683	0.627	0.742	0.342	0.313	0.371	INDETERMINATE	1	TRUE	0	0.527389817342746	2		658	916	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778822	76778822	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	100	579	0	ENST00000373344.5:c.6757G>C	p.Glu2253Gln	p.E2253Q	ENST00000373344	NM_000489.3	2253	Gaa/Caa	31/35	0.213414634879159	2	FACETS	0.647	0.579	0.719	0.324	0.289	0.36	INDETERMINATE	1	TRUE	0	0.527389817342746	2		579	586	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	109	460	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.711	0.642	0.783	0.711	0.642	0.783	SUBCLONAL	1	TRUE	1	0.689065122093636	2		460	445	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0052475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	124	400	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	0.637	0.578	0.698	0.637	0.578	0.698	SUBCLONAL	1	TRUE	1	0.689065122093636	2		400	565	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100983	27100983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	190	642	1	ENST00000324856.7:c.4268del	p.Pro1423LeufsTer58	p.P1423Lfs*58	ENST00000324856	NM_006015.4	1422	tCc/tc	18/20	0.462724318656623	1	FACETS	0.608	0.565	0.651	0.608	0.565	0.651	SUBCLONAL	1	TRUE	0	0.689065122093636	1		643	595	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858928	78858928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	396	556	0	ENST00000306801.3:c.1963G>A	p.Gly655Arg	p.G655R	ENST00000306801	NM_020761.2	655	Ggg/Agg	17/34	0.689065122093636	3	FACETS	0.887	0.848	0.926	0.887	0.848	0.926	CLONAL	2	TRUE	1	0.689065122093636	3		556	871	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0052484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	153	380	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.230902174497306	2	FACETS	1	0.974	1	0.566	0.521	0.613	INDETERMINATE	1	TRUE	0	0.521668585061986	2		380	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0052484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	455	753	0	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.481568984619547	2	FACETS	0.954	0.916	0.992	0.954	0.916	0.992	CLONAL	2	TRUE	0	0.521668585061986	2		753	914	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0052484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	43	478	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.69	0.582	0.807	0.69	0.582	0.807	SUBCLONAL	1	TRUE	1	0.521668585061986	2		478	239	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828827	26828827	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	153	372	0	ENST00000381527.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000381527	NM_001260.1	17	Gag/Aag	1/13	0.400576254675173	5	FACETS	1	0.953	1	0.355	0.324	0.387	CLONAL	1	TRUE	2	0.521668585061986	5		372	983	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587165	212587165	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	35	548	0	ENST00000342788.4:c.836T>G	p.Phe279Cys	p.F279C	ENST00000342788	NM_005235.2	279	tTc/tGc	7/28	0.230902174497306	2	FACETS	0.371	0.304	0.445	0.185	0.152	0.223	INDETERMINATE	1	TRUE	0	0.521668585061986	2		548	362	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934362	68934362	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745857499	NA	P-0052484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	63	514	1	ENST00000288368.4:c.428G>A	p.Arg143Gln	p.R143Q	ENST00000288368	NM_024870.2	143	cGg/cAg	4/40	0.169218847610159	2	FACETS	0.686	0.597	0.782	0.343	0.298	0.391	INDETERMINATE	1	TRUE	0	0.521668585061986	2		515	352	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464358	120464358	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	69	647	0	ENST00000256646.2:c.5288G>A	p.Gly1763Glu	p.G1763E	ENST00000256646	NM_024408.3	1763	gGg/gAg	29/34	1	2	FACETS	0.354	0.307	0.404	0.354	0.307	0.404	SUBCLONAL	1	TRUE	1	0.521668585061986	2		647	748	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117690	70117691	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0052484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	93	613	0	ENST00000245479.2:c.162dup	p.Lys55GlnfsTer197	p.K55Qfs*197	ENST00000245479	NM_000346.3	53	ttc/ttCc	1/3	0.481568984619547	2	FACETS	0.483	0.429	0.541	0.242	0.214	0.271	SUBCLONAL	1	TRUE	0	0.521668585061986	2		613	738	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0052485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	57	537	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.170589577325247	2		537	509	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0052485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	80	458	0	ENST00000311936.3:c.34_35delinsTT	p.Gly12Phe	p.G12F	ENST00000311936	NM_004985.3	12	GGt/TTt	2/5	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.170589577325247	2		458	793	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0052485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	19	208	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	1	2	FACETS	0.782	0.593	1	0.782	0.593	1	CLONAL	1	TRUE	1	0.170589577325247	2		208	285	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285837	39285837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397517164	NA	P-0052485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	39	450	0	ENST00000402219.2:c.322G>A	p.Glu108Lys	p.E108K	ENST00000402219	NM_005633.3	108	Gaa/Aaa	3/23	1	2	FACETS	0.65	0.538	0.777	0.65	0.538	0.777	SUBCLONAL	1	TRUE	1	0.170589577325247	2		450	703	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664562	29664562	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	95	484	0	ENST00000356175.3:c.6541T>G	p.Leu2181Val	p.L2181V	ENST00000356175	NM_000267.3	2181	Ttg/Gtg	42/57	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.170589577325247	2		484	910	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0052486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	245	719	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.197538210364009	2	FACETS	0.795	0.742	0.849	0.795	0.742	0.849	SUBCLONAL	2	TRUE	0	0.277722686779106	2		719	1110	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302595	15302595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1160655218	NA	P-0052486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	79	741	2	ENST00000263388.2:c.763G>A	p.Val255Ile	p.V255I	ENST00000263388	NM_000435.2	255	Gtc/Atc	5/33	0.197538210364009	2	FACETS	0.567	0.497	0.642	0.283	0.248	0.321	SUBCLONAL	1	TRUE	0	0.277722686779106	2		743	1004	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109323524	109323524	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	109	705	1	ENST00000436639.2:c.302G>T	p.Arg101Leu	p.R101L	ENST00000436639	NM_014454.2	101	cGa/cTa	2/10	0.190589284331487	2	FACETS	0.764	0.684	0.848	0.382	0.342	0.424	SUBCLONAL	1	TRUE	0	0.277722686779106	2		706	1028	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0052487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	255	558	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.509066506304144	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.509066506304144	1		558	604	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458698	120458698	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	245	484	0	ENST00000256646.2:c.6647C>G	p.Thr2216Ser	p.T2216S	ENST00000256646	NM_024408.3	2216	aCt/aGt	34/34	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.509066506304144	2		484	817	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593681	55593681	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	66	521	0	ENST00000288135.5:c.1747G>C	p.Glu583Gln	p.E583Q	ENST00000288135	NM_000222.2	583	Gag/Cag	11/21	0.509066506304144	1	FACETS	0.304	0.264	0.348	0.304	0.264	0.348	SUBCLONAL	1	TRUE	0	0.509066506304144	1		521	635	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0052488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	88	578	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.834	0.742	0.931	1	0.982	1	CLONAL	2	FALSE	1	0.224516351624023	2		578	470	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100696	67100696	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	62	573	0	ENST00000412916.2:c.394G>T	p.Ala132Ser	p.A132S	ENST00000412916		132	Gcc/Tcc	4/6	0.224516351624023	3	FACETS	1	0.969	1	0.731	0.634	0.837	CLONAL	1	FALSE	1	0.224516351624023	3		573	420	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781381	3781381	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	67	651	1	ENST00000262367.5:c.4984G>T	p.Asp1662Tyr	p.D1662Y	ENST00000262367	NM_004380.2	1662	Gat/Tat	30/31	0.224516351624023	3	FACETS	0.93	0.819	1	1	0.972	1	CLONAL	3	FALSE	1	0.224516351624023	3		652	238	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948770	55948770	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	50	468	0	ENST00000263923.4:c.3695G>T	p.Arg1232Leu	p.R1232L	ENST00000263923	NM_002253.2	1232	cGg/cTg	28/30	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	1	0.224516351624023	2		468	347	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044941	47044941	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	27	632	0	ENST00000377604.3:c.2268del	p.Trp756CysfsTer46	p.W756Cfs*46	ENST00000377604	NM_001204468.1	756	tGg/tg	20/24	0.224516351624023	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	FALSE	0	0.224516351624023	1		632	163	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0052489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	321	432	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.62966089830232	2	FACETS	0.99	0.949	1	0.99	0.949	1	CLONAL	2	TRUE	0	0.62966089830232	2		432	515	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508499	106508499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752602335	NA	P-0052489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	93	365	0	ENST00000359195.3:c.493G>A	p.Val165Ile	p.V165I	ENST00000359195	NM_002649.2	165	Gtc/Atc	2/11	0.62966089830232	4	FACETS	0.986	0.881	1	0.329	0.293	0.366	CLONAL	1	TRUE	1	0.62966089830232	4		365	488	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371734	55371734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	128	423	1	ENST00000297316.4:c.424C>T	p.Arg142Cys	p.R142C	ENST00000297316	NM_022454.3	142	Cgc/Tgc	2/2	0.62966089830232	7	FACETS	1	0.911	1	0.168	0.151	0.185	CLONAL	1	TRUE	1	0.62966089830232	7		424	1039	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562663	95562663	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	181	461	0	ENST00000393063.1:c.4594G>T	p.Glu1532Ter	p.E1532*	ENST00000393063	NM_030621.3	1532	Gaa/Taa	24/28	0.62966089830232	3	FACETS	1	0.98	1	0.584	0.541	0.629	CLONAL	1	TRUE	1	0.62966089830232	3		461	647	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579364	7579365	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGTAG	novel	NA	P-0052489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	412	774	1	ENST00000269305.4:c.318_322dup	p.Gly108AlafsTer17	p.G108Afs*17	ENST00000269305	NM_001126112.2	108	ggt/gCTACGgt	4/11	0.62966089830232	2	FACETS	0.932	0.897	0.967	0.932	0.897	0.967	CLONAL	2	TRUE	0	0.62966089830232	2		775	702	SUCCESS
ATR	545	MSKCC	GRCh37	3	142253923	142253923	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	129	165	0	ENST00000350721.4:c.3944A>T	p.Gln1315Leu	p.Q1315L	ENST00000350721	NM_001184.3	1315	cAg/cTg	21/47	0.62966089830232	3	FACETS	1	0.963	1	0.552	0.503	0.602	CLONAL	1	TRUE	1	0.62966089830232	3		165	488	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438166	110438166	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	44	186	0	ENST00000375856.3:c.235G>A	p.Glu79Lys	p.E79K	ENST00000375856	NM_003749.2	79	Gag/Aag	1/2	0.392576953847527	1	FACETS	0.23	0.193	0.271	0.23	0.193	0.271	INDETERMINATE	1	TRUE	0	0.676131253213113	1		186	374	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868405	117868405	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	79	402	0	ENST00000297338.2:c.937G>T	p.Val313Phe	p.V313F	ENST00000297338	NM_006265.2	313	Gtt/Ttt	8/14	0.392576953847527	1	FACETS	0.249	0.218	0.281	0.249	0.218	0.281	INDETERMINATE	1	TRUE	0	0.676131253213113	1		402	622	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934573	NA	P-0052491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	139	487	0	ENST00000269305.4:c.722C>G	p.Ser241Cys	p.S241C	ENST00000269305	NM_001126112.2	241	tCc/tGc	7/11	0.337846074342088	1	FACETS	0.993	0.907	1	0.993	0.907	1	CLONAL	1	TRUE	0	0.352504757424402	1		487	654	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060883	38060883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	129	437	0	ENST00000250448.2:c.1106C>T	p.Ser369Phe	p.S369F	ENST00000250448	NM_004496.3	369	tCt/tTt	2/2	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.352504757424402	2		437	701	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981475	201981475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	73	502	2	ENST00000359651.3:c.389C>T	p.Ser130Phe	p.S130F	ENST00000359651		130	tCc/tTc	3/8	1	2	FACETS	0.396	0.345	0.451	0.396	0.345	0.451	SUBCLONAL	1	TRUE	1	0.353102137729282	2		504	1045	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652329	206652329	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	90	547	0	ENST00000367120.3:c.1036G>A	p.Ala346Thr	p.A346T	ENST00000367120	NM_014002.3	346	Gcc/Acc	10/22	1	2	FACETS	0.398	0.352	0.448	0.398	0.352	0.448	SUBCLONAL	1	TRUE	1	0.353102137729282	2		547	1280	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771477	112771477	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	54	484	0	ENST00000369452.4:c.1650C>G	p.Asn550Lys	p.N550K	ENST00000369452	NM_007373.3	550	aaC/aaG	9/9	0.17998094346457	1	FACETS	0.489	0.418	0.567	0.489	0.418	0.567	INDETERMINATE	1	TRUE	0	0.353102137729282	1		484	515	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10283822	10283822	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762056108	NA	P-0052492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	52	544	0	ENST00000340748.4:c.664C>T	p.Pro222Ser	p.P222S	ENST00000340748		222	Cct/Tct	8/40	1	2	FACETS	0.45	0.383	0.525	0.45	0.383	0.525	SUBCLONAL	1	TRUE	1	0.353102137729282	2		544	654	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948787	17948788	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTA	novel	NA	P-0052492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	170	544	0	ENST00000458235.1:c.1654_1655insTAG	p.Thr551_Glu552insVal	p.T551_E552insV	ENST00000458235	NM_000215.3	552	gag/gTAGag	12/24	1	2	FACETS	0.82	0.753	0.891	0.82	0.753	0.891	CLONAL	1	TRUE	1	0.353102137729282	2		544	1174	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257573	19257573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	83	543	0	ENST00000162023.5:c.653C>T	p.Pro218Leu	p.P218L	ENST00000162023		218	cCc/cTc	10/13	1	2	FACETS	0.41	0.36	0.463	0.41	0.36	0.463	SUBCLONAL	1	TRUE	1	0.353102137729282	2		543	1147	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966559	25966559	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	164	604	0	ENST00000435504.4:c.2647A>C	p.Thr883Pro	p.T883P	ENST00000435504		883	Act/Cct	13/13	0.17998094346457	1	FACETS	0.915	0.841	0.992	0.915	0.841	0.992	INDETERMINATE	1	TRUE	0	0.353102137729282	1		604	836	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747890	41747890	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	114	289	0	ENST00000226382.2:c.879C>G	p.Ser293Arg	p.S293R	ENST00000226382	NM_003924.3	293	agC/agG	3/3	1	2	FACETS	0.951	0.857	1	0.951	0.857	1	CLONAL	1	TRUE	1	0.353102137729282	2		289	679	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630098	187630098	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	60	512	0	ENST00000441802.2:c.884T>C	p.Val295Ala	p.V295A	ENST00000441802	NM_005245.3	295	gTg/gCg	2/27	1	2	FACETS	0.479	0.412	0.552	0.479	0.412	0.552	SUBCLONAL	1	TRUE	1	0.353102137729282	2		512	710	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840006	27840063	+	frameshift_variant	Frame_Shift_Del	DEL	CGCTCTTGCGAGCCGCCTTGGTGGCCAGCTGCTTGCGCGGCGCTTTGCCGCCGGTGGA	CGCTCTTGCGAGCCGCCTTGGTGGCCAGCTGCTTGCGCGGCGCTTTGCCGCCGGTGGA	-	novel	NA	P-0052492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	117	468	0	ENST00000328488.2:c.31_88del	p.Ser11LeufsTer33	p.S11Lfs*33	ENST00000328488	NM_003533.2	11	TCCACCGGCGGCAAAGCGCCGCGCAAGCAGCTGGCCACCAAGGCGGCTCGCAAGAGCGct/ct	1/1	0.190034541570818	4	FACETS	0.959	0.864	1	0.48	0.432	0.53	INDETERMINATE	1	TRUE	2	0.353102137729282	4		468	935	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0052493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	212	449	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.32103022821971	5	FACETS	1	0.982	1	1	0.993	1	CLONAL	5	TRUE	1	0.32103022821971	5		449	360	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576258	88576258	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	83	381	0	ENST00000360948.2:c.1415G>T	p.Ser472Ile	p.S472I	ENST00000360948	NM_001012338.2	472	aGt/aTt	13/19	0.289320469169619	3	FACETS	1	0.942	1	0.722	0.645	0.802	CLONAL	2	TRUE	0	0.32103022821971	3		381	277	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519980	NA	P-0052493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	129	592	0	ENST00000269305.4:c.528C>G	p.Cys176Trp	p.C176W	ENST00000269305	NM_001126112.2	176	tgC/tgG	5/11	0.32103022821971	2	FACETS	0.933	0.862	1	1	0.987	1	CLONAL	3	TRUE	0	0.32103022821971	2		592	287	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524744	187524744	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375882967	NA	P-0052493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	59	643	1	ENST00000441802.2:c.10936C>T	p.Arg3646Cys	p.R3646C	ENST00000441802	NM_005245.3	3646	Cgc/Tgc	19/27	1	2	FACETS	0.978	0.845	1	0.978	0.845	1	CLONAL	1	TRUE	1	0.32103022821971	2		644	376	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830249	72830249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772830273	NA	P-0052493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	69	410	1	ENST00000268489.5:c.6332C>T	p.Pro2111Leu	p.P2111L	ENST00000268489	NM_006885.3	2111	cCg/cTg	9/10	0.289320469169619	3	FACETS	0.844	0.749	0.943	0.844	0.749	0.943	CLONAL	3	TRUE	0	0.32103022821971	3		411	197	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0052494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	651	507	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.859142079617325	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.859142079617325	2		507	751	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305454	65305454	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	39	525	0	ENST00000342505.4:c.2674del	p.Cys892AlafsTer19	p.C892Afs*19	ENST00000342505	NM_002227.2	892	Tgc/gc	20/25	0.859142079617325	1	FACETS	0.146	0.121	0.174	0.146	0.121	0.174	SUBCLONAL	1	TRUE	0	0.859142079617325	1		525	354	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	159	460	0				ENST00000310581	NM_198253.2	-/1132			0.604840760497748	4	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	2	0.708183023679357	4		460	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0052495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	483	928	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.708183023679357	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.708183023679357	2		928	638	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978935	25978935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	130	599	0	ENST00000435504.4:c.988G>A	p.Glu330Lys	p.E330K	ENST00000435504		330	Gaa/Aaa	10/13	0.636705449176053	3	FACETS	0.881	0.803	0.963	0.441	0.401	0.482	CLONAL	1	TRUE	1	0.708183023679357	3		599	564	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265579	198265579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	152	772	0	ENST00000335508.6:c.2578G>A	p.Glu860Lys	p.E860K	ENST00000335508	NM_012433.2	860	Gaa/Aaa	18/25	0.636705449176053	3	FACETS	0.953	0.875	1	0.476	0.437	0.517	CLONAL	1	TRUE	1	0.708183023679357	3		772	610	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138407755	138407755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371601853	NA	P-0052495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	137	681	1	ENST00000289153.2:c.2098C>T	p.Arg700Trp	p.R700W	ENST00000289153	NM_006219.2	700	Cgg/Tgg	14/22	0.604840760497748	4	FACETS	0.791	0.719	0.866	0.395	0.359	0.433	SUBCLONAL	1	TRUE	2	0.708183023679357	4		682	836	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523709	176523709	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761135791	NA	P-0052495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	180	887	0	ENST00000292408.4:c.2120G>A	p.Arg707Gln	p.R707Q	ENST00000292408	NM_213647.1	707	cGg/cAg	16/18	0.708183023679357	2	FACETS	0.892	0.827	0.958	0.446	0.413	0.479	CLONAL	1	TRUE	0	0.708183023679357	2		887	570	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089980	16089980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1431286801	NA	P-0052495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	130	463	0	ENST00000268712.3:c.130C>T	p.Arg44Cys	p.R44C	ENST00000268712	NM_006311.3	44	Cgt/Tgt	3/46	0.708183023679357	2	FACETS	1	0.934	1	0.51	0.468	0.553	CLONAL	1	TRUE	0	0.708183023679357	2		463	360	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094345	27094346	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	319	701	0	ENST00000324856.7:c.3054dup	p.Glu1019Ter	p.E1019*	ENST00000324856	NM_006015.4	1018	cct/ccTt	11/20	0.441474932987783	5	FACETS	0.887	0.844	0.931	0.887	0.844	0.931	CLONAL	3	TRUE	2	0.708183023679357	5		701	698	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555911	226555911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	191	697	1	ENST00000366794.5:c.2266G>A	p.Asp756Asn	p.D756N	ENST00000366794	NM_001618.3	756	Gac/Aac	16/23	0.708183023679357	3	FACETS	1	0.963	1	0.353	0.327	0.379	CLONAL	1	TRUE	0	0.708183023679357	3		698	690	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182177	99182177	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	204	782	0	ENST00000074304.5:c.2242C>T	p.Gln748Ter	p.Q748*	ENST00000074304	NM_001134224.1	748	Cag/Tag	21/26	0.636705449176053	3	FACETS	1	0.978	1	0.558	0.519	0.598	CLONAL	1	TRUE	1	0.708183023679357	3		782	699	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335891	73335891	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	398	672	0	ENST00000377767.4:c.2404C>G	p.Pro802Ala	p.P802A	ENST00000377767	NM_014953.3	802	Cca/Gca	18/21	0.708183023679357	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.708183023679357	3		672	500	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245993	16245993	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	150	563	0	ENST00000375759.3:c.1616G>C	p.Arg539Pro	p.R539P	ENST00000375759	NM_015001.2	539	cGa/cCa	8/15	0.708183023679357	3	FACETS	1	0.958	1	0.533	0.49	0.578	CLONAL	1	TRUE	1	0.708183023679357	3		563	538	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450704	70450704	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	192	769	0	ENST00000373644.4:c.5544C>G	p.Phe1848Leu	p.F1848L	ENST00000373644	NM_030625.2	1848	ttC/ttG	12/12	0.708183023679357	2	FACETS	1	0.97	1	0.534	0.498	0.57	CLONAL	1	TRUE	0	0.708183023679357	2		769	508	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451072	70451072	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0052495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	157	851	0	ENST00000373644.4:c.5912C>G	p.Ser1971Ter	p.S1971*	ENST00000373644	NM_030625.2	1971	tCa/tGa	12/12	0.708183023679357	2	FACETS	0.892	0.823	0.963	0.446	0.411	0.482	CLONAL	1	TRUE	0	0.708183023679357	2		851	497	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417835	32417835	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	137	670	0	ENST00000332351.3:c.1217C>G	p.Ser406Cys	p.S406C	ENST00000332351	NM_024426.4	406	tCc/tGc	7/10	1	2	FACETS	0.977	0.898	1	0.977	0.898	1	CLONAL	1	TRUE	1	0.708183023679357	2		670	396	SUCCESS
EED	8726	MSKCC	GRCh37	11	85967531	85967531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	113	569	0	ENST00000263360.6:c.529C>T	p.Pro177Ser	p.P177S	ENST00000263360	NM_003797.3	177	Cct/Tct	5/12	1	2	FACETS	0.994	0.906	1	0.994	0.906	1	CLONAL	1	TRUE	1	0.708183023679357	2		569	321	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436922	49436922	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	427	885	0	ENST00000301067.7:c.5581G>C	p.Glu1861Gln	p.E1861Q	ENST00000301067	NM_003482.3	1861	Gag/Cag	25/54	0.708183023679357	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.708183023679357	2		885	560	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254247	133254247	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	325	753	0	ENST00000320574.5:c.637G>C	p.Asp213His	p.D213H	ENST00000320574	NM_006231.2	213	Gac/Cac	7/49	0.708183023679357	3	FACETS	0.956	0.911	1	0.637	0.607	0.667	CLONAL	2	TRUE	0	0.708183023679357	3		753	650	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041731	42041731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	118	650	0	ENST00000219905.7:c.5926G>A	p.Asp1976Asn	p.D1976N	ENST00000219905	NM_001164273.1	1976	Gac/Aac	17/24	0.602386054929142	3	FACETS	0.881	0.799	0.967	0.441	0.399	0.484	CLONAL	1	TRUE	1	0.708183023679357	3		650	512	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478232	99478232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781148431	NA	P-0052495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	128	530	1	ENST00000268035.6:c.3136G>A	p.Glu1046Lys	p.E1046K	ENST00000268035	NM_000875.3	1046	Gag/Aag	16/21	0.602386054929142	3	FACETS	1	0.938	1	0.517	0.472	0.565	CLONAL	1	TRUE	1	0.708183023679357	3		531	473	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486167	99486167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	122	680	0	ENST00000268035.6:c.3473G>A	p.Arg1158Gln	p.R1158Q	ENST00000268035	NM_000875.3	1158	cGa/cAa	19/21	0.602386054929142	3	FACETS	0.89	0.809	0.976	0.445	0.404	0.488	CLONAL	1	TRUE	1	0.708183023679357	3		680	524	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813700	50813700	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	244	837	0	ENST00000398568.2:c.1254C>G	p.Phe418Leu	p.F418L	ENST00000398568	NM_001042412.1	418	ttC/ttG	8/18	0.649109721963485	5	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.708183023679357	5		837	1265	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821842	72821842	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	204	776	0	ENST00000268489.5:c.10333G>C	p.Glu3445Gln	p.E3445Q	ENST00000268489	NM_006885.3	3445	Gaa/Caa	10/10	0.708183023679357	6	FACETS	1	0.988	1	0.446	0.413	0.48	CLONAL	1	TRUE	3	0.708183023679357	6		776	1040	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752882	42752882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	159	1013	0	ENST00000222329.4:c.1382C>T	p.Pro461Leu	p.P461L	ENST00000222329	NM_006494.2	461	cCt/cTt	4/4	0.441474932987783	5	FACETS	1	0.976	1	0.389	0.356	0.422	CLONAL	1	TRUE	2	0.708183023679357	5		1013	794	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090413	37090413	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	141	739	0	ENST00000231790.2:c.2008A>G	p.Lys670Glu	p.K670E	ENST00000231790	NM_000249.3	670	Aag/Gag	18/19	0.708183023679357	3	FACETS	0.906	0.829	0.987	0.453	0.414	0.494	CLONAL	1	TRUE	1	0.708183023679357	3		739	595	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162634	47162634	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	118	603	0	ENST00000409792.3:c.3492G>C	p.Gln1164His	p.Q1164H	ENST00000409792	NM_014159.6	1164	caG/caC	3/21	0.708183023679357	3	FACETS	0.91	0.825	0.998	0.455	0.412	0.499	CLONAL	1	TRUE	1	0.708183023679357	3		603	496	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651382	52651382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	181	816	0	ENST00000394830.3:c.1714G>A	p.Glu572Lys	p.E572K	ENST00000394830	NM_018313.4	572	Gag/Aag	15/30	0.708183023679357	3	FACETS	0.983	0.91	1	0.492	0.455	0.53	CLONAL	1	TRUE	1	0.708183023679357	3		816	704	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702613	52702613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1372633093	NA	P-0052495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	163	679	1	ENST00000394830.3:c.285G>A	p.Met95Ile	p.M95I	ENST00000394830	NM_018313.4	95	atG/atA	4/30	0.708183023679357	3	FACETS	1	0.964	1	0.537	0.496	0.581	CLONAL	1	TRUE	1	0.708183023679357	3		680	580	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169991081	169991081	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs774546861	NA	P-0052495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	151	738	0	ENST00000295797.4:c.599T>C	p.Val200Ala	p.V200A	ENST00000295797	NM_002740.5	200	gTg/gCg	7/18	0.604840760497748	4	FACETS	0.974	0.892	1	0.487	0.446	0.53	CLONAL	1	TRUE	2	0.708183023679357	4		738	748	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172143	32172143	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	215	789	0	ENST00000375023.3:c.2889G>C	p.Gln963His	p.Q963H	ENST00000375023	NM_004557.3	963	caG/caC	19/30	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.708183023679357	2		789	544	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622275	162622275	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	115	602	0	ENST00000366898.1:c.422C>A	p.Ser141Ter	p.S141*	ENST00000366898	NM_004562.2	141	tCa/tAa	4/12	1	2	FACETS	0.964	0.879	1	0.964	0.879	1	CLONAL	1	TRUE	1	0.708183023679357	2		602	337	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845745	151845745	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	212	881	0	ENST00000262189.6:c.13267G>C	p.Asp4423His	p.D4423H	ENST00000262189	NM_170606.2	4423	Gac/Cac	52/59	0.708183023679357	4	FACETS	1	0.952	1	0.516	0.479	0.554	CLONAL	1	TRUE	2	0.708183023679357	4		881	991	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507321	8507321	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs750349056	NA	P-0052495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	95	608	0	ENST00000356435.5:c.1657G>C	p.Asp553His	p.D553H	ENST00000356435		553	Gat/Cat	11/35	0.253589525921074	3	FACETS	0.998	0.896	1	0.333	0.298	0.368	INDETERMINATE	1	TRUE	0	0.708183023679357	3		608	364	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	112	460	0				ENST00000310581	NM_198253.2	-/1132			0.251499621957603	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.415319846332616	4		460	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	310	928	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.365755004873324	2	FACETS	0.888	0.84	0.936	0.888	0.84	0.936	CLONAL	2	TRUE	0	0.415319846332616	2		928	841	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978935	25978935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	118	599	0	ENST00000435504.4:c.988G>A	p.Glu330Lys	p.E330K	ENST00000435504		330	Gaa/Aaa	10/13	0.364090305507409	3	FACETS	0.854	0.77	0.942	0.427	0.385	0.471	CLONAL	1	TRUE	1	0.415319846332616	3		599	804	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265579	198265579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	121	772	0	ENST00000335508.6:c.2578G>A	p.Glu860Lys	p.E860K	ENST00000335508	NM_012433.2	860	Gaa/Aaa	18/25	0.364090305507409	3	FACETS	0.819	0.74	0.903	0.41	0.37	0.452	CLONAL	1	TRUE	1	0.415319846332616	3		772	859	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138407755	138407755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371601853	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	113	681	1	ENST00000289153.2:c.2098C>T	p.Arg700Trp	p.R700W	ENST00000289153	NM_006219.2	700	Cgg/Tgg	14/22	0.251499621957603	4	FACETS	0.769	0.69	0.852	0.384	0.345	0.426	SUBCLONAL	1	TRUE	2	0.415319846332616	4		682	1002	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523709	176523709	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761135791	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	164	887	0	ENST00000292408.4:c.2120G>A	p.Arg707Gln	p.R707Q	ENST00000292408	NM_213647.1	707	cGg/cAg	16/18	0.365755004873324	2	FACETS	1	0.923	1	0.502	0.461	0.544	CLONAL	1	TRUE	0	0.415319846332616	2		887	787	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089980	16089980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1431286801	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	94	463	0	ENST00000268712.3:c.130C>T	p.Arg44Cys	p.R44C	ENST00000268712	NM_006311.3	44	Cgt/Tgt	3/46	0.365755004873324	2	FACETS	0.823	0.734	0.917	0.412	0.367	0.459	CLONAL	1	TRUE	0	0.415319846332616	2		463	550	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094345	27094346	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	287	701	0	ENST00000324856.7:c.3054dup	p.Glu1019Ter	p.E1019*	ENST00000324856	NM_006015.4	1018	cct/ccTt	11/20	0.251499621957603	4	FACETS	0.972	0.915	1	0.972	0.915	1	CLONAL	2	TRUE	2	0.415319846332616	4		701	1006	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100129	27100129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	72	557	0	ENST00000324856.7:c.3925C>T	p.Leu1309Phe	p.L1309F	ENST00000324856	NM_006015.4	1309	Ctc/Ttc	16/20	0.251499621957603	4	FACETS	0.473	0.412	0.539	0.236	0.206	0.27	SUBCLONAL	1	TRUE	2	0.415319846332616	4		557	1038	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555911	226555911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	140	697	1	ENST00000366794.5:c.2266G>A	p.Asp756Asn	p.D756N	ENST00000366794	NM_001618.3	756	Gac/Aac	16/23	0.415319846332616	4	FACETS	0.995	0.905	1	0.332	0.301	0.363	CLONAL	1	TRUE	1	0.415319846332616	4		698	959	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182177	99182177	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	148	782	0	ENST00000074304.5:c.2242C>T	p.Gln748Ter	p.Q748*	ENST00000074304	NM_001134224.1	748	Cag/Tag	21/26	0.364090305507409	3	FACETS	0.888	0.811	0.97	0.444	0.405	0.485	CLONAL	1	TRUE	1	0.415319846332616	3		782	969	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335891	73335891	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	470	672	0	ENST00000377767.4:c.2404C>G	p.Pro802Ala	p.P802A	ENST00000377767	NM_014953.3	802	Cca/Gca	18/21	0.415319846332616	3	FACETS	0.989	0.951	1	0.989	0.951	1	CLONAL	3	TRUE	0	0.415319846332616	3		672	921	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245993	16245993	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	104	563	0	ENST00000375759.3:c.1616G>C	p.Arg539Pro	p.R539P	ENST00000375759	NM_015001.2	539	cGa/cCa	8/15	0.251499621957603	4	FACETS	0.797	0.713	0.887	0.399	0.356	0.444	SUBCLONAL	1	TRUE	2	0.415319846332616	4		563	889	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450704	70450704	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	134	769	0	ENST00000373644.4:c.5544C>G	p.Phe1848Leu	p.F1848L	ENST00000373644	NM_030625.2	1848	ttC/ttG	12/12	0.365755004873324	2	FACETS	0.911	0.829	0.997	0.456	0.414	0.499	CLONAL	1	TRUE	0	0.415319846332616	2		769	708	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451072	70451072	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	142	851	0	ENST00000373644.4:c.5912C>G	p.Ser1971Ter	p.S1971*	ENST00000373644	NM_030625.2	1971	tCa/tGa	12/12	0.365755004873324	2	FACETS	0.915	0.835	0.999	0.458	0.417	0.5	CLONAL	1	TRUE	0	0.415319846332616	2		851	747	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417835	32417835	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	105	670	0	ENST00000332351.3:c.1217C>G	p.Ser406Cys	p.S406C	ENST00000332351	NM_024426.4	406	tCc/tGc	7/10	1	2	FACETS	0.804	0.721	0.891	0.804	0.721	0.891	CLONAL	1	TRUE	1	0.415319846332616	2		670	629	SUCCESS
EED	8726	MSKCC	GRCh37	11	85967531	85967531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	93	569	0	ENST00000263360.6:c.529C>T	p.Pro177Ser	p.P177S	ENST00000263360	NM_003797.3	177	Cct/Tct	5/12	1	2	FACETS	0.826	0.737	0.921	0.826	0.737	0.921	CLONAL	1	TRUE	1	0.415319846332616	2		569	542	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436922	49436922	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	321	885	0	ENST00000301067.7:c.5581G>C	p.Glu1861Gln	p.E1861Q	ENST00000301067	NM_003482.3	1861	Gag/Cag	25/54	0.336994967307948	3	FACETS	1	0.981	1	0.714	0.677	0.752	CLONAL	2	TRUE	0	0.415319846332616	3		885	871	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254247	133254247	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	246	753	0	ENST00000320574.5:c.637G>C	p.Asp213His	p.D213H	ENST00000320574	NM_006231.2	213	Gac/Cac	7/49	0.336994967307948	3	FACETS	0.86	0.806	0.915	0.573	0.537	0.61	CLONAL	2	TRUE	0	0.415319846332616	3		753	832	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041731	42041731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	93	650	0	ENST00000219905.7:c.5926G>A	p.Asp1976Asn	p.D1976N	ENST00000219905	NM_001164273.1	1976	Gac/Aac	17/24	0.377862448155277	3	FACETS	0.798	0.71	0.892	0.399	0.355	0.446	SUBCLONAL	1	TRUE	1	0.415319846332616	3		650	678	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478232	99478232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781148431	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	84	530	1	ENST00000268035.6:c.3136G>A	p.Glu1046Lys	p.E1046K	ENST00000268035	NM_000875.3	1046	Gag/Aag	16/21	0.377862448155277	3	FACETS	0.862	0.762	0.968	0.431	0.381	0.484	CLONAL	1	TRUE	1	0.415319846332616	3		531	567	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486167	99486167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	98	680	0	ENST00000268035.6:c.3473G>A	p.Arg1158Gln	p.R1158Q	ENST00000268035	NM_000875.3	1158	cGa/cAa	19/21	0.377862448155277	3	FACETS	0.769	0.686	0.857	0.385	0.343	0.429	SUBCLONAL	1	TRUE	1	0.415319846332616	3		680	741	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813700	50813700	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	158	837	0	ENST00000398568.2:c.1254C>G	p.Phe418Leu	p.F418L	ENST00000398568	NM_001042412.1	418	ttC/ttG	8/18	0.251499621957603	4	FACETS	0.868	0.793	0.946	0.434	0.396	0.473	CLONAL	1	TRUE	2	0.415319846332616	4		837	1241	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821842	72821842	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	142	776	0	ENST00000268489.5:c.10333G>C	p.Glu3445Gln	p.E3445Q	ENST00000268489	NM_006885.3	3445	Gaa/Caa	10/10	0.251499621957603	4	FACETS	0.987	0.898	1	0.493	0.449	0.54	CLONAL	1	TRUE	2	0.415319846332616	4		776	981	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752882	42752882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	172	1013	0	ENST00000222329.4:c.1382C>T	p.Pro461Leu	p.P461L	ENST00000222329	NM_006494.2	461	cCt/cTt	4/4	0.251499621957603	4	FACETS	0.911	0.836	0.989	0.455	0.418	0.495	CLONAL	1	TRUE	2	0.415319846332616	4		1013	1287	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090413	37090413	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	105	739	0	ENST00000231790.2:c.2008A>G	p.Lys670Glu	p.K670E	ENST00000231790	NM_000249.3	670	Aag/Gag	18/19	0.364090305507409	3	FACETS	0.774	0.693	0.86	0.387	0.346	0.43	SUBCLONAL	1	TRUE	1	0.415319846332616	3		739	789	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162634	47162634	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	124	603	0	ENST00000409792.3:c.3492G>C	p.Gln1164His	p.Q1164H	ENST00000409792	NM_014159.6	1164	caG/caC	3/21	0.364090305507409	3	FACETS	0.982	0.89	1	0.491	0.445	0.54	CLONAL	1	TRUE	1	0.415319846332616	3		603	734	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651382	52651382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	166	816	0	ENST00000394830.3:c.1714G>A	p.Glu572Lys	p.E572K	ENST00000394830	NM_018313.4	572	Gag/Aag	15/30	0.364090305507409	3	FACETS	0.983	0.903	1	0.492	0.451	0.534	CLONAL	1	TRUE	1	0.415319846332616	3		816	982	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702613	52702613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1372633093	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	96	679	1	ENST00000394830.3:c.285G>A	p.Met95Ile	p.M95I	ENST00000394830	NM_018313.4	95	atG/atA	4/30	0.364090305507409	3	FACETS	0.866	0.772	0.965	0.433	0.386	0.483	CLONAL	1	TRUE	1	0.415319846332616	3		680	645	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169991081	169991081	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs774546861	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	126	738	0	ENST00000295797.4:c.599T>C	p.Val200Ala	p.V200A	ENST00000295797	NM_002740.5	200	gTg/gCg	7/18	0.251499621957603	4	FACETS	0.89	0.805	0.98	0.445	0.402	0.49	CLONAL	1	TRUE	2	0.415319846332616	4		738	965	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172143	32172143	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	125	789	0	ENST00000375023.3:c.2889G>C	p.Gln963His	p.Q963H	ENST00000375023	NM_004557.3	963	caG/caC	19/30	1	2	FACETS	0.803	0.727	0.882	0.803	0.727	0.882	CLONAL	1	TRUE	1	0.415319846332616	2		789	750	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622275	162622275	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	125	602	0	ENST00000366898.1:c.422C>A	p.Ser141Ter	p.S141*	ENST00000366898	NM_004562.2	141	tCa/tAa	4/12	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.415319846332616	2		602	559	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845745	151845745	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	166	881	0	ENST00000262189.6:c.13267G>C	p.Asp4423His	p.D4423H	ENST00000262189	NM_170606.2	4423	Gac/Cac	52/59	0.415319846332616	4	FACETS	0.872	0.799	0.948			1	CLONAL	1	TRUE	NA	0.415319846332616	4		881	1298	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507321	8507321	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs750349056	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	90	608	0	ENST00000356435.5:c.1657G>C	p.Asp553His	p.D553H	ENST00000356435		553	Gat/Cat	11/35	0.117161605373574	3	FACETS	0.851	0.756	0.952	0.284	0.252	0.318	INDETERMINATE	1	TRUE	0	0.415319846332616	3		608	615	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556655	41556655	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052495-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	105	482	0	ENST00000263253.7:c.3600C>G	p.Phe1200Leu	p.F1200L	ENST00000263253	NM_001429.3	1200	ttC/ttG	20/31	0.415319846332616	3	FACETS	0.637	0.569	0.708	0.318	0.284	0.354	SUBCLONAL	1	TRUE	1	0.415319846332616	3		482	959	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0052496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	106	1087	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.667941060088403	2		1087	277	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0052496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	13	507	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.102	0.072	0.139	0.102	0.072	0.139	SUBCLONAL	1	TRUE	1	0.667941060088403	2		507	382	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398283	25398284	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCAGCT	novel	NA	P-0052496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	25	511	0	ENST00000311936.3:c.30_35dup	p.Ala11_Gly12dup	p.A11_G12dup	ENST00000311936	NM_004985.3	11	ggt/ggAGCTGGt	2/5	1	2	FACETS	0.169	0.133	0.211	0.169	0.133	0.211	SUBCLONAL	1	TRUE	1	0.667941060088403	2		511	443	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060728	38060728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	241	782	0	ENST00000250448.2:c.1261G>A	p.Glu421Lys	p.E421K	ENST00000250448	NM_004496.3	421	Gaa/Aaa	2/2	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.667941060088403	2		782	541	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170586	108170586	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	176	349	0	ENST00000278616.4:c.5151C>A	p.Tyr1717Ter	p.Y1717*	ENST00000278616	NM_000051.3	1717	taC/taA	34/63	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.667941060088403	2		349	464	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433217	49433217	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0052496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	183	711	0	ENST00000301067.7:c.8229+1G>A		p.X2743_splice	ENST00000301067	NM_003482.3	2743			1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.667941060088403	2		711	442	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438623	49438623	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	218	559	0	ENST00000301067.7:c.4867G>T	p.Glu1623Ter	p.E1623*	ENST00000301067	NM_003482.3	1623	Gag/Tag	19/54	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.667941060088403	2		559	500	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845346	151845346	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	183	575	0	ENST00000262189.6:c.13666del	p.His4556ThrfsTer70	p.H4556Tfs*70	ENST00000262189	NM_170606.2	4556	Cac/ac	52/59	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.667941060088403	2		575	493	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224567	123224582	+	frameshift_variant	Frame_Shift_Del	DEL	TGTTTATCCAATGCAG	TGTTTATCCAATGCAG	CAA	novel	NA	P-0052496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	26	570	0	ENST00000218089.9:c.3420_3435delinsCAA	p.Val1141LysfsTer15	p.V1141Kfs*15	ENST00000218089	NM_001042749.1	1140	agTGTTTATCCAATGCAG/agCAA	31/35	1	2	FACETS	0.157	0.123	0.195	0.157	0.123	0.195	SUBCLONAL	1	TRUE	1	0.667941060088403	2		570	497	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139648	202139648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	26	425	0	ENST00000358485.4:c.809C>T	p.Ser270Phe	p.S270F	ENST00000358485	NM_001080125.1	270	tCt/tTt	6/9	1	2	FACETS	0.398	0.314	0.494	0.398	0.314	0.494	SUBCLONAL	1	TRUE	1	0.284201345816063	2		425	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578187	7578187	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs878854071	NA	P-0052497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	123	647	0	ENST00000269305.4:c.662del	p.Glu221GlyfsTer26	p.E221Gfs*26	ENST00000269305	NM_001126112.2	221	gAg/gg	6/11	0.17718599859233	2	FACETS	1	0.938	1	0.525	0.474	0.578	CLONAL	1	TRUE	0	0.284201345816063	2		647	825	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612057	43612057	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356141763	NA	P-0052497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	152	771	1	ENST00000355710.3:c.2162G>A	p.Arg721Gln	p.R721Q	ENST00000355710	NM_020975.4	721	cGg/cAg	12/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.284201345816063	2		772	846	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262563	39262566	+	frameshift_variant	Frame_Shift_Del	DEL	ACTG	ACTG	-	novel	NA	P-0052497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	46	566	0	ENST00000402219.2:c.940_943del	p.Gln314TyrfsTer13	p.Q314Yfs*13	ENST00000402219	NM_005633.3	314	CAGTta/ta	7/23	1	2	FACETS	0.631	0.531	0.741	0.631	0.531	0.741	SUBCLONAL	1	TRUE	1	0.284201345816063	2		566	513	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434507	49434508	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0052497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	137	704	0	ENST00000301067.7:c.7044_7045dup	p.Pro2349ArgfsTer36	p.P2349Rfs*36	ENST00000301067	NM_003482.3	2349	ccc/cGCcc	31/54	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.284201345816063	2		704	841	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0052500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	481	536	1	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.318950068917754	6	FACETS	1	0.978	1			1	CLONAL	5	TRUE	NA	0.522454798858277	6		537	743	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0052500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	512	838	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.479157958243567	3	FACETS	1	0.996	1			1	CLONAL	3	TRUE	NA	0.522454798858277	3		838	708	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456585	32456585	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	13	90	0	ENST00000332351.3:c.307G>T	p.Ala103Ser	p.A103S	ENST00000332351	NM_024426.4	103	Gcg/Tcg	1/10	0.501702106201221	4	FACETS	0.621	0.446	0.83	0.311	0.223	0.415	SUBCLONAL	1	TRUE	2	0.522454798858277	4		90	122	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902560	1902560	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	81	739	0	ENST00000382891.5:c.179G>T	p.Gly60Val	p.G60V	ENST00000382891	NM_133335.3	60	gGg/gTg	2/22	0.330325726800372	4	FACETS	0.64	0.563	0.722	0.32	0.281	0.361	SUBCLONAL	1	TRUE	2	0.522454798858277	4		739	738	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916421	39916421	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	85	627	0	ENST00000378444.4:c.4582C>A	p.Gln1528Lys	p.Q1528K	ENST00000378444	NM_001123385.1	1528	Cag/Aag	11/15	0.308525244794717	2	FACETS	0.834	0.742	0.932	0.417	0.371	0.466	INDETERMINATE	1	TRUE	0	0.522454798858277	2		627	390	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986517	36986517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	460	541	0	ENST00000354822.5:c.1172C>T	p.Ser391Phe	p.S391F	ENST00000354822	NM_001079668.2	391	tCc/tTc	3/3	0.522454798858277	11	FACETS	1	0.974	1			1	CLONAL	4	TRUE	NA	0.522454798858277	11		541	1435	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560534	65560534	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0052500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	224	434	0	ENST00000358664.4:c.64-1G>T		p.X22_splice	ENST00000358664	NM_002382.4	22			0.532851526113108	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.522454798858277	2		434	350	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154784	2154784	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	173	797	1	ENST00000434045.2:c.437C>A	p.Ser146Tyr	p.S146Y	ENST00000434045	NM_001127598.1	146	tCc/tAc	4/5	0.501702106201221	4	FACETS	1	0.99	1	0.746	0.689	0.805	CLONAL	1	TRUE	2	0.522454798858277	4		798	676	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847303	68847303	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587778176	NA	P-0052500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	190	593	0	ENST00000261769.5:c.1225T>C	p.Trp409Arg	p.W409R	ENST00000261769	NM_004360.3	409	Tgg/Cgg	9/16	0.332995890585342	4	FACETS	0.921	0.857	0.988			1	CLONAL	2	TRUE	NA	0.522454798858277	4		593	601	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211625	5211625	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	212	619	0	ENST00000357368.4:c.5210A>T	p.Asn1737Ile	p.N1737I	ENST00000357368	NM_002850.3	1737	aAc/aTc	33/38	0.532851526113108	4	FACETS	0.803	0.748	0.86	0.536	0.499	0.573	CLONAL	2	TRUE	1	0.522454798858277	4		619	769	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354155	15354155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1477636105	NA	P-0052500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	57	629	0	ENST00000263377.2:c.2725C>T	p.Pro909Ser	p.P909S	ENST00000263377	NM_058243.2	909	Ccc/Tcc	14/20	0.522454798858277	5	FACETS	0.52	0.445	0.602	0.173	0.148	0.201	SUBCLONAL	1	TRUE	2	0.522454798858277	5		629	748	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18958624	18958624	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	151	671	0	ENST00000262803.5:c.443G>T	p.Arg148Leu	p.R148L	ENST00000262803	NM_002911.3	148	cGt/cTt	3/24	0.522454798858277	5	FACETS	0.995	0.909	1	0.332	0.303	0.362	CLONAL	1	TRUE	2	0.522454798858277	5		671	1036	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149387	61149387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750181088	NA	P-0052500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	331	534	0	ENST00000295025.8:c.1577C>T	p.Ser526Leu	p.S526L	ENST00000295025	NM_002908.2	526	tCa/tTa	11/11	0.342852451574822	5	FACETS	0.921	0.886	0.955	0.921	0.886	0.955	CLONAL	5	TRUE	0	0.522454798858277	5		534	491	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095755	178095755	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	73	482	0	ENST00000397062.3:c.1576G>T	p.Glu526Ter	p.E526*	ENST00000397062	NM_006164.4	526	Gag/Tag	5/5	0.374725081696956	5	FACETS	0.776	0.679	0.881	0.155	0.135	0.177	SUBCLONAL	1	TRUE	0	0.522454798858277	5		482	642	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251586	212251586	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	117	535	0	ENST00000342788.4:c.3473C>A	p.Pro1158His	p.P1158H	ENST00000342788	NM_005235.2	1158	cCc/cAc	27/28	0.374725081696956	5	FACETS	1	0.981	1	0.272	0.246	0.3	CLONAL	1	TRUE	0	0.522454798858277	5		535	587	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708984	117708984	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	184	566	0	ENST00000368508.3:c.1973G>T	p.Gly658Val	p.G658V	ENST00000368508	NM_002944.2	658	gGc/gTc	13/43	0.532851526113108	3	FACETS	0.814	0.756	0.872	0.542	0.504	0.582	CLONAL	2	TRUE	0	0.522454798858277	3		566	546	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877164	151877164	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	77	478	0	ENST00000262189.6:c.7197G>C	p.Lys2399Asn	p.K2399N	ENST00000262189	NM_170606.2	2399	aaG/aaC	37/59	0.281192579178102	4	FACETS	0.927	0.816	1	0.232	0.204	0.262	INDETERMINATE	1	TRUE	0	0.522454798858277	4		478	484	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932234	39932234	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1290420731	NA	P-0052500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	95	832	1	ENST00000378444.4:c.2365C>A	p.Pro789Thr	p.P789T	ENST00000378444	NM_001123385.1	789	Ccc/Acc	4/15	0.308525244794717	2	FACETS	0.695	0.621	0.774	0.348	0.31	0.387	INDETERMINATE	1	TRUE	0	0.522454798858277	2		833	523	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045726	47045726	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	60	776	0	ENST00000377604.3:c.2607G>T	p.Met869Ile	p.M869I	ENST00000377604	NM_001204468.1	869	atG/atT	23/24	0.475559861520197	1	FACETS	0.414	0.358	0.475	0.414	0.358	0.475	SUBCLONAL	1	TRUE	0	0.522454798858277	1		776	410	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0052514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	177	449	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.602009089114132	2		449	461	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790512	3790512	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	364	603	1	ENST00000262367.5:c.4021C>T	p.Arg1341Ter	p.R1341*	ENST00000262367	NM_004380.2	1341	Cga/Tga	24/31	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.602009089114132	2		604	881	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900499	3900502	+	frameshift_variant	Frame_Shift_Del	DEL	ATTA	ATTA	-	novel	NA	P-0052514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	337	696	0	ENST00000262367.5:c.594_597del	p.Asn199ArgfsTer10	p.N199Rfs*10	ENST00000262367	NM_004380.2	198	atTAAT/at	2/31	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.602009089114132	2		696	878	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176938	56176938	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0052514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	132	273	0	ENST00000399503.3:c.2208T>A	p.Tyr736Ter	p.Y736*	ENST00000399503	NM_005921.1	736	taT/taA	13/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.602009089114132	2		273	383	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390935	139390936	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGTGCGGCTGTGGTGGTGGT	novel	NA	P-0052514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	135	648	0	ENST00000277541.6:c.7236_7255dup	p.Leu2419HisfsTer10	p.L2419Hfs*10	ENST00000277541	NM_017617.3	2419	ctt/cACCACCACCACAGCCGCACCtt	34/34	1	2	FACETS	0.582	0.529	0.637	0.582	0.529	0.637	SUBCLONAL	1	TRUE	1	0.602009089114132	2		648	771	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	91	380	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.355635967960346	4	FACETS	0.913	0.817	1	0.913	0.817	1	CLONAL	2	FALSE	2	0.355635967960346	4		380	380	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	53	435	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	0.124998467050336	0	FACETS	0.61	0.523	0.704			1	INDETERMINATE	1	FALSE	0	0.355635967960346	0		435	315	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	88	495	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.752	0.673	0.835	1	0.981	1	SUBCLONAL	2	FALSE	1	0.355635967960346	2		495	329	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	117	749	6	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	0.124998467050336	0	FACETS	0.889	0.806	0.975			1	INDETERMINATE	1	FALSE	0	0.355635967960346	0		755	477	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	168	701	11	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.986	1	1	0.994	1	CLONAL	2	FALSE	1	0.355635967960346	2		712	382	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344476	118344476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782640926	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	79	343	0	ENST00000534358.1:c.2602G>A	p.Val868Met	p.V868M	ENST00000534358	NM_005933.3	868	Gtg/Atg	3/36	1	2	FACETS	0.929	0.83	1	1	0.984	1	CLONAL	2	FALSE	1	0.355635967960346	2		343	239	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	109	577	2	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	0.130467768173411	4	FACETS	0.768	0.692	0.848	0.768	0.692	0.848	INDETERMINATE	2	FALSE	2	0.355635967960346	4		579	541	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	244	641	1	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.18324186368337	3	FACETS	1	0.944	1	1	0.944	1	INDETERMINATE	2	FALSE	1	0.355635967960346	3		642	802	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607487	46607487	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	196	757	0	ENST00000263734.3:c.1681del	p.Gln561SerfsTer7	p.Q561Sfs*7	ENST00000263734	NM_001430.4	559	aCc/ac	12/16	1	2	FACETS	0.758	0.704	0.814	1	0.991	1	SUBCLONAL	2	FALSE	1	0.355635967960346	2		757	727	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	127	477	0	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.801	0.731	0.873	1	0.988	1	CLONAL	2	FALSE	1	0.355635967960346	2		477	446	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	120	639	2	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	0.18324186368337	3	FACETS	0.754	0.684	0.827	0.754	0.684	0.827	INDETERMINATE	2	FALSE	1	0.355635967960346	3		641	527	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	53	374	3	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	FALSE	1	0.355635967960346	2		377	286	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	112	675	1	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	0.124998467050336	0	FACETS	0.741	0.668	0.816			1	INDETERMINATE	1	FALSE	0	0.355635967960346	0		676	548	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573505	48573506	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	63	392	0	ENST00000342988.3:c.94_95del	p.Ser32Ter	p.S32*	ENST00000342988	NM_005359.5	30	gGA/g	2/12	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.355635967960346	2		392	247	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030479	49030479	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	59	441	0	ENST00000267163.4:c.1959del	p.Val654CysfsTer4	p.V654Cfs*4	ENST00000267163	NM_000321.2	652	Aaa/aa	19/27	0.130467768173411	4	FACETS	0.812	0.705	0.926	0.812	0.705	0.926	INDETERMINATE	2	FALSE	2	0.355635967960346	4		441	277	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	85	444	5	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.789	0.705	0.877	1	0.982	1	SUBCLONAL	2	FALSE	1	0.355635967960346	2		449	303	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	87	396	1	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	0.130467768173411	4	FACETS	0.984	0.879	1	0.984	0.879	1	INDETERMINATE	2	FALSE	2	0.355635967960346	4		397	337	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494908	56494908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs551223118	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	169	565	0	ENST00000267101.3:c.3265C>T	p.Arg1089Trp	p.R1089W	ENST00000267101	NM_001982.3	1089	Cgg/Tgg	27/28	0.355635967960346	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	FALSE	2	0.355635967960346	4		565	601	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646981	23646981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	86	750	0	ENST00000261584.4:c.886del	p.Met296Ter	p.M296*	ENST00000261584	NM_024675.3	296	Atg/tg	4/13	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.355635967960346	2		750	378	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391799	139391799	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1455334351	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	137	580	0	ENST00000277541.6:c.6392del	p.Gly2131AlafsTer117	p.G2131Afs*117	ENST00000277541	NM_017617.3	2131	gGc/gc	34/34	1	2	FACETS	0.82	0.751	0.891	1	0.989	1	CLONAL	2	FALSE	1	0.355635967960346	2		580	470	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656969	47656969	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779075	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	60	428	0	ENST00000233146.2:c.1165C>T	p.Arg389Ter	p.R389*	ENST00000233146	NM_000251.2	389	Cga/Tga	7/16	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	1	0.355635967960346	2		428	294	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17941419	17941420	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	167	669	0	ENST00000458235.1:c.2988dup	p.Glu997ArgfsTer45	p.E997Rfs*45	ENST00000458235	NM_000215.3	996	-/C	22/24	0.18324186368337	3	FACETS	0.834	0.769	0.902	0.834	0.769	0.902	INDETERMINATE	2	FALSE	1	0.355635967960346	3		669	663	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163374	108163374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754181173	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	65	501	0	ENST00000278616.4:c.4465C>T	p.Arg1489Cys	p.R1489C	ENST00000278616	NM_000051.3	1489	Cgt/Tgt	30/63	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.355635967960346	2		501	268	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212259	5212259	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	111	661	1	ENST00000357368.4:c.4772C>T	p.Ala1591Val	p.A1591V	ENST00000357368	NM_002850.3	1591	gCc/gTc	32/38	0.18324186368337	3	FACETS	0.859	0.778	0.944	0.859	0.778	0.944	INDETERMINATE	2	FALSE	1	0.355635967960346	3		662	428	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954321	48954321	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	69	411	0	ENST00000267163.4:c.1446del	p.His483IlefsTer12	p.H483Ifs*12	ENST00000267163	NM_000321.2	481	aTt/at	16/27	0.130467768173411	4	FACETS	0.892	0.784	1	0.892	0.784	1	INDETERMINATE	2	FALSE	2	0.355635967960346	4		411	295	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044464	5044464	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	83	666	0	ENST00000381652.3:c.412C>T	p.Arg138Ter	p.R138*	ENST00000381652	NM_004972.3	138	Cga/Tga	5/25	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.355635967960346	2		666	312	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023021	31023021	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs373580114	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	94	683	0	ENST00000375687.4:c.2506A>G	p.Thr836Ala	p.T836A	ENST00000375687	NM_015338.5	836	Act/Gct	13/13	0.124998467050336	0	FACETS	0.845	0.757	0.938			1	INDETERMINATE	1	FALSE	0	0.355635967960346	0		683	403	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316397	14316397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782457908	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	54	514	0	ENST00000256196.4:c.208G>A	p.Ala70Thr	p.A70T	ENST00000256196		70	Gca/Aca	3/6	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	FALSE	1	0.355635967960346	2		514	264	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526498	66526498	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	134	552	0	ENST00000358598.2:c.1054C>T	p.Arg352Ter	p.R352*	ENST00000358598	NM_212471.2	352	Cga/Tga	11/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.355635967960346	2		552	603	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	178	670	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.355635967960346	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	FALSE	2	0.355635967960346	4		670	583	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17743024	17743024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	99	449	0	ENST00000250003.3:c.932C>T	p.Ala311Val	p.A311V	ENST00000250003	NM_002478.4	311	gCg/gTg	3/3	1	2	FACETS	0.791	0.713	0.872	1	0.984	1	SUBCLONAL	2	FALSE	1	0.355635967960346	2		449	352	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526755	31526755	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	95	618	0	ENST00000344624.3:c.285del	p.Cys96AlafsTer12	p.C96Afs*12	ENST00000344624		95	ccC/cc	2/33	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	FALSE	1	0.355635967960346	2		618	503	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849457	68849457	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780112	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	153	653	0	ENST00000261769.5:c.1360G>A	p.Val454Ile	p.V454I	ENST00000261769	NM_004360.3	454	Gta/Ata	10/16	1	2	FACETS	0.791	0.728	0.856	1	0.989	1	SUBCLONAL	2	FALSE	1	0.355635967960346	2		653	544	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778282	3778282	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	122	723	0	ENST00000262367.5:c.6766del	p.Leu2256SerfsTer46	p.L2256Sfs*46	ENST00000262367	NM_004380.2	2256	Ctc/tc	31/31	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.355635967960346	2		723	473	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798378	42798378	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778167932	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	181	697	0	ENST00000575354.2:c.4249C>T	p.Arg1417Cys	p.R1417C	ENST00000575354	NM_015125.3	1417	Cgc/Tgc	18/20	0.18324186368337	3	FACETS	0.879	0.814	0.946	0.879	0.814	0.946	INDETERMINATE	2	FALSE	1	0.355635967960346	3		697	682	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129351	64129351	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	125	721	1	ENST00000334205.4:c.788del	p.Pro263LeufsTer112	p.P263Lfs*112	ENST00000334205	NM_003942.2	261	ttC/tt	8/17	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.355635967960346	2		722	589	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214714	36214714	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	88	645	1	ENST00000222270.7:c.3145del	p.Ala1049ArgfsTer133	p.A1049Rfs*133	ENST00000222270	NM_014727.1	1047	cGg/cg	8/37	0.18324186368337	3	FACETS	0.86	0.769	0.955	0.86	0.769	0.955	INDETERMINATE	2	FALSE	1	0.355635967960346	3		646	339	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250398	10250398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1010743136	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	146	534	2	ENST00000340748.4:c.3854G>A	p.Arg1285His	p.R1285H	ENST00000340748		1285	cGc/cAc	33/40	0.18324186368337	3	FACETS	1	0.953	1	1	0.953	1	INDETERMINATE	2	FALSE	1	0.355635967960346	3		536	460	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849994	151849994	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	88	425	0	ENST00000262189.6:c.12322C>T	p.Arg4108Ter	p.R4108*	ENST00000262189	NM_170606.2	4108	Cga/Tga	49/59	0.130467768173411	4	FACETS	0.978	0.874	1	0.978	0.874	1	INDETERMINATE	2	FALSE	2	0.355635967960346	4		425	343	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482202	87482202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	29	632	0	ENST00000277120.3:c.1489C>T	p.Leu497Phe	p.L497F	ENST00000277120		497	Ctc/Ttc	14/19	1	2	FACETS	0.347	0.278	0.426	0.347	0.278	0.426	SUBCLONAL	1	FALSE	1	0.355635967960346	2		632	470	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132814	152132815	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	102	312	0	ENST00000262189.6:c.57dup	p.Glu20ArgfsTer39	p.E20Rfs*39	ENST00000262189	NM_170606.2	19	-/C	1/59	0.130467768173411	4	FACETS	1	0.981	1	0.729	0.655	0.808	INDETERMINATE	1	FALSE	2	0.355635967960346	4		312	533	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634732	158634732	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771363719	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	102	442	1	ENST00000263640.3:c.454C>T	p.Arg152Cys	p.R152C	ENST00000263640	NM_001105.4	152	Cgc/Tgc	5/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.355635967960346	2		443	438	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418437	49418437	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	143	654	0	ENST00000301067.7:c.15976del	p.Met5327TrpfsTer6	p.M5327Wfs*6	ENST00000301067	NM_003482.3	5326	Ctt/tt	50/54	0.355635967960346	4	FACETS	0.76	0.694	0.829	0.76	0.694	0.829	SUBCLONAL	2	FALSE	2	0.355635967960346	4		654	717	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440169	220440169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777288649	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	136	762	1	ENST00000243786.2:c.1022G>A	p.Arg341His	p.R341H	ENST00000243786	NM_002191.3	341	cGc/cAc	2/2	1	2	FACETS	0.773	0.707	0.841	1	0.988	1	SUBCLONAL	2	FALSE	1	0.355635967960346	2		763	495	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405170	139405170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199506721	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	172	679	1	ENST00000277541.6:c.2675G>A	p.Arg892His	p.R892H	ENST00000277541	NM_017617.3	892	cGc/cAc	17/34	1	2	FACETS	0.809	0.748	0.871	1	0.991	1	CLONAL	2	FALSE	1	0.355635967960346	2		680	598	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808953	3808953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	117	605	0	ENST00000262367.5:c.3271C>T	p.Arg1091Cys	p.R1091C	ENST00000262367	NM_004380.2	1091	Cgc/Tgc	17/31	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.355635967960346	2		605	551	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259049	16259049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	103	578	0	ENST00000375759.3:c.6314C>T	p.Ala2105Val	p.A2105V	ENST00000375759	NM_015001.2	2105	gCt/gTt	11/15	0.124998467050336	0	FACETS	0.833	0.75	0.92			1	INDETERMINATE	1	FALSE	0	0.355635967960346	0		578	448	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649545	206649545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781928069	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	179	539	1	ENST00000367120.3:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000367120	NM_014002.3	127	cGg/cAg	6/22	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.355635967960346	2		540	680	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615578	43615578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373594744	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	126	694	1	ENST00000355710.3:c.2657G>A	p.Arg886Gln	p.R886Q	ENST00000355710	NM_020975.4	886	cGg/cAg	15/20	0.130467768173411	4	FACETS	1	0.948	1	1	0.948	1	INDETERMINATE	2	FALSE	2	0.355635967960346	4		695	455	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63700105	63700105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142921832	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	83	297	0	ENST00000279873.7:c.440G>A	p.Arg147Lys	p.R147K	ENST00000279873	NM_032199.2	147	aGg/aAg	3/10	0.130467768173411	4	FACETS	1	0.975	1	0.698	0.619	0.783	INDETERMINATE	1	FALSE	2	0.355635967960346	4		297	453	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118345032	118345032	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	51	253	0	ENST00000534358.1:c.3156+2T>C		p.X1052_splice	ENST00000534358	NM_005933.3	1052			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.355635967960346	2		253	195	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205263	46205263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	77	551	0	ENST00000334344.6:c.347G>A	p.Gly116Asp	p.G116D	ENST00000334344	NM_152641.2	116	gGc/gAc	4/21	0.355635967960346	4	FACETS	0.935	0.828	1	0.935	0.828	1	CLONAL	2	FALSE	2	0.355635967960346	4		551	314	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415600	49415600	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	25	500	0	ENST00000301067.7:c.16577A>G	p.His5526Arg	p.H5526R	ENST00000301067	NM_003482.3	5526	cAc/cGc	54/54	0.355635967960346	4	FACETS	0.403	0.317	0.502	0.201	0.158	0.251	SUBCLONAL	1	FALSE	2	0.355635967960346	4		500	473	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431193	49431193	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	59	627	0	ENST00000301067.7:c.9946G>T	p.Gly3316Cys	p.G3316C	ENST00000301067	NM_003482.3	3316	Ggt/Tgt	34/54	0.355635967960346	4	FACETS	0.774	0.666	0.892	0.387	0.333	0.446	SUBCLONAL	1	FALSE	2	0.355635967960346	4		627	581	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435385	110435385	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	166	439	0	ENST00000375856.3:c.3016C>A	p.Leu1006Met	p.L1006M	ENST00000375856	NM_003749.2	1006	Ctg/Atg	1/2	0.130467768173411	4	FACETS	1	0.982	1	1	0.982	1	INDETERMINATE	2	FALSE	2	0.355635967960346	4		439	529	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821382	72821382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766590724	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	19	481	0	ENST00000268489.5:c.10793C>T	p.Pro3598Leu	p.P3598L	ENST00000268489	NM_006885.3	3598	cCt/cTt	10/10	1	2	FACETS	0.335	0.254	0.43	0.335	0.254	0.43	SUBCLONAL	1	FALSE	1	0.355635967960346	2		481	319	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39629571	39629571	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	80	357	0	ENST00000262039.4:c.2263+2T>C		p.X755_splice	ENST00000262039	NM_002647.2	755			1	2	FACETS	0.945	0.845	1	1	0.985	1	CLONAL	2	FALSE	1	0.355635967960346	2		357	238	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220437	1220437	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	200	687	0	ENST00000326873.7:c.530T>G	p.Ile177Ser	p.I177S	ENST00000326873	NM_000455.4	177	aTc/aGc	4/10	0.18324186368337	3	FACETS	0.964	0.897	1	0.964	0.897	1	INDETERMINATE	2	FALSE	1	0.355635967960346	3		687	687	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249173	10249173	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	140	703	1	ENST00000340748.4:c.4009C>T	p.Arg1337Trp	p.R1337W	ENST00000340748		1337	Cgg/Tgg	34/40	0.18324186368337	3	FACETS	0.835	0.764	0.909	0.835	0.764	0.909	INDETERMINATE	2	FALSE	1	0.355635967960346	3		704	555	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349997	15349997	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	149	731	1	ENST00000263377.2:c.3655T>A	p.Ser1219Thr	p.S1219T	ENST00000263377	NM_058243.2	1219	Tca/Aca	18/20	0.18324186368337	3	FACETS	0.82	0.752	0.89	0.82	0.752	0.89	INDETERMINATE	2	FALSE	1	0.355635967960346	3		732	602	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635637	47635637	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	116	560	0	ENST00000233146.2:c.309T>G	p.Tyr103Ter	p.Y103*	ENST00000233146	NM_000251.2	103	taT/taG	2/16	1	2	FACETS	0.762	0.692	0.835	1	0.985	1	SUBCLONAL	2	FALSE	1	0.355635967960346	2		560	428	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015189	128015189	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	148	613	0	ENST00000285398.2:c.2332A>G	p.Lys778Glu	p.K778E	ENST00000285398	NM_000122.1	778	Aag/Gag	15/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.355635967960346	2		613	579	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104714	209104715	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	rs1559359182	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	64	347	0	ENST00000345146.2:c.863_864del	p.Leu288ArgfsTer59	p.L288Rfs*59	ENST00000345146	NM_005896.2	288	cTC/c	8/10	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	FALSE	1	0.355635967960346	2		347	330	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662266	227662266	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	158	655	0	ENST00000305123.5:c.1189A>G	p.Thr397Ala	p.T397A	ENST00000305123	NM_005544.2	397	Acc/Gcc	1/2	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.355635967960346	2		655	615	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024302	31024302	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	74	534	0	ENST00000375687.4:c.3787C>A	p.Pro1263Thr	p.P1263T	ENST00000375687	NM_015338.5	1263	Cca/Aca	13/13	0.124998467050336	0	FACETS	0.972	0.86	1			1	INDETERMINATE	1	FALSE	0	0.355635967960346	0		534	276	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944449	40944449	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	90	622	0	ENST00000373198.4:c.2053A>G	p.Lys685Glu	p.K685E	ENST00000373198	NM_133170.3	685	Aag/Gag	12/32	0.124998467050336	0	FACETS	0.794	0.708	0.883			1	INDETERMINATE	1	FALSE	0	0.355635967960346	0		622	411	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934193	49934193	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148081612	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	201	714	0	ENST00000296474.3:c.2314G>A	p.Val772Met	p.V772M	ENST00000296474	NM_002447.2	772	Gtg/Atg	8/20	1	2	FACETS	0.896	0.835	0.958	1	0.993	1	CLONAL	2	FALSE	1	0.355635967960346	2		714	631	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259541	89259541	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	60	488	0	ENST00000336596.2:c.685T>C	p.Ser229Pro	p.S229P	ENST00000336596	NM_005233.5	229	Tct/Cct	3/17	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	FALSE	1	0.355635967960346	2		488	314	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186774	142186774	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	45	311	0	ENST00000350721.4:c.6687+2T>C		p.X2229_splice	ENST00000350721	NM_001184.3	2229			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.355635967960346	2		311	186	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1978235	1978235	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	142	739	0	ENST00000382891.5:c.3659del	p.Lys1220ArgfsTer109	p.K1220Rfs*109	ENST00000382891	NM_133335.3	1219	Aaa/aa	21/22	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.355635967960346	2		739	628	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973829	131973829	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	97	468	0	ENST00000265335.6:c.3535del	p.Arg1179GlyfsTer9	p.R1179Gfs*9	ENST00000265335		1178	Aaa/aa	23/25	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.355635967960346	2		468	414	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324919	31324919	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	170	831	0	ENST00000412585.2:c.17C>G	p.Pro6Arg	p.P6R	ENST00000412585	NM_005514.6	6	cCc/cGc	1/8	0.204649683628456	4	FACETS	0.768	0.707	0.831	0.768	0.707	0.831	INDETERMINATE	2	FALSE	2	0.355635967960346	4		831	844	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420085	152420085	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs748564686	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	113	432	0	ENST00000206249.3:c.1772T>C	p.Phe591Ser	p.F591S	ENST00000206249	NM_000125.3	591	tTc/tCc	8/8	0.204649683628456	4	FACETS	1	0.936	1	1	0.936	1	INDETERMINATE	2	FALSE	2	0.355635967960346	4		432	414	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97887462	97887462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	86	478	0	ENST00000289081.3:c.902C>T	p.Ala301Val	p.A301V	ENST00000289081	NM_000136.2	301	gCa/gTa	10/15	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.355635967960346	2		478	422	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422380	47422380	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	74	449	0	ENST00000377045.4:c.17del	p.Gly6AlafsTer28	p.G6Afs*28	ENST00000377045	NM_001654.4	5	cGg/cg	2/16	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	FALSE	1	0.355635967960346	2		449	387	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413086	63413086	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	164	706	1	ENST00000330258.3:c.81del	p.Gly28GlufsTer25	p.G28Efs*25	ENST00000330258	NM_152424.3	27	aaA/aa	2/2	1	2	FACETS	0.774	0.714	0.836	1	0.99	1	SUBCLONAL	2	FALSE	1	0.355635967960346	2		707	596	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861500	152861500	+	synonymous_variant	Silent	SNP	C	C	T	rs781977080	NA	P-0052515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	57	413	1	ENST00000406277.2:c.252G>A	p.Gln84=	p.Q84=	ENST00000406277	NM_152274.4	84	caG/caA	4/7	1		FACETS		0.962	1				CLONAL	1	FALSE	1	0.355635967960346	2		414	241	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	64	460	0				ENST00000310581	NM_198253.2	-/1132			0.33645347733623	1	FACETS	0.873	0.776	0.972	0.873	0.776	0.972	INDETERMINATE	1	TRUE	0	0.647903022011832	1		460	153	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019861	123019861	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	257	492	0	ENST00000355640.3:c.349G>T	p.Val117Phe	p.V117F	ENST00000355640		117	Gtt/Ttt	2/7	1	2	FACETS	0.969	0.91	1	0.969	0.91	1	CLONAL	1	TRUE	1	0.647903022011832	2		492	819	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0052525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	55	240	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.778	0.669	0.896	0.778	0.669	0.896	SUBCLONAL	1	TRUE	1	0.4208812894664	2		240	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882025	NA	P-0052525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	156	589	0	ENST00000269305.4:c.646G>T	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ttg	6/11	0.4208812894664	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.4208812894664	1		589	438	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139977	50139977	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs533583599	NA	P-0052525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	72	686	0	ENST00000246792.3:c.352G>A	p.Glu118Lys	p.E118K	ENST00000246792	NM_006270.3	118	Gag/Aag	4/6	0.397894400785286	1	FACETS	0.545	0.477	0.617	0.545	0.477	0.617	SUBCLONAL	1	TRUE	0	0.4208812894664	1		686	496	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554305	29554305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs917302286	NA	P-0052525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	97	540	0	ENST00000356175.3:c.2321C>T	p.Thr774Ile	p.T774I	ENST00000356175	NM_000267.3	774	aCt/aTt	19/57	0.280988403513633	1	FACETS	0.724	0.647	0.804	0.724	0.647	0.804	SUBCLONAL	1	TRUE	0	0.4208812894664	1		540	503	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120249	70120250	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0052525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	136	545	1	ENST00000245479.2:c.1252_1253dup	p.Ala419SerfsTer52	p.A419Sfs*52	ENST00000245479	NM_000346.3	417	-/AT	3/3	0.280988403513633	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.4208812894664	1		546	468	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086110	16086110	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	25	555	0	ENST00000281043.3:c.1286A>G	p.Tyr429Cys	p.Y429C	ENST00000281043	NM_005378.4	429	tAt/tGt	3/3	1	2	FACETS	0.296	0.232	0.368	0.296	0.232	0.368	SUBCLONAL	1	TRUE	1	0.4208812894664	2		555	402	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206827	36206827	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	113	470	0	ENST00000300305.3:c.685G>T	p.Glu229Ter	p.E229*	ENST00000300305		229	Gag/Tag	6/8	0.404454051011799	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.4208812894664	1		470	334	SUCCESS
APC	324	MSKCC	GRCh37	5	112128219	112128219	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	60	290	0	ENST00000257430.4:c.723del	p.Ala242GlnfsTer51	p.A242Qfs*51	ENST00000257430	NM_000038.5	241	gAa/ga	7/16	1	2	FACETS	0.771	0.667	0.882	0.771	0.667	0.882	SUBCLONAL	1	TRUE	1	0.4208812894664	2		290	370	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0052526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	99	549	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.381050662605133	2	FACETS	0.896	0.811	0.984	0.896	0.811	0.984	CLONAL	2	TRUE	0	0.381050662605133	2		549	290	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612632	228612632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	86	553	1	ENST00000366696.1:c.395G>A	p.Arg132His	p.R132H	ENST00000366696	NM_003493.2	132	cGc/cAc	1/1	0.381050662605133	5	FACETS	0.974	0.862	1	0.244	0.215	0.274	CLONAL	1	TRUE	1	0.381050662605133	5		554	728	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602505	10602505	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	200	766	0	ENST00000171111.5:c.1073T>G	p.Leu358Arg	p.L358R	ENST00000171111	NM_203500.1	358	cTg/cGg	3/6	0.381050662605133	2	FACETS	0.972	0.908	1	0.972	0.908	1	CLONAL	2	TRUE	0	0.381050662605133	2		766	540	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098404	11098404	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	113	482	0	ENST00000358026.2:c.922A>G	p.Thr308Ala	p.T308A	ENST00000358026	NM_001128849.1	308	Acg/Gcg	6/36	0.381050662605133	2	FACETS	0.835	0.76	0.913	0.835	0.76	0.913	CLONAL	2	TRUE	0	0.381050662605133	2		482	355	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967033	25967033	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0052526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	166	544	0	ENST00000435504.4:c.2173A>T	p.Lys725Ter	p.K725*	ENST00000435504		725	Aag/Tag	13/13	0.381050662605133	3	FACETS	0.825	0.761	0.891			1	CLONAL	2	TRUE	NA	0.381050662605133	3		544	629	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757407	40757407	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	135	481	0	ENST00000373198.4:c.2891C>A	p.Ala964Asp	p.A964D	ENST00000373198	NM_133170.3	964	gCc/gAc	20/32	0.326774273658408	4	FACETS	0.952	0.87	1	0.952	0.87	1	CLONAL	2	TRUE	2	0.381050662605133	4		481	514	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411660	116411660	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	72	513	0	ENST00000397752.3:c.2839T>G	p.Leu947Val	p.L947V	ENST00000397752	NM_000245.2	947	Tta/Gta	13/21	0.35110455131755	3	FACETS	1	0.897	1	0.512	0.449	0.58	CLONAL	1	TRUE	1	0.381050662605133	3		513	439	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891265	101891265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	106	393	0	ENST00000374994.4:c.226G>A	p.Asp76Asn	p.D76N	ENST00000374994	NM_004612.2	76	Gac/Aac	2/9	0.381050662605133	2	FACETS	0.909	0.826	0.995	0.909	0.826	0.995	CLONAL	2	TRUE	0	0.381050662605133	2		393	306	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891349	101891349	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	109	409	0	ENST00000374994.4:c.310G>C	p.Asp104His	p.D104H	ENST00000374994	NM_004612.2	104	Gac/Cac	2/9	0.381050662605133	2	FACETS	0.99	0.902	1	0.99	0.902	1	CLONAL	2	TRUE	0	0.381050662605133	2		409	289	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0052526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	194	549	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.525598920812482	1	FACETS	0.942	0.877	1	0.942	0.877	1	CLONAL	1	TRUE	0	0.525598920812482	1		549	578	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612632	228612632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	145	553	1	ENST00000366696.1:c.395G>A	p.Arg132His	p.R132H	ENST00000366696	NM_003493.2	132	cGc/cAc	1/1	0.272953375107186	2	FACETS	0.464	0.422	0.508	0.232	0.211	0.254	INDETERMINATE	1	TRUE	0	0.525598920812482	2		554	1190	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459688	40459688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780900178	NA	P-0052526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	123	950	0	ENST00000345506.4:c.1853G>A	p.Arg618His	p.R618H	ENST00000345506	NM_003152.3	618	cGc/cAc	16/20	1	2	FACETS	0.399	0.36	0.441	0.399	0.36	0.441	SUBCLONAL	1	TRUE	1	0.525598920812482	2		950	1172	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602505	10602505	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	348	766	0	ENST00000171111.5:c.1073T>G	p.Leu358Arg	p.L358R	ENST00000171111	NM_203500.1	358	cTg/cGg	3/6	0.525598920812482	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.525598920812482	1		766	970	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098404	11098404	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	214	482	0	ENST00000358026.2:c.922A>G	p.Thr308Ala	p.T308A	ENST00000358026	NM_001128849.1	308	Acg/Gcg	6/36	0.525598920812482	1	FACETS	0.904	0.844	0.965	0.904	0.844	0.965	CLONAL	1	TRUE	0	0.525598920812482	1		482	664	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967033	25967033	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0052526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	316	544	0	ENST00000435504.4:c.2173A>T	p.Lys725Ter	p.K725*	ENST00000435504		725	Aag/Tag	13/13	0.242813617904775	1	FACETS	0.875	0.827	0.924	0.875	0.827	0.924	INDETERMINATE	1	TRUE	0	0.525598920812482	1		544	1013	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757407	40757407	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	261	481	0	ENST00000373198.4:c.2891C>A	p.Ala964Asp	p.A964D	ENST00000373198	NM_133170.3	964	gCc/gAc	20/32	1	2	FACETS	0.999	0.937	1	0.999	0.937	1	CLONAL	1	TRUE	1	0.525598920812482	2		481	994	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411660	116411660	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	235	513	0	ENST00000397752.3:c.2839T>G	p.Leu947Val	p.L947V	ENST00000397752	NM_000245.2	947	Tta/Gta	13/21	1	2	FACETS	0.937	0.875	1	0.937	0.875	1	CLONAL	1	TRUE	1	0.525598920812482	2		513	954	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891265	101891265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	190	393	0	ENST00000374994.4:c.226G>A	p.Asp76Asn	p.D76N	ENST00000374994	NM_004612.2	76	Gac/Aac	2/9	0.525598920812482	1	FACETS	0.991	0.923	1	0.991	0.923	1	CLONAL	1	TRUE	0	0.525598920812482	1		393	538	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891349	101891349	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052526-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	170	409	0	ENST00000374994.4:c.310G>C	p.Asp104His	p.D104H	ENST00000374994	NM_004612.2	104	Gac/Cac	2/9	0.525598920812482	1	FACETS	0.975	0.904	1	0.975	0.904	1	CLONAL	1	TRUE	0	0.525598920812482	1		409	489	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0052527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	127	537	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.397262499963285	2		537	501	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0052527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	124	432	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.944	0.856	1	0.944	0.856	1	CLONAL	1	TRUE	1	0.397262499963285	2		432	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0052527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	211	475	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.397262499963285	2		476	888	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0052527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	64	414	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.953	0.831	1	0.953	0.831	1	CLONAL	1	TRUE	1	0.397262499963285	2		414	338	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986569	36986569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	176	671	0	ENST00000354822.5:c.1120G>A	p.Val374Ile	p.V374I	ENST00000354822	NM_001079668.2	374	Gta/Ata	3/3	1	2	FACETS	0.993	0.915	1	0.993	0.915	1	CLONAL	1	TRUE	1	0.397262499963285	2		671	892	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0052527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	148	600	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.397262499963285	2		600	686	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562628	29562628	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1555615431	NA	P-0052527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	66	408	0	ENST00000356175.3:c.3709-1G>A		p.X1237_splice	ENST00000356175	NM_000267.3	1237			1	2	FACETS	0.782	0.681	0.89	0.782	0.681	0.89	SUBCLONAL	1	TRUE	1	0.397262499963285	2		408	425	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221236	1221236	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	416	700	0	ENST00000326873.7:c.762del	p.Phe255SerfsTer32	p.F255Sfs*32	ENST00000326873	NM_000455.4	253	taC/ta	6/10	0.397262499963285	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.397262499963285	2		700	976	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196514	106196514	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	98	409	0	ENST00000380013.4:c.4847A>C	p.Asn1616Thr	p.N1616T	ENST00000380013	NM_001127208.2	1616	aAc/aCc	11/11	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.397262499963285	2		409	453	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532624	187532624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200112487	NA	P-0052527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	83	431	0	ENST00000441802.2:c.9769C>T	p.Arg3257Trp	p.R3257W	ENST00000441802	NM_005245.3	3257	Cgg/Tgg	14/27	1	2	FACETS	0.863	0.764	0.969	0.863	0.764	0.969	CLONAL	1	TRUE	1	0.397262499963285	2		431	484	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064689	80064689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	74	461	1	ENST00000265081.6:c.2120C>T	p.Ser707Phe	p.S707F	ENST00000265081	NM_002439.4	707	tCt/tTt	15/24	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.397262499963285	2		462	313	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26046032	26046032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749656611	NA	P-0052527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	83	428	0	ENST00000540144.1:c.394C>T	p.Arg132Cys	p.R132C	ENST00000540144	NM_003531.2	132	Cgt/Tgt	1/1	0.397262499963285	4	FACETS	0.821	0.724	0.925	0.274	0.241	0.309	CLONAL	1	TRUE	1	0.397262499963285	4		428	711	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974361	93974361	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	99	450	1	ENST00000369303.4:c.1693G>A	p.Gly565Arg	p.G565R	ENST00000369303	NM_004440.3	565	Ggg/Agg	8/17	0.397262499963285	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.397262499963285	1		451	373	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492910	8492910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767627241	NA	P-0052527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	128	599	0	ENST00000356435.5:c.2419G>A	p.Gly807Arg	p.G807R	ENST00000356435		807	Gga/Aga	16/35	1	2	FACETS	0.799	0.724	0.877	0.799	0.724	0.877	SUBCLONAL	1	TRUE	1	0.397262499963285	2		599	807	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007182	62007182	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147194821	NA	P-0052528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	188	596	0	ENST00000392795.3:c.500C>T	p.Thr167Met	p.T167M	ENST00000392795	NM_001039933.1	167	aCg/aTg	4/6	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.580840720674456	2		596	603	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430770	181430770	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	179	736	0	ENST00000325404.1:c.622A>G	p.Asn208Asp	p.N208D	ENST00000325404	NM_003106.3	208	Aac/Gac	1/1	1	2	FACETS	0.92	0.851	0.991	0.92	0.851	0.991	CLONAL	1	TRUE	1	0.580840720674456	2		736	670	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061195	38061195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	129	415	0	ENST00000250448.2:c.794G>A	p.Arg265His	p.R265H	ENST00000250448	NM_004496.3	265	cGc/cAc	2/2	0.580840720674456	4	FACETS	0.93	0.844	1	0.31	0.281	0.341	CLONAL	1	TRUE	1	0.580840720674456	4		415	755	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69210708	69210708	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	140	278	0	ENST00000462284.1:c.291C>G	p.Phe97Leu	p.F97L	ENST00000462284	NM_002392.5	97	ttC/ttG	4/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.580840720674456	2		278	403	SUCCESS
APC	324	MSKCC	GRCh37	5	112175324	112175324	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1211642532	NA	P-0052531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	161	344	0	ENST00000257430.4:c.4033G>T	p.Glu1345Ter	p.E1345*	ENST00000257430	NM_000038.5	1345	Gaa/Taa	16/16	0.683622351071465	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.683622351071465	2		344	223	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955064	93955064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151105732	NA	P-0052531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	146	244	1	ENST00000369303.4:c.2834C>T	p.Thr945Met	p.T945M	ENST00000369303	NM_004440.3	945	aCg/aTg	16/17	0.683622351071465	3	FACETS	0.965	0.897	1	0.965	0.897	1	CLONAL	2	TRUE	1	0.683622351071465	3		245	297	SUCCESS
ATR	545	MSKCC	GRCh37	3	142234342	142234342	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	133	363	1	ENST00000350721.4:c.4398G>C	p.Gln1466His	p.Q1466H	ENST00000350721	NM_001184.3	1466	caG/caC	25/47	0.683622351071465	3	FACETS	1	0.939	1	0.517	0.472	0.564	CLONAL	1	TRUE	1	0.683622351071465	3		364	505	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879258	151879258	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	123	457	0	ENST00000262189.6:c.5687A>G	p.Asp1896Gly	p.D1896G	ENST00000262189	NM_170606.2	1896	gAt/gGt	36/59	0.683622351071465	3	FACETS	0.835	0.758	0.916	0.418	0.379	0.458	CLONAL	1	TRUE	1	0.683622351071465	3		457	578	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274794	123274794	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913478	NA	P-0052533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	149	535	2	ENST00000358487.5:c.1124A>G	p.Tyr375Cys	p.Y375C	ENST00000358487	NM_000141.4	375	tAc/tGc	9/18	1	2	FACETS	0.881	0.807	0.959	0.881	0.807	0.959	CLONAL	1	TRUE	1	0.480942817234778	2		537	703	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637689	52637689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	108	342	0	ENST00000394830.3:c.2627G>A	p.Arg876His	p.R876H	ENST00000394830	NM_018313.4	876	cGt/cAt	18/30	0.452843205110157	1	FACETS	0.95	0.861	1	0.95	0.861	1	CLONAL	1	TRUE	0	0.480942817234778	1		342	359	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439874	52439874	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	185	639	1	ENST00000460680.1:c.838C>T	p.Gln280Ter	p.Q280*	ENST00000460680	NM_004656.3	280	Cag/Tag	10/17	0.452843205110157	1	FACETS	0.893	0.828	0.96	0.893	0.828	0.96	CLONAL	1	TRUE	0	0.480942817234778	1		640	654	SUCCESS
APC	324	MSKCC	GRCh37	5	112177418	112177418	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876660233	NA	P-0052533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	81	273	0	ENST00000257430.4:c.6127A>G	p.Ile2043Val	p.I2043V	ENST00000257430	NM_000038.5	2043	Ata/Gta	16/16	1	2	FACETS	0.923	0.819	1	0.923	0.819	1	CLONAL	1	TRUE	1	0.480942817234778	2		273	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577115	7577115	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519983	NA	P-0052534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	173	563	0	ENST00000269305.4:c.823T>C	p.Cys275Arg	p.C275R	ENST00000269305	NM_001126112.2	275	Tgt/Cgt	8/11	0.379660876140657	2	FACETS	0.758	0.703	0.814	0.758	0.703	0.814	SUBCLONAL	2	TRUE	0	0.44756635549051	2		563	510	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422880	49422880	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	61	623	0	ENST00000301067.7:c.14215C>T	p.Pro4739Ser	p.P4739S	ENST00000301067	NM_003482.3	4739	Cct/Tct	44/54	0.331452161159468	3	FACETS	0.615	0.531	0.707	0.205	0.177	0.236	SUBCLONAL	1	TRUE	0	0.44756635549051	3		623	542	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060942	38060942	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	46	435	0	ENST00000250448.2:c.1047G>C	p.Leu349Phe	p.L349F	ENST00000250448	NM_004496.3	349	ttG/ttC	2/2	1	2	FACETS	0.672	0.569	0.784	0.672	0.569	0.784	SUBCLONAL	1	TRUE	1	0.44756635549051	2		435	306	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820770	3820772	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs752216328	NA	P-0052534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	74	744	1	ENST00000262367.5:c.2679_2681del	p.Ser895del	p.S895del	ENST00000262367	NM_004380.2	893	tcGTCt/tct	14/31	0.363455050654424	3	FACETS	0.715	0.627	0.81	0.238	0.209	0.27	SUBCLONAL	1	TRUE	0	0.44756635549051	3		745	566	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101639	27101655	+	frameshift_variant	Frame_Shift_Del	DEL	TTCCCACCTGGCTCTGT	TTCCCACCTGGCTCTGT	-	novel	NA	P-0052535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	121	468	0	ENST00000324856.7:c.4922_4938del	p.Phe1641Ter	p.F1641*	ENST00000324856	NM_006015.4	1641	TTCCCACCTGGCTCTGTt/t	18/20	0.270485401388491	1	FACETS	0.74	0.668	0.816	0.74	0.668	0.816	SUBCLONAL	1	FALSE	0	0.308701100072641	1		468	896	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591135	67591152	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GAGAGACCAATACTTGAT	GAGAGACCAATACTTGAT	-	novel	NA	P-0052535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	23	44	0	ENST00000274335.5:c.1729_1745+1del		p.TRDQYLMdel	ENST00000274335		576	acGAGAGACCAATACTTGATg/acg	12/15	0.279348678801223	1	FACETS	0.696	0.547	0.867	0.696	0.547	0.867	SUBCLONAL	1	FALSE	0	0.308701100072641	1		44	181	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674341	86674341	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0052535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	18	69	0	ENST00000274376.6:c.2473A>T	p.Lys825Ter	p.K825*	ENST00000274376	NM_002890.2	825	Aag/Tag	18/25	0.279348678801223	1	FACETS	0.548	0.414	0.704	0.548	0.414	0.704	SUBCLONAL	1	FALSE	0	0.308701100072641	1		69	180	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0052537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	30	542	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.412	0.331	0.505	0.412	0.331	0.505	SUBCLONAL	1	TRUE	1	0.25	2		542	582	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370226	40370226	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	101	835	1	ENST00000293328.3:c.1112C>T	p.Ala371Val	p.A371V	ENST00000293328	NM_012448.3	371	gCc/gTc	9/19	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.25	2		836	780	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207118	1207123	+	inframe_deletion	In_Frame_Del	DEL	CGGAGA	CGGAGA	-	novel	NA	P-0052537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	87	675	1	ENST00000326873.7:c.208_213del	p.Glu70_Thr71del	p.E70_T71del	ENST00000326873	NM_000455.4	69	tCGGAGAcg/tcg	1/10	0.3	1	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	0	0.25	1		676	605	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610481	10610481	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	89	715	1	ENST00000171111.5:c.229T>C	p.Cys77Arg	p.C77R	ENST00000171111	NM_203500.1	77	Tgt/Cgt	2/6	0.3	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.25	1		716	585	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198263263	198263263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	66	406	0	ENST00000335508.6:c.3056G>A	p.Arg1019Lys	p.R1019K	ENST00000335508	NM_012433.2	1019	aGa/aAa	21/25	1	2	FACETS	0.967	0.84	1	0.967	0.84	1	CLONAL	1	TRUE	1	0.25	2		406	546	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521543	8521543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	62	397	0	ENST00000356435.5:c.695G>T	p.Arg232Leu	p.R232L	ENST00000356435		232	cGc/cTc	9/35	0.3	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	0	0.25	1		397	408	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0052538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	134	449	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.996	0.916	1	0.996	0.916	1	CLONAL	1	TRUE	1	0.745143797989538	2		449	361	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0052538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	86	220	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.745143797989538	1	FACETS	0.809	0.735	0.884	0.809	0.735	0.884	CLONAL	1	TRUE	0	0.745143797989538	1		220	179	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061310	38061310	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs745876197	NA	P-0052538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	375	664	1	ENST00000250448.2:c.679T>C	p.Cys227Arg	p.C227R	ENST00000250448	NM_004496.3	227	Tgc/Cgc	2/2	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.745143797989538	2		665	951	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910647	29910647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	182	941	0	ENST00000376809.5:c.187G>A	p.Asp63Asn	p.D63N	ENST00000376809	NM_002116.7	63	Gac/Aac	2/8	1	2	FACETS	0.386	0.355	0.419	0.386	0.355	0.419	SUBCLONAL	1	TRUE	1	0.745143797989538	2		941	1264	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306927	65306927	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0052538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	190	466	0	ENST00000342505.4:c.2649+1del		p.X883_splice	ENST00000342505	NM_002227.2	883			0.737821786331546	1	FACETS	0.919	0.866	0.973	0.919	0.866	0.973	CLONAL	1	TRUE	0	0.745143797989538	1		466	348	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933148	49933148	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	90	530	0	ENST00000296474.3:c.2962G>C	p.Val988Leu	p.V988L	ENST00000296474	NM_002447.2	988	Gtt/Ctt	12/20	1	2	FACETS	0.358	0.317	0.401	0.358	0.317	0.401	SUBCLONAL	1	TRUE	1	0.745143797989538	2		530	675	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014284	70014284	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	144	493	0	ENST00000394351.3:c.1145C>G	p.Thr382Ser	p.T382S	ENST00000394351	NM_000248.3	382	aCc/aGc	9/9	1	2	FACETS	0.949	0.866	1	0.949	0.866	1	CLONAL	1	TRUE	1	0.353714045792373	2		493	858	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	23	413	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	1	2	FACETS	0.566	0.442	0.708	0.566	0.442	0.708	SUBCLONAL	1	TRUE	1	0.32	2		413	254	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866454	42866454	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	27	658	1	ENST00000398585.3:c.178G>A	p.Glu60Lys	p.E60K	ENST00000398585	NM_001135099.1	60	Gaa/Aaa	3/14	1	2	FACETS	0.504	0.401	0.621	0.504	0.401	0.621	SUBCLONAL	1	TRUE	1	0.32	2		659	335	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312725	91312725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	15	338	0	ENST00000355112.3:c.2464C>T	p.Pro822Ser	p.P822S	ENST00000355112	NM_000057.2	822	Cct/Tct	12/22	1	2	FACETS	0.329	0.24	0.436	0.329	0.24	0.436	SUBCLONAL	1	TRUE	1	0.32	2		338	285	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561396	9561396	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1262495622	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	10	426	0	ENST00000353224.5:c.386C>T	p.Ser129Phe	p.S129F	ENST00000353224	NM_177990.2	129	tCc/tTc	4/10	1	2	FACETS	0.381	0.258	0.535	0.381	0.258	0.535	SUBCLONAL	1	TRUE	1	0.32	2		426	164	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003784	+	frameshift_variant	Frame_Shift_Del	DEL	CTCT	CTCT	-	novel	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	18	446	0	ENST00000558401.1:c.41_44del	p.Ser14PhefsTer29	p.S14Ffs*29	ENST00000558401	NM_004048.2	13	CTCTct/ct	1/4	1	2	FACETS	0.365	0.275	0.472	0.365	0.275	0.472	SUBCLONAL	1	TRUE	1	0.32	2		446	308	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467191	99467191	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773555066	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	10	347	0	ENST00000268035.6:c.2572C>T	p.Pro858Ser	p.P858S	ENST00000268035	NM_000875.3	858	Ccc/Tcc	12/21	1	2	FACETS	0.45	0.305	0.629	0.45	0.305	0.629	SUBCLONAL	1	TRUE	1	0.32	2		347	139	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828504	72828504	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	12	562	0	ENST00000268489.5:c.8077C>T	p.Arg2693Ter	p.R2693*	ENST00000268489	NM_006885.3	2693	Cga/Tga	9/10	1	2	FACETS	0.377	0.265	0.514	0.377	0.265	0.514	SUBCLONAL	1	TRUE	1	0.32	2		562	199	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375088	31375088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	37	678	0	ENST00000328111.2:c.485C>T	p.Pro162Leu	p.P162L	ENST00000328111	NM_006892.3	162	cCc/cTc	6/23	1	2	FACETS	0.732	0.605	0.872	0.732	0.605	0.872	SUBCLONAL	1	TRUE	1	0.32	2		678	316	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155953	119155953	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764340189	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	35	531	0	ENST00000264033.4:c.1618C>T	p.Arg540Ter	p.R540*	ENST00000264033	NM_005188.3	540	Cga/Tga	11/16	1	2	FACETS	0.835	0.688	0.998	0.835	0.688	0.998	CLONAL	1	TRUE	1	0.32	2		531	262	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760610	133760610	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	74	733	0	ENST00000318560.5:c.2933C>T	p.Pro978Leu	p.P978L	ENST00000318560	NM_005157.4	978	cCa/cTa	11/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.32	2		733	338	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460399	149460399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	27	483	0	ENST00000286301.3:c.238G>A	p.Gly80Arg	p.G80R	ENST00000286301	NM_005211.3	80	Ggg/Agg	3/22	1	2	FACETS	0.625	0.499	0.768	0.625	0.499	0.768	SUBCLONAL	1	TRUE	1	0.32	2		483	270	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673473	30673473	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	34	610	0	ENST00000376406.3:c.3487C>T	p.Pro1163Ser	p.P1163S	ENST00000376406	NM_014641.2	1163	Ccc/Tcc	10/15	0.3	7	FACETS	1	0.916	1			1	CLONAL	1	TRUE	NA	0.32	7		610	314	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999347	100999347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	14	677	0	ENST00000325455.5:c.455C>T	p.Pro152Leu	p.P152L	ENST00000325455	NM_001202474.3	152	cCg/cTg	1/8	1	2	FACETS	0.442	0.32	0.589	0.442	0.32	0.589	SUBCLONAL	1	TRUE	1	0.32	2		677	198	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250125	110250125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1020085505	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	29	443	0	ENST00000374672.4:c.550C>T	p.Pro184Ser	p.P184S	ENST00000374672	NM_004235.4	184	Ccc/Tcc	3/5	1	2	FACETS	0.775	0.625	0.943	0.775	0.625	0.943	CLONAL	1	TRUE	1	0.32	2		443	234	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223460	36223460	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	107	704	0	ENST00000222270.7:c.6010C>T	p.Gln2004Ter	p.Q2004*	ENST00000222270	NM_014727.1	2004	Cag/Tag	28/37	1	2	FACETS	1	0.911	1	1	0.989	1	CLONAL	2	TRUE	1	0.32	2		704	333	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733326	85733326	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	15	322	0	ENST00000370580.1:c.686C>T	p.Thr229Ile	p.T229I	ENST00000370580	NM_003921.4	229	aCt/aTt	3/3	1	2	FACETS	0.493	0.362	0.651	0.493	0.362	0.651	SUBCLONAL	1	TRUE	1	0.32	2		322	190	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462933	120462933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1450649026	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	19	415	1	ENST00000256646.2:c.5398C>T	p.Arg1800Cys	p.R1800C	ENST00000256646	NM_024408.3	1800	Cgt/Tgt	30/34	1	2	FACETS	0.542	0.413	0.694	0.542	0.413	0.694	SUBCLONAL	1	TRUE	1	0.32	2		416	219	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837960	156837960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770401327	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	21	721	0	ENST00000524377.1:c.493G>A	p.Glu165Lys	p.E165K	ENST00000524377	NM_002529.3	165	Gag/Aag	5/17	1	2	FACETS	0.566	0.437	0.715	0.566	0.437	0.715	SUBCLONAL	1	TRUE	1	0.32	2		721	232	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944938	31944938	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	12	274	0	ENST00000340398.3:c.163C>T	p.Gln55Ter	p.Q55*	ENST00000340398	NM_001013699.2	55	Cag/Tag	1/1	1	2	FACETS	0.6	0.424	0.813	0.6	0.424	0.813	SUBCLONAL	1	TRUE	1	0.32	2		274	125	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115111993	115111993	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	26	498	0	ENST00000257566.3:c.1747C>T	p.Gln583Ter	p.Q583*	ENST00000257566	NM_016569.3	583	Cag/Tag	7/8	1	2	FACETS	0.6	0.476	0.74	0.6	0.476	0.74	SUBCLONAL	1	TRUE	1	0.32	2		498	271	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436448	110436486	+	inframe_deletion	In_Frame_Del	DEL	GTCGTCTGCCCCCAGGTTGCTGCTGGAGCTCCTGTGGGA	GTCGTCTGCCCCCAGGTTGCTGCTGGAGCTCCTGTGGGA	-	novel	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	94	536	0	ENST00000375856.3:c.1915_1953del	p.Ser639_Asp651del	p.S639_D651del	ENST00000375856	NM_003749.2	639	TCCCACAGGAGCTCCAGCAGCAACCTGGGGGCAGACGAC/-	1/2	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.32	2		536	403	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459318	99459318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1427895738	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	40	434	0	ENST00000268035.6:c.1954C>T	p.Pro652Ser	p.P652S	ENST00000268035	NM_000875.3	652	Cct/Tct	9/21	1	2	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	1	0.32	2		434	245	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341223	341223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	68	678	0	ENST00000262320.3:c.2261C>T	p.Pro754Leu	p.P754L	ENST00000262320	NM_003502.3	754	cCa/cTa	9/11	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.32	2		678	386	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633110	3633110	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs569861974	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	30	519	0	ENST00000294008.3:c.5141T>G	p.Leu1714Trp	p.L1714W	ENST00000294008	NM_032444.2	1714	tTg/tGg	14/15	1	2	FACETS	0.772	0.625	0.936	0.772	0.625	0.936	CLONAL	1	TRUE	1	0.32	2		519	243	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559744	29559744	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	15	235	0	ENST00000356175.3:c.3341T>A	p.Leu1114Ter	p.L1114*	ENST00000356175	NM_000267.3	1114	tTg/tAg	26/57	1	2	FACETS	0.738	0.544	0.967	0.738	0.544	0.967	CLONAL	1	TRUE	1	0.32	2		235	127	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866640	78866640	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	33	470	0	ENST00000306801.3:c.2213C>T	p.Ser738Phe	p.S738F	ENST00000306801	NM_020761.2	738	tCt/tTt	19/34	1	2	FACETS	0.755	0.618	0.909	0.755	0.618	0.909	CLONAL	1	TRUE	1	0.32	2		470	273	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632113	1632114	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	39	532	0	ENST00000344749.5:c.221_222delinsTT	p.Thr74Ile	p.T74I	ENST00000344749	NM_001136139.2	74	aCC/aTT	5/19	1	2	FACETS	0.755	0.628	0.895	0.755	0.628	0.895	SUBCLONAL	1	TRUE	1	0.32	2		532	323	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10279028	10279028	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	30	367	0	ENST00000340748.4:c.733C>T	p.Leu245Phe	p.L245F	ENST00000340748		245	Ctc/Ttc	9/40	1	2	FACETS	0.727	0.588	0.883	0.727	0.588	0.883	SUBCLONAL	1	TRUE	1	0.32	2		367	258	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291855	15291855	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	42	814	0	ENST00000263388.2:c.2911T>C	p.Cys971Arg	p.C971R	ENST00000263388	NM_000435.2	971	Tgc/Cgc	18/33	1	2	FACETS	0.875	0.734	1	0.875	0.734	1	CLONAL	1	TRUE	1	0.32	2		814	300	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948806	17948806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1284790510	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	32	588	1	ENST00000458235.1:c.1636G>A	p.Gly546Arg	p.G546R	ENST00000458235	NM_000215.3	546	Ggg/Agg	12/24	1	2	FACETS	0.629	0.512	0.761	0.629	0.512	0.761	SUBCLONAL	1	TRUE	1	0.32	2		589	318	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971759	18971759	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	53	609	0	ENST00000262803.5:c.2425T>C	p.Phe809Leu	p.F809L	ENST00000262803	NM_002911.3	809	Ttc/Ctc	17/24	1	2	FACETS	0.874	0.748	1	0.874	0.748	1	CLONAL	1	TRUE	1	0.32	2		609	379	SUCCESS
ALK	238	MSKCC	GRCh37	2	29473986	29473986	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	15	535	0	ENST00000389048.3:c.2189C>G	p.Ala730Gly	p.A730G	ENST00000389048	NM_004304.4	730	gCc/gGc	12/29	1	2	FACETS	0.533	0.391	0.702	0.533	0.391	0.702	SUBCLONAL	1	TRUE	1	0.32	2		535	176	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374336	31374336	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	21	569	0	ENST00000328111.2:c.335C>T	p.Ser112Phe	p.S112F	ENST00000328111	NM_006892.3	112	tCc/tTc	5/23	1	2	FACETS	0.573	0.443	0.724	0.573	0.443	0.724	SUBCLONAL	1	TRUE	1	0.32	2		569	229	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860379	42860380	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	17	592	1	ENST00000398585.3:c.497_498delinsTT	p.Pro166Leu	p.P166L	ENST00000398585	NM_001135099.1	166	cCC/cTT	5/14	1	2	FACETS	0.373	0.278	0.486	0.373	0.278	0.486	SUBCLONAL	1	TRUE	1	0.32	2		593	285	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514529	149514529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	18	457	0	ENST00000261799.4:c.415C>T	p.Leu139Phe	p.L139F	ENST00000261799	NM_002609.3	139	Ctc/Ttc	4/23	1	2	FACETS	0.563	0.425	0.724	0.563	0.425	0.724	SUBCLONAL	1	TRUE	1	0.32	2		457	200	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112035566	112035566	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	12	268	0	ENST00000368678.4:c.328C>T	p.Gln110Ter	p.Q110*	ENST00000368678		110	Caa/Taa	4/13	0.206659829502636	1	FACETS	0.315	0.221	0.43	0.315	0.221	0.43	SUBCLONAL	1	TRUE	0	0.32	1		268	200	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372172	55372172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	11	125	2	ENST00000297316.4:c.862G>A	p.Ala288Thr	p.A288T	ENST00000297316	NM_022454.3	288	Gcg/Acg	2/2	0.134804951061916	0	FACETS	0.437	0.304	0.599			1	INDETERMINATE	1	TRUE	0	0.32	0		127	107	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023307	27023307	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0052541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	35	58	0	ENST00000324856.7:c.413C>G	p.Ser138Ter	p.S138*	ENST00000324856	NM_006015.4	138	tCa/tGa	1/20	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.2	2		58	300	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0052541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	34	1087	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.48	0.391	0.581	0.48	0.391	0.581	SUBCLONAL	1	TRUE	1	0.2	2		1087	708	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0052541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	76	455	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.776	0.682	0.875	1	0.977	1	SUBCLONAL	2	TRUE	1	0.2	2		455	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555525857	NA	P-0052541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	84	693	0	ENST00000269305.4:c.596G>A	p.Gly199Glu	p.G199E	ENST00000269305	NM_001126112.2	199	gGa/gAa	6/11	0.20360181881857	1	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	0	0.2	1		693	743	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982728	90982728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	48	389	0	ENST00000265433.3:c.760G>A	p.Glu254Lys	p.E254K	ENST00000265433	NM_002485.4	254	Gaa/Aaa	7/16	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.2	2		389	398	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651951	36651952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	149	706	0	ENST00000244741.5:c.74dup	p.Asp26GlyfsTer10	p.D26Gfs*10	ENST00000244741	NM_000389.4	25	gtg/gTtg	2/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.2	2		706	1175	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138623	11138623	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	80	486	0	ENST00000358026.2:c.3379G>C	p.Asp1127His	p.D1127H	ENST00000358026	NM_001128849.1	1127	Gat/Cat	24/36	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.2	2		486	714	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929080	32929080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358940	NA	P-0052541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	67	478	0	ENST00000380152.3:c.7090G>A	p.Glu2364Lys	p.E2364K	ENST00000380152		2364	Gaa/Aaa	14/27	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.2	2		478	630	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981167	201981168	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2177	220	798	1	ENST00000359651.3:c.248dup	p.Asn83LysfsTer9	p.N83Kfs*9	ENST00000359651		82	-/A	2/8	0.3	10	FACETS	0.826	0.764	0.89			1	CLONAL	2	TRUE	NA	0.2	10		799	2397	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231831	36231831	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	45	635	0	ENST00000300305.3:c.553C>T	p.Gln185Ter	p.Q185*	ENST00000300305		185	Caa/Taa	5/8	1	2	FACETS	0.515	0.431	0.608	0.515	0.431	0.608	SUBCLONAL	1	TRUE	1	0.2	2		635	874	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448358	56448358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771597876	NA	P-0052541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	152	695	1	ENST00000407977.2:c.289G>A	p.Asp97Asn	p.D97N	ENST00000407977		97	Gac/Aac	3/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.2	2		696	1049	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61708370	61708370	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	52	398	0	ENST00000401558.2:c.3019G>C	p.Asp1007His	p.D1007H	ENST00000401558	NM_003400.3	1007	Gat/Cat	24/25	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.2	2		398	397	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983019	201983019	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1976	218	745	0	ENST00000359651.3:c.868G>T	p.Glu290Ter	p.E290*	ENST00000359651		290	Gag/Tag	7/8	0.3	10	FACETS	0.894	0.828	0.964			1	CLONAL	2	TRUE	NA	0.2	10		745	2194	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056435	26056435	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs769566015	NA	P-0052541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	84	387	0	ENST00000343677.2:c.222G>C	p.Glu74Asp	p.E74D	ENST00000343677	NM_005319.3	74	gaG/gaC	1/1	0.3	3	FACETS	1	0.922	1			1	CLONAL	1	TRUE	NA	0.2	3		387	872	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39321489	39321489	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	66	480	0	ENST00000373001.3:c.532C>T	p.His178Tyr	p.H178Y	ENST00000373001	NM_022157.3	178	Cac/Tac	3/7	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.2	2		480	639	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736277	243736277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	87	450	0	ENST00000263826.5:c.770C>T	p.Ser257Phe	p.S257F	ENST00000263826	NM_005465.4	257	tCt/tTt	8/13	0.3	3	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.2	3		450	684	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375222	118375222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	26	504	1	ENST00000534358.1:c.8615C>T	p.Ser2872Leu	p.S2872L	ENST00000534358	NM_005933.3	2872	tCa/tTa	27/36	1	2	FACETS	0.525	0.415	0.652	0.525	0.415	0.652	SUBCLONAL	1	TRUE	1	0.2	2		505	495	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929025	32929025	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	60	463	0	ENST00000380152.3:c.7035G>C	p.Gln2345His	p.Q2345H	ENST00000380152		2345	caG/caC	14/27	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.2	2		463	587	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929169	32929169	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	74	508	0	ENST00000380152.3:c.7179G>A	p.Met2393Ile	p.M2393I	ENST00000380152		2393	atG/atA	14/27	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.2	2		508	596	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490382	29490382	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	48	433	0	ENST00000356175.3:c.467G>C	p.Arg156Pro	p.R156P	ENST00000356175	NM_000267.3	156	cGc/cCc	4/57	0.3	1	FACETS	0.824	0.697	0.965	0.824	0.697	0.965	CLONAL	1	TRUE	0	0.2	1		433	524	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78854264	78854264	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	140	596	0	ENST00000306801.3:c.1559C>G	p.Ser520Trp	p.S520W	ENST00000306801	NM_020761.2	520	tCg/tGg	14/34	1	2	FACETS	0.792	0.721	0.866	1	0.988	1	SUBCLONAL	2	TRUE	1	0.2	2		596	884	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272180	15272180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1022220282	NA	P-0052541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	72	246	0	ENST00000263388.2:c.6259G>A	p.Ala2087Thr	p.A2087T	ENST00000263388	NM_000435.2	2087	Gcc/Acc	33/33	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.2	2		246	499	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127162	22127162	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	55	409	0	ENST00000215832.6:c.966G>C	p.Glu322Asp	p.E322D	ENST00000215832	NM_002745.4	322	gaG/gaC	7/9	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.2	2		409	540	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458400	12458400	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	116	614	0	ENST00000287820.6:c.1017G>C	p.Leu339Phe	p.L339F	ENST00000287820	NM_015869.4	339	ttG/ttC	6/7	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.2	2		614	878	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440864	52440864	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1301594623	NA	P-0052541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	125	661	0	ENST00000460680.1:c.640A>G	p.Ile214Val	p.I214V	ENST00000460680	NM_004656.3	214	Atc/Gtc	8/17	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.2	2		661	1157	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955090	55955090	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs373562441	NA	P-0052541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	100	499	0	ENST00000263923.4:c.3455C>A	p.Thr1152Lys	p.T1152K	ENST00000263923	NM_002253.2	1152	aCg/aAg	26/30	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.2	2		499	791	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950030	38950030	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	32	432	0	ENST00000357387.3:c.3920C>G	p.Ser1307Cys	p.S1307C	ENST00000357387	NM_152756.3	1307	tCt/tGt	31/38	0.136555997896405	1	FACETS	0.598	0.484	0.726	0.598	0.484	0.726	SUBCLONAL	1	TRUE	0	0.2	1		432	482	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827164	170827164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600552	NA	P-0052541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	27	258	0	ENST00000296930.5:c.532G>A	p.Asp178Asn	p.D178N	ENST00000296930	NM_002520.6	178	Gat/Aat	7/11	0.136555997896405	1	FACETS	0.992	0.793	1	0.992	0.793	1	CLONAL	1	TRUE	0	0.2	1		258	245	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637594	176637594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151111670	NA	P-0052541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	32	516	0	ENST00000439151.2:c.2194G>A	p.Asp732Asn	p.D732N	ENST00000439151	NM_022455.4	732	Gat/Aat	5/23	0.136555997896405	1	FACETS	0.509	0.412	0.619	0.509	0.412	0.619	SUBCLONAL	1	TRUE	0	0.2	1		516	566	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100197	157100197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	14	37	0	ENST00000346085.5:c.1134G>A	p.Met378Ile	p.M378I	ENST00000346085	NM_020732.3	378	atG/atA	1/20	1	2	FACETS	0.66	0.478	0.881	0.66	0.478	0.881	SUBCLONAL	1	TRUE	1	0.2	2		37	212	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249134	55249134	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1378775962	NA	P-0052541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	164	663	0	ENST00000275493.2:c.2432C>G	p.Ser811Cys	p.S811C	ENST00000275493	NM_005228.3	811	tCc/tGc	20/28	0.136555997896405	3	FACETS	1	0.987	1	0.72	0.66	0.784	CLONAL	1	TRUE	1	0.2	3		663	1252	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589575	67589576	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	17	257	0	ENST00000274335.5:c.1344dup	p.Leu449IlefsTer3	p.L449Ifs*3	ENST00000274335		446	-/A	10/15	0.301747413354005	4	FACETS	0.424	0.316	0.552	0.212	0.158	0.276	SUBCLONAL	1	TRUE	2	0.346107574058612	4		257	312	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248998	55248999	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCAGCG	rs727504263	NA	P-0052542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	189	622	0	ENST00000275493.2:c.2300_2308dup	p.Ala767_Val769dup	p.A767_V769dup	ENST00000275493	NM_005228.3	767	atg/aTGGCCAGCGtg	20/28	0.325071799979926	4	FACETS	1	0.971	1	0.727	0.675	0.781	CLONAL	2	TRUE	1	0.346107574058612	4		622	674	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185061	123185061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	45	271	0	ENST00000218089.9:c.1108C>T	p.Arg370Trp	p.R370W	ENST00000218089	NM_001042749.1	370	Cgg/Tgg	12/35	0.327136355928853	2	FACETS	0.828	0.699	0.969			1	CLONAL	1	TRUE	NA	0.346107574058612	2		271	314	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	89	504	3	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.579	0.513	0.65	0.579	0.513	0.65	SUBCLONAL	1	TRUE	1	0.393826604002778	2		507	781	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	46	495	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.461	0.388	0.541	0.461	0.388	0.541	SUBCLONAL	1	TRUE	1	0.393826604002778	2		495	507	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	127	749	6	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.882	0.8	0.969	0.882	0.8	0.969	CLONAL	1	TRUE	1	0.393826604002778	2		755	731	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	110	435	0	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.393826604002778	2		435	529	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715697	30715697	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	62	309	0	ENST00000295754.5:c.1355T>C	p.Leu452Pro	p.L452P	ENST00000295754	NM_003242.5	452	cTg/cCg	5/7	1	2	FACETS	0.592	0.512	0.679	0.592	0.512	0.679	SUBCLONAL	1	TRUE	1	0.393826604002778	2		309	532	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682399	52682400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	39	321	0	ENST00000394830.3:c.773dup	p.Asn258LysfsTer6	p.N258Kfs*6	ENST00000394830	NM_018313.4	258	aat/aaAt	8/30	1	2	FACETS	0.669	0.557	0.793	0.669	0.557	0.793	SUBCLONAL	1	TRUE	1	0.393826604002778	2		321	296	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298740	15298740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	128	792	1	ENST00000263388.2:c.1558G>A	p.Ala520Thr	p.A520T	ENST00000263388	NM_000435.2	520	Gcc/Acc	10/33	1	2	FACETS	0.644	0.582	0.708	0.644	0.582	0.708	SUBCLONAL	1	TRUE	1	0.393826604002778	2		793	1010	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561423	9561423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201131316	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	75	530	2	ENST00000353224.5:c.359C>T	p.Ala120Val	p.A120V	ENST00000353224	NM_177990.2	120	gCg/gTg	4/10	1	2	FACETS	0.572	0.501	0.648	0.572	0.501	0.648	SUBCLONAL	1	TRUE	1	0.393826604002778	2		532	666	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175836	24175837	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555881563	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	156	595	0	ENST00000263121.7:c.1066_1067del	p.Leu356AspfsTer4	p.L356Dfs*4	ENST00000263121	NM_003073.3	355	aCT/a	8/9	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.393826604002778	2		595	790	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	166	715	2	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.915	0.841	0.993	0.915	0.841	0.993	CLONAL	1	TRUE	1	0.393826604002778	2		717	921	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	127	572	6	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	NA	2	FACETS	1	0.953	1			1	INDETERMINATE	1	TRUE	NA	0.393826604002778	2		578	599	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912103	50912103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237089094	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	190	695	0	ENST00000440232.2:c.1837G>A	p.Ala613Thr	p.A613T	ENST00000440232	NM_002691.3	613	Gcc/Acc	15/27	0.393826604002778	4	FACETS	1	0.954	1	0.349	0.322	0.378	CLONAL	1	TRUE	1	0.393826604002778	4		695	1283	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465651	8465651	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772237001	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	28	646	0	ENST00000356435.5:c.3529C>T	p.Arg1177Cys	p.R1177C	ENST00000356435		1177	Cgc/Tgc	21/35	1	2	FACETS	0.288	0.23	0.355	0.288	0.23	0.355	SUBCLONAL	1	TRUE	1	0.393826604002778	2		646	493	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231788	36231788	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	175	574	0	ENST00000300305.3:c.596G>T	p.Gly199Val	p.G199V	ENST00000300305		199	gGg/gTg	5/8	1	2	FACETS	0.912	0.839	0.987	0.912	0.839	0.987	CLONAL	1	TRUE	1	0.393826604002778	2		574	975	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222309	53222309	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	132	669	1	ENST00000375401.3:c.4523del	p.Pro1508LeufsTer36	p.P1508Lfs*36	ENST00000375401	NM_004187.3	1508	cCt/ct	26/26	1	2	FACETS	0.797	0.724	0.874	0.797	0.724	0.874	SUBCLONAL	1	TRUE	1	0.393826604002778	2		670	841	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577093	7577093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882008	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	174	606	0	ENST00000269305.4:c.845G>A	p.Arg282Gln	p.R282Q	ENST00000269305	NM_001126112.2	282	cGg/cAg	8/11	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.393826604002778	2		606	864	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944264	81944264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1009796025	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	91	637	0	ENST00000359376.3:c.1873G>A	p.Ala625Thr	p.A625T	ENST00000359376	NM_002661.3	625	Gcc/Acc	18/33	1	2	FACETS	0.553	0.491	0.621	0.553	0.491	0.621	SUBCLONAL	1	TRUE	1	0.393826604002778	2		637	835	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279645	18279645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	77	541	0	ENST00000222254.8:c.1918C>T	p.Arg640Trp	p.R640W	ENST00000222254	NM_005027.3	640	Cgg/Tgg	15/16	1	2	FACETS	0.4	0.35	0.454	0.4	0.35	0.454	SUBCLONAL	1	TRUE	1	0.393826604002778	2		541	977	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405953	157405954	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1554294674	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	96	629	0	ENST00000346085.5:c.2201dup	p.Ser736IlefsTer27	p.S736Ifs*27	ENST00000346085	NM_020732.3	732	ccg/ccGg	6/20	1	2	FACETS	0.597	0.531	0.667	0.597	0.531	0.667	SUBCLONAL	1	TRUE	1	0.393826604002778	2		629	817	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760024	133760024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	82	1063	3	ENST00000318560.5:c.2352del	p.Arg785GlyfsTer3	p.R785Gfs*3	ENST00000318560	NM_005157.4	783	Ccc/cc	11/11	1	2	FACETS	0.507	0.446	0.572	0.507	0.446	0.572	SUBCLONAL	1	TRUE	1	0.393826604002778	2		1066	822	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	139	468	2	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.393826604002778	2		470	683	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460476	149460476	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	183	633	2	ENST00000286301.3:c.161del	p.Pro54HisfsTer58	p.P54Hfs*58	ENST00000286301	NM_005211.3	54	cCa/ca	3/22	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.393826604002778	2		635	918	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467434	66467434	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369606981	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	98	312	0	ENST00000273854.3:c.835G>A	p.Glu279Lys	p.E279K	ENST00000273854	NM_004439.5	279	Gaa/Aaa	3/18	1	2	FACETS	0.984	0.881	1	0.984	0.881	1	CLONAL	1	TRUE	1	0.393826604002778	2		312	506	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021232	31021232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148964601	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	160	545	3	ENST00000375687.4:c.1231C>T	p.Arg411Cys	p.R411C	ENST00000375687	NM_015338.5	411	Cgc/Tgc	12/13	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.393826604002778	2		548	758	SUCCESS
APC	324	MSKCC	GRCh37	5	112154703	112154703	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs730881221	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	80	362	0	ENST00000257430.4:c.974A>G	p.His325Arg	p.H325R	ENST00000257430	NM_000038.5	325	cAt/cGt	10/16	1	2	FACETS	0.755	0.666	0.85	0.755	0.666	0.85	SUBCLONAL	1	TRUE	1	0.393826604002778	2		362	538	SUCCESS
AR	367	MSKCC	GRCh37	X	66765877	66765877	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749006575	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	195	740	0	ENST00000374690.3:c.889G>A	p.Asp297Asn	p.D297N	ENST00000374690	NM_000044.3	297	Gac/Aac	1/8	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.393826604002778	2		740	933	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905061	50905061	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	150	594	0	ENST00000440232.2:c.347del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	115	Ccc/cc	4/27	0.393826604002778	4	FACETS	0.916	0.836	1	0.305	0.278	0.334	CLONAL	1	TRUE	1	0.393826604002778	4		594	1159	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225449690	225449690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	65	292	0	ENST00000264414.4:c.37G>A	p.Asp13Asn	p.D13N	ENST00000264414	NM_003590.4	13	Gac/Aac	1/16	1	2	FACETS	0.664	0.577	0.759	0.664	0.577	0.759	SUBCLONAL	1	TRUE	1	0.393826604002778	2		292	497	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273029	55273029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770749711	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	174	521	0	ENST00000275493.2:c.3352G>A	p.Ala1118Thr	p.A1118T	ENST00000275493	NM_005228.3	1118	Gcg/Acg	28/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.393826604002778	2		521	777	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512370	38512370	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567767560	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	37	194	0	ENST00000254066.5:c.1286del	p.Gly429ValfsTer214	p.G429Vfs*214	ENST00000254066	NM_000964.3	427	ccG/cc	9/9	1	2	FACETS	0.602	0.498	0.718	0.602	0.498	0.718	SUBCLONAL	1	TRUE	1	0.393826604002778	2		194	312	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	88	701	11	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.393826604002778	2		712	422	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	36	706	4	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.284	0.233	0.342	0.284	0.233	0.342	SUBCLONAL	1	TRUE	1	0.393826604002778	2		710	643	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599234	28599234	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	164	705	1	ENST00000253063.3:c.685del	p.Gln229ArgfsTer18	p.Q229Rfs*18	ENST00000253063	NM_031459.4	227	gCc/gc	5/10	1	2	FACETS	0.879	0.806	0.954	0.879	0.806	0.954	CLONAL	1	TRUE	1	0.393826604002778	2		706	948	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619792	1619792	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	176	747	0	ENST00000344749.5:c.1154del	p.Gly385ValfsTer9	p.G385Vfs*9	ENST00000344749	NM_001136139.2	385	gGt/gt	14/19	1	2	FACETS	0.989	0.911	1	0.989	0.911	1	CLONAL	1	TRUE	1	0.393826604002778	2		747	904	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324576	31324576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs151341159	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	121	648	0	ENST00000412585.2:c.232C>T	p.Gln78Ter	p.Q78*	ENST00000412585	NM_005514.6	78	Cag/Tag	2/8	1	2	FACETS	0.575	0.519	0.636	0.575	0.519	0.636	SUBCLONAL	1	TRUE	1	0.393826604002778	2		648	1068	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180310	27180310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1286718039	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	161	456	1	ENST00000380036.4:c.974G>A	p.Arg325His	p.R325H	ENST00000380036	NM_000459.3	325	cGc/cAc	7/23	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.393826604002778	2		457	763	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38631981	38631981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1255149646	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	74	431	3	ENST00000299084.4:c.471del	p.Gln158SerfsTer16	p.Q158Sfs*16	ENST00000299084	NM_152594.2	156	cTt/ct	5/7	1	2	FACETS	0.735	0.645	0.832	0.735	0.645	0.832	SUBCLONAL	1	TRUE	1	0.393826604002778	2		434	511	SUCCESS
BTK	695	MSKCC	GRCh37	X	100629549	100629549	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	94	523	0	ENST00000308731.7:c.215del	p.Asn72IlefsTer49	p.N72Ifs*49	ENST00000308731	NM_000061.2	72	aAt/at	3/19	1	2	FACETS	0.804	0.716	0.896	0.804	0.716	0.896	CLONAL	1	TRUE	1	0.393826604002778	2		523	594	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279522	1279522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368430301	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	170	614	0	ENST00000310581.5:c.2014C>T	p.Arg672Cys	p.R672C	ENST00000310581	NM_198253.2	672	Cgc/Tgc	5/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.393826604002778	2		614	736	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133898	41133898	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	63	436	0	ENST00000379561.5:c.1730del	p.Gly577AlafsTer5	p.G577Afs*5	ENST00000379561	NM_002015.3	577	gGc/gc	2/3	1	2	FACETS	0.5	0.432	0.574	0.5	0.432	0.574	SUBCLONAL	1	TRUE	1	0.393826604002778	2		436	640	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564667	86564667	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	184	637	0	ENST00000274376.6:c.402del	p.Pro136LeufsTer38	p.P136Lfs*38	ENST00000274376	NM_002890.2	133	ggT/gg	1/25	1	2	FACETS	0.874	0.806	0.945	0.874	0.806	0.945	CLONAL	1	TRUE	1	0.393826604002778	2		637	1069	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805537	32805539	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	190	664	0	ENST00000374899.4:c.472_474del	p.Phe158del	p.F158del	ENST00000374899	NM_018833.2	158	TTC/-	2/12	0.115378854997616	4	FACETS	1	0.988	1	0.672	0.621	0.726	INDETERMINATE	1	TRUE	2	0.393826604002778	4		664	1000	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543834	212543834	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761773013	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	50	413	0	ENST00000342788.4:c.1565C>T	p.Ser522Leu	p.S522L	ENST00000342788	NM_005235.2	522	tCg/tTg	13/28	1	2	FACETS	0.381	0.323	0.446	0.381	0.323	0.446	SUBCLONAL	1	TRUE	1	0.393826604002778	2		413	666	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345760	152345760	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	49	220	2	ENST00000359321.1:c.810del	p.Phe270LeufsTer27	p.F270Lfs*27	ENST00000359321	NM_005431.1	270	ttT/tt	3/3	1	2	FACETS	0.898	0.766	1	0.898	0.766	1	CLONAL	1	TRUE	1	0.393826604002778	2		222	277	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224128	53224128	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	160	652	0	ENST00000375401.3:c.3423G>T	p.Arg1141Ser	p.R1141S	ENST00000375401	NM_004187.3	1141	agG/agT	22/26	1	2	FACETS	0.999	0.917	1	0.999	0.917	1	CLONAL	1	TRUE	1	0.393826604002778	2		652	813	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612870	228612870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	94	622	0	ENST00000366696.1:c.157C>T	p.Arg53Cys	p.R53C	ENST00000366696	NM_003493.2	53	Cgc/Tgc	1/1	0.382737050577838	3	FACETS	0.62	0.55	0.694	0.31	0.275	0.347	SUBCLONAL	1	TRUE	1	0.393826604002778	3		622	922	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504578	103504578	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	94	357	0	ENST00000355739.4:c.204del	p.Arg69GlufsTer15	p.R69Efs*15	ENST00000355739	NM_000123.3	67	Ttt/tt	2/15	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.393826604002778	2		357	473	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117191	7117191	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	105	595	0	ENST00000302850.5:c.4025del	p.Gly1342AlafsTer23	p.G1342Afs*23	ENST00000302850	NM_000208.2	1342	gGc/gc	22/22	1	2	FACETS	0.679	0.608	0.755	0.679	0.608	0.755	SUBCLONAL	1	TRUE	1	0.393826604002778	2		595	785	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245898	5245898	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376695892	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	65	766	0	ENST00000357368.4:c.877G>A	p.Val293Met	p.V293M	ENST00000357368	NM_002850.3	293	Gtg/Atg	10/38	1	2	FACETS	0.362	0.313	0.416	0.362	0.313	0.416	SUBCLONAL	1	TRUE	1	0.393826604002778	2		766	911	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143165	30143165	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746089013	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	83	299	0	ENST00000389048.3:c.361C>T	p.Arg121Trp	p.R121W	ENST00000389048	NM_004304.4	121	Cgg/Tgg	1/29	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.393826604002778	2		299	409	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190885	185190885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746928773	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	204	554	1	ENST00000265026.3:c.1766G>A	p.Arg589His	p.R589H	ENST00000265026	NM_004721.4	589	cGc/cAc	11/14	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.393826604002778	2		555	920	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169536	11169536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	70	617	0	ENST00000358026.2:c.4702G>A	p.Ala1568Thr	p.A1568T	ENST00000358026	NM_001128849.1	1568	Gca/Aca	33/36	1	2	FACETS	0.453	0.394	0.517	0.453	0.394	0.517	SUBCLONAL	1	TRUE	1	0.393826604002778	2		617	784	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579885	7579885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs535274413	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	200	520	0	ENST00000269305.4:c.28G>A	p.Val10Ile	p.V10I	ENST00000269305	NM_001126112.2	10	Gtc/Atc	2/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.393826604002778	2		520	907	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775749	9775749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150205370	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	227	755	0	ENST00000377346.4:c.292G>A	p.Val98Ile	p.V98I	ENST00000377346	NM_005026.3	98	Gtc/Atc	4/24	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.393826604002778	2		755	1009	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657596	37657596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748453656	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	105	479	0	ENST00000447079.4:c.2513C>T	p.Ser838Leu	p.S838L	ENST00000447079	NM_015083.1	838	tCg/tTg	6/14	1	2	FACETS	0.984	0.885	1	0.984	0.885	1	CLONAL	1	TRUE	1	0.393826604002778	2		479	542	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187767	11187767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868627779	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	174	538	0	ENST00000361445.4:c.6130G>A	p.Val2044Met	p.V2044M	ENST00000361445	NM_004958.3	2044	Gtg/Atg	44/58	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.393826604002778	2		538	732	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023837	27023837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	21	108	0	ENST00000324856.7:c.943G>A	p.Asp315Asn	p.D315N	ENST00000324856	NM_006015.4	315	Gac/Aac	1/20	1	2	FACETS	0.359	0.276	0.455	0.359	0.276	0.455	SUBCLONAL	1	TRUE	1	0.393826604002778	2		108	297	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099426	27099426	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	164	462	0	ENST00000324856.7:c.3666del	p.Arg1223AlafsTer14	p.R1223Afs*14	ENST00000324856	NM_006015.4	1221	atG/at	14/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.393826604002778	2		462	747	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138885	64138885	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	87	264	1	ENST00000334205.4:c.2252C>A	p.Pro751Gln	p.P751Q	ENST00000334205	NM_003942.2	751	cCg/cAg	17/17	1	2	FACETS	0.993	0.883	1	0.993	0.883	1	CLONAL	1	TRUE	1	0.393826604002778	2		265	445	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981752	101981752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	47	245	0	ENST00000282441.5:c.173G>A	p.Arg58His	p.R58H	ENST00000282441	NM_001130145.2	58	cGc/cAc	1/9	1	2	FACETS	0.512	0.432	0.6	0.512	0.432	0.6	SUBCLONAL	1	TRUE	1	0.393826604002778	2		245	466	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377339	118377339	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	83	250	0	ENST00000534358.1:c.10732A>G	p.Thr3578Ala	p.T3578A	ENST00000534358	NM_005933.3	3578	Aca/Gca	27/36	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.393826604002778	2		250	418	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420203	49420204	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	159	590	0	ENST00000301067.7:c.15545dup	p.Leu5183ProfsTer16	p.L5183Pfs*16	ENST00000301067	NM_003482.3	5182	ggc/ggGc	48/54	1	2	FACETS	0.918	0.841	0.997	0.918	0.841	0.997	CLONAL	1	TRUE	1	0.393826604002778	2		590	880	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439702	49439702	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	66	510	0	ENST00000301067.7:c.4741+1del		p.X1581_splice	ENST00000301067	NM_003482.3	1581			1	2	FACETS	0.439	0.38	0.503	0.439	0.38	0.503	SUBCLONAL	1	TRUE	1	0.393826604002778	2		510	764	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120993	115120993	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	118	371	0	ENST00000257566.3:c.13A>G	p.Met5Val	p.M5V	ENST00000257566	NM_016569.3	5	Atg/Gtg	1/8	1	2	FACETS	0.992	0.898	1	0.992	0.898	1	CLONAL	1	TRUE	1	0.393826604002778	2		371	604	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257209	133257209	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs903149427	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	116	427	0	ENST00000320574.5:c.269A>G	p.Asp90Gly	p.D90G	ENST00000320574	NM_006231.2	90	gAc/gGc	3/49	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.393826604002778	2		427	582	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103508446	103508446	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	35	133	0	ENST00000355739.4:c.516del	p.Lys172AsnfsTer15	p.K172Nfs*15	ENST00000355739	NM_000123.3	171	cAa/ca	5/15	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.393826604002778	2		133	168	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437865	110437894	+	inframe_deletion	In_Frame_Del	DEL	CCGGCGGCGCCGGCAGAGCCGCCCAGGGCG	CCGGCGGCGCCGGCAGAGCCGCCCAGGGCG	-	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	28	97	0	ENST00000375856.3:c.507_536del	p.Leu171_Ala180del	p.L171_A180del	ENST00000375856	NM_003749.2	169	ggCGCCCTGGGCGGCTCTGCCGGCGCCGCCGGg/ggg	1/2	1	2	FACETS	0.76	0.613	0.926	0.76	0.613	0.926	CLONAL	1	TRUE	1	0.393826604002778	2		97	187	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242036	105242036	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	136	694	0	ENST00000349310.3:c.388G>T	p.Gly130Trp	p.G130W	ENST00000349310	NM_001014432.1	130	Ggg/Tgg	6/15	1	2	FACETS	0.776	0.705	0.85	0.776	0.705	0.85	SUBCLONAL	1	TRUE	1	0.393826604002778	2		694	890	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029473	14029473	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55736359	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	130	371	0	ENST00000311895.7:c.1684G>A	p.Asp562Asn	p.D562N	ENST00000311895	NM_005236.2	562	Gac/Aac	8/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.393826604002778	2		371	618	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953183	81953183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762414923	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	124	323	1	ENST00000359376.3:c.2149G>A	p.Val717Ile	p.V717I	ENST00000359376	NM_002661.3	717	Gtc/Atc	20/33	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.393826604002778	2		324	498	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663779	29663779	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	103	445	0	ENST00000356175.3:c.6211A>G	p.Asn2071Asp	p.N2071D	ENST00000356175	NM_000267.3	2071	Aat/Gat	41/57	1	2	FACETS	0.689	0.617	0.766	0.689	0.617	0.766	SUBCLONAL	1	TRUE	1	0.393826604002778	2		445	759	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33433403	33433403	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	110	539	1	ENST00000345365.6:c.576+2T>C		p.X192_splice	ENST00000345365	NM_002878.3	192			1	2	FACETS	0.654	0.587	0.725	0.654	0.587	0.725	SUBCLONAL	1	TRUE	1	0.393826604002778	2		540	854	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858204	40858204	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	158	443	0	ENST00000428826.2:c.1661-1G>T		p.X554_splice	ENST00000428826		554			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.393826604002778	2		443	711	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270535	10270535	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	189	584	1	ENST00000340748.4:c.1105C>T	p.Gln369Ter	p.Q369*	ENST00000340748		369	Cag/Tag	15/40	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.393826604002778	2		585	886	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629044	14629044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	78	346	0	ENST00000254322.2:c.118G>A	p.Gly40Ser	p.G40S	ENST00000254322	NM_006145.1	40	Ggc/Agc	1/3	1	2	FACETS	0.591	0.519	0.668	0.591	0.519	0.668	SUBCLONAL	1	TRUE	1	0.393826604002778	2		346	670	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212290	36212292	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	rs1243252928	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	155	615	0	ENST00000222270.7:c.2047_2049del	p.Pro683del	p.P683del	ENST00000222270	NM_014727.1	681	CCT/-	3/37	0.393826604002778	4	FACETS	0.936	0.855	1	0.312	0.285	0.341	CLONAL	1	TRUE	1	0.393826604002778	4		615	1172	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218089	36218089	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	353	373	0	ENST00000222270.7:c.4036G>T	p.Glu1346Ter	p.E1346*	ENST00000222270	NM_014727.1	1346	Gaa/Taa	15/37	0.393826604002778	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	1	0.393826604002778	4		373	786	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220124	36220124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	198	688	3	ENST00000222270.7:c.4844C>T	p.Ser1615Leu	p.S1615L	ENST00000222270	NM_014727.1	1615	tCg/tTg	22/37	0.393826604002778	4	FACETS	1	0.973	1	0.37	0.342	0.4	CLONAL	1	TRUE	1	0.393826604002778	4		691	1262	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753303	42753303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479167706	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	618	687	1	ENST00000222329.4:c.961G>A	p.Val321Ile	p.V321I	ENST00000222329	NM_006494.2	321	Gtc/Atc	4/4	0.393826604002778	4	FACETS	0.983	0.947	1	0.983	0.947	1	CLONAL	3	TRUE	1	0.393826604002778	4		688	1483	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918217	50918217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	577	687	0	ENST00000440232.2:c.2534C>T	p.Thr845Ile	p.T845I	ENST00000440232	NM_002691.3	845	aCt/aTt	20/27	0.393826604002778	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	1	0.393826604002778	4		687	1314	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416542	29416542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201759867	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	198	567	1	ENST00000389048.3:c.4411G>A	p.Val1471Met	p.V1471M	ENST00000389048	NM_004304.4	1471	Gtg/Atg	29/29	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.393826604002778	2		568	860	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449818	29449818	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs776510871	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	78	710	0	ENST00000389048.3:c.3037G>T	p.Val1013Leu	p.V1013L	ENST00000389048	NM_004304.4	1013	Gtg/Ttg	18/29	1	2	FACETS	0.419	0.367	0.475	0.419	0.367	0.475	SUBCLONAL	1	TRUE	1	0.393826604002778	2		710	945	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098063	178098063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	71	288	0	ENST00000397062.3:c.317C>T	p.Ala106Val	p.A106V	ENST00000397062	NM_006164.4	106	gCc/gTc	3/5	1	2	FACETS	0.711	0.622	0.807	0.711	0.622	0.807	SUBCLONAL	1	TRUE	1	0.393826604002778	2		288	507	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573326	41573326	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	179	695	0	ENST00000263253.7:c.5611C>T	p.Pro1871Ser	p.P1871S	ENST00000263253	NM_001429.3	1871	Ccc/Tcc	31/31	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.393826604002778	2		695	866	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670880	134670880	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868864751	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	61	356	0	ENST00000398015.3:c.791G>A	p.Ser264Asn	p.S264N	ENST00000398015	NM_004441.4	264	aGc/aAc	3/16	1	2	FACETS	0.605	0.522	0.695	0.605	0.522	0.695	SUBCLONAL	1	TRUE	1	0.393826604002778	2		356	512	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190884	106190884	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	111	348	0	ENST00000380013.4:c.4162A>G	p.Met1388Val	p.M1388V	ENST00000380013	NM_001127208.2	1388	Atg/Gtg	9/11	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.393826604002778	2		348	560	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250901	153250916	+	frameshift_variant	Frame_Shift_Del	DEL	AGCATGTGATCACATG	AGCATGTGATCACATG	-	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	48	309	0	ENST00000281708.4:c.1144_1159del	p.His382TyrfsTer8	p.H382Yfs*8	ENST00000281708	NM_033632.3	382	CATGTGATCACATGCTta/ta	8/12	1	2	FACETS	0.786	0.668	0.915	0.786	0.668	0.915	CLONAL	1	TRUE	1	0.393826604002778	2		309	310	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225657	225658	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	164	606	0	ENST00000264932.6:c.441dup	p.Ala148ArgfsTer14	p.A148Rfs*14	ENST00000264932	NM_004168.2	146	gcc/gCcc	4/15	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.393826604002778	2		606	826	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233738	233738	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs371484111	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	21	239	0	ENST00000264932.6:c.1042A>G	p.Thr348Ala	p.T348A	ENST00000264932	NM_004168.2	348	Act/Gct	8/15	1	2	FACETS	0.301	0.231	0.383	0.301	0.231	0.383	SUBCLONAL	1	TRUE	1	0.393826604002778	2		239	354	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38991088	38991091	+	frameshift_variant	Frame_Shift_Del	DEL	TCTG	TCTG	-	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	79	439	0	ENST00000357387.3:c.543_546del	p.Asp181GlufsTer13	p.D181Efs*13	ENST00000357387	NM_152756.3	181	gaCAGA/ga	7/38	0.264680342903309	3	FACETS	1	0.897	1			1	CLONAL	1	TRUE	NA	0.393826604002778	3		439	472	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665695	86665696	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	33	210	0	ENST00000274376.6:c.1678_1679del	p.Glu560AsnfsTer22	p.E560Nfs*22	ENST00000274376	NM_002890.2	559	gGA/g	12/25	1	2	FACETS	0.868	0.714	1	0.868	0.714	1	CLONAL	1	TRUE	1	0.393826604002778	2		210	193	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435690	149435690	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	168	620	0	ENST00000286301.3:c.2453C>A	p.Pro818His	p.P818H	ENST00000286301	NM_005211.3	818	cCt/cAt	19/22	1	2	FACETS	0.981	0.902	1	0.981	0.902	1	CLONAL	1	TRUE	1	0.393826604002778	2		620	870	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911108	29911108	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199474502	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1250	191	963	0	ENST00000376809.5:c.407G>T	p.Gly136Val	p.G136V	ENST00000376809	NM_002116.7	136	gGg/gTg	3/8	1	2	FACETS	0.673	0.62	0.728	0.673	0.62	0.728	SUBCLONAL	1	TRUE	1	0.393826604002778	2		963	1441	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679693	30679693	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	156	545	0	ENST00000376406.3:c.2026C>T	p.Gln676Ter	p.Q676*	ENST00000376406	NM_014641.2	676	Caa/Taa	5/15	1	2	FACETS	0.917	0.84	0.997	0.917	0.84	0.997	CLONAL	1	TRUE	1	0.393826604002778	2		545	864	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188279	32188281	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	189	709	0	ENST00000375023.3:c.1060_1062del	p.Glu354del	p.E354del	ENST00000375023	NM_004557.3	354	GAG/-	6/30	NA	2	FACETS	0.987	0.913	1			1	INDETERMINATE	1	TRUE	NA	0.393826604002778	2		709	972	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289587	33289587	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	172	554	0	ENST00000374542.5:c.116C>A	p.Pro39His	p.P39H	ENST00000374542	NM_001141970.1	39	cCt/cAt	2/8	0.115378854997616	4	FACETS	1	0.983	1	0.63	0.579	0.682	INDETERMINATE	1	TRUE	2	0.393826604002778	4		554	967	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41905114	41905114	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	114	351	0	ENST00000372991.4:c.433C>A	p.Leu145Ile	p.L145I	ENST00000372991	NM_001760.3	145	Cta/Ata	3/5	0.115378854997616	4	FACETS	1	0.978	1	0.652	0.588	0.719	INDETERMINATE	1	TRUE	2	0.393826604002778	4		351	619	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939558	68939558	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	34	210	0	ENST00000288368.4:c.543G>T	p.Lys181Asn	p.K181N	ENST00000288368	NM_024870.2	181	aaG/aaT	5/40	1	2	FACETS	0.741	0.609	0.887	0.741	0.609	0.887	SUBCLONAL	1	TRUE	1	0.393826604002778	2		210	233	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869541	117869541	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	61	251	0	ENST00000297338.2:c.653A>G	p.Asp218Gly	p.D218G	ENST00000297338	NM_006265.2	218	gAt/gGt	6/14	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.393826604002778	2		251	302	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27228272	27228272	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	78	453	0	ENST00000380036.4:c.3269T>A	p.Val1090Glu	p.V1090E	ENST00000380036	NM_000459.3	1090	gTg/gAg	22/23	1	2	FACETS	0.599	0.526	0.677	0.599	0.526	0.677	SUBCLONAL	1	TRUE	1	0.393826604002778	2		453	661	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624523	93624523	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	134	442	0	ENST00000375746.1:c.614T>C	p.Leu205Pro	p.L205P	ENST00000375746	NM_001174167.1	205	cTg/cCg	4/14	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.393826604002778	2		442	643	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242790	98242790	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	94	484	0	ENST00000331920.6:c.827A>T	p.Asp276Val	p.D276V	ENST00000331920	NM_000264.3	276	gAc/gTc	6/24	1	2	FACETS	0.629	0.559	0.703	0.629	0.559	0.703	SUBCLONAL	1	TRUE	1	0.393826604002778	2		484	759	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128230358	128230358	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	83	482	0	ENST00000265960.3:c.1238C>A	p.Pro413His	p.P413H	ENST00000265960	NM_001006617.1	413	cCt/cAt	10/12	1	2	FACETS	0.665	0.587	0.748	0.665	0.587	0.748	SUBCLONAL	1	TRUE	1	0.393826604002778	2		482	634	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929301	44929301	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	197	587	0	ENST00000377967.4:c.2401A>G	p.Asn801Asp	p.N801D	ENST00000377967	NM_021140.2	801	Aat/Gat	17/29	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.393826604002778	2		587	903	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223742	53223742	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	139	688	0	ENST00000375401.3:c.3617A>C	p.Gln1206Pro	p.Q1206P	ENST00000375401	NM_004187.3	1206	cAg/cCg	23/26	1	2	FACETS	0.875	0.797	0.957	0.875	0.797	0.957	CLONAL	1	TRUE	1	0.393826604002778	2		688	807	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224145	53224145	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	173	638	0	ENST00000375401.3:c.3406T>G	p.Ser1136Ala	p.S1136A	ENST00000375401	NM_004187.3	1136	Tct/Gct	22/26	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.393826604002778	2		638	860	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889145	76889145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1135401793	NA	P-0052543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	67	349	0	ENST00000373344.5:c.4865C>T	p.Ala1622Val	p.A1622V	ENST00000373344	NM_000489.3	1622	gCg/gTg	18/35	1	2	FACETS	0.838	0.731	0.953	0.838	0.731	0.953	CLONAL	1	TRUE	1	0.393826604002778	2		349	406	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250329	39250329	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	132	586	0	ENST00000402219.2:c.1240G>C	p.Gly414Arg	p.G414R	ENST00000402219	NM_005633.3	414	Ggg/Cgg	10/23	0.297911210521936	3	FACETS	0.497	0.45	0.546	0.248	0.225	0.273	INDETERMINATE	1	TRUE	1	0.783561325301763	3		586	944	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028044	69028044	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	31	467	0	ENST00000288368.4:c.3203T>A	p.Ile1068Lys	p.I1068K	ENST00000288368	NM_024870.2	1068	aTa/aAa	26/40	1	2	FACETS	0.141	0.113	0.172	0.141	0.113	0.172	SUBCLONAL	1	TRUE	1	0.783561325301763	2		467	562	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080351	5080351	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0052562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	144	276	0	ENST00000381652.3:c.2254A>T	p.Lys752Ter	p.K752*	ENST00000381652	NM_004972.3	752	Aaa/Taa	17/25	0.697776575062673	1	FACETS	0.844	0.787	0.9	0.844	0.787	0.9	CLONAL	1	TRUE	0	0.783561325301763	1		276	265	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873409	136873409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs923351521	NA	P-0052565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	23	342	1	ENST00000241393.3:c.89G>A	p.Arg30His	p.R30H	ENST00000241393	NM_003467.2	30	cGt/cAt	2/2	0.679493761278122	3	FACETS	0.863	0.686	1	0.432	0.343	0.53	CLONAL	1	TRUE	1	0.679962006357624	3		343	105	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210241	123210241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	267	571	0	ENST00000218089.9:c.2593C>T	p.Leu865Phe	p.L865F	ENST00000218089	NM_001042749.1	865	Ctt/Ttt	26/35	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.865040814315111	2		571	536	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	183	460	0				ENST00000310581	NM_198253.2	-/1132			0.275999375135699	2	FACETS	1	0.992	1	0.713	0.67	0.757	INDETERMINATE	1	TRUE	0	0.724603092181111	2		460	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780071	NA	P-0052567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	239	729	0	ENST00000269305.4:c.580C>T	p.Leu194Phe	p.L194F	ENST00000269305	NM_001126112.2	194	Ctt/Ttt	6/11	0.724603092181111	1	FACETS	0.729	0.686	0.772	0.729	0.686	0.772	SUBCLONAL	1	TRUE	0	0.724603092181111	1		729	577	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0052567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	97	471	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	NA	2	FACETS	0.371	0.33	0.414			1	INDETERMINATE	1	TRUE	NA	0.724603092181111	2		472	722	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651970	36651971	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0052567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	123	774	0	ENST00000244741.5:c.94dup	p.Arg32ProfsTer4	p.R32Pfs*4	ENST00000244741	NM_000389.4	31	agc/agCc	2/3	1	2	FACETS	0.362	0.327	0.4	0.362	0.327	0.4	SUBCLONAL	1	TRUE	1	0.724603092181111	2		774	937	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061250	38061250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1459219194	NA	P-0052567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	156	693	0	ENST00000250448.2:c.739C>T	p.His247Tyr	p.H247Y	ENST00000250448	NM_004496.3	247	Cac/Tac	2/2	NA	2	FACETS	0.439	0.402	0.479			1	INDETERMINATE	1	TRUE	NA	0.724603092181111	2		693	980	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665360	138665360	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906920	NA	P-0052567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	329	828	0	ENST00000330315.3:c.205G>A	p.Glu69Lys	p.E69K	ENST00000330315	NM_023067.3	69	Gag/Aag	1/1	0.188890557066927	4	FACETS	1	0.993	1	0.683	0.645	0.721	INDETERMINATE	1	TRUE	2	0.724603092181111	4		828	1147	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212230	5212230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367918810	NA	P-0052567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	98	741	1	ENST00000357368.4:c.4801G>A	p.Val1601Ile	p.V1601I	ENST00000357368	NM_002850.3	1601	Gtc/Atc	32/38	1	2	FACETS	0.349	0.311	0.39	0.349	0.311	0.39	SUBCLONAL	1	TRUE	1	0.724603092181111	2		742	775	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201747	66201747	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs146343247	NA	P-0052567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	201	509	0	ENST00000273854.3:c.2755C>T	p.Arg919Ter	p.R919*	ENST00000273854	NM_004439.5	919	Cga/Tga	16/18	1	2	FACETS	0.767	0.713	0.823	0.767	0.713	0.823	SUBCLONAL	1	TRUE	1	0.724603092181111	2		509	723	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934623	9934623	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267604688	NA	P-0052567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	73	421	0	ENST00000330684.3:c.1532C>T	p.Ser511Leu	p.S511L	ENST00000330684	NM_001134407.1	511	tCg/tTg	7/13	NA	2	FACETS	0.392	0.343	0.444			1	INDETERMINATE	1	TRUE	NA	0.724603092181111	2		421	514	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982105	201982106	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	140	772	0	ENST00000359651.3:c.630dup	p.Asp211ArgfsTer6	p.D211Rfs*6	ENST00000359651		210	tca/tcAa	5/8	NA	2	FACETS	0.451	0.41	0.493			1	INDETERMINATE	1	TRUE	NA	0.724603092181111	2		772	857	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945134	44945134	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	243	495	1	ENST00000377967.4:c.3458G>T	p.Cys1153Phe	p.C1153F	ENST00000377967	NM_021140.2	1153	tGt/tTt	24/29	0.695908875831388	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.724603092181111	1		496	412	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124704	108124704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769338089	NA	P-0052567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	48	448	0	ENST00000278616.4:c.2062G>A	p.Glu688Lys	p.E688K	ENST00000278616	NM_000051.3	688	Gaa/Aaa	13/63	0.280495813403769	1	FACETS	0.192	0.162	0.225	0.192	0.162	0.225	INDETERMINATE	1	TRUE	0	0.724603092181111	1		448	440	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28979997	28979997	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	54	456	1	ENST00000282397.4:c.1471A>T	p.Ile491Phe	p.I491F	ENST00000282397	NM_002019.4	491	Atc/Ttc	11/30	1	2	FACETS	0.207	0.176	0.241	0.207	0.176	0.241	SUBCLONAL	1	TRUE	1	0.724603092181111	2		457	720	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778895	3778914	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCCCAGCCACGGCCGCCT	GGGCCCAGCCACGGCCGCCT	-	novel	NA	P-0052567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	77	657	0	ENST00000262367.5:c.6134_6153del	p.Gln2045ProfsTer289	p.Q2045Pfs*289	ENST00000262367	NM_004380.2	2045	cAGGCGGCCGTGGCTGGGCCC/c	31/31	1	2	FACETS	0.242	0.212	0.275	0.242	0.212	0.275	SUBCLONAL	1	TRUE	1	0.724603092181111	2		657	877	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821508	72821508	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1188564840	NA	P-0052567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	77	443	0	ENST00000268489.5:c.10667G>C	p.Arg3556Thr	p.R3556T	ENST00000268489	NM_006885.3	3556	aGa/aCa	10/10	0.490314812424264	1	FACETS	0.29	0.255	0.327	0.29	0.255	0.327	SUBCLONAL	1	TRUE	0	0.724603092181111	1		443	467	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610510	10610510	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	218	768	0	ENST00000171111.5:c.200T>G	p.Met67Arg	p.M67R	ENST00000171111	NM_203500.1	67	aTg/aGg	2/6	1	2	FACETS	0.695	0.647	0.744	0.695	0.647	0.744	SUBCLONAL	1	TRUE	1	0.724603092181111	2		768	866	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610522	10610522	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	229	817	0	ENST00000171111.5:c.188C>G	p.Ala63Gly	p.A63G	ENST00000171111	NM_203500.1	63	gCc/gGc	2/6	1	2	FACETS	0.669	0.624	0.715	0.669	0.624	0.715	SUBCLONAL	1	TRUE	1	0.724603092181111	2		817	945	SUCCESS
ATR	545	MSKCC	GRCh37	3	142211986	142211986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	79	388	0	ENST00000350721.4:c.6066G>A	p.Met2022Ile	p.M2022I	ENST00000350721	NM_001184.3	2022	atG/atA	35/47	0.188890557066927	4	FACETS	0.543	0.478	0.614	0.272	0.239	0.307	INDETERMINATE	1	TRUE	2	0.724603092181111	4		388	692	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189431	56189431	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	51	515	0	ENST00000399503.3:c.4463G>T	p.Cys1488Phe	p.C1488F	ENST00000399503	NM_005921.1	1488	tGt/tTt	20/20	1	2	FACETS	0.205	0.173	0.239	0.205	0.173	0.239	SUBCLONAL	1	TRUE	1	0.724603092181111	2		515	688	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578281	7578281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	261	671	0	ENST00000269305.4:c.568C>T	p.Pro190Ser	p.P190S	ENST00000269305	NM_001126112.2	190	Cct/Tct	6/11	0.810548647470016	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.810548647470016	1		671	334	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	68	460	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.709	0.622	0.801	0.709	0.622	0.801	SUBCLONAL	1	TRUE	1	0.632914339714277	2		460	303	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0052572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	275	646	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.632914339714277	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.632914339714277	1		646	550	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711891	89711891	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660507	NA	P-0052572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	246	441	0	ENST00000371953.3:c.509G>T	p.Ser170Ile	p.S170I	ENST00000371953	NM_000314.4	170	aGt/aTt	6/9	0.632914339714277	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.632914339714277	1		441	468	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916800	48916804	+	frameshift_variant	Frame_Shift_Del	DEL	AGATG	AGATG	-	rs1064795438	NA	P-0052572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	239	414	0	ENST00000267163.4:c.335_339del	p.Glu112ValfsTer6	p.E112Vfs*6	ENST00000267163	NM_000321.2	110	ctAGATGag/ctag	3/27	0.632914339714277	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.632914339714277	1		414	452	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483019	29483019	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060500363	NA	P-0052572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	192	346	1	ENST00000356175.3:c.79C>T	p.Gln27Ter	p.Q27*	ENST00000356175	NM_000267.3	27	Cag/Tag	2/57	0.632914339714277	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.632914339714277	1		347	340	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0052573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	87	401	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.899	0.797	1	0.899	0.797	1	CLONAL	1	TRUE	1	0.3	2		401	645	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0052573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	167	719	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.304287676876702	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.3	1		719	878	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142068	108142068	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	126	560	1	ENST00000278616.4:c.3012C>A	p.Ser1004Arg	p.S1004R	ENST00000278616	NM_000051.3	1004	agC/agA	20/63	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.3	2		561	836	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663149	227663149	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	135	851	0	ENST00000305123.5:c.306G>T	p.Glu102Asp	p.E102D	ENST00000305123	NM_005544.2	102	gaG/gaT	1/2	0.304287676876702	3	FACETS	0.873	0.791	0.959	0.436	0.395	0.48	CLONAL	1	TRUE	1	0.3	3		851	1186	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686365	117686365	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	17	245	0	ENST00000368508.3:c.2976C>G	p.Phe992Leu	p.F992L	ENST00000368508	NM_002944.2	992	ttC/ttG	20/43	0.304287676876702	1	FACETS	0.304	0.226	0.396	0.304	0.226	0.396	SUBCLONAL	1	TRUE	0	0.3	1		245	317	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001359	150001359	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	216	619	0	ENST00000253339.5:c.2245C>G	p.His749Asp	p.H749D	ENST00000253339		749	Cat/Gat	4/7	0.285511194155325	2	FACETS	0.878	0.818	0.94	0.878	0.818	0.94	CLONAL	2	TRUE	0	0.3	2		619	820	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0052574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	194	531	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.192470436473999	4	FACETS	0.901	0.835	0.969	0.901	0.835	0.969	INDETERMINATE	2	TRUE	2	0.350980587129656	4		531	829	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394805	45394805	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	124	414	1	ENST00000262160.6:c.544C>T	p.Arg182Ter	p.R182*	ENST00000262160	NM_005901.5	182	Cga/Tga	5/11	0.269880767569657	2	FACETS	0.761	0.693	0.832	0.761	0.693	0.832	SUBCLONAL	2	TRUE	0	0.350980587129656	2		415	464	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134234	11134234	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1085307769	NA	P-0052574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	105	890	0	ENST00000358026.2:c.2900G>A	p.Arg967His	p.R967H	ENST00000358026	NM_001128849.1	967	cGt/cAt	20/36	1	2	FACETS	0.676	0.605	0.752	0.676	0.605	0.752	SUBCLONAL	1	TRUE	1	0.350980587129656	2		890	885	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934576	NA	P-0052574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	264	927	0	ENST00000269305.4:c.818G>C	p.Arg273Pro	p.R273P	ENST00000269305	NM_001126112.2	273	cGt/cCt	8/11	0.269880767569657	2	FACETS	1	0.993	1	0.726	0.681	0.773	CLONAL	1	TRUE	0	0.350980587129656	2		927	1036	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969813	81969813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371326699	NA	P-0052574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	154	734	0	ENST00000359376.3:c.2882C>T	p.Thr961Met	p.T961M	ENST00000359376	NM_002661.3	961	aCg/aTg	27/33	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.350980587129656	2		734	795	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249442	153249442	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	216	653	0	ENST00000281708.4:c.1336T>A	p.Trp446Arg	p.W446R	ENST00000281708	NM_033632.3	446	Tgg/Agg	9/12	0.350980587129656	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.350980587129656	1		653	755	SUCCESS
APC	324	MSKCC	GRCh37	5	112175599	112175599	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	121	433	0	ENST00000257430.4:c.4308del	p.Ser1436ArgfsTer37	p.S1436Rfs*37	ENST00000257430	NM_000038.5	1436	agT/ag	16/16	0.269880767569657	2	FACETS	1	0.985	1	0.743	0.676	0.813	CLONAL	1	TRUE	0	0.350980587129656	2		433	464	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0052576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	64	414	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	0.0524839496113394	3	FACETS	1	0.93	1	0.555	0.482	0.634	INDETERMINATE	1	TRUE	1	0.306225733336302	3		414	434	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0052576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	75	408	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.306225733336302	2		408	471	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058707	180058707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs918215332	NA	P-0052576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	122	916	0	ENST00000261937.6:c.130G>A	p.Gly44Ser	p.G44S	ENST00000261937	NM_182925.4	44	Ggt/Agt	2/30	0.306225733336302	1	FACETS	0.626	0.564	0.691	0.626	0.564	0.691	SUBCLONAL	1	TRUE	0	0.306225733336302	1		916	1078	SUCCESS
APC	324	MSKCC	GRCh37	5	112175530	112175530	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	49	324	0	ENST00000257430.4:c.4240del	p.Val1414Ter	p.V1414*	ENST00000257430	NM_000038.5	1413	atG/at	16/16	1	2	FACETS	0.688	0.583	0.803	0.688	0.583	0.803	SUBCLONAL	1	TRUE	1	0.306225733336302	2		324	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576851	7576851	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0052576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	144	691	0	ENST00000269305.4:c.993+2T>C		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.287245509953443	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.306225733336302	1		691	781	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776346	76776347	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCTAACGCCTGTACT	novel	NA	P-0052576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	17	285	0	ENST00000373344.5:c.7104_7119dup	p.Leu2374SerfsTer8	p.L2374Sfs*8	ENST00000373344	NM_000489.3	2373	-/AGTACAGGCGTTAGCA	34/35	0.266838453651018	2	FACETS	0.328	0.245	0.429			1	SUBCLONAL	1	TRUE	NA	0.306225733336302	2		285	338	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3827963	3828039	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAACCAAGGAAACAGGCTAAGGGATGGCAGTAGGAAATAAAATCCTTACTTGGAGGTCTCACAGGTTGTGCCTGTGG	AAACCAAGGAAACAGGCTAAGGGATGGCAGTAGGAAATAAAATCCTTACTTGGAGGTCTCACAGGTTGTGCCTGTGG	-	novel	NA	P-0052577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	22	296	0	ENST00000262367.5:c.2086_2113+49del		p.X696_splice	ENST00000262367	NM_004380.2	696		10/31	1	2	FACETS	0.96	0.751	1	0.96	0.751	1	CLONAL	1	TRUE	1	0.29	2		296	158	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525643	137525643	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0052577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	11	396	0	ENST00000367739.4:c.374-2A>T		p.X125_splice	ENST00000367739	NM_000416.2	125			1	2	FACETS	0.379	0.262	0.525	0.379	0.262	0.525	SUBCLONAL	1	TRUE	1	0.29	2		396	200	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873497	151873497	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	23	541	0	ENST00000262189.6:c.9041G>C	p.Gly3014Ala	p.G3014A	ENST00000262189	NM_170606.2	3014	gGg/gCg	38/59	1	2	FACETS	0.355	0.276	0.447	0.355	0.276	0.447	SUBCLONAL	1	TRUE	1	0.29	2		541	447	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	77	460	0				ENST00000310581	NM_198253.2	-/1132			0.260298658045996	4	FACETS	1	0.974	1	0.71	0.626	0.8	CLONAL	1	TRUE	2	0.328049416194819	4		460	439	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	92	451	0	ENST00000335508.6:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000335508	NM_012433.2	902	Gaa/Aaa	18/25	0.183464070561856	4	FACETS	1	0.977	1	0.691	0.616	0.771	INDETERMINATE	1	TRUE	2	0.328049416194819	4		451	539	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520006	NA	P-0052578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	186	657	0	ENST00000269305.4:c.821T>C	p.Val274Ala	p.V274A	ENST00000269305	NM_001126112.2	274	gTt/gCt	8/11	0.209848793793486	2	FACETS	1	0.99	1	0.747	0.691	0.804	CLONAL	1	TRUE	0	0.328049416194819	2		657	759	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	211	1162	0	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	0.183464070561856	4	FACETS	0.817	0.759	0.878	0.817	0.759	0.878	INDETERMINATE	2	TRUE	2	0.328049416194819	4		1162	1045	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913250	NA	P-0052578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	126	352	0	ENST00000369535.4:c.34G>T	p.Gly12Cys	p.G12C	ENST00000369535	NM_002524.4	12	Ggt/Tgt	2/7	0.183464070561856	4	FACETS	0.953	0.867	1	0.953	0.867	1	INDETERMINATE	2	TRUE	2	0.328049416194819	4		352	535	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675071	40675071	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	97	781	0	ENST00000249776.8:c.35T>G	p.Val12Gly	p.V12G	ENST00000249776	NM_033286.3	12	gTt/gGt	1/9	1	2	FACETS	0.628	0.559	0.702	0.628	0.559	0.702	SUBCLONAL	1	TRUE	1	0.328049416194819	2		781	941	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376191	118376191	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147412214	NA	P-0052578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	131	432	1	ENST00000534358.1:c.9584C>T	p.Pro3195Leu	p.P3195L	ENST00000534358	NM_005933.3	3195	cCg/cTg	27/36	0.281674861290472	2	FACETS	0.761	0.694	0.83	0.761	0.694	0.83	SUBCLONAL	2	TRUE	0	0.328049416194819	2		433	525	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481403	140481403	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913357	NA	P-0052578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	61	341	0	ENST00000288602.6:c.1405G>C	p.Gly469Arg	p.G469R	ENST00000288602	NM_004333.4	469	Gga/Cga	11/18	0.328049416194819	3	FACETS	0.875	0.756	1	0.437	0.378	0.502	CLONAL	1	TRUE	1	0.328049416194819	3		341	495	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259274	16259274	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	64	449	0	ENST00000375759.3:c.6539A>T	p.Lys2180Met	p.K2180M	ENST00000375759	NM_015001.2	2180	aAg/aTg	11/15	0.328049416194819	3	FACETS	0.779	0.675	0.892			1	SUBCLONAL	1	TRUE	NA	0.328049416194819	3		449	583	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22413205	22413216	+	inframe_deletion	In_Frame_Del	DEL	TGCTTGTTGGGA	TGCTTGTTGGGA	-	novel	NA	P-0052578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	29	204	0	ENST00000344548.3:c.332_343del	p.Leu111_Thr115delinsSer	p.L111_T115delinsS	ENST00000344548	NM_001039802.1	111	tTGCTTGTTGGGAct/tct	6/7	1	2	FACETS	0.772	0.623	0.939	0.772	0.623	0.939	CLONAL	1	TRUE	1	0.328049416194819	2		204	229	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438611	49438612	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0052578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	113	731	1	ENST00000301067.7:c.4878_4879delinsTT	p.Leu1626_Glu1627delinsPheTer	p.L1626_E1627delinsF*	ENST00000301067	NM_003482.3	1626	ttGGag/ttTTag	19/54	NA	2	FACETS	0.818	0.736	0.905			1	INDETERMINATE	1	TRUE	NA	0.328049416194819	2		732	842	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438620	49438620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	117	742	0	ENST00000301067.7:c.4870G>A	p.Ala1624Thr	p.A1624T	ENST00000301067	NM_003482.3	1624	Gca/Aca	19/54	NA	2	FACETS	0.84	0.757	0.928			1	INDETERMINATE	1	TRUE	NA	0.328049416194819	2		742	849	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492632	56492633	+	missense_variant	Missense_Mutation	DNP	GA	GA	TG	novel	NA	P-0052578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	223	566	1	ENST00000267101.3:c.2782_2783delinsTG	p.Glu928Trp	p.E928W	ENST00000267101	NM_001982.3	928	GAg/TGg	23/28	0.328049416194819	3	FACETS	0.966	0.902	1	0.966	0.902	1	CLONAL	2	TRUE	1	0.328049416194819	3		567	819	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495441	56495441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1340330119	NA	P-0052578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	130	724	0	ENST00000267101.3:c.3631C>T	p.Pro1211Ser	p.P1211S	ENST00000267101	NM_001982.3	1211	Ccc/Tcc	28/28	0.328049416194819	3	FACETS	0.845	0.765	0.93	0.422	0.382	0.465	CLONAL	1	TRUE	1	0.328049416194819	3		724	1092	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027120	49027130	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCATATAGGA	TTCATATAGGA	-	novel	NA	P-0052578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	66	230	0	ENST00000267163.4:c.1696-5_1701del		p.X566_splice	ENST00000267163	NM_000321.2	566		18/27	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.328049416194819	2		230	280	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061418	38061418	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	154	597	0	ENST00000250448.2:c.571C>G	p.Leu191Val	p.L191V	ENST00000250448	NM_004496.3	191	Ctc/Gtc	2/2	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.328049416194819	2		597	730	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242102	105242102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	311	875	0	ENST00000349310.3:c.322G>A	p.Asp108Asn	p.D108N	ENST00000349310	NM_001014432.1	108	Gac/Aac	6/15	0.260298658045996	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.328049416194819	4		875	1086	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552261	29552343	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTCTATGGTCAGCTTCTTCTGTACTTTTTCTGTATCATTTTATGTGCTCTGTTTGTTTTCTGAATGAAATTTGGTAAATTTC	CCTCTATGGTCAGCTTCTTCTGTACTTTTTCTGTATCATTTTATGTGCTCTGTTTGTTTTCTGAATGAAATTTGGTAAATTTC	-	novel	NA	P-0052578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	63	504	1	ENST00000356175.3:c.1994_2001+75del		p.X665_splice	ENST00000356175	NM_000267.3	665		17/57	0.183464070561856	4	FACETS	0.946	0.819	1	0.473	0.409	0.542	INDETERMINATE	1	TRUE	2	0.328049416194819	4		505	539	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45854957	45854972	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGACAGGCCCAGCT	AGGGACAGGCCCAGCT	-	novel	NA	P-0052578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	180	847	0	ENST00000391945.4:c.2198_2213del	p.Gln733ArgfsTer7	p.Q733Rfs*7	ENST00000391945	NM_000400.3	733	cAGCTGGGCCTGTCCCTg/cg	23/23	0.183464070561856	4	FACETS	1	0.988	1	0.692	0.637	0.749	INDETERMINATE	1	TRUE	2	0.328049416194819	4		847	1053	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027104	48027104	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	64	419	0	ENST00000234420.5:c.1982G>T	p.Gly661Val	p.G661V	ENST00000234420	NM_000179.2	661	gGt/gTt	4/10	1	2	FACETS	0.686	0.594	0.785	0.686	0.594	0.785	SUBCLONAL	1	TRUE	1	0.328049416194819	2		419	569	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712579	52712579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1402616012	NA	P-0052578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	49	436	0	ENST00000394830.3:c.173G>A	p.Arg58Gln	p.R58Q	ENST00000394830	NM_018313.4	58	cGa/cAa	3/30	0.129630010669493	4	FACETS	0.603	0.51	0.706	0.301	0.255	0.353	INDETERMINATE	1	TRUE	2	0.328049416194819	4		436	658	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495648	72495648	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	67	284	0	ENST00000477973.2:c.424A>G	p.Arg142Gly	p.R142G	ENST00000477973	NM_012234.5	142	Aga/Gga	1/4	0.129630010669493	4	FACETS	1	0.949	1	0.591	0.515	0.673	INDETERMINATE	1	TRUE	2	0.328049416194819	4		284	459	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190459	32190459	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	100	867	0	ENST00000375023.3:c.280C>G	p.Pro94Ala	p.P94A	ENST00000375023	NM_004557.3	94	Ccc/Gcc	3/30	1	2	FACETS	0.563	0.502	0.629	0.563	0.502	0.629	SUBCLONAL	1	TRUE	1	0.328049416194819	2		867	1082	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846179	151846215	+	frameshift_variant	Frame_Shift_Del	DEL	TGAAATGCTTTGGAAGGCGTTTCTCTCATAGGTGATT	TGAAATGCTTTGGAAGGCGTTTCTCTCATAGGTGATT	-	novel	NA	P-0052578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	46	569	0	ENST00000262189.6:c.12797_12833del	p.Gln4266LeufsTer48	p.Q4266Lfs*48	ENST00000262189	NM_170606.2	4266	cAATCACCTATGAGAGAAACGCCTTCCAAAGCATTTCAt/ct	52/59	0.328049416194819	3	FACETS	0.457	0.384	0.538	0.229	0.192	0.269	SUBCLONAL	1	TRUE	1	0.328049416194819	3		569	714	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846225	151846225	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	48	486	0	ENST00000262189.6:c.12787T>G	p.Ser4263Ala	p.S4263A	ENST00000262189	NM_170606.2	4263	Tca/Gca	52/59	0.328049416194819	3	FACETS	0.575	0.486	0.674	0.288	0.243	0.337	SUBCLONAL	1	TRUE	1	0.328049416194819	3		486	592	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410486	139410486	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	472	980	0	ENST00000277541.6:c.1616A>C	p.Asn539Thr	p.N539T	ENST00000277541	NM_017617.3	539	aAt/aCt	10/34	0.328049416194819	3	FACETS	0.902	0.863	0.941	0.902	0.863	0.941	CLONAL	3	TRUE	0	0.328049416194819	3		980	1238	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141524	11141524	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	96	695	0	ENST00000358026.2:c.3502del	p.Ala1168GlnfsTer4	p.A1168Qfs*4	ENST00000358026	NM_001128849.1	1167	tcG/tc	25/36	0.214987486028038	1	FACETS	0.78	0.697	0.867	1	0.982	1	SUBCLONAL	2	FALSE	0	0.214987486028038	1		695	511	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	58	495	0	ENST00000342988.3:c.1067C>A	p.Pro356His	p.P356H	ENST00000342988	NM_005359.5	356	cCt/cAt	9/12	1	2	FACETS	0.89	0.771	1	1	0.976	1	CLONAL	2	FALSE	1	0.214987486028038	2		495	303	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0052579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	42	565	1	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	0.214987486028038	5	FACETS	1	0.876	1	0.353	0.294	0.418	CLONAL	1	FALSE	2	0.214987486028038	5		566	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0052579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	125	1142	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.155258273861944	2	FACETS	0.855	0.775	0.939	0.855	0.775	0.939	CLONAL	2	FALSE	0	0.214987486028038	2		1142	680	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0052580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	235	464	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.454527180274188	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.454527180274188	3		464	616	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357173	89357173	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	49	719	0	ENST00000301030.4:c.461C>T	p.Ala154Val	p.A154V	ENST00000301030	NM_001256183.1	154	gCc/gTc	6/13	1	2	FACETS	0.33	0.279	0.387	0.33	0.279	0.387	SUBCLONAL	1	TRUE	1	0.454527180274188	2		719	653	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74868231	74868231	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	65	254	0	ENST00000284811.8:c.63G>T	p.Leu21Phe	p.L21F	ENST00000284811		21	ttG/ttT	3/4	1	2	FACETS	0.938	0.82	1	0.938	0.82	1	CLONAL	1	TRUE	1	0.454527180274188	2		254	305	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	175	460	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.977	0.911	1	0.977	0.911	1	CLONAL	1	TRUE	1	0.882359289571792	2		460	406	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0052581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	177	379	3	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.882359289571792	2		382	393	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791806	42791806	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	98	869	0	ENST00000575354.2:c.692G>A	p.Ser231Asn	p.S231N	ENST00000575354	NM_015125.3	231	aGc/aAc	5/20	0.882359289571792	1	FACETS	0.21	0.188	0.234	0.21	0.188	0.234	SUBCLONAL	1	TRUE	0	0.882359289571792	1		869	590	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799130	42799131	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0052581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	169	831	0	ENST00000575354.2:c.4620dup	p.Thr1541HisfsTer18	p.T1541Hfs*18	ENST00000575354	NM_015125.3	1538	-/C	20/20	0.882359289571792	1	FACETS	0.384	0.355	0.414	0.384	0.355	0.414	SUBCLONAL	1	TRUE	0	0.882359289571792	1		831	558	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428462	78428463	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0052581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	198	351	0	ENST00000370768.2:c.1336_1337del	p.Lys446AspfsTer44	p.K446Dfs*44	ENST00000370768	NM_003902.3	446	AAg/g	14/20	0.882359289571792	1	FACETS	0.984	0.943	1	0.984	0.943	1	CLONAL	1	TRUE	0	0.882359289571792	1		351	255	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791773	42791773	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	85	868	0	ENST00000575354.2:c.659A>C	p.Gln220Pro	p.Q220P	ENST00000575354	NM_015125.3	220	cAg/cCg	5/20	0.882359289571792	1	FACETS	0.19	0.168	0.214	0.19	0.168	0.214	SUBCLONAL	1	TRUE	0	0.882359289571792	1		868	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0052583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	385	693	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	0.907	0.862	0.953	0.907	0.862	0.953	CLONAL	1	TRUE	1	0.700992444250325	2		693	1211	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628455	187628455	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	400	759	0	ENST00000441802.2:c.2527C>T	p.Gln843Ter	p.Q843*	ENST00000441802	NM_005245.3	843	Cag/Tag	2/27	0.694517104161938	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.700992444250325	1		759	716	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	410	712	1	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.700992444250325	2		713	1150	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391887	139391887	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	1633	1035	0	ENST00000277541.6:c.6304C>T	p.Gln2102Ter	p.Q2102*	ENST00000277541	NM_017617.3	2102	Cag/Tag	34/34	0.699781980435366	3	FACETS	0.993	0.979	1	0.993	0.979	1	CLONAL	3	TRUE	0	0.700992444250325	3		1035	2112	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261338	16261338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	581	655	0	ENST00000375759.3:c.8603C>T	p.Ser2868Phe	p.S2868F	ENST00000375759	NM_015001.2	2868	tCc/tTc	11/15	0.689262343463056	3	FACETS	0.793	0.763	0.823	0.528	0.508	0.549	SUBCLONAL	2	TRUE	0	0.700992444250325	3		655	1412	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70360757	70360757	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	183	256	0	ENST00000373644.4:c.1934G>A	p.Arg645Lys	p.R645K	ENST00000373644	NM_030625.2	645	aGg/aAg	3/12	1	2	FACETS	0.987	0.918	1	0.987	0.918	1	CLONAL	1	TRUE	1	0.700992444250325	2		256	529	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872795	136872795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1272938495	NA	P-0052583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	303	471	4	ENST00000241393.3:c.703C>T	p.Arg235Cys	p.R235C	ENST00000241393	NM_003467.2	235	Cgc/Tgc	2/2	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.700992444250325	2		475	833	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413948	139413948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1288	758	847	2	ENST00000277541.6:c.812C>T	p.Ala271Val	p.A271V	ENST00000277541	NM_017617.3	271	gCc/gTc	5/34	0.699781980435366	3	FACETS	1	0.997	1	0.476	0.459	0.493	CLONAL	1	TRUE	0	0.700992444250325	3		849	2046	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510783	120510783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	495	600	1	ENST00000256646.2:c.1181C>T	p.Pro394Leu	p.P394L	ENST00000256646	NM_024408.3	394	cCc/cTc	7/34	0.647812945402645	2	FACETS	0.841	0.812	0.87	0.841	0.812	0.87	CLONAL	2	TRUE	0	0.700992444250325	2		601	840	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138974	37138974	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1418	265	856	0	ENST00000373509.5:c.314G>A	p.Arg105Lys	p.R105K	ENST00000373509	NM_002648.3	105	aGg/aAg	4/6	0.313107872980108	3	FACETS	0.607	0.567	0.648	0.303	0.283	0.324	INDETERMINATE	1	TRUE	1	0.700992444250325	3		856	1683	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188625	32188625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	573	757	0	ENST00000375023.3:c.830C>T	p.Pro277Leu	p.P277L	ENST00000375023	NM_004557.3	277	cCa/cTa	5/30	0.313107872980108	3	FACETS	0.763	0.733	0.793	0.763	0.733	0.793	INDETERMINATE	2	TRUE	1	0.700992444250325	3		757	1447	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961409	41961409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	428	462	0	ENST00000219905.7:c.317C>T	p.Pro106Leu	p.P106L	ENST00000219905	NM_001164273.1	106	cCt/cTt	2/24	0.34778890498375	2	FACETS	0.754	0.724	0.784	0.754	0.724	0.784	INDETERMINATE	2	TRUE	0	0.700992444250325	2		462	810	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406302	406302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	330	534	1	ENST00000399788.2:c.4139C>T	p.Pro1380Leu	p.P1380L	ENST00000399788	NM_001042603.1	1380	cCc/cTc	25/28	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.700992444250325	2		535	923	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444252	49444252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	558	1008	0	ENST00000301067.7:c.3119C>T	p.Ser1040Phe	p.S1040F	ENST00000301067	NM_003482.3	1040	tCc/tTc	11/54	1	2	FACETS	0.964	0.925	1	0.964	0.925	1	CLONAL	1	TRUE	1	0.700992444250325	2		1008	1651	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533851	63533851	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1451720453	NA	P-0052583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	377	644	1	ENST00000307078.5:c.1303C>T	p.Pro435Ser	p.P435S	ENST00000307078	NM_004655.3	435	Ccg/Tcg	6/11	1	2	FACETS	0.991	0.943	1	0.991	0.943	1	CLONAL	1	TRUE	1	0.700992444250325	2		645	1085	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251177	251177	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	135	320	1	ENST00000264932.6:c.1622A>G	p.Lys541Arg	p.K541R	ENST00000264932	NM_004168.2	541	aAg/aGg	12/15	NA	2	FACETS	0.813	0.744	0.884			1	INDETERMINATE	1	TRUE	NA	0.700992444250325	2		321	474	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31472232	31472232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1293897279	NA	P-0052583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	368	609	0	ENST00000344624.3:c.2179G>A	p.Glu727Lys	p.E727K	ENST00000344624		727	Gag/Aag	14/33	1	2	FACETS	0.947	0.899	0.995	0.947	0.899	0.995	CLONAL	1	TRUE	1	0.700992444250325	2		609	1109	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609798	117609798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	149	585	0	ENST00000368508.3:c.6901G>A	p.Gly2301Ser	p.G2301S	ENST00000368508	NM_002944.2	2301	Ggt/Agt	43/43	0.345722915946239	1	FACETS	0.356	0.326	0.388	0.356	0.326	0.388	INDETERMINATE	1	TRUE	0	0.700992444250325	1		585	775	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117730754	117730754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373938735	NA	P-0052583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	133	538	0	ENST00000368508.3:c.280G>A	p.Glu94Lys	p.E94K	ENST00000368508	NM_002944.2	94	Gaa/Aaa	4/43	0.345722915946239	1	FACETS	0.342	0.311	0.375	0.342	0.311	0.375	INDETERMINATE	1	TRUE	0	0.700992444250325	1		538	721	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878352	151878352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	305	537	0	ENST00000262189.6:c.6593G>A	p.Arg2198Lys	p.R2198K	ENST00000262189	NM_170606.2	2198	aGg/aAg	36/59	0.385816519176402	3	FACETS	1	0.98	1	0.542	0.51	0.573	INDETERMINATE	1	TRUE	1	0.700992444250325	3		537	1085	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772676	135772676	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	847	491	2	ENST00000298552.3:c.2870T>G	p.Val957Gly	p.V957G	ENST00000298552	NM_001162426.1	957	gTg/gGg	22/23	0.689262343463056	3	FACETS	0.962	0.942	0.982	0.962	0.942	0.982	CLONAL	3	TRUE	0	0.700992444250325	3		493	1131	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0052602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	501	724	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.525828536603684	3	FACETS	0.972	0.939	1	0.972	0.939	1	CLONAL	3	TRUE	0	0.518916411555874	3		724	834	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440297	52440297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759024400	NA	P-0052602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	117	655	2	ENST00000460680.1:c.755G>A	p.Arg252His	p.R252H	ENST00000460680	NM_004656.3	252	cGt/cAt	9/17	0.477975362706687	2	FACETS	0.74	0.669	0.815	0.37	0.334	0.408	SUBCLONAL	1	TRUE	0	0.518916411555874	2		657	609	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853774	59853774	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	223	429	0	ENST00000259008.2:c.2085G>C	p.Leu695Phe	p.L695F	ENST00000259008	NM_032043.2	695	ttG/ttC	14/20	0.525828536603684	3	FACETS	0.979	0.919	1	0.652	0.613	0.693	CLONAL	2	TRUE	0	0.518916411555874	3		429	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0052603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	251	656	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.309211435355312	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.37696763065699	1		657	902	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017724	31017724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1005458245	NA	P-0052603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	95	538	0	ENST00000375687.4:c.586G>A	p.Asp196Asn	p.D196N	ENST00000375687	NM_015338.5	196	Gat/Aat	8/13	1	2	FACETS	0.57	0.506	0.637	0.57	0.506	0.637	SUBCLONAL	1	TRUE	1	0.37696763065699	2		538	885	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342775	118342775	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	83	285	1	ENST00000534358.1:c.901C>T	p.Arg301Ter	p.R301*	ENST00000534358	NM_005933.3	301	Cga/Tga	3/36	0.37696763065699	1	FACETS	0.966	0.858	1	0.966	0.858	1	CLONAL	1	TRUE	0	0.37696763065699	1		286	370	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106726	27106727	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0052603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	158	572	0	ENST00000324856.7:c.6341dup	p.Gln2115AlafsTer35	p.Q2115Afs*35	ENST00000324856	NM_006015.4	2113	tcc/tCcc	20/20	0.235987600982893	1	FACETS	0.826	0.757	0.897	0.826	0.757	0.897	CLONAL	1	TRUE	0	0.37696763065699	1		572	824	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868115	56868115	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	51	504	0	ENST00000308159.5:c.1613A>C	p.Lys538Thr	p.K538T	ENST00000308159	NM_014669.4	538	aAg/aCg	14/22	0.168952285052405	2	FACETS	0.306	0.259	0.358	0.153	0.129	0.179	INDETERMINATE	1	TRUE	0	0.37696763065699	2		504	884	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100108	11100108	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	93	609	0	ENST00000358026.2:c.1234T>G	p.Phe412Val	p.F412V	ENST00000358026	NM_001128849.1	412	Ttc/Gtc	7/36	0.290421581358406	1	FACETS	0.469	0.416	0.525	0.469	0.416	0.525	SUBCLONAL	1	TRUE	0	0.37696763065699	1		609	854	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166220	7166220	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	92	612	0	ENST00000302850.5:c.1806A>C	p.Glu602Asp	p.E602D	ENST00000302850	NM_000208.2	602	gaA/gaC	8/22	0.290421581358406	1	FACETS	0.468	0.415	0.524	0.468	0.415	0.524	SUBCLONAL	1	TRUE	0	0.37696763065699	1		612	847	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89478259	89478259	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	90	262	0	ENST00000336596.2:c.2078A>G	p.Lys693Arg	p.K693R	ENST00000336596	NM_005233.5	693	aAg/aGg	12/17	1	2	FACETS	0.758	0.68	0.84	1	0.982	1	SUBCLONAL	2	TRUE	1	0.37696763065699	2		262	315	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790726	89790726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs933708411	NA	P-0052603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	128	890	1	ENST00000336032.3:c.113C>T	p.Ala38Val	p.A38V	ENST00000336032	NM_006813.2	38	gCt/gTt	1/2	1	2	FACETS	0.562	0.508	0.62	0.562	0.508	0.62	SUBCLONAL	1	TRUE	1	0.37696763065699	2		891	1208	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221735	55221735	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	139	471	0	ENST00000275493.2:c.779G>A	p.Cys260Tyr	p.C260Y	ENST00000275493	NM_005228.3	260	tGc/tAc	7/28	0.205958164533559	3	FACETS	0.933	0.849	1	0.467	0.424	0.511	INDETERMINATE	1	TRUE	1	0.37696763065699	3		471	939	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813035	76813035	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	58	436	0	ENST00000373344.5:c.6586G>T	p.Glu2196Ter	p.E2196*	ENST00000373344	NM_000489.3	2196	Gag/Tag	30/35	1	2	FACETS	0.534	0.459	0.616	0.534	0.459	0.616	SUBCLONAL	1	TRUE	1	0.37696763065699	2		436	576	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378648	25378648	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	149	382	0	ENST00000311936.3:c.350A>G	p.Lys117Arg	p.K117R	ENST00000311936	NM_004985.3	117	aAa/aGa	4/5	0.185377500128316	3	FACETS	0.904	0.842	0.965	0.904	0.842	0.965	INDETERMINATE	3	TRUE	0	0.457953783389892	3		382	295	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	69	302	0	ENST00000288602.6:c.1742A>T	p.Asn581Ile	p.N581I	ENST00000288602	NM_004333.4	581	aAt/aTt	15/18	0.184697963167799	4	FACETS	0.943	0.833	1	0.943	0.833	1	INDETERMINATE	2	TRUE	2	0.457953783389892	4		302	233	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs878854073	NA	P-0052604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	201	542	0	ENST00000269305.4:c.673-1G>A		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.457953783389892	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.457953783389892	2		542	412	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219357	1219357	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730881970	NA	P-0052604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	206	677	2	ENST00000326873.7:c.409C>T	p.Gln137Ter	p.Q137*	ENST00000326873	NM_000455.4	137	Cag/Tag	3/10	0.432527018250039	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.457953783389892	2		679	416	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193172945	193172945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	149	390	0	ENST00000367435.3:c.993G>C	p.Lys331Asn	p.K331N	ENST00000367435	NM_024529.4	331	aaG/aaC	11/17	0.45852641239334	4	FACETS	0.978	0.9	1	0.652	0.6	0.706	CLONAL	2	TRUE	1	0.457953783389892	4		390	485	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231103	46231103	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0052604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	25	218	0	ENST00000334344.6:c.1024-1G>C		p.X342_splice	ENST00000334344	NM_152641.2	342			0.373228477391399	4	FACETS	0.629	0.497	0.78			1	SUBCLONAL	1	TRUE	NA	0.457953783389892	4		218	253	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425347	49425347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	62	814	0	ENST00000301067.7:c.13141G>A	p.Asp4381Asn	p.D4381N	ENST00000301067	NM_003482.3	4381	Gac/Aac	39/54	0.457953783389892	5	FACETS	0.465	0.4	0.536			1	SUBCLONAL	1	TRUE	NA	0.457953783389892	5		814	982	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587780070	NA	P-0052605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	453	854	0	ENST00000269305.4:c.535C>A	p.His179Asn	p.H179N	ENST00000269305	NM_001126112.2	179	Cat/Aat	5/11	0.690024530645211	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.690024530645211	2		854	636	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523313	9523313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866291709	NA	P-0052605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	148	596	0	ENST00000353224.5:c.1924C>T	p.Pro642Ser	p.P642S	ENST00000353224	NM_177990.2	642	Ccc/Tcc	9/10	0.674243071680257	4	FACETS	0.96	0.878	1	0.48	0.439	0.523	CLONAL	1	TRUE	2	0.690024530645211	4		596	755	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261680	16261680	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	107	632	0	ENST00000375759.3:c.8945T>G	p.Leu2982Arg	p.L2982R	ENST00000375759	NM_015001.2	2982	cTc/cGc	11/15	0.690024530645211	2	FACETS	0.552	0.496	0.61	0.276	0.248	0.305	SUBCLONAL	1	TRUE	0	0.690024530645211	2		632	562	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251196	115251196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	183	627	1	ENST00000369535.4:c.530G>A	p.Gly177Glu	p.G177E	ENST00000369535	NM_002524.4	177	gGg/gAg	5/7	0.690024530645211	3	FACETS	1	0.954	1	0.521	0.482	0.561	CLONAL	1	TRUE	1	0.690024530645211	3		628	685	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137004	64137004	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	107	603	0	ENST00000334205.4:c.1515A>C	p.Glu505Asp	p.E505D	ENST00000334205	NM_003942.2	505	gaA/gaC	13/17	0.690024530645211	3	FACETS	0.642	0.576	0.711	0.321	0.288	0.356	SUBCLONAL	1	TRUE	1	0.690024530645211	3		603	650	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039155	49039155	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0052605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	203	395	0	ENST00000267163.4:c.2233A>T	p.Lys745Ter	p.K745*	ENST00000267163	NM_000321.2	745	Aaa/Taa	22/27	0.690024530645211	2	FACETS	0.943	0.896	0.989	0.943	0.896	0.989	CLONAL	2	TRUE	0	0.690024530645211	2		395	312	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604719	48604719	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	282	501	0	ENST00000342988.3:c.1541C>G	p.Pro514Arg	p.P514R	ENST00000342988	NM_005359.5	514	cCa/cGa	12/12	0.690024530645211	4	FACETS	0.936	0.884	0.988	0.936	0.884	0.988	CLONAL	2	TRUE	2	0.690024530645211	4		501	738	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546767	9546767	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	88	463	0	ENST00000353224.5:c.1255T>C	p.Ser419Pro	p.S419P	ENST00000353224	NM_177990.2	419	Tcc/Ccc	5/10	0.674243071680257	4	FACETS	0.742	0.658	0.831	0.371	0.329	0.416	SUBCLONAL	1	TRUE	2	0.690024530645211	4		463	581	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670673	134670673	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	164	746	0	ENST00000398015.3:c.584A>C	p.Lys195Thr	p.K195T	ENST00000398015	NM_004441.4	195	aAg/aCg	3/16	0.690024530645211	4	FACETS	0.781	0.717	0.849	0.391	0.358	0.425	SUBCLONAL	1	TRUE	2	0.690024530645211	4		746	1028	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0052606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	114	449	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.978	0.888	1	0.978	0.888	1	CLONAL	1	TRUE	1	0.590304008830213	2		449	395	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0052606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	151	401	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.590304008830213	2		401	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0052606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	237	851	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.586286554143929	1	FACETS	0.946	0.89	1	0.946	0.89	1	CLONAL	1	TRUE	0	0.590304008830213	1		851	598	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	166	446	0	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	1	2	FACETS	0.942	0.87	1	0.942	0.87	1	CLONAL	1	TRUE	1	0.590304008830213	2		446	597	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323186	31323186	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	281	1068	1	ENST00000412585.2:c.803G>A	p.Trp268Ter	p.W268*	ENST00000412585	NM_005514.6	268	tGg/tAg	4/8	1	2	FACETS	0.989	0.93	1	0.989	0.93	1	CLONAL	1	TRUE	1	0.590304008830213	2		1069	963	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266078	41266358	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATA	GCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATA	-	novel	NA	P-0052606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	145	457	0	ENST00000349496.5:c.78_242-84del		p.X26_splice	ENST00000349496	NM_001904.3	26		3/15	0.590304008830213	2	FACETS	1	0.989	1	0.725	0.671	0.779	CLONAL	1	TRUE	0	0.590304008830213	2		457	339	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247178	153247179	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGTA	novel	NA	P-0052606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	113	405	0	ENST00000281708.4:c.1620_1623dup	p.Asn542TyrfsTer2	p.N542Yfs*2	ENST00000281708	NM_033632.3	541	-/TACT	10/12	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.590304008830213	2		405	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0052607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	142	668	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	0.814	0.745	0.885	1	0.989	1	CLONAL	2	FALSE	1	0.315552666253615	2		669	553	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1978376	1978376	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	59	885	0	ENST00000382891.5:c.3796T>C	p.Ser1266Pro	p.S1266P	ENST00000382891	NM_133335.3	1266	Tcc/Ccc	21/22	0.315552666253615	1	FACETS	0.669	0.576	0.769	0.669	0.576	0.769	SUBCLONAL	1	FALSE	0	0.315552666253615	1		885	471	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438156	438156	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	39	433	0	ENST00000399788.2:c.1813C>A	p.Leu605Ile	p.L605I	ENST00000399788	NM_001042603.1	605	Cta/Ata	14/28	1	2	FACETS	0.574	0.475	0.683	0.574	0.475	0.683	SUBCLONAL	1	FALSE	1	0.315552666253615	2		433	431	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348762	11348762	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1333675855	NA	P-0052607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	64	491	0	ENST00000332029.2:c.574G>C	p.Ala192Pro	p.A192P	ENST00000332029	NM_003745.1	192	Gct/Cct	2/2	0.315552666253615	3	FACETS	1	0.95	1	0.598	0.519	0.681	CLONAL	1	FALSE	1	0.315552666253615	3		491	393	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591313	67591412	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGAGTAAGTAGTTACTAAAGATGGTGATAGCAGAAGATTTTTCTCATTTTAGGAAAATGCATGACTTGCTTTGTTTTTAGAACAAGTGAGGAATTTTAC	AAGAGTAAGTAGTTACTAAAGATGGTGATAGCAGAAGATTTTTCTCATTTTAGGAAAATGCATGACTTGCTTTGTTTTTAGAACAAGTGAGGAATTTTAC	-	novel	NA	P-0052607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	56	311	0	ENST00000274335.5:c.1811_1814+96del		p.X604_splice	ENST00000274335		604		13/15	1	2	FACETS	0.936	0.805	1	0.936	0.805	1	CLONAL	1	FALSE	1	0.315552666253615	2		311	379	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673696	176673696	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	23	382	0	ENST00000439151.2:c.4396G>C	p.Asp1466His	p.D1466H	ENST00000439151	NM_022455.4	1466	Gac/Cac	10/23	1	2	FACETS	0.392	0.305	0.492	0.392	0.305	0.492	SUBCLONAL	1	FALSE	1	0.315552666253615	2		382	372	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0052608-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	175	856	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.36119693476722	1	FACETS	0.923	0.851	0.999	0.923	0.851	0.999	CLONAL	1	TRUE	0	0.36119693476722	1		856	860	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044556	47044556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052608-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	179	882	1	ENST00000377604.3:c.2053C>T	p.Arg685Trp	p.R685W	ENST00000377604	NM_001204468.1	685	Cgg/Tgg	18/24	NA	2	FACETS	0.889	0.818	0.963			1	INDETERMINATE	1	TRUE	NA	0.36119693476722	2		883	1115	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550438	29550464	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACAATGAACTTTATGTTACTGCAGCTC	ACAATGAACTTTATGTTACTGCAGCTC	-	novel	NA	P-0052608-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	43	143	0	ENST00000356175.3:c.1722-20_1728del		p.X574_splice	ENST00000356175	NM_000267.3	574		16/57	0.36119693476722	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.36119693476722	1		143	170	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514314	69514314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377419016	NA	P-0052608-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1184	109	614	0	ENST00000294312.3:c.367G>A	p.Glu123Lys	p.E123K	ENST00000294312	NM_005117.2	123	Gag/Aag	3/3	0.36119693476722	5	FACETS	0.72	0.644	0.8	0.18	0.161	0.2	SUBCLONAL	1	TRUE	1	0.36119693476722	5		614	1293	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89842149	89842149	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0052608-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	164	610	0	ENST00000389301.3:c.1900+1del		p.X634_splice	ENST00000389301	NM_000135.2	634			1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.36119693476722	2		610	890	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582146	52582146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1367900513	NA	P-0052608-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	103	435	1	ENST00000394830.3:c.4682G>A	p.Arg1561His	p.R1561H	ENST00000394830	NM_018313.4	1561	cGc/cAc	30/30	1	2	FACETS	0.894	0.801	0.992	0.894	0.801	0.992	CLONAL	1	TRUE	1	0.36119693476722	2		436	638	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	412	378	0	ENST00000256196.4:c.68G>T	p.Gly23Val	p.G23V	ENST00000256196		23	gGc/gTc	1/6	0.573290962385286	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	4	TRUE	0	0.596355194295986	4		378	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793881	NA	P-0052618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	501	917	0	ENST00000269305.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGg/gAg	8/11	0.469864274841525	3	FACETS	0.944	0.914	0.974	0.944	0.914	0.974	CLONAL	3	TRUE	0	0.596355194295986	3		917	770	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940083	76940083	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	17	296	1	ENST00000373344.5:c.665G>T	p.Trp222Leu	p.W222L	ENST00000373344	NM_000489.3	222	tGg/tTg	9/35	0.540529766647717	2	FACETS	0.177	0.131	0.23			1	SUBCLONAL	1	TRUE	NA	0.596355194295986	2		297	323	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46215272	46215272	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0052618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	29	389	0	ENST00000334344.6:c.705+2T>A		p.X235_splice	ENST00000334344	NM_152641.2	235			0.208823746114575	4	FACETS	0.761	0.615	0.924	0.381	0.307	0.462	INDETERMINATE	1	TRUE	2	0.596355194295986	4		389	204	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105655	30105655	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	145	804	0	ENST00000331968.5:c.1031G>A	p.Gly344Glu	p.G344E	ENST00000331968	NM_002742.2	344	gGg/gAg	7/18	0.596355194295986	3	FACETS	0.841	0.768	0.917	0.42	0.384	0.459	CLONAL	1	TRUE	1	0.596355194295986	3		804	751	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946822	17946899	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTATGGCCCCCAGGTGTACAAATTCCTGCACCATGGTGCCTGGTTGGCAGCAGGGAGAGGCGGGGTTGGGAGACTGAA	CTATGGCCCCCAGGTGTACAAATTCCTGCACCATGGTGCCTGGTTGGCAGCAGGGAGAGGCGGGGTTGGGAGACTGAA	-	novel	NA	P-0052618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	47	1033	0	ENST00000458235.1:c.1787-39_1825del		p.X596_splice	ENST00000458235	NM_000215.3	596		14/24	0.477955369671992	2	FACETS	0.332	0.28	0.389	0.166	0.14	0.195	SUBCLONAL	1	TRUE	0	0.596355194295986	2		1033	475	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821151	32821151	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	51	1053	0	ENST00000354258.4:c.443G>T	p.Gly148Val	p.G148V	ENST00000354258	NM_000593.5	148	gGt/gTt	1/11	1	2	FACETS	0.298	0.253	0.348	0.298	0.253	0.348	SUBCLONAL	1	TRUE	1	0.596355194295986	2		1053	573	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188200	10188200	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	98	606	0	ENST00000256474.2:c.343C>A	p.His115Asn	p.H115N	ENST00000256474	NM_000551.3	115	Cac/Aac	2/3	0.343133928551606	1	FACETS	0.946	0.848	1	0.946	0.848	1	CLONAL	1	TRUE	0	0.343133928551606	1		606	500	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174440	11174440	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	141	855	1	ENST00000361445.4:c.7235A>T	p.Asp2412Val	p.D2412V	ENST00000361445	NM_004958.3	2412	gAc/gTc	53/58	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.343133928551606	2		856	735	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112893764	112893764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	32	422	0	ENST00000351677.2:c.653C>T	p.Thr218Met	p.T218M	ENST00000351677	NM_002834.3	218	aCg/aTg	6/16	1	2	FACETS	0.681	0.555	0.822	0.681	0.555	0.822	SUBCLONAL	1	TRUE	1	0.343133928551606	2		422	274	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012393	29012393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs539329072	NA	P-0052619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	64	662	0	ENST00000282397.4:c.478G>A	p.Val160Ile	p.V160I	ENST00000282397	NM_002019.4	160	Gtt/Att	4/30	1	2	FACETS	0.822	0.713	0.938	0.822	0.713	0.938	CLONAL	1	TRUE	1	0.343133928551606	2		662	454	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436683	52436689	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TCATCAA	TCATCAA	-	novel	NA	P-0052619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	95	843	0	ENST00000460680.1:c.1985_1991del	p.Ile662ThrfsTer28	p.I662Tfs*28	ENST00000460680	NM_004656.3	662	aTTGATGAc/ac	16/17	0.343133928551606	1	FACETS	0.97	0.867	1	0.97	0.867	1	CLONAL	1	TRUE	0	0.343133928551606	1		843	473	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215960	142215960	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	80	566	0	ENST00000350721.4:c.5633A>T	p.Glu1878Val	p.E1878V	ENST00000350721	NM_001184.3	1878	gAa/gTa	33/47	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.343133928551606	2		566	435	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	148	460	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.881	0.813	0.949	0.881	0.813	0.949	CLONAL	1	TRUE	1	0.838274882395706	2		460	401	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0052620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	669	1049	1	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	0.876	0.855	0.897	1	0.998	1	CLONAL	2	TRUE	1	0.838274882395706	2		1050	911	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348110	89348110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1170699512	NA	P-0052620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	409	1117	1	ENST00000301030.4:c.4840C>T	p.Arg1614Trp	p.R1614W	ENST00000301030	NM_001256183.1	1614	Cgg/Tgg	9/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.838274882395706	2		1118	927	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029415	16029415	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	24	154	0	ENST00000268712.3:c.1615G>C	p.Asp539His	p.D539H	ENST00000268712	NM_006311.3	539	Gat/Cat	15/46	0.462181116619384	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.838274882395706	0		154	347	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184978	123184981	+	frameshift_variant	Frame_Shift_Del	DEL	AAGT	AAGT	-	novel	NA	P-0052620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	142	30	0	ENST00000218089.9:c.1028_1031del	p.Val343AspfsTer35	p.V343Dfs*35	ENST00000218089	NM_001042749.1	342	gAAGTa/ga	12/35	1	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.838274882395706	1		30	187	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	89	460	0				ENST00000310581	NM_198253.2	-/1132			0.553833511308155	3	FACETS	1	0.952	1	0.558	0.498	0.62	CLONAL	1	TRUE	1	0.553833511308155	3		460	368	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873005	134873005	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs183234182	NA	P-0052621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	308	596	1	ENST00000398015.3:c.1309G>A	p.Val437Ile	p.V437I	ENST00000398015	NM_004441.4	437	Gtt/Att	6/16	0.496839309554692	4	FACETS	0.993	0.94	1	0.993	0.94	1	CLONAL	2	TRUE	2	0.553833511308155	4		597	870	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107013	27107013	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	561	573	0	ENST00000324856.7:c.6625del	p.Gln2209SerfsTer22	p.Q2209Sfs*22	ENST00000324856	NM_006015.4	2208	ttC/tt	20/20	0.553833511308155	5	FACETS	0.93	0.899	0.961	0.93	0.899	0.961	CLONAL	4	TRUE	1	0.553833511308155	5		573	997	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0052622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	176	495	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.404095087796973	4	FACETS	0.838	0.775	0.903	0.838	0.775	0.903	CLONAL	2	TRUE	2	0.482503445170745	4		495	645	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	158	623	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.345510692942354	2	FACETS	0.811	0.743	0.881	0.405	0.371	0.441	CLONAL	1	TRUE	0	0.482503445170745	2		623	808	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0052622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	294	679	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.345510692942354	2	FACETS	1	0.993	1	0.685	0.647	0.725	CLONAL	1	TRUE	0	0.482503445170745	2		679	889	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781467	135781467	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203537	NA	P-0052622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	131	584	0	ENST00000298552.3:c.1498C>T	p.Arg500Ter	p.R500*	ENST00000298552	NM_001162426.1	500	Cga/Tga	15/23	0.44470703914827	4	FACETS	0.751	0.68	0.826	0.375	0.34	0.413	SUBCLONAL	1	TRUE	2	0.482503445170745	4		584	1072	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163816	32163816	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	173	627	0	ENST00000375023.3:c.5410G>A	p.Ala1804Thr	p.A1804T	ENST00000375023	NM_004557.3	1804	Gcg/Acg	30/30	0.358859637976489	3	FACETS	0.909	0.836	0.985	0.303	0.278	0.329	CLONAL	1	TRUE	0	0.482503445170745	3		627	979	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641098	117641098	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	111	673	0	ENST00000368508.3:c.5873A>G	p.Glu1958Gly	p.E1958G	ENST00000368508	NM_002944.2	1958	gAa/gGa	36/43	0.345510692942354	2	FACETS	0.655	0.59	0.725	0.328	0.295	0.363	SUBCLONAL	1	TRUE	0	0.482503445170745	2		673	702	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922025	39922025	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	146	784	0	ENST00000378444.4:c.4147T>A	p.Tyr1383Asn	p.Y1383N	ENST00000378444	NM_001123385.1	1383	Tac/Aac	9/15	0.361108996483313	4	FACETS	0.751	0.684	0.822	0.375	0.342	0.411	SUBCLONAL	1	TRUE	2	0.482503445170745	4		784	1195	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922043	39922043	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	168	853	1	ENST00000378444.4:c.4129T>A	p.Leu1377Met	p.L1377M	ENST00000378444	NM_001123385.1	1377	Ttg/Atg	9/15	0.361108996483313	4	FACETS	0.805	0.738	0.876	0.403	0.369	0.438	CLONAL	1	TRUE	2	0.482503445170745	4		854	1282	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	94	451	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.951	0.848	1	0.951	0.848	1	CLONAL	1	TRUE	1	0.334465845141381	2		452	591	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	146	701	11	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.334465845141381	2		712	819	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	206	1227	2	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.956	0.885	1	0.956	0.885	1	CLONAL	1	TRUE	1	0.334465845141381	2		1229	1288	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	244	507	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.334465845141381	3	FACETS	0.916	0.857	0.976	0.916	0.857	0.976	CLONAL	2	TRUE	1	0.334465845141381	3		507	930	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429978	78429978	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	80	330	1	ENST00000370768.2:c.901del	p.Ile301TyrfsTer22	p.I301Yfs*22	ENST00000370768	NM_003902.3	301	Ata/ta	11/20	1	2	FACETS	0.903	0.796	1	0.903	0.796	1	CLONAL	1	TRUE	1	0.334465845141381	2		331	530	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	295	944	4	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	0.24816897448026	3	FACETS	0.968	0.912	1	0.968	0.912	1	CLONAL	2	TRUE	1	0.334465845141381	3		948	1063	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913837	32913837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359507	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	78	400	0	ENST00000380152.3:c.5351del	p.Asn1784ThrfsTer7	p.N1784Tfs*7	ENST00000380152		1782	cAa/ca	11/27	1	2	FACETS	0.877	0.772	0.989	0.877	0.772	0.989	CLONAL	1	TRUE	1	0.334465845141381	2		400	532	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	136	549	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.334465845141381	2		549	794	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	125	408	2	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.334465845141381	2		410	679	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578397	7578398	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	178	737	0	ENST00000269305.4:c.532dup	p.His178ProfsTer3	p.H178Pfs*3	ENST00000269305	NM_001126112.2	178	cac/cCac	5/11	NA	2	FACETS	0.972	0.895	1			1	INDETERMINATE	1	TRUE	NA	0.334465845141381	2		737	1095	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332273	70332273	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	95	361	0	ENST00000373644.4:c.184del	p.Thr62GlnfsTer13	p.T62Qfs*13	ENST00000373644	NM_030625.2	60	Aaa/aa	2/12	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.334465845141381	2		361	565	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101829	11101829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	162	673	0	ENST00000358026.2:c.1249C>T	p.Arg417Cys	p.R417C	ENST00000358026	NM_001128849.1	417	Cgc/Tgc	8/36	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.334465845141381	2		673	960	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001374	150001376	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs753305883	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	131	519	0	ENST00000253339.5:c.2228_2230del	p.Leu743del	p.L743del	ENST00000253339		743	cTTCga/cga	4/7	1	2	FACETS	0.979	0.889	1	0.979	0.889	1	CLONAL	1	TRUE	1	0.334465845141381	2		519	800	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059170	42059170	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs756744691	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	143	407	2	ENST00000219905.7:c.8895del	p.Thr2966ProfsTer4	p.T2966Pfs*4	ENST00000219905	NM_001164273.1	2964	Ccc/cc	24/24	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.334465845141381	2		409	692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	192	739	1	ENST00000269305.4:c.376T>C	p.Tyr126His	p.Y126H	ENST00000269305	NM_001126112.2	126	Tac/Cac	5/11	NA	2	FACETS	1	0.944	1			1	INDETERMINATE	1	TRUE	NA	0.334465845141381	2		740	1118	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572092	64572093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767319284	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	173	720	0	ENST00000312049.6:c.1546dup	p.Arg516ProfsTer15	p.R516Pfs*15	ENST00000312049	NM_130799.2	516	cgg/cCgg	10/10	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.334465845141381	2		720	1009	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413710	138413710	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	132	439	5	ENST00000289153.2:c.1810del	p.Arg604GlyfsTer4	p.R604Gfs*4	ENST00000289153	NM_006219.2	604	Cgg/gg	12/22	1	2	FACETS	0.97	0.881	1	0.97	0.881	1	CLONAL	1	TRUE	1	0.334465845141381	2		444	814	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	108	533	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	0.804	0.722	0.892	0.804	0.722	0.892	CLONAL	1	TRUE	1	0.334465845141381	2		533	803	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752695	42752695	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1366176199	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	209	808	3	ENST00000222329.4:c.1569del	p.Leu525SerfsTer6	p.L525Sfs*6	ENST00000222329	NM_006494.2	523	ggG/gg	4/4	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.334465845141381	2		811	1117	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424178	49424178	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs886040960	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	108	417	2	ENST00000301067.7:c.13884del	p.Thr4629ProfsTer11	p.T4629Pfs*11	ENST00000301067	NM_003482.3	4628	ccC/cc	42/54	1	2	FACETS	0.943	0.847	1	0.943	0.847	1	CLONAL	1	TRUE	1	0.334465845141381	2		419	685	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917611	151917611	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs938655561	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	110	493	0	ENST00000262189.6:c.3709C>T	p.Arg1237Ter	p.R1237*	ENST00000262189	NM_170606.2	1237	Cga/Tga	23/59	1	2	FACETS	0.938	0.844	1	0.938	0.844	1	CLONAL	1	TRUE	1	0.334465845141381	2		493	701	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434959	49434959	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555192751	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	142	686	1	ENST00000301067.7:c.6594del	p.Tyr2199IlefsTer65	p.Y2199Ifs*65	ENST00000301067	NM_003482.3	2198	ccC/cc	31/54	1	2	FACETS	0.843	0.767	0.923	0.843	0.767	0.923	CLONAL	1	TRUE	1	0.334465845141381	2		687	1007	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942031	81942031	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	130	500	0	ENST00000359376.3:c.1568C>A	p.Pro523His	p.P523H	ENST00000359376	NM_002661.3	523	cCt/cAt	17/33	0.334465845141381	3	FACETS	1	0.952	1	0.538	0.488	0.591	CLONAL	1	TRUE	1	0.334465845141381	3		500	843	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273104	18273105	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	172	770	0	ENST00000222254.8:c.1000dup	p.Asp334GlyfsTer26	p.D334Gfs*26	ENST00000222254	NM_005027.3	332	tgg/tGgg	8/16	1	2	FACETS	0.871	0.8	0.945	0.871	0.8	0.945	CLONAL	1	TRUE	1	0.334465845141381	2		770	1181	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273026	18273026	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	178	808	0	ENST00000222254.8:c.921del	p.Lys308ArgfsTer33	p.K308Rfs*33	ENST00000222254	NM_005027.3	306	Ccc/cc	8/16	1	2	FACETS	0.934	0.86	1	0.934	0.86	1	CLONAL	1	TRUE	1	0.334465845141381	2		808	1139	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216758	7216758	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1567615533	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	159	525	0	ENST00000380728.2:c.665T>C	p.Leu222Pro	p.L222P	ENST00000380728		222	cTa/cCa	8/11	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.334465845141381	2		525	833	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881428	37881428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375637720	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	126	753	2	ENST00000269571.5:c.2620G>A	p.Glu874Lys	p.E874K	ENST00000269571		874	Gag/Aag	21/27	1	2	FACETS	0.724	0.654	0.797	0.724	0.654	0.797	SUBCLONAL	1	TRUE	1	0.334465845141381	2		755	1041	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098425	11098425	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	129	471	1	ENST00000358026.2:c.947del	p.Pro316LeufsTer10	p.P316Lfs*10	ENST00000358026	NM_001128849.1	315	Ccc/cc	6/36	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.334465845141381	2		472	714	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162915	38162915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199766344	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	324	624	1	ENST00000317025.8:c.2291G>A	p.Arg764His	p.R764H	ENST00000317025	NM_023034.1	764	cGt/cAt	13/24	0.334465845141381	3	FACETS	0.977	0.923	1	0.977	0.923	1	CLONAL	2	TRUE	1	0.334465845141381	3		625	1157	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106847	27106847	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747780610	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	189	566	2	ENST00000324856.7:c.6458G>A	p.Arg2153His	p.R2153H	ENST00000324856	NM_006015.4	2153	cGc/cAc	20/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.334465845141381	2		568	982	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95578563	95578563	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886037684	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	87	306	0	ENST00000393063.1:c.2062C>T	p.Arg688Ter	p.R688*	ENST00000393063	NM_030621.3	688	Cga/Tga	14/28	0.334465845141381	3	FACETS	1	0.899	1	0.508	0.45	0.569	CLONAL	1	TRUE	1	0.334465845141381	3		306	598	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993830	72993831	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	75	586	0	ENST00000268489.5:c.214_215insG	p.Ser72CysfsTer47	p.S72Cfs*47	ENST00000268489	NM_006885.3	72	tcc/tGcc	2/10	0.334465845141381	3	FACETS	0.565	0.494	0.642	0.282	0.247	0.321	SUBCLONAL	1	TRUE	1	0.334465845141381	3		586	927	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054618	13054618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	143	541	0	ENST00000316448.5:c.1145C>T	p.Ala382Val	p.A382V	ENST00000316448	NM_004343.3	382	gCa/gTa	9/9	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.334465845141381	2		541	823	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532613	63532613	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121908568	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	208	906	0	ENST00000307078.5:c.1966C>T	p.Arg656Ter	p.R656*	ENST00000307078	NM_004655.3	656	Cga/Tga	8/11	1	2	FACETS	0.988	0.915	1	0.988	0.915	1	CLONAL	1	TRUE	1	0.334465845141381	2		906	1259	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962899	2962899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3735134	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	218	867	0	ENST00000396946.4:c.2009C>T	p.Thr670Met	p.T670M	ENST00000396946	NM_032415.4	670	aCg/aTg	16/25	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.334465845141381	2		867	1218	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439918	56439919	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1567876313	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	169	651	1	ENST00000407977.2:c.673dup	p.Arg225ProfsTer34	p.R225Pfs*34	ENST00000407977		225	cgc/cCgc	6/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.334465845141381	2		652	979	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197330	94197330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	99	424	0	ENST00000323929.3:c.1174C>T	p.Pro392Ser	p.P392S	ENST00000323929	NM_005591.3	392	Cca/Tca	11/20	1	2	FACETS	0.886	0.792	0.986	0.886	0.792	0.986	CLONAL	1	TRUE	1	0.334465845141381	2		424	668	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610167	43610167	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	183	820	1	ENST00000355710.3:c.2119G>T	p.Asp707Tyr	p.D707Y	ENST00000355710	NM_020975.4	707	Gat/Tat	11/20	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.334465845141381	2		821	1079	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447236	187447236	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	182	687	0	ENST00000232014.4:c.957del	p.Asn320MetfsTer4	p.N320Mfs*4	ENST00000232014	NM_001130845.1	319	ccC/cc	5/10	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.334465845141381	2		687	1067	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291474	10291474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753673660	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	149	601	2	ENST00000340748.4:c.205C>T	p.Arg69Cys	p.R69C	ENST00000340748		69	Cgt/Tgt	3/40	1	2	FACETS	0.994	0.908	1	0.994	0.908	1	CLONAL	1	TRUE	1	0.334465845141381	2		603	896	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546815	9546815	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	107	444	0	ENST00000353224.5:c.1207T>C	p.Ser403Pro	p.S403P	ENST00000353224	NM_177990.2	403	Tcc/Ccc	5/10	1	2	FACETS	0.992	0.891	1	0.992	0.891	1	CLONAL	1	TRUE	1	0.334465845141381	2		444	645	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346912	70346912	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760933452	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	160	616	0	ENST00000374080.3:c.2779G>A	p.Val927Met	p.V927M	ENST00000374080		927	Gtg/Atg	20/45	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.334465845141381	2		616	823	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257832	16257832	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	154	497	0	ENST00000375759.3:c.5097A>C	p.Gln1699His	p.Q1699H	ENST00000375759	NM_015001.2	1699	caA/caC	11/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.334465845141381	2		497	785	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799185	45799185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370124822	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	169	677	1	ENST00000450313.1:c.248C>T	p.Ser83Leu	p.S83L	ENST00000450313	NM_012222.2	83	tCa/tTa	3/16	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.334465845141381	2		678	994	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012360	176012360	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	114	394	0	ENST00000367669.3:c.1574A>T	p.Asp525Val	p.D525V	ENST00000367669	NM_022457.5	525	gAt/gTt	14/20	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.334465845141381	2		394	667	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61213539	61213539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768048172	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	122	375	0	ENST00000301761.2:c.497G>A	p.Arg166His	p.R166H	ENST00000301761	NM_017841.2	166	cGt/cAt	4/4	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.334465845141381	2		375	568	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573750	64573750	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371364206	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	166	685	1	ENST00000312049.6:c.1003C>T	p.Arg335Trp	p.R335W	ENST00000312049	NM_130799.2	335	Cgg/Tgg	7/10	1	2	FACETS	0.983	0.902	1	0.983	0.902	1	CLONAL	1	TRUE	1	0.334465845141381	2		686	1010	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493779	56493779	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	144	479	0	ENST00000267101.3:c.3095G>A	p.Ser1032Asn	p.S1032N	ENST00000267101	NM_001982.3	1032	aGc/aAc	25/28	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.334465845141381	2		479	796	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495400	56495400	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	189	612	0	ENST00000267101.3:c.3590A>G	p.Tyr1197Cys	p.Y1197C	ENST00000267101	NM_001982.3	1197	tAt/tGt	28/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.334465845141381	2		612	1029	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351931	89351931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765769874	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	432	823	1	ENST00000301030.4:c.1019C>T	p.Thr340Met	p.T340M	ENST00000301030	NM_001256183.1	340	aCg/aTg	9/13	0.334465845141381	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.334465845141381	3		824	1438	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435668	56435669	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	161	605	1	ENST00000407977.2:c.1468dup	p.Val490GlyfsTer15	p.V490Gfs*15	ENST00000407977		490	gtc/gGtc	9/10	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.334465845141381	2		606	946	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570510	39570510	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	35	171	0	ENST00000262039.4:c.706T>C	p.Tyr236His	p.Y236H	ENST00000262039	NM_002647.2	236	Tat/Cat	6/25	1	2	FACETS	0.91	0.751	1	0.91	0.751	1	CLONAL	1	TRUE	1	0.334465845141381	2		171	230	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348494	56348494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	83	353	0	ENST00000348428.3:c.302G>A	p.Cys101Tyr	p.C101Y	ENST00000348428	NM_006785.3	101	tGc/tAc	2/17	1	2	FACETS	0.919	0.813	1	0.919	0.813	1	CLONAL	1	TRUE	1	0.334465845141381	2		353	540	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976489	18976489	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	213	863	0	ENST00000262803.5:c.3139C>T	p.Gln1047Ter	p.Q1047*	ENST00000262803	NM_002911.3	1047	Cag/Tag	22/24	1	2	FACETS	0.991	0.919	1	0.991	0.919	1	CLONAL	1	TRUE	1	0.334465845141381	2		863	1285	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607704	46607704	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	218	830	1	ENST00000263734.3:c.1898del	p.Gly633AlafsTer63	p.G633Afs*63	ENST00000263734	NM_001430.4	631	atG/at	12/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.334465845141381	2		831	1207	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626697	12626697	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	142	514	0	ENST00000251849.4:c.1592T>C	p.Val531Ala	p.V531A	ENST00000251849	NM_002880.3	531	gTc/gCc	15/17	1	2	FACETS	0.993	0.905	1	0.993	0.905	1	CLONAL	1	TRUE	1	0.334465845141381	2		514	855	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391039	89391039	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	122	534	0	ENST00000336596.2:c.1105A>G	p.Asn369Asp	p.N369D	ENST00000336596	NM_005233.5	369	Aat/Gat	5/17	1	2	FACETS	0.939	0.849	1	0.939	0.849	1	CLONAL	1	TRUE	1	0.334465845141381	2		534	777	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980595	1980595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761501519	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	204	660	2	ENST00000382891.5:c.4057C>T	p.Arg1353Trp	p.R1353W	ENST00000382891	NM_133335.3	1353	Cgg/Tgg	22/22	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.334465845141381	2		662	940	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520464	176520464	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558220864	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	183	787	0	ENST00000292408.4:c.1309C>T	p.Arg437Cys	p.R437C	ENST00000292408	NM_213647.1	437	Cgt/Tgt	10/18	1	2	FACETS	0.938	0.865	1	0.938	0.865	1	CLONAL	1	TRUE	1	0.334465845141381	2		787	1166	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673751	30673751	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	156	519	0	ENST00000376406.3:c.3209T>C	p.Leu1070Pro	p.L1070P	ENST00000376406	NM_014641.2	1070	cTt/cCt	10/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.334465845141381	2		519	776	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875096	151875097	+	splice_acceptor_variant	Splice_Site	INS	-	-	TTT	rs753425356	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	17	83	0	ENST00000262189.6:c.7443-4_7443-2dup		p.X2481_splice	ENST00000262189	NM_170606.2	2481			1	2	FACETS	0.588	0.441	0.76	0.588	0.441	0.76	SUBCLONAL	1	TRUE	1	0.334465845141381	2		83	173	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271704	38271704	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1242	222	893	0	ENST00000425967.3:c.2245C>T	p.Arg749Cys	p.R749C	ENST00000425967	NM_001174067.1	749	Cgc/Tgc	17/19	0.334465845141381	3	FACETS	1	0.963	1	0.529	0.491	0.569	CLONAL	1	TRUE	1	0.334465845141381	3		893	1464	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039692	47039692	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	217	830	0	ENST00000377604.3:c.1144G>A	p.Ala382Thr	p.A382T	ENST00000377604	NM_001204468.1	382	Gcc/Acc	11/24	0.334465845141381	3	FACETS	1	0.963	1	0.53	0.492	0.571	CLONAL	1	TRUE	1	0.334465845141381	3		830	1428	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344188	70344188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556335288	NA	P-0052628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	105	470	1	ENST00000374080.3:c.1924G>A	p.Asp642Asn	p.D642N	ENST00000374080		642	Gat/Aat	13/45	1	2	FACETS	0.855	0.767	0.95	0.855	0.767	0.95	CLONAL	1	TRUE	1	0.334465845141381	2		471	734	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129735	30129735	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769159731	NA	P-0052629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	134	678	0	ENST00000263025.4:c.478G>A	p.Ala160Thr	p.A160T	ENST00000263025	NM_002746.2	160	Gcc/Acc	3/9	0.682252005276716	4	FACETS	0.887	0.806	0.971			1	CLONAL	1	TRUE	NA	0.675224126315694	4		678	750	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691003	NA	P-0052636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	70	820	0	ENST00000269305.4:c.96+1G>T		p.X32_splice	ENST00000269305	NM_001126112.2	32			1	2	FACETS	0.973	0.847	1	0.973	0.847	1	CLONAL	1	TRUE	1	0.18	2		820	799	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100919	27100919	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	87	799	0	ENST00000324856.7:c.4201C>T	p.Gln1401Ter	p.Q1401*	ENST00000324856	NM_006015.4	1401	Cag/Tag	18/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.18	2		799	821	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427615	49427615	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	154	801	0	ENST00000301067.7:c.10873C>A	p.Pro3625Thr	p.P3625T	ENST00000301067	NM_003482.3	3625	Ccc/Acc	39/54	0.738810301118439	3	FACETS	1	0.963	1	0.539	0.496	0.583	CLONAL	1	FALSE	1	0.738810301118439	3		801	530	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905750	50905751	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0052637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	45	1079	1	ENST00000440232.2:c.798_799delinsTT	p.Glu267Ter	p.E267*	ENST00000440232	NM_002691.3	266	ctGGag/ctTTag	7/27	0.584865792687805	4	FACETS	0.297	0.248	0.35	0.148	0.124	0.175	SUBCLONAL	1	FALSE	2	0.738810301118439	4		1080	714	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0052661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	223	856	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.467538382781672	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.467538382781672	1		856	592	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111855996	111855996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779622961	NA	P-0052661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	155	374	1	ENST00000341259.2:c.47C>T	p.Ser16Leu	p.S16L	ENST00000341259	NM_005475.2	16	tCa/tTa	2/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.467538382781672	2		375	499	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609751	81609751	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs189261858	NA	P-0052661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	95	401	1	ENST00000298171.2:c.1349G>A	p.Arg450His	p.R450H	ENST00000298171	NM_000369.2	450	cGc/cAc	10/10	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.467538382781672	2		402	404	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43699735	43699735	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137879443	NA	P-0052661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	132	452	0	ENST00000382044.4:c.5780C>T	p.Thr1927Met	p.T1927M	ENST00000382044	NM_001141980.1	1927	aCg/aTg	28/28	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.467538382781672	2		452	560	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81954867	81954867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757834798	NA	P-0052661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	172	568	0	ENST00000359376.3:c.2300C>T	p.Pro767Leu	p.P767L	ENST00000359376	NM_002661.3	767	cCg/cTg	21/33	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.467538382781672	2		568	725	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276696	15276696	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752169336	NA	P-0052661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	208	758	2	ENST00000263388.2:c.5569C>T	p.Arg1857Trp	p.R1857W	ENST00000263388	NM_000435.2	1857	Cgg/Tgg	30/33	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.467538382781672	2		760	757	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22405015	22405015	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	29	61	0	ENST00000344548.3:c.44G>T	p.Gly15Val	p.G15V	ENST00000344548	NM_001039802.1	15	gGt/gTt	3/7	1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.467538382781672	2		61	120	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023628	27023634	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCTGC	CGGCTGC	-	novel	NA	P-0052661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	65	152	0	ENST00000324856.7:c.739_745del	p.Ala247ProfsTer114	p.A247Pfs*114	ENST00000324856	NM_006015.4	245	gCGGCTGCc/gc	1/20	1	2	FACETS	0.858	0.762	0.957	1	0.98	1	CLONAL	2	TRUE	1	0.467538382781672	2		152	162	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187116	38187116	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374483765	NA	P-0052661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	188	661	1	ENST00000317025.8:c.1361G>A	p.Arg454Gln	p.R454Q	ENST00000317025	NM_023034.1	454	cGg/cAg	6/24	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.467538382781672	2		662	764	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143320	108143320	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587778071	NA	P-0052662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	33	294	0	ENST00000278616.4:c.3139A>G	p.Lys1047Glu	p.K1047E	ENST00000278616	NM_000051.3	1047	Aaa/Gaa	21/63	1	2	FACETS	0.354	0.287	0.429	0.354	0.287	0.429	SUBCLONAL	1	TRUE	1	0.34	2		294	549	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198470	108198470	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	79	318	0	ENST00000278616.4:c.7074G>C	p.Gln2358His	p.Q2358H	ENST00000278616	NM_000051.3	2358	caG/caC	48/63	0.136414517091605	6	FACETS	1	0.961	1	0.8	0.709	0.896	INDETERMINATE	2	FALSE	3	0.305954495571621	6		318	347	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813441	102813441	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	107	503	0	ENST00000307046.8:c.248G>C	p.Ser83Thr	p.S83T	ENST00000307046	NM_001111285.1	83	aGt/aCt	3/4	0.305954495571621	7	FACETS	0.97	0.872	1	0.388	0.349	0.43	CLONAL	2	FALSE	2	0.305954495571621	7		503	636	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41222946	41222946	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	98	477	0	ENST00000357654.3:c.4985T>A	p.Phe1662Tyr	p.F1662Y	ENST00000357654	NM_007294.3	1662	tTt/tAt	15/23	0.135264142923429	4	FACETS	1	0.915	1	1	0.915	1	INDETERMINATE	2	FALSE	2	0.305954495571621	4		477	410	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188272	10188273	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs869025649	NA	P-0052663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	79	502	0	ENST00000256474.2:c.419_420del	p.Leu140GlnfsTer3	p.L140Qfs*3	ENST00000256474	NM_000551.3	139	TCt/t	2/3	0.240394648548048	3	FACETS	0.933	0.828	1	0.622	0.552	0.696	CLONAL	2	FALSE	0	0.305954495571621	3		502	319	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52649438	52649438	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	91	480	0	ENST00000394830.3:c.1853T>C	p.Leu618Pro	p.L618P	ENST00000394830	NM_018313.4	618	cTc/cCc	16/30	0.240394648548048	3	FACETS	1	0.934	1	0.703	0.631	0.779	CLONAL	2	FALSE	0	0.305954495571621	3		480	325	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027771	152027771	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	119	605	0	ENST00000262189.6:c.304A>C	p.Lys102Gln	p.K102Q	ENST00000262189	NM_170606.2	102	Aaa/Caa	3/59	0.239140962199095	4	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	FALSE	2	0.305954495571621	4		605	488	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055906	180055906	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057518359	NA	P-0052665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	252	596	3	ENST00000261937.6:c.1079C>T	p.Ala360Val	p.A360V	ENST00000261937	NM_182925.4	360	gCg/gTg	8/30	0.399612949430159	1	FACETS	0.859	0.811	0.908	0.859	0.811	0.908	INDETERMINATE	1	TRUE	0	0.675478754344416	1		599	575	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577050	7577052	+	frameshift_variant	Frame_Shift_Del	DEL	GTG	GTG	TA	novel	NA	P-0052665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	294	619	3	ENST00000269305.4:c.886_888delinsTA	p.His296TyrfsTer49	p.H296Yfs*49	ENST00000269305	NM_001126112.2	296	CAC/TA	8/11	0.675478754344416	1	FACETS	0.961	0.913	1	0.961	0.913	1	CLONAL	1	TRUE	0	0.675478754344416	1		622	600	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399822	139399828	+	protein_altering_variant	In_Frame_Del	DEL	CACTGGC	CACTGGC	T	novel	NA	P-0052665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	916	687	19	ENST00000277541.6:c.4520_4526delinsA	p.Ser1507_Cys1509delinsAsn	p.S1507_C1509delinsN	ENST00000277541	NM_017617.3	1507	aGCCAGTGc/aAc	25/34	0.668738103122837	3	FACETS	0.97	0.95	0.99	0.97	0.95	0.99	CLONAL	3	TRUE	0	0.675478754344416	3		706	1247	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311619	15311621	+	inframe_deletion	In_Frame_Del	DEL	AGC	AGC	-	rs746497955	NA	P-0052671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	11	99	0	ENST00000263388.2:c.96_98del	p.Leu33del	p.L33del	ENST00000263388	NM_000435.2	32	ctGCTa/cta	1/33	0.73600457108684	3	FACETS	0.187	0.129	0.259	0.093	0.064	0.13	SUBCLONAL	1	TRUE	1	0.73600457108684	3		99	219	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	27	460	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.734	0.587	0.901	0.734	0.587	0.901	CLONAL	1	TRUE	1	0.306336408918198	2		460	240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577567	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1567549651	NA	P-0052673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	61	480	0	ENST00000269305.4:c.714dup	p.Asn239Ter	p.N239*	ENST00000269305	NM_001126112.2	238	-/T	7/11	1	2	FACETS	0.939	0.813	1	0.939	0.813	1	CLONAL	1	TRUE	1	0.306336408918198	2		480	424	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974759	21974759	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	13	242	0	ENST00000304494.5:c.68G>T	p.Gly23Val	p.G23V	ENST00000304494	NM_000077.4	23	gGt/gTt	1/3	1	2	FACETS	0.786	0.566	1	0.786	0.566	1	CLONAL	1	TRUE	1	0.306336408918198	2		242	108	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104356918	104356918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775245784	NA	P-0052674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	152	445	0	ENST00000369902.3:c.778G>A	p.Glu260Lys	p.E260K	ENST00000369902	NM_016169.3	260	Gag/Aag	7/12	0.606039895445926	4	FACETS	1	0.933	1	0.673	0.622	0.725	CLONAL	2	TRUE	1	0.606039895445926	4		445	399	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345342	70345342	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	50	266	0	ENST00000374080.3:c.2368A>G	p.Thr790Ala	p.T790A	ENST00000374080		790	Act/Gct	16/45	0.500136405976244	2	FACETS	0.927	0.8	1			1	CLONAL	1	TRUE	NA	0.606039895445926	2		266	178	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0052675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	317	578	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.357363542832401	3	FACETS	0.993	0.951	1	0.993	0.951	1	CLONAL	3	FALSE	0	0.511091100337053	3		578	523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138729528	NA	P-0052675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	94	687	0	ENST00000269305.4:c.523C>G	p.Arg175Gly	p.R175G	ENST00000269305	NM_001126112.2	175	Cgc/Ggc	5/11	0.494638299242518	1	FACETS	0.869	0.782	0.96	0.869	0.782	0.96	CLONAL	1	FALSE	0	0.511091100337053	1		687	315	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0052675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	37	346	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	0.198223389546785	5	FACETS	1	0.886	1			1	INDETERMINATE	1	FALSE	NA	0.511091100337053	5		346	235	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943740	71943740	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	113	815	0	ENST00000298229.2:c.1783A>G	p.Ile595Val	p.I595V	ENST00000298229	NM_001567.3	595	Atc/Gtc	15/28	1	2	FACETS	0.978	0.886	1	0.978	0.886	1	CLONAL	1	FALSE	1	0.511091100337053	2		815	452	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771794	135771794	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	111	751	0	ENST00000298552.3:c.3323G>T	p.Gly1108Val	p.G1108V	ENST00000298552	NM_001162426.1	1108	gGc/gTc	23/23	1	2	FACETS	0.976	0.883	1	0.976	0.883	1	CLONAL	1	FALSE	1	0.511091100337053	2		751	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	478	515	2	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.650833770474691	2	FACETS	0.939	0.907	0.971	0.939	0.907	0.971	CLONAL	2	TRUE	0	0.650833770474691	2		517	782	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31483728	31483728	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762172048	NA	P-0052676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	148	149	0	ENST00000344624.3:c.2004G>T	p.Leu668Phe	p.L668F	ENST00000344624		668	ttG/ttT	13/33	0.5331992461621	4	FACETS	0.97	0.897	1	0.97	0.897	1	CLONAL	2	TRUE	2	0.650833770474691	4		149	387	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974790	21974790	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	94	129	0	ENST00000304494.5:c.37del	p.Ala13LeufsTer13	p.A13Lfs*13	ENST00000304494	NM_000077.4	13	Gct/ct	1/3	0.650833770474691	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.650833770474691	1		129	175	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990703	7990703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	192	593	0	ENST00000319144.4:c.58G>A	p.Asp20Asn	p.D20N	ENST00000319144	NM_001139.2	20	Gac/Aac	1/15	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.43157143024627	2		593	889	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	430	435	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.971	0.945	0.996	1	0.998	1	CLONAL	2	TRUE	1	0.82	2		435	540	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	244	701	11	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.982	0.925	1	0.982	0.925	1	CLONAL	1	TRUE	1	0.82	2		712	606	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029457	16029457	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	46	455	0	ENST00000268712.3:c.1573del	p.Thr525GlnfsTer30	p.T525Qfs*30	ENST00000268712	NM_006311.3	525	Aca/ca	15/46	1	2	FACETS	0.231	0.195	0.272	0.231	0.195	0.272	SUBCLONAL	1	TRUE	1	0.82	2		455	485	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	205	333	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.82	2		333	454	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132438	11132438	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794284	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	408	659	2	ENST00000358026.2:c.2654G>A	p.Arg885His	p.R885H	ENST00000358026	NM_001128849.1	885	cGc/cAc	19/36	1	2	FACETS	0.963	0.919	1	0.963	0.919	1	CLONAL	1	TRUE	1	0.82	2		661	1033	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	56	618	2	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	1	2	FACETS	0.128	0.109	0.149	0.128	0.109	0.149	SUBCLONAL	1	TRUE	1	0.82	2		620	1065	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274172	10274173	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1555491538	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	331	449	0	ENST00000330684.3:c.96dup	p.Ala33ArgfsTer105	p.A33Rfs*105	ENST00000330684	NM_001134407.1	32	-/C	2/13	1	2	FACETS	0.911	0.864	0.959	0.911	0.864	0.959	CLONAL	1	TRUE	1	0.82	2		449	886	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	468	1227	2	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.949	0.908	0.99	0.949	0.908	0.99	CLONAL	1	TRUE	1	0.82	2		1229	1203	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589147	67589147	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	122	263	0	ENST00000274335.5:c.1135A>G	p.Lys379Glu	p.K379E	ENST00000274335		379	Aaa/Gaa	9/15	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.82	2		263	288	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690847	89690847	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776667	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	141	308	1	ENST00000371953.3:c.253+1G>A		p.X85_splice	ENST00000371953	NM_000314.4	85			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.82	2		309	329	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882050	36882050	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs780753361	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	807	670	5	ENST00000358127.4:c.963del	p.Ala322LeufsTer11	p.A322Lfs*11	ENST00000358127	NM_001280556.1	321	ccC/cc	8/10	1	2	FACETS	0.828	0.808	0.848	1	0.998	1	CLONAL	2	TRUE	1	0.82	2		675	1188	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720741	89720741	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs371387815	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	30	158	0	ENST00000371953.3:c.892C>T	p.Gln298Ter	p.Q298*	ENST00000371953	NM_000314.4	298	Caa/Taa	8/9	1	2	FACETS	0.585	0.48	0.7	0.585	0.48	0.7	SUBCLONAL	1	TRUE	1	0.82	2		158	125	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499363	89499363	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1317589623	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	46	321	0	ENST00000336596.2:c.2538del	p.Met847TrpfsTer10	p.M847Wfs*10	ENST00000336596	NM_005233.5	845	Ccc/cc	15/17	1	2	FACETS	0.17	0.143	0.201	0.17	0.143	0.201	SUBCLONAL	1	TRUE	1	0.82	2		321	659	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138915	64138915	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	192	368	0	ENST00000334205.4:c.2287del	p.Arg763AlafsTer21	p.R763Afs*21	ENST00000334205	NM_003942.2	761	gCc/gc	17/17	1	2	FACETS	0.755	0.702	0.81	0.755	0.702	0.81	SUBCLONAL	1	TRUE	1	0.82	2		368	620	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370985	55370985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	403	488	0	ENST00000297316.4:c.287C>G	p.Ala96Gly	p.A96G	ENST00000297316	NM_022454.3	96	gCc/gGc	1/2	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.82	2		488	951	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661663	227661664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761880048	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	265	493	12	ENST00000305123.5:c.1791dup	p.His598AlafsTer13	p.H598Afs*13	ENST00000305123	NM_005544.2	597	-/G	1/2	1	2	FACETS	0.764	0.718	0.811	0.764	0.718	0.811	SUBCLONAL	1	TRUE	1	0.82	2		505	846	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263974	104263974	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776579	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	126	395	1	ENST00000369902.3:c.71del	p.Pro24ArgfsTer72	p.P24Rfs*72	ENST00000369902	NM_016169.3	22	gCc/gc	1/12	1	2	FACETS	0.655	0.597	0.716	0.655	0.597	0.716	SUBCLONAL	1	TRUE	1	0.82	2		396	469	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361160	70361161	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCAGCAA	rs1433422316	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	184	591	0	ENST00000374080.3:c.6361_6369dup	p.Gln2121_Gln2123dup	p.Q2121_Q2123dup	ENST00000374080		2121	-/CAGCAGCAA	43/45	1	2	FACETS	0.472	0.436	0.51	0.472	0.436	0.51	SUBCLONAL	1	TRUE	1	0.82	2		591	950	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445500	49445500	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs886042284	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	390	800	3	ENST00000301067.7:c.1966del	p.Leu656CysfsTer274	p.L656Cfs*274	ENST00000301067	NM_003482.3	656	Ctg/tg	10/54	1	2	FACETS	0.785	0.747	0.825	0.785	0.747	0.825	SUBCLONAL	1	TRUE	1	0.82	2		803	1211	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	247	494	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	1	2	FACETS	0.991	0.934	1	0.991	0.934	1	CLONAL	1	TRUE	1	0.82	2		494	608	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	rs267608078	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	88	417	0	ENST00000234420.5:c.3260_3261dup	p.Phe1088ProfsTer3	p.F1088Pfs*3	ENST00000234420	NM_000179.2	1085	acc/aCCcc	5/10	1	2	FACETS	0.336	0.298	0.377	0.336	0.298	0.377	SUBCLONAL	1	TRUE	1	0.82	2		417	639	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435199	49435199	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	344	481	1	ENST00000301067.7:c.6354del	p.Ala2119LeufsTer25	p.A2119Lfs*25	ENST00000301067	NM_003482.3	2118	ccC/cc	31/54	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.82	2		482	831	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86658425	86658425	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	80	179	0	ENST00000274376.6:c.1390C>T	p.Arg464Cys	p.R464C	ENST00000274376	NM_002890.2	464	Cgt/Tgt	10/25	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.82	2		179	179	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602310	10602310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	504	631	0	ENST00000171111.5:c.1268G>A	p.Gly423Asp	p.G423D	ENST00000171111	NM_203500.1	423	gGc/gAc	3/6	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.82	2		631	1181	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646865	37646865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749022057	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	322	451	0	ENST00000447079.4:c.1987C>T	p.Arg663Cys	p.R663C	ENST00000447079	NM_015083.1	663	Cgt/Tgt	3/14	1	2	FACETS	0.939	0.891	0.989	0.939	0.891	0.989	CLONAL	1	TRUE	1	0.82	2		451	836	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32905070	32905070	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80359630	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	129	177	0	ENST00000380152.3:c.700del	p.Ser234ProfsTer7	p.S234Pfs*7	ENST00000380152		232	taT/ta	9/27	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.82	2		177	305	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720928	119720928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	222	410	0	ENST00000316626.5:c.247G>A	p.Ala83Thr	p.A83T	ENST00000316626		83	Gcc/Acc	2/12	1	2	FACETS	0.992	0.931	1	0.992	0.931	1	CLONAL	1	TRUE	1	0.82	2		410	546	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466036	69466038	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	430	598	0	ENST00000227507.2:c.875_877del	p.Asp292del	p.D292del	ENST00000227507	NM_053056.2	292	GAC/-	5/5	1	2	FACETS	0.969	0.926	1	0.969	0.926	1	CLONAL	1	TRUE	1	0.82	2		598	1082	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867363	45867363	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	323	579	0	ENST00000391945.4:c.830A>C	p.Asp277Ala	p.D277A	ENST00000391945	NM_000400.3	277	gAc/gCc	10/23	1	2	FACETS	0.718	0.679	0.759	0.718	0.679	0.759	SUBCLONAL	1	TRUE	1	0.82	2		579	1097	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187221	38187222	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	417	687	1	ENST00000317025.8:c.1255dup	p.Thr419AsnfsTer28	p.T419Nfs*28	ENST00000317025	NM_023034.1	419	acc/aAcc	6/24	1	2	FACETS	0.921	0.879	0.964	0.921	0.879	0.964	CLONAL	1	TRUE	1	0.82	2		688	1104	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81399214	81399214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	305	512	0	ENST00000222390.5:c.74C>T	p.Ala25Val	p.A25V	ENST00000222390	NM_000601.4	25	gCc/gTc	1/18	1	2	FACETS	0.965	0.914	1	0.965	0.914	1	CLONAL	1	TRUE	1	0.82	2		512	771	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056362	26056362	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	303	336	0	ENST00000343677.2:c.295A>G	p.Thr99Ala	p.T99A	ENST00000343677	NM_005319.3	99	Acc/Gcc	1/1	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.82	2		336	701	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17349174	17349174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	338	469	2	ENST00000375499.3:c.694G>A	p.Ala232Thr	p.A232T	ENST00000375499	NM_003000.2	232	Gcc/Acc	7/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.82	2		471	821	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023219	27023223	+	frameshift_variant	Frame_Shift_Del	DEL	CCTAG	CCTAG	-	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	92	134	0	ENST00000324856.7:c.325_329del	p.Pro109AlafsTer6	p.P109Afs*6	ENST00000324856	NM_006015.4	109	CCTAGg/g	1/20	1	2	FACETS	0.92	0.831	1	0.92	0.831	1	CLONAL	1	TRUE	1	0.82	2		134	244	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099425	27099426	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	353	486	0	ENST00000324856.7:c.3666dup	p.Arg1223AlafsTer5	p.R1223Afs*5	ENST00000324856	NM_006015.4	1221	atg/atGg	14/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.82	2		486	827	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112259	115112259	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1208681777	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	135	118	1	ENST00000257566.3:c.1481C>T	p.Ala494Val	p.A494V	ENST00000257566	NM_016569.3	494	gCc/gTc	7/8	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.82	2		119	269	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911955	32911955	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555283257	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	239	534	0	ENST00000380152.3:c.3463A>G	p.Thr1155Ala	p.T1155A	ENST00000380152		1155	Act/Gct	11/27	1	2	FACETS	0.828	0.777	0.88	0.828	0.777	0.88	CLONAL	1	TRUE	1	0.82	2		534	704	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858130	9858130	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	365	495	0	ENST00000330684.3:c.3271G>A	p.Ala1091Thr	p.A1091T	ENST00000330684	NM_001134407.1	1091	Gcc/Acc	13/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.82	2		495	831	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645032	67645035	+	frameshift_variant	Frame_Shift_Del	DEL	GGTT	GGTT	-	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	321	516	0	ENST00000264010.4:c.298_301del	p.Val100Ter	p.V100*	ENST00000264010	NM_006565.3	99	caGGTT/ca	3/12	1	2	FACETS	0.989	0.938	1	0.989	0.938	1	CLONAL	1	TRUE	1	0.82	2		516	792	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829125	72829125	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	406	521	0	ENST00000268489.5:c.7456C>T	p.Gln2486Ter	p.Q2486*	ENST00000268489	NM_006885.3	2486	Caa/Taa	9/10	1	2	FACETS	0.992	0.947	1	0.992	0.947	1	CLONAL	1	TRUE	1	0.82	2		521	998	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89345512	89345512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	254	326	0	ENST00000301030.4:c.7438G>A	p.Gly2480Ser	p.G2480S	ENST00000301030	NM_001256183.1	2480	Ggc/Agc	9/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.82	2		326	575	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983953	15983953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	251	303	0	ENST00000268712.3:c.3266G>A	p.Gly1089Glu	p.G1089E	ENST00000268712	NM_006311.3	1089	gGa/gAa	24/46	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.82	2		303	577	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732422	74732422	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	207	292	0	ENST00000359995.5:c.487T>A	p.Ser163Thr	p.S163T	ENST00000359995	NM_001195427.1	163	Tcc/Acc	2/3	1	2	FACETS	0.816	0.761	0.871	0.816	0.761	0.871	CLONAL	1	TRUE	1	0.82	2		292	619	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18962957	18962957	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	74	702	0	ENST00000262803.5:c.824C>T	p.Ala275Val	p.A275V	ENST00000262803	NM_002911.3	275	gCc/gTc	6/24	1	2	FACETS	0.146	0.127	0.167	0.146	0.127	0.167	SUBCLONAL	1	TRUE	1	0.82	2		702	1234	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258532	19258532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754381519	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	358	665	1	ENST00000162023.5:c.368C>T	p.Pro123Leu	p.P123L	ENST00000162023		123	cCg/cTg	8/13	1	2	FACETS	0.784	0.744	0.825	0.784	0.744	0.825	SUBCLONAL	1	TRUE	1	0.82	2		666	1114	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212416	36212416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	382	641	0	ENST00000222270.7:c.2167G>A	p.Gly723Arg	p.G723R	ENST00000222270	NM_014727.1	723	Ggg/Agg	3/37	1	2	FACETS	0.801	0.761	0.841	0.801	0.761	0.841	CLONAL	1	TRUE	1	0.82	2		641	1163	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216129	36216129	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	386	508	0	ENST00000222270.7:c.3537T>A	p.Cys1179Ter	p.C1179*	ENST00000222270	NM_014727.1	1179	tgT/tgA	11/37	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.82	2		508	903	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149842	99149842	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	248	277	0	ENST00000074304.5:c.154T>C	p.Cys52Arg	p.C52R	ENST00000074304	NM_001134224.1	52	Tgc/Cgc	5/26	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.82	2		277	550	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775602	39775602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1195312059	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	45	370	2	ENST00000288319.7:c.418C>T	p.Arg140Trp	p.R140W	ENST00000288319	NM_182918.3	140	Cgg/Tgg	4/10	1	2	FACETS	0.192	0.161	0.227	0.192	0.161	0.227	SUBCLONAL	1	TRUE	1	0.82	2		372	571	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008469	70008469	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	169	301	0	ENST00000394351.3:c.756C>A	p.Asp252Glu	p.D252E	ENST00000394351	NM_000248.3	252	gaC/gaA	8/9	1	2	FACETS	0.9	0.835	0.966	0.9	0.835	0.966	CLONAL	1	TRUE	1	0.82	2		301	458	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138431115	138431115	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	146	359	0	ENST00000289153.2:c.1334T>G	p.Val445Gly	p.V445G	ENST00000289153	NM_006219.2	445	gTt/gGt	8/22	1	2	FACETS	0.873	0.805	0.942	0.873	0.805	0.942	CLONAL	1	TRUE	1	0.82	2		359	408	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524920	187524920	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	57	527	0	ENST00000441802.2:c.10760A>G	p.Asp3587Gly	p.D3587G	ENST00000441802	NM_005245.3	3587	gAc/gGc	19/27	1	2	FACETS	0.144	0.123	0.167	0.144	0.123	0.167	SUBCLONAL	1	TRUE	1	0.82	2		527	967	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225554	225554	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	55	126	0	ENST00000264932.6:c.336del	p.Asn113ThrfsTer15	p.N113Tfs*15	ENST00000264932	NM_004168.2	111	ctG/ct	4/15	1	2	FACETS	0.699	0.607	0.795	0.699	0.607	0.795	SUBCLONAL	1	TRUE	1	0.82	2		126	192	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959097	2959097	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	359	613	0	ENST00000396946.4:c.2419A>G	p.Met807Val	p.M807V	ENST00000396946	NM_032415.4	807	Atg/Gtg	18/25	1	2	FACETS	0.855	0.812	0.899	0.855	0.812	0.899	CLONAL	1	TRUE	1	0.82	2		613	1024	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878199	151878199	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	271	480	0	ENST00000262189.6:c.6746C>A	p.Pro2249His	p.P2249H	ENST00000262189	NM_170606.2	2249	cCt/cAt	36/59	1	2	FACETS	0.815	0.767	0.864	0.815	0.767	0.864	CLONAL	1	TRUE	1	0.82	2		480	811	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220484	98220484	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	369	536	0	ENST00000331920.6:c.2979del	p.Val994Ter	p.V994*	ENST00000331920	NM_000264.3	993	aaA/aa	18/24	1	2	FACETS	0.965	0.918	1	0.965	0.918	1	CLONAL	1	TRUE	1	0.82	2		536	933	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730388	133730388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	47	416	0	ENST00000318560.5:c.454C>T	p.Arg152Cys	p.R152C	ENST00000318560	NM_005157.4	152	Cgt/Tgt	3/11	1	2	FACETS	0.154	0.13	0.182	0.154	0.13	0.182	SUBCLONAL	1	TRUE	1	0.82	2		416	742	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782142	135782142	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	265	462	0	ENST00000298552.3:c.1414A>G	p.Ser472Gly	p.S472G	ENST00000298552	NM_001162426.1	472	Agt/Ggt	14/23	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.82	2		462	628	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293627	137293627	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773076567	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	500	739	0	ENST00000481739.1:c.178G>A	p.Gly60Ser	p.G60S	ENST00000481739	NM_002957.4	60	Ggc/Agc	2/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.82	2		739	1162	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247024	53247024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	371	499	2	ENST00000375401.3:c.476G>A	p.Arg159His	p.R159H	ENST00000375401	NM_004187.3	159	cGc/cAc	4/26	1	2	FACETS	0.963	0.917	1	0.963	0.917	1	CLONAL	1	TRUE	1	0.82	2		501	940	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361092	70361103	+	inframe_deletion	In_Frame_Del	DEL	CAGCAACAGCAG	CAGCAACAGCAG	-	novel	NA	P-0052678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	154	323	0	ENST00000374080.3:c.6285_6296del	p.Gln2112_Gln2115del	p.Q2112_Q2115del	ENST00000374080		2094	CAGCAACAGCAG/-	43/45	1	2	FACETS	0.646	0.594	0.7	0.646	0.594	0.7	SUBCLONAL	1	TRUE	1	0.82	2		323	581	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	187	460	0				ENST00000310581	NM_198253.2	-/1132			0.538190295918244	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.538112338803763	3		460	414	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117753470	117753470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1248358199	NA	P-0052679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	138	479	0	ENST00000369458.3:c.8C>T	p.Ser3Phe	p.S3F	ENST00000369458	NM_024626.3	3	tCc/tTc	1/6	0.533232991160421	1	FACETS	0.886	0.814	0.961	0.886	0.814	0.961	CLONAL	1	TRUE	0	0.538112338803763	1		479	423	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236197	108236197	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555152033	NA	P-0052679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	171	473	0	ENST00000278616.4:c.9133C>G	p.Leu3045Val	p.L3045V	ENST00000278616	NM_000051.3	3045	Ctc/Gtc	63/63	1	2	FACETS	0.937	0.865	1	0.937	0.865	1	CLONAL	1	TRUE	1	0.538112338803763	2		473	678	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025522	1025522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	201	569	0	ENST00000358495.3:c.853G>A	p.Glu285Lys	p.E285K	ENST00000358495	NM_134424.2	285	Gag/Aag	9/12	0.406952055225935	5	FACETS	1	0.973	1	0.37	0.342	0.399	CLONAL	1	TRUE	2	0.538112338803763	5		569	1217	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560229	95560229	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	84	262	0	ENST00000393063.1:c.5360C>G	p.Ser1787Cys	p.S1787C	ENST00000393063	NM_030621.3	1787	tCt/tGt	25/28	0.522828297469682	2	FACETS	1	0.904	1	0.507	0.452	0.564	CLONAL	1	TRUE	0	0.538112338803763	2		262	308	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866444	37866444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	236	684	0	ENST00000269571.5:c.749C>T	p.Ser250Phe	p.S250F	ENST00000269571		250	tCt/tTt	6/27	0.524240363062751	3	FACETS	1	0.955	1	0.515	0.48	0.551	CLONAL	1	TRUE	1	0.538112338803763	3		684	1081	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	234	590	0	ENST00000269571.5:c.829G>C	p.Asp277His	p.D277H	ENST00000269571		277	Gac/Cac	7/27	0.524240363062751	3	FACETS	1	0.981	1	0.568	0.53	0.607	CLONAL	1	TRUE	1	0.538112338803763	3		590	972	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0052679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	213	853	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.524240363062751	3	FACETS	1	0.967	1	0.534	0.496	0.573	CLONAL	1	TRUE	1	0.538112338803763	3		853	941	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272488	15272488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	192	585	0	ENST00000263388.2:c.5951G>A	p.Ser1984Asn	p.S1984N	ENST00000263388	NM_000435.2	1984	aGc/aAc	33/33	0.416474415881583	2	FACETS	0.863	0.799	0.929	0.431	0.399	0.465	CLONAL	1	TRUE	0	0.538112338803763	2		585	827	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557272	187557273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1279779959	NA	P-0052679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	151	485	0	ENST00000441802.2:c.4089dup	p.Thr1364TyrfsTer8	p.T1364Yfs*8	ENST00000441802	NM_005245.3	1363	-/T	6/27	0.470069304936229	1	FACETS	0.934	0.862	1	0.934	0.862	1	CLONAL	1	TRUE	0	0.538112338803763	1		485	439	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233640	233643	+	missense_variant	Missense_Mutation	ONP	GAGG	GAGG	AAGA	novel	NA	P-0052679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	202	124	0	ENST00000264932.6:c.944_947delinsAAGA	p.Gly315_Gly316delinsGluAsp	p.G315_G316delinsED	ENST00000264932	NM_004168.2	315	gGAGGc/gAAGAc	8/15	0.538112338803763	7	FACETS	0.939	0.886	0.992	0.939	0.886	0.992	CLONAL	5	TRUE	2	0.538112338803763	7		124	375	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651983	36651984	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0052679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	342	558	0	ENST00000244741.5:c.108_109dup	p.Leu37ArgfsTer2	p.L37Rfs*2	ENST00000244741	NM_000389.4	35	-/GC	2/3	0.504218493239473	2	FACETS	0.909	0.867	0.951	0.909	0.867	0.951	CLONAL	2	TRUE	0	0.538112338803763	2		558	699	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0052686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	290	825	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.177555237058066	3	FACETS	1	0.979	1	0.719	0.677	0.762	INDETERMINATE	2	TRUE	0	0.315662060149672	3		826	986	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171631	36171631	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs751191137	NA	P-0052686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	52	370	0	ENST00000300305.3:c.934A>G	p.Thr312Ala	p.T312A	ENST00000300305		312	Acc/Gcc	7/8	0.217248625589766	2	FACETS	0.667	0.568	0.775	0.333	0.284	0.388	SUBCLONAL	1	TRUE	0	0.315662060149672	2		370	494	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404824	70404824	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs750068661	NA	P-0052686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	86	428	0	ENST00000373644.4:c.2338G>C	p.Glu780Gln	p.E780Q	ENST00000373644	NM_030625.2	780	Gaa/Caa	4/12	0.233331839124878	3	FACETS	0.839	0.742	0.943	0.419	0.371	0.472	CLONAL	1	TRUE	1	0.315662060149672	3		428	752	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900237	32900237	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1060502485	NA	P-0052686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	154	321	0	ENST00000380152.3:c.426-1G>A		p.X142_splice	ENST00000380152		142			0.173169281564891	4	FACETS	1	0.977	1			1	INDETERMINATE	2	TRUE	NA	0.315662060149672	4		321	553	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640911	3640911	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	108	507	0	ENST00000294008.3:c.2728G>C	p.Glu910Gln	p.E910Q	ENST00000294008	NM_032444.2	910	Gag/Cag	12/15	0.233331839124878	3	FACETS	0.743	0.665	0.825	0.371	0.332	0.413	SUBCLONAL	1	TRUE	1	0.315662060149672	3		507	1067	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228316	228316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766421069	NA	P-0052686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	37	237	0	ENST00000264932.6:c.638C>T	p.Thr213Ile	p.T213I	ENST00000264932	NM_004168.2	213	aCc/aTc	6/15	0.229849523530565	5	FACETS	0.743	0.612	0.889	0.248	0.204	0.297	SUBCLONAL	1	TRUE	2	0.315662060149672	5		237	465	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542654	141542654	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	115	523	0	ENST00000220592.5:c.2332G>C	p.Glu778Gln	p.E778Q	ENST00000220592	NM_012154.3	778	Gag/Cag	18/19	0.315662060149672	3	FACETS	0.712	0.639	0.789	0.356	0.319	0.395	SUBCLONAL	1	TRUE	1	0.315662060149672	3		523	1185	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0052687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	71	401	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.978	0.853	1	0.978	0.853	1	CLONAL	1	TRUE	1	0.22	2		401	660	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0052687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	29	594	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.365	0.291	0.449	0.365	0.291	0.449	SUBCLONAL	1	TRUE	1	0.22	2		594	723	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409060	4409060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781695497	NA	P-0052687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	48	657	0	ENST00000261254.3:c.755C>T	p.Ala252Val	p.A252V	ENST00000261254	NM_001759.3	252	gCg/gTg	5/5	1	2	FACETS	0.841	0.711	0.984	0.841	0.711	0.984	CLONAL	1	TRUE	1	0.22	2		657	519	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928833	49928833	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	88	1127	0	ENST00000296474.3:c.3533G>C	p.Arg1178Pro	p.R1178P	ENST00000296474	NM_002447.2	1178	cGg/cCg	16/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.22	2		1127	738	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0052688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	319	491	0	ENST00000374690.3:c.2105T>A	p.Leu702His	p.L702H	ENST00000374690	NM_000044.3	702	cTc/cAc	4/8	0.600750218154659	3	FACETS	1	0.956	1			1	CLONAL	2	FALSE	NA	0.600750218154659	3		491	687	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611336	28611336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201905189	NA	P-0052688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	45	667	0	ENST00000241453.7:c.1295C>T	p.Thr432Met	p.T432M	ENST00000241453	NM_004119.2	432	aCg/aTg	10/24	0.177171674210293	2	FACETS	0.42	0.354	0.492	0.21	0.177	0.246	INDETERMINATE	1	FALSE	0	0.600750218154659	2		667	357	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68982089	68982089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376775544	NA	P-0052688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	69	690	0	ENST00000288368.4:c.1463G>A	p.Arg488His	p.R488H	ENST00000288368	NM_024870.2	488	cGt/cAt	13/40	0.416943997349085	5	FACETS	0.528	0.459	0.603	0.106	0.091	0.121	SUBCLONAL	1	FALSE	0	0.600750218154659	5		690	827	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858038	40858038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748173627	NA	P-0052688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	119	956	1	ENST00000428826.2:c.1826G>A	p.Arg609His	p.R609H	ENST00000428826		609	cGt/cAt	16/21	1	2	FACETS	0.525	0.474	0.579	0.525	0.474	0.579	SUBCLONAL	1	FALSE	1	0.600750218154659	2		957	755	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085821	16085821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	61	791	0	ENST00000281043.3:c.997G>A	p.Ala333Thr	p.A333T	ENST00000281043	NM_005378.4	333	Gcc/Acc	3/3	0.195516636730814	2	FACETS	0.585	0.508	0.669	0.293	0.254	0.335	INDETERMINATE	1	FALSE	0	0.600750218154659	2		791	347	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776098	9776098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754531708	NA	P-0052688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	102	1090	2	ENST00000377346.4:c.562C>T	p.Arg188Trp	p.R188W	ENST00000377346	NM_005026.3	188	Cgg/Tgg	5/24	0.195516636730814	2	FACETS	0.536	0.48	0.595	0.268	0.24	0.298	INDETERMINATE	1	FALSE	0	0.600750218154659	2		1092	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578258	7578261	+	frameshift_variant	Frame_Shift_Del	DEL	CACT	CACT	-	novel	NA	P-0052688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	207	968	0	ENST00000269305.4:c.588_591del	p.Val197LysfsTer49	p.V197Kfs*49	ENST00000269305	NM_001126112.2	196	cgAGTG/cg	6/11	0.600750218154659	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	0	0.600750218154659	1		968	407	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207033	1207033	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	157	985	0	ENST00000326873.7:c.122del	p.Lys41SerfsTer10	p.K41Sfs*10	ENST00000326873	NM_000455.4	41	Aag/ag	1/10	0.342925816495579	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.342925816495579	1		985	631	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260029	16260029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	120	821	0	ENST00000375759.3:c.7294C>T	p.Pro2432Ser	p.P2432S	ENST00000375759	NM_015001.2	2432	Ccc/Tcc	11/15	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.342925816495579	2		821	699	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662944	52662944	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs781546758	NA	P-0052689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	94	602	0	ENST00000394830.3:c.1409A>G	p.Tyr470Cys	p.Y470C	ENST00000394830	NM_018313.4	470	tAc/tGc	13/30	1	2	FACETS	0.993	0.886	1	0.993	0.886	1	CLONAL	1	TRUE	1	0.342925816495579	2		602	552	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805920	32805920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	316	1113	1	ENST00000374899.4:c.91C>T	p.Leu31Phe	p.L31F	ENST00000374899	NM_018833.2	31	Ctt/Ttt	2/12	0.329921755179647	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.342925816495579	3		1114	982	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045168	47045175	+	frameshift_variant	Frame_Shift_Del	DEL	ACTAGAGA	ACTAGAGA	C	novel	NA	P-0052689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	119	411	0	ENST00000377604.3:c.2409_2416delinsC	p.Leu804ArgfsTer7	p.L804Rfs*7	ENST00000377604	NM_001204468.1	803	gcACTAGAGAag/gcCag	21/24	1	1	FACETS	0.759	0.691	0.828	1	0.986	1	SUBCLONAL	2	TRUE	0	0.342925816495579	1		411	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0052692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	798	656	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.78658561943627	2	FACETS	0.978	0.958	0.997	0.978	0.958	0.997	CLONAL	2	TRUE	0	0.799435463404619	2		657	1021	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0052692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	179	379	3	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.995	0.927	1	0.995	0.927	1	CLONAL	1	TRUE	1	0.799435463404619	2		382	450	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909629	76909629	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs919106518	NA	P-0052692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	196	571	0	ENST00000373344.5:c.4276C>T	p.Arg1426Ter	p.R1426*	ENST00000373344	NM_000489.3	1426	Cga/Tga	14/35	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.799435463404619	1		571	246	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280328	1280328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	149	1087	0	ENST00000310581.5:c.1895C>T	p.Pro632Leu	p.P632L	ENST00000310581	NM_198253.2	632	cCg/cTg	4/16	1	2	FACETS	0.311	0.283	0.34	0.311	0.283	0.34	SUBCLONAL	1	TRUE	1	0.799435463404619	2		1087	1199	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0052693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	565	677	0	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	0.960350012394807	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.960350012394807	1		677	595	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0052693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	639	873	0	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.960350012394807	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.960350012394807	1		873	668	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975376	13975376	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	327	612	0	ENST00000405192.2:c.511C>G	p.Pro171Ala	p.P171A	ENST00000405192	NM_001163147.1	171	Cca/Gca	7/12	1	2	FACETS	0.95	0.904	0.996	0.95	0.904	0.996	CLONAL	1	TRUE	1	0.960350012394807	2		612	717	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714659	52714659	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	81	999	0	ENST00000322088.6:c.417C>A	p.Asp139Glu	p.D139E	ENST00000322088	NM_014225.5	139	gaC/gaA	4/15	0.960350012394807	1	FACETS	0.118	0.103	0.133	0.118	0.103	0.133	SUBCLONAL	1	TRUE	0	0.960350012394807	1		999	744	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039340	49039341	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0052693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	307	651	0	ENST00000267163.4:c.2330dup	p.Thr778TyrfsTer17	p.T778Yfs*17	ENST00000267163	NM_000321.2	775	-/C		0.960350012394807	1	FACETS	0.889	0.862	0.914	0.889	0.862	0.914	CLONAL	1	TRUE	0	0.960350012394807	1		651	374	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0052694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	64	495	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.713787329429911	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.742475244014848	3		495	107	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0052694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	131	548	2	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.597535803568994	4	FACETS	1	0.984	1	1	0.992	1	CLONAL	3	TRUE	2	0.742475244014848	4		550	181	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0052694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	72	542	4	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.713787329429911	3	FACETS	0.978	0.884	1	0.978	0.884	1	CLONAL	2	TRUE	1	0.742475244014848	3		546	136	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	79	623	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.742475244014848	3	FACETS	0.986	0.896	1	0.657	0.597	0.717	CLONAL	2	TRUE	0	0.742475244014848	3		623	148	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0052694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	115	567	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.742475244014848	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	3	TRUE	0	0.742475244014848	3		567	139	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615083	43615083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377767422	NA	P-0052694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	45	989	4	ENST00000355710.3:c.2497C>T	p.Arg833Cys	p.R833C	ENST00000355710	NM_020975.4	833	Cgc/Tgc	14/20	0.742475244014848	3	FACETS	0.903	0.79	1	0.903	0.79	1	CLONAL	2	TRUE	1	0.742475244014848	3		993	92	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176104189	176104189	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	30	447	1	ENST00000367669.3:c.925G>C	p.Asp309His	p.D309H	ENST00000367669	NM_022457.5	309	Gat/Cat	8/20	0.597535803568994	4	FACETS	0.607	0.492	0.736	0.303	0.246	0.368	SUBCLONAL	1	TRUE	2	0.742475244014848	4		448	232	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2949692	2949692	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	21	711	0	ENST00000396946.4:c.3252G>C	p.Lys1084Asn	p.K1084N	ENST00000396946	NM_032415.4	1084	aaG/aaC	24/25	0.438689033537618	5	FACETS	0.396	0.305	0.502	0.132	0.101	0.168	INDETERMINATE	1	TRUE	2	0.742475244014848	5		711	302	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636307	87636307	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	24	714	0	ENST00000277120.3:c.2472G>C	p.Gln824His	p.Q824H	ENST00000277120		824	caG/caC	19/19	0.742475244014848	4	FACETS	0.552	0.435	0.685	0.184	0.145	0.229	SUBCLONAL	1	TRUE	1	0.742475244014848	4		714	204	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741849	162741849	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	148	600	0	ENST00000367921.3:c.1540G>C	p.Gly514Arg	p.G514R	ENST00000367921	NM_006182.2	514	Ggc/Cgc	13/18	0.371190078445293	1	FACETS	0.441	0.404	0.479	0.441	0.404	0.479	INDETERMINATE	1	TRUE	0	0.712737129665486	1		600	606	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653807	89653807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554893782	NA	P-0052695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	269	442	0	ENST00000371953.3:c.105G>A	p.Met35Ile	p.M35I	ENST00000371953	NM_000314.4	35	atG/atA	2/9	0.684192636453745	2	FACETS	0.955	0.916	0.994	0.955	0.916	0.994	CLONAL	2	TRUE	0	0.712737129665486	2		442	395	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114169	115114169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773465537	NA	P-0052695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	500	780	2	ENST00000257566.3:c.1048G>A	p.Ala350Thr	p.A350T	ENST00000257566	NM_016569.3	350	Gcc/Acc	6/8	0.19173252270087	3	FACETS	0.979	0.942	1	0.653	0.628	0.677	INDETERMINATE	2	TRUE	0	0.712737129665486	3		782	972	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423508	88423508	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	267	586	0	ENST00000360948.2:c.2327A>T	p.Asn776Ile	p.N776I	ENST00000360948	NM_001012338.2	776	aAc/aTc	18/19	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.712737129665486	2		586	702	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680740	88680740	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	355	913	1	ENST00000360948.2:c.517C>A	p.Leu173Ile	p.L173I	ENST00000360948	NM_001012338.2	173	Ctc/Atc	6/19	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.712737129665486	2		914	933	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0052695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	654	1040	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.625264933371095	2	FACETS	0.929	0.903	0.954	0.929	0.903	0.954	CLONAL	2	TRUE	0	0.712737129665486	2		1040	988	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30733020	30733020	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	125	605	1	ENST00000295754.5:c.1633G>T	p.Asp545Tyr	p.D545Y	ENST00000295754	NM_003242.5	545	Gac/Tac	7/7	0.712737129665486	1	FACETS	0.345	0.313	0.379	0.345	0.313	0.379	SUBCLONAL	1	TRUE	0	0.712737129665486	1		606	654	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197299	26197299	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	340	844	0	ENST00000356476.2:c.180G>T	p.Glu60Asp	p.E60D	ENST00000356476		60	gaG/gaT	1/1	0.311008355832222	3	FACETS	1	0.988	1	0.575	0.544	0.607	INDETERMINATE	1	TRUE	1	0.712737129665486	3		844	1125	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93973599	93973599	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	108	453	0	ENST00000369303.4:c.1777G>C	p.Asp593His	p.D593H	ENST00000369303	NM_004440.3	593	Gat/Cat	9/17	0.313657312107286	1	FACETS	0.426	0.384	0.47	0.426	0.384	0.47	INDETERMINATE	1	TRUE	0	0.712737129665486	1		453	458	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989680	68989680	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	241	678	0	ENST00000288368.4:c.1618T>C	p.Cys540Arg	p.C540R	ENST00000288368	NM_024870.2	540	Tgt/Cgt	15/40	0.433783911771429	3	FACETS	0.983	0.919	1	0.492	0.459	0.525	CLONAL	1	TRUE	1	0.712737129665486	3		678	933	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981857	70981857	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	605	984	0	ENST00000276594.2:c.239C>A	p.Pro80Gln	p.P80Q	ENST00000276594	NM_024504.3	80	cCg/cAg	2/8	0.433783911771429	3	FACETS	0.895	0.864	0.927	0.895	0.864	0.927	CLONAL	2	TRUE	1	0.712737129665486	3		984	1286	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5077512	5077512	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0052695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	170	467	1	ENST00000381652.3:c.1924A>T	p.Lys642Ter	p.K642*	ENST00000381652	NM_004972.3	642	Aaa/Taa	15/25	0.712737129665486	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.712737129665486	1		468	283	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180601	56180602	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	T	novel	NA	P-0052695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	174	519	0	ENST00000399503.3:c.3930_3931delinsT	p.Leu1310PhefsTer26	p.L1310Ffs*26	ENST00000399503	NM_005921.1	1310	ttGGga/ttTga	16/20	0.712737129665486	1	FACETS	0.935	0.877	0.994	0.935	0.877	0.994	CLONAL	1	TRUE	0	0.712737129665486	1		519	336	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0052696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	143	521	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.434399897260572	3	FACETS	0.887	0.808	0.969	0.443	0.404	0.485	CLONAL	1	TRUE	1	0.434345110686547	3		521	904	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532827	187532827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	150	660	0	ENST00000441802.2:c.9566G>A	p.Arg3189Lys	p.R3189K	ENST00000441802	NM_005245.3	3189	aGa/aAa	14/27	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.434345110686547	2		660	666	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505492	157505502	+	frameshift_variant	Frame_Shift_Del	DEL	GTGGGGAGGAG	GTGGGGAGGAG	-	novel	NA	P-0052696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	95	593	0	ENST00000346085.5:c.3473_3483del	p.Arg1158ProfsTer24	p.R1158Pfs*24	ENST00000346085	NM_020732.3	1158	cGTGGGGAGGAG/c	13/20	0.434345110686547	2	FACETS	0.843	0.753	0.938	0.421	0.376	0.469	CLONAL	1	TRUE	0	0.434345110686547	2		593	519	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0052699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	253	451	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.40350939013983	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.458759037594888	4		452	746	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0052699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	202	534	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	0.458759037594888	2	FACETS	0.961	0.902	1	0.961	0.902	1	CLONAL	2	TRUE	0	0.458759037594888	2		534	458	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953887	17953887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750606059	NA	P-0052699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	213	1050	1	ENST00000458235.1:c.515G>A	p.Arg172Gln	p.R172Q	ENST00000458235	NM_000215.3	172	cGg/cAg	5/24	0.450300792176952	3	FACETS	0.994	0.923	1	0.497	0.461	0.535	CLONAL	1	TRUE	1	0.458759037594888	3		1051	1148	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55991436	55991436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	412	925	1	ENST00000263923.4:c.25G>A	p.Val9Ile	p.V9I	ENST00000263923	NM_002253.2	9	Gtc/Atc	1/30	0.458759037594888	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.458759037594888	2		926	829	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259202	89259202	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	192	496	0	ENST00000336596.2:c.346T>G	p.Cys116Gly	p.C116G	ENST00000336596	NM_005233.5	116	Tgc/Ggc	3/17	0.458759037594888	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.458759037594888	2		496	379	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477134	67477134	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	187	877	0	ENST00000327367.4:c.941T>A	p.Phe314Tyr	p.F314Y	ENST00000327367	NM_005902.3	314	tTt/tAt	7/9	0.458759037594888	2	FACETS	0.979	0.905	1	0.489	0.452	0.528	CLONAL	1	TRUE	0	0.458759037594888	2		877	833	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578285	7578288	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CAGA	CAGA	-	novel	NA	P-0052699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	360	766	0	ENST00000269305.4:c.561_564del	p.Leu188ProfsTer58	p.L188Pfs*58	ENST00000269305	NM_001126112.2	187	ggTCTG/gg	6/11	0.458759037594888	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.458759037594888	2		766	718	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512339	38512339	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	44	733	0	ENST00000254066.5:c.1250C>T	p.Ser417Leu	p.S417L	ENST00000254066	NM_000964.3	417	tCa/tTa	9/9	0.458759037594888	2	FACETS	0.313	0.262	0.37	0.156	0.131	0.185	SUBCLONAL	1	TRUE	0	0.458759037594888	2		733	613	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440667	56440667	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	370	878	1	ENST00000407977.2:c.551T>A	p.Val184Glu	p.V184E	ENST00000407977		184	gTg/gAg	5/10	0.458759037594888	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.458759037594888	2		879	747	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298084	15298084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs75068032	NA	P-0052699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	421	1061	1	ENST00000263388.2:c.1672C>T	p.Arg558Cys	p.R558C	ENST00000263388	NM_000435.2	558	Cgc/Tgc	11/33	0.450300792176952	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.458759037594888	3		1062	1116	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176678803	176678803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	253	564	0	ENST00000439151.2:c.4714G>A	p.Gly1572Arg	p.G1572R	ENST00000439151	NM_022455.4	1572	Gga/Aga	12/23	0.18100356280585	5	FACETS	1	0.988	1	0.808	0.759	0.858	INDETERMINATE	2	TRUE	2	0.458759037594888	5		564	768	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151168649	151168649	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1248045931	NA	P-0052699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	219	546	0	ENST00000262187.5:c.318G>A	p.Met106Ile	p.M106I	ENST00000262187	NM_005614.3	106	atG/atA	5/8	0.40350939013983	4	FACETS	0.97	0.906	1	0.97	0.906	1	CLONAL	2	TRUE	2	0.458759037594888	4		546	718	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69103998	69103998	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	229	638	0	ENST00000288368.4:c.4388C>T	p.Thr1463Ile	p.T1463I	ENST00000288368	NM_024870.2	1463	aCa/aTa	36/40	0.18100356280585	5	FACETS	1	0.974	1	0.719	0.672	0.767	INDETERMINATE	2	TRUE	2	0.458759037594888	5		638	781	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0052701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	19	401	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.149646921473488	3	FACETS	0.148	0.111	0.191	0.074	0.055	0.096	INDETERMINATE	1	TRUE	1	0.480969023399015	3		401	664	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0052701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	353	839	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.344498360825097	2	FACETS	1	0.994	1	0.688	0.652	0.724	CLONAL	1	TRUE	0	0.480969023399015	2		839	1067	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098950	178098950	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	83	399	0	ENST00000397062.3:c.95T>G	p.Val32Gly	p.V32G	ENST00000397062	NM_006164.4	32	gTa/gGa	2/5	1	2	FACETS	0.707	0.626	0.794	0.707	0.626	0.794	SUBCLONAL	1	TRUE	1	0.480969023399015	2		399	488	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105586	27105586	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	141	661	0	ENST00000324856.7:c.5197G>T	p.Glu1733Ter	p.E1733*	ENST00000324856	NM_006015.4	1733	Gag/Tag	20/20	0.149646921473488	3	FACETS	0.856	0.78	0.936	0.428	0.39	0.468	INDETERMINATE	1	TRUE	1	0.480969023399015	3		661	850	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005442	29005443	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	23	368	0	ENST00000282397.4:c.818dup	p.Asn273LysfsTer2	p.N273Kfs*2	ENST00000282397	NM_002019.4	273	aat/aaAt	7/30	0.480969023399015	1	FACETS	0.304	0.237	0.38	0.304	0.237	0.38	SUBCLONAL	1	TRUE	0	0.480969023399015	1		368	239	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869545	102869545	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	63	730	0	ENST00000307046.8:c.96del	p.Phe33SerfsTer70	p.F33Sfs*70	ENST00000307046	NM_001111285.1	32	ctC/ct	2/4	1	2	FACETS	0.313	0.27	0.361	0.313	0.27	0.361	SUBCLONAL	1	TRUE	1	0.480969023399015	2		730	836	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246200	41246200	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	196	700	0	ENST00000357654.3:c.1348A>G	p.Lys450Glu	p.K450E	ENST00000357654	NM_007294.3	450	Aaa/Gaa	10/23	0.344498360825097	2	FACETS	1	0.989	1	0.657	0.612	0.704	CLONAL	1	TRUE	0	0.480969023399015	2		700	620	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374324	31374324	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	151	888	0	ENST00000328111.2:c.323A>C	p.Asn108Thr	p.N108T	ENST00000328111	NM_006892.3	108	aAc/aCc	5/23	1	2	FACETS	0.672	0.614	0.732	0.672	0.614	0.732	SUBCLONAL	1	TRUE	1	0.480969023399015	2		888	935	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217168	66217168	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	220	681	0	ENST00000273854.3:c.2447del	p.Val816GlyfsTer35	p.V816Gfs*35	ENST00000273854	NM_004439.5	816	gTg/gg	14/18	0.480969023399015	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.480969023399015	1		681	600	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279472	1279472	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1537	203	1237	0	ENST00000310581.5:c.2064G>T	p.Arg688Ser	p.R688S	ENST00000310581	NM_198253.2	688	agG/agT	5/16	0.480969023399015	3	FACETS	0.602	0.556	0.65	0.301	0.278	0.325	SUBCLONAL	1	TRUE	1	0.480969023399015	3		1237	1740	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051019	180051019	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	165	1007	0	ENST00000261937.6:c.1464C>A	p.Asp488Glu	p.D488E	ENST00000261937	NM_182925.4	488	gaC/gaA	11/30	0.42654946951064	1	FACETS	0.617	0.567	0.67	0.617	0.567	0.67	SUBCLONAL	1	TRUE	0	0.480969023399015	1		1007	844	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141557653	141557653	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	199	1089	0	ENST00000220592.5:c.1662G>T	p.Arg554Ser	p.R554S	ENST00000220592	NM_012154.3	554	agG/agT	13/19	1	2	FACETS	0.64	0.592	0.691	0.64	0.592	0.691	SUBCLONAL	1	TRUE	1	0.480969023399015	2		1089	1292	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755982	133755982	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0052701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	74	883	0	ENST00000318560.5:c.1609A>T	p.Arg537Ter	p.R537*	ENST00000318560	NM_005157.4	537	Aga/Tga	10/11	1	2	FACETS	0.298	0.26	0.34	0.298	0.26	0.34	SUBCLONAL	1	TRUE	1	0.480969023399015	2		883	1032	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041651	47041651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	90	893	0	ENST00000377604.3:c.1876C>T	p.His626Tyr	p.H626Y	ENST00000377604	NM_001204468.1	626	Cat/Tat	17/24	0.368582958114838	1	FACETS	0.339	0.3	0.38	0.339	0.3	0.38	SUBCLONAL	1	TRUE	0	0.480969023399015	1		893	839	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938740	76938740	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	65	809	1	ENST00000373344.5:c.2008A>T	p.Thr670Ser	p.T670S	ENST00000373344	NM_000489.3	670	Act/Tct	9/35	0.368582958114838	1	FACETS	0.34	0.295	0.39	0.34	0.295	0.39	SUBCLONAL	1	TRUE	0	0.480969023399015	1		810	603	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152864462	152864462	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1557027732	NA	P-0052701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	36	102	0	ENST00000406277.2:c.64G>T	p.Ala22Ser	p.A22S	ENST00000406277	NM_152274.4	22	Gcc/Tcc	3/7	NA		FACETS		NA	1				INDETERMINATE	NA	TRUE	NA	0.480969023399015	NA		102	230	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0052702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	81	636	2	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	0.901	0.801	1	0.901	0.801	1	CLONAL	1	TRUE	1	0.576575053829923	2		638	312	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439229	52439229	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	158	1134	9	ENST00000460680.1:c.1013del	p.Pro338LeufsTer24	p.P338Lfs*24	ENST00000460680	NM_004656.3	338	cCt/ct	11/17	0.576575053829923	1	FACETS	0.907	0.84	0.976	0.907	0.84	0.976	CLONAL	1	TRUE	0	0.576575053829923	1		1143	430	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0052703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	130	825	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		826	931	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0052703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	71	453	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		453	669	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855019	76855019	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	24	216	0	ENST00000373344.5:c.5817del	p.Asp1940IlefsTer15	p.D1940Ifs*15	ENST00000373344	NM_000489.3	1939	aaA/aa	25/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		216	345	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247165	153247165	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	15	167	0	ENST00000281708.4:c.1637C>A	p.Ser546Ter	p.S546*	ENST00000281708	NM_033632.3	546	tCa/tAa	10/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		167	181	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133187	30133187	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	94	370	0	ENST00000263025.4:c.311G>C	p.Arg104Pro	p.R104P	ENST00000263025	NM_002746.2	104	cGa/cCa	2/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		370	756	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412911	49412911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	84	517	1	ENST00000418115.1:c.112G>A	p.Val38Met	p.V38M	ENST00000418115	NM_001664.2	38	Gtg/Atg	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		518	660	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	91	460	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.988	0.888	1	0.988	0.888	1	CLONAL	1	TRUE	1	0.605961951716572	2		460	304	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266713	198266713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776846119	NA	P-0052704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	162	497	0	ENST00000335508.6:c.2219G>A	p.Gly740Glu	p.G740E	ENST00000335508	NM_012433.2	740	gGa/gAa	15/25	1	2	FACETS	0.878	0.809	0.949	0.878	0.809	0.949	CLONAL	1	TRUE	1	0.605961951716572	2		497	609	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042361	42042361	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	238	635	0	ENST00000219905.7:c.6556T>C	p.Cys2186Arg	p.C2186R	ENST00000219905	NM_001164273.1	2186	Tgt/Cgt	17/24	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.605961951716572	2		635	754	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441266	52441274	+	inframe_deletion	In_Frame_Del	DEL	GAACGCCTC	GAACGCCTC	-	novel	NA	P-0052704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	180	695	0	ENST00000460680.1:c.496_504del	p.Glu166_Phe168del	p.E166_F168del	ENST00000460680	NM_004656.3	166	GAGGCGTTC/-	7/17	0.605961951716572	1	FACETS	0.854	0.794	0.914	0.854	0.794	0.914	CLONAL	1	TRUE	0	0.605961951716572	1		695	485	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69998205	69998205	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	140	502	0	ENST00000394351.3:c.445C>G	p.Pro149Ala	p.P149A	ENST00000394351	NM_000248.3	149	Cct/Gct	5/9	0.605961951716572	3	FACETS	0.874	0.797	0.954	0.437	0.398	0.477	CLONAL	1	TRUE	1	0.605961951716572	3		502	689	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0052705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	97	537	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		537	248	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	24	460	0				ENST00000310581	NM_198253.2	-/1132			0.171239380179388	2	FACETS	0.433	0.343	0.536	0.217	0.171	0.268	INDETERMINATE	1	TRUE	0	0.692152305193625	2		460	160	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0052706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	234	455	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.61122193870092	4	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	2	0.692152305193625	4		455	568	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163720	32163720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253487294	NA	P-0052706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	299	636	1	ENST00000375023.3:c.5506G>A	p.Glu1836Lys	p.E1836K	ENST00000375023	NM_004557.3	1836	Gag/Aag	30/30	0.576335643340872	5	FACETS	0.936	0.89	0.983	0.936	0.89	0.983	CLONAL	3	TRUE	2	0.692152305193625	5		637	627	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806089	1806089	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913479	NA	P-0052706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	801	834	1	ENST00000260795.2:c.1108G>T	p.Gly370Cys	p.G370C	ENST00000260795		370	Ggc/Tgc	8/17	0.637365781419757	4	FACETS	1	0.997	1	1	0.997	1	CLONAL	4	TRUE	0	0.692152305193625	4		835	903	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	232	451	0	ENST00000335508.6:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000335508	NM_012433.2	902	Gaa/Aaa	18/25	0.684312161884059	2	FACETS	0.986	0.942	1	0.986	0.942	1	CLONAL	2	TRUE	0	0.692152305193625	2		451	340	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456424	99456424	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774280289	NA	P-0052706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	295	628	2	ENST00000268035.6:c.1741G>A	p.Val581Ile	p.V581I	ENST00000268035	NM_000875.3	581	Gtc/Atc	8/21	0.23272395248226	2	FACETS	1	0.994	1	0.68	0.645	0.714	INDETERMINATE	1	TRUE	0	0.692152305193625	2		630	627	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937668	44937669	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0052706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	250	255	0	ENST00000377967.4:c.2858_2859dup	p.Pro954PhefsTer17	p.P954Ffs*17	ENST00000377967	NM_021140.2	952	-/TT	19/29	0.681999645036873	2	FACETS	1	0.968	1			1	CLONAL	2	TRUE	NA	0.692152305193625	2		255	357	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	249	649	0	ENST00000397752.3:c.3028G>C	p.Asp1010His	p.D1010H	ENST00000397752	NM_000245.2	1010	Gat/Cat	14/21	0.220515536729195	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.242078864197413	2		649	957	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279558	1279558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	279	897	1	ENST00000310581.5:c.1978G>A	p.Ala660Thr	p.A660T	ENST00000310581	NM_198253.2	660	Gca/Aca	5/16	0.209672193619932	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.242078864197413	3		898	1153	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81891951	81891951	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs554363067	NA	P-0052707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	66	518	0	ENST00000359376.3:c.421A>G	p.Ile141Val	p.I141V	ENST00000359376	NM_002661.3	141	Att/Gtt	4/33	1	2	FACETS	0.765	0.663	0.875	0.765	0.663	0.875	SUBCLONAL	1	TRUE	1	0.242078864197413	2		518	713	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0052708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	49	479	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.548829168817514	1	FACETS	0.216	0.182	0.253	0.216	0.182	0.253	SUBCLONAL	1	TRUE	0	0.548829168817514	1		479	600	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0052708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	19	692	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	0.548829168817514	1	FACETS	0.086	0.065	0.112	0.086	0.065	0.112	SUBCLONAL	1	TRUE	0	0.548829168817514	1		692	582	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267203	41267203	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	129	499	0	ENST00000349496.5:c.787T>G	p.Leu263Val	p.L263V	ENST00000349496	NM_001904.3	263	Tta/Gta	6/15	1	2	FACETS	0.675	0.613	0.741	0.675	0.613	0.741	SUBCLONAL	1	TRUE	1	0.548829168817514	2		499	696	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778003	135778003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs781371665	NA	P-0052709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	314	586	0	ENST00000298552.3:c.2380C>T	p.Gln794Ter	p.Q794*	ENST00000298552	NM_001162426.1	794	Cag/Tag	18/23	0.633090155157336	2	FACETS	0.931	0.892	0.97	0.931	0.892	0.97	CLONAL	2	TRUE	0	0.659804447186029	2		586	511	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0052710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	264	680	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.916	0.859	0.975	0.916	0.859	0.975	CLONAL	1	TRUE	1	0.537583551344123	2		680	1072	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876658468	NA	P-0052710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	416	716	0	ENST00000269305.4:c.577C>A	p.His193Asn	p.H193N	ENST00000269305	NM_001126112.2	193	Cat/Aat	6/11	0.519461871186036	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.537583551344123	2		716	756	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519896	NA	P-0052710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	176	401	0	ENST00000281708.4:c.1514G>T	p.Arg505Leu	p.R505L	ENST00000281708	NM_033632.3	505	cGc/cTc	10/12	0.218509687693641	2	FACETS	1	0.985	1	0.614	0.57	0.66	INDETERMINATE	1	TRUE	0	0.537583551344123	2		401	533	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205768	108205768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555127166	NA	P-0052710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	113	400	0	ENST00000278616.4:c.8083G>A	p.Gly2695Ser	p.G2695S	ENST00000278616	NM_000051.3	2695	Ggt/Agt	55/63	0.333674748072148	1	FACETS	0.755	0.685	0.828	0.755	0.685	0.828	SUBCLONAL	1	TRUE	0	0.537583551344123	1		400	407	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165729	108165729	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs762083530	NA	P-0052710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	74	394	0	ENST00000278616.4:c.4852C>T	p.Arg1618Ter	p.R1618*	ENST00000278616	NM_000051.3	1618	Cga/Tga	32/63	0.333674748072148	1	FACETS	0.464	0.407	0.524	0.464	0.407	0.524	SUBCLONAL	1	TRUE	0	0.537583551344123	1		394	434	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508373	106508373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	167	512	0	ENST00000359195.3:c.367C>T	p.Arg123Cys	p.R123C	ENST00000359195	NM_002649.2	123	Cgc/Tgc	2/11	0.116572312747162	3	FACETS	1	0.983	1	0.614	0.566	0.663	INDETERMINATE	1	TRUE	1	0.537583551344123	3		512	642	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633862	86633862	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	124	383	3	ENST00000274376.6:c.971G>A	p.Arg324Lys	p.R324K	ENST00000274376	NM_002890.2	324	aGa/aAa	5/25	0.537583551344123	2	FACETS	1	0.975	1	0.59	0.539	0.643	CLONAL	1	TRUE	0	0.537583551344123	2		386	391	SUCCESS
APC	324	MSKCC	GRCh37	5	112175626	112175722	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTCAAACCAAGCGAGAAGTACCTAAAAATAAAGCACCTACTGCTGAAAAGAGAGAGAGTGGACCTAAGCAAGCTGCAGTAAATGCTGCAGTTCAG	AGCTCAAACCAAGCGAGAAGTACCTAAAAATAAAGCACCTACTGCTGAAAAGAGAGAGAGTGGACCTAAGCAAGCTGCAGTAAATGCTGCAGTTCAG	-	novel	NA	P-0052710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	225	374	0	ENST00000257430.4:c.4337_4433del	p.Ala1446GlyfsTer29	p.A1446Gfs*29	ENST00000257430	NM_000038.5	1445	acAGCTCAAACCAAGCGAGAAGTACCTAAAAATAAAGCACCTACTGCTGAAAAGAGAGAGAGTGGACCTAAGCAAGCTGCAGTAAATGCTGCAGTTCAG/ac	16/16	0.537583551344123	2	FACETS	0.877	0.827	0.928	0.877	0.827	0.928	CLONAL	2	TRUE	0	0.537583551344123	2		374	477	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720808	89720808	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	16	278	0	ENST00000371953.3:c.959T>C	p.Leu320Ser	p.L320S	ENST00000371953	NM_000314.4	320	tTa/tCa	8/9	0.457663645658859	1	FACETS	0.155	0.114	0.203	0.155	0.114	0.203	SUBCLONAL	1	TRUE	0	0.558357482674833	1		278	267	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0052711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	121	379	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	0.541995882667574	1	FACETS	0.88	0.804	0.958	0.88	0.804	0.958	CLONAL	1	TRUE	0	0.558357482674833	1		379	355	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789591	3789591	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	193	632	0	ENST00000262367.5:c.4268del	p.Pro1423LeufsTer36	p.P1423Lfs*36	ENST00000262367	NM_004380.2	1423	cCt/ct	25/31	0.546447411112359	1	FACETS	0.675	0.626	0.726	0.675	0.626	0.726	SUBCLONAL	1	TRUE	0	0.558357482674833	1		632	738	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	150	415	0	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	1	2	FACETS	0.714	0.654	0.778	0.714	0.654	0.778	SUBCLONAL	1	TRUE	1	0.558357482674833	2		415	752	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838324	156838324	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs146201511	NA	P-0052711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1878	452	1053	0	ENST00000524377.1:c.602C>A	p.Pro201His	p.P201H	ENST00000524377	NM_002529.3	201	cCc/cAc	6/17	0.545557931588041	3	FACETS	0.889	0.845	0.934	0.444	0.422	0.467	CLONAL	1	TRUE	1	0.558357482674833	3		1053	2330	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007871	45007872	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0052711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	224	522	0	ENST00000558401.1:c.319_320del	p.Leu107ValfsTer7	p.L107Vfs*7	ENST00000558401	NM_004048.2	106	acTTtg/actg	2/4	0.541995882667574	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.558357482674833	1		522	562	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276895	123276895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	226	561	1	ENST00000358487.5:c.1022C>T	p.Thr341Met	p.T341M	ENST00000358487	NM_000141.4	341	aCg/aTg	8/18	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.558357482674833	2		562	806	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39618751	39618751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752104656	NA	P-0052711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	113	289	0	ENST00000262039.4:c.1975C>T	p.Arg659Trp	p.R659W	ENST00000262039	NM_002647.2	659	Cgg/Tgg	18/25	1	2	FACETS	0.957	0.868	1	0.957	0.868	1	CLONAL	1	TRUE	1	0.558357482674833	2		289	423	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825519	50825519	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	140	503	0	ENST00000398568.2:c.2156del	p.Asn719MetfsTer13	p.N719Mfs*13	ENST00000398568	NM_001042412.1	717	gAa/ga	14/18	0.546447411112359	1	FACETS	0.956	0.881	1	0.956	0.881	1	CLONAL	1	TRUE	0	0.558357482674833	1		503	378	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307291	118307291	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	24	84	0	ENST00000534358.1:c.69del	p.Arg24AlafsTer4	p.R24Afs*4	ENST00000534358	NM_005933.3	22	Ggg/gg	1/36	0.541995882667574	1	FACETS	0.579	0.462	0.708	0.579	0.462	0.708	SUBCLONAL	1	TRUE	0	0.558357482674833	1		84	107	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058342	42058342	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201470885	NA	P-0052711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	199	445	0	ENST00000219905.7:c.8062G>A	p.Val2688Ile	p.V2688I	ENST00000219905	NM_001164273.1	2688	Gtc/Atc	24/24	0.541995882667574	1	FACETS	0.953	0.89	1	0.953	0.89	1	CLONAL	1	TRUE	0	0.558357482674833	1		445	539	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40468917	40468917	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs869312892	NA	P-0052711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	145	345	2	ENST00000264657.5:c.2147C>T	p.Thr716Met	p.T716M	ENST00000264657	NM_139276.2	716	aCg/aTg	23/24	1	2	FACETS	0.677	0.618	0.739	0.677	0.618	0.739	SUBCLONAL	1	TRUE	1	0.558357482674833	2		347	767	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804952	43804953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0052711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	212	492	0	ENST00000372470.3:c.408dup	p.Ser137GlnfsTer27	p.S137Qfs*27	ENST00000372470	NM_005373.2	134	-/C	4/12	1	2	FACETS	0.823	0.765	0.883	0.823	0.765	0.883	CLONAL	1	TRUE	1	0.558357482674833	2		492	923	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8105971	8105971	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	249	622	0	ENST00000346208.3:c.791T>C	p.Val264Ala	p.V264A	ENST00000346208		264	gTg/gCg	4/6	1	2	FACETS	0.827	0.773	0.882	0.827	0.773	0.882	CLONAL	1	TRUE	1	0.558357482674833	2		622	1079	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685311	89685311	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	97	331	0	ENST00000371953.3:c.206A>T	p.Asn69Ile	p.N69I	ENST00000371953	NM_000314.4	69	aAt/aTt	3/9	0.457663645658859	1	FACETS	0.846	0.764	0.931	0.846	0.764	0.931	CLONAL	1	TRUE	0	0.558357482674833	1		331	296	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692848	89692869	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTAAGTGAAGATGACAATCA	GGCTAAGTGAAGATGACAATCA	-	novel	NA	P-0052711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	33	201	0	ENST00000371953.3:c.332_353del	p.Trp111LeufsTer16	p.W111Lfs*16	ENST00000371953	NM_000314.4	111	tGGCTAAGTGAAGATGACAATCAt/tt	5/9	0.457663645658859	1	FACETS	0.408	0.334	0.489	0.408	0.334	0.489	SUBCLONAL	1	TRUE	0	0.558357482674833	1		201	209	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298778	46298778	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	211	503	1	ENST00000334344.6:c.5425T>C	p.Ser1809Pro	p.S1809P	ENST00000334344	NM_152641.2	1809	Tcc/Ccc	21/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.558357482674833	2		504	673	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349249	89349249	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	332	849	0	ENST00000301030.4:c.3701A>G	p.Asn1234Ser	p.N1234S	ENST00000301030	NM_001256183.1	1234	aAt/aGt	9/13	1	2	FACETS	0.804	0.758	0.85	0.804	0.758	0.85	CLONAL	1	TRUE	1	0.558357482674833	2		849	1480	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659287	86659287	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	82	298	0	ENST00000274376.6:c.1576T>C	p.Ser526Pro	p.S526P	ENST00000274376	NM_002890.2	526	Tct/Cct	11/25	0.541995882667574	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.558357482674833	1		298	176	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800159	32800159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	251	529	0	ENST00000374899.4:c.1223G>A	p.Ser408Asn	p.S408N	ENST00000374899	NM_018833.2	408	aGc/aAc	7/12	1	2	FACETS	0.847	0.793	0.904	0.847	0.793	0.904	CLONAL	1	TRUE	1	0.558357482674833	2		529	1061	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519741	137519741	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	133	397	0	ENST00000367739.4:c.897del	p.Lys299AsnfsTer18	p.K299Nfs*18	ENST00000367739	NM_000416.2	299	aaA/aa	7/7	0.546447411112359	1	FACETS	0.852	0.781	0.925	0.852	0.781	0.925	CLONAL	1	TRUE	0	0.558357482674833	1		397	403	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821499	32821499	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs776294658	NA	P-0052712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	649	973	0	ENST00000354258.4:c.95G>C	p.Gly32Ala	p.G32A	ENST00000354258	NM_000593.5	32	gGa/gCa	1/11	0.180390474879191	3	FACETS	1	0.975	1	1	0.997	1	CLONAL	3	TRUE	1	0.28	3		973	1734	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578463	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371524413	NA	P-0052713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	1498	862	0	ENST00000269305.4:c.467G>C	p.Arg156Pro	p.R156P	ENST00000269305	NM_001126112.2	156	cGc/cCc	5/11	0.762609391449181	4	FACETS	0.986	0.974	0.997	0.986	0.974	0.997	CLONAL	4	TRUE	0	0.772959143510946	4		862	1743	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22413282	22413282	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs142108830	NA	P-0052713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	31	53	0	ENST00000344548.3:c.409A>G	p.Ile137Val	p.I137V	ENST00000344548	NM_001039802.1	137	Atc/Gtc	6/7	0.290543088418558	4	FACETS	1	0.901	1	0.573	0.472	0.683	INDETERMINATE	1	TRUE	2	0.772959143510946	4		53	124	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197825	123197825	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	164	560	0	ENST00000218089.9:c.1949T>G	p.Val650Gly	p.V650G	ENST00000218089	NM_001042749.1	650	gTa/gGa	20/35	0.26471488793126	1	FACETS	0.405	0.373	0.438	0.405	0.373	0.438	INDETERMINATE	1	TRUE	0	0.772959143510946	1		560	643	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0052716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	217	400	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	0.790700931405188	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.790700931405188	1		400	317	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579703	7579703	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	350	773	0	ENST00000269305.4:c.93del	p.Leu32CysfsTer12	p.L32Cfs*12	ENST00000269305	NM_001126112.2	31	gtT/gt	3/11	0.790700931405188	1	FACETS	0.971	0.934	1	0.971	0.934	1	CLONAL	1	TRUE	0	0.790700931405188	1		773	551	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992179	72992179	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	530	1185	0	ENST00000268489.5:c.1866C>G	p.His622Gln	p.H622Q	ENST00000268489	NM_006885.3	622	caC/caG	2/10	0.790700931405188	1	FACETS	0.979	0.948	1	0.979	0.948	1	CLONAL	1	TRUE	0	0.790700931405188	1		1185	828	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0052717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	508	542	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.872377157448787	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.872377157448787	3		542	547	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339680	116339680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	370	487	0	ENST00000397752.3:c.542G>A	p.Gly181Glu	p.G181E	ENST00000397752	NM_000245.2	181	gGa/gAa	2/21	0.872377157448787	4	FACETS	0.934	0.891	0.978	0.934	0.891	0.978	CLONAL	2	TRUE	2	0.872377157448787	4		487	850	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619946	21619946	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	251	764	1	ENST00000382592.4:c.220C>T	p.Gln74Ter	p.Q74*	ENST00000382592	NM_014572.2	74	Cag/Tag	2/8	0.872377157448787	3	FACETS	0.999	0.938	1	0.5	0.469	0.532	CLONAL	1	TRUE	1	0.872377157448787	3		765	827	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222973	5222973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	502	677	2	ENST00000357368.4:c.2830G>C	p.Gly944Arg	p.G944R	ENST00000357368	NM_002850.3	944	Ggg/Cgg	18/38	0.739035870611566	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.872377157448787	4		679	1050	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162097	22162098	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	372	560	0	ENST00000215832.6:c.157dup	p.Ile53AsnfsTer8	p.I53Nfs*8	ENST00000215832	NM_002745.4	53	atc/aAtc	2/9	0.872377157448787	3	FACETS	0.986	0.947	1	0.986	0.947	1	CLONAL	2	TRUE	1	0.872377157448787	3		560	621	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244265	153244265	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	264	417	0	ENST00000281708.4:c.1892A>T	p.Gln631Leu	p.Q631L	ENST00000281708	NM_033632.3	631	cAg/cTg	12/12	0.872377157448787	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.872377157448787	3		417	413	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293694	1293694	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	871	1187	2	ENST00000310581.5:c.1307C>G	p.Ala436Gly	p.A436G	ENST00000310581	NM_198253.2	436	gCg/gGg	2/16	0.786873868111788	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	2	0.872377157448787	4		1189	1777	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755741	57755741	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	331	816	4	ENST00000274289.3:c.46A>G	p.Lys16Glu	p.K16E	ENST00000274289	NM_006622.3	16	Aaa/Gaa	1/14	0.872377157448787	3	FACETS	0.997	0.943	1	0.499	0.471	0.526	CLONAL	1	TRUE	1	0.872377157448787	3		820	1093	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334827	81334827	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	338	617	1	ENST00000222390.5:c.1889G>T	p.Arg630Leu	p.R630L	ENST00000222390	NM_000601.4	630	cGa/cTa	17/18	0.872377157448787	4	FACETS	0.953	0.907	0.999	0.953	0.907	0.999	CLONAL	2	TRUE	2	0.872377157448787	4		618	761	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482242	87482242	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	291	841	1	ENST00000277120.3:c.1529C>A	p.Ser510Ter	p.S510*	ENST00000277120		510	tCg/tAg	14/19	0.872377157448787	3	FACETS	1	0.979	1	0.538	0.507	0.569	CLONAL	1	TRUE	1	0.872377157448787	3		842	891	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400173	139400173	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	439	1059	1	ENST00000277541.6:c.4175T>A	p.Leu1392Gln	p.L1392Q	ENST00000277541	NM_017617.3	1392	cTg/cAg	25/34	0.872377157448787	3	FACETS	1	0.989	1	0.553	0.528	0.579	CLONAL	1	TRUE	1	0.872377157448787	3		1060	1306	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258040	16258040	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	97	587	0	ENST00000375759.3:c.5305G>T	p.Ala1769Ser	p.A1769S	ENST00000375759	NM_015001.2	1769	Gcc/Tcc	11/15	1	2	FACETS	0.956	0.852	1	0.956	0.852	1	CLONAL	1	TRUE	1	0.29	2		587	700	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266197	198266197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	67	558	0	ENST00000335508.6:c.2423C>T	p.Thr808Ile	p.T808I	ENST00000335508	NM_012433.2	808	aCa/aTa	17/25	1	2	FACETS	0.793	0.689	0.905	0.793	0.689	0.905	CLONAL	1	TRUE	1	0.29	2		558	583	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	39	460	0				ENST00000310581	NM_198253.2	-/1132			0.176161111453362	2	FACETS	0.443	0.367	0.527	0.222	0.183	0.264	INDETERMINATE	1	TRUE	0	0.430370223313977	2		460	409	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0052719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	283	1087	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.372484917995648	2	FACETS	0.812	0.766	0.859	0.812	0.766	0.859	CLONAL	2	TRUE	0	0.430370223313977	2		1087	810	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023267	27023286	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGGCGGCAGCAGCGATGG	GGTGGCGGCAGCAGCGATGG	-	novel	NA	P-0052719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	76	232	0	ENST00000324856.7:c.378_397del	p.Ser128AlafsTer265	p.S128Afs*265	ENST00000324856	NM_006015.4	125	GGTGGCGGCAGCAGCGATGGg/g	1/20	0.190726116391612	2	FACETS	1	0.921	1	0.527	0.466	0.592	INDETERMINATE	1	TRUE	0	0.430370223313977	2		232	335	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354342	354342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375396918	NA	P-0052719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	251	908	3	ENST00000262320.3:c.1216G>A	p.Glu406Lys	p.E406K	ENST00000262320	NM_003502.3	406	Gag/Aag	5/11	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.430370223313977	2		911	1160	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096201	2096201	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	242	903	0	ENST00000219066.1:c.306G>T	p.Met102Ile	p.M102I	ENST00000219066	NM_002528.5	102	atG/atT	2/6	1	2	FACETS	0.932	0.869	0.996	0.932	0.869	0.996	CLONAL	1	TRUE	1	0.430370223313977	2		903	1207	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799668	3799668	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	86	301	0	ENST00000262367.5:c.3796C>T	p.Gln1266Ter	p.Q1266*	ENST00000262367	NM_004380.2	1266	Cag/Tag	21/31	1	2	FACETS	0.898	0.798	1	0.898	0.798	1	CLONAL	1	TRUE	1	0.430370223313977	2		301	445	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116209	67116209	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	198	569	0	ENST00000412916.2:c.493G>C	p.Glu165Gln	p.E165Q	ENST00000412916		165	Gag/Cag	5/6	1	2	FACETS	0.985	0.913	1	0.985	0.913	1	CLONAL	1	TRUE	1	0.430370223313977	2		569	934	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579855	7579855	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1131691018	NA	P-0052719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	333	705	0	ENST00000269305.4:c.58del	p.Ser20GlnfsTer24	p.S20Qfs*24	ENST00000269305	NM_001126112.2	20	Tca/ca	2/11	0.380589240656982	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.430370223313977	1		705	938	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853857	59853857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	162	570	0	ENST00000259008.2:c.2002G>A	p.Glu668Lys	p.E668K	ENST00000259008	NM_032043.2	668	Gaa/Aaa	14/20	0.388871476076885	1	FACETS	0.863	0.794	0.934	0.863	0.794	0.934	CLONAL	1	TRUE	0	0.430370223313977	1		570	685	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132549	11132549	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	280	837	0	ENST00000358026.2:c.2765G>A	p.Trp922Ter	p.W922*	ENST00000358026	NM_001128849.1	922	tGg/tAg	19/36	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.430370223313977	2		837	1211	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209240	36209240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	69	389	0	ENST00000222270.7:c.320G>A	p.Cys107Tyr	p.C107Y	ENST00000222270	NM_014727.1	107	tGc/tAc	1/37	1	2	FACETS	0.676	0.591	0.769	0.676	0.591	0.769	SUBCLONAL	1	TRUE	1	0.430370223313977	2		389	474	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009095	27009095	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	33	246	1	ENST00000335756.4:c.31G>T	p.Glu11Ter	p.E11*	ENST00000335756	NM_001809.3	11	Gag/Tag	1/5	0.176161111453362	2	FACETS	0.397	0.324	0.48	0.199	0.162	0.24	INDETERMINATE	1	TRUE	0	0.430370223313977	2		247	386	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881576	111881576	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	116	757	0	ENST00000393256.3:c.254G>T	p.Arg85Ile	p.R85I	ENST00000393256	NM_006538.4	85	aGa/aTa	2/4	0.430370223313977	1	FACETS	0.518	0.466	0.572	0.518	0.466	0.572	SUBCLONAL	1	TRUE	0	0.430370223313977	1		757	817	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770633	40770633	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	164	456	0	ENST00000373198.4:c.2749G>A	p.Glu917Lys	p.E917K	ENST00000373198	NM_133170.3	917	Gag/Aag	19/32	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.430370223313977	2		456	666	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721207	176721207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	63	513	1	ENST00000439151.2:c.6838G>A	p.Glu2280Lys	p.E2280K	ENST00000439151	NM_022455.4	2280	Gaa/Aaa	23/23	0.176161111453362	2	FACETS	0.45	0.388	0.516	0.225	0.194	0.258	INDETERMINATE	1	TRUE	0	0.430370223313977	2		514	651	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721223	176721223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	73	507	0	ENST00000439151.2:c.6854G>A	p.Arg2285Lys	p.R2285K	ENST00000439151	NM_022455.4	2285	aGa/aAa	23/23	0.176161111453362	2	FACETS	0.524	0.458	0.595	0.262	0.229	0.298	INDETERMINATE	1	TRUE	0	0.430370223313977	2		507	647	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522599	157522599	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762183842	NA	P-0052719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	259	611	1	ENST00000346085.5:c.4871G>A	p.Arg1624Gln	p.R1624Q	ENST00000346085	NM_020732.3	1624	cGa/cAa	18/20	0.203566775613809	2	FACETS	1	0.991	1	0.662	0.621	0.704	INDETERMINATE	1	TRUE	0	0.430370223313977	2		612	909	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880184	151880184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	87	439	0	ENST00000262189.6:c.5140G>A	p.Asp1714Asn	p.D1714N	ENST00000262189	NM_170606.2	1714	Gat/Aat	35/59	1	2	FACETS	0.848	0.753	0.948	0.848	0.753	0.948	CLONAL	1	TRUE	1	0.430370223313977	2		439	477	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38157017	38157017	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1331481409	NA	P-0052719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	185	612	0	ENST00000317025.8:c.2703G>C	p.Leu901Phe	p.L901F	ENST00000317025	NM_023034.1	901	ttG/ttC	15/24	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.430370223313977	2		612	721	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738508	145738508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770800467	NA	P-0052719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	310	865	1	ENST00000428558.2:c.2477G>A	p.Arg826Gln	p.R826Q	ENST00000428558	NM_004260.3	826	cGa/cAa	16/22	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.430370223313977	2		866	1133	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137323775	137323775	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	255	984	0	ENST00000481739.1:c.1068G>C	p.Lys356Asn	p.K356N	ENST00000481739	NM_002957.4	356	aaG/aaC	8/10	1	2	FACETS	0.971	0.908	1	0.971	0.908	1	CLONAL	1	TRUE	1	0.430370223313977	2		984	1220	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44970636	44970636	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	122	259	0	ENST00000377967.4:c.4187del	p.Leu1396TyrfsTer142	p.L1396Yfs*142	ENST00000377967	NM_021140.2	1396	Tta/ta	29/29	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.430370223313977	1		259	302	SUCCESS
APC	324	MSKCC	GRCh37	5	112175852	112175852	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	55	383	0	ENST00000257430.4:c.4561G>T	p.Glu1521Ter	p.E1521*	ENST00000257430	NM_000038.5	1521	Gaa/Taa	16/16	0.3866740223997	1	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	0	0.409836036789925	1		383	204	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0052721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	359	1103	0	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	0.40307390144328	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.409836036789925	2		1103	801	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589629	67589630	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGATTATATGAAGAATATACCCGCACA	novel	NA	P-0052721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	17	414	0	ENST00000274335.5:c.1393_1419dup	p.Arg465_Thr473dup	p.R465_T473dup	ENST00000274335		465	-/AGATTATATGAAGAATATACCCGCACA	10/15	0.3866740223997	1	FACETS	0.215	0.16	0.28	0.215	0.16	0.28	SUBCLONAL	1	TRUE	0	0.409836036789925	1		414	307	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0052722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	150	542	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.239366299404528	2	FACETS	1	0.986	1	0.705	0.646	0.767	CLONAL	1	TRUE	0	0.310901905441999	2		542	684	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220370	1220370	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0052722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	107	818	0	ENST00000326873.7:c.465-2A>T		p.X155_splice	ENST00000326873	NM_000455.4	155			0.310901905441999	1	FACETS	0.89	0.8	0.986	0.89	0.8	0.986	CLONAL	1	TRUE	0	0.310901905441999	1		818	653	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150030	202150030	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs931648756	NA	P-0052722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	110	730	1	ENST00000358485.4:c.1471C>T	p.Arg491Ter	p.R491*	ENST00000358485	NM_001080125.1	491	Cga/Tga	8/9	1	2	FACETS	0.835	0.75	0.926	0.835	0.75	0.926	CLONAL	1	TRUE	1	0.310901905441999	2		731	847	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041519	14041519	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161291089	NA	P-0052722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	77	555	0	ENST00000311895.7:c.2066G>A	p.Arg689His	p.R689H	ENST00000311895	NM_005236.2	689	cGt/cAt	11/11	0.310901905441999	3	FACETS	0.737	0.646	0.834	0.368	0.323	0.417	SUBCLONAL	1	TRUE	1	0.310901905441999	3		555	777	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39746916	39746916	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	82	484	0	ENST00000361337.2:c.1930A>G	p.Met644Val	p.M644V	ENST00000361337	NM_003286.2	644	Atg/Gtg	18/21	0.310901905441999	1	FACETS	0.756	0.668	0.851	0.756	0.668	0.851	SUBCLONAL	1	TRUE	0	0.310901905441999	1		484	589	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69143600	69143600	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	69	437	0	ENST00000288368.4:c.4808C>A	p.Ala1603Asp	p.A1603D	ENST00000288368	NM_024870.2	1603	gCt/gAt	40/40	0.310901905441999	1	FACETS	0.658	0.573	0.749	0.658	0.573	0.749	SUBCLONAL	1	TRUE	0	0.310901905441999	1		437	570	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0052723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	90	449	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.326212947047633	4	FACETS	0.827	0.738	0.921	0.827	0.738	0.921	CLONAL	2	TRUE	2	0.36240943127035	4		449	409	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0052723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	78	566	1	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	1	2	FACETS	0.864	0.762	0.974	0.864	0.762	0.974	CLONAL	1	TRUE	1	0.36240943127035	2		567	498	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245486	46245486	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	67	452	0	ENST00000334344.6:c.3580C>T	p.Gln1194Ter	p.Q1194*	ENST00000334344	NM_152641.2	1194	Cag/Tag	15/21	1	2	FACETS	0.797	0.694	0.907	0.797	0.694	0.907	CLONAL	1	TRUE	1	0.36240943127035	2		452	464	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477100	67477100	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	150	831	0	ENST00000327367.4:c.907G>T	p.Val303Phe	p.V303F	ENST00000327367	NM_005902.3	303	Gtc/Ttc	7/9	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.36240943127035	2		831	823	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587397	29587397	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	67	464	0	ENST00000356175.3:c.4378G>C	p.Asp1460His	p.D1460H	ENST00000356175	NM_000267.3	1460	Gat/Cat	33/57	1	2	FACETS	0.864	0.753	0.983	0.864	0.753	0.983	CLONAL	1	TRUE	1	0.36240943127035	2		464	428	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125430	7125430	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	175	906	0	ENST00000302850.5:c.3122A>G	p.Asn1041Ser	p.N1041S	ENST00000302850	NM_000208.2	1041	aAt/aGt	17/22	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.36240943127035	2		906	898	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979505	55979505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	106	555	0	ENST00000263923.4:c.942G>A	p.Met314Ile	p.M314I	ENST00000263923	NM_002253.2	314	atG/atA	7/30	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.36240943127035	2		555	585	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29913034	29913034	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760978052	NA	P-0052723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	278	792	0	ENST00000376809.5:c.1069G>A	p.Asp357Asn	p.D357N	ENST00000376809	NM_002116.7	357	Gat/Aat	7/8	0.36240943127035	2	FACETS	0.955	0.901	1	0.955	0.901	1	CLONAL	2	TRUE	0	0.36240943127035	2		792	803	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27109610	27109610	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	102	685	0	ENST00000380036.4:c.22G>T	p.Val8Phe	p.V8F	ENST00000380036	NM_000459.3	8	Gtt/Ttt	1/23	1	2	FACETS	0.921	0.826	1	0.921	0.826	1	CLONAL	1	TRUE	1	0.36240943127035	2		685	611	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981165	55981167	+	missense_variant	Missense_Mutation	TNP	GGA	GGA	AGG	novel	NA	P-0052723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	59	600	0	ENST00000263923.4:c.532_534delinsCCT	p.Ser178Pro	p.S178P	ENST00000263923	NM_002253.2	178	TCC/CCT	5/30	1	2	FACETS	0.705	0.608	0.81	0.705	0.608	0.81	SUBCLONAL	1	TRUE	1	0.36240943127035	2		600	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0052724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	329	825	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.520532080697354	2		826	1258	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0052724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	110	449	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.520532080697354	2	FACETS	0.937	0.847	1	0.469	0.423	0.516	CLONAL	1	TRUE	0	0.520532080697354	2		449	451	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	97	460	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.956	0.858	1	0.956	0.858	1	CLONAL	1	TRUE	1	0.520532080697354	2		460	390	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121242	29121242	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137853007	NA	P-0052724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	179	842	0	ENST00000328354.6:c.433C>T	p.Arg145Trp	p.R145W	ENST00000328354	NM_007194.3	145	Cgg/Tgg	3/15	0.520532080697354	1	FACETS	0.971	0.902	1	0.971	0.902	1	CLONAL	1	TRUE	0	0.520532080697354	1		842	524	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526287	189526287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	299	678	0	ENST00000264731.3:c.551C>T	p.Ser184Leu	p.S184L	ENST00000264731	NM_003722.4	184	tCg/tTg	4/14	0.520532080697354	2	FACETS	1	0.985	1	0.563	0.531	0.596	CLONAL	1	TRUE	0	0.520532080697354	2		678	1020	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555526268	NA	P-0052724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	417	1013	0	ENST00000269305.4:c.406C>G	p.Gln136Glu	p.Q136E	ENST00000269305	NM_001126112.2	136	Caa/Gaa	5/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.520532080697354	2		1013	1491	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913384	NA	P-0052724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	238	553	0	ENST00000304494.5:c.262G>T	p.Glu88Ter	p.E88*	ENST00000304494	NM_000077.4	88	Gag/Tag	2/3	0.520532080697354	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.520532080697354	1		553	526	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501260	140501260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730880413	NA	P-0052724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	124	573	0	ENST00000288602.6:c.812G>A	p.Arg271His	p.R271H	ENST00000288602	NM_004333.4	271	cGt/cAt	6/18	0.520532080697354	1	FACETS	0.747	0.68	0.816	0.747	0.68	0.816	SUBCLONAL	1	TRUE	0	0.520532080697354	1		573	472	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402794	139402794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	430	1099	3	ENST00000277541.6:c.3215G>A	p.Gly1072Asp	p.G1072D	ENST00000277541	NM_017617.3	1072	gGc/gAc	20/34	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.520532080697354	2		1102	1505	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280418	1280418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759017540	NA	P-0052724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	282	984	1	ENST00000310581.5:c.1805C>T	p.Ser602Leu	p.S602L	ENST00000310581	NM_198253.2	602	tCg/tTg	4/16	1	2	FACETS	0.966	0.907	1	0.966	0.907	1	CLONAL	1	TRUE	1	0.520532080697354	2		985	1122	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284970	15284970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	379	1021	1	ENST00000263388.2:c.4645G>A	p.Ala1549Thr	p.A1549T	ENST00000263388	NM_000435.2	1549	Gcg/Acg	25/33	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.520532080697354	2		1022	1394	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384664	31384664	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	265	859	1	ENST00000328111.2:c.1366C>T	p.Gln456Ter	p.Q456*	ENST00000328111	NM_006892.3	456	Cag/Tag	13/23	1	2	FACETS	0.96	0.9	1	0.96	0.9	1	CLONAL	1	TRUE	1	0.520532080697354	2		860	1061	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856054	151856063	+	frameshift_variant	Frame_Shift_Del	DEL	TGAGTCCGTT	TGAGTCCGTT	-	novel	NA	P-0052724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	193	614	0	ENST00000262189.6:c.11555_11564del	p.Lys3852ArgfsTer34	p.K3852Rfs*34	ENST00000262189	NM_170606.2	3852	aAACGGACTCAg/ag	44/59	0.520532080697354	1	FACETS	0.908	0.845	0.973	0.908	0.845	0.973	CLONAL	1	TRUE	0	0.520532080697354	1		614	604	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427357	49427357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	235	950	0	ENST00000301067.7:c.11131C>T	p.Pro3711Ser	p.P3711S	ENST00000301067	NM_003482.3	3711	Cct/Tct	39/54	1	2	FACETS	0.9	0.84	0.962	0.9	0.84	0.962	CLONAL	1	TRUE	1	0.520532080697354	2		950	1003	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0052724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	392	825	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.554732836743239	2		826	1330	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0052724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	39	449	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.509189668395074	2	FACETS	1	0.898	1	0.541	0.458	0.629	CLONAL	1	TRUE	0	0.554732836743239	2		449	130	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	102	460	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.978	0.882	1	0.978	0.882	1	CLONAL	1	TRUE	1	0.554732836743239	2		460	376	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121242	29121242	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137853007	NA	P-0052724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	74	842	0	ENST00000328354.6:c.433C>T	p.Arg145Trp	p.R145W	ENST00000328354	NM_007194.3	145	Cgg/Tgg	3/15	1	2	FACETS	0.85	0.75	0.955	0.85	0.75	0.955	CLONAL	1	TRUE	1	0.554732836743239	2		842	314	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526287	189526287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	282	678	0	ENST00000264731.3:c.551C>T	p.Ser184Leu	p.S184L	ENST00000264731	NM_003722.4	184	tCg/tTg	4/14	0.509189668395074	2	FACETS	1	0.957	1	0.51	0.48	0.542	CLONAL	1	TRUE	0	0.554732836743239	2		678	996	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555526268	NA	P-0052724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	326	1013	0	ENST00000269305.4:c.406C>G	p.Gln136Glu	p.Q136E	ENST00000269305	NM_001126112.2	136	Caa/Gaa	5/11	1	2	FACETS	0.964	0.911	1	0.964	0.911	1	CLONAL	1	TRUE	1	0.554732836743239	2		1013	1219	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913384	NA	P-0052724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	272	553	0	ENST00000304494.5:c.262G>T	p.Glu88Ter	p.E88*	ENST00000304494	NM_000077.4	88	Gag/Tag	2/3	0.554732836743239	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.554732836743239	1		553	615	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402794	139402794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	424	1099	3	ENST00000277541.6:c.3215G>A	p.Gly1072Asp	p.G1072D	ENST00000277541	NM_017617.3	1072	gGc/gAc	20/34	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.554732836743239	2		1102	1465	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280418	1280418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759017540	NA	P-0052724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	329	984	1	ENST00000310581.5:c.1805C>T	p.Ser602Leu	p.S602L	ENST00000310581	NM_198253.2	602	tCg/tTg	4/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.554732836743239	2		985	1115	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284970	15284970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	456	1021	1	ENST00000263388.2:c.4645G>A	p.Ala1549Thr	p.A1549T	ENST00000263388	NM_000435.2	1549	Gcg/Acg	25/33	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.554732836743239	2		1022	1528	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384664	31384664	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	194	859	1	ENST00000328111.2:c.1366C>T	p.Gln456Ter	p.Q456*	ENST00000328111	NM_006892.3	456	Cag/Tag	13/23	1	2	FACETS	0.946	0.878	1	0.946	0.878	1	CLONAL	1	TRUE	1	0.554732836743239	2		860	739	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856054	151856063	+	frameshift_variant	Frame_Shift_Del	DEL	TGAGTCCGTT	TGAGTCCGTT	-	novel	NA	P-0052724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	113	614	0	ENST00000262189.6:c.11555_11564del	p.Lys3852ArgfsTer34	p.K3852Rfs*34	ENST00000262189	NM_170606.2	3852	aAACGGACTCAg/ag	44/59	0.554732836743239	1	FACETS	0.978	0.893	1	0.978	0.893	1	CLONAL	1	TRUE	0	0.554732836743239	1		614	301	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0052724-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	41	472	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	0.439792812025736	3	FACETS	0.527	0.44	0.624	0.264	0.22	0.312	SUBCLONAL	1	TRUE	1	0.554732836743239	3		472	358	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0052725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	86	401	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.221541961583913	2		401	750	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4090603	4090603	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs912154933	NA	P-0052725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	43	702	1	ENST00000262948.5:c.1196C>T	p.Ala399Val	p.A399V	ENST00000262948	NM_030662.3	399	gCc/gTc	11/11	1	2	FACETS	0.497	0.415	0.589	0.497	0.415	0.589	SUBCLONAL	1	TRUE	1	0.221541961583913	2		703	781	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629513	187629513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	121	831	0	ENST00000441802.2:c.1469C>T	p.Pro490Leu	p.P490L	ENST00000441802	NM_005245.3	490	cCt/cTt	2/27	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.221541961583913	2		831	923	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371722	55371722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052731-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	192	366	1	ENST00000297316.4:c.412C>T	p.Arg138Trp	p.R138W	ENST00000297316	NM_022454.3	138	Cgg/Tgg	2/2	0.3	3	FACETS	0.802	0.743	0.862	0.802	0.743	0.862	CLONAL	2	TRUE	1	0.38	3		367	750	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577543	7577551	+	inframe_deletion	In_Frame_Del	DEL	CATGCCGCC	CATGCCGCC	-	novel	NA	P-0052731-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	128	523	0	ENST00000269305.4:c.730_738del	p.Gly244_Met246del	p.G244_M246del	ENST00000269305	NM_001126112.2	244	GGCGGCATG/-	7/11	0.3	3	FACETS	0.816	0.739	0.898	0.408	0.369	0.449	CLONAL	1	TRUE	1	0.38	3		523	982	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260571	10260571	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052731-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	149	511	0	ENST00000340748.4:c.2291C>G	p.Ser764Cys	p.S764C	ENST00000340748		764	tCt/tGt	24/40	1	2	FACETS	0.834	0.762	0.91	0.834	0.762	0.91	CLONAL	1	TRUE	1	0.38	2		511	940	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522413	157522413	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052731-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	94	602	0	ENST00000346085.5:c.4685C>G	p.Ser1562Cys	p.S1562C	ENST00000346085	NM_020732.3	1562	tCc/tGc	18/20	1	2	FACETS	0.538	0.478	0.603	0.538	0.478	0.603	SUBCLONAL	1	TRUE	1	0.38	2		602	919	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415130	116415130	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052731-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1198	64	554	0	ENST00000397752.3:c.3224G>C	p.Ser1075Thr	p.S1075T	ENST00000397752	NM_000245.2	1075	aGc/aCc	15/21	0.189921587661838	4	FACETS	0.368	0.317	0.424	0.184	0.158	0.212	INDETERMINATE	1	TRUE	2	0.38	4		554	1262	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0052733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	48	754	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.905	0.763	1	0.905	0.763	1	CLONAL	1	TRUE	1	0.13	2		754	816	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216753	7216753	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs745671551	NA	P-0052733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	38	477	0	ENST00000380728.2:c.670C>T	p.Gln224Ter	p.Q224*	ENST00000380728		224	Cag/Tag	8/11	1	2	FACETS	0.841	0.694	1	0.841	0.694	1	CLONAL	1	TRUE	1	0.13	2		477	695	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482343	56482343	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	10	155	0	ENST00000267101.3:c.891T>G	p.Asp297Glu	p.D297E	ENST00000267101	NM_001982.3	297	gaT/gaG	8/28	1	2	FACETS	0.095	0.064	0.135	0.095	0.064	0.135	SUBCLONAL	1	TRUE	1	0.424316807513403	2		155	494	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696644	47696644	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519964	NA	P-0052737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	81	467	0	ENST00000347630.2:c.304T>G	p.Phe102Val	p.F102V	ENST00000347630	NM_001007230.1	102	Ttc/Gtc	5/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.474290476381285	2		467	248	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31451710	31451710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1466433904	NA	P-0052737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	25	329	0	ENST00000344624.3:c.2612G>A	p.Arg871His	p.R871H	ENST00000344624		871	cGc/cAc	18/33	1	2	FACETS	0.659	0.524	0.81	0.659	0.524	0.81	SUBCLONAL	1	FALSE	1	0.474290476381285	2		329	160	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035075	42035075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	29	587	0	ENST00000219905.7:c.4918del	p.Val1640SerfsTer10	p.V1640Sfs*10	ENST00000219905	NM_001164273.1	1639	gaG/ga	15/24	1	2	FACETS	0.523	0.421	0.636	0.523	0.421	0.636	SUBCLONAL	1	FALSE	1	0.474290476381285	2		587	234	SUCCESS
APC	324	MSKCC	GRCh37	5	112157641	112157648	+	frameshift_variant	Frame_Shift_Del	DEL	TGAAACTT	TGAAACTT	-	novel	NA	P-0052737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	47	492	0	ENST00000257430.4:c.1362_1369del	p.Met454IlefsTer3	p.M454Ifs*3	ENST00000257430	NM_000038.5	454	aTGAAACTT/a	11/16	0.474290476381285	1	FACETS	0.71	0.606	0.822	0.71	0.606	0.822	SUBCLONAL	1	FALSE	0	0.474290476381285	1		492	213	SUCCESS
APC	324	MSKCC	GRCh37	5	112175692	112175695	+	frameshift_variant	Frame_Shift_Del	DEL	TAAG	TAAG	-	novel	NA	P-0052737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	34	354	0	ENST00000257430.4:c.4401_4404del	p.Gln1469LeufsTer3	p.Q1469Lfs*3	ENST00000257430	NM_000038.5	1467	ccTAAG/cc	16/16	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	FALSE	1	0.474290476381285	2		354	139	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	122	460	0				ENST00000310581	NM_198253.2	-/1132			0.404713844783527	3	FACETS	0.891	0.819	0.963	0.891	0.819	0.963	CLONAL	2	TRUE	1	0.638565244922456	3		460	283	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0052738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	287	432	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.638565244922456	2	FACETS	0.942	0.9	0.984	0.942	0.9	0.984	CLONAL	2	TRUE	0	0.638565244922456	2		432	477	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457264	67457264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750707381	NA	P-0052738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	167	725	1	ENST00000327367.4:c.238C>T	p.Arg80Trp	p.R80W	ENST00000327367	NM_005902.3	80	Cgg/Tgg	2/9	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.638565244922456	2		726	519	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101131	41101131	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	189	726	0	ENST00000373198.4:c.1225C>T	p.Pro409Ser	p.P409S	ENST00000373198	NM_133170.3	409	Ccc/Tcc	8/32	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.638565244922456	2		726	517	SUCCESS
ATM	472	MSKCC	GRCh37	11	108213949	108213949	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs761625350	NA	P-0052738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	87	365	0	ENST00000278616.4:c.8269G>A	p.Val2757Met	p.V2757M	ENST00000278616	NM_000051.3	2757	Gtg/Atg	57/63	1	2	FACETS	0.888	0.794	0.985	0.888	0.794	0.985	CLONAL	1	TRUE	1	0.638565244922456	2		365	307	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458437	12458437	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530007199	NA	P-0052738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	182	689	1	ENST00000287820.6:c.1054G>A	p.Glu352Lys	p.E352K	ENST00000287820	NM_015869.4	352	Gag/Aag	6/7	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.638565244922456	2		690	568	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989689	68989689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1428676809	NA	P-0052738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	150	728	0	ENST00000288368.4:c.1627G>A	p.Gly543Arg	p.G543R	ENST00000288368	NM_024870.2	543	Gga/Aga	15/40	1	2	FACETS	0.854	0.785	0.926	0.854	0.785	0.926	CLONAL	1	TRUE	1	0.638565244922456	2		728	550	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165760	108165760	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	130	507	0	ENST00000278616.4:c.4883T>A	p.Met1628Lys	p.M1628K	ENST00000278616	NM_000051.3	1628	aTg/aAg	32/63	1	2	FACETS	0.925	0.846	1	0.925	0.846	1	CLONAL	1	TRUE	1	0.638565244922456	2		507	440	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197320	106197320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	99	502	0	ENST00000380013.4:c.5653C>T	p.Pro1885Ser	p.P1885S	ENST00000380013	NM_001127208.2	1885	Cct/Tct	11/11	1	2	FACETS	0.859	0.774	0.948	0.859	0.774	0.948	CLONAL	1	TRUE	1	0.638565244922456	2		502	361	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876541	35876541	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	145	630	0	ENST00000303115.3:c.1333C>T	p.Gln445Ter	p.Q445*	ENST00000303115	NM_002185.3	445	Caa/Taa	8/8	0.404713844783527	3	FACETS	1	0.954	1	0.53	0.486	0.576	CLONAL	1	TRUE	1	0.638565244922456	3		630	565	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133725	55133725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	127	579	0	ENST00000257290.5:c.938G>A	p.Gly313Asp	p.G313D	ENST00000257290	NM_006206.4	313	gGt/gAt	7/23	1	2	FACETS	0.936	0.855	1	0.936	0.855	1	CLONAL	1	TRUE	1	0.638565244922456	2		579	425	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0052739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	92	540	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.172917506224295	3	FACETS	0.838	0.747	0.935	0.838	0.747	0.935	CLONAL	2	TRUE	1	0.23	3		540	532	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0052739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	53	699	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.23	2		699	427	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249155	10249155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765098980	NA	P-0052739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	47	676	1	ENST00000340748.4:c.4027G>A	p.Val1343Met	p.V1343M	ENST00000340748		1343	Gtg/Atg	34/40	1	2	FACETS	0.894	0.755	1	0.894	0.755	1	CLONAL	1	TRUE	1	0.23	2		677	457	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986928	36986928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	25	412	0	ENST00000354822.5:c.761C>T	p.Ala254Val	p.A254V	ENST00000354822	NM_001079668.2	254	gCg/gTg	3/3	1	2	FACETS	0.651	0.513	0.809	0.651	0.513	0.809	SUBCLONAL	1	TRUE	1	0.23	2		412	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0052740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	571	479	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.0710466748715608	3	FACETS	0.972	0.956	0.987			1	INDETERMINATE	3	TRUE	NA	0.891244115510132	3		479	635	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874274	155874274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1185965337	NA	P-0052740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	615	513	2	ENST00000368323.3:c.257G>A	p.Arg86Gln	p.R86Q	ENST00000368323	NM_006912.5	86	cGg/cAg	5/6	0.353040509800181	5	FACETS	1	0.989	1			1	INDETERMINATE	3	TRUE	NA	0.891244115510132	5		515	1030	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851294	156851294	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	577	652	0	ENST00000524377.1:c.2251G>T	p.Ala751Ser	p.A751S	ENST00000524377	NM_002529.3	751	Gcc/Tcc	17/17	0.362673865557737	3	FACETS	0.996	0.965	1	0.996	0.965	1	INDETERMINATE	2	TRUE	1	0.891244115510132	3		652	940	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405421	70405421	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	307	609	0	ENST00000373644.4:c.2935A>G	p.Asn979Asp	p.N979D	ENST00000373644	NM_030625.2	979	Aac/Gac	4/12	NA	2	FACETS	1	0.962	1			1	INDETERMINATE	1	TRUE	NA	0.891244115510132	2		609	679	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432373	432373	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0052740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	147	123	0	ENST00000399788.2:c.2151-1G>C		p.X717_splice	ENST00000399788	NM_001042603.1	717			0.874020758213783	3	FACETS	1	0.967	1			1	CLONAL	2	TRUE	NA	0.891244115510132	3		123	229	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257758	133257758	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	571	550	0	ENST00000320574.5:c.170G>T	p.Gly57Val	p.G57V	ENST00000320574	NM_006231.2	57	gGt/gTt	2/49	0.794361402232519	3	FACETS	0.952	0.921	0.982	0.952	0.921	0.982	CLONAL	2	TRUE	1	0.891244115510132	3		550	973	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782924	66782924	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1199306921	NA	P-0052740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	181	421	0	ENST00000307102.5:c.1153A>C	p.Ser385Arg	p.S385R	ENST00000307102	NM_002755.3	385	Agc/Cgc	11/11	1	2	FACETS	0.768	0.713	0.823	0.768	0.713	0.823	SUBCLONAL	1	TRUE	1	0.891244115510132	2		421	529	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420314	88420314	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	165	445	0	ENST00000360948.2:c.2372G>T	p.Arg791Leu	p.R791L	ENST00000360948	NM_001012338.2	791	cGg/cTg	19/19	1	2	FACETS	0.947	0.881	1	0.947	0.881	1	CLONAL	1	TRUE	1	0.891244115510132	2		445	391	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223789	2223789	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	319	580	0	ENST00000326181.6:c.1087G>T	p.Asp363Tyr	p.D363Y	ENST00000326181	NM_032271.2	363	Gac/Tac	12/21	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.891244115510132	2		580	695	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925191	81925191	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	229	464	0	ENST00000359376.3:c.982A>T	p.Asn328Tyr	p.N328Y	ENST00000359376	NM_002661.3	328	Aac/Tac	11/33	0.891244115510132	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.891244115510132	1		464	272	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390432	56390432	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	207	356	0	ENST00000348428.3:c.1171A>T	p.Met391Leu	p.M391L	ENST00000348428	NM_006785.3	391	Atg/Ttg	10/17	0.449695537330235	4	FACETS	1	0.988	1	0.425	0.396	0.455	INDETERMINATE	1	TRUE	1	0.891244115510132	4		356	689	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520152	9520152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201686986	NA	P-0052740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	233	492	0	ENST00000353224.5:c.2117C>T	p.Pro706Leu	p.P706L	ENST00000353224	NM_177990.2	706	cCg/cTg	10/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.891244115510132	2		492	516	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385152	41385152	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs751630191	NA	P-0052740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	338	585	0	ENST00000373198.4:c.809G>T	p.Arg270Leu	p.R270L	ENST00000373198	NM_133170.3	270	cGc/cTc	6/32	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.891244115510132	2		585	739	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456456	89456456	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	163	367	0	ENST00000336596.2:c.1632G>T	p.Met544Ile	p.M544I	ENST00000336596	NM_005233.5	544	atG/atT	8/17	0.891244115510132	1	FACETS	0.994	0.951	1	0.994	0.951	1	CLONAL	1	TRUE	0	0.891244115510132	1		367	204	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31504699	31504699	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1032572786	NA	P-0052740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	234	481	1	ENST00000344624.3:c.1631G>T	p.Arg544Leu	p.R544L	ENST00000344624		544	cGc/cTc	8/33	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.891244115510132	2		482	508	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751936	57751936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	146	543	1	ENST00000274289.3:c.1301C>T	p.Ala434Val	p.A434V	ENST00000274289	NM_006622.3	434	gCa/gTa	10/14	1	2	FACETS	0.531	0.486	0.578	0.531	0.486	0.578	SUBCLONAL	1	TRUE	1	0.891244115510132	2		544	617	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576525	67576525	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	168	442	0	ENST00000274335.5:c.804C>G	p.Phe268Leu	p.F268L	ENST00000274335		268	ttC/ttG	5/15	1	2	FACETS	0.935	0.871	1	0.935	0.871	1	CLONAL	1	TRUE	1	0.891244115510132	2		442	403	SUCCESS
APC	324	MSKCC	GRCh37	5	112177358	112177358	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0052740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	144	342	0	ENST00000257430.4:c.6067A>T	p.Arg2023Ter	p.R2023*	ENST00000257430	NM_000038.5	2023	Aga/Tga	16/16	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.891244115510132	2		342	322	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813546	32813546	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	213	405	0	ENST00000354258.4:c.2237A>G	p.Tyr746Cys	p.Y746C	ENST00000354258	NM_000593.5	746	tAc/tGc	11/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.891244115510132	2		405	462	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43749707	43749707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	167	449	0	ENST00000523873.1:c.560G>A	p.Cys187Tyr	p.C187Y	ENST00000523873		187	tGc/tAc	7/8	1	2	FACETS	0.578	0.533	0.625	0.578	0.533	0.625	SUBCLONAL	1	TRUE	1	0.891244115510132	2		449	648	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972955	68972955	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	167	466	0	ENST00000288368.4:c.1280G>C	p.Arg427Thr	p.R427T	ENST00000288368	NM_024870.2	427	aGg/aCg	11/40	0.224581088829074	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.891244115510132	0		466	399	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436651	8436651	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	214	459	0	ENST00000356435.5:c.4027G>T	p.Ala1343Ser	p.A1343S	ENST00000356435		1343	Gca/Tca	24/35	0.394473304386046	3	FACETS	1	0.982	1	0.566	0.529	0.604	INDETERMINATE	1	TRUE	1	0.891244115510132	3		459	613	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015040	37015040	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	282	537	0	ENST00000358127.4:c.364C>G	p.Arg122Gly	p.R122G	ENST00000358127	NM_001280556.1	122	Cgg/Ggg	3/10	0.224581088829074	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.891244115510132	0		537	625	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285753	87285753	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	219	612	0	ENST00000277120.3:c.90C>G	p.Phe30Leu	p.F30L	ENST00000277120		30	ttC/ttG	2/19	0.224581088829074	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.891244115510132	0		612	499	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933511	39933511	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	212	634	1	ENST00000378444.4:c.1088G>T	p.Arg363Met	p.R363M	ENST00000378444	NM_001123385.1	363	aGg/aTg	4/15	0.891244115510132	3	FACETS	0.694	0.645	0.745	0.347	0.322	0.373	SUBCLONAL	1	TRUE	1	0.891244115510132	3		635	991	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426823	47426823	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	383	398	0	ENST00000377045.4:c.1068G>T	p.Gln356His	p.Q356H	ENST00000377045	NM_001654.4	356	caG/caT	10/16	NA	2	FACETS	0.82	0.794	0.846			1	INDETERMINATE	2	TRUE	NA	0.891244115510132	2		398	524	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410971	63410971	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	125	659	0	ENST00000330258.3:c.2196G>T	p.Met732Ile	p.M732I	ENST00000330258	NM_152424.3	732	atG/atT	2/2	NA	2	FACETS	0.511	0.464	0.56			1	INDETERMINATE	1	TRUE	NA	0.891244115510132	2		659	549	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411069	63411069	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	139	573	0	ENST00000330258.3:c.2098C>A	p.Pro700Thr	p.P700T	ENST00000330258	NM_152424.3	700	Cct/Act	2/2	NA	2	FACETS	0.564	0.516	0.614			1	INDETERMINATE	1	TRUE	NA	0.891244115510132	2		573	553	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340908	70340908	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	145	566	1	ENST00000374080.3:c.641G>T	p.Gly214Val	p.G214V	ENST00000374080		214	gGc/gTc	5/45	0.429094802787056	3	FACETS	0.574	0.523	0.626	0.191	0.174	0.209	INDETERMINATE	1	TRUE	0	0.891244115510132	3		567	820	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343027	70343027	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	634	604	0	ENST00000374080.3:c.1568T>C	p.Met523Thr	p.M523T	ENST00000374080		523	aTg/aCg	11/45	0.429094802787056	3	FACETS	1	0.996	1	0.765	0.745	0.785	INDETERMINATE	2	TRUE	0	0.891244115510132	3		604	896	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937491	76937491	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	118	515	0	ENST00000373344.5:c.3257C>A	p.Ala1086Glu	p.A1086E	ENST00000373344	NM_000489.3	1086	gCa/gAa	9/35	0.344576490343239	3	FACETS	0.596	0.539	0.657	0.199	0.179	0.219	INDETERMINATE	1	TRUE	0	0.891244115510132	3		515	642	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0052815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	94	537	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.881495873014887	2		537	203	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427558	427558	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	145	280	0	ENST00000399788.2:c.2611T>C	p.Ser871Pro	p.S871P	ENST00000399788	NM_001042603.1	871	Tct/Cct	19/28	NA	2	FACETS	0.617	0.566	0.67			1	INDETERMINATE	1	TRUE	NA	0.881495873014887	2		280	533	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784668	43784672	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TGGAA	TGGAA	-	novel	NA	P-0052815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	131	267	1	ENST00000382044.4:c.8-6_8-2del		p.X3_splice	ENST00000382044	NM_001141980.1	3			1	2	FACETS	0.576	0.525	0.629	0.576	0.525	0.629	SUBCLONAL	1	TRUE	1	0.881495873014887	2		268	516	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0013582-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	107	532	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.3	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.14	3		532	674	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs967461896	NA	P-0013582-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	60	621	0	ENST00000269305.4:c.526T>A	p.Cys176Ser	p.C176S	ENST00000269305	NM_001126112.2	176	Tgc/Agc	5/11	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.14	2		621	771	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217556	142217557	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1268253442	NA	P-0013582-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	22	0	0	ENST00000350721.4:c.5440dup	p.Arg1814LysfsTer8	p.R1814Kfs*8	ENST00000350721	NM_001184.3	1814	aga/aAga	32/47	1	2	FACETS	0.538	0.415	0.682	0.538	0.415	0.682	SUBCLONAL	1	TRUE	1	0.14	2		0	584	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527665	157527668	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs1554237269	NA	P-0014189-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	314	502	0	ENST00000346085.5:c.5394_5397del	p.Phe1798LeufsTer52	p.F1798Lfs*52	ENST00000346085	NM_020732.3	1797	cTGTTt/ct	20/20	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		502	697	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916840	48916841	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs1566186125	NA	P-0014189-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	60	116	0	ENST00000267163.4:c.371_372del	p.Ile124ArgfsTer6	p.I124Rfs*6	ENST00000267163	NM_000321.2	124	ATa/a	3/27	0.3	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		116	67	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347762	89347762	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748736120	NA	P-0016049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	92	679	1	ENST00000301030.4:c.5188G>A	p.Asp1730Asn	p.D1730N	ENST00000301030	NM_001256183.1	1730	Gat/Aat	9/13	0.360506731702675	1	FACETS	0.805	0.717	0.897	0.805	0.717	0.897	CLONAL	1	TRUE	0	0.360506731702675	1		680	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0016731-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	544	727	3	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.81367215384808	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.81367215384808	1		730	636	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0016731-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	97	360	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.307472375695767	2	FACETS	0.828	0.748	0.91	0.414	0.374	0.455	INDETERMINATE	1	TRUE	0	0.81367215384808	2		360	288	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0016731-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	149	657	2	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.176125568356009	2	FACETS	0.703	0.646	0.762	0.351	0.323	0.381	INDETERMINATE	1	TRUE	0	0.81367215384808	2		659	521	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0016731-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	234	630	1	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.81367215384808	2		631	508	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278102	15278102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143939165	NA	P-0016731-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	387	945	0	ENST00000263388.2:c.5320G>A	p.Asp1774Asn	p.D1774N	ENST00000263388	NM_000435.2	1774	Gac/Aac	29/33	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.81367215384808	2		945	851	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514655	103514655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758046666	NA	P-0016731-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	176	460	0	ENST00000355739.4:c.1156C>T	p.Arg386Trp	p.R386W	ENST00000355739	NM_000123.3	386	Cgg/Tgg	8/15	0.295720647218366	3	FACETS	1	0.982	1	0.591	0.548	0.634	INDETERMINATE	1	TRUE	1	0.81367215384808	3		460	515	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39311679	39311679	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016731-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	312	766	0	ENST00000373001.3:c.980A>T	p.Tyr327Phe	p.Y327F	ENST00000373001	NM_022157.3	327	tAt/tTt	6/7	0.176125568356009	2	FACETS	1	0.994	1	0.665	0.634	0.695	INDETERMINATE	1	TRUE	0	0.81367215384808	2		766	577	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551933	150551933	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016731-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	369	536	0	ENST00000369026.2:c.74G>T	p.Ser25Ile	p.S25I	ENST00000369026	NM_021960.4	25	aGc/aTc	1/3	0.356631024846128	1	FACETS	0.824	0.79	0.858	0.824	0.79	0.858	INDETERMINATE	1	TRUE	0	0.81367215384808	1		536	653	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31939889	31939889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016731-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	289	893	2	ENST00000375333.2:c.116C>T	p.Ala39Val	p.A39V	ENST00000375333	NM_032454.1	39	gCc/gTc	1/8	0.307472375695767	2	FACETS	0.751	0.708	0.795	0.375	0.354	0.398	INDETERMINATE	1	TRUE	0	0.81367215384808	2		895	946	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579364	7579364	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	434	489	0	ENST00000269305.4:c.323del	p.Gly108ValfsTer15	p.G108Vfs*15	ENST00000269305	NM_001126112.2	108	gGt/gt	4/11	0.370638932998547	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.414265654696471	2		489	997	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559203	29559206	+	missense_variant,splice_region_variant	Missense_Mutation	ONP	CTTA	CTTA	TCAC	novel	NA	P-0016745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	115	364	0	ENST00000356175.3:c.3310_3313delinsTCAC	p.Leu1104_Lys1105delinsSerGln	p.L1104_K1105delinsSQ	ENST00000356175	NM_000267.3	1104	CTTAaa/TCACaa	25/57	0.39477516323192	4	FACETS	0.661	0.594	0.733			1	SUBCLONAL	1	TRUE	NA	0.414265654696471	4		364	1188	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554657	63554657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	73	230	0	ENST00000307078.5:c.82G>A	p.Gly28Arg	p.G28R	ENST00000307078	NM_004655.3	28	Ggg/Agg	2/11	0.414265654696471	6	FACETS	0.809	0.706	0.919	0.202	0.176	0.23	CLONAL	1	TRUE	2	0.414265654696471	6		230	797	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128016869	128016869	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	rs1464665144	NA	P-0016745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	133	334	1	ENST00000285398.2:c.2217+3G>A		p.X739_splice	ENST00000285398	NM_000122.1	739			0.414265654696471	2	FACETS	0.81	0.736	0.887	0.405	0.368	0.444	CLONAL	1	TRUE	0	0.414265654696471	2		335	793	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478058	138478058	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	232	465	0	ENST00000289153.2:c.128A>T	p.Gln43Leu	p.Q43L	ENST00000289153	NM_006219.2	43	cAg/cTg	1/22	0.18693623515243	3	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.414265654696471	3		465	1061	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504940	186504940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1204	194	216	0	ENST00000323963.5:c.796G>A	p.Asp266Asn	p.D266N	ENST00000323963		266	Gac/Aac	8/11	0.414265654696471	9	FACETS	0.821	0.757	0.887	0.182	0.168	0.197	CLONAL	2	TRUE	0	0.414265654696471	9		216	1398	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445213	29445213	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017592-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	93	505	0	ENST00000389048.3:c.3512T>G	p.Ile1171Ser	p.I1171S	ENST00000389048	NM_004304.4	1171	aTc/aGc	22/29	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.317118174609952	2		505	530	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947596	48947596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1566196458	NA	P-0017973-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	140	233	0	ENST00000267163.4:c.1183C>T	p.Gln395Ter	p.Q395*	ENST00000267163	NM_000321.2	395	Caa/Taa	12/27	0.821776949649471	2	FACETS	0.959	0.913	1	0.959	0.913	1	CLONAL	2	TRUE	0	0.824831339474514	2		233	177	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587781525	NA	P-0017973-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	826	511	0	ENST00000269305.4:c.842A>T	p.Asp281Val	p.D281V	ENST00000269305	NM_001126112.2	281	gAc/gTc	8/11	0.611670347937172	3	FACETS	1	0.996	1			1	CLONAL	3	TRUE	NA	0.824831339474514	3		511	919	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221211	1221211	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0017973-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	597	440	1	ENST00000326873.7:c.735-1G>T		p.X245_splice	ENST00000326873	NM_000455.4	245			0.81122097690938	3	FACETS	0.985	0.966	1	0.985	0.966	1	CLONAL	3	TRUE	0	0.824831339474514	3		441	692	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465025	120465025	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017973-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	293	335	1	ENST00000256646.2:c.5047G>T	p.Ala1683Ser	p.A1683S	ENST00000256646	NM_024408.3	1683	Gct/Tct	28/34	0.824941162243378	3	FACETS	0.912	0.869	0.955	0.912	0.869	0.955	CLONAL	2	TRUE	1	0.824831339474514	3		336	550	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636140	28636140	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769807030	NA	P-0017973-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	374	351	3	ENST00000241453.7:c.232G>A	p.Ala78Thr	p.A78T	ENST00000241453	NM_004119.2	78	Gct/Act	3/24	0.821776949649471	2	FACETS	0.997	0.97	1	0.997	0.97	1	CLONAL	2	TRUE	0	0.824831339474514	2		354	455	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264426	46264426	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017973-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1376	149	298	0	ENST00000371998.3:c.1473G>T	p.Lys491Asn	p.K491N	ENST00000371998		491	aaG/aaT	11/23	0.824831339474514	10	FACETS	1	0.926	1			1	CLONAL	1	TRUE	NA	0.824831339474514	10		298	1525	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295237	1295237	+	upstream_gene_variant	5'Flank	SNP	G	G	C	novel	NA	P-0017973-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	474	212	0				ENST00000310581	NM_198253.2	-/1132			0.801077687003732	4	FACETS	0.92	0.889	0.951	1	0.997	1	CLONAL	3	TRUE	2	0.824831339474514	4		212	760	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517530	176517530	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017973-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	567	605	0	ENST00000292408.4:c.232del	p.Arg78ValfsTer9	p.R78Vfs*9	ENST00000292408	NM_213647.1	77	ggC/gg	3/18	0.821776949649471	2	FACETS	0.986	0.964	1	0.986	0.964	1	CLONAL	2	TRUE	0	0.824831339474514	2		605	697	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70971001	70971001	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017973-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	472	518	1	ENST00000276594.2:c.1260G>T	p.Lys420Asn	p.K420N	ENST00000276594	NM_024504.3	420	aaG/aaT	6/8	0.801077687003732	4	FACETS	0.965	0.925	1	0.965	0.925	1	CLONAL	2	TRUE	2	0.824831339474514	4		519	1082	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090788	5090788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1443056014	NA	P-0017973-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	102	152	0	ENST00000381652.3:c.2936C>T	p.Thr979Met	p.T979M	ENST00000381652	NM_004972.3	979	aCg/aTg	22/25	0.66808144294239	4	FACETS	0.885	0.805	0.966	0.885	0.805	0.966	CLONAL	2	TRUE	2	0.824831339474514	4		152	255	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229249	123229249	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017973-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	208	207	0	ENST00000218089.9:c.3733A>G	p.Thr1245Ala	p.T1245A	ENST00000218089	NM_001042749.1	1245	Aca/Gca	34/35	0.824941162243378	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.824831339474514	2		207	250	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281155	15281155	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017973-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	288	590	0	ENST00000263388.2:c.5101G>C	p.Ala1701Pro	p.A1701P	ENST00000263388	NM_000435.2	1701	Gcg/Ccg	27/33	0.81122097690938	3	FACETS	1	0.953	1	0.338	0.318	0.358	CLONAL	1	TRUE	0	0.824831339474514	3		590	973	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018942-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	293	373	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.827100571850784	2		373	550	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0018942-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	402	622	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.827100571850784	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.827100571850784	1		622	527	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974744	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAGCAGCGCCCGCA	CCTCCAGCAGCGCCCGCA	-	novel	NA	P-0018942-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	166	378	0	ENST00000304494.5:c.83_100del	p.Val28_Glu33del	p.V28_E33del	ENST00000304494	NM_000077.4	28	gTGCGGGCGCTGCTGGAGGcg/gcg	1/3	0.827100571850784	1	FACETS	0.898	0.848	0.948	0.898	0.848	0.948	CLONAL	1	TRUE	0	0.827100571850784	1		378	262	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482870	67482870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018942-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	287	479	0	ENST00000327367.4:c.1274C>T	p.Ser425Phe	p.S425F	ENST00000327367	NM_005902.3	425	tCt/tTt	9/9	0.827100571850784	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.827100571850784	1		479	387	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593466	48593466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064796102	NA	P-0018942-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	207	397	1	ENST00000342988.3:c.1217C>T	p.Ala406Val	p.A406V	ENST00000342988	NM_005359.5	406	gCg/gTg	10/12	0.827100571850784	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.827100571850784	1		398	291	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479763	67479763	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs140880290	NA	P-0018942-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	361	592	0	ENST00000327367.4:c.1070A>G	p.Asn357Ser	p.N357S	ENST00000327367	NM_005902.3	357	aAc/aGc	8/9	0.827100571850784	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.827100571850784	1		592	449	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100085	157100085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1271802085	NA	P-0018942-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	13	38	1	ENST00000346085.5:c.1022C>T	p.Ala341Val	p.A341V	ENST00000346085	NM_020732.3	341	gCg/gTg	1/20	1	2	FACETS	0.443	0.322	0.583	0.443	0.322	0.583	SUBCLONAL	1	TRUE	1	0.827100571850784	2		39	71	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053354	37053355	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0018942-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	58	449	0	ENST00000231790.2:c.588+2dup		p.X196_splice	ENST00000231790	NM_000249.3	196			0.36654272277756	1	FACETS	0.171	0.147	0.198	0.171	0.147	0.198	INDETERMINATE	1	TRUE	0	0.827100571850784	1		449	480	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119789	70119789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778047936	NA	P-0019631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	303	619	1	ENST00000245479.2:c.791G>A	p.Arg264Lys	p.R264K	ENST00000245479	NM_000346.3	264	aGa/aAa	3/3	0.172011154963218	6	FACETS	1	0.98	1			1	INDETERMINATE	2	TRUE	NA	0.777798140695143	6		620	922	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808901	3808901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	311	657	0	ENST00000262367.5:c.3323C>T	p.Ser1108Leu	p.S1108L	ENST00000262367	NM_004380.2	1108	tCa/tTa	17/31	0.754239061447054	3	FACETS	0.967	0.912	1	0.483	0.456	0.512	CLONAL	1	TRUE	1	0.777798140695143	3		657	1149	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983361	15983361	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	205	412	0	ENST00000268712.3:c.3418C>T	p.Gln1140Ter	p.Q1140*	ENST00000268712	NM_006311.3	1140	Caa/Taa	26/46	0.777798140695143	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.777798140695143	1		412	290	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100093	157100120	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCGGCGGCGGCAGCAGCAGGAGGCG	GCGGCGGCGGCGGCAGCAGCAGGAGGCG	-	rs1554247989	NA	P-0019631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	47	44	0	ENST00000346085.5:c.1044_1071del	p.Ala349MetfsTer11	p.A349Mfs*11	ENST00000346085	NM_020732.3	344	GCGGCGGCGGCGGCAGCAGCAGGAGGCGgc/gc	1/20	NA	2	FACETS	1	0.942	1			1	INDETERMINATE	1	TRUE	NA	0.777798140695143	2		44	105	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912128	32912343	+	inframe_deletion	In_Frame_Del	DEL	TGAAGTGGGGTTTAGGGGCTTTTATTCTGCTCATGGCACAAAACTGAATGTTTCTACTGAAGCTCTGCAAAAAGCTGTGAAACTGTTTAGTGATATTGAGAATATTAGTGAGGAAACTTCTGCAGAGGTACATCCAATAAGTTTATCTTCAAGTAAATGTCATGATTCTGTTGTTTCAATGTTTAAGATAGAAAATCATAATGATAAAACTGTAAG	TGAAGTGGGGTTTAGGGGCTTTTATTCTGCTCATGGCACAAAACTGAATGTTTCTACTGAAGCTCTGCAAAAAGCTGTGAAACTGTTTAGTGATATTGAGAATATTAGTGAGGAAACTTCTGCAGAGGTACATCCAATAAGTTTATCTTCAAGTAAATGTCATGATTCTGTTGTTTCAATGTTTAAGATAGAAAATCATAATGATAAAACTGTAAG	-	novel	NA	P-0019631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	236	627	1	ENST00000380152.3:c.3640_3855del	p.Val1214_Glu1285del	p.V1214_E1285del	ENST00000380152		1212	aaTGAAGTGGGGTTTAGGGGCTTTTATTCTGCTCATGGCACAAAACTGAATGTTTCTACTGAAGCTCTGCAAAAAGCTGTGAAACTGTTTAGTGATATTGAGAATATTAGTGAGGAAACTTCTGCAGAGGTACATCCAATAAGTTTATCTTCAAGTAAATGTCATGATTCTGTTGTTTCAATGTTTAAGATAGAAAATCATAATGATAAAACTGTAAGt/aat	11/27	0.777798140695143	2	FACETS	0.759	0.71	0.808	0.379	0.355	0.404	SUBCLONAL	1	TRUE	0	0.777798140695143	2		628	800	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135262	2135262	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019631-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	325	717	0	ENST00000219476.3:c.4601T>C	p.Leu1534Pro	p.L1534P	ENST00000219476	NM_000548.3	1534	cTc/cCc	36/42	0.754239061447054	3	FACETS	0.993	0.938	1	0.496	0.469	0.525	CLONAL	1	TRUE	1	0.777798140695143	3		717	1169	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332607	153332607	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020503-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	116	399	0	ENST00000281708.4:c.349G>T	p.Glu117Ter	p.E117*	ENST00000281708	NM_033632.3	117	Gag/Tag	2/12	0.581941660585559	3	FACETS	1	0.927	1	0.514	0.465	0.564	CLONAL	1	TRUE	1	0.581941660585559	3		399	501	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578476	7578476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767328513	NA	P-0020503-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	454	962	0	ENST00000269305.4:c.454C>T	p.Pro152Ser	p.P152S	ENST00000269305	NM_001126112.2	152	Ccg/Tcg	5/11	0.581941660585559	2	FACETS	0.995	0.959	1	0.995	0.959	1	CLONAL	2	TRUE	0	0.581941660585559	2		962	784	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354425	354425	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548567255	NA	P-0020503-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	163	631	0	ENST00000262320.3:c.1133C>T	p.Pro378Leu	p.P378L	ENST00000262320	NM_003502.3	378	cCg/cTg	5/11	1	2	FACETS	0.956	0.882	1	0.956	0.882	1	CLONAL	1	TRUE	1	0.581941660585559	2		631	586	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949207	71949207	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020503-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	200	784	0	ENST00000298229.2:c.3674T>C	p.Leu1225Pro	p.L1225P	ENST00000298229	NM_001567.3	1225	cTg/cCg	27/28	1	2	FACETS	0.895	0.831	0.961	0.895	0.831	0.961	CLONAL	1	TRUE	1	0.581941660585559	2		784	768	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863698	68863698	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020503-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	111	365	0	ENST00000261769.5:c.2437G>T	p.Glu813Ter	p.E813*	ENST00000261769	NM_004360.3	813	Gaa/Taa	15/16	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.581941660585559	2		365	347	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218467	1218467	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020503-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	318	604	0	ENST00000326873.7:c.343del	p.Asp115MetfsTer14	p.D115Mfs*14	ENST00000326873	NM_000455.4	114	gtG/gt	2/10	0.581941660585559	2	FACETS	0.955	0.913	0.998	0.955	0.913	0.998	CLONAL	2	TRUE	0	0.581941660585559	2		604	572	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524492	187524492	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020503-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	154	622	0	ENST00000441802.2:c.11188A>T	p.Ile3730Leu	p.I3730L	ENST00000441802	NM_005245.3	3730	Ata/Tta	19/27	0.581941660585559	3	FACETS	0.953	0.874	1	0.476	0.437	0.518	CLONAL	1	TRUE	1	0.581941660585559	3		622	717	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946134	13946134	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020503-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	303	531	0	ENST00000405192.2:c.962T>C	p.Leu321Pro	p.L321P	ENST00000405192	NM_001163147.1	321	cTt/cCt	10/12	0.50113982077518	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.581941660585559	4		531	800	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866531	56866531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020503-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	221	722	1	ENST00000519728.1:c.778G>A	p.Glu260Lys	p.E260K	ENST00000519728	NM_002350.3	260	Gaa/Aaa	8/13	0.581941660585559	3	FACETS	1	0.938	1	0.504	0.469	0.54	CLONAL	1	TRUE	1	0.581941660585559	3		723	973	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727912	78727912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020503-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	172	649	0	ENST00000306801.3:c.757C>T	p.Pro253Ser	p.P253S	ENST00000306801	NM_020761.2	253	Ccc/Tcc	6/34	0.581941660585559	3	FACETS	1	0.948	1	0.518	0.477	0.56	CLONAL	1	TRUE	1	0.581941660585559	3		649	737	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734065	58734065	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020503-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	417	615	0	ENST00000305921.3:c.1123A>G	p.Ile375Val	p.I375V	ENST00000305921	NM_003620.3	375	Atc/Gtc	5/6	0.581941660585559	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.581941660585559	3		615	876	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911599	39911601	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0020503-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	172	307	0	ENST00000378444.4:c.5029_5031del	p.Ser1677del	p.S1677del	ENST00000378444	NM_001123385.1	1677	TCC/-	15/15	0.162779174100596	0	FACETS	0.841	0.791	0.889			1	INDETERMINATE	1	TRUE	NA	0.581941660585559	0		307	294	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	67	230	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.850815512451269	2		230	143	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313274	65313274	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	218	480	0	ENST00000342505.4:c.1840G>C	p.Glu614Gln	p.E614Q	ENST00000342505	NM_002227.2	614	Gag/Cag	13/25	1	2	FACETS	0.969	0.909	1	0.969	0.909	1	CLONAL	1	TRUE	1	0.850815512451269	2		480	529	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426235	49426235	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	306	799	0	ENST00000301067.7:c.12253C>T	p.Gln4085Ter	p.Q4085*	ENST00000301067	NM_003482.3	4085	Cag/Tag	39/54	1	2	FACETS	0.931	0.882	0.98	0.931	0.882	0.98	CLONAL	1	TRUE	1	0.850815512451269	2		799	773	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40681810	40681810	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs768877625	NA	P-0022605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	117	267	0	ENST00000249776.8:c.589C>G	p.Gln197Glu	p.Q197E	ENST00000249776	NM_033286.3	197	Cag/Gag	5/9	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.850815512451269	2		267	268	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832898	3832898	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	173	390	0	ENST00000262367.5:c.1360C>T	p.Gln454Ter	p.Q454*	ENST00000262367	NM_004380.2	454	Caa/Taa	6/31	1	2	FACETS	0.939	0.874	1	0.939	0.874	1	CLONAL	1	TRUE	1	0.850815512451269	2		390	433	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368369	225368370	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	139	250	0	ENST00000264414.4:c.1376dup	p.Thr460AspfsTer2	p.T460Dfs*2	ENST00000264414	NM_003590.4	459	aag/aaAg	9/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.850815512451269	2		250	288	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269112	142269112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	36	304	0	ENST00000350721.4:c.2838G>A	p.Met946Ile	p.M946I	ENST00000350721	NM_001184.3	946	atG/atA	14/47	1	2	FACETS	0.193	0.158	0.232	0.193	0.158	0.232	SUBCLONAL	1	TRUE	1	0.850815512451269	2		304	438	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0022605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	151	356	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.97	0.899	1	0.97	0.899	1	CLONAL	1	TRUE	1	0.850815512451269	2		356	366	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0022605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	177	520	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.861	0.801	0.923	0.861	0.801	0.923	CLONAL	1	TRUE	1	0.850815512451269	2		520	483	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652225	36652226	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	291	780	0	ENST00000244741.5:c.349dup	p.Cys117LeufsTer12	p.C117Lfs*12	ENST00000244741	NM_000389.4	116	tct/tcTt	2/3	1	2	FACETS	0.877	0.829	0.926	0.877	0.829	0.926	CLONAL	1	TRUE	1	0.850815512451269	2		780	780	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913381	NA	P-0022605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	147	274	0	ENST00000304494.5:c.322G>T	p.Asp108Tyr	p.D108Y	ENST00000304494	NM_000077.4	108	Gat/Tat	2/3	0.850815512451269	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.850815512451269	1		274	186	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922932	44922947	+	frameshift_variant	Frame_Shift_Del	DEL	TAACAGGAAGTGGAAG	TAACAGGAAGTGGAAG	-	novel	NA	P-0022605-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	202	256	0	ENST00000377967.4:c.1796_1811del	p.Thr599MetfsTer21	p.T599Mfs*21	ENST00000377967	NM_021140.2	598	aTAACAGGAAGTGGAAGt/at	16/29	1	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.850815512451269	1		256	264	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657336	29657362	+	inframe_deletion	In_Frame_Del	DEL	TGTGCCTTAACTTGTACCTTTAATTTA	TGTGCCTTAACTTGTACCTTTAATTTA	-	novel	NA	P-0026733-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	104	483	0	ENST00000356175.3:c.5569_5595del	p.Cys1857_Leu1865del	p.C1857_L1865del	ENST00000356175	NM_000267.3	1857	TGTGCCTTAACTTGTACCTTTAATTTA/-	38/57	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.260605380653845	2		483	736	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0026772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	202	407	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.287686191502537	5	FACETS	1	0.984	1	0.789	0.735	0.845	CLONAL	2	TRUE	2	0.41289264810754	5		408	669	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0026772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	96	396	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.411366258308798	3	FACETS	0.948	0.846	1	0.474	0.423	0.528	CLONAL	1	TRUE	1	0.41289264810754	3		396	592	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923211	26923211	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	123	213	0	ENST00000381527.3:c.207A>C	p.Leu69Phe	p.L69F	ENST00000381527	NM_001260.1	69	ttA/ttC	3/13	0.41289264810754	5	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	3	0.41289264810754	5		213	389	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634343	23634343	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	343	629	0	ENST00000261584.4:c.2943del	p.Ser981ArgfsTer9	p.S981Rfs*9	ENST00000261584	NM_024675.3	981	agT/ag	9/13	0.411366258308798	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.41289264810754	3		629	927	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214586	5214586	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0026772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	194	556	0	ENST00000357368.4:c.4480G>T	p.Glu1494Ter	p.E1494*	ENST00000357368	NM_002850.3	1494	Gag/Tag	29/38	0.279231611909987	3	FACETS	1	0.991	1	0.745	0.691	0.801	CLONAL	1	TRUE	1	0.41289264810754	3		556	761	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408896	41408896	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	197	477	0	ENST00000373198.4:c.530T>A	p.Ile177Asn	p.I177N	ENST00000373198	NM_133170.3	177	aTc/aAc	4/32	0.41289264810754	8	FACETS	0.96	0.888	1	0.32	0.296	0.345	CLONAL	2	TRUE	2	0.41289264810754	8		477	1113	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294258	1294258	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	192	575	0	ENST00000310581.5:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000310581	NM_198253.2	248	cGg/cAg	2/16	0.207595469222414	4	FACETS	1	0.99	1	0.494	0.457	0.533	INDETERMINATE	1	TRUE	1	0.41289264810754	4		575	886	SUCCESS
APC	324	MSKCC	GRCh37	5	112175437	112175438	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATGTTTAGCAGATGTACTT	novel	NA	P-0026772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	79	228	0	ENST00000257430.4:c.4147_4165dup	p.Ser1389TyrfsTer3	p.S1389Yfs*3	ENST00000257430	NM_000038.5	1382	-/ATGTTTAGCAGATGTACTT	16/16	0.411366258308798	3	FACETS	0.782	0.696	0.874	0.782	0.696	0.874	SUBCLONAL	2	TRUE	1	0.41289264810754	3		228	295	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976648	90976648	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	27	396	0	ENST00000265433.3:c.984T>A	p.His328Gln	p.H328Q	ENST00000265433	NM_002485.4	328	caT/caA	8/16	0.287686191502537	5	FACETS	0.423	0.335	0.523	0.141	0.111	0.175	SUBCLONAL	1	TRUE	2	0.41289264810754	5		396	501	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339575	70339575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266838743	NA	P-0026772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	310	543	0	ENST00000374080.3:c.244C>T	p.Arg82Cys	p.R82C	ENST00000374080		82	Cgt/Tgt	3/45	0.18624787144812	6	FACETS	1	0.97	1	1	0.97	1	INDETERMINATE	3	TRUE	3	0.41289264810754	6		543	881	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0027083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	273	515	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	0.93	0.875	0.986	0.93	0.875	0.986	CLONAL	1	TRUE	1	0.677790229335219	2		515	866	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280598	115280598	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	296	470	0	ENST00000438362.2:c.433C>T	p.Arg145Ter	p.R145*	ENST00000438362	NM_001242891.1	145	Cga/Tga	4/20	0.677790229335219	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.677790229335219	1		470	576	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0027087-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	121	507	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.303351863911238	4	FACETS	0.898	0.816	0.984	0.898	0.816	0.984	CLONAL	2	TRUE	2	0.387922464461512	4		507	482	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0027087-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	14	318	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.387922464461512	1	FACETS	0.217	0.156	0.291	0.217	0.156	0.291	SUBCLONAL	1	TRUE	0	0.387922464461512	1		318	268	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0027087-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	9	356	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.340707714943436	3	FACETS	0.281	0.186	0.403	0.094	0.062	0.135	SUBCLONAL	1	TRUE	0	0.387922464461512	3		356	197	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133208934	133208934	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027087-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	37	520	0	ENST00000320574.5:c.6297C>G	p.Asn2099Lys	p.N2099K	ENST00000320574	NM_006231.2	2099	aaC/aaG	45/49	0.387922464461512	1	FACETS	0.45	0.371	0.537	0.45	0.371	0.537	SUBCLONAL	1	TRUE	0	0.387922464461512	1		520	342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578383	7578384	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0027087-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	151	531	0	ENST00000269305.4:c.546dup	p.Ser183LeufsTer3	p.S183Lfs*3	ENST00000269305	NM_001126112.2	182	-/C	5/11	0.384496047176777	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.387922464461512	2		531	363	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866689	37866689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149210045	NA	P-0027087-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	39	599	1	ENST00000269571.5:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269571		286	Gag/Aag	7/27	0.384496047176777	2	FACETS	0.449	0.372	0.535	0.224	0.186	0.268	SUBCLONAL	1	TRUE	0	0.387922464461512	2		600	448	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212430	5212431	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTCGGGCACGCCATGG	novel	NA	P-0027087-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	37	642	0	ENST00000357368.4:c.4671_4686dup	p.Tyr1563ProfsTer50	p.Y1563Pfs*50	ENST00000357368	NM_002850.3	1562	-/CCATGGCGTGCCCGAA	31/38	0.387922464461512	1	FACETS	0.388	0.32	0.464	0.388	0.32	0.464	SUBCLONAL	1	TRUE	0	0.387922464461512	1		642	396	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577121	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCA	novel	NA	P-0027532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	471	484	0	ENST00000269305.4:c.815_817dup	p.Val272_Arg273insLeu	p.V272_R273insL	ENST00000269305	NM_001126112.2	273	cgt/cTGCgt	8/11	0.408805049347384	4	FACETS	0.992	0.956	1			1	CLONAL	4	TRUE	NA	0.408805049347384	4		484	818	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46603863	46603863	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	80	503	0	ENST00000263734.3:c.1220C>G	p.Pro407Arg	p.P407R	ENST00000263734	NM_001430.4	407	cCa/cGa	9/16	0.344941867885288	3	FACETS	0.816	0.719	0.919	0.272	0.239	0.307	CLONAL	1	TRUE	0	0.408805049347384	3		503	578	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714198	43714198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28903076	NA	P-0028971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	414	990	0	ENST00000382044.4:c.3955C>T	p.Arg1319Cys	p.R1319C	ENST00000382044	NM_001141980.1	1319	Cgc/Tgc	19/28	0.094067053185614	6	FACETS	0.954	0.912	0.995	0.954	0.912	0.995	INDETERMINATE	3	FALSE	3	0.821874248618216	6		990	931	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714198	43714198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28903076	NA	P-0028971-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	349	990	0	ENST00000382044.4:c.3955C>T	p.Arg1319Cys	p.R1319C	ENST00000382044	NM_001141980.1	1319	Cgc/Tgc	19/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.666415036044486	2		990	984	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356748	70356748	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028971-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1403	120	773	0	ENST00000374080.3:c.5420G>T	p.Gly1807Val	p.G1807V	ENST00000374080		1807	gGt/gTt	38/45	0.666415036044486	5	FACETS	0.473	0.425	0.524	0.118	0.106	0.131	SUBCLONAL	1	TRUE	1	0.666415036044486	5		773	1523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577113	7577113	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0029931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	111	479	0	ENST00000269305.4:c.825T>A	p.Cys275Ter	p.C275*	ENST00000269305	NM_001126112.2	275	tgT/tgA	8/11	0.208090158150259	3	FACETS	0.913	0.822	1	0.913	0.822	1	CLONAL	2	TRUE	1	0.208090158150259	3		479	645	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312924	30312924	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	54	447	0	ENST00000262643.3:c.727C>A	p.Pro243Thr	p.P243T	ENST00000262643	NM_001238.2	243	Ccc/Acc	9/12	0.208090158150259	10	FACETS	1	0.915	1			1	CLONAL	1	TRUE	NA	0.208090158150259	10		447	856	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965571	25965571	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0029931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	51	463	0	ENST00000435504.4:c.3635C>G	p.Ser1212Ter	p.S1212*	ENST00000435504		1212	tCa/tGa	13/13	0.208090158150259	5	FACETS	0.95	0.806	1	0.317	0.268	0.37	CLONAL	1	TRUE	2	0.208090158150259	5		463	677	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	115	435	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.545587015470547	2		436	406	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	139	805	4	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.628	0.571	0.686	0.628	0.571	0.686	SUBCLONAL	1	TRUE	1	0.545587015470547	2		809	812	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	424	713	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.987	1	1	0.997	1	CLONAL	2	TRUE	1	0.545587015470547	2		715	735	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	167	430	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.821	0.765	0.877	1	0.992	1	CLONAL	2	TRUE	1	0.545587015470547	2		434	373	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591246	67591246	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	42	292	0	ENST00000274335.5:c.1746-2A>G		p.X582_splice	ENST00000274335		582			1	2	FACETS	0.664	0.559	0.778	0.664	0.559	0.778	SUBCLONAL	1	TRUE	1	0.545587015470547	2		292	232	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	169	558	3	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.545587015470547	2		561	619	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	109	431	28	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	1	2	FACETS	0.826	0.756	0.895	1	0.988	1	CLONAL	2	TRUE	1	0.545587015470547	2		459	242	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913837	32913837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359507	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	10	417	1	ENST00000380152.3:c.5351del	p.Asn1784ThrfsTer7	p.N1784Tfs*7	ENST00000380152		1782	cAa/ca	11/27	1	2	FACETS	0.205	0.138	0.288	0.205	0.138	0.288	SUBCLONAL	1	TRUE	1	0.545587015470547	2		418	179	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	44	183	2	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	1	FACETS	0.986	0.849	1	0.986	0.849	1	CLONAL	1	TRUE	0	0.545587015470547	1		185	119	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	216	752	2	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.545587015470547	2		754	755	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089706	27089706	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	185	612	0	ENST00000324856.7:c.2666del	p.Gly889AlafsTer2	p.G889Afs*2	ENST00000324856	NM_006015.4	888	Ggg/gg	8/20	1	2	FACETS	0.997	0.924	1	0.997	0.924	1	CLONAL	1	TRUE	1	0.545587015470547	2		612	680	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	58	316	0	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.545587015470547	2		316	210	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	201	737	13	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.95	0.882	1	0.95	0.882	1	CLONAL	1	TRUE	1	0.545587015470547	2		750	776	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042242	6042242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs114090343	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	199	513	0	ENST00000265849.7:c.379G>A	p.Ala127Thr	p.A127T	ENST00000265849	NM_000535.5	127	Gca/Aca	5/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.545587015470547	2		513	673	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053022	180053023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750808726	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	157	746	2	ENST00000261937.6:c.1267dup	p.Gln423ProfsTer4	p.Q423Pfs*4	ENST00000261937	NM_182925.4	423	cag/cCag	10/30	1	2	FACETS	0.786	0.722	0.854	0.786	0.722	0.854	SUBCLONAL	1	TRUE	1	0.545587015470547	2		748	732	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164805	36164805	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	72	769	0	ENST00000300305.3:c.1070del	p.Pro357ArgfsTer237	p.P357Rfs*237	ENST00000300305		357	cCg/cg	8/8	1	2	FACETS	0.274	0.238	0.312	0.274	0.238	0.312	SUBCLONAL	1	TRUE	1	0.545587015470547	2		769	965	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	61	308	1	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.545587015470547	2		309	205	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28934577	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	218	603	0	ENST00000269305.4:c.770T>C	p.Leu257Pro	p.L257P	ENST00000269305	NM_001126112.2	257	cTg/cCg	7/11	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.545587015470547	2		603	711	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	201	630	7	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.545587015470547	2		637	715	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202491	67202491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375129435	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	77	820	3	ENST00000312629.5:c.1300C>T	p.Arg434Trp	p.R434W	ENST00000312629	NM_003952.2	434	Cgg/Tgg	15/15	1	2	FACETS	0.347	0.304	0.394	0.347	0.304	0.394	SUBCLONAL	1	TRUE	1	0.545587015470547	2		823	813	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795103	242795104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768249210	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	169	833	3	ENST00000334409.5:c.105dup	p.Thr36HisfsTer70	p.T36Hfs*70	ENST00000334409	NM_005018.2	35	-/C	2/5	1	2	FACETS	0.777	0.716	0.842	0.777	0.716	0.842	SUBCLONAL	1	TRUE	1	0.545587015470547	2		836	797	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821890	72821890	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	118	395	0	ENST00000268489.5:c.10285del	p.Arg3429ValfsTer56	p.R3429Vfs*56	ENST00000268489	NM_006885.3	3429	Cgt/gt	10/10	1	2	FACETS	0.981	0.891	1	0.981	0.891	1	CLONAL	1	TRUE	1	0.545587015470547	2		395	441	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971138	21971138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760640852	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	236	472	0	ENST00000304494.5:c.220G>A	p.Asp74Asn	p.D74N	ENST00000304494	NM_000077.4	74	Gac/Aac	2/3	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.545587015470547	2		472	673	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141587	202141587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771150445	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	89	309	1	ENST00000358485.4:c.875G>A	p.Arg292Gln	p.R292Q	ENST00000358485	NM_001080125.1	292	cGg/cAg	7/9	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.545587015470547	2		310	320	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793008	33793010	+	inframe_deletion	In_Frame_Del	DEL	CGC	CGC	-	rs780345232	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	30	95	2	ENST00000498907.2:c.311_313del	p.Gly104del	p.G104del	ENST00000498907	NM_004364.3	104	gGCGac/gac	1/1	0.503301483138926	3	FACETS	0.946	0.773	1	0.473	0.386	0.568	CLONAL	1	TRUE	1	0.545587015470547	3		97	148	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120326	94120326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370195460	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	23	266	1	ENST00000369303.4:c.725C>T	p.Ala242Val	p.A242V	ENST00000369303	NM_004440.3	242	gCg/gTg	3/17	1	2	FACETS	0.34	0.266	0.426	0.34	0.266	0.426	SUBCLONAL	1	TRUE	1	0.545587015470547	2		267	248	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971012	21971012	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1477500164	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	98	544	0	ENST00000304494.5:c.346G>T	p.Asp116Tyr	p.D116Y	ENST00000304494	NM_000077.4	116	Gac/Tac	2/3	1	2	FACETS	0.459	0.409	0.513	0.459	0.409	0.513	SUBCLONAL	1	TRUE	1	0.545587015470547	2		544	782	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926270	112926270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918457	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	143	467	0	ENST00000351677.2:c.1403C>T	p.Thr468Met	p.T468M	ENST00000351677	NM_002834.3	468	aCg/aTg	12/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.545587015470547	2		467	439	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217557	142217557	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1268253442	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	60	402	0	ENST00000350721.4:c.5440del	p.Arg1814GlufsTer10	p.R1814Efs*10	ENST00000350721	NM_001184.3	1814	Aga/ga	32/47	1	2	FACETS	0.898	0.782	1	0.898	0.782	1	CLONAL	1	TRUE	1	0.545587015470547	2		402	245	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625219	69625219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	244	813	1	ENST00000334134.2:c.574C>T	p.Arg192Trp	p.R192W	ENST00000334134	NM_005247.2	192	Cgg/Tgg	3/3	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.545587015470547	2		814	780	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139794896	139794896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	182	478	0	ENST00000247668.2:c.290G>A	p.Arg97His	p.R97H	ENST00000247668	NM_021138.3	97	cGc/cAc	4/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.545587015470547	2		478	616	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822586	72822586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	154	574	5	ENST00000268489.5:c.9589del	p.Gln3197SerfsTer44	p.Q3197Sfs*44	ENST00000268489	NM_006885.3	3197	Cag/ag	10/10	1	2	FACETS	0.944	0.868	1	0.944	0.868	1	CLONAL	1	TRUE	1	0.545587015470547	2		579	598	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176666775	176666775	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776547552	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	53	279	0	ENST00000439151.2:c.4211G>A	p.Arg1404His	p.R1404H	ENST00000439151	NM_022455.4	1404	cGt/cAt	8/23	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.545587015470547	2		279	189	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947119	178947119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199943173	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	59	286	0	ENST00000263967.3:c.2555G>A	p.Arg852Gln	p.R852Q	ENST00000263967	NM_006218.2	852	cGa/cAa	18/21	1	2	FACETS	0.801	0.696	0.914	0.801	0.696	0.914	CLONAL	1	TRUE	1	0.545587015470547	2		286	270	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504347	149504347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	146	718	0	ENST00000261799.4:c.1855G>A	p.Ala619Thr	p.A619T	ENST00000261799	NM_002609.3	619	Gct/Act	13/23	1	2	FACETS	0.726	0.664	0.791	0.726	0.664	0.791	SUBCLONAL	1	TRUE	1	0.545587015470547	2		718	737	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039405	47039405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	60	324	0	ENST00000377604.3:c.1028G>A	p.Arg343His	p.R343H	ENST00000377604	NM_001204468.1	343	cGc/cAc	10/24	1	1	FACETS	0.457	0.396	0.523	0.457	0.396	0.523	SUBCLONAL	1	TRUE	0	0.545587015470547	1		324	350	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047888	180047888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	178	846	0	ENST00000261937.6:c.2287G>A	p.Val763Met	p.V763M	ENST00000261937	NM_182925.4	763	Gtg/Atg	15/30	1	2	FACETS	0.871	0.805	0.94	0.871	0.805	0.94	CLONAL	1	TRUE	1	0.545587015470547	2		846	749	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992720	68992720	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs182978151	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	66	468	0	ENST00000288368.4:c.1685G>A	p.Arg562His	p.R562H	ENST00000288368	NM_024870.2	562	cGt/cAt	16/40	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.545587015470547	2		468	230	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649712	48649712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149753411	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	46	375	1	ENST00000376670.3:c.196G>A	p.Ala66Thr	p.A66T	ENST00000376670	NM_002049.3	66	Gct/Act	2/6	1	1	FACETS	0.323	0.272	0.378	0.323	0.272	0.378	SUBCLONAL	1	TRUE	0	0.545587015470547	1		376	380	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214871	36214871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	373	756	12	ENST00000222270.7:c.3302del	p.Pro1101LeufsTer81	p.P1101Lfs*81	ENST00000222270	NM_014727.1	1099	ggC/gg	8/37	0.503301483138926	3	FACETS	0.893	0.85	0.937	0.893	0.85	0.937	CLONAL	2	TRUE	1	0.545587015470547	3		768	974	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24134057	24134057	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	50	382	0	ENST00000263121.7:c.214del	p.Thr72GlnfsTer13	p.T72Qfs*13	ENST00000263121	NM_003073.3	70	Aaa/aa	2/9	1	2	FACETS	0.549	0.468	0.637	0.549	0.468	0.637	SUBCLONAL	1	TRUE	1	0.545587015470547	2		382	334	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937723	44937723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	86	232	0	ENST00000377967.4:c.2911C>T	p.Arg971Cys	p.R971C	ENST00000377967	NM_021140.2	971	Cgt/Tgt	19/29	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.545587015470547	1		232	153	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942193	71942193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749091098	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	227	706	0	ENST00000298229.2:c.1457G>A	p.Arg486His	p.R486H	ENST00000298229	NM_001567.3	486	cGc/cAc	12/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.545587015470547	2		706	760	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707977	43707977	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	197	649	1	ENST00000382044.4:c.4904G>A	p.Arg1635His	p.R1635H	ENST00000382044	NM_001141980.1	1635	cGc/cAc	23/28	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.545587015470547	2		650	703	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940571	71940571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760513714	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	56	647	0	ENST00000298229.2:c.722C>T	p.Ser241Leu	p.S241L	ENST00000298229	NM_001567.3	241	tCg/tTg	6/28	1	2	FACETS	0.298	0.255	0.346	0.298	0.255	0.346	SUBCLONAL	1	TRUE	1	0.545587015470547	2		647	688	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731545	47731545	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	11	42	0	ENST00000449228.1:c.247del	p.Arg83AlafsTer146	p.R83Afs*146	ENST00000449228	NM_001127240.2	83	Cgc/gc	2/4	0.503301483138926	3	FACETS	0.513	0.358	0.702	0.257	0.179	0.351	SUBCLONAL	1	TRUE	1	0.545587015470547	3		42	100	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210725	36210725	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	269	759	1	ENST00000222270.7:c.481del	p.Leu161PhefsTer6	p.L161Ffs*6	ENST00000222270	NM_014727.1	159	aCc/ac	3/37	0.503301483138926	3	FACETS	1	0.99	1	0.637	0.598	0.677	CLONAL	1	TRUE	1	0.545587015470547	3		760	985	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675607	86675607	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	30	282	0	ENST00000274376.6:c.2543T>C	p.Leu848Pro	p.L848P	ENST00000274376	NM_002890.2	848	cTa/cCa	19/25	1	2	FACETS	0.71	0.579	0.853	0.71	0.579	0.853	SUBCLONAL	1	TRUE	1	0.545587015470547	2		282	155	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629475	187629475	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765412973	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	37	560	0	ENST00000441802.2:c.1507G>A	p.Ala503Thr	p.A503T	ENST00000441802	NM_005245.3	503	Gca/Aca	2/27	1	2	FACETS	0.269	0.221	0.322	0.269	0.221	0.322	SUBCLONAL	1	TRUE	1	0.545587015470547	2		560	505	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993366	72993366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140855443	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	193	693	1	ENST00000268489.5:c.679G>A	p.Val227Ile	p.V227I	ENST00000268489	NM_006885.3	227	Gtc/Atc	2/10	1	2	FACETS	0.884	0.82	0.951	0.884	0.82	0.951	CLONAL	1	TRUE	1	0.545587015470547	2		694	800	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976742	2976742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1225008718	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	193	648	0	ENST00000396946.4:c.1270C>T	p.Arg424Trp	p.R424W	ENST00000396946	NM_032415.4	424	Cgg/Tgg	9/25	1	2	FACETS	0.955	0.886	1	0.955	0.886	1	CLONAL	1	TRUE	1	0.545587015470547	2		648	741	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540974	187540974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752611276	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	108	351	0	ENST00000441802.2:c.6766G>A	p.Ala2256Thr	p.A2256T	ENST00000441802	NM_005245.3	2256	Gca/Aca	10/27	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.545587015470547	2		351	331	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395158	139395158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554826860	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	280	843	1	ENST00000277541.6:c.5780C>T	p.Thr1927Met	p.T1927M	ENST00000277541	NM_017617.3	1927	aCg/aTg	31/34	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.545587015470547	2		844	881	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876974	151876974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750213944	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	63	333	2	ENST00000262189.6:c.7387C>T	p.Arg2463Cys	p.R2463C	ENST00000262189	NM_170606.2	2463	Cgt/Tgt	37/59	1	2	FACETS	0.767	0.669	0.872	0.767	0.669	0.872	SUBCLONAL	1	TRUE	1	0.545587015470547	2		335	301	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716081	52716081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	131	629	4	ENST00000322088.6:c.646G>A	p.Glu216Lys	p.E216K	ENST00000322088	NM_014225.5	216	Gag/Aag	5/15	0.503301483138926	3	FACETS	0.749	0.68	0.822	0.375	0.34	0.411	SUBCLONAL	1	TRUE	1	0.545587015470547	3		633	816	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867316	45867316	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	68	760	0	ENST00000391945.4:c.877C>T	p.Arg293Trp	p.R293W	ENST00000391945	NM_000400.3	293	Cgg/Tgg	10/23	0.503301483138926	3	FACETS	0.329	0.286	0.377	0.165	0.143	0.189	SUBCLONAL	1	TRUE	1	0.545587015470547	3		760	963	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177585	56177585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768180463	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	94	375	0	ENST00000399503.3:c.2558G>A	p.Arg853His	p.R853H	ENST00000399503	NM_005921.1	853	cGt/cAt	14/20	0.122814333729992	6	FACETS	1	0.943	1			1	INDETERMINATE	2	TRUE	NA	0.545587015470547	6		375	336	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225600	225600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777600956	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	104	327	0	ENST00000264932.6:c.379G>A	p.Val127Met	p.V127M	ENST00000264932	NM_004168.2	127	Gtg/Atg	4/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.545587015470547	2		327	340	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775780	9775780	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765031777	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	227	735	1	ENST00000377346.4:c.323G>A	p.Arg108His	p.R108H	ENST00000377346	NM_005026.3	108	cGc/cAc	4/24	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.545587015470547	2		736	824	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915579	131915579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28903087	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	31	243	0	ENST00000265335.6:c.577C>T	p.Arg193Trp	p.R193W	ENST00000265335		193	Cgg/Tgg	5/25	1	2	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	TRUE	1	0.545587015470547	2		243	111	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943645	17943645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200579386	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	249	857	1	ENST00000458235.1:c.2444C>T	p.Thr815Met	p.T815M	ENST00000458235	NM_000215.3	815	aCg/aTg	18/24	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.545587015470547	2		858	858	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639543	3639543	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368434737	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	258	828	1	ENST00000294008.3:c.4096C>T	p.Arg1366Cys	p.R1366C	ENST00000294008	NM_032444.2	1366	Cgc/Tgc	12/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.545587015470547	2		829	873	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976867	2976867	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs776851896	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	113	446	1	ENST00000396946.4:c.1145C>T	p.Ala382Val	p.A382V	ENST00000396946	NM_032415.4	382	gCc/gTc	9/25	1	2	FACETS	0.806	0.728	0.887	0.806	0.728	0.887	CLONAL	1	TRUE	1	0.545587015470547	2		447	514	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743919	41743919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201003955	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	396	809	1	ENST00000301178.4:c.854C>T	p.Ser285Leu	p.S285L	ENST00000301178	NM_021913.4	285	tCg/tTg	7/20	0.503301483138926	3	FACETS	0.919	0.877	0.962	0.919	0.877	0.962	CLONAL	2	TRUE	1	0.545587015470547	3		810	1005	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322556	39322556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761415462	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	19	433	0	ENST00000373001.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000373001	NM_022157.3	146	Gca/Aca	2/7	1	2	FACETS	0.283	0.215	0.363	0.283	0.215	0.363	SUBCLONAL	1	TRUE	1	0.545587015470547	2		433	246	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881387	111881387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1429573443	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	138	501	0	ENST00000393256.3:c.65C>T	p.Ala22Val	p.A22V	ENST00000393256	NM_006538.4	22	gCg/gTg	2/4	1	2	FACETS	0.984	0.901	1	0.984	0.901	1	CLONAL	1	TRUE	1	0.545587015470547	2		501	514	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418371	139418371	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	186	757	0	ENST00000277541.6:c.201del	p.Cys68AlafsTer32	p.C68Afs*32	ENST00000277541	NM_017617.3	67	ccC/cc	3/34	1	2	FACETS	0.74	0.684	0.799	0.74	0.684	0.799	SUBCLONAL	1	TRUE	1	0.545587015470547	2		757	921	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127760	64127760	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	233	665	0	ENST00000334205.4:c.253G>A	p.Glu85Lys	p.E85K	ENST00000334205	NM_003942.2	85	Gag/Aag	3/17	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.545587015470547	2		665	757	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112272	115112272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544562535	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	97	136	0	ENST00000257566.3:c.1468G>A	p.Ala490Thr	p.A490T	ENST00000257566	NM_016569.3	490	Gcc/Acc	7/8	1	2	FACETS	0.757	0.687	0.827	1	0.984	1	SUBCLONAL	2	TRUE	1	0.545587015470547	2		136	235	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938436	76938436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376906761	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	59	264	0	ENST00000373344.5:c.2312C>T	p.Ala771Val	p.A771V	ENST00000373344	NM_000489.3	771	gCg/gTg	9/35	1	1	FACETS	0.763	0.686	0.839	1	0.979	1	SUBCLONAL	2	TRUE	0	0.545587015470547	1		264	103	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73340158	73340158	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	20	310	0	ENST00000377767.4:c.1922T>C	p.Met641Thr	p.M641T	ENST00000377767	NM_014953.3	641	aTg/aCg	15/21	1	2	FACETS	0.368	0.283	0.468	0.368	0.283	0.468	SUBCLONAL	1	TRUE	1	0.545587015470547	2		310	199	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743910	46743910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754995325	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	176	562	1	ENST00000371975.4:c.2200G>A	p.Val734Ile	p.V734I	ENST00000371975	NM_003579.3	734	Gtc/Atc	18/18	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.545587015470547	2		563	632	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268937	115268937	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765999933	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	91	444	0	ENST00000438362.2:c.1673G>A	p.Arg558His	p.R558H	ENST00000438362	NM_001242891.1	558	cGt/cAt	14/20	1	2	FACETS	0.894	0.8	0.993	0.894	0.8	0.993	CLONAL	1	TRUE	1	0.545587015470547	2		444	373	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226574098	226574098	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	83	475	0	ENST00000366794.5:c.763G>T	p.Val255Leu	p.V255L	ENST00000366794	NM_001618.3	255	Gtg/Ttg	6/23	1	2	FACETS	0.67	0.594	0.751	0.67	0.594	0.751	SUBCLONAL	1	TRUE	1	0.545587015470547	2		475	454	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589536	69589536	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	79	160	0	ENST00000168712.1:c.317G>A	p.Gly106Asp	p.G106D	ENST00000168712	NM_002007.2	106	gGc/gAc	1/3	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.545587015470547	2		160	254	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205762	108205762	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	67	340	0	ENST00000278616.4:c.8077G>A	p.Ala2693Thr	p.A2693T	ENST00000278616	NM_000051.3	2693	Gca/Aca	55/63	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.545587015470547	2		340	238	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628422	21628422	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1275285634	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	37	446	1	ENST00000421138.2:c.1196A>G	p.Tyr399Cys	p.Y399C	ENST00000421138		399	tAc/tGc	11/16	0.292699297888964	1	FACETS	0.519	0.433	0.614	0.519	0.433	0.614	INDETERMINATE	1	TRUE	0	0.545587015470547	1		447	190	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432426	49432426	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1170466072	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	71	726	1	ENST00000301067.7:c.8713C>T	p.Arg2905Cys	p.R2905C	ENST00000301067	NM_003482.3	2905	Cgt/Tgt	34/54	1	2	FACETS	0.308	0.268	0.352	0.308	0.268	0.352	SUBCLONAL	1	TRUE	1	0.545587015470547	2		727	844	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238230	133238230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766707934	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	135	500	0	ENST00000320574.5:c.2747C>T	p.Pro916Leu	p.P916L	ENST00000320574	NM_006231.2	916	cCg/cTg	24/49	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.545587015470547	2		500	484	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563416	21563416	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1163593629	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	250	862	0	ENST00000382592.4:c.503C>T	p.Thr168Met	p.T168M	ENST00000382592	NM_014572.2	168	aCg/aTg	4/8	1	2	FACETS	0.986	0.924	1	0.986	0.924	1	CLONAL	1	TRUE	1	0.545587015470547	2		862	929	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873766	35873766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	165	447	0	ENST00000216797.5:c.85C>T	p.Arg29Cys	p.R29C	ENST00000216797	NM_020529.2	29	Cgc/Tgc	1/6	1	2	FACETS	0.935	0.862	1	0.935	0.862	1	CLONAL	1	TRUE	1	0.545587015470547	2		447	647	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68758673	68758673	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	72	271	0	ENST00000487270.1:c.829G>T	p.Ala277Ser	p.A277S	ENST00000487270	NM_133509.3	277	Gct/Tct	8/11	1	2	FACETS	0.849	0.748	0.955	0.849	0.748	0.955	CLONAL	1	TRUE	1	0.545587015470547	2		271	311	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000055	42000055	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	49	530	0	ENST00000219905.7:c.2318C>A	p.Pro773His	p.P773H	ENST00000219905	NM_001164273.1	773	cCt/cAt	6/24	1	2	FACETS	0.567	0.482	0.658	0.567	0.482	0.658	SUBCLONAL	1	TRUE	1	0.545587015470547	2		530	317	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343619	343619	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	45	779	0	ENST00000262320.3:c.2055del	p.Ser686ProfsTer19	p.S686Pfs*19	ENST00000262320	NM_003502.3	685	ccC/cc	8/11	1	2	FACETS	0.196	0.164	0.232	0.196	0.164	0.232	SUBCLONAL	1	TRUE	1	0.545587015470547	2		779	840	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647504	3647504	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	194	765	0	ENST00000294008.3:c.1559C>A	p.Pro520His	p.P520H	ENST00000294008	NM_032444.2	520	cCt/cAt	7/15	1	2	FACETS	0.93	0.862	0.999	0.93	0.862	0.999	CLONAL	1	TRUE	1	0.545587015470547	2		765	765	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81939079	81939079	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	129	518	0	ENST00000359376.3:c.1438del	p.Glu480SerfsTer118	p.E480Sfs*118	ENST00000359376	NM_002661.3	478	caG/ca	15/33	1	2	FACETS	0.851	0.774	0.93	0.851	0.774	0.93	CLONAL	1	TRUE	1	0.545587015470547	2		518	556	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942872	15942872	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	109	432	0	ENST00000268712.3:c.6830A>G	p.Asp2277Gly	p.D2277G	ENST00000268712	NM_006311.3	2277	gAc/gGc	44/46	0.409340844621003	3	FACETS	1	0.974	1	0.613	0.554	0.674	CLONAL	1	TRUE	1	0.545587015470547	3		432	415	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670055	29670055	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555535407	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	71	382	0	ENST00000356175.3:c.7028G>A	p.Arg2343Gln	p.R2343Q	ENST00000356175	NM_000267.3	2343	cGg/cAg	47/57	1	2	FACETS	0.957	0.845	1	0.957	0.845	1	CLONAL	1	TRUE	1	0.545587015470547	2		382	272	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40856676	40856676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	84	344	0	ENST00000428826.2:c.1961G>A	p.Arg654Gln	p.R654Q	ENST00000428826		654	cGa/cAa	18/21	1	2	FACETS	0.93	0.829	1	0.93	0.829	1	CLONAL	1	TRUE	1	0.545587015470547	2		344	331	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733202	74733202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	137	602	0	ENST00000359995.5:c.41C>T	p.Thr14Ile	p.T14I	ENST00000359995	NM_001195427.1	14	aCc/aTc	1/3	1	2	FACETS	0.618	0.562	0.676	0.618	0.562	0.676	SUBCLONAL	1	TRUE	1	0.545587015470547	2		602	813	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919472	78919472	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	134	431	0	ENST00000306801.3:c.3031A>G	p.Thr1011Ala	p.T1011A	ENST00000306801	NM_020761.2	1011	Acg/Gcg	26/34	1	2	FACETS	0.95	0.868	1	0.95	0.868	1	CLONAL	1	TRUE	1	0.545587015470547	2		431	517	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45396876	45396876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	17	369	0	ENST00000262160.6:c.296C>T	p.Thr99Ile	p.T99I	ENST00000262160	NM_005901.5	99	aCa/aTa	3/11	1	2	FACETS	0.213	0.158	0.277	0.213	0.158	0.277	SUBCLONAL	1	TRUE	1	0.545587015470547	2		369	293	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210807	2210807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	42	557	0	ENST00000398665.3:c.1304C>T	p.Ala435Val	p.A435V	ENST00000398665	NM_032482.2	435	gCc/gTc	14/28	1	2	FACETS	0.249	0.207	0.295	0.249	0.207	0.295	SUBCLONAL	1	TRUE	1	0.545587015470547	2		557	619	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099406	4099406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1233377512	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	229	738	1	ENST00000262948.5:c.712C>T	p.Arg238Trp	p.R238W	ENST00000262948	NM_030662.3	238	Cgg/Tgg	7/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.545587015470547	2		739	809	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18267003	18267003	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	63	205	0	ENST00000222254.8:c.314C>A	p.Pro105His	p.P105H	ENST00000222254	NM_005027.3	105	cCt/cAt	2/16	1	2	FACETS	0.738	0.643	0.839	0.738	0.643	0.839	SUBCLONAL	1	TRUE	1	0.545587015470547	2		205	313	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40740954	40740954	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs778976738	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	328	706	0	ENST00000392038.2:c.1364G>A	p.Arg455His	p.R455H	ENST00000392038	NM_001626.4	455	cGc/cAc	13/14	0.503301483138926	3	FACETS	0.88	0.834	0.925	0.88	0.834	0.925	CLONAL	2	TRUE	1	0.545587015470547	3		706	870	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99162528	99162528	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	52	258	0	ENST00000074304.5:c.1046G>T	p.Gly349Val	p.G349V	ENST00000074304	NM_001134224.1	349	gGa/gTa	12/26	1	2	FACETS	0.983	0.849	1	0.983	0.849	1	CLONAL	1	TRUE	1	0.545587015470547	2		258	194	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589862	212589862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	107	459	0	ENST00000342788.4:c.680G>A	p.Ser227Asn	p.S227N	ENST00000342788	NM_005235.2	227	aGt/aAt	6/28	1	2	FACETS	0.717	0.645	0.793	0.717	0.645	0.793	SUBCLONAL	1	TRUE	1	0.545587015470547	2		459	547	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727185	40727185	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	132	466	0	ENST00000373198.4:c.3779A>C	p.Lys1260Thr	p.K1260T	ENST00000373198	NM_133170.3	1260	aAg/aCg	28/32	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.545587015470547	2		466	470	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691880	30691880	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	48	331	0	ENST00000295754.5:c.382A>G	p.Lys128Glu	p.K128E	ENST00000295754	NM_003242.5	128	Aag/Gag	3/7	1	2	FACETS	0.645	0.549	0.748	0.645	0.549	0.748	SUBCLONAL	1	TRUE	1	0.545587015470547	2		331	273	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998090	169998090	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	27	614	0	ENST00000295797.4:c.781G>T	p.Gly261Ter	p.G261*	ENST00000295797	NM_002740.5	261	Gga/Tga	9/18	1	2	FACETS	0.225	0.178	0.278	0.225	0.178	0.278	SUBCLONAL	1	TRUE	1	0.545587015470547	2		614	440	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332679	153332679	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	50	415	1	ENST00000281708.4:c.277G>T	p.Gly93Ter	p.G93*	ENST00000281708	NM_033632.3	93	Gga/Tga	2/12	1	2	FACETS	0.599	0.511	0.694	0.599	0.511	0.694	SUBCLONAL	1	TRUE	1	0.545587015470547	2		416	306	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235425	235425	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	56	562	0	ENST00000264932.6:c.1231G>T	p.Gly411Cys	p.G411C	ENST00000264932	NM_004168.2	411	Ggc/Tgc	9/15	1	2	FACETS	0.275	0.235	0.319	0.275	0.235	0.319	SUBCLONAL	1	TRUE	1	0.545587015470547	2		562	747	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294960	1294960	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	31	63	0	ENST00000310581.5:c.145G>A	p.Ala49Thr	p.A49T	ENST00000310581	NM_198253.2	49	Gcg/Acg	1/16	1	2	FACETS	0.728	0.597	0.873	0.728	0.597	0.873	SUBCLONAL	1	TRUE	1	0.545587015470547	2		63	156	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178126	56178126	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	60	301	0	ENST00000399503.3:c.3099T>A	p.Cys1033Ter	p.C1033*	ENST00000399503	NM_005921.1	1033	tgT/tgA	14/20	0.122814333729992	6	FACETS	1	0.903	1			1	INDETERMINATE	2	TRUE	NA	0.545587015470547	6		301	221	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80169094	80169094	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs377191897	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	20	406	0	ENST00000265081.6:c.3290T>C	p.Ile1097Thr	p.I1097T	ENST00000265081	NM_002439.4	1097	aTa/aCa	23/24	1	2	FACETS	0.363	0.278	0.461	0.363	0.278	0.461	SUBCLONAL	1	TRUE	1	0.545587015470547	2		406	202	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86658482	86658482	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs34028699	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	18	131	0	ENST00000274376.6:c.1451del	p.Lys484ArgfsTer14	p.K484Rfs*14	ENST00000274376	NM_002890.2	483	Aaa/aa	10/25	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.545587015470547	2		131	55	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514441	149514441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	141	517	0	ENST00000261799.4:c.503C>T	p.Ala168Val	p.A168V	ENST00000261799	NM_002609.3	168	gCa/gTa	4/23	1	2	FACETS	0.961	0.88	1	0.961	0.88	1	CLONAL	1	TRUE	1	0.545587015470547	2		517	538	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020805	26020805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs929355621	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	164	402	0	ENST00000357647.3:c.88G>A	p.Ala30Thr	p.A30T	ENST00000357647	NM_003529.2	30	Gct/Act	1/1	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.545587015470547	2		402	528	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30676014	30676014	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1286578052	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	148	573	1	ENST00000376406.3:c.2342C>T	p.Pro781Leu	p.P781L	ENST00000376406	NM_014641.2	781	cCa/cTa	8/15	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.545587015470547	2		574	536	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324571	31324571	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	144	336	0	ENST00000412585.2:c.237G>T	p.Glu79Asp	p.E79D	ENST00000412585	NM_005514.6	79	gaG/gaT	2/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.545587015470547	2		336	368	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140937	37140937	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	30	390	0	ENST00000373509.5:c.773G>T	p.Arg258Met	p.R258M	ENST00000373509	NM_002648.3	258	aGg/aTg	5/6	1	2	FACETS	0.257	0.207	0.314	0.257	0.207	0.314	SUBCLONAL	1	TRUE	1	0.545587015470547	2		390	428	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37141769	37141769	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761967890	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	30	523	1	ENST00000373509.5:c.844G>A	p.Glu282Lys	p.E282K	ENST00000373509	NM_002648.3	282	Gaa/Aaa	6/6	1	2	FACETS	0.198	0.159	0.243	0.198	0.159	0.243	SUBCLONAL	1	TRUE	1	0.545587015470547	2		524	555	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046354	69046354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	32	482	0	ENST00000288368.4:c.3827G>A	p.Cys1276Tyr	p.C1276Y	ENST00000288368	NM_024870.2	1276	tGt/tAt	32/40	1	2	FACETS	0.221	0.179	0.269	0.221	0.179	0.269	SUBCLONAL	1	TRUE	1	0.545587015470547	2		482	530	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209270	98209270	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1213795569	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	220	691	1	ENST00000331920.6:c.4268G>T	p.Arg1423Met	p.R1423M	ENST00000331920	NM_000264.3	1423	aGg/aTg	23/24	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.545587015470547	2		692	721	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209349	98209349	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	178	683	0	ENST00000331920.6:c.4189C>T	p.Leu1397Phe	p.L1397F	ENST00000331920	NM_000264.3	1397	Ctc/Ttc	23/24	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.545587015470547	2		683	643	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221955	98221955	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	117	461	1	ENST00000331920.6:c.2814G>T	p.Gln938His	p.Q938H	ENST00000331920	NM_000264.3	938	caG/caT	17/24	1	2	FACETS	0.705	0.638	0.777	0.705	0.638	0.777	SUBCLONAL	1	TRUE	1	0.545587015470547	2		462	608	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760136	133760136	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769405342	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	171	618	1	ENST00000318560.5:c.2459G>A	p.Arg820Gln	p.R820Q	ENST00000318560	NM_005157.4	820	cGg/cAg	11/11	1	2	FACETS	0.992	0.916	1	0.992	0.916	1	CLONAL	1	TRUE	1	0.545587015470547	2		619	632	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139811027	139811027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758339862	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	217	655	0	ENST00000247668.2:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000247668	NM_021138.3	213	cGa/cAa	7/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.545587015470547	2		655	715	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230838	53230838	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	85	352	2	ENST00000375401.3:c.1955C>T	p.Ala652Val	p.A652V	ENST00000375401	NM_004187.3	652	gCt/gTt	14/26	1	1	FACETS	0.553	0.491	0.618	0.553	0.491	0.618	SUBCLONAL	1	TRUE	0	0.545587015470547	1		354	410	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808051	3808051	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0030383-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	30	244	0	ENST00000262367.5:c.3370-2A>C		p.X1124_splice	ENST00000262367	NM_004380.2	1124			1	2	FACETS	0.466	0.377	0.565	0.466	0.377	0.565	SUBCLONAL	1	TRUE	1	0.545587015470547	2		244	236	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0030822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	75	655	4	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.189646966876787	2	FACETS	0.556	0.486	0.631	0.278	0.243	0.316	INDETERMINATE	1	TRUE	0	0.335177484490354	2		659	805	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637076	93637076	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	51	528	0	ENST00000375746.1:c.1126G>T	p.Glu376Ter	p.E376*	ENST00000375746	NM_001174167.1	376	Gaa/Taa	9/14	0.168371918209534	2	FACETS	0.573	0.487	0.668	0.287	0.243	0.334	INDETERMINATE	1	TRUE	0	0.335177484490354	2		528	531	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144877	47144877	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	75	581	0	ENST00000409792.3:c.4876T>G	p.Phe1626Val	p.F1626V	ENST00000409792	NM_014159.6	1626	Ttc/Gtc	7/21	0.168371918209534	2	FACETS	0.772	0.677	0.873	0.386	0.338	0.437	INDETERMINATE	1	TRUE	0	0.335177484490354	2		581	580	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166584	118166584	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	50	383	0	ENST00000369448.3:c.1094A>T	p.Asp365Val	p.D365V	ENST00000369448	NM_017709.3	365	gAt/gTt	2/2	0.0844687265620401	3	FACETS	0.726	0.616	0.846	0.363	0.308	0.423	INDETERMINATE	1	TRUE	1	0.335177484490354	3		383	480	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885526	111885526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199694759	NA	P-0030822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	82	769	1	ENST00000341259.2:c.1303G>A	p.Val435Met	p.V435M	ENST00000341259	NM_005475.2	435	Gtg/Atg	7/8	0.067956552932577	4	FACETS	0.716	0.63	0.808	0.358	0.315	0.404	INDETERMINATE	1	TRUE	2	0.335177484490354	4		770	913	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665641	86665671	+	frameshift_variant	Frame_Shift_Del	DEL	TTCAGATAGTAGTTCAGCACTTTAGTGAAGA	TTCAGATAGTAGTTCAGCACTTTAGTGAAGA	-	novel	NA	P-0030822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	30	307	0	ENST00000274376.6:c.1622_1652del	p.Phe541TyrfsTer19	p.F541Yfs*19	ENST00000274376	NM_002890.2	541	tTTCAGATAGTAGTTCAGCACTTTAGTGAAGAa/ta	12/25	1	2	FACETS	0.658	0.532	0.8	0.658	0.532	0.8	SUBCLONAL	1	TRUE	1	0.335177484490354	2		307	272	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440904	56440904	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1458799446	NA	P-0033575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	172	621	0	ENST00000407977.2:c.433C>T	p.Arg145Ter	p.R145*	ENST00000407977		145	Cga/Tga	4/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.332896364127225	2		621	950	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339565	116339565	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs779093896	NA	P-0033575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	73	331	0	ENST00000397752.3:c.427C>T	p.Arg143Ter	p.R143*	ENST00000397752	NM_000245.2	143	Cga/Tga	2/21	0.324890616641231	3	FACETS	0.949	0.831	1	0.475	0.415	0.538	CLONAL	1	TRUE	1	0.332896364127225	3		331	539	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624783	9624783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	84	418	0	ENST00000353224.5:c.194C>T	p.Ala65Val	p.A65V	ENST00000353224	NM_177990.2	65	gCt/gTt	3/10	1	2	FACETS	0.898	0.795	1	0.898	0.795	1	CLONAL	1	TRUE	1	0.332896364127225	2		418	562	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627933	187627933	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	141	658	1	ENST00000441802.2:c.3049T>C	p.Tyr1017His	p.Y1017H	ENST00000441802	NM_005245.3	1017	Tat/Cat	2/27	1	2	FACETS	0.845	0.769	0.926	0.845	0.769	0.926	CLONAL	1	TRUE	1	0.332896364127225	2		659	1002	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920401	114920401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1422891742	NA	P-0034302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	136	671	2	ENST00000543371.1:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000543371	NM_001198531.1	448	Cgg/Tgg	13/14	0.452515080554371	3	FACETS	0.89	0.828	0.951	0.89	0.828	0.951	CLONAL	3	TRUE	0	0.511956248281019	3		673	250	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166285	7166285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555743340	NA	P-0034302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	58	837	3	ENST00000302850.5:c.1741C>T	p.Arg581Trp	p.R581W	ENST00000302850	NM_000208.2	581	Cgg/Tgg	8/22	0.199832718316166	3	FACETS	1	0.888	1	0.342	0.297	0.392	INDETERMINATE	1	TRUE	0	0.511956248281019	3		840	277	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578497	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	novel	NA	P-0034302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	128	1113	0	ENST00000269305.4:c.431_433dup	p.Gln144dup	p.Q144dup	ENST00000269305	NM_001126112.2	144	ctg/cAGCtg	5/11	0.511956248281019	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.511956248281019	2		1113	242	SUCCESS
APC	324	MSKCC	GRCh37	5	112174968	112174969	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0034302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	36	269	0	ENST00000257430.4:c.3679_3680del	p.Arg1227AlafsTer12	p.R1227Afs*12	ENST00000257430	NM_000038.5	1226	aAG/a	16/16	0.511956248281019	2	FACETS	0.827	0.706	0.952	0.827	0.706	0.952	CLONAL	2	TRUE	0	0.511956248281019	2		269	85	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020775	37020775	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	42	596	0	ENST00000358127.4:c.70G>T	p.Gly24Trp	p.G24W	ENST00000358127	NM_001280556.1	24	Ggg/Tgg	2/10	0.511956248281019	3	FACETS	0.862	0.726	1	0.431	0.363	0.506	CLONAL	1	TRUE	1	0.511956248281019	3		596	239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0034798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	196	751	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.29172341023533	2	FACETS	0.984	0.917	1	0.984	0.917	1	CLONAL	2	TRUE	0	0.34597340479288	2		751	576	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342592	87342592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1456574135	NA	P-0034798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	62	377	1	ENST00000277120.3:c.877G>A	p.Glu293Lys	p.E293K	ENST00000277120		293	Gaa/Aaa	9/19	0.34597340479288	1	FACETS	0.918	0.798	1	0.918	0.798	1	CLONAL	1	TRUE	0	0.34597340479288	1		378	323	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182662899	182662899	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	47	452	0	ENST00000292782.4:c.763A>G	p.Lys255Glu	p.K255E	ENST00000292782	NM_020640.2	255	Aaa/Gaa	7/7	1	2	FACETS	0.579	0.489	0.679	0.579	0.489	0.679	SUBCLONAL	1	TRUE	1	0.34597340479288	2		452	469	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091782	29091782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373073383	NA	P-0034842-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	46	412	2	ENST00000328354.6:c.1175C>T	p.Ala392Val	p.A392V	ENST00000328354	NM_007194.3	392	gCg/gTg	11/15	0.23559927597803	3	FACETS	0.387	0.325	0.455	0.193	0.162	0.228	INDETERMINATE	1	TRUE	1	0.46522926618224	3		414	630	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374828	149374828	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034842-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	262	245	0	ENST00000360632.3:c.266C>G	p.Ser89Trp	p.S89W	ENST00000360632	NM_015472.4	89	tCg/tGg	2/7	0.288868841517518	5	FACETS	1	0.973	1	0.826	0.786	0.866	CLONAL	4	TRUE	0	0.46522926618224	5		245	463	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779700	3779701	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034842-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	63	634	0	ENST00000262367.5:c.5347dup	p.Cys1783LeufsTer183	p.C1783Lfs*183	ENST00000262367	NM_004380.2	1783	tgc/tTgc	31/31	0.338883467411931	1	FACETS	0.319	0.275	0.366	0.319	0.275	0.366	SUBCLONAL	1	TRUE	0	0.46522926618224	1		634	652	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86676324	86676324	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0034842-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	37	167	0	ENST00000274376.6:c.2604-2A>T		p.X868_splice	ENST00000274376	NM_002890.2	868			1	2	FACETS	0.899	0.75	1	0.899	0.75	1	CLONAL	1	TRUE	1	0.46522926618224	2		167	177	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426879	6426880	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACC	novel	NA	P-0034842-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	170	384	0	ENST00000356142.4:c.74_76dup	p.Thr25dup	p.T25dup	ENST00000356142	NM_018890.3	25	-/ACC	2/7	0.309560226357911	2	FACETS	0.779	0.723	0.836	0.779	0.723	0.836	SUBCLONAL	2	TRUE	0	0.46522926618224	2		384	469	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448692	49448692	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034842-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	39	378	0	ENST00000301067.7:c.167A>G	p.Gln56Arg	p.Q56R	ENST00000301067	NM_003482.3	56	cAg/cGg	2/54	0.46522926618224	3	FACETS	0.337	0.279	0.403	0.169	0.139	0.202	SUBCLONAL	1	TRUE	1	0.46522926618224	3		378	613	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495808	56495808	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034842-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	124	299	0	ENST00000267101.3:c.3998T>C	p.Leu1333Pro	p.L1333P	ENST00000267101	NM_001982.3	1333	cTt/cCt	28/28	0.46522926618224	3	FACETS	0.766	0.698	0.836	0.766	0.698	0.836	SUBCLONAL	2	TRUE	1	0.46522926618224	3		299	429	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649216	23649216	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034842-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	39	361	0	ENST00000261584.4:c.166del	p.Asp56IlefsTer12	p.D56Ifs*12	ENST00000261584	NM_024675.3	56	Gat/at	3/13	0.267244551757048	3	FACETS	0.389	0.322	0.464	0.195	0.161	0.232	INDETERMINATE	1	TRUE	1	0.46522926618224	3		361	531	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573382	55573382	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034842-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	24	360	0	ENST00000288135.5:c.1044G>T	p.Trp348Cys	p.W348C	ENST00000288135	NM_000222.2	348	tgG/tgT	6/21	0.215438799592807	1	FACETS	0.238	0.186	0.297	0.238	0.186	0.297	INDETERMINATE	1	TRUE	0	0.46522926618224	1		360	333	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155964	106155964	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034842-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	30	265	0	ENST00000380013.4:c.865G>C	p.Ala289Pro	p.A289P	ENST00000380013	NM_001127208.2	289	Gct/Cct	3/11	0.215438799592807	1	FACETS	0.33	0.266	0.402	0.33	0.266	0.402	INDETERMINATE	1	TRUE	0	0.46522926618224	1		265	300	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344845	70344845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034842-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	56	464	1	ENST00000374080.3:c.2075C>T	p.Pro692Leu	p.P692L	ENST00000374080		692	cCc/cTc	15/45	0.400711930887966	1	FACETS	0.447	0.384	0.516	0.447	0.384	0.516	SUBCLONAL	1	TRUE	0	0.46522926618224	1		465	413	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344991	70345004	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCCAGGTACTATT	CCCCAGGTACTATT	-	novel	NA	P-0034842-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	43	399	0	ENST00000374080.3:c.2226+1_2226+14del		p.X742_splice	ENST00000374080		742		15/45	0.400711930887966	1	FACETS	0.318	0.266	0.376	0.318	0.266	0.376	SUBCLONAL	1	TRUE	0	0.46522926618224	1		399	446	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042199	6042199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	116	531	0	ENST00000265849.7:c.422G>A	p.Gly141Glu	p.G141E	ENST00000265849	NM_000535.5	141	gGg/gAg	5/15	0.308749141370432	3	FACETS	0.437	0.393	0.484	0.146	0.131	0.162	INDETERMINATE	1	TRUE	0	0.790781925896231	3		531	936	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261670	16261670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	58	551	0	ENST00000375759.3:c.8935G>A	p.Gly2979Arg	p.G2979R	ENST00000375759	NM_015001.2	2979	Ggg/Agg	11/15	0.790781925896231	2	FACETS	0.223	0.191	0.258	0.111	0.095	0.129	SUBCLONAL	1	TRUE	0	0.790781925896231	2		551	658	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636895	2636895	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0036025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	59	578	0	ENST00000342085.4:c.1343+1G>C		p.X448_splice	ENST00000342085	NM_002613.4	448			0.790781925896231	2	FACETS	0.203	0.174	0.234	0.101	0.087	0.117	SUBCLONAL	1	TRUE	0	0.790781925896231	2		578	736	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219961	36219961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	154	592	2	ENST00000222270.7:c.4763G>A	p.Gly1588Glu	p.G1588E	ENST00000222270	NM_014727.1	1588	gGg/gAg	21/37	NA	2	FACETS	0.497	0.456	0.541			1	INDETERMINATE	1	TRUE	NA	0.790781925896231	2		594	783	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378247	225378247	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	107	210	0	ENST00000264414.4:c.648T>G	p.Phe216Leu	p.F216L	ENST00000264414	NM_003590.4	216	ttT/ttG	5/16	0.356580622481915	1	FACETS	0.676	0.619	0.734	0.676	0.619	0.734	INDETERMINATE	1	TRUE	0	0.790781925896231	1		210	242	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591104	67591104	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	51	256	1	ENST00000274335.5:c.1697T>C	p.Ile566Thr	p.I566T	ENST00000274335		566	aTt/aCt	12/15	0.371092528284033	1	FACETS	0.359	0.309	0.413	0.359	0.309	0.413	INDETERMINATE	1	TRUE	0	0.790781925896231	1		257	217	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37006488	37006488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036025-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	29	340	0	ENST00000358127.4:c.457G>A	p.Ala153Thr	p.A153T	ENST00000358127	NM_001280556.1	153	Gct/Act	4/10	0.532706672100401	1	FACETS	0.125	0.1	0.154	0.125	0.1	0.154	SUBCLONAL	1	TRUE	0	0.790781925896231	1		340	354	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0121487-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	197	610	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.902	0.843	0.961	0.902	0.843	0.961	CLONAL	1	NA	1	0.891585759380486	2		610	490	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166182	7166182	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0121487-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	181	680	0	ENST00000302850.5:c.1844T>C	p.Val615Ala	p.V615A	ENST00000302850	NM_000208.2	615	gTc/gCc	8/22	1	2	FACETS	0.974	0.909	1	0.974	0.909	1	CLONAL	1	NA	1	0.891585759380486	2		680	417	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0037280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	316	388	1	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	0.879576950770545	2	FACETS	1	0.994	1	0.643	0.614	0.671	CLONAL	1	TRUE	0	0.897478536881331	2		389	548	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0037280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	355	159	1	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.879576950770545	2	FACETS	0.929	0.904	0.952	0.929	0.904	0.952	CLONAL	2	TRUE	0	0.897478536881331	2		160	426	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772950	135772951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs118203724	NA	P-0037280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	226	424	0	ENST00000298552.3:c.2672dup	p.Asn891LysfsTer13	p.N891Kfs*13	ENST00000298552	NM_001162426.1	891	aac/aaAc	21/23	0.897478536881331	1	FACETS	0.765	0.727	0.802	0.765	0.727	0.802	SUBCLONAL	1	TRUE	0	0.897478536881331	1		424	363	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	99	230	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.58	2		230	336	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0037428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	20	325	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.198	0.151	0.253	0.198	0.151	0.253	SUBCLONAL	1	TRUE	1	0.58	2		325	348	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0037428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	130	520	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.811	0.738	0.886	0.811	0.738	0.886	CLONAL	1	TRUE	1	0.58	2		520	553	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465316	120465316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769177875	NA	P-0037428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	148	562	0	ENST00000256646.2:c.4945C>T	p.Leu1649Phe	p.L1649F	ENST00000256646	NM_024408.3	1649	Ctc/Ttc	27/34	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.58	2		562	491	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004664	16004664	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	68	654	0	ENST00000268712.3:c.2590C>T	p.Gln864Ter	p.Q864*	ENST00000268712	NM_006311.3	864	Cag/Tag	20/46	0.3	1	FACETS	0.317	0.276	0.361	0.317	0.276	0.361	INDETERMINATE	1	TRUE	0	0.58	1		654	525	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	20	449	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	1	2	FACETS	0.171	0.13	0.219	0.171	0.13	0.219	SUBCLONAL	1	TRUE	1	0.58	2		449	403	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100518	157100519	+	missense_variant	Missense_Mutation	DNP	TG	TG	CT	novel	NA	P-0037428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	58	174	1	ENST00000346085.5:c.1455_1456delinsCT	p.Ala486Ser	p.A486S	ENST00000346085	NM_020732.3	485	gcTGcc/gcCTcc	1/20	1	2	FACETS	0.966	0.843	1	0.966	0.843	1	CLONAL	1	TRUE	1	0.58	2		175	207	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891193	151891193	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747882261	NA	P-0037428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	51	533	1	ENST00000262189.6:c.4561G>A	p.Glu1521Lys	p.E1521K	ENST00000262189	NM_170606.2	1521	Gaa/Aaa	31/59	1	2	FACETS	0.346	0.293	0.403	0.346	0.293	0.403	SUBCLONAL	1	TRUE	1	0.58	2		534	509	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180297	27180297	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	25	599	0	ENST00000380036.4:c.961G>T	p.Glu321Ter	p.E321*	ENST00000380036	NM_000459.3	321	Gag/Tag	7/23	1	2	FACETS	0.192	0.15	0.239	0.192	0.15	0.239	SUBCLONAL	1	TRUE	1	0.58	2		599	450	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945109	44945109	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0037428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	105	198	0	ENST00000377967.4:c.3434-1G>C		p.X1145_splice	ENST00000377967	NM_021140.2	1145			1	1	FACETS	0.761	0.706	0.814	1	0.988	1	SUBCLONAL	2	TRUE	0	0.58	1		198	169	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222222	53222222	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782534108	NA	P-0037428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	73	396	0	ENST00000375401.3:c.4610C>T	p.Ser1537Leu	p.S1537L	ENST00000375401	NM_004187.3	1537	tCg/tTg	26/26	1	1	FACETS	0.598	0.528	0.672	0.598	0.528	0.672	SUBCLONAL	1	TRUE	0	0.58	1		396	299	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981855	201981858	+	frameshift_variant	Frame_Shift_Del	DEL	CCTC	CCTC	GG	novel	NA	P-0037428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	170	762	0	ENST00000359651.3:c.566_569delinsGG	p.Pro189ArgfsTer6	p.P189Rfs*6	ENST00000359651		189	cCCTCc/cGGc	4/8	1	2	FACETS	0.91	0.84	0.982	0.91	0.84	0.982	CLONAL	1	TRUE	1	0.58	2		762	644	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0037695-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	103	283	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.852	0.766	0.941	0.852	0.766	0.941	CLONAL	1	TRUE	1	0.524765940035636	2		283	461	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682989	241682989	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037695-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	191	544	0	ENST00000366560.3:c.34C>G	p.Arg12Gly	p.R12G	ENST00000366560	NM_000143.3	12	Cgt/Ggt	1/10	1	2	FACETS	0.917	0.849	0.986	0.917	0.849	0.986	CLONAL	1	TRUE	1	0.524765940035636	2		544	794	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233110	55233110	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038389-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1227	147	466	0	ENST00000275493.2:c.1860C>G	p.Cys620Trp	p.C620W	ENST00000275493	NM_005228.3	620	tgC/tgG	15/28	0.95571904386485	6	FACETS	1	0.947	1	0.211	0.192	0.232	CLONAL	1	TRUE	1	0.34	6		466	1374	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866689	37866689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149210045	NA	P-0038570-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	26	599	1	ENST00000269571.5:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269571		286	Gag/Aag	7/27	1	2	FACETS	0.138	0.108	0.171	0.138	0.108	0.171	SUBCLONAL	1	TRUE	1	0.846973248479731	2		600	446	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988452	41988455	+	frameshift_variant	Frame_Shift_Del	DEL	CAAA	CAAA	-	novel	NA	P-0038570-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	188	374	0	ENST00000219905.7:c.1246_1249del	p.Asn416ValfsTer7	p.N416Vfs*7	ENST00000219905	NM_001164273.1	415	tCAAAc/tc	3/24	0.837546594932763	3	FACETS	0.859	0.807	0.911	0.859	0.807	0.911	CLONAL	2	TRUE	1	0.846973248479731	3		374	368	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965728	93965728	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038570-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	61	214	0	ENST00000369303.4:c.2200C>T	p.Gln734Ter	p.Q734*	ENST00000369303	NM_004440.3	734	Cag/Tag	13/17	0.837546594932763	3	FACETS	1	0.885	1	0.505	0.442	0.571	CLONAL	1	TRUE	1	0.846973248479731	3		214	203	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866674	117866675	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCTTCC	novel	NA	P-0038570-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	195	324	0	ENST00000297338.2:c.965_970dup	p.Arg322_Lys323dup	p.R322_K323dup	ENST00000297338	NM_006265.2	322	cta/cGGAAGCta	9/14	0.773915289431033	4	FACETS	0.77	0.718	0.824	0.77	0.718	0.824	SUBCLONAL	2	TRUE	2	0.846973248479731	4		324	552	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465478	99465478	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756897082	NA	P-0038570-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	89	379	1	ENST00000268035.6:c.2303C>T	p.Pro768Leu	p.P768L	ENST00000268035	NM_000875.3	768	cCg/cTg	11/21	0.837546594932763	3	FACETS	0.877	0.785	0.974	0.439	0.392	0.487	CLONAL	1	TRUE	1	0.846973248479731	3		380	341	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272845	142272845	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038570-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	104	264	0	ENST00000350721.4:c.2354A>G	p.Asn785Ser	p.N785S	ENST00000350721	NM_001184.3	785	aAt/aGt	11/47	1	2	FACETS	0.99	0.903	1	0.99	0.903	1	CLONAL	1	TRUE	1	0.846973248479731	2		264	248	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0038986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	411	575	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	0.609973375134033	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.609973375134033	1		575	738	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132428	11132428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	156	633	0	ENST00000358026.2:c.2644G>A	p.Glu882Lys	p.E882K	ENST00000358026	NM_001128849.1	882	Gaa/Aaa	19/36	0.609973375134033	1	FACETS	0.616	0.567	0.667	0.616	0.567	0.667	SUBCLONAL	1	TRUE	0	0.609973375134033	1		633	577	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477861	140477861	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs397507474	NA	P-0038986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	124	284	0	ENST00000288602.6:c.1447A>G	p.Lys483Glu	p.K483E	ENST00000288602	NM_004333.4	483	Aaa/Gaa	12/18	0.609973375134033	3	FACETS	0.873	0.802	0.945	0.873	0.802	0.945	CLONAL	2	TRUE	1	0.609973375134033	3		284	304	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339898	116339898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	74	243	0	ENST00000397752.3:c.760G>A	p.Glu254Lys	p.E254K	ENST00000397752	NM_000245.2	254	Gaa/Aaa	2/21	0.609973375134033	3	FACETS	0.915	0.807	1	0.458	0.403	0.515	CLONAL	1	TRUE	1	0.609973375134033	3		243	346	SUCCESS
APC	324	MSKCC	GRCh37	5	112175903	112175903	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	37	146	0	ENST00000257430.4:c.4612G>T	p.Glu1538Ter	p.E1538*	ENST00000257430	NM_000038.5	1538	Gaa/Taa	16/16	0.609973375134033	1	FACETS	0.947	0.809	1	0.947	0.809	1	CLONAL	1	TRUE	0	0.609973375134033	1		146	89	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030585	47030586	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAG	rs782535776	NA	P-0038986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	151	572	0	ENST00000377604.3:c.373_375dup	p.Glu125dup	p.E125dup	ENST00000377604	NM_001204468.1	125	-/GAG	4/24	0.161668139197049	4	FACETS	0.785	0.717	0.857	0.262	0.239	0.286	INDETERMINATE	1	TRUE	1	0.609973375134033	4		572	1015	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0039138-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	139	299	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.76	2		299	328	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0039138-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	240	520	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.809	0.758	0.861	0.809	0.758	0.861	CLONAL	1	TRUE	1	0.76	2		520	781	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0039138-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	127	396	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.76	2		396	305	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436054	49436054	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0039138-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	366	637	0	ENST00000301067.7:c.5927C>G	p.Ser1976Ter	p.S1976*	ENST00000301067	NM_003482.3	1976	tCa/tGa	28/54	1	2	FACETS	0.918	0.872	0.965	0.918	0.872	0.965	CLONAL	1	TRUE	1	0.76	2		637	1049	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982373	201982373	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039138-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	503	760	1	ENST00000359651.3:c.752G>T	p.Arg251Leu	p.R251L	ENST00000359651		251	cGa/cTa	6/8	0.221894720520826	3	FACETS	1	0.99	1	0.556	0.532	0.581	INDETERMINATE	1	TRUE	1	0.76	3		761	1642	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983035	201983035	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039138-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	506	732	0	ENST00000359651.3:c.884G>C	p.Trp295Ser	p.W295S	ENST00000359651		295	tGg/tCg	7/8	0.221894720520826	3	FACETS	1	0.995	1	0.635	0.607	0.662	INDETERMINATE	1	TRUE	1	0.76	3		732	1448	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432069	49432069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039138-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	408	733	0	ENST00000301067.7:c.9070G>A	p.Glu3024Lys	p.E3024K	ENST00000301067	NM_003482.3	3024	Gaa/Aaa	34/54	1	2	FACETS	0.879	0.837	0.922	0.879	0.837	0.922	CLONAL	1	TRUE	1	0.76	2		733	1221	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562736	29562736	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs756780735	NA	P-0039138-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	195	407	0	ENST00000356175.3:c.3816G>C	p.Gln1272His	p.Q1272H	ENST00000356175	NM_000267.3	1272	caG/caC	28/57	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.76	2		407	496	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55225418	55225418	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039138-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	32	429	0	ENST00000275493.2:c.1270G>C	p.Glu424Gln	p.E424Q	ENST00000275493	NM_005228.3	424	Gaa/Caa	11/28	1	2	FACETS	0.139	0.112	0.169	0.139	0.112	0.169	SUBCLONAL	1	TRUE	1	0.76	2		429	607	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0039332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	83	277	1	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.846	0.754	0.943	0.846	0.754	0.943	CLONAL	1	TRUE	1	0.607324409047501	2		278	323	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858738	9858738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149698593	NA	P-0039332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	41	266	0	ENST00000330684.3:c.2663C>T	p.Thr888Met	p.T888M	ENST00000330684	NM_001134407.1	888	aCg/aTg	13/13	0.607324409047501	3	FACETS	0.481	0.401	0.569	0.24	0.2	0.285	SUBCLONAL	1	TRUE	1	0.607324409047501	3		266	366	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733029	74733029	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	121	334	0	ENST00000359995.5:c.214A>G	p.Met72Val	p.M72V	ENST00000359995	NM_001195427.1	72	Atg/Gtg	1/3	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.607324409047501	2		334	383	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591236	67591268	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTGTTTTTCAGGTGGTTGACTCAAAAAGGTGT	ACTGTTTTTCAGGTGGTTGACTCAAAAAGGTGT	-	novel	NA	P-0039332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	78	302	0	ENST00000274335.5:c.1746-12_1766del		p.X582_splice	ENST00000274335		582		13/15	1	2	FACETS	0.71	0.628	0.796	0.71	0.628	0.796	SUBCLONAL	1	TRUE	1	0.607324409047501	2		302	362	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0039351-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	267	299	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.810607796789008	2		299	601	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692911	89692911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909241	NA	P-0039351-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	326	539	0	ENST00000371953.3:c.395G>A	p.Gly132Asp	p.G132D	ENST00000371953	NM_000314.4	132	gGt/gAt	5/9	0.810607796789008	1	FACETS	0.945	0.908	0.982	0.945	0.908	0.982	CLONAL	1	TRUE	0	0.810607796789008	1		539	506	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94211986	94211986	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039351-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	323	572	0	ENST00000323929.3:c.459T>G	p.Phe153Leu	p.F153L	ENST00000323929	NM_005591.3	153	ttT/ttG	6/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.810607796789008	2		572	773	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786740	3786740	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039351-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	405	825	1	ENST00000262367.5:c.4471C>G	p.Gln1491Glu	p.Q1491E	ENST00000262367	NM_004380.2	1491	Caa/Gaa	27/31	1	2	FACETS	0.916	0.873	0.959	0.916	0.873	0.959	CLONAL	1	TRUE	1	0.810607796789008	2		826	1091	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631301	117631301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199882276	NA	P-0039351-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	317	511	0	ENST00000368508.3:c.6377G>A	p.Arg2126Gln	p.R2126Q	ENST00000368508	NM_002944.2	2126	cGg/cAg	40/43	1	2	FACETS	0.948	0.899	0.998	0.948	0.899	0.998	CLONAL	1	TRUE	1	0.810607796789008	2		511	825	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244406	5244406	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039860-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	117	710	0	ENST00000357368.4:c.1076C>A	p.Pro359His	p.P359H	ENST00000357368	NM_002850.3	359	cCt/cAt	11/38	0.16971368823079	4	FACETS	0.912	0.842	0.983	1	0.991	1	CLONAL	5	TRUE	2	0.279197962222396	4		710	235	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828051	3828051	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039860-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	53	509	0	ENST00000262367.5:c.2074C>A	p.Pro692Thr	p.P692T	ENST00000262367	NM_004380.2	692	Ccc/Acc	10/31	0.279197962222396	0	FACETS	0.97	0.848	1			1	CLONAL	2	TRUE	0	0.279197962222396	0		509	141	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31466297	31466297	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039860-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	65	521	0	ENST00000344624.3:c.2458C>T	p.Gln820Ter	p.Q820*	ENST00000344624		820	Cag/Tag	16/33	0.274066339206208	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	0	0.279197962222396	2		521	216	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0040364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	220	655	4	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.740343212765033	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.740343212765033	1		659	361	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0040769-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	442	403	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.924918364230129	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.924918364230129	3		403	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0040769-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	652	913	1	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.924918364230129	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.924918364230129	2		914	676	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273306	55273306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35918369	NA	P-0040769-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	381	523	0	ENST00000275493.2:c.3629C>T	p.Ala1210Val	p.A1210V	ENST00000275493	NM_005228.3	1210	gCa/gTa	28/28	0.924918364230129	4	FACETS	0.991	0.947	1	0.991	0.947	1	CLONAL	2	TRUE	2	0.924918364230129	4		523	800	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125513723	125513723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040769-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	312	365	1	ENST00000428830.2:c.851C>T	p.Ser284Leu	p.S284L	ENST00000428830	NM_001114121.2	284	tCa/tTa	9/14	0.537950751582107	4	FACETS	0.975	0.927	1	0.65	0.618	0.682	INDETERMINATE	2	TRUE	1	0.924918364230129	4		366	666	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488689	212488689	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040769-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	240	480	0	ENST00000342788.4:c.2160G>T	p.Arg720Ser	p.R720S	ENST00000342788	NM_005235.2	720	agG/agT	18/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.924918364230129	2		480	472	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863641	68863641	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040769-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	272	631	0	ENST00000261769.5:c.2380G>T	p.Val794Phe	p.V794F	ENST00000261769	NM_004360.3	794	Gtc/Ttc	15/16	0.924918364230129	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.924918364230129	1		631	301	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0040854-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	316	359	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.90331139013469	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.90331139013469	3		359	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0040854-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	340	615	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.889720055940863	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.90331139013469	2		615	361	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040854-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	187	764	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	0.889720055940863	2	FACETS	0.758	0.721	0.795	0.758	0.721	0.795	SUBCLONAL	2	TRUE	0	0.90331139013469	2		764	273	SUCCESS
RET	5979	MSKCC	GRCh37	10	43614996	43614996	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79658334	NA	P-0040854-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	197	970	0	ENST00000355710.3:c.2410G>C	p.Val804Leu	p.V804L	ENST00000355710	NM_020975.4	804	Gtg/Ctg	14/20	0.764873068271522	4	FACETS	1	0.975	1	0.553	0.514	0.594	CLONAL	1	TRUE	2	0.90331139013469	4		970	750	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658295	18658295	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040854-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	361	617	0	ENST00000266497.5:c.3100C>G	p.Arg1034Gly	p.R1034G	ENST00000266497		1034	Cgt/Ggt	22/31	0.864728203206153	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.90331139013469	4		617	749	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0041586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	129	501	3	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.162039112987647	2	FACETS	0.945	0.857	1	0.945	0.857	1	CLONAL	2	TRUE	0	0.162039112987647	2		504	842	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0041586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	137	629	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.162039112987647	2	FACETS	0.873	0.793	0.956	0.873	0.793	0.956	CLONAL	2	TRUE	0	0.162039112987647	2		629	969	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247812	59247813	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0041586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	107	663	1	ENST00000371222.2:c.930_931del	p.Lys311SerfsTer6	p.K311Sfs*6	ENST00000371222	NM_002228.3	310	caGAaa/caaa	1/1	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.162039112987647	2		664	1071	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724542	162724542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1041487062	NA	P-0041586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	162	535	1	ENST00000367921.3:c.314G>A	p.Arg105His	p.R105H	ENST00000367921	NM_006182.2	105	cGc/cAc	5/18	0.162039112987647	4	FACETS	0.842	0.772	0.915	1	0.982	1	CLONAL	3	TRUE	2	0.162039112987647	4		536	920	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15818054	15818054	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	24	101	0	ENST00000307771.7:c.181G>T	p.Glu61Ter	p.E61*	ENST00000307771	NM_005089.3	61	Gag/Tag	3/11	1	1	FACETS	0.773	0.611	0.957	1	0.932	1	CLONAL	2	TRUE	0	0.162039112987647	1		101	176	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443607	49443607	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	57	667	0	ENST00000301067.7:c.3764del	p.Gly1255AlafsTer75	p.G1255Afs*75	ENST00000301067	NM_003482.3	1255	gGc/gc	11/54	1	2	FACETS	0.722	0.617	0.836	0.722	0.617	0.836	SUBCLONAL	1	TRUE	1	0.162039112987647	2		667	975	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248147	98248147	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375628555	NA	P-0041586-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	28	304	0	ENST00000331920.6:c.404G>A	p.Arg135Gln	p.R135Q	ENST00000331920	NM_000264.3	135	cGa/cAa	3/24	1	2	FACETS	0.714	0.57	0.879	0.714	0.57	0.879	SUBCLONAL	1	TRUE	1	0.162039112987647	2		304	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577584	7577584	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041872-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	204	559	0	ENST00000269305.4:c.697del	p.His233ThrfsTer14	p.H233Tfs*14	ENST00000269305	NM_001126112.2	233	Cac/ac	7/11	0.3365175927211	2	FACETS	0.781	0.729	0.834	0.781	0.729	0.834	SUBCLONAL	2	TRUE	0	0.446612185650858	2		559	585	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11172917	11172917	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041872-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	98	496	0	ENST00000361445.4:c.7358A>T	p.Gln2453Leu	p.Q2453L	ENST00000361445	NM_004958.3	2453	cAg/cTg	54/58	1	2	FACETS	0.781	0.698	0.868	0.781	0.698	0.868	SUBCLONAL	1	TRUE	1	0.446612185650858	2		496	562	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120478097	120478097	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041872-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	75	486	0	ENST00000256646.2:c.3653G>C	p.Arg1218Pro	p.R1218P	ENST00000256646	NM_024408.3	1218	cGg/cCg	22/34	1	2	FACETS	0.722	0.635	0.816	0.722	0.635	0.816	SUBCLONAL	1	TRUE	1	0.446612185650858	2		486	465	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499737	18499737	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041872-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	162	394	0	ENST00000266497.5:c.1592C>A	p.Ala531Glu	p.A531E	ENST00000266497		531	gCa/gAa	10/31	0.421849472103871	2	FACETS	1	0.989	1	0.737	0.682	0.794	CLONAL	1	TRUE	0	0.446612185650858	2		394	492	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556138	29556139	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0041872-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	10	135	0	ENST00000356175.3:c.2505_2506delinsTT	p.Gln835_Glu836delinsHisTer	p.Q835_E836delinsH*	ENST00000356175	NM_000267.3	835	caGGaa/caTTaa	21/57	0.3365175927211	2	FACETS	0.503	0.344	0.698	0.252	0.172	0.349	SUBCLONAL	1	TRUE	0	0.446612185650858	2		135	89	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58700975	58700975	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041872-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	242	606	1	ENST00000305921.3:c.566A>C	p.His189Pro	p.H189P	ENST00000305921	NM_003620.3	189	cAc/cCc	2/6	0.446612185650858	4	FACETS	0.765	0.714	0.817	0.382	0.357	0.409	SUBCLONAL	2	TRUE	0	0.446612185650858	4		607	1025	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661995	227661995	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041872-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	293	713	0	ENST00000305123.5:c.1460G>T	p.Arg487Leu	p.R487L	ENST00000305123	NM_005544.2	487	cGg/cTg	1/2	0.345004808530351	3	FACETS	0.862	0.818	0.905	0.862	0.818	0.905	CLONAL	3	TRUE	0	0.446612185650858	3		713	621	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204759	128204759	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs375298899	NA	P-0041872-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	98	797	1	ENST00000341105.2:c.682C>A	p.Pro228Thr	p.P228T	ENST00000341105	NM_032638.4	228	Ccc/Acc	3/6	0.421849472103871	2	FACETS	0.838	0.75	0.93	0.419	0.375	0.465	CLONAL	1	TRUE	0	0.446612185650858	2		798	524	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869637	117869637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041872-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	139	435	0	ENST00000297338.2:c.557C>T	p.Thr186Ile	p.T186I	ENST00000297338	NM_006265.2	186	aCt/aTt	6/14	0.344731450087237	2	FACETS	0.786	0.723	0.85	0.786	0.723	0.85	SUBCLONAL	2	TRUE	0	0.446612185650858	2		435	396	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441746	49441746	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0041872-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	76	476	1	ENST00000301067.7:c.4236+2T>A		p.X1412_splice	ENST00000301067	NM_003482.3	1412			0.345004808530351	3	FACETS	0.676	0.593	0.765	0.225	0.197	0.255	SUBCLONAL	1	TRUE	0	0.446612185650858	3		477	616	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58700908	58700908	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041872-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	274	537	0	ENST00000305921.3:c.499C>A	p.Leu167Ile	p.L167I	ENST00000305921	NM_003620.3	167	Ctt/Att	2/6	0.446612185650858	4	FACETS	1	0.962	1	0.514	0.484	0.545	CLONAL	2	TRUE	0	0.446612185650858	4		537	863	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0042681-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	325	644	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.330661152608942	0	FACETS	0.714	0.686	0.741			1	SUBCLONAL	3	TRUE	0	0.383523533054629	0		644	488	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696688	47696688	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519971	NA	P-0042681-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	69	415	0	ENST00000347630.2:c.260A>G	p.Tyr87Cys	p.Y87C	ENST00000347630	NM_001007230.1	87	tAc/tGc	5/11	1	2	FACETS	0.833	0.737	0.933	1	0.98	1	CLONAL	2	TRUE	1	0.383523533054629	2		415	216	SUCCESS
APC	324	MSKCC	GRCh37	5	112175861	112175862	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0042681-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	56	235	0	ENST00000257430.4:c.4571_4572del	p.Ile1524AsnfsTer8	p.I1524Nfs*8	ENST00000257430	NM_000038.5	1524	ATa/a	16/16	0.347384104389042	0	FACETS	0.659	0.594	0.723			1	SUBCLONAL	3	TRUE	0	0.383523533054629	0		235	91	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509338	149509349	+	inframe_deletion	In_Frame_Del	DEL	CCTCCTGCGTGT	CCTCCTGCGTGT	-	novel	NA	P-0042681-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	202	506	0	ENST00000261799.4:c.1550_1561del	p.Asp517_Glu520del	p.D517_E520del	ENST00000261799	NM_002609.3	517	gACACGCAGGAGGtc/gtc	10/23	0.383523533054629	1	FACETS	0.997	0.937	1	1	0.994	1	CLONAL	2	TRUE	0	0.383523533054629	1		506	427	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273492	5273501	+	frameshift_variant	Frame_Shift_Del	DEL	CAACCGAGTT	CAACCGAGTT	-	novel	NA	P-0042681-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	99	781	0	ENST00000357368.4:c.331_340del	p.Asn111GlyfsTer30	p.N111Gfs*30	ENST00000357368	NM_002850.3	111	AACTCGGTTGgg/gg	4/38	1	2	FACETS	0.755	0.674	0.84	0.755	0.674	0.84	SUBCLONAL	1	TRUE	1	0.383523533054629	2		781	684	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435300	110435302	+	inframe_deletion	In_Frame_Del	DEL	GGT	GGT	-	rs765493638	NA	P-0043007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	11	13	0	ENST00000375856.3:c.3099_3101del	p.Pro1036del	p.P1036del	ENST00000375856	NM_003749.2	1033	ccACCg/ccg	1/2	1	2	FACETS	0.521	0.365	0.708	0.521	0.365	0.708	SUBCLONAL	1	TRUE	1	0.534856903222724	2		13	79	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248120	110248120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	175	410	0	ENST00000374672.4:c.1352C>T	p.Thr451Met	p.T451M	ENST00000374672	NM_004235.4	451	aCg/aTg	5/5	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.534856903222724	2		410	648	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342474	118342474	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	98	202	0	ENST00000534358.1:c.600T>A	p.Asn200Lys	p.N200K	ENST00000534358	NM_005933.3	200	aaT/aaA	3/36	1	2	FACETS	0.896	0.805	0.992	0.896	0.805	0.992	CLONAL	1	TRUE	1	0.534856903222724	2		202	409	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	57	230	0				ENST00000310581	NM_198253.2	-/1132			0.113091920993125	4	FACETS	0.834	0.73	0.941	0.834	0.73	0.941	INDETERMINATE	2	TRUE	2	0.70772518788646	4		230	165	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0043247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	175	344	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.70772518788646	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.70772518788646	1		344	296	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233033	55233033	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7228	6112	575	0	ENST00000275493.2:c.1783T>G	p.Cys595Gly	p.C595G	ENST00000275493	NM_005228.3	595	Tgc/Ggc	15/28	0.70772518788646	52	FACETS	1	0.994	1	0.475	0.469	0.48	CLONAL	24	TRUE	1	0.70772518788646	52		575	13340	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628298	187628298	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs748807574	NA	P-0043247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	191	651	0	ENST00000441802.2:c.2684T>C	p.Ile895Thr	p.I895T	ENST00000441802	NM_005245.3	895	aTt/aCt	2/27	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.70772518788646	2		651	507	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97869407	97869407	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043247-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	162	794	0	ENST00000289081.3:c.1474del	p.Leu492SerfsTer20	p.L492Sfs*20	ENST00000289081	NM_000136.2	492	Ctc/tc	14/15	1	2	FACETS	0.856	0.79	0.923	0.856	0.79	0.923	CLONAL	1	TRUE	1	0.70772518788646	2		794	535	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0043310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	49	373	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.349632057600122	3	FACETS	0.956	0.827	1	0.956	0.827	1	CLONAL	2	TRUE	1	0.402289786385805	3		373	153	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0043310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	187	447	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.402289786385805	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.402289786385805	2		447	442	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870985	12870986	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1555085549	NA	P-0043310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	149	342	0	ENST00000228872.4:c.215dup	p.Lys73GlnfsTer52	p.K73Qfs*52	ENST00000228872	NM_004064.3	71	gag/gaGg	1/3	0.349632057600122	3	FACETS	0.912	0.839	0.986	0.912	0.839	0.986	CLONAL	2	TRUE	1	0.402289786385805	3		342	488	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168694	32168694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143040647	NA	P-0043310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	112	572	0	ENST00000375023.3:c.4229G>A	p.Arg1410His	p.R1410H	ENST00000375023	NM_004557.3	1410	cGc/cAc	23/30	1	2	FACETS	0.98	0.885	1	0.98	0.885	1	CLONAL	1	TRUE	1	0.402289786385805	2		572	568	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117955	70117956	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0043310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	99	248	0	ENST00000245479.2:c.424dup	p.Leu142ProfsTer110	p.L142Pfs*110	ENST00000245479	NM_000346.3	141	-/C	1/3	0.402289786385805	2	FACETS	0.898	0.814	0.985	0.898	0.814	0.985	CLONAL	2	TRUE	0	0.402289786385805	2		248	274	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149375036	149375036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	37	602	1	ENST00000360632.3:c.58G>A	p.Val20Ile	p.V20I	ENST00000360632	NM_015472.4	20	Gtc/Atc	2/7	0.349632057600122	3	FACETS	0.306	0.251	0.368	0.153	0.125	0.184	SUBCLONAL	1	TRUE	1	0.402289786385805	3		603	722	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514536	149514536	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	50	423	0	ENST00000261799.4:c.408C>A	p.Phe136Leu	p.F136L	ENST00000261799	NM_002609.3	136	ttC/ttA	4/23	0.356235396332953	3	FACETS	1	0.916	1	0.553	0.473	0.64	CLONAL	1	TRUE	1	0.402289786385805	3		423	270	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061212	38061232	+	inframe_deletion	In_Frame_Del	DEL	GTAGCAGCCGTTCTCGAACAT	GTAGCAGCCGTTCTCGAACAT	-	novel	NA	P-0043637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	376	518	0	ENST00000250448.2:c.757_777del	p.Met253_Tyr259del	p.M253_Y259del	ENST00000250448	NM_004496.3	253	ATGTTCGAGAACGGCTGCTAC/-	2/2	0.569700315707261	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.567107274764318	3		518	741	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43783907	43783907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	282	602	0	ENST00000382044.4:c.331C>T	p.Gln111Ter	p.Q111*	ENST00000382044	NM_001141980.1	111	Cag/Tag	4/28	0.569700315707261	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.567107274764318	1		602	529	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112764499	112764499	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	131	476	0	ENST00000369452.4:c.1108A>G	p.Ile370Val	p.I370V	ENST00000369452	NM_007373.3	370	Att/Gtt	5/9	0.547339905967305	2	FACETS	0.991	0.906	1	0.496	0.453	0.54	CLONAL	1	TRUE	0	0.567107274764318	2		476	466	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124610	108124611	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0043637-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	172	431	0	ENST00000278616.4:c.1970_1971del	p.Phe657Ter	p.F657*	ENST00000278616	NM_000051.3	656	acTTtt/actt	13/63	0.569700315707261	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.567107274764318	1		431	307	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600572	43600572	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044005-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	563	610	0	ENST00000355710.3:c.798C>G	p.Asp266Glu	p.D266E	ENST00000355710	NM_020975.4	266	gaC/gaG	4/20	0.808674075134584	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.808674075134584	1		610	727	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279540	123279540	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044005-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	499	586	0	ENST00000358487.5:c.892G>C	p.Gly298Arg	p.G298R	ENST00000358487	NM_000141.4	298	Ggc/Cgc	7/18	0.808674075134584	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.808674075134584	1		586	642	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435386	18435386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761165027	NA	P-0044005-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	16	254	0	ENST00000266497.5:c.371G>A	p.Cys124Tyr	p.C124Y	ENST00000266497		124	tGc/tAc	1/31	0.808674075134584	2	FACETS	0.152	0.112	0.199	0.076	0.056	0.1	SUBCLONAL	1	TRUE	0	0.808674075134584	2		254	261	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0044005-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	586	547	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.808674075134584	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.808674075134584	1		547	771	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732352	74732352	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs145534754	NA	P-0044005-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	494	387	0	ENST00000359995.5:c.557G>T	p.Arg186Leu	p.R186L	ENST00000359995	NM_001195427.1	186	cGg/cTg	2/3	0.808674075134584	3	FACETS	0.757	0.727	0.788	0.505	0.484	0.525	SUBCLONAL	2	TRUE	0	0.808674075134584	3		387	1133	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597396	10597396	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044005-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	657	670	0	ENST00000171111.5:c.1807G>T	p.Gly603Trp	p.G603W	ENST00000171111	NM_203500.1	603	Ggg/Tgg	6/6	0.808674075134584	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.808674075134584	1		670	870	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213619	36213619	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044005-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	564	800	0	ENST00000222270.7:c.2721G>T	p.Glu907Asp	p.E907D	ENST00000222270	NM_014727.1	907	gaG/gaT	5/37	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.808674075134584	2		800	1240	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221354	36221354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766608261	NA	P-0044005-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	174	649	0	ENST00000222270.7:c.5188G>A	p.Val1730Met	p.V1730M	ENST00000222270	NM_014727.1	1730	Gtg/Atg	24/37	NA	2	FACETS	0.387	0.356	0.42			1	INDETERMINATE	1	TRUE	NA	0.808674075134584	2		649	1111	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25459857	25459857	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044005-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	321	532	0	ENST00000264709.3:c.2426T>C	p.Val809Ala	p.V809A	ENST00000264709	NM_175629.2	809	gTg/gCg	21/23	0.808486837518965	3	FACETS	0.986	0.931	1	0.493	0.465	0.521	CLONAL	1	TRUE	1	0.808674075134584	3		532	1131	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426799	212426799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044005-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	80	332	0	ENST00000342788.4:c.2316G>T	p.Met772Ile	p.M772I	ENST00000342788	NM_005235.2	772	atG/atT	20/28	0.781860630326163	4	FACETS	0.413	0.363	0.467	0.138	0.121	0.156	SUBCLONAL	1	TRUE	1	0.808674075134584	4		332	866	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196553	106196553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044005-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	219	354	1	ENST00000380013.4:c.4886C>T	p.Pro1629Leu	p.P1629L	ENST00000380013	NM_001127208.2	1629	cCa/cTa	11/11	0.808674075134584	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.808674075134584	1		355	315	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0044005-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	93	370	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.808674075134584	1	FACETS	0.835	0.767	0.902	0.835	0.767	0.902	CLONAL	1	TRUE	0	0.808674075134584	1		370	164	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170136	32170136	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771019003	NA	P-0044005-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	203	747	0	ENST00000375023.3:c.3472C>T	p.Arg1158Ter	p.R1158*	ENST00000375023	NM_004557.3	1158	Cga/Tga	21/30	1	2	FACETS	0.485	0.449	0.522	0.485	0.449	0.522	SUBCLONAL	1	TRUE	1	0.808674075134584	2		747	1036	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397530	116397530	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044005-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	453	409	0	ENST00000397752.3:c.1902C>G	p.Phe634Leu	p.F634L	ENST00000397752	NM_000245.2	634	ttC/ttG	7/21	0.808674075134584	4	FACETS	0.865	0.833	0.896			1	CLONAL	3	TRUE	NA	0.808674075134584	4		409	781	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850288	128850290	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0044005-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2192	149	584	0	ENST00000249373.3:c.1552_1554del	p.Glu518del	p.E518del	ENST00000249373	NM_005631.4	517	gtGGAg/gtg	9/12	0.808674075134584	6	FACETS	0.412	0.374	0.452			1	SUBCLONAL	1	TRUE	NA	0.808674075134584	6		584	2341	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873836	151873836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044005-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	409	437	0	ENST00000262189.6:c.8702C>T	p.Pro2901Leu	p.P2901L	ENST00000262189	NM_170606.2	2901	cCt/cTt	38/59	0.808486837518965	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.808674075134584	3		437	705	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136072	64136072	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044005-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	281	0	0	ENST00000334205.4:c.1333A>T	p.Arg445Trp	p.R445W	ENST00000334205	NM_003942.2	445	Agg/Tgg	11/17	0.326219251436563	2	FACETS	0.792	0.746	0.838	0.396	0.373	0.419	INDETERMINATE	1	TRUE	0	0.808674075134584	2		0	878	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0045007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	99	373	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.236207936229804	2	FACETS	0.903	0.81	1	0.903	0.81	1	CLONAL	2	TRUE	0	0.236207936229804	2		373	464	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	41	200	0	ENST00000342988.3:c.1610A>T	p.Asp537Val	p.D537V	ENST00000342988	NM_005359.5	537	gAc/gTc	12/12	0.207394619148377	1	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	0	0.236207936229804	1		200	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs864622237	NA	P-0045007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	213	348	0	ENST00000269305.4:c.700T>C	p.Tyr234His	p.Y234H	ENST00000269305	NM_001126112.2	234	Tac/Cac	7/11	0.236207936229804	3	FACETS	1	0.953	1			1	CLONAL	3	TRUE	NA	0.236207936229804	3		348	656	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903755	41903755	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0045007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	171	525	1	ENST00000372991.4:c.802A>T	p.Lys268Ter	p.K268*	ENST00000372991	NM_001760.3	268	Aaa/Taa	5/5	0.236207936229804	2	FACETS	0.892	0.821	0.965	0.892	0.821	0.965	CLONAL	2	TRUE	0	0.236207936229804	2		526	812	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492797	56492798	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	142	362	0	ENST00000407977.2:c.141dup	p.Ile48TyrfsTer27	p.I48Yfs*27	ENST00000407977		47	-/T	2/10	0.236207936229804	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	0	0.236207936229804	2		362	586	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974754	21974754	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045007-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	53	196	0	ENST00000304494.5:c.73del	p.Val25Ter	p.V25*	ENST00000304494	NM_000077.4	25	Gta/ta	1/3	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.236207936229804	2		196	340	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123688	11123688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	55	443	2	ENST00000358026.2:c.2338G>A	p.Glu780Lys	p.E780K	ENST00000358026	NM_001128849.1	780	Gag/Aag	16/36	0.272745287152369	3	FACETS	1	0.953	1	0.401	0.35	0.454	INDETERMINATE	1	TRUE	0	0.814500847358837	3		445	158	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555526101	NA	P-0045180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	88	736	0	ENST00000269305.4:c.497C>G	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tGa	5/11	0.217564278623379	4	FACETS	0.916	0.864	0.962	0.916	0.864	0.962	INDETERMINATE	4	TRUE	0	0.814500847358837	4		736	107	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400858	72400858	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	24	334	0	ENST00000357731.5:c.313A>G	p.Ile105Val	p.I105V	ENST00000357731	NM_173808.2	105	Ata/Gta	2/7	0.814500847358837	3	FACETS	0.553	0.438	0.682	0.184	0.146	0.228	SUBCLONAL	1	TRUE	0	0.814500847358837	3		334	150	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896530	78896530	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	70	610	0	ENST00000306801.3:c.2527G>T	p.Val843Leu	p.V843L	ENST00000306801	NM_020761.2	843	Gtg/Ttg	22/34	0.814500847358837	7	FACETS	0.805	0.708	0.909	0.403	0.354	0.455	CLONAL	2	TRUE	3	0.814500847358837	7		610	324	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38631974	38631974	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045256-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	62	447	0	ENST00000299084.4:c.460G>A	p.Asp154Asn	p.D154N	ENST00000299084	NM_152594.2	154	Gat/Aat	5/7	0.283540137025926	1	FACETS	0.92	0.798	1	0.92	0.798	1	CLONAL	1	TRUE	0	0.283540137025926	1		447	408	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220578	1220578	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0045256-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	73	559	0	ENST00000326873.7:c.598-2A>C		p.X200_splice	ENST00000326873	NM_000455.4	200			0.283540137025926	1	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	0	0.283540137025926	1		559	442	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2202722	2202722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045256-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	95	599	0	ENST00000398665.3:c.731C>T	p.Ala244Val	p.A244V	ENST00000398665	NM_032482.2	244	gCc/gTc	9/28	0.283540137025926	1	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	0	0.283540137025926	1		599	573	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602328	10602328	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045256-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	113	724	0	ENST00000171111.5:c.1250G>T	p.Gly417Val	p.G417V	ENST00000171111	NM_203500.1	417	gGg/gTg	3/6	0.283540137025926	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.283540137025926	1		724	608	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61706062	61706062	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045256-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	75	500	0	ENST00000401558.2:c.3109G>C	p.Glu1037Gln	p.E1037Q	ENST00000401558	NM_003400.3	1037	Gag/Cag	25/25	1	2	FACETS	0.863	0.757	0.977	0.863	0.757	0.977	CLONAL	1	TRUE	1	0.283540137025926	2		500	613	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678369	88678370	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	A	novel	NA	P-0045256-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	133	692	0	ENST00000360948.2:c.1166_1167delinsT	p.Gln389LeufsTer25	p.Q389Lfs*25	ENST00000360948	NM_001012338.2	389	cAG/cT	9/19	0.207030902578003	3	FACETS	1	0.985	1	0.732	0.665	0.801	CLONAL	1	TRUE	1	0.283540137025926	3		692	732	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045449-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	166	230	0				ENST00000310581	NM_198253.2	-/1132			0.891891296884871	3	FACETS	0.948	0.891	1	0.948	0.891	1	CLONAL	2	TRUE	1	0.891891296884871	3		230	284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0045449-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	571	727	3	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.891891296884871	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.891891296884871	2		730	634	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955535	48955535	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045449-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	61	143	0	ENST00000267163.4:c.1651G>T	p.Glu551Ter	p.E551*	ENST00000267163	NM_000321.2	551	Gaa/Taa	17/27	0.879034991138869	1	FACETS	0.773	0.7	0.844	0.773	0.7	0.844	SUBCLONAL	1	TRUE	0	0.891891296884871	1		143	98	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	311	230	0				ENST00000310581	NM_198253.2	-/1132			0.559144009780472	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.843305540848442	4		230	610	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114679	108114679	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs778624615	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	94	187	0	ENST00000278616.4:c.497-1G>C		p.X166_splice	ENST00000278616	NM_000051.3	166			0.428714590267837	2	FACETS	1	0.964	1	0.557	0.508	0.607	INDETERMINATE	1	TRUE	0	0.843305540848442	2		187	200	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968136	55968136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747362899	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	124	440	0	ENST00000263923.4:c.2194G>A	p.Glu732Lys	p.E732K	ENST00000263923	NM_002253.2	732	Gaa/Aaa	15/30	0.694019532143467	1	FACETS	0.338	0.307	0.37	0.338	0.307	0.37	SUBCLONAL	1	TRUE	0	0.843305540848442	1		440	503	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183067	32183067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1273	217	632	0	ENST00000375023.3:c.1957G>A	p.Asp653Asn	p.D653N	ENST00000375023	NM_004557.3	653	Gat/Aat	12/30	0.843305540848442	3	FACETS	0.491	0.455	0.529	0.246	0.227	0.265	SUBCLONAL	1	TRUE	1	0.843305540848442	3		632	1490	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133488	55133488	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	143	380	0	ENST00000257290.5:c.792C>G	p.Ile264Met	p.I264M	ENST00000257290	NM_006206.4	264	atC/atG	6/23	0.694019532143467	1	FACETS	0.416	0.382	0.452	0.416	0.382	0.452	SUBCLONAL	1	TRUE	0	0.843305540848442	1		380	471	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178638	32178638	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140125037	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	182	651	0	ENST00000375023.3:c.2756C>T	p.Pro919Leu	p.P919L	ENST00000375023	NM_004557.3	919	cCc/cTc	18/30	0.843305540848442	3	FACETS	0.467	0.429	0.506	0.233	0.214	0.253	SUBCLONAL	1	TRUE	1	0.843305540848442	3		651	1315	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350198	89350198	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	181	636	0	ENST00000301030.4:c.2752G>C	p.Glu918Gln	p.E918Q	ENST00000301030	NM_001256183.1	918	Gag/Cag	9/13	1	2	FACETS	0.485	0.447	0.524	0.485	0.447	0.524	SUBCLONAL	1	TRUE	1	0.843305540848442	2		636	885	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030058	36030058	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	168	536	0	ENST00000358208.4:c.1093C>T	p.Gln365Ter	p.Q365*	ENST00000358208		365	Cag/Tag	9/12	NA	2	FACETS	0.392	0.359	0.426			1	INDETERMINATE	1	TRUE	NA	0.843305540848442	2		536	1017	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836846	151836846	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	413	427	0	ENST00000262189.6:c.14374G>C	p.Glu4792Gln	p.E4792Q	ENST00000262189	NM_170606.2	4792	Gag/Cag	56/59	0.492853491101801	2	FACETS	0.8	0.773	0.827	0.8	0.773	0.827	INDETERMINATE	2	TRUE	0	0.843305540848442	2		427	612	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484280	120484280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	106	427	0	ENST00000256646.2:c.2850G>A	p.Met950Ile	p.M950I	ENST00000256646	NM_024408.3	950	atG/atA	18/34	0.341888883091723	6	FACETS	0.585	0.523	0.651	0.195	0.174	0.217	INDETERMINATE	1	TRUE	3	0.843305540848442	6		427	1155	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466782	25466782	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	183	503	0	ENST00000264709.3:c.1921G>C	p.Asp641His	p.D641H	ENST00000264709	NM_175629.2	641	Gat/Cat	16/23	0.843305540848442	3	FACETS	0.551	0.507	0.596	0.184	0.169	0.199	SUBCLONAL	1	TRUE	0	0.843305540848442	3		503	1120	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177456	56177456	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	104	370	0	ENST00000399503.3:c.2429C>G	p.Ser810Ter	p.S810*	ENST00000399503	NM_005921.1	810	tCa/tGa	14/20	0.828578529625536	2	FACETS	0.667	0.602	0.734	0.333	0.301	0.367	SUBCLONAL	1	TRUE	0	0.843305540848442	2		370	370	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932138	39932138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201595640	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	320	602	0	ENST00000378444.4:c.2461G>A	p.Val821Met	p.V821M	ENST00000378444	NM_001123385.1	821	Gtg/Atg	4/15	0.843305540848442	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.843305540848442	1		602	429	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343550	118343550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	121	446	0	ENST00000534358.1:c.1676C>T	p.Ser559Leu	p.S559L	ENST00000534358	NM_005933.3	559	tCg/tTg	3/36	0.428714590267837	2	FACETS	0.488	0.442	0.536	0.244	0.221	0.268	INDETERMINATE	1	TRUE	0	0.843305540848442	2		446	588	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798510	32798510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746574637	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	199	595	0	ENST00000374899.4:c.1346G>A	p.Arg449Gln	p.R449Q	ENST00000374899	NM_018833.2	449	cGa/cAa	8/12	0.843305540848442	3	FACETS	0.527	0.487	0.569	0.264	0.243	0.285	SUBCLONAL	1	TRUE	1	0.843305540848442	3		595	1273	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998292	100998292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	31	93	0	ENST00000325455.5:c.1510G>A	p.Ala504Thr	p.A504T	ENST00000325455	NM_001202474.3	504	Gcc/Acc	1/8	0.428714590267837	2	FACETS	0.537	0.441	0.641	0.268	0.22	0.321	INDETERMINATE	1	TRUE	0	0.843305540848442	2		93	137	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247175	153247175	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	85	256	0	ENST00000281708.4:c.1627A>G	p.Arg543Gly	p.R543G	ENST00000281708	NM_033632.3	543	Aga/Gga	10/12	0.446984461379142	1	FACETS	0.367	0.327	0.408	0.367	0.327	0.408	INDETERMINATE	1	TRUE	0	0.843305540848442	1		256	318	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914305	32914305	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	87	463	0	ENST00000380152.3:c.5813G>A	p.Gly1938Glu	p.G1938E	ENST00000380152		1938	gGa/gAa	11/27	0.456449222956637	1	FACETS	0.42	0.376	0.466	0.42	0.376	0.466	INDETERMINATE	1	TRUE	0	0.843305540848442	1		463	284	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305460	65305460	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	349	444	0	ENST00000342505.4:c.2668G>C	p.Glu890Gln	p.E890Q	ENST00000342505	NM_002227.2	890	Gag/Cag	20/25	0.349907090442112	4	FACETS	0.929	0.884	0.974	0.929	0.884	0.974	INDETERMINATE	2	TRUE	2	0.843305540848442	4		444	821	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094319	193094319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	153	328	0	ENST00000367435.3:c.209C>T	p.Ser70Phe	p.S70F	ENST00000367435	NM_024529.4	70	tCt/tTt	2/17	0.693297151777935	3	FACETS	0.836	0.768	0.907	0.279	0.256	0.303	CLONAL	1	TRUE	0	0.843305540848442	3		328	617	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945363	71945363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	199	616	0	ENST00000298229.2:c.2251G>A	p.Glu751Lys	p.E751K	ENST00000298229	NM_001567.3	751	Gag/Aag	20/28	0.428714590267837	2	FACETS	0.5	0.464	0.539	0.25	0.232	0.27	INDETERMINATE	1	TRUE	0	0.843305540848442	2		616	943	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556179	29556179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	48	106	0	ENST00000356175.3:c.2546G>A	p.Gly849Glu	p.G849E	ENST00000356175	NM_000267.3	849	gGa/gAa	21/57	0.802424806615867	2	FACETS	0.711	0.613	0.816	0.356	0.306	0.408	SUBCLONAL	1	TRUE	0	0.843305540848442	2		106	160	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740678	58740678	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	154	441	0	ENST00000305921.3:c.1583G>A	p.Arg528Lys	p.R528K	ENST00000305921	NM_003620.3	528	aGa/aAa	6/6	1	2	FACETS	0.561	0.515	0.609	0.561	0.515	0.609	SUBCLONAL	1	TRUE	1	0.843305540848442	2		441	651	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249913	39249913	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs267607079	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	295	521	0	ENST00000402219.2:c.1656G>T	p.Arg552Ser	p.R552S	ENST00000402219	NM_005633.3	552	agG/agT	10/23	0.843305540848442	3	FACETS	1	0.978	1	0.357	0.336	0.378	CLONAL	1	TRUE	0	0.843305540848442	3		521	929	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010415	48010415	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs776745497	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1304	236	412	0	ENST00000234420.5:c.43C>G	p.Pro15Ala	p.P15A	ENST00000234420	NM_000179.2	15	Ccg/Gcg	1/10	0.843305540848442	3	FACETS	0.517	0.48	0.554	0.172	0.16	0.185	SUBCLONAL	1	TRUE	0	0.843305540848442	3		412	1540	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030837	36030837	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	119	347	0	ENST00000358208.4:c.1117-1G>A		p.X373_splice	ENST00000358208		373			NA	2	FACETS	0.446	0.403	0.491			1	INDETERMINATE	1	TRUE	NA	0.843305540848442	2		347	633	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24129386	24129386	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	186	293	0	ENST00000263121.7:c.30C>A	p.Phe10Leu	p.F10L	ENST00000263121	NM_003073.3	10	ttC/ttA	1/9	0.155984625355362	5	FACETS	0.964	0.89	1			1	INDETERMINATE	1	TRUE	NA	0.843305540848442	5		293	1036	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982103	38982103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	69	349	0	ENST00000357387.3:c.619G>A	p.Gly207Arg	p.G207R	ENST00000357387	NM_152756.3	207	Gga/Aga	8/38	0.777131031444942	6	FACETS	0.478	0.415	0.546	0.119	0.103	0.137	SUBCLONAL	1	TRUE	2	0.843305540848442	6		349	920	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652048	36652049	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	1114	662	0	ENST00000244741.5:c.171dup	p.Pro58ThrfsTer5	p.P58Tfs*5	ENST00000244741	NM_000389.4	57	aca/acAa	2/3	0.843305540848442	3	FACETS	0.932	0.917	0.945	1	0.999	1	CLONAL	3	TRUE	1	0.843305540848442	3		662	1344	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099233	157099233	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1478614436	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	189	380	0	ENST00000346085.5:c.170C>T	p.Ser57Leu	p.S57L	ENST00000346085	NM_020732.3	57	tCg/tTg	1/20	0.843305540848442	3	FACETS	0.605	0.558	0.653	0.202	0.186	0.218	SUBCLONAL	1	TRUE	0	0.843305540848442	3		380	1054	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187266	38187266	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	339	575	0	ENST00000317025.8:c.1211C>T	p.Ser404Phe	p.S404F	ENST00000317025	NM_023034.1	404	tCc/tTc	6/24	0.843305540848442	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.843305540848442	1		575	428	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778789	76778789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	74	498	0	ENST00000373344.5:c.6790G>A	p.Glu2264Lys	p.E2264K	ENST00000373344	NM_000489.3	2264	Gaa/Aaa	31/35	0.74896857877727	1	FACETS	0.327	0.289	0.368	0.327	0.289	0.368	SUBCLONAL	1	TRUE	0	0.843305540848442	1		498	310	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106123	27106123	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	190	467	0	ENST00000324856.7:c.5734G>T	p.Asp1912Tyr	p.D1912Y	ENST00000324856	NM_006015.4	1912	Gat/Tat	20/20	NA	2	FACETS	0.732	0.68	0.785			1	INDETERMINATE	1	TRUE	NA	0.843305540848442	2		467	616	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999190	100999190	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	136	605	0	ENST00000325455.5:c.612C>G	p.His204Gln	p.H204Q	ENST00000325455	NM_001202474.3	204	caC/caG	1/8	0.428714590267837	2	FACETS	0.435	0.395	0.476	0.217	0.197	0.238	INDETERMINATE	1	TRUE	0	0.843305540848442	2		605	742	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102094399	102094399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	147	375	0	ENST00000282441.5:c.1079G>A	p.Gly360Glu	p.G360E	ENST00000282441	NM_001130145.2	360	gGg/gAg	7/9	0.428714590267837	2	FACETS	0.503	0.46	0.548	0.252	0.23	0.274	INDETERMINATE	1	TRUE	0	0.843305540848442	2		375	693	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165171	47165171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045861-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	61	297	0	ENST00000409792.3:c.955C>T	p.Leu319Phe	p.L319F	ENST00000409792	NM_014159.6	319	Ctt/Ttt	3/21	1	2	FACETS	0.416	0.36	0.475	0.416	0.36	0.475	SUBCLONAL	1	TRUE	1	0.843305540848442	2		297	348	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0045867-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	126	277	1	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	0.925266869385147	2	FACETS	0.953	0.879	1	0.477	0.439	0.515	CLONAL	1	TRUE	0	0.927585089212457	2		278	285	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACAACCCCC	rs397517115	NA	P-0045867-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	387	476	0	ENST00000275493.2:c.2311_2319dup	p.Asn771_His773dup	p.N771_H773dup	ENST00000275493	NM_005228.3	771	gac/gACAACCCCCac	20/28	0.899836544936421	4	FACETS	0.864	0.824	0.904	0.864	0.824	0.904	CLONAL	2	TRUE	2	0.927585089212457	4		476	931	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs760043106	NA	P-0045867-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	384	576	0	ENST00000269305.4:c.584T>A	p.Ile195Asn	p.I195N	ENST00000269305	NM_001126112.2	195	aTc/aAc	6/11	0.927585089212457	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.927585089212457	2		576	411	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032284	26032284	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779303049	NA	P-0045867-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	64	291	0	ENST00000244661.2:c.5C>T	p.Ala2Val	p.A2V	ENST00000244661	NM_003537.3	2	gCt/gTt	1/1	0.377463678350826	6	FACETS	0.936	0.813	1	0.234	0.203	0.267	INDETERMINATE	1	TRUE	2	0.927585089212457	6		291	421	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444662	78444663	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGA	novel	NA	P-0045867-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	430	404	1	ENST00000370768.2:c.24_26dup	p.Pro10dup	p.P10dup	ENST00000370768	NM_003902.3	10	ccc/ccTCCc	1/20	0.811837082006382	4	FACETS	0.934	0.894	0.974	0.934	0.894	0.974	CLONAL	2	TRUE	2	0.927585089212457	4		405	957	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3841996	3841996	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1487159105	NA	P-0045867-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	239	297	0	ENST00000262367.5:c.1316A>T	p.Lys439Met	p.K439M	ENST00000262367	NM_004380.2	439	aAg/aTg	5/31	0.511058292485022	6	FACETS	0.929	0.876	0.982	0.929	0.876	0.982	INDETERMINATE	3	TRUE	3	0.927585089212457	6		297	528	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259475	55259475	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045867-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	447	440	0	ENST00000275493.2:c.2533G>T	p.Val845Leu	p.V845L	ENST00000275493	NM_005228.3	845	Gtg/Ttg	21/28	0.899836544936421	4	FACETS	0.888	0.85	0.926	0.888	0.85	0.926	CLONAL	2	TRUE	2	0.927585089212457	4		440	1046	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55270181	55270237	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGTAACCTTCCCTCATTTCCTCCTGCAGCTGCAAAGCTGTCCCATCAAGGAAGACA	GAGTAACCTTCCCTCATTTCCTCCTGCAGCTGCAAAGCTGTCCCATCAAGGAAGACA	-	novel	NA	P-0045867-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	521	642	0	ENST00000275493.2:c.3163-28_3191del		p.X1055_splice	ENST00000275493	NM_005228.3	1055		27/28	0.899836544936421	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.927585089212457	4		642	1053	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579559	7579559	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046558-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	48	690	0	ENST00000269305.4:c.128del	p.Leu43Ter	p.L43*	ENST00000269305	NM_001126112.2	43	tTg/tg	4/11	1	2	FACETS	0.979	0.827	1	0.979	0.827	1	CLONAL	1	TRUE	1	0.172090652530545	2		690	570	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0046558-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	37	481	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	1	2	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	TRUE	1	0.172090652530545	2		481	419	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112380	115112380	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374981272	NA	P-0046558-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	26	444	0	ENST00000257566.3:c.1360C>T	p.Arg454Cys	p.R454C	ENST00000257566	NM_016569.3	454	Cgc/Tgc	7/8	1	2	FACETS	0.842	0.667	1	0.842	0.667	1	CLONAL	1	TRUE	1	0.172090652530545	2		444	359	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46597039	46597039	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046558-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	24	416	0	ENST00000263734.3:c.853G>C	p.Asp285His	p.D285H	ENST00000263734	NM_001430.4	285	Gac/Cac	7/16	1	2	FACETS	0.638	0.499	0.799	0.638	0.499	0.799	SUBCLONAL	1	TRUE	1	0.172090652530545	2		416	437	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271480	26271480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046558-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	101	619	0	ENST00000305910.3:c.133G>A	p.Gly45Ser	p.G45S	ENST00000305910	NM_003534.2	45	Ggc/Agc	1/1	0.163825715854378	2	FACETS	0.978	0.876	1	0.978	0.876	1	CLONAL	2	TRUE	0	0.172090652530545	2		619	600	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030599	47030599	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046558-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	33	735	0	ENST00000377604.3:c.374A>G	p.Glu125Gly	p.E125G	ENST00000377604	NM_001204468.1	125	gAg/gGg	4/24	1	2	FACETS	0.746	0.607	0.904	0.746	0.607	0.904	CLONAL	1	TRUE	1	0.172090652530545	2		735	514	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0046836-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	46	235	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	0.977	0.827	1	0.977	0.827	1	CLONAL	1	TRUE	1	0.305646878144375	2		235	308	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164884	106164884	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1339287432	NA	P-0046836-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	76	496	0	ENST00000380013.4:c.3752C>T	p.Thr1251Met	p.T1251M	ENST00000380013	NM_001127208.2	1251	aCg/aTg	6/11	NA	2	FACETS	0.989	0.869	1			1	INDETERMINATE	1	TRUE	NA	0.305646878144375	2		496	503	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001429	29001429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753144948	NA	P-0046836-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	53	410	0	ENST00000282397.4:c.1303G>A	p.Val435Met	p.V435M	ENST00000282397	NM_002019.4	435	Gtg/Atg	10/30	0.295195259271927	2	FACETS	0.925	0.792	1	0.462	0.396	0.535	CLONAL	1	TRUE	0	0.305646878144375	2		410	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	G	rs1131691003	NA	P-0046836-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	199	633	0	ENST00000269305.4:c.96+1G>C		p.X32_splice	ENST00000269305	NM_001126112.2	32			0.295195259271927	2	FACETS	0.996	0.927	1	0.996	0.927	1	CLONAL	2	TRUE	0	0.305646878144375	2		633	654	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573133	64573133	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046836-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	171	511	0	ENST00000312049.6:c.1159G>T	p.Glu387Ter	p.E387*	ENST00000312049	NM_130799.2	387	Gag/Tag	8/10	0.305646878144375	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.305646878144375	3		511	586	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575555	64575570	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GCTGTCCAATTTGGTG	GCTGTCCAATTTGGTG	-	novel	NA	P-0046836-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	55	579	2	ENST00000312049.6:c.447_462del	p.Thr150ProfsTer30	p.T150Pfs*30	ENST00000312049	NM_130799.2	149	ggCACCAAATTGGACAGC/gg	3/10	0.305646878144375	3	FACETS	0.704	0.602	0.816	0.352	0.301	0.408	SUBCLONAL	1	TRUE	1	0.305646878144375	3		581	589	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629127	86629127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046836-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	44	351	0	ENST00000274376.6:c.872C>G	p.Thr291Arg	p.T291R	ENST00000274376	NM_002890.2	291	aCa/aGa	4/25	1	2	FACETS	0.827	0.696	0.972	0.827	0.696	0.972	CLONAL	1	TRUE	1	0.305646878144375	2		351	348	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0047113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	72	373	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.266948797512642	2		373	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0047113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	111	751	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.266948797512642	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.266948797512642	1		751	664	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0047113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	124	652	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.266948797512642	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.266948797512642	1		652	590	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423632	88423632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1478926904	NA	P-0047113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	66	522	0	ENST00000360948.2:c.2203C>T	p.Arg735Cys	p.R735C	ENST00000360948	NM_001012338.2	735	Cgc/Tgc	18/19	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.266948797512642	2		522	487	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662691	117662691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368206665	NA	P-0047113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	86	457	0	ENST00000368508.3:c.4774C>T	p.Arg1592Cys	p.R1592C	ENST00000368508	NM_002944.2	1592	Cgt/Tgt	29/43	0.176870855029199	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.266948797512642	1		457	524	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390071	89390071	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760135022	NA	P-0047342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	70	250	0	ENST00000336596.2:c.820C>T	p.Arg274Ter	p.R274*	ENST00000336596	NM_005233.5	274	Cga/Tga	4/17	0.167104982788847	0	FACETS	0.833	0.732	0.94			1	INDETERMINATE	1	FALSE	0	0.34795093776533	0		250	315	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609942	43609947	+	inframe_deletion	In_Frame_Del	DEL	GAGCTG	GAGCTG	-	rs121913312	NA	P-0047749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	231	518	0	ENST00000355710.3:c.1894_1899del	p.Glu632_Leu633del	p.E632_L633del	ENST00000355710	NM_020975.4	632	GAGCTG/-	11/20	0.297762507048141	1	FACETS	0.674	0.633	0.715	0.674	0.633	0.715	INDETERMINATE	1	TRUE	0	0.741287512172105	1		518	582	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058502	42058502	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	75	280	0	ENST00000219905.7:c.8222A>T	p.Glu2741Val	p.E2741V	ENST00000219905	NM_001164273.1	2741	gAg/gTg	24/24	0.316690545233911	1	FACETS	0.419	0.37	0.47	0.419	0.37	0.47	INDETERMINATE	1	TRUE	0	0.741287512172105	1		280	304	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27192565	27192565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	117	263	0	ENST00000380036.4:c.1568G>A	p.Gly523Glu	p.G523E	ENST00000380036	NM_000459.3	523	gGa/gAa	11/23	0.316690545233911	1	FACETS	0.493	0.448	0.539	0.493	0.448	0.539	INDETERMINATE	1	TRUE	0	0.741287512172105	1		263	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0047802-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	25	574	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.463813608714203	1	FACETS	0.82	0.66	0.995	0.82	0.66	0.995	CLONAL	1	TRUE	0	0.463813608714203	1		574	101	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133048	30133048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047802-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	24	341	0	ENST00000331968.5:c.553C>T	p.His185Tyr	p.H185Y	ENST00000331968	NM_002742.2	185	Cat/Tat	4/18	0.463813608714203	1	FACETS	0.764	0.611	0.933	0.764	0.611	0.933	CLONAL	1	TRUE	0	0.463813608714203	1		341	104	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68982094	68982094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047802-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	44	452	0	ENST00000288368.4:c.1468C>T	p.His490Tyr	p.H490Y	ENST00000288368	NM_024870.2	490	Cat/Tat	13/40	0.463813608714203	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	0	0.463813608714203	1		452	136	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661913	29661913	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047802-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	18	418	0	ENST00000356175.3:c.5808del	p.Arg1937ValfsTer21	p.R1937Vfs*21	ENST00000356175	NM_000267.3	1936	gTt/gt	39/57	0.463813608714203	1	FACETS	0.685	0.526	0.865	0.685	0.526	0.865	SUBCLONAL	1	TRUE	0	0.463813608714203	1		418	87	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64286802	64286802	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047802-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	20	370	0	ENST00000370651.3:c.17G>T	p.Arg6Leu	p.R6L	ENST00000370651	NM_003463.4	6	cGc/cTc	2/6	1	2	FACETS	0.695	0.538	0.874	0.695	0.538	0.874	SUBCLONAL	1	TRUE	1	0.463813608714203	2		370	124	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0048104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	87	359	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.279255976354849	2		359	549	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578538	7578538	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1131691037	NA	P-0048104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	175	714	0	ENST00000269305.4:c.392A>T	p.Asn131Ile	p.N131I	ENST00000269305	NM_001126112.2	131	aAc/aTc	5/11	0.279255976354849	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.279255976354849	1		714	986	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761121	59761121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	302	483	0	ENST00000259008.2:c.3286G>A	p.Glu1096Lys	p.E1096K	ENST00000259008	NM_032043.2	1096	Gaa/Aaa	20/20	0.161506612070208	5	FACETS	0.924	0.871	0.979			1	INDETERMINATE	3	TRUE	NA	0.279255976354849	5		483	1107	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761169	59761169	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	272	482	1	ENST00000259008.2:c.3238G>C	p.Asp1080His	p.D1080H	ENST00000259008	NM_032043.2	1080	Gat/Cat	20/20	0.161506612070208	5	FACETS	0.856	0.804	0.91			1	INDETERMINATE	3	TRUE	NA	0.279255976354849	5		483	1076	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761031	59761031	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	281	435	0	ENST00000259008.2:c.3376G>A	p.Glu1126Lys	p.E1126K	ENST00000259008	NM_032043.2	1126	Gaa/Aaa	20/20	0.161506612070208	5	FACETS	0.921	0.866	0.977			1	INDETERMINATE	3	TRUE	NA	0.279255976354849	5		435	1034	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761073	59761073	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	276	464	0	ENST00000259008.2:c.3334G>C	p.Asp1112His	p.D1112H	ENST00000259008	NM_032043.2	1112	Gat/Cat	20/20	0.161506612070208	5	FACETS	0.884	0.831	0.94			1	INDETERMINATE	3	TRUE	NA	0.279255976354849	5		464	1057	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	30	344	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.962	0.781	1	1	0.967	1	CLONAL	3	TRUE	1	0.1	2		344	208	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739030	145739030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199562131	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	112	717	1	ENST00000428558.2:c.2125C>T	p.Arg709Trp	p.R709W	ENST00000428558	NM_004260.3	709	Cgg/Tgg	13/22	1	2	FACETS	1	0.945	1	1	0.992	1	CLONAL	4	TRUE	1	0.1	2		718	524	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074178	8074178	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	26	364	0	ENST00000377482.5:c.481G>T	p.Ala161Ser	p.A161S	ENST00000377482	NM_018948.3	161	Gcc/Tcc	4/4	1	2	FACETS	1	0.846	1	1	0.954	1	CLONAL	2	TRUE	1	0.1	2		364	241	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775907	9775907	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	69	784	0	ENST00000377346.4:c.371G>A	p.Gly124Asp	p.G124D	ENST00000377346	NM_005026.3	124	gGc/gAc	5/24	1	2	FACETS	1	0.874	1	1	0.985	1	CLONAL	3	TRUE	1	0.1	2		784	460	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778848	9778848	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	113	770	0	ENST00000377346.4:c.1117C>T	p.Gln373Ter	p.Q373*	ENST00000377346	NM_005026.3	373	Cag/Tag	9/24	1	2	FACETS	1	0.963	1	1	0.991	1	CLONAL	3	TRUE	1	0.1	2		770	660	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782385	9782385	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	70	860	0	ENST00000377346.4:c.2318G>T	p.Ser773Ile	p.S773I	ENST00000377346	NM_005026.3	773	aGc/aTc	18/24	1	2	FACETS	1	0.904	1	1	0.982	1	CLONAL	2	TRUE	1	0.1	2		860	670	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184559	11184559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	62	617	0	ENST00000361445.4:c.6658C>T	p.Leu2220Phe	p.L2220F	ENST00000361445	NM_004958.3	2220	Ctc/Ttc	47/58	1	2	FACETS	1	0.903	1	1	0.986	1	CLONAL	4	TRUE	1	0.1	2		617	297	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187864	11187864	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	54	474	0	ENST00000361445.4:c.6034-1G>T		p.X2012_splice	ENST00000361445	NM_004958.3	2012			1	2	FACETS	0.912	0.785	1	1	0.983	1	CLONAL	4	TRUE	1	0.1	2		474	296	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264638	11264638	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	84	657	1	ENST00000361445.4:c.3924G>T	p.Gln1308His	p.Q1308H	ENST00000361445	NM_004958.3	1308	caG/caT	26/58	1	2	FACETS	0.913	0.81	1	1	0.989	1	CLONAL	4	TRUE	1	0.1	2		658	460	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11273589	11273589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140743545	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	29	501	2	ENST00000361445.4:c.3152C>T	p.Thr1051Met	p.T1051M	ENST00000361445	NM_004958.3	1051	aCg/aTg	21/58	1	2	FACETS	1	0.816	1	1	0.957	1	CLONAL	2	TRUE	1	0.1	2		503	286	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307982	11307982	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	66	561	0	ENST00000361445.4:c.1010G>T	p.Ser337Ile	p.S337I	ENST00000361445	NM_004958.3	337	aGc/aTc	7/58	1	2	FACETS	1	0.923	1	1	0.987	1	CLONAL	4	TRUE	1	0.1	2		561	307	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260984	16260984	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762266580	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	64	496	0	ENST00000375759.3:c.8249C>A	p.Ser2750Tyr	p.S2750Y	ENST00000375759	NM_015001.2	2750	tCt/tAt	11/15	1	2	FACETS	1	0.933	1	1	0.986	1	CLONAL	4	TRUE	1	0.1	2		496	289	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057932	27057932	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	131	679	0	ENST00000324856.7:c.1640G>T	p.Ser547Ile	p.S547I	ENST00000324856	NM_006015.4	547	aGc/aTc	3/20	1	2	FACETS	1	0.916	1	1	0.993	1	CLONAL	4	TRUE	1	0.1	2		679	650	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100129	27100129	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	35	691	0	ENST00000324856.7:c.3925C>A	p.Leu1309Ile	p.L1309I	ENST00000324856	NM_006015.4	1309	Ctc/Atc	16/20	1	2	FACETS	0.764	0.626	0.919	1	0.949	1	CLONAL	2	TRUE	1	0.1	2		691	458	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100978	27100978	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	83	695	0	ENST00000324856.7:c.4260G>T	p.Gln1420His	p.Q1420H	ENST00000324856	NM_006015.4	1420	caG/caT	18/20	1	2	FACETS	1	0.903	1	1	0.989	1	CLONAL	4	TRUE	1	0.1	2		695	407	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	60	502	0	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	1	2	FACETS	1	0.88	1	1	0.985	1	CLONAL	4	TRUE	1	0.1	2		502	296	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932151	36932151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	79	669	0	ENST00000361632.4:c.2318C>T	p.Thr773Ile	p.T773I	ENST00000361632		773	aCt/aTt	16/16	1	2	FACETS	0.959	0.848	1	1	0.988	1	CLONAL	4	TRUE	1	0.1	2		669	412	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36934849	36934849	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	30	407	1	ENST00000361632.4:c.1484G>T	p.Arg495Met	p.R495M	ENST00000361632		495	aGg/aTg	11/16	1	2	FACETS	0.888	0.723	1	1	0.97	1	CLONAL	4	TRUE	1	0.1	2		408	169	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532582	46532582	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	36	339	0	ENST00000262741.5:c.495+1G>A		p.X165_splice	ENST00000262741	NM_003629.3	165			1	2	FACETS	0.957	0.796	1	1	0.975	1	CLONAL	4	TRUE	1	0.1	2		339	188	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743608	46743608	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	70	679	2	ENST00000371975.4:c.1989G>T	p.Glu663Asp	p.E663D	ENST00000371975	NM_003579.3	663	gaG/gaT	17/18	1	2	FACETS	1	0.922	1	1	0.986	1	CLONAL	3	TRUE	1	0.1	2		681	435	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303726	65303726	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	17	554	0	ENST00000342505.4:c.3029T>C	p.Leu1010Pro	p.L1010P	ENST00000342505	NM_002227.2	1010	cTt/cCt	22/25	1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	1	0.1	2		554	281	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321281	65321281	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	98	624	0	ENST00000342505.4:c.1559G>T	p.Gly520Val	p.G520V	ENST00000342505	NM_002227.2	520	gGa/gTa	11/25	1	2	FACETS	1	0.96	1	1	0.99	1	CLONAL	3	TRUE	1	0.1	2		624	567	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430348	78430348	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	35	459	0	ENST00000370768.2:c.820G>T	p.Gly274Ter	p.G274*	ENST00000370768	NM_003902.3	274	Gga/Tga	10/20	1	2	FACETS	1	0.896	1	1	0.973	1	CLONAL	3	TRUE	1	0.1	2		459	208	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432751	78432751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	23	405	0	ENST00000370768.2:c.325G>A	p.Asp109Asn	p.D109N	ENST00000370768	NM_003902.3	109	Gat/Aat	5/20	1	2	FACETS	0.886	0.696	1	1	0.955	1	CLONAL	3	TRUE	1	0.1	2		405	173	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85741982	85741982	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	99	620	0	ENST00000370580.1:c.54G>T	p.Lys18Asn	p.K18N	ENST00000370580	NM_003921.4	18	aaG/aaT	1/3	1	2	FACETS	0.95	0.851	1	1	0.991	1	CLONAL	4	TRUE	1	0.1	2		620	521	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166375	118166375	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	30	410	0	ENST00000369448.3:c.885C>A	p.His295Gln	p.H295Q	ENST00000369448	NM_017709.3	295	caC/caA	2/2	1	2	FACETS	0.866	0.702	1	1	0.965	1	CLONAL	3	TRUE	1	0.1	2		410	231	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466378	120466378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779822957	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	57	562	1	ENST00000256646.2:c.4741C>T	p.Arg1581Trp	p.R1581W	ENST00000256646	NM_024408.3	1581	Cgg/Tgg	26/34	1	2	FACETS	1	0.897	1	1	0.983	1	CLONAL	3	TRUE	1	0.1	2		563	362	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150549952	150549952	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	23	255	0	ENST00000369026.2:c.952T>G	p.Phe318Val	p.F318V	ENST00000369026	NM_021960.4	318	Ttc/Gtc	3/3	1	2	FACETS	1	0.85	1	1	0.95	1	CLONAL	2	TRUE	1	0.1	2		255	207	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838026	156838026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749764095	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	82	844	1	ENST00000524377.1:c.559C>T	p.Pro187Ser	p.P187S	ENST00000524377	NM_002529.3	187	Ccc/Tcc	5/17	1	2	FACETS	1	0.921	1	1	0.988	1	CLONAL	3	TRUE	1	0.1	2		845	519	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306558	163306558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	42	449	0	ENST00000271452.3:c.355C>T	p.Arg119Trp	p.R119W	ENST00000271452	NM_145697.2	119	Cgg/Tgg	6/14	1	2	FACETS	1	0.919	1	1	0.978	1	CLONAL	3	TRUE	1	0.1	2		449	243	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175898	176175898	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	34	61	0	ENST00000367669.3:c.217G>T	p.Ala73Ser	p.A73S	ENST00000367669	NM_022457.5	73	Gcc/Tcc	1/20	1	2	FACETS	1	0.897	1	1	0.975	1	CLONAL	4	TRUE	1	0.1	2		61	152	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176176036	176176036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	87	549	0	ENST00000367669.3:c.79G>A	p.Ala27Thr	p.A27T	ENST00000367669	NM_022457.5	27	Gcc/Acc	1/20	1	2	FACETS	1	0.954	1	1	0.989	1	CLONAL	3	TRUE	1	0.1	2		549	508	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980347	201980347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	143	730	0	ENST00000359651.3:c.83C>T	p.Ser28Phe	p.S28F	ENST00000359651		28	tCt/tTt	1/8	1	2	FACETS	1	0.967	1	1	0.994	1	CLONAL	4	TRUE	1	0.1	2		730	641	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666675	206666675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	97	716	0	ENST00000367120.3:c.2009C>T	p.Pro670Leu	p.P670L	ENST00000367120	NM_014002.3	670	cCt/cTt	20/22	1	2	FACETS	0.926	0.828	1	1	0.99	1	CLONAL	4	TRUE	1	0.1	2		716	524	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675353	241675353	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs778399986	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	32	467	0	ENST00000366560.3:c.469A>G	p.Ile157Val	p.I157V	ENST00000366560	NM_000143.3	157	Att/Gtt	4/10	1	2	FACETS	0.857	0.699	1	1	0.967	1	CLONAL	3	TRUE	1	0.1	2		467	249	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115725	8115725	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	31	342	0	ENST00000346208.3:c.1071G>T	p.Lys357Asn	p.K357N	ENST00000346208		357	aaG/aaT	6/6	1	2	FACETS	1	0.9	1	1	0.97	1	CLONAL	3	TRUE	1	0.1	2		342	178	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63699942	63699942	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	11	235	0	ENST00000279873.7:c.277G>T	p.Asp93Tyr	p.D93Y	ENST00000279873	NM_032199.2	93	Gat/Tat	3/10	1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	1	0.1	2		235	152	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845516	63845516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	23	309	0	ENST00000279873.7:c.1255C>T	p.Pro419Ser	p.P419S	ENST00000279873	NM_032199.2	419	Cca/Tca	9/10	1	2	FACETS	1	0.838	1	1	0.949	1	CLONAL	2	TRUE	1	0.1	2		309	212	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405077	70405077	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1208117050	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	41	580	0	ENST00000373644.4:c.2591G>A	p.Ser864Asn	p.S864N	ENST00000373644	NM_030625.2	864	aGt/aAt	4/12	1	2	FACETS	0.903	0.759	1	1	0.978	1	CLONAL	4	TRUE	1	0.1	2		580	227	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624271	89624272	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs786204883	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	50	370	0	ENST00000371953.3:c.46dup	p.Tyr16LeufsTer28	p.Y16Lfs*28	ENST00000371953	NM_000314.4	15	-/T	1/9	1	2	FACETS	0.98	0.839	1	1	0.982	1	CLONAL	4	TRUE	1	0.1	2		370	255	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653844	89653844	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	34	472	0	ENST00000371953.3:c.142A>G	p.Asn48Asp	p.N48D	ENST00000371953	NM_000314.4	48	Aac/Gac	2/9	1	2	FACETS	1	0.837	1	1	0.974	1	CLONAL	4	TRUE	1	0.1	2		472	168	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309752	104309752	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	83	650	0	ENST00000369902.3:c.343G>T	p.Gly115Cys	p.G115C	ENST00000369902	NM_016169.3	115	Ggt/Tgt	3/12	1	2	FACETS	0.993	0.881	1	1	0.989	1	CLONAL	4	TRUE	1	0.1	2		650	418	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900992	114900992	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs916808807	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	75	549	1	ENST00000543371.1:c.602C>T	p.Thr201Met	p.T201M	ENST00000543371	NM_001198531.1	201	aCg/aTg	6/14	1	2	FACETS	0.974	0.858	1	1	0.988	1	CLONAL	4	TRUE	1	0.1	2		550	385	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239530	123239530	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	66	842	1	ENST00000358487.5:c.2307C>A	p.Tyr769Ter	p.Y769*	ENST00000358487	NM_000141.4	769	taC/taA	18/18	1	2	FACETS	0.962	0.841	1	1	0.986	1	CLONAL	4	TRUE	1	0.1	2		843	343	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533521	533521	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1350889077	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	125	798	2	ENST00000451590.1:c.382C>T	p.Arg128Trp	p.R128W	ENST00000451590	NM_001130442.1	128	Cgg/Tgg	4/5	1	2	FACETS	0.948	0.86	1	1	0.992	1	CLONAL	4	TRUE	1	0.1	2		800	659	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129112	64129112	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	58	639	0	ENST00000334205.4:c.652-2A>G		p.X218_splice	ENST00000334205	NM_003942.2	218			1	2	FACETS	1	0.937	1	1	0.984	1	CLONAL	3	TRUE	1	0.1	2		639	336	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138779	64138779	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	101	609	0	ENST00000334205.4:c.2146G>A	p.Gly716Ser	p.G716S	ENST00000334205	NM_003942.2	716	Ggc/Agc	17/17	1	2	FACETS	1	0.947	1	1	0.99	1	CLONAL	3	TRUE	1	0.1	2		609	617	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571852	64571852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	120	856	0	ENST00000312049.6:c.1787G>A	p.Ser596Asn	p.S596N	ENST00000312049	NM_130799.2	596	aGt/aAt	10/10	1	2	FACETS	0.888	0.803	0.977	1	0.992	1	CLONAL	4	TRUE	1	0.1	2		856	676	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941063	71941063	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	89	769	0	ENST00000298229.2:c.939G>T	p.Glu313Asp	p.E313D	ENST00000298229	NM_001567.3	313	gaG/gaT	8/28	1	2	FACETS	1	0.893	1	1	0.99	1	CLONAL	4	TRUE	1	0.1	2		769	444	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941843	71941843	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514511	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	61	590	1	ENST00000298229.2:c.1201C>T	p.Arg401Trp	p.R401W	ENST00000298229	NM_001567.3	401	Cgg/Tgg	11/28	1	2	FACETS	0.992	0.859	1	1	0.983	1	CLONAL	3	TRUE	1	0.1	2		591	410	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943379	71943379	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1165709765	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	71	454	0	ENST00000298229.2:c.1711C>T	p.Arg571Trp	p.R571W	ENST00000298229	NM_001567.3	571	Cgg/Tgg	14/28	1	2	FACETS	0.97	0.852	1	1	0.987	1	CLONAL	4	TRUE	1	0.1	2		454	366	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948172	71948172	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	111	840	0	ENST00000298229.2:c.2884A>G	p.Lys962Glu	p.K962E	ENST00000298229	NM_001567.3	962	Aag/Gag	26/28	1	2	FACETS	1	0.926	1	1	0.992	1	CLONAL	4	TRUE	1	0.1	2		840	538	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949363	71949363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	100	675	2	ENST00000298229.2:c.3743G>A	p.Arg1248His	p.R1248H	ENST00000298229	NM_001567.3	1248	cGc/cAc	28/28	1	2	FACETS	1	0.914	1	1	0.991	1	CLONAL	4	TRUE	1	0.1	2		677	490	SUCCESS
EED	8726	MSKCC	GRCh37	11	85975293	85975293	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	26	282	0	ENST00000263360.6:c.714A>C	p.Glu238Asp	p.E238D	ENST00000263360	NM_003797.3	238	gaA/gaC	7/12	1	2	FACETS	0.903	0.72	1	1	0.961	1	CLONAL	3	TRUE	1	0.1	2		282	192	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920762	100920762	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	62	487	0	ENST00000325455.5:c.2386T>C	p.Ser796Pro	p.S796P	ENST00000325455	NM_001202474.3	796	Tca/Cca	6/8	1	2	FACETS	1	0.916	1	1	0.986	1	CLONAL	4	TRUE	1	0.1	2		487	290	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139218	108139218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775371838	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	40	690	1	ENST00000278616.4:c.2720G>A	p.Cys907Tyr	p.C907Y	ENST00000278616	NM_000051.3	907	tGt/tAt	18/63	1	2	FACETS	0.977	0.816	1	1	0.975	1	CLONAL	3	TRUE	1	0.1	2		691	273	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199934	108199934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	13	242	0	ENST00000278616.4:c.7276C>T	p.Leu2426Phe	p.L2426F	ENST00000278616	NM_000051.3	2426	Ctc/Ttc	49/63	1	2	FACETS	1	0.762	1	1	0.929	1	CLONAL	3	TRUE	1	0.1	2		242	82	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204696	108204696	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	10	192	1	ENST00000278616.4:c.8010+1G>A		p.X2670_splice	ENST00000278616	NM_000051.3	2670			1	2	FACETS	0.926	0.637	1	1	0.904	1	CLONAL	3	TRUE	1	0.1	2		193	72	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118339495	118339495	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	25	352	0	ENST00000534358.1:c.438G>T	p.Glu146Asp	p.E146D	ENST00000534358	NM_005933.3	146	gaG/gaT	2/36	1	2	FACETS	0.975	0.775	1	1	0.961	1	CLONAL	3	TRUE	1	0.1	2		352	171	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118355670	118355670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	38	521	1	ENST00000534358.1:c.4312G>A	p.Ala1438Thr	p.A1438T	ENST00000534358	NM_005933.3	1438	Gcc/Acc	10/36	1	2	FACETS	0.895	0.744	1	1	0.972	1	CLONAL	3	TRUE	1	0.1	2		522	283	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390766	118390766	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	17	439	0	ENST00000534358.1:c.11416C>A	p.Leu3806Met	p.L3806M	ENST00000534358	NM_005933.3	3806	Ctg/Atg	33/36	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.1	2		439	240	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392749	118392749	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	57	601	1	ENST00000534358.1:c.11781G>T	p.Lys3927Asn	p.K3927N	ENST00000534358	NM_005933.3	3927	aaG/aaT	36/36	1	2	FACETS	1	0.937	1	1	0.983	1	CLONAL	3	TRUE	1	0.1	2		602	329	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142500	119142500	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	46	489	0	ENST00000264033.4:c.499G>T	p.Gly167Ter	p.G167*	ENST00000264033	NM_005188.3	167	Gga/Tga	3/16	1	2	FACETS	0.97	0.825	1	1	0.98	1	CLONAL	4	TRUE	1	0.1	2		489	237	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170448	119170448	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751198294	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	34	439	0	ENST00000264033.4:c.2678G>A	p.Arg893Gln	p.R893Q	ENST00000264033	NM_005188.3	893	cGg/cAg	16/16	1	2	FACETS	0.914	0.751	1	1	0.97	1	CLONAL	3	TRUE	1	0.1	2		439	248	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497620	125497620	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	30	425	0	ENST00000428830.2:c.184C>A	p.Leu62Ile	p.L62I	ENST00000428830	NM_001114121.2	62	Cta/Ata	3/14	1	2	FACETS	0.955	0.78	1	1	0.97	1	CLONAL	4	TRUE	1	0.1	2		425	157	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514027	125514027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761313560	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	57	550	1	ENST00000428830.2:c.965G>A	p.Arg322His	p.R322H	ENST00000428830	NM_001114121.2	322	cGc/cAc	10/14	1	2	FACETS	0.986	0.853	1	1	0.984	1	CLONAL	4	TRUE	1	0.1	2		551	289	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427453	427453	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780617531	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	62	648	0	ENST00000399788.2:c.2716G>A	p.Glu906Lys	p.E906K	ENST00000399788	NM_001042603.1	906	Gaa/Aaa	19/28	0.169619318347497	4	FACETS	0.963	0.837	1	1	0.979	1	CLONAL	4	TRUE	2	0.1	4		648	354	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992224	11992224	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565546170	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	23	376	1	ENST00000396373.4:c.314G>A	p.Arg105Gln	p.R105Q	ENST00000396373	NM_001987.4	105	cGa/cAa	3/8	0.169619318347497	4	FACETS	1	0.825	1	1	0.825	1	CLONAL	2	TRUE	2	0.1	4		377	238	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12043945	12043945	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	57	406	0	ENST00000396373.4:c.1324C>A	p.Leu442Met	p.L442M	ENST00000396373	NM_001987.4	442	Ctg/Atg	8/8	0.169619318347497	4	FACETS	1	0.907	1	1	0.979	1	CLONAL	4	TRUE	2	0.1	4		406	295	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870862	12870862	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	58	249	0	ENST00000228872.4:c.89G>A	p.Arg30Lys	p.R30K	ENST00000228872	NM_004064.3	30	aGg/aAg	1/3	0.169619318347497	4	FACETS	0.925	0.801	1	1	0.981	1	CLONAL	5	TRUE	2	0.1	4		249	276	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871858	12871858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	24	207	0	ENST00000228872.4:c.575G>A	p.Gly192Asp	p.G192D	ENST00000228872	NM_004064.3	192	gGc/gAc	2/3	0.169619318347497	4	FACETS	1	0.916	1	0.702	0.55	0.878	CLONAL	1	TRUE	2	0.1	4		207	376	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719955	18719955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1273800580	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	27	449	1	ENST00000266497.5:c.3852G>A	p.Met1284Ile	p.M1284I	ENST00000266497		1284	atG/atA	27/31	0.169619318347497	4	FACETS	1	0.877	1	1	0.946	1	CLONAL	3	TRUE	2	0.1	4		450	175	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636455	21636455	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	45	567	0	ENST00000421138.2:c.555G>T	p.Lys185Asn	p.K185N	ENST00000421138		185	aaG/aaT	7/16	0.169619318347497	4	FACETS	0.917	0.776	1	1	0.97	1	CLONAL	4	TRUE	2	0.1	4		567	270	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644546	21644546	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	64	603	1	ENST00000421138.2:c.121G>T	p.Val41Phe	p.V41F	ENST00000421138		41	Gtc/Ttc	4/16	0.169619318347497	4	FACETS	0.985	0.86	1	1	0.983	1	CLONAL	5	TRUE	2	0.1	4		604	286	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425584	49425584	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	67	868	0	ENST00000301067.7:c.12904C>A	p.Leu4302Ile	p.L4302I	ENST00000301067	NM_003482.3	4302	Ctt/Att	39/54	0.169619318347497	4	FACETS	0.972	0.849	1	1	0.98	1	CLONAL	4	TRUE	2	0.1	4		868	379	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425725	49425725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	85	811	0	ENST00000301067.7:c.12763G>A	p.Gly4255Ser	p.G4255S	ENST00000301067	NM_003482.3	4255	Ggc/Agc	39/54	0.169619318347497	4	FACETS	1	0.938	1	1	0.986	1	CLONAL	4	TRUE	2	0.1	4		811	431	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444783	49444783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	87	830	0	ENST00000301067.7:c.2683C>T	p.Leu895Phe	p.L895F	ENST00000301067	NM_003482.3	895	Ctt/Ttt	10/54	0.169619318347497	4	FACETS	0.917	0.814	1	1	0.984	1	CLONAL	4	TRUE	2	0.1	4		830	522	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492598	50492598	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	84	597	0	ENST00000394963.4:c.1494G>T	p.Lys498Asn	p.K498N	ENST00000394963	NM_003076.4	498	aaG/aaT	12/13	0.169619318347497	4	FACETS	0.901	0.801	1	1	0.986	1	CLONAL	5	TRUE	2	0.1	4		597	410	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494950	56494950	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	98	611	0	ENST00000267101.3:c.3307G>T	p.Gly1103Cys	p.G1103C	ENST00000267101	NM_001982.3	1103	Ggc/Tgc	27/28	0.169619318347497	4	FACETS	0.917	0.822	1	1	0.988	1	CLONAL	5	TRUE	2	0.1	4		611	470	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865244	57865244	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	62	711	1	ENST00000228682.2:c.2721G>T	p.Glu907Asp	p.E907D	ENST00000228682	NM_005269.2	907	gaG/gaT	12/12	0.169619318347497	4	FACETS	1	0.881	1	1	0.98	1	CLONAL	4	TRUE	2	0.1	4		712	336	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222704	69222704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	43	481	0	ENST00000462284.1:c.677C>T	p.Ser226Leu	p.S226L	ENST00000462284	NM_002392.5	226	tCg/tTg	8/11	0.169619318347497	4	FACETS	1	0.887	1	1	0.962	1	CLONAL	3	TRUE	2	0.1	4		481	295	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856533	111856533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	88	303	0	ENST00000341259.2:c.584C>T	p.Ala195Val	p.A195V	ENST00000341259	NM_005475.2	195	gCg/gTg	2/8	0.169619318347497	4	FACETS	0.922	0.821	1	1	0.987	1	CLONAL	5	TRUE	2	0.1	4		303	420	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856543	111856543	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	74	291	0	ENST00000341259.2:c.594G>T	p.Glu198Asp	p.E198D	ENST00000341259	NM_005475.2	198	gaG/gaT	2/8	0.169619318347497	4	FACETS	0.995	0.875	1	1	0.983	1	CLONAL	4	TRUE	2	0.1	4		291	409	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112892416	112892416	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1488672907	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	31	454	0	ENST00000351677.2:c.574G>T	p.Asp192Tyr	p.D192Y	ENST00000351677	NM_002834.3	192	Gat/Tat	5/16	0.169619318347497	4	FACETS	0.984	0.801	1	1	0.942	1	CLONAL	3	TRUE	2	0.1	4		454	231	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112893832	112893832	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	37	426	0	ENST00000351677.2:c.721G>A	p.Asp241Asn	p.D241N	ENST00000351677	NM_002834.3	241	Gat/Aat	6/16	0.169619318347497	4	FACETS	1	0.839	1	1	0.967	1	CLONAL	4	TRUE	2	0.1	4		426	202	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112163	115112163	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866220131	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	70	619	2	ENST00000257566.3:c.1577C>T	p.Ala526Val	p.A526V	ENST00000257566	NM_016569.3	526	gCc/gTc	7/8	0.169619318347497	4	FACETS	1	0.934	1	1	0.977	1	CLONAL	3	TRUE	2	0.1	4		621	464	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112283	115112283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1018135320	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	32	99	2	ENST00000257566.3:c.1457C>T	p.Thr486Met	p.T486M	ENST00000257566	NM_016569.3	486	aCg/aTg	7/8	0.169619318347497	4	FACETS	0.986	0.817	1	1	0.97	1	CLONAL	6	TRUE	2	0.1	4		101	119	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114148	115114148	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140580685	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	51	576	0	ENST00000257566.3:c.1069G>A	p.Ala357Thr	p.A357T	ENST00000257566	NM_016569.3	357	Gcc/Acc	6/8	0.169619318347497	4	FACETS	0.846	0.72	0.984	1	0.948	1	CLONAL	3	TRUE	2	0.1	4		576	442	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115406	115115406	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	25	647	1	ENST00000257566.3:c.920G>T	p.Gly307Val	p.G307V	ENST00000257566	NM_016569.3	307	gGa/gTa	5/8	0.169619318347497	4	FACETS	0.821	0.647	1	0.821	0.647	1	CLONAL	2	TRUE	2	0.1	4		648	335	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541645	120541645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	21	574	2	ENST00000229340.5:c.212G>A	p.Arg71His	p.R71H	ENST00000229340	NM_006861.6	71	cGc/cAc	3/6	0.169619318347497	4	FACETS	1	0.844	1	0.566	0.435	0.72	CLONAL	1	TRUE	2	0.1	4		576	408	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541697	120541697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs984926660	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	27	707	0	ENST00000229340.5:c.160G>A	p.Gly54Arg	p.G54R	ENST00000229340	NM_006861.6	54	Ggg/Agg	3/6	0.169619318347497	4	FACETS	1	0.899	1	0.619	0.491	0.765	CLONAL	1	TRUE	2	0.1	4		707	480	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794801	120794801	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	140	877	0	ENST00000257552.2:c.556C>G	p.Pro186Ala	p.P186A	ENST00000257552	NM_002442.3	186	Cca/Gca	9/15	0.169619318347497	4	FACETS	1	0.942	1	1	0.992	1	CLONAL	5	TRUE	2	0.1	4		877	593	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432008	121432009	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	129	852	0	ENST00000257555.6:c.755_756insT	p.Gln252HisfsTer65	p.Q252Hfs*65	ENST00000257555		252	cag/caTg	4/10	0.169619318347497	4	FACETS	1	0.96	1	1	0.991	1	CLONAL	4	TRUE	2	0.1	4		852	644	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226041	133226041	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373170535	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	89	688	0	ENST00000320574.5:c.3856C>T	p.Arg1286Cys	p.R1286C	ENST00000320574	NM_006231.2	1286	Cgc/Tgc	31/49	0.169619318347497	4	FACETS	0.94	0.836	1	1	0.985	1	CLONAL	4	TRUE	2	0.1	4		688	521	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253151	133253151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	52	505	0	ENST00000320574.5:c.890C>T	p.Ser297Phe	p.S297F	ENST00000320574	NM_006231.2	297	tCc/tTc	9/49	0.169619318347497	4	FACETS	1	0.909	1	1	0.977	1	CLONAL	4	TRUE	2	0.1	4		505	265	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257855	133257855	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773204331	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	52	466	0	ENST00000320574.5:c.73G>A	p.Ala25Thr	p.A25T	ENST00000320574	NM_006231.2	25	Gcc/Acc	2/49	0.169619318347497	4	FACETS	1	0.875	1	1	0.976	1	CLONAL	4	TRUE	2	0.1	4		466	280	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549155	21549155	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	80	679	0	ENST00000382592.4:c.3121A>G	p.Thr1041Ala	p.T1041A	ENST00000382592	NM_014572.2	1041	Acc/Gcc	8/8	1	2	FACETS	0.952	0.843	1	1	0.988	1	CLONAL	4	TRUE	1	0.1	2		679	420	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562850	21562850	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1418882962	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	117	641	1	ENST00000382592.4:c.1069G>A	p.Val357Met	p.V357M	ENST00000382592	NM_014572.2	357	Gtg/Atg	4/8	1	2	FACETS	0.902	0.817	0.991	1	0.992	1	CLONAL	5	TRUE	1	0.1	2		642	519	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975441	26975441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	11	435	0	ENST00000381527.3:c.1067G>A	p.Arg356Gln	p.R356Q	ENST00000381527	NM_001260.1	356	cGa/cAa	11/13	1	2	FACETS	1	0.691	1	1	0.691	1	CLONAL	1	TRUE	1	0.1	2		435	220	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610144	28610144	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	42	465	0	ENST00000241453.7:c.1346A>G	p.Gln449Arg	p.Q449R	ENST00000241453	NM_004119.2	449	cAg/cGg	11/24	1	2	FACETS	1	0.924	1	1	0.973	1	CLONAL	2	TRUE	1	0.1	2		465	354	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28883002	28883002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs115595062	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	32	529	2	ENST00000282397.4:c.3698C>T	p.Pro1233Leu	p.P1233L	ENST00000282397	NM_002019.4	1233	cCg/cTg	28/30	1	2	FACETS	1	0.819	1	1	0.969	1	CLONAL	3	TRUE	1	0.1	2		531	213	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964143	28964143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766569666	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	10	447	0	ENST00000282397.4:c.1759G>A	p.Val587Ile	p.V587I	ENST00000282397	NM_002019.4	587	Gtt/Att	13/30	1	2	FACETS	1	0.72	1	1	0.72	1	CLONAL	1	TRUE	1	0.1	2		447	187	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28979987	28979987	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	34	552	0	ENST00000282397.4:c.1481C>A	p.Ala494Asp	p.A494D	ENST00000282397	NM_002019.4	494	gCt/gAt	11/30	1	2	FACETS	0.918	0.754	1	1	0.97	1	CLONAL	3	TRUE	1	0.1	2		552	247	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907031	32907031	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	21	453	0	ENST00000380152.3:c.1416G>T	p.Gln472His	p.Q472H	ENST00000380152		472	caG/caT	10/27	1	2	FACETS	1	0.83	1	1	0.944	1	CLONAL	2	TRUE	1	0.1	2		453	193	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907442	32907442	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	23	302	0	ENST00000380152.3:c.1827A>T	p.Gln609His	p.Q609H	ENST00000380152		609	caA/caT	10/27	1	2	FACETS	0.97	0.764	1	1	0.957	1	CLONAL	3	TRUE	1	0.1	2		302	158	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910854	32910854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502434	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	16	560	0	ENST00000380152.3:c.2362G>A	p.Gly788Ser	p.G788S	ENST00000380152		788	Ggc/Agc	11/27	1	2	FACETS	0.988	0.734	1	1	0.922	1	CLONAL	2	TRUE	1	0.1	2		560	162	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913079	32913080	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs397507731	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	13	553	0	ENST00000380152.3:c.4593dup	p.Val1532SerfsTer2	p.V1532Sfs*2	ENST00000380152		1529	-/A	11/27	1	2	FACETS	1	0.799	1	1	0.799	1	CLONAL	1	TRUE	1	0.1	2		553	224	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972403	32972403	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs730881576	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	21	606	0	ENST00000380152.3:c.9753G>T	p.Lys3251Asn	p.K3251N	ENST00000380152		3251	aaG/aaT	27/27	1	2	FACETS	0.764	0.589	0.967	1	0.919	1	CLONAL	2	TRUE	1	0.1	2		606	275	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528152	103528152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760309416	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	48	322	2	ENST00000355739.4:c.3460G>A	p.Asp1154Asn	p.D1154N	ENST00000355739	NM_000123.3	1154	Gat/Aat	15/15	1	2	FACETS	0.988	0.843	1	1	0.981	1	CLONAL	4	TRUE	1	0.1	2		324	243	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435262	110435262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316344339	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	55	293	0	ENST00000375856.3:c.3139G>A	p.Ala1047Thr	p.A1047T	ENST00000375856	NM_003749.2	1047	Gcc/Acc	1/2	1	2	FACETS	1	0.91	1	1	0.982	1	CLONAL	3	TRUE	1	0.1	2		293	340	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435388	110435388	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	114	568	0	ENST00000375856.3:c.3013C>A	p.Leu1005Ile	p.L1005I	ENST00000375856	NM_003749.2	1005	Ctc/Atc	1/2	1	2	FACETS	0.964	0.871	1	1	0.992	1	CLONAL	4	TRUE	1	0.1	2		568	591	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437643	110437643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776368162	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	50	732	0	ENST00000375856.3:c.758G>A	p.Ser253Asn	p.S253N	ENST00000375856	NM_003749.2	253	aGc/aAc	1/2	1	2	FACETS	0.98	0.832	1	1	0.973	1	CLONAL	2	TRUE	1	0.1	2		732	510	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133000	30133000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771368542	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	66	579	0	ENST00000331968.5:c.601C>T	p.Arg201Trp	p.R201W	ENST00000331968	NM_002742.2	201	Cgg/Tgg	4/18	1	2	FACETS	1	0.879	1	1	0.985	1	CLONAL	3	TRUE	1	0.1	2		579	436	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610084	81610084	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	40	440	0	ENST00000298171.2:c.1682G>T	p.Ser561Ile	p.S561I	ENST00000298171	NM_000369.2	561	aGt/aTt	10/10	1	2	FACETS	1	0.894	1	1	0.976	1	CLONAL	3	TRUE	1	0.1	2		440	244	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95563031	95563031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776416084	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	35	348	2	ENST00000393063.1:c.4226C>T	p.Ala1409Val	p.A1409V	ENST00000393063	NM_030621.3	1409	gCg/gTg	24/28	1	2	FACETS	1	0.868	1	1	0.973	1	CLONAL	3	TRUE	1	0.1	2		350	220	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95591002	95591002	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	12	203	0	ENST00000393063.1:c.907C>A	p.Leu303Ile	p.L303I	ENST00000393063	NM_030621.3	303	Cta/Ata	9/28	1	2	FACETS	1	0.78	1	1	0.925	1	CLONAL	3	TRUE	1	0.1	2		203	72	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239243	105239243	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	53	588	0	ENST00000349310.3:c.1144G>T	p.Gly382Trp	p.G382W	ENST00000349310	NM_001014432.1	382	Ggg/Tgg	12/15	1	2	FACETS	1	0.942	1	1	0.979	1	CLONAL	2	TRUE	1	0.1	2		588	437	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675475	40675475	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	52	682	0	ENST00000249776.8:c.256G>T	p.Val86Leu	p.V86L	ENST00000249776	NM_033286.3	86	Gtg/Ttg	2/9	1	2	FACETS	0.912	0.776	1	1	0.972	1	CLONAL	2	TRUE	1	0.1	2		682	570	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40993326	40993326	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	45	453	0	ENST00000267868.3:c.152C>T	p.Ala51Val	p.A51V	ENST00000267868	NM_002875.4	51	gCt/gTt	3/10	1	2	FACETS	0.907	0.769	1	1	0.98	1	CLONAL	4	TRUE	1	0.1	2		453	248	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035008	42035008	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	58	640	0	ENST00000219905.7:c.4850C>T	p.Ala1617Val	p.A1617V	ENST00000219905	NM_001164273.1	1617	gCt/gTt	15/24	1	2	FACETS	1	0.907	1	1	0.985	1	CLONAL	4	TRUE	1	0.1	2		640	274	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041074	42041074	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	72	646	1	ENST00000219905.7:c.5452C>T	p.Arg1818Ter	p.R1818*	ENST00000219905	NM_001164273.1	1818	Cga/Tga	16/24	1	2	FACETS	1	0.882	1	1	0.987	1	CLONAL	4	TRUE	1	0.1	2		647	359	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052588	42052588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	93	446	0	ENST00000219905.7:c.7259C>T	p.Ala2420Val	p.A2420V	ENST00000219905	NM_001164273.1	2420	gCg/gTg	20/24	1	2	FACETS	1	0.954	1	1	0.99	1	CLONAL	4	TRUE	1	0.1	2		446	415	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059465	42059465	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	43	306	0	ENST00000219905.7:c.9185C>A	p.Ser3062Tyr	p.S3062Y	ENST00000219905	NM_001164273.1	3062	tCt/tAt	24/24	1	2	FACETS	1	0.873	1	1	0.977	1	CLONAL	3	TRUE	1	0.1	2		306	275	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748329	43748329	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	65	710	1	ENST00000382044.4:c.2477C>T	p.Ala826Val	p.A826V	ENST00000382044	NM_001141980.1	826	gCa/gTa	12/28	1	2	FACETS	0.883	0.77	1	1	0.986	1	CLONAL	4	TRUE	1	0.1	2		711	368	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007679	45007679	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	30	386	0	ENST00000558401.1:c.126C>A	p.Phe42Leu	p.F42L	ENST00000558401	NM_004048.2	42	ttC/ttA	2/4	1	2	FACETS	0.837	0.678	1	1	0.964	1	CLONAL	3	TRUE	1	0.1	2		386	239	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73991991	73991991	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	88	697	2	ENST00000318443.5:c.11G>A	p.Arg4Gln	p.R4Q	ENST00000318443	NM_001024736.1	4	cGg/cAg	2/10	1	2	FACETS	1	0.918	1	1	0.989	1	CLONAL	3	TRUE	1	0.1	2		699	563	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994595	73994595	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	74	868	0	ENST00000318443.5:c.80-1G>T		p.X27_splice	ENST00000318443	NM_001024736.1	27			1	2	FACETS	0.911	0.802	1	1	0.987	1	CLONAL	4	TRUE	1	0.1	2		868	406	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73995392	73995392	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	21	486	0	ENST00000318443.5:c.698G>T	p.Ser233Ile	p.S233I	ENST00000318443	NM_001024736.1	233	aGc/aTc	4/10	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.1	2		486	297	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996774	73996774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200175975	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	51	341	0	ENST00000318443.5:c.1330G>A	p.Val444Met	p.V444M	ENST00000318443	NM_001024736.1	444	Gtg/Atg	6/10	1	2	FACETS	1	0.901	1	1	0.983	1	CLONAL	4	TRUE	1	0.1	2		341	240	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74005274	74005274	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	51	583	0	ENST00000318443.5:c.1583-1G>T		p.X528_splice	ENST00000318443	NM_001024736.1	528			1	2	FACETS	1	0.912	1	1	0.983	1	CLONAL	4	TRUE	1	0.1	2		583	235	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472520	88472520	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	72	646	0	ENST00000360948.2:c.2035G>T	p.Asp679Tyr	p.D679Y	ENST00000360948	NM_001012338.2	679	Gac/Tac	16/19	1	2	FACETS	1	0.938	1	1	0.987	1	CLONAL	3	TRUE	1	0.1	2		646	431	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476387	88476387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202056599	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	36	613	0	ENST00000360948.2:c.1745G>A	p.Arg582Gln	p.R582Q	ENST00000360948	NM_001012338.2	582	cGg/cAg	15/19	1	2	FACETS	1	0.855	1	1	0.965	1	CLONAL	2	TRUE	1	0.1	2		613	345	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90627542	90627542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1222149957	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	81	662	1	ENST00000330062.3:c.1315G>A	p.Asp439Asn	p.D439N	ENST00000330062	NM_002168.2	439	Gac/Aac	11/11	1	2	FACETS	0.894	0.791	1	1	0.988	1	CLONAL	4	TRUE	1	0.1	2		663	453	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628303	90628303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	93	825	1	ENST00000330062.3:c.1108G>A	p.Ala370Thr	p.A370T	ENST00000330062	NM_002168.2	370	Gcc/Acc	9/11	1	2	FACETS	1	0.953	1	1	0.99	1	CLONAL	3	TRUE	1	0.1	2		826	549	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630704	90630704	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs118101777	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	86	706	0	ENST00000330062.3:c.782G>A	p.Arg261His	p.R261H	ENST00000330062	NM_002168.2	261	cGt/cAt	6/11	1	2	FACETS	1	0.915	1	1	0.989	1	CLONAL	4	TRUE	1	0.1	2		706	416	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631963	90631963	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	17	594	0	ENST00000330062.3:c.390G>T	p.Lys130Asn	p.K130N	ENST00000330062	NM_002168.2	130	aaG/aaT	4/11	1	2	FACETS	1	0.796	1	1	0.796	1	CLONAL	1	TRUE	1	0.1	2		594	315	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292692	91292692	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	10	424	0	ENST00000355112.3:c.194T>G	p.Val65Gly	p.V65G	ENST00000355112	NM_000057.2	65	gTt/gGt	3/22	1	2	FACETS	1	0.768	1	1	0.768	1	CLONAL	1	TRUE	1	0.1	2		424	170	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303873	91303873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	52	489	0	ENST00000355112.3:c.1270C>A	p.Leu424Ile	p.L424I	ENST00000355112	NM_000057.2	424	Ctt/Att	7/22	1	2	FACETS	0.937	0.807	1	1	0.984	1	CLONAL	5	TRUE	1	0.1	2		489	222	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434748	99434748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567180721	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	91	653	1	ENST00000268035.6:c.835C>T	p.Arg279Cys	p.R279C	ENST00000268035	NM_000875.3	279	Cgt/Tgt	3/21	1	2	FACETS	1	0.933	1	1	0.989	1	CLONAL	3	TRUE	1	0.1	2		654	568	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096184	2096184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	110	893	1	ENST00000219066.1:c.323C>T	p.Ala108Val	p.A108V	ENST00000219066	NM_002528.5	108	gCa/gTa	2/6	0.0961476558192928	0	FACETS	0.884	0.797	0.976			1	CLONAL	4	TRUE	0	0.1	0		894	560	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129127	2129127	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	123	773	0	ENST00000219476.3:c.3061G>A	p.Glu1021Lys	p.E1021K	ENST00000219476	NM_000548.3	1021	Gag/Aag	27/42	0.0961476558192928	0	FACETS	1	0.915	1			1	CLONAL	5	TRUE	0	0.1	0		773	441	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129187	2129187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1479870591	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	88	799	0	ENST00000219476.3:c.3121G>A	p.Val1041Ile	p.V1041I	ENST00000219476	NM_000548.3	1041	Gtc/Atc	27/42	0.0961476558192928	0	FACETS	1	0.898	1			1	CLONAL	3	TRUE	0	0.1	0		799	522	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2218100	2218100	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	110	872	0	ENST00000326181.6:c.162G>T	p.Lys54Asn	p.K54N	ENST00000326181	NM_032271.2	54	aaG/aaT	4/21	0.0961476558192928	0	FACETS	0.886	0.798	0.977			1	CLONAL	4	TRUE	0	0.1	0		872	559	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220693	2220693	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775280844	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	56	541	0	ENST00000326181.6:c.310C>T	p.Arg104Cys	p.R104C	ENST00000326181	NM_032271.2	104	Cgc/Tgc	5/21	0.0961476558192928	0	FACETS	1	0.874	1			1	CLONAL	3	TRUE	0	0.1	0		541	331	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639023	3639023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	98	630	0	ENST00000294008.3:c.4616C>T	p.Pro1539Leu	p.P1539L	ENST00000294008	NM_032444.2	1539	cCc/cTc	12/15	0.0961476558192928	0	FACETS	1	0.937	1			1	CLONAL	3	TRUE	0	0.1	0		630	551	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639591	3639591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767241703	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	105	818	1	ENST00000294008.3:c.4048G>A	p.Gly1350Ser	p.G1350S	ENST00000294008	NM_032444.2	1350	Ggc/Agc	12/15	0.0961476558192928	0	FACETS	1	0.928	1			1	CLONAL	3	TRUE	0	0.1	0		819	605	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639791	3639791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140103960	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	109	781	1	ENST00000294008.3:c.3848C>T	p.Ala1283Val	p.A1283V	ENST00000294008	NM_032444.2	1283	gCc/gTc	12/15	0.0961476558192928	0	FACETS	1	0.954	1			1	CLONAL	3	TRUE	0	0.1	0		782	592	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779271	3779271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370704436	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	87	555	0	ENST00000262367.5:c.5777G>A	p.Arg1926Gln	p.R1926Q	ENST00000262367	NM_004380.2	1926	cGg/cAg	31/31	0.0961476558192928	0	FACETS	0.868	0.774	0.966			1	CLONAL	5	TRUE	0	0.1	0		555	361	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779526	3779526	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	127	1038	3	ENST00000262367.5:c.5522C>A	p.Pro1841His	p.P1841H	ENST00000262367	NM_004380.2	1841	cCc/cAc	31/31	0.0961476558192928	0	FACETS	0.881	0.8	0.966			1	CLONAL	4	TRUE	0	0.1	0		1041	649	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819257	3819257	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	107	608	0	ENST00000262367.5:c.2978C>A	p.Pro993His	p.P993H	ENST00000262367	NM_004380.2	993	cCt/cAt	15/31	0.0961476558192928	0	FACETS	1	0.903	1			1	CLONAL	4	TRUE	0	0.1	0		608	481	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934906	9934906	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866473134	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	18	484	1	ENST00000330684.3:c.1384G>A	p.Asp462Asn	p.D462N	ENST00000330684	NM_001134407.1	462	Gat/Aat	6/13	0.0961476558192928	0	FACETS	0.85	0.647	1			1	CLONAL	3	TRUE	0	0.1	0		485	127	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024732	14024732	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	22	478	0	ENST00000311895.7:c.958T>G	p.Phe320Val	p.F320V	ENST00000311895	NM_005236.2	320	Ttt/Gtt	5/11	0.0961476558192928	0	FACETS	0.921	0.717	1			1	CLONAL	2	TRUE	0	0.1	0		478	215	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637637	23637637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555459971	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	19	626	0	ENST00000261584.4:c.2668G>A	p.Ala890Thr	p.A890T	ENST00000261584	NM_024675.3	890	Gct/Act	7/13	0.0961476558192928	0	FACETS	1	0.837	1			1	CLONAL	1	TRUE	0	0.1	0		626	300	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649222	23649222	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	36	527	0	ENST00000261584.4:c.160G>T	p.Glu54Ter	p.E54*	ENST00000261584	NM_024675.3	54	Gaa/Taa	3/13	0.0961476558192928	0	FACETS	0.809	0.668	0.965			1	CLONAL	3	TRUE	0	0.1	0		527	267	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785743	50785743	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	42	605	0	ENST00000398568.2:c.733G>T	p.Glu245Ter	p.E245*	ENST00000398568	NM_001042412.1	245	Gaa/Taa	4/18	0.0961476558192928	0	FACETS	1	0.869	1			1	CLONAL	3	TRUE	0	0.1	0		605	243	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50827489	50827489	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	57	519	0	ENST00000398568.2:c.2374G>A	p.Ala792Thr	p.A792T	ENST00000398568	NM_001042412.1	792	Gca/Aca	16/18	0.0961476558192928	0	FACETS	0.861	0.744	0.986			1	CLONAL	4	TRUE	0	0.1	0		519	298	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782328	56782328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	87	545	1	ENST00000308159.5:c.169G>A	p.Asp57Asn	p.D57N	ENST00000308159	NM_014669.4	57	Gat/Aat	2/22	0.0961476558192928	0	FACETS	0.846	0.752	0.945			1	CLONAL	4	TRUE	0	0.1	0		546	463	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063333	67063333	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	34	272	0	ENST00000412916.2:c.23A>G	p.Gln8Arg	p.Q8R	ENST00000412916		8	cAg/cGg	1/6	0.0961476558192928	0	FACETS	0.877	0.718	1			1	CLONAL	2	TRUE	0	0.1	0		272	349	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650720	67650720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	84	576	0	ENST00000264010.4:c.1025G>A	p.Arg342His	p.R342H	ENST00000264010	NM_006565.3	342	cGt/cAt	5/12	0.0961476558192928	0	FACETS	1	0.916	1			1	CLONAL	3	TRUE	0	0.1	0		576	484	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660469	67660469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	47	378	2	ENST00000264010.4:c.1369C>T	p.Arg457Ter	p.R457*	ENST00000264010	NM_006565.3	457	Cga/Tga	8/12	0.0961476558192928	0	FACETS	0.9	0.77	1			1	CLONAL	5	TRUE	0	0.1	0		380	188	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821400	72821400	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1414695354	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	102	567	0	ENST00000268489.5:c.10775A>G	p.His3592Arg	p.H3592R	ENST00000268489	NM_006885.3	3592	cAc/cGc	10/10	0.0961476558192928	0	FACETS	1	0.936	1			1	CLONAL	4	TRUE	0	0.1	0		567	436	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829050	72829050	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	32	627	0	ENST00000268489.5:c.7531C>G	p.Pro2511Ala	p.P2511A	ENST00000268489	NM_006885.3	2511	Ccc/Gcc	9/10	0.0961476558192928	0	FACETS	1	0.915	1			1	CLONAL	1	TRUE	0	0.1	0		627	461	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831340	72831340	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	13	390	0	ENST00000268489.5:c.5241G>T	p.Gln1747His	p.Q1747H	ENST00000268489	NM_006885.3	1747	caG/caT	9/10	0.0961476558192928	0	FACETS	1	0.787	1			1	CLONAL	1	TRUE	0	0.1	0		390	207	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992345	72992345	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	106	906	1	ENST00000268489.5:c.1700G>T	p.Arg567Met	p.R567M	ENST00000268489	NM_006885.3	567	aGg/aTg	2/10	0.0961476558192928	0	FACETS	0.928	0.835	1			1	CLONAL	4	TRUE	0	0.1	0		907	514	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992931	72992931	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	99	812	0	ENST00000268489.5:c.1114C>T	p.Arg372Ter	p.R372*	ENST00000268489	NM_006885.3	372	Cga/Tga	2/10	0.0961476558192928	0	FACETS	0.857	0.77	0.948			1	CLONAL	5	TRUE	0	0.1	0		812	416	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992957	72992957	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	84	892	0	ENST00000268489.5:c.1088G>T	p.Ser363Ile	p.S363I	ENST00000268489	NM_006885.3	363	aGt/aTt	2/10	0.0961476558192928	0	FACETS	0.885	0.786	0.991			1	CLONAL	4	TRUE	0	0.1	0		892	427	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341527	89341527	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	101	581	0	ENST00000301030.4:c.7543C>A	p.Leu2515Met	p.L2515M	ENST00000301030	NM_001256183.1	2515	Ctg/Atg	10/13	0.0961476558192928	0	FACETS	1	0.923	1			1	CLONAL	4	TRUE	0	0.1	0		581	441	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346973	89346973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773403872	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	49	484	0	ENST00000301030.4:c.5977C>T	p.Arg1993Cys	p.R1993C	ENST00000301030	NM_001256183.1	1993	Cgt/Tgt	9/13	0.0961476558192928	0	FACETS	0.955	0.813	1			1	CLONAL	3	TRUE	0	0.1	0		484	308	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349786	89349786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	59	775	0	ENST00000301030.4:c.3164G>A	p.Cys1055Tyr	p.C1055Y	ENST00000301030	NM_001256183.1	1055	tGt/tAt	9/13	0.0961476558192928	0	FACETS	0.906	0.786	1			1	CLONAL	4	TRUE	0	0.1	0		775	293	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350196	89350196	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	76	845	1	ENST00000301030.4:c.2754G>T	p.Glu918Asp	p.E918D	ENST00000301030	NM_001256183.1	918	gaG/gaT	9/13	0.0961476558192928	0	FACETS	1	0.911	1			1	CLONAL	3	TRUE	0	0.1	0		846	438	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351578	89351578	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	68	772	2	ENST00000301030.4:c.1372C>T	p.Arg458Ter	p.R458*	ENST00000301030	NM_001256183.1	458	Cga/Tga	9/13	0.0961476558192928	0	FACETS	0.971	0.848	1			1	CLONAL	3	TRUE	0	0.1	0		774	420	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805037	89805037	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	123	783	0	ENST00000389301.3:c.4340A>G	p.Asp1447Gly	p.D1447G	ENST00000389301	NM_000135.2	1447	gAc/gGc	43/43	0.0961476558192928	0	FACETS	0.832	0.754	0.915			1	CLONAL	4	TRUE	0	0.1	0		783	665	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89815066	89815066	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs751266148	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	71	588	0	ENST00000389301.3:c.3348+1G>A		p.X1116_splice	ENST00000389301	NM_000135.2	1116			0.0961476558192928	0	FACETS	1	0.897	1			1	CLONAL	3	TRUE	0	0.1	0		588	415	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89871701	89871701	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	52	599	0	ENST00000389301.3:c.696G>T	p.Arg232Ser	p.R232S	ENST00000389301	NM_000135.2	232	agG/agT	7/43	0.0961476558192928	0	FACETS	0.872	0.742	1			1	CLONAL	2	TRUE	0	0.1	0		599	537	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89871793	89871793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779131886	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	50	569	0	ENST00000389301.3:c.604G>A	p.Asp202Asn	p.D202N	ENST00000389301	NM_000135.2	202	Gac/Aac	7/43	0.0961476558192928	0	FACETS	0.974	0.827	1			1	CLONAL	2	TRUE	0	0.1	0		569	462	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216785	7216785	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	58	551	0	ENST00000380728.2:c.638C>A	p.Pro213His	p.P213H	ENST00000380728		213	cCt/cAt	8/11	1	2	FACETS	1	0.93	1	1	0.984	1	CLONAL	3	TRUE	1	0.1	2		551	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578184	7578184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146340390	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	92	643	0	ENST00000269305.4:c.665C>T	p.Pro222Leu	p.P222L	ENST00000269305	NM_001126112.2	222	cCg/cTg	6/11	1	2	FACETS	1	0.94	1	1	0.99	1	CLONAL	4	TRUE	1	0.1	2		643	427	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984848	11984848	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	17	403	0	ENST00000353533.5:c.393+1G>T		p.X131_splice	ENST00000353533	NM_003010.3	131			1	2	FACETS	1	0.847	1	1	0.936	1	CLONAL	2	TRUE	1	0.1	2		403	143	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968301	15968301	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	23	356	0	ENST00000268712.3:c.4984A>C	p.Ile1662Leu	p.I1662L	ENST00000268712	NM_006311.3	1662	Att/Ctt	34/46	1	2	FACETS	1	0.794	1	1	0.958	1	CLONAL	3	TRUE	1	0.1	2		356	152	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16005044	16005044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	79	626	0	ENST00000268712.3:c.2210G>A	p.Ser737Asn	p.S737N	ENST00000268712	NM_006311.3	737	aGt/aAt	20/46	1	2	FACETS	0.99	0.876	1	1	0.988	1	CLONAL	4	TRUE	1	0.1	2		626	399	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687566	29687566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144178015	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	43	556	2	ENST00000356175.3:c.8159C>T	p.Thr2720Met	p.T2720M	ENST00000356175	NM_000267.3	2720	aCg/aTg	56/57	1	2	FACETS	1	0.871	1	1	0.977	1	CLONAL	3	TRUE	1	0.1	2		558	276	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676334	37676334	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	53	571	0	ENST00000447079.4:c.3089C>A	p.Pro1030His	p.P1030H	ENST00000447079	NM_015083.1	1030	cCt/cAt	11/14	1	2	FACETS	1	0.915	1	1	0.982	1	CLONAL	3	TRUE	1	0.1	2		571	322	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884278	37884278	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1389410789	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	77	585	0	ENST00000269571.5:c.3749G>A	p.Gly1250Asp	p.G1250D	ENST00000269571		1250	gGt/gAt	27/27	1	2	FACETS	0.937	0.827	1	1	0.988	1	CLONAL	4	TRUE	1	0.1	2		585	411	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38506138	38506138	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	60	617	0	ENST00000254066.5:c.430C>T	p.Arg144Ter	p.R144*	ENST00000254066	NM_000964.3	144	Cga/Tga	4/9	1	2	FACETS	1	0.947	1	1	0.981	1	CLONAL	2	TRUE	1	0.1	2		617	496	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40364010	40364010	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	61	913	0	ENST00000293328.3:c.1672T>C	p.Phe558Leu	p.F558L	ENST00000293328	NM_012448.3	558	Ttc/Ctc	13/19	1	2	FACETS	0.933	0.804	1	1	0.977	1	CLONAL	2	TRUE	1	0.1	2		913	654	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475320	40475320	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	60	627	0	ENST00000264657.5:c.1706T>C	p.Ile569Thr	p.I569T	ENST00000264657	NM_139276.2	569	aTt/aCt	19/24	1	2	FACETS	1	0.936	1	1	0.984	1	CLONAL	3	TRUE	1	0.1	2		627	351	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226399	41226399	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	79	704	0	ENST00000357654.3:c.4624T>G	p.Ser1542Ala	p.S1542A	ENST00000357654	NM_007294.3	1542	Tct/Gct	14/23	1	2	FACETS	0.888	0.784	0.998	1	0.988	1	CLONAL	4	TRUE	1	0.1	2		704	445	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804168	46804168	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	94	739	0	ENST00000290295.7:c.839A>G	p.Asn280Ser	p.N280S	ENST00000290295	NM_006361.5	280	aAc/aGc	2/2	1	2	FACETS	0.908	0.813	1	1	0.991	1	CLONAL	5	TRUE	1	0.1	2		739	414	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724441	724441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	62	811	0	ENST00000314574.4:c.1615C>T	p.Pro539Ser	p.P539S	ENST00000314574	NM_005433.3	539	Cca/Tca	12/12	0.0961476558192928	0	FACETS	0.889	0.773	1			1	CLONAL	4	TRUE	0	0.1	0		811	314	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550299	39550299	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374012011	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	20	285	1	ENST00000262039.4:c.410G>A	p.Arg137His	p.R137H	ENST00000262039	NM_002647.2	137	cGc/cAc	4/25	0.0961476558192928	0	FACETS	0.923	0.714	1			1	CLONAL	3	TRUE	0	0.1	0		286	130	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39567842	39567842	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	15	307	0	ENST00000262039.4:c.598G>T	p.Glu200Ter	p.E200*	ENST00000262039	NM_002647.2	200	Gaa/Taa	5/25	0.0961476558192928	0	FACETS	1	0.769	1			1	CLONAL	2	TRUE	0	0.1	0		307	129	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395793	45395793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1404495202	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	20	296	1	ENST00000262160.6:c.341G>A	p.Arg114His	p.R114H	ENST00000262160	NM_005901.5	114	cGt/cAt	4/11	0.0961476558192928	0	FACETS	1	0.817	1			1	CLONAL	2	TRUE	0	0.1	0		297	168	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575191	48575191	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	33	305	0	ENST00000342988.3:c.385A>G	p.Asn129Asp	p.N129D	ENST00000342988	NM_005359.5	129	Aat/Gat	3/12	0.0961476558192928	0	FACETS	0.853	0.703	1			1	CLONAL	4	TRUE	0	0.1	0		305	174	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400749	56400749	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	33	326	0	ENST00000348428.3:c.1343T>C	p.Leu448Ser	p.L448S	ENST00000348428	NM_006785.3	448	tTg/tCg	11/17	0.0961476558192928	0	FACETS	0.99	0.818	1			1	CLONAL	4	TRUE	0	0.1	0		326	150	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400783	56400783	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	16	291	0	ENST00000348428.3:c.1377C>A	p.Phe459Leu	p.F459L	ENST00000348428	NM_006785.3	459	ttC/ttA	11/17	0.0961476558192928	0	FACETS	0.95	0.713	1			1	CLONAL	3	TRUE	0	0.1	0		291	101	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57569912	57569912	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	14	301	0	ENST00000316660.6:c.92G>T	p.Arg31Ile	p.R31I	ENST00000316660	NM_021127.2	31	aGa/aTa	2/2	0.0961476558192928	0	FACETS	1	0.865	1			1	CLONAL	1	TRUE	0	0.1	0		301	183	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612427	1612427	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs187316941	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	68	743	0	ENST00000344749.5:c.1592C>T	p.Thr531Met	p.T531M	ENST00000344749	NM_001136139.2	531	aCg/aTg	18/19	1	2	FACETS	1	0.95	1	1	0.983	1	CLONAL	2	TRUE	1	0.1	2		743	572	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621184	1621184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1458537272	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	83	763	0	ENST00000344749.5:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000344749	NM_001136139.2	321	cGa/cAa	12/19	1	2	FACETS	1	0.932	1	1	0.988	1	CLONAL	3	TRUE	1	0.1	2		763	514	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621933	1621933	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	112	878	0	ENST00000344749.5:c.859C>A	p.Leu287Ile	p.L287I	ENST00000344749	NM_001136139.2	287	Ctc/Atc	11/19	1	2	FACETS	1	0.936	1	1	0.992	1	CLONAL	4	TRUE	1	0.1	2		878	535	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622388	1622388	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	112	801	1	ENST00000344749.5:c.576C>A	p.Asp192Glu	p.D192E	ENST00000344749	NM_001136139.2	192	gaC/gaA	9/19	1	2	FACETS	0.89	0.802	0.983	1	0.991	1	CLONAL	4	TRUE	1	0.1	2		802	629	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625652	1625652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533848977	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	117	835	3	ENST00000344749.5:c.422C>T	p.Ser141Leu	p.S141L	ENST00000344749	NM_001136139.2	141	tCg/tTg	7/19	1	2	FACETS	0.97	0.877	1	1	0.992	1	CLONAL	4	TRUE	1	0.1	2		838	603	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2180720	2180720	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	104	737	0	ENST00000398665.3:c.90T>G	p.His30Gln	p.H30Q	ENST00000398665	NM_032482.2	30	caT/caG	2/28	1	2	FACETS	1	0.909	1	1	0.991	1	CLONAL	4	TRUE	1	0.1	2		737	514	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217916	2217916	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs759690350	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	152	696	1	ENST00000398665.3:c.2690C>T	p.Ala897Val	p.A897V	ENST00000398665	NM_032482.2	897	gCg/gTg	22/28	1	2	FACETS	1	0.963	1	1	0.994	1	CLONAL	4	TRUE	1	0.1	2		697	699	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118954	3118954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	145	782	0	ENST00000078429.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000078429	NM_002067.2	213	cGg/cAg	5/7	1	2	FACETS	1	0.968	1	1	0.994	1	CLONAL	4	TRUE	1	0.1	2		782	647	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208025	5208025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768615091	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	95	700	0	ENST00000357368.4:c.5686G>A	p.Val1896Met	p.V1896M	ENST00000357368	NM_002850.3	1896	Gtg/Atg	37/38	1	2	FACETS	1	0.926	1	1	0.99	1	CLONAL	4	TRUE	1	0.1	2		700	455	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212459	5212459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs182037655	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	90	649	3	ENST00000357368.4:c.4658C>T	p.Thr1553Met	p.T1553M	ENST00000357368	NM_002850.3	1553	aCg/aTg	31/38	1	2	FACETS	0.941	0.839	1	1	0.99	1	CLONAL	4	TRUE	1	0.1	2		652	478	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117392	7117392	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	80	669	1	ENST00000302850.5:c.3824T>A	p.Phe1275Tyr	p.F1275Y	ENST00000302850	NM_000208.2	1275	tTc/tAc	22/22	1	2	FACETS	0.988	0.874	1	1	0.989	1	CLONAL	4	TRUE	1	0.1	2		670	405	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122777	7122777	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	32	570	0	ENST00000302850.5:c.3377C>A	p.Pro1126His	p.P1126H	ENST00000302850	NM_000208.2	1126	cCt/cAt	19/22	1	2	FACETS	1	0.91	1	1	0.965	1	CLONAL	2	TRUE	1	0.1	2		570	265	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170554	7170554	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	31	424	0	ENST00000302850.5:c.1477G>T	p.Ala493Ser	p.A493S	ENST00000302850	NM_000208.2	493	Gca/Tca	6/22	1	2	FACETS	1	0.833	1	1	0.96	1	CLONAL	2	TRUE	1	0.1	2		424	301	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251781	10251782	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	81	647	0	ENST00000340748.4:c.3345dup	p.Gly1116ArgfsTer11	p.G1116Rfs*11	ENST00000340748		1115	-/A	30/40	1	2	FACETS	0.942	0.837	1	1	0.989	1	CLONAL	5	TRUE	1	0.1	2		647	344	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599964	10599964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1364007421	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	124	793	1	ENST00000171111.5:c.1612G>A	p.Asp538Asn	p.D538N	ENST00000171111	NM_203500.1	538	Gat/Aat	5/6	1	2	FACETS	0.932	0.845	1	1	0.992	1	CLONAL	4	TRUE	1	0.1	2		794	665	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105666	11105666	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1414888106	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	117	604	0	ENST00000358026.2:c.1582C>T	p.Arg528Trp	p.R528W	ENST00000358026	NM_001128849.1	528	Cgg/Tgg	9/36	1	2	FACETS	0.947	0.856	1	1	0.992	1	CLONAL	4	TRUE	1	0.1	2		604	618	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132438	11132438	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794284	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	108	746	0	ENST00000358026.2:c.2654G>A	p.Arg885His	p.R885H	ENST00000358026	NM_001128849.1	885	cGc/cAc	19/36	1	2	FACETS	0.906	0.817	0.998	1	0.992	1	CLONAL	5	TRUE	1	0.1	2		746	477	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145808	11145808	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	46	581	0	ENST00000358026.2:c.4170G>T	p.Lys1390Asn	p.K1390N	ENST00000358026	NM_001128849.1	1390	aaG/aaT	29/36	1	2	FACETS	0.838	0.708	0.981	1	0.976	1	CLONAL	3	TRUE	1	0.1	2		581	366	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168971	11168971	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	131	607	0	ENST00000358026.2:c.4561C>T	p.Pro1521Ser	p.P1521S	ENST00000358026	NM_001128849.1	1521	Ccc/Tcc	32/36	1	2	FACETS	1	0.954	1	1	0.993	1	CLONAL	4	TRUE	1	0.1	2		607	609	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170735	11170735	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568565611	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	104	736	0	ENST00000358026.2:c.4879G>A	p.Val1627Met	p.V1627M	ENST00000358026	NM_001128849.1	1627	Gtg/Atg	35/36	1	2	FACETS	0.922	0.828	1	1	0.991	1	CLONAL	4	TRUE	1	0.1	2		736	564	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272056	15272056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	67	730	0	ENST00000263388.2:c.6383C>T	p.Ala2128Val	p.A2128V	ENST00000263388	NM_000435.2	2128	gCa/gTa	33/33	1	2	FACETS	1	0.944	1	1	0.986	1	CLONAL	3	TRUE	1	0.1	2		730	388	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276722	15276722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446718967	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	113	773	1	ENST00000263388.2:c.5543G>A	p.Arg1848His	p.R1848H	ENST00000263388	NM_000435.2	1848	cGt/cAt	30/33	1	2	FACETS	0.978	0.882	1	1	0.992	1	CLONAL	4	TRUE	1	0.1	2		774	578	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288435	15288435	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	66	474	2	ENST00000263388.2:c.4304G>A	p.Arg1435His	p.R1435H	ENST00000263388	NM_000435.2	1435	cGc/cAc	24/33	1	2	FACETS	0.962	0.841	1	1	0.986	1	CLONAL	4	TRUE	1	0.1	2		476	343	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295220	15295220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568357671	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	95	871	0	ENST00000263388.2:c.2452G>A	p.Ala818Thr	p.A818T	ENST00000263388	NM_000435.2	818	Gca/Aca	16/33	1	2	FACETS	1	0.95	1	1	0.99	1	CLONAL	3	TRUE	1	0.1	2		871	569	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296310	15296310	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	43	820	2	ENST00000263388.2:c.2132A>G	p.Asp711Gly	p.D711G	ENST00000263388	NM_000435.2	711	gAt/gGt	13/33	1	2	FACETS	0.885	0.74	1	1	0.966	1	CLONAL	2	TRUE	1	0.1	2		822	486	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350554	15350554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199839337	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	126	899	0	ENST00000263377.2:c.3361C>T	p.Arg1121Cys	p.R1121C	ENST00000263377	NM_058243.2	1121	Cgc/Tgc	16/20	1	2	FACETS	1	0.948	1	1	0.993	1	CLONAL	4	TRUE	1	0.1	2		899	593	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354182	15354182	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	68	695	1	ENST00000263377.2:c.2698C>A	p.Leu900Ile	p.L900I	ENST00000263377	NM_058243.2	900	Ctc/Atc	14/20	1	2	FACETS	1	0.895	1	1	0.985	1	CLONAL	3	TRUE	1	0.1	2		696	441	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354254	15354254	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	125	839	2	ENST00000263377.2:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000263377	NM_058243.2	876	Cga/Tga	14/20	1	2	FACETS	1	0.962	1	1	0.992	1	CLONAL	3	TRUE	1	0.1	2		841	744	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273795	18273795	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	75	626	0	ENST00000222254.8:c.1128G>T	p.Lys376Asn	p.K376N	ENST00000222254	NM_005027.3	376	aaG/aaT	10/16	1	2	FACETS	1	0.889	1	1	0.987	1	CLONAL	3	TRUE	1	0.1	2		626	494	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277042	18277042	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	79	632	0	ENST00000222254.8:c.1489A>G	p.Thr497Ala	p.T497A	ENST00000222254	NM_005027.3	497	Act/Gct	12/16	1	2	FACETS	1	0.952	1	1	0.988	1	CLONAL	3	TRUE	1	0.1	2		632	456	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18963073	18963073	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	118	811	0	ENST00000262803.5:c.940G>T	p.Ala314Ser	p.A314S	ENST00000262803	NM_002911.3	314	Gcc/Tcc	6/24	1	2	FACETS	1	0.951	1	1	0.992	1	CLONAL	4	TRUE	1	0.1	2		811	547	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313508	30313508	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	80	561	0	ENST00000262643.3:c.1108C>A	p.Leu370Met	p.L370M	ENST00000262643	NM_001238.2	370	Ctg/Atg	11/12	1	2	FACETS	1	0.946	1	1	0.989	1	CLONAL	4	TRUE	1	0.1	2		561	359	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314638	30314638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	64	589	1	ENST00000262643.3:c.1187C>T	p.Pro396Leu	p.P396L	ENST00000262643	NM_001238.2	396	cCg/cTg	12/12	1	2	FACETS	0.983	0.854	1	1	0.984	1	CLONAL	3	TRUE	1	0.1	2		590	434	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792720	33792720	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	14	71	0	ENST00000498907.2:c.601C>A	p.Leu201Met	p.L201M	ENST00000498907	NM_004364.3	201	Ctg/Atg	1/1	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.1	2		71	187	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211096	36211096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	115	878	0	ENST00000222270.7:c.847G>A	p.Gly283Arg	p.G283R	ENST00000222270	NM_014727.1	283	Gga/Aga	3/37	1	2	FACETS	1	0.957	1	1	0.991	1	CLONAL	3	TRUE	1	0.1	2		878	691	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211883	36211883	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202218975	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	119	879	0	ENST00000222270.7:c.1634G>A	p.Arg545Gln	p.R545Q	ENST00000222270	NM_014727.1	545	cGa/cAa	3/37	1	2	FACETS	1	0.941	1	1	0.992	1	CLONAL	4	TRUE	1	0.1	2		879	565	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212257	36212257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	70	685	1	ENST00000222270.7:c.2008C>T	p.Pro670Ser	p.P670S	ENST00000222270	NM_014727.1	670	Cct/Tct	3/37	1	2	FACETS	1	0.885	1	1	0.987	1	CLONAL	4	TRUE	1	0.1	2		686	347	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214019	36214019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	117	799	0	ENST00000222270.7:c.2845C>T	p.Pro949Ser	p.P949S	ENST00000222270	NM_014727.1	949	Ccc/Tcc	6/37	1	2	FACETS	1	0.94	1	1	0.992	1	CLONAL	4	TRUE	1	0.1	2		799	556	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214025	36214025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766488321	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	97	779	1	ENST00000222270.7:c.2851C>T	p.Arg951Cys	p.R951C	ENST00000222270	NM_014727.1	951	Cgc/Tgc	6/37	1	2	FACETS	0.9	0.805	1	1	0.99	1	CLONAL	4	TRUE	1	0.1	2		780	539	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215571	36215571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	104	812	1	ENST00000222270.7:c.3368G>A	p.Arg1123Gln	p.R1123Q	ENST00000222270	NM_014727.1	1123	cGg/cAg	9/37	1	2	FACETS	1	0.953	1	1	0.991	1	CLONAL	3	TRUE	1	0.1	2		813	625	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216440	36216440	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	37	845	1	ENST00000222270.7:c.3703C>T	p.Arg1235Trp	p.R1235W	ENST00000222270	NM_014727.1	1235	Cgg/Tgg	12/37	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.1	2		846	650	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218794	36218794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	85	812	0	ENST00000222270.7:c.4405G>A	p.Glu1469Lys	p.E1469K	ENST00000222270	NM_014727.1	1469	Gag/Aag	18/37	1	2	FACETS	0.968	0.86	1	1	0.989	1	CLONAL	4	TRUE	1	0.1	2		812	439	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223158	36223158	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	118	863	0	ENST00000222270.7:c.5708A>G	p.Asp1903Gly	p.D1903G	ENST00000222270	NM_014727.1	1903	gAc/gGc	28/37	1	2	FACETS	1	0.914	1	1	0.992	1	CLONAL	4	TRUE	1	0.1	2		863	584	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224133	36224133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879164926	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	76	649	0	ENST00000222270.7:c.6683C>T	p.Ala2228Val	p.A2228V	ENST00000222270	NM_014727.1	2228	gCt/gTt	28/37	1	2	FACETS	0.925	0.812	1	1	0.986	1	CLONAL	3	TRUE	1	0.1	2		649	548	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229342	36229342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	69	636	0	ENST00000222270.7:c.8032C>T	p.Arg2678Cys	p.R2678C	ENST00000222270	NM_014727.1	2678	Cgc/Tgc	37/37	1	2	FACETS	1	0.926	1	1	0.986	1	CLONAL	3	TRUE	1	0.1	2		636	424	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745110	41745110	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	97	699	0	ENST00000301178.4:c.1176G>T	p.Glu392Asp	p.E392D	ENST00000301178	NM_021913.4	392	gaG/gaT	9/20	1	2	FACETS	1	0.903	1	1	0.991	1	CLONAL	4	TRUE	1	0.1	2		699	481	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791832	42791832	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	64	690	0	ENST00000575354.2:c.718G>A	p.Ala240Thr	p.A240T	ENST00000575354	NM_015125.3	240	Gcc/Acc	5/20	1	2	FACETS	1	0.876	1	1	0.984	1	CLONAL	3	TRUE	1	0.1	2		690	423	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794850	42794850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761981948	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	77	698	1	ENST00000575354.2:c.1930G>A	p.Gly644Arg	p.G644R	ENST00000575354	NM_015125.3	644	Gga/Aga	10/20	1	2	FACETS	1	0.941	1	1	0.989	1	CLONAL	4	TRUE	1	0.1	2		699	349	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796805	42796805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1452309156	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	138	855	1	ENST00000575354.2:c.3263G>A	p.Gly1088Glu	p.G1088E	ENST00000575354	NM_015125.3	1088	gGa/gAa	14/20	1	2	FACETS	0.968	0.885	1	1	0.994	1	CLONAL	5	TRUE	1	0.1	2		856	570	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797270	42797270	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1392154159	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	87	755	0	ENST00000575354.2:c.3632G>T	p.Gly1211Val	p.G1211V	ENST00000575354	NM_015125.3	1211	gGc/gTc	15/20	1	2	FACETS	1	0.905	1	1	0.99	1	CLONAL	4	TRUE	1	0.1	2		755	427	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798451	42798451	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs969587337	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	84	688	1	ENST00000575354.2:c.4322G>A	p.Arg1441His	p.R1441H	ENST00000575354	NM_015125.3	1441	cGt/cAt	18/20	1	2	FACETS	0.884	0.784	0.991	1	0.989	1	CLONAL	4	TRUE	1	0.1	2		689	475	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799258	42799258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs530430600	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	31	666	0	ENST00000575354.2:c.4742C>T	p.Ser1581Leu	p.S1581L	ENST00000575354	NM_015125.3	1581	tCg/tTg	20/20	1	2	FACETS	0.873	0.707	1	1	0.952	1	CLONAL	2	TRUE	1	0.1	2		666	355	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871913	45871913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913020	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	138	671	4	ENST00000391945.4:c.335G>A	p.Arg112His	p.R112H	ENST00000391945	NM_000400.3	112	cGc/cAc	5/23	1	2	FACETS	1	0.95	1	1	0.994	1	CLONAL	5	TRUE	1	0.1	2		675	524	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731620	47731620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	53	112	0	ENST00000449228.1:c.172C>T	p.Pro58Ser	p.P58S	ENST00000449228	NM_001127240.2	58	Ccc/Tcc	2/4	1	2	FACETS	1	0.908	1	1	0.983	1	CLONAL	4	TRUE	1	0.1	2		112	247	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716212	52716212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555791268	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	100	646	2	ENST00000322088.6:c.656C>T	p.Ser219Leu	p.S219L	ENST00000322088	NM_014225.5	219	tCg/tTg	6/15	1	2	FACETS	0.907	0.815	1	1	0.991	1	CLONAL	5	TRUE	1	0.1	2		648	441	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716227	52716227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	120	667	1	ENST00000322088.6:c.671C>T	p.Ala224Val	p.A224V	ENST00000322088	NM_014225.5	224	gCg/gTg	6/15	1	2	FACETS	1	0.916	1	1	0.993	1	CLONAL	5	TRUE	1	0.1	2		668	476	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085953	16085953	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	78	563	0	ENST00000281043.3:c.1129T>C	p.Ser377Pro	p.S377P	ENST00000281043	NM_005378.4	377	Tcg/Ccg	3/3	1	2	FACETS	1	0.926	1	1	0.989	1	CLONAL	4	TRUE	1	0.1	2		563	367	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964903	25964903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561088610	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	30	436	0	ENST00000435504.4:c.4303C>T	p.Arg1435Trp	p.R1435W	ENST00000435504		1435	Cgg/Tgg	13/13	1	2	FACETS	0.987	0.797	1	1	0.957	1	CLONAL	2	TRUE	1	0.1	2		436	304	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966531	25966531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	65	665	1	ENST00000435504.4:c.2675C>T	p.Thr892Ile	p.T892I	ENST00000435504		892	aCc/aTc	13/13	1	2	FACETS	1	0.916	1	1	0.986	1	CLONAL	4	TRUE	1	0.1	2		666	306	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966700	25966700	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs780470199	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	31	621	0	ENST00000435504.4:c.2506A>G	p.Thr836Ala	p.T836A	ENST00000435504		836	Aca/Gca	13/13	1	2	FACETS	0.781	0.632	0.95	1	0.945	1	CLONAL	2	TRUE	1	0.1	2		621	397	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224176	39224176	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	25	377	0	ENST00000402219.2:c.2968T>A	p.Phe990Ile	p.F990I	ENST00000402219	NM_005633.3	990	Ttc/Atc	19/23	1	2	FACETS	1	0.87	1	1	0.966	1	CLONAL	4	TRUE	1	0.1	2		377	112	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241098	39241098	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1159717692	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	41	573	1	ENST00000402219.2:c.1973C>T	p.Ala658Val	p.A658V	ENST00000402219	NM_005633.3	658	gCt/gTt	12/23	1	2	FACETS	1	0.927	1	1	0.973	1	CLONAL	2	TRUE	1	0.1	2		574	339	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262572	39262572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1437202996	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	59	515	0	ENST00000402219.2:c.934C>T	p.Leu312Phe	p.L312F	ENST00000402219	NM_005633.3	312	Ctt/Ttt	7/23	1	2	FACETS	1	0.909	1	1	0.985	1	CLONAL	4	TRUE	1	0.1	2		515	278	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690230	47690230	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63749947	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	27	501	0	ENST00000233146.2:c.1447G>T	p.Glu483Ter	p.E483*	ENST00000233146	NM_000251.2	483	Gaa/Taa	9/16	1	2	FACETS	1	0.879	1	1	0.966	1	CLONAL	3	TRUE	1	0.1	2		501	159	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702390	47702390	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	16	300	0	ENST00000233146.2:c.1986G>T	p.Gln662His	p.Q662H	ENST00000233146	NM_000251.2	662	caG/caT	12/16	1	2	FACETS	1	0.811	1	1	0.943	1	CLONAL	3	TRUE	1	0.1	2		300	97	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707951	47707951	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63749830	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	51	477	0	ENST00000233146.2:c.2575G>T	p.Glu859Ter	p.E859*	ENST00000233146	NM_000251.2	859	Gaa/Taa	15/16	1	2	FACETS	0.985	0.844	1	1	0.982	1	CLONAL	4	TRUE	1	0.1	2		477	259	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47710037	47710037	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1553370893	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	12	254	0	ENST00000233146.2:c.2754G>T	p.Lys918Asn	p.K918N	ENST00000233146	NM_000251.2	918	aaG/aaT	16/16	1	2	FACETS	0.941	0.671	1	1	0.92	1	CLONAL	3	TRUE	1	0.1	2		254	85	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026497	48026497	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	31	515	0	ENST00000234420.5:c.1375T>C	p.Ser459Pro	p.S459P	ENST00000234420	NM_000179.2	459	Tct/Cct	4/10	1	2	FACETS	0.984	0.802	1	1	0.968	1	CLONAL	3	TRUE	1	0.1	2		515	210	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032118	48032118	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1558389423	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	34	362	0	ENST00000234420.5:c.3508A>C	p.Ile1170Leu	p.I1170L	ENST00000234420	NM_000179.2	1170	Att/Ctt	6/10	1	2	FACETS	1	0.885	1	1	0.972	1	CLONAL	3	TRUE	1	0.1	2		362	206	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634786	158634786	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765195676	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	38	376	0	ENST00000263640.3:c.400G>A	p.Ala134Thr	p.A134T	ENST00000263640	NM_001105.4	134	Gca/Aca	5/11	1	2	FACETS	1	0.898	1	1	0.975	1	CLONAL	3	TRUE	1	0.1	2		376	228	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095713	178095713	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	30	415	0	ENST00000397062.3:c.1618C>A	p.Leu540Ile	p.L540I	ENST00000397062	NM_006164.4	540	Ctc/Atc	5/5	1	2	FACETS	0.955	0.78	1	1	0.97	1	CLONAL	4	TRUE	1	0.1	2		415	157	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095941	178095941	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	19	465	0	ENST00000397062.3:c.1390C>A	p.Leu464Ile	p.L464I	ENST00000397062	NM_006164.4	464	Ctc/Atc	5/5	1	2	FACETS	0.856	0.652	1	1	0.923	1	CLONAL	2	TRUE	1	0.1	2		465	222	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190717496	190717496	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	20	294	0	ENST00000441310.2:c.815T>G	p.Ile272Ser	p.I272S	ENST00000441310	NM_000534.4	272	aTc/aGc	7/13	1	2	FACETS	0.971	0.755	1	1	0.956	1	CLONAL	4	TRUE	1	0.1	2		294	103	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265555	198265555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	59	574	0	ENST00000335508.6:c.2602G>A	p.Val868Met	p.V868M	ENST00000335508	NM_012433.2	868	Gtg/Atg	18/25	1	2	FACETS	1	0.867	1	1	0.985	1	CLONAL	4	TRUE	1	0.1	2		574	295	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131459	202131459	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	32	545	0	ENST00000358485.4:c.427G>T	p.Glu143Ter	p.E143*	ENST00000358485	NM_001080125.1	143	Gag/Tag	2/9	1	2	FACETS	0.84	0.685	1	1	0.966	1	CLONAL	3	TRUE	1	0.1	2		545	254	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149553	202149553	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	21	471	0	ENST00000358485.4:c.994A>T	p.Thr332Ser	p.T332S	ENST00000358485	NM_001080125.1	332	Acc/Tcc	8/9	1	2	FACETS	1	0.835	1	1	0.945	1	CLONAL	2	TRUE	1	0.1	2		471	191	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209110071	209110071	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	40	555	1	ENST00000345146.2:c.492G>T	p.Lys164Asn	p.K164N	ENST00000345146	NM_005896.2	164	aaG/aaT	5/10	1	2	FACETS	0.946	0.79	1	1	0.975	1	CLONAL	3	TRUE	1	0.1	2		556	282	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248519	212248519	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754829537	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	76	558	0	ENST00000342788.4:c.3748C>T	p.Arg1250Trp	p.R1250W	ENST00000342788	NM_005235.2	1250	Cgg/Tgg	28/28	1	2	FACETS	0.92	0.811	1	1	0.988	1	CLONAL	4	TRUE	1	0.1	2		558	413	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295774	212295774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754127388	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	81	531	0	ENST00000342788.4:c.2539C>T	p.Arg847Cys	p.R847C	ENST00000342788	NM_005235.2	847	Cgt/Tgt	21/28	1	2	FACETS	0.997	0.886	1	1	0.989	1	CLONAL	5	TRUE	1	0.1	2		531	325	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225365174	225365174	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	45	387	0	ENST00000264414.4:c.1516C>T	p.Arg506Trp	p.R506W	ENST00000264414	NM_003590.4	506	Cgg/Tgg	11/16	1	2	FACETS	1	0.891	1	1	0.979	1	CLONAL	3	TRUE	1	0.1	2		387	281	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378259	225378259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	20	355	0	ENST00000264414.4:c.636G>A	p.Met212Ile	p.M212I	ENST00000264414	NM_003590.4	212	atG/atA	5/16	1	2	FACETS	0.889	0.686	1	1	0.949	1	CLONAL	3	TRUE	1	0.1	2		355	150	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422393	225422393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1417750087	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	33	468	0	ENST00000264414.4:c.247G>A	p.Glu83Lys	p.E83K	ENST00000264414	NM_003590.4	83	Gaa/Aaa	2/16	1	2	FACETS	1	0.889	1	1	0.972	1	CLONAL	3	TRUE	1	0.1	2		468	197	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422536	225422536	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	39	404	0	ENST00000264414.4:c.104A>T	p.Asp35Val	p.D35V	ENST00000264414	NM_003590.4	35	gAc/gTc	2/16	1	2	FACETS	1	0.847	1	1	0.977	1	CLONAL	4	TRUE	1	0.1	2		404	193	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663159	227663159	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	93	635	1	ENST00000305123.5:c.296G>T	p.Ser99Ile	p.S99I	ENST00000305123	NM_005544.2	99	aGc/aTc	1/2	1	2	FACETS	0.957	0.854	1	1	0.99	1	CLONAL	4	TRUE	1	0.1	2		636	486	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546855	9546855	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	42	502	0	ENST00000353224.5:c.1167G>T	p.Gln389His	p.Q389H	ENST00000353224	NM_177990.2	389	caG/caT	5/10	0.0961476558192928	0	FACETS	1	0.86	1			1	CLONAL	3	TRUE	0	0.1	0		502	246	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024425	31024426	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	70	775	0	ENST00000375687.4:c.3915dup	p.Gly1306TrpfsTer23	p.G1306Wfs*23	ENST00000375687	NM_015338.5	1304	ctt/cTtt	13/13	0.0961476558192928	0	FACETS	1	0.893	1			1	CLONAL	3	TRUE	0	0.1	0		775	411	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383271	31383271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753291521	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	93	569	0	ENST00000328111.2:c.1183G>A	p.Ala395Thr	p.A395T	ENST00000328111	NM_006892.3	395	Gca/Aca	11/23	0.0961476558192928	0	FACETS	0.879	0.785	0.979			1	CLONAL	4	TRUE	0	0.1	0		569	476	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306566	41306566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	65	621	1	ENST00000373198.4:c.1093C>T	p.Pro365Ser	p.P365S	ENST00000373198	NM_133170.3	365	Cca/Tca	7/32	0.0961476558192928	0	FACETS	0.977	0.851	1			1	CLONAL	3	TRUE	0	0.1	0		622	399	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385204	41385204	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	81	671	0	ENST00000373198.4:c.757A>T	p.Ser253Cys	p.S253C	ENST00000373198	NM_133170.3	253	Agt/Tgt	6/32	0.0961476558192928	0	FACETS	1	0.91	1			1	CLONAL	3	TRUE	0	0.1	0		671	470	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408883	41408883	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	41	427	0	ENST00000373198.4:c.543G>T	p.Glu181Asp	p.E181D	ENST00000373198	NM_133170.3	181	gaG/gaT	4/32	0.0961476558192928	0	FACETS	1	0.888	1			1	CLONAL	2	TRUE	0	0.1	0		427	341	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39774502	39774502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769456407	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	35	499	0	ENST00000288319.7:c.650G>A	p.Arg217Gln	p.R217Q	ENST00000288319	NM_182918.3	217	cGg/cAg	5/10	1	2	FACETS	0.879	0.721	1	1	0.958	1	CLONAL	2	TRUE	1	0.1	2		499	398	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24135797	24135797	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	56	551	0	ENST00000263121.7:c.284A>T	p.Glu95Val	p.E95V	ENST00000263121	NM_003073.3	95	gAa/gTa	3/9	1	2	FACETS	0.99	0.852	1	1	0.982	1	CLONAL	3	TRUE	1	0.1	2		551	377	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143232	24143232	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	76	673	2	ENST00000263121.7:c.464G>A	p.Arg155His	p.R155H	ENST00000263121	NM_003073.3	155	cGc/cAc	4/9	1	2	FACETS	0.927	0.817	1	1	0.988	1	CLONAL	4	TRUE	1	0.1	2		675	410	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143243	24143243	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	78	666	0	ENST00000263121.7:c.475G>T	p.Asp159Tyr	p.D159Y	ENST00000263121	NM_003073.3	159	Gac/Tac	4/9	1	2	FACETS	0.942	0.832	1	1	0.988	1	CLONAL	4	TRUE	1	0.1	2		666	414	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092906	29092906	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	34	528	1	ENST00000328354.6:c.1078G>T	p.Glu360Ter	p.E360*	ENST00000328354	NM_007194.3	360	Gag/Tag	10/15	1	2	FACETS	0.956	0.787	1	1	0.97	1	CLONAL	3	TRUE	1	0.1	2		529	237	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527619	41527619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	61	426	0	ENST00000263253.7:c.1510C>T	p.Arg504Trp	p.R504W	ENST00000263253	NM_001429.3	504	Cgg/Tgg	6/31	1	2	FACETS	0.892	0.774	1	1	0.985	1	CLONAL	4	TRUE	1	0.1	2		426	342	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537115	41537115	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853039	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	46	417	1	ENST00000263253.7:c.1942C>T	p.Arg648Ter	p.R648*	ENST00000263253	NM_001429.3	648	Cga/Tga	10/31	1	2	FACETS	1	0.85	1	1	0.981	1	CLONAL	4	TRUE	1	0.1	2		418	230	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713704	30713704	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	61	504	0	ENST00000295754.5:c.1029C>A	p.Ser343Arg	p.S343R	ENST00000295754	NM_003242.5	343	agC/agA	4/7	1	2	FACETS	0.882	0.765	1	1	0.985	1	CLONAL	4	TRUE	1	0.1	2		504	346	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180365	38180365	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	101	714	0	ENST00000396334.3:c.213C>A	p.Tyr71Ter	p.Y71*	ENST00000396334	NM_002468.4	71	taC/taA	1/5	1	2	FACETS	0.92	0.825	1	1	0.991	1	CLONAL	4	TRUE	1	0.1	2		714	549	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180381	38180381	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	88	715	0	ENST00000396334.3:c.229C>A	p.Leu77Met	p.L77M	ENST00000396334	NM_002468.4	77	Ctg/Atg	1/5	1	2	FACETS	1	0.956	1	1	0.989	1	CLONAL	3	TRUE	1	0.1	2		715	510	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182047	38182047	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	68	491	0	ENST00000396334.3:c.671T>G	p.Leu224Arg	p.L224R	ENST00000396334	NM_002468.4	224	cTc/cGc	3/5	1	2	FACETS	1	0.947	1	1	0.986	1	CLONAL	3	TRUE	1	0.1	2		491	390	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	14	321	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.1	2		321	206	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164864	47164864	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	38	377	1	ENST00000409792.3:c.1262G>T	p.Arg421Met	p.R421M	ENST00000409792	NM_014159.6	421	aGg/aTg	3/21	1	2	FACETS	0.974	0.814	1	1	0.977	1	CLONAL	4	TRUE	1	0.1	2		378	195	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397700	49397700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	74	519	1	ENST00000418115.1:c.524C>T	p.Thr175Met	p.T175M	ENST00000418115	NM_001664.2	175	aCg/aTg	5/5	1	2	FACETS	0.974	0.857	1	1	0.988	1	CLONAL	4	TRUE	1	0.1	2		520	380	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933268	49933268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	127	787	0	ENST00000296474.3:c.2842C>T	p.Pro948Ser	p.P948S	ENST00000296474	NM_002447.2	948	Cca/Tca	12/20	1	2	FACETS	0.994	0.903	1	1	0.993	1	CLONAL	4	TRUE	1	0.1	2		787	639	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934752	49934752	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777611015	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	111	777	1	ENST00000296474.3:c.2144G>A	p.Arg715Gln	p.R715Q	ENST00000296474	NM_002447.2	715	cGg/cAg	7/20	1	2	FACETS	1	0.95	1	1	0.992	1	CLONAL	4	TRUE	1	0.1	2		778	513	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939829	49939829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	130	779	1	ENST00000296474.3:c.1214G>A	p.Ser405Asn	p.S405N	ENST00000296474	NM_002447.2	405	aGt/aAt	1/20	1	2	FACETS	0.97	0.882	1	1	0.993	1	CLONAL	4	TRUE	1	0.1	2		780	670	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014350	70014350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	81	606	0	ENST00000394351.3:c.1211G>A	p.Ser404Asn	p.S404N	ENST00000394351	NM_000248.3	404	aGc/aAc	9/9	1	2	FACETS	0.896	0.793	1	1	0.988	1	CLONAL	4	TRUE	1	0.1	2		606	452	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582311	119582311	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	42	397	0	ENST00000316626.5:c.1090C>T	p.Pro364Ser	p.P364S	ENST00000316626		364	Cca/Tca	10/12	1	2	FACETS	0.962	0.808	1	1	0.976	1	CLONAL	3	TRUE	1	0.1	2		397	291	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582380	119582380	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs753950587	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	42	355	0	ENST00000316626.5:c.1021C>T	p.Arg341Ter	p.R341*	ENST00000316626		341	Cga/Tga	10/12	1	2	FACETS	1	0.873	1	1	0.977	1	CLONAL	3	TRUE	1	0.1	2		355	268	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720967	119720967	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	50	487	0	ENST00000316626.5:c.208G>T	p.Val70Leu	p.V70L	ENST00000316626		70	Gta/Tta	2/12	1	2	FACETS	0.926	0.792	1	1	0.982	1	CLONAL	4	TRUE	1	0.1	2		487	270	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134885805	134885805	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	58	597	0	ENST00000398015.3:c.1716G>T	p.Glu572Asp	p.E572D	ENST00000398015	NM_004441.4	572	gaG/gaT	9/16	1	2	FACETS	0.948	0.82	1	1	0.984	1	CLONAL	4	TRUE	1	0.1	2		597	306	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977865	134977865	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	28	368	0	ENST00000398015.3:c.2858G>T	p.Arg953Ile	p.R953I	ENST00000398015	NM_004441.4	953	aGa/aTa	16/16	1	2	FACETS	1	0.889	1	1	0.967	1	CLONAL	3	TRUE	1	0.1	2		368	162	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138407749	138407749	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	29	457	0	ENST00000289153.2:c.2104A>C	p.Ser702Arg	p.S702R	ENST00000289153	NM_006219.2	702	Agt/Cgt	14/22	1	2	FACETS	1	0.824	1	1	0.957	1	CLONAL	2	TRUE	1	0.1	2		457	283	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278281	142278281	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs746970647	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	41	452	0	ENST00000350721.4:c.1544G>A	p.Arg515His	p.R515H	ENST00000350721	NM_001184.3	515	cGt/cAt	7/47	1	2	FACETS	1	0.91	1	1	0.977	1	CLONAL	3	TRUE	1	0.1	2		452	242	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998128	169998128	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs753143066	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	42	634	6	ENST00000295797.4:c.826del	p.Thr276GlnfsTer7	p.T276Qfs*7	ENST00000295797	NM_002740.5	273	ttA/tt	9/18	1	2	FACETS	1	0.884	1	1	0.977	1	CLONAL	3	TRUE	1	0.1	2		640	263	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916824	178916824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201269904	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	49	628	1	ENST00000263967.3:c.211G>A	p.Val71Ile	p.V71I	ENST00000263967	NM_006218.2	71	Gta/Ata	2/21	1	2	FACETS	0.95	0.811	1	1	0.981	1	CLONAL	4	TRUE	1	0.1	2		629	258	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430567	181430567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	32	411	1	ENST00000325404.1:c.419C>T	p.Ala140Val	p.A140V	ENST00000325404	NM_003106.3	140	gCg/gTg	1/1	1	2	FACETS	0.936	0.761	1	1	0.957	1	CLONAL	2	TRUE	1	0.1	2		412	342	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430614	181430614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	83	448	0	ENST00000325404.1:c.466C>T	p.Arg156Cys	p.R156C	ENST00000325404	NM_003106.3	156	Cgc/Tgc	1/1	1	2	FACETS	1	0.903	1	1	0.989	1	CLONAL	4	TRUE	1	0.1	2		448	407	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430986	181430986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334384230	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	86	736	0	ENST00000325404.1:c.838G>A	p.Gly280Ser	p.G280S	ENST00000325404	NM_003106.3	280	Ggc/Agc	1/1	1	2	FACETS	1	0.946	1	1	0.989	1	CLONAL	3	TRUE	1	0.1	2		736	516	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502465	186502465	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	30	316	0	ENST00000323963.5:c.188C>A	p.Ala63Asp	p.A63D	ENST00000323963		63	gCt/gAt	3/11	1	2	FACETS	1	0.887	1	1	0.969	1	CLONAL	3	TRUE	1	0.1	2		316	177	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504995	186504995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	47	404	0	ENST00000323963.5:c.851G>A	p.Arg284His	p.R284H	ENST00000323963		284	cGc/cAc	8/11	1	2	FACETS	1	0.917	1	1	0.98	1	CLONAL	3	TRUE	1	0.1	2		404	279	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505660	186505660	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	25	328	0	ENST00000323963.5:c.1068C>A	p.Asn356Lys	p.N356K	ENST00000323963		356	aaC/aaA	10/11	1	2	FACETS	1	0.866	1	1	0.963	1	CLONAL	3	TRUE	1	0.1	2		328	149	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440292	187440292	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750212558	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	96	539	0	ENST00000232014.4:c.2075G>A	p.Arg692His	p.R692H	ENST00000232014	NM_001130845.1	692	cGc/cAc	10/10	1	2	FACETS	0.941	0.842	1	1	0.99	1	CLONAL	4	TRUE	1	0.1	2		539	510	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444560	187444560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	106	701	0	ENST00000232014.4:c.1667G>A	p.Arg556His	p.R556H	ENST00000232014	NM_001130845.1	556	cGc/cAc	7/10	1	2	FACETS	0.927	0.833	1	1	0.991	1	CLONAL	4	TRUE	1	0.1	2		701	572	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803416	1803416	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368831528	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	35	729	2	ENST00000260795.2:c.685G>A	p.Val229Ile	p.V229I	ENST00000260795		229	Gtc/Atc	5/17	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.1	2		731	546	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808406	1808406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	122	1082	1	ENST00000260795.2:c.2164G>A	p.Asp722Asn	p.D722N	ENST00000260795		722	Gac/Aac	15/17	1	2	FACETS	1	0.923	1	1	0.992	1	CLONAL	4	TRUE	1	0.1	2		1083	598	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980527	1980527	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	116	781	1	ENST00000382891.5:c.3989C>A	p.Ala1330Glu	p.A1330E	ENST00000382891	NM_133335.3	1330	gCg/gAg	22/22	1	2	FACETS	1	0.934	1	1	0.992	1	CLONAL	4	TRUE	1	0.1	2		782	557	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748335	41748335	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	74	612	0	ENST00000226382.2:c.434G>A	p.Trp145Ter	p.W145*	ENST00000226382	NM_003924.3	145	tGg/tAg	3/3	1	2	FACETS	0.879	0.771	0.996	1	0.985	1	CLONAL	3	TRUE	1	0.1	2		612	561	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749509	41749509	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	85	555	1	ENST00000226382.2:c.286C>T	p.Arg96Cys	p.R96C	ENST00000226382	NM_003924.3	96	Cgc/Tgc	2/3	1	2	FACETS	1	0.952	1	1	0.989	1	CLONAL	3	TRUE	1	0.1	2		556	498	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55154983	55154983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1185214354	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	39	511	0	ENST00000257290.5:c.2692G>A	p.Gly898Ser	p.G898S	ENST00000257290	NM_006206.4	898	Ggc/Agc	20/23	1	2	FACETS	1	0.837	1	1	0.975	1	CLONAL	3	TRUE	1	0.1	2		511	259	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156540	55156540	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775205485	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	49	608	0	ENST00000257290.5:c.2941C>T	p.Arg981Cys	p.R981C	ENST00000257290	NM_006206.4	981	Cgt/Tgt	22/23	1	2	FACETS	1	0.902	1	1	0.98	1	CLONAL	3	TRUE	1	0.1	2		608	303	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535301	66535301	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	119	589	0	ENST00000273854.3:c.160C>A	p.Leu54Met	p.L54M	ENST00000273854	NM_004439.5	54	Ctg/Atg	1/18	1	2	FACETS	1	0.945	1	1	0.992	1	CLONAL	4	TRUE	1	0.1	2		589	561	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156081	106156081	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749904780	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	32	363	0	ENST00000380013.4:c.982G>A	p.Val328Ile	p.V328I	ENST00000380013	NM_001127208.2	328	Gtt/Att	3/11	1	2	FACETS	0.982	0.807	1	1	0.972	1	CLONAL	4	TRUE	1	0.1	2		363	163	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157472	106157472	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	20	334	0	ENST00000380013.4:c.2373T>G	p.Tyr791Ter	p.Y791*	ENST00000380013	NM_001127208.2	791	taT/taG	3/11	1	2	FACETS	0.909	0.706	1	1	0.955	1	CLONAL	4	TRUE	1	0.1	2		334	110	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157656	106157657	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1560546209	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	25	344	0	ENST00000380013.4:c.2562dup	p.Ala855CysfsTer17	p.A855Cfs*17	ENST00000380013	NM_001127208.2	853	ctt/cTtt	3/11	1	2	FACETS	1	0.869	1	1	0.963	1	CLONAL	3	TRUE	1	0.1	2		344	148	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164011	106164011	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	36	374	0	ENST00000380013.4:c.3521C>T	p.Ala1174Val	p.A1174V	ENST00000380013	NM_001127208.2	1174	gCt/gTt	5/11	1	2	FACETS	1	0.862	1	1	0.976	1	CLONAL	4	TRUE	1	0.1	2		374	173	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067103	143067103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	40	404	0	ENST00000262992.4:c.1610C>T	p.Ala537Val	p.A537V	ENST00000262992	NM_001101669.1	537	gCt/gTt	16/24	1	2	FACETS	1	0.89	1	1	0.976	1	CLONAL	3	TRUE	1	0.1	2		404	246	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244165	153244165	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	58	560	0	ENST00000281708.4:c.1992G>T	p.Glu664Asp	p.E664D	ENST00000281708	NM_033632.3	664	gaG/gaT	12/12	1	2	FACETS	1	0.934	1	1	0.984	1	CLONAL	3	TRUE	1	0.1	2		560	340	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516893	187516893	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	27	517	0	ENST00000441802.2:c.13088C>A	p.Ser4363Tyr	p.S4363Y	ENST00000441802	NM_005245.3	4363	tCt/tAt	26/27	1	2	FACETS	0.763	0.607	0.94	1	0.935	1	CLONAL	2	TRUE	1	0.1	2		517	354	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521102	187521102	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1317684793	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	61	457	0	ENST00000441802.2:c.12053C>T	p.Ala4018Val	p.A4018V	ENST00000441802	NM_005245.3	4018	gCc/gTc	22/27	1	2	FACETS	0.887	0.769	1	1	0.985	1	CLONAL	4	TRUE	1	0.1	2		457	344	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524377	187524377	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	60	559	0	ENST00000441802.2:c.11303G>T	p.Ser3768Ile	p.S3768I	ENST00000441802	NM_005245.3	3768	aGt/aTt	19/27	1	2	FACETS	1	0.873	1	1	0.983	1	CLONAL	3	TRUE	1	0.1	2		559	396	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524699	187524699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	91	724	0	ENST00000441802.2:c.10981C>T	p.Arg3661Cys	p.R3661C	ENST00000441802	NM_005245.3	3661	Cgc/Tgc	19/27	1	2	FACETS	0.905	0.806	1	1	0.99	1	CLONAL	4	TRUE	1	0.1	2		724	503	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540639	187540639	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	42	392	0	ENST00000441802.2:c.7101G>A	p.Met2367Ile	p.M2367I	ENST00000441802	NM_005245.3	2367	atG/atA	10/27	1	2	FACETS	1	0.896	1	1	0.977	1	CLONAL	3	TRUE	1	0.1	2		392	257	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554851	187554851	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	42	444	0	ENST00000441802.2:c.4310C>T	p.Thr1437Ile	p.T1437I	ENST00000441802	NM_005245.3	1437	aCt/aTt	7/27	1	2	FACETS	1	0.909	1	1	0.98	1	CLONAL	4	TRUE	1	0.1	2		444	189	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630062	187630062	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	55	693	0	ENST00000441802.2:c.920G>A	p.Arg307Lys	p.R307K	ENST00000441802	NM_005245.3	307	aGg/aAg	2/27	1	2	FACETS	1	0.927	1	1	0.984	1	CLONAL	4	TRUE	1	0.1	2		693	247	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630285	187630285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	45	645	0	ENST00000441802.2:c.697G>A	p.Gly233Arg	p.G233R	ENST00000441802	NM_005245.3	233	Ggg/Agg	2/27	1	2	FACETS	1	0.916	1	1	0.974	1	CLONAL	2	TRUE	1	0.1	2		645	395	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236579	236579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1560998056	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	19	106	0	ENST00000264932.6:c.1297C>T	p.Pro433Ser	p.P433S	ENST00000264932	NM_004168.2	433	Ccc/Tcc	10/15	1	2	FACETS	1	0.826	1	1	0.956	1	CLONAL	4	TRUE	1	0.1	2		106	88	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279426	1279426	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199422297	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	84	825	0	ENST00000310581.5:c.2110C>T	p.Pro704Ser	p.P704S	ENST00000310581	NM_198253.2	704	Cct/Tct	5/16	1	2	FACETS	0.911	0.808	1	1	0.989	1	CLONAL	4	TRUE	1	0.1	2		825	461	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293686	1293686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	92	855	0	ENST00000310581.5:c.1315G>A	p.Glu439Lys	p.E439K	ENST00000310581	NM_198253.2	439	Gag/Aag	2/16	1	2	FACETS	0.895	0.798	0.998	1	0.99	1	CLONAL	4	TRUE	1	0.1	2		855	514	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449399	31449399	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	51	457	0	ENST00000344624.3:c.2810T>C	p.Met937Thr	p.M937T	ENST00000344624		937	aTg/aCg	19/33	1	2	FACETS	1	0.921	1	1	0.983	1	CLONAL	4	TRUE	1	0.1	2		457	230	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183306	56183306	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	41	577	1	ENST00000399503.3:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000399503	NM_005921.1	1406	Cag/Tag	18/20	1	2	FACETS	0.936	0.784	1	1	0.975	1	CLONAL	3	TRUE	1	0.1	2		578	292	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754258	57754258	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	36	423	0	ENST00000274289.3:c.593A>C	p.Glu198Ala	p.E198A	ENST00000274289	NM_006622.3	198	gAa/gCa	4/14	1	2	FACETS	0.896	0.743	1	1	0.975	1	CLONAL	4	TRUE	1	0.1	2		423	201	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590427	67590427	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	24	245	0	ENST00000274335.5:c.1489C>T	p.Gln497Ter	p.Q497*	ENST00000274335		497	Cag/Tag	11/15	1	2	FACETS	1	0.866	1	1	0.962	1	CLONAL	3	TRUE	1	0.1	2		245	142	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593320	67593320	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	26	308	1	ENST00000274335.5:c.2066G>A	p.Ser689Asn	p.S689N	ENST00000274335		689	aGc/aAc	15/15	1	2	FACETS	1	0.882	1	1	0.957	1	CLONAL	2	TRUE	1	0.1	2		309	223	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629103	86629103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753769946	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	11	299	0	ENST00000274376.6:c.848G>A	p.Arg283His	p.R283H	ENST00000274376	NM_002890.2	283	cGt/cAt	4/25	1	2	FACETS	0.821	0.57	1	1	0.87	1	CLONAL	2	TRUE	1	0.1	2		299	134	SUCCESS
APC	324	MSKCC	GRCh37	5	112102927	112102927	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746592911	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	38	445	2	ENST00000257430.4:c.262C>T	p.Arg88Trp	p.R88W	ENST00000257430	NM_000038.5	88	Cgg/Tgg	4/16	1	2	FACETS	1	0.915	1	1	0.976	1	CLONAL	3	TRUE	1	0.1	2		447	218	SUCCESS
APC	324	MSKCC	GRCh37	5	112174315	112174315	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	24	361	0	ENST00000257430.4:c.3024A>G	p.Ile1008Met	p.I1008M	ENST00000257430	NM_000038.5	1008	atA/atG	16/16	1	2	FACETS	1	0.803	1	1	0.964	1	CLONAL	4	TRUE	1	0.1	2		361	119	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449529	149449529	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	77	699	0	ENST00000286301.3:c.1417A>G	p.Thr473Ala	p.T473A	ENST00000286301	NM_005211.3	473	Act/Gct	10/22	1	2	FACETS	1	0.914	1	1	0.987	1	CLONAL	3	TRUE	1	0.1	2		699	490	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517514	176517514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373397427	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	126	823	1	ENST00000292408.4:c.215G>A	p.Arg72His	p.R72H	ENST00000292408	NM_213647.1	72	cGc/cAc	3/18	1	2	FACETS	0.916	0.833	1	1	0.993	1	CLONAL	5	TRUE	1	0.1	2		824	550	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637122	176637122	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	13	594	0	ENST00000439151.2:c.1727del	p.Asn576ThrfsTer23	p.N576Tfs*23	ENST00000439151	NM_022455.4	574	ggA/gg	5/23	1	2	FACETS	0.778	0.557	1	1	0.879	1	CLONAL	2	TRUE	1	0.1	2		594	167	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665280	176665280	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784107	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	54	358	0	ENST00000439151.2:c.3964C>T	p.Arg1322Ter	p.R1322*	ENST00000439151	NM_022455.4	1322	Cga/Tga	7/23	1	2	FACETS	1	0.891	1	1	0.984	1	CLONAL	4	TRUE	1	0.1	2		358	260	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694712	176694712	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	24	395	0	ENST00000439151.2:c.5296C>T	p.Arg1766Ter	p.R1766*	ENST00000439151	NM_022455.4	1766	Cga/Tga	15/23	1	2	FACETS	1	0.871	1	1	0.953	1	CLONAL	2	TRUE	1	0.1	2		395	208	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721324	176721324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	59	502	0	ENST00000439151.2:c.6955C>T	p.Pro2319Ser	p.P2319S	ENST00000439151	NM_022455.4	2319	Cca/Tca	23/23	1	2	FACETS	0.955	0.827	1	1	0.985	1	CLONAL	4	TRUE	1	0.1	2		502	309	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030329	180030329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142322370	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	81	776	2	ENST00000261937.6:c.3955C>T	p.Arg1319Trp	p.R1319W	ENST00000261937	NM_182925.4	1319	Cgg/Tgg	30/30	1	2	FACETS	1	0.912	1	1	0.988	1	CLONAL	3	TRUE	1	0.1	2		778	520	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057800	180057800	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	29	428	1	ENST00000261937.6:c.156-1G>T		p.X52_splice	ENST00000261937	NM_182925.4	52			1	2	FACETS	0.991	0.802	1	1	0.966	1	CLONAL	3	TRUE	1	0.1	2		429	195	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671203	30671203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	103	706	3	ENST00000376406.3:c.5674G>A	p.Ala1892Thr	p.A1892T	ENST00000376406	NM_014641.2	1892	Gcc/Acc	11/15	0.0961476558192928	3	FACETS	1	0.935	1	1	0.988	1	CLONAL	4	TRUE	1	0.1	3		709	513	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671780	30671780	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	87	668	0	ENST00000376406.3:c.5180C>A	p.Ala1727Asp	p.A1727D	ENST00000376406	NM_014641.2	1727	gCt/gAt	10/15	0.0961476558192928	3	FACETS	1	0.948	1	1	0.987	1	CLONAL	4	TRUE	1	0.1	3		668	411	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672242	30672242	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	104	797	0	ENST00000376406.3:c.4718C>T	p.Pro1573Leu	p.P1573L	ENST00000376406	NM_014641.2	1573	cCt/cTt	10/15	0.0961476558192928	3	FACETS	0.952	0.857	1	1	0.989	1	CLONAL	5	TRUE	1	0.1	3		797	459	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673725	30673725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs78556678	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	22	619	1	ENST00000376406.3:c.3235C>T	p.Arg1079Cys	p.R1079C	ENST00000376406	NM_014641.2	1079	Cgt/Tgt	10/15	0.0961476558192928	3	FACETS	1	0.871	1	0.598	0.463	0.756	CLONAL	1	TRUE	1	0.1	3		620	386	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679902	30679902	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	65	454	0	ENST00000376406.3:c.1817C>A	p.Ala606Asp	p.A606D	ENST00000376406	NM_014641.2	606	gCt/gAt	5/15	0.0961476558192928	3	FACETS	1	0.936	1	1	0.982	1	CLONAL	4	TRUE	1	0.1	3		454	306	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166818	32166818	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1441415979	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	95	777	2	ENST00000375023.3:c.4420C>T	p.Arg1474Ter	p.R1474*	ENST00000375023	NM_004557.3	1474	Cga/Tga	24/30	0.0961476558192928	3	FACETS	1	0.948	1	1	0.983	1	CLONAL	3	TRUE	1	0.1	3		779	601	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166845	32166845	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	117	806	0	ENST00000375023.3:c.4393C>T	p.Leu1465Phe	p.L1465F	ENST00000375023	NM_004557.3	1465	Ctt/Ttt	24/30	0.0961476558192928	3	FACETS	0.942	0.851	1	1	0.988	1	CLONAL	4	TRUE	1	0.1	3		806	652	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188767	32188767	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	58	720	0	ENST00000375023.3:c.787C>A	p.Leu263Ile	p.L263I	ENST00000375023	NM_004557.3	263	Ctc/Atc	4/30	0.0961476558192928	3	FACETS	0.953	0.821	1	1	0.965	1	CLONAL	3	TRUE	1	0.1	3		720	426	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798112	32798112	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	114	705	0	ENST00000374899.4:c.1567A>G	p.Thr523Ala	p.T523A	ENST00000374899	NM_018833.2	523	Aca/Gca	9/12	0.0961476558192928	3	FACETS	1	0.942	1	1	0.989	1	CLONAL	4	TRUE	1	0.1	3		705	565	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798183	32798183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146801469	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	94	651	2	ENST00000374899.4:c.1496C>T	p.Thr499Met	p.T499M	ENST00000374899	NM_018833.2	499	aCg/aTg	9/12	0.0961476558192928	3	FACETS	0.991	0.885	1	1	0.986	1	CLONAL	4	TRUE	1	0.1	3		653	498	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805928	32805928	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	176	804	1	ENST00000374899.4:c.83G>T	p.Gly28Val	p.G28V	ENST00000374899	NM_018833.2	28	gGg/gTg	2/12	0.0961476558192928	3	FACETS	0.994	0.917	1	1	0.994	1	CLONAL	5	TRUE	1	0.1	3		805	744	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286966	33286966	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	40	791	0	ENST00000374542.5:c.1971G>T	p.Glu657Asp	p.E657D	ENST00000374542	NM_001141970.1	657	gaG/gaT	7/8	0.0961476558192928	3	FACETS	1	0.95	1	0.724	0.601	0.862	CLONAL	1	TRUE	1	0.1	3		791	580	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979210	93979210	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	18	277	0	ENST00000369303.4:c.1618G>T	p.Gly540Cys	p.G540C	ENST00000369303	NM_004440.3	540	Ggt/Tgt	7/17	0.0961476558192928	3	FACETS	1	0.77	1	1	0.934	1	CLONAL	4	TRUE	1	0.1	3		277	94	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554351	106554351	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	51	416	0	ENST00000369096.4:c.1879G>T	p.Gly627Ter	p.G627*	ENST00000369096	NM_001198.3	627	Gga/Tga	6/7	0.0961476558192928	3	FACETS	0.997	0.851	1	1	0.964	1	CLONAL	3	TRUE	1	0.1	3		416	358	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554834	106554834	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	50	391	0	ENST00000369096.4:c.1951C>T	p.Arg651Ter	p.R651*	ENST00000369096	NM_001198.3	651	Cga/Tga	7/7	0.0961476558192928	3	FACETS	1	0.928	1	1	0.971	1	CLONAL	3	TRUE	1	0.1	3		391	305	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109315718	109315718	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1429593576	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	72	692	0	ENST00000436639.2:c.1067T>G	p.Met356Arg	p.M356R	ENST00000436639	NM_014454.2	356	aTg/aGg	6/10	0.0961476558192928	3	FACETS	1	0.931	1	1	0.984	1	CLONAL	4	TRUE	1	0.1	3		692	348	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662297	117662297	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1029038641	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	37	574	0	ENST00000368508.3:c.5079+1G>A		p.X1693_splice	ENST00000368508	NM_002944.2	1693			0.0961476558192928	3	FACETS	0.938	0.781	1	1	0.964	1	CLONAL	4	TRUE	1	0.1	3		574	207	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200102	138200102	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	61	517	0	ENST00000237289.4:c.1520G>T	p.Ser507Ile	p.S507I	ENST00000237289	NM_001270507.1	507	aGc/aTc	7/9	0.0961476558192928	3	FACETS	1	0.904	1	1	0.973	1	CLONAL	3	TRUE	1	0.1	3		517	405	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415582	152415582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	71	648	0	ENST00000206249.3:c.1432G>A	p.Val478Ile	p.V478I	ENST00000206249	NM_000125.3	478	Gtc/Atc	7/8	0.0961476558192928	3	FACETS	0.875	0.767	0.991	1	0.979	1	CLONAL	4	TRUE	1	0.1	3		648	426	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222566	157222566	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	90	662	0	ENST00000346085.5:c.1833G>T	p.Gln611His	p.Q611H	ENST00000346085	NM_020732.3	611	caG/caT	4/20	0.0961476558192928	3	FACETS	0.914	0.813	1	1	0.984	1	CLONAL	4	TRUE	1	0.1	3		662	517	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157406025	157406025	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	41	485	0	ENST00000346085.5:c.2267C>A	p.Pro756His	p.P756H	ENST00000346085	NM_020732.3	756	cCt/cAt	6/20	0.0961476558192928	3	FACETS	1	0.849	1	1	0.957	1	CLONAL	3	TRUE	1	0.1	3		485	283	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157454262	157454262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	52	453	2	ENST00000346085.5:c.2472G>A	p.Met824Ile	p.M824I	ENST00000346085	NM_020732.3	824	atG/atA	8/20	0.0961476558192928	3	FACETS	0.904	0.775	1	1	0.973	1	CLONAL	4	TRUE	1	0.1	3		455	302	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505566	157505566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	33	252	0	ENST00000346085.5:c.3547C>T	p.Pro1183Ser	p.P1183S	ENST00000346085	NM_020732.3	1183	Cct/Tct	13/20	0.0961476558192928	3	FACETS	1	0.844	1	1	0.964	1	CLONAL	4	TRUE	1	0.1	3		252	169	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527679	157527679	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs797045282	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	85	595	1	ENST00000346085.5:c.5404C>T	p.Arg1802Ter	p.R1802*	ENST00000346085	NM_020732.3	1802	Cga/Tga	20/20	0.0961476558192928	3	FACETS	0.956	0.848	1	1	0.984	1	CLONAL	4	TRUE	1	0.1	3		596	467	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771132	161771132	+	stop_lost	Nonstop_Mutation	SNP	T	T	C	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	130	633	0	ENST00000366898.1:c.1397A>G	p.Ter466TrpextTer23	p.*466Wext*23	ENST00000366898	NM_004562.2	466	tAg/tGg	12/12	0.0961476558192928	3	FACETS	0.977	0.89	1	1	0.991	1	CLONAL	5	TRUE	1	0.1	3		633	559	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042233	6042233	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	96	565	0	ENST00000265849.7:c.388A>G	p.Lys130Glu	p.K130E	ENST00000265849	NM_000535.5	130	Aag/Gag	5/15	0.169619318347497	1	FACETS	0.952	0.852	1	1	0.99	1	CLONAL	4	TRUE	0	0.1	1		565	479	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729399	41729399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	53	601	1	ENST00000242208.4:c.1130G>A	p.Arg377His	p.R377H	ENST00000242208	NM_002192.2	377	cGc/cAc	3/3	0.169619318347497	1	FACETS	1	0.932	1	1	0.978	1	CLONAL	2	TRUE	0	0.1	1		602	433	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729789	41729789	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	30	391	0	ENST00000242208.4:c.740G>T	p.Cys247Phe	p.C247F	ENST00000242208	NM_002192.2	247	tGc/tTc	3/3	0.169619318347497	1	FACETS	0.979	0.796	1	1	0.967	1	CLONAL	3	TRUE	0	0.1	1		391	194	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468080	50468080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	50	504	1	ENST00000331340.3:c.1315C>T	p.Arg439Cys	p.R439C	ENST00000331340	NM_006060.4	439	Cgc/Tgc	8/8	0.169619318347497	1	FACETS	1	0.886	1	1	0.98	1	CLONAL	3	TRUE	0	0.1	1		505	303	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55272988	55272988	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	68	558	0	ENST00000275493.2:c.3311C>A	p.Ser1104Tyr	p.S1104Y	ENST00000275493	NM_005228.3	1104	tCt/tAt	28/28	0.169619318347497	1	FACETS	1	0.877	1	1	0.985	1	CLONAL	3	TRUE	0	0.1	1		558	429	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508082	106508082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	34	256	2	ENST00000359195.3:c.76C>T	p.Arg26Cys	p.R26C	ENST00000359195	NM_002649.2	26	Cgc/Tgc	2/11	0.169619318347497	4	FACETS	1	0.876	1	1	0.954	1	CLONAL	3	TRUE	2	0.1	4		258	230	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522613	106522613	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	30	508	0	ENST00000359195.3:c.2590C>A	p.Leu864Ile	p.L864I	ENST00000359195	NM_002649.2	864	Ctc/Atc	7/11	0.169619318347497	4	FACETS	0.987	0.8	1	1	0.94	1	CLONAL	3	TRUE	2	0.1	4		508	223	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545690	106545690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	48	587	1	ENST00000359195.3:c.3167C>T	p.Thr1056Ile	p.T1056I	ENST00000359195	NM_002649.2	1056	aCa/aTa	11/11	0.169619318347497	4	FACETS	0.989	0.842	1	1	0.974	1	CLONAL	4	TRUE	2	0.1	4		588	267	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339493	116339493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766874293	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	27	367	0	ENST00000397752.3:c.355G>A	p.Ala119Thr	p.A119T	ENST00000397752	NM_000245.2	119	Gct/Act	2/21	0.169619318347497	4	FACETS	0.889	0.715	1	1	0.949	1	CLONAL	4	TRUE	2	0.1	4		367	167	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340276	116340276	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	14	308	1	ENST00000397752.3:c.1142del	p.Asn381ThrfsTer3	p.N381Tfs*3	ENST00000397752	NM_000245.2	380	Aaa/aa	2/21	0.169619318347497	4	FACETS	0.928	0.673	1	0.928	0.673	1	CLONAL	2	TRUE	2	0.1	4		309	166	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411756	116411756	+	intron_variant	Intron	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	53	918	1	ENST00000397752.3:c.2887+48G>A		p.*963*	ENST00000397752	NM_000245.2	-/1390			0.169619318347497	4	FACETS	1	0.866	1	1	0.966	1	CLONAL	3	TRUE	2	0.1	4		919	384	SUCCESS
MET	4233	MSKCC	GRCh37	7	116417524	116417524	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	26	253	0	ENST00000397752.3:c.3340+1G>T		p.X1114_splice	ENST00000397752	NM_000245.2	1114			0.169619318347497	4	FACETS	1	0.865	1	1	0.957	1	CLONAL	4	TRUE	2	0.1	4		253	130	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852163	128852163	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	123	816	1	ENST00000249373.3:c.2235G>T	p.Gln745His	p.Q745H	ENST00000249373	NM_005631.4	745	caG/caT	12/12	0.169619318347497	4	FACETS	0.991	0.9	1	1	0.991	1	CLONAL	5	TRUE	2	0.1	4		817	546	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534449	140534449	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	24	541	0	ENST00000288602.6:c.464C>A	p.Pro155His	p.P155H	ENST00000288602	NM_004333.4	155	cCt/cAt	3/18	0.169619318347497	4	FACETS	0.854	0.671	1	0.854	0.671	1	CLONAL	2	TRUE	2	0.1	4		541	309	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523666	148523667	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	10	363	0	ENST00000320356.2:c.786dup	p.Asn263GlnfsTer8	p.N263Qfs*8	ENST00000320356	NM_004456.4	262	-/C	8/20	0.169619318347497	4	FACETS	1	0.756	1	0.573	0.388	0.805	CLONAL	1	TRUE	2	0.1	4		363	192	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524275	148524275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	31	412	0	ENST00000320356.2:c.709G>A	p.Ala237Thr	p.A237T	ENST00000320356	NM_004456.4	237	Gca/Aca	7/20	0.169619318347497	4	FACETS	1	0.891	1	1	0.953	1	CLONAL	3	TRUE	2	0.1	4		412	200	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151164240	151164240	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	32	239	0	ENST00000262187.5:c.520G>T	p.Ala174Ser	p.A174S	ENST00000262187	NM_005614.3	174	Gct/Tct	8/8	0.169619318347497	4	FACETS	0.939	0.773	1	1	0.966	1	CLONAL	5	TRUE	2	0.1	4		239	150	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848547	151848547	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	27	385	1	ENST00000262189.6:c.12646G>A	p.Asp4216Asn	p.D4216N	ENST00000262189	NM_170606.2	4216	Gat/Aat	50/59	0.169619318347497	4	FACETS	0.985	0.789	1	1	0.934	1	CLONAL	3	TRUE	2	0.1	4		386	201	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902253	151902253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1230955155	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	38	341	0	ENST00000262189.6:c.3899G>T	p.Arg1300Ile	p.R1300I	ENST00000262189	NM_170606.2	1300	aGa/aTa	25/59	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.1	NA		341	161	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539105	23539105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	50	476	0	ENST00000380871.4:c.334G>A	p.Ala112Thr	p.A112T	ENST00000380871	NM_006167.3	112	Gcc/Acc	2/2	1	2	FACETS	1	0.926	1	1	0.981	1	CLONAL	3	TRUE	1	0.1	2		476	292	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271189	38271189	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771680156	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	52	524	0	ENST00000425967.3:c.2519G>A	p.Arg840Gln	p.R840Q	ENST00000425967	NM_001174067.1	840	cGa/cAa	19/19	1	2	FACETS	0.945	0.807	1	1	0.98	1	CLONAL	3	TRUE	1	0.1	2		524	367	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275402	38275402	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	27	629	0	ENST00000425967.3:c.1631T>A	p.Val544Glu	p.V544E	ENST00000425967	NM_001174067.1	544	gTg/gAg	12/19	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.1	2		629	479	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277214	38277214	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121909631	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	92	766	0	ENST00000425967.3:c.1214A>G	p.Tyr405Cys	p.Y405C	ENST00000425967	NM_001174067.1	405	tAc/tGc	10/19	1	2	FACETS	0.933	0.832	1	1	0.99	1	CLONAL	4	TRUE	1	0.1	2		766	493	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002946	69002946	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146486437	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	20	300	0	ENST00000288368.4:c.2246C>T	p.Thr749Met	p.T749M	ENST00000288368	NM_024870.2	749	aCg/aTg	20/40	1	2	FACETS	1	0.838	1	1	0.943	1	CLONAL	2	TRUE	1	0.1	2		300	179	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021769	69021769	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	38	559	0	ENST00000288368.4:c.3057C>A	p.Asp1019Glu	p.D1019E	ENST00000288368	NM_024870.2	1019	gaC/gaA	25/40	1	2	FACETS	1	0.921	1	1	0.971	1	CLONAL	2	TRUE	1	0.1	2		559	316	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69032484	69032484	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	72	647	0	ENST00000288368.4:c.3558C>A	p.Asp1186Glu	p.D1186E	ENST00000288368	NM_024870.2	1186	gaC/gaA	29/40	1	2	FACETS	0.933	0.819	1	1	0.987	1	CLONAL	4	TRUE	1	0.1	2		647	386	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69143582	69143582	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777006292	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	29	377	0	ENST00000288368.4:c.4790G>A	p.Cys1597Tyr	p.C1597Y	ENST00000288368	NM_024870.2	1597	tGc/tAc	40/40	1	2	FACETS	0.837	0.675	1	1	0.963	1	CLONAL	3	TRUE	1	0.1	2		377	231	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978707	70978707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763796290	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	23	596	0	ENST00000276594.2:c.946G>A	p.Asp316Asn	p.D316N	ENST00000276594	NM_024504.3	316	Gat/Aat	5/8	1	2	FACETS	0.996	0.779	1	1	0.945	1	CLONAL	2	TRUE	1	0.1	2		596	231	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859804	117859804	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	26	294	0	ENST00000297338.2:c.1831C>A	p.Leu611Met	p.L611M	ENST00000297338	NM_006265.2	611	Ctg/Atg	14/14	1	2	FACETS	1	0.875	1	1	0.964	1	CLONAL	3	TRUE	1	0.1	2		294	153	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752974	128752974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	73	481	0	ENST00000377970.2:c.1135C>T	p.Arg379Cys	p.R379C	ENST00000377970	NM_002467.4	379	Cgc/Tgc	3/3	1	2	FACETS	0.931	0.819	1	1	0.987	1	CLONAL	4	TRUE	1	0.1	2		481	392	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572645	141572645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372742713	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	50	652	0	ENST00000220592.5:c.425C>T	p.Ala142Val	p.A142V	ENST00000220592	NM_012154.3	142	gCg/gTg	4/19	1	2	FACETS	1	0.861	1	1	0.974	1	CLONAL	2	TRUE	1	0.1	2		652	493	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739584	145739584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772515188	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	102	862	2	ENST00000428558.2:c.1867C>T	p.Arg623Cys	p.R623C	ENST00000428558	NM_004260.3	623	Cgc/Tgc	11/22	1	2	FACETS	1	0.922	1	1	0.991	1	CLONAL	4	TRUE	1	0.1	2		864	495	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054599	5054599	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	14	265	1	ENST00000381652.3:c.651G>T	p.Lys217Asn	p.K217N	ENST00000381652	NM_004972.3	217	aaG/aaT	7/25	0.0961476558192928	0	FACETS	1	0.797	1			1	CLONAL	2	TRUE	0	0.1	0		266	113	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404575	8404575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1168914682	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	25	320	1	ENST00000356435.5:c.4172C>T	p.Ala1391Val	p.A1391V	ENST00000356435		1391	gCa/gTa	25/35	0.0961476558192928	0	FACETS	1	0.857	1			1	CLONAL	3	TRUE	0	0.1	0		321	137	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465480	8465480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	40	443	0	ENST00000356435.5:c.3700G>A	p.Glu1234Lys	p.E1234K	ENST00000356435		1234	Gaa/Aaa	21/35	0.0961476558192928	0	FACETS	0.963	0.81	1			1	CLONAL	4	TRUE	0	0.1	0		443	187	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486079	8486079	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	29	520	0	ENST00000356435.5:c.2738T>G	p.Ile913Ser	p.I913S	ENST00000356435		913	aTt/aGt	17/35	0.0961476558192928	0	FACETS	1	0.897	1			1	CLONAL	2	TRUE	0	0.1	0		520	221	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499651	8499651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	27	421	0	ENST00000356435.5:c.2318C>T	p.Ala773Val	p.A773V	ENST00000356435		773	gCa/gTa	14/35	0.0961476558192928	0	FACETS	0.931	0.743	1			1	CLONAL	2	TRUE	0	0.1	0		421	261	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971132	21971132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774633329	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	58	460	0	ENST00000304494.5:c.226G>A	p.Ala76Thr	p.A76T	ENST00000304494	NM_000077.4	76	Gcc/Acc	2/3	0.0961476558192928	0	FACETS	0.956	0.825	1			1	CLONAL	3	TRUE	0	0.1	0		460	364	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994327	21994327	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	71	449	0	ENST00000579755.1:c.4G>T	p.Val2Leu	p.V2L	ENST00000579755		2	Gtg/Ttg	1/3	0.0961476558192928		FACETS		0.786	1				CLONAL	4	TRUE	0	0.1	0		449	357	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180292	27180292	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	51	581	0	ENST00000380036.4:c.956A>T	p.Asn319Ile	p.N319I	ENST00000380036	NM_000459.3	319	aAt/aTt	7/23	0.0961476558192928	0	FACETS	0.812	0.692	0.942			1	CLONAL	3	TRUE	0	0.1	0		581	377	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197554	27197554	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	62	584	0	ENST00000380036.4:c.1866G>T	p.Gln622His	p.Q622H	ENST00000380036	NM_000459.3	622	caG/caT	12/23	0.0961476558192928	0	FACETS	0.864	0.751	0.984			1	CLONAL	4	TRUE	0	0.1	0		584	323	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325701	87325701	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	28	405	0	ENST00000277120.3:c.578A>C	p.Asn193Thr	p.N193T	ENST00000277120		193	aAt/aCt	6/19	0.0961476558192928	0	FACETS	1	0.866	1			1	CLONAL	3	TRUE	0	0.1	0		405	154	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636253	87636253	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	75	562	0	ENST00000277120.3:c.2418G>A	p.Trp806Ter	p.W806*	ENST00000277120		806	tgG/tgA	19/19	0.0961476558192928	0	FACETS	0.898	0.791	1			1	CLONAL	4	TRUE	0	0.1	0		562	376	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639939	93639939	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	43	293	0	ENST00000375746.1:c.1268T>A	p.Val423Asp	p.V423D	ENST00000375746	NM_001174167.1	423	gTc/gAc	10/14	0.0961476558192928	0	FACETS	0.896	0.757	1			1	CLONAL	4	TRUE	0	0.1	0		293	216	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639971	93639971	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	54	324	0	ENST00000375746.1:c.1300C>T	p.Arg434Trp	p.R434W	ENST00000375746	NM_001174167.1	434	Cgg/Tgg	10/14	0.0961476558192928	0	FACETS	0.914	0.787	1			1	CLONAL	4	TRUE	0	0.1	0		324	266	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641063	93641063	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs201930376	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	18	451	0	ENST00000375746.1:c.1409A>G	p.Asn470Ser	p.N470S	ENST00000375746	NM_001174167.1	470	aAc/aGc	11/14	0.0961476558192928	0	FACETS	1	0.763	1			1	CLONAL	2	TRUE	0	0.1	0		451	161	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97897654	97897654	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143181565	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	39	521	0	ENST00000289081.3:c.817G>A	p.Glu273Lys	p.E273K	ENST00000289081	NM_000136.2	273	Gaa/Aaa	8/15	0.0961476558192928	0	FACETS	0.932	0.778	1			1	CLONAL	3	TRUE	0	0.1	0		521	251	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135780990	135780990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs914628341	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	59	519	3	ENST00000298552.3:c.1975G>A	p.Ala659Thr	p.A659T	ENST00000298552	NM_001162426.1	659	Gcg/Acg	15/23	0.0961476558192928	0	FACETS	0.994	0.86	1			1	CLONAL	3	TRUE	0	0.1	0		522	356	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798781	135798781	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1214441043	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	41	351	0	ENST00000298552.3:c.462C>A	p.Phe154Leu	p.F154L	ENST00000298552	NM_001162426.1	154	ttC/ttA	6/23	0.0961476558192928	0	FACETS	1	0.896	1			1	CLONAL	3	TRUE	0	0.1	0		351	226	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402583	139402583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370696201	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	62	797	1	ENST00000277541.6:c.3334G>A	p.Val1112Ile	p.V1112I	ENST00000277541	NM_017617.3	1112	Gtt/Att	21/34	0.0961476558192928	0	FACETS	1	0.902	1			1	CLONAL	2	TRUE	0	0.1	0		798	530	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413915	139413915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758804728	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	96	667	0	ENST00000277541.6:c.845G>A	p.Arg282His	p.R282H	ENST00000277541	NM_017617.3	282	cGc/cAc	5/34	0.0961476558192928	0	FACETS	1	0.94	1			1	CLONAL	3	TRUE	0	0.1	0		667	535	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20152125	20152125	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	38	381	0	ENST00000379607.5:c.205G>A	p.Val69Ile	p.V69I	ENST00000379607	NM_001412.3	69	Gtt/Att	4/7	0.169619318347497	1	FACETS	1	0.861	1	1	0.977	1	CLONAL	4	TRUE	0	0.1	1		381	175	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911426	39911426	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	32	614	0	ENST00000378444.4:c.5204C>A	p.Thr1735Asn	p.T1735N	ENST00000378444	NM_001123385.1	1735	aCt/aAt	15/15	0.169619318347497	1	FACETS	1	0.864	1	1	0.962	1	CLONAL	2	TRUE	0	0.1	1		614	283	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913566	39913566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	46	464	0	ENST00000378444.4:c.4762G>A	p.Gly1588Ser	p.G1588S	ENST00000378444	NM_001123385.1	1588	Ggt/Agt	13/15	0.169619318347497	1	FACETS	1	0.926	1	1	0.98	1	CLONAL	3	TRUE	0	0.1	1		464	252	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931994	39931994	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	69	796	0	ENST00000378444.4:c.2605T>C	p.Tyr869His	p.Y869H	ENST00000378444	NM_001123385.1	869	Tat/Cat	4/15	0.169619318347497	1	FACETS	0.913	0.8	1	1	0.987	1	CLONAL	4	TRUE	0	0.1	1		796	359	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44920640	44920640	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	54	530	0	ENST00000377967.4:c.1401G>A	p.Trp467Ter	p.W467*	ENST00000377967	NM_021140.2	467	tgG/tgA	14/29	0.169619318347497	1	FACETS	1	0.897	1	1	0.984	1	CLONAL	4	TRUE	0	0.1	1		530	245	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929491	44929491	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	43	596	2	ENST00000377967.4:c.2591G>T	p.Ser864Ile	p.S864I	ENST00000377967	NM_021140.2	864	aGc/aTc	17/29	0.169619318347497	1	FACETS	1	0.895	1	1	0.978	1	CLONAL	3	TRUE	0	0.1	1		598	252	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424250	47424250	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	87	644	0	ENST00000377045.4:c.255G>T	p.Glu85Asp	p.E85D	ENST00000377045	NM_001654.4	85	gaG/gaT	4/16	0.169619318347497	1	FACETS	0.894	0.795	1	1	0.989	1	CLONAL	4	TRUE	0	0.1	1		644	462	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650729	48650729	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	50	603	1	ENST00000376670.3:c.599-1G>T		p.X200_splice	ENST00000376670	NM_002049.3	200			0.169619318347497	1	FACETS	1	0.926	1	1	0.981	1	CLONAL	3	TRUE	0	0.1	1		604	278	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652558	48652558	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781880992	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	23	469	1	ENST00000376670.3:c.1229C>T	p.Pro410Leu	p.P410L	ENST00000376670	NM_002049.3	410	cCg/cTg	6/6	0.169619318347497	1	FACETS	1	0.802	1	1	0.947	1	CLONAL	2	TRUE	0	0.1	1		470	213	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222173	53222173	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	56	634	0	ENST00000375401.3:c.4659G>T	p.Gln1553His	p.Q1553H	ENST00000375401	NM_004187.3	1553	caG/caT	26/26	0.169619318347497	1	FACETS	1	0.874	1	1	0.982	1	CLONAL	3	TRUE	0	0.1	1		634	349	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222757	53222757	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	71	877	0	ENST00000375401.3:c.4179G>T	p.Glu1393Asp	p.E1393D	ENST00000375401	NM_004187.3	1393	gaG/gaT	25/26	0.169619318347497	1	FACETS	0.925	0.81	1	1	0.985	1	CLONAL	3	TRUE	0	0.1	1		877	486	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223370	53223370	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	43	693	0	ENST00000375401.3:c.3989C>T	p.Ala1330Val	p.A1330V	ENST00000375401	NM_004187.3	1330	gCc/gTc	23/26	0.169619318347497	1	FACETS	1	0.849	1	1	0.97	1	CLONAL	2	TRUE	0	0.1	1		693	403	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223488	53223488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	63	609	1	ENST00000375401.3:c.3871C>T	p.Arg1291Cys	p.R1291C	ENST00000375401	NM_004187.3	1291	Cgc/Tgc	23/26	0.169619318347497	1	FACETS	0.972	0.847	1	1	0.986	1	CLONAL	4	TRUE	0	0.1	1		610	308	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224201	53224201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782064942	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	76	796	0	ENST00000375401.3:c.3350G>A	p.Arg1117Gln	p.R1117Q	ENST00000375401	NM_004187.3	1117	cGg/cAg	22/26	0.169619318347497	1	FACETS	0.915	0.804	1	1	0.986	1	CLONAL	3	TRUE	0	0.1	1		796	526	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240838	53240838	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	33	544	1	ENST00000375401.3:c.1243-1G>T		p.X415_splice	ENST00000375401	NM_004187.3	415			0.169619318347497	1	FACETS	1	0.847	1	1	0.971	1	CLONAL	3	TRUE	0	0.1	1		545	202	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412974	63412974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	61	912	1	ENST00000330258.3:c.193G>A	p.Gly65Ser	p.G65S	ENST00000330258	NM_152424.3	65	Ggt/Agt	2/2	0.169619318347497	1	FACETS	1	0.872	1	1	0.984	1	CLONAL	3	TRUE	0	0.1	1		913	384	SUCCESS
AR	367	MSKCC	GRCh37	X	66942713	66942713	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	34	519	2	ENST00000374690.3:c.2494C>T	p.Arg832Ter	p.R832*	ENST00000374690	NM_000044.3	832	Cga/Tga	7/8	0.169619318347497	1	FACETS	0.983	0.81	1	1	0.971	1	CLONAL	3	TRUE	0	0.1	1		521	219	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341238	70341238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754407926	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	28	546	0	ENST00000374080.3:c.797G>A	p.Arg266His	p.R266H	ENST00000374080		266	cGc/cAc	6/45	0.169619318347497	1	FACETS	1	0.879	1	1	0.959	1	CLONAL	2	TRUE	0	0.1	1		546	234	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346912	70346912	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760933452	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	77	594	0	ENST00000374080.3:c.2779G>A	p.Val927Met	p.V927M	ENST00000374080		927	Gtg/Atg	20/45	0.169619318347497	1	FACETS	0.888	0.783	0.999	1	0.988	1	CLONAL	4	TRUE	0	0.1	1		594	412	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875919	76875919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	14	529	1	ENST00000373344.5:c.5216G>A	p.Arg1739Gln	p.R1739Q	ENST00000373344	NM_000489.3	1739	cGa/cAa	20/35	0.169619318347497	1	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	0	0.1	1		530	193	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891541	76891541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	28	439	0	ENST00000373344.5:c.4564G>A	p.Glu1522Lys	p.E1522K	ENST00000373344	NM_000489.3	1522	Gaa/Aaa	16/35	0.169619318347497	1	FACETS	0.905	0.733	1	1	0.968	1	CLONAL	4	TRUE	0	0.1	1		439	147	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937874	76937874	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	26	673	0	ENST00000373344.5:c.2874G>T	p.Gln958His	p.Q958H	ENST00000373344	NM_000489.3	958	caG/caT	9/35	0.169619318347497	1	FACETS	1	0.903	1	1	0.959	1	CLONAL	2	TRUE	0	0.1	1		673	198	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937898	76937898	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	11	657	0	ENST00000373344.5:c.2850A>C	p.Lys950Asn	p.K950N	ENST00000373344	NM_000489.3	950	aaA/aaC	9/35	0.169619318347497	1	FACETS	1	0.794	1	1	0.794	1	CLONAL	1	TRUE	0	0.1	1		657	173	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939154	76939154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	34	620	0	ENST00000373344.5:c.1594C>T	p.Leu532Phe	p.L532F	ENST00000373344	NM_000489.3	532	Ctt/Ttt	9/35	0.169619318347497	1	FACETS	0.868	0.714	1	1	0.969	1	CLONAL	3	TRUE	0	0.1	1		620	248	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940449	76940449	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	34	562	0	ENST00000373344.5:c.644G>A	p.Gly215Glu	p.G215E	ENST00000373344	NM_000489.3	215	gGa/gAa	8/35	0.169619318347497	1	FACETS	1	0.829	1	1	0.971	1	CLONAL	3	TRUE	0	0.1	1		562	214	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613371	100613371	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	45	578	0	ENST00000308731.7:c.1029G>T	p.Gln343His	p.Q343H	ENST00000308731	NM_000061.2	343	caG/caT	12/19	0.169619318347497	1	FACETS	1	0.899	1	1	0.979	1	CLONAL	3	TRUE	0	0.1	1		578	263	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630184	100630184	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	48	638	0	ENST00000308731.7:c.89T>C	p.Phe30Ser	p.F30S	ENST00000308731	NM_000061.2	30	tTt/tCt	2/19	0.169619318347497	1	FACETS	0.891	0.759	1	1	0.981	1	CLONAL	4	TRUE	0	0.1	1		638	256	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210292	123210292	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	25	448	0	ENST00000218089.9:c.2644G>T	p.Ala882Ser	p.A882S	ENST00000218089	NM_001042749.1	882	Gct/Tct	26/35	0.169619318347497	1	FACETS	0.875	0.695	1	1	0.958	1	CLONAL	3	TRUE	0	0.1	1		448	181	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861572	152861572	+	synonymous_variant	Silent	SNP	G	G	T	novel	NA	P-0048683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	28	809	0	ENST00000406277.2:c.180C>A	p.Thr60=	p.T60=	ENST00000406277	NM_152274.4	60	acC/acA	4/7	0.169619318347497		FACETS		0.931	1				CLONAL	1	TRUE	0	0.1	1		809	368	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500488	149500488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1060499540	NA	P-0048880-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	129	646	0	ENST00000261799.4:c.2549A>T	p.Asp850Val	p.D850V	ENST00000261799	NM_002609.3	850	gAc/gTc	18/23	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.3	2		646	634	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073551	8073551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs547029591	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	65	318	0	ENST00000377482.5:c.1108G>A	p.Glu370Lys	p.E370K	ENST00000377482	NM_018948.3	370	Gaa/Aaa	4/4	1	2	FACETS	0.804	0.701	0.913	0.804	0.701	0.913	CLONAL	1	TRUE	1	0.48	2		318	337	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777640	9777640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148703447	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	199	623	0	ENST00000377346.4:c.976G>A	p.Glu326Lys	p.E326K	ENST00000377346	NM_005026.3	326	Gag/Aag	8/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.48	2		623	737	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783289	9783289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	180	558	0	ENST00000377346.4:c.2533G>A	p.Ala845Thr	p.A845T	ENST00000377346	NM_005026.3	845	Gca/Aca	20/24	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.48	2		558	704	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307708	11307708	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	102	375	0	ENST00000361445.4:c.1199C>T	p.Ala400Val	p.A400V	ENST00000361445	NM_004958.3	400	gCt/gTt	8/58	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.48	2		375	419	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11318542	11318542	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	52	252	0	ENST00000361445.4:c.271G>T	p.Ala91Ser	p.A91S	ENST00000361445	NM_004958.3	91	Gct/Tct	3/58	1	2	FACETS	0.739	0.634	0.854	0.739	0.634	0.854	SUBCLONAL	1	TRUE	1	0.48	2		252	293	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259759	16259759	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	121	402	1	ENST00000375759.3:c.7024C>T	p.Arg2342Ter	p.R2342*	ENST00000375759	NM_015001.2	2342	Cga/Tga	11/15	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.48	2		403	467	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260050	16260050	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	151	472	0	ENST00000375759.3:c.7315C>A	p.Pro2439Thr	p.P2439T	ENST00000375759	NM_015001.2	2439	Ccg/Acg	11/15	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.48	2		472	608	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087929	27087929	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	123	507	1	ENST00000324856.7:c.2216C>A	p.Pro739His	p.P739H	ENST00000324856	NM_006015.4	739	cCt/cAt	6/20	1	2	FACETS	0.893	0.81	0.979	0.893	0.81	0.979	CLONAL	1	TRUE	1	0.48	2		508	574	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101238	27101238	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	112	603	1	ENST00000324856.7:c.4520A>C	p.Asn1507Thr	p.N1507T	ENST00000324856	NM_006015.4	1507	aAt/aCt	18/20	1	2	FACETS	0.764	0.689	0.843	0.764	0.689	0.843	SUBCLONAL	1	TRUE	1	0.48	2		604	611	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102112	27102112	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	32	469	0	ENST00000324856.7:c.5038C>A	p.Leu1680Ile	p.L1680I	ENST00000324856	NM_006015.4	1680	Ctc/Atc	19/20	1	2	FACETS	0.259	0.21	0.315	0.259	0.21	0.315	SUBCLONAL	1	TRUE	1	0.48	2		469	514	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36931963	36931963	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs780460174	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	160	556	0	ENST00000361632.4:c.2506T>G	p.Phe836Val	p.F836V	ENST00000361632		836	Ttc/Gtc	16/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.48	2		556	627	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935357	36935357	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	205	648	0	ENST00000361632.4:c.1370A>G	p.Gln457Arg	p.Q457R	ENST00000361632		457	cAg/cGg	10/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.48	2		648	737	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325246	39325246	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	133	462	0	ENST00000373001.3:c.73G>T	p.Asp25Tyr	p.D25Y	ENST00000373001	NM_022157.3	25	Gac/Tac	1/7	1	2	FACETS	0.964	0.879	1	0.964	0.879	1	CLONAL	1	TRUE	1	0.48	2		462	575	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43817970	43817970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1419808054	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	87	529	0	ENST00000372470.3:c.1649G>A	p.Ser550Asn	p.S550N	ENST00000372470	NM_005373.2	550	aGc/aAc	11/12	1	2	FACETS	0.519	0.46	0.583	0.519	0.46	0.583	SUBCLONAL	1	TRUE	1	0.48	2		529	698	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65323437	65323437	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1240783724	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	103	401	2	ENST00000342505.4:c.1360C>T	p.Arg454Trp	p.R454W	ENST00000342505	NM_002227.2	454	Cgg/Tgg	10/25	1	2	FACETS	0.869	0.781	0.961	0.869	0.781	0.961	CLONAL	1	TRUE	1	0.48	2		403	494	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339110	65339110	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs747560156	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	26	366	0	ENST00000342505.4:c.426G>T	p.Lys142Asn	p.K142N	ENST00000342505	NM_002227.2	142	aaG/aaT	5/25	1	2	FACETS	0.233	0.184	0.29	0.233	0.184	0.29	SUBCLONAL	1	TRUE	1	0.48	2		366	464	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268832	115268832	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	46	347	0	ENST00000438362.2:c.1778G>T	p.Ser593Ile	p.S593I	ENST00000438362	NM_001242891.1	593	aGt/aTt	14/20	1	2	FACETS	0.551	0.465	0.644	0.551	0.465	0.644	SUBCLONAL	1	TRUE	1	0.48	2		347	348	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690405	117690405	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	85	310	0	ENST00000369458.3:c.725-1G>T		p.X242_splice	ENST00000369458	NM_024626.3	242			1	2	FACETS	0.95	0.845	1	0.95	0.845	1	CLONAL	1	TRUE	1	0.48	2		310	373	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510194	120510194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199565938	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	99	323	0	ENST00000256646.2:c.1315G>A	p.Ala439Thr	p.A439T	ENST00000256646	NM_024408.3	439	Gcc/Acc	8/34	1	2	FACETS	0.989	0.889	1	0.989	0.889	1	CLONAL	1	TRUE	1	0.48	2		323	417	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510705	120510705	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	109	463	1	ENST00000256646.2:c.1259C>T	p.Ala420Val	p.A420V	ENST00000256646	NM_024408.3	420	gCc/gTc	7/34	1	2	FACETS	0.977	0.882	1	0.977	0.882	1	CLONAL	1	TRUE	1	0.48	2		464	465	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843688	156843688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754611476	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	212	764	3	ENST00000524377.1:c.1114G>A	p.Ala372Thr	p.A372T	ENST00000524377	NM_002529.3	372	Gcc/Acc	8/17	1	2	FACETS	0.993	0.923	1	0.993	0.923	1	CLONAL	1	TRUE	1	0.48	2		767	890	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740183	162740183	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	92	413	0	ENST00000367921.3:c.1385C>A	p.Pro462His	p.P462H	ENST00000367921	NM_006182.2	462	cCt/cAt	12/18	1	2	FACETS	0.778	0.693	0.867	0.778	0.693	0.867	SUBCLONAL	1	TRUE	1	0.48	2		413	493	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740215	162740215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771675675	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	118	384	0	ENST00000367921.3:c.1417C>T	p.Arg473Cys	p.R473C	ENST00000367921	NM_006182.2	473	Cgc/Tgc	12/18	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.48	2		384	473	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748433	162748433	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	91	300	1	ENST00000367921.3:c.2350del	p.Cys784ValfsTer44	p.C784Vfs*44	ENST00000367921	NM_006182.2	783	Ttt/tt	17/18	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.48	2		301	366	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306606	163306606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373198630	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	50	287	0	ENST00000271452.3:c.403C>T	p.Arg135Cys	p.R135C	ENST00000271452	NM_145697.2	135	Cgt/Tgt	6/14	1	2	FACETS	0.739	0.631	0.855	0.739	0.631	0.855	SUBCLONAL	1	TRUE	1	0.48	2		287	282	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318779	163318779	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs116669228	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	37	304	0	ENST00000271452.3:c.1169G>A	p.Arg390Gln	p.R390Q	ENST00000271452	NM_145697.2	390	cGa/cAa	13/14	1	2	FACETS	0.517	0.428	0.616	0.517	0.428	0.616	SUBCLONAL	1	TRUE	1	0.48	2		304	298	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104572	193104572	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	57	288	0	ENST00000367435.3:c.359G>A	p.Arg120Gln	p.R120Q	ENST00000367435	NM_024529.4	120	cGa/cAa	4/17	1	2	FACETS	0.87	0.753	0.995	0.87	0.753	0.995	CLONAL	1	TRUE	1	0.48	2		288	273	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206943233	206943233	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	68	279	0	ENST00000423557.1:c.385T>G	p.Phe129Val	p.F129V	ENST00000423557	NM_000572.2	129	Ttt/Gtt	4/5	1	2	FACETS	0.929	0.815	1	0.929	0.815	1	CLONAL	1	TRUE	1	0.48	2		279	305	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226556015	226556015	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	74	346	0	ENST00000366794.5:c.2162C>A	p.Ser721Tyr	p.S721Y	ENST00000366794	NM_001618.3	721	tCt/tAt	16/23	1	2	FACETS	0.809	0.712	0.912	0.809	0.712	0.912	CLONAL	1	TRUE	1	0.48	2		346	381	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612807	228612807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	184	686	0	ENST00000366696.1:c.220G>A	p.Glu74Lys	p.E74K	ENST00000366696	NM_003493.2	74	Gag/Aag	1/1	1	2	FACETS	0.996	0.921	1	0.996	0.921	1	CLONAL	1	TRUE	1	0.48	2		686	770	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612980	228612980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571515258	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	126	486	0	ENST00000366696.1:c.47C>T	p.Ala16Val	p.A16V	ENST00000366696	NM_003493.2	16	gCg/gTg	1/1	1	2	FACETS	0.962	0.875	1	0.962	0.875	1	CLONAL	1	TRUE	1	0.48	2		486	546	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736307	243736307	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	89	331	2	ENST00000263826.5:c.740G>A	p.Arg247His	p.R247H	ENST00000263826	NM_005465.4	247	cGc/cAc	8/13	1	2	FACETS	0.932	0.832	1	0.932	0.832	1	CLONAL	1	TRUE	1	0.48	2		333	398	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243777030	243777030	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	52	272	0	ENST00000263826.5:c.639T>G	p.Tyr213Ter	p.Y213*	ENST00000263826	NM_005465.4	213	taT/taG	7/13	1	2	FACETS	0.998	0.861	1	0.998	0.861	1	CLONAL	1	TRUE	1	0.48	2		272	217	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858935	243858935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	52	353	0	ENST00000263826.5:c.130G>T	p.Asp44Tyr	p.D44Y	ENST00000263826	NM_005465.4	44	Gat/Tat	2/13	1	2	FACETS	0.824	0.707	0.949	0.824	0.707	0.949	CLONAL	1	TRUE	1	0.48	2		353	263	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021924	246021924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	179	491	1	ENST00000388985.4:c.950C>T	p.Ser317Phe	p.S317F	ENST00000388985		317	tCt/tTt	10/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.48	2		492	668	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246091336	246091336	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	90	213	0	ENST00000388985.4:c.600-1G>A		p.X200_splice	ENST00000388985		200			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.48	2		213	318	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246490619	246490619	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	46	307	0	ENST00000388985.4:c.415G>T	p.Asp139Tyr	p.D139Y	ENST00000388985		139	Gat/Tat	5/12	1	2	FACETS	0.734	0.623	0.855	0.734	0.623	0.855	SUBCLONAL	1	TRUE	1	0.48	2		307	261	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100708	8100708	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774889150	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	201	621	0	ENST00000346208.3:c.682G>A	p.Glu228Lys	p.E228K	ENST00000346208		228	Gag/Aag	3/6	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.48	2		621	746	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609103	43609103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs77503355	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	172	639	1	ENST00000355710.3:c.1859G>A	p.Cys620Tyr	p.C620Y	ENST00000355710	NM_020975.4	620	tGc/tAc	10/20	1	2	FACETS	0.972	0.897	1	0.972	0.897	1	CLONAL	1	TRUE	1	0.48	2		640	737	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617397	43617397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	97	318	0	ENST00000355710.3:c.2734C>T	p.Arg912Trp	p.R912W	ENST00000355710	NM_020975.4	912	Cgg/Tgg	16/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.48	2		318	339	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63661937	63661937	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	68	276	0	ENST00000279873.7:c.41G>T	p.Gly14Val	p.G14V	ENST00000279873	NM_032199.2	14	gGc/gTc	2/10	1	2	FACETS	0.944	0.829	1	0.944	0.829	1	CLONAL	1	TRUE	1	0.48	2		276	300	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845627	63845627	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	44	161	0	ENST00000279873.7:c.1366G>T	p.Glu456Ter	p.E456*	ENST00000279873	NM_032199.2	456	Gaa/Taa	9/10	1	2	FACETS	0.996	0.847	1	0.996	0.847	1	CLONAL	1	TRUE	1	0.48	2		161	184	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405304	70405304	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	92	432	0	ENST00000373644.4:c.2818G>T	p.Asp940Tyr	p.D940Y	ENST00000373644	NM_030625.2	940	Gac/Tac	4/12	1	2	FACETS	0.906	0.81	1	0.906	0.81	1	CLONAL	1	TRUE	1	0.48	2		432	423	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70442666	70442666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	96	367	0	ENST00000373644.4:c.4988C>T	p.Ala1663Val	p.A1663V	ENST00000373644	NM_030625.2	1663	gCt/gTt	10/12	1	2	FACETS	0.837	0.749	0.93	0.837	0.749	0.93	CLONAL	1	TRUE	1	0.48	2		367	478	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451374	70451374	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	114	404	0	ENST00000373644.4:c.6214G>T	p.Glu2072Ter	p.E2072*	ENST00000373644	NM_030625.2	2072	Gaa/Taa	12/12	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.48	2		404	431	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649856	88649856	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1564714776	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	21	244	0	ENST00000372037.3:c.105G>T	p.Met35Ile	p.M35I	ENST00000372037	NM_004329.2	35	atG/atT	4/13	1	2	FACETS	0.407	0.314	0.514	0.407	0.314	0.514	SUBCLONAL	1	TRUE	1	0.48	2		244	215	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681278	88681278	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	117	464	1	ENST00000372037.3:c.1168G>T	p.Asp390Tyr	p.D390Y	ENST00000372037	NM_004329.2	390	Gac/Tac	11/13	1	2	FACETS	0.967	0.877	1	0.967	0.877	1	CLONAL	1	TRUE	1	0.48	2		465	504	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681341	88681341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786202611	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	42	213	1	ENST00000372037.3:c.1231G>A	p.Glu411Lys	p.E411K	ENST00000372037	NM_004329.2	411	Gaa/Aaa	11/13	1	2	FACETS	0.764	0.644	0.895	0.764	0.644	0.895	SUBCLONAL	1	TRUE	1	0.48	2		214	229	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683433	88683433	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	19	107	0	ENST00000372037.3:c.1556A>C	p.Lys519Thr	p.K519T	ENST00000372037	NM_004329.2	519	aAg/aCg	13/13	1	2	FACETS	0.792	0.611	0.996	0.792	0.611	0.996	CLONAL	1	TRUE	1	0.48	2		107	100	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685313	89685313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	15	195	0	ENST00000371953.3:c.208C>A	p.Leu70Ile	p.L70I	ENST00000371953	NM_000314.4	70	Ctt/Att	3/9	1	2	FACETS	0.311	0.228	0.411	0.311	0.228	0.411	SUBCLONAL	1	TRUE	1	0.48	2		195	201	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	67	344	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.973	0.853	1	0.973	0.853	1	CLONAL	1	TRUE	1	0.48	2		344	287	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325146	123325146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199575491	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	156	485	0	ENST00000358487.5:c.182G>A	p.Arg61His	p.R61H	ENST00000358487	NM_000141.4	61	cGc/cAc	3/18	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.48	2		485	614	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533478	533478	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	199	677	0	ENST00000451590.1:c.425T>C	p.Ile142Thr	p.I142T	ENST00000451590	NM_001130442.1	142	aTc/aCc	4/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.48	2		677	756	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154267	2154267	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	174	555	0	ENST00000434045.2:c.661G>T	p.Asp221Tyr	p.D221Y	ENST00000434045	NM_001127598.1	221	Gac/Tac	5/5	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.48	2		555	649	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421507	32421507	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs150194429	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	155	421	0	ENST00000332351.3:c.1085T>G	p.Phe362Cys	p.F362C	ENST00000332351	NM_024426.4	362	tTc/tGc	6/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.48	2		421	562	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128638	64128638	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	136	470	0	ENST00000334205.4:c.495G>T	p.Glu165Asp	p.E165D	ENST00000334205	NM_003942.2	165	gaG/gaT	5/17	1	2	FACETS	0.98	0.895	1	0.98	0.895	1	CLONAL	1	TRUE	1	0.48	2		470	578	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572612	64572612	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	50	704	0	ENST00000312049.6:c.1244G>T	p.Arg415Leu	p.R415L	ENST00000312049	NM_130799.2	415	cGa/cTa	9/10	1	2	FACETS	0.252	0.213	0.295	0.252	0.213	0.295	SUBCLONAL	1	TRUE	1	0.48	2		704	826	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67197055	67197055	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	76	319	1	ENST00000312629.5:c.298G>T	p.Val100Phe	p.V100F	ENST00000312629	NM_003952.2	100	Gtc/Ttc	4/15	1	2	FACETS	0.759	0.669	0.856	0.759	0.669	0.856	SUBCLONAL	1	TRUE	1	0.48	2		320	417	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198975	67198975	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	95	335	0	ENST00000312629.5:c.446A>G	p.Glu149Gly	p.E149G	ENST00000312629	NM_003952.2	149	gAg/gGg	5/15	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.48	2		335	394	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588217	69588217	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140567674	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	39	437	0	ENST00000168712.1:c.481C>T	p.Leu161Phe	p.L161F	ENST00000168712	NM_002007.2	161	Ctc/Ttc	3/3	1	2	FACETS	0.298	0.247	0.356	0.298	0.247	0.356	SUBCLONAL	1	TRUE	1	0.48	2		437	545	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625398	69625398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1408695395	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	185	707	0	ENST00000334134.2:c.395G>A	p.Arg132Gln	p.R132Q	ENST00000334134	NM_005247.2	132	cGg/cAg	3/3	1	2	FACETS	0.995	0.92	1	0.995	0.92	1	CLONAL	1	TRUE	1	0.48	2		707	775	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939804	71939804	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773663316	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	222	729	0	ENST00000298229.2:c.431G>A	p.Arg144His	p.R144H	ENST00000298229	NM_001567.3	144	cGc/cAc	4/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.48	2		729	848	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942155	71942155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	191	648	1	ENST00000298229.2:c.1419G>T	p.Glu473Asp	p.E473D	ENST00000298229	NM_001567.3	473	gaG/gaT	12/28	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.48	2		649	751	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945335	71945335	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs745723030	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	98	509	1	ENST00000298229.2:c.2223G>T	p.Lys741Asn	p.K741N	ENST00000298229	NM_001567.3	741	aaG/aaT	20/28	1	2	FACETS	0.591	0.527	0.659	0.591	0.527	0.659	SUBCLONAL	1	TRUE	1	0.48	2		510	691	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989511	85989511	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	73	332	0	ENST00000263360.6:c.1270A>G	p.Ile424Val	p.I424V	ENST00000263360	NM_003797.3	424	Att/Gtt	12/12	1	2	FACETS	0.872	0.768	0.982	0.872	0.768	0.982	CLONAL	1	TRUE	1	0.48	2		332	349	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989562	85989562	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs767548896	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	73	295	2	ENST00000263360.6:c.1321C>T	p.Arg441Ter	p.R441*	ENST00000263360	NM_003797.3	441	Cga/Tga	12/12	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.48	2		297	285	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204835	94204835	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	31	293	0	ENST00000323929.3:c.750A>C	p.Lys250Asn	p.K250N	ENST00000323929	NM_005591.3	250	aaA/aaC	8/20	1	2	FACETS	0.513	0.416	0.62	0.513	0.416	0.62	SUBCLONAL	1	TRUE	1	0.48	2		293	252	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219121	94219121	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	62	283	0	ENST00000323929.3:c.283A>C	p.Ser95Arg	p.S95R	ENST00000323929	NM_005591.3	95	Agt/Cgt	4/20	1	2	FACETS	0.823	0.716	0.937	0.823	0.716	0.937	CLONAL	1	TRUE	1	0.48	2		283	314	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911953	94911953	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764991422	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	64	414	0	ENST00000536441.1:c.977G>A	p.Arg326Gln	p.R326Q	ENST00000536441	NM_144665.3	326	cGa/cAa	7/10	1	2	FACETS	0.787	0.685	0.895	0.787	0.685	0.895	SUBCLONAL	1	TRUE	1	0.48	2		414	339	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195702	102195702	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	56	325	0	ENST00000263464.3:c.462T>G	p.Phe154Leu	p.F154L	ENST00000263464	NM_001165.4	154	ttT/ttG	2/9	1	2	FACETS	0.871	0.753	0.997	0.871	0.753	0.997	CLONAL	1	TRUE	1	0.48	2		325	268	SUCCESS
ATM	472	MSKCC	GRCh37	11	108100028	108100028	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	51	221	0	ENST00000278616.4:c.309C>A	p.Tyr103Ter	p.Y103*	ENST00000278616	NM_000051.3	103	taC/taA	4/63	1	2	FACETS	0.837	0.717	0.965	0.837	0.717	0.965	CLONAL	1	TRUE	1	0.48	2		221	254	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123575	108123575	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs747242300	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	45	308	0	ENST00000278616.4:c.1834C>A	p.Leu612Ile	p.L612I	ENST00000278616	NM_000051.3	612	Ctt/Att	12/63	1	2	FACETS	0.595	0.502	0.697	0.595	0.502	0.697	SUBCLONAL	1	TRUE	1	0.48	2		308	315	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142131	108142131	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	41	294	0	ENST00000278616.4:c.3075T>G	p.Phe1025Leu	p.F1025L	ENST00000278616	NM_000051.3	1025	ttT/ttG	20/63	1	2	FACETS	0.798	0.671	0.936	0.798	0.671	0.936	CLONAL	1	TRUE	1	0.48	2		294	214	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216472	108216472	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	34	177	0	ENST00000278616.4:c.8421G>T	p.Glu2807Asp	p.E2807D	ENST00000278616	NM_000051.3	2807	gaG/gaT	58/63	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.48	2		177	132	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373118	118373118	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	36	225	0	ENST00000534358.1:c.6511C>T	p.Pro2171Ser	p.P2171S	ENST00000534358	NM_005933.3	2171	Cct/Tct	27/36	1	2	FACETS	0.636	0.526	0.756	0.636	0.526	0.756	SUBCLONAL	1	TRUE	1	0.48	2		225	236	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374027	118374027	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	69	311	0	ENST00000534358.1:c.7420C>T	p.Pro2474Ser	p.P2474S	ENST00000534358	NM_005933.3	2474	Cct/Tct	27/36	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.48	2		311	267	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374309	118374309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	66	327	0	ENST00000534358.1:c.7702C>T	p.Pro2568Ser	p.P2568S	ENST00000534358	NM_005933.3	2568	Cca/Tca	27/36	1	2	FACETS	0.87	0.761	0.986	0.87	0.761	0.986	CLONAL	1	TRUE	1	0.48	2		327	316	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374708	118374708	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781925188	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	51	277	2	ENST00000534358.1:c.8101G>A	p.Ala2701Thr	p.A2701T	ENST00000534358	NM_005933.3	2701	Gca/Aca	27/36	1	2	FACETS	0.824	0.706	0.95	0.824	0.706	0.95	CLONAL	1	TRUE	1	0.48	2		279	258	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375309	118375309	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	68	295	0	ENST00000534358.1:c.8702C>A	p.Ser2901Tyr	p.S2901Y	ENST00000534358	NM_005933.3	2901	tCt/tAt	27/36	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.48	2		295	265	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376509	118376509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781852468	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	42	284	0	ENST00000534358.1:c.9902C>T	p.Pro3301Leu	p.P3301L	ENST00000534358	NM_005933.3	3301	cCg/cTg	27/36	1	2	FACETS	0.549	0.46	0.646	0.549	0.46	0.646	SUBCLONAL	1	TRUE	1	0.48	2		284	319	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118391539	118391539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782283493	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	61	256	0	ENST00000534358.1:c.11452C>T	p.Pro3818Ser	p.P3818S	ENST00000534358	NM_005933.3	3818	Cca/Tca	34/36	1	2	FACETS	0.807	0.701	0.92	0.807	0.701	0.92	CLONAL	1	TRUE	1	0.48	2		256	315	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144724	119144724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253824253	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	62	264	0	ENST00000264033.4:c.737G>A	p.Arg246Gln	p.R246Q	ENST00000264033	NM_005188.3	246	cGa/cAa	4/16	1	2	FACETS	0.906	0.79	1	0.906	0.79	1	CLONAL	1	TRUE	1	0.48	2		264	285	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148927	119148927	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1265704711	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	66	353	1	ENST00000264033.4:c.1147A>C	p.Ile383Leu	p.I383L	ENST00000264033	NM_005188.3	383	Ata/Cta	8/16	1	2	FACETS	0.873	0.764	0.989	0.873	0.764	0.989	CLONAL	1	TRUE	1	0.48	2		354	315	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404855	404855	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	134	327	0	ENST00000399788.2:c.4339G>T	p.Glu1447Ter	p.E1447*	ENST00000399788	NM_001042603.1	1447	Gaa/Taa	26/28	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.48	2		327	546	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463366	463366	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	46	234	0	ENST00000399788.2:c.905del	p.Gly302GlufsTer22	p.G302Efs*22	ENST00000399788	NM_001042603.1	302	gGa/ga	8/28	1	2	FACETS	0.723	0.613	0.843	0.723	0.613	0.843	SUBCLONAL	1	TRUE	1	0.48	2		234	265	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464349	464349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772720111	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	76	361	0	ENST00000399788.2:c.845G>A	p.Arg282Gln	p.R282Q	ENST00000399788	NM_001042603.1	282	cGg/cAg	7/28	1	2	FACETS	0.747	0.658	0.842	0.747	0.658	0.842	SUBCLONAL	1	TRUE	1	0.48	2		361	424	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1034690	1034690	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	57	289	0	ENST00000358495.3:c.469A>G	p.Ser157Gly	p.S157G	ENST00000358495	NM_134424.2	157	Agt/Ggt	7/12	1	2	FACETS	0.851	0.737	0.974	0.851	0.737	0.974	CLONAL	1	TRUE	1	0.48	2		289	279	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383380	4383380	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	103	444	0	ENST00000261254.3:c.174G>T	p.Met58Ile	p.M58I	ENST00000261254	NM_001759.3	58	atG/atT	1/5	1	2	FACETS	0.89	0.801	0.985	0.89	0.801	0.985	CLONAL	1	TRUE	1	0.48	2		444	482	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385169	4385169	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	60	203	0	ENST00000261254.3:c.196-2A>C		p.X66_splice	ENST00000261254	NM_001759.3	66			1	2	FACETS	0.954	0.83	1	0.954	0.83	1	CLONAL	1	TRUE	1	0.48	2		203	262	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385333	4385333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	40	337	0	ENST00000261254.3:c.358G>A	p.Ala120Thr	p.A120T	ENST00000261254	NM_001759.3	120	Gcg/Acg	2/5	1	2	FACETS	0.399	0.331	0.474	0.399	0.331	0.474	SUBCLONAL	1	TRUE	1	0.48	2		337	418	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398007	4398007	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	96	384	0	ENST00000261254.3:c.572-1G>T		p.X191_splice	ENST00000261254	NM_001759.3	191			1	2	FACETS	0.952	0.854	1	0.952	0.854	1	CLONAL	1	TRUE	1	0.48	2		384	420	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398153	4398153	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	130	413	0	ENST00000261254.3:c.717C>A	p.Asp239Glu	p.D239E	ENST00000261254	NM_001759.3	239	gaC/gaA	4/5	1	2	FACETS	0.966	0.88	1	0.966	0.88	1	CLONAL	1	TRUE	1	0.48	2		413	561	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435082	18435082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	50	247	0	ENST00000266497.5:c.67G>A	p.Glu23Lys	p.E23K	ENST00000266497		23	Gaa/Aaa	1/31	1	2	FACETS	0.744	0.636	0.861	0.744	0.636	0.861	SUBCLONAL	1	TRUE	1	0.48	2		247	280	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466937	18466937	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	58	227	0	ENST00000266497.5:c.1076A>G	p.Lys359Arg	p.K359R	ENST00000266497		359	aAa/aGa	5/31	1	2	FACETS	0.836	0.724	0.956	0.836	0.724	0.956	CLONAL	1	TRUE	1	0.48	2		227	289	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18576967	18576967	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	29	338	0	ENST00000266497.5:c.2375T>G	p.Leu792Arg	p.L792R	ENST00000266497		792	cTt/cGt	16/31	1	2	FACETS	0.348	0.279	0.426	0.348	0.279	0.426	SUBCLONAL	1	TRUE	1	0.48	2		338	347	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641559	18641559	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	49	255	0	ENST00000266497.5:c.2558G>T	p.Arg853Ile	p.R853I	ENST00000266497		853	aGa/aTa	17/31	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.48	2		255	202	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793430	18793430	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	64	302	0	ENST00000266497.5:c.4127T>G	p.Val1376Gly	p.V1376G	ENST00000266497		1376	gTt/gGt	30/31	1	2	FACETS	0.936	0.818	1	0.936	0.818	1	CLONAL	1	TRUE	1	0.48	2		302	285	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21639478	21639478	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	46	210	0	ENST00000421138.2:c.436G>T	p.Asp146Tyr	p.D146Y	ENST00000421138		146	Gac/Tac	6/16	1	2	FACETS	0.844	0.718	0.981	0.844	0.718	0.981	CLONAL	1	TRUE	1	0.48	2		210	227	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380309	25380309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1407509439	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	73	311	0	ENST00000311936.3:c.149C>T	p.Thr50Ile	p.T50I	ENST00000311936	NM_004985.3	50	aCc/aTc	3/5	1	2	FACETS	0.869	0.765	0.979	0.869	0.765	0.979	CLONAL	1	TRUE	1	0.48	2		311	350	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211668	46211668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767329695	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	38	168	0	ENST00000334344.6:c.634G>A	p.Asp212Asn	p.D212N	ENST00000334344	NM_152641.2	212	Gac/Aac	5/21	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.48	2		168	135	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244026	46244026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	58	349	0	ENST00000334344.6:c.2120C>A	p.Ala707Asp	p.A707D	ENST00000334344	NM_152641.2	707	gCt/gAt	15/21	1	2	FACETS	0.703	0.607	0.806	0.703	0.607	0.806	SUBCLONAL	1	TRUE	1	0.48	2		349	344	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244436	46244436	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	72	355	0	ENST00000334344.6:c.2530G>T	p.Asp844Tyr	p.D844Y	ENST00000334344	NM_152641.2	844	Gat/Tat	15/21	1	2	FACETS	0.912	0.803	1	0.912	0.803	1	CLONAL	1	TRUE	1	0.48	2		355	329	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246383	46246383	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	58	261	0	ENST00000334344.6:c.4477G>A	p.Val1493Ile	p.V1493I	ENST00000334344	NM_152641.2	1493	Gta/Ata	15/21	1	2	FACETS	0.922	0.8	1	0.922	0.8	1	CLONAL	1	TRUE	1	0.48	2		261	262	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431580	49431580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	186	648	0	ENST00000301067.7:c.9559G>A	p.Ala3187Thr	p.A3187T	ENST00000301067	NM_003482.3	3187	Gcc/Acc	34/54	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.48	2		648	689	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50490728	50490728	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	122	405	0	ENST00000394963.4:c.1365G>A	p.Trp455Ter	p.W455*	ENST00000394963	NM_003076.4	455	tgG/tgA	11/13	1	2	FACETS	0.956	0.868	1	0.956	0.868	1	CLONAL	1	TRUE	1	0.48	2		405	532	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	187	576	0	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.48	2		576	758	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864355	57864355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765569651	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	32	605	0	ENST00000228682.2:c.1832G>A	p.Arg611Gln	p.R611Q	ENST00000228682	NM_005269.2	611	cGg/cAg	12/12	1	2	FACETS	0.223	0.18	0.272	0.223	0.18	0.272	SUBCLONAL	1	TRUE	1	0.48	2		605	597	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865012	57865012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	109	617	2	ENST00000228682.2:c.2489C>T	p.Ala830Val	p.A830V	ENST00000228682	NM_005269.2	830	gCa/gTa	12/12	1	2	FACETS	0.727	0.654	0.804	0.727	0.654	0.804	SUBCLONAL	1	TRUE	1	0.48	2		619	625	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865408	57865408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	42	660	0	ENST00000228682.2:c.2885G>A	p.Gly962Asp	p.G962D	ENST00000228682	NM_005269.2	962	gGt/gAt	12/12	1	2	FACETS	0.265	0.221	0.315	0.265	0.221	0.315	SUBCLONAL	1	TRUE	1	0.48	2		660	660	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811667	102811667	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	155	550	0	ENST00000307046.8:c.517G>T	p.Gly173Ter	p.G173*	ENST00000307046	NM_001111285.1	173	Gga/Tga	4/4	1	2	FACETS	0.989	0.908	1	0.989	0.908	1	CLONAL	1	TRUE	1	0.48	2		550	653	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856130	111856130	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765237130	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	176	557	2	ENST00000341259.2:c.181G>A	p.Glu61Lys	p.E61K	ENST00000341259	NM_005475.2	61	Gag/Aag	2/8	1	2	FACETS	0.933	0.861	1	0.933	0.861	1	CLONAL	1	TRUE	1	0.48	2		559	786	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416734	121416734	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	156	702	0	ENST00000257555.6:c.163G>T	p.Gly55Trp	p.G55W	ENST00000257555		55	Ggg/Tgg	1/10	1	2	FACETS	0.78	0.715	0.849	0.78	0.715	0.849	SUBCLONAL	1	TRUE	1	0.48	2		702	833	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431486	121431486	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	40	444	0	ENST00000257555.6:c.690G>T	p.Glu230Asp	p.E230D	ENST00000257555		230	gaG/gaT	3/10	1	2	FACETS	0.279	0.231	0.332	0.279	0.231	0.332	SUBCLONAL	1	TRUE	1	0.48	2		444	598	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212495	133212495	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879254168	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	21	372	0	ENST00000320574.5:c.5794C>T	p.Arg1932Cys	p.R1932C	ENST00000320574	NM_006231.2	1932	Cgt/Tgt	42/49	1	2	FACETS	0.21	0.161	0.268	0.21	0.161	0.268	SUBCLONAL	1	TRUE	1	0.48	2		372	416	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218920	133218920	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	140	706	0	ENST00000320574.5:c.5016C>A	p.Phe1672Leu	p.F1672L	ENST00000320574	NM_006231.2	1672	ttC/ttA	38/49	1	2	FACETS	0.716	0.652	0.783	0.716	0.652	0.783	SUBCLONAL	1	TRUE	1	0.48	2		706	815	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220557	133220557	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747619107	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	68	353	0	ENST00000320574.5:c.4156C>T	p.Arg1386Trp	p.R1386W	ENST00000320574	NM_006231.2	1386	Cgg/Tgg	33/49	1	2	FACETS	0.613	0.535	0.698	0.613	0.535	0.698	SUBCLONAL	1	TRUE	1	0.48	2		353	462	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225601	133225601	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	186	605	0	ENST00000320574.5:c.4063T>G	p.Leu1355Val	p.L1355V	ENST00000320574	NM_006231.2	1355	Ttg/Gtg	32/49	1	2	FACETS	0.997	0.923	1	0.997	0.923	1	CLONAL	1	TRUE	1	0.48	2		605	777	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248860	133248860	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs116260568	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	161	501	0	ENST00000320574.5:c.1735C>T	p.Arg579Cys	p.R579C	ENST00000320574	NM_006231.2	579	Cgc/Tgc	16/49	1	2	FACETS	0.974	0.896	1	0.974	0.896	1	CLONAL	1	TRUE	1	0.48	2		501	689	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253157	133253157	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	98	325	0	ENST00000320574.5:c.884T>G	p.Met295Arg	p.M295R	ENST00000320574	NM_006231.2	295	aTg/aGg	9/49	1	2	FACETS	0.943	0.846	1	0.943	0.846	1	CLONAL	1	TRUE	1	0.48	2		325	433	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562477	21562477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757658067	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	13	247	0	ENST00000382592.4:c.1442C>T	p.Ala481Val	p.A481V	ENST00000382592	NM_014572.2	481	gCg/gTg	4/8	1	2	FACETS	0.279	0.199	0.376	0.279	0.199	0.376	SUBCLONAL	1	TRUE	1	0.48	2		247	194	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578310	28578310	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	59	310	0	ENST00000241453.7:c.2861T>G	p.Met954Arg	p.M954R	ENST00000241453	NM_004119.2	954	aTg/aGg	24/24	1	2	FACETS	0.747	0.647	0.855	0.747	0.647	0.855	SUBCLONAL	1	TRUE	1	0.48	2		310	329	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877366	28877366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1392528455	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	135	353	0	ENST00000282397.4:c.3955G>A	p.Ala1319Thr	p.A1319T	ENST00000282397	NM_002019.4	1319	Gcg/Acg	30/30	1	2	FACETS	0.941	0.858	1	0.941	0.858	1	CLONAL	1	TRUE	1	0.48	2		353	598	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897084	28897084	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	58	262	0	ENST00000282397.4:c.2797-1G>T		p.X933_splice	ENST00000282397	NM_002019.4	933			1	2	FACETS	0.905	0.785	1	0.905	0.785	1	CLONAL	1	TRUE	1	0.48	2		262	267	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008324	29008324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770377283	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	35	196	0	ENST00000282397.4:c.547C>T	p.Arg183Cys	p.R183C	ENST00000282397	NM_002019.4	183	Cgc/Tgc	5/30	1	2	FACETS	0.701	0.58	0.835	0.701	0.58	0.835	SUBCLONAL	1	TRUE	1	0.48	2		196	208	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012441	29012441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55974987	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	63	450	0	ENST00000282397.4:c.430G>A	p.Glu144Lys	p.E144K	ENST00000282397	NM_002019.4	144	Gaa/Aaa	4/30	1	2	FACETS	0.815	0.71	0.928	0.815	0.71	0.928	CLONAL	1	TRUE	1	0.48	2		450	322	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041233	29041233	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	101	434	0	ENST00000282397.4:c.195A>C	p.Glu65Asp	p.E65D	ENST00000282397	NM_002019.4	65	gaA/gaC	3/30	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.48	2		434	406	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900284	32900284	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs113114005	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	45	269	0	ENST00000380152.3:c.472T>C	p.Ser158Pro	p.S158P	ENST00000380152		158	Tca/Cca	5/27	1	2	FACETS	0.884	0.752	1	0.884	0.752	1	CLONAL	1	TRUE	1	0.48	2		269	212	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32903625	32903625	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	22	240	0	ENST00000380152.3:c.677C>T	p.Thr226Ile	p.T226I	ENST00000380152		226	aCt/aTt	8/27	1	2	FACETS	0.385	0.299	0.484	0.385	0.299	0.484	SUBCLONAL	1	TRUE	1	0.48	2		240	238	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911503	32911503	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	38	398	0	ENST00000380152.3:c.3011G>T	p.Ser1004Ile	p.S1004I	ENST00000380152		1004	aGt/aTt	11/27	1	2	FACETS	0.754	0.629	0.89	0.754	0.629	0.89	SUBCLONAL	1	TRUE	1	0.48	2		398	210	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913083	32913083	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	79	377	0	ENST00000380152.3:c.4591A>C	p.Lys1531Gln	p.K1531Q	ENST00000380152		1531	Aaa/Caa	11/27	1	2	FACETS	0.957	0.848	1	0.957	0.848	1	CLONAL	1	TRUE	1	0.48	2		377	344	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913557	32913557	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767200163	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	39	313	0	ENST00000380152.3:c.5065G>A	p.Ala1689Thr	p.A1689T	ENST00000380152		1689	Gca/Aca	11/27	1	2	FACETS	0.597	0.498	0.707	0.597	0.498	0.707	SUBCLONAL	1	TRUE	1	0.48	2		313	272	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914835	32914835	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	52	363	0	ENST00000380152.3:c.6343G>T	p.Glu2115Ter	p.E2115*	ENST00000380152		2115	Gag/Tag	11/27	1	2	FACETS	0.768	0.659	0.886	0.768	0.659	0.886	SUBCLONAL	1	TRUE	1	0.48	2		363	282	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929156	32929156	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	69	368	0	ENST00000380152.3:c.7166G>T	p.Arg2389Ile	p.R2389I	ENST00000380152		2389	aGa/aTa	14/27	1	2	FACETS	0.833	0.731	0.943	0.833	0.731	0.943	CLONAL	1	TRUE	1	0.48	2		368	345	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972800	32972800	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397507568	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	28	315	0	ENST00000380152.3:c.10150C>T	p.Arg3384Ter	p.R3384*	ENST00000380152		3384	Cga/Tga	27/27	1	2	FACETS	0.408	0.327	0.5	0.408	0.327	0.5	SUBCLONAL	1	TRUE	1	0.48	2		315	286	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134682	41134682	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	73	351	0	ENST00000379561.5:c.946C>T	p.Arg316Ter	p.R316*	ENST00000379561	NM_002015.3	316	Cga/Tga	2/3	1	2	FACETS	0.988	0.872	1	0.988	0.872	1	CLONAL	1	TRUE	1	0.48	2		351	308	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916843	48916843	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	59	226	0	ENST00000267163.4:c.373G>T	p.Glu125Ter	p.E125*	ENST00000267163	NM_000321.2	125	Gaa/Taa	3/27	1	2	FACETS	0.976	0.848	1	0.976	0.848	1	CLONAL	1	TRUE	1	0.48	2		226	252	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033886	49033886	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs137853295	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	72	302	0	ENST00000267163.4:c.2023G>T	p.Glu675Ter	p.E675*	ENST00000267163	NM_000321.2	675	Gaa/Taa	20/27	1	2	FACETS	0.875	0.77	0.986	0.875	0.77	0.986	CLONAL	1	TRUE	1	0.48	2		302	343	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281886	49281886	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs201885552	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	29	498	0	ENST00000282018.3:c.933T>A	p.Asn311Lys	p.N311K	ENST00000282018	NM_020377.2	311	aaT/aaA	1/1	1	2	FACETS	0.263	0.211	0.323	0.263	0.211	0.323	SUBCLONAL	1	TRUE	1	0.48	2		498	459	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73334762	73334762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	24	201	0	ENST00000377767.4:c.2698G>A	p.Val900Met	p.V900M	ENST00000377767	NM_014953.3	900	Gtg/Atg	20/21	1	2	FACETS	0.662	0.525	0.817	0.662	0.525	0.817	SUBCLONAL	1	TRUE	1	0.48	2		201	151	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506681	103506681	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766620389	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	47	173	0	ENST00000355739.4:c.424G>A	p.Asp142Asn	p.D142N	ENST00000355739	NM_000123.3	142	Gac/Aac	4/15	1	2	FACETS	0.933	0.796	1	0.933	0.796	1	CLONAL	1	TRUE	1	0.48	2		173	210	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514057	103514057	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	33	255	0	ENST00000355739.4:c.873G>T	p.Leu291Phe	p.L291F	ENST00000355739	NM_000123.3	291	ttG/ttT	7/15	1	2	FACETS	0.598	0.49	0.718	0.598	0.49	0.718	SUBCLONAL	1	TRUE	1	0.48	2		255	230	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514904	103514904	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	77	298	0	ENST00000355739.4:c.1405G>T	p.Asp469Tyr	p.D469Y	ENST00000355739	NM_000123.3	469	Gac/Tac	8/15	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.48	2		298	289	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518224	103518224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376753356	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	42	217	0	ENST00000355739.4:c.2162C>T	p.Ala721Val	p.A721V	ENST00000355739	NM_000123.3	721	gCg/gTg	9/15	1	2	FACETS	0.748	0.63	0.877	0.748	0.63	0.877	SUBCLONAL	1	TRUE	1	0.48	2		217	234	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436515	110436515	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	203	883	0	ENST00000375856.3:c.1886C>A	p.Pro629Gln	p.P629Q	ENST00000375856	NM_003749.2	629	cCa/cAa	1/2	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.48	2		883	840	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046502	30046502	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	105	449	0	ENST00000331968.5:c.2681C>A	p.Thr894Asn	p.T894N	ENST00000331968	NM_002742.2	894	aCt/aAt	18/18	1	2	FACETS	0.816	0.734	0.903	0.816	0.734	0.903	CLONAL	1	TRUE	1	0.48	2		449	536	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093381	30093381	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1469866177	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	38	386	0	ENST00000331968.5:c.1882C>T	p.Arg628Cys	p.R628C	ENST00000331968	NM_002742.2	628	Cgt/Tgt	13/18	1	2	FACETS	0.419	0.347	0.499	0.419	0.347	0.499	SUBCLONAL	1	TRUE	1	0.48	2		386	378	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093456	30093456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1008608681	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	39	271	0	ENST00000331968.5:c.1807C>T	p.Arg603Cys	p.R603C	ENST00000331968	NM_002742.2	603	Cgt/Tgt	13/18	1	2	FACETS	0.735	0.615	0.867	0.735	0.615	0.867	SUBCLONAL	1	TRUE	1	0.48	2		271	221	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30102152	30102152	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs775376594	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	68	334	0	ENST00000331968.5:c.1315C>T	p.Arg439Trp	p.R439W	ENST00000331968	NM_002742.2	439	Cgg/Tgg	9/18	1	2	FACETS	0.954	0.838	1	0.954	0.838	1	CLONAL	1	TRUE	1	0.48	2		334	297	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108020	30108020	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	29	466	0	ENST00000331968.5:c.787T>G	p.Leu263Val	p.L263V	ENST00000331968	NM_002742.2	263	Ttg/Gtg	5/18	1	2	FACETS	0.26	0.208	0.319	0.26	0.208	0.319	SUBCLONAL	1	TRUE	1	0.48	2		466	465	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060685	38060685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	253	759	0	ENST00000250448.2:c.1304C>T	p.Ala435Val	p.A435V	ENST00000250448	NM_004496.3	435	gCc/gTc	2/2	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.48	2		759	970	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060728	38060728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	252	789	2	ENST00000250448.2:c.1261G>A	p.Glu421Lys	p.E421K	ENST00000250448	NM_004496.3	421	Gaa/Aaa	2/2	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.48	2		791	990	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060919	38060919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867404999	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	144	457	0	ENST00000250448.2:c.1070C>T	p.Ala357Val	p.A357V	ENST00000250448	NM_004496.3	357	gCg/gTg	2/2	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.48	2		457	547	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422185	81422185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241423317	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	108	408	0	ENST00000298171.2:c.161C>T	p.Thr54Met	p.T54M	ENST00000298171	NM_000369.2	54	aCg/aTg	1/10	1	2	FACETS	0.846	0.762	0.934	0.846	0.762	0.934	CLONAL	1	TRUE	1	0.48	2		408	532	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570036	95570036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1454503348	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	88	429	0	ENST00000393063.1:c.3697G>A	p.Asp1233Asn	p.D1233N	ENST00000393063	NM_030621.3	1233	Gat/Aat	22/28	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.48	2		429	352	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572438	95572438	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	47	282	0	ENST00000393063.1:c.2927A>G	p.Tyr976Cys	p.Y976C	ENST00000393063	NM_030621.3	976	tAc/tGc	19/28	1	2	FACETS	0.62	0.525	0.723	0.62	0.525	0.723	SUBCLONAL	1	TRUE	1	0.48	2		282	316	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574033	95574033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770335698	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	16	218	0	ENST00000393063.1:c.2716C>T	p.Arg906Cys	p.R906C	ENST00000393063	NM_030621.3	906	Cgc/Tgc	18/28	1	2	FACETS	0.368	0.273	0.481	0.368	0.273	0.481	SUBCLONAL	1	TRUE	1	0.48	2		218	181	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574292	95574292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144649926	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	11	281	0	ENST00000393063.1:c.2575C>T	p.Arg859Trp	p.R859W	ENST00000393063	NM_030621.3	859	Cgg/Tgg	17/28	1	2	FACETS	0.227	0.156	0.314	0.227	0.156	0.314	SUBCLONAL	1	TRUE	1	0.48	2		281	202	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582819	95582819	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	33	230	0	ENST00000393063.1:c.1723G>T	p.Asp575Tyr	p.D575Y	ENST00000393063	NM_030621.3	575	Gac/Tac	11/28	1	2	FACETS	0.859	0.709	1	0.859	0.709	1	CLONAL	1	TRUE	1	0.48	2		230	160	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675070	40675070	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	116	552	0	ENST00000249776.8:c.34G>T	p.Val12Phe	p.V12F	ENST00000249776	NM_033286.3	12	Gtt/Ttt	1/9	1	2	FACETS	0.724	0.653	0.798	0.724	0.653	0.798	SUBCLONAL	1	TRUE	1	0.48	2		552	668	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961418	41961418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	59	389	0	ENST00000219905.7:c.326G>A	p.Arg109His	p.R109H	ENST00000219905	NM_001164273.1	109	cGt/cAt	2/24	1	2	FACETS	0.869	0.754	0.991	0.869	0.754	0.991	CLONAL	1	TRUE	1	0.48	2		389	283	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961652	41961652	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	88	363	0	ENST00000219905.7:c.560A>G	p.Asp187Gly	p.D187G	ENST00000219905	NM_001164273.1	187	gAc/gGc	2/24	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.48	2		363	320	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961900	41961900	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	13	312	0	ENST00000219905.7:c.808G>T	p.Asp270Tyr	p.D270Y	ENST00000219905	NM_001164273.1	270	Gat/Tat	2/24	1	2	FACETS	0.209	0.149	0.283	0.209	0.149	0.283	SUBCLONAL	1	TRUE	1	0.48	2		312	259	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988918	41988918	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	75	384	1	ENST00000219905.7:c.1710G>T	p.Lys570Asn	p.K570N	ENST00000219905	NM_001164273.1	570	aaG/aaT	3/24	1	2	FACETS	0.901	0.795	1	0.901	0.795	1	CLONAL	1	TRUE	1	0.48	2		385	347	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989221	41989221	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	62	334	0	ENST00000219905.7:c.2013G>T	p.Lys671Asn	p.K671N	ENST00000219905	NM_001164273.1	671	aaG/aaT	3/24	1	2	FACETS	0.841	0.732	0.958	0.841	0.732	0.958	CLONAL	1	TRUE	1	0.48	2		334	307	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021428	42021428	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	78	316	1	ENST00000219905.7:c.3724C>T	p.Arg1242Ter	p.R1242*	ENST00000219905	NM_001164273.1	1242	Cga/Tga	11/24	1	2	FACETS	0.876	0.775	0.983	0.876	0.775	0.983	CLONAL	1	TRUE	1	0.48	2		317	371	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041075	42041075	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1309775039	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	119	484	0	ENST00000219905.7:c.5453G>A	p.Arg1818Gln	p.R1818Q	ENST00000219905	NM_001164273.1	1818	cGa/cAa	16/24	1	2	FACETS	0.976	0.885	1	0.976	0.885	1	CLONAL	1	TRUE	1	0.48	2		484	508	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720237	43720237	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	111	317	0	ENST00000382044.4:c.3805G>T	p.Glu1269Ter	p.E1269*	ENST00000382044	NM_001141980.1	1269	Gaa/Taa	18/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.48	2		317	383	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762205	43762205	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	100	475	0	ENST00000382044.4:c.1240C>A	p.Leu414Ile	p.L414I	ENST00000382044	NM_001141980.1	414	Ctt/Att	11/28	1	2	FACETS	0.78	0.699	0.866	0.78	0.699	0.866	SUBCLONAL	1	TRUE	1	0.48	2		475	534	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483928	88483928	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	147	514	0	ENST00000360948.2:c.1642G>T	p.Ala548Ser	p.A548S	ENST00000360948	NM_001012338.2	548	Gcc/Tcc	14/19	1	2	FACETS	0.899	0.823	0.979	0.899	0.823	0.979	CLONAL	1	TRUE	1	0.48	2		514	681	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669507	88669507	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs767212935	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	51	328	0	ENST00000360948.2:c.1391T>C	p.Met464Thr	p.M464T	ENST00000360948	NM_001012338.2	464	aTg/aCg	12/19	1	2	FACETS	0.629	0.537	0.729	0.629	0.537	0.729	SUBCLONAL	1	TRUE	1	0.48	2		328	338	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678473	88678473	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	132	573	0	ENST00000360948.2:c.1063G>T	p.Glu355Ter	p.E355*	ENST00000360948	NM_001012338.2	355	Gag/Tag	9/19	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.48	2		573	546	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292938	91292938	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	81	423	0	ENST00000355112.3:c.440C>A	p.Ser147Tyr	p.S147Y	ENST00000355112	NM_000057.2	147	tCt/tAt	3/22	1	2	FACETS	0.953	0.846	1	0.953	0.846	1	CLONAL	1	TRUE	1	0.48	2		423	354	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295040	91295040	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	53	215	0	ENST00000355112.3:c.823T>G	p.Leu275Val	p.L275V	ENST00000355112	NM_000057.2	275	Ttg/Gtg	4/22	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.48	2		215	208	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303420	91303420	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	44	315	0	ENST00000355112.3:c.1131G>T	p.Glu377Asp	p.E377D	ENST00000355112	NM_000057.2	377	gaG/gaT	6/22	1	2	FACETS	0.657	0.554	0.769	0.657	0.554	0.769	SUBCLONAL	1	TRUE	1	0.48	2		315	279	SUCCESS
BLM	641	MSKCC	GRCh37	15	91306240	91306240	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373090621	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	49	245	0	ENST00000355112.3:c.1927C>T	p.Arg643Cys	p.R643C	ENST00000355112	NM_000057.2	643	Cgt/Tgt	8/22	1	2	FACETS	0.827	0.706	0.956	0.827	0.706	0.956	CLONAL	1	TRUE	1	0.48	2		245	247	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310233	91310233	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs896043726	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	12	215	0	ENST00000355112.3:c.2287C>A	p.Leu763Ile	p.L763I	ENST00000355112	NM_000057.2	763	Cta/Ata	10/22	1	2	FACETS	0.262	0.184	0.357	0.262	0.184	0.357	SUBCLONAL	1	TRUE	1	0.48	2		215	191	SUCCESS
BLM	641	MSKCC	GRCh37	15	91341447	91341447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771767745	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	28	298	0	ENST00000355112.3:c.3238G>A	p.Asp1080Asn	p.D1080N	ENST00000355112	NM_000057.2	1080	Gat/Aat	17/22	1	2	FACETS	0.449	0.36	0.549	0.449	0.36	0.549	SUBCLONAL	1	TRUE	1	0.48	2		298	260	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347210	347210	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	144	627	0	ENST00000262320.3:c.1801G>A	p.Ala601Thr	p.A601T	ENST00000262320	NM_003502.3	601	Gcg/Acg	7/11	1	2	FACETS	0.946	0.866	1	0.946	0.866	1	CLONAL	1	TRUE	1	0.48	2		627	634	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396155	396155	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	118	356	0	ENST00000262320.3:c.871G>T	p.Glu291Ter	p.E291*	ENST00000262320	NM_003502.3	291	Gag/Tag	2/11	1	2	FACETS	0.916	0.829	1	0.916	0.829	1	CLONAL	1	TRUE	1	0.48	2		356	537	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138118	2138118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45517395	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	58	763	3	ENST00000219476.3:c.5138G>A	p.Arg1713His	p.R1713H	ENST00000219476	NM_000548.3	1713	cGc/cAc	40/42	1	2	FACETS	0.269	0.23	0.312	0.269	0.23	0.312	SUBCLONAL	1	TRUE	1	0.48	2		766	898	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778977	3778977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745551441	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	146	619	0	ENST00000262367.5:c.6071C>T	p.Ala2024Val	p.A2024V	ENST00000262367	NM_004380.2	2024	gCg/gTg	31/31	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.48	2		619	608	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819235	3819235	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	43	397	0	ENST00000262367.5:c.3000G>T	p.Glu1000Asp	p.E1000D	ENST00000262367	NM_004380.2	1000	gaG/gaT	15/31	1	2	FACETS	0.282	0.235	0.334	0.282	0.235	0.334	SUBCLONAL	1	TRUE	1	0.48	2		397	635	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828120	3828120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	132	406	1	ENST00000262367.5:c.2005C>T	p.Arg669Trp	p.R669W	ENST00000262367	NM_004380.2	669	Cgg/Tgg	10/31	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.48	2		407	531	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858247	9858247	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	67	358	0	ENST00000330684.3:c.3154C>A	p.Leu1052Ile	p.L1052I	ENST00000330684	NM_001134407.1	1052	Ctt/Att	13/13	1	2	FACETS	0.812	0.71	0.92	0.812	0.71	0.92	CLONAL	1	TRUE	1	0.48	2		358	344	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858260	9858260	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	24	340	0	ENST00000330684.3:c.3141G>T	p.Lys1047Asn	p.K1047N	ENST00000330684	NM_001134407.1	1047	aaG/aaT	13/13	1	2	FACETS	0.296	0.232	0.37	0.296	0.232	0.37	SUBCLONAL	1	TRUE	1	0.48	2		340	338	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923444	9923444	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	94	479	0	ENST00000330684.3:c.1843A>C	p.Asn615His	p.N615H	ENST00000330684	NM_001134407.1	615	Aac/Cac	9/13	1	2	FACETS	0.868	0.777	0.965	0.868	0.777	0.965	CLONAL	1	TRUE	1	0.48	2		479	451	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031921	10031921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	120	499	0	ENST00000330684.3:c.902C>T	p.Thr301Ile	p.T301I	ENST00000330684	NM_001134407.1	301	aCc/aTc	3/13	1	2	FACETS	0.938	0.851	1	0.938	0.851	1	CLONAL	1	TRUE	1	0.48	2		499	533	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274136	10274136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866582475	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	154	557	0	ENST00000330684.3:c.133G>A	p.Asp45Asn	p.D45N	ENST00000330684	NM_001134407.1	45	Gac/Aac	2/13	1	2	FACETS	0.965	0.886	1	0.965	0.886	1	CLONAL	1	TRUE	1	0.48	2		557	665	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020454	14020454	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764093404	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	79	239	0	ENST00000311895.7:c.425C>A	p.Ser142Tyr	p.S142Y	ENST00000311895	NM_005236.2	142	tCt/tAt	3/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.48	2		239	280	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14022004	14022004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	29	398	0	ENST00000311895.7:c.704C>T	p.Ala235Val	p.A235V	ENST00000311895	NM_005236.2	235	gCa/gTa	4/11	1	2	FACETS	0.335	0.269	0.41	0.335	0.269	0.41	SUBCLONAL	1	TRUE	1	0.48	2		398	361	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637636	23637636	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	102	499	0	ENST00000261584.4:c.2669C>A	p.Ala890Asp	p.A890D	ENST00000261584	NM_024675.3	890	gCt/gAt	7/13	1	2	FACETS	0.814	0.731	0.902	0.814	0.731	0.902	CLONAL	1	TRUE	1	0.48	2		499	522	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23640966	23640966	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778587	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	89	339	0	ENST00000261584.4:c.2509G>A	p.Glu837Lys	p.E837K	ENST00000261584	NM_024675.3	837	Gaa/Aaa	5/13	1	2	FACETS	0.981	0.876	1	0.981	0.876	1	CLONAL	1	TRUE	1	0.48	2		339	378	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641779	23641779	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746582620	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	34	219	0	ENST00000261584.4:c.1696C>T	p.Arg566Cys	p.R566C	ENST00000261584	NM_024675.3	566	Cgt/Tgt	5/13	1	2	FACETS	0.897	0.743	1	0.897	0.743	1	CLONAL	1	TRUE	1	0.48	2		219	158	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50815252	50815252	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	105	509	0	ENST00000398568.2:c.1605C>A	p.Ser535Arg	p.S535R	ENST00000398568	NM_001042412.1	535	agC/agA	9/18	1	2	FACETS	0.617	0.553	0.685	0.617	0.553	0.685	SUBCLONAL	1	TRUE	1	0.48	2		509	709	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650710	67650710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243010179	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	153	492	0	ENST00000264010.4:c.1015C>T	p.Arg339Trp	p.R339W	ENST00000264010	NM_006565.3	339	Cgg/Tgg	5/12	1	2	FACETS	0.995	0.913	1	0.995	0.913	1	CLONAL	1	TRUE	1	0.48	2		492	641	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856122	68856122	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781696	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	100	378	0	ENST00000261769.5:c.1930G>A	p.Asp644Asn	p.D644N	ENST00000261769	NM_004360.3	644	Gac/Aac	12/16	1	2	FACETS	0.87	0.781	0.964	0.87	0.781	0.964	CLONAL	1	TRUE	1	0.48	2		378	479	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827916	72827916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758610922	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	155	566	1	ENST00000268489.5:c.8665C>T	p.Arg2889Trp	p.R2889W	ENST00000268489	NM_006885.3	2889	Cgg/Tgg	9/10	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.48	2		567	644	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830135	72830135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	111	486	0	ENST00000268489.5:c.6446G>A	p.Arg2149His	p.R2149H	ENST00000268489	NM_006885.3	2149	cGc/cAc	9/10	1	2	FACETS	0.719	0.648	0.795	0.719	0.648	0.795	SUBCLONAL	1	TRUE	1	0.48	2		486	643	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830385	72830385	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	60	269	0	ENST00000268489.5:c.6196G>T	p.Ala2066Ser	p.A2066S	ENST00000268489	NM_006885.3	2066	Gca/Tca	9/10	1	2	FACETS	0.865	0.752	0.986	0.865	0.752	0.986	CLONAL	1	TRUE	1	0.48	2		269	289	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831456	72831456	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	36	448	0	ENST00000268489.5:c.5125G>T	p.Glu1709Ter	p.E1709*	ENST00000268489	NM_006885.3	1709	Gag/Tag	9/10	1	2	FACETS	0.305	0.25	0.366	0.305	0.25	0.366	SUBCLONAL	1	TRUE	1	0.48	2		448	492	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984685	72984685	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776123634	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	224	614	1	ENST00000268489.5:c.2899G>A	p.Val967Met	p.V967M	ENST00000268489	NM_006885.3	967	Gtg/Atg	3/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.48	2		615	797	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991901	72991901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147160019	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	186	526	0	ENST00000268489.5:c.2144G>A	p.Arg715Gln	p.R715Q	ENST00000268489	NM_006885.3	715	cGa/cAa	2/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.48	2		526	684	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992235	72992235	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	89	585	0	ENST00000268489.5:c.1810G>T	p.Glu604Ter	p.E604*	ENST00000268489	NM_006885.3	604	Gaa/Taa	2/10	1	2	FACETS	0.466	0.412	0.523	0.466	0.412	0.523	SUBCLONAL	1	TRUE	1	0.48	2		585	796	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348068	89348068	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	107	722	0	ENST00000301030.4:c.4882G>T	p.Asp1628Tyr	p.D1628Y	ENST00000301030	NM_001256183.1	1628	Gac/Tac	9/13	1	2	FACETS	0.517	0.463	0.574	0.517	0.463	0.574	SUBCLONAL	1	TRUE	1	0.48	2		722	863	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348743	89348743	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542863039	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	193	610	0	ENST00000301030.4:c.4207G>A	p.Gly1403Arg	p.G1403R	ENST00000301030	NM_001256183.1	1403	Gga/Aga	9/13	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.48	2		610	786	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351332	89351332	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	181	725	1	ENST00000301030.4:c.1618G>T	p.Asp540Tyr	p.D540Y	ENST00000301030	NM_001256183.1	540	Gac/Tac	9/13	1	2	FACETS	0.924	0.854	0.997	0.924	0.854	0.997	CLONAL	1	TRUE	1	0.48	2		726	816	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89837020	89837020	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	177	572	0	ENST00000389301.3:c.2174C>A	p.Ser725Tyr	p.S725Y	ENST00000389301	NM_000135.2	725	tCt/tAt	24/43	1	2	FACETS	0.909	0.839	0.982	0.909	0.839	0.982	CLONAL	1	TRUE	1	0.48	2		572	811	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882364	89882364	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	30	474	0	ENST00000389301.3:c.110C>A	p.Pro37His	p.P37H	ENST00000389301	NM_000135.2	37	cCt/cAt	2/43	1	2	FACETS	0.21	0.168	0.258	0.21	0.168	0.258	SUBCLONAL	1	TRUE	1	0.48	2		474	595	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216087	7216087	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	21	278	1	ENST00000380728.2:c.972C>A	p.Phe324Leu	p.F324L	ENST00000380728		324	ttC/ttA	11/11	1	2	FACETS	0.213	0.164	0.272	0.213	0.164	0.272	SUBCLONAL	1	TRUE	1	0.48	2		279	410	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983258	7983258	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	113	488	0	ENST00000319144.4:c.756G>T	p.Glu252Asp	p.E252D	ENST00000319144	NM_001139.2	252	gaG/gaT	7/15	1	2	FACETS	0.969	0.876	1	0.969	0.876	1	CLONAL	1	TRUE	1	0.48	2		488	486	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984505	7984505	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	27	404	0	ENST00000319144.4:c.353G>T	p.Gly118Val	p.G118V	ENST00000319144	NM_001139.2	118	gGa/gTa	3/15	1	2	FACETS	0.214	0.169	0.265	0.214	0.169	0.265	SUBCLONAL	1	TRUE	1	0.48	2		404	526	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032537	12032537	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	69	299	0	ENST00000353533.5:c.973C>T	p.Pro325Ser	p.P325S	ENST00000353533	NM_003010.3	325	Cct/Tct	9/11	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.48	2		299	278	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119768	17119768	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	162	633	0	ENST00000285071.4:c.1226A>G	p.Tyr409Cys	p.Y409C	ENST00000285071	NM_144997.5	409	tAc/tGc	11/14	1	2	FACETS	0.925	0.85	1	0.925	0.85	1	CLONAL	1	TRUE	1	0.48	2		633	730	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483134	29483134	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	31	289	0	ENST00000356175.3:c.194T>C	p.Val65Ala	p.V65A	ENST00000356175	NM_000267.3	65	gTt/gCt	2/57	1	2	FACETS	0.465	0.377	0.563	0.465	0.377	0.563	SUBCLONAL	1	TRUE	1	0.48	2		289	278	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559872	29559872	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375845704	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	77	216	0	ENST00000356175.3:c.3469G>A	p.Val1157Ile	p.V1157I	ENST00000356175	NM_000267.3	1157	Gta/Ata	26/57	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.48	2		216	294	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562641	29562641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854562	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	65	307	0	ENST00000356175.3:c.3721C>T	p.Arg1241Ter	p.R1241*	ENST00000356175	NM_000267.3	1241	Cga/Tga	28/57	1	2	FACETS	0.846	0.739	0.961	0.846	0.739	0.961	CLONAL	1	TRUE	1	0.48	2		307	320	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592246	29592246	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	24	132	0	ENST00000356175.3:c.4662-1G>T		p.X1554_splice	ENST00000356175	NM_000267.3	1554			1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.48	2		132	93	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627589	37627589	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1567685867	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	91	427	0	ENST00000447079.4:c.1504G>T	p.Asp502Tyr	p.D502Y	ENST00000447079	NM_015083.1	502	Gac/Tac	2/14	1	2	FACETS	0.98	0.876	1	0.98	0.876	1	CLONAL	1	TRUE	1	0.48	2		427	387	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475082	40475082	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	129	452	0	ENST00000264657.5:c.1828T>C	p.Phe610Leu	p.F610L	ENST00000264657	NM_139276.2	610	Ttc/Ctc	20/24	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.48	2		452	529	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696381	47696381	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	95	415	0	ENST00000347630.2:c.442G>T	p.Gly148Trp	p.G148W	ENST00000347630	NM_001007230.1	148	Ggg/Tgg	6/11	1	2	FACETS	0.861	0.77	0.956	0.861	0.77	0.956	CLONAL	1	TRUE	1	0.48	2		415	460	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436128	56436128	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	159	518	0	ENST00000407977.2:c.1009C>T	p.Arg337Ter	p.R337*	ENST00000407977		337	Cga/Tga	9/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.48	2		518	606	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740668	58740668	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs759850701	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	88	377	0	ENST00000305921.3:c.1573G>T	p.Glu525Ter	p.E525*	ENST00000305921	NM_003620.3	525	Gaa/Taa	6/6	1	2	FACETS	0.943	0.841	1	0.943	0.841	1	CLONAL	1	TRUE	1	0.48	2		377	389	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885995	59885995	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752309409	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	96	358	0	ENST00000259008.2:c.751C>T	p.Arg251Cys	p.R251C	ENST00000259008	NM_032043.2	251	Cgc/Tgc	7/20	1	2	FACETS	0.905	0.811	1	0.905	0.811	1	CLONAL	1	TRUE	1	0.48	2		358	442	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554530	63554530	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	111	497	0	ENST00000307078.5:c.209C>A	p.Ser70Tyr	p.S70Y	ENST00000307078	NM_004655.3	70	tCt/tAt	2/11	1	2	FACETS	0.881	0.795	0.971	0.881	0.795	0.971	CLONAL	1	TRUE	1	0.48	2		497	525	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78599496	78599496	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	84	322	0	ENST00000306801.3:c.168G>T	p.Lys56Asn	p.K56N	ENST00000306801	NM_020761.2	56	aaG/aaT	2/34	1	2	FACETS	0.843	0.749	0.943	0.843	0.749	0.943	CLONAL	1	TRUE	1	0.48	2		322	415	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681713	78681713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1299432885	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	102	446	0	ENST00000306801.3:c.421G>A	p.Ala141Thr	p.A141T	ENST00000306801	NM_020761.2	141	Gcc/Acc	4/34	1	2	FACETS	0.651	0.583	0.723	0.651	0.583	0.723	SUBCLONAL	1	TRUE	1	0.48	2		446	653	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743020	743020	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	95	445	0	ENST00000314574.4:c.958G>T	p.Glu320Ter	p.E320*	ENST00000314574	NM_005433.3	320	Gaa/Taa	8/12	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.48	2		445	385	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743338	743338	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	94	375	0	ENST00000314574.4:c.802G>T	p.Asp268Tyr	p.D268Y	ENST00000314574	NM_005433.3	268	Gat/Tat	7/12	1	2	FACETS	0.919	0.823	1	0.919	0.823	1	CLONAL	1	TRUE	1	0.48	2		375	426	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39575856	39575856	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs140660681	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	48	187	0	ENST00000262039.4:c.789G>T	p.Glu263Asp	p.E263D	ENST00000262039	NM_002647.2	263	gaG/gaT	8/25	1	2	FACETS	0.781	0.666	0.906	0.781	0.666	0.906	CLONAL	1	TRUE	1	0.48	2		187	256	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394731	45394731	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	67	347	0	ENST00000262160.6:c.618C>A	p.Phe206Leu	p.F206L	ENST00000262160	NM_005901.5	206	ttC/ttA	5/11	1	2	FACETS	0.752	0.657	0.854	0.752	0.657	0.854	SUBCLONAL	1	TRUE	1	0.48	2		347	371	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422959	45422959	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	86	234	0	ENST00000262160.6:c.169C>T	p.Arg57Ter	p.R57*	ENST00000262160	NM_005901.5	57	Cga/Tga	2/11	1	2	FACETS	0.998	0.89	1	0.998	0.89	1	CLONAL	1	TRUE	1	0.48	2		234	359	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573560	48573560	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	20	197	1	ENST00000342988.3:c.144G>T	p.Lys48Asn	p.K48N	ENST00000342988	NM_005359.5	48	aaG/aaT	2/12	1	2	FACETS	0.493	0.379	0.624	0.493	0.379	0.624	SUBCLONAL	1	TRUE	1	0.48	2		198	169	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584577	48584577	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	61	350	0	ENST00000342988.3:c.750G>T	p.Gln250His	p.Q250H	ENST00000342988	NM_005359.5	250	caG/caT	6/12	1	2	FACETS	0.704	0.61	0.805	0.704	0.61	0.805	SUBCLONAL	1	TRUE	1	0.48	2		350	361	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604832	48604832	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	62	224	0	ENST00000342988.3:c.1654G>T	p.Asp552Tyr	p.D552Y	ENST00000342988	NM_005359.5	552	Gac/Tac	12/12	1	2	FACETS	0.994	0.867	1	0.994	0.867	1	CLONAL	1	TRUE	1	0.48	2		224	260	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218484	1218484	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	122	392	0	ENST00000326873.7:c.359A>T	p.Glu120Val	p.E120V	ENST00000326873	NM_000455.4	120	gAa/gTa	2/10	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.48	2		392	480	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619401	1619401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200307903	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	235	759	2	ENST00000344749.5:c.1240G>A	p.Asp414Asn	p.D414N	ENST00000344749	NM_001136139.2	414	Gac/Aac	15/19	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.48	2		761	947	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099307	4099307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758031424	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	209	781	0	ENST00000262948.5:c.811G>A	p.Asp271Asn	p.D271N	ENST00000262948	NM_030662.3	271	Gac/Aac	7/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.48	2		781	823	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099411	4099411	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1309234276	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	202	600	0	ENST00000262948.5:c.707C>T	p.Pro236Leu	p.P236L	ENST00000262948	NM_030662.3	236	cCg/cTg	7/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.48	2		600	753	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220365	5220365	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	117	391	3	ENST00000357368.4:c.3456-1G>T		p.X1152_splice	ENST00000357368	NM_002850.3	1152			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.48	2		394	444	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229660	5229660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	34	68	0	ENST00000357368.4:c.2191G>A	p.Ala731Thr	p.A731T	ENST00000357368	NM_002850.3	731	Gcg/Acg	15/38	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.48	2		68	119	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267479	7267479	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	45	406	0	ENST00000302850.5:c.529G>T	p.Asp177Tyr	p.D177Y	ENST00000302850	NM_000208.2	177	Gat/Tat	2/22	1	2	FACETS	0.378	0.317	0.445	0.378	0.317	0.445	SUBCLONAL	1	TRUE	1	0.48	2		406	496	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602404	10602404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1432914621	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	244	757	2	ENST00000171111.5:c.1174G>A	p.Ala392Thr	p.A392T	ENST00000171111	NM_203500.1	392	Gcc/Acc	3/6	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.48	2		759	921	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100016	11100016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749059769	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	140	534	0	ENST00000358026.2:c.1142G>A	p.Arg381Gln	p.R381Q	ENST00000358026	NM_001128849.1	381	cGa/cAa	7/36	1	2	FACETS	0.823	0.751	0.898	0.823	0.751	0.898	CLONAL	1	TRUE	1	0.48	2		534	709	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051678	13051678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1026947469	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	61	408	0	ENST00000316448.5:c.937G>A	p.Val313Met	p.V313M	ENST00000316448	NM_004343.3	313	Gtg/Atg	7/9	1	2	FACETS	0.513	0.443	0.589	0.513	0.443	0.589	SUBCLONAL	1	TRUE	1	0.48	2		408	495	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291588	15291588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1333396423	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	51	749	0	ENST00000263388.2:c.3046G>A	p.Val1016Ile	p.V1016I	ENST00000263388	NM_000435.2	1016	Gtc/Atc	19/33	1	2	FACETS	0.241	0.204	0.283	0.241	0.204	0.283	SUBCLONAL	1	TRUE	1	0.48	2		749	880	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299917	15299917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555729068	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	220	807	0	ENST00000263388.2:c.1261C>T	p.Arg421Cys	p.R421C	ENST00000263388	NM_000435.2	421	Cgt/Tgt	8/33	1	2	FACETS	0.982	0.915	1	0.982	0.915	1	CLONAL	1	TRUE	1	0.48	2		807	933	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300192	15300192	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771875329	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	38	602	0	ENST00000263388.2:c.1084G>A	p.Glu362Lys	p.E362K	ENST00000263388	NM_000435.2	362	Gag/Aag	7/33	1	2	FACETS	0.212	0.174	0.254	0.212	0.174	0.254	SUBCLONAL	1	TRUE	1	0.48	2		602	747	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303052	15303052	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151016108	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	206	836	2	ENST00000263388.2:c.398G>A	p.Arg133His	p.R133H	ENST00000263388	NM_000435.2	133	cGc/cAc	4/33	1	2	FACETS	0.976	0.907	1	0.976	0.907	1	CLONAL	1	TRUE	1	0.48	2		838	879	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950379	17950379	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	49	641	0	ENST00000458235.1:c.1348C>A	p.Leu450Ile	p.L450I	ENST00000458235	NM_000215.3	450	Ctt/Att	10/24	1	2	FACETS	0.229	0.193	0.269	0.229	0.193	0.269	SUBCLONAL	1	TRUE	1	0.48	2		641	890	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953230	17953230	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	177	749	0	ENST00000458235.1:c.756G>T	p.Glu252Asp	p.E252D	ENST00000458235	NM_000215.3	252	gaG/gaT	6/24	1	2	FACETS	0.985	0.909	1	0.985	0.909	1	CLONAL	1	TRUE	1	0.48	2		749	749	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971733	18971733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	217	580	0	ENST00000262803.5:c.2399G>A	p.Arg800His	p.R800H	ENST00000262803	NM_002911.3	800	cGc/cAc	17/24	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.48	2		580	788	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260037	19260037	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs769182595	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	42	506	0	ENST00000162023.5:c.256G>A	p.Glu86Lys	p.E86K	ENST00000162023		86	Gag/Aag	7/13	1	2	FACETS	0.262	0.218	0.312	0.262	0.218	0.312	SUBCLONAL	1	TRUE	1	0.48	2		506	667	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792496	33792496	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	96	376	0	ENST00000498907.2:c.825G>T	p.Lys275Asn	p.K275N	ENST00000498907	NM_004364.3	275	aaG/aaT	1/1	1	2	FACETS	0.868	0.777	0.963	0.868	0.777	0.963	CLONAL	1	TRUE	1	0.48	2		376	461	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212191	36212191	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1313945983	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	120	439	0	ENST00000222270.7:c.1942C>T	p.Arg648Trp	p.R648W	ENST00000222270	NM_014727.1	648	Cgg/Tgg	3/37	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.48	2		439	497	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213563	36213563	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	216	784	0	ENST00000222270.7:c.2665G>T	p.Asp889Tyr	p.D889Y	ENST00000222270	NM_014727.1	889	Gat/Tat	5/37	1	2	FACETS	0.958	0.892	1	0.958	0.892	1	CLONAL	1	TRUE	1	0.48	2		784	939	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213599	36213599	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754201347	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	210	739	1	ENST00000222270.7:c.2701C>T	p.Arg901Trp	p.R901W	ENST00000222270	NM_014727.1	901	Cgg/Tgg	5/37	1	2	FACETS	0.936	0.87	1	0.936	0.87	1	CLONAL	1	TRUE	1	0.48	2		740	935	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213989	36213989	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	52	736	0	ENST00000222270.7:c.2815A>G	p.Thr939Ala	p.T939A	ENST00000222270	NM_014727.1	939	Aca/Gca	6/37	1	2	FACETS	0.243	0.206	0.284	0.243	0.206	0.284	SUBCLONAL	1	TRUE	1	0.48	2		736	890	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216490	36216490	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	225	712	2	ENST00000222270.7:c.3753C>A	p.Phe1251Leu	p.F1251L	ENST00000222270	NM_014727.1	1251	ttC/ttA	12/37	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.48	2		714	876	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220895	36220895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	46	274	0	ENST00000222270.7:c.4945G>A	p.Ala1649Thr	p.A1649T	ENST00000222270	NM_014727.1	1649	Gcc/Acc	23/37	1	2	FACETS	0.713	0.604	0.83	0.713	0.604	0.83	SUBCLONAL	1	TRUE	1	0.48	2		274	269	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223523	36223523	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368364777	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	177	807	0	ENST00000222270.7:c.6073G>A	p.Glu2025Lys	p.E2025K	ENST00000222270	NM_014727.1	2025	Gag/Aag	28/37	1	2	FACETS	0.899	0.83	0.972	0.899	0.83	0.972	CLONAL	1	TRUE	1	0.48	2		807	820	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223977	36223977	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	224	822	0	ENST00000222270.7:c.6527G>A	p.Ser2176Asn	p.S2176N	ENST00000222270	NM_014727.1	2176	aGc/aAc	28/37	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.48	2		822	915	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224532	36224532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759167832	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	224	1054	4	ENST00000222270.7:c.6994C>T	p.Arg2332Cys	p.R2332C	ENST00000222270	NM_014727.1	2332	Cgt/Tgt	29/37	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.48	2		1058	902	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743987	41743987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1306116384	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	224	661	0	ENST00000301178.4:c.922C>T	p.Arg308Cys	p.R308C	ENST00000301178	NM_021913.4	308	Cgc/Tgc	7/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.48	2		661	825	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754460	41754460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374709166	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	192	577	0	ENST00000301178.4:c.1579C>T	p.Arg527Trp	p.R527W	ENST00000301178	NM_021913.4	527	Cgg/Tgg	13/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.48	2		577	780	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765508	41765508	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	133	551	0	ENST00000301178.4:c.2384G>T	p.Ser795Ile	p.S795I	ENST00000301178	NM_021913.4	795	aGt/aTt	20/20	1	2	FACETS	0.964	0.879	1	0.964	0.879	1	CLONAL	1	TRUE	1	0.48	2		551	575	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383267	42383267	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	123	487	0	ENST00000221972.3:c.287T>C	p.Val96Ala	p.V96A	ENST00000221972	NM_021601.3	96	gTg/gCg	2/5	1	2	FACETS	0.837	0.759	0.919	0.837	0.759	0.919	CLONAL	1	TRUE	1	0.48	2		487	612	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383679	42383679	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	191	602	0	ENST00000221972.3:c.454C>A	p.Leu152Ile	p.L152I	ENST00000221972	NM_021601.3	152	Ctc/Atc	3/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.48	2		602	725	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791292	42791292	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	185	620	0	ENST00000575354.2:c.352G>T	p.Glu118Ter	p.E118*	ENST00000575354	NM_015125.3	118	Gaa/Taa	3/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.48	2		620	735	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797228	42797228	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	186	774	0	ENST00000575354.2:c.3590C>A	p.Ser1197Tyr	p.S1197Y	ENST00000575354	NM_015125.3	1197	tCt/tAt	15/20	1	2	FACETS	0.976	0.903	1	0.976	0.903	1	CLONAL	1	TRUE	1	0.48	2		774	794	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868176	45868176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559154781	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	57	668	2	ENST00000391945.4:c.514G>A	p.Ala172Thr	p.A172T	ENST00000391945	NM_000400.3	172	Gct/Act	7/23	1	2	FACETS	0.259	0.221	0.3	0.259	0.221	0.3	SUBCLONAL	1	TRUE	1	0.48	2		670	918	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873414	45873414	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	152	606	0	ENST00000391945.4:c.82C>T	p.Leu28Phe	p.L28F	ENST00000391945	NM_000400.3	28	Ctc/Ttc	2/23	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.48	2		606	617	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906378	50906378	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1235062032	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	122	779	2	ENST00000440232.2:c.1039C>T	p.Pro347Ser	p.P347S	ENST00000440232	NM_002691.3	347	Ccg/Tcg	9/27	1	2	FACETS	0.583	0.526	0.643	0.583	0.526	0.643	SUBCLONAL	1	TRUE	1	0.48	2		781	872	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910303	50910303	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	152	682	0	ENST00000440232.2:c.1558C>A	p.Leu520Met	p.L520M	ENST00000440232	NM_002691.3	520	Ctg/Atg	13/27	1	2	FACETS	0.753	0.689	0.82	0.753	0.689	0.82	SUBCLONAL	1	TRUE	1	0.48	2		682	841	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910352	50910352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779735891	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	203	675	1	ENST00000440232.2:c.1607C>T	p.Ala536Val	p.A536V	ENST00000440232	NM_002691.3	536	gCg/gTg	13/27	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.48	2		676	810	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714546	52714546	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	37	549	0	ENST00000322088.6:c.304A>G	p.Thr102Ala	p.T102A	ENST00000322088	NM_014225.5	102	Aca/Gca	4/15	1	2	FACETS	0.22	0.18	0.264	0.22	0.18	0.264	SUBCLONAL	1	TRUE	1	0.48	2		549	701	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470480	25470480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760854242	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	192	571	1	ENST00000264709.3:c.994G>A	p.Gly332Arg	p.G332R	ENST00000264709	NM_175629.2	332	Gga/Aga	8/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.48	2		572	703	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142885	30142885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766999851	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	187	618	1	ENST00000389048.3:c.641G>A	p.Arg214His	p.R214H	ENST00000389048	NM_004304.4	214	cGc/cAc	1/29	1	2	FACETS	0.988	0.914	1	0.988	0.914	1	CLONAL	1	TRUE	1	0.48	2		619	789	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39240640	39240640	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	66	323	0	ENST00000402219.2:c.2128C>A	p.Leu710Ile	p.L710I	ENST00000402219	NM_005633.3	710	Ctt/Att	13/23	1	2	FACETS	0.862	0.754	0.977	0.862	0.754	0.977	CLONAL	1	TRUE	1	0.48	2		323	319	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250039	39250039	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	24	408	0	ENST00000402219.2:c.1530C>A	p.Tyr510Ter	p.Y510*	ENST00000402219	NM_005633.3	510	taC/taA	10/23	1	2	FACETS	0.344	0.27	0.429	0.344	0.27	0.429	SUBCLONAL	1	TRUE	1	0.48	2		408	291	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46588129	46588129	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	155	560	0	ENST00000263734.3:c.679G>T	p.Glu227Ter	p.E227*	ENST00000263734	NM_001430.4	227	Gaa/Taa	6/16	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.48	2		560	638	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607473	46607473	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	169	660	0	ENST00000263734.3:c.1662G>T	p.Glu554Asp	p.E554D	ENST00000263734	NM_001430.4	554	gaG/gaT	12/16	1	2	FACETS	0.817	0.751	0.885	0.817	0.751	0.885	CLONAL	1	TRUE	1	0.48	2		660	862	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47601018	47601018	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	83	458	2	ENST00000263735.4:c.256G>T	p.Gly86Trp	p.G86W	ENST00000263735	NM_002354.2	86	Ggg/Tgg	3/9	1	2	FACETS	0.704	0.623	0.79	0.704	0.623	0.79	SUBCLONAL	1	TRUE	1	0.48	2		460	491	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47602439	47602439	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs606231203	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	58	289	0	ENST00000263735.4:c.491+1G>A		p.X164_splice	ENST00000263735	NM_002354.2	164			1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.48	2		289	236	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656952	47656952	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376934727	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	67	242	1	ENST00000233146.2:c.1148G>A	p.Arg383Gln	p.R383Q	ENST00000233146	NM_000251.2	383	cGa/cAa	7/16	1	2	FACETS	0.99	0.869	1	0.99	0.869	1	CLONAL	1	TRUE	1	0.48	2		243	282	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026567	48026567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773226008	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	73	306	0	ENST00000234420.5:c.1445G>A	p.Arg482Gln	p.R482Q	ENST00000234420	NM_000179.2	482	cGa/cAa	4/10	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.48	2		306	298	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030755	48030755	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	48	243	0	ENST00000234420.5:c.3369A>C	p.Glu1123Asp	p.E1123D	ENST00000234420	NM_000179.2	1123	gaA/gaC	5/10	1	2	FACETS	0.816	0.696	0.946	0.816	0.696	0.946	CLONAL	1	TRUE	1	0.48	2		243	245	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033753	48033753	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1553333707	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	44	237	0	ENST00000234420.5:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000234420	NM_000179.2	1322	Gaa/Taa	9/10	1	2	FACETS	0.996	0.847	1	0.996	0.847	1	CLONAL	1	TRUE	1	0.48	2		237	184	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711231	61711231	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	45	339	0	ENST00000401558.2:c.2518G>T	p.Glu840Ter	p.E840*	ENST00000401558	NM_003400.3	840	Gaa/Taa	21/25	1	2	FACETS	0.781	0.662	0.91	0.781	0.662	0.91	CLONAL	1	TRUE	1	0.48	2		339	240	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920688	96920688	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369144563	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	105	390	3	ENST00000258439.3:c.292G>A	p.Ala98Thr	p.A98T	ENST00000258439	NM_001193304.2	98	Gcc/Acc	3/4	1	2	FACETS	0.939	0.846	1	0.939	0.846	1	CLONAL	1	TRUE	1	0.48	2		393	466	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99154436	99154436	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	116	421	0	ENST00000074304.5:c.578G>T	p.Arg193Met	p.R193M	ENST00000074304	NM_001134224.1	193	aGg/aTg	8/26	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.48	2		421	470	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047286	128047286	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	93	342	0	ENST00000285398.2:c.636G>T	p.Glu212Asp	p.E212D	ENST00000285398	NM_000122.1	212	gaG/gaT	5/15	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.48	2		342	384	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622585	158622585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	27	389	0	ENST00000263640.3:c.914G>A	p.Cys305Tyr	p.C305Y	ENST00000263640	NM_001105.4	305	tGc/tAc	8/11	1	2	FACETS	0.313	0.248	0.386	0.313	0.248	0.386	SUBCLONAL	1	TRUE	1	0.48	2		389	360	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095799	178095799	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	57	339	0	ENST00000397062.3:c.1532C>A	p.Ala511Asp	p.A511D	ENST00000397062	NM_006164.4	511	gCt/gAt	5/5	1	2	FACETS	0.903	0.782	1	0.903	0.782	1	CLONAL	1	TRUE	1	0.48	2		339	263	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096135	178096135	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	28	359	1	ENST00000397062.3:c.1196C>A	p.Ser399Tyr	p.S399Y	ENST00000397062	NM_006164.4	399	tCt/tAt	5/5	1	2	FACETS	0.331	0.265	0.407	0.331	0.265	0.407	SUBCLONAL	1	TRUE	1	0.48	2		360	352	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096667	178096667	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	53	297	0	ENST00000397062.3:c.664G>T	p.Glu222Ter	p.E222*	ENST00000397062	NM_006164.4	222	Gaa/Taa	5/5	1	2	FACETS	0.932	0.803	1	0.932	0.803	1	CLONAL	1	TRUE	1	0.48	2		297	237	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098889	178098889	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	92	339	0	ENST00000397062.3:c.156A>C	p.Lys52Asn	p.K52N	ENST00000397062	NM_006164.4	52	aaA/aaC	2/5	1	2	FACETS	0.961	0.859	1	0.961	0.859	1	CLONAL	1	TRUE	1	0.48	2		339	399	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682810	190682810	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	58	293	0	ENST00000441310.2:c.492del	p.Lys164AsnfsTer6	p.K164Nfs*6	ENST00000441310	NM_000534.4	162	gcA/gc	5/13	1	2	FACETS	0.951	0.826	1	0.951	0.826	1	CLONAL	1	TRUE	1	0.48	2		293	254	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718969	190718969	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	19	190	0	ENST00000441310.2:c.971C>A	p.Ser324Tyr	p.S324Y	ENST00000441310	NM_000534.4	324	tCt/tAt	9/13	1	2	FACETS	0.55	0.421	0.698	0.55	0.421	0.698	SUBCLONAL	1	TRUE	1	0.48	2		190	144	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257139	198257139	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	63	297	0	ENST00000335508.6:c.3803T>A	p.Ile1268Asn	p.I1268N	ENST00000335508	NM_012433.2	1268	aTt/aAt	25/25	1	2	FACETS	0.924	0.807	1	0.924	0.807	1	CLONAL	1	TRUE	1	0.48	2		297	284	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285224	198285224	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757758244	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	26	361	0	ENST00000335508.6:c.343C>T	p.Arg115Trp	p.R115W	ENST00000335508	NM_012433.2	115	Cgg/Tgg	4/25	1	2	FACETS	0.334	0.265	0.414	0.334	0.265	0.414	SUBCLONAL	1	TRUE	1	0.48	2		361	324	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288699	198288699	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	43	263	0	ENST00000335508.6:c.29-1G>T		p.X10_splice	ENST00000335508	NM_012433.2	10			1	2	FACETS	0.703	0.592	0.823	0.703	0.592	0.823	SUBCLONAL	1	TRUE	1	0.48	2		263	255	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136264	202136264	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	85	374	0	ENST00000358485.4:c.508G>T	p.Glu170Ter	p.E170*	ENST00000358485	NM_001080125.1	170	Gaa/Taa	3/9	1	2	FACETS	0.937	0.834	1	0.937	0.834	1	CLONAL	1	TRUE	1	0.48	2		374	378	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251759	212251759	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1232890148	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	91	258	0	ENST00000342788.4:c.3300G>T	p.Glu1100Asp	p.E1100D	ENST00000342788	NM_005235.2	1100	gaG/gaT	27/28	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.48	2		258	351	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589809	212589809	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	93	307	0	ENST00000342788.4:c.733G>T	p.Asp245Tyr	p.D245Y	ENST00000342788	NM_005235.2	245	Gac/Tac	6/28	1	2	FACETS	0.966	0.865	1	0.966	0.865	1	CLONAL	1	TRUE	1	0.48	2		307	401	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589875	212589875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758827443	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	35	383	2	ENST00000342788.4:c.667G>A	p.Gly223Arg	p.G223R	ENST00000342788	NM_005235.2	223	Gga/Aga	6/28	1	2	FACETS	0.226	0.184	0.273	0.226	0.184	0.273	SUBCLONAL	1	TRUE	1	0.48	2		385	645	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215595163	215595163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377227840	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	28	289	0	ENST00000260947.4:c.1973G>A	p.Arg658His	p.R658H	ENST00000260947	NM_000465.2	658	cGc/cAc	10/11	1	2	FACETS	0.418	0.335	0.512	0.418	0.335	0.512	SUBCLONAL	1	TRUE	1	0.48	2		289	279	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379427	225379427	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	24	401	0	ENST00000264414.4:c.441del	p.Arg148GlufsTer21	p.R148Efs*21	ENST00000264414	NM_003590.4	147	ttT/tt	4/16	1	2	FACETS	0.283	0.222	0.354	0.283	0.222	0.354	SUBCLONAL	1	TRUE	1	0.48	2		401	353	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662143	227662143	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	135	582	0	ENST00000305123.5:c.1312T>C	p.Phe438Leu	p.F438L	ENST00000305123	NM_005544.2	438	Ttc/Ctc	1/2	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.48	2		582	537	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663379	227663379	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	95	448	0	ENST00000305123.5:c.76C>T	p.His26Tyr	p.H26Y	ENST00000305123	NM_005544.2	26	Cac/Tac	1/2	1	2	FACETS	0.75	0.67	0.834	0.75	0.67	0.834	SUBCLONAL	1	TRUE	1	0.48	2		448	528	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561186	9561186	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	26	386	0	ENST00000353224.5:c.596A>G	p.Tyr199Cys	p.Y199C	ENST00000353224	NM_177990.2	199	tAt/tGt	4/10	1	2	FACETS	0.292	0.231	0.362	0.292	0.231	0.362	SUBCLONAL	1	TRUE	1	0.48	2		386	371	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022569	31022569	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	109	427	0	ENST00000375687.4:c.2054G>A	p.Gly685Glu	p.G685E	ENST00000375687	NM_015338.5	685	gGa/gAa	13/13	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.48	2		427	429	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31025088	31025088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139397200	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	92	404	0	ENST00000375687.4:c.4573G>A	p.Asp1525Asn	p.D1525N	ENST00000375687	NM_015338.5	1525	Gat/Aat	13/13	1	2	FACETS	0.8	0.714	0.892	0.8	0.714	0.892	SUBCLONAL	1	TRUE	1	0.48	2		404	479	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383280	31383280	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778547539	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	138	427	1	ENST00000328111.2:c.1192C>T	p.Arg398Cys	p.R398C	ENST00000328111	NM_006892.3	398	Cgc/Tgc	11/23	1	2	FACETS	0.933	0.852	1	0.933	0.852	1	CLONAL	1	TRUE	1	0.48	2		428	616	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386391	31386391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1051749732	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	204	597	0	ENST00000328111.2:c.1616G>A	p.Arg539Gln	p.R539Q	ENST00000328111	NM_006892.3	539	cGg/cAg	15/23	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.48	2		597	707	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39725963	39725963	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	32	198	0	ENST00000361337.2:c.834C>A	p.Phe278Leu	p.F278L	ENST00000361337	NM_003286.2	278	ttC/ttA	10/21	1	2	FACETS	0.725	0.594	0.869	0.725	0.594	0.869	SUBCLONAL	1	TRUE	1	0.48	2		198	184	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728706	39728706	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	41	165	0	ENST00000361337.2:c.986A>G	p.Glu329Gly	p.E329G	ENST00000361337	NM_003286.2	329	gAg/gGg	12/21	1	2	FACETS	0.85	0.716	0.995	0.85	0.716	0.995	CLONAL	1	TRUE	1	0.48	2		165	201	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827900	40827900	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	125	408	0	ENST00000373198.4:c.2528C>A	p.Ser843Tyr	p.S843Y	ENST00000373198	NM_133170.3	843	tCt/tAt	17/32	1	2	FACETS	0.949	0.862	1	0.949	0.862	1	CLONAL	1	TRUE	1	0.48	2		408	549	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980730	40980730	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	20	321	1	ENST00000373198.4:c.1756A>C	p.Ile586Leu	p.I586L	ENST00000373198	NM_133170.3	586	Att/Ctt	10/32	1	2	FACETS	0.228	0.174	0.291	0.228	0.174	0.291	SUBCLONAL	1	TRUE	1	0.48	2		322	366	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101086	41101086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776769442	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	142	590	1	ENST00000373198.4:c.1270G>A	p.Val424Met	p.V424M	ENST00000373198	NM_133170.3	424	Gtg/Atg	8/32	1	2	FACETS	0.92	0.841	1	0.92	0.841	1	CLONAL	1	TRUE	1	0.48	2		591	643	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101118	41101118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751886972	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	162	610	0	ENST00000373198.4:c.1238C>T	p.Ala413Val	p.A413V	ENST00000373198	NM_133170.3	413	gCg/gTg	8/32	1	2	FACETS	0.999	0.919	1	0.999	0.919	1	CLONAL	1	TRUE	1	0.48	2		610	676	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306800	41306800	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	64	272	0	ENST00000373198.4:c.860-1G>T		p.X287_splice	ENST00000373198	NM_133170.3	287			1	2	FACETS	0.956	0.836	1	0.956	0.836	1	CLONAL	1	TRUE	1	0.48	2		272	279	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62290764	62290764	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	29	181	0	ENST00000360203.5:c.9G>T	p.Lys3Asn	p.K3N	ENST00000360203	NM_001283009.1	3	aaG/aaT	2/35	1	2	FACETS	0.573	0.463	0.696	0.573	0.463	0.696	SUBCLONAL	1	TRUE	1	0.48	2		181	211	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62311264	62311264	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1412076234	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	103	324	0	ENST00000360203.5:c.1100A>G	p.Asp367Gly	p.D367G	ENST00000360203	NM_001283009.1	367	gAc/gGc	13/35	1	2	FACETS	0.917	0.825	1	0.917	0.825	1	CLONAL	1	TRUE	1	0.48	2		324	468	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62320883	62320883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200847054	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	213	801	0	ENST00000360203.5:c.1907C>T	p.Thr636Met	p.T636M	ENST00000360203	NM_001283009.1	636	aCg/aTg	23/35	1	2	FACETS	0.956	0.889	1	0.956	0.889	1	CLONAL	1	TRUE	1	0.48	2		801	928	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171607	36171607	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1569008655	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	21	252	0	ENST00000300305.3:c.958C>T	p.Arg320Ter	p.R320*	ENST00000300305		320	Cga/Tga	7/8	1	2	FACETS	0.278	0.214	0.353	0.278	0.214	0.353	SUBCLONAL	1	TRUE	1	0.48	2		252	315	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839671	42839671	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs572530227	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	140	473	0	ENST00000398585.3:c.1568G>A	p.Arg523Gln	p.R523Q	ENST00000398585	NM_001135099.1	523	cGa/cAa	13/14	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.48	2		473	519	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866439	42866439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61735791	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	231	613	3	ENST00000398585.3:c.193G>A	p.Ala65Thr	p.A65T	ENST00000398585	NM_001135099.1	65	Gca/Aca	3/14	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.48	2		616	915	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655272	45655272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764295138	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	173	607	1	ENST00000407780.3:c.580C>T	p.Arg194Trp	p.R194W	ENST00000407780	NM_001283052.1	194	Cgg/Tgg	4/7	1	2	FACETS	0.945	0.871	1	0.945	0.871	1	CLONAL	1	TRUE	1	0.48	2		608	763	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162026	22162026	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	39	344	0	ENST00000215832.6:c.229C>T	p.Arg77Cys	p.R77C	ENST00000215832	NM_002745.4	77	Cgc/Tgc	2/9	1	2	FACETS	0.455	0.378	0.541	0.455	0.378	0.541	SUBCLONAL	1	TRUE	1	0.48	2		344	357	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175890	24175890	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	92	373	0	ENST00000263121.7:c.1118G>T	p.Arg373Met	p.R373M	ENST00000263121	NM_003073.3	373	aGg/aTg	8/9	1	2	FACETS	0.832	0.742	0.926	0.832	0.742	0.926	CLONAL	1	TRUE	1	0.48	2		373	461	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130460	29130460	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	113	509	0	ENST00000328354.6:c.250G>T	p.Glu84Ter	p.E84*	ENST00000328354	NM_007194.3	84	Gaa/Taa	2/15	1	2	FACETS	0.94	0.85	1	0.94	0.85	1	CLONAL	1	TRUE	1	0.48	2		509	501	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038202	30038202	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	62	361	0	ENST00000338641.4:c.375G>T	p.Gln125His	p.Q125H	ENST00000338641	NM_000268.3	125	caG/caT	4/16	1	2	FACETS	0.574	0.497	0.657	0.574	0.497	0.657	SUBCLONAL	1	TRUE	1	0.48	2		361	450	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536262	41536262	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	62	342	1	ENST00000263253.7:c.1878+1G>T		p.X626_splice	ENST00000263253	NM_001429.3	626			1	2	FACETS	0.957	0.835	1	0.957	0.835	1	CLONAL	1	TRUE	1	0.48	2		343	270	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422845	12422845	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	47	328	0	ENST00000287820.6:c.335C>A	p.Ser112Tyr	p.S112Y	ENST00000287820	NM_015869.4	112	tCt/tAt	3/7	1	2	FACETS	0.558	0.472	0.652	0.558	0.472	0.652	SUBCLONAL	1	TRUE	1	0.48	2		328	351	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475445	12475445	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	136	442	0	ENST00000287820.6:c.1319A>G	p.Asn440Ser	p.N440S	ENST00000287820	NM_015869.4	440	aAc/aGc	7/7	1	2	FACETS	0.959	0.875	1	0.959	0.875	1	CLONAL	1	TRUE	1	0.48	2		442	591	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650270	12650270	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	73	342	0	ENST00000251849.4:c.576A>C	p.Gln192His	p.Q192H	ENST00000251849	NM_002880.3	192	caA/caC	5/17	1	2	FACETS	0.966	0.852	1	0.966	0.852	1	CLONAL	1	TRUE	1	0.48	2		342	315	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729962	30729962	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs104893819	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	111	290	0	ENST00000295754.5:c.1483C>T	p.Arg495Ter	p.R495*	ENST00000295754	NM_003242.5	495	Cga/Tga	6/7	1	2	FACETS	0.921	0.832	1	0.921	0.832	1	CLONAL	1	TRUE	1	0.48	2		290	502	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266898	41266898	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1172941347	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	48	345	0	ENST00000349496.5:c.569G>A	p.Arg190His	p.R190H	ENST00000349496	NM_001904.3	190	cGt/cAt	5/15	1	2	FACETS	0.641	0.545	0.746	0.641	0.545	0.746	SUBCLONAL	1	TRUE	1	0.48	2		345	312	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144907	47144907	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	54	281	0	ENST00000409792.3:c.4846G>T	p.Asp1616Tyr	p.D1616Y	ENST00000409792	NM_014159.6	1616	Gat/Tat	7/21	1	2	FACETS	0.896	0.773	1	0.896	0.773	1	CLONAL	1	TRUE	1	0.48	2		281	251	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158212	47158212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553699111	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	55	346	0	ENST00000409792.3:c.4487G>A	p.Arg1496Gln	p.R1496Q	ENST00000409792	NM_014159.6	1496	cGa/cAa	4/21	1	2	FACETS	0.852	0.735	0.977	0.852	0.735	0.977	CLONAL	1	TRUE	1	0.48	2		346	269	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164311	47164311	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	15	249	0	ENST00000409792.3:c.1815A>C	p.Lys605Asn	p.K605N	ENST00000409792	NM_014159.6	605	aaA/aaC	3/21	1	2	FACETS	0.293	0.215	0.388	0.293	0.215	0.388	SUBCLONAL	1	TRUE	1	0.48	2		249	213	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164573	47164573	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	56	257	0	ENST00000409792.3:c.1553C>A	p.Ser518Tyr	p.S518Y	ENST00000409792	NM_014159.6	518	tCt/tAt	3/21	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.48	2		257	222	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164963	47164963	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1450528900	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	32	263	0	ENST00000409792.3:c.1163G>A	p.Arg388Gln	p.R388Q	ENST00000409792	NM_014159.6	388	cGg/cAg	3/21	1	2	FACETS	0.58	0.473	0.698	0.58	0.473	0.698	SUBCLONAL	1	TRUE	1	0.48	2		263	230	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939856	49939856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781591594	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	189	674	0	ENST00000296474.3:c.1187G>A	p.Arg396Gln	p.R396Q	ENST00000296474	NM_002447.2	396	cGa/cAa	1/20	1	2	FACETS	0.956	0.885	1	0.956	0.885	1	CLONAL	1	TRUE	1	0.48	2		674	824	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620629	52620629	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	124	365	0	ENST00000394830.3:c.3124A>G	p.Thr1042Ala	p.T1042A	ENST00000394830	NM_018313.4	1042	Acc/Gcc	21/30	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.48	2		365	473	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668641	52668641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	62	372	0	ENST00000394830.3:c.1278G>A	p.Met426Ile	p.M426I	ENST00000394830	NM_018313.4	426	atG/atA	12/30	1	2	FACETS	0.747	0.649	0.852	0.747	0.649	0.852	SUBCLONAL	1	TRUE	1	0.48	2		372	346	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52692244	52692244	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1359676390	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	82	259	0	ENST00000394830.3:c.616G>A	p.Glu206Lys	p.E206K	ENST00000394830	NM_018313.4	206	Gaa/Aaa	6/30	1	2	FACETS	0.946	0.841	1	0.946	0.841	1	CLONAL	1	TRUE	1	0.48	2		259	361	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014052	70014052	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	79	366	0	ENST00000394351.3:c.913C>A	p.Leu305Ile	p.L305I	ENST00000394351	NM_000248.3	305	Ctc/Atc	9/9	1	2	FACETS	0.897	0.794	1	0.897	0.794	1	CLONAL	1	TRUE	1	0.48	2		366	367	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026835	71026835	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1233328410	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	17	231	0	ENST00000318789.4:c.1387G>T	p.Glu463Ter	p.E463*	ENST00000318789	NM_032682.5	463	Gaa/Taa	16/21	1	2	FACETS	0.363	0.272	0.471	0.363	0.272	0.471	SUBCLONAL	1	TRUE	1	0.48	2		231	195	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102918	71102918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148369068	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	30	189	0	ENST00000318789.4:c.289G>A	p.Val97Met	p.V97M	ENST00000318789	NM_032682.5	97	Gtg/Atg	8/21	1	2	FACETS	0.484	0.392	0.589	0.484	0.392	0.589	SUBCLONAL	1	TRUE	1	0.48	2		189	258	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73108219	73108219	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	13	61	0	ENST00000356692.5:c.319T>G	p.Leu107Val	p.L107V	ENST00000356692		107	Ttg/Gtg	4/9	1	2	FACETS	1	0.777	1	1	0.777	1	CLONAL	1	TRUE	1	0.48	2		61	51	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114168	73114168	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	48	263	1	ENST00000356692.5:c.804T>G	p.Ile268Met	p.I268M	ENST00000356692		268	atT/atG	8/9	1	2	FACETS	0.571	0.485	0.666	0.571	0.485	0.666	SUBCLONAL	1	TRUE	1	0.48	2		264	350	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259085	89259085	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	59	268	0	ENST00000336596.2:c.229A>T	p.Ser77Cys	p.S77C	ENST00000336596	NM_005233.5	77	Agt/Tgt	3/17	1	2	FACETS	0.972	0.845	1	0.972	0.845	1	CLONAL	1	TRUE	1	0.48	2		268	253	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259104	89259104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1019076961	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	63	303	0	ENST00000336596.2:c.248G>T	p.Arg83Ile	p.R83I	ENST00000336596	NM_005233.5	83	aGa/aTa	3/17	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.48	2		303	257	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89478279	89478279	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	47	294	0	ENST00000336596.2:c.2098G>T	p.Glu700Ter	p.E700*	ENST00000336596	NM_005233.5	700	Gaa/Taa	12/17	1	2	FACETS	0.768	0.653	0.892	0.768	0.653	0.892	SUBCLONAL	1	TRUE	1	0.48	2		294	255	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498444	89498444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	46	369	0	ENST00000336596.2:c.2416G>A	p.Asp806Asn	p.D806N	ENST00000336596	NM_005233.5	806	Gat/Aat	14/17	1	2	FACETS	0.707	0.6	0.824	0.707	0.6	0.824	SUBCLONAL	1	TRUE	1	0.48	2		369	271	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582379	119582379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	52	258	0	ENST00000316626.5:c.1022G>A	p.Arg341Gln	p.R341Q	ENST00000316626		341	cGa/cAa	10/12	1	2	FACETS	0.572	0.488	0.663	0.572	0.488	0.663	SUBCLONAL	1	TRUE	1	0.48	2		258	379	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200090	128200090	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs779797858	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	48	647	0	ENST00000341105.2:c.1215G>T	p.Lys405Asn	p.K405N	ENST00000341105	NM_032638.4	405	aaG/aaT	6/6	1	2	FACETS	0.259	0.218	0.304	0.259	0.218	0.304	SUBCLONAL	1	TRUE	1	0.48	2		647	773	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873039	134873039	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	136	445	0	ENST00000398015.3:c.1343G>T	p.Arg448Met	p.R448M	ENST00000398015	NM_004441.4	448	aGg/aTg	6/16	1	2	FACETS	0.92	0.839	1	0.92	0.839	1	CLONAL	1	TRUE	1	0.48	2		445	616	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138383891	138383891	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	54	329	0	ENST00000289153.2:c.2659G>T	p.Glu887Ter	p.E887*	ENST00000289153	NM_006219.2	887	Gaa/Taa	18/22	1	2	FACETS	0.549	0.47	0.635	0.549	0.47	0.635	SUBCLONAL	1	TRUE	1	0.48	2		329	410	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453486	138453486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451809865	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	55	267	0	ENST00000289153.2:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000289153	NM_006219.2	321	cGa/cAa	5/22	1	2	FACETS	0.955	0.826	1	0.955	0.826	1	CLONAL	1	TRUE	1	0.48	2		267	240	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665257	138665257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	182	685	0	ENST00000330315.3:c.308G>C	p.Arg103Pro	p.R103P	ENST00000330315	NM_023067.3	103	cGc/cCc	1/1	1	2	FACETS	0.986	0.912	1	0.986	0.912	1	CLONAL	1	TRUE	1	0.48	2		685	769	SUCCESS
ATR	545	MSKCC	GRCh37	3	142185243	142185243	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	49	397	0	ENST00000350721.4:c.6820C>A	p.Leu2274Met	p.L2274M	ENST00000350721	NM_001184.3	2274	Ctg/Atg	40/47	1	2	FACETS	0.714	0.609	0.828	0.714	0.609	0.828	SUBCLONAL	1	TRUE	1	0.48	2		397	286	SUCCESS
ATR	545	MSKCC	GRCh37	3	142224067	142224067	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	81	445	0	ENST00000350721.4:c.5110G>T	p.Glu1704Ter	p.E1704*	ENST00000350721	NM_001184.3	1704	Gaa/Taa	29/47	1	2	FACETS	0.743	0.658	0.835	0.743	0.658	0.835	SUBCLONAL	1	TRUE	1	0.48	2		445	454	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279272	142279272	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	60	339	0	ENST00000350721.4:c.1374A>C	p.Gln458His	p.Q458H	ENST00000350721	NM_001184.3	458	caA/caC	6/47	1	2	FACETS	0.887	0.77	1	0.887	0.77	1	CLONAL	1	TRUE	1	0.48	2		339	282	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280234	142280234	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	65	249	0	ENST00000350721.4:c.1200G>T	p.Leu400Phe	p.L400F	ENST00000350721	NM_001184.3	400	ttG/ttT	5/47	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.48	2		249	244	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169999726	169999726	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	68	333	0	ENST00000295797.4:c.1037G>A	p.Arg346Gln	p.R346Q	ENST00000295797	NM_002740.5	346	cGa/cAa	11/18	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.48	2		333	272	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170002311	170002311	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	24	115	1	ENST00000295797.4:c.1130G>T	p.Arg377Ile	p.R377I	ENST00000295797	NM_002740.5	377	aGa/aTa	12/18	1	2	FACETS	0.952	0.761	1	0.952	0.761	1	CLONAL	1	TRUE	1	0.48	2		116	105	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170009708	170009708	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	42	238	0	ENST00000295797.4:c.1270A>T	p.Ile424Phe	p.I424F	ENST00000295797	NM_002740.5	424	Att/Ttt	13/18	1	2	FACETS	0.854	0.721	0.998	0.854	0.721	0.998	CLONAL	1	TRUE	1	0.48	2		238	205	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916855	178916855	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	85	410	0	ENST00000263967.3:c.242A>C	p.Glu81Ala	p.E81A	ENST00000263967	NM_006218.2	81	gAa/gCa	2/21	1	2	FACETS	0.976	0.869	1	0.976	0.869	1	CLONAL	1	TRUE	1	0.48	2		410	363	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917553	178917553	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	47	309	0	ENST00000263967.3:c.428T>G	p.Ile143Ser	p.I143S	ENST00000263967	NM_006218.2	143	aTt/aGt	3/21	1	2	FACETS	0.837	0.713	0.971	0.837	0.713	0.971	CLONAL	1	TRUE	1	0.48	2		309	234	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928067	178928067	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	70	423	0	ENST00000263967.3:c.1345C>A	p.Pro449Thr	p.P449T	ENST00000263967	NM_006218.2	449	Cct/Act	8/21	1	2	FACETS	0.843	0.74	0.953	0.843	0.74	0.953	CLONAL	1	TRUE	1	0.48	2		423	346	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928074	178928074	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	70	409	0	ENST00000263967.3:c.1352G>T	p.Gly451Val	p.G451V	ENST00000263967	NM_006218.2	451	gGa/gTa	8/21	1	2	FACETS	0.855	0.751	0.966	0.855	0.751	0.966	CLONAL	1	TRUE	1	0.48	2		409	341	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178943818	178943818	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs199926184	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	20	214	0	ENST00000263967.3:c.2485C>A	p.Leu829Ile	p.L829I	ENST00000263967	NM_006218.2	829	Ctt/Att	17/21	1	2	FACETS	0.362	0.278	0.461	0.362	0.278	0.461	SUBCLONAL	1	TRUE	1	0.48	2		214	230	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430440	181430440	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	209	640	0	ENST00000325404.1:c.292C>T	p.Arg98Ter	p.R98*	ENST00000325404	NM_003106.3	98	Cga/Tga	1/1	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.48	2		640	776	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430744	181430744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	194	760	1	ENST00000325404.1:c.596G>A	p.Arg199His	p.R199H	ENST00000325404	NM_003106.3	199	cGc/cAc	1/1	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.48	2		761	777	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430990	181430990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	200	617	0	ENST00000325404.1:c.842C>T	p.Ala281Val	p.A281V	ENST00000325404	NM_003106.3	281	gCc/gTc	1/1	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.48	2		617	774	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146527	185146527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35961174	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	144	386	0	ENST00000265026.3:c.158G>A	p.Arg53Gln	p.R53Q	ENST00000265026	NM_004721.4	53	cGa/cAa	2/14	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.48	2		386	474	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155246	185155246	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	113	304	0	ENST00000265026.3:c.487G>A	p.Val163Met	p.V163M	ENST00000265026	NM_004721.4	163	Gtg/Atg	3/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.48	2		304	363	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181393	185181393	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	76	328	0	ENST00000265026.3:c.1334C>A	p.Thr445Asn	p.T445N	ENST00000265026	NM_004721.4	445	aCt/aAt	8/14	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.48	2		328	284	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183602	185183602	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	89	365	0	ENST00000265026.3:c.1456T>G	p.Leu486Val	p.L486V	ENST00000265026	NM_004721.4	486	Ttg/Gtg	9/14	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.48	2		365	369	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191502	185191502	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	173	542	0	ENST00000265026.3:c.2383C>A	p.Leu795Ile	p.L795I	ENST00000265026	NM_004721.4	795	Ctc/Atc	11/14	1	2	FACETS	0.986	0.91	1	0.986	0.91	1	CLONAL	1	TRUE	1	0.48	2		542	731	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443345	187443345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	111	317	0	ENST00000232014.4:c.1781G>A	p.Arg594Gln	p.R594Q	ENST00000232014	NM_001130845.1	594	cGa/cAa	8/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.48	2		317	412	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446227	187446227	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	42	609	0	ENST00000232014.4:c.1461G>T	p.Glu487Asp	p.E487D	ENST00000232014	NM_001130845.1	487	gaG/gaT	6/10	1	2	FACETS	0.236	0.196	0.28	0.236	0.196	0.28	SUBCLONAL	1	TRUE	1	0.48	2		609	743	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189585700	189585700	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	117	332	0	ENST00000264731.3:c.961A>C	p.Ile321Leu	p.I321L	ENST00000264731	NM_003722.4	321	Att/Ctt	7/14	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.48	2		332	464	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612212	189612212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764601563	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	90	425	0	ENST00000264731.3:c.1964G>A	p.Arg655Gln	p.R655Q	ENST00000264731	NM_003722.4	655	cGa/cAa	14/14	1	2	FACETS	0.732	0.652	0.818	0.732	0.652	0.818	SUBCLONAL	1	TRUE	1	0.48	2		425	512	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127414	55127414	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501504	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	113	443	0	ENST00000257290.5:c.202G>A	p.Asp68Asn	p.D68N	ENST00000257290	NM_006206.4	68	Gat/Aat	3/23	1	2	FACETS	0.887	0.801	0.976	0.887	0.801	0.976	CLONAL	1	TRUE	1	0.48	2		443	531	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127534	55127534	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	79	268	0	ENST00000257290.5:c.322G>T	p.Glu108Ter	p.E108*	ENST00000257290	NM_006206.4	108	Gaa/Taa	3/23	1	2	FACETS	0.885	0.783	0.992	0.885	0.783	0.992	CLONAL	1	TRUE	1	0.48	2		268	372	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133628	55133628	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	57	362	0	ENST00000257290.5:c.931+1G>A		p.X311_splice	ENST00000257290	NM_006206.4	311			1	2	FACETS	0.769	0.664	0.881	0.769	0.664	0.881	SUBCLONAL	1	TRUE	1	0.48	2		362	309	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141123	55141123	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	17	299	0	ENST00000257290.5:c.1769G>T	p.Arg590Ile	p.R590I	ENST00000257290	NM_006206.4	590	aGa/aTa	12/23	1	2	FACETS	0.242	0.18	0.315	0.242	0.18	0.315	SUBCLONAL	1	TRUE	1	0.48	2		299	293	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161380	55161380	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376544204	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	117	378	0	ENST00000257290.5:c.3211G>A	p.Asp1071Asn	p.D1071N	ENST00000257290	NM_006206.4	1071	Gac/Aac	23/23	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.48	2		378	440	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565871	55565871	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767174569	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	53	389	0	ENST00000288135.5:c.695C>T	p.Thr232Met	p.T232M	ENST00000288135	NM_000222.2	232	aCg/aTg	4/21	1	2	FACETS	0.58	0.496	0.671	0.58	0.496	0.671	SUBCLONAL	1	TRUE	1	0.48	2		389	381	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604658	55604658	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778433	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	101	439	2	ENST00000288135.5:c.2866C>T	p.Arg956Trp	p.R956W	ENST00000288135	NM_000222.2	956	Cgg/Tgg	21/21	1	2	FACETS	0.738	0.662	0.819	0.738	0.662	0.819	SUBCLONAL	1	TRUE	1	0.48	2		441	570	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55962463	55962463	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	61	327	0	ENST00000263923.4:c.2661G>T	p.Lys887Asn	p.K887N	ENST00000263923	NM_002253.2	887	aaG/aaT	19/30	1	2	FACETS	0.7	0.607	0.8	0.7	0.607	0.8	SUBCLONAL	1	TRUE	1	0.48	2		327	363	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976641	55976641	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	61	437	0	ENST00000263923.4:c.1184A>C	p.Asn395Thr	p.N395T	ENST00000263923	NM_002253.2	395	aAt/aCt	9/30	1	2	FACETS	0.628	0.543	0.719	0.628	0.543	0.719	SUBCLONAL	1	TRUE	1	0.48	2		437	405	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55987327	55987327	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	40	317	0	ENST00000263923.4:c.98G>T	p.Arg33Met	p.R33M	ENST00000263923	NM_002253.2	33	aGg/aTg	2/30	1	2	FACETS	0.611	0.51	0.721	0.611	0.51	0.721	SUBCLONAL	1	TRUE	1	0.48	2		317	273	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197796	66197796	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	31	238	0	ENST00000273854.3:c.2903G>T	p.Arg968Ile	p.R968I	ENST00000273854	NM_004439.5	968	aGa/aTa	17/18	1	2	FACETS	0.624	0.508	0.753	0.624	0.508	0.753	SUBCLONAL	1	TRUE	1	0.48	2		238	207	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286229	66286229	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	32	249	0	ENST00000273854.3:c.1457C>A	p.Ser486Tyr	p.S486Y	ENST00000273854	NM_004439.5	486	tCt/tAt	6/18	1	2	FACETS	0.525	0.428	0.633	0.525	0.428	0.633	SUBCLONAL	1	TRUE	1	0.48	2		249	254	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356200	66356200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770587480	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	97	427	1	ENST00000273854.3:c.1297G>A	p.Ala433Thr	p.A433T	ENST00000273854	NM_004439.5	433	Gct/Act	5/18	1	2	FACETS	0.853	0.764	0.946	0.853	0.764	0.946	CLONAL	1	TRUE	1	0.48	2		428	474	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361207	66361207	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370682403	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	54	265	0	ENST00000273854.3:c.965G>A	p.Cys322Tyr	p.C322Y	ENST00000273854	NM_004439.5	322	tGt/tAt	4/18	1	2	FACETS	0.801	0.689	0.921	0.801	0.689	0.921	CLONAL	1	TRUE	1	0.48	2		265	281	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467554	66467554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	66	255	0	ENST00000273854.3:c.715C>T	p.His239Tyr	p.H239Y	ENST00000273854	NM_004439.5	239	Cac/Tac	3/18	1	2	FACETS	0.955	0.837	1	0.955	0.837	1	CLONAL	1	TRUE	1	0.48	2		255	288	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467751	66467751	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	63	286	0	ENST00000273854.3:c.518A>C	p.Lys173Thr	p.K173T	ENST00000273854	NM_004439.5	173	aAa/aCa	3/18	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.48	2		286	230	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467942	66467942	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	53	278	0	ENST00000273854.3:c.327G>T	p.Gln109His	p.Q109H	ENST00000273854	NM_004439.5	109	caG/caT	3/18	1	2	FACETS	0.84	0.722	0.966	0.84	0.722	0.966	CLONAL	1	TRUE	1	0.48	2		278	263	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535316	66535316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	200	647	0	ENST00000273854.3:c.145G>A	p.Ala49Thr	p.A49T	ENST00000273854	NM_004439.5	49	Gca/Aca	1/18	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.48	2		647	775	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155596	106155596	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	47	318	0	ENST00000380013.4:c.497T>A	p.Phe166Tyr	p.F166Y	ENST00000380013	NM_001127208.2	166	tTt/tAt	3/11	1	2	FACETS	0.702	0.596	0.817	0.702	0.596	0.817	SUBCLONAL	1	TRUE	1	0.48	2		318	279	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156196	106156196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	73	228	0	ENST00000380013.4:c.1097G>A	p.Ser366Asn	p.S366N	ENST00000380013	NM_001127208.2	366	aGc/aAc	3/11	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.48	2		228	296	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003187	143003187	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	45	252	0	ENST00000262992.4:c.2639G>T	p.Arg880Ile	p.R880I	ENST00000262992	NM_001101669.1	880	aGa/aTa	23/24	1	2	FACETS	0.83	0.704	0.965	0.83	0.704	0.965	CLONAL	1	TRUE	1	0.48	2		252	226	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143129653	143129653	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	163	308	0	ENST00000262992.4:c.997G>T	p.Gly333Ter	p.G333*	ENST00000262992	NM_001101669.1	333	Gga/Tga	12/24	1	2	FACETS	0.967	0.902	1	1	0.993	1	CLONAL	2	TRUE	1	0.48	2		308	351	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	133	357	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.48	2		357	517	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517778	187517778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	74	237	0	ENST00000441802.2:c.12916C>T	p.Pro4306Ser	p.P4306S	ENST00000441802	NM_005245.3	4306	Cca/Tca	25/27	1	2	FACETS	0.937	0.827	1	0.937	0.827	1	CLONAL	1	TRUE	1	0.48	2		237	329	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524834	187524834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771664786	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	82	470	0	ENST00000441802.2:c.10846G>A	p.Val3616Ile	p.V3616I	ENST00000441802	NM_005245.3	3616	Gta/Ata	19/27	1	2	FACETS	0.629	0.556	0.708	0.629	0.556	0.708	SUBCLONAL	1	TRUE	1	0.48	2		470	543	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530465	187530465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1389992570	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	59	278	0	ENST00000441802.2:c.10078G>A	p.Asp3360Asn	p.D3360N	ENST00000441802	NM_005245.3	3360	Gat/Aat	16/27	1	2	FACETS	0.796	0.689	0.91	0.796	0.689	0.91	CLONAL	1	TRUE	1	0.48	2		278	309	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540091	187540091	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs545138363	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	59	308	0	ENST00000441802.2:c.7649C>A	p.Thr2550Asn	p.T2550N	ENST00000441802	NM_005245.3	2550	aCt/aAt	10/27	1	2	FACETS	0.866	0.751	0.988	0.866	0.751	0.988	CLONAL	1	TRUE	1	0.48	2		308	284	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554873	187554873	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1014814755	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	44	314	0	ENST00000441802.2:c.4288G>A	p.Glu1430Lys	p.E1430K	ENST00000441802	NM_005245.3	1430	Gag/Aag	7/27	1	2	FACETS	0.512	0.431	0.602	0.512	0.431	0.602	SUBCLONAL	1	TRUE	1	0.48	2		314	358	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628413	187628413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1425439780	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	121	518	0	ENST00000441802.2:c.2569G>A	p.Val857Met	p.V857M	ENST00000441802	NM_005245.3	857	Gtg/Atg	2/27	1	2	FACETS	0.74	0.67	0.814	0.74	0.67	0.814	SUBCLONAL	1	TRUE	1	0.48	2		518	681	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629037	187629037	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	25	438	0	ENST00000441802.2:c.1945G>T	p.Asp649Tyr	p.D649Y	ENST00000441802	NM_005245.3	649	Gat/Tat	2/27	1	2	FACETS	0.279	0.219	0.347	0.279	0.219	0.347	SUBCLONAL	1	TRUE	1	0.48	2		438	374	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629277	187629277	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	98	447	0	ENST00000441802.2:c.1705T>C	p.Phe569Leu	p.F569L	ENST00000441802	NM_005245.3	569	Ttt/Ctt	2/27	1	2	FACETS	0.874	0.784	0.97	0.874	0.784	0.97	CLONAL	1	TRUE	1	0.48	2		447	467	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251552	251552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	143	445	0	ENST00000264932.6:c.1763C>T	p.Ser588Leu	p.S588L	ENST00000264932	NM_004168.2	588	tCa/tTa	13/15	1	2	FACETS	0.956	0.875	1	0.956	0.875	1	CLONAL	1	TRUE	1	0.48	2		445	623	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293665	1293665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567650961	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	166	862	0	ENST00000310581.5:c.1336C>T	p.Arg446Cys	p.R446C	ENST00000310581	NM_198253.2	446	Cgt/Tgt	2/16	1	2	FACETS	0.72	0.661	0.782	0.72	0.661	0.782	SUBCLONAL	1	TRUE	1	0.48	2		862	960	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293898	1293898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	227	821	1	ENST00000310581.5:c.1103C>T	p.Ser368Phe	p.S368F	ENST00000310581	NM_198253.2	368	tCc/tTc	2/16	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.48	2		822	939	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38942979	38942979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	43	261	0	ENST00000357387.3:c.5008C>T	p.Arg1670Trp	p.R1670W	ENST00000357387	NM_152756.3	1670	Cgg/Tgg	37/38	1	2	FACETS	0.681	0.574	0.798	0.681	0.574	0.798	SUBCLONAL	1	TRUE	1	0.48	2		261	263	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950352	38950352	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	36	350	1	ENST00000357387.3:c.3598C>T	p.Arg1200Ter	p.R1200*	ENST00000357387	NM_152756.3	1200	Cga/Tga	31/38	1	2	FACETS	0.581	0.481	0.693	0.581	0.481	0.693	SUBCLONAL	1	TRUE	1	0.48	2		351	258	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39021178	39021178	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	45	254	0	ENST00000357387.3:c.158A>G	p.Asn53Ser	p.N53S	ENST00000357387	NM_152756.3	53	aAt/aGt	3/38	1	2	FACETS	0.694	0.588	0.811	0.694	0.588	0.811	SUBCLONAL	1	TRUE	1	0.48	2		254	270	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178426	56178426	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	27	270	0	ENST00000399503.3:c.3399G>T	p.Glu1133Asp	p.E1133D	ENST00000399503	NM_005921.1	1133	gaG/gaT	14/20	1	2	FACETS	0.521	0.417	0.638	0.521	0.417	0.638	SUBCLONAL	1	TRUE	1	0.48	2		270	216	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754638	57754638	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	47	288	0	ENST00000274289.3:c.409C>A	p.Leu137Ile	p.L137I	ENST00000274289	NM_006622.3	137	Ctt/Att	3/14	1	2	FACETS	0.863	0.735	1	0.863	0.735	1	CLONAL	1	TRUE	1	0.48	2		288	227	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575489	67575489	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs547196342	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	81	274	0	ENST00000274335.5:c.562C>T	p.Arg188Cys	p.R188C	ENST00000274335		188	Cgc/Tgc	4/15	1	2	FACETS	0.879	0.779	0.984	0.879	0.779	0.984	CLONAL	1	TRUE	1	0.48	2		274	384	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588096	67588096	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	18	237	0	ENST00000274335.5:c.926C>A	p.Pro309His	p.P309H	ENST00000274335		309	cCt/cAt	7/15	1	2	FACETS	0.424	0.32	0.544	0.424	0.32	0.544	SUBCLONAL	1	TRUE	1	0.48	2		237	177	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	30	235	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	0.786	0.641	0.946	0.786	0.641	0.946	CLONAL	1	TRUE	1	0.48	2		235	159	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589618	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519838	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	25	219	0	ENST00000274335.5:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000274335		461	Cga/Tga	10/15	1	2	FACETS	0.543	0.43	0.669	0.543	0.43	0.669	SUBCLONAL	1	TRUE	1	0.48	2		219	192	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80074556	80074556	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199791286	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	79	320	1	ENST00000265081.6:c.2336G>A	p.Arg779His	p.R779H	ENST00000265081	NM_002439.4	779	cGc/cAc	17/24	1	2	FACETS	0.899	0.796	1	0.899	0.796	1	CLONAL	1	TRUE	1	0.48	2		321	366	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80149977	80149977	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	47	341	0	ENST00000265081.6:c.2842G>T	p.Gly948Ter	p.G948*	ENST00000265081	NM_002439.4	948	Gga/Tga	21/24	1	2	FACETS	0.89	0.759	1	0.89	0.759	1	CLONAL	1	TRUE	1	0.48	2		341	220	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564527	86564527	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	31	543	0	ENST00000274376.6:c.259A>G	p.Thr87Ala	p.T87A	ENST00000274376	NM_002890.2	87	Aca/Gca	1/25	1	2	FACETS	0.219	0.177	0.268	0.219	0.177	0.268	SUBCLONAL	1	TRUE	1	0.48	2		543	589	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86637116	86637116	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	31	147	0	ENST00000274376.6:c.1027G>T	p.Glu343Ter	p.E343*	ENST00000274376	NM_002890.2	343	Gaa/Taa	6/25	1	2	FACETS	0.726	0.593	0.872	0.726	0.593	0.872	SUBCLONAL	1	TRUE	1	0.48	2		147	178	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681153	86681153	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	13	245	0	ENST00000274376.6:c.2794T>G	p.Leu932Val	p.L932V	ENST00000274376	NM_002890.2	932	Tta/Gta	22/25	1	2	FACETS	0.272	0.194	0.367	0.272	0.194	0.367	SUBCLONAL	1	TRUE	1	0.48	2		245	199	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685312	86685312	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	45	142	0	ENST00000274376.6:c.3028C>T	p.Arg1010Ter	p.R1010*	ENST00000274376	NM_002890.2	1010	Cga/Tga	24/25	1	2	FACETS	0.889	0.755	1	0.889	0.755	1	CLONAL	1	TRUE	1	0.48	2		142	211	SUCCESS
APC	324	MSKCC	GRCh37	5	112173606	112173606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	38	233	0	ENST00000257430.4:c.2315C>T	p.Thr772Ile	p.T772I	ENST00000257430	NM_000038.5	772	aCt/aTt	16/16	1	2	FACETS	0.8	0.668	0.943	0.8	0.668	0.943	CLONAL	1	TRUE	1	0.48	2		233	198	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	44	368	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.861	0.73	1	0.861	0.73	1	CLONAL	1	TRUE	1	0.48	2		368	213	SUCCESS
APC	324	MSKCC	GRCh37	5	112174526	112174526	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1456190774	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	44	275	0	ENST00000257430.4:c.3235A>G	p.Thr1079Ala	p.T1079A	ENST00000257430	NM_000038.5	1079	Act/Gct	16/16	1	2	FACETS	0.808	0.684	0.942	0.808	0.684	0.942	CLONAL	1	TRUE	1	0.48	2		275	227	SUCCESS
APC	324	MSKCC	GRCh37	5	112176846	112176846	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	48	290	0	ENST00000257430.4:c.5555C>A	p.Thr1852Asn	p.T1852N	ENST00000257430	NM_000038.5	1852	aCt/aAt	16/16	1	2	FACETS	0.714	0.608	0.83	0.714	0.608	0.83	SUBCLONAL	1	TRUE	1	0.48	2		290	280	SUCCESS
APC	324	MSKCC	GRCh37	5	112177991	112177991	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	65	272	0	ENST00000257430.4:c.6700C>A	p.Pro2234Thr	p.P2234T	ENST00000257430	NM_000038.5	2234	Cca/Aca	16/16	1	2	FACETS	0.844	0.737	0.958	0.844	0.737	0.958	CLONAL	1	TRUE	1	0.48	2		272	321	SUCCESS
APC	324	MSKCC	GRCh37	5	112179017	112179017	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	45	247	0	ENST00000257430.4:c.7726G>C	p.Ala2576Pro	p.A2576P	ENST00000257430	NM_000038.5	2576	Gct/Cct	16/16	1	2	FACETS	0.845	0.717	0.982	0.845	0.717	0.982	CLONAL	1	TRUE	1	0.48	2		247	222	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915673	131915673	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28903088	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	36	313	0	ENST00000265335.6:c.671G>A	p.Arg224His	p.R224H	ENST00000265335		224	cGt/cAt	5/25	1	2	FACETS	0.512	0.422	0.611	0.512	0.422	0.611	SUBCLONAL	1	TRUE	1	0.48	2		313	293	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940521	131940521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs181961360	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	34	301	1	ENST00000265335.6:c.2548C>T	p.Arg850Cys	p.R850C	ENST00000265335		850	Cgt/Tgt	16/25	1	2	FACETS	0.632	0.52	0.756	0.632	0.52	0.756	SUBCLONAL	1	TRUE	1	0.48	2		302	224	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953794	131953794	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	43	245	0	ENST00000265335.6:c.3197A>C	p.Asn1066Thr	p.N1066T	ENST00000265335		1066	aAt/aCt	21/25	1	2	FACETS	0.857	0.725	1	0.857	0.725	1	CLONAL	1	TRUE	1	0.48	2		245	209	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441071	149441071	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	85	367	0	ENST00000286301.3:c.1841C>T	p.Ala614Val	p.A614V	ENST00000286301	NM_005211.3	614	gCt/gTt	13/22	1	2	FACETS	0.67	0.593	0.751	0.67	0.593	0.751	SUBCLONAL	1	TRUE	1	0.48	2		367	529	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505096	149505096	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	33	509	0	ENST00000261799.4:c.1719C>A	p.Ser573Arg	p.S573R	ENST00000261799	NM_002609.3	573	agC/agA	12/23	1	2	FACETS	0.228	0.185	0.276	0.228	0.185	0.276	SUBCLONAL	1	TRUE	1	0.48	2		509	604	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517993	176517993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765844308	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	39	576	0	ENST00000292408.4:c.491C>T	p.Ala164Val	p.A164V	ENST00000292408	NM_213647.1	164	gCg/gTg	5/18	1	2	FACETS	0.225	0.186	0.27	0.225	0.186	0.27	SUBCLONAL	1	TRUE	1	0.48	2		576	721	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562752	176562752	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	97	428	0	ENST00000439151.2:c.648G>T	p.Glu216Asp	p.E216D	ENST00000439151	NM_022455.4	216	gaG/gaT	2/23	1	2	FACETS	0.823	0.737	0.914	0.823	0.737	0.914	CLONAL	1	TRUE	1	0.48	2		428	491	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636760	176636760	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	39	343	0	ENST00000439151.2:c.1360G>T	p.Asp454Tyr	p.D454Y	ENST00000439151	NM_022455.4	454	Gat/Tat	5/23	1	2	FACETS	0.484	0.402	0.574	0.484	0.402	0.574	SUBCLONAL	1	TRUE	1	0.48	2		343	336	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687153	176687153	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	82	352	0	ENST00000439151.2:c.5130C>A	p.Cys1710Ter	p.C1710*	ENST00000439151	NM_022455.4	1710	tgC/tgA	14/23	1	2	FACETS	0.979	0.87	1	0.979	0.87	1	CLONAL	1	TRUE	1	0.48	2		352	349	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180037026	180037026	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	63	455	0	ENST00000261937.6:c.3687-1G>T		p.X1229_splice	ENST00000261937	NM_182925.4	1229			1	2	FACETS	0.489	0.423	0.56	0.489	0.423	0.56	SUBCLONAL	1	TRUE	1	0.48	2		455	537	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041081	180041081	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs201431522	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	53	671	0	ENST00000261937.6:c.3318G>T	p.Glu1106Asp	p.E1106D	ENST00000261937	NM_182925.4	1106	gaG/gaT	24/30	1	2	FACETS	0.27	0.229	0.314	0.27	0.229	0.314	SUBCLONAL	1	TRUE	1	0.48	2		671	819	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180050958	180050958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781305649	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	186	629	0	ENST00000261937.6:c.1525G>A	p.Glu509Lys	p.E509K	ENST00000261937	NM_182925.4	509	Gag/Aag	11/30	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.48	2		629	751	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056376	180056376	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	50	627	0	ENST00000261937.6:c.868G>T	p.Glu290Ter	p.E290*	ENST00000261937	NM_182925.4	290	Gaa/Taa	7/30	1	2	FACETS	0.345	0.292	0.403	0.345	0.292	0.403	SUBCLONAL	1	TRUE	1	0.48	2		627	604	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393226	393226	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	166	538	0	ENST00000380956.4:c.74G>A	p.Arg25His	p.R25H	ENST00000380956	NM_001195286.1	25	cGc/cAc	2/9	1	2	FACETS	0.977	0.9	1	0.977	0.9	1	CLONAL	1	TRUE	1	0.48	2		538	708	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481461	20481461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	69	209	1	ENST00000346618.3:c.530C>T	p.Thr177Met	p.T177M	ENST00000346618	NM_001949.4	177	aCg/aTg	3/7	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.48	2		210	274	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225582	26225582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752115135	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	129	552	0	ENST00000360408.1:c.200C>T	p.Pro67Leu	p.P67L	ENST00000360408	NM_003532.2	67	cCg/cTg	1/1	1	2	FACETS	0.94	0.855	1	0.94	0.855	1	CLONAL	1	TRUE	1	0.48	2		552	572	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858349	27858349	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	143	598	0	ENST00000359303.2:c.222A>C	p.Glu74Asp	p.E74D	ENST00000359303	NM_003535.2	74	gaA/gaC	1/1	1	2	FACETS	0.969	0.886	1	0.969	0.886	1	CLONAL	1	TRUE	1	0.48	2		598	615	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910404	29910404	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	169	737	0	ENST00000376809.5:c.73+1G>A		p.X25_splice	ENST00000376809	NM_002116.7	25			1	2	FACETS	0.971	0.895	1	0.971	0.895	1	CLONAL	1	TRUE	1	0.48	2		737	725	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911095	29911095	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199474499	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	57	784	0	ENST00000376809.5:c.394C>T	p.Arg132Cys	p.R132C	ENST00000376809	NM_002116.7	132	Cgc/Tgc	3/8	1	2	FACETS	0.299	0.256	0.347	0.299	0.256	0.347	SUBCLONAL	1	TRUE	1	0.48	2		784	794	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911128	29911128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41554014	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	60	603	2	ENST00000376809.5:c.427G>A	p.Asp143Asn	p.D143N	ENST00000376809	NM_002116.7	143	Gac/Aac	3/8	1	2	FACETS	0.431	0.371	0.496	0.431	0.371	0.496	SUBCLONAL	1	TRUE	1	0.48	2		605	580	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912169	29912169	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	43	179	0	ENST00000376809.5:c.890G>T	p.Arg297Ile	p.R297I	ENST00000376809	NM_002116.7	297	aGa/aTa	4/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.48	2		179	137	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671741	30671741	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	156	491	0	ENST00000376406.3:c.5219A>T	p.Lys1740Met	p.K1740M	ENST00000376406	NM_014641.2	1740	aAg/aTg	10/15	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.48	2		491	617	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673634	30673634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1386319473	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	47	519	0	ENST00000376406.3:c.3326C>T	p.Thr1109Ile	p.T1109I	ENST00000376406	NM_014641.2	1109	aCt/aTt	10/15	1	2	FACETS	0.292	0.245	0.343	0.292	0.245	0.343	SUBCLONAL	1	TRUE	1	0.48	2		519	671	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681489	30681489	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	53	332	2	ENST00000376406.3:c.523C>A	p.Leu175Ile	p.L175I	ENST00000376406	NM_014641.2	175	Ctt/Att	4/15	1	2	FACETS	0.759	0.652	0.874	0.759	0.652	0.874	SUBCLONAL	1	TRUE	1	0.48	2		334	291	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681495	30681495	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	51	324	1	ENST00000376406.3:c.518-1G>T		p.X173_splice	ENST00000376406	NM_014641.2	173			1	2	FACETS	0.776	0.664	0.896	0.776	0.664	0.896	SUBCLONAL	1	TRUE	1	0.48	2		325	274	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169935	32169935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142477287	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	161	660	1	ENST00000375023.3:c.3673C>T	p.Arg1225Trp	p.R1225W	ENST00000375023	NM_004557.3	1225	Cgg/Tgg	21/30	1	2	FACETS	0.875	0.803	0.949	0.875	0.803	0.949	CLONAL	1	TRUE	1	0.48	2		661	767	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169955	32169955	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	166	706	0	ENST00000375023.3:c.3653C>A	p.Ser1218Tyr	p.S1218Y	ENST00000375023	NM_004557.3	1218	tCt/tAt	21/30	1	2	FACETS	0.89	0.819	0.964	0.89	0.819	0.964	CLONAL	1	TRUE	1	0.48	2		706	777	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170103	32170103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764352594	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	47	753	1	ENST00000375023.3:c.3505C>T	p.Arg1169Trp	p.R1169W	ENST00000375023	NM_004557.3	1169	Cgg/Tgg	21/30	1	2	FACETS	0.244	0.205	0.287	0.244	0.205	0.287	SUBCLONAL	1	TRUE	1	0.48	2		754	803	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178588	32178588	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	161	598	0	ENST00000375023.3:c.2806T>A	p.Ser936Thr	p.S936T	ENST00000375023	NM_004557.3	936	Tcc/Acc	18/30	1	2	FACETS	0.941	0.865	1	0.941	0.865	1	CLONAL	1	TRUE	1	0.48	2		598	713	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181952	32181952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	155	606	1	ENST00000375023.3:c.2102C>T	p.Ala701Val	p.A701V	ENST00000375023	NM_004557.3	701	gCc/gTc	13/30	1	2	FACETS	0.814	0.746	0.885	0.814	0.746	0.885	CLONAL	1	TRUE	1	0.48	2		607	793	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184804	32184804	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	137	513	0	ENST00000375023.3:c.1779C>A	p.Cys593Ter	p.C593*	ENST00000375023	NM_004557.3	593	tgC/tgA	11/30	1	2	FACETS	0.983	0.897	1	0.983	0.897	1	CLONAL	1	TRUE	1	0.48	2		513	581	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187447	32187447	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779321619	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	183	623	1	ENST00000375023.3:c.1432G>A	p.Glu478Lys	p.E478K	ENST00000375023	NM_004557.3	478	Gag/Aag	8/30	1	2	FACETS	0.969	0.896	1	0.969	0.896	1	CLONAL	1	TRUE	1	0.48	2		624	787	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797232	32797232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1247287824	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	194	642	0	ENST00000374899.4:c.1877G>A	p.Arg626Gln	p.R626Q	ENST00000374899	NM_018833.2	626	cGg/cAg	11/12	1	2	FACETS	0.977	0.906	1	0.977	0.906	1	CLONAL	1	TRUE	1	0.48	2		642	827	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798533	32798533	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	160	552	0	ENST00000374899.4:c.1323G>T	p.Glu441Asp	p.E441D	ENST00000374899	NM_018833.2	441	gaG/gaT	8/12	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.48	2		552	593	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805984	32805984	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	150	560	0	ENST00000374899.4:c.27G>T	p.Trp9Cys	p.W9C	ENST00000374899	NM_018833.2	9	tgG/tgT	2/12	1	2	FACETS	0.94	0.861	1	0.94	0.861	1	CLONAL	1	TRUE	1	0.48	2		560	665	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287941	33287941	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756719415	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	75	377	0	ENST00000374542.5:c.1312G>A	p.Glu438Lys	p.E438K	ENST00000374542	NM_001141970.1	438	Gaa/Aaa	5/8	1	2	FACETS	0.757	0.666	0.853	0.757	0.666	0.853	SUBCLONAL	1	TRUE	1	0.48	2		377	413	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288561	33288561	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1373347535	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	110	358	4	ENST00000374542.5:c.991G>A	p.Asp331Asn	p.D331N	ENST00000374542	NM_001141970.1	331	Gat/Aat	3/8	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.48	2		362	402	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288599	33288599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	99	369	0	ENST00000374542.5:c.953G>A	p.Arg318Gln	p.R318Q	ENST00000374542	NM_001141970.1	318	cGa/cAa	3/8	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.48	2		369	379	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652243	36652243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs558863376	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	185	578	0	ENST00000244741.5:c.365G>A	p.Arg122His	p.R122H	ENST00000244741	NM_000389.4	122	cGc/cAc	2/3	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.48	2		578	716	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748500	43748500	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	63	249	0	ENST00000523873.1:c.454A>C	p.Lys152Gln	p.K152Q	ENST00000523873		152	Aaa/Caa	6/8	1	2	FACETS	0.836	0.728	0.951	0.836	0.728	0.951	CLONAL	1	TRUE	1	0.48	2		249	314	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793691	89793691	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	45	275	0	ENST00000336032.3:c.760A>C	p.Lys254Gln	p.K254Q	ENST00000336032	NM_006813.2	254	Aaa/Caa	2/2	1	2	FACETS	0.798	0.677	0.929	0.798	0.677	0.929	CLONAL	1	TRUE	1	0.48	2		275	235	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322654	109322654	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	83	377	0	ENST00000436639.2:c.383C>A	p.Ala128Asp	p.A128D	ENST00000436639	NM_014454.2	128	gCt/gAt	3/10	1	2	FACETS	0.969	0.862	1	0.969	0.862	1	CLONAL	1	TRUE	1	0.48	2		377	357	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415068	109415068	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	115	454	0	ENST00000436639.2:c.209T>G	p.Leu70Arg	p.L70R	ENST00000436639	NM_014454.2	70	cTt/cGt	1/10	1	2	FACETS	0.976	0.884	1	0.976	0.884	1	CLONAL	1	TRUE	1	0.48	2		454	491	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638362	117638362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	60	311	0	ENST00000368508.3:c.6079G>A	p.Glu2027Lys	p.E2027K	ENST00000368508	NM_002944.2	2027	Gaa/Aaa	38/43	1	2	FACETS	0.833	0.723	0.951	0.833	0.723	0.951	CLONAL	1	TRUE	1	0.48	2		311	300	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117645540	117645540	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	58	437	0	ENST00000368508.3:c.5596A>G	p.Ile1866Val	p.I1866V	ENST00000368508	NM_002944.2	1866	Att/Gtt	34/43	1	2	FACETS	0.898	0.779	1	0.898	0.779	1	CLONAL	1	TRUE	1	0.48	2		437	269	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663689	117663689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	29	222	0	ENST00000368508.3:c.4543G>A	p.Ala1515Thr	p.A1515T	ENST00000368508	NM_002944.2	1515	Gct/Act	28/43	1	2	FACETS	0.646	0.523	0.783	0.646	0.523	0.783	SUBCLONAL	1	TRUE	1	0.48	2		222	187	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681540	117681540	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	49	212	0	ENST00000368508.3:c.3410G>T	p.Gly1137Val	p.G1137V	ENST00000368508	NM_002944.2	1137	gGa/gTa	22/43	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.48	2		212	197	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117707025	117707025	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	39	288	0	ENST00000368508.3:c.2126-1G>T		p.X709_splice	ENST00000368508	NM_002944.2	709			1	2	FACETS	0.502	0.417	0.595	0.502	0.417	0.595	SUBCLONAL	1	TRUE	1	0.48	2		288	324	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710549	117710549	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	32	172	0	ENST00000368508.3:c.1723G>A	p.Val575Ile	p.V575I	ENST00000368508	NM_002944.2	575	Gtt/Att	12/43	1	2	FACETS	0.687	0.563	0.825	0.687	0.563	0.825	SUBCLONAL	1	TRUE	1	0.48	2		172	194	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710846	117710846	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	61	339	0	ENST00000368508.3:c.1426G>T	p.Val476Phe	p.V476F	ENST00000368508	NM_002944.2	476	Gtc/Ttc	12/43	1	2	FACETS	0.637	0.552	0.729	0.637	0.552	0.729	SUBCLONAL	1	TRUE	1	0.48	2		339	399	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715423	117715423	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	47	284	0	ENST00000368508.3:c.1066G>T	p.Val356Leu	p.V356L	ENST00000368508	NM_002944.2	356	Gta/Tta	10/43	1	2	FACETS	0.756	0.643	0.879	0.756	0.643	0.879	SUBCLONAL	1	TRUE	1	0.48	2		284	259	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715787	117715787	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	55	293	0	ENST00000368508.3:c.971A>C	p.Asn324Thr	p.N324T	ENST00000368508	NM_002944.2	324	aAt/aCt	9/43	1	2	FACETS	0.955	0.826	1	0.955	0.826	1	CLONAL	1	TRUE	1	0.48	2		293	240	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718123	117718123	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	83	410	0	ENST00000368508.3:c.734G>T	p.Arg245Ile	p.R245I	ENST00000368508	NM_002944.2	245	aGa/aTa	7/43	1	2	FACETS	0.935	0.831	1	0.935	0.831	1	CLONAL	1	TRUE	1	0.48	2		410	370	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117737437	117737437	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	52	258	0	ENST00000368508.3:c.212A>G	p.Asn71Ser	p.N71S	ENST00000368508	NM_002944.2	71	aAc/aGc	3/43	1	2	FACETS	0.895	0.77	1	0.895	0.77	1	CLONAL	1	TRUE	1	0.48	2		258	242	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519451	137519451	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747769538	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	37	245	0	ENST00000367739.4:c.1187C>T	p.Ser396Leu	p.S396L	ENST00000367739	NM_000416.2	396	tCg/tTg	7/7	1	2	FACETS	0.65	0.54	0.772	0.65	0.54	0.772	SUBCLONAL	1	TRUE	1	0.48	2		245	237	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192486	138192486	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	74	258	0	ENST00000237289.4:c.122A>C	p.Lys41Thr	p.K41T	ENST00000237289	NM_001270507.1	41	aAa/aCa	2/9	1	2	FACETS	0.961	0.848	1	0.961	0.848	1	CLONAL	1	TRUE	1	0.48	2		258	321	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004246	150004246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	39	212	0	ENST00000253339.5:c.1979G>A	p.Arg660His	p.R660H	ENST00000253339		660	cGt/cAt	3/7	1	2	FACETS	0.793	0.664	0.933	0.793	0.664	0.933	CLONAL	1	TRUE	1	0.48	2		212	205	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004723	150004723	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	99	429	0	ENST00000253339.5:c.1502T>C	p.Met501Thr	p.M501T	ENST00000253339		501	aTg/aCg	3/7	1	2	FACETS	0.989	0.889	1	0.989	0.889	1	CLONAL	1	TRUE	1	0.48	2		429	417	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522443	157522443	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	151	528	0	ENST00000346085.5:c.4715C>A	p.Ser1572Tyr	p.S1572Y	ENST00000346085	NM_020732.3	1572	tCt/tAt	18/20	1	2	FACETS	0.974	0.893	1	0.974	0.893	1	CLONAL	1	TRUE	1	0.48	2		528	646	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522598	157522598	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554236040	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	30	415	1	ENST00000346085.5:c.4870C>T	p.Arg1624Ter	p.R1624*	ENST00000346085	NM_020732.3	1624	Cga/Tga	18/20	1	2	FACETS	0.222	0.178	0.272	0.222	0.178	0.272	SUBCLONAL	1	TRUE	1	0.48	2		416	563	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528230	157528230	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	104	445	0	ENST00000346085.5:c.5955T>G	p.His1985Gln	p.H1985Q	ENST00000346085	NM_020732.3	1985	caT/caG	20/20	1	2	FACETS	0.838	0.753	0.927	0.838	0.753	0.927	CLONAL	1	TRUE	1	0.48	2		445	517	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622212	162622212	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	24	332	0	ENST00000366898.1:c.485T>G	p.Leu162Arg	p.L162R	ENST00000366898	NM_004562.2	162	cTc/cGc	4/12	1	2	FACETS	0.228	0.178	0.285	0.228	0.178	0.285	SUBCLONAL	1	TRUE	1	0.48	2		332	439	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963878	2963878	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	139	468	1	ENST00000396946.4:c.1929C>A	p.Phe643Leu	p.F643L	ENST00000396946	NM_032415.4	643	ttC/ttA	15/25	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.48	2		469	545	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987422	2987422	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	80	317	0	ENST00000396946.4:c.8-1G>T		p.X3_splice	ENST00000396946	NM_032415.4	3			1	2	FACETS	0.992	0.881	1	0.992	0.881	1	CLONAL	1	TRUE	1	0.48	2		317	336	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026990	6026990	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	29	348	0	ENST00000265849.7:c.1406G>T	p.Arg469Ile	p.R469I	ENST00000265849	NM_000535.5	469	aGa/aTa	11/15	1	2	FACETS	0.245	0.196	0.301	0.245	0.196	0.301	SUBCLONAL	1	TRUE	1	0.48	2		348	493	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035238	6035238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1805322	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	18	267	0	ENST00000265849.7:c.830C>T	p.Thr277Met	p.T277M	ENST00000265849	NM_000535.5	277	aCg/aTg	8/15	1	2	FACETS	0.251	0.188	0.325	0.251	0.188	0.325	SUBCLONAL	1	TRUE	1	0.48	2		267	299	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946176	13946176	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	105	423	0	ENST00000405192.2:c.920A>G	p.Gln307Arg	p.Q307R	ENST00000405192	NM_001163147.1	307	cAa/cGa	10/12	1	2	FACETS	0.911	0.821	1	0.911	0.821	1	CLONAL	1	TRUE	1	0.48	2		423	480	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971164	13971164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	26	258	0	ENST00000405192.2:c.765G>A	p.Met255Ile	p.M255I	ENST00000405192	NM_001163147.1	255	atG/atA	8/12	1	2	FACETS	0.358	0.283	0.442	0.358	0.283	0.442	SUBCLONAL	1	TRUE	1	0.48	2		258	303	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729652	41729652	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	48	486	0	ENST00000242208.4:c.877C>A	p.Leu293Ile	p.L293I	ENST00000242208	NM_002192.2	293	Ctc/Atc	3/3	1	2	FACETS	0.344	0.29	0.404	0.344	0.29	0.404	SUBCLONAL	1	TRUE	1	0.48	2		486	581	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730108	41730108	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	97	339	0	ENST00000242208.4:c.421T>G	p.Ser141Ala	p.S141A	ENST00000242208	NM_002192.2	141	Tcc/Gcc	3/3	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.48	2		339	397	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739838	41739838	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	108	420	0	ENST00000242208.4:c.135G>T	p.Lys45Asn	p.K45N	ENST00000242208	NM_002192.2	45	aaG/aaT	2/3	1	2	FACETS	0.904	0.815	0.997	0.904	0.815	0.997	CLONAL	1	TRUE	1	0.48	2		420	498	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459493	50459493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	53	246	0	ENST00000331340.3:c.782C>A	p.Ser261Tyr	p.S261Y	ENST00000331340	NM_006060.4	261	tCt/tAt	7/8	1	2	FACETS	0.679	0.583	0.784	0.679	0.583	0.784	SUBCLONAL	1	TRUE	1	0.48	2		246	325	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459563	50459563	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	30	197	0	ENST00000331340.3:c.850+2T>C		p.X284_splice	ENST00000331340	NM_006060.4	284			1	2	FACETS	0.539	0.436	0.653	0.539	0.436	0.653	SUBCLONAL	1	TRUE	1	0.48	2		197	232	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55087054	55087054	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	89	262	0	ENST00000275493.2:c.84G>T	p.Lys28Asn	p.K28N	ENST00000275493	NM_005228.3	28	aaG/aaT	1/28	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.48	2		262	329	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240678	55240678	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	182	625	0	ENST00000275493.2:c.1922C>A	p.Pro641His	p.P641H	ENST00000275493	NM_005228.3	641	cCt/cAt	17/28	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.48	2		625	742	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241659	55241659	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	159	584	0	ENST00000275493.2:c.2107C>A	p.Leu703Ile	p.L703I	ENST00000275493	NM_005228.3	703	Ctc/Atc	18/28	1	2	FACETS	0.93	0.855	1	0.93	0.855	1	CLONAL	1	TRUE	1	0.48	2		584	712	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335730	81335730	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	39	273	0	ENST00000222390.5:c.1630T>C	p.Tyr544His	p.Y544H	ENST00000222390	NM_000601.4	544	Tat/Cat	15/18	1	2	FACETS	0.829	0.695	0.975	0.829	0.695	0.975	CLONAL	1	TRUE	1	0.48	2		273	196	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92404119	92404119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761377867	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	39	299	0	ENST00000265734.4:c.260G>A	p.Arg87Gln	p.R87Q	ENST00000265734	NM_001259.6	87	cGa/cAa	3/8	1	2	FACETS	0.589	0.49	0.697	0.589	0.49	0.697	SUBCLONAL	1	TRUE	1	0.48	2		299	276	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845485	128845485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779548739	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	110	646	0	ENST00000249373.3:c.782G>A	p.Arg261His	p.R261H	ENST00000249373	NM_005631.4	261	cGc/cAc	4/12	1	2	FACETS	0.634	0.57	0.702	0.634	0.57	0.702	SUBCLONAL	1	TRUE	1	0.48	2		646	723	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506449	148506449	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	50	328	0	ENST00000320356.2:c.2063A>C	p.Lys688Thr	p.K688T	ENST00000320356	NM_004456.4	688	aAa/aCa	18/20	1	2	FACETS	0.692	0.591	0.802	0.692	0.591	0.802	SUBCLONAL	1	TRUE	1	0.48	2		328	301	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514990	148514990	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	49	343	0	ENST00000320356.2:c.1219G>T	p.Asp407Tyr	p.D407Y	ENST00000320356	NM_004456.4	407	Gat/Tat	10/20	1	2	FACETS	0.546	0.464	0.636	0.546	0.464	0.636	SUBCLONAL	1	TRUE	1	0.48	2		343	374	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523560	148523560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	43	145	1	ENST00000320356.2:c.893G>A	p.Arg298His	p.R298H	ENST00000320356	NM_004456.4	298	cGt/cAt	8/20	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.48	2		146	177	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151167659	151167659	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1368836455	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	78	253	0	ENST00000262187.5:c.460C>A	p.Gln154Lys	p.Q154K	ENST00000262187	NM_005614.3	154	Cag/Aag	7/8	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.48	2		253	279	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845874	151845874	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764548280	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	62	470	2	ENST00000262189.6:c.13138G>T	p.Asp4380Tyr	p.D4380Y	ENST00000262189	NM_170606.2	4380	Gat/Tat	52/59	1	2	FACETS	0.552	0.478	0.632	0.552	0.478	0.632	SUBCLONAL	1	TRUE	1	0.48	2		472	468	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860512	151860512	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	124	421	1	ENST00000262189.6:c.10150G>T	p.Glu3384Ter	p.E3384*	ENST00000262189	NM_170606.2	3384	Gaa/Taa	43/59	1	2	FACETS	0.994	0.903	1	0.994	0.903	1	CLONAL	1	TRUE	1	0.48	2		422	520	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860865	151860865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766514400	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	85	311	0	ENST00000262189.6:c.9797G>A	p.Arg3266Gln	p.R3266Q	ENST00000262189	NM_170606.2	3266	cGg/cAg	43/59	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.48	2		311	319	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880153	151880153	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs138819584	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	49	354	0	ENST00000262189.6:c.5171G>T	p.Ser1724Ile	p.S1724I	ENST00000262189	NM_170606.2	1724	aGc/aTc	35/59	1	2	FACETS	0.727	0.62	0.842	0.727	0.62	0.842	SUBCLONAL	1	TRUE	1	0.48	2		354	281	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891204	151891204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	33	357	0	ENST00000262189.6:c.4550G>A	p.Gly1517Glu	p.G1517E	ENST00000262189	NM_170606.2	1517	gGa/gAa	31/59	1	2	FACETS	0.338	0.275	0.409	0.338	0.275	0.409	SUBCLONAL	1	TRUE	1	0.48	2		357	407	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902232	151902232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559949839	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	83	305	0	ENST00000262189.6:c.3920C>T	p.Ser1307Phe	p.S1307F	ENST00000262189	NM_170606.2	1307	tCc/tTc	25/59	1	2	FACETS	0.991	0.882	1	0.991	0.882	1	CLONAL	1	TRUE	1	0.48	2		305	349	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945102	151945102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	24	295	0	ENST00000262189.6:c.2417C>T	p.Ser806Phe	p.S806F	ENST00000262189	NM_170606.2	806	tCc/tTc	14/59	1	2	FACETS	0.4	0.314	0.498	0.4	0.314	0.498	SUBCLONAL	1	TRUE	1	0.48	2		295	250	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945109	151945109	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	25	289	0	ENST00000262189.6:c.2410C>A	p.Leu804Ile	p.L804I	ENST00000262189	NM_170606.2	804	Ctt/Att	14/59	1	2	FACETS	0.44	0.348	0.544	0.44	0.348	0.544	SUBCLONAL	1	TRUE	1	0.48	2		289	237	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012410	152012410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	26	202	0	ENST00000262189.6:c.403G>A	p.Ala135Thr	p.A135T	ENST00000262189	NM_170606.2	135	Gct/Act	4/59	1	2	FACETS	0.595	0.475	0.73	0.595	0.475	0.73	SUBCLONAL	1	TRUE	1	0.48	2		202	182	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540300	23540300	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	150	488	1	ENST00000380871.4:c.103C>A	p.Leu35Met	p.L35M	ENST00000380871	NM_006167.3	35	Ctg/Atg	1/2	1	2	FACETS	0.974	0.893	1	0.974	0.893	1	CLONAL	1	TRUE	1	0.48	2		489	642	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540358	23540359	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	115	446	0	ENST00000380871.4:c.44_45insT	p.Glu15AspfsTer93	p.E15Dfs*93	ENST00000380871	NM_006167.3	15	gag/gaTg	1/2	1	2	FACETS	0.789	0.713	0.87	0.789	0.713	0.87	SUBCLONAL	1	TRUE	1	0.48	2		446	607	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133224	38133224	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	29	463	0	ENST00000317025.8:c.4249G>T	p.Glu1417Ter	p.E1417*	ENST00000317025	NM_023034.1	1417	Gaa/Taa	24/24	1	2	FACETS	0.218	0.174	0.268	0.218	0.174	0.268	SUBCLONAL	1	TRUE	1	0.48	2		463	554	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38135923	38135923	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	95	310	0	ENST00000317025.8:c.3768G>T	p.Glu1256Asp	p.E1256D	ENST00000317025	NM_023034.1	1256	gaG/gaT	22/24	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.48	2		310	365	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38184295	38184295	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	95	410	0	ENST00000317025.8:c.1661A>C	p.Lys554Thr	p.K554T	ENST00000317025	NM_023034.1	554	aAg/aCg	7/24	1	2	FACETS	0.91	0.815	1	0.91	0.815	1	CLONAL	1	TRUE	1	0.48	2		410	435	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187065	38187065	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	168	581	0	ENST00000317025.8:c.1412A>C	p.Lys471Thr	p.K471T	ENST00000317025	NM_023034.1	471	aAa/aCa	6/24	1	2	FACETS	0.96	0.885	1	0.96	0.885	1	CLONAL	1	TRUE	1	0.48	2		581	729	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38194933	38194933	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	130	425	0	ENST00000317025.8:c.800A>C	p.Lys267Thr	p.K267T	ENST00000317025	NM_023034.1	267	aAg/aCg	4/24	1	2	FACETS	0.99	0.902	1	0.99	0.902	1	CLONAL	1	TRUE	1	0.48	2		425	547	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205323	38205323	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	165	602	1	ENST00000317025.8:c.367G>T	p.Glu123Ter	p.E123*	ENST00000317025	NM_023034.1	123	Gaa/Taa	2/24	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.48	2		603	637	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56910911	56910911	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	93	381	0	ENST00000519728.1:c.1057G>A	p.Glu353Lys	p.E353K	ENST00000519728	NM_002350.3	353	Gag/Aag	11/13	1	2	FACETS	0.873	0.78	0.97	0.873	0.78	0.97	CLONAL	1	TRUE	1	0.48	2		381	444	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005921	69005921	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	51	451	0	ENST00000288368.4:c.2332G>T	p.Asp778Tyr	p.D778Y	ENST00000288368	NM_024870.2	778	Gat/Tat	21/40	1	2	FACETS	0.581	0.495	0.674	0.581	0.495	0.674	SUBCLONAL	1	TRUE	1	0.48	2		451	366	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978488	70978488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	79	346	0	ENST00000276594.2:c.1165C>T	p.Pro389Ser	p.P389S	ENST00000276594	NM_024504.3	389	Cca/Tca	5/8	1	2	FACETS	0.974	0.864	1	0.974	0.864	1	CLONAL	1	TRUE	1	0.48	2		346	338	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978658	70978658	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	110	530	1	ENST00000276594.2:c.995G>A	p.Arg332His	p.R332H	ENST00000276594	NM_024504.3	332	cGc/cAc	5/8	1	2	FACETS	0.854	0.77	0.942	0.854	0.77	0.942	CLONAL	1	TRUE	1	0.48	2		531	537	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981903	70981903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747860295	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	36	709	2	ENST00000276594.2:c.193G>A	p.Ala65Thr	p.A65T	ENST00000276594	NM_024504.3	65	Gcc/Acc	2/8	1	2	FACETS	0.228	0.187	0.275	0.228	0.187	0.275	SUBCLONAL	1	TRUE	1	0.48	2		711	657	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90949275	90949275	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	26	170	0	ENST00000265433.3:c.2213C>A	p.Ser738Tyr	p.S738Y	ENST00000265433	NM_002485.4	738	tCt/tAt	15/16	1	2	FACETS	0.681	0.545	0.834	0.681	0.545	0.834	SUBCLONAL	1	TRUE	1	0.48	2		170	159	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958490	90958490	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	77	278	0	ENST00000265433.3:c.1948C>A	p.Leu650Ile	p.L650I	ENST00000265433	NM_002485.4	650	Ctt/Att	13/16	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.48	2		278	284	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752646	128752646	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	20	184	0	ENST00000377970.2:c.807G>T	p.Glu269Asp	p.E269D	ENST00000377970	NM_002467.4	269	gaG/gaT	3/3	1	2	FACETS	0.352	0.269	0.447	0.352	0.269	0.447	SUBCLONAL	1	TRUE	1	0.48	2		184	237	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742557	145742557	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	161	671	0	ENST00000428558.2:c.231C>A	p.Cys77Ter	p.C77*	ENST00000428558	NM_004260.3	77	tgC/tgA	4/22	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.48	2		671	613	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054625	5054625	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	38	191	0	ENST00000381652.3:c.677G>T	p.Arg226Met	p.R226M	ENST00000381652	NM_004972.3	226	aGg/aTg	7/25	1	2	FACETS	0.825	0.689	0.972	0.825	0.689	0.972	CLONAL	1	TRUE	1	0.48	2		191	192	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054643	5054643	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	37	191	0	ENST00000381652.3:c.695G>T	p.Arg232Ile	p.R232I	ENST00000381652	NM_004972.3	232	aGa/aTa	7/25	1	2	FACETS	0.807	0.673	0.954	0.807	0.673	0.954	CLONAL	1	TRUE	1	0.48	2		191	191	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5055687	5055687	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1338813094	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	17	211	0	ENST00000381652.3:c.955G>A	p.Asp319Asn	p.D319N	ENST00000381652	NM_004972.3	319	Gat/Aat	8/25	1	2	FACETS	0.448	0.336	0.579	0.448	0.336	0.579	SUBCLONAL	1	TRUE	1	0.48	2		211	158	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5078311	5078311	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	33	254	0	ENST00000381652.3:c.1998A>C	p.Glu666Asp	p.E666D	ENST00000381652	NM_004972.3	666	gaA/gaC	16/25	1	2	FACETS	0.859	0.709	1	0.859	0.709	1	CLONAL	1	TRUE	1	0.48	2		254	160	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080614	5080614	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1414977743	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	39	283	0	ENST00000381652.3:c.2365G>T	p.Asp789Tyr	p.D789Y	ENST00000381652	NM_004972.3	789	Gat/Tat	18/25	1	2	FACETS	0.666	0.556	0.787	0.666	0.556	0.787	SUBCLONAL	1	TRUE	1	0.48	2		283	244	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126730	5126730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1437629509	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	44	334	0	ENST00000381652.3:c.3338G>A	p.Arg1113His	p.R1113H	ENST00000381652	NM_004972.3	1113	cGc/cAc	25/25	1	2	FACETS	0.641	0.541	0.751	0.641	0.541	0.751	SUBCLONAL	1	TRUE	1	0.48	2		334	286	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341701	8341701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766088715	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	52	349	0	ENST00000356435.5:c.4939G>A	p.Glu1647Lys	p.E1647K	ENST00000356435		1647	Gaa/Aaa	29/35	1	2	FACETS	0.815	0.699	0.939	0.815	0.699	0.939	CLONAL	1	TRUE	1	0.48	2		349	266	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341907	8341907	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753625198	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	49	312	0	ENST00000356435.5:c.4733C>T	p.Thr1578Ile	p.T1578I	ENST00000356435		1578	aCt/aTt	29/35	1	2	FACETS	0.869	0.743	1	0.869	0.743	1	CLONAL	1	TRUE	1	0.48	2		312	235	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389304	8389304	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	20	412	0	ENST00000356435.5:c.4314C>A	p.Asp1438Glu	p.D1438E	ENST00000356435		1438	gaC/gaA	26/35	1	2	FACETS	0.222	0.169	0.284	0.222	0.169	0.284	SUBCLONAL	1	TRUE	1	0.48	2		412	376	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486301	8486301	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	70	219	0	ENST00000356435.5:c.2516C>A	p.Ala839Asp	p.A839D	ENST00000356435		839	gCt/gAt	17/35	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.48	2		219	257	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507340	8507340	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	46	297	1	ENST00000356435.5:c.1638C>A	p.Asn546Lys	p.N546K	ENST00000356435		546	aaC/aaA	11/35	1	2	FACETS	0.856	0.728	0.993	0.856	0.728	0.993	CLONAL	1	TRUE	1	0.48	2		298	224	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507360	8507360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770164058	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	49	290	1	ENST00000356435.5:c.1618C>T	p.Arg540Cys	p.R540C	ENST00000356435		540	Cgt/Tgt	11/35	1	2	FACETS	0.851	0.727	0.983	0.851	0.727	0.983	CLONAL	1	TRUE	1	0.48	2		291	240	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636826	8636826	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1353675904	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	73	289	0	ENST00000356435.5:c.83G>A	p.Arg28Gln	p.R28Q	ENST00000356435		28	cGa/cAa	2/35	1	2	FACETS	0.694	0.61	0.785	0.694	0.61	0.785	SUBCLONAL	1	TRUE	1	0.48	2		289	438	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971105	21971105	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878853646	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	114	560	1	ENST00000304494.5:c.253G>A	p.Ala85Thr	p.A85T	ENST00000304494	NM_000077.4	85	Gct/Act	2/3	1	2	FACETS	0.652	0.587	0.72	0.652	0.587	0.72	SUBCLONAL	1	TRUE	1	0.48	2		561	729	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27190599	27190599	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	30	495	0	ENST00000380036.4:c.1400C>A	p.Ser467Tyr	p.S467Y	ENST00000380036	NM_000459.3	467	tCt/tAt	10/23	1	2	FACETS	0.263	0.211	0.321	0.263	0.211	0.321	SUBCLONAL	1	TRUE	1	0.48	2		495	476	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212743	27212743	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	128	530	0	ENST00000380036.4:c.2725A>C	p.Asn909His	p.N909H	ENST00000380036	NM_000459.3	909	Aac/Cac	17/23	1	2	FACETS	0.751	0.682	0.824	0.751	0.682	0.824	SUBCLONAL	1	TRUE	1	0.48	2		530	710	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336291	80336291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	62	255	1	ENST00000286548.4:c.1028C>T	p.Ala343Val	p.A343V	ENST00000286548	NM_002072.3	343	gCc/gTc	7/7	1	2	FACETS	0.647	0.561	0.74	0.647	0.561	0.74	SUBCLONAL	1	TRUE	1	0.48	2		256	399	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430538	80430538	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	17	430	0	ENST00000286548.4:c.470C>T	p.Thr157Ile	p.T157I	ENST00000286548	NM_002072.3	157	aCc/aTc	3/7	1	2	FACETS	0.213	0.158	0.278	0.213	0.158	0.278	SUBCLONAL	1	TRUE	1	0.48	2		430	333	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317073	87317073	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	89	311	0	ENST00000277120.3:c.213-1G>T		p.X71_splice	ENST00000277120		71			1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.48	2		311	362	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87366970	87366970	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	106	451	0	ENST00000277120.3:c.1366T>G	p.Leu456Val	p.L456V	ENST00000277120		456	Ttg/Gtg	12/19	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.48	2		451	438	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482282	87482282	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	32	441	0	ENST00000277120.3:c.1569G>T	p.Lys523Asn	p.K523N	ENST00000277120		523	aaG/aaT	14/19	1	2	FACETS	0.317	0.257	0.385	0.317	0.257	0.385	SUBCLONAL	1	TRUE	1	0.48	2		441	420	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570220	87570220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	28	388	0	ENST00000277120.3:c.1960C>A	p.Leu654Met	p.L654M	ENST00000277120		654	Ctg/Atg	17/19	1	2	FACETS	0.297	0.237	0.365	0.297	0.237	0.365	SUBCLONAL	1	TRUE	1	0.48	2		388	393	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636293	87636293	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	72	495	2	ENST00000277120.3:c.2458C>A	p.His820Asn	p.H820N	ENST00000277120		820	Cat/Aat	19/19	1	2	FACETS	0.533	0.466	0.605	0.533	0.466	0.605	SUBCLONAL	1	TRUE	1	0.48	2		497	563	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641149	93641149	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	80	386	0	ENST00000375746.1:c.1495A>C	p.Asn499His	p.N499H	ENST00000375746	NM_001174167.1	499	Aat/Cat	11/14	1	2	FACETS	0.693	0.612	0.779	0.693	0.612	0.779	SUBCLONAL	1	TRUE	1	0.48	2		386	481	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229575	98229575	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	62	315	0	ENST00000331920.6:c.2383T>A	p.Phe795Ile	p.F795I	ENST00000331920	NM_000264.3	795	Ttc/Atc	15/24	1	2	FACETS	0.773	0.672	0.882	0.773	0.672	0.882	SUBCLONAL	1	TRUE	1	0.48	2		315	334	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907037	101907037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	46	197	0	ENST00000374994.4:c.997G>A	p.Asp333Asn	p.D333N	ENST00000374994	NM_004612.2	333	Gat/Aat	6/9	1	2	FACETS	0.786	0.667	0.914	0.786	0.667	0.914	CLONAL	1	TRUE	1	0.48	2		197	244	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250031	110250031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747308187	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	199	680	0	ENST00000374672.4:c.644C>T	p.Pro215Leu	p.P215L	ENST00000374672	NM_004235.4	215	cCg/cTg	3/5	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.48	2		680	695	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759956	133759956	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564994914	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	197	655	0	ENST00000318560.5:c.2279C>T	p.Pro760Leu	p.P760L	ENST00000318560	NM_005157.4	760	cCg/cTg	11/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.48	2		655	769	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776996	135776996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	122	381	0	ENST00000298552.3:c.2482C>T	p.Leu828Phe	p.L828F	ENST00000298552	NM_001162426.1	828	Ctc/Ttc	19/23	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.48	2		381	478	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778000	135778000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	109	372	0	ENST00000298552.3:c.2383G>T	p.Glu795Ter	p.E795*	ENST00000298552	NM_001162426.1	795	Gaa/Taa	18/23	1	2	FACETS	0.962	0.869	1	0.962	0.869	1	CLONAL	1	TRUE	1	0.48	2		372	472	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781380	135781380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751125011	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	145	515	0	ENST00000298552.3:c.1585G>A	p.Ala529Thr	p.A529T	ENST00000298552	NM_001162426.1	529	Gcc/Acc	15/23	1	2	FACETS	0.914	0.836	0.995	0.914	0.836	0.995	CLONAL	1	TRUE	1	0.48	2		515	661	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787731	135787731	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151309813	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	143	378	0	ENST00000298552.3:c.851G>A	p.Arg284His	p.R284H	ENST00000298552	NM_001162426.1	284	cGc/cAc	9/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.48	2		378	489	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796804	135796804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223799508	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	46	231	0	ENST00000298552.3:c.683G>A	p.Arg228Gln	p.R228Q	ENST00000298552	NM_001162426.1	228	cGa/cAa	8/23	1	2	FACETS	0.988	0.843	1	0.988	0.843	1	CLONAL	1	TRUE	1	0.48	2		231	194	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798786	135798786	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	71	250	0	ENST00000298552.3:c.457G>T	p.Asp153Tyr	p.D153Y	ENST00000298552	NM_001162426.1	153	Gat/Tat	6/23	1	2	FACETS	0.922	0.811	1	0.922	0.811	1	CLONAL	1	TRUE	1	0.48	2		250	321	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391602	139391602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	235	798	0	ENST00000277541.6:c.6589C>T	p.Leu2197Phe	p.L2197F	ENST00000277541	NM_017617.3	2197	Ctc/Ttc	34/34	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.48	2		798	837	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396460	139396460	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1414106410	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	134	638	0	ENST00000277541.6:c.5465A>C	p.Lys1822Thr	p.K1822T	ENST00000277541	NM_017617.3	1822	aAg/aCg	29/34	1	2	FACETS	0.731	0.664	0.8	0.731	0.664	0.8	SUBCLONAL	1	TRUE	1	0.48	2		638	764	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139414004	139414004	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	165	503	0	ENST00000277541.6:c.756G>T	p.Gln252His	p.Q252H	ENST00000277541	NM_017617.3	252	caG/caT	5/34	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.48	2		503	662	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317531	1317531	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	31	413	0	ENST00000400841.2:c.534G>T	p.Glu178Asp	p.E178D	ENST00000400841		178	gaG/gaT	5/6	1	2	FACETS	0.236	0.19	0.288	0.236	0.19	0.288	SUBCLONAL	1	TRUE	1	0.48	2		413	548	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321319	1321319	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	128	440	1	ENST00000400841.2:c.436C>A	p.Leu146Ile	p.L146I	ENST00000400841		146	Ctc/Atc	4/6	1	2	FACETS	0.959	0.873	1	0.959	0.873	1	CLONAL	1	TRUE	1	0.48	2		441	556	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911630	39911630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754470140	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	147	476	0	ENST00000378444.4:c.5000C>T	p.Ser1667Leu	p.S1667L	ENST00000378444	NM_001123385.1	1667	tCg/tTg	15/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.48	2		476	497	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922303	39922303	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	71	317	0	ENST00000378444.4:c.3869C>A	p.Ser1290Tyr	p.S1290Y	ENST00000378444	NM_001123385.1	1290	tCt/tAt	9/15	1	2	FACETS	0.793	0.696	0.896	0.793	0.696	0.896	SUBCLONAL	1	TRUE	1	0.48	2		317	373	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932212	39932212	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	218	672	1	ENST00000378444.4:c.2387C>A	p.Thr796Asn	p.T796N	ENST00000378444	NM_001123385.1	796	aCt/aAt	4/15	1	2	FACETS	0.992	0.923	1	0.992	0.923	1	CLONAL	1	TRUE	1	0.48	2		673	916	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932732	39932732	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	204	633	0	ENST00000378444.4:c.1867G>T	p.Glu623Ter	p.E623*	ENST00000378444	NM_001123385.1	623	Gaa/Taa	4/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.48	2		633	798	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44920632	44920632	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	73	367	0	ENST00000377967.4:c.1393C>A	p.His465Asn	p.H465N	ENST00000377967	NM_021140.2	465	Cat/Aat	14/29	1	2	FACETS	0.818	0.719	0.922	0.818	0.719	0.922	CLONAL	1	TRUE	1	0.48	2		367	372	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044865	47044865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	199	778	0	ENST00000377604.3:c.2191G>A	p.Ala731Thr	p.A731T	ENST00000377604	NM_001204468.1	731	Gcc/Acc	20/24	1	2	FACETS	0.971	0.901	1	0.971	0.901	1	CLONAL	1	TRUE	1	0.48	2		778	854	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428417	47428417	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	134	488	0	ENST00000377045.4:c.1285G>T	p.Asp429Tyr	p.D429Y	ENST00000377045	NM_001654.4	429	Gat/Tat	12/16	1	2	FACETS	0.938	0.856	1	0.938	0.856	1	CLONAL	1	TRUE	1	0.48	2		488	595	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430809	47430809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	222	662	0	ENST00000377045.4:c.1774G>A	p.Asp592Asn	p.D592N	ENST00000377045	NM_001654.4	592	Gat/Aat	16/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.48	2		662	846	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247103	53247103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782434611	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	123	443	0	ENST00000375401.3:c.397C>T	p.Arg133Trp	p.R133W	ENST00000375401	NM_004187.3	133	Cgg/Tgg	4/26	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.48	2		443	503	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247506	53247506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1556853080	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	84	456	0	ENST00000375401.3:c.303G>T	p.Lys101Asn	p.K101N	ENST00000375401	NM_004187.3	101	aaG/aaT	3/26	1	2	FACETS	0.657	0.581	0.737	0.657	0.581	0.737	SUBCLONAL	1	TRUE	1	0.48	2		456	533	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410467	63410467	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	142	628	0	ENST00000330258.3:c.2700G>T	p.Glu900Asp	p.E900D	ENST00000330258	NM_152424.3	900	gaG/gaT	2/2	1	2	FACETS	0.945	0.864	1	0.945	0.864	1	CLONAL	1	TRUE	1	0.48	2		628	626	SUCCESS
AR	367	MSKCC	GRCh37	X	66942740	66942740	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852577	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	103	362	0	ENST00000374690.3:c.2521C>T	p.Arg841Cys	p.R841C	ENST00000374690	NM_000044.3	841	Cgt/Tgt	7/8	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.48	2		362	400	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345277	70345277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	98	474	0	ENST00000374080.3:c.2303G>A	p.Arg768His	p.R768H	ENST00000374080		768	cGc/cAc	16/45	1	2	FACETS	0.667	0.596	0.743	0.667	0.596	0.743	SUBCLONAL	1	TRUE	1	0.48	2		474	612	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346956	70346956	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	95	391	0	ENST00000374080.3:c.2823G>T	p.Gln941His	p.Q941H	ENST00000374080		941	caG/caT	20/45	1	2	FACETS	0.787	0.703	0.875	0.787	0.703	0.875	SUBCLONAL	1	TRUE	1	0.48	2		391	503	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356449	70356449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1224410841	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	175	512	0	ENST00000374080.3:c.5344C>T	p.Arg1782Cys	p.R1782C	ENST00000374080		1782	Cgc/Tgc	37/45	1	2	FACETS	0.999	0.922	1	0.999	0.922	1	CLONAL	1	TRUE	1	0.48	2		512	730	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356469	70356469	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	126	498	0	ENST00000374080.3:c.5364G>T	p.Lys1788Asn	p.K1788N	ENST00000374080		1788	aaG/aaT	37/45	1	2	FACETS	0.663	0.6	0.729	0.663	0.6	0.729	SUBCLONAL	1	TRUE	1	0.48	2		498	792	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763869	76763869	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	90	448	0	ENST00000373344.5:c.7439G>T	p.Arg2480Ile	p.R2480I	ENST00000373344	NM_000489.3	2480	aGa/aTa	35/35	1	2	FACETS	0.788	0.702	0.879	0.788	0.702	0.879	SUBCLONAL	1	TRUE	1	0.48	2		448	476	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855926	76855926	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	46	310	0	ENST00000373344.5:c.5674G>T	p.Asp1892Tyr	p.D1892Y	ENST00000373344	NM_000489.3	1892	Gac/Tac	23/35	1	2	FACETS	0.702	0.595	0.818	0.702	0.595	0.818	SUBCLONAL	1	TRUE	1	0.48	2		310	273	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891466	76891466	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	56	359	0	ENST00000373344.5:c.4639G>T	p.Glu1547Ter	p.E1547*	ENST00000373344	NM_000489.3	1547	Gaa/Taa	16/35	1	2	FACETS	0.592	0.509	0.682	0.592	0.509	0.682	SUBCLONAL	1	TRUE	1	0.48	2		359	394	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920208	76920208	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	34	348	0	ENST00000373344.5:c.3869G>T	p.Gly1290Val	p.G1290V	ENST00000373344	NM_000489.3	1290	gGa/gTa	11/35	1	2	FACETS	0.444	0.364	0.534	0.444	0.364	0.534	SUBCLONAL	1	TRUE	1	0.48	2		348	319	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937745	76937745	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	64	376	0	ENST00000373344.5:c.3003del	p.Val1002Ter	p.V1002*	ENST00000373344	NM_000489.3	1001	aaA/aa	9/35	1	2	FACETS	0.847	0.739	0.962	0.847	0.739	0.962	CLONAL	1	TRUE	1	0.48	2		376	315	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937896	76937896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	21	452	0	ENST00000373344.5:c.2852C>T	p.Thr951Ile	p.T951I	ENST00000373344	NM_000489.3	951	aCc/aTc	9/35	1	2	FACETS	0.222	0.17	0.282	0.222	0.17	0.282	SUBCLONAL	1	TRUE	1	0.48	2		452	394	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939766	76939766	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	68	426	0	ENST00000373344.5:c.982G>T	p.Glu328Ter	p.E328*	ENST00000373344	NM_000489.3	328	Gaa/Taa	9/35	1	2	FACETS	0.864	0.757	0.977	0.864	0.757	0.977	CLONAL	1	TRUE	1	0.48	2		426	328	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76949318	76949318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	25	303	0	ENST00000373344.5:c.479G>A	p.Arg160His	p.R160H	ENST00000373344	NM_000489.3	160	cGc/cAc	6/35	1	2	FACETS	0.354	0.279	0.44	0.354	0.279	0.44	SUBCLONAL	1	TRUE	1	0.48	2		303	294	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76949388	76949388	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	52	300	0	ENST00000373344.5:c.409G>T	p.Asp137Tyr	p.D137Y	ENST00000373344	NM_000489.3	137	Gac/Tac	6/35	1	2	FACETS	0.805	0.691	0.928	0.805	0.691	0.928	CLONAL	1	TRUE	1	0.48	2		300	269	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952145	76952145	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	32	330	0	ENST00000373344.5:c.290C>A	p.Pro97His	p.P97H	ENST00000373344	NM_000489.3	97	cCt/cAt	5/35	1	2	FACETS	0.431	0.351	0.522	0.431	0.351	0.522	SUBCLONAL	1	TRUE	1	0.48	2		330	309	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972715	76972715	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	46	269	0	ENST00000373344.5:c.26G>T	p.Ser9Ile	p.S9I	ENST00000373344	NM_000489.3	9	aGc/aTc	2/35	1	2	FACETS	0.718	0.609	0.836	0.718	0.609	0.836	SUBCLONAL	1	TRUE	1	0.48	2		269	267	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611909	100611909	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	28	454	0	ENST00000308731.7:c.1212C>A	p.Phe404Leu	p.F404L	ENST00000308731	NM_000061.2	404	ttC/ttA	14/19	1	2	FACETS	0.233	0.185	0.287	0.233	0.185	0.287	SUBCLONAL	1	TRUE	1	0.48	2		454	501	SUCCESS
BTK	695	MSKCC	GRCh37	X	100629546	100629546	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	32	461	1	ENST00000308731.7:c.218C>A	p.Pro73His	p.P73H	ENST00000308731	NM_000061.2	73	cCt/cAt	3/19	1	2	FACETS	0.337	0.273	0.408	0.337	0.273	0.408	SUBCLONAL	1	TRUE	1	0.48	2		462	396	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630242	100630242	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	93	267	0	ENST00000308731.7:c.31C>A	p.Leu11Met	p.L11M	ENST00000308731	NM_000061.2	11	Ctg/Atg	2/19	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.48	2		267	374	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019660	123019660	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	74	437	0	ENST00000355640.3:c.148G>T	p.Ala50Ser	p.A50S	ENST00000355640		50	Gca/Tca	2/7	1	2	FACETS	0.662	0.581	0.748	0.662	0.581	0.748	SUBCLONAL	1	TRUE	1	0.48	2		437	466	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020196	123020196	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	115	515	0	ENST00000355640.3:c.684C>A	p.Phe228Leu	p.F228L	ENST00000355640		228	ttC/ttA	2/7	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.48	2		515	472	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020224	123020224	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs111978474	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	89	493	0	ENST00000355640.3:c.712C>T	p.Arg238Ter	p.R238*	ENST00000355640		238	Cga/Tga	2/7	1	2	FACETS	0.898	0.801	1	0.898	0.801	1	CLONAL	1	TRUE	1	0.48	2		493	413	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123026591	123026591	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	81	386	0	ENST00000355640.3:c.1067C>A	p.Thr356Asn	p.T356N	ENST00000355640		356	aCt/aAt	5/7	1	2	FACETS	0.872	0.773	0.977	0.872	0.773	0.977	CLONAL	1	TRUE	1	0.48	2		386	387	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123040913	123040913	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	57	328	0	ENST00000355640.3:c.1376C>A	p.Ala459Asp	p.A459D	ENST00000355640		459	gCt/gAt	7/7	1	2	FACETS	0.83	0.718	0.951	0.83	0.718	0.951	CLONAL	1	TRUE	1	0.48	2		328	286	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205170	123205170	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	27	271	0	ENST00000218089.9:c.2530G>A	p.Ala844Thr	p.A844T	ENST00000218089	NM_001042749.1	844	Gca/Aca	25/35	1	2	FACETS	0.608	0.488	0.743	0.608	0.488	0.743	SUBCLONAL	1	TRUE	1	0.48	2		271	185	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215247	123215247	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	46	312	0	ENST00000218089.9:c.2793A>G	p.Ile931Met	p.I931M	ENST00000218089	NM_001042749.1	931	atA/atG	28/35	1	2	FACETS	0.792	0.673	0.921	0.792	0.673	0.921	CLONAL	1	TRUE	1	0.48	2		312	242	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217326	123217326	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	26	449	0	ENST00000218089.9:c.2980C>T	p.Pro994Ser	p.P994S	ENST00000218089	NM_001042749.1	994	Cct/Tct	29/35	1	2	FACETS	0.3	0.237	0.372	0.3	0.237	0.372	SUBCLONAL	1	TRUE	1	0.48	2		449	361	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217392	123217392	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	60	321	0	ENST00000218089.9:c.3046A>G	p.Arg1016Gly	p.R1016G	ENST00000218089	NM_001042749.1	1016	Aga/Gga	29/35	1	2	FACETS	0.94	0.818	1	0.94	0.818	1	CLONAL	1	TRUE	1	0.48	2		321	266	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224762	123224762	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	23	418	0	ENST00000218089.9:c.3526G>T	p.Glu1176Ter	p.E1176*	ENST00000218089	NM_001042749.1	1176	Gag/Tag	32/35	1	2	FACETS	0.255	0.198	0.321	0.255	0.198	0.321	SUBCLONAL	1	TRUE	1	0.48	2		418	376	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224771	123224771	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	90	403	0	ENST00000218089.9:c.3535G>T	p.Ala1179Ser	p.A1179S	ENST00000218089	NM_001042749.1	1179	Gca/Tca	32/35	1	2	FACETS	0.987	0.882	1	0.987	0.882	1	CLONAL	1	TRUE	1	0.48	2		403	380	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123234433	123234433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	47	270	0	ENST00000218089.9:c.3793G>A	p.Val1265Met	p.V1265M	ENST00000218089	NM_001042749.1	1265	Gtg/Atg	35/35	1	2	FACETS	0.874	0.745	1	0.874	0.745	1	CLONAL	1	TRUE	1	0.48	2		270	224	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504138	123504138	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	65	313	0	ENST00000371139.4:c.314A>C	p.Lys105Thr	p.K105T	ENST00000371139	NM_001114937.2	105	aAg/aCg	3/4	1	2	FACETS	0.903	0.789	1	0.903	0.789	1	CLONAL	1	TRUE	1	0.48	2		313	300	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858047	152858047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1432027234	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	136	450	1	ENST00000406277.2:c.568G>A	p.Ala190Thr	p.A190T	ENST00000406277	NM_152274.4	190	Gcc/Acc	6/7	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.48	2		451	521	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225537	225537	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	20	140	0	ENST00000264932.6:c.316G>T	p.Gly106Ter	p.G106*	ENST00000264932	NM_004168.2	106	Gga/Tga	4/15	1	2	FACETS	0.706	0.547	0.887	0.706	0.547	0.887	SUBCLONAL	1	TRUE	1	0.48	2		140	118	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197805	66197805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	25	244	0	ENST00000273854.3:c.2894G>A	p.Gly965Glu	p.G965E	ENST00000273854	NM_004439.5	965	gGg/gAg	17/18	1	2	FACETS	0.523	0.415	0.646	0.523	0.415	0.646	SUBCLONAL	1	TRUE	1	0.48	2		244	199	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026133	71026133	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs775136381	NA	P-0049135-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	189	282	0	ENST00000318789.4:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000318789	NM_032682.5	497	Cga/Tga	17/21	0.579916632343344	2	FACETS	0.899	0.847	0.951	0.899	0.847	0.951	CLONAL	2	TRUE	0	0.616179141758107	2		282	341	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0049243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	45	344	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	FALSE	1	0.32447416803256	2		344	262	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692922	89692922	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201044	NA	P-0049243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	33	559	0	ENST00000371953.3:c.406T>C	p.Cys136Arg	p.C136R	ENST00000371953	NM_000314.4	136	Tgt/Cgt	5/9	1	2	FACETS	0.64	0.522	0.771	0.64	0.522	0.771	SUBCLONAL	1	FALSE	1	0.32447416803256	2		559	318	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591246	67591265	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGGTGGTTGACTCAAAAAGG	AGGTGGTTGACTCAAAAAGG	-	novel	NA	P-0049243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	24	356	0	ENST00000274335.5:c.1746-2_1763del		p.X582_splice	ENST00000274335		582		13/15	1	2	FACETS	0.698	0.55	0.867	0.698	0.55	0.867	SUBCLONAL	1	FALSE	1	0.32447416803256	2		356	212	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230863	53230863	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	142	746	0	ENST00000375401.3:c.1930C>T	p.His644Tyr	p.H644Y	ENST00000375401	NM_004187.3	644	Cat/Tat	14/26	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.32447416803256	2		746	755	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0049249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	142	403	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.315827799884375	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.315827799884375	2		403	420	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431421	49431421	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	164	732	0	ENST00000301067.7:c.9718C>G	p.Leu3240Val	p.L3240V	ENST00000301067	NM_003482.3	3240	Ctg/Gtg	34/54	0.311805886458694	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.315827799884375	3		732	580	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73350141	73350141	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	59	483	0	ENST00000377767.4:c.744A>T	p.Gln248His	p.Q248H	ENST00000377767	NM_014953.3	248	caA/caT	5/21	0.315827799884375	3	FACETS	1	0.868	1	0.503	0.434	0.578	CLONAL	1	TRUE	1	0.315827799884375	3		483	430	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348059	89348059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1402377065	NA	P-0049249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	259	791	0	ENST00000301030.4:c.4891C>T	p.Arg1631Trp	p.R1631W	ENST00000301030	NM_001256183.1	1631	Cgg/Tgg	9/13	0.311805886458694	3	FACETS	0.849	0.798	0.9	1	0.991	1	CLONAL	3	TRUE	1	0.315827799884375	3		791	746	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207064	1207065	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1131690917	NA	P-0049249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	177	761	0	ENST00000326873.7:c.157dup	p.Asp53GlyfsTer110	p.D53Gfs*110	ENST00000326873	NM_000455.4	51	atg/atGg	1/10	0.315827799884375	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.315827799884375	2		761	538	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250861	10250861	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	203	792	1	ENST00000340748.4:c.3619C>A	p.Arg1207Ser	p.R1207S	ENST00000340748		1207	Cgc/Agc	32/40	0.315827799884375	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.315827799884375	2		793	565	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602746	10602746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	251	917	0	ENST00000171111.5:c.832C>T	p.Pro278Ser	p.P278S	ENST00000171111	NM_203500.1	278	Ccg/Tcg	3/6	0.315827799884375	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.315827799884375	2		917	756	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146592	185146592	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	72	620	0	ENST00000265026.3:c.223G>A	p.Asp75Asn	p.D75N	ENST00000265026	NM_004721.4	75	Gat/Aat	2/14	1	2	FACETS	0.993	0.871	1	0.993	0.871	1	CLONAL	1	TRUE	1	0.315827799884375	2		620	459	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215332	123215332	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	75	556	0	ENST00000218089.9:c.2879del	p.Gly960AspfsTer5	p.G960Dfs*5	ENST00000218089	NM_001042749.1	960	Gga/ga	28/35	0.305843811070147	3	FACETS	0.965	0.846	1	0.482	0.423	0.546	CLONAL	1	TRUE	1	0.315827799884375	3		556	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0049254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	247	751	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.544574380118685	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.544574380118685	1		751	573	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967046	18967048	+	inframe_deletion	In_Frame_Del	DEL	GTC	GTC	-	rs754213556	NA	P-0049254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	232	599	2	ENST00000262803.5:c.1764_1766del	p.Ser589del	p.S589del	ENST00000262803	NM_002911.3	587	ctGTCg/ctg	13/24	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.544574380118685	2		601	745	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526163	189526163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	49	610	0	ENST00000264731.3:c.427G>A	p.Val143Ile	p.V143I	ENST00000264731	NM_003722.4	143	Gtc/Atc	4/14	0.38015386433019	1	FACETS	0.174	0.147	0.204	0.174	0.147	0.204	SUBCLONAL	1	TRUE	0	0.544574380118685	1		610	752	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956221	55956221	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs767542615	NA	P-0049254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	67	479	1	ENST00000263923.4:c.3094C>T	p.Arg1032Ter	p.R1032*	ENST00000263923	NM_002253.2	1032	Cga/Tga	23/30	0.186366465952874	2	FACETS	0.82	0.719	0.928	0.41	0.359	0.464	INDETERMINATE	1	TRUE	0	0.544574380118685	2		480	300	SUCCESS
APC	324	MSKCC	GRCh37	5	112173268	112173269	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	23	190	0	ENST00000257430.4:c.1979dup	p.Asn660LysfsTer14	p.N660Kfs*14	ENST00000257430	NM_000038.5	659	-/A	16/16	1	2	FACETS	0.845	0.672	1	0.845	0.672	1	CLONAL	1	TRUE	1	0.544574380118685	2		190	100	SUCCESS
APC	324	MSKCC	GRCh37	5	112175214	112175216	+	frameshift_variant	Frame_Shift_Ins	INS	AAG	AAG	TAAA	novel	NA	P-0049254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	30	284	0	ENST00000257430.4:c.3923_3925delinsTAAA	p.Lys1308IlefsTer7	p.K1308Ifs*7	ENST00000257430	NM_000038.5	1308	aAAGaa/aTAAAaa	16/16	1	2	FACETS	0.75	0.612	0.9	0.75	0.612	0.9	SUBCLONAL	1	TRUE	1	0.544574380118685	2		284	147	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0049265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	141	396	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.563588178878531	5	FACETS	0.713	0.648	0.782	0.238	0.216	0.261	SUBCLONAL	1	TRUE	2	0.563588178878531	5		396	1295	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574548	64574548	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	265	666	0	ENST00000312049.6:c.847C>G	p.Leu283Val	p.L283V	ENST00000312049	NM_130799.2	283	Ctg/Gtg	6/10	1	2	FACETS	0.989	0.928	1	0.989	0.928	1	CLONAL	1	TRUE	1	0.563588178878531	2		666	951	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577507	7577507	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	216	571	0	ENST00000269305.4:c.774A>C	p.Glu258Asp	p.E258D	ENST00000269305	NM_001126112.2	258	gaA/gaC	7/11	0.563588178878531	1	FACETS	0.887	0.829	0.945	0.887	0.829	0.945	CLONAL	1	TRUE	0	0.563588178878531	1		571	621	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924233	11924280	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCTCCGGGGGCGGCAGCGGCAGCGGCACCCCCGGCCCCGTAGGGTC	CGGCTCCGGGGGCGGCAGCGGCAGCGGCACCCCCGGCCCCGTAGGGTC	A	novel	NA	P-0049265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	81	23	0	ENST00000353533.5:c.30_77delinsA	p.Gly11ProfsTer14	p.G11Pfs*14	ENST00000353533	NM_003010.3	10	ggCGGCTCCGGGGGCGGCAGCGGCAGCGGCACCCCCGGCCCCGTAGGGTCc/ggAc	1/11	0.563588178878531	1	FACETS	1	0.966	1	1	0.99	1	CLONAL	2	TRUE	0	0.563588178878531	1		23	99	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629071	14629071	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	146	381	0	ENST00000254322.2:c.91T>C	p.Tyr31His	p.Y31H	ENST00000254322	NM_006145.1	31	Tac/Cac	1/3	1	2	FACETS	0.987	0.906	1	0.987	0.906	1	CLONAL	1	TRUE	1	0.563588178878531	2		381	525	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033976	48033976	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	172	336	0	ENST00000234420.5:c.4060C>G	p.Leu1354Val	p.L1354V	ENST00000234420	NM_000179.2	1354	Ctg/Gtg	10/10	1	2	FACETS	0.986	0.912	1	0.986	0.912	1	CLONAL	1	TRUE	1	0.563588178878531	2		336	619	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028885	47028885	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049741-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	65	375	0	ENST00000377604.3:c.189G>T	p.Glu63Asp	p.E63D	ENST00000377604	NM_001204468.1	63	gaG/gaT	3/24	0.131623999797074	2	FACETS	1	0.972	1			1	INDETERMINATE	1	FALSE	NA	0.357037535814498	2		375	254	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049741-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	88	731	0	ENST00000269305.4:c.880del	p.Glu294SerfsTer51	p.E294Sfs*51	ENST00000269305	NM_001126112.2	294	Gag/ag	8/11	0.12382187162766	3	FACETS	0.782	0.692	0.878	0.391	0.346	0.439	INDETERMINATE	1	FALSE	1	0.357037535814498	3		731	743	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233158	69233159	+	stop_gained	Nonsense_Mutation	DNP	GA	GA	TT	novel	NA	P-0049741-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	49	451	0	ENST00000462284.1:c.1023_1024delinsTT	p.Lys342Ter	p.K342*	ENST00000462284	NM_002392.5	341	ggGAaa/ggTTaa	11/11	1	2	FACETS	0.549	0.465	0.641	0.549	0.465	0.641	SUBCLONAL	1	FALSE	1	0.357037535814498	2		451	500	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280229	142280229	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049741-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	55	454	0	ENST00000350721.4:c.1205T>C	p.Met402Thr	p.M402T	ENST00000350721	NM_001184.3	402	aTg/aCg	5/47	0.246274257057919	4	FACETS	0.762	0.651	0.882	0.381	0.325	0.441	SUBCLONAL	1	FALSE	2	0.357037535814498	4		454	549	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0049783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	29	495	0	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		495	309	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592358	29592358	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1085307819	NA	P-0049783-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	26	354	0	ENST00000356175.3:c.4772+1G>T		p.X1591_splice	ENST00000356175	NM_000267.3	1591			1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		354	440	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2218147	2218147	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762923537	NA	P-0049964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	30	597	0	ENST00000326181.6:c.209C>T	p.Pro70Leu	p.P70L	ENST00000326181	NM_032271.2	70	cCg/cTg	4/21	0.424590367479292	3	FACETS	0.381	0.308	0.465	0.191	0.154	0.233	SUBCLONAL	1	TRUE	1	0.652122756067348	3		597	320	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183873	10183873	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0050037-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	41	429	0	ENST00000256474.2:c.340+2T>A		p.X114_splice	ENST00000256474	NM_000551.3	114			1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.28	2		429	284	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104425	2104425	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs45444196	NA	P-0050037-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	59	691	0	ENST00000219476.3:c.465C>G	p.Tyr155Ter	p.Y155*	ENST00000219476	NM_000548.3	155	taC/taG	5/42	1	2	FACETS	0.949	0.819	1	0.949	0.819	1	CLONAL	1	TRUE	1	0.28	2		691	444	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0050045-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	62	318	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.833	0.721	0.953	0.833	0.721	0.953	CLONAL	1	TRUE	1	0.332461003671613	2		318	448	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405962	70405962	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140289196	NA	P-0050045-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	170	488	1	ENST00000373644.4:c.3476G>A	p.Arg1159Gln	p.R1159Q	ENST00000373644	NM_030625.2	1159	cGg/cAg	4/12	0.29012794803864	3	FACETS	0.856	0.789	0.924	0.856	0.789	0.924	CLONAL	2	TRUE	1	0.332461003671613	3		489	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578260	7578260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204041	NA	P-0050045-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	247	760	0	ENST00000269305.4:c.589G>A	p.Val197Met	p.V197M	ENST00000269305	NM_001126112.2	197	Gtg/Atg	6/11	0.275859825284344	2	FACETS	0.865	0.81	0.921	0.865	0.81	0.921	CLONAL	2	TRUE	0	0.332461003671613	2		760	859	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858492	9858492	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148669437	NA	P-0050045-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	121	552	1	ENST00000330684.3:c.2909G>A	p.Arg970Gln	p.R970Q	ENST00000330684	NM_001134407.1	970	cGg/cAg	13/13	0.116710242474378	3	FACETS	1	0.975	1	0.617	0.558	0.679	INDETERMINATE	1	TRUE	1	0.332461003671613	3		553	688	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085789	16085789	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050045-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	201	533	0	ENST00000281043.3:c.965G>A	p.Arg322Gln	p.R322Q	ENST00000281043	NM_005378.4	322	cGa/cAa	3/3	0.143532205662295	4	FACETS	1	0.947	1	1	0.947	1	INDETERMINATE	2	TRUE	2	0.332461003671613	4		533	787	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050045-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	64	244	0	ENST00000257430.4:c.3916G>C	p.Glu1306Gln	p.E1306Q	ENST00000257430	NM_000038.5	1306	Gaa/Caa	16/16	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.332461003671613	2		244	313	SUCCESS
APC	324	MSKCC	GRCh37	5	112175334	112175503	+	frameshift_variant	Frame_Shift_Del	DEL	GGCACAAAGCTGTTGAATTTTCTTCAGGAGCGAAATCTCCCTCCAAAAGTGGTGCTCAGACACCCAAAAGTCCACCTGAACACTATGTTCAGGAGACCCCACTCATGTTTAGCAGATGTACTTCTGTCAGTTCACTTGATAGTTTTGAGAGTCGTTCGATTGCCAGCTCC	GGCACAAAGCTGTTGAATTTTCTTCAGGAGCGAAATCTCCCTCCAAAAGTGGTGCTCAGACACCCAAAAGTCCACCTGAACACTATGTTCAGGAGACCCCACTCATGTTTAGCAGATGTACTTCTGTCAGTTCACTTGATAGTTTTGAGAGTCGTTCGATTGCCAGCTCC	-	novel	NA	P-0050045-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	67	230	0	ENST00000257430.4:c.4044_4213del	p.Arg1348SerfsTer4	p.R1348Sfs*4	ENST00000257430	NM_000038.5	1348	aGGCACAAAGCTGTTGAATTTTCTTCAGGAGCGAAATCTCCCTCCAAAAGTGGTGCTCAGACACCCAAAAGTCCACCTGAACACTATGTTCAGGAGACCCCACTCATGTTTAGCAGATGTACTTCTGTCAGTTCACTTGATAGTTTTGAGAGTCGTTCGATTGCCAGCTCC/a	16/16	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.332461003671613	2		230	360	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222727	53222727	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050045-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1341	92	939	2	ENST00000375401.3:c.4209G>A	p.Met1403Ile	p.M1403I	ENST00000375401	NM_004187.3	1403	atG/atA	25/26	0.170336784711172	4	FACETS	0.515	0.455	0.578	0.257	0.227	0.289	INDETERMINATE	1	TRUE	2	0.332461003671613	4		941	1433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0050147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	321	959	2	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	0.262461980862339	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	FALSE	0	0.27255551115669	3		961	836	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945008	31945008	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	84	821	0	ENST00000340398.3:c.93del	p.Ser32LeufsTer5	p.S32Lfs*5	ENST00000340398	NM_001013699.2	31	ccC/cc	1/1	0.27255551115669	6	FACETS	0.802	0.706	0.905	0.267	0.235	0.302	CLONAL	1	FALSE	3	0.27255551115669	6		821	1188	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050200-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	42	230	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.764	0.639	0.902	0.764	0.639	0.902	CLONAL	1	TRUE	1	0.29	2		230	379	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796547	42796547	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050200-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1364	117	918	0	ENST00000575354.2:c.3104C>A	p.Thr1035Lys	p.T1035K	ENST00000575354	NM_015125.3	1035	aCg/aAg	13/20	1	2	FACETS	0.545	0.489	0.604	0.545	0.489	0.604	SUBCLONAL	1	TRUE	1	0.29	2		918	1481	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526750	31526750	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050200-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	69	562	0	ENST00000344624.3:c.290C>G	p.Pro97Arg	p.P97R	ENST00000344624		97	cCa/cGa	2/33	1	2	FACETS	0.508	0.441	0.581	0.508	0.441	0.581	SUBCLONAL	1	TRUE	1	0.29	2		562	937	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786910	135786910	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0050200-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	103	403	0	ENST00000298552.3:c.959T>A	p.Leu320Ter	p.L320*	ENST00000298552	NM_001162426.1	320	tTa/tAa	10/23	0.3	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	0	0.29	1		403	598	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0050218-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	198	454	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.284827875815313	2	FACETS	0.84	0.782	0.899	0.84	0.782	0.899	CLONAL	2	FALSE	0	0.376114677641849	2		454	627	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0050218-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	123	507	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.334261146181961	4	FACETS	1	0.983	1	0.706	0.64	0.776	CLONAL	1	FALSE	2	0.376114677641849	4		507	637	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980609	70980609	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050222-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	370	648	1	ENST00000276594.2:c.768G>T	p.Met256Ile	p.M256I	ENST00000276594	NM_024504.3	256	atG/atT	4/8	1	2	FACETS	0.793	0.754	0.832	0.793	0.754	0.832	SUBCLONAL	1	TRUE	1	0.913462638244428	2		649	1022	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220446	1220447	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAACCTGCTGC	novel	NA	P-0050222-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1587	606	908	0	ENST00000326873.7:c.540_550dup	p.Leu184ArgfsTer107	p.L184Rfs*107	ENST00000326873	NM_000455.4	180	ggg/ggGAACCTGCTGCg	4/10	0.913462638244428	3	FACETS	0.881	0.845	0.918	0.441	0.422	0.459	CLONAL	1	TRUE	1	0.913462638244428	3		908	2193	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939053	48939053	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050222-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	156	337	0	ENST00000267163.4:c.888del	p.Phe296LeufsTer5	p.F296Lfs*5	ENST00000267163	NM_000321.2	295	aaT/aa	9/27	1	2	FACETS	0.936	0.869	1	0.936	0.869	1	CLONAL	1	TRUE	1	0.913462638244428	2		337	365	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940967	71940967	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0050222-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	639	813	1	ENST00000298229.2:c.844-1G>A		p.X282_splice	ENST00000298229	NM_001567.3	282			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.913462638244428	2		814	1395	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003414	42003415	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0050222-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	404	580	0	ENST00000219905.7:c.2954dup	p.Pro986SerfsTer5	p.P986Sfs*5	ENST00000219905	NM_001164273.1	984	cgc/cgCc	8/24	1	2	FACETS	0.913	0.872	0.954	0.913	0.872	0.954	CLONAL	1	TRUE	1	0.913462638244428	2		580	969	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038826	47038826	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050222-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	677	897	0	ENST00000377604.3:c.833C>A	p.Ala278Asp	p.A278D	ENST00000377604	NM_001204468.1	278	gCc/gAc	9/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.913462638244428	2		897	1440	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191469	10191469	+	splice_acceptor_variant	Splice_Site	DEL	A	A	-	novel	NA	P-0050228-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	52	344	0	ENST00000256474.2:c.464-2del		p.X155_splice	ENST00000256474	NM_000551.3	155			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		344	134	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0050262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	212	454	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.803	0.748	0.86	0.803	0.748	0.86	CLONAL	1	TRUE	1	0.677562662502393	2		454	779	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129632	47129632	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	145	391	0	ENST00000409792.3:c.5248C>T	p.Gln1750Ter	p.Q1750*	ENST00000409792	NM_014159.6	1750	Cag/Tag	10/21	0.632475910181832	3	FACETS	0.946	0.866	1	0.473	0.433	0.514	CLONAL	1	TRUE	1	0.677562662502393	3		391	606	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098859	47098859	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	566	647	1	ENST00000409792.3:c.6415C>T	p.Gln2139Ter	p.Q2139*	ENST00000409792	NM_014159.6	2139	Caa/Taa	15/21	0.632475910181832	3	FACETS	0.972	0.937	1	0.972	0.937	1	CLONAL	2	TRUE	1	0.677562662502393	3		648	1151	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931617	39931617	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	171	440	0	ENST00000378444.4:c.2982del	p.Glu994AspfsTer27	p.E994Dfs*27	ENST00000378444	NM_001123385.1	994	gaG/ga	4/15	1	2	FACETS	0.918	0.85	0.988	0.918	0.85	0.988	CLONAL	1	TRUE	1	0.677562662502393	2		440	550	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743988	41743988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776310618	NA	P-0050298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	145	694	0	ENST00000301178.4:c.923G>A	p.Arg308His	p.R308H	ENST00000301178	NM_021913.4	308	cGc/cAc	7/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.221128299967433	2		694	1103	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912489	50912495	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGAGGTG	AGAGGTG	-	novel	NA	P-0050298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	97	638	0	ENST00000440232.2:c.2005_2006+5del		p.X669_splice	ENST00000440232	NM_002691.3	669		16/27	1	2	FACETS	0.863	0.767	0.965	0.863	0.767	0.965	CLONAL	1	TRUE	1	0.221128299967433	2		638	1017	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342985	225342985	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	83	374	0	ENST00000264414.4:c.2107A>G	p.Ile703Val	p.I703V	ENST00000264414	NM_003590.4	703	Ata/Gta	15/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.221128299967433	2		374	635	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229618	98229618	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	54	293	0	ENST00000331920.6:c.2340T>G	p.Ile780Met	p.I780M	ENST00000331920	NM_000264.3	780	atT/atG	15/24	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.221128299967433	2		293	467	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0050465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	26	314	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.178447916061924	1	FACETS	1	0.796	1	1	0.796	1	CLONAL	1	TRUE	0	0.13	1		314	372	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577111	7577111	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs786202082	NA	P-0050465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	37	430	0	ENST00000269305.4:c.827C>G	p.Ala276Gly	p.A276G	ENST00000269305	NM_001126112.2	276	gCc/gGc	8/11	1	2	FACETS	0.963	0.793	1	0.963	0.793	1	CLONAL	1	TRUE	1	0.13	2		430	591	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692793	89692793	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786204927	NA	P-0050465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	10	211	0	ENST00000371953.3:c.277C>G	p.His93Asp	p.H93D	ENST00000371953	NM_000314.4	93	Cat/Gat	5/9	0.178447916061924	1	FACETS	0.501	0.338	0.707	0.501	0.338	0.707	SUBCLONAL	1	TRUE	0	0.13	1		211	287	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939141	36939141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757569036	NA	P-0050465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	38	600	0	ENST00000361632.4:c.568C>T	p.Arg190Cys	p.R190C	ENST00000361632		190	Cgc/Tgc	5/16	1	2	FACETS	0.82	0.676	0.982	0.82	0.676	0.982	CLONAL	1	TRUE	1	0.13	2		600	713	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128848611	128848611	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	19	0	0	ENST00000249373.3:c.1276C>G	p.Leu426Val	p.L426V	ENST00000249373	NM_005631.4	426	Ctg/Gtg	7/12	1	2	FACETS	0.469	0.354	0.605	0.469	0.354	0.605	SUBCLONAL	1	TRUE	1	0.13	2		0	623	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589574	67589600	+	inframe_deletion	In_Frame_Del	DEL	GGAAAAAATTACATGAATATAACACTC	GGAAAAAATTACATGAATATAACACTC	-	novel	NA	P-0050465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	27	153	0	ENST00000274335.5:c.1337_1363del	p.Gly446_Gln455delinsGlu	p.G446_Q455delinsE	ENST00000274335		446	gGGAAAAAATTACATGAATATAACACTCag/gag	10/15	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.13	2		153	307	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636739	176636739	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1485814265	NA	P-0050465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	28	299	0	ENST00000439151.2:c.1339A>G	p.Ile447Val	p.I447V	ENST00000439151	NM_022455.4	447	Atc/Gtc	5/23	0.3	3	FACETS	0.948	0.756	1			1	CLONAL	1	TRUE	NA	0.13	3		299	484	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0050471-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	182	726	0	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.228795489654494	2	FACETS	0.943	0.872	1	0.943	0.872	1	CLONAL	2	TRUE	0	0.251669611188321	2		726	767	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0050471-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	265	637	0	ENST00000269305.4:c.560-1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.23802692040648	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	3	TRUE	0	0.251669611188321	3		637	776	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667552	29667552	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050471-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	90	595	0	ENST00000356175.3:c.6888G>A	p.Trp2296Ter	p.W2296*	ENST00000356175	NM_000267.3	2296	tgG/tgA	46/57	0.201047142113255	3	FACETS	1	0.917	1	0.521	0.462	0.584	CLONAL	1	TRUE	1	0.251669611188321	3		595	773	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750842	57750842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050471-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	46	385	0	ENST00000274289.3:c.1762G>T	p.Asp588Tyr	p.D588Y	ENST00000274289	NM_006622.3	588	Gat/Tat	13/14	1	2	FACETS	0.837	0.705	0.981	0.837	0.705	0.981	CLONAL	1	TRUE	1	0.251669611188321	2		385	437	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597400	10597401	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0050471-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	172	766	0	ENST00000171111.5:c.1802_1803delinsTT	p.Arg601Leu	p.R601L	ENST00000171111	NM_203500.1	601	cGG/cTT	6/6	0.228795489654494	2	FACETS	0.865	0.797	0.936	0.865	0.797	0.936	CLONAL	2	TRUE	0	0.251669611188321	2		766	790	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935703	13935703	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050471-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	103	473	0	ENST00000405192.2:c.1153G>T	p.Glu385Ter	p.E385*	ENST00000405192	NM_001163147.1	385	Gag/Tag	12/12	0.251669611188321	3	FACETS	0.817	0.733	0.905	0.817	0.733	0.905	CLONAL	2	TRUE	1	0.251669611188321	3		473	564	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100186	27100186	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050471-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	132	524	1	ENST00000324856.7:c.3982C>T	p.Gln1328Ter	p.Q1328*	ENST00000324856	NM_006015.4	1328	Cag/Tag	16/20	0.201047142113255	3	FACETS	0.881	0.802	0.965	0.881	0.802	0.965	CLONAL	2	TRUE	1	0.251669611188321	3		525	670	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000057	30000057	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050473-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	154	483	0	ENST00000338641.4:c.70del	p.Val24Ter	p.V24*	ENST00000338641	NM_000268.3	24	Gtg/tg	1/16	0.621481912391796	1	FACETS	0.899	0.833	0.966	0.899	0.833	0.966	CLONAL	1	TRUE	0	0.621481912391796	1		483	380	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115813	8115847	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAACAGCTCGTTTAACCCGGCCGCCCTCTCCAG	AAGAACAGCTCGTTTAACCCGGCCGCCCTCTCCAG	-	novel	NA	P-0050519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	82	513	0	ENST00000346208.3:c.1160_1194del	p.Lys387ThrfsTer108	p.K387Tfs*108	ENST00000346208		387	AAGAACAGCTCGTTTAACCCGGCCGCCCTCTCCAGa/a	6/6	0.374917677705268	3	FACETS	0.775	0.684	0.873	0.388	0.342	0.437	SUBCLONAL	1	TRUE	1	0.374917677705268	3		513	670	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913351	NA	P-0050520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	150	285	0	ENST00000288602.6:c.1397G>C	p.Gly466Ala	p.G466A	ENST00000288602	NM_004333.4	466	gGa/gCa	11/18	1	2	FACETS	0.964	0.885	1	0.964	0.885	1	CLONAL	1	TRUE	1	0.531127285358348	2		285	586	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562772	29562772	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	206	323	0	ENST00000356175.3:c.3853del	p.Met1285Ter	p.M1285*	ENST00000356175	NM_000267.3	1284	atA/at	28/57	0.531127285358348	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.531127285358348	1		323	549	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30060992	30060998	+	frameshift_variant	Frame_Shift_Del	DEL	CACTGGA	CACTGGA	-	novel	NA	P-0050520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	35	342	0	ENST00000338641.4:c.824_830del	p.Pro275LeufsTer19	p.P275Lfs*19	ENST00000338641	NM_000268.3	275	cCACTGGAt/ct	9/16	0.531127285358348	1	FACETS	0.189	0.155	0.228	0.189	0.155	0.228	SUBCLONAL	1	TRUE	0	0.531127285358348	1		342	511	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606305	93606305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408106520	NA	P-0050520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	292	626	1	ENST00000375746.1:c.125G>A	p.Arg42His	p.R42H	ENST00000375746	NM_001174167.1	42	cGc/cAc	2/14	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.531127285358348	2		627	1046	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005143	150005143	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050570-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	144	415	0	ENST00000253339.5:c.1082del	p.Asn361MetfsTer8	p.N361Mfs*8	ENST00000253339		361	aAt/at	3/7	1	2	FACETS	0.93	0.854	1	0.93	0.854	1	CLONAL	1	TRUE	1	0.633399174344606	2		415	489	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135777067	135777086	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CTGCAGTCCTCCAGCTTCGT	CTGCAGTCCTCCAGCTTCGT	-	novel	NA	P-0050570-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	130	378	0	ENST00000298552.3:c.2392_2411del	p.Thr798GlufsTer21	p.T798Efs*21	ENST00000298552	NM_001162426.1	798	ACGAAGCTGGAGGACTGCAGg/g	19/23	0.633399174344606	1	FACETS	0.79	0.725	0.856	0.79	0.725	0.856	SUBCLONAL	1	TRUE	0	0.633399174344606	1		378	355	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696430	47696430	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519970	NA	P-0050572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	48	498	0	ENST00000347630.2:c.393G>T	p.Trp131Cys	p.W131C	ENST00000347630	NM_001007230.1	131	tgG/tgT	6/11	1	2	FACETS	0.926	0.782	1	0.926	0.782	1	CLONAL	1	TRUE	1	0.18	2		498	576	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165570	47165571	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0050572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	60	557	0	ENST00000409792.3:c.555dup	p.Pro186ThrfsTer51	p.P186Tfs*51	ENST00000409792	NM_014159.6	185	-/A	3/21	1	2	FACETS	0.947	0.815	1	0.947	0.815	1	CLONAL	1	TRUE	1	0.18	2		557	704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0050582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	232	513	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.577754239254895	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.577754239254895	1		513	502	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042006	14042006	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	120	313	0	ENST00000311895.7:c.2553C>A	p.Phe851Leu	p.F851L	ENST00000311895	NM_005236.2	851	ttC/ttA	11/11	0.240916938990421	2	FACETS	1	0.979	1	0.618	0.565	0.673	INDETERMINATE	1	TRUE	0	0.577754239254895	2		313	336	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802567	139802567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138185376	NA	P-0050582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	513	665	0	ENST00000247668.2:c.412G>A	p.Ala138Thr	p.A138T	ENST00000247668	NM_021138.3	138	Gcg/Acg	5/11	0.577754239254895	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.577754239254895	2		665	875	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098806	178098806	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1553487947	NA	P-0050582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	81	490	0	ENST00000397062.3:c.239C>A	p.Thr80Lys	p.T80K	ENST00000397062	NM_006164.4	80	aCa/aAa	2/5	1	2	FACETS	0.74	0.656	0.829	0.74	0.656	0.829	SUBCLONAL	1	TRUE	1	0.577754239254895	2		490	379	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510305	187510305	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs758757364	NA	P-0050582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	54	302	0	ENST00000441802.2:c.13208A>G	p.Tyr4403Cys	p.Y4403C	ENST00000441802	NM_005245.3	4403	tAt/tGt	27/27	0.240916938990421	2	FACETS	0.647	0.556	0.744	0.323	0.278	0.372	INDETERMINATE	1	TRUE	0	0.577754239254895	2		302	289	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132602	11132602	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	317	652	0	ENST00000358026.2:c.2818G>T	p.Glu940Ter	p.E940*	ENST00000358026	NM_001128849.1	940	Gag/Tag	19/36	0.577754239254895	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.577754239254895	1		652	689	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422191	81422191	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	77	429	0	ENST00000298171.2:c.167C>G	p.Thr56Ser	p.T56S	ENST00000298171	NM_000369.2	56	aCt/aGt	1/10	0.488124523819932	1	FACETS	0.549	0.486	0.617	0.549	0.486	0.617	SUBCLONAL	1	TRUE	0	0.577754239254895	1		429	345	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670265	134670265	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	163	371	0	ENST00000398015.3:c.176A>G	p.Gln59Arg	p.Q59R	ENST00000398015	NM_004441.4	59	cAg/cGg	3/16	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.577754239254895	2		371	403	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628934	187628934	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	72	465	0	ENST00000441802.2:c.2048T>A	p.Leu683Gln	p.L683Q	ENST00000441802	NM_005245.3	683	cTg/cAg	2/27	0.240916938990421	2	FACETS	0.629	0.553	0.711	0.315	0.276	0.356	INDETERMINATE	1	TRUE	0	0.577754239254895	2		465	396	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163818	152163818	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	53	356	0	ENST00000206249.3:c.539A>T	p.Lys180Met	p.K180M	ENST00000206249	NM_000125.3	180	aAg/aTg	2/8	1	2	FACETS	0.556	0.476	0.642	0.556	0.476	0.642	SUBCLONAL	1	TRUE	1	0.577754239254895	2		356	330	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	127	299	0				ENST00000310581	NM_198253.2	-/1132			0.385528285138775	1	FACETS	0.852	0.788	0.917	0.852	0.788	0.917	INDETERMINATE	1	TRUE	0	0.721535822188701	1		299	264	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	182	448	1	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	NA	2	FACETS	1	0.948	1			1	INDETERMINATE	1	TRUE	NA	0.721535822188701	2		449	494	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266713	198266713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776846119	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	122	415	1	ENST00000335508.6:c.2219G>A	p.Gly740Glu	p.G740E	ENST00000335508	NM_012433.2	740	gGa/gAa	15/25	1	2	FACETS	0.907	0.828	0.988	0.907	0.828	0.988	CLONAL	1	TRUE	1	0.721535822188701	2		416	373	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528489	29528489	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764079291	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	76	410	0	ENST00000356175.3:c.1246C>T	p.Arg416Ter	p.R416*	ENST00000356175	NM_000267.3	416	Cga/Tga	11/57	0.171494991316465	3	FACETS	1	0.973	1	0.657	0.587	0.731	INDETERMINATE	1	TRUE	1	0.721535822188701	3		410	218	SUCCESS
APC	324	MSKCC	GRCh37	5	112177901	112177901	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs752654519	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	217	356	0	ENST00000257430.4:c.6610C>T	p.Arg2204Ter	p.R2204*	ENST00000257430	NM_000038.5	2204	Cga/Tga	16/16	0.721535822188701	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.721535822188701	2		356	280	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991721	72991721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370398587	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	196	239	0	ENST00000268489.5:c.2324C>T	p.Ala775Val	p.A775V	ENST00000268489	NM_006885.3	775	gCg/gTg	2/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.721535822188701	2		239	404	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972909	55972909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	105	490	0	ENST00000263923.4:c.1481G>A	p.Gly494Glu	p.G494E	ENST00000263923	NM_002253.2	494	gGa/gAa	11/30	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.721535822188701	2		490	278	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624595	93624595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	202	585	0	ENST00000375746.1:c.686C>T	p.Pro229Leu	p.P229L	ENST00000375746	NM_001174167.1	229	cCc/cTc	4/14	1	2	FACETS	0.902	0.841	0.964	0.902	0.841	0.964	CLONAL	1	TRUE	1	0.721535822188701	2		585	621	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214404	55214404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770290445	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	220	619	0	ENST00000275493.2:c.530C>T	p.Ser177Leu	p.S177L	ENST00000275493	NM_005228.3	177	tCg/tTg	4/28	1	2	FACETS	0.962	0.9	1	0.962	0.9	1	CLONAL	1	TRUE	1	0.721535822188701	2		619	634	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381466	81381466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	138	293	0	ENST00000222390.5:c.595G>A	p.Glu199Lys	p.E199K	ENST00000222390	NM_000601.4	199	Gaa/Aaa	5/18	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.721535822188701	2		293	348	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955046	93955046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141581954	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	59	264	0	ENST00000369303.4:c.2852C>T	p.Ser951Phe	p.S951F	ENST00000369303	NM_004440.3	951	tCc/tTc	16/17	0.721535822188701	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.721535822188701	1		264	91	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993833	72993833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374747520	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	234	663	1	ENST00000268489.5:c.212C>T	p.Pro71Leu	p.P71L	ENST00000268489	NM_006885.3	71	cCc/cTc	2/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.721535822188701	2		664	637	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78931513	78931513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750857501	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	237	612	0	ENST00000306801.3:c.3460C>T	p.Arg1154Cys	p.R1154C	ENST00000306801	NM_020761.2	1154	Cgt/Tgt	29/34	NA	2	FACETS	0.916	0.859	0.975			1	INDETERMINATE	1	TRUE	NA	0.721535822188701	2		612	717	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556397	29556397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1135402831	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	152	563	0	ENST00000356175.3:c.2764G>A	p.Gly922Ser	p.G922S	ENST00000356175	NM_000267.3	922	Ggt/Agt	21/57	0.171494991316465	3	FACETS	1	0.984	1	0.629	0.58	0.679	INDETERMINATE	1	TRUE	1	0.721535822188701	3		563	456	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518768	176518768	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781285001	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	643	828	1	ENST00000292408.4:c.686C>T	p.Ala229Val	p.A229V	ENST00000292408	NM_213647.1	229	gCt/gTt	6/18	0.721535822188701	2	FACETS	0.944	0.919	0.969	0.944	0.919	0.969	CLONAL	2	TRUE	0	0.721535822188701	2		829	944	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121329	29121329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	156	638	0	ENST00000328354.6:c.346G>A	p.Gly116Arg	p.G116R	ENST00000328354	NM_007194.3	116	Ggg/Agg	3/15	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.721535822188701	2		638	388	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518073	8518073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1480778931	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	177	436	0	ENST00000356435.5:c.1318G>A	p.Glu440Lys	p.E440K	ENST00000356435		440	Gaa/Aaa	10/35	0.721535822188701	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.721535822188701	1		436	299	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102196	27102196	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	160	360	0	ENST00000324856.7:c.5122C>T	p.Gln1708Ter	p.Q1708*	ENST00000324856	NM_006015.4	1708	Cag/Tag	19/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.721535822188701	2		360	427	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656272	18656272	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	127	490	1	ENST00000266497.5:c.2951G>A	p.Gly984Glu	p.G984E	ENST00000266497		984	gGa/gAa	21/31	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.721535822188701	2		491	317	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406072	70406072	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	140	580	0	ENST00000373644.4:c.3586C>T	p.Gln1196Ter	p.Q1196*	ENST00000373644	NM_030625.2	1196	Caa/Taa	4/12	1	2	FACETS	0.98	0.902	1	0.98	0.902	1	CLONAL	1	TRUE	1	0.721535822188701	2		580	396	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517885	187517885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1222913841	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	177	535	0	ENST00000441802.2:c.12809G>A	p.Arg4270Gln	p.R4270Q	ENST00000441802	NM_005245.3	4270	cGa/cAa	25/27	1	2	FACETS	0.933	0.866	1	0.933	0.866	1	CLONAL	1	TRUE	1	0.721535822188701	2		535	526	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552243	29552243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151138158	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	91	482	1	ENST00000356175.3:c.1976G>A	p.Arg659Gln	p.R659Q	ENST00000356175	NM_000267.3	659	cGg/cAg	17/57	0.171494991316465	3	FACETS	1	0.959	1	0.568	0.51	0.628	INDETERMINATE	1	TRUE	1	0.721535822188701	3		483	302	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989026	85989026	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	54	289	0	ENST00000263360.6:c.1192A>T	p.Lys398Ter	p.K398*	ENST00000263360	NM_003797.3	398	Aaa/Taa	11/12	1	2	FACETS	0.953	0.832	1	0.953	0.832	1	CLONAL	1	TRUE	1	0.721535822188701	2		289	157	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133912	41133912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	206	479	0	ENST00000379561.5:c.1716G>A	p.Met572Ile	p.M572I	ENST00000379561	NM_002015.3	572	atG/atA	2/3	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.721535822188701	2		479	569	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582912	95582912	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852979	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	85	364	0	ENST00000393063.1:c.1630C>T	p.Arg544Ter	p.R544*	ENST00000393063	NM_030621.3	544	Cga/Tga	11/28	1	2	FACETS	0.879	0.788	0.974	0.879	0.788	0.974	CLONAL	1	TRUE	1	0.721535822188701	2		364	268	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019469	42019470	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	173	595	0	ENST00000219905.7:c.3522_3523delinsTT	p.Pro1175Ser	p.P1175S	ENST00000219905	NM_001164273.1	1174	atCCcc/atTTcc	10/24	0.721535822188701	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.721535822188701	1		595	271	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652282	3652282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	259	705	0	ENST00000294008.3:c.787G>A	p.Glu263Lys	p.E263K	ENST00000294008	NM_032444.2	263	Gag/Aag	4/15	NA	2	FACETS	0.942	0.886	0.999			1	INDETERMINATE	1	TRUE	NA	0.721535822188701	2		705	762	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371752	89371752	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs781056489	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	186	424	0	ENST00000301030.4:c.88G>A	p.Asp30Asn	p.D30N	ENST00000301030	NM_001256183.1	30	Gat/Aat	4/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.721535822188701	2		424	487	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37680934	37680934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	143	419	0	ENST00000447079.4:c.3103C>T	p.His1035Tyr	p.H1035Y	ENST00000447079	NM_015083.1	1035	Cac/Tac	12/14	1	2	FACETS	0.96	0.884	1	0.96	0.884	1	CLONAL	1	TRUE	1	0.721535822188701	2		419	413	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216313	2216313	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	249	805	0	ENST00000398665.3:c.1957C>G	p.Gln653Glu	p.Q653E	ENST00000398665	NM_032482.2	653	Cag/Gag	20/28	1	2	FACETS	0.917	0.861	0.974	0.917	0.861	0.974	CLONAL	1	TRUE	1	0.721535822188701	2		805	753	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291119	10291120	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	258	768	2	ENST00000340748.4:c.351_352delinsTT	p.Arg118Cys	p.R118C	ENST00000340748		117	gcCCgt/gcTTgt	4/40	1	2	FACETS	0.936	0.88	0.993	0.936	0.88	0.993	CLONAL	1	TRUE	1	0.721535822188701	2		770	764	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366386	15366386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1238456472	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	191	559	0	ENST00000263377.2:c.1769C>T	p.Pro590Leu	p.P590L	ENST00000263377	NM_058243.2	590	cCc/cTc	10/20	1	2	FACETS	0.952	0.887	1	0.952	0.887	1	CLONAL	1	TRUE	1	0.721535822188701	2		559	556	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18963010	18963010	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568276400	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	323	917	0	ENST00000262803.5:c.877C>T	p.Leu293Phe	p.L293F	ENST00000262803	NM_002911.3	293	Ctc/Ttc	6/24	1	2	FACETS	0.957	0.906	1	0.957	0.906	1	CLONAL	1	TRUE	1	0.721535822188701	2		917	936	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221241	36221241	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	269	701	2	ENST00000222270.7:c.5077-2A>C		p.X1693_splice	ENST00000222270	NM_014727.1	1693			1	2	FACETS	0.997	0.94	1	0.997	0.94	1	CLONAL	1	TRUE	1	0.721535822188701	2		703	748	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754582	42754583	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	293	871	1	ENST00000222329.4:c.157_158delinsAA	p.Gly53Lys	p.G53K	ENST00000222329	NM_006494.2	53	GGg/AAg	2/4	1	2	FACETS	0.992	0.937	1	0.992	0.937	1	CLONAL	1	TRUE	1	0.721535822188701	2		872	819	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25536840	25536841	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	299	771	2	ENST00000264709.3:c.13_14delinsTT	p.Pro5Phe	p.P5F	ENST00000264709	NM_175629.2	5	CCc/TTc	2/23	1	2	FACETS	0.965	0.912	1	0.965	0.912	1	CLONAL	1	TRUE	1	0.721535822188701	2		773	859	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972978	25972978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	166	376	0	ENST00000435504.4:c.1447C>T	p.Pro483Ser	p.P483S	ENST00000435504		483	Cca/Tca	12/13	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.721535822188701	2		376	455	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445382	29445382	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	296	748	3	ENST00000389048.3:c.3450+1G>A		p.X1150_splice	ENST00000389048	NM_004304.4	1150			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.721535822188701	2		751	817	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546571	9546571	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	179	492	0	ENST00000353224.5:c.1451A>G	p.Lys484Arg	p.K484R	ENST00000353224	NM_177990.2	484	aAg/aGg	5/10	1	2	FACETS	0.943	0.876	1	0.943	0.876	1	CLONAL	1	TRUE	1	0.721535822188701	2		492	526	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252959	36252959	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	170	409	0	ENST00000300305.3:c.403G>T	p.Gly135Cys	p.G135C	ENST00000300305		135	Ggc/Tgc	4/8	1	2	FACETS	0.994	0.923	1	0.994	0.923	1	CLONAL	1	TRUE	1	0.721535822188701	2		409	474	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162410	47162410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	148	395	0	ENST00000409792.3:c.3716C>T	p.Ser1239Phe	p.S1239F	ENST00000409792	NM_014159.6	1239	tCc/tTc	3/21	1	2	FACETS	0.954	0.88	1	0.954	0.88	1	CLONAL	1	TRUE	1	0.721535822188701	2		395	430	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014341	70014341	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	268	560	0	ENST00000394351.3:c.1202C>T	p.Ser401Phe	p.S401F	ENST00000394351	NM_000248.3	401	tCc/tTc	9/9	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.721535822188701	2		560	684	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428263	72428264	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	128	486	0	ENST00000477973.2:c.626_627delinsTT	p.Pro210Phe	p.P210F	ENST00000477973	NM_012234.5	210	CCt/TTt	3/4	1	2	FACETS	0.951	0.872	1	0.951	0.872	1	CLONAL	1	TRUE	1	0.721535822188701	2		486	373	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181957	32181958	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	286	752	1	ENST00000375023.3:c.2096_2097delinsTT	p.Pro699Leu	p.P699L	ENST00000375023	NM_004557.3	699	cCC/cTT	13/30	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.721535822188701	2		753	751	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813375	32813375	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	336	840	0	ENST00000354258.4:c.2408C>T	p.Pro803Leu	p.P803L	ENST00000354258	NM_000593.5	803	cCt/cTt	11/11	1	2	FACETS	0.961	0.911	1	0.961	0.911	1	CLONAL	1	TRUE	1	0.721535822188701	2		840	969	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845556	128845557	+	missense_variant	Missense_Mutation	DNP	TT	TT	CA	novel	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	291	680	1	ENST00000249373.3:c.853_854delinsCA	p.Phe285His	p.F285H	ENST00000249373	NM_005631.4	285	TTc/CAc	4/12	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.721535822188701	2		681	790	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880106	151880106	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	95	474	0	ENST00000262189.6:c.5218T>A	p.Leu1740Ile	p.L1740I	ENST00000262189	NM_170606.2	1740	Tta/Ata	35/59	1	2	FACETS	0.961	0.868	1	0.961	0.868	1	CLONAL	1	TRUE	1	0.721535822188701	2		474	274	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38178649	38178649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	54	440	0	ENST00000317025.8:c.1750C>T	p.Arg584Cys	p.R584C	ENST00000317025	NM_023034.1	584	Cgt/Tgt	8/24	1	2	FACETS	0.651	0.562	0.745	0.651	0.562	0.745	SUBCLONAL	1	TRUE	1	0.721535822188701	2		440	230	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389292	8389292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	145	570	0	ENST00000356435.5:c.4326G>A	p.Met1442Ile	p.M1442I	ENST00000356435		1442	atG/atA	26/35	0.721535822188701	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.721535822188701	1		570	244	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639959	93639959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1350208195	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	136	336	0	ENST00000375746.1:c.1288C>T	p.Pro430Ser	p.P430S	ENST00000375746	NM_001174167.1	430	Ccg/Tcg	10/14	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.721535822188701	2		336	366	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019621	123019621	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	220	271	0	ENST00000355640.3:c.109C>T	p.Pro37Ser	p.P37S	ENST00000355640		37	Cca/Tca	2/7	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.721535822188701	1		271	278	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0050590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	937	713	0	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	0.320597293795427	3	FACETS	1	0.995	1			1	CLONAL	6	FALSE	NA	0.329872932504764	3		713	1080	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0050590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	4107	742	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.329872932504764	25	FACETS	1	0.998	1			1	CLONAL	26	FALSE	NA	0.329872932504764	25		742	4527	SUCCESS
ATR	545	MSKCC	GRCh37	3	142185215	142185215	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	196	369	0	ENST00000350721.4:c.6848A>G	p.His2283Arg	p.H2283R	ENST00000350721	NM_001184.3	2283	cAt/cGt	40/47	0.33230689811943	1	FACETS	0.971	0.907	1	1	0.994	1	CLONAL	2	FALSE	0	0.329872932504764	1		369	511	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0050677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	127	314	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.310459881838183	4	FACETS	0.973	0.886	1	0.973	0.886	1	CLONAL	2	TRUE	2	0.339393587422638	4		314	515	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004589	16004589	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	18	461	0	ENST00000268712.3:c.2665G>A	p.Val889Met	p.V889M	ENST00000268712	NM_006311.3	889	Gtg/Atg	20/46	0.339393587422638	1	FACETS	0.25	0.188	0.324	0.25	0.188	0.324	SUBCLONAL	1	TRUE	0	0.339393587422638	1		461	352	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984672	11984672	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0050677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	12	286	0	ENST00000353533.5:c.219-1G>C		p.X73_splice	ENST00000353533	NM_003010.3	73			0.339393587422638	1	FACETS	0.345	0.243	0.47	0.345	0.243	0.47	SUBCLONAL	1	TRUE	0	0.339393587422638	1		286	170	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923272	26923272	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	23	327	0	ENST00000381527.3:c.268G>A	p.Asp90Asn	p.D90N	ENST00000381527	NM_001260.1	90	Gat/Aat	3/13	0.219980019587207	4	FACETS	0.396	0.307	0.498	0.198	0.153	0.249	SUBCLONAL	1	TRUE	2	0.339393587422638	4		327	459	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176678824	176678825	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0050677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	33	417	0	ENST00000439151.2:c.4735_4736delinsAA	p.Gly1579Lys	p.G1579K	ENST00000439151	NM_022455.4	1579	GGa/AAa	12/23	0.310459881838183	4	FACETS	0.533	0.433	0.645	0.266	0.216	0.323	SUBCLONAL	1	TRUE	2	0.339393587422638	4		417	489	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685315	89685315	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1554897280	NA	P-0050716-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	23	273	0	ENST00000371953.3:c.209+1G>A		p.X70_splice	ENST00000371953	NM_000314.4	70			0.341481130798032	2	FACETS	1	0.889	1	0.601	0.477	0.74	CLONAL	1	TRUE	0	0.341481130798032	2		273	112	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0050716-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	68	819	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	1	2	FACETS	0.526	0.457	0.601	0.526	0.457	0.601	SUBCLONAL	1	TRUE	1	0.341481130798032	2		819	757	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69230510	69230510	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050716-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	27	318	0	ENST00000462284.1:c.899A>T	p.Asp300Val	p.D300V	ENST00000462284	NM_002392.5	300	gAt/gTt	10/11	0.0760029993020366	3	FACETS	0.72	0.575	0.885	0.36	0.287	0.443	INDETERMINATE	1	TRUE	1	0.341481130798032	3		318	257	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535461	187535461	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050716-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	23	363	0	ENST00000441802.2:c.9113C>T	p.Pro3038Leu	p.P3038L	ENST00000441802	NM_005245.3	3038	cCt/cTt	12/27	1	2	FACETS	0.604	0.473	0.755	0.604	0.473	0.755	SUBCLONAL	1	TRUE	1	0.341481130798032	2		363	223	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0050725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	161	570	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.224713404930605	1	FACETS	0.816	0.75	0.886	1	0.99	1	CLONAL	2	TRUE	0	0.224713404930605	1		570	779	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880211	151880211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1405586437	NA	P-0050725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	67	384	4	ENST00000262189.6:c.5113C>T	p.Arg1705Cys	p.R1705C	ENST00000262189	NM_170606.2	1705	Cgc/Tgc	35/59	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.224713404930605	2		388	458	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168750	56168753	+	frameshift_variant	Frame_Shift_Del	DEL	AAGA	AAGA	-	novel	NA	P-0050725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	186	378	0	ENST00000399503.3:c.1604_1607del	p.Gln535ArgfsTer21	p.Q535Rfs*21	ENST00000399503	NM_005921.1	535	cAAGAg/cg	9/20	0.224713404930605	6	FACETS	1	0.968	1			1	CLONAL	3	TRUE	NA	0.224713404930605	6		378	741	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052633	42052633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	63	393	0	ENST00000219905.7:c.7304G>A	p.Arg2435Gln	p.R2435Q	ENST00000219905	NM_001164273.1	2435	cGg/cAg	20/24	1	2	FACETS	0.233	0.201	0.268	0.233	0.201	0.268	SUBCLONAL	1	TRUE	1	0.886174822952199	2		393	610	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	95	684	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.231	0.205	0.259	0.231	0.205	0.259	SUBCLONAL	1	TRUE	1	0.886174822952199	2		684	928	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0050754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	50	277	1	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.231	0.196	0.269	0.231	0.196	0.269	SUBCLONAL	1	TRUE	1	0.886174822952199	2		278	489	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17345380	17345380	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	69	360	0	ENST00000375499.3:c.839T>C	p.Val280Ala	p.V280A	ENST00000375499	NM_003000.2	280	gTt/gCt	8/8	0.209535275673944	2	FACETS	0.249	0.217	0.284	0.125	0.108	0.142	INDETERMINATE	1	TRUE	0	0.886174822952199	2		360	625	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105562	27105563	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0050754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	142	403	0	ENST00000324856.7:c.5175dup	p.Glu1726Ter	p.E1726*	ENST00000324856	NM_006015.4	1725	att/aTtt	20/20	0.209535275673944	2	FACETS	0.519	0.475	0.566	0.26	0.237	0.283	INDETERMINATE	1	TRUE	0	0.886174822952199	2		403	617	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0050754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	59	454	3	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	0.209535275673944	2	FACETS	0.207	0.177	0.239	0.103	0.088	0.12	INDETERMINATE	1	TRUE	0	0.886174822952199	2		457	644	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339111	65339111	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	88	450	0	ENST00000342505.4:c.425del	p.Lys142ArgfsTer26	p.K142Rfs*26	ENST00000342505	NM_002227.2	142	aAg/ag	5/25	0.209535275673944	2	FACETS	0.281	0.249	0.316	0.14	0.124	0.158	INDETERMINATE	1	TRUE	0	0.886174822952199	2		450	707	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834202	156834202	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	90	616	0	ENST00000524377.1:c.269T>C	p.Leu90Pro	p.L90P	ENST00000524377	NM_002529.3	90	cTg/cCg	2/17	1	2	FACETS	0.244	0.216	0.275	0.244	0.216	0.275	SUBCLONAL	1	TRUE	1	0.886174822952199	2		616	831	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597813	43597813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770548816	NA	P-0050754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	86	641	0	ENST00000355710.3:c.361G>A	p.Val121Ile	p.V121I	ENST00000355710	NM_020975.4	121	Gtc/Atc	3/20	1	2	FACETS	0.237	0.209	0.267	0.237	0.209	0.267	SUBCLONAL	1	TRUE	1	0.886174822952199	2		641	818	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683208	88683209	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0050754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	44	310	0	ENST00000372037.3:c.1426_1427dup	p.Lys477SerfsTer22	p.K477Sfs*22	ENST00000372037	NM_004329.2	473	gtt/gtTGt	12/13	1	2	FACETS	0.222	0.186	0.261	0.222	0.186	0.261	SUBCLONAL	1	TRUE	1	0.886174822952199	2		310	448	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711887	89711887	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776673	NA	P-0050754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	48	387	1	ENST00000371953.3:c.507del	p.Ser170ValfsTer13	p.S170Vfs*13	ENST00000371953	NM_000314.4	169	Ccc/cc	6/9	1	2	FACETS	0.217	0.183	0.254	0.217	0.183	0.254	SUBCLONAL	1	TRUE	1	0.886174822952199	2		388	500	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720664	89720664	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1114167648	NA	P-0050754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	30	270	0	ENST00000371953.3:c.815A>C	p.His272Pro	p.H272P	ENST00000371953	NM_000314.4	272	cAc/cCc	8/9	1	2	FACETS	0.174	0.14	0.212	0.174	0.14	0.212	SUBCLONAL	1	TRUE	1	0.886174822952199	2		270	390	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115550	108115550	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	56	330	1	ENST00000278616.4:c.698T>C	p.Leu233Ser	p.L233S	ENST00000278616	NM_000051.3	233	tTa/tCa	7/63	1	2	FACETS	0.275	0.236	0.318	0.275	0.236	0.318	SUBCLONAL	1	TRUE	1	0.886174822952199	2		331	459	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0050754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	86	467	3	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.292	0.258	0.328	0.292	0.258	0.328	SUBCLONAL	1	TRUE	1	0.886174822952199	2		470	665	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641389	18641389	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1229278001	NA	P-0050754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	28	184	0	ENST00000266497.5:c.2393del	p.Asn798MetfsTer16	p.N798Mfs*16	ENST00000266497		796	ctA/ct	17/31	NA	2	FACETS	0.255	0.204	0.312			1	INDETERMINATE	1	TRUE	NA	0.886174822952199	2		184	248	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218831	133218831	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754086131	NA	P-0050754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	88	555	0	ENST00000320574.5:c.5105A>G	p.Asn1702Ser	p.N1702S	ENST00000320574	NM_006231.2	1702	aAc/aGc	38/49	1	2	FACETS	0.271	0.24	0.305	0.271	0.24	0.305	SUBCLONAL	1	TRUE	1	0.886174822952199	2		555	732	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235865	133235892	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGGGGGAGCCCTCACCTCTCCGTGACA	TGGGGGGAGCCCTCACCTCTCCGTGACA	CGG	novel	NA	P-0050754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	60	459	2	ENST00000320574.5:c.3264_3275+16delinsCCG		p.X1088_splice	ENST00000320574	NM_006231.2	1088		26/49	1	2	FACETS	0.216	0.185	0.249	0.216	0.185	0.249	SUBCLONAL	1	TRUE	1	0.886174822952199	2		461	628	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105237174	105237174	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	86	418	1	ENST00000349310.3:c.1271C>A	p.Pro424His	p.P424H	ENST00000349310	NM_001014432.1	424	cCc/cAc	14/15	1	2	FACETS	0.296	0.262	0.333	0.296	0.262	0.333	SUBCLONAL	1	TRUE	1	0.886174822952199	2		419	656	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660465	67660465	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	50	325	0	ENST00000264010.4:c.1365C>G	p.His455Gln	p.H455Q	ENST00000264010	NM_006565.3	455	caC/caG	8/12	1	2	FACETS	0.223	0.189	0.261	0.223	0.189	0.261	SUBCLONAL	1	TRUE	1	0.886174822952199	2		325	505	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11019816	11019816	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	63	494	0	ENST00000327064.4:c.491A>C	p.Gln164Pro	p.Q164P	ENST00000327064	NM_199141.1	164	cAg/cCg	4/16	1	2	FACETS	0.211	0.182	0.243	0.211	0.182	0.243	SUBCLONAL	1	TRUE	1	0.886174822952199	2		494	673	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0050754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	40	210	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.269	0.224	0.319	0.269	0.224	0.319	SUBCLONAL	1	TRUE	1	0.886174822952199	2		210	335	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152566	56152566	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	70	265	0	ENST00000399503.3:c.622C>T	p.Arg208Ter	p.R208*	ENST00000399503	NM_005921.1	208	Cga/Tga	2/20	1	2	FACETS	0.343	0.3	0.39	0.343	0.3	0.39	SUBCLONAL	1	TRUE	1	0.886174822952199	2		265	460	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721336	176721336	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	62	457	0	ENST00000439151.2:c.6967G>A	p.Ala2323Thr	p.A2323T	ENST00000439151	NM_022455.4	2323	Gca/Aca	23/23	1	2	FACETS	0.222	0.191	0.255	0.222	0.191	0.255	SUBCLONAL	1	TRUE	1	0.886174822952199	2		457	630	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271605	26271605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753112584	NA	P-0050754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	55	306	0	ENST00000305910.3:c.8G>A	p.Arg3His	p.R3H	ENST00000305910	NM_003534.2	3	cGc/cAc	1/1	1	2	FACETS	0.294	0.252	0.34	0.294	0.252	0.34	SUBCLONAL	1	TRUE	1	0.886174822952199	2		306	422	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935543	13935543	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763469375	NA	P-0050754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	58	339	0	ENST00000405192.2:c.1313C>T	p.Pro438Leu	p.P438L	ENST00000405192	NM_001163147.1	438	cCg/cTg	12/12	1	2	FACETS	0.241	0.207	0.278	0.241	0.207	0.278	SUBCLONAL	1	TRUE	1	0.886174822952199	2		339	543	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338639	70338650	+	protein_altering_variant	In_Frame_Del	DEL	GGCCCCTGAAGC	GGCCCCTGAAGC	AGG	novel	NA	P-0050754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	89	449	2	ENST00000374080.3:c.35_46delinsAGG	p.Arg12_Arg16delinsGlnGly	p.R12_R16delinsQG	ENST00000374080		12	cGGCCCCTGAAGCgg/cAGGgg	1/45	1	2	FACETS	0.273	0.242	0.306	0.273	0.242	0.306	SUBCLONAL	1	TRUE	1	0.886174822952199	2		451	736	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778854	76778854	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	44	381	0	ENST00000373344.5:c.6725A>G	p.Gln2242Arg	p.Q2242R	ENST00000373344	NM_000489.3	2242	cAg/cGg	31/35	1	2	FACETS	0.245	0.205	0.288	0.245	0.205	0.288	SUBCLONAL	1	TRUE	1	0.886174822952199	2		381	406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0050756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	332	547	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.467929664557395	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.528000673754664	2		547	615	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468391	89468391	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	11	210	0	ENST00000336596.2:c.1925T>G	p.Leu642Arg	p.L642R	ENST00000336596	NM_005233.5	642	cTt/cGt	11/17	0.29241724004698	3	FACETS	0.288	0.199	0.398	0.096	0.066	0.133	INDETERMINATE	1	TRUE	0	0.528000673754664	3		210	183	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800930	243800930	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	64	357	0	ENST00000263826.5:c.544G>T	p.Glu182Ter	p.E182*	ENST00000263826	NM_005465.4	182	Gaa/Taa	5/13	0.23955384544221	3	FACETS	1	0.954	1	0.401	0.351	0.453	INDETERMINATE	1	TRUE	0	0.528000673754664	3		357	255	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796784	42796784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746217053	NA	P-0050756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	180	911	2	ENST00000575354.2:c.3242C>T	p.Pro1081Leu	p.P1081L	ENST00000575354	NM_015125.3	1081	cCg/cTg	14/20	1	2	FACETS	0.982	0.909	1	0.982	0.909	1	CLONAL	1	TRUE	1	0.528000673754664	2		913	694	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876392	35876392	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	133	617	0	ENST00000303115.3:c.1184A>C	p.Lys395Thr	p.K395T	ENST00000303115	NM_002185.3	395	aAg/aCg	8/8	0.463969737088545	4	FACETS	1	0.912	1	0.502	0.456	0.55	CLONAL	1	TRUE	2	0.528000673754664	4		617	767	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948823	17948823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199649035	NA	P-0050756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	183	770	3	ENST00000458235.1:c.1619G>A	p.Arg540His	p.R540H	ENST00000458235	NM_000215.3	540	cGc/cAc	12/24	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.528000673754664	2		773	672	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858934	45858934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772572683	NA	P-0050756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	140	712	0	ENST00000391945.4:c.1532G>A	p.Arg511Gln	p.R511Q	ENST00000391945	NM_000400.3	511	cGg/cAg	16/23	1	2	FACETS	0.896	0.819	0.976	0.896	0.819	0.976	CLONAL	1	TRUE	1	0.528000673754664	2		712	592	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249755	133249755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755463796	NA	P-0050756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	123	490	0	ENST00000320574.5:c.1468G>A	p.Asp490Asn	p.D490N	ENST00000320574	NM_006231.2	490	Gac/Aac	14/49	0.528000673754664	2	FACETS	1	0.97	1	0.572	0.522	0.624	CLONAL	1	TRUE	0	0.528000673754664	2		490	407	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100905	41100905	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0050756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	116	568	0	ENST00000373198.4:c.1450+1G>T		p.X484_splice	ENST00000373198	NM_133170.3	484			0.463969737088545	4	FACETS	0.999	0.902	1	0.5	0.451	0.551	CLONAL	1	TRUE	2	0.528000673754664	4		568	672	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601929	43601929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779719517	NA	P-0050756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	53	880	0	ENST00000355710.3:c.973G>A	p.Ala325Thr	p.A325T	ENST00000355710	NM_020975.4	325	Gcc/Acc	5/20	NA	2	FACETS	0.281	0.239	0.327			1	INDETERMINATE	1	TRUE	NA	0.528000673754664	2		880	715	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29068943	29068943	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	173	293	1	ENST00000282397.4:c.38C>T	p.Ala13Val	p.A13V	ENST00000282397	NM_002019.4	13	gCg/gTg	1/30	0.33111138465939	6	FACETS	0.849	0.787	0.913	0.637	0.59	0.685	CLONAL	3	TRUE	2	0.528000673754664	6		294	529	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231154	98231154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1402724349	NA	P-0050756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	164	798	0	ENST00000331920.6:c.2129A>G	p.Asp710Gly	p.D710G	ENST00000331920	NM_000264.3	710	gAc/gGc	14/24	0.104900881647453	3	FACETS	1	0.983	1	0.416	0.383	0.45	INDETERMINATE	1	TRUE	0	0.528000673754664	3		798	629	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609819	81609819	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	45	438	0	ENST00000298171.2:c.1417G>T	p.Val473Leu	p.V473L	ENST00000298171	NM_000369.2	473	Gta/Tta	10/10	1	2	FACETS	0.512	0.432	0.6	0.512	0.432	0.6	SUBCLONAL	1	TRUE	1	0.528000673754664	2		438	333	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186777	142186777	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs112373905	NA	P-0050756-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	52	273	0	ENST00000350721.4:c.6686C>T	p.Pro2229Leu	p.P2229L	ENST00000350721	NM_001184.3	2229	cCg/cTg	39/47	0.29241724004698	3	FACETS	1	0.962	1	0.451	0.39	0.516	INDETERMINATE	1	TRUE	0	0.528000673754664	3		273	184	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574026	7574026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	71	583	0	ENST00000269305.4:c.1001G>T	p.Gly334Val	p.G334V	ENST00000269305	NM_001126112.2	334	gGg/gTg	10/11	0.456279789806881	2	FACETS	0.934	0.836	1	0.934	0.836	1	CLONAL	2	TRUE	0	0.460574139868548	2		583	165	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247174	153247174	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	34	258	0	ENST00000281708.4:c.1628G>C	p.Arg543Thr	p.R543T	ENST00000281708	NM_033632.3	543	aGa/aCa	10/12	0.462466313516182	2	FACETS	0.9	0.763	1	0.9	0.763	1	CLONAL	2	TRUE	0	0.460574139868548	2		258	82	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645901	67645901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	52	441	0	ENST00000264010.4:c.829C>T	p.Arg277Trp	p.R277W	ENST00000264010	NM_006565.3	277	Cgg/Tgg	4/12	0.320338354219438	5	FACETS	0.94	0.812	1	0.627	0.541	0.718	CLONAL	2	TRUE	2	0.460574139868548	5		441	203	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561030	9561030	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs745765163	NA	P-0050775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	44	398	0	ENST00000353224.5:c.752C>A	p.Ala251Glu	p.A251E	ENST00000353224	NM_177990.2	251	gCg/gAg	4/10	0.320338354219438	5	FACETS	0.878	0.746	1	0.585	0.497	0.679	CLONAL	2	TRUE	2	0.460574139868548	5		398	184	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670241	134670241	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050775-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	93	424	0	ENST00000398015.3:c.152A>T	p.Asn51Ile	p.N51I	ENST00000398015	NM_004441.4	51	aAc/aTc	3/16	0.462466313516182	3	FACETS	0.905	0.827	0.983	0.905	0.827	0.983	CLONAL	3	TRUE	0	0.460574139868548	3		424	183	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624401	140624440	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCGGCGCCGGCGCCGGCGCCGGCCTCGGGCTCCATGTC	CCGCGGCGCCGGCGCCGGCGCCGGCCTCGGGCTCCATGTC	-	novel	NA	P-0050799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	29	192	0	ENST00000288602.6:c.64_103del	p.Asp22ProfsTer19	p.D22Pfs*19	ENST00000288602	NM_004333.4	22	GACATGGAGCCCGAGGCCGGCGCCGGCGCCGGCGCCGCGGcc/cc	1/18	0.809925558951544	3	FACETS	0.37	0.298	0.451	0.185	0.149	0.226	SUBCLONAL	1	TRUE	1	0.809798883585481	3		192	272	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0050832-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	118	507	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.220561660610195	4	FACETS	1	0.972	1	0.603	0.544	0.665	CLONAL	1	TRUE	2	0.353478777447674	4		507	749	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0050832-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	74	331	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.260784401020246	2	FACETS	1	0.898	1	0.512	0.45	0.578	CLONAL	1	TRUE	0	0.353478777447674	2		331	409	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0050832-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	86	277	1	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	0.25019120130663	3	FACETS	1	0.969	1	0.635	0.564	0.71	CLONAL	1	TRUE	1	0.353478777447674	3		278	451	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259439	55259439	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs397517126	NA	P-0050832-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	103	424	0	ENST00000275493.2:c.2497T>G	p.Leu833Val	p.L833V	ENST00000275493	NM_005228.3	833	Ttg/Gtg	21/28	0.220561660610195	4	FACETS	1	0.976	1	0.654	0.586	0.726	CLONAL	1	TRUE	2	0.353478777447674	4		424	603	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374890	45374890	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050832-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	133	416	0	ENST00000262160.6:c.953A>T	p.Asn318Ile	p.N318I	ENST00000262160	NM_005901.5	318	aAt/aTt	8/11	0.260784401020246	2	FACETS	0.823	0.753	0.896	0.823	0.753	0.896	CLONAL	2	TRUE	0	0.353478777447674	2		416	457	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100009	30100009	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050832-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	156	525	0	ENST00000331968.5:c.1611G>C	p.Gln537His	p.Q537H	ENST00000331968	NM_002742.2	537	caG/caC	10/18	0.250123756226708	3	FACETS	0.767	0.704	0.832	0.767	0.704	0.832	SUBCLONAL	2	TRUE	1	0.353478777447674	3		525	677	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650846	37650846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050832-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	109	447	2	ENST00000447079.4:c.2318G>A	p.Arg773His	p.R773H	ENST00000447079	NM_015083.1	773	cGt/cAt	5/14	0.220561660610195	4	FACETS	1	0.976	1	0.647	0.582	0.716	CLONAL	1	TRUE	2	0.353478777447674	4		449	645	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111537	8111550	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	TGGGCTCTACTACA	TGGGCTCTACTACA	GTAG	novel	NA	P-0050842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	242	625	2	ENST00000346208.3:c.1023_1036delinsGTAG	p.Cys341TrpfsTer2	p.C341Wfs*2	ENST00000346208		341	tgTGGGCTCTACTACAag/tgGTAGag	5/6	1	2	FACETS	0.827	0.775	0.881	1	0.994	1	CLONAL	2	TRUE	1	0.361576324920054	2		627	809	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	347	778	1	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.361576324920054	0	FACETS	0.888	0.848	0.928			1	CLONAL	2	TRUE	0	0.361576324920054	0		779	690	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842405	68842405	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050842-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	261	559	0	ENST00000261769.5:c.466T>G	p.Trp156Gly	p.W156G	ENST00000261769	NM_004360.3	156	Tgg/Ggg	4/16	0.742417470074241	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.742417470074241	1		559	430	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0050855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	176	727	3	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	NA	2	FACETS	0.912	0.841	0.987			1	INDETERMINATE	2	TRUE	NA	0.213873372346932	2		730	902	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351864	89351864	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	89	700	0	ENST00000301030.4:c.1086C>A	p.Asp362Glu	p.D362E	ENST00000301030	NM_001256183.1	362	gaC/gaA	9/13	1	2	FACETS	0.838	0.741	0.942	0.838	0.741	0.942	CLONAL	1	TRUE	1	0.213873372346932	2		700	993	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0050906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	83	325	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.646580684203007	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.646580684203007	2		325	123	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0050906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	78	396	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.646580684203007	2	FACETS	0.989	0.908	1	0.989	0.908	1	CLONAL	2	TRUE	0	0.646580684203007	2		396	122	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591825	48591825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767342	NA	P-0050906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	119	130	0	ENST00000342988.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000342988	NM_005359.5	330	Gaa/Aaa	9/12	0.646580684203007	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.646580684203007	2		130	179	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40498589	40498589	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	143	158	0	ENST00000264657.5:c.271C>T	p.Gln91Ter	p.Q91*	ENST00000264657	NM_139276.2	91	Cag/Tag	3/24	0.646580684203007	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.646580684203007	2		158	215	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464454	25464454	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1183198167	NA	P-0050906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	269	704	0	ENST00000264709.3:c.2059G>A	p.Val687Ile	p.V687I	ENST00000264709	NM_175629.2	687	Gtc/Atc	17/23	0.646580684203007	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.646580684203007	2		704	379	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732967	30732967	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	169	466	0	ENST00000295754.5:c.1582del	p.Arg528ValfsTer36	p.R528Vfs*36	ENST00000295754	NM_003242.5	527	gCc/gc	7/7	0.646580684203007	2	FACETS	0.983	0.928	1	0.983	0.928	1	CLONAL	2	TRUE	0	0.646580684203007	2		466	266	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42002898	42002898	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0050906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	94	100	0	ENST00000219905.7:c.2435C>G	p.Ser812Ter	p.S812*	ENST00000219905	NM_001164273.1	812	tCa/tGa	8/24	0.646580684203007	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.646580684203007	2		100	140	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133720	2133720	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	244	1043	1	ENST00000219476.3:c.3908G>T	p.Gly1303Val	p.G1303V	ENST00000219476	NM_000548.3	1303	gGa/gTa	33/42	0.604503105819069	4	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	2	0.646580684203007	4		1044	618	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639035	3639035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1425908713	NA	P-0050906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	253	809	0	ENST00000294008.3:c.4604G>A	p.Gly1535Glu	p.G1535E	ENST00000294008	NM_032444.2	1535	gGa/gAa	12/15	0.604503105819069	4	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	2	0.646580684203007	4		809	639	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619278	23619278	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146377793	NA	P-0050906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	180	403	0	ENST00000261584.4:c.3257G>A	p.Arg1086Gln	p.R1086Q	ENST00000261584	NM_024675.3	1086	cGa/cAa	12/13	0.604503105819069	4	FACETS	0.911	0.847	0.977	0.911	0.847	0.977	CLONAL	2	TRUE	2	0.646580684203007	4		403	503	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663704	29663704	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1340390812	NA	P-0050906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	131	143	0	ENST00000356175.3:c.6136C>T	p.Pro2046Ser	p.P2046S	ENST00000356175	NM_000267.3	2046	Cct/Tct	41/57	0.646580684203007	2	FACETS	0.938	0.876	0.998	0.938	0.876	0.998	CLONAL	2	TRUE	0	0.646580684203007	2		143	216	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468261	120468261	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	269	771	1	ENST00000256646.2:c.4178G>T	p.Arg1393Leu	p.R1393L	ENST00000256646	NM_024408.3	1393	cGc/cTc	25/34	0.351829457920715	3	FACETS	0.904	0.854	0.955	1	0.993	1	CLONAL	3	TRUE	1	0.351829457920715	3		772	663	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845895	156845895	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	69	1009	2	ENST00000524377.1:c.1525G>T	p.Asp509Tyr	p.D509Y	ENST00000524377	NM_002529.3	509	Gac/Tac	13/17	0.327131093297477	4	FACETS	0.553	0.481	0.633	0.277	0.24	0.317	SUBCLONAL	1	TRUE	2	0.351829457920715	4		1011	958	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518749	204518749	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	86	319	0	ENST00000367182.3:c.1412G>T	p.Gly471Val	p.G471V	ENST00000367182	NM_001278516.1	471	gGg/gTg	11/11	0.327131093297477	4	FACETS	0.753	0.669	0.841	0.753	0.669	0.841	SUBCLONAL	2	TRUE	2	0.351829457920715	4		319	439	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682946	241682946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs187226800	NA	P-0050930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	164	591	0	ENST00000366560.3:c.77C>T	p.Pro26Leu	p.P26L	ENST00000366560	NM_000143.3	26	cCc/cTc	1/10	0.327131093297477	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.351829457920715	4		591	528	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103486	77103486	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1231385297	NA	P-0050930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	185	348	0	ENST00000356341.3:c.80G>T	p.Gly27Val	p.G27V	ENST00000356341	NM_002576.4	27	gGc/gTc	2/15	0.300597788108492	4	FACETS	1	0.976	1	0.819	0.765	0.873	CLONAL	3	TRUE	0	0.351829457920715	4		348	434	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254220	133254220	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767503360	NA	P-0050930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	43	611	0	ENST00000320574.5:c.664C>T	p.Arg222Cys	p.R222C	ENST00000320574	NM_006231.2	222	Cgc/Tgc	7/49	1	2	FACETS	0.512	0.429	0.605	0.512	0.429	0.605	SUBCLONAL	1	TRUE	1	0.351829457920715	2		611	477	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914626	32914626	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	46	572	0	ENST00000380152.3:c.6134T>C	p.Phe2045Ser	p.F2045S	ENST00000380152		2045	tTt/tCt	11/27	0.276933311620369	2	FACETS	0.607	0.511	0.712	0.303	0.255	0.356	SUBCLONAL	1	TRUE	0	0.351829457920715	2		572	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0050930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	163	712	0	ENST00000269305.4:c.375+1del		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.252390528219554	2	FACETS	0.861	0.795	0.929	0.861	0.795	0.929	CLONAL	2	TRUE	0	0.351829457920715	2		712	538	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960894	15960894	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	29	322	0	ENST00000268712.3:c.6326C>G	p.Ser2109Cys	p.S2109C	ENST00000268712	NM_006311.3	2109	tCt/tGt	40/46	0.252390528219554	2	FACETS	0.55	0.442	0.671	0.275	0.221	0.336	SUBCLONAL	1	TRUE	0	0.351829457920715	2		322	300	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576138	29576138	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1555617383	NA	P-0050930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	88	393	0	ENST00000356175.3:c.4110+1G>A		p.X1370_splice	ENST00000356175	NM_000267.3	1370			0.177430747182458	4	FACETS	0.756	0.673	0.844	0.756	0.673	0.844	INDETERMINATE	2	TRUE	2	0.351829457920715	4		393	447	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670033	29670033	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	80	306	0	ENST00000356175.3:c.7006G>T	p.Glu2336Ter	p.E2336*	ENST00000356175	NM_000267.3	2336	Gag/Tag	47/57	0.177430747182458	4	FACETS	1	0.975	1	0.708	0.626	0.795	INDETERMINATE	1	TRUE	2	0.351829457920715	4		306	434	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0050930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	59	629	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.177430747182458	4	FACETS	0.794	0.683	0.915	0.397	0.341	0.458	INDETERMINATE	1	TRUE	2	0.351829457920715	4		629	571	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600407	10600407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867398451	NA	P-0050930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	61	930	0	ENST00000171111.5:c.1448G>A	p.Arg483His	p.R483H	ENST00000171111	NM_203500.1	483	cGc/cAc	4/6	0.351829457920715	3	FACETS	0.477	0.41	0.55	0.238	0.205	0.275	SUBCLONAL	1	TRUE	1	0.351829457920715	3		930	855	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728470	190728470	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	26	293	0	ENST00000441310.2:c.1858T>C	p.Tyr620His	p.Y620H	ENST00000441310	NM_000534.4	620	Tat/Cat	10/13	0.280633051802048	3	FACETS	0.574	0.455	0.709	0.287	0.227	0.355	SUBCLONAL	1	TRUE	1	0.351829457920715	3		293	303	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624783	9624783	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	79	464	0	ENST00000353224.5:c.194C>A	p.Ala65Asp	p.A65D	ENST00000353224	NM_177990.2	65	gCt/gAt	3/10	0.295071335225738	3	FACETS	1	0.97	1	0.439	0.388	0.493	CLONAL	1	TRUE	0	0.351829457920715	3		464	401	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485013	57485013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	47	391	1	ENST00000371085.3:c.847C>T	p.Arg283Cys	p.R283C	ENST00000371085	NM_000516.4	283	Cgc/Tgc	11/13	0.295071335225738	3	FACETS	0.816	0.69	0.954	0.272	0.23	0.318	CLONAL	1	TRUE	0	0.351829457920715	3		392	385	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503976	186503977	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0050930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	26	260	0	ENST00000323963.5:c.545dup	p.Leu182PhefsTer3	p.L182Ffs*3	ENST00000323963		181	gtt/gTtt	6/11	0.252390528219554	2	FACETS	0.478	0.379	0.592	0.239	0.189	0.296	SUBCLONAL	1	TRUE	0	0.351829457920715	2		260	309	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264661	1264661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199422304	NA	P-0050930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1249	87	950	1	ENST00000310581.5:c.2701C>T	p.Arg901Trp	p.R901W	ENST00000310581	NM_198253.2	901	Cgg/Tgg	11/16	0.351829457920715	9	FACETS	0.826	0.729	0.931	0.118	0.104	0.133	CLONAL	1	TRUE	2	0.351829457920715	9		951	1336	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350065	81350065	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	130	329	1	ENST00000222390.5:c.1267C>G	p.His423Asp	p.H423D	ENST00000222390	NM_000601.4	423	Cat/Gat	10/18	0.333824556748437	4	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	2	0.351829457920715	4		330	488	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410340	63410340	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	67	968	1	ENST00000330258.3:c.2827G>T	p.Asp943Tyr	p.D943Y	ENST00000330258	NM_152424.3	943	Gac/Tac	2/2	1	2	FACETS	0.675	0.587	0.771	0.675	0.587	0.771	SUBCLONAL	1	TRUE	1	0.351829457920715	2		969	564	SUCCESS
AR	367	MSKCC	GRCh37	X	66766412	66766412	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	45	358	0	ENST00000374690.3:c.1424C>G	p.Ala475Gly	p.A475G	ENST00000374690	NM_000044.3	475	gCg/gGg	1/8	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.351829457920715	2		358	214	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938241	76938241	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	45	539	0	ENST00000373344.5:c.2507C>G	p.Thr836Ser	p.T836S	ENST00000373344	NM_000489.3	836	aCc/aGc	9/35	1	2	FACETS	0.523	0.44	0.615	0.523	0.44	0.615	SUBCLONAL	1	TRUE	1	0.351829457920715	2		539	489	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858011	152858011	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	25	451	0	ENST00000406277.2:c.604G>A	p.Gly202Arg	p.G202R	ENST00000406277	NM_152274.4	202	Gga/Aga	6/7	0.280633051802048	3	FACETS	0.389	0.306	0.484	0.194	0.153	0.242	SUBCLONAL	1	TRUE	1	0.351829457920715	3		451	430	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188294	32188295	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs766348245	NA	P-0050930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	57	603	5	ENST00000375023.3:c.1046dup	p.Thr350HisfsTer4	p.T350Hfs*4	ENST00000375023	NM_004557.3	349	ggc/ggGc	6/30	0.351829457920715	3	FACETS	0.479	0.41	0.554	0.239	0.205	0.277	SUBCLONAL	1	TRUE	1	0.351829457920715	3		608	796	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0050930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	62	446	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.457	0.395	0.525	0.457	0.395	0.525	SUBCLONAL	1	TRUE	1	0.467424624399073	2		446	580	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560181	29560181	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	80	264	1	ENST00000356175.3:c.3658G>T	p.Glu1220Ter	p.E1220*	ENST00000356175	NM_000267.3	1220	Gaa/Taa	27/57	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.467424624399073	2		265	330	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477161	67477161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758586312	NA	P-0050930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	50	490	2	ENST00000327367.4:c.968G>A	p.Arg323His	p.R323H	ENST00000327367	NM_005902.3	323	cGc/cAc	7/9	1	2	FACETS	0.356	0.301	0.416	0.356	0.301	0.416	SUBCLONAL	1	TRUE	1	0.467424624399073	2		492	601	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101985107	101985107	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	84	498	1	ENST00000282441.5:c.554G>T	p.Gly185Val	p.G185V	ENST00000282441	NM_001130145.2	185	gGt/gTt	2/9	1	2	FACETS	0.545	0.481	0.613	0.545	0.481	0.613	SUBCLONAL	1	TRUE	1	0.467424624399073	2		499	660	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14021952	14021952	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs145138851	NA	P-0050930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	63	323	0	ENST00000311895.7:c.652A>G	p.Met218Val	p.M218V	ENST00000311895	NM_005236.2	218	Atg/Gtg	4/11	1	2	FACETS	0.576	0.499	0.659	0.576	0.499	0.659	SUBCLONAL	1	TRUE	1	0.467424624399073	2		323	468	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657411	29657411	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	53	406	0	ENST00000356175.3:c.5644A>G	p.Asn1882Asp	p.N1882D	ENST00000356175	NM_000267.3	1882	Aac/Gac	38/57	1	2	FACETS	0.427	0.364	0.496	0.427	0.364	0.496	SUBCLONAL	1	TRUE	1	0.467424624399073	2		406	531	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684095	29684095	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs916881278	NA	P-0050930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	48	321	0	ENST00000356175.3:c.7793T>G	p.Leu2598Arg	p.L2598R	ENST00000356175	NM_000267.3	2598	cTt/cGt	52/57	1	2	FACETS	0.411	0.347	0.481	0.411	0.347	0.481	SUBCLONAL	1	TRUE	1	0.467424624399073	2		321	500	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440226	220440226	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	84	654	0	ENST00000243786.2:c.1079C>A	p.Thr360Lys	p.T360K	ENST00000243786	NM_002191.3	360	aCg/aAg	2/2	1	2	FACETS	0.524	0.463	0.59	0.524	0.463	0.59	SUBCLONAL	1	TRUE	1	0.467424624399073	2		654	686	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968275	2968275	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050930-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	103	764	0	ENST00000396946.4:c.1711G>C	p.Asp571His	p.D571H	ENST00000396946	NM_032415.4	571	Gac/Cac	13/25	0.467424624399073	1	FACETS	0.43	0.384	0.478	0.43	0.384	0.478	SUBCLONAL	1	TRUE	0	0.467424624399073	1		764	786	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0050959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	70	423	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.23049928770255	2		423	512	SUCCESS
AR	367	MSKCC	GRCh37	X	66765730	66765730	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	83	514	1	ENST00000374690.3:c.742G>T	p.Gly248Cys	p.G248C	ENST00000374690	NM_000044.3	248	Ggc/Tgc	1/8	1	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.23049928770255	1		515	455	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346365	73346365	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	49	338	0	ENST00000377767.4:c.1435G>T	p.Asp479Tyr	p.D479Y	ENST00000377767	NM_014953.3	479	Gac/Tac	10/21	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.23049928770255	2		338	383	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991727	72991727	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755455411	NA	P-0050959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	23	196	0	ENST00000268489.5:c.2318C>T	p.Ala773Val	p.A773V	ENST00000268489	NM_006885.3	773	gCg/gTg	2/10	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.23049928770255	2		196	180	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858567	57858567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	52	686	1	ENST00000228682.2:c.305C>T	p.Ser102Leu	p.S102L	ENST00000228682	NM_005269.2	102	tCa/tTa	4/12	1	2	FACETS	0.648	0.551	0.755	0.648	0.551	0.755	SUBCLONAL	1	TRUE	1	0.23049928770255	2		687	696	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156016	119156016	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1246882963	NA	P-0050959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	73	647	0	ENST00000264033.4:c.1681C>G	p.Gln561Glu	p.Q561E	ENST00000264033	NM_005188.3	561	Caa/Gaa	11/16	1	2	FACETS	0.877	0.767	0.997	0.877	0.767	0.997	CLONAL	1	TRUE	1	0.23049928770255	2		647	722	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161851	47161851	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	41	368	0	ENST00000409792.3:c.4275G>C	p.Lys1425Asn	p.K1425N	ENST00000409792	NM_014159.6	1425	aaG/aaC	3/21	1	2	FACETS	0.775	0.646	0.919	0.775	0.646	0.919	CLONAL	1	TRUE	1	0.23049928770255	2		368	459	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11205059	11205059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	46	586	0	ENST00000361445.4:c.4730C>T	p.Ala1577Val	p.A1577V	ENST00000361445	NM_004958.3	1577	gCg/gTg	33/58	1	2	FACETS	0.634	0.533	0.745	0.634	0.533	0.745	SUBCLONAL	1	TRUE	1	0.23049928770255	2		586	630	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098594	47098594	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	70	555	0	ENST00000409792.3:c.6680del	p.Pro2227HisfsTer21	p.P2227Hfs*21	ENST00000409792	NM_014159.6	2227	cCa/ca	15/21	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.23049928770255	2		555	552	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161706	47161706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	39	253	0	ENST00000409792.3:c.4420G>A	p.Asp1474Asn	p.D1474N	ENST00000409792	NM_014159.6	1474	Gat/Aat	3/21	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.23049928770255	2		253	322	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161742	47161742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	36	310	0	ENST00000409792.3:c.4384G>A	p.Glu1462Lys	p.E1462K	ENST00000409792	NM_014159.6	1462	Gaa/Aaa	3/21	1	2	FACETS	0.842	0.693	1	0.842	0.693	1	CLONAL	1	TRUE	1	0.23049928770255	2		310	371	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161886	47161886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	34	394	0	ENST00000409792.3:c.4240G>A	p.Asp1414Asn	p.D1414N	ENST00000409792	NM_014159.6	1414	Gat/Aat	3/21	1	2	FACETS	0.596	0.486	0.72	0.596	0.486	0.72	SUBCLONAL	1	TRUE	1	0.23049928770255	2		394	495	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759388	133759388	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	73	631	0	ENST00000318560.5:c.1711T>G	p.Leu571Val	p.L571V	ENST00000318560	NM_005157.4	571	Ttg/Gtg	11/11	0.23049928770255	1	FACETS	0.89	0.778	1	0.89	0.778	1	CLONAL	1	TRUE	0	0.23049928770255	1		631	630	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692816	89692817	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554898084	NA	P-0050961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	134	212	0	ENST00000371953.3:c.301dup	p.Ile101AsnfsTer6	p.I101Nfs*6	ENST00000371953	NM_000314.4	100	-/A	5/9	0.432979736410157	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.432979736410157	2		212	288	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117799	108117799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202160435	NA	P-0050961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	14	345	0	ENST00000278616.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000278616	NM_000051.3	337	cGt/cAt	8/63	1	2	FACETS	0.142	0.102	0.191	0.142	0.102	0.191	SUBCLONAL	1	TRUE	1	0.432979736410157	2		345	455	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916937	+	inframe_deletion	In_Frame_Del	DEL	GGCAACCGT	GGCAACCGT	-	novel	NA	P-0050961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	91	338	0	ENST00000263967.3:c.317_325del	p.Gly106_Arg108del	p.G106_R108del	ENST00000263967	NM_006218.2	106	GGCAACCGT/-	2/21	1	2	FACETS	0.786	0.7	0.877	0.786	0.7	0.877	SUBCLONAL	1	TRUE	1	0.432979736410157	2		338	535	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851171	151851191	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGACGCAAAATATAAAGTG	GGTGACGCAAAATATAAAGTG	A	novel	NA	P-0050961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	86	289	0	ENST00000262189.6:c.12180_12200delinsT	p.Thr4061PhefsTer25	p.T4061Ffs*25	ENST00000262189	NM_170606.2	4060	ggCACTTTATATTTTGCGTCACCt/ggTt	48/59	0.432979736410157	3	FACETS	1	0.979	1	0.721	0.644	0.803	CLONAL	1	TRUE	1	0.432979736410157	3		289	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0050963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	312	655	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.613879547122132	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.613879547122132	1		655	652	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0050963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	52	351	1	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	0.308236469750125	0	FACETS	0.178	0.152	0.207			1	INDETERMINATE	1	TRUE	0	0.613879547122132	0		352	367	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355310	81355310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	102	203	0	ENST00000222390.5:c.1064G>A	p.Arg355Gln	p.R355Q	ENST00000222390	NM_000601.4	355	cGa/cAa	9/18	0.474158600947449	3	FACETS	1	0.909	1	0.505	0.454	0.558	CLONAL	1	TRUE	1	0.613879547122132	3		203	430	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979319	40979319	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1217327426	NA	P-0050963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	340	540	10	ENST00000373198.4:c.1814C>T	p.Thr605Met	p.T605M	ENST00000373198	NM_133170.3	605	aCg/aTg	11/32	0.112890527718044	5	FACETS	1	0.986	1	0.736	0.698	0.775	INDETERMINATE	2	TRUE	2	0.613879547122132	5		550	963	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043408	180043408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778806900	NA	P-0050963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	123	615	2	ENST00000261937.6:c.3178C>T	p.Arg1060Trp	p.R1060W	ENST00000261937	NM_182925.4	1060	Cgg/Tgg	23/30	0.410298223236226	1	FACETS	0.394	0.356	0.433	0.394	0.356	0.433	SUBCLONAL	1	TRUE	0	0.613879547122132	1		617	705	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023401	27023404	+	frameshift_variant	Frame_Shift_Del	DEL	CCAC	CCAC	-	novel	NA	P-0050963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	75	269	0	ENST00000324856.7:c.508_511del	p.His170AsnfsTer61	p.H170Nfs*61	ENST00000324856	NM_006015.4	169	ttCCAC/tt	1/20	0.284181898513167	1	FACETS	0.427	0.376	0.481	0.427	0.376	0.481	INDETERMINATE	1	TRUE	0	0.613879547122132	1		269	397	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244137	153244138	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCACACAACTCCCCCACTC	novel	NA	P-0050963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	118	405	1	ENST00000281708.4:c.2001_2019dup	p.Arg674GlufsTer26	p.R674Efs*26	ENST00000281708	NM_033632.3	673	-/GAGTGGGGGAGTTGTGTGG	12/12	0.294321808057153	1	FACETS	0.337	0.304	0.372	0.337	0.304	0.372	INDETERMINATE	1	TRUE	0	0.613879547122132	1		406	791	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0050970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	145	211	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.270098640041958	0	FACETS	0.789	0.739	0.838			1	SUBCLONAL	3	FALSE	0	0.335217037632906	0		211	243	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0050970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	243	518	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	FALSE	1	0.335217037632906	2		518	604	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061238	38061239	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGAGTCCGGGTGCAGCGTCCAGTA	novel	NA	P-0050970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	254	566	0	ENST00000250448.2:c.727_750dup	p.Tyr243_Ser250dup	p.Y243_S250dup	ENST00000250448	NM_004496.3	243	-/TACTGGACGCTGCACCCGGACTCC	2/2	1	2	FACETS	0.758	0.71	0.808	1	0.993	1	SUBCLONAL	2	FALSE	1	0.335217037632906	2		566	999	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061529	38061538	+	protein_altering_variant	In_Frame_Del	DEL	CCGCGCGGCT	CCGCGCGGCT	GGCGGCG	novel	NA	P-0050970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	67	276	1	ENST00000250448.2:c.451_460delinsCGCCGCC	p.Ser151_Gly154delinsArgArgArg	p.S151_G154delinsRRR	ENST00000250448	NM_004496.3	151	AGCCGCGCGGgc/CGCCGCCgc	2/2	1	2	FACETS	0.875	0.762	0.996	0.875	0.762	0.996	CLONAL	1	FALSE	1	0.335217037632906	2		277	457	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981518	70981518	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	219	918	1	ENST00000276594.2:c.578C>A	p.Ala193Asp	p.A193D	ENST00000276594	NM_024504.3	193	gCt/gAt	2/8	0.335217037632906	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	0	0.335217037632906	1		919	902	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	37	629	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.657	0.541	0.787	0.657	0.541	0.787	SUBCLONAL	1	TRUE	1	0.209047365683255	2		631	539	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	134	713	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.963	1	1	0.991	1	CLONAL	2	TRUE	1	0.209047365683255	2		715	581	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	60	681	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.884	0.761	1	0.884	0.761	1	CLONAL	1	TRUE	1	0.209047365683255	2		681	649	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	12	183	2	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	0.0797059124379285	2	FACETS	1	0.743	1			1	INDETERMINATE	1	TRUE	NA	0.209047365683255	2		185	109	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	39	465	5	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.822	0.681	0.979	0.822	0.681	0.979	CLONAL	1	TRUE	1	0.209047365683255	2		470	454	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736166	204736166	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	22	332	0	ENST00000302823.3:c.529del	p.Tyr177IlefsTer10	p.Y177Ifs*10	ENST00000302823	NM_005214.4	175	Ttt/tt	3/4	1	2	FACETS	0.591	0.458	0.746	0.591	0.458	0.746	SUBCLONAL	1	TRUE	1	0.209047365683255	2		332	356	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434367	121434367	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	52	872	4	ENST00000257555.6:c.1136del	p.Pro379LeufsTer5	p.P379Lfs*5	ENST00000257555		377	ctC/ct	6/10	1	2	FACETS	0.895	0.762	1	0.895	0.762	1	CLONAL	1	TRUE	1	0.209047365683255	2		876	556	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793211	139793212	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748531430	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	48	751	3	ENST00000247668.2:c.26dup	p.Gly10TrpfsTer70	p.G10Wfs*70	ENST00000247668	NM_021138.3	7	acc/aCcc	2/11	0.199951250291497	3	FACETS	0.922	0.779	1	0.461	0.389	0.54	CLONAL	1	TRUE	1	0.209047365683255	3		754	550	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770588	40770588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1389160956	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	27	470	0	ENST00000373198.4:c.2794C>T	p.Arg932Cys	p.R932C	ENST00000373198	NM_133170.3	932	Cgc/Tgc	19/32	1	2	FACETS	0.661	0.525	0.815	0.661	0.525	0.815	SUBCLONAL	1	TRUE	1	0.209047365683255	2		470	391	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115780	8115780	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	43	525	0	ENST00000346208.3:c.1131del	p.Val378CysfsTer26	p.V378Cfs*26	ENST00000346208		376	Aaa/aa	6/6	1	2	FACETS	0.85	0.711	1	0.85	0.711	1	CLONAL	1	TRUE	1	0.209047365683255	2		525	484	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510561	38510561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1457382271	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	30	578	0	ENST00000254066.5:c.815G>A	p.Arg272Gln	p.R272Q	ENST00000254066	NM_000964.3	272	cGg/cAg	7/9	1	2	FACETS	0.747	0.602	0.912	0.747	0.602	0.912	CLONAL	1	TRUE	1	0.209047365683255	2		578	384	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	70	388	3	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	0.179681597495717	4	FACETS	1	0.968	1	0.69	0.602	0.785	CLONAL	1	TRUE	2	0.209047365683255	4		391	587	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007619	45007619	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs111482205	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	38	211	0	ENST00000558401.1:c.68-2A>G		p.X23_splice	ENST00000558401	NM_004048.2	23			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.209047365683255	2		211	251	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385183	41385183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1423243089	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	58	690	1	ENST00000373198.4:c.778C>T	p.Arg260Trp	p.R260W	ENST00000373198	NM_133170.3	260	Cgg/Tgg	6/32	1	2	FACETS	0.979	0.841	1	0.979	0.841	1	CLONAL	1	TRUE	1	0.209047365683255	2		691	567	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180972	108180972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	31	268	0	ENST00000278616.4:c.5848G>A	p.Ala1950Thr	p.A1950T	ENST00000278616	NM_000051.3	1950	Gct/Act	39/63	0.190195427305805	2	FACETS	0.716	0.579	0.872	0.358	0.289	0.436	SUBCLONAL	1	TRUE	0	0.209047365683255	2		268	414	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982386	25982386	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	32	239	0	ENST00000435504.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000435504		302	Cga/Tga	9/13	NA	2	FACETS	0.942	0.766	1			1	INDETERMINATE	1	TRUE	NA	0.209047365683255	2		239	325	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574391	41574391	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752587236	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	23	668	0	ENST00000263253.7:c.6676C>T	p.Arg2226Trp	p.R2226W	ENST00000263253	NM_001429.3	2226	Cgg/Tgg	31/31	1	2	FACETS	0.493	0.384	0.621	0.493	0.384	0.621	SUBCLONAL	1	TRUE	1	0.209047365683255	2		668	446	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562745	21562745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778627422	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	47	288	0	ENST00000382592.4:c.1174G>A	p.Ala392Thr	p.A392T	ENST00000382592	NM_014572.2	392	Gcg/Acg	4/8	0.199951250291497	3	FACETS	0.804	0.682	0.937	0.804	0.682	0.937	CLONAL	2	TRUE	1	0.209047365683255	3		288	309	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604518	43604518	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199529397	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	41	690	3	ENST00000355710.3:c.1103G>A	p.Arg368His	p.R368H	ENST00000355710	NM_020975.4	368	cGc/cAc	6/20	1	2	FACETS	0.772	0.643	0.916	0.772	0.643	0.916	CLONAL	1	TRUE	1	0.209047365683255	2		693	508	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737051	162737051	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762369382	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	45	466	1	ENST00000367921.3:c.1195C>T	p.Arg399Trp	p.R399W	ENST00000367921	NM_006182.2	399	Cgg/Tgg	11/18	1	2	FACETS	0.872	0.732	1	0.872	0.732	1	CLONAL	1	TRUE	1	0.209047365683255	2		467	494	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726051	61726052	+	splice_region_variant,intron_variant	Splice_Region	DEL	AA	AA	-	rs372688892	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	52	230	0	ENST00000401558.2:c.591-4_591-3del		p.X197_splice	ENST00000401558	NM_003400.3	197			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.209047365683255	2		230	379	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214728	36214728	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	34	724	2	ENST00000222270.7:c.3159del	p.Arg1055GlyfsTer127	p.R1055Gfs*127	ENST00000222270	NM_014727.1	1052	Ggg/gg	8/37	1	2	FACETS	0.741	0.605	0.894	0.741	0.605	0.894	SUBCLONAL	1	TRUE	1	0.209047365683255	2		726	439	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435199	49435199	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	54	700	0	ENST00000301067.7:c.6354del	p.Ala2119LeufsTer25	p.A2119Lfs*25	ENST00000301067	NM_003482.3	2118	ccC/cc	31/54	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.209047365683255	2		700	450	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510072	187510072	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35485176	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	36	405	1	ENST00000441802.2:c.13441C>T	p.Arg4481Trp	p.R4481W	ENST00000441802	NM_005245.3	4481	Cgg/Tgg	27/27	1	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	TRUE	1	0.209047365683255	2		406	337	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78422338	78422338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1244295456	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	47	354	0	ENST00000370768.2:c.1624G>A	p.Ala542Thr	p.A542T	ENST00000370768	NM_003902.3	542	Gct/Act	17/20	1	2	FACETS	0.935	0.789	1	0.935	0.789	1	CLONAL	1	TRUE	1	0.209047365683255	2		354	481	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384765	17384765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754532648	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	54	734	0	ENST00000359435.4:c.397C>T	p.Arg133Trp	p.R133W	ENST00000359435	NM_001033549.1	133	Cgg/Tgg	4/9	1	2	FACETS	0.84	0.717	0.975	0.84	0.717	0.975	CLONAL	1	TRUE	1	0.209047365683255	2		734	615	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981516	70981516	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	59	973	1	ENST00000276594.2:c.580C>T	p.Arg194Trp	p.R194W	ENST00000276594	NM_024504.3	194	Cgg/Tgg	2/8	0.186301290542264	3	FACETS	0.748	0.642	0.864	0.374	0.321	0.432	SUBCLONAL	1	TRUE	1	0.209047365683255	3		974	834	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139642	202139642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1351320412	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	39	295	1	ENST00000358485.4:c.803C>T	p.Ser268Leu	p.S268L	ENST00000358485	NM_001080125.1	268	tCg/tTg	6/9	1	2	FACETS	0.915	0.759	1	0.915	0.759	1	CLONAL	1	TRUE	1	0.209047365683255	2		296	408	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524687	187524687	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs928653182	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	75	615	0	ENST00000441802.2:c.10993C>T	p.Arg3665Ter	p.R3665*	ENST00000441802	NM_005245.3	3665	Cga/Tga	19/27	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.209047365683255	2		615	582	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948584	71948584	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	45	1001	0	ENST00000298229.2:c.3296T>G	p.Leu1099Arg	p.L1099R	ENST00000298229	NM_001567.3	1099	cTg/cGg	26/28	0.190195427305805	2	FACETS	0.79	0.663	0.93	0.395	0.331	0.465	CLONAL	1	TRUE	0	0.209047365683255	2		1001	545	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570217	87570217	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200114699	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	54	457	0	ENST00000277120.3:c.1957G>A	p.Val653Met	p.V653M	ENST00000277120		653	Gtg/Atg	17/19	0.199951250291497	3	FACETS	1	0.966	1	0.741	0.635	0.856	CLONAL	1	TRUE	1	0.209047365683255	3		457	385	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588757	52588757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269557269	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	53	704	1	ENST00000394830.3:c.4271C>T	p.Pro1424Leu	p.P1424L	ENST00000394830	NM_018313.4	1424	cCg/cTg	27/30	1	2	FACETS	0.946	0.807	1	0.946	0.807	1	CLONAL	1	TRUE	1	0.209047365683255	2		705	536	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968840	32968840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80359194	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	35	271	0	ENST00000380152.3:c.9271G>A	p.Val3091Ile	p.V3091I	ENST00000380152		3091	Gtc/Atc	25/27	0.179681597495717	4	FACETS	1	0.922	1	0.619	0.509	0.742	CLONAL	1	TRUE	2	0.209047365683255	4		271	327	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244110	5244110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141022401	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	42	836	0	ENST00000357368.4:c.1372C>T	p.Arg458Cys	p.R458C	ENST00000357368	NM_002850.3	458	Cgc/Tgc	11/38	1	2	FACETS	0.762	0.636	0.903	0.762	0.636	0.903	CLONAL	1	TRUE	1	0.209047365683255	2		836	527	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342966	225342966	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1159640544	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	55	437	0	ENST00000264414.4:c.2126G>A	p.Arg709Gln	p.R709Q	ENST00000264414	NM_003590.4	709	cGg/cAg	15/16	1	2	FACETS	0.935	0.8	1	0.935	0.8	1	CLONAL	1	TRUE	1	0.209047365683255	2		437	563	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172510	108172510	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs876660289	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	19	231	0	ENST00000278616.4:c.5318del	p.Lys1773SerfsTer3	p.K1773Sfs*3	ENST00000278616	NM_000051.3	1771	agA/ag	35/63	0.190195427305805	2	FACETS	0.592	0.449	0.76	0.296	0.224	0.38	SUBCLONAL	1	TRUE	0	0.209047365683255	2		231	307	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191783	123191783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	50	170	0	ENST00000218089.9:c.1372G>A	p.Ala458Thr	p.A458T	ENST00000218089	NM_001042749.1	458	Gcc/Acc	15/35	0.0797059124379285	2	FACETS	0.903	0.772	1			1	INDETERMINATE	2	TRUE	NA	0.209047365683255	2		170	265	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618866	37618868	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs955200004	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	49	529	0	ENST00000447079.4:c.544_546del	p.Glu182del	p.E182del	ENST00000447079	NM_015083.1	181	aAGGag/aag	1/14	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.209047365683255	2		529	449	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194648	29194648	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	83	987	0	ENST00000240100.2:c.1080del	p.Thr361ProfsTer62	p.T361Pfs*62	ENST00000240100	NM_001394.6	360	ccC/cc	4/4	0.186301290542264	3	FACETS	1	0.954	1	0.584	0.515	0.658	CLONAL	1	TRUE	1	0.209047365683255	3		987	751	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749376	41749376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	25	364	0	ENST00000226382.2:c.419C>T	p.Ala140Val	p.A140V	ENST00000226382	NM_003924.3	140	gCg/gTg	2/3	1	2	FACETS	0.899	0.711	1	0.899	0.711	1	CLONAL	1	TRUE	1	0.209047365683255	2		364	266	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11313966	11313966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	55	635	0	ENST00000361445.4:c.770G>A	p.Arg257Gln	p.R257Q	ENST00000361445	NM_004958.3	257	cGg/cAg	6/58	1	2	FACETS	0.993	0.85	1	0.993	0.85	1	CLONAL	1	TRUE	1	0.209047365683255	2		635	530	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023880	27023880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1311879638	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	14	139	1	ENST00000324856.7:c.986C>T	p.Pro329Leu	p.P329L	ENST00000324856	NM_006015.4	329	cCg/cTg	1/20	1	2	FACETS	0.943	0.686	1	0.943	0.686	1	CLONAL	1	TRUE	1	0.209047365683255	2		140	142	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748125	72748125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199585673	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	42	482	3	ENST00000357731.5:c.53C>T	p.Ala18Val	p.A18V	ENST00000357731	NM_173808.2	18	gCg/gTg	1/7	1	2	FACETS	1	0.836	1	1	0.836	1	CLONAL	1	TRUE	1	0.209047365683255	2		485	402	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119446	193119446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754070093	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	45	319	0	ENST00000367435.3:c.841C>T	p.Arg281Cys	p.R281C	ENST00000367435	NM_024529.4	281	Cgc/Tgc	9/17	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.209047365683255	2		319	369	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115855	8115855	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	47	603	0	ENST00000346208.3:c.1201T>C	p.Ser401Pro	p.S401P	ENST00000346208		401	Tcc/Ccc	6/6	1	2	FACETS	0.871	0.735	1	0.871	0.735	1	CLONAL	1	TRUE	1	0.209047365683255	2		603	516	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624556	21624557	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1282388962	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	48	463	0	ENST00000421138.2:c.1472_1473del	p.Glu491ValfsTer17	p.E491Vfs*17	ENST00000421138		491	gAG/g	14/16	1	2	FACETS	0.844	0.713	0.988	0.844	0.713	0.988	CLONAL	1	TRUE	1	0.209047365683255	2		463	544	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431709	49431709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752428122	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	51	863	2	ENST00000301067.7:c.9430G>A	p.Ala3144Thr	p.A3144T	ENST00000301067	NM_003482.3	3144	Gca/Aca	34/54	1	2	FACETS	0.884	0.751	1	0.884	0.751	1	CLONAL	1	TRUE	1	0.209047365683255	2		865	552	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432035	49432035	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	49	861	0	ENST00000301067.7:c.9104A>G	p.Asp3035Gly	p.D3035G	ENST00000301067	NM_003482.3	3035	gAc/gGc	34/54	1	2	FACETS	0.804	0.68	0.94	0.804	0.68	0.94	CLONAL	1	TRUE	1	0.209047365683255	2		861	583	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443503	49443503	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769946520	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	61	679	0	ENST00000301067.7:c.3868C>T	p.Arg1290Trp	p.R1290W	ENST00000301067	NM_003482.3	1290	Cgg/Tgg	11/54	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.209047365683255	2		679	507	SUCCESS
BLM	641	MSKCC	GRCh37	15	91328285	91328285	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	88	477	0	ENST00000355112.3:c.2797A>C	p.Lys933Gln	p.K933Q	ENST00000355112	NM_000057.2	933	Aag/Cag	14/22	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.209047365683255	2		477	563	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341250	341250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371459615	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	30	941	3	ENST00000262320.3:c.2234C>T	p.Ala745Val	p.A745V	ENST00000262320	NM_003502.3	745	gCg/gTg	9/11	1	2	FACETS	0.542	0.435	0.663	0.542	0.435	0.663	SUBCLONAL	1	TRUE	1	0.209047365683255	2		944	530	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55478773	55478773	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369720643	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	47	490	0	ENST00000284073.2:c.346G>A	p.Gly116Arg	p.G116R	ENST00000284073	NM_138962.2	116	Ggg/Agg	6/14	1	2	FACETS	0.929	0.784	1	0.929	0.784	1	CLONAL	1	TRUE	1	0.209047365683255	2		490	484	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166387	7166387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747554207	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	51	582	0	ENST00000302850.5:c.1639G>A	p.Gly547Arg	p.G547R	ENST00000302850	NM_000208.2	547	Ggg/Agg	8/22	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.209047365683255	2		582	480	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912145	50912145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	47	851	3	ENST00000440232.2:c.1879G>A	p.Ala627Thr	p.A627T	ENST00000440232	NM_002691.3	627	Gca/Aca	15/27	1	2	FACETS	0.762	0.642	0.895	0.762	0.642	0.895	SUBCLONAL	1	TRUE	1	0.209047365683255	2		854	590	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471033	25471033	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	55	879	2	ENST00000264709.3:c.728G>T	p.Ser243Ile	p.S243I	ENST00000264709	NM_175629.2	243	aGc/aTc	7/23	1	2	FACETS	0.842	0.72	0.976	0.842	0.72	0.976	CLONAL	1	TRUE	1	0.209047365683255	2		881	625	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617511	158617511	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	44	542	0	ENST00000263640.3:c.1145T>C	p.Met382Thr	p.M382T	ENST00000263640	NM_001105.4	382	aTg/aCg	9/11	1	2	FACETS	0.859	0.721	1	0.859	0.721	1	CLONAL	1	TRUE	1	0.209047365683255	2		542	490	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438554	52438554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373809972	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	38	583	0	ENST00000460680.1:c.1165C>T	p.Arg389Cys	p.R389C	ENST00000460680	NM_004656.3	389	Cgc/Tgc	12/17	1	2	FACETS	0.784	0.648	0.935	0.784	0.648	0.935	CLONAL	1	TRUE	1	0.209047365683255	2		583	464	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902610	1902610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749595883	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	44	630	0	ENST00000382891.5:c.229G>A	p.Asp77Asn	p.D77N	ENST00000382891	NM_133335.3	77	Gac/Aac	2/22	1	2	FACETS	0.77	0.645	0.908	0.77	0.645	0.908	CLONAL	1	TRUE	1	0.209047365683255	2		630	547	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143043282	143043282	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs1364646936	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	27	315	0	ENST00000262992.4:c.2134C>T	p.Arg712Ter	p.R712*	ENST00000262992	NM_001101669.1	712	Cga/Tga	19/24	1	2	FACETS	0.698	0.555	0.861	0.698	0.555	0.861	SUBCLONAL	1	TRUE	1	0.209047365683255	2		315	370	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279504	1279504	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1278095401	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	43	1019	1	ENST00000310581.5:c.2032G>A	p.Ala678Thr	p.A678T	ENST00000310581	NM_198253.2	678	Gcc/Acc	5/16	1	2	FACETS	0.74	0.619	0.875	0.74	0.619	0.875	SUBCLONAL	1	TRUE	1	0.209047365683255	2		1020	556	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947421	38947421	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	25	272	0	ENST00000357387.3:c.4259del	p.Gly1420ValfsTer14	p.G1420Vfs*14	ENST00000357387	NM_152756.3	1420	gGt/gt	32/38	1	2	FACETS	0.828	0.653	1	0.828	0.653	1	CLONAL	1	TRUE	1	0.209047365683255	2		272	289	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950626	38950626	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	36	374	0	ENST00000357387.3:c.3324del	p.Lys1108AsnfsTer52	p.K1108Nfs*52	ENST00000357387	NM_152756.3	1108	aaA/aa	31/38	1	2	FACETS	0.76	0.625	0.912	0.76	0.625	0.912	CLONAL	1	TRUE	1	0.209047365683255	2		374	453	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29197685	29197685	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	61	791	3	ENST00000240100.2:c.509del	p.Pro170ArgfsTer57	p.P170Rfs*57	ENST00000240100	NM_001394.6	170	cCg/cg	2/4	0.186301290542264	3	FACETS	0.872	0.751	1	0.436	0.375	0.502	CLONAL	1	TRUE	1	0.209047365683255	3		794	739	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285934	38285934	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs758823379	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	43	522	0	ENST00000425967.3:c.477G>T	p.Glu159Asp	p.E159D	ENST00000425967	NM_001174067.1	159	gaG/gaT	5/19	0.186301290542264	3	FACETS	1	0.901	1	0.553	0.463	0.652	CLONAL	1	TRUE	1	0.209047365683255	3		522	411	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27229172	27229172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751768682	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	37	519	0	ENST00000380036.4:c.3317C>T	p.Thr1106Met	p.T1106M	ENST00000380036	NM_000459.3	1106	aCg/aTg	23/23	0.199951250291497	3	FACETS	0.715	0.588	0.857	0.357	0.294	0.429	SUBCLONAL	1	TRUE	1	0.209047365683255	3		519	547	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911574	101911574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	34	330	0	ENST00000374994.4:c.1499G>A	p.Gly500Asp	p.G500D	ENST00000374994	NM_004612.2	500	gGc/gAc	9/9	0.199951250291497	3	FACETS	0.839	0.686	1	0.42	0.343	0.506	CLONAL	1	TRUE	1	0.209047365683255	3		330	428	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802631	135802631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750512029	NA	P-0050977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	31	341	0	ENST00000298552.3:c.167C>T	p.Pro56Leu	p.P56L	ENST00000298552	NM_001162426.1	56	cCg/cTg	4/23	0.199951250291497	3	FACETS	0.862	0.698	1	0.431	0.349	0.524	CLONAL	1	TRUE	1	0.209047365683255	3		341	380	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0050981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	131	322	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.231463462113319	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	0	0.234229742865962	2		322	543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0050981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	201	516	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.234229742865962	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.234229742865962	2		516	745	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602764	10602764	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	247	730	0	ENST00000171111.5:c.814C>T	p.Arg272Cys	p.R272C	ENST00000171111	NM_203500.1	272	Cgc/Tgc	3/6	0.234229742865962	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.234229742865962	2		730	960	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480383	89480383	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	86	267	0	ENST00000336596.2:c.2220G>T	p.Met740Ile	p.M740I	ENST00000336596	NM_005233.5	740	atG/atT	13/17	0.120064830908548	4	FACETS	0.906	0.804	1	0.906	0.804	1	INDETERMINATE	2	TRUE	2	0.234229742865962	4		267	500	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220505	1220505	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs886039554	NA	P-0050981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	194	546	0	ENST00000326873.7:c.597+1G>T		p.X199_splice	ENST00000326873	NM_000455.4	199			0.234229742865962	2	FACETS	0.997	0.924	1	0.997	0.924	1	CLONAL	2	TRUE	0	0.234229742865962	2		546	831	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092813	27092884	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACCCCCATATTCCATGGGTGGAACCATGGCCAACAATTCTGCAGGTAAGTGCTAGTCATTCTCACTAGGGA	GACCCCCATATTCCATGGGTGGAACCATGGCCAACAATTCTGCAGGTAAGTGCTAGTCATTCTCACTAGGGA	-	novel	NA	P-0050981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	63	419	0	ENST00000324856.7:c.2834_2878+27del		p.X945_splice	ENST00000324856	NM_006015.4	945		9/20	1	2	FACETS	0.901	0.779	1	0.901	0.779	1	CLONAL	1	TRUE	1	0.234229742865962	2		419	597	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658833	3658833	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	152	409	0	ENST00000294008.3:c.133G>C	p.Asp45His	p.D45H	ENST00000294008	NM_032444.2	45	Gat/Cat	2/15	0.234229742865962	2	FACETS	0.934	0.856	1	0.934	0.856	1	CLONAL	2	TRUE	0	0.234229742865962	2		409	695	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641547	23641547	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	151	471	0	ENST00000261584.4:c.1928T>G	p.Phe643Cys	p.F643C	ENST00000261584	NM_024675.3	643	tTt/tGt	5/13	0.234229742865962	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	0	0.234229742865962	2		471	628	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78820274	78820274	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	121	490	0	ENST00000306801.3:c.1214A>G	p.His405Arg	p.H405R	ENST00000306801	NM_020761.2	405	cAc/cGc	11/34	0.120064830908548	4	FACETS	0.768	0.694	0.847	0.768	0.694	0.847	INDETERMINATE	2	TRUE	2	0.234229742865962	4		490	830	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378333	225378333	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	86	235	0	ENST00000264414.4:c.562C>T	p.Gln188Ter	p.Q188*	ENST00000264414	NM_003590.4	188	Cag/Tag	5/16	0.220355103720593	3	FACETS	0.932	0.829	1			1	CLONAL	2	TRUE	NA	0.234229742865962	3		235	440	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051619	30051619	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	114	307	0	ENST00000338641.4:c.553G>T	p.Glu185Ter	p.E185*	ENST00000338641	NM_000268.3	185	Gag/Tag	6/16	0.234229742865962	2	FACETS	0.958	0.867	1	0.958	0.867	1	CLONAL	2	TRUE	0	0.234229742865962	2		307	508	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528638	89528638	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs748204014	NA	P-0050981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	60	194	0	ENST00000336596.2:c.2938C>G	p.Pro980Ala	p.P980A	ENST00000336596	NM_005233.5	980	Cca/Gca	17/17	0.120064830908548	4	FACETS	0.927	0.803	1	0.927	0.803	1	INDETERMINATE	2	TRUE	2	0.234229742865962	4		194	341	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972956	68972956	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050981-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	52	368	0	ENST00000288368.4:c.1281G>T	p.Arg427Ser	p.R427S	ENST00000288368	NM_024870.2	427	agG/agT	11/40	0.234229742865962	3	FACETS	0.771	0.656	0.898	0.386	0.328	0.449	SUBCLONAL	1	TRUE	1	0.234229742865962	3		368	643	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050982-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	336	373	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.174121914714442	2	FACETS	1	0.993	1	0.633	0.601	0.666	INDETERMINATE	1	TRUE	0	0.620353270388465	2		373	855	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0050982-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	339	644	2	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.620353270388465	1	FACETS	0.927	0.882	0.973	0.927	0.882	0.973	CLONAL	1	TRUE	0	0.620353270388465	1		646	813	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105616	27105620	+	frameshift_variant	Frame_Shift_Del	DEL	ACGCT	ACGCT	-	novel	NA	P-0050982-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	432	492	0	ENST00000324856.7:c.5229_5233del	p.Leu1744GlyfsTer10	p.L1744Gfs*10	ENST00000324856	NM_006015.4	1743	ACGCTa/a	20/20	0.587755259338558	2	FACETS	0.872	0.838	0.905	0.872	0.838	0.905	CLONAL	2	TRUE	0	0.620353270388465	2		492	799	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913783	32913784	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1555284157	NA	P-0050982-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	269	477	0	ENST00000380152.3:c.5297dup	p.Asn1766LysfsTer2	p.N1766Kfs*2	ENST00000380152		1764	tca/tcAa	11/27	0.620353270388465	1	FACETS	0.999	0.945	1	0.999	0.945	1	CLONAL	1	TRUE	0	0.620353270388465	1		477	599	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533689	63533689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764728243	NA	P-0050982-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	317	576	0	ENST00000307078.5:c.1465C>T	p.Pro489Ser	p.P489S	ENST00000307078	NM_004655.3	489	Ccc/Tcc	6/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.620353270388465	2		576	913	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221300	36221301	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0050982-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	758	732	3	ENST00000222270.7:c.5134_5135delinsTT	p.Gly1712Phe	p.G1712F	ENST00000222270	NM_014727.1	1712	GGc/TTc	24/37	0.590109994814875	3	FACETS	0.936	0.905	0.966	0.936	0.905	0.966	CLONAL	2	TRUE	1	0.620353270388465	3		735	1711	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103811	209103811	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050982-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	258	531	0	ENST00000345146.2:c.1138A>T	p.Ile380Phe	p.I380F	ENST00000345146	NM_005896.2	380	Att/Ttt	9/10	0.620353270388465	1	FACETS	0.872	0.822	0.923	0.872	0.822	0.923	CLONAL	1	TRUE	0	0.620353270388465	1		531	658	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265076	46265076	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050982-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	310	486	1	ENST00000371998.3:c.1946C>G	p.Ser649Cys	p.S649C	ENST00000371998		649	tCt/tGt	12/23	0.29785421467946	3	FACETS	0.787	0.745	0.829	0.787	0.745	0.829	INDETERMINATE	2	TRUE	1	0.620353270388465	3		487	832	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970813	55970813	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs779902862	NA	P-0050982-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	61	556	0	ENST00000263923.4:c.1984C>G	p.Leu662Val	p.L662V	ENST00000263923	NM_002253.2	662	Cta/Gta	13/30	1	2	FACETS	0.239	0.206	0.276	0.239	0.206	0.276	SUBCLONAL	1	TRUE	1	0.620353270388465	2		556	822	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813108	76813108	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050982-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	246	532	1	ENST00000373344.5:c.6513G>T	p.Met2171Ile	p.M2171I	ENST00000373344	NM_000489.3	2171	atG/atT	30/35	NA	2	FACETS	0.928	0.869	0.988			1	INDETERMINATE	1	TRUE	NA	0.620353270388465	2		533	855	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0050983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	116	913	1	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.293666211013899	1	FACETS	0.768	0.691	0.849	0.768	0.691	0.849	SUBCLONAL	1	TRUE	0	0.293912009751611	1		914	877	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509624	106509624	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	92	417	0	ENST00000359195.3:c.1618G>T	p.Gly540Trp	p.G540W	ENST00000359195	NM_002649.2	540	Ggg/Tgg	2/11	0.236309889004459	4	FACETS	0.858	0.761	0.962			1	CLONAL	1	TRUE	NA	0.293912009751611	4		417	944	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610601	10610601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	197	629	1	ENST00000171111.5:c.109G>A	p.Glu37Lys	p.E37K	ENST00000171111	NM_203500.1	37	Gag/Aag	2/6	0.293912009751611	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.293912009751611	1		630	886	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120460343	120460343	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	93	491	0	ENST00000256646.2:c.5972A>C	p.Glu1991Ala	p.E1991A	ENST00000256646	NM_024408.3	1991	gAg/gCg	33/34	0.151720993196696	1	FACETS	0.773	0.688	0.865	0.773	0.688	0.865	INDETERMINATE	1	TRUE	0	0.293912009751611	1		491	698	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678521	88678521	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	119	425	1	ENST00000360948.2:c.1015G>T	p.Gly339Trp	p.G339W	ENST00000360948	NM_001012338.2	339	Ggg/Tgg	9/19	0.151720993196696	1	FACETS	1	0.92	1	1	0.92	1	INDETERMINATE	1	TRUE	0	0.293912009751611	1		426	677	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213961	2213961	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs542651972	NA	P-0050983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	240	617	1	ENST00000326181.6:c.40G>T	p.Gly14Trp	p.G14W	ENST00000326181	NM_032271.2	14	Ggg/Tgg	2/21	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.293912009751611	2		618	1091	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681779	78681779	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	78	577	0	ENST00000306801.3:c.487G>T	p.Glu163Ter	p.E163*	ENST00000306801	NM_020761.2	163	Gag/Tag	4/34	0.291636281563126	3	FACETS	0.696	0.61	0.788	0.348	0.305	0.394	SUBCLONAL	1	TRUE	1	0.293912009751611	3		577	875	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293157	212293157	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	68	352	0	ENST00000342788.4:c.2695del	p.His899IlefsTer15	p.H899Ifs*15	ENST00000342788	NM_005235.2	899	Cat/at	22/28	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.293912009751611	2		352	419	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713336	30713336	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	142	345	0	ENST00000295754.5:c.661G>C	p.Glu221Gln	p.E221Q	ENST00000295754	NM_003242.5	221	Gaa/Caa	4/7	0.293912009751611	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.293912009751611	1		345	648	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873098	134873098	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	104	515	0	ENST00000398015.3:c.1402G>T	p.Glu468Ter	p.E468*	ENST00000398015	NM_004441.4	468	Gag/Tag	6/16	0.293912009751611	1	FACETS	0.795	0.712	0.884	0.795	0.712	0.884	SUBCLONAL	1	TRUE	0	0.293912009751611	1		515	759	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201828	66201828	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	65	367	0	ENST00000273854.3:c.2674G>T	p.Glu892Ter	p.E892*	ENST00000273854	NM_004439.5	892	Gag/Tag	16/18	1	2	FACETS	0.655	0.568	0.75	0.655	0.568	0.75	SUBCLONAL	1	TRUE	1	0.293912009751611	2		367	675	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280370	1280370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746434205	NA	P-0050983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	183	567	2	ENST00000310581.5:c.1853C>T	p.Thr618Met	p.T618M	ENST00000310581	NM_198253.2	618	aCg/aTg	4/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.293912009751611	2		569	1067	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81340829	81340829	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050983-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	31	244	0	ENST00000222390.5:c.1412G>T	p.Gly471Val	p.G471V	ENST00000222390	NM_000601.4	471	gGt/gTt	12/18	1	2	FACETS	0.718	0.582	0.87	0.718	0.582	0.87	SUBCLONAL	1	TRUE	1	0.293912009751611	2		244	294	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050984-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	208	289	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.45153915181072	3	FACETS	0.949	0.887	1	0.949	0.887	1	CLONAL	2	TRUE	1	0.45153915181072	3		289	595	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0050984-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	398	622	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.45153915181072	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.45153915181072	2		622	833	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876449	35876449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2229232	NA	P-0050984-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	356	641	0	ENST00000303115.3:c.1241C>T	p.Thr414Met	p.T414M	ENST00000303115	NM_002185.3	414	aCg/aTg	8/8	0.44112891886262	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.45153915181072	3		641	926	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591837	48591837	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867764109	NA	P-0050984-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	267	540	0	ENST00000342988.3:c.1000C>T	p.Gln334Ter	p.Q334*	ENST00000342988	NM_005359.5	334	Cag/Tag	9/12	0.45153915181072	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.45153915181072	2		540	566	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440943	56440943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786205215	NA	P-0050984-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	180	541	1	ENST00000407977.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000407977		132	Cga/Tga	4/10	0.45153915181072	3	FACETS	1	0.952	1	0.521	0.481	0.564	CLONAL	1	TRUE	1	0.45153915181072	3		542	937	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950487	68950487	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050984-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	111	538	0	ENST00000288368.4:c.799C>A	p.Leu267Ile	p.L267I	ENST00000288368	NM_024870.2	267	Ctt/Att	7/40	0.361300027599261	4	FACETS	0.935	0.841	1	0.468	0.42	0.518	CLONAL	1	TRUE	2	0.45153915181072	4		538	763	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050985-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	25	373	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.242	0.19	0.301	0.242	0.19	0.301	SUBCLONAL	1	TRUE	1	0.5	2		373	414	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221264	1221267	+	frameshift_variant	Frame_Shift_Del	DEL	TTGT	TTGT	-	rs121913320	NA	P-0050985-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	75	610	0	ENST00000326873.7:c.790_793del	p.Phe264ArgfsTer22	p.F264Rfs*22	ENST00000326873	NM_000455.4	263	TTGTtt/tt	6/10	NA	2	FACETS	0.367	0.321	0.417			1	INDETERMINATE	1	TRUE	NA	0.5	2		610	818	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050986-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	61	373	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.269043446190117	4	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	2	0.26	4		373	250	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207168	1207168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520039	NA	P-0050986-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	84	750	1	ENST00000326873.7:c.256C>T	p.Arg86Ter	p.R86*	ENST00000326873	NM_000455.4	86	Cga/Tga	1/10	0.3	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.26	1		751	468	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602688	10602688	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050986-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	51	798	2	ENST00000171111.5:c.890G>T	p.Cys297Phe	p.C297F	ENST00000171111	NM_203500.1	297	tGc/tTc	3/6	0.3	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.26	1		800	285	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506194	103506194	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050986-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	17	401	0	ENST00000355739.4:c.352G>T	p.Ala118Ser	p.A118S	ENST00000355739	NM_000123.3	118	Gcc/Tcc	3/15	1	2	FACETS	0.769	0.577	0.995	0.769	0.577	0.995	CLONAL	1	TRUE	1	0.26	2		401	170	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937608	32937608	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050986-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	28	506	0	ENST00000380152.3:c.8269G>T	p.Glu2757Ter	p.E2757*	ENST00000380152		2757	Gaa/Taa	18/27	1	2	FACETS	1	0.817	1	1	0.817	1	CLONAL	1	TRUE	1	0.26	2		506	212	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569931	95569931	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050986-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	33	469	0	ENST00000393063.1:c.3802A>G	p.Ile1268Val	p.I1268V	ENST00000393063	NM_030621.3	1268	Att/Gtt	22/28	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.26	2		469	222	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135074	11135079	+	inframe_deletion	In_Frame_Del	DEL	AGGGCG	AGGGCG	-	novel	NA	P-0050986-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	61	844	0	ENST00000358026.2:c.3041_3046del	p.Lys1014_Val1016delinsMet	p.K1014_V1016delinsM	ENST00000358026	NM_001128849.1	1014	aAGGGCGtg/atg	21/36	0.3	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.26	1		844	334	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955051	17955051	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050986-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	53	806	0	ENST00000458235.1:c.176A>C	p.Lys59Thr	p.K59T	ENST00000458235	NM_000215.3	59	aAg/aCg	2/24	0.3	1	FACETS	0.871	0.745	1	0.871	0.745	1	CLONAL	1	TRUE	0	0.26	1		806	407	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438024	438024	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050986-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	34	334	0	ENST00000399788.2:c.1945T>G	p.Leu649Val	p.L649V	ENST00000399788	NM_001042603.1	649	Tta/Gta	14/28	0.258390835056245	1	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	0	0.26	1		334	204	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18649069	18649069	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050986-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	28	433	0	ENST00000266497.5:c.2744A>T	p.Asn915Ile	p.N915I	ENST00000266497		915	aAc/aTc	19/31	0.269043446190117	4	FACETS	0.933	0.747	1	0.466	0.373	0.572	CLONAL	1	TRUE	2	0.26	4		433	291	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40678561	40678561	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0050986-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	33	480	0	ENST00000249776.8:c.305-2A>T		p.X102_splice	ENST00000249776	NM_033286.3	102			1	2	FACETS	0.92	0.752	1	0.92	0.752	1	CLONAL	1	TRUE	1	0.26	2		480	276	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0050990-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	273	341	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.245253321736807	5	FACETS	0.895	0.842	0.948	1	0.988	1	CLONAL	4	TRUE	2	0.245253321736807	5		341	851	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0050990-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	227	564	1	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.232166898465243	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	0	0.245253321736807	2		565	921	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274929	38274929	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749758370	NA	P-0050990-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	110	633	0	ENST00000425967.3:c.1651G>A	p.Ala551Thr	p.A551T	ENST00000425967	NM_001174067.1	551	Gca/Aca	13/19	0.245253321736807	1	FACETS	0.818	0.734	0.908	0.818	0.734	0.908	CLONAL	1	TRUE	0	0.245253321736807	1		633	962	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602748	10602748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050990-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	226	658	0	ENST00000171111.5:c.830C>T	p.Thr277Met	p.T277M	ENST00000171111	NM_203500.1	277	aCg/aTg	3/6	0.232166898465243	2	FACETS	0.948	0.884	1	0.948	0.884	1	CLONAL	2	TRUE	0	0.245253321736807	2		658	972	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002659	37002659	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1385943435	NA	P-0050990-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	68	487	0	ENST00000358127.4:c.590G>T	p.Arg197Leu	p.R197L	ENST00000358127	NM_001280556.1	197	cGc/cTc	5/10	0.234130004544125	2	FACETS	0.787	0.684	0.898	0.393	0.342	0.449	SUBCLONAL	1	TRUE	0	0.245253321736807	2		487	705	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050999-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	120	230	0				ENST00000310581	NM_198253.2	-/1132			0.404300976311695	4	FACETS	0.954	0.868	1	0.954	0.868	1	CLONAL	2	TRUE	2	0.416156524503199	4		230	428	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0050999-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	516	615	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.331037293836198	3	FACETS	0.944	0.908	0.979	0.944	0.908	0.979	CLONAL	3	TRUE	0	0.416156524503199	3		615	1058	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000029	30000099	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CAAGAGGAAGCAACCCAAGACGTTCACCGTGAGGATCGTCACCATGGACGCCGAGATGGAGTTCAATTGCG	CAAGAGGAAGCAACCCAAGACGTTCACCGTGAGGATCGTCACCATGGACGCCGAGATGGAGTTCAATTGCG	-	novel	NA	P-0050999-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	81	440	0	ENST00000338641.4:c.42_112del	p.Lys15AspfsTer10	p.K15Dfs*10	ENST00000338641	NM_000268.3	14	ctCAAGAGGAAGCAACCCAAGACGTTCACCGTGAGGATCGTCACCATGGACGCCGAGATGGAGTTCAATTGCGag/ctag	1/16	0.320204862213074	3	FACETS	1	0.932	1	0.359	0.317	0.403	CLONAL	1	TRUE	0	0.416156524503199	3		440	437	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390794	139390794	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369167555	NA	P-0051004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	85	844	0	ENST00000277541.6:c.7397C>T	p.Thr2466Met	p.T2466M	ENST00000277541	NM_017617.3	2466	aCg/aTg	34/34	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.532961952989298	2		844	311	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965848	25965848	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs767987419	NA	P-0051004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	102	528	0	ENST00000435504.4:c.3358A>G	p.Met1120Val	p.M1120V	ENST00000435504		1120	Atg/Gtg	13/13	0.155471341122641	0	FACETS	0.569	0.515	0.625			1	INDETERMINATE	1	TRUE	0	0.532961952989298	0		528	314	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281053	49281053	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	152	586	0	ENST00000282018.3:c.100G>C	p.Glu34Gln	p.E34Q	ENST00000282018	NM_020377.2	34	Gaa/Caa	1/1	0.474981466535204	4	FACETS	0.967	0.884	1	0.322	0.294	0.352	CLONAL	1	TRUE	1	0.509636632084506	4		586	931	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436185	56436185	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0051021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	317	506	0	ENST00000407977.2:c.953-1G>A		p.X318_splice	ENST00000407977		318			0.509636632084506	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.509636632084506	2		506	574	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0051024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	43	299	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.28312688393955	2		299	282	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127460	55127460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779332376	NA	P-0051024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	36	470	1	ENST00000257290.5:c.248C>T	p.Thr83Met	p.T83M	ENST00000257290	NM_006206.4	83	aCg/aTg	3/23	0.28312688393955	1	FACETS	0.393	0.322	0.472	0.393	0.322	0.472	SUBCLONAL	1	TRUE	0	0.28312688393955	1		471	556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0051044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	129	762	1	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	0.258423524671062	1	FACETS	0.985	0.892	1	0.985	0.892	1	CLONAL	1	TRUE	0	0.258423524671062	1		763	883	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615168	43615168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	67	594	0	ENST00000355710.3:c.2582G>A	p.Gly861Glu	p.G861E	ENST00000355710	NM_020975.4	861	gGg/gAg	14/20	1	2	FACETS	0.729	0.633	0.834	0.729	0.633	0.834	SUBCLONAL	1	TRUE	1	0.258423524671062	2		594	711	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939856	49939856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781591594	NA	P-0051045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	65	674	0	ENST00000296474.3:c.1187G>A	p.Arg396Gln	p.R396Q	ENST00000296474	NM_002447.2	396	cGa/cAa	1/20	1	2	FACETS	0.521	0.451	0.598	0.521	0.451	0.598	SUBCLONAL	1	FALSE	1	0.326818796047652	2		674	763	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729945	30729947	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0051045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	50	512	0	ENST00000295754.5:c.1468_1470del	p.Asn490del	p.N490del	ENST00000295754	NM_003242.5	489	gACAac/gac	6/7	1	2	FACETS	0.549	0.466	0.641	0.549	0.466	0.641	SUBCLONAL	1	FALSE	1	0.326818796047652	2		512	557	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99181170	99181170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759905070	NA	P-0051051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	333	529	0	ENST00000074304.5:c.2111G>A	p.Arg704His	p.R704H	ENST00000074304	NM_001134224.1	704	cGc/cAc	20/26	1	2	FACETS	0.909	0.863	0.955	0.909	0.863	0.955	CLONAL	1	TRUE	1	0.877508163239594	2		529	835	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527605	29527605	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	180	332	0	ENST00000356175.3:c.1054del	p.Asp352IlefsTer24	p.D352Ifs*24	ENST00000356175	NM_000267.3	352	Gat/at	9/57	0.866311349589149	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.877508163239594	1		332	225	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0051063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	22	396	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.835	1	1	0.835	1	CLONAL	1	TRUE	1	0.21992550192516	2		396	184	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0051063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1457	191	747	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.21992550192516	2		747	1648	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0051063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	23	358	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	1	2	FACETS	0.778	0.607	0.974	0.778	0.607	0.974	CLONAL	1	TRUE	1	0.21992550192516	2		358	269	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023069	27023069	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	78	113	0	ENST00000324856.7:c.175G>T	p.Glu59Ter	p.E59*	ENST00000324856	NM_006015.4	59	Gag/Tag	1/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.21992550192516	2		113	503	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030346	11030346	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	112	629	0	ENST00000327064.4:c.1096G>C	p.Asp366His	p.D366H	ENST00000327064	NM_199141.1	366	Gat/Cat	9/16	1	2	FACETS	0.788	0.707	0.875	0.788	0.707	0.875	SUBCLONAL	1	TRUE	1	0.21992550192516	2		629	1292	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0051064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	165	289	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.301003216615433	1	FACETS	0.726	0.67	0.783	0.726	0.67	0.783	INDETERMINATE	1	TRUE	0	0.58424119351661	1		289	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764146326	NA	P-0051064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	357	631	0	ENST00000269305.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000269305	NM_001126112.2	281	Gac/Aac	8/11	0.58424119351661	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.58424119351661	1		631	818	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288297	33288297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1186523174	NA	P-0051064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	136	540	1	ENST00000374542.5:c.1111C>T	p.Arg371Trp	p.R371W	ENST00000374542	NM_001141970.1	371	Cgg/Tgg	4/8	1	2	FACETS	0.452	0.41	0.496	0.452	0.41	0.496	SUBCLONAL	1	TRUE	1	0.58424119351661	2		541	1031	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591912	48591912	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	235	450	0	ENST00000342988.3:c.1075G>T	p.Gly359Ter	p.G359*	ENST00000342988	NM_005359.5	359	Gga/Tga	9/12	0.58424119351661	1	FACETS	0.941	0.885	0.999	0.941	0.885	0.999	CLONAL	1	TRUE	0	0.58424119351661	1		450	605	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	8	373	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.307009683343056	1	FACETS	0.345	0.222	0.502	0.345	0.222	0.502	SUBCLONAL	1	TRUE	0	0.307009683343056	1		373	128	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0051065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	34	396	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.225919647117264	3	FACETS	1	0.926	1	1	0.926	1	CLONAL	3	TRUE	0	0.307009683343056	3		396	74	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111554	8111554	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	90	666	0	ENST00000346208.3:c.1040T>G	p.Leu347Arg	p.L347R	ENST00000346208		347	cTt/cGt	5/6	1	2	FACETS	0.867	0.777	0.962	1	0.984	1	CLONAL	2	TRUE	1	0.307009683343056	2		666	338	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100531	8100532	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0051065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	144	893	1	ENST00000346208.3:c.509dup	p.Gly171ArgfsTer132	p.G171Rfs*132	ENST00000346208		169	acc/aCcc	3/6	1	2	FACETS	1	0.982	1	1	0.993	1	CLONAL	2	TRUE	1	0.307009683343056	2		894	382	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828796	72828796	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1448393163	NA	P-0051065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	47	655	0	ENST00000268489.5:c.7785G>T	p.Gln2595His	p.Q2595H	ENST00000268489	NM_006885.3	2595	caG/caT	9/10	0.307009683343056	0	FACETS	0.996	0.85	1			1	CLONAL	1	TRUE	0	0.307009683343056	0		655	213	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264341	30264341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1421240953	NA	P-0051065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	10	178	1	ENST00000322652.5:c.76G>T	p.Gly26Trp	p.G26W	ENST00000322652	NM_015355.2	26	Ggg/Tgg	1/16	0.307009683343056	3	FACETS	0.759	0.519	1	0.38	0.259	0.528	CLONAL	1	TRUE	1	0.307009683343056	3		179	99	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0051067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	75	289	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.291808872618902	2		289	403	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0051067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	183	713	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.755	0.697	0.814	1	0.99	1	SUBCLONAL	2	TRUE	1	0.291808872618902	2		715	831	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	81	541	1	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.884	0.779	0.996	0.884	0.779	0.996	CLONAL	1	TRUE	1	0.291808872618902	2		542	628	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0051067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	162	529	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.81	0.746	0.878	1	0.99	1	CLONAL	2	TRUE	1	0.291808872618902	2		529	685	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874637	35874637	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	43	348	1	ENST00000303115.3:c.799del	p.Arg267GlyfsTer28	p.R267Gfs*28	ENST00000303115	NM_002185.3	265	Aaa/aa	6/8	1	2	FACETS	0.642	0.537	0.758	0.642	0.537	0.758	SUBCLONAL	1	TRUE	1	0.291808872618902	2		349	459	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917496	178917496	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	49	319	0	ENST00000263967.3:c.371C>A	p.Pro124Gln	p.P124Q	ENST00000263967	NM_006218.2	124	cCa/cAa	3/21	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.291808872618902	2		319	261	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509685	29509685	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0051067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	52	387	0	ENST00000356175.3:c.888+2T>C		p.X296_splice	ENST00000356175	NM_000267.3	296			1	2	FACETS	0.99	0.846	1	0.99	0.846	1	CLONAL	1	TRUE	1	0.291808872618902	2		387	360	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466022	69466022	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	48	791	0	ENST00000227507.2:c.860C>A	p.Pro287His	p.P287H	ENST00000227507	NM_053056.2	287	cCc/cAc	5/5	1	2	FACETS	0.392	0.33	0.46	0.392	0.33	0.46	SUBCLONAL	1	TRUE	1	0.291808872618902	2		791	840	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102199	27102199	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0051067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	68	354	1	ENST00000324856.7:c.5124+1G>A		p.X1708_splice	ENST00000324856	NM_006015.4	1708			1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.291808872618902	2		355	414	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218158	36218158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1311138959	NA	P-0051067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	114	526	1	ENST00000222270.7:c.4105G>A	p.Glu1369Lys	p.E1369K	ENST00000222270	NM_014727.1	1369	Gag/Aag	15/37	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.291808872618902	2		527	567	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653843	89653848	+	inframe_deletion	In_Frame_Del	DEL	GAACAA	GAACAA	-	novel	NA	P-0051067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	81	401	0	ENST00000371953.3:c.141_146del	p.Arg47_Asn49delinsSer	p.R47_N49delinsS	ENST00000371953	NM_000314.4	47	agGAACAAt/agt	2/9	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.291808872618902	2		401	379	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711909	89711928	+	frameshift_variant	Frame_Shift_Del	DEL	ATTATTATAGCTACCTGTTA	ATTATTATAGCTACCTGTTA	-	novel	NA	P-0051067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	50	485	0	ENST00000371953.3:c.528_547del	p.Tyr176Ter	p.Y176*	ENST00000371953	NM_000314.4	176	tATTATTATAGCTACCTGTTA/t	6/9	1	2	FACETS	0.844	0.718	0.982	0.844	0.718	0.982	CLONAL	1	TRUE	1	0.291808872618902	2		485	406	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121481	108121481	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	55	367	0	ENST00000278616.4:c.1289G>A	p.Cys430Tyr	p.C430Y	ENST00000278616	NM_000051.3	430	tGt/tAt	10/63	1	2	FACETS	0.906	0.777	1	0.906	0.777	1	CLONAL	1	TRUE	1	0.291808872618902	2		367	416	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660463	227660463	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	48	699	0	ENST00000305123.5:c.2992del	p.Arg998ValfsTer13	p.R998Vfs*13	ENST00000305123	NM_005544.2	998	Cgt/gt	1/2	1	2	FACETS	0.474	0.4	0.556	0.474	0.4	0.556	SUBCLONAL	1	TRUE	1	0.291808872618902	2		699	694	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197137	106197137	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	37	401	1	ENST00000380013.4:c.5470G>T	p.Gly1824Cys	p.G1824C	ENST00000380013	NM_001127208.2	1824	Ggt/Tgt	11/11	1	2	FACETS	0.511	0.421	0.612	0.511	0.421	0.612	SUBCLONAL	1	TRUE	1	0.291808872618902	2		402	496	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287907	33287907	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	55	445	0	ENST00000374542.5:c.1346A>C	p.Glu449Ala	p.E449A	ENST00000374542	NM_001141970.1	449	gAg/gCg	5/8	1	2	FACETS	0.752	0.644	0.871	0.752	0.644	0.871	SUBCLONAL	1	TRUE	1	0.291808872618902	2		445	501	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909676	76909676	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	27	312	0	ENST00000373344.5:c.4229C>A	p.Ala1410Glu	p.A1410E	ENST00000373344	NM_000489.3	1410	gCa/gAa	14/35	1	2	FACETS	0.52	0.414	0.641	0.52	0.414	0.641	SUBCLONAL	1	TRUE	1	0.291808872618902	2		312	356	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0051069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	732	289	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.5486667597436	4	FACETS	0.912	0.888	0.936			1	CLONAL	4	TRUE	NA	0.5486667597436	4		289	1133	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0051069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	300	533	1	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	0.498007749806747	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.5486667597436	1		534	772	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696716	47696716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	90	351	0	ENST00000347630.2:c.232G>A	p.Glu78Lys	p.E78K	ENST00000347630	NM_001007230.1	78	Gaa/Aaa	5/11	0.276482980439897	1	FACETS	0.402	0.357	0.45	0.402	0.357	0.45	INDETERMINATE	1	TRUE	0	0.5486667597436	1		351	592	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487334	56487334	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	34	295	0	ENST00000267101.3:c.1480G>A	p.Val494Met	p.V494M	ENST00000267101	NM_001982.3	494	Gtg/Atg	12/28	0.179005621735312	4	FACETS	0.299	0.243	0.361			1	INDETERMINATE	1	TRUE	NA	0.5486667597436	4		295	643	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174439	11174439	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	137	686	0	ENST00000361445.4:c.7236C>G	p.Asp2412Glu	p.D2412E	ENST00000361445	NM_004958.3	2412	gaC/gaG	53/58	1	2	FACETS	0.826	0.749	0.906	0.826	0.749	0.906	CLONAL	1	TRUE	1	0.284824056172111	2		686	1165	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100802	8100802	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	109	718	0	ENST00000346208.3:c.776C>G	p.Thr259Arg	p.T259R	ENST00000346208		259	aCa/aGa	3/6	1	2	FACETS	0.783	0.701	0.869	0.783	0.701	0.869	SUBCLONAL	1	TRUE	1	0.284824056172111	2		718	978	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817793	3817794	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0051070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	63	586	0	ENST00000262367.5:c.3177dup	p.Lys1060Ter	p.K1060*	ENST00000262367	NM_004380.2	1059	-/T	16/31	1	2	FACETS	0.793	0.686	0.909	0.793	0.686	0.909	CLONAL	1	TRUE	1	0.284824056172111	2		586	558	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967227	134967227	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	95	616	0	ENST00000398015.3:c.2566C>A	p.Leu856Ile	p.L856I	ENST00000398015	NM_004441.4	856	Ctc/Atc	14/16	1	2	FACETS	0.736	0.654	0.824	0.736	0.654	0.824	SUBCLONAL	1	TRUE	1	0.284824056172111	2		616	906	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590655	189590655	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	40	442	0	ENST00000264731.3:c.1220G>T	p.Gly407Val	p.G407V	ENST00000264731	NM_003722.4	407	gGc/gTc	10/14	1	2	FACETS	0.68	0.566	0.807	0.68	0.566	0.807	SUBCLONAL	1	TRUE	1	0.284824056172111	2		442	413	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549314	187549314	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	74	481	0	ENST00000441802.2:c.4804G>T	p.Glu1602Ter	p.E1602*	ENST00000441802	NM_005245.3	1602	Gag/Tag	9/27	1	2	FACETS	0.859	0.752	0.974	0.859	0.752	0.974	CLONAL	1	TRUE	1	0.284824056172111	2		481	605	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	206	647	0	ENST00000397752.3:c.3028G>C	p.Asp1010His	p.D1010H	ENST00000397752	NM_000245.2	1010	Gat/Cat	14/21	0.284824056172111	4	FACETS	0.95	0.891	1	1	0.989	1	CLONAL	4	TRUE	1	0.284824056172111	4		647	489	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0051072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	184	289	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.43869614174347	3	FACETS	0.944	0.877	1	0.944	0.877	1	CLONAL	2	TRUE	1	0.43869614174347	3		289	542	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0051072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	350	562	1	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.365208032442852	2	FACETS	0.811	0.77	0.853	0.811	0.77	0.853	CLONAL	2	TRUE	0	0.43869614174347	2		563	984	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575209	48575209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767326	NA	P-0051072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	14	291	0	ENST00000342988.3:c.403C>T	p.Arg135Ter	p.R135*	ENST00000342988	NM_005359.5	135	Cga/Tga	3/12	0.369893006874625	1	FACETS	0.213	0.154	0.285	0.213	0.154	0.285	SUBCLONAL	1	TRUE	0	0.43869614174347	1		291	234	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974783	21974783	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658556	NA	P-0051072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	202	316	0	ENST00000304494.5:c.44G>A	p.Trp15Ter	p.W15*	ENST00000304494	NM_000077.4	15	tGg/tAg	1/3	0.32539367775415	2	FACETS	0.831	0.776	0.887	0.831	0.776	0.887	CLONAL	2	TRUE	0	0.43869614174347	2		316	554	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426355	49426355	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	356	794	2	ENST00000301067.7:c.12133C>T	p.Gln4045Ter	p.Q4045*	ENST00000301067	NM_003482.3	4045	Cag/Tag	39/54	0.306426306154226	4	FACETS	0.782	0.739	0.826	0.782	0.739	0.826	SUBCLONAL	2	TRUE	2	0.43869614174347	4		796	1493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	225	555	0	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		555	320	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	286	766	0	ENST00000326873.7:c.667G>T	p.Glu223Ter	p.E223*	ENST00000326873	NM_000455.4	223	Gag/Tag	5/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		766	399	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610364	10610364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	307	771	4	ENST00000171111.5:c.346C>T	p.Arg116Trp	p.R116W	ENST00000171111	NM_203500.1	116	Cgg/Tgg	2/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		775	409	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518091	69518091	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	337	691	2	ENST00000294312.3:c.274A>T	p.Ile92Phe	p.I92F	ENST00000294312	NM_005117.2	92	Atc/Ttc	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		693	737	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90971032	90971032	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	180	374	1	ENST00000265433.3:c.1045G>T	p.Asp349Tyr	p.D349Y	ENST00000265433	NM_002485.4	349	Gat/Tat	9/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		375	1000	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20150350	20150350	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	166	430	0	ENST00000379607.5:c.287A>T	p.Asn96Ile	p.N96I	ENST00000379607	NM_001412.3	96	aAt/aTt	5/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		430	229	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	103	230	0				ENST00000310581	NM_198253.2	-/1132			0.753967343138606	3	FACETS	0.894	0.806	0.987	0.447	0.403	0.494	CLONAL	1	TRUE	1	0.77068973997214	3		230	414	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0051074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	269	866	1	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.77068973997214	2		867	690	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0051074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	289	747	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.77068973997214	1	FACETS	0.998	0.955	1	0.998	0.955	1	CLONAL	1	TRUE	0	0.77068973997214	1		747	462	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030426	49030426	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0051074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	779	538	0	ENST00000267163.4:c.1901C>G	p.Ser634Ter	p.S634*	ENST00000267163	NM_000321.2	634	tCa/tGa	19/27	0.753160994963592	4	FACETS	0.968	0.951	0.985	0.968	0.951	0.985	CLONAL	4	TRUE	0	0.77068973997214	4		538	924	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0051074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	46	486	0	ENST00000311936.3:c.34_35delinsTT	p.Gly12Phe	p.G12F	ENST00000311936	NM_004985.3	12	GGt/TTt	2/5	0.767439180478512	2	FACETS	0.212	0.178	0.25	0.106	0.089	0.125	SUBCLONAL	1	TRUE	0	0.77068973997214	2		486	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	274	785	0	ENST00000269305.4:c.853G>C	p.Glu285Gln	p.E285Q	ENST00000269305	NM_001126112.2	285	Gag/Cag	8/11	0.77068973997214	1	FACETS	0.984	0.94	1	0.984	0.94	1	CLONAL	1	TRUE	0	0.77068973997214	1		785	444	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030378	49030378	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0051074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	685	452	0	ENST00000267163.4:c.1853C>G	p.Ser618Ter	p.S618*	ENST00000267163	NM_000321.2	618	tCa/tGa	19/27	0.753160994963592	4	FACETS	0.961	0.942	0.978	0.961	0.942	0.978	CLONAL	4	TRUE	0	0.77068973997214	4		452	819	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485448	57485448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	158	429	0	ENST00000371085.3:c.1030G>A	p.Glu344Lys	p.E344K	ENST00000371085	NM_000516.4	344	Gag/Aag	12/13	0.753967343138606	3	FACETS	0.924	0.85	1	0.462	0.425	0.5	CLONAL	1	TRUE	1	0.77068973997214	3		429	615	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988237	36988237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	186	597	0	ENST00000354822.5:c.416C>T	p.Ser139Phe	p.S139F	ENST00000354822	NM_001079668.2	139	tCt/tTt	2/3	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.77068973997214	2		597	473	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170543	11170543	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	227	819	2	ENST00000358026.2:c.4846G>T	p.Glu1616Ter	p.E1616*	ENST00000358026	NM_001128849.1	1616	Gaa/Taa	34/36	0.77068973997214	1	FACETS	0.96	0.912	1	0.96	0.912	1	CLONAL	1	TRUE	0	0.77068973997214	1		821	377	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514152	69514152	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	495	779	0	ENST00000294312.3:c.529G>C	p.Glu177Gln	p.E177Q	ENST00000294312	NM_005117.2	177	Gag/Cag	3/3	0.767439180478512	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.77068973997214	2		779	636	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945020	31945020	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	565	763	0	ENST00000340398.3:c.81G>C	p.Arg27Ser	p.R27S	ENST00000340398	NM_001013699.2	27	agG/agC	1/1	0.767439180478512	2	FACETS	0.968	0.943	0.993	0.968	0.943	0.993	CLONAL	2	TRUE	0	0.77068973997214	2		763	757	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109712	115109712	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	651	837	0	ENST00000257566.3:c.2166G>C	p.Gln722His	p.Q722H	ENST00000257566	NM_016569.3	722	caG/caC	8/8	0.77068973997214	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	1	0.77068973997214	3		837	1068	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652920	29652920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	378	418	0	ENST00000356175.3:c.4855G>A	p.Glu1619Lys	p.E1619K	ENST00000356175	NM_000267.3	1619	Gaa/Aaa	36/57	0.77068973997214	3	FACETS	0.992	0.951	1	0.992	0.951	1	CLONAL	2	TRUE	1	0.77068973997214	3		418	685	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0051075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	96	289	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	FALSE	1	0.284879429256799	2		289	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579536	7579536	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567556930	NA	P-0051075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	113	645	0	ENST00000269305.4:c.151G>T	p.Glu51Ter	p.E51*	ENST00000269305	NM_001126112.2	51	Gaa/Taa	4/11	0.283997012800325	1	FACETS	0.788	0.709	0.873	0.788	0.709	0.873	SUBCLONAL	1	FALSE	0	0.284879429256799	1		645	863	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650591	18650591	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs751731010	NA	P-0051075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	115	464	0	ENST00000266497.5:c.2802G>T	p.Gln934His	p.Q934H	ENST00000266497		934	caG/caT	20/31	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.284879429256799	2		464	702	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045533	47045533	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0051075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	143	788	0	ENST00000377604.3:c.2500A>T	p.Lys834Ter	p.K834*	ENST00000377604	NM_001204468.1	834	Aag/Tag	22/24	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	1	0.284879429256799	2		788	953	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760462	133760462	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	163	800	0	ENST00000318560.5:c.2785G>T	p.Gly929Cys	p.G929C	ENST00000318560	NM_005157.4	929	Ggc/Tgc	11/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.284879429256799	2		800	1035	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436136	51436136	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	75	355	0	ENST00000262662.1:c.96T>A	p.Asn32Lys	p.N32K	ENST00000262662		32	aaT/aaA	3/4	1	2	FACETS	0.977	0.858	1	0.977	0.858	1	CLONAL	1	FALSE	1	0.284879429256799	2		355	539	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332630	70332630	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	53	542	0	ENST00000373644.4:c.535T>A	p.Ser179Thr	p.S179T	ENST00000373644	NM_030625.2	179	Tct/Act	2/12	1	2	FACETS	0.561	0.478	0.653	0.561	0.478	0.653	SUBCLONAL	1	FALSE	1	0.284879429256799	2		542	663	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098407	108098407	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	56	406	0	ENST00000278616.4:c.56G>T	p.Arg19Ile	p.R19I	ENST00000278616	NM_000051.3	19	aGa/aTa	2/63	1	2	FACETS	0.802	0.688	0.927	0.802	0.688	0.927	CLONAL	1	FALSE	1	0.284879429256799	2		406	490	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864711	57864711	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	142	817	0	ENST00000228682.2:c.2188C>A	p.Leu730Met	p.L730M	ENST00000228682	NM_005269.2	730	Ctg/Atg	12/12	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	FALSE	1	0.284879429256799	2		817	968	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003680	45003750	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	CGTTTAATATAAGTGGAGGCGTCGCGCTGGCGGGCATTCCTGAAGCTGACAGCATTCGGGCCGAGATGTCT	CGTTTAATATAAGTGGAGGCGTCGCGCTGGCGGGCATTCCTGAAGCTGACAGCATTCGGGCCGAGATGTCT	-	novel	NA	P-0051075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	39	281	0	ENST00000558401.1:c.-63_8del		p.*21*	ENST00000558401	NM_004048.2	?-2/119		1/4	0.130491216616655	0	FACETS	0.578	0.48	0.686			1	INDETERMINATE	1	FALSE	0	0.284879429256799	0		281	339	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427703	72427703	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	91	473	0	ENST00000477973.2:c.787A>G	p.Lys263Glu	p.K263E	ENST00000477973	NM_012234.5	263	Aag/Gag	4/4	1	2	FACETS	0.958	0.851	1	0.958	0.851	1	CLONAL	1	FALSE	1	0.284879429256799	2		473	667	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209522	98209522	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	147	822	1	ENST00000331920.6:c.4016G>T	p.Trp1339Leu	p.W1339L	ENST00000331920	NM_000264.3	1339	tGg/tTg	23/24	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	1	0.284879429256799	2		823	966	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411027	63411027	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	135	728	0	ENST00000330258.3:c.2140C>T	p.Gln714Ter	p.Q714*	ENST00000330258	NM_152424.3	714	Caa/Taa	2/2	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.284879429256799	2		728	876	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253880	30253880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	120	441	1	ENST00000307677.4:c.574G>A	p.Val192Met	p.V192M	ENST00000307677	NM_138578.1	192	Gtg/Atg	3/3	1	2	FACETS	0.647	0.587	0.71	0.647	0.587	0.71	SUBCLONAL	1	TRUE	1	0.690868173709178	2		442	537	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061228	38061228	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	258	560	0	ENST00000250448.2:c.761del	p.Phe254SerfsTer67	p.F254Sfs*67	ENST00000250448	NM_004496.3	254	tTc/tc	2/2	0.167402274348641	3	FACETS	1	0.954	1	1	0.954	1	INDETERMINATE	2	TRUE	1	0.563072205455151	3		560	581	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466582	120466582	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	48	453	0	ENST00000256646.2:c.4537T>C	p.Phe1513Leu	p.F1513L	ENST00000256646	NM_024408.3	1513	Ttc/Ctc	26/34	1	2	FACETS	0.531	0.451	0.618	0.531	0.451	0.618	SUBCLONAL	1	TRUE	1	0.563072205455151	2		453	321	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0051078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	57	578	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		578	652	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0051078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	47	442	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		442	692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0051079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	681	655	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.802050219274273	2		655	823	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11273473	11273473	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761539813	NA	P-0051079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	104	393	0	ENST00000361445.4:c.3268C>T	p.Arg1090Cys	p.R1090C	ENST00000361445	NM_004958.3	1090	Cgc/Tgc	21/58	0.580685407981538	3	FACETS	0.461	0.413	0.513			1	SUBCLONAL	1	TRUE	NA	0.802050219274273	3		393	788	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492608	56492610	+	missense_variant	Missense_Mutation	TNP	GTA	GTA	TTC	novel	NA	P-0051079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	245	450	0	ENST00000267101.3:c.2758_2760delinsTTC	p.Val920Phe	p.V920F	ENST00000267101	NM_001982.3	920	GTA/TTC	23/28	0.580685407981538	3	FACETS	0.972	0.91	1			1	CLONAL	1	TRUE	NA	0.802050219274273	3		450	881	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778789	3778829	+	frameshift_variant	Frame_Shift_Del	DEL	GCACCTGCTGTTGCTGCTGAGGGGAGCTGGGCGACTTCAGG	GCACCTGCTGTTGCTGCTGAGGGGAGCTGGGCGACTTCAGG	-	novel	NA	P-0051079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	300	725	0	ENST00000262367.5:c.6219_6259del	p.Leu2074GlufsTer253	p.L2074Efs*253	ENST00000262367	NM_004380.2	2073	acCCTGAAGTCGCCCAGCTCCCCTCAGCAGCAACAGCAGGTGCtg/actg	31/31	0.773027869823729	1	FACETS	0.932	0.892	0.971	0.932	0.892	0.971	CLONAL	1	TRUE	0	0.802050219274273	1		725	481	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202795	128202795	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	149	761	0	ENST00000341105.2:c.925G>C	p.Asp309His	p.D309H	ENST00000341105	NM_032638.4	309	Gac/Cac	4/6	0.177467992217062	3	FACETS	0.455	0.415	0.498	0.152	0.138	0.166	INDETERMINATE	1	TRUE	0	0.802050219274273	3		761	1143	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636314	87636314	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	113	588	0	ENST00000277120.3:c.2479G>T	p.Ala827Ser	p.A827S	ENST00000277120		827	Gcc/Tcc	19/19	0.801324630038233	2	FACETS	0.44	0.397	0.486	0.22	0.198	0.243	SUBCLONAL	1	TRUE	0	0.802050219274273	2		588	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0051080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	188	666	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.305658357530879	3	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.305658357530879	3		666	568	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437465	52437465	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	134	592	0	ENST00000460680.1:c.1696G>T	p.Glu566Ter	p.E566*	ENST00000460680	NM_004656.3	566	Gag/Tag	13/17	0.305658357530879	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.305658357530879	1		592	516	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493461	56493461	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1259152291	NA	P-0051080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	51	438	0	ENST00000267101.3:c.2869A>T	p.Thr957Ser	p.T957S	ENST00000267101	NM_001982.3	957	Acc/Tcc	24/28	1	2	FACETS	0.667	0.567	0.777	0.667	0.567	0.777	SUBCLONAL	1	TRUE	1	0.305658357530879	2		438	500	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	240	373	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.510668965183401	2	FACETS	0.971	0.918	1	0.971	0.918	1	CLONAL	2	TRUE	0	0.510668965183401	2		373	484	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0051081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	315	435	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.510668965183401	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.510668965183401	3		436	756	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0051081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	79	283	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.897	0.795	1	0.897	0.795	1	CLONAL	1	TRUE	1	0.510668965183401	2		283	345	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166282	7166282	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	227	617	0	ENST00000302850.5:c.1744G>T	p.Gly582Cys	p.G582C	ENST00000302850	NM_000208.2	582	Ggt/Tgt	8/22	0.510668965183401	2	FACETS	0.986	0.92	1	0.493	0.46	0.527	CLONAL	1	TRUE	0	0.510668965183401	2		617	902	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713544	30713546	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0051081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	118	513	0	ENST00000295754.5:c.871_873del	p.Lys291del	p.K291del	ENST00000295754	NM_003242.5	290	gAGAag/gag	4/7	1	2	FACETS	0.727	0.657	0.8	0.727	0.657	0.8	SUBCLONAL	1	TRUE	1	0.510668965183401	2		513	636	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016564	12016564	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	86	260	0	ENST00000353533.5:c.700A>T	p.Asn234Tyr	p.N234Y	ENST00000353533	NM_003010.3	234	Aat/Tat	7/11	1	2	FACETS	0.857	0.763	0.956	0.857	0.763	0.956	CLONAL	1	TRUE	1	0.510668965183401	2		260	393	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713129	30713129	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0051081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	101	273	1	ENST00000295754.5:c.455-1G>T		p.X152_splice	ENST00000295754	NM_003242.5	152			1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.510668965183401	2		274	382	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47205386	47205386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773221585	NA	P-0051081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	142	454	1	ENST00000409792.3:c.29C>T	p.Pro10Leu	p.P10L	ENST00000409792	NM_014159.6	10	cCg/cTg	1/21	1	2	FACETS	0.966	0.884	1	0.966	0.884	1	CLONAL	1	TRUE	1	0.510668965183401	2		455	576	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12043184	12043184	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0051081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	72	242	0	ENST00000353533.5:c.1069A>T	p.Lys357Ter	p.K357*	ENST00000353533	NM_003010.3	357	Aag/Tag	10/11	1	2	FACETS	0.813	0.715	0.916	0.813	0.715	0.916	CLONAL	1	TRUE	1	0.510668965183401	2		242	347	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933455	39933455	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	225	341	0	ENST00000378444.4:c.1144G>T	p.Glu382Ter	p.E382*	ENST00000378444	NM_001123385.1	382	Gag/Tag	4/15	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.510668965183401	1		341	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0051082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	514	587	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.859903823890281	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.859903823890281	1		587	655	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776650038	NA	P-0051082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	98	416	1	ENST00000334205.4:c.2308C>T	p.Pro770Ser	p.P770S	ENST00000334205	NM_003942.2	770	Ccc/Tcc	17/17	1	2	FACETS	0.368	0.329	0.41	0.368	0.329	0.41	SUBCLONAL	1	TRUE	1	0.859903823890281	2		417	619	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533378	29533378	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs878853865	NA	P-0051082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	166	264	0	ENST00000356175.3:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000356175	NM_000267.3	461	Cga/Tga	12/57	0.78553917297955	1	FACETS	0.949	0.901	0.994	0.949	0.901	0.994	CLONAL	1	TRUE	0	0.859903823890281	1		264	232	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912050	76912050	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	197	166	0	ENST00000373344.5:c.4214G>T	p.Arg1405Met	p.R1405M	ENST00000373344	NM_000489.3	1405	aGg/aTg	13/35	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.859903823890281	1		166	228	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220437	1220437	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	119	757	0	ENST00000326873.7:c.530T>C	p.Ile177Thr	p.I177T	ENST00000326873	NM_000455.4	177	aTc/aCc	4/10	0.859903823890281	1	FACETS	0.216	0.195	0.239	0.216	0.195	0.239	SUBCLONAL	1	TRUE	0	0.859903823890281	1		757	729	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0051083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	29	344	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.356	0.286	0.436	0.356	0.286	0.436	SUBCLONAL	1	TRUE	1	0.482940770559071	2		344	337	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0051083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	40	371	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	0.483	0.402	0.572	0.483	0.402	0.572	SUBCLONAL	1	TRUE	1	0.482940770559071	2		371	343	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0051083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	46	289	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	0.375	0.316	0.441	0.375	0.316	0.441	SUBCLONAL	1	TRUE	1	0.482940770559071	2		289	508	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624296	89624296	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786201995	NA	P-0051083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	78	426	0	ENST00000371953.3:c.70G>T	p.Asp24Tyr	p.D24Y	ENST00000371953	NM_000314.4	24	Gac/Tac	1/9	1	2	FACETS	0.598	0.526	0.675	0.598	0.526	0.675	SUBCLONAL	1	TRUE	1	0.482940770559071	2		426	540	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650661	67650661	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	83	355	0	ENST00000264010.4:c.966del	p.His322GlnfsTer11	p.H322Qfs*11	ENST00000264010	NM_006565.3	322	caC/ca	5/12	1	2	FACETS	0.498	0.439	0.561	0.498	0.439	0.561	SUBCLONAL	1	TRUE	1	0.482940770559071	2		355	690	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180833	106180833	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	44	349	0	ENST00000380013.4:c.3861T>G	p.Phe1287Leu	p.F1287L	ENST00000380013	NM_001127208.2	1287	ttT/ttG	7/11	1	2	FACETS	0.409	0.343	0.482	0.409	0.343	0.482	SUBCLONAL	1	TRUE	1	0.482940770559071	2		349	445	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061312	38061312	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	194	646	0	ENST00000250448.2:c.677A>C	p.Asp226Ala	p.D226A	ENST00000250448	NM_004496.3	226	gAc/gCc	2/2	0.313439023109773	4	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.34285758938582	4		646	1083	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696425	47696425	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519967	NA	P-0051084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	139	536	0	ENST00000347630.2:c.398T>G	p.Phe133Cys	p.F133C	ENST00000347630	NM_001007230.1	133	tTc/tGc	6/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.34285758938582	2		536	714	SUCCESS
APC	324	MSKCC	GRCh37	5	112173813	112173813	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0051084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	148	365	0	ENST00000257430.4:c.2522T>G	p.Leu841Ter	p.L841*	ENST00000257430	NM_000038.5	841	tTa/tGa	16/16	NA	2	FACETS	0.992	0.915	1			1	INDETERMINATE	2	TRUE	NA	0.34285758938582	2		365	435	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725032	49725032	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	GGT	novel	NA	P-0051084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	116	764	0	ENST00000449682.2:c.312delinsACC	p.Arg105ProfsTer23	p.R105Pfs*23	ENST00000449682	NM_020998.3	104	acG/acACC	3/18	1	2	FACETS	0.829	0.747	0.916	0.829	0.747	0.916	CLONAL	1	TRUE	1	0.34285758938582	2		764	816	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427538	427538	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	85	487	0	ENST00000399788.2:c.2631G>T	p.Leu877Phe	p.L877F	ENST00000399788	NM_001042603.1	877	ttG/ttT	19/28	0.239802655790522	2	FACETS	0.822	0.731	0.92	0.822	0.731	0.92	CLONAL	2	TRUE	0	0.239802655790522	2		487	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574008	+	frameshift_variant	Frame_Shift_Del	DEL	GGAACA	GGAACA	TC	novel	NA	P-0051085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	127	653	0	ENST00000269305.4:c.1019_1024delinsGA	p.Met340ArgfsTer4	p.M340Rfs*4	ENST00000269305	NM_001126112.2	340	aTGTTCCga/aGAga	10/11	0.230611804881509	2	FACETS	0.965	0.878	1	0.965	0.878	1	CLONAL	2	TRUE	0	0.239802655790522	2		653	549	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108329	8108329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	95	664	0	ENST00000585124.1:c.895G>A	p.Gly299Arg	p.G299R	ENST00000585124	NM_004217.3	299	Gga/Aga	9/9	0.230611804881509	2	FACETS	0.799	0.714	0.888	0.799	0.714	0.888	SUBCLONAL	2	TRUE	0	0.239802655790522	2		664	496	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599910	10599910	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	143	684	0	ENST00000171111.5:c.1666G>T	p.Ala556Ser	p.A556S	ENST00000171111	NM_203500.1	556	Gcc/Tcc	5/6	0.230611804881509	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.239802655790522	2		684	567	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431047	181431047	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	65	704	0	ENST00000325404.1:c.899G>C	p.Ser300Thr	p.S300T	ENST00000325404	NM_003106.3	300	aGc/aCc	1/1	0.219430079375792	5	FACETS	1	0.923	1	0.366	0.316	0.419	CLONAL	1	TRUE	2	0.239802655790522	5		704	672	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0051088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	74	578	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.748	0.655	0.848	0.748	0.655	0.848	SUBCLONAL	1	TRUE	1	0.327495143201954	2		578	604	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720720	89720721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs786204905	NA	P-0051088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	11	174	0	ENST00000371953.3:c.875dup	p.Asn292LysfsTer6	p.N292Kfs*6	ENST00000371953	NM_000314.4	291	gaa/gAaa	8/9	0.319545413397055	1	FACETS	0.367	0.254	0.506	0.367	0.254	0.506	SUBCLONAL	1	TRUE	0	0.327495143201954	1		174	153	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579716	7579716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1192416464	NA	P-0051088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	120	647	0	ENST00000269305.4:c.80del	p.Pro27LeufsTer17	p.P27Lfs*17	ENST00000269305	NM_001126112.2	27	cCt/ct	3/11	0.271599601113316	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.327495143201954	1		647	493	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934994	49934994	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771121262	NA	P-0051088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	116	788	0	ENST00000296474.3:c.2005C>T	p.Arg669Trp	p.R669W	ENST00000296474	NM_002447.2	669	Cgg/Tgg	6/20	1	2	FACETS	0.931	0.839	1	0.931	0.839	1	CLONAL	1	TRUE	1	0.327495143201954	2		788	761	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152009026	152009026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	20	329	0	ENST00000262189.6:c.596G>T	p.Arg199Leu	p.R199L	ENST00000262189	NM_170606.2	199	cGa/cTa	5/59	1	2	FACETS	0.325	0.248	0.415	0.325	0.248	0.415	SUBCLONAL	1	TRUE	1	0.327495143201954	2		329	376	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0051089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	200	515	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	0.453558149232737	4	FACETS	0.915	0.851	0.98	0.915	0.851	0.98	CLONAL	2	TRUE	2	0.47899746978937	4		515	675	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961589	41961589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	181	512	0	ENST00000219905.7:c.497G>A	p.Gly166Asp	p.G166D	ENST00000219905	NM_001164273.1	166	gGt/gAt	2/24	0.47899746978937	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.47899746978937	2		512	347	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0051090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	16	229	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	1	0.816	1	1	0.816	1	CLONAL	1	TRUE	1	0.12	2		229	235	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0051090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	20	314	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.868	0.663	1	0.868	0.663	1	CLONAL	1	TRUE	1	0.12	2		314	384	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	14	449	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.441	0.317	0.593	0.441	0.317	0.593	SUBCLONAL	1	TRUE	1	0.12	2		449	529	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097818	27097818	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0051090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	19	372	0	ENST00000324856.7:c.3406+1G>T		p.X1136_splice	ENST00000324856	NM_006015.4	1136			1	2	FACETS	0.861	0.652	1	0.861	0.652	1	CLONAL	1	TRUE	1	0.12	2		372	368	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238986	5238986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756351666	NA	P-0051090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	39	669	0	ENST00000357368.4:c.1793C>T	p.Ser598Leu	p.S598L	ENST00000357368	NM_002850.3	598	tCg/tTg	13/38	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.12	2		669	627	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	32	321	0	ENST00000263967.3:c.333G>T	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaT	2/21	1	2	FACETS	0.762	0.618	0.923	0.762	0.618	0.923	CLONAL	1	TRUE	1	0.22	2		321	382	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	44	407	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.935	0.785	1	0.935	0.785	1	CLONAL	1	TRUE	1	0.22	2		408	428	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	14	404	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.212	0.152	0.285	0.212	0.152	0.285	SUBCLONAL	1	TRUE	1	0.22	2		404	601	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692953	89692953	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs786204933	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	39	472	0	ENST00000371953.3:c.437T>G	p.Leu146Ter	p.L146*	ENST00000371953	NM_000314.4	146	tTa/tGa	5/9	1	2	FACETS	0.728	0.603	0.867	0.728	0.603	0.867	SUBCLONAL	1	TRUE	1	0.22	2		472	487	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	51	344	0	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	0.974	0.829	1	0.974	0.829	1	CLONAL	1	TRUE	1	0.22	2		344	476	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717769	89717770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	16	249	0	ENST00000371953.3:c.800dup	p.Asp268GlyfsTer30	p.D268Gfs*30	ENST00000371953	NM_000314.4	265	cta/ctAa	7/9	1	2	FACETS	0.466	0.344	0.613	0.466	0.344	0.613	SUBCLONAL	1	TRUE	1	0.22	2		249	312	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578193	28578193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs968020606	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	66	437	0	ENST00000241453.7:c.2978C>T	p.Ser993Leu	p.S993L	ENST00000241453	NM_004119.2	993	tCg/tTg	24/24	1	2	FACETS	0.979	0.85	1	0.979	0.85	1	CLONAL	1	TRUE	1	0.22	2		437	613	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	47	362	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.976	0.824	1	0.976	0.824	1	CLONAL	1	TRUE	1	0.22	2		362	438	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	60	473	0	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	1	2	FACETS	0.874	0.753	1	0.874	0.753	1	CLONAL	1	TRUE	1	0.22	2		473	624	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727521	88727521	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	53	413	0	ENST00000360948.2:c.258G>T	p.Glu86Asp	p.E86D	ENST00000360948	NM_001012338.2	86	gaG/gaT	3/19	1	2	FACETS	0.775	0.66	0.901	0.775	0.66	0.901	CLONAL	1	TRUE	1	0.22	2		413	622	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	51	474	0	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	1	2	FACETS	0.899	0.764	1	0.899	0.764	1	CLONAL	1	TRUE	1	0.22	2		474	516	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	30	295	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.814	0.657	0.992	0.814	0.657	0.992	CLONAL	1	TRUE	1	0.22	2		295	335	SUCCESS
APC	324	MSKCC	GRCh37	5	112178211	112178211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs901983934	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	38	398	0	ENST00000257430.4:c.6920C>T	p.Ser2307Leu	p.S2307L	ENST00000257430	NM_000038.5	2307	tCg/tTg	16/16	1	2	FACETS	0.74	0.611	0.883	0.74	0.611	0.883	SUBCLONAL	1	TRUE	1	0.22	2		398	467	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971370	13971370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748346103	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	11	299	0	ENST00000405192.2:c.559C>T	p.Arg187Cys	p.R187C	ENST00000405192	NM_001163147.1	187	Cgc/Tgc	8/12	1	2	FACETS	0.223	0.153	0.311	0.223	0.153	0.311	SUBCLONAL	1	TRUE	1	0.22	2		299	448	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556079	29556079	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886041347	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	19	200	0	ENST00000356175.3:c.2446C>T	p.Arg816Ter	p.R816*	ENST00000356175	NM_000267.3	816	Cga/Tga	21/57	1	2	FACETS	0.677	0.515	0.868	0.677	0.515	0.868	SUBCLONAL	1	TRUE	1	0.22	2		200	255	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162161	47162161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147170912	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	30	391	1	ENST00000409792.3:c.3965G>A	p.Arg1322Gln	p.R1322Q	ENST00000409792	NM_014159.6	1322	cGa/cAa	3/21	1	2	FACETS	0.516	0.414	0.631	0.516	0.414	0.631	SUBCLONAL	1	TRUE	1	0.22	2		392	529	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687122	176687122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	31	381	1	ENST00000439151.2:c.5099G>A	p.Arg1700Gln	p.R1700Q	ENST00000439151	NM_022455.4	1700	cGa/cAa	14/23	1	2	FACETS	0.469	0.378	0.572	0.469	0.378	0.572	SUBCLONAL	1	TRUE	1	0.22	2		382	601	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226308	2226308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	82	713	1	ENST00000326181.6:c.1921C>T	p.Arg641Cys	p.R641C	ENST00000326181	NM_032271.2	641	Cgt/Tgt	20/21	1	2	FACETS	0.855	0.752	0.965	0.855	0.752	0.965	CLONAL	1	TRUE	1	0.22	2		714	872	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267797	7267797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	72	474	0	ENST00000302850.5:c.211G>A	p.Glu71Lys	p.E71K	ENST00000302850	NM_000208.2	71	Gaa/Aaa	2/22	1	2	FACETS	0.914	0.798	1	0.914	0.798	1	CLONAL	1	TRUE	1	0.22	2		474	716	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637121	176637122	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1299932363	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	46	469	0	ENST00000439151.2:c.1727dup	p.Asn576LysfsTer8	p.N576Kfs*8	ENST00000439151	NM_022455.4	574	gga/ggAa	5/23	1	2	FACETS	0.748	0.629	0.879	0.748	0.629	0.879	SUBCLONAL	1	TRUE	1	0.22	2		469	559	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050414	176050414	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148950158	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	18	266	0	ENST00000367669.3:c.1151G>A	p.Arg384Gln	p.R384Q	ENST00000367669	NM_022457.5	384	cGa/cAa	11/20	1	2	FACETS	0.544	0.409	0.703	0.544	0.409	0.703	SUBCLONAL	1	TRUE	1	0.22	2		266	301	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131951755	131951755	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	32	247	1	ENST00000265335.6:c.3097G>T	p.Glu1033Ter	p.E1033*	ENST00000265335		1033	Gaa/Taa	20/25	1	2	FACETS	0.924	0.751	1	0.924	0.751	1	CLONAL	1	TRUE	1	0.22	2		248	315	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720928	176720928	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784209	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	74	456	0	ENST00000439151.2:c.6559C>T	p.Arg2187Ter	p.R2187*	ENST00000439151	NM_022455.4	2187	Cga/Tga	23/23	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.22	2		456	601	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115681	108115681	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs876660933	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	24	297	0	ENST00000278616.4:c.829G>T	p.Glu277Ter	p.E277*	ENST00000278616	NM_000051.3	277	Gaa/Taa	7/63	1	2	FACETS	0.788	0.619	0.982	0.788	0.619	0.982	CLONAL	1	TRUE	1	0.22	2		297	277	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740436	58740436	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs769061997	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	43	481	1	ENST00000305921.3:c.1341G>T	p.Glu447Asp	p.E447D	ENST00000305921	NM_003620.3	447	gaG/gaT	6/6	1	2	FACETS	0.739	0.618	0.873	0.739	0.618	0.873	SUBCLONAL	1	TRUE	1	0.22	2		482	529	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813432	102813432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751304020	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	93	523	0	ENST00000307046.8:c.257C>T	p.Ala86Val	p.A86V	ENST00000307046	NM_001111285.1	86	gCg/gTg	3/4	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.22	2		523	717	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376881	118376881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140200473	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	50	388	1	ENST00000534358.1:c.10274C>T	p.Ala3425Val	p.A3425V	ENST00000534358	NM_005933.3	3425	gCg/gTg	27/36	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.22	2		389	449	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245519	46245519	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371267186	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	52	326	0	ENST00000334344.6:c.3613G>A	p.Gly1205Arg	p.G1205R	ENST00000334344	NM_152641.2	1205	Gga/Aga	15/21	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.22	2		326	390	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609954	117609954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369184938	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	22	342	1	ENST00000368508.3:c.6745G>A	p.Asp2249Asn	p.D2249N	ENST00000368508	NM_002944.2	2249	Gat/Aat	43/43	1	2	FACETS	0.606	0.47	0.765	0.606	0.47	0.765	SUBCLONAL	1	TRUE	1	0.22	2		343	330	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485783	57485783	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	41	366	1	ENST00000371085.3:c.1084C>A	p.His362Asn	p.H362N	ENST00000371085	NM_000516.4	362	Cat/Aat	13/13	1	2	FACETS	0.609	0.506	0.724	0.609	0.506	0.724	SUBCLONAL	1	TRUE	1	0.22	2		367	612	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851828	63851828	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs201944744	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	40	501	0	ENST00000279873.7:c.2606C>A	p.Ser869Tyr	p.S869Y	ENST00000279873	NM_032199.2	869	tCt/tAt	10/10	1	2	FACETS	0.497	0.412	0.593	0.497	0.412	0.593	SUBCLONAL	1	TRUE	1	0.22	2		501	731	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277291	41277291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	38	335	1	ENST00000349496.5:c.1760G>A	p.Arg587Gln	p.R587Q	ENST00000349496	NM_001904.3	587	cGa/cAa	11/15	1	2	FACETS	0.73	0.604	0.872	0.73	0.604	0.872	SUBCLONAL	1	TRUE	1	0.22	2		336	473	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845479	128845479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	84	569	3	ENST00000249373.3:c.776C>T	p.Ser259Leu	p.S259L	ENST00000249373	NM_005631.4	259	tCg/tTg	4/12	1	2	FACETS	0.899	0.793	1	0.899	0.793	1	CLONAL	1	TRUE	1	0.22	2		572	849	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872009	35872009	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	69	455	0	ENST00000216797.5:c.604T>G	p.Leu202Val	p.L202V	ENST00000216797	NM_020529.2	202	Ttg/Gtg	4/6	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.22	2		455	588	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69011978	69011978	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	89	448	0	ENST00000288368.4:c.2615C>A	p.Ser872Tyr	p.S872Y	ENST00000288368	NM_024870.2	872	tCt/tAt	23/40	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.22	2		448	649	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463197	25463197	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	69	536	0	ENST00000264709.3:c.2296A>G	p.Lys766Glu	p.K766E	ENST00000264709	NM_175629.2	766	Aag/Gag	19/23	1	2	FACETS	0.899	0.782	1	0.899	0.782	1	CLONAL	1	TRUE	1	0.22	2		536	698	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248553	8248553	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757437334	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	86	608	1	ENST00000335790.3:c.334G>A	p.Asp112Asn	p.D112N	ENST00000335790	NM_002315.2	112	Gac/Aac	3/4	1	2	FACETS	0.97	0.857	1	0.97	0.857	1	CLONAL	1	TRUE	1	0.22	2		609	806	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430201	181430201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	37	319	0	ENST00000325404.1:c.53C>T	p.Ser18Leu	p.S18L	ENST00000325404	NM_003106.3	18	tCg/tTg	1/1	1	2	FACETS	0.807	0.665	0.964	0.807	0.665	0.964	CLONAL	1	TRUE	1	0.22	2		319	417	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944857	131944857	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	15	240	0	ENST00000265335.6:c.2878G>T	p.Asp960Tyr	p.D960Y	ENST00000265335		960	Gac/Tac	18/25	1	2	FACETS	0.489	0.357	0.647	0.489	0.357	0.647	SUBCLONAL	1	TRUE	1	0.22	2		240	279	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656601	3656601	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1395992833	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	99	586	2	ENST00000294008.3:c.634C>T	p.Arg212Ter	p.R212*	ENST00000294008	NM_032444.2	212	Cga/Tga	3/15	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.22	2		588	897	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47061267	47061267	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	60	433	0	ENST00000409792.3:c.7414G>T	p.Glu2472Ter	p.E2472*	ENST00000409792	NM_014159.6	2472	Gaa/Taa	19/21	1	2	FACETS	0.909	0.783	1	0.909	0.783	1	CLONAL	1	TRUE	1	0.22	2		433	600	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294420	1294420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	96	696	0	ENST00000310581.5:c.581G>A	p.Arg194Gln	p.R194Q	ENST00000310581	NM_198253.2	194	cGa/cAa	2/16	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.22	2		696	802	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254535	10254535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746527645	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	73	526	0	ENST00000340748.4:c.2975G>A	p.Arg992Gln	p.R992Q	ENST00000340748		992	cGa/cAa	28/40	1	2	FACETS	0.988	0.863	1	0.988	0.863	1	CLONAL	1	TRUE	1	0.22	2		526	672	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50482348	50482348	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	66	439	1	ENST00000394963.4:c.699C>A	p.Phe233Leu	p.F233L	ENST00000394963	NM_003076.4	233	ttC/ttA	6/13	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.22	2		440	550	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177644	56177644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149242419	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	45	386	2	ENST00000399503.3:c.2617G>A	p.Val873Ile	p.V873I	ENST00000399503	NM_005921.1	873	Gta/Ata	14/20	1	2	FACETS	0.778	0.653	0.915	0.778	0.653	0.915	CLONAL	1	TRUE	1	0.22	2		388	526	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023343	27023343	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	25	219	0	ENST00000324856.7:c.449T>C	p.Phe150Ser	p.F150S	ENST00000324856	NM_006015.4	150	tTc/tCc	1/20	1	2	FACETS	0.695	0.548	0.864	0.695	0.548	0.864	SUBCLONAL	1	TRUE	1	0.22	2		219	327	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303757	65303757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs897926965	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	36	482	0	ENST00000342505.4:c.2998G>A	p.Val1000Ile	p.V1000I	ENST00000342505	NM_002227.2	1000	Gtt/Att	22/25	1	2	FACETS	0.507	0.416	0.61	0.507	0.416	0.61	SUBCLONAL	1	TRUE	1	0.22	2		482	645	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280103	115280103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs538505760	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	57	382	0	ENST00000438362.2:c.529G>A	p.Glu177Lys	p.E177K	ENST00000438362	NM_001242891.1	177	Gaa/Aaa	5/20	1	2	FACETS	0.798	0.684	0.923	0.798	0.684	0.923	CLONAL	1	TRUE	1	0.22	2		382	649	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830919	156830919	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	66	547	1	ENST00000524377.1:c.193G>A	p.Ala65Thr	p.A65T	ENST00000524377	NM_002529.3	65	Gca/Aca	1/17	1	2	FACETS	0.881	0.764	1	0.881	0.764	1	CLONAL	1	TRUE	1	0.22	2		548	681	SUCCESS
RET	5979	MSKCC	GRCh37	10	43598036	43598036	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	108	675	0	ENST00000355710.3:c.584T>G	p.Phe195Cys	p.F195C	ENST00000355710	NM_020975.4	195	tTc/tGc	3/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.22	2		675	884	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717619	89717619	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	26	337	0	ENST00000371953.3:c.644T>C	p.Phe215Ser	p.F215S	ENST00000371953	NM_000314.4	215	tTt/tCt	7/9	1	2	FACETS	0.634	0.502	0.785	0.634	0.502	0.785	SUBCLONAL	1	TRUE	1	0.22	2		337	373	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119762	108119762	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	20	229	0	ENST00000278616.4:c.1168G>T	p.Glu390Ter	p.E390*	ENST00000278616	NM_000051.3	390	Gaa/Taa	9/63	1	2	FACETS	0.525	0.401	0.671	0.525	0.401	0.671	SUBCLONAL	1	TRUE	1	0.22	2		229	346	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158372	108158372	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	45	361	0	ENST00000278616.4:c.4039T>G	p.Leu1347Val	p.L1347V	ENST00000278616	NM_000051.3	1347	Tta/Gta	27/63	1	2	FACETS	0.872	0.733	1	0.872	0.733	1	CLONAL	1	TRUE	1	0.22	2		361	469	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438149	438149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	48	359	0	ENST00000399788.2:c.1820G>A	p.Arg607His	p.R607H	ENST00000399788	NM_001042603.1	607	cGc/cAc	14/28	0.3	1	FACETS	0.75	0.634	0.877	0.75	0.634	0.877	SUBCLONAL	1	TRUE	0	0.22	1		359	518	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145317	58145317	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs745481376	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	70	514	0	ENST00000257904.6:c.184C>T	p.Arg62Ter	p.R62*	ENST00000257904	NM_000075.3	62	Cga/Tga	2/8	1	2	FACETS	0.898	0.782	1	0.898	0.782	1	CLONAL	1	TRUE	1	0.22	2		514	709	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435139	110435139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	74	631	2	ENST00000375856.3:c.3262G>A	p.Ala1088Thr	p.A1088T	ENST00000375856	NM_003749.2	1088	Gcg/Acg	1/2	1	2	FACETS	0.78	0.681	0.886	0.78	0.681	0.886	SUBCLONAL	1	TRUE	1	0.22	2		633	863	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245269	41245269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161074446	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	61	550	0	ENST00000357654.3:c.2279C>T	p.Thr760Ile	p.T760I	ENST00000357654	NM_007294.3	760	aCt/aTt	10/23	1	2	FACETS	0.93	0.803	1	0.93	0.803	1	CLONAL	1	TRUE	1	0.22	2		550	596	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610079	10610079	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	59	564	0	ENST00000171111.5:c.631T>G	p.Phe211Val	p.F211V	ENST00000171111	NM_203500.1	211	Ttt/Gtt	2/6	1	2	FACETS	0.707	0.607	0.816	0.707	0.607	0.816	SUBCLONAL	1	TRUE	1	0.22	2		564	759	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610379	10610379	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	95	783	0	ENST00000171111.5:c.331T>C	p.Phe111Leu	p.F111L	ENST00000171111	NM_203500.1	111	Ttc/Ctc	2/6	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.22	2		783	864	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617410	158617410	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	46	371	0	ENST00000263640.3:c.1246A>G	p.Arg416Gly	p.R416G	ENST00000263640	NM_001105.4	416	Agg/Ggg	9/11	1	2	FACETS	0.871	0.734	1	0.871	0.734	1	CLONAL	1	TRUE	1	0.22	2		371	480	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719477	190719477	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	30	306	0	ENST00000441310.2:c.1479T>G	p.Ile493Met	p.I493M	ENST00000441310	NM_000534.4	493	atT/atG	9/13	1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	1	0.22	2		306	259	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376145	225376145	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	47	441	4	ENST00000264414.4:c.809C>A	p.Ser270Tyr	p.S270Y	ENST00000264414	NM_003590.4	270	tCc/tAc	6/16	1	2	FACETS	0.819	0.691	0.96	0.819	0.691	0.96	CLONAL	1	TRUE	1	0.22	2		445	522	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660855	227660855	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	69	612	0	ENST00000305123.5:c.2600A>C	p.Lys867Thr	p.K867T	ENST00000305123	NM_005544.2	867	aAg/aCg	1/2	1	2	FACETS	0.94	0.819	1	0.94	0.819	1	CLONAL	1	TRUE	1	0.22	2		612	667	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162130	22162130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	38	291	0	ENST00000215832.6:c.125C>T	p.Ala42Val	p.A42V	ENST00000215832	NM_002745.4	42	gCt/gTt	2/9	1	2	FACETS	0.884	0.731	1	0.884	0.731	1	CLONAL	1	TRUE	1	0.22	2		291	391	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545144	41545144	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	61	494	0	ENST00000263253.7:c.2344T>G	p.Leu782Val	p.L782V	ENST00000263253	NM_001429.3	782	Ttg/Gtg	13/31	1	2	FACETS	0.883	0.761	1	0.883	0.761	1	CLONAL	1	TRUE	1	0.22	2		494	628	SUCCESS
ATR	545	MSKCC	GRCh37	3	142171996	142171996	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	44	485	0	ENST00000350721.4:c.7735G>T	p.Glu2579Ter	p.E2579*	ENST00000350721	NM_001184.3	2579	Gaa/Taa	46/47	1	2	FACETS	0.686	0.575	0.81	0.686	0.575	0.81	SUBCLONAL	1	TRUE	1	0.22	2		485	583	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211133	55211133	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	59	425	0	ENST00000275493.2:c.376G>T	p.Asp126Tyr	p.D126Y	ENST00000275493	NM_005228.3	126	Gat/Tat	3/28	1	2	FACETS	0.961	0.827	1	0.961	0.827	1	CLONAL	1	TRUE	1	0.22	2		425	558	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509115	106509115	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	77	543	0	ENST00000359195.3:c.1109T>C	p.Ile370Thr	p.I370T	ENST00000359195	NM_002649.2	370	aTc/aCc	2/11	1	2	FACETS	0.921	0.808	1	0.921	0.808	1	CLONAL	1	TRUE	1	0.22	2		543	760	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418991	116418991	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	32	230	0	ENST00000397752.3:c.3502T>G	p.Phe1168Val	p.F1168V	ENST00000397752	NM_000245.2	1168	Ttc/Gtc	17/21	1	2	FACETS	0.938	0.764	1	0.938	0.764	1	CLONAL	1	TRUE	1	0.22	2		230	310	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989692	68989692	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	60	469	1	ENST00000288368.4:c.1630T>G	p.Phe544Val	p.F544V	ENST00000288368	NM_024870.2	544	Ttt/Gtt	15/40	1	2	FACETS	0.887	0.764	1	0.887	0.764	1	CLONAL	1	TRUE	1	0.22	2		470	615	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248028	98248028	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	49	449	0	ENST00000331920.6:c.523C>T	p.Leu175Phe	p.L175F	ENST00000331920	NM_000264.3	175	Ctc/Ttc	3/24	1	2	FACETS	0.717	0.607	0.839	0.717	0.607	0.839	SUBCLONAL	1	TRUE	1	0.22	2		449	621	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411643	63411643	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1288332581	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	61	638	0	ENST00000330258.3:c.1524C>A	p.Phe508Leu	p.F508L	ENST00000330258	NM_152424.3	508	ttC/ttA	2/2	1	2	FACETS	0.775	0.667	0.892	0.775	0.667	0.892	SUBCLONAL	1	TRUE	1	0.22	2		638	716	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849307	76849307	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	43	371	0	ENST00000373344.5:c.5969C>A	p.Ser1990Tyr	p.S1990Y	ENST00000373344	NM_000489.3	1990	tCt/tAt	26/35	1	2	FACETS	0.842	0.705	0.994	0.842	0.705	0.994	CLONAL	1	TRUE	1	0.22	2		371	464	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617582	100617582	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs782454588	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	93	572	0	ENST00000308731.7:c.487A>G	p.Met163Val	p.M163V	ENST00000308731	NM_000061.2	163	Atg/Gtg	6/19	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.22	2		572	719	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023116	48023116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569728764	NA	P-0051091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	36	383	0	ENST00000234420.5:c.541G>A	p.Glu181Lys	p.E181K	ENST00000234420	NM_000179.2	181	Gaa/Aaa	3/10	1	2	FACETS	0.617	0.507	0.742	0.617	0.507	0.742	SUBCLONAL	1	TRUE	1	0.22	2		383	530	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	63	230	0				ENST00000310581	NM_198253.2	-/1132			0.263844511873782	3	FACETS	1	0.964	1	0.663	0.577	0.754	CLONAL	1	TRUE	1	0.347741512623632	3		230	321	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974783	21974783	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658556	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	109	316	0	ENST00000304494.5:c.44G>A	p.Trp15Ter	p.W15*	ENST00000304494	NM_000077.4	15	tGg/tAg	1/3	0.337750366489652	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.347741512623632	2		316	285	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	130	718	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	1	2	FACETS	0.975	0.885	1	0.975	0.885	1	CLONAL	1	TRUE	1	0.347741512623632	2		718	767	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780071	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	84	562	0	ENST00000269305.4:c.580C>T	p.Leu194Phe	p.L194F	ENST00000269305	NM_001126112.2	194	Ctt/Ttt	6/11	1	2	FACETS	0.756	0.668	0.85	0.756	0.668	0.85	SUBCLONAL	1	TRUE	1	0.347741512623632	2		562	639	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041739	29041739	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	34	327	0	ENST00000282397.4:c.80C>T	p.Ser27Leu	p.S27L	ENST00000282397	NM_002019.4	27	tCa/tTa	2/30	1	2	FACETS	0.486	0.397	0.586	0.486	0.397	0.586	SUBCLONAL	1	TRUE	1	0.347741512623632	2		327	402	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642495	117642495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs9489124	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	89	644	0	ENST00000368508.3:c.5704G>A	p.Glu1902Lys	p.E1902K	ENST00000368508	NM_002944.2	1902	Gaa/Aaa	35/43	1	2	FACETS	0.824	0.732	0.923	0.824	0.732	0.923	CLONAL	1	TRUE	1	0.347741512623632	2		644	621	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054194	30054194	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	86	450	0	ENST00000338641.4:c.616G>T	p.Glu206Ter	p.E206*	ENST00000338641	NM_000268.3	206	Gaa/Taa	7/16	0.305938638551807	1	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	0	0.347741512623632	1		450	406	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249626	110249626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	281	869	1	ENST00000374672.4:c.1049C>T	p.Ser350Phe	p.S350F	ENST00000374672	NM_004235.4	350	tCc/tTc	3/5	0.340012620977856	3	FACETS	1	0.982	1	0.733	0.69	0.776	CLONAL	2	TRUE	0	0.347741512623632	3		870	863	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916917	178916917	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	69	430	0	ENST00000263967.3:c.304A>T	p.Ile102Phe	p.I102F	ENST00000263967	NM_006218.2	102	Att/Ttt	2/21	1	2	FACETS	0.756	0.659	0.86	0.756	0.659	0.86	SUBCLONAL	1	TRUE	1	0.347741512623632	2		430	525	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225449690	225449690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	72	392	0	ENST00000264414.4:c.37G>A	p.Asp13Asn	p.D13N	ENST00000264414	NM_003590.4	13	Gac/Aac	1/16	0.26795479357674	2	FACETS	1	0.965	1	0.633	0.557	0.713	CLONAL	1	TRUE	0	0.347741512623632	2		392	327	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953871	55953871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	60	476	0	ENST00000263923.4:c.3565G>A	p.Asp1189Asn	p.D1189N	ENST00000263923	NM_002253.2	1189	Gat/Aat	27/30	1	2	FACETS	0.769	0.664	0.882	0.769	0.664	0.882	SUBCLONAL	1	TRUE	1	0.347741512623632	2		476	449	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223358	36223358	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	114	895	0	ENST00000222270.7:c.5908C>T	p.Pro1970Ser	p.P1970S	ENST00000222270	NM_014727.1	1970	Cct/Tct	28/37	1	2	FACETS	0.847	0.763	0.936	0.847	0.763	0.936	CLONAL	1	TRUE	1	0.347741512623632	2		895	774	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125476	7125476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	119	740	0	ENST00000302850.5:c.3076C>T	p.Leu1026Phe	p.L1026F	ENST00000302850	NM_000208.2	1026	Ctt/Ttt	17/22	1	2	FACETS	0.972	0.879	1	0.972	0.879	1	CLONAL	1	TRUE	1	0.347741512623632	2		740	704	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606353	93606353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	272	684	0	ENST00000375746.1:c.173G>A	p.Gly58Glu	p.G58E	ENST00000375746	NM_001174167.1	58	gGg/gAg	2/14	0.340012620977856	3	FACETS	0.918	0.867	0.969	0.918	0.867	0.969	CLONAL	3	TRUE	0	0.347741512623632	3		684	667	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420955	49420955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	36	558	2	ENST00000301067.7:c.14794C>T	p.Pro4932Ser	p.P4932S	ENST00000301067	NM_003482.3	4932	Ccc/Tcc	48/54	1	2	FACETS	0.536	0.441	0.643	0.536	0.441	0.643	SUBCLONAL	1	TRUE	1	0.347741512623632	2		560	386	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217458	142217458	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	47	420	0	ENST00000350721.4:c.5539G>A	p.Gly1847Arg	p.G1847R	ENST00000350721	NM_001184.3	1847	Gga/Aga	32/47	1	2	FACETS	0.727	0.615	0.849	0.727	0.615	0.849	SUBCLONAL	1	TRUE	1	0.347741512623632	2		420	372	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884605	111884605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1402866378	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	75	511	0	ENST00000341259.2:c.781C>T	p.Arg261Trp	p.R261W	ENST00000341259	NM_005475.2	261	Cgg/Tgg	3/8	1	2	FACETS	0.87	0.764	0.983	0.87	0.764	0.983	CLONAL	1	TRUE	1	0.347741512623632	2		511	496	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347623	118347623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	114	562	0	ENST00000534358.1:c.3260C>T	p.Pro1087Leu	p.P1087L	ENST00000534358	NM_005933.3	1087	cCt/cTt	4/36	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.347741512623632	2		562	636	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2492116	2492117	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	106	729	0	ENST00000355716.4:c.514_515delinsTT	p.Pro172Phe	p.P172F	ENST00000355716	NM_003820.2	172	CCc/TTc	5/8	1	2	FACETS	0.865	0.776	0.959	0.865	0.776	0.959	CLONAL	1	TRUE	1	0.347741512623632	2		729	705	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782335	9782335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	105	739	0	ENST00000377346.4:c.2268G>A	p.Met756Ile	p.M756I	ENST00000377346	NM_005026.3	756	atG/atA	18/24	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.347741512623632	2		739	582	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307212	65307213	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	95	510	0	ENST00000342505.4:c.2475_2476delinsTT	p.Arg826Cys	p.R826C	ENST00000342505	NM_002227.2	825	acCCgc/acTTgc	18/25	1	2	FACETS	0.974	0.869	1	0.974	0.869	1	CLONAL	1	TRUE	1	0.347741512623632	2		510	561	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483263	120483263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	63	476	0	ENST00000256646.2:c.3098C>T	p.Pro1033Leu	p.P1033L	ENST00000256646	NM_024408.3	1033	cCa/cTa	19/34	1	2	FACETS	0.774	0.671	0.886	0.774	0.671	0.886	SUBCLONAL	1	TRUE	1	0.347741512623632	2		476	468	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226558200	226558200	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	81	465	0	ENST00000366794.5:c.2089C>T	p.Pro697Ser	p.P697S	ENST00000366794	NM_001618.3	697	Ccc/Tcc	15/23	1	2	FACETS	0.987	0.873	1	0.987	0.873	1	CLONAL	1	TRUE	1	0.347741512623632	2		465	472	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850890	63850891	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	63	455	1	ENST00000279873.7:c.1668_1669delinsTT	p.Pro557Ser	p.P557S	ENST00000279873	NM_032199.2	556	gtCCct/gtTTct	10/10	1	2	FACETS	0.735	0.637	0.841	0.735	0.637	0.841	SUBCLONAL	1	TRUE	1	0.347741512623632	2		456	493	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947618	48947618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	23	177	0	ENST00000267163.4:c.1205C>T	p.Ser402Phe	p.S402F	ENST00000267163	NM_000321.2	402	tCc/tTc	12/27	1	2	FACETS	0.471	0.367	0.59	0.471	0.367	0.59	SUBCLONAL	1	TRUE	1	0.347741512623632	2		177	281	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213962	2213962	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	126	635	0	ENST00000326181.6:c.41G>A	p.Gly14Glu	p.G14E	ENST00000326181	NM_032271.2	14	gGg/gAg	2/21	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.347741512623632	2		635	685	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656667	3656667	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753758188	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	119	784	3	ENST00000294008.3:c.568C>T	p.Pro190Ser	p.P190S	ENST00000294008	NM_032444.2	190	Cct/Tct	3/15	1	2	FACETS	0.811	0.732	0.895	0.811	0.732	0.895	CLONAL	1	TRUE	1	0.347741512623632	2		787	844	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845901	72845901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	97	501	1	ENST00000268489.5:c.3566C>T	p.Ser1189Phe	p.S1189F	ENST00000268489	NM_006885.3	1189	tCt/tTt	6/10	1	2	FACETS	0.965	0.863	1	0.965	0.863	1	CLONAL	1	TRUE	1	0.347741512623632	2		502	578	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78617537	78617537	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759088888	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	57	368	0	ENST00000306801.3:c.275C>T	p.Ser92Leu	p.S92L	ENST00000306801	NM_020761.2	92	tCg/tTg	3/34	1	2	FACETS	0.826	0.711	0.95	0.826	0.711	0.95	CLONAL	1	TRUE	1	0.347741512623632	2		368	397	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950291	17950291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	128	641	0	ENST00000458235.1:c.1436C>T	p.Pro479Leu	p.P479L	ENST00000458235	NM_000215.3	479	cCc/cTc	10/24	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.347741512623632	2		641	731	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731619	47731620	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	97	175	1	ENST00000449228.1:c.172_173delinsTT	p.Pro58Phe	p.P58F	ENST00000449228	NM_001127240.2	58	CCc/TTc	2/4	0.337750366489652	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.347741512623632	2		176	260	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469166	25469166	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	179	639	0	ENST00000264709.3:c.1292C>T	p.Pro431Leu	p.P431L	ENST00000264709	NM_175629.2	431	cCc/cTc	11/23	0.26795479357674	2	FACETS	0.908	0.842	0.975	0.908	0.842	0.975	CLONAL	2	TRUE	0	0.347741512623632	2		639	567	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39751934	39751934	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	77	350	1	ENST00000361337.2:c.2295T>A	p.Phe765Leu	p.F765L	ENST00000361337	NM_003286.2	765	ttT/ttA	21/21	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.347741512623632	2		351	440	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927945	49927946	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	84	573	1	ENST00000296474.3:c.3782_3783delinsTT	p.Thr1261Ile	p.T1261I	ENST00000296474	NM_002447.2	1261	aCC/aTT	18/20	1	2	FACETS	0.852	0.754	0.957	0.852	0.754	0.957	CLONAL	1	TRUE	1	0.347741512623632	2		574	567	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499453	89499453	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	65	466	0	ENST00000336596.2:c.2623G>T	p.Val875Phe	p.V875F	ENST00000336596	NM_005233.5	875	Gtt/Ttt	15/17	1	2	FACETS	0.715	0.62	0.817	0.715	0.62	0.817	SUBCLONAL	1	TRUE	1	0.347741512623632	2		466	523	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161357	185161358	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	68	539	1	ENST00000265026.3:c.784_785delinsAA	p.Gly262Lys	p.G262K	ENST00000265026	NM_004721.4	262	GGa/AAa	4/14	1	2	FACETS	0.703	0.612	0.802	0.703	0.612	0.802	SUBCLONAL	1	TRUE	1	0.347741512623632	2		540	556	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861019	35861020	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	105	379	0	ENST00000303115.3:c.148_149delinsAA	p.Gly50Lys	p.G50K	ENST00000303115	NM_002185.3	50	GGa/AAa	2/8	0.263844511873782	3	FACETS	1	0.978	1	0.664	0.597	0.734	CLONAL	1	TRUE	1	0.347741512623632	3		379	534	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627245	86627245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	112	323	0	ENST00000274376.6:c.620G>A	p.Arg207Lys	p.R207K	ENST00000274376	NM_002890.2	207	aGa/aAa	2/25	0.26795479357674	2	FACETS	0.765	0.693	0.84	0.765	0.693	0.84	SUBCLONAL	2	TRUE	0	0.347741512623632	2		323	421	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501539	149501539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	163	574	0	ENST00000261799.4:c.2248G>A	p.Asp750Asn	p.D750N	ENST00000261799	NM_002609.3	750	Gac/Aac	16/23	0.26795479357674	2	FACETS	0.786	0.725	0.85	0.786	0.725	0.85	SUBCLONAL	2	TRUE	0	0.347741512623632	2		574	596	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508940	106508940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	68	420	0	ENST00000359195.3:c.934G>A	p.Asp312Asn	p.D312N	ENST00000359195	NM_002649.2	312	Gac/Aac	2/11	1	2	FACETS	0.901	0.787	1	0.901	0.787	1	CLONAL	1	TRUE	1	0.347741512623632	2		420	434	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434474	140434475	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	87	393	1	ENST00000288602.6:c.2223_2224delinsAA	p.Asp742Asn	p.D742N	ENST00000288602	NM_004333.4	741	gaGGat/gaAAat	18/18	1	2	FACETS	0.949	0.843	1	0.949	0.843	1	CLONAL	1	TRUE	1	0.347741512623632	2		394	527	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98222059	98222059	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	229	354	0	ENST00000331920.6:c.2710A>T	p.Lys904Ter	p.K904*	ENST00000331920	NM_000264.3	904	Aaa/Taa	17/24	0.340012620977856	3	FACETS	0.96	0.903	1	0.96	0.903	1	CLONAL	3	TRUE	0	0.347741512623632	3		354	537	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231163	98231163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	264	719	0	ENST00000331920.6:c.2120C>T	p.Ser707Phe	p.S707F	ENST00000331920	NM_000264.3	707	tCc/tTc	14/24	0.340012620977856	3	FACETS	1	0.985	1	0.756	0.711	0.801	CLONAL	2	TRUE	0	0.347741512623632	3		719	786	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403482	139403482	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs201163739	NA	P-0051092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	452	841	1	ENST00000277541.6:c.3011C>A	p.Ser1004Ter	p.S1004*	ENST00000277541	NM_017617.3	1004	tCg/tAg	19/34	0.340012620977856	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	0	0.347741512623632	3		842	985	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	26	230	0				ENST00000310581	NM_198253.2	-/1132			0.246470487816303	0	FACETS	0.669	0.537	0.816			1	SUBCLONAL	1	FALSE	0	0.361987141322278	0		230	137	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	88	718	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.242907821070149	3	FACETS	1	0.954	1	0.571	0.507	0.638	CLONAL	1	FALSE	1	0.361987141322278	3		718	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780071	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	82	562	0	ENST00000269305.4:c.580C>T	p.Leu194Phe	p.L194F	ENST00000269305	NM_001126112.2	194	Ctt/Ttt	6/11	0.242907821070149	3	FACETS	1	0.964	1	0.612	0.542	0.687	CLONAL	1	FALSE	1	0.361987141322278	3		562	437	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642495	117642495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs9489124	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	66	644	0	ENST00000368508.3:c.5704G>A	p.Glu1902Lys	p.E1902K	ENST00000368508	NM_002944.2	1902	Gaa/Aaa	35/43	0.280704502735192	1	FACETS	0.863	0.754	0.98	0.863	0.754	0.98	CLONAL	1	FALSE	0	0.361987141322278	1		644	346	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249626	110249626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	73	869	1	ENST00000374672.4:c.1049C>T	p.Ser350Phe	p.S350F	ENST00000374672	NM_004235.4	350	tCc/tTc	3/5	0.348444832711709	2	FACETS	0.789	0.692	0.894	0.395	0.346	0.447	SUBCLONAL	1	FALSE	0	0.361987141322278	2		870	511	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916917	178916917	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	48	430	0	ENST00000263967.3:c.304A>T	p.Ile102Phe	p.I102F	ENST00000263967	NM_006218.2	102	Att/Ttt	2/21	1	2	FACETS	0.536	0.453	0.627	0.536	0.453	0.627	SUBCLONAL	1	FALSE	1	0.361987141322278	2		430	495	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225449690	225449690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	63	392	0	ENST00000264414.4:c.37G>A	p.Asp13Asn	p.D13N	ENST00000264414	NM_003590.4	13	Gac/Aac	1/16	0.16883960452085	4	FACETS	1	0.959	1	0.637	0.554	0.727	INDETERMINATE	1	FALSE	2	0.361987141322278	4		392	372	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953871	55953871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	22	476	0	ENST00000263923.4:c.3565G>A	p.Asp1189Asn	p.D1189N	ENST00000263923	NM_002253.2	1189	Gat/Aat	27/30	0.362017512991925	0	FACETS	0.375	0.291	0.47			1	SUBCLONAL	1	FALSE	0	0.361987141322278	0		476	207	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223358	36223358	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	72	895	0	ENST00000222270.7:c.5908C>T	p.Pro1970Ser	p.P1970S	ENST00000222270	NM_014727.1	1970	Cct/Tct	28/37	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	FALSE	1	0.361987141322278	2		895	391	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125476	7125476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	51	740	0	ENST00000302850.5:c.3076C>T	p.Leu1026Phe	p.L1026F	ENST00000302850	NM_000208.2	1026	Ctt/Ttt	17/22	0.225782523851511	0	FACETS	0.524	0.447	0.608			1	SUBCLONAL	1	FALSE	0	0.361987141322278	0		740	343	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606353	93606353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	108	684	0	ENST00000375746.1:c.173G>A	p.Gly58Glu	p.G58E	ENST00000375746	NM_001174167.1	58	gGg/gAg	2/14	0.348444832711709	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	FALSE	0	0.361987141322278	2		684	279	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420955	49420955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	62	558	2	ENST00000301067.7:c.14794C>T	p.Pro4932Ser	p.P4932S	ENST00000301067	NM_003482.3	4932	Ccc/Tcc	48/54	0.328611535460859	4	FACETS	1	0.932	1	0.561	0.486	0.642	CLONAL	1	FALSE	2	0.361987141322278	4		560	416	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217458	142217458	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	58	420	0	ENST00000350721.4:c.5539G>A	p.Gly1847Arg	p.G1847R	ENST00000350721	NM_001184.3	1847	Gga/Aga	32/47	1	2	FACETS	0.94	0.812	1	0.94	0.812	1	CLONAL	1	FALSE	1	0.361987141322278	2		420	341	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884605	111884605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1402866378	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	44	511	0	ENST00000341259.2:c.781C>T	p.Arg261Trp	p.R261W	ENST00000341259	NM_005475.2	261	Cgg/Tgg	3/8	0.328611535460859	4	FACETS	0.838	0.704	0.986	0.419	0.352	0.493	CLONAL	1	FALSE	2	0.361987141322278	4		511	395	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347623	118347623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	63	562	0	ENST00000534358.1:c.3260C>T	p.Pro1087Leu	p.P1087L	ENST00000534358	NM_005933.3	1087	cCt/cTt	4/36	1	2	FACETS	0.827	0.717	0.945	0.827	0.717	0.945	CLONAL	1	FALSE	1	0.361987141322278	2		562	421	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2492116	2492117	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	49	729	0	ENST00000355716.4:c.514_515delinsTT	p.Pro172Phe	p.P172F	ENST00000355716	NM_003820.2	172	CCc/TTc	5/8	0.280704502735192	1	FACETS	0.601	0.51	0.7	0.601	0.51	0.7	SUBCLONAL	1	FALSE	0	0.361987141322278	1		729	369	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782335	9782335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	41	739	0	ENST00000377346.4:c.2268G>A	p.Met756Ile	p.M756I	ENST00000377346	NM_005026.3	756	atG/atA	18/24	0.280704502735192	1	FACETS	0.53	0.443	0.627	0.53	0.443	0.627	SUBCLONAL	1	FALSE	0	0.361987141322278	1		739	350	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307212	65307213	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	48	510	0	ENST00000342505.4:c.2475_2476delinsTT	p.Arg826Cys	p.R826C	ENST00000342505	NM_002227.2	825	acCCgc/acTTgc	18/25	1	2	FACETS	0.691	0.585	0.806	0.691	0.585	0.806	SUBCLONAL	1	FALSE	1	0.361987141322278	2		510	384	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483263	120483263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	67	476	0	ENST00000256646.2:c.3098C>T	p.Pro1033Leu	p.P1033L	ENST00000256646	NM_024408.3	1033	cCa/cTa	19/34	1	2	FACETS	0.974	0.851	1	0.974	0.851	1	CLONAL	1	FALSE	1	0.361987141322278	2		476	380	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226558200	226558200	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	61	465	0	ENST00000366794.5:c.2089C>T	p.Pro697Ser	p.P697S	ENST00000366794	NM_001618.3	697	Ccc/Tcc	15/23	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	FALSE	1	0.361987141322278	2		465	314	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850890	63850891	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	67	455	1	ENST00000279873.7:c.1668_1669delinsTT	p.Pro557Ser	p.P557S	ENST00000279873	NM_032199.2	556	gtCCct/gtTTct	10/10	0.361987141322278	9	FACETS	0.801	0.697	0.913			1	CLONAL	2	FALSE	NA	0.361987141322278	9		456	524	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947618	48947618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	47	177	0	ENST00000267163.4:c.1205C>T	p.Ser402Phe	p.S402F	ENST00000267163	NM_000321.2	402	tCc/tTc	12/27	0.341634619754662	4	FACETS	0.869	0.735	1			1	CLONAL	1	FALSE	NA	0.361987141322278	4		177	407	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213962	2213962	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	84	635	0	ENST00000326181.6:c.41G>A	p.Gly14Glu	p.G14E	ENST00000326181	NM_032271.2	14	gGg/gAg	2/21	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	FALSE	1	0.361987141322278	2		635	432	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656667	3656667	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753758188	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	66	784	3	ENST00000294008.3:c.568C>T	p.Pro190Ser	p.P190S	ENST00000294008	NM_032444.2	190	Cct/Tct	3/15	1	2	FACETS	0.725	0.63	0.827	0.725	0.63	0.827	SUBCLONAL	1	FALSE	1	0.361987141322278	2		787	503	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845901	72845901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	36	501	1	ENST00000268489.5:c.3566C>T	p.Ser1189Phe	p.S1189F	ENST00000268489	NM_006885.3	1189	tCt/tTt	6/10	1	2	FACETS	0.633	0.522	0.757	0.633	0.522	0.757	SUBCLONAL	1	FALSE	1	0.361987141322278	2		502	314	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78617537	78617537	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759088888	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	41	368	0	ENST00000306801.3:c.275C>T	p.Ser92Leu	p.S92L	ENST00000306801	NM_020761.2	92	tCg/tTg	3/34	0.242907821070149	3	FACETS	0.828	0.692	0.978	0.414	0.346	0.489	CLONAL	1	FALSE	1	0.361987141322278	3		368	323	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950291	17950291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	45	641	0	ENST00000458235.1:c.1436C>T	p.Pro479Leu	p.P479L	ENST00000458235	NM_000215.3	479	cCc/cTc	10/24	1	2	FACETS	0.756	0.638	0.885	0.756	0.638	0.885	SUBCLONAL	1	FALSE	1	0.361987141322278	2		641	329	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731619	47731620	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	53	175	1	ENST00000449228.1:c.172_173delinsTT	p.Pro58Phe	p.P58F	ENST00000449228	NM_001127240.2	58	CCc/TTc	2/4	0.196329718092327	3	FACETS	0.762	0.657	0.873			1	INDETERMINATE	2	FALSE	NA	0.361987141322278	3		176	227	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469166	25469166	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	65	639	0	ENST00000264709.3:c.1292C>T	p.Pro431Leu	p.P431L	ENST00000264709	NM_175629.2	431	cCc/cTc	11/23	1	2	FACETS	0.96	0.837	1	0.96	0.837	1	CLONAL	1	FALSE	1	0.361987141322278	2		639	374	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39751934	39751934	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	41	350	1	ENST00000361337.2:c.2295T>A	p.Phe765Leu	p.F765L	ENST00000361337	NM_003286.2	765	ttT/ttA	21/21	1	2	FACETS	0.792	0.663	0.934	0.792	0.663	0.934	CLONAL	1	FALSE	1	0.361987141322278	2		351	286	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927945	49927946	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	46	573	1	ENST00000296474.3:c.3782_3783delinsTT	p.Thr1261Ile	p.T1261I	ENST00000296474	NM_002447.2	1261	aCC/aTT	18/20	0.242907821070149	3	FACETS	1	0.887	1	0.528	0.448	0.616	CLONAL	1	FALSE	1	0.361987141322278	3		574	284	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499453	89499453	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	38	466	0	ENST00000336596.2:c.2623G>T	p.Val875Phe	p.V875F	ENST00000336596	NM_005233.5	875	Gtt/Ttt	15/17	0.242907821070149	3	FACETS	0.79	0.655	0.939	0.395	0.327	0.47	CLONAL	1	FALSE	1	0.361987141322278	3		466	314	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161357	185161358	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	48	539	1	ENST00000265026.3:c.784_785delinsAA	p.Gly262Lys	p.G262K	ENST00000265026	NM_004721.4	262	GGa/AAa	4/14	1	2	FACETS	0.764	0.649	0.891	0.764	0.649	0.891	SUBCLONAL	1	FALSE	1	0.361987141322278	2		540	347	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861019	35861020	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	24	379	0	ENST00000303115.3:c.148_149delinsAA	p.Gly50Lys	p.G50K	ENST00000303115	NM_002185.3	50	GGa/AAa	2/8	0.16883960452085	4	FACETS	0.502	0.393	0.627	0.251	0.196	0.314	INDETERMINATE	1	FALSE	2	0.361987141322278	4		379	360	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627245	86627245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	61	323	0	ENST00000274376.6:c.620G>A	p.Arg207Lys	p.R207K	ENST00000274376	NM_002890.2	207	aGa/aAa	2/25	0.16883960452085	4	FACETS	1	0.935	1	0.568	0.492	0.65	INDETERMINATE	1	FALSE	2	0.361987141322278	4		323	404	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501539	149501539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	78	574	0	ENST00000261799.4:c.2248G>A	p.Asp750Asn	p.D750N	ENST00000261799	NM_002609.3	750	Gac/Aac	16/23	0.16883960452085	4	FACETS	1	0.968	1	0.652	0.575	0.734	INDETERMINATE	1	FALSE	2	0.361987141322278	4		574	450	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508940	106508940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	38	420	0	ENST00000359195.3:c.934G>A	p.Asp312Asn	p.D312N	ENST00000359195	NM_002649.2	312	Gac/Aac	2/11	0.242907821070149	3	FACETS	0.792	0.657	0.942	0.396	0.328	0.471	CLONAL	1	FALSE	1	0.361987141322278	3		420	313	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434474	140434475	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	33	393	1	ENST00000288602.6:c.2223_2224delinsAA	p.Asp742Asn	p.D742N	ENST00000288602	NM_004333.4	741	gaGGat/gaAAat	18/18	0.242907821070149	3	FACETS	0.725	0.592	0.873	0.363	0.296	0.437	SUBCLONAL	1	FALSE	1	0.361987141322278	3		394	297	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98222059	98222059	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	181	354	0	ENST00000331920.6:c.2710A>T	p.Lys904Ter	p.K904*	ENST00000331920	NM_000264.3	904	Aaa/Taa	17/24	0.348444832711709	2	FACETS	1	0.954	1	1	0.992	1	CLONAL	3	FALSE	0	0.361987141322278	2		354	328	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231163	98231163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	103	719	0	ENST00000331920.6:c.2120C>T	p.Ser707Phe	p.S707F	ENST00000331920	NM_000264.3	707	tCc/tTc	14/24	0.348444832711709	2	FACETS	1	0.978	1	0.66	0.594	0.729	CLONAL	1	FALSE	0	0.361987141322278	2		719	431	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403482	139403482	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs201163739	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	121	841	1	ENST00000277541.6:c.3011C>A	p.Ser1004Ter	p.S1004*	ENST00000277541	NM_017617.3	1004	tCg/tAg	19/34	0.348444832711709	2	FACETS	0.838	0.764	0.914	0.838	0.764	0.914	CLONAL	2	FALSE	0	0.361987141322278	2		842	399	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161358	185161358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	46	540	0	ENST00000265026.3:c.785G>A	p.Gly262Glu	p.G262E	ENST00000265026	NM_004721.4	262	gGa/gAa	4/14	1	2	FACETS	0.732	0.619	0.857	0.732	0.619	0.857	SUBCLONAL	1	FALSE	1	0.361987141322278	2		540	347	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190742121	190742122	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0051092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	37	340	1	ENST00000441310.2:c.2758_2759delinsTT	p.Pro920Leu	p.P920L	ENST00000441310	NM_000534.4	920	CCa/TTa	13/13	0.242907821070149	3	FACETS	0.891	0.738	1	0.445	0.369	0.53	CLONAL	1	FALSE	1	0.361987141322278	3		341	271	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	21	404	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.559	0.429	0.711	0.559	0.429	0.711	SUBCLONAL	1	TRUE	1	0.15	2		404	501	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498444	89498444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	31	369	0	ENST00000336596.2:c.2416G>A	p.Asp806Asn	p.D806N	ENST00000336596	NM_005233.5	806	Gat/Aat	14/17	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.15	2		369	345	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	13	235	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	0.71	0.506	0.959	0.71	0.506	0.959	CLONAL	1	TRUE	1	0.15	2		235	244	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176614	56176614	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	23	315	0	ENST00000399503.3:c.2164G>T	p.Glu722Ter	p.E722*	ENST00000399503	NM_005921.1	722	Gaa/Taa	12/20	1	2	FACETS	0.752	0.585	0.945	0.752	0.585	0.945	CLONAL	1	TRUE	1	0.15	2		315	408	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277291	41277291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	25	335	1	ENST00000349496.5:c.1760G>A	p.Arg587Gln	p.R587Q	ENST00000349496	NM_001904.3	587	cGa/cAa	11/15	1	2	FACETS	0.792	0.623	0.986	0.792	0.623	0.986	CLONAL	1	TRUE	1	0.15	2		336	421	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518099	8518099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764400127	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	28	445	0	ENST00000356435.5:c.1292C>T	p.Ser431Leu	p.S431L	ENST00000356435		431	tCg/tTg	10/35	1	2	FACETS	0.765	0.61	0.942	0.765	0.61	0.942	CLONAL	1	TRUE	1	0.15	2		445	488	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111958593	111958593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555186772	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	30	425	0	ENST00000375549.3:c.65G>A	p.Arg22Gln	p.R22Q	ENST00000375549	NM_003002.3	22	cGa/cAa	2/4	1	2	FACETS	0.849	0.683	1	0.849	0.683	1	CLONAL	1	TRUE	1	0.15	2		425	471	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	38	507	1	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.949	0.784	1	0.949	0.784	1	CLONAL	1	TRUE	1	0.15	2		508	534	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145543	61145543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767519747	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	22	258	0	ENST00000295025.8:c.655C>T	p.Arg219Cys	p.R219C	ENST00000295025	NM_002908.2	219	Cgt/Tgt	7/11	1	2	FACETS	1	0.785	1	1	0.785	1	CLONAL	1	TRUE	1	0.15	2		258	290	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912815	100912815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1000609240	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	22	348	0	ENST00000325455.5:c.2507G>A	p.Arg836Gln	p.R836Q	ENST00000325455	NM_001202474.3	836	cGa/cAa	7/8	1	2	FACETS	0.789	0.611	0.996	0.789	0.611	0.996	CLONAL	1	TRUE	1	0.15	2		348	372	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	26	392	0	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	1	2	FACETS	0.839	0.664	1	0.839	0.664	1	CLONAL	1	TRUE	1	0.15	2		392	413	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858390	9858390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	24	416	0	ENST00000330684.3:c.3011C>T	p.Ser1004Phe	p.S1004F	ENST00000330684	NM_001134407.1	1004	tCc/tTc	13/13	1	2	FACETS	0.788	0.617	0.986	0.788	0.617	0.986	CLONAL	1	TRUE	1	0.15	2		416	406	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617589	158617589	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121912679	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	23	380	0	ENST00000263640.3:c.1067G>A	p.Gly356Asp	p.G356D	ENST00000263640	NM_001105.4	356	gGc/gAc	9/11	1	2	FACETS	0.765	0.595	0.961	0.765	0.595	0.961	CLONAL	1	TRUE	1	0.15	2		380	401	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692791	89692791	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	16	202	0	ENST00000371953.3:c.275A>T	p.Asp92Val	p.D92V	ENST00000371953	NM_000314.4	92	gAc/gTc	5/9	1	2	FACETS	0.796	0.588	1	0.796	0.588	1	CLONAL	1	TRUE	1	0.15	2		202	268	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649000	86649000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755634472	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	14	236	0	ENST00000274376.6:c.1280G>A	p.Arg427Gln	p.R427Q	ENST00000274376	NM_002890.2	427	cGa/cAa	9/25	1	2	FACETS	0.699	0.505	0.935	0.699	0.505	0.935	SUBCLONAL	1	TRUE	1	0.15	2		236	267	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152108	55152108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377487797	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	36	640	1	ENST00000257290.5:c.2540C>T	p.Ser847Leu	p.S847L	ENST00000257290	NM_006206.4	847	tCg/tTg	18/23	1	2	FACETS	0.725	0.594	0.872	0.725	0.594	0.872	SUBCLONAL	1	TRUE	1	0.15	2		641	662	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554305	81554305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777252114	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	35	345	0	ENST00000298171.2:c.325C>T	p.Arg109Trp	p.R109W	ENST00000298171	NM_000369.2	109	Cgg/Tgg	4/10	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.15	2		345	339	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462920	120462920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372061331	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	33	519	0	ENST00000256646.2:c.5411C>T	p.Ser1804Leu	p.S1804L	ENST00000256646	NM_024408.3	1804	tCg/tTg	30/34	1	2	FACETS	0.848	0.689	1	0.848	0.689	1	CLONAL	1	TRUE	1	0.15	2		519	519	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203492	108203492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs138941496	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	13	169	0	ENST00000278616.4:c.7792C>T	p.Arg2598Ter	p.R2598*	ENST00000278616	NM_000051.3	2598	Cga/Tga	53/63	1	2	FACETS	0.841	0.601	1	0.841	0.601	1	CLONAL	1	TRUE	1	0.15	2		169	206	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39706272	39706272	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	17	255	0	ENST00000361337.2:c.330C>A	p.Phe110Leu	p.F110L	ENST00000361337	NM_003286.2	110	ttC/ttA	5/21	1	2	FACETS	0.7	0.521	0.912	0.7	0.521	0.912	SUBCLONAL	1	TRUE	1	0.15	2		255	324	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	44	359	0	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.15	2		359	409	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44910975	44910975	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	19	228	0	ENST00000377967.4:c.676G>T	p.Glu226Ter	p.E226*	ENST00000377967	NM_021140.2	226	Gaa/Taa	9/29	1	2	FACETS	0.925	0.702	1	0.925	0.702	1	CLONAL	1	TRUE	1	0.15	2		228	274	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624245	89624245	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554890335	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	16	163	0	ENST00000371953.3:c.19G>T	p.Glu7Ter	p.E7*	ENST00000371953	NM_000314.4	7	Gag/Tag	1/9	1	2	FACETS	1	0.837	1	1	0.837	1	CLONAL	1	TRUE	1	0.15	2		163	180	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	28	495	0	ENST00000320574.5:c.1231G>C	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ctg	13/49	1	2	FACETS	0.972	0.777	1	0.972	0.777	1	CLONAL	1	TRUE	1	0.15	2		495	384	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11308103	11308103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141936187	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	36	543	2	ENST00000361445.4:c.889G>A	p.Asp297Asn	p.D297N	ENST00000361445	NM_004958.3	297	Gac/Aac	7/58	1	2	FACETS	0.862	0.707	1	0.862	0.707	1	CLONAL	1	TRUE	1	0.15	2		545	557	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268419	142268419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs980426116	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	30	291	1	ENST00000350721.4:c.3073C>T	p.Arg1025Cys	p.R1025C	ENST00000350721	NM_001184.3	1025	Cgt/Tgt	15/47	1	2	FACETS	0.995	0.802	1	0.995	0.802	1	CLONAL	1	TRUE	1	0.15	2		292	402	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045832	143045832	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	29	552	0	ENST00000262992.4:c.1802C>T	p.Ser601Phe	p.S601F	ENST00000262992	NM_001101669.1	601	tCc/tTc	17/24	1	2	FACETS	0.7	0.561	0.86	0.7	0.561	0.86	SUBCLONAL	1	TRUE	1	0.15	2		552	552	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32920978	32920978	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs80358920	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	32	289	0	ENST00000380152.3:c.6952C>T	p.Arg2318Ter	p.R2318*	ENST00000380152		2318	Cga/Tga	13/27	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.15	2		289	340	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223725	53223725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	38	706	1	ENST00000375401.3:c.3634C>T	p.Arg1212Trp	p.R1212W	ENST00000375401	NM_004187.3	1212	Cgg/Tgg	23/26	1	2	FACETS	0.692	0.57	0.829	0.692	0.57	0.829	SUBCLONAL	1	TRUE	1	0.15	2		707	732	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564503	55564503	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1044091916	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	21	442	0	ENST00000288135.5:c.391G>A	p.Asp131Asn	p.D131N	ENST00000288135	NM_000222.2	131	Gac/Aac	3/21	1	2	FACETS	0.67	0.515	0.851	0.67	0.515	0.851	SUBCLONAL	1	TRUE	1	0.15	2		442	418	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709524	176709524	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587784169	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	18	298	0	ENST00000439151.2:c.5951G>A	p.Arg1984Gln	p.R1984Q	ENST00000439151	NM_022455.4	1984	cGa/cAa	19/23	1	2	FACETS	0.787	0.592	1	0.787	0.592	1	CLONAL	1	TRUE	1	0.15	2		298	305	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938995	76938995	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs886044898	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	25	391	0	ENST00000373344.5:c.1753G>T	p.Glu585Ter	p.E585*	ENST00000373344	NM_000489.3	585	Gaa/Taa	9/35	1	2	FACETS	0.754	0.593	0.94	0.754	0.593	0.94	CLONAL	1	TRUE	1	0.15	2		391	442	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992217	11992217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	29	444	1	ENST00000396373.4:c.307C>T	p.Arg103Cys	p.R103C	ENST00000396373	NM_001987.4	103	Cgc/Tgc	3/8	1	2	FACETS	0.855	0.686	1	0.855	0.686	1	CLONAL	1	TRUE	1	0.15	2		445	452	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152215	11152215	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	30	537	1	ENST00000358026.2:c.4499C>T	p.Ala1500Val	p.A1500V	ENST00000358026	NM_001128849.1	1500	gCc/gTc	31/36	1	2	FACETS	0.84	0.676	1	0.84	0.676	1	CLONAL	1	TRUE	1	0.15	2		538	476	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202424	138202424	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	45	675	0	ENST00000237289.4:c.2341G>A	p.Glu781Lys	p.E781K	ENST00000237289	NM_001270507.1	781	Gaa/Aaa	9/9	1	2	FACETS	0.955	0.802	1	0.955	0.802	1	CLONAL	1	TRUE	1	0.15	2		675	628	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441434	40441434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	38	624	0	ENST00000345506.4:c.5C>T	p.Ala2Val	p.A2V	ENST00000345506	NM_003152.3	2	gCg/gTg	3/20	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.15	2		624	475	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369218	118369218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782785673	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	35	362	0	ENST00000534358.1:c.5936G>A	p.Arg1979Gln	p.R1979Q	ENST00000534358	NM_005933.3	1979	cGa/cAa	22/36	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.15	2		362	380	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419072	419072	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	26	333	0	ENST00000399788.2:c.3275A>C	p.Lys1092Thr	p.K1092T	ENST00000399788	NM_001042603.1	1092	aAa/aCa	22/28	1	2	FACETS	0.846	0.669	1	0.846	0.669	1	CLONAL	1	TRUE	1	0.15	2		333	410	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41999978	41999978	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	28	463	0	ENST00000219905.7:c.2241C>A	p.Tyr747Ter	p.Y747*	ENST00000219905	NM_001164273.1	747	taC/taA	6/24	1	2	FACETS	0.741	0.591	0.912	0.741	0.591	0.912	CLONAL	1	TRUE	1	0.15	2		463	504	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133283	30133283	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	35	698	0	ENST00000263025.4:c.215A>G	p.Lys72Arg	p.K72R	ENST00000263025	NM_002746.2	72	aAg/aGg	2/9	1	2	FACETS	0.731	0.598	0.882	0.731	0.598	0.882	SUBCLONAL	1	TRUE	1	0.15	2		698	638	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16022741	16022741	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	21	298	0	ENST00000268712.3:c.1911A>C	p.Lys637Asn	p.K637N	ENST00000268712	NM_006311.3	637	aaA/aaC	17/46	1	2	FACETS	0.9	0.693	1	0.9	0.693	1	CLONAL	1	TRUE	1	0.15	2		298	311	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698123	47698123	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63750328	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	16	216	1	ENST00000233146.2:c.1681G>T	p.Glu561Ter	p.E561*	ENST00000233146	NM_000251.2	561	Gaa/Taa	11/16	1	2	FACETS	0.83	0.614	1	0.83	0.614	1	CLONAL	1	TRUE	1	0.15	2		217	257	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433464	138433464	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	21	343	0	ENST00000289153.2:c.1148A>C	p.Glu383Ala	p.E383A	ENST00000289153	NM_006219.2	383	gAa/gCa	7/22	1	2	FACETS	0.741	0.57	0.941	0.741	0.57	0.941	CLONAL	1	TRUE	1	0.15	2		343	378	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526244	189526244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	36	674	0	ENST00000264731.3:c.508G>A	p.Asp170Asn	p.D170N	ENST00000264731	NM_003722.4	170	Gac/Aac	4/14	1	2	FACETS	0.77	0.632	0.927	0.77	0.632	0.927	CLONAL	1	TRUE	1	0.15	2		674	623	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178098	56178098	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	19	299	0	ENST00000399503.3:c.3071A>C	p.Lys1024Thr	p.K1024T	ENST00000399503	NM_005921.1	1024	aAg/aCg	14/20	1	2	FACETS	0.761	0.577	0.977	0.761	0.577	0.977	CLONAL	1	TRUE	1	0.15	2		299	333	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534854	5534854	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	28	500	0	ENST00000397747.3:c.165A>G	p.Ile55Met	p.I55M	ENST00000397747	NM_025239.3	55	atA/atG	3/7	1	2	FACETS	0.778	0.621	0.958	0.778	0.621	0.958	CLONAL	1	TRUE	1	0.15	2		500	480	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27209205	27209205	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	21	390	0	ENST00000380036.4:c.2662C>A	p.Leu888Ile	p.L888I	ENST00000380036	NM_000459.3	888	Ctc/Atc	16/23	1	2	FACETS	0.69	0.53	0.876	0.69	0.53	0.876	SUBCLONAL	1	TRUE	1	0.15	2		390	406	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890147	76890147	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	31	405	0	ENST00000373344.5:c.4747A>C	p.Lys1583Gln	p.K1583Q	ENST00000373344	NM_000489.3	1583	Aag/Cag	17/35	1	2	FACETS	0.817	0.66	0.995	0.817	0.66	0.995	CLONAL	1	TRUE	1	0.15	2		405	506	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	158	230	0				ENST00000310581	NM_198253.2	-/1132			0.179384314011442	5	FACETS	1	0.933	1	1	0.933	1	INDETERMINATE	3	TRUE	2	0.33246907703916	5		230	470	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654550	29654550	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	117	327	0	ENST00000356175.3:c.5239G>T	p.Glu1747Ter	p.E1747*	ENST00000356175	NM_000267.3	1747	Gag/Tag	37/57	0.128992772958673	3	FACETS	0.918	0.841	0.997	0.918	0.841	0.997	INDETERMINATE	3	TRUE	0	0.33246907703916	3		327	298	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152157	11152157	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568528491	NA	P-0051094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	130	611	0	ENST00000358026.2:c.4441G>A	p.Glu1481Lys	p.E1481K	ENST00000358026	NM_001128849.1	1481	Gag/Aag	31/36	0.128992772958673	3	FACETS	1	0.982	1	0.446	0.405	0.489	INDETERMINATE	1	TRUE	0	0.33246907703916	3		611	681	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190763	108190769	+	frameshift_variant	Frame_Shift_Del	DEL	TATGAAA	TATGAAA	-	novel	NA	P-0051094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	88	344	0	ENST00000278616.4:c.6430_6436del	p.Tyr2144ValfsTer7	p.Y2144Vfs*7	ENST00000278616	NM_000051.3	2144	TATGAAAgt/gt	44/63	0.33246907703916	3	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	1	0.33246907703916	3		344	285	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794542	42794542	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	133	805	1	ENST00000575354.2:c.1622C>A	p.Ser541Tyr	p.S541Y	ENST00000575354	NM_015125.3	541	tCc/tAc	10/20	0.103936874241134	6	FACETS	0.773	0.701	0.848	0.515	0.467	0.565	INDETERMINATE	2	TRUE	3	0.33246907703916	6		806	862	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991651	25991651	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	139	456	0	ENST00000435504.4:c.591G>C	p.Lys197Asn	p.K197N	ENST00000435504		197	aaG/aaC	7/13	0.33246907703916	3	FACETS	0.807	0.738	0.88	0.807	0.738	0.88	CLONAL	2	TRUE	1	0.33246907703916	3		456	604	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443688	29443688	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	123	574	1	ENST00000389048.3:c.3529C>T	p.Gln1177Ter	p.Q1177*	ENST00000389048	NM_004304.4	1177	Cag/Tag	23/29	0.33246907703916	3	FACETS	1	0.979	1	0.649	0.588	0.713	CLONAL	1	TRUE	1	0.33246907703916	3		575	665	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574853	41574853	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	132	661	0	ENST00000263253.7:c.7138C>G	p.Pro2380Ala	p.P2380A	ENST00000263253	NM_001429.3	2380	Cca/Gca	31/31	0.128992772958673	3	FACETS	1	0.973	1	0.397	0.36	0.435	INDETERMINATE	1	TRUE	0	0.33246907703916	3		661	778	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902487	1902487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	139	629	0	ENST00000382891.5:c.106C>T	p.Pro36Ser	p.P36S	ENST00000382891	NM_133335.3	36	Ccg/Tcg	2/22	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.33246907703916	2		629	609	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752860	128752860	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	172	377	0	ENST00000377970.2:c.1021A>G	p.Lys341Glu	p.K341E	ENST00000377970	NM_002467.4	341	Aag/Gag	3/3	0.33246907703916	6	FACETS	1	0.976	1	0.571	0.526	0.618	CLONAL	2	TRUE	2	0.33246907703916	6		377	754	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391879	139391905	+	inframe_deletion	In_Frame_Del	DEL	GCGCTCCTGTGCGATGTCGCGCGGCAG	GCGCTCCTGTGCGATGTCGCGCGGCAG	-	novel	NA	P-0051094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	128	937	0	ENST00000277541.6:c.6286_6312del	p.Leu2096_Arg2104del	p.L2096_R2104del	ENST00000277541	NM_017617.3	2096	CTGCCGCGCGACATCGCACAGGAGCGC/-	34/34	0.33246907703916	3	FACETS	1	0.957	1	0.549	0.497	0.603	CLONAL	1	TRUE	1	0.33246907703916	3		937	818	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412210	139412211	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCA	novel	NA	P-0051094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	259	719	0	ENST00000277541.6:c.1432_1434dup	p.Cys478dup	p.C478dup	ENST00000277541	NM_017617.3	478	-/TGC	8/34	0.33246907703916	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.33246907703916	3		719	743	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0051095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	142	341	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.544741222348722	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.544741222348722	1		341	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0051095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	244	745	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.544741222348722	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.544741222348722	1		745	641	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331962	81331962	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs201768315	NA	P-0051095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	59	286	0	ENST00000222390.5:c.2122C>T	p.Arg708Ter	p.R708*	ENST00000222390	NM_000601.4	708	Cga/Tga	18/18	1	2	FACETS	0.658	0.57	0.754	0.658	0.57	0.754	SUBCLONAL	1	TRUE	1	0.544741222348722	2		286	329	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475550	12475550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479145908	NA	P-0051095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	218	500	0	ENST00000287820.6:c.1424C>T	p.Thr475Met	p.T475M	ENST00000287820	NM_015869.4	475	aCg/aTg	7/7	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.544741222348722	2		500	639	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302307	15302307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115029695	NA	P-0051095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	248	723	2	ENST00000263388.2:c.964G>A	p.Val322Met	p.V322M	ENST00000263388	NM_000435.2	322	Gtg/Atg	6/33	0.544741222348722	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.544741222348722	1		725	616	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265062	198265062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	154	344	1	ENST00000335508.6:c.2815C>T	p.Arg939Cys	p.R939C	ENST00000335508	NM_012433.2	939	Cgt/Tgt	19/25	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.544741222348722	2		345	467	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971092	21971093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0051095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	387	481	2	ENST00000304494.5:c.265_266insT	p.Gly89ValfsTer31	p.G89Vfs*31	ENST00000304494	NM_000077.4	89	ggc/gTgc	2/3	0.544741222348722	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.544741222348722	2		483	644	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519975	NA	P-0051097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	624	839	0	ENST00000269305.4:c.403T>C	p.Cys135Arg	p.C135R	ENST00000269305	NM_001126112.2	135	Tgc/Cgc	5/11	0.735514069665256	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.735514069665256	2		839	791	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556727	41556727	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0051097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	245	390	0	ENST00000263253.7:c.3671+1G>A		p.X1224_splice	ENST00000263253	NM_001429.3	1224			0.735514069665256	3	FACETS	0.978	0.926	1	0.978	0.926	1	CLONAL	2	TRUE	1	0.735514069665256	3		390	466	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300159	15300159	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1435305678	NA	P-0051097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1251	107	857	1	ENST00000263388.2:c.1117G>T	p.Gly373Cys	p.G373C	ENST00000263388	NM_000435.2	373	Ggc/Tgc	7/33	0.622934490558691	4	FACETS	0.372	0.332	0.414	0.186	0.166	0.207	SUBCLONAL	1	TRUE	2	0.735514069665256	4		858	1358	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	151	230	0				ENST00000310581	NM_198253.2	-/1132			0.304183163800474	5	FACETS	1	0.96	1	0.708	0.653	0.763	INDETERMINATE	2	FALSE	2	0.669338522437871	5		230	426	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	297	255	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	0.662177407961039	2	FACETS	1	0.994	1			1	CLONAL	2	FALSE	NA	0.669338522437871	2		255	379	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872210	45872210	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	427	732	0	ENST00000391945.4:c.224G>A	p.Arg75Lys	p.R75K	ENST00000391945	NM_000400.3	75	aGa/aAa	4/23	0.512722259492802	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	FALSE	2	0.669338522437871	4		732	1002	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735466	40735466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182388300	NA	P-0051098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	398	662	1	ENST00000373198.4:c.3407G>A	p.Arg1136His	p.R1136H	ENST00000373198	NM_133170.3	1136	cGt/cAt	25/32	0.395674834024588	4	FACETS	1	0.982	1			1	INDETERMINATE	2	FALSE	NA	0.669338522437871	4		663	943	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100667	8100667	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	100	734	0	ENST00000346208.3:c.641C>G	p.Ser214Trp	p.S214W	ENST00000346208		214	tCg/tGg	3/6	0.669338522437871	3	FACETS	0.377	0.336	0.421	0.189	0.168	0.211	SUBCLONAL	1	FALSE	1	0.669338522437871	3		734	1057	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894230	NA	P-0051098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	324	609	0	ENST00000451590.1:c.35G>A	p.Gly12Asp	p.G12D	ENST00000451590	NM_001130442.1	12	gGc/gAc	2/5	0.669338522437871	2	FACETS	0.931	0.893	0.968	0.931	0.893	0.968	CLONAL	2	FALSE	0	0.669338522437871	2		609	520	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114793	108114793	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs147915571	NA	P-0051098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	269	355	0	ENST00000278616.4:c.610G>T	p.Gly204Ter	p.G204*	ENST00000278616	NM_000051.3	204	Gga/Tga	6/63	0.669338522437871	5	FACETS	0.909	0.855	0.965			1	CLONAL	2	FALSE	NA	0.669338522437871	5		355	886	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654619	67654619	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	257	436	0	ENST00000264010.4:c.1106A>G	p.His369Arg	p.H369R	ENST00000264010	NM_006565.3	369	cAc/cGc	6/12	0.270426074180218	5	FACETS	1	0.98	1	0.727	0.684	0.77	INDETERMINATE	2	FALSE	2	0.669338522437871	5		436	706	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0051098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	406	689	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.669338522437871	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	FALSE	0	0.669338522437871	2		689	604	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289838	15289838	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	98	882	0	ENST00000263388.2:c.3716C>T	p.Ser1239Leu	p.S1239L	ENST00000263388	NM_000435.2	1239	tCa/tTa	22/33	0.669338522437871	3	FACETS	0.375	0.334	0.42	0.188	0.167	0.21	SUBCLONAL	1	FALSE	1	0.669338522437871	3		882	1041	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965463	18965463	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	132	680	0	ENST00000262803.5:c.1210G>C	p.Glu404Gln	p.E404Q	ENST00000262803	NM_002911.3	404	Gag/Cag	9/24	0.669338522437871	3	FACETS	0.693	0.629	0.759	0.346	0.314	0.38	SUBCLONAL	1	FALSE	1	0.669338522437871	3		680	760	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271292	1271292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	344	615	0	ENST00000310581.5:c.2410G>A	p.Gly804Ser	p.G804S	ENST00000310581	NM_198253.2	804	Ggc/Agc	8/16	0.304183163800474	5	FACETS	1	0.992	1	0.809	0.769	0.849	INDETERMINATE	2	FALSE	2	0.669338522437871	5		615	849	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651923	36651930	+	frameshift_variant	Frame_Shift_Del	DEL	CAAGGCCT	CAAGGCCT	-	novel	NA	P-0051098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	505	695	0	ENST00000244741.5:c.45_52del	p.Ser15ArgfsTer18	p.S15Rfs*18	ENST00000244741	NM_000389.4	15	agCAAGGCCTgc/aggc	2/3	0.669338522437871	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	FALSE	1	0.669338522437871	3		695	977	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	545	230	0				ENST00000310581	NM_198253.2	-/1132			0.459693305208948	6	FACETS	0.946	0.918	0.974			1	CLONAL	5	TRUE	NA	0.637396925644691	6		230	822	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0051099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	239	396	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.287573519595562	3	FACETS	0.805	0.757	0.854	0.805	0.757	0.854	INDETERMINATE	2	TRUE	1	0.637396925644691	3		396	614	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037865	49037865	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0051099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	168	286	0	ENST00000267163.4:c.2107-2A>G		p.X703_splice	ENST00000267163	NM_000321.2	703			NA	2	FACETS	0.925	0.87	0.979			1	INDETERMINATE	2	TRUE	NA	0.637396925644691	2		286	285	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992765	68992765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs900217349	NA	P-0051099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	62	487	1	ENST00000288368.4:c.1730G>A	p.Arg577Gln	p.R577Q	ENST00000288368	NM_024870.2	577	cGa/cAa	16/40	1	2	FACETS	0.271	0.233	0.311	0.271	0.233	0.311	SUBCLONAL	1	TRUE	1	0.637396925644691	2		488	719	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107275	193107275	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	27	265	0	ENST00000367435.3:c.484G>C	p.Glu162Gln	p.E162Q	ENST00000367435	NM_024529.4	162	Gaa/Caa	6/17	1	2	FACETS	0.18	0.143	0.223	0.18	0.143	0.223	SUBCLONAL	1	TRUE	1	0.637396925644691	2		265	470	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137737	64137737	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	335	883	0	ENST00000334205.4:c.1838C>G	p.Ser613Cys	p.S613C	ENST00000334205	NM_003942.2	613	tCt/tGt	15/17	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.637396925644691	2		883	906	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426649	49426649	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	205	473	0	ENST00000301067.7:c.11839C>T	p.Gln3947Ter	p.Q3947*	ENST00000301067	NM_003482.3	3947	Cag/Tag	39/54	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.637396925644691	2		473	608	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606033	81606033	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	62	432	0	ENST00000298171.2:c.703C>G	p.Gln235Glu	p.Q235E	ENST00000298171	NM_000369.2	235	Caa/Gaa	9/10	0.477946139129276	1	FACETS	0.312	0.27	0.357	0.312	0.27	0.357	SUBCLONAL	1	TRUE	0	0.637396925644691	1		432	425	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696700	47696705	+	inframe_deletion	In_Frame_Del	DEL	TAATCT	TAATCT	-	novel	NA	P-0051099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	239	423	0	ENST00000347630.2:c.243_248del	p.Lys81_Tyr83delinsAsn	p.K81_Y83delinsN	ENST00000347630	NM_001007230.1	81	aaAGATTAc/aac	5/11	0.202730670103871	2	FACETS	1	0.989	1	0.619	0.582	0.656	INDETERMINATE	1	TRUE	0	0.637396925644691	2		423	606	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047062	128047062	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	206	526	0	ENST00000285398.2:c.673G>C	p.Glu225Gln	p.E225Q	ENST00000285398	NM_000122.1	225	Gaa/Caa	6/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.637396925644691	2		526	568	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282218	38282218	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0051099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	218	521	0	ENST00000425967.3:c.839-1G>C		p.X280_splice	ENST00000425967	NM_001174067.1	280			0.637396925644691	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.637396925644691	1		521	439	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521517	8521517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	241	450	1	ENST00000356435.5:c.721C>T	p.Pro241Ser	p.P241S	ENST00000356435		241	Cca/Tca	9/35	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.637396925644691	2		451	727	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942724	44942724	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	217	455	0	ENST00000377967.4:c.3304G>C	p.Glu1102Gln	p.E1102Q	ENST00000377967	NM_021140.2	1102	Gag/Cag	23/29	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.637396925644691	2		455	670	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227947	123227947	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	138	429	0	ENST00000218089.9:c.3658G>T	p.Glu1220Ter	p.E1220*	ENST00000218089	NM_001042749.1	1220	Gag/Tag	33/35	1	2	FACETS	0.745	0.681	0.812	0.745	0.681	0.812	SUBCLONAL	1	TRUE	1	0.637396925644691	2		429	581	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	42	230	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.741	0.62	0.876	0.741	0.62	0.876	SUBCLONAL	1	TRUE	1	0.278422381453294	2		230	407	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309857	65309857	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	43	560	0	ENST00000342505.4:c.2293G>C	p.Glu765Gln	p.E765Q	ENST00000342505	NM_002227.2	765	Gag/Cag	17/25	1	2	FACETS	0.446	0.372	0.529	0.446	0.372	0.529	SUBCLONAL	1	TRUE	1	0.278422381453294	2		560	692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577560	7577560	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520002	NA	P-0051100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	174	626	0	ENST00000269305.4:c.721T>G	p.Ser241Ala	p.S241A	ENST00000269305	NM_001126112.2	241	Tcc/Gcc	7/11	0.278422381453294	1	FACETS	0.783	0.723	0.845	1	0.99	1	SUBCLONAL	2	TRUE	0	0.278422381453294	1		626	687	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25498372	25498372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	86	475	1	ENST00000264709.3:c.489G>A	p.Met163Ile	p.M163I	ENST00000264709	NM_175629.2	163	atG/atA	5/23	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.278422381453294	2		476	582	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860781	45860781	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	124	742	2	ENST00000391945.4:c.1328C>T	p.Ala443Val	p.A443V	ENST00000391945	NM_000400.3	443	gCc/gTc	14/23	1	2	FACETS	0.995	0.9	1	0.995	0.9	1	CLONAL	1	TRUE	1	0.278422381453294	2		744	895	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097648	27097649	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTCAATGTGGGCACATCAAGCAGAG	novel	NA	P-0051100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	65	647	0	ENST00000324856.7:c.3260_3261insAGCTCAATGTGGGCACATCAAGCAG	p.Ser1087ArgfsTer26	p.S1087Rfs*26	ENST00000324856	NM_006015.4	1079	-/CTCAATGTGGGCACATCAAGCAGAG	12/20	1	2	FACETS	0.614	0.532	0.704	0.614	0.532	0.704	SUBCLONAL	1	TRUE	1	0.278422381453294	2		647	760	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949178	71949178	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	166	938	0	ENST00000298229.2:c.3647del	p.Gly1216AlafsTer52	p.G1216Afs*52	ENST00000298229	NM_001567.3	1215	gaG/ga	27/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.278422381453294	2		938	919	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033955	49033956	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0051100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	41	331	0	ENST00000267163.4:c.2094dup	p.His699AlafsTer22	p.H699Afs*22	ENST00000267163	NM_000321.2	698	agg/aGgg	20/27	1	2	FACETS	0.775	0.647	0.917	0.775	0.647	0.917	CLONAL	1	TRUE	1	0.278422381453294	2		331	380	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40998441	40998441	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	46	482	0	ENST00000267868.3:c.292G>C	p.Glu98Gln	p.E98Q	ENST00000267868	NM_002875.4	98	Gag/Cag	4/10	1	2	FACETS	0.553	0.465	0.651	0.553	0.465	0.651	SUBCLONAL	1	TRUE	1	0.278422381453294	2		482	597	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40379633	40379633	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	68	697	0	ENST00000293328.3:c.199G>A	p.Glu67Lys	p.E67K	ENST00000293328	NM_012448.3	67	Gag/Aag	3/19	1	2	FACETS	0.655	0.569	0.748	0.655	0.569	0.748	SUBCLONAL	1	TRUE	1	0.278422381453294	2		697	746	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332631	153332631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	27	391	0	ENST00000281708.4:c.325G>A	p.Asp109Asn	p.D109N	ENST00000281708	NM_033632.3	109	Gat/Aat	2/12	1	2	FACETS	0.424	0.337	0.525	0.424	0.337	0.525	SUBCLONAL	1	TRUE	1	0.278422381453294	2		391	457	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120269	94120269	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	28	388	0	ENST00000369303.4:c.782G>C	p.Gly261Ala	p.G261A	ENST00000369303	NM_004440.3	261	gGa/gCa	3/17	1	2	FACETS	0.384	0.306	0.473	0.384	0.306	0.473	SUBCLONAL	1	TRUE	1	0.278422381453294	2		388	524	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918259	44918259	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	44	258	0	ENST00000377967.4:c.884C>A	p.Ser295Ter	p.S295*	ENST00000377967	NM_021140.2	295	tCa/tAa	11/29	0.278422381453294	1	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	0	0.278422381453294	1		258	269	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0051101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	34	434	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.679	0.553	0.822	0.679	0.553	0.822	SUBCLONAL	1	TRUE	1	0.13	2		435	770	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045978	47045978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	30	377	0	ENST00000377604.3:c.2773C>T	p.Arg925Cys	p.R925C	ENST00000377604	NM_001204468.1	925	Cgc/Tgc	24/24	1	1	FACETS	0.756	0.607	0.925	0.756	0.607	0.925	CLONAL	1	TRUE	0	0.13	1		377	571	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578471	7578472	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCGGGGGT	novel	NA	P-0051107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	100	925	0	ENST00000269305.4:c.450_458dup	p.Pro151_Pro153dup	p.P151_P153dup	ENST00000269305	NM_001126112.2	151	ccc/ccACCCCCGCCc	5/11	0.233689871022424	2	FACETS	0.641	0.571	0.715	0.32	0.285	0.358	SUBCLONAL	1	TRUE	0	0.323104260242929	2		925	966	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750387	41750388	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CT	CT	AC	novel	NA	P-0051107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	48	566	1	ENST00000226382.2:c.240_241delinsGT	p.Val81Phe	p.V81F	ENST00000226382	NM_003924.3	80	gcAGtt/gcGTtt	1/3	NA	2	FACETS	0.626	0.529	0.732			1	INDETERMINATE	1	TRUE	NA	0.323104260242929	2		567	475	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183788	10183788	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882034	NA	P-0051108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	288	829	0	ENST00000256474.2:c.257C>G	p.Pro86Arg	p.P86R	ENST00000256474	NM_000551.3	86	cCc/cGc	1/3	0.668586539348704	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.668586539348704	2		829	406	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014209	70014209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	265	704	0	ENST00000394351.3:c.1070G>A	p.Gly357Glu	p.G357E	ENST00000394351	NM_000248.3	357	gGg/gAg	9/9	0.570270957356027	4	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	2	0.668586539348704	4		704	660	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	151	230	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.793525708017105	2		230	363	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0051109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	232	423	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.983	0.923	1	0.983	0.923	1	CLONAL	1	TRUE	1	0.793525708017105	2		423	595	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282480	115282480	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs777883903	NA	P-0051109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	221	453	0	ENST00000438362.2:c.170A>G	p.Asn57Ser	p.N57S	ENST00000438362	NM_001242891.1	57	aAt/aGt	3/20	1	2	FACETS	0.995	0.933	1	0.995	0.933	1	CLONAL	1	TRUE	1	0.793525708017105	2		453	560	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933595	39933620	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGGCAACAGGAGAGCTGTGTCCCC	GGGGGCAACAGGAGAGCTGTGTCCCC	-	novel	NA	P-0051109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	78	333	0	ENST00000378444.4:c.979_1004del	p.Gly327LeufsTer45	p.G327Lfs*45	ENST00000378444	NM_001123385.1	327	GGGGACACAGCTCTCCTGTTGCCCCCc/c	4/15	1	1	FACETS	0.265	0.233	0.298	0.265	0.233	0.298	SUBCLONAL	1	TRUE	0	0.793525708017105	1		333	448	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	47	230	0				ENST00000310581	NM_198253.2	-/1132			0.216999218209693	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.23	1		230	279	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0051110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	102	731	0	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	0.3	2	FACETS	1	0.954	1			1	CLONAL	1	TRUE	NA	0.23	2		731	791	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69143593	69143593	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	54	461	0	ENST00000288368.4:c.4801C>T	p.Pro1601Ser	p.P1601S	ENST00000288368	NM_024870.2	1601	Ccc/Tcc	40/40	1	2	FACETS	0.896	0.766	1	0.896	0.766	1	CLONAL	1	TRUE	1	0.23	2		461	524	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030859	36030859	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1190315469	NA	P-0051110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	82	517	0	ENST00000358208.4:c.1138G>A	p.Val380Met	p.V380M	ENST00000358208		380	Gtg/Atg	10/12	0.138728513290441	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.23	1		517	492	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215351	123215351	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	77	273	0	ENST00000218089.9:c.2897C>G	p.Thr966Arg	p.T966R	ENST00000218089	NM_001042749.1	966	aCa/aGa	28/35	0.3	2	FACETS	0.912	0.806	1	0.912	0.806	1	CLONAL	2	TRUE	0	0.23	2		273	367	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692911	89692911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909241	NA	P-0051111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	51	539	0	ENST00000371953.3:c.395G>A	p.Gly132Asp	p.G132D	ENST00000371953	NM_000314.4	132	gGt/gAt	5/9	0.22201720382976	3	FACETS	0.982	0.866	1	1	0.981	1	CLONAL	5	FALSE	1	0.22201720382976	3		539	104	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692961	89692961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060500122	NA	P-0051111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	15	647	0	ENST00000371953.3:c.445C>T	p.Gln149Ter	p.Q149*	ENST00000371953	NM_000314.4	149	Caa/Taa	5/9	0.22201720382976	3	FACETS	1	0.891	1	0.743	0.551	0.968	CLONAL	1	FALSE	1	0.22201720382976	3		647	101	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054402	42054402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752413385	NA	P-0051111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	13	425	0	ENST00000219905.7:c.7586G>A	p.Arg2529Lys	p.R2529K	ENST00000219905	NM_001164273.1	2529	aGa/aAa	22/24	1	2	FACETS	1	0.744	1	1	0.744	1	CLONAL	1	FALSE	1	0.22201720382976	2		425	113	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs371769427	NA	P-0051111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	44	339	0	ENST00000291552.4:c.101C>A	p.Ser34Tyr	p.S34Y	ENST00000291552	NM_006758.2	34	tCt/tAt	2/8	0.22201720382976	3	FACETS	1	0.925	1	1	0.977	1	CLONAL	4	FALSE	1	0.22201720382976	3		339	100	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100949	27100949	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	35	729	0	ENST00000324856.7:c.4231C>T	p.Gln1411Ter	p.Q1411*	ENST00000324856	NM_006015.4	1411	Cag/Tag	18/20	0.22201720382976	8	FACETS	1	0.844	1	1	0.844	1	CLONAL	4	FALSE	4	0.22201720382976	8		729	130	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907691	111907691	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	42	492	0	ENST00000393256.3:c.465T>G	p.Ile155Met	p.I155M	ENST00000393256	NM_006538.4	155	atT/atG	3/4	1	2	FACETS	1	0.911	1	1	0.979	1	CLONAL	3	FALSE	1	0.22201720382976	2		492	116	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589602	67589604	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	novel	NA	P-0051111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	86	354	0	ENST00000274335.5:c.1365_1367del	p.Gln455_Phe456delinsHis	p.Q455_F456delinsH	ENST00000274335		455	caGTTt/cat	10/15	0.22201720382976	30	FACETS	1	0.924	1			1	CLONAL	14	FALSE	NA	0.22201720382976	30		354	221	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0051112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	203	629	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.280319804460732	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.280319804460732	1		631	957	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118361988	118361988	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	120	388	0	ENST00000534358.1:c.4774G>T	p.Asp1592Tyr	p.D1592Y	ENST00000534358	NM_005933.3	1592	Gat/Tat	14/36	NA	2	FACETS	0.783	0.71	0.859			1	INDETERMINATE	2	TRUE	NA	0.280319804460732	2		388	547	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928002	178928002	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs756193341	NA	P-0051112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	61	401	0	ENST00000263967.3:c.1280T>A	p.Ile427Lys	p.I427K	ENST00000263967	NM_006218.2	427	aTa/aAa	8/21	1	2	FACETS	0.74	0.638	0.851	0.74	0.638	0.851	SUBCLONAL	1	TRUE	1	0.280319804460732	2		401	588	SUCCESS
APC	324	MSKCC	GRCh37	5	112175106	112175106	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	30	297	0	ENST00000257430.4:c.3815C>A	p.Ser1272Ter	p.S1272*	ENST00000257430	NM_000038.5	1272	tCa/tAa	16/16	1	2	FACETS	0.578	0.466	0.706	0.578	0.466	0.706	SUBCLONAL	1	TRUE	1	0.280319804460732	2		297	370	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802620	135802620	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	94	408	0	ENST00000298552.3:c.178A>T	p.Ile60Phe	p.I60F	ENST00000298552	NM_001162426.1	60	Atc/Ttc	4/23	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.280319804460732	2		408	656	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032570	12032573	+	frameshift_variant	Frame_Shift_Del	DEL	TTCT	TTCT	CCC	novel	NA	P-0051113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	42	598	0	ENST00000353533.5:c.1006_1009delinsCCC	p.Phe336ProfsTer27	p.F336Pfs*27	ENST00000353533	NM_003010.3	336	TTCTcc/CCCcc	9/11	0.329523621406012	2	FACETS	1	0.959	1	0.733	0.62	0.853	CLONAL	1	TRUE	0	0.329523621406012	2		598	174	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267324	198267324	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	26	544	0	ENST00000335508.6:c.2033C>T	p.Ala678Val	p.A678V	ENST00000335508	NM_012433.2	678	gCc/gTc	14/25	0.255011193173597	3	FACETS	1	0.838	1	0.528	0.422	0.648	CLONAL	1	TRUE	1	0.329523621406012	3		544	174	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120867	94120867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	30	433	0	ENST00000369303.4:c.184G>A	p.Asp62Asn	p.D62N	ENST00000369303	NM_004440.3	62	Gat/Aat	3/17	0.255011193173597	3	FACETS	1	0.94	1	0.721	0.589	0.867	CLONAL	1	TRUE	1	0.329523621406012	3		433	147	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183739	10183739	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs5030802	NA	P-0051114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	42	774	1	ENST00000256474.2:c.208G>T	p.Glu70Ter	p.E70*	ENST00000256474	NM_000551.3	70	Gag/Tag	1/3	0.220634682034005	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.220634682034005	1		775	242	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297722	15297725	+	frameshift_variant	Frame_Shift_Del	DEL	GGTT	GGTT	-	novel	NA	P-0051114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	46	732	0	ENST00000263388.2:c.1915_1918del	p.Asn639AlafsTer220	p.N639Afs*220	ENST00000263388	NM_000435.2	639	AACCgc/gc	12/33	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.220634682034005	2		732	333	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772950	135772951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs118203724	NA	P-0051118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	63	424	0	ENST00000298552.3:c.2672dup	p.Asn891LysfsTer13	p.N891Kfs*13	ENST00000298552	NM_001162426.1	891	aac/aaAc	21/23	0.249974755606969	1	FACETS	0.978	0.848	1	0.978	0.848	1	CLONAL	1	TRUE	0	0.249974755606969	1		424	451	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923035	44923036	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0051118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	151	610	0	ENST00000377967.4:c.1901dup	p.Asn634LysfsTer5	p.N634Kfs*5	ENST00000377967	NM_021140.2	632	-/A	16/29	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.249974755606969	2		610	918	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444370	49444370	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	152	693	0	ENST00000301067.7:c.3001C>A	p.Leu1001Ile	p.L1001I	ENST00000301067	NM_003482.3	1001	Ctt/Att	11/54	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.249974755606969	2		693	1019	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945788	17945788	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	183	754	0	ENST00000458235.1:c.2072T>G	p.Val691Gly	p.V691G	ENST00000458235	NM_000215.3	691	gTg/gGg	16/24	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.249974755606969	2		754	1057	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796843	42796843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	146	846	0	ENST00000575354.2:c.3301G>A	p.Ala1101Thr	p.A1101T	ENST00000575354	NM_015125.3	1101	Gca/Aca	14/20	1	2	FACETS	0.982	0.894	1	0.982	0.894	1	CLONAL	1	TRUE	1	0.249974755606969	2		846	1190	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188279	10188282	+	frameshift_variant	Frame_Shift_Del	DEL	ATGT	ATGT	-	novel	NA	P-0051118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	104	569	0	ENST00000256474.2:c.422_425del	p.Asn141MetfsTer17	p.N141Mfs*17	ENST00000256474	NM_000551.3	141	aATGTt/at	2/3	0.224431078463585	1	FACETS	0.968	0.867	1	0.968	0.867	1	CLONAL	1	TRUE	0	0.249974755606969	1		569	752	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090077	37090077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	101	587	0	ENST00000231790.2:c.1966T>A	p.Phe656Ile	p.F656I	ENST00000231790	NM_000249.3	656	Ttc/Atc	17/19	0.224431078463585	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.249974755606969	1		587	627	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437532	52437532	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	142	700	1	ENST00000460680.1:c.1629C>A	p.Cys543Ter	p.C543*	ENST00000460680	NM_004656.3	543	tgC/tgA	13/17	0.224431078463585	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.249974755606969	1		701	866	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52685784	52685785	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0051118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	61	445	0	ENST00000394830.3:c.687dup	p.Leu230SerfsTer34	p.L230Sfs*34	ENST00000394830	NM_018313.4	229	-/T	7/30	0.224431078463585	1	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	0	0.249974755606969	1		445	417	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848021	151848022	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0051118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	46	342	0	ENST00000262189.6:c.12737dup	p.Tyr4246Ter	p.Y4246*	ENST00000262189	NM_170606.2	4246	tat/taAt	51/59	0.249974755606969	3	FACETS	0.928	0.783	1	0.464	0.391	0.545	CLONAL	1	TRUE	1	0.249974755606969	3		342	446	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422383	47422383	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	116	566	1	ENST00000377045.4:c.17G>C	p.Gly6Ala	p.G6A	ENST00000377045	NM_001654.4	6	gGc/gCc	2/16	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.249974755606969	2		567	887	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849241	76849241	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	94	525	0	ENST00000373344.5:c.6035A>G	p.Glu2012Gly	p.E2012G	ENST00000373344	NM_000489.3	2012	gAg/gGg	26/35	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.249974755606969	2		525	574	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0051119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	118	359	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.546588777257837	2		359	423	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0051119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	119	403	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.909	0.825	0.996	0.909	0.825	0.996	CLONAL	1	TRUE	1	0.546588777257837	2		403	479	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18943136	18943136	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	33	223	0	ENST00000262803.5:c.118C>A	p.Leu40Ile	p.L40I	ENST00000262803	NM_002911.3	40	Ctt/Att	1/24	0.546588777257837	4	FACETS	0.351	0.285	0.426	0.117	0.095	0.142	SUBCLONAL	1	TRUE	1	0.546588777257837	4		223	532	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976541	18976541	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	324	884	0	ENST00000262803.5:c.3191C>G	p.Pro1064Arg	p.P1064R	ENST00000262803	NM_002911.3	1064	cCt/cGt	22/24	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.546588777257837	2		884	863	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198260849	198260849	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	134	533	0	ENST00000335508.6:c.3470A>G	p.Tyr1157Cys	p.Y1157C	ENST00000335508	NM_012433.2	1157	tAt/tGt	23/25	1	2	FACETS	0.859	0.783	0.937	0.859	0.783	0.937	CLONAL	1	TRUE	1	0.546588777257837	2		533	571	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0051120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	135	692	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.208076845956744	4	FACETS	0.865	0.787	0.947	0.865	0.787	0.947	CLONAL	2	TRUE	2	0.26	4		692	756	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207078	1207078	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	212	858	0	ENST00000326873.7:c.166G>T	p.Gly56Trp	p.G56W	ENST00000326873	NM_000455.4	56	Ggg/Tgg	1/10	0.245299320162141	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	0	0.26	2		858	807	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0051120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	96	870	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	0.208076845956744	4	FACETS	1	0.954	1	0.568	0.506	0.635	CLONAL	1	TRUE	2	0.26	4		870	819	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610154	10610154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	220	852	0	ENST00000171111.5:c.556G>A	p.Gly186Ser	p.G186S	ENST00000171111	NM_203500.1	186	Ggc/Agc	2/6	0.0743922534277597	3	FACETS	1	0.984	1			1	INDETERMINATE	2	TRUE	NA	0.26	3		852	816	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019697	123019697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755189208	NA	P-0051120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	58	345	0	ENST00000355640.3:c.185G>A	p.Arg62Gln	p.R62Q	ENST00000355640		62	cGg/cAg	2/7	0.297929147035353	4	FACETS	1	0.913	1			1	CLONAL	1	TRUE	NA	0.26	4		345	518	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912787	100912787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	66	478	0	ENST00000325455.5:c.2535G>T	p.Arg845Ser	p.R845S	ENST00000325455	NM_001202474.3	845	agG/agT	7/8	0.297929147035353	3	FACETS	0.854	0.741	0.976	0.427	0.37	0.488	CLONAL	1	TRUE	1	0.26	3		478	672	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431392	121431392	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	108	655	0	ENST00000257555.6:c.596G>T	p.Gly199Val	p.G199V	ENST00000257555		199	gGg/gTg	3/10	0.16010974062882	3	FACETS	0.837	0.753	0.925	0.837	0.753	0.925	CLONAL	2	TRUE	1	0.26	3		655	561	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871653	35871653	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	200	467	0	ENST00000216797.5:c.853G>T	p.Asp285Tyr	p.D285Y	ENST00000216797	NM_020529.2	285	Gat/Tat	5/6	0.282722221383988	5	FACETS	1	0.983	1	0.872	0.813	0.933	CLONAL	3	TRUE	1	0.26	5		467	613	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003195	143003195	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	150	395	0	ENST00000262992.4:c.2631T>A	p.Asp877Glu	p.D877E	ENST00000262992	NM_001101669.1	877	gaT/gaA	23/24	0.215947459957027	3	FACETS	0.933	0.859	1	0.933	0.859	1	CLONAL	3	TRUE	0	0.26	3		395	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	210	687	0	ENST00000269305.4:c.470T>G	p.Val157Gly	p.V157G	ENST00000269305	NM_001126112.2	157	gTc/gGc	5/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.486166948508033	2		687	835	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0051121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	154	636	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	1	2	FACETS	0.78	0.715	0.849	0.78	0.715	0.849	SUBCLONAL	1	TRUE	1	0.486166948508033	2		636	812	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867598	78867598	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	208	640	0	ENST00000306801.3:c.2334C>G	p.Ile778Met	p.I778M	ENST00000306801	NM_020761.2	778	atC/atG	20/34	0.44380685947262	3	FACETS	1	0.974	1	0.551	0.511	0.592	CLONAL	1	TRUE	1	0.486166948508033	3		640	965	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120794	94120794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs570778929	NA	P-0051121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	125	433	1	ENST00000369303.4:c.257G>A	p.Arg86Gln	p.R86Q	ENST00000369303	NM_004440.3	86	cGg/cAg	3/17	1	2	FACETS	0.94	0.855	1	0.94	0.855	1	CLONAL	1	TRUE	1	0.486166948508033	2		434	547	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335602	81335602	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0051121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	80	337	0	ENST00000222390.5:c.1757+1G>A		p.X586_splice	ENST00000222390	NM_000601.4	586			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.486166948508033	2		337	298	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608222	100608222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	235	461	0	ENST00000308731.7:c.1868C>T	p.Ser623Leu	p.S623L	ENST00000308731	NM_000061.2	623	tCa/tTa	18/19	0.329812751605437	2	FACETS	1	0.993	1	0.745	0.699	0.791	CLONAL	1	TRUE	0	0.486166948508033	2		461	649	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971113	21971135	+	frameshift_variant	Frame_Shift_Del	DEL	ACGGGTCGGGTGAGAGTGGCGGG	ACGGGTCGGGTGAGAGTGGCGGG	C	novel	NA	P-0051121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	47	560	0	ENST00000304494.5:c.223_245delinsG	p.Pro75GlyfsTer64	p.P75Gfs*64	ENST00000304494	NM_000077.4	75	CCCGCCACTCTCACCCGACCCGTg/Gg	2/3	0.475392329576586	1	FACETS	0.443	0.376	0.518	0.443	0.376	0.518	SUBCLONAL	1	TRUE	0	0.486166948508033	1		560	330	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0051122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	24	299	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.954	0.747	1	0.954	0.747	1	CLONAL	1	TRUE	1	0.13	2		299	387	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971153	21971153	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913383	NA	P-0051122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	43	586	0	ENST00000304494.5:c.205G>T	p.Glu69Ter	p.E69*	ENST00000304494	NM_000077.4	69	Gag/Tag	2/3	1	2	FACETS	0.967	0.808	1	0.967	0.808	1	CLONAL	1	TRUE	1	0.13	2		586	684	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0051122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	23	588	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	1	2	FACETS	0.453	0.351	0.572	0.453	0.351	0.572	SUBCLONAL	1	TRUE	1	0.13	2		588	781	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89791122	89791122	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	21	214	0	ENST00000336032.3:c.509C>T	p.Ala170Val	p.A170V	ENST00000336032	NM_006813.2	170	gCg/gTg	1/2	1	2	FACETS	1	0.81	1	1	0.81	1	CLONAL	1	TRUE	1	0.13	2		214	305	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931794	68931794	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0051122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	26	397	0	ENST00000288368.4:c.224C>G	p.Ser75Ter	p.S75*	ENST00000288368	NM_024870.2	75	tCa/tGa	3/40	0.0958664323484528	3	FACETS	0.868	0.686	1	0.434	0.343	0.539	CLONAL	1	TRUE	1	0.13	3		397	491	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855985	68855985	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	33	492	0	ENST00000261769.5:c.1793G>C	p.Arg598Pro	p.R598P	ENST00000261769	NM_004360.3	598	cGa/cCa	12/16	1	2	FACETS	0.772	0.627	0.936	0.772	0.627	0.936	CLONAL	1	TRUE	1	0.13	2		492	658	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539192	187539192	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	45	444	0	ENST00000441802.2:c.8548C>T	p.Gln2850Ter	p.Q2850*	ENST00000441802	NM_005245.3	2850	Cag/Tag	10/27	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.13	2		444	565	SUCCESS
APC	324	MSKCC	GRCh37	5	112176087	112176087	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1554086212	NA	P-0051122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	23	378	0	ENST00000257430.4:c.4796C>G	p.Ser1599Ter	p.S1599*	ENST00000257430	NM_000038.5	1599	tCa/tGa	16/16	1	2	FACETS	0.802	0.624	1	0.802	0.624	1	CLONAL	1	TRUE	1	0.13	2		378	441	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412697	139412697	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	47	816	0	ENST00000277541.6:c.1147G>T	p.Glu383Ter	p.E383*	ENST00000277541	NM_017617.3	383	Gag/Tag	7/34	1	2	FACETS	0.816	0.686	0.96	0.816	0.686	0.96	CLONAL	1	TRUE	1	0.13	2		816	886	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276696	15276696	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752169336	NA	P-0051123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	365	738	1	ENST00000263388.2:c.5569C>T	p.Arg1857Trp	p.R1857W	ENST00000263388	NM_000435.2	1857	Cgg/Tgg	30/33	0.411190644499551	4	FACETS	0.924	0.878	0.97	0.924	0.878	0.97	CLONAL	2	TRUE	2	0.631111751108697	4		739	1021	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285274	212285274	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	154	411	0	ENST00000342788.4:c.3027T>G	p.Asp1009Glu	p.D1009E	ENST00000342788	NM_005235.2	1009	gaT/gaG	25/28	0.433928723262524	3	FACETS	1	0.988	1	0.709	0.654	0.764	CLONAL	1	TRUE	1	0.631111751108697	3		411	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0051124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	296	570	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.527987734797823	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.527987734797823	1		570	759	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494697	2494697	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	199	737	0	ENST00000355716.4:c.837G>C	p.Arg279Ser	p.R279S	ENST00000355716	NM_003820.2	279	agG/agC	8/8	0.29905136957754	3	FACETS	0.889	0.823	0.958			1	INDETERMINATE	1	TRUE	NA	0.527987734797823	3		737	1072	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0051125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	198	514	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.410853251088139	1	FACETS	1	0.98	1	1	0.995	1	CLONAL	2	TRUE	0	0.410853251088139	1		514	353	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029333	14029333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766111215	NA	P-0051125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	30	334	0	ENST00000311895.7:c.1544G>A	p.Arg515His	p.R515H	ENST00000311895	NM_005236.2	515	cGt/cAt	8/11	0.410853251088139	1	FACETS	0.488	0.395	0.592	0.488	0.395	0.592	SUBCLONAL	1	TRUE	0	0.410853251088139	1		334	238	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42057113	42057113	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	93	528	0	ENST00000219905.7:c.7774A>C	p.Thr2592Pro	p.T2592P	ENST00000219905	NM_001164273.1	2592	Acc/Ccc	23/24	0.410853251088139	1	FACETS	0.869	0.777	0.965	0.869	0.777	0.965	CLONAL	1	TRUE	0	0.410853251088139	1		528	414	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535480	187535480	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	109	299	0	ENST00000441802.2:c.9094A>T	p.Ile3032Phe	p.I3032F	ENST00000441802	NM_005245.3	3032	Att/Ttt	12/27	0.410853251088139	1	FACETS	0.843	0.772	0.915	1	0.988	1	CLONAL	2	TRUE	0	0.410853251088139	1		299	250	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0051128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	57	507	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	0.896	0.77	1	0.896	0.77	1	CLONAL	1	TRUE	1	0.268987006768859	2		507	473	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471703	120471703	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	38	611	1	ENST00000256646.2:c.3788G>T	p.Gly1263Val	p.G1263V	ENST00000256646	NM_024408.3	1263	gGa/gTa	23/34	1	2	FACETS	0.421	0.347	0.504	0.421	0.347	0.504	SUBCLONAL	1	TRUE	1	0.268987006768859	2		612	671	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0051129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	198	430	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.187242293691021	4	FACETS	0.891	0.828	0.956	0.891	0.828	0.956	INDETERMINATE	2	TRUE	2	0.449160402650845	4		434	717	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874637	35874637	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	178	348	1	ENST00000303115.3:c.799del	p.Arg267GlyfsTer28	p.R267Gfs*28	ENST00000303115	NM_002185.3	265	Aaa/aa	6/8	0.187242293691021	4	FACETS	0.906	0.839	0.975	0.906	0.839	0.975	INDETERMINATE	2	TRUE	2	0.449160402650845	4		349	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0051129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	550	695	2	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.362908660035494	4	FACETS	0.93	0.899	0.961	0.93	0.899	0.961	CLONAL	4	TRUE	0	0.449160402650845	4		697	954	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556481	29556481	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1060500357	NA	P-0051129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	124	262	0	ENST00000356175.3:c.2848C>T	p.Gln950Ter	p.Q950*	ENST00000356175	NM_000267.3	950	Cag/Tag	21/57	0.449160402650845	2	FACETS	0.986	0.908	1	0.986	0.908	1	CLONAL	2	TRUE	0	0.449160402650845	2		262	280	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0051129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	238	427	13	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	0.430681531816304	2	FACETS	0.864	0.813	0.917	0.864	0.813	0.917	CLONAL	2	TRUE	0	0.449160402650845	2		440	613	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220544	133220544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200776293	NA	P-0051129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	233	513	0	ENST00000320574.5:c.4169G>A	p.Arg1390His	p.R1390H	ENST00000320574	NM_006231.2	1390	cGc/cAc	33/49	0.430681531816304	2	FACETS	0.928	0.873	0.983	0.928	0.873	0.983	CLONAL	2	TRUE	0	0.449160402650845	2		513	559	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199896	108199896	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	98	252	0	ENST00000278616.4:c.7238A>G	p.Lys2413Arg	p.K2413R	ENST00000278616	NM_000051.3	2413	aAg/aGg	49/63	0.449160402650845	2	FACETS	0.823	0.746	0.902	0.823	0.746	0.902	CLONAL	2	TRUE	0	0.449160402650845	2		252	265	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845209	128845209	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762783453	NA	P-0051129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	84	654	3	ENST00000249373.3:c.703G>A	p.Ala235Thr	p.A235T	ENST00000249373	NM_005631.4	235	Gcg/Acg	3/12	0.430681531816304	2	FACETS	0.625	0.553	0.703	0.313	0.276	0.352	SUBCLONAL	1	TRUE	0	0.449160402650845	2		657	598	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760465	133760465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758209901	NA	P-0051129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	308	665	2	ENST00000318560.5:c.2788G>A	p.Ala930Thr	p.A930T	ENST00000318560	NM_005157.4	930	Gca/Aca	11/11	0.449160402650845	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.449160402650845	2		667	630	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939047	48939048	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587778828	NA	P-0051129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	140	299	0	ENST00000267163.4:c.884dup	p.Asn295LysfsTer15	p.N295Kfs*15	ENST00000267163	NM_000321.2	293	-/A	9/27	0.430681531816304	2	FACETS	0.933	0.863	1	0.933	0.863	1	CLONAL	2	TRUE	0	0.449160402650845	2		299	334	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951096	48951096	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	115	305	0	ENST00000267163.4:c.1258A>G	p.Lys420Glu	p.K420E	ENST00000267163	NM_000321.2	420	Aag/Gag	13/27	0.430681531816304	2	FACETS	0.865	0.791	0.94	0.865	0.791	0.94	CLONAL	2	TRUE	0	0.449160402650845	2		305	296	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142860	7142860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	101	602	1	ENST00000302850.5:c.2509G>A	p.Ala837Thr	p.A837T	ENST00000302850	NM_000208.2	837	Gca/Aca	12/22	0.430681531816304	2	FACETS	0.631	0.564	0.702	0.315	0.282	0.351	SUBCLONAL	1	TRUE	0	0.449160402650845	2		603	713	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288605	33288605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	70	433	0	ENST00000374542.5:c.947C>T	p.Ala316Val	p.A316V	ENST00000374542	NM_001141970.1	316	gCc/gTc	3/8	0.430681531816304	2	FACETS	0.712	0.623	0.807	0.356	0.311	0.404	SUBCLONAL	1	TRUE	0	0.449160402650845	2		433	438	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551498	150551498	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1710	316	772	0	ENST00000369026.2:c.509A>G	p.Glu170Gly	p.E170G	ENST00000369026	NM_021960.4	170	gAg/gGg	1/3	0.794267749623297	9	FACETS	1	0.994	1			1	CLONAL	1	TRUE	NA	0.794267749623297	9		772	2026	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980255	201980256	+	5_prime_UTR_variant	5'UTR	DEL	AG	AG	-	novel	NA	P-0051130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	141	486	0	ENST00000359651.3:c.-10_-9del		p.*4*	ENST00000359651		-/371		1/8	0.389012822883798	6	FACETS	1	0.987	1	0.371	0.338	0.404	INDETERMINATE	1	TRUE	2	0.794267749623297	6		486	620	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424741	49424741	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783692	NA	P-0051130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	580	762	1	ENST00000301067.7:c.13606C>T	p.Arg4536Ter	p.R4536*	ENST00000301067	NM_003482.3	4536	Cga/Tga	40/54	0.794267749623297	7	FACETS	0.966	0.929	1	0.725	0.697	0.753	CLONAL	3	TRUE	3	0.794267749623297	7		763	1504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577504	7577504	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	604	611	0	ENST00000269305.4:c.777del	p.Ser260ProfsTer85	p.S260Pfs*85	ENST00000269305	NM_001126112.2	259	gaC/ga	7/11	0.794267749623297	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.794267749623297	3		611	699	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379748	17379748	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202199976	NA	P-0051130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	739	825	0	ENST00000359435.4:c.133G>A	p.Val45Met	p.V45M	ENST00000359435	NM_001033549.1	45	Gtg/Atg	2/9	0.794267749623297	6	FACETS	1	0.994	1	0.827	0.801	0.853	CLONAL	3	TRUE	2	0.794267749623297	6		825	1456	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921370	178921370	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051130-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	67	503	0	ENST00000263967.3:c.852T>G	p.Asn284Lys	p.N284K	ENST00000263967	NM_006218.2	284	aaT/aaG	5/21	0.794267749623297	4	FACETS	0.434	0.376	0.496	0.145	0.125	0.166	SUBCLONAL	1	TRUE	1	0.794267749623297	4		503	698	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424731	47424731	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	227	618	0	ENST00000377045.4:c.539T>C	p.Leu180Pro	p.L180P	ENST00000377045	NM_001654.4	180	cTa/cCa	6/16	1	2	FACETS	0.995	0.929	1	0.995	0.929	1	CLONAL	1	TRUE	1	0.529306535509592	2		618	862	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937855	76937855	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	195	564	0	ENST00000373344.5:c.2893G>A	p.Ala965Thr	p.A965T	ENST00000373344	NM_000489.3	965	Gca/Aca	9/35	1	2	FACETS	0.979	0.908	1	0.979	0.908	1	CLONAL	1	TRUE	1	0.529306535509592	2		564	753	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933593	39933594	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0051134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	86	412	0	ENST00000378444.4:c.1005dup	p.Ser336LeufsTer45	p.S336Lfs*45	ENST00000378444	NM_001123385.1	335	-/C	4/15	1	1	FACETS	0.764	0.679	0.855	1	0.98	1	SUBCLONAL	2	TRUE	0	0.218443751276523	1		412	459	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218338	69218338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	62	429	0	ENST00000462284.1:c.430C>T	p.Leu144Phe	p.L144F	ENST00000462284	NM_002392.5	144	Ctt/Ttt	7/11	1	2	FACETS	0.945	0.816	1	0.945	0.816	1	CLONAL	1	TRUE	1	0.218443751276523	2		429	601	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796550	42796550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	138	1075	1	ENST00000575354.2:c.3107G>T	p.Ser1036Ile	p.S1036I	ENST00000575354	NM_015125.3	1036	aGc/aTc	13/20	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.218443751276523	2		1076	1186	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484603	57484603	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	80	566	1	ENST00000371085.3:c.687T>G	p.Asp229Glu	p.D229E	ENST00000371085	NM_000516.4	229	gaT/gaG	9/13	1	2	FACETS	0.944	0.83	1	0.944	0.83	1	CLONAL	1	TRUE	1	0.218443751276523	2		567	776	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480396	89480396	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	89	339	0	ENST00000336596.2:c.2233C>G	p.Arg745Gly	p.R745G	ENST00000336596	NM_005233.5	745	Cga/Gga	13/17	0.218443751276523	1	FACETS	0.78	0.695	0.871	1	0.981	1	SUBCLONAL	2	TRUE	0	0.218443751276523	1		339	465	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0051135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	84	250	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.331176090937002	2		250	479	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0051135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	99	403	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.331176090937002	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.331176090937002	1		403	485	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163848	32163848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1210630301	NA	P-0051135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	90	671	0	ENST00000375023.3:c.5378G>A	p.Arg1793Gln	p.R1793Q	ENST00000375023	NM_004557.3	1793	cGa/cAa	30/30	0.286907081618908	3	FACETS	0.864	0.767	0.969	0.432	0.383	0.485	CLONAL	1	TRUE	1	0.331176090937002	3		671	733	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220626	1220626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057520038	NA	P-0051135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	120	774	0	ENST00000326873.7:c.644G>A	p.Gly215Asp	p.G215D	ENST00000326873	NM_000455.4	215	gGc/gAc	5/10	0.331176090937002	1	FACETS	0.827	0.748	0.911	0.827	0.748	0.911	CLONAL	1	TRUE	0	0.331176090937002	1		774	731	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980777	40980777	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	120	519	0	ENST00000373198.4:c.1709C>G	p.Thr570Arg	p.T570R	ENST00000373198	NM_133170.3	570	aCa/aGa	10/32	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.331176090937002	2		519	632	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867414	35867415	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0051135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	42	342	1	ENST00000303115.3:c.228_229delinsAG	p.Leu77Val	p.L77V	ENST00000303115	NM_002185.3	76	gcCCtc/gcAGtc	3/8	1	2	FACETS	0.611	0.511	0.722	0.611	0.511	0.722	SUBCLONAL	1	TRUE	1	0.331176090937002	2		343	415	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0051141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	189	423	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.634224434076767	2		423	495	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239420	105239420	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051141-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	293	716	0	ENST00000349310.3:c.967G>C	p.Asp323His	p.D323H	ENST00000349310	NM_001014432.1	323	Gac/Cac	12/15	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.634224434076767	2		716	780	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443695	29443695	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863225281	NA	P-0121597-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	169	559	0	ENST00000389048.3:c.3522C>G	p.Phe1174Leu	p.F1174L	ENST00000389048	NM_004304.4	1174	ttC/ttG	23/29	0.362861376476199	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	NA	1	0.466330750488894	4		559	321	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747955	41747956	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0121597-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	80	207	0	ENST00000226382.2:c.813dup	p.Gly272ArgfsTer88	p.G272Rfs*88	ENST00000226382	NM_003924.3	271	-/A	3/3	1	2	FACETS	0.975	0.88	1	1	0.986	1	CLONAL	2	NA	1	0.466330750488894	2		207	176	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205768	108205768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555127166	NA	P-0051146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	52	232	0	ENST00000278616.4:c.8083G>A	p.Gly2695Ser	p.G2695S	ENST00000278616	NM_000051.3	2695	Ggt/Agt	55/63	1	2	FACETS	0.744	0.641	0.853	0.744	0.641	0.853	SUBCLONAL	1	TRUE	1	0.656459876358159	2		232	213	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178655	108178656	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587781730	NA	P-0051146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	42	150	0	ENST00000278616.4:c.5712dup	p.Ser1905IlefsTer25	p.S1905Ifs*25	ENST00000278616	NM_000051.3	1902	-/A	38/63	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.656459876358159	2		150	127	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435754	110435770	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCCAAGAAGCCCTCC	GGCCCAAGAAGCCCTCC	-	novel	NA	P-0051146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	217	143	0	ENST00000375856.3:c.2631_2647del	p.Glu878AlafsTer107	p.E878Afs*107	ENST00000375856	NM_003749.2	877	ccGGAGGGCTTCTTGGGCCag/ccag	1/2	0.656459876358159	27	FACETS	1	0.934	1			1	CLONAL	5	TRUE	NA	0.656459876358159	27		143	1210	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435782	110435792	+	frameshift_variant	Frame_Shift_Del	DEL	GCTAGGCCGCA	GCTAGGCCGCA	-	novel	NA	P-0051146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	236	134	0	ENST00000375856.3:c.2609_2619del	p.Val870GlyfsTer117	p.V870Gfs*117	ENST00000375856	NM_003749.2	870	gTGCGGCCTAGC/g	1/2	0.656459876358159	27	FACETS	0.971	0.905	1			1	CLONAL	6	TRUE	NA	0.656459876358159	27		134	1136	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061044	38061054	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGTGCACAC	CCCGTGCACAC	-	novel	NA	P-0051146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	22	261	0	ENST00000250448.2:c.935_945del	p.Gly312GlufsTer99	p.G312Efs*99	ENST00000250448	NM_004496.3	312	gGTGTGCACGGG/g	2/2	1	2	FACETS	0.305	0.237	0.383	0.305	0.237	0.383	SUBCLONAL	1	TRUE	1	0.656459876358159	2		261	220	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315357	30315357	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	27	229	0	ENST00000322652.5:c.1042A>G	p.Thr348Ala	p.T348A	ENST00000322652	NM_015355.2	348	Aca/Gca	10/16	1	2	FACETS	0.383	0.306	0.469	0.383	0.306	0.469	SUBCLONAL	1	TRUE	1	0.656459876358159	2		229	215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0051147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	115	454	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.282628370629528	2	FACETS	1	0.98	1	0.658	0.596	0.722	CLONAL	1	TRUE	0	0.387808971571644	2		454	451	SUCCESS
APC	324	MSKCC	GRCh37	5	112175494	112175500	+	frameshift_variant	Frame_Shift_Del	DEL	TGCCAGC	TGCCAGC	-	novel	NA	P-0051147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	51	192	0	ENST00000257430.4:c.4204_4210del	p.Ala1402ProfsTer11	p.A1402Pfs*11	ENST00000257430	NM_000038.5	1401	atTGCCAGC/at	16/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.387808971571644	2		192	210	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745967	745967	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	61	317	0	ENST00000314574.4:c.555A>T	p.Arg185Ser	p.R185S	ENST00000314574	NM_005433.3	185	agA/agT	5/12	0.282628370629528	2	FACETS	0.881	0.764	1	0.441	0.382	0.504	CLONAL	1	TRUE	0	0.387808971571644	2		317	357	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187998	32187998	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	87	548	1	ENST00000375023.3:c.1223G>T	p.Ser408Ile	p.S408I	ENST00000375023	NM_004557.3	408	aGc/aTc	7/30	0.173069392916594	4	FACETS	0.895	0.792	1	0.447	0.396	0.502	INDETERMINATE	1	TRUE	2	0.387808971571644	4		549	696	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	14	230	0				ENST00000310581	NM_198253.2	-/1132			0.217818873360397	1	FACETS	0.542	0.392	0.725	0.542	0.392	0.725	SUBCLONAL	1	TRUE	0	0.18	1		230	261	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0051148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	94	520	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.995	0.888	1	1	0.986	1	CLONAL	2	TRUE	1	0.18	2		520	525	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0051148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	49	482	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	1	2	FACETS	0.995	0.843	1	0.995	0.843	1	CLONAL	1	TRUE	1	0.18	2		482	547	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044907	47044907	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	40	357	0	ENST00000377604.3:c.2237del	p.Gly746AlafsTer56	p.G746Afs*56	ENST00000377604	NM_001204468.1	745	Ggg/gg	20/24	1	1	FACETS	0.999	0.831	1	0.999	0.831	1	CLONAL	1	TRUE	0	0.18	1		357	405	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564530	86564530	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	38	521	0	ENST00000274376.6:c.266del	p.Gly89GlufsTer7	p.G89Efs*7	ENST00000274376	NM_002890.2	88	Ggg/gg	1/25	1	2	FACETS	0.704	0.581	0.842	0.704	0.581	0.842	SUBCLONAL	1	TRUE	1	0.18	2		521	600	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038756	47038756	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	19	347	0	ENST00000377604.3:c.763C>T	p.Gln255Ter	p.Q255*	ENST00000377604	NM_001204468.1	255	Cag/Tag	9/24	1	1	FACETS	0.55	0.417	0.708	0.55	0.417	0.708	SUBCLONAL	1	TRUE	0	0.18	1		347	349	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044488	12044488	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1168805084	NA	P-0051148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	17	216	0	ENST00000353533.5:c.1111G>A	p.Glu371Lys	p.E371K	ENST00000353533	NM_003010.3	371	Gaa/Aaa	11/11	1	2	FACETS	0.784	0.586	1	0.784	0.586	1	CLONAL	1	TRUE	1	0.18	2		216	241	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422905	49422905	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	57	584	0	ENST00000301067.7:c.14190G>A	p.Trp4730Ter	p.W4730*	ENST00000301067	NM_003482.3	4730	tgG/tgA	44/54	1	2	FACETS	0.94	0.805	1	0.94	0.805	1	CLONAL	1	TRUE	1	0.18	2		584	674	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433935	49433935	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	55	717	2	ENST00000301067.7:c.7618C>T	p.Gln2540Ter	p.Q2540*	ENST00000301067	NM_003482.3	2540	Cag/Tag	31/54	1	2	FACETS	0.814	0.695	0.944	0.814	0.695	0.944	CLONAL	1	TRUE	1	0.18	2		719	751	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211661	36211661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210126385	NA	P-0051148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	48	429	2	ENST00000222270.7:c.1412G>A	p.Arg471Gln	p.R471Q	ENST00000222270	NM_014727.1	471	cGg/cAg	3/37	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.18	2		431	498	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967186	134967186	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	22	364	0	ENST00000398015.3:c.2526del	p.Leu843CysfsTer36	p.L843Cfs*36	ENST00000398015	NM_004441.4	842	cGg/cg	14/16	0.232643431132164	0	FACETS	0.664	0.515	0.837			1	SUBCLONAL	1	TRUE	0	0.18	0		364	302	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909246	41909246	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	48	637	0	ENST00000372991.4:c.142del	p.Val48CysfsTer35	p.V48Cfs*35	ENST00000372991	NM_001760.3	48	Gtg/tg	1/5	1	2	FACETS	0.731	0.616	0.857	0.731	0.616	0.857	SUBCLONAL	1	TRUE	1	0.18	2		637	730	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300840	137300840	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	55	615	1	ENST00000481739.1:c.485C>T	p.Thr162Met	p.T162M	ENST00000481739	NM_002957.4	162	aCg/aTg	4/10	1	2	FACETS	0.947	0.81	1	0.947	0.81	1	CLONAL	1	TRUE	1	0.18	2		616	645	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0051149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	107	454	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.303896731633728	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.31	1		454	397	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	20	230	0				ENST00000310581	NM_198253.2	-/1132			0.193389140838182	1	FACETS	0.553	0.425	0.702	0.553	0.425	0.702	SUBCLONAL	1	TRUE	0	0.31	1		230	197	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913381	NA	P-0051149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	95	321	0	ENST00000304494.5:c.322G>A	p.Asp108Asn	p.D108N	ENST00000304494	NM_000077.4	108	Gat/Aat	2/3	0.303896731633728	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.31	1		321	380	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781386	135781386	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203549	NA	P-0051149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	148	543	0	ENST00000298552.3:c.1579C>T	p.Gln527Ter	p.Q527*	ENST00000298552	NM_001162426.1	527	Cag/Tag	15/23	0.299929576857581	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.31	2		543	452	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871053	12871053	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	76	373	1	ENST00000228872.4:c.285del	p.Gly97ValfsTer22	p.G97Vfs*22	ENST00000228872	NM_004064.3	94	Ccc/cc	1/3	0.264966958245958	3	FACETS	0.809	0.715	0.909	0.809	0.715	0.909	CLONAL	2	TRUE	1	0.31	3		374	350	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465517	99465517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	24	435	0	ENST00000268035.6:c.2342G>A	p.Arg781Lys	p.R781K	ENST00000268035	NM_000875.3	781	aGa/aAa	11/21	1	2	FACETS	0.462	0.362	0.577	0.462	0.362	0.577	SUBCLONAL	1	TRUE	1	0.31	2		435	335	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509603	106509603	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	37	471	0	ENST00000359195.3:c.1597C>G	p.Gln533Glu	p.Q533E	ENST00000359195	NM_002649.2	533	Cag/Gag	2/11	1	2	FACETS	0.635	0.524	0.758	0.635	0.524	0.758	SUBCLONAL	1	TRUE	1	0.31	2		471	376	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27209227	27209227	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	44	360	0	ENST00000380036.4:c.2684G>C	p.Arg895Pro	p.R895P	ENST00000380036	NM_000459.3	895	cGa/cCa	16/23	0.303896731633728	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.31	1		360	209	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733140	74733140	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	161	574	0	ENST00000359995.5:c.103G>C	p.Glu35Gln	p.E35Q	ENST00000359995	NM_001195427.1	35	Gag/Cag	1/3	0.11323808320988	4	FACETS	1	0.947	1	1	0.947	1	INDETERMINATE	2	TRUE	2	0.31	4		574	656	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023685	27023685	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	69	258	0	ENST00000324856.7:c.791C>A	p.Ser264Ter	p.S264*	ENST00000324856	NM_006015.4	264	tCg/tAg	1/20	0.218000650037345	4	FACETS	1	0.974	1	0.746	0.653	0.845	CLONAL	1	TRUE	2	0.31	4		258	391	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181978	38181978	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs566004944	NA	P-0051149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	90	511	3	ENST00000396334.3:c.602G>A	p.Arg201Gln	p.R201Q	ENST00000396334	NM_002468.4	201	cGa/cAa	3/5	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.31	2		514	436	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176684086	176684086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	20	415	0	ENST00000439151.2:c.4900C>T	p.Arg1634Trp	p.R1634W	ENST00000439151	NM_022455.4	1634	Cgg/Tgg	13/23	1	2	FACETS	0.345	0.263	0.441	0.345	0.263	0.441	SUBCLONAL	1	TRUE	1	0.31	2		415	374	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691118	18691118	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	52	359	0	ENST00000266497.5:c.3229G>A	p.Glu1077Lys	p.E1077K	ENST00000266497		1077	Gag/Aag	23/31	0.264966958245958	3	FACETS	0.821	0.706	0.944	0.821	0.706	0.944	CLONAL	2	TRUE	1	0.31	3		359	236	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828872	26828872	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	83	295	0	ENST00000381527.3:c.94T>G	p.Tyr32Asp	p.Y32D	ENST00000381527	NM_001260.1	32	Tat/Gat	1/13	0.299594916871986	2	FACETS	0.809	0.72	0.902	0.809	0.72	0.902	CLONAL	2	TRUE	0	0.31	2		295	331	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741922	40741922	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	130	695	0	ENST00000392038.2:c.1050C>G	p.Phe350Leu	p.F350L	ENST00000392038	NM_001626.4	350	ttC/ttG	11/14	0.218000650037345	4	FACETS	0.802	0.729	0.879	0.802	0.729	0.879	CLONAL	2	TRUE	2	0.31	4		695	685	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143236	30143236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	158	445	0	ENST00000389048.3:c.290C>T	p.Pro97Leu	p.P97L	ENST00000389048	NM_004304.4	97	cCg/cTg	1/29	0.167126185371229	3	FACETS	1	0.975	1	0.758	0.699	0.818	INDETERMINATE	2	TRUE	0	0.31	3		445	518	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54959332	54959332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	23	297	0	ENST00000312783.6:c.368C>T	p.Ser123Leu	p.S123L	ENST00000312783	NM_198436.1	123	tCa/tTa	5/10	1	2	FACETS	0.554	0.432	0.693	0.554	0.432	0.693	SUBCLONAL	1	TRUE	1	0.31	2		297	268	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259335	36259335	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555899861	NA	P-0051149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	191	235	1	ENST00000300305.3:c.156G>A	p.Met52Ile	p.M52I	ENST00000300305		52	atG/atA	3/8	0.303896731633728	6	FACETS	0.886	0.825	0.949	0.886	0.825	0.949	CLONAL	4	TRUE	2	0.31	6		236	563	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162312	47162312	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	45	408	0	ENST00000409792.3:c.3814C>G	p.Gln1272Glu	p.Q1272E	ENST00000409792	NM_014159.6	1272	Cag/Gag	3/21	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.31	2		408	283	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588991	67588991	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	20	231	0	ENST00000274335.5:c.1082C>G	p.Ser361Cys	p.S361C	ENST00000274335		361	tCt/tGt	8/15	0.193389140838182	1	FACETS	0.872	0.675	1	0.872	0.675	1	CLONAL	1	TRUE	0	0.31	1		231	125	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505121	149505121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140081345	NA	P-0051149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	42	496	2	ENST00000261799.4:c.1694G>A	p.Arg565Gln	p.R565Q	ENST00000261799	NM_002609.3	565	cGa/cAa	12/23	1	2	FACETS	0.698	0.584	0.825	0.698	0.584	0.825	SUBCLONAL	1	TRUE	1	0.31	2		498	388	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519502	137519502	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	64	325	0	ENST00000367739.4:c.1136C>G	p.Ser379Cys	p.S379C	ENST00000367739	NM_000416.2	379	tCt/tGt	7/7	0.299594916871986	2	FACETS	0.832	0.729	0.941	0.832	0.729	0.941	CLONAL	2	TRUE	0	0.31	2		325	248	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509523	106509523	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	47	500	0	ENST00000359195.3:c.1517C>G	p.Thr506Ser	p.T506S	ENST00000359195	NM_002649.2	506	aCt/aGt	2/11	1	2	FACETS	0.749	0.633	0.876	0.749	0.633	0.876	SUBCLONAL	1	TRUE	1	0.31	2		500	405	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045128	47045128	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	61	527	0	ENST00000377604.3:c.2370del	p.His791ThrfsTer11	p.H791Tfs*11	ENST00000377604	NM_001204468.1	790	aTt/at	21/24	1	2	FACETS	0.859	0.743	0.985	0.859	0.743	0.985	CLONAL	1	TRUE	1	0.31	2		527	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0051149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	262	454	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.524481661848033	2	FACETS	0.991	0.945	1	0.991	0.945	1	CLONAL	2	TRUE	0	0.604826979993207	2		454	437	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	34	230	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.75	0.622	0.888	0.75	0.622	0.888	SUBCLONAL	1	TRUE	1	0.604826979993207	2		230	150	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913381	NA	P-0051149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	234	321	0	ENST00000304494.5:c.322G>A	p.Asp108Asn	p.D108N	ENST00000304494	NM_000077.4	108	Gat/Aat	2/3	0.536827853296753	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	3	TRUE	0	0.604826979993207	3		321	335	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781386	135781386	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203549	NA	P-0051149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	246	543	0	ENST00000298552.3:c.1579C>T	p.Gln527Ter	p.Q527*	ENST00000298552	NM_001162426.1	527	Cag/Tag	15/23	0.604826979993207	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.604826979993207	2		543	363	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871053	12871053	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	156	373	1	ENST00000228872.4:c.285del	p.Gly97ValfsTer22	p.G97Vfs*22	ENST00000228872	NM_004064.3	94	Ccc/cc	1/3	0.604826979993207	3	FACETS	0.77	0.712	0.83	0.77	0.712	0.83	SUBCLONAL	2	TRUE	1	0.604826979993207	3		374	436	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465517	99465517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	88	435	0	ENST00000268035.6:c.2342G>A	p.Arg781Lys	p.R781K	ENST00000268035	NM_000875.3	781	aGa/aAa	11/21	0.604826979993207	3	FACETS	0.907	0.808	1	0.453	0.404	0.506	CLONAL	1	TRUE	1	0.604826979993207	3		435	418	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509603	106509603	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	93	471	0	ENST00000359195.3:c.1597C>G	p.Gln533Glu	p.Q533E	ENST00000359195	NM_002649.2	533	Cag/Gag	2/11	0.220337146473185	3	FACETS	1	0.94	1	0.535	0.48	0.594	INDETERMINATE	1	TRUE	1	0.604826979993207	3		471	374	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27209227	27209227	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	176	360	0	ENST00000380036.4:c.2684G>C	p.Arg895Pro	p.R895P	ENST00000380036	NM_000459.3	895	cGa/cCa	16/23	0.536827853296753	3	FACETS	0.865	0.816	0.914	0.865	0.816	0.914	CLONAL	3	TRUE	0	0.604826979993207	3		360	292	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733140	74733140	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	282	574	0	ENST00000359995.5:c.103G>C	p.Glu35Gln	p.E35Q	ENST00000359995	NM_001195427.1	35	Gag/Cag	1/3	0.316838862830952	5	FACETS	1	0.99	1	0.809	0.764	0.854	INDETERMINATE	2	TRUE	2	0.604826979993207	5		574	733	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023685	27023685	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	126	258	0	ENST00000324856.7:c.791C>A	p.Ser264Ter	p.S264*	ENST00000324856	NM_006015.4	264	tCg/tAg	1/20	0.451289720515214	4	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.604826979993207	4		258	446	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181978	38181978	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs566004944	NA	P-0051149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	247	511	3	ENST00000396334.3:c.602G>A	p.Arg201Gln	p.R201Q	ENST00000396334	NM_002468.4	201	cGa/cAa	3/5	0.604826979993207	3	FACETS	0.935	0.882	0.988	0.935	0.882	0.988	CLONAL	2	TRUE	1	0.604826979993207	3		514	569	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176684086	176684086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	40	415	0	ENST00000439151.2:c.4900C>T	p.Arg1634Trp	p.R1634W	ENST00000439151	NM_022455.4	1634	Cgg/Tgg	13/23	0.220337146473185	3	FACETS	0.402	0.334	0.477	0.201	0.167	0.239	INDETERMINATE	1	TRUE	1	0.604826979993207	3		415	429	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691118	18691118	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	94	359	0	ENST00000266497.5:c.3229G>A	p.Glu1077Lys	p.E1077K	ENST00000266497		1077	Gag/Aag	23/31	0.604826979993207	3	FACETS	1	0.977	1	0.655	0.59	0.723	CLONAL	1	TRUE	1	0.604826979993207	3		359	309	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828872	26828872	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	178	295	0	ENST00000381527.3:c.94T>G	p.Tyr32Asp	p.Y32D	ENST00000381527	NM_001260.1	32	Tat/Gat	1/13	0.45095453740659	3	FACETS	0.855	0.806	0.903	0.855	0.806	0.903	CLONAL	3	TRUE	0	0.604826979993207	3		295	299	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741922	40741922	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	277	695	0	ENST00000392038.2:c.1050C>G	p.Phe350Leu	p.F350L	ENST00000392038	NM_001626.4	350	ttC/ttG	11/14	0.193277509769295	5	FACETS	1	0.978	1			1	INDETERMINATE	2	TRUE	NA	0.604826979993207	5		695	815	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143236	30143236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	330	445	0	ENST00000389048.3:c.290C>T	p.Pro97Leu	p.P97L	ENST00000389048	NM_004304.4	97	cCg/cTg	1/29	0.26979400339405	5	FACETS	1	0.967	1	0.807	0.774	0.838	INDETERMINATE	4	TRUE	0	0.604826979993207	5		445	516	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54959332	54959332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	37	297	0	ENST00000312783.6:c.368C>T	p.Ser123Leu	p.S123L	ENST00000312783	NM_198436.1	123	tCa/tTa	5/10	0.604826979993207	3	FACETS	0.687	0.57	0.815	0.343	0.285	0.408	SUBCLONAL	1	TRUE	1	0.604826979993207	3		297	232	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259335	36259335	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555899861	NA	P-0051149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	272	235	1	ENST00000300305.3:c.156G>A	p.Met52Ile	p.M52I	ENST00000300305		52	atG/atA	3/8	0.604826979993207	5	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	2	0.604826979993207	5		236	537	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162312	47162312	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	139	408	0	ENST00000409792.3:c.3814C>G	p.Gln1272Glu	p.Q1272E	ENST00000409792	NM_014159.6	1272	Cag/Gag	3/21	0.604826979993207	3	FACETS	0.924	0.854	0.994	0.924	0.854	0.994	CLONAL	2	TRUE	1	0.604826979993207	3		408	324	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588991	67588991	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	40	231	0	ENST00000274335.5:c.1082C>G	p.Ser361Cys	p.S361C	ENST00000274335		361	tCt/tGt	8/15	1	2	FACETS	0.9	0.761	1	0.9	0.761	1	CLONAL	1	TRUE	1	0.604826979993207	2		231	147	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505121	149505121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140081345	NA	P-0051149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	134	496	2	ENST00000261799.4:c.1694G>A	p.Arg565Gln	p.R565Q	ENST00000261799	NM_002609.3	565	cGa/cAa	12/23	0.220337146473185	3	FACETS	1	0.978	1	0.607	0.556	0.661	INDETERMINATE	1	TRUE	1	0.604826979993207	3		498	475	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519502	137519502	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	174	325	0	ENST00000367739.4:c.1136C>G	p.Ser379Cys	p.S379C	ENST00000367739	NM_000416.2	379	tCt/tGt	7/7	0.397105968172828	3	FACETS	0.85	0.8	0.898	0.85	0.8	0.898	CLONAL	3	TRUE	0	0.604826979993207	3		325	294	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509523	106509523	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	95	500	0	ENST00000359195.3:c.1517C>G	p.Thr506Ser	p.T506S	ENST00000359195	NM_002649.2	506	aCt/aGt	2/11	0.220337146473185	3	FACETS	1	0.918	1	0.514	0.461	0.57	INDETERMINATE	1	TRUE	1	0.604826979993207	3		500	398	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045128	47045128	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	165	527	0	ENST00000377604.3:c.2370del	p.His791ThrfsTer11	p.H791Tfs*11	ENST00000377604	NM_001204468.1	790	aTt/at	21/24	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.604826979993207	2		527	431	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144716	119144716	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	66	325	0	ENST00000264033.4:c.729C>G	p.Ile243Met	p.I243M	ENST00000264033	NM_005188.3	243	atC/atG	4/16	0.604826979993207	3	FACETS	0.872	0.762	0.989	0.436	0.381	0.495	CLONAL	1	TRUE	1	0.604826979993207	3		325	326	SUCCESS
CBL	867	MSKCC	GRCh37	11	119145552	119145552	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051149-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	54	285	0	ENST00000264033.4:c.758C>G	p.Ser253Cys	p.S253C	ENST00000264033	NM_005188.3	253	tCt/tGt	5/16	0.604826979993207	3	FACETS	0.711	0.611	0.82	0.356	0.305	0.41	SUBCLONAL	1	TRUE	1	0.604826979993207	3		285	327	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0051150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	30	610	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.818	1	1	0.818	1	CLONAL	1	TRUE	1	0.13	2		610	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0051150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	40	623	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	1	2	FACETS	0.896	0.743	1	0.896	0.743	1	CLONAL	1	TRUE	1	0.13	2		623	687	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972525	32972525	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56121817	NA	P-0051150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	30	337	0	ENST00000380152.3:c.9875C>T	p.Pro3292Leu	p.P3292L	ENST00000380152		3292	cCg/cTg	27/27	1	2	FACETS	0.877	0.706	1	0.877	0.706	1	CLONAL	1	TRUE	1	0.13	2		337	526	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670622	67670622	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	21	239	0	ENST00000264010.4:c.1867G>T	p.Glu623Ter	p.E623*	ENST00000264010	NM_006565.3	623	Gag/Tag	11/12	1	2	FACETS	0.798	0.613	1	0.798	0.613	1	CLONAL	1	TRUE	1	0.13	2		239	405	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024558	11024558	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	27	330	0	ENST00000327064.4:c.675G>T	p.Leu225Phe	p.L225F	ENST00000327064	NM_199141.1	225	ttG/ttT	6/16	1	2	FACETS	0.837	0.665	1	0.837	0.665	1	CLONAL	1	TRUE	1	0.13	2		330	496	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	14	230	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.867	0.629	1	0.867	0.629	1	CLONAL	1	TRUE	1	0.19	2		230	170	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0051151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	95	790	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	1	0.935	1	1	0.987	1	CLONAL	2	TRUE	1	0.19	2		790	471	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941629	48941629	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1131690860	NA	P-0051151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	17	133	0	ENST00000267163.4:c.940-1G>A		p.X314_splice	ENST00000267163	NM_000321.2	314			1	2	FACETS	1	0.789	1	1	0.789	1	CLONAL	1	TRUE	1	0.19	2		133	169	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553362	41553362	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	28	317	0	ENST00000263253.7:c.3451C>T	p.Gln1151Ter	p.Q1151*	ENST00000263253	NM_001429.3	1151	Caa/Taa	18/31	1	2	FACETS	0.81	0.647	0.995	0.81	0.647	0.995	CLONAL	1	TRUE	1	0.19	2		317	364	SUCCESS
APC	324	MSKCC	GRCh37	5	112154936	112154936	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	24	443	0	ENST00000257430.4:c.1207G>T	p.Glu403Ter	p.E403*	ENST00000257430	NM_000038.5	403	Gaa/Taa	10/16	1	2	FACETS	0.627	0.491	0.784	0.627	0.491	0.784	SUBCLONAL	1	TRUE	1	0.19	2		443	403	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922711	44922712	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0051151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	12	127	0	ENST00000377967.4:c.1574dup	p.Asn525LysfsTer6	p.N525Kfs*6	ENST00000377967	NM_021140.2	524	-/A	16/29	0.3	2	FACETS	1	0.752	1	0.535	0.379	0.724	CLONAL	1	TRUE	0	0.19	2		127	118	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579350	7579350	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587781642	NA	P-0051152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	165	479	0	ENST00000269305.4:c.337T>G	p.Phe113Val	p.F113V	ENST00000269305	NM_001126112.2	113	Ttc/Gtc	4/11	0.245561723777235	3	FACETS	0.947	0.876	1	0.947	0.876	1	CLONAL	3	TRUE	0	0.245561723777235	3		479	531	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098803	178098803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	70	355	0	ENST00000397062.3:c.242G>A	p.Gly81Asp	p.G81D	ENST00000397062	NM_006164.4	81	gGt/gAt	2/5	0.215586800731821	3	FACETS	0.783	0.685	0.887	0.783	0.685	0.887	SUBCLONAL	2	TRUE	1	0.245561723777235	3		355	409	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524551	187524551	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	74	378	0	ENST00000441802.2:c.11129A>T	p.Gln3710Leu	p.Q3710L	ENST00000441802	NM_005245.3	3710	cAa/cTa	19/27	0.215586800731821	3	FACETS	0.752	0.661	0.85	0.752	0.661	0.85	SUBCLONAL	2	TRUE	1	0.245561723777235	3		378	450	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449769	149449769	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	83	432	0	ENST00000286301.3:c.1295T>C	p.Leu432Pro	p.L432P	ENST00000286301	NM_005211.3	432	cTg/cCg	9/22	0.144491233762815	2	FACETS	0.909	0.807	1	0.909	0.807	1	INDETERMINATE	2	TRUE	0	0.245561723777235	2		432	372	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819810	170819810	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	67	311	0	ENST00000296930.5:c.449A>G	p.Lys150Arg	p.K150R	ENST00000296930	NM_002520.6	150	aAg/aGg	5/11	0.144491233762815	2	FACETS	0.798	0.698	0.904	0.798	0.698	0.904	INDETERMINATE	2	TRUE	0	0.245561723777235	2		311	342	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956953	2956953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	118	383	0	ENST00000396946.4:c.2674G>A	p.Ala892Thr	p.A892T	ENST00000396946	NM_032415.4	892	Gca/Aca	20/25	NA	3	FACETS	1	0.949	1			1	INDETERMINATE	2	TRUE	NA	0.245561723777235	3		383	504	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971189	21971195	+	frameshift_variant	Frame_Shift_Del	DEL	CGCTGCC	CGCTGCC	AT	novel	NA	P-0051152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	82	293	1	ENST00000304494.5:c.163_169delinsAT	p.Gly55IlefsTer63	p.G55Ifs*63	ENST00000304494	NM_000077.4	55	GGCAGCGcc/ATcc	2/3	0.245561723777235	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.245561723777235	2		294	299	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579410	7579410	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567556123	NA	P-0051153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	256	504	0	ENST00000269305.4:c.277del	p.Leu93CysfsTer30	p.L93Cfs*30	ENST00000269305	NM_001126112.2	93	Ctg/tg	4/11	0.68669106668542	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.68669106668542	1		504	462	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104353820	104353820	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	142	358	0	ENST00000369902.3:c.754C>T	p.Gln252Ter	p.Q252*	ENST00000369902	NM_016169.3	252	Caa/Taa	6/12	0.444939388226656	1	FACETS	0.811	0.75	0.872	0.811	0.75	0.872	CLONAL	1	TRUE	0	0.68669106668542	1		358	335	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880992	134880992	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1435865991	NA	P-0051153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	169	386	0	ENST00000398015.3:c.1555G>A	p.Gly519Ser	p.G519S	ENST00000398015	NM_004441.4	519	Ggc/Agc	7/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.68669106668542	2		386	448	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867546	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs11466445	NA	P-0051154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	10	17	1	ENST00000374994.4:c.70_78del	p.Ala24_Ala26del	p.A24_A26del	ENST00000374994	NM_004612.2	17	ctGGCGGCGGCg/ctg	1/9	1	2	FACETS	1	0.837	1	1	0.837	1	CLONAL	1	TRUE	1	0.426880414523914	2		18	35	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183778	10183778	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	111	576	0	ENST00000256474.2:c.247del	p.Val83SerfsTer76	p.V83Sfs*76	ENST00000256474	NM_000551.3	83	Gtc/tc	1/3	0.313802292932282	2	FACETS	1	0.984	1	0.728	0.661	0.798	CLONAL	1	TRUE	0	0.426880414523914	2		576	357	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165692	47165693	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0051154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	61	315	0	ENST00000409792.3:c.433_434del	p.Lys145GlufsTer91	p.K145Efs*91	ENST00000409792	NM_014159.6	145	AAg/g	3/21	0.313802292932282	2	FACETS	1	0.967	1	0.674	0.59	0.762	CLONAL	1	TRUE	0	0.426880414523914	2		315	212	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620511	52620512	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0051154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	96	361	0	ENST00000394830.3:c.3241_3242insT	p.Lys1081IlefsTer3	p.K1081Ifs*3	ENST00000394830	NM_018313.4	1081	aaa/aTaa	21/30	0.313802292932282	2	FACETS	0.885	0.802	0.971	0.885	0.802	0.971	CLONAL	2	TRUE	0	0.426880414523914	2		361	254	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540396	187540398	+	inframe_deletion	In_Frame_Del	DEL	GGT	GGT	-	novel	NA	P-0051154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	102	277	0	ENST00000441802.2:c.7342_7344del	p.Thr2448del	p.T2448del	ENST00000441802	NM_005245.3	2448	ACC/-	10/27	0.295261540544995	3	FACETS	1	0.974	1	0.795	0.725	0.867	CLONAL	2	TRUE	0	0.426880414523914	3		277	243	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183706	10183713	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCGGCC	CCGCGGCC	-	novel	NA	P-0051158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	50	492	0	ENST00000256474.2:c.176_183del	p.Pro59ArgfsTer70	p.P59Rfs*70	ENST00000256474	NM_000551.3	59	CCGCGGCCc/c	1/3	1	2	FACETS	0.99	0.841	1	0.99	0.841	1	CLONAL	1	TRUE	1	0.21	2		492	481	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165119	47165119	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	21	173	0	ENST00000409792.3:c.1007C>A	p.Ser336Ter	p.S336*	ENST00000409792	NM_014159.6	336	tCa/tAa	3/21	1	2	FACETS	0.901	0.696	1	0.901	0.696	1	CLONAL	1	TRUE	1	0.21	2		173	222	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437677	52437678	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0051158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	50	485	0	ENST00000460680.1:c.1483_1484del	p.Thr495GlyfsTer3	p.T495Gfs*3	ENST00000460680	NM_004656.3	495	ACg/g	13/17	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.21	2		485	463	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32182025	32182025	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	35	482	1	ENST00000375023.3:c.2029T>C	p.Cys677Arg	p.C677R	ENST00000375023	NM_004557.3	677	Tgt/Cgt	13/30	1	2	FACETS	0.595	0.487	0.717	0.595	0.487	0.717	SUBCLONAL	1	TRUE	1	0.21	2		483	560	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506168	103506168	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	47	218	0	ENST00000355739.4:c.326T>C	p.Leu109Pro	p.L109P	ENST00000355739	NM_000123.3	109	cTt/cCt	3/15	1	2	FACETS	0.921	0.78	1	0.921	0.78	1	CLONAL	1	TRUE	1	0.29	2		218	352	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60795992	60795992	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	41	288	1	ENST00000333681.4:c.586G>T	p.Asp196Tyr	p.D196Y	ENST00000333681		196	Gat/Tat	3/3	1	2	FACETS	0.754	0.629	0.892	0.754	0.629	0.892	SUBCLONAL	1	TRUE	1	0.29	2		289	375	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	246	751	1	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.67	2		752	734	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	113	502	4	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.953	0.867	1	0.953	0.867	1	CLONAL	1	TRUE	1	0.67	2		506	354	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	115	335	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.986	0.899	1	0.986	0.899	1	CLONAL	1	TRUE	1	0.67	2		335	348	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602773	10602773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	265	812	0	ENST00000171111.5:c.805C>T	p.Arg269Trp	p.R269W	ENST00000171111	NM_203500.1	269	Cgg/Tgg	3/6	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.67	2		812	785	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	210	752	2	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.998	0.932	1	0.998	0.932	1	CLONAL	1	TRUE	1	0.67	2		754	628	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597813	43597813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770548816	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	177	641	0	ENST00000355710.3:c.361G>A	p.Val121Ile	p.V121I	ENST00000355710	NM_020975.4	121	Gtc/Atc	3/20	1	2	FACETS	0.861	0.797	0.926	0.861	0.797	0.926	CLONAL	1	TRUE	1	0.67	2		641	614	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188294	32188295	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs766348245	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	55	603	5	ENST00000375023.3:c.1046dup	p.Thr350HisfsTer4	p.T350Hfs*4	ENST00000375023	NM_004557.3	349	ggc/ggGc	6/30	1	2	FACETS	0.268	0.229	0.311	0.268	0.229	0.311	SUBCLONAL	1	TRUE	1	0.67	2		608	612	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475550	12475550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479145908	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	171	500	0	ENST00000287820.6:c.1424C>T	p.Thr475Met	p.T475M	ENST00000287820	NM_015869.4	475	aCg/aTg	7/7	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.67	2		500	502	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760465	133760465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758209901	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	174	665	2	ENST00000318560.5:c.2788G>A	p.Ala930Thr	p.A930T	ENST00000318560	NM_005157.4	930	Gca/Aca	11/11	1	2	FACETS	0.943	0.874	1	0.943	0.874	1	CLONAL	1	TRUE	1	0.67	2		667	551	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	110	330	1	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.67	2		331	326	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	147	421	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.243726634809805	1	FACETS	0.669	0.617	0.723	0.669	0.617	0.723	INDETERMINATE	1	TRUE	0	0.67	1		421	436	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	82	327	2	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	0.777	0.692	0.866	0.777	0.692	0.866	SUBCLONAL	1	TRUE	1	0.67	2		329	315	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781324	3781326	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs587783502	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	240	816	1	ENST00000262367.5:c.5039_5041del	p.Ser1680del	p.S1680del	ENST00000262367	NM_004380.2	1680	tCCTtg/ttg	30/31	1	2	FACETS	0.983	0.922	1	0.983	0.922	1	CLONAL	1	TRUE	1	0.67	2		817	729	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	259	673	0	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.67	2		673	723	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258253	16258253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771599410	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	190	468	0	ENST00000375759.3:c.5518G>A	p.Val1840Ile	p.V1840I	ENST00000375759	NM_015001.2	1840	Gtc/Atc	11/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.67	2		468	548	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37061889	37061889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793519	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	120	403	0	ENST00000231790.2:c.973C>T	p.Arg325Trp	p.R325W	ENST00000231790	NM_000249.3	325	Cgg/Tgg	11/19	1	2	FACETS	0.876	0.798	0.957	0.876	0.798	0.957	CLONAL	1	TRUE	1	0.67	2		403	409	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	133	401	3	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	0.825	0.755	0.899	0.825	0.755	0.899	CLONAL	1	TRUE	1	0.67	2		404	481	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	177	659	3	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	0.733	0.677	0.791	0.733	0.677	0.791	SUBCLONAL	1	TRUE	1	0.67	2		662	721	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	81	266	7	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	1	2	FACETS	0.785	0.699	0.876	0.785	0.699	0.876	SUBCLONAL	1	TRUE	1	0.67	2		273	308	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805318	89805318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201494304	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	169	524	0	ENST00000389301.3:c.4232C>T	p.Pro1411Leu	p.P1411L	ENST00000389301	NM_000135.2	1411	cCg/cTg	42/43	1	2	FACETS	0.916	0.847	0.986	0.916	0.847	0.986	CLONAL	1	TRUE	1	0.67	2		524	551	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300570	11300570	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764486955	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	164	553	0	ENST00000361445.4:c.1576C>T	p.Arg526Cys	p.R526C	ENST00000361445	NM_004958.3	526	Cgt/Tgt	11/58	1	2	FACETS	0.847	0.782	0.914	0.847	0.782	0.914	CLONAL	1	TRUE	1	0.67	2		553	578	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330629	65330630	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	106	322	1	ENST00000342505.4:c.1016dup	p.Asn339LysfsTer2	p.N339Kfs*2	ENST00000342505	NM_002227.2	339	aat/aaAt	8/25	1	2	FACETS	0.909	0.824	0.998	0.909	0.824	0.998	CLONAL	1	TRUE	1	0.67	2		323	348	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606273	93606273	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	83	667	2	ENST00000375746.1:c.98del	p.Gly33AlafsTer2	p.G33Afs*2	ENST00000375746	NM_001174167.1	31	caG/ca	2/14	1	2	FACETS	0.367	0.324	0.414	0.367	0.324	0.414	SUBCLONAL	1	TRUE	1	0.67	2		669	675	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971324	13971324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752431857	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	68	307	3	ENST00000405192.2:c.605C>T	p.Thr202Met	p.T202M	ENST00000405192	NM_001163147.1	202	aCg/aTg	8/12	1	2	FACETS	0.702	0.617	0.793	0.702	0.617	0.793	SUBCLONAL	1	TRUE	1	0.67	2		310	289	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226124	53226124	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs951268570	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	202	684	0	ENST00000375401.3:c.2725C>T	p.Arg909Trp	p.R909W	ENST00000375401	NM_004187.3	909	Cgg/Tgg	19/26	1	2	FACETS	0.956	0.891	1	0.956	0.891	1	CLONAL	1	TRUE	1	0.67	2		684	631	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021211	31021211	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs373145711	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	159	403	0	ENST00000375687.4:c.1210C>T	p.Arg404Ter	p.R404*	ENST00000375687	NM_015338.5	404	Cga/Tga	12/13	1	2	FACETS	0.977	0.902	1	0.977	0.902	1	CLONAL	1	TRUE	1	0.67	2		403	486	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69458697	69458697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1373641771	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	37	496	2	ENST00000227507.2:c.512C>T	p.Ala171Val	p.A171V	ENST00000227507	NM_053056.2	171	gCg/gTg	3/5	1	2	FACETS	0.189	0.155	0.227	0.189	0.155	0.227	SUBCLONAL	1	TRUE	1	0.67	2		498	585	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541438	187541438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755378789	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	108	318	0	ENST00000441802.2:c.6302G>A	p.Arg2101His	p.R2101H	ENST00000441802	NM_005245.3	2101	cGc/cAc	10/27	1	2	FACETS	0.926	0.84	1	0.926	0.84	1	CLONAL	1	TRUE	1	0.67	2		318	348	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968172	55968172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	129	403	1	ENST00000263923.4:c.2158C>T	p.Arg720Trp	p.R720W	ENST00000263923	NM_002253.2	720	Cgg/Tgg	15/30	1	2	FACETS	0.858	0.783	0.934	0.858	0.783	0.934	CLONAL	1	TRUE	1	0.67	2		404	449	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843306	128843306	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752289293	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	221	709	1	ENST00000249373.3:c.413G>A	p.Arg138Gln	p.R138Q	ENST00000249373	NM_005631.4	138	cGg/cAg	2/12	1	2	FACETS	0.906	0.847	0.967	0.906	0.847	0.967	CLONAL	1	TRUE	1	0.67	2		710	728	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856304	111856304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	30	62	0	ENST00000341259.2:c.355C>T	p.Arg119Cys	p.R119C	ENST00000341259	NM_005475.2	119	Cgc/Tgc	2/8	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.67	2		62	84	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738485	145738485	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767722327	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	289	716	1	ENST00000428558.2:c.2500G>A	p.Ala834Thr	p.A834T	ENST00000428558	NM_004260.3	834	Gcc/Acc	16/22	0.243726634809805	3	FACETS	0.808	0.764	0.851	0.808	0.764	0.851	INDETERMINATE	2	TRUE	1	0.67	3		717	713	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048667	180048667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749960761	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	201	660	1	ENST00000261937.6:c.1895G>A	p.Arg632His	p.R632H	ENST00000261937	NM_182925.4	632	cGc/cAc	13/30	0.3	1	FACETS	0.614	0.572	0.657	0.614	0.572	0.657	INDETERMINATE	1	TRUE	0	0.67	1		661	650	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281310	15281310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	285	750	0	ENST00000263388.2:c.4946C>T	p.Ala1649Val	p.A1649V	ENST00000263388	NM_000435.2	1649	gCg/gTg	27/33	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.67	2		750	774	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879925	44879925	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs189751539	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	158	408	0	ENST00000377967.4:c.514C>T	p.Arg172Ter	p.R172*	ENST00000377967	NM_021140.2	172	Cga/Tga	6/29	1	2	FACETS	0.981	0.906	1	0.981	0.906	1	CLONAL	1	TRUE	1	0.67	2		408	481	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426544	49426544	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555188379	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	270	769	1	ENST00000301067.7:c.11944C>T	p.Arg3982Ter	p.R3982*	ENST00000301067	NM_003482.3	3982	Cga/Tga	39/54	1	2	FACETS	0.958	0.902	1	0.958	0.902	1	CLONAL	1	TRUE	1	0.67	2		770	841	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965019	25965019	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750809033	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	143	452	0	ENST00000435504.4:c.4187C>T	p.Thr1396Met	p.T1396M	ENST00000435504		1396	aCg/aTg	13/13	1	2	FACETS	0.889	0.817	0.964	0.889	0.817	0.964	CLONAL	1	TRUE	1	0.67	2		452	480	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457614	67457614	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253901433	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	180	537	0	ENST00000327367.4:c.424C>T	p.Arg142Cys	p.R142C	ENST00000327367	NM_005902.3	142	Cgc/Tgc	3/9	1	2	FACETS	0.906	0.84	0.974	0.906	0.84	0.974	CLONAL	1	TRUE	1	0.67	2		537	593	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478947	56478947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760053751	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	177	583	2	ENST00000267101.3:c.403C>T	p.Arg135Cys	p.R135C	ENST00000267101	NM_001982.3	135	Cgc/Tgc	3/28	1	2	FACETS	0.884	0.818	0.951	0.884	0.818	0.951	CLONAL	1	TRUE	1	0.67	2		585	598	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275750	41275750	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1210247690	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	157	410	0	ENST00000349496.5:c.1645C>T	p.Arg549Cys	p.R549C	ENST00000349496	NM_001904.3	549	Cgc/Tgc	10/15	1	2	FACETS	0.951	0.877	1	0.951	0.877	1	CLONAL	1	TRUE	1	0.67	2		410	493	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108097	30108097	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	121	421	0	ENST00000331968.5:c.710C>T	p.Ser237Leu	p.S237L	ENST00000331968	NM_002742.2	237	tCa/tTa	5/18	1	2	FACETS	0.852	0.776	0.931	0.852	0.776	0.931	CLONAL	1	TRUE	1	0.67	2		421	424	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427730	49427732	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	161	610	0	ENST00000301067.7:c.10756_10758del	p.Lys3586del	p.K3586del	ENST00000301067	NM_003482.3	3586	AAG/-	39/54	1	2	FACETS	0.769	0.708	0.832	0.769	0.708	0.832	SUBCLONAL	1	TRUE	1	0.67	2		610	625	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392700	118392700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	165	474	0	ENST00000534358.1:c.11732C>T	p.Ser3911Leu	p.S3911L	ENST00000534358	NM_005933.3	3911	tCg/tTg	36/36	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.67	2		474	489	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797191	42797191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778202	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	273	782	1	ENST00000575354.2:c.3553G>A	p.Ala1185Thr	p.A1185T	ENST00000575354	NM_015125.3	1185	Gcc/Acc	15/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.67	2		783	799	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10286250	10286250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781646588	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	78	554	0	ENST00000340748.4:c.566C>T	p.Ser189Leu	p.S189L	ENST00000340748		189	tCg/tTg	6/40	1	2	FACETS	0.438	0.385	0.494	0.438	0.385	0.494	SUBCLONAL	1	TRUE	1	0.67	2		554	532	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206933	162206933	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777074432	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	61	240	0	ENST00000366898.1:c.742G>A	p.Val248Ile	p.V248I	ENST00000366898	NM_004562.2	248	Gtc/Atc	7/12	1	2	FACETS	0.785	0.686	0.89	0.785	0.686	0.89	SUBCLONAL	1	TRUE	1	0.67	2		240	232	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971042	21971042	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	87	547	0	ENST00000304494.5:c.316del	p.Val106CysfsTer40	p.V106Cfs*40	ENST00000304494	NM_000077.4	106	Gtg/tg	2/3	0.243726634809805	1	FACETS	0.345	0.306	0.386	0.345	0.306	0.386	INDETERMINATE	1	TRUE	0	0.67	1		547	501	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438734	49438734	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759873461	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	176	540	1	ENST00000301067.7:c.4756C>T	p.Arg1586Cys	p.R1586C	ENST00000301067	NM_003482.3	1586	Cgc/Tgc	19/54	1	2	FACETS	0.847	0.784	0.912	0.847	0.784	0.912	CLONAL	1	TRUE	1	0.67	2		541	620	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775662	9775662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	66	652	1	ENST00000377346.4:c.205G>A	p.Val69Met	p.V69M	ENST00000377346	NM_005026.3	69	Gtg/Atg	4/24	1	2	FACETS	0.29	0.251	0.332	0.29	0.251	0.332	SUBCLONAL	1	TRUE	1	0.67	2		653	680	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69458696	69458697	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	37	495	3	ENST00000227507.2:c.511_512delinsTT	p.Ala171Leu	p.A171L	ENST00000227507	NM_053056.2	171	GCg/TTg	3/5	1	2	FACETS	0.189	0.155	0.227	0.189	0.155	0.227	SUBCLONAL	1	TRUE	1	0.67	2		498	585	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625362	69625362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781807006	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	237	746	1	ENST00000334134.2:c.431G>A	p.Arg144His	p.R144H	ENST00000334134	NM_005247.2	144	cGc/cAc	3/3	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.67	2		747	685	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992099	11992099	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	104	330	0	ENST00000396373.4:c.189G>T	p.Arg63Ser	p.R63S	ENST00000396373	NM_001987.4	63	agG/agT	3/8	0.140764131893472	3	FACETS	1	0.965	1	0.572	0.517	0.63	INDETERMINATE	1	TRUE	1	0.67	3		330	362	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50481242	50481242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	133	341	0	ENST00000394963.4:c.628C>T	p.Arg210Trp	p.R210W	ENST00000394963	NM_003076.4	210	Cgg/Tgg	5/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.67	2		341	361	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143048	58143048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370258992	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	246	665	1	ENST00000257904.6:c.736C>T	p.Arg246Cys	p.R246C	ENST00000257904	NM_000075.3	246	Cgt/Tgt	7/8	1	2	FACETS	0.998	0.937	1	0.998	0.937	1	CLONAL	1	TRUE	1	0.67	2		666	736	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194789	30194789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761853569	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	161	488	0	ENST00000331968.5:c.356C>T	p.Ala119Val	p.A119V	ENST00000331968	NM_002742.2	119	gCg/gTg	2/18	1	2	FACETS	0.893	0.824	0.964	0.893	0.824	0.964	CLONAL	1	TRUE	1	0.67	2		488	538	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987162	36987162	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1228705369	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	226	687	0	ENST00000354822.5:c.527T>C	p.Leu176Pro	p.L176P	ENST00000354822	NM_001079668.2	176	cTg/cCg	3/3	1	2	FACETS	0.944	0.883	1	0.944	0.883	1	CLONAL	1	TRUE	1	0.67	2		687	715	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944264	81944264	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1009796025	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	227	602	1	ENST00000359376.3:c.1873G>T	p.Ala625Ser	p.A625S	ENST00000359376	NM_002661.3	625	Gcc/Tcc	18/33	1	2	FACETS	0.976	0.914	1	0.976	0.914	1	CLONAL	1	TRUE	1	0.67	2		603	694	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346504	89346504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	162	672	0	ENST00000301030.4:c.6446C>T	p.Ala2149Val	p.A2149V	ENST00000301030	NM_001256183.1	2149	gCa/gTa	9/13	1	2	FACETS	0.887	0.819	0.958	0.887	0.819	0.958	CLONAL	1	TRUE	1	0.67	2		672	545	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967084	18967084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1388762291	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	96	553	1	ENST00000262803.5:c.1799G>A	p.Arg600His	p.R600H	ENST00000262803	NM_002911.3	600	cGc/cAc	13/24	1	2	FACETS	0.444	0.395	0.495	0.444	0.395	0.495	SUBCLONAL	1	TRUE	1	0.67	2		554	646	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46597010	46597010	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759634197	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	149	348	0	ENST00000263734.3:c.824G>A	p.Arg275His	p.R275H	ENST00000263734	NM_001430.4	275	cGc/cAc	7/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.67	2		348	431	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698067	47698104	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTAATATTTTTAATAAAACTGTTATTTCGATTTGCAGC	TTAATATTTTTAATAAAACTGTTATTTCGATTTGCAGC	AT	novel	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	56	257	1	ENST00000233146.2:c.1662-37_1662delinsAT		p.X554_splice	ENST00000233146	NM_000251.2	554		11/16	1	2	FACETS	0.699	0.606	0.799	0.699	0.606	0.799	SUBCLONAL	1	TRUE	1	0.67	2		258	239	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61708333	61708333	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	39	258	0	ENST00000401558.2:c.3056T>C	p.Leu1019Pro	p.L1019P	ENST00000401558	NM_003400.3	1019	cTa/cCa	24/25	1	2	FACETS	0.348	0.289	0.413	0.348	0.289	0.413	SUBCLONAL	1	TRUE	1	0.67	2		258	335	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294282	1294282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751231538	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	202	685	0	ENST00000310581.5:c.719G>A	p.Arg240His	p.R240H	ENST00000310581	NM_198253.2	240	cGt/cAt	2/16	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.67	2		685	594	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755629	57755629	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	194	523	1	ENST00000274289.3:c.158del	p.Pro53ArgfsTer47	p.P53Rfs*47	ENST00000274289	NM_006622.3	53	cCg/cg	1/14	1	2	FACETS	0.879	0.817	0.942	0.879	0.817	0.942	CLONAL	1	TRUE	1	0.67	2		524	659	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128246832	128246834	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	76	608	0	ENST00000265960.3:c.1095_1097del	p.Glu365del	p.E365del	ENST00000265960	NM_001006617.1	365	gaGGAt/gat	9/12	1	2	FACETS	0.401	0.352	0.453	0.401	0.352	0.453	SUBCLONAL	1	TRUE	1	0.67	2		608	566	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412311	139412311	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752919688	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	243	715	2	ENST00000277541.6:c.1334C>T	p.Thr445Met	p.T445M	ENST00000277541	NM_017617.3	445	aCg/aTg	8/34	1	2	FACETS	0.991	0.93	1	0.991	0.93	1	CLONAL	1	TRUE	1	0.67	2		717	732	SUCCESS
ATRX	546	MSKCC	GRCh37	X	77041481	77041481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	94	437	4	ENST00000373344.5:c.7G>A	p.Ala3Thr	p.A3T	ENST00000373344	NM_000489.3	3	Gct/Act	1/35	1	2	FACETS	0.507	0.452	0.566	0.507	0.452	0.566	SUBCLONAL	1	TRUE	1	0.67	2		441	553	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69458696	69458696	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	34	497	0	ENST00000227507.2:c.511G>T	p.Ala171Ser	p.A171S	ENST00000227507	NM_053056.2	171	Gcg/Tcg	3/5	1	2	FACETS	0.174	0.141	0.21	0.174	0.141	0.21	SUBCLONAL	1	TRUE	1	0.67	2		497	584	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371708	225371708	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	70	335	0	ENST00000264414.4:c.896T>G	p.Met299Arg	p.M299R	ENST00000264414	NM_003590.4	299	aTg/aGg	7/16	0.124479064335535	4	FACETS	0.991	0.877	1	0.991	0.877	1	INDETERMINATE	2	TRUE	2	0.466884079021051	4		335	222	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720737	89720737	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0051162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	15	90	0	ENST00000371953.3:c.888T>A	p.Cys296Ter	p.C296*	ENST00000371953	NM_000314.4	296	tgT/tgA	8/9	1	2	FACETS	0.616	0.451	0.813	0.616	0.451	0.813	SUBCLONAL	1	TRUE	1	0.24	2		90	203	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499477	89499477	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752560194	NA	P-0051162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	44	319	0	ENST00000336596.2:c.2647C>T	p.Arg883Trp	p.R883W	ENST00000336596	NM_005233.5	883	Cgg/Tgg	15/17	1	2	FACETS	0.817	0.685	0.962	0.817	0.685	0.962	CLONAL	1	TRUE	1	0.24	2		319	449	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857046	9857046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774039446	NA	P-0051164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	10	232	0	ENST00000330684.3:c.4355G>A	p.Arg1452His	p.R1452H	ENST00000330684	NM_001134407.1	1452	cGc/cAc	13/13	1	2	FACETS	0.81	0.554	1	0.81	0.554	1	CLONAL	1	TRUE	1	0.26	2		232	95	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	47	230	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.915	1			1	INDETERMINATE	1	TRUE	NA	0.382384368493823	2		230	222	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165679	118165680	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0051165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	58	279	0	ENST00000369448.3:c.189_190del	p.Ile64GlnfsTer45	p.I64Qfs*45	ENST00000369448	NM_017709.3	63	ggCAtc/ggtc	2/2	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.382384368493823	2		279	303	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405964	70405964	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	38	389	0	ENST00000373644.4:c.3482del	p.Lys1161ArgfsTer6	p.K1161Rfs*6	ENST00000373644	NM_030625.2	1160	Aaa/aa	4/12	0.222813575048782	2	FACETS	0.617	0.512	0.734	0.309	0.256	0.367	INDETERMINATE	1	TRUE	0	0.382384368493823	2		389	322	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368378	225368380	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0051165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	38	235	0	ENST00000264414.4:c.1366_1368del	p.Ser456del	p.S456del	ENST00000264414	NM_003590.4	456	TCT/-	9/16	0.382384368493823	1	FACETS	0.792	0.661	0.935	0.792	0.661	0.935	CLONAL	1	TRUE	0	0.382384368493823	1		235	203	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183846	10183846	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	83	588	0	ENST00000256474.2:c.317del	p.Gly106AlafsTer53	p.G106Afs*53	ENST00000256474	NM_000551.3	105	acG/ac	1/3	0.382384368493823	1	FACETS	0.822	0.729	0.921	0.822	0.729	0.921	CLONAL	1	TRUE	0	0.382384368493823	1		588	427	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610343	10610343	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	95	686	1	ENST00000171111.5:c.367G>A	p.Val123Met	p.V123M	ENST00000171111	NM_203500.1	123	Gtg/Atg	2/6	0.589802171025169	3	FACETS	0.643	0.573	0.717	0.321	0.286	0.359	SUBCLONAL	1	TRUE	1	0.589802171025169	3		687	649	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602523	10602523	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1419752356	NA	P-0051167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	109	682	0	ENST00000171111.5:c.1055G>A	p.Trp352Ter	p.W352*	ENST00000171111	NM_203500.1	352	tGg/tAg	3/6	0.589802171025169	3	FACETS	0.844	0.76	0.932	0.422	0.38	0.466	CLONAL	1	TRUE	1	0.589802171025169	3		682	567	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937048	178937048	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	54	257	0	ENST00000263967.3:c.1729A>G	p.Arg577Gly	p.R577G	ENST00000263967	NM_006218.2	577	Aga/Gga	11/21	0.589802171025169	4	FACETS	0.789	0.676	0.911	0.394	0.338	0.456	CLONAL	1	TRUE	2	0.589802171025169	4		257	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0051172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	158	644	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.152508178732006	2	FACETS	1	0.981	1	0.624	0.572	0.679	INDETERMINATE	1	TRUE	0	0.28	2		644	904	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585361	29585361	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1555618492	NA	P-0051172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	81	394	0	ENST00000356175.3:c.4111-1G>A		p.X1371_splice	ENST00000356175	NM_000267.3	1371			0.152508178732006	2	FACETS	1	0.945	1	0.56	0.494	0.629	INDETERMINATE	1	TRUE	0	0.28	2		394	517	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79974857	79974857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	97	447	0	ENST00000265081.6:c.1285C>T	p.Pro429Ser	p.P429S	ENST00000265081	NM_002439.4	429	Cct/Tct	8/24	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.28	2		447	600	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748300	43748300	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	63	677	0	ENST00000382044.4:c.2506T>C	p.Ser836Pro	p.S836P	ENST00000382044	NM_001141980.1	836	Tca/Cca	12/28	1	2	FACETS	0.521	0.449	0.599	0.521	0.449	0.599	SUBCLONAL	1	TRUE	1	0.28	2		677	864	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969101	93969101	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	35	283	0	ENST00000369303.4:c.1895G>T	p.Cys632Phe	p.C632F	ENST00000369303	NM_004440.3	632	tGt/tTt	10/17	1	2	FACETS	0.694	0.57	0.834	0.694	0.57	0.834	SUBCLONAL	1	TRUE	1	0.28	2		283	360	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679016	117679016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	39	421	0	ENST00000368508.3:c.3805C>T	p.His1269Tyr	p.H1269Y	ENST00000368508	NM_002944.2	1269	Cac/Tac	24/43	1	2	FACETS	0.53	0.438	0.632	0.53	0.438	0.632	SUBCLONAL	1	TRUE	1	0.28	2		421	526	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974752	21974753	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAG	novel	NA	P-0051172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	30	180	0	ENST00000304494.5:c.74_75insCTT	p.Val25_Glu26insLeu	p.V25_E26insL	ENST00000304494	NM_000077.4	25	gta/gtCTTa	1/3	1	2	FACETS	0.878	0.711	1	0.878	0.711	1	CLONAL	1	TRUE	1	0.28	2		180	244	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909644	76909644	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051172-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	46	209	1	ENST00000373344.5:c.4261C>T	p.Gln1421Ter	p.Q1421*	ENST00000373344	NM_000489.3	1421	Cag/Tag	14/35	0.12530529535701	2	FACETS	1	0.927	1			1	INDETERMINATE	1	TRUE	NA	0.28	2		210	282	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051173-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	80	230	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.731739521212147	2		230	213	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508499	106508499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752602335	NA	P-0051173-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	127	323	0	ENST00000359195.3:c.493G>A	p.Val165Ile	p.V165I	ENST00000359195	NM_002649.2	165	Gtc/Atc	2/11	0.731739521212147	3	FACETS	0.907	0.825	0.991	0.453	0.412	0.496	CLONAL	1	TRUE	1	0.731739521212147	3		323	523	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221743	55221743	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519829	NA	P-0051173-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	186	478	0	ENST00000275493.2:c.787A>C	p.Thr263Pro	p.T263P	ENST00000275493	NM_005228.3	263	Acc/Ccc	7/28	0.731739521212147	3	FACETS	0.901	0.834	0.97	0.45	0.417	0.485	CLONAL	1	TRUE	1	0.731739521212147	3		478	771	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129420	2129420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781774	NA	P-0051173-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	207	585	1	ENST00000219476.3:c.3275C>T	p.Pro1092Leu	p.P1092L	ENST00000219476	NM_000548.3	1092	cCg/cTg	28/42	1	2	FACETS	0.904	0.843	0.965	0.904	0.843	0.965	CLONAL	1	TRUE	1	0.731739521212147	2		586	626	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95579443	95579443	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs878855246	NA	P-0051173-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	131	246	0	ENST00000393063.1:c.2026C>T	p.Arg676Ter	p.R676*	ENST00000393063	NM_030621.3	676	Cga/Tga	13/28	1	2	FACETS	0.942	0.864	1	0.942	0.864	1	CLONAL	1	TRUE	1	0.731739521212147	2		246	380	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155399	47155399	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051173-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	62	400	0	ENST00000409792.3:c.4682G>C	p.Gly1561Ala	p.G1561A	ENST00000409792	NM_014159.6	1561	gGc/gCc	5/21	1	2	FACETS	0.366	0.317	0.419	0.366	0.317	0.419	SUBCLONAL	1	TRUE	1	0.731739521212147	2		400	463	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47088090	47088090	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051173-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	114	409	0	ENST00000409792.3:c.6985C>T	p.Gln2329Ter	p.Q2329*	ENST00000409792	NM_014159.6	2329	Cag/Tag	16/21	1	2	FACETS	0.571	0.516	0.628	0.571	0.516	0.628	SUBCLONAL	1	TRUE	1	0.731739521212147	2		409	546	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161755	47161756	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGGTCCCTGAAGTCATCCATGACACAGGAGGGCCCAAA	novel	NA	P-0051173-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	79	262	0	ENST00000409792.3:c.4370_4371insTTTGGGCCCTCCTGTGTCATGGATGACTTCAGGGACCC	p.Gln1458LeufsTer38	p.Q1458Lfs*38	ENST00000409792	NM_014159.6	1457	cca/ccTTTGGGCCCTCCTGTGTCATGGATGACTTCAGGGACCCa	3/21	1	2	FACETS	0.489	0.431	0.549	0.489	0.431	0.549	SUBCLONAL	1	TRUE	1	0.731739521212147	2		262	442	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211849	123211850	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAACAAGGCAGATAGACAAAATTCAGTGTGCTAAGACCCTTATTCTC	novel	NA	P-0051173-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	96	407	0	ENST00000218089.9:c.2718_2764dup	p.Ser922LysfsTer5	p.S922Kfs*5	ENST00000218089	NM_001042749.1	906	aaa/aAAACAAGGCAGATAGACAAAATTCAGTGTGCTAAGACCCTTATTCTCaa	27/35	1	2	FACETS	0.42	0.375	0.469	0.42	0.375	0.469	SUBCLONAL	1	TRUE	1	0.731739521212147	2		407	624	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0051177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	213	975	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.620576901817551	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.625600165056839	1		977	434	SUCCESS
APC	324	MSKCC	GRCh37	5	112163677	112163677	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0051177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	59	506	0	ENST00000257430.4:c.1600A>T	p.Lys534Ter	p.K534*	ENST00000257430	NM_000038.5	534	Aaa/Taa	13/16	1	2	FACETS	0.861	0.751	0.978	0.861	0.751	0.978	CLONAL	1	TRUE	1	0.625600165056839	2		506	219	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0051177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	39	232	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.866	0.731	1	0.866	0.731	1	CLONAL	1	TRUE	1	0.625600165056839	2		232	144	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044541	47044541	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	173	525	0	ENST00000377604.3:c.2038C>T	p.Arg680Ter	p.R680*	ENST00000377604	NM_001204468.1	680	Cga/Tga	18/24	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.625600165056839	1		525	270	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909851	100909851	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	12	314	0	ENST00000325455.5:c.2798A>T	p.Lys933Met	p.K933M	ENST00000325455	NM_001202474.3	933	aAg/aTg	8/8	1	2	FACETS	0.422	0.3	0.567	0.422	0.3	0.567	SUBCLONAL	1	TRUE	1	0.625600165056839	2		314	91	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523073	25523073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779208522	NA	P-0051177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	198	937	2	ENST00000264709.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000264709	NM_175629.2	38	Cgc/Tgc	3/23	1	2	FACETS	0.966	0.899	1	0.966	0.899	1	CLONAL	1	TRUE	1	0.625600165056839	2		939	655	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226561935	226561935	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	81	616	0	ENST00000366794.5:c.2062G>T	p.Glu688Ter	p.E688*	ENST00000366794	NM_001618.3	688	Gag/Tag	14/23	1	2	FACETS	0.878	0.782	0.978	0.878	0.782	0.978	CLONAL	1	TRUE	1	0.625600165056839	2		616	295	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828612	72828615	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	novel	NA	P-0051179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	41	689	1	ENST00000268489.5:c.7966_7969del	p.Leu2656ThrfsTer24	p.L2656Tfs*24	ENST00000268489	NM_006885.3	2656	CTCTac/ac	9/10	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.18	2		690	411	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60795898	60795898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	55	569	0	ENST00000333681.4:c.680G>A	p.Gly227Glu	p.G227E	ENST00000333681		227	gGa/gAa	3/3	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.18	2		569	556	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222979	36222979	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1178719022	NA	P-0051179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	33	868	0	ENST00000222270.7:c.5608T>C	p.Tyr1870His	p.Y1870H	ENST00000222270	NM_014727.1	1870	Tac/Cac	27/37	1	2	FACETS	0.661	0.537	0.801	0.661	0.537	0.801	SUBCLONAL	1	TRUE	1	0.18	2		868	555	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391524	84391524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200068246	NA	P-0051179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	20	401	0	ENST00000321945.7:c.308G>A	p.Arg103His	p.R103H	ENST00000321945	NM_139076.2	103	cGt/cAt	5/9	1	2	FACETS	0.839	0.642	1	0.839	0.642	1	CLONAL	1	TRUE	1	0.18	2		401	265	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0051180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	160	454	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.387749435167261	1	FACETS	0.895	0.823	0.971	0.895	0.823	0.971	CLONAL	1	TRUE	0	0.387749435167261	1		454	743	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0051180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	120	454	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.370061215558381	1	FACETS	0.968	0.878	1	0.968	0.878	1	CLONAL	1	TRUE	0	0.370061215558381	1		454	546	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975740	26975755	+	frameshift_variant	Frame_Shift_Del	DEL	TATCATGACCTCAGAC	TATCATGACCTCAGAC	-	novel	NA	P-0051180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	61	282	0	ENST00000381527.3:c.1253_1268del	p.Met418SerfsTer59	p.M418Sfs*59	ENST00000381527	NM_001260.1	416	ctTATCATGACCTCAGAC/ct	12/13	1	2	FACETS	0.85	0.736	0.972	0.85	0.736	0.972	CLONAL	1	TRUE	1	0.370061215558381	2		282	388	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0051181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	144	299	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.812	0.741	0.886	1	0.989	1	CLONAL	2	TRUE	1	0.23742622629037	2		299	747	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0051181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	138	866	1	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.23742622629037	1	FACETS	0.949	0.862	1	0.949	0.862	1	CLONAL	1	TRUE	0	0.23742622629037	1		867	1080	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525620	187525621	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0051181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	88	638	0	ENST00000441802.2:c.10458dup	p.Lys3487GlufsTer4	p.K3487Efs*4	ENST00000441802	NM_005245.3	3486	-/G	18/27	1	2	FACETS	0.751	0.664	0.845	0.751	0.664	0.845	SUBCLONAL	1	TRUE	1	0.23742622629037	2		638	987	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056141	26056141	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	56	497	0	ENST00000343677.2:c.516G>C	p.Lys172Asn	p.K172N	ENST00000343677	NM_005319.3	172	aaG/aaC	1/1	1	2	FACETS	0.626	0.536	0.726	0.626	0.536	0.726	SUBCLONAL	1	TRUE	1	0.23742622629037	2		497	753	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652097	36652098	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0051181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	111	783	0	ENST00000244741.5:c.222dup	p.Lys75GlnfsTer14	p.K75Qfs*14	ENST00000244741	NM_000389.4	73	-/C	2/3	1	2	FACETS	0.804	0.721	0.893	0.804	0.721	0.893	CLONAL	1	TRUE	1	0.23742622629037	2		783	1163	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222693	53222693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	111	486	0	ENST00000375401.3:c.4243G>A	p.Glu1415Lys	p.E1415K	ENST00000375401	NM_004187.3	1415	Gag/Aag	25/26	1	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.23742622629037	1		486	628	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222991	53222991	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	79	355	0	ENST00000375401.3:c.4081G>C	p.Glu1361Gln	p.E1361Q	ENST00000375401	NM_004187.3	1361	Gag/Cag	24/26	1	1	FACETS	0.961	0.846	1	0.961	0.846	1	CLONAL	1	TRUE	0	0.23742622629037	1		355	610	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223395	53223395	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	87	445	0	ENST00000375401.3:c.3964G>C	p.Glu1322Gln	p.E1322Q	ENST00000375401	NM_004187.3	1322	Gag/Cag	23/26	1	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.23742622629037	1		445	620	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223407	53223407	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	90	463	2	ENST00000375401.3:c.3952G>T	p.Glu1318Ter	p.E1318*	ENST00000375401	NM_004187.3	1318	Gaa/Taa	23/26	1	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.23742622629037	1		465	642	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	36	360	0	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	1	FACETS	0.091	0.075	0.11	0.091	0.075	0.11	SUBCLONAL	1	TRUE	0	0.868321854353652	1		360	513	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	308	502	4	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.988	0.938	1	0.988	0.938	1	CLONAL	1	TRUE	1	0.868321854353652	2		506	718	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	57	732	1	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	0.142	0.121	0.165	0.142	0.121	0.165	SUBCLONAL	1	TRUE	1	0.868321854353652	2		733	924	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	398	770	5	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.995	0.951	1	0.995	0.951	1	CLONAL	1	TRUE	1	0.868321854353652	2		775	921	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217380	123217380	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	346	338	0	ENST00000218089.9:c.3034C>T	p.Arg1012Ter	p.R1012*	ENST00000218089	NM_001042749.1	1012	Cga/Tga	29/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.868321854353652	1		338	397	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	450	558	3	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.868321854353652	2		561	761	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	436	752	2	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.995	0.953	1	0.995	0.953	1	CLONAL	1	TRUE	1	0.868321854353652	2		754	1009	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	72	653	1	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.167	0.145	0.191	0.167	0.145	0.191	SUBCLONAL	1	TRUE	1	0.868321854353652	2		654	991	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430832	78430832	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	90	717	0	ENST00000370768.2:c.557C>T	p.Ala186Val	p.A186V	ENST00000370768	NM_003902.3	186	gCa/gTa	8/20	1	2	FACETS	0.184	0.163	0.208	0.184	0.163	0.208	SUBCLONAL	1	TRUE	1	0.868321854353652	2		717	1124	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849884	156849884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770727871	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	412	722	0	ENST00000524377.1:c.2140G>A	p.Gly714Ser	p.G714S	ENST00000524377	NM_002529.3	714	Ggc/Agc	16/17	1	2	FACETS	0.935	0.893	0.977	0.935	0.893	0.977	CLONAL	1	TRUE	1	0.868321854353652	2		722	1015	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925621	114925621	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763934346	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	258	667	0	ENST00000543371.1:c.1699G>A	p.Ala567Thr	p.A567T	ENST00000543371	NM_001198531.1	567	Gcc/Acc	14/14	1	2	FACETS	0.622	0.583	0.662	0.622	0.583	0.662	SUBCLONAL	1	TRUE	1	0.868321854353652	2		667	956	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138923	64138923	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs747874901	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	56	462	0	ENST00000334205.4:c.2290C>T	p.Arg764Ter	p.R764*	ENST00000334205	NM_003942.2	764	Cga/Tga	17/17	1	2	FACETS	0.211	0.181	0.245	0.211	0.181	0.245	SUBCLONAL	1	TRUE	1	0.868321854353652	2		462	610	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214012	108214012	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	282	508	0	ENST00000278616.4:c.8332G>A	p.Glu2778Lys	p.E2778K	ENST00000278616	NM_000051.3	2778	Gaa/Aaa	57/63	1	2	FACETS	0.999	0.946	1	0.999	0.946	1	CLONAL	1	TRUE	1	0.868321854353652	2		508	650	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344476	118344476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782640926	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	35	344	0	ENST00000534358.1:c.2602G>A	p.Val868Met	p.V868M	ENST00000534358	NM_005933.3	868	Gtg/Atg	3/36	1	2	FACETS	0.175	0.143	0.211	0.175	0.143	0.211	SUBCLONAL	1	TRUE	1	0.868321854353652	2		344	460	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420184	49420184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555185701	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	405	746	1	ENST00000301067.7:c.15565G>A	p.Gly5189Arg	p.G5189R	ENST00000301067	NM_003482.3	5189	Gga/Aga	48/54	1	2	FACETS	0.982	0.938	1	0.982	0.938	1	CLONAL	1	TRUE	1	0.868321854353652	2		747	950	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428417	49428417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1439926284	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	488	750	2	ENST00000301067.7:c.10388C>T	p.Ser3463Leu	p.S3463L	ENST00000301067	NM_003482.3	3463	tCg/tTg	36/54	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.868321854353652	2		752	1117	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864534	57864534	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	51	803	1	ENST00000228682.2:c.2015del	p.Gly672GlufsTer47	p.G672Efs*47	ENST00000228682	NM_005269.2	671	Ggg/gg	12/12	1	2	FACETS	0.116	0.097	0.136	0.116	0.097	0.136	SUBCLONAL	1	TRUE	1	0.868321854353652	2		804	1017	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919631	28919631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200840674	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	104	642	0	ENST00000282397.4:c.2306C>T	p.Ala769Val	p.A769V	ENST00000282397	NM_002019.4	769	gCg/gTg	16/30	1	2	FACETS	0.271	0.242	0.301	0.271	0.242	0.301	SUBCLONAL	1	TRUE	1	0.868321854353652	2		642	885	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465636	99465636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775915596	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	329	571	1	ENST00000268035.6:c.2461G>A	p.Val821Ile	p.V821I	ENST00000268035	NM_000875.3	821	Gtc/Atc	11/21	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.868321854353652	2		572	755	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354432	354432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761954300	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	260	686	0	ENST00000262320.3:c.1126C>T	p.Arg376Trp	p.R376W	ENST00000262320	NM_003502.3	376	Cgg/Tgg	5/11	1	2	FACETS	0.662	0.621	0.703	0.662	0.621	0.703	SUBCLONAL	1	TRUE	1	0.868321854353652	2		686	905	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221320	2221320	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	113	725	0	ENST00000326181.6:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000326181	NM_032271.2	135	tGc/tAc	6/21	1	2	FACETS	0.273	0.245	0.302	0.273	0.245	0.302	SUBCLONAL	1	TRUE	1	0.868321854353652	2		725	955	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67646012	67646013	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	97	476	1	ENST00000264010.4:c.950_951dup	p.Gly318GlnfsTer16	p.G318Qfs*16	ENST00000264010	NM_006565.3	314	aac/aACac	4/12	1	2	FACETS	0.275	0.244	0.307	0.275	0.244	0.307	SUBCLONAL	1	TRUE	1	0.868321854353652	2		477	813	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654625	67654625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	245	591	1	ENST00000264010.4:c.1112G>A	p.Arg371His	p.R371H	ENST00000264010	NM_006565.3	371	cGc/cAc	6/12	1	2	FACETS	0.633	0.593	0.675	0.633	0.593	0.675	SUBCLONAL	1	TRUE	1	0.868321854353652	2		592	891	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654642	67654642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	290	622	3	ENST00000264010.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000264010	NM_006565.3	377	Cgt/Tgt	6/12	1	2	FACETS	0.684	0.644	0.724	0.684	0.644	0.724	SUBCLONAL	1	TRUE	1	0.868321854353652	2		625	977	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81922843	81922843	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs988595873	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	126	523	0	ENST00000359376.3:c.832C>T	p.Arg278Cys	p.R278C	ENST00000359376	NM_002661.3	278	Cgt/Tgt	10/33	1	2	FACETS	0.354	0.321	0.39	0.354	0.321	0.39	SUBCLONAL	1	TRUE	1	0.868321854353652	2		523	819	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836612	89836612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	309	825	1	ENST00000389301.3:c.2278G>A	p.Ala760Thr	p.A760T	ENST00000389301	NM_000135.2	760	Gca/Aca	25/43	1	2	FACETS	0.666	0.628	0.704	0.666	0.628	0.704	SUBCLONAL	1	TRUE	1	0.868321854353652	2		826	1069	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7978994	7978994	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367693196	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	263	643	0	ENST00000319144.4:c.1573G>A	p.Ala525Thr	p.A525T	ENST00000319144	NM_001139.2	525	Gca/Aca	12/15	1	2	FACETS	0.674	0.633	0.716	0.674	0.633	0.716	SUBCLONAL	1	TRUE	1	0.868321854353652	2		643	899	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554556	29554556	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	176	257	0	ENST00000356175.3:c.2341del	p.His781MetfsTer10	p.H781Mfs*10	ENST00000356175	NM_000267.3	781	Cat/at	20/57	1	2	FACETS	0.943	0.878	1	0.943	0.878	1	CLONAL	1	TRUE	1	0.868321854353652	2		257	430	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554674	63554674	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	228	540	0	ENST00000307078.5:c.65C>A	p.Pro22Gln	p.P22Q	ENST00000307078	NM_004655.3	22	cCg/cAg	2/11	1	2	FACETS	0.672	0.628	0.718	0.672	0.628	0.718	SUBCLONAL	1	TRUE	1	0.868321854353652	2		540	781	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2189769	2189769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	510	820	3	ENST00000398665.3:c.239G>A	p.Arg80His	p.R80H	ENST00000398665	NM_032482.2	80	cGt/cAt	4/28	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.868321854353652	2		823	1069	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244190	5244190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760369713	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	371	711	0	ENST00000357368.4:c.1292G>A	p.Arg431Gln	p.R431Q	ENST00000357368	NM_002850.3	431	cGg/cAg	11/38	1	2	FACETS	0.904	0.861	0.948	0.904	0.861	0.948	CLONAL	1	TRUE	1	0.868321854353652	2		711	945	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024706	11024706	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139789571	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	232	418	0	ENST00000327064.4:c.823G>A	p.Ala275Thr	p.A275T	ENST00000327064	NM_199141.1	275	Gcc/Acc	6/16	1	2	FACETS	0.966	0.909	1	0.966	0.909	1	CLONAL	1	TRUE	1	0.868321854353652	2		418	553	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132491	11132491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	311	712	0	ENST00000358026.2:c.2707G>A	p.Ala903Thr	p.A903T	ENST00000358026	NM_001128849.1	903	Gca/Aca	19/36	1	2	FACETS	0.697	0.658	0.737	0.697	0.658	0.737	SUBCLONAL	1	TRUE	1	0.868321854353652	2		712	1028	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141492	11141492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	430	776	0	ENST00000358026.2:c.3469C>T	p.Arg1157Trp	p.R1157W	ENST00000358026	NM_001128849.1	1157	Cgg/Tgg	25/36	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.868321854353652	2		776	957	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281488	15281488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	444	741	0	ENST00000263388.2:c.4885G>A	p.Val1629Met	p.V1629M	ENST00000263388	NM_000435.2	1629	Gtg/Atg	26/33	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.868321854353652	2		741	953	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285086	15285086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	271	745	1	ENST00000263388.2:c.4529G>A	p.Arg1510His	p.R1510H	ENST00000263388	NM_000435.2	1510	cGc/cAc	25/33	1	2	FACETS	0.62	0.582	0.659	0.62	0.582	0.659	SUBCLONAL	1	TRUE	1	0.868321854353652	2		746	1007	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868350	45868350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765679315	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	153	873	2	ENST00000391945.4:c.427C>T	p.Arg143Trp	p.R143W	ENST00000391945	NM_000400.3	143	Cgg/Tgg	6/23	1	2	FACETS	0.296	0.27	0.324	0.296	0.27	0.324	SUBCLONAL	1	TRUE	1	0.868321854353652	2		875	1189	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724361	52724361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	47	474	1	ENST00000322088.6:c.1493G>A	p.Arg498His	p.R498H	ENST00000322088	NM_014225.5	498	cGc/cAc	12/15	1	2	FACETS	0.162	0.136	0.19	0.162	0.136	0.19	SUBCLONAL	1	TRUE	1	0.868321854353652	2		475	670	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635575	47635576	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	285	545	0	ENST00000233146.2:c.248dup	p.Met83IlefsTer4	p.M83Ifs*4	ENST00000233146	NM_000251.2	83	atg/aTtg	2/16	1	2	FACETS	0.898	0.849	0.948	0.898	0.849	0.948	CLONAL	1	TRUE	1	0.868321854353652	2		545	731	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672741	47672741	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs557339938	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	414	666	2	ENST00000233146.2:c.1331G>A	p.Arg444His	p.R444H	ENST00000233146	NM_000251.2	444	cGt/cAt	8/16	1	2	FACETS	0.951	0.908	0.994	0.951	0.908	0.994	CLONAL	1	TRUE	1	0.868321854353652	2		668	1003	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026176	48026176	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881787	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	281	477	0	ENST00000234420.5:c.1054G>A	p.Val352Ile	p.V352I	ENST00000234420	NM_000179.2	352	Gtt/Att	4/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.868321854353652	2		477	617	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265573	198265573	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	61	649	1	ENST00000335508.6:c.2584G>A	p.Glu862Lys	p.E862K	ENST00000335508	NM_012433.2	862	Gaa/Aaa	18/25	1	2	FACETS	0.167	0.144	0.193	0.167	0.144	0.193	SUBCLONAL	1	TRUE	1	0.868321854353652	2		650	840	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39713141	39713141	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	25	319	0	ENST00000361337.2:c.552del	p.Val185PhefsTer36	p.V185Ffs*36	ENST00000361337	NM_003286.2	183	Aaa/aa	8/21	1	2	FACETS	0.165	0.129	0.205	0.165	0.129	0.205	SUBCLONAL	1	TRUE	1	0.868321854353652	2		319	350	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42861441	42861441	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	46	501	0	ENST00000398585.3:c.429G>A	p.Trp143Ter	p.W143*	ENST00000398585	NM_001135099.1	143	tgG/tgA	4/14	1	2	FACETS	0.155	0.13	0.183	0.155	0.13	0.183	SUBCLONAL	1	TRUE	1	0.868321854353652	2		501	684	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436312	52436312	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	349	651	0	ENST00000460680.1:c.2182C>T	p.Arg728Cys	p.R728C	ENST00000460680	NM_004656.3	728	Cgc/Tgc	17/17	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.868321854353652	2		651	784	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037144	71037144	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	260	404	0	ENST00000318789.4:c.1146+1G>A		p.X382_splice	ENST00000318789	NM_032682.5	382			1	2	FACETS	0.971	0.916	1	0.971	0.916	1	CLONAL	1	TRUE	1	0.868321854353652	2		404	617	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696631	176696631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs794727176	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	34	364	1	ENST00000439151.2:c.5332C>T	p.Arg1778Ter	p.R1778*	ENST00000439151	NM_022455.4	1778	Cga/Tga	16/23	1	2	FACETS	0.167	0.136	0.201	0.167	0.136	0.201	SUBCLONAL	1	TRUE	1	0.868321854353652	2		365	470	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012386	152012386	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	199	422	1	ENST00000262189.6:c.427del	p.Ser143ValfsTer3	p.S143Vfs*3	ENST00000262189	NM_170606.2	143	Agt/gt	4/59	1	2	FACETS	0.86	0.803	0.918	0.86	0.803	0.918	CLONAL	1	TRUE	1	0.868321854353652	2		423	533	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559285	141559285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1185404860	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	324	741	0	ENST00000220592.5:c.1516C>T	p.Arg506Trp	p.R506W	ENST00000220592	NM_012154.3	506	Cgg/Tgg	12/19	1	2	FACETS	0.687	0.649	0.726	0.687	0.649	0.726	SUBCLONAL	1	TRUE	1	0.868321854353652	2		741	1086	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411912	63411912	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	63	521	0	ENST00000330258.3:c.1255C>G	p.Pro419Ala	p.P419A	ENST00000330258	NM_152424.3	419	Ccc/Gcc	2/2	1	1	FACETS	0.12	0.103	0.138	0.12	0.103	0.138	SUBCLONAL	1	TRUE	0	0.868321854353652	1		521	686	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357196	70357196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200663107	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	70	382	1	ENST00000374080.3:c.5711C>T	p.Ala1904Val	p.A1904V	ENST00000374080		1904	gCg/gTg	39/45	1	1	FACETS	0.182	0.159	0.208	0.182	0.159	0.208	SUBCLONAL	1	TRUE	0	0.868321854353652	1		383	500	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939847	76939847	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	384	363	0	ENST00000373344.5:c.901G>C	p.Asp301His	p.D301H	ENST00000373344	NM_000489.3	301	Gac/Cac	9/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.868321854353652	1		363	464	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939895	76939895	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	410	372	0	ENST00000373344.5:c.853G>C	p.Glu285Gln	p.E285Q	ENST00000373344	NM_000489.3	285	Gag/Cag	9/35	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.868321854353652	1		372	490	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940025	76940025	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	431	327	0	ENST00000373344.5:c.723G>C	p.Lys241Asn	p.K241N	ENST00000373344	NM_000489.3	241	aaG/aaC	9/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.868321854353652	1		327	495	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940459	76940459	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	401	324	0	ENST00000373344.5:c.634G>C	p.Asp212His	p.D212H	ENST00000373344	NM_000489.3	212	Gac/Cac	8/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.868321854353652	1		324	464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934578	NA	P-0051183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	41	675	0	ENST00000269305.4:c.524G>T	p.Arg175Leu	p.R175L	ENST00000269305	NM_001126112.2	175	cGc/cTc	5/11	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.15	2		675	428	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798329	45798329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780748	NA	P-0051183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	34	745	0	ENST00000450313.1:c.607C>T	p.Arg203Cys	p.R203C	ENST00000450313	NM_012222.2	203	Cgt/Tgt	8/16	1	2	FACETS	0.937	0.765	1	0.937	0.765	1	CLONAL	1	TRUE	1	0.15	2		745	484	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555189	106555189	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	21	606	0	ENST00000369096.4:c.2306A>T	p.Glu769Val	p.E769V	ENST00000369096	NM_001198.3	769	gAa/gTa	7/7	0.0887123949278257	3	FACETS	0.818	0.629	1	0.409	0.314	0.52	INDETERMINATE	1	TRUE	1	0.15	3		606	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0051213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	429	705	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.791789234797669	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.791789234797669	1		705	602	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0051213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	529	968	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.791789234797669	2		968	1268	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159754	20159754	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	308	300	0	ENST00000379607.5:c.5C>G	p.Pro2Arg	p.P2R	ENST00000379607	NM_001412.3	2	cCc/cGc	1/7	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.791789234797669	1		300	388	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149946	99149947	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0051213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	301	660	0	ENST00000074304.5:c.258_259del	p.Glu87AspfsTer3	p.E87Dfs*3	ENST00000074304	NM_001134224.1	86	acGGag/acag	5/26	1	2	FACETS	0.926	0.876	0.977	0.926	0.876	0.977	CLONAL	1	TRUE	1	0.791789234797669	2		660	821	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0051215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	227	289	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.525932714726942	2	FACETS	0.882	0.831	0.933	0.882	0.831	0.933	CLONAL	2	TRUE	0	0.531917898375458	2		289	484	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0051215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	101	351	1	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.9	0.81	0.994	0.9	0.81	0.994	CLONAL	1	TRUE	1	0.531917898375458	2		352	422	SUCCESS
APC	324	MSKCC	GRCh37	5	112175754	112175754	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0051215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	83	367	0	ENST00000257430.4:c.4463T>A	p.Leu1488Ter	p.L1488*	ENST00000257430	NM_000038.5	1488	tTa/tAa	16/16	1	2	FACETS	0.819	0.728	0.916	0.819	0.728	0.916	CLONAL	1	TRUE	1	0.531917898375458	2		367	381	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411000	63411000	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	387	375	0	ENST00000330258.3:c.2167C>T	p.Gln723Ter	p.Q723*	ENST00000330258	NM_152424.3	723	Cag/Tag	2/2	0.48389993100026	2	FACETS	0.888	0.859	0.917			1	CLONAL	3	TRUE	NA	0.531917898375458	2		375	546	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115277091	115277091	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754952923	NA	P-0051215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	131	520	0	ENST00000438362.2:c.692G>A	p.Arg231His	p.R231H	ENST00000438362	NM_001242891.1	231	cGc/cAc	7/20	1	2	FACETS	0.77	0.7	0.842	0.77	0.7	0.842	SUBCLONAL	1	TRUE	1	0.531917898375458	2		520	640	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808587	1808587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188849608	NA	P-0051215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	499	1024	1	ENST00000260795.2:c.2200G>A	p.Ala734Thr	p.A734T	ENST00000260795		734	Gcg/Acg	16/17	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.531917898375458	2		1025	904	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813592	50813592	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	192	470	0	ENST00000398568.2:c.1149del	p.Lys383AsnfsTer22	p.K383Nfs*22	ENST00000398568	NM_001042412.1	382	gcA/gc	8/18	0.698246413790928	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.698246413790928	1		470	349	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758268	41758268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs555593485	NA	P-0051220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	80	589	1	ENST00000301178.4:c.1724C>T	p.Thr575Met	p.T575M	ENST00000301178	NM_021913.4	575	aCg/aTg	15/20	1	2	FACETS	0.899	0.796	1	0.899	0.796	1	CLONAL	1	TRUE	1	0.430695099311659	2		590	413	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631138	176631138	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	74	437	0	ENST00000439151.2:c.1081T>A	p.Tyr361Asn	p.Y361N	ENST00000439151	NM_022455.4	361	Tat/Aat	4/23	1	2	FACETS	0.836	0.735	0.943	0.836	0.735	0.943	CLONAL	1	TRUE	1	0.430695099311659	2		437	411	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243952	53243952	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	115	429	0	ENST00000375401.3:c.1041del	p.Asp347GlufsTer83	p.D347Efs*83	ENST00000375401	NM_004187.3	347	gaC/ga	8/26	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.430695099311659	1		429	286	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	78	230	0				ENST00000310581	NM_198253.2	-/1132			0.17185785760376	2	FACETS	0.954	0.849	1	0.477	0.424	0.532	INDETERMINATE	1	TRUE	0	0.621634331279757	2		230	263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578188	7578188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201592	NA	P-0051221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	288	708	1	ENST00000269305.4:c.661G>A	p.Glu221Lys	p.E221K	ENST00000269305	NM_001126112.2	221	Gag/Aag	6/11	0.621634331279757	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.621634331279757	1		709	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0051221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	261	790	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.621634331279757	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.621634331279757	1		790	561	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971029	21971029	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519852	NA	P-0051221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	231	429	0	ENST00000304494.5:c.329G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tGg/tAg	2/3	1	2	FACETS	0.929	0.881	0.976	1	0.995	1	CLONAL	2	TRUE	1	0.621634331279757	2		429	400	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	295	593	0	ENST00000397062.3:c.246A>T	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaT	2/5	0.315566867531375	3	FACETS	1	0.993	1	0.701	0.661	0.741	INDETERMINATE	1	TRUE	1	0.621634331279757	3		593	888	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	220	674	0	ENST00000269305.4:c.811G>C	p.Glu271Gln	p.E271Q	ENST00000269305	NM_001126112.2	271	Gag/Cag	8/11	0.621634331279757	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.621634331279757	1		674	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579714	7579714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	296	665	0	ENST00000269305.4:c.82G>A	p.Glu28Lys	p.E28K	ENST00000269305	NM_001126112.2	28	Gaa/Aaa	3/11	0.621634331279757	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.621634331279757	1		665	549	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983106	201983107	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0051221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	190	624	0	ENST00000359651.3:c.958_959del	p.Lys320GlufsTer150	p.K320Efs*150	ENST00000359651		319	AAa/a	7/8	0.478028513818304	1	FACETS	0.721	0.671	0.773	0.721	0.671	0.773	SUBCLONAL	1	TRUE	0	0.621634331279757	1		624	584	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342580	118342580	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	144	227	0	ENST00000534358.1:c.706A>G	p.Thr236Ala	p.T236A	ENST00000534358	NM_005933.3	236	Aca/Gca	3/36	0.460142265301987	3	FACETS	0.943	0.874	1	0.943	0.874	1	CLONAL	2	TRUE	1	0.621634331279757	3		227	322	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362635	118362635	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	278	429	0	ENST00000534358.1:c.4996T>C	p.Tyr1666His	p.Y1666H	ENST00000534358	NM_005933.3	1666	Tac/Cac	15/36	0.460142265301987	3	FACETS	0.907	0.859	0.956	0.907	0.859	0.956	CLONAL	2	TRUE	1	0.621634331279757	3		429	646	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125507419	125507432	+	frameshift_variant	Frame_Shift_Del	DEL	ACAACAAACCCCTC	ACAACAAACCCCTC	-	novel	NA	P-0051221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	69	286	0	ENST00000428830.2:c.795_808del	p.Tyr265Ter	p.Y265*	ENST00000428830	NM_001114121.2	265	tACAACAAACCCCTC/t	8/14	0.460142265301987	3	FACETS	0.778	0.681	0.881	0.389	0.34	0.441	SUBCLONAL	1	TRUE	1	0.621634331279757	3		286	374	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714248	43714248	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	274	753	0	ENST00000382044.4:c.3905G>T	p.Gly1302Val	p.G1302V	ENST00000382044	NM_001141980.1	1302	gGt/gTt	19/28	1	2	FACETS	0.936	0.88	0.993	0.936	0.88	0.993	CLONAL	1	TRUE	1	0.621634331279757	2		753	942	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215817	133215817	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	114	622	0	ENST00000320574.5:c.5446A>C	p.Asn1816His	p.N1816H	ENST00000320574	NM_006231.2	1816	Aac/Cac	40/49	0.246883121878119	3	FACETS	0.83	0.75	0.915	0.415	0.375	0.458	INDETERMINATE	1	TRUE	1	0.613371141272198	3		622	585	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224532	36224532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759167832	NA	P-0051223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	129	1054	4	ENST00000222270.7:c.6994C>T	p.Arg2332Cys	p.R2332C	ENST00000222270	NM_014727.1	2332	Cgt/Tgt	29/37	0.145587355837085	2	FACETS	0.686	0.62	0.756	0.343	0.31	0.378	INDETERMINATE	1	TRUE	0	0.312849912383763	2		1058	1202	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254929	16254929	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs751475729	NA	P-0051223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	45	588	0	ENST00000375759.3:c.2194C>T	p.Arg732Ter	p.R732*	ENST00000375759	NM_015001.2	732	Cga/Tga	11/15	1	2	FACETS	0.409	0.342	0.482	0.409	0.342	0.482	SUBCLONAL	1	TRUE	1	0.312849912383763	2		588	704	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43699735	43699735	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137879443	NA	P-0051223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	93	599	1	ENST00000382044.4:c.5780C>T	p.Thr1927Met	p.T1927M	ENST00000382044	NM_001141980.1	1927	aCg/aTg	28/28	0.312849912383763	1	FACETS	0.746	0.664	0.834	0.746	0.664	0.834	SUBCLONAL	1	TRUE	0	0.312849912383763	1		600	672	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822177	72822177	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	49	878	0	ENST00000268489.5:c.9998A>G	p.Gln3333Arg	p.Q3333R	ENST00000268489	NM_006885.3	3333	cAg/cGg	10/10	0.312849912383763	1	FACETS	0.324	0.274	0.38	0.324	0.274	0.38	SUBCLONAL	1	TRUE	0	0.312849912383763	1		878	815	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81962220	81962230	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TATAACGTCGG	TATAACGTCGG	-	novel	NA	P-0051223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	115	531	0	ENST00000359376.3:c.2574_2581+3del		p.X858_splice	ENST00000359376	NM_002661.3	858		24/33	0.312849912383763	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.312849912383763	1		531	535	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249726	39249726	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	26	445	0	ENST00000402219.2:c.1843T>C	p.Tyr615His	p.Y615H	ENST00000402219	NM_005633.3	615	Tac/Cac	10/23	0.145587355837085	2	FACETS	0.321	0.253	0.399	0.16	0.126	0.2	INDETERMINATE	1	TRUE	0	0.312849912383763	2		445	518	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900558	3900560	+	frameshift_variant	Frame_Shift_Del	DEL	TAG	TAG	A	novel	NA	P-0051223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	242	975	0	ENST00000262367.5:c.536_538delinsT	p.Ala179ValfsTer3	p.A179Vfs*3	ENST00000262367	NM_004380.2	179	gCTAac/gTac	2/31	0.312849912383763	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.312849912383763	1		975	931	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928067	178928093	+	inframe_deletion	In_Frame_Del	DEL	CCTCATGGATTAGAAGATTTGCTGAAC	CCTCATGGATTAGAAGATTTGCTGAAC	-	novel	NA	P-0051224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	199	389	0	ENST00000263967.3:c.1348_1374del	p.His450_Pro458del	p.H450_P458del	ENST00000263967	NM_006218.2	449	CCTCATGGATTAGAAGATTTGCTGAAC/-	8/21	0.322944092812849	11	FACETS	0.923	0.859	0.989	0.659	0.614	0.706	CLONAL	5	TRUE	4	0.322944092812849	11		389	655	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625225	69625225	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	108	809	0	ENST00000334134.2:c.568A>G	p.Met190Val	p.M190V	ENST00000334134	NM_005247.2	190	Atg/Gtg	3/3	0.322944092812849	6	FACETS	1	0.918	1			1	CLONAL	1	TRUE	NA	0.322944092812849	6		809	1070	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672725	30672725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	215	691	1	ENST00000376406.3:c.4235C>T	p.Pro1412Leu	p.P1412L	ENST00000376406	NM_014641.2	1412	cCt/cTt	10/15	0.300201266620355	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.322944092812849	4		692	815	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0051228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	85	359	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.378627412639465	2		359	345	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114816	108114817	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0051228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	38	413	1	ENST00000278616.4:c.640dup	p.Ser214PhefsTer40	p.S214Ffs*40	ENST00000278616	NM_000051.3	211	-/T	6/63	1	2	FACETS	0.473	0.391	0.565	0.473	0.391	0.565	SUBCLONAL	1	TRUE	1	0.378627412639465	2		414	424	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293694	1293694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs986886145	NA	P-0051228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	304	838	4	ENST00000310581.5:c.1307C>T	p.Ala436Val	p.A436V	ENST00000310581	NM_198253.2	436	gCg/gTg	2/16	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.378627412639465	2		842	1194	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199926	108199926	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121434221	NA	P-0051228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	17	208	0	ENST00000278616.4:c.7268A>G	p.Glu2423Gly	p.E2423G	ENST00000278616	NM_000051.3	2423	gAa/gGa	49/63	1	2	FACETS	0.434	0.324	0.563	0.434	0.324	0.563	SUBCLONAL	1	TRUE	1	0.378627412639465	2		208	207	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874011	123874013	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs780061449	NA	P-0051228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	10	26	0	ENST00000330479.4:c.62_64del	p.Ala21del	p.A21del	ENST00000330479	NM_020382.3	14	gaGGCg/gag	2/9	1	2	FACETS	0.724	0.498	0.998	0.724	0.498	0.998	CLONAL	1	TRUE	1	0.378627412639465	2		26	73	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs377622327	NA	P-0051228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	142	505	0	ENST00000324856.7:c.3972C>A	p.Tyr1324Ter	p.Y1324*	ENST00000324856	NM_006015.4	1324	taC/taA	16/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.378627412639465	2		505	669	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058535	72058535	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	119	390	0	ENST00000357731.5:c.905A>T	p.Lys302Met	p.K302M	ENST00000357731	NM_173808.2	302	aAg/aTg	6/7	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.378627412639465	2		390	615	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052936	180052936	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	179	799	0	ENST00000261937.6:c.1354C>G	p.Leu452Val	p.L452V	ENST00000261937	NM_182925.4	452	Ctg/Gtg	10/30	1	2	FACETS	0.987	0.91	1	0.987	0.91	1	CLONAL	1	TRUE	1	0.378627412639465	2		799	958	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0051229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	67	299	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.594008806241631	2		299	180	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803121	1803121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745863884	NA	P-0051229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	40	713	0	ENST00000260795.2:c.473G>A	p.Arg158Gln	p.R158Q	ENST00000260795		158	cGg/cAg	4/17	0.550633650556717	3	FACETS	0.255	0.211	0.304			1	SUBCLONAL	1	TRUE	NA	0.594008806241631	3		713	685	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579568	7579568	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	430	575	0	ENST00000269305.4:c.119del	p.Met40ArgfsTer4	p.M40Rfs*4	ENST00000269305	NM_001126112.2	40	aTg/ag	4/11	0.594008806241631	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.594008806241631	3		575	597	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037885	49037885	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	141	239	0	ENST00000267163.4:c.2125T>G	p.Tyr709Asp	p.Y709D	ENST00000267163	NM_000321.2	709	Tat/Gat	21/27	0.594008806241631	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.594008806241631	2		239	226	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681111	37681111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	353	417	0	ENST00000447079.4:c.3280G>A	p.Val1094Met	p.V1094M	ENST00000447079	NM_015083.1	1094	Gtg/Atg	12/14	0.594008806241631	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.594008806241631	3		417	469	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774947	73774947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	190	360	0	ENST00000254810.4:c.226G>A	p.Ala76Thr	p.A76T	ENST00000254810	NM_005324.3	76	Gcg/Acg	3/4	0.594008806241631	3	FACETS	1	0.963	1	0.691	0.648	0.735	CLONAL	2	TRUE	0	0.594008806241631	3		360	400	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589129	67589130	+	splice_acceptor_variant	Splice_Site	INS	-	-	GGAAAGGGG	novel	NA	P-0051229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	51	196	0	ENST00000274335.5:c.1119_1127dup		p.X373_splice	ENST00000274335		373			1	2	FACETS	0.791	0.681	0.91	0.791	0.681	0.91	CLONAL	1	TRUE	1	0.594008806241631	2		196	217	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445213	29445213	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	95	505	0	ENST00000389048.3:c.3512T>G	p.Ile1171Ser	p.I1171S	ENST00000389048	NM_004304.4	1171	aTc/aGc	22/29	0.39368470808543	1	FACETS	0.83	0.742	0.922	0.83	0.742	0.922	CLONAL	1	TRUE	0	0.39368470808543	1		505	467	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092809	27092809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	75	435	0	ENST00000324856.7:c.2830C>T	p.Gln944Ter	p.Q944*	ENST00000324856	NM_006015.4	944	Cag/Tag	9/20	1	2	FACETS	0.927	0.816	1	0.927	0.816	1	CLONAL	1	TRUE	1	0.39368470808543	2		435	411	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459182	120459182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	81	488	0	ENST00000256646.2:c.6163C>T	p.His2055Tyr	p.H2055Y	ENST00000256646	NM_024408.3	2055	Cac/Tac	34/34	1	2	FACETS	0.931	0.824	1	0.931	0.824	1	CLONAL	1	TRUE	1	0.39368470808543	2		488	442	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103898	209103898	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	104	390	1	ENST00000345146.2:c.1051G>C	p.Glu351Gln	p.E351Q	ENST00000345146	NM_005896.2	351	Gag/Cag	9/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.39368470808543	2		391	475	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732942	30732942	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	54	272	0	ENST00000295754.5:c.1555G>A	p.Glu519Lys	p.E519K	ENST00000295754	NM_003242.5	519	Gag/Aag	7/7	1	2	FACETS	0.809	0.695	0.933	0.809	0.695	0.933	CLONAL	1	TRUE	1	0.39368470808543	2		272	339	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33290684	33290684	+	5_prime_UTR_variant	5'UTR	SNP	C	C	T	novel	NA	P-0051231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	79	497	1	ENST00000374542.5:c.-98G>A		p.*33*	ENST00000374542	NM_001141970.1	-/740		1/8	0.39368470808543	3	FACETS	0.758	0.667	0.855	0.379	0.333	0.428	SUBCLONAL	1	TRUE	1	0.39368470808543	3		498	634	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651983	36651984	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0051231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	205	617	0	ENST00000244741.5:c.106dup	p.Ala36GlyfsTer12	p.A36Gfs*12	ENST00000244741	NM_000389.4	35	-/G	2/3	0.39368470808543	3	FACETS	0.91	0.848	0.974	0.91	0.848	0.974	CLONAL	2	TRUE	1	0.39368470808543	3		617	685	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0051232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	108	325	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.354765013510688	2		325	512	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412905	49412905	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519951	NA	P-0051232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	48	570	0	ENST00000418115.1:c.118G>C	p.Glu40Gln	p.E40Q	ENST00000418115	NM_001664.2	40	Gag/Cag	2/5	1	2	FACETS	0.319	0.268	0.375	0.319	0.268	0.375	SUBCLONAL	1	TRUE	1	0.354765013510688	2		570	849	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0051232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	146	396	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.354765013510688	2		396	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579536	7579536	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567556930	NA	P-0051232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	112	645	0	ENST00000269305.4:c.151G>T	p.Glu51Ter	p.E51*	ENST00000269305	NM_001126112.2	51	Gaa/Taa	4/11	1	2	FACETS	0.612	0.549	0.679	0.612	0.549	0.679	SUBCLONAL	1	TRUE	1	0.354765013510688	2		645	1032	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776107	9776107	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	56	635	0	ENST00000377346.4:c.571C>G	p.Leu191Val	p.L191V	ENST00000377346	NM_005026.3	191	Ctg/Gtg	5/24	0.320675393626544	1	FACETS	0.363	0.31	0.421	0.363	0.31	0.421	SUBCLONAL	1	TRUE	0	0.354765013510688	1		635	716	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107195	27107195	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0051232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	70	425	0	ENST00000324856.7:c.6806C>G	p.Ser2269Ter	p.S2269*	ENST00000324856	NM_006015.4	2269	tCa/tGa	20/20	0.320675393626544	1	FACETS	0.59	0.515	0.671	0.59	0.515	0.671	SUBCLONAL	1	TRUE	0	0.354765013510688	1		425	550	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46733158	46733158	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	44	417	0	ENST00000371975.4:c.919C>G	p.Gln307Glu	p.Q307E	ENST00000371975	NM_003579.3	307	Cag/Gag	9/18	1	2	FACETS	0.399	0.334	0.472	0.399	0.334	0.472	SUBCLONAL	1	TRUE	1	0.354765013510688	2		417	621	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456833	32456833	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	43	535	0	ENST00000332351.3:c.59C>G	p.Ser20Cys	p.S20C	ENST00000332351	NM_024426.4	20	tCc/tGc	1/10	1	2	FACETS	0.32	0.267	0.38	0.32	0.267	0.38	SUBCLONAL	1	TRUE	1	0.354765013510688	2		535	757	SUCCESS
ATM	472	MSKCC	GRCh37	11	108099992	108099992	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	20	252	0	ENST00000278616.4:c.273G>C	p.Gln91His	p.Q91H	ENST00000278616	NM_000051.3	91	caG/caC	4/63	1	2	FACETS	0.283	0.215	0.362	0.283	0.215	0.362	SUBCLONAL	1	TRUE	1	0.354765013510688	2		252	399	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143332	108143332	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs774935453	NA	P-0051232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	38	306	0	ENST00000278616.4:c.3151G>C	p.Glu1051Gln	p.E1051Q	ENST00000278616	NM_000051.3	1051	Gag/Cag	21/63	1	2	FACETS	0.383	0.316	0.458	0.383	0.316	0.458	SUBCLONAL	1	TRUE	1	0.354765013510688	2		306	560	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939065	48939066	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0051232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	96	213	0	ENST00000267163.4:c.898_899del	p.Met300GlufsTer9	p.M300Efs*9	ENST00000267163	NM_000321.2	299	ttTAtg/tttg	9/27	0.282827438991703	2	FACETS	1	0.975	1	0.652	0.585	0.723	CLONAL	1	TRUE	0	0.354765013510688	2		213	415	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396809	396809	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	79	598	0	ENST00000262320.3:c.217G>C	p.Glu73Gln	p.E73Q	ENST00000262320	NM_003502.3	73	Gag/Cag	2/11	1	2	FACETS	0.503	0.441	0.569	0.503	0.441	0.569	SUBCLONAL	1	TRUE	1	0.354765013510688	2		598	886	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	397013	397013	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	125	863	0	ENST00000262320.3:c.13G>C	p.Glu5Gln	p.E5Q	ENST00000262320	NM_003502.3	5	Gag/Cag	2/11	1	2	FACETS	0.76	0.687	0.837	0.76	0.687	0.837	SUBCLONAL	1	TRUE	1	0.354765013510688	2		863	927	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830853	3830853	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs764580876	NA	P-0051232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	31	418	0	ENST00000262367.5:c.1703C>G	p.Ser568Cys	p.S568C	ENST00000262367	NM_004380.2	568	tCt/tGt	8/31	1	2	FACETS	0.291	0.235	0.356	0.291	0.235	0.356	SUBCLONAL	1	TRUE	1	0.354765013510688	2		418	600	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619245	37619245	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	40	440	0	ENST00000447079.4:c.921G>C	p.Arg307Ser	p.R307S	ENST00000447079	NM_015083.1	307	agG/agC	1/14	1	2	FACETS	0.315	0.261	0.376	0.315	0.261	0.376	SUBCLONAL	1	TRUE	1	0.354765013510688	2		440	716	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1623958	1623958	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	115	518	1	ENST00000344749.5:c.541C>A	p.Pro181Thr	p.P181T	ENST00000344749	NM_001136139.2	181	Cca/Aca	8/19	0.354765013510688	1	FACETS	0.905	0.818	0.997	0.905	0.818	0.997	CLONAL	1	TRUE	0	0.354765013510688	1		519	589	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145672	11145672	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746533073	NA	P-0051232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	62	655	1	ENST00000358026.2:c.4034C>T	p.Ser1345Leu	p.S1345L	ENST00000358026	NM_001128849.1	1345	tCg/tTg	29/36	1	2	FACETS	0.397	0.342	0.457	0.397	0.342	0.457	SUBCLONAL	1	TRUE	1	0.354765013510688	2		656	880	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47600989	47600989	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0051232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	116	483	0	ENST00000263735.4:c.227C>G	p.Ser76Ter	p.S76*	ENST00000263735	NM_002354.2	76	tCa/tGa	3/9	1	2	FACETS	0.952	0.859	1	0.952	0.859	1	CLONAL	1	TRUE	1	0.354765013510688	2		483	687	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252856	36252856	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	53	251	0	ENST00000300305.3:c.506G>C	p.Arg169Thr	p.R169T	ENST00000300305		169	aGa/aCa	4/8	0.230916496964512	5	FACETS	0.806	0.687	0.936	0.269	0.229	0.312	CLONAL	1	TRUE	2	0.354765013510688	5		251	568	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412929	49412929	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	53	590	0	ENST00000418115.1:c.94G>C	p.Glu32Gln	p.E32Q	ENST00000418115	NM_001664.2	32	Gag/Cag	2/5	1	2	FACETS	0.333	0.283	0.389	0.333	0.283	0.389	SUBCLONAL	1	TRUE	1	0.354765013510688	2		590	896	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509975	187509975	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	68	365	0	ENST00000441802.2:c.13538G>C	p.Arg4513Thr	p.R4513T	ENST00000441802	NM_005245.3	4513	aGa/aCa	27/27	1	2	FACETS	0.74	0.645	0.843	0.74	0.645	0.843	SUBCLONAL	1	TRUE	1	0.354765013510688	2		365	518	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394913	394913	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	44	413	0	ENST00000380956.4:c.309G>C	p.Lys103Asn	p.K103N	ENST00000380956	NM_001195286.1	103	aaG/aaC	3/9	0.34439317376761	4	FACETS	0.403	0.337	0.477			1	SUBCLONAL	1	TRUE	NA	0.354765013510688	4		413	834	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777996	27777996	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	132	588	0	ENST00000369163.2:c.145C>G	p.Leu49Val	p.L49V	ENST00000369163	NM_003536.2	49	Ctc/Gtc	1/1	0.354765013510688	3	FACETS	0.965	0.875	1	0.482	0.437	0.53	CLONAL	1	TRUE	1	0.354765013510688	3		588	908	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323293	31323293	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	54	239	0	ENST00000412585.2:c.696C>A	p.Phe232Leu	p.F232L	ENST00000412585	NM_005514.6	232	ttC/ttA	4/8	0.354765013510688	3	FACETS	0.745	0.637	0.863	0.373	0.318	0.432	SUBCLONAL	1	TRUE	1	0.354765013510688	3		239	481	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038895	47038895	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0051232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	63	309	1	ENST00000377604.3:c.901+1G>A		p.X301_splice	ENST00000377604	NM_001204468.1	301			1	1	FACETS	0.646	0.56	0.739	0.646	0.56	0.739	SUBCLONAL	1	TRUE	0	0.354765013510688	1		310	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	548	790	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.787810173905961	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.787810173905961	2		790	673	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519925	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	175	476	0	ENST00000263967.3:c.1357G>C	p.Glu453Gln	p.E453Q	ENST00000263967	NM_006218.2	453	Gaa/Caa	8/21	0.694336017923339	4	FACETS	0.858	0.798	0.919	0.858	0.798	0.919	CLONAL	2	TRUE	2	0.787810173905961	4		476	463	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	230	532	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	0.787810173905961	3	FACETS	1	0.982	1	0.567	0.53	0.604	CLONAL	1	TRUE	1	0.787810173905961	3		532	718	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711350	114711350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243981730	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	67	266	0	ENST00000543371.1:c.365C>T	p.Ser122Leu	p.S122L	ENST00000543371	NM_001198531.1	122	tCg/tTg	3/14	0.403191206305134	3	FACETS	0.704	0.615	0.797			1	INDETERMINATE	1	TRUE	NA	0.787810173905961	3		266	337	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565601	41565601	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	91	315	0	ENST00000263253.7:c.4267G>T	p.Glu1423Ter	p.E1423*	ENST00000263253	NM_001429.3	1423	Gaa/Taa	26/31	0.694336017923339	4	FACETS	0.981	0.876	1	0.491	0.438	0.546	CLONAL	1	TRUE	2	0.787810173905961	4		315	421	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793483	18793483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603405	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	65	308	0	ENST00000266497.5:c.4180G>A	p.Glu1394Lys	p.E1394K	ENST00000266497		1394	Gaa/Aaa	30/31	0.403191206305134	3	FACETS	0.983	0.864	1			1	INDETERMINATE	1	TRUE	NA	0.787810173905961	3		308	234	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527607	41527607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	296	438	0	ENST00000263253.7:c.1498C>T	p.Pro500Ser	p.P500S	ENST00000263253	NM_001429.3	500	Ccc/Tcc	6/31	0.694336017923339	4	FACETS	0.974	0.923	1	0.974	0.923	1	CLONAL	2	TRUE	2	0.787810173905961	4		438	690	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385069	31385069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867242533	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	775	737	1	ENST00000328111.2:c.1454G>A	p.Arg485Gln	p.R485Q	ENST00000328111	NM_006892.3	485	cGa/cAa	14/23	0.643243332577129	4	FACETS	0.938	0.913	0.963	0.938	0.913	0.963	CLONAL	3	TRUE	1	0.787810173905961	4		738	1250	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347144	89347144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765986335	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	196	741	1	ENST00000301030.4:c.5806G>A	p.Glu1936Lys	p.E1936K	ENST00000301030	NM_001256183.1	1936	Gag/Aag	9/13	0.234165132124851	2	FACETS	0.846	0.788	0.905	0.423	0.394	0.453	INDETERMINATE	1	TRUE	0	0.787810173905961	2		742	588	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277609	142277609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs983647070	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	161	336	1	ENST00000350721.4:c.1742C>T	p.Ser581Leu	p.S581L	ENST00000350721	NM_001184.3	581	tCa/tTa	8/47	0.694336017923339	4	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	2	0.787810173905961	4		337	361	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244778	46244778	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057524391	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	181	490	0	ENST00000334344.6:c.2872C>T	p.Gln958Ter	p.Q958*	ENST00000334344	NM_152641.2	958	Cag/Tag	15/21	0.787810173905961	3	FACETS	1	0.971	1	0.545	0.505	0.585	CLONAL	1	TRUE	1	0.787810173905961	3		490	588	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976494	25976494	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	113	314	0	ENST00000435504.4:c.1051G>C	p.Glu351Gln	p.E351Q	ENST00000435504		351	Gag/Cag	11/13	0.428806852114562	4	FACETS	0.787	0.717	0.858	0.787	0.717	0.858	INDETERMINATE	2	TRUE	2	0.787810173905961	4		314	326	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716359	18716359	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	33	320	0	ENST00000266497.5:c.3706G>C	p.Glu1236Gln	p.E1236Q	ENST00000266497		1236	Gaa/Caa	26/31	0.403191206305134	3	FACETS	0.342	0.279	0.414			1	INDETERMINATE	1	TRUE	NA	0.787810173905961	3		320	341	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276815	15276815	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161550693	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	69	837	1	ENST00000263388.2:c.5450C>T	p.Ser1817Leu	p.S1817L	ENST00000263388	NM_000435.2	1817	tCa/tTa	30/33	0.693563577671579	3	FACETS	0.237	0.206	0.272	0.119	0.103	0.136	SUBCLONAL	1	TRUE	1	0.787810173905961	3		838	1029	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437296	121437296	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	375	998	0	ENST00000257555.6:c.1634C>G	p.Ser545Ter	p.S545*	ENST00000257555		545	tCa/tGa	9/10	0.693563577671579	3	FACETS	1	0.967	1	0.512	0.486	0.539	CLONAL	1	TRUE	1	0.787810173905961	3		998	1295	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031912	10031912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	181	657	1	ENST00000330684.3:c.911C>T	p.Ser304Phe	p.S304F	ENST00000330684	NM_001134407.1	304	tCt/tTt	3/13	0.234165132124851	2	FACETS	0.829	0.77	0.89	0.415	0.385	0.445	INDETERMINATE	1	TRUE	0	0.787810173905961	2		658	554	SUCCESS
AR	367	MSKCC	GRCh37	X	66765623	66765623	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	45	550	0	ENST00000374690.3:c.635G>C	p.Arg212Thr	p.R212T	ENST00000374690	NM_000044.3	212	aGg/aCg	1/8	0.591251922464458	2	FACETS	0.172	0.144	0.203			1	SUBCLONAL	1	TRUE	NA	0.787810173905961	2		550	664	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206881	36206881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	21	309	0	ENST00000300305.3:c.631G>A	p.Asp211Asn	p.D211N	ENST00000300305		211	Gat/Aat	6/8	0.787810173905961	2	FACETS	0.178	0.137	0.226	0.089	0.068	0.113	SUBCLONAL	1	TRUE	0	0.787810173905961	2		309	299	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340348	8340348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1372695674	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	273	500	0	ENST00000356435.5:c.5248G>A	p.Gly1750Ser	p.G1750S	ENST00000356435		1750	Ggc/Agc	31/35	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	2	TRUE	NA	0.787810173905961	2		500	344	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282499	115282499	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	145	375	0	ENST00000438362.2:c.151C>G	p.Pro51Ala	p.P51A	ENST00000438362	NM_001242891.1	51	Cca/Gca	3/20	0.753906132684522	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.787810173905961	3		375	246	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70442617	70442617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	117	554	0	ENST00000373644.4:c.4939G>A	p.Glu1647Lys	p.E1647K	ENST00000373644	NM_030625.2	1647	Gaa/Aaa	10/12	0.781945660367263	3	FACETS	0.658	0.595	0.725	0.329	0.297	0.363	SUBCLONAL	1	TRUE	1	0.787810173905961	3		554	629	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230420	46230420	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	63	349	0	ENST00000334344.6:c.754G>C	p.Asp252His	p.D252H	ENST00000334344	NM_152641.2	252	Gac/Cac	7/21	0.787810173905961	3	FACETS	0.667	0.581	0.76	0.334	0.29	0.38	SUBCLONAL	1	TRUE	1	0.787810173905961	3		349	334	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425552	49425552	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	637	950	0	ENST00000301067.7:c.12936del	p.Ser4313AlafsTer71	p.S4313Afs*71	ENST00000301067	NM_003482.3	4312	tcC/tc	39/54	0.787810173905961	3	FACETS	0.968	0.937	0.999	0.968	0.937	0.999	CLONAL	2	TRUE	1	0.787810173905961	3		950	1164	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426667	49426667	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	212	445	0	ENST00000301067.7:c.11821C>T	p.Gln3941Ter	p.Q3941*	ENST00000301067	NM_003482.3	3941	Caa/Taa	39/54	0.787810173905961	3	FACETS	1	0.982	1	0.571	0.533	0.61	CLONAL	1	TRUE	1	0.787810173905961	3		445	657	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620128	21620128	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	326	509	0	ENST00000382592.4:c.38G>C	p.Gly13Ala	p.G13A	ENST00000382592	NM_014572.2	13	gGa/gCa	2/8	0.257500997846424	4	FACETS	1	0.984	1	1	0.984	1	INDETERMINATE	2	TRUE	2	0.787810173905961	4		509	688	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041235	29041235	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	214	495	0	ENST00000282397.4:c.193G>A	p.Glu65Lys	p.E65K	ENST00000282397	NM_002019.4	65	Gaa/Aaa	3/30	0.257500997846424	4	FACETS	1	0.98	1	1	0.98	1	INDETERMINATE	2	TRUE	2	0.787810173905961	4		495	446	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436620	110436620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	126	973	0	ENST00000375856.3:c.1781C>T	p.Ser594Leu	p.S594L	ENST00000375856	NM_003749.2	594	tCg/tTg	1/2	0.50383215825285	2	FACETS	0.398	0.36	0.438	0.199	0.18	0.219	SUBCLONAL	1	TRUE	0	0.787810173905961	2		973	804	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748885	43748885	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	406	768	0	ENST00000382044.4:c.1921G>C	p.Glu641Gln	p.E641Q	ENST00000382044	NM_001141980.1	641	Gag/Cag	12/28	0.781945660367263	3	FACETS	0.945	0.907	0.983	0.945	0.907	0.983	CLONAL	2	TRUE	1	0.787810173905961	3		768	760	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293183	91293183	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	251	461	0	ENST00000355112.3:c.685G>A	p.Glu229Lys	p.E229K	ENST00000355112	NM_000057.2	229	Gaa/Aaa	3/22	0.781945660367263	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.787810173905961	3		461	416	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23625365	23625365	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	200	605	0	ENST00000261584.4:c.3161C>G	p.Ser1054Cys	p.S1054C	ENST00000261584	NM_024675.3	1054	tCt/tGt	11/13	0.234165132124851	2	FACETS	1	0.991	1	0.668	0.629	0.707	INDETERMINATE	1	TRUE	0	0.787810173905961	2		605	380	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660517	67660517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	292	452	1	ENST00000264010.4:c.1417G>A	p.Asp473Asn	p.D473N	ENST00000264010	NM_006565.3	473	Gat/Aat	8/12	0.234165132124851	2	FACETS	1	0.995	1	0.741	0.708	0.775	INDETERMINATE	1	TRUE	0	0.787810173905961	2		453	500	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662310	67662310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	190	477	0	ENST00000264010.4:c.1556G>A	p.Gly519Glu	p.G519E	ENST00000264010	NM_006565.3	519	gGg/gAg	9/12	0.234165132124851	2	FACETS	0.857	0.797	0.917	0.428	0.398	0.459	INDETERMINATE	1	TRUE	0	0.787810173905961	2		477	563	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349018	89349018	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs534628110	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	166	794	0	ENST00000301030.4:c.3932G>C	p.Arg1311Pro	p.R1311P	ENST00000301030	NM_001256183.1	1311	cGa/cCa	9/13	0.234165132124851	2	FACETS	0.543	0.499	0.588	0.272	0.249	0.294	INDETERMINATE	1	TRUE	0	0.787810173905961	2		794	776	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989657	15989657	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	335	386	0	ENST00000268712.3:c.3116C>G	p.Ser1039Ter	p.S1039*	ENST00000268712	NM_006311.3	1039	tCa/tGa	23/46	0.787810173905961	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.787810173905961	2		386	404	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649098	37649098	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	273	437	0	ENST00000447079.4:c.2203G>C	p.Glu735Gln	p.E735Q	ENST00000447079	NM_015083.1	735	Gaa/Caa	4/14	0.787810173905961	3	FACETS	0.96	0.913	1	0.96	0.913	1	CLONAL	2	TRUE	1	0.787810173905961	3		437	503	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243512	41243512	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	346	625	0	ENST00000357654.3:c.4036G>T	p.Glu1346Ter	p.E1346*	ENST00000357654	NM_007294.3	1346	Gaa/Taa	10/23	0.787810173905961	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.787810173905961	3		625	571	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243576	41243576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	364	647	0	ENST00000357654.3:c.3972G>A	p.Met1324Ile	p.M1324I	ENST00000357654	NM_007294.3	1324	atG/atA	10/23	0.787810173905961	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.787810173905961	3		647	630	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4123794	4123794	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	122	468	0	ENST00000262948.5:c.79G>C	p.Glu27Gln	p.E27Q	ENST00000262948	NM_030662.3	27	Gag/Cag	1/11	0.597318768732558	3	FACETS	0.73	0.662	0.802	0.365	0.331	0.401	SUBCLONAL	1	TRUE	1	0.787810173905961	3		468	591	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152257	99152257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1419963032	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	82	407	0	ENST00000074304.5:c.336G>A	p.Met112Ile	p.M112I	ENST00000074304	NM_001134224.1	112	atG/atA	6/26	0.477270144785966	4	FACETS	0.949	0.842	1	0.475	0.421	0.532	CLONAL	1	TRUE	2	0.787810173905961	4		407	392	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155990	99155990	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	338	603	0	ENST00000074304.5:c.671-1G>C		p.X224_splice	ENST00000074304	NM_001134224.1	224			0.477270144785966	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.787810173905961	4		603	748	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256713	46256713	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	82	422	0	ENST00000371998.3:c.769G>C	p.Glu257Gln	p.E257Q	ENST00000371998		257	Gaa/Caa	8/23	0.643243332577129	4	FACETS	0.784	0.693	0.88	0.261	0.231	0.294	SUBCLONAL	1	TRUE	1	0.787810173905961	4		422	475	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485036	57485036	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	106	387	0	ENST00000371085.3:c.870C>G	p.Phe290Leu	p.F290L	ENST00000371085	NM_000516.4	290	ttC/ttG	11/13	0.643243332577129	4	FACETS	0.916	0.825	1	0.305	0.275	0.338	CLONAL	1	TRUE	1	0.787810173905961	4		387	525	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37622754	37622754	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	586	934	1	ENST00000249071.6:c.538C>T	p.Gln180Ter	p.Q180*	ENST00000249071	NM_002872.4	180	Cag/Tag	6/7	0.694336017923339	4	FACETS	0.933	0.898	0.969	0.933	0.898	0.969	CLONAL	2	TRUE	2	0.787810173905961	4		935	1425	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566483	41566483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	93	454	0	ENST00000263253.7:c.4360G>A	p.Asp1454Asn	p.D1454N	ENST00000263253	NM_001429.3	1454	Gac/Aac	27/31	0.694336017923339	4	FACETS	0.737	0.656	0.822	0.368	0.328	0.411	SUBCLONAL	1	TRUE	2	0.787810173905961	4		454	573	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089136	37089136	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	109	489	0	ENST00000231790.2:c.1858G>T	p.Glu620Ter	p.E620*	ENST00000231790	NM_000249.3	620	Gag/Tag	16/19	0.597318768732558	3	FACETS	0.859	0.776	0.946	0.43	0.388	0.473	CLONAL	1	TRUE	1	0.787810173905961	3		489	449	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66468004	66468004	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	45	239	0	ENST00000273854.3:c.265G>T	p.Val89Leu	p.V89L	ENST00000273854	NM_004439.5	89	Gtg/Ttg	3/18	1	2	FACETS	0.81	0.696	0.931	0.81	0.696	0.931	CLONAL	1	TRUE	1	0.787810173905961	2		239	141	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876184	35876184	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	178	521	0	ENST00000303115.3:c.976G>C	p.Asp326His	p.D326H	ENST00000303115	NM_002185.3	326	Gat/Cat	8/8	0.643243332577129	4	FACETS	1	0.989	1	0.457	0.423	0.492	CLONAL	1	TRUE	1	0.787810173905961	4		521	589	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161236	56161236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	94	445	0	ENST00000399503.3:c.1105G>A	p.Glu369Lys	p.E369K	ENST00000399503	NM_005921.1	369	Gaa/Aaa	5/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.787810173905961	2		445	207	SUCCESS
APC	324	MSKCC	GRCh37	5	112174014	112174014	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs746393911	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	80	313	0	ENST00000257430.4:c.2723C>G	p.Ser908Cys	p.S908C	ENST00000257430	NM_000038.5	908	tCt/tGt	16/16	0.56152712357812	1	FACETS	0.692	0.624	0.76	0.692	0.624	0.76	SUBCLONAL	1	TRUE	0	0.787810173905961	1		313	178	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638823	176638823	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	40	614	1	ENST00000439151.2:c.3423G>A	p.Met1141Ile	p.M1141I	ENST00000439151	NM_022455.4	1141	atG/atA	5/23	1	2	FACETS	0.212	0.176	0.252	0.212	0.176	0.252	SUBCLONAL	1	TRUE	1	0.787810173905961	2		615	479	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687130	176687130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	160	508	0	ENST00000439151.2:c.5107G>A	p.Glu1703Lys	p.E1703K	ENST00000439151	NM_022455.4	1703	Gag/Aag	14/23	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.787810173905961	2		508	402	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29913231	29913231	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	315	527	0	ENST00000376809.5:c.1097G>C	p.Ter366SerextTer8	p.*366Sext*8	ENST00000376809	NM_002116.7	366	tGa/tCa	8/8	0.679961094292478	2	FACETS	0.934	0.901	0.966	0.934	0.901	0.966	CLONAL	2	TRUE	0	0.787810173905961	2		527	428	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672269	30672269	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	224	825	0	ENST00000376406.3:c.4691C>G	p.Ser1564Cys	p.S1564C	ENST00000376406	NM_014641.2	1564	tCt/tGt	10/15	0.679961094292478	2	FACETS	0.729	0.681	0.779	0.365	0.34	0.39	SUBCLONAL	1	TRUE	0	0.787810173905961	2		825	780	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188091	151188091	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	68	357	0	ENST00000262187.5:c.62C>G	p.Ser21Ter	p.S21*	ENST00000262187	NM_005614.3	21	tCa/tGa	2/8	0.694336017923339	4	FACETS	0.841	0.736	0.953	0.42	0.368	0.477	CLONAL	1	TRUE	2	0.787810173905961	4		357	367	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271322	38271322	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1326	301	835	1	ENST00000425967.3:c.2386G>T	p.Glu796Ter	p.E796*	ENST00000425967	NM_001174067.1	796	Gag/Tag	19/19	0.666404329245825	6	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.787810173905961	6		836	1627	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507399	8507399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1327108344	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	73	295	0	ENST00000356435.5:c.1579G>A	p.Glu527Lys	p.E527K	ENST00000356435		527	Gag/Aag	11/35	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.787810173905961	NA		295	185	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285861	87285861	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	145	508	0	ENST00000277120.3:c.198G>C	p.Glu66Asp	p.E66D	ENST00000277120		66	gaG/gaC	2/19	0.787810173905961	2	FACETS	0.907	0.836	0.979	0.453	0.418	0.49	CLONAL	1	TRUE	0	0.787810173905961	2		508	406	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923194	39923194	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	30	229	0	ENST00000378444.4:c.3514G>A	p.Glu1172Lys	p.E1172K	ENST00000378444	NM_001123385.1	1172	Gag/Aag	8/15	0.591251922464458	2	FACETS	0.238	0.192	0.29			1	SUBCLONAL	1	TRUE	NA	0.787810173905961	2		229	320	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409875	63409875	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	22	271	1	ENST00000330258.3:c.3292C>G	p.Gln1098Glu	p.Q1098E	ENST00000330258	NM_152424.3	1098	Cag/Gag	2/2	0.591251922464458	2	FACETS	0.134	0.103	0.169			1	SUBCLONAL	1	TRUE	NA	0.787810173905961	2		272	418	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410058	63410058	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs748190147	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	209	372	0	ENST00000330258.3:c.3109C>T	p.Gln1037Ter	p.Q1037*	ENST00000330258	NM_152424.3	1037	Cag/Tag	2/2	0.591251922464458	2	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.787810173905961	2		372	486	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411252	63411252	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	546	415	0	ENST00000330258.3:c.1915C>T	p.Gln639Ter	p.Q639*	ENST00000330258	NM_152424.3	639	Caa/Taa	2/2	0.591251922464458	2	FACETS	1	0.998	1			1	CLONAL	2	TRUE	NA	0.787810173905961	2		415	600	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	119	230	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.83	0.76	0.9	0.83	0.76	0.9	CLONAL	1	TRUE	1	0.95	2		230	302	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0051234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	284	565	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.955	0.905	1	0.955	0.905	1	CLONAL	1	TRUE	1	0.95	2		565	626	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806092	1806092	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913484	NA	P-0051234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	329	778	0	ENST00000260795.2:c.1111A>T	p.Ser371Cys	p.S371C	ENST00000260795		371	Agt/Tgt	8/17	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.95	2		778	678	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288549	15288549	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	61	70	0	ENST00000263388.2:c.4190G>A	p.Gly1397Glu	p.G1397E	ENST00000263388	NM_000435.2	1397	gGg/gAg	24/33	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.95	2		70	106	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652083	36652084	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0051234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	133	815	0	ENST00000244741.5:c.209dup	p.Leu71ProfsTer18	p.L71Pfs*18	ENST00000244741	NM_000389.4	69	cgg/cGgg	2/3	1	2	FACETS	0.375	0.341	0.411	0.375	0.341	0.411	SUBCLONAL	1	TRUE	1	0.95	2		815	746	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984365	201984366	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0051234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	285	658	0	ENST00000359651.3:c.1032_1033dup	p.Val345GlyfsTer103	p.V345Gfs*103	ENST00000359651		344	cgg/cGGgg	8/8	1	2	FACETS	0.893	0.845	0.941	0.893	0.845	0.941	CLONAL	1	TRUE	1	0.95	2		658	672	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256730	19256730	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	297	887	1	ENST00000162023.5:c.983G>A	p.Gly328Glu	p.G328E	ENST00000162023		328	gGg/gAg	13/13	1	2	FACETS	0.947	0.899	0.996	0.947	0.899	0.996	CLONAL	1	TRUE	1	0.95	2		888	660	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539021	187539022	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0051234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	282	470	0	ENST00000441802.2:c.8718dup	p.Thr2907TyrfsTer8	p.T2907Yfs*8	ENST00000441802	NM_005245.3	2906	-/T	10/27	1	2	FACETS	0.965	0.915	1	0.965	0.915	1	CLONAL	1	TRUE	1	0.95	2		470	615	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967940	93967940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs953493697	NA	P-0051234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	233	431	0	ENST00000369303.4:c.1987G>A	p.Ala663Thr	p.A663T	ENST00000369303	NM_004440.3	663	Gcc/Acc	11/17	1	2	FACETS	0.971	0.916	1	0.971	0.916	1	CLONAL	1	TRUE	1	0.95	2		431	505	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938523	44938523	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	279	443	1	ENST00000377967.4:c.3071A>T	p.Glu1024Val	p.E1024V	ENST00000377967	NM_021140.2	1024	gAa/gTa	20/29	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.95	2		444	587	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0051237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	100	799	2	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	0.246039484969759	2	FACETS	1	0.955	1	0.546	0.495	0.599	INDETERMINATE	1	TRUE	0	0.649167925316124	2		801	282	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396233	396233	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145696080	NA	P-0051237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	151	735	0	ENST00000262320.3:c.793G>A	p.Gly265Arg	p.G265R	ENST00000262320	NM_003502.3	265	Gga/Aga	2/11	0.246039484969759	2	FACETS	0.791	0.738	0.844	0.791	0.738	0.844	INDETERMINATE	2	TRUE	0	0.649167925316124	2		735	294	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123701	11123701	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	123	665	2	ENST00000358026.2:c.2351G>A	p.Gly784Glu	p.G784E	ENST00000358026	NM_001128849.1	784	gGg/gAg	16/36	0.296056955023681	4	FACETS	0.959	0.879	1	0.959	0.879	1	INDETERMINATE	2	TRUE	2	0.649167925316124	4		667	326	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021356	31021356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	33	630	0	ENST00000375687.4:c.1355G>A	p.Gly452Glu	p.G452E	ENST00000375687	NM_015338.5	452	gGg/gAg	12/13	0.276655094035009	3	FACETS	0.736	0.606	0.879	0.368	0.303	0.44	INDETERMINATE	1	TRUE	1	0.649167925316124	3		630	183	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439298	52439298	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	103	748	0	ENST00000460680.1:c.944A>G	p.Glu315Gly	p.E315G	ENST00000460680	NM_004656.3	315	gAg/gGg	11/17	0.531170857511068	2	FACETS	0.763	0.7	0.826	0.763	0.7	0.826	SUBCLONAL	2	TRUE	0	0.649167925316124	2		748	208	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841488	156841488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1023556915	NA	P-0051238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	222	671	1	ENST00000524377.1:c.791C>T	p.Thr264Met	p.T264M	ENST00000524377	NM_002529.3	264	aCg/aTg	7/17	0.488999065595199	3	FACETS	0.972	0.903	1	0.486	0.451	0.521	CLONAL	1	TRUE	1	0.488999065595199	3		672	1163	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248415	59248415	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	146	451	0	ENST00000371222.2:c.328T>G	p.Phe110Val	p.F110V	ENST00000371222	NM_002228.3	110	Ttc/Gtc	1/1	0.488999065595199	3	FACETS	0.95	0.868	1	0.475	0.434	0.518	CLONAL	1	TRUE	1	0.488999065595199	3		451	782	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639840	3639840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201422743	NA	P-0051238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	50	698	0	ENST00000294008.3:c.3799C>T	p.Arg1267Cys	p.R1267C	ENST00000294008	NM_032444.2	1267	Cgt/Tgt	12/15	1	2	FACETS	0.218	0.184	0.256	0.218	0.184	0.256	SUBCLONAL	1	TRUE	1	0.488999065595199	2		698	937	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662337	227662337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762739828	NA	P-0051238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	215	651	0	ENST00000305123.5:c.1118G>A	p.Arg373His	p.R373H	ENST00000305123	NM_005544.2	373	cGc/cAc	1/2	1	2	FACETS	0.989	0.921	1	0.989	0.921	1	CLONAL	1	TRUE	1	0.488999065595199	2		651	889	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430748	181430748	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	242	732	0	ENST00000325404.1:c.600C>A	p.Tyr200Ter	p.Y200*	ENST00000325404	NM_003106.3	200	taC/taA	1/1	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.488999065595199	2		732	935	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43746274	43746274	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0051238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	158	381	0	ENST00000523873.1:c.392+1G>C		p.X131_splice	ENST00000523873		131			1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.488999065595199	2		381	631	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	88	230	0				ENST00000310581	NM_198253.2	-/1132			0.325461870088623	3	FACETS	0.816	0.728	0.909	0.816	0.728	0.909	CLONAL	2	TRUE	1	0.327656849820472	3		230	383	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260643	16260643	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	292	642	0	ENST00000375759.3:c.7908G>C	p.Lys2636Asn	p.K2636N	ENST00000375759	NM_015001.2	2636	aaG/aaC	11/15	0.327656849820472	3	FACETS	0.882	0.834	0.931	0.882	0.834	0.931	CLONAL	3	TRUE	0	0.327656849820472	3		642	784	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059194	27059194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	199	390	0	ENST00000324856.7:c.1831C>T	p.Gln611Ter	p.Q611*	ENST00000324856	NM_006015.4	611	Cag/Tag	4/20	0.327656849820472	3	FACETS	0.851	0.794	0.908	0.851	0.794	0.908	CLONAL	3	TRUE	0	0.327656849820472	3		390	554	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851255	156851255	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	73	745	0	ENST00000524377.1:c.2212G>C	p.Asp738His	p.D738H	ENST00000524377	NM_002529.3	738	Gac/Cac	17/17	0.259625881426334	5	FACETS	0.73	0.636	0.83	0.243	0.212	0.277	SUBCLONAL	1	TRUE	2	0.327656849820472	5		745	911	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725030	162725030	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	60	375	0	ENST00000367921.3:c.502C>T	p.Pro168Ser	p.P168S	ENST00000367921	NM_006182.2	168	Cca/Tca	6/18	0.259625881426334	5	FACETS	0.904	0.779	1	0.301	0.259	0.347	CLONAL	1	TRUE	2	0.327656849820472	5		375	604	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981210	201981210	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	131	922	0	ENST00000359651.3:c.289A>G	p.Met97Val	p.M97V	ENST00000359651		97	Atg/Gtg	2/8	0.292407142421512	3	FACETS	0.995	0.902	1			1	CLONAL	1	TRUE	NA	0.327656849820472	3		922	935	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600624	43600624	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	96	706	0	ENST00000355710.3:c.850G>C	p.Glu284Gln	p.E284Q	ENST00000355710	NM_020975.4	284	Gag/Cag	4/20	0.325461870088623	3	FACETS	0.891	0.794	0.995	0.446	0.397	0.498	CLONAL	1	TRUE	1	0.327656849820472	3		706	765	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279522	123279522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370877537	NA	P-0051239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	102	704	1	ENST00000358487.5:c.910G>A	p.Asp304Asn	p.D304N	ENST00000358487	NM_000141.4	304	Gac/Aac	7/18	0.212608247187187	3	FACETS	0.987	0.883	1			1	CLONAL	1	TRUE	NA	0.327656849820472	3		705	734	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217654	7217654	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	161	335	0	ENST00000380728.2:c.273G>C	p.Lys91Asn	p.K91N	ENST00000380728		91	aaG/aaC	4/11	0.221221821852542	2	FACETS	0.929	0.858	1	0.929	0.858	1	CLONAL	2	TRUE	0	0.327656849820472	2		335	529	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670053	29670053	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	50	223	0	ENST00000356175.3:c.7026C>G	p.Ile2342Met	p.I2342M	ENST00000356175	NM_000267.3	2342	atC/atG	47/57	0.327656849820472	5	FACETS	0.903	0.767	1	0.301	0.255	0.351	CLONAL	1	TRUE	2	0.327656849820472	5		223	504	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18276981	18276981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	67	440	0	ENST00000222254.8:c.1428G>A	p.Met476Ile	p.M476I	ENST00000222254	NM_005027.3	476	atG/atA	12/16	0.180489287951998	5	FACETS	1	0.949	1	0.396	0.344	0.451	INDETERMINATE	1	TRUE	2	0.327656849820472	5		440	514	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630442	47630442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	120	873	0	ENST00000233146.2:c.112G>A	p.Asp38Asn	p.D38N	ENST00000233146	NM_000251.2	38	Gac/Aac	1/16	0.246973835836711	4	FACETS	1	0.943	1	0.355	0.32	0.392	CLONAL	1	TRUE	1	0.327656849820472	4		873	914	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182505	99182505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	90	638	1	ENST00000074304.5:c.2308G>A	p.Val770Met	p.V770M	ENST00000074304	NM_001134224.1	770	Gtg/Atg	22/26	1	2	FACETS	0.731	0.648	0.819	0.731	0.648	0.819	SUBCLONAL	1	TRUE	1	0.327656849820472	2		639	752	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662752	227662752	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	131	831	0	ENST00000305123.5:c.703G>C	p.Glu235Gln	p.E235Q	ENST00000305123	NM_005544.2	235	Gag/Cag	1/2	1	2	FACETS	0.958	0.869	1	0.958	0.869	1	CLONAL	1	TRUE	1	0.327656849820472	2		831	835	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31393193	31393193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	82	349	0	ENST00000328111.2:c.2281G>A	p.Glu761Lys	p.E761K	ENST00000328111	NM_006892.3	761	Gaa/Aaa	21/23	0.180489287951998	5	FACETS	1	0.97	1	0.44	0.388	0.495	INDETERMINATE	1	TRUE	2	0.327656849820472	5		349	566	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916851	178916851	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	186	259	0	ENST00000263967.3:c.238G>A	p.Glu80Lys	p.E80K	ENST00000263967	NM_006218.2	80	Gaa/Aaa	2/21	0.282498155175341	5	FACETS	1	0.983	1	0.875	0.815	0.935	CLONAL	3	TRUE	1	0.327656849820472	5		259	484	SUCCESS
APC	324	MSKCC	GRCh37	5	112179677	112179677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	40	253	1	ENST00000257430.4:c.8386G>A	p.Asp2796Asn	p.D2796N	ENST00000257430	NM_000038.5	2796	Gat/Aat	16/16	0.246973835836711	4	FACETS	0.979	0.817	1	0.326	0.272	0.387	CLONAL	1	TRUE	1	0.327656849820472	4		254	331	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056430	26056430	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	128	351	0	ENST00000343677.2:c.227del	p.Asn76ThrfsTer13	p.N76Tfs*13	ENST00000343677	NM_005319.3	76	aAc/ac	1/1	0.327656849820472	5	FACETS	1	0.946	1			1	CLONAL	2	TRUE	NA	0.327656849820472	5		351	552	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673673	30673673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	106	686	1	ENST00000376406.3:c.3287C>T	p.Ser1096Leu	p.S1096L	ENST00000376406	NM_014641.2	1096	tCa/tTa	10/15	0.180489287951998	5	FACETS	1	0.969	1	0.405	0.362	0.449	INDETERMINATE	1	TRUE	2	0.327656849820472	5		687	795	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168996	32168996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs8192573	NA	P-0051239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	114	926	1	ENST00000375023.3:c.4037G>A	p.Arg1346Gln	p.R1346Q	ENST00000375023	NM_004557.3	1346	cGg/cAg	22/30	1	2	FACETS	0.89	0.801	0.984	0.89	0.801	0.984	CLONAL	1	TRUE	1	0.327656849820472	2		927	782	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226031	133226031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781298285	NA	P-0051241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	64	597	0	ENST00000320574.5:c.3866G>A	p.Arg1289His	p.R1289H	ENST00000320574	NM_006231.2	1289	cGc/cAc	31/49	1	2	FACETS	0.929	0.812	1	1	0.979	1	CLONAL	2	FALSE	1	0.2295147903424	2		597	300	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860690	151860690	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	38	378	0	ENST00000262189.6:c.9972del	p.Ser3325AlafsTer36	p.S3325Afs*36	ENST00000262189	NM_170606.2	3324	acT/ac	43/59	1	2	FACETS	0.93	0.779	1	1	0.966	1	CLONAL	2	FALSE	1	0.2295147903424	2		378	178	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239871	53239871	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	38	234	0	ENST00000375401.3:c.1570A>G	p.Asn524Asp	p.N524D	ENST00000375401	NM_004187.3	524	Aac/Gac	11/26	0.154012946054524	2	FACETS	0.935	0.792	1			1	CLONAL	3	FALSE	NA	0.2295147903424	2		234	118	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982149	201982149	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	22	558	0	ENST00000359651.3:c.673A>C	p.Lys225Gln	p.K225Q	ENST00000359651		225	Aag/Cag	5/8	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		558	321	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435919	110435919	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	102	622	0	ENST00000375856.3:c.2482T>G	p.Ser828Ala	p.S828A	ENST00000375856	NM_003749.2	828	Tcc/Gcc	1/2	0.134695103553751	4	FACETS	1	0.956	1	1	0.956	1	INDETERMINATE	2	TRUE	2	0.514114272832466	4		622	276	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063347	67063347	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	34	256	0	ENST00000412916.2:c.37G>T	p.Glu13Ter	p.E13*	ENST00000412916		13	Gag/Tag	1/6	0.514114272832466	1	FACETS	0.812	0.678	0.956	0.812	0.678	0.956	CLONAL	1	TRUE	0	0.514114272832466	1		256	121	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579407	7579419	+	frameshift_variant	Frame_Shift_Del	DEL	ACAGGGGCCAGGA	ACAGGGGCCAGGA	GCC	novel	NA	P-0051246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	128	756	1	ENST00000269305.4:c.268_280delinsGGC	p.Ser90GlyfsTer30	p.S90Gfs*30	ENST00000269305	NM_001126112.2	90	TCCTGGCCCCTGTca/GGCca	4/11	0.514114272832466	1	FACETS	0.916	0.857	0.973	1	0.992	1	CLONAL	2	TRUE	0	0.514114272832466	1		757	202	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541504	187541504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1272319296	NA	P-0051246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	39	322	1	ENST00000441802.2:c.6236C>T	p.Pro2079Leu	p.P2079L	ENST00000441802	NM_005245.3	2079	cCg/cTg	10/27	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.514114272832466	2		323	146	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391728	139391728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035043614	NA	P-0051246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	102	750	0	ENST00000277541.6:c.6463G>A	p.Gly2155Ser	p.G2155S	ENST00000277541	NM_017617.3	2155	Ggc/Agc	34/34	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.514114272832466	2		750	303	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779662	3779662	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0121492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	79	633	1	ENST00000262367.5:c.5386C>T	p.Gln1796Ter	p.Q1796*	ENST00000262367	NM_004380.2	1796	Cag/Tag	31/31	1	2	FACETS	0.933	0.823	1	0.933	0.823	1	CLONAL	1	NA	1	0.31	2		634	546	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	961	373	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.595877918046256	10	FACETS	1	0.991	1			1	CLONAL	8	TRUE	NA	0.595877918046256	10		373	1335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0051249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	416	629	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.553892944762205	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.595877918046256	2		631	682	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44896902	44896902	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	242	129	0	ENST00000377967.4:c.622C>T	p.Gln208Ter	p.Q208*	ENST00000377967	NM_021140.2	208	Caa/Taa	8/29	0.543711875395132	2	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.595877918046256	2		129	354	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185004	123185005	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0051249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	33	76	0	ENST00000218089.9:c.1052_1053dup	p.Gln352TyrfsTer28	p.Q352Yfs*28	ENST00000218089	NM_001042749.1	351	cta/cTAta	12/35	0.543711875395132	2	FACETS	0.465	0.381	0.559			1	SUBCLONAL	1	TRUE	NA	0.595877918046256	2		76	238	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0051250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	16	359	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.33	2		359	77	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	72	230	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.949	0.831	1	0.949	0.831	1	CLONAL	1	TRUE	1	0.33	2		230	460	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0051250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	6	233	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.826	0.504	1	0.826	0.504	1	CLONAL	1	TRUE	1	0.33	2		234	44	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795817	42795817	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	141	670	0	ENST00000575354.2:c.2806G>T	p.Gly936Ter	p.G936*	ENST00000575354	NM_015125.3	936	Gga/Tga	11/20	0.149095104725419	3	FACETS	1	0.986	1	0.487	0.445	0.532	INDETERMINATE	1	TRUE	0	0.33	3		670	681	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637690	52637690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239654517	NA	P-0051252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	44	363	0	ENST00000394830.3:c.2626C>T	p.Arg876Cys	p.R876C	ENST00000394830	NM_018313.4	876	Cgt/Tgt	18/30	0.243437509242169	1	FACETS	0.786	0.66	0.924	0.786	0.66	0.924	CLONAL	1	TRUE	0	0.243437509242169	1		363	404	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17947999	17947999	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	71	665	0	ENST00000458235.1:c.1725G>C	p.Leu575Phe	p.L575F	ENST00000458235	NM_000215.3	575	ttG/ttC	13/24	0.243437509242169	1	FACETS	0.782	0.682	0.89	0.782	0.682	0.89	SUBCLONAL	1	TRUE	0	0.243437509242169	1		665	655	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183746	10183746	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	67	630	0	ENST00000256474.2:c.217del	p.Gln73ArgfsTer86	p.Q73Rfs*86	ENST00000256474	NM_000551.3	72	tCc/tc	1/3	0.243437509242169	1	FACETS	0.935	0.814	1	0.935	0.814	1	CLONAL	1	TRUE	0	0.243437509242169	1		630	517	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442591	52442591	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	47	293	0	ENST00000460680.1:c.154T>G	p.Trp52Gly	p.W52G	ENST00000460680	NM_004656.3	52	Tgg/Ggg	4/17	0.243437509242169	1	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	0	0.243437509242169	1		293	316	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133471	55133472	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	novel	NA	P-0051252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	46	355	0	ENST00000257290.5:c.775_776delinsTT	p.Thr259Leu	p.T259L	ENST00000257290	NM_006206.4	259	ACa/TTa	6/23	1	2	FACETS	0.879	0.741	1	0.879	0.741	1	CLONAL	1	TRUE	1	0.243437509242169	2		355	430	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858168	27858168	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	65	411	0	ENST00000359303.2:c.403del	p.Arg135GlufsTer?	p.R135Efs*?	ENST00000359303	NM_003535.2	135	Cga/ga	1/1	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.243437509242169	2		411	420	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188081	151188081	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	52	347	0	ENST00000262187.5:c.72T>G	p.Ile24Met	p.I24M	ENST00000262187	NM_005614.3	24	atT/atG	2/8	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.243437509242169	2		347	385	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231142	53231142	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	69	228	0	ENST00000375401.3:c.1760del	p.Asn587ThrfsTer72	p.N587Tfs*72	ENST00000375401	NM_004187.3	587	aAc/ac	13/26	1	1	FACETS	0.902	0.794	1	1	0.98	1	CLONAL	2	TRUE	0	0.243437509242169	1		228	276	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918582	44918582	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	112	413	0	ENST00000377967.4:c.1065G>A	p.Trp355Ter	p.W355*	ENST00000377967	NM_021140.2	355	tgG/tgA	12/29	0.379257284321221	1	FACETS	0.799	0.725	0.876	0.799	0.725	0.876	SUBCLONAL	1	FALSE	0	0.534877619691945	1		413	384	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399350	139399350	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	118	625	0	ENST00000277541.6:c.4793G>C	p.Arg1598Pro	p.R1598P	ENST00000277541	NM_017617.3	1598	cGc/cCc	26/34	1	2	FACETS	0.759	0.687	0.835	0.759	0.687	0.835	SUBCLONAL	1	FALSE	1	0.534877619691945	2		625	581	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390873	139390912	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTCGGCTCTCCACTCAGGAAGCTCCGGCCCAGGTGGCC	GGCTCGGCTCTCCACTCAGGAAGCTCCGGCCCAGGTGGCC	-	novel	NA	P-0051253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	152	741	0	ENST00000277541.6:c.7279_7318del	p.Gly2427ArgfsTer37	p.G2427Rfs*37	ENST00000277541	NM_017617.3	2427	GGCCACCTGGGCCGGAGCTTCCTGAGTGGAGAGCCGAGCCag/ag	34/34	1	2	FACETS	0.963	0.885	1	0.963	0.885	1	CLONAL	1	FALSE	1	0.534877619691945	2		741	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0051254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	178	751	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	NA	2	FACETS	0.924	0.856	0.995			1	INDETERMINATE	2	TRUE	NA	0.308656991115961	2		751	624	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0051254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	157	448	1	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.245229843629303	4	FACETS	0.923	0.848	1	0.923	0.848	1	CLONAL	2	TRUE	2	0.308656991115961	4		449	721	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866355	42866355	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	85	544	0	ENST00000398585.3:c.277G>T	p.Val93Phe	p.V93F	ENST00000398585	NM_001135099.1	93	Gtc/Ttc	3/14	0.245229843629303	4	FACETS	0.773	0.682	0.871	0.387	0.341	0.436	SUBCLONAL	1	TRUE	2	0.308656991115961	4		544	932	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606899	43606899	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1226167606	NA	P-0051254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	114	728	0	ENST00000355710.3:c.1508C>G	p.Thr503Arg	p.T503R	ENST00000355710	NM_020975.4	503	aCa/aGa	7/20	0.281096815183578	3	FACETS	0.882	0.793	0.976	0.441	0.396	0.488	CLONAL	1	TRUE	1	0.308656991115961	3		728	967	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999500	100999500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	120	729	0	ENST00000325455.5:c.302C>T	p.Ser101Phe	p.S101F	ENST00000325455	NM_001202474.3	101	tCt/tTt	1/8	0.297544392641338	3	FACETS	0.991	0.894	1	0.495	0.447	0.547	CLONAL	1	TRUE	1	0.308656991115961	3		729	906	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435238	110435238	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	112	340	0	ENST00000375856.3:c.3163G>T	p.Gly1055Cys	p.G1055C	ENST00000375856	NM_003749.2	1055	Ggc/Tgc	1/2	0.281096815183578	3	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	1	0.308656991115961	3		340	405	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220651	1220651	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	131	690	0	ENST00000326873.7:c.669G>T	p.Glu223Asp	p.E223D	ENST00000326873	NM_000455.4	223	gaG/gaT	5/10	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.308656991115961	2		690	824	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11137007	11137007	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	108	493	0	ENST00000358026.2:c.3200G>T	p.Gly1067Val	p.G1067V	ENST00000358026	NM_001128849.1	1067	gGc/gTc	23/36	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.308656991115961	2		493	671	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546950	9546950	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	122	285	0	ENST00000353224.5:c.1072C>G	p.Pro358Ala	p.P358A	ENST00000353224	NM_177990.2	358	Cct/Gct	5/10	0.308656991115961	3	FACETS	0.883	0.802	0.967			1	CLONAL	2	TRUE	NA	0.308656991115961	3		285	517	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200703	128200703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	195	671	0	ENST00000341105.2:c.1102C>T	p.Pro368Ser	p.P368S	ENST00000341105	NM_032638.4	368	Cct/Tct	5/6	0.308656991115961	6	FACETS	0.941	0.87	1	0.47	0.435	0.508	CLONAL	2	TRUE	2	0.308656991115961	6		671	1086	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670212	134670212	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0051254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	207	232	0	ENST00000398015.3:c.124-1G>T		p.X42_splice	ENST00000398015	NM_004441.4	42			0.308656991115961	6	FACETS	1	0.956	1	1	0.956	1	CLONAL	4	TRUE	2	0.308656991115961	6		232	528	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149453034	149453034	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	159	289	0	ENST00000286301.3:c.912C>A	p.Ser304Arg	p.S304R	ENST00000286301	NM_005211.3	304	agC/agA	7/22	0.301640852111228	3	FACETS	0.845	0.781	0.911	0.845	0.781	0.911	CLONAL	3	TRUE	0	0.308656991115961	3		289	469	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611236	100611236	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	208	377	0	ENST00000308731.7:c.1370T>A	p.Leu457Gln	p.L457Q	ENST00000308731	NM_000061.2	457	cTg/cAg	15/19	NA	2	FACETS	0.862	0.808	0.918			1	INDETERMINATE	3	TRUE	NA	0.308656991115961	2		377	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0051255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	110	623	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.19944671925875	2		623	752	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95596505	95596505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745802492	NA	P-0051256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	58	255	0	ENST00000393063.1:c.463G>A	p.Ala155Thr	p.A155T	ENST00000393063	NM_030621.3	155	Gcc/Acc	6/28	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.406252786853233	2		255	255	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	28	230	0				ENST00000310581	NM_198253.2	-/1132			0.344309105899321	3	FACETS	1	0.925	1	0.653	0.531	0.786	CLONAL	1	FALSE	1	0.434906503733499	3		230	120	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0051257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	76	188	0	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	0.434906503733499	5	FACETS	1	0.951	1	0.752	0.668	0.839	CLONAL	2	FALSE	2	0.434906503733499	5		188	256	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431634	6431634	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	86	186	0	ENST00000356142.4:c.187G>A	p.Asp63Asn	p.D63N	ENST00000356142	NM_018890.3	63	Gat/Aat	3/7	0.379423755586562	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	FALSE	2	0.434906503733499	4		186	234	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	67	387	0	ENST00000361445.4:c.5930C>G	p.Thr1977Arg	p.T1977R	ENST00000361445	NM_004958.3	1977	aCa/aGa	43/58	0.436239689163043	1	FACETS	0.798	0.713	0.885	1	0.98	1	SUBCLONAL	2	FALSE	0	0.434906503733499	1		387	151	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023876	27023889	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCCGGCGGACAT	GGCCCGGCGGACAT	-	novel	NA	P-0051257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	41	113	0	ENST00000324856.7:c.986_999del	p.Pro329LeufsTer66	p.P329Lfs*66	ENST00000324856	NM_006015.4	328	GGCCCGGCGGACATg/g	1/20	NA	2	FACETS	0.773	0.66	0.892			1	INDETERMINATE	2	FALSE	NA	0.434906503733499	2		113	122	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578518	7578518	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934875	NA	P-0051258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	142	687	0	ENST00000269305.4:c.412G>C	p.Ala138Pro	p.A138P	ENST00000269305	NM_001126112.2	138	Gcc/Ccc	5/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.204203096961728	2		687	1018	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47700160	47700161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0051258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	41	364	0	ENST00000347630.2:c.12dup	p.Pro5SerfsTer16	p.P5Sfs*16	ENST00000347630	NM_001007230.1	4	-/T	3/11	1	2	FACETS	0.862	0.718	1	0.862	0.718	1	CLONAL	1	TRUE	1	0.204203096961728	2		364	466	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223637	36223637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	63	767	1	ENST00000222270.7:c.6187G>A	p.Gly2063Ser	p.G2063S	ENST00000222270	NM_014727.1	2063	Ggc/Agc	28/37	1	2	FACETS	0.565	0.487	0.651	0.565	0.487	0.651	SUBCLONAL	1	TRUE	1	0.204203096961728	2		768	1092	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0051259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	119	629	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.260402727363817	2		631	907	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999713	100999713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	144	746	1	ENST00000325455.5:c.89G>A	p.Arg30His	p.R30H	ENST00000325455	NM_001202474.3	30	cGc/cAc	1/8	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.260402727363817	2		747	1074	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926884	112926884	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	44	497	0	ENST00000351677.2:c.1504T>C	p.Ser502Pro	p.S502P	ENST00000351677	NM_002834.3	502	Tca/Cca	13/16	1	2	FACETS	0.469	0.392	0.554	0.469	0.392	0.554	SUBCLONAL	1	TRUE	1	0.260402727363817	2		497	721	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0051259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	94	560	1	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.944	0.839	1	0.944	0.839	1	CLONAL	1	TRUE	1	0.260402727363817	2		561	765	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117825	70117830	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGCA	CCAGCA	GG	novel	NA	P-0051259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	107	500	2	ENST00000245479.2:c.293_298delinsGG	p.Ser98TrpfsTer11	p.S98Wfs*11	ENST00000245479	NM_000346.3	98	tCCAGCAag/tGGag	1/3	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.260402727363817	2		502	720	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604706	48604706	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	77	356	0	ENST00000342988.3:c.1528G>A	p.Gly510Arg	p.G510R	ENST00000342988	NM_005359.5	510	Gga/Aga	12/12	0.260402727363817	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.260402727363817	1		356	434	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164914	106164914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771761785	NA	P-0051259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	32	319	0	ENST00000380013.4:c.3782G>A	p.Arg1261His	p.R1261H	ENST00000380013	NM_001127208.2	1261	cGc/cAc	6/11	1	2	FACETS	0.544	0.441	0.66	0.544	0.441	0.66	SUBCLONAL	1	TRUE	1	0.260402727363817	2		319	452	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929070	44929071	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0051259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	89	207	0	ENST00000377967.4:c.2172_2173del	p.Leu725AspfsTer4	p.L725Dfs*4	ENST00000377967	NM_021140.2	724	ATa/a	17/29	1	1	FACETS	0.915	0.819	1	1	0.985	1	CLONAL	2	TRUE	0	0.260402727363817	1		207	325	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910732	29910732	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	150	779	0	ENST00000376809.5:c.272T>A	p.Val91Glu	p.V91E	ENST00000376809	NM_002116.7	91	gTg/gAg	2/8	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.260402727363817	2		779	1118	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0051260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	462	629	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.392896642036351	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.392896642036351	1		631	1296	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955550	48955550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913304	NA	P-0051260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	28	188	0	ENST00000267163.4:c.1666C>T	p.Arg556Ter	p.R556*	ENST00000267163	NM_000321.2	556	Cga/Tga	17/27	0.392896642036351	1	FACETS	0.779	0.631	0.943	0.779	0.631	0.943	CLONAL	1	TRUE	0	0.392896642036351	1		188	147	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057302	30057302	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315496	NA	P-0051260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	200	378	0	ENST00000338641.4:c.784C>T	p.Arg262Ter	p.R262*	ENST00000338641	NM_000268.3	262	Cga/Tga	8/16	0.392896642036351	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.392896642036351	1		378	678	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883719	37883719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143958183	NA	P-0051260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	505	844	1	ENST00000269571.5:c.3331C>T	p.Arg1111Trp	p.R1111W	ENST00000269571		1111	Cgg/Tgg	26/27	0.392896642036351	1	FACETS	0.762	0.73	0.795	1	0.996	1	SUBCLONAL	2	TRUE	0	0.392896642036351	1		845	1355	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230752	53230752	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	162	278	0	ENST00000375401.3:c.2041C>T	p.Arg681Ter	p.R681*	ENST00000375401	NM_004187.3	681	Cga/Tga	14/26	0.356277652307297	2	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.392896642036351	2		278	642	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739374	145739374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776218553	NA	P-0051260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	637	672	0	ENST00000428558.2:c.1996G>A	p.Gly666Arg	p.G666R	ENST00000428558	NM_004260.3	666	Ggg/Agg	12/22	0.361232539883501	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.392896642036351	2		672	1492	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816139	89816139	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs760392231	NA	P-0051260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	303	557	1	ENST00000389301.3:c.3238C>T	p.Arg1080Trp	p.R1080W	ENST00000389301	NM_000135.2	1080	Cgg/Tgg	32/43	0.392896642036351	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.392896642036351	1		558	943	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536939	120536939	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760171048	NA	P-0051260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	349	617	0	ENST00000229340.5:c.247G>A	p.Gly83Arg	p.G83R	ENST00000229340	NM_006861.6	83	Ggg/Agg	4/6	0.392896642036351	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.392896642036351	1		617	1026	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255141	16255142	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0051260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	54	298	1	ENST00000375759.3:c.2417_2418dup	p.Arg807AspfsTer3	p.R807Dfs*3	ENST00000375759	NM_015001.2	802	-/GA	11/15	0.392896642036351	1	FACETS	0.437	0.374	0.507	0.437	0.374	0.507	SUBCLONAL	1	TRUE	0	0.392896642036351	1		299	505	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139001	50139001	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs538230538	NA	P-0051260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	426	647	0	ENST00000246792.3:c.562C>T	p.Arg188Trp	p.R188W	ENST00000246792	NM_006270.3	188	Cgg/Tgg	5/6	0.392896642036351	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.392896642036351	1		647	1292	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11269466	11269466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	196	428	0	ENST00000361445.4:c.3704G>A	p.Arg1235Gln	p.R1235Q	ENST00000361445	NM_004958.3	1235	cGg/cAg	25/58	0.392896642036351	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.392896642036351	1		428	684	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681326	88681326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781332	NA	P-0051260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	58	283	0	ENST00000372037.3:c.1216C>T	p.Arg406Cys	p.R406C	ENST00000372037	NM_004329.2	406	Cgc/Tgc	11/13	0.392896642036351	1	FACETS	0.518	0.446	0.596	0.518	0.446	0.596	SUBCLONAL	1	TRUE	0	0.392896642036351	1		283	458	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013729	170013729	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1389006052	NA	P-0051260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	22	237	0	ENST00000295797.4:c.1448G>A	p.Arg483His	p.R483H	ENST00000295797	NM_002740.5	483	cGt/cAt	15/18	0.340085576359817	3	FACETS	0.354	0.273	0.447	0.118	0.091	0.149	SUBCLONAL	1	TRUE	0	0.392896642036351	3		237	379	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317715	163317715	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199764107	NA	P-0051260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	20	119	0	ENST00000271452.3:c.1111C>T	p.Arg371Cys	p.R371C	ENST00000271452	NM_145697.2	371	Cgc/Tgc	12/14	0.392896642036351	1	FACETS	0.889	0.694	1	0.889	0.694	1	CLONAL	1	TRUE	0	0.392896642036351	1		119	92	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628520	90628520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1237752648	NA	P-0051260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	192	669	0	ENST00000330062.3:c.1067G>A	p.Arg356Gln	p.R356Q	ENST00000330062	NM_002168.2	356	cGg/cAg	8/11	0.392896642036351	1	FACETS	0.694	0.641	0.749	0.694	0.641	0.749	SUBCLONAL	1	TRUE	0	0.392896642036351	1		669	1132	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010462	48010480	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCGGCCGTGCCGCCGCT	AGGCGGCCGTGCCGCCGCT	-	novel	NA	P-0051260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	469	500	0	ENST00000234420.5:c.90_108del	p.Gly31ProfsTer44	p.G31Pfs*44	ENST00000234420	NM_000179.2	30	gaAGGCGGCCGTGCCGCCGCT/ga	1/10	0.392896642036351	1	FACETS	0.965	0.926	1	1	0.997	1	CLONAL	2	TRUE	0	0.392896642036351	1		500	994	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220237	55220237	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0051262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	83	404	0	ENST00000275493.2:c.629-2A>C		p.X210_splice	ENST00000275493	NM_005228.3	210			1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	FALSE	1	0.232267745211342	2		404	687	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041262	29041262	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	34	214	1	ENST00000282397.4:c.166del	p.Glu56LysfsTer12	p.E56Kfs*12	ENST00000282397	NM_002019.4	56	Gaa/aa	3/30	1	2	FACETS	0.82	0.671	0.987	0.82	0.671	0.987	CLONAL	1	FALSE	1	0.232267745211342	2		215	357	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183788	10183788	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	67	482	0	ENST00000256474.2:c.257C>A	p.Pro86His	p.P86H	ENST00000256474	NM_000551.3	86	cCc/cAc	1/3	0.232267745211342	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	FALSE	0	0.232267745211342	1		482	482	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12653507	12653507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	73	260	0	ENST00000251849.4:c.262G>A	p.Val88Met	p.V88M	ENST00000251849	NM_002880.3	88	Gtg/Atg	3/17	0.232267745211342	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	0	0.232267745211342	1		260	488	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504310	186504311	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0051262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	18	112	0	ENST00000323963.5:c.649dup	p.Met217AsnfsTer4	p.M217Nfs*4	ENST00000323963		216	aca/acAa	7/11	1	2	FACETS	1	0.824	1	1	0.824	1	CLONAL	1	FALSE	1	0.232267745211342	2		112	140	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0051263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	253	289	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.649199874843937	2	FACETS	0.906	0.863	0.95	0.906	0.863	0.95	CLONAL	2	TRUE	0	0.649199874843937	2		289	430	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0051263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	122	247	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.649199874843937	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.649199874843937	1		247	246	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578242	7578242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882003	NA	P-0051263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	247	484	0	ENST00000269305.4:c.607G>A	p.Val203Met	p.V203M	ENST00000269305	NM_001126112.2	203	Gtg/Atg	6/11	NA	2	FACETS	0.926	0.868	0.985			1	INDETERMINATE	1	TRUE	NA	0.649199874843937	2		484	822	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223334	2223334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757410464	NA	P-0051263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	109	565	0	ENST00000326181.6:c.946C>T	p.Arg316Cys	p.R316C	ENST00000326181	NM_032271.2	316	Cgc/Tgc	10/21	1	2	FACETS	0.355	0.318	0.395	0.355	0.318	0.395	SUBCLONAL	1	TRUE	1	0.649199874843937	2		565	945	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1064795203	NA	P-0051264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	161	686	0	ENST00000269305.4:c.532C>G	p.His178Asp	p.H178D	ENST00000269305	NM_001126112.2	178	Cac/Gac	5/11	1	2	FACETS	0.995	0.917	1	0.995	0.917	1	CLONAL	1	TRUE	1	0.522800607779301	2		686	619	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696430	47696430	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	104	390	0	ENST00000347630.2:c.393G>C	p.Trp131Cys	p.W131C	ENST00000347630	NM_001007230.1	131	tgG/tgC	6/11	1	2	FACETS	0.902	0.813	0.996	0.902	0.813	0.996	CLONAL	1	TRUE	1	0.522800607779301	2		390	441	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696450	47696450	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	53	342	0	ENST00000347630.2:c.373T>G	p.Phe125Val	p.F125V	ENST00000347630	NM_001007230.1	125	Ttt/Gtt	6/11	1	2	FACETS	0.511	0.437	0.591	0.511	0.437	0.591	SUBCLONAL	1	TRUE	1	0.522800607779301	2		342	397	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624942	9624942	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	98	316	0	ENST00000353224.5:c.35C>A	p.Ser12Tyr	p.S12Y	ENST00000353224	NM_177990.2	12	tCt/tAt	3/10	0.379884438200685	3	FACETS	0.924	0.827	1	0.462	0.413	0.513	CLONAL	1	TRUE	1	0.522800607779301	3		316	512	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	86	230	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.899	0.799	1	0.899	0.799	1	CLONAL	1	TRUE	1	0.454638456738025	2		230	421	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339981	70339981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	217	240	0	ENST00000374080.3:c.514G>A	p.Glu172Lys	p.E172K	ENST00000374080		172	Gag/Aag	4/45	1	1	FACETS	0.84	0.792	0.888	1	0.994	1	CLONAL	2	TRUE	0	0.454638456738025	1		240	439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576885	7576885	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0051267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	531	603	0	ENST00000269305.4:c.961A>T	p.Lys321Ter	p.K321*	ENST00000269305	NM_001126112.2	321	Aaa/Taa	9/11	0.454638456738025	2	FACETS	0.993	0.955	1	0.993	0.955	1	CLONAL	2	TRUE	0	0.454638456738025	2		603	1176	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873733	37873733	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs199726056	NA	P-0051267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	163	574	0	ENST00000269571.5:c.1898C>T	p.Ser633Phe	p.S633F	ENST00000269571		633	tCc/tTc	15/27	1	2	FACETS	0.746	0.684	0.811	0.746	0.684	0.811	SUBCLONAL	1	TRUE	1	0.454638456738025	2		574	961	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475218	475218	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1404815403	NA	P-0051267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	189	568	0	ENST00000399788.2:c.419C>G	p.Ser140Cys	p.S140C	ENST00000399788	NM_001042603.1	140	tCt/tGt	4/28	1	2	FACETS	0.884	0.817	0.953	0.884	0.817	0.953	CLONAL	1	TRUE	1	0.454638456738025	2		568	941	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864889	117864889	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	160	431	0	ENST00000297338.2:c.1220G>T	p.Gly407Val	p.G407V	ENST00000297338	NM_006265.2	407	gGa/gTa	10/14	1	2	FACETS	0.997	0.916	1	0.997	0.916	1	CLONAL	1	TRUE	1	0.454638456738025	2		431	706	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949126	151949126	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	141	506	1	ENST00000262189.6:c.1519C>T	p.Gln507Ter	p.Q507*	ENST00000262189	NM_170606.2	507	Cag/Tag	11/59	1	2	FACETS	0.798	0.728	0.872	0.798	0.728	0.872	SUBCLONAL	1	TRUE	1	0.454638456738025	2		507	777	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922994	44922994	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	234	267	0	ENST00000377967.4:c.1855C>T	p.His619Tyr	p.H619Y	ENST00000377967	NM_021140.2	619	Cat/Tat	16/29	1	1	FACETS	0.799	0.753	0.844	1	0.994	1	SUBCLONAL	2	TRUE	0	0.454638456738025	1		267	498	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339496	81339496	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	133	404	0	ENST00000222390.5:c.1508C>A	p.Thr503Lys	p.T503K	ENST00000222390	NM_000601.4	503	aCa/aAa	13/18	1	2	FACETS	0.869	0.791	0.951	0.869	0.791	0.951	CLONAL	1	TRUE	1	0.454638456738025	2		404	673	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491401	2491401	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	284	756	0	ENST00000355716.4:c.444G>C	p.Gln148His	p.Q148H	ENST00000355716	NM_003820.2	148	caG/caC	4/8	0.190135977333862	3	FACETS	1	0.982	1	0.56	0.525	0.595	INDETERMINATE	1	TRUE	1	0.454638456738025	3		756	1370	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107079	27107079	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	158	503	0	ENST00000324856.7:c.6690G>C	p.Met2230Ile	p.M2230I	ENST00000324856	NM_006015.4	2230	atG/atC	20/20	1	2	FACETS	0.892	0.819	0.969	0.892	0.819	0.969	CLONAL	1	TRUE	1	0.454638456738025	2		503	779	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415634	49415634	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	127	369	0	ENST00000301067.7:c.16543G>C	p.Asp5515His	p.D5515H	ENST00000301067	NM_003482.3	5515	Gat/Cat	54/54	1	2	FACETS	0.904	0.821	0.991	0.904	0.821	0.991	CLONAL	1	TRUE	1	0.454638456738025	2		369	618	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991634	72991634	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	64	578	0	ENST00000268489.5:c.2411G>A	p.Trp804Ter	p.W804*	ENST00000268489	NM_006885.3	804	tGg/tAg	2/10	0.346374823908325	1	FACETS	0.252	0.217	0.289	0.252	0.217	0.289	SUBCLONAL	1	TRUE	0	0.454638456738025	1		578	864	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81939013	81939013	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	59	424	0	ENST00000359376.3:c.1368G>T	p.Lys456Asn	p.K456N	ENST00000359376	NM_002661.3	456	aaG/aaT	15/33	0.346374823908325	1	FACETS	0.35	0.301	0.403	0.35	0.301	0.403	SUBCLONAL	1	TRUE	0	0.454638456738025	1		424	573	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564756	41564756	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1353213083	NA	P-0051267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	105	589	0	ENST00000263253.7:c.4057T>G	p.Phe1353Val	p.F1353V	ENST00000263253	NM_001429.3	1353	Ttt/Gtt	25/31	1	2	FACETS	0.486	0.435	0.541	0.486	0.435	0.541	SUBCLONAL	1	TRUE	1	0.454638456738025	2		589	950	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422860	12422860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148037954	NA	P-0051267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	202	438	0	ENST00000287820.6:c.350C>T	p.Ser117Phe	p.S117F	ENST00000287820	NM_015869.4	117	tCt/tTt	3/7	1	2	FACETS	0.964	0.894	1	0.964	0.894	1	CLONAL	1	TRUE	1	0.454638456738025	2		438	922	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964443	70964443	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	273	589	0	ENST00000276594.2:c.1585C>T	p.His529Tyr	p.H529Y	ENST00000276594	NM_024504.3	529	Cat/Tat	8/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.454638456738025	2		589	1003	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941824	44941824	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	115	147	1	ENST00000377967.4:c.3148G>T	p.Glu1050Ter	p.E1050*	ENST00000377967	NM_021140.2	1050	Gaa/Taa	21/29	1	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.454638456738025	1		148	298	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0051269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	124	439	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.326087039348892	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.326087039348892	1		439	628	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879672	151879672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	40	229	0	ENST00000262189.6:c.5273G>A	p.Arg1758His	p.R1758H	ENST00000262189	NM_170606.2	1758	cGt/cAt	36/59	1	2	FACETS	0.743	0.62	0.88	0.743	0.62	0.88	SUBCLONAL	1	TRUE	1	0.326087039348892	2		229	330	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027153	49027154	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0051269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	69	234	0	ENST00000267163.4:c.1721_1722del	p.Lys574ThrfsTer10	p.K574Tfs*10	ENST00000267163	NM_000321.2	574	AAa/a	18/27	0.326087039348892	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.326087039348892	1		234	307	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396961	396962	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0051269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	184	831	0	ENST00000262320.3:c.64dup	p.Arg22ProfsTer7	p.R22Pfs*7	ENST00000262320	NM_003502.3	22	cga/cCga	2/11	0.326087039348892	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.326087039348892	1		831	915	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566540	41566540	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	77	348	0	ENST00000263253.7:c.4417A>C	p.Lys1473Gln	p.K1473Q	ENST00000263253	NM_001429.3	1473	Aag/Cag	27/31	1	2	FACETS	0.787	0.692	0.89	0.787	0.692	0.89	SUBCLONAL	1	TRUE	1	0.326087039348892	2		348	600	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455025	50455055	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAATTGTGTTTTCTGCAGTTGGTAAACCTCA	CAATTGTGTTTTCTGCAGTTGGTAAACCTCA	-	novel	NA	P-0051269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	39	301	0	ENST00000331340.3:c.590-15_605del		p.X197_splice	ENST00000331340	NM_006060.4	197		6/8	1	2	FACETS	0.641	0.532	0.762	0.641	0.532	0.762	SUBCLONAL	1	TRUE	1	0.326087039348892	2		301	373	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97869373	97869373	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	76	699	0	ENST00000289081.3:c.1508C>G	p.Thr503Arg	p.T503R	ENST00000289081	NM_000136.2	503	aCg/aGg	14/15	1	2	FACETS	0.508	0.444	0.577	0.508	0.444	0.577	SUBCLONAL	1	TRUE	1	0.326087039348892	2		699	918	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593613	55593613	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913521	NA	P-0051271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	268	411	0	ENST00000288135.5:c.1679T>A	p.Val560Asp	p.V560D	ENST00000288135	NM_000222.2	560	gTt/gAt	11/21	0.253344232005731	2	FACETS	1	0.992	1	0.619	0.59	0.648	INDETERMINATE	1	TRUE	0	0.943168548998782	2		411	459	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748510	43748510	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774265827	NA	P-0051271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	57	310	0	ENST00000523873.1:c.464G>A	p.Arg155His	p.R155H	ENST00000523873		155	cGc/cAc	6/8	1	2	FACETS	0.25	0.215	0.289	0.25	0.215	0.289	SUBCLONAL	1	TRUE	1	0.943168548998782	2		310	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0051272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	142	751	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.413964601803456	2		751	665	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526104	63526104	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs562176077	NA	P-0051272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	89	673	1	ENST00000307078.5:c.2522G>A	p.Arg841Gln	p.R841Q	ENST00000307078	NM_004655.3	841	cGg/cAg	11/11	0.413964601803456	4	FACETS	0.69	0.611	0.775	0.23	0.203	0.259	SUBCLONAL	1	TRUE	1	0.413964601803456	4		674	881	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341129	8341129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	91	379	0	ENST00000356435.5:c.5087G>A	p.Gly1696Glu	p.G1696E	ENST00000356435		1696	gGa/gAa	30/35	0.413964601803456	3	FACETS	0.965	0.859	1	0.482	0.429	0.539	CLONAL	1	TRUE	1	0.413964601803456	3		379	550	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056223	27056223	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	76	756	1	ENST00000324856.7:c.1219C>A	p.Pro407Thr	p.P407T	ENST00000324856	NM_006015.4	407	Cct/Act	2/20	NA	2	FACETS	0.657	0.577	0.743			1	INDETERMINATE	1	TRUE	NA	0.413964601803456	2		757	559	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005348	42005348	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0051272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	179	384	0	ENST00000219905.7:c.3085-1G>C		p.X1029_splice	ENST00000219905	NM_001164273.1	1029			0.413964601803456	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.413964601803456	2		384	397	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831723	72831723	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	135	692	0	ENST00000268489.5:c.4858C>T	p.His1620Tyr	p.H1620Y	ENST00000268489	NM_006885.3	1620	Cat/Tat	9/10	0.413964601803456	2	FACETS	1	0.972	1	0.579	0.529	0.632	CLONAL	1	TRUE	0	0.413964601803456	2		692	563	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456490	29456490	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	64	825	0	ENST00000389048.3:c.2428A>C	p.Ser810Arg	p.S810R	ENST00000389048	NM_004304.4	810	Agc/Cgc	14/29	0.251631669291459	4	FACETS	0.389	0.335	0.448	0.194	0.167	0.224	SUBCLONAL	1	TRUE	2	0.413964601803456	4		825	1124	SUCCESS
APC	324	MSKCC	GRCh37	5	112179669	112179669	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	63	339	0	ENST00000257430.4:c.8378G>C	p.Ser2793Thr	p.S2793T	ENST00000257430	NM_000038.5	2793	aGc/aCc	16/16	0.251631669291459	4	FACETS	0.976	0.847	1	0.488	0.423	0.558	CLONAL	1	TRUE	2	0.413964601803456	4		339	441	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410978	63410978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	41	801	0	ENST00000330258.3:c.2189C>T	p.Pro730Leu	p.P730L	ENST00000330258	NM_152424.3	730	cCa/cTa	2/2	0.28322828011223	3	FACETS	0.366	0.304	0.435	0.183	0.152	0.218	SUBCLONAL	1	TRUE	1	0.413964601803456	3		801	653	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555526101	NA	P-0051273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	185	736	0	ENST00000269305.4:c.497C>G	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tGa	5/11	NA	2	FACETS	0.814	0.757	0.872			1	INDETERMINATE	2	TRUE	NA	0.425484497376835	2		736	534	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659240	86659240	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	61	211	0	ENST00000274376.6:c.1533del	p.Lys511AsnfsTer9	p.K511Nfs*9	ENST00000274376	NM_002890.2	510	gAa/ga	11/25	0.362870758342134	2	FACETS	1	0.966	1	0.67	0.586	0.758	CLONAL	1	TRUE	0	0.425484497376835	2		211	214	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84393442	84393442	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0051273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	62	157	1	ENST00000321945.7:c.216-1G>A		p.X72_splice	ENST00000321945	NM_139076.2	72			0.425484497376835	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.425484497376835	1		158	183	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0051277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	281	359	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.647378078688685	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.647378078688685	3		359	505	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0051277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	83	368	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.77	0.686	0.859	0.77	0.686	0.859	SUBCLONAL	1	TRUE	1	0.647378078688685	2		368	333	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0051277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	201	610	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.647378078688685	2		610	608	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0051277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	85	232	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.647378078688685	2		232	233	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	397013	397013	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	104	863	0	ENST00000262320.3:c.13G>C	p.Glu5Gln	p.E5Q	ENST00000262320	NM_003502.3	5	Gag/Cag	2/11	1	2	FACETS	0.328	0.293	0.366	0.328	0.293	0.366	SUBCLONAL	1	TRUE	1	0.647378078688685	2		863	979	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0051277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	313	996	1	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	0.575423456772736	1	FACETS	0.959	0.912	1	0.959	0.912	1	CLONAL	1	TRUE	0	0.647378078688685	1		997	682	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118862	70118867	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TTCTGA	TTCTGA	-	novel	NA	P-0051277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	188	575	0	ENST00000245479.2:c.434_439del	p.Leu145_Asn147delinsHis	p.L145_N147delinsH	ENST00000245479	NM_000346.3	145	cTTCTGAac/cac	2/3	1	2	FACETS	0.813	0.754	0.875	0.813	0.754	0.875	CLONAL	1	TRUE	1	0.647378078688685	2		575	714	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220105	36220105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368307141	NA	P-0051277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	104	914	0	ENST00000222270.7:c.4825G>A	p.Val1609Ile	p.V1609I	ENST00000222270	NM_014727.1	1609	Gtc/Atc	22/37	1	2	FACETS	0.321	0.287	0.358	0.321	0.287	0.358	SUBCLONAL	1	TRUE	1	0.647378078688685	2		914	1000	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961348	54961348	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	63	620	0	ENST00000312783.6:c.284C>G	p.Thr95Ser	p.T95S	ENST00000312783	NM_198436.1	95	aCc/aGc	4/10	0.588277230349346	4	FACETS	0.318	0.274	0.366	0.106	0.091	0.122	SUBCLONAL	1	TRUE	1	0.647378078688685	4		620	1009	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535320	66535320	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	75	712	1	ENST00000273854.3:c.141C>A	p.Cys47Ter	p.C47*	ENST00000273854	NM_004439.5	47	tgC/tgA	1/18	0.647378078688685	1	FACETS	0.332	0.292	0.375	0.332	0.292	0.375	SUBCLONAL	1	TRUE	0	0.647378078688685	1		713	472	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190584	32190584	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0051277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	101	788	0	ENST00000375023.3:c.156-1G>T		p.X52_splice	ENST00000375023	NM_004557.3	52			NA	2	FACETS	0.325	0.29	0.363			1	INDETERMINATE	1	TRUE	NA	0.647378078688685	2		788	960	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068120	94068120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1056840976	NA	P-0051277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	131	245	0	ENST00000369303.4:c.842G>A	p.Arg281His	p.R281H	ENST00000369303	NM_004440.3	281	cGt/cAt	4/17	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.647378078688685	2		245	310	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109308791	109308791	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	47	286	0	ENST00000436639.2:c.1612G>C	p.Glu538Gln	p.E538Q	ENST00000436639	NM_014454.2	538	Gaa/Caa	10/10	0.647378078688685	3	FACETS	0.424	0.358	0.497	0.212	0.179	0.249	SUBCLONAL	1	TRUE	1	0.647378078688685	3		286	453	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0051281-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	646	507	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.261879137883988	15	FACETS	1	0.972	1			1	CLONAL	12	TRUE	NA	0.261879137883988	15		507	1108	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0051281-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	223	975	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.261879137883988	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.261879137883988	2		977	838	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920691	96920691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752938517	NA	P-0051281-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	87	405	2	ENST00000258439.3:c.289G>A	p.Ala97Thr	p.A97T	ENST00000258439	NM_001193304.2	97	Gcc/Acc	3/4	0.22947003725535	3	FACETS	0.96	0.849	1	0.48	0.424	0.539	CLONAL	1	TRUE	1	0.261879137883988	3		407	783	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0051282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	102	890	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	1	2	FACETS	0.309	0.276	0.345	0.309	0.276	0.345	SUBCLONAL	1	TRUE	1	0.674334724555474	2		890	978	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0051282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	50	941	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			1	2	FACETS	0.155	0.13	0.181	0.155	0.13	0.181	SUBCLONAL	1	TRUE	1	0.674334724555474	2		941	959	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490316	29490327	+	inframe_deletion	In_Frame_Del	DEL	TTCGGAATTCTG	TTCGGAATTCTG	-	novel	NA	P-0051282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	44	481	0	ENST00000356175.3:c.401_412del	p.Leu134_Ala138delinsPro	p.L134_A138delinsP	ENST00000356175	NM_000267.3	134	cTTCGGAATTCTGcc/ccc	4/57	1	2	FACETS	0.196	0.164	0.232	0.196	0.164	0.232	SUBCLONAL	1	TRUE	1	0.674334724555474	2		481	665	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405866	49405866	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	56	610	0	ENST00000418115.1:c.272G>A	p.Ser91Asn	p.S91N	ENST00000418115	NM_001664.2	91	aGt/aAt	3/5	1	2	FACETS	0.237	0.202	0.275	0.237	0.202	0.275	SUBCLONAL	1	TRUE	1	0.674334724555474	2		610	701	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0051284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	113	289	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.559281552408788	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.559281552408788	1		289	242	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0051284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	15	331	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.559281552408788	1	FACETS	0.196	0.143	0.259	0.196	0.143	0.259	SUBCLONAL	1	TRUE	0	0.559281552408788	1		331	197	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	91	230	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.84	0.757	0.924	0.84	0.757	0.924	CLONAL	1	TRUE	1	0.846731915160457	2		230	256	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0051298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	175	423	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.833758896740836	3	FACETS	0.955	0.884	1	0.478	0.442	0.515	CLONAL	1	TRUE	1	0.846731915160457	3		423	616	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624266	89624268	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0051298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	146	283	0	ENST00000371953.3:c.42_44del	p.Arg15del	p.R15del	ENST00000371953	NM_000314.4	14	AGG/-	1/9	0.846731915160457	1	FACETS	0.97	0.918	1	0.97	0.918	1	CLONAL	1	TRUE	0	0.846731915160457	1		283	205	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941718	48941719	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0051298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	103	217	0	ENST00000267163.4:c.1028_1029del	p.Leu343ProfsTer3	p.L343Pfs*3	ENST00000267163	NM_000321.2	343	cTT/c	10/27	NA	2	FACETS	0.785	0.731	0.837			1	INDETERMINATE	2	TRUE	NA	0.846731915160457	2		217	155	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	61	230	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.942	0.83	1	0.942	0.83	1	CLONAL	1	TRUE	1	0.780570356269178	2		230	166	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0051301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	372	633	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.780570356269178	2		633	444	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2214516	2214516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	220	636	1	ENST00000398665.3:c.1844C>T	p.Ser615Leu	p.S615L	ENST00000398665	NM_032482.2	615	tCg/tTg	19/28	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.780570356269178	2		637	488	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	113	377	1	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		378	552	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439797	52439798	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0051303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	278	537	0	ENST00000460680.1:c.914_915del	p.Ser305Ter	p.S305*	ENST00000460680	NM_004656.3	305	tCT/t	10/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		537	467	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965568	93965568	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	90	308	0	ENST00000369303.4:c.2360C>T	p.Pro787Leu	p.P787L	ENST00000369303	NM_004440.3	787	cCa/cTa	13/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		308	400	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0051304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	19	210	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.319	0.241	0.41	0.319	0.241	0.41	SUBCLONAL	1	TRUE	1	0.332981233675038	2		210	358	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692900	89692900	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1114167645	NA	P-0051304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	38	290	0	ENST00000371953.3:c.384G>C	p.Lys128Asn	p.K128N	ENST00000371953	NM_000314.4	128	aaG/aaC	5/9	1	2	FACETS	0.593	0.491	0.707	0.593	0.491	0.707	SUBCLONAL	1	TRUE	1	0.332981233675038	2		290	385	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260301	16260302	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0051304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	69	423	0	ENST00000375759.3:c.7567_7568del	p.Lys2523GlyfsTer3	p.K2523Gfs*3	ENST00000375759	NM_015001.2	2522	acAAag/acag	11/15	1	2	FACETS	0.811	0.708	0.922	0.811	0.708	0.922	CLONAL	1	TRUE	1	0.332981233675038	2		423	511	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645418	67645418	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	23	358	0	ENST00000264010.4:c.683T>G	p.Phe228Cys	p.F228C	ENST00000264010	NM_006565.3	228	tTt/tGt	3/12	0.332981233675038	1	FACETS	0.321	0.25	0.403	0.321	0.25	0.403	SUBCLONAL	1	TRUE	0	0.332981233675038	1		358	359	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772275	68772275	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	94	593	0	ENST00000261769.5:c.127del	p.Arg43GlyfsTer13	p.R43Gfs*13	ENST00000261769	NM_004360.3	42	Ccc/cc	2/16	0.332981233675038	1	FACETS	0.932	0.832	1	0.932	0.832	1	CLONAL	1	TRUE	0	0.332981233675038	1		593	505	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206845	36206858	+	frameshift_variant	Frame_Shift_Del	DEL	CGGAAAAGGACAAG	CGGAAAAGGACAAG	-	novel	NA	P-0051304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	71	360	0	ENST00000300305.3:c.654_667del	p.Ser218ArgfsTer5	p.S218Rfs*5	ENST00000300305		218	agCTTGTCCTTTTCCGag/agag	6/8	1	2	FACETS	0.885	0.774	1	0.885	0.774	1	CLONAL	1	TRUE	1	0.332981233675038	2		360	482	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843728	151843728	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	66	318	0	ENST00000262189.6:c.13987C>G	p.Leu4663Val	p.L4663V	ENST00000262189	NM_170606.2	4663	Ctg/Gtg	53/59	1	2	FACETS	0.887	0.772	1	0.887	0.772	1	CLONAL	1	TRUE	1	0.332981233675038	2		318	447	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920590	127920590	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	44	416	0	ENST00000373547.4:c.309G>A	p.Trp103Ter	p.W103*	ENST00000373547	NM_002721.4	103	tgG/tgA	4/7	1	2	FACETS	0.523	0.439	0.617	0.523	0.439	0.617	SUBCLONAL	1	TRUE	1	0.332981233675038	2		416	505	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0051316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	218	396	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.902	0.842	0.963	0.902	0.842	0.963	CLONAL	1	TRUE	1	0.661611821431849	2		396	731	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063717	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0051316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	107	213	0	ENST00000412916.2:c.165+1G>C		p.X55_splice	ENST00000412916		55			0.661611821431849	1	FACETS	0.988	0.908	1	0.988	0.908	1	CLONAL	1	TRUE	0	0.661611821431849	1		213	219	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115718	8115719	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0051316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	150	275	0	ENST00000346208.3:c.1066_1067dup	p.Met356IlefsTer2	p.M356Ifs*2	ENST00000346208		355	act/acTAt	6/6	1	2	FACETS	0.935	0.861	1	0.935	0.861	1	CLONAL	1	TRUE	1	0.661611821431849	2		275	485	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118851	115118851	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0051316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	229	338	1	ENST00000257566.3:c.490A>T	p.Lys164Ter	p.K164*	ENST00000257566	NM_016569.3	164	Aaa/Taa	2/8	1	2	FACETS	0.964	0.902	1	0.964	0.902	1	CLONAL	1	TRUE	1	0.661611821431849	2		339	718	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120142	70120143	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0051316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	281	222	0	ENST00000245479.2:c.1145_1146dup	p.Thr383Ter	p.T383*	ENST00000245479	NM_000346.3	382	ctg/cTGtg	3/3	0.661611821431849	2	FACETS	0.97	0.928	1	0.97	0.928	1	CLONAL	2	TRUE	0	0.661611821431849	2		222	438	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218464	36218464	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	263	529	1	ENST00000222270.7:c.4243C>T	p.Gln1415Ter	p.Q1415*	ENST00000222270	NM_014727.1	1415	Cag/Tag	16/37	1	2	FACETS	0.956	0.898	1	0.956	0.898	1	CLONAL	1	TRUE	1	0.661611821431849	2		530	832	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676198	29676199	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0051347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	166	246	0	ENST00000356175.3:c.7189dup	p.Thr2397AsnfsTer4	p.T2397Nfs*4	ENST00000356175	NM_000267.3	2396	cta/ctAa	48/57	1	2	FACETS	0.965	0.894	1	0.965	0.894	1	CLONAL	1	TRUE	1	0.716737938968041	2		246	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0051379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	180	751	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.196268627901055	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.2628325000645	2		751	613	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039195	49039195	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	227	402	0	ENST00000267163.4:c.2273C>A	p.Ser758Ter	p.S758*	ENST00000267163	NM_000321.2	758	tCg/tAg	22/27	0.25840751925405	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.2628325000645	2		402	794	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477136	67477136	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	190	506	0	ENST00000327367.4:c.943G>T	p.Val315Phe	p.V315F	ENST00000327367	NM_005902.3	315	Gtc/Ttc	7/9	0.257586220552841	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	1	0.2628325000645	3		506	792	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109314067	109314067	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs557313505	NA	P-0051379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	170	424	1	ENST00000436639.2:c.1156C>T	p.Arg386Cys	p.R386C	ENST00000436639	NM_014454.2	386	Cgt/Tgt	7/10	0.2628325000645	3	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	1	0.2628325000645	3		425	725	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136013	64136013	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	79	632	0	ENST00000334205.4:c.1274G>C	p.Cys425Ser	p.C425S	ENST00000334205	NM_003942.2	425	tGt/tCt	11/17	0.255933352269629	3	FACETS	0.959	0.843	1	0.48	0.421	0.542	CLONAL	1	TRUE	1	0.2628325000645	3		632	709	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349516	89349516	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	134	528	0	ENST00000301030.4:c.3434G>T	p.Arg1145Met	p.R1145M	ENST00000301030	NM_001256183.1	1145	aGg/aTg	9/13	0.257586220552841	3	FACETS	0.842	0.767	0.921	0.842	0.767	0.921	CLONAL	2	TRUE	1	0.2628325000645	3		528	685	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353790	40353790	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	154	472	0	ENST00000293328.3:c.2330T>A	p.Met777Lys	p.M777K	ENST00000293328	NM_012448.3	777	aTg/aAg	19/19	0.257586220552841	3	FACETS	0.947	0.869	1	0.947	0.869	1	CLONAL	2	TRUE	1	0.2628325000645	3		472	700	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526099	63526099	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	128	411	0	ENST00000307078.5:c.2527G>T	p.Asp843Tyr	p.D843Y	ENST00000307078	NM_004655.3	843	Gat/Tat	11/11	0.257586220552841	3	FACETS	0.854	0.776	0.936	0.854	0.776	0.936	CLONAL	2	TRUE	1	0.2628325000645	3		411	645	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374418	81374418	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	106	284	0	ENST00000222390.5:c.644A>G	p.Asn215Ser	p.N215S	ENST00000222390	NM_000601.4	215	aAt/aGt	6/18	0.2628325000645	5	FACETS	0.858	0.771	0.951	0.858	0.771	0.951	CLONAL	2	TRUE	3	0.2628325000645	5		284	655	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939546	76939546	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	190	234	0	ENST00000373344.5:c.1202A>G	p.Asp401Gly	p.D401G	ENST00000373344	NM_000489.3	401	gAt/gGt	9/35	0.2628325000645	2	FACETS	1	0.968	1			1	CLONAL	3	TRUE	NA	0.2628325000645	2		234	455	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	88	230	0				ENST00000310581	NM_198253.2	-/1132			0.278026115279523	3	FACETS	1	0.974	1	0.67	0.596	0.75	CLONAL	1	TRUE	1	0.291442247282117	3		230	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0051408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	131	442	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.291442247282117	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.291442247282117	1		442	761	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0051408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	111	408	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	1	2	FACETS	0.982	0.882	1	0.982	0.882	1	CLONAL	1	TRUE	1	0.291442247282117	2		408	776	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012660	36012660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	52	134	0	ENST00000358208.4:c.104C>T	p.Ser35Leu	p.S35L	ENST00000358208		35	tCg/tTg	2/12	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.291442247282117	2		134	289	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518428	204518428	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	61	251	0	ENST00000367182.3:c.1091G>T	p.Arg364Ile	p.R364I	ENST00000367182	NM_001278516.1	364	aGa/aTa	11/11	1	2	FACETS	0.777	0.67	0.892	0.777	0.67	0.892	SUBCLONAL	1	TRUE	1	0.291442247282117	2		251	539	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412958	49412958	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	124	441	1	ENST00000418115.1:c.65T>C	p.Leu22Pro	p.L22P	ENST00000418115	NM_001664.2	22	cTc/cCc	2/5	1	2	FACETS	0.911	0.823	1	0.911	0.823	1	CLONAL	1	TRUE	1	0.291442247282117	2		442	934	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217236	7217236	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs775804583	NA	P-0051408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	155	404	0	ENST00000380728.2:c.469del	p.Gln157LysfsTer188	p.Q157Kfs*188	ENST00000380728		157	Caa/aa	6/11	0.291442247282117	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.291442247282117	1		404	757	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244113	46244113	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	94	275	0	ENST00000334344.6:c.2207G>T	p.Gly736Val	p.G736V	ENST00000334344	NM_152641.2	736	gGa/gTa	15/21	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.291442247282117	2		275	584	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369186	40369186	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	92	354	0	ENST00000293328.3:c.1372C>G	p.Gln458Glu	p.Q458E	ENST00000293328	NM_012448.3	458	Caa/Gaa	11/19	1	2	FACETS	0.996	0.886	1	0.996	0.886	1	CLONAL	1	TRUE	1	0.291442247282117	2		354	634	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628890	187628890	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1420808439	NA	P-0051408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	127	381	0	ENST00000441802.2:c.2092G>C	p.Glu698Gln	p.E698Q	ENST00000441802	NM_005245.3	698	Gag/Cag	2/27	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.291442247282117	2		381	758	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0051449-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	27	408	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.246638354128695	4	FACETS	1	0.89	1	0.591	0.472	0.725	CLONAL	1	FALSE	2	0.246638354128695	4		408	231	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136245	202136245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051449-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	34	506	0	ENST00000358485.4:c.489G>A	p.Met163Ile	p.M163I	ENST00000358485	NM_001080125.1	163	atG/atA	3/9	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	1	0.246638354128695	2		506	222	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577590	7577590	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051449-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	43	587	0	ENST00000269305.4:c.691del	p.Thr231ProfsTer16	p.T231Pfs*16	ENST00000269305	NM_001126112.2	231	Acc/cc	7/11	0.178572122880492	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	0	0.246638354128695	1		587	210	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245660	46245660	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051449-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	26	427	0	ENST00000334344.6:c.3754G>T	p.Glu1252Ter	p.E1252*	ENST00000334344	NM_152641.2	1252	Gaa/Taa	15/21	0.110546672011278	4	FACETS	1	0.93	1	0.726	0.58	0.891	INDETERMINATE	1	FALSE	2	0.246638354128695	4		427	181	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532642	187532642	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051449-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	27	520	0	ENST00000441802.2:c.9751C>T	p.Gln3251Ter	p.Q3251*	ENST00000441802	NM_005245.3	3251	Caa/Taa	14/27	0.246638354128695	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	FALSE	0	0.246638354128695	1		520	156	SUCCESS
APC	324	MSKCC	GRCh37	5	112154762	112154762	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs767126766	NA	P-0051449-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	23	514	0	ENST00000257430.4:c.1033A>G	p.Ile345Val	p.I345V	ENST00000257430	NM_000038.5	345	Ata/Gta	10/16	0.246638354128695	3	FACETS	1	0.871	1	0.582	0.457	0.724	CLONAL	1	FALSE	1	0.246638354128695	3		514	180	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981464	201981471	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTTGTCAG	CTTGTCAG	-	novel	NA	P-0051529-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	147	642	0	ENST00000359651.3:c.386-5_388del		p.X129_splice	ENST00000359651		129			0.269515429704162	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.330173791218877	4		642	480	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981565	201981565	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0051529-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	158	806	0	ENST00000359651.3:c.478+1G>C		p.X160_splice	ENST00000359651		160			0.269515429704162	4	FACETS	0.863	0.792	0.936	0.863	0.792	0.936	CLONAL	2	TRUE	2	0.330173791218877	4		806	738	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111965564	111965564	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051529-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	32	222	0	ENST00000375549.3:c.350G>C	p.Gly117Ala	p.G117A	ENST00000375549	NM_003002.3	117	gGg/gCg	4/4	0.298712860256415	3	FACETS	1	0.862	1	0.533	0.435	0.641	CLONAL	1	TRUE	1	0.330173791218877	3		222	212	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533469	63533469	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051529-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	164	808	0	ENST00000307078.5:c.1685C>G	p.Pro562Arg	p.P562R	ENST00000307078	NM_004655.3	562	cCg/cGg	6/11	0.330173791218877	3	FACETS	0.757	0.696	0.821	0.757	0.696	0.821	SUBCLONAL	2	TRUE	1	0.330173791218877	3		808	764	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593387	48593387	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0051529-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	59	279	0	ENST00000342988.3:c.1140-2A>T		p.X380_splice	ENST00000342988	NM_005359.5	380			0.330173791218877	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.330173791218877	1		279	218	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056404	26056404	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051529-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	106	405	0	ENST00000343677.2:c.253A>G	p.Lys85Glu	p.K85E	ENST00000343677	NM_005319.3	85	Aag/Gag	1/1	0.330173791218877	4	FACETS	0.934	0.843	1	0.934	0.843	1	CLONAL	2	TRUE	2	0.330173791218877	4		405	457	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850333	128850333	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051529-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	85	700	0	ENST00000249373.3:c.1596G>C	p.Met532Ile	p.M532I	ENST00000249373	NM_005631.4	532	atG/atC	9/12	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.330173791218877	2		700	500	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934301	68934301	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051529-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	92	485	0	ENST00000288368.4:c.367T>A	p.Cys123Ser	p.C123S	ENST00000288368	NM_024870.2	123	Tgt/Agt	4/40	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.330173791218877	2		485	493	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970955	21971355	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCGCAGCCGCGCGCAGGTACCGTGCGACATCGCGATGGCCCAGCTCCTCAGCCAGGTCCACGGGCAGACGGCCCCAGGCATCGCGCACGTCCAGCCGCGCCCCGGCCCGGTGCAGCACCACCAGCGTGTCCAGGAAGCCCTCCCGGGCAGCGTCGTGCACGGGTCGGGTGAGAGTGGCGGGGTCGGCGCAGTTGGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCTGCCCATCATCATGACCTGCCAGAGAGAACAGAATGGTCAGAGCCAGGGTGGGGGCCGGCATGACGGAAAGGAAGCTTGTGTAGAGCCCCCTCACCGCCAAGCAGACCCCCACACAAGCCCCAGGTGTCTAATTACCCCTACATTTGCTTCCAGTTTCCAATTT	CCGCAGCCGCGCGCAGGTACCGTGCGACATCGCGATGGCCCAGCTCCTCAGCCAGGTCCACGGGCAGACGGCCCCAGGCATCGCGCACGTCCAGCCGCGCCCCGGCCCGGTGCAGCACCACCAGCGTGTCCAGGAAGCCCTCCCGGGCAGCGTCGTGCACGGGTCGGGTGAGAGTGGCGGGGTCGGCGCAGTTGGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCTGCCCATCATCATGACCTGCCAGAGAGAACAGAATGGTCAGAGCCAGGGTGGGGGCCGGCATGACGGAAAGGAAGCTTGTGTAGAGCCCCCTCACCGCCAAGCAGACCCCCACACAAGCCCCAGGTGTCTAATTACCCCTACATTTGCTTCCAGTTTCCAATTT	-	novel	NA	P-0051529-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	143	814	0	ENST00000304494.5:c.151-148_403del		p.X51_splice	ENST00000304494	NM_000077.4	51		2/3	0.330173791218877	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.330173791218877	1		814	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0051571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	442	547	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.467583217969724	2	FACETS	0.978	0.937	1	0.978	0.937	1	CLONAL	2	TRUE	0	0.476972651218419	2		547	948	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341230	341230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756690670	NA	P-0051571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	225	584	2	ENST00000262320.3:c.2254G>A	p.Val752Met	p.V752M	ENST00000262320	NM_003502.3	752	Gtg/Atg	9/11	0.476972651218419	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.476972651218419	1		586	632	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006685	62006685	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0051571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	60	560	1	ENST00000392795.3:c.595-1G>T		p.X199_splice	ENST00000392795	NM_001039933.1	199			0.476972651218419	3	FACETS	0.369	0.317	0.426	0.123	0.105	0.142	SUBCLONAL	1	TRUE	0	0.476972651218419	3		561	845	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980921	40980921	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	112	314	0	ENST00000373198.4:c.1565A>C	p.Asn522Thr	p.N522T	ENST00000373198	NM_133170.3	522	aAc/aCc	10/32	1	2	FACETS	0.987	0.892	1	0.987	0.892	1	CLONAL	1	TRUE	1	0.476972651218419	2		314	476	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0051572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	17	254	0	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	0.817999280649681	1	FACETS	0.076	0.056	0.1	0.076	0.056	0.1	SUBCLONAL	1	TRUE	0	0.817999280649681	1		254	323	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741837	17741837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199584989	NA	P-0051572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	78	169	0	ENST00000250003.3:c.508G>A	p.Ala170Thr	p.A170T	ENST00000250003	NM_002478.4	170	Gcg/Acg	1/3	1	2	FACETS	0.978	0.878	1	0.978	0.878	1	CLONAL	1	TRUE	1	0.817999280649681	2		169	195	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024671	11024671	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	233	477	1	ENST00000327064.4:c.788T>A	p.Leu263His	p.L263H	ENST00000327064	NM_199141.1	263	cTc/cAc	6/16	1	2	FACETS	0.962	0.904	1	0.962	0.904	1	CLONAL	1	TRUE	1	0.817999280649681	2		478	592	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	129	230	0				ENST00000310581	NM_198253.2	-/1132			0.702385185668172	1	FACETS	0.906	0.839	0.974	0.906	0.839	0.974	CLONAL	1	TRUE	0	0.702385185668172	1		230	263	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	149	299	0				ENST00000310581	NM_198253.2	-/1132			0.702385185668172	1	FACETS	0.952	0.888	1	0.952	0.888	1	CLONAL	1	TRUE	0	0.702385185668172	1		299	289	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	9	396	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.702385185668172	2	FACETS	0.089	0.058	0.128	0.044	0.029	0.064	SUBCLONAL	1	TRUE	0	0.702385185668172	2		396	289	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212495	133212495	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879254168	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	189	372	0	ENST00000320574.5:c.5794C>T	p.Arg1932Cys	p.R1932C	ENST00000320574	NM_006231.2	1932	Cgt/Tgt	42/49	1	2	FACETS	0.912	0.848	0.978	0.912	0.848	0.978	CLONAL	1	TRUE	1	0.702385185668172	2		372	590	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498444	89498444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	148	369	0	ENST00000336596.2:c.2416G>A	p.Asp806Asn	p.D806N	ENST00000336596	NM_005233.5	806	Gat/Aat	14/17	1	2	FACETS	0.928	0.855	1	0.928	0.855	1	CLONAL	1	TRUE	1	0.702385185668172	2		369	454	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	14	432	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	1	2	FACETS	0.09	0.065	0.122	0.09	0.065	0.122	SUBCLONAL	1	TRUE	1	0.702385185668172	2		432	441	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770597	40770597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761441812	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	179	441	0	ENST00000373198.4:c.2785G>A	p.Asp929Asn	p.D929N	ENST00000373198	NM_133170.3	929	Gat/Aat	19/32	1	2	FACETS	0.92	0.854	0.988	0.92	0.854	0.988	CLONAL	1	TRUE	1	0.702385185668172	2		441	554	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841545	156841545	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	926	613	0	ENST00000524377.1:c.848C>T	p.Ser283Phe	p.S283F	ENST00000524377	NM_002529.3	283	tCc/tTc	7/17	0.631502646719412	5	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	2	0.702385185668172	5		613	1770	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943349	17943349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759015510	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	601	548	0	ENST00000458235.1:c.2659C>T	p.Arg887Cys	p.R887C	ENST00000458235	NM_000215.3	887	Cgt/Tgt	19/24	0.702385185668172	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.702385185668172	3		548	1098	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805178	43805178	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	251	522	0	ENST00000372470.3:c.628C>T	p.Pro210Ser	p.P210S	ENST00000372470	NM_005373.2	210	Cca/Tca	4/12	1	2	FACETS	0.952	0.894	1	0.952	0.894	1	CLONAL	1	TRUE	1	0.702385185668172	2		522	751	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950487	68950487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138740482	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	139	367	0	ENST00000288368.4:c.799C>T	p.Leu267Phe	p.L267F	ENST00000288368	NM_024870.2	267	Ctt/Ttt	7/40	0.702385185668172	3	FACETS	0.804	0.734	0.878	0.402	0.367	0.439	CLONAL	1	TRUE	1	0.702385185668172	3		367	665	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211154	36211154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	549	704	0	ENST00000222270.7:c.905C>T	p.Pro302Leu	p.P302L	ENST00000222270	NM_014727.1	302	cCc/cTc	3/37	0.260893526187633	3	FACETS	0.913	0.879	0.947	0.913	0.879	0.947	INDETERMINATE	2	TRUE	1	0.702385185668172	3		704	1157	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790000	40790000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159843	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	228	435	1	ENST00000373198.4:c.2731G>A	p.Glu911Lys	p.E911K	ENST00000373198	NM_133170.3	911	Gaa/Aaa	18/32	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.702385185668172	2		436	641	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858195	40858195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777686988	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	513	512	0	ENST00000428826.2:c.1669C>T	p.Arg557Cys	p.R557C	ENST00000428826		557	Cgt/Tgt	16/21	0.702385185668172	3	FACETS	0.968	0.932	1	0.968	0.932	1	CLONAL	2	TRUE	1	0.702385185668172	3		512	1019	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978414	2978414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	303	593	0	ENST00000396946.4:c.916G>A	p.Glu306Lys	p.E306K	ENST00000396946	NM_032415.4	306	Gaa/Aaa	7/25	1	2	FACETS	0.983	0.929	1	0.983	0.929	1	CLONAL	1	TRUE	1	0.702385185668172	2		593	878	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419974	41419974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	271	508	0	ENST00000373198.4:c.347G>A	p.Ser116Asn	p.S116N	ENST00000373198	NM_133170.3	116	aGc/aAc	3/32	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.702385185668172	2		508	730	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670529	134670529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	582	615	1	ENST00000398015.3:c.440C>T	p.Ser147Phe	p.S147F	ENST00000398015	NM_004441.4	147	tCc/tTc	3/16	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.702385185668172	2		616	813	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089777	27089777	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	40	421	0	ENST00000324856.7:c.2732+1G>A		p.X911_splice	ENST00000324856	NM_006015.4	911			1	2	FACETS	0.195	0.161	0.232	0.195	0.161	0.232	SUBCLONAL	1	TRUE	1	0.702385185668172	2		421	585	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281364	15281364	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1487491390	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	195	426	0	ENST00000263388.2:c.4892G>A	p.Gly1631Glu	p.G1631E	ENST00000263388	NM_000435.2	1631	gGg/gAg	27/33	0.702385185668172	3	FACETS	0.799	0.74	0.861	0.399	0.37	0.431	SUBCLONAL	1	TRUE	1	0.702385185668172	3		426	939	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069640	69069640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	128	502	0	ENST00000288368.4:c.4315G>A	p.Glu1439Lys	p.E1439K	ENST00000288368	NM_024870.2	1439	Gaa/Aaa	35/40	0.702385185668172	3	FACETS	0.962	0.876	1	0.481	0.438	0.526	CLONAL	1	TRUE	1	0.702385185668172	3		502	512	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198260870	198260870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	165	449	0	ENST00000335508.6:c.3449C>T	p.Ser1150Leu	p.S1150L	ENST00000335508	NM_012433.2	1150	tCg/tTg	23/25	1	2	FACETS	0.969	0.897	1	0.969	0.897	1	CLONAL	1	TRUE	1	0.702385185668172	2		449	485	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073797	8073797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	149	352	0	ENST00000377482.5:c.862C>T	p.Pro288Ser	p.P288S	ENST00000377482	NM_018948.3	288	Ccc/Tcc	4/4	1	2	FACETS	0.914	0.842	0.989	0.914	0.842	0.989	CLONAL	1	TRUE	1	0.702385185668172	2		352	464	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609660	117609660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	133	320	0	ENST00000368508.3:c.7039G>A	p.Asp2347Asn	p.D2347N	ENST00000368508	NM_002944.2	2347	Gat/Aat	43/43	0.699694871478993	1	FACETS	0.971	0.902	1	0.971	0.902	1	CLONAL	1	TRUE	0	0.702385185668172	1		320	253	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669529	88669529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	220	436	0	ENST00000360948.2:c.1369G>A	p.Gly457Ser	p.G457S	ENST00000360948	NM_001012338.2	457	Ggt/Agt	12/19	1	2	FACETS	0.958	0.896	1	0.958	0.896	1	CLONAL	1	TRUE	1	0.702385185668172	2		436	654	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154225	2154225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1014211286	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	238	534	0	ENST00000434045.2:c.703C>T	p.Arg235Trp	p.R235W	ENST00000434045	NM_001127598.1	235	Cgg/Tgg	5/5	1	2	FACETS	0.913	0.856	0.972	0.913	0.856	0.972	CLONAL	1	TRUE	1	0.702385185668172	2		534	742	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422736	49422736	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1332350348	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	211	462	0	ENST00000301067.7:c.14257C>T	p.Pro4753Ser	p.P4753S	ENST00000301067	NM_003482.3	4753	Cca/Tca	45/54	1	2	FACETS	0.966	0.903	1	0.966	0.903	1	CLONAL	1	TRUE	1	0.702385185668172	2		462	622	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005353	42005353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	180	325	0	ENST00000219905.7:c.3089C>T	p.Ser1030Phe	p.S1030F	ENST00000219905	NM_001164273.1	1030	tCc/tTc	9/24	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.702385185668172	2		325	512	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032405	10032405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	143	311	0	ENST00000330684.3:c.418C>T	p.Pro140Ser	p.P140S	ENST00000330684	NM_001134407.1	140	Ccg/Tcg	3/13	0.699327305385642	2	FACETS	0.986	0.908	1	0.493	0.454	0.533	CLONAL	1	TRUE	0	0.702385185668172	2		311	413	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50811774	50811774	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	103	369	0	ENST00000398568.2:c.1051T>A	p.Leu351Ile	p.L351I	ENST00000398568	NM_001042412.1	351	Tta/Ata	7/18	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.702385185668172	2		369	268	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579433	7579433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	322	541	1	ENST00000269305.4:c.254C>T	p.Pro85Leu	p.P85L	ENST00000269305	NM_001126112.2	85	cCt/cTt	4/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.702385185668172	2		542	829	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687342	37687342	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	228	473	0	ENST00000447079.4:c.4246G>T	p.Val1416Phe	p.V1416F	ENST00000447079	NM_015083.1	1416	Gtc/Ttc	14/14	0.702385185668172	3	FACETS	1	0.948	1	0.509	0.475	0.544	CLONAL	1	TRUE	1	0.702385185668172	3		473	862	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110636	4110653	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GATCTCAAGGTGGATCAG	GATCTCAAGGTGGATCAG	-	novel	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	501	472	0	ENST00000262948.5:c.304_321del	p.Leu102_Ile107del	p.L102_I107del	ENST00000262948	NM_030662.3	102	CTGATCCACCTTGAGATC/-	3/11	0.702385185668172	3	FACETS	0.987	0.951	1	0.987	0.951	1	CLONAL	2	TRUE	1	0.702385185668172	3		472	976	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212132	36212132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	265	371	0	ENST00000222270.7:c.1883C>T	p.Pro628Leu	p.P628L	ENST00000222270	NM_014727.1	628	cCc/cTc	3/37	0.260893526187633	3	FACETS	0.87	0.823	0.917	0.87	0.823	0.917	INDETERMINATE	2	TRUE	1	0.702385185668172	3		371	586	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868179	45868179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	383	605	1	ENST00000391945.4:c.511C>T	p.Pro171Ser	p.P171S	ENST00000391945	NM_000400.3	171	Ccc/Tcc	7/23	0.260893526187633	3	FACETS	0.811	0.773	0.848	0.811	0.773	0.848	INDETERMINATE	2	TRUE	1	0.702385185668172	3		606	909	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52709266	52709266	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	324	513	0	ENST00000322088.6:c.220G>A	p.Gly74Arg	p.G74R	ENST00000322088	NM_014225.5	74	Gga/Aga	3/15	0.260893526187633	3	FACETS	0.787	0.747	0.827	0.787	0.747	0.827	INDETERMINATE	2	TRUE	1	0.702385185668172	3		513	792	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561038	9561038	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1192887616	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	178	368	0	ENST00000353224.5:c.744G>C	p.Glu248Asp	p.E248D	ENST00000353224	NM_177990.2	248	gaG/gaC	4/10	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.702385185668172	2		368	505	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264421	46264421	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	183	455	0	ENST00000371998.3:c.1468C>T	p.Pro490Ser	p.P490S	ENST00000371998		490	Cca/Tca	11/23	1	2	FACETS	0.877	0.814	0.942	0.877	0.814	0.942	CLONAL	1	TRUE	1	0.702385185668172	2		455	594	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662417	117662417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	187	457	0	ENST00000368508.3:c.4960G>A	p.Glu1654Lys	p.E1654K	ENST00000368508	NM_002944.2	1654	Gaa/Aaa	30/43	0.699694871478993	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.702385185668172	1		457	342	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	163148693	163148693	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs397518439	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	160	280	0	ENST00000366898.1:c.7+1G>T		p.X3_splice	ENST00000366898	NM_004562.2	3			0.699694871478993	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.702385185668172	1		280	285	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370817	55370817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	339	379	0	ENST00000297316.4:c.119G>A	p.Gly40Glu	p.G40E	ENST00000297316	NM_022454.3	40	gGg/gAg	1/2	0.702385185668172	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.702385185668172	3		379	637	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465467	8465467	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	153	364	0	ENST00000356435.5:c.3713C>T	p.Ser1238Phe	p.S1238F	ENST00000356435		1238	tCt/tTt	21/35	0.702385185668172	2	FACETS	0.939	0.866	1	0.469	0.433	0.507	CLONAL	1	TRUE	0	0.702385185668172	2		364	464	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504261	8504261	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	342	358	0	ENST00000356435.5:c.1822A>T	p.Lys608Ter	p.K608*	ENST00000356435		608	Aag/Tag	12/35	0.702385185668172	2	FACETS	0.964	0.928	0.999	0.964	0.928	0.999	CLONAL	2	TRUE	0	0.702385185668172	2		358	505	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606220	93606220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	239	492	0	ENST00000375746.1:c.40C>T	p.Pro14Ser	p.P14S	ENST00000375746	NM_001174167.1	14	Ccc/Tcc	2/14	1	2	FACETS	0.943	0.884	1	0.943	0.884	1	CLONAL	1	TRUE	1	0.702385185668172	2		492	722	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650137	93650138	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0051574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	182	509	1	ENST00000375746.1:c.1688_1689delinsAA	p.Trp563Ter	p.W563*	ENST00000375746	NM_001174167.1	563	tGG/tAA	12/14	1	2	FACETS	0.814	0.754	0.875	0.814	0.754	0.875	CLONAL	1	TRUE	1	0.702385185668172	2		510	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578502	7578502	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	318	488	0	ENST00000269305.4:c.428T>C	p.Val143Ala	p.V143A	ENST00000269305	NM_001126112.2	143	gTg/gCg	5/11	0.47262593636919	2	FACETS	0.798	0.757	0.84	0.798	0.757	0.84	SUBCLONAL	2	TRUE	0	0.504240049837952	2		488	790	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101976	11101976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555757709	NA	P-0051575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	175	535	0	ENST00000358026.2:c.1396C>T	p.Arg466Cys	p.R466C	ENST00000358026	NM_001128849.1	466	Cgc/Tgc	8/36	1	2	FACETS	0.872	0.804	0.942	0.872	0.804	0.942	CLONAL	1	TRUE	1	0.504240049837952	2		535	796	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057318	30057318	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	28	254	2	ENST00000338641.4:c.800G>A	p.Ser267Asn	p.S267N	ENST00000338641	NM_000268.3	267	aGt/aAt	8/16	0.47262593636919	2	FACETS	0.237	0.189	0.292	0.118	0.094	0.146	SUBCLONAL	1	TRUE	0	0.504240049837952	2		256	469	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0051578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	38	283	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.898	0.749	1	0.898	0.749	1	CLONAL	1	TRUE	1	0.395453670719892	2		283	214	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937648	76937648	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	25	423	1	ENST00000373344.5:c.3100C>A	p.Gln1034Lys	p.Q1034K	ENST00000373344	NM_000489.3	1034	Caa/Aaa	9/35	0.395453670719892	1	FACETS	0.537	0.426	0.662	0.537	0.426	0.662	SUBCLONAL	1	TRUE	0	0.395453670719892	1		424	189	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274775	123274792	+	inframe_deletion	In_Frame_Del	DEL	GTAAATGGCTATCTCCAG	GTAAATGGCTATCTCCAG	-	novel	NA	P-0051578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	130	540	0	ENST00000358487.5:c.1126_1143del	p.Leu376_Tyr381del	p.L376_Y381del	ENST00000358487	NM_000141.4	376	CTGGAGATAGCCATTTAC/-	9/18	0.290232223035801	2	FACETS	1	0.985	1	0.708	0.647	0.772	CLONAL	1	TRUE	0	0.395453670719892	2		540	464	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696689	47696689	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519972	NA	P-0051589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	116	457	0	ENST00000347630.2:c.259T>A	p.Tyr87Asn	p.Y87N	ENST00000347630	NM_001007230.1	87	Tac/Aac	5/11	1	2	FACETS	0.912	0.824	1	1	0.988	1	CLONAL	2	TRUE	1	0.21	2		457	606	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445005	89445005	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112239794	NA	P-0051589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	45	388	0	ENST00000336596.2:c.1325C>T	p.Thr442Met	p.T442M	ENST00000336596	NM_005233.5	442	aCg/aTg	6/17	1	2	FACETS	0.747	0.627	0.879	0.747	0.627	0.879	SUBCLONAL	1	TRUE	1	0.21	2		388	574	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5070053	5070054	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0051589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	16	282	0	ENST00000381652.3:c.1641+2dup		p.X547_splice	ENST00000381652	NM_004972.3	547			1	2	FACETS	0.55	0.406	0.722	0.55	0.406	0.722	SUBCLONAL	1	TRUE	1	0.21	2		282	277	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0051604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	278	578	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.316881426409062	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.324612542922206	4		578	986	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0051604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	271	408	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.321809017691096	4	FACETS	0.991	0.934	1	0.991	0.934	1	CLONAL	3	TRUE	1	0.324612542922206	4		408	744	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0051604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	252	562	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.324612542922206	2	FACETS	0.988	0.927	1	0.988	0.927	1	CLONAL	2	TRUE	0	0.324612542922206	2		562	786	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032318	11032318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1422712222	NA	P-0051604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	247	546	0	ENST00000327064.4:c.1712G>A	p.Gly571Asp	p.G571D	ENST00000327064	NM_199141.1	571	gGt/gAt	16/16	0.181689804318626	5	FACETS	1	0.981	1	0.746	0.698	0.796	INDETERMINATE	2	TRUE	2	0.324612542922206	5		546	1011	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31511281	31511281	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	210	449	0	ENST00000344624.3:c.1293del	p.Asp432IlefsTer46	p.D432Ifs*46	ENST00000344624		431	ggA/gg	6/33	0.324612542922206	5	FACETS	0.938	0.87	1			1	CLONAL	2	TRUE	NA	0.324612542922206	5		449	1026	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321655	30321655	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051607-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	386	423	0	ENST00000322652.5:c.1510C>T	p.Gln504Ter	p.Q504*	ENST00000322652	NM_015355.2	504	Cag/Tag	13/16	0.810187045220032	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.810187045220032	2		423	470	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56171024	56171024	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051607-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	285	224	0	ENST00000399503.3:c.1852G>T	p.Ala618Ser	p.A618S	ENST00000399503	NM_005921.1	618	Gcc/Tcc	10/20	0.744583451192065	3	FACETS	0.963	0.918	1	0.963	0.918	1	CLONAL	2	TRUE	1	0.810187045220032	3		224	513	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216782	7216782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324992597	NA	P-0051674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	25	452	0	ENST00000380728.2:c.641C>T	p.Ser214Leu	p.S214L	ENST00000380728		214	tCg/tTg	8/11	0.383608328950555	1	FACETS	0.234	0.183	0.291	0.234	0.183	0.291	SUBCLONAL	1	TRUE	0	0.383608328950555	1		452	451	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115854	8115855	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCCTCCCTGAGCCACATCTCGCCCTTCAGCCACTCCAGCCACATGCTGACCACGCCCACGCCGA	novel	NA	P-0051674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	39	531	0	ENST00000346208.3:c.1202_1265dup	p.Met422IlefsTer106	p.M422Ifs*106	ENST00000346208		400	-/TCCTCCCTGAGCCACATCTCGCCCTTCAGCCACTCCAGCCACATGCTGACCACGCCCACGCCGA	6/6	1	2	FACETS	0.28	0.231	0.334	0.28	0.231	0.334	SUBCLONAL	1	TRUE	1	0.383608328950555	2		531	727	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216401	7216401	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756358952	NA	P-0051674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	103	680	1	ENST00000380728.2:c.847C>T	p.Pro283Ser	p.P283S	ENST00000380728		283	Cct/Tct	10/11	0.383608328950555	1	FACETS	0.612	0.548	0.68	0.612	0.548	0.68	SUBCLONAL	1	TRUE	0	0.383608328950555	1		681	709	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734129	58734129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1271913502	NA	P-0051680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	90	399	0	ENST00000305921.3:c.1187C>T	p.Thr396Ile	p.T396I	ENST00000305921	NM_003620.3	396	aCt/aTt	5/6	0.899562010848206	4	FACETS	0.999	0.893	1	0.499	0.446	0.555	CLONAL	1	FALSE	2	0.991425553899897	4		399	362	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	182	299	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.650513391074602	2		299	397	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	38	520	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.183	0.151	0.22	0.183	0.151	0.22	SUBCLONAL	1	TRUE	1	0.650513391074602	2		520	637	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928067	178928093	+	inframe_deletion	In_Frame_Del	DEL	CCTCATGGATTAGAAGATTTGCTGAAC	CCTCATGGATTAGAAGATTTGCTGAAC	-	novel	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	248	389	0	ENST00000263967.3:c.1348_1374del	p.His450_Pro458del	p.H450_P458del	ENST00000263967	NM_006218.2	449	CCTCATGGATTAGAAGATTTGCTGAAC/-	8/21	0.31925013287932	3	FACETS	0.778	0.733	0.825	0.778	0.733	0.825	INDETERMINATE	2	TRUE	1	0.650513391074602	3		389	649	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	259	455	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.650513391074602	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.650513391074602	1		455	518	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	42	255	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	1	1	FACETS	0.293	0.246	0.346	0.293	0.246	0.346	SUBCLONAL	1	TRUE	0	0.650513391074602	1		255	297	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	371	564	0	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.650513391074602	2		564	838	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874261	155874261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352822	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	58	399	0	ENST00000368323.3:c.270G>A	p.Met90Ile	p.M90I	ENST00000368323	NM_006912.5	90	atG/atA	5/6	0.574376397337486	3	FACETS	0.281	0.24	0.325	0.14	0.12	0.163	SUBCLONAL	1	TRUE	1	0.650513391074602	3		399	842	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263948	16263948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1289724532	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	293	706	0	ENST00000375759.3:c.10317G>A	p.Met3439Ile	p.M3439I	ENST00000375759	NM_015001.2	3439	atG/atA	12/15	1	2	FACETS	0.93	0.876	0.984	0.93	0.876	0.984	CLONAL	1	TRUE	1	0.650513391074602	2		706	969	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514032	69514032	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	novel	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	286	447	0	ENST00000294312.3:c.649T>C	p.Ter217GlnextTer29	p.*217Qext*29	ENST00000294312	NM_005117.2	217	Taa/Caa	3/3	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.650513391074602	2		447	692	SUCCESS
EED	8726	MSKCC	GRCh37	11	85956291	85956291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369888376	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	126	212	0	ENST00000263360.6:c.20C>T	p.Ser7Leu	p.S7L	ENST00000263360	NM_003797.3	7	tCg/tTg	1/12	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.650513391074602	2		212	355	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236211	108236211	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	211	431	0	ENST00000278616.4:c.9147C>A	p.Phe3049Leu	p.F3049L	ENST00000278616	NM_000051.3	3049	ttC/ttA	63/63	1	2	FACETS	0.891	0.831	0.953	0.891	0.831	0.953	CLONAL	1	TRUE	1	0.650513391074602	2		431	728	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416788	416788	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	139	277	0	ENST00000399788.2:c.3762G>A	p.Met1254Ile	p.M1254I	ENST00000399788	NM_001042603.1	1254	atG/atA	23/28	1	2	FACETS	0.969	0.89	1	0.969	0.89	1	CLONAL	1	TRUE	1	0.650513391074602	2		277	441	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11803068	11803068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	35	208	0	ENST00000396373.4:c.7G>A	p.Glu3Lys	p.E3K	ENST00000396373	NM_001987.4	3	Gag/Aag	1/8	1	2	FACETS	0.267	0.219	0.321	0.267	0.219	0.321	SUBCLONAL	1	TRUE	1	0.650513391074602	2		208	403	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422925	49422925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1275148461	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	74	601	1	ENST00000301067.7:c.14170C>T	p.His4724Tyr	p.H4724Y	ENST00000301067	NM_003482.3	4724	Cat/Tat	44/54	1	2	FACETS	0.27	0.236	0.307	0.27	0.236	0.307	SUBCLONAL	1	TRUE	1	0.650513391074602	2		602	842	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582825	95582825	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	106	217	0	ENST00000393063.1:c.1717G>A	p.Glu573Lys	p.E573K	ENST00000393063	NM_030621.3	573	Gaa/Aaa	11/28	1	2	FACETS	0.871	0.788	0.958	0.871	0.788	0.958	CLONAL	1	TRUE	1	0.650513391074602	2		217	374	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295148	91295148	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs753911420	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	142	271	0	ENST00000355112.3:c.931G>T	p.Ala311Ser	p.A311S	ENST00000355112	NM_000057.2	311	Gct/Tct	4/22	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.650513391074602	2		271	382	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434864	99434864	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	234	405	0	ENST00000268035.6:c.951G>C	p.Gln317His	p.Q317H	ENST00000268035	NM_000875.3	317	caG/caC	3/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.650513391074602	2		405	669	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	76	377	1	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	1	2	FACETS	0.401	0.352	0.454	0.401	0.352	0.454	SUBCLONAL	1	TRUE	1	0.650513391074602	2		378	583	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847234	68847234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	187	357	0	ENST00000261769.5:c.1156G>A	p.Glu386Lys	p.E386K	ENST00000261769	NM_004360.3	386	Gag/Aag	9/16	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.650513391074602	2		357	558	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618638	37618638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	172	378	0	ENST00000447079.4:c.314G>A	p.Ser105Asn	p.S105N	ENST00000447079	NM_015083.1	105	aGc/aAc	1/14	1	2	FACETS	0.902	0.835	0.972	0.902	0.835	0.972	CLONAL	1	TRUE	1	0.650513391074602	2		378	586	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222829	5222829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	209	443	0	ENST00000357368.4:c.2974G>A	p.Glu992Lys	p.E992K	ENST00000357368	NM_002850.3	992	Gag/Aag	18/38	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.650513391074602	2		443	612	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279766	46279766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	205	385	1	ENST00000371998.3:c.3692G>A	p.Arg1231Lys	p.R1231K	ENST00000371998		1231	aGa/aAa	20/23	1	2	FACETS	0.961	0.896	1	0.961	0.896	1	CLONAL	1	TRUE	1	0.650513391074602	2		386	656	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130391	29130391	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs775320614	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	175	338	0	ENST00000328354.6:c.319G>A	p.Glu107Lys	p.E107K	ENST00000328354	NM_007194.3	107	Gaa/Aaa	2/15	1	2	FACETS	0.978	0.907	1	0.978	0.907	1	CLONAL	1	TRUE	1	0.650513391074602	2		338	550	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723626	49723626	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	100	212	0	ENST00000449682.2:c.1017-1G>C		p.X339_splice	ENST00000449682	NM_020998.3	339			1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.650513391074602	2		212	288	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440379	52440379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	276	441	1	ENST00000460680.1:c.673G>A	p.Asp225Asn	p.D225N	ENST00000460680	NM_004656.3	225	Gac/Aac	9/17	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.650513391074602	2		442	695	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281357	142281357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	59	412	0	ENST00000350721.4:c.887C>T	p.Ser296Leu	p.S296L	ENST00000350721	NM_001184.3	296	tCa/tTa	4/47	1	2	FACETS	0.279	0.24	0.323	0.279	0.24	0.323	SUBCLONAL	1	TRUE	1	0.650513391074602	2		412	649	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	234	799	2	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.650513391074602	2		801	631	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530399	187530399	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	175	300	0	ENST00000441802.2:c.10144T>C	p.Ser3382Pro	p.S3382P	ENST00000441802	NM_005245.3	3382	Tcg/Ccg	16/27	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.650513391074602	2		300	494	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940147	31940147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	84	509	0	ENST00000375333.2:c.289C>T	p.Leu97Phe	p.L97F	ENST00000375333	NM_032454.1	97	Ctc/Ttc	2/8	1	2	FACETS	0.278	0.244	0.313	0.278	0.244	0.313	SUBCLONAL	1	TRUE	1	0.650513391074602	2		509	930	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547247	106547247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	201	290	0	ENST00000369096.4:c.484G>A	p.Val162Met	p.V162M	ENST00000369096	NM_001198.3	162	Gtg/Atg	4/7	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.650513391074602	2		290	457	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004942	150004942	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	36	326	0	ENST00000253339.5:c.1283G>A	p.Gly428Glu	p.G428E	ENST00000253339		428	gGa/gAa	3/7	1	2	FACETS	0.197	0.162	0.237	0.197	0.162	0.237	SUBCLONAL	1	TRUE	1	0.650513391074602	2		326	561	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8497269	8497269	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	36	236	0	ENST00000356435.5:c.2323-1G>A		p.X775_splice	ENST00000356435		775			1	2	FACETS	0.302	0.248	0.361	0.302	0.248	0.361	SUBCLONAL	1	TRUE	1	0.650513391074602	2		236	367	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918295	44918295	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	219	200	0	ENST00000377967.4:c.920A>G	p.Tyr307Cys	p.Y307C	ENST00000377967	NM_021140.2	307	tAc/tGc	11/29	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.650513391074602	1		200	357	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44919349	44919349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	144	160	0	ENST00000377967.4:c.1277C>T	p.Pro426Leu	p.P426L	ENST00000377967	NM_021140.2	426	cCa/cTa	13/29	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.650513391074602	1		160	218	SUCCESS
AR	367	MSKCC	GRCh37	X	66765625	66765625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1480539040	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	373	368	0	ENST00000374690.3:c.637G>A	p.Glu213Lys	p.E213K	ENST00000374690	NM_000044.3	213	Gag/Aag	1/8	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.650513391074602	1		368	535	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202465	123202465	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	149	187	0	ENST00000218089.9:c.2317C>T	p.Gln773Ter	p.Q773*	ENST00000218089	NM_001042749.1	773	Caa/Taa	24/35	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.650513391074602	1		187	260	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427027	49427042	+	stop_gained	Nonsense_Mutation	DEL	GGGGGCCCAAAGCTCC	GGGGGCCCAAAGCTCC	A	novel	NA	P-0051682-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	51	497	0	ENST00000301067.7:c.11446_11461delinsT	p.Gly3816_Gln3821delinsTer	p.G3816_Q3821delins*	ENST00000301067	NM_003482.3	3816	GGAGCTTTGGGCCCCCag/Tag	39/54	1	2	FACETS	0.234	0.198	0.273	0.234	0.198	0.273	SUBCLONAL	1	TRUE	1	0.650513391074602	2		497	670	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0051683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	32	403	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.206991782863088	3	FACETS	0.752	0.61	0.912	0.376	0.305	0.456	CLONAL	1	FALSE	1	0.225392298414794	3		403	420	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923504	9923504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs565111836	NA	P-0051683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	24	297	0	ENST00000330684.3:c.1783C>T	p.His595Tyr	p.H595Y	ENST00000330684	NM_001134407.1	595	Cat/Tat	9/13	1	2	FACETS	0.59	0.462	0.737	0.59	0.462	0.737	SUBCLONAL	1	FALSE	1	0.225392298414794	2		297	361	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836600	89836600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751572448	NA	P-0051683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	78	635	8	ENST00000389301.3:c.2290C>T	p.Arg764Trp	p.R764W	ENST00000389301	NM_000135.2	764	Cgg/Tgg	25/43	1	2	FACETS	0.902	0.792	1	0.902	0.792	1	CLONAL	1	FALSE	1	0.225392298414794	2		643	767	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976506	25976506	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	63	205	0	ENST00000435504.4:c.1039G>T	p.Glu347Ter	p.E347*	ENST00000435504		347	Gag/Tag	11/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.488592015265992	2		205	195	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851653	134851654	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0051684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	112	406	0	ENST00000398015.3:c.1061_1062del	p.Val354AspfsTer20	p.V354Dfs*20	ENST00000398015	NM_004441.4	353	gaTGtg/gatg	5/16	1	2	FACETS	0.885	0.8	0.975	0.885	0.8	0.975	CLONAL	1	TRUE	1	0.488592015265992	2		406	518	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057765	180057765	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	56	444	1	ENST00000261937.6:c.190G>T	p.Ala64Ser	p.A64S	ENST00000261937	NM_182925.4	64	Gct/Tct	3/30	1	2	FACETS	0.537	0.461	0.619	0.537	0.461	0.619	SUBCLONAL	1	TRUE	1	0.488592015265992	2		445	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0051685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	340	644	2	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.320394202875125	4	FACETS	0.882	0.835	0.929	0.882	0.835	0.929	INDETERMINATE	2	TRUE	2	0.561724036560893	4		646	1072	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069060	5069060	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	30	275	0	ENST00000381652.3:c.1370del	p.Asn457MetfsTer22	p.N457Mfs*22	ENST00000381652	NM_004972.3	455	acA/ac	11/25	0.561724036560893	1	FACETS	0.565	0.462	0.677	0.565	0.462	0.677	SUBCLONAL	1	TRUE	0	0.561724036560893	1		275	136	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11308032	11308032	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	690	491	0	ENST00000361445.4:c.960G>T	p.Gln320His	p.Q320H	ENST00000361445	NM_004958.3	320	caG/caT	7/58	0.561724036560893	3	FACETS	1	0.986	1			1	CLONAL	3	TRUE	NA	0.561724036560893	3		491	1028	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246445	105246445	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	554	455	0	ENST00000349310.3:c.155T>A	p.Leu52His	p.L52H	ENST00000349310	NM_001014432.1	52	cTc/cAc	4/15	0.477479753202974	4	FACETS	0.979	0.945	1			1	CLONAL	3	TRUE	NA	0.561724036560893	4		455	1049	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39542509	39542509	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	100	318	0	ENST00000262039.4:c.313C>T	p.Gln105Ter	p.Q105*	ENST00000262039	NM_002647.2	105	Caa/Taa	3/25	0.561724036560893	3	FACETS	0.929	0.833	1	0.464	0.416	0.515	CLONAL	1	TRUE	1	0.561724036560893	3		318	491	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573393	55573393	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1560402002	NA	P-0051685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	289	349	0	ENST00000288135.5:c.1055A>G	p.Asn352Ser	p.N352S	ENST00000288135	NM_000222.2	352	aAc/aGc	6/21	0.561724036560893	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.561724036560893	3		349	554	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562443	95562443	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs939314926	NA	P-0051685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	562	364	0	ENST00000393063.1:c.4814C>G	p.Pro1605Arg	p.P1605R	ENST00000393063	NM_030621.3	1605	cCt/cGt	24/28	0.477479753202974	4	FACETS	1	0.979	1			1	CLONAL	4	TRUE	NA	0.561724036560893	4		364	776	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78426087	78426087	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	164	436	0	ENST00000370768.2:c.1438C>G	p.Pro480Ala	p.P480A	ENST00000370768	NM_003902.3	480	Cca/Gca	15/20	0.477479753202974	4	FACETS	1	0.934	1			1	CLONAL	1	TRUE	NA	0.561724036560893	4		436	894	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275422	115275422	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	190	344	0	ENST00000438362.2:c.991G>T	p.Gly331Ter	p.G331*	ENST00000438362	NM_001242891.1	331	Gga/Tga	10/20	0.561724036560893	3	FACETS	0.971	0.908	1	0.971	0.908	1	CLONAL	2	TRUE	1	0.561724036560893	3		344	446	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18477968	18477968	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0051685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	45	285	0	ENST00000266497.5:c.1209-1G>A		p.X403_splice	ENST00000266497		403			0.561724036560893	2	FACETS	0.607	0.514	0.708	0.303	0.257	0.354	SUBCLONAL	1	TRUE	0	0.561724036560893	2		285	264	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691146	18691146	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	152	340	0	ENST00000266497.5:c.3257G>T	p.Gly1086Val	p.G1086V	ENST00000266497		1086	gGg/gTg	23/31	0.561724036560893	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.561724036560893	2		340	262	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95596452	95596452	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	268	241	0	ENST00000393063.1:c.516G>T	p.Leu172Phe	p.L172F	ENST00000393063	NM_030621.3	172	ttG/ttT	6/28	0.477479753202974	4	FACETS	0.948	0.908	0.986			1	CLONAL	4	TRUE	NA	0.561724036560893	4		241	393	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81926767	81927326	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAACACAAATTTTAAAAAAGTTGGGGTGAATCATGACAAGGAGGAAAGTGCATTAAAGAGTCATTCTTACGGCAGTTTTGGTGGATATGGCTCCTAGCATAGCCGATTGCACCAACAGTTGTTGAATATCTGTTCTGTGCCTGGCCTCAAGCCTTGATATCAAAAGAAGTGCCCATCTTTGTTTAGACCGAGGACCCAGAGAGCGGCCATGGGGCCTTGTTAATTCATCTTCTGCAGCTTTTTTTGCTTCTGACGTGCTTTGACCAACTTCTCCTCAAAAGAACACGTCCTCTCCACGCTTGCATTGCCCAGGTGGTCAGCAGTCACTTCCTGCGATTGTGGCCTGACTTCAGAGCTCATGCCCAGTGTGACCGTGGGATTGTGTATTTCTGTCCTAGGCCTTAGCTTTGAGTCTTTCTACATGGAAGAACTCAGAGCTTTGGCGGCTCGGGCGGAGAAGTTCCCCCACAACACCCTGAGGTGCAGGCTTGCCCCCCAACCCCTGTGGCTGCCACTCTCACACGGCCACCTGCCTTCTCTCCTGCAGGTACCTTACAGGT	GAACACAAATTTTAAAAAAGTTGGGGTGAATCATGACAAGGAGGAAAGTGCATTAAAGAGTCATTCTTACGGCAGTTTTGGTGGATATGGCTCCTAGCATAGCCGATTGCACCAACAGTTGTTGAATATCTGTTCTGTGCCTGGCCTCAAGCCTTGATATCAAAAGAAGTGCCCATCTTTGTTTAGACCGAGGACCCAGAGAGCGGCCATGGGGCCTTGTTAATTCATCTTCTGCAGCTTTTTTTGCTTCTGACGTGCTTTGACCAACTTCTCCTCAAAAGAACACGTCCTCTCCACGCTTGCATTGCCCAGGTGGTCAGCAGTCACTTCCTGCGATTGTGGCCTGACTTCAGAGCTCATGCCCAGTGTGACCGTGGGATTGTGTATTTCTGTCCTAGGCCTTAGCTTTGAGTCTTTCTACATGGAAGAACTCAGAGCTTTGGCGGCTCGGGCGGAGAAGTTCCCCCACAACACCCTGAGGTGCAGGCTTGCCCCCCAACCCCTGTGGCTGCCACTCTCACACGGCCACCTGCCTTCTCTCCTGCAGGTACCTTACAGGT	-	novel	NA	P-0051685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2	32	0	0	ENST00000359376.3:c.987-545_1001del		p.X329_splice	ENST00000359376	NM_002661.3	329		12/33	0.147706788213119	3	FACETS	1	0.965	1	1	0.975	1	INDETERMINATE	4	TRUE	0	0.561724036560893	3		0	34	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960975	15960975	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	229	288	0	ENST00000268712.3:c.6245A>C	p.Gln2082Pro	p.Q2082P	ENST00000268712	NM_006311.3	2082	cAg/cCg	40/46	0.320394202875125	4	FACETS	1	0.977	1	1	0.977	1	INDETERMINATE	2	TRUE	2	0.561724036560893	4		288	590	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557870	29557870	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	95	200	0	ENST00000356175.3:c.3124G>T	p.Val1042Leu	p.V1042L	ENST00000356175	NM_000267.3	1042	Gta/Tta	24/57	0.561724036560893	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.561724036560893	3		200	187	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474351	40474351	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	281	370	1	ENST00000264657.5:c.2050G>T	p.Gly684Ter	p.G684*	ENST00000264657	NM_139276.2	684	Gga/Tga	21/24	0.429906152832083	4	FACETS	0.948	0.894	1	0.948	0.894	1	CLONAL	2	TRUE	2	0.561724036560893	4		371	824	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007658	62007659	+	missense_variant	Missense_Mutation	DNP	CT	CT	AG	novel	NA	P-0051685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	165	467	1	ENST00000392795.3:c.208_209inv	p.Ser70Leu	p.S70L	ENST00000392795	NM_001039933.1	70	AGc/CTc	3/6	0.561724036560893	3	FACETS	1	0.973	1	0.563	0.519	0.609	CLONAL	1	TRUE	1	0.561724036560893	3		468	668	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270433	10270433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	116	530	0	ENST00000340748.4:c.1133C>T	p.Pro378Leu	p.P378L	ENST00000340748		378	cCa/cTa	16/40	0.561724036560893	2	FACETS	0.534	0.481	0.589	0.267	0.24	0.295	SUBCLONAL	1	TRUE	0	0.561724036560893	2		530	774	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627458	14627458	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	167	454	0	ENST00000254322.2:c.612G>C	p.Leu204Phe	p.L204F	ENST00000254322	NM_006145.1	204	ttG/ttC	2/3	0.561724036560893	2	FACETS	1	0.968	1	0.544	0.502	0.586	CLONAL	1	TRUE	0	0.561724036560893	2		454	547	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288846	15288846	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	78	146	0	ENST00000263388.2:c.3893G>T	p.Cys1298Phe	p.C1298F	ENST00000263388	NM_000435.2	1298	tGc/tTc	24/33	0.561724036560893	2	FACETS	1	0.958	1	0.579	0.516	0.644	CLONAL	1	TRUE	0	0.561724036560893	2		146	240	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306506	41306506	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	52	284	0	ENST00000373198.4:c.1153G>T	p.Asp385Tyr	p.D385Y	ENST00000373198	NM_133170.3	385	Gat/Tat	7/32	0.561724036560893	3	FACETS	0.473	0.403	0.55	0.237	0.201	0.275	SUBCLONAL	1	TRUE	1	0.561724036560893	3		284	501	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518201	187518201	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	95	276	0	ENST00000441802.2:c.12493G>C	p.Ala4165Pro	p.A4165P	ENST00000441802	NM_005245.3	4165	Gct/Cct	25/27	1	2	FACETS	0.811	0.727	0.9	0.811	0.727	0.9	CLONAL	1	TRUE	1	0.561724036560893	2		276	417	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969924	161969924	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	152	407	0	ENST00000366898.1:c.1045A>G	p.Lys349Glu	p.K349E	ENST00000366898	NM_004562.2	349	Aaa/Gaa	9/12	0.511525520978066	3	FACETS	1	0.979	1	0.397	0.365	0.431	CLONAL	1	TRUE	0	0.561724036560893	3		407	582	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367331	50367331	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	110	304	0	ENST00000331340.3:c.138C>A	p.Ser46Arg	p.S46R	ENST00000331340	NM_006060.4	46	agC/agA	3/8	0.561724036560893	4	FACETS	0.883	0.794	0.976	0.294	0.264	0.326	CLONAL	1	TRUE	1	0.561724036560893	4		304	693	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151167723	151167723	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	68	266	0	ENST00000262187.5:c.396del	p.Glu133LysfsTer31	p.E133Kfs*31	ENST00000262187	NM_005614.3	132	gaA/ga	7/8	0.561724036560893	3	FACETS	0.869	0.76	0.984	0.434	0.38	0.492	CLONAL	1	TRUE	1	0.561724036560893	3		266	357	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275512	38276059	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCGGGGGAAACAGAGAGTGGCATAAGTTGGGGCTGGTGAAGTTCAAACCTTGAGAGGCACCCCATCTCCACCTCTCTGTATTTCACCCAACTGCGAGCAGAAAGTGGAATGAATGTTTCTGCAGGCATTTCATGAACCTTCACCGCCCAGAAGGTGTTAGTATACACACCTTCCACCACTAGAATAGCAAGCAAGGAATGCCTTCAAAAAGTTGGGAGTCAAAGTATTATTACCTGTCCCGAGGCAGCTCCCAGCGAGGGTCTTCGGGAAGCTCATACTCAGAGACCCCTGCTAGCATGGGAGTCCCACTGGAGGAGAGCCGTGATGGCCGAACCAGAAGAACCCCAGAGTTCATGGATGCACTGGAGTCAGCAGACACCTGCAAGGAAGAGTGGGGTCACCCTAGAGCAAGGAGGGGGGACGGGGTGACTCCTTCCCATTCTTAGTCAGGGCTTCCCAACAATGGCAGAGGCACATGTCTGTGTATCTGATGTTCTTTCCTCAACACAGAGTGGTCCAAAGACCATGGTAGGCCAGGAGGCCCAAC	TTCGGGGGAAACAGAGAGTGGCATAAGTTGGGGCTGGTGAAGTTCAAACCTTGAGAGGCACCCCATCTCCACCTCTCTGTATTTCACCCAACTGCGAGCAGAAAGTGGAATGAATGTTTCTGCAGGCATTTCATGAACCTTCACCGCCCAGAAGGTGTTAGTATACACACCTTCCACCACTAGAATAGCAAGCAAGGAATGCCTTCAAAAAGTTGGGAGTCAAAGTATTATTACCTGTCCCGAGGCAGCTCCCAGCGAGGGTCTTCGGGAAGCTCATACTCAGAGACCCCTGCTAGCATGGGAGTCCCACTGGAGGAGAGCCGTGATGGCCGAACCAGAAGAACCCCAGAGTTCATGGATGCACTGGAGTCAGCAGACACCTGCAAGGAAGAGTGGGGTCACCCTAGAGCAAGGAGGGGGGACGGGGTGACTCCTTCCCATTCTTAGTCAGGGCTTCCCAACAATGGCAGAGGCACATGTCTGTGTATCTGATGTTCTTTCCTCAACACAGAGTGGTCCAAAGACCATGGTAGGCCAGGAGGCCCAAC	-	novel	NA	P-0051685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	120	393	0	ENST00000425967.3:c.1378-168_1524-3del		p.X460_splice	ENST00000425967	NM_001174067.1	460		11/19	0.561724036560893	3	FACETS	0.9	0.815	0.989	0.45	0.407	0.495	CLONAL	1	TRUE	1	0.561724036560893	3		393	608	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220423	123220423	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	66	205	0	ENST00000218089.9:c.3080C>G	p.Thr1027Ser	p.T1027S	ENST00000218089	NM_001042749.1	1027	aCc/aGc	30/35	0.477479753202974	2	FACETS	0.592	0.516	0.673			1	SUBCLONAL	1	TRUE	NA	0.561724036560893	2		205	397	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	59	230	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.941	0.823	1	0.941	0.823	1	CLONAL	1	TRUE	1	0.64	2		230	196	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873161	71873161	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	113	293	0	ENST00000357731.5:c.1033A>G	p.Ile345Val	p.I345V	ENST00000357731	NM_173808.2	345	Ata/Gta	7/7	1	2	FACETS	0.998	0.907	1	0.998	0.907	1	CLONAL	1	TRUE	1	0.64	2		293	354	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0051687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	79	439	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.261049682533711	1	FACETS	0.967	0.852	1	0.967	0.852	1	CLONAL	1	TRUE	0	0.261049682533711	1		439	544	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964224	28964224	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	57	165	0	ENST00000282397.4:c.1678C>T	p.His560Tyr	p.H560Y	ENST00000282397	NM_002019.4	560	Cat/Tat	13/30	0.231460781898819	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.261049682533711	1		165	320	SUCCESS
CBL	867	MSKCC	GRCh37	11	119146771	119146771	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	39	362	2	ENST00000264033.4:c.934G>T	p.Gly312Trp	p.G312W	ENST00000264033	NM_005188.3	312	Ggg/Tgg	6/16	1	2	FACETS	0.564	0.467	0.672	0.564	0.467	0.672	SUBCLONAL	1	TRUE	1	0.261049682533711	2		364	530	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968244	18968244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	120	542	0	ENST00000262803.5:c.2084C>T	p.Pro695Leu	p.P695L	ENST00000262803	NM_002911.3	695	cCc/cTc	15/24	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.261049682533711	2		542	697	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796361	42796361	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0051687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	125	594	1	ENST00000575354.2:c.3008+2T>A		p.X1003_splice	ENST00000575354	NM_015125.3	1003			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.261049682533711	2		595	795	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416275	29416275	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	37	527	0	ENST00000389048.3:c.4678T>A	p.Ser1560Thr	p.S1560T	ENST00000389048	NM_004304.4	1560	Tct/Act	29/29	1	2	FACETS	0.408	0.335	0.49	0.408	0.335	0.49	SUBCLONAL	1	TRUE	1	0.261049682533711	2		527	695	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026342	48026342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	66	314	0	ENST00000234420.5:c.1220C>T	p.Thr407Ile	p.T407I	ENST00000234420	NM_000179.2	407	aCt/aTt	4/10	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.261049682533711	2		314	459	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484206	8484206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768568228	NA	P-0051688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	95	451	0	ENST00000356435.5:c.3326G>A	p.Arg1109His	p.R1109H	ENST00000356435		1109	cGt/cAt	19/35	0.244250285194318	3	FACETS	0.959	0.858	1	0.959	0.858	1	CLONAL	2	TRUE	1	0.244250285194318	3		451	455	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779616	3779634	+	frameshift_variant	Frame_Shift_Del	DEL	TTGCGTTTGCAGCCCTTGG	TTGCGTTTGCAGCCCTTGG	-	novel	NA	P-0051688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	117	768	0	ENST00000262367.5:c.5414_5432del	p.Thr1805ArgfsTer62	p.T1805Rfs*62	ENST00000262367	NM_004380.2	1805	aCCAAGGGCTGCAAACGCAAg/ag	31/31	1	2	FACETS	0.79	0.715	0.87	1	0.986	1	SUBCLONAL	2	TRUE	1	0.244250285194318	2		768	606	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947541	38947541	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	14	121	0	ENST00000357387.3:c.4139T>C	p.Phe1380Ser	p.F1380S	ENST00000357387	NM_152756.3	1380	tTc/tCc	32/38	0.244250285194318	3	FACETS	0.681	0.493	0.906	0.34	0.246	0.453	SUBCLONAL	1	TRUE	1	0.244250285194318	3		121	189	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183681	10183705	+	frameshift_variant	Frame_Shift_Del	DEL	CGAGGAGGAGATGGAGGCCGGGCGG	CGAGGAGGAGATGGAGGCCGGGCGG	-	novel	NA	P-0051691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	87	602	0	ENST00000256474.2:c.151_175del	p.Glu51ArgfsTer8	p.E51Rfs*8	ENST00000256474	NM_000551.3	50	gcCGAGGAGGAGATGGAGGCCGGGCGG/gc	1/3	0.441620689691488	1	FACETS	0.85	0.759	0.947	0.85	0.759	0.947	CLONAL	1	TRUE	0	0.441620689691488	1		602	361	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0051738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	181	404	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.972	0.899	1	0.972	0.899	1	CLONAL	1	TRUE	1	0.54	2		404	690	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0051738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	252	403	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.539757362289357	3	FACETS	0.897	0.844	0.95	0.897	0.844	0.95	CLONAL	2	TRUE	1	0.54	3		403	661	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0051738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	82	556	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.539	0.476	0.607	0.539	0.476	0.607	SUBCLONAL	1	TRUE	1	0.54	2		556	563	SUCCESS
APC	324	MSKCC	GRCh37	5	112170813	112170813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554083227	NA	P-0051738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	193	551	0	ENST00000257430.4:c.1909G>A	p.Gly637Arg	p.G637R	ENST00000257430	NM_000038.5	637	Ggg/Agg	15/16	1	2	FACETS	0.907	0.841	0.976	0.907	0.841	0.976	CLONAL	1	TRUE	1	0.54	2		551	788	SUCCESS
APC	324	MSKCC	GRCh37	5	112174091	112174094	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1131691143	NA	P-0051738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	109	339	0	ENST00000257430.4:c.2802_2805del	p.Tyr935IlefsTer19	p.Y935Ifs*19	ENST00000257430	NM_000038.5	934	ACTTac/ac	16/16	1	2	FACETS	0.905	0.818	0.996	0.905	0.818	0.996	CLONAL	1	TRUE	1	0.54	2		339	446	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571448	95571448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373412959	NA	P-0051738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	77	300	0	ENST00000393063.1:c.3229G>A	p.Asp1077Asn	p.D1077N	ENST00000393063	NM_030621.3	1077	Gat/Aat	21/28	1	2	FACETS	0.653	0.575	0.735	0.653	0.575	0.735	SUBCLONAL	1	TRUE	1	0.54	2		300	437	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798342	42798342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	250	677	0	ENST00000575354.2:c.4213G>A	p.Glu1405Lys	p.E1405K	ENST00000575354	NM_015125.3	1405	Gag/Aag	18/20	0.539757362289357	3	FACETS	1	0.96	1	0.518	0.484	0.554	CLONAL	1	TRUE	1	0.54	3		677	1134	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120094	70120094	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	27	55	0	ENST00000245479.2:c.1100del	p.Pro367HisfsTer16	p.P367Hfs*16	ENST00000245479	NM_000346.3	366	Ccc/cc	3/3	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.54	2		55	84	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261676	16261677	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CG	novel	NA	P-0051738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	52	467	0	ENST00000375759.3:c.8943_8944dup	p.Leu2982ArgfsTer41	p.L2982Rfs*41	ENST00000375759	NM_015001.2	2981	acg/aCGcg	11/15	1	2	FACETS	0.292	0.248	0.34	0.292	0.248	0.34	SUBCLONAL	1	TRUE	1	0.54	2		467	660	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982371	25982371	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	132	246	0	ENST00000435504.4:c.919C>A	p.Leu307Ile	p.L307I	ENST00000435504		307	Ctc/Atc	9/13	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.54	2		246	454	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023354	31023354	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	52	498	2	ENST00000375687.4:c.2839G>T	p.Glu947Ter	p.E947*	ENST00000375687	NM_015338.5	947	Gag/Tag	13/13	1	2	FACETS	0.282	0.239	0.329	0.282	0.239	0.329	SUBCLONAL	1	TRUE	1	0.54	2		500	683	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	129	386	0	ENST00000263967.3:c.3073A>T	p.Thr1025Ser	p.T1025S	ENST00000263967	NM_006218.2	1025	Acc/Tcc	21/21	1	2	FACETS	0.948	0.864	1	0.948	0.864	1	CLONAL	1	TRUE	1	0.54	2		386	504	SUCCESS
APC	324	MSKCC	GRCh37	5	112175991	112175991	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	77	258	0	ENST00000257430.4:c.4700del	p.Ser1567Ter	p.S1567*	ENST00000257430	NM_000038.5	1567	tCa/ta	16/16	1	2	FACETS	0.797	0.704	0.894	0.797	0.704	0.894	SUBCLONAL	1	TRUE	1	0.54	2		258	358	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910423	29911042	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGAAACCGCCTCTGCGGGGAGAAGCAAGGGGCCCTCCTGGCGGGGGCGCAGGACCGGGGGAGCCGCGCCGGGACGAGGGTCGGGCAGGTCTCAGCCACTGCTCGCCCCCAGGCTCCCACTCCATGAGGTATTTCTTCACATCCGTGTCCCGGCCCGGCCGCGGGGAGCCCCGCTTCATCGCCGTGGGCTACGTGGACGACACGCAGTTCGTGCGGTTCGACAGCGACGCCGCGAGCCAGAGGATGGAGCCGCGGGCGCCGTGGATAGAGCAGGAGGGGCCGGAGTATTGGGACCAGGAGACACGGAATGTGAAGGCCCAGTCACAGACTGACCGAGTGGACCTGGGGACCCTGCGCGGCTACTACAACCAGAGCGAGGCCGGTGAGTGACCCCGGCCGGGGGCGCAGGTCAGGACCCCTCATCCCCCACGGACGGGCCAGGTCGCCCACAGTCTCCGGGTCCGAGATCCACCCCGAAGCCGCGGGACCCCGAGACCCTTGCCCCGGGAGAGGCCCAGGCGCCTTTACCCGGTTTCATTTTCAGTTTAGGCCAAAAATCCCCCCGGGTTGGTCGGGGCTGGGCGGGGCTCGGGGGACTGGGCTGACCGCGGGGTCGGGGCC	GGAAACCGCCTCTGCGGGGAGAAGCAAGGGGCCCTCCTGGCGGGGGCGCAGGACCGGGGGAGCCGCGCCGGGACGAGGGTCGGGCAGGTCTCAGCCACTGCTCGCCCCCAGGCTCCCACTCCATGAGGTATTTCTTCACATCCGTGTCCCGGCCCGGCCGCGGGGAGCCCCGCTTCATCGCCGTGGGCTACGTGGACGACACGCAGTTCGTGCGGTTCGACAGCGACGCCGCGAGCCAGAGGATGGAGCCGCGGGCGCCGTGGATAGAGCAGGAGGGGCCGGAGTATTGGGACCAGGAGACACGGAATGTGAAGGCCCAGTCACAGACTGACCGAGTGGACCTGGGGACCCTGCGCGGCTACTACAACCAGAGCGAGGCCGGTGAGTGACCCCGGCCGGGGGCGCAGGTCAGGACCCCTCATCCCCCACGGACGGGCCAGGTCGCCCACAGTCTCCGGGTCCGAGATCCACCCCGAAGCCGCGGGACCCCGAGACCCTTGCCCCGGGAGAGGCCCAGGCGCCTTTACCCGGTTTCATTTTCAGTTTAGGCCAAAAATCCCCCCGGGTTGGTCGGGGCTGGGCGGGGCTCGGGGGACTGGGCTGACCGCGGGGTCGGGGCC	-	novel	NA	P-0051738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	289	482	0	ENST00000376809.5:c.73+20_344-3del		p.X25_splice	ENST00000376809	NM_002116.7	25		2/8	1	2	FACETS	0.812	0.77	0.855	1	0.995	1	CLONAL	2	TRUE	1	0.54	2		482	659	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450375	50450375	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	149	499	0	ENST00000331340.3:c.559G>T	p.Ala187Ser	p.A187S	ENST00000331340	NM_006060.4	187	Gcc/Tcc	5/8	0.539757362289357	3	FACETS	0.845	0.773	0.921	0.423	0.386	0.461	CLONAL	1	TRUE	1	0.54	3		499	829	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120200	70120201	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	C	novel	NA	P-0051738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	176	496	0	ENST00000245479.2:c.1202_1203delinsC	p.Gln401ProfsTer2	p.Q401Pfs*2	ENST00000245479	NM_000346.3	401	cAG/cC	3/3	1	2	FACETS	0.875	0.808	0.945	0.875	0.808	0.945	CLONAL	1	TRUE	1	0.54	2		496	745	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	282	316	0	ENST00000346208.3:c.878T>A	p.Met293Lys	p.M293K	ENST00000346208		293	aTg/aAg	4/6	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.745260806505201	2		316	747	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870878	12870878	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	16	249	0	ENST00000228872.4:c.106del	p.Val36TrpfsTer6	p.V36Wfs*6	ENST00000228872	NM_004064.3	35	ccG/cc	1/3	0.225348711136977	3	FACETS	0.62	0.461	0.809	0.31	0.23	0.405	SUBCLONAL	1	TRUE	1	0.360298180907293	3		249	169	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385031	31385031	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	39	672	0	ENST00000328111.2:c.1416T>A	p.Asp472Glu	p.D472E	ENST00000328111	NM_006892.3	472	gaT/gaA	14/23	0.14844563417298	4	FACETS	1	0.947	1	0.685	0.573	0.807	INDETERMINATE	1	TRUE	2	0.360298180907293	4		672	215	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0051743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	35	289	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.200287774617434	2		289	288	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061748	38061748	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	21	452	2	ENST00000250448.2:c.241G>A	p.Ala81Thr	p.A81T	ENST00000250448	NM_004496.3	81	Gca/Aca	2/2	1	2	FACETS	0.912	0.704	1	0.912	0.704	1	CLONAL	1	TRUE	1	0.200287774617434	2		454	230	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0051743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	50	644	1	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.178621167042509	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.200287774617434	1		645	331	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101578	27101580	+	frameshift_variant	Frame_Shift_Del	DEL	ACC	ACC	G	novel	NA	P-0051743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	59	642	0	ENST00000324856.7:c.4860_4862delinsG	p.Pro1621CysfsTer26	p.P1621Cfs*26	ENST00000324856	NM_006015.4	1620	gtACCt/gtGt	18/20	1	2	FACETS	0.856	0.741	0.981	1	0.975	1	CLONAL	2	TRUE	1	0.200287774617434	2		642	344	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0051744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	94	176	0	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.391643987630068	2		176	450	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	149	610	2	ENST00000324856.7:c.666C>A	p.Tyr222Ter	p.Y222*	ENST00000324856	NM_006015.4	222	taC/taA	1/20	0.391643987630068	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.391643987630068	1		612	596	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637871	39637871	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	96	309	0	ENST00000262039.4:c.2288G>C	p.Gly763Ala	p.G763A	ENST00000262039	NM_002647.2	763	gGa/gCa	22/25	1	2	FACETS	0.797	0.711	0.888	0.797	0.711	0.888	SUBCLONAL	1	TRUE	1	0.391643987630068	2		309	615	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001410	29001410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771714708	NA	P-0051746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	41	316	0	ENST00000282397.4:c.1322C>T	p.Pro441Leu	p.P441L	ENST00000282397	NM_002019.4	441	cCg/cTg	10/30	0.249965170644416	0	FACETS	0.216	0.18	0.257			1	INDETERMINATE	1	TRUE	0	0.454360377734966	0		316	455	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272263	18272263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1255802241	NA	P-0051746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	10	18	0	ENST00000222254.8:c.773C>T	p.Pro258Leu	p.P258L	ENST00000222254	NM_005027.3	258	cCg/cTg	6/16	0.297908416059087	1	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	0	0.454360377734966	1		18	26	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111491	8111492	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACTCTGG	novel	NA	P-0051746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	164	543	0	ENST00000346208.3:c.979_985dup	p.Arg329ThrfsTer25	p.R329Tfs*25	ENST00000346208		326	aca/acACTCTGGa	5/6	1	2	FACETS	0.802	0.736	0.871	0.802	0.736	0.871	CLONAL	1	TRUE	1	0.454360377734966	2		543	900	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63537676	63537676	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0051746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	36	440	0	ENST00000307078.5:c.957-1G>A		p.X319_splice	ENST00000307078	NM_004655.3	319			0.32825345956334	3	FACETS	0.332	0.272	0.4	0.166	0.136	0.2	SUBCLONAL	1	TRUE	1	0.454360377734966	3		440	585	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115012	3115012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555702147	NA	P-0051747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	412	871	1	ENST00000078429.4:c.547C>T	p.Arg183Cys	p.R183C	ENST00000078429	NM_002067.2	183	Cgc/Tgc	4/7	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.787435979205717	2		872	825	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307484	118307484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1343124835	NA	P-0051747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	222	570	0	ENST00000534358.1:c.257C>T	p.Ser86Leu	p.S86L	ENST00000534358	NM_005933.3	86	tCg/tTg	1/36	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.787435979205717	2		570	536	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442490	52442504	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CTGGTGGGCAAAGAA	CTGGTGGGCAAAGAA	-	novel	NA	P-0051747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	129	417	0	ENST00000460680.1:c.241_255del	p.Phe81_Gln85del	p.F81_Q85del	ENST00000460680	NM_004656.3	81	TTCTTTGCCCACCAG/-	4/17	0.787435979205717	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.787435979205717	1		417	187	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953730	48953730	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs3092891	NA	P-0051749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	227	181	0	ENST00000267163.4:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000267163	NM_000321.2	445	Cga/Tga	14/27	0.808553575289604	2	FACETS	0.937	0.901	0.971	0.937	0.901	0.971	CLONAL	2	TRUE	0	0.830001314781676	2		181	292	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881392	37881392	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	606	908	0	ENST00000269571.5:c.2584A>G	p.Thr862Ala	p.T862A	ENST00000269571		862	Aca/Gca	21/27	0.830001314781676	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.830001314781676	1		908	805	SUCCESS
APC	324	MSKCC	GRCh37	5	112175939	112175939	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	147	265	0	ENST00000257430.4:c.4648G>T	p.Glu1550Ter	p.E1550*	ENST00000257430	NM_000038.5	1550	Gag/Tag	16/16	0.720152205562462	1	FACETS	0.702	0.654	0.751	0.702	0.654	0.751	SUBCLONAL	1	TRUE	0	0.830001314781676	1		265	295	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711993	89711993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	262	341	0	ENST00000371953.3:c.611C>T	p.Pro204Leu	p.P204L	ENST00000371953	NM_000314.4	204	cCa/cTa	6/9	0.830001314781676	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.830001314781676	1		341	343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577118	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs1567547933	NA	P-0051749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	601	848	1	ENST00000269305.4:c.820_821del	p.Val274LeufsTer31	p.V274Lfs*31	ENST00000269305	NM_001126112.2	274	GTt/t	8/11	0.830001314781676	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.830001314781676	1		849	834	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593523	48593539	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTTCATAAGATCTAC	CTGTTCATAAGATCTAC	-	novel	NA	P-0051749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	176	218	0	ENST00000342988.3:c.1275_1291del	p.Val426LysfsTer8	p.V426Kfs*8	ENST00000342988	NM_005359.5	425	gCTGTTCATAAGATCTAC/g	10/12	0.830001314781676	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.830001314781676	1		218	245	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368461	225368461	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	37	333	0	ENST00000264414.4:c.1285G>C	p.Glu429Gln	p.E429Q	ENST00000264414	NM_003590.4	429	Gaa/Caa	9/16	0.625220774210214	1	FACETS	0.083	0.067	0.099	0.083	0.067	0.099	SUBCLONAL	1	TRUE	0	0.830001314781676	1		333	632	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950743	79950743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	57	305	0	ENST00000265081.6:c.197C>T	p.Pro66Leu	p.P66L	ENST00000265081	NM_002439.4	66	cCc/cTc	1/24	0.830001314781676	1	FACETS	0.339	0.294	0.387	0.339	0.294	0.387	SUBCLONAL	1	TRUE	0	0.830001314781676	1		305	237	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163801	32163801	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	477	749	0	ENST00000375023.3:c.5425C>A	p.Gln1809Lys	p.Q1809K	ENST00000375023	NM_004557.3	1809	Caa/Aaa	30/30	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.830001314781676	2		749	1049	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902246	151902247	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0051749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	91	479	0	ENST00000262189.6:c.3905_3906del	p.Val1302AspfsTer18	p.V1302Dfs*18	ENST00000262189	NM_170606.2	1302	gTG/g	25/59	0.326422660506227	1	FACETS	0.208	0.185	0.233	0.208	0.185	0.233	INDETERMINATE	1	TRUE	0	0.830001314781676	1		479	616	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0051750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	162	233	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		234	439	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909629	76909629	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs919106518	NA	P-0051750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	195	242	0	ENST00000373344.5:c.4276C>T	p.Arg1426Ter	p.R1426*	ENST00000373344	NM_000489.3	1426	Cga/Tga	14/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		242	323	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134236	11134236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	251	575	0	ENST00000358026.2:c.2902C>T	p.Leu968Phe	p.L968F	ENST00000358026	NM_001128849.1	968	Ctc/Ttc	20/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		575	703	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436855	110436855	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	266	703	0	ENST00000375856.3:c.1546C>T	p.His516Tyr	p.H516Y	ENST00000375856	NM_003749.2	516	Cac/Tac	1/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		703	865	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138729528	NA	P-0051751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	478	701	0	ENST00000269305.4:c.523C>G	p.Arg175Gly	p.R175G	ENST00000269305	NM_001126112.2	175	Cgc/Ggc	5/11	0.643019992639915	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.730861768677566	2		701	642	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955086	93955086	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	120	420	0	ENST00000369303.4:c.2812G>T	p.Glu938Ter	p.E938*	ENST00000369303	NM_004440.3	938	Gaa/Taa	16/17	0.721160301730825	3	FACETS	0.954	0.867	1	0.477	0.433	0.523	CLONAL	1	TRUE	1	0.730861768677566	3		420	470	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94067986	94067986	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	80	359	0	ENST00000369303.4:c.976G>T	p.Val326Phe	p.V326F	ENST00000369303	NM_004440.3	326	Gtt/Ttt	4/17	0.721160301730825	3	FACETS	0.812	0.72	0.91	0.406	0.36	0.455	CLONAL	1	TRUE	1	0.730861768677566	3		359	368	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0051752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	29	321	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.232	0.186	0.285	0.232	0.186	0.285	SUBCLONAL	1	TRUE	1	0.544766662870803	2		321	458	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0051752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	188	403	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.544766662870803	2		403	682	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094483	27094483	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0051752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	49	442	0	ENST00000324856.7:c.3191T>A	p.Leu1064Ter	p.L1064*	ENST00000324856	NM_006015.4	1064	tTg/tAg	11/20	1	2	FACETS	0.309	0.261	0.362	0.309	0.261	0.362	SUBCLONAL	1	TRUE	1	0.544766662870803	2		442	582	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436082	49436082	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	150	429	0	ENST00000301067.7:c.5899G>T	p.Gly1967Cys	p.G1967C	ENST00000301067	NM_003482.3	1967	Ggt/Tgt	28/54	1	2	FACETS	0.963	0.884	1	0.963	0.884	1	CLONAL	1	TRUE	1	0.544766662870803	2		429	572	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555740	21555740	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1353172366	NA	P-0051752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	72	682	1	ENST00000382592.4:c.2530G>A	p.Asp844Asn	p.D844N	ENST00000382592	NM_014572.2	844	Gat/Aat	6/8	1	2	FACETS	0.271	0.235	0.309	0.271	0.235	0.309	SUBCLONAL	1	TRUE	1	0.544766662870803	2		683	977	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368436	225368436	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	35	521	0	ENST00000264414.4:c.1310C>T	p.Ala437Val	p.A437V	ENST00000264414	NM_003590.4	437	gCa/gTa	9/16	1	2	FACETS	0.242	0.197	0.291	0.242	0.197	0.291	SUBCLONAL	1	TRUE	1	0.544766662870803	2		521	532	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524489	44524489	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	28	330	0	ENST00000291552.4:c.68A>G	p.Lys23Arg	p.K23R	ENST00000291552	NM_006758.2	23	aAa/aGa	2/8	1	2	FACETS	0.232	0.185	0.286	0.232	0.185	0.286	SUBCLONAL	1	TRUE	1	0.544766662870803	2		330	443	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162747	47162747	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	52	485	2	ENST00000409792.3:c.3379C>T	p.Gln1127Ter	p.Q1127*	ENST00000409792	NM_014159.6	1127	Caa/Taa	3/21	1	2	FACETS	0.345	0.294	0.402	0.345	0.294	0.402	SUBCLONAL	1	TRUE	1	0.544766662870803	2		487	553	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72842138	72842138	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	125	356	0	ENST00000325599.8:c.1110G>T	p.Gln370His	p.Q370H	ENST00000325599	NM_018130.2	370	caG/caT	10/11	1	2	FACETS	0.954	0.869	1	0.954	0.869	1	CLONAL	1	TRUE	1	0.544766662870803	2		356	481	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456448	89456448	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs377041029	NA	P-0051752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	164	402	0	ENST00000336596.2:c.1624G>C	p.Val542Leu	p.V542L	ENST00000336596	NM_005233.5	542	Gtg/Ctg	8/17	1	2	FACETS	0.916	0.844	0.991	0.916	0.844	0.991	CLONAL	1	TRUE	1	0.544766662870803	2		402	657	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359014	81359014	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	191	567	0	ENST00000222390.5:c.947C>A	p.Thr316Asn	p.T316N	ENST00000222390	NM_000601.4	316	aCt/aAt	8/18	1	2	FACETS	0.948	0.879	1	0.948	0.879	1	CLONAL	1	TRUE	1	0.544766662870803	2		567	740	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040991	47040992	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0051752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	154	762	0	ENST00000377604.3:c.1522dup	p.Tyr508LeufsTer10	p.Y508Lfs*10	ENST00000377604	NM_001204468.1	507	-/T	14/24	1	2	FACETS	0.598	0.546	0.651	0.598	0.546	0.651	SUBCLONAL	1	TRUE	1	0.544766662870803	2		762	946	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	168	435	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.515282451526526	2		436	626	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	124	344	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.959	0.872	1	0.959	0.872	1	CLONAL	1	TRUE	1	0.515282451526526	2		344	502	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998128	169998128	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs753143066	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	230	634	6	ENST00000295797.4:c.826del	p.Thr276GlnfsTer7	p.T276Qfs*7	ENST00000295797	NM_002740.5	273	ttA/tt	9/18	1	2	FACETS	0.995	0.929	1	0.995	0.929	1	CLONAL	1	TRUE	1	0.515282451526526	2		640	897	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	274	745	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.515282451526526	2		745	1047	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	246	681	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.515282451526526	2		681	926	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	153	613	1	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.964	0.885	1	0.964	0.885	1	CLONAL	1	TRUE	1	0.515282451526526	2		614	616	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	142	439	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.954	0.873	1	0.954	0.873	1	CLONAL	1	TRUE	1	0.515282451526526	2		439	578	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	167	558	3	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.934	0.861	1	0.934	0.861	1	CLONAL	1	TRUE	1	0.515282451526526	2		561	694	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	193	548	2	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.515282451526526	2		550	737	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679576	86679576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	112	489	0	ENST00000274376.6:c.2737C>T	p.Arg913Trp	p.R913W	ENST00000274376	NM_002890.2	913	Cgg/Tgg	21/25	1	2	FACETS	0.856	0.773	0.942	0.856	0.773	0.942	CLONAL	1	TRUE	1	0.515282451526526	2		489	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	201	684	1	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	1	2	FACETS	0.885	0.821	0.951	0.885	0.821	0.951	CLONAL	1	TRUE	1	0.515282451526526	2		685	882	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432040	121432040	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771108132	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	245	712	0	ENST00000257555.6:c.787C>T	p.Arg263Cys	p.R263C	ENST00000257555		263	Cgt/Tgt	4/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.515282451526526	2		712	931	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942685	48942685	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913301	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	67	250	0	ENST00000267163.4:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000267163	NM_000321.2	358	Cga/Tga	11/27	0.211109882687544	5	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.515282451526526	5		250	340	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	126	503	0	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	0.867	0.788	0.949	0.867	0.788	0.949	CLONAL	1	TRUE	1	0.515282451526526	2		503	564	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796882	42796883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761345552	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	209	820	1	ENST00000575354.2:c.3347dup	p.Ser1117LysfsTer34	p.S1117Kfs*34	ENST00000575354	NM_015125.3	1114	gcc/gCcc	14/20	1	2	FACETS	0.893	0.83	0.959	0.893	0.83	0.959	CLONAL	1	TRUE	1	0.515282451526526	2		821	908	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222308	2222308	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750329755	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	202	717	0	ENST00000326181.6:c.592G>A	p.Gly198Arg	p.G198R	ENST00000326181	NM_032271.2	198	Ggg/Agg	8/21	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.515282451526526	2		717	780	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039340	49039340	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	157	520	0	ENST00000267163.4:c.2326-1G>A		p.X776_splice	ENST00000267163	NM_000321.2	776			1	2	FACETS	0.932	0.856	1	0.932	0.856	1	CLONAL	1	TRUE	1	0.515282451526526	2		520	654	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725018	47725019	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs762488821	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	189	882	0	ENST00000449228.1:c.725dup	p.Arg243GlnfsTer7	p.R243Qfs*7	ENST00000449228	NM_001127240.2	242	ggc/ggGc	4/4	1	2	FACETS	0.825	0.763	0.89	0.825	0.763	0.89	CLONAL	1	TRUE	1	0.515282451526526	2		882	889	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905061	50905061	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	171	572	1	ENST00000440232.2:c.347del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	115	Ccc/cc	4/27	1	2	FACETS	0.992	0.916	1	0.992	0.916	1	CLONAL	1	TRUE	1	0.515282451526526	2		573	669	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346220	152346220	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	188	592	4	ENST00000359321.1:c.350del	p.Leu117TrpfsTer17	p.L117Wfs*17	ENST00000359321	NM_005431.1	117	tTg/tg	3/3	1	2	FACETS	0.965	0.894	1	0.965	0.894	1	CLONAL	1	TRUE	1	0.515282451526526	2		596	756	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099341	157099341	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587779741	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	21	296	0	ENST00000346085.5:c.278A>T	p.His93Leu	p.H93L	ENST00000346085	NM_020732.3	93	cAc/cTc	1/20	1	2	FACETS	0.225	0.173	0.286	0.225	0.173	0.286	SUBCLONAL	1	TRUE	1	0.515282451526526	2		296	362	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619391	1619391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779358744	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	226	686	0	ENST00000344749.5:c.1250C>T	p.Thr417Met	p.T417M	ENST00000344749	NM_001136139.2	417	aCg/aTg	15/19	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.515282451526526	2		686	856	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	314	431	28	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	1	2	FACETS	0.863	0.82	0.906	1	0.996	1	CLONAL	2	TRUE	1	0.515282451526526	2		459	706	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998496	100998496	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	156	515	0	ENST00000325455.5:c.1306del	p.Glu436LysfsTer4	p.E436Kfs*4	ENST00000325455	NM_001202474.3	436	Gaa/aa	1/8	1	2	FACETS	0.996	0.916	1	0.996	0.916	1	CLONAL	1	TRUE	1	0.515282451526526	2		515	608	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857365	9857365	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	109	470	0	ENST00000330684.3:c.4036del	p.Gln1346LysfsTer51	p.Q1346Kfs*51	ENST00000330684	NM_001134407.1	1346	Caa/aa	13/13	1	2	FACETS	0.867	0.782	0.956	0.867	0.782	0.956	CLONAL	1	TRUE	1	0.515282451526526	2		470	488	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944877	31944877	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	135	425	0	ENST00000340398.3:c.224C>T	p.Ala75Val	p.A75V	ENST00000340398	NM_001013699.2	75	gCg/gTg	1/1	1	2	FACETS	0.963	0.88	1	0.963	0.88	1	CLONAL	1	TRUE	1	0.515282451526526	2		425	544	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424697	49424697	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	213	659	0	ENST00000301067.7:c.13650del	p.Leu4551CysfsTer2	p.L4551Cfs*2	ENST00000301067	NM_003482.3	4550	gcC/gc	40/54	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.515282451526526	2		659	791	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600011	10600011	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	227	708	0	ENST00000171111.5:c.1565C>A	p.Ala522Asp	p.A522D	ENST00000171111	NM_203500.1	522	gCt/gAt	5/6	1	2	FACETS	0.971	0.906	1	0.971	0.906	1	CLONAL	1	TRUE	1	0.515282451526526	2		708	907	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051094	13051094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1031122373	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	187	479	0	ENST00000316448.5:c.530G>A	p.Arg177Gln	p.R177Q	ENST00000316448	NM_004343.3	177	cGg/cAg	5/9	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.515282451526526	2		479	648	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288766	15288766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	51	154	0	ENST00000263388.2:c.3973C>T	p.Arg1325Cys	p.R1325C	ENST00000263388	NM_000435.2	1325	Cgc/Tgc	24/33	1	2	FACETS	0.798	0.685	0.92	0.798	0.685	0.92	CLONAL	1	TRUE	1	0.515282451526526	2		154	248	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47643526	47643526	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs63751027	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	188	571	0	ENST00000233146.2:c.1034G>A	p.Trp345Ter	p.W345*	ENST00000233146	NM_000251.2	345	tGg/tAg	6/16	1	2	FACETS	0.949	0.879	1	0.949	0.879	1	CLONAL	1	TRUE	1	0.515282451526526	2		571	769	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702289	47702290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	154	527	0	ENST00000233146.2:c.1887dup	p.Gly630ArgfsTer14	p.G630Rfs*14	ENST00000233146	NM_000251.2	629	caa/cAaa	12/16	1	2	FACETS	0.868	0.796	0.942	0.868	0.796	0.942	CLONAL	1	TRUE	1	0.515282451526526	2		527	689	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62311267	62311267	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765792997	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	115	387	0	ENST00000360203.5:c.1103C>T	p.Ser368Leu	p.S368L	ENST00000360203	NM_001283009.1	368	tCg/tTg	13/35	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.515282451526526	2		387	445	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845418	42845418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1051913801	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	150	555	0	ENST00000398585.3:c.844G>A	p.Gly282Arg	p.G282R	ENST00000398585	NM_001135099.1	282	Ggg/Agg	9/14	1	2	FACETS	0.97	0.891	1	0.97	0.891	1	CLONAL	1	TRUE	1	0.515282451526526	2		555	600	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098724	47098724	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	187	578	2	ENST00000409792.3:c.6550G>A	p.Ala2184Thr	p.A2184T	ENST00000409792	NM_014159.6	2184	Gct/Act	15/21	1	2	FACETS	0.964	0.893	1	0.964	0.893	1	CLONAL	1	TRUE	1	0.515282451526526	2		580	753	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031922	26031922	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	121	413	0	ENST00000244661.2:c.367A>G	p.Lys123Glu	p.K123E	ENST00000244661	NM_003537.3	123	Aaa/Gaa	1/1	1	2	FACETS	0.867	0.786	0.951	0.867	0.786	0.951	CLONAL	1	TRUE	1	0.515282451526526	2		413	542	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741409	145741409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs549497811	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	299	794	1	ENST00000428558.2:c.1094G>A	p.Arg365Gln	p.R365Q	ENST00000428558	NM_004260.3	365	cGg/cAg	5/22	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.515282451526526	2		795	1090	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139804414	139804414	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144636458	NA	P-0051753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	216	625	2	ENST00000247668.2:c.571G>A	p.Gly191Ser	p.G191S	ENST00000247668	NM_021138.3	191	Ggc/Agc	6/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.515282451526526	2		627	827	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0051754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	291	396	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.798465520955339	7	FACETS	0.995	0.937	1	0.332	0.312	0.352	CLONAL	2	TRUE	1	0.798465520955339	7		396	1097	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974721	21974721	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	191	366	0	ENST00000304494.5:c.106del	p.Ala36ArgfsTer17	p.A36Rfs*17	ENST00000304494	NM_000077.4	36	Gcg/cg	1/3	0.798465520955339	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.798465520955339	1		366	275	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427647	49427647	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0051754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	304	629	0	ENST00000301067.7:c.10841C>G	p.Ser3614Ter	p.S3614*	ENST00000301067	NM_003482.3	3614	tCa/tGa	39/54	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.798465520955339	2		629	707	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8338947	8338947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	166	453	0	ENST00000356435.5:c.5354G>A	p.Arg1785Lys	p.R1785K	ENST00000356435		1785	aGg/aAg	32/35	0.798465520955339	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.798465520955339	1		453	237	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307285	65307285	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0051754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	16	309	0	ENST00000342505.4:c.2404-1G>C		p.X802_splice	ENST00000342505	NM_002227.2	802			0.798465520955339	1	FACETS	0.096	0.071	0.127	0.096	0.071	0.127	SUBCLONAL	1	TRUE	0	0.798465520955339	1		309	250	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746044	162746044	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	173	372	0	ENST00000367921.3:c.2167A>T	p.Thr723Ser	p.T723S	ENST00000367921	NM_006182.2	723	Aca/Tca	16/18	1	2	FACETS	0.944	0.878	1	0.944	0.878	1	CLONAL	1	TRUE	1	0.798465520955339	2		372	459	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318864	163318864	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	84	378	1	ENST00000271452.3:c.1254G>T	p.Lys418Asn	p.K418N	ENST00000271452	NM_145697.2	418	aaG/aaT	13/14	1	2	FACETS	0.895	0.804	0.989	0.895	0.804	0.989	CLONAL	1	TRUE	1	0.798465520955339	2		379	235	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675437	241675437	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	79	256	0	ENST00000366560.3:c.385G>A	p.Glu129Lys	p.E129K	ENST00000366560	NM_000143.3	129	Gaa/Aaa	4/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.798465520955339	2		256	170	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	532757	532759	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TGG	TGG	-	novel	NA	P-0051754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	306	539	0	ENST00000451590.1:c.451-4_451-2del		p.X151_splice	ENST00000451590	NM_001130442.1	151			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.798465520955339	2		539	751	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251955	8251955	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	388	701	0	ENST00000335790.3:c.122A>G	p.Asp41Gly	p.D41G	ENST00000335790	NM_002315.2	41	gAc/gGc	2/4	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.798465520955339	2		701	919	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557719	21557719	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	328	642	0	ENST00000382592.4:c.2126A>C	p.Gln709Pro	p.Q709P	ENST00000382592	NM_014572.2	709	cAg/cCg	5/8	0.798465520955339	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.798465520955339	1		642	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	627	655	0	ENST00000269305.4:c.535del	p.His179MetfsTer68	p.H179Mfs*68	ENST00000269305	NM_001126112.2	179	Cat/at	5/11	0.798465520955339	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.798465520955339	2		655	744	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581325	48581325	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	165	468	0	ENST00000342988.3:c.629G>T	p.Ser210Ile	p.S210I	ENST00000342988	NM_005359.5	210	aGc/aTc	5/12	1	2	FACETS	0.898	0.833	0.966	0.898	0.833	0.966	CLONAL	1	TRUE	1	0.798465520955339	2		468	460	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295256	15295256	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1251987844	NA	P-0051754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1386	420	731	1	ENST00000263388.2:c.2416C>T	p.Arg806Ter	p.R806*	ENST00000263388	NM_000435.2	806	Cga/Tga	16/33	0.781759480292934	4	FACETS	1	0.977	1	0.349	0.331	0.367	CLONAL	1	TRUE	1	0.798465520955339	4		732	1806	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1255501	1255501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	288	581	0	ENST00000310581.5:c.3058C>T	p.Pro1020Ser	p.P1020S	ENST00000310581	NM_198253.2	1020	Cca/Tca	14/16	1	2	FACETS	0.987	0.933	1	0.987	0.933	1	CLONAL	1	TRUE	1	0.798465520955339	2		581	731	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591025	67591025	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374948680	NA	P-0051754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	104	292	0	ENST00000274335.5:c.1618G>A	p.Asp540Asn	p.D540N	ENST00000274335		540	Gac/Aac	12/15	0.798465520955339	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.798465520955339	1		292	155	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524687	137524687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	137	515	0	ENST00000367739.4:c.682A>G	p.Thr228Ala	p.T228A	ENST00000367739	NM_000416.2	228	Act/Gct	5/7	1	2	FACETS	0.927	0.854	1	0.927	0.854	1	CLONAL	1	TRUE	1	0.798465520955339	2		515	370	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410106	139410106	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	761	726	2	ENST00000277541.6:c.1732G>T	p.Gly578Cys	p.G578C	ENST00000277541	NM_017617.3	578	Ggc/Tgc	11/34	0.798465520955339	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.798465520955339	3		728	1310	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	186	230	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.873297785031288	2		230	397	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076824	72076824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	196	328	0	ENST00000357731.5:c.673C>T	p.Pro225Ser	p.P225S	ENST00000357731	NM_173808.2	225	Cct/Tct	5/7	1	2	FACETS	0.927	0.867	0.988	0.927	0.867	0.988	CLONAL	1	TRUE	1	0.873297785031288	2		328	484	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2214596	2214596	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0051755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	268	583	0	ENST00000398665.3:c.1923+1G>C		p.X641_splice	ENST00000398665	NM_032482.2	641			0.858613810883918	3	FACETS	0.877	0.824	0.933	0.439	0.412	0.467	CLONAL	1	TRUE	1	0.873297785031288	3		583	1005	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001293	150001293	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	281	533	0	ENST00000253339.5:c.2311T>C	p.Ser771Pro	p.S771P	ENST00000253339		771	Tca/Cca	4/7	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.873297785031288	2		533	620	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0051756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	53	213	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.33597745253913	1	FACETS	0.798	0.684	0.921	0.798	0.684	0.921	CLONAL	1	TRUE	0	0.33597745253913	1		213	329	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0051756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	144	650	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.33597745253913	1	FACETS	0.94	0.858	1	0.94	0.858	1	CLONAL	1	TRUE	0	0.33597745253913	1		650	759	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0051757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	592	341	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.227867654054023	8	FACETS	1	0.983	1			1	CLONAL	7	TRUE	NA	0.227867654054023	8		341	1213	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0051757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	107	331	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.227867654054023	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.227867654054023	1		331	637	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	360001	360001	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs771361430	NA	P-0051757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	66	775	0	ENST00000262320.3:c.1088A>G	p.Asn363Ser	p.N363S	ENST00000262320	NM_003502.3	363	aAt/aGt	4/11	1	2	FACETS	0.65	0.563	0.745	0.65	0.563	0.745	SUBCLONAL	1	TRUE	1	0.227867654054023	2		775	891	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633488	69633488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1419524448	NA	P-0051757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	37	291	2	ENST00000334134.2:c.214G>A	p.Ala72Thr	p.A72T	ENST00000334134	NM_005247.2	72	Gcc/Acc	1/3	0.191732700399344	3	FACETS	0.997	0.823	1	0.332	0.274	0.397	CLONAL	1	TRUE	0	0.227867654054023	3		293	363	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508743	148508743	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	58	443	0	ENST00000320356.2:c.1921G>T	p.Glu641Ter	p.E641*	ENST00000320356	NM_004456.4	641	Gaa/Taa	16/20	1	2	FACETS	0.671	0.575	0.775	0.671	0.575	0.775	SUBCLONAL	1	TRUE	1	0.227867654054023	2		443	759	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971202	21971205	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CATG	CATG	-	novel	NA	P-0051757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	97	470	0	ENST00000304494.5:c.153_156del	p.Met52Ter	p.M52*	ENST00000304494	NM_000077.4	51	gtCATG/gt	2/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.227867654054023	2		470	658	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0051758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	155	507	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.163044100660616	3	FACETS	0.833	0.762	0.907	0.833	0.762	0.907	CLONAL	2	TRUE	1	0.212704024081208	3		507	968	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0051758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	19	509	1	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.183249428441839	1	FACETS	0.25	0.189	0.323	0.25	0.189	0.323	SUBCLONAL	1	TRUE	0	0.212704024081208	1		510	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0051758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	177	764	0	ENST00000269305.4:c.560-2A>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			NA	2	FACETS	0.926	0.853	1			1	INDETERMINATE	2	TRUE	NA	0.212704024081208	2		764	899	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023559	27023560	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0051759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	265	519	0	ENST00000324856.7:c.671dup	p.Pro225AlafsTer175	p.P225Afs*175	ENST00000324856	NM_006015.4	222	tac/taCc	1/20	0.603754291020713	4	FACETS	0.842	0.792	0.893	0.842	0.792	0.893	CLONAL	2	TRUE	2	0.603754291020713	4		519	836	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023432	27023432	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	296	494	0	ENST00000324856.7:c.539del	p.Gly180AlafsTer52	p.G180Afs*52	ENST00000324856	NM_006015.4	180	Ggc/gc	1/20	0.603754291020713	4	FACETS	0.964	0.911	1	0.964	0.911	1	CLONAL	2	TRUE	2	0.603754291020713	4		494	816	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246002	46246002	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	294	401	0	ENST00000334344.6:c.4098del	p.Gly1367GlufsTer6	p.G1367Efs*6	ENST00000334344	NM_152641.2	1366	Aaa/aa	15/21	0.603754291020713	3	FACETS	0.981	0.942	1	0.981	0.942	1	CLONAL	3	TRUE	0	0.603754291020713	3		401	431	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001322	29001322	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	140	343	0	ENST00000282397.4:c.1410del	p.Cys471ValfsTer41	p.C471Vfs*41	ENST00000282397	NM_002019.4	470	ccC/cc	10/30	0.603754291020713	5	FACETS	0.873	0.8	0.949	0.582	0.533	0.633	CLONAL	2	TRUE	2	0.603754291020713	5		343	506	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212252695	212252695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1438732641	NA	P-0051759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	67	260	0	ENST00000342788.4:c.3158C>T	p.Pro1053Leu	p.P1053L	ENST00000342788	NM_005235.2	1053	cCt/cTt	26/28	0.603754291020713	4	FACETS	0.981	0.857	1	0.327	0.285	0.371	CLONAL	1	TRUE	1	0.603754291020713	4		260	363	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889121	76889121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	104	421	0	ENST00000373344.5:c.4889C>T	p.Thr1630Ile	p.T1630I	ENST00000373344	NM_000489.3	1630	aCt/aTt	18/35	1	2	FACETS	0.911	0.823	1	0.911	0.823	1	CLONAL	1	TRUE	1	0.603754291020713	2		421	378	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0051760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	53	283	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.855	0.736	0.982	0.855	0.736	0.982	CLONAL	1	TRUE	1	0.497810666987548	2		283	249	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526594	31526594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	276	581	0	ENST00000344624.3:c.446C>T	p.Pro149Leu	p.P149L	ENST00000344624		149	cCc/cTc	2/33	0.497810666987548	1	FACETS	0.888	0.847	0.928	1	0.996	1	CLONAL	2	TRUE	0	0.497810666987548	1		581	469	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945118	151945118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774935898	NA	P-0051760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	23	425	0	ENST00000262189.6:c.2401C>T	p.Pro801Ser	p.P801S	ENST00000262189	NM_170606.2	801	Cct/Tct	14/59	1	2	FACETS	0.291	0.227	0.366	0.291	0.227	0.366	SUBCLONAL	1	TRUE	1	0.497810666987548	2		425	317	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524343	148524343	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs973062748	NA	P-0051760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	66	310	0	ENST00000320356.2:c.641C>T	p.Pro214Leu	p.P214L	ENST00000320356	NM_004456.4	214	cCa/cTa	7/20	1	2	FACETS	0.989	0.868	1	0.989	0.868	1	CLONAL	1	TRUE	1	0.497810666987548	2		310	268	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797201	45797201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529008617	NA	P-0051760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	136	666	2	ENST00000450313.1:c.1214C>T	p.Pro405Leu	p.P405L	ENST00000450313	NM_012222.2	405	cCg/cTg	13/16	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.497810666987548	2		668	540	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136341	2136341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771289256	NA	P-0051760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	152	634	1	ENST00000219476.3:c.4810G>A	p.Gly1604Ser	p.G1604S	ENST00000219476	NM_000548.3	1604	Ggc/Agc	37/42	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.497810666987548	2		635	537	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830226	72830226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	80	379	0	ENST00000268489.5:c.6355G>A	p.Gly2119Arg	p.G2119R	ENST00000268489	NM_006885.3	2119	Gga/Aga	9/10	0.497810666987548	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.497810666987548	1		379	223	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434903	56434903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370703233	NA	P-0051760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	168	565	0	ENST00000407977.2:c.2234C>T	p.Ser745Phe	p.S745F	ENST00000407977		745	tCt/tTt	9/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.497810666987548	2		565	570	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78617545	78617545	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	82	352	0	ENST00000306801.3:c.283C>T	p.Pro95Ser	p.P95S	ENST00000306801	NM_020761.2	95	Cct/Tct	3/34	1	2	FACETS	0.811	0.719	0.909	0.811	0.719	0.909	CLONAL	1	TRUE	1	0.497810666987548	2		352	406	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78882674	78882674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	167	562	0	ENST00000306801.3:c.2465C>T	p.Pro822Leu	p.P822L	ENST00000306801	NM_020761.2	822	cCc/cTc	21/34	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.497810666987548	2		562	641	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212035	5212036	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0051760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	121	552	0	ENST00000357368.4:c.4995_4996delinsTT	p.Gln1666Ter	p.Q1666*	ENST00000357368	NM_002850.3	1665	atCCag/atTTag	32/38	1	2	FACETS	0.951	0.864	1	0.951	0.864	1	CLONAL	1	TRUE	1	0.497810666987548	2		552	511	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47604166	47604166	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	88	427	0	ENST00000263735.4:c.505G>A	p.Glu169Lys	p.E169K	ENST00000263735	NM_002354.2	169	Gag/Aag	5/9	1	2	FACETS	0.895	0.798	0.997	0.895	0.798	0.997	CLONAL	1	TRUE	1	0.497810666987548	2		427	395	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180375	38180375	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	114	644	1	ENST00000396334.3:c.223C>T	p.Arg75Trp	p.R75W	ENST00000396334	NM_002468.4	75	Cgg/Tgg	1/5	0.497810666987548	3	FACETS	0.908	0.819	1	0.454	0.409	0.501	CLONAL	1	TRUE	1	0.497810666987548	3		645	630	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106194018	106194018	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	68	292	0	ENST00000380013.4:c.4480T>A	p.Ser1494Thr	p.S1494T	ENST00000380013	NM_001127208.2	1494	Tca/Aca	10/11	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.497810666987548	2		292	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0051761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	239	655	4	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.640360634685743	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.640360634685743	1		659	482	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970969	21970969	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	234	586	0	ENST00000304494.5:c.389T>A	p.Leu130Gln	p.L130Q	ENST00000304494	NM_000077.4	130	cTg/cAg	2/3	0.640360634685743	1	FACETS	0.998	0.941	1	0.998	0.941	1	CLONAL	1	TRUE	0	0.640360634685743	1		586	498	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879854	37879854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	240	591	0	ENST00000269571.5:c.2149G>A	p.Glu717Lys	p.E717K	ENST00000269571		717	Gag/Aag	18/27	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.640360634685743	2		591	672	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082444	16082444	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	186	647	0	ENST00000281043.3:c.258G>C	p.Glu86Asp	p.E86D	ENST00000281043	NM_005378.4	86	gaG/gaC	2/3	0.386429321614951	1	FACETS	0.726	0.675	0.778	0.726	0.675	0.778	SUBCLONAL	1	TRUE	0	0.640360634685743	1		647	544	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0051764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	175	507	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.130577908797191	5	FACETS	0.999	0.922	1	0.666	0.615	0.719	INDETERMINATE	2	FALSE	2	0.39360318293811	5		507	708	SUCCESS
EED	8726	MSKCC	GRCh37	11	85968567	85968567	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	93	314	0	ENST00000263360.6:c.563G>T	p.Gly188Val	p.G188V	ENST00000263360	NM_003797.3	188	gGc/gTc	6/12	0.361916918504603	3	FACETS	0.977	0.87	1	0.488	0.435	0.545	CLONAL	1	FALSE	1	0.39360318293811	3		314	579	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233727	233727	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2247	244	666	0	ENST00000264932.6:c.1031C>G	p.Ser344Cys	p.S344C	ENST00000264932	NM_004168.2	344	tCt/tGt	8/15	0.39360318293811	11	FACETS	1	0.99	1			1	CLONAL	1	FALSE	NA	0.39360318293811	11		666	2491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0051765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	254	629	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.894	0.836	0.954	0.894	0.836	0.954	CLONAL	1	TRUE	1	0.477468006682785	2		631	1190	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11308017	11308017	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	97	730	0	ENST00000361445.4:c.975G>C	p.Gln325His	p.Q325H	ENST00000361445	NM_004958.3	325	caG/caC	7/58	0.178525980306423	1	FACETS	0.317	0.281	0.354	0.317	0.281	0.354	INDETERMINATE	1	TRUE	0	0.477468006682785	1		730	977	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78422307	78422308	+	frameshift_variant	Frame_Shift_Ins	INS	GG	GG	AGTGGC	novel	NA	P-0051765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	104	495	0	ENST00000370768.2:c.1654_1655delinsGCCACT	p.Pro552AlafsTer16	p.P552Afs*16	ENST00000370768	NM_003902.3	552	CCa/GCCACTa	17/20	0.423223284402153	3	FACETS	0.571	0.51	0.636			1	SUBCLONAL	1	TRUE	NA	0.477468006682785	3		495	945	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456472	32456472	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	114	415	0	ENST00000332351.3:c.420C>G	p.Ile140Met	p.I140M	ENST00000332351	NM_024426.4	140	atC/atG	1/10	1	2	FACETS	0.888	0.802	0.977	0.888	0.802	0.977	CLONAL	1	TRUE	1	0.477468006682785	2		415	538	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0051765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	20	533	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.101	0.077	0.131	0.101	0.077	0.131	SUBCLONAL	1	TRUE	1	0.477468006682785	2		533	826	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434673	110434673	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	111	854	0	ENST00000375856.3:c.3728C>G	p.Thr1243Ser	p.T1243S	ENST00000375856	NM_003749.2	1243	aCc/aGc	1/2	0.232273872762734	1	FACETS	0.366	0.328	0.406	0.366	0.328	0.406	INDETERMINATE	1	TRUE	0	0.477468006682785	1		854	967	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23640569	23640569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	211	678	1	ENST00000261584.4:c.2542G>A	p.Asp848Asn	p.D848N	ENST00000261584	NM_024675.3	848	Gat/Aat	6/13	0.404007054183647	1	FACETS	0.823	0.765	0.881	0.823	0.765	0.881	CLONAL	1	TRUE	0	0.477468006682785	1		679	818	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560172	29560172	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	131	415	0	ENST00000356175.3:c.3649G>T	p.Asp1217Tyr	p.D1217Y	ENST00000356175	NM_000267.3	1217	Gat/Tat	27/57	1	2	FACETS	0.785	0.713	0.86	0.785	0.713	0.86	SUBCLONAL	1	TRUE	1	0.477468006682785	2		415	699	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40461480	40461480	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1215	276	1213	2	ENST00000345506.4:c.2200C>A	p.Pro734Thr	p.P734T	ENST00000345506	NM_003152.3	734	Ccc/Acc	19/20	1	2	FACETS	0.775	0.726	0.826	0.775	0.726	0.826	SUBCLONAL	1	TRUE	1	0.477468006682785	2		1215	1491	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384932	17384932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	248	869	0	ENST00000359435.4:c.482C>T	p.Ser161Phe	p.S161F	ENST00000359435	NM_001033549.1	161	tCc/tTc	5/9	0.404007054183647	1	FACETS	0.774	0.724	0.825	0.774	0.724	0.825	SUBCLONAL	1	TRUE	0	0.477468006682785	1		869	1022	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954591	17954591	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	253	915	0	ENST00000458235.1:c.303G>C	p.Arg101Ser	p.R101S	ENST00000458235	NM_000215.3	101	agG/agC	3/24	0.404007054183647	1	FACETS	0.77	0.72	0.821	0.77	0.72	0.821	SUBCLONAL	1	TRUE	0	0.477468006682785	1		915	1048	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791797	42791797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	96	849	1	ENST00000575354.2:c.683G>A	p.Arg228Gln	p.R228Q	ENST00000575354	NM_015125.3	228	cGg/cAg	5/20	1	2	FACETS	0.338	0.3	0.379	0.338	0.3	0.379	SUBCLONAL	1	TRUE	1	0.477468006682785	2		850	1188	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716298	52716298	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	207	768	0	ENST00000322088.6:c.742C>G	p.Leu248Val	p.L248V	ENST00000322088	NM_014225.5	248	Ctg/Gtg	6/15	NA	2	FACETS	0.792	0.734	0.852			1	INDETERMINATE	1	TRUE	NA	0.477468006682785	2		768	1095	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659982	227659982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1166934768	NA	P-0051765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	108	815	0	ENST00000305123.5:c.3473G>A	p.Gly1158Glu	p.G1158E	ENST00000305123	NM_005544.2	1158	gGa/gAa	1/2	0.196445924200243	2	FACETS	0.407	0.364	0.453	0.204	0.182	0.227	INDETERMINATE	1	TRUE	0	0.477468006682785	2		815	1111	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680584	30680584	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	201	654	0	ENST00000376406.3:c.1135G>C	p.Asp379His	p.D379H	ENST00000376406	NM_014641.2	379	Gat/Cat	5/15	0.27654618930844	3	FACETS	1	0.964	1	0.533	0.493	0.573	INDETERMINATE	1	TRUE	1	0.477468006682785	3		654	979	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683777	162683777	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	127	495	0	ENST00000366898.1:c.192G>C	p.Gln64His	p.Q64H	ENST00000366898	NM_004562.2	64	caG/caC	3/12	0.232273872762734	1	FACETS	0.684	0.622	0.749	0.684	0.622	0.749	INDETERMINATE	1	TRUE	0	0.477468006682785	1		495	592	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633439	8633440	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0051765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	123	456	1	ENST00000356435.5:c.229_230delinsTT	p.Gly77Leu	p.G77L	ENST00000356435		77	GGg/TTg	3/35	0.477468006682785	1	FACETS	0.842	0.766	0.92	0.842	0.766	0.92	CLONAL	1	TRUE	0	0.477468006682785	1		457	466	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	203	230	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.716560205356926	2		230	540	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0051767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	201	497	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.716560205356926	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.716560205356926	1		498	311	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915523	112915523	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28933386	NA	P-0051767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	302	570	0	ENST00000351677.2:c.922A>G	p.Asn308Asp	p.N308D	ENST00000351677	NM_002834.3	308	Aat/Gat	8/16	1	2	FACETS	0.95	0.898	1	0.95	0.898	1	CLONAL	1	TRUE	1	0.716560205356926	2		570	887	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141567331	141567331	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	247	506	0	ENST00000220592.5:c.883C>T	p.Pro295Ser	p.P295S	ENST00000220592	NM_012154.3	295	Ccg/Tcg	8/19	1	2	FACETS	0.996	0.936	1	0.996	0.936	1	CLONAL	1	TRUE	1	0.716560205356926	2		506	692	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0051768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	91	289	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.184768365277382	4	FACETS	0.884	0.793	0.979	1	0.965	1	CLONAL	4	FALSE	1	0.184766378709424	4		289	330	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0051768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	68	556	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.184768365277382	3	FACETS	0.995	0.87	1	0.995	0.87	1	CLONAL	2	FALSE	1	0.184766378709424	3		556	404	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0051768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	70	529	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.146919087526009	0	FACETS	1	0.905	1			1	CLONAL	2	FALSE	0	0.184766378709424	0		529	299	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692848	89692848	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	17	208	0	ENST00000371953.3:c.332G>A	p.Trp111Ter	p.W111*	ENST00000371953	NM_000314.4	111	tGg/tAg	5/9	0.184766378709424	5	FACETS	1	0.777	1	0.687	0.519	0.881	CLONAL	2	FALSE	2	0.184766378709424	5		208	114	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058072	27058072	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	31	486	0	ENST00000324856.7:c.1780C>T	p.Gln594Ter	p.Q594*	ENST00000324856	NM_006015.4	594	Cag/Tag	3/20	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	FALSE	1	0.184766378709424	2		486	261	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	33	540	0	ENST00000263967.3:c.3012G>T	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atT	21/21	0.184768365277382	3	FACETS	1	0.901	1	0.584	0.477	0.705	CLONAL	1	FALSE	1	0.184766378709424	3		540	334	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247172	153247173	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0051768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	34	355	0	ENST00000281708.4:c.1629_1630del	p.Arg543SerfsTer7	p.R543Sfs*7	ENST00000281708	NM_033632.3	543	agAGtc/agtc	10/12	1	2	FACETS	0.825	0.679	0.987	1	0.955	1	CLONAL	2	FALSE	1	0.184766378709424	2		355	223	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711990	89712025	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCCAATGTTCAGTGGCGGAACTTGCAGTAAGTGCT	TTCCAATGTTCAGTGGCGGAACTTGCAGTAAGTGCT	-	novel	NA	P-0051768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	53	417	0	ENST00000371953.3:c.609_634+10del		p.X203_splice	ENST00000371953	NM_000314.4	203		6/9	0.184766378709424	5	FACETS	1	0.937	1	1	0.937	1	CLONAL	3	FALSE	2	0.184766378709424	5		417	212	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920765	100920781	+	frameshift_variant	Frame_Shift_Del	DEL	AGAATGATGATTCTTTC	AGAATGATGATTCTTTC	-	novel	NA	P-0051768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	51	513	0	ENST00000325455.5:c.2367_2383del	p.Met789IlefsTer20	p.M789Ifs*20	ENST00000325455	NM_001202474.3	789	atGAAAGAATCATCATTCTat/atat	6/8	1	2	FACETS	1	0.94	1	1	0.979	1	CLONAL	2	FALSE	1	0.184766378709424	2		513	233	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199941	128199941	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754242887	NA	P-0051768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	42	603	1	ENST00000341105.2:c.1364C>T	p.Thr455Ile	p.T455I	ENST00000341105	NM_032638.4	455	aCt/aTt	6/6	0.184768365277382	3	FACETS	1	0.952	1	0.705	0.591	0.832	CLONAL	1	FALSE	1	0.184766378709424	3		604	352	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508767	148508767	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	51	462	0	ENST00000320356.2:c.1897A>C	p.Ile633Leu	p.I633L	ENST00000320356	NM_004456.4	633	Atc/Ctc	16/20	0.184766378709424	5	FACETS	1	0.904	1	0.539	0.46	0.624	CLONAL	2	FALSE	1	0.184766378709424	5		462	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0051769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	203	655	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.316729898801707	6	FACETS	0.879	0.822	0.937	0.659	0.616	0.703	INDETERMINATE	3	TRUE	2	0.690568533037725	6		655	531	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0051769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	93	408	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.323093655568487	4	FACETS	0.925	0.837	1	0.925	0.837	1	INDETERMINATE	2	TRUE	2	0.690568533037725	4		408	246	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0051769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	192	655	4	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.316729898801707	6	FACETS	0.923	0.863	0.985	0.693	0.647	0.739	INDETERMINATE	3	TRUE	2	0.690568533037725	6		659	478	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0051769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	21	322	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.638791200364651	5	FACETS	0.118	0.09	0.152	0.039	0.03	0.051	SUBCLONAL	1	TRUE	2	0.690568533037725	5		322	1046	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861563	152861563	+	synonymous_variant	Silent	SNP	G	G	A	rs139660436	NA	P-0051769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	22	721	1	ENST00000406277.2:c.189C>T	p.Asp63=	p.D63=	ENST00000406277	NM_152274.4	63	gaC/gaT	4/7	0.290781442629481		FACETS		NA	1				INDETERMINATE	1	TRUE	0	0.690568533037725	0		722	275	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0051769-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	96	655	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.190644170255587	3	FACETS	1	0.942	1	0.543	0.484	0.605	INDETERMINATE	1	TRUE	1	0.35	3		655	594	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0051769-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	32	408	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.35	2		408	172	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0051769-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	57	655	4	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.190644170255587	3	FACETS	0.758	0.651	0.874	0.379	0.325	0.437	INDETERMINATE	1	TRUE	1	0.35	3		659	505	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0051770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	250	435	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.384182780456274	3	FACETS	0.913	0.856	0.971	0.913	0.856	0.971	CLONAL	2	TRUE	1	0.384182780456274	3		436	850	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0051770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	262	289	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.384182780456274	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.384182780456274	3		289	733	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0051770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	293	535	0	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	0.384182780456274	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.384182780456274	2		535	720	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434491	110434491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	184	627	2	ENST00000375856.3:c.3910G>A	p.Gly1304Ser	p.G1304S	ENST00000375856	NM_003749.2	1304	Ggc/Agc	1/2	0.384182780456274	3	FACETS	1	0.934	1	0.508	0.468	0.549	CLONAL	1	TRUE	1	0.384182780456274	3		629	1125	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	249	230	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.816977992139937	2		230	574	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0051772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	861	822	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	1	0.992	1	1	0.999	1	CLONAL	2	TRUE	1	0.816977992139937	2		822	1037	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38173513	38173513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	330	615	2	ENST00000317025.8:c.1903C>T	p.Arg635Cys	p.R635C	ENST00000317025	NM_023034.1	635	Cgc/Tgc	10/24	1	2	FACETS	0.902	0.855	0.949	0.902	0.855	0.949	CLONAL	1	TRUE	1	0.816977992139937	2		617	896	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275782	38275782	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	323	703	1	ENST00000425967.3:c.1487T>G	p.Leu496Arg	p.L496R	ENST00000425967	NM_001174067.1	496	cTt/cGt	11/19	1	2	FACETS	0.926	0.878	0.975	0.926	0.878	0.975	CLONAL	1	TRUE	1	0.816977992139937	2		704	854	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218349	69218349	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2384	185	512	0	ENST00000462284.1:c.441G>C	p.Glu147Asp	p.E147D	ENST00000462284	NM_002392.5	147	gaG/gaC	7/11	0.583189105576879	12	FACETS	0.967	0.888	1			1	CLONAL	1	TRUE	NA	0.583189105576879	12		512	2569	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712646	43712646	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	62	800	0	ENST00000382044.4:c.4538G>C	p.Arg1513Pro	p.R1513P	ENST00000382044	NM_001141980.1	1513	cGa/cCa	21/28	0.29167124334525	3	FACETS	0.285	0.245	0.328	0.142	0.122	0.164	INDETERMINATE	1	TRUE	1	0.583189105576879	3		800	965	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944376	131944376	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	48	248	0	ENST00000265335.6:c.2788A>T	p.Ile930Phe	p.I930F	ENST00000265335		930	Atc/Ttc	17/25	0.292266379720369	1	FACETS	0.301	0.255	0.352	0.301	0.255	0.352	INDETERMINATE	1	TRUE	0	0.583189105576879	1		248	387	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034451	47034451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	291	693	1	ENST00000377604.3:c.536G>A	p.Ser179Asn	p.S179N	ENST00000377604	NM_001204468.1	179	aGt/aAt	6/24	0.18540804175507	5	FACETS	1	0.968	1	0.692	0.653	0.732	INDETERMINATE	2	TRUE	2	0.583189105576879	5		694	901	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0051776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	224	727	3	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.255121408705869	2	FACETS	0.866	0.807	0.927	0.866	0.807	0.927	CLONAL	2	TRUE	0	0.283237825931014	2		730	913	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88651892	88651892	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	137	353	0	ENST00000372037.3:c.239G>C	p.Gly80Ala	p.G80A	ENST00000372037	NM_004329.2	80	gGa/gCa	5/13	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.283237825931014	2		353	651	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681438	88681438	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659155	NA	P-0051776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	117	551	0	ENST00000372037.3:c.1328G>A	p.Arg443His	p.R443H	ENST00000372037	NM_004329.2	443	cGt/cAt	11/13	1	2	FACETS	0.889	0.801	0.983	0.889	0.801	0.983	CLONAL	1	TRUE	1	0.283237825931014	2		551	929	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221493	36221493	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	120	775	0	ENST00000222270.7:c.5252G>T	p.Gly1751Val	p.G1751V	ENST00000222270	NM_014727.1	1751	gGa/gTa	25/37	0.283237825931014	3	FACETS	0.838	0.755	0.927	0.419	0.377	0.464	CLONAL	1	TRUE	1	0.283237825931014	3		775	1154	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	157	373	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.502363310566907	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.502363310566907	1		373	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	242	734	0	ENST00000269305.4:c.166G>T	p.Glu56Ter	p.E56*	ENST00000269305	NM_001126112.2	56	Gaa/Taa	4/11	0.502363310566907	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.502363310566907	1		734	698	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561764	55561764	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913505	NA	P-0051777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	71	337	0	ENST00000288135.5:c.154G>A	p.Asp52Asn	p.D52N	ENST00000288135	NM_000222.2	52	Gac/Aac	2/21	0.322929213198365	1	FACETS	0.556	0.487	0.628	0.556	0.487	0.628	SUBCLONAL	1	TRUE	0	0.502363310566907	1		337	381	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs730881677	NA	P-0051777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	139	409	0	ENST00000304494.5:c.151-1G>C		p.X51_splice	ENST00000304494	NM_000077.4	51			0.502363310566907	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.502363310566907	1		409	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912654	NA	P-0051777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	281	799	1	ENST00000269305.4:c.469G>A	p.Val157Ile	p.V157I	ENST00000269305	NM_001126112.2	157	Gtc/Atc	5/11	0.502363310566907	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.502363310566907	1		800	724	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090395	37090395	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1320565129	NA	P-0051777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	60	405	0	ENST00000231790.2:c.1990G>A	p.Val664Met	p.V664M	ENST00000231790	NM_000249.3	664	Gtg/Atg	18/19	1	2	FACETS	0.433	0.373	0.498	0.433	0.373	0.498	SUBCLONAL	1	TRUE	1	0.502363310566907	2		405	552	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0051782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	984	289	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.726198712828778	8	FACETS	1	0.988	1	1	0.988	1	CLONAL	8	TRUE	0	0.726198712828778	8		289	1077	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	258	458	2	ENST00000304494.5:c.172del	p.Arg58GlufsTer88	p.R58Efs*88	ENST00000304494	NM_000077.4	58	Cga/ga	2/3	0.726198712828778	2	FACETS	0.973	0.934	1	0.973	0.934	1	CLONAL	2	TRUE	0	0.726198712828778	2		460	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576899	7576900	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0051782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	640	650	2	ENST00000269305.4:c.946_947insT	p.Pro316LeufsTer21	p.P316Lfs*21	ENST00000269305	NM_001126112.2	316	ccc/cTcc	9/11	0.726198712828778	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	0	0.726198712828778	3		652	792	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432495	49432495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	630	610	3	ENST00000301067.7:c.8644C>T	p.His2882Tyr	p.H2882Y	ENST00000301067	NM_003482.3	2882	Cac/Tac	34/54	0.726198712828778	3	FACETS	1	0.993	1			1	CLONAL	3	TRUE	NA	0.726198712828778	3		613	762	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347363	89347363	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769501359	NA	P-0051782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	478	674	1	ENST00000301030.4:c.5587G>T	p.Asp1863Tyr	p.D1863Y	ENST00000301030	NM_001256183.1	1863	Gac/Tac	9/13	0.726198712828778	6	FACETS	1	0.966	1	0.507	0.484	0.531	CLONAL	2	TRUE	2	0.726198712828778	6		675	1592	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0051783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	59	289	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.18	2		289	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0051783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	38	508	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	1	2	FACETS	0.707	0.583	0.846	0.707	0.583	0.846	SUBCLONAL	1	TRUE	1	0.18	2		508	597	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974697	21974697	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	35	373	0	ENST00000304494.5:c.130del	p.Tyr44ThrfsTer9	p.Y44Tfs*9	ENST00000304494	NM_000077.4	44	Tac/ac	1/3	1	2	FACETS	0.878	0.719	1	0.878	0.719	1	CLONAL	1	TRUE	1	0.18	2		373	443	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0051784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	149	423	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.968	0.892	1	0.968	0.892	1	CLONAL	1	TRUE	1	0.684191792100313	2		423	450	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164136	47164136	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0051784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	129	320	0	ENST00000409792.3:c.1990A>T	p.Arg664Ter	p.R664*	ENST00000409792	NM_014159.6	664	Aga/Tga	3/21	1	2	FACETS	0.936	0.856	1	0.936	0.856	1	CLONAL	1	TRUE	1	0.684191792100313	2		320	403	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084124	47084124	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	174	574	0	ENST00000409792.3:c.7165del	p.Ile2389LeufsTer22	p.I2389Lfs*22	ENST00000409792	NM_014159.6	2389	Att/tt	17/21	1	2	FACETS	0.886	0.821	0.954	0.886	0.821	0.954	CLONAL	1	TRUE	1	0.684191792100313	2		574	574	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099929	157099929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761134074	NA	P-0051784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	165	545	0	ENST00000346085.5:c.866G>A	p.Gly289Glu	p.G289E	ENST00000346085	NM_020732.3	289	gGg/gAg	1/20	0.684191792100313	1	FACETS	0.899	0.839	0.96	0.899	0.839	0.96	CLONAL	1	TRUE	0	0.684191792100313	1		545	353	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425056	49425056	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs562043836	NA	P-0051784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	79	785	2	ENST00000301067.7:c.13432C>T	p.Arg4478Trp	p.R4478W	ENST00000301067	NM_003482.3	4478	Cgg/Tgg	39/54	1	2	FACETS	0.258	0.226	0.292	0.258	0.226	0.292	SUBCLONAL	1	TRUE	1	0.684191792100313	2		787	895	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593422	48593423	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0051784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	38	355	0	ENST00000342988.3:c.1176dup	p.Gly393ArgfsTer2	p.G393Rfs*2	ENST00000342988	NM_005359.5	391	-/A	10/12	0.650270041351809	1	FACETS	0.241	0.2	0.287	0.241	0.2	0.287	SUBCLONAL	1	TRUE	0	0.684191792100313	1		355	303	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0051784-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	84	423	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.367202724884018	2		423	368	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0051784-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	104	533	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.367202724884018	2		533	519	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164136	47164136	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0051784-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	72	320	0	ENST00000409792.3:c.1990A>T	p.Arg664Ter	p.R664*	ENST00000409792	NM_014159.6	664	Aga/Tga	3/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.367202724884018	2		320	312	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084124	47084124	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051784-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	95	574	0	ENST00000409792.3:c.7165del	p.Ile2389LeufsTer22	p.I2389Lfs*22	ENST00000409792	NM_014159.6	2389	Att/tt	17/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.367202724884018	2		574	441	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099929	157099929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761134074	NA	P-0051784-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	77	545	0	ENST00000346085.5:c.866G>A	p.Gly289Glu	p.G289E	ENST00000346085	NM_020732.3	289	gGg/gAg	1/20	0.367202724884018	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.367202724884018	1		545	265	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524547	103524547	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs773559180	NA	P-0051784-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	29	174	0	ENST00000355739.4:c.2679-1G>A		p.X893_splice	ENST00000355739	NM_000123.3	893			1	2	FACETS	0.878	0.711	1	0.878	0.711	1	CLONAL	1	TRUE	1	0.367202724884018	2		174	180	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0051785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	195	509	1	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.794329242580622	1	FACETS	0.977	0.927	1	0.977	0.927	1	CLONAL	1	TRUE	0	0.794329242580622	1		510	303	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881329	37881329	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	609	742	0	ENST00000269571.5:c.2521C>A	p.Leu841Ile	p.L841I	ENST00000269571		841	Ctc/Atc	21/27	0.393560466182329	3	FACETS	1	0.997	1	0.808	0.786	0.83	INDETERMINATE	2	TRUE	0	0.794329242580622	3		742	884	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221951	1221951	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	134	728	1	ENST00000326873.7:c.866T>A	p.Met289Lys	p.M289K	ENST00000326873	NM_000455.4	289	aTg/aAg	7/10	0.794329242580622	1	FACETS	0.427	0.391	0.465	0.427	0.391	0.465	SUBCLONAL	1	TRUE	0	0.794329242580622	1		729	476	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221966	1221966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	225	726	0	ENST00000326873.7:c.881C>T	p.Pro294Leu	p.P294L	ENST00000326873	NM_000455.4	294	cCg/cTg	7/10	0.794329242580622	1	FACETS	0.707	0.666	0.748	0.707	0.666	0.748	SUBCLONAL	1	TRUE	0	0.794329242580622	1		726	483	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602335	10602335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	311	825	0	ENST00000171111.5:c.1243C>T	p.Arg415Cys	p.R415C	ENST00000171111	NM_203500.1	415	Cgc/Tgc	3/6	0.794329242580622	1	FACETS	0.981	0.942	1	0.981	0.942	1	CLONAL	1	TRUE	0	0.794329242580622	1		825	481	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735466	40735466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182388300	NA	P-0051785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	182	662	1	ENST00000373198.4:c.3407G>A	p.Arg1136His	p.R1136H	ENST00000373198	NM_133170.3	1136	cGt/cAt	25/32	0.237720576248252	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.794329242580622	0		663	519	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713622	52713622	+	frameshift_variant	Frame_Shift_Ins	INS	T	T	ACA	novel	NA	P-0051785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	83	441	0	ENST00000394830.3:c.106delinsTGT	p.Arg36CysfsTer10	p.R36Cfs*10	ENST00000394830	NM_018313.4	36	Agg/TGTgg	2/30	0.794329242580622	1	FACETS	0.36	0.32	0.402	0.36	0.32	0.402	SUBCLONAL	1	TRUE	0	0.794329242580622	1		441	350	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280151	142280151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	174	369	0	ENST00000350721.4:c.1283C>T	p.Ser428Leu	p.S428L	ENST00000350721	NM_001184.3	428	tCa/tTa	5/47	1	2	FACETS	0.907	0.843	0.973	0.907	0.843	0.973	CLONAL	1	TRUE	1	0.794329242580622	2		369	483	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240783	53240783	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	268	584	0	ENST00000375401.3:c.1297G>C	p.Glu433Gln	p.E433Q	ENST00000375401	NM_004187.3	433	Gag/Cag	10/26	0.794329242580622	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.794329242580622	1		584	387	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78426047	78426047	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	298	531	0	ENST00000370768.2:c.1478C>T	p.Pro493Leu	p.P493L	ENST00000370768	NM_003902.3	493	cCa/cTa	15/20	1	2	FACETS	0.979	0.928	1	0.979	0.928	1	CLONAL	1	TRUE	1	0.902202451946189	2		531	675	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28883020	28883020	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1238611113	NA	P-0051786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	239	418	0	ENST00000282397.4:c.3680C>T	p.Thr1227Ile	p.T1227I	ENST00000282397	NM_002019.4	1227	aCc/aTc	28/30	1	2	FACETS	0.953	0.898	1	0.953	0.898	1	CLONAL	1	TRUE	1	0.902202451946189	2		418	556	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488718	212488718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267599191	NA	P-0051786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	344	397	0	ENST00000342788.4:c.2131C>T	p.Arg711Cys	p.R711C	ENST00000342788	NM_005235.2	711	Cgt/Tgt	18/28	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.902202451946189	2		397	688	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525104	9525104	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	214	394	0	ENST00000353224.5:c.1781C>T	p.Ser594Phe	p.S594F	ENST00000353224	NM_177990.2	594	tCc/tTc	8/10	1	2	FACETS	0.962	0.904	1	0.962	0.904	1	CLONAL	1	TRUE	1	0.902202451946189	2		394	493	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1959713	1959713	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs548600548	NA	P-0051786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	178	276	0	ENST00000382891.5:c.2935C>T	p.Arg979Ter	p.R979*	ENST00000382891	NM_133335.3	979	Cga/Tga	16/22	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.902202451946189	2		276	362	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453124	140453136	+	protein_altering_variant	In_Frame_Del	DEL	CATCGAGATTTCA	CATCGAGATTTCA	T	novel	NA	P-0051786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	413	328	0	ENST00000288602.6:c.1799_1811delinsA	p.Val600_Trp604delinsGlu	p.V600_W604delinsE	ENST00000288602	NM_004333.4	600	gTGAAATCTCGATGg/gAg	15/18	0.316628402003402	5	FACETS	0.923	0.886	0.96			1	INDETERMINATE	3	TRUE	NA	0.902202451946189	5		328	778	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156720	20156720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	335	371	0	ENST00000379607.5:c.37C>T	p.Arg13Cys	p.R13C	ENST00000379607	NM_001412.3	13	Cgc/Tgc	2/7	0.840731197493376	1	FACETS	0.989	0.961	1	0.989	0.961	1	CLONAL	1	TRUE	0	0.902202451946189	1		371	412	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0051787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	15	591	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	0.3	1	FACETS	0.843	0.62	1	0.843	0.62	1	CLONAL	1	TRUE	0	0.22	1		591	144	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971029	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0051787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	17	522	0	ENST00000304494.5:c.329_330delinsAA	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tGG/tAA	2/3	1	2	FACETS	0.773	0.585	0.988	1	0.909	1	CLONAL	2	TRUE	1	0.22	2		522	100	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450080	32450080	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1060501259	NA	P-0051787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	11	586	0	ENST00000332351.3:c.732C>G	p.Phe244Leu	p.F244L	ENST00000332351	NM_024426.4	244	ttC/ttG	2/10	1	2	FACETS	0.676	0.468	0.931	0.676	0.468	0.931	SUBCLONAL	1	TRUE	1	0.22	2		586	148	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622250	117622250	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	23	372	0	ENST00000368508.3:c.6620C>T	p.Thr2207Ile	p.T2207I	ENST00000368508	NM_002944.2	2207	aCt/aTt	42/43	0.3	2	FACETS	1	0.877	1			1	CLONAL	1	TRUE	NA	0.22	2		372	177	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346540	89346540	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	10	583	0	ENST00000301030.4:c.6410C>T	p.Ser2137Phe	p.S2137F	ENST00000301030	NM_001256183.1	2137	tCc/tTc	9/13	1	2	FACETS	0.866	0.591	1	0.866	0.591	1	CLONAL	1	TRUE	1	0.22	2		583	105	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396844	396844	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747093980	NA	P-0051787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	11	705	1	ENST00000262320.3:c.182C>T	p.Pro61Leu	p.P61L	ENST00000262320	NM_003502.3	61	cCg/cTg	2/11	0.3	1	FACETS	0.695	0.483	0.956	0.695	0.483	0.956	SUBCLONAL	1	TRUE	0	0.22	1		706	128	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726954	46726954	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	11	442	0	ENST00000371975.4:c.788G>C	p.Gly263Ala	p.G263A	ENST00000371975	NM_003579.3	263	gGa/gCa	8/18	1	2	FACETS	0.621	0.43	0.857	0.621	0.43	0.857	SUBCLONAL	1	TRUE	1	0.22	2		442	161	SUCCESS
ATM	472	MSKCC	GRCh37	11	108099997	108099997	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	16	269	0	ENST00000278616.4:c.278A>C	p.Lys93Thr	p.K93T	ENST00000278616	NM_000051.3	93	aAg/aCg	4/63	1	2	FACETS	0.938	0.698	1	0.938	0.698	1	CLONAL	1	TRUE	1	0.22	2		269	155	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684076	29684076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138839077	NA	P-0051787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	17	468	0	ENST00000356175.3:c.7774C>T	p.Pro2592Ser	p.P2592S	ENST00000356175	NM_000267.3	2592	Ccg/Tcg	52/57	1	2	FACETS	1	0.764	1	1	0.764	1	CLONAL	1	TRUE	1	0.22	2		468	152	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676255	37676255	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	17	470	0	ENST00000447079.4:c.3010G>C	p.Asp1004His	p.D1004H	ENST00000447079	NM_015083.1	1004	Gat/Cat	11/14	1	2	FACETS	1	0.768	1	1	0.768	1	CLONAL	1	TRUE	1	0.22	2		470	151	SUCCESS
YES1	7525	MSKCC	GRCh37	18	739752	739752	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	23	428	0	ENST00000314574.4:c.1120G>T	p.Val374Phe	p.V374F	ENST00000314574	NM_005433.3	374	Gtt/Ttt	9/12	0.152832296910827	3	FACETS	1	0.916	1	0.695	0.546	0.864	CLONAL	1	TRUE	1	0.22	3		428	167	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223048	5223048	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	11	751	0	ENST00000357368.4:c.2755G>C	p.Glu919Gln	p.E919Q	ENST00000357368	NM_002850.3	919	Gag/Cag	18/38	0.115093900880749	0	FACETS	0.743	0.518	1			1	INDETERMINATE	1	TRUE	0	0.22	0		751	105	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11015675	11015675	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	18	580	0	ENST00000327064.4:c.269G>A	p.Cys90Tyr	p.C90Y	ENST00000327064	NM_199141.1	90	tGc/tAc	2/16	0.115093900880749	0	FACETS	0.868	0.659	1			1	INDETERMINATE	1	TRUE	0	0.22	0		580	147	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256694	19256694	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	20	907	0	ENST00000162023.5:c.1019C>T	p.Pro340Leu	p.P340L	ENST00000162023		340	cCc/cTc	13/13	0.115093900880749	0	FACETS	1	0.846	1			1	INDETERMINATE	1	TRUE	0	0.22	0		907	126	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49399990	49399990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	10	602	0	ENST00000418115.1:c.347G>A	p.Gly116Glu	p.G116E	ENST00000418115	NM_001664.2	116	gGg/gAg	4/5	1	2	FACETS	0.61	0.414	0.855	0.61	0.414	0.855	SUBCLONAL	1	TRUE	1	0.22	2		602	149	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138400808	138400809	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AT	novel	NA	P-0051787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	12	300	0	ENST00000289153.2:c.2504_2504+1delinsAT		p.X835_splice	ENST00000289153	NM_006219.2	835		17/22	1	2	FACETS	1	0.716	1	1	0.716	1	CLONAL	1	TRUE	1	0.22	2		300	108	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602754	55602754	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	21	325	0	ENST00000288135.5:c.2575C>G	p.Leu859Val	p.L859V	ENST00000288135	NM_000222.2	859	Ctt/Gtt	18/21	0.115093900880749	0	FACETS	1	0.865	1			1	INDETERMINATE	1	TRUE	0	0.22	0		325	128	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924487	131924487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1052007421	NA	P-0051787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	23	329	0	ENST00000265335.6:c.1160C>T	p.Pro387Leu	p.P387L	ENST00000265335		387	cCa/cTa	8/25	0.152832296910827	3	FACETS	0.936	0.74	1	0.936	0.74	1	CLONAL	2	TRUE	1	0.22	3		329	124	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030819	69030819	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1452937015	NA	P-0051787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	13	330	2	ENST00000288368.4:c.3361T>C	p.Phe1121Leu	p.F1121L	ENST00000288368	NM_024870.2	1121	Ttc/Ctc	27/40	0.152832296910827	0	FACETS	0.668	0.479	0.895			1	SUBCLONAL	1	TRUE	0	0.22	0		332	138	SUCCESS
AR	367	MSKCC	GRCh37	X	66765815	66765815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	13	853	0	ENST00000374690.3:c.827C>T	p.Pro276Leu	p.P276L	ENST00000374690	NM_000044.3	276	cCa/cTa	1/8	0.152832296910827	0	FACETS	0.545	0.39	0.733			1	SUBCLONAL	1	TRUE	0	0.22	0		853	169	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356492	70356492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	11	519	0	ENST00000374080.3:c.5387C>T	p.Ala1796Val	p.A1796V	ENST00000374080		1796	gCt/gTt	37/45	0.152832296910827	0	FACETS	0.65	0.452	0.893			1	SUBCLONAL	1	TRUE	0	0.22	0		519	120	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0051789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	157	629	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.241835076316436	2	FACETS	1	0.979	1	0.593	0.545	0.642	INDETERMINATE	1	TRUE	0	0.446592506541962	2		631	593	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0051789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	67	316	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.947	0.829	1	0.947	0.829	1	CLONAL	1	TRUE	1	0.446592506541962	2		316	317	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873066	134873066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762457030	NA	P-0051789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	104	617	0	ENST00000398015.3:c.1370C>T	p.Pro457Leu	p.P457L	ENST00000398015	NM_004441.4	457	cCg/cTg	6/16	0.27023733491587	0	FACETS	0.529	0.476	0.585			1	SUBCLONAL	1	TRUE	0	0.446592506541962	0		617	487	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175876	176175876	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	11	239	0	ENST00000367669.3:c.239G>T	p.Gly80Val	p.G80V	ENST00000367669	NM_022457.5	80	gGg/gTg	1/20	1	2	FACETS	0.31	0.214	0.428	0.31	0.214	0.428	SUBCLONAL	1	TRUE	1	0.446592506541962	2		239	159	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380264	25380265	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGTACTCCTCTTGACCTGCTGTGTCGAGAATATCCA	novel	NA	P-0051789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	80	489	0	ENST00000311936.3:c.158_193dup	p.Tyr64_Ser65insMetAspIleLeuAspThrAlaGlyGlnGluGluTyr	p.Y64_S65insMDILDTAGQEEY	ENST00000311936	NM_004985.3	65	agt/aTGGATATTCTCGACACAGCAGGTCAAGAGGAGTACAgt	3/5	1	2	FACETS	0.68	0.6	0.765	0.68	0.6	0.765	SUBCLONAL	1	TRUE	1	0.446592506541962	2		489	527	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962899	2962899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3735134	NA	P-0051790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	186	753	1	ENST00000396946.4:c.2009C>T	p.Thr670Met	p.T670M	ENST00000396946	NM_032415.4	670	aCg/aTg	16/25	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.566578041824666	2		754	622	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0051791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	65	442	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.24336550001744	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.24336550001744	1		442	364	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	47	230	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	1	0.192969506279528	2		230	485	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0051792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	217	799	2	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	1	0.982	1	1	0.994	1	CLONAL	2	TRUE	1	0.192969506279528	2		801	969	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397742	49397742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552757	NA	P-0051792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	81	489	0	ENST00000418115.1:c.482C>T	p.Ala161Val	p.A161V	ENST00000418115	NM_001664.2	161	gCa/gTa	5/5	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.192969506279528	2		489	781	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891308	101891308	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0051792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	68	501	0	ENST00000374994.4:c.269C>G	p.Ser90Ter	p.S90*	ENST00000374994	NM_004612.2	90	tCa/tGa	2/9	0.192969506279528	1	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	0	0.192969506279528	1		501	620	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295170	1295170	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0051792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	46	289	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.192969506279528	2		289	392	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27098997	27098997	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0051792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	57	467	0	ENST00000324856.7:c.3413C>G	p.Ser1138Ter	p.S1138*	ENST00000324856	NM_006015.4	1138	tCa/tGa	13/20	1	2	FACETS	0.892	0.765	1	0.892	0.765	1	CLONAL	1	TRUE	1	0.192969506279528	2		467	662	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980398	201980399	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAAC	novel	NA	P-0051792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	94	681	0	ENST00000359651.3:c.136_139dup	p.Pro47GlnfsTer46	p.P47Qfs*46	ENST00000359651		45	agc/agCAACc	1/8	1	2	FACETS	0.976	0.867	1	0.976	0.867	1	CLONAL	1	TRUE	1	0.192969506279528	2		681	998	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981129	201981130	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CG	novel	NA	P-0051792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	101	709	0	ENST00000359651.3:c.210_211dup	p.Gln71ArgfsTer85	p.Q71Rfs*85	ENST00000359651		70	acg/aCGcg	2/8	1	2	FACETS	0.966	0.861	1	0.966	0.861	1	CLONAL	1	TRUE	1	0.192969506279528	2		709	1084	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434136	49434136	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	114	733	0	ENST00000301067.7:c.7417C>T	p.Gln2473Ter	p.Q2473*	ENST00000301067	NM_003482.3	2473	Cag/Tag	31/54	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.192969506279528	2		733	1181	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18972883	18972883	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	79	622	1	ENST00000262803.5:c.2522G>T	p.Cys841Phe	p.C841F	ENST00000262803	NM_002911.3	841	tGt/tTt	18/24	1	2	FACETS	0.898	0.788	1	0.898	0.788	1	CLONAL	1	TRUE	1	0.192969506279528	2		623	912	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18972889	18972889	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	81	620	0	ENST00000262803.5:c.2528G>T	p.Arg843Leu	p.R843L	ENST00000262803	NM_002911.3	843	cGg/cTg	18/24	1	2	FACETS	0.9	0.791	1	0.9	0.791	1	CLONAL	1	TRUE	1	0.192969506279528	2		620	933	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782191	135782192	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0051792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	55	366	0	ENST00000298552.3:c.1364dup	p.Leu456SerfsTer3	p.L456Sfs*3	ENST00000298552	NM_001162426.1	455	act/acCt	14/23	0.192969506279528	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.192969506279528	1		366	448	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0051793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	42	657	2	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.719	0.599	0.853	0.719	0.599	0.853	SUBCLONAL	1	TRUE	1	0.17	2		659	687	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842705	68842705	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	57	437	0	ENST00000261769.5:c.641T>C	p.Leu214Pro	p.L214P	ENST00000261769	NM_004360.3	214	cTg/cCg	5/16	1	2	FACETS	0.938	0.803	1	0.938	0.803	1	CLONAL	1	TRUE	1	0.17	2		437	715	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619916	21619916	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	37	417	0	ENST00000382592.4:c.250T>G	p.Leu84Val	p.L84V	ENST00000382592	NM_014572.2	84	Ttg/Gtg	2/8	1	2	FACETS	0.64	0.526	0.768	0.64	0.526	0.768	SUBCLONAL	1	TRUE	1	0.17	2		417	680	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961630	18961631	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCAG	novel	NA	P-0051794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	128	594	0	ENST00000262803.5:c.764_768dup	p.Ile257AlafsTer66	p.I257Afs*66	ENST00000262803	NM_002911.3	255	cgc/cGCCAGgc	5/24	0.141217521090681	4	FACETS	1	0.98	1	0.428	0.389	0.469	INDETERMINATE	1	TRUE	1	0.436578925127224	4		594	656	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0051795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	360	490	3	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	0.182784864411933	6	FACETS	1	0.99	1	0.78	0.74	0.82	INDETERMINATE	2	TRUE	3	0.654225386778226	6		493	1086	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0051795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	159	188	0	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	0.654225386778226	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.654225386778226	1		188	263	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702512	52702512	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0051795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	204	302	1	ENST00000394830.3:c.384+2T>C		p.X128_splice	ENST00000394830	NM_018313.4	128			0.654225386778226	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.654225386778226	1		303	330	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281276	142281276	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	140	374	0	ENST00000350721.4:c.968A>G	p.Glu323Gly	p.E323G	ENST00000350721	NM_001184.3	323	gAa/gGa	4/47	0.182784864411933	6	FACETS	1	0.98	1	0.423	0.385	0.462	INDETERMINATE	1	TRUE	3	0.654225386778226	6		374	779	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157406019	157406020	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0051795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	91	374	0	ENST00000346085.5:c.2265_2266del	p.Pro756CysfsTer6	p.P756Cfs*6	ENST00000346085	NM_020732.3	754	aTC/a	6/20	0.17928244989591	0	FACETS	0.262	0.234	0.291			1	INDETERMINATE	1	TRUE	0	0.654225386778226	0		374	367	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938046	76938046	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	348	586	0	ENST00000373344.5:c.2702T>C	p.Ile901Thr	p.I901T	ENST00000373344	NM_000489.3	901	aTc/aCc	9/35	0.182784864411933	6	FACETS	1	0.99	1	0.774	0.734	0.815	INDETERMINATE	2	TRUE	3	0.654225386778226	6		586	1057	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074178	8074179	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0051797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	401	389	0	ENST00000377482.5:c.480_481insCA	p.Ala161GlnfsTer15	p.A161Qfs*15	ENST00000377482	NM_018948.3	160	-/CA	4/4	0.404999700139199	6	FACETS	0.964	0.924	1	0.964	0.924	1	CLONAL	5	TRUE	1	0.404999700139199	6		389	744	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491666	120491666	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	30	343	0	ENST00000256646.2:c.2563G>C	p.Glu855Gln	p.E855Q	ENST00000256646	NM_024408.3	855	Gag/Cag	16/34	1	2	FACETS	0.412	0.332	0.502	0.412	0.332	0.502	SUBCLONAL	1	TRUE	1	0.404999700139199	2		343	360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0051797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	229	516	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.404999700139199	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.404999700139199	2		516	546	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	173	397	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	0.34343940084973	4	FACETS	0.971	0.898	1	0.971	0.898	1	CLONAL	2	TRUE	2	0.404999700139199	4		397	618	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808052	1808052	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	50	973	0	ENST00000260795.2:c.2028C>A	p.Asp676Glu	p.D676E	ENST00000260795		676	gaC/gaA	14/17	0.363548504127946	3	FACETS	0.318	0.269	0.373	0.159	0.134	0.187	SUBCLONAL	1	TRUE	1	0.404999700139199	3		973	934	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0051798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	132	520	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.158002232727975	3	FACETS	0.964	0.881	1	0.642	0.587	0.7	INDETERMINATE	2	TRUE	0	0.347204888417548	3		520	463	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164095	108164095	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	43	125	0	ENST00000278616.4:c.4667A>T	p.Tyr1556Phe	p.Y1556F	ENST00000278616	NM_000051.3	1556	tAt/tTt	31/63	0.296792428741118	4	FACETS	1	0.925	1	0.392	0.329	0.46	CLONAL	1	TRUE	1	0.347204888417548	4		125	284	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665752	29665755	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1555535032	NA	P-0051798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	60	152	0	ENST00000356175.3:c.6789_6792del	p.Tyr2264ThrfsTer5	p.Y2264Tfs*5	ENST00000356175	NM_000267.3	2263	ACTTac/ac	45/57	1	2	FACETS	0.768	0.67	0.871	1	0.973	1	SUBCLONAL	2	TRUE	1	0.347204888417548	2		152	225	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244252	41244252	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80357815	NA	P-0051798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	135	411	0	ENST00000357654.3:c.3296del	p.Pro1099LeufsTer10	p.P1099Lfs*10	ENST00000357654	NM_007294.3	1099	cCt/ct	10/23	0.347204888417548	2	FACETS	0.864	0.792	0.939	0.864	0.792	0.939	CLONAL	2	TRUE	0	0.347204888417548	2		411	450	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796944	42796980	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCAAGGGCCCGCCAGCCCCTGCCACTGCCACCCCA	GCCCAAGGGCCCGCCAGCCCCTGCCACTGCCACCCCA	-	novel	NA	P-0051798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	75	699	0	ENST00000575354.2:c.3406_3442del	p.Lys1136ArgfsTer13	p.K1136Rfs*13	ENST00000575354	NM_015125.3	1134	ctGCCCAAGGGCCCGCCAGCCCCTGCCACTGCCACCCCA/ct	14/20	0.197749872790022	5	FACETS	0.753	0.659	0.856	0.251	0.219	0.286	INDETERMINATE	1	TRUE	2	0.347204888417548	5		699	872	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573545	48573546	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0051798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	15	186	0	ENST00000342988.3:c.129_130delinsTT	p.Leu43_Val44delinsPheLeu	p.L43_V44delinsFL	ENST00000342988	NM_005359.5	43	ttGGta/ttTTta	2/12	0.158002232727975	3	FACETS	0.488	0.357	0.644	0.163	0.119	0.215	INDETERMINATE	1	TRUE	0	0.347204888417548	3		186	208	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0051799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	163	435	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.329445315716658	3	FACETS	0.967	0.893	1	0.967	0.893	1	CLONAL	2	FALSE	1	0.346837950758126	3		436	570	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0051799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	129	289	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.241181302754116	4	FACETS	1	0.975	1	0.782	0.715	0.851	CLONAL	2	FALSE	1	0.346837950758126	4		289	427	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0051799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	73	356	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.19499708515988	3	FACETS	0.797	0.703	0.896	0.797	0.703	0.896	INDETERMINATE	2	FALSE	1	0.346837950758126	3		356	310	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0051799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	43	282	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.78	0.655	0.916	0.78	0.655	0.916	CLONAL	1	FALSE	1	0.346837950758126	2		282	318	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781504	NA	P-0051799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	45	703	1	ENST00000269305.4:c.314G>T	p.Gly105Val	p.G105V	ENST00000269305	NM_001126112.2	105	gGc/gTc	4/11	1	2	FACETS	0.311	0.26	0.367	0.311	0.26	0.367	SUBCLONAL	1	FALSE	1	0.346837950758126	2		704	835	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527783	103527783	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1279336454	NA	P-0051799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	25	346	0	ENST00000355739.4:c.3091G>A	p.Ala1031Thr	p.A1031T	ENST00000355739	NM_000123.3	1031	Gcc/Acc	15/15	0.346837950758126	2	FACETS	0.47	0.37	0.583	0.235	0.185	0.292	SUBCLONAL	1	FALSE	0	0.346837950758126	2		346	307	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353903	15353903	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	48	584	1	ENST00000263377.2:c.2977C>T	p.Pro993Ser	p.P993S	ENST00000263377	NM_058243.2	993	Cct/Tct	14/20	1	2	FACETS	0.495	0.418	0.58	0.495	0.418	0.58	SUBCLONAL	1	FALSE	1	0.346837950758126	2		585	559	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981851	201981852	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0051799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	228	842	0	ENST00000359651.3:c.566_567dup	p.Ser190ProfsTer65	p.S190Pfs*65	ENST00000359651		188	gcc/gCCcc	4/8	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.346837950758126	2		842	961	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120517	70120521	+	frameshift_variant	Frame_Shift_Del	DEL	ACTCG	ACTCG	-	novel	NA	P-0051799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	157	770	0	ENST00000245479.2:c.1521_1525del	p.Arg508LeufsTer68	p.R508Lfs*68	ENST00000245479	NM_000346.3	507	ACTCGa/a	3/3	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.346837950758126	2		770	808	SUCCESS
APC	324	MSKCC	GRCh37	5	112173994	112173994	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	45	326	0	ENST00000257430.4:c.2704del	p.Glu902LysfsTer14	p.E902Kfs*14	ENST00000257430	NM_000038.5	901	caG/ca	16/16	1	2	FACETS	0.927	0.784	1	0.927	0.784	1	CLONAL	1	FALSE	1	0.346837950758126	2		326	280	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0051801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	194	845	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.223657637122368	2	FACETS	0.868	0.805	0.935	0.868	0.805	0.935	CLONAL	2	TRUE	0	0.263419458597255	2		845	848	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951964	178951964	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	253	341	0	ENST00000263967.3:c.3019G>C	p.Gly1007Arg	p.G1007R	ENST00000263967	NM_006218.2	1007	Ggc/Cgc	21/21	0.263419458597255	5	FACETS	1	0.973	1	1	0.973	1	CLONAL	5	TRUE	0	0.263419458597255	5		341	514	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629108	86629108	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853218	NA	P-0051801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	59	301	0	ENST00000274376.6:c.853C>T	p.Arg285Ter	p.R285*	ENST00000274376	NM_002890.2	285	Cga/Tga	4/25	0.263419458597255	2	FACETS	0.961	0.837	1	0.961	0.837	1	CLONAL	2	TRUE	0	0.263419458597255	2		301	233	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727938	41727938	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1320068051	NA	P-0051801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	158	636	0	ENST00000301178.4:c.563C>T	p.Pro188Leu	p.P188L	ENST00000301178	NM_021913.4	188	cCc/cTc	4/20	0.263419458597255	3	FACETS	0.899	0.825	0.976	0.899	0.825	0.976	CLONAL	2	TRUE	1	0.263419458597255	3		636	755	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259412	16259412	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	93	419	1	ENST00000375759.3:c.6677T>A	p.Ile2226Asn	p.I2226N	ENST00000375759	NM_015001.2	2226	aTt/aAt	11/15	0.263419458597255	3	FACETS	0.777	0.693	0.866			1	SUBCLONAL	2	TRUE	NA	0.263419458597255	3		420	514	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748131	72748131	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	116	458	0	ENST00000357731.5:c.47G>T	p.Trp16Leu	p.W16L	ENST00000357731	NM_173808.2	16	tGg/tTg	1/7	0.263419458597255	3	FACETS	0.846	0.765	0.932	0.846	0.765	0.932	CLONAL	2	TRUE	1	0.263419458597255	3		458	589	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661726	227661726	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	176	635	0	ENST00000305123.5:c.1729G>C	p.Val577Leu	p.V577L	ENST00000305123	NM_005544.2	577	Gtg/Ctg	1/2	0.263419458597255	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	1	0.263419458597255	3		635	738	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109314058	109314058	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	55	400	0	ENST00000436639.2:c.1165G>C	p.Glu389Gln	p.E389Q	ENST00000436639	NM_014454.2	389	Gag/Cag	7/10	0.263419458597255	3	FACETS	1	0.889	1	0.522	0.447	0.603	CLONAL	1	TRUE	1	0.263419458597255	3		400	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0051802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	399	520	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.845269514669689	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.845269514669689	1		520	540	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001188	150001188	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	161	515	0	ENST00000253339.5:c.2416C>T	p.Arg806Ter	p.R806*	ENST00000253339		806	Cga/Tga	4/7	0.845269514669689	1	FACETS	0.969	0.919	1	0.969	0.919	1	CLONAL	1	TRUE	0	0.845269514669689	1		515	227	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0051803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	60	547	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.213235721328407	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.16	1		547	626	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	54	613	1	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	0.213235721328407	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.16	1		614	508	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602773	10602773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	89	812	0	ENST00000171111.5:c.805C>T	p.Arg269Trp	p.R269W	ENST00000171111	NM_203500.1	269	Cgg/Tgg	3/6	0.160214294405471	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.16	1		812	775	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902658	50902658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750825686	NA	P-0051803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	89	786	0	ENST00000440232.2:c.233G>A	p.Arg78His	p.R78H	ENST00000440232	NM_002691.3	78	cGc/cAc	3/27	0.160214294405471	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.16	1		786	684	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100727	8100728	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs771019738	NA	P-0051803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	48	766	4	ENST00000346208.3:c.708dup	p.Ser237GlnfsTer66	p.S237Qfs*66	ENST00000346208		234	ttc/ttCc	3/6	0.160214294405471	1	FACETS	0.948	0.801	1	0.948	0.801	1	CLONAL	1	TRUE	0	0.16	1		770	582	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244967	46244967	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	48	480	2	ENST00000334344.6:c.3065del	p.Pro1022HisfsTer38	p.P1022Hfs*38	ENST00000334344	NM_152641.2	1021	Ccc/cc	15/21	0.160214294405471	3	FACETS	1	0.917	1	0.567	0.479	0.665	CLONAL	1	TRUE	1	0.16	3		482	571	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400029	139400029	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs778742968	NA	P-0051803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	36	774	0	ENST00000277541.6:c.4319T>C	p.Ile1440Thr	p.I1440T	ENST00000277541	NM_017617.3	1440	aTc/aCc	25/34	0.213235721328407	1	FACETS	0.703	0.577	0.845	0.703	0.577	0.845	SUBCLONAL	1	TRUE	0	0.16	1		774	589	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434542	140434542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368528867	NA	P-0051803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	20	298	0	ENST00000288602.6:c.2156G>A	p.Arg719His	p.R719H	ENST00000288602	NM_004333.4	719	cGc/cAc	18/18	1	2	FACETS	0.804	0.615	1	0.804	0.615	1	CLONAL	1	TRUE	1	0.16	2		298	311	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319690	62319692	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs779176651	NA	P-0051803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	49	727	0	ENST00000360203.5:c.1678_1680del	p.Phe560del	p.F560del	ENST00000360203	NM_001283009.1	558	aTCTtc/atc	20/35	0.0755018290518443	0	FACETS	0.798	0.675	0.934			1	INDETERMINATE	1	TRUE	0	0.16	0		727	645	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941442	71941442	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	41	703	0	ENST00000298229.2:c.1127A>G	p.Lys376Arg	p.K376R	ENST00000298229	NM_001567.3	376	aAg/aGg	10/28	0.160214294405471	1	FACETS	0.796	0.662	0.946	0.796	0.662	0.946	CLONAL	1	TRUE	0	0.16	1		703	592	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093429	30093429	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	35	417	0	ENST00000331968.5:c.1834A>G	p.Lys612Glu	p.K612E	ENST00000331968	NM_002742.2	612	Aaa/Gaa	13/18	0.160214294405471	1	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	0	0.16	1		417	374	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003001	42003001	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	33	636	1	ENST00000219905.7:c.2538del	p.Asn847MetfsTer26	p.N847Mfs*26	ENST00000219905	NM_001164273.1	846	tcT/tc	8/24	1	2	FACETS	0.771	0.627	0.934	0.771	0.627	0.934	CLONAL	1	TRUE	1	0.16	2		637	535	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89811470	89811470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	62	610	1	ENST00000389301.3:c.3523C>T	p.Pro1175Ser	p.P1175S	ENST00000389301	NM_000135.2	1175	Ccg/Tcg	36/43	0.213235721328407	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.16	1		611	549	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16097832	16097833	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0051803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	59	417	0	ENST00000268712.3:c.51_52del	p.Arg19LeufsTer23	p.R19Lfs*23	ENST00000268712	NM_006311.3	17	caAAgt/cagt	2/46	0.213235721328407	1	FACETS	0.782	0.674	0.898	1	0.971	1	SUBCLONAL	2	TRUE	0	0.16	1		417	434	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84406138	84406138	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1283259911	NA	P-0051803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	34	257	0	ENST00000321945.7:c.87+1G>A		p.X29_splice	ENST00000321945	NM_139076.2	29			0.160214294405471	1	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	0	0.16	1		257	357	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371938	55371938	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	41	294	0	ENST00000297316.4:c.628G>A	p.Gly210Ser	p.G210S	ENST00000297316	NM_022454.3	210	Ggc/Agc	2/2	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.16	2		294	495	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859900	117859900	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs780599047	NA	P-0051803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	22	223	0	ENST00000297338.2:c.1735A>G	p.Ile579Val	p.I579V	ENST00000297338	NM_006265.2	579	Atc/Gtc	14/14	1	2	FACETS	0.939	0.728	1	0.939	0.728	1	CLONAL	1	TRUE	1	0.16	2		223	293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0051804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	99	975	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.306820163714452	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.312721813594633	1		977	515	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099872	157099872	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs762100979	NA	P-0051804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	117	449	0	ENST00000346085.5:c.809C>G	p.Ser270Cys	p.S270C	ENST00000346085	NM_020732.3	270	tCc/tGc	1/20	0.312721813594633	2	FACETS	0.783	0.71	0.859	0.783	0.71	0.859	SUBCLONAL	2	TRUE	0	0.312721813594633	2		449	478	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333687	70333687	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	41	422	0	ENST00000373644.4:c.1592C>G	p.Ala531Gly	p.A531G	ENST00000373644	NM_030625.2	531	gCc/gGc	2/12	0.281321433824248	1	FACETS	0.48	0.4	0.569	0.48	0.4	0.569	SUBCLONAL	1	TRUE	0	0.312721813594633	1		422	461	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335891	73335891	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	163	332	0	ENST00000377767.4:c.2404C>G	p.Pro802Ala	p.P802A	ENST00000377767	NM_014953.3	802	Cca/Gca	18/21	0.265856552073919	3	FACETS	1	0.981	1	0.793	0.733	0.854	CLONAL	2	TRUE	0	0.312721813594633	3		332	507	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258581	19258581	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	104	759	0	ENST00000162023.5:c.319G>A	p.Glu107Lys	p.E107K	ENST00000162023		107	Gag/Aag	8/13	1	2	FACETS	0.86	0.77	0.956	0.86	0.77	0.956	CLONAL	1	TRUE	1	0.312721813594633	2		759	773	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728624	190728624	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0051804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	98	390	0	ENST00000441310.2:c.2012C>G	p.Ser671Ter	p.S671*	ENST00000441310	NM_000534.4	671	tCa/tGa	10/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.312721813594633	2		390	522	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961499	54961499	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	107	456	0	ENST00000312783.6:c.133C>T	p.Gln45Ter	p.Q45*	ENST00000312783	NM_198436.1	45	Cag/Tag	4/10	0.218492912559352	3	FACETS	1	0.977	1	0.653	0.587	0.723	CLONAL	1	TRUE	1	0.312721813594633	3		456	606	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052892	180052892	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	52	718	0	ENST00000261937.6:c.1398C>A	p.Cys466Ter	p.C466*	ENST00000261937	NM_182925.4	466	tgC/tgA	10/30	0.312721813594633	1	FACETS	0.458	0.39	0.534	0.458	0.39	0.534	SUBCLONAL	1	TRUE	0	0.312721813594633	1		718	612	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974685	21974685	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	70	477	0	ENST00000304494.5:c.142C>G	p.Pro48Ala	p.P48A	ENST00000304494	NM_000077.4	48	Ccg/Gcg	1/3	0.281321433824248	1	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	0	0.312721813594633	1		477	373	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	69	485	0	ENST00000304494.5:c.143del	p.Pro48ArgfsTer5	p.P48Rfs*5	ENST00000304494	NM_000077.4	48	cCg/cg	1/3	0.281321433824248	1	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	0	0.312721813594633	1		485	372	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0051806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	29	211	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.386628929350298	2	FACETS	1	0.855	1	0.525	0.43	0.628	CLONAL	1	TRUE	0	0.493105537177334	2		211	112	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1023835002	NA	P-0051806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	18	421	0	ENST00000558401.1:c.1A>G	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Gtg	1/4	0.4521908753962	2	FACETS	0.465	0.352	0.596	0.233	0.176	0.298	SUBCLONAL	1	TRUE	0	0.493105537177334	2		421	157	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0051806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	66	475	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.386628929350298	2	FACETS	0.853	0.759	0.948	0.853	0.759	0.948	CLONAL	2	TRUE	0	0.493105537177334	2		475	157	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431638	6431638	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	36	316	0	ENST00000356142.4:c.191A>G	p.Tyr64Cys	p.Y64C	ENST00000356142	NM_018890.3	64	tAt/tGt	3/7	1	2	FACETS	0.987	0.824	1	0.987	0.824	1	CLONAL	1	TRUE	1	0.493105537177334	2		316	148	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827442	72827442	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	51	538	0	ENST00000268489.5:c.9139C>T	p.Gln3047Ter	p.Q3047*	ENST00000268489	NM_006885.3	3047	Cag/Tag	9/10	0.337640808853673	2	FACETS	0.778	0.678	0.88	0.778	0.678	0.88	SUBCLONAL	2	TRUE	0	0.493105537177334	2		538	133	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858078	40858078	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	27	529	0	ENST00000428826.2:c.1786del	p.Asp596ThrfsTer34	p.D596Tfs*34	ENST00000428826		596	Gac/ac	16/21	0.134557884423384	5	FACETS	1	0.836	1	0.262	0.21	0.32	INDETERMINATE	1	TRUE	1	0.493105537177334	5		529	182	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119945	70119946	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0051806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	67	362	0	ENST00000245479.2:c.949_950dup	p.Ser318AlafsTer66	p.S318Afs*66	ENST00000245479	NM_000346.3	316	acg/acGGg	3/3	0.386628929350298	2	FACETS	0.855	0.762	0.949	0.855	0.762	0.949	CLONAL	2	TRUE	0	0.493105537177334	2		362	159	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609839	117609839	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	33	492	0	ENST00000368508.3:c.6860A>C	p.Lys2287Thr	p.K2287T	ENST00000368508	NM_002944.2	2287	aAg/aCg	43/43	0.382803120437333	1	FACETS	0.862	0.717	1	0.862	0.717	1	CLONAL	1	TRUE	0	0.493105537177334	1		492	117	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399124	139399124	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0051806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	37	614	1	ENST00000277541.6:c.5018+1G>A		p.X1673_splice	ENST00000277541	NM_017617.3	1673			0.272372905340083	3	FACETS	1	0.951	1	0.703	0.591	0.823	INDETERMINATE	1	TRUE	1	0.493105537177334	3		615	133	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437894	52437894	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	158	678	0	ENST00000460680.1:c.1267del	p.Thr423GlnfsTer7	p.T423Qfs*7	ENST00000460680	NM_004656.3	423	Aca/ca	13/17	0.438097276247888	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.460653825110677	1		678	526	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877184	151877184	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	141	353	0	ENST00000262189.6:c.7177C>T	p.Gln2393Ter	p.Q2393*	ENST00000262189	NM_170606.2	2393	Cag/Tag	37/59	0.190147251278081	4	FACETS	0.858	0.786	0.933	0.858	0.786	0.933	INDETERMINATE	2	TRUE	2	0.460653825110677	4		353	521	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994137	21994163	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CCTGGTCTTCTAGGAAGCGGCTGCTGC	CCTGGTCTTCTAGGAAGCGGCTGCTGC	-	novel	NA	P-0051807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	97	602	0	ENST00000579755.1:c.168_193+1del		p.X56_splice	ENST00000579755		56		1/3	0.460653825110677		FACETS		0.638	0.79				SUBCLONAL	1	TRUE	0	0.460653825110677	1		602	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	50	579	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	1	2	FACETS	0.581	0.493	0.679	0.581	0.493	0.679	SUBCLONAL	1	TRUE	1	0.267885995974974	2		579	642	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923297	9923297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	77	447	0	ENST00000330684.3:c.1990G>A	p.Gly664Ser	p.G664S	ENST00000330684	NM_001134407.1	664	Ggc/Agc	9/13	0.128231339975471	6	FACETS	1	0.945	1	0.376	0.331	0.424	INDETERMINATE	1	TRUE	3	0.620820026958192	6		447	493	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0051811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	185	435	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.156742350309367	3	FACETS	0.947	0.878	1	0.631	0.585	0.679	INDETERMINATE	2	TRUE	0	0.358848758128944	3		436	642	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0051811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	105	396	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.358848758128944	2		396	584	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940521	131940521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs181961360	NA	P-0051813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	18	301	1	ENST00000265335.6:c.2548C>T	p.Arg850Cys	p.R850C	ENST00000265335		850	Cgt/Tgt	16/25	1	2	FACETS	0.144	0.108	0.186	0.144	0.108	0.186	SUBCLONAL	1	TRUE	1	0.795389347021682	2		302	315	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261739	16261739	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	205	565	0	ENST00000375759.3:c.9004C>T	p.Pro3002Ser	p.P3002S	ENST00000375759	NM_015001.2	3002	Ccc/Tcc	11/15	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.795389347021682	2		565	514	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0051813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	380	453	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.795389347021682	2		453	711	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843748	156843748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537263008	NA	P-0051813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	265	757	1	ENST00000524377.1:c.1174C>T	p.Pro392Ser	p.P392S	ENST00000524377	NM_002529.3	392	Cct/Tct	8/17	1	2	FACETS	0.94	0.886	0.995	0.94	0.886	0.995	CLONAL	1	TRUE	1	0.795389347021682	2		758	709	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650147	206650147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	211	554	0	ENST00000367120.3:c.667C>T	p.Pro223Ser	p.P223S	ENST00000367120	NM_014002.3	223	Ccc/Tcc	7/22	1	2	FACETS	0.995	0.933	1	0.995	0.933	1	CLONAL	1	TRUE	1	0.795389347021682	2		554	533	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472553	88472553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	210	595	0	ENST00000360948.2:c.2002G>A	p.Val668Met	p.V668M	ENST00000360948	NM_001012338.2	668	Gtg/Atg	16/19	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.795389347021682	2		595	523	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797870	42797870	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	252	778	0	ENST00000575354.2:c.3922G>T	p.Glu1308Ter	p.E1308*	ENST00000575354	NM_015125.3	1308	Gag/Tag	16/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.795389347021682	2		778	601	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513234	44513234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780011533	NA	P-0051813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	167	259	0	ENST00000291552.4:c.701G>A	p.Arg234His	p.R234H	ENST00000291552	NM_006758.2	234	cGt/cAt	8/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.795389347021682	2		259	379	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155904	106155904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	128	383	0	ENST00000380013.4:c.805C>T	p.His269Tyr	p.H269Y	ENST00000380013	NM_001127208.2	269	Cat/Tat	3/11	NA	2	FACETS	0.875	0.802	0.95			1	INDETERMINATE	1	TRUE	NA	0.795389347021682	2		383	368	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0051813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	114	226	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.795389347021682	2		227	286	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477804	140477804	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	23	439	0	ENST00000288602.6:c.1504G>A	p.Val502Ile	p.V502I	ENST00000288602	NM_004333.4	502	Gta/Ata	12/18	1	2	FACETS	0.135	0.105	0.17	0.135	0.105	0.17	SUBCLONAL	1	TRUE	1	0.795389347021682	2		439	429	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932000	39932000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	246	584	0	ENST00000378444.4:c.2599G>A	p.Glu867Lys	p.E867K	ENST00000378444	NM_001123385.1	867	Gaa/Aaa	4/15	1	2	FACETS	0.899	0.845	0.954	0.899	0.845	0.954	CLONAL	1	TRUE	1	0.795389347021682	2		584	688	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410327	63410327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	241	690	0	ENST00000330258.3:c.2840C>T	p.Ser947Phe	p.S947F	ENST00000330258	NM_152424.3	947	tCc/tTc	2/2	1	2	FACETS	0.984	0.925	1	0.984	0.925	1	CLONAL	1	TRUE	1	0.795389347021682	2		690	616	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0051814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	104	289	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.491532853726838	1	FACETS	0.642	0.577	0.71	0.642	0.577	0.71	SUBCLONAL	1	TRUE	0	0.491532853726838	1		289	497	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0051814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	93	356	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.923	0.826	1	0.923	0.826	1	CLONAL	1	TRUE	1	0.491532853726838	2		356	410	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0051814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	90	247	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.491532853726838	1	FACETS	0.725	0.648	0.806	0.725	0.648	0.806	SUBCLONAL	1	TRUE	0	0.491532853726838	1		247	381	SUCCESS
APC	324	MSKCC	GRCh37	5	112173926	112173926	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060503287	NA	P-0051814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	63	290	0	ENST00000257430.4:c.2635C>T	p.Gln879Ter	p.Q879*	ENST00000257430	NM_000038.5	879	Cag/Tag	16/16	0.491532853726838	1	FACETS	0.525	0.457	0.599	0.525	0.457	0.599	SUBCLONAL	1	TRUE	0	0.491532853726838	1		290	368	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214666	5214666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs116660613	NA	P-0051814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	163	735	0	ENST00000357368.4:c.4400C>T	p.Pro1467Leu	p.P1467L	ENST00000357368	NM_002850.3	1467	cCg/cTg	29/38	1	2	FACETS	0.831	0.764	0.901	0.831	0.764	0.901	CLONAL	1	TRUE	1	0.491532853726838	2		735	798	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265446	152265446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371610514	NA	P-0051814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	140	421	0	ENST00000206249.3:c.899G>A	p.Arg300His	p.R300H	ENST00000206249	NM_000125.3	300	cGc/cAc	4/8	1	2	FACETS	0.904	0.826	0.986	0.904	0.826	0.986	CLONAL	1	TRUE	1	0.491532853726838	2		421	630	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202261	133202261	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	199	565	0	ENST00000320574.5:c.6627G>C	p.Lys2209Asn	p.K2209N	ENST00000320574	NM_006231.2	2209	aaG/aaC	47/49	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.491532853726838	2		565	650	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394712	45394712	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	98	287	0	ENST00000262160.6:c.637C>T	p.Gln213Ter	p.Q213*	ENST00000262160	NM_005901.5	213	Cag/Tag	5/11	0.491532853726838	1	FACETS	0.845	0.761	0.933	0.845	0.761	0.933	CLONAL	1	TRUE	0	0.491532853726838	1		287	356	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968164	68968164	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	224	413	0	ENST00000288368.4:c.1193A>T	p.Asp398Val	p.D398V	ENST00000288368	NM_024870.2	398	gAc/gTc	10/40	0.487875813838114	3	FACETS	0.812	0.76	0.866	0.812	0.76	0.866	CLONAL	2	TRUE	1	0.491532853726838	3		413	699	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	138	373	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.197564964350071	4	FACETS	1	0.973	1	1	0.973	1	INDETERMINATE	2	TRUE	2	0.343831542288599	4		373	471	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0051816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	166	396	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.343831542288599	5	FACETS	0.986	0.919	1	0.986	0.919	1	CLONAL	4	TRUE	1	0.343831542288599	5		396	371	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0051816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	66	211	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.343831542288599	3	FACETS	1	0.902	1	1	0.902	1	CLONAL	2	TRUE	1	0.343831542288599	3		211	219	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411246	63411246	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	308	289	2	ENST00000330258.3:c.1921C>T	p.Arg641Ter	p.R641*	ENST00000330258	NM_152424.3	641	Cga/Tga	2/2	0.343831542288599	4	FACETS	1	0.98	1			1	CLONAL	5	TRUE	NA	0.343831542288599	4		291	466	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38949917	38949917	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs747557548	NA	P-0051816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	26	279	0	ENST00000357387.3:c.4033T>G	p.Leu1345Val	p.L1345V	ENST00000357387	NM_152756.3	1345	Tta/Gta	31/38	0.283935347031011	4	FACETS	0.641	0.508	0.793	0.214	0.169	0.265	SUBCLONAL	1	TRUE	1	0.343831542288599	4		279	317	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100600	8100600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778161799	NA	P-0051816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	201	593	0	ENST00000346208.3:c.574G>A	p.Asp192Asn	p.D192N	ENST00000346208		192	Gac/Aac	3/6	0.110028719836813	5	FACETS	0.862	0.803	0.924	0.647	0.602	0.693	INDETERMINATE	3	TRUE	1	0.343831542288599	5		593	685	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281607	15281607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	124	542	0	ENST00000263388.2:c.4766G>A	p.Arg1589Gln	p.R1589Q	ENST00000263388	NM_000435.2	1589	cGg/cAg	26/33	0.283935347031011	4	FACETS	1	0.969	1	0.389	0.352	0.429	CLONAL	1	TRUE	1	0.343831542288599	4		542	830	SUCCESS
APC	324	MSKCC	GRCh37	5	112173826	112173826	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	53	261	0	ENST00000257430.4:c.2536del	p.Ser846LeufsTer15	p.S846Lfs*15	ENST00000257430	NM_000038.5	845	cgT/cg	16/16	0.343831542288599	3	FACETS	1	0.955	1	0.65	0.558	0.748	CLONAL	1	TRUE	1	0.343831542288599	3		261	278	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420409	49420409	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	38	663	1	ENST00000301067.7:c.15340del	p.His5114IlefsTer33	p.H5114Ifs*33	ENST00000301067	NM_003482.3	5114	Cat/at	48/54	0.571415221494906	3	FACETS	0.236	0.194	0.282	0.118	0.097	0.141	SUBCLONAL	1	TRUE	1	0.571415221494906	3		664	726	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096047	11096048	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0051817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	58	756	0	ENST00000358026.2:c.326dup	p.Pro110AlafsTer19	p.P110Afs*19	ENST00000358026	NM_001128849.1	107	-/C	3/36	0.571415221494906	3	FACETS	0.414	0.355	0.478	0.207	0.177	0.239	SUBCLONAL	1	TRUE	1	0.571415221494906	3		756	631	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875872	76875872	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	107	206	0	ENST00000373344.5:c.5263C>G	p.Leu1755Val	p.L1755V	ENST00000373344	NM_000489.3	1755	Cta/Gta	20/35	1	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.571415221494906	1		206	227	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920238	76920238	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	15	190	0	ENST00000373344.5:c.3839T>A	p.Ile1280Asn	p.I1280N	ENST00000373344	NM_000489.3	1280	aTt/aAt	11/35	1	1	FACETS	0.186	0.136	0.245	0.186	0.136	0.245	SUBCLONAL	1	TRUE	0	0.571415221494906	1		190	202	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340288	116340288	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0051818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	261	325	0	ENST00000397752.3:c.1150A>T	p.Arg384Ter	p.R384*	ENST00000397752	NM_000245.2	384	Aga/Tga	2/21	0.691739221749658	5	FACETS	0.991	0.932	1	0.496	0.466	0.526	CLONAL	2	TRUE	1	0.687621229913068	5		325	778	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0051818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	468	508	0	ENST00000269305.4:c.375+1G>C		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.691739221749658	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.687621229913068	3		508	554	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754720	41754720	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs913467939	NA	P-0051818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	38	526	0	ENST00000301178.4:c.1706T>C	p.Met569Thr	p.M569T	ENST00000301178	NM_021913.4	569	aTg/aCg	14/20	0.691739221749658	3	FACETS	0.211	0.174	0.253	0.106	0.087	0.127	SUBCLONAL	1	TRUE	1	0.687621229913068	3		526	703	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41905073	41905073	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	30	422	0	ENST00000372991.4:c.474T>A	p.His158Gln	p.H158Q	ENST00000372991	NM_001760.3	158	caT/caA	3/5	NA	2	FACETS	0.213	0.171	0.26			1	INDETERMINATE	1	TRUE	NA	0.687621229913068	2		422	410	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002752	37002752	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	118	498	0	ENST00000358127.4:c.497A>T	p.Gln166Leu	p.Q166L	ENST00000358127	NM_001280556.1	166	cAg/cTg	5/10	1	2	FACETS	0.789	0.717	0.864	0.789	0.717	0.864	SUBCLONAL	1	TRUE	1	0.687621229913068	2		498	435	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971138	21971138	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs760640852	NA	P-0051819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	29	382	0	ENST00000304494.5:c.220G>T	p.Asp74Tyr	p.D74Y	ENST00000304494	NM_000077.4	74	Gac/Tac	2/3	0.244004228180165	1	FACETS	0.165	0.132	0.203	0.165	0.132	0.203	INDETERMINATE	1	TRUE	0	0.496530970403998	1		382	531	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566488	41566488	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	136	335	0	ENST00000263253.7:c.4365G>C	p.Gln1455His	p.Q1455H	ENST00000263253	NM_001429.3	1455	caG/caC	27/31	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.496530970403998	2		335	547	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579346	7579348	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs764486868	NA	P-0051819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	241	612	0	ENST00000269305.4:c.339_341del	p.Phe113del	p.F113del	ENST00000269305	NM_001126112.2	113	ttCTTg/ttg	4/11	0.447494389616678	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.496530970403998	1		612	696	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105667	27105667	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	90	403	0	ENST00000324856.7:c.5278G>T	p.Glu1760Ter	p.E1760*	ENST00000324856	NM_006015.4	1760	Gag/Tag	20/20	0.244004228180165	1	FACETS	0.643	0.573	0.716	0.643	0.573	0.716	INDETERMINATE	1	TRUE	0	0.496530970403998	1		403	424	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88671966	88671966	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0051819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	24	238	0	ENST00000360948.2:c.1205-1G>A		p.X402_splice	ENST00000360948	NM_001012338.2	402			1	2	FACETS	0.252	0.197	0.315	0.252	0.197	0.315	SUBCLONAL	1	TRUE	1	0.496530970403998	2		238	384	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039340	49039341	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0051819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	126	457	0	ENST00000267163.4:c.2330dup	p.Thr778TyrfsTer17	p.T778Yfs*17	ENST00000267163	NM_000321.2	775	-/C		0.496530970403998	1	FACETS	0.723	0.657	0.791	0.723	0.657	0.791	SUBCLONAL	1	TRUE	0	0.496530970403998	1		457	528	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156870	106156870	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1365072838	NA	P-0051819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	43	403	0	ENST00000380013.4:c.1771C>T	p.Gln591Ter	p.Q591*	ENST00000380013	NM_001127208.2	591	Cag/Tag	3/11	0.323681744331798	1	FACETS	0.261	0.218	0.309	0.261	0.218	0.309	SUBCLONAL	1	TRUE	0	0.496530970403998	1		403	499	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713129	30713129	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0051819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	19	266	0	ENST00000295754.5:c.455-1G>A		p.X152_splice	ENST00000295754	NM_003242.5	152			0.496530970403998	1	FACETS	0.171	0.129	0.22	0.171	0.129	0.22	SUBCLONAL	1	TRUE	0	0.496530970403998	1		266	337	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264319	16264319	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1405875555	NA	P-0051819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	95	536	0	ENST00000375759.3:c.10522G>A	p.Val3508Met	p.V3508M	ENST00000375759	NM_015001.2	3508	Gtg/Atg	13/15	0.244004228180165	1	FACETS	0.534	0.476	0.594	0.534	0.476	0.594	INDETERMINATE	1	TRUE	0	0.496530970403998	1		536	539	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252089	226252089	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	26	121	0	ENST00000366813.1:c.37G>T	p.Gly13Cys	p.G13C	ENST00000366813		13	Ggt/Tgt	1/3	1	2	FACETS	0.635	0.508	0.777	0.635	0.508	0.777	SUBCLONAL	1	TRUE	1	0.496530970403998	2		121	165	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212923	94212923	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	17	279	0	ENST00000323929.3:c.319C>T	p.Pro107Ser	p.P107S	ENST00000323929	NM_005591.3	107	Cca/Tca	5/20	0.447494389616678	1	FACETS	0.178	0.132	0.232	0.178	0.132	0.232	SUBCLONAL	1	TRUE	0	0.496530970403998	1		279	289	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895689	28895689	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	33	470	0	ENST00000282397.4:c.3085del	p.Leu1029PhefsTer8	p.L1029Ffs*8	ENST00000282397	NM_002019.4	1029	Ctt/tt	23/30	0.496530970403998	1	FACETS	0.184	0.149	0.223	0.184	0.149	0.223	SUBCLONAL	1	TRUE	0	0.496530970403998	1		470	544	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59820460	59820460	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	126	389	0	ENST00000259008.2:c.2293G>C	p.Val765Leu	p.V765L	ENST00000259008	NM_032043.2	765	Gtg/Ctg	16/20	0.496530970403998	1	FACETS	0.885	0.808	0.965	0.885	0.808	0.965	CLONAL	1	TRUE	0	0.496530970403998	1		389	431	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250390	10250390	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	30	495	0	ENST00000340748.4:c.3862G>T	p.Val1288Phe	p.V1288F	ENST00000340748		1288	Gtc/Ttc	33/40	0.447494389616678	1	FACETS	0.183	0.147	0.224	0.183	0.147	0.224	SUBCLONAL	1	TRUE	0	0.496530970403998	1		495	496	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719725	190719725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	69	282	0	ENST00000441310.2:c.1727C>T	p.Ser576Leu	p.S576L	ENST00000441310	NM_000534.4	576	tCa/tTa	9/13	1	2	FACETS	0.822	0.721	0.93	0.822	0.721	0.93	CLONAL	1	TRUE	1	0.496530970403998	2		282	338	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73047233	73047233	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	43	383	0	ENST00000356692.5:c.40G>C	p.Glu14Gln	p.E14Q	ENST00000356692		14	Gag/Cag	2/9	0.496530970403998	1	FACETS	0.286	0.239	0.337	0.286	0.239	0.337	SUBCLONAL	1	TRUE	0	0.496530970403998	1		383	456	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591245	67591246	+	splice_acceptor_variant,intron_variant	Splice_Site	DNP	CA	CA	TT	novel	NA	P-0051819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	89	344	0	ENST00000274335.5:c.1746-3_1746-2delinsTT		p.X582_splice	ENST00000274335		582			0.459288335893554	1	FACETS	0.627	0.559	0.699	0.627	0.559	0.699	SUBCLONAL	1	TRUE	0	0.496530970403998	1		344	430	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722098	176722098	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1337506511	NA	P-0051819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	101	505	0	ENST00000439151.2:c.7729G>C	p.Val2577Leu	p.V2577L	ENST00000439151	NM_022455.4	2577	Gtg/Ctg	23/23	0.335178986611748	2	FACETS	0.617	0.552	0.686	0.309	0.276	0.343	SUBCLONAL	1	TRUE	0	0.496530970403998	2		505	659	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250718	26250718	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	125	524	0	ENST00000446824.2:c.116C>T	p.Pro39Leu	p.P39L	ENST00000446824	NM_021018.2	39	cCc/cTc	1/1	1	2	FACETS	0.802	0.727	0.88	0.802	0.727	0.88	CLONAL	1	TRUE	1	0.496530970403998	2		524	628	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188395	32188395	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	110	566	0	ENST00000375023.3:c.946G>C	p.Asp316His	p.D316H	ENST00000375023	NM_004557.3	316	Gat/Cat	6/30	1	2	FACETS	0.715	0.643	0.79	0.715	0.643	0.79	SUBCLONAL	1	TRUE	1	0.496530970403998	2		566	620	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0051820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	107	745	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	1	2	FACETS	0.981	0.884	1	1	0.988	1	CLONAL	2	TRUE	1	0.22	2		745	496	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256202	133256202	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs371147799	NA	P-0051820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	67	463	0	ENST00000320574.5:c.459C>G	p.Ile153Met	p.I153M	ENST00000320574	NM_006231.2	153	atC/atG	6/49	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.22	2		463	419	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	167	805	4	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	1	0.981	1	1	0.993	1	CLONAL	2	TRUE	1	0.238155755522878	2		809	589	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	33	360	0	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	0.1237613169068	0	FACETS	0.347	0.282	0.421			1	INDETERMINATE	1	TRUE	0	0.238155755522878	0		360	608	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	308	713	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.875	0.83	0.921	1	0.997	1	CLONAL	4	TRUE	1	0.238155755522878	2		715	739	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	91	308	3	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	1	2	FACETS	1	0.948	1	1	0.987	1	CLONAL	2	TRUE	1	0.238155755522878	2		311	349	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70441157	70441157	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	rs764225020	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	77	355	0	ENST00000373644.4:c.4832del	p.Asn1611ThrfsTer13	p.N1611Tfs*13	ENST00000373644	NM_030625.2	1609	gAa/ga	9/12	1	2	FACETS	1	0.895	1	1	0.984	1	CLONAL	2	TRUE	1	0.238155755522878	2		355	320	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851286	156851286	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745776726	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	177	702	2	ENST00000524377.1:c.2243G>A	p.Arg748Gln	p.R748Q	ENST00000524377	NM_002529.3	748	cGg/cAg	17/17	1	2	FACETS	1	0.977	1	1	0.993	1	CLONAL	2	TRUE	1	0.238155755522878	2		704	654	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	42	477	0	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	0.566	0.472	0.671	0.566	0.472	0.671	SUBCLONAL	1	TRUE	1	0.238155755522878	2		477	623	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	26	256	3	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	0.238155755522878	4	FACETS	0.723	0.572	0.895	0.241	0.19	0.299	SUBCLONAL	1	TRUE	1	0.238155755522878	4		259	374	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376690	31376690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	54	488	0	ENST00000328111.2:c.685G>A	p.Val229Met	p.V229M	ENST00000328111	NM_006892.3	229	Gtg/Atg	7/23	0.238155755522878	2	FACETS	0.967	0.827	1	0.483	0.413	0.56	CLONAL	1	TRUE	0	0.238155755522878	2		488	469	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	88	661	4	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	1	2	FACETS	0.992	0.879	1	0.992	0.879	1	CLONAL	1	TRUE	1	0.238155755522878	2		665	745	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742463	17742463	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	25	554	1	ENST00000250003.3:c.650del	p.Pro217ArgfsTer33	p.P217Rfs*33	ENST00000250003	NM_002478.4	215	ggC/gg	2/3	1	2	FACETS	0.43	0.338	0.537	0.43	0.338	0.537	SUBCLONAL	1	TRUE	1	0.238155755522878	2		555	488	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158447	106158447	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	13	291	0	ENST00000380013.4:c.3353del	p.Asn1118IlefsTer19	p.N1118Ifs*19	ENST00000380013	NM_001127208.2	1116	atA/at	3/11	1	2	FACETS	0.463	0.33	0.625	0.463	0.33	0.625	SUBCLONAL	1	TRUE	1	0.238155755522878	2		291	236	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739581	145739581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375100228	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	200	768	0	ENST00000428558.2:c.1870G>A	p.Val624Ile	p.V624I	ENST00000428558	NM_004260.3	624	Gtc/Atc	11/22	0.238155755522878	4	FACETS	1	0.981	1	0.775	0.719	0.834	CLONAL	2	TRUE	1	0.238155755522878	4		768	894	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	101	751	1	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.238155755522878	2		752	820	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	243	691	10	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.887	0.832	0.943	1	0.995	1	CLONAL	3	TRUE	1	0.238155755522878	2		701	767	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	86	675	0	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	0.238155755522878	5	FACETS	1	0.962	1	0.606	0.535	0.682	CLONAL	1	TRUE	3	0.238155755522878	5		675	809	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	36	541	1	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.238155755522878	2		542	286	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	69	605	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	0.238155755522878	4	FACETS	1	0.914	1	0.355	0.309	0.405	CLONAL	1	TRUE	1	0.238155755522878	4		605	674	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847400	68847400	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	29	433	0	ENST00000261769.5:c.1320+2T>G		p.X440_splice	ENST00000261769	NM_004360.3	440			1	2	FACETS	0.507	0.406	0.623	0.507	0.406	0.623	SUBCLONAL	1	TRUE	1	0.238155755522878	2		433	480	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	111	427	10	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	0.238155755522878	1	FACETS	0.931	0.843	1	1	0.988	1	CLONAL	2	TRUE	0	0.238155755522878	1		437	441	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913253	39913253	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	44	508	0	ENST00000378444.4:c.4862del	p.Pro1621GlnfsTer53	p.P1621Qfs*53	ENST00000378444	NM_001123385.1	1621	cCa/ca	14/15	0.1237613169068	0	FACETS	0.604	0.507	0.712			1	INDETERMINATE	1	TRUE	0	0.238155755522878	0		508	466	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	38	492	2	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	0.722	0.597	0.862	0.722	0.597	0.862	SUBCLONAL	1	TRUE	1	0.238155755522878	2		494	442	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739030	145739030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199562131	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	175	717	1	ENST00000428558.2:c.2125C>T	p.Arg709Trp	p.R709W	ENST00000428558	NM_004260.3	709	Cgg/Tgg	13/22	0.238155755522878	4	FACETS	1	0.921	1	0.667	0.614	0.721	CLONAL	2	TRUE	1	0.238155755522878	4		718	910	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025569	1025569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	43	658	2	ENST00000358495.3:c.806G>A	p.Arg269Gln	p.R269Q	ENST00000358495	NM_134424.2	269	cGg/cAg	9/12	0.238155755522878	1	FACETS	0.475	0.397	0.563	0.475	0.397	0.563	SUBCLONAL	1	TRUE	0	0.238155755522878	1		660	669	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	175	502	4	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.965	1	1	0.994	1	CLONAL	3	TRUE	1	0.238155755522878	2		506	462	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	117	624	0	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	0.1237613169068	0	FACETS	0.749	0.678	0.822			1	INDETERMINATE	2	TRUE	0	0.238155755522878	0		624	500	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38283643	38283643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs186746130	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	129	382	1	ENST00000425967.3:c.835G>A	p.Val279Met	p.V279M	ENST00000425967	NM_001174067.1	279	Gtg/Atg	7/19	0.238155755522878	4	FACETS	0.834	0.76	0.912	0.834	0.76	0.912	CLONAL	3	TRUE	1	0.238155755522878	4		383	536	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829040	128829042	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	rs570242755	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	34	51	0	ENST00000249373.3:c.67_69del	p.Leu23del	p.L23del	ENST00000249373	NM_005631.4	16	ggGCTg/ggg	1/12	1	2	FACETS	1	0.908	1	1	0.968	1	CLONAL	2	TRUE	1	0.238155755522878	2		51	125	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120115	70120115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	12	140	0	ENST00000245479.2:c.1121del	p.Pro374ArgfsTer9	p.P374Rfs*9	ENST00000245479	NM_000346.3	373	Ccc/cc	3/3	1	2	FACETS	0.763	0.54	1	0.763	0.54	1	CLONAL	1	TRUE	1	0.238155755522878	2		140	132	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401385	139401385	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	88	695	1	ENST00000277541.6:c.3684del	p.Val1229LeufsTer216	p.V1229Lfs*216	ENST00000277541	NM_017617.3	1228	ccC/cc	23/34	0.238155755522878	4	FACETS	0.93	0.822	1	0.31	0.274	0.349	CLONAL	1	TRUE	1	0.238155755522878	4		696	984	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259967	16259967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	48	571	1	ENST00000375759.3:c.7232C>T	p.Ser2411Leu	p.S2411L	ENST00000375759	NM_015001.2	2411	tCg/tTg	11/15	1	2	FACETS	0.689	0.582	0.807	0.689	0.582	0.807	SUBCLONAL	1	TRUE	1	0.238155755522878	2		572	585	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372193	55372193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753081636	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	108	271	1	ENST00000297316.4:c.883G>A	p.Val295Met	p.V295M	ENST00000297316	NM_022454.3	295	Gtg/Atg	2/2	0.238155755522878	4	FACETS	1	0.954	1	0.733	0.66	0.809	CLONAL	2	TRUE	1	0.238155755522878	4		272	511	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639588	47639588	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63749897	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	32	315	0	ENST00000233146.2:c.687del	p.Ala230LeufsTer16	p.A230Lfs*16	ENST00000233146	NM_000251.2	227	agA/ag	4/16	1	2	FACETS	0.746	0.607	0.904	0.746	0.607	0.904	CLONAL	1	TRUE	1	0.238155755522878	2		315	360	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434595	110434595	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs555841746	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	42	452	0	ENST00000375856.3:c.3806A>C	p.Gln1269Pro	p.Q1269P	ENST00000375856	NM_003749.2	1269	cAg/cCg	1/2	0.166195876129294	3	FACETS	0.728	0.607	0.863	0.364	0.303	0.432	SUBCLONAL	1	TRUE	1	0.238155755522878	3		452	542	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119910	70119910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1297203260	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	66	514	1	ENST00000245479.2:c.916del	p.Val306CysfsTer77	p.V306Cfs*77	ENST00000245479	NM_000346.3	304	ccG/cc	3/3	1	2	FACETS	0.967	0.84	1	0.967	0.84	1	CLONAL	1	TRUE	1	0.238155755522878	2		515	573	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506428	148506428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	96	419	1	ENST00000320356.2:c.2084C>T	p.Ser695Leu	p.S695L	ENST00000320356	NM_004456.4	695	tCg/tTg	18/20	1	2	FACETS	1	0.952	1	1	0.988	1	CLONAL	2	TRUE	1	0.238155755522878	2		420	366	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028805	47028805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	55	590	1	ENST00000377604.3:c.109C>T	p.Arg37Trp	p.R37W	ENST00000377604	NM_001204468.1	37	Cgg/Tgg	3/24	0.1237613169068	0	FACETS	0.536	0.457	0.621			1	INDETERMINATE	1	TRUE	0	0.238155755522878	0		591	657	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	104	430	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.866	0.779	0.958	1	0.986	1	CLONAL	2	TRUE	1	0.238155755522878	2		434	504	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324892	31324892	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs765875917	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	35	317	0	ENST00000412585.2:c.44del	p.Ala15GlyfsTer5	p.A15Gfs*5	ENST00000412585	NM_005514.6	15	gCg/gg	1/8	0.139292488157321	4	FACETS	1	0.944	1	0.711	0.586	0.849	INDETERMINATE	1	TRUE	2	0.238155755522878	4		317	256	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	42	528	5	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.604	0.503	0.716	0.604	0.503	0.716	SUBCLONAL	1	TRUE	1	0.238155755522878	2		533	584	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	79	670	5	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	0.139292488157321	4	FACETS	1	0.883	1	0.503	0.441	0.569	INDETERMINATE	1	TRUE	2	0.238155755522878	4		675	817	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614463	38614463	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	23	374	1	ENST00000299084.4:c.234del	p.Asp79ThrfsTer42	p.D79Tfs*42	ENST00000299084	NM_152594.2	77	Aaa/aa	3/7	1	2	FACETS	0.57	0.444	0.715	0.57	0.444	0.715	SUBCLONAL	1	TRUE	1	0.238155755522878	2		375	339	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624558	93624558	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867241355	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	150	554	2	ENST00000375746.1:c.649C>T	p.Arg217Cys	p.R217C	ENST00000375746	NM_001174167.1	217	Cgc/Tgc	4/14	0.238155755522878	4	FACETS	1	0.969	1	0.747	0.684	0.812	CLONAL	2	TRUE	1	0.238155755522878	4		556	696	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	81	456	0	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	0.238155755522878	5	FACETS	0.771	0.68	0.868	0.771	0.68	0.868	SUBCLONAL	2	TRUE	3	0.238155755522878	5		456	599	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214398	36214398	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs868041281	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	45	514	2	ENST00000222270.7:c.3057del	p.Gly1020AlafsTer4	p.G1020Afs*4	ENST00000222270	NM_014727.1	1018	Aaa/aa	7/37	1	2	FACETS	0.704	0.591	0.828	0.704	0.591	0.828	SUBCLONAL	1	TRUE	1	0.238155755522878	2		516	537	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	217	684	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.238155755522878	5	FACETS	1	0.97	1	1	0.993	1	CLONAL	3	TRUE	3	0.238155755522878	5		684	770	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863054	56863054	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1266824391	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	117	547	0	ENST00000519728.1:c.327del	p.Glu110LysfsTer15	p.E110Kfs*15	ENST00000519728	NM_002350.3	107	acA/ac	5/13	0.238155755522878	4	FACETS	0.978	0.884	1	0.652	0.589	0.718	CLONAL	2	TRUE	1	0.238155755522878	4		547	622	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161938	47161939	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	88	342	0	ENST00000409792.3:c.4187dup	p.Asn1396LysfsTer2	p.N1396Kfs*2	ENST00000409792	NM_014159.6	1396	aat/aaAt	3/21	1	2	FACETS	0.899	0.801	1	1	0.984	1	CLONAL	2	TRUE	1	0.238155755522878	2		342	411	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324886	31324887	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760037174	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	21	312	1	ENST00000412585.2:c.49_50insG	p.Leu17ArgfsTer82	p.L17Rfs*82	ENST00000412585	NM_005514.6	17	ctg/cGtg	1/8	0.139292488157321	4	FACETS	0.866	0.669	1	0.433	0.334	0.548	INDETERMINATE	1	TRUE	2	0.238155755522878	4		313	252	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858268	59858268	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	37	501	1	ENST00000259008.2:c.1727del	p.Asn576IlefsTer14	p.N576Ifs*14	ENST00000259008	NM_032043.2	576	aAt/at	12/20	1	2	FACETS	0.591	0.486	0.708	0.591	0.486	0.708	SUBCLONAL	1	TRUE	1	0.238155755522878	2		502	526	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524725	187524725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756919389	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	189	646	1	ENST00000441802.2:c.10955C>T	p.Pro3652Leu	p.P3652L	ENST00000441802	NM_005245.3	3652	cCg/cTg	19/27	1	2	FACETS	1	0.97	1	1	0.994	1	CLONAL	2	TRUE	1	0.238155755522878	2		647	730	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	143	732	1	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	0.996	0.911	1	1	0.991	1	CLONAL	2	TRUE	1	0.238155755522878	2		733	603	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753149	42753151	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs199960550	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	182	640	7	ENST00000222329.4:c.1113_1115del	p.Ser373del	p.S373del	ENST00000222329	NM_006494.2	371	tcTTCc/tcc	4/4	1	2	FACETS	1	0.983	1	1	0.994	1	CLONAL	2	TRUE	1	0.238155755522878	2		647	632	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187222	38187222	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	61	624	2	ENST00000317025.8:c.1255del	p.Thr419ProfsTer8	p.T419Pfs*8	ENST00000317025	NM_023034.1	419	Acc/cc	6/24	0.238155755522878	4	FACETS	0.582	0.501	0.672	0.194	0.167	0.224	SUBCLONAL	1	TRUE	1	0.238155755522878	4		626	1089	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648329	206648329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55721947	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	232	506	1	ENST00000367120.3:c.350G>A	p.Arg117His	p.R117H	ENST00000367120	NM_014002.3	117	cGc/cAc	5/22	1	2	FACETS	0.925	0.867	0.985	1	0.995	1	CLONAL	3	TRUE	1	0.238155755522878	2		507	702	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821082	72821082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458157669	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	164	490	0	ENST00000268489.5:c.11093C>T	p.Thr3698Met	p.T3698M	ENST00000268489	NM_006885.3	3698	aCg/aTg	10/10	1	2	FACETS	1	0.974	1	1	0.993	1	CLONAL	2	TRUE	1	0.238155755522878	2		490	609	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504426	186504427	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	100	447	0	ENST00000323963.5:c.770_771del	p.Glu257GlyfsTer9	p.E257Gfs*9	ENST00000323963		255	GAg/g	7/11	1	2	FACETS	0.905	0.813	1	1	0.986	1	CLONAL	2	TRUE	1	0.238155755522878	2		447	464	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483053	29483055	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	45	432	0	ENST00000356175.3:c.117_119del	p.Asn39del	p.N39del	ENST00000356175	NM_000267.3	38	cACAac/cac	2/57	1	2	FACETS	0.794	0.667	0.934	0.794	0.667	0.934	CLONAL	1	TRUE	1	0.238155755522878	2		432	476	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054395	42054396	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	29	378	0	ENST00000219905.7:c.7585dup	p.Arg2529LysfsTer9	p.R2529Kfs*9	ENST00000219905	NM_001164273.1	2527	caa/cAaa	22/24	1	2	FACETS	0.815	0.655	0.995	0.815	0.655	0.995	CLONAL	1	TRUE	1	0.238155755522878	2		378	299	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184561	11184561	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	181	510	0	ENST00000361445.4:c.6656del	p.Asn2219ThrfsTer60	p.N2219Tfs*60	ENST00000361445	NM_004958.3	2219	aAc/ac	47/58	1	2	FACETS	0.916	0.851	0.983	1	0.994	1	CLONAL	3	TRUE	1	0.238155755522878	2		510	553	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002719	37002719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757277825	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	108	483	1	ENST00000358127.4:c.530C>T	p.Ser177Leu	p.S177L	ENST00000358127	NM_001280556.1	177	tCg/tTg	5/10	0.238155755522878	4	FACETS	1	0.981	1	0.476	0.427	0.528	CLONAL	1	TRUE	1	0.238155755522878	4		484	787	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323185	31323185	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs151341353	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	49	659	0	ENST00000412585.2:c.804G>A	p.Trp268Ter	p.W268*	ENST00000412585	NM_005514.6	268	tgG/tgA	4/8	0.139292488157321	4	FACETS	0.721	0.609	0.844	0.36	0.304	0.422	INDETERMINATE	1	TRUE	2	0.238155755522878	4		659	707	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562789	21562789	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766346109	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	171	359	0	ENST00000382592.4:c.1130G>A	p.Arg377His	p.R377H	ENST00000382592	NM_014572.2	377	cGc/cAc	4/8	0.238155755522878	0	FACETS	0.75	0.696	0.806			1	SUBCLONAL	3	TRUE	0	0.238155755522878	0		359	486	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324680	31324681	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	44	401	0	ENST00000412585.2:c.127dup	p.Glu43GlyfsTer56	p.E43Gfs*56	ENST00000412585	NM_005514.6	43	gag/gGag	2/8	0.139292488157321	4	FACETS	1	0.946	1	0.655	0.551	0.77	INDETERMINATE	1	TRUE	2	0.238155755522878	4		401	349	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31466379	31466379	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	114	478	4	ENST00000344624.3:c.2376del	p.Lys792AsnfsTer7	p.K792Nfs*7	ENST00000344624		792	aaA/aa	16/33	1	2	FACETS	1	0.935	1	1	0.989	1	CLONAL	2	TRUE	1	0.238155755522878	2		482	460	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187135	38187135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356401338	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	193	610	0	ENST00000317025.8:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000317025	NM_023034.1	448	Cgg/Tgg	6/24	0.238155755522878	4	FACETS	1	0.958	1	0.7	0.648	0.755	CLONAL	2	TRUE	1	0.238155755522878	4		610	955	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32899249	32899249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358603	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	89	301	0	ENST00000380152.3:c.353G>A	p.Arg118His	p.R118H	ENST00000380152		118	cGc/cAc	4/27	0.166195876129294	3	FACETS	0.847	0.759	0.94	1	0.972	1	CLONAL	3	TRUE	1	0.238155755522878	3		301	329	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599885	28599885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371066600	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	155	571	0	ENST00000253063.3:c.767G>A	p.Arg256His	p.R256H	ENST00000253063	NM_031459.4	256	cGc/cAc	6/10	1	2	FACETS	1	0.954	1	1	0.992	1	CLONAL	2	TRUE	1	0.238155755522878	2		571	617	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124454	94124457	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	97	394	0	ENST00000369303.4:c.126_129del	p.Thr43SerfsTer57	p.T43Sfs*57	ENST00000369303	NM_004440.3	42	caAACA/ca	2/17	0.139292488157321	4	FACETS	1	0.969	1	1	0.969	1	INDETERMINATE	2	TRUE	2	0.238155755522878	4		394	415	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435327	110435327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1450582670	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	40	262	1	ENST00000375856.3:c.3074C>T	p.Pro1025Leu	p.P1025L	ENST00000375856	NM_003749.2	1025	cCg/cTg	1/2	0.166195876129294	3	FACETS	0.942	0.784	1	0.471	0.392	0.559	CLONAL	1	TRUE	1	0.238155755522878	3		263	399	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551354	150551354	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs866377910	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	112	687	1	ENST00000369026.2:c.653A>G	p.Asp218Gly	p.D218G	ENST00000369026	NM_021960.4	218	gAt/gGt	1/3	1	2	FACETS	0.831	0.745	0.922	0.831	0.745	0.922	CLONAL	1	TRUE	1	0.238155755522878	2		688	1132	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138870	64138870	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	190	457	0	ENST00000334205.4:c.2237C>A	p.Pro746His	p.P746H	ENST00000334205	NM_003942.2	746	cCt/cAt	17/17	1	2	FACETS	0.976	0.909	1	1	0.995	1	CLONAL	3	TRUE	1	0.238155755522878	2		457	545	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998189	100998189	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1462925567	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	51	245	0	ENST00000325455.5:c.1613A>G	p.Tyr538Cys	p.Y538C	ENST00000325455	NM_001202474.3	538	tAc/tGc	1/8	1	2	FACETS	0.917	0.78	1	0.917	0.78	1	CLONAL	1	TRUE	1	0.238155755522878	2		245	467	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913126	32913126	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1322421694	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	124	420	0	ENST00000380152.3:c.4634T>C	p.Leu1545Pro	p.L1545P	ENST00000380152		1545	cTt/cCt	11/27	0.166195876129294	3	FACETS	0.861	0.785	0.941	1	0.981	1	CLONAL	3	TRUE	1	0.238155755522878	3		420	451	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514511	103514511	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	57	314	0	ENST00000355739.4:c.1012A>G	p.Thr338Ala	p.T338A	ENST00000355739	NM_000123.3	338	Acc/Gcc	8/15	0.166195876129294	3	FACETS	0.878	0.759	1	0.878	0.759	1	CLONAL	2	TRUE	1	0.238155755522878	3		314	305	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871253	35871253	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	42	360	0	ENST00000216797.5:c.920A>G	p.Asp307Gly	p.D307G	ENST00000216797	NM_020529.2	307	gAc/gGc	6/6	1	2	FACETS	0.543	0.453	0.645	0.543	0.453	0.645	SUBCLONAL	1	TRUE	1	0.238155755522878	2		360	649	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748135	43748136	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	75	503	1	ENST00000382044.4:c.2670dup	p.Lys891GlufsTer12	p.K891Efs*12	ENST00000382044	NM_001141980.1	890	-/G	12/28	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.238155755522878	2		504	579	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312401	91312402	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	111	423	0	ENST00000355112.3:c.2349_2350del	p.Tyr784Ter	p.Y784*	ENST00000355112	NM_000057.2	782	aaTCtc/aatc	11/22	1	2	FACETS	0.876	0.791	0.966	1	0.987	1	CLONAL	2	TRUE	1	0.238155755522878	2		423	532	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396161	396161	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	133	512	0	ENST00000262320.3:c.865G>T	p.Gly289Cys	p.G289C	ENST00000262320	NM_003502.3	289	Ggc/Tgc	2/11	1	2	FACETS	0.87	0.792	0.951	1	0.989	1	CLONAL	2	TRUE	1	0.238155755522878	2		512	642	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104372	2104372	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173061992	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	53	602	1	ENST00000219476.3:c.412G>A	p.Glu138Lys	p.E138K	ENST00000219476	NM_000548.3	138	Gaa/Aaa	5/42	1	2	FACETS	0.58	0.494	0.676	0.58	0.494	0.676	SUBCLONAL	1	TRUE	1	0.238155755522878	2		603	767	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50827539	50827539	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	59	392	0	ENST00000398568.2:c.2428del	p.Ile810SerfsTer19	p.I810Sfs*19	ENST00000398568	NM_001042412.1	808	ggA/gg	16/18	1	2	FACETS	0.955	0.822	1	0.955	0.822	1	CLONAL	1	TRUE	1	0.238155755522878	2		392	519	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357487	89357487	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	73	662	0	ENST00000301030.4:c.331del	p.Leu111SerfsTer13	p.L111Sfs*13	ENST00000301030	NM_001256183.1	111	Ctc/tc	5/13	1	2	FACETS	0.882	0.771	1	0.882	0.771	1	CLONAL	1	TRUE	1	0.238155755522878	2		662	695	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610672	10610672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	137	613	2	ENST00000171111.5:c.38G>A	p.Cys13Tyr	p.C13Y	ENST00000171111	NM_203500.1	13	tGc/tAc	2/6	1	2	FACETS	0.973	0.889	1	1	0.99	1	CLONAL	2	TRUE	1	0.238155755522878	2		615	591	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098369	11098369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781066262	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	173	485	0	ENST00000358026.2:c.887C>T	p.Thr296Met	p.T296M	ENST00000358026	NM_001128849.1	296	aCg/aTg	6/36	1	2	FACETS	1	0.976	1	1	0.993	1	CLONAL	2	TRUE	1	0.238155755522878	2		485	639	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279955	18279955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1202529789	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	85	559	0	ENST00000222254.8:c.2038G>A	p.Ala680Thr	p.A680T	ENST00000222254	NM_005027.3	680	Gcg/Acg	16/16	1	2	FACETS	0.852	0.752	0.959	0.852	0.752	0.959	CLONAL	1	TRUE	1	0.238155755522878	2		559	838	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439667	220439667	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	210	741	0	ENST00000243786.2:c.520C>A	p.Pro174Thr	p.P174T	ENST00000243786	NM_002191.3	174	Cct/Act	2/2	1	2	FACETS	0.859	0.802	0.919	1	0.995	1	CLONAL	3	TRUE	1	0.238155755522878	2		741	684	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253819	30253819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763223337	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	138	547	1	ENST00000307677.4:c.635G>A	p.Arg212His	p.R212H	ENST00000307677	NM_138578.1	212	cGc/cAc	3/3	0.238155755522878	2	FACETS	1	0.986	1	0.725	0.66	0.793	CLONAL	1	TRUE	0	0.238155755522878	2		548	799	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158124	47158125	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	99	387	0	ENST00000409792.3:c.4574_4575del	p.Leu1525HisfsTer3	p.L1525Hfs*3	ENST00000409792	NM_014159.6	1525	cTC/c	4/21	1	2	FACETS	1	0.934	1	1	0.988	1	CLONAL	2	TRUE	1	0.238155755522878	2		387	396	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430435	181430435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	51	619	0	ENST00000325404.1:c.287G>A	p.Arg96Gln	p.R96Q	ENST00000325404	NM_003106.3	96	cGg/cAg	1/1	1	2	FACETS	0.562	0.476	0.656	0.562	0.476	0.656	SUBCLONAL	1	TRUE	1	0.238155755522878	2		619	762	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449588	187449588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867240773	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	40	376	1	ENST00000232014.4:c.292C>T	p.Arg98Trp	p.R98W	ENST00000232014	NM_001130845.1	98	Cgg/Tgg	4/10	1	2	FACETS	0.737	0.612	0.875	0.737	0.612	0.875	SUBCLONAL	1	TRUE	1	0.238155755522878	2		377	456	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805347	32805347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	46	478	0	ENST00000374899.4:c.575C>T	p.Ala192Val	p.A192V	ENST00000374899	NM_018833.2	192	gCc/gTc	3/12	0.139292488157321	4	FACETS	0.87	0.732	1	0.435	0.366	0.511	INDETERMINATE	1	TRUE	2	0.238155755522878	4		478	550	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163922	152163922	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	27	389	0	ENST00000206249.3:c.643G>C	p.Gly215Arg	p.G215R	ENST00000206249	NM_000125.3	215	Gga/Cga	2/8	0.139292488157321	4	FACETS	0.872	0.695	1	0.436	0.347	0.537	INDETERMINATE	1	TRUE	2	0.238155755522878	4		389	322	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339371	116339371	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	139	407	0	ENST00000397752.3:c.233T>C	p.Leu78Pro	p.L78P	ENST00000397752	NM_000245.2	78	cTt/cCt	2/21	1	2	FACETS	1	0.981	1	1	0.992	1	CLONAL	2	TRUE	1	0.238155755522878	2		407	467	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540162	23540162	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	123	240	0	ENST00000380871.4:c.241del	p.Arg81AlafsTer56	p.R81Afs*56	ENST00000380871	NM_006167.3	81	Cgc/gc	1/2	0.238155755522878	4	FACETS	0.853	0.775	0.933	0.853	0.775	0.933	CLONAL	3	TRUE	1	0.238155755522878	4		240	500	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126354	5126354	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	33	304	0	ENST00000381652.3:c.3199A>G	p.Asn1067Asp	p.N1067D	ENST00000381652	NM_004972.3	1067	Aat/Gat	24/25	0.238155755522878	4	FACETS	0.858	0.699	1	0.286	0.233	0.346	CLONAL	1	TRUE	1	0.238155755522878	4		304	400	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485322	8485322	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	64	297	0	ENST00000356435.5:c.3058T>C	p.Phe1020Leu	p.F1020L	ENST00000356435		1020	Ttt/Ctt	18/35	0.238155755522878	4	FACETS	1	0.881	1	0.674	0.588	0.767	CLONAL	2	TRUE	1	0.238155755522878	4		297	329	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248055	98248057	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1201611173	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	123	489	0	ENST00000331920.6:c.494_496del	p.Glu165del	p.E165del	ENST00000331920	NM_000264.3	165	gAAGgt/ggt	3/24	0.238155755522878	4	FACETS	0.882	0.798	0.97	0.588	0.532	0.647	CLONAL	2	TRUE	1	0.238155755522878	4		489	725	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913262	39913262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	45	503	0	ENST00000378444.4:c.4853C>T	p.Ala1618Val	p.A1618V	ENST00000378444	NM_001123385.1	1618	gCc/gTc	14/15	0.1237613169068	0	FACETS	0.651	0.548	0.766			1	INDETERMINATE	1	TRUE	0	0.238155755522878	0		503	442	SUCCESS
AR	367	MSKCC	GRCh37	X	66863111	66863111	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	28	538	1	ENST00000374690.3:c.1630A>G	p.Arg544Gly	p.R544G	ENST00000374690	NM_000044.3	544	Agg/Ggg	2/8	0.1237613169068	0	FACETS	0.389	0.31	0.479			1	INDETERMINATE	1	TRUE	0	0.238155755522878	0		539	461	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	146	230	0				ENST00000310581	NM_198253.2	-/1132			0.463626200762376	7	FACETS	1	0.94	1	1	0.94	1	CLONAL	5	TRUE	2	0.463626200762376	7		230	270	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0051822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	321	408	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	0.463626200762376	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	1	0.463626200762376	4		408	584	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937001	48937001	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	118	441	0	ENST00000267163.4:c.769C>T	p.Gln257Ter	p.Q257*	ENST00000267163	NM_000321.2	257	Cag/Tag	8/27	0.463626200762376	4	FACETS	0.819	0.743	0.897	0.819	0.743	0.897	CLONAL	2	TRUE	2	0.463626200762376	4		441	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578227	7578227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	261	658	0	ENST00000269305.4:c.622G>A	p.Asp208Asn	p.D208N	ENST00000269305	NM_001126112.2	208	Gac/Aac	6/11	0.260565540140362	5	FACETS	0.912	0.859	0.965	0.912	0.859	0.965	INDETERMINATE	3	TRUE	2	0.463626200762376	5		658	698	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573991	7573991	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567542019	NA	P-0051822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	254	673	0	ENST00000269305.4:c.1036G>T	p.Glu346Ter	p.E346*	ENST00000269305	NM_001126112.2	346	Gag/Tag	10/11	0.260565540140362	5	FACETS	1	0.984	1	0.756	0.71	0.803	INDETERMINATE	2	TRUE	2	0.463626200762376	5		673	819	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916851	48916851	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0051822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	126	258	0	ENST00000267163.4:c.380+1G>T		p.X127_splice	ENST00000267163	NM_000321.2	127			0.463626200762376	4	FACETS	0.994	0.909	1	0.994	0.909	1	CLONAL	2	TRUE	2	0.463626200762376	4		258	400	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432480	49432480	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	333	717	0	ENST00000301067.7:c.8659G>T	p.Gly2887Ter	p.G2887*	ENST00000301067	NM_003482.3	2887	Gga/Tga	34/54	0.463626200762376	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	TRUE	1	0.463626200762376	4		717	676	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879337	151879337	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	152	491	0	ENST00000262189.6:c.5608C>T	p.Gln1870Ter	p.Q1870*	ENST00000262189	NM_170606.2	1870	Cag/Tag	36/59	0.212631719916216	3	FACETS	1	0.951	1	1	0.951	1	INDETERMINATE	2	TRUE	1	0.463626200762376	3		491	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578188	7578188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201592	NA	P-0051822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	253	708	1	ENST00000269305.4:c.661G>A	p.Glu221Lys	p.E221K	ENST00000269305	NM_001126112.2	221	Gag/Aag	6/11	0.260565540140362	5	FACETS	0.88	0.828	0.933	0.88	0.828	0.933	INDETERMINATE	3	TRUE	2	0.463626200762376	5		709	701	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298847	46298847	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs12319797	NA	P-0051822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	33	258	0	ENST00000334344.6:c.5494G>C	p.Glu1832Gln	p.E1832Q	ENST00000334344	NM_152641.2	1832	Gaa/Caa	21/21	0.463626200762376	4	FACETS	0.681	0.556	0.821	0.227	0.185	0.274	SUBCLONAL	1	TRUE	1	0.463626200762376	4		258	306	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957889	1957889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1040367399	NA	P-0051822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	269	466	0	ENST00000382891.5:c.2855G>A	p.Arg952Lys	p.R952K	ENST00000382891	NM_133335.3	952	aGa/aAa	15/22	0.463626200762376	2	FACETS	0.839	0.799	0.878	1	0.993	1	CLONAL	3	TRUE	0	0.463626200762376	2		466	461	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045001	47045001	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	233	392	1	ENST00000377604.3:c.2327G>A	p.Arg776Gln	p.R776Q	ENST00000377604	NM_001204468.1	776	cGg/cAg	20/24	0.242169614523482	2	FACETS	0.98	0.936	1			1	INDETERMINATE	3	TRUE	NA	0.463626200762376	2		393	342	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340946	70340946	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	248	358	0	ENST00000374080.3:c.679G>C	p.Glu227Gln	p.E227Q	ENST00000374080		227	Gag/Cag	5/45	0.242169614523482	2	FACETS	0.972	0.929	1			1	INDETERMINATE	3	TRUE	NA	0.463626200762376	2		358	367	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571932	64571932	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	101	739	0	ENST00000312049.6:c.1707del	p.Ile570SerfsTer18	p.I570Sfs*18	ENST00000312049	NM_130799.2	569	aaG/aa	10/10	0.359655872264125	6	FACETS	0.929	0.833	1			1	CLONAL	2	TRUE	NA	0.359655872264125	6		739	520	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500637	99500637	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	57	595	0	ENST00000268035.6:c.4070G>T	p.Arg1357Leu	p.R1357L	ENST00000268035	NM_000875.3	1357	cGg/cTg	21/21	0.0609492772662388	3	FACETS	0.776	0.673	0.885	0.776	0.673	0.885	INDETERMINATE	2	TRUE	1	0.359655872264125	3		595	241	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641575	23641575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	38	603	0	ENST00000261584.4:c.1900C>T	p.Pro634Ser	p.P634S	ENST00000261584	NM_024675.3	634	Cca/Tca	5/13	0.359655872264125	1	FACETS	0.731	0.609	0.866	0.731	0.609	0.866	SUBCLONAL	1	TRUE	0	0.359655872264125	1		603	237	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991610	72991610	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	31	592	0	ENST00000268489.5:c.2435A>G	p.Glu812Gly	p.E812G	ENST00000268489	NM_006885.3	812	gAg/gGg	2/10	0.359655872264125	1	FACETS	0.607	0.494	0.733	0.607	0.494	0.733	SUBCLONAL	1	TRUE	0	0.359655872264125	1		592	233	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271898	15271898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	62	915	0	ENST00000263388.2:c.6541C>T	p.Pro2181Ser	p.P2181S	ENST00000263388	NM_000435.2	2181	Cca/Tca	33/33	0.148861203830329	3	FACETS	1	0.958	1	0.632	0.549	0.72	INDETERMINATE	1	TRUE	1	0.359655872264125	3		915	322	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412032	116412046	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTTTCCAGAAGGTA	CTTTTCCAGAAGGTA	AGGTG	novel	NA	P-0051823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	540	639	1	ENST00000397752.3:c.3017_3028+3delinsAGGTG		p.X1006_splice	ENST00000397752	NM_000245.2	1006		14/21	0.359655872264125	10	FACETS	0.995	0.965	1			1	CLONAL	9	TRUE	NA	0.359655872264125	10		640	818	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	330	230	0				ENST00000310581	NM_198253.2	-/1132			0.234856386765692	8	FACETS	1	0.983	1	1	0.993	1	CLONAL	8	TRUE	1	0.234856386765692	8		230	568	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	118	325	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	1	0.956	1	1	0.992	1	CLONAL	3	TRUE	1	0.234856386765692	2		325	313	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	188	408	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	0.0572575886908084	3	FACETS	1	0.96	1	1	0.992	1	INDETERMINATE	3	TRUE	1	0.234856386765692	3		408	570	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	28	518	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.334	0.266	0.412	0.334	0.266	0.412	SUBCLONAL	1	TRUE	1	0.234856386765692	2		518	714	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	14	365	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.0572575886908084	3	FACETS	0.544	0.393	0.726	0.272	0.196	0.363	INDETERMINATE	1	TRUE	1	0.234856386765692	3		365	245	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405899	70405899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	26	478	0	ENST00000373644.4:c.3413C>T	p.Ser1138Leu	p.S1138L	ENST00000373644	NM_030625.2	1138	tCa/tTa	4/12	0.0572575886908084	3	FACETS	0.691	0.547	0.856	0.346	0.273	0.428	INDETERMINATE	1	TRUE	1	0.234856386765692	3		478	358	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	401	564	0	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	1	2	FACETS	1	0.99	1	1	0.997	1	CLONAL	3	TRUE	1	0.234856386765692	2		564	1007	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721812	49721812	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs142690032	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	13	16	0	ENST00000449682.2:c.1951C>T	p.Arg651Ter	p.R651*	ENST00000449682	NM_020998.3	651	Cga/Tga	17/18	1	2	FACETS	1	0.838	1	1	0.924	1	CLONAL	2	TRUE	1	0.234856386765692	2		16	46	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868193	37868193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	41	721	0	ENST00000269571.5:c.914C>T	p.Ser305Phe	p.S305F	ENST00000269571		305	tCt/tTt	8/27	1	2	FACETS	0.431	0.357	0.513	0.431	0.357	0.513	SUBCLONAL	1	TRUE	1	0.234856386765692	2		721	811	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100564	8100564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1178153797	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	66	754	0	ENST00000346208.3:c.538G>A	p.Glu180Lys	p.E180K	ENST00000346208		180	Gag/Aag	3/6	0.0572575886908084	3	FACETS	0.626	0.541	0.717	0.313	0.27	0.359	INDETERMINATE	1	TRUE	1	0.234856386765692	3		754	1004	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629199	187629199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	161	561	0	ENST00000441802.2:c.1783G>A	p.Asp595Asn	p.D595N	ENST00000441802	NM_005245.3	595	Gat/Aat	2/27	0.0572575886908084	3	FACETS	0.91	0.844	0.977	1	0.992	1	INDETERMINATE	4	TRUE	1	0.234856386765692	3		561	421	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2218080	2218080	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	90	857	0	ENST00000326181.6:c.142G>A	p.Asp48Asn	p.D48N	ENST00000326181	NM_032271.2	48	Gac/Aac	4/21	1	2	FACETS	0.703	0.622	0.79	0.703	0.622	0.79	SUBCLONAL	1	TRUE	1	0.234856386765692	2		857	1090	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372127	45372127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	134	549	0	ENST00000262160.6:c.1042G>A	p.Glu348Lys	p.E348K	ENST00000262160	NM_005901.5	348	Gag/Aag	9/11	1	2	FACETS	0.951	0.873	1	1	0.993	1	CLONAL	3	TRUE	1	0.234856386765692	2		549	400	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307316	118307316	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs9332745	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	22	4	0	ENST00000534358.1:c.89C>G	p.Ala30Gly	p.A30G	ENST00000534358	NM_005933.3	30	gCc/gGc	1/36	1	2	FACETS	1	0.879	1	1	0.964	1	CLONAL	4	TRUE	1	0.234856386765692	2		4	43	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581234	48581234	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767332	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	189	502	3	ENST00000342988.3:c.538C>T	p.Gln180Ter	p.Q180*	ENST00000342988	NM_005359.5	180	Caa/Taa	5/12	1	2	FACETS	1	0.962	1	1	0.995	1	CLONAL	3	TRUE	1	0.234856386765692	2		505	512	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164748	106164748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	151	444	0	ENST00000380013.4:c.3616G>A	p.Glu1206Lys	p.E1206K	ENST00000380013	NM_001127208.2	1206	Gaa/Aaa	6/11	0.0572575886908084	3	FACETS	1	0.971	1	1	0.971	1	INDETERMINATE	2	TRUE	1	0.234856386765692	3		444	636	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554497	63554497	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146238336	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	43	676	2	ENST00000307078.5:c.242C>T	p.Ser81Phe	p.S81F	ENST00000307078	NM_004655.3	81	tCc/tTc	2/11	1	2	FACETS	0.492	0.411	0.583	0.492	0.411	0.583	SUBCLONAL	1	TRUE	1	0.234856386765692	2		678	744	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950189	38950189	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	302	523	0	ENST00000357387.3:c.3761G>A	p.Ser1254Asn	p.S1254N	ENST00000357387	NM_152756.3	1254	aGc/aAc	31/38	0.234856386765692	8	FACETS	0.973	0.922	1	0.834	0.79	0.878	CLONAL	6	TRUE	1	0.234856386765692	8		523	751	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156947	89156947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	248	586	1	ENST00000336596.2:c.49G>A	p.Asp17Asn	p.D17N	ENST00000336596	NM_005233.5	17	Gac/Aac	1/17	1	2	FACETS	0.972	0.913	1	1	0.996	1	CLONAL	3	TRUE	1	0.234856386765692	2		587	724	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197360	106197360	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767475870	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	174	400	0	ENST00000380013.4:c.5693C>T	p.Ser1898Phe	p.S1898F	ENST00000380013	NM_001127208.2	1898	tCc/tTc	11/11	0.0572575886908084	3	FACETS	0.983	0.916	1	1	0.993	1	INDETERMINATE	4	TRUE	1	0.234856386765692	3		400	421	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162475176	162475176	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761430731	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	125	396	0	ENST00000366898.1:c.565C>T	p.Pro189Ser	p.P189S	ENST00000366898	NM_004562.2	189	Cca/Tca	5/12	0.0572575886908084	3	FACETS	0.903	0.824	0.985	1	0.983	1	INDETERMINATE	3	TRUE	1	0.234856386765692	3		396	439	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16097838	16097838	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	23	385	0	ENST00000268712.3:c.46G>A	p.Glu16Lys	p.E16K	ENST00000268712	NM_006311.3	16	Gaa/Aaa	2/46	1	2	FACETS	0.616	0.48	0.773	0.616	0.48	0.773	SUBCLONAL	1	TRUE	1	0.234856386765692	2		385	318	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278198	41278198	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	25	380	1	ENST00000349496.5:c.2074G>A	p.Glu692Lys	p.E692K	ENST00000349496	NM_001904.3	692	Gag/Aag	13/15	1	2	FACETS	0.572	0.451	0.712	0.572	0.451	0.712	SUBCLONAL	1	TRUE	1	0.234856386765692	2		381	372	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262270	115262270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	210	492	0	ENST00000438362.2:c.2284G>A	p.Glu762Lys	p.E762K	ENST00000438362	NM_001242891.1	762	Gag/Aag	18/20	1	2	FACETS	0.994	0.929	1	1	0.995	1	CLONAL	3	TRUE	1	0.234856386765692	2		492	600	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115277086	115277086	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	26	555	0	ENST00000438362.2:c.697C>T	p.Gln233Ter	p.Q233*	ENST00000438362	NM_001242891.1	233	Cag/Tag	7/20	1	2	FACETS	0.563	0.446	0.698	0.563	0.446	0.698	SUBCLONAL	1	TRUE	1	0.234856386765692	2		555	393	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871765	12871765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373917399	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	84	169	1	ENST00000228872.4:c.482C>T	p.Ser161Phe	p.S161F	ENST00000228872	NM_004064.3	161	tCt/tTt	2/3	0.234856386765692	1	FACETS	0.961	0.865	1	1	0.989	1	CLONAL	3	TRUE	0	0.234856386765692	1		170	219	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117723	115117723	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	120	459	0	ENST00000257566.3:c.712A>G	p.Thr238Ala	p.T238A	ENST00000257566	NM_016569.3	238	Act/Gct	3/8	0.0572575886908084	3	FACETS	0.998	0.917	1	1	0.99	1	INDETERMINATE	4	TRUE	1	0.234856386765692	3		459	286	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120806851	120806851	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	69	54	0	ENST00000257552.2:c.44C>T	p.Ser15Leu	p.S15L	ENST00000257552	NM_002442.3	15	tCg/tTg	1/15	0.0572575886908084	3	FACETS	0.968	0.856	1	1	0.975	1	INDETERMINATE	3	TRUE	1	0.234856386765692	3		54	226	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435444	121435444	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	385	821	0	ENST00000257555.6:c.1477A>G	p.Met493Val	p.M493V	ENST00000257555		493	Atg/Gtg	7/10	0.0572575886908084	3	FACETS	0.882	0.839	0.924	1	0.996	1	INDETERMINATE	4	TRUE	1	0.234856386765692	3		821	1039	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897017	28897017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	45	551	0	ENST00000282397.4:c.2863C>T	p.Pro955Ser	p.P955S	ENST00000282397	NM_002019.4	955	Cca/Tca	21/30	1	2	FACETS	0.57	0.478	0.673	0.57	0.478	0.673	SUBCLONAL	1	TRUE	1	0.234856386765692	2		551	672	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052693	42052693	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	237	520	0	ENST00000219905.7:c.7364C>G	p.Ser2455Cys	p.S2455C	ENST00000219905	NM_001164273.1	2455	tCt/tGt	20/24	1	2	FACETS	1	0.984	1	1	0.996	1	CLONAL	3	TRUE	1	0.234856386765692	2		520	594	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828175	3828175	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	93	264	0	ENST00000262367.5:c.1950T>G	p.Tyr650Ter	p.Y650*	ENST00000262367	NM_004380.2	650	taT/taG	10/31	1	2	FACETS	0.99	0.902	1	1	0.991	1	CLONAL	4	TRUE	1	0.234856386765692	2		264	200	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864498	56864498	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	327	642	0	ENST00000308159.5:c.986G>C	p.Gly329Ala	p.G329A	ENST00000308159	NM_014669.4	329	gGa/gCa	10/22	1	2	FACETS	1	0.986	1	1	0.997	1	CLONAL	3	TRUE	1	0.234856386765692	2		642	836	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7977025	7977025	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	394	698	0	ENST00000319144.4:c.1705A>C	p.Ile569Leu	p.I569L	ENST00000319144	NM_001139.2	569	Ata/Cta	13/15	1	2	FACETS	0.888	0.847	0.928	1	0.997	1	CLONAL	4	TRUE	1	0.234856386765692	2		698	945	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978925	25978925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	183	423	0	ENST00000435504.4:c.998C>T	p.Thr333Ile	p.T333I	ENST00000435504		333	aCt/aTt	10/13	1	2	FACETS	0.93	0.869	0.991	1	0.995	1	CLONAL	4	TRUE	1	0.234856386765692	2		423	419	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46608820	46608820	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	343	681	0	ENST00000263734.3:c.2131C>T	p.Gln711Ter	p.Q711*	ENST00000263734	NM_001430.4	711	Cag/Tag	13/16	1	2	FACETS	1	0.972	1	1	0.997	1	CLONAL	3	TRUE	1	0.234856386765692	2		681	940	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050320	128050320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	280	609	0	ENST00000285398.2:c.337G>A	p.Val113Met	p.V113M	ENST00000285398	NM_000122.1	113	Gtg/Atg	3/15	1	2	FACETS	1	0.986	1	1	0.996	1	CLONAL	3	TRUE	1	0.234856386765692	2		609	705	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279990	46279990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	246	688	0	ENST00000371998.3:c.3916C>T	p.Pro1306Ser	p.P1306S	ENST00000371998		1306	Ccg/Tcg	20/23	1	2	FACETS	0.932	0.875	0.991	1	0.996	1	CLONAL	3	TRUE	1	0.234856386765692	2		688	749	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595818	52595818	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	212	538	0	ENST00000394830.3:c.4097del	p.Arg1366LysfsTer14	p.R1366Kfs*14	ENST00000394830	NM_018313.4	1366	aGa/aa	26/30	1	2	FACETS	0.862	0.804	0.922	1	0.995	1	CLONAL	3	TRUE	1	0.234856386765692	2		538	698	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595825	52595825	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	238	501	0	ENST00000394830.3:c.4090G>A	p.Glu1364Lys	p.E1364K	ENST00000394830	NM_018313.4	1364	Gaa/Aaa	26/30	1	2	FACETS	0.915	0.858	0.974	1	0.995	1	CLONAL	3	TRUE	1	0.234856386765692	2		501	738	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164796	106164796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	216	558	0	ENST00000380013.4:c.3664G>A	p.Glu1222Lys	p.E1222K	ENST00000380013	NM_001127208.2	1222	Gag/Aag	6/11	0.0572575886908084	3	FACETS	1	0.986	1	1	0.986	1	INDETERMINATE	2	TRUE	1	0.234856386765692	3		558	834	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247194	153247195	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTGTGTAGACAGGTTTCAGTCTCT	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	84	378	0	ENST00000281708.4:c.1584_1607dup	p.Glu529_Thr536dup	p.E529_T536dup	ENST00000281708	NM_033632.3	529	acg/acAGAGACTGAAACCTGTCTACACACg	10/12	0.0572575886908084	3	FACETS	1	0.967	1	1	0.967	1	INDETERMINATE	2	TRUE	1	0.234856386765692	3		378	325	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340042	116340042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	12	294	0	ENST00000397752.3:c.904G>A	p.Glu302Lys	p.E302K	ENST00000397752	NM_000245.2	302	Gaa/Aaa	2/21	0.0572575886908084	3	FACETS	0.565	0.397	0.771	0.283	0.198	0.386	INDETERMINATE	1	TRUE	1	0.234856386765692	3		294	202	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189005	38189005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	20	590	0	ENST00000317025.8:c.1009G>A	p.Glu337Lys	p.E337K	ENST00000317025	NM_023034.1	337	Gaa/Aaa	5/24	1	2	FACETS	0.426	0.325	0.544	0.426	0.325	0.544	SUBCLONAL	1	TRUE	1	0.234856386765692	2		590	400	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942824	44942846	+	frameshift_variant	Frame_Shift_Del	DEL	ACATGAAAGTTCCAGGGAGCAGA	ACATGAAAGTTCCAGGGAGCAGA	-	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	84	291	0	ENST00000377967.4:c.3407_3429del	p.Met1136ThrfsTer7	p.M1136Tfs*7	ENST00000377967	NM_021140.2	1135	tACATGAAAGTTCCAGGGAGCAGA/t	23/29	0.0369544265186867	2	FACETS	0.917	0.845	0.986			1	INDETERMINATE	6	TRUE	NA	0.234856386765692	2		291	130	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038556	47038556	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	459	370	0	ENST00000377604.3:c.718A>T	p.Lys240Ter	p.K240*	ENST00000377604	NM_001204468.1	240	Aag/Tag	8/24	0.0369544265186867	2	FACETS	0.999	0.975	1			1	INDETERMINATE	7	TRUE	NA	0.234856386765692	2		370	559	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182890	123182890	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	10	169	0	ENST00000218089.9:c.855G>A	p.Met285Ile	p.M285I	ENST00000218089	NM_001042749.1	285	atG/atA	10/35	0.0369544265186867	2	FACETS	0.64	0.435	0.895			1	INDETERMINATE	1	TRUE	NA	0.234856386765692	2		169	133	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052689	42052693	+	missense_variant	Missense_Mutation	ONP	CATTC	CATTC	TATTG	novel	NA	P-0051839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	249	517	0	ENST00000219905.7:c.7360_7364delinsTATTG	p.His2454_Ser2455delinsTyrCys	p.H2454_S2455delinsYC	ENST00000219905	NM_001164273.1	2454	CATTCt/TATTGt	20/24	1	2	FACETS	1	0.986	1	1	0.996	1	CLONAL	3	TRUE	1	0.234856386765692	2		517	618	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799176	42799176	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762480443	NA	P-0051840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	73	665	1	ENST00000575354.2:c.4660G>A	p.Ala1554Thr	p.A1554T	ENST00000575354	NM_015125.3	1554	Gca/Aca	20/20	1	2	FACETS	0.263	0.229	0.299	0.263	0.229	0.299	SUBCLONAL	1	TRUE	1	0.814286477425486	2		666	682	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098956	178098956	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	79	267	0	ENST00000397062.3:c.89T>C	p.Leu30Pro	p.L30P	ENST00000397062	NM_006164.4	30	cTt/cCt	2/5	0.118283891577265	0	FACETS	0.485	0.431	0.542			1	INDETERMINATE	1	FALSE	0	0.530568270958896	0		267	288	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434850	99434850	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1282070639	NA	P-0051841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	229	501	0	ENST00000268035.6:c.937C>T	p.Arg313Cys	p.R313C	ENST00000268035	NM_000875.3	313	Cgc/Tgc	3/21	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.530568270958896	2		501	831	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456593	40456594	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0051841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	236	690	0	ENST00000345506.4:c.1304dup	p.Thr436AspfsTer10	p.T436Dfs*10	ENST00000345506	NM_003152.3	435	gtg/gTtg	12/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.530568270958896	2		690	781	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442071	52442071	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	221	550	0	ENST00000460680.1:c.278C>A	p.Thr93Asn	p.T93N	ENST00000460680	NM_004656.3	93	aCt/aAt	5/17	0.470465914505594	2	FACETS	0.928	0.875	0.981	0.928	0.875	0.981	CLONAL	2	FALSE	0	0.530568270958896	2		550	449	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584538	52584539	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0051841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	179	625	0	ENST00000394830.3:c.4474_4475insTA	p.Pro1492LeufsTer14	p.P1492Lfs*14	ENST00000394830	NM_018313.4	1492	cca/cTAca	29/30	0.470465914505594	2	FACETS	0.825	0.77	0.88	0.825	0.77	0.88	CLONAL	2	FALSE	0	0.530568270958896	2		625	409	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31495452	31495452	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	148	484	0	ENST00000344624.3:c.1696A>G	p.Asn566Asp	p.N566D	ENST00000344624		566	Aac/Gac	9/33	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.530568270958896	2		484	456	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	213	590	2	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.144331907437963	6	FACETS	1	0.976	1	0.737	0.686	0.79	INDETERMINATE	2	TRUE	3	0.432121294236668	6		592	831	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0051843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	269	562	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.432121294236668	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.432121294236668	2		562	543	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028670	12028670	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	155	448	0	ENST00000353533.5:c.873G>T	p.Trp291Cys	p.W291C	ENST00000353533	NM_003010.3	291	tgG/tgT	8/11	0.432121294236668	2	FACETS	0.98	0.91	1	0.98	0.91	1	CLONAL	2	TRUE	0	0.432121294236668	2		448	366	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834585	156834585	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	243	797	0	ENST00000524377.1:c.353G>T	p.Ser118Ile	p.S118I	ENST00000524377	NM_002529.3	118	aGt/aTt	3/17	0.337571148610211	3	FACETS	0.901	0.845	0.958	0.901	0.845	0.958	CLONAL	2	TRUE	1	0.432121294236668	3		797	759	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94201060	94201060	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0051843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	55	249	0	ENST00000323929.3:c.1018-1G>C		p.X340_splice	ENST00000323929	NM_005591.3	340			0.432121294236668	2	FACETS	1	0.924	1	0.551	0.477	0.63	CLONAL	1	TRUE	0	0.432121294236668	2		249	231	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119812256	119812256	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	81	438	1	ENST00000316626.5:c.26C>A	p.Ser9Tyr	p.S9Y	ENST00000316626		9	tCc/tAc	1/12	0.432121294236668	3	FACETS	0.912	0.806	1	0.456	0.403	0.513	CLONAL	1	TRUE	1	0.432121294236668	3		439	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0051844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	148	513	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.295079509230235	2	FACETS	1	0.979	1	0.605	0.554	0.658	CLONAL	1	TRUE	0	0.38389170506635	2		513	637	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs869025608	NA	P-0051844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	148	527	0	ENST00000307102.5:c.171G>T	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaT	2/11	0.295079509230235	2	FACETS	1	0.984	1	0.659	0.604	0.716	CLONAL	1	TRUE	0	0.38389170506635	2		527	585	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549504	21549504	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0051844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	180	461	0	ENST00000382592.4:c.2773-1G>T		p.X925_splice	ENST00000382592	NM_014572.2	925			0.295079509230235	2	FACETS	0.761	0.705	0.819	0.761	0.705	0.819	SUBCLONAL	2	TRUE	0	0.38389170506635	2		461	616	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257617	16257617	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	171	455	0	ENST00000375759.3:c.4882G>C	p.Asp1628His	p.D1628H	ENST00000375759	NM_015001.2	1628	Gat/Cat	11/15	0.295079509230235	2	FACETS	1	0.989	1	0.73	0.675	0.787	CLONAL	1	TRUE	0	0.38389170506635	2		455	610	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462825	69462825	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	175	688	0	ENST00000227507.2:c.638A>G	p.Gln213Arg	p.Q213R	ENST00000227507	NM_053056.2	213	cAa/cGa	4/5	0.38389170506635	4	FACETS	1	0.936	1	0.34	0.312	0.369	CLONAL	1	TRUE	1	0.38389170506635	4		688	1236	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199955	108199955	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	68	226	0	ENST00000278616.4:c.7297C>G	p.Gln2433Glu	p.Q2433E	ENST00000278616	NM_000051.3	2433	Cag/Gag	49/63	0.38389170506635	5	FACETS	1	0.964	1			1	CLONAL	1	TRUE	NA	0.38389170506635	5		226	429	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118365018	118365018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	97	356	0	ENST00000534358.1:c.5194G>A	p.Asp1732Asn	p.D1732N	ENST00000534358	NM_005933.3	1732	Gat/Aat	17/36	0.38389170506635	3	FACETS	1	0.938	1	0.357	0.319	0.398	CLONAL	1	TRUE	0	0.38389170506635	3		356	562	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021360	42021360	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0051844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	133	271	0	ENST00000219905.7:c.3658-2A>G		p.X1220_splice	ENST00000219905	NM_001164273.1	1220			0.295079509230235	2	FACETS	0.862	0.79	0.935	0.862	0.79	0.935	CLONAL	2	TRUE	0	0.38389170506635	2		271	402	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229049	36229049	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	273	706	0	ENST00000222270.7:c.7829G>T	p.Arg2610Leu	p.R2610L	ENST00000222270	NM_014727.1	2610	cGc/cTc	36/37	0.295079509230235	2	FACETS	0.773	0.727	0.82	0.773	0.727	0.82	SUBCLONAL	2	TRUE	0	0.38389170506635	2		706	920	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645769	215645769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1426045227	NA	P-0051844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	83	479	0	ENST00000260947.4:c.829G>A	p.Glu277Lys	p.E277K	ENST00000260947	NM_000465.2	277	Gaa/Aaa	4/11	1	2	FACETS	0.674	0.595	0.758	0.674	0.595	0.758	SUBCLONAL	1	TRUE	1	0.38389170506635	2		479	642	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683739	162683739	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	188	598	0	ENST00000366898.1:c.230G>T	p.Gly77Val	p.G77V	ENST00000366898	NM_004562.2	77	gGt/gTt	3/12	0.288343458333101	3	FACETS	1	0.99	1	0.493	0.456	0.531	CLONAL	1	TRUE	0	0.38389170506635	3		598	790	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141567278	141567278	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	316	627	0	ENST00000220592.5:c.936C>G	p.Phe312Leu	p.F312L	ENST00000220592	NM_012154.3	312	ttC/ttG	8/19	0.288343458333101	3	FACETS	1	0.984	1	0.734	0.695	0.774	CLONAL	2	TRUE	0	0.38389170506635	3		627	891	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359948	87359949	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0051844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	123	382	0	ENST00000277120.3:c.1256_1257insA	p.Thr420HisfsTer5	p.T420Hfs*5	ENST00000277120		419	tcc/tcAc	11/19	0.295079509230235	2	FACETS	1	0.984	1	0.706	0.643	0.771	CLONAL	1	TRUE	0	0.38389170506635	2		382	454	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0051845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	78	591	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.22	2		591	620	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856070	151856070	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	75	495	1	ENST00000262189.6:c.11548C>T	p.Arg3850Ter	p.R3850*	ENST00000262189	NM_170606.2	3850	Cga/Tga	44/59	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.22	2		496	639	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818810	32818810	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	87	677	0	ENST00000354258.4:c.1141C>G	p.Leu381Val	p.L381V	ENST00000354258	NM_000593.5	381	Ctc/Gtc	4/11	1	2	FACETS	0.984	0.87	1	0.984	0.87	1	CLONAL	1	TRUE	1	0.22	2		677	804	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838299	156838299	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	70	888	0	ENST00000524377.1:c.577G>T	p.Val193Leu	p.V193L	ENST00000524377	NM_002529.3	193	Gtg/Ttg	6/17	1	2	FACETS	0.885	0.771	1	0.885	0.771	1	CLONAL	1	TRUE	1	0.22	2		888	719	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850633	63850633	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	27	294	0	ENST00000279873.7:c.1411C>T	p.Gln471Ter	p.Q471*	ENST00000279873	NM_032199.2	471	Caa/Taa	10/10	1	2	FACETS	0.718	0.571	0.885	0.718	0.571	0.885	SUBCLONAL	1	TRUE	1	0.22	2		294	342	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554232	63554232	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	36	655	0	ENST00000307078.5:c.507C>G	p.Ile169Met	p.I169M	ENST00000307078	NM_004655.3	169	atC/atG	2/11	0.295239620568678	1	FACETS	0.428	0.35	0.515	0.428	0.35	0.515	SUBCLONAL	1	TRUE	0	0.22	1		655	681	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965098	25965098	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	64	601	0	ENST00000435504.4:c.4108A>T	p.Ser1370Cys	p.S1370C	ENST00000435504		1370	Agc/Tgc	13/13	1	2	FACETS	0.912	0.789	1	0.912	0.789	1	CLONAL	1	TRUE	1	0.22	2		601	638	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	94	373	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.822	0.731	0.918	0.822	0.731	0.918	CLONAL	1	TRUE	1	0.34	2		373	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576870	7576871	+	stop_gained	Nonsense_Mutation	DNP	CT	CT	AA	novel	NA	P-0051847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	118	783	0	ENST00000269305.4:c.975_976delinsTT	p.Glu326Ter	p.E326*	ENST00000269305	NM_001126112.2	325	ggAGaa/ggTTaa	9/11	0.304526197076975	1	FACETS	0.788	0.712	0.869	0.788	0.712	0.869	SUBCLONAL	1	TRUE	0	0.34	1		783	731	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513358	44513358	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	68	679	0	ENST00000291552.4:c.577C>G	p.His193Asp	p.H193D	ENST00000291552	NM_006758.2	193	Cat/Gat	8/8	1	2	FACETS	0.624	0.543	0.712	0.624	0.543	0.712	SUBCLONAL	1	TRUE	1	0.34	2		679	641	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864295	151864295	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	129	557	0	ENST00000262189.6:c.9686A>T	p.Glu3229Val	p.E3229V	ENST00000262189	NM_170606.2	3229	gAa/gTa	42/59	1	2	FACETS	0.95	0.861	1	0.95	0.861	1	CLONAL	1	TRUE	1	0.34	2		557	799	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0051848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	49	466	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.1188488999541	0	FACETS	0.787	0.677	0.905			1	INDETERMINATE	2	FALSE	0	0.24875754378578	0		466	188	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745244	43745244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	289	834	0	ENST00000523873.1:c.157C>T	p.His53Tyr	p.H53Y	ENST00000523873		53	Cat/Tat	3/8	0.24875754378578	9	FACETS	0.986	0.932	1	1	0.989	1	CLONAL	6	FALSE	4	0.24875754378578	9		834	735	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0051848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	236	555	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	1	0.981	1	1	0.996	1	CLONAL	3	FALSE	1	0.24875754378578	2		555	575	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845153	151845154	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0051848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	235	700	0	ENST00000262189.6:c.13858dup	p.His4620ProfsTer2	p.H4620Pfs*2	ENST00000262189	NM_170606.2	4620	cat/cCat	52/59	0.24875754378578	8	FACETS	0.97	0.916	1	1	0.986	1	CLONAL	7	FALSE	2	0.24875754378578	8		700	486	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063632	67063635	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TAAG	TAAG	-	novel	NA	P-0051848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	168	342	0	ENST00000412916.2:c.83_86del	p.Lys28ThrfsTer60	p.K28Tfs*60	ENST00000412916		27	atTAAG/at	2/6	NA	2	FACETS	0.896	0.835	0.957			1	INDETERMINATE	4	FALSE	NA	0.24875754378578	2		342	377	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913109	44913109	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0051848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	16	658	0	ENST00000377967.4:c.784A>T	p.Lys262Ter	p.K262*	ENST00000377967	NM_021140.2	262	Aaa/Taa	10/29	0.24875754378578	1	FACETS	0.39	0.288	0.512	0.39	0.288	0.512	SUBCLONAL	1	FALSE	0	0.24875754378578	1		658	289	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	14	230	0				ENST00000310581	NM_198253.2	-/1132			0.263252265834986	0	FACETS	0.808	0.592	1			1	CLONAL	1	TRUE	0	0.263252265834986	0		230	97	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0051849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	34	356	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.712	0.582	0.857	0.712	0.582	0.857	SUBCLONAL	1	TRUE	1	0.263252265834986	2		356	363	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0051849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	61	423	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.263252265834986	2		423	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0051849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	55	747	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.263252265834986	1	FACETS	0.933	0.801	1	0.933	0.801	1	CLONAL	1	TRUE	0	0.263252265834986	1		747	389	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974695	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691187	NA	P-0051849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	56	413	0	ENST00000304494.5:c.132del	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	taC/ta	1/3	0.263252265834986	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.263252265834986	1		413	278	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864333	117864333	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	36	321	0	ENST00000297338.2:c.1324G>A	p.Glu442Lys	p.E442K	ENST00000297338	NM_006265.2	442	Gag/Aag	11/14	1	2	FACETS	0.824	0.679	0.985	0.824	0.679	0.985	CLONAL	1	TRUE	1	0.263252265834986	2		321	332	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222263	53222263	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	34	350	0	ENST00000375401.3:c.4569G>C	p.Gln1523His	p.Q1523H	ENST00000375401	NM_004187.3	1523	caG/caC	26/26	1	1	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	0	0.263252265834986	1		350	211	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922820	44922833	+	frameshift_variant	Frame_Shift_Del	DEL	GCCTGCCCTGGGCA	GCCTGCCCTGGGCA	-	novel	NA	P-0051851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	114	272	0	ENST00000377967.4:c.1685_1698del	p.Cys562PhefsTer14	p.C562Ffs*14	ENST00000377967	NM_021140.2	561	GCCTGCCCTGGGCAg/g	16/29	1	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.355147072313028	1		272	408	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882025	NA	P-0051852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	162	667	1	ENST00000269305.4:c.646G>T	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ttg	6/11	0.211826269603282	2	FACETS	1	0.987	1	0.702	0.645	0.762	CLONAL	1	TRUE	0	0.273364329295205	2		668	844	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874261	155874261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352822	NA	P-0051852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	196	399	0	ENST00000368323.3:c.270G>A	p.Met90Ile	p.M90I	ENST00000368323	NM_006912.5	90	atG/atA	5/6	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.273364329295205	NA		399	680	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602583	10602583	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	186	856	0	ENST00000171111.5:c.995G>A	p.Gly332Asp	p.G332D	ENST00000171111	NM_203500.1	332	gGc/gAc	3/6	0.211826269603282	2	FACETS	0.81	0.749	0.873	0.81	0.749	0.873	CLONAL	2	TRUE	0	0.273364329295205	2		856	840	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293661	1293661	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	102	872	0	ENST00000310581.5:c.1340G>T	p.Arg447Leu	p.R447L	ENST00000310581	NM_198253.2	447	cGc/cTc	2/16	0.145688409411407	5	FACETS	0.93	0.83	1	0.31	0.276	0.346	INDETERMINATE	1	TRUE	2	0.273364329295205	5		872	1131	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589776	28589776	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	56	515	0	ENST00000241453.7:c.2604G>C	p.Lys868Asn	p.K868N	ENST00000241453	NM_004119.2	868	aaG/aaC	21/24	0.211541029080614	3	FACETS	0.73	0.625	0.845	0.365	0.312	0.423	SUBCLONAL	1	TRUE	1	0.273364329295205	3		515	638	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670455	88670456	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0051852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	33	328	0	ENST00000360948.2:c.1230dup	p.Asp411Ter	p.D411*	ENST00000360948	NM_001012338.2	410	-/T	11/19	0.211541029080614	3	FACETS	0.679	0.553	0.821	0.34	0.276	0.411	SUBCLONAL	1	TRUE	1	0.273364329295205	3		328	404	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446266	29446266	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	99	685	0	ENST00000389048.3:c.3301A>C	p.Lys1101Gln	p.K1101Q	ENST00000389048	NM_004304.4	1101	Aag/Cag	20/29	0.194004821135161	3	FACETS	1	0.92	1	0.518	0.462	0.578	CLONAL	1	TRUE	1	0.273364329295205	3		685	794	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919763	96919763	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	58	557	0	ENST00000258439.3:c.500C>A	p.Ser167Tyr	p.S167Y	ENST00000258439	NM_001193304.2	167	tCc/tAc	4/4	0.194004821135161	3	FACETS	0.626	0.537	0.724	0.313	0.268	0.362	SUBCLONAL	1	TRUE	1	0.273364329295205	3		557	770	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067156	37067156	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	71	299	0	ENST00000231790.2:c.1067C>G	p.Ser356Cys	p.S356C	ENST00000231790	NM_000249.3	356	tCt/tGt	12/19	0.211826269603282	2	FACETS	0.869	0.765	0.978	0.869	0.765	0.978	CLONAL	2	TRUE	0	0.273364329295205	2		299	299	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964932	55964932	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	65	367	0	ENST00000263923.4:c.2305G>T	p.Val769Leu	p.V769L	ENST00000263923	NM_002253.2	769	Gta/Tta	16/30	1	2	FACETS	0.995	0.865	1	0.995	0.865	1	CLONAL	1	TRUE	1	0.273364329295205	2		367	478	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505090	149505090	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	138	659	0	ENST00000261799.4:c.1725C>A	p.Asp575Glu	p.D575E	ENST00000261799	NM_002609.3	575	gaC/gaA	12/23	0.211826269603282	2	FACETS	1	0.983	1	0.667	0.607	0.729	CLONAL	1	TRUE	0	0.273364329295205	2		659	757	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553584	106553584	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	63	469	0	ENST00000369096.4:c.1549C>T	p.Pro517Ser	p.P517S	ENST00000369096	NM_001198.3	517	Ccc/Tcc	5/7	0.194004821135161	3	FACETS	0.893	0.772	1	0.446	0.386	0.512	CLONAL	1	TRUE	1	0.273364329295205	3		469	587	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386583	81386583	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	67	507	0	ENST00000222390.5:c.404G>C	p.Ser135Thr	p.S135T	ENST00000222390	NM_000601.4	135	aGc/aCc	4/18	0.194004821135161	3	FACETS	1	0.961	1	0.638	0.556	0.725	CLONAL	1	TRUE	1	0.273364329295205	3		507	437	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117875391	117875391	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	88	385	0	ENST00000297338.2:c.252G>C	p.Lys84Asn	p.K84N	ENST00000297338	NM_006265.2	84	aaG/aaC	3/14	0.0633345069661666	4	FACETS	0.895	0.796	0.999	0.895	0.796	0.999	INDETERMINATE	2	TRUE	2	0.273364329295205	4		385	458	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220421	123220421	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	137	509	0	ENST00000218089.9:c.3078G>T	p.Met1026Ile	p.M1026I	ENST00000218089	NM_001042749.1	1026	atG/atT	30/35	0.15417270474933	3	FACETS	0.84	0.766	0.918	0.84	0.766	0.918	INDETERMINATE	2	TRUE	1	0.273364329295205	3		509	678	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0051853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	56	341	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.21507897795182	1	FACETS	0.9	0.771	1	0.9	0.771	1	CLONAL	1	TRUE	0	0.221451038256026	1		341	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579356	7579359	+	frameshift_variant	Frame_Shift_Del	DEL	GACG	GACG	-	novel	NA	P-0051853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	100	786	0	ENST00000269305.4:c.328_331del	p.Arg110TrpfsTer12	p.R110Wfs*12	ENST00000269305	NM_001126112.2	110	CGTCtg/tg	4/11	0.21507897795182	1	FACETS	0.948	0.846	1	0.948	0.846	1	CLONAL	1	TRUE	0	0.221451038256026	1		786	847	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974809	21974809	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	21	140	0	ENST00000304494.5:c.18del	p.Ser7AlafsTer19	p.S7Afs*19	ENST00000304494	NM_000077.4	6	ggG/gg	1/3	0.221451038256026	1	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	0	0.221451038256026	1		140	146	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226980	2226980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	74	514	0	ENST00000398665.3:c.4460C>T	p.Ser1487Phe	p.S1487F	ENST00000398665	NM_032482.2	1487	tCc/tTc	27/28	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.221451038256026	2		514	662	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603038	48603039	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCAGCAGCAGGCGGCTACTGCACAAGC	rs876660720	NA	P-0051853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	38	430	0	ENST00000342988.3:c.1349_1376dup	p.Ala460GlyfsTer43	p.A460Gfs*43	ENST00000342988	NM_005359.5	447	atg/aTGCAGCAGCAGGCGGCTACTGCACAAGCtg	11/12	0.21507897795182	1	FACETS	0.557	0.46	0.666	0.557	0.46	0.666	SUBCLONAL	1	TRUE	0	0.221451038256026	1		430	548	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221340	1221340	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0051854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	112	635	1	ENST00000326873.7:c.862+1G>A		p.X288_splice	ENST00000326873	NM_000455.4	288			0.391573548317012	1	FACETS	0.866	0.782	0.955	0.866	0.782	0.955	CLONAL	1	TRUE	0	0.391573548317012	1		636	531	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110208	8110208	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0051854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	139	636	0	ENST00000585124.1:c.399-2A>T		p.X133_splice	ENST00000585124	NM_004217.3	133			1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.391573548317012	2		636	697	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619332	37619332	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	116	552	0	ENST00000447079.4:c.1009del	p.Leu337Ter	p.L337*	ENST00000447079	NM_015083.1	336	ttC/tt	1/14	1	2	FACETS	0.957	0.865	1	0.957	0.865	1	CLONAL	1	TRUE	1	0.391573548317012	2		552	619	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600364	10600364	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	174	745	0	ENST00000171111.5:c.1491G>T	p.Trp497Cys	p.W497C	ENST00000171111	NM_203500.1	497	tgG/tgT	4/6	0.391573548317012	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.391573548317012	1		745	640	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057268	180057268	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	139	806	1	ENST00000261937.6:c.470C>A	p.Pro157His	p.P157H	ENST00000261937	NM_182925.4	157	cCc/cAc	4/30	0.391573548317012	1	FACETS	0.919	0.84	1	0.919	0.84	1	CLONAL	1	TRUE	0	0.391573548317012	1		807	621	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539098	23539098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	30	475	0	ENST00000380871.4:c.341C>T	p.Pro114Leu	p.P114L	ENST00000380871	NM_006167.3	114	cCa/cTa	2/2	1	2	FACETS	0.26	0.208	0.318	0.26	0.208	0.318	SUBCLONAL	1	TRUE	1	0.391573548317012	2		475	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0051855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	76	689	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.573859020394529	1	FACETS	0.271	0.238	0.308	0.271	0.238	0.308	SUBCLONAL	1	TRUE	0	0.573859020394529	1		689	696	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333164	70333164	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	326	677	0	ENST00000373644.4:c.1069G>T	p.Glu357Ter	p.E357*	ENST00000373644	NM_030625.2	357	Gaa/Taa	2/12	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.573859020394529	2		677	927	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562110	21562110	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	324	812	0	ENST00000382592.4:c.1809G>T	p.Lys603Asn	p.K603N	ENST00000382592	NM_014572.2	603	aaG/aaT	4/8	0.573859020394529	1	FACETS	0.894	0.847	0.941	0.894	0.847	0.941	CLONAL	1	TRUE	0	0.573859020394529	1		812	901	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443726	52443735	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTACCGAAAT	TTACCGAAAT	-	novel	NA	P-0051855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	372	720	0	ENST00000460680.1:c.62_67+4del		p.X21_splice	ENST00000460680	NM_004656.3	21		2/17	0.573859020394529	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.573859020394529	1		720	863	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0051858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	434	655	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.536424855946291	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	FALSE	0	0.538073762016729	3		655	624	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200961	108200961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782310	NA	P-0051858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	126	296	0	ENST00000278616.4:c.7328G>A	p.Arg2443Gln	p.R2443Q	ENST00000278616	NM_000051.3	2443	cGa/cAa	50/63	0.536424855946291	2	FACETS	1	0.98	1	0.624	0.571	0.679	CLONAL	1	FALSE	0	0.538073762016729	2		296	375	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878676	151878676	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0051858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	99	446	0	ENST00000262189.6:c.6269C>G	p.Ser2090Ter	p.S2090*	ENST00000262189	NM_170606.2	2090	tCa/tGa	36/59	0.538073762016729	5	FACETS	0.941	0.84	1	0.314	0.28	0.349	CLONAL	1	FALSE	2	0.538073762016729	5		446	707	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974393	93974393	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	79	347	0	ENST00000369303.4:c.1661C>T	p.Pro554Leu	p.P554L	ENST00000369303	NM_004440.3	554	cCt/cTt	8/17	0.536424855946291	1	FACETS	0.902	0.806	1	0.902	0.806	1	CLONAL	1	FALSE	0	0.538073762016729	1		347	238	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246642	41246642	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	324	473	0	ENST00000357654.3:c.906del	p.Glu303AsnfsTer11	p.E303Nfs*11	ENST00000357654	NM_007294.3	302	gcT/gc	10/23	0.536424855946291	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	FALSE	0	0.538073762016729	3		473	487	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260148	10260148	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs868584117	NA	P-0051858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	34	613	0	ENST00000340748.4:c.2519C>G	p.Ser840Cys	p.S840C	ENST00000340748		840	tCc/tGc	25/40	0.536424855946291	3	FACETS	0.243	0.198	0.295	0.122	0.099	0.148	SUBCLONAL	1	FALSE	1	0.538073762016729	3		613	659	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036990	180036990	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	183	657	0	ENST00000261937.6:c.3722C>G	p.Ala1241Gly	p.A1241G	ENST00000261937	NM_182925.4	1241	gCc/gGc	28/30	0.536424855946291	3	FACETS	1	0.984	1	0.617	0.572	0.665	CLONAL	1	FALSE	1	0.538073762016729	3		657	699	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851877	128851877	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	208	748	0	ENST00000249373.3:c.1949A>G	p.Glu650Gly	p.E650G	ENST00000249373	NM_005631.4	650	gAa/gGa	12/12	0.536424855946291	4	FACETS	1	0.986	1			1	CLONAL	1	FALSE	NA	0.538073762016729	4		748	962	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0051859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	347	676	0	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	0.723965259043262	2	FACETS	0.986	0.959	1	0.986	0.959	1	CLONAL	2	TRUE	0	0.850269618181641	2		676	414	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023944	27023948	+	frameshift_variant	Frame_Shift_Del	DEL	GGGAG	GGGAG	-	novel	NA	P-0051859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	58	86	0	ENST00000324856.7:c.1053_1057del	p.Gly352ProfsTer46	p.G352Pfs*46	ENST00000324856	NM_006015.4	350	tcGGGAGgg/tcgg	1/20	0.723965259043262	2	FACETS	0.863	0.791	0.929	0.863	0.791	0.929	CLONAL	2	TRUE	0	0.850269618181641	2		86	79	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450132	32450132	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	158	672	0	ENST00000332351.3:c.680G>T	p.Ser227Ile	p.S227I	ENST00000332351	NM_024426.4	227	aGc/aTc	2/10	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.850269618181641	2		672	359	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042099	14042099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs538267970	NA	P-0051859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	87	382	0	ENST00000311895.7:c.2646C>A	p.Asp882Glu	p.D882E	ENST00000311895	NM_005236.2	882	gaC/gaA	11/11	1	2	FACETS	0.979	0.885	1	0.979	0.885	1	CLONAL	1	TRUE	1	0.850269618181641	2		382	209	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390931	139390952	+	frameshift_variant	Frame_Shift_Del	DEL	GCCAAGGTGCGGCTGTGGTGGT	GCCAAGGTGCGGCTGTGGTGGT	-	novel	NA	P-0051859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	157	963	0	ENST00000277541.6:c.7239_7260del	p.Pro2414Ter	p.P2414*	ENST00000277541	NM_017617.3	2413	ccACCACCACAGCCGCACCTTGGC/cc	34/34	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.850269618181641	2		963	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912660	NA	P-0051860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	98	822	0	ENST00000269305.4:c.839G>T	p.Arg280Ile	p.R280I	ENST00000269305	NM_001126112.2	280	aGa/aTa	8/11	0.282188483476711	1	FACETS	0.872	0.779	0.972	0.872	0.779	0.972	CLONAL	1	TRUE	0	0.283269880190742	1		822	681	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913355	NA	P-0051860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	53	386	0	ENST00000288602.6:c.1406G>T	p.Gly469Val	p.G469V	ENST00000288602	NM_004333.4	469	gGa/gTa	11/18	1	2	FACETS	0.969	0.829	1	0.969	0.829	1	CLONAL	1	TRUE	1	0.283269880190742	2		386	386	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691105	18691105	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	42	459	0	ENST00000266497.5:c.3216C>A	p.Phe1072Leu	p.F1072L	ENST00000266497		1072	ttC/ttA	23/31	0.193610650124129	1	FACETS	0.769	0.644	0.906	0.769	0.644	0.906	CLONAL	1	TRUE	0	0.283269880190742	1		459	331	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484043	50484043	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	80	681	1	ENST00000394963.4:c.893A>T	p.Asp298Val	p.D298V	ENST00000394963	NM_003076.4	298	gAc/gTc	8/13	1	2	FACETS	0.908	0.8	1	0.908	0.8	1	CLONAL	1	TRUE	1	0.283269880190742	2		682	622	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274078	10274078	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	56	850	0	ENST00000330684.3:c.191C>A	p.Pro64His	p.P64H	ENST00000330684	NM_001134407.1	64	cCc/cAc	2/13	0.193610650124129	1	FACETS	0.469	0.401	0.544	0.469	0.401	0.544	SUBCLONAL	1	TRUE	0	0.283269880190742	1		850	723	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219345	1219345	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	110	707	0	ENST00000326873.7:c.397G>C	p.Val133Leu	p.V133L	ENST00000326873	NM_000455.4	133	Gtg/Ctg	3/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.283269880190742	2		707	672	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	69	344	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.935	1	1	0.983	1	CLONAL	2	TRUE	1	0.22	2		344	286	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942155	71942155	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	41	648	1	ENST00000298229.2:c.1419G>T	p.Glu473Asp	p.E473D	ENST00000298229	NM_001567.3	473	gaG/gaT	12/28	1	2	FACETS	0.521	0.433	0.62	0.521	0.433	0.62	SUBCLONAL	1	TRUE	1	0.22	2		649	715	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650710	67650710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243010179	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	200	492	0	ENST00000264010.4:c.1015C>T	p.Arg339Trp	p.R339W	ENST00000264010	NM_006565.3	339	Cgg/Tgg	5/12	1	2	FACETS	1	0.983	1	1	0.994	1	CLONAL	2	TRUE	1	0.22	2		492	765	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554834	106554834	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	106	391	0	ENST00000369096.4:c.1951C>T	p.Arg651Ter	p.R651*	ENST00000369096	NM_001198.3	651	Cga/Tga	7/7	1	2	FACETS	1	0.949	1	1	0.989	1	CLONAL	2	TRUE	1	0.22	2		391	445	SUCCESS
B2M	567	MSKCC	GRCh37	15	45008529	45008529	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	15	249	0	ENST00000558401.1:c.349C>T	p.Arg117Ter	p.R117*	ENST00000558401	NM_004048.2	117	Cga/Tga	3/4	0.251026068322716	2	FACETS	0.478	0.349	0.634	0.239	0.174	0.317	SUBCLONAL	1	TRUE	0	0.22	2		249	285	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099338	193099338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	70	297	0	ENST00000367435.3:c.272G>A	p.Arg91Gln	p.R91Q	ENST00000367435	NM_024529.4	91	cGa/cAa	3/17	1	2	FACETS	1	0.96	1	1	0.985	1	CLONAL	2	TRUE	1	0.22	2		297	262	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068357	26068357	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	11	304	0	ENST00000435504.4:c.133G>T	p.Glu45Ter	p.E45*	ENST00000435504		45	Gaa/Taa	2/13	1	2	FACETS	0.455	0.314	0.63	0.455	0.314	0.63	SUBCLONAL	1	TRUE	1	0.22	2		304	220	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288964	212288964	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	79	399	0	ENST00000342788.4:c.2782G>T	p.Glu928Ter	p.E928*	ENST00000342788	NM_005235.2	928	Gaa/Taa	23/28	1	2	FACETS	1	0.941	1	1	0.985	1	CLONAL	2	TRUE	1	0.22	2		399	328	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267600319	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	128	310	0	ENST00000257430.4:c.4199C>T	p.Ser1400Leu	p.S1400L	ENST00000257430	NM_000038.5	1400	tCg/tTg	16/16	1	2	FACETS	0.944	0.863	1	1	0.992	1	CLONAL	3	TRUE	1	0.22	2		310	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371409680	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	174	553	0	ENST00000269305.4:c.848G>A	p.Arg283His	p.R283H	ENST00000269305	NM_001126112.2	283	cGc/cAc	8/11	1	2	FACETS	1	0.959	1	1	0.993	1	CLONAL	2	TRUE	1	0.22	2		553	746	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891367	101891367	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	55	306	0	ENST00000374994.4:c.328G>T	p.Glu110Ter	p.E110*	ENST00000374994	NM_004612.2	110	Gaa/Taa	2/9	1	2	FACETS	0.833	0.718	0.958	1	0.972	1	CLONAL	2	TRUE	1	0.22	2		306	300	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125356	47125356	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	114	418	0	ENST00000409792.3:c.5914G>T	p.Glu1972Ter	p.E1972*	ENST00000409792	NM_014159.6	1972	Gaa/Taa	12/21	1	2	FACETS	0.866	0.786	0.948	1	0.991	1	CLONAL	3	TRUE	1	0.22	2		418	399	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286171	66286171	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	16	264	0	ENST00000273854.3:c.1515G>T	p.Lys505Asn	p.K505N	ENST00000273854	NM_004439.5	505	aaG/aaT	6/18	1	2	FACETS	0.782	0.58	1	0.782	0.58	1	CLONAL	1	TRUE	1	0.22	2		264	186	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965761	25965761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377352572	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	161	600	0	ENST00000435504.4:c.3445C>T	p.Arg1149Cys	p.R1149C	ENST00000435504		1149	Cgt/Tgt	13/13	1	2	FACETS	1	0.977	1	1	0.993	1	CLONAL	2	TRUE	1	0.22	2		600	629	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542357	187542357	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs769432838	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	65	372	0	ENST00000441802.2:c.5383C>T	p.Arg1795Ter	p.R1795*	ENST00000441802	NM_005245.3	1795	Cga/Tga	10/27	1	2	FACETS	0.975	0.852	1	1	0.98	1	CLONAL	2	TRUE	1	0.22	2		372	303	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649005	86649005	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	68	291	0	ENST00000274376.6:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000274376	NM_002890.2	429	Gaa/Taa	9/25	1	2	FACETS	0.991	0.877	1	1	0.986	1	CLONAL	3	TRUE	1	0.22	2		291	208	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895689	28895689	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	82	418	0	ENST00000282397.4:c.3085C>A	p.Leu1029Ile	p.L1029I	ENST00000282397	NM_002019.4	1029	Ctt/Att	23/30	1	2	FACETS	0.898	0.796	1	1	0.983	1	CLONAL	2	TRUE	1	0.22	2		418	415	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520192	9520192	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	163	448	0	ENST00000353224.5:c.2077G>A	p.Glu693Lys	p.E693K	ENST00000353224	NM_177990.2	693	Gaa/Aaa	10/10	1	2	FACETS	0.879	0.811	0.949	1	0.993	1	CLONAL	3	TRUE	1	0.22	2		448	562	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137487	202137487	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	123	385	0	ENST00000358485.4:c.715G>T	p.Glu239Ter	p.E239*	ENST00000358485	NM_001080125.1	239	Gaa/Taa	4/9	1	2	FACETS	0.892	0.813	0.973	1	0.992	1	CLONAL	3	TRUE	1	0.22	2		385	418	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788637	3788637	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	92	390	0	ENST00000262367.5:c.4317C>A	p.Phe1439Leu	p.F1439L	ENST00000262367	NM_004380.2	1439	ttC/ttA	26/31	1	2	FACETS	0.955	0.853	1	1	0.986	1	CLONAL	2	TRUE	1	0.22	2		390	438	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176614	56176614	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	97	315	0	ENST00000399503.3:c.2164G>T	p.Glu722Ter	p.E722*	ENST00000399503	NM_005921.1	722	Gaa/Taa	12/20	1	2	FACETS	1	0.971	1	1	0.989	1	CLONAL	2	TRUE	1	0.22	2		315	362	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850948	63850948	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	157	451	1	ENST00000279873.7:c.1726G>T	p.Glu576Ter	p.E576*	ENST00000279873	NM_032199.2	576	Gaa/Taa	10/10	1	2	FACETS	1	0.974	1	1	0.993	1	CLONAL	2	TRUE	1	0.22	2		452	626	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562710	29562710	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs863224660	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	89	395	0	ENST00000356175.3:c.3790G>T	p.Glu1264Ter	p.E1264*	ENST00000356175	NM_000267.3	1264	Gaa/Taa	28/57	1	2	FACETS	1	0.952	1	1	0.987	1	CLONAL	2	TRUE	1	0.22	2		395	363	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286205	66286205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777851171	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	63	330	0	ENST00000273854.3:c.1481G>A	p.Arg494His	p.R494H	ENST00000273854	NM_004439.5	494	cGt/cAt	6/18	1	2	FACETS	1	0.924	1	1	0.982	1	CLONAL	2	TRUE	1	0.22	2		330	265	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591246	67591246	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	86	292	0	ENST00000274335.5:c.1746-2A>G		p.X582_splice	ENST00000274335		582			1	2	FACETS	0.875	0.782	0.971	1	0.988	1	CLONAL	3	TRUE	1	0.22	2		292	298	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001395	150001395	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	109	424	0	ENST00000253339.5:c.2209C>T	p.Arg737Ter	p.R737*	ENST00000253339		737	Cga/Tga	4/7	1	2	FACETS	0.915	0.83	1	1	0.991	1	CLONAL	3	TRUE	1	0.22	2		424	361	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720900	119720900	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	45	357	0	ENST00000316626.5:c.275G>T	p.Arg92Ile	p.R92I	ENST00000316626		92	aGa/aTa	2/12	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.22	2		357	392	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934254	48934254	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1131690904	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	71	380	0	ENST00000267163.4:c.709G>T	p.Glu237Ter	p.E237*	ENST00000267163	NM_000321.2	237	Gaa/Taa	7/27	1	2	FACETS	1	0.964	1	1	0.985	1	CLONAL	2	TRUE	1	0.22	2		380	259	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520202	176520202	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763979974	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	206	675	1	ENST00000292408.4:c.1121C>T	p.Ala374Val	p.A374V	ENST00000292408	NM_213647.1	374	gCg/gTg	9/18	1	2	FACETS	1	0.978	1	1	0.994	1	CLONAL	2	TRUE	1	0.22	2		676	833	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106571	27106571	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	214	566	0	ENST00000324856.7:c.6182T>C	p.Leu2061Ser	p.L2061S	ENST00000324856	NM_006015.4	2061	tTg/tCg	20/20	1	2	FACETS	0.872	0.813	0.932	1	0.995	1	CLONAL	3	TRUE	1	0.22	2		566	744	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344759	65344759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	99	334	1	ENST00000342505.4:c.278G>A	p.Arg93His	p.R93H	ENST00000342505	NM_002227.2	93	cGc/cAc	4/25	1	2	FACETS	1	0.968	1	1	0.989	1	CLONAL	2	TRUE	1	0.22	2		335	380	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446976	187446976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369842677	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	182	595	0	ENST00000232014.4:c.1217G>A	p.Arg406Gln	p.R406Q	ENST00000232014	NM_001130845.1	406	cGa/cAa	5/10	1	2	FACETS	1	0.982	1	1	0.994	1	CLONAL	2	TRUE	1	0.22	2		595	696	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523280	9523280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769363113	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	179	482	0	ENST00000353224.5:c.1957C>T	p.Arg653Trp	p.R653W	ENST00000353224	NM_177990.2	653	Cgg/Tgg	9/10	1	2	FACETS	0.906	0.839	0.974	1	0.994	1	CLONAL	3	TRUE	1	0.22	2		482	599	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445674	49445674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778514296	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	175	716	0	ENST00000301067.7:c.1792C>T	p.Arg598Cys	p.R598C	ENST00000301067	NM_003482.3	598	Cgt/Tgt	10/54	1	2	FACETS	1	0.96	1	1	0.993	1	CLONAL	2	TRUE	1	0.22	2		716	749	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622214	117622214	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	73	348	0	ENST00000368508.3:c.6656G>T	p.Arg2219Ile	p.R2219I	ENST00000368508	NM_002944.2	2219	aGa/aTa	42/43	1	2	FACETS	1	0.934	1	1	0.984	1	CLONAL	2	TRUE	1	0.22	2		348	305	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152446	56152446	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	57	179	1	ENST00000399503.3:c.502G>T	p.Glu168Ter	p.E168*	ENST00000399503	NM_005921.1	168	Gaa/Taa	2/20	1	2	FACETS	1	0.956	1	1	0.982	1	CLONAL	2	TRUE	1	0.22	2		180	208	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911481	101911481	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	49	246	0	ENST00000374994.4:c.1406A>C	p.Lys469Thr	p.K469T	ENST00000374994	NM_004612.2	469	aAa/aCa	9/9	1	2	FACETS	1	0.904	1	1	0.976	1	CLONAL	2	TRUE	1	0.22	2		246	208	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250189	133250189	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	133	565	0	ENST00000320574.5:c.1331T>A	p.Met444Lys	p.M444K	ENST00000320574	NM_006231.2	444	aTg/aAg	13/49	1	2	FACETS	1	0.968	1	1	0.991	1	CLONAL	2	TRUE	1	0.22	2		565	536	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416103	49416103	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	171	454	1	ENST00000301067.7:c.16372G>T	p.Glu5458Ter	p.E5458*	ENST00000301067	NM_003482.3	5458	Gaa/Taa	52/54	1	2	FACETS	0.89	0.824	0.959	1	0.994	1	CLONAL	3	TRUE	1	0.22	2		455	582	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	430229	430229	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	77	338	0	ENST00000399788.2:c.2473G>T	p.Glu825Ter	p.E825*	ENST00000399788	NM_001042603.1	825	Gaa/Taa	18/28	1	2	FACETS	0.856	0.755	0.963	1	0.981	1	CLONAL	2	TRUE	1	0.22	2		338	409	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657596	37657596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748453656	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	122	446	0	ENST00000447079.4:c.2513C>T	p.Ser838Leu	p.S838L	ENST00000447079	NM_015083.1	838	tCg/tTg	6/14	1	2	FACETS	0.86	0.783	0.939	1	0.991	1	CLONAL	3	TRUE	1	0.22	2		446	430	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138383915	138383915	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	118	416	0	ENST00000289153.2:c.2635G>T	p.Asp879Tyr	p.D879Y	ENST00000289153	NM_006219.2	879	Gat/Tat	18/22	1	2	FACETS	1	0.973	1	1	0.991	1	CLONAL	2	TRUE	1	0.22	2		416	452	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143326433	143326433	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	121	355	0	ENST00000262992.4:c.181A>G	p.Thr61Ala	p.T61A	ENST00000262992	NM_001101669.1	61	Aca/Gca	4/24	1	2	FACETS	0.879	0.801	0.96	1	0.991	1	CLONAL	3	TRUE	1	0.22	2		355	417	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509810	106509810	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	133	527	0	ENST00000359195.3:c.1804G>T	p.Glu602Ter	p.E602*	ENST00000359195	NM_002649.2	602	Gaa/Taa	2/11	1	2	FACETS	1	0.979	1	1	0.992	1	CLONAL	2	TRUE	1	0.22	2		527	493	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192672	94192672	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	126	438	0	ENST00000323929.3:c.1402G>T	p.Asp468Tyr	p.D468Y	ENST00000323929	NM_005591.3	468	Gat/Tat	13/20	1	2	FACETS	0.977	0.893	1	1	0.992	1	CLONAL	3	TRUE	1	0.22	2		438	391	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087555	27087555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1171422700	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	234	549	1	ENST00000324856.7:c.2129G>A	p.Arg710His	p.R710H	ENST00000324856	NM_006015.4	710	cGc/cAc	5/20	1	2	FACETS	0.922	0.863	0.982	1	0.995	1	CLONAL	3	TRUE	1	0.22	2		550	769	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248452	59248452	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	155	504	1	ENST00000371222.2:c.291C>A	p.Phe97Leu	p.F97L	ENST00000371222	NM_002228.3	97	ttC/ttA	1/1	1	2	FACETS	0.914	0.842	0.988	1	0.993	1	CLONAL	3	TRUE	1	0.22	2		505	514	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743378	162743378	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	90	321	0	ENST00000367921.3:c.1848G>T	p.Lys616Asn	p.K616N	ENST00000367921	NM_006182.2	616	aaG/aaT	14/18	1	2	FACETS	0.983	0.878	1	1	0.986	1	CLONAL	2	TRUE	1	0.22	2		321	416	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716103	243716103	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	110	415	0	ENST00000263826.5:c.1091A>G	p.Lys364Arg	p.K364R	ENST00000263826	NM_005465.4	364	aAa/aGa	10/13	1	2	FACETS	0.894	0.811	0.98	1	0.991	1	CLONAL	3	TRUE	1	0.22	2		415	373	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809202	243809202	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	73	372	0	ENST00000263826.5:c.422A>C	p.Lys141Thr	p.K141T	ENST00000263826	NM_005465.4	141	aAa/aCa	4/13	1	2	FACETS	1	0.958	1	1	0.985	1	CLONAL	2	TRUE	1	0.22	2		372	280	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649889	88649889	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	22	335	0	ENST00000372037.3:c.138T>G	p.Asn46Lys	p.N46K	ENST00000372037	NM_004329.2	46	aaT/aaG	4/13	1	2	FACETS	0.727	0.564	0.916	0.727	0.564	0.916	CLONAL	1	TRUE	1	0.22	2		335	275	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725055	89725055	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	39	156	0	ENST00000371953.3:c.1038C>A	p.Tyr346Ter	p.Y346*	ENST00000371953	NM_000314.4	346	taC/taA	9/9	1	2	FACETS	1	0.902	1	1	0.971	1	CLONAL	2	TRUE	1	0.22	2		156	161	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514083	69514083	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	179	551	0	ENST00000294312.3:c.598T>A	p.Phe200Ile	p.F200I	ENST00000294312	NM_005117.2	200	Ttt/Att	3/3	1	2	FACETS	0.849	0.786	0.914	1	0.994	1	CLONAL	3	TRUE	1	0.22	2		551	639	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518551	69518551	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	96	430	0	ENST00000294312.3:c.94C>A	p.Pro32Thr	p.P32T	ENST00000294312	NM_005117.2	32	Ccc/Acc	1/3	1	2	FACETS	0.974	0.873	1	1	0.986	1	CLONAL	2	TRUE	1	0.22	2		430	448	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912696	100912696	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	75	330	0	ENST00000325455.5:c.2626C>A	p.Leu876Ile	p.L876I	ENST00000325455	NM_001202474.3	876	Ctt/Att	7/8	1	2	FACETS	1	0.941	1	1	0.985	1	CLONAL	2	TRUE	1	0.22	2		330	309	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912045	32912045	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786202485	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	119	531	0	ENST00000380152.3:c.3553A>G	p.Thr1185Ala	p.T1185A	ENST00000380152		1185	Aca/Gca	11/27	1	2	FACETS	1	0.958	1	1	0.99	1	CLONAL	2	TRUE	1	0.22	2		531	493	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039169	49039169	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs587778861	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	84	336	0	ENST00000267163.4:c.2247T>A	p.Tyr749Ter	p.Y749*	ENST00000267163	NM_000321.2	749	taT/taA	22/27	1	2	FACETS	1	0.968	1	1	0.987	1	CLONAL	2	TRUE	1	0.22	2		336	309	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438060	110438060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	109	362	0	ENST00000375856.3:c.341C>T	p.Ala114Val	p.A114V	ENST00000375856	NM_003749.2	114	gCc/gTc	1/2	1	2	FACETS	1	0.96	1	1	0.989	1	CLONAL	2	TRUE	1	0.22	2		362	443	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007695	45007695	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	126	344	0	ENST00000558401.1:c.142T>C	p.Ser48Pro	p.S48P	ENST00000558401	NM_004048.2	48	Tct/Cct	2/4	0.251026068322716	2	FACETS	1	0.936	1	1	0.987	1	CLONAL	3	TRUE	0	0.22	2		344	372	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007723	45007723	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	19	355	0	ENST00000558401.1:c.171del	p.Asp58ThrfsTer3	p.D58Tfs*3	ENST00000558401	NM_004048.2	57	gTt/gt	2/4	0.251026068322716	2	FACETS	0.48	0.363	0.617	0.24	0.181	0.309	SUBCLONAL	1	TRUE	0	0.22	2		355	360	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857520	9857520	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs756382250	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	121	390	0	ENST00000330684.3:c.3881A>G	p.Asn1294Ser	p.N1294S	ENST00000330684	NM_001134407.1	1294	aAc/aGc	13/13	1	2	FACETS	0.867	0.789	0.947	1	0.991	1	CLONAL	3	TRUE	1	0.22	2		390	423	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858167	9858167	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	118	512	0	ENST00000330684.3:c.3234G>T	p.Lys1078Asn	p.K1078N	ENST00000330684	NM_001134407.1	1078	aaG/aaT	13/13	1	2	FACETS	0.965	0.874	1	1	0.989	1	CLONAL	2	TRUE	1	0.22	2		512	556	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350921	89350921	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	156	588	3	ENST00000301030.4:c.2029G>T	p.Asp677Tyr	p.D677Y	ENST00000301030	NM_001256183.1	677	Gat/Tat	9/13	1	2	FACETS	1	0.982	1	1	0.993	1	CLONAL	2	TRUE	1	0.22	2		591	573	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492774	56492774	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	148	539	0	ENST00000407977.2:c.165G>T	p.Met55Ile	p.M55I	ENST00000407977		55	atG/atT	2/10	1	2	FACETS	0.846	0.777	0.917	1	0.993	1	CLONAL	3	TRUE	1	0.22	2		539	530	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59878739	59878739	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	92	384	0	ENST00000259008.2:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000259008	NM_032043.2	339	Gaa/Taa	8/20	1	2	FACETS	1	0.958	1	1	0.988	1	CLONAL	2	TRUE	1	0.22	2		384	368	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763485	41763485	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	136	476	0	ENST00000301178.4:c.2284C>A	p.Leu762Met	p.L762M	ENST00000301178	NM_021913.4	762	Ctg/Atg	19/20	1	2	FACETS	1	0.948	1	1	0.991	1	CLONAL	2	TRUE	1	0.22	2		476	587	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030720	48030720	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	98	318	0	ENST00000234420.5:c.3334G>T	p.Asp1112Tyr	p.D1112Y	ENST00000234420	NM_000179.2	1112	Gac/Tac	5/10	1	2	FACETS	0.919	0.829	1	1	0.99	1	CLONAL	3	TRUE	1	0.22	2		318	323	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881365	111881365	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776207874	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	127	390	0	ENST00000393256.3:c.43G>A	p.Glu15Lys	p.E15K	ENST00000393256	NM_006538.4	15	Gaa/Aaa	2/4	1	2	FACETS	1	0.953	1	1	0.99	1	CLONAL	2	TRUE	1	0.22	2		390	538	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151189	202151189	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	49	268	1	ENST00000358485.4:c.1489G>T	p.Asp497Tyr	p.D497Y	ENST00000358485	NM_001080125.1	497	Gat/Tat	9/9	1	2	FACETS	1	0.859	1	1	0.975	1	CLONAL	2	TRUE	1	0.22	2		269	222	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989612	212989612	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	75	283	0	ENST00000342788.4:c.99G>T	p.Glu33Asp	p.E33D	ENST00000342788	NM_005235.2	33	gaG/gaT	2/28	1	2	FACETS	1	0.954	1	1	0.985	1	CLONAL	2	TRUE	1	0.22	2		283	295	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30954262	30954262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	88	353	1	ENST00000375687.4:c.133G>A	p.Glu45Lys	p.E45K	ENST00000375687	NM_015338.5	45	Gaa/Aaa	2/13	1	2	FACETS	1	0.962	1	1	0.987	1	CLONAL	2	TRUE	1	0.22	2		354	341	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445016	89445016	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	97	323	0	ENST00000336596.2:c.1336G>T	p.Asp446Tyr	p.D446Y	ENST00000336596	NM_005233.5	446	Gat/Tat	6/17	1	2	FACETS	1	0.967	1	1	0.989	1	CLONAL	2	TRUE	1	0.22	2		323	371	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480472	89480472	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	101	294	0	ENST00000336596.2:c.2309T>C	p.Val770Ala	p.V770A	ENST00000336596	NM_005233.5	770	gTc/gCc	13/17	1	2	FACETS	1	0.971	1	1	0.989	1	CLONAL	2	TRUE	1	0.22	2		294	380	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503687	186503687	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	87	347	0	ENST00000323963.5:c.364C>A	p.Leu122Met	p.L122M	ENST00000323963		122	Ctg/Atg	5/11	1	2	FACETS	1	0.968	1	1	0.988	1	CLONAL	2	TRUE	1	0.22	2		347	323	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55569903	55569903	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	41	215	0	ENST00000288135.5:c.770A>T	p.Glu257Val	p.E257V	ENST00000288135	NM_000222.2	257	gAg/gTg	5/21	1	2	FACETS	1	0.906	1	1	0.973	1	CLONAL	2	TRUE	1	0.22	2		215	169	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280091	66280091	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	94	312	0	ENST00000273854.3:c.1598C>A	p.Ala533Asp	p.A533D	ENST00000273854	NM_004439.5	533	gCt/gAt	7/18	1	2	FACETS	1	0.972	1	1	0.989	1	CLONAL	2	TRUE	1	0.22	2		312	344	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589148	67589148	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	19	258	0	ENST00000274335.5:c.1136A>C	p.Lys379Thr	p.K379T	ENST00000274335		379	aAa/aCa	9/15	1	2	FACETS	0.919	0.701	1	0.919	0.701	1	CLONAL	1	TRUE	1	0.22	2		258	188	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681142	86681142	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	71	303	0	ENST00000274376.6:c.2783G>T	p.Arg928Ile	p.R928I	ENST00000274376	NM_002890.2	928	aGa/aTa	22/25	1	2	FACETS	0.991	0.88	1	1	0.987	1	CLONAL	3	TRUE	1	0.22	2		303	217	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401661	401661	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	146	465	0	ENST00000380956.4:c.983G>T	p.Arg328Ile	p.R328I	ENST00000380956	NM_001195286.1	328	aGa/aTa	7/9	1	2	FACETS	1	0.974	1	1	0.992	1	CLONAL	2	TRUE	1	0.22	2		465	574	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739766	41739766	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	156	507	0	ENST00000242208.4:c.207G>T	p.Lys69Asn	p.K69N	ENST00000242208	NM_002192.2	69	aaG/aaT	2/3	1	2	FACETS	1	0.98	1	1	0.993	1	CLONAL	2	TRUE	1	0.22	2		507	592	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202952	27202952	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	109	480	0	ENST00000380036.4:c.2044G>T	p.Asp682Tyr	p.D682Y	ENST00000380036	NM_000459.3	682	Gac/Tac	13/23	1	2	FACETS	1	0.955	1	1	0.989	1	CLONAL	2	TRUE	1	0.22	2		480	451	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753954	133753954	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	46	385	0	ENST00000318560.5:c.1423T>G	p.Cys475Gly	p.C475G	ENST00000318560	NM_005157.4	475	Tgt/Ggt	8/11	1	2	FACETS	0.961	0.811	1	0.961	0.811	1	CLONAL	1	TRUE	1	0.22	2		385	435	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348994	70348994	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	195	563	0	ENST00000374080.3:c.3506C>T	p.Ala1169Val	p.A1169V	ENST00000374080		1169	gCc/gTc	25/45	1	2	FACETS	1	0.984	1	1	0.994	1	CLONAL	2	TRUE	1	0.22	2		563	738	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0051862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	180	435	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.710377405853439	3	FACETS	0.883	0.826	0.94	0.883	0.826	0.94	CLONAL	2	TRUE	1	0.722526961187149	3		435	384	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796805	135796805	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203427	NA	P-0051862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	25	319	0	ENST00000298552.3:c.682C>T	p.Arg228Ter	p.R228*	ENST00000298552	NM_001162426.1	228	Cga/Tga	8/23	1	2	FACETS	0.618	0.496	0.753	0.618	0.496	0.753	SUBCLONAL	1	TRUE	1	0.722526961187149	2		319	112	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125397	7125397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1288021639	NA	P-0051862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	165	615	0	ENST00000302850.5:c.3155C>T	p.Thr1052Ile	p.T1052I	ENST00000302850	NM_000208.2	1052	aCc/aTc	17/22	0.722526961187149	6	FACETS	0.875	0.802	0.952	0.219	0.2	0.238	CLONAL	1	TRUE	2	0.722526961187149	6		615	1276	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323268	31323268	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	121	189	0	ENST00000412585.2:c.721T>A	p.Trp241Arg	p.W241R	ENST00000412585	NM_005514.6	241	Tgg/Agg	4/8	0.722526961187149	3	FACETS	0.93	0.859	1	0.93	0.859	1	CLONAL	2	TRUE	1	0.722526961187149	3		189	245	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	139	373	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.277919962925133	4	FACETS	1	0.968	1	0.74	0.679	0.804	CLONAL	2	TRUE	1	0.367281704015676	4		373	466	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0051865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	34	356	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.350673803649214	3	FACETS	0.891	0.732	1	0.445	0.366	0.534	CLONAL	1	TRUE	1	0.367281704015676	3		356	246	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0051865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	69	238	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.270764118245104	3	FACETS	0.751	0.66	0.848	0.751	0.66	0.848	SUBCLONAL	2	TRUE	1	0.367281704015676	3		238	296	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0051865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	66	360	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.270764118245104	3	FACETS	1	0.952	1	0.597	0.521	0.679	CLONAL	1	TRUE	1	0.367281704015676	3		360	356	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944260	206944260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746523858	NA	P-0051865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	23	339	0	ENST00000423557.1:c.370C>T	p.Arg124Trp	p.R124W	ENST00000423557	NM_000572.2	124	Cgg/Tgg	3/5	0.350673803649214	3	FACETS	0.332	0.258	0.418	0.166	0.129	0.209	SUBCLONAL	1	TRUE	1	0.367281704015676	3		339	446	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139760	55139760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751618661	NA	P-0051865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	58	514	1	ENST00000257290.5:c.1421C>T	p.Thr474Met	p.T474M	ENST00000257290	NM_006206.4	474	aCg/aTg	10/23	0.350673803649214	3	FACETS	0.692	0.595	0.798	0.346	0.297	0.399	SUBCLONAL	1	TRUE	1	0.367281704015676	3		515	540	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039456	49039456	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1566237785	NA	P-0051865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	77	315	0	ENST00000267163.4:c.2441A>G	p.Lys814Arg	p.K814R	ENST00000267163	NM_000321.2	814	aAa/aGa	23/27	0.288029222868693	5	FACETS	1	0.894	1	0.34	0.298	0.385	CLONAL	1	TRUE	2	0.367281704015676	5		315	638	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720320	43720320	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0051865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	323	526	0	ENST00000382044.4:c.3722T>A	p.Leu1241Ter	p.L1241*	ENST00000382044	NM_001141980.1	1241	tTa/tAa	18/28	0.367131917335062	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	3	TRUE	0	0.367281704015676	3		526	694	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119891	70119891	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	139	484	0	ENST00000245479.2:c.893del	p.Leu298ArgfsTer85	p.L298Rfs*85	ENST00000245479	NM_000346.3	298	cTg/cg	3/3	0.270764118245104	3	FACETS	1	0.985	1	0.708	0.646	0.772	CLONAL	1	TRUE	1	0.367281704015676	3		484	633	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119930	70119930	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	44	416	0	ENST00000245479.2:c.932G>T	p.Gly311Val	p.G311V	ENST00000245479	NM_000346.3	311	gGc/gTc	3/3	0.270764118245104	3	FACETS	0.537	0.45	0.634	0.269	0.225	0.317	SUBCLONAL	1	TRUE	1	0.367281704015676	3		416	528	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561018	9561018	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	51	409	0	ENST00000353224.5:c.764G>A	p.Ser255Asn	p.S255N	ENST00000353224	NM_177990.2	255	aGt/aAt	4/10	0.286450734498382	4	FACETS	0.712	0.605	0.83	0.356	0.302	0.415	SUBCLONAL	1	TRUE	2	0.367281704015676	4		409	533	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713910	30713910	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	80	436	0	ENST00000295754.5:c.1235A>G	p.Asp412Gly	p.D412G	ENST00000295754	NM_003242.5	412	gAc/gGc	4/7	0.350673803649214	3	FACETS	1	0.884	1	0.501	0.442	0.564	CLONAL	1	TRUE	1	0.367281704015676	3		436	515	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907813	76907813	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	22	194	0	ENST00000373344.5:c.4348G>T	p.Glu1450Ter	p.E1450*	ENST00000373344	NM_000489.3	1450	Gaa/Taa	15/35	0.350673803649214	3	FACETS	0.619	0.481	0.778	0.31	0.24	0.389	SUBCLONAL	1	TRUE	1	0.367281704015676	3		194	229	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0051866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	245	289	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.449231555155398	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.547298160701032	4		289	660	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0051866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	229	509	1	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.547298160701032	2	FACETS	0.886	0.837	0.936	0.886	0.837	0.936	CLONAL	2	TRUE	0	0.547298160701032	2		510	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579310	7579310	+	splice_donor_variant	Splice_Site	SNP	A	A	C	rs1555526469	NA	P-0051866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	282	470	0	ENST00000269305.4:c.375+2T>G		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.494693038899059	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.547298160701032	2		470	515	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966768	44966768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	237	209	0	ENST00000377967.4:c.3992G>A	p.Cys1331Tyr	p.C1331Y	ENST00000377967	NM_021140.2	1331	tGt/tAt	27/29	0.413065866879992	2	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.547298160701032	2		209	380	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574366	95574366	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	352	207	0	ENST00000393063.1:c.2501C>A	p.Ser834Tyr	p.S834Y	ENST00000393063	NM_030621.3	834	tCt/tAt	17/28	0.547298160701032	7	FACETS	0.91	0.866	0.954			1	CLONAL	4	TRUE	NA	0.547298160701032	7		207	837	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0051867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	223	337	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	0.190486297058964	3	FACETS	1	0.944	1	0.671	0.629	0.714	INDETERMINATE	2	TRUE	0	0.460063209803748	3		337	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567546196	NA	P-0051867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	391	659	3	ENST00000269305.4:c.949del	p.Gln317SerfsTer28	p.Q317Sfs*28	ENST00000269305	NM_001126112.2	317	Cag/ag	9/11	0.460063209803748	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.460063209803748	2		662	768	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961847	15961847	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763880485	NA	P-0051867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	192	503	1	ENST00000268712.3:c.5948C>T	p.Ala1983Val	p.A1983V	ENST00000268712	NM_006311.3	1983	gCg/gTg	38/46	0.460063209803748	4	FACETS	1	0.955	1	0.524	0.484	0.566	CLONAL	1	TRUE	2	0.460063209803748	4		504	1163	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446848	49446848	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	273	538	0	ENST00000301067.7:c.962G>C	p.Arg321Pro	p.R321P	ENST00000301067	NM_003482.3	321	cGg/cCg	8/54	0.373648659392614	1	FACETS	0.781	0.74	0.822	1	0.995	1	SUBCLONAL	2	TRUE	0	0.460063209803748	1		538	585	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959357	26959357	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	42	336	0	ENST00000381527.3:c.524G>C	p.Gly175Ala	p.G175A	ENST00000381527	NM_001260.1	175	gGc/gCc	6/13	0.460063209803748	5	FACETS	0.367	0.305	0.437			1	SUBCLONAL	1	TRUE	NA	0.460063209803748	5		336	840	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562591	95562591	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	63	370	0	ENST00000393063.1:c.4666G>C	p.Asp1556His	p.D1556H	ENST00000393063	NM_030621.3	1556	Gac/Cac	24/28	0.20312535704945	5	FACETS	0.685	0.592	0.786			1	INDETERMINATE	1	TRUE	NA	0.460063209803748	5		370	676	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670716	67670716	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	213	531	0	ENST00000264010.4:c.1961G>A	p.Arg654Gln	p.R654Q	ENST00000264010	NM_006565.3	654	cGa/cAa	11/12	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.460063209803748	2		531	670	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375489	15375489	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	401	654	0	ENST00000263377.2:c.938C>A	p.Pro313His	p.P313H	ENST00000263377	NM_058243.2	313	cCc/cAc	6/20	0.289751870013957	4	FACETS	1	0.984	1			1	CLONAL	2	TRUE	NA	0.460063209803748	4		654	1185	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306544	41306544	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	303	486	1	ENST00000373198.4:c.1115C>A	p.Pro372Gln	p.P372Q	ENST00000373198	NM_133170.3	372	cCg/cAg	7/32	0.417942068832942	3	FACETS	0.882	0.834	0.932	0.882	0.834	0.932	CLONAL	2	TRUE	1	0.460063209803748	3		487	918	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421274	12421274	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	83	615	0	ENST00000287820.6:c.154G>T	p.Val52Leu	p.V52L	ENST00000287820	NM_015869.4	52	Gta/Tta	2/7	0.262330561496534	3	FACETS	0.545	0.48	0.615	0.182	0.16	0.205	INDETERMINATE	1	TRUE	0	0.460063209803748	3		615	814	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271483	26271483	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	124	658	0	ENST00000305910.3:c.130C>A	p.Pro44Thr	p.P44T	ENST00000305910	NM_003534.2	44	Ccc/Acc	1/1	0.169648620055515	2	FACETS	0.765	0.693	0.84	0.382	0.346	0.42	INDETERMINATE	1	TRUE	0	0.460063209803748	2		658	705	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729888	41729888	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1043609570	NA	P-0051867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	109	509	0	ENST00000242208.4:c.641G>T	p.Arg214Leu	p.R214L	ENST00000242208	NM_002192.2	214	cGg/cTg	3/3	0.214892404815111	1	FACETS	0.695	0.626	0.767	0.695	0.626	0.767	INDETERMINATE	1	TRUE	0	0.460063209803748	1		509	525	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624526	93624526	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	139	481	0	ENST00000375746.1:c.617G>T	p.Cys206Phe	p.C206F	ENST00000375746	NM_001174167.1	206	tGc/tTc	4/14	0.437457615602217	1	FACETS	0.907	0.831	0.986	0.907	0.831	0.986	CLONAL	1	TRUE	0	0.460063209803748	1		481	513	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0051868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	159	299	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.92	2		299	345	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0051868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	491	520	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.753	0.73	0.775	1	0.997	1	SUBCLONAL	2	TRUE	1	0.92	2		520	709	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217380	123217380	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	246	338	0	ENST00000218089.9:c.3034C>T	p.Arg1012Ter	p.R1012*	ENST00000218089	NM_001042749.1	1012	Cga/Tga	29/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.92	1		338	268	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798769	135798769	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	33	325	1	ENST00000298552.3:c.474del	p.Phe158LeufsTer9	p.F158Lfs*9	ENST00000298552	NM_001162426.1	158	ttT/tt	6/23	0.155064487240556	1	FACETS	0.086	0.07	0.105	0.086	0.07	0.105	INDETERMINATE	1	TRUE	0	0.92	1		326	449	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258030	123258030	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	328	474	1	ENST00000358487.5:c.1651C>T	p.Leu551Phe	p.L551F	ENST00000358487	NM_000141.4	551	Ctt/Ttt	12/18	1	2	FACETS	0.944	0.898	0.991	0.944	0.898	0.991	CLONAL	1	TRUE	1	0.92	2		475	755	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77034331	77034331	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	410	619	0	ENST00000356341.3:c.1626G>C	p.Lys542Asn	p.K542N	ENST00000356341	NM_002576.4	542	aaG/aaC	15/15	1	2	FACETS	0.996	0.953	1	0.996	0.953	1	CLONAL	1	TRUE	1	0.92	2		619	895	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237652	133237652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138391248	NA	P-0051868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	356	599	3	ENST00000320574.5:c.2963C>T	p.Ser988Leu	p.S988L	ENST00000320574	NM_006231.2	988	tCg/tTg	25/49	1	2	FACETS	0.873	0.83	0.915	0.873	0.83	0.915	CLONAL	1	TRUE	1	0.92	2		602	887	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923243	26923243	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	203	323	0	ENST00000381527.3:c.239C>T	p.Ser80Phe	p.S80F	ENST00000381527	NM_001260.1	80	tCt/tTt	3/13	1	2	FACETS	0.881	0.825	0.938	0.881	0.825	0.938	CLONAL	1	TRUE	1	0.92	2		323	501	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923248	26923248	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	209	323	0	ENST00000381527.3:c.244C>A	p.Gln82Lys	p.Q82K	ENST00000381527	NM_001260.1	82	Caa/Aaa	3/13	1	2	FACETS	0.893	0.837	0.949	0.893	0.837	0.949	CLONAL	1	TRUE	1	0.92	2		323	509	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29007954	29007954	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0051868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	22	208	0	ENST00000282397.4:c.813+2T>C		p.X271_splice	ENST00000282397	NM_002019.4	271			1	2	FACETS	0.123	0.095	0.156	0.123	0.095	0.156	SUBCLONAL	1	TRUE	1	0.92	2		208	389	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352389	73352389	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	269	475	0	ENST00000377767.4:c.516C>G	p.Ile172Met	p.I172M	ENST00000377767	NM_014953.3	172	atC/atG	3/21	1	2	FACETS	0.995	0.942	1	0.995	0.942	1	CLONAL	1	TRUE	1	0.92	2		475	588	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545666	63545666	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	272	504	0	ENST00000307078.5:c.928G>C	p.Asp310His	p.D310H	ENST00000307078	NM_004655.3	310	Gat/Cat	3/11	1	2	FACETS	0.801	0.756	0.848	0.801	0.756	0.848	CLONAL	1	TRUE	1	0.92	2		504	738	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621916	1621917	+	missense_variant	Missense_Mutation	DNP	GG	GG	TA	novel	NA	P-0051868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	405	684	0	ENST00000344749.5:c.875_876delinsTA	p.Ser292Leu	p.S292L	ENST00000344749	NM_001136139.2	292	tCC/tTA	11/19	1	2	FACETS	0.923	0.882	0.964	0.923	0.882	0.964	CLONAL	1	TRUE	1	0.92	2		684	954	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227827	36227827	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	387	706	0	ENST00000222270.7:c.7312C>G	p.Leu2438Val	p.L2438V	ENST00000222270	NM_014727.1	2438	Ctg/Gtg	32/37	1	2	FACETS	0.825	0.786	0.864	0.825	0.786	0.864	CLONAL	1	TRUE	1	0.92	2		706	1020	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021828	71021828	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0051868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	131	190	0	ENST00000318789.4:c.1531-1G>T		p.X511_splice	ENST00000318789	NM_032682.5	511			1	2	FACETS	0.999	0.924	1	0.999	0.924	1	CLONAL	1	TRUE	1	0.92	2		190	285	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433344	138433344	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	164	402	0	ENST00000289153.2:c.1268C>G	p.Ser423Cys	p.S423C	ENST00000289153	NM_006219.2	423	tCt/tGt	7/22	1	2	FACETS	0.77	0.713	0.828	0.77	0.713	0.828	SUBCLONAL	1	TRUE	1	0.92	2		402	463	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846099	128846099	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	477	689	0	ENST00000249373.3:c.1029C>G	p.Phe343Leu	p.F343L	ENST00000249373	NM_005631.4	343	ttC/ttG	5/12	1	2	FACETS	0.937	0.898	0.975	0.937	0.898	0.975	CLONAL	1	TRUE	1	0.92	2		689	1107	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782289	NA	P-0051869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	174	517	1	ENST00000269305.4:c.706T>C	p.Tyr236His	p.Y236H	ENST00000269305	NM_001126112.2	236	Tac/Cac	7/11	0.450860374031966	3	FACETS	1	0.988	1	0.823	0.771	0.874	CLONAL	2	TRUE	0	0.532980687658563	3		518	335	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520273	176520273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759709290	NA	P-0051869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	88	640	0	ENST00000292408.4:c.1192C>T	p.Arg398Trp	p.R398W	ENST00000292408	NM_213647.1	398	Cgg/Tgg	9/18	1	2	FACETS	0.971	0.868	1	0.971	0.868	1	CLONAL	1	TRUE	1	0.532980687658563	2		640	340	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026524	48026524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369456858	NA	P-0051869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	36	489	0	ENST00000234420.5:c.1402C>T	p.Arg468Cys	p.R468C	ENST00000234420	NM_000179.2	468	Cgt/Tgt	4/10	0.426142957672991	3	FACETS	0.781	0.647	0.928	0.391	0.323	0.464	CLONAL	1	TRUE	1	0.532980687658563	3		489	219	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831629	72831629	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs117283459	NA	P-0051869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	93	612	0	ENST00000268489.5:c.4952C>T	p.Thr1651Met	p.T1651M	ENST00000268489	NM_006885.3	1651	aCg/aTg	9/10	0.450860374031966	3	FACETS	1	0.971	1	0.413	0.37	0.457	CLONAL	1	TRUE	0	0.532980687658563	3		612	357	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710622	114710622	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1282664682	NA	P-0051869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	68	454	0	ENST00000543371.1:c.107C>T	p.Ser36Leu	p.S36L	ENST00000543371	NM_001198531.1	36	tCg/tTg	1/14	1	2	FACETS	0.837	0.734	0.945	0.837	0.734	0.945	CLONAL	1	TRUE	1	0.532980687658563	2		454	305	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382185	152382185	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	80	458	0	ENST00000206249.3:c.1295C>A	p.Ser432Ter	p.S432*	ENST00000206249	NM_000125.3	432	tCa/tAa	6/8	0.532980687658563	3	FACETS	1	0.972	1	0.802	0.728	0.877	CLONAL	2	TRUE	0	0.532980687658563	3		458	158	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248111	59248111	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	43	250	0	ENST00000371222.2:c.632T>G	p.Leu211Arg	p.L211R	ENST00000371222	NM_002228.3	211	cTg/cGg	1/1	0.481380081666334	4	FACETS	1	0.948	1	0.654	0.555	0.762	CLONAL	1	TRUE	2	0.532980687658563	4		250	189	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446857	49446857	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0051869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	88	497	0	ENST00000301067.7:c.955-2A>G		p.X319_splice	ENST00000301067	NM_003482.3	319			0.532980687658563	4	FACETS	1	0.968	1			1	CLONAL	1	TRUE	NA	0.532980687658563	4		497	409	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30103732	30103732	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	13	374	0	ENST00000331968.5:c.1206C>A	p.Asn402Lys	p.N402K	ENST00000331968	NM_002742.2	402	aaC/aaA	8/18	0.196321914032013	1	FACETS	0.407	0.294	0.54	0.407	0.294	0.54	INDETERMINATE	1	TRUE	0	0.532980687658563	1		374	88	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16062129	16062129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	48	499	0	ENST00000268712.3:c.677C>T	p.Pro226Leu	p.P226L	ENST00000268712	NM_006311.3	226	cCt/cTt	6/46	0.450860374031966	3	FACETS	1	0.879	1	0.344	0.294	0.398	CLONAL	1	TRUE	0	0.532980687658563	3		499	221	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326568	62326568	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	331	715	2	ENST00000360203.5:c.3493C>A	p.Gln1165Lys	p.Q1165K	ENST00000360203	NM_001283009.1	1165	Caa/Aaa	33/35	0.388809919802793	4	FACETS	0.959	0.914	1	0.959	0.914	1	CLONAL	3	TRUE	1	0.532980687658563	4		717	662	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515146	149515146	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	71	554	0	ENST00000261799.4:c.336G>T	p.Glu112Asp	p.E112D	ENST00000261799	NM_002609.3	112	gaG/gaT	3/23	1	2	FACETS	0.726	0.637	0.82	0.726	0.637	0.82	SUBCLONAL	1	TRUE	1	0.532980687658563	2		554	367	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0051870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	192	403	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.224125040983633	4	FACETS	0.969	0.903	1	1	0.988	1	CLONAL	4	TRUE	1	0.224125040983633	4		403	541	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223967	36223967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	73	676	0	ENST00000222270.7:c.6517C>T	p.Arg2173Trp	p.R2173W	ENST00000222270	NM_014727.1	2173	Cgg/Tgg	28/37	0.162691747080051	0	FACETS	0.938	0.821	1			1	CLONAL	1	TRUE	0	0.224125040983633	0		676	539	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376437	118376437	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	86	350	0	ENST00000534358.1:c.9830T>G	p.Leu3277Arg	p.L3277R	ENST00000534358	NM_005933.3	3277	cTt/cGt	27/36	1	2	FACETS	0.905	0.805	1	1	0.984	1	CLONAL	2	TRUE	1	0.224125040983633	2		350	424	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031743	26032022	+	coding_sequence_variant,3_prime_UTR_variant	Frame_Shift_Del	DEL	GCTTTCCGGGGGGGTCCTTAGAAATTTGTTCTGTTAAGACAACAAAAAATTATCACAGCTACTTTCGTTGGAATAAGTGGGTGGCTCTGAAAAGAGCCTTTGGGTTTTAAGACTGATGAAAAAGTGACTTTACATTTACGCTCTTTCTCCGCGAATGCGGCGAGCGAGCTGGATGTCTTTGGGCATAATAGTCACTCGCTTAGCATGGATGGCGCAAAGGTTTGTGTCCTCAAAGAGCCCTACCAAGTAGGCCTCACAAGCCTCCTGCAGCGCCATCACC	GCTTTCCGGGGGGGTCCTTAGAAATTTGTTCTGTTAAGACAACAAAAAATTATCACAGCTACTTTCGTTGGAATAAGTGGGTGGCTCTGAAAAGAGCCTTTGGGTTTTAAGACTGATGAAAAAGTGACTTTACATTTACGCTCTTTCTCCGCGAATGCGGCGAGCGAGCTGGATGTCTTTGGGCATAATAGTCACTCGCTTAGCATGGATGGCGCAAAGGTTTGTGTCCTCAAAGAGCCCTACCAAGTAGGCCTCACAAGCCTCCTGCAGCGCCATCACC	-	novel	NA	P-0051870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	47	35	0				ENST00000244661	NM_003537.3	89		1/1	1	2	FACETS	0.962	0.839	1	1	0.982	1	CLONAL	4	TRUE	1	0.224125040983633	2		35	109	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929266	44929266	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs747545667	NA	P-0051870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	97	267	0	ENST00000377967.4:c.2366A>G	p.Asn789Ser	p.N789S	ENST00000377967	NM_021140.2	789	aAt/aGt	17/29	1	1	FACETS	0.982	0.889	1	1	0.99	1	CLONAL	3	TRUE	0	0.224125040983633	1		267	261	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	114	230	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.845867734302182	2		230	238	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0051871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	112	229	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.996	0.912	1	0.996	0.912	1	CLONAL	1	TRUE	1	0.845867734302182	2		229	266	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888211	112888211	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121918465	NA	P-0051871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	252	496	0	ENST00000351677.2:c.227A>G	p.Glu76Gly	p.E76G	ENST00000351677	NM_002834.3	76	gAg/gGg	3/16	1	2	FACETS	0.98	0.924	1	0.98	0.924	1	CLONAL	1	TRUE	1	0.845867734302182	2		496	608	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684337	29684337	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs1060500333	NA	P-0051871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	190	440	0	ENST00000356175.3:c.7857T>G	p.Tyr2619Ter	p.Y2619*	ENST00000356175	NM_000267.3	2619	taT/taG	53/57	1	2	FACETS	0.956	0.893	1	0.956	0.893	1	CLONAL	1	TRUE	1	0.845867734302182	2		440	470	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552212	29552212	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	169	355	0	ENST00000356175.3:c.1945del	p.Glu649AsnfsTer39	p.E649Nfs*39	ENST00000356175	NM_000267.3	649	Gaa/aa	17/57	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.845867734302182	2		355	389	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872105	76872105	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	138	234	0	ENST00000373344.5:c.5542C>T	p.Gln1848Ter	p.Q1848*	ENST00000373344	NM_000489.3	1848	Cag/Tag	22/35	0.3698143769988	2	FACETS	0.933	0.871	0.994			1	CLONAL	3	TRUE	NA	0.409110825110912	2		234	241	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916146	9916146	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	49	466	1	ENST00000330684.3:c.2143G>T	p.Asp715Tyr	p.D715Y	ENST00000330684	NM_001134407.1	715	Gac/Tac	10/13	1	2	FACETS	0.424	0.359	0.496	0.424	0.359	0.496	SUBCLONAL	1	TRUE	1	0.409110825110912	2		467	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0051873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	139	632	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.116753914427136	5	FACETS	0.989	0.904	1	1	0.989	1	CLONAL	5	FALSE	2	0.116753914427136	5		632	566	SUCCESS
AR	367	MSKCC	GRCh37	X	66765159	66765191	+	inframe_deletion	In_Frame_Del	DEL	GCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA	GCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA	-	rs3032358	NA	P-0051873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	41	135	0	ENST00000374690.3:c.207_239del	p.Gln70_Gln80del	p.Q70_Q80del	ENST00000374690	NM_000044.3	57	ctGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAg/ctg	1/8	0.116753914427136	4	FACETS	0.912	0.771	1			1	CLONAL	5	FALSE	NA	0.116753914427136	4		135	172	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	166	255	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	0.116753914427136	4	FACETS	1	0.938	1			1	CLONAL	10	FALSE	NA	0.116753914427136	4		255	317	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099403	157099432	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAGCAACAGCAG	CAGCAGCAGCAGCAGCAGCAGCAACAGCAG	-	novel	NA	P-0051873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	63	299	0	ENST00000346085.5:c.357_386del	p.Gln122_Gln131del	p.Q122_Q131del	ENST00000346085	NM_020732.3	114	CAGCAGCAGCAGCAGCAGCAGCAACAGCAG/-	1/20	0.116753914427136	2	FACETS	1	0.912	1	1	0.981	1	CLONAL	4	FALSE	0	0.116753914427136	2		299	256	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057835	27057835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	207	682	0	ENST00000324856.7:c.1543C>T	p.Gln515Ter	p.Q515*	ENST00000324856	NM_006015.4	515	Cag/Tag	3/20	0.116753914427136	3	FACETS	0.957	0.895	1	1	0.994	1	CLONAL	7	FALSE	0	0.116753914427136	3		682	560	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247165	153247165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	30	286	0	ENST00000281708.4:c.1637C>T	p.Ser546Leu	p.S546L	ENST00000281708	NM_033632.3	546	tCa/tTa	10/12	0.116753914427136	3	FACETS	0.88	0.711	1	0.587	0.474	0.714	CLONAL	2	FALSE	0	0.116753914427136	3		286	309	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593383	55593383	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0051873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	35	294	0	ENST00000288135.5:c.1541-1G>A		p.X514_splice	ENST00000288135	NM_000222.2	514			0.116753914427136	3	FACETS	1	0.881	1	0.729	0.6	0.873	CLONAL	2	FALSE	0	0.116753914427136	3		294	290	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774771	73774771	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	170	449	0	ENST00000254810.4:c.316G>A	p.Glu106Lys	p.E106K	ENST00000254810	NM_005324.3	106	Gaa/Aaa	4/4	0.116753914427136	6	FACETS	0.94	0.87	1	1	0.991	1	CLONAL	7	FALSE	2	0.116753914427136	6		449	546	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807890	1807890	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913105	NA	P-0051873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	87	809	0	ENST00000260795.2:c.1949A>T	p.Lys650Met	p.K650M	ENST00000260795		650	aAg/aTg	13/17	0.116753914427136	3	FACETS	1	0.959	1	0.789	0.699	0.886	CLONAL	2	FALSE	0	0.116753914427136	3		809	666	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97887418	97887418	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs776529713	NA	P-0051873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	69	479	1	ENST00000289081.3:c.946C>T	p.Gln316Ter	p.Q316*	ENST00000289081	NM_000136.2	316	Cag/Tag	10/15	0.116753914427136	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	FALSE	1	0.116753914427136	3		480	539	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112555	2112555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	168	701	0	ENST00000219476.3:c.1315G>A	p.Asp439Asn	p.D439N	ENST00000219476	NM_000548.3	439	Gac/Aac	13/42	1	2	FACETS	1	0.945	1	1	0.995	1	CLONAL	6	FALSE	1	0.116753914427136	2		701	469	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423497	116423497	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	146	344	0	ENST00000397752.3:c.3772C>T	p.Gln1258Ter	p.Q1258*	ENST00000397752	NM_000245.2	1258	Caa/Taa	19/21	0.116753914427136	6	FACETS	0.995	0.916	1	1	0.987	1	CLONAL	7	FALSE	1	0.116753914427136	6		344	443	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106009	8106009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	266	497	0	ENST00000346208.3:c.829G>A	p.Asp277Asn	p.D277N	ENST00000346208		277	Gat/Aat	4/6	0.116753914427136	13	FACETS	0.998	0.94	1	1	0.99	1	CLONAL	10	FALSE	5	0.116753914427136	13		497	750	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390745	118390745	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	92	419	0	ENST00000534358.1:c.11395G>C	p.Glu3799Gln	p.E3799Q	ENST00000534358	NM_005933.3	3799	Gaa/Caa	33/36	1	2	FACETS	0.908	0.814	1	1	0.99	1	CLONAL	5	FALSE	1	0.116753914427136	2		419	347	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123889597	123889597	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	15	304	0	ENST00000330479.4:c.824T>G	p.Phe275Cys	p.F275C	ENST00000330479	NM_020382.3	275	tTt/tGt	7/9	0.116753914427136	3	FACETS	0.916	0.669	1	0.458	0.334	0.607	CLONAL	1	FALSE	1	0.116753914427136	3		304	297	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871197	35871234	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	TGTTCTTTCAGCCCCTTTGCGCTCATAACGTCAGACGC	TGTTCTTTCAGCCCCTTTGCGCTCATAACGTCAGACGC	-	novel	NA	P-0051873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	37	363	0	ENST00000216797.5:c.939_*22del		p.*313*	ENST00000216797	NM_020529.2	313		6/6	0.116753914427136	6	FACETS	1	0.883	1	0.728	0.601	0.869	CLONAL	2	FALSE	3	0.116753914427136	6		363	358	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590961	95590962	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGGGTCCCAGAACTACCAATACGGCACGA	novel	NA	P-0051873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	36	306	0	ENST00000393063.1:c.918_947dup	p.Cys306_Pro315dup	p.C306_P315dup	ENST00000393063	NM_030621.3	306	tgg/tgTCGTGCCGTATTGGTAGTTCTGGGACCCTGg	9/28	0.116753914427136	6	FACETS	1	0.91	1	0.783	0.645	0.936	CLONAL	2	FALSE	3	0.116753914427136	6		306	324	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38631999	38631999	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	99	473	0	ENST00000299084.4:c.485T>C	p.Val162Ala	p.V162A	ENST00000299084	NM_152594.2	162	gTt/gCt	5/7	0.116753914427136	6	FACETS	1	0.925	1	1	0.925	1	CLONAL	4	FALSE	2	0.116753914427136	6		473	503	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782893	66782893	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	105	439	0	ENST00000307102.5:c.1122G>C	p.Trp374Cys	p.W374C	ENST00000307102	NM_002755.3	374	tgG/tgC	11/11	0.116753914427136	2	FACETS	0.964	0.872	1	1	0.99	1	CLONAL	5	FALSE	0	0.116753914427136	2		439	373	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112002	2112003	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0051873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	33	530	0	ENST00000219476.3:c.1252_1253del	p.Arg418AlafsTer2	p.R418Afs*2	ENST00000219476	NM_000548.3	417	cAG/c	12/42	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	FALSE	1	0.116753914427136	2		530	388	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134460	2134460	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	34	839	1	ENST00000219476.3:c.4237G>A	p.Glu1413Lys	p.E1413K	ENST00000219476	NM_000548.3	1413	Gag/Aag	34/42	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	FALSE	1	0.116753914427136	2		840	504	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853187	68853187	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs373605261	NA	P-0051873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	66	461	0	ENST00000261769.5:c.1570C>G	p.Arg524Gly	p.R524G	ENST00000261769	NM_004360.3	524	Cgg/Ggg	11/16	1	2	FACETS	1	0.883	1	1	0.985	1	CLONAL	3	FALSE	1	0.116753914427136	2		461	372	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618790	37618790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	92	545	1	ENST00000447079.4:c.466G>A	p.Glu156Lys	p.E156K	ENST00000447079	NM_015083.1	156	Gag/Aag	1/14	0.116753914427136	7	FACETS	1	0.919	1	0.829	0.74	0.924	CLONAL	4	FALSE	2	0.116753914427136	7		546	491	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871990	45871990	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	178	504	0	ENST00000391945.4:c.258G>T	p.Glu86Asp	p.E86D	ENST00000391945	NM_000400.3	86	gaG/gaT	5/23	0.116753914427136	5	FACETS	0.971	0.902	1	1	0.994	1	CLONAL	7	FALSE	2	0.116753914427136	5		504	527	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241111	39241111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	94	455	0	ENST00000402219.2:c.1960G>A	p.Glu654Lys	p.E654K	ENST00000402219	NM_005633.3	654	Gag/Aag	12/23	0.116753914427136	6	FACETS	1	0.905	1	1	0.905	1	CLONAL	4	FALSE	2	0.116753914427136	6		455	490	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202122991	202122991	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	67	442	0	ENST00000358485.4:c.37A>G	p.Ser13Gly	p.S13G	ENST00000358485	NM_001080125.1	13	Agt/Ggt	1/9	0.116753914427136	6	FACETS	1	0.957	1			1	CLONAL	2	FALSE	NA	0.116753914427136	6		442	568	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249498	153249498	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0051873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	129	460	0	ENST00000281708.4:c.1280C>G	p.Ser427Ter	p.S427*	ENST00000281708	NM_033632.3	427	tCa/tGa	9/12	0.116753914427136	3	FACETS	1	0.95	1	1	0.989	1	CLONAL	5	FALSE	0	0.116753914427136	3		460	443	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109315761	109315761	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs75780557	NA	P-0051873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	97	538	0	ENST00000436639.2:c.1024T>A	p.Leu342Ile	p.L342I	ENST00000436639	NM_014454.2	342	Tta/Ata	6/10	0.116753914427136	5	FACETS	1	0.933	1	0.637	0.569	0.709	CLONAL	3	FALSE	0	0.116753914427136	5		538	613	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346374	152346374	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	87	542	0	ENST00000359321.1:c.196A>G	p.Ile66Val	p.I66V	ENST00000359321	NM_005431.1	66	Ata/Gta	3/3	0.116753914427136	6	FACETS	0.968	0.86	1	0.774	0.688	0.865	CLONAL	4	FALSE	1	0.116753914427136	6		542	475	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918580	44918580	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	172	261	0	ENST00000377967.4:c.1063T>G	p.Trp355Gly	p.W355G	ENST00000377967	NM_021140.2	355	Tgg/Ggg	12/29	0.116753914427136	4	FACETS	0.982	0.92	1			1	CLONAL	10	FALSE	NA	0.116753914427136	4		261	335	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0051879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	168	463	2	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	1	2	FACETS	0.992	0.92	1	0.992	0.92	1	CLONAL	1	TRUE	1	0.683989968497115	2		465	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0051879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	214	528	7	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	0.623708727455326	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.683989968497115	1		535	395	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061463	38061463	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	193	478	5	ENST00000250448.2:c.526A>G	p.Ile176Val	p.I176V	ENST00000250448	NM_004496.3	176	Atc/Gtc	2/2	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.683989968497115	2		483	517	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853184	68853185	+	stop_gained,frameshift_variant,splice_region_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0051879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	151	475	0	ENST00000261769.5:c.1568dup	p.Tyr523Ter	p.Y523*	ENST00000261769	NM_004360.3	523	tat/tAat	11/16	0.683989968497115	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.683989968497115	1		475	286	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987418	2987418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	27	459	0	ENST00000396946.4:c.11G>A	p.Gly4Glu	p.G4E	ENST00000396946	NM_032415.4	4	gGa/gAa	3/25	1	2	FACETS	0.171	0.135	0.211	0.171	0.135	0.211	SUBCLONAL	1	TRUE	1	0.683989968497115	2		459	463	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120642	115120642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	269	629	3	ENST00000257566.3:c.364G>A	p.Glu122Lys	p.E122K	ENST00000257566	NM_016569.3	122	Gag/Aag	1/8	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.683989968497115	2		632	707	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936950	48936950	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0051879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	86	292	0	ENST00000267163.4:c.719-1G>A		p.X240_splice	ENST00000267163	NM_000321.2	240			0.683989968497115	1	FACETS	0.979	0.892	1	0.979	0.892	1	CLONAL	1	TRUE	0	0.683989968497115	1		292	169	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218419	69218419	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051879-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	129	424	4	ENST00000462284.1:c.511A>T	p.Ile171Phe	p.I171F	ENST00000462284	NM_002392.5	171	Att/Ttt	7/11	1	2	FACETS	0.95	0.87	1	0.95	0.87	1	CLONAL	1	TRUE	1	0.683989968497115	2		428	397	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0051892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	360	488	1	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	0.675730937995947	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.675730937995947	1		489	642	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428422	49428422	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs915492855	NA	P-0051892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	51	644	0	ENST00000301067.7:c.10383G>T	p.Arg3461Ser	p.R3461S	ENST00000301067	NM_003482.3	3461	agG/agT	36/54	0.344410962717588	1	FACETS	0.1	0.084	0.118	0.1	0.084	0.118	INDETERMINATE	1	TRUE	0	0.675730937995947	1		644	997	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656563	3656563	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs777059567	NA	P-0051892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	435	708	0	ENST00000294008.3:c.672G>C	p.Leu224Phe	p.L224F	ENST00000294008	NM_032444.2	224	ttG/ttC	3/15	0.675730937995947	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.675730937995947	1		708	821	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656505	3656505	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	397	695	0	ENST00000294008.3:c.730G>C	p.Asp244His	p.D244H	ENST00000294008	NM_032444.2	244	Gat/Cat	3/15	0.675730937995947	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.675730937995947	1		695	760	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602850	10602850	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	486	933	0	ENST00000171111.5:c.728C>A	p.Ser243Tyr	p.S243Y	ENST00000171111	NM_203500.1	243	tCc/tAc	3/6	0.675730937995947	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.675730937995947	1		933	910	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1953943	1953943	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1226	398	787	1	ENST00000382891.5:c.2122A>T	p.Ser708Cys	p.S708C	ENST00000382891	NM_133335.3	708	Agc/Tgc	11/22	0.675730937995947	3	FACETS	0.97	0.921	1			1	CLONAL	1	TRUE	NA	0.675730937995947	3		788	1624	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980396	1980397	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0051892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1955	443	847	0	ENST00000382891.5:c.3864_3865dup	p.Gly1289ValfsTer41	p.G1289Vfs*41	ENST00000382891	NM_133335.3	1286	-/GT	22/22	0.675730937995947	3	FACETS	0.732	0.695	0.769			1	SUBCLONAL	1	TRUE	NA	0.675730937995947	3		847	2398	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873593	35873593	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	129	192	0	ENST00000303115.3:c.549A>C	p.Leu183Phe	p.L183F	ENST00000303115	NM_002185.3	183	ttA/ttC	5/8	0.436208685841124	3	FACETS	1	0.975	1	0.591	0.54	0.644	CLONAL	1	TRUE	1	0.675730937995947	3		192	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057519990	NA	P-0051894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	267	516	0	ENST00000269305.4:c.796G>T	p.Gly266Ter	p.G266*	ENST00000269305	NM_001126112.2	266	Gga/Tga	8/11	0.355956929500079	2	FACETS	0.897	0.845	0.95	0.897	0.845	0.95	CLONAL	2	TRUE	0	0.393672171010832	2		516	756	SUCCESS
CALR	811	MSKCC	GRCh37	19	13049967	13049967	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	190	426	3	ENST00000316448.5:c.111G>T	p.Trp37Cys	p.W37C	ENST00000316448	NM_004343.3	37	tgG/tgT	2/9	0.151767655497359	4	FACETS	0.883	0.818	0.95	0.883	0.818	0.95	INDETERMINATE	2	TRUE	2	0.393672171010832	4		429	762	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120469132	120469133	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0051894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	101	470	0	ENST00000256646.2:c.3994_3995delinsTT	p.Arg1332Phe	p.R1332F	ENST00000256646	NM_024408.3	1332	CGt/TTt	24/34	0.350046284477071	3	FACETS	0.787	0.703	0.877	0.394	0.351	0.439	SUBCLONAL	1	TRUE	1	0.393672171010832	3		470	780	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712593	43712593	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	278	725	0	ENST00000382044.4:c.4591G>A	p.Asp1531Asn	p.D1531N	ENST00000382044	NM_001141980.1	1531	Gat/Aat	21/28	0.322689615897208	4	FACETS	0.865	0.812	0.919	0.865	0.812	0.919	CLONAL	2	TRUE	2	0.393672171010832	4		725	1138	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783825	50783825	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	93	543	1	ENST00000398568.2:c.220del	p.Ile74PhefsTer2	p.I74Ffs*2	ENST00000398568	NM_001042412.1	72	ttA/tt	3/18	0.338593086140295	1	FACETS	0.816	0.729	0.908	0.816	0.729	0.908	CLONAL	1	TRUE	0	0.393672171010832	1		544	465	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320330	30320330	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	98	239	0	ENST00000322652.5:c.1271A>T	p.Gln424Leu	p.Q424L	ENST00000322652	NM_015355.2	424	cAa/cTa	11/16	0.355956929500079	2	FACETS	0.87	0.787	0.956	0.87	0.787	0.956	CLONAL	2	TRUE	0	0.393672171010832	2		239	286	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5225743	5225743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	106	693	0	ENST00000357368.4:c.2489G>A	p.Gly830Glu	p.G830E	ENST00000357368	NM_002850.3	830	gGa/gAa	17/38	0.151767655497359	4	FACETS	0.704	0.63	0.783	0.352	0.315	0.392	INDETERMINATE	1	TRUE	2	0.393672171010832	4		693	1066	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918754	50918754	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs754832710	NA	P-0051894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	299	794	1	ENST00000440232.2:c.2624G>T	p.Arg875Leu	p.R875L	ENST00000440232	NM_002691.3	875	cGc/cTc	21/27	0.22808199471555	4	FACETS	0.811	0.763	0.861	0.811	0.763	0.861	INDETERMINATE	2	TRUE	2	0.393672171010832	4		795	1305	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101038	41101038	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	357	675	0	ENST00000373198.4:c.1318G>T	p.Val440Phe	p.V440F	ENST00000373198	NM_133170.3	440	Gtc/Ttc	8/32	0.355956929500079	2	FACETS	0.937	0.89	0.984	0.937	0.89	0.984	CLONAL	2	TRUE	0	0.393672171010832	2		675	968	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627798	187627798	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	230	485	0	ENST00000441802.2:c.3184G>T	p.Asp1062Tyr	p.D1062Y	ENST00000441802	NM_005245.3	1062	Gac/Tac	2/27	0.355956929500079	2	FACETS	0.884	0.829	0.94	0.884	0.829	0.94	CLONAL	2	TRUE	0	0.393672171010832	2		485	661	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386541	81386541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753731630	NA	P-0051894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	132	431	0	ENST00000222390.5:c.446G>A	p.Cys149Tyr	p.C149Y	ENST00000222390	NM_000601.4	149	tGt/tAt	4/18	0.393672171010832	3	FACETS	0.854	0.78	0.93	0.854	0.78	0.93	CLONAL	2	TRUE	1	0.393672171010832	3		431	470	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272337	38272337	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	262	578	0	ENST00000425967.3:c.2030G>T	p.Arg677Leu	p.R677L	ENST00000425967	NM_001174067.1	677	cGg/cTg	15/19	0.365469187902611	4	FACETS	0.89	0.834	0.947			1	CLONAL	2	TRUE	NA	0.393672171010832	4		578	1042	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0051896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	35	283	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.891	0.736	1	0.891	0.736	1	CLONAL	1	TRUE	1	0.339916074974638	2		283	231	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115252285	115252285	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	71	338	0	ENST00000369535.4:c.355G>C	p.Asp119His	p.D119H	ENST00000369535	NM_002524.4	119	Gat/Cat	4/7	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.339916074974638	2		338	403	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651516	52651516	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	65	439	0	ENST00000394830.3:c.1580del	p.Phe527SerfsTer42	p.F527Sfs*42	ENST00000394830	NM_018313.4	527	tTc/tc	15/30	0.330771821123487	1	FACETS	0.977	0.853	1	0.977	0.853	1	CLONAL	1	TRUE	0	0.339916074974638	1		439	325	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007111	152007111	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	54	416	0	ENST00000262189.6:c.789C>A	p.Cys263Ter	p.C263*	ENST00000262189	NM_170606.2	263	tgC/tgA	6/59	0.331306783599576	4	FACETS	0.693	0.592	0.805	0.231	0.197	0.269	SUBCLONAL	1	TRUE	1	0.339916074974638	4		416	614	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0051897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	75	454	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.29965799264012	1	FACETS	0.683	0.599	0.773	0.683	0.599	0.773	SUBCLONAL	1	TRUE	0	0.322513749809715	1		454	571	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0051897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	43	289	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.801	0.673	0.942	0.801	0.673	0.942	CLONAL	1	TRUE	1	0.322513749809715	2		289	333	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633320	8633320	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866980874	NA	P-0051897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	90	375	0	ENST00000356435.5:c.349C>T	p.Arg117Trp	p.R117W	ENST00000356435		117	Cgg/Tgg	3/35	0.302752510697992	2	FACETS	0.918	0.824	1	0.918	0.824	1	CLONAL	2	TRUE	0	0.322513749809715	2		375	304	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778731	76778732	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	TT	TT	AC	novel	NA	P-0051897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	42	341	0	ENST00000373344.5:c.6847_6848delinsGT	p.Lys2283Val	p.K2283V	ENST00000373344	NM_000489.3	2283	AAg/GTg	31/35	0.322513749809715	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.322513749809715	1		341	195	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0051898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	242	435	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.425730976859426	3	FACETS	0.989	0.938	1	0.989	0.938	1	CLONAL	3	TRUE	0	0.43658533446391	3		435	455	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221998	1221998	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690945	NA	P-0051898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	205	670	1	ENST00000326873.7:c.913C>T	p.Gln305Ter	p.Q305*	ENST00000326873	NM_000455.4	305	Cag/Tag	7/10	0.418014204362035	2	FACETS	0.898	0.84	0.956	0.898	0.84	0.956	CLONAL	2	TRUE	0	0.43658533446391	2		671	523	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64286881	64286884	+	frameshift_variant	Frame_Shift_Del	DEL	ATTT	ATTT	-	novel	NA	P-0051898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	49	298	0	ENST00000370651.3:c.98_101del	p.Phe33Ter	p.F33*	ENST00000370651	NM_003463.4	32	aaATTT/aa	2/6	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.43658533446391	NA		298	244	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599949	10599950	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0051898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	135	799	0	ENST00000171111.5:c.1626_1627del	p.Glu542AspfsTer31	p.E542Dfs*31	ENST00000171111	NM_203500.1	542	gaGAcg/gacg	5/6	0.418014204362035	2	FACETS	0.926	0.843	1	0.463	0.421	0.506	CLONAL	1	TRUE	0	0.43658533446391	2		799	668	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599948	10599950	+	frameshift_variant	Frame_Shift_Del	DEL	GTC	GTC	A	novel	NA	P-0051898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	151	795	0	ENST00000171111.5:c.1626_1628delinsT	p.Glu542AspfsTer31	p.E542Dfs*31	ENST00000171111	NM_203500.1	542	gaGACg/gaTg	5/6	0.418014204362035	2	FACETS	1	0.944	1	0.519	0.475	0.564	CLONAL	1	TRUE	0	0.43658533446391	2		795	667	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	72	373	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.906	0.793	1	0.906	0.793	1	CLONAL	1	TRUE	1	0.312231589308171	2		373	509	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602715	10602715	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	98	974	0	ENST00000171111.5:c.863G>T	p.Cys288Phe	p.C288F	ENST00000171111	NM_203500.1	288	tGc/tTc	3/6	0.312231589308171	1	FACETS	0.953	0.852	1	0.953	0.852	1	CLONAL	1	TRUE	0	0.312231589308171	1		974	556	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411011	63411011	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	41	671	0	ENST00000330258.3:c.2156T>A	p.Met719Lys	p.M719K	ENST00000330258	NM_152424.3	719	aTg/aAg	2/2	0.312231589308171	1	FACETS	0.546	0.455	0.646	0.546	0.455	0.646	SUBCLONAL	1	TRUE	0	0.312231589308171	1		671	406	SUCCESS
ATR	545	MSKCC	GRCh37	3	142211977	142211977	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0051899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	60	339	1	ENST00000350721.4:c.6075T>A	p.Tyr2025Ter	p.Y2025*	ENST00000350721	NM_001184.3	2025	taT/taA	35/47	1	2	FACETS	0.896	0.774	1	0.896	0.774	1	CLONAL	1	TRUE	1	0.312231589308171	2		340	429	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129957	55129957	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	86	558	0	ENST00000257290.5:c.491G>T	p.Ser164Ile	p.S164I	ENST00000257290	NM_006206.4	164	aGt/aTt	4/23	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.312231589308171	2		558	514	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962294	2962294	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1003847451	NA	P-0051899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	87	800	0	ENST00000396946.4:c.2243C>A	p.Thr748Lys	p.T748K	ENST00000396946	NM_032415.4	748	aCg/aAg	17/25	0.312231589308171	1	FACETS	0.871	0.773	0.975	0.871	0.773	0.975	CLONAL	1	TRUE	0	0.312231589308171	1		800	540	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730044	41730044	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1397640362	NA	P-0051899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	46	576	1	ENST00000242208.4:c.485C>T	p.Pro162Leu	p.P162L	ENST00000242208	NM_002192.2	162	cCc/cTc	3/3	1	2	FACETS	0.67	0.564	0.785	0.67	0.564	0.785	SUBCLONAL	1	TRUE	1	0.312231589308171	2		577	440	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763983	76763983	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	57	636	0	ENST00000373344.5:c.7325del	p.Pro2442GlnfsTer3	p.P2442Qfs*3	ENST00000373344	NM_000489.3	2442	cCa/ca	35/35	0.312231589308171	1	FACETS	0.547	0.469	0.632	0.547	0.469	0.632	SUBCLONAL	1	TRUE	0	0.312231589308171	1		636	563	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	37	373	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.761	0.631	0.905	0.761	0.631	0.905	CLONAL	1	TRUE	1	0.364190949096436	2		373	267	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0051900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	109	476	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.364190949096436	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.364190949096436	1		476	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577505	7577506	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0051900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	80	641	0	ENST00000269305.4:c.775_776delinsTT	p.Asp259Phe	p.D259F	ENST00000269305	NM_001126112.2	259	GAc/TTc	7/11	0.364190949096436	1	FACETS	0.646	0.57	0.728	0.646	0.57	0.728	SUBCLONAL	1	TRUE	0	0.364190949096436	1		641	556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0051901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	132	604	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.357465963356916	1	FACETS	0.998	0.909	1	0.998	0.909	1	CLONAL	1	TRUE	0	0.357465963356916	1		604	608	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035920	47035920	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	148	679	1	ENST00000377604.3:c.598C>T	p.Gln200Ter	p.Q200*	ENST00000377604	NM_001204468.1	200	Cag/Tag	7/24	0.357465963356916	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.357465963356916	1		680	651	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs869320707	NA	P-0051901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	1159	573	0	ENST00000397752.3:c.3028+1G>T		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.357465963356916	11	FACETS	1	0.992	1			1	CLONAL	10	TRUE	NA	0.357465963356916	11		573	1658	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738829	145738829	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758736784	NA	P-0051901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	105	1076	2	ENST00000428558.2:c.2236G>A	p.Ala746Thr	p.A746T	ENST00000428558	NM_004260.3	746	Gcg/Acg	14/22	0.138071867701503	5	FACETS	0.703	0.628	0.784	0.234	0.209	0.262	INDETERMINATE	1	TRUE	2	0.357465963356916	5		1078	1283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0051904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	200	454	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.246975301011597	3	FACETS	0.897	0.835	0.961	1	0.989	1	CLONAL	3	TRUE	1	0.246975301011597	3		454	676	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	149	373	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.974	1	1	0.992	1	CLONAL	2	TRUE	1	0.246975301011597	2		373	527	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046634	42046634	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0051904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	71	253	0	ENST00000219905.7:c.7009-1G>T		p.X2337_splice	ENST00000219905	NM_001164273.1	2337			0.202053949511834	2	FACETS	0.913	0.803	1	0.913	0.803	1	CLONAL	2	TRUE	0	0.246975301011597	2		253	315	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	362	373	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.184251242901278	7	FACETS	1	0.981	1	1	0.996	1	CLONAL	9	FALSE	1	0.184251242901278	7		373	614	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245931	5245931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	134	835	0	ENST00000357368.4:c.844G>A	p.Ala282Thr	p.A282T	ENST00000357368	NM_002850.3	282	Gcc/Acc	10/38	0.184251242901278	0	FACETS	0.815	0.749	0.882			1	CLONAL	4	FALSE	0	0.184251242901278	0		835	364	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0051906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	406	449	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	0.667575048517877	3	FACETS	0.973	0.931	1	0.973	0.931	1	CLONAL	2	TRUE	1	0.667575048517877	3		449	834	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155983	119155983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202065722	NA	P-0051906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	355	614	0	ENST00000264033.4:c.1648C>T	p.Arg550Trp	p.R550W	ENST00000264033	NM_005188.3	550	Cgg/Tgg	11/16	1	2	FACETS	0.956	0.907	1	0.956	0.907	1	CLONAL	1	TRUE	1	0.667575048517877	2		614	1112	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333932	70333932	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0051906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	182	320	0	ENST00000373644.4:c.1837A>T	p.Lys613Ter	p.K613*	ENST00000373644	NM_030625.2	613	Aag/Tag	2/12	0.326646292303514	1	FACETS	0.795	0.741	0.85	0.795	0.741	0.85	INDETERMINATE	1	TRUE	0	0.667575048517877	1		320	457	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098502	108098502	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0051906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	96	161	0	ENST00000278616.4:c.73-1G>T		p.X25_splice	ENST00000278616	NM_000051.3	25			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.667575048517877	2		161	266	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033276	69033276	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	39	404	0	ENST00000288368.4:c.3716T>A	p.Phe1239Tyr	p.F1239Y	ENST00000288368	NM_024870.2	1239	tTt/tAt	30/40	1	2	FACETS	0.228	0.188	0.272	0.228	0.188	0.272	SUBCLONAL	1	TRUE	1	0.667575048517877	2		404	513	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	249	373	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.566036325123663	2	FACETS	0.956	0.908	1	0.956	0.908	1	CLONAL	2	TRUE	0	0.592215755605701	2		373	440	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578537	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs879254214	NA	P-0051907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	304	853	1	ENST00000269305.4:c.393_395del	p.Asn131del	p.N131del	ENST00000269305	NM_001126112.2	131	aaCAAg/aag	5/11	0.592215755605701	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.592215755605701	1		854	680	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500417	99500417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777816523	NA	P-0051907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	109	715	0	ENST00000268035.6:c.3850G>A	p.Glu1284Lys	p.E1284K	ENST00000268035	NM_000875.3	1284	Gag/Aag	21/21	0.376648816657666	1	FACETS	0.367	0.33	0.407	0.367	0.33	0.407	SUBCLONAL	1	TRUE	0	0.592215755605701	1		715	706	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092947	27092947	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0051907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	39	260	0	ENST00000324856.7:c.2879-1G>A		p.X960_splice	ENST00000324856	NM_006015.4	960			0.376648816657666	1	FACETS	0.365	0.304	0.432	0.365	0.304	0.432	SUBCLONAL	1	TRUE	0	0.592215755605701	1		260	254	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673794	30673794	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	89	448	1	ENST00000376406.3:c.3166C>G	p.Gln1056Glu	p.Q1056E	ENST00000376406	NM_014641.2	1056	Cag/Gag	10/15	1	2	FACETS	0.516	0.458	0.577	0.516	0.458	0.577	SUBCLONAL	1	TRUE	1	0.592215755605701	2		449	583	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912777	100912777	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	123	355	0	ENST00000325455.5:c.2545A>G	p.Ile849Val	p.I849V	ENST00000325455	NM_001202474.3	849	Att/Gtt	7/8	1	2	FACETS	0.957	0.872	1	0.957	0.872	1	CLONAL	1	TRUE	1	0.592215755605701	2		355	434	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99451961	99451961	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	81	393	0	ENST00000268035.6:c.1295G>T	p.Trp432Leu	p.W432L	ENST00000268035	NM_000875.3	432	tGg/tTg	6/21	0.376648816657666	1	FACETS	0.456	0.404	0.512	0.456	0.404	0.512	SUBCLONAL	1	TRUE	0	0.592215755605701	1		393	422	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210914	36210914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749729184	NA	P-0051907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	157	841	0	ENST00000222270.7:c.665G>A	p.Arg222Gln	p.R222Q	ENST00000222270	NM_014727.1	222	cGg/cAg	3/37	1	2	FACETS	0.537	0.491	0.585	0.537	0.491	0.585	SUBCLONAL	1	TRUE	1	0.592215755605701	2		841	987	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753675	42753675	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	147	900	0	ENST00000222329.4:c.589G>T	p.Glu197Ter	p.E197*	ENST00000222329	NM_006494.2	197	Gag/Tag	4/4	1	2	FACETS	0.506	0.461	0.552	0.506	0.461	0.552	SUBCLONAL	1	TRUE	1	0.592215755605701	2		900	982	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39233636	39233636	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	161	426	0	ENST00000402219.2:c.2708A>C	p.Glu903Ala	p.E903A	ENST00000402219	NM_005633.3	903	gAa/gCa	17/23	0.592215755605701	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.592215755605701	1		426	354	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70005608	70005608	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	86	346	0	ENST00000394351.3:c.637G>A	p.Glu213Lys	p.E213K	ENST00000394351	NM_000248.3	213	Gaa/Aaa	7/9	0.376648816657666	1	FACETS	0.73	0.654	0.809	0.73	0.654	0.809	SUBCLONAL	1	TRUE	0	0.592215755605701	1		346	280	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482282	87482282	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs201888268	NA	P-0051907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	62	547	0	ENST00000277120.3:c.1569G>C	p.Lys523Asn	p.K523N	ENST00000277120		523	aaG/aaC	14/19	0.592215755605701	1	FACETS	0.409	0.355	0.468	0.409	0.355	0.468	SUBCLONAL	1	TRUE	0	0.592215755605701	1		547	360	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98011412	98011412	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	110	348	0	ENST00000289081.3:c.162G>C	p.Glu54Asp	p.E54D	ENST00000289081	NM_000136.2	54	gaG/gaC	2/15	0.592215755605701	1	FACETS	0.921	0.84	1	0.921	0.84	1	CLONAL	1	TRUE	0	0.592215755605701	1		348	284	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115842	8115843	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0051908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	206	491	0	ENST00000346208.3:c.1189dup	p.Ser397PhefsTer110	p.S397Ffs*110	ENST00000346208		396	-/T	6/6	0.233541572366099	3	FACETS	1	0.953	1	0.344	0.32	0.369	INDETERMINATE	1	TRUE	0	0.643066373818552	3		491	820	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965075	25965076	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0051908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	71	465	0	ENST00000435504.4:c.4130dup	p.Ser1377ArgfsTer43	p.S1377Rfs*43	ENST00000435504		1377	agc/agGc	13/13	0.197439012683506	2	FACETS	0.506	0.443	0.574	0.253	0.221	0.287	INDETERMINATE	1	TRUE	0	0.643066373818552	2		465	436	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032784	48032784	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs758428552	NA	P-0051908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	21	253	0	ENST00000234420.5:c.3584G>C	p.Ser1195Thr	p.S1195T	ENST00000234420	NM_000179.2	1195	aGt/aCt	7/10	0.197439012683506	2	FACETS	0.403	0.313	0.507	0.202	0.156	0.254	INDETERMINATE	1	TRUE	0	0.643066373818552	2		253	162	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060822	38060822	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	115	834	0	ENST00000250448.2:c.1167A>T	p.Lys389Asn	p.K389N	ENST00000250448	NM_004496.3	389	aaA/aaT	2/2	0.787784436925752	2	FACETS	0.991	0.939	1	0.991	0.939	1	CLONAL	2	TRUE	0	0.800377279362431	2		834	145	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794626	42794626	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	124	796	0	ENST00000575354.2:c.1706G>T	p.Gly569Val	p.G569V	ENST00000575354	NM_015125.3	569	gGc/gTc	10/20	0.445935399544249	5	FACETS	1	0.976	1	0.773	0.711	0.836	INDETERMINATE	2	TRUE	2	0.800377279362431	5		796	294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579419	7579419	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	168	771	0	ENST00000269305.4:c.268del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	90	Tcc/cc	4/11	0.354431232049357	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.354431232049357	1		771	592	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874373	151874373	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	25	295	0	ENST00000262189.6:c.8165T>C	p.Leu2722Ser	p.L2722S	ENST00000262189	NM_170606.2	2722	tTa/tCa	38/59	1	2	FACETS	0.455	0.359	0.565	0.455	0.359	0.565	SUBCLONAL	1	TRUE	1	0.354431232049357	2		295	310	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404348	139404348	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	144	772	0	ENST00000277541.6:c.2806G>T	p.Gly936Cys	p.G936C	ENST00000277541	NM_017617.3	936	Ggc/Tgc	18/34	1	2	FACETS	0.995	0.908	1	0.995	0.908	1	CLONAL	1	TRUE	1	0.354431232049357	2		772	817	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	29	373	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.0673622208536915	3	FACETS	0.598	0.479	0.732	0.299	0.239	0.366	INDETERMINATE	1	TRUE	1	0.275348329765712	3		373	401	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183540	185183540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	40	298	0	ENST00000265026.3:c.1394C>T	p.Ala465Val	p.A465V	ENST00000265026	NM_004721.4	465	gCg/gTg	9/14	1	2	FACETS	0.8	0.667	0.949	0.8	0.667	0.949	CLONAL	1	TRUE	1	0.275348329765712	2		298	363	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444519	187444519	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	39	545	0	ENST00000232014.4:c.1708G>A	p.Gly570Ser	p.G570S	ENST00000232014	NM_001130845.1	570	Ggt/Agt	7/10	1	2	FACETS	0.421	0.348	0.503	0.421	0.348	0.503	SUBCLONAL	1	TRUE	1	0.275348329765712	2		545	673	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675556	86675556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	15	194	0	ENST00000274376.6:c.2492G>A	p.Ser831Asn	p.S831N	ENST00000274376	NM_002890.2	831	aGt/aAt	19/25	1	2	FACETS	0.576	0.423	0.76	0.576	0.423	0.76	SUBCLONAL	1	TRUE	1	0.275348329765712	2		194	189	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124541	108124541	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0051911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	17	216	0	ENST00000278616.4:c.1899T>A	p.Cys633Ter	p.C633*	ENST00000278616	NM_000051.3	633	tgT/tgA	13/63	1	2	FACETS	0.722	0.542	0.934	0.722	0.542	0.934	CLONAL	1	TRUE	1	0.275348329765712	2		216	171	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478599	57478599	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	24	373	0	ENST00000371085.3:c.271A>G	p.Lys91Glu	p.K91E	ENST00000371085	NM_000516.4	91	Aaa/Gaa	4/13	1	2	FACETS	0.441	0.345	0.552	0.441	0.345	0.552	SUBCLONAL	1	TRUE	1	0.275348329765712	2		373	395	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781121	161781122	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	rs758718482	NA	P-0051921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	84	426	0	ENST00000366898.1:c.1283dup	p.Asn428LysfsTer141	p.N428Kfs*141	ENST00000366898	NM_004562.2	428	aat/aaAt	11/12	0.328754155106113	3	FACETS	0.742	0.656	0.833	0.371	0.328	0.417	SUBCLONAL	1	TRUE	1	0.467229265687474	3		426	598	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023189	33023189	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0051921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	202	563	0	ENST00000300177.4:c.298A>T	p.Lys100Ter	p.K100*	ENST00000300177	NM_001191322.1	100	Aag/Tag	2/2	0.268693395139586	2	FACETS	0.83	0.776	0.885	0.83	0.776	0.885	INDETERMINATE	2	TRUE	0	0.467229265687474	2		563	521	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724661	43724661	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	179	637	0	ENST00000382044.4:c.3406G>T	p.Gly1136Ter	p.G1136*	ENST00000382044	NM_001141980.1	1136	Gga/Tga	17/28	0.417431149788522	3	FACETS	1	0.985	1	0.426	0.393	0.459	CLONAL	1	TRUE	0	0.467229265687474	3		637	740	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628962	187628962	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	87	502	0	ENST00000441802.2:c.2020T>C	p.Cys674Arg	p.C674R	ENST00000441802	NM_005245.3	674	Tgt/Cgt	2/27	0.268693395139586	2	FACETS	0.763	0.678	0.854	0.382	0.339	0.427	INDETERMINATE	1	TRUE	0	0.467229265687474	2		502	488	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	84	230	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.3	2		230	430	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0051922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	11	325	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.220825678131042	3	FACETS	0.203	0.139	0.282	0.101	0.069	0.141	SUBCLONAL	1	TRUE	1	0.3	3		325	416	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278106	41278106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	70	360	0	ENST00000349496.5:c.1982G>A	p.Arg661Gln	p.R661Q	ENST00000349496	NM_001904.3	661	cGa/cAa	13/15	0.220825678131042	3	FACETS	1	0.914	1	0.529	0.462	0.601	CLONAL	1	TRUE	1	0.3	3		360	507	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0051922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	107	579	0	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	1	2	FACETS	0.957	0.859	1	0.957	0.859	1	CLONAL	1	TRUE	1	0.3	2		579	745	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0051922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	68	866	1	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.142726453472826	1	FACETS	0.432	0.374	0.494	0.432	0.374	0.494	INDETERMINATE	1	TRUE	0	0.3	1		867	893	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873223	71873223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	41	386	0	ENST00000357731.5:c.971G>A	p.Gly324Glu	p.G324E	ENST00000357731	NM_173808.2	324	gGg/gAg	7/7	1	2	FACETS	0.617	0.514	0.731	0.617	0.514	0.731	SUBCLONAL	1	TRUE	1	0.3	2		386	443	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106159	27106172	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGATGGAGCTAA	GAGGATGGAGCTAA	-	novel	NA	P-0051922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	45	461	0	ENST00000324856.7:c.5773_5786del	p.Asp1925PhefsTer15	p.D1925Ffs*15	ENST00000324856	NM_006015.4	1924	GAGGATGGAGCTAAg/g	20/20	1	2	FACETS	0.527	0.442	0.621	0.527	0.442	0.621	SUBCLONAL	1	TRUE	1	0.3	2		461	569	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021410	31021410	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	132	527	0	ENST00000375687.4:c.1409C>G	p.Ser470Cys	p.S470C	ENST00000375687	NM_015338.5	470	tCc/tGc	12/13	0.220825678131042	3	FACETS	1	0.98	1	0.65	0.59	0.712	CLONAL	1	TRUE	1	0.3	3		527	779	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143350350	143350350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	14	214	0	ENST00000262992.4:c.112G>A	p.Glu38Lys	p.E38K	ENST00000262992	NM_001101669.1	38	Gaa/Aaa	3/24	1	2	FACETS	0.691	0.503	0.916	0.691	0.503	0.916	SUBCLONAL	1	TRUE	1	0.3	2		214	135	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171400	123171402	+	inframe_deletion	In_Frame_Del	DEL	ATC	ATC	-	novel	NA	P-0051922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	29	197	0	ENST00000218089.9:c.314_316del	p.Ser105del	p.S105del	ENST00000218089	NM_001042749.1	104	gaATCa/gaa	6/35	1	1	FACETS	0.934	0.757	1	0.934	0.757	1	CLONAL	1	TRUE	0	0.3	1		197	176	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45800087	45800087	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	77	546	0	ENST00000450313.1:c.133C>T	p.Gln45Ter	p.Q45*	ENST00000450313	NM_012222.2	45	Cag/Tag	2/16	0.460902830885433	3	FACETS	0.889	0.787	0.997	0.296	0.262	0.333	CLONAL	1	TRUE	0	0.699754284131695	3		546	334	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445269	49445269	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	772	944	1	ENST00000301067.7:c.2197C>T	p.Gln733Ter	p.Q733*	ENST00000301067	NM_003482.3	733	Caa/Taa	10/54	0.699754284131695	8	FACETS	1	0.992	1			1	CLONAL	6	TRUE	NA	0.699754284131695	8		945	1097	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445487	49445487	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	165	804	0	ENST00000301067.7:c.1979C>A	p.Ser660Ter	p.S660*	ENST00000301067	NM_003482.3	660	tCa/tAa	10/54	0.699754284131695	8	FACETS	0.885	0.813	0.959			1	CLONAL	2	TRUE	NA	0.699754284131695	8		804	826	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346732	89346732	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770387752	NA	P-0051923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	16	582	0	ENST00000301030.4:c.6218C>T	p.Pro2073Leu	p.P2073L	ENST00000301030	NM_001256183.1	2073	cCg/cTg	9/13	1	2	FACETS	0.179	0.132	0.235	0.179	0.132	0.235	SUBCLONAL	1	TRUE	1	0.699754284131695	2		582	255	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519988	NA	P-0051923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	262	592	0	ENST00000269305.4:c.808T>C	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	Ttt/Ctt	8/11	0.162888990970714	6	FACETS	1	0.984	1			1	INDETERMINATE	6	TRUE	NA	0.699754284131695	6		592	295	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11172460	11172460	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	176	735	0	ENST00000358026.2:c.5008G>C	p.Asp1670His	p.D1670H	ENST00000358026	NM_001128849.1	1670	Gac/Cac	36/36	0.487726218927848	3	FACETS	1	0.989	1	0.682	0.633	0.731	CLONAL	1	TRUE	1	0.699754284131695	3		735	498	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719779	190719779	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	58	44	0	ENST00000441310.2:c.1781C>T	p.Pro594Leu	p.P594L	ENST00000441310	NM_000534.4	594	cCt/cTt	9/13	0.311449567851466	6	FACETS	1	0.952	1	0.395	0.346	0.445	INDETERMINATE	2	TRUE	0	0.699754284131695	6		44	168	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637588	176637588	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	40	240	0	ENST00000439151.2:c.2188C>G	p.Leu730Val	p.L730V	ENST00000439151	NM_022455.4	730	Ctc/Gtc	5/23	0.699754284131695	3	FACETS	0.721	0.605	0.848	0.24	0.201	0.283	SUBCLONAL	1	TRUE	0	0.699754284131695	3		240	214	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638483	176638483	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	74	544	0	ENST00000439151.2:c.3083C>A	p.Ser1028Tyr	p.S1028Y	ENST00000439151	NM_022455.4	1028	tCc/tAc	5/23	0.699754284131695	3	FACETS	0.995	0.88	1	0.332	0.293	0.372	CLONAL	1	TRUE	0	0.699754284131695	3		544	287	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158610	26158610	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	34	380	1	ENST00000289316.2:c.213C>G	p.Phe71Leu	p.F71L	ENST00000289316	NM_138720.2	71	ttC/ttG	1/2	0.334200762033655	6	FACETS	1	0.908	1	0.389	0.32	0.464	INDETERMINATE	1	TRUE	3	0.699754284131695	6		381	200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0051925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	125	629	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.224288400099295	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.224288400099295	1		631	777	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456414	32456414	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	136	731	0	ENST00000332351.3:c.478T>C	p.Phe160Leu	p.F160L	ENST00000332351	NM_024426.4	160	Ttc/Ctc	1/10	1	2	FACETS	0.771	0.702	0.844	1	0.987	1	SUBCLONAL	2	TRUE	1	0.224288400099295	2		731	786	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39708781	39708782	+	missense_variant	Missense_Mutation	DNP	AG	AG	TT	novel	NA	P-0051925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	59	244	0	ENST00000361337.2:c.392_393delinsTT	p.Glu131Val	p.E131V	ENST00000361337	NM_003286.2	131	gAG/gTT	6/21	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.224288400099295	2		244	502	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0051941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	162	276	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.870167626923518	2		276	356	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0051941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	195	410	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	0.515499296759915	1	FACETS	0.715	0.674	0.756	0.715	0.674	0.756	INDETERMINATE	1	TRUE	0	0.870167626923518	1		410	354	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176338	24176338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	265	769	0	ENST00000263121.7:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000263121	NM_003073.3	377	Cgt/Tgt	9/9	1	2	FACETS	0.937	0.885	0.99	0.937	0.885	0.99	CLONAL	1	TRUE	1	0.870167626923518	2		769	650	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148892	119148892	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs387906666	NA	P-0051941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	212	264	0	ENST00000264033.4:c.1112A>C	p.Tyr371Ser	p.Y371S	ENST00000264033	NM_005188.3	371	tAc/tCc	8/16	0.865401162378274	2	FACETS	0.955	0.922	0.986	0.955	0.922	0.986	CLONAL	2	TRUE	0	0.870167626923518	2		264	255	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415622	49415622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	75	349	0	ENST00000301067.7:c.16555G>A	p.Asp5519Asn	p.D5519N	ENST00000301067	NM_003482.3	5519	Gat/Aat	54/54	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.870167626923518	NA		349	611	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586439	189586439	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	60	393	0	ENST00000264731.3:c.1063G>T	p.Asp355Tyr	p.D355Y	ENST00000264731	NM_003722.4	355	Gat/Tat	8/14	1	2	FACETS	0.46	0.399	0.525	0.46	0.399	0.525	SUBCLONAL	1	TRUE	1	0.870167626923518	2		393	300	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622478	158622478	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	143	339	0	ENST00000263640.3:c.1021A>G	p.Asn341Asp	p.N341D	ENST00000263640	NM_001105.4	341	Aat/Gat	8/11	0.252629567588301	3	FACETS	0.942	0.861	1	0.942	0.861	1	CLONAL	2	TRUE	1	0.252629567588301	3		339	677	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069292	30069292	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1161410708	NA	P-0051943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	92	543	2	ENST00000338641.4:c.1160del	p.Lys387ArgfsTer39	p.K387Rfs*39	ENST00000338641	NM_000268.3	386	gAa/ga	12/16	0.252629567588301	1	FACETS	0.778	0.69	0.871	0.778	0.69	0.871	SUBCLONAL	1	TRUE	0	0.252629567588301	1		545	818	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519126	187519126	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs1439921171	NA	P-0051943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	32	348	0	ENST00000441802.2:c.12257G>C	p.Arg4086Thr	p.R4086T	ENST00000441802	NM_005245.3	4086	aGg/aCg	23/27	1	2	FACETS	0.448	0.362	0.544	0.448	0.362	0.544	SUBCLONAL	1	TRUE	1	0.252629567588301	2		348	566	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	43	230	0				ENST00000310581	NM_198253.2	-/1132			0.245200770548335	0	FACETS	0.49	0.426	0.554			1	INDETERMINATE	1	TRUE	0	0.658590411538592	0		230	91	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0051944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	555	790	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.658590411538592	2	FACETS	0.889	0.872	0.904	1	0.998	1	CLONAL	3	TRUE	0	0.658590411538592	2		790	632	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548322	41548322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	136	309	1	ENST00000263253.7:c.3110C>T	p.Ser1037Leu	p.S1037L	ENST00000263253	NM_001429.3	1037	tCa/tTa	16/31	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.658590411538592	2		310	329	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045981	26045981	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1377734473	NA	P-0051944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	148	402	1	ENST00000540144.1:c.343G>A	p.Ala115Thr	p.A115T	ENST00000540144	NM_003531.2	115	Gct/Act	1/1	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.658590411538592	2		403	379	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815580	139815580	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747252505	NA	P-0051944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	262	633	0	ENST00000247668.2:c.1051G>A	p.Asp351Asn	p.D351N	ENST00000247668	NM_021138.3	351	Gat/Aat	9/11	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.658590411538592	2		633	629	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881495	48881495	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0051944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	112	248	1	ENST00000267163.4:c.217A>T	p.Arg73Ter	p.R73*	ENST00000267163	NM_000321.2	73	Aga/Tga	2/27	0.658590411538592	1	FACETS	0.776	0.732	0.817	1	0.991	1	SUBCLONAL	2	TRUE	0	0.658590411538592	1		249	147	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63700059	63700059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	110	236	0	ENST00000279873.7:c.394G>A	p.Glu132Lys	p.E132K	ENST00000279873	NM_032199.2	132	Gag/Aag	3/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.658590411538592	2		236	249	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720860	89720861	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0051944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	161	268	0	ENST00000371953.3:c.1011_1012insC	p.Ser338LeufsTer5	p.S338Lfs*5	ENST00000371953	NM_000314.4	337	-/C	8/9	0.658590411538592	1	FACETS	0.8	0.764	0.833	1	0.994	1	SUBCLONAL	2	TRUE	0	0.658590411538592	1		268	205	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562673	95562673	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	144	310	0	ENST00000393063.1:c.4584G>C	p.Trp1528Cys	p.W1528C	ENST00000393063	NM_030621.3	1528	tgG/tgC	24/28	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.658590411538592	2		310	309	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860626	3860626	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0051944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	224	574	0	ENST00000262367.5:c.953C>G	p.Ser318Ter	p.S318*	ENST00000262367	NM_004380.2	318	tCa/tGa	3/31	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.658590411538592	2		574	540	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661663	227661663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	175	551	1	ENST00000305123.5:c.1792C>T	p.His598Tyr	p.H598Y	ENST00000305123	NM_005544.2	598	Cac/Tac	1/2	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.658590411538592	2		552	389	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181944	38181944	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	161	489	0	ENST00000396334.3:c.568G>C	p.Glu190Gln	p.E190Q	ENST00000396334	NM_002468.4	190	Gag/Cag	3/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.658590411538592	2		489	424	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177853	142177853	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	121	278	0	ENST00000350721.4:c.7450G>C	p.Asp2484His	p.D2484H	ENST00000350721	NM_001184.3	2484	Gat/Cat	44/47	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.658590411538592	2		278	278	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670667	86670667	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	82	226	0	ENST00000274376.6:c.1945C>T	p.Pro649Ser	p.P649S	ENST00000274376	NM_002890.2	649	Cct/Tct	15/25	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.658590411538592	2		226	192	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041589	47041611	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTGTACTGGGATGGGGAGAGG	ACCTGTACTGGGATGGGGAGAGG	-	novel	NA	P-0051944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	215	323	0	ENST00000377604.3:c.1814_1836del	p.Tyr605SerfsTer15	p.Y605Sfs*15	ENST00000377604	NM_001204468.1	605	tACCTGTACTGGGATGGGGAGAGG/t	17/24	0.189717933178882	2	FACETS	0.857	0.828	0.883			1	INDETERMINATE	3	TRUE	NA	0.658590411538592	2		323	254	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696688	47696688	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519971	NA	P-0051945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	42	415	0	ENST00000347630.2:c.260A>G	p.Tyr87Cys	p.Y87C	ENST00000347630	NM_001007230.1	87	tAc/tGc	5/11	1	2	FACETS	0.962	0.805	1	0.962	0.805	1	CLONAL	1	TRUE	1	0.24	2		415	364	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061192	38061194	+	missense_variant	Missense_Mutation	TNP	AAG	AAG	CTT	novel	NA	P-0051945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	16	334	0	ENST00000250448.2:c.795_797inv	p.Phe266Ser	p.F266S	ENST00000250448	NM_004496.3	265	cgCTTc/cgAAGc	2/2	1	2	FACETS	0.57	0.422	0.746	0.57	0.422	0.746	SUBCLONAL	1	TRUE	1	0.24	2		334	234	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288573	33288573	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs202141130	NA	P-0051969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	167	448	1	ENST00000374542.5:c.979C>T	p.Arg327Ter	p.R327*	ENST00000374542	NM_001141970.1	327	Cga/Tga	3/8	0.10201063223213	8	FACETS	0.974	0.899	1	1	0.991	1	CLONAL	7	FALSE	4	0.10201063223213	8		449	627	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37083803	37083803	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	281	430	0	ENST00000231790.2:c.1712T>G	p.Phe571Cys	p.F571C	ENST00000231790	NM_000249.3	571	tTt/tGt	15/19	0.10201063223213	8	FACETS	1	0.976	1	1	0.995	1	CLONAL	7	FALSE	4	0.10201063223213	8		430	963	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281177	142281177	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	45	440	0	ENST00000350721.4:c.1067T>A	p.Phe356Tyr	p.F356Y	ENST00000350721	NM_001184.3	356	tTt/tAt	4/47	0.10201063223213	8	FACETS	1	0.954	1	0.358	0.3	0.423	CLONAL	1	FALSE	4	0.10201063223213	8		440	805	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755128667	NA	P-0051971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	152	736	0	ENST00000407977.2:c.1976dup	p.Pro660SerfsTer87	p.P660Sfs*87	ENST00000407977		659	ggt/ggGt	9/10	0.305672529496473	3	FACETS	0.87	0.793	0.951	0.29	0.264	0.317	CLONAL	1	TRUE	0	0.305672529496473	3		736	1318	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636766	8636766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776233840	NA	P-0051971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	101	471	0	ENST00000356435.5:c.143C>T	p.Thr48Met	p.T48M	ENST00000356435		48	aCg/aTg	2/35	0.291901908598217	2	FACETS	0.9	0.805	1	0.45	0.402	0.501	CLONAL	1	TRUE	0	0.305672529496473	2		471	734	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577063	7577064	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCTTGCGG	novel	NA	P-0051971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	585	720	0	ENST00000269305.4:c.867_874dup	p.Lys292ThrfsTer56	p.K292Tfs*56	ENST00000269305	NM_001126112.2	292	aaa/aCCGCAAGAaa	8/11	0.305672529496473	3	FACETS	0.961	0.924	0.999	0.961	0.924	0.999	CLONAL	3	TRUE	0	0.305672529496473	3		720	1530	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092951	29092951	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	306	493	0	ENST00000328354.6:c.1033C>A	p.His345Asn	p.H345N	ENST00000328354	NM_007194.3	345	Cac/Aac	10/15	0.286988080344816	3	FACETS	0.924	0.874	0.974	0.924	0.874	0.974	CLONAL	3	TRUE	0	0.305672529496473	3		493	833	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426907	6426907	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	311	434	0	ENST00000356142.4:c.100C>G	p.Pro34Ala	p.P34A	ENST00000356142	NM_018890.3	34	Cct/Gct	2/7	0.305672529496473	6	FACETS	0.956	0.905	1	0.956	0.905	1	CLONAL	4	TRUE	2	0.305672529496473	6		434	857	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0051972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	298	435	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.986	1	1	0.996	1	CLONAL	2	TRUE	1	0.271355479083246	2		436	967	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0051972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	370	502	0	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	0.238805908370888	1	FACETS	0.993	0.949	1	1	0.997	1	CLONAL	3	TRUE	0	0.271355479083246	1		502	791	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477837	140477851	+	inframe_deletion	In_Frame_Del	DEL	TAGGTGCTGTCACAT	TAGGTGCTGTCACAT	-	novel	NA	P-0051972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	374	531	0	ENST00000288602.6:c.1457_1471del	p.Asn486_Pro490del	p.N486_P490del	ENST00000288602	NM_004333.4	486	aATGTGACAGCACCTAca/aca	12/18	0.271355479083246	3	FACETS	0.893	0.848	0.939	1	0.994	1	CLONAL	3	TRUE	1	0.271355479083246	3		531	1168	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183739	10183739	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs5030802	NA	P-0051975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	160	774	1	ENST00000256474.2:c.208G>T	p.Glu70Ter	p.E70*	ENST00000256474	NM_000551.3	70	Gag/Tag	1/3	0.486652580359651	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.486652580359651	1		775	482	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348739	11348741	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	novel	NA	P-0051975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	179	458	0	ENST00000332029.2:c.595_597del	p.Val199del	p.V199del	ENST00000332029	NM_003745.1	199	GTC/-	2/2	1	2	FACETS	0.885	0.817	0.956	0.885	0.817	0.956	CLONAL	1	TRUE	1	0.486652580359651	2		458	831	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295315	1295315	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0051975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	257	376	0				ENST00000310581	NM_198253.2	-/1132			0.372342585222299	3	FACETS	0.974	0.918	1	0.974	0.918	1	CLONAL	2	TRUE	1	0.486652580359651	3		376	674	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146233	38146233	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	162	533	0	ENST00000317025.8:c.3273C>G	p.Asp1091Glu	p.D1091E	ENST00000317025	NM_023034.1	1091	gaC/gaG	19/24	1	2	FACETS	0.884	0.813	0.959	0.884	0.813	0.959	CLONAL	1	TRUE	1	0.486652580359651	2		533	753	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0051976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	51	629	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.32	0.27	0.375	0.32	0.27	0.375	SUBCLONAL	1	TRUE	1	0.270765806227911	2		631	1178	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0051976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1277	114	681	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.605	0.543	0.672	0.605	0.543	0.672	SUBCLONAL	1	TRUE	1	0.270765806227911	2		681	1391	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482926	140482927	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs777474487	NA	P-0051976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	61	539	0	ENST00000288602.6:c.1208dup	p.Ala404CysfsTer9	p.A404Cfs*9	ENST00000288602	NM_004333.4	403	cct/ccCt	10/18	0.270765806227911	3	FACETS	0.452	0.388	0.521	0.226	0.194	0.261	SUBCLONAL	1	TRUE	1	0.270765806227911	3		539	1133	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847275	68847277	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0051976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	146	528	0	ENST00000261769.5:c.1199_1201del	p.Asp400del	p.D400del	ENST00000261769	NM_004360.3	399	acTGAt/act	9/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.270765806227911	2		528	895	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405962	49405962	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	157	548	0	ENST00000418115.1:c.176A>G	p.Asp59Gly	p.D59G	ENST00000418115	NM_001664.2	59	gAc/gGc	3/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.270765806227911	2		548	978	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441815	49441816	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs756471180	NA	P-0051976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	157	558	2	ENST00000301067.7:c.4168dup	p.Ala1390GlyfsTer42	p.A1390Gfs*42	ENST00000301067	NM_003482.3	1390	gca/gGca	14/54	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.270765806227911	2		560	1041	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466039	69466039	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1225090625	NA	P-0051976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	188	704	0	ENST00000227507.2:c.877G>A	p.Val293Met	p.V293M	ENST00000227507	NM_053056.2	293	Gtg/Atg	5/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.270765806227911	2		704	1207	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441822	49441823	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0051976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	171	544	2	ENST00000301067.7:c.4161_4162delinsTT	p.Arg1388Trp	p.R1388W	ENST00000301067	NM_003482.3	1387	ggCCgg/ggTTgg	14/54	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.270765806227911	2		546	1021	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988447	36988447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1004953614	NA	P-0051976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	45	468	0	ENST00000354822.5:c.206C>T	p.Ala69Val	p.A69V	ENST00000354822	NM_001079668.2	69	gCg/gTg	2/3	1	2	FACETS	0.404	0.339	0.478	0.404	0.339	0.478	SUBCLONAL	1	TRUE	1	0.270765806227911	2		468	822	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957772	1957772	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	179	677	0	ENST00000382891.5:c.2738A>G	p.His913Arg	p.H913R	ENST00000382891	NM_133335.3	913	cAc/cGc	15/22	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.270765806227911	2		677	1214	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285571	38285571	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	52	463	0	ENST00000425967.3:c.582G>T	p.Lys194Asn	p.K194N	ENST00000425967	NM_001174067.1	194	aaG/aaT	6/19	0.270765806227911	3	FACETS	0.427	0.362	0.499	0.213	0.181	0.25	SUBCLONAL	1	TRUE	1	0.270765806227911	3		463	1022	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0051977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	158	652	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.162768074772265	2	FACETS	0.976	0.895	1	0.976	0.895	1	CLONAL	2	FALSE	0	0.205189643047799	2		652	789	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0051977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	94	621	2	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	0.205189643047799	1	FACETS	0.878	0.779	0.983	0.878	0.779	0.983	CLONAL	1	FALSE	0	0.205189643047799	1		623	937	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371633	55371633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs931390946	NA	P-0051977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	79	634	1	ENST00000297316.4:c.323C>T	p.Ala108Val	p.A108V	ENST00000297316	NM_022454.3	108	gCg/gTg	2/2	0.205189643047799	3	FACETS	0.858	0.752	0.971	0.429	0.376	0.486	CLONAL	1	FALSE	1	0.205189643047799	3		635	990	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270108	66270108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756653935	NA	P-0051977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	66	413	0	ENST00000273854.3:c.1774G>A	p.Val592Ile	p.V592I	ENST00000273854	NM_004439.5	592	Gtc/Atc	8/18	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	1	0.205189643047799	2		413	564	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804396	46804396	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1206296287	NA	P-0051977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	135	485	0	ENST00000290295.7:c.611G>A	p.Gly204Glu	p.G204E	ENST00000290295	NM_006361.5	204	gGg/gAg	2/2	0.205189643047799	3	FACETS	1	0.916	1	1	0.916	1	CLONAL	2	FALSE	1	0.205189643047799	3		485	721	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164458	47164458	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	76	390	0	ENST00000409792.3:c.1668del	p.Lys556AsnfsTer23	p.K556Nfs*23	ENST00000409792	NM_014159.6	556	aaA/aa	3/21	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	FALSE	1	0.205189643047799	2		390	705	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149434799	149434799	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0051977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	66	545	2	ENST00000286301.3:c.2654+1G>A		p.X885_splice	ENST00000286301	NM_005211.3	885			1	2	FACETS	0.768	0.665	0.879	0.768	0.665	0.879	SUBCLONAL	1	FALSE	1	0.205189643047799	2		547	838	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0051978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	192	396	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.532852075969541	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.566832059471817	1		396	447	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	76	312	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.566832059471817	1	FACETS	0.709	0.629	0.793	0.709	0.629	0.793	SUBCLONAL	1	TRUE	0	0.566832059471817	1		312	271	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921566	178921566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793349	NA	P-0051978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	104	336	0	ENST00000263967.3:c.1048G>A	p.Asp350Asn	p.D350N	ENST00000263967	NM_006218.2	350	Gac/Aac	5/21	0.532852075969541	1	FACETS	0.949	0.863	1	0.949	0.863	1	CLONAL	1	TRUE	0	0.566832059471817	1		336	277	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117311	115117311	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	114	310	0	ENST00000257566.3:c.863del	p.Lys288ArgfsTer2	p.K288Rfs*2	ENST00000257566	NM_016569.3	288	aAg/ag	4/8	0.566832059471817	3	FACETS	0.91	0.822	1	0.455	0.411	0.502	CLONAL	1	TRUE	1	0.566832059471817	3		310	567	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111475	8111479	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAC	CAGAC	-	novel	NA	P-0051978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	236	632	1	ENST00000346208.3:c.963_967del	p.Gln321HisfsTer29	p.Q321Hfs*29	ENST00000346208		321	CAGACc/c	5/6	1	2	FACETS	0.974	0.911	1	0.974	0.911	1	CLONAL	1	TRUE	1	0.566832059471817	2		633	855	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998865	100998865	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	266	765	0	ENST00000325455.5:c.937C>G	p.His313Asp	p.H313D	ENST00000325455	NM_001202474.3	313	Cac/Gac	1/8	1	2	FACETS	0.962	0.903	1	0.962	0.903	1	CLONAL	1	TRUE	1	0.566832059471817	2		765	976	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0051979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	73	368	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	0.458769296195201	3	FACETS	1	0.97	1	0.641	0.571	0.713	INDETERMINATE	1	TRUE	1	0.780198866811036	3		368	203	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0051979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	347	561	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	0.780198866811036	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.780198866811036	1		561	529	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398280	25398281	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0051979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	119	423	0	ENST00000311936.3:c.38_39delinsTT	p.Gly13Val	p.G13V	ENST00000311936	NM_004985.3	13	gGC/gTT	2/5	0.329840466809461	1	FACETS	0.547	0.5	0.596	0.547	0.5	0.596	INDETERMINATE	1	TRUE	0	0.780198866811036	1		423	340	SUCCESS
APC	324	MSKCC	GRCh37	5	112175588	112175588	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	155	343	0	ENST00000257430.4:c.4298del	p.Pro1433GlnfsTer40	p.P1433Qfs*40	ENST00000257430	NM_000038.5	1433	Cca/ca	16/16	0.458769296195201	3	FACETS	0.858	0.799	0.917	0.858	0.799	0.917	INDETERMINATE	2	TRUE	1	0.780198866811036	3		343	322	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349019	89349019	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	216	706	0	ENST00000301030.4:c.3931C>T	p.Arg1311Ter	p.R1311*	ENST00000301030	NM_001256183.1	1311	Cga/Tga	9/13	0.253118143939443	2	FACETS	0.668	0.622	0.715	0.334	0.311	0.358	INDETERMINATE	1	TRUE	0	0.780198866811036	2		706	829	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201828	66201828	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779738574	NA	P-0051979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	134	371	0	ENST00000273854.3:c.2674G>A	p.Glu892Lys	p.E892K	ENST00000273854	NM_004439.5	892	Gag/Aag	16/18	0.244495828911941	1	FACETS	0.593	0.546	0.642	0.593	0.546	0.642	INDETERMINATE	1	TRUE	0	0.780198866811036	1		371	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0051980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	157	924	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.158007877869683	2	FACETS	0.793	0.727	0.863	0.793	0.727	0.863	SUBCLONAL	2	TRUE	0	0.230625433247559	2		924	858	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274568	198274568	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	69	628	0	ENST00000335508.6:c.830C>G	p.Ala277Gly	p.A277G	ENST00000335508	NM_012433.2	277	gCg/gGg	7/25	0.214554974998619	3	FACETS	0.945	0.823	1	0.473	0.411	0.539	CLONAL	1	TRUE	1	0.230625433247559	3		628	706	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808916	3808916	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	367	642	0	ENST00000262367.5:c.3308G>A	p.Arg1103Gln	p.R1103Q	ENST00000262367	NM_004380.2	1103	cGa/cAa	17/31	1	2	FACETS	0.983	0.938	1	0.983	0.938	1	CLONAL	1	TRUE	1	0.912973381565385	2		642	818	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593607	+	protein_altering_variant	In_Frame_Del	DEL	AGTGGAA	AGTGGAA	G	novel	NA	P-0051981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	153	411	0	ENST00000288135.5:c.1667_1673delinsG	p.Gln556_Lys558delinsArg	p.Q556_K558delinsR	ENST00000288135	NM_000222.2	556	cAGTGGAAg/cGg	11/21	0.912973381565385	1	FACETS	0.925	0.881	0.965	0.925	0.881	0.965	CLONAL	1	TRUE	0	0.912973381565385	1		411	197	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822460	72822460	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	300	737	0	ENST00000268489.5:c.9715A>G	p.Lys3239Glu	p.K3239E	ENST00000268489	NM_006885.3	3239	Aaa/Gaa	10/10	1	2	FACETS	1	0.967	1	1	0.997	1	CLONAL	4	TRUE	1	0.164253133134596	2		737	885	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593648	55593649	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACCCAACACAACTTCCTTATGATTTCA	novel	NA	P-0051982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	156	431	0	ENST00000288135.5:c.1737_1738insTTCAACCCAACACAACTTCCTTATGAT	p.Asp579_His580insPheAsnProThrGlnLeuProTyrAsp	p.D579_H580insFNPTQLPYD	ENST00000288135	NM_000222.2	572	gac/gACCCAACACAACTTCCTTATGATTTCAac	11/21	1	2	FACETS	0.967	0.888	1	1	0.993	1	CLONAL	3	TRUE	1	0.164253133134596	2		431	655	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0051983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	45	299	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.989	0.835	1	0.989	0.835	1	CLONAL	1	TRUE	1	0.28	2		299	325	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138729528	NA	P-0051983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	131	701	0	ENST00000269305.4:c.523C>G	p.Arg175Gly	p.R175G	ENST00000269305	NM_001126112.2	175	Cgc/Ggc	5/11	0.298027581523697	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.28	1		701	549	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027153	49027156	+	frameshift_variant	Frame_Shift_Del	DEL	AAAC	AAAC	-	novel	NA	P-0051983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	57	394	0	ENST00000267163.4:c.1722_1725del	p.Lys574AsnfsTer36	p.K574Nfs*36	ENST00000267163	NM_000321.2	574	AAACaa/aa	18/27	1	2	FACETS	0.932	0.801	1	0.932	0.801	1	CLONAL	1	TRUE	1	0.28	2		394	437	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653782	89653783	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	TC	rs786203477	NA	P-0051983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	32	364	0	ENST00000371953.3:c.81_82insCT	p.Ile28LeufsTer27	p.I28Lfs*27	ENST00000371953	NM_000314.4	27	tat/taTCt	2/9	0.298027581523697	1	FACETS	0.533	0.433	0.646	0.533	0.433	0.646	SUBCLONAL	1	TRUE	0	0.28	1		364	369	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228085	36228085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	36	784	0	ENST00000222270.7:c.7471C>T	p.Arg2491Cys	p.R2491C	ENST00000222270	NM_014727.1	2491	Cgt/Tgt	33/37	1	2	FACETS	0.388	0.318	0.468	0.388	0.318	0.468	SUBCLONAL	1	TRUE	1	0.28	2		784	662	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78420971	78420972	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0051984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	123	401	1	ENST00000370768.2:c.1748_1749del	p.Thr583LysfsTer29	p.T583Kfs*29	ENST00000370768	NM_003902.3	583	aCC/a	18/20	1	2	FACETS	0.517	0.468	0.568	0.517	0.468	0.568	SUBCLONAL	1	TRUE	1	0.736847960059423	2		402	646	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913517	NA	P-0051984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	213	405	0	ENST00000288135.5:c.1676T>G	p.Val559Gly	p.V559G	ENST00000288135	NM_000222.2	559	gTt/gGt	11/21	1	2	FACETS	0.993	0.93	1	0.993	0.93	1	CLONAL	1	TRUE	1	0.736847960059423	2		405	582	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436680	8436680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201582858	NA	P-0051984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	101	349	0	ENST00000356435.5:c.3998G>A	p.Ser1333Asn	p.S1333N	ENST00000356435		1333	aGc/aAc	24/35	1	2	FACETS	0.563	0.505	0.624	0.563	0.505	0.624	SUBCLONAL	1	TRUE	1	0.736847960059423	2		349	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0051986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	47	655	4	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.989	0.832	1	0.989	0.832	1	CLONAL	1	TRUE	1	0.11	2		659	864	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844180	68844180	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	48	716	0	ENST00000261769.5:c.768T>G	p.Asn256Lys	p.N256K	ENST00000261769	NM_004360.3	256	aaT/aaG	6/16	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.11	2		716	833	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990463	69990463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868605472	NA	P-0051986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	32	432	0	ENST00000394351.3:c.422C>T	p.Ala141Val	p.A141V	ENST00000394351	NM_000248.3	141	gCt/gTt	4/9	1	2	FACETS	0.946	0.766	1	0.946	0.766	1	CLONAL	1	TRUE	1	0.11	2		432	615	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560464	95560464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	571	607	0	ENST00000393063.1:c.5125G>A	p.Asp1709Asn	p.D1709N	ENST00000393063	NM_030621.3	1709	Gat/Aat	25/28	0.790647920521532	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.790746786201682	3		607	986	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562837	95562837	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	187	396	0	ENST00000393063.1:c.4420A>G	p.Thr1474Ala	p.T1474A	ENST00000393063	NM_030621.3	1474	Acc/Gcc	24/28	0.790647920521532	3	FACETS	1	0.962	1	0.528	0.49	0.567	CLONAL	1	TRUE	1	0.790746786201682	3		396	625	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781199	3781211	+	frameshift_variant	Frame_Shift_Del	DEL	CACAGTGCAGTGC	CACAGTGCAGTGC	-	novel	NA	P-0051990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	359	791	0	ENST00000262367.5:c.5154_5166del	p.Trp1718CysfsTer22	p.W1718Cfs*22	ENST00000262367	NM_004380.2	1718	tgGCACTGCACTGTG/tg	30/31	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.790746786201682	2		791	876	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857626	9857626	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	211	514	0	ENST00000330684.3:c.3775A>G	p.Asn1259Asp	p.N1259D	ENST00000330684	NM_001134407.1	1259	Aac/Gac	13/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.790746786201682	2		514	494	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143447	30143447	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	204	410	0	ENST00000389048.3:c.79C>T	p.Gln27Ter	p.Q27*	ENST00000389048	NM_004304.4	27	Cag/Tag	1/29	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.790746786201682	2		410	431	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131271	202131271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	197	600	0	ENST00000358485.4:c.239C>T	p.Ser80Phe	p.S80F	ENST00000358485	NM_001080125.1	80	tCc/tTc	2/9	1	2	FACETS	0.968	0.904	1	0.968	0.904	1	CLONAL	1	TRUE	1	0.790746786201682	2		600	515	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50490683	50490684	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	T	novel	NA	P-0051990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	354	632	0	ENST00000394963.4:c.1320_1321delinsT	p.Met441CysfsTer2	p.M441Cfs*2	ENST00000394963	NM_003076.4	440	ttCAtg/ttTtg	11/13	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.790746786201682	2		632	777	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0051994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	254	423	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.46932729918417	2		423	727	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0051994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	70	99	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	1	2	FACETS	0.909	0.813	1	1	0.983	1	CLONAL	2	TRUE	1	0.46932729918417	2		99	164	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814157	76814157	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	201	204	0	ENST00000373344.5:c.6487T>G	p.Tyr2163Asp	p.Y2163D	ENST00000373344	NM_000489.3	2163	Tat/Gat	29/35	1	1	FACETS	1	0.985	1	1	0.995	1	CLONAL	2	TRUE	0	0.46932729918417	1		204	300	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	102	230	0				ENST00000310581	NM_198253.2	-/1132			0.510624595190867	1	FACETS	0.425	0.383	0.469	0.425	0.383	0.469	SUBCLONAL	1	TRUE	0	0.754408885458836	1		230	396	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39317380	39317380	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	305	596	0	ENST00000373001.3:c.806A>G	p.Tyr269Cys	p.Y269C	ENST00000373001	NM_022157.3	269	tAc/tGc	5/7	1	2	FACETS	0.938	0.887	0.99	0.938	0.887	0.99	CLONAL	1	TRUE	1	0.754408885458836	2		596	862	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571892	64571892	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	339	788	0	ENST00000312049.6:c.1747T>C	p.Ser583Pro	p.S583P	ENST00000312049	NM_130799.2	583	Tcg/Ccg	10/10	0.543068706178247	1	FACETS	0.596	0.565	0.627	0.596	0.565	0.627	SUBCLONAL	1	TRUE	0	0.754408885458836	1		788	939	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788617	3788617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519884	NA	P-0051995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	509	419	1	ENST00000262367.5:c.4337G>A	p.Arg1446His	p.R1446H	ENST00000262367	NM_004380.2	1446	cGc/cAc	26/31	0.445502452476974	2	FACETS	0.828	0.801	0.855	0.828	0.801	0.855	INDETERMINATE	2	TRUE	0	0.754408885458836	2		420	815	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579349	7579349	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1567555667	NA	P-0051995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	412	681	0	ENST00000269305.4:c.338T>G	p.Phe113Cys	p.F113C	ENST00000269305	NM_001126112.2	113	tTc/tGc	4/11	0.693531462681826	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.754408885458836	1		681	665	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56411614	56411614	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1325186559	NA	P-0051995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	231	403	0	ENST00000348428.3:c.1798A>G	p.Ile600Val	p.I600V	ENST00000348428	NM_006785.3	600	Att/Gtt	15/17	0.754408885458836	1	FACETS	0.97	0.921	1	0.97	0.921	1	CLONAL	1	TRUE	0	0.754408885458836	1		403	393	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048638	180048638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	161	711	0	ENST00000261937.6:c.1924C>T	p.Arg642Cys	p.R642C	ENST00000261937	NM_182925.4	642	Cgc/Tgc	13/30	0.543068706178247	1	FACETS	0.327	0.299	0.355	0.327	0.299	0.355	SUBCLONAL	1	TRUE	0	0.754408885458836	1		711	814	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8733783	8733783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	565	491	0	ENST00000356435.5:c.61G>A	p.Glu21Lys	p.E21K	ENST00000356435		21	Gag/Aag	1/35	0.749121045269887	2	FACETS	0.973	0.947	0.998	0.973	0.947	0.998	CLONAL	2	TRUE	0	0.754408885458836	2		491	770	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950055	44950057	+	frameshift_variant	Frame_Shift_Del	DEL	GGA	GGA	C	novel	NA	P-0051995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	277	464	0	ENST00000377967.4:c.3824_3826delinsC	p.Trp1275SerfsTer15	p.W1275Sfs*15	ENST00000377967	NM_021140.2	1275	tGGAat/tCat	26/29	0.754408885458836	1	FACETS	0.996	0.951	1	0.996	0.951	1	CLONAL	1	TRUE	0	0.754408885458836	1		464	459	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0051996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	53	359	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.873	0.745	1	0.873	0.745	1	CLONAL	1	TRUE	1	0.237662554833845	2		359	511	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849442	68849453	+	inframe_deletion	In_Frame_Del	DEL	CAGTACATTCTA	CAGTACATTCTA	-	novel	NA	P-0051996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	73	596	0	ENST00000261769.5:c.1347_1358del	p.Gln449_Leu452del	p.Q449_L452del	ENST00000261769	NM_004360.3	449	CAGTACATTCTA/-	10/16	0.237662554833845	1	FACETS	0.753	0.658	0.856	0.753	0.658	0.856	SUBCLONAL	1	TRUE	0	0.237662554833845	1		596	719	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0051997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	59	419	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.120266944365818	3	FACETS	0.911	0.785	1	0.455	0.392	0.524	INDETERMINATE	1	TRUE	1	0.33201405609902	3		419	455	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998891	11998891	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0051997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	35	226	0	ENST00000353533.5:c.394-1del		p.X132_splice	ENST00000353533	NM_003010.3	132			1	2	FACETS	0.847	0.698	1	0.847	0.698	1	CLONAL	1	TRUE	1	0.33201405609902	2		226	249	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	101	373	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	1	FALSE	NA	0.3540360964595	2		373	463	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0051998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	54	435	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.115984430968395	0	FACETS	0.503	0.431	0.581			1	INDETERMINATE	1	FALSE	0	0.3540360964595	0		436	392	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0051998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	54	435	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	1	2	FACETS	0.889	0.763	1	0.889	0.763	1	CLONAL	1	FALSE	1	0.3540360964595	2		435	343	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0051998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	113	561	1	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	1	2	FACETS	0.973	0.877	1	0.973	0.877	1	CLONAL	1	FALSE	1	0.3540360964595	2		562	656	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730008	41730008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537531066	NA	P-0051998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	72	630	0	ENST00000242208.4:c.521G>A	p.Arg174His	p.R174H	ENST00000242208	NM_002192.2	174	cGc/cAc	3/3	1	2	FACETS	0.882	0.773	0.999	0.882	0.773	0.999	CLONAL	1	FALSE	1	0.3540360964595	2		630	461	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584605	48584606	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0051998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	36	479	0	ENST00000342988.3:c.779dup	p.Tyr260Ter	p.Y260*	ENST00000342988	NM_005359.5	260	tac/tAac	6/12	0.3540360964595	1	FACETS	0.528	0.435	0.631	0.528	0.435	0.631	SUBCLONAL	1	FALSE	0	0.3540360964595	1		479	317	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937896	36937896	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	86	821	0	ENST00000361632.4:c.940del	p.Leu314CysfsTer14	p.L314Cfs*14	ENST00000361632		314	Ctg/tg	7/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.3540360964595	2		821	419	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492877	56492877	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	44	366	0	ENST00000407977.2:c.62T>A	p.Leu21Gln	p.L21Q	ENST00000407977		21	cTg/cAg	2/10	0.298277379865493	0	FACETS	0.692	0.586	0.808			1	SUBCLONAL	1	FALSE	0	0.3540360964595	0		366	232	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0051999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	39	321	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.313	0.259	0.373	0.313	0.259	0.373	SUBCLONAL	1	TRUE	1	0.54	2		321	462	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624302	89624302	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876661010	NA	P-0051999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	248	626	0	ENST00000371953.3:c.76A>C	p.Thr26Pro	p.T26P	ENST00000371953	NM_000314.4	26	Acc/Ccc	1/9	0.555997987468711	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.54	1		626	575	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521061	187521061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	135	459	0	ENST00000441802.2:c.12094C>T	p.Pro4032Ser	p.P4032S	ENST00000441802	NM_005245.3	4032	Cct/Tct	22/27	1	2	FACETS	0.994	0.909	1	0.994	0.909	1	CLONAL	1	TRUE	1	0.54	2		459	503	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125379	7125379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778982272	NA	P-0052000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	64	890	2	ENST00000302850.5:c.3173C>T	p.Thr1058Met	p.T1058M	ENST00000302850	NM_000208.2	1058	aCg/aTg	17/22	0.647382365461551	4	FACETS	0.252	0.217	0.29	0.126	0.108	0.145	SUBCLONAL	1	TRUE	2	0.748018416837757	4		892	1187	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574025	7574025	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	864	680	0	ENST00000269305.4:c.1002del	p.Arg335ValfsTer10	p.R335Vfs*10	ENST00000269305	NM_001126112.2	334	ggG/gg	10/11	0.71792826320668	4	FACETS	0.989	0.972	1	0.989	0.972	1	CLONAL	4	TRUE	0	0.748018416837757	4		680	1021	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62322275	62322275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758245234	NA	P-0052000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	202	918	0	ENST00000360203.5:c.2531G>A	p.Arg844Gln	p.R844Q	ENST00000360203	NM_001283009.1	844	cGg/cAg	27/35	NA	2	FACETS	0.578	0.536	0.621			1	INDETERMINATE	1	TRUE	NA	0.748018416837757	2		918	935	SUCCESS
ATM	472	MSKCC	GRCh37	11	108099904	108099904	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0052000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	50	182	0	ENST00000278616.4:c.186-1G>C		p.X62_splice	ENST00000278616	NM_000051.3	62			0.227723801162657	3	FACETS	1	0.898	1			1	INDETERMINATE	1	TRUE	NA	0.748018416837757	3		182	175	SUCCESS
ATM	472	MSKCC	GRCh37	11	108099930	108099930	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	75	249	0	ENST00000278616.4:c.211G>C	p.Glu71Gln	p.E71Q	ENST00000278616	NM_000051.3	71	Gaa/Caa	4/63	0.227723801162657	3	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.748018416837757	3		249	226	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737513	204737513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	224	354	0	ENST00000302823.3:c.650C>T	p.Pro217Leu	p.P217L	ENST00000302823	NM_005214.4	217	cCt/cTt	4/4	0.647382365461551	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	2	0.748018416837757	4		354	504	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984858	55984858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	26	616	0	ENST00000263923.4:c.271C>T	p.Pro91Ser	p.P91S	ENST00000263923	NM_002253.2	91	Cca/Tca	3/30	0.748018416837757	2	FACETS	0.137	0.108	0.171	0.069	0.054	0.086	SUBCLONAL	1	TRUE	0	0.748018416837757	2		616	506	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	258	230	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.853532573618114	2		230	515	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578281	7578281	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660254	NA	P-0052001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	362	711	0	ENST00000269305.4:c.568C>A	p.Pro190Thr	p.P190T	ENST00000269305	NM_001126112.2	190	Cct/Act	6/11	1	2	FACETS	0.956	0.911	1	0.956	0.911	1	CLONAL	1	TRUE	1	0.853532573618114	2		711	887	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0052001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	434	765	1	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	1	2	FACETS	0.901	0.861	0.941	0.901	0.861	0.941	CLONAL	1	TRUE	1	0.853532573618114	2		766	1129	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577599	7577599	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	338	580	0	ENST00000269305.4:c.682G>C	p.Asp228His	p.D228H	ENST00000269305	NM_001126112.2	228	Gac/Cac	7/11	1	2	FACETS	0.98	0.932	1	0.98	0.932	1	CLONAL	1	TRUE	1	0.853532573618114	2		580	808	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1284	54	849	0	ENST00000269305.4:c.455C>G	p.Pro152Arg	p.P152R	ENST00000269305	NM_001126112.2	152	cCg/cGg	5/11	1	2	FACETS	0.095	0.08	0.111	0.095	0.08	0.111	SUBCLONAL	1	TRUE	1	0.853532573618114	2		849	1338	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0052001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	364	572	1	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	0.94	0.895	0.986	0.94	0.895	0.986	CLONAL	1	TRUE	1	0.853532573618114	2		573	907	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872210	45872210	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	494	732	0	ENST00000391945.4:c.224G>A	p.Arg75Lys	p.R75K	ENST00000391945	NM_000400.3	75	aGa/aAa	4/23	0.853532573618114	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.853532573618114	1		732	626	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063389	67063389	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0052001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	456	354	0	ENST00000412916.2:c.78+1G>A		p.X26_splice	ENST00000412916		26			0.853532573618114	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.853532573618114	2		354	526	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18975016	18975016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761111860	NA	P-0052001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	227	533	2	ENST00000262803.5:c.2813G>A	p.Arg938Gln	p.R938Q	ENST00000262803	NM_002911.3	938	cGg/cAg	20/24	0.339132940271435	1	FACETS	0.445	0.416	0.474	0.445	0.416	0.474	INDETERMINATE	1	TRUE	0	0.853532573618114	1		535	685	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800503	32800503	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1336	144	878	2	ENST00000374899.4:c.1044G>T	p.Glu348Asp	p.E348D	ENST00000374899	NM_018833.2	348	gaG/gaT	6/12	1	2	FACETS	0.228	0.207	0.25	0.228	0.207	0.25	SUBCLONAL	1	TRUE	1	0.853532573618114	2		880	1480	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541901	187541901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751134485	NA	P-0052019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	50	497	0	ENST00000441802.2:c.5839C>T	p.Arg1947Cys	p.R1947C	ENST00000441802	NM_005245.3	1947	Cgc/Tgc	10/27	0.548910757512959	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.539458121817585	1		497	97	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155686	106155686	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	18	325	0	ENST00000380013.4:c.587A>G	p.Asn196Ser	p.N196S	ENST00000380013	NM_001127208.2	196	aAc/aGc	3/11	0.163990921852599	4	FACETS	0.776	0.59	0.991	0.388	0.295	0.496	INDETERMINATE	1	TRUE	2	0.535809723496846	4		325	133	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56911995	56911995	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	13	492	0	ENST00000519728.1:c.1223A>G	p.Lys408Arg	p.K408R	ENST00000519728	NM_002350.3	408	aAg/aGg	12/13	0.531926859373359	1	FACETS	0.39	0.282	0.519	0.39	0.282	0.519	SUBCLONAL	1	TRUE	0	0.535809723496846	1		492	91	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936995	48936995	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778842	NA	P-0052025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	131	401	0	ENST00000267163.4:c.763C>T	p.Arg255Ter	p.R255*	ENST00000267163	NM_000321.2	255	Cga/Tga	8/27	0.455781759541453	2	FACETS	0.858	0.79	0.926	0.858	0.79	0.926	CLONAL	2	TRUE	0	0.488031601816426	2		401	313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578425	+	protein_altering_variant	In_Frame_Del	DEL	TGGTGGGGGCAGCGCCTCACAACCTCCGTCAT	TGGTGGGGGCAGCGCCTCACAACCTCCGTCAT	CC	novel	NA	P-0052025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	287	815	4	ENST00000269305.4:c.505_536delinsGG	p.Met169_His179delinsGly	p.M169_H179delinsG	ENST00000269305	NM_001126112.2	169	ATGACGGAGGTTGTGAGGCGCTGCCCCCACCAt/GGt	5/11	0.488031601816426	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.488031601816426	1		819	704	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604790	48604790	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1568211615	NA	P-0052025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	126	373	1	ENST00000342988.3:c.1612G>T	p.Glu538Ter	p.E538*	ENST00000342988	NM_005359.5	538	Gaa/Taa	12/12	0.455781759541453	2	FACETS	0.768	0.705	0.833	0.768	0.705	0.833	SUBCLONAL	2	TRUE	0	0.488031601816426	2		374	336	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106648	27106648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553153748	NA	P-0052026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	102	645	0	ENST00000324856.7:c.6259G>A	p.Gly2087Arg	p.G2087R	ENST00000324856	NM_006015.4	2087	Gga/Aga	20/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.28234408696515	2		645	613	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0052026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	55	318	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.943	0.809	1	0.943	0.809	1	CLONAL	1	TRUE	1	0.28234408696515	2		318	413	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589589	67589591	+	inframe_deletion	In_Frame_Del	DEL	AAT	AAT	-	novel	NA	P-0052026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	51	222	0	ENST00000274335.5:c.1353_1355del	p.Glu451_Tyr452delinsAsp	p.E451_Y452delinsD	ENST00000274335		451	gAATat/gat	10/15	1	2	FACETS	0.969	0.826	1	0.969	0.826	1	CLONAL	1	TRUE	1	0.28234408696515	2		222	373	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711891	89711891	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660507	NA	P-0052026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	154	404	0	ENST00000371953.3:c.509G>T	p.Ser170Ile	p.S170I	ENST00000371953	NM_000314.4	170	aGt/aTt	6/9	0.259175693967792	3	FACETS	0.946	0.868	1	0.946	0.868	1	CLONAL	2	TRUE	1	0.28234408696515	3		404	658	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740552	145740552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1250323268	NA	P-0052026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	157	886	0	ENST00000428558.2:c.1465G>A	p.Val489Ile	p.V489I	ENST00000428558	NM_004260.3	489	Gtc/Atc	8/22	0.116676761701316	5	FACETS	0.844	0.773	0.918	0.422	0.386	0.459	INDETERMINATE	2	TRUE	1	0.28234408696515	5		886	938	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0052027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	34	373	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.22	2		373	240	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956205	55956205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148668147	NA	P-0052027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	32	569	2	ENST00000263923.4:c.3110C>T	p.Ser1037Leu	p.S1037L	ENST00000263923	NM_002253.2	1037	tCg/tTg	23/30	0.3	1	FACETS	0.721	0.586	0.873	0.721	0.586	0.873	SUBCLONAL	1	TRUE	0	0.22	1		571	359	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048788	180048788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375315719	NA	P-0052027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	62	964	1	ENST00000261937.6:c.1774C>T	p.Arg592Cys	p.R592C	ENST00000261937	NM_182925.4	592	Cgc/Tgc	13/30	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.22	2		965	513	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0052027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	37	698	2	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			1	2	FACETS	0.795	0.656	0.951	0.795	0.656	0.951	CLONAL	1	TRUE	1	0.22	2		700	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578373	7578374	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0052028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	197	762	0	ENST00000269305.4:c.556_557del	p.Asp186TrpfsTer22	p.D186Wfs*22	ENST00000269305	NM_001126112.2	186	GAt/t	5/11	0.557961700091758	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.574320389875319	1		762	459	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485995	40485995	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	169	677	0	ENST00000264657.5:c.870A>T	p.Lys290Asn	p.K290N	ENST00000264657	NM_139276.2	290	aaA/aaT	9/24	0.562188584275381	2	FACETS	0.771	0.71	0.835	0.386	0.355	0.418	SUBCLONAL	1	TRUE	0	0.574320389875319	2		677	763	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660090	227660090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112888661	NA	P-0052028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	134	848	0	ENST00000305123.5:c.3365G>A	p.Gly1122Glu	p.G1122E	ENST00000305123	NM_005544.2	1122	gGg/gAg	1/2	0.556909865988943	3	FACETS	0.858	0.781	0.939	0.429	0.39	0.47	CLONAL	1	TRUE	1	0.574320389875319	3		848	700	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403183	116403183	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	86	614	0	ENST00000397752.3:c.2444T>A	p.Leu815Gln	p.L815Q	ENST00000397752	NM_000245.2	815	cTg/cAg	11/21	0.523299421527588	4	FACETS	0.972	0.863	1	0.324	0.287	0.363	CLONAL	1	TRUE	1	0.574320389875319	4		614	485	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0052029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	114	435	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.902	0.815	0.994	1	0.988	1	CLONAL	2	TRUE	1	0.223237552667981	2		436	566	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933406	100933406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150584881	NA	P-0052029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	115	540	1	ENST00000325455.5:c.1984G>A	p.Val662Ile	p.V662I	ENST00000325455	NM_001202474.3	662	Gtt/Att	4/8	1	2	FACETS	0.965	0.873	1	1	0.989	1	CLONAL	2	TRUE	1	0.223237552667981	2		541	534	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790171	40790171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760735173	NA	P-0052029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	91	448	0	ENST00000373198.4:c.2560C>T	p.Arg854Cys	p.R854C	ENST00000373198	NM_133170.3	854	Cgc/Tgc	18/32	1	2	FACETS	0.815	0.726	0.909	1	0.982	1	CLONAL	2	TRUE	1	0.223237552667981	2		448	500	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414242	32414242	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	53	422	0	ENST00000332351.3:c.1309C>T	p.Gln437Ter	p.Q437*	ENST00000332351	NM_024426.4	437	Cag/Tag	8/10	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.223237552667981	2		422	402	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964927	15964927	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs768556634	NA	P-0052029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	75	553	0	ENST00000268712.3:c.5669G>T	p.Gly1890Val	p.G1890V	ENST00000268712	NM_006311.3	1890	gGc/gTc	37/46	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.223237552667981	2		553	506	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120216	70120217	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	119	642	0	ENST00000245479.2:c.1219dup	p.Tyr407LeufsTer171	p.Y407Lfs*171	ENST00000245479	NM_000346.3	406	-/T	3/3	1	2	FACETS	0.823	0.744	0.905	1	0.987	1	CLONAL	2	TRUE	1	0.223237552667981	2		642	648	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477790	140477791	+	inframe_insertion,splice_region_variant	In_Frame_Ins	INS	-	-	CTGAGTACT	novel	NA	P-0052029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	60	449	0	ENST00000288602.6:c.1509_1517dup	p.Val504_Arg506dup	p.V504_R506dup	ENST00000288602	NM_004333.4	504	agg/agAGTACTCAGg		1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.223237552667981	2		449	422	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443482	49443482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746084513	NA	P-0052030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	228	648	0	ENST00000301067.7:c.3889C>T	p.Arg1297Cys	p.R1297C	ENST00000301067	NM_003482.3	1297	Cgt/Tgt	11/54	0.384220694160448	3	FACETS	0.959	0.892	1	0.48	0.446	0.515	CLONAL	1	TRUE	1	0.441775664026356	3		648	1314	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443703	49443703	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0052030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1362	345	852	0	ENST00000301067.7:c.3668C>G	p.Ser1223Ter	p.S1223*	ENST00000301067	NM_003482.3	1223	tCa/tGa	11/54	0.384220694160448	3	FACETS	1	0.985	1	0.559	0.527	0.591	CLONAL	1	TRUE	1	0.441775664026356	3		852	1707	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445379	49445380	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	T	novel	NA	P-0052030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1271	696	1035	0	ENST00000301067.7:c.2086_2087delinsA	p.Ser696ThrfsTer234	p.S696Tfs*234	ENST00000301067	NM_003482.3	696	TCc/Ac	10/54	0.384220694160448	3	FACETS	0.978	0.942	1	0.978	0.942	1	CLONAL	2	TRUE	1	0.441775664026356	3		1035	1967	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131459	202131459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	277	535	0	ENST00000358485.4:c.427G>A	p.Glu143Lys	p.E143K	ENST00000358485	NM_001080125.1	143	Gag/Aag	2/9	0.375116118981016	2	FACETS	0.884	0.835	0.934	0.884	0.835	0.934	CLONAL	2	TRUE	0	0.441775664026356	2		535	709	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513474	41513474	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	219	624	0	ENST00000263253.7:c.378G>C	p.Met126Ile	p.M126I	ENST00000263253	NM_001429.3	126	atG/atC	2/31	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.441775664026356	2		624	984	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41562602	41562602	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0052030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	54	460	0	ENST00000263253.7:c.3807-1G>C		p.X1269_splice	ENST00000263253	NM_001429.3	1269			1	2	FACETS	0.407	0.348	0.473	0.407	0.348	0.473	SUBCLONAL	1	TRUE	1	0.441775664026356	2		460	600	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41562627	41562627	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	53	464	0	ENST00000263253.7:c.3831G>C	p.Lys1277Asn	p.K1277N	ENST00000263253	NM_001429.3	1277	aaG/aaC	23/31	1	2	FACETS	0.422	0.359	0.49	0.422	0.359	0.49	SUBCLONAL	1	TRUE	1	0.441775664026356	2		464	569	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564536	41564536	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	166	603	0	ENST00000263253.7:c.3958G>C	p.Glu1320Gln	p.E1320Q	ENST00000263253	NM_001429.3	1320	Gag/Cag	24/31	1	2	FACETS	0.805	0.739	0.873	0.805	0.739	0.873	CLONAL	1	TRUE	1	0.441775664026356	2		603	934	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564849	41564849	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	201	609	0	ENST00000263253.7:c.4150G>A	p.Asp1384Asn	p.D1384N	ENST00000263253	NM_001429.3	1384	Gac/Aac	25/31	1	2	FACETS	0.921	0.854	0.991	0.921	0.854	0.991	CLONAL	1	TRUE	1	0.441775664026356	2		609	988	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568638	41568638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	39	390	0	ENST00000263253.7:c.4588G>A	p.Glu1530Lys	p.E1530K	ENST00000263253	NM_001429.3	1530	Gag/Aag	28/31	1	2	FACETS	0.38	0.314	0.452	0.38	0.314	0.452	SUBCLONAL	1	TRUE	1	0.441775664026356	2		390	465	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	92	321	0	ENST00000263967.3:c.333G>T	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaT	2/21	0.326747055997967	4	FACETS	1	0.951	1	0.56	0.499	0.625	CLONAL	1	TRUE	2	0.441775664026356	4		321	536	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250840	153250840	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	50	427	0	ENST00000281708.4:c.1220C>A	p.Ser407Ter	p.S407*	ENST00000281708	NM_033632.3	407	tCa/tAa	8/12	1	2	FACETS	0.62	0.528	0.721	0.62	0.528	0.721	SUBCLONAL	1	TRUE	1	0.441775664026356	2		427	365	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0052031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	188	578	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.921	0.851	0.994	0.921	0.851	0.994	CLONAL	1	TRUE	1	0.407075904778507	2		578	1003	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577507	7577507	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	197	651	0	ENST00000269305.4:c.774A>T	p.Glu258Asp	p.E258D	ENST00000269305	NM_001126112.2	258	gaA/gaT	7/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.407075904778507	2		651	877	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830733	72830733	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	171	504	0	ENST00000268489.5:c.5848G>T	p.Glu1950Ter	p.E1950*	ENST00000268489	NM_006885.3	1950	Gag/Tag	9/10	0.407075904778507	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.407075904778507	1		504	667	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576873	7576874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	192	635	0	ENST00000269305.4:c.972dup	p.Gly325TrpfsTer12	p.G325Wfs*12	ENST00000269305	NM_001126112.2	324	-/T	9/11	1	2	FACETS	0.919	0.85	0.992	0.919	0.85	0.992	CLONAL	1	TRUE	1	0.407075904778507	2		635	1026	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0052032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	590	655	4	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.82448486913241	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.82469812962272	2		659	654	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023313	27023313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1189437882	NA	P-0052032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	96	102	0	ENST00000324856.7:c.419C>T	p.Ala140Val	p.A140V	ENST00000324856	NM_006015.4	140	gCg/gTg	1/20	0.82448486913241	3	FACETS	1	0.984	1	0.734	0.667	0.802	CLONAL	1	TRUE	1	0.82469812962272	3		102	224	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115972	8115973	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0052032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	220	399	0	ENST00000346208.3:c.1320dup	p.Ala441ArgfsTer66	p.A441Rfs*66	ENST00000346208		440	acc/aCcc	6/6	0.455798190164162	6	FACETS	0.915	0.86	0.971	0.915	0.86	0.971	INDETERMINATE	3	TRUE	3	0.82469812962272	6		399	515	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435289	121435289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371544082	NA	P-0052032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	213	749	0	ENST00000257555.6:c.1322C>T	p.Thr441Met	p.T441M	ENST00000257555		441	aCg/aTg	7/10	0.58965781541546	4	FACETS	0.87	0.807	0.934	0.435	0.403	0.467	CLONAL	1	TRUE	2	0.82469812962272	4		749	1084	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237591	133237591	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	201	606	0	ENST00000320574.5:c.3024G>T	p.Lys1008Asn	p.K1008N	ENST00000320574	NM_006231.2	1008	aaG/aaT	25/49	0.58965781541546	4	FACETS	1	0.928	1	0.5	0.464	0.538	CLONAL	1	TRUE	2	0.82469812962272	4		606	889	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047507	49047507	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1131690906	NA	P-0052032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	75	306	0	ENST00000267163.4:c.2501C>A	p.Ser834Ter	p.S834*	ENST00000267163	NM_000321.2	834	tCa/tAa	24/27	0.82448486913241	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.82469812962272	1		306	99	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437872	110437872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	89	171	0	ENST00000375856.3:c.529G>A	p.Ala177Thr	p.A177T	ENST00000375856	NM_003749.2	177	Gcc/Acc	1/2	0.82469812962272	10	FACETS	1	0.95	1			1	CLONAL	1	TRUE	NA	0.82469812962272	10		171	819	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835634	68835634	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs767019668	NA	P-0052032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	198	643	0	ENST00000261769.5:c.225C>G	p.Phe75Leu	p.F75L	ENST00000261769	NM_004360.3	75	ttC/ttG	3/16	0.82448486913241	3	FACETS	0.941	0.874	1	0.47	0.437	0.505	CLONAL	1	TRUE	1	0.82469812962272	3		643	721	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670043	29670102	+	inframe_deletion	In_Frame_Del	DEL	TTATGGCAATCCGGAATCCTCTGGAGTGGCACTGCAAGCAAATGGATCATTTTGTTGGAC	TTATGGCAATCCGGAATCCTCTGGAGTGGCACTGCAAGCAAATGGATCATTTTGTTGGAC	-	novel	NA	P-0052032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	109	389	0	ENST00000356175.3:c.7017_7076del	p.Met2340_Leu2359del	p.M2340_L2359del	ENST00000356175	NM_000267.3	2339	tTTATGGCAATCCGGAATCCTCTGGAGTGGCACTGCAAGCAAATGGATCATTTTGTTGGACtc/ttc	47/57	0.82448486913241	1	FACETS	0.582	0.531	0.633	0.582	0.531	0.633	SUBCLONAL	1	TRUE	0	0.82469812962272	1		389	267	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006599	62006599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1658	216	669	0	ENST00000392795.3:c.680C>T	p.Pro227Leu	p.P227L	ENST00000392795	NM_001039933.1	227	cCa/cTa	6/6	0.82469812962272	7	FACETS	0.856	0.792	0.922			1	CLONAL	1	TRUE	NA	0.82469812962272	7		669	1874	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526153	63526153	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	189	599	0	ENST00000307078.5:c.2473G>C	p.Glu825Gln	p.E825Q	ENST00000307078	NM_004655.3	825	Gag/Cag	11/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.82469812962272	NA		599	990	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299127	15299127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	213	787	1	ENST00000263388.2:c.1411G>A	p.Asp471Asn	p.D471N	ENST00000263388	NM_000435.2	471	Gac/Aac	9/33	0.684485327953165	4	FACETS	0.814	0.755	0.875	0.407	0.377	0.438	CLONAL	1	TRUE	2	0.82469812962272	4		788	1158	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355556	15355556	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	203	710	1	ENST00000263377.2:c.2176A>C	p.Lys726Gln	p.K726Q	ENST00000263377	NM_058243.2	726	Aaa/Caa	12/20	0.684485327953165	4	FACETS	0.814	0.754	0.876	0.407	0.377	0.438	CLONAL	1	TRUE	2	0.82469812962272	4		711	1104	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218843	36218843	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs569194163	NA	P-0052032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	95	932	0	ENST00000222270.7:c.4454C>T	p.Pro1485Leu	p.P1485L	ENST00000222270	NM_014727.1	1485	cCg/cTg	18/37	1	2	FACETS	0.277	0.246	0.31	0.277	0.246	0.31	SUBCLONAL	1	TRUE	1	0.82469812962272	2		932	832	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223628	36223628	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1281558460	NA	P-0052032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	392	1048	2	ENST00000222270.7:c.6178C>T	p.Gln2060Ter	p.Q2060*	ENST00000222270	NM_014727.1	2060	Cag/Tag	28/37	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.82469812962272	2		1050	884	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49929005	49929005	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	335	692	0	ENST00000296474.3:c.3361G>C	p.Glu1121Gln	p.E1121Q	ENST00000296474	NM_002447.2	1121	Gag/Cag	16/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.82469812962272	2		692	715	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280007	66280007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	74	208	0	ENST00000273854.3:c.1682C>T	p.Pro561Leu	p.P561L	ENST00000273854	NM_004439.5	561	cCa/cTa	7/18	0.409860579203909	4	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.82469812962272	4		208	226	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549491	187549491	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs888946039	NA	P-0052032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	156	492	0	ENST00000441802.2:c.4627C>T	p.Arg1543Cys	p.R1543C	ENST00000441802	NM_005245.3	1543	Cgc/Tgc	9/27	0.82448486913241	4	FACETS	0.878	0.805	0.954	0.22	0.201	0.239	CLONAL	1	TRUE	0	0.82469812962272	4		492	786	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414378	6414378	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	67	147	0	ENST00000356142.4:c.12C>G	p.Ile4Met	p.I4M	ENST00000356142	NM_018890.3	4	atC/atG	1/7	0.684485327953165	4	FACETS	0.877	0.767	0.994	0.439	0.383	0.497	CLONAL	1	TRUE	2	0.82469812962272	4		147	338	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737362	145737362	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	341	1038	0	ENST00000428558.2:c.3325G>C	p.Glu1109Gln	p.E1109Q	ENST00000428558	NM_004260.3	1109	Gag/Cag	20/22	0.82448486913241	3	FACETS	1	0.976	1	0.526	0.498	0.554	CLONAL	1	TRUE	1	0.82469812962272	3		1038	1111	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517961	8517961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	129	446	0	ENST00000356435.5:c.1430C>T	p.Thr477Ile	p.T477I	ENST00000356435		477	aCt/aTt	10/35	0.82448486913241	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.82469812962272	1		446	183	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815662	139815662	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	366	607	0	ENST00000247668.2:c.1133C>A	p.Ser378Tyr	p.S378Y	ENST00000247668	NM_021138.3	378	tCc/tAc	9/11	0.706217315741049	3	FACETS	0.933	0.893	0.972	0.933	0.893	0.972	CLONAL	2	TRUE	1	0.82469812962272	3		607	672	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593580	55593606	+	splice_acceptor_variant,coding_sequence_variant	In_Frame_Del	DEL	AGAAACCCATGTATGAAGTACAGTGGA	AGAAACCCATGTATGAAGTACAGTGGA	-	rs121913234	NA	P-0052033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	334	365	0	ENST00000288135.5:c.1648_1674del		p.K550_K558del	ENST00000288135	NM_000222.2	550		11/21	0.863230160969708	3	FACETS	0.92	0.88	0.96	0.92	0.88	0.96	CLONAL	2	TRUE	1	0.863254322721432	3		365	602	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0052034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	171	449	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	0.201299175428397	4	FACETS	0.778	0.716	0.843	0.778	0.716	0.843	SUBCLONAL	2	TRUE	2	0.321056426287098	4		449	904	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221302	1221302	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	416	825	0	ENST00000326873.7:c.827del	p.Gly276AlafsTer11	p.G276Afs*11	ENST00000326873	NM_000455.4	275	ccG/cc	6/10	0.214136742734351	3	FACETS	0.855	0.815	0.895			1	CLONAL	3	TRUE	NA	0.321056426287098	3		825	1173	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610222	10610222	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	458	810	0	ENST00000171111.5:c.488A>T	p.Gln163Leu	p.Q163L	ENST00000171111	NM_203500.1	163	cAg/cTg	2/6	0.244088948840942	3	FACETS	0.866	0.827	0.905	0.866	0.827	0.905	CLONAL	3	TRUE	0	0.321056426287098	3		810	1275	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172457	108172457	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0052034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	61	406	0	ENST00000278616.4:c.5260A>T	p.Lys1754Ter	p.K1754*	ENST00000278616	NM_000051.3	1754	Aag/Tag	35/63	1	2	FACETS	0.605	0.522	0.696	0.605	0.522	0.696	SUBCLONAL	1	TRUE	1	0.321056426287098	2		406	628	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333869	70333869	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	135	369	0	ENST00000373644.4:c.1774G>T	p.Gly592Trp	p.G592W	ENST00000373644	NM_030625.2	592	Ggg/Tgg	2/12	0.231555053425489	3	FACETS	1	0.986	1	0.75	0.683	0.819	CLONAL	1	TRUE	1	0.321056426287098	3		369	651	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164038	108164038	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0052034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	42	135	0	ENST00000278616.4:c.4612-2A>T		p.X1538_splice	ENST00000278616	NM_000051.3	1538			1	2	FACETS	0.962	0.808	1	0.962	0.808	1	CLONAL	1	TRUE	1	0.321056426287098	2		135	272	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17947977	17947977	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	317	807	1	ENST00000458235.1:c.1747C>A	p.His583Asn	p.H583N	ENST00000458235	NM_000215.3	583	Cat/Aat	13/24	0.244088948840942	3	FACETS	0.967	0.912	1	0.645	0.608	0.682	CLONAL	2	TRUE	0	0.321056426287098	3		808	1185	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163808	152163808	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	183	460	0	ENST00000206249.3:c.529G>T	p.Glu177Ter	p.E177*	ENST00000206249	NM_000125.3	177	Gaa/Taa	2/8	0.245263479958254	2	FACETS	0.797	0.738	0.859	0.797	0.738	0.859	SUBCLONAL	2	TRUE	0	0.321056426287098	2		460	715	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0052038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	27	283	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.935	0.749	1	0.935	0.749	1	CLONAL	1	TRUE	1	0.291694454158755	2		283	198	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	55	230	0				ENST00000310581	NM_198253.2	-/1132			0.260146272163135	1	FACETS	1	0.907	1	1	0.985	1	CLONAL	4	FALSE	0	0.260146272163135	1		230	91	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0052039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	229	423	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.260146272163135	12	FACETS	1	0.976	1			1	CLONAL	7	FALSE	NA	0.260146272163135	12		423	541	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861037	35861037	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	112	328	0	ENST00000303115.3:c.166A>T	p.Thr56Ser	p.T56S	ENST00000303115	NM_002185.3	56	Acc/Tcc	2/8	0.260146272163135	5	FACETS	0.891	0.811	0.973	1	0.973	1	CLONAL	4	FALSE	2	0.260146272163135	5		328	336	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417559	139417559	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	128	879	0	ENST00000277541.6:c.485A>T	p.Tyr162Phe	p.Y162F	ENST00000277541	NM_017617.3	162	tAc/tTc	4/34	0.25379231732069	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	FALSE	2	0.260146272163135	4		879	510	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0052040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	97	607	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	0.231411684533525	2	FACETS	1	0.957	1	0.568	0.508	0.631	CLONAL	1	TRUE	0	0.329651184471673	2		607	518	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965572	25965572	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	134	609	0	ENST00000435504.4:c.3634T>G	p.Ser1212Ala	p.S1212A	ENST00000435504		1212	Tca/Gca	13/13	0.0128856422145185	3	FACETS	1	0.986	1	0.738	0.672	0.806	INDETERMINATE	1	TRUE	1	0.329651184471673	3		609	642	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0052041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	41	396	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.907	0.762	1	0.907	0.762	1	CLONAL	1	TRUE	1	0.384552572036271	2		396	235	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0052041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	104	629	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.875	0.785	0.97	0.875	0.785	0.97	CLONAL	1	TRUE	1	0.384552572036271	2		631	618	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742994	17742994	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113719982	NA	P-0052041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	109	772	1	ENST00000250003.3:c.902C>T	p.Pro301Leu	p.P301L	ENST00000250003	NM_002478.4	301	cCg/cTg	3/3	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.384552572036271	2		773	553	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235935	108235935	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770641163	NA	P-0052041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	34	418	0	ENST00000278616.4:c.8977C>T	p.Arg2993Ter	p.R2993*	ENST00000278616	NM_000051.3	2993	Cga/Tga	62/63	1	2	FACETS	0.765	0.63	0.916	0.765	0.63	0.916	CLONAL	1	TRUE	1	0.384552572036271	2		418	231	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427451	427451	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0052041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	84	598	0	ENST00000399788.2:c.2718A>C	p.Glu906Asp	p.E906D	ENST00000399788	NM_001042603.1	906	gaA/gaC	19/28	0.335914405792957	2	FACETS	0.717	0.634	0.806	0.359	0.317	0.403	SUBCLONAL	1	TRUE	0	0.384552572036271	2		598	609	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0052041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	75	322	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.191761688340562	3	FACETS	0.953	0.847	1	0.953	0.847	1	INDETERMINATE	2	TRUE	1	0.384552572036271	3		322	244	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424779	49424779	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	79	658	0	ENST00000301067.7:c.13568A>T	p.Lys4523Met	p.K4523M	ENST00000301067	NM_003482.3	4523	aAg/aTg	40/54	0.191761688340562	3	FACETS	0.727	0.639	0.821	0.363	0.319	0.411	INDETERMINATE	1	TRUE	1	0.384552572036271	3		658	674	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440206	49440206	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	45	559	0	ENST00000301067.7:c.4420T>G	p.Cys1474Gly	p.C1474G	ENST00000301067	NM_003482.3	1474	Tgt/Ggt	16/54	0.191761688340562	3	FACETS	0.613	0.516	0.721	0.307	0.258	0.361	INDETERMINATE	1	TRUE	1	0.384552572036271	3		559	455	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345073	73345073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765260071	NA	P-0052041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	27	399	1	ENST00000377767.4:c.1724C>T	p.Thr575Met	p.T575M	ENST00000377767	NM_014953.3	575	aCg/aTg	13/21	0.34406428913729	4	FACETS	0.759	0.606	0.933	0.253	0.202	0.311	CLONAL	1	TRUE	1	0.384552572036271	4		400	256	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99482548	99482548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs794727201	NA	P-0052041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	106	656	0	ENST00000268035.6:c.3416G>A	p.Arg1139Gln	p.R1139Q	ENST00000268035	NM_000875.3	1139	cGg/cAg	18/21	1	2	FACETS	0.865	0.777	0.959	0.865	0.777	0.959	CLONAL	1	TRUE	1	0.384552572036271	2		656	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578528	7578528	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	126	918	0	ENST00000269305.4:c.402T>G	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	ttT/ttG	5/11	1	2	FACETS	0.751	0.68	0.827	0.751	0.68	0.827	SUBCLONAL	1	TRUE	1	0.384552572036271	2		918	872	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0052041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	60	509	1	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.304114948982499	2	FACETS	1	0.934	1	0.561	0.488	0.64	CLONAL	1	TRUE	0	0.384552572036271	2		510	278	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627634	14627636	+	missense_variant	Missense_Mutation	TNP	AGT	AGT	CGG	novel	NA	P-0052041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	74	600	0	ENST00000254322.2:c.434_436delinsCCG	p.Asn145_Phe146delinsThrVal	p.N145_F146delinsTV	ENST00000254322	NM_006145.1	145	aACTtt/aCCGtt	2/3	1	2	FACETS	0.668	0.585	0.757	0.668	0.585	0.757	SUBCLONAL	1	TRUE	1	0.384552572036271	2		600	576	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752714	42752714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	97	874	1	ENST00000222329.4:c.1550G>A	p.Gly517Glu	p.G517E	ENST00000222329	NM_006494.2	517	gGg/gAg	4/4	1	2	FACETS	0.896	0.801	0.997	0.896	0.801	0.997	CLONAL	1	TRUE	1	0.384552572036271	2		875	563	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266072	41266664	+	splice_acceptor_variant,splice_donor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	TCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCAAGATGATGCAGAACTTGCCACACGTGCAATCCC	TCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCAAGATGATGCAGAACTTGCCACACGTGCAATCCC	-	novel	NA	P-0052041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	30	354	0	ENST00000349496.5:c.70_462del		p.X24_splice	ENST00000349496	NM_001904.3	24	agTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCAAGATGATGCAGAACTTGCCACACGTGCAATCCCt/agt	3-4/15	1	2	FACETS	0.476	0.384	0.58	0.476	0.384	0.58	SUBCLONAL	1	TRUE	1	0.384552572036271	2		354	328	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125500	47125500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	34	445	1	ENST00000409792.3:c.5770C>T	p.Gln1924Ter	p.Q1924*	ENST00000409792	NM_014159.6	1924	Cag/Tag	12/21	0.384552572036271	1	FACETS	0.646	0.532	0.773	0.646	0.532	0.773	SUBCLONAL	1	TRUE	0	0.384552572036271	1		446	221	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983328	149983328	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs766845191	NA	P-0052041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	58	479	0	ENST00000253339.5:c.2930T>G	p.Leu977Arg	p.L977R	ENST00000253339		977	cTc/cGc	7/7	1	2	FACETS	0.79	0.681	0.907	0.79	0.681	0.907	CLONAL	1	TRUE	1	0.384552572036271	2		479	382	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	37	230	0				ENST00000310581	NM_198253.2	-/1132			0.186958172099149	4	FACETS	0.831	0.693	0.982	0.831	0.693	0.982	INDETERMINATE	2	TRUE	2	0.314531918755344	4		230	186	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039340	49039341	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0052042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	120	457	0	ENST00000267163.4:c.2330dup	p.Thr778TyrfsTer17	p.T778Yfs*17	ENST00000267163	NM_000321.2	775	-/C		0.314531918755344	4	FACETS	1	0.981	1	0.45	0.406	0.496	CLONAL	1	TRUE	1	0.314531918755344	4		457	743	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0052042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	163	455	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.223258371330897	2	FACETS	0.98	0.905	1	0.98	0.905	1	CLONAL	2	TRUE	0	0.314531918755344	2		455	529	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59934581	59934581	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	71	238	0	ENST00000259008.2:c.217G>A	p.Asp73Asn	p.D73N	ENST00000259008	NM_032043.2	73	Gat/Aat	4/20	0.110856704932861	5	FACETS	1	0.946	1	0.567	0.499	0.638	INDETERMINATE	2	TRUE	1	0.314531918755344	5		238	293	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280125	66280125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	37	246	0	ENST00000273854.3:c.1564G>A	p.Glu522Lys	p.E522K	ENST00000273854	NM_004439.5	522	Gag/Aag	7/18	0.181603774339647	3	FACETS	0.738	0.609	0.881	0.246	0.203	0.294	INDETERMINATE	1	TRUE	0	0.314531918755344	3		246	369	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805601	46805601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	62	845	0	ENST00000290295.7:c.355G>A	p.Glu119Lys	p.E119K	ENST00000290295	NM_006361.5	119	Gag/Aag	1/2	0.110856704932861	5	FACETS	1	0.905	1	0.265	0.228	0.304	INDETERMINATE	1	TRUE	1	0.314531918755344	5		845	548	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303359	11303359	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0052042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	41	409	0	ENST00000361445.4:c.1226-2A>G		p.X409_splice	ENST00000361445	NM_004958.3	409			0.314531918755344	1	FACETS	0.67	0.56	0.791	0.67	0.56	0.791	SUBCLONAL	1	TRUE	0	0.314531918755344	1		409	328	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292751	62292751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	70	563	0	ENST00000360203.5:c.203C>T	p.Ser68Phe	p.S68F	ENST00000360203	NM_001283009.1	68	tCt/tTt	3/35	0.311701257133574	3	FACETS	0.872	0.76	0.992	0.436	0.38	0.496	CLONAL	1	TRUE	1	0.314531918755344	3		563	591	SUCCESS
ATR	545	MSKCC	GRCh37	3	142189021	142189021	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs372864251	NA	P-0052042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	43	246	0	ENST00000350721.4:c.6226C>G	p.Leu2076Val	p.L2076V	ENST00000350721	NM_001184.3	2076	Cta/Gta	37/47	0.314531918755344	6	FACETS	0.804	0.672	0.95	0.201	0.168	0.238	CLONAL	1	TRUE	2	0.314531918755344	6		246	554	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555261	226555261	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	55	471	0	ENST00000366794.5:c.2326A>G	p.Ser776Gly	p.S776G	ENST00000366794	NM_001618.3	776	Agt/Ggt	17/23	1	2	FACETS	0.857	0.735	0.989	0.857	0.735	0.989	CLONAL	1	TRUE	1	0.314531918755344	2		471	408	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480324	56480324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	120	379	1	ENST00000267101.3:c.431C>T	p.Ser144Leu	p.S144L	ENST00000267101	NM_001982.3	144	tCa/tTa	4/28	0.314531918755344	5	FACETS	1	0.975	1	0.81	0.736	0.887	CLONAL	2	TRUE	2	0.314531918755344	5		380	462	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984689	72984689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	151	661	2	ENST00000268489.5:c.2895G>A	p.Met965Ile	p.M965I	ENST00000268489	NM_006885.3	965	atG/atA	3/10	0.314531918755344	1	FACETS	0.891	0.822	0.962	1	0.991	1	CLONAL	2	TRUE	0	0.314531918755344	1		663	454	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953221	81953221	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1160757509	NA	P-0052042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	59	294	0	ENST00000359376.3:c.2187G>A	p.Met729Ile	p.M729I	ENST00000359376	NM_002661.3	729	atG/atA	20/33	0.314531918755344	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.314531918755344	1		294	246	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240319	5240319	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	113	719	1	ENST00000357368.4:c.1595G>T	p.Arg532Leu	p.R532L	ENST00000357368	NM_002850.3	532	cGg/cTg	12/38	0.314531918755344	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.314531918755344	1		720	425	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270426	10270426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	85	614	0	ENST00000340748.4:c.1140G>A	p.Met380Ile	p.M380I	ENST00000340748		380	atG/atA	16/40	0.314531918755344	8	FACETS	1	0.949	1	0.19	0.167	0.214	CLONAL	1	TRUE	2	0.314531918755344	8		614	922	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655376	45655376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	76	730	0	ENST00000407780.3:c.476C>T	p.Thr159Ile	p.T159I	ENST00000407780	NM_001283052.1	159	aCa/aTa	4/7	0.110856704932861	5	FACETS	0.886	0.776	1	0.221	0.194	0.251	INDETERMINATE	1	TRUE	1	0.314531918755344	5		730	803	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626746	12626746	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	68	420	0	ENST00000251849.4:c.1543G>A	p.Glu515Lys	p.E515K	ENST00000251849	NM_002880.3	515	Gag/Aag	15/17	0.314531918755344	6	FACETS	1	0.972	1	0.37	0.322	0.421	CLONAL	1	TRUE	2	0.314531918755344	6		420	476	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665057	138665057	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395169710	NA	P-0052042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	15	95	1	ENST00000330315.3:c.508G>A	p.Gly170Arg	p.G170R	ENST00000330315	NM_023067.3	170	Gga/Aga	1/1	NA	2	FACETS	0.983	0.729	1			1	INDETERMINATE	1	TRUE	NA	0.314531918755344	2		96	97	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176516679	176516679	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	133	552	0	ENST00000292408.4:c.76G>A	p.Glu26Lys	p.E26K	ENST00000292408	NM_213647.1	26	Gag/Aag	2/18	0.261938294613723	3	FACETS	0.924	0.85	1	0.924	0.85	1	CLONAL	3	TRUE	0	0.314531918755344	3		552	353	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978484	70978484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	15	358	1	ENST00000276594.2:c.1169C>T	p.Ser390Phe	p.S390F	ENST00000276594	NM_024504.3	390	tCt/tTt	5/8	NA	2	FACETS	0.386	0.282	0.511			1	INDETERMINATE	1	TRUE	NA	0.314531918755344	2		359	247	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0052043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	71	435	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.987	0.865	1	1	0.982	1	CLONAL	2	TRUE	1	0.17	2		436	423	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	53	684	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.188880967836296	5	FACETS	1	0.858	1	0.336	0.286	0.392	CLONAL	1	TRUE	2	0.17	5		684	776	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	19	335	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.588	0.446	0.757	0.588	0.446	0.757	SUBCLONAL	1	TRUE	1	0.17	2		335	380	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0052043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	85	862	1	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	NA	2	FACETS	0.862	0.763	0.968			1	INDETERMINATE	2	TRUE	NA	0.17	2		863	580	SUCCESS
RET	5979	MSKCC	GRCh37	10	43598018	43598018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753707182	NA	P-0052043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	40	777	0	ENST00000355710.3:c.566G>A	p.Arg189His	p.R189H	ENST00000355710	NM_020975.4	189	cGc/cAc	3/20	1	2	FACETS	0.88	0.73	1	0.88	0.73	1	CLONAL	1	TRUE	1	0.17	2		777	535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782329	NA	P-0052043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	30	576	0	ENST00000269305.4:c.746G>T	p.Arg249Met	p.R249M	ENST00000269305	NM_001126112.2	249	aGg/aTg	7/11	1	2	FACETS	0.589	0.473	0.721	0.589	0.473	0.721	SUBCLONAL	1	TRUE	1	0.17	2		576	599	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913237	NA	P-0052043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	27	347	0	ENST00000369535.4:c.35G>T	p.Gly12Val	p.G12V	ENST00000369535	NM_002524.4	12	gGt/gTt	2/7	1	2	FACETS	0.722	0.574	0.892	0.722	0.574	0.892	SUBCLONAL	1	TRUE	1	0.17	2		347	440	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222475	2222475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200919682	NA	P-0052043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	33	674	2	ENST00000398665.3:c.3307G>A	p.Val1103Met	p.V1103M	ENST00000398665	NM_032482.2	1103	Gtg/Atg	24/28	0.3	0	FACETS	0.644	0.524	0.78			1	SUBCLONAL	1	TRUE	0	0.17	0		676	500	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0052043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	32	770	5	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	0.188880967836296	5	FACETS	0.826	0.669	1	0.275	0.223	0.335	CLONAL	1	TRUE	2	0.17	5		775	572	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421848	49421848	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	135	853	1	ENST00000301067.7:c.14459del	p.Pro4820GlnfsTer38	p.P4820Qfs*38	ENST00000301067	NM_003482.3	4820	cCa/ca	46/54	0.188880967836296	5	FACETS	0.864	0.786	0.946	0.864	0.786	0.946	CLONAL	3	TRUE	2	0.17	5		854	769	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321298	1321298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757079410	NA	P-0052043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	50	463	0	ENST00000400841.2:c.457C>T	p.Arg153Trp	p.R153W	ENST00000400841		153	Cgg/Tgg	4/6	1	2	FACETS	0.801	0.682	0.931	1	0.967	1	CLONAL	2	TRUE	1	0.17	2		463	367	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142022	108142023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0052043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	81	481	0	ENST00000278616.4:c.2967dup	p.Ile990TyrfsTer20	p.I990Yfs*20	ENST00000278616	NM_000051.3	989	act/acTt	20/63	0.160759730667387	2	FACETS	0.894	0.789	1	0.894	0.789	1	CLONAL	2	TRUE	0	0.17	2		481	533	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2224309	2224309	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	32	768	0	ENST00000326181.6:c.1321A>T	p.Ile441Phe	p.I441F	ENST00000326181	NM_032271.2	441	Atc/Ttc	14/21	0.3	1	FACETS	0.553	0.447	0.673	0.553	0.447	0.673	SUBCLONAL	1	TRUE	0	0.17	1		768	623	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022385	26022385	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	30	399	0	ENST00000435504.4:c.272T>C	p.Val91Ala	p.V91A	ENST00000435504		91	gTg/gCg	5/13	NA	2	FACETS	0.622	0.5	0.762			1	INDETERMINATE	1	TRUE	NA	0.17	2		399	567	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170009639	170009642	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGG	AAGG	-	novel	NA	P-0052043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	33	334	0	ENST00000295797.4:c.1206_1209del		p.X402_splice	ENST00000295797	NM_002740.5	402		13/18	0.0763569293434987	3	FACETS	0.858	0.698	1	0.429	0.349	0.52	INDETERMINATE	1	TRUE	1	0.17	3		334	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577557	7577557	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519982	NA	P-0052044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	110	661	0	ENST00000269305.4:c.724T>G	p.Cys242Gly	p.C242G	ENST00000269305	NM_001126112.2	242	Tgc/Ggc	7/11	0.297697045109534	1	FACETS	0.854	0.77	0.943	0.854	0.77	0.943	CLONAL	1	TRUE	0	0.38	1		661	549	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101099	27101099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	79	741	0	ENST00000324856.7:c.4381C>T	p.Arg1461Ter	p.R1461*	ENST00000324856	NM_006015.4	1461	Cga/Tga	18/20	1	2	FACETS	0.628	0.552	0.709	0.628	0.552	0.709	SUBCLONAL	1	TRUE	1	0.38	2		741	662	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212473	36212473	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	84	899	3	ENST00000222270.7:c.2224C>T	p.Gln742Ter	p.Q742*	ENST00000222270	NM_014727.1	742	Cag/Tag	3/37	0.297645456750743	1	FACETS	0.479	0.422	0.539	0.479	0.422	0.539	SUBCLONAL	1	TRUE	0	0.38	1		902	748	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223372	36223372	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	123	1086	0	ENST00000222270.7:c.5924del	p.Pro1975GlnfsTer12	p.P1975Qfs*12	ENST00000222270	NM_014727.1	1974	ggC/gg	28/37	0.297645456750743	1	FACETS	0.645	0.583	0.71	0.645	0.583	0.71	SUBCLONAL	1	TRUE	0	0.38	1		1086	813	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0052045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	421	373	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.689074737776757	3	FACETS	0.939	0.9	0.978	0.939	0.9	0.978	CLONAL	2	TRUE	1	0.689074737776757	3		373	875	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845292	42845294	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0052055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	272	783	0	ENST00000398585.3:c.968_970del	p.Ile323del	p.I323del	ENST00000398585	NM_001135099.1	323	aTCAcc/acc	9/14	0.641870536200833	3	FACETS	1	0.978	1	0.542	0.509	0.577	CLONAL	1	TRUE	1	0.641870536200833	3		783	1032	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061248	38061248	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	169	581	0	ENST00000250448.2:c.741C>G	p.His247Gln	p.H247Q	ENST00000250448	NM_004496.3	247	caC/caG	2/2	1	2	FACETS	0.858	0.792	0.925	0.858	0.792	0.925	CLONAL	1	TRUE	1	0.641870536200833	2		581	614	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858086	152858086	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	56	621	0	ENST00000406277.2:c.529C>T	p.His177Tyr	p.H177Y	ENST00000406277	NM_152274.4	177	Cat/Tat	6/7	0.172217663509906	4	FACETS	0.819	0.701	0.949	0.41	0.35	0.475	CLONAL	1	TRUE	2	0.2525208343864	4		621	678	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115712	8115752	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGA	CCCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGA	-	novel	NA	P-0052057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	52	261	0	ENST00000346208.3:c.1058_1098del	p.Pro353GlnfsTer4	p.P353Qfs*4	ENST00000346208		353	cCCCTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGA/c	6/6	0.220612032929497	4	FACETS	0.819	0.701	0.946	0.819	0.701	0.946	CLONAL	2	TRUE	2	0.2525208343864	4		261	315	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100664	67100664	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	112	394	0	ENST00000412916.2:c.362G>T	p.Gly121Val	p.G121V	ENST00000412916		121	gGt/gTt	4/6	0.2525208343864	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.2525208343864	2		394	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0052058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	263	622	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.585764882230011	1	FACETS	0.965	0.911	1	0.965	0.911	1	CLONAL	1	TRUE	0	0.585764882230011	1		622	658	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245948	41245948	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs142074233	NA	P-0052058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	132	471	0	ENST00000357654.3:c.1600C>T	p.Gln534Ter	p.Q534*	ENST00000357654	NM_007294.3	534	Cag/Tag	10/23	0.585764882230011	1	FACETS	0.996	0.918	1	0.996	0.918	1	CLONAL	1	TRUE	0	0.585764882230011	1		471	320	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911320	32911320	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	91	419	0	ENST00000380152.3:c.2828T>C	p.Ile943Thr	p.I943T	ENST00000380152		943	aTt/aCt	11/27	0.231921273236697	1	FACETS	0.693	0.622	0.767	0.693	0.622	0.767	INDETERMINATE	1	TRUE	0	0.585764882230011	1		419	317	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160243	22160243	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	134	242	0	ENST00000215832.6:c.388C>A	p.Leu130Ile	p.L130I	ENST00000215832	NM_002745.4	130	Ctc/Atc	3/9	NA	2	FACETS	1	0.947	1			1	INDETERMINATE	1	TRUE	NA	0.585764882230011	2		242	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0052060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	207	751	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.869930535890955	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.869930535890955	1		751	254	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0052060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	105	349	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.869930535890955	2		349	234	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0052061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	173	652	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.691861355515724	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.691861355515724	1		652	296	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593606	55593611	+	inframe_deletion	In_Frame_Del	DEL	AAGGTT	AAGGTT	-	novel	NA	P-0052061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	146	326	0	ENST00000288135.5:c.1672_1677del	p.Lys558_Val559del	p.K558_V559del	ENST00000288135	NM_000222.2	558	AAGGTT/-	11/21	1	2	FACETS	0.868	0.798	0.941	0.868	0.798	0.941	CLONAL	1	TRUE	1	0.691861355515724	2		326	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0052085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	170	655	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.338932555131431	2	FACETS	1	0.989	1	0.704	0.652	0.758	CLONAL	1	TRUE	0	0.438097582827387	2		655	551	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0052085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	28	250	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.360243881237948	3	FACETS	0.514	0.412	0.631	0.257	0.206	0.316	SUBCLONAL	1	TRUE	1	0.438097582827387	3		250	303	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913535	NA	P-0052085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	127	503	0	ENST00000311936.3:c.37G>C	p.Gly13Arg	p.G13R	ENST00000311936	NM_004985.3	13	Ggc/Cgc	2/5	0.37792040007768	3	FACETS	0.77	0.702	0.84			1	SUBCLONAL	2	TRUE	NA	0.438097582827387	3		503	459	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573210	64573210	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	81	682	0	ENST00000312049.6:c.1082A>G	p.Tyr361Cys	p.Y361C	ENST00000312049	NM_130799.2	361	tAc/tGc	8/10	0.360243881237948	3	FACETS	0.746	0.658	0.841	0.373	0.329	0.421	SUBCLONAL	1	TRUE	1	0.438097582827387	3		682	604	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969327	44969327	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	55	271	0	ENST00000377967.4:c.4009G>T	p.Glu1337Ter	p.E1337*	ENST00000377967	NM_021140.2	1337	Gag/Tag	28/29	0.351736258800771	2	FACETS	0.77	0.672	0.872	0.77	0.672	0.872	SUBCLONAL	2	TRUE	0	0.438097582827387	2		271	163	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44515829	44515829	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	152	509	1	ENST00000291552.4:c.224A>G	p.Gln75Arg	p.Q75R	ENST00000291552	NM_006758.2	75	cAg/cGg	4/8	0.360243881237948	3	FACETS	0.826	0.76	0.894	0.826	0.76	0.894	CLONAL	2	TRUE	1	0.438097582827387	3		510	512	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913386	NA	P-0052085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	172	580	0	ENST00000304494.5:c.341C>A	p.Pro114His	p.P114H	ENST00000304494	NM_000077.4	114	cCc/cAc	2/3	0.338932555131431	2	FACETS	0.848	0.788	0.909	0.848	0.788	0.909	CLONAL	2	TRUE	0	0.438097582827387	2		580	463	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316228	11316228	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	58	450	0	ENST00000361445.4:c.526G>T	p.Ala176Ser	p.A176S	ENST00000361445	NM_004958.3	176	Gcc/Tcc	5/58	0.360243881237948	3	FACETS	0.729	0.627	0.838	0.364	0.313	0.419	SUBCLONAL	1	TRUE	1	0.438097582827387	3		450	443	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221933	1222955	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCGGCTTCTCCTCAGGGATGCTTGAGTACGAACCGGCCAAGAGGTTCTCCATCCGGCAGATCCGGCAGCACAGGTGAGCGGCCCCTGGGGGCAGTGGGGCCGAGGCTGCAGGGAGGCCGGCCATGTGGGCAGCTGGTTGAGCGGGCGCTAGAGCAGGGCGTGGTGGGGGTGCCAGGCTGGGCTGGGGCCAGACCCCGTGCAGCGCCCGCAGTTCTCGGGGCCCGAGTGGGGTCTCTGGGCAGTGTCCTGTTACCGGCCAGACCCAGGCGCCTTGTCCGAACTGGGGTCTGAGTGAGGACATGCGTCCGTCCCTGCCCTAGGCATGGAGATGCGCCAGGAAGGGCACAGCTGGTCCCAAACACTGGCGAGAGCCTCTCTTTTTCCCCTCCTCCTGGGGCTCCCAGCAGCAGGGTGTGGCTGGGATCCAGCCCAGGGCCCCCAGCTCCATGACAGGGAAGACAGAGCAGCGGACGGGGTCAGCAGGCCCCACAGTGCCGCCTCCCTCACTTCGTGGGCTCTGCTCCTCTGCACCAGCCCCTGGAGGCCCTTGAGCCGTCTGCTGGAGCCCCTCCGAGCCCCGAGGCCACCCACTGAGACCGGCTCTGGGAGTGGGAGTGTCCGGACCCCTGAGGCGCTGGTGCTGATTGTGCCTTGGGGGTCTCTGCACAGCTCGGGTCATCTGGGCGCCTGGCGGGGACTGGGGCTGCCCCCCGATAGCCTCCTGGGCTGGGATGTGCTCAGGGCCCCCCAGACCCCCTTCTGGCCTTTGCTGGCTTTGCAGCCAGCATCCATCTGGTGGGTGCTGGCTTCTGAGTGCCACCTGGGACACAGGCCTCAGGGTGGAGGGGACATCTGTCAGGCTTGGAGTCAGGTCAGCCTGCCTGCTCCTAGAGGACATGGCTGAGCTTCTGTGGTCACAGCCACCCCTTGCACGGCCTGGTCCCAGCTCCTGAGTGTGTGGCAGGTACCCTGGGCCCAGAGGAGCTGGGTCGGAAAACTGGACCGCCCTGGTGCCAGCCTGAC	CCGGCTTCTCCTCAGGGATGCTTGAGTACGAACCGGCCAAGAGGTTCTCCATCCGGCAGATCCGGCAGCACAGGTGAGCGGCCCCTGGGGGCAGTGGGGCCGAGGCTGCAGGGAGGCCGGCCATGTGGGCAGCTGGTTGAGCGGGCGCTAGAGCAGGGCGTGGTGGGGGTGCCAGGCTGGGCTGGGGCCAGACCCCGTGCAGCGCCCGCAGTTCTCGGGGCCCGAGTGGGGTCTCTGGGCAGTGTCCTGTTACCGGCCAGACCCAGGCGCCTTGTCCGAACTGGGGTCTGAGTGAGGACATGCGTCCGTCCCTGCCCTAGGCATGGAGATGCGCCAGGAAGGGCACAGCTGGTCCCAAACACTGGCGAGAGCCTCTCTTTTTCCCCTCCTCCTGGGGCTCCCAGCAGCAGGGTGTGGCTGGGATCCAGCCCAGGGCCCCCAGCTCCATGACAGGGAAGACAGAGCAGCGGACGGGGTCAGCAGGCCCCACAGTGCCGCCTCCCTCACTTCGTGGGCTCTGCTCCTCTGCACCAGCCCCTGGAGGCCCTTGAGCCGTCTGCTGGAGCCCCTCCGAGCCCCGAGGCCACCCACTGAGACCGGCTCTGGGAGTGGGAGTGTCCGGACCCCTGAGGCGCTGGTGCTGATTGTGCCTTGGGGGTCTCTGCACAGCTCGGGTCATCTGGGCGCCTGGCGGGGACTGGGGCTGCCCCCCGATAGCCTCCTGGGCTGGGATGTGCTCAGGGCCCCCCAGACCCCCTTCTGGCCTTTGCTGGCTTTGCAGCCAGCATCCATCTGGTGGGTGCTGGCTTCTGAGTGCCACCTGGGACACAGGCCTCAGGGTGGAGGGGACATCTGTCAGGCTTGGAGTCAGGTCAGCCTGCCTGCTCCTAGAGGACATGGCTGAGCTTCTGTGGTCACAGCCACCCCTTGCACGGCCTGGTCCCAGCTCCTGAGTGTGTGGCAGGTACCCTGGGCCCAGAGGAGCTGGGTCGGAAAACTGGACCGCCCTGGTGCCAGCCTGAC	-	novel	NA	P-0052085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	60	670	0	ENST00000326873.7:c.863-15_921-29del		p.X288_splice	ENST00000326873	NM_000455.4	288		7/10	0.351736258800771	2	FACETS	0.736	0.637	0.843	0.368	0.318	0.422	SUBCLONAL	1	TRUE	0	0.438097582827387	2		670	372	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451801	29451801	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	34	375	0	ENST00000389048.3:c.2764G>C	p.Gly922Arg	p.G922R	ENST00000389048	NM_004304.4	922	Gga/Cga	16/29	0.32626631955362	3	FACETS	0.577	0.472	0.694	0.288	0.236	0.347	SUBCLONAL	1	TRUE	1	0.438097582827387	3		375	328	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286784	212286784	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	29	394	0	ENST00000342788.4:c.2912C>A	p.Ala971Asp	p.A971D	ENST00000342788	NM_005235.2	971	gCt/gAt	24/28	0.360243881237948	3	FACETS	0.504	0.405	0.617	0.252	0.202	0.309	SUBCLONAL	1	TRUE	1	0.438097582827387	3		394	320	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332888	153332888	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	56	412	0	ENST00000281708.4:c.68C>G	p.Pro23Arg	p.P23R	ENST00000281708	NM_033632.3	23	cCt/cGt	2/12	1	2	FACETS	0.662	0.569	0.763	0.662	0.569	0.763	SUBCLONAL	1	TRUE	1	0.438097582827387	2		412	386	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001579	150001579	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs112659070	NA	P-0052085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	30	237	0	ENST00000253339.5:c.2025A>T	p.Gln675His	p.Q675H	ENST00000253339		675	caA/caT	4/7	1	2	FACETS	0.964	0.789	1	0.964	0.789	1	CLONAL	1	TRUE	1	0.438097582827387	2		237	142	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411659	116411659	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	50	470	0	ENST00000397752.3:c.2838A>T	p.Leu946Phe	p.L946F	ENST00000397752	NM_000245.2	946	ttA/ttT	13/21	1	2	FACETS	0.885	0.757	1	0.885	0.757	1	CLONAL	1	TRUE	1	0.438097582827387	2		470	258	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0052086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	31	407	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.296	0.238	0.361	0.296	0.238	0.361	SUBCLONAL	1	TRUE	1	0.32	2		408	655	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729271	41729271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749989847	NA	P-0052086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	74	467	1	ENST00000242208.4:c.1258G>A	p.Val420Met	p.V420M	ENST00000242208	NM_002192.2	420	Gtg/Atg	3/3	0.234136193202329	3	FACETS	1	0.948	1	0.576	0.505	0.651	CLONAL	1	TRUE	1	0.32	3		468	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578281	7578281	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660254	NA	P-0052086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	138	711	0	ENST00000269305.4:c.568C>A	p.Pro190Thr	p.P190T	ENST00000269305	NM_001126112.2	190	Cct/Act	6/11	0.223766329976893	2	FACETS	1	0.987	1	0.737	0.673	0.804	CLONAL	1	TRUE	0	0.32	2		711	585	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40461070	40461070	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778121170	NA	P-0052086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	57	883	0	ENST00000345506.4:c.2068G>A	p.Ala690Thr	p.A690T	ENST00000345506	NM_003152.3	690	Gct/Act	18/20	1	2	FACETS	0.405	0.346	0.469	0.405	0.346	0.469	SUBCLONAL	1	TRUE	1	0.32	2		883	880	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46276004	46276004	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs970774570	NA	P-0052086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	47	610	0	ENST00000371998.3:c.3440A>G	p.Asn1147Ser	p.N1147S	ENST00000371998		1147	aAt/aGt	18/23	0.12543917733268	5	FACETS	0.672	0.566	0.789	0.168	0.141	0.198	INDETERMINATE	1	TRUE	1	0.32	5		610	647	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30323836	30323836	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	11	270	0	ENST00000322652.5:c.1814A>T	p.Asp605Val	p.D605V	ENST00000322652	NM_015355.2	605	gAt/gTt	15/16	1	2	FACETS	0.409	0.283	0.565	0.409	0.283	0.565	SUBCLONAL	1	TRUE	1	0.32	2		270	168	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000373	42000373	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0052086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	25	456	0	ENST00000219905.7:c.2392A>T	p.Lys798Ter	p.K798*	ENST00000219905	NM_001164273.1	798	Aaa/Taa	7/24	0.301048359924591	1	FACETS	0.573	0.454	0.709	0.573	0.454	0.709	SUBCLONAL	1	TRUE	0	0.32	1		456	229	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645128	67645151	+	inframe_deletion	In_Frame_Del	DEL	AGAAGAACTTCAGGGGGCTTATGA	AGAAGAACTTCAGGGGGCTTATGA	-	novel	NA	P-0052086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	53	676	0	ENST00000264010.4:c.394_417del	p.Glu132_Glu139del	p.E132_E139del	ENST00000264010	NM_006565.3	131	gtAGAAGAACTTCAGGGGGCTTATGAa/gta	3/12	1	2	FACETS	0.663	0.565	0.769	0.663	0.565	0.769	SUBCLONAL	1	TRUE	1	0.32	2		676	500	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120398	70120408	+	frameshift_variant	Frame_Shift_Del	DEL	CCTACATGAAC	CCTACATGAAC	-	novel	NA	P-0052086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	105	821	0	ENST00000245479.2:c.1402_1412del	p.Tyr468ArgfsTer106	p.Y468Rfs*106	ENST00000245479	NM_000346.3	467	aCCTACATGAAC/a	3/3	1	2	FACETS	0.837	0.75	0.93	0.837	0.75	0.93	CLONAL	1	TRUE	1	0.32	2		821	784	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279557	18279557	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1443129832	NA	P-0052086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	110	590	0	ENST00000222254.8:c.1830C>A	p.Asp610Glu	p.D610E	ENST00000222254	NM_005027.3	610	gaC/gaA	15/16	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.32	2		590	670	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70005672	70005672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	19	437	0	ENST00000394351.3:c.701C>T	p.Ser234Leu	p.S234L	ENST00000394351	NM_000248.3	234	tCa/tTa	7/9	1	2	FACETS	0.533	0.405	0.681	0.533	0.405	0.681	SUBCLONAL	1	TRUE	1	0.32	2		437	223	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069645	69069645	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	27	474	0	ENST00000288368.4:c.4320G>C	p.Lys1440Asn	p.K1440N	ENST00000288368	NM_024870.2	1440	aaG/aaC	35/40	1	2	FACETS	0.559	0.445	0.688	0.559	0.445	0.688	SUBCLONAL	1	TRUE	1	0.32	2		474	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0052089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	499	1000	4	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.320351761675658	1	FACETS	1	0.994	1	1	0.994	1	INDETERMINATE	1	TRUE	0	0.659085578303011	1		1004	889	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162323	47162323	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs773098323	NA	P-0052089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	31	419	0	ENST00000409792.3:c.3803C>G	p.Ser1268Cys	p.S1268C	ENST00000409792	NM_014159.6	1268	tCt/tGt	3/21	0.650514376764467	3	FACETS	0.218	0.176	0.267	0.109	0.088	0.134	SUBCLONAL	1	TRUE	1	0.659085578303011	3		419	573	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157256597	157256598	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	novel	NA	P-0052089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	12	258	2	ENST00000346085.5:c.1927-2dup		p.X643_splice	ENST00000346085	NM_020732.3	643			0.659085578303011	1	FACETS	0.104	0.073	0.143	0.104	0.073	0.143	SUBCLONAL	1	TRUE	0	0.659085578303011	1		260	234	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941242	36941242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	114	883	2	ENST00000361632.4:c.97G>A	p.Ala33Thr	p.A33T	ENST00000361632		33	Gcc/Acc	3/16	0.211178916221086	2	FACETS	0.436	0.392	0.482	0.218	0.196	0.241	INDETERMINATE	1	TRUE	0	0.659085578303011	2		885	793	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971241	18971241	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	105	745	0	ENST00000262803.5:c.2294T>C	p.Leu765Pro	p.L765P	ENST00000262803	NM_002911.3	765	cTg/cCg	16/24	0.360089943656078	3	FACETS	0.46	0.411	0.512	0.23	0.205	0.256	INDETERMINATE	1	TRUE	1	0.659085578303011	3		745	921	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578525	7578525	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519976	NA	P-0052091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	170	929	0	ENST00000269305.4:c.405C>G	p.Cys135Trp	p.C135W	ENST00000269305	NM_001126112.2	135	tgC/tgG	5/11	0.704169532770034	1	FACETS	0.992	0.934	1	0.992	0.934	1	CLONAL	1	TRUE	0	0.742674649285003	1		929	290	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664915	138664915	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	58	271	0	ENST00000330315.3:c.650C>G	p.Ser217Cys	p.S217C	ENST00000330315	NM_023067.3	217	tCc/tGc	1/1	0.525263215548529	3	FACETS	1	0.925	1	0.544	0.474	0.616	CLONAL	1	TRUE	1	0.742674649285003	3		271	197	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	protein_altering_variant	In_Frame_Ins	INS	-	-	GTT	rs1554350347	NA	P-0052091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	385	832	0	ENST00000275493.2:c.2308_2309insGTT	p.Asp770delinsGlyTyr	p.D770delinsGY	ENST00000275493	NM_005228.3	770	gac/gGTTac	20/28	0.605829075141467	4	FACETS	0.951	0.915	0.987			1	CLONAL	3	TRUE	NA	0.742674649285003	4		832	633	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578242	7578242	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882003	NA	P-0052092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	301	714	0	ENST00000269305.4:c.607G>T	p.Val203Leu	p.V203L	ENST00000269305	NM_001126112.2	203	Gtg/Ttg	6/11	0.509170070574057	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.509170070574057	1		714	720	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851697	134851697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370730579	NA	P-0052092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	239	774	0	ENST00000398015.3:c.1103G>A	p.Arg368Gln	p.R368Q	ENST00000398015	NM_004441.4	368	cGg/cAg	5/16	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.509170070574057	2		774	767	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56477589	56477589	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	305	682	0	ENST00000267101.3:c.137A>C	p.Tyr46Ser	p.Y46S	ENST00000267101	NM_001982.3	46	tAc/tCc	2/28	0.0979422980108362	4	FACETS	0.846	0.798	0.895	0.846	0.798	0.895	INDETERMINATE	2	TRUE	2	0.509170070574057	4		682	1069	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0052093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	102	404	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	FALSE	1	0.288363137841617	2		404	685	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101327	27101327	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	144	1030	0	ENST00000324856.7:c.4609C>T	p.Gln1537Ter	p.Q1537*	ENST00000324856	NM_006015.4	1537	Cag/Tag	18/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.288363137841617	2		1030	898	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052633	42052633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	88	393	0	ENST00000219905.7:c.7304G>A	p.Arg2435Gln	p.R2435Q	ENST00000219905	NM_001164273.1	2435	cGg/cAg	20/24	1	2	FACETS	0.994	0.882	1	0.994	0.882	1	CLONAL	1	FALSE	1	0.288363137841617	2		393	614	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574620	41574620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	130	932	0	ENST00000263253.7:c.6905C>T	p.Ser2302Phe	p.S2302F	ENST00000263253	NM_001429.3	2302	tCt/tTt	31/31	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	1	0.288363137841617	2		932	874	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0052094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	276	454	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.340458071965974	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.340458071965974	2		454	728	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0052094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	286	373	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.28391104165288	4	FACETS	1	0.971	1	1	0.995	1	CLONAL	3	TRUE	2	0.340458071965974	4		373	721	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836985	89836985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs539161141	NA	P-0052094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	221	587	1	ENST00000389301.3:c.2209G>A	p.Ala737Thr	p.A737T	ENST00000389301	NM_000135.2	737	Gct/Act	24/43	0.215273271926986	4	FACETS	0.946	0.881	1	0.946	0.881	1	CLONAL	2	TRUE	2	0.340458071965974	4		588	920	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431810	49431810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769315900	NA	P-0052094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	145	583	0	ENST00000301067.7:c.9329G>A	p.Arg3110His	p.R3110H	ENST00000301067	NM_003482.3	3110	cGc/cAc	34/54	0.28391104165288	4	FACETS	1	0.98	1	0.625	0.57	0.683	CLONAL	1	TRUE	2	0.340458071965974	4		583	913	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087395	27087396	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0052094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	260	509	0	ENST00000324856.7:c.1969_1970insA	p.Leu657HisfsTer19	p.L657Hfs*19	ENST00000324856	NM_006015.4	657	ctg/cAtg	5/20	0.312733406752329	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.340458071965974	3		509	820	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95592973	95592973	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	85	170	0	ENST00000393063.1:c.847G>T	p.Asp283Tyr	p.D283Y	ENST00000393063	NM_030621.3	283	Gat/Tat	8/28	0.28391104165288	4	FACETS	1	0.894	1	1	0.894	1	CLONAL	2	TRUE	2	0.340458071965974	4		170	334	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993867	72993867	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200390317	NA	P-0052094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	70	529	1	ENST00000268489.5:c.178C>T	p.Arg60Cys	p.R60C	ENST00000268489	NM_006885.3	60	Cgc/Tgc	2/10	0.215273271926986	4	FACETS	0.777	0.677	0.886	0.389	0.338	0.443	SUBCLONAL	1	TRUE	2	0.340458071965974	4		530	709	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038810	47038810	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	485	692	0	ENST00000377604.3:c.817C>A	p.Pro273Thr	p.P273T	ENST00000377604	NM_001204468.1	273	Ccg/Acg	9/24	0.340458071965974	8	FACETS	1	0.992	1			1	CLONAL	3	TRUE	NA	0.340458071965974	8		692	1648	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038875	47038875	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	428	600	0	ENST00000377604.3:c.882C>G	p.Ser294Arg	p.S294R	ENST00000377604	NM_001204468.1	294	agC/agG	9/24	0.340458071965974	8	FACETS	1	0.987	1			1	CLONAL	3	TRUE	NA	0.340458071965974	8		600	1547	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039421	47039421	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	389	615	0	ENST00000377604.3:c.1044C>G	p.Ile348Met	p.I348M	ENST00000377604	NM_001204468.1	348	atC/atG	10/24	0.340458071965974	8	FACETS	1	0.983	1			1	CLONAL	3	TRUE	NA	0.340458071965974	8		615	1431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121912651	NA	P-0052095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	369	716	0	ENST00000269305.4:c.742C>G	p.Arg248Gly	p.R248G	ENST00000269305	NM_001126112.2	248	Cgg/Ggg	7/11	0.388826452703863	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.516719392036272	2		716	711	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100175	27100176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0052095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	249	662	3	ENST00000324856.7:c.3977dup	p.Gln1327AlafsTer11	p.Q1327Afs*11	ENST00000324856	NM_006015.4	1324	tac/taCc	16/20	0.516719392036272	3	FACETS	0.778	0.731	0.827	0.778	0.731	0.827	SUBCLONAL	2	TRUE	1	0.516719392036272	3		665	779	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596057	43596057	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	71	872	0	ENST00000355710.3:c.224C>A	p.Thr75Lys	p.T75K	ENST00000355710	NM_020975.4	75	aCg/aAg	2/20	0.23719046968838	3	FACETS	0.361	0.314	0.412			1	INDETERMINATE	1	TRUE	NA	0.516719392036272	3		872	957	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70441196	70441196	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	40	513	0	ENST00000373644.4:c.4865del	p.Arg1622HisfsTer2	p.R1622Hfs*2	ENST00000373644	NM_030625.2	1622	cGa/ca	9/12	0.23719046968838	3	FACETS	0.466	0.387	0.553			1	INDETERMINATE	1	TRUE	NA	0.516719392036272	3		513	418	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562218	95562218	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	68	420	1	ENST00000393063.1:c.5039A>T	p.Lys1680Met	p.K1680M	ENST00000393063	NM_030621.3	1680	aAg/aTg	24/28	1	2	FACETS	0.698	0.61	0.792	0.698	0.61	0.792	SUBCLONAL	1	TRUE	1	0.516719392036272	2		421	377	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222196	5222196	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0052095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	306	718	0	ENST00000357368.4:c.3139A>T	p.Lys1047Ter	p.K1047*	ENST00000357368	NM_002850.3	1047	Aag/Tag	19/38	0.516719392036272	2	FACETS	0.92	0.874	0.965	0.92	0.874	0.965	CLONAL	2	TRUE	0	0.516719392036272	2		718	644	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107035	11107038	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	novel	NA	P-0052095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	276	598	0	ENST00000358026.2:c.1742_1745del	p.Lys581ArgfsTer31	p.K581Rfs*31	ENST00000358026	NM_001128849.1	580	aaAAAG/aa	10/36	0.516719392036272	2	FACETS	0.944	0.895	0.992	0.944	0.895	0.992	CLONAL	2	TRUE	0	0.516719392036272	2		598	566	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965237	25965237	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	470	635	0	ENST00000435504.4:c.3969A>G	p.Ile1323Met	p.I1323M	ENST00000435504		1323	atA/atG	13/13	0.516719392036272	5	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	2	0.516719392036272	5		635	990	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754890	29754890	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	311	618	0	ENST00000389048.3:c.1045G>T	p.Val349Phe	p.V349F	ENST00000389048	NM_004304.4	349	Gtc/Ttc	4/29	0.516719392036272	5	FACETS	0.94	0.887	0.995	0.627	0.591	0.664	CLONAL	2	TRUE	2	0.516719392036272	5		618	1136	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138384010	138384010	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	74	576	0	ENST00000289153.2:c.2540G>C	p.Arg847Pro	p.R847P	ENST00000289153	NM_006219.2	847	cGc/cCc	18/22	0.516719392036272	3	FACETS	0.603	0.528	0.683	0.301	0.264	0.342	SUBCLONAL	1	TRUE	1	0.516719392036272	3		576	598	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169953106	169953106	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	61	531	0	ENST00000295797.4:c.190C>G	p.Gln64Glu	p.Q64E	ENST00000295797	NM_002740.5	64	Cag/Gag	2/18	0.516719392036272	3	FACETS	0.498	0.43	0.573	0.249	0.215	0.287	SUBCLONAL	1	TRUE	1	0.516719392036272	3		531	596	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430354	181430354	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	225	479	0	ENST00000325404.1:c.206C>A	p.Ser69Ter	p.S69*	ENST00000325404	NM_003106.3	69	tCg/tAg	1/1	0.516719392036272	3	FACETS	0.903	0.846	0.96	0.903	0.846	0.96	CLONAL	2	TRUE	1	0.516719392036272	3		479	607	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557738	187557738	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0052095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	81	373	0	ENST00000441802.2:c.3972+1G>T		p.X1324_splice	ENST00000441802	NM_005245.3	1324			1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.516719392036272	2		373	298	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803101	32803101	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	67	798	0	ENST00000374899.4:c.775del	p.Leu259Ter	p.L259*	ENST00000374899	NM_018833.2	259	Ctg/tg	5/12	0.516719392036272	3	FACETS	0.399	0.346	0.457	0.199	0.173	0.229	SUBCLONAL	1	TRUE	1	0.516719392036272	3		798	818	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023210	150023210	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0052095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	110	534	0	ENST00000253339.5:c.53T>C	p.Phe18Ser	p.F18S	ENST00000253339		18	tTt/tCt	1/7	0.367483188673323	2	FACETS	0.97	0.877	1	0.485	0.438	0.534	CLONAL	1	TRUE	0	0.516719392036272	2		534	439	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0052096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	325	315	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	0.77719778461041	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.77719778461041	4		315	718	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0052096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	519	727	3	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.77719778461041	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.77719778461041	2		730	634	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	497	748	1	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.77719778461041	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.77719778461041	3		749	853	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389107	31389107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749860839	NA	P-0052096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	176	556	0	ENST00000328111.2:c.2020G>A	p.Glu674Lys	p.E674K	ENST00000328111	NM_006892.3	674	Gaa/Aaa	19/23	0.690469378682723	4	FACETS	0.905	0.834	0.979	0.453	0.417	0.49	CLONAL	1	TRUE	2	0.77719778461041	4		556	889	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350822	15350822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200902225	NA	P-0052096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1233	217	718	0	ENST00000263377.2:c.3181G>A	p.Glu1061Lys	p.E1061K	ENST00000263377	NM_058243.2	1061	Gaa/Aaa	15/20	0.77719778461041	6	FACETS	0.984	0.912	1	0.246	0.228	0.265	CLONAL	1	TRUE	2	0.77719778461041	6		718	1450	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998940	100998940	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	561	773	0	ENST00000325455.5:c.862C>G	p.Pro288Ala	p.P288A	ENST00000325455	NM_001202474.3	288	Ccg/Gcg	1/8	0.776191140767024	4	FACETS	1	0.98	1	0.759	0.736	0.781	CLONAL	3	TRUE	0	0.77719778461041	4		773	845	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952942	2952942	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	216	759	0	ENST00000396946.4:c.2998G>C	p.Glu1000Gln	p.E1000Q	ENST00000396946	NM_032415.4	1000	Gag/Cag	22/25	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.77719778461041	2		759	542	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	89	230	0				ENST00000310581	NM_198253.2	-/1132			0.235765404702477	4	FACETS	0.972	0.869	1	0.972	0.869	1	CLONAL	2	TRUE	2	0.322875551804662	4		230	375	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057961	27057961	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	C	C	TA	novel	NA	P-0052097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	347	799	0	ENST00000324856.7:c.1669delinsTA	p.Gln557Ter	p.Q557*	ENST00000324856	NM_006015.4	557	Cag/TAag	3/20	0.254612181423051	4	FACETS	0.964	0.915	1	1	0.995	1	CLONAL	3	TRUE	2	0.322875551804662	4		799	983	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597942	43597942	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	282	1128	0	ENST00000355710.3:c.490G>C	p.Glu164Gln	p.E164Q	ENST00000355710	NM_020975.4	164	Gag/Cag	3/20	0.255986734805944	5	FACETS	1	0.968	1	0.698	0.655	0.742	CLONAL	2	TRUE	2	0.322875551804662	5		1128	1238	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019398	42019398	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	36	544	0	ENST00000219905.7:c.3451G>A	p.Glu1151Lys	p.E1151K	ENST00000219905	NM_001164273.1	1151	Gaa/Aaa	10/24	0.291983977238673	3	FACETS	0.909	0.75	1	0.454	0.375	0.543	CLONAL	1	TRUE	1	0.322875551804662	3		544	285	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0052097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	210	615	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.255986734805944	5	FACETS	1	0.973	1	0.729	0.678	0.782	CLONAL	2	TRUE	2	0.322875551804662	5		615	883	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0052097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	302	923	0	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	0.255986734805944	5	FACETS	0.879	0.829	0.93	0.879	0.829	0.93	CLONAL	3	TRUE	2	0.322875551804662	5		923	1053	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761202	59761202	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	92	647	0	ENST00000259008.2:c.3205C>G	p.Gln1069Glu	p.Q1069E	ENST00000259008	NM_032043.2	1069	Caa/Gaa	20/20	0.235765404702477	4	FACETS	0.865	0.772	0.962	0.865	0.772	0.962	CLONAL	2	TRUE	2	0.322875551804662	4		647	436	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	78	387	1	ENST00000335508.6:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000335508	NM_012433.2	902	Gaa/Aaa	18/25	0.322875551804662	3	FACETS	0.888	0.803	0.973	1	0.969	1	CLONAL	4	TRUE	0	0.322875551804662	3		388	158	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265582	198265582	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	86	473	0	ENST00000335508.6:c.2575G>C	p.Asp859His	p.D859H	ENST00000335508	NM_012433.2	859	Gat/Cat	18/25	0.322875551804662	3	FACETS	0.946	0.853	1	0.946	0.853	1	CLONAL	3	TRUE	0	0.322875551804662	3		473	218	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412905	49412905	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519951	NA	P-0052097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	121	570	0	ENST00000418115.1:c.118G>C	p.Glu40Gln	p.E40Q	ENST00000418115	NM_001664.2	40	Gag/Cag	2/5	0.182785358985682	4	FACETS	0.93	0.844	1	0.93	0.844	1	INDETERMINATE	2	TRUE	2	0.322875551804662	4		570	533	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412986	49412986	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	118	778	0	ENST00000418115.1:c.37G>C	p.Asp13His	p.D13H	ENST00000418115	NM_001664.2	13	Gat/Cat	2/5	0.182785358985682	4	FACETS	0.795	0.719	0.875	0.795	0.719	0.875	INDETERMINATE	2	TRUE	2	0.322875551804662	4		778	608	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433500	138433500	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0052097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	38	449	0	ENST00000289153.2:c.1112C>G	p.Ser371Ter	p.S371*	ENST00000289153	NM_006219.2	371	tCa/tGa	7/22	0.182785358985682	4	FACETS	1	0.915	1	0.585	0.486	0.694	INDETERMINATE	1	TRUE	2	0.322875551804662	4		449	266	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280135	66280135	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	15	418	0	ENST00000273854.3:c.1554C>G	p.Ile518Met	p.I518M	ENST00000273854	NM_004439.5	518	atC/atG	7/18	0.235765404702477	4	FACETS	0.475	0.347	0.628	0.237	0.173	0.314	SUBCLONAL	1	TRUE	2	0.322875551804662	4		418	259	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918622	44918622	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	272	362	0	ENST00000377967.4:c.1105C>T	p.Gln369Ter	p.Q369*	ENST00000377967	NM_021140.2	369	Cag/Tag	12/29	0.322875551804662	4	FACETS	1	0.985	1			1	CLONAL	5	TRUE	NA	0.322875551804662	4		362	418	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338683	70338683	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	312	363	0	ENST00000374080.3:c.79C>G	p.Gln27Glu	p.Q27E	ENST00000374080		27	Cag/Gag	1/45	0.322875551804662	4	FACETS	0.995	0.952	1			1	CLONAL	5	TRUE	NA	0.322875551804662	4		363	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0052098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	145	442	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.135183223752293	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.176412672280915	2		442	727	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0052098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	39	367	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	0.162051623289093	3	FACETS	1	0.933	1	0.635	0.527	0.755	CLONAL	1	TRUE	1	0.176412672280915	3		367	379	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864461	162864461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146288080	NA	P-0052098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	49	480	0	ENST00000366898.1:c.52G>A	p.Asp18Asn	p.D18N	ENST00000366898	NM_004562.2	18	Gat/Aat	2/12	0.176412672280915	3	FACETS	1	0.906	1	0.55	0.465	0.643	CLONAL	1	TRUE	1	0.176412672280915	3		480	550	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56792506	56792506	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0052098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	113	629	0	ENST00000308159.5:c.236A>C	p.Glu79Ala	p.E79A	ENST00000308159	NM_014669.4	79	gAg/gCg	3/22	0.10395570284044	5	FACETS	0.846	0.763	0.934	0.635	0.572	0.701	INDETERMINATE	3	TRUE	1	0.176412672280915	5		629	638	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645556	215645556	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	65	500	0	ENST00000260947.4:c.1042G>T	p.Val348Phe	p.V348F	ENST00000260947	NM_000465.2	348	Gtt/Ttt	4/11	0.135183223752293	2	FACETS	0.98	0.854	1	0.98	0.854	1	CLONAL	2	TRUE	0	0.176412672280915	2		500	376	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590415	67590447	+	inframe_deletion	In_Frame_Del	DEL	ATATTTGAAGAACAGTGCCAGACCCAAGAGCGG	ATATTTGAAGAACAGTGCCAGACCCAAGAGCGG	-	novel	NA	P-0052098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	17	146	0	ENST00000274335.5:c.1477_1509del	p.Ile493_Arg503del	p.I493_R503del	ENST00000274335		493	ATATTTGAAGAACAGTGCCAGACCCAAGAGCGG/-	11/15	0.176412672280915	2	FACETS	1	0.892	1	0.703	0.529	0.906	CLONAL	1	TRUE	0	0.176412672280915	2		146	137	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0052099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	383	885	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	0.349769252490913	4	FACETS	0.947	0.9	0.995	0.947	0.9	0.995	CLONAL	2	TRUE	2	0.50462979539766	4		885	1206	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717699	89717699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	215	530	0	ENST00000371953.3:c.724G>A	p.Glu242Lys	p.E242K	ENST00000371953	NM_000314.4	242	Gag/Aag	7/9	0.50462979539766	3	FACETS	0.928	0.869	0.988	0.928	0.869	0.988	CLONAL	2	TRUE	1	0.50462979539766	3		530	575	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200975	108200975	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	319	491	0	ENST00000278616.4:c.7342G>C	p.Asp2448His	p.D2448H	ENST00000278616	NM_000051.3	2448	Gat/Cat	50/63	0.503024636197358	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.50462979539766	3		491	502	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36253011	36253011	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587776809	NA	P-0052099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	266	456	0	ENST00000300305.3:c.352-1G>A		p.X118_splice	ENST00000300305		118			0.42339109776177	5	FACETS	0.944	0.891	0.997	0.944	0.891	0.997	CLONAL	3	TRUE	2	0.50462979539766	5		456	654	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941842	44941843	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTAA	novel	NA	P-0052099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	82	247	0	ENST00000377967.4:c.3166_3167insTTAA	p.His1056LeufsTer4	p.H1056Lfs*4	ENST00000377967	NM_021140.2	1056	cat/cTTAAat	21/29	0.429516159403282	2	FACETS	1	0.951	1			1	CLONAL	2	TRUE	NA	0.50462979539766	2		247	152	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224609	123224609	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0052099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	172	283	0	ENST00000218089.9:c.3463del	p.Tyr1155IlefsTer5	p.Y1155Ifs*5	ENST00000218089	NM_001042749.1	1154	gaT/ga	31/35	0.429516159403282	2	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.50462979539766	2		283	278	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604750	48604750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	123	544	0	ENST00000342988.3:c.1572G>T	p.Trp524Cys	p.W524C	ENST00000342988	NM_005359.5	524	tgG/tgT	12/12	0.337771773048597	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.337771773048597	1		544	557	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611047	100611047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs128621202	NA	P-0052100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	136	420	0	ENST00000308731.7:c.1559G>A	p.Arg520Gln	p.R520Q	ENST00000308731	NM_000061.2	520	cGa/cAa	15/19	1	1	FACETS	0.824	0.757	0.893	1	0.989	1	CLONAL	2	TRUE	0	0.337771773048597	1		420	406	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602329	10602329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	156	915	1	ENST00000171111.5:c.1249G>A	p.Gly417Arg	p.G417R	ENST00000171111	NM_203500.1	417	Ggg/Agg	3/6	1	2	FACETS	0.957	0.876	1	0.957	0.876	1	CLONAL	1	TRUE	1	0.337771773048597	2		916	965	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104356978	104356978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761003435	NA	P-0052100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	147	731	2	ENST00000369902.3:c.838C>T	p.Arg280Trp	p.R280W	ENST00000369902	NM_016169.3	280	Cgg/Tgg	7/12	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.337771773048597	2		733	816	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856605	111856605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	115	360	0	ENST00000341259.2:c.656G>A	p.Arg219His	p.R219H	ENST00000341259	NM_005475.2	219	cGc/cAc	2/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.337771773048597	2		360	548	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440685	56440686	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0052100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	73	758	0	ENST00000407977.2:c.531_532dup	p.Lys178ThrfsTer8	p.K178Tfs*8	ENST00000407977		178	aag/aCAag	5/10	1	2	FACETS	0.526	0.459	0.598	0.526	0.459	0.598	SUBCLONAL	1	TRUE	1	0.337771773048597	2		758	822	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180958	108180959	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0052101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	98	412	0	ENST00000278616.4:c.5835_5836del	p.Gln1946ValfsTer18	p.Q1946Vfs*18	ENST00000278616	NM_000051.3	1945	gCT/g	39/63	0.881720639440176	1	FACETS	0.956	0.897	1	0.956	0.897	1	CLONAL	1	TRUE	0	0.881720639440176	1		412	130	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696689	47696689	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519972	NA	P-0052102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	173	457	0	ENST00000347630.2:c.259T>A	p.Tyr87Asn	p.Y87N	ENST00000347630	NM_001007230.1	87	Tac/Aac	5/11	0.182394150423105	2	FACETS	1	0.989	1	0.695	0.643	0.747	INDETERMINATE	1	TRUE	0	0.458677588063706	2		457	543	SUCCESS
APC	324	MSKCC	GRCh37	5	112175651	112175651	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	111	370	0	ENST00000257430.4:c.4364del	p.Asn1455IlefsTer18	p.N1455Ifs*18	ENST00000257430	NM_000038.5	1454	Aaa/aa	16/16	0.458677588063706	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.458677588063706	1		370	357	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143044480	143044480	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1428613850	NA	P-0052102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	20	417	0	ENST00000262992.4:c.1982T>C	p.Leu661Ser	p.L661S	ENST00000262992	NM_001101669.1	661	tTg/tCg	18/24	1	2	FACETS	0.295	0.225	0.376	0.295	0.225	0.376	SUBCLONAL	1	TRUE	1	0.458677588063706	2		417	296	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0052103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	23	164	1	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.635	0.494	0.8	0.635	0.494	0.8	SUBCLONAL	1	TRUE	1	0.13	2		165	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0052103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	26	713	0	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	1	2	FACETS	0.441	0.347	0.549	0.441	0.347	0.549	SUBCLONAL	1	TRUE	1	0.13	2		713	907	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0052104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	175	578	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.413428027811966	2		578	698	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0052104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	139	442	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.413428027811966	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.413428027811966	1		442	521	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248548	8248548	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	171	644	0	ENST00000335790.3:c.339C>G	p.Cys113Trp	p.C113W	ENST00000335790	NM_002315.2	113	tgC/tgG	3/4	0.312308299107444	1	FACETS	0.993	0.917	1	0.993	0.917	1	CLONAL	1	TRUE	0	0.413428027811966	1		644	661	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521385	8521385	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	123	545	0	ENST00000356435.5:c.853G>A	p.Gly285Arg	p.G285R	ENST00000356435		285	Gga/Aga	9/35	1	2	FACETS	0.985	0.894	1	0.985	0.894	1	CLONAL	1	TRUE	1	0.413428027811966	2		545	604	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354793	40354794	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	C	novel	NA	P-0052104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	43	533	0	ENST00000293328.3:c.2110_2111delinsG	p.Ile704AlafsTer9	p.I704Afs*9	ENST00000293328	NM_012448.3	704	ATc/Gc	17/19	0.413428027811966	1	FACETS	0.333	0.278	0.393	0.333	0.278	0.393	SUBCLONAL	1	TRUE	0	0.413428027811966	1		533	496	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445329	49445329	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1184	134	848	2	ENST00000301067.7:c.2137G>T	p.Asp713Tyr	p.D713Y	ENST00000301067	NM_003482.3	713	Gac/Tac	10/54	0.285346000237801	3	FACETS	0.815	0.738	0.896	0.408	0.369	0.448	CLONAL	1	TRUE	1	0.285045066322417	3		850	1318	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643306	38643312	+	frameshift_variant	Frame_Shift_Del	DEL	CAGACTA	CAGACTA	-	novel	NA	P-0052105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	54	466	1	ENST00000299084.4:c.781_787del	p.Tyr261IlefsTer40	p.Y261Ifs*40	ENST00000299084	NM_152594.2	259	gCAGACTAc/gc	7/7	0.21698871166423	4	FACETS	0.742	0.633	0.862	0.371	0.316	0.431	SUBCLONAL	1	TRUE	2	0.285045066322417	4		467	656	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858420	9858420	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	93	508	0	ENST00000330684.3:c.2981A>G	p.Asn994Ser	p.N994S	ENST00000330684	NM_001134407.1	994	aAc/aGc	13/13	0.222254471992524	3	FACETS	1	0.956	1	0.574	0.511	0.642	CLONAL	1	TRUE	1	0.285045066322417	3		508	649	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578506	7578523	+	inframe_deletion	In_Frame_Del	DEL	GGCAGGTCTTGGCCAGTT	GGCAGGTCTTGGCCAGTT	-	novel	NA	P-0052105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	245	778	0	ENST00000269305.4:c.407_424del	p.Gln136_Cys141del	p.Q136_C141del	ENST00000269305	NM_001126112.2	136	cAACTGGCCAAGACCTGCCct/cct	5/11	0.277724829245959	2	FACETS	0.812	0.758	0.866	0.812	0.758	0.866	CLONAL	2	TRUE	0	0.285045066322417	2		778	1059	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220715	1220716	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	TGTA	novel	NA	P-0052105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	230	630	0	ENST00000326873.7:c.734_734+3dup		p.L245fs	ENST00000326873	NM_000455.4	245	ctc/cTGTAtc	5/10	0.284112801507612	2	FACETS	0.95	0.888	1	0.95	0.888	1	CLONAL	2	TRUE	0	0.285045066322417	2		630	849	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128036758	128036758	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	135	445	0	ENST00000285398.2:c.1721G>T	p.Arg574Leu	p.R574L	ENST00000285398	NM_000122.1	574	cGa/cTa	10/15	0.228285263130755	3	FACETS	0.776	0.707	0.849	0.776	0.707	0.849	SUBCLONAL	2	TRUE	1	0.285045066322417	3		445	697	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576887	212576887	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0052105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	61	407	0	ENST00000342788.4:c.1012G>C	p.Gly338Arg	p.G338R	ENST00000342788	NM_005235.2	338	Ggc/Cgc	9/28	0.228285263130755	3	FACETS	0.974	0.842	1	0.487	0.421	0.559	CLONAL	1	TRUE	1	0.285045066322417	3		407	502	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484858	57485003	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTTTGTGGAGTGACCGCCCACCCCCTGCGCTTGCCCAGGAGGCCCTGGTCTGCACTGTTTATAGAGAAGAACCCCGTGCAAGCATTCCAGACCCCTGGCCGAAAGCGCGCTTCTCCCAAGCATTCACACGGCCTCCCTTCTTGT	AGGTTTGTGGAGTGACCGCCCACCCCCTGCGCTTGCCCAGGAGGCCCTGGTCTGCACTGTTTATAGAGAAGAACCCCGTGCAAGCATTCCAGACCCCTGGCCGAAAGCGCGCTTCTCCCAAGCATTCACACGGCCTCCCTTCTTGT	-	novel	NA	P-0052105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	84	526	2	ENST00000371085.3:c.839+1_840-1del		p.X280_splice	ENST00000371085	NM_000516.4	280		10/13	0.21698871166423	4	FACETS	0.834	0.735	0.94	0.417	0.367	0.47	CLONAL	1	TRUE	2	0.285045066322417	4		528	908	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485136	57485387	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTGTGTATGGCTTCCACTCTTGCTGGCTGTTCATTGCGGTGGTTCTTTTTCAAACGGTCAGGCTGAAAACCCCCATCCCCCTCCCACCACCAAACCATAAAGGATCTATAAGAGAAGCAAGAAAAACGCACTCCCACTAATTCTCATATGGAAAAATCAGGGTTTTGAAGACTTCAGGAGCTACAGAGATGCTAGCACCCCAGCTCTGCTTGAATTTTAAATTACATTAATATGTATTCCCTTTTTATATA	GGTGTGTATGGCTTCCACTCTTGCTGGCTGTTCATTGCGGTGGTTCTTTTTCAAACGGTCAGGCTGAAAACCCCCATCCCCCTCCCACCACCAAACCATAAAGGATCTATAAGAGAAGCAAGAAAAACGCACTCCCACTAATTCTCATATGGAAAAATCAGGGTTTTGAAGACTTCAGGAGCTACAGAGATGCTAGCACCCCAGCTCTGCTTGAATTTTAAATTACATTAATATGTATTCCCTTTTTATATA	-	novel	NA	P-0052105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	54	330	0	ENST00000371085.3:c.970+1_971-1del		p.X324_splice	ENST00000371085	NM_000516.4	324		11/13	0.21698871166423	4	FACETS	0.665	0.567	0.773	0.333	0.283	0.387	SUBCLONAL	1	TRUE	2	0.285045066322417	4		330	732	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485456	57485736	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTGAGTCGAGCCTGTCTTTAGTTTCCTCTCTTGTTCCTCCTCTTTTTCTCATGGATGTAAATTTACTTAATTCCAAATTCAGGGGTTCAGCTACCCAGTTCCATGGTTTTAGTTCACGCACATCCAGTGTGGATTTGAGCTCTTTGCGCCCCTCTTTTTGCTTTTGTTTTCATATGACATCAGAGGCTGGCTGACAGCCGTCCCTGGTAGGTGTCCCCATCAGGGATAGGGTGGTTCCTGGCGAGGGTGTCACTGACAAGTCCCCTTGTTTGTGCCCGCA	GGTGAGTCGAGCCTGTCTTTAGTTTCCTCTCTTGTTCCTCCTCTTTTTCTCATGGATGTAAATTTACTTAATTCCAAATTCAGGGGTTCAGCTACCCAGTTCCATGGTTTTAGTTCACGCACATCCAGTGTGGATTTGAGCTCTTTGCGCCCCTCTTTTTGCTTTTGTTTTCATATGACATCAGAGGCTGGCTGACAGCCGTCCCTGGTAGGTGTCCCCATCAGGGATAGGGTGGTTCCTGGCGAGGGTGTCACTGACAAGTCCCCTTGTTTGTGCCCGCA	-	novel	NA	P-0052105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	37	333	0	ENST00000371085.3:c.1038+1_1039-1del		p.X346_splice	ENST00000371085	NM_000516.4	346		12/13	0.21698871166423	4	FACETS	0.461	0.379	0.553	0.23	0.189	0.277	SUBCLONAL	1	TRUE	2	0.285045066322417	4		333	724	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713483	30713483	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0052105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	257	546	0	ENST00000295754.5:c.808C>T	p.Gln270Ter	p.Q270*	ENST00000295754	NM_003242.5	270	Cag/Tag	4/7	0.249021929918491	3	FACETS	0.884	0.831	0.938	0.884	0.831	0.938	CLONAL	3	TRUE	0	0.285045066322417	3		546	777	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0052105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	204	325	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.285045066322417	6	FACETS	0.979	0.914	1	0.979	0.914	1	CLONAL	4	TRUE	2	0.285045066322417	6		325	574	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039704	47039704	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0052105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	209	306	0	ENST00000377604.3:c.1156A>T	p.Lys386Ter	p.K386*	ENST00000377604	NM_001204468.1	386	Aag/Tag	11/24	0.205943914561491	2	FACETS	0.953	0.893	1			1	CLONAL	3	TRUE	NA	0.285045066322417	2		306	513	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890140	76890140	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	56	246	0	ENST00000373344.5:c.4754C>A	p.Ser1585Tyr	p.S1585Y	ENST00000373344	NM_000489.3	1585	tCt/tAt	17/35	0.205943914561491	2	FACETS	1	0.91	1			1	CLONAL	1	TRUE	NA	0.285045066322417	2		246	365	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793253	33793253	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs137852728	NA	P-0052106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	20	178	0	ENST00000498907.2:c.68del	p.Pro23ArgfsTer137	p.P23Rfs*137	ENST00000498907	NM_004364.3	23	cCg/cg	1/1	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.17	2		178	204	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528448	29528448	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0052106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	21	339	0	ENST00000356175.3:c.1205C>A	p.Ser402Ter	p.S402*	ENST00000356175	NM_000267.3	402	tCa/tAa	11/57	1	2	FACETS	1	0.791	1	1	0.791	1	CLONAL	1	TRUE	1	0.17	2		339	241	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736839	736839	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	17	521	0	ENST00000314574.4:c.1260A>T	p.Leu420Phe	p.L420F	ENST00000314574	NM_005433.3	420	ttA/ttT	10/12	1	2	FACETS	0.678	0.506	0.883	0.678	0.506	0.883	SUBCLONAL	1	TRUE	1	0.17	2		521	295	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45864860	45864871	+	inframe_deletion	In_Frame_Del	DEL	CCAGAGTATGCA	CCAGAGTATGCA	-	novel	NA	P-0052106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	43	807	0	ENST00000391945.4:c.1148_1159del	p.Leu383_Glu387delinsGln	p.L383_E387delinsQ	ENST00000391945	NM_000400.3	383	cTGCATACTCTGGag/cag	12/23	0.3	3	FACETS	0.919	0.768	1			1	CLONAL	1	TRUE	NA	0.17	3		807	597	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198046	185198046	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	23	386	0	ENST00000265026.3:c.2528A>T	p.Gln843Leu	p.Q843L	ENST00000265026	NM_004721.4	843	cAg/cTg	13/14	1	2	FACETS	0.671	0.523	0.844	0.671	0.523	0.844	SUBCLONAL	1	TRUE	1	0.17	2		386	403	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198153	185198153	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	40	567	0	ENST00000265026.3:c.2635G>C	p.Asp879His	p.D879H	ENST00000265026	NM_004721.4	879	Gac/Cac	13/14	1	2	FACETS	0.871	0.723	1	0.871	0.723	1	CLONAL	1	TRUE	1	0.17	2		567	540	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628235	187628235	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	29	614	0	ENST00000441802.2:c.2747C>A	p.Ser916Ter	p.S916*	ENST00000441802	NM_005245.3	916	tCa/tAa	2/27	0.3	1	FACETS	0.811	0.651	0.993	0.811	0.651	0.993	CLONAL	1	TRUE	0	0.17	1		614	385	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793258	33793258	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs867113214	NA	P-0052106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	22	178	0	ENST00000498907.2:c.63C>A	p.Ser21Arg	p.S21R	ENST00000498907	NM_004364.3	21	agC/agA	1/1	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.17	2		178	208	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579451	7579458	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGCTGG	GCTGCTGG	A	novel	NA	P-0052106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	41	819	3	ENST00000269305.4:c.229_236delinsT	p.Pro77PhefsTer44	p.P77Ffs*44	ENST00000269305	NM_001126112.2	77	CCAGCAGCt/Tt	4/11	1	2	FACETS	0.852	0.709	1	0.852	0.709	1	CLONAL	1	TRUE	1	0.17	2		822	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0052107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	591	845	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.589306695315587	3	FACETS	0.953	0.925	0.981	0.953	0.925	0.981	CLONAL	3	TRUE	0	0.589306695315587	3		845	908	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819237	3819237	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	174	681	2	ENST00000262367.5:c.2998G>A	p.Glu1000Lys	p.E1000K	ENST00000262367	NM_004380.2	1000	Gag/Aag	15/31	0.575130960959237	4	FACETS	1	0.967	1	0.363	0.334	0.393	CLONAL	1	TRUE	1	0.589306695315587	4		683	861	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413100	139413100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201236538	NA	P-0052107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	612	984	2	ENST00000277541.6:c.1042G>A	p.Ala348Thr	p.A348T	ENST00000277541	NM_017617.3	348	Gcc/Acc	6/34	0.589306695315587	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.589306695315587	3		986	868	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599209	28599209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	218	1027	0	ENST00000253063.3:c.655G>A	p.Glu219Lys	p.E219K	ENST00000253063	NM_031459.4	219	Gag/Aag	5/10	0.589306695315587	3	FACETS	1	0.945	1	0.509	0.473	0.546	CLONAL	1	TRUE	1	0.589306695315587	3		1027	941	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599944	28599944	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	186	907	0	ENST00000253063.3:c.826G>C	p.Glu276Gln	p.E276Q	ENST00000253063	NM_031459.4	276	Gag/Cag	6/10	0.589306695315587	3	FACETS	1	0.942	1	0.511	0.472	0.551	CLONAL	1	TRUE	1	0.589306695315587	3		907	800	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873137	71873137	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	73	418	0	ENST00000357731.5:c.1057C>G	p.Leu353Val	p.L353V	ENST00000357731	NM_173808.2	353	Cta/Gta	7/7	1	2	FACETS	0.789	0.696	0.887	0.789	0.696	0.887	SUBCLONAL	1	TRUE	1	0.589306695315587	2		418	314	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450049	32450049	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0052107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	161	618	0	ENST00000332351.3:c.763T>A	p.Ser255Thr	p.S255T	ENST00000332351	NM_024426.4	255	Tcg/Acg	2/10	0.589306695315587	3	FACETS	1	0.956	1	0.529	0.487	0.574	CLONAL	1	TRUE	1	0.589306695315587	3		618	668	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533712	41533712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1433822758	NA	P-0052107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	207	681	1	ENST00000263253.7:c.1678G>A	p.Ala560Thr	p.A560T	ENST00000263253	NM_001429.3	560	Gct/Act	8/31	0.589306695315587	5	FACETS	1	0.985	1	0.307	0.284	0.33	CLONAL	1	TRUE	1	0.589306695315587	5		682	1079	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630357	187630357	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0052107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	459	676	0	ENST00000441802.2:c.625A>T	p.Arg209Ter	p.R209*	ENST00000441802	NM_005245.3	209	Aga/Tga	2/27	0.589306695315587	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	0	0.589306695315587	3		676	672	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399851	139399851	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0052107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	199	1019	0	ENST00000277541.6:c.4497C>A	p.Tyr1499Ter	p.Y1499*	ENST00000277541	NM_017617.3	1499	taC/taA	25/34	0.589306695315587	3	FACETS	0.873	0.809	0.94	0.291	0.269	0.314	CLONAL	1	TRUE	0	0.589306695315587	3		1019	1001	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0052109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	357	789	0	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.729184800498196	5	FACETS	0.898	0.852	0.945	0.449	0.426	0.473	CLONAL	2	TRUE	1	0.737777720806727	5		789	1135	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711875	89711875	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587782603	NA	P-0052109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	231	416	0	ENST00000371953.3:c.493G>A	p.Gly165Arg	p.G165R	ENST00000371953	NM_000314.4	165	Gga/Aga	6/9	0.737777720806727	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.737777720806727	2		416	291	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0052109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	199	299	0				ENST00000310581	NM_198253.2	-/1132			0.736967658957413	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.737777720806727	3		299	351	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439775	51439775	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	159	427	0	ENST00000262662.1:c.340G>A	p.Gly114Ser	p.G114S	ENST00000262662		114	Ggc/Agc	4/4	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.737777720806727	2		427	384	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041703	29041703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	185	559	0	ENST00000282397.4:c.116C>T	p.Thr39Ile	p.T39I	ENST00000282397	NM_002019.4	39	aCc/aTc	2/30	0.435513459662138	3	FACETS	0.785	0.734	0.838	0.785	0.734	0.838	INDETERMINATE	2	TRUE	1	0.737777720806727	3		559	437	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218476	36218476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	350	805	0	ENST00000222270.7:c.4255G>A	p.Gly1419Ser	p.G1419S	ENST00000222270	NM_014727.1	1419	Ggc/Agc	16/37	0.736967658957413	3	FACETS	0.959	0.917	1	0.959	0.917	1	CLONAL	2	TRUE	1	0.737777720806727	3		805	677	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873683	151873683	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0052122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	111	622	0	ENST00000262189.6:c.8855C>G	p.Ser2952Ter	p.S2952*	ENST00000262189	NM_170606.2	2952	tCa/tGa	38/59	1	2	FACETS	0.881	0.796	0.969	0.881	0.796	0.969	CLONAL	1	FALSE	1	0.543236449824832	2		622	464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577144	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs879253942	NA	P-0052124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	380	600	0	ENST00000269305.4:c.794T>C	p.Leu265Pro	p.L265P	ENST00000269305	NM_001126112.2	265	cTg/cCg	8/11	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.463393774048658	2		600	688	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858147	40858147	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	65	728	0	ENST00000428826.2:c.1717C>T	p.Pro573Ser	p.P573S	ENST00000428826		573	Cct/Tct	16/21	0.463393774048658	1	FACETS	0.38	0.329	0.435	0.38	0.329	0.435	SUBCLONAL	1	TRUE	0	0.463393774048658	1		728	567	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262484	10262484	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0052124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	156	704	0	ENST00000340748.4:c.2011A>G	p.Lys671Glu	p.K671E	ENST00000340748		671	Aag/Gag	22/40	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.463393774048658	2		704	617	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177053	56177053	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	86	361	0	ENST00000399503.3:c.2323C>T	p.His775Tyr	p.H775Y	ENST00000399503	NM_005921.1	775	Cat/Tat	13/20	0.280736768417266	1	FACETS	0.76	0.677	0.848	0.76	0.677	0.848	SUBCLONAL	1	TRUE	0	0.463393774048658	1		361	375	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057703	180057703	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0052124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	66	855	0	ENST00000261937.6:c.252C>G	p.Cys84Trp	p.C84W	ENST00000261937	NM_182925.4	84	tgC/tgG	3/30	0.247977163559972	2	FACETS	0.418	0.363	0.479	0.209	0.181	0.24	INDETERMINATE	1	TRUE	0	0.463393774048658	2		855	681	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913517	NA	P-0052126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	133	430	0	ENST00000288135.5:c.1676T>C	p.Val559Ala	p.V559A	ENST00000288135	NM_000222.2	559	gTt/gCt	11/21	1	2	FACETS	0.974	0.896	1	0.974	0.896	1	CLONAL	1	TRUE	1	0.752047406485717	2		430	363	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0052126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	175	388	1	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	1	2	FACETS	0.931	0.864	0.999	0.931	0.864	0.999	CLONAL	1	TRUE	1	0.752047406485717	2		389	500	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420204	49420204	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0052129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	214	715	0	ENST00000301067.7:c.15545del	p.Gly5182AlafsTer61	p.G5182Afs*61	ENST00000301067	NM_003482.3	5182	gGc/gc	48/54	0.287416446031976	4	FACETS	0.956	0.89	1	0.956	0.89	1	CLONAL	2	TRUE	2	0.35403430875024	4		715	856	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784110	120784110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs538550275	NA	P-0052129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	89	767	1	ENST00000257552.2:c.875C>T	p.Thr292Met	p.T292M	ENST00000257552	NM_002442.3	292	aCg/aTg	13/15	0.287416446031976	4	FACETS	0.8	0.708	0.898	0.4	0.354	0.449	SUBCLONAL	1	TRUE	2	0.35403430875024	4		768	851	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224206	98224206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750373573	NA	P-0052129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	68	434	0	ENST00000331920.6:c.2635G>A	p.Asp879Asn	p.D879N	ENST00000331920	NM_000264.3	879	Gat/Aat	16/24	0.35403430875024	3	FACETS	0.96	0.837	1	0.48	0.418	0.546	CLONAL	1	TRUE	1	0.35403430875024	3		434	471	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637586	23637587	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0052129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	464	504	1	ENST00000261584.4:c.2718_2719delinsTT	p.Trp906_Glu907delinsCysTer	p.W906_E907delinsC*	ENST00000261584	NM_024675.3	906	tgGGaa/tgTTaa	7/13	0.35403430875024	7	FACETS	1	0.969	1			1	CLONAL	5	TRUE	NA	0.35403430875024	7		505	978	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579376	+	inframe_deletion	In_Frame_Del	DEL	GGAAACCGTAGCTGCCCT	GGAAACCGTAGCTGCCCT	-	novel	NA	P-0052129-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	253	712	1	ENST00000269305.4:c.311_328del	p.Gln104_Phe109del	p.Q104_F109del	ENST00000269305	NM_001126112.2	104	cAGGGCAGCTACGGTTTCCgt/cgt	4/11	0.309816409816595	3	FACETS	1	0.99	1	0.831	0.782	0.88	CLONAL	2	TRUE	0	0.35403430875024	3		713	675	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0052132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	58	655	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.914	0.783	1	0.914	0.783	1	CLONAL	1	TRUE	1	0.14	2		655	907	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631129	69631129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs281860303	NA	P-0052132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	49	600	1	ENST00000334134.2:c.283C>T	p.Arg95Trp	p.R95W	ENST00000334134	NM_005247.2	95	Cgg/Tgg	2/3	1	2	FACETS	0.728	0.614	0.854	0.728	0.614	0.854	SUBCLONAL	1	TRUE	1	0.14	2		601	962	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600470	10600470	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0052132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	69	671	0	ENST00000171111.5:c.1385G>T	p.Gly462Val	p.G462V	ENST00000171111	NM_203500.1	462	gGg/gTg	4/6	1	2	FACETS	0.951	0.825	1	0.951	0.825	1	CLONAL	1	TRUE	1	0.14	2		671	1037	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264321	30264321	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0052132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	16	102	0	ENST00000322652.5:c.56G>T	p.Gly19Val	p.G19V	ENST00000322652	NM_015355.2	19	gGg/gTg	1/16	1	2	FACETS	0.879	0.656	1	1	0.915	1	CLONAL	2	TRUE	1	0.14	2		102	130	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0052133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	27	359	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.909	0.733	1	1	0.951	1	CLONAL	2	FALSE	1	0.20618866308171	2		359	144	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463181	25463181	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757823678	NA	P-0052133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	61	625	1	ENST00000264709.3:c.2312G>A	p.Arg771Gln	p.R771Q	ENST00000264709	NM_175629.2	771	cGa/cAa	19/23	0.20618866308171	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	FALSE	1	0.20618866308171	3		626	262	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013728	12013728	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0052133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	38	426	0	ENST00000353533.5:c.673del	p.Ile225LeufsTer51	p.I225Lfs*51	ENST00000353533	NM_003010.3	224	Aaa/aa	6/11	0.20618866308171	0	FACETS	1	0.865	1			1	CLONAL	2	FALSE	0	0.20618866308171	0		426	142	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370918	55370918	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	62	785	1	ENST00000297316.4:c.220G>A	p.Ala74Thr	p.A74T	ENST00000297316	NM_022454.3	74	Gct/Act	1/2	1	2	FACETS	1	0.941	1	1	0.982	1	CLONAL	2	FALSE	1	0.20618866308171	2		786	264	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022932	27022932	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0052133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	12	72	1	ENST00000324856.7:c.38T>A	p.Leu13Gln	p.L13Q	ENST00000324856	NM_006015.4	13	cTg/cAg	1/20	0.20618866308171	3	FACETS	0.813	0.58	1	0.813	0.58	1	CLONAL	2	FALSE	1	0.20618866308171	3		73	79	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024570	16024570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0052133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	44	549	0	ENST00000268712.3:c.1648G>A	p.Glu550Lys	p.E550K	ENST00000268712	NM_006311.3	550	Gaa/Aaa	16/46	0.20618866308171	0	FACETS	0.931	0.792	1			1	CLONAL	2	FALSE	0	0.20618866308171	0		549	182	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227887	36227887	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0052133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	34	869	0	ENST00000222270.7:c.7372+1del		p.G2458fs	ENST00000222270	NM_014727.1	2458	Gga/ga	32/37	0.112369433988529	4	FACETS	0.792	0.651	0.949	0.792	0.651	0.949	INDETERMINATE	2	FALSE	2	0.20618866308171	4		869	251	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0052136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	41	230	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.984	0.818	1	0.984	0.818	1	CLONAL	1	TRUE	1	0.13	2		230	641	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969327	44969327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0052136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	26	174	0	ENST00000377967.4:c.4009G>A	p.Glu1337Lys	p.E1337K	ENST00000377967	NM_021140.2	1337	Gag/Aag	28/29	1	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.13	1		174	261	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044453	47044453	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0052136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	48	356	0	ENST00000377604.3:c.1951-1G>T		p.X651_splice	ENST00000377604	NM_001204468.1	651			1	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.13	1		356	507	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202926	27202926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772637203	NA	P-0052137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	70	592	0	ENST00000380036.4:c.2018G>A	p.Arg673His	p.R673H	ENST00000380036	NM_000459.3	673	cGt/cAt	13/23	1	2	FACETS	0.642	0.559	0.732	0.642	0.559	0.732	SUBCLONAL	1	FALSE	1	0.3	2		592	727	SUCCESS
APC	324	MSKCC	GRCh37	5	112154969	112154969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137854567	NA	P-0003018-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	205	516	0	ENST00000257430.4:c.1240C>T	p.Arg414Cys	p.R414C	ENST00000257430	NM_000038.5	414	Cgc/Tgc	10/16	0.423699186419853	3	FACETS	0.882	0.817	0.949			1	CLONAL	1	TRUE	NA	0.504661392682534	3		516	1154	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488679	212488679	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003018-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	234	528	1	ENST00000342788.4:c.2170C>A	p.Leu724Ile	p.L724I	ENST00000342788	NM_005235.2	724	Ctt/Att	18/28	0.420153494733163	3	FACETS	0.84	0.782	0.901	0.42	0.391	0.451	CLONAL	1	TRUE	1	0.504661392682534	3		529	1382	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468474	89468474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003018-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	176	449	0	ENST00000336596.2:c.2008G>A	p.Glu670Lys	p.E670K	ENST00000336596	NM_005233.5	670	Gaa/Aaa	11/17	0.420153494733163	3	FACETS	0.788	0.725	0.854	0.394	0.362	0.427	SUBCLONAL	1	TRUE	1	0.504661392682534	3		449	1108	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126095	2126095	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003018-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	240	552	0	ENST00000219476.3:c.2666C>G	p.Ala889Gly	p.A889G	ENST00000219476	NM_000548.3	889	gCc/gGc	24/42	1	2	FACETS	0.973	0.909	1	0.973	0.909	1	CLONAL	1	TRUE	1	0.504661392682534	2		552	978	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430798	47430804	+	frameshift_variant	Frame_Shift_Del	DEL	GCACCCA	GCACCCA	-	novel	NA	P-0003018-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	221	248	0	ENST00000377045.4:c.1764_1770del	p.Thr589ProfsTer?	p.T589Pfs*?	ENST00000377045	NM_001654.4	588	cGCACCCAg/cg	16/16	0.504661392682534	2	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.504661392682534	2		248	692	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979987	7979987	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746723399	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	177	635	0	ENST00000319144.4:c.1350del	p.Leu451SerfsTer16	p.L451Sfs*16	ENST00000319144	NM_001139.2	450	ggG/gg	10/15	0.387922982209155	3	FACETS	1	0.988	1	0.457	0.421	0.494	CLONAL	1	TRUE	0	0.387922982209155	3		635	795	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579410	7579410	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567556123	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	368	618	0	ENST00000269305.4:c.277del	p.Leu93CysfsTer30	p.L93Cfs*30	ENST00000269305	NM_001126112.2	93	Ctg/tg	4/11	0.387922982209155	3	FACETS	0.86	0.819	0.901	0.86	0.819	0.901	CLONAL	3	TRUE	0	0.387922982209155	3		618	878	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593468	55593468	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	139	305	0	ENST00000288135.5:c.1625T>C	p.Ile542Thr	p.I542T	ENST00000288135	NM_000222.2	542	aTt/aCt	10/21	0.330772524762897	3	FACETS	1	0.961	1	0.715	0.657	0.774	CLONAL	2	TRUE	0	0.387922982209155	3		305	399	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248150	110248150	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	60	379	0	ENST00000374672.4:c.1322A>G	p.Asp441Gly	p.D441G	ENST00000374672	NM_004235.4	441	gAt/gGt	5/5	0.336614758278676	3	FACETS	0.781	0.674	0.897	0.39	0.337	0.449	SUBCLONAL	1	TRUE	1	0.387922982209155	3		379	473	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851561	134851561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	92	447	1	ENST00000398015.3:c.967C>T	p.Pro323Ser	p.P323S	ENST00000398015	NM_004441.4	323	Cca/Tca	5/16	NA	2	FACETS	1	0.934	1			1	INDETERMINATE	1	TRUE	NA	0.387922982209155	2		448	446	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193820	106193820	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	56	306	1	ENST00000380013.4:c.4282G>A	p.Glu1428Lys	p.E1428K	ENST00000380013	NM_001127208.2	1428	Gag/Aag	10/11	0.250872338864787	3	FACETS	0.977	0.841	1			1	CLONAL	1	TRUE	NA	0.387922982209155	3		307	353	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2105513	2105513	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	132	484	0	ENST00000219476.3:c.592A>T	p.Met198Leu	p.M198L	ENST00000219476	NM_000548.3	198	Atg/Ttg	6/42	0.278589056320216	3	FACETS	1	0.986	1	0.728	0.664	0.795	CLONAL	1	TRUE	1	0.387922982209155	3		484	558	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560965	9560965	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	124	431	0	ENST00000353224.5:c.817C>A	p.Leu273Met	p.L273M	ENST00000353224	NM_177990.2	273	Ctg/Atg	4/10	0.278589056320216	3	FACETS	0.814	0.741	0.889	0.814	0.741	0.889	CLONAL	2	TRUE	1	0.387922982209155	3		431	469	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874218	155874218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	283	524	0	ENST00000368323.3:c.313C>T	p.Arg105Cys	p.R105C	ENST00000368323	NM_006912.5	105	Cgt/Tgt	5/6	0.320479485853769	5	FACETS	0.897	0.845	0.949	0.897	0.845	0.949	CLONAL	3	TRUE	2	0.387922982209155	5		524	858	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11297967	11297967	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	75	557	0	ENST00000361445.4:c.2141C>G	p.Thr714Ser	p.T714S	ENST00000361445	NM_004958.3	714	aCt/aGt	13/58	1	2	FACETS	0.655	0.575	0.742	0.655	0.575	0.742	SUBCLONAL	1	TRUE	1	0.387922982209155	2		557	590	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256485	115256485	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753954415	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	101	525	1	ENST00000369535.4:c.226G>A	p.Glu76Lys	p.E76K	ENST00000369535	NM_002524.4	76	Gaa/Aaa	3/7	0.387922982209155	5	FACETS	0.856	0.764	0.955	0.214	0.191	0.239	CLONAL	1	TRUE	1	0.387922982209155	5		526	962	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771569	112771570	+	missense_variant	Missense_Mutation	DNP	TG	TG	AT	novel	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	169	399	1	ENST00000369452.4:c.1742_1743delinsAT	p.Met581Asn	p.M581N	ENST00000369452	NM_007373.3	581	aTG/aAT	9/9	0.387922982209155	2	FACETS	0.929	0.862	0.997	0.929	0.862	0.997	CLONAL	2	TRUE	0	0.387922982209155	2		400	469	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195485	102195485	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	118	408	0	ENST00000263464.3:c.245C>A	p.Pro82His	p.P82H	ENST00000263464	NM_001165.4	82	cCt/cAt	2/9	0.336614758278676	3	FACETS	1	0.985	1	0.746	0.676	0.818	CLONAL	1	TRUE	1	0.387922982209155	3		408	487	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122670	108122670	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	118	478	0	ENST00000278616.4:c.1714T>A	p.Leu572Ile	p.L572I	ENST00000278616	NM_000051.3	572	Tta/Ata	11/63	0.336614758278676	3	FACETS	0.917	0.835	1	0.917	0.835	1	CLONAL	2	TRUE	1	0.387922982209155	3		478	396	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248877	133248877	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	294	543	1	ENST00000320574.5:c.1718G>T	p.Arg573Leu	p.R573L	ENST00000320574	NM_006231.2	573	cGg/cTg	16/49	0.387922982209155	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.387922982209155	4		544	914	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877353	28877353	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs536239359	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	150	417	0	ENST00000282397.4:c.3968C>G	p.Pro1323Arg	p.P1323R	ENST00000282397	NM_002019.4	1323	cCg/cGg	30/30	0.327487168542093	3	FACETS	0.827	0.76	0.897	0.552	0.507	0.598	CLONAL	2	TRUE	0	0.387922982209155	3		417	558	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041231	29041231	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1210263660	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	65	487	0	ENST00000282397.4:c.197T>C	p.Met66Thr	p.M66T	ENST00000282397	NM_002019.4	66	aTg/aCg	3/30	0.327487168542093	3	FACETS	0.703	0.61	0.804	0.234	0.203	0.268	SUBCLONAL	1	TRUE	0	0.387922982209155	3		487	569	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858664	9858664	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	103	452	0	ENST00000330684.3:c.2737T>G	p.Ser913Ala	p.S913A	ENST00000330684	NM_001134407.1	913	Tca/Gca	13/13	NA	2	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.387922982209155	2		452	448	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649199	23649199	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	58	431	0	ENST00000261584.4:c.183G>C	p.Gln61His	p.Q61H	ENST00000261584	NM_024675.3	61	caG/caC	3/13	0.327880653301952	3	FACETS	0.634	0.545	0.732			1	SUBCLONAL	1	TRUE	NA	0.387922982209155	3		431	563	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89825070	89825070	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	137	518	0	ENST00000389301.3:c.2896G>C	p.Glu966Gln	p.E966Q	ENST00000389301	NM_000135.2	966	Gag/Cag	30/43	0.278589056320216	3	FACETS	1	0.986	1	0.718	0.656	0.783	CLONAL	1	TRUE	1	0.387922982209155	3		518	587	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763494	59763494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	114	464	0	ENST00000259008.2:c.2608C>T	p.His870Tyr	p.H870Y	ENST00000259008	NM_032043.2	870	Cac/Tac	19/20	0.278589056320216	3	FACETS	0.826	0.749	0.905	0.826	0.749	0.905	CLONAL	2	TRUE	1	0.387922982209155	3		464	425	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223138	1223138	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	364	600	1	ENST00000326873.7:c.1075G>C	p.Asp359His	p.D359H	ENST00000326873	NM_000455.4	359	Gac/Cac	8/10	0.294127091353115	4	FACETS	1	0.986	1			1	CLONAL	3	TRUE	NA	0.387922982209155	4		601	802	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226470	1226470	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	425	754	0	ENST00000326873.7:c.1126G>T	p.Glu376Ter	p.E376*	ENST00000326873	NM_000455.4	376	Gag/Tag	9/10	0.294127091353115	4	FACETS	1	0.993	1			1	CLONAL	3	TRUE	NA	0.387922982209155	4		754	873	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599964	10599964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1364007421	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	329	618	0	ENST00000171111.5:c.1612G>A	p.Asp538Asn	p.D538N	ENST00000171111	NM_203500.1	538	Gat/Aat	5/6	0.332337270493705	3	FACETS	0.88	0.837	0.924	0.88	0.837	0.924	CLONAL	3	TRUE	0	0.387922982209155	3		618	767	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602666	10602671	+	inframe_deletion	In_Frame_Del	DEL	GATCTT	GATCTT	-	novel	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	321	631	0	ENST00000171111.5:c.907_912del	p.Lys303_Ile304del	p.K303_I304del	ENST00000171111	NM_203500.1	303	AAGATC/-	3/6	0.332337270493705	3	FACETS	1	0.991	1	0.793	0.752	0.834	CLONAL	2	TRUE	0	0.387922982209155	3		631	831	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661603	227661603	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	168	551	1	ENST00000305123.5:c.1852G>T	p.Gly618Trp	p.G618W	ENST00000305123	NM_005544.2	618	Ggg/Tgg	1/2	0.278589056320216	3	FACETS	0.819	0.756	0.885	0.819	0.756	0.885	CLONAL	2	TRUE	1	0.387922982209155	3		552	631	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546852	9546852	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1438419751	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	53	405	0	ENST00000353224.5:c.1170C>A	p.Ser390Arg	p.S390R	ENST00000353224	NM_177990.2	390	agC/agA	5/10	0.278589056320216	3	FACETS	0.788	0.674	0.913	0.394	0.337	0.457	CLONAL	1	TRUE	1	0.387922982209155	3		405	414	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37055985	37055985	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	118	322	1	ENST00000231790.2:c.740C>T	p.Ser247Phe	p.S247F	ENST00000231790	NM_000249.3	247	tCc/tTc	9/19	0.387922982209155	3	FACETS	1	0.983	1	0.476	0.431	0.522	CLONAL	1	TRUE	0	0.387922982209155	3		323	509	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71064736	71064736	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	133	421	0	ENST00000318789.4:c.938G>T	p.Cys313Phe	p.C313F	ENST00000318789	NM_032682.5	313	tGt/tTt	12/21	0.387922982209155	5	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.387922982209155	5		421	766	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391135	89391135	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1367928047	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	109	490	0	ENST00000336596.2:c.1201G>T	p.Ala401Ser	p.A401S	ENST00000336596	NM_005233.5	401	Gca/Tca	5/17	0.387922982209155	3	FACETS	1	0.936	1	0.351	0.316	0.389	CLONAL	1	TRUE	0	0.387922982209155	3		490	637	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155052	55155052	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	47	376	0	ENST00000257290.5:c.2761G>C	p.Ala921Pro	p.A921P	ENST00000257290	NM_006206.4	921	Gct/Cct	20/23	0.330772524762897	3	FACETS	0.579	0.488	0.678	0.193	0.162	0.226	SUBCLONAL	1	TRUE	0	0.387922982209155	3		376	500	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213846	66213846	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	55	425	1	ENST00000273854.3:c.2584T>A	p.Trp862Arg	p.W862R	ENST00000273854	NM_004439.5	862	Tgg/Agg	15/18	NA	2	FACETS	0.762	0.655	0.879			1	INDETERMINATE	1	TRUE	NA	0.387922982209155	2		426	372	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213898	66213899	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	52	390	0	ENST00000273854.3:c.2531_2532delinsTT	p.Trp844Phe	p.W844F	ENST00000273854	NM_004439.5	844	tGG/tTT	15/18	NA	2	FACETS	0.798	0.683	0.923			1	INDETERMINATE	1	TRUE	NA	0.387922982209155	2		390	336	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683679	162683679	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs369634041	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	125	464	0	ENST00000366898.1:c.290G>T	p.Arg97Leu	p.R97L	ENST00000366898	NM_004562.2	97	cGg/cTg	3/12	0.38193436360942	3	FACETS	1	0.984	1	0.709	0.644	0.776	CLONAL	1	TRUE	1	0.387922982209155	3		464	543	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739772	41739772	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	100	577	0	ENST00000242208.4:c.201C>G	p.His67Gln	p.H67Q	ENST00000242208	NM_002192.2	67	caC/caG	2/3	0.294127091353115	4	FACETS	0.81	0.723	0.904			1	CLONAL	1	TRUE	NA	0.387922982209155	4		577	883	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468262	50468262	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	132	537	1	ENST00000331340.3:c.1497C>A	p.Ser499Arg	p.S499R	ENST00000331340	NM_006060.4	499	agC/agA	8/8	0.387922982209155	4	FACETS	1	0.979	1	0.636	0.578	0.697	CLONAL	1	TRUE	2	0.387922982209155	4		538	743	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976654	90976654	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	124	430	0	ENST00000265433.3:c.978G>C	p.Gln326His	p.Q326H	ENST00000265433	NM_002485.4	326	caG/caC	8/16	0.175970775424849	5	FACETS	0.783	0.71	0.859	0.522	0.473	0.573	INDETERMINATE	2	TRUE	2	0.387922982209155	5		430	646	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486148	8486148	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	97	370	1	ENST00000356435.5:c.2669C>T	p.Ser890Leu	p.S890L	ENST00000356435		890	tCa/tTa	17/35	0.327913108474844	2	FACETS	1	0.976	1	0.649	0.583	0.719	CLONAL	1	TRUE	0	0.387922982209155	2		371	385	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521390	8521390	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	138	558	0	ENST00000356435.5:c.848C>A	p.Pro283Gln	p.P283Q	ENST00000356435		283	cCa/cAa	9/35	0.327913108474844	2	FACETS	1	0.987	1	0.723	0.662	0.786	CLONAL	1	TRUE	0	0.387922982209155	2		558	492	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922219	39922219	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	143	221	0	ENST00000378444.4:c.3953C>G	p.Pro1318Arg	p.P1318R	ENST00000378444	NM_001123385.1	1318	cCt/cGt	9/15	0.387922982209155	2	FACETS	1	0.98	1			1	CLONAL	2	TRUE	NA	0.387922982209155	2		221	315	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414401	6414401	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003576-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	37	110	0	ENST00000356142.4:c.35G>T	p.Gly12Val	p.G12V	ENST00000356142	NM_018890.3	12	gGa/gTa	1/7	0.347454282970617	5	FACETS	0.995	0.823	1	0.332	0.274	0.395	CLONAL	1	TRUE	2	0.388766378066113	5		110	303	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725198	49725198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759497617	NA	P-0003576-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	15	113	1	ENST00000449682.2:c.227C>T	p.Pro76Leu	p.P76L	ENST00000449682	NM_020998.3	76	cCc/cTc	2/18	1	2	FACETS	0.336	0.245	0.444	0.336	0.245	0.444	SUBCLONAL	1	TRUE	1	0.388766378066113	2		114	230	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344724	65344724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003576-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	76	257	0	ENST00000342505.4:c.313C>T	p.Leu105Phe	p.L105F	ENST00000342505	NM_002227.2	105	Ctc/Ttc	4/25	0.212083292961523	3	FACETS	0.863	0.758	0.975	0.432	0.379	0.488	INDETERMINATE	1	TRUE	1	0.388766378066113	3		257	541	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519430	137519430	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003576-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	23	213	0	ENST00000367739.4:c.1208C>G	p.Ser403Cys	p.S403C	ENST00000367739	NM_000416.2	403	tCt/tGt	7/7	0.222262634132901	4	FACETS	0.406	0.316	0.51	0.135	0.105	0.17	INDETERMINATE	1	TRUE	1	0.388766378066113	4		213	405	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132948	30132948	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0121517-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	237	626	0	ENST00000331968.5:c.653C>A	p.Ser218Ter	p.S218*	ENST00000331968	NM_002742.2	218	tCa/tAa	4/18	0.363813412369988	3	FACETS	1	0.982	1	0.562	0.527	0.598	INDETERMINATE	1	NA	1	0.87426945152567	3		626	693	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286182	66286182	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0121517-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	151	373	0	ENST00000273854.3:c.1504T>A	p.Tyr502Asn	p.Y502N	ENST00000273854	NM_004439.5	502	Tat/Aat	6/18	1	2	FACETS	0.907	0.839	0.975	0.907	0.839	0.975	CLONAL	1	NA	1	0.87426945152567	2		373	381	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747902	41747903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0121517-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	211	457	0	ENST00000226382.2:c.866dup	p.Pro290SerfsTer70	p.P290Sfs*70	ENST00000226382	NM_003924.3	289	ggt/ggGt	3/3	1	2	FACETS	0.919	0.862	0.978	0.919	0.862	0.978	CLONAL	1	NA	1	0.87426945152567	2		457	525	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273268	115273268	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121517-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	176	459	0	ENST00000438362.2:c.1190G>T	p.Gly397Val	p.G397V	ENST00000438362	NM_001242891.1	397	gGt/gTt	11/20	1	2	FACETS	0.928	0.864	0.992	0.928	0.864	0.992	CLONAL	1	NA	1	0.87426945152567	2		459	434	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0005759-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	111	394	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.872	0.793	0.954	0.872	0.793	0.954	CLONAL	1	TRUE	1	0.735727093376417	2		394	346	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858184	9858184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005759-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	82	514	0	ENST00000330684.3:c.3217G>A	p.Glu1073Lys	p.E1073K	ENST00000330684	NM_001134407.1	1073	Gaa/Aaa	13/13	0.468014836608854	1	FACETS	0.341	0.302	0.383	0.341	0.302	0.383	SUBCLONAL	1	TRUE	0	0.735727093376417	1		514	413	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222500	39222500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005759-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	171	444	0	ENST00000402219.2:c.3110C>T	p.Ser1037Phe	p.S1037F	ENST00000402219	NM_005633.3	1037	tCt/tTt	20/23	0.198681571852718	2	FACETS	0.709	0.654	0.765	0.354	0.327	0.383	INDETERMINATE	1	TRUE	0	0.735727093376417	2		444	656	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437267	52437267	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1064795638	NA	P-0005759-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	236	657	1	ENST00000460680.1:c.1777C>T	p.Gln593Ter	p.Q593*	ENST00000460680	NM_004656.3	593	Cag/Tag	14/17	0.735727093376417	1	FACETS	0.954	0.905	1	0.954	0.905	1	CLONAL	1	TRUE	0	0.735727093376417	1		658	425	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593615	+	frameshift_variant	Frame_Shift_Del	DEL	AGTGGAAGGTTGTTG	AGTGGAAGGTTGTTG	GTGGA	novel	NA	P-0006875-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	272	348	0	ENST00000288135.5:c.1667_1681delinsGTGGA	p.Gln556ArgfsTer5	p.Q556Rfs*5	ENST00000288135	NM_000222.2	556	cAGTGGAAGGTTGTTGag/cGTGGAag	11/21	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.7	2		348	757	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435765	110435765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781697899	NA	P-0012773-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	24	129	0	ENST00000375856.3:c.2636G>A	p.Gly879Asp	p.G879D	ENST00000375856	NM_003749.2	879	gGc/gAc	1/2	1	2	FACETS	0.373	0.292	0.466	0.373	0.292	0.466	SUBCLONAL	1	TRUE	1	0.399451233777679	2		129	322	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748510	162748510	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012773-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	30	0	0	ENST00000367921.3:c.2424A>T	p.Gln808His	p.Q808H	ENST00000367921	NM_006182.2	808	caA/caT	17/18	1	2	FACETS	0.231	0.186	0.284	0.231	0.186	0.284	SUBCLONAL	1	TRUE	1	0.399451233777679	2		0	649	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530177	212530177	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012773-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	11	0	0	ENST00000342788.4:c.1742C>G	p.Ser581Cys	p.S581C	ENST00000342788	NM_005235.2	581	tCt/tGt	15/28	1	2	FACETS	0.1	0.069	0.14	0.1	0.069	0.14	SUBCLONAL	1	TRUE	1	0.399451233777679	2		0	549	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569229	67569229	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012773-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	27	0	0	ENST00000274335.5:c.346C>G	p.Pro116Ala	p.P116A	ENST00000274335		116	Ccg/Gcg	2/15	1	2	FACETS	0.236	0.187	0.292	0.236	0.187	0.292	SUBCLONAL	1	TRUE	1	0.399451233777679	2		0	573	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858518	27858518	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371964190	NA	P-0012773-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	32	0	0	ENST00000359303.2:c.53G>C	p.Arg18Pro	p.R18P	ENST00000359303	NM_003535.2	18	cGg/cCg	1/1	1	2	FACETS	0.18	0.145	0.22	0.18	0.145	0.22	SUBCLONAL	1	TRUE	1	0.399451233777679	2		0	888	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0013106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	730	390	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.299437629893674	10	FACETS	1	0.986	1			1	CLONAL	8	TRUE	NA	0.27	10		390	1369	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670708	134670708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	44	460	0	ENST00000398015.3:c.619C>T	p.Pro207Ser	p.P207S	ENST00000398015	NM_004441.4	207	Cca/Tca	3/16	0.104670887565121	4	FACETS	1	0.884	1	0.532	0.447	0.626	INDETERMINATE	1	TRUE	2	0.27	4		460	389	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037486	12037486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	81	317	0	ENST00000396373.4:c.1117C>T	p.Pro373Ser	p.P373S	ENST00000396373	NM_001987.4	373	Ccc/Tcc	6/8	0.299437629893674	8	FACETS	0.928	0.823	1	0.464	0.411	0.52	CLONAL	3	TRUE	2	0.27	8		317	390	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163720	32163720	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	42	648	0	ENST00000375023.3:c.5506G>C	p.Glu1836Gln	p.E1836Q	ENST00000375023	NM_004557.3	1836	Gag/Cag	30/30	0.299437629893674	5	FACETS	0.696	0.58	0.825	0.232	0.193	0.275	SUBCLONAL	1	TRUE	2	0.27	5		648	628	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942524	17942524	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	22	667	0	ENST00000458235.1:c.2764G>C	p.Asp922His	p.D922H	ENST00000458235	NM_000215.3	922	Gat/Cat	20/24	0.299437629893674	2	FACETS	0.471	0.365	0.595	0.235	0.182	0.298	SUBCLONAL	1	TRUE	0	0.27	2		667	346	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880244	155880244	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	164	416	0	ENST00000368323.3:c.160A>T	p.Ile54Phe	p.I54F	ENST00000368323	NM_006912.5	54	Att/Ttt	3/6	0.299437629893674	3	FACETS	0.889	0.822	0.958	1	0.987	1	CLONAL	3	TRUE	1	0.27	3		416	517	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645922	215645922	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs876659965	NA	P-0013106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	44	486	0	ENST00000260947.4:c.676G>C	p.Asp226His	p.D226H	ENST00000260947	NM_000465.2	226	Gat/Cat	4/11	0.148732748844277	5	FACETS	0.872	0.731	1	0.291	0.243	0.343	INDETERMINATE	1	TRUE	2	0.27	5		486	525	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032120	10032120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	32	519	0	ENST00000330684.3:c.703G>A	p.Glu235Lys	p.E235K	ENST00000330684	NM_001134407.1	235	Gag/Aag	3/13	0.0482341931478718	3	FACETS	0.623	0.505	0.756			1	INDETERMINATE	1	TRUE	NA	0.27	3		519	432	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427647	49427647	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0013106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	18	531	0	ENST00000301067.7:c.10841C>G	p.Ser3614Ter	p.S3614*	ENST00000301067	NM_003482.3	3614	tCa/tGa	39/54	0.299437629893674	5	FACETS	0.556	0.418	0.719	0.185	0.139	0.24	SUBCLONAL	1	TRUE	2	0.27	5		531	337	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009087	27009087	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	16	269	0	ENST00000335756.4:c.23G>A	p.Arg8Gln	p.R8Q	ENST00000335756	NM_001809.3	8	cGa/cAa	1/5	0.148732748844277	5	FACETS	0.767	0.568	1	0.256	0.189	0.335	INDETERMINATE	1	TRUE	2	0.27	5		269	217	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966586	36966586	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0013106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	24	604	0	ENST00000358127.4:c.740C>G	p.Ser247Ter	p.S247*	ENST00000358127	NM_001280556.1	247	tCa/tGa	6/10	0.299437629893674	2	FACETS	0.552	0.433	0.689	0.276	0.216	0.345	SUBCLONAL	1	TRUE	0	0.27	2		604	322	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227700	53227700	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	13	244	0	ENST00000375401.3:c.2488C>A	p.Leu830Met	p.L830M	ENST00000375401	NM_004187.3	830	Ctg/Atg	17/26	0.20410027491706	2	FACETS	0.448	0.319	0.604			1	SUBCLONAL	1	TRUE	NA	0.27	2		244	215	SUCCESS
AR	367	MSKCC	GRCh37	X	66942780	66942780	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0013106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	23	207	0	ENST00000374690.3:c.2561C>G	p.Ser854Ter	p.S854*	ENST00000374690	NM_000044.3	854	tCa/tGa	7/8	0.20410027491706	2	FACETS	0.936	0.735	1			1	CLONAL	1	TRUE	NA	0.27	2		207	182	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937950	76937950	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013106-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	34	233	0	ENST00000373344.5:c.2798C>T	p.Ser933Phe	p.S933F	ENST00000373344	NM_000489.3	933	tCt/tTt	9/35	0.20410027491706	2	FACETS	0.874	0.717	1			1	CLONAL	1	TRUE	NA	0.27	2		233	288	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0013106-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	18	390	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.237791340249677	5	FACETS	0.901	0.68	1	0.3	0.226	0.387	CLONAL	1	TRUE	2	0.237791340249677	5		390	228	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880244	155880244	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013106-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	80	416	0	ENST00000368323.3:c.160A>T	p.Ile54Phe	p.I54F	ENST00000368323	NM_006912.5	54	Att/Ttt	3/6	0.237791340249677	3	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	1	0.237791340249677	3		416	348	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950689	38950689	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013106-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	10	314	0	ENST00000357387.3:c.3261C>G	p.Phe1087Leu	p.F1087L	ENST00000357387	NM_152756.3	1087	ttC/ttG	31/38	0.237791340249677	4	FACETS	0.575	0.39	0.808	0.288	0.195	0.404	SUBCLONAL	1	TRUE	2	0.237791340249677	4		314	181	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0015665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	24	396	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.459	0.359	0.575	0.459	0.359	0.575	SUBCLONAL	1	TRUE	1	0.200405675101561	2		396	522	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520000	NA	P-0015665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	123	740	1	ENST00000269305.4:c.452C>A	p.Pro151His	p.P151H	ENST00000269305	NM_001126112.2	151	cCc/cAc	5/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.200405675101561	2		741	1100	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	43	273	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.200405675101561	1	FACETS	0.856	0.717	1	0.856	0.717	1	CLONAL	1	TRUE	0	0.200405675101561	1		273	451	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26970485	26970485	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	19	243	0	ENST00000381527.3:c.854G>A	p.Arg285Lys	p.R285K	ENST00000381527	NM_001260.1	285	aGa/aAa	8/13	0.200405675101561	3	FACETS	0.966	0.735	1	0.483	0.367	0.618	CLONAL	1	TRUE	1	0.200405675101561	3		243	216	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007620	45007620	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0015665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	23	243	0	ENST00000558401.1:c.68del		p.X23_splice	ENST00000558401	NM_004048.2	23			1	2	FACETS	0.604	0.47	0.759	0.604	0.47	0.759	SUBCLONAL	1	TRUE	1	0.200405675101561	2		243	380	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996194	73996194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759425133	NA	P-0015665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	45	501	0	ENST00000318443.5:c.928C>T	p.Arg310Cys	p.R310C	ENST00000318443	NM_001024736.1	310	Cgc/Tgc	5/10	1	2	FACETS	0.634	0.532	0.748	0.634	0.532	0.748	SUBCLONAL	1	TRUE	1	0.200405675101561	2		501	708	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238989	5238989	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1294241597	NA	P-0015665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	58	604	1	ENST00000357368.4:c.1790G>A	p.Arg597His	p.R597H	ENST00000357368	NM_002850.3	597	cGc/cAc	13/38	1	2	FACETS	0.68	0.583	0.787	0.68	0.583	0.787	SUBCLONAL	1	TRUE	1	0.200405675101561	2		605	851	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28929495	NA	P-0017319-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	286	610	0	ENST00000275493.2:c.2155G>T	p.Gly719Cys	p.G719C	ENST00000275493	NM_005228.3	719	Ggc/Tgc	18/28	0.810669863950735	7	FACETS	1	0.985	1	1	0.985	1	CLONAL	4	FALSE	3	0.810669863950735	7		610	495	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0017319-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	336	554	1	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.810669863950735	7	FACETS	1	0.983	1	1	0.983	1	CLONAL	4	FALSE	3	0.810669863950735	7		555	595	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242742	46242742	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0017319-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	118	342	0	ENST00000334344.6:c.1704T>A	p.Tyr568Ter	p.Y568*	ENST00000334344	NM_152641.2	568	taT/taA	13/21	0.810669863950735	3	FACETS	1	0.973	1	0.391	0.356	0.426	CLONAL	1	FALSE	0	0.810669863950735	3		342	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577521	7577521	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017319-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	102	618	0	ENST00000269305.4:c.760A>T	p.Ile254Phe	p.I254F	ENST00000269305	NM_001126112.2	254	Atc/Ttc	7/11	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	2	FALSE	NA	0.810669863950735	2		618	117	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772349	56772349	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017319-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	98	517	0	ENST00000337432.4:c.203G>T	p.Cys68Phe	p.C68F	ENST00000337432	NM_058216.2	68	tGt/tTt	2/9	0.738217175148291	4	FACETS	0.805	0.729	0.883	0.536	0.486	0.589	CLONAL	2	FALSE	1	0.810669863950735	4		517	272	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453145	140453145	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913366	NA	P-0121563-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	16	268	0	ENST00000288602.6:c.1790T>G	p.Leu597Arg	p.L597R	ENST00000288602	NM_004333.4	597	cTa/cGa	15/18	1	2	FACETS		NA	1			1	NA	NA	NA	1	NA	2		268	548	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0017628-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	83	355	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.259121710241034	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.291381705137125	1		355	470	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218483	1218483	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs775595174	NA	P-0017628-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	26	425	1	ENST00000326873.7:c.358G>T	p.Glu120Ter	p.E120*	ENST00000326873	NM_000455.4	120	Gaa/Taa	2/10	0.291381705137125	1	FACETS	0.386	0.305	0.479	0.386	0.305	0.479	SUBCLONAL	1	TRUE	0	0.291381705137125	1		426	395	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600506	10600506	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017628-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	74	521	0	ENST00000171111.5:c.1349G>T	p.Trp450Leu	p.W450L	ENST00000171111	NM_203500.1	450	tGg/tTg	4/6	0.291381705137125	1	FACETS	0.941	0.827	1	0.941	0.827	1	CLONAL	1	TRUE	0	0.291381705137125	1		521	461	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685572	29685572	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017628-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	89	414	0	ENST00000356175.3:c.7982A>T	p.His2661Leu	p.H2661L	ENST00000356175	NM_000267.3	2661	cAt/cTt	54/57	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.291381705137125	2		414	475	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300188	15300188	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017628-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	65	675	0	ENST00000263388.2:c.1088A>C	p.Asp363Ala	p.D363A	ENST00000263388	NM_000435.2	363	gAt/gCt	7/33	0.291381705137125	1	FACETS	0.628	0.544	0.719	0.628	0.544	0.719	SUBCLONAL	1	TRUE	0	0.291381705137125	1		675	607	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721177	61721178	+	stop_gained	Nonsense_Mutation	INS	-	-	ATT	novel	NA	P-0017628-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	61	416	0	ENST00000401558.2:c.1096_1097insAAT	p.Ile365_Phe366insTer	p.I365_F366ins*	ENST00000401558	NM_003400.3	366	ttt/tAATtt	12/25	1	2	FACETS	0.745	0.643	0.856	0.745	0.643	0.856	SUBCLONAL	1	TRUE	1	0.291381705137125	2		416	562	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0018173-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	186	295	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.873107840540535	2		295	415	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561376	9561376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774715756	NA	P-0018173-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	38	486	0	ENST00000353224.5:c.406G>A	p.Asp136Asn	p.D136N	ENST00000353224	NM_177990.2	136	Gat/Aat	4/10	1	2	FACETS	0.213	0.176	0.255	0.213	0.176	0.255	SUBCLONAL	1	TRUE	1	0.873107840540535	2		486	408	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0019459-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	264	308	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	0.743069921669975	3	FACETS	1	0.993	1	0.721	0.68	0.762	CLONAL	1	TRUE	1	0.743069921669975	3		308	676	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913400	NA	P-0019459-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	188	220	0	ENST00000349496.5:c.98C>A	p.Ser33Tyr	p.S33Y	ENST00000349496	NM_001904.3	33	tCt/tAt	3/15	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.743069921669975	2		220	488	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241722	55241722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1051753269	NA	P-0019459-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	491	398	1	ENST00000275493.2:c.2170G>A	p.Gly724Ser	p.G724S	ENST00000275493	NM_005228.3	724	Ggc/Agc	18/28	0.743069921669975	3	FACETS	0.967	0.931	1	0.967	0.931	1	CLONAL	2	TRUE	1	0.743069921669975	3		399	937	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685270	89685271	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0019459-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	103	116	0	ENST00000371953.3:c.170dup	p.Leu57PhefsTer6	p.L57Ffs*6	ENST00000371953	NM_000314.4	55	-/T	3/9	0.743069921669975	1	FACETS	0.963	0.888	1	0.963	0.888	1	CLONAL	1	TRUE	0	0.743069921669975	1		116	181	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366883	40366883	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019459-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	402	508	0	ENST00000397332.2:c.314C>A	p.Ser105Tyr	p.S105Y	ENST00000397332	NM_001033082.2	105	tCc/tAc	2/3	1	2	FACETS	0.977	0.931	1	0.977	0.931	1	CLONAL	1	TRUE	1	0.743069921669975	2		508	1108	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357753	70357753	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019459-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	340	253	0	ENST00000374080.3:c.6004C>T	p.Gln2002Ter	p.Q2002*	ENST00000374080		2002	Cag/Tag	41/45	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.743069921669975	1		253	453	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0019659-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	453	404	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.686085904637439	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.686085904637439	3		404	785	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019659-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	115	397	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.686085904637439	3	FACETS	0.886	0.802	0.974	0.443	0.401	0.487	CLONAL	1	TRUE	1	0.686085904637439	3		397	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0019659-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	294	395	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.686085904637439	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.686085904637439	2		395	382	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916935	178916935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019659-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	328	287	0	ENST00000263967.3:c.322C>A	p.Arg108Ser	p.R108S	ENST00000263967	NM_006218.2	108	Cgt/Agt	2/21	0.686085904637439	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.686085904637439	3		287	581	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0022777-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	329	407	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.441266461493168	5	FACETS	0.884	0.842	0.926	0.884	0.842	0.926	CLONAL	4	TRUE	1	0.441266461493168	5		407	701	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0022777-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	182	615	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.441754063819519	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.441266461493168	1		617	609	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187374	32187374	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022777-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	81	596	0	ENST00000375023.3:c.1505C>A	p.Pro502Gln	p.P502Q	ENST00000375023	NM_004557.3	502	cCg/cAg	8/30	1	2	FACETS	0.504	0.444	0.569	0.504	0.444	0.569	SUBCLONAL	1	TRUE	1	0.441266461493168	2		596	728	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749037	43749037	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022777-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	98	739	1	ENST00000382044.4:c.1769A>T	p.Lys590Ile	p.K590I	ENST00000382044	NM_001141980.1	590	aAa/aTa	12/28	NA	2	FACETS	0.555	0.495	0.62			1	INDETERMINATE	1	TRUE	NA	0.441266461493168	2		740	800	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055895	180055895	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022777-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	85	645	0	ENST00000261937.6:c.1090C>A	p.Pro364Thr	p.P364T	ENST00000261937	NM_182925.4	364	Ccc/Acc	8/30	0.264856765459269	4	FACETS	0.724	0.639	0.815	0.362	0.319	0.408	SUBCLONAL	1	TRUE	2	0.441266461493168	4		645	767	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	79	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.301357501430103	2	FACETS	0.923	0.822	1	0.923	0.822	1	CLONAL	2	TRUE	0	0.322989691600266	2		334	265	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579357	7579358	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTTT	novel	NA	P-0022793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	157	753	0	ENST00000269305.4:c.329_330insAAAG	p.Leu111LysfsTer39	p.L111Kfs*39	ENST00000269305	NM_001126112.2	110	cgt/cgAAAGt	4/11	0.301357501430103	2	FACETS	0.86	0.792	0.931	0.86	0.792	0.931	CLONAL	2	TRUE	0	0.322989691600266	2		753	565	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126409	5126409	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs371455894	NA	P-0022793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	20	345	0	ENST00000381652.3:c.3254A>G	p.Asn1085Ser	p.N1085S	ENST00000381652	NM_004972.3	1085	aAt/aGt	24/25	1	2	FACETS	0.904	0.699	1	0.904	0.699	1	CLONAL	1	TRUE	1	0.322989691600266	2		345	137	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022793-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	72	672	0	ENST00000304494.5:c.341C>G	p.Pro114Arg	p.P114R	ENST00000304494	NM_000077.4	114	cCc/cGc	2/3	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.322989691600266	2		672	392	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640658	3640662	+	missense_variant	Missense_Mutation	ONP	ATCTC	ATCTC	CTCTT	novel	NA	P-0023000-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	65	761	0	ENST00000294008.3:c.2977_2981delinsAAGAG	p.Glu993_Ile994delinsLysSer	p.E993_I994delinsKS	ENST00000294008	NM_032444.2	993	GAGATc/AAGAGc	12/15	1	2	FACETS	0.939	0.815	1	0.939	0.815	1	CLONAL	1	TRUE	1	0.280908654624164	2		761	493	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610468	10610468	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023000-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	66	652	0	ENST00000171111.5:c.242T>G	p.Leu81Arg	p.L81R	ENST00000171111	NM_203500.1	81	cTg/cGg	2/6	0.280908654624164	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.280908654624164	1		652	380	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577329	64577330	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs386134253	NA	P-0023717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	249	662	0	ENST00000312049.6:c.252dup	p.Ile85TyrfsTer32	p.I85Yfs*32	ENST00000312049	NM_130799.2	84	-/T	2/10	0.334725615587328	2	FACETS	1	0.992	1	0.707	0.663	0.752	CLONAL	1	FALSE	0	0.434654407822501	2		662	810	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136370	2136372	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	rs137854331	NA	P-0023717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	235	742	0	ENST00000219476.3:c.4842_4844del	p.Ile1614del	p.I1614del	ENST00000219476	NM_000548.3	1613	gaCATc/gac	37/42	0.363068471616924	2	FACETS	1	0.987	1	0.606	0.566	0.647	CLONAL	1	FALSE	0	0.434654407822501	2		742	892	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288261	33288261	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	256	608	0	ENST00000374542.5:c.1147C>T	p.Gln383Ter	p.Q383*	ENST00000374542	NM_001141970.1	383	Caa/Taa	4/8	0.334725615587328	2	FACETS	1	0.992	1	0.706	0.663	0.75	CLONAL	1	FALSE	0	0.434654407822501	2		608	834	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0024568-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	257	451	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.717172740721202	3	FACETS	0.968	0.918	1	0.968	0.918	1	CLONAL	2	TRUE	1	0.717172740721202	3		451	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577595	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0024568-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	631	551	0	ENST00000269305.4:c.686_687del	p.Cys229TyrfsTer10	p.C229Yfs*10	ENST00000269305	NM_001126112.2	229	tGT/t	7/11	0.717172740721202	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	4	TRUE	0	0.717172740721202	4		551	750	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722347	176722347	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024568-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	127	434	0	ENST00000439151.2:c.7978C>A	p.Gln2660Lys	p.Q2660K	ENST00000439151	NM_022455.4	2660	Cag/Aag	23/23	0.717172740721202	8	FACETS	1	0.912	1			1	CLONAL	1	TRUE	NA	0.717172740721202	8		434	1106	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070639	67070639	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0024568-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	155	161	0	ENST00000412916.2:c.263T>G	p.Leu88Ter	p.L88*	ENST00000412916		88	tTa/tGa	3/6	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	2	TRUE	NA	0.717172740721202	2		161	209	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115696	8115724	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTTTAGATTAACAGACCCCTGACTATGAA	GTTTAGATTAACAGACCCCTGACTATGAA	-	novel	NA	P-0024568-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	139	230	0	ENST00000346208.3:c.1048-5_1071del		p.X350_splice	ENST00000346208		350		6/6	0.717172740721202	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.717172740721202	2		230	176	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845521	63845521	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024568-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	101	272	0	ENST00000279873.7:c.1260C>G	p.Ile420Met	p.I420M	ENST00000279873	NM_032199.2	420	atC/atG	9/10	0.717172740721202	2	FACETS	1	0.932	1	0.516	0.468	0.565	CLONAL	1	TRUE	0	0.717172740721202	2		272	273	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371742	45371742	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024568-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	129	363	0	ENST00000262160.6:c.1249A>T	p.Ser417Cys	p.S417C	ENST00000262160	NM_005901.5	417	Agt/Tgt	10/11	0.489171341347962	4	FACETS	0.998	0.908	1	0.499	0.454	0.547	CLONAL	1	TRUE	2	0.717172740721202	4		363	619	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748880	41748880	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024568-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	140	573	0	ENST00000301178.4:c.1405C>G	p.Leu469Val	p.L469V	ENST00000301178	NM_021913.4	469	Ctc/Gtc	11/20	0.677816922426637	5	FACETS	1	0.961	1	0.274	0.249	0.299	CLONAL	1	TRUE	1	0.717172740721202	5		573	740	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163437	47163437	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024568-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	87	353	0	ENST00000409792.3:c.2689C>G	p.Leu897Val	p.L897V	ENST00000409792	NM_014159.6	897	Ctc/Gtc	3/21	0.614178691929136	2	FACETS	0.814	0.729	0.903	0.407	0.364	0.452	CLONAL	1	TRUE	0	0.717172740721202	2		353	298	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662727	117662727	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024568-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	25	404	1	ENST00000368508.3:c.4738G>C	p.Glu1580Gln	p.E1580Q	ENST00000368508	NM_002944.2	1580	Gaa/Caa	29/43	0.472984790571222	3	FACETS	0.265	0.208	0.329	0.088	0.069	0.11	SUBCLONAL	1	TRUE	0	0.717172740721202	3		405	358	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974813	21974813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554656700	NA	P-0024568-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	59	158	2	ENST00000304494.5:c.14C>T	p.Ala5Val	p.A5V	ENST00000304494	NM_000077.4	5	gCg/gTg	1/3	0.717172740721202	2	FACETS	1	0.968	1	0.643	0.57	0.716	CLONAL	1	TRUE	0	0.717172740721202	2		160	128	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692817	89692819	+	inframe_deletion	In_Frame_Del	DEL	ATC	ATC	-	novel	NA	P-0027054-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	95	210	0	ENST00000371953.3:c.302_304del	p.Ile101del	p.I101del	ENST00000371953	NM_000314.4	101	ATC/-	5/9	0.705097693425776	2	FACETS	1	0.984	1	0.708	0.649	0.767	CLONAL	1	TRUE	0	0.744955622372436	2		210	180	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578541	7578541	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027054-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	170	731	0	ENST00000269305.4:c.389T>A	p.Leu130His	p.L130H	ENST00000269305	NM_001126112.2	130	cTc/cAc	5/11	0.713202190970347	2	FACETS	0.684	0.631	0.739	0.342	0.315	0.37	SUBCLONAL	1	TRUE	0	0.744955622372436	2		731	667	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185570	27185570	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027054-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	379	554	1	ENST00000380036.4:c.1270T>A	p.Cys424Ser	p.C424S	ENST00000380036	NM_000459.3	424	Tgc/Agc	9/23	0.730015873828174	2	FACETS	0.904	0.872	0.935	0.904	0.872	0.935	CLONAL	2	TRUE	0	0.744955622372436	2		555	563	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875981	76875984	+	frameshift_variant	Frame_Shift_Del	DEL	ACAA	ACAA	-	novel	NA	P-0027054-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	26	321	0	ENST00000373344.5:c.5151_5154del	p.Cys1718MetfsTer6	p.C1718Mfs*6	ENST00000373344	NM_000489.3	1717	gtTTGT/gt	20/35	0.717622073798687	2	FACETS	0.332	0.265	0.409	0.166	0.132	0.205	SUBCLONAL	1	TRUE	0	0.744955622372436	2		321	210	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028777-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	51	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.265958301277672	2		276	367	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0028777-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	347	525	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.265958301277672	3	FACETS	1	0.987	1			1	CLONAL	3	TRUE	NA	0.265958301277672	3		525	889	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0028777-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	97	513	0	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	0.265958301277672	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.265958301277672	1		513	591	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566488	41566488	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028777-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	64	361	0	ENST00000263253.7:c.4365G>T	p.Gln1455His	p.Q1455H	ENST00000263253	NM_001429.3	1455	caG/caT	27/31	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.265958301277672	2		361	464	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666674	206666674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553391211	NA	P-0028777-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	81	630	0	ENST00000367120.3:c.2008C>T	p.Pro670Ser	p.P670S	ENST00000367120	NM_014002.3	670	Cct/Tct	20/22	1	2	FACETS	0.785	0.691	0.886	0.785	0.691	0.886	SUBCLONAL	1	TRUE	1	0.265958301277672	2		630	776	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281802	46281802	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs769002244	NA	P-0028777-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	105	593	0	ENST00000371998.3:c.4249A>G	p.Met1417Val	p.M1417V	ENST00000371998		1417	Atg/Gtg	22/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.265958301277672	2		593	646	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573052	41573052	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028777-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	165	978	0	ENST00000263253.7:c.5337C>A	p.Cys1779Ter	p.C1779*	ENST00000263253	NM_001429.3	1779	tgC/tgA	31/31	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.265958301277672	2		978	1066	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531837	46531837	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028777-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	48	200	0	ENST00000262741.5:c.510A>C	p.Lys170Asn	p.K170N	ENST00000262741	NM_003629.3	170	aaA/aaC	5/10	1	2	FACETS	0.945	0.801	1	0.945	0.801	1	CLONAL	1	TRUE	1	0.265958301277672	2		200	382	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916211	9916211	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028777-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	74	436	0	ENST00000330684.3:c.2078A>T	p.Asn693Ile	p.N693I	ENST00000330684	NM_001134407.1	693	aAc/aTc	10/13	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.265958301277672	2		436	532	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677775	47677775	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028777-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	59	438	0	ENST00000347630.2:c.1090C>G	p.Leu364Val	p.L364V	ENST00000347630	NM_001007230.1	364	Ctg/Gtg	11/11	1	2	FACETS	0.766	0.659	0.883	0.766	0.659	0.883	SUBCLONAL	1	TRUE	1	0.265958301277672	2		438	579	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164380	47164380	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028777-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	20	246	0	ENST00000409792.3:c.1746C>G	p.Ile582Met	p.I582M	ENST00000409792	NM_014159.6	582	atC/atG	3/21	0.265958301277672	1	FACETS	0.364	0.278	0.465	0.364	0.278	0.465	SUBCLONAL	1	TRUE	0	0.265958301277672	1		246	358	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0029664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	79	577	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.210440277278861	5	FACETS	1	0.957	1	0.785	0.693	0.882	CLONAL	2	FALSE	2	0.208912712394066	5		577	422	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971209	21971209	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1554654224	NA	P-0029664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	108	416	2	ENST00000304494.5:c.151-2A>G		p.X51_splice	ENST00000304494	NM_000077.4	51			0.210440277278861	2	FACETS	0.915	0.84	0.99	1	0.991	1	CLONAL	5	FALSE	0	0.208912712394066	2		418	226	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0029664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	19	332	0				ENST00000310581	NM_198253.2	-/1132			0.210440277278861	1	FACETS	0.783	0.604	0.986	1	0.919	1	CLONAL	2	FALSE	0	0.208912712394066	1		332	104	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053022	180053023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750808726	NA	P-0029664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	17	577	0	ENST00000261937.6:c.1267dup	p.Gln423ProfsTer4	p.Q423Pfs*4	ENST00000261937	NM_182925.4	423	cag/cCag	10/30	0.210440277278861	0	FACETS	0.766	0.575	0.991			1	CLONAL	1	FALSE	0	0.208912712394066	0		577	168	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533552	533552	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	171	689	1	ENST00000451590.1:c.351G>T	p.Lys117Asn	p.K117N	ENST00000451590	NM_001130442.1	117	aaG/aaT	4/5	0.210440277278861	1	FACETS	0.991	0.925	1	1	0.995	1	CLONAL	4	FALSE	0	0.208912712394066	1		690	370	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950309	17950309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	64	629	1	ENST00000458235.1:c.1418C>T	p.Ser473Phe	p.S473F	ENST00000458235	NM_000215.3	473	tCc/tTc	10/24	0.151937669325001	3	FACETS	0.907	0.789	1	0.907	0.789	1	CLONAL	2	FALSE	1	0.208912712394066	3		630	373	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937178	36937178	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	72	617	1	ENST00000361632.4:c.1141G>A	p.Ala381Thr	p.A381T	ENST00000361632		381	Gct/Act	9/16	0.144263877566412	4	FACETS	0.917	0.808	1	1	0.972	1	CLONAL	3	FALSE	2	0.208912712394066	4		618	303	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046476	69046476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	65	544	0	ENST00000288368.4:c.3949C>T	p.Leu1317Phe	p.L1317F	ENST00000288368	NM_024870.2	1317	Ctt/Ttt	32/40	0.210440277278861	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	0	0.208912712394066	1		544	374	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882021	36882021	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs982302460	NA	P-0029664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	59	593	1	ENST00000358127.4:c.992C>T	p.Thr331Met	p.T331M	ENST00000358127	NM_001280556.1	331	aCg/aTg	8/10	1	2	FACETS	1	0.894	1	1	0.98	1	CLONAL	2	FALSE	1	0.208912712394066	2		594	273	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741897	162741897	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	31	416	0	ENST00000367921.3:c.1588C>T	p.Gln530Ter	p.Q530*	ENST00000367921	NM_006182.2	530	Caa/Taa	13/18	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	FALSE	1	0.208912712394066	2		416	246	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11205062	11205062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	80	589	0	ENST00000361445.4:c.4727C>T	p.Thr1576Ile	p.T1576I	ENST00000361445	NM_004958.3	1576	aCt/aTt	33/58	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	2	FALSE	NA	0.208912712394066	2		589	310	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22412937	22412937	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	27	174	0	ENST00000344548.3:c.184G>A	p.Glu62Lys	p.E62K	ENST00000344548	NM_001039802.1	62	Gag/Aag	5/7	0.208912712394066	7	FACETS	1	0.877	1			1	CLONAL	2	FALSE	NA	0.208912712394066	7		174	174	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948536	71948536	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11548491	NA	P-0029664-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	31	609	0	ENST00000298229.2:c.3248C>T	p.Ala1083Val	p.A1083V	ENST00000298229	NM_001567.3	1083	gCt/gTt	26/28	0.210440277278861	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	FALSE	0	0.208912712394066	1		609	222	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0030562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	18	384	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.738518994223315	1	FACETS	0.115	0.086	0.149	0.115	0.086	0.149	SUBCLONAL	1	TRUE	0	0.738518994223315	1		384	267	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0030562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	60	474	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.738518994223315	3	FACETS	0.283	0.243	0.327	0.142	0.121	0.164	SUBCLONAL	1	TRUE	1	0.738518994223315	3		474	785	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0030562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1266	104	608	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.738518994223315	7	FACETS	0.585	0.522	0.653	0.117	0.104	0.131	SUBCLONAL	1	TRUE	2	0.738518994223315	7		609	1370	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28929495	NA	P-0030562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	956	610	0	ENST00000275493.2:c.2155G>T	p.Gly719Cys	p.G719C	ENST00000275493	NM_005228.3	719	Ggc/Tgc	18/28	0.738518994223315	7	FACETS	0.98	0.957	1	0.98	0.957	1	CLONAL	5	TRUE	2	0.738518994223315	7		610	1504	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0030562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	779	554	1	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.738518994223315	7	FACETS	1	0.986	1	1	0.986	1	CLONAL	5	TRUE	2	0.738518994223315	7		555	1181	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578283	7578283	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	315	506	1	ENST00000269305.4:c.566C>A	p.Ala189Asp	p.A189D	ENST00000269305	NM_001126112.2	189	gCc/gAc	6/11	0.738518994223315	2	FACETS	0.987	0.952	1	0.987	0.952	1	CLONAL	2	TRUE	0	0.738518994223315	2		507	432	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249808	133249808	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	230	450	0	ENST00000320574.5:c.1415A>C	p.Lys472Thr	p.K472T	ENST00000320574	NM_006231.2	472	aAg/aCg	14/49	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.738518994223315	2		450	517	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131361	17131361	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	414	605	0	ENST00000285071.4:c.91C>T	p.Gln31Ter	p.Q31*	ENST00000285071	NM_144997.5	31	Caa/Taa	4/14	0.738518994223315	2	FACETS	0.997	0.967	1	0.997	0.967	1	CLONAL	2	TRUE	0	0.738518994223315	2		605	562	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961000	55961000	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	151	388	1	ENST00000263923.4:c.2940G>T	p.Glu980Asp	p.E980D	ENST00000263923	NM_002253.2	980	gaG/gaT	21/30	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.738518994223315	2		389	392	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545714	106545714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	133	466	0	ENST00000359195.3:c.3191C>T	p.Ala1064Val	p.A1064V	ENST00000359195	NM_002649.2	1064	gCt/gTt	11/11	0.738518994223315	3	FACETS	0.794	0.723	0.868	0.397	0.361	0.434	SUBCLONAL	1	TRUE	1	0.738518994223315	3		466	621	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859587	151859587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	26	370	0	ENST00000262189.6:c.11075C>T	p.Ala3692Val	p.A3692V	ENST00000262189	NM_170606.2	3692	gCa/gTa	43/59	0.738518994223315	3	FACETS	0.192	0.151	0.238	0.096	0.075	0.119	SUBCLONAL	1	TRUE	1	0.738518994223315	3		370	503	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641523	23641536	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTCTTTAAGATG	CCCTCTTTAAGATG	T	novel	NA	P-0030562-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	150	493	0	ENST00000261584.4:c.1939_1952delinsA	p.His647LysfsTer9	p.H647Kfs*9	ENST00000261584	NM_024675.3	647	CATCTTAAAGAGGGa/Aa	5/13	0.649512139856783	4	FACETS	0.859	0.786	0.936	0.43	0.393	0.468	CLONAL	1	TRUE	2	0.738518994223315	4		493	822	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	116	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.631902504253782	2		276	265	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48921987	48921989	+	frameshift_variant	Frame_Shift_Del	DEL	AAC	AAC	GA	novel	NA	P-0030866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	176	344	0	ENST00000267163.4:c.527_529delinsGA	p.Gln176ArgfsTer10	p.Q176Rfs*10	ENST00000267163	NM_000321.2	176	cAACcc/cGAcc	5/27	0.631902504253782	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.631902504253782	1		344	321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578393	7578393	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876660821	NA	P-0030866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	434	643	0	ENST00000269305.4:c.537T>G	p.His179Gln	p.H179Q	ENST00000269305	NM_001126112.2	179	caT/caG	5/11	0.127053227080706	5	FACETS	0.998	0.973	1			1	INDETERMINATE	5	TRUE	NA	0.631902504253782	5		643	536	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0031355-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	340	807	1	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.264255503786562	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	TRUE	0	0.291097386254594	3		808	864	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651233	52651318	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTCCCGCAAAATGTGCCTACTTCAGGACCGCTGGCCCTCCTTACCTGGGAGCCCTCCTCATTATAGTGCCTGGCATTCCGGAACA	TCTCCCGCAAAATGTGCCTACTTCAGGACCGCTGGCCCTCCTTACCTGGGAGCCCTCCTCATTATAGTGCCTGGCATTCCGGAACA	-	novel	NA	P-0031355-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	33	214	0	ENST00000394830.3:c.1778_1818+45del		p.X593_splice	ENST00000394830	NM_018313.4	593		15/30	0.227461136426299	2	FACETS	1	0.932	1	0.652	0.537	0.778	CLONAL	1	TRUE	0	0.291097386254594	2		214	174	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820977	32820977	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031355-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	69	792	0	ENST00000354258.4:c.617C>A	p.Ala206Glu	p.A206E	ENST00000354258	NM_000593.5	206	gCg/gAg	1/11	0.227461136426299	2	FACETS	0.648	0.563	0.739	0.324	0.281	0.37	SUBCLONAL	1	TRUE	0	0.291097386254594	2		792	732	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988128	85988128	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042748-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	187	452	0	ENST00000263360.6:c.1073A>G	p.Tyr358Cys	p.Y358C	ENST00000263360	NM_003797.3	358	tAc/tGc	10/12	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.415326392039098	2		452	626	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875985	76875985	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042748-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	184	396	0	ENST00000373344.5:c.5150T>G	p.Val1717Gly	p.V1717G	ENST00000373344	NM_000489.3	1717	gTt/gGt	20/35	1	2	FACETS	0.83	0.772	0.889	1	0.992	1	CLONAL	2	TRUE	1	0.415326392039098	2		396	534	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317070	11317070	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766996808	NA	P-0042998-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	41	704	1	ENST00000361445.4:c.424G>A	p.Ala142Thr	p.A142T	ENST00000361445	NM_004958.3	142	Gct/Act	4/58	1	2	FACETS	0.779	0.647	0.926	0.779	0.647	0.926	CLONAL	1	TRUE	1	0.14	2		705	752	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895641	28895641	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1475572191	NA	P-0042998-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	60	662	0	ENST00000282397.4:c.3133C>T	p.Arg1045Trp	p.R1045W	ENST00000282397	NM_002019.4	1045	Cgg/Tgg	23/30	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.14	2		662	803	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577151	7577152	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0042998-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	41	684	1	ENST00000269305.4:c.786dup	p.Asn263Ter	p.N263*	ENST00000269305	NM_001126112.2	262	-/T	8/11	1	2	FACETS	0.865	0.719	1	0.865	0.719	1	CLONAL	1	TRUE	1	0.14	2		685	677	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374890	45374890	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042998-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	65	740	0	ENST00000262160.6:c.953A>T	p.Asn318Ile	p.N318I	ENST00000262160	NM_005901.5	318	aAt/aTt	8/11	0.204090119797003	3	FACETS	1	0.95	1	0.607	0.525	0.696	CLONAL	1	TRUE	1	0.14	3		740	819	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874169	155874169	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042998-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	24	0	0	ENST00000368323.3:c.362T>C	p.Val121Ala	p.V121A	ENST00000368323	NM_006912.5	121	gTc/gCc	5/6	1	2	FACETS	0.376	0.293	0.473	0.376	0.293	0.473	SUBCLONAL	1	TRUE	1	0.14	2		0	911	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88651892	88651892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042998-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	28	0	0	ENST00000372037.3:c.239G>A	p.Gly80Glu	p.G80E	ENST00000372037	NM_004329.2	80	gGa/gAa	5/13	1	2	FACETS	0.579	0.461	0.714	0.579	0.461	0.714	SUBCLONAL	1	TRUE	1	0.14	2		0	691	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99472846	99472846	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778465734	NA	P-0042998-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	25	0	0	ENST00000268035.6:c.2842G>A	p.Val948Met	p.V948M	ENST00000268035	NM_000875.3	948	Gtg/Atg	14/21	1	2	FACETS	0.404	0.317	0.505	0.404	0.317	0.505	SUBCLONAL	1	TRUE	1	0.14	2		0	884	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332874	152332874	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs755020320	NA	P-0042998-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	19	0	0	ENST00000206249.3:c.1180C>A	p.Arg394Ser	p.R394S	ENST00000206249	NM_000125.3	394	Cgc/Agc	5/8	1	2	FACETS	0.396	0.299	0.512	0.396	0.299	0.512	SUBCLONAL	1	TRUE	1	0.14	2		0	685	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0043139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	16	518	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.433	0.319	0.57	0.433	0.319	0.57	SUBCLONAL	1	TRUE	1	0.1884526506571	2		518	392	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772235	68772236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0043139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	124	885	0	ENST00000261769.5:c.84_85insAG	p.His29SerfsTer28	p.H29Sfs*28	ENST00000261769	NM_004360.3	28	-/AG	2/16	0.1884526506571	0	FACETS	1	0.961	1			1	CLONAL	2	TRUE	0	0.1884526506571	0		885	484	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043146-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	334	276	0				ENST00000310581	NM_198253.2	-/1132			0.79821808597634	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.831772342266916	3		276	548	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0043146-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	253	396	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.958	0.903	1	0.958	0.903	1	CLONAL	1	TRUE	1	0.831772342266916	2		396	635	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577266	64577273	+	frameshift_variant	Frame_Shift_Del	DEL	AGAGGGAC	AGAGGGAC	-	novel	NA	P-0043146-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	432	610	2	ENST00000312049.6:c.309_316del	p.Leu105SerfsTer9	p.L105Sfs*9	ENST00000312049	NM_130799.2	103	ctGTCCCTCTat/ctat	2/10	0.829445315522947	1	FACETS	0.966	0.935	0.997	0.966	0.935	0.997	CLONAL	1	TRUE	0	0.831772342266916	1		612	628	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272121	142272121	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043146-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	284	448	0	ENST00000350721.4:c.2753A>T	p.Lys918Ile	p.K918I	ENST00000350721	NM_001184.3	918	aAa/aTa	13/47	1	2	FACETS	0.907	0.857	0.958	0.907	0.857	0.958	CLONAL	1	TRUE	1	0.831772342266916	2		448	753	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153563	108153575	+	protein_altering_variant	In_Frame_Del	DEL	CCTTTTATTTTAT	CCTTTTATTTTAT	TTAA	novel	NA	P-0043800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	37	312	2	ENST00000278616.4:c.3703_3715delinsTTAA	p.Pro1235_Leu1239delinsLeuIle	p.P1235_L1239delinsLI	ENST00000278616	NM_000051.3	1235	CCTTTTATTTTATta/TTAAta	25/63	0.248576151923361	1	FACETS	0.902	0.747	1	0.902	0.747	1	CLONAL	1	TRUE	0	0.248634221098823	1		314	289	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864269	57864269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200441300	NA	P-0043800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	68	585	0	ENST00000228682.2:c.1746G>A	p.Met582Ile	p.M582I	ENST00000228682	NM_005269.2	582	atG/atA	12/12	1	2	FACETS	0.789	0.686	0.901	0.789	0.686	0.901	CLONAL	1	TRUE	1	0.248634221098823	2		585	693	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220493	1220493	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	78	628	0	ENST00000326873.7:c.586G>C	p.Gly196Arg	p.G196R	ENST00000326873	NM_000455.4	196	Ggc/Cgc	4/10	0.248634221098823	1	FACETS	0.961	0.845	1	0.961	0.845	1	CLONAL	1	TRUE	0	0.248634221098823	1		628	572	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602390	10602391	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0043800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	95	792	0	ENST00000171111.5:c.1187dup	p.Tyr396Ter	p.Y396*	ENST00000171111	NM_203500.1	396	tac/taAc	3/6	0.248634221098823	1	FACETS	0.91	0.811	1	0.91	0.811	1	CLONAL	1	TRUE	0	0.248634221098823	1		792	735	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212084	36212084	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043800-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	91	776	0	ENST00000222270.7:c.1835C>T	p.Thr612Ile	p.T612I	ENST00000222270	NM_014727.1	612	aCc/aTc	3/37	1	2	FACETS	0.861	0.764	0.966	0.861	0.764	0.966	CLONAL	1	TRUE	1	0.248634221098823	2		776	850	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043824-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	93	276	0				ENST00000310581	NM_198253.2	-/1132			0.251115457484411	3	FACETS	0.832	0.743	0.927	0.832	0.743	0.927	CLONAL	2	FALSE	1	0.251115457484411	3		276	501	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0043824-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	65	221	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.251115457484411	3	FACETS	0.777	0.677	0.884	0.777	0.677	0.884	SUBCLONAL	2	FALSE	1	0.251115457484411	3		221	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567556006	NA	P-0043824-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	128	617	1	ENST00000269305.4:c.298del	p.Gln100ArgfsTer23	p.Q100Rfs*23	ENST00000269305	NM_001126112.2	100	Cag/ag	4/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.251115457484411	2		618	872	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211537	46211537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043824-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	35	249	0	ENST00000334344.6:c.503G>A	p.Gly168Glu	p.G168E	ENST00000334344	NM_152641.2	168	gGa/gAa	5/21	1	2	FACETS	0.593	0.486	0.714	0.593	0.486	0.714	SUBCLONAL	1	FALSE	1	0.251115457484411	2		249	470	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216962	7216963	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043824-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	75	492	0	ENST00000380728.2:c.558dup	p.Ala187CysfsTer19	p.A187Cfs*19	ENST00000380728		186	-/T	7/11	1	2	FACETS	0.855	0.748	0.969	0.855	0.748	0.969	CLONAL	1	FALSE	1	0.251115457484411	2		492	699	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958803	55958803	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043824-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	102	518	0	ENST00000263923.4:c.3050A>G	p.Glu1017Gly	p.E1017G	ENST00000263923	NM_002253.2	1017	gAg/gGg	22/30	0.251115457484411	3	FACETS	1	0.914	1			1	CLONAL	1	FALSE	NA	0.251115457484411	3		518	891	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195073	123195073	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0043824-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	76	206	0	ENST00000218089.9:c.1417-1G>C		p.X473_splice	ENST00000218089	NM_001042749.1	473			1	1	FACETS	0.922	0.818	1	1	0.983	1	CLONAL	2	FALSE	0	0.251115457484411	1		206	287	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0044268-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	56	434	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	1	2	FACETS	0.567	0.485	0.656	0.567	0.485	0.656	SUBCLONAL	1	TRUE	1	0.34	2		434	581	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118339521	118339521	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044268-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	72	453	0	ENST00000534358.1:c.464A>T	p.Glu155Val	p.E155V	ENST00000534358	NM_005933.3	155	gAa/gTa	2/36	1	2	FACETS	0.907	0.795	1	0.907	0.795	1	CLONAL	1	TRUE	1	0.34	2		453	467	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658373	18658373	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044268-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	37	362	0	ENST00000266497.5:c.3178C>T	p.Gln1060Ter	p.Q1060*	ENST00000266497		1060	Caa/Taa	22/31	1	2	FACETS	0.535	0.441	0.639	0.535	0.441	0.639	SUBCLONAL	1	TRUE	1	0.34	2		362	407	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39002737	39002737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1161334352	NA	P-0044268-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	52	340	0	ENST00000357387.3:c.292G>A	p.Glu98Lys	p.E98K	ENST00000357387	NM_152756.3	98	Gaa/Aaa	5/38	NA	3	FACETS	0.86	0.734	0.998	0.43	0.367	0.499	INDETERMINATE	1	TRUE	1	0.34	3		340	416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28934577	NA	P-0044294-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	171	602	0	ENST00000269305.4:c.770T>C	p.Leu257Pro	p.L257P	ENST00000269305	NM_001126112.2	257	cTg/cCg	7/11	0.590667228753697	1	FACETS	0.962	0.896	1	0.962	0.896	1	CLONAL	1	TRUE	0	0.607984948752151	1		602	407	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	195	366	0				ENST00000310581	NM_198253.2	-/1132			0.414334463621958	5	FACETS	1	0.961	1	1	0.961	1	INDETERMINATE	3	TRUE	2	0.871574943538941	5		366	337	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684350	29684350	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	195	584	0	ENST00000356175.3:c.7870G>T	p.Glu2624Ter	p.E2624*	ENST00000356175	NM_000267.3	2624	Gag/Tag	53/57	0.695169310906592	4	FACETS	0.853	0.797	0.91	0.853	0.797	0.91	CLONAL	2	TRUE	2	0.871574943538941	4		584	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	249	581	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.871574943538941	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.871574943538941	2		581	280	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163297	32163297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1239036035	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	478	869	0	ENST00000375023.3:c.5929G>A	p.Glu1977Lys	p.E1977K	ENST00000375023	NM_004557.3	1977	Gag/Aag	30/30	0.534577498155115	4	FACETS	0.932	0.902	0.962	0.932	0.902	0.962	CLONAL	3	TRUE	1	0.871574943538941	4		869	734	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099402	157099403	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAG	rs587779743	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	31	341	0	ENST00000346085.5:c.360_362dup	p.Gln131dup	p.Q131dup	ENST00000346085	NM_020732.3	131	-/CAG	1/20	0.871574943538941	2	FACETS	0.447	0.366	0.537	0.224	0.183	0.269	SUBCLONAL	1	TRUE	0	0.871574943538941	2		341	159	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023037	33023037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	124	660	0	ENST00000300177.4:c.146C>T	p.Ser49Leu	p.S49L	ENST00000300177	NM_001191322.1	49	tCg/tTg	2/2	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.871574943538941	2		660	268	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339981	70339981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	216	284	0	ENST00000374080.3:c.514G>A	p.Glu172Lys	p.E172K	ENST00000374080		172	Gag/Aag	4/45	0.871574943538941	2	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.871574943538941	2		284	231	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	230	440	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	0.871574943538941	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.871574943538941	2		440	240	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843447	3843447	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783461	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	152	607	1	ENST00000262367.5:c.1156C>T	p.Arg386Ter	p.R386*	ENST00000262367	NM_004380.2	386	Cga/Tga	4/31	1	2	FACETS	0.977	0.906	1	0.977	0.906	1	CLONAL	1	TRUE	1	0.871574943538941	2		608	357	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193530	99193530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	378	857	2	ENST00000074304.5:c.2725G>A	p.Glu909Lys	p.E909K	ENST00000074304	NM_001134224.1	909	Gag/Aag	25/26	0.871574943538941	3	FACETS	0.995	0.956	1	0.995	0.956	1	CLONAL	2	TRUE	1	0.871574943538941	3		859	626	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793134	33793134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1452063514	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	124	306	0	ENST00000498907.2:c.187G>A	p.Asp63Asn	p.D63N	ENST00000498907	NM_004364.3	63	Gac/Aac	1/1	0.871574943538941	5	FACETS	0.782	0.713	0.853	0.521	0.475	0.569	SUBCLONAL	2	TRUE	2	0.871574943538941	5		306	420	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870966	12870966	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	198	310	0	ENST00000228872.4:c.193C>T	p.Gln65Ter	p.Q65*	ENST00000228872	NM_004064.3	65	Cag/Tag	1/3	0.544312203636555	6	FACETS	0.957	0.898	1	0.957	0.898	1	CLONAL	3	TRUE	3	0.871574943538941	6		310	434	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618547	37618547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	274	651	1	ENST00000447079.4:c.223G>A	p.Asp75Asn	p.D75N	ENST00000447079	NM_015083.1	75	Gat/Aat	1/14	0.695169310906592	4	FACETS	0.954	0.903	1	0.954	0.903	1	CLONAL	2	TRUE	2	0.871574943538941	4		652	617	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619292	37619292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	291	665	1	ENST00000447079.4:c.968C>T	p.Ser323Leu	p.S323L	ENST00000447079	NM_015083.1	323	tCg/tTg	1/14	0.695169310906592	4	FACETS	0.978	0.928	1	0.978	0.928	1	CLONAL	2	TRUE	2	0.871574943538941	4		666	639	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855787	45855787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	172	861	0	ENST00000391945.4:c.2023G>T	p.Gly675Cys	p.G675C	ENST00000391945	NM_000400.3	675	Ggc/Tgc	21/23	1	2	FACETS	0.984	0.917	1	0.984	0.917	1	CLONAL	1	TRUE	1	0.871574943538941	2		861	401	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952304	17952304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	173	875	1	ENST00000458235.1:c.1036G>A	p.Asp346Asn	p.D346N	ENST00000458235	NM_000215.3	346	Gac/Aac	8/24	0.796020395382855	3	FACETS	0.885	0.818	0.954	0.443	0.409	0.477	CLONAL	1	TRUE	1	0.871574943538941	3		876	644	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374909	149374909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	577	654	0	ENST00000360632.3:c.185C>T	p.Ser62Leu	p.S62L	ENST00000360632	NM_015472.4	62	tCg/tTg	2/7	0.871574943538941	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	1	0.871574943538941	4		654	806	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794999	242794999	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424422486	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	150	968	1	ENST00000334409.5:c.210G>A	p.Met70Ile	p.M70I	ENST00000334409	NM_005018.2	70	atG/atA	2/5	0.871574943538941	3	FACETS	0.883	0.811	0.957	0.441	0.405	0.479	CLONAL	1	TRUE	1	0.871574943538941	3		969	560	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660138	227660138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1448309277	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	173	830	1	ENST00000305123.5:c.3317C>T	p.Ser1106Leu	p.S1106L	ENST00000305123	NM_005544.2	1106	tCa/tTa	1/2	0.871574943538941	3	FACETS	1	0.943	1	0.511	0.473	0.55	CLONAL	1	TRUE	1	0.871574943538941	3		831	558	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851228	151851228	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	34	310	0	ENST00000262189.6:c.12143C>T	p.Ser4048Leu	p.S4048L	ENST00000262189	NM_170606.2	4048	tCa/tTa	48/59	1	2	FACETS	0.821	0.691	0.957	0.821	0.691	0.957	CLONAL	1	TRUE	1	0.871574943538941	2		310	95	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023943	27023943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	47	117	0	ENST00000324856.7:c.1049C>T	p.Ser350Leu	p.S350L	ENST00000324856	NM_006015.4	350	tCg/tTg	1/20	0.855571048471701	3	FACETS	0.895	0.768	1	0.448	0.384	0.516	CLONAL	1	TRUE	1	0.871574943538941	3		117	173	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247882	59247882	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	236	815	0	ENST00000371222.2:c.861G>C	p.Leu287Phe	p.L287F	ENST00000371222	NM_002228.3	287	ttG/ttC	1/1	0.534577498155115	4	FACETS	1	0.99	1	0.43	0.402	0.458	CLONAL	1	TRUE	1	0.871574943538941	4		815	786	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78425916	78425916	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	194	547	0	ENST00000370768.2:c.1529G>A	p.Trp510Ter	p.W510*	ENST00000370768	NM_003902.3	510	tGg/tAg	16/20	0.534577498155115	4	FACETS	0.887	0.84	0.933	0.887	0.84	0.933	CLONAL	3	TRUE	1	0.871574943538941	4		547	313	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466576	120466576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	127	519	0	ENST00000256646.2:c.4543G>A	p.Asp1515Asn	p.D1515N	ENST00000256646	NM_024408.3	1515	Gac/Aac	26/34	0.534577498155115	4	FACETS	1	0.985	1	0.464	0.424	0.505	CLONAL	1	TRUE	1	0.871574943538941	4		519	392	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551376	150551376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	216	899	0	ENST00000369026.2:c.631G>A	p.Glu211Lys	p.E211K	ENST00000369026	NM_021960.4	211	Gag/Aag	1/3	0.871574943538941	4	FACETS	0.715	0.663	0.768	0.238	0.221	0.256	SUBCLONAL	1	TRUE	1	0.871574943538941	4		899	1298	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119447	193119447	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	97	429	0	ENST00000367435.3:c.842G>C	p.Arg281Pro	p.R281P	ENST00000367435	NM_024529.4	281	cGc/cCc	9/17	0.871574943538941	4	FACETS	0.997	0.894	1	0.332	0.298	0.368	CLONAL	1	TRUE	1	0.871574943538941	4		429	418	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575515	64575525	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCCTGGCAG	GGGCCTGGCAG	-	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	322	712	0	ENST00000312049.6:c.492_502del	p.Cys165GlyfsTer11	p.C165Gfs*11	ENST00000312049	NM_130799.2	164	gcCTGCCAGGCCCtg/gctg	3/10	0.534577498155115	4	FACETS	1	0.994	1	0.829	0.793	0.865	CLONAL	2	TRUE	1	0.871574943538941	4		712	556	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206918	102206918	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	61	436	0	ENST00000263464.3:c.1546G>A	p.Glu516Lys	p.E516K	ENST00000263464	NM_001165.4	516	Gaa/Aaa	7/9	0.534577498155115	4	FACETS	1	0.966	1	0.443	0.389	0.5	CLONAL	1	TRUE	1	0.871574943538941	4		436	197	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352519	118352519	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	130	600	0	ENST00000534358.1:c.3724C>T	p.Gln1242Ter	p.Q1242*	ENST00000534358	NM_005933.3	1242	Cag/Tag	7/36	0.534577498155115	4	FACETS	1	0.974	1	0.39	0.356	0.426	CLONAL	1	TRUE	1	0.871574943538941	4		600	477	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427885	49427885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	376	780	1	ENST00000301067.7:c.10705G>A	p.Glu3569Lys	p.E3569K	ENST00000301067	NM_003482.3	3569	Gag/Aag	38/54	0.544312203636555	6	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	TRUE	3	0.871574943538941	6		781	775	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444499	49444499	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	174	700	0	ENST00000301067.7:c.2872G>C	p.Glu958Gln	p.E958Q	ENST00000301067	NM_003482.3	958	Gag/Cag	11/54	0.544312203636555	6	FACETS	1	0.989	1	0.495	0.456	0.534	CLONAL	1	TRUE	3	0.871574943538941	6		700	738	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023114	33023114	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	131	711	0	ENST00000300177.4:c.223G>A	p.Glu75Lys	p.E75K	ENST00000300177	NM_001191322.1	75	Gag/Aag	2/2	1	2	FACETS	0.931	0.857	1	0.931	0.857	1	CLONAL	1	TRUE	1	0.871574943538941	2		711	323	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591728	38591728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	89	465	0	ENST00000299084.4:c.187G>A	p.Glu63Lys	p.E63K	ENST00000299084	NM_152594.2	63	Gag/Aag	2/7	1	2	FACETS	0.88	0.795	0.968	0.88	0.795	0.968	CLONAL	1	TRUE	1	0.871574943538941	2		465	232	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041908	42041908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	105	632	0	ENST00000219905.7:c.6103G>A	p.Glu2035Lys	p.E2035K	ENST00000219905	NM_001164273.1	2035	Gaa/Aaa	17/24	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.871574943538941	2		632	219	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762144	43762144	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	150	723	0	ENST00000382044.4:c.1301C>T	p.Ser434Leu	p.S434L	ENST00000382044	NM_001141980.1	434	tCa/tTa	11/28	1	2	FACETS	0.992	0.92	1	0.992	0.92	1	CLONAL	1	TRUE	1	0.871574943538941	2		723	347	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138583	2138583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778484981	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	218	766	1	ENST00000219476.3:c.5396C>T	p.Ser1799Leu	p.S1799L	ENST00000219476	NM_000548.3	1799	tCg/tTg	42/42	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.871574943538941	2		767	461	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817781	3817781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886041006	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	150	618	0	ENST00000262367.5:c.3190G>A	p.Glu1064Lys	p.E1064K	ENST00000262367	NM_004380.2	1064	Gag/Aag	16/31	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.871574943538941	2		618	312	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14021937	14021937	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	85	560	1	ENST00000311895.7:c.637G>A	p.Glu213Lys	p.E213K	ENST00000311895	NM_005236.2	213	Gaa/Aaa	4/11	1	2	FACETS	0.938	0.846	1	0.938	0.846	1	CLONAL	1	TRUE	1	0.871574943538941	2		561	208	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821848	72821848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1287091663	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	163	591	0	ENST00000268489.5:c.10327G>A	p.Glu3443Lys	p.E3443K	ENST00000268489	NM_006885.3	3443	Gaa/Aaa	10/10	1	2	FACETS	0.974	0.906	1	0.974	0.906	1	CLONAL	1	TRUE	1	0.871574943538941	2		591	384	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942499	17942499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	165	836	1	ENST00000458235.1:c.2789C>T	p.Ser930Phe	p.S930F	ENST00000458235	NM_000215.3	930	tCc/tTc	20/24	0.796020395382855	3	FACETS	0.952	0.879	1	0.476	0.439	0.514	CLONAL	1	TRUE	1	0.871574943538941	3		837	571	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18956873	18956873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758924331	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	164	662	0	ENST00000262803.5:c.316G>A	p.Glu106Lys	p.E106K	ENST00000262803	NM_002911.3	106	Gag/Aag	2/24	0.796020395382855	3	FACETS	1	0.933	1	0.505	0.466	0.545	CLONAL	1	TRUE	1	0.871574943538941	3		662	535	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18958573	18958573	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	278	681	0	ENST00000262803.5:c.392C>T	p.Pro131Leu	p.P131L	ENST00000262803	NM_002911.3	131	cCt/cTt	3/24	0.796020395382855	3	FACETS	0.916	0.872	0.959	0.916	0.872	0.959	CLONAL	2	TRUE	1	0.871574943538941	3		681	500	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211411	36211411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	484	831	0	ENST00000222270.7:c.1162G>A	p.Glu388Lys	p.E388K	ENST00000222270	NM_014727.1	388	Gag/Aag	3/37	0.871574943538941	5	FACETS	0.974	0.939	1	0.974	0.939	1	CLONAL	3	TRUE	2	0.871574943538941	5		831	877	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753786	42753786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765102149	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	431	925	1	ENST00000222329.4:c.478C>T	p.Arg160Cys	p.R160C	ENST00000222329	NM_006494.2	160	Cgc/Tgc	4/4	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.871574943538941	2		926	708	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796483	42796483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751173226	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	445	977	1	ENST00000575354.2:c.3040G>A	p.Ala1014Thr	p.A1014T	ENST00000575354	NM_015125.3	1014	Gcg/Acg	13/20	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.871574943538941	2		978	738	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967335	25967335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	176	401	0	ENST00000435504.4:c.1871C>T	p.Ser624Phe	p.S624F	ENST00000435504		624	tCc/tTc	13/13	0.871574943538941	3	FACETS	0.996	0.94	1	0.996	0.94	1	CLONAL	2	TRUE	1	0.871574943538941	3		401	291	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047360	128047360	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	249	529	0	ENST00000285398.2:c.562C>T	p.Leu188Phe	p.L188F	ENST00000285398	NM_000122.1	188	Ctt/Ttt	5/15	0.871574943538941	3	FACETS	0.958	0.911	1	0.958	0.911	1	CLONAL	2	TRUE	1	0.871574943538941	3		529	428	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989531	212989531	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1443958987	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	231	422	0	ENST00000342788.4:c.180G>A	p.Met60Ile	p.M60I	ENST00000342788	NM_005235.2	60	atG/atA	2/28	0.871574943538941	3	FACETS	0.971	0.922	1	0.971	0.922	1	CLONAL	2	TRUE	1	0.871574943538941	3		422	392	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659740	227659740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	291	504	0	ENST00000305123.5:c.3715G>A	p.Glu1239Lys	p.E1239K	ENST00000305123	NM_005544.2	1239	Gag/Aag	1/2	0.871574943538941	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.871574943538941	3		504	443	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661616	227661616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	206	866	0	ENST00000305123.5:c.1839G>A	p.Met613Ile	p.M613I	ENST00000305123	NM_005544.2	613	atG/atA	1/2	0.871574943538941	3	FACETS	1	0.985	1	0.589	0.55	0.629	CLONAL	1	TRUE	1	0.871574943538941	3		866	576	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309757	30309757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs996600059	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	289	688	1	ENST00000307677.4:c.265G>A	p.Ala89Thr	p.A89T	ENST00000307677	NM_138578.1	89	Gcg/Acg	2/3	0.837448043456627	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	2	0.871574943538941	4		689	612	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385023	31385023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	323	778	0	ENST00000328111.2:c.1408G>A	p.Asp470Asn	p.D470N	ENST00000328111	NM_006892.3	470	Gat/Aat	14/23	0.837448043456627	4	FACETS	0.94	0.893	0.987	0.94	0.893	0.987	CLONAL	2	TRUE	2	0.871574943538941	4		778	738	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280649	41280649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	254	687	0	ENST00000349496.5:c.2162C>T	p.Ser721Phe	p.S721F	ENST00000349496	NM_001904.3	721	tCt/tTt	15/15	0.603120082518482	4	FACETS	0.858	0.817	0.898	0.858	0.817	0.898	CLONAL	3	TRUE	1	0.871574943538941	4		687	424	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502882	186502882	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	290	512	0	ENST00000323963.5:c.340G>C	p.Ala114Pro	p.A114P	ENST00000323963		114	Gct/Cct	4/11	0.871574943538941	4	FACETS	0.927	0.888	0.965	0.927	0.888	0.965	CLONAL	3	TRUE	1	0.871574943538941	4		512	448	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806615	1806615	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761325047	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	210	898	0	ENST00000260795.2:c.1331C>T	p.Ser444Phe	p.S444F	ENST00000260795		444	tCc/tTc	9/17	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.871574943538941	2		898	441	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146626	55146626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	99	560	0	ENST00000257290.5:c.2300C>T	p.Ser767Leu	p.S767L	ENST00000257290	NM_006206.4	767	tCa/tTa	16/23	1	2	FACETS	0.959	0.872	1	0.959	0.872	1	CLONAL	1	TRUE	1	0.871574943538941	2		560	237	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029321	143029321	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	55	329	0	ENST00000262992.4:c.2299G>C	p.Glu767Gln	p.E767Q	ENST00000262992	NM_001101669.1	767	Gaa/Caa	21/24	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.871574943538941	2		329	123	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519281	187519281	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	73	425	0	ENST00000441802.2:c.12104-2A>C		p.X4035_splice	ENST00000441802	NM_005245.3	4035			1	2	FACETS	0.957	0.857	1	0.957	0.857	1	CLONAL	1	TRUE	1	0.871574943538941	2		425	175	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542269	187542269	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	50	490	0	ENST00000441802.2:c.5471C>T	p.Ser1824Phe	p.S1824F	ENST00000441802	NM_005245.3	1824	tCt/tTt	10/27	1	2	FACETS	0.964	0.843	1	0.964	0.843	1	CLONAL	1	TRUE	1	0.871574943538941	2		490	119	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629169	187629169	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	67	632	1	ENST00000441802.2:c.1813C>T	p.Gln605Ter	p.Q605*	ENST00000441802	NM_005245.3	605	Cag/Tag	2/27	1	2	FACETS	0.869	0.771	0.969	0.869	0.771	0.969	CLONAL	1	TRUE	1	0.871574943538941	2		633	177	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630295	187630295	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	126	651	0	ENST00000441802.2:c.687G>A	p.Met229Ile	p.M229I	ENST00000441802	NM_005245.3	229	atG/atA	2/27	1	2	FACETS	0.997	0.918	1	0.997	0.918	1	CLONAL	1	TRUE	1	0.871574943538941	2		651	290	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915627	131915627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	152	370	0	ENST00000265335.6:c.625G>A	p.Glu209Lys	p.E209K	ENST00000265335		209	Gaa/Aaa	5/25	0.871574943538941	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.871574943538941	3		370	226	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158737	26158737	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	251	508	0	ENST00000289316.2:c.340G>C	p.Glu114Gln	p.E114Q	ENST00000289316	NM_138720.2	114	Gag/Cag	1/2	0.534577498155115	4	FACETS	0.951	0.909	0.991	0.951	0.909	0.991	CLONAL	3	TRUE	1	0.871574943538941	4		508	378	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181961	32181961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	291	809	0	ENST00000375023.3:c.2093C>T	p.Ala698Val	p.A698V	ENST00000375023	NM_004557.3	698	gCa/gTa	13/30	0.534577498155115	4	FACETS	0.864	0.826	0.902	0.864	0.826	0.902	CLONAL	3	TRUE	1	0.871574943538941	4		809	482	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821421	32821421	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	167	876	0	ENST00000354258.4:c.173G>A	p.Arg58Gln	p.R58Q	ENST00000354258	NM_000593.5	58	cGa/cAa	1/11	0.534577498155115	4	FACETS	1	0.984	1	0.416	0.384	0.449	CLONAL	1	TRUE	1	0.871574943538941	4		876	575	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864457	162864457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	318	527	0	ENST00000366898.1:c.56C>T	p.Ser19Phe	p.S19F	ENST00000366898	NM_004562.2	19	tCt/tTt	2/12	0.871574943538941	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.871574943538941	2		527	355	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6037009	6037009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142434011	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	254	526	0	ENST00000265849.7:c.751G>A	p.Val251Met	p.V251M	ENST00000265849	NM_000535.5	251	Gtg/Atg	7/15	0.326173371214601	2	FACETS	1	0.994	1	0.678	0.645	0.71	INDETERMINATE	1	TRUE	0	0.871574943538941	2		526	430	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859429	151859429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	116	580	0	ENST00000262189.6:c.11233G>A	p.Glu3745Lys	p.E3745K	ENST00000262189	NM_170606.2	3745	Gaa/Aaa	43/59	1	2	FACETS	0.954	0.875	1	0.954	0.875	1	CLONAL	1	TRUE	1	0.871574943538941	2		580	279	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56911053	56911053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	168	561	1	ENST00000519728.1:c.1199G>A	p.Arg400Lys	p.R400K	ENST00000519728	NM_002350.3	400	aGg/aAg	11/13	0.855571048471701	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.871574943538941	3		562	264	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021812	69021812	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	233	633	0	ENST00000288368.4:c.3100C>T	p.Gln1034Ter	p.Q1034*	ENST00000288368	NM_024870.2	1034	Cag/Tag	25/40	0.855571048471701	3	FACETS	0.957	0.909	1	0.957	0.909	1	CLONAL	2	TRUE	1	0.871574943538941	3		633	401	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76949351	76949351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	196	245	0	ENST00000373344.5:c.446G>A	p.Arg149Lys	p.R149K	ENST00000373344	NM_000489.3	149	aGa/aAa	6/35	0.871574943538941	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.871574943538941	2		245	203	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28903794	28903794	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs770140431	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	137	652	1	ENST00000282397.4:c.2665C>A	p.Leu889Met	p.L889M	ENST00000282397	NM_002019.4	889	Ctg/Atg	19/30	0.871574943538941	2	FACETS	0.998	0.923	1	0.499	0.461	0.537	CLONAL	1	TRUE	0	0.871574943538941	2		653	315	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633104	3633104	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	117	655	0	ENST00000294008.3:c.5147C>T	p.Ser1716Leu	p.S1716L	ENST00000294008	NM_032444.2	1716	tCa/tTa	14/15	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.871574943538941	2		655	266	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149437110	149437110	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs899883054	NA	P-0044446-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	151	843	0	ENST00000286301.3:c.2178G>A	p.Met726Ile	p.M726I	ENST00000286301	NM_005211.3	726	atG/atA	16/22	0.871574943538941	3	FACETS	1	0.931	1	0.506	0.465	0.547	CLONAL	1	TRUE	1	0.871574943538941	3		843	492	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044707-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	144	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.939	0.858	1	0.939	0.858	1	CLONAL	1	TRUE	1	0.424734224883274	2		436	722	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578232	7578232	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0044707-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	187	565	0	ENST00000269305.4:c.617T>A	p.Leu206Ter	p.L206*	ENST00000269305	NM_001126112.2	206	tTg/tAg	6/11	0.366102452817906	1	FACETS	0.851	0.787	0.917	0.851	0.787	0.917	CLONAL	1	TRUE	0	0.424734224883274	1		565	815	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271393	26271393	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044707-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	131	424	0	ENST00000305910.3:c.220G>T	p.Glu74Ter	p.E74*	ENST00000305910	NM_003534.2	74	Gaa/Taa	1/1	0.366102452817906	1	FACETS	0.742	0.675	0.812	0.742	0.675	0.812	SUBCLONAL	1	TRUE	0	0.424734224883274	1		424	655	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986989	36986990	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	AA	novel	NA	P-0044707-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	381	345	1	ENST00000354822.5:c.699_700delinsTT	p.Gln234Ter	p.Q234*	ENST00000354822	NM_001079668.2	233	acGCag/acTTag	3/3	0.424734224883274	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.424734224883274	2		346	746	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595924	43595924	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044707-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	64	595	0	ENST00000355710.3:c.91T>A	p.Phe31Ile	p.F31I	ENST00000355710	NM_020975.4	31	Ttc/Atc	2/20	0.269331865660855	0	FACETS	0.234	0.202	0.269			1	SUBCLONAL	1	TRUE	0	0.424734224883274	0		595	740	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0044708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	325	564	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.409684289627753	2	FACETS	0.776	0.737	0.815	0.776	0.737	0.815	SUBCLONAL	2	TRUE	0	0.536552113747099	2		564	781	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941858	44941858	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0044708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	40	205	0	ENST00000377967.4:c.3182C>G	p.Ser1061Ter	p.S1061*	ENST00000377967	NM_021140.2	1061	tCa/tGa	21/29	1	1	FACETS	0.276	0.23	0.328	0.276	0.23	0.328	SUBCLONAL	1	TRUE	0	0.536552113747099	1		205	395	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643248	38643248	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	54	400	0	ENST00000299084.4:c.718C>G	p.Gln240Glu	p.Q240E	ENST00000299084	NM_152594.2	240	Caa/Gaa	7/7	0.536552113747099	1	FACETS	0.327	0.28	0.379	0.327	0.28	0.379	SUBCLONAL	1	TRUE	0	0.536552113747099	1		400	450	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155411	47155412	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044708-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	174	438	0	ENST00000409792.3:c.4669dup	p.Thr1557AsnfsTer31	p.T1557Nfs*31	ENST00000409792	NM_014159.6	1557	aca/aAca	5/21	1	2	FACETS	0.816	0.752	0.882	0.816	0.752	0.882	CLONAL	1	TRUE	1	0.536552113747099	2		438	795	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027133	49027133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853292	NA	P-0045414-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	35	528	0	ENST00000267163.4:c.1700C>T	p.Ser567Leu	p.S567L	ENST00000267163	NM_000321.2	567	tCa/tTa	18/27	0.360188388559164	3	FACETS	0.403	0.329	0.486	0.202	0.164	0.243	SUBCLONAL	1	TRUE	1	0.360188388559164	3		528	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0045414-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	123	839	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.360188388559164	1	FACETS	0.896	0.812	0.984	0.896	0.812	0.984	CLONAL	1	TRUE	0	0.360188388559164	1		839	625	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528611	8528611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201846121	NA	P-0045414-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	78	639	0	ENST00000356435.5:c.521G>A	p.Arg174His	p.R174H	ENST00000356435		174	cGt/cAt	4/35	1	2	FACETS	0.685	0.602	0.774	0.685	0.602	0.774	SUBCLONAL	1	TRUE	1	0.360188388559164	2		639	632	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448391	49448391	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045414-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	64	948	0	ENST00000301067.7:c.320A>G	p.Glu107Gly	p.E107G	ENST00000301067	NM_003482.3	107	gAg/gGg	3/54	1	2	FACETS	0.534	0.462	0.613	0.534	0.462	0.613	SUBCLONAL	1	TRUE	1	0.360188388559164	2		948	665	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136277	202136277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045414-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	213	927	0	ENST00000358485.4:c.521C>T	p.Ser174Leu	p.S174L	ENST00000358485	NM_001080125.1	174	tCa/tTa	3/9	0.203414863986535	2	FACETS	1	0.991	1	0.746	0.695	0.798	INDETERMINATE	1	TRUE	0	0.360188388559164	2		927	793	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259152	36259156	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCA	GGGCA	-	novel	NA	P-0045414-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	42	676	1	ENST00000300305.3:c.335_339del	p.Leu112HisfsTer24	p.L112Hfs*24	ENST00000300305		112	cTGCCC/c	3/8	1	2	FACETS	0.371	0.309	0.441	0.371	0.309	0.441	SUBCLONAL	1	TRUE	1	0.360188388559164	2		677	628	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565544	41565544	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045414-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	164	694	0	ENST00000263253.7:c.4211del	p.Phe1404SerfsTer6	p.F1404Sfs*6	ENST00000263253	NM_001429.3	1404	Ttc/tc	26/31	0.271446166509355	2	FACETS	1	0.986	1	0.675	0.621	0.73	CLONAL	1	TRUE	0	0.360188388559164	2		694	675	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665299	138665299	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1226344391	NA	P-0045414-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	200	906	0	ENST00000330315.3:c.266C>G	p.Pro89Arg	p.P89R	ENST00000330315	NM_023067.3	89	cCg/cGg	1/1	0.172884180458215	3	FACETS	0.783	0.726	0.841	0.783	0.726	0.841	INDETERMINATE	2	TRUE	1	0.360188388559164	3		906	837	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918557	44918557	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0045414-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	108	398	0	ENST00000377967.4:c.1040T>A	p.Leu347Ter	p.L347*	ENST00000377967	NM_021140.2	347	tTg/tAg	12/29	1	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.360188388559164	1		398	353	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998898	11998898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046982-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	22	355	0	ENST00000353533.5:c.400C>T	p.Arg134Trp	p.R134W	ENST00000353533	NM_003010.3	134	Cgg/Tgg	4/11	0.234059031736601	5	FACETS	0.439	0.341	0.553	0.146	0.113	0.185	INDETERMINATE	1	TRUE	2	0.983886521310526	5		355	252	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	32	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.826	1	1	0.826	1	CLONAL	1	TRUE	1	0.28	2		276	226	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0047585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	84	595	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.766	0.676	0.863	0.766	0.676	0.863	SUBCLONAL	1	TRUE	1	0.28	2		596	783	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	81	934	0	ENST00000269305.4:c.470T>G	p.Val157Gly	p.V157G	ENST00000269305	NM_001126112.2	157	gTc/gGc	5/11	1	2	FACETS	0.578	0.508	0.654	0.578	0.508	0.654	SUBCLONAL	1	TRUE	1	0.28	2		934	1001	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971145	21971159	+	inframe_deletion	In_Frame_Del	DEL	GTTGGGCTCCGCGCC	GTTGGGCTCCGCGCC	-	novel	NA	P-0047585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	43	480	0	ENST00000304494.5:c.199_213del	p.Gly67_Asn71del	p.G67_N71del	ENST00000304494	NM_000077.4	67	GGCGCGGAGCCCAAC/-	2/3	1	2	FACETS	0.627	0.524	0.74	0.627	0.524	0.74	SUBCLONAL	1	TRUE	1	0.28	2		480	490	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940765	49940765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540212347	NA	P-0047585-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	69	852	0	ENST00000296474.3:c.278C>T	p.Thr93Met	p.T93M	ENST00000296474	NM_002447.2	93	aCg/aTg	1/20	1	2	FACETS	0.638	0.554	0.728	0.638	0.554	0.728	SUBCLONAL	1	TRUE	1	0.28	2		852	773	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061011	38061011	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	81	491	0	ENST00000250448.2:c.978del	p.Ala329ProfsTer21	p.A329Pfs*21	ENST00000250448	NM_004496.3	326	ccC/cc	2/2	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.241177927950491	2		491	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0047832-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	253	554	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.435915605395557	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.435915605395557	1		554	692	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0047832-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	118	340	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.435915605395557	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.435915605395557	1		340	387	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412647	63412648	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047832-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	47	567	1	ENST00000330258.3:c.519dup	p.Ser174Ter	p.S174*	ENST00000330258	NM_152424.3	173	-/T	2/2	0.214415118774088	3	FACETS	0.286	0.24	0.337	0.143	0.12	0.169	INDETERMINATE	1	TRUE	1	0.435915605395557	3		568	918	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332337	70332337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761821309	NA	P-0048097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	169	433	0	ENST00000373644.4:c.242G>A	p.Arg81His	p.R81H	ENST00000373644	NM_030625.2	81	cGc/cAc	2/12	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.639490253706121	2		433	528	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479833	67479833	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	401	484	1	ENST00000327367.4:c.1140G>A	p.Trp380Ter	p.W380*	ENST00000327367	NM_005902.3	380	tgG/tgA	8/9	0.639490253706121	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.639490253706121	2		485	607	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149002	119149902	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGCAGGTACGGATCTAAACAGCGACTTTTTTCAGCTATGTAATAACCTTGGAAAATTCGGTATTATATAGCCTTTACTGATACAAGGGGTGGCCTGGCTTTTGGGGTTAGGTTTAAACTTTTACTTTTTTTTGATCTCTAGGAAATGTATTTTCTAGTAGATTAATATTTTAAGTATTTTCAGATGCATCTGTTACTATCTTTTGCTTCTTCTGCAGGAATCAGAAGGTCAGGGCTGTCCTTTCTGCCGATGTGAAATTAAAGGTACTGAACCCATCGTGGTAGATCCGTTTGATCCTAGAGGGAGTGGCAGCCTGTTGAGGCAAGGAGCAGAGGGAGCTCCCTCCCCAAATTATGATGATGATGATGATGAACGAGCTGATGATACTCTCTTCATGATGAAGGAATTGGCTGGTGCCAAGGTAAGATGGCAGTTTAGGAGACTGGCAAAATCCATTGTGAGTTGTCTTCTAAAGCCGTAAAACACTTAACGATATCCAAACTACAATGATAGGTAGTATTAATAGCTAATATTTATTGAGCATTTACTATATGACAGATATTGTGTTAAGCACTTTACTTGTTTTTTACTCAATCTTTACTACAGCCCTATGAGTACATACTACTATTATCCTTATTTAACAGATGAAGAAACTGAGGCACAAAGAGGTTAAGGAATTTGCCGAAGACCACACAGCTAGTAGGTTGAAGCATCTGTGAGCTGCATCTATGACCAGGCATTCCAGCTTAAGGCCCATGTTCTTACTGTCTGTATTTTTTAGGACTAAGACTTTATTCATATCTGTTGGTGGAGAATATGAGGGAGAAATAAAAGAACTGGACCCTCTTTTGCTAATGCAACTAGAATAAGTTCTGTTCCCTTTTTTTTTTTTTATTTTAA	TGGCAGGTACGGATCTAAACAGCGACTTTTTTCAGCTATGTAATAACCTTGGAAAATTCGGTATTATATAGCCTTTACTGATACAAGGGGTGGCCTGGCTTTTGGGGTTAGGTTTAAACTTTTACTTTTTTTTGATCTCTAGGAAATGTATTTTCTAGTAGATTAATATTTTAAGTATTTTCAGATGCATCTGTTACTATCTTTTGCTTCTTCTGCAGGAATCAGAAGGTCAGGGCTGTCCTTTCTGCCGATGTGAAATTAAAGGTACTGAACCCATCGTGGTAGATCCGTTTGATCCTAGAGGGAGTGGCAGCCTGTTGAGGCAAGGAGCAGAGGGAGCTCCCTCCCCAAATTATGATGATGATGATGATGAACGAGCTGATGATACTCTCTTCATGATGAAGGAATTGGCTGGTGCCAAGGTAAGATGGCAGTTTAGGAGACTGGCAAAATCCATTGTGAGTTGTCTTCTAAAGCCGTAAAACACTTAACGATATCCAAACTACAATGATAGGTAGTATTAATAGCTAATATTTATTGAGCATTTACTATATGACAGATATTGTGTTAAGCACTTTACTTGTTTTTTACTCAATCTTTACTACAGCCCTATGAGTACATACTACTATTATCCTTATTTAACAGATGAAGAAACTGAGGCACAAAGAGGTTAAGGAATTTGCCGAAGACCACACAGCTAGTAGGTTGAAGCATCTGTGAGCTGCATCTATGACCAGGCATTCCAGCTTAAGGCCCATGTTCTTACTGTCTGTATTTTTTAGGACTAAGACTTTATTCATATCTGTTGGTGGAGAATATGAGGGAGAAATAAAAGAACTGGACCCTCTTTTGCTAATGCAACTAGAATAAGTTCTGTTCCCTTTTTTTTTTTTTATTTTAA	-	novel	NA	P-0048097-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	115	439	0	ENST00000264033.4:c.1225_1431+482del		p.X409_splice	ENST00000264033	NM_005188.3	409		8-9/16	1	2	FACETS	0.869	0.789	0.952	0.869	0.789	0.952	CLONAL	1	TRUE	1	0.639490253706121	2		439	414	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048140-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	275	390	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.583965519880031	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.583965519880031	3		390	568	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955060	55955060	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs771413759	NA	P-0048140-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	65	378	0	ENST00000263923.4:c.3485A>C	p.Asn1162Thr	p.N1162T	ENST00000263923	NM_002253.2	1162	aAt/aCt	26/30	0.583965519880031	3	FACETS	0.505	0.438	0.577	0.252	0.219	0.289	SUBCLONAL	1	TRUE	1	0.583965519880031	3		378	570	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481768	40481768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048140-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	77	347	0	ENST00000264657.5:c.1136G>A	p.Arg379Lys	p.R379K	ENST00000264657	NM_139276.2	379	aGa/aAa	12/24	0.294809683826007	5	FACETS	0.838	0.737	0.948	0.279	0.245	0.316	INDETERMINATE	1	TRUE	2	0.583965519880031	5		347	590	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131976419	131976419	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048140-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	162	466	0	ENST00000265335.6:c.3674G>A	p.Cys1225Tyr	p.C1225Y	ENST00000265335		1225	tGt/tAt	24/25	0.583965519880031	5	FACETS	1	0.986	1	0.455	0.418	0.494	CLONAL	1	TRUE	2	0.583965519880031	5		466	762	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0048700-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	43	355	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	TRUE	1	0.21	2		355	408	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178095	56178095	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374455781	NA	P-0048700-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	27	335	0	ENST00000399503.3:c.3068G>A	p.Arg1023His	p.R1023H	ENST00000399503	NM_005921.1	1023	cGc/cAc	14/20	1	2	FACETS	0.688	0.547	0.848	0.688	0.547	0.848	SUBCLONAL	1	TRUE	1	0.21	2		335	374	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249037	55249037	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397517119	NA	P-0048700-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	57	470	0	ENST00000275493.2:c.2335G>T	p.Gly779Cys	p.G779C	ENST00000275493	NM_005228.3	779	Ggc/Tgc	20/28	1	2	FACETS	0.942	0.809	1	0.942	0.809	1	CLONAL	1	TRUE	1	0.21	2		470	576	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101546	27101546	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048700-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	60	564	1	ENST00000324856.7:c.4830del	p.Met1611Ter	p.M1611*	ENST00000324856	NM_006015.4	1610	Ggg/gg	18/20	1	2	FACETS	0.879	0.757	1	0.879	0.757	1	CLONAL	1	TRUE	1	0.21	2		565	650	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264463	30264477	+	inframe_deletion	In_Frame_Del	DEL	TGCGGTGTTACCGGT	TGCGGTGTTACCGGT	-	novel	NA	P-0048700-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	29	430	0	ENST00000322652.5:c.198_212del	p.Ala67_Val71del	p.A67_V71del	ENST00000322652	NM_015355.2	66	gcTGCGGTGTTACCGGTg/gcg	1/16	1	2	FACETS	0.533	0.427	0.655	0.533	0.427	0.655	SUBCLONAL	1	TRUE	1	0.21	2		430	518	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873328	136873328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048700-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	55	418	1	ENST00000241393.3:c.170G>A	p.Gly57Glu	p.G57E	ENST00000241393	NM_003467.2	57	gGa/gAa	2/2	0.142824634569798	3	FACETS	1	0.94	1	0.595	0.51	0.689	CLONAL	1	TRUE	1	0.21	3		419	486	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962585	38962585	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0048700-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	28	323	0	ENST00000357387.3:c.1668+2T>G		p.X556_splice	ENST00000357387	NM_152756.3	556			1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.21	2		323	247	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507315	8507315	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048700-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	54	360	0	ENST00000356435.5:c.1663G>T	p.Glu555Ter	p.E555*	ENST00000356435		555	Gag/Tag	11/35	1	2	FACETS	0.832	0.715	0.958	1	0.972	1	CLONAL	2	TRUE	1	0.21	2		360	309	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034416	47034416	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0048700-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	63	553	0	ENST00000377604.3:c.503-2A>C		p.X168_splice	ENST00000377604	NM_001204468.1	168			1	2	FACETS	0.82	0.708	0.941	0.82	0.708	0.941	CLONAL	1	TRUE	1	0.21	2		553	732	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317024	11317024	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048700-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	29	480	0	ENST00000361445.4:c.470G>T	p.Gly157Val	p.G157V	ENST00000361445	NM_004958.3	157	gGt/gTt	4/58	1	2	FACETS	0.464	0.372	0.569	0.464	0.372	0.569	SUBCLONAL	1	TRUE	1	0.309114253911844	2		480	404	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112259	115112259	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048700-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	10	272	0	ENST00000257566.3:c.1481C>A	p.Ala494Asp	p.A494D	ENST00000257566	NM_016569.3	494	gCc/gAc	7/8	1	2	FACETS	0.354	0.239	0.497	0.354	0.239	0.497	SUBCLONAL	1	TRUE	1	0.309114253911844	2		272	183	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112404	115112404	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048700-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	24	769	0	ENST00000257566.3:c.1336A>T	p.Thr446Ser	p.T446S	ENST00000257566	NM_016569.3	446	Act/Tct	7/8	1	2	FACETS	0.378	0.296	0.473	0.378	0.296	0.473	SUBCLONAL	1	TRUE	1	0.309114253911844	2		769	411	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061892	38061892	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048700-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	63	830	0	ENST00000250448.2:c.97A>C	p.Asn33His	p.N33H	ENST00000250448	NM_004496.3	33	Aac/Cac	2/2	0.163269324800806	4	FACETS	0.701	0.605	0.806	0.351	0.302	0.403	INDETERMINATE	1	TRUE	2	0.309114253911844	4		830	761	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576195	88576195	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048700-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	52	649	1	ENST00000360948.2:c.1478C>T	p.Ser493Leu	p.S493L	ENST00000360948	NM_001012338.2	493	tCa/tTa	13/19	1	2	FACETS	0.655	0.557	0.761	0.655	0.557	0.761	SUBCLONAL	1	TRUE	1	0.309114253911844	2		650	514	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632482	3632482	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048700-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	91	967	1	ENST00000294008.3:c.5366G>T	p.Gly1789Val	p.G1789V	ENST00000294008	NM_032444.2	1789	gGc/gTc	15/15	0.151814946489887	3	FACETS	0.878	0.779	0.984	0.439	0.389	0.492	INDETERMINATE	1	TRUE	1	0.309114253911844	3		968	774	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832029	72832029	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048700-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	84	523	0	ENST00000268489.5:c.4552G>T	p.Gly1518Cys	p.G1518C	ENST00000268489	NM_006885.3	1518	Ggc/Tgc	9/10	0.167582737659755	2	FACETS	1	0.972	1	0.66	0.586	0.738	INDETERMINATE	1	TRUE	0	0.309114253911844	2		523	412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0048700-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	79	606	1	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	0.872	0.768	0.984	0.872	0.768	0.984	CLONAL	1	TRUE	1	0.309114253911844	2		607	586	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051698	13051698	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048700-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	20	492	1	ENST00000316448.5:c.957G>T	p.Trp319Cys	p.W319C	ENST00000316448	NM_004343.3	319	tgG/tgT	7/9	0.165038546908726	2	FACETS	0.332	0.253	0.424	0.166	0.126	0.212	INDETERMINATE	1	TRUE	0	0.309114253911844	2		493	390	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25458648	25458648	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048700-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	37	460	0	ENST00000264709.3:c.2525A>T	p.Gln842Leu	p.Q842L	ENST00000264709	NM_175629.2	842	cAg/cTg	22/23	0.292571419579789	1	FACETS	0.585	0.483	0.698	0.585	0.483	0.698	SUBCLONAL	1	TRUE	0	0.309114253911844	1		460	346	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40828028	40828028	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048700-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	28	380	0	ENST00000373198.4:c.2400G>T	p.Leu800Phe	p.L800F	ENST00000373198	NM_133170.3	800	ttG/ttT	17/32	0.292571419579789	1	FACETS	0.699	0.562	0.854	0.699	0.562	0.854	SUBCLONAL	1	TRUE	0	0.309114253911844	1		380	219	SUCCESS
APC	324	MSKCC	GRCh37	5	112175415	112175415	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048700-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	34	278	0	ENST00000257430.4:c.4124A>T	p.His1375Leu	p.H1375L	ENST00000257430	NM_000038.5	1375	cAc/cTc	16/16	1	2	FACETS	0.936	0.77	1	0.936	0.77	1	CLONAL	1	TRUE	1	0.309114253911844	2		278	235	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401518	401518	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048700-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	24	499	0	ENST00000380956.4:c.840T>A	p.His280Gln	p.H280Q	ENST00000380956	NM_001195286.1	280	caT/caA	7/9	0.151814946489887	3	FACETS	0.562	0.441	0.702	0.281	0.22	0.351	INDETERMINATE	1	TRUE	1	0.309114253911844	3		499	319	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206804	162206804	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1262180713	NA	P-0048700-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	27	362	0	ENST00000366898.1:c.871G>T	p.Ala291Ser	p.A291S	ENST00000366898	NM_004562.2	291	Gct/Tct	7/12	1	2	FACETS	0.514	0.409	0.633	0.514	0.409	0.633	SUBCLONAL	1	TRUE	1	0.309114253911844	2		362	340	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361796	70361796	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048700-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	32	680	0	ENST00000374080.3:c.6472C>A	p.Leu2158Ile	p.L2158I	ENST00000374080		2158	Ctt/Att	44/45	0.292571419579789	1	FACETS	0.346	0.28	0.421	0.346	0.28	0.421	SUBCLONAL	1	TRUE	0	0.309114253911844	1		680	506	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938007	76938007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048700-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	41	579	0	ENST00000373344.5:c.2741C>T	p.Ala914Val	p.A914V	ENST00000373344	NM_000489.3	914	gCa/gTa	9/35	0.292571419579789	1	FACETS	0.475	0.396	0.564	0.475	0.396	0.564	SUBCLONAL	1	TRUE	0	0.309114253911844	1		579	472	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0048700-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	84	380	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.190368146907509	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.200253001248913	2		380	355	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0048700-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	54	620	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.200253001248913	2		620	416	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045006	47045006	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048700-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	50	852	0	ENST00000377604.3:c.2332C>T	p.Gln778Ter	p.Q778*	ENST00000377604	NM_001204468.1	778	Cag/Tag	20/24	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.200253001248913	2		852	487	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514056	69514056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138132534	NA	P-0048700-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	45	677	0	ENST00000294312.3:c.625G>A	p.Val209Met	p.V209M	ENST00000294312	NM_005117.2	209	Gtg/Atg	3/3	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.200253001248913	2		677	385	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360557	118360558	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0048700-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	33	425	1	ENST00000534358.1:c.4530_4531delinsTT	p.Gly1511Ter	p.G1511*	ENST00000534358	NM_005933.3	1510	ctGGga/ctTTga	12/36	1	2	FACETS	0.8	0.652	0.967	0.8	0.652	0.967	CLONAL	1	TRUE	1	0.200253001248913	2		426	412	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210926	36210926	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048700-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	66	892	0	ENST00000222270.7:c.677G>T	p.Arg226Leu	p.R226L	ENST00000222270	NM_014727.1	226	cGg/cTg	3/37	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.200253001248913	2		892	522	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319959	8319959	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048700-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	12	198	0	ENST00000356435.5:c.5542G>T	p.Val1848Phe	p.V1848F	ENST00000356435		1848	Gtt/Ttt	34/35	1	2	FACETS	0.81	0.571	1	0.81	0.571	1	CLONAL	1	TRUE	1	0.200253001248913	2		198	148	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402468	139402468	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1048656395	NA	P-0048700-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	74	1042	0	ENST00000277541.6:c.3449C>T	p.Ser1150Leu	p.S1150L	ENST00000277541	NM_017617.3	1150	tCa/tTa	21/34	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.200253001248913	2		1042	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0048760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	477	725	1	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.692250652711271	2	FACETS	0.969	0.939	0.999	0.969	0.939	0.999	CLONAL	2	TRUE	0	0.696938884226229	2		726	706	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142913	7142913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1283504748	NA	P-0048760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4741	256	667	0	ENST00000302850.5:c.2456G>A	p.Arg819His	p.R819H	ENST00000302850	NM_000208.2	819	cGc/cAc	12/22	0.696938884226229	22	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.696938884226229	22		667	4997	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713421	40713421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199947379	NA	P-0048760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	53	668	1	ENST00000373198.4:c.4094C>T	p.Thr1365Met	p.T1365M	ENST00000373198	NM_133170.3	1365	aCg/aTg	30/32	0.442024013536379	3	FACETS	0.289	0.246	0.336	0.144	0.123	0.168	SUBCLONAL	1	TRUE	1	0.696938884226229	3		669	710	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247469	71247469	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs794727811	NA	P-0048760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	24	464	0	ENST00000318789.4:c.64G>A	p.Gly22Ser	p.G22S	ENST00000318789	NM_032682.5	22	Ggc/Agc	6/21	0.643668828339384	2	FACETS	0.166	0.13	0.208	0.083	0.065	0.104	SUBCLONAL	1	TRUE	0	0.696938884226229	2		464	415	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43730591	43730591	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	23	382	0	ENST00000382044.4:c.3122T>C	p.Leu1041Ser	p.L1041S	ENST00000382044	NM_001141980.1	1041	tTg/tCg	16/28	0.424168339845152	2	FACETS	0.184	0.143	0.232	0.092	0.071	0.116	SUBCLONAL	1	TRUE	0	0.696938884226229	2		382	358	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285903	39285903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	27	323	0	ENST00000402219.2:c.256G>A	p.Ala86Thr	p.A86T	ENST00000402219	NM_005633.3	86	Gca/Aca	3/23	0.595578535449689	3	FACETS	0.331	0.263	0.407	0.165	0.131	0.204	SUBCLONAL	1	TRUE	1	0.696938884226229	3		323	316	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93607756	93607756	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	28	273	0	ENST00000375746.1:c.458A>G	p.Gln153Arg	p.Q153R	ENST00000375746	NM_001174167.1	153	cAg/cGg	3/14	0.696938884226229	3	FACETS	0.281	0.225	0.346	0.141	0.112	0.173	SUBCLONAL	1	TRUE	1	0.696938884226229	3		273	385	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048773-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	168	276	0				ENST00000310581	NM_198253.2	-/1132			0.62726765214342	5	FACETS	0.942	0.878	1	0.942	0.878	1	CLONAL	3	TRUE	2	0.62726765214342	5		276	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0048773-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	511	643	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.62726765214342	3	FACETS	0.951	0.922	0.979	0.951	0.922	0.979	CLONAL	3	TRUE	0	0.62726765214342	3		643	750	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481806	56481806	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048773-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	288	548	0	ENST00000267101.3:c.734C>T	p.Ala245Val	p.A245V	ENST00000267101	NM_001982.3	245	gCc/gTc	7/28	0.560759215504131	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.62726765214342	3		548	596	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923093	48923094	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0048773-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	100	224	0	ENST00000267163.4:c.543_544del	p.Ser182TyrfsTer2	p.S182Yfs*2	ENST00000267163	NM_000321.2	181	ATa/a	6/27	0.56570999116243	4	FACETS	0.907	0.822	0.995	0.907	0.822	0.995	CLONAL	2	TRUE	2	0.62726765214342	4		224	286	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037866	49037866	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0048773-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	97	221	1	ENST00000267163.4:c.2107-1G>T		p.X703_splice	ENST00000267163	NM_000321.2	703			0.56570999116243	4	FACETS	0.83	0.75	0.914	0.83	0.75	0.914	CLONAL	2	TRUE	2	0.62726765214342	4		222	303	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464961	120464961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764895571	NA	P-0048773-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	124	475	0	ENST00000256646.2:c.5111G>A	p.Arg1704His	p.R1704H	ENST00000256646	NM_024408.3	1704	cGt/cAt	28/34	1	2	FACETS	0.907	0.827	0.99	0.907	0.827	0.99	CLONAL	1	TRUE	1	0.62726765214342	2		475	436	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350517	15350517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048773-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	118	682	1	ENST00000263377.2:c.3398C>T	p.Pro1133Leu	p.P1133L	ENST00000263377	NM_058243.2	1133	cCc/cTc	16/20	0.130652969655093	6	FACETS	1	0.982	1	0.466	0.421	0.513	INDETERMINATE	1	TRUE	3	0.62726765214342	6		683	607	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50816350	50816350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868852255	NA	P-0048773-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	129	321	0	ENST00000398568.2:c.1790C>T	p.Ser597Phe	p.S597F	ENST00000398568	NM_001042412.1	597	tCt/tTt	10/18	0.619616661739825	2	FACETS	0.948	0.884	1	0.948	0.884	1	CLONAL	2	TRUE	0	0.62726765214342	2		321	217	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748081	72748081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048773-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	119	544	0	ENST00000357731.5:c.97C>T	p.Pro33Ser	p.P33S	ENST00000357731	NM_173808.2	33	Ccg/Tcg	1/7	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.62726765214342	2		544	340	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717685	89717708	+	inframe_deletion	In_Frame_Del	DEL	AGTTCATGTACTTTGAGTTCCCTC	AGTTCATGTACTTTGAGTTCCCTC	-	novel	NA	P-0048773-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	127	381	0	ENST00000371953.3:c.712_735del	p.Phe238_Gln245del	p.F238_Q245del	ENST00000371953	NM_000314.4	237	aAGTTCATGTACTTTGAGTTCCCTCag/aag	7/9	0.619616661739825	2	FACETS	1	0.985	1	0.67	0.617	0.725	CLONAL	1	TRUE	0	0.62726765214342	2		381	302	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574748	95574748	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048773-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	76	377	0	ENST00000393063.1:c.2349T>G	p.Asp783Glu	p.D783E	ENST00000393063	NM_030621.3	783	gaT/gaG	16/28	0.62726765214342	3	FACETS	1	0.902	1	0.51	0.451	0.572	CLONAL	1	TRUE	1	0.62726765214342	3		377	312	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349738	15349738	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048773-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	274	751	0	ENST00000263377.2:c.3836C>G	p.Ala1279Gly	p.A1279G	ENST00000263377	NM_058243.2	1279	gCa/gGa	19/20	0.130652969655093	6	FACETS	0.942	0.89	0.995	0.942	0.89	0.995	INDETERMINATE	3	TRUE	3	0.62726765214342	6		751	697	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147720	61147735	+	frameshift_variant	Frame_Shift_Del	DEL	GAGAGACCAAGACCTG	GAGAGACCAAGACCTG	-	novel	NA	P-0048773-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	100	293	0	ENST00000295025.8:c.1031_1046del	p.Glu344ValfsTer25	p.E344Vfs*25	ENST00000295025	NM_002908.2	344	GAGAGACCAAGACCTGgt/gt	10/11	0.619616661739825	2	FACETS	0.781	0.715	0.848	0.781	0.715	0.848	SUBCLONAL	2	TRUE	0	0.62726765214342	2		293	204	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513586	41513586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148575477	NA	P-0048773-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	108	573	1	ENST00000263253.7:c.490G>A	p.Gly164Arg	p.G164R	ENST00000263253	NM_001429.3	164	Gga/Aga	2/31	1	2	FACETS	0.82	0.741	0.902	0.82	0.741	0.902	CLONAL	1	TRUE	1	0.62726765214342	2		574	420	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935631	13935631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048773-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	208	449	0	ENST00000405192.2:c.1225C>A	p.Pro409Thr	p.P409T	ENST00000405192	NM_001163147.1	409	Cca/Aca	12/12	0.62726765214342	3	FACETS	0.88	0.825	0.935	0.88	0.825	0.935	CLONAL	2	TRUE	1	0.62726765214342	3		449	495	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798773	135798773	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048773-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	139	301	0	ENST00000298552.3:c.470T>G	p.Ile157Ser	p.I157S	ENST00000298552	NM_001162426.1	157	aTt/aGt	6/23	0.62726765214342	3	FACETS	0.967	0.896	1	0.967	0.896	1	CLONAL	2	TRUE	1	0.62726765214342	3		301	301	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048773-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	234	276	0				ENST00000310581	NM_198253.2	-/1132			0.79216427016968	5	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	FALSE	2	0.792083607474838	5		276	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0048773-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	649	643	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.580307570907301	6	FACETS	1	0.996	1	0.895	0.876	0.912	CLONAL	5	FALSE	0	0.792083607474838	6		643	789	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481806	56481806	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048773-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	301	548	0	ENST00000267101.3:c.734C>T	p.Ala245Val	p.A245V	ENST00000267101	NM_001982.3	245	gCc/gTc	7/28	0.79216427016968	4	FACETS	0.855	0.816	0.893	0.855	0.816	0.893	CLONAL	3	FALSE	1	0.792083607474838	4		548	531	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923093	48923094	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0048773-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	155	224	0	ENST00000267163.4:c.543_544del	p.Ser182TyrfsTer2	p.S182Yfs*2	ENST00000267163	NM_000321.2	181	ATa/a	6/27	0.625210098276865	6	FACETS	1	0.984	1	0.828	0.767	0.891	CLONAL	2	FALSE	3	0.792083607474838	6		224	407	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037866	49037866	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0048773-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	118	221	1	ENST00000267163.4:c.2107-1G>T		p.X703_splice	ENST00000267163	NM_000321.2	703			0.625210098276865	6	FACETS	1	0.98	1	0.833	0.763	0.905	CLONAL	2	FALSE	3	0.792083607474838	6		222	308	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464961	120464961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764895571	NA	P-0048773-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	181	475	0	ENST00000256646.2:c.5111G>A	p.Arg1704His	p.R1704H	ENST00000256646	NM_024408.3	1704	cGt/cAt	28/34	0.544013996090531	4	FACETS	1	0.99	1	0.49	0.455	0.526	CLONAL	1	FALSE	1	0.792083607474838	4		475	557	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350517	15350517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048773-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	71	682	1	ENST00000263377.2:c.3398C>T	p.Pro1133Leu	p.P1133L	ENST00000263377	NM_058243.2	1133	cCc/cTc	16/20	0.638844344831524	4	FACETS	0.504	0.439	0.573	0.252	0.219	0.287	SUBCLONAL	1	FALSE	2	0.792083607474838	4		683	638	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50816350	50816350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868852255	NA	P-0048773-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	164	321	0	ENST00000398568.2:c.1790C>T	p.Ser597Phe	p.S597F	ENST00000398568	NM_001042412.1	597	tCt/tTt	10/18	0.77934300503364	2	FACETS	0.945	0.9	0.988	0.945	0.9	0.988	CLONAL	2	FALSE	0	0.792083607474838	2		321	219	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748081	72748081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048773-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	102	544	0	ENST00000357731.5:c.97C>T	p.Pro33Ser	p.P33S	ENST00000357731	NM_173808.2	33	Ccg/Tcg	1/7	0.544013996090531	4	FACETS	1	0.964	1	0.385	0.346	0.425	CLONAL	1	FALSE	1	0.792083607474838	4		544	400	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717685	89717708	+	inframe_deletion	In_Frame_Del	DEL	AGTTCATGTACTTTGAGTTCCCTC	AGTTCATGTACTTTGAGTTCCCTC	-	novel	NA	P-0048773-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	146	381	0	ENST00000371953.3:c.712_735del	p.Phe238_Gln245del	p.F238_Q245del	ENST00000371953	NM_000314.4	237	aAGTTCATGTACTTTGAGTTCCCTCag/aag	7/9	0.792083607474838	2	FACETS	0.819	0.771	0.866	0.819	0.771	0.866	CLONAL	2	FALSE	0	0.792083607474838	2		381	225	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349738	15349738	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048773-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	271	751	0	ENST00000263377.2:c.3836C>G	p.Ala1279Gly	p.A1279G	ENST00000263377	NM_058243.2	1279	gCa/gGa	19/20	0.638844344831524	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	FALSE	2	0.792083607474838	4		751	608	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147720	61147735	+	frameshift_variant	Frame_Shift_Del	DEL	GAGAGACCAAGACCTG	GAGAGACCAAGACCTG	-	novel	NA	P-0048773-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	88	293	0	ENST00000295025.8:c.1031_1046del	p.Glu344ValfsTer25	p.E344Vfs*25	ENST00000295025	NM_002908.2	344	GAGAGACCAAGACCTGgt/gt	10/11	0.287594851563938	3	FACETS	0.808	0.733	0.883	0.539	0.489	0.589	INDETERMINATE	2	FALSE	0	0.792083607474838	3		293	192	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935631	13935631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048773-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	160	449	0	ENST00000405192.2:c.1225C>A	p.Pro409Thr	p.P409T	ENST00000405192	NM_001163147.1	409	Cca/Aca	12/12	0.260899412177514	6	FACETS	1	0.976	1	0.566	0.524	0.61	INDETERMINATE	2	FALSE	2	0.792083607474838	6		449	461	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798773	135798773	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048773-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	179	301	0	ENST00000298552.3:c.470T>G	p.Ile157Ser	p.I157S	ENST00000298552	NM_001162426.1	157	aTt/aGt	6/23	0.325596303177564	4	FACETS	0.978	0.926	1	0.734	0.694	0.772	INDETERMINATE	3	FALSE	0	0.792083607474838	4		301	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578179	7578179	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048773-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	20	599	0	ENST00000269305.4:c.670G>T	p.Glu224Ter	p.E224*	ENST00000269305	NM_001126112.2	224	Gag/Tag	6/11	0.580307570907301	6	FACETS	0.153	0.116	0.196	0.025	0.019	0.033	SUBCLONAL	1	FALSE	0	0.792083607474838	6		599	855	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755536	57755536	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1438314086	NA	P-0048773-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	20	580	0	ENST00000274289.3:c.251G>A	p.Arg84Gln	p.R84Q	ENST00000274289	NM_006622.3	84	cGg/cAg	1/14	0.576477793935633	2	FACETS	0.18	0.138	0.23	0.09	0.069	0.115	SUBCLONAL	1	FALSE	0	0.792083607474838	2		580	280	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17125830	17125830	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048865-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	419	684	0	ENST00000285071.4:c.764A>G	p.His255Arg	p.H255R	ENST00000285071	NM_144997.5	255	cAc/cGc	7/14	0.586487590777461	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.586487590777461	2		684	642	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023582	27023583	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	T	novel	NA	P-0048865-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	329	369	0	ENST00000324856.7:c.688_689delinsT	p.Ala230CysfsTer2	p.A230Cfs*2	ENST00000324856	NM_006015.4	230	GCg/Tg	1/20	0.586487590777461	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.586487590777461	2		369	478	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0048881-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	126	366	0				ENST00000310581	NM_198253.2	-/1132			0.315268727091124	3	FACETS	1	0.98	1	0.629	0.574	0.685	INDETERMINATE	1	TRUE	1	0.630561095166522	3		366	418	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467457	25467457	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048881-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	287	784	0	ENST00000264709.3:c.1619G>T	p.Cys540Phe	p.C540F	ENST00000264709	NM_175629.2	540	tGc/tTc	14/23	0.377611200183039	1	FACETS	0.872	0.825	0.919	0.872	0.825	0.919	INDETERMINATE	1	TRUE	0	0.630561095166522	1		784	715	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505064	149505064	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048881-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	143	651	0	ENST00000261799.4:c.1751C>A	p.Pro584His	p.P584H	ENST00000261799	NM_002609.3	584	cCc/cAc	12/23	0.377611200183039	1	FACETS	0.463	0.423	0.505	0.463	0.423	0.505	INDETERMINATE	1	TRUE	0	0.630561095166522	1		651	671	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500486	149500488	+	missense_variant	Missense_Mutation	TNP	TGT	TGT	AGA	novel	NA	P-0048881-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	116	727	1	ENST00000261799.4:c.2549_2551delinsTCT	p.Asp850_Ile851delinsValPhe	p.D850_I851delinsVF	ENST00000261799	NM_002609.3	850	gACAtc/gTCTtc	18/23	0.377611200183039	1	FACETS	0.332	0.299	0.367	0.332	0.299	0.367	INDETERMINATE	1	TRUE	0	0.630561095166522	1		728	759	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612286	189612286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048929-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	115	436	0	ENST00000264731.3:c.2038G>A	p.Glu680Lys	p.E680K	ENST00000264731	NM_003722.4	680	Gag/Aag	14/14	1	2	FACETS	0.87	0.795	0.947	0.87	0.795	0.947	CLONAL	1	TRUE	1	0.869506392521017	2		436	304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0049071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	57	614	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.856	0.734	0.989	0.856	0.734	0.989	CLONAL	1	TRUE	1	0.21011011353296	2		614	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0049071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	41	580	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	1	2	FACETS	0.707	0.588	0.839	0.707	0.588	0.839	SUBCLONAL	1	TRUE	1	0.21011011353296	2		580	552	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402595	20402595	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	76	471	0	ENST00000346618.3:c.132C>A	p.Phe44Leu	p.F44L	ENST00000346618	NM_001949.4	44	ttC/ttA	1/7	0.21011011353296	1	FACETS	0.773	0.681	0.87	1	0.977	1	SUBCLONAL	2	TRUE	0	0.21011011353296	1		471	419	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736256	243736256	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	22	340	0	ENST00000263826.5:c.791C>A	p.Ser264Tyr	p.S264Y	ENST00000263826	NM_005465.4	264	tCc/tAc	8/13	0.18154521269349	2	FACETS	0.571	0.442	0.721	0.285	0.221	0.361	SUBCLONAL	1	TRUE	0	0.21011011353296	2		340	367	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574663	95574663	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	11	298	0	ENST00000393063.1:c.2434C>T	p.Gln812Ter	p.Q812*	ENST00000393063	NM_030621.3	812	Cag/Tag	16/28	1	2	FACETS	0.575	0.398	0.795	0.575	0.398	0.795	SUBCLONAL	1	TRUE	1	0.21011011353296	2		298	182	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42790923	42790932	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TGTGGACGAA	TGTGGACGAA	-	novel	NA	P-0049071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	43	663	0	ENST00000575354.2:c.74_83del	p.Thr25AsnfsTer13	p.T25Nfs*13	ENST00000575354	NM_015125.3	23	gTGTGGACGAAt/gt	2/20	0.21011011353296	1	FACETS	0.768	0.643	0.907	0.768	0.643	0.907	CLONAL	1	TRUE	0	0.21011011353296	1		663	477	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151882712	151882712	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	28	245	0	ENST00000262189.6:c.5013G>A	p.Trp1671Ter	p.W1671*	ENST00000262189	NM_170606.2	1671	tgG/tgA	34/59	0.18154521269349	2	FACETS	0.877	0.709	1	0.877	0.709	1	CLONAL	2	TRUE	0	0.21011011353296	2		245	152	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0049305-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	438	705	1	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.82860530595101	2	FACETS	0.955	0.93	0.978	0.955	0.93	0.978	CLONAL	2	TRUE	0	0.851297437410962	2		706	539	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248573	8248573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780757257	NA	P-0049305-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	211	1007	1	ENST00000335790.3:c.314G>A	p.Arg105Gln	p.R105Q	ENST00000335790	NM_002315.2	105	cGg/cAg	3/4	0.482110590880546	1	FACETS	0.392	0.365	0.419	0.392	0.365	0.419	INDETERMINATE	1	TRUE	0	0.851297437410962	1		1008	727	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120732	94120732	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049305-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	510	497	0	ENST00000369303.4:c.319A>T	p.Arg107Trp	p.R107W	ENST00000369303	NM_004440.3	107	Agg/Tgg	3/17	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.851297437410962	2		497	589	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220463	1220464	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049305-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	652	966	0	ENST00000326873.7:c.558dup	p.Gly187ArgfsTer79	p.G187Rfs*79	ENST00000326873	NM_000455.4	186	acc/aCcc	4/10	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.851297437410962	NA		966	814	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589779	55589779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1560414379	NA	P-0049305-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	297	418	0	ENST00000288135.5:c.1261C>T	p.Leu421Phe	p.L421F	ENST00000288135	NM_000222.2	421	Ctc/Ttc	8/21	0.851297437410962	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.851297437410962	1		418	339	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600015	10600015	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049305-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	751	959	0	ENST00000171111.5:c.1561G>C	p.Ala521Pro	p.A521P	ENST00000171111	NM_203500.1	521	Gct/Cct	5/6	0.840323338023351	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.851297437410962	2		959	881	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834536	156834536	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049305-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	183	941	0	ENST00000524377.1:c.304G>T	p.Gly102Cys	p.G102C	ENST00000524377	NM_002529.3	102	Ggt/Tgt	3/17	0.851297437410962	2	FACETS	0.498	0.46	0.538	0.249	0.23	0.269	SUBCLONAL	1	TRUE	0	0.851297437410962	2		941	863	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498388	89498388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049305-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	173	268	0	ENST00000336596.2:c.2360C>T	p.Pro787Leu	p.P787L	ENST00000336596	NM_005233.5	787	cCa/cTa	14/17	0.427158581769978	3	FACETS	0.979	0.921	1	0.979	0.921	1	INDETERMINATE	2	TRUE	1	0.851297437410962	3		268	296	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967332	134967332	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049305-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	250	530	0	ENST00000398015.3:c.2671G>T	p.Val891Leu	p.V891L	ENST00000398015	NM_004441.4	891	Gtg/Ttg	14/16	0.427158581769978	3	FACETS	1	0.987	1	0.588	0.553	0.624	INDETERMINATE	1	TRUE	1	0.851297437410962	3		530	712	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143066998	143066998	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1561280492	NA	P-0049305-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	254	363	0	ENST00000262992.4:c.1715C>G	p.Pro572Arg	p.P572R	ENST00000262992	NM_001101669.1	572	cCa/cGa	16/24	0.824950642358801	2	FACETS	0.962	0.931	0.992	0.962	0.931	0.992	CLONAL	2	TRUE	0	0.851297437410962	2		363	310	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38978707	38978707	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049305-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	279	315	0	ENST00000357387.3:c.799G>T	p.Asp267Tyr	p.D267Y	ENST00000357387	NM_152756.3	267	Gat/Tat	9/38	0.431218713357173	3	FACETS	0.89	0.846	0.933	0.89	0.846	0.933	INDETERMINATE	2	TRUE	1	0.851297437410962	3		315	525	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564587	86564587	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138308013	NA	P-0049305-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	384	984	0	ENST00000274376.6:c.319G>C	p.Val107Leu	p.V107L	ENST00000274376	NM_002890.2	107	Gtt/Ctt	1/25	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.851297437410962	2		984	852	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951932	2951932	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0049305-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	261	659	0	ENST00000396946.4:c.3020-2A>T		p.X1007_splice	ENST00000396946	NM_032415.4	1007			0.427158581769978	3	FACETS	1	0.987	1	0.584	0.55	0.62	INDETERMINATE	1	TRUE	1	0.851297437410962	3		659	748	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571417	95571487	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGGAAGTGATCTGACTCCCACGCCAGCATCGCTGGCAGTCTGGGCTCTTAGCTCCTCTGCAGTCAAAAG	GCAGGAAGTGATCTGACTCCCACGCCAGCATCGCTGGCAGTCTGGGCTCTTAGCTCCTCTGCAGTCAAAAG	-	novel	NA	P-0049305-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	99	287	0	ENST00000393063.1:c.3190_3260del	p.Leu1064GlyfsTer3	p.L1064Gfs*3	ENST00000393063	NM_030621.3	1064	CTTTTGACTGCAGAGGAGCTAAGAGCCCAGACTGCCAGCGATGCTGGCGTGGGAGTCAGATCACTTCCTGCg/g	21/28	0.851297437410962	2	FACETS	0.805	0.728	0.884	0.402	0.364	0.442	CLONAL	1	TRUE	0	0.851297437410962	2		287	289	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796000	78796000	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0049305-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	144	706	0	ENST00000306801.3:c.891-1G>A		p.X297_splice	ENST00000306801	NM_020761.2	297			0.32036754664019	4	FACETS	0.621	0.566	0.68	0.311	0.283	0.34	INDETERMINATE	1	TRUE	2	0.851297437410962	4		706	1008	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288549	33288549	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049305-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	110	568	1	ENST00000374542.5:c.1003A>T	p.Asn335Tyr	p.N335Y	ENST00000374542	NM_001141970.1	335	Aac/Tac	3/8	0.481369360729418	3	FACETS	0.533	0.479	0.59	0.178	0.159	0.197	INDETERMINATE	1	TRUE	0	0.851297437410962	3		569	691	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412143	63412143	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs200303647	NA	P-0049305-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	133	508	0	ENST00000330258.3:c.1024G>C	p.Asp342His	p.D342H	ENST00000330258	NM_152424.3	342	Gac/Cac	2/2	0.666580992562999	2	FACETS	0.405	0.368	0.444			1	SUBCLONAL	1	TRUE	NA	0.851297437410962	2		508	772	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230571	46230571	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	30	300	0	ENST00000334344.6:c.820C>T	p.Arg274Ter	p.R274*	ENST00000334344	NM_152641.2	274	Cga/Tga	8/21	1	2	FACETS	0.76	0.612	0.93	0.76	0.612	0.93	CLONAL	1	TRUE	1	0.15	2		300	526	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173645	108173645	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	18	371	0	ENST00000278616.4:c.5385G>A	p.Trp1795Ter	p.W1795*	ENST00000278616	NM_000051.3	1795	tgG/tgA	36/63	1	2	FACETS	0.795	0.598	1	0.795	0.598	1	CLONAL	1	TRUE	1	0.15	2		371	302	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0049382-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	21	716	0	ENST00000397752.3:c.3028+1G>A		p.X1010_splice	ENST00000397752	NM_000245.2	1010			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		716	179	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897289	78897289	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0049382-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	55	603	0	ENST00000306801.3:c.2625-1G>C		p.X875_splice	ENST00000306801	NM_020761.2	875			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		603	407	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187102	11187102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	121	587	0	ENST00000361445.4:c.6316C>T	p.His2106Tyr	p.H2106Y	ENST00000361445	NM_004958.3	2106	Cat/Tat	45/58	0.50851227913943	1	FACETS	0.341	0.308	0.375	0.341	0.308	0.375	SUBCLONAL	1	TRUE	0	0.6890793177083	1		587	675	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11318554	11318554	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs773018103	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	244	376	0	ENST00000361445.4:c.259A>G	p.Ile87Val	p.I87V	ENST00000361445	NM_004958.3	87	Atc/Gtc	3/58	0.50851227913943	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.6890793177083	1		376	464	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094422	27094422	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	87	514	0	ENST00000324856.7:c.3130G>C	p.Val1044Leu	p.V1044L	ENST00000324856	NM_006015.4	1044	Gtg/Ctg	11/20	0.50851227913943	1	FACETS	0.28	0.248	0.314	0.28	0.248	0.314	SUBCLONAL	1	TRUE	0	0.6890793177083	1		514	592	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097815	27097815	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	73	360	0	ENST00000324856.7:c.3404C>A	p.Pro1135His	p.P1135H	ENST00000324856	NM_006015.4	1135	cCt/cAt	12/20	0.50851227913943	1	FACETS	0.35	0.307	0.395	0.35	0.307	0.395	SUBCLONAL	1	TRUE	0	0.6890793177083	1		360	397	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805639	43805639	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	86	443	0	ENST00000372470.3:c.695C>T	p.Ser232Leu	p.S232L	ENST00000372470	NM_005373.2	232	tCa/tTa	5/12	0.437597698580228	2	FACETS	0.49	0.435	0.549	0.245	0.217	0.275	SUBCLONAL	1	TRUE	0	0.6890793177083	2		443	509	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78422272	78422272	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	66	308	0	ENST00000370768.2:c.1690C>G	p.Gln564Glu	p.Q564E	ENST00000370768	NM_003902.3	564	Caa/Gaa	17/20	0.437597698580228	2	FACETS	0.391	0.34	0.446	0.195	0.17	0.223	SUBCLONAL	1	TRUE	0	0.6890793177083	2		308	490	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459275	120459275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	359	482	0	ENST00000256646.2:c.6070G>A	p.Glu2024Lys	p.E2024K	ENST00000256646	NM_024408.3	2024	Gaa/Aaa	34/34	0.648398332860209	5	FACETS	0.791	0.749	0.834			1	SUBCLONAL	2	TRUE	NA	0.6890793177083	5		482	1340	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459283	120459283	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	338	457	0	ENST00000256646.2:c.6062G>A	p.Gly2021Glu	p.G2021E	ENST00000256646	NM_024408.3	2021	gGg/gAg	34/34	0.648398332860209	5	FACETS	0.776	0.733	0.819			1	SUBCLONAL	2	TRUE	NA	0.6890793177083	5		457	1286	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120460386	120460386	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs312262798	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	368	425	0	ENST00000256646.2:c.5930-1G>A		p.X1977_splice	ENST00000256646	NM_024408.3	1977			0.648398332860209	5	FACETS	0.86	0.815	0.905			1	CLONAL	2	TRUE	NA	0.6890793177083	5		425	1263	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464433	120464433	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	338	384	0	ENST00000256646.2:c.5214-1G>A		p.X1738_splice	ENST00000256646	NM_024408.3	1738			0.648398332860209	5	FACETS	0.828	0.784	0.874			1	CLONAL	2	TRUE	NA	0.6890793177083	5		384	1204	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464875	120464875	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	412	453	0	ENST00000256646.2:c.5197G>A	p.Asp1733Asn	p.D1733N	ENST00000256646	NM_024408.3	1733	Gat/Aat	28/34	0.648398332860209	5	FACETS	0.882	0.839	0.926			1	CLONAL	2	TRUE	NA	0.6890793177083	5		453	1378	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851298	63851298	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	101	567	0	ENST00000279873.7:c.2076G>C	p.Lys692Asn	p.K692N	ENST00000279873	NM_032199.2	692	aaG/aaC	10/10	0.407669056006353	1	FACETS	0.31	0.277	0.345	0.31	0.277	0.345	INDETERMINATE	1	TRUE	0	0.6890793177083	1		567	620	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104269018	104269018	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	119	585	0	ENST00000369902.3:c.275G>T	p.Ser92Ile	p.S92I	ENST00000369902	NM_016169.3	92	aGc/aTc	2/12	0.407669056006353	1	FACETS	0.329	0.297	0.362	0.329	0.297	0.362	INDETERMINATE	1	TRUE	0	0.6890793177083	1		585	689	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136015	64136015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1440181729	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	121	629	3	ENST00000334205.4:c.1276C>T	p.Arg426Cys	p.R426C	ENST00000334205	NM_003942.2	426	Cgc/Tgc	11/17	0.36112671075798	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.6890793177083	0		632	702	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466927	18466927	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	86	369	0	ENST00000266497.5:c.1066C>T	p.Gln356Ter	p.Q356*	ENST00000266497		356	Caa/Taa	5/31	0.240092674648362	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.6890793177083	0		369	456	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426373	49426373	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	140	916	0	ENST00000301067.7:c.12115G>C	p.Glu4039Gln	p.E4039Q	ENST00000301067	NM_003482.3	4039	Gag/Cag	39/54	0.573646644205487	3	FACETS	0.461	0.418	0.505			1	SUBCLONAL	1	TRUE	NA	0.6890793177083	3		916	1186	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434861	49434861	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	268	789	1	ENST00000301067.7:c.6692C>A	p.Pro2231His	p.P2231H	ENST00000301067	NM_003482.3	2231	cCt/cAt	31/54	0.573646644205487	3	FACETS	1	0.971	1			1	CLONAL	1	TRUE	NA	0.6890793177083	3		790	989	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487139	56487139	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	93	439	0	ENST00000267101.3:c.1285T>C	p.Ser429Pro	p.S429P	ENST00000267101	NM_001982.3	429	Tca/Cca	12/28	0.407669056006353	1	FACETS	0.335	0.299	0.374	0.335	0.299	0.374	INDETERMINATE	1	TRUE	0	0.6890793177083	1		439	528	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865656	57865656	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	274	842	0	ENST00000228682.2:c.3133A>G	p.Thr1045Ala	p.T1045A	ENST00000228682	NM_005269.2	1045	Act/Gct	12/12	0.407669056006353	1	FACETS	0.676	0.637	0.716	0.676	0.637	0.716	INDETERMINATE	1	TRUE	0	0.6890793177083	1		842	771	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120714	115120714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	122	699	0	ENST00000257566.3:c.292G>A	p.Glu98Lys	p.E98K	ENST00000257566	NM_016569.3	98	Gag/Aag	1/8	0.407669056006353	1	FACETS	0.324	0.293	0.356	0.324	0.293	0.356	INDETERMINATE	1	TRUE	0	0.6890793177083	1		699	717	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936807	32936807	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	79	364	0	ENST00000380152.3:c.7953G>C	p.Arg2651Ser	p.R2651S	ENST00000380152		2651	agG/agC	17/27	0.194490095018497	6	FACETS	0.723	0.635	0.818	0.241	0.211	0.273	INDETERMINATE	1	TRUE	3	0.6890793177083	6		364	754	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954208	48954248	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCAAAATTTTAGGTAAATTTTTTACTTTTAGTAAAAAATT	TTCAAAATTTTAGGTAAATTTTTTACTTTTAGTAAAAAATT	-	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	118	272	0	ENST00000267163.4:c.1411_1421+30del		p.X471_splice	ENST00000267163	NM_000321.2	471		15/27	0.194490095018497	6	FACETS	1	0.984	1	0.485	0.439	0.533	INDETERMINATE	1	TRUE	3	0.6890793177083	6		272	560	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281629	49281629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749662416	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	442	767	1	ENST00000282018.3:c.676C>T	p.Arg226Trp	p.R226W	ENST00000282018	NM_020377.2	226	Cgg/Tgg	1/1	0.194490095018497	6	FACETS	0.868	0.829	0.907	0.868	0.829	0.907	INDETERMINATE	3	TRUE	3	0.6890793177083	6		768	1172	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81558946	81558946	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	74	395	0	ENST00000298171.2:c.539T>A	p.Leu180Ter	p.L180*	ENST00000298171	NM_000369.2	180	tTg/tAg	6/10	1	2	FACETS	0.366	0.32	0.415	0.366	0.32	0.415	SUBCLONAL	1	TRUE	1	0.6890793177083	2		395	587	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2132493	2132493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201135184	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	157	738	0	ENST00000219476.3:c.3871G>A	p.Val1291Ile	p.V1291I	ENST00000219476	NM_000548.3	1291	Gtt/Att	32/42	0.594491902119855	1	FACETS	0.396	0.363	0.43	0.396	0.363	0.43	SUBCLONAL	1	TRUE	0	0.6890793177083	1		738	755	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789684	3789719	+	inframe_deletion	In_Frame_Del	DEL	CGATATGGGAAAGATTCAGACATTTCCCCAGAATCC	CGATATGGGAAAGATTCAGACATTTCCCCAGAATCC	-	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	181	446	0	ENST00000262367.5:c.4140_4175del	p.Asp1381_Arg1392del	p.D1381_R1392del	ENST00000262367	NM_004380.2	1380	gtGGATTCTGGGGAAATGTCTGAATCTTTCCCATATCGa/gta	25/31	0.594491902119855	1	FACETS	0.779	0.727	0.832	0.779	0.727	0.832	SUBCLONAL	1	TRUE	0	0.6890793177083	1		446	442	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831088	72831104	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGCCTGGGCCTGTCC	CAGGCCTGGGCCTGTCC	-	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	72	416	0	ENST00000268489.5:c.5477_5493del	p.Gly1826AlafsTer97	p.G1826Afs*97	ENST00000268489	NM_006885.3	1826	gGGACAGGCCCAGGCCTG/g	9/10	0.407669056006353	1	FACETS	0.33	0.289	0.374	0.33	0.289	0.374	INDETERMINATE	1	TRUE	0	0.6890793177083	1		416	415	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679316	29679316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	97	372	0	ENST00000356175.3:c.7436C>T	p.Ser2479Phe	p.S2479F	ENST00000356175	NM_000267.3	2479	tCt/tTt	50/57	0.334413687359965	2	FACETS	0.556	0.498	0.618	0.278	0.249	0.309	INDETERMINATE	1	TRUE	0	0.6890793177083	2		372	506	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805601	46805601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1652	101	781	0	ENST00000290295.7:c.355G>A	p.Glu119Lys	p.E119K	ENST00000290295	NM_006361.5	119	Gag/Aag	1/2	0.413158365434373	2	FACETS	0.167	0.148	0.187	0.084	0.074	0.094	INDETERMINATE	1	TRUE	0	0.6890793177083	2		781	1753	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774170	56774170	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	642	491	0	ENST00000337432.4:c.521C>G	p.Thr174Ser	p.T174S	ENST00000337432	NM_058216.2	174	aCt/aGt	3/9	0.403736651164832	4	FACETS	1	0.993	1	0.8	0.777	0.822	INDETERMINATE	3	TRUE	0	0.6890793177083	4		491	984	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78865592	78865592	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs751472732	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	102	606	0	ENST00000306801.3:c.2056A>G	p.Ile686Val	p.I686V	ENST00000306801	NM_020761.2	686	Ata/Gta	18/34	0.126638024338899	6	FACETS	0.657	0.586	0.733			1	INDETERMINATE	1	TRUE	NA	0.6890793177083	6		606	1071	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724606	724606	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	219	554	0	ENST00000314574.4:c.1450C>G	p.Gln484Glu	p.Q484E	ENST00000314574	NM_005433.3	484	Caa/Gaa	12/12	0.672590102852936	1	FACETS	0.749	0.703	0.797	0.749	0.703	0.797	SUBCLONAL	1	TRUE	0	0.6890793177083	1		554	556	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45391445	45391445	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	73	378	0	ENST00000262160.6:c.715C>T	p.Gln239Ter	p.Q239*	ENST00000262160	NM_005901.5	239	Caa/Taa	6/11	0.256299753755238	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.6890793177083	0		378	363	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985608	60985608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	68	258	0	ENST00000333681.4:c.292C>T	p.Arg98Cys	p.R98C	ENST00000333681		98	Cgc/Tgc	2/3	0.256299753755238	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.6890793177083	0		258	223	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7152878	7152878	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	96	560	0	ENST00000302850.5:c.2090A>G	p.His697Arg	p.H697R	ENST00000302850	NM_000208.2	697	cAc/cGc	10/22	0.594491902119855	1	FACETS	0.353	0.315	0.392	0.353	0.315	0.392	SUBCLONAL	1	TRUE	0	0.6890793177083	1		560	518	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	218	650	0	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	0.256299753755238	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.6890793177083	0		650	634	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46597021	46597021	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	105	460	0	ENST00000263734.3:c.835G>A	p.Glu279Lys	p.E279K	ENST00000263734	NM_001430.4	279	Gaa/Aaa	7/16	0.277825847606557	1	FACETS	0.328	0.294	0.364	0.328	0.294	0.364	INDETERMINATE	1	TRUE	0	0.6890793177083	1		460	609	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790156	40790156	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	94	496	0	ENST00000373198.4:c.2575C>G	p.Gln859Glu	p.Q859E	ENST00000373198	NM_133170.3	859	Cag/Gag	18/32	0.177736488489112	3	FACETS	0.537	0.478	0.6	0.269	0.239	0.3	INDETERMINATE	1	TRUE	1	0.6890793177083	3		496	683	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256704	46256704	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	288	462	1	ENST00000371998.3:c.760A>G	p.Thr254Ala	p.T254A	ENST00000371998		254	Act/Gct	8/23	0.177736488489112	3	FACETS	1	0.991	1	0.627	0.591	0.664	INDETERMINATE	1	TRUE	1	0.6890793177083	3		463	896	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1254	132	692	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	0.6890793177083	3	FACETS	0.372	0.336	0.409	0.186	0.168	0.205	SUBCLONAL	1	TRUE	1	0.6890793177083	3		692	1386	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412982	49412982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1254	137	682	0	ENST00000418115.1:c.41G>A	p.Gly14Glu	p.G14E	ENST00000418115	NM_001664.2	14	gGa/gAa	2/5	0.6890793177083	3	FACETS	0.384	0.348	0.423	0.192	0.174	0.212	SUBCLONAL	1	TRUE	1	0.6890793177083	3		682	1391	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436404	52436404	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	88	672	0	ENST00000460680.1:c.2090C>G	p.Ser697Cys	p.S697C	ENST00000460680	NM_004656.3	697	tCc/tGc	17/17	0.6890793177083	3	FACETS	0.335	0.296	0.377	0.168	0.148	0.189	SUBCLONAL	1	TRUE	1	0.6890793177083	3		672	1025	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433485	138433485	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	117	448	0	ENST00000289153.2:c.1127A>C	p.Lys376Thr	p.K376T	ENST00000289153	NM_006219.2	376	aAa/aCa	7/22	0.642537837814372	4	FACETS	0.56	0.503	0.619	0.187	0.167	0.207	SUBCLONAL	1	TRUE	1	0.6890793177083	4		448	1025	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226870	142226870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1216055957	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	96	526	0	ENST00000350721.4:c.4934C>T	p.Ser1645Phe	p.S1645F	ENST00000350721	NM_001184.3	1645	tCc/tTc	28/47	0.642537837814372	4	FACETS	0.391	0.347	0.438	0.13	0.115	0.146	SUBCLONAL	1	TRUE	1	0.6890793177083	4		526	1205	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127397	55127397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	115	597	0	ENST00000257290.5:c.185C>T	p.Ser62Phe	p.S62F	ENST00000257290	NM_006206.4	62	tCt/tTt	3/23	1	2	FACETS	0.464	0.418	0.512	0.464	0.418	0.512	SUBCLONAL	1	TRUE	1	0.6890793177083	2		597	720	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247177	153247177	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	67	297	0	ENST00000281708.4:c.1625A>C	p.Asn542Thr	p.N542T	ENST00000281708	NM_033632.3	542	aAt/aCt	10/12	1	2	FACETS	0.439	0.382	0.5	0.439	0.382	0.5	SUBCLONAL	1	TRUE	1	0.6890793177083	2		297	443	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532737	187532737	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	108	559	0	ENST00000441802.2:c.9656C>G	p.Ser3219Ter	p.S3219*	ENST00000441802	NM_005245.3	3219	tCa/tGa	14/27	1	2	FACETS	0.446	0.4	0.494	0.446	0.4	0.494	SUBCLONAL	1	TRUE	1	0.6890793177083	2		559	703	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449429	31449429	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	405	451	0	ENST00000344624.3:c.2780A>G	p.Tyr927Cys	p.Y927C	ENST00000344624		927	tAc/tGc	19/33	0.520087955337647	5	FACETS	1	0.992	1	0.778	0.742	0.814	CLONAL	2	TRUE	2	0.6890793177083	5		451	1024	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593299	67593299	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	69	283	0	ENST00000274335.5:c.2045C>G	p.Ala682Gly	p.A682G	ENST00000274335		682	gCc/gGc	15/15	0.334413687359965	2	FACETS	0.555	0.486	0.628	0.277	0.243	0.314	INDETERMINATE	1	TRUE	0	0.6890793177083	2		283	361	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509431	149509431	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	130	700	0	ENST00000261799.4:c.1468G>C	p.Glu490Gln	p.E490Q	ENST00000261799	NM_002609.3	490	Gag/Cag	10/23	0.587369721340196	1	FACETS	0.339	0.308	0.372	0.339	0.308	0.372	SUBCLONAL	1	TRUE	0	0.6890793177083	1		700	729	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051041	180051041	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	95	635	0	ENST00000261937.6:c.1442A>G	p.Asp481Gly	p.D481G	ENST00000261937	NM_182925.4	481	gAc/gGc	11/30	0.587369721340196	1	FACETS	0.409	0.366	0.454	0.409	0.366	0.454	SUBCLONAL	1	TRUE	0	0.6890793177083	1		635	442	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505387	157505387	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	53	427	0	ENST00000346085.5:c.3368G>C	p.Arg1123Pro	p.R1123P	ENST00000346085	NM_020732.3	1123	cGt/cCt	13/20	0.6890793177083	1	FACETS	0.279	0.239	0.323	0.279	0.239	0.323	SUBCLONAL	1	TRUE	0	0.6890793177083	1		427	361	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849826	151849826	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	49	305	0	ENST00000262189.6:c.12490A>C	p.Lys4164Gln	p.K4164Q	ENST00000262189	NM_170606.2	4164	Aag/Cag	49/59	0.376808501501107	2	FACETS	0.476	0.405	0.552	0.238	0.202	0.276	INDETERMINATE	1	TRUE	0	0.6890793177083	2		305	299	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878775	151878775	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	78	441	0	ENST00000262189.6:c.6170A>G	p.Tyr2057Cys	p.Y2057C	ENST00000262189	NM_170606.2	2057	tAt/tGt	36/59	0.376808501501107	2	FACETS	0.447	0.394	0.505	0.224	0.197	0.253	INDETERMINATE	1	TRUE	0	0.6890793177083	2		441	506	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371818	55371818	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	88	157	0	ENST00000297316.4:c.508G>A	p.Glu170Lys	p.E170K	ENST00000297316	NM_022454.3	170	Gag/Aag	2/2	0.407669056006353	1	FACETS	0.817	0.739	0.895	0.817	0.739	0.895	INDETERMINATE	1	TRUE	0	0.6890793177083	1		157	205	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484164	8484164	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs766454892	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	87	544	0	ENST00000356435.5:c.3368T>C	p.Met1123Thr	p.M1123T	ENST00000356435		1123	aTg/aCg	19/35	1	2	FACETS	0.392	0.347	0.44	0.392	0.347	0.44	SUBCLONAL	1	TRUE	1	0.6890793177083	2		544	644	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8525005	8525005	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	70	356	1	ENST00000356435.5:c.599C>A	p.Ser200Tyr	p.S200Y	ENST00000356435		200	tCt/tAt	7/35	1	2	FACETS	0.43	0.376	0.489	0.43	0.376	0.489	SUBCLONAL	1	TRUE	1	0.6890793177083	2		357	472	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923468	36923468	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	43	668	0	ENST00000358127.4:c.794C>T	p.Ser265Leu	p.S265L	ENST00000358127	NM_001280556.1	265	tCa/tTa	7/10	1	2	FACETS	0.155	0.129	0.184	0.155	0.129	0.184	SUBCLONAL	1	TRUE	1	0.6890793177083	2		668	805	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797293	135797308	+	frameshift_variant	Frame_Shift_Del	DEL	ATAAAGGCGATGAAAG	ATAAAGGCGATGAAAG	-	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	43	227	0	ENST00000298552.3:c.561_576del	p.Phe188GlufsTer17	p.F188Efs*17	ENST00000298552	NM_001162426.1	187	ctCTTTCATCGCCTTTAT/ct	7/23	0.413158365434373	2	FACETS	0.322	0.27	0.38	0.161	0.135	0.19	INDETERMINATE	1	TRUE	0	0.6890793177083	2		227	387	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399865	139399865	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	220	774	1	ENST00000277541.6:c.4483C>T	p.Gln1495Ter	p.Q1495*	ENST00000277541	NM_017617.3	1495	Cag/Tag	25/34	0.494573917870591	1	FACETS	0.448	0.417	0.48	0.448	0.417	0.48	SUBCLONAL	1	TRUE	0	0.6890793177083	1		775	934	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566418	139566418	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs374930413	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	51	631	0	ENST00000308874.7:c.677C>G	p.Ser226Trp	p.S226W	ENST00000308874		226	tCg/tGg	9/10	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.6890793177083	NA		631	793	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027147	49027147	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	TG	novel	NA	P-0049587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	223	348	0	ENST00000267163.4:c.1714delinsTG	p.Leu572CysfsTer3	p.L572Cfs*3	ENST00000267163	NM_000321.2	572	Ctt/TGtt	18/27	0.194490095018497	6	FACETS	1	0.988	1	0.82	0.768	0.872	INDETERMINATE	2	TRUE	3	0.6890793177083	6		348	626	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049597-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	134	276	0				ENST00000310581	NM_198253.2	-/1132			0.387757025376217	9	FACETS	1	0.917	1	0.336	0.305	0.369	CLONAL	2	TRUE	3	0.387757025376217	9		276	807	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652129	36652129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34916193	NA	P-0049597-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	256	760	1	ENST00000244741.5:c.251G>A	p.Arg84Gln	p.R84Q	ENST00000244741	NM_000389.4	84	cGa/cAa	2/3	0.387757025376217	5	FACETS	1	0.974	1	0.715	0.67	0.762	CLONAL	2	TRUE	2	0.387757025376217	5		761	973	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733217	40733217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049597-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	148	493	0	ENST00000373198.4:c.3589G>A	p.Glu1197Lys	p.E1197K	ENST00000373198	NM_133170.3	1197	Gaa/Aaa	26/32	0.169917162060521	5	FACETS	0.936	0.858	1	0.624	0.572	0.679	INDETERMINATE	2	TRUE	2	0.387757025376217	5		493	645	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030637	47030637	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049597-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	220	690	0	ENST00000377604.3:c.412C>T	p.Gln138Ter	p.Q138*	ENST00000377604	NM_001204468.1	138	Cag/Tag	4/24	0.338742783547019	2	FACETS	0.923	0.864	0.982	0.923	0.864	0.982	CLONAL	2	TRUE	0	0.387757025376217	2		690	615	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410883	31410883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049597-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1533	120	570	0	ENST00000344624.3:c.3637C>T	p.Arg1213Cys	p.R1213C	ENST00000344624		1213	Cgc/Tgc	28/33	0.387757025376217	9	FACETS	0.883	0.794	0.977	0.147	0.132	0.163	CLONAL	1	TRUE	3	0.387757025376217	9		570	1653	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252856	36252856	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049597-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	56	284	0	ENST00000300305.3:c.506G>C	p.Arg169Thr	p.R169T	ENST00000300305		169	aGa/aCa	4/8	0.387757025376217	1	FACETS	0.82	0.708	0.94	0.82	0.708	0.94	CLONAL	1	TRUE	0	0.387757025376217	1		284	284	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983150	201983150	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049597-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	166	514	1	ENST00000359651.3:c.999G>A	p.Met333Ile	p.M333I	ENST00000359651		333	atG/atA	7/8	1	2	FACETS	0.758	0.7	0.817	1	0.99	1	SUBCLONAL	2	TRUE	1	0.387757025376217	2		515	565	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023090	27023090	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs962566886	NA	P-0049597-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	30	166	0	ENST00000324856.7:c.196C>A	p.Pro66Thr	p.P66T	ENST00000324856	NM_006015.4	66	Ccg/Acg	1/20	0.387757025376217	4	FACETS	1	0.836	1	0.344	0.279	0.417	CLONAL	1	TRUE	1	0.387757025376217	4		166	208	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796325	42796325	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049597-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	318	769	0	ENST00000575354.2:c.2974C>G	p.Gln992Glu	p.Q992E	ENST00000575354	NM_015125.3	992	Cag/Gag	12/20	0.387757025376217	5	FACETS	0.911	0.862	0.961	0.911	0.862	0.961	CLONAL	3	TRUE	2	0.387757025376217	5		769	949	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213589	27213589	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049597-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	532	386	0	ENST00000380036.4:c.2985G>C	p.Lys995Asn	p.K995N	ENST00000380036	NM_000459.3	995	aaG/aaC	18/23	0.387757025376217	9	FACETS	1	0.984	1	0.58	0.557	0.602	CLONAL	5	TRUE	0	0.387757025376217	9		386	1240	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216972	2216972	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049597-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	127	706	0	ENST00000398665.3:c.2427G>C	p.Glu809Asp	p.E809D	ENST00000398665	NM_032482.2	809	gaG/gaC	21/28	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.387757025376217	2		706	579	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630726	187630726	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049597-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	76	488	0	ENST00000441802.2:c.256G>C	p.Glu86Gln	p.E86Q	ENST00000441802	NM_005245.3	86	Gaa/Caa	2/27	0.358059513700214	3	FACETS	0.818	0.718	0.925	0.409	0.359	0.463	CLONAL	1	TRUE	1	0.387757025376217	3		488	572	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672272	30672272	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049597-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	97	571	0	ENST00000376406.3:c.4688C>G	p.Ser1563Cys	p.S1563C	ENST00000376406	NM_014641.2	1563	tCc/tGc	10/15	0.387757025376217	5	FACETS	0.941	0.838	1	0.314	0.279	0.351	CLONAL	1	TRUE	2	0.387757025376217	5		571	841	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672302	30672302	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049597-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	91	580	0	ENST00000376406.3:c.4658C>G	p.Ser1553Cys	p.S1553C	ENST00000376406	NM_014641.2	1553	tCt/tGt	10/15	0.387757025376217	5	FACETS	0.871	0.773	0.977	0.29	0.257	0.326	CLONAL	1	TRUE	2	0.387757025376217	5		580	852	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0049598-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	91	614	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.24	2		614	624	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771344	68771344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555509646	NA	P-0049598-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	18	0	0	ENST00000261769.5:c.26C>T	p.Ser9Leu	p.S9L	ENST00000261769	NM_004360.3	9	tCg/tTg	1/16	0.286595755242479	4	FACETS	0.441	0.331	0.571	0.22	0.165	0.286	SUBCLONAL	1	TRUE	2	0.24	4		0	422	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428225	33428225	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs750621215	NA	P-0049598-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	26	496	0	ENST00000345365.6:c.898C>T	p.Arg300Ter	p.R300*	ENST00000345365	NM_002878.3	300	Cga/Tga	9/10	0.3	1	FACETS	0.403	0.318	0.501	0.403	0.318	0.501	SUBCLONAL	1	TRUE	0	0.24	1		496	473	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275290	115275290	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049598-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	11	0	0	ENST00000438362.2:c.1123G>C	p.Glu375Gln	p.E375Q	ENST00000438362	NM_001242891.1	375	Gag/Cag	10/20	1	2	FACETS	0.332	0.229	0.461	0.332	0.229	0.461	SUBCLONAL	1	TRUE	1	0.24	2		0	276	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426889	49426890	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	AA	novel	NA	P-0049598-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	65	519	2	ENST00000301067.7:c.11598_11599delinsTT	p.Gln3866_Gln3867delinsHisTer	p.Q3866_Q3867delinsH*	ENST00000301067	NM_003482.3	3866	caGCaa/caTTaa	39/54	0.211713985886013	2	FACETS	1	0.957	1	0.625	0.544	0.713	CLONAL	1	TRUE	0	0.24	2		521	433	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89865574	89865574	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049598-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	121	556	0	ENST00000389301.3:c.893G>C	p.Trp298Ser	p.W298S	ENST00000389301	NM_000135.2	298	tGg/tCg	10/43	0.286595755242479	4	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	2	0.24	4		556	600	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16062082	16062082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049598-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	34	367	1	ENST00000268712.3:c.724G>A	p.Glu242Lys	p.E242K	ENST00000268712	NM_006311.3	242	Gag/Aag	6/46	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.24	2		368	244	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16062148	16062148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049598-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	63	521	0	ENST00000268712.3:c.658G>A	p.Glu220Lys	p.E220K	ENST00000268712	NM_006311.3	220	Gag/Aag	6/46	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.24	2		521	445	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159101	24159101	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049598-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	11	0	0	ENST00000263121.7:c.773C>A	p.Ser258Ter	p.S258*	ENST00000263121	NM_003073.3	258	tCa/tAa	6/9	1	2	FACETS	0.174	0.119	0.243	0.174	0.119	0.243	SUBCLONAL	1	TRUE	1	0.24	2		0	526	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138383966	138383966	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049598-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	39	512	0	ENST00000289153.2:c.2584G>C	p.Asp862His	p.D862H	ENST00000289153	NM_006219.2	862	Gac/Cac	18/22	1	2	FACETS	0.73	0.605	0.869	0.73	0.605	0.869	SUBCLONAL	1	TRUE	1	0.24	2		512	445	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049763-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	47	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.3	1	FACETS	0.612	0.518	0.716	0.612	0.518	0.716	SUBCLONAL	1	TRUE	0	0.32	1		334	403	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911311	29911311	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs199474579	NA	P-0049763-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	68	601	0	ENST00000376809.5:c.610C>T	p.Gln204Ter	p.Q204*	ENST00000376809	NM_002116.7	204	Cag/Tag	3/8	0.3	3	FACETS	0.705	0.613	0.805	0.353	0.306	0.403	SUBCLONAL	1	TRUE	1	0.32	3		601	699	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438169	56438169	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049763-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	155	855	0	ENST00000407977.2:c.824G>T	p.Cys275Phe	p.C275F	ENST00000407977		275	tGt/tTt	7/10	0.3	1	FACETS	0.818	0.748	0.891	0.818	0.748	0.891	CLONAL	1	TRUE	0	0.32	1		855	995	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911752	32911752	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs80359379	NA	P-0049763-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	58	593	0	ENST00000380152.3:c.3263del	p.Pro1088LeufsTer16	p.P1088Lfs*16	ENST00000380152		1087	aCc/ac	11/27	1	2	FACETS	0.738	0.635	0.85	0.738	0.635	0.85	SUBCLONAL	1	TRUE	1	0.32	2		593	491	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575103	48575103	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049763-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	60	443	0	ENST00000342988.3:c.297G>C	p.Trp99Cys	p.W99C	ENST00000342988	NM_005359.5	99	tgG/tgC	3/12	0.24312015405512	1	FACETS	0.842	0.729	0.964	0.842	0.729	0.964	CLONAL	1	TRUE	0	0.32	1		443	374	SUCCESS
APC	324	MSKCC	GRCh37	5	112178625	112178646	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAAGCTCCAAGCCCAACCTT	AAGAAGCTCCAAGCCCAACCTT	-	novel	NA	P-0049763-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	43	379	0	ENST00000257430.4:c.7340_7361del	p.Ala2447GlufsTer31	p.A2447Efs*31	ENST00000257430	NM_000038.5	2445	aAAGAAGCTCCAAGCCCAACCTTa/aa	16/16	0.3	1	FACETS	0.618	0.519	0.728	0.618	0.519	0.728	SUBCLONAL	1	TRUE	0	0.32	1		379	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0049974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	237	603	2	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	NA	2	FACETS	1	0.949	1			1	INDETERMINATE	2	TRUE	NA	0.421925277920212	2		605	557	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0050012-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	74	265	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.511819385235129	1	FACETS	0.803	0.711	0.899	0.803	0.711	0.899	CLONAL	1	TRUE	0	0.511819385235129	1		265	268	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263973	104263974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776579	NA	P-0050012-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	12	199	0	ENST00000369902.3:c.71dup	p.Ala25GlyfsTer23	p.A25Gfs*23	ENST00000369902	NM_016169.3	22	gcc/gCcc	1/12	0.511819385235129	1	FACETS	0.162	0.113	0.221	0.162	0.113	0.221	SUBCLONAL	1	TRUE	0	0.511819385235129	1		199	216	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578397	7578398	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0050012-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	244	642	2	ENST00000269305.4:c.532dup	p.His178ProfsTer3	p.H178Pfs*3	ENST00000269305	NM_001126112.2	178	cac/cCac	5/11	0.511819385235129	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.511819385235129	1		644	589	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934155	48934155	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050012-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	143	284	0	ENST00000267163.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000267163	NM_000321.2	204	Gaa/Taa	7/27	0.511819385235129	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.511819385235129	1		284	327	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294075	1294075	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050012-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	68	850	0	ENST00000310581.5:c.926C>G	p.Ser309Cys	p.S309C	ENST00000310581	NM_198253.2	309	tCc/tGc	2/16	0.511819385235129	1	FACETS	0.269	0.233	0.307	0.269	0.233	0.307	SUBCLONAL	1	TRUE	0	0.511819385235129	1		850	736	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249037	55249038	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0050016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	179	720	0	ENST00000275493.2:c.2335_2336delinsTT	p.Gly779Phe	p.G779F	ENST00000275493	NM_005228.3	779	GGc/TTc	20/28	0.3	3	FACETS	1	0.975	1	1	0.991	1	CLONAL	3	TRUE	1	0.13	3		720	864	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913628	32913628	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs886038120	NA	P-0050016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	23	356	0	ENST00000380152.3:c.5138del	p.Asn1713IlefsTer12	p.N1713Ifs*12	ENST00000380152		1712	ggA/gg	11/27	1	2	FACETS	1	0.781	1	1	0.781	1	CLONAL	1	TRUE	1	0.13	2		356	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0050022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	239	558	1	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	NA	2	FACETS	1	0.957	1			1	INDETERMINATE	2	TRUE	NA	0.550215802116932	2		559	430	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484429	57484429	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	93	466	0	ENST00000371085.3:c.610A>G	p.Thr204Ala	p.T204A	ENST00000371085	NM_000516.4	204	Act/Gct	8/13	0.550215802116932	3	FACETS	0.943	0.843	1	0.472	0.421	0.525	CLONAL	1	TRUE	1	0.550215802116932	3		466	457	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372160	45372160	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1040132520	NA	P-0050022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	201	351	0	ENST00000262160.6:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000262160	NM_005901.5	337	Cgc/Tgc	9/11	0.370660082878379	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.550215802116932	4		351	481	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951076	48951076	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050022-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	85	224	0	ENST00000267163.4:c.1240del	p.Ser414ValfsTer3	p.S414Vfs*3	ENST00000267163	NM_000321.2	413	gAa/ga	13/27	0.550215802116932	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.550215802116932	1		224	201	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098421	47098421	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050039-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	85	442	0	ENST00000409792.3:c.6853C>T	p.Gln2285Ter	p.Q2285*	ENST00000409792	NM_014159.6	2285	Cag/Tag	15/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		442	586	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692893	89692893	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	34	296	0	ENST00000371953.3:c.377C>A	p.Ala126Asp	p.A126D	ENST00000371953	NM_000314.4	126	gCt/gAt	5/9	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		296	548	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0050060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	19	343	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		343	643	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0050184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	397	691	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.898780097608074	2		691	435	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039220	49039220	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	228	501	0	ENST00000267163.4:c.2300del	p.Asn767IlefsTer43	p.N767Ifs*43	ENST00000267163	NM_000321.2	766	acA/ac	22/27	0.883425769828569	2	FACETS	0.979	0.951	1	0.979	0.951	1	CLONAL	2	TRUE	0	0.898780097608074	2		501	259	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479213	50479213	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	332	598	0	ENST00000394963.4:c.61G>T	p.Gly21Trp	p.G21W	ENST00000394963	NM_003076.4	21	Ggg/Tgg	1/13	0.687835702283879	4	FACETS	0.94	0.895	0.986	0.94	0.895	0.986	CLONAL	2	TRUE	2	0.898780097608074	4		598	746	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166467	118166467	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	122	425	0	ENST00000369448.3:c.977G>C	p.Arg326Pro	p.R326P	ENST00000369448	NM_017709.3	326	cGc/cCc	2/2	0.898780097608074	3	FACETS	1	0.971	1	0.57	0.522	0.62	CLONAL	1	TRUE	1	0.898780097608074	3		425	345	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871728	35871728	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	126	656	0	ENST00000216797.5:c.778del	p.Arg260AlafsTer13	p.R260Afs*13	ENST00000216797	NM_020529.2	260	Cgc/gc	5/6	0.363934640533577	3	FACETS	0.65	0.59	0.713	0.217	0.196	0.238	INDETERMINATE	1	TRUE	0	0.898780097608074	3		656	625	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007221	62007221	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	357	928	1	ENST00000392795.3:c.461A>T	p.Gln154Leu	p.Q154L	ENST00000392795	NM_001039933.1	154	cAg/cTg	4/6	0.754036170960368	4	FACETS	0.976	0.931	1	0.976	0.931	1	CLONAL	2	TRUE	2	0.898780097608074	4		929	773	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400666	56400667	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0050184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	163	361	0	ENST00000348428.3:c.1263dup	p.Asn422GlufsTer8	p.N422Efs*8	ENST00000348428	NM_006785.3	420	-/G	11/17	0.898780097608074	5	FACETS	0.845	0.781	0.91	0.563	0.521	0.607	CLONAL	2	TRUE	2	0.898780097608074	5		361	504	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25458666	25458666	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	277	586	0	ENST00000264709.3:c.2507G>T	p.Arg836Met	p.R836M	ENST00000264709	NM_175629.2	836	aGg/aTg	22/23	0.855323172200156	3	FACETS	0.921	0.878	0.964	0.921	0.878	0.964	CLONAL	2	TRUE	1	0.898780097608074	3		586	485	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99179966	99179966	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1334248840	NA	P-0050184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	228	817	0	ENST00000074304.5:c.1909C>G	p.Leu637Val	p.L637V	ENST00000074304	NM_001134224.1	637	Ctc/Gtc	19/26	0.898780097608074	3	FACETS	0.953	0.89	1	0.476	0.445	0.508	CLONAL	1	TRUE	1	0.898780097608074	3		817	772	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141141	55141142	+	splice_donor_variant	Splice_Site	INS	-	-	A	novel	NA	P-0050184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	149	343	0	ENST00000257290.5:c.1786+1_1786+2insA		p.X596_splice	ENST00000257290	NM_006206.4	596			0.855323172200156	3	FACETS	0.985	0.924	1	0.985	0.924	1	CLONAL	2	TRUE	1	0.898780097608074	3		343	244	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244098	153244098	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	174	541	0	ENST00000281708.4:c.2059G>T	p.Gly687Trp	p.G687W	ENST00000281708	NM_033632.3	687	Ggg/Tgg	12/12	0.722928175391396	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.898780097608074	1		541	211	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048716	180048716	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	325	987	2	ENST00000261937.6:c.1846T>A	p.Phe616Ile	p.F616I	ENST00000261937	NM_182925.4	616	Ttc/Atc	13/30	0.0892394925686453	6	FACETS	0.913	0.868	0.958	0.913	0.868	0.958	INDETERMINATE	3	TRUE	3	0.898780097608074	6		989	739	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6037033	6037033	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs867655834	NA	P-0050184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	274	419	0	ENST00000265849.7:c.727G>T	p.Val243Phe	p.V243F	ENST00000265849	NM_000535.5	243	Gtt/Ttt	7/15	0.896138206467923	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.898780097608074	2		419	302	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197399	27197399	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	278	606	0	ENST00000380036.4:c.1711G>T	p.Glu571Ter	p.E571*	ENST00000380036	NM_000459.3	571	Gaa/Taa	12/23	0.687835702283879	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	2	0.898780097608074	4		606	583	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	565	633	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.891	0.866	0.915	1	0.998	1	CLONAL	4	TRUE	1	0.393438475539559	2		633	806	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048760	180048760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754245879	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	286	826	0	ENST00000261937.6:c.1802C>T	p.Ala601Val	p.A601V	ENST00000261937	NM_182925.4	601	gCg/gTg	13/30	0.393438475539559	1	FACETS	0.846	0.801	0.892	1	0.995	1	CLONAL	2	TRUE	0	0.393438475539559	1		826	690	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	235	430	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.862	0.808	0.917	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		430	693	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939260	71939260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	99	762	0	ENST00000298229.2:c.209G>A	p.Arg70His	p.R70H	ENST00000298229	NM_001567.3	70	cGc/cAc	2/28	1	2	FACETS	0.683	0.61	0.761	0.683	0.61	0.761	SUBCLONAL	1	TRUE	1	0.393438475539559	2		762	737	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	116	350	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	0.788	0.718	0.862	1	0.987	1	SUBCLONAL	2	TRUE	1	0.393438475539559	2		350	374	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926888	112926888	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507546	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	183	572	0	ENST00000351677.2:c.1508G>T	p.Gly503Val	p.G503V	ENST00000351677	NM_002834.3	503	gGg/gTg	13/16	1	2	FACETS	0.795	0.738	0.854	1	0.991	1	SUBCLONAL	2	TRUE	1	0.393438475539559	2		572	585	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	76	494	2	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	1	2	FACETS	0.594	0.521	0.673	0.594	0.521	0.673	SUBCLONAL	1	TRUE	1	0.393438475539559	2		496	650	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489264	2489264	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	273	702	0	ENST00000355716.4:c.169T>C	p.Cys57Arg	p.C57R	ENST00000355716	NM_003820.2	57	Tgc/Cgc	2/8	1	2	FACETS	0.908	0.856	0.961	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		702	764	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9787015	9787015	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	245	481	1	ENST00000377346.4:c.3046C>T	p.Arg1016Ter	p.R1016*	ENST00000377346	NM_005026.3	1016	Cga/Tga	24/24	1	2	FACETS	0.932	0.876	0.989	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		482	668	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169362	11169362	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	169	476	0	ENST00000361445.4:c.7513C>T	p.Arg2505Ter	p.R2505*	ENST00000361445	NM_004958.3	2505	Cga/Tga	56/58	1	2	FACETS	0.824	0.763	0.887	1	0.991	1	CLONAL	2	TRUE	1	0.393438475539559	2		476	521	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187170	11187170	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	93	594	0	ENST00000361445.4:c.6248A>G	p.Glu2083Gly	p.E2083G	ENST00000361445	NM_004958.3	2083	gAg/gGg	45/58	1	2	FACETS	0.792	0.705	0.884	0.792	0.705	0.884	SUBCLONAL	1	TRUE	1	0.393438475539559	2		594	597	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11194462	11194462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	214	618	0	ENST00000361445.4:c.5192C>T	p.Ala1731Val	p.A1731V	ENST00000361445	NM_004958.3	1731	gCc/gTc	37/58	1	2	FACETS	0.843	0.788	0.9	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	2		618	645	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294267	11294267	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1187856229	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	107	545	1	ENST00000361445.4:c.2264G>A	p.Arg755His	p.R755H	ENST00000361445	NM_004958.3	755	cGc/cAc	14/58	1	2	FACETS	0.898	0.807	0.993	0.898	0.807	0.993	CLONAL	1	TRUE	1	0.393438475539559	2		546	606	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202989	16202989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	161	454	0	ENST00000375759.3:c.697C>T	p.Pro233Ser	p.P233S	ENST00000375759	NM_015001.2	233	Cca/Tca	3/15	1	2	FACETS	0.807	0.746	0.87	1	0.991	1	CLONAL	2	TRUE	1	0.393438475539559	2		454	507	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237796	16237796	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	66	293	0	ENST00000375759.3:c.1243G>T	p.Glu415Ter	p.E415*	ENST00000375759	NM_015001.2	415	Gaa/Taa	5/15	1	2	FACETS	0.784	0.683	0.893	0.784	0.683	0.893	SUBCLONAL	1	TRUE	1	0.393438475539559	2		293	428	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256136	16256136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	189	509	0	ENST00000375759.3:c.3401G>A	p.Cys1134Tyr	p.C1134Y	ENST00000375759	NM_015001.2	1134	tGc/tAc	11/15	1	2	FACETS	0.833	0.774	0.892	1	0.992	1	CLONAL	2	TRUE	1	0.393438475539559	2		509	577	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257039	16257039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1224202162	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	191	444	1	ENST00000375759.3:c.4304C>T	p.Ala1435Val	p.A1435V	ENST00000375759	NM_015001.2	1435	gCa/gTa	11/15	1	2	FACETS	0.859	0.8	0.92	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	2		445	565	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262715	16262715	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149328916	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	177	393	0	ENST00000375759.3:c.9980C>T	p.Ala3327Val	p.A3327V	ENST00000375759	NM_015001.2	3327	gCc/gTc	11/15	1	2	FACETS	0.903	0.839	0.969	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	2		393	498	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089568	27089568	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	256	702	0	ENST00000324856.7:c.2524C>A	p.His842Asn	p.H842N	ENST00000324856	NM_006015.4	842	Cat/Aat	8/20	1	2	FACETS	0.902	0.849	0.957	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		702	721	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101523	27101523	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1295471823	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	262	829	0	ENST00000324856.7:c.4805G>A	p.Ser1602Asn	p.S1602N	ENST00000324856	NM_006015.4	1602	aGc/aAc	18/20	1	2	FACETS	0.899	0.846	0.952	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		829	741	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	118	509	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.958	0.867	1	0.958	0.867	1	CLONAL	1	TRUE	1	0.393438475539559	2		509	626	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598272	28598272	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	267	798	1	ENST00000253063.3:c.244G>A	p.Val82Met	p.V82M	ENST00000253063	NM_031459.4	82	Gtg/Atg	3/10	1	2	FACETS	0.791	0.744	0.839	1	0.994	1	SUBCLONAL	2	TRUE	1	0.393438475539559	2		799	858	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939219	36939219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762191036	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	246	801	1	ENST00000361632.4:c.490C>T	p.Arg164Trp	p.R164W	ENST00000361632		164	Cgg/Tgg	5/16	1	2	FACETS	0.858	0.805	0.911	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		802	729	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36945078	36945078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	66	682	2	ENST00000361632.4:c.20G>A	p.Cys7Tyr	p.C7Y	ENST00000361632		7	tGc/tAc	2/16	1	2	FACETS	0.444	0.384	0.508	0.444	0.384	0.508	SUBCLONAL	1	TRUE	1	0.393438475539559	2		684	756	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803593	43803593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	240	666	0	ENST00000372470.3:c.74G>A	p.Ser25Asn	p.S25N	ENST00000372470	NM_005373.2	25	aGc/aAc	1/12	1	2	FACETS	0.99	0.931	1	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		666	616	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818265	43818265	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	237	672	1	ENST00000372470.3:c.1730G>T	p.Arg577Met	p.R577M	ENST00000372470	NM_005373.2	577	aGg/aTg	12/12	1	2	FACETS	0.879	0.825	0.935	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		673	685	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799087	45799087	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs373766973	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	231	682	0	ENST00000450313.1:c.346C>T	p.Arg116Trp	p.R116W	ENST00000450313	NM_012222.2	116	Cgg/Tgg	3/16	1	2	FACETS	0.826	0.773	0.879	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	2		682	711	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511669	46511669	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557548214	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	159	468	0	ENST00000262741.5:c.1108G>A	p.Asp370Asn	p.D370N	ENST00000262741	NM_003629.3	370	Gac/Aac	9/10	1	2	FACETS	0.84	0.776	0.906	1	0.991	1	CLONAL	2	TRUE	1	0.393438475539559	2		468	481	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46736445	46736445	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	182	479	0	ENST00000371975.4:c.1157G>T	p.Ser386Ile	p.S386I	ENST00000371975	NM_003579.3	386	aGc/aTc	10/18	1	2	FACETS	0.884	0.822	0.948	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	2		479	523	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65300268	65300268	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	39	225	0	ENST00000342505.4:c.3442G>T	p.Gly1148Ter	p.G1148*	ENST00000342505	NM_002227.2	1148	Gga/Tga	25/25	1	2	FACETS	0.608	0.506	0.722	0.608	0.506	0.722	SUBCLONAL	1	TRUE	1	0.393438475539559	2		225	326	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262332	115262332	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	35	328	0	ENST00000438362.2:c.2222G>T	p.Ser741Ile	p.S741I	ENST00000438362	NM_001242891.1	741	aGc/aTc	18/20	1	2	FACETS	0.38	0.311	0.458	0.38	0.311	0.458	SUBCLONAL	1	TRUE	1	0.393438475539559	2		328	468	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273203	115273203	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	90	416	0	ENST00000438362.2:c.1255T>G	p.Phe419Val	p.F419V	ENST00000438362	NM_001242891.1	419	Ttc/Gtc	11/20	1	2	FACETS	0.789	0.701	0.882	0.789	0.701	0.882	SUBCLONAL	1	TRUE	1	0.393438475539559	2		416	580	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165761	118165761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	161	370	0	ENST00000369448.3:c.271C>A	p.Leu91Met	p.L91M	ENST00000369448	NM_017709.3	91	Ctg/Atg	2/2	1	2	FACETS	0.977	0.906	1	1	0.992	1	CLONAL	2	TRUE	1	0.393438475539559	2		370	419	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483320	120483320	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	64	366	1	ENST00000256646.2:c.3041C>A	p.Pro1014His	p.P1014H	ENST00000256646	NM_024408.3	1014	cCt/cAt	19/34	1	2	FACETS	0.707	0.614	0.808	0.707	0.614	0.808	SUBCLONAL	1	TRUE	1	0.393438475539559	2		367	460	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497768	120497768	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781902176	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	187	483	1	ENST00000256646.2:c.2114G>A	p.Arg705His	p.R705H	ENST00000256646	NM_024408.3	705	cGc/cAc	13/34	1	2	FACETS	0.909	0.846	0.973	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	2		484	523	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512280	120512280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	189	515	1	ENST00000256646.2:c.962G>A	p.Gly321Asp	p.G321D	ENST00000256646	NM_024408.3	321	gGc/gAc	6/34	1	2	FACETS	0.77	0.715	0.826	1	0.991	1	SUBCLONAL	2	TRUE	1	0.393438475539559	2		516	624	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834519	156834519	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	216	709	0	ENST00000524377.1:c.288-1G>A		p.X96_splice	ENST00000524377	NM_002529.3	96			1	2	FACETS	0.856	0.801	0.913	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	2		709	641	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838380	156838380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202030811	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	167	919	1	ENST00000524377.1:c.658C>T	p.Arg220Trp	p.R220W	ENST00000524377	NM_002529.3	220	Cgg/Tgg	6/17	1	2	FACETS	0.985	0.905	1	0.985	0.905	1	CLONAL	1	TRUE	1	0.393438475539559	2		920	862	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849089	156849089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	267	828	0	ENST00000524377.1:c.1981G>A	p.Gly661Arg	p.G661R	ENST00000524377	NM_002529.3	661	Gga/Aga	15/17	1	2	FACETS	0.827	0.778	0.877	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		828	821	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849152	156849152	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs768180688	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	189	605	1	ENST00000524377.1:c.2044C>T	p.Arg682Cys	p.R682C	ENST00000524377	NM_002529.3	682	Cgt/Tgt	15/17	1	2	FACETS	0.759	0.705	0.815	1	0.991	1	SUBCLONAL	2	TRUE	1	0.393438475539559	2		606	633	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851255	156851255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1480681042	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	132	651	0	ENST00000524377.1:c.2212G>A	p.Asp738Asn	p.D738N	ENST00000524377	NM_002529.3	738	Gac/Aac	17/17	1	2	FACETS	0.964	0.877	1	0.964	0.877	1	CLONAL	1	TRUE	1	0.393438475539559	2		651	696	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163295897	163295897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770685564	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	104	301	0	ENST00000271452.3:c.56G>A	p.Arg19His	p.R19H	ENST00000271452	NM_145697.2	19	cGc/cAc	2/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.393438475539559	2		301	390	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111145	193111146	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	rs760591174	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	42	255	1	ENST00000367435.3:c.687_688dup	p.Val230GlufsTer28	p.V230Efs*28	ENST00000367435	NM_024529.4	226	-/AG	7/17	1	2	FACETS	0.635	0.532	0.749	0.635	0.532	0.749	SUBCLONAL	1	TRUE	1	0.393438475539559	2		256	336	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111149	193111149	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	50	251	0	ENST00000367435.3:c.682G>T	p.Glu228Ter	p.E228*	ENST00000367435	NM_024529.4	228	Gag/Tag	7/17	1	2	FACETS	0.782	0.667	0.907	0.782	0.667	0.907	CLONAL	1	TRUE	1	0.393438475539559	2		251	325	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518514	204518514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	109	312	0	ENST00000367182.3:c.1177G>A	p.Glu393Lys	p.E393K	ENST00000367182	NM_001278516.1	393	Gaa/Aaa	11/11	1	2	FACETS	0.808	0.733	0.885	1	0.986	1	CLONAL	2	TRUE	1	0.393438475539559	2		312	343	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518634	204518634	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	131	302	0	ENST00000367182.3:c.1297C>A	p.Leu433Ile	p.L433I	ENST00000367182	NM_001278516.1	433	Ctc/Atc	11/11	1	2	FACETS	0.922	0.847	0.999	1	0.99	1	CLONAL	2	TRUE	1	0.393438475539559	2		302	361	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206646650	206646650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553384304	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	272	833	1	ENST00000367120.3:c.80G>A	p.Arg27His	p.R27H	ENST00000367120	NM_014002.3	27	cGc/cAc	3/22	1	2	FACETS	0.869	0.818	0.92	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		834	796	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649530	206649530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	179	446	0	ENST00000367120.3:c.365G>A	p.Gly122Asp	p.G122D	ENST00000367120	NM_014002.3	122	gGc/gAc	6/22	1	2	FACETS	0.906	0.843	0.971	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	2		446	502	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206665021	206665021	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	197	483	0	ENST00000367120.3:c.1774T>G	p.Phe592Val	p.F592V	ENST00000367120	NM_014002.3	592	Ttc/Gtc	18/22	1	2	FACETS	0.872	0.813	0.933	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	2		483	574	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944310	206944310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755490123	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	185	500	0	ENST00000423557.1:c.320C>T	p.Ala107Val	p.A107V	ENST00000423557	NM_000572.2	107	gCg/gTg	3/5	1	2	FACETS	0.752	0.698	0.808	1	0.991	1	SUBCLONAL	2	TRUE	1	0.393438475539559	2		500	625	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552729	226552729	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746139482	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	162	485	0	ENST00000366794.5:c.2632C>T	p.Arg878Trp	p.R878W	ENST00000366794	NM_001618.3	878	Cgg/Tgg	19/23	1	2	FACETS	0.86	0.795	0.926	1	0.991	1	CLONAL	2	TRUE	1	0.393438475539559	2		485	479	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226556023	226556023	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	53	347	0	ENST00000366794.5:c.2155-1G>A		p.X719_splice	ENST00000366794	NM_001618.3	719			1	2	FACETS	0.761	0.652	0.88	0.761	0.652	0.88	SUBCLONAL	1	TRUE	1	0.393438475539559	2		347	354	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612659	228612659	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	301	679	0	ENST00000366696.1:c.368A>G	p.Lys123Arg	p.K123R	ENST00000366696	NM_003493.2	123	aAg/aGg	1/1	1	2	FACETS	0.959	0.907	1	1	0.996	1	CLONAL	2	TRUE	1	0.393438475539559	2		679	798	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612801	228612801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369460992	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	290	713	2	ENST00000366696.1:c.226G>A	p.Ala76Thr	p.A76T	ENST00000366696	NM_003493.2	76	Gct/Act	1/1	1	2	FACETS	0.887	0.837	0.937	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		715	831	SUCCESS
FH	2271	MSKCC	GRCh37	1	241672012	241672012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	141	419	0	ENST00000366560.3:c.629G>A	p.Gly210Glu	p.G210E	ENST00000366560	NM_000143.3	210	gGa/gAa	5/10	1	2	FACETS	0.779	0.715	0.845	1	0.989	1	SUBCLONAL	2	TRUE	1	0.393438475539559	2		419	460	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736239	243736239	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	75	300	0	ENST00000263826.5:c.808C>T	p.Arg270Cys	p.R270C	ENST00000263826	NM_005465.4	270	Cgt/Tgt	8/13	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.393438475539559	2		300	365	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246490640	246490641	+	splice_acceptor_variant	Splice_Site	INS	-	-	T	rs773077071	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	90	264	0	ENST00000388985.4:c.395-2dup		p.X132_splice	ENST00000388985		132			1	2	FACETS	0.752	0.675	0.833	1	0.982	1	SUBCLONAL	2	TRUE	1	0.393438475539559	2		264	304	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100645	8100645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1218595084	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	252	782	3	ENST00000346208.3:c.619G>A	p.Ala207Thr	p.A207T	ENST00000346208		207	Gcc/Acc	3/6	1	2	FACETS	0.88	0.827	0.934	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		785	728	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596068	43596068	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537523906	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	232	735	1	ENST00000355710.3:c.235C>T	p.Arg79Trp	p.R79W	ENST00000355710	NM_020975.4	79	Cgg/Tgg	2/20	1	2	FACETS	0.881	0.826	0.938	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		736	669	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620378	43620378	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	169	499	0	ENST00000355710.3:c.2987C>T	p.Pro996Leu	p.P996L	ENST00000355710	NM_020975.4	996	cCg/cTg	18/20	1	2	FACETS	0.762	0.704	0.821	1	0.99	1	SUBCLONAL	2	TRUE	1	0.393438475539559	2		499	564	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622099	43622099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs79853121	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	168	499	0	ENST00000355710.3:c.3116C>T	p.Pro1039Leu	p.P1039L	ENST00000355710	NM_020975.4	1039	cCg/cTg	19/20	1	2	FACETS	0.781	0.722	0.841	1	0.99	1	SUBCLONAL	2	TRUE	1	0.393438475539559	2		499	547	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759868	63759868	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766186442	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	136	307	0	ENST00000279873.7:c.521C>T	p.Thr174Met	p.T174M	ENST00000279873	NM_032199.2	174	aCg/aTg	4/10	1	2	FACETS	0.95	0.874	1	1	0.991	1	CLONAL	2	TRUE	1	0.393438475539559	2		307	364	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759902	63759902	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	139	327	0	ENST00000279873.7:c.555C>A	p.Cys185Ter	p.C185*	ENST00000279873	NM_032199.2	185	tgC/tgA	4/10	1	2	FACETS	0.894	0.823	0.968	1	0.99	1	CLONAL	2	TRUE	1	0.393438475539559	2		327	395	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63816959	63816959	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	108	248	0	ENST00000279873.7:c.930G>T	p.Lys310Asn	p.K310N	ENST00000279873	NM_032199.2	310	aaG/aaT	6/10	1	2	FACETS	0.934	0.85	1	1	0.989	1	CLONAL	2	TRUE	1	0.393438475539559	2		248	294	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332565	70332565	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs185830524	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	175	442	0	ENST00000373644.4:c.470C>T	p.Ser157Leu	p.S157L	ENST00000373644	NM_030625.2	157	tCg/tTg	2/12	1	2	FACETS	0.869	0.806	0.933	1	0.992	1	CLONAL	2	TRUE	1	0.393438475539559	2		442	512	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406127	70406127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	75	491	1	ENST00000373644.4:c.3641C>T	p.Ser1214Phe	p.S1214F	ENST00000373644	NM_030625.2	1214	tCt/tTt	4/12	1	2	FACETS	0.658	0.577	0.745	0.658	0.577	0.745	SUBCLONAL	1	TRUE	1	0.393438475539559	2		492	579	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406468	70406468	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	213	622	0	ENST00000373644.4:c.3982C>T	p.Gln1328Ter	p.Q1328*	ENST00000373644	NM_030625.2	1328	Caa/Taa	4/12	1	2	FACETS	0.828	0.773	0.884	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	2		622	654	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450655	70450655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771857626	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	227	411	0	ENST00000373644.4:c.5495C>T	p.Ser1832Leu	p.S1832L	ENST00000373644	NM_030625.2	1832	tCg/tTg	12/12	1	2	FACETS	0.938	0.88	0.997	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		411	615	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451288	70451288	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771754741	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	109	635	0	ENST00000373644.4:c.6128G>A	p.Arg2043His	p.R2043H	ENST00000373644	NM_030625.2	2043	cGc/cAc	12/12	1	2	FACETS	0.764	0.687	0.846	0.764	0.687	0.846	SUBCLONAL	1	TRUE	1	0.393438475539559	2		635	725	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653826	89653826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	98	250	0	ENST00000371953.3:c.124C>T	p.Leu42Phe	p.L42F	ENST00000371953	NM_000314.4	42	Ctt/Ttt	2/9	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.393438475539559	2		250	339	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690808	89690808	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	42	145	0	ENST00000371953.3:c.215C>T	p.Ala72Val	p.A72V	ENST00000371953	NM_000314.4	72	gCt/gTt	4/9	1	2	FACETS	0.768	0.645	0.903	0.768	0.645	0.903	CLONAL	1	TRUE	1	0.393438475539559	2		145	278	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309753	104309753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	228	577	0	ENST00000369902.3:c.344G>A	p.Gly115Asp	p.G115D	ENST00000369902	NM_016169.3	115	gGt/gAt	3/12	1	2	FACETS	0.878	0.823	0.934	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		577	660	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724197	112724197	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	58	290	0	ENST00000369452.4:c.81G>T	p.Glu27Asp	p.E27D	ENST00000369452	NM_007373.3	27	gaG/gaT	2/9	1	2	FACETS	0.679	0.585	0.782	0.679	0.585	0.782	SUBCLONAL	1	TRUE	1	0.393438475539559	2		290	434	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769038	112769038	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	57	283	0	ENST00000369452.4:c.1317G>T	p.Lys439Asn	p.K439N	ENST00000369452	NM_007373.3	439	aaG/aaT	7/9	1	2	FACETS	0.765	0.659	0.879	0.765	0.659	0.879	SUBCLONAL	1	TRUE	1	0.393438475539559	2		283	379	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129448	64129448	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	294	875	0	ENST00000334205.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000334205	NM_003942.2	294	Gaa/Taa	8/17	1	2	FACETS	0.96	0.908	1	1	0.996	1	CLONAL	2	TRUE	1	0.393438475539559	2		875	778	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138755	64138755	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	211	600	0	ENST00000334205.4:c.2122G>A	p.Ala708Thr	p.A708T	ENST00000334205	NM_003942.2	708	Gca/Aca	17/17	1	2	FACETS	0.847	0.791	0.904	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	2		600	633	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572059	64572059	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1085307502	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	290	783	0	ENST00000312049.6:c.1580G>A	p.Arg527Gln	p.R527Q	ENST00000312049	NM_130799.2	527	cGa/cAa	10/10	1	2	FACETS	0.814	0.768	0.862	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		783	905	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198846	67198846	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	148	376	0	ENST00000312629.5:c.317T>G	p.Ile106Ser	p.I106S	ENST00000312629	NM_003952.2	106	aTt/aGt	5/15	1	2	FACETS	0.787	0.724	0.852	1	0.989	1	SUBCLONAL	2	TRUE	1	0.393438475539559	2		376	478	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514089	69514089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	277	677	0	ENST00000294312.3:c.592G>A	p.Asp198Asn	p.D198N	ENST00000294312	NM_005117.2	198	Gac/Aac	3/3	1	2	FACETS	0.949	0.896	1	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		677	742	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588124	69588124	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	91	615	0	ENST00000168712.1:c.574C>T	p.Arg192Ter	p.R192*	ENST00000168712	NM_002007.2	192	Cga/Tga	3/3	1	2	FACETS	0.724	0.643	0.81	0.724	0.643	0.81	SUBCLONAL	1	TRUE	1	0.393438475539559	2		615	639	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942153	71942153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	262	823	1	ENST00000298229.2:c.1417G>A	p.Glu473Lys	p.E473K	ENST00000298229	NM_001567.3	473	Gag/Aag	12/28	1	2	FACETS	0.822	0.773	0.872	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		824	810	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944182	71944182	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	119	650	0	ENST00000298229.2:c.2015C>A	p.Ala672Asp	p.A672D	ENST00000298229	NM_001567.3	672	gCc/gAc	17/28	1	2	FACETS	0.858	0.775	0.945	0.858	0.775	0.945	CLONAL	1	TRUE	1	0.393438475539559	2		650	705	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122736	108122736	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	124	309	0	ENST00000278616.4:c.1780G>T	p.Glu594Ter	p.E594*	ENST00000278616	NM_000051.3	594	Gaa/Taa	11/63	1	2	FACETS	0.792	0.723	0.863	1	0.987	1	SUBCLONAL	2	TRUE	1	0.393438475539559	2		309	398	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198378	108198378	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769606850	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	120	324	0	ENST00000278616.4:c.6982C>T	p.Pro2328Ser	p.P2328S	ENST00000278616	NM_000051.3	2328	Ccc/Tcc	48/63	1	2	FACETS	0.889	0.813	0.968	1	0.989	1	CLONAL	2	TRUE	1	0.393438475539559	2		324	343	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200960	108200960	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434220	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	159	311	0	ENST00000278616.4:c.7327C>T	p.Arg2443Ter	p.R2443*	ENST00000278616	NM_000051.3	2443	Cga/Tga	50/63	1	2	FACETS	0.91	0.842	0.979	1	0.992	1	CLONAL	2	TRUE	1	0.393438475539559	2		311	444	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203496	108203496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	83	167	0	ENST00000278616.4:c.7796C>T	p.Thr2599Ile	p.T2599I	ENST00000278616	NM_000051.3	2599	aCa/aTa	53/63	1	2	FACETS	0.84	0.753	0.931	1	0.983	1	CLONAL	2	TRUE	1	0.393438475539559	2		167	251	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205708	108205708	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	21	222	0	ENST00000278616.4:c.8023G>A	p.Gly2675Arg	p.G2675R	ENST00000278616	NM_000051.3	2675	Gga/Aga	55/63	1	2	FACETS	0.434	0.335	0.549	0.434	0.335	0.549	SUBCLONAL	1	TRUE	1	0.393438475539559	2		222	246	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111959736	111959736	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1555187083	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	278	628	0	ENST00000375549.3:c.314+1G>A		p.X105_splice	ENST00000375549	NM_003002.3	105			1	2	FACETS	0.821	0.773	0.869	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		628	861	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343271	118343271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	113	321	0	ENST00000534358.1:c.1397C>T	p.Ser466Phe	p.S466F	ENST00000534358	NM_005933.3	466	tCt/tTt	3/36	1	2	FACETS	0.898	0.818	0.979	1	0.988	1	CLONAL	2	TRUE	1	0.393438475539559	2		321	320	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374526	118374526	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	80	333	0	ENST00000534358.1:c.7919T>G	p.Val2640Gly	p.V2640G	ENST00000534358	NM_005933.3	2640	gTa/gGa	27/36	1	2	FACETS	0.975	0.863	1	0.975	0.863	1	CLONAL	1	TRUE	1	0.393438475539559	2		333	417	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376958	118376958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139366882	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	138	388	1	ENST00000534358.1:c.10351G>A	p.Glu3451Lys	p.E3451K	ENST00000534358	NM_005933.3	3451	Gaa/Aaa	27/36	1	2	FACETS	0.928	0.854	1	1	0.991	1	CLONAL	2	TRUE	1	0.393438475539559	2		389	378	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503100	125503100	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3731410	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	114	248	0	ENST00000428830.2:c.467G>A	p.Arg156Gln	p.R156Q	ENST00000428830	NM_001114121.2	156	cGg/cAg	6/14	1	2	FACETS	0.823	0.749	0.899	1	0.987	1	CLONAL	2	TRUE	1	0.393438475539559	2		248	352	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416756	416756	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	139	311	0	ENST00000399788.2:c.3794C>T	p.Ala1265Val	p.A1265V	ENST00000399788	NM_001042603.1	1265	gCc/gTc	23/28	1	2	FACETS	0.901	0.829	0.975	1	0.991	1	CLONAL	2	TRUE	1	0.393438475539559	2		311	392	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420097	420097	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	217	521	1	ENST00000399788.2:c.3170C>T	p.Thr1057Ile	p.T1057I	ENST00000399788	NM_001042603.1	1057	aCt/aTt	21/28	1	2	FACETS	0.877	0.82	0.935	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		522	629	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025614	1025614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200657132	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	225	670	2	ENST00000358495.3:c.761C>T	p.Thr254Met	p.T254M	ENST00000358495	NM_134424.2	254	aCg/aTg	9/12	1	2	FACETS	0.831	0.778	0.886	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	2		672	688	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1040396	1040396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	225	547	2	ENST00000358495.3:c.176G>A	p.Gly59Glu	p.G59E	ENST00000358495	NM_134424.2	59	gGa/gAa	3/12	1	2	FACETS	0.921	0.863	0.98	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		549	621	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992114	11992114	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs202004830	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	60	388	0	ENST00000396373.4:c.204G>T	p.Gln68His	p.Q68H	ENST00000396373	NM_001987.4	68	caG/caT	3/8	NA	2	FACETS	0.639	0.552	0.734			1	INDETERMINATE	1	TRUE	NA	0.393438475539559	2		388	477	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871007	12871007	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	140	389	0	ENST00000228872.4:c.234G>T	p.Glu78Asp	p.E78D	ENST00000228872	NM_004064.3	78	gaG/gaT	1/3	NA	2	FACETS	0.936	0.863	1			1	INDETERMINATE	2	TRUE	NA	0.393438475539559	2		389	380	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624582	21624582	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	151	325	0	ENST00000421138.2:c.1448-1G>T		p.X483_splice	ENST00000421138		483			1	2	FACETS	0.842	0.776	0.909	1	0.991	1	CLONAL	2	TRUE	1	0.393438475539559	2		325	456	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21626571	21626571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776939203	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	126	280	0	ENST00000421138.2:c.1361G>A	p.Arg454His	p.R454H	ENST00000421138		454	cGt/cAt	13/16	1	2	FACETS	0.887	0.813	0.964	1	0.989	1	CLONAL	2	TRUE	1	0.393438475539559	2		280	361	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628410	21628410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	110	338	0	ENST00000421138.2:c.1208G>A	p.Gly403Glu	p.G403E	ENST00000421138		403	gGa/gAa	11/16	1	2	FACETS	0.818	0.743	0.895	1	0.987	1	CLONAL	2	TRUE	1	0.393438475539559	2		338	342	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644468	21644468	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754016839	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	24	384	1	ENST00000421138.2:c.199G>A	p.Ala67Thr	p.A67T	ENST00000421138		67	Gct/Act	4/16	1	2	FACETS	0.274	0.214	0.343	0.274	0.214	0.343	SUBCLONAL	1	TRUE	1	0.393438475539559	2		385	445	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420229	49420229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	125	679	2	ENST00000301067.7:c.15520C>T	p.Arg5174Trp	p.R5174W	ENST00000301067	NM_003482.3	5174	Cgg/Tgg	48/54	1	2	FACETS	0.858	0.777	0.942	0.858	0.777	0.942	CLONAL	1	TRUE	1	0.393438475539559	2		681	741	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420454	49420454	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	96	701	0	ENST00000301067.7:c.15295G>T	p.Gly5099Cys	p.G5099C	ENST00000301067	NM_003482.3	5099	Ggt/Tgt	48/54	1	2	FACETS	0.722	0.644	0.805	0.722	0.644	0.805	SUBCLONAL	1	TRUE	1	0.393438475539559	2		701	676	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420456	49420456	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	218	704	0	ENST00000301067.7:c.15293C>A	p.Thr5098Asn	p.T5098N	ENST00000301067	NM_003482.3	5098	aCt/aAt	48/54	1	2	FACETS	0.814	0.76	0.868	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	2		704	681	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420460	49420460	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	237	693	1	ENST00000301067.7:c.15289C>T	p.Arg5097Ter	p.R5097*	ENST00000301067	NM_003482.3	5097	Cga/Tga	48/54	1	2	FACETS	0.883	0.829	0.939	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		694	682	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422957	49422957	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	117	745	0	ENST00000301067.7:c.14138G>A	p.Ser4713Asn	p.S4713N	ENST00000301067	NM_003482.3	4713	aGc/aAc	44/54	1	2	FACETS	0.825	0.744	0.91	0.825	0.744	0.91	CLONAL	1	TRUE	1	0.393438475539559	2		745	721	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424710	49424710	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	120	668	0	ENST00000301067.7:c.13637G>T	p.Arg4546Met	p.R4546M	ENST00000301067	NM_003482.3	4546	aGg/aTg	40/54	1	2	FACETS	0.88	0.796	0.969	0.88	0.796	0.969	CLONAL	1	TRUE	1	0.393438475539559	2		668	693	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425037	49425037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1480605988	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	140	758	0	ENST00000301067.7:c.13451G>A	p.Arg4484Gln	p.R4484Q	ENST00000301067	NM_003482.3	4484	cGa/cAa	39/54	1	2	FACETS	0.823	0.749	0.9	0.823	0.749	0.9	CLONAL	1	TRUE	1	0.393438475539559	2		758	865	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425456	49425456	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs398123716	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	136	866	2	ENST00000301067.7:c.13032del	p.Lys4345AsnfsTer39	p.K4345Nfs*39	ENST00000301067	NM_003482.3	4344	ccC/cc	39/54	1	2	FACETS	0.883	0.803	0.966	0.883	0.803	0.966	CLONAL	1	TRUE	1	0.393438475539559	2		868	783	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431919	49431919	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	268	749	0	ENST00000301067.7:c.9220G>T	p.Glu3074Ter	p.E3074*	ENST00000301067	NM_003482.3	3074	Gaa/Taa	34/54	1	2	FACETS	0.899	0.847	0.952	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		749	758	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431950	49431950	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	117	724	0	ENST00000301067.7:c.9189G>T	p.Lys3063Asn	p.K3063N	ENST00000301067	NM_003482.3	3063	aaG/aaT	34/54	1	2	FACETS	0.81	0.731	0.894	0.81	0.731	0.894	CLONAL	1	TRUE	1	0.393438475539559	2		724	734	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432129	49432129	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	106	727	1	ENST00000301067.7:c.9010G>T	p.Glu3004Ter	p.E3004*	ENST00000301067	NM_003482.3	3004	Gag/Tag	34/54	1	2	FACETS	0.735	0.659	0.816	0.735	0.659	0.816	SUBCLONAL	1	TRUE	1	0.393438475539559	2		728	733	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434485	49434485	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	86	874	0	ENST00000301067.7:c.7068G>T	p.Gln2356His	p.Q2356H	ENST00000301067	NM_003482.3	2356	caG/caT	31/54	1	2	FACETS	0.566	0.5	0.636	0.566	0.5	0.636	SUBCLONAL	1	TRUE	1	0.393438475539559	2		874	773	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	235	732	8	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.851	0.798	0.905	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		740	702	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445403	49445403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368472158	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	262	881	1	ENST00000301067.7:c.2063G>A	p.Arg688His	p.R688H	ENST00000301067	NM_003482.3	688	cGc/cAc	10/54	1	2	FACETS	0.825	0.776	0.876	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		882	807	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445712	49445712	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	296	883	2	ENST00000301067.7:c.1754C>A	p.Pro585His	p.P585H	ENST00000301067	NM_003482.3	585	cCt/cAt	10/54	1	2	FACETS	0.82	0.773	0.867	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		885	918	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484292	50484292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746406610	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	247	549	0	ENST00000394963.4:c.1052G>A	p.Arg351His	p.R351H	ENST00000394963	NM_003076.4	351	cGt/cAt	9/13	1	2	FACETS	0.888	0.834	0.943	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		549	707	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486584	56486584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs570637025	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	248	581	1	ENST00000267101.3:c.1163G>A	p.Arg388Gln	p.R388Q	ENST00000267101	NM_001982.3	388	cGg/cAg	10/28	1	2	FACETS	0.873	0.82	0.927	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		582	722	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858561	57858561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763470494	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	226	687	3	ENST00000228682.2:c.299G>A	p.Arg100His	p.R100H	ENST00000228682	NM_005269.2	100	cGc/cAc	4/12	1	2	FACETS	0.85	0.796	0.905	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		690	676	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860053	57860053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200444628	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	278	732	1	ENST00000228682.2:c.793C>T	p.Arg265Trp	p.R265W	ENST00000228682	NM_005269.2	265	Cgg/Tgg	8/12	1	2	FACETS	0.809	0.762	0.858	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		733	873	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111886044	111886044	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769682050	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	203	559	0	ENST00000341259.2:c.1666G>A	p.Glu556Lys	p.E556K	ENST00000341259	NM_005475.2	556	Gaa/Aaa	8/8	1	2	FACETS	0.768	0.715	0.822	1	0.992	1	SUBCLONAL	2	TRUE	1	0.393438475539559	2		559	672	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109824	115109824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	255	707	1	ENST00000257566.3:c.2054C>T	p.Ala685Val	p.A685V	ENST00000257566	NM_016569.3	685	gCa/gTa	8/8	1	2	FACETS	0.91	0.857	0.965	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		708	712	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109963	115109963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	288	758	0	ENST00000257566.3:c.1915C>T	p.Arg639Cys	p.R639C	ENST00000257566	NM_016569.3	639	Cgc/Tgc	8/8	1	2	FACETS	0.899	0.849	0.95	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		758	814	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117443	115117443	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	126	338	0	ENST00000257566.3:c.731C>T	p.Ser244Phe	p.S244F	ENST00000257566	NM_016569.3	244	tCc/tTc	4/8	1	2	FACETS	0.89	0.815	0.966	1	0.99	1	CLONAL	2	TRUE	1	0.393438475539559	2		338	360	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120651	115120651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	273	702	2	ENST00000257566.3:c.355C>T	p.Arg119Trp	p.R119W	ENST00000257566	NM_016569.3	119	Cgg/Tgg	1/8	1	2	FACETS	0.813	0.766	0.862	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		704	853	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120795649	120795649	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	112	398	0	ENST00000257552.2:c.504A>C	p.Glu168Asp	p.E168D	ENST00000257552	NM_002442.3	168	gaA/gaC	8/15	1	2	FACETS	0.987	0.89	1	0.987	0.89	1	CLONAL	1	TRUE	1	0.393438475539559	2		398	577	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437163	121437163	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1421619915	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	359	938	0	ENST00000257555.6:c.1594G>A	p.Ala532Thr	p.A532T	ENST00000257555		532	Gcc/Acc	8/10	1	2	FACETS	0.973	0.925	1	1	0.996	1	CLONAL	2	TRUE	1	0.393438475539559	2		938	938	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202250	133202250	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	253	734	0	ENST00000320574.5:c.6638C>T	p.Ala2213Val	p.A2213V	ENST00000320574	NM_006231.2	2213	gCc/gTc	47/49	1	2	FACETS	0.87	0.818	0.923	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		734	739	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209381	133209381	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1247397969	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	253	591	2	ENST00000320574.5:c.6005C>T	p.Ala2002Val	p.A2002V	ENST00000320574	NM_006231.2	2002	gCg/gTg	44/49	1	2	FACETS	0.977	0.92	1	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		593	658	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219153	133219153	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs565413729	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	267	746	1	ENST00000320574.5:c.4891C>T	p.Arg1631Cys	p.R1631C	ENST00000320574	NM_006231.2	1631	Cgc/Tgc	37/49	1	2	FACETS	0.884	0.832	0.936	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		747	768	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235965	133235965	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	68	633	0	ENST00000320574.5:c.3191T>C	p.Leu1064Pro	p.L1064P	ENST00000320574	NM_006231.2	1064	cTg/cCg	26/49	1	2	FACETS	0.538	0.468	0.614	0.538	0.468	0.614	SUBCLONAL	1	TRUE	1	0.393438475539559	2		633	642	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	179	535	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	0.854	0.793	0.916	1	0.992	1	CLONAL	2	TRUE	1	0.393438475539559	2		535	533	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257827	133257827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747005851	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	93	425	0	ENST00000320574.5:c.101G>A	p.Arg34His	p.R34H	ENST00000320574	NM_006231.2	34	cGc/cAc	2/49	1	2	FACETS	0.963	0.86	1	0.963	0.86	1	CLONAL	1	TRUE	1	0.393438475539559	2		425	491	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592645	28592645	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs770772264	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	175	419	0	ENST00000241453.7:c.2500C>T	p.Arg834Ter	p.R834*	ENST00000241453	NM_004119.2	834	Cga/Tga	20/24	1	2	FACETS	0.904	0.84	0.97	1	0.992	1	CLONAL	2	TRUE	1	0.393438475539559	2		419	492	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895602	28895602	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	79	311	0	ENST00000282397.4:c.3172G>A	p.Asp1058Asn	p.D1058N	ENST00000282397	NM_002019.4	1058	Gat/Aat	23/30	1	2	FACETS	0.93	0.821	1	0.93	0.821	1	CLONAL	1	TRUE	1	0.393438475539559	2		311	432	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041668	29041668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767792497	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	171	444	0	ENST00000282397.4:c.151C>T	p.Leu51Phe	p.L51F	ENST00000282397	NM_002019.4	51	Ctc/Ttc	2/30	1	2	FACETS	0.882	0.818	0.947	1	0.992	1	CLONAL	2	TRUE	1	0.393438475539559	2		444	493	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906789	32906789	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	150	538	0	ENST00000380152.3:c.1174G>A	p.Ala392Thr	p.A392T	ENST00000380152		392	Gcc/Acc	10/27	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.393438475539559	2		538	559	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913299	32913299	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	161	376	0	ENST00000380152.3:c.4807A>C	p.Asn1603His	p.N1603H	ENST00000380152		1603	Aac/Cac	11/27	1	2	FACETS	0.874	0.809	0.941	1	0.991	1	CLONAL	2	TRUE	1	0.393438475539559	2		376	468	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914212	32914212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555284376	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	136	340	1	ENST00000380152.3:c.5720C>T	p.Ser1907Phe	p.S1907F	ENST00000380152		1907	tCt/tTt	11/27	1	2	FACETS	0.817	0.75	0.887	1	0.989	1	CLONAL	2	TRUE	1	0.393438475539559	2		341	423	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914379	32914379	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	98	363	0	ENST00000380152.3:c.5887G>T	p.Gly1963Trp	p.G1963W	ENST00000380152		1963	Ggg/Tgg	11/27	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.393438475539559	2		363	461	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915177	32915177	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs730881548	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	39	338	0	ENST00000380152.3:c.6685G>T	p.Glu2229Ter	p.E2229*	ENST00000380152		2229	Gaa/Taa	11/27	1	2	FACETS	0.406	0.336	0.484	0.406	0.336	0.484	SUBCLONAL	1	TRUE	1	0.393438475539559	2		338	488	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936757	32936757	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	149	342	0	ENST00000380152.3:c.7903G>T	p.Glu2635Ter	p.E2635*	ENST00000380152		2635	Gaa/Taa	17/27	1	2	FACETS	0.964	0.891	1	1	0.992	1	CLONAL	2	TRUE	1	0.393438475539559	2		342	393	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030339	49030339	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	75	200	0	ENST00000267163.4:c.1815-1G>T		p.X605_splice	ENST00000267163	NM_000321.2	605			1	2	FACETS	0.832	0.741	0.927	1	0.981	1	CLONAL	2	TRUE	1	0.393438475539559	2		200	229	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281066	49281066	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs924137042	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	115	533	2	ENST00000282018.3:c.113G>T	p.Arg38Ile	p.R38I	ENST00000282018	NM_020377.2	38	aGa/aTa	1/1	1	2	FACETS	0.921	0.831	1	0.921	0.831	1	CLONAL	1	TRUE	1	0.393438475539559	2		535	635	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514527	103514527	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	114	244	0	ENST00000355739.4:c.1028G>T	p.Arg343Ile	p.R343I	ENST00000355739	NM_000123.3	343	aGa/aTa	8/15	1	2	FACETS	0.914	0.834	0.996	1	0.989	1	CLONAL	2	TRUE	1	0.393438475539559	2		244	317	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514814	103514814	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	136	338	0	ENST00000355739.4:c.1315G>T	p.Gly439Ter	p.G439*	ENST00000355739	NM_000123.3	439	Gga/Tga	8/15	1	2	FACETS	0.934	0.86	1	1	0.991	1	CLONAL	2	TRUE	1	0.393438475539559	2		338	370	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435832	110435832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	201	579	0	ENST00000375856.3:c.2569G>A	p.Gly857Ser	p.G857S	ENST00000375856	NM_003749.2	857	Ggc/Agc	1/2	1	2	FACETS	0.893	0.834	0.954	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	2		579	572	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093381	30093381	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1469866177	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	157	362	0	ENST00000331968.5:c.1882C>T	p.Arg628Cys	p.R628C	ENST00000331968	NM_002742.2	628	Cgt/Tgt	13/18	1	2	FACETS	0.913	0.845	0.983	1	0.992	1	CLONAL	2	TRUE	1	0.393438475539559	2		362	437	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194766	30194766	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370180862	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	89	492	0	ENST00000331968.5:c.379G>A	p.Asp127Asn	p.D127N	ENST00000331968	NM_002742.2	127	Gat/Aat	2/18	1	2	FACETS	0.749	0.665	0.839	0.749	0.665	0.839	SUBCLONAL	1	TRUE	1	0.393438475539559	2		492	604	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396613	30396613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	97	230	0	ENST00000331968.5:c.106G>A	p.Ala36Thr	p.A36T	ENST00000331968	NM_002742.2	36	Gcg/Acg	1/18	1	2	FACETS	0.971	0.88	1	1	0.988	1	CLONAL	2	TRUE	1	0.393438475539559	2		230	254	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543313	65543313	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	204	586	0	ENST00000358664.4:c.364C>T	p.Leu122Phe	p.L122F	ENST00000358664	NM_002382.4	122	Ctc/Ttc	5/5	1	2	FACETS	0.851	0.794	0.91	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	2		586	609	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569708	95569708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767166092	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	48	195	3	ENST00000393063.1:c.4025G>A	p.Arg1342His	p.R1342H	ENST00000393063	NM_030621.3	1342	cGc/cAc	22/28	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.393438475539559	2		198	188	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572376	95572376	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	113	319	0	ENST00000393063.1:c.2987+2T>C		p.X996_splice	ENST00000393063	NM_030621.3	996			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.393438475539559	2		319	391	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582957	95582957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	62	245	0	ENST00000393063.1:c.1585C>T	p.Pro529Ser	p.P529S	ENST00000393063	NM_030621.3	529	Cca/Tca	11/28	1	2	FACETS	0.832	0.722	0.95	0.832	0.722	0.95	CLONAL	1	TRUE	1	0.393438475539559	2		245	379	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105238762	105238762	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	108	802	0	ENST00000349310.3:c.1200G>T	p.Lys400Asn	p.K400N	ENST00000349310	NM_001014432.1	400	aaG/aaT	13/15	1	2	FACETS	0.71	0.637	0.788	0.71	0.637	0.788	SUBCLONAL	1	TRUE	1	0.393438475539559	2		802	773	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239288	105239288	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762705090	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	263	743	1	ENST00000349310.3:c.1099C>T	p.Arg367Cys	p.R367C	ENST00000349310	NM_001014432.1	367	Cgc/Tgc	12/15	1	2	FACETS	0.944	0.89	0.999	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		744	708	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241439	105241439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	68	687	0	ENST00000349310.3:c.541C>T	p.Leu181Phe	p.L181F	ENST00000349310	NM_001014432.1	181	Ctc/Ttc	7/15	1	2	FACETS	0.5	0.435	0.571	0.5	0.435	0.571	SUBCLONAL	1	TRUE	1	0.393438475539559	2		687	691	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40685763	40685763	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777913445	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	129	364	0	ENST00000249776.8:c.916G>A	p.Ala306Thr	p.A306T	ENST00000249776	NM_033286.3	306	Gcc/Acc	9/9	1	2	FACETS	0.786	0.719	0.856	1	0.988	1	SUBCLONAL	2	TRUE	1	0.393438475539559	2		364	417	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028768	42028768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	173	550	0	ENST00000219905.7:c.4306G>A	p.Ala1436Thr	p.A1436T	ENST00000219905	NM_001164273.1	1436	Gcc/Acc	13/24	1	2	FACETS	0.852	0.79	0.916	1	0.992	1	CLONAL	2	TRUE	1	0.393438475539559	2		550	516	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040864	42040864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	149	416	0	ENST00000219905.7:c.5242C>T	p.Pro1748Ser	p.P1748S	ENST00000219905	NM_001164273.1	1748	Cca/Tca	16/24	1	2	FACETS	0.816	0.752	0.882	1	0.99	1	CLONAL	2	TRUE	1	0.393438475539559	2		416	464	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041551	42041551	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	213	532	0	ENST00000219905.7:c.5746A>C	p.Thr1916Pro	p.T1916P	ENST00000219905	NM_001164273.1	1916	Aca/Cca	17/24	1	2	FACETS	0.838	0.783	0.894	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	2		532	646	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041696	42041696	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	170	433	1	ENST00000219905.7:c.5891C>A	p.Ala1964Asp	p.A1964D	ENST00000219905	NM_001164273.1	1964	gCt/gAt	17/24	1	2	FACETS	0.95	0.882	1	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	2		434	455	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054006	42054006	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	121	318	0	ENST00000219905.7:c.7468C>T	p.Arg2490Ter	p.R2490*	ENST00000219905	NM_001164273.1	2490	Cga/Tga	21/24	1	2	FACETS	0.836	0.763	0.911	1	0.988	1	CLONAL	2	TRUE	1	0.393438475539559	2		318	368	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712512	43712512	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	201	532	0	ENST00000382044.4:c.4672T>G	p.Phe1558Val	p.F1558V	ENST00000382044	NM_001141980.1	1558	Ttc/Gtc	21/28	1	2	FACETS	0.772	0.718	0.826	1	0.992	1	SUBCLONAL	2	TRUE	1	0.393438475539559	2		532	662	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714099	43714099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139105949	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	268	720	1	ENST00000382044.4:c.4054G>A	p.Ala1352Thr	p.A1352T	ENST00000382044	NM_001141980.1	1352	Gca/Aca	19/28	1	2	FACETS	0.894	0.842	0.947	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		721	762	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994914	73994914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	47	171	0	ENST00000318443.5:c.398C>T	p.Ala133Val	p.A133V	ENST00000318443	NM_001024736.1	133	gCc/gTc	3/10	1	2	FACETS	0.885	0.765	1	1	0.973	1	CLONAL	2	TRUE	1	0.393438475539559	2		171	135	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996745	73996745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1320648606	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	89	291	0	ENST00000318443.5:c.1301G>A	p.Gly434Asp	p.G434D	ENST00000318443	NM_001024736.1	434	gGc/gAc	6/10	1	2	FACETS	0.788	0.708	0.872	1	0.983	1	SUBCLONAL	2	TRUE	1	0.393438475539559	2		291	287	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631980	90631980	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	189	415	1	ENST00000330062.3:c.374-1G>T		p.X125_splice	ENST00000330062	NM_002168.2	125			1	2	FACETS	0.926	0.863	0.99	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	2		416	519	SUCCESS
BLM	641	MSKCC	GRCh37	15	91352442	91352442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760554566	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	57	351	0	ENST00000355112.3:c.3827C>T	p.Ala1276Val	p.A1276V	ENST00000355112	NM_000057.2	1276	gCg/gTg	20/22	1	2	FACETS	0.703	0.605	0.81	0.703	0.605	0.81	SUBCLONAL	1	TRUE	1	0.393438475539559	2		351	412	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396245	396245	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	56	704	2	ENST00000262320.3:c.781G>A	p.Ala261Thr	p.A261T	ENST00000262320	NM_003502.3	261	Gct/Act	2/11	1	2	FACETS	0.402	0.343	0.465	0.402	0.343	0.465	SUBCLONAL	1	TRUE	1	0.393438475539559	2		706	709	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094723	2094723	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs374489979	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	355	914	3	ENST00000219066.1:c.457C>T	p.Arg153Ter	p.R153*	ENST00000219066	NM_002528.5	153	Cga/Tga	3/6	1	2	FACETS	0.854	0.81	0.898	1	0.996	1	CLONAL	2	TRUE	1	0.393438475539559	2		917	1057	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098696	2098696	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	225	595	0	ENST00000219476.3:c.80A>C	p.Asn27Thr	p.N27T	ENST00000219476	NM_000548.3	27	aAt/aCt	2/42	1	2	FACETS	0.81	0.758	0.864	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	2		595	706	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122964	2122964	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	230	651	0	ENST00000219476.3:c.2335T>C	p.Tyr779His	p.Y779H	ENST00000219476	NM_000548.3	779	Tac/Cac	21/42	1	2	FACETS	0.875	0.82	0.931	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		651	668	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134310	2134310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751203255	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	270	1013	0	ENST00000219476.3:c.4087G>A	p.Val1363Ile	p.V1363I	ENST00000219476	NM_000548.3	1363	Gtc/Atc	34/42	1	2	FACETS	0.881	0.83	0.933	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		1013	779	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135027	2135027	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	110	721	0	ENST00000219476.3:c.4569G>T	p.Glu1523Asp	p.E1523D	ENST00000219476	NM_000548.3	1523	gaG/gaT	35/42	1	2	FACETS	0.828	0.745	0.916	0.828	0.745	0.916	CLONAL	1	TRUE	1	0.393438475539559	2		721	675	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138534	2138534	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777166275	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	294	779	0	ENST00000219476.3:c.5347G>A	p.Glu1783Lys	p.E1783K	ENST00000219476	NM_000548.3	1783	Gag/Aag	42/42	1	2	FACETS	0.909	0.859	0.96	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		779	822	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222243	2222243	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753021184	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	287	773	0	ENST00000326181.6:c.527C>T	p.Ala176Val	p.A176V	ENST00000326181	NM_032271.2	176	gCg/gTg	8/21	1	2	FACETS	0.945	0.893	0.998	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		773	772	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639977	3639977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3827530	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	273	704	3	ENST00000294008.3:c.3662C>T	p.Ala1221Val	p.A1221V	ENST00000294008	NM_032444.2	1221	gCg/gTg	12/15	1	2	FACETS	0.969	0.915	1	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		707	716	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641150	3641150	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757069261	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	117	825	4	ENST00000294008.3:c.2489C>T	p.Ala830Val	p.A830V	ENST00000294008	NM_032444.2	830	gCg/gTg	12/15	1	2	FACETS	0.598	0.538	0.662	0.598	0.538	0.662	SUBCLONAL	1	TRUE	1	0.393438475539559	2		829	994	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641177	3641177	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	331	845	0	ENST00000294008.3:c.2462C>T	p.Ser821Leu	p.S821L	ENST00000294008	NM_032444.2	821	tCa/tTa	12/15	1	2	FACETS	0.871	0.825	0.917	1	0.996	1	CLONAL	2	TRUE	1	0.393438475539559	2		845	966	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778911	3778911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753688167	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	178	630	3	ENST00000262367.5:c.6137C>T	p.Ala2046Val	p.A2046V	ENST00000262367	NM_004380.2	2046	gCg/gTg	31/31	1	2	FACETS	0.754	0.699	0.811	1	0.99	1	SUBCLONAL	2	TRUE	1	0.393438475539559	2		633	600	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781375	3781375	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	267	744	1	ENST00000262367.5:c.4990C>T	p.Arg1664Cys	p.R1664C	ENST00000262367	NM_004380.2	1664	Cgc/Tgc	30/31	1	2	FACETS	0.9	0.848	0.953	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		745	754	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788630	3788630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	93	386	0	ENST00000262367.5:c.4324C>T	p.Pro1442Ser	p.P1442S	ENST00000262367	NM_004380.2	1442	Cca/Tca	26/31	1	2	FACETS	0.897	0.8	1	0.897	0.8	1	CLONAL	1	TRUE	1	0.393438475539559	2		386	527	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820662	3820662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	305	851	0	ENST00000262367.5:c.2789C>A	p.Pro930His	p.P930H	ENST00000262367	NM_004380.2	930	cCt/cAt	14/31	1	2	FACETS	0.844	0.798	0.892	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		851	918	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828768	3828768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	231	571	2	ENST00000262367.5:c.1874G>A	p.Arg625His	p.R625H	ENST00000262367	NM_004380.2	625	cGc/cAc	9/31	1	2	FACETS	0.884	0.829	0.941	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		573	664	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842041	3842041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	157	410	1	ENST00000262367.5:c.1271G>A	p.Arg424Gln	p.R424Q	ENST00000262367	NM_004380.2	424	cGa/cAa	5/31	1	2	FACETS	0.854	0.789	0.921	1	0.991	1	CLONAL	2	TRUE	1	0.393438475539559	2		411	467	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862811	9862811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	211	664	0	ENST00000330684.3:c.2492G>A	p.Ser831Asn	p.S831N	ENST00000330684	NM_001134407.1	831	aGc/aAc	12/13	1	2	FACETS	0.772	0.72	0.825	1	0.992	1	SUBCLONAL	2	TRUE	1	0.393438475539559	2		664	695	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020454	14020454	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764093404	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	122	334	0	ENST00000311895.7:c.425C>A	p.Ser142Tyr	p.S142Y	ENST00000311895	NM_005236.2	142	tCt/tAt	3/11	1	2	FACETS	0.805	0.735	0.878	1	0.988	1	CLONAL	2	TRUE	1	0.393438475539559	2		334	385	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041927	14041927	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765253522	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	84	330	1	ENST00000311895.7:c.2474C>T	p.Ala825Val	p.A825V	ENST00000311895	NM_005236.2	825	gCg/gTg	11/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.393438475539559	2		331	382	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646516	23646516	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs772691867	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	92	436	0	ENST00000261584.4:c.1351T>G	p.Leu451Val	p.L451V	ENST00000261584	NM_024675.3	451	Tta/Gta	4/13	1	2	FACETS	0.793	0.706	0.885	0.793	0.706	0.885	SUBCLONAL	1	TRUE	1	0.393438475539559	2		436	590	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785524	50785524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201836260	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	76	430	0	ENST00000398568.2:c.514C>T	p.Arg172Cys	p.R172C	ENST00000398568	NM_001042412.1	172	Cgt/Tgt	4/18	1	2	FACETS	0.726	0.638	0.821	0.726	0.638	0.821	SUBCLONAL	1	TRUE	1	0.393438475539559	2		430	532	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828337	50828337	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	124	334	0	ENST00000398568.2:c.2675A>G	p.Asp892Gly	p.D892G	ENST00000398568	NM_001042412.1	892	gAt/gGt	17/18	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.393438475539559	2		334	423	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56832433	56832433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367699010	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	113	316	0	ENST00000308159.5:c.343G>A	p.Glu115Lys	p.E115K	ENST00000308159	NM_014669.4	115	Gaa/Aaa	4/22	1	2	FACETS	0.802	0.73	0.877	1	0.987	1	CLONAL	2	TRUE	1	0.393438475539559	2		316	358	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663331	67663331	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	73	315	0	ENST00000264010.4:c.1732G>A	p.Ala578Thr	p.A578T	ENST00000264010	NM_006565.3	578	Gct/Act	10/12	1	2	FACETS	0.845	0.742	0.956	0.845	0.742	0.956	CLONAL	1	TRUE	1	0.393438475539559	2		315	439	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845655	68845655	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749056300	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	212	624	2	ENST00000261769.5:c.901G>A	p.Ala301Thr	p.A301T	ENST00000261769	NM_004360.3	301	Gct/Act	7/16	1	2	FACETS	0.816	0.762	0.872	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	2		626	660	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855985	68855985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780759537	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	164	505	2	ENST00000261769.5:c.1793G>A	p.Arg598Gln	p.R598Q	ENST00000261769	NM_004360.3	598	cGa/cAa	12/16	1	2	FACETS	0.8	0.74	0.862	1	0.991	1	SUBCLONAL	2	TRUE	1	0.393438475539559	2		507	521	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830348	72830348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774246895	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	60	435	0	ENST00000268489.5:c.6233C>T	p.Pro2078Leu	p.P2078L	ENST00000268489	NM_006885.3	2078	cCg/cTg	9/10	1	2	FACETS	0.716	0.619	0.821	0.716	0.619	0.821	SUBCLONAL	1	TRUE	1	0.393438475539559	2		435	426	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831602	72831602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	215	572	1	ENST00000268489.5:c.4979G>A	p.Ser1660Asn	p.S1660N	ENST00000268489	NM_006885.3	1660	aGt/aAt	9/10	1	2	FACETS	0.88	0.823	0.938	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		573	621	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991865	72991865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374002759	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	271	678	1	ENST00000268489.5:c.2180G>A	p.Arg727His	p.R727H	ENST00000268489	NM_006885.3	727	cGc/cAc	2/10	1	2	FACETS	0.871	0.82	0.922	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		679	791	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993335	72993335	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773329700	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	152	779	0	ENST00000268489.5:c.710G>A	p.Arg237Gln	p.R237Q	ENST00000268489	NM_006885.3	237	cGa/cAa	2/10	1	2	FACETS	0.861	0.788	0.939	0.861	0.788	0.939	CLONAL	1	TRUE	1	0.393438475539559	2		779	897	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81927337	81927337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1164040767	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	357	711	0	ENST00000359376.3:c.1010G>A	p.Arg337Gln	p.R337Q	ENST00000359376	NM_002661.3	337	cGg/cAg	12/33	1	2	FACETS	0.99	0.941	1	1	0.996	1	CLONAL	2	TRUE	1	0.393438475539559	2		711	917	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965124	81965124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691537	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	180	530	0	ENST00000359376.3:c.2604C>A	p.Asn868Lys	p.N868K	ENST00000359376	NM_002661.3	868	aaC/aaA	25/33	1	2	FACETS	0.832	0.772	0.893	1	0.992	1	CLONAL	2	TRUE	1	0.393438475539559	2		530	550	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969848	81969848	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568724894	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	87	537	4	ENST00000359376.3:c.2917G>A	p.Asp973Asn	p.D973N	ENST00000359376	NM_002661.3	973	Gac/Aac	27/33	1	2	FACETS	0.729	0.646	0.817	0.729	0.646	0.817	SUBCLONAL	1	TRUE	1	0.393438475539559	2		541	607	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346783	89346783	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	157	505	0	ENST00000301030.4:c.6167A>G	p.Tyr2056Cys	p.Y2056C	ENST00000301030	NM_001256183.1	2056	tAc/tGc	9/13	1	2	FACETS	0.866	0.8	0.933	1	0.991	1	CLONAL	2	TRUE	1	0.393438475539559	2		505	461	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346871	89346871	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	64	375	0	ENST00000301030.4:c.6079C>A	p.Leu2027Met	p.L2027M	ENST00000301030	NM_001256183.1	2027	Ctg/Atg	9/13	1	2	FACETS	0.841	0.731	0.958	0.841	0.731	0.958	CLONAL	1	TRUE	1	0.393438475539559	2		375	387	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348010	89348010	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	168	812	0	ENST00000301030.4:c.4940C>A	p.Pro1647His	p.P1647H	ENST00000301030	NM_001256183.1	1647	cCt/cAt	9/13	1	2	FACETS	0.924	0.849	1	0.924	0.849	1	CLONAL	1	TRUE	1	0.393438475539559	2		812	924	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349114	89349114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1319132440	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	176	825	0	ENST00000301030.4:c.3836G>T	p.Ser1279Ile	p.S1279I	ENST00000301030	NM_001256183.1	1279	aGc/aTc	9/13	1	2	FACETS	0.902	0.83	0.976	0.902	0.83	0.976	CLONAL	1	TRUE	1	0.393438475539559	2		825	992	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349484	89349484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs964523960	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	279	646	1	ENST00000301030.4:c.3466C>T	p.Arg1156Trp	p.R1156W	ENST00000301030	NM_001256183.1	1156	Cgg/Tgg	9/13	1	2	FACETS	0.888	0.837	0.939	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		647	799	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351582	89351582	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	320	737	0	ENST00000301030.4:c.1368G>T	p.Lys456Asn	p.K456N	ENST00000301030	NM_001256183.1	456	aaG/aaT	9/13	1	2	FACETS	0.959	0.909	1	1	0.996	1	CLONAL	2	TRUE	1	0.393438475539559	2		737	848	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351829	89351829	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	145	707	0	ENST00000301030.4:c.1121A>C	p.Glu374Ala	p.E374A	ENST00000301030	NM_001256183.1	374	gAa/gCa	9/13	1	2	FACETS	0.774	0.706	0.846	0.774	0.706	0.846	SUBCLONAL	1	TRUE	1	0.393438475539559	2		707	952	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357496	89357496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1419112752	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	202	756	0	ENST00000301030.4:c.322G>A	p.Gly108Ser	p.G108S	ENST00000301030	NM_001256183.1	108	Ggc/Agc	5/13	1	2	FACETS	0.777	0.723	0.832	1	0.992	1	SUBCLONAL	2	TRUE	1	0.393438475539559	2		756	661	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89809275	89809275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs545742908	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	266	598	0	ENST00000389301.3:c.3698C>T	p.Ala1233Val	p.A1233V	ENST00000389301	NM_000135.2	1233	gCg/gTg	37/43	1	2	FACETS	0.842	0.792	0.893	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		598	803	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816307	89816307	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	156	473	1	ENST00000389301.3:c.3070A>C	p.Met1024Leu	p.M1024L	ENST00000389301	NM_000135.2	1024	Atg/Ctg	32/43	1	2	FACETS	0.806	0.744	0.87	1	0.99	1	CLONAL	2	TRUE	1	0.393438475539559	2		474	492	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849470	89849470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778045457	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	113	612	5	ENST00000389301.3:c.1511G>A	p.Arg504His	p.R504H	ENST00000389301	NM_000135.2	504	cGc/cAc	16/43	1	2	FACETS	0.801	0.721	0.885	0.801	0.721	0.885	CLONAL	1	TRUE	1	0.393438475539559	2		617	717	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216961	7216961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs920323510	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	222	510	0	ENST00000380728.2:c.560C>T	p.Ala187Val	p.A187V	ENST00000380728		187	gCc/gTc	7/11	1	2	FACETS	0.894	0.837	0.952	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		510	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576858	7576858	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	130	572	0	ENST00000269305.4:c.988C>A	p.Leu330Ile	p.L330I	ENST00000269305	NM_001126112.2	330	Ctt/Att	9/11	1	2	FACETS	0.889	0.808	0.975	0.889	0.808	0.975	CLONAL	1	TRUE	1	0.393438475539559	2		572	743	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577504	7577504	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	224	604	1	ENST00000269305.4:c.777C>A	p.Asp259Glu	p.D259E	ENST00000269305	NM_001126112.2	259	gaC/gaA	7/11	1	2	FACETS	0.902	0.845	0.96	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		605	631	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950396	15950396	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201721277	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	144	384	1	ENST00000268712.3:c.6548G>A	p.Arg2183His	p.R2183H	ENST00000268712	NM_006311.3	2183	cGc/cAc	42/46	1	2	FACETS	0.83	0.764	0.898	1	0.99	1	CLONAL	2	TRUE	1	0.393438475539559	2		385	441	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964969	15964969	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	96	477	0	ENST00000268712.3:c.5627G>T	p.Arg1876Ile	p.R1876I	ENST00000268712	NM_006311.3	1876	aGa/aTa	37/46	1	2	FACETS	0.895	0.8	0.996	0.895	0.8	0.996	CLONAL	1	TRUE	1	0.393438475539559	2		477	545	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049786	16049786	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	137	246	4	ENST00000268712.3:c.986C>A	p.Pro329His	p.P329H	ENST00000268712	NM_006311.3	329	cCt/cAt	10/46	1	2	FACETS	0.833	0.765	0.903	1	0.989	1	CLONAL	2	TRUE	1	0.393438475539559	2		250	418	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556079	29556079	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886041347	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	84	213	0	ENST00000356175.3:c.2446C>T	p.Arg816Ter	p.R816*	ENST00000356175	NM_000267.3	816	Cga/Tga	21/57	1	2	FACETS	0.854	0.766	0.945	1	0.984	1	CLONAL	2	TRUE	1	0.393438475539559	2		213	250	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586143	29586143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771420960	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	127	373	0	ENST00000356175.3:c.4363C>T	p.Arg1455Cys	p.R1455C	ENST00000356175	NM_000267.3	1455	Cgc/Tgc	32/57	1	2	FACETS	0.841	0.769	0.914	1	0.989	1	CLONAL	2	TRUE	1	0.393438475539559	2		373	384	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664842	29664842	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	114	321	0	ENST00000356175.3:c.6585C>A	p.Cys2195Ter	p.C2195*	ENST00000356175	NM_000267.3	2195	tgC/tgA	43/57	1	2	FACETS	0.873	0.795	0.952	1	0.988	1	CLONAL	2	TRUE	1	0.393438475539559	2		321	332	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667784	37667784	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	150	351	0	ENST00000447079.4:c.2669G>A	p.Arg890His	p.R890H	ENST00000447079	NM_015083.1	890	cGc/cAc	8/14	1	2	FACETS	0.813	0.749	0.879	1	0.99	1	CLONAL	2	TRUE	1	0.393438475539559	2		351	469	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687303	37687303	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	233	589	0	ENST00000447079.4:c.4207C>A	p.Leu1403Ile	p.L1403I	ENST00000447079	NM_015083.1	1403	Ctc/Atc	14/14	1	2	FACETS	0.907	0.851	0.964	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		589	653	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864607	37864607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775382058	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	202	603	0	ENST00000269571.5:c.259G>A	p.Ala87Thr	p.A87T	ENST00000269571		87	Gct/Act	3/27	1	2	FACETS	0.753	0.701	0.806	1	0.991	1	SUBCLONAL	2	TRUE	1	0.393438475539559	2		603	682	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868604	37868604	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	32	468	0	ENST00000269571.5:c.1051C>T	p.Arg351Ter	p.R351*	ENST00000269571		351	Cga/Tga	9/27	1	2	FACETS	0.323	0.261	0.392	0.323	0.261	0.392	SUBCLONAL	1	TRUE	1	0.393438475539559	2		468	504	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872139	37872139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371450390	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	269	795	1	ENST00000269571.5:c.1460G>A	p.Arg487Gln	p.R487Q	ENST00000269571		487	cGg/cAg	12/27	1	2	FACETS	0.83	0.781	0.88	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		796	824	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38506052	38506052	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	230	515	0	ENST00000254066.5:c.344G>T	p.Ser115Ile	p.S115I	ENST00000254066	NM_000964.3	115	aGc/aTc	4/9	1	2	FACETS	0.925	0.868	0.983	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		515	632	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475362	40475362	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	82	461	0	ENST00000264657.5:c.1664C>A	p.Ala555Asp	p.A555D	ENST00000264657	NM_139276.2	555	gCt/gAt	19/24	1	2	FACETS	0.881	0.78	0.989	0.881	0.78	0.989	CLONAL	1	TRUE	1	0.393438475539559	2		461	473	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870539	40870539	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	139	640	0	ENST00000428826.2:c.864G>T	p.Glu288Asp	p.E288D	ENST00000428826		288	gaG/gaT	9/21	1	2	FACETS	0.891	0.812	0.974	0.891	0.812	0.974	CLONAL	1	TRUE	1	0.393438475539559	2		640	793	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243662	41243662	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	92	562	0	ENST00000357654.3:c.3886T>G	p.Phe1296Val	p.F1296V	ENST00000357654	NM_007294.3	1296	Ttt/Gtt	10/23	1	2	FACETS	0.732	0.651	0.818	0.732	0.651	0.818	SUBCLONAL	1	TRUE	1	0.393438475539559	2		562	639	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243976	41243976	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	196	505	0	ENST00000357654.3:c.3572G>T	p.Ser1191Ile	p.S1191I	ENST00000357654	NM_007294.3	1191	aGc/aTc	10/23	1	2	FACETS	0.844	0.787	0.904	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	2		505	590	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246856	41246856	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357001	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	110	314	0	ENST00000357654.3:c.692C>T	p.Thr231Met	p.T231M	ENST00000357654	NM_007294.3	231	aCg/aTg	10/23	1	2	FACETS	0.788	0.715	0.863	1	0.986	1	SUBCLONAL	2	TRUE	1	0.393438475539559	2		314	355	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41276047	41276047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	68	371	0	ENST00000357654.3:c.67G>A	p.Glu23Lys	p.E23K	ENST00000357654	NM_007294.3	23	Gag/Aag	2/23	1	2	FACETS	0.578	0.503	0.659	0.578	0.503	0.659	SUBCLONAL	1	TRUE	1	0.393438475539559	2		371	598	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47679297	47679297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	200	456	0	ENST00000347630.2:c.910G>A	p.Glu304Lys	p.E304K	ENST00000347630	NM_001007230.1	304	Gaa/Aaa	10/11	1	2	FACETS	0.908	0.847	0.969	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	2		456	560	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696465	47696465	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	131	383	0	ENST00000347630.2:c.358C>T	p.Gln120Ter	p.Q120*	ENST00000347630	NM_001007230.1	120	Caa/Taa	6/11	1	2	FACETS	0.797	0.729	0.866	1	0.988	1	SUBCLONAL	2	TRUE	1	0.393438475539559	2		383	418	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696695	47696695	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	178	398	0	ENST00000347630.2:c.253T>C	p.Ser85Pro	p.S85P	ENST00000347630	NM_001007230.1	85	Tca/Cca	5/11	1	2	FACETS	0.832	0.772	0.893	1	0.992	1	CLONAL	2	TRUE	1	0.393438475539559	2		398	544	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435407	56435407	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	124	772	0	ENST00000407977.2:c.1730A>C	p.Gln577Pro	p.Q577P	ENST00000407977		577	cAg/cCg	9/10	1	2	FACETS	0.817	0.739	0.898	0.817	0.739	0.898	CLONAL	1	TRUE	1	0.393438475539559	2		772	772	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770112	56770112	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	209	578	0	ENST00000337432.4:c.108G>T	p.Glu36Asp	p.E36D	ENST00000337432	NM_058216.2	36	gaG/gaT	1/9	1	2	FACETS	0.865	0.808	0.923	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	2		578	614	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772427	56772427	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	113	565	0	ENST00000337432.4:c.281A>G	p.Glu94Gly	p.E94G	ENST00000337432	NM_058216.2	94	gAg/gGg	2/9	1	2	FACETS	0.864	0.778	0.954	0.864	0.778	0.954	CLONAL	1	TRUE	1	0.393438475539559	2		565	665	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56798158	56798158	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	61	260	0	ENST00000337432.4:c.889C>A	p.Leu297Ile	p.L297I	ENST00000337432	NM_058216.2	297	Ctt/Att	6/9	1	2	FACETS	0.753	0.651	0.862	0.753	0.651	0.862	SUBCLONAL	1	TRUE	1	0.393438475539559	2		260	412	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677957	58677957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	114	351	0	ENST00000305921.3:c.182G>A	p.Gly61Asp	p.G61D	ENST00000305921	NM_003620.3	61	gGc/gAc	1/6	1	2	FACETS	0.84	0.765	0.917	1	0.988	1	CLONAL	2	TRUE	1	0.393438475539559	2		351	345	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761304	59761304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45437094	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	187	570	0	ENST00000259008.2:c.3103C>T	p.Arg1035Cys	p.R1035C	ENST00000259008	NM_032043.2	1035	Cgt/Tgt	20/20	1	2	FACETS	0.78	0.725	0.838	1	0.991	1	SUBCLONAL	2	TRUE	1	0.393438475539559	2		570	609	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853790	59853790	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	52	387	0	ENST00000259008.2:c.2069G>T	p.Gly690Val	p.G690V	ENST00000259008	NM_032043.2	690	gGa/gTa	14/20	1	2	FACETS	0.544	0.463	0.632	0.544	0.463	0.632	SUBCLONAL	1	TRUE	1	0.393438475539559	2		387	486	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861659	59861659	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	104	217	0	ENST00000259008.2:c.1600C>A	p.Leu534Ile	p.L534I	ENST00000259008	NM_032043.2	534	Ctt/Att	11/20	1	2	FACETS	0.839	0.761	0.92	1	0.986	1	CLONAL	2	TRUE	1	0.393438475539559	2		217	315	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926578	59926578	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	49	358	0	ENST00000259008.2:c.419C>A	p.Ala140Asp	p.A140D	ENST00000259008	NM_032043.2	140	gCt/gAt	5/20	1	2	FACETS	0.599	0.508	0.698	0.599	0.508	0.698	SUBCLONAL	1	TRUE	1	0.393438475539559	2		358	416	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006677	62006677	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	253	729	0	ENST00000392795.3:c.602A>G	p.Asp201Gly	p.D201G	ENST00000392795	NM_001039933.1	201	gAc/gGc	6/6	1	2	FACETS	0.896	0.842	0.95	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		729	718	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532439	63532439	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs148765149	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	123	799	2	ENST00000307078.5:c.2140C>T	p.Arg714Trp	p.R714W	ENST00000307078	NM_004655.3	714	Cgg/Tgg	8/11	1	2	FACETS	0.76	0.687	0.837	0.76	0.687	0.837	SUBCLONAL	1	TRUE	1	0.393438475539559	2		801	823	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119809	70119809	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771635102	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	110	630	0	ENST00000245479.2:c.811C>T	p.Arg271Cys	p.R271C	ENST00000245479	NM_000346.3	271	Cgc/Tgc	3/3	1	2	FACETS	0.801	0.72	0.886	0.801	0.72	0.886	CLONAL	1	TRUE	1	0.393438475539559	2		630	698	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732926	74732926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776880365	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	149	369	0	ENST00000359995.5:c.317C>T	p.Pro106Leu	p.P106L	ENST00000359995	NM_001195427.1	106	cCa/cTa	1/3	1	2	FACETS	1	0.954	1	1	0.992	1	CLONAL	2	TRUE	1	0.393438475539559	2		369	364	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78765249	78765249	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	117	331	0	ENST00000306801.3:c.831-1G>A		p.X277_splice	ENST00000306801	NM_020761.2	277			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.393438475539559	2		331	397	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78820376	78820376	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	47	610	0	ENST00000306801.3:c.1314+2T>C		p.X438_splice	ENST00000306801	NM_020761.2	438			1	2	FACETS	0.383	0.323	0.451	0.383	0.323	0.451	SUBCLONAL	1	TRUE	1	0.393438475539559	2		610	623	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78854287	78854287	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	190	501	0	ENST00000306801.3:c.1582C>T	p.Pro528Ser	p.P528S	ENST00000306801	NM_020761.2	528	Cca/Tca	14/34	1	2	FACETS	0.891	0.83	0.953	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	2		501	542	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923252	78923252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	76	594	0	ENST00000306801.3:c.3275C>T	p.Ala1092Val	p.A1092V	ENST00000306801	NM_020761.2	1092	gCc/gTc	28/34	1	2	FACETS	0.686	0.603	0.776	0.686	0.603	0.776	SUBCLONAL	1	TRUE	1	0.393438475539559	2		594	563	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591894	48591894	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	167	406	0	ENST00000342988.3:c.1057T>C	p.Tyr353His	p.Y353H	ENST00000342988	NM_005359.5	353	Tac/Cac	9/12	0.342527508039289	1	FACETS	0.902	0.84	0.964	1	0.993	1	CLONAL	2	TRUE	0	0.393438475539559	1		406	378	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400800	56400800	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	33	172	0	ENST00000348428.3:c.1394G>A	p.Arg465Lys	p.R465K	ENST00000348428	NM_006785.3	465	aGg/aAg	11/17	0.342527508039289	1	FACETS	0.688	0.565	0.823	0.688	0.565	0.823	SUBCLONAL	1	TRUE	0	0.393438475539559	1		172	196	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56411684	56411684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1004957123	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	120	253	0	ENST00000348428.3:c.1868C>T	p.Pro623Leu	p.P623L	ENST00000348428	NM_006785.3	623	cCg/cTg	15/17	0.342527508039289	1	FACETS	0.828	0.759	0.897	1	0.989	1	CLONAL	2	TRUE	0	0.393438475539559	1		253	296	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223059	1223059	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913325	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	304	756	2	ENST00000326873.7:c.996G>A	p.Trp332Ter	p.W332*	ENST00000326873	NM_000455.4	332	tgG/tgA	8/10	1	2	FACETS	0.885	0.837	0.934	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		758	873	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612347	1612347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200962332	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	349	831	2	ENST00000344749.5:c.1672C>T	p.Arg558Cys	p.R558C	ENST00000344749	NM_001136139.2	558	Cgc/Tgc	18/19	1	2	FACETS	0.948	0.9	0.996	1	0.996	1	CLONAL	2	TRUE	1	0.393438475539559	2		833	936	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615775	1615775	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149277795	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	239	652	1	ENST00000344749.5:c.1496G>A	p.Arg499Gln	p.R499Q	ENST00000344749	NM_001136139.2	499	cGg/cAg	17/19	1	2	FACETS	0.922	0.866	0.979	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		653	659	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1646389	1646389	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	302	747	0	ENST00000344749.5:c.110C>A	p.Pro37His	p.P37H	ENST00000344749	NM_001136139.2	37	cCc/cAc	3/19	1	2	FACETS	0.899	0.85	0.949	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		747	854	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207621	2207621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1208115143	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	169	744	0	ENST00000398665.3:c.905C>T	p.Ser302Leu	p.S302L	ENST00000398665	NM_032482.2	302	tCg/tTg	11/28	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.393438475539559	2		744	781	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210501	2210501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368335495	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	279	845	2	ENST00000398665.3:c.1108G>A	p.Ala370Thr	p.A370T	ENST00000398665	NM_032482.2	370	Gcc/Acc	13/28	1	2	FACETS	0.922	0.87	0.975	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		847	769	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211139	2211139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	354	893	1	ENST00000398665.3:c.1393C>T	p.Pro465Ser	p.P465S	ENST00000398665	NM_032482.2	465	Ccg/Tcg	15/28	1	2	FACETS	0.958	0.911	1	1	0.996	1	CLONAL	2	TRUE	1	0.393438475539559	2		894	939	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216310	2216310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780465036	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	185	698	3	ENST00000398665.3:c.1954C>T	p.Arg652Trp	p.R652W	ENST00000398665	NM_032482.2	652	Cgg/Tgg	20/28	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.393438475539559	2		701	690	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216548	2216548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371878008	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	324	921	1	ENST00000398665.3:c.2192C>T	p.Ser731Leu	p.S731L	ENST00000398665	NM_032482.2	731	tCg/tTg	20/28	1	2	FACETS	0.932	0.883	0.981	1	0.996	1	CLONAL	2	TRUE	1	0.393438475539559	2		922	884	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2220218	2220218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376474660	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	238	696	1	ENST00000398665.3:c.2803G>A	p.Ala935Thr	p.A935T	ENST00000398665	NM_032482.2	935	Gca/Aca	23/28	1	2	FACETS	0.906	0.85	0.962	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		697	668	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226812	2226812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs911763223	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	224	517	0	ENST00000398665.3:c.4292C>T	p.Ala1431Val	p.A1431V	ENST00000398665	NM_032482.2	1431	gCg/gTg	27/28	1	2	FACETS	0.876	0.82	0.933	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		517	650	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226949	2226949	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	205	641	0	ENST00000398665.3:c.4429G>A	p.Gly1477Ser	p.G1477S	ENST00000398665	NM_032482.2	1477	Ggc/Agc	27/28	1	2	FACETS	0.813	0.758	0.869	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	2		641	641	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3113422	3113422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	254	670	1	ENST00000078429.4:c.416C>T	p.Pro139Leu	p.P139L	ENST00000078429	NM_002067.2	139	cCg/cTg	3/7	1	2	FACETS	0.883	0.83	0.937	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		671	731	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119263	3119263	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	119	684	0	ENST00000078429.4:c.795G>T	p.Gln265His	p.Q265H	ENST00000078429	NM_002067.2	265	caG/caT	6/7	1	2	FACETS	0.77	0.695	0.849	0.77	0.695	0.849	SUBCLONAL	1	TRUE	1	0.393438475539559	2		684	786	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221102	5221102	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	241	693	0	ENST00000357368.4:c.3364C>A	p.Leu1122Ile	p.L1122I	ENST00000357368	NM_002850.3	1122	Ctc/Atc	20/38	1	2	FACETS	0.862	0.808	0.916	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		693	711	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222756	5222756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374799314	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	271	878	1	ENST00000357368.4:c.3047G>A	p.Arg1016Gln	p.R1016Q	ENST00000357368	NM_002850.3	1016	cGg/cAg	18/38	1	2	FACETS	0.905	0.853	0.958	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		879	761	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184412	7184412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752147545	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	312	730	0	ENST00000302850.5:c.889C>T	p.Arg297Trp	p.R297W	ENST00000302850	NM_000208.2	297	Cgg/Tgg	3/22	1	2	FACETS	0.848	0.802	0.895	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		730	935	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251579	10251579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770370709	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	120	541	2	ENST00000340748.4:c.3353G>A	p.Gly1118Asp	p.G1118D	ENST00000340748		1118	gGc/gAc	31/40	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.393438475539559	2		543	592	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098464	11098464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	183	507	0	ENST00000358026.2:c.982C>T	p.Pro328Ser	p.P328S	ENST00000358026	NM_001128849.1	328	Ccg/Tcg	6/36	1	2	FACETS	0.879	0.818	0.942	1	0.992	1	CLONAL	2	TRUE	1	0.393438475539559	2		507	529	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105567	11105567	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	86	569	0	ENST00000358026.2:c.1483G>T	p.Gly495Cys	p.G495C	ENST00000358026	NM_001128849.1	495	Ggc/Tgc	9/36	1	2	FACETS	0.581	0.514	0.654	0.581	0.514	0.654	SUBCLONAL	1	TRUE	1	0.393438475539559	2		569	752	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121076	11121076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1131691371	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	50	623	0	ENST00000358026.2:c.2143G>A	p.Asp715Asn	p.D715N	ENST00000358026	NM_001128849.1	715	Gat/Aat	15/36	1	2	FACETS	0.392	0.332	0.459	0.392	0.332	0.459	SUBCLONAL	1	TRUE	1	0.393438475539559	2		623	648	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135100	11135100	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555780047	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	248	832	1	ENST00000358026.2:c.3067G>A	p.Glu1023Lys	p.E1023K	ENST00000358026	NM_001128849.1	1023	Gag/Aag	21/36	1	2	FACETS	0.854	0.802	0.907	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		833	738	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145692	11145692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1228120902	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	249	811	4	ENST00000358026.2:c.4054G>A	p.Ala1352Thr	p.A1352T	ENST00000358026	NM_001128849.1	1352	Gcg/Acg	29/36	1	2	FACETS	0.769	0.721	0.818	1	0.993	1	SUBCLONAL	2	TRUE	1	0.393438475539559	2		815	823	SUCCESS
CALR	811	MSKCC	GRCh37	19	13049547	13049547	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	265	791	0	ENST00000316448.5:c.54G>T	p.Glu18Asp	p.E18D	ENST00000316448	NM_004343.3	18	gaG/gaT	1/9	1	2	FACETS	0.819	0.771	0.869	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		791	822	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276316	15276316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372834264	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	291	774	1	ENST00000263388.2:c.5678G>A	p.Arg1893Gln	p.R1893Q	ENST00000263388	NM_000435.2	1893	cGa/cAa	31/33	1	2	FACETS	0.94	0.888	0.992	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		775	787	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297716	15297716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568359179	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	270	726	2	ENST00000263388.2:c.1924G>A	p.Asp642Asn	p.D642N	ENST00000263388	NM_000435.2	642	Gac/Aac	12/33	1	2	FACETS	0.815	0.767	0.864	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		728	842	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297788	15297788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748963864	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	297	861	0	ENST00000263388.2:c.1852G>A	p.Glu618Lys	p.E618K	ENST00000263388	NM_000435.2	618	Gaa/Aaa	12/33	1	2	FACETS	0.883	0.834	0.933	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		861	855	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375286	15375286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	250	691	0	ENST00000263377.2:c.1141G>A	p.Asp381Asn	p.D381N	ENST00000263377	NM_058243.2	381	Gac/Aac	6/20	1	2	FACETS	0.866	0.813	0.919	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		691	734	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965969	18965969	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	211	718	0	ENST00000262803.5:c.1462A>G	p.Ser488Gly	p.S488G	ENST00000262803	NM_002911.3	488	Agc/Ggc	11/24	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.393438475539559	2		718	749	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968243	18968243	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	253	801	1	ENST00000262803.5:c.2083C>T	p.Pro695Ser	p.P695S	ENST00000262803	NM_002911.3	695	Ccc/Tcc	15/24	1	2	FACETS	0.889	0.836	0.943	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		802	723	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257409	19257409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs546609857	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	342	887	1	ENST00000162023.5:c.724G>A	p.Gly242Arg	p.G242R	ENST00000162023		242	Gga/Aga	11/13	1	2	FACETS	0.928	0.88	0.976	1	0.996	1	CLONAL	2	TRUE	1	0.393438475539559	2		888	937	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257607	19257607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750384916	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	301	866	1	ENST00000162023.5:c.619C>T	p.Arg207Trp	p.R207W	ENST00000162023		207	Cgg/Tgg	10/13	1	2	FACETS	0.855	0.807	0.903	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		867	895	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257874	19257874	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780635430	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	159	994	0	ENST00000162023.5:c.512G>A	p.Arg171Gln	p.R171Q	ENST00000162023		171	cGa/cAa	9/13	1	2	FACETS	0.91	0.834	0.989	0.91	0.834	0.989	CLONAL	1	TRUE	1	0.393438475539559	2		994	888	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260061	19260061	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	324	708	0	ENST00000162023.5:c.232A>C	p.Ser78Arg	p.S78R	ENST00000162023		78	Agc/Cgc	7/13	1	2	FACETS	0.998	0.947	1	1	0.996	1	CLONAL	2	TRUE	1	0.393438475539559	2		708	825	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308339	30308339	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	180	456	0	ENST00000262643.3:c.353A>C	p.Lys118Thr	p.K118T	ENST00000262643	NM_001238.2	118	aAa/aCa	6/12	1	2	FACETS	0.873	0.811	0.936	1	0.992	1	CLONAL	2	TRUE	1	0.393438475539559	2		456	524	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793049	33793049	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	57	266	1	ENST00000498907.2:c.272C>A	p.Ala91Asp	p.A91D	ENST00000498907	NM_004364.3	91	gCc/gAc	1/1	1	2	FACETS	0.917	0.792	1	0.917	0.792	1	CLONAL	1	TRUE	1	0.393438475539559	2		267	316	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210688	36210688	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	250	634	0	ENST00000222270.7:c.439C>T	p.Arg147Ter	p.R147*	ENST00000222270	NM_014727.1	147	Cga/Tga	3/37	1	2	FACETS	0.993	0.935	1	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		634	640	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210907	36210907	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770426704	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	303	933	0	ENST00000222270.7:c.658C>T	p.Arg220Trp	p.R220W	ENST00000222270	NM_014727.1	220	Cgg/Tgg	3/37	1	2	FACETS	0.871	0.823	0.92	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		933	884	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214046	36214046	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	289	836	2	ENST00000222270.7:c.2872G>A	p.Gly958Ser	p.G958S	ENST00000222270	NM_014727.1	958	Ggc/Agc	6/37	1	2	FACETS	0.833	0.786	0.881	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		838	882	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214059	36214059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	154	820	0	ENST00000222270.7:c.2885G>A	p.Arg962His	p.R962H	ENST00000222270	NM_014727.1	962	cGc/cAc	6/37	1	2	FACETS	0.868	0.794	0.945	0.868	0.794	0.945	CLONAL	1	TRUE	1	0.393438475539559	2		820	902	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214081	36214081	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	307	843	1	ENST00000222270.7:c.2907T>G	p.Cys969Trp	p.C969W	ENST00000222270	NM_014727.1	969	tgT/tgG	6/37	1	2	FACETS	0.848	0.802	0.896	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		844	920	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216712	36216712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780411851	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	188	518	0	ENST00000222270.7:c.3878G>A	p.Arg1293His	p.R1293H	ENST00000222270	NM_014727.1	1293	cGc/cAc	13/37	1	2	FACETS	0.824	0.766	0.883	1	0.992	1	CLONAL	2	TRUE	1	0.393438475539559	2		518	580	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221280	36221280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555731980	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	162	781	1	ENST00000222270.7:c.5114G>A	p.Arg1705Gln	p.R1705Q	ENST00000222270	NM_014727.1	1705	cGa/cAa	24/37	1	2	FACETS	0.941	0.864	1	0.941	0.864	1	CLONAL	1	TRUE	1	0.393438475539559	2		782	875	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227996	36227996	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	221	769	0	ENST00000222270.7:c.7382G>T	p.Gly2461Val	p.G2461V	ENST00000222270	NM_014727.1	2461	gGg/gTg	33/37	1	2	FACETS	0.838	0.784	0.894	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	2		769	670	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229422	36229422	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	203	511	0	ENST00000222270.7:c.8112C>A	p.Asn2704Lys	p.N2704K	ENST00000222270	NM_014727.1	2704	aaC/aaA	37/37	1	2	FACETS	0.883	0.825	0.944	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	2		511	584	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748581	40748581	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761956794	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	211	608	0	ENST00000392038.2:c.301C>T	p.Arg101Trp	p.R101W	ENST00000392038	NM_001626.4	101	Cgg/Tgg	5/14	1	2	FACETS	0.809	0.755	0.864	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	2		608	663	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748898	41748898	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1307122843	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	204	623	0	ENST00000301178.4:c.1423C>T	p.Arg475Ter	p.R475*	ENST00000301178	NM_021913.4	475	Cga/Tga	11/20	1	2	FACETS	0.843	0.786	0.901	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	2		623	615	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42381432	42381432	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	123	657	0	ENST00000221972.3:c.58C>A	p.Leu20Met	p.L20M	ENST00000221972	NM_021601.3	20	Ctg/Atg	1/5	1	2	FACETS	0.889	0.805	0.978	0.889	0.805	0.978	CLONAL	1	TRUE	1	0.393438475539559	2		657	703	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752808	42752808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1233632467	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	318	828	1	ENST00000222329.4:c.1456C>T	p.Arg486Trp	p.R486W	ENST00000222329	NM_006494.2	486	Cgg/Tgg	4/4	1	2	FACETS	0.941	0.892	0.991	1	0.996	1	CLONAL	2	TRUE	1	0.393438475539559	2		829	859	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753795	42753795	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1433054936	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	133	948	3	ENST00000222329.4:c.469G>A	p.Glu157Lys	p.E157K	ENST00000222329	NM_006494.2	157	Gag/Aag	4/4	1	2	FACETS	0.774	0.703	0.85	0.774	0.703	0.85	SUBCLONAL	1	TRUE	1	0.393438475539559	2		951	873	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754555	42754555	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	215	861	0	ENST00000222329.4:c.185A>G	p.Glu62Gly	p.E62G	ENST00000222329	NM_006494.2	62	gAg/gGg	2/4	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.393438475539559	2		861	729	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796502	42796502	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	168	994	1	ENST00000575354.2:c.3059G>T	p.Ser1020Ile	p.S1020I	ENST00000575354	NM_015125.3	1020	aGc/aTc	13/20	1	2	FACETS	0.891	0.818	0.966	0.891	0.818	0.966	CLONAL	1	TRUE	1	0.393438475539559	2		995	959	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797126	42797126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	142	942	0	ENST00000575354.2:c.3488G>A	p.Ser1163Asn	p.S1163N	ENST00000575354	NM_015125.3	1163	aGc/aAc	15/20	1	2	FACETS	0.761	0.693	0.833	0.761	0.693	0.833	SUBCLONAL	1	TRUE	1	0.393438475539559	2		942	948	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856060	45856060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913024	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	108	755	2	ENST00000391945.4:c.1846C>T	p.Arg616Trp	p.R616W	ENST00000391945	NM_000400.3	616	Cgg/Tgg	20/23	1	2	FACETS	0.765	0.687	0.847	0.765	0.687	0.847	SUBCLONAL	1	TRUE	1	0.393438475539559	2		757	718	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45864851	45864851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369191500	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	338	889	1	ENST00000391945.4:c.1168G>A	p.Asp390Asn	p.D390N	ENST00000391945	NM_000400.3	390	Gac/Aac	12/23	1	2	FACETS	0.917	0.87	0.965	1	0.996	1	CLONAL	2	TRUE	1	0.393438475539559	2		890	937	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731550	47731550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	12	34	0	ENST00000449228.1:c.242G>A	p.Arg81His	p.R81H	ENST00000449228	NM_001127240.2	81	cGc/cAc	2/4	1	2	FACETS	0.897	0.664	1	1	0.904	1	CLONAL	2	TRUE	1	0.393438475539559	2		34	34	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139929	50139929	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374650566	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	327	883	0	ENST00000246792.3:c.400G>A	p.Asp134Asn	p.D134N	ENST00000246792	NM_006270.3	134	Gac/Aac	4/6	1	2	FACETS	0.897	0.85	0.944	1	0.996	1	CLONAL	2	TRUE	1	0.393438475539559	2		883	927	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905267	50905267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs969950434	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	280	896	0	ENST00000440232.2:c.475G>A	p.Glu159Lys	p.E159K	ENST00000440232	NM_002691.3	159	Gag/Aag	5/27	1	2	FACETS	0.848	0.8	0.898	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		896	839	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715947	52715947	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1029209344	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	174	587	0	ENST00000322088.6:c.512G>A	p.Arg171Gln	p.R171Q	ENST00000322088	NM_014225.5	171	cGg/cAg	5/15	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.393438475539559	2		587	618	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082414	16082414	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	425	813	0	ENST00000281043.3:c.228C>A	p.Ser76Arg	p.S76R	ENST00000281043	NM_005378.4	76	agC/agA	2/3	0.292407850503411	2	FACETS	0.847	0.813	0.882	1	0.995	1	CLONAL	3	TRUE	0	0.393438475539559	2		813	850	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505369	25505369	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	186	727	0	ENST00000264709.3:c.389G>T	p.Arg130Ile	p.R130I	ENST00000264709	NM_175629.2	130	aGa/aTa	4/23	0.292407850503411	2	FACETS	1	0.989	1	0.682	0.632	0.734	CLONAL	1	TRUE	0	0.393438475539559	2		727	693	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523095	25523095	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	162	697	0	ENST00000264709.3:c.90G>T	p.Glu30Asp	p.E30D	ENST00000264709	NM_175629.2	30	gaG/gaT	3/23	0.292407850503411	2	FACETS	1	0.974	1	0.568	0.522	0.616	CLONAL	1	TRUE	0	0.393438475539559	2		697	725	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917821	29917821	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	108	772	0	ENST00000389048.3:c.847C>A	p.Leu283Ile	p.L283I	ENST00000389048	NM_004304.4	283	Ctc/Atc	3/29	0.292407850503411	2	FACETS	0.706	0.633	0.783	0.353	0.316	0.392	SUBCLONAL	1	TRUE	0	0.393438475539559	2		772	778	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940452	29940452	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	66	281	0	ENST00000389048.3:c.779G>T	p.Ser260Ile	p.S260I	ENST00000389048	NM_004304.4	260	aGc/aTc	2/29	0.292407850503411	2	FACETS	1	0.916	1	0.531	0.464	0.602	CLONAL	1	TRUE	0	0.393438475539559	2		281	316	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143227	30143227	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	156	794	0	ENST00000389048.3:c.299G>T	p.Arg100Met	p.R100M	ENST00000389048	NM_004304.4	100	aGg/aTg	1/29	0.292407850503411	2	FACETS	1	0.973	1	0.568	0.521	0.617	CLONAL	1	TRUE	0	0.393438475539559	2		794	698	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46608841	46608841	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	31	651	0	ENST00000263734.3:c.2152G>T	p.Ala718Ser	p.A718S	ENST00000263734	NM_001430.4	718	Gcc/Tcc	13/16	0.265128340346136	2	FACETS	0.266	0.214	0.325	0.133	0.107	0.163	SUBCLONAL	1	TRUE	0	0.393438475539559	2		651	592	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690230	47690230	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63749947	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	201	230	0	ENST00000233146.2:c.1447G>T	p.Glu483Ter	p.E483*	ENST00000233146	NM_000251.2	483	Gaa/Taa	9/16	0.265128340346136	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.393438475539559	2		230	505	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698180	47698180	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63751411	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	58	159	0	ENST00000233146.2:c.1738G>T	p.Glu580Ter	p.E580*	ENST00000233146	NM_000251.2	580	Gaa/Taa	11/16	0.265128340346136	2	FACETS	0.989	0.857	1	0.495	0.428	0.566	CLONAL	1	TRUE	0	0.393438475539559	2		159	298	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705610	47705610	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	181	269	0	ENST00000233146.2:c.2410G>T	p.Ala804Ser	p.A804S	ENST00000233146	NM_000251.2	804	Gca/Tca	14/16	0.265128340346136	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.393438475539559	2		269	371	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026290	48026290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147737737	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	103	335	1	ENST00000234420.5:c.1168G>A	p.Asp390Asn	p.D390N	ENST00000234420	NM_000179.2	390	Gat/Aat	4/10	0.265128340346136	2	FACETS	1	0.983	1	0.742	0.67	0.816	CLONAL	1	TRUE	0	0.393438475539559	2		336	353	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026729	48026729	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	95	355	0	ENST00000234420.5:c.1607G>T	p.Ser536Ile	p.S536I	ENST00000234420	NM_000179.2	536	aGt/aTt	4/10	0.265128340346136	2	FACETS	1	0.944	1	0.541	0.484	0.601	CLONAL	1	TRUE	0	0.393438475539559	2		355	446	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026852	48026852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376220212	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	80	381	0	ENST00000234420.5:c.1730G>A	p.Arg577His	p.R577H	ENST00000234420	NM_000179.2	577	cGc/cAc	4/10	0.265128340346136	2	FACETS	0.875	0.773	0.983	0.437	0.386	0.492	CLONAL	1	TRUE	0	0.393438475539559	2		381	465	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032107	48032107	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	93	317	0	ENST00000234420.5:c.3497G>T	p.Arg1166Met	p.R1166M	ENST00000234420	NM_000179.2	1166	aGg/aTg	6/10	0.265128340346136	2	FACETS	0.983	0.878	1	0.491	0.439	0.547	CLONAL	1	TRUE	0	0.393438475539559	2		317	481	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61717799	61717799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	273	402	0	ENST00000401558.2:c.2000G>T	p.Ser667Ile	p.S667I	ENST00000401558	NM_003400.3	667	aGt/aTt	17/25	0.265128340346136	2	FACETS	0.89	0.845	0.934	1	0.993	1	CLONAL	3	TRUE	0	0.393438475539559	2		402	520	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721153	61721153	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	145	384	0	ENST00000401558.2:c.1121A>C	p.Asn374Thr	p.N374T	ENST00000401558	NM_003400.3	374	aAt/aCt	12/25	0.265128340346136	2	FACETS	1	0.986	1	0.694	0.637	0.753	CLONAL	1	TRUE	0	0.393438475539559	2		384	531	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921765	111921765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572257286	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	209	385	0	ENST00000393256.3:c.554G>A	p.Arg185Gln	p.R185Q	ENST00000393256	NM_006538.4	185	cGa/cAa	4/4	0.265128340346136	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.393438475539559	2		385	444	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015278	128015278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	248	461	0	ENST00000285398.2:c.2243G>A	p.Ser748Asn	p.S748N	ENST00000285398	NM_000122.1	748	aGt/aAt	15/15	0.265128340346136	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.393438475539559	2		461	525	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128018818	128018818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	38	422	1	ENST00000285398.2:c.2050G>A	p.Gly684Ser	p.G684S	ENST00000285398	NM_000122.1	684	Ggt/Agt	13/15	0.265128340346136	2	FACETS	0.389	0.321	0.465	0.194	0.16	0.233	SUBCLONAL	1	TRUE	0	0.393438475539559	2		423	497	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872872	136872872	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	81	357	0	ENST00000241393.3:c.626T>G	p.Ile209Ser	p.I209S	ENST00000241393	NM_003467.2	209	aTc/aGc	2/2	0.265128340346136	2	FACETS	1	0.948	1	0.561	0.498	0.628	CLONAL	1	TRUE	0	0.393438475539559	2		357	367	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873384	136873384	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	214	317	0	ENST00000241393.3:c.114A>C	p.Lys38Asn	p.K38N	ENST00000241393	NM_003467.2	38	aaA/aaC	2/2	0.265128340346136	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.393438475539559	2		317	438	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622534	158622534	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	105	454	0	ENST00000263640.3:c.965A>C	p.Glu322Ala	p.E322A	ENST00000263640	NM_001105.4	322	gAg/gCg	8/11	0.265128340346136	2	FACETS	0.958	0.861	1	0.479	0.43	0.531	CLONAL	1	TRUE	0	0.393438475539559	2		454	557	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634684	158634684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764097240	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	46	340	0	ENST00000263640.3:c.502G>A	p.Glu168Lys	p.E168K	ENST00000263640	NM_001105.4	168	Gaa/Aaa	5/11	0.265128340346136	2	FACETS	0.536	0.452	0.629	0.268	0.226	0.315	SUBCLONAL	1	TRUE	0	0.393438475539559	2		340	436	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718999	190718999	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147084726	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	45	150	0	ENST00000441310.2:c.1001C>T	p.Thr334Met	p.T334M	ENST00000441310	NM_000534.4	334	aCg/aTg	9/13	0.265128340346136	2	FACETS	1	0.893	1	0.532	0.452	0.619	CLONAL	1	TRUE	0	0.393438475539559	2		150	215	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719176	190719176	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	119	197	0	ENST00000441310.2:c.1178A>G	p.Asp393Gly	p.D393G	ENST00000441310	NM_000534.4	393	gAt/gGt	9/13	0.265128340346136	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.393438475539559	2		197	277	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266828	198266828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs16865307	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	103	420	0	ENST00000335508.6:c.2104C>T	p.Arg702Trp	p.R702W	ENST00000335508	NM_012433.2	702	Cgg/Tgg	15/25	0.265128340346136	2	FACETS	0.919	0.824	1	0.459	0.412	0.509	CLONAL	1	TRUE	0	0.393438475539559	2		420	570	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268355	198268355	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	205	346	0	ENST00000335508.6:c.1673G>T	p.Arg558Met	p.R558M	ENST00000335508	NM_012433.2	558	aGg/aTg	12/25	0.265128340346136	2	FACETS	0.835	0.786	0.884	1	0.99	1	CLONAL	3	TRUE	0	0.393438475539559	2		346	416	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274608	198274608	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746096232	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	165	523	0	ENST00000335508.6:c.790G>A	p.Gly264Arg	p.G264R	ENST00000335508	NM_012433.2	264	Gga/Aga	7/25	0.265128340346136	2	FACETS	1	0.972	1	0.561	0.516	0.607	CLONAL	1	TRUE	0	0.393438475539559	2		523	748	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281558	198281558	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	335	471	0	ENST00000335508.6:c.573G>T	p.Gln191His	p.Q191H	ENST00000335508	NM_012433.2	191	caG/caT	6/25	0.265128340346136	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.393438475539559	2		471	705	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735465	204735465	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	102	452	0	ENST00000302823.3:c.266A>C	p.Tyr89Ser	p.Y89S	ENST00000302823	NM_005214.4	89	tAc/tCc	2/4	0.265128340346136	2	FACETS	1	0.966	1	0.587	0.528	0.648	CLONAL	1	TRUE	0	0.393438475539559	2		452	442	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593492	215593492	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs879253880	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	57	289	0	ENST00000260947.4:c.2242G>T	p.Glu748Ter	p.E748*	ENST00000260947	NM_000465.2	748	Gag/Tag	11/11	0.251942456589204	2	FACETS	0.783	0.675	0.9	0.392	0.337	0.45	SUBCLONAL	1	TRUE	0	0.393438475539559	2		289	370	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439610	220439610	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	396	815	0	ENST00000243786.2:c.463C>A	p.Leu155Met	p.L155M	ENST00000243786	NM_002191.3	155	Ctg/Atg	2/2	0.251942456589204	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.393438475539559	2		815	825	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660690	227660690	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	199	835	0	ENST00000305123.5:c.2765G>T	p.Arg922Met	p.R922M	ENST00000305123	NM_005544.2	922	aGg/aTg	1/2	0.251942456589204	2	FACETS	1	0.987	1	0.638	0.592	0.685	CLONAL	1	TRUE	0	0.393438475539559	2		835	793	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662409	227662409	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	115	702	0	ENST00000305123.5:c.1046C>A	p.Pro349His	p.P349H	ENST00000305123	NM_005544.2	349	cCc/cAc	1/2	0.251942456589204	2	FACETS	0.833	0.751	0.919	0.416	0.375	0.46	CLONAL	1	TRUE	0	0.393438475539559	2		702	702	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561114	9561114	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867074457	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	109	330	0	ENST00000353224.5:c.668C>T	p.Ser223Leu	p.S223L	ENST00000353224	NM_177990.2	223	tCg/tTg	4/10	1	2	FACETS	0.805	0.731	0.882	1	0.986	1	CLONAL	2	TRUE	1	0.393438475539559	2		330	344	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022374	31022374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750708574	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	124	391	1	ENST00000375687.4:c.1859G>A	p.Arg620His	p.R620H	ENST00000375687	NM_015338.5	620	cGt/cAt	13/13	1	2	FACETS	0.888	0.813	0.965	1	0.989	1	CLONAL	2	TRUE	1	0.393438475539559	2		392	355	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022422	31022422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370230857	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	77	285	0	ENST00000375687.4:c.1907C>T	p.Ala636Val	p.A636V	ENST00000375687	NM_015338.5	636	gCg/gTg	13/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.393438475539559	2		285	289	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375108	31375108	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375097618	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	129	817	0	ENST00000328111.2:c.505G>A	p.Asp169Asn	p.D169N	ENST00000328111	NM_006892.3	169	Gac/Aac	6/23	1	2	FACETS	0.824	0.747	0.904	0.824	0.747	0.904	CLONAL	1	TRUE	1	0.393438475539559	2		817	796	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022576	36022576	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	84	576	0	ENST00000358208.4:c.450-1G>A		p.X150_splice	ENST00000358208		150			1	2	FACETS	0.797	0.705	0.894	0.797	0.705	0.894	SUBCLONAL	1	TRUE	1	0.393438475539559	2		576	536	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741494	39741494	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	193	402	0	ENST00000361337.2:c.1381T>C	p.Tyr461His	p.Y461H	ENST00000361337	NM_003286.2	461	Tat/Cat	14/21	1	2	FACETS	0.973	0.909	1	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		402	504	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714370	40714370	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs956451753	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	66	475	0	ENST00000373198.4:c.4027C>T	p.Arg1343Trp	p.R1343W	ENST00000373198	NM_133170.3	1343	Cgg/Tgg	29/32	1	2	FACETS	0.709	0.617	0.809	0.709	0.617	0.809	SUBCLONAL	1	TRUE	1	0.393438475539559	2		475	473	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739109	40739109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1166590993	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	66	574	1	ENST00000373198.4:c.3175C>T	p.Arg1059Trp	p.R1059W	ENST00000373198	NM_133170.3	1059	Cgg/Tgg	24/32	1	2	FACETS	0.629	0.547	0.719	0.629	0.547	0.719	SUBCLONAL	1	TRUE	1	0.393438475539559	2		575	533	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419926	41419926	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	234	607	0	ENST00000373198.4:c.395G>T	p.Gly132Val	p.G132V	ENST00000373198	NM_133170.3	132	gGg/gTg	3/32	1	2	FACETS	0.943	0.885	1	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		607	631	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264374	46264374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768671146	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	73	385	2	ENST00000371998.3:c.1421C>T	p.Ala474Val	p.A474V	ENST00000371998		474	gCc/gTc	11/23	1	2	FACETS	0.781	0.685	0.884	0.781	0.685	0.884	SUBCLONAL	1	TRUE	1	0.393438475539559	2		387	475	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264452	46264452	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	149	380	0	ENST00000371998.3:c.1499T>C	p.Val500Ala	p.V500A	ENST00000371998		500	gTt/gCt	11/23	1	2	FACETS	0.806	0.742	0.871	1	0.99	1	CLONAL	2	TRUE	1	0.393438475539559	2		380	470	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267785	46267785	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756751050	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	87	504	0	ENST00000371998.3:c.2546G>A	p.Arg849His	p.R849H	ENST00000371998		849	cGt/cAt	14/23	1	2	FACETS	0.772	0.684	0.865	0.772	0.684	0.865	SUBCLONAL	1	TRUE	1	0.393438475539559	2		504	573	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46271079	46271079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1328250517	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	179	421	1	ENST00000371998.3:c.3203G>A	p.Gly1068Asp	p.G1068D	ENST00000371998		1068	gGc/gAc	17/23	1	2	FACETS	0.826	0.766	0.887	1	0.992	1	CLONAL	2	TRUE	1	0.393438475539559	2		422	551	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945261	54945261	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	164	345	0	ENST00000312783.6:c.1165A>G	p.Lys389Glu	p.K389E	ENST00000312783	NM_198436.1	389	Aaa/Gaa	10/10	1	2	FACETS	0.916	0.849	0.985	1	0.992	1	CLONAL	2	TRUE	1	0.393438475539559	2		345	455	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480443	57480443	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	46	221	0	ENST00000371085.3:c.438C>A	p.Phe146Leu	p.F146L	ENST00000371085	NM_000516.4	146	ttC/ttA	6/13	1	2	FACETS	0.769	0.651	0.898	0.769	0.651	0.898	SUBCLONAL	1	TRUE	1	0.393438475539559	2		221	304	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484813	57484813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555891595	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	208	583	1	ENST00000371085.3:c.793C>T	p.Arg265Cys	p.R265C	ENST00000371085	NM_000516.4	265	Cgc/Tgc	10/13	1	2	FACETS	0.855	0.799	0.913	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	2		584	618	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62320441	62320441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	143	753	0	ENST00000360203.5:c.1834C>T	p.Pro612Ser	p.P612S	ENST00000360203	NM_001283009.1	612	Cct/Tct	22/35	1	2	FACETS	0.882	0.805	0.963	0.882	0.805	0.963	CLONAL	1	TRUE	1	0.393438475539559	2		753	824	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42870081	42870081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375223866	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	178	524	0	ENST00000398585.3:c.91G>A	p.Asp31Asn	p.D31N	ENST00000398585	NM_001135099.1	31	Gat/Aat	2/14	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.393438475539559	2		524	617	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45649946	45649946	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	109	638	1	ENST00000407780.3:c.889G>T	p.Glu297Ter	p.E297*	ENST00000407780	NM_001283052.1	297	Gag/Tag	6/7	1	2	FACETS	0.786	0.706	0.87	0.786	0.706	0.87	SUBCLONAL	1	TRUE	1	0.393438475539559	2		639	705	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45649954	45649954	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs186459476	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	130	632	0	ENST00000407780.3:c.881C>T	p.Pro294Leu	p.P294L	ENST00000407780	NM_001283052.1	294	cCg/cTg	6/7	1	2	FACETS	0.983	0.894	1	0.983	0.894	1	CLONAL	1	TRUE	1	0.393438475539559	2		632	672	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288089	21288089	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	64	304	0	ENST00000354336.3:c.334T>G	p.Ser112Ala	p.S112A	ENST00000354336	NM_005207.3	112	Tct/Gct	2/3	1	2	FACETS	0.858	0.747	0.978	0.858	0.747	0.978	CLONAL	1	TRUE	1	0.393438475539559	2		304	379	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288497	21288497	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	222	535	0	ENST00000354336.3:c.742C>T	p.Pro248Ser	p.P248S	ENST00000354336	NM_005207.3	248	Ccc/Tcc	2/3	1	2	FACETS	0.851	0.796	0.907	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	2		535	663	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175857	24175859	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs875989800	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	207	567	0	ENST00000263121.7:c.1091_1093del	p.Lys364del	p.K364del	ENST00000263121	NM_003073.3	362	gAGAag/gag	8/9	1	2	FACETS	0.802	0.748	0.857	1	0.992	1	CLONAL	2	TRUE	1	0.393438475539559	2		567	656	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175871	24175871	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	117	518	0	ENST00000263121.7:c.1099G>A	p.Asp367Asn	p.D367N	ENST00000263121	NM_003073.3	367	Gac/Aac	8/9	1	2	FACETS	0.981	0.887	1	0.981	0.887	1	CLONAL	1	TRUE	1	0.393438475539559	2		518	606	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176338	24176338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	25	824	0	ENST00000263121.7:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000263121	NM_003073.3	377	Cgt/Tgt	9/9	1	2	FACETS	0.158	0.123	0.197	0.158	0.123	0.197	SUBCLONAL	1	TRUE	1	0.393438475539559	2		824	806	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054200	30054200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	64	369	1	ENST00000338641.4:c.622C>A	p.Leu208Met	p.L208M	ENST00000338641	NM_000268.3	208	Ctg/Atg	7/16	1	2	FACETS	0.675	0.586	0.772	0.675	0.586	0.772	SUBCLONAL	1	TRUE	1	0.393438475539559	2		370	482	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37622817	37622817	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	127	825	0	ENST00000249071.6:c.475G>T	p.Ala159Ser	p.A159S	ENST00000249071	NM_002872.4	159	Gct/Tct	6/7	1	2	FACETS	0.775	0.702	0.852	0.775	0.702	0.852	SUBCLONAL	1	TRUE	1	0.393438475539559	2		825	833	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513694	41513694	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	206	615	0	ENST00000263253.7:c.598C>T	p.Arg200Ter	p.R200*	ENST00000263253	NM_001429.3	200	Cga/Tga	2/31	1	2	FACETS	0.844	0.788	0.902	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	2		615	620	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572907	41572907	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	136	715	0	ENST00000263253.7:c.5192G>A	p.Arg1731His	p.R1731H	ENST00000263253	NM_001429.3	1731	cGc/cAc	31/31	1	2	FACETS	0.906	0.825	0.991	0.906	0.825	0.991	CLONAL	1	TRUE	1	0.393438475539559	2		715	763	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572952	41572952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	259	737	0	ENST00000263253.7:c.5237G>A	p.Cys1746Tyr	p.C1746Y	ENST00000263253	NM_001429.3	1746	tGc/tAc	31/31	1	2	FACETS	0.846	0.796	0.898	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		737	778	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181992	38181992	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	40	578	0	ENST00000396334.3:c.616G>C	p.Val206Leu	p.V206L	ENST00000396334	NM_002468.4	206	Gtg/Ctg	3/5	1	2	FACETS	0.323	0.268	0.385	0.323	0.268	0.385	SUBCLONAL	1	TRUE	1	0.393438475539559	2		578	629	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41279559	41279559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200308943	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	135	414	1	ENST00000349496.5:c.2129G>A	p.Arg710His	p.R710H	ENST00000349496	NM_001904.3	710	cGc/cAc	14/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.393438475539559	2		415	471	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162582	47162582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	140	315	0	ENST00000409792.3:c.3544G>A	p.Gly1182Ser	p.G1182S	ENST00000409792	NM_014159.6	1182	Ggt/Agt	3/21	1	2	FACETS	0.946	0.872	1	1	0.991	1	CLONAL	2	TRUE	1	0.393438475539559	2		315	376	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164291	47164291	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	52	235	0	ENST00000409792.3:c.1835C>A	p.Ala612Asp	p.A612D	ENST00000409792	NM_014159.6	612	gCt/gAt	3/21	1	2	FACETS	0.762	0.651	0.882	0.762	0.651	0.882	SUBCLONAL	1	TRUE	1	0.393438475539559	2		235	347	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165105	47165106	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	49	208	0	ENST00000409792.3:c.1020dup	p.Phe341IlefsTer6	p.F341Ifs*6	ENST00000409792	NM_014159.6	340	-/A	3/21	1	2	FACETS	0.791	0.673	0.919	0.791	0.673	0.919	CLONAL	1	TRUE	1	0.393438475539559	2		208	315	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397717	49397717	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	106	432	1	ENST00000418115.1:c.507G>T	p.Glu169Asp	p.E169D	ENST00000418115	NM_001664.2	169	gaG/gaT	5/5	1	2	FACETS	0.815	0.732	0.903	0.815	0.732	0.903	CLONAL	1	TRUE	1	0.393438475539559	2		433	661	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436622	52436622	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	93	657	0	ENST00000460680.1:c.2052G>T	p.Gln684His	p.Q684H	ENST00000460680	NM_004656.3	684	caG/caT	16/17	1	2	FACETS	0.771	0.687	0.861	0.771	0.687	0.861	SUBCLONAL	1	TRUE	1	0.393438475539559	2		657	613	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643844	52643844	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	148	449	0	ENST00000394830.3:c.2052T>G	p.Phe684Leu	p.F684L	ENST00000394830	NM_018313.4	684	ttT/ttG	17/30	1	2	FACETS	0.863	0.795	0.932	1	0.991	1	CLONAL	2	TRUE	1	0.393438475539559	2		449	436	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090572	71090572	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	32	347	0	ENST00000318789.4:c.776T>C	p.Val259Ala	p.V259A	ENST00000318789	NM_032682.5	259	gTc/gCc	11/21	1	2	FACETS	0.332	0.269	0.403	0.332	0.269	0.403	SUBCLONAL	1	TRUE	1	0.393438475539559	2		347	490	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71161761	71161761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	98	314	0	ENST00000318789.4:c.208C>T	p.Leu70Phe	p.L70F	ENST00000318789	NM_032682.5	70	Ctt/Ttt	7/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.393438475539559	2		314	366	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114549	73114549	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	18	147	0	ENST00000356692.5:c.930G>T	p.Glu310Asp	p.E310D	ENST00000356692		310	gaG/gaT	9/9	1	2	FACETS	0.464	0.351	0.598	0.464	0.351	0.598	SUBCLONAL	1	TRUE	1	0.393438475539559	2		147	197	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521680	89521680	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	184	449	0	ENST00000336596.2:c.2757G>A	p.Trp919Ter	p.W919*	ENST00000336596	NM_005233.5	919	tgG/tgA	16/17	1	2	FACETS	0.811	0.753	0.87	1	0.992	1	CLONAL	2	TRUE	1	0.393438475539559	2		449	577	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582302	119582302	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	160	397	0	ENST00000316626.5:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000316626		367	Cga/Tga	10/12	1	2	FACETS	0.817	0.754	0.881	1	0.991	1	CLONAL	2	TRUE	1	0.393438475539559	2		397	498	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670789	134670789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368276671	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	172	515	0	ENST00000398015.3:c.700G>A	p.Val234Met	p.V234M	ENST00000398015	NM_004441.4	234	Gtg/Atg	3/16	0.393438475539559	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.393438475539559	1		515	541	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898789	134898789	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	90	357	0	ENST00000398015.3:c.1847T>C	p.Val616Ala	p.V616A	ENST00000398015	NM_004441.4	616	gTa/gCa	10/16	0.393438475539559	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.393438475539559	1		357	336	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138407751	138407751	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	51	383	0	ENST00000289153.2:c.2102del	p.Gly701GlufsTer6	p.G701Efs*6	ENST00000289153	NM_006219.2	701	gGa/ga	14/22	1	2	FACETS	0.524	0.445	0.61	0.524	0.445	0.61	SUBCLONAL	1	TRUE	1	0.393438475539559	2		383	495	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138409876	138409876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760002387	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	131	368	0	ENST00000289153.2:c.2002C>T	p.Arg668Trp	p.R668W	ENST00000289153	NM_006219.2	668	Cgg/Tgg	13/22	1	2	FACETS	0.808	0.74	0.878	1	0.988	1	CLONAL	2	TRUE	1	0.393438475539559	2		368	412	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433411	138433411	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	157	367	0	ENST00000289153.2:c.1201T>C	p.Cys401Arg	p.C401R	ENST00000289153	NM_006219.2	401	Tgt/Cgt	7/22	1	2	FACETS	0.895	0.827	0.964	1	0.992	1	CLONAL	2	TRUE	1	0.393438475539559	2		367	446	SUCCESS
ATR	545	MSKCC	GRCh37	3	142211993	142211993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	135	367	0	ENST00000350721.4:c.6059C>T	p.Ala2020Val	p.A2020V	ENST00000350721	NM_001184.3	2020	gCa/gTa	35/47	1	2	FACETS	0.884	0.812	0.958	1	0.99	1	CLONAL	2	TRUE	1	0.393438475539559	2		367	388	SUCCESS
ATR	545	MSKCC	GRCh37	3	142218543	142218543	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	138	357	0	ENST00000350721.4:c.5306A>C	p.Glu1769Ala	p.E1769A	ENST00000350721	NM_001184.3	1769	gAa/gCa	31/47	1	2	FACETS	0.821	0.754	0.891	1	0.989	1	CLONAL	2	TRUE	1	0.393438475539559	2		357	427	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274872	142274872	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	155	432	0	ENST00000350721.4:c.2188G>T	p.Glu730Ter	p.E730*	ENST00000350721	NM_001184.3	730	Gaa/Taa	10/47	1	2	FACETS	0.788	0.726	0.851	1	0.99	1	SUBCLONAL	2	TRUE	1	0.393438475539559	2		432	500	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149243838	149243838	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1338920465	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	264	613	0	ENST00000360632.3:c.980C>T	p.Pro327Leu	p.P327L	ENST00000360632	NM_015472.4	327	cCg/cTg	6/7	1	2	FACETS	0.949	0.895	1	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		613	707	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374828	149374828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	30	449	0	ENST00000360632.3:c.266C>T	p.Ser89Leu	p.S89L	ENST00000360632	NM_015472.4	89	tCg/tTg	2/7	1	2	FACETS	0.296	0.237	0.362	0.296	0.237	0.362	SUBCLONAL	1	TRUE	1	0.393438475539559	2		449	516	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917688	178917688	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	37	146	0	ENST00000263967.3:c.562+1G>A		p.X188_splice	ENST00000263967	NM_006218.2	188			1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.393438475539559	2		146	183	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922301	178922301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	108	287	0	ENST00000263967.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000263967	NM_006218.2	357	cGa/cAa	6/21	1	2	FACETS	0.775	0.703	0.85	1	0.985	1	SUBCLONAL	2	TRUE	1	0.393438475539559	2		287	354	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442797	187442797	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	105	605	0	ENST00000232014.4:c.1909A>G	p.Thr637Ala	p.T637A	ENST00000232014	NM_001130845.1	637	Acc/Gcc	9/10	1	2	FACETS	0.872	0.783	0.966	0.872	0.783	0.966	CLONAL	1	TRUE	1	0.393438475539559	2		605	612	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447219	187447219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147914986	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	234	641	0	ENST00000232014.4:c.974G>A	p.Arg325Gln	p.R325Q	ENST00000232014	NM_001130845.1	325	cGg/cAg	5/10	1	2	FACETS	0.85	0.796	0.904	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		641	700	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447565	187447565	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151194132	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	105	615	1	ENST00000232014.4:c.628G>A	p.Asp210Asn	p.D210N	ENST00000232014	NM_001130845.1	210	Gat/Aat	5/10	1	2	FACETS	0.857	0.769	0.949	0.857	0.769	0.949	CLONAL	1	TRUE	1	0.393438475539559	2		616	623	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526184	189526184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762371837	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	239	631	1	ENST00000264731.3:c.448G>A	p.Ala150Thr	p.A150T	ENST00000264731	NM_003722.4	150	Gca/Aca	4/14	1	2	FACETS	0.846	0.793	0.9	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		632	718	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582120	189582120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	195	435	2	ENST00000264731.3:c.679G>A	p.Ala227Thr	p.A227T	ENST00000264731	NM_003722.4	227	Gcc/Acc	5/14	1	2	FACETS	0.89	0.83	0.951	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	2		437	557	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803117	1803117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1330260382	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	283	895	0	ENST00000260795.2:c.469G>A	p.Glu157Lys	p.E157K	ENST00000260795		157	Gag/Aag	4/17	0.393438475539559	1	FACETS	0.914	0.866	0.962	1	0.995	1	CLONAL	2	TRUE	0	0.393438475539559	1		895	632	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808388	1808388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	328	1027	0	ENST00000260795.2:c.2146C>T	p.Pro716Ser	p.P716S	ENST00000260795		716	Ccc/Tcc	15/17	0.393438475539559	1	FACETS	0.85	0.807	0.893	1	0.996	1	CLONAL	2	TRUE	0	0.393438475539559	1		1027	788	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153671	55153671	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	199	585	1	ENST00000257290.5:c.2637G>A	p.Trp879Ter	p.W879*	ENST00000257290	NM_006206.4	879	tgG/tgA	19/23	0.393438475539559	1	FACETS	0.781	0.73	0.833	1	0.992	1	SUBCLONAL	2	TRUE	0	0.393438475539559	1		586	520	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189879	66189879	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	126	392	0	ENST00000273854.3:c.3067C>A	p.Leu1023Ile	p.L1023I	ENST00000273854	NM_004439.5	1023	Ctt/Att	18/18	0.393438475539559	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.393438475539559	1		392	344	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286194	66286194	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	17	288	0	ENST00000273854.3:c.1492A>C	p.Ile498Leu	p.I498L	ENST00000273854	NM_004439.5	498	Atc/Ctc	6/18	0.393438475539559	1	FACETS	0.245	0.183	0.32	0.245	0.183	0.32	SUBCLONAL	1	TRUE	0	0.393438475539559	1		288	283	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383933	84383933	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	75	411	0	ENST00000321945.7:c.919T>A	p.Ser307Thr	p.S307T	ENST00000321945	NM_139076.2	307	Tct/Act	9/9	0.393438475539559	1	FACETS	0.707	0.622	0.798	0.707	0.622	0.798	SUBCLONAL	1	TRUE	0	0.393438475539559	1		411	433	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808339	99808339	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	51	315	0	ENST00000280892.6:c.350G>A	p.Gly117Asp	p.G117D	ENST00000280892	NM_001130678.1	117	gGt/gAt	5/7	0.393438475539559	1	FACETS	0.639	0.546	0.74	0.639	0.546	0.74	SUBCLONAL	1	TRUE	0	0.393438475539559	1		315	326	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155557	106155557	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	132	299	0	ENST00000380013.4:c.458C>A	p.Ser153Tyr	p.S153Y	ENST00000380013	NM_001127208.2	153	tCt/tAt	3/11	0.393438475539559	1	FACETS	0.812	0.747	0.877	1	0.989	1	CLONAL	2	TRUE	0	0.393438475539559	1		299	332	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142950056	142950056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568595082	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	85	279	0	ENST00000262992.4:c.2654G>A	p.Arg885His	p.R885H	ENST00000262992	NM_001101669.1	885	cGc/cAc	24/24	0.393438475539559	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.393438475539559	1		279	239	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143033701	143033701	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	52	290	0	ENST00000262992.4:c.2270C>A	p.Ala757Asp	p.A757D	ENST00000262992	NM_001101669.1	757	gCt/gAt	20/24	0.393438475539559	1	FACETS	0.687	0.588	0.794	0.687	0.588	0.794	SUBCLONAL	1	TRUE	0	0.393438475539559	1		290	309	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250895	153250895	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	104	248	0	ENST00000281708.4:c.1165T>A	p.Phe389Ile	p.F389I	ENST00000281708	NM_033632.3	389	Ttt/Att	8/12	0.393438475539559	1	FACETS	0.823	0.75	0.898	1	0.987	1	CLONAL	2	TRUE	0	0.393438475539559	1		248	258	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518179	187518179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	167	404	0	ENST00000441802.2:c.12515C>T	p.Ser4172Phe	p.S4172F	ENST00000441802	NM_005245.3	4172	tCc/tTc	25/27	0.393438475539559	1	FACETS	0.863	0.803	0.924	1	0.992	1	CLONAL	2	TRUE	0	0.393438475539559	1		404	395	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524755	187524755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	240	668	0	ENST00000441802.2:c.10925C>T	p.Thr3642Ile	p.T3642I	ENST00000441802	NM_005245.3	3642	aCc/aTc	19/27	0.393438475539559	1	FACETS	0.861	0.811	0.912	1	0.994	1	CLONAL	2	TRUE	0	0.393438475539559	1		668	569	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524950	187524950	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	195	577	0	ENST00000441802.2:c.10730C>T	p.Thr3577Ile	p.T3577I	ENST00000441802	NM_005245.3	3577	aCt/aTt	19/27	0.393438475539559	1	FACETS	0.796	0.744	0.85	1	0.992	1	SUBCLONAL	2	TRUE	0	0.393438475539559	1		577	500	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540721	187540721	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	141	411	0	ENST00000441802.2:c.7019G>A	p.Gly2340Asp	p.G2340D	ENST00000441802	NM_005245.3	2340	gGc/gAc	10/27	0.393438475539559	1	FACETS	0.834	0.771	0.899	1	0.99	1	CLONAL	2	TRUE	0	0.393438475539559	1		411	345	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628392	187628392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	35	595	1	ENST00000441802.2:c.2590G>A	p.Asp864Asn	p.D864N	ENST00000441802	NM_005245.3	864	Gac/Aac	2/27	0.393438475539559	1	FACETS	0.232	0.189	0.28	0.232	0.189	0.28	SUBCLONAL	1	TRUE	0	0.393438475539559	1		596	617	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629400	187629400	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1018407179	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	247	587	2	ENST00000441802.2:c.1582G>A	p.Glu528Lys	p.E528K	ENST00000441802	NM_005245.3	528	Gaa/Aaa	2/27	0.393438475539559	1	FACETS	0.842	0.793	0.891	1	0.994	1	CLONAL	2	TRUE	0	0.393438475539559	1		589	599	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254570	1254570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	549	843	2	ENST00000310581.5:c.3208G>A	p.Val1070Met	p.V1070M	ENST00000310581	NM_198253.2	1070	Gtg/Atg	15/16	0.336811910637431	3	FACETS	0.919	0.889	0.948	1	0.996	1	CLONAL	4	TRUE	0	0.393438475539559	3		845	909	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279521	1279521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1353891039	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	602	991	1	ENST00000310581.5:c.2015G>A	p.Arg672His	p.R672H	ENST00000310581	NM_198253.2	672	cGc/cAc	5/16	0.336811910637431	3	FACETS	0.908	0.88	0.936	1	0.996	1	CLONAL	4	TRUE	0	0.393438475539559	3		992	1008	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293545	1293545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199422293	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	161	973	1	ENST00000310581.5:c.1456C>T	p.Arg486Cys	p.R486C	ENST00000310581	NM_198253.2	486	Cgc/Tgc	2/16	0.336811910637431	3	FACETS	0.861	0.788	0.937	0.287	0.262	0.313	CLONAL	1	TRUE	0	0.393438475539559	3		974	1138	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294283	1294283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	131	848	2	ENST00000310581.5:c.718C>T	p.Arg240Cys	p.R240C	ENST00000310581	NM_198253.2	240	Cgt/Tgt	2/16	0.336811910637431	3	FACETS	0.905	0.82	0.993	0.302	0.273	0.331	CLONAL	1	TRUE	0	0.393438475539559	3		850	881	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468079	31468079	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	100	445	0	ENST00000344624.3:c.2333G>T	p.Arg778Leu	p.R778L	ENST00000344624		778	cGc/cTc	15/33	0.336811910637431	3	FACETS	0.859	0.768	0.956	0.286	0.256	0.319	CLONAL	1	TRUE	0	0.393438475539559	3		445	708	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515274	31515274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201711846	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	469	603	0	ENST00000344624.3:c.1111C>T	p.Arg371Cys	p.R371C	ENST00000344624		371	Cgt/Tgt	5/33	0.336811910637431	3	FACETS	0.897	0.865	0.929	1	0.995	1	CLONAL	4	TRUE	0	0.393438475539559	3		603	795	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31521312	31521312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746400926	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	41	435	1	ENST00000344624.3:c.865C>T	p.Arg289Trp	p.R289W	ENST00000344624		289	Cgg/Tgg	3/33	0.336811910637431	3	FACETS	0.397	0.329	0.471	0.132	0.109	0.157	SUBCLONAL	1	TRUE	0	0.393438475539559	3		436	629	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950030	38950030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1367871779	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	38	368	0	ENST00000357387.3:c.3920C>T	p.Ser1307Phe	p.S1307F	ENST00000357387	NM_152756.3	1307	tCt/tTt	31/38	0.336811910637431	3	FACETS	0.524	0.433	0.626	0.175	0.144	0.209	SUBCLONAL	1	TRUE	0	0.393438475539559	3		368	441	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38968131	38968131	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs143280630	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	44	208	0	ENST00000357387.3:c.974G>A	p.Arg325Gln	p.R325Q	ENST00000357387	NM_152756.3	325	cGa/cAa	12/38	0.336811910637431	3	FACETS	0.794	0.669	0.932	0.265	0.223	0.311	CLONAL	1	TRUE	0	0.393438475539559	3		208	337	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39002715	39002715	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	238	354	0	ENST00000357387.3:c.314G>A	p.Arg105Gln	p.R105Q	ENST00000357387	NM_152756.3	105	cGa/cAa	5/38	0.336811910637431	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	3	TRUE	0	0.393438475539559	3		354	481	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177486	56177486	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs775087404	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	69	346	0	ENST00000399503.3:c.2459A>G	p.Tyr820Cys	p.Y820C	ENST00000399503	NM_005921.1	820	tAc/tGc	14/20	0.342527508039289	1	FACETS	0.829	0.727	0.937	0.829	0.727	0.937	CLONAL	1	TRUE	0	0.393438475539559	1		346	340	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177605	56177605	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	78	349	0	ENST00000399503.3:c.2578G>T	p.Ala860Ser	p.A860S	ENST00000399503	NM_005921.1	860	Gca/Tca	14/20	0.342527508039289	1	FACETS	0.794	0.702	0.893	0.794	0.702	0.893	SUBCLONAL	1	TRUE	0	0.393438475539559	1		349	401	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179413	56179413	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	64	233	0	ENST00000399503.3:c.3726A>C	p.Glu1242Asp	p.E1242D	ENST00000399503	NM_005921.1	1242	gaA/gaC	15/20	0.342527508039289	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.393438475539559	1		233	251	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751365	57751365	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	27	274	0	ENST00000274289.3:c.1625+1G>A		p.X542_splice	ENST00000274289	NM_006622.3	542			0.342527508039289	1	FACETS	0.411	0.328	0.506	0.411	0.328	0.506	SUBCLONAL	1	TRUE	0	0.393438475539559	1		274	268	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522624	67522624	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	128	297	0	ENST00000274335.5:c.121G>A	p.Gly41Arg	p.G41R	ENST00000274335		41	Gga/Aga	1/15	0.342527508039289	1	FACETS	0.822	0.756	0.889	1	0.989	1	CLONAL	2	TRUE	0	0.393438475539559	1		297	318	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576493	67576493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	116	310	0	ENST00000274335.5:c.772C>A	p.Leu258Met	p.L258M	ENST00000274335		258	Ctg/Atg	5/15	0.342527508039289	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.393438475539559	1		310	318	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	83	189	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	0.342527508039289	1	FACETS	0.878	0.793	0.965	1	0.985	1	CLONAL	2	TRUE	0	0.393438475539559	1		189	193	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80168983	80168983	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	237	535	0	ENST00000265081.6:c.3179C>A	p.Thr1060Asn	p.T1060N	ENST00000265081	NM_002439.4	1060	aCt/aAt	23/24	0.342527508039289	1	FACETS	0.94	0.886	0.993	1	0.995	1	CLONAL	2	TRUE	0	0.393438475539559	1		535	515	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564512	86564512	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs767017718	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	225	634	0	ENST00000274376.6:c.244G>T	p.Gly82Trp	p.G82W	ENST00000274376	NM_002890.2	82	Ggg/Tgg	1/25	0.342527508039289	1	FACETS	0.868	0.817	0.921	1	0.994	1	CLONAL	2	TRUE	0	0.393438475539559	1		634	529	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564573	86564573	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	100	692	0	ENST00000274376.6:c.305T>G	p.Val102Gly	p.V102G	ENST00000274376	NM_002890.2	102	gTg/gGg	1/25	0.342527508039289	1	FACETS	0.729	0.653	0.81	0.729	0.653	0.81	SUBCLONAL	1	TRUE	0	0.393438475539559	1		692	560	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670673	86670673	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	25	117	0	ENST00000274376.6:c.1951A>T	p.Ile651Phe	p.I651F	ENST00000274376	NM_002890.2	651	Atc/Ttc	15/25	0.342527508039289	1	FACETS	0.54	0.429	0.666	0.54	0.429	0.666	SUBCLONAL	1	TRUE	0	0.393438475539559	1		117	189	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674234	86674234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	67	294	0	ENST00000274376.6:c.2366G>A	p.Arg789Gln	p.R789Q	ENST00000274376	NM_002890.2	789	cGa/cAa	18/25	0.342527508039289	1	FACETS	0.869	0.761	0.983	0.869	0.761	0.983	CLONAL	1	TRUE	0	0.393438475539559	1		294	315	SUCCESS
APC	324	MSKCC	GRCh37	5	112164560	112164560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	20	226	0	ENST00000257430.4:c.1634C>T	p.Ala545Val	p.A545V	ENST00000257430	NM_000038.5	545	gCg/gTg	14/16	0.342527508039289	1	FACETS	0.361	0.277	0.46	0.361	0.277	0.46	SUBCLONAL	1	TRUE	0	0.393438475539559	1		226	226	SUCCESS
APC	324	MSKCC	GRCh37	5	112173524	112173524	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	51	340	0	ENST00000257430.4:c.2233C>T	p.Pro745Ser	p.P745S	ENST00000257430	NM_000038.5	745	Cct/Tct	16/16	0.342527508039289	1	FACETS	0.807	0.692	0.931	0.807	0.692	0.931	CLONAL	1	TRUE	0	0.393438475539559	1		340	258	SUCCESS
APC	324	MSKCC	GRCh37	5	112174611	112174611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	66	360	0	ENST00000257430.4:c.3320C>T	p.Ala1107Val	p.A1107V	ENST00000257430	NM_000038.5	1107	gCc/gTc	16/16	0.342527508039289	1	FACETS	0.856	0.748	0.97	0.856	0.748	0.97	CLONAL	1	TRUE	0	0.393438475539559	1		360	315	SUCCESS
APC	324	MSKCC	GRCh37	5	112179365	112179365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	70	351	0	ENST00000257430.4:c.8074C>T	p.Pro2692Ser	p.P2692S	ENST00000257430	NM_000038.5	2692	Cca/Tca	16/16	0.342527508039289	1	FACETS	0.824	0.723	0.931	0.824	0.723	0.931	CLONAL	1	TRUE	0	0.393438475539559	1		351	347	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927019	131927019	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140333740	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	42	251	1	ENST00000265335.6:c.1556G>A	p.Arg519His	p.R519H	ENST00000265335		519	cGt/cAt	10/25	0.342527508039289	1	FACETS	0.849	0.717	0.992	0.849	0.717	0.992	CLONAL	1	TRUE	0	0.393438475539559	1		252	202	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973875	131973875	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	39	339	0	ENST00000265335.6:c.3578C>T	p.Thr1193Ile	p.T1193I	ENST00000265335		1193	aCa/aTa	23/25	0.342527508039289	1	FACETS	0.438	0.363	0.52	0.438	0.363	0.52	SUBCLONAL	1	TRUE	0	0.393438475539559	1		339	364	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131976385	131976385	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs546479838	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	184	470	1	ENST00000265335.6:c.3640C>T	p.Arg1214Cys	p.R1214C	ENST00000265335		1214	Cgc/Tgc	24/25	0.342527508039289	1	FACETS	0.81	0.755	0.865	1	0.992	1	CLONAL	2	TRUE	0	0.393438475539559	1		471	464	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433785	149433785	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	229	684	0	ENST00000286301.3:c.2766C>A	p.Asp922Glu	p.D922E	ENST00000286301	NM_005211.3	922	gaC/gaA	22/22	0.393438475539559	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.393438475539559	1		684	624	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497340	149497340	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	131	604	0	ENST00000261799.4:c.2978C>A	p.Pro993His	p.P993H	ENST00000261799	NM_002609.3	993	cCt/cAt	22/23	0.393438475539559	1	FACETS	0.985	0.898	1	0.985	0.898	1	CLONAL	1	TRUE	0	0.393438475539559	1		604	543	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637850	176637850	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115722008	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	100	525	0	ENST00000439151.2:c.2450C>T	p.Ser817Phe	p.S817F	ENST00000439151	NM_022455.4	817	tCt/tTt	5/23	0.393438475539559	1	FACETS	0.79	0.708	0.876	0.79	0.708	0.876	SUBCLONAL	1	TRUE	0	0.393438475539559	1		525	517	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176684153	176684153	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587784131	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	69	308	0	ENST00000439151.2:c.4966+1G>A		p.X1656_splice	ENST00000439151	NM_022455.4	1656			0.393438475539559	1	FACETS	0.807	0.708	0.914	0.807	0.708	0.914	CLONAL	1	TRUE	0	0.393438475539559	1		308	349	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720891	176720891	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	197	497	1	ENST00000439151.2:c.6522C>A	p.Phe2174Leu	p.F2174L	ENST00000439151	NM_022455.4	2174	ttC/ttA	23/23	0.393438475539559	1	FACETS	0.886	0.83	0.943	1	0.993	1	CLONAL	2	TRUE	0	0.393438475539559	1		498	454	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721361	176721361	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	87	519	0	ENST00000439151.2:c.6992A>G	p.Asp2331Gly	p.D2331G	ENST00000439151	NM_022455.4	2331	gAc/gGc	23/23	0.393438475539559	1	FACETS	0.788	0.7	0.88	0.788	0.7	0.88	SUBCLONAL	1	TRUE	0	0.393438475539559	1		519	451	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721760	176721760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587784216	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	82	468	0	ENST00000439151.2:c.7391G>A	p.Arg2464His	p.R2464H	ENST00000439151	NM_022455.4	2464	cGc/cAc	23/23	0.393438475539559	1	FACETS	0.823	0.729	0.921	0.823	0.729	0.921	CLONAL	1	TRUE	0	0.393438475539559	1		468	407	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046349	180046349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	115	698	0	ENST00000261937.6:c.2665G>A	p.Glu889Lys	p.E889K	ENST00000261937	NM_182925.4	889	Gag/Aag	19/30	0.393438475539559	1	FACETS	0.919	0.832	1	0.919	0.832	1	CLONAL	1	TRUE	0	0.393438475539559	1		698	511	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052971	180052971	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753074837	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	152	921	3	ENST00000261937.6:c.1319G>A	p.Arg440His	p.R440H	ENST00000261937	NM_182925.4	440	cGc/cAc	10/30	0.393438475539559	1	FACETS	0.885	0.812	0.962	0.885	0.812	0.962	CLONAL	1	TRUE	0	0.393438475539559	1		924	701	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056059	26056059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356957360	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	63	361	0	ENST00000343677.2:c.598C>T	p.Pro200Ser	p.P200S	ENST00000343677	NM_005319.3	200	Ccc/Tcc	1/1	0.321353483667012	3	FACETS	0.767	0.664	0.877	0.383	0.332	0.439	SUBCLONAL	1	TRUE	1	0.393438475539559	3		361	500	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056533	26056533	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1332170864	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	39	294	0	ENST00000343677.2:c.124G>C	p.Glu42Gln	p.E42Q	ENST00000343677	NM_005319.3	42	Gag/Cag	1/1	0.321353483667012	3	FACETS	0.582	0.482	0.692	0.291	0.241	0.346	SUBCLONAL	1	TRUE	1	0.393438475539559	3		294	408	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056654	26056654	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	19	212	0	ENST00000343677.2:c.3G>A	p.Met1?	p.M1?	ENST00000343677	NM_005319.3	1	atG/atA	1/1	0.321353483667012	3	FACETS	0.408	0.31	0.524	0.204	0.155	0.262	SUBCLONAL	1	TRUE	1	0.393438475539559	3		212	283	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680425	30680425	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	85	587	0	ENST00000376406.3:c.1294G>T	p.Glu432Ter	p.E432*	ENST00000376406	NM_014641.2	432	Gaa/Taa	5/15	0.321353483667012	3	FACETS	0.689	0.609	0.776	0.345	0.304	0.388	SUBCLONAL	1	TRUE	1	0.393438475539559	3		587	750	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166875	32166875	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	176	830	0	ENST00000375023.3:c.4363G>A	p.Ala1455Thr	p.A1455T	ENST00000375023	NM_004557.3	1455	Gcc/Acc	24/30	0.321353483667012	3	FACETS	0.974	0.896	1	0.487	0.448	0.528	CLONAL	1	TRUE	1	0.393438475539559	3		830	1099	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171546	32171546	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	318	586	1	ENST00000375023.3:c.3231+1G>A		p.X1077_splice	ENST00000375023	NM_004557.3	1077			0.321353483667012	3	FACETS	0.936	0.89	0.982	1	0.994	1	CLONAL	3	TRUE	1	0.393438475539559	3		587	689	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190527	32190527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775207648	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	366	712	0	ENST00000375023.3:c.212C>T	p.Ala71Val	p.A71V	ENST00000375023	NM_004557.3	71	gCc/gTc	3/30	0.321353483667012	3	FACETS	0.896	0.855	0.938	1	0.995	1	CLONAL	3	TRUE	1	0.393438475539559	3		712	828	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798417	32798417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770778501	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	218	628	1	ENST00000374899.4:c.1439G>A	p.Arg480His	p.R480H	ENST00000374899	NM_018833.2	480	cGc/cAc	8/12	0.321353483667012	3	FACETS	0.79	0.736	0.846	0.79	0.736	0.846	SUBCLONAL	2	TRUE	1	0.393438475539559	3		629	839	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32819922	32819922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1257301662	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	272	613	0	ENST00000354258.4:c.988C>T	p.Arg330Cys	p.R330C	ENST00000354258	NM_000593.5	330	Cgc/Tgc	3/11	0.321353483667012	3	FACETS	0.831	0.78	0.882	0.831	0.78	0.882	CLONAL	2	TRUE	1	0.393438475539559	3		613	996	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287986	33287986	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	166	403	0	ENST00000374542.5:c.1267G>T	p.Ala423Ser	p.A423S	ENST00000374542	NM_001141970.1	423	Gca/Tca	5/8	0.321353483667012	3	FACETS	0.964	0.891	1	0.964	0.891	1	CLONAL	2	TRUE	1	0.393438475539559	3		403	524	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288897	33288897	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	69	419	0	ENST00000374542.5:c.655G>T	p.Asp219Tyr	p.D219Y	ENST00000374542	NM_001141970.1	219	Gac/Tac	3/8	0.321353483667012	3	FACETS	0.759	0.662	0.864	0.38	0.331	0.432	SUBCLONAL	1	TRUE	1	0.393438475539559	3		419	553	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652243	36652243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs558863376	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	388	713	1	ENST00000244741.5:c.365G>A	p.Arg122His	p.R122H	ENST00000244741	NM_000389.4	122	cGc/cAc	2/3	0.321353483667012	3	FACETS	0.865	0.825	0.904	1	0.994	1	CLONAL	3	TRUE	1	0.393438475539559	3		714	910	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112035587	112035587	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs778511334	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	137	321	0	ENST00000368678.4:c.307T>G	p.Phe103Val	p.F103V	ENST00000368678		103	Ttt/Gtt	4/13	0.393438475539559	1	FACETS	0.808	0.745	0.873	1	0.99	1	CLONAL	2	TRUE	0	0.393438475539559	1		321	346	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674183	117674183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	83	463	0	ENST00000368508.3:c.4291G>A	p.Ala1431Thr	p.A1431T	ENST00000368508	NM_002944.2	1431	Gct/Act	26/43	0.393438475539559	1	FACETS	0.77	0.683	0.863	0.77	0.683	0.863	SUBCLONAL	1	TRUE	0	0.393438475539559	1		463	440	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677864	117677864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	64	324	0	ENST00000368508.3:c.4069G>A	p.Ala1357Thr	p.A1357T	ENST00000368508	NM_002944.2	1357	Gca/Aca	25/43	0.393438475539559	1	FACETS	0.79	0.688	0.898	0.79	0.688	0.898	SUBCLONAL	1	TRUE	0	0.393438475539559	1		324	331	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724440	117724440	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	23	422	0	ENST00000368508.3:c.439A>G	p.Thr147Ala	p.T147A	ENST00000368508	NM_002944.2	147	Act/Gct	6/43	0.393438475539559	1	FACETS	0.24	0.187	0.302	0.24	0.187	0.302	SUBCLONAL	1	TRUE	0	0.393438475539559	1		422	391	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196086	138196086	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	65	297	0	ENST00000237289.4:c.400G>T	p.Asp134Tyr	p.D134Y	ENST00000237289	NM_001270507.1	134	Gac/Tac	3/9	0.393438475539559	1	FACETS	0.891	0.779	1	0.891	0.779	1	CLONAL	1	TRUE	0	0.393438475539559	1		297	298	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199855	138199855	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781186525	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	88	499	0	ENST00000237289.4:c.1273C>T	p.Pro425Ser	p.P425S	ENST00000237289	NM_001270507.1	425	Ccg/Tcg	7/9	0.393438475539559	1	FACETS	0.79	0.703	0.882	0.79	0.703	0.882	SUBCLONAL	1	TRUE	0	0.393438475539559	1		499	455	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004702	150004702	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	160	455	0	ENST00000253339.5:c.1523T>C	p.Leu508Pro	p.L508P	ENST00000253339		508	cTa/cCa	3/7	0.393438475539559	1	FACETS	0.783	0.726	0.842	1	0.991	1	SUBCLONAL	2	TRUE	0	0.393438475539559	1		455	417	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005506	150005506	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	64	377	0	ENST00000253339.5:c.719C>A	p.Pro240His	p.P240H	ENST00000253339		240	cCt/cAt	3/7	0.393438475539559	1	FACETS	0.773	0.674	0.88	0.773	0.674	0.88	SUBCLONAL	1	TRUE	0	0.393438475539559	1		377	338	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382166	152382166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752526411	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	162	381	0	ENST00000206249.3:c.1276G>A	p.Asp426Asn	p.D426N	ENST00000206249	NM_000125.3	426	Gac/Aac	6/8	0.393438475539559	1	FACETS	0.844	0.784	0.904	1	0.992	1	CLONAL	2	TRUE	0	0.393438475539559	1		381	392	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150532	157150532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151093357	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	166	476	0	ENST00000346085.5:c.1714G>A	p.Gly572Arg	p.G572R	ENST00000346085	NM_020732.3	572	Gga/Aga	2/20	0.393438475539559	1	FACETS	0.809	0.751	0.867	1	0.991	1	CLONAL	2	TRUE	0	0.393438475539559	1		476	419	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527898	157527898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	40	508	0	ENST00000346085.5:c.5623G>A	p.Ala1875Thr	p.A1875T	ENST00000346085	NM_020732.3	1875	Gca/Aca	20/20	0.393438475539559	1	FACETS	0.357	0.297	0.425	0.357	0.297	0.425	SUBCLONAL	1	TRUE	0	0.393438475539559	1		508	457	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161807881	161807881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375036403	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	164	364	2	ENST00000366898.1:c.1112C>T	p.Ala371Val	p.A371V	ENST00000366898	NM_004562.2	371	gCg/gTg	10/12	0.393438475539559	1	FACETS	0.905	0.843	0.968	1	0.992	1	CLONAL	2	TRUE	0	0.393438475539559	1		366	370	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864349	162864349	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	78	355	0	ENST00000366898.1:c.164C>A	p.Thr55Asn	p.T55N	ENST00000366898	NM_004562.2	55	aCt/aAt	2/12	0.393438475539559	1	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	0	0.393438475539559	1		355	316	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864380	162864380	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	181	429	0	ENST00000366898.1:c.133T>G	p.Phe45Val	p.F45V	ENST00000366898	NM_004562.2	45	Ttc/Gtc	2/12	0.393438475539559	1	FACETS	0.882	0.824	0.941	1	0.993	1	CLONAL	2	TRUE	0	0.393438475539559	1		429	419	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958187	2958187	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	324	642	0	ENST00000396946.4:c.2545C>A	p.Leu849Met	p.L849M	ENST00000396946	NM_032415.4	849	Ctg/Atg	19/25	0.242480283348898	3	FACETS	0.851	0.808	0.894	1	0.993	1	CLONAL	3	TRUE	1	0.393438475539559	3		642	772	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959201	2959201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1466997751	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	356	699	0	ENST00000396946.4:c.2315C>T	p.Ser772Leu	p.S772L	ENST00000396946	NM_032415.4	772	tCg/tTg	18/25	0.242480283348898	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	3		699	874	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987272	2987272	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	149	533	1	ENST00000396946.4:c.157G>T	p.Asp53Tyr	p.D53Y	ENST00000396946	NM_032415.4	53	Gat/Tat	3/25	0.242480283348898	3	FACETS	0.801	0.735	0.869	0.801	0.735	0.869	CLONAL	2	TRUE	1	0.393438475539559	3		534	566	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971155	13971155	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	102	310	0	ENST00000405192.2:c.774G>T	p.Gln258His	p.Q258H	ENST00000405192	NM_001163147.1	258	caG/caT	8/12	0.242480283348898	3	FACETS	0.81	0.73	0.893	0.81	0.73	0.893	CLONAL	2	TRUE	1	0.393438475539559	3		310	383	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971171	13971171	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	117	360	1	ENST00000405192.2:c.758C>A	p.Pro253His	p.P253H	ENST00000405192	NM_001163147.1	253	cCt/cAt	8/12	0.242480283348898	3	FACETS	0.784	0.711	0.859	0.784	0.711	0.859	SUBCLONAL	2	TRUE	1	0.393438475539559	3		361	454	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978824	13978824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	218	458	0	ENST00000405192.2:c.283C>T	p.Pro95Ser	p.P95S	ENST00000405192	NM_001163147.1	95	Cca/Tca	6/12	0.242480283348898	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.393438475539559	3		458	549	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739759	41739759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	237	654	0	ENST00000242208.4:c.214C>T	p.Pro72Ser	p.P72S	ENST00000242208	NM_002192.2	72	Ccc/Tcc	2/3	0.242480283348898	3	FACETS	0.97	0.909	1	0.97	0.909	1	CLONAL	2	TRUE	1	0.393438475539559	3		654	743	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55225428	55225428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	78	432	1	ENST00000275493.2:c.1280G>A	p.Arg427His	p.R427H	ENST00000275493	NM_005228.3	427	cGc/cAc	11/28	0.242480283348898	3	FACETS	0.923	0.813	1	0.462	0.406	0.521	CLONAL	1	TRUE	1	0.393438475539559	3		433	514	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240779	55240779	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	117	826	0	ENST00000275493.2:c.2023C>T	p.Arg675Trp	p.R675W	ENST00000275493	NM_005228.3	675	Cgg/Tgg	17/28	0.242480283348898	3	FACETS	0.835	0.753	0.923	0.418	0.376	0.462	CLONAL	1	TRUE	1	0.393438475539559	3		826	852	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268086	55268086	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	382	687	0	ENST00000275493.2:c.2926C>T	p.Gln976Ter	p.Q976*	ENST00000275493	NM_005228.3	976	Cag/Tag	24/28	0.242480283348898	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.393438475539559	3		687	959	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55272969	55272969	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	159	502	0	ENST00000275493.2:c.3294del	p.Arg1100GlyfsTer16	p.R1100Gfs*16	ENST00000275493	NM_005228.3	1098	Ccc/cc	28/28	0.242480283348898	3	FACETS	0.778	0.716	0.842	0.778	0.716	0.842	SUBCLONAL	2	TRUE	1	0.393438475539559	3		502	622	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273039	55273039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	254	631	0	ENST00000275493.2:c.3362G>A	p.Arg1121Lys	p.R1121K	ENST00000275493	NM_005228.3	1121	aGa/aAa	28/28	0.242480283348898	3	FACETS	0.956	0.898	1	0.956	0.898	1	CLONAL	2	TRUE	1	0.393438475539559	3		631	808	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273145	55273145	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	214	603	0	ENST00000275493.2:c.3468C>A	p.His1156Gln	p.H1156Q	ENST00000275493	NM_005228.3	1156	caC/caA	28/28	0.242480283348898	3	FACETS	0.909	0.848	0.972	0.909	0.848	0.972	CLONAL	2	TRUE	1	0.393438475539559	3		603	716	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346592	81346592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764869064	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	170	393	0	ENST00000222390.5:c.1361C>T	p.Thr454Met	p.T454M	ENST00000222390	NM_000601.4	454	aCg/aTg	11/18	0.242480283348898	3	FACETS	0.855	0.797	0.915	1	0.987	1	CLONAL	3	TRUE	1	0.393438475539559	3		393	403	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508064	106508064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	84	291	0	ENST00000359195.3:c.58C>T	p.Arg20Cys	p.R20C	ENST00000359195	NM_002649.2	20	Cgc/Tgc	2/11	0.242480283348898	3	FACETS	0.919	0.822	1	0.919	0.822	1	CLONAL	2	TRUE	1	0.393438475539559	3		291	278	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508578	106508578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1445337101	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	196	438	0	ENST00000359195.3:c.572G>A	p.Arg191His	p.R191H	ENST00000359195	NM_002649.2	191	cGc/cAc	2/11	0.242480283348898	3	FACETS	0.872	0.816	0.928	1	0.99	1	CLONAL	3	TRUE	1	0.393438475539559	3		438	456	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845536	128845536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	348	664	0	ENST00000249373.3:c.833G>A	p.Ser278Asn	p.S278N	ENST00000249373	NM_005631.4	278	aGc/aAc	4/12	0.242480283348898	3	FACETS	0.848	0.807	0.89	1	0.993	1	CLONAL	3	TRUE	1	0.393438475539559	3		664	832	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534584	140534584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	72	396	1	ENST00000288602.6:c.329C>T	p.Ser110Phe	p.S110F	ENST00000288602	NM_004333.4	110	tCt/tTt	3/18	0.242480283348898	3	FACETS	0.867	0.759	0.983	0.434	0.379	0.492	CLONAL	1	TRUE	1	0.393438475539559	3		397	505	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511197	148511197	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	102	470	1	ENST00000320356.2:c.1705G>A	p.Ala569Thr	p.A569T	ENST00000320356	NM_004456.4	569	Gca/Aca	15/20	0.242480283348898	3	FACETS	0.929	0.832	1	0.464	0.416	0.516	CLONAL	1	TRUE	1	0.393438475539559	3		471	668	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515148	148515148	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775942317	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	200	365	0	ENST00000320356.2:c.1061G>A	p.Arg354His	p.R354H	ENST00000320356	NM_004456.4	354	cGt/cAt	10/20	0.242480283348898	3	FACETS	0.848	0.794	0.903	1	0.989	1	CLONAL	3	TRUE	1	0.393438475539559	3		365	478	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835984	151835984	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	62	385	0	ENST00000262189.6:c.14540T>C	p.Ile4847Thr	p.I4847T	ENST00000262189	NM_170606.2	4847	aTc/aCc	58/59	0.242480283348898	3	FACETS	0.818	0.708	0.937	0.409	0.354	0.469	CLONAL	1	TRUE	1	0.393438475539559	3		385	461	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860908	151860908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	94	264	0	ENST00000262189.6:c.9754C>T	p.Arg3252Cys	p.R3252C	ENST00000262189	NM_170606.2	3252	Cgt/Tgt	43/59	0.242480283348898	3	FACETS	0.869	0.781	0.96	0.869	0.781	0.96	CLONAL	2	TRUE	1	0.393438475539559	3		264	329	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151947038	151947038	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs760517811	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	143	287	1	ENST00000262189.6:c.1736C>T	p.Ala579Val	p.A579V	ENST00000262189	NM_170606.2	579	gCg/gTg	13/59	0.242480283348898	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.393438475539559	3		288	390	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055711	152055711	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	84	545	1	ENST00000262189.6:c.211G>T	p.Gly71Trp	p.G71W	ENST00000262189	NM_170606.2	71	Ggg/Tgg	2/59	0.242480283348898	3	FACETS	0.79	0.698	0.888	0.395	0.349	0.444	SUBCLONAL	1	TRUE	1	0.393438475539559	3		546	647	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540238	23540238	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	96	513	0	ENST00000380871.4:c.165G>C	p.Glu55Asp	p.E55D	ENST00000380871	NM_006167.3	55	gaG/gaC	1/2	0.321353483667012	3	FACETS	0.993	0.887	1	0.497	0.443	0.553	CLONAL	1	TRUE	1	0.393438475539559	3		513	588	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146171	38146171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	423	653	1	ENST00000317025.8:c.3335C>T	p.Ser1112Leu	p.S1112L	ENST00000317025	NM_023034.1	1112	tCg/tTg	19/24	0.321353483667012	3	FACETS	0.922	0.883	0.962	1	0.996	1	CLONAL	3	TRUE	1	0.393438475539559	3		654	930	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934365	68934365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	95	249	0	ENST00000288368.4:c.431C>T	p.Thr144Ile	p.T144I	ENST00000288368	NM_024870.2	144	aCa/aTa	4/40	0.321353483667012	3	FACETS	1	0.951	1	0.556	0.496	0.619	CLONAL	1	TRUE	1	0.393438475539559	3		249	520	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995523	68995523	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	63	475	0	ENST00000288368.4:c.1927C>A	p.Leu643Ile	p.L643I	ENST00000288368	NM_024870.2	643	Cta/Ata	18/40	0.321353483667012	3	FACETS	0.591	0.51	0.678	0.295	0.255	0.339	SUBCLONAL	1	TRUE	1	0.393438475539559	3		475	649	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002939	69002939	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773432628	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	107	291	0	ENST00000288368.4:c.2239C>T	p.Arg747Trp	p.R747W	ENST00000288368	NM_024870.2	747	Cgg/Tgg	20/40	0.321353483667012	3	FACETS	0.766	0.692	0.843	0.766	0.692	0.843	SUBCLONAL	2	TRUE	1	0.393438475539559	3		291	425	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74872001	74872001	+	start_lost,splice_region_variant	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	72	148	0	ENST00000284811.8:c.3G>A	p.Met1?	p.M1?	ENST00000284811		1	atG/atA	2/4	0.321353483667012	3	FACETS	1	0.975	1	0.737	0.65	0.829	CLONAL	1	TRUE	1	0.393438475539559	3		148	297	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967703	90967703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	84	225	0	ENST00000265433.3:c.1205C>T	p.Thr402Ile	p.T402I	ENST00000265433	NM_002485.4	402	aCt/aTt	10/16	0.321353483667012	3	FACETS	1	0.976	1	0.702	0.624	0.784	CLONAL	1	TRUE	1	0.393438475539559	3		225	364	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141557654	141557654	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	105	904	0	ENST00000220592.5:c.1661G>T	p.Arg554Met	p.R554M	ENST00000220592	NM_012154.3	554	aGg/aTg	13/19	0.321353483667012	3	FACETS	0.53	0.473	0.591	0.265	0.236	0.296	SUBCLONAL	1	TRUE	1	0.393438475539559	3		904	1205	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561436	141561436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	306	552	2	ENST00000220592.5:c.1369G>A	p.Ala457Thr	p.A457T	ENST00000220592	NM_012154.3	457	Gcc/Acc	11/19	0.321353483667012	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.393438475539559	3		554	775	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566312	141566312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754710399	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	293	461	0	ENST00000220592.5:c.1100C>T	p.Ala367Val	p.A367V	ENST00000220592	NM_012154.3	367	gCg/gTg	9/19	0.321353483667012	3	FACETS	0.88	0.834	0.926	1	0.993	1	CLONAL	3	TRUE	1	0.393438475539559	3		461	675	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737820	145737820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs36023964	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	392	887	2	ENST00000428558.2:c.3010C>T	p.Arg1004Trp	p.R1004W	ENST00000428558	NM_004260.3	1004	Cgg/Tgg	18/22	0.321353483667012	3	FACETS	0.906	0.866	0.947	1	0.995	1	CLONAL	3	TRUE	1	0.393438475539559	3		889	877	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737902	145737902	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	175	935	0	ENST00000428558.2:c.2928G>T	p.Glu976Asp	p.E976D	ENST00000428558	NM_004260.3	976	gaG/gaT	18/22	0.321353483667012	3	FACETS	1	0.966	1	0.544	0.501	0.59	CLONAL	1	TRUE	1	0.393438475539559	3		935	978	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126342	5126342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746602942	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	90	199	1	ENST00000381652.3:c.3187C>T	p.Arg1063Cys	p.R1063C	ENST00000381652	NM_004972.3	1063	Cgt/Tgt	24/25	0.375453045293922	0	FACETS	0.836	0.765	0.906			1	CLONAL	2	TRUE	0	0.393438475539559	0		200	166	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465625	8465625	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	76	373	1	ENST00000356435.5:c.3555A>C	p.Glu1185Asp	p.E1185D	ENST00000356435		1185	gaA/gaC	21/35	0.375453045293922	0	FACETS	0.843	0.748	0.943			1	CLONAL	1	TRUE	0	0.393438475539559	0		374	278	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504315	8504315	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774444064	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	192	547	0	ENST00000356435.5:c.1768C>T	p.Pro590Ser	p.P590S	ENST00000356435		590	Cct/Tct	12/35	0.375453045293922	0	FACETS	0.789	0.742	0.837			1	SUBCLONAL	2	TRUE	0	0.393438475539559	0		547	375	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518229	8518229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	109	332	0	ENST00000356435.5:c.1162G>A	p.Asp388Asn	p.D388N	ENST00000356435		388	Gat/Aat	10/35	0.375453045293922	0	FACETS	0.683	0.626	0.741			1	SUBCLONAL	2	TRUE	0	0.393438475539559	0		332	246	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157829	27157829	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	157	390	0	ENST00000380036.4:c.53G>A	p.Gly18Glu	p.G18E	ENST00000380036	NM_000459.3	18	gGa/gAa	2/23	0.375453045293922	0	FACETS	0.807	0.754	0.859			1	CLONAL	2	TRUE	0	0.393438475539559	0		390	300	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27172641	27172641	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	162	501	0	ENST00000380036.4:c.656A>C	p.Glu219Ala	p.E219A	ENST00000380036	NM_000459.3	219	gAa/gCa	5/23	0.375453045293922	0	FACETS	0.739	0.689	0.789			1	SUBCLONAL	2	TRUE	0	0.393438475539559	0		501	338	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180310	27180310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1286718039	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	175	498	1	ENST00000380036.4:c.974G>A	p.Arg325His	p.R325H	ENST00000380036	NM_000459.3	325	cGc/cAc	7/23	0.375453045293922	0	FACETS	0.747	0.699	0.796			1	SUBCLONAL	2	TRUE	0	0.393438475539559	0		499	361	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606492	93606492	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs752276138	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	169	857	0	ENST00000375746.1:c.312G>T	p.Lys104Asn	p.K104N	ENST00000375746	NM_001174167.1	104	aaG/aaT	2/14	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.393438475539559	2		857	853	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641212	93641212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200320837	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	111	390	0	ENST00000375746.1:c.1558C>T	p.Arg520Cys	p.R520C	ENST00000375746	NM_001174167.1	520	Cgt/Tgt	11/14	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.393438475539559	2		390	415	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97869368	97869368	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780179187	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	229	585	0	ENST00000289081.3:c.1513G>A	p.Ala505Thr	p.A505T	ENST00000289081	NM_000136.2	505	Gcc/Acc	14/15	1	2	FACETS	0.864	0.809	0.919	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		585	674	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97934393	97934393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	52	232	0	ENST00000289081.3:c.382G>A	p.Asp128Asn	p.D128N	ENST00000289081	NM_000136.2	128	Gat/Aat	5/15	1	2	FACETS	0.771	0.659	0.892	0.771	0.659	0.892	SUBCLONAL	1	TRUE	1	0.393438475539559	2		232	343	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209411	98209411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	64	769	0	ENST00000331920.6:c.4127C>T	p.Ser1376Phe	p.S1376F	ENST00000331920	NM_000264.3	1376	tCc/tTc	23/24	1	2	FACETS	0.43	0.371	0.493	0.43	0.371	0.493	SUBCLONAL	1	TRUE	1	0.393438475539559	2		769	757	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209717	98209717	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	81	678	0	ENST00000331920.6:c.3821C>T	p.Ser1274Phe	p.S1274F	ENST00000331920	NM_000264.3	1274	tCc/tTc	23/24	1	2	FACETS	0.525	0.461	0.592	0.525	0.461	0.592	SUBCLONAL	1	TRUE	1	0.393438475539559	2		678	785	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347904	128347904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377752331	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	298	740	0	ENST00000265960.3:c.601G>A	p.Ala201Thr	p.A201T	ENST00000265960	NM_001006617.1	201	Gcc/Acc	5/12	1	2	FACETS	0.906	0.856	0.956	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		740	836	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347909	128347909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	298	732	1	ENST00000265960.3:c.596C>T	p.Ala199Val	p.A199V	ENST00000265960	NM_001006617.1	199	gCc/gTc	5/12	1	2	FACETS	0.881	0.832	0.93	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		733	860	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760373	133760373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777134913	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	256	687	0	ENST00000318560.5:c.2696C>T	p.Pro899Leu	p.P899L	ENST00000318560	NM_005157.4	899	cCg/cTg	11/11	1	2	FACETS	0.913	0.859	0.967	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		687	713	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133761029	133761029	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	129	697	0	ENST00000318560.5:c.3352C>A	p.Leu1118Ile	p.L1118I	ENST00000318560	NM_005157.4	1118	Ctc/Atc	11/11	1	2	FACETS	0.84	0.762	0.922	0.84	0.762	0.922	CLONAL	1	TRUE	1	0.393438475539559	2		697	781	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300848	137300848	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	178	786	0	ENST00000481739.1:c.493A>G	p.Lys165Glu	p.K165E	ENST00000481739	NM_002957.4	165	Aag/Gag	4/10	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.393438475539559	2		786	879	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390716	139390716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751367016	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	350	984	1	ENST00000277541.6:c.7475C>T	p.Ser2492Leu	p.S2492L	ENST00000277541	NM_017617.3	2492	tCg/tTg	34/34	1	2	FACETS	0.931	0.884	0.978	1	0.996	1	CLONAL	2	TRUE	1	0.393438475539559	2		985	956	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391666	139391666	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1450558564	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	145	949	0	ENST00000277541.6:c.6525C>A	p.Asp2175Glu	p.D2175E	ENST00000277541	NM_017617.3	2175	gaC/gaA	34/34	1	2	FACETS	0.818	0.746	0.894	0.818	0.746	0.894	CLONAL	1	TRUE	1	0.393438475539559	2		949	901	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391896	139391896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766745955	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	314	945	1	ENST00000277541.6:c.6295G>A	p.Asp2099Asn	p.D2099N	ENST00000277541	NM_017617.3	2099	Gac/Aac	34/34	1	2	FACETS	0.869	0.822	0.917	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		946	918	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391957	139391957	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	174	851	2	ENST00000277541.6:c.6234G>T	p.Lys2078Asn	p.K2078N	ENST00000277541	NM_017617.3	2078	aaG/aaT	34/34	1	2	FACETS	0.955	0.879	1	0.955	0.879	1	CLONAL	1	TRUE	1	0.393438475539559	2		853	926	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400185	139400185	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	300	907	0	ENST00000277541.6:c.4163G>A	p.Ser1388Asn	p.S1388N	ENST00000277541	NM_017617.3	1388	aGc/aAc	25/34	1	2	FACETS	0.894	0.845	0.944	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		907	853	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401802	139401802	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544640305	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	294	864	0	ENST00000277541.6:c.3598G>A	p.Asp1200Asn	p.D1200N	ENST00000277541	NM_017617.3	1200	Gac/Aac	22/34	1	2	FACETS	0.891	0.841	0.941	1	0.995	1	CLONAL	2	TRUE	1	0.393438475539559	2		864	839	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930319	39930319	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	134	641	0	ENST00000378444.4:c.3145G>T	p.Ala1049Ser	p.A1049S	ENST00000378444	NM_001123385.1	1049	Gcc/Tcc	6/15	0.303036108281108	0	FACETS	0.767	0.7	0.836			1	SUBCLONAL	1	TRUE	0	0.393438475539559	0		641	539	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833938	44833938	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	173	362	0	ENST00000377967.4:c.362G>A	p.Ser121Asn	p.S121N	ENST00000377967	NM_021140.2	121	aGt/aAt	4/29	0.303036108281108	0	FACETS	0.78	0.73	0.829			1	SUBCLONAL	2	TRUE	0	0.393438475539559	0		362	342	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44919337	44919337	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	103	438	0	ENST00000377967.4:c.1265C>T	p.Ala422Val	p.A422V	ENST00000377967	NM_021140.2	422	gCg/gTg	13/29	0.303036108281108	0	FACETS	0.628	0.572	0.685			1	SUBCLONAL	2	TRUE	0	0.393438475539559	0		438	253	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045776	47045776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs538880998	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	345	899	0	ENST00000377604.3:c.2657C>T	p.Thr886Met	p.T886M	ENST00000377604	NM_001204468.1	886	aCg/aTg	23/24	0.393438475539559	0	FACETS	0.936	0.898	0.974			1	CLONAL	2	TRUE	0	0.393438475539559	0		899	568	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424383	47424383	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	75	559	1	ENST00000377045.4:c.304-1G>A		p.X102_splice	ENST00000377045	NM_001654.4	102			0.393438475539559	0	FACETS	0.634	0.559	0.713			1	SUBCLONAL	1	TRUE	0	0.393438475539559	0		560	365	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651681	48651681	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	221	655	0	ENST00000376670.3:c.847G>A	p.Gly283Ser	p.G283S	ENST00000376670	NM_002049.3	283	Ggc/Agc	5/6	0.393438475539559	0	FACETS	0.815	0.77	0.86			1	CLONAL	2	TRUE	0	0.393438475539559	0		655	418	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230809	53230809	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	282	803	0	ENST00000375401.3:c.1984C>A	p.Leu662Met	p.L662M	ENST00000375401	NM_004187.3	662	Ctg/Atg	14/26	0.393438475539559	0	FACETS	0.807	0.767	0.846			1	CLONAL	2	TRUE	0	0.393438475539559	0		803	539	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246393	53246393	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	126	674	0	ENST00000375401.3:c.589C>A	p.Leu197Ile	p.L197I	ENST00000375401	NM_004187.3	197	Cta/Ata	5/26	0.393438475539559	0	FACETS	0.756	0.688	0.827			1	SUBCLONAL	1	TRUE	0	0.393438475539559	0		674	514	SUCCESS
AR	367	MSKCC	GRCh37	X	66931469	66931469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	116	631	0	ENST00000374690.3:c.2111G>A	p.Ser704Asn	p.S704N	ENST00000374690	NM_000044.3	704	aGc/aAc	4/8	0.393438475539559	0	FACETS	0.79	0.716	0.866			1	SUBCLONAL	1	TRUE	0	0.393438475539559	0		631	453	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342400	70342400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	275	616	0	ENST00000374080.3:c.1291C>T	p.Arg431Trp	p.R431W	ENST00000374080		431	Cgg/Tgg	9/45	0.393438475539559	0	FACETS	0.898	0.856	0.94			1	CLONAL	2	TRUE	0	0.393438475539559	0		616	472	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829787	76829787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057517948	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	147	418	0	ENST00000373344.5:c.6254G>A	p.Arg2085His	p.R2085H	ENST00000373344	NM_000489.3	2085	cGt/cAt	28/35	0.375453045293922	0	FACETS	0.741	0.688	0.793			1	SUBCLONAL	2	TRUE	0	0.393438475539559	0		418	306	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845361	76845361	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	38	192	0	ENST00000373344.5:c.6160C>A	p.Leu2054Ile	p.L2054I	ENST00000373344	NM_000489.3	2054	Ctt/Att	27/35	0.375453045293922	0	FACETS	0.553	0.461	0.653			1	SUBCLONAL	1	TRUE	0	0.393438475539559	0		192	212	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937432	76937432	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	15	286	0	ENST00000373344.5:c.3316G>A	p.Asp1106Asn	p.D1106N	ENST00000373344	NM_000489.3	1106	Gat/Aat	9/35	0.375453045293922	0	FACETS	0.157	0.115	0.209			1	SUBCLONAL	1	TRUE	0	0.393438475539559	0		286	294	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123022491	123022491	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	94	492	0	ENST00000355640.3:c.900C>A	p.Cys300Ter	p.C300*	ENST00000355640		300	tgC/tgA	3/7	0.375453045293922	0	FACETS	0.736	0.659	0.816			1	SUBCLONAL	1	TRUE	0	0.393438475539559	0		492	394	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860070	152860070	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557026564	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	129	635	0	ENST00000406277.2:c.358G>A	p.Val120Met	p.V120M	ENST00000406277	NM_152274.4	120	Gtg/Atg	5/7	0.375453045293922		FACETS		0.747	0.893				CLONAL	1	TRUE	0	0.393438475539559	0		635	486	SUCCESS
RET	5979	MSKCC	GRCh37	10	43613844	43613844	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775711017	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	237	728	2	ENST00000355710.3:c.2308C>T	p.Arg770Ter	p.R770*	ENST00000355710	NM_020975.4	770	Cga/Tga	13/20	1	2	FACETS	0.867	0.813	0.922	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		730	695	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852498	42852498	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	217	582	0	ENST00000398585.3:c.588G>T	p.Gln196His	p.Q196H	ENST00000398585	NM_001135099.1	196	caG/caT	6/14	1	2	FACETS	0.915	0.856	0.974	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		582	603	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105609	11105609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1263541939	NA	P-0050204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	254	652	0	ENST00000358026.2:c.1525G>A	p.Ala509Thr	p.A509T	ENST00000358026	NM_001128849.1	509	Gcc/Acc	9/36	1	2	FACETS	0.877	0.825	0.931	1	0.994	1	CLONAL	2	TRUE	1	0.393438475539559	2		652	736	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115279378	115279378	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0050211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	238	292	0	ENST00000438362.2:c.638+1G>C		p.X213_splice	ENST00000438362	NM_001242891.1	213			0.89048565085029	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.89048565085029	1		292	285	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593638	55593661	+	stop_gained	Nonsense_Mutation	DEL	TGTTTACATAGACCCAACACAACT	TGTTTACATAGACCCAACACAACT	GTG	novel	NA	P-0050211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	330	498	2	ENST00000288135.5:c.1704_1727delinsGTG	p.Tyr568_Leu576delinsTer	p.Y568_L576delins*	ENST00000288135	NM_000222.2	568	taTGTTTACATAGACCCAACACAACTt/taGTGt	11/21	1	2	FACETS	0.921	0.875	0.967	0.921	0.875	0.967	CLONAL	1	TRUE	1	0.89048565085029	2		500	805	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732996	30732996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893809	NA	P-0050223-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	77	374	0	ENST00000295754.5:c.1609C>T	p.Arg537Cys	p.R537C	ENST00000295754	NM_003242.5	537	Cgc/Tgc	7/7	0.324733207632452	1	FACETS	0.944	0.832	1	0.944	0.832	1	CLONAL	1	TRUE	0	0.324733207632452	1		374	421	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271772	38271772	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050223-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	80	646	0	ENST00000425967.3:c.2177C>G	p.Thr726Ser	p.T726S	ENST00000425967	NM_001174067.1	726	aCt/aGt	17/19	0.324733207632452	1	FACETS	0.997	0.882	1	0.997	0.882	1	CLONAL	1	TRUE	0	0.324733207632452	1		646	414	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981119	201981119	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050223-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	116	631	0	ENST00000359651.3:c.198del	p.Trp67GlyfsTer88	p.W67Gfs*88	ENST00000359651		66	ttC/tt	2/8	0.25691390449274	3	FACETS	1	0.978	1	0.646	0.583	0.712	CLONAL	1	TRUE	1	0.324733207632452	3		631	643	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984369	201984370	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050223-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	191	505	0	ENST00000359651.3:c.1034_1035insA	p.Asp346GlyfsTer125	p.D346Gfs*125	ENST00000359651		345	gtg/gtAg	8/8	0.25691390449274	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.324733207632452	3		505	615	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99823040	99823040	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	141	302	0	ENST00000280892.6:c.172C>T	p.Pro58Ser	p.P58S	ENST00000280892	NM_001130678.1	58	Ccc/Tcc	2/7	1	2	FACETS	0.924	0.852	0.998	0.924	0.852	0.998	CLONAL	1	TRUE	1	0.813655611765085	2		302	375	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989018	41989018	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050337-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	102	449	0	ENST00000219905.7:c.1810C>T	p.Gln604Ter	p.Q604*	ENST00000219905	NM_001164273.1	604	Cag/Tag	3/24	0.213043361626846	3	FACETS	1	0.934	1	0.702	0.63	0.778	CLONAL	2	TRUE	0	0.213043361626846	3		449	503	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058043	27058049	+	frameshift_variant	Frame_Shift_Del	DEL	CTCAGCA	CTCAGCA	-	novel	NA	P-0050337-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	93	416	0	ENST00000324856.7:c.1751_1757del	p.Ser584CysfsTer33	p.S584Cfs*33	ENST00000324856	NM_006015.4	584	tCTCAGCAg/tg	3/20	0.144448574873419	3	FACETS	0.815	0.726	0.909	0.543	0.484	0.606	CLONAL	2	TRUE	0	0.213043361626846	3		416	593	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654677	29654693	+	frameshift_variant	Frame_Shift_Del	DEL	TCACCTTCATGCACCAG	TCACCTTCATGCACCAG	-	novel	NA	P-0050337-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	109	239	0	ENST00000356175.3:c.5366_5382del	p.Leu1789ArgfsTer3	p.L1789Rfs*3	ENST00000356175	NM_000267.3	1789	cTCACCTTCATGCACCAG/c	37/57	0.213043361626846	3	FACETS	0.918	0.831	1	0.918	0.831	1	CLONAL	3	TRUE	0	0.213043361626846	3		239	411	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128036929	128036930	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0050337-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	94	351	0	ENST00000285398.2:c.1549_1550delinsTT	p.Glu517Leu	p.E517L	ENST00000285398	NM_000122.1	517	GAa/TTa	10/15	0.144448574873419	3	FACETS	1	0.948	1	0.733	0.656	0.815	CLONAL	2	TRUE	0	0.213043361626846	3		351	444	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30090740	30090741	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GC	GC	TT	novel	NA	P-0050337-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	161	469	1	ENST00000338641.4:c.1738-1_1738delinsTT		p.X580_splice	ENST00000338641	NM_000268.3	580		16/16	0.213043361626846	3	FACETS	1	0.975	1	0.765	0.703	0.829	CLONAL	2	TRUE	0	0.213043361626846	3		470	729	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227924	55227924	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050337-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	37	299	0	ENST00000275493.2:c.1391C>T	p.Ser464Leu	p.S464L	ENST00000275493	NM_005228.3	464	tCa/tTa	12/28	0.208459915607696	5	FACETS	1	0.902	1	0.381	0.314	0.456	CLONAL	1	TRUE	2	0.213043361626846	5		299	401	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0050340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	17	297	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	0.194	0.143	0.253	0.194	0.143	0.253	SUBCLONAL	1	TRUE	1	0.320046999438848	2		297	549	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100645	8100645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1218595084	NA	P-0050340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	55	782	3	ENST00000346208.3:c.619G>A	p.Ala207Thr	p.A207T	ENST00000346208		207	Gcc/Acc	3/6	0.320046999438848	1	FACETS	0.366	0.312	0.426	0.366	0.312	0.426	SUBCLONAL	1	TRUE	0	0.320046999438848	1		785	788	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0050340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	194	321	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.88	0.824	0.938	1	0.995	1	CLONAL	3	TRUE	1	0.320046999438848	2		321	459	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938589	44938589	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0050340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	312	389	0	ENST00000377967.4:c.3137C>G	p.Ser1046Ter	p.S1046*	ENST00000377967	NM_021140.2	1046	tCa/tGa	20/29	1	2	FACETS	0.998	0.95	1	1	0.997	1	CLONAL	3	TRUE	1	0.320046999438848	2		389	651	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562482	95562482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	55	364	0	ENST00000393063.1:c.4775C>T	p.Pro1592Leu	p.P1592L	ENST00000393063	NM_030621.3	1592	cCg/cTg	24/28	NA	2	FACETS	0.639	0.547	0.74			1	INDETERMINATE	1	TRUE	NA	0.320046999438848	2		364	538	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249196	10249196	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	455	691	0	ENST00000340748.4:c.3986A>C	p.Glu1329Ala	p.E1329A	ENST00000340748		1329	gAg/gCg	34/40	0.309713375791389	4	FACETS	1	0.984	1	0.795	0.76	0.83	CLONAL	3	TRUE	0	0.320046999438848	4		691	1180	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98241342	98241342	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1060502297	NA	P-0050340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	767	496	0	ENST00000331920.6:c.1155del	p.Asn386ThrfsTer46	p.N386Tfs*46	ENST00000331920	NM_000264.3	385	atC/at	8/24	0.320046999438848	3	FACETS	1	0.997	1	1	0.999	1	CLONAL	6	TRUE	0	0.320046999438848	3		496	857	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	43	366	0				ENST00000310581	NM_198253.2	-/1132			0.272137807229823	1	FACETS	0.617	0.519	0.725	0.617	0.519	0.725	SUBCLONAL	1	TRUE	0	0.376981705900092	1		366	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	72	577	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	1	2	FACETS	0.743	0.65	0.843	0.743	0.65	0.843	SUBCLONAL	1	TRUE	1	0.376981705900092	2		577	514	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256019	16256019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	163	473	0	ENST00000375759.3:c.3284C>T	p.Ser1095Phe	p.S1095F	ENST00000375759	NM_015001.2	1095	tCt/tTt	11/15	0.376981705900092	3	FACETS	0.908	0.838	0.98	0.908	0.838	0.98	CLONAL	2	TRUE	1	0.376981705900092	3		473	566	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257746	16257746	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	85	438	1	ENST00000375759.3:c.5011G>T	p.Glu1671Ter	p.E1671*	ENST00000375759	NM_015001.2	1671	Gag/Tag	11/15	0.376981705900092	3	FACETS	0.929	0.822	1	0.464	0.411	0.521	CLONAL	1	TRUE	1	0.376981705900092	3		439	577	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056313	27056313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	87	499	0	ENST00000324856.7:c.1309C>T	p.Arg437Trp	p.R437W	ENST00000324856	NM_006015.4	437	Cgg/Tgg	2/20	0.376981705900092	3	FACETS	0.883	0.783	0.991	0.442	0.391	0.496	CLONAL	1	TRUE	1	0.376981705900092	3		499	621	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363349	40363349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	92	533	0	ENST00000397332.2:c.880G>A	p.Ala294Thr	p.A294T	ENST00000397332	NM_001033082.2	294	Gct/Act	3/3	0.376981705900092	3	FACETS	0.894	0.795	0.999	0.447	0.397	0.5	CLONAL	1	TRUE	1	0.376981705900092	3		533	649	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439854	51439854	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	87	400	0	ENST00000262662.1:c.419C>T	p.Ala140Val	p.A140V	ENST00000262662		140	gCc/gTc	4/4	0.376981705900092	3	FACETS	0.976	0.866	1	0.488	0.433	0.547	CLONAL	1	TRUE	1	0.376981705900092	3		400	562	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430589	78430589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	64	359	0	ENST00000370768.2:c.701C>T	p.Pro234Leu	p.P234L	ENST00000370768	NM_003902.3	234	cCt/cTt	9/20	0.226106305237644	4	FACETS	1	0.928	1			1	INDETERMINATE	1	TRUE	NA	0.376981705900092	4		359	424	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166617	118166617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	42	285	0	ENST00000369448.3:c.1127C>T	p.Pro376Leu	p.P376L	ENST00000369448	NM_017709.3	376	cCt/cTt	2/2	1	2	FACETS	0.686	0.575	0.808	0.686	0.575	0.808	SUBCLONAL	1	TRUE	1	0.376981705900092	2		285	325	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649664	206649664	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374373296	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	106	608	0	ENST00000367120.3:c.499G>A	p.Asp167Asn	p.D167N	ENST00000367120	NM_014002.3	167	Gat/Aat	6/22	1	2	FACETS	0.919	0.825	1	0.919	0.825	1	CLONAL	1	TRUE	1	0.376981705900092	2		608	612	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570788	226570788	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	101	494	0	ENST00000366794.5:c.1108C>T	p.Pro370Ser	p.P370S	ENST00000366794	NM_001618.3	370	Ccg/Tcg	8/23	1	2	FACETS	0.851	0.761	0.945	0.851	0.761	0.945	CLONAL	1	TRUE	1	0.376981705900092	2		494	630	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604563	43604563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774139424	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	60	705	1	ENST00000355710.3:c.1148G>A	p.Gly383Asp	p.G383D	ENST00000355710	NM_020975.4	383	gGc/gAc	6/20	0.236406933271883	1	FACETS	0.433	0.372	0.498	0.433	0.372	0.498	SUBCLONAL	1	TRUE	0	0.376981705900092	1		706	597	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373158	118373158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555045986	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	67	324	0	ENST00000534358.1:c.6551C>T	p.Pro2184Leu	p.P2184L	ENST00000534358	NM_005933.3	2184	cCt/cTt	27/36	1	2	FACETS	0.987	0.863	1	0.987	0.863	1	CLONAL	1	TRUE	1	0.376981705900092	2		324	360	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945093	31945093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	78	514	0	ENST00000340398.3:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000340398	NM_001013699.2	3	cGa/cAa	1/1	1	2	FACETS	0.695	0.612	0.785	0.695	0.612	0.785	SUBCLONAL	1	TRUE	1	0.376981705900092	2		514	595	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230641	46230641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	80	323	0	ENST00000334344.6:c.890C>T	p.Ser297Phe	p.S297F	ENST00000334344	NM_152641.2	297	tCc/tTc	8/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.376981705900092	2		323	331	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244255	46244256	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	45	347	0	ENST00000334344.6:c.2349_2350delinsTT	p.Pro784Ser	p.P784S	ENST00000334344	NM_152641.2	783	atCCct/atTTct	15/21	1	2	FACETS	0.809	0.684	0.946	0.809	0.684	0.946	CLONAL	1	TRUE	1	0.376981705900092	2		347	295	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864571	57864571	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	140	711	0	ENST00000228682.2:c.2048C>T	p.Ser683Phe	p.S683F	ENST00000228682	NM_005269.2	683	tCt/tTt	12/12	1	2	FACETS	0.972	0.886	1	0.972	0.886	1	CLONAL	1	TRUE	1	0.376981705900092	2		711	764	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112578	115112578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	101	682	0	ENST00000257566.3:c.1162G>A	p.Glu388Lys	p.E388K	ENST00000257566	NM_016569.3	388	Gag/Aag	7/8	0.236406933271883	1	FACETS	0.637	0.569	0.708	0.637	0.569	0.708	SUBCLONAL	1	TRUE	0	0.376981705900092	1		682	683	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967585	26967585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	32	388	0	ENST00000381527.3:c.728C>T	p.Thr243Ile	p.T243I	ENST00000381527	NM_001260.1	243	aCt/aTt	7/13	0.272137807229823	1	FACETS	0.71	0.582	0.852	0.71	0.582	0.852	SUBCLONAL	1	TRUE	0	0.376981705900092	1		388	194	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906829	32906829	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	55	406	0	ENST00000380152.3:c.1214G>A	p.Gly405Glu	p.G405E	ENST00000380152		405	gGa/gAa	10/27	0.272137807229823	1	FACETS	0.701	0.602	0.807	0.701	0.602	0.807	SUBCLONAL	1	TRUE	0	0.376981705900092	1		406	338	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134315	41134315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	41	476	0	ENST00000379561.5:c.1313C>T	p.Pro438Leu	p.P438L	ENST00000379561	NM_002015.3	438	cCt/cTt	2/3	0.272137807229823	1	FACETS	0.424	0.354	0.503	0.424	0.354	0.503	SUBCLONAL	1	TRUE	0	0.376981705900092	1		476	416	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435592	110435592	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	73	489	0	ENST00000375856.3:c.2809C>T	p.Pro937Ser	p.P937S	ENST00000375856	NM_003749.2	937	Ccc/Tcc	1/2	0.272137807229823	1	FACETS	0.599	0.524	0.678	0.599	0.524	0.678	SUBCLONAL	1	TRUE	0	0.376981705900092	1		489	525	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100221	30100221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	40	286	0	ENST00000331968.5:c.1399C>T	p.Pro467Ser	p.P467S	ENST00000331968	NM_002742.2	467	Cct/Tct	10/18	1	2	FACETS	0.819	0.685	0.967	0.819	0.685	0.967	CLONAL	1	TRUE	1	0.376981705900092	2		286	259	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3645668	3645668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	144	778	0	ENST00000294008.3:c.1951C>T	p.Pro651Ser	p.P651S	ENST00000294008	NM_032444.2	651	Cct/Tct	9/15	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.376981705900092	2		778	705	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900720	3900720	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	117	654	1	ENST00000262367.5:c.376G>A	p.Gly126Arg	p.G126R	ENST00000262367	NM_004380.2	126	Gga/Aga	2/31	1	2	FACETS	0.877	0.791	0.967	0.877	0.791	0.967	CLONAL	1	TRUE	1	0.376981705900092	2		655	708	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	104	815	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	1	2	FACETS	0.709	0.635	0.788	0.709	0.635	0.788	SUBCLONAL	1	TRUE	1	0.376981705900092	2		815	778	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16052783	16052783	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	18	279	0	ENST00000268712.3:c.891T>G	p.Asn297Lys	p.N297K	ENST00000268712	NM_006311.3	297	aaT/aaG	9/46	1	2	FACETS	0.659	0.5	0.843	0.659	0.5	0.843	SUBCLONAL	1	TRUE	1	0.376981705900092	2		279	145	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682521	37682521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	64	416	0	ENST00000447079.4:c.3712C>T	p.Pro1238Ser	p.P1238S	ENST00000447079	NM_015083.1	1238	Cca/Tca	13/14	NA	2	FACETS	0.799	0.694	0.912			1	INDETERMINATE	1	TRUE	NA	0.376981705900092	2		416	425	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226409	2226409	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	154	840	0	ENST00000398665.3:c.3889C>A	p.Pro1297Thr	p.P1297T	ENST00000398665	NM_032482.2	1297	Ccc/Acc	27/28	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.376981705900092	2		840	763	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17940991	17940991	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	180	870	0	ENST00000458235.1:c.3133C>T	p.Pro1045Ser	p.P1045S	ENST00000458235	NM_000215.3	1045	Ccc/Tcc	23/24	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.376981705900092	2		870	881	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965761	25965761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377352572	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	106	590	0	ENST00000435504.4:c.3445C>T	p.Arg1149Cys	p.R1149C	ENST00000435504		1149	Cgt/Tgt	13/13	1	2	FACETS	0.961	0.864	1	0.961	0.864	1	CLONAL	1	TRUE	1	0.376981705900092	2		590	585	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422431	225422431	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	29	414	0	ENST00000264414.4:c.209G>C	p.Gly70Ala	p.G70A	ENST00000264414	NM_003590.4	70	gGa/gCa	2/16	1	2	FACETS	0.712	0.575	0.866	0.712	0.575	0.866	SUBCLONAL	1	TRUE	1	0.376981705900092	2		414	216	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546608	9546608	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763093827	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	81	425	0	ENST00000353224.5:c.1414G>A	p.Gly472Arg	p.G472R	ENST00000353224	NM_177990.2	472	Ggg/Agg	5/10	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.376981705900092	2		425	426	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023874	31023874	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	116	606	0	ENST00000375687.4:c.3359A>G	p.Lys1120Arg	p.K1120R	ENST00000375687	NM_015338.5	1120	aAg/aGg	13/13	1	2	FACETS	0.885	0.799	0.977	0.885	0.799	0.977	CLONAL	1	TRUE	1	0.376981705900092	2		606	695	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012660	36012660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	65	240	0	ENST00000358208.4:c.104C>T	p.Ser35Leu	p.S35L	ENST00000358208		35	tCg/tTg	2/12	1	2	FACETS	0.977	0.852	1	0.977	0.852	1	CLONAL	1	TRUE	1	0.376981705900092	2		240	353	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713469	40713469	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528913627	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	104	580	0	ENST00000373198.4:c.4046G>A	p.Arg1349His	p.R1349H	ENST00000373198	NM_133170.3	1349	cGt/cAt	30/32	0.376981705900092	1	FACETS	0.747	0.671	0.829	0.747	0.671	0.829	SUBCLONAL	1	TRUE	0	0.376981705900092	1		580	599	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757461	40757461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866132388	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	78	521	2	ENST00000373198.4:c.2837C>T	p.Ser946Phe	p.S946F	ENST00000373198	NM_133170.3	946	tCc/tTc	20/32	0.376981705900092	1	FACETS	0.648	0.571	0.731	0.648	0.571	0.731	SUBCLONAL	1	TRUE	0	0.376981705900092	1		523	518	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36421162	36421162	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750755857	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	41	348	0	ENST00000300305.3:c.35C>T	p.Ser12Leu	p.S12L	ENST00000300305		12	tCg/tTg	1/8	0.272137807229823	1	FACETS	0.384	0.319	0.455	0.384	0.319	0.455	SUBCLONAL	1	TRUE	0	0.376981705900092	1		348	460	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866441	42866441	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770444484	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	148	697	0	ENST00000398585.3:c.191C>T	p.Pro64Leu	p.P64L	ENST00000398585	NM_001135099.1	64	cCc/cTc	3/14	0.272137807229823	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.376981705900092	1		697	628	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026132	71026132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751543308	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	68	419	1	ENST00000318789.4:c.1490G>A	p.Arg497Gln	p.R497Q	ENST00000318789	NM_032682.5	497	cGa/cAa	17/21	0.376981705900092	4	FACETS	0.822	0.716	0.938	0.274	0.238	0.313	CLONAL	1	TRUE	1	0.376981705900092	4		420	604	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73108244	73108244	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	39	107	0	ENST00000356692.5:c.344A>G	p.Tyr115Cys	p.Y115C	ENST00000356692		115	tAt/tGt	4/9	0.376981705900092	4	FACETS	1	0.866	1	1	0.866	1	CLONAL	3	TRUE	1	0.376981705900092	4		107	94	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390207	89390207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	55	288	0	ENST00000336596.2:c.956C>T	p.Ser319Phe	p.S319F	ENST00000336596	NM_005233.5	319	tCc/tTc	4/17	0.376981705900092	4	FACETS	0.889	0.762	1	0.296	0.254	0.343	CLONAL	1	TRUE	1	0.376981705900092	4		288	452	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138402533	138402533	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	36	253	0	ENST00000289153.2:c.2412T>A	p.Phe804Leu	p.F804L	ENST00000289153	NM_006219.2	804	ttT/ttA	16/22	1	2	FACETS	0.95	0.789	1	0.95	0.789	1	CLONAL	1	TRUE	1	0.376981705900092	2		253	201	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176561	142176561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	36	308	0	ENST00000350721.4:c.7540C>T	p.Arg2514Cys	p.R2514C	ENST00000350721	NM_001184.3	2514	Cgc/Tgc	45/47	1	2	FACETS	0.568	0.468	0.68	0.568	0.468	0.68	SUBCLONAL	1	TRUE	1	0.376981705900092	2		308	336	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750440	41750440	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	86	503	0	ENST00000226382.2:c.188G>A	p.Gly63Glu	p.G63E	ENST00000226382	NM_003924.3	63	gGa/gAa	1/3	0.376981705900092	4	FACETS	0.814	0.719	0.915			1	CLONAL	1	TRUE	NA	0.376981705900092	4		503	772	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593591	55593591	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519704	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	372	336	0	ENST00000288135.5:c.1657T>A	p.Tyr553Asn	p.Y553N	ENST00000288135	NM_000222.2	553	Tat/Aat	11/21	0.376981705900092	7	FACETS	0.939	0.904	0.974			1	CLONAL	7	TRUE	NA	0.376981705900092	7		336	583	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599339	55599339	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs993022333	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	403	315	0	ENST00000288135.5:c.2465A>T	p.Asn822Ile	p.N822I	ENST00000288135	NM_000222.2	822	aAt/aTt	17/21	0.376981705900092	7	FACETS	0.954	0.92	0.987			1	CLONAL	7	TRUE	NA	0.376981705900092	7		315	622	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527246	187527246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	72	467	0	ENST00000441802.2:c.10328G>A	p.Gly3443Glu	p.G3443E	ENST00000441802	NM_005245.3	3443	gGa/gAa	17/27	1	2	FACETS	0.907	0.796	1	0.907	0.796	1	CLONAL	1	TRUE	1	0.376981705900092	2		467	421	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539888	187539888	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	49	399	0	ENST00000441802.2:c.7852G>T	p.Val2618Phe	p.V2618F	ENST00000441802	NM_005245.3	2618	Gtt/Ttt	10/27	1	2	FACETS	0.688	0.584	0.801	0.688	0.584	0.801	SUBCLONAL	1	TRUE	1	0.376981705900092	2		399	378	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629231	187629231	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	102	444	0	ENST00000441802.2:c.1751T>G	p.Val584Gly	p.V584G	ENST00000441802	NM_005245.3	584	gTg/gGg	2/27	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.376981705900092	2		444	487	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876362	35876362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	58	557	0	ENST00000303115.3:c.1154C>T	p.Ser385Phe	p.S385F	ENST00000303115	NM_002185.3	385	tCc/tTc	8/8	1	2	FACETS	0.575	0.494	0.663	0.575	0.494	0.663	SUBCLONAL	1	TRUE	1	0.376981705900092	2		557	535	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524603	176524603	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758782236	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	63	797	0	ENST00000292408.4:c.2335G>A	p.Asp779Asn	p.D779N	ENST00000292408	NM_213647.1	779	Gat/Aat	18/18	0.236406933271883	1	FACETS	0.428	0.37	0.491	0.428	0.37	0.491	SUBCLONAL	1	TRUE	0	0.376981705900092	1		797	634	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20483130	20483131	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	63	291	0	ENST00000346618.3:c.863_864delinsTT	p.Thr288Ile	p.T288I	ENST00000346618	NM_001949.4	288	aCC/aTT	4/7	0.230413057990714	3	FACETS	1	0.912	1			1	CLONAL	1	TRUE	NA	0.376981705900092	3		291	373	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188306	32188306	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	126	794	1	ENST00000375023.3:c.1035T>A	p.Ser345Arg	p.S345R	ENST00000375023	NM_004557.3	345	agT/agA	6/30	0.259390786749849	3	FACETS	1	0.961	1	0.37	0.336	0.407	CLONAL	1	TRUE	0	0.376981705900092	3		795	715	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956529	93956529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	33	288	0	ENST00000369303.4:c.2707C>T	p.Pro903Ser	p.P903S	ENST00000369303	NM_004440.3	903	Ccc/Tcc	15/17	1	2	FACETS	0.826	0.678	0.99	0.826	0.678	0.99	CLONAL	1	TRUE	1	0.376981705900092	2		288	212	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553295	106553295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	88	589	0	ENST00000369096.4:c.1260G>A	p.Met420Ile	p.M420I	ENST00000369096	NM_001198.3	420	atG/atA	5/7	1	2	FACETS	0.841	0.747	0.942	0.841	0.747	0.942	CLONAL	1	TRUE	1	0.376981705900092	2		589	555	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005543	150005543	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1393423529	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	64	347	1	ENST00000253339.5:c.682C>T	p.Pro228Ser	p.P228S	ENST00000253339		228	Cct/Tct	3/7	0.153679014030838	3	FACETS	1	0.889	1	0.512	0.445	0.584	INDETERMINATE	1	TRUE	1	0.376981705900092	3		348	394	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930094	68930098	+	missense_variant	Missense_Mutation	ONP	GAATG	GAATG	AAATA	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	33	331	0	ENST00000288368.4:c.155_159delinsAAATA	p.Arg52_Met53delinsLysIle	p.R52_M53delinsKI	ENST00000288368	NM_024870.2	52	aGAATG/aAAATA	2/40	0.172863138554581	0	FACETS	0.385	0.315	0.464			1	INDETERMINATE	1	TRUE	0	0.376981705900092	0		331	283	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126331	5126334	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	ONP	AGGA	AGGA	CGGG	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	17	216	0	ENST00000381652.3:c.3178-2_3179delinsCGGG		p.X1060_splice	ENST00000381652	NM_004972.3	1060		24/25	0.376981705900092	1	FACETS	0.711	0.538	0.909	0.711	0.538	0.909	CLONAL	1	TRUE	0	0.376981705900092	1		216	103	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400999	139400999	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	104	729	0	ENST00000277541.6:c.3994T>C	p.Phe1332Leu	p.F1332L	ENST00000277541	NM_017617.3	1332	Ttc/Ctc	24/34	1	2	FACETS	0.849	0.761	0.942	0.849	0.761	0.942	CLONAL	1	TRUE	1	0.376981705900092	2		729	650	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139811012	139811012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	111	603	0	ENST00000247668.2:c.623C>T	p.Thr208Ile	p.T208I	ENST00000247668	NM_021138.3	208	aCt/aTt	7/11	1	2	FACETS	0.944	0.85	1	0.944	0.85	1	CLONAL	1	TRUE	1	0.376981705900092	2		603	624	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314906	1314906	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	62	335	2	ENST00000400841.2:c.755G>A	p.Trp252Ter	p.W252*	ENST00000400841		252	tGg/tAg	6/6	1	1	FACETS	0.653	0.566	0.746	0.653	0.566	0.746	SUBCLONAL	1	TRUE	0	0.376981705900092	1		337	409	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411231	63411231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775711054	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	153	347	0	ENST00000330258.3:c.1936C>T	p.Arg646Trp	p.R646W	ENST00000330258	NM_152424.3	646	Cgg/Tgg	2/2	1	1	FACETS	0.915	0.849	0.982	1	0.992	1	CLONAL	2	TRUE	0	0.376981705900092	1		347	360	SUCCESS
AR	367	MSKCC	GRCh37	X	66937340	66937340	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	90	267	0	ENST00000374690.3:c.2194G>A	p.Asp732Asn	p.D732N	ENST00000374690	NM_000044.3	732	Gac/Aac	5/8	1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.376981705900092	1		267	271	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861594	152861597	+	frameshift_variant	Frame_Shift_Del	DEL	TAAA	TAAA	-	novel	NA	P-0050421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	140	281	0	ENST00000406277.2:c.155_158del	p.Ile52ThrfsTer17	p.I52Tfs*17	ENST00000406277	NM_152274.4	52	aTTTAc/ac	4/7	1		FACETS		0.761	0.891				CLONAL	2	TRUE	0	0.376981705900092	1		281	365	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249092	55249092	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	102	634	0	ENST00000275493.2:c.2390G>C	p.Cys797Ser	p.C797S	ENST00000275493	NM_005228.3	797	tGc/tCc	20/28	0.277069363853457	6	FACETS	1	0.96	1	0.192	0.172	0.214	INDETERMINATE	1	TRUE	0	0.478779577198349	6		634	723	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0050436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	220	608	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.277069363853457	6	FACETS	1	0.987	1	0.408	0.381	0.436	INDETERMINATE	2	TRUE	0	0.478779577198349	6		609	734	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0050436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	265	519	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.277069363853457	6	FACETS	0.996	0.944	1	0.664	0.629	0.699	INDETERMINATE	4	TRUE	0	0.478779577198349	6		519	544	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583304	46583304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370125133	NA	P-0050436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	57	417	1	ENST00000263734.3:c.232G>A	p.Glu78Lys	p.E78K	ENST00000263734	NM_001430.4	78	Gag/Aag	3/16	0.278471832437578	1	FACETS	0.461	0.397	0.53	0.461	0.397	0.53	INDETERMINATE	1	TRUE	0	0.478779577198349	1		418	393	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015677	112015677	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs751647014	NA	P-0050436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	63	536	1	ENST00000368678.4:c.1165C>T	p.Arg389Ter	p.R389*	ENST00000368678		389	Cga/Tga	11/13	0.222211822899552	1	FACETS	0.435	0.377	0.498	0.435	0.377	0.498	INDETERMINATE	1	TRUE	0	0.478779577198349	1		537	460	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911951	32911951	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	63	568	0	ENST00000380152.3:c.3459G>C	p.Lys1153Asn	p.K1153N	ENST00000380152		1153	aaG/aaC	11/27	0.222211822899552	1	FACETS	0.424	0.367	0.485	0.424	0.367	0.485	INDETERMINATE	1	TRUE	0	0.478779577198349	1		568	472	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40738997	40738997	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	54	508	0	ENST00000373198.4:c.3287C>A	p.Ala1096Asp	p.A1096D	ENST00000373198	NM_133170.3	1096	gCt/gAt	24/32	1	2	FACETS	0.537	0.46	0.621	0.537	0.46	0.621	SUBCLONAL	1	TRUE	1	0.478779577198349	2		508	420	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739666	41739666	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	50	632	1	ENST00000242208.4:c.307A>G	p.Ile103Val	p.I103V	ENST00000242208	NM_002192.2	103	Ata/Gta	2/3	0.277069363853457	6	FACETS	0.53	0.449	0.62	0.088	0.074	0.104	INDETERMINATE	1	TRUE	0	0.478779577198349	6		633	771	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579366	7579366	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs770776262	NA	P-0050442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	15	711	0	ENST00000269305.4:c.321C>A	p.Tyr107Ter	p.Y107*	ENST00000269305	NM_001126112.2	107	taC/taA	4/11	1	2	FACETS	0.158	0.115	0.211	0.158	0.115	0.211	SUBCLONAL	1	TRUE	1	0.32	2		711	592	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929412	44929415	+	frameshift_variant	Frame_Shift_Del	DEL	ACAA	ACAA	-	rs786205676	NA	P-0050442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	98	363	0	ENST00000377967.4:c.2515_2518del	p.Asn839ValfsTer27	p.N839Vfs*27	ENST00000377967	NM_021140.2	838	ACAAac/ac	17/29	0.229926317021182	2	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.32	2		363	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0050458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	268	475	1	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.703337468304747	1	FACETS	0.982	0.933	1	0.982	0.933	1	CLONAL	1	TRUE	0	0.703337468304747	1		476	503	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877347	28877347	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	45	442	2	ENST00000282397.4:c.3974C>A	p.Pro1325Gln	p.P1325Q	ENST00000282397	NM_002019.4	1325	cCa/cAa	30/30	0.260201265569276	1	FACETS	0.094	0.079	0.112	0.094	0.079	0.112	INDETERMINATE	1	TRUE	0	0.703337468304747	1		444	880	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992300	72992300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	410	621	0	ENST00000268489.5:c.1745C>T	p.Ala582Val	p.A582V	ENST00000268489	NM_006885.3	582	gCa/gTa	2/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.703337468304747	2		621	1091	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384667	84384667	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	349	388	0	ENST00000321945.7:c.776G>A	p.Gly259Glu	p.G259E	ENST00000321945	NM_139076.2	259	gGa/gAa	8/9	0.688374006513933	3	FACETS	0.845	0.805	0.885	0.845	0.805	0.885	CLONAL	2	TRUE	1	0.703337468304747	3		388	794	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0050459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	107	390	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.367362735327431	2	FACETS	1	0.954	1	0.552	0.497	0.61	CLONAL	1	TRUE	0	0.367362735327431	2		390	528	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0050459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	120	383	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.342048832045994	3	FACETS	0.835	0.759	0.914	0.835	0.759	0.914	CLONAL	2	TRUE	1	0.367362735327431	3		383	463	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0050459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	213	479	1	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.267253796985167	4	FACETS	1	0.984	1	0.781	0.729	0.834	CLONAL	2	TRUE	1	0.367362735327431	4		480	677	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175481	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0050459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	92	326	0	ENST00000257430.4:c.4192_4193del	p.Arg1399PhefsTer9	p.R1399Ffs*9	ENST00000257430	NM_000038.5	1397	GAg/g	16/16	0.342048832045994	3	FACETS	1	0.96	1	0.584	0.52	0.651	CLONAL	1	TRUE	1	0.367362735327431	3		326	508	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249517	153249517	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	102	439	0	ENST00000281708.4:c.1261A>G	p.Thr421Ala	p.T421A	ENST00000281708	NM_033632.3	421	Aca/Gca	9/12	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.367362735327431	2		439	536	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120662	94120662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	73	401	0	ENST00000369303.4:c.389C>A	p.Thr130Lys	p.T130K	ENST00000369303	NM_004440.3	130	aCa/aAa	3/17	0.240049487058733	3	FACETS	0.95	0.833	1	0.475	0.416	0.538	CLONAL	1	TRUE	1	0.367362735327431	3		401	495	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542569	141542569	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	108	498	0	ENST00000220592.5:c.2417C>T	p.Ala806Val	p.A806V	ENST00000220592	NM_012154.3	806	gCt/gTt	18/19	0.306867076634177	4	FACETS	1	0.957	1	0.374	0.335	0.414	CLONAL	1	TRUE	1	0.367362735327431	4		498	717	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0050461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	370	430	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.929464812877062	2		430	737	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410674	32410674	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	365	386	0	ENST00000332351.3:c.1484G>T	p.Arg495Leu	p.R495L	ENST00000332351	NM_024426.4	495	cGg/cTg	10/10	1	2	FACETS	0.965	0.92	1	0.965	0.92	1	CLONAL	1	TRUE	1	0.929464812877062	2		386	814	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270092	66270092	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	249	341	0	ENST00000273854.3:c.1790G>T	p.Ser597Ile	p.S597I	ENST00000273854	NM_004439.5	597	aGt/aTt	8/18	1	2	FACETS	0.807	0.759	0.855	0.807	0.759	0.855	CLONAL	1	TRUE	1	0.929464812877062	2		341	664	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215779	98215779	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	172	404	0	ENST00000331920.6:c.3430G>C	p.Glu1144Gln	p.E1144Q	ENST00000331920	NM_000264.3	1144	Gag/Cag	20/24	0.149072594879664	2	FACETS	0.891	0.821	0.963	0.891	0.821	0.963	CLONAL	2	TRUE	0	0.246669318089896	2		404	783	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590736	189590736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558374141	NA	P-0050462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	99	472	0	ENST00000264731.3:c.1301C>T	p.Thr434Met	p.T434M	ENST00000264731	NM_003722.4	434	aCg/aTg	10/14	0.246669318089896	5	FACETS	0.981	0.873	1	0.245	0.218	0.274	CLONAL	1	TRUE	1	0.246669318089896	5		472	1121	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493694	56493694	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	38	402	0	ENST00000267101.3:c.3010G>C	p.Glu1004Gln	p.E1004Q	ENST00000267101	NM_001982.3	1004	Gag/Cag	25/28	1	2	FACETS	0.453	0.373	0.543	0.453	0.373	0.543	SUBCLONAL	1	TRUE	1	0.246669318089896	2		402	680	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568590	41568590	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	145	437	0	ENST00000263253.7:c.4540G>C	p.Glu1514Gln	p.E1514Q	ENST00000263253	NM_001429.3	1514	Gaa/Caa	28/31	0.216142498667654	2	FACETS	0.816	0.746	0.89	0.816	0.746	0.89	CLONAL	2	TRUE	0	0.246669318089896	2		437	720	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	107	276	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.963	1			1	INDETERMINATE	1	TRUE	NA	0.663789438623032	2		276	290	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050412	13050412	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs756230073	NA	P-0050463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	207	442	0	ENST00000316448.5:c.364A>G	p.Met122Val	p.M122V	ENST00000316448	NM_004343.3	122	Atg/Gtg	3/9	0.663789438623032	3	FACETS	1	0.941	1	0.507	0.471	0.543	CLONAL	1	TRUE	1	0.663789438623032	3		442	820	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0050464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	124	513	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.206131970667358	2		516	875	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0050464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	105	441	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.206131970667358	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.206131970667358	1		441	808	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0050464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	23	397	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.206131970667358	3	FACETS	0.271	0.21	0.343	0.136	0.105	0.172	SUBCLONAL	1	TRUE	1	0.206131970667358	3		399	907	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0050464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	18	245	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.409	0.307	0.53	0.409	0.307	0.53	SUBCLONAL	1	TRUE	1	0.206131970667358	2		245	427	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0050464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	66	332	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.935	0.811	1	0.935	0.811	1	CLONAL	1	TRUE	1	0.206131970667358	2		333	685	SUCCESS
APC	324	MSKCC	GRCh37	5	112175171	112175171	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085373	NA	P-0050464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	72	210	0	ENST00000257430.4:c.3880C>T	p.Gln1294Ter	p.Q1294*	ENST00000257430	NM_000038.5	1294	Cag/Tag	16/16	0.206131970667358	2	FACETS	0.954	0.839	1	0.954	0.839	1	CLONAL	2	TRUE	0	0.206131970667358	2		210	366	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371684	55371684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	65	487	0	ENST00000297316.4:c.374G>A	p.Arg125His	p.R125H	ENST00000297316	NM_022454.3	125	cGc/cAc	2/2	1	2	FACETS	0.865	0.749	0.991	0.865	0.749	0.991	CLONAL	1	TRUE	1	0.206131970667358	2		487	729	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692910	89692910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	57	430	0	ENST00000371953.3:c.394G>A	p.Gly132Ser	p.G132S	ENST00000371953	NM_000314.4	132	Ggt/Agt	5/9	1	2	FACETS	0.982	0.843	1	0.982	0.843	1	CLONAL	1	TRUE	1	0.206131970667358	2		430	563	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910870	114910870	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0050464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	79	362	0	ENST00000543371.1:c.989C>G	p.Ser330Ter	p.S330*	ENST00000543371	NM_001198531.1	330	tCa/tGa	9/14	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.206131970667358	2		362	655	SUCCESS
ATR	545	MSKCC	GRCh37	3	142218477	142218477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	82	327	0	ENST00000350721.4:c.5372del	p.Leu1791TrpfsTer33	p.L1791Wfs*33	ENST00000350721	NM_001184.3	1791	tTg/tg	31/47	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.206131970667358	2		327	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0050465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	100	554	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.255398833542982	1	FACETS	0.797	0.711	0.889	0.797	0.711	0.889	SUBCLONAL	1	FALSE	0	0.255398833542982	1		554	857	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0050465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	64	431	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.873	0.756	1	0.873	0.756	1	CLONAL	1	FALSE	1	0.255398833542982	2		431	574	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165912	118165912	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	76	356	0	ENST00000369448.3:c.422A>C	p.Lys141Thr	p.K141T	ENST00000369448	NM_017709.3	141	aAg/aCg	2/2	1	2	FACETS	0.99	0.869	1	0.99	0.869	1	CLONAL	1	FALSE	1	0.255398833542982	2		356	601	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278343	39278343	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	136	479	0	ENST00000402219.2:c.806T>A	p.Met269Lys	p.M269K	ENST00000402219	NM_005633.3	269	aTg/aAg	6/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.255398833542982	2		479	716	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262217	46262240	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTTCCTTTTTTTGTTTAATAGG	TTTTTCCTTTTTTTGTTTAATAGG	AAAGGAAAA	novel	NA	P-0050465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	47	280	2	ENST00000371998.3:c.824-23_824delinsAAAGGAAAA		p.X275_splice	ENST00000371998		275		9/23	1	2	FACETS	0.798	0.674	0.935	0.798	0.674	0.935	CLONAL	1	FALSE	1	0.255398833542982	2		282	461	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128848611	128848611	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	115	526	0	ENST00000249373.3:c.1276C>G	p.Leu426Val	p.L426V	ENST00000249373	NM_005631.4	426	Ctg/Gtg	7/12	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	FALSE	1	0.255398833542982	2		526	832	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0050466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	185	439	0	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			NA	2	FACETS	0.859	0.8	0.92			1	INDETERMINATE	2	TRUE	NA	0.415767909594951	2		439	518	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509579	29509579	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	44	405	0	ENST00000356175.3:c.784C>G	p.Arg262Gly	p.R262G	ENST00000356175	NM_000267.3	262	Cgt/Ggt	8/57	0.272001854118368	3	FACETS	0.499	0.418	0.589	0.25	0.209	0.295	SUBCLONAL	1	TRUE	1	0.415767909594951	3		405	512	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051665	30051665	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	136	243	0	ENST00000338641.4:c.599+1del		p.R200fs	ENST00000338641	NM_000268.3	200	aGg/ag	6/16	0.415767909594951	2	FACETS	0.962	0.887	1	0.962	0.887	1	CLONAL	2	TRUE	0	0.415767909594951	2		243	340	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874286	76874289	+	frameshift_variant	Frame_Shift_Del	DEL	AGCT	AGCT	-	novel	NA	P-0050466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	42	396	0	ENST00000373344.5:c.5433_5436del	p.Ala1812AspfsTer11	p.A1812Dfs*11	ENST00000373344	NM_000489.3	1811	ttAGCT/tt	21/35	0.331825226344889	0	FACETS	0.468	0.394	0.55			1	SUBCLONAL	1	TRUE	0	0.415767909594951	0		396	252	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	210	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.281318131878144	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	TRUE	1	0.281318131878144	4		436	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0050468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	201	497	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.270981943657036	2	FACETS	0.964	0.896	1	0.964	0.896	1	CLONAL	2	TRUE	0	0.281318131878144	2		497	741	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974715	21974732	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCCCCCGCCTCCA	GCAGCGCCCCCGCCTCCA	-	novel	NA	P-0050468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	106	315	0	ENST00000304494.5:c.95_112del	p.Leu32_Leu37del	p.L32_L37del	ENST00000304494	NM_000077.4	32	cTGGAGGCGGGGGCGCTGCcc/ccc	1/3	0.281318131878144	2	FACETS	0.889	0.802	0.979	0.889	0.802	0.979	CLONAL	2	TRUE	0	0.281318131878144	2		315	424	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476763	140476763	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1562954580	NA	P-0050468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	104	386	0	ENST00000288602.6:c.1643T>C	p.Phe548Ser	p.F548S	ENST00000288602	NM_004333.4	548	tTt/tCt	13/18	0.125227377224321	4	FACETS	0.927	0.833	1	0.927	0.833	1	INDETERMINATE	2	TRUE	2	0.281318131878144	4		386	511	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0050469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	313	384	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.528663029891897	2	FACETS	0.905	0.861	0.949	0.905	0.861	0.949	CLONAL	2	TRUE	0	0.528663029891897	2		384	654	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579469	7579470	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CG	novel	NA	P-0050469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	224	596	0	ENST00000269305.4:c.216_217dup	p.Val73AlafsTer51	p.V73Afs*51	ENST00000269305	NM_001126112.2	73	gtg/gCGtg	4/11	0.528663029891897	1	FACETS	0.911	0.853	0.971	0.911	0.853	0.971	CLONAL	1	TRUE	0	0.528663029891897	1		596	684	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098917	178098917	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	174	344	0	ENST00000397062.3:c.128G>T	p.Arg43Leu	p.R43L	ENST00000397062	NM_006164.4	43	cGg/cTg	2/5	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.528663029891897	2		344	613	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0050470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	189	355	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.366541401503909	2	FACETS	0.937	0.873	1	0.937	0.873	1	CLONAL	2	TRUE	0	0.37211701739606	2		355	542	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987148	36987148	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0050470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	117	497	0	ENST00000354822.5:c.541A>T	p.Lys181Ter	p.K181*	ENST00000354822	NM_001079668.2	181	Aag/Tag	3/3	1	2	FACETS	0.998	0.902	1	0.998	0.902	1	CLONAL	1	TRUE	1	0.37211701739606	2		497	630	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987220	36987220	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	89	446	1	ENST00000354822.5:c.469del	p.Arg157AlafsTer9	p.R157Afs*9	ENST00000354822	NM_001079668.2	157	Cgc/gc	3/3	1	2	FACETS	0.859	0.763	0.961	0.859	0.763	0.961	CLONAL	1	TRUE	1	0.37211701739606	2		447	557	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0050471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	34	510	3	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	1	2	FACETS	0.59	0.482	0.712	0.59	0.482	0.712	SUBCLONAL	1	TRUE	1	0.26	2		513	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0050471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	43	465	0	ENST00000269305.4:c.560-1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			1	2	FACETS	0.748	0.627	0.883	0.748	0.627	0.883	SUBCLONAL	1	TRUE	1	0.26	2		465	442	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667552	29667552	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	19	0	0	ENST00000356175.3:c.6888G>A	p.Trp2296Ter	p.W2296*	ENST00000356175	NM_000267.3	2296	tgG/tgA	46/57	1	2	FACETS	0.304	0.23	0.392	0.304	0.23	0.392	SUBCLONAL	1	TRUE	1	0.26	2		0	480	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750842	57750842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	17	0	0	ENST00000274289.3:c.1762G>T	p.Asp588Tyr	p.D588Y	ENST00000274289	NM_006622.3	588	Gat/Tat	13/14	1	2	FACETS	0.396	0.295	0.517	0.396	0.295	0.517	SUBCLONAL	1	TRUE	1	0.26	2		0	330	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597400	10597401	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0050471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	55	560	1	ENST00000171111.5:c.1802_1803delinsTT	p.Arg601Leu	p.R601L	ENST00000171111	NM_203500.1	601	cGG/cTT	6/6	1	2	FACETS	0.771	0.659	0.892	0.771	0.659	0.892	SUBCLONAL	1	TRUE	1	0.26	2		561	549	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935703	13935703	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	30	359	0	ENST00000405192.2:c.1153G>T	p.Glu385Ter	p.E385*	ENST00000405192	NM_001163147.1	385	Gag/Tag	12/12	1	2	FACETS	0.636	0.512	0.775	0.636	0.512	0.775	SUBCLONAL	1	TRUE	1	0.26	2		359	363	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100186	27100186	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	27	383	0	ENST00000324856.7:c.3982C>T	p.Gln1328Ter	p.Q1328*	ENST00000324856	NM_006015.4	1328	Cag/Tag	16/20	1	2	FACETS	0.577	0.459	0.712	0.577	0.459	0.712	SUBCLONAL	1	TRUE	1	0.26	2		383	360	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	96	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.116590625326215	3	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.249096141097075	3		334	628	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947540	48947540	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0050524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	115	353	0	ENST00000267163.4:c.1128-1G>A		p.X376_splice	ENST00000267163	NM_000321.2	376			0.249096141097075	1	FACETS	0.77	0.696	0.847	1	0.985	1	SUBCLONAL	2	TRUE	0	0.249096141097075	1		353	525	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943743	71943743	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	174	670	0	ENST00000298229.2:c.1786T>A	p.Ser596Thr	p.S596T	ENST00000298229	NM_001567.3	596	Tct/Act	15/28	1	2	FACETS	0.796	0.733	0.861	1	0.99	1	SUBCLONAL	2	TRUE	1	0.249096141097075	2		670	878	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961651	41961651	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	94	371	0	ENST00000219905.7:c.559G>C	p.Asp187His	p.D187H	ENST00000219905	NM_001164273.1	187	Gac/Cac	2/24	1	2	FACETS	0.794	0.71	0.884	1	0.982	1	SUBCLONAL	2	TRUE	1	0.249096141097075	2		371	475	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579182	7579348	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAACTATAAAAAAACACTGACAGGAAGCCAAAGGGTGAAGAGGAATCCCAAAGTTCCAAACAAAAGAAATGCAGGGGGATACGGCCAGGCATTGAAGTCTCATGGAAGCCAGCCCCTCAGGGCAACTGACCGTGCAAGTCACAGACTTGGCTGTCCCAGAATGCAAG	AAACTATAAAAAAACACTGACAGGAAGCCAAAGGGTGAAGAGGAATCCCAAAGTTCCAAACAAAAGAAATGCAGGGGGATACGGCCAGGCATTGAAGTCTCATGGAAGCCAGCCCCTCAGGGCAACTGACCGTGCAAGTCACAGACTTGGCTGTCCCAGAATGCAAG	-	novel	NA	P-0050524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	42	108	1	ENST00000269305.4:c.339_375+130del		p.X113_splice	ENST00000269305	NM_001126112.2	113		4/11	0.249096141097075	1	FACETS	1	0.86	1	1	0.972	1	CLONAL	2	TRUE	0	0.249096141097075	1		109	146	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579185	7579351	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTATAAAAAAACACTGACAGGAAGCCAAAGGGTGAAGAGGAATCCCAAAGTTCCAAACAAAAGAAATGCAGGGGGATACGGCCAGGCATTGAAGTCTCATGGAAGCCAGCCCCTCAGGGCAACTGACCGTGCAAGTCACAGACTTGGCTGTCCCAGAATGCAAGAAG	CTATAAAAAAACACTGACAGGAAGCCAAAGGGTGAAGAGGAATCCCAAAGTTCCAAACAAAAGAAATGCAGGGGGATACGGCCAGGCATTGAAGTCTCATGGAAGCCAGCCCCTCAGGGCAACTGACCGTGCAAGTCACAGACTTGGCTGTCCCAGAATGCAAGAAG	-	novel	NA	P-0050524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	22	126	0	ENST00000269305.4:c.336_375+127del		p.X112_splice	ENST00000269305	NM_001126112.2	112		4/11	0.249096141097075	1	FACETS	0.998	0.78	1	0.998	0.78	1	CLONAL	1	TRUE	0	0.249096141097075	1		126	155	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311616	15311625	+	frameshift_variant	Frame_Shift_Del	DEL	GCTAGCAGCA	GCTAGCAGCA	-	novel	NA	P-0050524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	22	142	0	ENST00000263388.2:c.92_101del	p.Leu31ArgfsTer202	p.L31Rfs*202	ENST00000263388	NM_000435.2	31	cTGCTGCTAGCg/cg	1/33	1	2	FACETS	0.96	0.749	1	0.96	0.749	1	CLONAL	1	TRUE	1	0.249096141097075	2		142	184	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096076	178096076	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	46	400	0	ENST00000397062.3:c.1255G>C	p.Asp419His	p.D419H	ENST00000397062	NM_006164.4	419	Gat/Cat	5/5	0.249096141097075	6	FACETS	0.664	0.558	0.783	0.166	0.139	0.196	SUBCLONAL	1	TRUE	2	0.249096141097075	6		400	833	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5463032	5463032	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	60	275	0	ENST00000381577.3:c.593G>C	p.Arg198Thr	p.R198T	ENST00000381577	NM_014143.3	198	aGa/aCa	4/7	0.249096141097075	3	FACETS	1	0.896	1	0.523	0.451	0.601	CLONAL	1	TRUE	1	0.249096141097075	3		275	518	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0050526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	15	337	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.18	0.131	0.239	0.18	0.131	0.239	SUBCLONAL	1	TRUE	1	0.41139369993091	2		337	405	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101612	27101612	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	385	757	0	ENST00000324856.7:c.4899del	p.Met1634Ter	p.M1634*	ENST00000324856	NM_006015.4	1632	Ccc/cc	18/20	0.41139369993091	2	FACETS	0.913	0.87	0.957	0.913	0.87	0.957	CLONAL	2	TRUE	0	0.41139369993091	2		757	1025	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371849	55371850	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0050526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	19	102	0	ENST00000297316.4:c.541dup	p.Leu181ProfsTer184	p.L181Pfs*184	ENST00000297316	NM_022454.3	180	ggc/ggCc	2/2	1	2	FACETS	0.684	0.525	0.868	0.684	0.525	0.868	SUBCLONAL	1	TRUE	1	0.41139369993091	2		102	135	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942647	71942647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	146	546	0	ENST00000298229.2:c.1603G>A	p.Ala535Thr	p.A535T	ENST00000298229	NM_001567.3	535	Gcc/Acc	13/28	1	2	FACETS	0.912	0.834	0.995	0.912	0.834	0.995	CLONAL	1	TRUE	1	0.41139369993091	2		546	778	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720720	89720720	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	93	116	0	ENST00000371953.3:c.871del	p.Glu291LysfsTer16	p.E291Kfs*16	ENST00000371953	NM_000314.4	291	Gaa/aa	8/9	0.41139369993091	3	FACETS	0.988	0.902	1	0.988	0.902	1	CLONAL	3	TRUE	0	0.41139369993091	3		116	184	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944789	71944789	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0050526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	140	570	0	ENST00000298229.2:c.2212+1G>T		p.X738_splice	ENST00000298229	NM_001567.3	738			1	2	FACETS	0.907	0.827	0.991	0.907	0.827	0.991	CLONAL	1	TRUE	1	0.41139369993091	2		570	750	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830604	72830604	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	143	617	0	ENST00000268489.5:c.5977del	p.Ser1993ProfsTer4	p.S1993Pfs*4	ENST00000268489	NM_006885.3	1993	Tcc/cc	9/10	1	2	FACETS	0.982	0.897	1	0.982	0.897	1	CLONAL	1	TRUE	1	0.41139369993091	2		617	708	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591056	67591076	+	inframe_deletion	In_Frame_Del	DEL	AGAAGCAGGCAGCTGAGTATC	AGAAGCAGGCAGCTGAGTATC	-	novel	NA	P-0050526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	59	255	0	ENST00000274335.5:c.1649_1669del	p.Lys550_Tyr556del	p.K550_Y556del	ENST00000274335		550	aAGAAGCAGGCAGCTGAGTATCga/aga	12/15	1	2	FACETS	0.966	0.837	1	0.966	0.837	1	CLONAL	1	TRUE	1	0.41139369993091	2		255	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912655	NA	P-0050527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	450	519	14	ENST00000269305.4:c.725G>C	p.Cys242Ser	p.C242S	ENST00000269305	NM_001126112.2	242	tGc/tCc	7/11	0.912022435216162	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.912022435216162	1		533	525	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934602	9934602	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs397518470	NA	P-0050527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	196	427	7	ENST00000330684.3:c.1553G>T	p.Arg518Leu	p.R518L	ENST00000330684	NM_001134407.1	518	cGt/cTt	7/13	0.487826334397359	1	FACETS	0.361	0.336	0.388	0.361	0.336	0.388	INDETERMINATE	1	TRUE	0	0.912022435216162	1		434	647	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015395	176015395	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	189	376	5	ENST00000367669.3:c.1343A>G	p.Tyr448Cys	p.Y448C	ENST00000367669	NM_022457.5	448	tAt/tGt	12/20	1	2	FACETS	0.984	0.922	1	0.984	0.922	1	CLONAL	1	TRUE	1	0.912022435216162	2		381	421	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039505	49039505	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0050527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	239	336	2	ENST00000267163.4:c.2489+1G>T		p.X830_splice	ENST00000267163	NM_000321.2	830			0.912022435216162	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.912022435216162	1		338	284	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092967	27092967	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	237	347	6	ENST00000324856.7:c.2898G>T	p.Glu966Asp	p.E966D	ENST00000324856	NM_006015.4	966	gaG/gaT	10/20	1	2	FACETS	0.962	0.907	1	0.962	0.907	1	CLONAL	1	TRUE	1	0.912022435216162	2		353	540	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112588	2112588	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs45491095	NA	P-0050527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	468	625	12	ENST00000219476.3:c.1348G>T	p.Glu450Ter	p.E450*	ENST00000219476	NM_000548.3	450	Gag/Tag	13/42	0.487826334397359	1	FACETS	0.697	0.672	0.722	0.697	0.672	0.722	INDETERMINATE	1	TRUE	0	0.912022435216162	1		637	801	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234550	41234550	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs397509152	NA	P-0050527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	399	443	10	ENST00000357654.3:c.4228G>T	p.Glu1410Ter	p.E1410*	ENST00000357654	NM_007294.3	1410	Gaa/Taa	12/23	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.912022435216162	2		453	869	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422507	225422507	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	245	346	7	ENST00000264414.4:c.133C>T	p.Gln45Ter	p.Q45*	ENST00000264414	NM_003590.4	45	Cag/Tag	2/16	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.912022435216162	2		353	463	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306676	41306676	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	239	616	2	ENST00000373198.4:c.983G>C	p.Arg328Pro	p.R328P	ENST00000373198	NM_133170.3	328	cGc/cCc	7/32	1	2	FACETS	0.522	0.487	0.558	0.522	0.487	0.558	SUBCLONAL	1	TRUE	1	0.912022435216162	2		618	1004	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152087	55152087	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	416	614	4	ENST00000257290.5:c.2519C>A	p.Ala840Asp	p.A840D	ENST00000257290	NM_006206.4	840	gCc/gAc	18/23	1	2	FACETS	0.977	0.934	1	0.977	0.934	1	CLONAL	1	TRUE	1	0.912022435216162	2		618	934	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187426	32187426	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1465	279	682	11	ENST00000375023.3:c.1453C>A	p.His485Asn	p.H485N	ENST00000375023	NM_004557.3	485	Cac/Aac	8/30	0.889509236640391	3	FACETS	0.511	0.478	0.545	0.255	0.239	0.273	SUBCLONAL	1	TRUE	1	0.912022435216162	3		693	1744	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100132	157100132	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs993453560	NA	P-0050527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	54	45	0	ENST00000346085.5:c.1069G>T	p.Gly357Cys	p.G357C	ENST00000346085	NM_020732.3	357	Ggc/Tgc	1/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.912022435216162	2		45	101	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5029791	5029791	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	237	317	2	ENST00000381652.3:c.235C>G	p.Pro79Ala	p.P79A	ENST00000381652	NM_004972.3	79	Cct/Gct	4/25	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.912022435216162	2		319	497	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246459	53246459	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	184	253	3	ENST00000375401.3:c.523C>G	p.Gln175Glu	p.Q175E	ENST00000375401	NM_004187.3	175	Cag/Gag	5/26	1	1	FACETS	0.567	0.531	0.603	0.567	0.531	0.603	SUBCLONAL	1	TRUE	0	0.912022435216162	1		256	387	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	91	276	0				ENST00000310581	NM_198253.2	-/1132			0.494171145939794	5	FACETS	1	0.965	1	0.777	0.7	0.858	CLONAL	2	TRUE	2	0.494171145939794	5		276	275	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864693	68864693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	159	336	0	ENST00000288368.4:c.64C>T	p.Arg22Cys	p.R22C	ENST00000288368	NM_024870.2	22	Cgc/Tgc	1/40	0.494171145939794	6	FACETS	1	0.97	1	0.552	0.509	0.598	CLONAL	2	TRUE	2	0.494171145939794	6		336	579	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0050536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	4621	556	1	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.494171145939794	34	FACETS	0.995	0.989	1			1	CLONAL	32	TRUE	NA	0.494171145939794	34		557	5231	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40742257	40742257	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	104	609	0	ENST00000392038.2:c.867C>G	p.Ile289Met	p.I289M	ENST00000392038	NM_001626.4	289	atC/atG	10/14	0.494171145939794	5	FACETS	0.813	0.727	0.905	0.271	0.242	0.302	CLONAL	1	TRUE	2	0.494171145939794	5		609	901	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527461	29527461	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786203950	NA	P-0050536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	35	326	0	ENST00000356175.3:c.910C>T	p.Arg304Ter	p.R304*	ENST00000356175	NM_000267.3	304	Cga/Tga	9/57	0.314798605116642	6	FACETS	0.546	0.447	0.657	0.136	0.111	0.165	SUBCLONAL	1	TRUE	2	0.494171145939794	6		326	516	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	236	321	0	ENST00000335508.6:c.2704G>C	p.Glu902Gln	p.E902Q	ENST00000335508	NM_012433.2	902	Gaa/Caa	18/25	0.494171145939794	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	0	0.494171145939794	3		321	382	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651893	36651894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0050536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	104	603	0	ENST00000244741.5:c.19dup	p.Asp7GlyfsTer29	p.D7Gfs*29	ENST00000244741	NM_000389.4	5	-/G	2/3	0.455955118064841	4	FACETS	0.871	0.78	0.967	0.29	0.26	0.323	CLONAL	1	TRUE	1	0.494171145939794	4		603	722	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107135	27107135	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0050536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	256	504	0	ENST00000324856.7:c.6746C>G	p.Ser2249Ter	p.S2249*	ENST00000324856	NM_006015.4	2249	tCa/tGa	20/20	0.452347840398076	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.494171145939794	4		504	700	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193871	106193871	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	164	297	0	ENST00000380013.4:c.4333C>T	p.Gln1445Ter	p.Q1445*	ENST00000380013	NM_001127208.2	1445	Cag/Tag	10/11	0.455955118064841	4	FACETS	1	0.985	1	0.824	0.766	0.884	CLONAL	2	TRUE	1	0.494171145939794	4		297	401	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999078	100999078	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200987911	NA	P-0050536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	202	507	0	ENST00000325455.5:c.724C>T	p.Arg242Trp	p.R242W	ENST00000325455	NM_001202474.3	242	Cgg/Tgg	1/8	0.333651070239619	5	FACETS	0.997	0.927	1	0.665	0.618	0.712	CLONAL	2	TRUE	2	0.494171145939794	5		507	714	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265268	16265268	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	131	521	0	ENST00000375759.3:c.10760A>G	p.Asp3587Gly	p.D3587G	ENST00000375759	NM_015001.2	3587	gAt/gGt	14/15	0.452347840398076	4	FACETS	1	0.949	1	0.533	0.484	0.585	CLONAL	1	TRUE	2	0.494171145939794	4		521	743	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429833	78429833	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	52	297	0	ENST00000370768.2:c.955C>T	p.Pro319Ser	p.P319S	ENST00000370768	NM_003902.3	319	Ccc/Tcc	12/20	0.452347840398076	4	FACETS	0.845	0.722	0.979	0.423	0.361	0.49	CLONAL	1	TRUE	2	0.494171145939794	4		297	372	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104356901	104356901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	102	432	0	ENST00000369902.3:c.761G>A	p.Arg254Lys	p.R254K	ENST00000369902	NM_016169.3	254	aGa/aAa	7/12	0.494171145939794	3	FACETS	1	0.939	1	0.532	0.478	0.589	CLONAL	1	TRUE	1	0.494171145939794	3		432	484	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104356924	104356924	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	106	477	0	ENST00000369902.3:c.784G>C	p.Asp262His	p.D262H	ENST00000369902	NM_016169.3	262	Gat/Cat	7/12	0.494171145939794	3	FACETS	0.996	0.896	1	0.498	0.448	0.551	CLONAL	1	TRUE	1	0.494171145939794	3		477	537	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948404	71948404	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	308	713	1	ENST00000298229.2:c.3116C>T	p.Ser1039Phe	p.S1039F	ENST00000298229	NM_001567.3	1039	tCt/tTt	26/28	0.333651070239619	5	FACETS	1	0.987	1	0.765	0.723	0.808	CLONAL	2	TRUE	2	0.494171145939794	5		714	946	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996738	100996738	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	76	364	0	ENST00000325455.5:c.1789G>T	p.Gly597Trp	p.G597W	ENST00000325455	NM_001202474.3	597	Ggg/Tgg	2/8	0.333651070239619	5	FACETS	1	0.945	1	0.377	0.332	0.426	CLONAL	1	TRUE	2	0.494171145939794	5		364	473	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343984	118343984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	139	322	0	ENST00000534358.1:c.2110C>T	p.Pro704Ser	p.P704S	ENST00000534358	NM_005933.3	704	Cca/Tca	3/36	0.333651070239619	5	FACETS	1	0.963	1	0.724	0.664	0.786	CLONAL	2	TRUE	2	0.494171145939794	5		322	451	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861900	57861900	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	107	637	0	ENST00000228682.2:c.1201G>A	p.Gly401Ser	p.G401S	ENST00000228682	NM_005269.2	401	Ggc/Agc	10/12	0.494171145939794	5	FACETS	0.857	0.768	0.952	0.286	0.256	0.318	CLONAL	1	TRUE	2	0.494171145939794	5		637	880	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929375	32929375	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	81	368	0	ENST00000380152.3:c.7385C>G	p.Ser2462Cys	p.S2462C	ENST00000380152		2462	tCc/tGc	14/27	0.494171145939794	4	FACETS	0.931	0.822	1	0.31	0.274	0.349	CLONAL	1	TRUE	1	0.494171145939794	4		368	526	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78914341	78914341	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	313	606	0	ENST00000306801.3:c.2965G>C	p.Glu989Gln	p.E989Q	ENST00000306801	NM_020761.2	989	Gag/Cag	25/34	0.494171145939794	5	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	3	0.494171145939794	5		606	929	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222067	2222067	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	132	791	0	ENST00000398665.3:c.2899G>T	p.Glu967Ter	p.E967*	ENST00000398665	NM_032482.2	967	Gag/Tag	24/28	0.494171145939794	5	FACETS	0.799	0.724	0.879	0.266	0.241	0.293	SUBCLONAL	1	TRUE	2	0.494171145939794	5		791	1164	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18963845	18963845	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	165	449	0	ENST00000262803.5:c.1022G>C	p.Arg341Thr	p.R341T	ENST00000262803	NM_002911.3	341	aGa/aCa	7/24	0.494171145939794	5	FACETS	0.82	0.755	0.888	0.547	0.503	0.592	CLONAL	2	TRUE	2	0.494171145939794	5		449	709	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198264978	198264978	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	159	304	0	ENST00000335508.6:c.2899G>C	p.Glu967Gln	p.E967Q	ENST00000335508	NM_012433.2	967	Gag/Cag	19/25	0.494171145939794	3	FACETS	1	0.986	1	0.821	0.765	0.876	CLONAL	2	TRUE	0	0.494171145939794	3		304	326	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29099543	29099543	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	49	308	0	ENST00000328354.6:c.858C>G	p.Ile286Met	p.I286M	ENST00000328354	NM_007194.3	286	atC/atG	8/15	0.494171145939794	3	FACETS	0.734	0.624	0.853	0.367	0.312	0.427	SUBCLONAL	1	TRUE	1	0.494171145939794	3		308	337	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665280	138665280	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	253	589	0	ENST00000330315.3:c.285G>T	p.Lys95Asn	p.K95N	ENST00000330315	NM_023067.3	95	aaG/aaT	1/1	0.494171145939794	4	FACETS	0.918	0.862	0.976	0.918	0.862	0.976	CLONAL	2	TRUE	2	0.494171145939794	4		589	833	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277499	142277499	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	146	285	0	ENST00000350721.4:c.1852C>G	p.Leu618Val	p.L618V	ENST00000350721	NM_001184.3	618	Cta/Gta	8/47	0.494171145939794	4	FACETS	0.996	0.918	1	0.996	0.918	1	CLONAL	2	TRUE	2	0.494171145939794	4		285	443	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169977839	169977839	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	167	360	0	ENST00000295797.4:c.306G>C	p.Leu102Phe	p.L102F	ENST00000295797	NM_002740.5	102	ttG/ttC	3/18	0.494171145939794	5	FACETS	1	0.971	1	0.732	0.677	0.788	CLONAL	2	TRUE	2	0.494171145939794	5		360	536	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670341	30670341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1336113706	NA	P-0050536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	163	433	0	ENST00000376406.3:c.6091C>T	p.Arg2031Trp	p.R2031W	ENST00000376406	NM_014641.2	2031	Cgg/Tgg	14/15	0.455955118064841	4	FACETS	0.904	0.835	0.976	0.603	0.557	0.651	CLONAL	2	TRUE	1	0.494171145939794	4		433	545	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70967563	70967563	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	178	497	0	ENST00000276594.2:c.1460G>T	p.Arg487Ile	p.R487I	ENST00000276594	NM_024504.3	487	aGa/aTa	7/8	0.494171145939794	6	FACETS	0.929	0.858	1	0.464	0.429	0.502	CLONAL	2	TRUE	2	0.494171145939794	6		497	771	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70967613	70967613	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	115	399	0	ENST00000276594.2:c.1410C>G	p.Phe470Leu	p.F470L	ENST00000276594	NM_024504.3	470	ttC/ttG	7/8	0.494171145939794	6	FACETS	1	0.984	1	0.371	0.335	0.41	CLONAL	1	TRUE	2	0.494171145939794	6		399	623	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328345	137328346	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0050536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	139	673	0	ENST00000481739.1:c.1277_1278dup	p.Ser427AlafsTer36	p.S427Afs*36	ENST00000481739	NM_002957.4	425	ctg/ctGCg	10/10	0.494171145939794	3	FACETS	0.952	0.868	1	0.476	0.434	0.52	CLONAL	1	TRUE	1	0.494171145939794	3		673	737	SUCCESS
EED	8726	MSKCC	GRCh37	11	85968611	85968611	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	153	302	1	ENST00000263360.6:c.608del	p.Pro203GlnfsTer7	p.P203Qfs*7	ENST00000263360	NM_003797.3	203	Cca/ca	6/12	NA	2	FACETS	0.892	0.853	0.928			1	INDETERMINATE	2	TRUE	NA	0.907763050099715	2		303	189	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029329	14029332	+	frameshift_variant	Frame_Shift_Del	DEL	TATC	TATC	GAT	novel	NA	P-0050538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	29	318	1	ENST00000311895.7:c.1540_1543delinsGAT	p.Tyr514AspfsTer5	p.Y514Dfs*5	ENST00000311895	NM_005236.2	514	TATCgt/GATgt	8/11	0.817456034456461	2	FACETS	0.243	0.195	0.297	0.121	0.097	0.149	SUBCLONAL	1	TRUE	0	0.907763050099715	2		319	263	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588751	29588751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760703505	NA	P-0050538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	149	295	0	ENST00000356175.3:c.4537C>T	p.Arg1513Ter	p.R1513*	ENST00000356175	NM_000267.3	1513	Cga/Tga	34/57	0.795496720788224	4	FACETS	0.872	0.808	0.938	0.872	0.808	0.938	CLONAL	2	TRUE	2	0.907763050099715	4		295	359	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40364066	40364066	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	27	96	0	ENST00000293328.3:c.1616A>G	p.Asn539Ser	p.N539S	ENST00000293328	NM_012448.3	539	aAc/aGc	13/19	0.907763050099715	6	FACETS	0.842	0.674	1	0.21	0.168	0.258	CLONAL	1	TRUE	2	0.907763050099715	6		96	199	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117378	115117379	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	TA	TA	-	novel	NA	P-0050539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	364	342	0	ENST00000257566.3:c.795_796del	p.Tyr265Ter	p.Y265*	ENST00000257566	NM_016569.3	265	taTAgt/tagt	4/8	0.398310879206155	6	FACETS	0.94	0.904	0.976			1	CLONAL	6	FALSE	NA	0.398310879206155	6		342	582	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060696	38060697	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGCC	novel	NA	P-0050539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	144	929	1	ENST00000250448.2:c.1288_1292dup	p.Thr432AlafsTer10	p.T432Afs*10	ENST00000250448	NM_004496.3	431	tct/tcGGCTCt	2/2	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.398310879206155	2		930	600	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842374	68842375	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555515197	NA	P-0050539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	103	499	0	ENST00000261769.5:c.438_439del	p.Pro147TrpfsTer20	p.P147Wfs*20	ENST00000261769	NM_004360.3	145	tcCTct/tcct	4/16	0.343415805201824	0	FACETS	0.564	0.512	0.617			1	SUBCLONAL	2	FALSE	0	0.398310879206155	0		499	276	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646831	37646831	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	152	365	0	ENST00000447079.4:c.1956del	p.Lys652AsnfsTer3	p.K652Nfs*3	ENST00000447079	NM_015083.1	651	tcA/tc	3/14	0.398310879206155	6	FACETS	1	0.978	1			1	CLONAL	2	FALSE	NA	0.398310879206155	6		365	581	SUCCESS
APC	324	MSKCC	GRCh37	5	112173386	112173386	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	77	324	0	ENST00000257430.4:c.2095T>A	p.Trp699Arg	p.W699R	ENST00000257430	NM_000038.5	699	Tgg/Agg	16/16	1	2	FACETS	0.887	0.792	0.984	1	0.983	1	CLONAL	2	FALSE	1	0.398310879206155	2		324	218	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502735	149502735	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763239423	NA	P-0050539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	359	631	0	ENST00000261799.4:c.2053C>T	p.Arg685Cys	p.R685C	ENST00000261799	NM_002609.3	685	Cgc/Tgc	15/23	0.405786632840346	4	FACETS	0.956	0.916	0.997	1	0.994	1	CLONAL	4	FALSE	1	0.398310879206155	4		631	659	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730114	41730114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	105	398	0	ENST00000242208.4:c.415G>A	p.Glu139Lys	p.E139K	ENST00000242208	NM_002192.2	139	Gag/Aag	3/3	1	2	FACETS	0.861	0.782	0.943	1	0.987	1	CLONAL	2	FALSE	1	0.398310879206155	2		398	306	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569662	41569662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	82	284	0	ENST00000263253.7:c.4653G>T	p.Lys1551Asn	p.K1551N	ENST00000263253	NM_001429.3	1551	aaG/aaT	29/31	1	2	FACETS	0.847	0.754	0.943	0.847	0.754	0.943	CLONAL	1	TRUE	1	0.633094838714714	2		284	306	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495647	72495647	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	116	392	0	ENST00000477973.2:c.425G>C	p.Arg142Thr	p.R142T	ENST00000477973	NM_012234.5	142	aGa/aCa	1/4	1	2	FACETS	0.907	0.824	0.993	0.907	0.824	0.993	CLONAL	1	TRUE	1	0.633094838714714	2		392	404	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061105	38061134	+	frameshift_variant	Frame_Shift_Del	DEL	TTGCGGCTCTCAGGGCCGCCCTTGGCGCCG	TTGCGGCTCTCAGGGCCGCCCTTGGCGCCG	C	novel	NA	P-0050552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	24	122	0	ENST00000250448.2:c.855_884delinsG	p.Ser285ArgfsTer8	p.S285Rfs*8	ENST00000250448	NM_004496.3	285	agCGGCGCCAAGGGCGGCCCTGAGAGCCGCAAg/agGg	2/2	1	2	FACETS	0.486	0.385	0.6	0.486	0.385	0.6	SUBCLONAL	1	TRUE	1	0.633094838714714	2		122	156	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0050553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	77	518	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.2142445300354	4	FACETS	0.834	0.737	0.936	0.834	0.737	0.936	CLONAL	3	TRUE	1	0.2142445300354	4		518	349	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519966	NA	P-0050553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	66	738	0	ENST00000347630.2:c.397T>A	p.Phe133Ile	p.F133I	ENST00000347630	NM_001007230.1	133	Ttc/Atc	6/11	0.152668738309365	4	FACETS	0.99	0.863	1			1	CLONAL	2	TRUE	NA	0.2142445300354	4		738	378	SUCCESS
APC	324	MSKCC	GRCh37	5	112175574	112175575	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACAA	novel	NA	P-0050553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	61	531	0	ENST00000257430.4:c.4286_4289dup	p.Met1431AsnfsTer8	p.M1431Nfs*8	ENST00000257430	NM_000038.5	1428	gga/ggACAAa	16/16	0.2142445300354	1	FACETS	0.989	0.863	1	1	0.98	1	CLONAL	2	TRUE	0	0.2142445300354	1		531	257	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058535	69058535	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	87	715	0	ENST00000288368.4:c.4179A>T	p.Gln1393His	p.Q1393H	ENST00000288368	NM_024870.2	1393	caA/caT	34/40	0.2142445300354	7	FACETS	0.999	0.886	1	0.333	0.295	0.374	CLONAL	2	TRUE	1	0.2142445300354	7		715	624	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	521	276	0				ENST00000310581	NM_198253.2	-/1132			0.561281753627873	5	FACETS	0.932	0.905	0.958	1	0.996	1	CLONAL	5	TRUE	1	0.561281753627873	5		276	734	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0050554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	478	839	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.506924818340567	3	FACETS	0.895	0.864	0.927	0.895	0.864	0.927	CLONAL	3	TRUE	0	0.561281753627873	3		839	812	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044943	47044943	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	356	390	0	ENST00000377604.3:c.2269C>T	p.Gln757Ter	p.Q757*	ENST00000377604	NM_001204468.1	757	Cag/Tag	20/24	0.561281753627873	2	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.561281753627873	2		390	539	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027248	49027248	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0050554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	157	465	2	ENST00000267163.4:c.1814+1G>A		p.X605_splice	ENST00000267163	NM_000321.2	605			0.561281753627873	3	FACETS	0.872	0.817	0.925			1	CLONAL	3	TRUE	NA	0.561281753627873	3		467	274	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032257	26032257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	88	388	0	ENST00000244661.2:c.32C>T	p.Ser11Phe	p.S11F	ENST00000244661	NM_003537.3	11	tCc/tTc	1/1	0.561281753627873	6	FACETS	1	0.958	1	0.39	0.346	0.437	CLONAL	1	TRUE	3	0.561281753627873	6		388	569	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404710	70404710	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	37	600	0	ENST00000373644.4:c.2224G>C	p.Asp742His	p.D742H	ENST00000373644	NM_030625.2	742	Gac/Cac	4/12	0.424678750524117	2	FACETS	0.441	0.365	0.525	0.22	0.182	0.263	SUBCLONAL	1	TRUE	0	0.561281753627873	2		600	299	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157872	106157872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	22	433	0	ENST00000380013.4:c.2773G>A	p.Ala925Thr	p.A925T	ENST00000380013	NM_001127208.2	925	Gca/Aca	3/11	0.561281753627873	3	FACETS	0.268	0.207	0.338	0.089	0.069	0.113	SUBCLONAL	1	TRUE	0	0.561281753627873	3		433	375	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514364	149514364	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754682330	NA	P-0050554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	244	653	0	ENST00000261799.4:c.580A>G	p.Ile194Val	p.I194V	ENST00000261799	NM_002609.3	194	Att/Gtt	4/23	0.561281753627873	3	FACETS	0.944	0.889	0.999	0.944	0.889	0.999	CLONAL	2	TRUE	1	0.561281753627873	3		653	590	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158443	26158443	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	135	775	0	ENST00000289316.2:c.46A>C	p.Lys16Gln	p.K16Q	ENST00000289316	NM_138720.2	16	Aag/Cag	1/2	0.561281753627873	6	FACETS	1	0.932	1	0.344	0.312	0.378	CLONAL	1	TRUE	3	0.561281753627873	6		775	989	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200010	138200010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	117	581	0	ENST00000237289.4:c.1428G>A	p.Met476Ile	p.M476I	ENST00000237289	NM_001270507.1	476	atG/atA	7/9	0.319576924972394	4	FACETS	0.956	0.863	1	0.478	0.431	0.527	INDETERMINATE	1	TRUE	2	0.561281753627873	4		581	681	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157882	27157919	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGATGCTGAAACATCTCTCACCTGCATTGCCTCTGG	TCTGATGCTGAAACATCTCTCACCTGCATTGCCTCTGG	-	novel	NA	P-0050554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	86	584	0	ENST00000380036.4:c.106_143del	p.Ser36ValfsTer5	p.S36Vfs*5	ENST00000380036	NM_000459.3	36	TCTGATGCTGAAACATCTCTCACCTGCATTGCCTCTGGg/g	2/23	0.391987639160823	4	FACETS	0.779	0.69	0.874	0.39	0.345	0.437	SUBCLONAL	1	TRUE	2	0.561281753627873	4		584	614	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0050555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	16	339	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	1	2	FACETS	0.248	0.183	0.327	0.248	0.183	0.327	SUBCLONAL	1	FALSE	1	0.372625719730532	2		339	346	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0050555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	38	487	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.731	0.607	0.868	0.731	0.607	0.868	SUBCLONAL	1	FALSE	1	0.372625719730532	2		487	279	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032566	47032566	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	39	514	0	ENST00000377604.3:c.472G>T	p.Glu158Ter	p.E158*	ENST00000377604	NM_001204468.1	158	Gag/Tag	5/24	0.114441618524859	0	FACETS	0.515	0.429	0.609			1	INDETERMINATE	1	FALSE	0	0.372625719730532	0		514	255	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658295	18658295	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	99	503	0	ENST00000266497.5:c.3100C>G	p.Arg1034Gly	p.R1034G	ENST00000266497		1034	Cgt/Ggt	22/31	0.274430199495159	5	FACETS	0.981	0.897	1	1	0.981	1	CLONAL	4	TRUE	2	0.369891254182338	5		503	212	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443695	49443695	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	15	673	0	ENST00000301067.7:c.3676C>A	p.Leu1226Ile	p.L1226I	ENST00000301067	NM_003482.3	1226	Ctc/Atc	11/54	0.369891254182338	7	FACETS	0.531	0.388	0.704	0.133	0.097	0.176	SUBCLONAL	1	TRUE	3	0.369891254182338	7		673	294	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061137	38061186	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGC	GCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGC	-	novel	NA	P-0050556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	188	100	0	ENST00000250448.2:c.803_852del	p.Cys268Ter	p.C268*	ENST00000250448	NM_004496.3	268	tGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGC/t	2/2	0.369891254182338	5	FACETS	0.946	0.892	1	1	0.993	1	CLONAL	5	TRUE	2	0.369891254182338	5		100	334	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980488	70980488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267601982	NA	P-0050556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	62	626	1	ENST00000276594.2:c.889G>A	p.Gly297Arg	p.G297R	ENST00000276594	NM_024504.3	297	Gga/Aga	4/8	0.175937128948821	4	FACETS	0.973	0.851	1	0.973	0.851	1	INDETERMINATE	2	TRUE	2	0.369891254182338	4		627	236	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619137	37619137	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	CAGGC	novel	NA	P-0050556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	202	578	0	ENST00000447079.4:c.813delinsCAGGC	p.Arg271SerfsTer28	p.R271Sfs*28	ENST00000447079	NM_015083.1	271	agA/agCAGGC	1/14	0.369891254182338	7	FACETS	0.952	0.898	1			1	CLONAL	6	TRUE	NA	0.369891254182338	7		578	368	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0050557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	51	391	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	0.605	0.514	0.706	0.605	0.514	0.706	SUBCLONAL	1	TRUE	1	0.272170032242144	2		391	619	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793008	33793010	+	inframe_deletion	In_Frame_Del	DEL	CGC	CGC	-	rs780345232	NA	P-0050557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	13	66	0	ENST00000498907.2:c.311_313del	p.Gly104del	p.G104del	ENST00000498907	NM_004364.3	104	gGCGac/gac	1/1	0.272170032242144	13	FACETS	1	0.811	1			1	CLONAL	1	TRUE	NA	0.272170032242144	13		66	200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0050557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	142	653	0	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	0.272170032242144	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.272170032242144	1		653	718	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589579	67589593	+	inframe_deletion	In_Frame_Del	DEL	AAATTACATGAATAT	AAATTACATGAATAT	-	novel	NA	P-0050557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	85	304	0	ENST00000274335.5:c.1344_1358del	p.Lys448_Tyr452del	p.K448_Y452del	ENST00000274335		448	AAATTACATGAATAT/-	10/15	0.272170032242144	3	FACETS	1	0.976	1	0.711	0.63	0.797	CLONAL	1	TRUE	1	0.272170032242144	3		304	499	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047151	77047151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	95	550	0	ENST00000356341.3:c.1393C>T	p.Leu465Phe	p.L465F	ENST00000356341	NM_002576.4	465	Ctc/Ttc	13/15	1	2	FACETS	0.983	0.876	1	0.983	0.876	1	CLONAL	1	TRUE	1	0.272170032242144	2		550	710	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39251221	39251221	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	153	589	1	ENST00000402219.2:c.1132A>T	p.Thr378Ser	p.T378S	ENST00000402219	NM_005633.3	378	Aca/Tca	9/23	0.13070485025428	4	FACETS	1	0.985	1	0.688	0.628	0.75	INDETERMINATE	1	TRUE	2	0.272170032242144	4		590	1040	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931904	39931904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	118	724	0	ENST00000378444.4:c.2695C>T	p.Pro899Ser	p.P899S	ENST00000378444	NM_001123385.1	899	Cca/Tca	4/15	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.272170032242144	2		724	850	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0050558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1287	571	519	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.713031047928728	6	FACETS	1	0.983	1	0.523	0.501	0.545	CLONAL	2	TRUE	2	0.713031047928728	6		519	1858	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578206	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs886039484	NA	P-0050558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	656	712	0	ENST00000269305.4:c.643A>G	p.Ser215Gly	p.S215G	ENST00000269305	NM_001126112.2	215	Agt/Ggt	6/11	0.619659568783948	2	FACETS	0.92	0.895	0.945	0.92	0.895	0.945	CLONAL	2	TRUE	0	0.713031047928728	2		712	1000	SUCCESS
RET	5979	MSKCC	GRCh37	10	43613868	43613868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs75686697	NA	P-0050558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	66	746	1	ENST00000355710.3:c.2332G>A	p.Val778Ile	p.V778I	ENST00000355710	NM_020975.4	778	Gtc/Atc	13/20	0.555288647390265	2	FACETS	0.217	0.188	0.249	0.109	0.094	0.125	SUBCLONAL	1	TRUE	0	0.713031047928728	2		747	852	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121340	29121340	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660788	NA	P-0050558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	275	724	0	ENST00000328354.6:c.335A>G	p.Asn112Ser	p.N112S	ENST00000328354	NM_007194.3	112	aAc/aGc	3/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.713031047928728	2		724	744	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0050575-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	141	472	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	1	2	FACETS	0.827	0.755	0.901	0.827	0.755	0.901	CLONAL	1	TRUE	1	0.526482999210917	2		472	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0050637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	250	513	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.710201120578221	2		516	639	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0050637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	95	422	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.913	0.824	1	0.913	0.824	1	CLONAL	1	TRUE	1	0.710201120578221	2		422	293	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0050637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	110	318	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	0.710201120578221	3	FACETS	1	0.975	1	0.61	0.554	0.668	CLONAL	1	TRUE	1	0.710201120578221	3		318	344	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77070014	77070014	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	188	601	0	ENST00000356341.3:c.526G>C	p.Asp176His	p.D176H	ENST00000356341	NM_002576.4	176	Gat/Cat	6/15	1	2	FACETS	0.964	0.897	1	0.964	0.897	1	CLONAL	1	TRUE	1	0.710201120578221	2		601	549	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045895	180045895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	158	545	0	ENST00000261937.6:c.2876G>A	p.Arg959His	p.R959H	ENST00000261937	NM_182925.4	959	cGc/cAc	21/30	0.710201120578221	3	FACETS	0.993	0.914	1	0.497	0.457	0.538	CLONAL	1	TRUE	1	0.710201120578221	3		545	607	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813088	76813088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	183	659	0	ENST00000373344.5:c.6533G>A	p.Arg2178Gln	p.R2178Q	ENST00000373344	NM_000489.3	2178	cGg/cAg	30/35	0.45171519067563	3	FACETS	1	0.967	1	0.538	0.498	0.579	CLONAL	1	TRUE	1	0.710201120578221	3		659	649	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115928	8115929	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	112	391	0	ENST00000346208.3:c.1275dup	p.Ser426IlefsTer81	p.S426Ifs*81	ENST00000346208		425	cca/ccAa	6/6	0.272322237725626	2	FACETS	0.594	0.537	0.654	0.297	0.268	0.327	INDETERMINATE	1	TRUE	0	0.771448708882408	2		391	489	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401627	401627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	57	527	0	ENST00000380956.4:c.949C>T	p.Leu317Phe	p.L317F	ENST00000380956	NM_001195286.1	317	Ctc/Ttc	7/9	0.272322237725626	2	FACETS	0.293	0.251	0.339	0.147	0.125	0.17	INDETERMINATE	1	TRUE	0	0.771448708882408	2		527	504	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074067	8074067	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1449925618	NA	P-0050643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	63	315	0	ENST00000377482.5:c.592A>G	p.Arg198Gly	p.R198G	ENST00000377482	NM_018948.3	198	Agg/Ggg	4/4	0.318165926532292	1	FACETS	0.37	0.323	0.42	0.37	0.323	0.42	INDETERMINATE	1	TRUE	0	0.771448708882408	1		315	271	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18762564	18762565	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0050643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	80	270	0	ENST00000266497.5:c.4059+2dup		p.X1353_splice	ENST00000266497		1353			0.30920998773635	3	FACETS	1	0.972	1	0.639	0.572	0.708	INDETERMINATE	1	TRUE	1	0.771448708882408	3		270	225	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41242955	41242990	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTACCTGAGTGGTTAAAATGTCACTCTGAGAGGA	TTTTACCTGAGTGGTTAAAATGTCACTCTGAGAGGA	-	novel	NA	P-0050643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	190	320	0	ENST00000357654.3:c.4156_4185+6del		p.X1386_splice	ENST00000357654	NM_007294.3	1386		11/23	0.30920998773635	3	FACETS	1	0.986	1	0.618	0.576	0.662	INDETERMINATE	1	TRUE	1	0.771448708882408	3		320	552	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55603374	55603374	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	102	291	0	ENST00000288135.5:c.2730T>G	p.Asp910Glu	p.D910E	ENST00000288135	NM_000222.2	910	gaT/gaG	20/21	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.581666461267794	2		291	340	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974899	15974899	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	49	379	0	ENST00000268712.3:c.3976C>T	p.Arg1326Ter	p.R1326*	ENST00000268712	NM_006311.3	1326	Cga/Tga	30/46	1	2	FACETS	0.457	0.387	0.534	0.457	0.387	0.534	SUBCLONAL	1	TRUE	1	0.45015989698549	2		379	476	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238417	98238417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137903539	NA	P-0050645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	58	427	2	ENST00000331920.6:c.1627C>T	p.Arg543Cys	p.R543C	ENST00000331920	NM_000264.3	543	Cgc/Tgc	12/24	1	2	FACETS	0.561	0.483	0.646	0.561	0.483	0.646	SUBCLONAL	1	TRUE	1	0.45015989698549	2		429	459	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023637	27023638	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTCCAAGCCGC	novel	NA	P-0050645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	28	300	0	ENST00000324856.7:c.748_758dup	p.Ser255ArgfsTer112	p.S255Rfs*112	ENST00000324856	NM_006015.4	248	ggc/ggCTCCAAGCCGCc	1/20	1	2	FACETS	0.435	0.348	0.533	0.435	0.348	0.533	SUBCLONAL	1	TRUE	1	0.45015989698549	2		300	286	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087568	27087569	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0050645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	32	551	0	ENST00000324856.7:c.2143dup	p.Ser715PhefsTer102	p.S715Ffs*102	ENST00000324856	NM_006015.4	714	-/T	5/20	1	2	FACETS	0.237	0.191	0.289	0.237	0.191	0.289	SUBCLONAL	1	TRUE	1	0.45015989698549	2		551	600	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552773	226552773	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	119	490	0	ENST00000366794.5:c.2588G>T	p.Gly863Val	p.G863V	ENST00000366794	NM_001618.3	863	gGg/gTg	19/23	0.424906529291213	4	FACETS	0.914	0.825	1	0.305	0.275	0.336	CLONAL	1	TRUE	1	0.45015989698549	4		490	839	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115705	8115718	+	frameshift_variant	Frame_Shift_Del	DEL	AACAGACCCCTGAC	AACAGACCCCTGAC	-	novel	NA	P-0050645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	65	302	0	ENST00000346208.3:c.1051_1064del	p.Asn351TyrfsTer15	p.N351Yfs*15	ENST00000346208		351	AACAGACCCCTGACt/t	6/6	1	2	FACETS	0.832	0.726	0.946	0.832	0.726	0.946	CLONAL	1	TRUE	1	0.45015989698549	2		302	347	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063327	67063341	+	inframe_deletion	In_Frame_Del	DEL	CCGACCAGAGAAGCA	CCGACCAGAGAAGCA	-	novel	NA	P-0050645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	24	195	0	ENST00000412916.2:c.17_31del	p.Pro6_Lys11delinsGln	p.P6_K11delinsQ	ENST00000412916		6	cCCGACCAGAGAAGCAag/cag	1/6	0.45015989698549	1	FACETS	0.617	0.49	0.759	0.617	0.49	0.759	SUBCLONAL	1	TRUE	0	0.45015989698549	1		195	134	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724336	112724336	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	38	493	0	ENST00000369452.4:c.220C>T	p.Arg74Trp	p.R74W	ENST00000369452	NM_007373.3	74	Cgg/Tgg	2/9	1	2	FACETS	0.364	0.3	0.436	0.364	0.3	0.436	SUBCLONAL	1	TRUE	1	0.33	2		493	633	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39607429	39607429	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	37	268	0	ENST00000262039.4:c.1507G>A	p.Asp503Asn	p.D503N	ENST00000262039	NM_002647.2	503	Gat/Aat	14/25	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.33	2		268	207	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470597	25470597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	26	812	0	ENST00000264709.3:c.877G>A	p.Gly293Arg	p.G293R	ENST00000264709	NM_175629.2	293	Ggg/Agg	8/23	0.179561304866191	3	FACETS	1	0.893	1	0.597	0.477	0.732	CLONAL	1	TRUE	1	0.29	3		812	172	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403361	139403361	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	19	799	0	ENST00000277541.6:c.3132del	p.Arg1044SerfsTer135	p.R1044Sfs*135	ENST00000277541	NM_017617.3	1044	agG/ag	19/34	1	2	FACETS	0.749	0.572	0.954	0.749	0.572	0.954	CLONAL	1	TRUE	1	0.29	2		799	175	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292532	15292532	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	32	891	1	ENST00000263388.2:c.2647C>T	p.Arg883Ter	p.R883*	ENST00000263388	NM_000435.2	883	Cga/Tga	17/33	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.29	2		892	171	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400277	139400277	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1564191302	NA	P-0050647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	27	876	0	ENST00000277541.6:c.4071C>A	p.Cys1357Ter	p.C1357*	ENST00000277541	NM_017617.3	1357	tgC/tgA	25/34	1	2	FACETS	0.95	0.762	1	0.95	0.762	1	CLONAL	1	TRUE	1	0.29	2		876	196	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413142	139413142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	27	904	0	ENST00000277541.6:c.1000G>T	p.Glu334Ter	p.E334*	ENST00000277541	NM_017617.3	334	Gag/Tag	6/34	1	2	FACETS	0.922	0.739	1	0.922	0.739	1	CLONAL	1	TRUE	1	0.29	2		904	202	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611887	100611887	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	32	334	0	ENST00000308731.7:c.1234C>A	p.Gln412Lys	p.Q412K	ENST00000308731	NM_000061.2	412	Caa/Aaa	14/19	0.216059915085812	2	FACETS	0.897	0.743	1			1	CLONAL	2	TRUE	NA	0.29	2		334	123	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0050649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	139	525	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.916	0.835	1	1	0.99	1	CLONAL	2	TRUE	1	0.22	2		525	690	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786740	3786740	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	36	483	0	ENST00000262367.5:c.4471C>G	p.Gln1491Glu	p.Q1491E	ENST00000262367	NM_004380.2	1491	Caa/Gaa	27/31	1	2	FACETS	0.517	0.424	0.622	0.517	0.424	0.622	SUBCLONAL	1	TRUE	1	0.22	2		483	633	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866632	117866632	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	59	534	0	ENST00000297338.2:c.1013G>T	p.Arg338Ile	p.R338I	ENST00000297338	NM_006265.2	338	aGa/aTa	9/14	1	2	FACETS	0.874	0.751	1	0.874	0.751	1	CLONAL	1	TRUE	1	0.22	2		534	614	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	436	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.421999421195887	6	FACETS	1	0.981	1	0.848	0.822	0.874	CLONAL	5	TRUE	0	0.631506200741049	6		334	614	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0050651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	137	554	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.631506200741049	1	FACETS	0.925	0.854	0.996	0.925	0.854	0.996	CLONAL	1	TRUE	0	0.631506200741049	1		554	321	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845229	151845229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	178	496	1	ENST00000262189.6:c.13783C>T	p.Arg4595Cys	p.R4595C	ENST00000262189	NM_170606.2	4595	Cgc/Tgc	52/59	0.631506200741049	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.631506200741049	3		497	359	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101233	27101234	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0050651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	69	665	0	ENST00000324856.7:c.4515_4516del	p.Tyr1506Ter	p.Y1506*	ENST00000324856	NM_006015.4	1505	acCTat/acat	18/20	1	2	FACETS	0.756	0.665	0.853	0.756	0.665	0.853	SUBCLONAL	1	TRUE	1	0.631506200741049	2		665	289	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860117	152860117	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	95	627	1	ENST00000406277.2:c.311A>T	p.Glu104Val	p.E104V	ENST00000406277	NM_152274.4	104	gAg/gTg	5/7	1		FACETS		0.526	0.655				SUBCLONAL	1	TRUE	1	0.631506200741049	2		628	511	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0050652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	27	384	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.771	0.613	0.952	0.771	0.613	0.952	CLONAL	1	TRUE	1	0.17	2		384	412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0050652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	47	158	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	1	2	FACETS	0.967	0.815	1	0.967	0.815	1	CLONAL	1	TRUE	1	0.17	2		158	572	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604717	48604717	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	33	161	1	ENST00000342988.3:c.1541del	p.Pro514GlnfsTer23	p.P514Qfs*23	ENST00000342988	NM_005359.5	513	taC/ta	12/12	1	2	FACETS	1	0.832	1	1	0.832	1	CLONAL	1	TRUE	1	0.17	2		162	380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577138	7577138	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	72	642	0	ENST00000269305.4:c.800G>T	p.Arg267Leu	p.R267L	ENST00000269305	NM_001126112.2	267	cGg/cTg	8/11	0.3	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.2	1		642	463	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217856	7217856	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	84	624	0	ENST00000380728.2:c.155del	p.Lys52ArgfsTer11	p.K52Rfs*11	ENST00000380728		52	aAg/ag	3/11	0.0233328096410164	3	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.2	3		624	620	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0050655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	65	580	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.199189020577487	2	FACETS	0.82	0.711	0.938	0.41	0.355	0.469	CLONAL	1	TRUE	0	0.264601920682838	2		580	599	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	67	394	1	ENST00000263967.3:c.3012G>A	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atA	21/21	0.172634955510873	3	FACETS	1	0.937	1	0.564	0.491	0.643	CLONAL	1	TRUE	1	0.264601920682838	3		395	508	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054856	5054857	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0050655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	60	381	0	ENST00000381652.3:c.909_910del	p.His303GlnfsTer4	p.H303Qfs*4	ENST00000381652	NM_004972.3	303	cAT/c	7/25	NA	2	FACETS	0.982	0.848	1			1	INDETERMINATE	1	TRUE	NA	0.264601920682838	2		381	462	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514089	69514089	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	81	663	0	ENST00000294312.3:c.592G>T	p.Asp198Tyr	p.D198Y	ENST00000294312	NM_005117.2	198	Gac/Tac	3/3	1	2	FACETS	0.767	0.675	0.866	0.767	0.675	0.866	SUBCLONAL	1	TRUE	1	0.264601920682838	2		663	798	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235899	133235899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500778	NA	P-0050655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	144	590	0	ENST00000320574.5:c.3257G>A	p.Gly1086Asp	p.G1086D	ENST00000320574	NM_006231.2	1086	gGc/gAc	26/49	1	2	FACETS	0.796	0.727	0.867	1	0.988	1	SUBCLONAL	2	TRUE	1	0.264601920682838	2		590	684	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108782	2108782	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	102	711	0	ENST00000219476.3:c.883G>T	p.Ala295Ser	p.A295S	ENST00000219476	NM_000548.3	295	Gcc/Tcc	10/42	1	2	FACETS	0.869	0.776	0.968	0.869	0.776	0.968	CLONAL	1	TRUE	1	0.264601920682838	2		711	887	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984843	9984843	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	48	355	0	ENST00000330684.3:c.1122G>T	p.Lys374Asn	p.K374N	ENST00000330684	NM_001134407.1	374	aaG/aaT	4/13	1	2	FACETS	0.71	0.6	0.831	0.71	0.6	0.831	SUBCLONAL	1	TRUE	1	0.264601920682838	2		355	511	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46271015	46271015	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	97	526	1	ENST00000371998.3:c.3139C>T	p.Gln1047Ter	p.Q1047*	ENST00000371998		1047	Cag/Tag	17/23	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.264601920682838	2		527	729	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633857	86633858	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0050655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	49	361	0	ENST00000274376.6:c.967_968del	p.Leu323LysfsTer4	p.L323Kfs*4	ENST00000274376	NM_002890.2	322	aaTTta/aata	5/25	0.199189020577487	2	FACETS	0.796	0.675	0.93	0.398	0.337	0.465	CLONAL	1	TRUE	0	0.264601920682838	2		361	465	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0050656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	73	383	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.545562705854155	1	FACETS	0.94	0.837	1	0.94	0.837	1	CLONAL	1	TRUE	0	0.545562705854155	1		383	207	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831584	72831584	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	109	616	0	ENST00000268489.5:c.4997C>G	p.Ser1666Cys	p.S1666C	ENST00000268489	NM_006885.3	1666	tCc/tGc	9/10	1	2	FACETS	0.747	0.673	0.824	0.747	0.673	0.824	SUBCLONAL	1	TRUE	1	0.545562705854155	2		616	535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0050656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	239	704	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.514176029900807	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.545562705854155	1		704	618	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593491	48593494	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	rs80338965	NA	P-0050656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	71	275	0	ENST00000342988.3:c.1245_1248del	p.Asp415GlufsTer20	p.D415Efs*20	ENST00000342988	NM_005359.5	414	ttAGAC/tt	10/12	0.545562705854155	1	FACETS	0.714	0.631	0.802	0.714	0.631	0.802	SUBCLONAL	1	TRUE	0	0.545562705854155	1		275	265	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0050659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	92	366	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.537862198569936	2		366	301	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0050659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	73	236	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	0.722	0.635	0.814	0.722	0.635	0.814	SUBCLONAL	1	TRUE	1	0.537862198569936	2		236	376	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0050659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	450	640	0	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.537862198569936	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.537862198569936	3		640	1007	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	120	276	0				ENST00000310581	NM_198253.2	-/1132			0.616327915666383	4	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	2	0.683827561873386	4		276	292	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0050660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	278	525	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.683827561873386	3	FACETS	0.923	0.875	0.971	0.923	0.875	0.971	CLONAL	2	TRUE	1	0.683827561873386	3		525	591	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186598	108186598	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	59	233	0	ENST00000278616.4:c.6055del	p.Tyr2019MetfsTer28	p.Y2019Mfs*28	ENST00000278616	NM_000051.3	2019	Tat/at	41/63	0.683827561873386	3	FACETS	0.877	0.762	1	0.439	0.381	0.5	CLONAL	1	TRUE	1	0.683827561873386	3		233	264	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422690	49422690	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	406	584	0	ENST00000301067.7:c.14303del	p.Lys4768SerfsTer29	p.K4768Sfs*29	ENST00000301067	NM_003482.3	4768	aAg/ag	45/54	0.683827561873386	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.683827561873386	3		584	762	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2090190	2090190	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	482	691	0	ENST00000219066.1:c.759G>C	p.Lys253Asn	p.K253N	ENST00000219066	NM_002528.5	253	aaG/aaC	5/6	0.683827561873386	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.683827561873386	3		691	895	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001566	150001566	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	144	296	0	ENST00000253339.5:c.2038C>G	p.Gln680Glu	p.Q680E	ENST00000253339		680	Caa/Gaa	4/7	0.65266163916537	4	FACETS	0.999	0.923	1	0.999	0.923	1	CLONAL	2	TRUE	2	0.683827561873386	4		296	355	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104718	69104719	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0050660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	505	472	0	ENST00000288368.4:c.4565dup	p.Ala1523ArgfsTer109	p.A1523Rfs*109	ENST00000288368	NM_024870.2	1521	ctg/ctGg	37/40	0.683827561873386	4	FACETS	0.986	0.952	1	0.986	0.952	1	CLONAL	3	TRUE	1	0.683827561873386	4		472	841	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0050661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	560	649	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	NA	2	FACETS	0.922	0.897	0.947			1	INDETERMINATE	2	TRUE	NA	0.774296492948515	2		649	784	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	188	438	1	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.774296492948515	2		439	473	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106648	27106648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553153748	NA	P-0050663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	18	516	1	ENST00000324856.7:c.6259G>A	p.Gly2087Arg	p.G2087R	ENST00000324856	NM_006015.4	2087	Gga/Aga	20/20	1	2	FACETS	0.119	0.089	0.156	0.119	0.089	0.156	SUBCLONAL	1	TRUE	1	0.365540025358847	2		517	825	SUCCESS
APC	324	MSKCC	GRCh37	5	112179110	112179110	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	14	243	0	ENST00000257430.4:c.7819T>C	p.Ser2607Pro	p.S2607P	ENST00000257430	NM_000038.5	2607	Tcc/Ccc	16/16	1	2	FACETS	0.298	0.215	0.399	0.298	0.215	0.399	SUBCLONAL	1	TRUE	1	0.365540025358847	2		243	257	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106654	27106654	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	TCG	novel	NA	P-0050663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	65	519	0	ENST00000324856.7:c.6265delinsTCG	p.Leu2089SerfsTer47	p.L2089Sfs*47	ENST00000324856	NM_006015.4	2089	Cta/TCGta	20/20	1	2	FACETS	0.43	0.372	0.493	0.43	0.372	0.493	SUBCLONAL	1	TRUE	1	0.365540025358847	2		519	827	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0050664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	199	600	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.498163898276981	1	FACETS	0.963	0.897	1	0.963	0.897	1	CLONAL	1	TRUE	0	0.498163898276981	1		600	623	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0050664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	95	278	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.232815686600924	0	FACETS	0.539	0.484	0.597			1	INDETERMINATE	1	TRUE	0	0.498163898276981	0		278	355	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0050664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	48	252	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.232815686600924	0	FACETS	0.272	0.23	0.317			1	INDETERMINATE	1	TRUE	0	0.498163898276981	0		252	356	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664546	29664546	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	88	446	0	ENST00000356175.3:c.6528del	p.Phe2176LeufsTer3	p.F2176Lfs*3	ENST00000356175	NM_000267.3	2175	acT/ac	42/57	0.356633033994681	1	FACETS	0.483	0.429	0.541	0.483	0.429	0.541	SUBCLONAL	1	TRUE	0	0.498163898276981	1		446	549	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222221	5222221	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	62	436	1	ENST00000357368.4:c.3114G>T	p.Lys1038Asn	p.K1038N	ENST00000357368	NM_002850.3	1038	aaG/aaT	19/38	0.356633033994681	1	FACETS	0.47	0.407	0.537	0.47	0.407	0.537	SUBCLONAL	1	TRUE	0	0.498163898276981	1		437	398	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639851	93639851	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0050664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	12	206	0	ENST00000375746.1:c.1182-2A>G		p.X394_splice	ENST00000375746	NM_001174167.1	394			1	2	FACETS	0.202	0.142	0.277	0.202	0.142	0.277	SUBCLONAL	1	TRUE	1	0.498163898276981	2		206	238	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412087	63412087	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	163	341	0	ENST00000330258.3:c.1080del	p.Cys361AlafsTer3	p.C361Afs*3	ENST00000330258	NM_152424.3	360	tcC/tc	2/2	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.498163898276981	1		341	353	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845858	72845859	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0050665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	36	540	0	ENST00000268489.5:c.3608_3609del	p.Glu1203ValfsTer12	p.E1203Vfs*12	ENST00000268489	NM_006885.3	1203	gAG/g	6/10	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		540	539	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195138	123195138	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	17	478	0	ENST00000218089.9:c.1481A>T	p.Asp494Val	p.D494V	ENST00000218089	NM_001042749.1	494	gAc/gTc	16/35	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		478	306	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	185	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.399110636216769	4	FACETS	0.92	0.855	0.987	0.92	0.855	0.987	CLONAL	2	TRUE	2	0.552236119779741	4		436	565	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508824	106508824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226994105	NA	P-0050666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	389	615	1	ENST00000359195.3:c.818G>A	p.Arg273His	p.R273H	ENST00000359195	NM_002649.2	273	cGc/cAc	2/11	0.552236119779741	6	FACETS	0.95	0.91	0.991	0.95	0.91	0.991	CLONAL	4	TRUE	2	0.552236119779741	6		616	780	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577146	7577156	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	TAGATTACCAC	TAGATTACCAC	-	novel	NA	P-0050666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	227	577	0	ENST00000269305.4:c.783-1_792del		p.X261_splice	ENST00000269305	NM_001126112.2	261		8/11	NA	2	FACETS	0.913	0.863	0.964			1	INDETERMINATE	2	TRUE	NA	0.552236119779741	2		577	450	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141568614	141568614	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs755874332	NA	P-0050667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	217	614	0	ENST00000220592.5:c.848A>G	p.Asn283Ser	p.N283S	ENST00000220592	NM_012154.3	283	aAt/aGt	7/19	0.352534308345666	3	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	1	0.352534308345666	3		614	719	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166285	7166285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555743340	NA	P-0050667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	123	594	0	ENST00000302850.5:c.1741C>T	p.Arg581Trp	p.R581W	ENST00000302850	NM_000208.2	581	Cgg/Tgg	8/22	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.352534308345666	2		594	568	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0050668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	107	369	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	0.211948933636109	6	FACETS	0.853	0.764	0.947	0.426	0.382	0.474	CLONAL	2	TRUE	2	0.211948933636109	6		369	843	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483966	88483966	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	62	503	0	ENST00000360948.2:c.1604G>T	p.Arg535Met	p.R535M	ENST00000360948	NM_001012338.2	535	aGg/aTg	14/19	0.146517211603676	3	FACETS	0.95	0.82	1	0.475	0.41	0.546	CLONAL	1	TRUE	1	0.211948933636109	3		503	681	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602757	10602757	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	256	759	0	ENST00000171111.5:c.821A>C	p.His274Pro	p.H274P	ENST00000171111	NM_203500.1	274	cAc/cCc	3/6	0.211948933636109	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	0	0.211948933636109	2		759	1201	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796925	45796925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779701238	NA	P-0050668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	82	534	0	ENST00000450313.1:c.1405G>A	p.Val469Ile	p.V469I	ENST00000450313	NM_012222.2	469	Gta/Ata	14/16	0.157990013449881	2	FACETS	0.875	0.77	0.988	0.438	0.385	0.494	CLONAL	1	TRUE	0	0.211948933636109	2		534	884	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106717	27106717	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	150	558	0	ENST00000324856.7:c.6328G>T	p.Ala2110Ser	p.A2110S	ENST00000324856	NM_006015.4	2110	Gcc/Tcc	20/20	0.157990013449881	2	FACETS	0.856	0.783	0.932	0.856	0.783	0.932	CLONAL	2	TRUE	0	0.211948933636109	2		558	827	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670531	134670531	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs62270337	NA	P-0050668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	77	576	0	ENST00000398015.3:c.442C>A	p.Gln148Lys	p.Q148K	ENST00000398015	NM_004441.4	148	Cag/Aag	3/16	0.167714246335445	2	FACETS	0.749	0.656	0.85	0.375	0.328	0.425	SUBCLONAL	1	TRUE	0	0.211948933636109	2		576	970	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47709929	47709930	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	T	novel	NA	P-0050668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	42	254	0	ENST00000233146.2:c.2646_2647delinsT	p.Lys882AsnfsTer10	p.K882Nfs*10	ENST00000233146	NM_000251.2	882	aaAAtt/aaTtt	16/16	0.211948933636109	5	FACETS	0.976	0.815	1	0.325	0.271	0.386	CLONAL	1	TRUE	2	0.211948933636109	5		254	535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0050669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	417	807	1	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.637791054073477	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.637791054073477	2		808	601	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309024	137309024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1348109062	NA	P-0050669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	189	721	0	ENST00000481739.1:c.631C>T	p.Arg211Cys	p.R211C	ENST00000481739	NM_002957.4	211	Cgt/Tgt	5/10	0.637791054073477	3	FACETS	1	0.96	1	0.526	0.487	0.566	CLONAL	1	TRUE	1	0.637791054073477	3		721	743	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344633	70344633	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	163	584	0	ENST00000374080.3:c.1994C>A	p.Ser665Tyr	p.S665Y	ENST00000374080		665	tCt/tAt	14/45	0.637791054073477	3	FACETS	1	0.921	1	0.5	0.46	0.541	CLONAL	1	TRUE	1	0.637791054073477	3		584	674	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234455	41234456	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0050669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	285	520	0	ENST00000357654.3:c.4322dup	p.Asp1441GlufsTer21	p.D1441Efs*21	ENST00000357654	NM_007294.3	1441	gac/gaAc	12/23	0.637791054073477	2	FACETS	0.974	0.931	1	0.974	0.931	1	CLONAL	2	TRUE	0	0.637791054073477	2		520	459	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27192417	27192485	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	AACAACAACCCCGGCTTAAGGAATGTAAGAGAATGCCAACTTAAGTTTCCTGGACGTTTTCTCTTCTCA	AACAACAACCCCGGCTTAAGGAATGTAAGAGAATGCCAACTTAAGTTTCCTGGACGTTTTCTCTTCTCA	-	novel	NA	P-0050669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	103	192	0	ENST00000380036.4:c.1490-70_1490-2del		p.X497_splice	ENST00000380036	NM_000459.3	497			1	2	FACETS	0.832	0.766	0.899	1	0.988	1	CLONAL	2	TRUE	1	0.637791054073477	2		192	194	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274911	41274911	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	153	402	2	ENST00000349496.5:c.1161T>G	p.Asn387Lys	p.N387K	ENST00000349496	NM_001904.3	387	aaT/aaG	8/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.490613146573314	2		404	512	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244127	153244127	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	144	477	0	ENST00000281708.4:c.2030C>G	p.Ala677Gly	p.A677G	ENST00000281708	NM_033632.3	677	gCc/gGc	12/12	1	2	FACETS	0.845	0.772	0.92	0.845	0.772	0.92	CLONAL	1	TRUE	1	0.490613146573314	2		477	695	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397793	116397793	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1318989606	NA	P-0050670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	106	440	3	ENST00000397752.3:c.2067C>A	p.His689Gln	p.H689Q	ENST00000397752	NM_000245.2	689	caC/caA	8/21	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.490613146573314	2		443	425	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0050671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	138	390	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.212231874015921	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	2	0.31	4		390	513	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352058	89352058	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs1567583835	NA	P-0050671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	172	620	0	ENST00000301030.4:c.893-1G>C		p.X298_splice	ENST00000301030	NM_001256183.1	298			0.212231874015921	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	2	0.31	4		620	676	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129169	64129169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746466314	NA	P-0050671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	90	839	0	ENST00000334205.4:c.707C>T	p.Ser236Leu	p.S236L	ENST00000334205	NM_003942.2	236	tCg/tTg	7/17	0.212231874015921	4	FACETS	0.962	0.853	1	0.481	0.426	0.539	CLONAL	1	TRUE	2	0.31	4		839	791	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050349	176050349	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	248	506	0	ENST00000367669.3:c.1216C>T	p.Arg406Ter	p.R406*	ENST00000367669	NM_022457.5	406	Cga/Tga	11/20	0.300360158431161	7	FACETS	0.906	0.853	0.959	0.906	0.853	0.959	CLONAL	5	TRUE	2	0.31	7		506	627	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609395	39609395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	103	312	0	ENST00000262039.4:c.1697G>A	p.Arg566His	p.R566H	ENST00000262039	NM_002647.2	566	cGt/cAt	15/25	0.300360158431161	2	FACETS	0.963	0.871	1	0.963	0.871	1	CLONAL	2	TRUE	0	0.31	2		312	345	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741465	17741465	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	88	626	0	ENST00000250003.3:c.136C>A	p.Leu46Met	p.L46M	ENST00000250003	NM_002478.4	46	Ctg/Atg	1/3	0.212231874015921	4	FACETS	1	0.931	1	0.535	0.474	0.6	CLONAL	1	TRUE	2	0.31	4		626	695	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005475	42005475	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	207	668	0	ENST00000219905.7:c.3211T>A	p.Cys1071Ser	p.C1071S	ENST00000219905	NM_001164273.1	1071	Tgc/Agc	9/24	0.212231874015921	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.31	4		668	730	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955553	55955553	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	66	576	0	ENST00000263923.4:c.3392C>G	p.Thr1131Ser	p.T1131S	ENST00000263923	NM_002253.2	1131	aCt/aGt	25/30	0.300360158431161	3	FACETS	0.94	0.817	1	0.47	0.408	0.537	CLONAL	1	TRUE	1	0.31	3		576	523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0050672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	55	732	0	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	1	2	FACETS	0.568	0.484	0.66	0.568	0.484	0.66	SUBCLONAL	1	TRUE	1	0.21	2		732	922	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604750	48604750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	59	347	0	ENST00000342988.3:c.1572G>T	p.Trp524Cys	p.W524C	ENST00000342988	NM_005359.5	524	tgG/tgT	12/12	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.21	2		347	467	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0050673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	107	479	1	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.274903684877439	2		480	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	90	754	0	ENST00000269305.4:c.166G>T	p.Glu56Ter	p.E56*	ENST00000269305	NM_001126112.2	56	Gaa/Taa	4/11	0.252309464512267	1	FACETS	0.873	0.775	0.977	0.873	0.775	0.977	CLONAL	1	TRUE	0	0.274903684877439	1		754	647	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968235	2968235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1188731718	NA	P-0050673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	115	762	0	ENST00000396946.4:c.1751G>A	p.Arg584His	p.R584H	ENST00000396946	NM_032415.4	584	cGc/cAc	13/25	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.274903684877439	2		762	796	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	210	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.295521128413112	5	FACETS	1	0.981	1	1	0.981	1	CLONAL	4	TRUE	1	0.28	5		334	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0050674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	143	630	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.262533127745553	2	FACETS	0.964	0.884	1	0.964	0.884	1	CLONAL	2	TRUE	0	0.28	2		630	530	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905465	11905465	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1036410712	NA	P-0050674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	43	376	1	ENST00000396373.4:c.115C>T	p.Arg39Ter	p.R39*	ENST00000396373	NM_001987.4	39	Cga/Tga	2/8	0.295521128413112	6	FACETS	0.92	0.769	1	0.184	0.153	0.218	CLONAL	1	TRUE	1	0.28	6		377	521	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0050675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	266	355	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.386870640176565	4	FACETS	1	0.989	1	0.813	0.765	0.862	CLONAL	2	TRUE	1	0.386870640176565	4		355	782	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138642	55138642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143344944	NA	P-0050675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	47	479	0	ENST00000257290.5:c.1319C>T	p.Thr440Met	p.T440M	ENST00000257290	NM_006206.4	440	aCg/aTg	9/23	0.361905800389253	4	FACETS	0.387	0.325	0.455	0.193	0.162	0.228	SUBCLONAL	1	TRUE	2	0.386870640176565	4		479	871	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575152	48575152	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	147	295	0	ENST00000342988.3:c.346C>T	p.Gln116Ter	p.Q116*	ENST00000342988	NM_005359.5	116	Cag/Tag	3/12	0.386870640176565	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.386870640176565	2		295	368	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602323	10602323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	451	768	0	ENST00000171111.5:c.1255G>T	p.Gly419Trp	p.G419W	ENST00000171111	NM_203500.1	419	Ggg/Tgg	3/6	0.386870640176565	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.386870640176565	2		768	989	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387093	31387093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143300013	NA	P-0050675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	307	587	1	ENST00000328111.2:c.1718G>A	p.Arg573Gln	p.R573Q	ENST00000328111	NM_006892.3	573	cGg/cAg	16/23	0.35146811583607	4	FACETS	0.926	0.873	0.981			1	CLONAL	2	TRUE	NA	0.386870640176565	4		588	1188	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617655	39617655	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0050675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	119	258	0	ENST00000262039.4:c.1840-1G>T		p.X614_splice	ENST00000262039	NM_002647.2	614			0.33157272241059	3	FACETS	0.904	0.823	0.988			1	CLONAL	2	TRUE	NA	0.386870640176565	3		258	406	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087533	27087533	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	182	700	0	ENST00000324856.7:c.2109del	p.Ala704ProfsTer38	p.A704Pfs*38	ENST00000324856	NM_006015.4	703	Ccc/cc	5/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.386870640176565	2		700	921	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391634	139391634	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs757589247	NA	P-0050675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	419	865	0	ENST00000277541.6:c.6557G>T	p.Gly2186Val	p.G2186V	ENST00000277541	NM_017617.3	2186	gGc/gTc	34/34	0.321713910730552	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.386870640176565	4		865	1381	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318734	163318734	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0050675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	86	337	0	ENST00000271452.3:c.1125-1G>T		p.X375_splice	ENST00000271452	NM_145697.2	375			0.386870640176565	3	FACETS	1	0.944	1	0.552	0.49	0.617	CLONAL	1	TRUE	1	0.386870640176565	3		337	481	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588252	69588252	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	118	375	0	ENST00000168712.1:c.446C>A	p.Pro149His	p.P149H	ENST00000168712	NM_002007.2	149	cCc/cAc	3/3	0.386870640176565	4	FACETS	1	0.976	1	0.629	0.568	0.692	CLONAL	1	TRUE	2	0.386870640176565	4		375	673	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442527	49442527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1167060436	NA	P-0050675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	331	416	0	ENST00000301067.7:c.4046G>A	p.Ser1349Asn	p.S1349N	ENST00000301067	NM_003482.3	1349	aGt/aAt	13/54	0.386870640176565	3	FACETS	0.991	0.944	1	0.991	0.944	1	CLONAL	3	TRUE	0	0.386870640176565	3		416	687	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606177	81606177	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	208	419	0	ENST00000298171.2:c.847T>A	p.Cys283Ser	p.C283S	ENST00000298171	NM_000369.2	283	Tgc/Agc	9/10	0.386870640176565	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.386870640176565	2		419	515	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028724	42028724	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	269	511	0	ENST00000219905.7:c.4262T>G	p.Leu1421Trp	p.L1421W	ENST00000219905	NM_001164273.1	1421	tTg/tGg	13/24	0.35146811583607	4	FACETS	1	0.95	1			1	CLONAL	2	TRUE	NA	0.386870640176565	4		511	952	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478182	99478182	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	295	374	0	ENST00000268035.6:c.3086G>T	p.Arg1029Ile	p.R1029I	ENST00000268035	NM_000875.3	1029	aGa/aTa	16/21	0.386870640176565	5	FACETS	1	0.948	1	1	0.948	1	CLONAL	3	TRUE	2	0.386870640176565	5		374	801	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993897	72993897	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	192	603	0	ENST00000268489.5:c.148T>G	p.Leu50Val	p.L50V	ENST00000268489	NM_006885.3	50	Ttg/Gtg	2/10	0.344351052138143	3	FACETS	0.791	0.733	0.85	0.527	0.489	0.567	SUBCLONAL	2	TRUE	0	0.386870640176565	3		603	749	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579394	7579394	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	397	761	0	ENST00000269305.4:c.293C>G	p.Pro98Arg	p.P98R	ENST00000269305	NM_001126112.2	98	cCt/cGt	4/11	0.376083988995648	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.386870640176565	2		761	939	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589887	212589887	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	225	457	0	ENST00000342788.4:c.655G>T	p.Gly219Cys	p.G219C	ENST00000342788	NM_005235.2	219	Ggc/Tgc	6/28	0.386870640176565	3	FACETS	0.943	0.882	1	0.943	0.882	1	CLONAL	2	TRUE	1	0.386870640176565	3		457	736	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958821	55958821	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	134	497	0	ENST00000263923.4:c.3032A>T	p.Gln1011Leu	p.Q1011L	ENST00000263923	NM_002253.2	1011	cAa/cTa	22/30	0.284063131066796	3	FACETS	1	0.969	1	0.574	0.522	0.629	CLONAL	1	TRUE	1	0.386870640176565	3		497	720	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873723	35873723	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0050675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	83	304	0	ENST00000303115.3:c.679A>T	p.Arg227Ter	p.R227*	ENST00000303115	NM_002185.3	227	Aga/Tga	5/8	0.284063131066796	3	FACETS	1	0.939	1	0.547	0.484	0.614	CLONAL	1	TRUE	1	0.386870640176565	3		304	468	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169009	32169009	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs765918039	NA	P-0050675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	378	831	0	ENST00000375023.3:c.4024T>C	p.Tyr1342His	p.Y1342H	ENST00000375023	NM_004557.3	1342	Tat/Cat	22/30	0.361905800389253	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	2	0.386870640176565	4		831	1343	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188920	32188920	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	367	763	0	ENST00000375023.3:c.634C>G	p.His212Asp	p.H212D	ENST00000375023	NM_004557.3	212	Cat/Gat	4/30	0.361905800389253	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.386870640176565	4		763	1237	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233130	55233130	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	245	460	0	ENST00000275493.2:c.1880G>T	p.Gly627Val	p.G627V	ENST00000275493	NM_005228.3	627	gGa/gTa	15/28	0.361905800389253	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.386870640176565	4		460	841	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250482	110250482	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	288	624	0	ENST00000374672.4:c.193C>A	p.Leu65Met	p.L65M	ENST00000374672	NM_004235.4	65	Ctg/Atg	3/5	0.321713910730552	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.386870640176565	4		624	986	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040734	47040734	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs868980666	NA	P-0050675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	380	667	1	ENST00000377604.3:c.1369C>A	p.His457Asn	p.H457N	ENST00000377604	NM_001204468.1	457	Cat/Aat	13/24	0.321713910730552	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.386870640176565	4		668	1241	SUCCESS
AR	367	MSKCC	GRCh37	X	66765680	66765680	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	390	856	0	ENST00000374690.3:c.693del	p.Ile232PhefsTer26	p.I232Ffs*26	ENST00000374690	NM_000044.3	231	aCc/ac	1/8	0.321713910730552	4	FACETS	0.945	0.897	0.995	0.945	0.897	0.995	CLONAL	2	TRUE	2	0.386870640176565	4		856	1479	SUCCESS
AR	367	MSKCC	GRCh37	X	66765784	66765784	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1233351946	NA	P-0050675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	418	869	0	ENST00000374690.3:c.796G>T	p.Asp266Tyr	p.D266Y	ENST00000374690	NM_000044.3	266	Gat/Tat	1/8	0.321713910730552	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.386870640176565	4		869	1468	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185199	123185199	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	191	433	0	ENST00000218089.9:c.1151A>T	p.Tyr384Phe	p.Y384F	ENST00000218089	NM_001042749.1	384	tAt/tTt	13/35	0.321713910730552	4	FACETS	0.848	0.786	0.913	0.848	0.786	0.913	CLONAL	2	TRUE	2	0.386870640176565	4		433	807	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0050680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	74	978	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	1	2	FACETS	0.524	0.457	0.596	0.524	0.457	0.596	SUBCLONAL	1	TRUE	1	0.291416463919245	2		978	969	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0050680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	34	519	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.0462119114791593	3	FACETS	0.438	0.356	0.529	0.219	0.178	0.265	INDETERMINATE	1	TRUE	1	0.291416463919245	3		519	611	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0050701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	51	366	0				ENST00000310581	NM_198253.2	-/1132			0.210790507316958	5	FACETS	1	0.881	1			1	INDETERMINATE	2	TRUE	NA	0.693031797121201	5		366	148	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16203058	16203058	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	101	456	0	ENST00000375759.3:c.766C>G	p.Gln256Glu	p.Q256E	ENST00000375759	NM_015001.2	256	Cag/Gag	3/15	0.613805282775134	5	FACETS	0.842	0.76	0.927			1	CLONAL	2	TRUE	NA	0.693031797121201	5		456	353	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982968	201982969	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0050701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	36	711	0	ENST00000359651.3:c.820dup	p.His274ProfsTer27	p.H274Pfs*27	ENST00000359651		273	acc/aCcc	7/8	0.69918501859631	2	FACETS	0.191	0.156	0.229	0.095	0.078	0.115	SUBCLONAL	1	TRUE	0	0.693031797121201	2		711	545	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924729	94924729	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	92	600	0	ENST00000536441.1:c.181T>A	p.Phe61Ile	p.F61I	ENST00000536441	NM_144665.3	61	Ttt/Att	3/10	1	2	FACETS	0.941	0.848	1	0.941	0.848	1	CLONAL	1	TRUE	1	0.693031797121201	2		600	282	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178622	108178622	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0050701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	52	197	0	ENST00000278616.4:c.5675-2A>G		p.X1892_splice	ENST00000278616	NM_000051.3	1892			1	2	FACETS	0.981	0.853	1	0.981	0.853	1	CLONAL	1	TRUE	1	0.693031797121201	2		197	153	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495438	56495438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	127	599	0	ENST00000267101.3:c.3628C>T	p.His1210Tyr	p.H1210Y	ENST00000267101	NM_001982.3	1210	Cat/Tat	28/28	0.589440296378396	4	FACETS	1	0.983	1	0.667	0.608	0.728	CLONAL	1	TRUE	2	0.693031797121201	4		599	465	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118764	115118764	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1375	354	505	0	ENST00000257566.3:c.577A>T	p.Thr193Ser	p.T193S	ENST00000257566	NM_016569.3	193	Act/Tct	2/8	0.693031797121201	18	FACETS	0.967	0.913	1			1	CLONAL	4	TRUE	NA	0.693031797121201	18		505	1729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0050701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	148	520	0	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.64773430630003	3	FACETS	0.978	0.929	1	0.978	0.929	1	CLONAL	3	TRUE	0	0.693031797121201	3		520	196	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021828	71021828	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0050701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	23	189	0	ENST00000318789.4:c.1531-1G>A		p.X511_splice	ENST00000318789	NM_032682.5	511			NA	2	FACETS	0.657	0.522	0.806			1	INDETERMINATE	1	TRUE	NA	0.693031797121201	2		189	101	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170016888	170016888	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	56	414	0	ENST00000295797.4:c.1693C>G	p.Pro565Ala	p.P565A	ENST00000295797	NM_002740.5	565	Cca/Gca	17/18	0.693031797121201	6	FACETS	0.945	0.812	1			1	CLONAL	1	TRUE	NA	0.693031797121201	6		414	408	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803630	1803631	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACGTGGAGTTCCACTGCAAGGTGT	novel	NA	P-0050701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	29	773	0	ENST00000260795.2:c.811_834dup	p.Val271_Tyr278dup	p.V271_Y278dup	ENST00000260795		271	gac/gACGTGGAGTTCCACTGCAAGGTGTac	6/17	NA	2	FACETS	0.148	0.118	0.183			1	INDETERMINATE	1	TRUE	NA	0.693031797121201	2		773	564	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808029	1808029	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1490564667	NA	P-0050701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	279	755	0	ENST00000260795.2:c.2005C>G	p.Arg669Gly	p.R669G	ENST00000260795		669	Cga/Gga	14/17	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.693031797121201	2		755	560	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808870	1808870	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs560280646	NA	P-0050701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	29	768	0	ENST00000260795.2:c.2302G>T	p.Glu768Ter	p.E768*	ENST00000260795		768	Gag/Tag	17/17	NA	2	FACETS	0.16	0.128	0.197			1	INDETERMINATE	1	TRUE	NA	0.693031797121201	2		768	523	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694712	176694712	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	32	400	0	ENST00000439151.2:c.5296C>T	p.Arg1766Ter	p.R1766*	ENST00000439151	NM_022455.4	1766	Cga/Tga	15/23	1	2	FACETS	0.604	0.497	0.721	0.604	0.497	0.721	SUBCLONAL	1	TRUE	1	0.693031797121201	2		400	153	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696701	176696701	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	12	373	0	ENST00000439151.2:c.5402C>G	p.Ser1801Cys	p.S1801C	ENST00000439151	NM_022455.4	1801	tCt/tGt	16/23	1	2	FACETS	0.157	0.11	0.215	0.157	0.11	0.215	SUBCLONAL	1	TRUE	1	0.693031797121201	2		373	220	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708990	117708990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	109	464	0	ENST00000368508.3:c.1967G>A	p.Arg656Lys	p.R656K	ENST00000368508	NM_002944.2	656	aGg/aAg	13/43	0.69918501859631	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.693031797121201	1		464	200	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398629	116398629	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	69	428	0	ENST00000397752.3:c.2219A>G	p.Glu740Gly	p.E740G	ENST00000397752	NM_000245.2	740	gAa/gGa	9/21	0.693031797121201	6	FACETS	1	0.968	1			1	CLONAL	1	TRUE	NA	0.693031797121201	6		428	351	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44733180	44733180	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	278	295	0	ENST00000377967.4:c.174del	p.Phe59SerfsTer2	p.F59Sfs*2	ENST00000377967	NM_021140.2	58	Ggg/gg	2/29	0.595327387525086	2	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.693031797121201	2		295	364	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937815	76937815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	17	291	0	ENST00000373344.5:c.2933C>T	p.Ser978Phe	p.S978F	ENST00000373344	NM_000489.3	978	tCt/tTt	9/35	0.595327387525086	2	FACETS	0.319	0.239	0.412			1	SUBCLONAL	1	TRUE	NA	0.693031797121201	2		291	154	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	87	734	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.237419701577378	5	FACETS	0.77	0.682	0.864	0.514	0.455	0.576	SUBCLONAL	2	FALSE	2	0.237419701577378	5		735	645	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	53	390	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.237419701577378	5	FACETS	1	0.931	1	0.387	0.33	0.449	CLONAL	1	FALSE	2	0.237419701577378	5		390	522	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043904	180043904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56082504	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	64	518	0	ENST00000261937.6:c.3092G>A	p.Arg1031Gln	p.R1031Q	ENST00000261937	NM_182925.4	1031	cGa/cAa	22/30	0.172223363206345	3	FACETS	1	0.934	1	0.564	0.488	0.645	CLONAL	1	FALSE	1	0.237419701577378	3		518	535	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669553	88669553	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs200206241	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	121	379	0	ENST00000360948.2:c.1345C>G	p.Leu449Val	p.L449V	ENST00000360948	NM_001012338.2	449	Ctc/Gtc	12/19	0.237419701577378	5	FACETS	1	0.975	1	0.814	0.738	0.894	CLONAL	2	FALSE	2	0.237419701577378	5		379	566	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294275	11294275	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	148	433	0	ENST00000361445.4:c.2256G>C	p.Gln752His	p.Q752H	ENST00000361445	NM_004958.3	752	caG/caC	14/58	0.237419701577378	5	FACETS	0.93	0.853	1	0.93	0.853	1	CLONAL	3	FALSE	2	0.237419701577378	5		433	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780071	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	152	493	0	ENST00000269305.4:c.580C>T	p.Leu194Phe	p.L194F	ENST00000269305	NM_001126112.2	194	Ctt/Ttt	6/11	0.227852347569562	3	FACETS	0.871	0.801	0.944	0.871	0.801	0.944	CLONAL	3	FALSE	0	0.237419701577378	3		493	548	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596014	43596014	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	189	625	0	ENST00000355710.3:c.181G>A	p.Glu61Lys	p.E61K	ENST00000355710	NM_020975.4	61	Gag/Aag	2/20	0.226430619877683	3	FACETS	0.945	0.878	1	0.945	0.878	1	CLONAL	3	FALSE	0	0.237419701577378	3		625	628	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602493	10602493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	204	666	0	ENST00000171111.5:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000171111	NM_203500.1	362	cGg/cAg	3/6	0.237419701577378	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	FALSE	0	0.237419701577378	2		666	719	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456431	89456431	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs777508142	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	43	244	0	ENST00000336596.2:c.1607C>G	p.Ser536Cys	p.S536C	ENST00000336596	NM_005233.5	536	tCt/tGt	8/17	0.237419701577378	5	FACETS	0.99	0.829	1	0.33	0.276	0.39	CLONAL	1	FALSE	2	0.237419701577378	5		244	496	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989174	41989174	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	54	421	0	ENST00000219905.7:c.1966G>C	p.Asp656His	p.D656H	ENST00000219905	NM_001164273.1	656	Gat/Cat	3/24	0.237419701577378	5	FACETS	0.906	0.773	1	0.302	0.257	0.351	CLONAL	1	FALSE	2	0.237419701577378	5		421	681	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32969038	32969038	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	51	341	0	ENST00000380152.3:c.9469G>C	p.Glu3157Gln	p.E3157Q	ENST00000380152		3157	Gag/Cag	25/27	0.237419701577378	5	FACETS	1	0.93	1	0.389	0.331	0.453	CLONAL	1	FALSE	2	0.237419701577378	5		341	499	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967202	93967202	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	54	360	0	ENST00000369303.4:c.2150G>T	p.Gly717Val	p.G717V	ENST00000369303	NM_004440.3	717	gGa/gTa	12/17	0.237419701577378	5	FACETS	1	0.948	1	0.417	0.356	0.483	CLONAL	1	FALSE	2	0.237419701577378	5		360	493	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11204726	11204726	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	68	331	0	ENST00000361445.4:c.4851G>C	p.Gln1617His	p.Q1617H	ENST00000361445	NM_004958.3	1617	caG/caC	34/58	0.237419701577378	5	FACETS	0.794	0.692	0.904	0.53	0.461	0.603	CLONAL	2	FALSE	2	0.237419701577378	5		331	489	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513233	149513233	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	70	554	0	ENST00000261799.4:c.850G>C	p.Glu284Gln	p.E284Q	ENST00000261799	NM_002609.3	284	Gaa/Caa	6/23	0.172223363206345	3	FACETS	1	0.918	1	0.535	0.467	0.61	CLONAL	1	FALSE	1	0.237419701577378	3		554	616	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324576	31324576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs151341159	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	141	388	0	ENST00000412585.2:c.232C>T	p.Gln78Ter	p.Q78*	ENST00000412585	NM_005514.6	78	Cag/Tag	2/8	0.222301739856646	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	FALSE	0	0.237419701577378	3		388	403	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228414	228414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	78	273	0	ENST00000264932.6:c.736C>T	p.Arg246Cys	p.R246C	ENST00000264932	NM_004168.2	246	Cgc/Tgc	6/15	0.147863772526126	4	FACETS	0.818	0.721	0.922	0.545	0.48	0.615	CLONAL	2	FALSE	1	0.237419701577378	4		273	497	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148507464	148507464	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	137	368	0	ENST00000320356.2:c.1990G>C	p.Asp664His	p.D664H	ENST00000320356	NM_004456.4	664	Gat/Cat	17/20	0.237419701577378	5	FACETS	0.837	0.764	0.914	0.837	0.764	0.914	CLONAL	3	FALSE	2	0.237419701577378	5		368	623	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660441	227660441	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373248004	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	151	559	0	ENST00000305123.5:c.3014C>T	p.Ser1005Leu	p.S1005L	ENST00000305123	NM_005544.2	1005	tCg/tTg	1/2	0.237419701577378	5	FACETS	0.91	0.835	0.988	0.91	0.835	0.988	CLONAL	3	FALSE	2	0.237419701577378	5		559	632	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981767	201981767	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	164	546	0	ENST00000359651.3:c.479-1G>C		p.X160_splice	ENST00000359651		160			0.237419701577378	6	FACETS	0.974	0.897	1	0.974	0.897	1	CLONAL	3	FALSE	3	0.237419701577378	6		546	697	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858279	27858279	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	169	619	0	ENST00000359303.2:c.292G>T	p.Glu98Ter	p.E98*	ENST00000359303	NM_003535.2	98	Gag/Tag	1/1	0.222301739856646	3	FACETS	1	0.971	1	0.738	0.68	0.798	CLONAL	2	FALSE	0	0.237419701577378	3		619	719	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47079200	47079200	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	130	503	0	ENST00000409792.3:c.7306G>C	p.Glu2436Gln	p.E2436Q	ENST00000409792	NM_014159.6	2436	Gag/Cag	18/21	0.237419701577378	5	FACETS	1	0.956	1	0.725	0.659	0.794	CLONAL	2	FALSE	2	0.237419701577378	5		503	683	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926910	112926910	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	14	403	1	ENST00000351677.2:c.1530G>T	p.Gln510His	p.Q510H	ENST00000351677	NM_002834.3	510	caG/caT	13/16	0.237419701577378	6	FACETS	0.296	0.213	0.398	0.074	0.053	0.1	SUBCLONAL	1	FALSE	2	0.237419701577378	6		404	587	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282391	115282391	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	143	428	0	ENST00000438362.2:c.259C>T	p.Gln87Ter	p.Q87*	ENST00000438362	NM_001242891.1	87	Cag/Tag	3/20	0.227852347569562	3	FACETS	1	0.979	1	0.812	0.744	0.883	CLONAL	2	FALSE	0	0.237419701577378	3		428	553	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030774	48030774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752164796	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	108	276	0	ENST00000234420.5:c.3388G>A	p.Val1130Met	p.V1130M	ENST00000234420	NM_000179.2	1130	Gtg/Atg	5/10	0.237419701577378	5	FACETS	0.972	0.879	1	0.972	0.879	1	CLONAL	3	FALSE	2	0.237419701577378	5		276	423	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255646	16255646	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	55	417	0	ENST00000375759.3:c.2911G>C	p.Asp971His	p.D971H	ENST00000375759	NM_015001.2	971	Gat/Cat	11/15	0.237419701577378	5	FACETS	1	0.956	1	0.44	0.377	0.509	CLONAL	1	FALSE	2	0.237419701577378	5		417	476	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598203	28598203	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	110	577	0	ENST00000253063.3:c.175G>A	p.Glu59Lys	p.E59K	ENST00000253063	NM_031459.4	59	Gag/Aag	3/10	0.237419701577378	5	FACETS	0.868	0.78	0.961	0.579	0.52	0.641	CLONAL	2	FALSE	2	0.237419701577378	5		577	724	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282490	115282490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	109	358	0	ENST00000438362.2:c.160C>T	p.Leu54Phe	p.L54F	ENST00000438362	NM_001242891.1	54	Ctc/Ttc	3/20	0.227852347569562	3	FACETS	1	0.974	1	0.821	0.743	0.903	CLONAL	2	FALSE	0	0.237419701577378	3		358	417	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506199	120506199	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	91	233	0	ENST00000256646.2:c.1913C>G	p.Ser638Ter	p.S638*	ENST00000256646	NM_024408.3	638	tCa/tGa	11/34	0.227852347569562	3	FACETS	0.919	0.825	1	0.919	0.825	1	CLONAL	3	FALSE	0	0.237419701577378	3		233	311	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740177	162740177	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	152	426	0	ENST00000367921.3:c.1379C>T	p.Ser460Leu	p.S460L	ENST00000367921	NM_006182.2	460	tCa/tTa	12/18	0.237419701577378	6	FACETS	0.964	0.884	1	0.964	0.884	1	CLONAL	3	FALSE	3	0.237419701577378	6		426	653	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749914	162749914	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	136	431	0	ENST00000367921.3:c.2446C>T	p.Gln816Ter	p.Q816*	ENST00000367921	NM_006182.2	816	Caa/Taa	18/18	0.237419701577378	6	FACETS	0.876	0.799	0.957	0.876	0.799	0.957	CLONAL	3	FALSE	3	0.237419701577378	6		431	643	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667387	241667387	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	159	401	1	ENST00000366560.3:c.1063G>A	p.Glu355Lys	p.E355K	ENST00000366560	NM_000143.3	355	Gaa/Aaa	7/10	0.237419701577378	6	FACETS	1	0.937	1	1	0.937	1	CLONAL	3	FALSE	3	0.237419701577378	6		402	645	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851932	63851932	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	195	459	0	ENST00000279873.7:c.2710C>G	p.Gln904Glu	p.Q904E	ENST00000279873	NM_032199.2	904	Cag/Gag	10/10	0.226430619877683	3	FACETS	0.93	0.864	0.997	0.93	0.864	0.997	CLONAL	3	FALSE	0	0.237419701577378	3		459	659	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344490	118344490	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs782263390	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	91	231	0	ENST00000534358.1:c.2616G>C	p.Lys872Asn	p.K872N	ENST00000534358	NM_005933.3	872	aaG/aaC	3/36	0.237419701577378	6	FACETS	1	0.906	1	0.507	0.453	0.563	CLONAL	3	FALSE	0	0.237419701577378	6		231	372	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944860	31944860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1288725636	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	69	402	0	ENST00000340398.3:c.241G>A	p.Asp81Asn	p.D81N	ENST00000340398	NM_001013699.2	81	Gac/Aac	1/1	0.237419701577378	6	FACETS	1	0.966	1	0.336	0.292	0.383	CLONAL	1	FALSE	2	0.237419701577378	6		402	638	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428059	49428059	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	101	554	0	ENST00000301067.7:c.10531G>C	p.Glu3511Gln	p.E3511Q	ENST00000301067	NM_003482.3	3511	Gag/Cag	38/54	0.237419701577378	6	FACETS	0.859	0.768	0.956	0.43	0.384	0.478	CLONAL	2	FALSE	2	0.237419701577378	6		554	730	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915216	32915216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786202002	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	68	376	1	ENST00000380152.3:c.6724G>A	p.Asp2242Asn	p.D2242N	ENST00000380152		2242	Gat/Aat	11/27	0.237419701577378	5	FACETS	1	0.961	1	0.427	0.372	0.488	CLONAL	1	FALSE	2	0.237419701577378	5		377	606	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240320	41240320	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	50	388	0	ENST00000379561.5:c.30C>G	p.Ile10Met	p.I10M	ENST00000379561	NM_002015.3	10	atC/atG	1/3	0.237419701577378	5	FACETS	1	0.879	1	0.347	0.294	0.406	CLONAL	1	FALSE	2	0.237419701577378	5		388	548	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436620	110436620	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	118	788	0	ENST00000375856.3:c.1781C>G	p.Ser594Trp	p.S594W	ENST00000375856	NM_003749.2	594	tCg/tGg	1/2	0.237419701577378	5	FACETS	0.872	0.787	0.962	0.581	0.524	0.641	CLONAL	2	FALSE	2	0.237419701577378	5		788	773	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988530	36988530	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	182	539	0	ENST00000354822.5:c.123C>G	p.Phe41Leu	p.F41L	ENST00000354822	NM_001079668.2	41	ttC/ttG	2/3	0.237419701577378	5	FACETS	1	0.984	1	0.831	0.768	0.897	CLONAL	2	FALSE	2	0.237419701577378	5		539	834	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724442	43724442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	194	562	0	ENST00000382044.4:c.3625G>A	p.Glu1209Lys	p.E1209K	ENST00000382044	NM_001141980.1	1209	Gag/Aag	17/28	0.237419701577378	5	FACETS	0.87	0.806	0.936	0.87	0.806	0.936	CLONAL	3	FALSE	2	0.237419701577378	5		562	849	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467116	99467116	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	66	387	0	ENST00000268035.6:c.2497G>C	p.Asp833His	p.D833H	ENST00000268035	NM_000875.3	833	Gac/Cac	12/21	0.237419701577378	5	FACETS	1	0.971	1	0.491	0.427	0.56	CLONAL	1	FALSE	2	0.237419701577378	5		387	512	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658830	3658830	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	137	475	0	ENST00000294008.3:c.136G>C	p.Glu46Gln	p.E46Q	ENST00000294008	NM_032444.2	46	Gag/Cag	2/15	0.227852347569562	3	FACETS	0.842	0.771	0.916	0.842	0.771	0.916	CLONAL	3	FALSE	0	0.237419701577378	3		475	511	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883753	37883753	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	110	684	0	ENST00000269571.5:c.3365C>T	p.Ser1122Phe	p.S1122F	ENST00000269571		1122	tCt/tTt	26/27	0.237419701577378	5	FACETS	0.76	0.682	0.842	0.507	0.455	0.561	SUBCLONAL	2	FALSE	2	0.237419701577378	5		684	827	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453459	40453459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1186642966	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	185	752	0	ENST00000345506.4:c.1156G>A	p.Glu386Lys	p.E386K	ENST00000345506	NM_003152.3	386	Gag/Aag	10/20	0.237419701577378	5	FACETS	0.889	0.823	0.959	0.889	0.823	0.959	CLONAL	3	FALSE	2	0.237419701577378	5		752	792	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448285	56448285	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	169	493	0	ENST00000407977.2:c.362C>G	p.Ser121Ter	p.S121*	ENST00000407977		121	tCa/tGa	3/10	0.237419701577378	6	FACETS	0.852	0.785	0.923	0.852	0.785	0.923	CLONAL	3	FALSE	3	0.237419701577378	6		493	821	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395623	45395623	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1221585986	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	51	292	0	ENST00000262160.6:c.511G>C	p.Glu171Gln	p.E171Q	ENST00000262160	NM_005901.5	171	Gag/Cag	4/11	0.237419701577378	5	FACETS	1	0.929	1	0.388	0.329	0.451	CLONAL	1	FALSE	2	0.237419701577378	5		292	501	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593536	48593536	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555686621	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	80	179	0	ENST00000342988.3:c.1287C>G	p.Ile429Met	p.I429M	ENST00000342988	NM_005359.5	429	atC/atG	10/12	0.237419701577378	5	FACETS	0.97	0.862	1	0.97	0.862	1	CLONAL	3	FALSE	2	0.237419701577378	5		179	314	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953921	17953921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	204	657	1	ENST00000458235.1:c.481G>A	p.Glu161Lys	p.E161K	ENST00000458235	NM_000215.3	161	Gag/Aag	5/24	0.237419701577378	8	FACETS	0.896	0.83	0.964	0.537	0.498	0.579	CLONAL	3	FALSE	3	0.237419701577378	8		658	1095	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213920	36213920	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	206	620	0	ENST00000222270.7:c.2746G>C	p.Glu916Gln	p.E916Q	ENST00000222270	NM_014727.1	916	Gag/Cag	6/37	0.237419701577378	6	FACETS	0.973	0.904	1	0.973	0.904	1	CLONAL	3	FALSE	3	0.237419701577378	6		620	877	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918223	50918223	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	180	609	0	ENST00000440232.2:c.2540C>G	p.Ser847Ter	p.S847*	ENST00000440232	NM_002691.3	847	tCa/tGa	20/27	0.237419701577378	6	FACETS	0.993	0.917	1	0.993	0.917	1	CLONAL	3	FALSE	3	0.237419701577378	6		609	751	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015665	27015665	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	74	462	0	ENST00000335756.4:c.252C>G	p.Phe84Leu	p.F84L	ENST00000335756	NM_001809.3	84	ttC/ttG	3/5	0.237419701577378	5	FACETS	1	0.965	1	0.433	0.379	0.491	CLONAL	1	FALSE	2	0.237419701577378	5		462	651	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116222	209116222	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	57	331	0	ENST00000345146.2:c.54G>C	p.Met18Ile	p.M18I	ENST00000345146	NM_005896.2	18	atG/atC	3/10	0.237419701577378	5	FACETS	1	0.961	1	0.458	0.393	0.528	CLONAL	1	FALSE	2	0.237419701577378	5		331	474	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376122	225376122	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	81	458	0	ENST00000264414.4:c.832G>C	p.Glu278Gln	p.E278Q	ENST00000264414	NM_003590.4	278	Gaa/Caa	6/16	0.237419701577378	5	FACETS	1	0.976	1	0.489	0.431	0.551	CLONAL	1	FALSE	2	0.237419701577378	5		458	631	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376224	225376224	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	72	398	0	ENST00000264414.4:c.730G>C	p.Glu244Gln	p.E244Q	ENST00000264414	NM_003590.4	244	Gaa/Caa	6/16	0.237419701577378	5	FACETS	1	0.973	1	0.49	0.428	0.556	CLONAL	1	FALSE	2	0.237419701577378	5		398	560	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378302	225378302	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	40	280	0	ENST00000264414.4:c.593G>C	p.Arg198Thr	p.R198T	ENST00000264414	NM_003590.4	198	aGa/aCa	5/16	0.237419701577378	5	FACETS	0.907	0.753	1	0.302	0.251	0.36	CLONAL	1	FALSE	2	0.237419701577378	5		280	504	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162054	47162054	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	55	323	0	ENST00000409792.3:c.4072C>G	p.Leu1358Val	p.L1358V	ENST00000409792	NM_014159.6	1358	Cta/Gta	3/21	0.237419701577378	5	FACETS	1	0.96	1	0.459	0.393	0.531	CLONAL	1	FALSE	2	0.237419701577378	5		323	456	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499444	89499444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	146	460	0	ENST00000336596.2:c.2614G>A	p.Glu872Lys	p.E872K	ENST00000336596	NM_005233.5	872	Gag/Aag	15/17	0.237419701577378	5	FACETS	0.917	0.841	0.997	0.917	0.841	0.997	CLONAL	3	FALSE	2	0.237419701577378	5		460	606	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665151	138665151	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	59	452	0	ENST00000330315.3:c.414C>G	p.Phe138Leu	p.F138L	ENST00000330315	NM_023067.3	138	ttC/ttG	1/1	0.237419701577378	5	FACETS	1	0.951	1	0.415	0.357	0.478	CLONAL	1	FALSE	2	0.237419701577378	5		452	541	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665542	138665542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	84	513	0	ENST00000330315.3:c.23C>T	p.Pro8Leu	p.P8L	ENST00000330315	NM_023067.3	8	cCc/cTc	1/1	0.237419701577378	5	FACETS	0.842	0.745	0.945	0.561	0.496	0.63	CLONAL	2	FALSE	2	0.237419701577378	5		513	570	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443289	187443289	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	31	243	0	ENST00000232014.4:c.1837C>T	p.Gln613Ter	p.Q613*	ENST00000232014	NM_001130845.1	613	Cag/Tag	8/10	0.237419701577378	5	FACETS	1	0.812	1	0.334	0.27	0.407	CLONAL	1	FALSE	2	0.237419701577378	5		243	353	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231666	66231666	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	94	332	0	ENST00000273854.3:c.2034G>C	p.Glu678Asp	p.E678D	ENST00000273854	NM_004439.5	678	gaG/gaC	11/18	0.237419701577378	5	FACETS	1	0.971	1	0.832	0.745	0.925	CLONAL	2	FALSE	2	0.237419701577378	5		332	430	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067123	143067123	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	103	341	0	ENST00000262992.4:c.1590G>C	p.Lys530Asn	p.K530N	ENST00000262992	NM_001101669.1	530	aaG/aaC	16/24	0.237419701577378	5	FACETS	1	0.931	1	0.699	0.627	0.775	CLONAL	2	FALSE	2	0.237419701577378	5		341	561	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517907	187517907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	152	448	0	ENST00000441802.2:c.12787G>A	p.Asp4263Asn	p.D4263N	ENST00000441802	NM_005245.3	4263	Gac/Aac	25/27	0.237419701577378	5	FACETS	0.974	0.895	1	0.974	0.895	1	CLONAL	3	FALSE	2	0.237419701577378	5		448	594	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628008	187628008	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs937758046	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	136	451	0	ENST00000441802.2:c.2974G>C	p.Glu992Gln	p.E992Q	ENST00000441802	NM_005245.3	992	Gag/Cag	2/27	0.237419701577378	5	FACETS	0.904	0.825	0.986	0.904	0.825	0.986	CLONAL	3	FALSE	2	0.237419701577378	5		451	573	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629169	187629169	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	79	484	0	ENST00000441802.2:c.1813C>G	p.Gln605Glu	p.Q605E	ENST00000441802	NM_005245.3	605	Cag/Gag	2/27	0.237419701577378	5	FACETS	0.825	0.727	0.93	0.55	0.484	0.62	CLONAL	2	FALSE	2	0.237419701577378	5		484	547	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750794	57750794	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	124	351	1	ENST00000274289.3:c.1810C>T	p.Gln604Ter	p.Q604*	ENST00000274289	NM_006622.3	604	Cag/Tag	13/14	0.237419701577378	5	FACETS	0.84	0.763	0.921	0.84	0.763	0.921	CLONAL	3	FALSE	2	0.237419701577378	5		352	562	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674274	86674274	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	131	353	0	ENST00000274376.6:c.2406G>A	p.Met802Ile	p.M802I	ENST00000274376	NM_002890.2	802	atG/atA	18/25	0.237419701577378	5	FACETS	0.866	0.789	0.946	0.866	0.789	0.946	CLONAL	3	FALSE	2	0.237419701577378	5		353	576	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515391	149515391	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	143	542	0	ENST00000261799.4:c.91C>G	p.Gln31Glu	p.Q31E	ENST00000261799	NM_002609.3	31	Cag/Gag	3/23	0.172223363206345	3	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	FALSE	1	0.237419701577378	3		542	646	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053198	180053198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	95	601	1	ENST00000261937.6:c.1171G>A	p.Glu391Lys	p.E391K	ENST00000261937	NM_182925.4	391	Gag/Aag	9/30	0.172223363206345	3	FACETS	1	0.979	1	0.722	0.644	0.805	CLONAL	1	FALSE	1	0.237419701577378	3		602	620	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32802933	32802933	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	115	278	0	ENST00000374899.4:c.943C>A	p.Gln315Lys	p.Q315K	ENST00000374899	NM_018833.2	315	Cag/Aag	5/12	0.222301739856646	3	FACETS	0.879	0.798	0.963	0.879	0.798	0.963	CLONAL	3	FALSE	0	0.237419701577378	3		278	411	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157495228	157495228	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	77	447	0	ENST00000346085.5:c.3112C>G	p.Pro1038Ala	p.P1038A	ENST00000346085	NM_020732.3	1038	Cca/Gca	11/20	0.237419701577378	5	FACETS	1	0.972	1	0.463	0.407	0.524	CLONAL	1	FALSE	2	0.237419701577378	5		447	633	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435997	116435997	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	123	513	0	ENST00000397752.3:c.3992C>G	p.Ser1331Cys	p.S1331C	ENST00000397752	NM_000245.2	1331	tCt/tGt	21/21	0.237419701577378	5	FACETS	0.882	0.797	0.97	0.588	0.531	0.647	CLONAL	2	FALSE	2	0.237419701577378	5		513	797	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008972	152008972	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	152	387	0	ENST00000262189.6:c.650C>A	p.Ser217Ter	p.S217*	ENST00000262189	NM_170606.2	217	tCa/tAa	5/59	0.237419701577378	5	FACETS	0.907	0.833	0.985	0.907	0.833	0.985	CLONAL	3	FALSE	2	0.237419701577378	5		387	638	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863323	56863323	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	129	357	0	ENST00000519728.1:c.467G>C	p.Arg156Thr	p.R156T	ENST00000519728	NM_002350.3	156	aGa/aCa	6/13	0.237419701577378	6	FACETS	1	0.976	1	0.811	0.737	0.888	CLONAL	2	FALSE	3	0.237419701577378	6		357	659	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031690	69031690	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371787029	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	136	350	0	ENST00000288368.4:c.3445C>G	p.Arg1149Gly	p.R1149G	ENST00000288368	NM_024870.2	1149	Cgc/Ggc	28/40	0.237419701577378	6	FACETS	0.903	0.823	0.985	0.903	0.823	0.985	CLONAL	3	FALSE	3	0.237419701577378	6		350	624	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993685	90993685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	94	266	1	ENST00000265433.3:c.238G>A	p.Glu80Lys	p.E80K	ENST00000265433	NM_002485.4	80	Gag/Aag	3/16	0.237419701577378	6	FACETS	1	0.929	1	0.703	0.627	0.783	CLONAL	2	FALSE	3	0.237419701577378	6		267	554	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270496	98270496	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	74	422	0	ENST00000331920.6:c.148C>G	p.Leu50Val	p.L50V	ENST00000331920	NM_000264.3	50	Ctg/Gtg	1/24	0.237419701577378	5	FACETS	1	0.973	1	0.485	0.425	0.55	CLONAL	1	FALSE	2	0.237419701577378	5		422	581	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910697	29910697	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs199474414	NA	P-0050703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	209	1044	0	ENST00000376809.5:c.237G>C	p.Glu79Asp	p.E79D	ENST00000376809	NM_002116.7	79	gaG/gaC	2/8	0.222301739856646	3	FACETS	1	0.948	1	0.683	0.634	0.734	CLONAL	2	FALSE	0	0.237419701577378	3		1044	961	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0050704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	236	336	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	0.77980028006142	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	FALSE	2	0.77980028006142	4		336	513	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559764	29559764	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1567851029	NA	P-0050704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	161	242	0	ENST00000356175.3:c.3361G>T	p.Glu1121Ter	p.E1121*	ENST00000356175	NM_000267.3	1121	Gaa/Taa	26/57	0.77980028006142	4	FACETS	0.97	0.901	1	0.97	0.901	1	CLONAL	2	FALSE	2	0.77980028006142	4		242	379	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148929	119148929	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	226	355	0	ENST00000264033.4:c.1149A>G	p.Ile383Met	p.I383M	ENST00000264033	NM_005188.3	383	atA/atG	8/16	0.77980028006142	2	FACETS	0.973	0.934	1	0.973	0.934	1	CLONAL	2	FALSE	0	0.77980028006142	2		355	298	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436678	110436678	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	332	739	0	ENST00000375856.3:c.1723A>T	p.Thr575Ser	p.T575S	ENST00000375856	NM_003749.2	575	Acc/Tcc	1/2	0.736617722086088	3	FACETS	0.986	0.943	1	0.986	0.943	1	CLONAL	2	FALSE	1	0.77980028006142	3		739	600	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591139	67591141	+	frameshift_variant	Frame_Shift_Del	DEL	GAC	GAC	T	novel	NA	P-0050704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	15	223	0	ENST00000274335.5:c.1732_1734delinsT	p.Asp578SerfsTer23	p.D578Sfs*23	ENST00000274335		578	GAC/T	12/15	0.736617722086088	3	FACETS	0.194	0.141	0.257	0.097	0.07	0.129	SUBCLONAL	1	FALSE	1	0.77980028006142	3		223	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0050705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	108	637	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.36082813706245	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.36082813706245	1		637	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0050706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	241	430	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.329951192232527	3	FACETS	0.848	0.799	0.897	0.848	0.799	0.897	CLONAL	3	FALSE	0	0.411815546041846	3		430	555	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874011	123874013	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs780061449	NA	P-0050708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	10	79	0	ENST00000330479.4:c.62_64del	p.Ala21del	p.A21del	ENST00000330479	NM_020382.3	14	gaGGCg/gag	2/9	1	2	FACETS	0.912	0.621	1	0.912	0.621	1	CLONAL	1	TRUE	1	0.17	2		79	129	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061228	38061228	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	71	711	0	ENST00000250448.2:c.761del	p.Phe254SerfsTer67	p.F254Sfs*67	ENST00000250448	NM_004496.3	254	tTc/tc	2/2	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.17	2		711	796	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79974798	79974798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	57	561	0	ENST00000265081.6:c.1226C>T	p.Ala409Val	p.A409V	ENST00000265081	NM_002439.4	409	gCt/gTt	8/24	1	2	FACETS	0.93	0.797	1	0.93	0.797	1	CLONAL	1	TRUE	1	0.17	2		561	721	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099452	27099452	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1171440222	NA	P-0050710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	90	400	0	ENST00000324856.7:c.3689A>C	p.Lys1230Thr	p.K1230T	ENST00000324856	NM_006015.4	1230	aAg/aCg	14/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.224168611415711	2		400	585	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119839	70119839	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	99	602	1	ENST00000245479.2:c.841G>A	p.Asp281Asn	p.D281N	ENST00000245479	NM_000346.3	281	Gac/Aac	3/3	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.224168611415711	2		603	756	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873167	136873167	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	50	346	0	ENST00000241393.3:c.331G>T	p.Ala111Ser	p.A111S	ENST00000241393	NM_003467.2	111	Gca/Tca	2/2	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.224168611415711	2		346	428	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944338	131944338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs562172843	NA	P-0050710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	33	188	0	ENST00000265335.6:c.2750C>T	p.Thr917Ile	p.T917I	ENST00000265335		917	aCa/aTa	17/25	0.166947833441776	3	FACETS	0.955	0.779	1			1	CLONAL	1	TRUE	NA	0.224168611415711	3		188	343	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553171	106553171	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	75	446	0	ENST00000369096.4:c.1136C>G	p.Ala379Gly	p.A379G	ENST00000369096	NM_001198.3	379	gCg/gGg	5/7	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.224168611415711	2		446	613	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981701	70981701	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	87	643	0	ENST00000276594.2:c.395A>G	p.Gln132Arg	p.Q132R	ENST00000276594	NM_024504.3	132	cAa/cGa	2/8	1	2	FACETS	0.95	0.84	1	0.95	0.84	1	CLONAL	1	TRUE	1	0.224168611415711	2		643	817	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0050711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	42	355	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.759	0.633	0.898	0.759	0.633	0.898	SUBCLONAL	1	FALSE	1	0.22010887063585	2		355	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579362	7579362	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	36	590	1	ENST00000269305.4:c.325T>A	p.Phe109Ile	p.F109I	ENST00000269305	NM_001126112.2	109	Ttc/Atc	4/11	0.22010887063585	1	FACETS	0.612	0.502	0.734	0.612	0.502	0.734	SUBCLONAL	1	FALSE	0	0.22010887063585	1		591	476	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81973512	81973512	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	45	393	0	ENST00000359376.3:c.3329G>T	p.Ser1110Ile	p.S1110I	ENST00000359376	NM_002661.3	1110	aGc/aTc	30/33	0.22010887063585	1	FACETS	0.896	0.755	1	0.896	0.755	1	CLONAL	1	FALSE	0	0.22010887063585	1		393	406	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739056	40739056	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	38	540	0	ENST00000373198.4:c.3228C>A	p.Cys1076Ter	p.C1076*	ENST00000373198	NM_133170.3	1076	tgC/tgA	24/32	0.22010887063585	1	FACETS	0.644	0.532	0.769	0.644	0.532	0.769	SUBCLONAL	1	FALSE	0	0.22010887063585	1		540	477	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37628898	37628898	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	49	635	0	ENST00000249071.6:c.168G>T	p.Trp56Cys	p.W56C	ENST00000249071	NM_002872.4	56	tgG/tgT	3/7	0.22010887063585	1	FACETS	0.649	0.549	0.759	0.649	0.549	0.759	SUBCLONAL	1	FALSE	0	0.22010887063585	1		635	611	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540017	187540017	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	36	318	0	ENST00000441802.2:c.7723G>T	p.Gly2575Ter	p.G2575*	ENST00000441802	NM_005245.3	2575	Gga/Tga	10/27	1	2	FACETS	0.768	0.631	0.921	0.768	0.631	0.921	CLONAL	1	FALSE	1	0.22010887063585	2		318	426	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720871	176720871	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	41	435	0	ENST00000439151.2:c.6502G>T	p.Gly2168Trp	p.G2168W	ENST00000439151	NM_022455.4	2168	Ggg/Tgg	23/23	0.22010887063585	1	FACETS	0.65	0.541	0.771	0.65	0.541	0.771	SUBCLONAL	1	FALSE	0	0.22010887063585	1		435	510	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0050712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	196	536	0	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	1	2	FACETS	0.89	0.826	0.955	0.89	0.826	0.955	CLONAL	1	TRUE	1	0.603480067558052	2		536	730	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0050712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	130	517	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.949	0.867	1	0.949	0.867	1	CLONAL	1	TRUE	1	0.603480067558052	2		517	454	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0050712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	74	219	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.882	0.781	0.989	0.882	0.781	0.989	CLONAL	1	TRUE	1	0.603480067558052	2		219	278	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213358	36213359	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0050712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	89	758	0	ENST00000222270.7:c.2561_2562del	p.Glu854AlafsTer34	p.E854Afs*34	ENST00000222270	NM_014727.1	852	aAG/a	4/37	1	2	FACETS	0.32	0.282	0.359	0.32	0.282	0.359	SUBCLONAL	1	TRUE	1	0.603480067558052	2		758	923	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0050712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	87	383	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.871	0.778	0.968	0.871	0.778	0.968	CLONAL	1	TRUE	1	0.603480067558052	2		383	331	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0050712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	137	740	4	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.476	0.433	0.522	0.476	0.433	0.522	SUBCLONAL	1	TRUE	1	0.603480067558052	2		744	953	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0050712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	120	376	4	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.756	0.686	0.83	0.756	0.686	0.83	SUBCLONAL	1	TRUE	1	0.603480067558052	2		380	526	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261373	16261373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773726905	NA	P-0050712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	44	552	1	ENST00000375759.3:c.8638G>A	p.Val2880Met	p.V2880M	ENST00000375759	NM_015001.2	2880	Gtg/Atg	11/15	0.603480067558052	2	FACETS	0.218	0.182	0.257	0.109	0.091	0.129	SUBCLONAL	1	TRUE	0	0.603480067558052	2		553	670	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46512266	46512266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34168524	NA	P-0050712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	148	466	0	ENST00000262741.5:c.973C>T	p.Arg325Cys	p.R325C	ENST00000262741	NM_003629.3	325	Cgc/Tgc	8/10	0.603480067558052	2	FACETS	0.931	0.855	1	0.465	0.427	0.505	CLONAL	1	TRUE	0	0.603480067558052	2		466	527	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163313635	163313635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149575845	NA	P-0050712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	65	172	0	ENST00000271452.3:c.782C>T	p.Thr261Met	p.T261M	ENST00000271452	NM_145697.2	261	aCg/aTg	10/14	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.603480067558052	2		172	189	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606815	43606815	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138624658	NA	P-0050712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	233	736	0	ENST00000355710.3:c.1424G>A	p.Arg475Gln	p.R475Q	ENST00000355710	NM_020975.4	475	cGg/cAg	7/20	1	2	FACETS	0.935	0.874	0.997	0.935	0.874	0.997	CLONAL	1	TRUE	1	0.603480067558052	2		736	826	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111886063	111886063	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770527337	NA	P-0050712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	38	506	2	ENST00000341259.2:c.1685G>A	p.Arg562Gln	p.R562Q	ENST00000341259	NM_005475.2	562	cGg/cAg	8/8	1	2	FACETS	0.175	0.144	0.21	0.175	0.144	0.21	SUBCLONAL	1	TRUE	1	0.603480067558052	2		508	719	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220501	133220501	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	197	536	0	ENST00000320574.5:c.4212G>T	p.Glu1404Asp	p.E1404D	ENST00000320574	NM_006231.2	1404	gaG/gaT	33/49	1	2	FACETS	0.949	0.882	1	0.949	0.882	1	CLONAL	1	TRUE	1	0.603480067558052	2		536	688	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2105507	2105507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45517113	NA	P-0050712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	80	426	0	ENST00000219476.3:c.586G>A	p.Ala196Thr	p.A196T	ENST00000219476	NM_000548.3	196	Gca/Aca	6/42	1	2	FACETS	0.433	0.381	0.488	0.433	0.381	0.488	SUBCLONAL	1	TRUE	1	0.603480067558052	2		426	613	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652947	29652947	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770124316	NA	P-0050712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	128	371	0	ENST00000356175.3:c.4882G>A	p.Gly1628Arg	p.G1628R	ENST00000356175	NM_000267.3	1628	Ggg/Agg	36/57	1	2	FACETS	0.882	0.804	0.962	0.882	0.804	0.962	CLONAL	1	TRUE	1	0.603480067558052	2		371	481	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532648	63532648	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1025003994	NA	P-0050712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	230	653	0	ENST00000307078.5:c.1931A>G	p.Tyr644Cys	p.Y644C	ENST00000307078	NM_004655.3	644	tAc/tGc	8/11	1	2	FACETS	0.927	0.867	0.99	0.927	0.867	0.99	CLONAL	1	TRUE	1	0.603480067558052	2		653	822	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526486	66526486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772571340	NA	P-0050712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	159	412	1	ENST00000358598.2:c.1042G>A	p.Val348Ile	p.V348I	ENST00000358598	NM_212471.2	348	Gtt/Att	11/11	1	2	FACETS	0.857	0.789	0.927	0.857	0.789	0.927	CLONAL	1	TRUE	1	0.603480067558052	2		413	615	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120040	70120040	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	38	84	0	ENST00000245479.2:c.1042C>T	p.Gln348Ter	p.Q348*	ENST00000245479	NM_000346.3	348	Cag/Tag	3/3	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.603480067558052	2		84	122	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762376	41762376	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763877877	NA	P-0050712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	191	442	0	ENST00000301178.4:c.2056G>A	p.Val686Met	p.V686M	ENST00000301178	NM_021913.4	686	Gtg/Atg	18/20	1	2	FACETS	0.975	0.906	1	0.975	0.906	1	CLONAL	1	TRUE	1	0.603480067558052	2		442	649	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703631	47703631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750636	NA	P-0050712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	197	457	0	ENST00000233146.2:c.2131C>T	p.Arg711Ter	p.R711*	ENST00000233146	NM_000251.2	711	Cga/Tga	13/16	0.603480067558052	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.603480067558052	1		457	446	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026204	48026204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750440	NA	P-0050712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	35	328	1	ENST00000234420.5:c.1082G>A	p.Arg361His	p.R361H	ENST00000234420	NM_000179.2	361	cGc/cAc	4/10	0.603480067558052	1	FACETS	0.26	0.214	0.312	0.26	0.214	0.312	SUBCLONAL	1	TRUE	0	0.603480067558052	1		329	311	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151289	202151290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	50	303	0	ENST00000358485.4:c.1596dup	p.Leu533ThrfsTer6	p.L533Tfs*6	ENST00000358485	NM_001080125.1	530	aga/agAa	9/9	1	2	FACETS	0.359	0.304	0.418	0.359	0.304	0.418	SUBCLONAL	1	TRUE	1	0.603480067558052	2		303	462	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439583	220439583	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	218	746	0	ENST00000243786.2:c.436A>G	p.Asn146Asp	p.N146D	ENST00000243786	NM_002191.3	146	Aat/Gat	2/2	1	2	FACETS	0.892	0.832	0.954	0.892	0.832	0.954	CLONAL	1	TRUE	1	0.603480067558052	2		746	810	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790074	40790074	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	173	580	0	ENST00000373198.4:c.2657C>A	p.Pro886His	p.P886H	ENST00000373198	NM_133170.3	886	cCc/cAc	18/32	1	2	FACETS	0.763	0.704	0.825	0.763	0.704	0.825	SUBCLONAL	1	TRUE	1	0.603480067558052	2		580	751	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165213	47165213	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	95	331	0	ENST00000409792.3:c.913del	p.Thr305GlnfsTer35	p.T305Qfs*35	ENST00000409792	NM_014159.6	305	Aca/ca	3/21	1	2	FACETS	0.719	0.643	0.798	0.719	0.643	0.798	SUBCLONAL	1	TRUE	1	0.603480067558052	2		331	438	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517609	176517609	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs755455944	NA	P-0050712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	229	702	0	ENST00000292408.4:c.310C>T	p.Arg104Ter	p.R104*	ENST00000292408	NM_213647.1	104	Cga/Tga	3/18	1	2	FACETS	0.926	0.865	0.988	0.926	0.865	0.988	CLONAL	1	TRUE	1	0.603480067558052	2		702	820	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481625	20481627	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0050712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	99	266	0	ENST00000346618.3:c.700_702del	p.Lys234del	p.K234del	ENST00000346618	NM_001949.4	232	AAG/-	3/7	1	2	FACETS	0.824	0.741	0.911	0.824	0.741	0.911	CLONAL	1	TRUE	1	0.603480067558052	2		266	398	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405929	157405929	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs563771544	NA	P-0050712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	180	476	1	ENST00000346085.5:c.2171C>T	p.Ala724Val	p.A724V	ENST00000346085	NM_020732.3	724	gCg/gTg	6/20	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.603480067558052	2		477	595	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527862	157527862	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	74	427	0	ENST00000346085.5:c.5587G>T	p.Gly1863Cys	p.G1863C	ENST00000346085	NM_020732.3	1863	Ggc/Tgc	20/20	1	2	FACETS	0.498	0.437	0.564	0.498	0.437	0.564	SUBCLONAL	1	TRUE	1	0.603480067558052	2		427	492	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	189	584	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	0.852	0.79	0.917	0.852	0.79	0.917	CLONAL	1	TRUE	1	0.603480067558052	2		584	735	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8338977	8338977	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	56	409	0	ENST00000356435.5:c.5324C>T	p.Ala1775Val	p.A1775V	ENST00000356435		1775	gCt/gTt	32/35	1	2	FACETS	0.364	0.312	0.421	0.364	0.312	0.421	SUBCLONAL	1	TRUE	1	0.603480067558052	2		409	510	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169625	27169625	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs775884054	NA	P-0050712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	205	494	0	ENST00000380036.4:c.626G>A	p.Arg209Gln	p.R209Q	ENST00000380036	NM_000459.3	209	cGg/cAg	4/23	1	2	FACETS	0.983	0.916	1	0.983	0.916	1	CLONAL	1	TRUE	1	0.603480067558052	2		494	691	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564080	139564080	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537251168	NA	P-0050712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	79	757	0	ENST00000308874.7:c.220C>T	p.Arg74Cys	p.R74C	ENST00000308874		74	Cgc/Tgc	5/10	1	2	FACETS	0.298	0.261	0.338	0.298	0.261	0.338	SUBCLONAL	1	TRUE	1	0.603480067558052	2		757	878	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	421	276	0				ENST00000310581	NM_198253.2	-/1132			0.276833441198685	9	FACETS	1	0.983	1	1	0.983	1	CLONAL	8	TRUE	1	0.276833441198685	9		276	721	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0050713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	98	596	0	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.276833441198685	2		596	559	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936072	44936072	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1135401809	NA	P-0050713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	35	198	0	ENST00000377967.4:c.2832+1G>A		p.X944_splice	ENST00000377967	NM_021140.2	944			1	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.276833441198685	1		198	164	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068405	26068405	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	37	319	0	ENST00000435504.4:c.85A>G	p.Met29Val	p.M29V	ENST00000435504		29	Atg/Gtg	2/13	1	2	FACETS	0.649	0.535	0.776	0.649	0.535	0.776	SUBCLONAL	1	TRUE	1	0.276833441198685	2		319	412	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231506	5231506	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1386910242	NA	P-0050713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	72	697	0	ENST00000357368.4:c.1970G>A	p.Arg657His	p.R657H	ENST00000357368	NM_002850.3	657	cGc/cAc	14/38	1	2	FACETS	0.843	0.737	0.958	0.843	0.737	0.958	CLONAL	1	TRUE	1	0.276833441198685	2		697	617	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982989	201982990	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0050713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	115	686	0	ENST00000359651.3:c.841dup	p.Asp281GlyfsTer20	p.D281Gfs*20	ENST00000359651		280	cgg/cGgg	7/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.276833441198685	2		686	666	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026839	71026839	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	33	343	0	ENST00000318789.4:c.1383del	p.Asn461LysfsTer13	p.N461Kfs*13	ENST00000318789	NM_032682.5	461	aaC/aa	16/21	1	2	FACETS	0.714	0.582	0.861	0.714	0.582	0.861	SUBCLONAL	1	TRUE	1	0.276833441198685	2		343	334	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443373	187443373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	34	452	1	ENST00000232014.4:c.1753C>T	p.Arg585Trp	p.R585W	ENST00000232014	NM_001130845.1	585	Cgg/Tgg	8/10	0.208852772898479	4	FACETS	0.321	0.262	0.388	0.107	0.087	0.13	INDETERMINATE	1	TRUE	1	0.58943876077387	4		453	571	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874961	151874961	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0050714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	40	283	0	ENST00000262189.6:c.7577T>A	p.Leu2526Ter	p.L2526*	ENST00000262189	NM_170606.2	2526	tTa/tAa	38/59	1	2	FACETS	0.556	0.465	0.656	0.556	0.465	0.656	SUBCLONAL	1	TRUE	1	0.58943876077387	2		283	244	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	59	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.983	0.845	1	0.983	0.845	1	CLONAL	1	TRUE	1	0.17	2		334	706	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0050715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	122	853	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.17	2		853	1074	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956675	93956675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776802108	NA	P-0050715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	42	351	0	ENST00000369303.4:c.2561G>A	p.Arg854His	p.R854H	ENST00000369303	NM_004440.3	854	cGt/cAt	15/17	1	2	FACETS	0.961	0.802	1	0.961	0.802	1	CLONAL	1	TRUE	1	0.17	2		351	514	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444794	49444794	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0050715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	75	821	1	ENST00000301067.7:c.2672T>G	p.Leu891Ter	p.L891*	ENST00000301067	NM_003482.3	891	tTa/tGa	10/54	1	2	FACETS	0.932	0.815	1	0.932	0.815	1	CLONAL	1	TRUE	1	0.17	2		822	947	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685315	89685315	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1554897280	NA	P-0050716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	95	227	0	ENST00000371953.3:c.209+1G>A		p.X70_splice	ENST00000371953	NM_000314.4	70			NA	2	FACETS	0.863	0.776	0.954			1	INDETERMINATE	2	TRUE	NA	0.316247876586495	2		227	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0050716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	253	651	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.316247876586495	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	0	0.316247876586495	2		651	797	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172457	108172457	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0050716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	76	359	0	ENST00000278616.4:c.5260A>T	p.Lys1754Ter	p.K1754*	ENST00000278616	NM_000051.3	1754	Aag/Tag	35/63	NA	2	FACETS	1	0.952	1			1	INDETERMINATE	1	TRUE	NA	0.316247876586495	2		359	415	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69230510	69230510	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	67	308	0	ENST00000462284.1:c.899A>T	p.Asp300Val	p.D300V	ENST00000462284	NM_002392.5	300	gAt/gTt	10/11	0.220992925013788	3	FACETS	0.912	0.794	1			1	CLONAL	1	TRUE	NA	0.316247876586495	3		308	538	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619783	1619783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	102	663	0	ENST00000344749.5:c.1163G>A	p.Gly388Asp	p.G388D	ENST00000344749	NM_001136139.2	388	gGc/gAc	14/19	0.316247876586495	2	FACETS	0.779	0.696	0.867	0.39	0.348	0.434	SUBCLONAL	1	TRUE	0	0.316247876586495	2		663	828	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535461	187535461	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	56	310	0	ENST00000441802.2:c.9113C>T	p.Pro3038Leu	p.P3038L	ENST00000441802	NM_005245.3	3038	cCt/cTt	12/27	0.316247876586495	3	FACETS	0.853	0.732	0.985	0.426	0.366	0.493	CLONAL	1	TRUE	1	0.316247876586495	3		310	481	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38137144	38137144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	118	509	0	ENST00000317025.8:c.3674G>A	p.Ser1225Asn	p.S1225N	ENST00000317025	NM_023034.1	1225	aGt/aAt	21/24	0.255798046530523	4	FACETS	1	0.95	1			1	CLONAL	1	TRUE	NA	0.316247876586495	4		509	904	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981877	70981877	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	115	676	0	ENST00000276594.2:c.219G>A	p.Met73Ile	p.M73I	ENST00000276594	NM_024504.3	73	atG/atA	2/8	0.295157705841957	3	FACETS	0.914	0.822	1	0.457	0.411	0.506	CLONAL	1	TRUE	1	0.316247876586495	3		676	922	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087395	27087396	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0050726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	90	580	0	ENST00000324856.7:c.1970dup	p.Ser658GlufsTer18	p.S658Efs*18	ENST00000324856	NM_006015.4	657	ctg/cTtg	5/20	1	2	FACETS	0.937	0.833	1	0.937	0.833	1	CLONAL	1	TRUE	1	0.305307349294675	2		580	629	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105611	27105611	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	63	537	0	ENST00000324856.7:c.5222A>G	p.Gln1741Arg	p.Q1741R	ENST00000324856	NM_006015.4	1741	cAg/cGg	20/20	1	2	FACETS	0.724	0.626	0.83	0.724	0.626	0.83	SUBCLONAL	1	TRUE	1	0.305307349294675	2		537	570	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56787253	56787253	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	90	485	0	ENST00000337432.4:c.739C>A	p.Pro247Thr	p.P247T	ENST00000337432	NM_058216.2	247	Cca/Aca	5/9	1	2	FACETS	0.97	0.862	1	0.97	0.862	1	CLONAL	1	TRUE	1	0.305307349294675	2		485	608	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876260	35876260	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	42	508	0	ENST00000303115.3:c.1052C>G	p.Ser351Cys	p.S351C	ENST00000303115	NM_002185.3	351	tCt/tGt	8/8	0.133998205171409	3	FACETS	0.717	0.599	0.848	0.359	0.299	0.424	INDETERMINATE	1	TRUE	1	0.305307349294675	3		508	442	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373757	118373757	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	AA	novel	NA	P-0050726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	50	332	0	ENST00000534358.1:c.7150delinsAA	p.Gln2384LysfsTer15	p.Q2384Kfs*15	ENST00000534358	NM_005933.3	2384	Caa/AAaa	27/36	0.292083740363609	1	FACETS	0.907	0.774	1	0.907	0.774	1	CLONAL	1	TRUE	0	0.305307349294675	1		332	306	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216382	2216382	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs967712936	NA	P-0050728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	276	794	0	ENST00000398665.3:c.2026A>G	p.Lys676Glu	p.K676E	ENST00000398665	NM_032482.2	676	Aag/Gag	20/28	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.610023520779517	2		794	894	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21565543	21565543	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	220	513	0	ENST00000382592.4:c.343G>T	p.Glu115Ter	p.E115*	ENST00000382592	NM_014572.2	115	Gag/Tag	3/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.610023520779517	2		513	648	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469606	25469606	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	273	762	2	ENST00000264709.3:c.1162C>A	p.His388Asn	p.H388N	ENST00000264709	NM_175629.2	388	Cac/Aac	10/23	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.610023520779517	2		764	891	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103741	47103741	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	196	484	0	ENST00000409792.3:c.6205del	p.Thr2069LeufsTer78	p.T2069Lfs*78	ENST00000409792	NM_014159.6	2069	Act/ct	14/21	0.610023520779517	1	FACETS	0.997	0.934	1	0.997	0.934	1	CLONAL	1	TRUE	0	0.610023520779517	1		484	448	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940243	49940244	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCGGCTGTACAGTCAGGAAGTATA	novel	NA	P-0050728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	165	770	0	ENST00000296474.3:c.776_799dup	p.Val259_Pro266dup	p.V259_P266dup	ENST00000296474	NM_002447.2	259	gcc/gTATACTTCCTGACTGTACAGCCGGcc	1/20	0.610023520779517	1	FACETS	0.539	0.496	0.583	0.539	0.496	0.583	SUBCLONAL	1	TRUE	0	0.610023520779517	1		770	698	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613116	52613116	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	198	441	0	ENST00000394830.3:c.3412T>C	p.Cys1138Arg	p.C1138R	ENST00000394830	NM_018313.4	1138	Tgt/Cgt	22/30	0.610023520779517	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.610023520779517	1		441	443	SUCCESS
APC	324	MSKCC	GRCh37	5	112178342	112178342	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	139	410	0	ENST00000257430.4:c.7051C>G	p.Pro2351Ala	p.P2351A	ENST00000257430	NM_000038.5	2351	Cct/Gct	16/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.610023520779517	2		410	427	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877869	151877887	+	frameshift_variant	Frame_Shift_Del	DEL	ACAGGTCCAGGAAGTTGGG	ACAGGTCCAGGAAGTTGGG	-	novel	NA	P-0050729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	22	336	0	ENST00000262189.6:c.7058_7076del	p.Ser2353CysfsTer6	p.S2353Cfs*6	ENST00000262189	NM_170606.2	2353	tCCCAACTTCCTGGACCTGTg/tg	36/59	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		336	254	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808979	1808979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751115449	NA	P-0050729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	61	513	0	ENST00000260795.2:c.2411C>T	p.Ser804Leu	p.S804L	ENST00000260795		804	tCg/tTg	17/17	0.0817868310585695	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		513	326	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38064160	38064160	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	55	362	0	ENST00000250448.2:c.18G>C	p.Lys6Asn	p.K6N	ENST00000250448	NM_004496.3	6	aaG/aaC	1/2	0.133354573678914	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		362	433	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942035	44942035	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0050729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	33	118	0	ENST00000377967.4:c.3284+1G>T		p.X1095_splice	ENST00000377967	NM_021140.2	1095			1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		118	133	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061137	38061160	+	inframe_deletion	In_Frame_Del	DEL	GCCCCCGCTTCCGCTCCCGCCCCC	GCCCCCGCTTCCGCTCCCGCCCCC	-	novel	NA	P-0050729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	67	369	0	ENST00000250448.2:c.829_852del	p.Gly277_Gly284del	p.G277_G284del	ENST00000250448	NM_004496.3	277	GGGGGCGGGAGCGGAAGCGGGGGC/-	2/2	0.133354573678914	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		369	369	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061169	38061200	+	protein_altering_variant	In_Frame_Del	DEL	CCCCCGGCTGCTTCTCGCACTTGAAGCGCTTC	CCCCCGGCTGCTTCTCGCACTTGAAGCGCTTC	GG	novel	NA	P-0050729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	73	517	2	ENST00000250448.2:c.789_820delinsCC	p.Gln263_Ala274delinsHisPro	p.Q263_A274delinsHP	ENST00000250448	NM_004496.3	263	caGAAGCGCTTCAAGTGCGAGAAGCAGCCGGGGGcc/caCCcc	2/2	0.133354573678914	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		519	511	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66777352	66777352	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	204	765	0	ENST00000307102.5:c.718T>C	p.Tyr240His	p.Y240H	ENST00000307102	NM_002755.3	240	Tac/Cac	7/11	1	2	FACETS	0.958	0.896	1	0.958	0.896	1	CLONAL	1	TRUE	1	0.822321828094543	2		765	518	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536220	41536221	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0050731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	170	569	0	ENST00000263253.7:c.1837_1838del	p.Arg613GlufsTer3	p.R613Efs*3	ENST00000263253	NM_001429.3	613	CGg/g	9/31	0.732803526621043	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.822321828094543	1		569	234	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	71	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.754	0.665	0.847	0.754	0.665	0.847	SUBCLONAL	1	TRUE	1	0.700257358167386	2		276	269	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220274	55220274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8919	8163	571	1	ENST00000275493.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000275493	NM_005228.3	222	Cgc/Tgc	6/28	0.700257358167386	35	FACETS	1	0.995	1	0.49	0.484	0.495	CLONAL	17	TRUE	0	0.700257358167386	35		572	17082	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168520	56168520	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	110	187	0	ENST00000399503.3:c.1476A>C	p.Arg492Ser	p.R492S	ENST00000399503	NM_005921.1	492	agA/agC	8/20	1	2	FACETS	0.976	0.888	1	0.976	0.888	1	CLONAL	1	TRUE	1	0.700257358167386	2		187	322	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0050733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	27	474	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.449	0.357	0.554	0.449	0.357	0.554	SUBCLONAL	1	TRUE	1	0.31	2		474	388	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252156	226252156	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	17	91	0	ENST00000366813.1:c.104G>T	p.Gly35Val	p.G35V	ENST00000366813		35	gGg/gTg	1/3	1	2	FACETS	0.914	0.69	1	0.914	0.69	1	CLONAL	1	TRUE	1	0.31	2		91	120	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879893	37879893	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1452141491	NA	P-0050733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	94	632	0	ENST00000269571.5:c.2188G>A	p.Ala730Thr	p.A730T	ENST00000269571		730	Gct/Act	18/27	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.31	2		632	565	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0050734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	170	247	0	ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	4/10	0.346571867669626	3	FACETS	1	0.941	1	1	0.941	1	CLONAL	3	TRUE	0	0.346571867669626	3		247	380	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250808	26250808	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768964817	NA	P-0050734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	77	373	0	ENST00000446824.2:c.26G>A	p.Arg9His	p.R9H	ENST00000446824	NM_021018.2	9	cGt/cAt	1/1	0.335994192313994	3	FACETS	0.934	0.822	1	0.467	0.411	0.528	CLONAL	1	TRUE	1	0.346571867669626	3		373	558	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0050735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	172	441	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.725550955404099	3	FACETS	0.838	0.772	0.906	0.419	0.386	0.453	CLONAL	1	TRUE	1	0.725550955404099	3		441	771	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs786203436	NA	P-0050735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	669	705	4	ENST00000269305.4:c.487T>G	p.Tyr163Asp	p.Y163D	ENST00000269305	NM_001126112.2	163	Tac/Gac	5/11	0.725550955404099	2	FACETS	0.977	0.952	1	0.977	0.952	1	CLONAL	2	TRUE	0	0.725550955404099	2		709	944	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431538	49431556	+	frameshift_variant	Frame_Shift_Del	DEL	GTGGGCTGGGGGTCAGCAG	GTGGGCTGGGGGTCAGCAG	-	novel	NA	P-0050735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	51	646	1	ENST00000301067.7:c.9583_9601del	p.Leu3195Ter	p.L3195*	ENST00000301067	NM_003482.3	3195	CTGCTGACCCCCAGCCCACtg/tg	34/54	0.408977436450591	3	FACETS	0.189	0.159	0.221	0.063	0.053	0.074	INDETERMINATE	1	TRUE	0	0.725550955404099	3		647	1015	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346360	89346360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767358927	NA	P-0050735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	133	550	0	ENST00000301030.4:c.6590C>T	p.Thr2197Ile	p.T2197I	ENST00000301030	NM_001256183.1	2197	aCc/aTc	9/13	NA	2	FACETS	0.555	0.505	0.607			1	INDETERMINATE	1	TRUE	NA	0.725550955404099	2		550	661	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144121	11144121	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	327	581	1	ENST00000358026.2:c.3702C>G	p.Phe1234Leu	p.F1234L	ENST00000358026	NM_001128849.1	1234	ttC/ttG	26/36	0.580193346276795	4	FACETS	1	0.983	1	0.553	0.521	0.586	CLONAL	1	TRUE	2	0.725550955404099	4		582	1406	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242483	55242506	+	inframe_deletion	In_Frame_Del	DEL	ATCTCCGAAAGCCAACAAGGAAAT	ATCTCCGAAAGCCAACAAGGAAAT	-	rs727504232	NA	P-0050736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	2786	498	0	ENST00000275493.2:c.2253_2276del	p.Ser752_Ile759del	p.S752_I759del	ENST00000275493	NM_005228.3	751	acATCTCCGAAAGCCAACAAGGAAATc/acc	19/28	0.844824953026611	27	FACETS	1	0.992	1	0.923	0.915	0.931	CLONAL	24	TRUE	1	0.844824953026611	27		498	3176	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782082	NA	P-0050736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	621	710	0	ENST00000269305.4:c.745A>T	p.Arg249Trp	p.R249W	ENST00000269305	NM_001126112.2	249	Agg/Tgg	7/11	0.828921362876454	3	FACETS	1	0.985	1			1	CLONAL	3	TRUE	NA	0.844824953026611	3		710	696	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793408	18793408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	129	501	0	ENST00000266497.5:c.4105C>T	p.Leu1369Phe	p.L1369F	ENST00000266497		1369	Ctt/Ttt	30/31	0.840951182829089	2	FACETS	0.904	0.83	0.978	0.452	0.415	0.489	CLONAL	1	TRUE	0	0.844824953026611	2		501	338	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983019	201983019	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	264	860	0	ENST00000359651.3:c.868G>C	p.Glu290Gln	p.E290Q	ENST00000359651		290	Gag/Cag	7/8	0.844824953026611	4	FACETS	0.813	0.76	0.867	0.271	0.253	0.289	CLONAL	1	TRUE	1	0.844824953026611	4		860	1419	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256124	133256124	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	354	636	0	ENST00000320574.5:c.537G>T	p.Glu179Asp	p.E179D	ENST00000320574	NM_006231.2	179	gaG/gaT	6/49	0.840951182829089	2	FACETS	0.991	0.964	1	0.991	0.964	1	CLONAL	2	TRUE	0	0.844824953026611	2		636	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0050741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	510	479	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	0.82406596463717	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.833057843986851	1		479	673	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846073	128846073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	451	542	0	ENST00000249373.3:c.1003C>T	p.Leu335Phe	p.L335F	ENST00000249373	NM_005631.4	335	Ctc/Ttc	5/12	1	2	FACETS	0.975	0.933	1	0.975	0.933	1	CLONAL	1	TRUE	1	0.833057843986851	2		542	1111	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670483	134670483	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	300	384	0	ENST00000398015.3:c.394G>T	p.Ala132Ser	p.A132S	ENST00000398015	NM_004441.4	132	Gcc/Tcc	3/16	1	2	FACETS	0.888	0.84	0.937	0.888	0.84	0.937	CLONAL	1	TRUE	1	0.833057843986851	2		384	811	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715643	18715643	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	106	219	0	ENST00000266497.5:c.3474A>G	p.Ile1158Met	p.I1158M	ENST00000266497		1158	atA/atG	25/31	0.105023597225796	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.833057843986851	0		219	276	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112079	115112079	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	543	598	1	ENST00000257566.3:c.1661C>A	p.Ser554Ter	p.S554*	ENST00000257566	NM_016569.3	554	tCg/tAg	7/8	1	2	FACETS	0.963	0.925	1	0.963	0.925	1	CLONAL	1	TRUE	1	0.833057843986851	2		599	1354	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951162	48951162	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	158	254	0	ENST00000267163.4:c.1324G>T	p.Gly442Ter	p.G442*	ENST00000267163	NM_000321.2	442	Gga/Tga	13/27	0.833057843986851	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.833057843986851	1		254	211	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715500	117715500	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	103	255	0	ENST00000368508.3:c.989T>C	p.Val330Ala	p.V330A	ENST00000368508	NM_002944.2	330	gTt/gCt	10/43	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.833057843986851	2		255	219	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509775	106509775	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140864387	NA	P-0050741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	275	429	1	ENST00000359195.3:c.1769C>T	p.Pro590Leu	p.P590L	ENST00000359195	NM_002649.2	590	cCt/cTt	2/11	1	2	FACETS	0.996	0.942	1	0.996	0.942	1	CLONAL	1	TRUE	1	0.833057843986851	2		430	663	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	15	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.215	0.156	0.286	0.215	0.156	0.286	SUBCLONAL	1	TRUE	1	0.32	2		334	436	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484596	57484596	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913494	NA	P-0050742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	70	503	0	ENST00000371085.3:c.680A>G	p.Gln227Arg	p.Q227R	ENST00000371085	NM_000516.4	227	cAg/cGg	9/13	1	2	FACETS	0.827	0.722	0.94	0.827	0.722	0.94	CLONAL	1	TRUE	1	0.32	2		503	529	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355080	73355080	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	35	405	0	ENST00000377767.4:c.290A>G	p.Glu97Gly	p.E97G	ENST00000377767	NM_014953.3	97	gAa/gGa	2/21	1	2	FACETS	0.432	0.354	0.521	0.432	0.354	0.521	SUBCLONAL	1	TRUE	1	0.32	2		405	506	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774905	73774905	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	33	577	0	ENST00000254810.4:c.268A>G	p.Ile90Val	p.I90V	ENST00000254810	NM_005324.3	90	Atc/Gtc	3/4	1	2	FACETS	0.333	0.27	0.404	0.333	0.27	0.404	SUBCLONAL	1	TRUE	1	0.32	2		577	619	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755548	39755548	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	29	513	0	ENST00000288319.7:c.1217C>A	p.Ser406Ter	p.S406*	ENST00000288319	NM_182918.3	406	tCa/tAa	10/10	1	2	FACETS	0.397	0.318	0.488	0.397	0.318	0.488	SUBCLONAL	1	TRUE	1	0.32	2		513	456	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	36	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.917	0.753	1	0.917	0.753	1	CLONAL	1	TRUE	1	0.17	2		334	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0050743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	42	467	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	1	2	FACETS	0.703	0.585	0.834	0.703	0.585	0.834	SUBCLONAL	1	TRUE	1	0.17	2		467	703	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128321993	128321993	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	47	530	0	ENST00000265960.3:c.767A>C	p.Lys256Thr	p.K256T	ENST00000265960	NM_001006617.1	256	aAg/aCg	6/12	1	2	FACETS	0.711	0.598	0.836	0.711	0.598	0.836	SUBCLONAL	1	TRUE	1	0.17	2		530	778	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	37	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.288294053389768	4	FACETS	1	0.854	1	1	0.854	1	CLONAL	2	FALSE	2	0.3	4		334	157	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0050744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	66	580	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.205449629119012	2	FACETS	0.797	0.699	0.901	0.797	0.699	0.901	CLONAL	2	FALSE	0	0.3	2		580	276	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0050744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	20	550	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.164568131778231	2	FACETS	0.567	0.435	0.722	0.284	0.217	0.361	INDETERMINATE	1	FALSE	0	0.3	2		550	235	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495442	149495442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576668629	NA	P-0050744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	58	889	1	ENST00000261799.4:c.3205G>A	p.Glu1069Lys	p.E1069K	ENST00000261799	NM_002609.3	1069	Gaa/Aaa	23/23	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	FALSE	1	0.3	2		890	337	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535316	66535316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	26	603	2	ENST00000273854.3:c.145G>A	p.Ala49Thr	p.A49T	ENST00000273854	NM_004439.5	49	Gca/Aca	1/18	1	2	FACETS	0.561	0.445	0.694	0.561	0.445	0.694	SUBCLONAL	1	FALSE	1	0.3	2		605	309	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	288	580	31	ENST00000269305.4:c.859G>T	p.Glu287Ter	p.E287*	ENST00000269305	NM_001126112.2	287	Gag/Tag	8/11	0.602685462206722	1	FACETS	0.994	0.941	1	0.994	0.941	1	CLONAL	1	TRUE	0	0.602685462206722	1		611	672	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940512	71940512	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	147	506	0	ENST00000298229.2:c.663G>C	p.Glu221Asp	p.E221D	ENST00000298229	NM_001567.3	221	gaG/gaC	6/28	1	2	FACETS	0.729	0.667	0.793	0.729	0.667	0.793	SUBCLONAL	1	TRUE	1	0.602685462206722	2		506	669	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942048	17942048	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	289	649	30	ENST00000458235.1:c.2967C>A	p.Ser989Arg	p.S989R	ENST00000458235	NM_000215.3	989	agC/agA	21/24	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.602685462206722	2		679	888	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951905	178951905	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	158	327	9	ENST00000263967.3:c.2960C>A	p.Ala987Asp	p.A987D	ENST00000263967	NM_006218.2	987	gCt/gAt	21/21	1	2	FACETS	0.925	0.852	1	0.925	0.852	1	CLONAL	1	TRUE	1	0.602685462206722	2		336	567	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978530	70978530	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	185	452	24	ENST00000276594.2:c.1123G>C	p.Asp375His	p.D375H	ENST00000276594	NM_024504.3	375	Gat/Cat	5/8	0.602685462206722	1	FACETS	0.962	0.898	1	0.962	0.898	1	CLONAL	1	TRUE	0	0.602685462206722	1		476	446	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933908	39933908	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	274	717	36	ENST00000378444.4:c.691C>G	p.Gln231Glu	p.Q231E	ENST00000378444	NM_001123385.1	231	Cag/Gag	4/15	0.602685462206722	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.602685462206722	1		753	607	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	165	518	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.860771747979798	4	FACETS	1	0.921	1	0.5	0.46	0.542	CLONAL	1	TRUE	2	0.860771747979798	4		518	713	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240686	55240686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1217	560	598	0	ENST00000275493.2:c.1930C>T	p.Pro644Ser	p.P644S	ENST00000275493	NM_005228.3	644	Ccg/Tcg	17/28	0.860771747979798	6	FACETS	0.996	0.955	1	0.498	0.477	0.519	CLONAL	2	TRUE	2	0.860771747979798	6		598	1777	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781572	9781572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1287221059	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	617	550	0	ENST00000377346.4:c.1882G>A	p.Glu628Lys	p.E628K	ENST00000377346	NM_005026.3	628	Gag/Aag	15/24	0.860771747979798	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.860771747979798	4		550	1333	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254672	16254672	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	201	370	0	ENST00000375759.3:c.1937C>G	p.Ser646Cys	p.S646C	ENST00000375759	NM_015001.2	646	tCc/tGc	11/15	0.860771747979798	4	FACETS	0.956	0.887	1	0.478	0.443	0.514	CLONAL	1	TRUE	2	0.860771747979798	4		370	909	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259484	16259484	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	470	466	0	ENST00000375759.3:c.6749C>T	p.Pro2250Leu	p.P2250L	ENST00000375759	NM_015001.2	2250	cCc/cTc	11/15	0.860771747979798	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	2	0.860771747979798	4		466	1002	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089629	27089630	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	618	586	0	ENST00000324856.7:c.2585_2586delinsTA	p.Ser862Leu	p.S862L	ENST00000324856	NM_006015.4	862	tCC/tTA	8/20	0.860771747979798	4	FACETS	0.991	0.956	1	0.991	0.956	1	CLONAL	2	TRUE	2	0.860771747979798	4		586	1348	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107204	27107204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1476138197	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	454	390	0	ENST00000324856.7:c.6815C>T	p.Ser2272Leu	p.S2272L	ENST00000324856	NM_006015.4	2272	tCa/tTa	20/20	0.860771747979798	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.860771747979798	4		390	943	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28600566	28600566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	453	406	0	ENST00000253063.3:c.917C>T	p.Pro306Leu	p.P306L	ENST00000253063	NM_031459.4	306	cCc/cTc	7/10	0.860771747979798	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.860771747979798	4		406	973	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812601	43812601	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	272	477	0	ENST00000372470.3:c.1304G>A	p.Trp435Ter	p.W435*	ENST00000372470	NM_005373.2	435	tGg/tAg	8/12	0.860771747979798	4	FACETS	1	0.978	1	0.544	0.511	0.579	CLONAL	1	TRUE	2	0.860771747979798	4		477	1080	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166491	118166491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	334	342	1	ENST00000369448.3:c.1001C>T	p.Ser334Phe	p.S334F	ENST00000369448	NM_017709.3	334	tCc/tTc	2/2	0.860771747979798	4	FACETS	0.99	0.943	1	0.99	0.943	1	CLONAL	2	TRUE	2	0.860771747979798	4		343	729	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874179	155874187	+	inframe_deletion	In_Frame_Del	DEL	TAAGCTGTT	TAAGCTGTT	-	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	439	455	0	ENST00000368323.3:c.344_352del	p.Lys115_Leu117del	p.K115_L117del	ENST00000368323	NM_006912.5	115	aAACAGCTTAtt/att	5/6	0.81180115281683	4	FACETS	0.883	0.844	0.922	0.883	0.844	0.922	CLONAL	2	TRUE	2	0.860771747979798	4		455	1075	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849018	156849018	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	547	587	0	ENST00000524377.1:c.1910G>A	p.Gly637Glu	p.G637E	ENST00000524377	NM_002529.3	637	gGg/gAg	15/17	0.81180115281683	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.860771747979798	4		587	1159	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849818	156849818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761967383	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	238	491	0	ENST00000524377.1:c.2074C>T	p.Arg692Cys	p.R692C	ENST00000524377	NM_002529.3	692	Cgc/Tgc	16/17	0.81180115281683	4	FACETS	1	0.945	1	0.506	0.473	0.541	CLONAL	1	TRUE	2	0.860771747979798	4		491	1016	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927446	245927446	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	365	384	0	ENST00000388985.4:c.1082T>A	p.Phe361Tyr	p.F361Y	ENST00000388985		361	tTt/tAt	11/12	0.775329445090173	6	FACETS	0.982	0.932	1	0.655	0.621	0.689	CLONAL	2	TRUE	3	0.860771747979798	6		384	1175	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310845	123310845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1474313509	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	242	468	0	ENST00000358487.5:c.583G>A	p.Gly195Arg	p.G195R	ENST00000358487	NM_000141.4	195	Ggg/Agg	5/18	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.860771747979798	2		468	539	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417854	32417854	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	215	410	0	ENST00000332351.3:c.1198A>G	p.Lys400Glu	p.K400E	ENST00000332351	NM_024426.4	400	Aag/Gag	7/10	1	2	FACETS	0.957	0.898	1	0.957	0.898	1	CLONAL	1	TRUE	1	0.860771747979798	2		410	522	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115743	108115744	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	79	178	0	ENST00000278616.4:c.891_892delinsTT	p.Gln298Ter	p.Q298*	ENST00000278616	NM_000051.3	297	acCCaa/acTTaa	7/63	0.189425431802637	3	FACETS	1	0.979	1	0.698	0.628	0.77	INDETERMINATE	1	TRUE	1	0.860771747979798	3		178	188	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231198	46231198	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	241	264	0	ENST00000334344.6:c.1118G>A	p.Arg373Lys	p.R373K	ENST00000334344	NM_152641.2	373	aGa/aAa	9/21	0.860771747979798	4	FACETS	0.939	0.885	0.993			1	CLONAL	2	TRUE	NA	0.860771747979798	4		264	555	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445046	49445046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757089451	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	246	529	0	ENST00000301067.7:c.2420C>T	p.Ser807Phe	p.S807F	ENST00000301067	NM_003482.3	807	tCc/tTc	10/54	0.84775656740758	3	FACETS	1	0.963	1	0.518	0.486	0.551	CLONAL	1	TRUE	1	0.860771747979798	3		529	789	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144477	58144477	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	106	259	0	ENST00000257904.6:c.594G>A	p.Trp198Ter	p.W198*	ENST00000257904	NM_000075.3	198	tgG/tgA	5/8	0.84775656740758	3	FACETS	0.833	0.752	0.918	0.416	0.376	0.459	CLONAL	1	TRUE	1	0.860771747979798	3		259	423	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111855952	111855952	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	603	506	0	ENST00000341259.2:c.3G>A	p.Met1?	p.M1?	ENST00000341259	NM_005475.2	1	atG/atA	2/8	0.84775656740758	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.860771747979798	3		506	986	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115401	115115401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs910695260	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	201	449	0	ENST00000257566.3:c.925G>A	p.Gly309Ser	p.G309S	ENST00000257566	NM_016569.3	309	Ggc/Agc	5/8	0.84775656740758	3	FACETS	0.97	0.902	1	0.485	0.451	0.52	CLONAL	1	TRUE	1	0.860771747979798	3		449	689	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570348	95570349	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	221	272	0	ENST00000393063.1:c.3384_3385delinsTT	p.Pro1129Ser	p.P1129S	ENST00000393063	NM_030621.3	1128	gtCCct/gtTTct	22/28	0.860771747979798	3	FACETS	0.907	0.858	0.955	0.907	0.858	0.955	CLONAL	2	TRUE	1	0.860771747979798	3		272	405	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058882	42058882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	330	328	0	ENST00000219905.7:c.8602C>T	p.Pro2868Ser	p.P2868S	ENST00000219905	NM_001164273.1	2868	Cct/Tct	24/24	0.81180115281683	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.860771747979798	4		328	655	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43773116	43773116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775544576	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	416	476	1	ENST00000382044.4:c.476C>T	p.Thr159Ile	p.T159I	ENST00000382044	NM_001141980.1	159	aCt/aTt	5/28	0.81180115281683	4	FACETS	0.962	0.92	1	0.962	0.92	1	CLONAL	2	TRUE	2	0.860771747979798	4		477	935	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823918	3823919	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	221	518	0	ENST00000262367.5:c.2296_2297delinsTT	p.Pro766Phe	p.P766F	ENST00000262367	NM_004380.2	766	CCt/TTt	13/31	0.84775656740758	3	FACETS	0.925	0.863	0.989	0.463	0.431	0.495	CLONAL	1	TRUE	1	0.860771747979798	3		518	794	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858006	9858006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	166	408	0	ENST00000330684.3:c.3395C>T	p.Pro1132Leu	p.P1132L	ENST00000330684	NM_001134407.1	1132	cCa/cTa	13/13	0.84775656740758	3	FACETS	0.854	0.787	0.923	0.427	0.393	0.462	CLONAL	1	TRUE	1	0.860771747979798	3		408	646	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934567	9934567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	187	448	1	ENST00000330684.3:c.1588G>A	p.Glu530Lys	p.E530K	ENST00000330684	NM_001134407.1	530	Gaa/Aaa	7/13	0.84775656740758	3	FACETS	0.928	0.86	0.997	0.464	0.43	0.499	CLONAL	1	TRUE	1	0.860771747979798	3		449	670	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984919	9984919	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	397	419	0	ENST00000330684.3:c.1046C>T	p.Ser349Phe	p.S349F	ENST00000330684	NM_001134407.1	349	tCc/tTc	4/13	0.84775656740758	3	FACETS	0.945	0.908	0.982	0.945	0.908	0.982	CLONAL	2	TRUE	1	0.860771747979798	3		419	698	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031882	10031882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	232	520	0	ENST00000330684.3:c.941C>T	p.Pro314Leu	p.P314L	ENST00000330684	NM_001134407.1	314	cCc/cTc	3/13	0.84775656740758	3	FACETS	0.946	0.885	1	0.473	0.442	0.505	CLONAL	1	TRUE	1	0.860771747979798	3		520	815	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032089	10032089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	442	448	0	ENST00000330684.3:c.734C>T	p.Ser245Phe	p.S245F	ENST00000330684	NM_001134407.1	245	tCc/tTc	3/13	0.84775656740758	3	FACETS	0.993	0.957	1	0.993	0.957	1	CLONAL	2	TRUE	1	0.860771747979798	3		448	740	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347980	89347982	+	missense_variant	Missense_Mutation	TNP	GAC	GAC	AAA	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	574	680	1	ENST00000301030.4:c.4968_4970delinsTTT	p.Glu1656_Ser1657delinsAspLeu	p.E1656_S1657delinsDL	ENST00000301030	NM_001256183.1	1656	gaGTCg/gaTTTg	9/13	0.84775656740758	3	FACETS	0.977	0.946	1	0.977	0.946	1	CLONAL	2	TRUE	1	0.860771747979798	3		681	976	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351379	89351379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1040338311	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	292	631	2	ENST00000301030.4:c.1571C>T	p.Ser524Leu	p.S524L	ENST00000301030	NM_001256183.1	524	tCg/tTg	9/13	0.84775656740758	3	FACETS	0.972	0.916	1	0.486	0.458	0.515	CLONAL	1	TRUE	1	0.860771747979798	3		633	998	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044500	12044500	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	138	297	0	ENST00000353533.5:c.1123G>C	p.Val375Leu	p.V375L	ENST00000353533	NM_003010.3	375	Gtt/Ctt	11/11	0.860771747979798	3	FACETS	0.982	0.9	1	0.491	0.45	0.534	CLONAL	1	TRUE	1	0.860771747979798	3		297	467	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16001803	16001803	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771889820	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	166	341	0	ENST00000268712.3:c.2698C>T	p.Pro900Ser	p.P900S	ENST00000268712	NM_006311.3	900	Cct/Tct	21/46	0.860771747979798	3	FACETS	0.935	0.863	1	0.468	0.431	0.505	CLONAL	1	TRUE	1	0.860771747979798	3		341	590	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556424	29556424	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	347	386	0	ENST00000356175.3:c.2791C>T	p.Pro931Ser	p.P931S	ENST00000356175	NM_000267.3	931	Cca/Tca	21/57	0.253114476180965	5	FACETS	1	0.991	1	0.662	0.636	0.688	INDETERMINATE	3	TRUE	0	0.860771747979798	5		386	558	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654535	29654535	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	189	201	0	ENST00000356175.3:c.5224C>T	p.Gln1742Ter	p.Q1742*	ENST00000356175	NM_000267.3	1742	Caa/Taa	37/57	0.253114476180965	5	FACETS	1	0.958	1	0.612	0.577	0.646	INDETERMINATE	3	TRUE	0	0.860771747979798	5		201	329	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687382	37687382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	418	458	0	ENST00000447079.4:c.4286C>T	p.Ser1429Phe	p.S1429F	ENST00000447079	NM_015083.1	1429	tCt/tTt	14/14	0.253114476180965	5	FACETS	1	0.993	1	0.672	0.648	0.696	INDETERMINATE	3	TRUE	0	0.860771747979798	5		458	662	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554000	63554000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755206242	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	465	447	0	ENST00000307078.5:c.739G>A	p.Val247Met	p.V247M	ENST00000307078	NM_004655.3	247	Gtg/Atg	2/11	0.860771747979798	6	FACETS	1	0.986	1	0.536	0.512	0.56	CLONAL	2	TRUE	2	0.860771747979798	6		447	1372	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117545	70117545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	477	512	0	ENST00000245479.2:c.13G>A	p.Asp5Asn	p.D5N	ENST00000245479	NM_000346.3	5	Gac/Aac	1/3	0.860771747979798	6	FACETS	1	0.971	1	0.511	0.488	0.534	CLONAL	2	TRUE	2	0.860771747979798	6		512	1477	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78931475	78931475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1236	594	634	0	ENST00000306801.3:c.3422C>T	p.Ser1141Leu	p.S1141L	ENST00000306801	NM_020761.2	1141	tCa/tTa	29/34	0.860771747979798	6	FACETS	1	0.978	1	0.513	0.492	0.534	CLONAL	2	TRUE	2	0.860771747979798	6		634	1830	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619164	1619164	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	678	682	0	ENST00000344749.5:c.1396C>T	p.Pro466Ser	p.P466S	ENST00000344749	NM_001136139.2	466	Ccc/Tcc	16/19	0.81180115281683	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.860771747979798	4		682	1437	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244371	5244372	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	625	681	1	ENST00000357368.4:c.1110_1111delinsAT	p.Ser371Cys	p.S371C	ENST00000357368	NM_002850.3	370	aaGAgc/aaATgc	11/38	0.81180115281683	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.860771747979798	4		682	1347	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251567	10251567	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	469	497	0	ENST00000340748.4:c.3365C>T	p.Ser1122Phe	p.S1122F	ENST00000340748		1122	tCc/tTc	31/40	0.81180115281683	4	FACETS	0.927	0.888	0.965	0.927	0.888	0.965	CLONAL	2	TRUE	2	0.860771747979798	4		497	1094	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291043	10291043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	411	446	0	ENST00000340748.4:c.428C>T	p.Ser143Phe	p.S143F	ENST00000340748		143	tCc/tTc	4/40	0.81180115281683	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.860771747979798	4		446	840	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272326	15272326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545621067	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	637	734	0	ENST00000263388.2:c.6113G>A	p.Gly2038Asp	p.G2038D	ENST00000263388	NM_000435.2	2038	gGc/gAc	33/33	0.81180115281683	4	FACETS	0.959	0.925	0.993	0.959	0.925	0.993	CLONAL	2	TRUE	2	0.860771747979798	4		734	1436	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290984	15290984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1438626607	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	323	701	1	ENST00000263388.2:c.3226C>T	p.Arg1076Cys	p.R1076C	ENST00000263388	NM_000435.2	1076	Cgt/Tgt	20/33	0.81180115281683	4	FACETS	0.937	0.883	0.992	0.468	0.441	0.496	CLONAL	1	TRUE	2	0.860771747979798	4		702	1491	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297970	15297970	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	723	733	0	ENST00000263388.2:c.1786A>G	p.Lys596Glu	p.K596E	ENST00000263388	NM_000435.2	596	Aaa/Gaa	11/33	0.81180115281683	4	FACETS	0.983	0.951	1	0.983	0.951	1	CLONAL	2	TRUE	2	0.860771747979798	4		733	1590	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353815	15353815	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780028668	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	289	276	0	ENST00000263377.2:c.3065C>T	p.Pro1022Leu	p.P1022L	ENST00000263377	NM_058243.2	1022	cCg/cTg	14/20	0.81180115281683	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.860771747979798	4		276	575	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753353	42753353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1162	735	751	0	ENST00000222329.4:c.911C>T	p.Ser304Phe	p.S304F	ENST00000222329	NM_006494.2	304	tCc/tTc	4/4	0.764902872242421	5	FACETS	1	0.984	1	0.688	0.664	0.712	CLONAL	2	TRUE	2	0.860771747979798	5		751	1897	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42759142	42759142	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	329	377	0	ENST00000222329.4:c.10C>T	p.Pro4Ser	p.P4S	ENST00000222329	NM_006494.2	4	Ccg/Tcg	1/4	0.764902872242421	5	FACETS	0.912	0.864	0.961	0.608	0.576	0.641	CLONAL	2	TRUE	2	0.860771747979798	5		377	960	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705240	52705240	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	412	396	1	ENST00000322088.6:c.122C>T	p.Ala41Val	p.A41V	ENST00000322088	NM_014225.5	41	gCc/gTc	2/15	0.367288589234889	6	FACETS	0.994	0.951	1	0.994	0.951	1	INDETERMINATE	3	TRUE	3	0.860771747979798	6		397	874	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451826	29451826	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	299	388	0	ENST00000389048.3:c.2739G>A	p.Trp913Ter	p.W913*	ENST00000389048	NM_004304.4	913	tgG/tgA	16/29	0.84775656740758	3	FACETS	0.941	0.898	0.984	0.941	0.898	0.984	CLONAL	2	TRUE	1	0.860771747979798	3		388	528	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917881	29917881	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	225	507	1	ENST00000389048.3:c.788-1G>A		p.X263_splice	ENST00000389048	NM_004304.4	263			0.84775656740758	3	FACETS	1	0.961	1	0.519	0.485	0.553	CLONAL	1	TRUE	1	0.860771747979798	3		508	721	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118940	61118940	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	173	388	0	ENST00000295025.8:c.133C>T	p.Arg45Ter	p.R45*	ENST00000295025	NM_002908.2	45	Cga/Tga	2/11	0.860771747979798	3	FACETS	1	0.929	1	0.502	0.464	0.54	CLONAL	1	TRUE	1	0.860771747979798	3		388	573	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873080	136873080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	363	349	0	ENST00000241393.3:c.418C>T	p.His140Tyr	p.H140Y	ENST00000241393	NM_003467.2	140	Cac/Tac	2/2	0.81180115281683	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.860771747979798	4		349	749	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268449	198268449	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	372	411	0	ENST00000335508.6:c.1579G>A	p.Gly527Arg	p.G527R	ENST00000335508	NM_012433.2	527	Gga/Aga	12/25	0.764902872242421	5	FACETS	0.865	0.827	0.903	0.865	0.827	0.903	CLONAL	3	TRUE	2	0.860771747979798	5		411	763	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295801	212295801	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1423325504	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	512	418	0	ENST00000342788.4:c.2512C>T	p.Arg838Ter	p.R838*	ENST00000342788	NM_005235.2	838	Cga/Tga	21/28	0.764902872242421	5	FACETS	0.932	0.898	0.966	0.932	0.898	0.966	CLONAL	3	TRUE	2	0.860771747979798	5		418	975	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794454	242794454	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	297	652	0	ENST00000334409.5:c.488C>T	p.Ala163Val	p.A163V	ENST00000334409	NM_005018.2	163	gCc/gTc	3/5	0.832733621342359	4	FACETS	0.951	0.894	1			1	CLONAL	1	TRUE	NA	0.860771747979798	4		652	1350	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546761	9546761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768724288	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	335	337	0	ENST00000353224.5:c.1261G>A	p.Asp421Asn	p.D421N	ENST00000353224	NM_177990.2	421	Gac/Aac	5/10	0.81180115281683	4	FACETS	0.964	0.918	1	0.964	0.918	1	CLONAL	2	TRUE	2	0.860771747979798	4		337	751	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730801	40730801	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	208	483	0	ENST00000373198.4:c.3734G>A	p.Gly1245Glu	p.G1245E	ENST00000373198	NM_133170.3	1245	gGa/gAa	27/32	0.81180115281683	4	FACETS	0.867	0.805	0.932	0.434	0.402	0.466	CLONAL	1	TRUE	2	0.860771747979798	4		483	1037	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400125	41400125	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	198	436	0	ENST00000373198.4:c.634C>T	p.Gln212Ter	p.Q212*	ENST00000373198	NM_133170.3	212	Cag/Tag	5/32	0.81180115281683	4	FACETS	0.898	0.832	0.967	0.449	0.416	0.484	CLONAL	1	TRUE	2	0.860771747979798	4		436	953	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69998309	69998310	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	179	302	0	ENST00000394351.3:c.549_550delinsAA	p.Glu184Lys	p.E184K	ENST00000394351	NM_000248.3	183	agGGag/agAAag	5/9	0.860771747979798	3	FACETS	0.963	0.892	1	0.481	0.446	0.518	CLONAL	1	TRUE	1	0.860771747979798	3		302	618	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683372	182683372	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	130	353	0	ENST00000292782.4:c.173G>T	p.Gly58Val	p.G58V	ENST00000292782	NM_020640.2	58	gGa/gTa	2/7	0.860771747979798	4	FACETS	0.735	0.667	0.806	0.367	0.333	0.403	SUBCLONAL	1	TRUE	2	0.860771747979798	4		353	765	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197612	106197612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	316	251	0	ENST00000380013.4:c.5945C>T	p.Ser1982Phe	p.S1982F	ENST00000380013	NM_001127208.2	1982	tCc/tTc	11/11	0.860771747979798	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.860771747979798	3		251	504	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629247	187629247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	438	490	0	ENST00000441802.2:c.1735C>T	p.Pro579Ser	p.P579S	ENST00000441802	NM_005245.3	579	Ccc/Tcc	2/27	0.860771747979798	4	FACETS	0.959	0.919	1			1	CLONAL	2	TRUE	NA	0.860771747979798	4		490	987	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	156	332	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.860771747979798	2		332	354	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526267	31526267	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1039084165	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	334	614	0	ENST00000344624.3:c.773G>A	p.Arg258Lys	p.R258K	ENST00000344624		258	aGg/aAg	2/33	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.860771747979798	2		614	750	SUCCESS
APC	324	MSKCC	GRCh37	5	112090679	112090679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1270741856	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	234	248	0	ENST00000257430.4:c.92C>T	p.Ser31Phe	p.S31F	ENST00000257430	NM_000038.5	31	tCc/tTc	2/16	0.860771747979798	2	FACETS	0.992	0.961	1	0.992	0.961	1	CLONAL	2	TRUE	0	0.860771747979798	2		248	274	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721042	176721042	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1418961998	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	219	418	0	ENST00000439151.2:c.6673C>T	p.Pro2225Ser	p.P2225S	ENST00000439151	NM_022455.4	2225	Cca/Tca	23/23	0.860771747979798	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.860771747979798	1		418	278	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057572	180057572	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	290	566	0	ENST00000261937.6:c.383C>T	p.Ser128Phe	p.S128F	ENST00000261937	NM_182925.4	128	tCc/tTc	3/30	0.860771747979798	1	FACETS	0.994	0.959	1	0.994	0.959	1	CLONAL	1	TRUE	0	0.860771747979798	1		566	386	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673065	30673065	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1362687413	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	238	574	1	ENST00000376406.3:c.3895C>T	p.Arg1299Ter	p.R1299*	ENST00000376406	NM_014641.2	1299	Cga/Tga	10/15	0.84775656740758	3	FACETS	0.889	0.831	0.948	0.444	0.415	0.474	CLONAL	1	TRUE	1	0.860771747979798	3		575	890	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168622	32168623	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	498	568	1	ENST00000375023.3:c.4300_4301delinsTT	p.Pro1434Phe	p.P1434F	ENST00000375023	NM_004557.3	1434	CCt/TTt	23/30	0.84775656740758	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.860771747979798	3		569	821	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190296	32190296	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	364	340	0	ENST00000375023.3:c.443G>A	p.Gly148Glu	p.G148E	ENST00000375023	NM_004557.3	148	gGa/gAa	3/30	0.84775656740758	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.860771747979798	3		340	574	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552997	106552997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	503	502	0	ENST00000369096.4:c.962C>T	p.Pro321Leu	p.P321L	ENST00000369096	NM_001198.3	321	cCc/cTc	5/7	0.84775656740758	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.860771747979798	3		502	826	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609888	117609888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	178	392	1	ENST00000368508.3:c.6811G>A	p.Gly2271Arg	p.G2271R	ENST00000368508	NM_002944.2	2271	Ggg/Agg	43/43	0.84775656740758	3	FACETS	0.875	0.809	0.943	0.438	0.404	0.472	CLONAL	1	TRUE	1	0.860771747979798	3		393	676	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631298	117631298	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	331	394	1	ENST00000368508.3:c.6380G>A	p.Trp2127Ter	p.W2127*	ENST00000368508	NM_002944.2	2127	tGg/tAg	40/43	0.84775656740758	3	FACETS	0.95	0.909	0.991	0.95	0.909	0.991	CLONAL	2	TRUE	1	0.860771747979798	3		395	579	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522243	157522243	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	247	529	1	ENST00000346085.5:c.4515G>T	p.Arg1505Ser	p.R1505S	ENST00000346085	NM_020732.3	1505	agG/agT	18/20	0.84775656740758	3	FACETS	0.908	0.85	0.967	0.454	0.425	0.484	CLONAL	1	TRUE	1	0.860771747979798	3		530	904	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522622	157522623	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	116	348	0	ENST00000346085.5:c.4894_4894+1delinsAA		p.X1632_splice	ENST00000346085	NM_020732.3	1632		18/20	0.84775656740758	3	FACETS	0.733	0.663	0.806	0.366	0.331	0.403	SUBCLONAL	1	TRUE	1	0.860771747979798	3		348	526	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974094	2974095	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	317	325	0	ENST00000396946.4:c.1510_1511delinsAT	p.Gly504Ile	p.G504I	ENST00000396946	NM_032415.4	504	GGc/ATc	10/25	0.860771747979798	6	FACETS	0.879	0.83	0.93	0.44	0.415	0.465	CLONAL	2	TRUE	2	0.860771747979798	6		325	1140	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6045540	6045540	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	169	147	0	ENST00000265849.7:c.146C>T	p.Ala49Val	p.A49V	ENST00000265849	NM_000535.5	49	gCt/gTt	2/15	0.860771747979798	6	FACETS	1	0.936	1	0.506	0.468	0.545	CLONAL	2	TRUE	2	0.860771747979798	6		147	528	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214415	55214415	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	428	464	0	ENST00000275493.2:c.541C>T	p.Gln181Ter	p.Q181*	ENST00000275493	NM_005228.3	181	Cag/Tag	4/28	0.860771747979798	6	FACETS	0.983	0.937	1	0.492	0.468	0.516	CLONAL	2	TRUE	2	0.860771747979798	6		464	1376	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55219001	55219001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	370	362	0	ENST00000275493.2:c.574C>T	p.Pro192Ser	p.P192S	ENST00000275493	NM_005228.3	192	Cca/Tca	5/28	0.860771747979798	6	FACETS	1	0.979	1	0.528	0.501	0.555	CLONAL	2	TRUE	2	0.860771747979798	6		362	1108	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140500172	140500172	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	597	543	1	ENST00000288602.6:c.970G>A	p.Asp324Asn	p.D324N	ENST00000288602	NM_004333.4	324	Gac/Aac	7/18	0.81180115281683	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.860771747979798	4		544	1234	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879009	151879009	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1300239688	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	437	494	0	ENST00000262189.6:c.5936C>T	p.Pro1979Leu	p.P1979L	ENST00000262189	NM_170606.2	1979	cCc/cTc	36/59	0.81180115281683	4	FACETS	0.948	0.907	0.988	0.948	0.907	0.988	CLONAL	2	TRUE	2	0.860771747979798	4		494	997	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971187	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	455	496	1	ENST00000304494.5:c.171_172delinsTT	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	57	gcCCga/gcTTga	2/3	0.860771747979798	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.860771747979798	2		497	517	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922039	39922039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	606	270	0	ENST00000378444.4:c.4133C>T	p.Pro1378Leu	p.P1378L	ENST00000378444	NM_001123385.1	1378	cCa/cTa	9/15	0.832733621342359	2	FACETS	1	0.998	1			1	CLONAL	2	TRUE	NA	0.860771747979798	2		270	642	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861645	152861646	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0050746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	438	272	0	ENST00000406277.2:c.107-1_107delinsAA		p.X36_splice	ENST00000406277	NM_152274.4	36		4/7	0.832733621342359		FACETS		0.995	1				CLONAL	2	TRUE	NA	0.860771747979798	2		272	484	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	109	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.113728645504072	3	FACETS	1	0.921	1	1	0.921	1	INDETERMINATE	2	TRUE	1	0.305687357985058	3		436	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0050747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	122	630	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.254037961411429	1	FACETS	0.937	0.847	1	0.937	0.847	1	CLONAL	1	TRUE	0	0.305687357985058	1		630	722	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971115	21971133	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTCGGGTGAGAGTGGCG	GGGTCGGGTGAGAGTGGCG	-	rs730881674	NA	P-0050747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	76	575	0	ENST00000304494.5:c.225_243del	p.Ala76CysfsTer64	p.A76Cfs*64	ENST00000304494	NM_000077.4	75	ccCGCCACTCTCACCCGACCC/cc	2/3	0.305687357985058	1	FACETS	0.496	0.434	0.562	0.496	0.434	0.562	SUBCLONAL	1	TRUE	0	0.305687357985058	1		575	850	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358526	67358526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	90	358	0	ENST00000327367.4:c.34G>A	p.Val12Met	p.V12M	ENST00000327367	NM_005902.3	12	Gtg/Atg	1/9	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.305687357985058	2		358	576	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584808	48584808	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	109	401	0	ENST00000342988.3:c.889del	p.His297IlefsTer39	p.H297Ifs*39	ENST00000342988	NM_005359.5	296	Ccc/cc	7/12	0.254037961411429	1	FACETS	0.845	0.759	0.936	0.845	0.759	0.936	CLONAL	1	TRUE	0	0.305687357985058	1		401	715	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138376589	138376589	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	101	432	0	ENST00000289153.2:c.2885A>G	p.Tyr962Cys	p.Y962C	ENST00000289153	NM_006219.2	962	tAt/tGt	20/22	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.305687357985058	2		432	522	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0050748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	38	384	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.220007514792678	2		384	329	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0050748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	80	496	0	ENST00000269305.4:c.560-2A>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.211973223784124	1	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	0	0.220007514792678	1		496	633	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	157	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.244140572289071	NA		334	447	SUCCESS
APC	324	MSKCC	GRCh37	5	112162945	112162945	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1114167599	NA	P-0050749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	150	278	0	ENST00000257430.4:c.1548+1G>T		p.X516_splice	ENST00000257430	NM_000038.5	516			0.244140572289071	6	FACETS	1	0.957	1	1	0.957	1	CLONAL	5	FALSE	1	0.244140572289071	6		278	350	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591085	67591085	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519839	NA	P-0050749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	214	265	0	ENST00000274335.5:c.1678G>T	p.Asp560Tyr	p.D560Y	ENST00000274335		560	Gac/Tac	12/15	0.244140572289071	6	FACETS	1	0.973	1	1	0.991	1	CLONAL	6	FALSE	1	0.244140572289071	6		265	413	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106861	27106861	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	117	608	0	ENST00000324856.7:c.6472C>T	p.Arg2158Ter	p.R2158*	ENST00000324856	NM_006015.4	2158	Cga/Tga	20/20	1	2	FACETS	0.867	0.784	0.953	1	0.987	1	CLONAL	2	FALSE	1	0.244140572289071	2		608	553	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164733	106164733	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1373336171	NA	P-0050749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	124	332	0	ENST00000380013.4:c.3601C>T	p.Arg1201Cys	p.R1201C	ENST00000380013	NM_001127208.2	1201	Cgc/Tgc	6/11	0.162454527363767	5	FACETS	1	0.938	1	1	0.938	1	CLONAL	3	FALSE	2	0.244140572289071	5		332	446	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990399	81990399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199530350	NA	P-0050749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	85	505	2	ENST00000359376.3:c.3670C>T	p.Arg1224Cys	p.R1224C	ENST00000359376	NM_002661.3	1224	Cgc/Tgc	32/33	0.244818520407424	3	FACETS	1	0.974	1	0.685	0.607	0.769	CLONAL	1	FALSE	1	0.244140572289071	3		507	570	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14317388	14317388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782670869	NA	P-0050749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	70	302	1	ENST00000256196.4:c.122C>T	p.Thr41Met	p.T41M	ENST00000256196		41	aCg/aTg	2/6	0.244818520407424	3	FACETS	0.853	0.748	0.966	0.853	0.748	0.966	CLONAL	2	FALSE	1	0.244140572289071	3		303	377	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539077	187539077	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	68	495	0	ENST00000441802.2:c.8663T>C	p.Val2888Ala	p.V2888A	ENST00000441802	NM_005245.3	2888	gTt/gCt	10/27	0.162454527363767	5	FACETS	1	0.964	1	0.439	0.382	0.501	CLONAL	1	FALSE	2	0.244140572289071	5		495	578	SUCCESS
APC	324	MSKCC	GRCh37	5	112173420	112173420	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167584	NA	P-0050749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	41	321	0	ENST00000257430.4:c.2129del	p.Leu710ProfsTer8	p.L710Pfs*8	ENST00000257430	NM_000038.5	710	cTc/cc	16/16	0.244140572289071	6	FACETS	1	0.934	1	0.251	0.209	0.298	CLONAL	1	FALSE	1	0.244140572289071	6		321	398	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2214514	2214516	+	missense_variant	Missense_Mutation	TNP	GTC	GTC	TTT	novel	NA	P-0050749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	125	702	0	ENST00000398665.3:c.1842_1844delinsTTT	p.Ser615Leu	p.S615L	ENST00000398665	NM_032482.2	614	ctGTCg/ctTTTg	19/28	0.244140572289071	5	FACETS	0.777	0.703	0.856	0.777	0.703	0.856	SUBCLONAL	2	FALSE	3	0.244140572289071	5		702	900	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	209	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.464884980860746	4	FACETS	1	0.951	1	1	0.951	1	CLONAL	3	TRUE	1	0.464884980860746	4		334	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0050750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	168	513	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.449069412939817	1	FACETS	0.942	0.87	1	0.942	0.87	1	CLONAL	1	TRUE	0	0.464884980860746	1		516	589	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670327	134670327	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373140258	NA	P-0050750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	88	348	0	ENST00000398015.3:c.238C>T	p.Arg80Trp	p.R80W	ENST00000398015	NM_004441.4	80	Cgg/Tgg	3/16	1	2	FACETS	0.797	0.709	0.89	0.797	0.709	0.89	SUBCLONAL	1	TRUE	1	0.464884980860746	2		348	475	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389303	8389303	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	92	407	0	ENST00000356435.5:c.4315T>A	p.Phe1439Ile	p.F1439I	ENST00000356435		1439	Ttt/Att	26/35	0.464884980860746	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.464884980860746	1		407	301	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971048	21971077	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGCGCCCCGGCCCGGTGCAGCACCACCA	GCCGCGCCCCGGCCCGGTGCAGCACCACCA	C	novel	NA	P-0050750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	182	475	0	ENST00000304494.5:c.281_310delinsG	p.Leu94ArgfsTer16	p.L94Rfs*16	ENST00000304494	NM_000077.4	94	cTGGTGGTGCTGCACCGGGCCGGGGCGCGGCtg/cGtg	2/3	0.464884980860746	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.464884980860746	1		475	580	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0050753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	250	551	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.915	0.86	0.971	0.915	0.86	0.971	CLONAL	1	TRUE	1	0.758293739889155	2		551	721	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0050753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	423	853	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.758293739889155	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.758293739889155	1		853	680	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692892	89692892	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554898129	NA	P-0050753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	80	279	0	ENST00000371953.3:c.376G>T	p.Ala126Ser	p.A126S	ENST00000371953	NM_000314.4	126	Gct/Tct	5/9	1	2	FACETS	0.784	0.699	0.873	0.784	0.699	0.873	SUBCLONAL	1	TRUE	1	0.758293739889155	2		279	269	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992720	68992721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs764112302	NA	P-0050753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	119	391	7	ENST00000288368.4:c.1693dup	p.Ser565PhefsTer3	p.S565Ffs*3	ENST00000288368	NM_024870.2	562	cgt/cgTt	16/40	1	2	FACETS	0.727	0.661	0.795	0.727	0.661	0.795	SUBCLONAL	1	TRUE	1	0.758293739889155	2		398	432	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	118	349	0	ENST00000371953.3:c.511C>G	p.Gln171Glu	p.Q171E	ENST00000371953	NM_000314.4	171	Cag/Gag	6/9	1	2	FACETS	0.926	0.846	1	0.926	0.846	1	CLONAL	1	TRUE	1	0.758293739889155	2		349	336	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047501	49047501	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0050753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	104	308	0	ENST00000267163.4:c.2495T>G	p.Leu832Ter	p.L832*	ENST00000267163	NM_000321.2	832	tTa/tGa	24/27	0.758293739889155	1	FACETS	0.951	0.879	1	0.951	0.879	1	CLONAL	1	TRUE	0	0.758293739889155	1		308	179	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591082	67591102	+	inframe_deletion	In_Frame_Del	DEL	ATTGACAAACGTATGAACAGC	ATTGACAAACGTATGAACAGC	-	novel	NA	P-0050753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	156	251	0	ENST00000274335.5:c.1678_1698del	p.Asp560_Ile566del	p.D560_I566del	ENST00000274335		559	ATTGACAAACGTATGAACAGC/-	12/15	0.7549925051523	2	FACETS	0.918	0.869	0.965	0.918	0.869	0.965	CLONAL	2	TRUE	0	0.758293739889155	2		251	224	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189032	38189032	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	360	492	0	ENST00000317025.8:c.982C>G	p.Arg328Gly	p.R328G	ENST00000317025	NM_023034.1	328	Cga/Gga	5/24	0.687791977474986	3	FACETS	0.933	0.892	0.974	0.933	0.892	0.974	CLONAL	2	TRUE	1	0.758293739889155	3		492	702	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0050754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	39	221	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	1	0.908	1	1	0.973	1	CLONAL	2	TRUE	1	0.312276573821979	2		221	114	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0050754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	81	320	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.816	0.725	0.91	1	0.981	1	CLONAL	2	TRUE	1	0.312276573821979	2		320	318	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711887	89711887	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776673	NA	P-0050754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	58	326	0	ENST00000371953.3:c.507del	p.Ser170ValfsTer13	p.S170Vfs*13	ENST00000371953	NM_000314.4	169	Ccc/cc	6/9	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.312276573821979	2		326	286	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835781	68835781	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060501215	NA	P-0050754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	133	401	0	ENST00000261769.5:c.377del	p.Pro126ArgfsTer89	p.P126Rfs*89	ENST00000261769	NM_004360.3	124	cgC/cg	3/16	0.11553714245895	4	FACETS	0.877	0.799	0.959			1	INDETERMINATE	2	TRUE	NA	0.312276573821979	4		401	637	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052633	42052633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	146	364	1	ENST00000219905.7:c.7304G>A	p.Arg2435Gln	p.R2435Q	ENST00000219905	NM_001164273.1	2435	cGg/cAg	20/24	1	2	FACETS	0.88	0.808	0.955	1	0.99	1	CLONAL	2	TRUE	1	0.312276573821979	2		365	531	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152566	56152566	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	52	281	0	ENST00000399503.3:c.622C>T	p.Arg208Ter	p.R208*	ENST00000399503	NM_005921.1	208	Cga/Tga	2/20	1	2	FACETS	0.812	0.701	0.931	1	0.971	1	CLONAL	2	TRUE	1	0.312276573821979	2		281	205	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090482	37090482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	18	359	0	ENST00000231790.2:c.2077G>A	p.Glu693Lys	p.E693K	ENST00000231790	NM_000249.3	693	Gag/Aag	18/19	1	2	FACETS	0.342	0.257	0.443	0.342	0.257	0.443	SUBCLONAL	1	TRUE	1	0.312276573821979	2		359	337	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195481	102195481	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	20	354	0	ENST00000263464.3:c.241A>C	p.Ser81Arg	p.S81R	ENST00000263464	NM_001165.4	81	Agt/Cgt	2/9	1	2	FACETS	0.437	0.334	0.558	0.437	0.334	0.558	SUBCLONAL	1	TRUE	1	0.312276573821979	2		354	293	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800486	32800486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773325619	NA	P-0050754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	42	555	0	ENST00000374899.4:c.1061G>A	p.Arg354His	p.R354H	ENST00000374899	NM_018833.2	354	cGc/cAc	6/12	1	2	FACETS	0.357	0.297	0.424	0.357	0.297	0.424	SUBCLONAL	1	TRUE	1	0.312276573821979	2		555	754	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105562	27105563	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0050754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	258	423	0	ENST00000324856.7:c.5175dup	p.Glu1726Ter	p.E1726*	ENST00000324856	NM_006015.4	1725	att/aTtt	20/20	0.312276573821979	3	FACETS	1	0.955	1	1	0.993	1	CLONAL	4	TRUE	0	0.312276573821979	3		423	475	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759560	133759560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755654666	NA	P-0050754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	56	660	0	ENST00000318560.5:c.1883C>T	p.Pro628Leu	p.P628L	ENST00000318560	NM_005157.4	628	cCg/cTg	11/11	1	2	FACETS	0.421	0.359	0.489	0.421	0.359	0.489	SUBCLONAL	1	TRUE	1	0.312276573821979	2		660	852	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720664	89720664	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1114167648	NA	P-0050754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	62	278	0	ENST00000371953.3:c.815A>C	p.His272Pro	p.H272P	ENST00000371953	NM_000314.4	272	cAc/cCc	8/9	1	2	FACETS	0.82	0.717	0.93	1	0.976	1	CLONAL	2	TRUE	1	0.312276573821979	2		278	242	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239838	105239838	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	96	588	0	ENST00000349310.3:c.782T>C	p.Leu261Pro	p.L261P	ENST00000349310	NM_001014432.1	261	cTg/cCg	10/15	1	2	FACETS	0.782	0.697	0.874	0.782	0.697	0.874	SUBCLONAL	1	TRUE	1	0.312276573821979	2		588	786	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660465	67660465	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	89	292	0	ENST00000264010.4:c.1365C>G	p.His455Gln	p.H455Q	ENST00000264010	NM_006565.3	455	caC/caG	8/12	0.11553714245895	4	FACETS	1	0.915	1			1	INDETERMINATE	2	TRUE	NA	0.312276573821979	4		292	364	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242920	142242921	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0050754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	35	465	0	ENST00000350721.4:c.4066dup	p.Glu1356GlyfsTer20	p.E1356Gfs*20	ENST00000350721	NM_001184.3	1356	gaa/gGaa	22/47	1	2	FACETS	0.752	0.619	0.901	0.752	0.619	0.901	CLONAL	1	TRUE	1	0.312276573821979	2		465	298	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372767	81372767	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	28	367	0	ENST00000222390.5:c.767A>G	p.Asp256Gly	p.D256G	ENST00000222390	NM_000601.4	256	gAt/gGt	7/18	1	2	FACETS	0.539	0.431	0.661	0.539	0.431	0.661	SUBCLONAL	1	TRUE	1	0.312276573821979	2		367	333	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932436	39932436	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	71	561	0	ENST00000378444.4:c.2163del	p.Leu722TrpfsTer8	p.L722Wfs*8	ENST00000378444	NM_001123385.1	721	ggG/gg	4/15	0.312276573821979	1	FACETS	0.827	0.724	0.938	0.827	0.724	0.938	CLONAL	1	TRUE	0	0.312276573821979	1		561	464	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338650	70338650	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	127	505	0	ENST00000374080.3:c.46C>G	p.Arg16Gly	p.R16G	ENST00000374080		16	Cgg/Ggg	1/45	0.312276573821979	1	FACETS	0.769	0.702	0.839	1	0.987	1	SUBCLONAL	2	TRUE	0	0.312276573821979	1		505	446	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338639	70338650	+	protein_altering_variant	In_Frame_Del	DEL	GGCCCCTGAAGC	GGCCCCTGAAGC	AGG	novel	NA	P-0050754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	127	519	2	ENST00000374080.3:c.35_46delinsAGG	p.Arg12_Arg16delinsGlnGly	p.R12_R16delinsQG	ENST00000374080		12	cGGCCCCTGAAGCgg/cAGGgg	1/45	0.312276573821979	1	FACETS	0.756	0.69	0.825	1	0.987	1	SUBCLONAL	2	TRUE	0	0.312276573821979	1		521	454	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235865	133235892	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGGGGGAGCCCTCACCTCTCCGTGACA	TGGGGGGAGCCCTCACCTCTCCGTGACA	CGG	novel	NA	P-0050754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	108	468	2	ENST00000320574.5:c.3264_3275+16delinsCCG		p.X1088_splice	ENST00000320574	NM_006231.2	1088		26/49	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.312276573821979	2		470	485	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	36	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.13	2		334	483	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765753	41765753	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761731744	NA	P-0050755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	24	527	0	ENST00000301178.4:c.2629G>A	p.Ala877Thr	p.A877T	ENST00000301178	NM_021913.4	877	Gct/Act	20/20	1	2	FACETS	0.792	0.62	0.992	0.792	0.62	0.992	CLONAL	1	TRUE	1	0.13	2		527	466	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504392	149504392	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs541926152	NA	P-0050755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	33	535	0	ENST00000261799.4:c.1810C>T	p.Arg604Cys	p.R604C	ENST00000261799	NM_002609.3	604	Cgc/Tgc	13/23	1	2	FACETS	0.849	0.69	1	0.849	0.69	1	CLONAL	1	TRUE	1	0.13	2		535	598	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013719	170013719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388201066	NA	P-0050755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	33	390	0	ENST00000295797.4:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000295797	NM_002740.5	480	Cgc/Tgc	15/18	1	2	FACETS	0.918	0.746	1	0.918	0.746	1	CLONAL	1	TRUE	1	0.13	2		390	553	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494667	2494669	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0050755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	39	729	2	ENST00000355716.4:c.811_813del	p.Glu271del	p.E271del	ENST00000355716	NM_003820.2	269	gtGGAg/gtg	8/8	1	2	FACETS	0.971	0.803	1	0.971	0.803	1	CLONAL	1	TRUE	1	0.13	2		731	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0050756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	217	567	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.457014152572897	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.457014152572897	1		567	667	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800930	243800930	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	48	336	0	ENST00000263826.5:c.544G>T	p.Glu182Ter	p.E182*	ENST00000263826	NM_005465.4	182	Gaa/Taa	5/13	0.23814027510421	3	FACETS	0.585	0.495	0.684	0.293	0.247	0.342	INDETERMINATE	1	TRUE	1	0.457014152572897	3		336	441	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796784	42796784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746217053	NA	P-0050756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	157	676	0	ENST00000575354.2:c.3242C>T	p.Pro1081Leu	p.P1081L	ENST00000575354	NM_015125.3	1081	cCg/cTg	14/20	1	2	FACETS	0.865	0.794	0.94	0.865	0.794	0.94	CLONAL	1	TRUE	1	0.457014152572897	2		676	794	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876392	35876392	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	83	467	0	ENST00000303115.3:c.1184A>C	p.Lys395Thr	p.K395T	ENST00000303115	NM_002185.3	395	aAg/aCg	8/8	0.210776645478043	5	FACETS	0.864	0.762	0.973	0.288	0.254	0.325	INDETERMINATE	1	TRUE	2	0.457014152572897	5		467	709	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948823	17948823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199649035	NA	P-0050756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	153	607	2	ENST00000458235.1:c.1619G>A	p.Arg540His	p.R540H	ENST00000458235	NM_000215.3	540	cGc/cAc	12/24	1	2	FACETS	0.892	0.817	0.969	0.892	0.817	0.969	CLONAL	1	TRUE	1	0.457014152572897	2		609	751	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858934	45858934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772572683	NA	P-0050756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	140	521	0	ENST00000391945.4:c.1532G>A	p.Arg511Gln	p.R511Q	ENST00000391945	NM_000400.3	511	cGg/cAg	16/23	1	2	FACETS	0.937	0.855	1	0.937	0.855	1	CLONAL	1	TRUE	1	0.457014152572897	2		521	654	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249755	133249755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755463796	NA	P-0050756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	91	426	0	ENST00000320574.5:c.1468G>A	p.Asp490Asn	p.D490N	ENST00000320574	NM_006231.2	490	Gac/Aac	14/49	0.294809239356876	1	FACETS	0.742	0.663	0.826	0.742	0.663	0.826	SUBCLONAL	1	TRUE	0	0.457014152572897	1		426	414	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100905	41100905	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0050756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	81	464	0	ENST00000373198.4:c.1450+1G>T		p.X484_splice	ENST00000373198	NM_133170.3	484			NA	2	FACETS	0.56	0.493	0.631			1	INDETERMINATE	1	TRUE	NA	0.457014152572897	2		464	633	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601929	43601929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779719517	NA	P-0050756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	119	736	0	ENST00000355710.3:c.973G>A	p.Ala325Thr	p.A325T	ENST00000355710	NM_020975.4	325	Gcc/Acc	5/20	1	2	FACETS	0.726	0.656	0.8	0.726	0.656	0.8	SUBCLONAL	1	TRUE	1	0.457014152572897	2		736	717	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29068943	29068943	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	204	377	1	ENST00000282397.4:c.38C>T	p.Ala13Val	p.A13V	ENST00000282397	NM_002019.4	13	gCg/gTg	1/30	0.222758430317607	5	FACETS	1	0.975	1	0.731	0.681	0.783	INDETERMINATE	2	TRUE	2	0.457014152572897	5		378	686	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129484	152129484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs17847065	NA	P-0050756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	15	257	0	ENST00000206249.3:c.437C>T	p.Pro146Leu	p.P146L	ENST00000206249	NM_000125.3	146	cCg/cTg	1/8	0.457014152572897	1	FACETS	0.209	0.153	0.277	0.209	0.153	0.277	SUBCLONAL	1	TRUE	0	0.457014152572897	1		257	242	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231154	98231154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1402724349	NA	P-0050756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	83	619	0	ENST00000331920.6:c.2129A>G	p.Asp710Gly	p.D710G	ENST00000331920	NM_000264.3	710	gAc/gGc	14/24	0.162596295185322	2	FACETS	0.583	0.515	0.656	0.292	0.257	0.328	INDETERMINATE	1	TRUE	0	0.457014152572897	2		619	623	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	24	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.737	0.579	0.92	0.737	0.579	0.92	CLONAL	1	TRUE	1	0.204046177020795	2		276	319	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0050757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	20	518	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.895	0.687	1	0.895	0.687	1	CLONAL	1	TRUE	1	0.204046177020795	2		518	219	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092809	27092809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	49	481	1	ENST00000324856.7:c.2830C>T	p.Gln944Ter	p.Q944*	ENST00000324856	NM_006015.4	944	Cag/Tag	9/20	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.204046177020795	2		482	473	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868663	37868663	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1275492389	NA	P-0050757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	68	550	0	ENST00000269571.5:c.1110C>G	p.Ile370Met	p.I370M	ENST00000269571		370	atC/atG	9/27	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.204046177020795	2		550	649	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0050757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	58	556	1	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	1	2	FACETS	0.872	0.748	1	0.872	0.748	1	CLONAL	1	TRUE	1	0.204046177020795	2		557	652	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263850	133263850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	50	361	0	ENST00000320574.5:c.52G>A	p.Glu18Lys	p.E18K	ENST00000320574	NM_006231.2	18	Gag/Aag	1/49	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.204046177020795	2		361	444	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987067	36987067	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	67	677	1	ENST00000354822.5:c.622C>T	p.Arg208Ter	p.R208*	ENST00000354822	NM_001079668.2	208	Cga/Tga	3/3	1	2	FACETS	0.971	0.844	1	0.971	0.844	1	CLONAL	1	TRUE	1	0.204046177020795	2		678	676	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087548	27087548	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	82	636	0	ENST00000324856.7:c.2122C>T	p.Gln708Ter	p.Q708*	ENST00000324856	NM_006015.4	708	Cag/Tag	5/20	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.204046177020795	2		636	757	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587782272	NA	P-0050757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	77	490	0	ENST00000269305.4:c.994-1G>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.204046177020795	2		490	523	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211928	36211928	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0050757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	78	598	0	ENST00000222270.7:c.1679C>G	p.Ser560Ter	p.S560*	ENST00000222270	NM_014727.1	560	tCa/tGa	3/37	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.204046177020795	2		598	748	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89824998	89824998	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501883	NA	P-0050757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	68	515	1	ENST00000389301.3:c.2968G>A	p.Asp990Asn	p.D990N	ENST00000389301	NM_000135.2	990	Gat/Aat	30/43	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.204046177020795	2		516	495	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308324	30308324	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	34	456	0	ENST00000262643.3:c.338G>C	p.Arg113Thr	p.R113T	ENST00000262643	NM_001238.2	113	aGa/aCa	6/12	1	2	FACETS	0.829	0.678	0.999	0.829	0.678	0.999	CLONAL	1	TRUE	1	0.204046177020795	2		456	402	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44894227	44894228	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	62	410	0	ENST00000377967.4:c.619dup	p.Ile207AsnfsTer10	p.I207Nfs*10	ENST00000377967	NM_021140.2	206	gaa/gAaa	7/29	0.204046177020795	1	FACETS	1	0.893	1	1	0.98	1	CLONAL	2	TRUE	0	0.204046177020795	1		410	266	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662386	117662386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	29	466	0	ENST00000368508.3:c.4991C>T	p.Ser1664Phe	p.S1664F	ENST00000368508	NM_002944.2	1664	tCc/tTc	30/43	1	2	FACETS	0.938	0.755	1	0.938	0.755	1	CLONAL	1	TRUE	1	0.204046177020795	2		466	303	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266845	18266845	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	84	523	1	ENST00000222254.8:c.156G>T	p.Gln52His	p.Q52H	ENST00000222254	NM_005027.3	52	caG/caT	2/16	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.204046177020795	2		524	670	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195769	102195769	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	21	349	0	ENST00000263464.3:c.529C>T	p.Gln177Ter	p.Q177*	ENST00000263464	NM_001165.4	177	Cag/Tag	2/9	0.150433071983544	4	FACETS	0.742	0.571	0.941			1	CLONAL	1	TRUE	NA	0.204046177020795	4		349	334	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380680	118380680	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	11	332	1	ENST00000534358.1:c.10918G>T	p.Glu3640Ter	p.E3640*	ENST00000534358	NM_005933.3	3640	Gaa/Taa	30/36	NA	2	FACETS	0.609	0.421	0.842			1	INDETERMINATE	1	TRUE	NA	0.204046177020795	2		333	177	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233162	69233162	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	15	351	0	ENST00000462284.1:c.1027G>C	p.Asp343His	p.D343H	ENST00000462284	NM_002392.5	343	Gat/Cat	11/11	1	2	FACETS	0.551	0.402	0.729	0.551	0.402	0.729	SUBCLONAL	1	TRUE	1	0.204046177020795	2		351	267	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423592	88423592	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	53	526	0	ENST00000360948.2:c.2243C>G	p.Thr748Ser	p.T748S	ENST00000360948	NM_001012338.2	748	aCt/aGt	18/19	0.204046177020795	1	FACETS	0.964	0.823	1	0.964	0.823	1	CLONAL	1	TRUE	0	0.204046177020795	1		526	484	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224384	36224384	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs868232650	NA	P-0050757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	107	790	0	ENST00000222270.7:c.6934C>G	p.Gln2312Glu	p.Q2312E	ENST00000222270	NM_014727.1	2312	Cag/Gag	28/37	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.204046177020795	2		790	841	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791166	42791166	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	88	664	0	ENST00000575354.2:c.226G>A	p.Glu76Lys	p.E76K	ENST00000575354	NM_015125.3	76	Gag/Aag	3/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.204046177020795	2		664	662	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791252	42791252	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1256325889	NA	P-0050757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	88	666	0	ENST00000575354.2:c.312G>C	p.Glu104Asp	p.E104D	ENST00000575354	NM_015125.3	104	gaG/gaC	3/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.204046177020795	2		666	677	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792055	42792055	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	70	732	0	ENST00000575354.2:c.859G>A	p.Gly287Arg	p.G287R	ENST00000575354	NM_015125.3	287	Ggg/Agg	6/20	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.204046177020795	2		732	654	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792078	42792078	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	61	718	0	ENST00000575354.2:c.882G>C	p.Glu294Asp	p.E294D	ENST00000575354	NM_015125.3	294	gaG/gaC	6/20	1	2	FACETS	0.921	0.794	1	0.921	0.794	1	CLONAL	1	TRUE	1	0.204046177020795	2		718	649	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715419	117715419	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	18	400	0	ENST00000368508.3:c.1070C>G	p.Ser357Cys	p.S357C	ENST00000368508	NM_002944.2	357	tCt/tGt	10/43	1	2	FACETS	0.757	0.571	0.976	0.757	0.571	0.976	CLONAL	1	TRUE	1	0.204046177020795	2		400	233	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397729	116397729	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	28	519	0	ENST00000397752.3:c.2003C>G	p.Pro668Arg	p.P668R	ENST00000397752	NM_000245.2	668	cCt/cGt	8/21	NA	3	FACETS	1	0.827	1	0.518	0.415	0.635	INDETERMINATE	1	TRUE	1	0.204046177020795	3		519	292	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879415	151879415	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	65	497	0	ENST00000262189.6:c.5530G>C	p.Asp1844His	p.D1844H	ENST00000262189	NM_170606.2	1844	Gat/Cat	36/59	NA	3	FACETS	1	0.966	1	0.684	0.594	0.782	INDETERMINATE	1	TRUE	1	0.204046177020795	3		497	513	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772733	135772733	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0050757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	26	431	0	ENST00000298552.3:c.2814-1G>C		p.X938_splice	ENST00000298552	NM_001162426.1	938			0.204046177020795	1	FACETS	0.88	0.699	1	0.88	0.699	1	CLONAL	1	TRUE	0	0.204046177020795	1		431	260	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913385	NA	P-0050758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	63	395	0	ENST00000304494.5:c.247C>G	p.His83Asp	p.H83D	ENST00000304494	NM_000077.4	83	Cac/Gac	2/3	0.226273967942257	1	FACETS	0.98	0.849	1	0.98	0.849	1	CLONAL	1	TRUE	0	0.226273967942257	1		395	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0050758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	85	475	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.226273967942257	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.226273967942257	1		475	588	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61197622	61197623	+	missense_variant	Missense_Mutation	DNP	GC	GC	CT	novel	NA	P-0050758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	40	342	1	ENST00000301761.2:c.4_5delinsCT	p.Ala2Leu	p.A2L	ENST00000301761	NM_017841.2	2	GCg/CTg	1/4	0.177309820505873	2	FACETS	0.6	0.498	0.715	0.3	0.249	0.358	SUBCLONAL	1	TRUE	0	0.226273967942257	2		343	589	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281784	46281784	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	63	449	0	ENST00000371998.3:c.4231C>G	p.Pro1411Ala	p.P1411A	ENST00000371998		1411	Ccc/Gcc	22/23	0.226273967942257	3	FACETS	0.892	0.771	1	0.446	0.385	0.512	CLONAL	1	TRUE	1	0.226273967942257	3		449	695	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78599575	78599575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375687715	NA	P-0050759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	91	353	0	ENST00000306801.3:c.247C>T	p.Arg83Cys	p.R83C	ENST00000306801	NM_020761.2	83	Cgc/Tgc	2/34	1	2	FACETS	0.312	0.277	0.35	0.312	0.277	0.35	SUBCLONAL	1	TRUE	1	0.845236914041149	2		353	690	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951062	48951091	+	inframe_deletion	In_Frame_Del	DEL	AGTGAATCCAAAAGAAAGTATACTGAAAAG	AGTGAATCCAAAAGAAAGTATACTGAAAAG	-	novel	NA	P-0050759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	108	226	0	ENST00000267163.4:c.1230_1259del	p.Asn410_Val419del	p.N410_V419del	ENST00000267163	NM_000321.2	408	acAGTGAATCCAAAAGAAAGTATACTGAAAAGa/aca	13/27	0.845236914041149	1	FACETS	0.811	0.751	0.869	0.811	0.751	0.869	CLONAL	1	TRUE	0	0.845236914041149	1		226	182	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563420	87563420	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs183344464	NA	P-0050759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	46	545	1	ENST00000277120.3:c.1808G>A	p.Arg603His	p.R603H	ENST00000277120		603	cGt/cAt	16/19	1	2	FACETS	0.122	0.102	0.145	0.122	0.102	0.145	SUBCLONAL	1	TRUE	1	0.845236914041149	2		546	889	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0050760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	379	392	1	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	0.847244728306032	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.847244728306032	1		393	479	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28882987	28882987	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1459098012	NA	P-0050760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	98	374	0	ENST00000282397.4:c.3713T>C	p.Met1238Thr	p.M1238T	ENST00000282397	NM_002019.4	1238	aTg/aCg	28/30	0.844540234191191	2	FACETS	0.351	0.313	0.391	0.176	0.156	0.196	SUBCLONAL	1	TRUE	0	0.847244728306032	2		374	659	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696432	47696432	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519968	NA	P-0050761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	117	525	0	ENST00000347630.2:c.391T>G	p.Trp131Gly	p.W131G	ENST00000347630	NM_001007230.1	131	Tgg/Ggg	6/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.36174265377265	2		525	610	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005400	42005400	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	139	547	1	ENST00000219905.7:c.3138del	p.Cys1047AlafsTer15	p.C1047Afs*15	ENST00000219905	NM_001164273.1	1046	Ccc/cc	9/24	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.36174265377265	2		548	696	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743579	46743579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144347182	NA	P-0050762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	39	702	0	ENST00000371975.4:c.1960C>T	p.Arg654Cys	p.R654C	ENST00000371975	NM_003579.3	654	Cgc/Tgc	17/18	1	2	FACETS	0.334	0.276	0.4	0.334	0.276	0.4	SUBCLONAL	1	TRUE	1	0.337103789193442	2		702	692	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102874100	102874100	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1237646173	NA	P-0050762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	61	353	0	ENST00000307046.8:c.60G>T	p.Leu20Phe	p.L20F	ENST00000307046	NM_001111285.1	20	ttG/ttT	1/4	0.254953367654285	4	FACETS	0.768	0.667	0.876	0.768	0.667	0.876	SUBCLONAL	2	TRUE	2	0.337103789193442	4		353	315	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023433	31023433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773277713	NA	P-0050762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	176	567	0	ENST00000375687.4:c.2918G>A	p.Ser973Asn	p.S973N	ENST00000375687	NM_015338.5	973	aGt/aAt	13/13	0.182126669340998	4	FACETS	1	0.929	1	1	0.929	1	INDETERMINATE	2	TRUE	2	0.337103789193442	4		567	694	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188318	10188318	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	157	575	0	ENST00000256474.2:c.461C>T	p.Pro154Leu	p.P154L	ENST00000256474	NM_000551.3	154	cCa/cTa	2/3	0.337103789193442	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.337103789193442	2		575	426	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651544	52651544	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	93	453	0	ENST00000394830.3:c.1552del	p.Ile518Ter	p.I518*	ENST00000394830	NM_018313.4	518	Ata/ta	15/30	0.337103789193442	2	FACETS	0.948	0.854	1	0.948	0.854	1	CLONAL	2	TRUE	0	0.337103789193442	2		453	291	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0050764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	33	507	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.1505881463568	3	FACETS	1	0.945	1	0.748	0.611	0.903	CLONAL	1	TRUE	1	0.14	3		507	337	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0050764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	28	458	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	1	2	FACETS	0.969	0.774	1	0.969	0.774	1	CLONAL	1	TRUE	1	0.14	2		458	413	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0050764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	69	767	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.14	2		767	689	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123260429	123260429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	36	552	0	ENST00000358487.5:c.1472G>A	p.Cys491Tyr	p.C491Y	ENST00000358487	NM_000141.4	491	tGc/tAc	11/18	1	2	FACETS	1	0.828	1	1	0.828	1	CLONAL	1	TRUE	1	0.14	2		552	510	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436792	52436803	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CACCTTGAACTT	CACCTTGAACTT	-	novel	NA	P-0050764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	22	630	0	ENST00000460680.1:c.1975_1983+3del		p.X659_splice	ENST00000460680	NM_004656.3	659		15/17	1	2	FACETS	0.731	0.565	0.924	0.731	0.565	0.924	CLONAL	1	TRUE	1	0.14	2		630	430	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0050766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	32	220	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	0.604	0.491	0.731	0.604	0.491	0.731	SUBCLONAL	1	TRUE	1	0.33	2		220	321	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693003	89693003	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs786204900	NA	P-0050766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	56	340	0	ENST00000371953.3:c.491del	p.Lys164ArgfsTer3	p.K164Rfs*3	ENST00000371953	NM_000314.4	163	Aaa/aa	5/9	1	2	FACETS	0.799	0.686	0.921	0.799	0.686	0.921	CLONAL	1	TRUE	1	0.33	2		340	425	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845615	63845618	+	frameshift_variant	Frame_Shift_Del	DEL	AAGA	AAGA	-	novel	NA	P-0050766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	64	318	0	ENST00000279873.7:c.1360_1363del	p.Glu454LysfsTer24	p.E454Kfs*24	ENST00000279873	NM_032199.2	452	AAGAaa/aa	9/10	1	2	FACETS	0.989	0.861	1	0.989	0.861	1	CLONAL	1	TRUE	1	0.33	2		318	392	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591246	67591246	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0050766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	94	406	0	ENST00000274335.5:c.1746-2A>G		p.X582_splice	ENST00000274335		582			1	2	FACETS	0.996	0.888	1	0.996	0.888	1	CLONAL	1	TRUE	1	0.33	2		406	572	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441434	40441434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	32	481	0	ENST00000345506.4:c.5C>T	p.Ala2Val	p.A2V	ENST00000345506	NM_003152.3	2	gCg/gTg	3/20	1	2	FACETS	0.352	0.285	0.428	0.352	0.285	0.428	SUBCLONAL	1	TRUE	1	0.33	2		481	551	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0050768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	29	525	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.922	0.739	1	0.922	0.739	1	CLONAL	1	TRUE	1	0.13	2		525	484	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923060	44923060	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	43	279	0	ENST00000377967.4:c.1921C>T	p.Gln641Ter	p.Q641*	ENST00000377967	NM_021140.2	641	Cag/Tag	16/29	1	1	FACETS	0.834	0.699	0.982	1	0.964	1	CLONAL	2	TRUE	0	0.13	1		279	371	SUCCESS
ATR	545	MSKCC	GRCh37	3	142180796	142180796	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	34	330	0	ENST00000350721.4:c.7178T>C	p.Leu2393Pro	p.L2393P	ENST00000350721	NM_001184.3	2393	cTa/cCa	42/47	1	2	FACETS	0.993	0.81	1	0.993	0.81	1	CLONAL	1	TRUE	1	0.13	2		330	527	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557629	95557629	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	273	499	0	ENST00000393063.1:c.5438A>G	p.Glu1813Gly	p.E1813G	ENST00000393063	NM_030621.3	1813	gAg/gGg	26/28	0.858468746503115	3	FACETS	0.955	0.91	1	0.955	0.91	1	CLONAL	2	TRUE	1	0.870948475361426	3		499	471	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885314	111885314	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	206	424	0	ENST00000341259.2:c.1202A>G	p.Tyr401Cys	p.Y401C	ENST00000341259	NM_005475.2	401	tAc/tGc	6/8	0.588477012194351	4	FACETS	1	0.986	1	0.409	0.381	0.438	CLONAL	1	TRUE	1	0.870948475361426	4		424	721	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574841	95574841	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0050770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	39	312	0	ENST00000393063.1:c.2257-1G>A		p.X753_splice	ENST00000393063	NM_030621.3	753			0.858468746503115	3	FACETS	0.691	0.58	0.812	0.346	0.29	0.406	SUBCLONAL	1	TRUE	1	0.870948475361426	3		312	186	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36028545	36028545	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	307	599	1	ENST00000358208.4:c.887C>T	p.Ala296Val	p.A296V	ENST00000358208		296	gCc/gTc	8/12	0.835527437952042	2	FACETS	0.929	0.88	0.978	0.464	0.44	0.489	CLONAL	1	TRUE	0	0.870948475361426	2		600	759	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417547	139417547	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	298	645	0	ENST00000277541.6:c.497G>T	p.Cys166Phe	p.C166F	ENST00000277541	NM_017617.3	166	tGc/tTc	4/34	0.870948475361426	3	FACETS	0.984	0.928	1	0.492	0.464	0.521	CLONAL	1	TRUE	1	0.870948475361426	3		645	998	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	136	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.599630728788974	2		276	417	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0050771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	80	396	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.599630728788974	2		396	242	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435797	56435797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	197	501	0	ENST00000407977.2:c.1340G>A	p.Gly447Glu	p.G447E	ENST00000407977		447	gGa/gAa	9/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.599630728788974	2		501	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0050774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	277	547	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.507333124055636	1	FACETS	0.77	0.732	0.808	1	0.995	1	SUBCLONAL	2	TRUE	0	0.507333124055636	1		547	529	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974744	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAGCAGCGCCCGCA	CCTCCAGCAGCGCCCGCA	-	novel	NA	P-0050774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	107	290	0	ENST00000304494.5:c.83_100del	p.Val28_Glu33del	p.V28_E33del	ENST00000304494	NM_000077.4	28	gTGCGGGCGCTGCTGGAGGcg/gcg	1/3	0.507333124055636	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.507333124055636	1		290	238	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0050774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	148	350	0	ENST00000311936.3:c.34_35delinsCT	p.Gly12Leu	p.G12L	ENST00000311936	NM_004985.3	12	GGt/CTt	2/5	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.507333124055636	2		350	424	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743940	46743940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372007047	NA	P-0050774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	103	402	0	ENST00000371975.4:c.2230C>T	p.Arg744Trp	p.R744W	ENST00000371975	NM_003579.3	744	Cgg/Tgg	18/18	0.266829578957005	3	FACETS	0.988	0.888	1	0.494	0.444	0.547	INDETERMINATE	1	TRUE	1	0.507333124055636	3		402	515	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953978	17953978	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773590163	NA	P-0050774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	202	521	0	ENST00000458235.1:c.424C>T	p.Arg142Cys	p.R142C	ENST00000458235	NM_000215.3	142	Cgc/Tgc	5/24	0.126747269675605	3	FACETS	0.843	0.787	0.901	0.562	0.524	0.601	INDETERMINATE	2	TRUE	0	0.507333124055636	3		521	592	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955095	93955095	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	81	332	0	ENST00000369303.4:c.2803A>C	p.Ile935Leu	p.I935L	ENST00000369303	NM_004440.3	935	Att/Ctt	16/17	0.507333124055636	2	FACETS	0.696	0.615	0.781	0.348	0.307	0.391	SUBCLONAL	1	TRUE	0	0.507333124055636	2		332	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579408	7579430	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGGGCCAGGAGGGGGCTGGTG	CAGGGGCCAGGAGGGGGCTGGTG	-	rs886041861	NA	P-0050775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	83	669	0	ENST00000269305.4:c.257_279del	p.Ala86ValfsTer55	p.A86Vfs*55	ENST00000269305	NM_001126112.2	86	gCACCAGCCCCCTCCTGGCCCCTG/g	4/11	0.275629920057027	1	FACETS	0.657	0.579	0.741	0.657	0.579	0.741	SUBCLONAL	1	TRUE	0	0.275629920057027	1		669	790	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853298	68853299	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0050775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	79	602	0	ENST00000261769.5:c.1685_1686dup	p.Ala563GlnfsTer3	p.A563Qfs*3	ENST00000261769	NM_004360.3	561	tac/tACac	11/16	0.199807822745578	1	FACETS	0.749	0.659	0.846	0.749	0.659	0.846	SUBCLONAL	1	TRUE	0	0.275629920057027	1		602	660	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0050778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	124	494	2	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	0.345116019135055	3	FACETS	0.819	0.74	0.902	0.409	0.37	0.451	CLONAL	1	TRUE	1	0.38570486281744	3		496	937	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618570	37618572	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0050778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	38	488	0	ENST00000447079.4:c.248_250del	p.Phe83del	p.F83del	ENST00000447079	NM_015083.1	82	acCTTc/acc	1/14	0.38570486281744	3	FACETS	0.359	0.296	0.43	0.179	0.148	0.215	SUBCLONAL	1	TRUE	1	0.38570486281744	3		488	655	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406127	70406127	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	35	600	0	ENST00000373644.4:c.3641C>A	p.Ser1214Tyr	p.S1214Y	ENST00000373644	NM_030625.2	1214	tCt/tAt	4/12	0.38570486281744	3	FACETS	0.315	0.257	0.38	0.158	0.128	0.19	SUBCLONAL	1	TRUE	1	0.38570486281744	3		600	687	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928935	44928936	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	102	454	0	ENST00000377967.4:c.2036dup	p.Asn680GlufsTer8	p.N680Efs*8	ENST00000377967	NM_021140.2	679	cag/cAag	17/29	1	2	FACETS	0.915	0.82	1	0.915	0.82	1	CLONAL	1	TRUE	1	0.38570486281744	2		454	578	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0050779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	208	581	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.369178535631116	2		581	783	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39283981	39283981	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	84	391	0	ENST00000402219.2:c.372C>G	p.His124Gln	p.H124Q	ENST00000402219	NM_005633.3	124	caC/caG	4/23	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.369178535631116	2		391	405	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437652	52437652	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	49	541	0	ENST00000460680.1:c.1509del	p.Phe503LeufsTer68	p.F503Lfs*68	ENST00000460680	NM_004656.3	503	ttC/tt	13/17	0.369178535631116	1	FACETS	0.302	0.255	0.354	0.302	0.255	0.354	SUBCLONAL	1	TRUE	0	0.369178535631116	1		541	717	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441128	52441228	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGCCCCAGCTCCCTAGGAGGTAGGCAGAGACACCCAACAGGCCTCCAGCTCATGGTGCCTACCATGGTCAATGGGGTAGACCTTCAGCCCATCCAGCTCAA	AGCCCCAGCTCCCTAGGAGGTAGGCAGAGACACCCAACAGGCCTCCAGCTCATGGTGCCTACCATGGTCAATGGGGTAGACCTTCAGCCCATCCAGCTCAA	-	novel	NA	P-0050779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	155	171	0	ENST00000460680.1:c.542_580+62del		p.X181_splice	ENST00000460680	NM_004656.3	181		7/17	0.369178535631116	1	FACETS	1	0.955	1	1	0.993	1	CLONAL	2	TRUE	0	0.369178535631116	1		171	331	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	67	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.30556955307543	2		334	372	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0050781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	13	401	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.332	0.237	0.449	0.332	0.237	0.449	SUBCLONAL	1	TRUE	1	0.30556955307543	2		401	256	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0050781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	20	90	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	0.984	0.761	1	0.984	0.761	1	CLONAL	1	TRUE	1	0.30556955307543	2		90	133	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601893	43601893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057521089	NA	P-0050781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	128	622	0	ENST00000355710.3:c.937C>T	p.Arg313Trp	p.R313W	ENST00000355710	NM_020975.4	313	Cgg/Tgg	5/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.30556955307543	2		622	665	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120535104	120535104	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	99	536	0	ENST00000229340.5:c.551A>G	p.Gln184Arg	p.Q184R	ENST00000229340	NM_006861.6	184	cAg/cGg	6/6	1	2	FACETS	0.983	0.879	1	0.983	0.879	1	CLONAL	1	TRUE	1	0.30556955307543	2		536	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578410	7578415	+	frameshift_variant	Frame_Shift_Del	DEL	TCACAA	TCACAA	AT	novel	NA	P-0050781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	128	653	1	ENST00000269305.4:c.515_520delinsAT	p.Val172AspfsTer74	p.V172Dfs*74	ENST00000269305	NM_001126112.2	172	gTTGTGAgg/gATgg	5/11	0.30556955307543	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.30556955307543	1		654	605	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011180	12011180	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0050781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	32	356	0	ENST00000353533.5:c.587T>G	p.Leu196Ter	p.L196*	ENST00000353533	NM_003010.3	196	tTa/tGa	5/11	0.30556955307543	1	FACETS	0.716	0.584	0.863	0.716	0.584	0.863	SUBCLONAL	1	TRUE	0	0.30556955307543	1		356	248	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0050781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	10	466	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	1	2	FACETS	0.178	0.12	0.252	0.178	0.12	0.252	SUBCLONAL	1	TRUE	1	0.30556955307543	2		466	367	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0050781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	54	431	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.913	0.783	1	0.913	0.783	1	CLONAL	1	TRUE	1	0.30556955307543	2		431	387	SUCCESS
APC	324	MSKCC	GRCh37	5	112174308	112174308	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	45	343	0	ENST00000257430.4:c.3017del	p.His1006LeufsTer16	p.H1006Lfs*16	ENST00000257430	NM_000038.5	1006	cAt/ct	16/16	0.30556955307543	1	FACETS	0.863	0.73	1	0.863	0.73	1	CLONAL	1	TRUE	0	0.30556955307543	1		343	289	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0050781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	66	278	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.30556955307543	1	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	0	0.30556955307543	1		278	365	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009255	69009255	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	93	375	0	ENST00000288368.4:c.2372T>C	p.Val791Ala	p.V791A	ENST00000288368	NM_024870.2	791	gTt/gCt	22/40	1	2	FACETS	0.855	0.767	0.947	1	0.985	1	CLONAL	2	TRUE	1	0.30556955307543	2		375	356	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404360	139404360	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758642073	NA	P-0050781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	184	636	1	ENST00000277541.6:c.2794G>A	p.Asp932Asn	p.D932N	ENST00000277541	NM_017617.3	932	Gac/Aac	18/34	1	2	FACETS	0.765	0.708	0.825	1	0.99	1	SUBCLONAL	2	TRUE	1	0.30556955307543	2		637	787	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0050782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	26	390	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.651	0.515	0.807	0.651	0.515	0.807	SUBCLONAL	1	TRUE	1	0.18	2		390	444	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0050782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	50	517	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.18	2		517	462	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0050782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	27	465	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.709	0.564	0.876	0.709	0.564	0.876	SUBCLONAL	1	TRUE	1	0.18	2		465	423	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0050782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	43	611	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.654	0.546	0.775	0.654	0.546	0.775	SUBCLONAL	1	TRUE	1	0.18	2		611	730	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0050782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	40	470	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.18	2		470	433	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444650	187444650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1246753673	NA	P-0050782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	35	504	0	ENST00000232014.4:c.1577G>A	p.Arg526His	p.R526H	ENST00000232014	NM_001130845.1	526	cGc/cAc	7/10	1	2	FACETS	0.615	0.503	0.742	0.615	0.503	0.742	SUBCLONAL	1	TRUE	1	0.18	2		504	632	SUCCESS
ATM	472	MSKCC	GRCh37	11	108181042	108181042	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	14	195	0	ENST00000278616.4:c.5918G>C	p.Arg1973Thr	p.R1973T	ENST00000278616	NM_000051.3	1973	aGa/aCa	39/63	1	2	FACETS	0.591	0.427	0.791	0.591	0.427	0.791	SUBCLONAL	1	TRUE	1	0.18	2		195	263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577137	7577137	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	91	610	0	ENST00000269305.4:c.801del	p.Asn268ThrfsTer77	p.N268Tfs*77	ENST00000269305	NM_001126112.2	267	cgG/cg	8/11	0.216214357544548	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.216214357544548	1		610	682	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	142	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.404279068177852	3	FACETS	1	0.977	1	0.6	0.548	0.654	CLONAL	1	TRUE	1	0.404279068177852	3		436	704	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0050785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	121	397	2	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.893	0.809	0.983	0.893	0.809	0.983	CLONAL	1	TRUE	1	0.404279068177852	2		399	670	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121531	193121531	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	59	337	0	ENST00000367435.3:c.929A>G	p.Asp310Gly	p.D310G	ENST00000367435	NM_024529.4	310	gAc/gGc	10/17	1	2	FACETS	0.671	0.579	0.771	0.671	0.579	0.771	SUBCLONAL	1	TRUE	1	0.404279068177852	2		337	435	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941938	71941943	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CATGGG	CATGGG	-	novel	NA	P-0050785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	99	726	0	ENST00000298229.2:c.1296_1300+1del		p.X432_splice	ENST00000298229	NM_001567.3	432		11/28	1	2	FACETS	0.739	0.66	0.822	0.739	0.66	0.822	SUBCLONAL	1	TRUE	1	0.404279068177852	2		726	663	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595216	52595902	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGATTTAATTAGAATAAAAGGAAAATAAAGGCAGTTGAGCTTTATAAAAAAGACCCAAATACCTTAGAAGTAGCTATGAATACAGACACAGTATAGGCCAGGACTGACCTAGGAAACCAAGCACTTTAGCAAAGACTCAGCCTGAAGTTTAAATATATGGCTTACCAAGAGCTGTAACACAAGATCACTGATTTTAAGAGGCCCTTTTCAGACGAATTTTAATTAAAATTATATTTAACATCATTGTACAATAATTCCCTAGCTCAACATGTGTGCTTACAGGGCTCAATGAAAGAAAAAAATCATGCAATTTTTAGTAGCAAAATATTTTGGAGAAATTTGCAGGGGAAAATACAACACCAGGATCAGAGGCCAAGTCAGGGGCAGTGCTCTGCTCAGTCAGGACAAGGCTAGCATCTAAAATACTGGTTGGGTGCCATTTGGAACAGTCCCCAAAATAAAAGTTCATGTGCAAGTGGTAAGAACAAGAGTAAAACCTGTCTGTGCGCGTGCATTCCTGAAACACCCCCTTGCTTCGAAAGACAGTTGTGCCTAGGCTCTATTTACCTTCATATTCTGCTTTCTTGGCTGTCTCAAGATTTCTCCATTCTGTCCCCACCAGGCGGCTGAGCTCCCCGAAAGAGTAGTCTGGGTGTTGGGCCTTAATCACAGCCCTCATCTCACTGC	TGATTTAATTAGAATAAAAGGAAAATAAAGGCAGTTGAGCTTTATAAAAAAGACCCAAATACCTTAGAAGTAGCTATGAATACAGACACAGTATAGGCCAGGACTGACCTAGGAAACCAAGCACTTTAGCAAAGACTCAGCCTGAAGTTTAAATATATGGCTTACCAAGAGCTGTAACACAAGATCACTGATTTTAAGAGGCCCTTTTCAGACGAATTTTAATTAAAATTATATTTAACATCATTGTACAATAATTCCCTAGCTCAACATGTGTGCTTACAGGGCTCAATGAAAGAAAAAAATCATGCAATTTTTAGTAGCAAAATATTTTGGAGAAATTTGCAGGGGAAAATACAACACCAGGATCAGAGGCCAAGTCAGGGGCAGTGCTCTGCTCAGTCAGGACAAGGCTAGCATCTAAAATACTGGTTGGGTGCCATTTGGAACAGTCCCCAAAATAAAAGTTCATGTGCAAGTGGTAAGAACAAGAGTAAAACCTGTCTGTGCGCGTGCATTCCTGAAACACCCCCTTGCTTCGAAAGACAGTTGTGCCTAGGCTCTATTTACCTTCATATTCTGCTTTCTTGGCTGTCTCAAGATTTCTCCATTCTGTCCCCACCAGGCGGCTGAGCTCCCCGAAAGAGTAGTCTGGGTGTTGGGCCTTAATCACAGCCCTCATCTCACTGC	-	novel	NA	P-0050785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2	94	0	0	ENST00000394830.3:c.4013_4132+567del		p.X1338_splice	ENST00000394830	NM_018313.4	1338		26/30	1	2	FACETS		NA	1	1	0.992	1	NA	5	TRUE	1	0.404279068177852	2		0	96	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0050786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	58	517	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.62	0.534	0.713	0.62	0.534	0.713	SUBCLONAL	1	TRUE	1	0.436281778284333	2		517	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0050786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	135	598	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.436281778284333	2		598	571	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669523	88669523	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750055690	NA	P-0050786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	82	475	0	ENST00000360948.2:c.1375C>T	p.Arg459Trp	p.R459W	ENST00000360948	NM_001012338.2	459	Cgg/Tgg	12/19	1	2	FACETS	0.681	0.602	0.766	0.681	0.602	0.766	SUBCLONAL	1	TRUE	1	0.436281778284333	2		475	552	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374334	15374334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201883209	NA	P-0050786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	143	558	1	ENST00000263377.2:c.1238G>A	p.Arg413His	p.R413H	ENST00000263377	NM_058243.2	413	cGt/cAt	7/20	1	2	FACETS	0.788	0.719	0.861	0.788	0.719	0.861	SUBCLONAL	1	TRUE	1	0.436281778284333	2		559	832	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435375	56435375	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	75	720	0	ENST00000407977.2:c.1762del	p.Gln588SerfsTer112	p.Q588Sfs*112	ENST00000407977		588	Cag/ag	9/10	1	2	FACETS	0.359	0.314	0.409	0.359	0.314	0.409	SUBCLONAL	1	TRUE	1	0.436281778284333	2		720	957	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620662	52620662	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	88	351	0	ENST00000394830.3:c.3091G>T	p.Val1031Phe	p.V1031F	ENST00000394830	NM_018313.4	1031	Gtt/Ttt	21/30	0.423292470307104	1	FACETS	0.734	0.653	0.818	0.734	0.653	0.818	SUBCLONAL	1	TRUE	0	0.436281778284333	1		351	430	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	95	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.306136052237615	2		334	453	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721237	176721237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767645475	NA	P-0050787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	66	365	0	ENST00000439151.2:c.6868C>T	p.Pro2290Ser	p.P2290S	ENST00000439151	NM_022455.4	2290	Ccc/Tcc	23/23	1	2	FACETS	0.982	0.855	1	0.982	0.855	1	CLONAL	1	TRUE	1	0.306136052237615	2		365	439	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680128	30680128	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	126	508	0	ENST00000376406.3:c.1591C>G	p.Pro531Ala	p.P531A	ENST00000376406	NM_014641.2	531	Cca/Gca	5/15	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.306136052237615	2		508	759	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	322	276	0				ENST00000310581	NM_198253.2	-/1132			0.239776303366483	4	FACETS	0.91	0.869	0.951	0.91	0.869	0.951	INDETERMINATE	3	TRUE	1	0.65	4		276	599	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0050788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	347	788	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.65	2		788	930	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0050788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	258	674	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	0.944	0.886	1	0.944	0.886	1	CLONAL	1	TRUE	1	0.65	2		674	841	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916747	48916747	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690915	NA	P-0050788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	269	337	1	ENST00000267163.4:c.277C>T	p.Gln93Ter	p.Q93*	ENST00000267163	NM_000321.2	93	Caa/Taa	3/27	0.303054301837359	1	FACETS	0.753	0.724	0.781	1	0.996	1	INDETERMINATE	2	TRUE	0	0.65	1		338	371	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423511	88423511	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0050788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	286	538	0	ENST00000360948.2:c.2324C>G	p.Ser775Ter	p.S775*	ENST00000360948	NM_001012338.2	775	tCa/tGa	18/19	0.245430059791821	1	FACETS	0.75	0.708	0.793	0.75	0.708	0.793	INDETERMINATE	1	TRUE	0	0.65	1		538	792	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127167	22127167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	135	472	0	ENST00000215832.6:c.961G>A	p.Asp321Asn	p.D321N	ENST00000215832	NM_002745.4	321	Gac/Aac	7/9	1	2	FACETS	0.681	0.621	0.744	0.681	0.621	0.744	SUBCLONAL	1	TRUE	1	0.65	2		472	610	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387689	17387689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	53	585	0	ENST00000359435.4:c.757G>A	p.Glu253Lys	p.E253K	ENST00000359435	NM_001033549.1	253	Gag/Aag	8/9	1	2	FACETS	0.206	0.175	0.24	0.206	0.175	0.24	SUBCLONAL	1	TRUE	1	0.65	2		585	792	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045687	26045687	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	86	403	0	ENST00000540144.1:c.49C>G	p.Pro17Ala	p.P17A	ENST00000540144	NM_003531.2	17	Ccg/Gcg	1/1	1	2	FACETS	0.492	0.436	0.551	0.492	0.436	0.551	SUBCLONAL	1	TRUE	1	0.65	2		403	538	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941886	44941886	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0050788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	308	208	0	ENST00000377967.4:c.3209+1G>A		p.X1070_splice	ENST00000377967	NM_021140.2	1070			0.137927645846154	2	FACETS	0.849	0.824	0.872			1	INDETERMINATE	3	TRUE	NA	0.65	2		208	372	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074401	8074401	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	223	517	0	ENST00000377482.5:c.258del	p.Ser87LeufsTer34	p.S87Lfs*34	ENST00000377482	NM_018948.3	86	ccA/cc	4/4	0.303054301837359	3	FACETS	1	0.991	1	0.673	0.63	0.718	INDETERMINATE	1	TRUE	1	0.65	3		517	675	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023209	27023227	+	frameshift_variant	Frame_Shift_Del	DEL	GAACGCGGGCCCTAGGCCC	GAACGCGGGCCCTAGGCCC	-	novel	NA	P-0050788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	105	153	0	ENST00000324856.7:c.316_334del	p.Asn106ProfsTer2	p.N106Pfs*2	ENST00000324856	NM_006015.4	105	ggGAACGCGGGCCCTAGGCCC/gg	1/20	0.303054301837359	3	FACETS	0.867	0.791	0.943	0.867	0.791	0.943	INDETERMINATE	2	TRUE	1	0.65	3		153	247	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100075	27100075	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	68	763	0	ENST00000324856.7:c.3871G>C	p.Glu1291Gln	p.E1291Q	ENST00000324856	NM_006015.4	1291	Gag/Cag	16/20	0.303054301837359	3	FACETS	0.295	0.255	0.337	0.147	0.127	0.169	INDETERMINATE	1	TRUE	1	0.65	3		763	941	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998724	100998724	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766312564	NA	P-0050788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	119	700	1	ENST00000325455.5:c.1078G>A	p.Asp360Asn	p.D360N	ENST00000325455	NM_001202474.3	360	Gac/Aac	1/8	0.245430059791821	1	FACETS	0.34	0.307	0.375	0.34	0.307	0.375	INDETERMINATE	1	TRUE	0	0.65	1		701	726	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999111	100999111	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1052227689	NA	P-0050788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	102	697	0	ENST00000325455.5:c.691G>A	p.Glu231Lys	p.E231K	ENST00000325455	NM_001202474.3	231	Gag/Aag	1/8	0.245430059791821	1	FACETS	0.296	0.264	0.329	0.296	0.264	0.329	INDETERMINATE	1	TRUE	0	0.65	1		697	716	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118353204	118353216	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGAAAAGGTGAGG	AGAAAAGGTGAGG	-	novel	NA	P-0050788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	119	282	0	ENST00000534358.1:c.4083_4086+9del		p.X1361_splice	ENST00000534358	NM_005933.3	1361		8/36	0.245430059791821	1	FACETS	0.775	0.709	0.842	0.775	0.709	0.842	INDETERMINATE	1	TRUE	0	0.65	1		282	319	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727489	66727489	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	268	575	0	ENST00000307102.5:c.205G>C	p.Glu69Gln	p.E69Q	ENST00000307102	NM_002755.3	69	Gag/Cag	2/11	0.245430059791821	1	FACETS	0.733	0.691	0.777	0.733	0.691	0.777	INDETERMINATE	1	TRUE	0	0.65	1		575	759	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245871	5245871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	92	863	0	ENST00000357368.4:c.904G>A	p.Asp302Asn	p.D302N	ENST00000357368	NM_002850.3	302	Gat/Aat	10/38	1	2	FACETS	0.301	0.266	0.338	0.301	0.266	0.338	SUBCLONAL	1	TRUE	1	0.65	2		863	941	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387701	17387701	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	39	522	0	ENST00000359435.4:c.769G>A	p.Glu257Lys	p.E257K	ENST00000359435	NM_001033549.1	257	Gag/Aag	8/9	1	2	FACETS	0.167	0.138	0.2	0.167	0.138	0.2	SUBCLONAL	1	TRUE	1	0.65	2		522	717	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545081	41545081	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	138	542	1	ENST00000263253.7:c.2281C>T	p.Gln761Ter	p.Q761*	ENST00000263253	NM_001429.3	761	Cag/Tag	13/31	1	2	FACETS	0.56	0.51	0.613	0.56	0.51	0.613	SUBCLONAL	1	TRUE	1	0.65	2		543	758	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565580	41565580	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	157	442	0	ENST00000263253.7:c.4246G>A	p.Glu1416Lys	p.E1416K	ENST00000263253	NM_001429.3	1416	Gaa/Aaa	26/31	1	2	FACETS	0.655	0.601	0.711	0.655	0.601	0.711	SUBCLONAL	1	TRUE	1	0.65	2		442	738	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539398	187539398	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	120	456	0	ENST00000441802.2:c.8342G>A	p.Arg2781Lys	p.R2781K	ENST00000441802	NM_005245.3	2781	aGg/aAg	10/27	1	2	FACETS	0.551	0.498	0.607	0.551	0.498	0.607	SUBCLONAL	1	TRUE	1	0.65	2		456	670	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104626	69104626	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	78	690	0	ENST00000288368.4:c.4470C>G	p.Ile1490Met	p.I1490M	ENST00000288368	NM_024870.2	1490	atC/atG	37/40	0.303054301837359	3	FACETS	0.283	0.248	0.322	0.142	0.124	0.161	INDETERMINATE	1	TRUE	1	0.65	3		690	1123	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0050789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	83	517	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.25006619260243	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.804706198780997	0		517	208	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0050789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	105	341	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.551394011495489	3	FACETS	0.803	0.735	0.871	0.803	0.735	0.871	CLONAL	2	TRUE	1	0.804706198780997	3		341	228	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922321	178922321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	112	464	1	ENST00000263967.3:c.1090G>A	p.Gly364Arg	p.G364R	ENST00000263967	NM_006218.2	364	Gga/Aga	6/21	0.551394011495489	3	FACETS	0.81	0.744	0.876	0.81	0.744	0.876	CLONAL	2	TRUE	1	0.804706198780997	3		465	241	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	132	428	0	ENST00000263967.3:c.3127A>C	p.Met1043Leu	p.M1043L	ENST00000263967	NM_006218.2	1043	Atg/Ctg	21/21	0.551394011495489	3	FACETS	0.967	0.9	1	0.967	0.9	1	CLONAL	2	TRUE	1	0.804706198780997	3		428	238	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804300	43804300	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	368	607	0	ENST00000372470.3:c.300A>C	p.Glu100Asp	p.E100D	ENST00000372470	NM_005373.2	100	gaA/gaC	3/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.804706198780997	2		607	864	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118365088	118365088	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	54	542	0	ENST00000534358.1:c.5264G>C	p.Ser1755Thr	p.S1755T	ENST00000534358	NM_005933.3	1755	aGc/aCc	17/36	1	2	FACETS	0.624	0.54	0.714	0.624	0.54	0.714	SUBCLONAL	1	TRUE	1	0.804706198780997	2		542	215	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119810	70119810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	337	577	1	ENST00000245479.2:c.812G>A	p.Arg271His	p.R271H	ENST00000245479	NM_000346.3	271	cGc/cAc	3/3	1	2	FACETS	0.905	0.858	0.952	0.905	0.858	0.952	CLONAL	1	TRUE	1	0.804706198780997	2		578	926	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40739858	40739858	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	339	577	1	ENST00000392038.2:c.1367A>G	p.Tyr456Cys	p.Y456C	ENST00000392038	NM_001626.4	456	tAt/tGt	14/14	0.372702796726533	3	FACETS	1	0.994	1	0.67	0.636	0.704	INDETERMINATE	1	TRUE	1	0.804706198780997	3		578	882	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037216	71037216	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	165	385	0	ENST00000318789.4:c.1075A>C	p.Lys359Gln	p.K359Q	ENST00000318789	NM_032682.5	359	Aaa/Caa	14/21	1	2	FACETS	0.969	0.9	1	0.969	0.9	1	CLONAL	1	TRUE	1	0.804706198780997	2		385	423	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608650	189608650	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	43	503	0	ENST00000264731.3:c.1725G>C	p.Gln575His	p.Q575H	ENST00000264731	NM_003722.4	575	caG/caC	13/14	0.551394011495489	3	FACETS	0.258	0.216	0.306	0.129	0.108	0.153	SUBCLONAL	1	TRUE	1	0.804706198780997	3		503	580	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056707	180056707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	25	614	0	ENST00000261937.6:c.805C>T	p.Pro269Ser	p.P269S	ENST00000261937	NM_182925.4	269	Cca/Tca	6/30	0.744374126351906	1	FACETS	0.088	0.068	0.11	0.088	0.068	0.11	SUBCLONAL	1	TRUE	0	0.804706198780997	1		614	424	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028061	69028061	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	19	547	2	ENST00000288368.4:c.3220G>T	p.Asp1074Tyr	p.D1074Y	ENST00000288368	NM_024870.2	1074	Gac/Tac	26/40	1	2	FACETS	0.218	0.165	0.279	0.218	0.165	0.279	SUBCLONAL	1	TRUE	1	0.804706198780997	2		549	217	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0050791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	59	517	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.21	2		517	552	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0050791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	14	425	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.247	0.177	0.332	0.247	0.177	0.332	SUBCLONAL	1	TRUE	1	0.21	2		425	540	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0050791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	55	611	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.979	0.838	1	0.979	0.838	1	CLONAL	1	TRUE	1	0.21	2		611	535	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0050791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	53	433	1	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.903	0.77	1	0.903	0.77	1	CLONAL	1	TRUE	1	0.21	2		434	559	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089777	27089777	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0050791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	49	499	1	ENST00000324856.7:c.2732+1G>T		p.X911_splice	ENST00000324856	NM_006015.4	911			1	2	FACETS	0.901	0.763	1	0.901	0.763	1	CLONAL	1	TRUE	1	0.21	2		500	518	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057991	27057991	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	34	569	0	ENST00000324856.7:c.1699C>T	p.Gln567Ter	p.Q567*	ENST00000324856	NM_006015.4	567	Cag/Tag	3/20	1	2	FACETS	0.524	0.427	0.634	0.524	0.427	0.634	SUBCLONAL	1	TRUE	1	0.21	2		569	618	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653853	89653853	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	95	326	0	ENST00000371953.3:c.151del	p.Asp51MetfsTer3	p.D51Mfs*3	ENST00000371953	NM_000314.4	51	Gat/at	2/9	0.248110467753585	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	2	TRUE	0	0.21	2		326	449	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098016	178098016	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	26	482	0	ENST00000397062.3:c.364C>G	p.Leu122Val	p.L122V	ENST00000397062	NM_006164.4	122	Ctt/Gtt	3/5	1	2	FACETS	0.482	0.38	0.598	0.482	0.38	0.598	SUBCLONAL	1	TRUE	1	0.21	2		482	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519985	NA	P-0050792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	503	699	0	ENST00000269305.4:c.857A>T	p.Glu286Val	p.E286V	ENST00000269305	NM_001126112.2	286	gAa/gTa	8/11	0.852280555267721	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.852280555267721	1		699	655	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447425	49447425	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0050792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	260	578	0	ENST00000301067.7:c.674-1G>C		p.X225_splice	ENST00000301067	NM_003482.3	225			1	2	FACETS	0.8	0.752	0.848	0.8	0.752	0.848	SUBCLONAL	1	TRUE	1	0.852280555267721	2		578	763	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646863	37646863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	31	564	0	ENST00000447079.4:c.1985C>T	p.Thr662Ile	p.T662I	ENST00000447079	NM_015083.1	662	aCa/aTa	3/14	0.852280555267721	1	FACETS	0.069	0.056	0.085	0.069	0.056	0.085	SUBCLONAL	1	TRUE	0	0.852280555267721	1		564	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	440	513	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.57704014276344	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.57704014276344	2		516	681	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	249	518	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.525964948873822	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.57704014276344	4		518	655	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	41	352	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	0.195838429773659	2	FACETS	0.353	0.294	0.418	0.176	0.147	0.209	INDETERMINATE	1	TRUE	0	0.57704014276344	2		352	403	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588849	69588849	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	117	567	1	ENST00000168712.1:c.387C>A	p.Phe129Leu	p.F129L	ENST00000168712	NM_002007.2	129	ttC/ttA	2/3	0.57704014276344	5	FACETS	0.708	0.637	0.784			1	SUBCLONAL	1	TRUE	NA	0.57704014276344	5		568	1068	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032031	26032031	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	110	472	0	ENST00000244661.2:c.258G>C	p.Gln86His	p.Q86H	ENST00000244661	NM_003537.3	86	caG/caC	1/1	0.568457204222024	5	FACETS	0.736	0.66	0.817	0.245	0.22	0.273	SUBCLONAL	1	TRUE	2	0.57704014276344	5		472	966	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675183	30675183	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs748112559	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	164	574	0	ENST00000376406.3:c.3062G>C	p.Arg1021Thr	p.R1021T	ENST00000376406	NM_014641.2	1021	aGa/aCa	9/15	0.3986553256363	5	FACETS	0.887	0.812	0.965	0.296	0.27	0.322	CLONAL	1	TRUE	2	0.57704014276344	5		574	1196	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004998	150004998	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	148	431	0	ENST00000253339.5:c.1227G>C	p.Met409Ile	p.M409I	ENST00000253339		409	atG/atC	3/7	0.57704014276344	3	FACETS	1	0.951	1	0.526	0.482	0.572	CLONAL	1	TRUE	1	0.57704014276344	3		431	628	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522581	176522581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	159	605	0	ENST00000292408.4:c.1678G>A	p.Glu560Lys	p.E560K	ENST00000292408	NM_213647.1	560	Gag/Aag	13/18	0.574161358931072	4	FACETS	0.89	0.816	0.969			1	CLONAL	1	TRUE	NA	0.57704014276344	4		605	976	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528774	8528774	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	45	346	0	ENST00000356435.5:c.358C>A	p.Gln120Lys	p.Q120K	ENST00000356435		120	Caa/Aaa	4/35	0.57704014276344	3	FACETS	0.405	0.34	0.477	0.203	0.17	0.239	SUBCLONAL	1	TRUE	1	0.57704014276344	3		346	496	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177011	56177011	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	248	363	0	ENST00000399503.3:c.2281del	p.Ile761Ter	p.I761*	ENST00000399503	NM_005921.1	761	Ata/ta	13/20	0.564975920651282	2	FACETS	0.961	0.913	1	0.961	0.913	1	CLONAL	2	TRUE	0	0.57704014276344	2		363	447	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259934	16259934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs988832507	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	157	562	1	ENST00000375759.3:c.7199C>T	p.Ser2400Phe	p.S2400F	ENST00000375759	NM_015001.2	2400	tCt/tTt	11/15	0.57704014276344	3	FACETS	0.983	0.903	1	0.492	0.451	0.534	CLONAL	1	TRUE	1	0.57704014276344	3		563	713	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248067	110248067	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	57	481	0	ENST00000374672.4:c.1405G>C	p.Asp469His	p.D469H	ENST00000374672	NM_004235.4	469	Gac/Cac	5/5	0.57704014276344	3	FACETS	0.406	0.348	0.47	0.203	0.174	0.235	SUBCLONAL	1	TRUE	1	0.57704014276344	3		481	627	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257272	16257272	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	140	553	0	ENST00000375759.3:c.4537G>C	p.Glu1513Gln	p.E1513Q	ENST00000375759	NM_015001.2	1513	Gag/Cag	11/15	0.57704014276344	3	FACETS	0.856	0.781	0.935	0.428	0.39	0.468	CLONAL	1	TRUE	1	0.57704014276344	3		553	730	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032111	26032111	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	109	473	0	ENST00000244661.2:c.178G>C	p.Glu60Gln	p.E60Q	ENST00000244661	NM_003537.3	60	Gag/Cag	1/1	0.568457204222024	5	FACETS	0.747	0.669	0.829	0.249	0.223	0.277	SUBCLONAL	1	TRUE	2	0.57704014276344	5		473	944	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964366	70964366	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	49	386	0	ENST00000276594.2:c.1662C>G	p.Ile554Met	p.I554M	ENST00000276594	NM_024504.3	554	atC/atG	8/8	0.57704014276344	4	FACETS	0.503	0.426	0.588	0.168	0.142	0.196	SUBCLONAL	1	TRUE	1	0.57704014276344	4		386	532	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678077	117678077	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs199725375	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	73	312	0	ENST00000368508.3:c.3856C>T	p.Arg1286Cys	p.R1286C	ENST00000368508	NM_002944.2	1286	Cgc/Tgc	25/43	0.57704014276344	3	FACETS	0.84	0.739	0.948	0.42	0.369	0.474	CLONAL	1	TRUE	1	0.57704014276344	3		312	388	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871836	12871836	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	111	264	0	ENST00000228872.4:c.553G>C	p.Glu185Gln	p.E185Q	ENST00000228872	NM_004064.3	185	Gag/Cag	2/3	0.357416759178615	4	FACETS	1	0.968	1	0.586	0.529	0.646	CLONAL	1	TRUE	2	0.57704014276344	4		264	518	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390923	89390923	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	105	336	0	ENST00000336596.2:c.989G>C	p.Arg330Thr	p.R330T	ENST00000336596	NM_005233.5	330	aGa/aCa	5/17	1	2	FACETS	0.856	0.772	0.944	0.856	0.772	0.944	CLONAL	1	TRUE	1	0.57704014276344	2		336	425	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031939	26031939	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	75	439	0	ENST00000244661.2:c.350G>C	p.Arg117Pro	p.R117P	ENST00000244661	NM_003537.3	117	cGa/cCa	1/1	0.568457204222024	5	FACETS	0.573	0.501	0.651	0.191	0.167	0.217	SUBCLONAL	1	TRUE	2	0.57704014276344	5		439	846	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030845	36030845	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	83	351	0	ENST00000358208.4:c.1124C>G	p.Ser375Ter	p.S375*	ENST00000358208		375	tCa/tGa	10/12	0.57704014276344	3	FACETS	0.721	0.638	0.81	0.361	0.319	0.405	SUBCLONAL	1	TRUE	1	0.57704014276344	3		351	514	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831584	72831584	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	158	616	0	ENST00000268489.5:c.4997C>G	p.Ser1666Cys	p.S1666C	ENST00000268489	NM_006885.3	1666	tCc/tGc	9/10	0.57704014276344	3	FACETS	0.897	0.823	0.974	0.448	0.411	0.487	CLONAL	1	TRUE	1	0.57704014276344	3		616	787	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352058	89352058	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs1567583835	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	144	620	0	ENST00000301030.4:c.893-1G>C		p.X298_splice	ENST00000301030	NM_001256183.1	298			0.57704014276344	3	FACETS	0.901	0.823	0.982	0.45	0.411	0.491	CLONAL	1	TRUE	1	0.57704014276344	3		620	714	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261277	16261277	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	39	510	0	ENST00000375759.3:c.8542C>T	p.Gln2848Ter	p.Q2848*	ENST00000375759	NM_015001.2	2848	Cag/Tag	11/15	0.57704014276344	3	FACETS	0.249	0.206	0.298	0.125	0.103	0.149	SUBCLONAL	1	TRUE	1	0.57704014276344	3		510	699	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023733	27023733	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	131	367	0	ENST00000324856.7:c.839C>A	p.Ser280Tyr	p.S280Y	ENST00000324856	NM_006015.4	280	tCc/tAc	1/20	0.57704014276344	3	FACETS	1	0.967	1	0.561	0.512	0.613	CLONAL	1	TRUE	1	0.57704014276344	3		367	521	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092802	27092802	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	146	509	0	ENST00000324856.7:c.2823C>G	p.Ile941Met	p.I941M	ENST00000324856	NM_006015.4	941	atC/atG	9/20	0.57704014276344	3	FACETS	0.815	0.744	0.889	0.408	0.372	0.445	CLONAL	1	TRUE	1	0.57704014276344	3		509	800	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304213	65304213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	105	397	0	ENST00000342505.4:c.2902C>T	p.Leu968Phe	p.L968F	ENST00000342505	NM_002227.2	968	Ctt/Ttt	21/25	0.57704014276344	3	FACETS	0.716	0.642	0.794	0.358	0.321	0.397	SUBCLONAL	1	TRUE	1	0.57704014276344	3		397	655	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917583	94917583	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	67	327	0	ENST00000536441.1:c.937+1G>C		p.X313_splice	ENST00000536441	NM_144665.3	313			0.560422979274825	3	FACETS	0.671	0.585	0.764	0.224	0.195	0.255	SUBCLONAL	1	TRUE	0	0.57704014276344	3		327	446	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999114	100999114	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	71	591	0	ENST00000325455.5:c.688G>C	p.Glu230Gln	p.E230Q	ENST00000325455	NM_001202474.3	230	Gag/Cag	1/8	0.560422979274825	3	FACETS	0.474	0.413	0.54	0.158	0.137	0.18	SUBCLONAL	1	TRUE	0	0.57704014276344	3		591	669	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445476	49445476	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs558509938	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1282	161	678	0	ENST00000301067.7:c.1990C>G	p.Pro664Ala	p.P664A	ENST00000301067	NM_003482.3	664	Cca/Gca	10/54	0.57704014276344	5	FACETS	0.721	0.659	0.787	0.24	0.219	0.263	SUBCLONAL	1	TRUE	2	0.57704014276344	5		678	1443	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479282	50479282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	103	376	0	ENST00000394963.4:c.130C>T	p.Pro44Ser	p.P44S	ENST00000394963	NM_003076.4	44	Ccg/Tcg	1/13	0.57704014276344	5	FACETS	0.749	0.67	0.834	0.25	0.223	0.278	SUBCLONAL	1	TRUE	2	0.57704014276344	5		376	889	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858636	57858636	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	138	431	0	ENST00000228682.2:c.374C>A	p.Ser125Tyr	p.S125Y	ENST00000228682	NM_005269.2	125	tCc/tAc	4/12	0.57704014276344	5	FACETS	0.945	0.859	1	0.315	0.286	0.345	CLONAL	1	TRUE	2	0.57704014276344	5		431	944	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120805836	120805836	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	197	630	0	ENST00000257552.2:c.242C>G	p.Ser81Trp	p.S81W	ENST00000257552	NM_002442.3	81	tCg/tGg	4/15	0.57704014276344	3	FACETS	1	0.972	1	0.548	0.508	0.589	CLONAL	1	TRUE	1	0.57704014276344	3		630	803	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562878	95562878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	86	344	0	ENST00000393063.1:c.4379C>T	p.Ser1460Leu	p.S1460L	ENST00000393063	NM_030621.3	1460	tCa/tTa	24/28	0.563145560406817	2	FACETS	0.857	0.764	0.954	0.428	0.382	0.477	CLONAL	1	TRUE	0	0.57704014276344	2		344	348	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630700	90630700	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	173	580	0	ENST00000330062.3:c.786C>G	p.Phe262Leu	p.F262L	ENST00000330062	NM_002168.2	262	ttC/ttG	6/11	0.194439187480012	3	FACETS	0.923	0.85	0.999	0.308	0.283	0.333	INDETERMINATE	1	TRUE	0	0.57704014276344	3		580	837	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351842	89351842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1357660606	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	190	688	1	ENST00000301030.4:c.1108G>A	p.Asp370Asn	p.D370N	ENST00000301030	NM_001256183.1	370	Gac/Aac	9/13	0.57704014276344	3	FACETS	0.853	0.788	0.92	0.426	0.394	0.46	CLONAL	1	TRUE	1	0.57704014276344	3		689	995	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448364	56448364	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	245	672	0	ENST00000407977.2:c.283G>C	p.Asp95His	p.D95H	ENST00000407977		95	Gat/Cat	3/10	0.57704014276344	3	FACETS	0.93	0.869	0.994	0.31	0.289	0.332	CLONAL	1	TRUE	0	0.57704014276344	3		672	1176	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625613	1625613	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	170	623	0	ENST00000344749.5:c.461C>G	p.Ser154Cys	p.S154C	ENST00000344749	NM_001136139.2	154	tCc/tGc	7/19	0.57704014276344	3	FACETS	0.847	0.779	0.918	0.424	0.389	0.459	CLONAL	1	TRUE	1	0.57704014276344	3		623	896	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18943097	18943097	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	110	324	0	ENST00000262803.5:c.79G>C	p.Asp27His	p.D27H	ENST00000262803	NM_002911.3	27	Gac/Cac	1/24	0.194439187480012	3	FACETS	0.95	0.857	1	0.317	0.285	0.35	INDETERMINATE	1	TRUE	0	0.57704014276344	3		324	517	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210423	36210423	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866027702	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	58	532	0	ENST00000222270.7:c.416C>G	p.Ser139Cys	p.S139C	ENST00000222270	NM_014727.1	139	tCt/tGt	2/37	0.194439187480012	3	FACETS	0.377	0.323	0.436	0.126	0.107	0.146	INDETERMINATE	1	TRUE	0	0.57704014276344	3		532	687	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762869	40762869	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	146	589	0	ENST00000392038.2:c.139C>G	p.Gln47Glu	p.Q47E	ENST00000392038	NM_001626.4	47	Cag/Gag	3/14	0.194439187480012	3	FACETS	0.885	0.809	0.964	0.295	0.269	0.322	INDETERMINATE	1	TRUE	0	0.57704014276344	3		589	737	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721139	61721139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	133	455	0	ENST00000401558.2:c.1135G>A	p.Glu379Lys	p.E379K	ENST00000401558	NM_003400.3	379	Gaa/Aaa	12/25	0.57704014276344	3	FACETS	0.818	0.744	0.896	0.409	0.372	0.448	CLONAL	1	TRUE	1	0.57704014276344	3		455	726	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610520	215610520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	142	446	0	ENST00000260947.4:c.1736C>T	p.Ser579Leu	p.S579L	ENST00000260947	NM_000465.2	579	tCa/tTa	8/11	0.54257958614697	3	FACETS	0.884	0.807	0.965	0.442	0.403	0.483	CLONAL	1	TRUE	1	0.57704014276344	3		446	717	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281219	46281219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1402011307	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	113	488	0	ENST00000371998.3:c.4016G>A	p.Arg1339Lys	p.R1339K	ENST00000371998		1339	aGa/aAa	21/23	0.57704014276344	6	FACETS	0.733	0.658	0.813	0.183	0.164	0.204	SUBCLONAL	1	TRUE	2	0.57704014276344	6		488	1151	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069267	30069268	+	missense_variant	Missense_Mutation	DNP	GA	GA	CT	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	128	484	0	ENST00000338641.4:c.1132_1133delinsCT	p.Glu378Leu	p.E378L	ENST00000338641	NM_000268.3	378	GAg/CTg	12/16	0.57704014276344	3	FACETS	0.926	0.842	1	0.463	0.421	0.508	CLONAL	1	TRUE	1	0.57704014276344	3		484	617	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545766	41545766	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	138	401	0	ENST00000263253.7:c.2381C>T	p.Ala794Val	p.A794V	ENST00000263253	NM_001429.3	794	gCa/gTa	14/31	0.57704014276344	3	FACETS	1	0.951	1	0.529	0.484	0.577	CLONAL	1	TRUE	1	0.57704014276344	3		401	582	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042470	37042470	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	101	365	1	ENST00000231790.2:c.232G>T	p.Glu78Ter	p.E78*	ENST00000231790	NM_000249.3	78	Gaa/Taa	3/19	1	2	FACETS	0.799	0.719	0.884	0.799	0.719	0.884	SUBCLONAL	1	TRUE	1	0.57704014276344	2		366	438	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595864	52595864	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	152	551	0	ENST00000394830.3:c.4051G>C	p.Asp1351His	p.D1351H	ENST00000394830	NM_018313.4	1351	Gac/Cac	26/30	1	2	FACETS	0.806	0.739	0.875	0.806	0.739	0.875	CLONAL	1	TRUE	1	0.57704014276344	2		551	654	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534289	187534289	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	109	520	0	ENST00000441802.2:c.9437G>C	p.Arg3146Thr	p.R3146T	ENST00000441802	NM_005245.3	3146	aGa/aCa	13/27	0.525964948873822	4	FACETS	0.65	0.583	0.721	0.325	0.291	0.361	SUBCLONAL	1	TRUE	2	0.57704014276344	4		520	917	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540899	187540899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	108	341	0	ENST00000441802.2:c.6841C>T	p.Pro2281Ser	p.P2281S	ENST00000441802	NM_005245.3	2281	Cct/Tct	10/27	0.525964948873822	4	FACETS	0.89	0.8	0.986	0.445	0.4	0.493	CLONAL	1	TRUE	2	0.57704014276344	4		341	663	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637250	176637250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	164	592	1	ENST00000439151.2:c.1850C>T	p.Ser617Leu	p.S617L	ENST00000439151	NM_022455.4	617	tCa/tTa	5/23	0.574161358931072	4	FACETS	0.851	0.781	0.925			1	CLONAL	1	TRUE	NA	0.57704014276344	4		593	1053	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637597	176637597	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	181	519	1	ENST00000439151.2:c.2197C>A	p.Leu733Met	p.L733M	ENST00000439151	NM_022455.4	733	Ctg/Atg	5/23	0.574161358931072	4	FACETS	1	0.948	1			1	CLONAL	1	TRUE	NA	0.57704014276344	4		520	956	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158619	26158619	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1358692800	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	68	281	0	ENST00000289316.2:c.222C>G	p.Ile74Met	p.I74M	ENST00000289316	NM_138720.2	74	atC/atG	1/2	0.568457204222024	5	FACETS	0.892	0.778	1	0.297	0.259	0.339	CLONAL	1	TRUE	2	0.57704014276344	5		281	493	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681601	30681601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	146	485	0	ENST00000376406.3:c.496G>A	p.Glu166Lys	p.E166K	ENST00000376406	NM_014641.2	166	Gag/Aag	3/15	0.3986553256363	5	FACETS	0.967	0.882	1	0.322	0.294	0.353	CLONAL	1	TRUE	2	0.57704014276344	5		485	976	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100145	157100145	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	23	71	0	ENST00000346085.5:c.1082C>A	p.Ser361Ter	p.S361*	ENST00000346085	NM_020732.3	361	tCg/tAg	1/20	0.57704014276344	3	FACETS	1	0.895	1	0.604	0.483	0.736	CLONAL	1	TRUE	1	0.57704014276344	3		71	85	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527522	157527522	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	159	537	0	ENST00000346085.5:c.5247G>C	p.Glu1749Asp	p.E1749D	ENST00000346085	NM_020732.3	1749	gaG/gaC	20/20	0.57704014276344	3	FACETS	0.965	0.886	1	0.482	0.443	0.524	CLONAL	1	TRUE	1	0.57704014276344	3		537	736	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878431	151878431	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	192	643	0	ENST00000262189.6:c.6514G>C	p.Asp2172His	p.D2172H	ENST00000262189	NM_170606.2	2172	Gac/Cac	36/59	0.54257958614697	3	FACETS	0.86	0.795	0.927	0.43	0.397	0.464	CLONAL	1	TRUE	1	0.57704014276344	3		643	997	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80646056	80646056	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	61	225	0	ENST00000286548.4:c.96C>A	p.Asp32Glu	p.D32E	ENST00000286548	NM_002072.3	32	gaC/gaA	1/7	0.57704014276344	3	FACETS	0.876	0.761	0.999	0.438	0.38	0.5	CLONAL	1	TRUE	1	0.57704014276344	3		225	311	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0050794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	159	366	0				ENST00000310581	NM_198253.2	-/1132			0.550913975350418	1	FACETS	0.808	0.754	0.862	0.808	0.754	0.862	CLONAL	1	TRUE	0	0.763110039560446	1		366	319	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0050794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	463	627	3	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.577471214322868	1	FACETS	0.925	0.892	0.959	0.925	0.892	0.959	CLONAL	1	TRUE	0	0.763110039560446	1		630	811	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	396	581	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.763110039560446	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.763110039560446	1		581	575	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835741	68835741	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	329	592	0	ENST00000261769.5:c.332C>A	p.Ser111Tyr	p.S111Y	ENST00000261769	NM_004360.3	111	tCc/tAc	3/16	0.354845469933589	1	FACETS	0.717	0.682	0.752	0.717	0.682	0.752	INDETERMINATE	1	TRUE	0	0.763110039560446	1		592	744	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346418	89346418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	165	653	1	ENST00000301030.4:c.6532G>A	p.Asp2178Asn	p.D2178N	ENST00000301030	NM_001256183.1	2178	Gat/Aat	9/13	0.354845469933589	1	FACETS	0.434	0.4	0.469	0.434	0.4	0.469	INDETERMINATE	1	TRUE	0	0.763110039560446	1		654	616	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617490	158617490	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	189	533	0	ENST00000263640.3:c.1166A>G	p.Glu389Gly	p.E389G	ENST00000263640	NM_001105.4	389	gAa/gGa	9/11	0.354845469933589	1	FACETS	0.505	0.469	0.541	0.505	0.469	0.541	INDETERMINATE	1	TRUE	0	0.763110039560446	1		533	607	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660180	227660180	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1205546039	NA	P-0050794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	217	740	0	ENST00000305123.5:c.3275C>T	p.Pro1092Leu	p.P1092L	ENST00000305123	NM_005544.2	1092	cCa/cTa	1/2	0.763110039560446	1	FACETS	0.715	0.672	0.758	0.715	0.672	0.758	SUBCLONAL	1	TRUE	0	0.763110039560446	1		740	492	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552973	106552973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	176	634	0	ENST00000369096.4:c.938C>T	p.Ser313Phe	p.S313F	ENST00000369096	NM_001198.3	313	tCc/tTc	5/7	0.250091552031934	2	FACETS	0.648	0.598	0.699	0.324	0.299	0.35	INDETERMINATE	1	TRUE	0	0.763110039560446	2		634	712	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058566	69058566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866534903	NA	P-0050794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	164	565	0	ENST00000288368.4:c.4210C>T	p.His1404Tyr	p.H1404Y	ENST00000288368	NM_024870.2	1404	Cat/Tat	34/40	0.250091552031934	2	FACETS	0.642	0.591	0.694	0.321	0.295	0.347	INDETERMINATE	1	TRUE	0	0.763110039560446	2		565	670	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0050795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	28	252	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.633	0.506	0.779	0.633	0.506	0.779	SUBCLONAL	1	TRUE	1	0.216157396566331	2		252	409	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119775	70119776	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0050795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	137	667	0	ENST00000245479.2:c.779dup	p.Glu261ArgfsTer35	p.E261Rfs*35	ENST00000245479	NM_000346.3	259	-/C	3/3	0.183578189219213	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	2	0.216157396566331	4		667	711	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0050796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	226	396	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.67895512822923	2		396	610	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0050803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	8104	396	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.553668778356584	91	FACETS	0.996	0.993	0.998			1	CLONAL	91	TRUE	NA	0.553668778356584	91		396	8283	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262336	115262336	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	54	300	0	ENST00000438362.2:c.2218G>A	p.Asp740Asn	p.D740N	ENST00000438362	NM_001242891.1	740	Gat/Aat	18/20	0.553668778356584	3	FACETS	0.743	0.638	0.857	0.372	0.319	0.429	SUBCLONAL	1	TRUE	1	0.553668778356584	3		300	335	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069459	30069460	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	T	novel	NA	P-0050803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	231	578	0	ENST00000338641.4:c.1324_1325delinsT	p.Glu442TrpfsTer13	p.E442Wfs*13	ENST00000338641	NM_000268.3	442	GAg/Tg	12/16	0.553668778356584	2	FACETS	0.929	0.879	0.98	0.929	0.879	0.98	CLONAL	2	TRUE	0	0.553668778356584	2		578	449	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111496	8111503	+	frameshift_variant	Frame_Shift_Del	DEL	TGGAGGAG	TGGAGGAG	-	novel	NA	P-0050805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	101	557	0	ENST00000346208.3:c.982_989del	p.Trp328GlufsTer21	p.W328Efs*21	ENST00000346208		328	TGGAGGAGg/g	5/6	1	2	FACETS	0.875	0.783	0.973	0.875	0.783	0.973	CLONAL	1	TRUE	1	0.351341087662483	2		557	657	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873606	151873607	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0050805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	81	482	0	ENST00000262189.6:c.8930_8931dup	p.Arg2978LeufsTer3	p.R2978Lfs*3	ENST00000262189	NM_170606.2	2977	-/CT	38/59	0.255608471644919	3	FACETS	0.794	0.699	0.895	0.397	0.349	0.448	SUBCLONAL	1	TRUE	1	0.351341087662483	3		482	683	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0050806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	21	390	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.304856196478092	4	FACETS	1	0.91	1	0.693	0.54	0.865	CLONAL	1	FALSE	2	0.316847830059043	4		390	126	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0050806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	137	600	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.28864166476942	2	FACETS	0.819	0.749	0.892	0.819	0.749	0.892	CLONAL	2	FALSE	0	0.316847830059043	2		600	528	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0050806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	57	431	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.260740432771444	2	FACETS	0.818	0.711	0.931	0.818	0.711	0.931	CLONAL	2	FALSE	0	0.316847830059043	2		431	220	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0050806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	70	417	1	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.316847830059043	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	FALSE	1	0.316847830059043	3		418	214	SUCCESS
APC	324	MSKCC	GRCh37	5	112175322	112175322	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1114167578	NA	P-0050806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	62	252	0	ENST00000257430.4:c.4031C>G	p.Ser1344Ter	p.S1344*	ENST00000257430	NM_000038.5	1344	tCa/tGa	16/16	0.316847830059043	3	FACETS	1	0.955	1	0.795	0.699	0.895	CLONAL	2	FALSE	0	0.316847830059043	3		252	190	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244257	5244257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	90	992	0	ENST00000357368.4:c.1225G>A	p.Gly409Ser	p.G409S	ENST00000357368	NM_002850.3	409	Ggc/Agc	11/38	1	2	FACETS	0.942	0.837	1	0.942	0.837	1	CLONAL	1	FALSE	1	0.316847830059043	2		992	603	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797269	32797269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs972577711	NA	P-0050806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	119	800	2	ENST00000374899.4:c.1840C>T	p.Arg614Cys	p.R614C	ENST00000374899	NM_018833.2	614	Cgt/Tgt	11/12	0.316847830059043	4	FACETS	1	0.984	1	0.739	0.668	0.814	CLONAL	1	FALSE	2	0.316847830059043	4		802	669	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47685242	47685242	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1343939111	NA	P-0050806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	22	364	0	ENST00000347630.2:c.708C>A	p.Ser236Arg	p.S236R	ENST00000347630	NM_001007230.1	236	agC/agA	8/11	0.278008765618262	3	FACETS	0.829	0.646	1	0.415	0.323	0.52	CLONAL	1	FALSE	1	0.316847830059043	3		364	194	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	461	734	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.589501130617234	5	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	2	0.589501130617234	5		735	895	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	108	276	0				ENST00000310581	NM_198253.2	-/1132			0.589501130617234	3	FACETS	0.844	0.77	0.92	0.844	0.77	0.92	CLONAL	2	TRUE	1	0.589501130617234	3		276	281	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991700	72991711	+	inframe_deletion	In_Frame_Del	DEL	GCCGCCGCCGCA	GCCGCCGCCGCA	-	novel	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	39	538	0	ENST00000268489.5:c.2334_2345del	p.Ala781_Ala784del	p.A781_A784del	ENST00000268489	NM_006885.3	778	gcTGCGGCGGCGGCg/gcg	2/10	0.475584933760845	4	FACETS	0.493	0.408	0.586	0.246	0.204	0.293	SUBCLONAL	1	TRUE	2	0.589501130617234	4		538	427	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423511	88423511	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	160	538	0	ENST00000360948.2:c.2324C>G	p.Ser775Ter	p.S775*	ENST00000360948	NM_001012338.2	775	tCa/tGa	18/19	0.475584933760845	4	FACETS	0.812	0.75	0.877	0.812	0.75	0.877	CLONAL	2	TRUE	2	0.589501130617234	4		538	531	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	235	765	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	0.264912969748508	2	FACETS	0.936	0.887	0.984	0.936	0.887	0.984	INDETERMINATE	2	TRUE	0	0.589501130617234	2		765	426	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681353	88681353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140592056	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	41	148	0	ENST00000372037.3:c.1243G>A	p.Glu415Lys	p.E415K	ENST00000372037	NM_004329.2	415	Gaa/Aaa	11/13	0.513671954888205	4	FACETS	1	0.959	1	0.737	0.625	0.857	CLONAL	1	TRUE	2	0.589501130617234	4		148	150	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	170	501	1	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	0.475584933760845	4	FACETS	0.949	0.88	1	0.949	0.88	1	CLONAL	2	TRUE	2	0.589501130617234	4		502	483	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	293	835	1	ENST00000269571.5:c.829G>T	p.Asp277Tyr	p.D277Y	ENST00000269571		277	Gac/Tac	7/27	0.589501130617234	5	FACETS	1	0.984	1	0.739	0.698	0.781	CLONAL	2	TRUE	2	0.589501130617234	5		836	845	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619935	21619935	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1421639293	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	212	628	0	ENST00000382592.4:c.231G>C	p.Leu77Phe	p.L77F	ENST00000382592	NM_014572.2	77	ttG/ttC	2/8	0.513671954888205	4	FACETS	0.961	0.899	1	0.961	0.899	1	CLONAL	2	TRUE	2	0.589501130617234	4		628	595	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458572	12458572	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	95	601	0	ENST00000287820.6:c.1189G>C	p.Glu397Gln	p.E397Q	ENST00000287820	NM_015869.4	397	Gag/Cag	6/7	0.513671954888205	4	FACETS	0.865	0.772	0.964	0.433	0.386	0.482	CLONAL	1	TRUE	2	0.589501130617234	4		601	592	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288412	15288412	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	55	723	0	ENST00000263388.2:c.4327G>A	p.Asp1443Asn	p.D1443N	ENST00000263388	NM_000435.2	1443	Gac/Aac	24/33	0.145586395920836	6	FACETS	0.487	0.415	0.566	0.162	0.138	0.189	INDETERMINATE	1	TRUE	3	0.589501130617234	6		723	835	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108641	8108641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	227	763	0	ENST00000585124.1:c.754G>A	p.Glu252Lys	p.E252K	ENST00000585124	NM_004217.3	252	Gag/Aag	8/9	0.475584933760845	4	FACETS	0.883	0.827	0.941	0.883	0.827	0.941	CLONAL	2	TRUE	2	0.589501130617234	4		763	693	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817505	39817505	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	179	567	0	ENST00000288319.7:c.58G>C	p.Glu20Gln	p.E20Q	ENST00000288319	NM_182918.3	20	Gag/Cag	2/10	0.475584933760845	4	FACETS	0.867	0.804	0.931	0.867	0.804	0.931	CLONAL	2	TRUE	2	0.589501130617234	4		567	557	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350747	89350747	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	218	672	0	ENST00000301030.4:c.2203G>C	p.Glu735Gln	p.E735Q	ENST00000301030	NM_001256183.1	735	Gag/Cag	9/13	0.475584933760845	4	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	2	0.589501130617234	4		672	588	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219785	36219785	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	307	844	0	ENST00000222270.7:c.4682C>G	p.Ser1561Ter	p.S1561*	ENST00000222270	NM_014727.1	1561	tCa/tGa	20/37	0.145586395920836	6	FACETS	0.975	0.924	1	0.975	0.924	1	INDETERMINATE	3	TRUE	3	0.589501130617234	6		844	776	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841800	151841800	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	99	274	0	ENST00000262189.6:c.14341C>T	p.Gln4781Ter	p.Q4781*	ENST00000262189	NM_170606.2	4781	Cag/Tag	55/59	0.475584933760845	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	2	0.589501130617234	4		274	245	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363883	118363883	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	74	476	0	ENST00000534358.1:c.5116C>T	p.Gln1706Ter	p.Q1706*	ENST00000534358	NM_005933.3	1706	Cag/Tag	16/36	1	2	FACETS	0.884	0.782	0.991	0.884	0.782	0.991	CLONAL	1	TRUE	1	0.589501130617234	2		476	284	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057768	27057768	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	330	759	1	ENST00000324856.7:c.1476del	p.Thr493ProfsTer126	p.T493Pfs*126	ENST00000324856	NM_006015.4	492	caG/ca	3/20	0.513671954888205	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	2	0.589501130617234	4		760	754	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100739	8100739	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	254	773	1	ENST00000346208.3:c.713G>A	p.Ser238Asn	p.S238N	ENST00000346208		238	aGc/aAc	3/6	0.513671954888205	4	FACETS	0.977	0.919	1	0.977	0.919	1	CLONAL	2	TRUE	2	0.589501130617234	4		774	701	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415876	49415876	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1477916093	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	155	452	0	ENST00000301067.7:c.16471G>C	p.Glu5491Gln	p.E5491Q	ENST00000301067	NM_003482.3	5491	Gag/Cag	53/54	0.513671954888205	4	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	2	0.589501130617234	4		452	410	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112401	115112401	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	252	832	0	ENST00000257566.3:c.1339C>G	p.Arg447Gly	p.R447G	ENST00000257566	NM_016569.3	447	Cgc/Ggc	7/8	0.513671954888205	4	FACETS	0.992	0.933	1	0.992	0.933	1	CLONAL	2	TRUE	2	0.589501130617234	4		832	685	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619898	21619898	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	201	574	0	ENST00000382592.4:c.268G>C	p.Glu90Gln	p.E90Q	ENST00000382592	NM_014572.2	90	Gaa/Caa	2/8	0.513671954888205	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	2	0.589501130617234	4		574	526	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437028	110437028	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	107	127	1	ENST00000375856.3:c.1373C>T	p.Ser458Phe	p.S458F	ENST00000375856	NM_003749.2	458	tCc/tTc	1/2	0.513671954888205	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.589501130617234	4		128	241	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100401	2100401	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	155	458	0	ENST00000219476.3:c.139G>A	p.Glu47Lys	p.E47K	ENST00000219476	NM_000548.3	47	Gaa/Aaa	3/42	0.461351086414025	5	FACETS	1	0.976	1	0.756	0.699	0.814	CLONAL	2	TRUE	2	0.589501130617234	5		458	437	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100408	2100408	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	155	470	0	ENST00000219476.3:c.146del	p.Ser49ThrfsTer12	p.S49Tfs*12	ENST00000219476	NM_000548.3	49	aGc/ac	3/42	0.461351086414025	5	FACETS	1	0.972	1	0.741	0.684	0.798	CLONAL	2	TRUE	2	0.589501130617234	5		470	446	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134302	11134302	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	193	641	1	ENST00000358026.2:c.2968G>T	p.Glu990Ter	p.E990*	ENST00000358026	NM_001128849.1	990	Gaa/Taa	20/36	0.145586395920836	6	FACETS	0.933	0.87	0.996	0.933	0.87	0.996	INDETERMINATE	3	TRUE	3	0.589501130617234	6		642	510	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919626	96919626	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	190	610	0	ENST00000258439.3:c.637G>C	p.Glu213Gln	p.E213Q	ENST00000258439	NM_001193304.2	213	Gag/Cag	4/4	0.461351086414025	5	FACETS	0.861	0.805	0.919	0.861	0.805	0.919	CLONAL	3	TRUE	2	0.589501130617234	5		610	470	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980907	40980907	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs926083986	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	173	445	0	ENST00000373198.4:c.1579G>A	p.Gly527Ser	p.G527S	ENST00000373198	NM_133170.3	527	Ggc/Agc	10/32	0.145586395920836	6	FACETS	0.901	0.837	0.967	0.901	0.837	0.967	INDETERMINATE	3	TRUE	3	0.589501130617234	6		445	473	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817469	39817469	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	205	597	0	ENST00000288319.7:c.94G>T	p.Glu32Ter	p.E32*	ENST00000288319	NM_182918.3	32	Gag/Tag	2/10	0.475584933760845	4	FACETS	0.942	0.879	1	0.942	0.879	1	CLONAL	2	TRUE	2	0.589501130617234	4		597	587	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458605	12458605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	80	526	0	ENST00000287820.6:c.1222G>A	p.Asp408Asn	p.D408N	ENST00000287820	NM_015869.4	408	Gat/Aat	6/7	0.513671954888205	4	FACETS	0.828	0.731	0.932	0.414	0.365	0.466	CLONAL	1	TRUE	2	0.589501130617234	4		526	521	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035075	37035075	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587779008	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	249	536	0	ENST00000231790.2:c.37G>A	p.Glu13Lys	p.E13K	ENST00000231790	NM_000249.3	13	Gag/Aag	1/19	0.513671954888205	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.589501130617234	4		536	612	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260136	149260136	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	193	487	0	ENST00000360632.3:c.757G>C	p.Glu253Gln	p.E253Q	ENST00000360632	NM_015472.4	253	Gag/Cag	4/7	0.475584933760845	4	FACETS	0.948	0.883	1	0.948	0.883	1	CLONAL	2	TRUE	2	0.589501130617234	4		487	549	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169953073	169953073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	196	475	1	ENST00000295797.4:c.157G>A	p.Glu53Lys	p.E53K	ENST00000295797	NM_002740.5	53	Gag/Aag	2/18	0.475584933760845	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.589501130617234	4		476	503	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196728	106196728	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	133	452	0	ENST00000380013.4:c.5061G>C	p.Gln1687His	p.Q1687H	ENST00000380013	NM_001127208.2	1687	caG/caC	11/11	0.246395738190597	4	FACETS	1	0.982	1	1	0.982	1	INDETERMINATE	2	TRUE	2	0.589501130617234	4		452	295	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976715	2976716	+	missense_variant	Missense_Mutation	DNP	TC	TC	CG	novel	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	94	677	0	ENST00000396946.4:c.1296_1297delinsCG	p.Glu432_Ser433delinsAspGly	p.E432_S433delinsDG	ENST00000396946	NM_032415.4	432	gaGAgc/gaCGgc	9/25	0.246395738190597	4	FACETS	0.819	0.73	0.914	0.409	0.365	0.457	INDETERMINATE	1	TRUE	2	0.589501130617234	4		677	619	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457159	5457159	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	106	351	0	ENST00000381577.3:c.133G>C	p.Glu45Gln	p.E45Q	ENST00000381577	NM_014143.3	45	Gaa/Caa	3/7	0.264912969748508	2	FACETS	0.972	0.898	1	0.972	0.898	1	INDETERMINATE	2	TRUE	0	0.589501130617234	2		351	185	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346868	70346868	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	366	384	0	ENST00000374080.3:c.2735C>T	p.Ser912Leu	p.S912L	ENST00000374080		912	tCg/tTg	20/45	0.589501130617234	3	FACETS	0.905	0.881	0.928			1	CLONAL	4	TRUE	NA	0.589501130617234	3		384	444	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169988332	169988332	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141965722	NA	P-0050808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	52	299	2	ENST00000295797.4:c.574C>T	p.Arg192Trp	p.R192W	ENST00000295797	NM_002740.5	192	Cgg/Tgg	6/18	1	2	FACETS	0.588	0.505	0.677	0.588	0.505	0.677	SUBCLONAL	1	TRUE	1	0.709983122743442	2		301	249	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627174	86627175	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGAAAACTTGACAGAACGAT	novel	NA	P-0050808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	14	186	0	ENST00000274376.6:c.550_569dup	p.Ile190MetfsTer8	p.I190Mfs*8	ENST00000274376	NM_002890.2	183	-/GGAAAACTTGACAGAACGAT	2/25	1	2	FACETS	0.306	0.222	0.405	0.306	0.222	0.405	SUBCLONAL	1	TRUE	1	0.709983122743442	2		186	129	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86676335	86676336	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0050808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	46	222	0	ENST00000274376.6:c.2617_2618del	p.Ile873LeufsTer11	p.I873Lfs*11	ENST00000274376	NM_002890.2	871	agATat/agat	20/25	1	2	FACETS	0.906	0.78	1	0.906	0.78	1	CLONAL	1	TRUE	1	0.709983122743442	2		222	143	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637651	176637651	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs775181583	NA	P-0050808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	119	483	0	ENST00000439151.2:c.2251C>G	p.Leu751Val	p.L751V	ENST00000439151	NM_022455.4	751	Ctc/Gtc	5/23	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.709983122743442	2		483	332	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658326	18658326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560894742	NA	P-0050809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	14	496	1	ENST00000266497.5:c.3131C>T	p.Ser1044Leu	p.S1044L	ENST00000266497		1044	tCg/tTg	22/31	0.3	1	FACETS	0.329	0.238	0.439	0.329	0.238	0.439	SUBCLONAL	1	TRUE	0	0.31	1		497	232	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066675	94066675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	19	496	1	ENST00000369303.4:c.1084G>A	p.Asp362Asn	p.D362N	ENST00000369303	NM_004440.3	362	Gat/Aat	5/17	0.148732268217973	5	FACETS	0.601	0.456	0.771	0.2	0.152	0.257	INDETERMINATE	1	TRUE	2	0.31	5		497	299	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892206	9892206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	13	633	0	ENST00000330684.3:c.2284G>A	p.Gly762Arg	p.G762R	ENST00000330684	NM_001134407.1	762	Gga/Aga	11/13	1	2	FACETS	0.453	0.324	0.61	0.453	0.324	0.61	SUBCLONAL	1	TRUE	1	0.31	2		633	185	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476272	88476272	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	25	641	0	ENST00000360948.2:c.1860G>A	p.Met620Ile	p.M620I	ENST00000360948	NM_001012338.2	620	atG/atA	15/19	1	2	FACETS	0.743	0.589	0.919	0.743	0.589	0.919	CLONAL	1	TRUE	1	0.31	2		641	217	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048898	180048898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	12	985	1	ENST00000261937.6:c.1664C>T	p.Pro555Leu	p.P555L	ENST00000261937	NM_182925.4	555	cCc/cTc	13/30	0.215882617821785	0	FACETS	0.334	0.235	0.454			1	SUBCLONAL	1	TRUE	0	0.31	0		986	160	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499829	8499829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1220058466	NA	P-0050809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	17	513	0	ENST00000356435.5:c.2140C>T	p.Pro714Ser	p.P714S	ENST00000356435		714	Cct/Tct	14/35	1	2	FACETS	0.451	0.337	0.587	0.451	0.337	0.587	SUBCLONAL	1	TRUE	1	0.31	2		513	243	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026771	48026771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878853710	NA	P-0050809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	13	402	0	ENST00000234420.5:c.1649C>T	p.Ser550Phe	p.S550F	ENST00000234420	NM_000179.2	550	tCt/tTt	4/10	0.148732268217973	3	FACETS	0.47	0.336	0.634	0.235	0.168	0.317	INDETERMINATE	1	TRUE	1	0.31	3		402	206	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273994	10273994	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	27	1049	0	ENST00000330684.3:c.275G>A	p.Gly92Glu	p.G92E	ENST00000330684	NM_001134407.1	92	gGg/gAg	2/13	1	2	FACETS	0.884	0.709	1	0.884	0.709	1	CLONAL	1	TRUE	1	0.31	2		1049	197	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16052787	16052787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	35	300	1	ENST00000268712.3:c.887G>A	p.Arg296Lys	p.R296K	ENST00000268712	NM_006311.3	296	aGa/aAa	9/46	1	2	FACETS	0.765	0.63	0.917	0.765	0.63	0.917	CLONAL	1	TRUE	1	0.31	2		301	295	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745997	162745997	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	17	342	0	ENST00000367921.3:c.2120T>C	p.Val707Ala	p.V707A	ENST00000367921	NM_006182.2	707	gTt/gCt	16/18	0.215882617821785	3	FACETS	0.615	0.46	0.798	0.307	0.23	0.399	SUBCLONAL	1	TRUE	1	0.31	3		342	206	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404458	70404458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755655526	NA	P-0050809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	10	316	0	ENST00000373644.4:c.1972G>A	p.Asp658Asn	p.D658N	ENST00000373644	NM_030625.2	658	Gat/Aat	4/12	1	2	FACETS	0.436	0.296	0.611	0.436	0.296	0.611	SUBCLONAL	1	TRUE	1	0.31	2		316	148	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981860	101981861	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0050809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	29	825	2	ENST00000282441.5:c.281_282delinsTT	p.Ser94Phe	p.S94F	ENST00000282441	NM_001130145.2	94	tCC/tTT	1/9	0.148732268217973	3	FACETS	0.649	0.521	0.794	0.324	0.26	0.397	INDETERMINATE	1	TRUE	1	0.31	3		827	333	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432386	49432386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1485781380	NA	P-0050809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	24	928	0	ENST00000301067.7:c.8753C>T	p.Pro2918Leu	p.P2918L	ENST00000301067	NM_003482.3	2918	cCt/cTt	34/54	0.215882617821785	5	FACETS	0.89	0.699	1	0.297	0.233	0.369	CLONAL	1	TRUE	2	0.31	5		928	255	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120789177	120789177	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	15	593	0	ENST00000257552.2:c.760C>A	p.Pro254Thr	p.P254T	ENST00000257552	NM_002442.3	254	Ccg/Acg	11/15	0.148732268217973	0	FACETS	0.448	0.33	0.589			1	INDETERMINATE	1	TRUE	0	0.31	0		593	149	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005634	42005634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373831853	NA	P-0050809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	24	337	0	ENST00000219905.7:c.3370G>A	p.Gly1124Arg	p.G1124R	ENST00000219905	NM_001164273.1	1124	Gga/Aga	9/24	0.3	1	FACETS	0.935	0.742	1	0.935	0.742	1	CLONAL	1	TRUE	0	0.31	1		337	140	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17116996	17116996	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	33	724	0	ENST00000285071.4:c.1713C>G	p.Ser571Arg	p.S571R	ENST00000285071	NM_144997.5	571	agC/agG	14/14	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.31	2		724	196	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652932	29652932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	17	387	0	ENST00000356175.3:c.4867G>A	p.Asp1623Asn	p.D1623N	ENST00000356175	NM_000267.3	1623	Gac/Aac	36/57	1	2	FACETS	0.414	0.309	0.539	0.414	0.309	0.539	SUBCLONAL	1	TRUE	1	0.31	2		387	265	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451858	29451858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	13	651	0	ENST00000389048.3:c.2707G>A	p.Gly903Arg	p.G903R	ENST00000389048	NM_004304.4	903	Gga/Aga	16/29	0.3	1	FACETS	0.36	0.257	0.485	0.36	0.257	0.485	SUBCLONAL	1	TRUE	0	0.31	1		651	197	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272079	142272079	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	21	447	0	ENST00000350721.4:c.2795C>T	p.Pro932Leu	p.P932L	ENST00000350721	NM_001184.3	932	cCc/cTc	13/47	0.215882617821785	3	FACETS	0.636	0.491	0.804	0.318	0.245	0.402	SUBCLONAL	1	TRUE	1	0.31	3		447	246	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584513	189584513	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs79939938	NA	P-0050809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	16	347	0	ENST00000264731.3:c.809A>G	p.Asn270Ser	p.N270S	ENST00000264731	NM_003722.4	270	aAc/aGc	6/14	0.215882617821785	3	FACETS	0.518	0.383	0.679	0.259	0.191	0.34	SUBCLONAL	1	TRUE	1	0.31	3		347	230	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264577	1264577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	15	769	0	ENST00000310581.5:c.2785C>T	p.Pro929Ser	p.P929S	ENST00000310581	NM_198253.2	929	Ccc/Tcc	11/16	0.3	1	FACETS	0.639	0.471	0.837	0.639	0.471	0.837	SUBCLONAL	1	TRUE	0	0.31	1		769	128	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38960517	38960517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	13	229	0	ENST00000357387.3:c.1834C>T	p.Leu612Phe	p.L612F	ENST00000357387	NM_152756.3	612	Ctt/Ttt	20/38	0.148732268217973	5	FACETS	0.683	0.488	0.919	0.228	0.162	0.307	INDETERMINATE	1	TRUE	2	0.31	5		229	180	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	155	276	0				ENST00000310581	NM_198253.2	-/1132			0.547236315243556	1	FACETS	0.76	0.708	0.811	0.76	0.708	0.811	SUBCLONAL	1	TRUE	0	0.7906466970413	1		276	312	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0050829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	700	474	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.781748969846184	3	FACETS	0.982	0.963	0.999	0.982	0.963	0.999	CLONAL	3	TRUE	0	0.7906466970413	3		474	839	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0050829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	431	786	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	1	2	FACETS	0.963	0.92	1	0.963	0.92	1	CLONAL	1	TRUE	1	0.7906466970413	2		786	1132	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459522	50459522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1410124404	NA	P-0050829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	80	387	0	ENST00000331340.3:c.811G>A	p.Val271Ile	p.V271I	ENST00000331340	NM_006060.4	271	Gtc/Atc	7/8	0.7906466970413	1	FACETS	0.408	0.363	0.455	0.408	0.363	0.455	SUBCLONAL	1	TRUE	0	0.7906466970413	1		387	300	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916226	9916226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	166	493	0	ENST00000330684.3:c.2063G>A	p.Gly688Glu	p.G688E	ENST00000330684	NM_001134407.1	688	gGa/gAa	10/13	1	2	FACETS	0.886	0.821	0.952	0.886	0.821	0.952	CLONAL	1	TRUE	1	0.7906466970413	2		493	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579717	7579717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs922736614	NA	P-0050829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	297	645	0	ENST00000269305.4:c.79C>T	p.Pro27Ser	p.P27S	ENST00000269305	NM_001126112.2	27	Cct/Tct	3/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.7906466970413	2		645	747	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577469	64577469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs794728616	NA	P-0050829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	314	653	1	ENST00000312049.6:c.113C>T	p.Ser38Phe	p.S38F	ENST00000312049	NM_130799.2	38	tCc/tTc	2/10	0.7906466970413	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.7906466970413	1		654	455	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499393	89499393	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	272	488	1	ENST00000336596.2:c.2563C>T	p.Gln855Ter	p.Q855*	ENST00000336596	NM_005233.5	855	Cag/Tag	15/17	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.7906466970413	2		489	627	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278788	1278788	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	343	830	0	ENST00000310581.5:c.2254C>T	p.His752Tyr	p.H752Y	ENST00000310581	NM_198253.2	752	Cat/Tat	6/16	0.547236315243556	1	FACETS	0.748	0.714	0.783	0.748	0.714	0.783	SUBCLONAL	1	TRUE	0	0.7906466970413	1		830	701	SUCCESS
APC	324	MSKCC	GRCh37	5	112178748	112178748	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	183	410	0	ENST00000257430.4:c.7457C>T	p.Pro2486Leu	p.P2486L	ENST00000257430	NM_000038.5	2486	cCt/cTt	16/16	0.41995652995545	1	FACETS	0.691	0.646	0.736	0.691	0.646	0.736	INDETERMINATE	1	TRUE	0	0.7906466970413	1		410	405	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156695	2156695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142012621	NA	P-0050829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	181	932	3	ENST00000434045.2:c.227C>T	p.Ser76Leu	p.S76L	ENST00000434045	NM_001127598.1	76	tCg/tTg	3/5	0.322339708795258	1	FACETS	0.338	0.312	0.365	0.338	0.312	0.365	INDETERMINATE	1	TRUE	0	0.7906466970413	1		935	819	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495322	56495322	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1323241399	NA	P-0050829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	141	565	0	ENST00000267101.3:c.3512C>T	p.Ser1171Phe	p.S1171F	ENST00000267101	NM_001982.3	1171	tCc/tTc	28/28	0.486412262872925	1	FACETS	0.414	0.379	0.45	0.414	0.379	0.45	SUBCLONAL	1	TRUE	0	0.7906466970413	1		565	521	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100412	2100412	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	258	486	0	ENST00000219476.3:c.150G>A	p.Met50Ile	p.M50I	ENST00000219476	NM_000548.3	50	atG/atA	3/42	1	2	FACETS	0.992	0.935	1	0.992	0.935	1	CLONAL	1	TRUE	1	0.7906466970413	2		486	658	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211325	36211325	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	337	774	0	ENST00000222270.7:c.1076A>G	p.Gln359Arg	p.Q359R	ENST00000222270	NM_014727.1	359	cAg/cGg	3/37	0.486412262872925	1	FACETS	0.76	0.725	0.795	0.76	0.725	0.795	SUBCLONAL	1	TRUE	0	0.7906466970413	1		774	678	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274652	198274653	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0050829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	123	637	1	ENST00000335508.6:c.745_746delinsTT	p.Pro249Leu	p.P249L	ENST00000335508	NM_012433.2	249	CCa/TTa	7/25	0.41995652995545	1	FACETS	0.333	0.302	0.365	0.333	0.302	0.365	INDETERMINATE	1	TRUE	0	0.7906466970413	1		638	565	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183746	10183746	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs962558566	NA	P-0050829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	380	951	0	ENST00000256474.2:c.215C>T	p.Ser72Phe	p.S72F	ENST00000256474	NM_000551.3	72	tCc/tTc	1/3	1	2	FACETS	0.931	0.886	0.976	0.931	0.886	0.976	CLONAL	1	TRUE	1	0.7906466970413	2		951	1033	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027107	71027107	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	263	609	0	ENST00000318789.4:c.1220C>T	p.Pro407Leu	p.P407L	ENST00000318789	NM_032682.5	407	cCa/cTa	15/21	1	2	FACETS	0.954	0.9	1	0.954	0.9	1	CLONAL	1	TRUE	1	0.7906466970413	2		609	697	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417368	139417368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	516	1157	0	ENST00000277541.6:c.676C>T	p.Pro226Ser	p.P226S	ENST00000277541	NM_017617.3	226	Ccc/Tcc	4/34	0.7906466970413	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.7906466970413	1		1157	719	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932815	39932815	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	413	374	1	ENST00000378444.4:c.1784T>A	p.Ile595Asn	p.I595N	ENST00000378444	NM_001123385.1	595	aTt/aAt	4/15	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.7906466970413	1		375	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781504	NA	P-0050830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	339	864	1	ENST00000269305.4:c.314G>T	p.Gly105Val	p.G105V	ENST00000269305	NM_001126112.2	105	gGc/gTc	4/11	0.809480104073409	1	FACETS	0.977	0.941	1	0.977	0.941	1	CLONAL	1	TRUE	0	0.831114097630646	1		865	488	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556484	29556484	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1131691122	NA	P-0050830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	135	330	0	ENST00000356175.3:c.2850+1G>T		p.X950_splice	ENST00000356175	NM_000267.3	950			0.831114097630646	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.831114097630646	1		330	173	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089478	27089478	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	260	710	1	ENST00000324856.7:c.2434C>T	p.Gln812Ter	p.Q812*	ENST00000324856	NM_006015.4	812	Cag/Tag	8/20	0.831114097630646	1	FACETS	0.883	0.843	0.923	0.883	0.843	0.923	CLONAL	1	TRUE	0	0.831114097630646	1		711	414	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156988	89156988	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0050830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	186	447	0	ENST00000336596.2:c.88+2T>G		p.X30_splice	ENST00000336596	NM_005233.5	30			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.831114097630646	2		447	427	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0050831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	213	630	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.797	0.743	0.852	0.797	0.743	0.852	SUBCLONAL	1	TRUE	1	0.706331355712152	2		630	757	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0050831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	163	518	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.962	0.89	1	0.962	0.89	1	CLONAL	1	TRUE	1	0.706331355712152	2		518	480	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0050831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	164	320	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.706331355712152	2		320	437	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	364	419	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	0.706331355712152	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.706331355712152	2		419	495	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380346	14380346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	158	379	2	ENST00000256196.4:c.71G>A	p.Gly24Asp	p.G24D	ENST00000256196		24	gGc/gAc	1/6	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.706331355712152	2		381	444	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033438	48033438	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs63750882	NA	P-0050831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	175	488	0	ENST00000234420.5:c.3742C>G	p.His1248Asp	p.H1248D	ENST00000234420	NM_000179.2	1248	Cac/Gac	8/10	1	2	FACETS	0.885	0.82	0.951	0.885	0.82	0.951	CLONAL	1	TRUE	1	0.706331355712152	2		488	560	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845614	63845614	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	120	217	0	ENST00000279873.7:c.1353del	p.Ser451ArgfsTer28	p.S451Rfs*28	ENST00000279873	NM_032199.2	451	agC/ag	9/10	1	2	FACETS	0.985	0.9	1	0.985	0.9	1	CLONAL	1	TRUE	1	0.706331355712152	2		217	345	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487311	56487311	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	215	475	0	ENST00000267101.3:c.1457A>G	p.His486Arg	p.H486R	ENST00000267101	NM_001982.3	486	cAt/cGt	12/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.706331355712152	2		475	543	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274640	198274640	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	298	629	1	ENST00000335508.6:c.758T>A	p.Ile253Lys	p.I253K	ENST00000335508	NM_012433.2	253	aTa/aAa	7/25	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.706331355712152	2		630	756	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	36	894	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.489	0.401	0.588	0.489	0.401	0.588	SUBCLONAL	1	TRUE	1	0.25	2		899	589	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391024	89391024	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	27	572	0	ENST00000336596.2:c.1095del	p.Lys365AsnfsTer6	p.K365Nfs*6	ENST00000336596	NM_005233.5	364	Aaa/aa	5/17	1	2	FACETS	0.492	0.391	0.608	0.492	0.391	0.608	SUBCLONAL	1	TRUE	1	0.25	2		572	439	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	19	325	3	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	1	2	FACETS	0.61	0.464	0.782	0.61	0.464	0.782	SUBCLONAL	1	TRUE	1	0.25	2		328	249	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	34	364	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.898	0.736	1	0.898	0.736	1	CLONAL	1	TRUE	1	0.25	2		364	303	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	23	350	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	0.455	0.354	0.573	0.455	0.354	0.573	SUBCLONAL	1	TRUE	1	0.25	2		350	404	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	30	859	2	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.464	0.373	0.568	0.464	0.373	0.568	SUBCLONAL	1	TRUE	1	0.25	2		861	517	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250883	153250883	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	36	368	1	ENST00000281708.4:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000281708	NM_033632.3	393	Cga/Tga	8/12	1	2	FACETS	0.74	0.609	0.887	0.74	0.609	0.887	SUBCLONAL	1	TRUE	1	0.25	2		369	389	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	27	329	0	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	1	2	FACETS	0.771	0.615	0.949	0.771	0.615	0.949	CLONAL	1	TRUE	1	0.25	2		329	280	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	35	304	4	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	1	2	FACETS	0.895	0.735	1	0.895	0.735	1	CLONAL	1	TRUE	1	0.25	2		308	313	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380279	25380279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	32	463	0	ENST00000311936.3:c.179G>A	p.Gly60Asp	p.G60D	ENST00000311936	NM_004985.3	60	gGt/gAt	3/5	1	2	FACETS	0.525	0.425	0.637	0.525	0.425	0.637	SUBCLONAL	1	TRUE	1	0.25	2		463	488	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262309	46262309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	27	550	0	ENST00000371998.3:c.893G>A	p.Arg298Gln	p.R298Q	ENST00000371998		298	cGa/cAa	9/23	1	2	FACETS	0.458	0.363	0.566	0.458	0.363	0.566	SUBCLONAL	1	TRUE	1	0.25	2		550	472	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226308	2226308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	61	1078	2	ENST00000326181.6:c.1921C>T	p.Arg641Cys	p.R641C	ENST00000326181	NM_032271.2	641	Cgt/Tgt	20/21	1	2	FACETS	0.695	0.599	0.8	0.695	0.599	0.8	SUBCLONAL	1	TRUE	1	0.25	2		1080	702	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426774	49426774	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1334139538	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	28	447	3	ENST00000301067.7:c.11714A>T	p.Gln3905Leu	p.Q3905L	ENST00000301067	NM_003482.3	3905	cAg/cTg	39/54	1	2	FACETS	0.742	0.594	0.909	0.742	0.594	0.909	CLONAL	1	TRUE	1	0.25	2		450	302	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112190	115112190	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1450269147	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	36	749	1	ENST00000257566.3:c.1550C>T	p.Pro517Leu	p.P517L	ENST00000257566	NM_016569.3	517	cCg/cTg	7/8	1	2	FACETS	0.611	0.502	0.734	0.611	0.502	0.734	SUBCLONAL	1	TRUE	1	0.25	2		750	471	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431722	49431722	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555190550	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	44	1033	0	ENST00000301067.7:c.9417del	p.Lys3140ArgfsTer2	p.K3140Rfs*2	ENST00000301067	NM_003482.3	3139	ccC/cc	34/54	1	2	FACETS	0.67	0.562	0.791	0.67	0.562	0.791	SUBCLONAL	1	TRUE	1	0.25	2		1033	525	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033193	69033193	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	23	500	0	ENST00000288368.4:c.3637del	p.Arg1213GlyfsTer31	p.R1213Gfs*31	ENST00000288368	NM_024870.2	1211	ccA/cc	30/40	1	2	FACETS	0.422	0.328	0.531	0.422	0.328	0.531	SUBCLONAL	1	TRUE	1	0.25	2		500	436	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478927	56478927	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	45	798	1	ENST00000267101.3:c.383G>A	p.Ser128Asn	p.S128N	ENST00000267101	NM_001982.3	128	aGc/aAc	3/28	1	2	FACETS	0.609	0.511	0.718	0.609	0.511	0.718	SUBCLONAL	1	TRUE	1	0.25	2		799	591	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31493321	31493322	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1330233722	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	20	366	0	ENST00000344624.3:c.1834dup	p.Leu612ProfsTer8	p.L612Pfs*8	ENST00000344624		612	ctg/cCtg	10/33	1	2	FACETS	0.446	0.34	0.569	0.446	0.34	0.569	SUBCLONAL	1	TRUE	1	0.25	2		366	359	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559777	29559777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs902739109	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	21	324	1	ENST00000356175.3:c.3374C>T	p.Ala1125Val	p.A1125V	ENST00000356175	NM_000267.3	1125	gCg/gTg	26/57	1	2	FACETS	0.587	0.453	0.744	0.587	0.453	0.744	SUBCLONAL	1	TRUE	1	0.25	2		325	286	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467590	66467590	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746706656	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	24	378	0	ENST00000273854.3:c.679C>T	p.Arg227Cys	p.R227C	ENST00000273854	NM_004439.5	227	Cgt/Tgt	3/18	1	2	FACETS	0.64	0.502	0.798	0.64	0.502	0.798	SUBCLONAL	1	TRUE	1	0.25	2		378	300	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095881	29095881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143611747	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	53	689	0	ENST00000328354.6:c.953G>A	p.Arg318His	p.R318H	ENST00000328354	NM_007194.3	318	cGc/cAc	9/15	1	2	FACETS	0.668	0.569	0.776	0.668	0.569	0.776	SUBCLONAL	1	TRUE	1	0.25	2		689	635	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050349	37050349	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63749959	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	27	398	0	ENST00000231790.2:c.503del	p.Asn168IlefsTer34	p.N168Ifs*34	ENST00000231790	NM_000249.3	166	ttA/tt	6/19	1	2	FACETS	0.535	0.425	0.66	0.535	0.425	0.66	SUBCLONAL	1	TRUE	1	0.25	2		398	404	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23635355	23635355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555459712	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	29	500	0	ENST00000261584.4:c.2809G>A	p.Gly937Arg	p.G937R	ENST00000261584	NM_024675.3	937	Gga/Aga	8/13	1	2	FACETS	0.468	0.375	0.574	0.468	0.375	0.574	SUBCLONAL	1	TRUE	1	0.25	2		500	496	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213894	2213896	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	89	1064	3	ENST00000398665.3:c.1708_1710del	p.Glu570del	p.E570del	ENST00000398665	NM_032482.2	569	aAGGag/aag	18/28	1	2	FACETS	0.985	0.873	1	0.985	0.873	1	CLONAL	1	TRUE	1	0.25	2		1067	723	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938875	178938875	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	11	96	0	ENST00000263967.3:c.2117T>A	p.Val706Asp	p.V706D	ENST00000263967	NM_006218.2	706	gTc/gAc	14/21	1	2	FACETS	1	0.808	1	1	0.808	1	CLONAL	1	TRUE	1	0.25	2		96	72	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961391	1961391	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	38	710	0	ENST00000382891.5:c.3179G>A	p.Arg1060His	p.R1060H	ENST00000382891	NM_133335.3	1060	cGc/cAc	17/22	1	2	FACETS	0.534	0.441	0.639	0.534	0.441	0.639	SUBCLONAL	1	TRUE	1	0.25	2		710	569	SUCCESS
APC	324	MSKCC	GRCh37	5	112151229	112151229	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	30	447	0	ENST00000257430.4:c.875del	p.Leu292Ter	p.L292*	ENST00000257430	NM_000038.5	291	gTt/gt	9/16	1	2	FACETS	0.536	0.431	0.655	0.536	0.431	0.655	SUBCLONAL	1	TRUE	1	0.25	2		447	448	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435879	149435879	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs281860281	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	48	824	0	ENST00000286301.3:c.2345G>A	p.Arg782His	p.R782H	ENST00000286301	NM_005211.3	782	cGt/cAt	18/22	0.261053278437459	0	FACETS	0.488	0.412	0.572			1	SUBCLONAL	1	TRUE	0	0.25	0		824	590	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983086	201983086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	129	781	0	ENST00000359651.3:c.935C>T	p.Ala312Val	p.A312V	ENST00000359651		312	gCc/gTc	7/8	0.280380685514011	3	FACETS	0.939	0.854	1	0.939	0.854	1	CLONAL	2	TRUE	1	0.25	3		781	618	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138924	64138924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1268525057	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	26	687	0	ENST00000334205.4:c.2291G>A	p.Arg764Gln	p.R764Q	ENST00000334205	NM_003942.2	764	cGa/cAa	17/17	1	2	FACETS	0.502	0.397	0.623	0.502	0.397	0.623	SUBCLONAL	1	TRUE	1	0.25	2		687	414	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948266	71948266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759985176	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	52	1034	1	ENST00000298229.2:c.2978C>T	p.Pro993Leu	p.P993L	ENST00000298229	NM_001567.3	993	cCg/cTg	26/28	1	2	FACETS	0.583	0.496	0.68	0.583	0.496	0.68	SUBCLONAL	1	TRUE	1	0.25	2		1035	713	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380207	25380207	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	29	433	0	ENST00000311936.3:c.251T>C	p.Ile84Thr	p.I84T	ENST00000311936	NM_004985.3	84	aTa/aCa	3/5	1	2	FACETS	0.542	0.435	0.664	0.542	0.435	0.664	SUBCLONAL	1	TRUE	1	0.25	2		433	428	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120806041	120806041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	49	901	1	ENST00000257552.2:c.136G>A	p.Val46Met	p.V46M	ENST00000257552	NM_002442.3	46	Gtg/Atg	3/15	1	2	FACETS	0.635	0.537	0.743	0.635	0.537	0.743	SUBCLONAL	1	TRUE	1	0.25	2		902	617	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993134	72993134	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	70	906	0	ENST00000268489.5:c.911A>T	p.Asp304Val	p.D304V	ENST00000268489	NM_006885.3	304	gAc/gTc	2/10	1	2	FACETS	0.781	0.68	0.89	0.781	0.68	0.89	SUBCLONAL	1	TRUE	1	0.25	2		906	717	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276789	15276789	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	38	971	1	ENST00000263388.2:c.5476T>C	p.Cys1826Arg	p.C1826R	ENST00000263388	NM_000435.2	1826	Tgc/Cgc	30/33	1	2	FACETS	0.486	0.4	0.581	0.486	0.4	0.581	SUBCLONAL	1	TRUE	1	0.25	2		972	626	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719263	52719263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	29	713	1	ENST00000322088.6:c.929G>A	p.Cys310Tyr	p.C310Y	ENST00000322088	NM_014225.5	310	tGt/tAt	8/15	1	2	FACETS	0.433	0.346	0.532	0.433	0.346	0.532	SUBCLONAL	1	TRUE	1	0.25	2		714	536	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400033	49400033	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	27	614	1	ENST00000418115.1:c.304G>T	p.Glu102Ter	p.E102*	ENST00000418115	NM_001664.2	102	Gaa/Taa	4/5	1	2	FACETS	0.404	0.32	0.5	0.404	0.32	0.5	SUBCLONAL	1	TRUE	1	0.25	2		615	535	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927456	49927456	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	67	1016	0	ENST00000296474.3:c.3848G>T	p.Arg1283Leu	p.R1283L	ENST00000296474	NM_002447.2	1283	cGg/cTg	19/20	1	2	FACETS	0.939	0.816	1	0.939	0.816	1	CLONAL	1	TRUE	1	0.25	2		1016	571	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798184	32798184	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1042109790	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	49	788	0	ENST00000374899.4:c.1495A>G	p.Thr499Ala	p.T499A	ENST00000374899	NM_018833.2	499	Acg/Gcg	9/12	1	2	FACETS	0.616	0.521	0.721	0.616	0.521	0.721	SUBCLONAL	1	TRUE	1	0.25	2		788	636	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415693	152415693	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	35	634	0	ENST00000206249.3:c.1543A>G	p.Arg515Gly	p.R515G	ENST00000206249	NM_000125.3	515	Agg/Ggg	7/8	1	2	FACETS	0.632	0.518	0.76	0.632	0.518	0.76	SUBCLONAL	1	TRUE	1	0.25	2		634	443	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099414	157099415	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCAGCAGCAA	rs797045275	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	13	389	0	ENST00000346085.5:c.363_374dup	p.Gln128_Gln131dup	p.Q128_Q131dup	ENST00000346085	NM_020732.3	128	-/CAGCAGCAGCAA	1/20	1	2	FACETS	0.437	0.311	0.59	0.437	0.311	0.59	SUBCLONAL	1	TRUE	1	0.25	2		389	238	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739069	145739069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs531970883	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	38	641	0	ENST00000428558.2:c.2086C>T	p.Arg696Cys	p.R696C	ENST00000428558	NM_004260.3	696	Cgt/Tgt	13/22	1	2	FACETS	0.595	0.491	0.711	0.595	0.491	0.711	SUBCLONAL	1	TRUE	1	0.25	2		641	511	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27209203	27209203	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs776358378	NA	P-0050833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	36	537	0	ENST00000380036.4:c.2660A>G	p.Asn887Ser	p.N887S	ENST00000380036	NM_000459.3	887	aAt/aGt	16/23	1	2	FACETS	0.713	0.586	0.854	0.713	0.586	0.854	SUBCLONAL	1	TRUE	1	0.25	2		537	404	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	70	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.264842459291822	2		334	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0050834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	254	946	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.264842459291822	1	FACETS	0.956	0.897	1	1	0.995	1	CLONAL	2	TRUE	0	0.264842459291822	1		946	870	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371942	55371942	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	231	666	1	ENST00000297316.4:c.632C>T	p.Ala211Val	p.A211V	ENST00000297316	NM_022454.3	211	gCg/gTg	2/2	0.264842459291822	1	FACETS	1	0.966	1	1	0.995	1	CLONAL	2	TRUE	0	0.264842459291822	1		667	723	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120351	70120352	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0050834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	252	1041	0	ENST00000245479.2:c.1354dup	p.Tyr452LeufsTer126	p.Y452Lfs*126	ENST00000245479	NM_000346.3	451	-/T	3/3	0.264842459291822	0	FACETS	0.868	0.815	0.922			1	CLONAL	2	TRUE	0	0.264842459291822	0		1041	806	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383338	42383338	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782282654	NA	P-0050834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	41	799	0	ENST00000221972.3:c.358G>A	p.Gly120Ser	p.G120S	ENST00000221972	NM_021601.3	120	Ggc/Agc	2/5	1	2	FACETS	0.474	0.394	0.564	0.474	0.394	0.564	SUBCLONAL	1	TRUE	1	0.264842459291822	2		799	653	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710666	114710666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	95	512	0	ENST00000543371.1:c.151G>A	p.Glu51Lys	p.E51K	ENST00000543371	NM_001198531.1	51	Gaa/Aaa	1/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.264842459291822	2		512	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0050835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	416	603	2	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.288712760782184	4	FACETS	0.933	0.895	0.972	1	0.994	1	CLONAL	4	TRUE	1	0.364614224377004	4		605	834	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693002	89693003	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	43	443	0	ENST00000371953.3:c.491dup	p.Val166SerfsTer14	p.V166Sfs*14	ENST00000371953	NM_000314.4	162	-/A	5/9	0.287572973861402	3	FACETS	0.728	0.611	0.858	0.364	0.305	0.429	SUBCLONAL	1	TRUE	1	0.364614224377004	3		443	383	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692831	89692831	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	44	179	0	ENST00000371953.3:c.315T>G	p.Cys105Trp	p.C105W	ENST00000371953	NM_000314.4	105	tgT/tgG	5/9	0.287572973861402	3	FACETS	0.849	0.724	0.983	0.849	0.724	0.983	CLONAL	2	TRUE	1	0.364614224377004	3		179	168	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602473	10602473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	183	1074	0	ENST00000171111.5:c.1105G>A	p.Val369Met	p.V369M	ENST00000171111	NM_203500.1	369	Gtg/Atg	3/6	0.244313244524338	4	FACETS	1	0.963	1	0.538	0.496	0.583	CLONAL	1	TRUE	2	0.364614224377004	4		1074	1272	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691218	18691218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	45	321	1	ENST00000266497.5:c.3329G>A	p.Ser1110Asn	p.S1110N	ENST00000266497		1110	aGc/aAc	23/31	0.287572973861402	3	FACETS	0.793	0.668	0.93	0.397	0.334	0.465	CLONAL	1	TRUE	1	0.364614224377004	3		322	368	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163862	152163862	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	108	569	0	ENST00000206249.3:c.583T>C	p.Tyr195His	p.Y195H	ENST00000206249	NM_000125.3	195	Tac/Cac	2/8	0.337140257553182	2	FACETS	1	0.95	1	0.543	0.489	0.601	CLONAL	1	TRUE	0	0.364614224377004	2		569	545	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505399	157505399	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	76	447	0	ENST00000346085.5:c.3380C>G	p.Thr1127Ser	p.T1127S	ENST00000346085	NM_020732.3	1127	aCc/aGc	13/20	0.337140257553182	2	FACETS	0.766	0.673	0.866	0.383	0.336	0.433	SUBCLONAL	1	TRUE	0	0.364614224377004	2		447	544	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935012	49935012	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	130	962	0	ENST00000296474.3:c.1987C>G	p.Pro663Ala	p.P663A	ENST00000296474	NM_002447.2	663	Cca/Gca	6/20	0.273418133599974	4	FACETS	0.773	0.699	0.851			1	SUBCLONAL	1	TRUE	NA	0.364614224377004	4		962	1259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576857	7576857	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	362	702	0	ENST00000269305.4:c.989T>G	p.Leu330Arg	p.L330R	ENST00000269305	NM_001126112.2	330	cTt/cGt	9/11	0.776239902943475	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	0	0.776239902943475	1		702	570	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	36	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.862	0.716	1	0.862	0.716	1	CLONAL	1	TRUE	1	0.413333184018815	2		334	202	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	67	1021	0	ENST00000269305.4:c.403del	p.Cys135AlafsTer35	p.C135Afs*35	ENST00000269305	NM_001126112.2	135	Tgc/gc	5/11	0.413333184018815	1	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	0	0.413333184018815	1		1021	254	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851762	134851762	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753407361	NA	P-0050838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	63	798	0	ENST00000398015.3:c.1168C>T	p.Arg390Cys	p.R390C	ENST00000398015	NM_004441.4	390	Cgc/Tgc	5/16	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.413333184018815	2		798	295	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0050839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	146	430	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.544243929007	1	FACETS	0.868	0.799	0.939	0.868	0.799	0.939	CLONAL	1	TRUE	0	0.544243929007	1		430	450	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0050839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	682	487	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.544243929007	5	FACETS	0.976	0.947	1	0.976	0.947	1	CLONAL	4	TRUE	1	0.544243929007	5		487	1166	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908816	101908816	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	141	566	0	ENST00000374994.4:c.1180G>T	p.Glu394Ter	p.E394*	ENST00000374994	NM_004612.2	394	Gaa/Taa	7/9	0.544243929007	1	FACETS	0.982	0.905	1	0.982	0.905	1	CLONAL	1	TRUE	0	0.544243929007	1		566	384	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032458	12032459	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	122	541	0	ENST00000353533.5:c.894_895insA	p.Glu299ArgfsTer14	p.E299Rfs*14	ENST00000353533	NM_003010.3	298	-/A	9/11	0.544243929007	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.544243929007	1		541	298	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246027164	246027164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768027957	NA	P-0050839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	72	702	0	ENST00000388985.4:c.838G>A	p.Glu280Lys	p.E280K	ENST00000388985		280	Gag/Aag	9/12	0.329136529902097	3	FACETS	0.487	0.425	0.554	0.244	0.212	0.277	SUBCLONAL	1	TRUE	1	0.544243929007	3		702	691	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0050846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	33	396	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.688	0.563	0.829	0.688	0.563	0.829	SUBCLONAL	1	FALSE	1	0.331702228674969	2		396	289	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755128667	NA	P-0050846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	109	735	0	ENST00000407977.2:c.1976dup	p.Pro660SerfsTer87	p.P660Sfs*87	ENST00000407977		659	ggt/ggGt	9/10	1	2	FACETS	0.922	0.828	1	0.922	0.828	1	CLONAL	1	FALSE	1	0.331702228674969	2		735	713	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175951	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1392778905	NA	P-0050846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	50	233	0	ENST00000257430.4:c.4660G>T	p.Glu1554Ter	p.E1554*	ENST00000257430	NM_000038.5	1554	Gaa/Taa	16/16	0.277386622187263	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	2	FALSE	0	0.331702228674969	2		233	149	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999077	100999077	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	88	808	0	ENST00000325455.5:c.725G>A	p.Arg242Gln	p.R242Q	ENST00000325455	NM_001202474.3	242	cGg/cAg	1/8	1	2	FACETS	0.884	0.785	0.991	0.884	0.785	0.991	CLONAL	1	FALSE	1	0.331702228674969	2		808	600	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104604	209104604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1229651962	NA	P-0050846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	48	440	1	ENST00000345146.2:c.974C>T	p.Thr325Met	p.T325M	ENST00000345146	NM_005896.2	325	aCg/aTg	8/10	1	2	FACETS	0.604	0.511	0.707	0.604	0.511	0.707	SUBCLONAL	1	FALSE	1	0.331702228674969	2		441	479	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374908	45374908	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs797044882	NA	P-0050846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	90	513	0	ENST00000262160.6:c.935G>C	p.Cys312Ser	p.C312S	ENST00000262160	NM_005901.5	312	tGc/tCc	8/11	0.213941120525899	2	FACETS	1	0.979	1	0.72	0.643	0.8	CLONAL	1	FALSE	0	0.331702228674969	2		513	377	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045979	26045979	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	107	509	0	ENST00000540144.1:c.341A>C	p.His114Pro	p.H114P	ENST00000540144	NM_003531.2	114	cAc/cCc	1/1	0.267844645905658	2	FACETS	1	0.978	1	0.658	0.593	0.727	CLONAL	1	FALSE	0	0.331702228674969	2		509	490	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404719	70404719	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs568996501	NA	P-0050846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	91	362	0	ENST00000373644.4:c.2233C>T	p.Arg745Ter	p.R745*	ENST00000373644	NM_030625.2	745	Cga/Tga	4/12	0.311052746644655	2	FACETS	0.871	0.782	0.964	0.871	0.782	0.964	CLONAL	2	FALSE	0	0.331702228674969	2		362	315	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160365	108160365	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	38	315	1	ENST00000278616.4:c.4273C>T	p.Gln1425Ter	p.Q1425*	ENST00000278616	NM_000051.3	1425	Caa/Taa	29/63	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	1	0.331702228674969	2		316	176	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905480	11905480	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	61	409	0	ENST00000396373.4:c.130G>C	p.Glu44Gln	p.E44Q	ENST00000396373	NM_001987.4	44	Gag/Cag	2/8	0.158853759857003	5	FACETS	1	0.937	1	0.383	0.33	0.439	INDETERMINATE	1	FALSE	2	0.331702228674969	5		409	480	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686349	30686349	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	81	395	0	ENST00000295754.5:c.205A>G	p.Ser69Gly	p.S69G	ENST00000295754	NM_003242.5	69	Agc/Ggc	2/7	0.331702228674969	1	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	FALSE	0	0.331702228674969	1		395	400	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589577	67589687	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAAATTACATGAATATAACACTCAGTTTCAAGAAAAAAGTCGAGAATATGATAGATTATATGAAGAATATACCCGCACATCCCAGGTGAGTTTTCTATGAAAATCAGATT	AAAAATTACATGAATATAACACTCAGTTTCAAGAAAAAAGTCGAGAATATGATAGATTATATGAAGAATATACCCGCACATCCCAGGTGAGTTTTCTATGAAAATCAGATT	-	novel	NA	P-0050846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	18	207	0	ENST00000274335.5:c.1345_1425+30del		p.X449_splice	ENST00000274335		449		10/15	0.277386622187263	2	FACETS	0.77	0.585	0.984	0.385	0.292	0.492	CLONAL	1	FALSE	0	0.331702228674969	2		207	141	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020392	69020392	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	83	495	0	ENST00000288368.4:c.2764A>C	p.Lys922Gln	p.K922Q	ENST00000288368	NM_024870.2	922	Aaa/Caa	24/40	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.331702228674969	2		495	383	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	178	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.471403619720415	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.471403619720415	3		436	267	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603044	48603044	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781359	NA	P-0050847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	62	411	0	ENST00000342988.3:c.1345C>T	p.Gln449Ter	p.Q449*	ENST00000342988	NM_005359.5	449	Cag/Tag	11/12	1	2	FACETS	0.865	0.767	0.966	1	0.98	1	CLONAL	2	TRUE	1	0.471403619720415	2		411	152	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038956	12038967	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCAGGTAGCAC	TTCAGGTAGCAC	-	novel	NA	P-0050847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	105	292	0	ENST00000396373.4:c.1252_1253+10del		p.X418_splice	ENST00000396373	NM_001987.4	418		7/8	0.471403619720415	5	FACETS	0.933	0.868	0.996	0.933	0.868	0.996	CLONAL	5	TRUE	0	0.471403619720415	5		292	163	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610099	43610099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760088950	NA	P-0050848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	239	775	2	ENST00000355710.3:c.2051C>T	p.Pro684Leu	p.P684L	ENST00000355710	NM_020975.4	684	cCg/cTg	11/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.669420084317821	2		777	704	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482861	67482861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	335	480	0	ENST00000327367.4:c.1265C>T	p.Ser422Phe	p.S422F	ENST00000327367	NM_005902.3	422	tCc/tTc	9/9	0.669420084317821	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.669420084317821	1		480	527	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0050848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	240	590	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.669420084317821	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.669420084317821	1		590	457	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980849	40980849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs548511212	NA	P-0050848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	174	541	0	ENST00000373198.4:c.1637G>A	p.Arg546Gln	p.R546Q	ENST00000373198	NM_133170.3	546	cGg/cAg	10/32	0.669420084317821	3	FACETS	0.867	0.8	0.938	0.434	0.4	0.469	CLONAL	1	TRUE	1	0.669420084317821	3		541	800	SUCCESS
APC	324	MSKCC	GRCh37	5	112175130	112175145	+	frameshift_variant	Frame_Shift_Del	DEL	TGTCATCAGCTGAAGA	TGTCATCAGCTGAAGA	-	novel	NA	P-0050848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	121	239	0	ENST00000257430.4:c.3841_3856del	p.Ser1281LysfsTer2	p.S1281Kfs*2	ENST00000257430	NM_000038.5	1280	tTGTCATCAGCTGAAGAt/tt	16/16	0.669420084317821	2	FACETS	0.918	0.855	0.978	0.918	0.855	0.978	CLONAL	2	TRUE	0	0.669420084317821	2		239	197	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399895	139399895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	209	1046	0	ENST00000277541.6:c.4453G>A	p.Asp1485Asn	p.D1485N	ENST00000277541	NM_017617.3	1485	Gac/Aac	25/34	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.492475699793879	2		1046	786	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663442	29663443	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0050849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	91	517	0	ENST00000356175.3:c.6036_6037del	p.Thr2013CysfsTer25	p.T2013Cfs*25	ENST00000356175	NM_000267.3	2012	gAT/g	40/57	1	2	FACETS	0.827	0.738	0.921	0.827	0.738	0.921	CLONAL	1	TRUE	1	0.492475699793879	2		517	447	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163843	152163843	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	55	577	0	ENST00000206249.3:c.564C>G	p.Cys188Trp	p.C188W	ENST00000206249	NM_000125.3	188	tgC/tgG	2/8	0.389092302457226	3	FACETS	0.538	0.461	0.623	0.269	0.23	0.312	SUBCLONAL	1	TRUE	1	0.492475699793879	3		577	517	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151932991	151932991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759973306	NA	P-0050849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	13	101	0	ENST00000262189.6:c.2680C>T	p.Arg894Trp	p.R894W	ENST00000262189	NM_170606.2	894	Cgg/Tgg	16/59	0.394345493406452	1	FACETS	0.553	0.402	0.729	0.553	0.402	0.729	SUBCLONAL	1	TRUE	0	0.492475699793879	1		101	72	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	25	524	2	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.277	0.218	0.346	0.277	0.218	0.346	SUBCLONAL	1	TRUE	1	0.37	2		526	487	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	247	894	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.975	1	1	0.995	1	CLONAL	2	TRUE	1	0.37	2		899	628	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	196	530	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.96	0.895	1	1	0.994	1	CLONAL	2	TRUE	1	0.37	2		533	552	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	132	819	2	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.37	2		821	681	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	111	531	2	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.37	2		533	469	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	91	396	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.244638945337107	3	FACETS	1	0.977	1	0.687	0.614	0.765	CLONAL	1	TRUE	1	0.37	3		396	424	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	30	390	0	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	0.389	0.313	0.475	0.389	0.313	0.475	SUBCLONAL	1	TRUE	1	0.37	2		390	417	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	64	455	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.37	2		455	345	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	28	329	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.529	0.424	0.649	0.529	0.424	0.649	SUBCLONAL	1	TRUE	1	0.37	2		330	286	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	38	305	1	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.619	0.513	0.736	0.619	0.513	0.736	SUBCLONAL	1	TRUE	1	0.37	2		306	332	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	121	409	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	1	0.936	1	1	0.99	1	CLONAL	2	TRUE	1	0.37	2		409	319	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144146	11144146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	73	770	0	ENST00000358026.2:c.3727C>T	p.Arg1243Trp	p.R1243W	ENST00000358026	NM_001128849.1	1243	Cgg/Tgg	26/36	1	2	FACETS	0.604	0.528	0.686	0.604	0.528	0.686	SUBCLONAL	1	TRUE	1	0.37	2		770	653	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675571	86675571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1561325048	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	31	277	0	ENST00000274376.6:c.2513del	p.Asn838MetfsTer4	p.N838Mfs*4	ENST00000274376	NM_002890.2	836	gAa/ga	19/25	1	2	FACETS	0.738	0.601	0.892	0.738	0.601	0.892	SUBCLONAL	1	TRUE	1	0.37	2		277	227	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523009	25523009	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	144	831	2	ENST00000264709.3:c.176del	p.Pro59ArgfsTer13	p.P59Rfs*13	ENST00000264709	NM_175629.2	59	cCg/cg	3/23	1	2	FACETS	0.989	0.903	1	0.989	0.903	1	CLONAL	1	TRUE	1	0.37	2		833	787	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	104	669	7	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.861	0.772	0.955	0.861	0.772	0.955	CLONAL	1	TRUE	1	0.37	2		676	653	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335810	73335810	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs183862178	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	66	370	0	ENST00000377767.4:c.2485C>T	p.Arg829Cys	p.R829C	ENST00000377767	NM_014953.3	829	Cgt/Tgt	18/21	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.37	2		370	333	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446284	70446284	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	105	549	0	ENST00000373644.4:c.5230del	p.Arg1744GlufsTer18	p.R1744Efs*18	ENST00000373644	NM_030625.2	1742	Aaa/aa	11/12	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.37	2		549	557	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438317	110438322	+	inframe_deletion	In_Frame_Del	DEL	GTTGTT	GTTGTT	-	rs532810290	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	35	231	0	ENST00000375856.3:c.79_84del	p.Asn27_Asn28del	p.N27_N28del	ENST00000375856	NM_003749.2	27	AACAAC/-	1/2	1	2	FACETS	0.719	0.593	0.86	0.719	0.593	0.86	SUBCLONAL	1	TRUE	1	0.37	2		231	263	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	168	740	4	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.37	2		744	775	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144049	11144051	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	130	828	1	ENST00000358026.2:c.3634_3636del	p.Glu1212del	p.E1212del	ENST00000358026	NM_001128849.1	1210	gtGGAg/gtg	26/36	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.37	2		829	688	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726490	46726490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149246216	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	90	546	1	ENST00000371975.4:c.569C>T	p.Thr190Met	p.T190M	ENST00000371975	NM_003579.3	190	aCg/aTg	7/18	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.37	2		547	410	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	84	505	6	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.96	0.851	1	0.96	0.851	1	CLONAL	1	TRUE	1	0.37	2		511	473	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217557	142217557	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1268253442	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	49	413	0	ENST00000350721.4:c.5440del	p.Arg1814GlufsTer10	p.R1814Efs*10	ENST00000350721	NM_001184.3	1814	Aga/ga	32/47	1	2	FACETS	0.708	0.602	0.825	0.708	0.602	0.825	SUBCLONAL	1	TRUE	1	0.37	2		413	374	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627418	37627418	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	40	588	0	ENST00000447079.4:c.1337del	p.Lys446SerfsTer6	p.K446Sfs*6	ENST00000447079	NM_015083.1	445	Aaa/aa	2/14	1	2	FACETS	0.402	0.333	0.478	0.402	0.333	0.478	SUBCLONAL	1	TRUE	1	0.37	2		588	538	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238356	98238356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	111	628	1	ENST00000331920.6:c.1688C>T	p.Ala563Val	p.A563V	ENST00000331920	NM_000264.3	563	gCg/gTg	12/24	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.37	2		629	549	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955112	17955112	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755706305	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	117	881	4	ENST00000458235.1:c.115del	p.Gln39SerfsTer108	p.Q39Sfs*108	ENST00000458235	NM_000215.3	39	Cag/ag	2/24	1	2	FACETS	0.871	0.786	0.961	0.871	0.786	0.961	CLONAL	1	TRUE	1	0.37	2		885	726	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945961	17945961	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	137	1049	0	ENST00000458235.1:c.1978del	p.Ala660LeufsTer10	p.A660Lfs*10	ENST00000458235	NM_000215.3	660	Gct/ct	15/24	1	2	FACETS	0.877	0.798	0.961	0.877	0.798	0.961	CLONAL	1	TRUE	1	0.37	2		1049	844	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981721	101981721	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555075353	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	64	353	0	ENST00000282441.5:c.147del	p.Ala50ProfsTer24	p.A50Pfs*24	ENST00000282441	NM_001130145.2	48	Ccc/cc	1/9	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.37	2		353	271	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106042	8106042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	75	552	0	ENST00000346208.3:c.862G>A	p.Gly288Arg	p.G288R	ENST00000346208		288	Ggg/Agg	4/6	1	2	FACETS	0.901	0.792	1	0.901	0.792	1	CLONAL	1	TRUE	1	0.37	2		552	450	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827892	40827892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573377632	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	81	524	1	ENST00000373198.4:c.2536G>A	p.Val846Ile	p.V846I	ENST00000373198	NM_133170.3	846	Gtc/Atc	17/32	1	2	FACETS	0.984	0.871	1	0.984	0.871	1	CLONAL	1	TRUE	1	0.37	2		525	445	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100283	8100283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	70	785	0	ENST00000346208.3:c.257G>A	p.Arg86His	p.R86H	ENST00000346208		86	cGc/cAc	3/6	1	2	FACETS	0.589	0.514	0.671	0.589	0.514	0.671	SUBCLONAL	1	TRUE	1	0.37	2		785	642	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426820	121426820	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520291	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	111	630	0	ENST00000257555.6:c.511C>T	p.Arg171Ter	p.R171*	ENST00000257555		171	Cga/Tga	2/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.37	2		630	524	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863054	56863054	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1266824391	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	34	525	0	ENST00000519728.1:c.327del	p.Glu110LysfsTer15	p.E110Kfs*15	ENST00000519728	NM_002350.3	107	acA/ac	5/13	1	2	FACETS	0.402	0.328	0.485	0.402	0.328	0.485	SUBCLONAL	1	TRUE	1	0.37	2		525	457	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682249	37682249	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	101	676	0	ENST00000447079.4:c.3440A>T	p.Gln1147Leu	p.Q1147L	ENST00000447079	NM_015083.1	1147	cAg/cTg	13/14	1	2	FACETS	0.963	0.863	1	0.963	0.863	1	CLONAL	1	TRUE	1	0.37	2		676	567	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738365	133738365	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	31	652	0	ENST00000318560.5:c.765G>T	p.Glu255Asp	p.E255D	ENST00000318560	NM_005157.4	255	gaG/gaT	4/11	1	2	FACETS	0.323	0.261	0.395	0.323	0.261	0.395	SUBCLONAL	1	TRUE	1	0.37	2		652	518	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534444	140534444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1258111302	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	101	481	0	ENST00000288602.6:c.469G>A	p.Val157Ile	p.V157I	ENST00000288602	NM_004333.4	157	Gtt/Att	3/18	0.244638945337107	3	FACETS	0.754	0.678	0.834	0.754	0.678	0.834	SUBCLONAL	2	TRUE	1	0.37	3		481	429	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799979	72799979	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	56	306	0	ENST00000325599.8:c.1190del	p.Lys397SerfsTer9	p.K397Sfs*9	ENST00000325599	NM_018130.2	397	aAg/ag	11/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.37	2		306	257	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390697	139390697	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	125	959	3	ENST00000277541.6:c.7494del	p.Ser2499AlafsTer90	p.S2499Afs*90	ENST00000277541	NM_017617.3	2498	ccC/cc	34/34	1	2	FACETS	0.891	0.807	0.98	0.891	0.807	0.98	CLONAL	1	TRUE	1	0.37	2		962	758	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626661	12626661	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	82	471	0	ENST00000251849.4:c.1628C>T	p.Thr543Met	p.T543M	ENST00000251849	NM_002880.3	543	aCg/aTg	15/17	1	2	FACETS	0.994	0.88	1	0.994	0.88	1	CLONAL	1	TRUE	1	0.37	2		471	446	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430206	181430208	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	51	413	2	ENST00000325404.1:c.67_69del	p.Gly23del	p.G23del	ENST00000325404	NM_003106.3	20	GGC/-	1/1	1	2	FACETS	0.934	0.8	1	0.934	0.8	1	CLONAL	1	TRUE	1	0.37	2		415	295	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205092	38205092	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	57	556	1	ENST00000317025.8:c.598del	p.Ser200AlafsTer20	p.S200Afs*20	ENST00000317025	NM_023034.1	200	Agc/gc	2/24	1	2	FACETS	0.712	0.612	0.82	0.712	0.612	0.82	SUBCLONAL	1	TRUE	1	0.37	2		557	433	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097740	8097740	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1436692613	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	154	719	0	ENST00000346208.3:c.122A>G	p.Tyr41Cys	p.Y41C	ENST00000346208		41	tAc/tGc	2/6	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.37	2		719	635	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055745	152055745	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	120	431	0	ENST00000262189.6:c.177del	p.Thr61LeufsTer44	p.T61Lfs*44	ENST00000262189	NM_170606.2	59	ggG/gg	2/59	0.244638945337107	3	FACETS	0.906	0.825	0.991	0.906	0.825	0.991	CLONAL	2	TRUE	1	0.37	3		431	424	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248736	212248737	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	52	339	0	ENST00000342788.4:c.3530dup	p.Asn1177LysfsTer9	p.N1177Kfs*9	ENST00000342788	NM_005235.2	1177	aat/aaAt	28/28	1	2	FACETS	0.997	0.855	1	0.997	0.855	1	CLONAL	1	TRUE	1	0.37	2		339	282	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369257	40369257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1449203089	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	118	596	0	ENST00000293328.3:c.1301C>T	p.Ser434Leu	p.S434L	ENST00000293328	NM_012448.3	434	tCg/tTg	11/19	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.37	2		596	577	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378245	15378245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	51	431	0	ENST00000263377.2:c.541C>T	p.Arg181Cys	p.R181C	ENST00000263377	NM_058243.2	181	Cgt/Tgt	4/20	1	2	FACETS	0.785	0.67	0.911	0.785	0.67	0.911	CLONAL	1	TRUE	1	0.37	2		431	351	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583373	46583373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs181240421	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	117	631	0	ENST00000263734.3:c.301G>A	p.Val101Met	p.V101M	ENST00000263734	NM_001430.4	101	Gtg/Atg	3/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.37	2		631	530	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191783	123191783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	66	439	1	ENST00000218089.9:c.1372G>A	p.Ala458Thr	p.A458T	ENST00000218089	NM_001042749.1	458	Gcc/Acc	15/35	1	2	FACETS	0.941	0.821	1	0.941	0.821	1	CLONAL	1	TRUE	1	0.37	2		440	379	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262670	16262670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765359153	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	75	448	2	ENST00000375759.3:c.9935G>A	p.Arg3312His	p.R3312H	ENST00000375759	NM_015001.2	3312	cGc/cAc	11/15	1	2	FACETS	0.977	0.86	1	0.977	0.86	1	CLONAL	1	TRUE	1	0.37	2		450	415	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166203	118166203	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	48	409	0	ENST00000369448.3:c.715del	p.Ile239SerfsTer28	p.I239Sfs*28	ENST00000369448	NM_017709.3	238	gAa/ga	2/2	1	2	FACETS	0.786	0.668	0.916	0.786	0.668	0.916	CLONAL	1	TRUE	1	0.37	2		409	330	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120509104	120509104	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	71	335	0	ENST00000256646.2:c.1462G>T	p.Gly488Cys	p.G488C	ENST00000256646	NM_024408.3	488	Ggt/Tgt	9/34	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.37	2		335	323	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615117	43615117	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs55947360	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	47	1038	0	ENST00000355710.3:c.2531G>T	p.Arg844Leu	p.R844L	ENST00000355710	NM_020975.4	844	cGg/cTg	14/20	1	2	FACETS	0.365	0.307	0.429	0.365	0.307	0.429	SUBCLONAL	1	TRUE	1	0.37	2		1038	696	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111958640	111958640	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs80338843	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	71	449	1	ENST00000375549.3:c.112C>T	p.Arg38Ter	p.R38*	ENST00000375549	NM_003002.3	38	Cga/Tga	2/4	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.37	2		450	376	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793457	18793458	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	52	423	2	ENST00000266497.5:c.4158dup	p.Cys1387MetfsTer8	p.C1387Mfs*8	ENST00000266497		1385	cca/ccAa	30/31	1	2	FACETS	0.922	0.79	1	0.922	0.79	1	CLONAL	1	TRUE	1	0.37	2		425	305	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486592	56486592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139868331	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	97	628	0	ENST00000267101.3:c.1171C>T	p.Arg391Trp	p.R391W	ENST00000267101	NM_001982.3	391	Cgg/Tgg	10/28	1	2	FACETS	0.969	0.867	1	0.969	0.867	1	CLONAL	1	TRUE	1	0.37	2		628	541	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034971	42034971	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	122	643	0	ENST00000219905.7:c.4817del	p.Leu1606Ter	p.L1606*	ENST00000219905	NM_001164273.1	1605	Ttt/tt	15/24	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.37	2		643	548	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134260	2134260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45517326	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	133	924	1	ENST00000219476.3:c.4037C>T	p.Ser1346Leu	p.S1346L	ENST00000219476	NM_000548.3	1346	tCg/tTg	34/42	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.37	2		925	664	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16055280	16055290	+	frameshift_variant	Frame_Shift_Del	DEL	CACCTTGGTAT	CACCTTGGTAT	-	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	41	385	0	ENST00000268712.3:c.812_822del	p.Asp271ValfsTer3	p.D271Vfs*3	ENST00000268712	NM_006311.3	271	gATACCAAGGTG/g	8/46	1	2	FACETS	0.678	0.566	0.8	0.678	0.566	0.8	SUBCLONAL	1	TRUE	1	0.37	2		385	327	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16097805	16097805	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	109	601	0	ENST00000268712.3:c.79T>C	p.Tyr27His	p.Y27H	ENST00000268712	NM_006311.3	27	Tat/Cat	2/46	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.37	2		601	556	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007694	62007694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746592632	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	88	543	0	ENST00000392795.3:c.173G>A	p.Arg58Gln	p.R58Q	ENST00000392795	NM_001039933.1	58	cGg/cAg	3/6	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.37	2		543	463	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210916	36210916	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	149	1112	0	ENST00000222270.7:c.671del	p.Pro224GlnfsTer15	p.P224Qfs*15	ENST00000222270	NM_014727.1	223	Ccc/cc	3/37	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.37	2		1112	747	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213498	36213498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	90	1100	2	ENST00000222270.7:c.2600G>A	p.Arg867His	p.R867H	ENST00000222270	NM_014727.1	867	cGc/cAc	5/37	1	2	FACETS	0.56	0.496	0.629	0.56	0.496	0.629	SUBCLONAL	1	TRUE	1	0.37	2		1102	868	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416790	29416790	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	39	320	0	ENST00000389048.3:c.4165-2A>C		p.X1389_splice	ENST00000389048	NM_004304.4	1389			1	2	FACETS	0.933	0.78	1	0.933	0.78	1	CLONAL	1	TRUE	1	0.37	2		320	226	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023405	31023405	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	84	486	0	ENST00000375687.4:c.2890T>C	p.Ser964Pro	p.S964P	ENST00000375687	NM_015338.5	964	Tct/Cct	13/13	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.37	2		486	392	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026107	36026107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34881773	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	133	950	0	ENST00000358208.4:c.709G>A	p.Ala237Thr	p.A237T	ENST00000358208		237	Gcc/Acc	7/12	1	2	FACETS	0.973	0.885	1	0.973	0.885	1	CLONAL	1	TRUE	1	0.37	2		950	739	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620666	52620666	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	85	382	1	ENST00000394830.3:c.3087G>T	p.Glu1029Asp	p.E1029D	ENST00000394830	NM_018313.4	1029	gaG/gaT	21/30	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.37	2		383	385	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519133	187519133	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	86	429	0	ENST00000441802.2:c.12250G>T	p.Gly4084Cys	p.G4084C	ENST00000441802	NM_005245.3	4084	Ggt/Tgt	23/27	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.37	2		429	399	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845240	151845240	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	136	605	0	ENST00000262189.6:c.13772A>G	p.Tyr4591Cys	p.Y4591C	ENST00000262189	NM_170606.2	4591	tAt/tGt	52/59	0.244638945337107	3	FACETS	0.921	0.843	1	0.921	0.843	1	CLONAL	2	TRUE	1	0.37	3		605	473	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129326	64129326	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs755246792	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	116	884	0	ENST00000334205.4:c.758G>A	p.Arg253Gln	p.R253Q	ENST00000334205	NM_003942.2	253	cGg/cAg	8/17	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.37	2		884	621	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138774	64138774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs901715491	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	155	826	0	ENST00000334205.4:c.2141G>A	p.Arg714Gln	p.R714Q	ENST00000334205	NM_003942.2	714	cGg/cAg	17/17	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.37	2		826	710	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253977	133253977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196808684	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	102	586	0	ENST00000320574.5:c.773C>T	p.Thr258Ile	p.T258I	ENST00000320574	NM_006231.2	258	aCc/aTc	8/49	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.37	2		586	524	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612353	1612353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs999701904	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	168	1044	4	ENST00000344749.5:c.1666C>T	p.Arg556Trp	p.R556W	ENST00000344749	NM_001136139.2	556	Cgg/Tgg	18/19	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.37	2		1048	788	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047266	128047266	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	62	399	0	ENST00000285398.2:c.656C>A	p.Ala219Asp	p.A219D	ENST00000285398	NM_000122.1	219	gCc/gAc	5/15	1	2	FACETS	0.926	0.804	1	0.926	0.804	1	CLONAL	1	TRUE	1	0.37	2		399	362	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84388671	84388673	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs759905964	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	60	386	0	ENST00000321945.7:c.615_617del	p.Glu205del	p.E205del	ENST00000321945	NM_139076.2	205	gaAGAt/gat	7/9	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.37	2		386	291	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80021356	80021357	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	89	532	0	ENST00000265081.6:c.1425_1426insA	p.Tyr476IlefsTer7	p.Y476Ifs*7	ENST00000265081	NM_002439.4	475	-/A	9/24	1	2	FACETS	0.99	0.881	1	0.99	0.881	1	CLONAL	1	TRUE	1	0.37	2		532	486	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633857	86633857	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	21	335	0	ENST00000274376.6:c.966T>G	p.Asn322Lys	p.N322K	ENST00000274376	NM_002890.2	322	aaT/aaG	5/25	1	2	FACETS	0.445	0.343	0.563	0.445	0.343	0.563	SUBCLONAL	1	TRUE	1	0.37	2		335	255	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670340	30670340	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	94	481	0	ENST00000376406.3:c.6092G>T	p.Arg2031Leu	p.R2031L	ENST00000376406	NM_014641.2	2031	cGg/cTg	14/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.37	2		481	447	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43739024	43739024	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	84	482	0	ENST00000523873.1:c.41T>C	p.Leu14Ser	p.L14S	ENST00000523873		14	tTg/tCg	1/8	1	2	FACETS	0.948	0.84	1	0.948	0.84	1	CLONAL	1	TRUE	1	0.37	2		482	479	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989700	68989700	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1235901571	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	92	535	1	ENST00000288368.4:c.1638C>A	p.His546Gln	p.H546Q	ENST00000288368	NM_024870.2	546	caC/caA	15/40	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.37	2		536	453	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128305418	128305418	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	93	545	0	ENST00000265960.3:c.878A>G	p.Gln293Arg	p.Q293R	ENST00000265960	NM_001006617.1	293	cAg/cGg	7/12	1	2	FACETS	0.963	0.859	1	0.963	0.859	1	CLONAL	1	TRUE	1	0.37	2		545	522	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	106	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.969	0.877	1	0.969	0.877	1	CLONAL	1	TRUE	1	0.577075742129866	2		276	379	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0050852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	101	401	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.794	0.714	0.878	0.794	0.714	0.878	SUBCLONAL	1	TRUE	1	0.577075742129866	2		401	441	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29662034	29662034	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs876660696	NA	P-0050852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	78	357	0	ENST00000356175.3:c.5928G>A	p.Trp1976Ter	p.W1976*	ENST00000356175	NM_000267.3	1976	tgG/tgA	39/57	1	2	FACETS	0.959	0.852	1	0.959	0.852	1	CLONAL	1	TRUE	1	0.577075742129866	2		357	282	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331961	81331961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763072412	NA	P-0050852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	71	296	1	ENST00000222390.5:c.2123G>A	p.Arg708Gln	p.R708Q	ENST00000222390	NM_000601.4	708	cGa/cAa	18/18	0.515862781828536	3	FACETS	0.97	0.853	1	0.485	0.426	0.547	CLONAL	1	TRUE	1	0.577075742129866	3		297	327	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28631601	28631602	+	splice_acceptor_variant,intron_variant	Splice_Site	DNP	TG	TG	CA	novel	NA	P-0050852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	72	275	1	ENST00000241453.7:c.369-3_369-2inv		p.X123_splice	ENST00000241453	NM_004119.2	123			1	2	FACETS	0.81	0.714	0.912	0.81	0.714	0.912	CLONAL	1	TRUE	1	0.577075742129866	2		276	308	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179034	123179035	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	153	282	0	ENST00000218089.9:c.484dup	p.Thr162AsnfsTer16	p.T162Nfs*16	ENST00000218089	NM_001042749.1	161	-/A	8/35	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.577075742129866	1		282	264	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39283844	39283844	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs730881037	NA	P-0050852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	86	337	0	ENST00000402219.2:c.509A>C	p.Lys170Thr	p.K170T	ENST00000402219	NM_005633.3	170	aAg/aCg	4/23	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.577075742129866	2		337	298	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0050853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	151	649	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.194922701167867	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.194922701167867	1		649	1046	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940498	29940498	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	202	413	0	ENST00000389048.3:c.733C>A	p.Leu245Ile	p.L245I	ENST00000389048	NM_004304.4	245	Ctc/Atc	2/29	0.568916700177926	3	FACETS	0.989	0.928	1	0.989	0.928	1	CLONAL	2	TRUE	1	0.568916700177926	3		413	461	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115742	8115742	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	87	347	0	ENST00000346208.3:c.1088C>A	p.Thr363Asn	p.T363N	ENST00000346208		363	aCc/aAc	6/6	0.198759379554597	6	FACETS	1	0.97	1	0.426	0.378	0.477	INDETERMINATE	1	TRUE	3	0.568916700177926	6		347	512	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445623	49445623	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	123	728	0	ENST00000301067.7:c.1843T>A	p.Ser615Thr	p.S615T	ENST00000301067	NM_003482.3	615	Tct/Act	10/54	0.531021082843703	4	FACETS	0.682	0.615	0.752	0.341	0.307	0.376	SUBCLONAL	1	TRUE	2	0.568916700177926	4		728	995	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870332	155870332	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0050854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	131	467	0	ENST00000368323.3:c.507C>G	p.Tyr169Ter	p.Y169*	ENST00000368323	NM_006912.5	169	taC/taG	6/6	0.198759379554597	6	FACETS	1	0.985	1	0.476	0.433	0.522	INDETERMINATE	1	TRUE	3	0.568916700177926	6		467	689	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32799804	32800111	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GATGAAAGTATACAATATCTTGGATTTGCTTCAGAATAATATGGGTGGGGGGAAGTGGCTGGGGATACAGATCCAACAAGATTGGGCATGAGTTGATCATTGTTAAAGCACAGGATGTATACATGTGAGTTTGTAATATTATTTTGTCTCATTTTTGGCATATGTTTAAAATTCTCCATAGCAAAATTACTTGCGGGTTTTGGTTTTGTATTGTATTGTTAAAAAGAACAAATAAAGCCCAAGGCCCAGGAGTCCACAAAGAAAAAGAGAGGGAAAAAAGGAGAGCAGGCTTGGCTTCTCGCTCACCT	GATGAAAGTATACAATATCTTGGATTTGCTTCAGAATAATATGGGTGGGGGGAAGTGGCTGGGGATACAGATCCAACAAGATTGGGCATGAGTTGATCATTGTTAAAGCACAGGATGTATACATGTGAGTTTGTAATATTATTTTGTCTCATTTTTGGCATATGTTTAAAATTCTCCATAGCAAAATTACTTGCGGGTTTTGGTTTTGTATTGTATTGTTAAAAAGAACAAATAAAGCCCAAGGCCCAGGAGTCCACAAAGAAAAAGAGAGGGAAAAAAGGAGAGCAGGCTTGGCTTCTCGCTCACCT	-	novel	NA	P-0050854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1	85	6	0	ENST00000374899.4:c.1271_1272+306del		p.X424_splice	ENST00000374899	NM_018833.2	424		7/12	0.568916700177926	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	4	TRUE	1	0.568916700177926	3		6	86	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0050861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	59	487	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.892	0.768	1	0.892	0.768	1	CLONAL	1	TRUE	1	0.23	2		487	575	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275733	41275733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	29	531	0	ENST00000349496.5:c.1628C>T	p.Ala543Val	p.A543V	ENST00000349496	NM_001904.3	543	gCa/gTa	10/15	1	2	FACETS	0.501	0.401	0.615	0.501	0.401	0.615	SUBCLONAL	1	TRUE	1	0.23	2		531	503	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687279	117687280	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0050861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	45	346	0	ENST00000368508.3:c.2771dup	p.Asn924LysfsTer11	p.N924Kfs*11	ENST00000368508	NM_002944.2	924	aat/aaAt	18/43	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.23	2		346	352	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041566	47041566	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0050861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	67	635	0	ENST00000377604.3:c.1791C>G	p.Tyr597Ter	p.Y597*	ENST00000377604	NM_001204468.1	597	taC/taG	17/24	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.23	2		635	579	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861563	152861563	+	synonymous_variant	Silent	SNP	G	G	A	rs139660436	NA	P-0050862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	224	569	1	ENST00000406277.2:c.189C>T	p.Asp63=	p.D63=	ENST00000406277	NM_152274.4	63	gaC/gaT	4/7	0.447652534961718		FACETS		0.944	1				CLONAL	1	TRUE	0	0.447652534961718	1		570	768	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444951	49444951	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs781145102	NA	P-0050862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	78	564	0	ENST00000301067.7:c.2515G>T	p.Glu839Ter	p.E839*	ENST00000301067	NM_003482.3	839	Gag/Tag	10/54	1	2	FACETS	0.386	0.339	0.438	0.386	0.339	0.438	SUBCLONAL	1	TRUE	1	0.447652534961718	2		564	902	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919710	50919710	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs761160001	NA	P-0050862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	302	828	0	ENST00000440232.2:c.2878C>A	p.Gln960Lys	p.Q960K	ENST00000440232	NM_002691.3	960	Cag/Aag	23/27	0.447652534961718	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.447652534961718	1		828	1014	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157711	106157711	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	79	213	0	ENST00000380013.4:c.2612A>C	p.Asn871Thr	p.N871T	ENST00000380013	NM_001127208.2	871	aAt/aCt	3/11	1	2	FACETS	0.934	0.826	1	0.934	0.826	1	CLONAL	1	TRUE	1	0.447652534961718	2		213	378	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93636954	93636955	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0050862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	88	236	0	ENST00000375746.1:c.1009dup	p.Gln337ProfsTer45	p.Q337Pfs*45	ENST00000375746	NM_001174167.1	335	ggc/ggCc	9/14	1	2	FACETS	0.919	0.818	1	0.919	0.818	1	CLONAL	1	TRUE	1	0.447652534961718	2		236	428	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	20	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		436	352	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520006	NA	P-0050863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	53	652	0	ENST00000269305.4:c.821T>G	p.Val274Gly	p.V274G	ENST00000269305	NM_001126112.2	274	gTt/gGt	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		652	773	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	56	276	0				ENST00000310581	NM_198253.2	-/1132			0.368118265725801	4	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	2	0.368118265725801	4		276	191	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427404	49427404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	42	826	0	ENST00000301067.7:c.11084C>T	p.Pro3695Leu	p.P3695L	ENST00000301067	NM_003482.3	3695	cCt/cTt	39/54	0.368118265725801	4	FACETS	0.855	0.716	1	0.428	0.358	0.505	CLONAL	1	TRUE	2	0.368118265725801	4		826	365	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657509	37657509	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	54	347	0	ENST00000447079.4:c.2426T>C	p.Phe809Ser	p.F809S	ENST00000447079	NM_015083.1	809	tTt/tCt	6/14	0.368118265725801	4	FACETS	0.892	0.771	1	0.892	0.771	1	CLONAL	2	TRUE	2	0.368118265725801	4		347	225	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443625	52443625	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0050864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	86	582	0	ENST00000460680.1:c.68-1G>A		p.X23_splice	ENST00000460680	NM_004656.3	23			0.338328246619481	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.368118265725801	2		582	216	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630224	100630224	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	35	440	0	ENST00000308731.7:c.49A>G	p.Lys17Glu	p.K17E	ENST00000308731	NM_000061.2	17	Aaa/Gaa	2/19	0.32393065552987	4	FACETS	1	0.883	1	0.547	0.451	0.653	CLONAL	1	TRUE	2	0.368118265725801	4		440	238	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0050865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	391	627	3	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.113160746151813	4	FACETS	1	0.992	1			1	INDETERMINATE	3	TRUE	NA	0.630760164481946	4		630	605	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524124	18524124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1161481962	NA	P-0050865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	53	266	0	ENST00000266497.5:c.1636C>T	p.Pro546Ser	p.P546S	ENST00000266497		546	Ccc/Tcc	11/31	0.556537646934681	1	FACETS	0.669	0.581	0.761	0.669	0.581	0.761	SUBCLONAL	1	TRUE	0	0.630760164481946	1		266	172	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849994	151849994	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	91	308	0	ENST00000262189.6:c.12322C>T	p.Arg4108Ter	p.R4108*	ENST00000262189	NM_170606.2	4108	Cga/Tga	49/59	1	2	FACETS	0.907	0.814	1	0.907	0.814	1	CLONAL	1	TRUE	1	0.630760164481946	2		308	318	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943721	9943721	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	135	620	0	ENST00000330684.3:c.1220G>A	p.Ser407Asn	p.S407N	ENST00000330684	NM_001134407.1	407	aGc/aAc	5/13	1	2	FACETS	0.759	0.693	0.828	0.759	0.693	0.828	SUBCLONAL	1	TRUE	1	0.630760164481946	2		620	564	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799667	72799667	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540952628	NA	P-0050865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	154	560	0	ENST00000325599.8:c.1502C>T	p.Ala501Val	p.A501V	ENST00000325599	NM_018130.2	501	gCc/gTc	11/11	1	2	FACETS	0.961	0.886	1	0.961	0.886	1	CLONAL	1	TRUE	1	0.630760164481946	2		560	508	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915106	32915106	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs730881546	NA	P-0050867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	141	464	0	ENST00000380152.3:c.6614T>G	p.Val2205Gly	p.V2205G	ENST00000380152		2205	gTg/gGg	11/27	0.583490308181198	2	FACETS	1	0.952	1	0.525	0.482	0.569	CLONAL	1	TRUE	0	0.62178962648424	2		464	432	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156711	106156711	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	157	357	0	ENST00000380013.4:c.1612C>G	p.Gln538Glu	p.Q538E	ENST00000380013	NM_001127208.2	538	Caa/Gaa	3/11	0.498981551679222	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.62178962648424	1		357	294	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940483	76940486	+	frameshift_variant	Frame_Shift_Del	DEL	AATA	AATA	-	novel	NA	P-0050867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	129	444	0	ENST00000373344.5:c.607_610del	p.Tyr203ThrfsTer2	p.Y203Tfs*2	ENST00000373344	NM_000489.3	203	TATTac/ac	8/35	1	2	FACETS	0.979	0.895	1	0.979	0.895	1	CLONAL	1	TRUE	1	0.62178962648424	2		444	424	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441414	52441414	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1553645838	NA	P-0050887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	116	456	0	ENST00000460680.1:c.437+1G>T		p.X146_splice	ENST00000460680	NM_004656.3	146			0.790018087863533	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	0	0.790018087863533	1		456	168	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264737	46264737	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	106	377	0	ENST00000371998.3:c.1609del	p.Leu537PhefsTer18	p.L537Ffs*18	ENST00000371998		536	tCc/tc	12/23	0.103304816985485	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.790018087863533	0		377	261	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051639	30051639	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	112	301	0	ENST00000338641.4:c.573G>A	p.Trp191Ter	p.W191*	ENST00000338641	NM_000268.3	191	tgG/tgA	6/16	0.790018087863533	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	0	0.790018087863533	1		301	165	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188265	10188266	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0050887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	151	545	0	ENST00000256474.2:c.410_411del	p.Val137AlafsTer6	p.V137Afs*6	ENST00000256474	NM_000551.3	136	ttTGtg/tttg	2/3	0.790018087863533	1	FACETS	0.918	0.861	0.973	0.918	0.861	0.973	CLONAL	1	FALSE	0	0.790018087863533	1		545	252	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0050888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	325	463	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	0.934	0.887	0.981	0.934	0.887	0.981	CLONAL	1	TRUE	1	0.896918500579151	2		463	776	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0050888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	15	193	0	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	1	1	FACETS	0.068	0.049	0.09	0.068	0.049	0.09	SUBCLONAL	1	TRUE	0	0.896918500579151	1		193	273	SUCCESS
AR	367	MSKCC	GRCh37	X	66943606	66943606	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	330	256	0	ENST00000374690.3:c.2686A>T	p.Met896Leu	p.M896L	ENST00000374690	NM_000044.3	896	Atg/Ttg	8/8	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.896918500579151	1		256	387	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852414	63852414	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	TT	novel	NA	P-0050888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	127	507	0	ENST00000279873.7:c.3192delinsTT	p.Gly1065TrpfsTer24	p.G1065Wfs*24	ENST00000279873	NM_032199.2	1064	ggC/ggTT	10/10	1	2	FACETS	0.39	0.353	0.428	0.39	0.353	0.428	SUBCLONAL	1	TRUE	1	0.896918500579151	2		507	726	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	122	276	0				ENST00000310581	NM_198253.2	-/1132			0.210539347724197	4	FACETS	0.956	0.869	1	0.956	0.869	1	CLONAL	2	TRUE	2	0.339787991702005	4		276	503	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280658	115280658	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	64	508	0	ENST00000438362.2:c.373A>T	p.Thr125Ser	p.T125S	ENST00000438362	NM_001242891.1	125	Act/Tct	4/20	1	2	FACETS	0.785	0.681	0.897	0.785	0.681	0.897	SUBCLONAL	1	TRUE	1	0.339787991702005	2		508	480	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739031	40739031	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	84	450	0	ENST00000373198.4:c.3253G>T	p.Val1085Phe	p.V1085F	ENST00000373198	NM_133170.3	1085	Gtc/Ttc	24/32	0.27050660643354	3	FACETS	0.879	0.777	0.989	0.44	0.388	0.495	CLONAL	1	TRUE	1	0.339787991702005	3		450	658	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651943	36651944	+	stop_gained	Nonsense_Mutation	DNP	TC	TC	AA	novel	NA	P-0050890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	274	530	0	ENST00000244741.5:c.65_66delinsAA	p.Phe22Ter	p.F22*	ENST00000244741	NM_000389.4	22	tTC/tAA	2/3	0.289291982419704	4	FACETS	1	0.98	1	0.807	0.763	0.852	CLONAL	3	TRUE	0	0.339787991702005	4		530	669	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409974	63409974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	42	446	0	ENST00000330258.3:c.3193G>A	p.Gly1065Arg	p.G1065R	ENST00000330258	NM_152424.3	1065	Gga/Aga	2/2	1	2	FACETS	0.652	0.546	0.77	0.652	0.546	0.77	SUBCLONAL	1	TRUE	1	0.339787991702005	2		446	379	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0050891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	84	390	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.343824465092156	3	FACETS	0.944	0.835	1	0.472	0.417	0.53	CLONAL	1	TRUE	1	0.386964806468768	3		390	549	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155721	56155722	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0050891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	65	417	0	ENST00000399503.3:c.816_817del	p.Arg273SerfsTer27	p.R273Sfs*27	ENST00000399503	NM_005921.1	271	agAAaa/agaa	3/20	0.386964806468768	3	FACETS	0.885	0.769	1	0.443	0.384	0.505	CLONAL	1	TRUE	1	0.386964806468768	3		417	453	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160755	56160756	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0050891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	134	354	0	ENST00000399503.3:c.1031dup	p.Gln345SerfsTer40	p.Q345Sfs*40	ENST00000399503	NM_005921.1	343	-/C	4/20	0.386964806468768	3	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	1	0.386964806468768	3		354	405	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637738	176637738	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	98	624	0	ENST00000439151.2:c.2338T>C	p.Ser780Pro	p.S780P	ENST00000439151	NM_022455.4	780	Tcg/Ccg	5/23	0.344954866312942	4	FACETS	0.916	0.817	1	0.458	0.408	0.511	CLONAL	1	TRUE	2	0.386964806468768	4		624	767	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0050893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	22	384	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.542	0.419	0.687	0.542	0.419	0.687	SUBCLONAL	1	TRUE	1	0.15	2		384	541	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218423	1218423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	29	536	1	ENST00000326873.7:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000326873	NM_000455.4	100	Caa/Taa	2/10	0.3	1	FACETS	0.631	0.505	0.775	0.631	0.505	0.775	SUBCLONAL	1	TRUE	0	0.15	1		537	567	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602698	10602698	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	48	667	0	ENST00000171111.5:c.880G>T	p.Asp294Tyr	p.D294Y	ENST00000171111	NM_203500.1	294	Gac/Tac	3/6	0.126857379155115	1	FACETS	0.881	0.743	1	0.881	0.743	1	CLONAL	1	TRUE	0	0.15	1		667	672	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830445	72830445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	20	323	0	ENST00000268489.5:c.6136C>T	p.Pro2046Ser	p.P2046S	ENST00000268489	NM_006885.3	2046	Ccc/Tcc	9/10	1	2	FACETS	0.926	0.709	1	0.926	0.709	1	CLONAL	1	TRUE	1	0.15	2		323	288	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820535	44820535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780238270	NA	P-0050893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	24	400	0	ENST00000377967.4:c.232C>T	p.Arg78Cys	p.R78C	ENST00000377967	NM_021140.2	78	Cgc/Tgc	3/29	1	2	FACETS	0.705	0.552	0.882	0.705	0.552	0.882	SUBCLONAL	1	TRUE	1	0.15	2		400	454	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249510	153249510	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1157879635	NA	P-0050894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	242	479	1	ENST00000281708.4:c.1268G>T	p.Gly423Val	p.G423V	ENST00000281708	NM_033632.3	423	gGa/gTa	9/12	0.169343841066229	3	FACETS	0.753	0.707	0.8	0.753	0.707	0.8	INDETERMINATE	2	TRUE	1	0.588014105014697	3		480	707	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577144	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs879253942	NA	P-0050894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	423	514	0	ENST00000269305.4:c.794T>C	p.Leu265Pro	p.L265P	ENST00000269305	NM_001126112.2	265	cTg/cCg	8/11	NA	2	FACETS	1	0.968	1			1	INDETERMINATE	2	TRUE	NA	0.588014105014697	2		514	715	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849430	68849462	+	inframe_deletion	In_Frame_Del	DEL	GAGGCCAAGCAGCAGTACATTCTACACGTAGCA	GAGGCCAAGCAGCAGTACATTCTACACGTAGCA	-	novel	NA	P-0050894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	84	480	1	ENST00000261769.5:c.1334_1366del	p.Glu445_Ala455del	p.E445_A455del	ENST00000261769	NM_004360.3	445	GAGGCCAAGCAGCAGTACATTCTACACGTAGCA/-	10/16	0.586624421363145	2	FACETS	0.439	0.388	0.494	0.219	0.194	0.247	SUBCLONAL	1	TRUE	0	0.588014105014697	2		481	651	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17125948	17125948	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	215	468	0	ENST00000285071.4:c.646C>A	p.Pro216Thr	p.P216T	ENST00000285071	NM_144997.5	216	Cca/Aca	7/14	0.541000051667076	2	FACETS	0.971	0.906	1	0.486	0.453	0.519	CLONAL	1	TRUE	0	0.588014105014697	2		468	753	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78829339	78829339	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	170	462	0	ENST00000306801.3:c.1390G>C	p.Val464Leu	p.V464L	ENST00000306801	NM_020761.2	464	Gtg/Ctg	12/34	0.588014105014697	2	FACETS	0.975	0.901	1	0.488	0.45	0.526	CLONAL	1	TRUE	0	0.588014105014697	2		462	593	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459831	149459831	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	248	632	0	ENST00000286301.3:c.376C>T	p.Pro126Ser	p.P126S	ENST00000286301	NM_005211.3	126	Ccc/Tcc	4/22	NA	2	FACETS	1	0.953	1			1	INDETERMINATE	1	TRUE	NA	0.588014105014697	2		632	828	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052872	180052872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	423	588	0	ENST00000261937.6:c.1418G>A	p.Ser473Asn	p.S473N	ENST00000261937	NM_182925.4	473	aGt/aAt	10/30	0.443690133722395	3	FACETS	0.972	0.93	1			1	CLONAL	2	TRUE	NA	0.588014105014697	3		588	958	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0050895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	76	518	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.284709961271693	5	FACETS	0.907	0.805	1	0.907	0.805	1	CLONAL	3	TRUE	2	0.284709961271693	5		518	280	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	82	513	0	ENST00000269305.4:c.569del	p.Pro190LeufsTer57	p.P190Lfs*57	ENST00000269305	NM_001126112.2	190	cCt/ct	6/11	0.284709961271693	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.284709961271693	3		513	268	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744059	39744059	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	25	347	0	ENST00000361337.2:c.1687G>C	p.Asp563His	p.D563H	ENST00000361337	NM_003286.2	563	Gat/Cat	16/21	0.216025585762025	3	FACETS	0.678	0.535	0.841	0.339	0.267	0.421	SUBCLONAL	1	TRUE	1	0.284709961271693	3		347	296	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111517	8111518	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	130	575	0	ENST00000346208.3:c.1004dup	p.Asp335GlufsTer17	p.D335Efs*17	ENST00000346208		335	gac/gAac	5/6	1	2	FACETS	0.668	0.607	0.732	0.668	0.607	0.732	SUBCLONAL	1	TRUE	1	0.566641680746123	2		575	687	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105672	27105673	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0050900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	169	384	0	ENST00000324856.7:c.5287dup	p.Glu1763GlyfsTer10	p.E1763Gfs*10	ENST00000324856	NM_006015.4	1761	-/G	20/20	0.517538653314332	2	FACETS	0.88	0.823	0.937	0.88	0.823	0.937	CLONAL	2	TRUE	0	0.566641680746123	2		384	339	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0050901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	98	396	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.617036920570849	4	FACETS	0.999	0.91	1	0.999	0.91	1	CLONAL	2	TRUE	2	0.773055783424006	4		396	225	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041849	14041849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs968717590	NA	P-0050901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	56	357	2	ENST00000311895.7:c.2396G>A	p.Arg799Gln	p.R799Q	ENST00000311895	NM_005236.2	799	cGg/cAg	11/11	1	2	FACETS	0.837	0.731	0.949	0.837	0.731	0.949	CLONAL	1	TRUE	1	0.773055783424006	2		359	173	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882025	NA	P-0050901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	213	612	1	ENST00000269305.4:c.646G>T	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ttg	6/11	0.691097609589181	3	FACETS	0.906	0.869	0.942	0.906	0.869	0.942	CLONAL	3	TRUE	0	0.773055783424006	3		613	281	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213998	2213998	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1189829990	NA	P-0050901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	23	560	0	ENST00000326181.6:c.77C>T	p.Thr26Ile	p.T26I	ENST00000326181	NM_032271.2	26	aCa/aTa	2/21	1	2	FACETS	0.208	0.162	0.261	0.208	0.162	0.261	SUBCLONAL	1	TRUE	1	0.773055783424006	2		560	286	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627442	37627442	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	104	481	0	ENST00000447079.4:c.1357T>A	p.Leu453Met	p.L453M	ENST00000447079	NM_015083.1	453	Ttg/Atg	2/14	0.691097609589181	3	FACETS	1	0.981	1	0.443	0.402	0.484	CLONAL	1	TRUE	0	0.773055783424006	3		481	281	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545737	63545737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371327205	NA	P-0050901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	149	431	0	ENST00000307078.5:c.857G>A	p.Gly286Asp	p.G286D	ENST00000307078	NM_004655.3	286	gGt/gAt	3/11	0.691097609589181	3	FACETS	0.857	0.811	0.9	0.857	0.811	0.9	CLONAL	3	TRUE	0	0.773055783424006	3		431	208	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244044	5244044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372290737	NA	P-0050901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	91	702	0	ENST00000357368.4:c.1438G>A	p.Val480Met	p.V480M	ENST00000357368	NM_002850.3	480	Gtg/Atg	11/38	0.756679975848467	3	FACETS	0.98	0.879	1	0.49	0.439	0.543	CLONAL	1	TRUE	1	0.773055783424006	3		702	333	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518909	187518909	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1323366048	NA	P-0050901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	145	514	0	ENST00000441802.2:c.12295A>T	p.Lys4099Ter	p.K4099*	ENST00000441802	NM_005245.3	4099	Aag/Tag	24/27	0.402403705433434	4	FACETS	1	0.977	1	1	0.977	1	INDETERMINATE	2	TRUE	2	0.773055783424006	4		514	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579355	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519997	NA	P-0050902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	345	616	0	ENST00000269305.4:c.332T>G	p.Leu111Arg	p.L111R	ENST00000269305	NM_001126112.2	111	cTg/cGg	4/11	0.471026968140086	3	FACETS	0.953	0.915	0.99	0.953	0.915	0.99	CLONAL	3	FALSE	0	0.564748969113435	3		616	548	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986546	36986546	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	94	506	0	ENST00000354822.5:c.1143C>A	p.Asn381Lys	p.N381K	ENST00000354822	NM_001079668.2	381	aaC/aaA	3/3	0.386513046031747	1	FACETS	0.711	0.639	0.786	0.711	0.639	0.786	SUBCLONAL	1	FALSE	0	0.564748969113435	1		506	336	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074165	8074165	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	79	318	0	ENST00000377482.5:c.494A>G	p.Asp165Gly	p.D165G	ENST00000377482	NM_018948.3	165	gAt/gGt	4/4	0.40858464787379	0	FACETS	0.522	0.462	0.586			1	SUBCLONAL	1	FALSE	0	0.441287841896502	0		318	383	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374703	118374703	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs956313303	NA	P-0050904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	53	371	1	ENST00000534358.1:c.8096G>A	p.Arg2699Gln	p.R2699Q	ENST00000534358	NM_005933.3	2699	cGa/cAa	27/36	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	FALSE	1	0.441287841896502	2		372	208	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439924	49439924	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	116	500	0	ENST00000301067.7:c.4617del	p.Glu1540ArgfsTer22	p.E1540Rfs*22	ENST00000301067	NM_003482.3	1539	acA/ac	17/54	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.441287841896502	2		500	475	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865680	57865680	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	115	664	0	ENST00000228682.2:c.3157C>G	p.Leu1053Val	p.L1053V	ENST00000228682	NM_005269.2	1053	Ctg/Gtg	12/12	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	FALSE	1	0.441287841896502	2		664	509	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135311	30135311	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	55	379	0	ENST00000331968.5:c.507del	p.Leu170TrpfsTer13	p.L170Wfs*13	ENST00000331968	NM_002742.2	169	ggG/gg	3/18	0.441287841896502	1	FACETS	0.627	0.539	0.721	0.627	0.539	0.721	SUBCLONAL	1	FALSE	0	0.441287841896502	1		379	310	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917794	29917794	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201750304	NA	P-0050904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	151	594	3	ENST00000389048.3:c.874C>T	p.Arg292Cys	p.R292C	ENST00000389048	NM_004304.4	292	Cgc/Tgc	3/29	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.441287841896502	2		597	621	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023640	31023640	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	262	500	0	ENST00000375687.4:c.3125C>A	p.Pro1042Gln	p.P1042Q	ENST00000375687	NM_015338.5	1042	cCa/cAa	13/13	0.336133515212167	3	FACETS	0.84	0.795	0.886	1	0.991	1	CLONAL	3	FALSE	1	0.441287841896502	3		500	575	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183711	10183712	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	T	novel	NA	P-0050904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	78	519	0	ENST00000256474.2:c.180_181delinsT	p.Val62CysfsTer5	p.V62Cfs*5	ENST00000256474	NM_000551.3	60	cgGCcc/cgTcc	1/3	0.441287841896502	1	FACETS	0.998	0.888	1	0.998	0.888	1	CLONAL	1	FALSE	0	0.441287841896502	1		519	276	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52649453	52649456	+	frameshift_variant	Frame_Shift_Del	DEL	ATAT	ATAT	-	novel	NA	P-0050904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	79	387	0	ENST00000394830.3:c.1835_1838del	p.His612ProfsTer29	p.H612Pfs*29	ENST00000394830	NM_018313.4	612	cATATc/cc	16/30	0.441287841896502	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	0	0.441287841896502	1		387	240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577541	7577541	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201762	NA	P-0050905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	34	655	1	ENST00000269305.4:c.740A>T	p.Asn247Ile	p.N247I	ENST00000269305	NM_001126112.2	247	aAc/aTc	7/11	0.45435485027639	2	FACETS	1	0.943	1	0.656	0.552	0.765	CLONAL	1	TRUE	0	0.545344822089644	2		656	95	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602611	10602611	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	35	776	0	ENST00000171111.5:c.967A>G	p.Lys323Glu	p.K323E	ENST00000171111	NM_203500.1	323	Aag/Gag	3/6	0.469134209098916	2	FACETS	1	0.955	1	0.721	0.611	0.835	CLONAL	1	TRUE	0	0.545344822089644	2		776	89	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574485	64574485	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	43	690	0	ENST00000312049.6:c.910A>G	p.Lys304Glu	p.K304E	ENST00000312049	NM_130799.2	304	Aag/Gag	6/10	0.284706039194178	5	FACETS	0.861	0.742	0.984	0.861	0.742	0.984	INDETERMINATE	3	TRUE	2	0.545344822089644	5		690	111	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466970	18466971	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0050905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	24	398	0	ENST00000266497.5:c.1109_1110delinsAT	p.Arg370Asn	p.R370N	ENST00000266497		370	aGG/aAT	5/31	0.211049135376942	5	FACETS	0.899	0.722	1	0.599	0.481	0.728	INDETERMINATE	2	TRUE	2	0.545344822089644	5		398	89	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965173	25965173	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	13	621	1	ENST00000435504.4:c.4033G>T	p.Val1345Leu	p.V1345L	ENST00000435504		1345	Gta/Tta	13/13	0.37401508526148	3	FACETS	0.619	0.447	0.824	0.31	0.223	0.412	SUBCLONAL	1	TRUE	1	0.545344822089644	3		622	98	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146574	185146574	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	20	628	0	ENST00000265026.3:c.205T>A	p.Leu69Met	p.L69M	ENST00000265026	NM_004721.4	69	Ttg/Atg	2/14	0.545344822089644	4	FACETS	0.81	0.625	1	0.405	0.312	0.511	CLONAL	1	TRUE	2	0.545344822089644	4		628	140	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1253862	1253862	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	15	528	0	ENST00000310581.5:c.3380T>C	p.Phe1127Ser	p.F1127S	ENST00000310581	NM_198253.2	1127	tTc/tCc	16/16	0.192483330413889	1	FACETS	0.44	0.326	0.571	0.44	0.326	0.571	INDETERMINATE	1	TRUE	0	0.545344822089644	1		528	91	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400226	139400226	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	32	818	2	ENST00000277541.6:c.4122C>A	p.Cys1374Ter	p.C1374*	ENST00000277541	NM_017617.3	1374	tgC/tgA	25/34	0.210069865365746	3	FACETS	1	0.95	1	0.739	0.616	0.871	INDETERMINATE	1	TRUE	1	0.545344822089644	3		820	101	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0050907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	40	366	0				ENST00000310581	NM_198253.2	-/1132			0.21603881287857	1	FACETS	0.86	0.716	1	0.86	0.716	1	CLONAL	1	TRUE	0	0.21603881287857	1		366	384	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0050907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	58	627	3	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.707	0.607	0.818	0.707	0.607	0.818	SUBCLONAL	1	TRUE	1	0.21603881287857	2		630	759	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239508	123239508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374993905	NA	P-0050907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	109	824	0	ENST00000358487.5:c.2329G>A	p.Glu777Lys	p.E777K	ENST00000358487	NM_000141.4	777	Gaa/Aaa	18/18	0.21603881287857	0	FACETS	1	0.901	1			1	CLONAL	1	TRUE	0	0.21603881287857	0		824	788	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577559	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0050907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	82	621	1	ENST00000269305.4:c.722_723delinsTT	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCC/tTT	7/11	0.21603881287857	1	FACETS	0.981	0.865	1	0.981	0.865	1	CLONAL	1	TRUE	0	0.21603881287857	1		622	690	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144132	11144132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	79	719	0	ENST00000358026.2:c.3713C>T	p.Ser1238Phe	p.S1238F	ENST00000358026	NM_001128849.1	1238	tCc/tTc	26/36	1	2	FACETS	0.964	0.847	1	0.964	0.847	1	CLONAL	1	TRUE	1	0.21603881287857	2		719	759	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484270	8484270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867884876	NA	P-0050907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	82	501	0	ENST00000356435.5:c.3262C>T	p.Arg1088Cys	p.R1088C	ENST00000356435		1088	Cgt/Tgt	19/35	0.21603881287857	0	FACETS	0.931	0.822	1			1	CLONAL	1	TRUE	0	0.21603881287857	0		501	639	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47709985	47709985	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	42	317	0	ENST00000233146.2:c.2702A>G	p.Glu901Gly	p.E901G	ENST00000233146	NM_000251.2	901	gAa/gGa	16/16	1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.21603881287857	2		317	386	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511088	148511088	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	74	453	0	ENST00000320356.2:c.1814C>T	p.Ser605Phe	p.S605F	ENST00000320356	NM_004456.4	605	tCc/tTc	15/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.21603881287857	2		453	505	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227026	53227026	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	63	402	1	ENST00000375401.3:c.2549T>G	p.Leu850Arg	p.L850R	ENST00000375401	NM_004187.3	850	cTg/cGg	18/26	NA	2	FACETS	0.763	0.663	0.871			1	INDETERMINATE	2	TRUE	NA	0.21603881287857	2		403	382	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	85	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.177286742835614	3	FACETS	0.998	0.889	1	0.666	0.593	0.743	CLONAL	2	TRUE	0	0.26	3		334	370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0050908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	151	567	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.241061834891689	2	FACETS	1	0.987	1	0.722	0.661	0.787	CLONAL	1	TRUE	0	0.26	2		567	804	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0050908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	31	337	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.998	0.812	1	0.998	0.812	1	CLONAL	1	TRUE	1	0.26	2		337	239	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222717	5222717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767586201	NA	P-0050908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	55	498	1	ENST00000357368.4:c.3086C>T	p.Thr1029Met	p.T1029M	ENST00000357368	NM_002850.3	1029	aCg/aTg	18/38	1	2	FACETS	0.735	0.628	0.851	0.735	0.628	0.851	SUBCLONAL	1	TRUE	1	0.26	2		499	576	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280814	41280814	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	34	322	0	ENST00000349496.5:c.2327G>A	p.Trp776Ter	p.W776*	ENST00000349496	NM_001904.3	776	tGg/tAg	15/15	1	2	FACETS	0.703	0.575	0.847	0.703	0.575	0.847	SUBCLONAL	1	TRUE	1	0.26	2		322	372	SUCCESS
APC	324	MSKCC	GRCh37	5	112174944	112174944	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	28	218	0	ENST00000257430.4:c.3653C>A	p.Thr1218Lys	p.T1218K	ENST00000257430	NM_000038.5	1218	aCg/aAg	16/16	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.26	2		218	202	SUCCESS
APC	324	MSKCC	GRCh37	5	112175230	112175230	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	23	222	0	ENST00000257430.4:c.3939del	p.Arg1314GlyfsTer7	p.R1314Gfs*7	ENST00000257430	NM_000038.5	1313	acT/ac	16/16	1	2	FACETS	0.847	0.663	1	0.847	0.663	1	CLONAL	1	TRUE	1	0.26	2		222	209	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279374	38279374	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	183	652	0	ENST00000425967.3:c.1115G>C	p.Cys372Ser	p.C372S	ENST00000425967	NM_001174067.1	372	tGc/tCc	9/19	0.3	4	FACETS	1	0.973	1	0.742	0.686	0.8	CLONAL	2	TRUE	1	0.26	4		652	797	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0050926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	181	366	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.789688119279904	2		366	415	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073956	8073956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1283318754	NA	P-0050926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	220	426	0	ENST00000377482.5:c.703C>T	p.Pro235Ser	p.P235S	ENST00000377482	NM_018948.3	235	Cca/Tca	4/4	1	2	FACETS	0.999	0.937	1	0.999	0.937	1	CLONAL	1	TRUE	1	0.789688119279904	2		426	558	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300560	11300560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775796479	NA	P-0050926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	413	665	0	ENST00000361445.4:c.1586C>T	p.Pro529Leu	p.P529L	ENST00000361445	NM_004958.3	529	cCa/cTa	11/58	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.789688119279904	2		665	994	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534285	534285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894226	NA	P-0050926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	295	605	1	ENST00000451590.1:c.38G>T	p.Gly13Val	p.G13V	ENST00000451590	NM_001130442.1	13	gGt/gTt	2/5	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.789688119279904	2		606	739	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061753	38061753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	327	534	0	ENST00000250448.2:c.236C>T	p.Pro79Leu	p.P79L	ENST00000250448	NM_004496.3	79	cCc/cTc	2/2	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.789688119279904	2		534	781	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95597967	95597967	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	156	257	0	ENST00000393063.1:c.317T>C	p.Val106Ala	p.V106A	ENST00000393063	NM_030621.3	106	gTt/gCt	5/28	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.789688119279904	2		257	394	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857284	9857284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	249	501	0	ENST00000330684.3:c.4117G>A	p.Asp1373Asn	p.D1373N	ENST00000330684	NM_001134407.1	1373	Gat/Aat	13/13	0.735001974985157	1	FACETS	0.763	0.722	0.804	0.763	0.722	0.804	SUBCLONAL	1	TRUE	0	0.789688119279904	1		501	500	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50830325	50830325	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	286	419	0	ENST00000398568.2:c.2768T>C	p.Leu923Ser	p.L923S	ENST00000398568	NM_001042412.1	923	tTg/tCg	18/18	0.29776410648946	3	FACETS	1	0.991	1	0.635	0.6	0.672	INDETERMINATE	1	TRUE	1	0.789688119279904	3		419	795	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508736	29508736	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555608737	NA	P-0050926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	184	411	0	ENST00000356175.3:c.663G>A	p.Trp221Ter	p.W221*	ENST00000356175	NM_000267.3	221	tgG/tgA	7/57	0.789688119279904	3	FACETS	0.852	0.788	0.918	0.426	0.394	0.459	CLONAL	1	TRUE	1	0.789688119279904	3		411	763	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556857	29556860	+	stop_gained	Nonsense_Mutation	ONP	TATT	TATT	GATG	novel	NA	P-0050926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	293	278	0	ENST00000356175.3:c.2855_2858delinsGATG	p.Leu952_Leu953delinsTer	p.L952_L953delins*	ENST00000356175	NM_000267.3	952	tTATTg/tGATGg	22/57	0.789688119279904	3	FACETS	0.984	0.938	1	0.984	0.938	1	CLONAL	2	TRUE	1	0.789688119279904	3		278	526	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687013	37687013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	332	543	0	ENST00000447079.4:c.3917C>T	p.Ser1306Phe	p.S1306F	ENST00000447079	NM_015083.1	1306	tCc/tTc	14/14	0.789688119279904	3	FACETS	1	0.968	1	0.516	0.488	0.545	CLONAL	1	TRUE	1	0.789688119279904	3		543	1136	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164910	47164910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	124	234	0	ENST00000409792.3:c.1216C>T	p.His406Tyr	p.H406Y	ENST00000409792	NM_014159.6	406	Cac/Tac	3/21	1	2	FACETS	0.849	0.776	0.923	0.849	0.776	0.923	CLONAL	1	TRUE	1	0.789688119279904	2		234	370	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971104	55971104	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781752678	NA	P-0050926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	310	530	0	ENST00000263923.4:c.1693G>A	p.Glu565Lys	p.E565K	ENST00000263923	NM_002253.2	565	Gag/Aag	13/30	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.789688119279904	2		530	751	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522561	67522561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs969825259	NA	P-0050926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	165	206	0	ENST00000274335.5:c.58G>A	p.Glu20Lys	p.E20K	ENST00000274335		20	Gaa/Aaa	1/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.789688119279904	2		206	399	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502729	149502729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777708927	NA	P-0050926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	354	599	1	ENST00000261799.4:c.2059G>A	p.Gly687Arg	p.G687R	ENST00000261799	NM_002609.3	687	Gga/Aga	15/23	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.789688119279904	2		600	881	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390657	139390657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	478	907	1	ENST00000277541.6:c.7534C>T	p.Pro2512Ser	p.P2512S	ENST00000277541	NM_017617.3	2512	Ccg/Tcg	34/34	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.789688119279904	2		908	1175	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0050927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	3374	519	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.600017888759553	25	FACETS	0.981	0.974	0.988			1	CLONAL	24	TRUE	NA	0.600017888759553	25		519	3774	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360504	70360504	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	301	1087	1	ENST00000374080.3:c.6064C>T	p.Gln2022Ter	p.Q2022*	ENST00000374080		2022	Cag/Tag	42/45	1	2	FACETS	0.93	0.876	0.985	0.93	0.876	0.985	CLONAL	1	TRUE	1	0.600017888759553	2		1088	1079	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575104	48575114	+	frameshift_variant	Frame_Shift_Del	DEL	AGGTGGCCTGA	AGGTGGCCTGA	-	novel	NA	P-0050927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	102	312	0	ENST00000342988.3:c.298_308del	p.Arg100SerfsTer5	p.R100Sfs*5	ENST00000342988	NM_005359.5	100	AGGTGGCCTGAt/t	3/12	0.553157011322633	1	FACETS	0.841	0.763	0.921	0.841	0.763	0.921	CLONAL	1	TRUE	0	0.600017888759553	1		312	283	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138554	11138554	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	236	821	0	ENST00000358026.2:c.3310C>G	p.Gln1104Glu	p.Q1104E	ENST00000358026	NM_001128849.1	1104	Caa/Gaa	24/36	0.562262743808775	1	FACETS	0.871	0.818	0.925	0.871	0.818	0.925	CLONAL	1	TRUE	0	0.600017888759553	1		821	632	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29085197	29085197	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	16	11	0	ENST00000328354.6:c.1468G>C	p.Asp490His	p.D490H	ENST00000328354	NM_007194.3	490	Gac/Cac	14/15	0.566630495773333	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.600017888759553	1		11	28	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840032	27840032	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	73	621	0	ENST00000328488.2:c.62T>A	p.Leu21Gln	p.L21Q	ENST00000328488	NM_003533.2	21	cTg/cAg	1/1	0.543491347839794	2	FACETS	0.37	0.324	0.421	0.185	0.162	0.211	SUBCLONAL	1	TRUE	0	0.600017888759553	2		621	657	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0050933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	142	355	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.931	1	1	0.991	1	CLONAL	2	TRUE	1	0.22	2		355	632	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382145	152382145	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	20	0	0	ENST00000206249.3:c.1255G>C	p.Glu419Gln	p.E419Q	ENST00000206249	NM_000125.3	419	Gag/Cag	6/8	1	2	FACETS	0.367	0.279	0.469	0.367	0.279	0.469	SUBCLONAL	1	TRUE	1	0.22	2		0	496	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0050935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	110	390	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.873	0.786	0.965	0.873	0.786	0.965	CLONAL	1	TRUE	1	0.397997130113121	2		390	633	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150336	108150336	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0050935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	79	323	0	ENST00000278616.4:c.3402+1G>A		p.X1134_splice	ENST00000278616	NM_000051.3	1134			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.397997130113121	2		323	314	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039883	47039883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	107	864	0	ENST00000377604.3:c.1226C>T	p.Ala409Val	p.A409V	ENST00000377604	NM_001204468.1	409	gCg/gTg	12/24	1	2	FACETS	0.879	0.79	0.972	0.879	0.79	0.972	CLONAL	1	TRUE	1	0.397997130113121	2		864	612	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586072	29586072	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	72	380	0	ENST00000356175.3:c.4292del	p.His1431LeufsTer17	p.H1431Lfs*17	ENST00000356175	NM_000267.3	1431	cAt/ct	32/57	0.397997130113121	1	FACETS	0.767	0.674	0.866	0.767	0.674	0.866	SUBCLONAL	1	TRUE	0	0.397997130113121	1		380	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0050937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	176	567	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.287228306305694	2	FACETS	0.905	0.838	0.974	0.905	0.838	0.974	CLONAL	2	TRUE	0	0.318314520478023	2		567	611	SUCCESS
APC	324	MSKCC	GRCh37	5	112157627	112157628	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs1554080698	NA	P-0050937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	41	917	1	ENST00000257430.4:c.1354_1355del	p.Val452SerfsTer7	p.V452Sfs*7	ENST00000257430	NM_000038.5	449	gcTGtg/gctg	11/16	0.318314520478023	3	FACETS	1	0.942	1	0.644	0.54	0.756	CLONAL	1	TRUE	1	0.318314520478023	3		918	232	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087893	27087904	+	inframe_deletion	In_Frame_Del	DEL	GGCCACCCAGTG	GGCCACCCAGTG	-	novel	NA	P-0050937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	84	1437	0	ENST00000324856.7:c.2181_2192del	p.Pro728_Gly731del	p.P728_G731del	ENST00000324856	NM_006015.4	727	cGGCCACCCAGTGgc/cgc	6/20	1	2	FACETS	0.949	0.84	1	0.949	0.84	1	CLONAL	1	TRUE	1	0.318314520478023	2		1437	556	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517442	157517442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772095737	NA	P-0050937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	144	1045	2	ENST00000346085.5:c.4006G>A	p.Asp1336Asn	p.D1336N	ENST00000346085	NM_020732.3	1336	Gac/Aac	16/20	0.318314520478023	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.318314520478023	3		1047	494	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	151	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.87	0.803	0.939	1	0.991	1	CLONAL	2	TRUE	1	0.39518401059256	2		436	439	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	44	258	0	ENST00000257430.4:c.3964del	p.Glu1322LysfsTer93	p.E1322Kfs*93	ENST00000257430	NM_000038.5	1322	Gaa/aa	16/16	1	2	FACETS	0.873	0.738	1	0.873	0.738	1	CLONAL	1	TRUE	1	0.39518401059256	2		258	255	SUCCESS
APC	324	MSKCC	GRCh37	5	112175770	112175770	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	84	338	0	ENST00000257430.4:c.4480del	p.Glu1494LysfsTer13	p.E1494Kfs*13	ENST00000257430	NM_000038.5	1493	acG/ac	16/16	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.39518401059256	2		338	365	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368203	45368203	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	120	333	0	ENST00000262160.6:c.1399T>C	p.Ser467Pro	p.S467P	ENST00000262160	NM_005901.5	467	Tca/Cca	11/11	0.348861348072516	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.39518401059256	2		333	280	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309757	65309757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs929273412	NA	P-0050939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	121	546	0	ENST00000342505.4:c.2393C>T	p.Thr798Met	p.T798M	ENST00000342505	NM_002227.2	798	aCg/aTg	17/25	1	2	FACETS	0.858	0.776	0.944	0.858	0.776	0.944	CLONAL	1	TRUE	1	0.39518401059256	2		546	714	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711357	114711379	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGCCCGAACCGTAAGTGCCTCCG	CGCCCGAACCGTAAGTGCCTCCG	-	novel	NA	P-0050939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	27	231	0	ENST00000543371.1:c.378_381+19del		p.X126_splice	ENST00000543371	NM_001198531.1	126		3/14	1	2	FACETS	0.403	0.321	0.497	0.403	0.321	0.497	SUBCLONAL	1	TRUE	1	0.39518401059256	2		231	339	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424200	49424200	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	84	333	0	ENST00000301067.7:c.13862C>T	p.Thr4621Ile	p.T4621I	ENST00000301067	NM_003482.3	4621	aCa/aTa	42/54	0.39518401059256	3	FACETS	0.87	0.77	0.978	0.435	0.385	0.489	CLONAL	1	TRUE	1	0.39518401059256	3		333	585	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477143	67477143	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	180	749	0	ENST00000327367.4:c.950C>A	p.Ser317Tyr	p.S317Y	ENST00000327367	NM_005902.3	317	tCt/tAt	7/9	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.39518401059256	2		749	910	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795612	42795612	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	222	995	0	ENST00000575354.2:c.2692C>A	p.Pro898Thr	p.P898T	ENST00000575354	NM_015125.3	898	Ccc/Acc	10/20	1	2	FACETS	0.951	0.884	1	0.951	0.884	1	CLONAL	1	TRUE	1	0.39518401059256	2		995	1182	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028842	47028843	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGCC	novel	NA	P-0050939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	429	884	0	ENST00000377604.3:c.147_151dup	p.Gln51ProfsTer85	p.Q51Pfs*85	ENST00000377604	NM_001204468.1	49	ggc/ggCAGCCc	3/24	0.39518401059256	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.39518401059256	3		884	1286	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	82	276	0				ENST00000310581	NM_198253.2	-/1132			0.432017128965004	5	FACETS	1	0.97	1	0.434	0.384	0.488	CLONAL	1	TRUE	2	0.432017128965004	5		276	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0050940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	454	852	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.340705375006463	3	FACETS	1	0.995	1	0.832	0.797	0.867	CLONAL	2	TRUE	0	0.432017128965004	3		852	1024	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113139	209113139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	23	432	0	ENST00000345146.2:c.368G>A	p.Gly123Glu	p.G123E	ENST00000345146	NM_005896.2	123	gGa/gAa	4/10	0.432017128965004	1	FACETS	0.321	0.251	0.402	0.321	0.251	0.402	SUBCLONAL	1	TRUE	0	0.432017128965004	1		432	260	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041576	47041576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	279	415	1	ENST00000377604.3:c.1801C>T	p.Gln601Ter	p.Q601*	ENST00000377604	NM_001204468.1	601	Cag/Tag	17/24	0.420876540523214	2	FACETS	0.853	0.812	0.893			1	CLONAL	3	TRUE	NA	0.432017128965004	2		416	505	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982311	201982312	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0050940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	371	999	0	ENST00000359651.3:c.692dup	p.Arg233SerfsTer2	p.R233Sfs*2	ENST00000359651		230	-/G	6/8	0.432017128965004	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	1	0.432017128965004	3		999	1043	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807562	36807562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	90	843	0	ENST00000373129.3:c.1102G>A	p.Glu368Lys	p.E368K	ENST00000373129	NM_032017.1	368	Gag/Aag	12/12	0.432017128965004	3	FACETS	0.587	0.52	0.659	0.294	0.26	0.33	SUBCLONAL	1	TRUE	1	0.432017128965004	3		843	863	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951166	48951166	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0050940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	55	392	0	ENST00000267163.4:c.1328C>G	p.Ser443Ter	p.S443*	ENST00000267163	NM_000321.2	443	tCa/tGa	13/27	0.432017128965004	0	FACETS	0.709	0.615	0.808			1	SUBCLONAL	1	TRUE	0	0.432017128965004	0		392	204	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209110136	209110136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	33	480	0	ENST00000345146.2:c.427G>A	p.Asp143Asn	p.D143N	ENST00000345146	NM_005896.2	143	Gat/Aat	5/10	0.432017128965004	1	FACETS	0.468	0.383	0.563	0.468	0.383	0.563	SUBCLONAL	1	TRUE	0	0.432017128965004	1		480	256	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714485	117714485	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0050940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	16	263	0	ENST00000368508.3:c.1165-1G>T		p.X389_splice	ENST00000368508	NM_002944.2	389			0.432017128965004	0	FACETS	0.351	0.262	0.454			1	SUBCLONAL	1	TRUE	0	0.432017128965004	0		263	120	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0050941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	246	366	0				ENST00000310581	NM_198253.2	-/1132			0.374776784673868	2	FACETS	0.899	0.855	0.942	0.899	0.855	0.942	INDETERMINATE	2	TRUE	0	0.658004949702448	2		366	416	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0050941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	207	1081	3	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	0.407469629980576	1	FACETS	0.443	0.411	0.476	0.443	0.411	0.476	SUBCLONAL	1	TRUE	0	0.658004949702448	1		1084	953	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715979	52715979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205227	NA	P-0050942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	43	753	0	ENST00000322088.6:c.544C>T	p.Arg182Trp	p.R182W	ENST00000322088	NM_014225.5	182	Cgg/Tgg	5/15	1	2	FACETS	0.584	0.487	0.693	0.584	0.487	0.693	SUBCLONAL	1	TRUE	1	0.17	2		753	866	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578509	7578509	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519978	NA	P-0050942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	110	936	0	ENST00000269305.4:c.421T>C	p.Cys141Arg	p.C141R	ENST00000269305	NM_001126112.2	141	Tgc/Cgc	5/11	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.17	2		936	1222	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202773	16202773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140309172	NA	P-0050942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	31	450	2	ENST00000375759.3:c.481C>T	p.Arg161Trp	p.R161W	ENST00000375759	NM_015001.2	161	Cgg/Tgg	3/15	1	2	FACETS	0.612	0.494	0.747	0.612	0.494	0.747	SUBCLONAL	1	TRUE	1	0.17	2		452	596	SUCCESS
APC	324	MSKCC	GRCh37	5	112162945	112162945	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1114167599	NA	P-0050942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	37	278	0	ENST00000257430.4:c.1548+1G>T		p.X516_splice	ENST00000257430	NM_000038.5	516			1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.17	2		278	425	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661717	227661717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144912682	NA	P-0050942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	59	694	0	ENST00000305123.5:c.1738C>T	p.Arg580Cys	p.R580C	ENST00000305123	NM_005544.2	580	Cgc/Tgc	1/2	NA	2	FACETS	0.845	0.726	0.976			1	INDETERMINATE	1	TRUE	NA	0.17	2		694	821	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	88	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.974	0.868	1	0.974	0.868	1	CLONAL	1	TRUE	1	0.451860741274739	2		334	400	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954192	48954192	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	64	261	0	ENST00000267163.4:c.1393G>T	p.Glu465Ter	p.E465*	ENST00000267163	NM_000321.2	465	Gaa/Taa	15/27	0.451860741274739	1	FACETS	0.933	0.819	1	0.933	0.819	1	CLONAL	1	TRUE	0	0.451860741274739	1		261	235	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579408	7579430	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGGGCCAGGAGGGGGCTGGTG	CAGGGGCCAGGAGGGGGCTGGTG	-	rs886041861	NA	P-0050943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	212	669	0	ENST00000269305.4:c.257_279del	p.Ala86ValfsTer55	p.A86Vfs*55	ENST00000269305	NM_001126112.2	86	gCACCAGCCCCCTCCTGGCCCCTG/g	4/11	0.451860741274739	1	FACETS	0.807	0.75	0.866	0.807	0.75	0.866	CLONAL	1	TRUE	0	0.451860741274739	1		669	900	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858195	40858195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777686988	NA	P-0050943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	207	827	2	ENST00000428826.2:c.1669C>T	p.Arg557Cys	p.R557C	ENST00000428826		557	Cgt/Tgt	16/21	1	2	FACETS	0.932	0.865	1	0.932	0.865	1	CLONAL	1	TRUE	1	0.451860741274739	2		829	983	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983121	201983122	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0050943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	182	843	0	ENST00000359651.3:c.971dup	p.Met324IlefsTer147	p.M324Ifs*147	ENST00000359651		324	atg/aTtg	7/8	1	2	FACETS	0.976	0.902	1	0.976	0.902	1	CLONAL	1	TRUE	1	0.451860741274739	2		843	825	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349765	89349765	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	220	918	1	ENST00000301030.4:c.3185C>A	p.Thr1062Asn	p.T1062N	ENST00000301030	NM_001256183.1	1062	aCc/aAc	9/13	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.451860741274739	2		919	969	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47088112	47088112	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0050944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	62	458	0	ENST00000409792.3:c.6964-1G>C		p.X2322_splice	ENST00000409792	NM_014159.6	2322			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		458	265	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985468	2985468	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	30	510	0	ENST00000396946.4:c.343T>A	p.Phe115Ile	p.F115I	ENST00000396946	NM_032415.4	115	Ttc/Atc	4/25	0.1034778512887	0	FACETS	0.385	0.309	0.47			1	INDETERMINATE	1	TRUE	0	0.26	0		510	444	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490393	29490393	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	28	454	0	ENST00000356175.3:c.478A>T	p.Arg160Trp	p.R160W	ENST00000356175	NM_000267.3	160	Agg/Tgg	4/57	1	2	FACETS	0.437	0.348	0.538	0.437	0.348	0.538	SUBCLONAL	1	TRUE	1	0.26	2		454	493	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152476	56152476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	20	283	0	ENST00000399503.3:c.532G>A	p.Asp178Asn	p.D178N	ENST00000399503	NM_005921.1	178	Gat/Aat	2/20	0.166106022148874	3	FACETS	0.483	0.369	0.617	0.241	0.184	0.309	SUBCLONAL	1	TRUE	1	0.26	3		283	360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0050946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	332	896	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.2894417609795	3	FACETS	1	0.987	1	0.749	0.71	0.788	CLONAL	2	TRUE	0	0.384259507325804	3		896	917	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367288	50367288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775793261	NA	P-0050946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	128	528	3	ENST00000331340.3:c.95C>T	p.Pro32Leu	p.P32L	ENST00000331340	NM_006060.4	32	cCg/cTg	3/8	0.269941312192109	4	FACETS	0.751	0.683	0.823	0.751	0.683	0.823	SUBCLONAL	2	TRUE	2	0.384259507325804	4		531	614	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636819	2636820	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0050946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	240	914	0	ENST00000342085.4:c.1268_1269delinsTT	p.Ser423Phe	p.S423F	ENST00000342085	NM_002613.4	423	tCC/tTT	11/14	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.384259507325804	2		914	850	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713470	40713470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318044562	NA	P-0050946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	259	924	1	ENST00000373198.4:c.4045C>T	p.Arg1349Cys	p.R1349C	ENST00000373198	NM_133170.3	1349	Cgt/Tgt	30/32	0.356732261411077	3	FACETS	1	0.992	1			1	CLONAL	1	TRUE	NA	0.384259507325804	3		925	1135	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435581	56435581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200166143	NA	P-0050946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	138	1016	0	ENST00000407977.2:c.1556G>A	p.Arg519Gln	p.R519Q	ENST00000407977		519	cGa/cAa	9/10	0.384259507325804	3	FACETS	0.715	0.649	0.784	0.357	0.324	0.392	SUBCLONAL	1	TRUE	1	0.384259507325804	3		1016	1198	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164842	106164842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	77	677	0	ENST00000380013.4:c.3710C>T	p.Pro1237Leu	p.P1237L	ENST00000380013	NM_001127208.2	1237	cCg/cTg	6/11	0.27833892840332	3	FACETS	0.692	0.608	0.784	0.346	0.304	0.392	SUBCLONAL	1	TRUE	1	0.384259507325804	3		677	690	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300092	15300092	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	262	971	0	ENST00000263388.2:c.1184G>T	p.Cys395Phe	p.C395F	ENST00000263388	NM_000435.2	395	tGc/tTc	7/33	0.269941312192109	4	FACETS	0.836	0.783	0.891	0.836	0.783	0.891	CLONAL	2	TRUE	2	0.384259507325804	4		971	1129	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217300	11217300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	848	993	0	ENST00000361445.4:c.4378C>T	p.Leu1460Phe	p.L1460F	ENST00000361445	NM_004958.3	1460	Ctt/Ttt	30/58	0.384259507325804	7	FACETS	0.982	0.953	1	0.982	0.953	1	CLONAL	5	TRUE	2	0.384259507325804	7		993	1762	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916193	9916194	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0050946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	153	627	1	ENST00000330684.3:c.2095_2096delinsTT	p.Pro699Phe	p.P699F	ENST00000330684	NM_001134407.1	699	CCc/TTc	10/13	0.293736093792363	2	FACETS	1	0.986	1	0.682	0.627	0.739	CLONAL	1	TRUE	0	0.384259507325804	2		628	584	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805494	1805494	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1474909212	NA	P-0050946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	288	1014	0	ENST00000260795.2:c.1006G>A	p.Glu336Lys	p.E336K	ENST00000260795		336	Gag/Aag	7/17	0.293736093792363	2	FACETS	0.761	0.717	0.806	0.761	0.717	0.806	SUBCLONAL	2	TRUE	0	0.384259507325804	2		1014	985	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467782	66467782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	61	422	0	ENST00000273854.3:c.487G>A	p.Gly163Arg	p.G163R	ENST00000273854	NM_004439.5	163	Ggg/Agg	3/18	0.27833892840332	3	FACETS	0.832	0.719	0.954	0.416	0.359	0.477	CLONAL	1	TRUE	1	0.384259507325804	3		422	455	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165190	32165191	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0050946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	155	1092	3	ENST00000375023.3:c.4937_4938delinsAA	p.Arg1646Gln	p.R1646Q	ENST00000375023	NM_004557.3	1646	cGG/cAA	27/30	0.27833892840332	3	FACETS	0.842	0.769	0.919	0.421	0.384	0.46	CLONAL	1	TRUE	1	0.384259507325804	3		1095	1142	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120581	94120581	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	120	542	0	ENST00000369303.4:c.470A>G	p.Gln157Arg	p.Q157R	ENST00000369303	NM_004440.3	157	cAa/cGa	3/17	0.269941312192109	4	FACETS	1	0.985	1	0.743	0.673	0.816	CLONAL	1	TRUE	2	0.384259507325804	4		542	582	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0050947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1329	52	872	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	1	2	FACETS	0.471	0.399	0.55	0.471	0.399	0.55	SUBCLONAL	1	TRUE	1	0.16	2		872	1381	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736292	243736292	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	49	533	0	ENST00000263826.5:c.755G>T	p.Gly252Val	p.G252V	ENST00000263826	NM_005465.4	252	gGt/gTt	8/13	0.231596599645268	4	FACETS	0.497	0.42	0.583	0.249	0.21	0.292	SUBCLONAL	1	TRUE	2	0.309605555720061	4		533	834	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0050948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	279	734	1	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.247746873333659	3	FACETS	0.927	0.876	0.98	0.927	0.876	0.98	CLONAL	3	TRUE	0	0.309605555720061	3		735	748	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226712	2226712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780009010	NA	P-0050948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	171	922	2	ENST00000398665.3:c.4192G>A	p.Gly1398Arg	p.G1398R	ENST00000398665	NM_032482.2	1398	Ggg/Agg	27/28	0.0135312699948038	3	FACETS	1	0.989	1	0.731	0.672	0.791	INDETERMINATE	1	TRUE	1	0.309605555720061	3		924	873	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664856	138664856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	20	124	1	ENST00000330315.3:c.709G>A	p.Gly237Ser	p.G237S	ENST00000330315	NM_023067.3	237	Ggt/Agt	1/1	0.199765349257257	3	FACETS	1	0.788	1	0.511	0.394	0.645	CLONAL	1	TRUE	1	0.309605555720061	3		125	146	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0050948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	167	550	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.286650283540852	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	0	0.309605555720061	2		550	539	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0050949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	868	946	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.651534217823242	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	4	TRUE	0	0.651534217823242	4		946	1095	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602314	10602314	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	433	997	1	ENST00000171111.5:c.1264G>C	p.Asp422His	p.D422H	ENST00000171111	NM_203500.1	422	Gat/Cat	3/6	0.642624504095892	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.651534217823242	2		998	629	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667466	241667466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	93	314	0	ENST00000366560.3:c.984G>A	p.Met328Ile	p.M328I	ENST00000366560	NM_000143.3	328	atG/atA	7/10	0.651534217823242	6	FACETS	1	0.961	1	0.235	0.209	0.262	CLONAL	1	TRUE	1	0.651534217823242	6		314	560	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624258	89624258	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	86	243	0	ENST00000371953.3:c.32G>C	p.Arg11Thr	p.R11T	ENST00000371953	NM_000314.4	11	aGa/aCa	1/9	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.651534217823242	2		243	208	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128616	64128616	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	106	647	0	ENST00000334205.4:c.473T>C	p.Ile158Thr	p.I158T	ENST00000334205	NM_003942.2	158	aTt/aCt	5/17	0.651534217823242	3	FACETS	0.849	0.764	0.938	0.425	0.382	0.469	CLONAL	1	TRUE	1	0.651534217823242	3		647	508	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716374	18716374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	178	394	0	ENST00000266497.5:c.3721C>A	p.Gln1241Lys	p.Q1241K	ENST00000266497		1241	Cag/Aag	26/31	0.651534217823242	5	FACETS	0.906	0.84	0.975	0.604	0.56	0.65	CLONAL	2	TRUE	2	0.651534217823242	5		394	596	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842598	68842598	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	128	517	0	ENST00000261769.5:c.534C>G	p.Ile178Met	p.I178M	ENST00000261769	NM_004360.3	178	atC/atG	5/16	0.571531025867911	3	FACETS	0.998	0.909	1	0.499	0.454	0.545	CLONAL	1	TRUE	1	0.651534217823242	3		517	522	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579353	7579353	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	696	818	0	ENST00000269305.4:c.334G>C	p.Gly112Arg	p.G112R	ENST00000269305	NM_001126112.2	112	Ggc/Cgc	4/11	0.651534217823242	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	4	TRUE	0	0.651534217823242	4		818	870	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288428	15288428	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	146	570	0	ENST00000263388.2:c.4311C>G	p.Phe1437Leu	p.F1437L	ENST00000263388	NM_000435.2	1437	ttC/ttG	24/33	0.651328135084492	2	FACETS	1	0.972	1	0.557	0.514	0.602	CLONAL	1	TRUE	0	0.651534217823242	2		570	402	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660606	190660606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	73	346	0	ENST00000441310.2:c.244G>A	p.Glu82Lys	p.E82K	ENST00000441310	NM_000534.4	82	Gaa/Aaa	3/13	0.57416444314589	5	FACETS	0.923	0.81	1	0.308	0.27	0.349	CLONAL	1	TRUE	2	0.651534217823242	5		346	480	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662309	227662310	+	missense_variant	Missense_Mutation	DNP	GC	GC	CA	novel	NA	P-0050949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	320	803	2	ENST00000305123.5:c.1145_1146delinsTG	p.Cys382Leu	p.C382L	ENST00000305123	NM_005544.2	382	tGC/tTG	1/2	0.642624504095892	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.651534217823242	2		805	482	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033204	69033205	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0050949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	101	541	1	ENST00000288368.4:c.3644_3645delinsTT	p.Arg1215Leu	p.R1215L	ENST00000288368	NM_024870.2	1215	cGG/cTT	30/40	1	2	FACETS	0.886	0.8	0.975	0.886	0.8	0.975	CLONAL	1	TRUE	1	0.651534217823242	2		542	350	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224234	98224234	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	85	412	0	ENST00000331920.6:c.2607G>A	p.Met869Ile	p.M869I	ENST00000331920	NM_000264.3	869	atG/atA	16/24	0.651534217823242	2	FACETS	0.912	0.816	1	0.456	0.408	0.506	CLONAL	1	TRUE	0	0.651534217823242	2		412	286	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074181	8074182	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0050950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	94	465	0	ENST00000377482.5:c.477_478del	p.Glu160SerfsTer6	p.E160Sfs*6	ENST00000377482	NM_018948.3	159	tcTGaa/tcaa	4/4	1	2	FACETS	0.97	0.865	1	0.97	0.865	1	CLONAL	1	TRUE	1	0.344220965538157	2		465	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0050950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	109	808	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.262426114480123	1	FACETS	0.674	0.605	0.747	0.674	0.605	0.747	SUBCLONAL	1	TRUE	0	0.344220965538157	1		808	778	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0050950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	92	308	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	0.265989132466456	3	FACETS	0.842	0.748	0.943	0.421	0.374	0.472	CLONAL	1	TRUE	1	0.344220965538157	3		308	744	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	25	276	0				ENST00000310581	NM_198253.2	-/1132			0.343049505454254	3	FACETS	0.954	0.758	1	0.477	0.379	0.588	CLONAL	1	TRUE	1	0.343049505454254	3		276	179	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0050951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	135	380	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.343049505454254	4	FACETS	1	0.94	1	1	0.94	1	CLONAL	3	TRUE	1	0.343049505454254	4		380	344	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431873	49431874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1333678798	NA	P-0050951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	54	815	0	ENST00000301067.7:c.9265dup	p.Val3089GlyfsTer9	p.V3089Gfs*9	ENST00000301067	NM_003482.3	3089	gtg/gGtg	34/54	1	2	FACETS	0.698	0.597	0.808	0.698	0.597	0.808	SUBCLONAL	1	TRUE	1	0.343049505454254	2		815	451	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041046	47041046	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0050951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	64	787	0	ENST00000377604.3:c.1575+1G>T		p.X525_splice	ENST00000377604	NM_001204468.1	525			1	2	FACETS	0.87	0.756	0.993	0.87	0.756	0.993	CLONAL	1	TRUE	1	0.343049505454254	2		787	429	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398211	25398211	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs727503109	NA	P-0050951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	41	352	0	ENST00000311936.3:c.108A>G	p.Ile36Met	p.I36M	ENST00000311936	NM_004985.3	36	atA/atG	2/5	0.343049505454254	4	FACETS	1	0.9	1	0.369	0.309	0.435	CLONAL	1	TRUE	1	0.343049505454254	4		352	290	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626805	14626805	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377706903	NA	P-0050951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	49	627	0	ENST00000254322.2:c.970G>A	p.Glu324Lys	p.E324K	ENST00000254322	NM_006145.1	324	Gaa/Aaa	3/3	1	2	FACETS	0.781	0.663	0.909	0.781	0.663	0.909	CLONAL	1	TRUE	1	0.343049505454254	2		627	366	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111514	8111514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	67	625	0	ENST00000346208.3:c.1000G>A	p.Gly334Arg	p.G334R	ENST00000346208		334	Ggg/Agg	5/6	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.343049505454254	2		625	336	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602343	28602343	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	62	505	1	ENST00000241453.7:c.2025del	p.Asn676ThrfsTer14	p.N676Tfs*14	ENST00000241453	NM_004119.2	675	gtG/gt	16/24	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.343049505454254	2		506	337	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011128	12011128	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	46	368	0	ENST00000353533.5:c.535G>C	p.Glu179Gln	p.E179Q	ENST00000353533	NM_003010.3	179	Gaa/Caa	5/11	0.343049505454254	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.343049505454254	1		368	202	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119761	70119761	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	58	627	0	ENST00000245479.2:c.763G>C	p.Glu255Gln	p.E255Q	ENST00000245479	NM_000346.3	255	Gag/Cag	3/3	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.343049505454254	2		627	277	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650341	12650341	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs886039607	NA	P-0050951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	47	502	0	ENST00000251849.4:c.505G>C	p.Gly169Arg	p.G169R	ENST00000251849	NM_002880.3	169	Ggc/Cgc	5/17	1	2	FACETS	0.838	0.71	0.977	0.838	0.71	0.977	CLONAL	1	TRUE	1	0.343049505454254	2		502	327	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222739	53222739	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	84	941	1	ENST00000375401.3:c.4197G>T	p.Leu1399Phe	p.L1399F	ENST00000375401	NM_004187.3	1399	ttG/ttT	25/26	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.343049505454254	2		942	456	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731049	162731049	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	302	385	0	ENST00000367921.3:c.904G>T	p.Val302Leu	p.V302L	ENST00000367921	NM_006182.2	302	Gta/Tta	9/18	0.872240116877411	4	FACETS	0.876	0.83	0.922	0.876	0.83	0.922	CLONAL	2	TRUE	2	0.872240116877411	4		385	740	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226568823	226568823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779381164	NA	P-0050953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	560	669	2	ENST00000366794.5:c.1246G>A	p.Gly416Arg	p.G416R	ENST00000366794	NM_001618.3	416	Ggg/Agg	9/23	0.872240116877411	4	FACETS	0.963	0.927	0.999	0.963	0.927	0.999	CLONAL	2	TRUE	2	0.872240116877411	4		671	1248	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954221	48954221	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0050953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	151	204	0	ENST00000267163.4:c.1421+1G>A		p.X474_splice	ENST00000267163	NM_000321.2	474			0.872240116877411	2	FACETS	0.956	0.917	0.992	0.956	0.917	0.992	CLONAL	2	TRUE	0	0.872240116877411	2		204	181	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0050953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	604	658	0	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	0.872240116877411	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.872240116877411	2		658	690	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486032	29486032	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	59	252	0	ENST00000356175.3:c.209T>C	p.Ile70Thr	p.I70T	ENST00000356175	NM_000267.3	70	aTa/aCa	3/57	0.872240116877411	3	FACETS	0.952	0.832	1	0.476	0.416	0.54	CLONAL	1	TRUE	1	0.872240116877411	3		252	204	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290110	15290197	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGGGTGGTCAAGAGGGAATGAAGACAGCCTCTCATCCTGTCCCCCCAACCCTGGCCCTGGCATACCCAGCGTTCCTGGGGGACAGGAG	GGGGTGGTCAAGAGGGAATGAAGACAGCCTCTCATCCTGTCCCCCCAACCCTGGCCCTGGCATACCCAGCGTTCCTGGGGGACAGGAG	-	novel	NA	P-0050953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	386	676	0	ENST00000263388.2:c.3438_3461-17del		p.X1146_splice	ENST00000263388	NM_000435.2	1146		21/33	0.872240116877411	3	FACETS	1	0.99	1	0.568	0.541	0.597	CLONAL	1	TRUE	1	0.872240116877411	3		676	1118	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290255	15290255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	415	776	2	ENST00000263388.2:c.3380C>T	p.Ala1127Val	p.A1127V	ENST00000263388	NM_000435.2	1127	gCc/gTc	21/33	0.872240116877411	3	FACETS	1	0.986	1	0.545	0.519	0.572	CLONAL	1	TRUE	1	0.872240116877411	3		778	1253	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426674	212426674	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs112196222	NA	P-0050953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	204	497	0	ENST00000342788.4:c.2441A>G	p.Asn814Ser	p.N814S	ENST00000342788	NM_005235.2	814	aAc/aGc	20/28	0.872240116877411	3	FACETS	0.96	0.894	1	0.48	0.447	0.514	CLONAL	1	TRUE	1	0.872240116877411	3		497	700	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268670	46268670	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	202	432	2	ENST00000371998.3:c.2955G>T	p.Arg985Ser	p.R985S	ENST00000371998		985	agG/agT	16/23	0.872240116877411	3	FACETS	0.983	0.915	1	0.491	0.457	0.526	CLONAL	1	TRUE	1	0.872240116877411	3		434	677	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760288	133760288	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	551	574	1	ENST00000318560.5:c.2611G>T	p.Glu871Ter	p.E871*	ENST00000318560	NM_005157.4	871	Gag/Tag	11/11	0.872240116877411	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	2	0.872240116877411	4		575	1064	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0050954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	743	696	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.283773701449449	9	FACETS	1	0.987	1			1	CLONAL	6	TRUE	NA	0.283773701449449	9		696	1674	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579585	7579585	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	209	587	1	ENST00000269305.4:c.102del	p.Leu35CysfsTer9	p.L35Cfs*9	ENST00000269305	NM_001126112.2	34	ccC/cc	4/11	0.283773701449449	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.283773701449449	2		588	656	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451518	70451518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	73	559	2	ENST00000373644.4:c.6358G>A	p.Val2120Met	p.V2120M	ENST00000373644	NM_030625.2	2120	Gtg/Atg	12/12	1	2	FACETS	0.784	0.686	0.891	0.784	0.686	0.891	SUBCLONAL	1	TRUE	1	0.283773701449449	2		561	656	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913236	32913236	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	80	472	0	ENST00000380152.3:c.4744A>G	p.Thr1582Ala	p.T1582A	ENST00000380152		1582	Acc/Gcc	11/27	NA	2	FACETS	1	0.943	1			1	INDETERMINATE	2	TRUE	NA	0.283773701449449	2		472	259	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0050955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	841	734	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.847007002527679	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.845878310096046	3		735	902	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0050955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	567	595	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.847007002527679	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.845878310096046	2		596	662	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212302	36212302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779172651	NA	P-0050955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	278	778	0	ENST00000222270.7:c.2053G>A	p.Asp685Asn	p.D685N	ENST00000222270	NM_014727.1	685	Gat/Aat	3/37	0.847007002527679	4	FACETS	0.936	0.878	0.996			1	CLONAL	1	TRUE	NA	0.845878310096046	4		778	1296	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940748	71940748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	602	779	0	ENST00000298229.2:c.795del	p.Leu266Ter	p.L266*	ENST00000298229	NM_001567.3	265	gtG/gt	7/28	0.847007002527679	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.845878310096046	2		779	678	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061132	38061132	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	57	125	0	ENST00000250448.2:c.857G>T	p.Gly286Val	p.G286V	ENST00000250448	NM_004496.3	286	gGc/gTc	2/2	0.847007002527679	4	FACETS	1	0.962	1	0.434	0.378	0.493	CLONAL	1	TRUE	1	0.845878310096046	4		125	191	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940863	49940871	+	inframe_deletion	In_Frame_Del	DEL	GGTCACCAT	GGTCACCAT	-	novel	NA	P-0050955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1198	389	908	0	ENST00000296474.3:c.172_180del	p.Met58_Thr60del	p.M58_T60del	ENST00000296474	NM_002447.2	58	ATGGTGACC/-	1/20	0.502122980571873	6	FACETS	0.78	0.74	0.821	0.52	0.493	0.548	INDETERMINATE	2	TRUE	3	0.845878310096046	6		908	1587	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739732	41739732	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	203	586	0	ENST00000242208.4:c.241G>T	p.Ala81Ser	p.A81S	ENST00000242208	NM_002192.2	81	Gcg/Tcg	2/3	0.847007002527679	4	FACETS	1	0.955	1	0.346	0.321	0.372	CLONAL	1	TRUE	1	0.845878310096046	4		586	854	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007635	45007635	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	95	273	0	ENST00000558401.1:c.82C>T	p.Gln28Ter	p.Q28*	ENST00000558401	NM_004048.2	28	Cag/Tag	2/4	0.620062574500871	1	FACETS	0.988	0.899	1	0.988	0.899	1	CLONAL	1	TRUE	0	0.620062574500871	1		273	214	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309528	30309528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1468552717	NA	P-0050956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	56	630	1	ENST00000307677.4:c.494G>A	p.Arg165Gln	p.R165Q	ENST00000307677	NM_138578.1	165	cGg/cAg	2/3	0.57859093399868	3	FACETS	0.213	0.181	0.247	0.106	0.09	0.124	SUBCLONAL	1	TRUE	1	0.620062574500871	3		631	1113	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0050957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	88	366	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.921	0.83	1	0.921	0.83	1	CLONAL	1	TRUE	1	0.816712750688296	2		366	234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579559	7579559	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	242	771	0	ENST00000269305.4:c.128del	p.Leu43Ter	p.L43*	ENST00000269305	NM_001126112.2	43	tTg/tg	4/11	1	2	FACETS	0.948	0.892	1	0.948	0.892	1	CLONAL	1	TRUE	1	0.816712750688296	2		771	625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579317	7579317	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	250	652	0	ENST00000269305.4:c.370T>C	p.Cys124Arg	p.C124R	ENST00000269305	NM_001126112.2	124	Tgc/Cgc	4/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.816712750688296	2		652	577	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591141	67591141	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	126	248	0	ENST00000274335.5:c.1735del	p.Gln579AsnfsTer3	p.Q579Nfs*3	ENST00000274335		578	gaC/ga	12/15	0.13834853367189	3	FACETS	1	0.986	1	0.701	0.644	0.758	INDETERMINATE	1	TRUE	1	0.816712750688296	3		248	310	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051204	128051204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1251238422	NA	P-0050958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	130	589	0	ENST00000285398.2:c.119C>T	p.Ser40Leu	p.S40L	ENST00000285398	NM_000122.1	40	tCg/tTg	2/15	1	2	FACETS	0.975	0.896	1	0.975	0.896	1	CLONAL	1	TRUE	1	0.784556246066729	2		589	340	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864693	68864693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	97	336	0	ENST00000288368.4:c.64C>T	p.Arg22Cys	p.R22C	ENST00000288368	NM_024870.2	22	Cgc/Tgc	1/40	0.784556246066729	6	FACETS	0.94	0.838	1	0.188	0.167	0.21	CLONAL	1	TRUE	1	0.784556246066729	6		336	676	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528072	103528072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	91	324	0	ENST00000355739.4:c.3380C>T	p.Ser1127Leu	p.S1127L	ENST00000355739	NM_000123.3	1127	tCa/tTa	15/15	0.77370570211899	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.784556246066729	1		324	136	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111957681	111957681	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	133	533	0	ENST00000375549.3:c.50G>C	p.Arg17Pro	p.R17P	ENST00000375549	NM_003002.3	17	cGa/cCa	1/4	0.713443615257187	3	FACETS	1	0.947	1	0.523	0.479	0.569	CLONAL	1	TRUE	1	0.784556246066729	3		533	451	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992616	72992619	+	frameshift_variant	Frame_Shift_Del	DEL	CCTC	CCTC	-	novel	NA	P-0050958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	83	464	0	ENST00000268489.5:c.1426_1429del	p.Glu476LysfsTer59	p.E476Kfs*59	ENST00000268489	NM_006885.3	476	GAGGaa/aa	2/10	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.784556246066729	2		464	195	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196351	106196351	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	91	291	0	ENST00000380013.4:c.4684G>C	p.Ala1562Pro	p.A1562P	ENST00000380013	NM_001127208.2	1562	Gct/Cct	11/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.784556246066729	2		291	223	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562396	176562396	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	114	554	2	ENST00000439151.2:c.292C>T	p.Gln98Ter	p.Q98*	ENST00000439151	NM_022455.4	98	Caa/Taa	2/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.784556246066729	2		556	248	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635245	87635245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	134	550	4	ENST00000277120.3:c.2297G>A	p.Gly766Asp	p.G766D	ENST00000277120		766	gGc/gAc	18/19	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.784556246066729	2		554	325	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106072	8106072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	26	437	1	ENST00000346208.3:c.892C>T	p.Arg298Trp	p.R298W	ENST00000346208		298	Cgg/Tgg	4/6	1	2	FACETS	0.359	0.283	0.446	0.359	0.283	0.446	SUBCLONAL	1	TRUE	1	0.280856493793746	2		438	516	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916747	48916747	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690915	NA	P-0050962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	83	337	1	ENST00000267163.4:c.277C>T	p.Gln93Ter	p.Q93*	ENST00000267163	NM_000321.2	93	Caa/Taa	3/27	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.280856493793746	2		338	423	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793386	242793386	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs756100729	NA	P-0050962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	59	755	0	ENST00000334409.5:c.691C>T	p.Arg231Ter	p.R231*	ENST00000334409	NM_005018.2	231	Cga/Tga	5/5	1	2	FACETS	0.598	0.513	0.69	0.598	0.513	0.69	SUBCLONAL	1	TRUE	1	0.280856493793746	2		755	703	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478816	56478816	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	51	564	0	ENST00000267101.3:c.272T>C	p.Met91Thr	p.M91T	ENST00000267101	NM_001982.3	91	aTg/aCg	3/28	0.177928301918039	2	FACETS	0.501	0.425	0.585	0.25	0.212	0.293	SUBCLONAL	1	TRUE	0	0.280856493793746	2		564	725	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562113	176562113	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	29	413	0	ENST00000439151.2:c.9G>C	p.Gln3His	p.Q3H	ENST00000439151	NM_022455.4	3	caG/caC	2/23	1	2	FACETS	0.361	0.289	0.444	0.361	0.289	0.444	SUBCLONAL	1	TRUE	1	0.280856493793746	2		413	572	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193202164	193202164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1223664442	NA	P-0050964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	47	280	0	ENST00000367435.3:c.1196G>A	p.Arg399Gln	p.R399Q	ENST00000367435	NM_024529.4	399	cGa/cAa	14/17	0.43528885608458	5	FACETS	0.731	0.617	0.857	0.183	0.154	0.215	SUBCLONAL	1	TRUE	1	0.43528885608458	5		280	488	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	83	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.865	0.775	0.958	0.865	0.775	0.958	CLONAL	1	TRUE	1	0.773751411290596	2		276	248	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202854	133202854	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199613242	NA	P-0050965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	329	733	2	ENST00000320574.5:c.6380G>A	p.Arg2127Gln	p.R2127Q	ENST00000320574	NM_006231.2	2127	cGa/cAa	46/49	1	2	FACETS	0.933	0.885	0.983	0.933	0.885	0.983	CLONAL	1	TRUE	1	0.773751411290596	2		735	911	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069271	30069271	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	312	661	0	ENST00000338641.4:c.1136del	p.Glu379GlyfsTer47	p.E379Gfs*47	ENST00000338641	NM_000268.3	379	gAg/gg	12/16	0.773751411290596	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.773751411290596	1		661	482	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	21	401	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.93	0.719	1	0.93	0.719	1	CLONAL	1	TRUE	1	0.21	2		401	215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	42	872	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	1	2	FACETS	0.99	0.828	1	0.99	0.828	1	CLONAL	1	TRUE	1	0.21	2		872	404	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	9	391	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.429	0.283	0.614	0.429	0.283	0.614	SUBCLONAL	1	TRUE	1	0.21	2		391	200	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951053	48951053	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	15	242	0	ENST00000267163.4:c.1216-1G>T		p.X406_splice	ENST00000267163	NM_000321.2	406			0.164885149755444	2	FACETS	1	0.784	1	0.537	0.396	0.704	CLONAL	1	TRUE	0	0.21	2		242	133	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007792	45007792	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	31	453	0	ENST00000558401.1:c.239G>A	p.Trp80Ter	p.W80*	ENST00000558401	NM_004048.2	80	tGg/tAg	2/4	0.164885149755444	1	FACETS	0.954	0.774	1	0.954	0.774	1	CLONAL	1	TRUE	0	0.21	1		453	277	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69230456	69230456	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	25	368	0	ENST00000462284.1:c.845A>G	p.Tyr282Cys	p.Y282C	ENST00000462284	NM_002392.5	282	tAt/tGt	10/11	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.21	2		368	215	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508614	106508614	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377001952	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	30	588	1	ENST00000359195.3:c.608C>T	p.Thr203Met	p.T203M	ENST00000359195	NM_002649.2	203	aCg/aTg	2/11	1	2	FACETS	0.74	0.596	0.903	0.74	0.596	0.903	CLONAL	1	TRUE	1	0.21	2		589	386	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974095	2974095	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	26	524	0	ENST00000396946.4:c.1510G>T	p.Gly504Cys	p.G504C	ENST00000396946	NM_032415.4	504	Ggc/Tgc	10/25	1	2	FACETS	0.807	0.64	0.997	0.807	0.64	0.997	CLONAL	1	TRUE	1	0.21	2		524	307	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117759	115117759	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	26	444	0	ENST00000257566.3:c.676G>T	p.Asp226Tyr	p.D226Y	ENST00000257566	NM_016569.3	226	Gat/Tat	3/8	1	2	FACETS	1	0.827	1	1	0.827	1	CLONAL	1	TRUE	1	0.21	2		444	237	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711875	89711875	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	rs587782603	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	12	401	0	ENST00000371953.3:c.493G>T	p.Gly165Ter	p.G165*	ENST00000371953	NM_000314.4	165	Gga/Tga	6/9	1	2	FACETS	0.484	0.34	0.662	0.484	0.34	0.662	SUBCLONAL	1	TRUE	1	0.21	2		401	236	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592727	28592727	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	31	500	0	ENST00000241453.7:c.2419-1G>T		p.X807_splice	ENST00000241453	NM_004119.2	807			0.164885149755444	1	FACETS	0.842	0.682	1	0.842	0.682	1	CLONAL	1	TRUE	0	0.21	1		500	314	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36846912	36846912	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	26	622	0	ENST00000358127.4:c.1027G>T	p.Gly343Trp	p.G343W	ENST00000358127	NM_001280556.1	343	Ggg/Tgg	9/10	0.164885149755444	1	FACETS	0.731	0.58	0.904	0.731	0.58	0.904	CLONAL	1	TRUE	0	0.21	1		622	303	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720650	89720650	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	22	418	0	ENST00000371953.3:c.802-1G>T		p.X268_splice	ENST00000371953	NM_000314.4	268			1	2	FACETS	0.988	0.769	1	0.988	0.769	1	CLONAL	1	TRUE	1	0.21	2		418	212	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851762	134851762	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	22	792	0	ENST00000398015.3:c.1168C>A	p.Arg390Ser	p.R390S	ENST00000398015	NM_004441.4	390	Cgc/Agc	5/16	1	2	FACETS	0.534	0.414	0.675	0.534	0.414	0.675	SUBCLONAL	1	TRUE	1	0.21	2		792	392	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11297985	11297985	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	63	788	0	ENST00000361445.4:c.2123G>T	p.Arg708Leu	p.R708L	ENST00000361445	NM_004958.3	708	cGg/cTg	13/58	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.21	2		788	428	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307877	11307877	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	44	612	0	ENST00000361445.4:c.1115A>T	p.Gln372Leu	p.Q372L	ENST00000361445	NM_004958.3	372	cAg/cTg	7/58	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.21	2		612	378	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202969	16202969	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	33	608	0	ENST00000375759.3:c.677G>T	p.Arg226Leu	p.R226L	ENST00000375759	NM_015001.2	226	cGg/cTg	3/15	1	2	FACETS	0.849	0.693	1	0.849	0.693	1	CLONAL	1	TRUE	1	0.21	2		608	370	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106594	27106594	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	46	781	2	ENST00000324856.7:c.6205G>T	p.Gly2069Trp	p.G2069W	ENST00000324856	NM_006015.4	2069	Ggg/Tgg	20/20	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.21	2		783	418	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932422	36932422	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	48	831	0	ENST00000361632.4:c.2047T>G	p.Phe683Val	p.F683V	ENST00000361632		683	Ttc/Gtc	16/16	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.21	2		831	453	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845411	156845411	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	45	1107	1	ENST00000524377.1:c.1454G>T	p.Gly485Val	p.G485V	ENST00000524377	NM_002529.3	485	gGg/gTg	12/17	1	2	FACETS	0.924	0.777	1	0.924	0.777	1	CLONAL	1	TRUE	1	0.21	2		1108	464	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156848963	156848963	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	31	886	0	ENST00000524377.1:c.1855C>A	p.Pro619Thr	p.P619T	ENST00000524377	NM_002529.3	619	Cca/Aca	15/17	1	2	FACETS	0.722	0.584	0.878	0.722	0.584	0.878	SUBCLONAL	1	TRUE	1	0.21	2		886	409	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243668570	243668570	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	40	434	0	ENST00000263826.5:c.1421C>A	p.Ser474Tyr	p.S474Y	ENST00000263826	NM_005465.4	474	tCt/tAt	13/13	0.258220763327652	3	FACETS	0.765	0.64	0.904	0.765	0.64	0.904	CLONAL	2	TRUE	1	0.21	3		434	275	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332820	70332820	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	44	673	0	ENST00000373644.4:c.725T>G	p.Met242Arg	p.M242R	ENST00000373644	NM_030625.2	242	aTg/aGg	2/12	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.21	2		673	346	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88679198	88679198	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	14	257	0	ENST00000372037.3:c.1138G>C	p.Asp380His	p.D380H	ENST00000372037	NM_004329.2	380	Gac/Cac	10/13	1	2	FACETS	0.745	0.54	0.991	0.745	0.54	0.991	CLONAL	1	TRUE	1	0.21	2		257	179	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574655	64574655	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	26	954	0	ENST00000312049.6:c.820G>T	p.Glu274Ter	p.E274*	ENST00000312049	NM_130799.2	274	Gaa/Taa	5/10	1	2	FACETS	0.643	0.509	0.797	0.643	0.509	0.797	SUBCLONAL	1	TRUE	1	0.21	2		954	385	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200272	67200272	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	33	841	1	ENST00000312629.5:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000312629	NM_003952.2	194	Gac/Tac	7/15	1	2	FACETS	0.77	0.627	0.931	0.77	0.627	0.931	CLONAL	1	TRUE	1	0.21	2		842	408	SUCCESS
ATM	472	MSKCC	GRCh37	11	108159774	108159774	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	16	370	0	ENST00000278616.4:c.4180A>G	p.Ser1394Gly	p.S1394G	ENST00000278616	NM_000051.3	1394	Agc/Ggc	28/63	1	2	FACETS	0.866	0.643	1	0.866	0.643	1	CLONAL	1	TRUE	1	0.21	2		370	176	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	493231	493231	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	33	477	0	ENST00000399788.2:c.332A>T	p.Glu111Val	p.E111V	ENST00000399788	NM_001042603.1	111	gAg/gTg	3/28	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.21	2		477	295	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443925	18443925	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	11	355	0	ENST00000266497.5:c.898C>A	p.Pro300Thr	p.P300T	ENST00000266497		300	Cct/Act	3/31	1	2	FACETS	0.776	0.539	1	0.776	0.539	1	CLONAL	1	TRUE	1	0.21	2		355	135	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21627858	21627858	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	34	651	0	ENST00000421138.2:c.1272C>A	p.Phe424Leu	p.F424L	ENST00000421138		424	ttC/ttA	12/16	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.21	2		651	266	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906774	32906774	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs869320791	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	25	677	1	ENST00000380152.3:c.1159G>T	p.Val387Phe	p.V387F	ENST00000380152		387	Gtt/Ttt	10/27	0.164885149755444	1	FACETS	0.74	0.584	0.918	0.74	0.584	0.918	CLONAL	1	TRUE	0	0.21	1		678	288	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614611	38614611	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	14	379	0	ENST00000299084.4:c.376+1G>T		p.X126_splice	ENST00000299084	NM_152594.2	126			0.164885149755444	1	FACETS	0.751	0.545	0.997	0.751	0.545	0.997	CLONAL	1	TRUE	0	0.21	1		379	159	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991358	41991358	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	18	464	0	ENST00000219905.7:c.2188+1G>A		p.X730_splice	ENST00000219905	NM_001164273.1	730			0.164885149755444	1	FACETS	0.701	0.529	0.902	0.701	0.529	0.902	CLONAL	1	TRUE	0	0.21	1		464	219	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996212	73996212	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	15	595	0	ENST00000318443.5:c.946G>T	p.Asp316Tyr	p.D316Y	ENST00000318443	NM_001024736.1	316	Gac/Tac	5/10	0.164885149755444	1	FACETS	0.587	0.429	0.775	0.587	0.429	0.775	SUBCLONAL	1	TRUE	0	0.21	1		595	218	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680776	88680776	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	40	707	0	ENST00000360948.2:c.481T>A	p.Phe161Ile	p.F161I	ENST00000360948	NM_001012338.2	161	Ttt/Att	6/19	0.164885149755444	1	FACETS	0.888	0.739	1	0.888	0.739	1	CLONAL	1	TRUE	0	0.21	1		707	384	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222563	2222563	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	30	942	0	ENST00000326181.6:c.757G>T	p.Glu253Ter	p.E253*	ENST00000326181	NM_032271.2	253	Gag/Tag	9/21	1	2	FACETS	0.74	0.596	0.903	0.74	0.596	0.903	CLONAL	1	TRUE	1	0.21	2		942	386	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842062	3842062	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	16	460	0	ENST00000262367.5:c.1250C>G	p.Ser417Cys	p.S417C	ENST00000262367	NM_004380.2	417	tCt/tGt	5/31	1	2	FACETS	0.643	0.476	0.842	0.643	0.476	0.842	SUBCLONAL	1	TRUE	1	0.21	2		460	237	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862869	9862869	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	33	680	0	ENST00000330684.3:c.2434C>A	p.Leu812Met	p.L812M	ENST00000330684	NM_001134407.1	812	Ctg/Atg	12/13	1	2	FACETS	0.812	0.662	0.981	0.812	0.662	0.981	CLONAL	1	TRUE	1	0.21	2		680	387	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041484	14041484	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	26	395	0	ENST00000311895.7:c.2031G>C	p.Gln677His	p.Q677H	ENST00000311895	NM_005236.2	677	caG/caC	11/11	1	2	FACETS	1	0.816	1	1	0.816	1	CLONAL	1	TRUE	1	0.21	2		395	241	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992547	72992547	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	31	826	0	ENST00000268489.5:c.1498G>C	p.Asp500His	p.D500H	ENST00000268489	NM_006885.3	500	Gat/Cat	2/10	1	2	FACETS	0.695	0.562	0.845	0.695	0.562	0.845	SUBCLONAL	1	TRUE	1	0.21	2		826	425	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969954	81969954	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	29	500	0	ENST00000359376.3:c.3023A>C	p.Gln1008Pro	p.Q1008P	ENST00000359376	NM_002661.3	1008	cAg/cCg	27/33	1	2	FACETS	0.939	0.756	1	0.939	0.756	1	CLONAL	1	TRUE	1	0.21	2		500	294	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550460	29550460	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	13	232	0	ENST00000356175.3:c.1722-2A>T		p.X574_splice	ENST00000356175	NM_000267.3	574			1	2	FACETS	1	0.831	1	1	0.831	1	CLONAL	1	TRUE	1	0.21	2		232	100	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553513	29553513	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	25	615	0	ENST00000356175.3:c.2062G>C	p.Glu688Gln	p.E688Q	ENST00000356175	NM_000267.3	688	Gaa/Caa	18/57	1	2	FACETS	0.73	0.576	0.908	0.73	0.576	0.908	CLONAL	1	TRUE	1	0.21	2		615	326	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322660	30322660	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	36	594	0	ENST00000322652.5:c.1673G>C	p.Ser558Thr	p.S558T	ENST00000322652	NM_015355.2	558	aGt/aCt	14/16	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.21	2		594	307	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533676	63533677	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	34	785	0	ENST00000307078.5:c.1477dup	p.Ser493PhefsTer135	p.S493Ffs*135	ENST00000307078	NM_004655.3	493	tcg/tTcg	6/11	1	2	FACETS	0.967	0.792	1	0.967	0.792	1	CLONAL	1	TRUE	1	0.21	2		785	335	SUCCESS
YES1	7525	MSKCC	GRCh37	18	739791	739791	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	42	486	1	ENST00000314574.4:c.1081A>T	p.Lys361Ter	p.K361*	ENST00000314574	NM_005433.3	361	Aag/Tag	9/12	0.164885149755444	3	FACETS	1	0.953	1	0.711	0.596	0.837	CLONAL	1	TRUE	1	0.21	3		487	311	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622393	1622393	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	27	849	0	ENST00000344749.5:c.571G>T	p.Glu191Ter	p.E191*	ENST00000344749	NM_001136139.2	191	Gag/Tag	9/19	1	2	FACETS	0.737	0.587	0.908	0.737	0.587	0.908	CLONAL	1	TRUE	1	0.21	2		849	349	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3113366	3113366	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	39	805	0	ENST00000078429.4:c.360G>T	p.Lys120Asn	p.K120N	ENST00000078429	NM_002067.2	120	aaG/aaT	3/7	1	2	FACETS	0.996	0.827	1	0.996	0.827	1	CLONAL	1	TRUE	1	0.21	2		805	373	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272239	15272239	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	52	744	0	ENST00000263388.2:c.6200C>T	p.Pro2067Leu	p.P2067L	ENST00000263388	NM_000435.2	2067	cCc/cTc	33/33	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.21	2		744	338	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42385042	42385042	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	37	824	0	ENST00000221972.3:c.676C>A	p.Pro226Thr	p.P226T	ENST00000221972	NM_021601.3	226	Ccg/Acg	5/5	1	2	FACETS	0.808	0.666	0.967	0.808	0.666	0.967	CLONAL	1	TRUE	1	0.21	2		824	436	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61717885	61717886	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	35	504	0	ENST00000401558.2:c.1913_1914del	p.Gly638ValfsTer24	p.G638Vfs*24	ENST00000401558	NM_003400.3	638	gGG/g	17/25	1	2	FACETS	0.913	0.75	1	0.913	0.75	1	CLONAL	1	TRUE	1	0.21	2		504	365	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149709	202149709	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	34	670	0	ENST00000358485.4:c.1150G>C	p.Gly384Arg	p.G384R	ENST00000358485	NM_001080125.1	384	Ggc/Cgc	8/9	1	2	FACETS	0.933	0.764	1	0.933	0.764	1	CLONAL	1	TRUE	1	0.21	2		670	347	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661250	227661250	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	42	865	0	ENST00000305123.5:c.2205G>T	p.Met735Ile	p.M735I	ENST00000305123	NM_005544.2	735	atG/atT	1/2	1	2	FACETS	0.976	0.816	1	0.976	0.816	1	CLONAL	1	TRUE	1	0.21	2		865	410	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560815	9560815	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	24	507	1	ENST00000353224.5:c.967G>T	p.Glu323Ter	p.E323*	ENST00000353224	NM_177990.2	323	Gag/Tag	4/10	1	2	FACETS	0.825	0.648	1	0.825	0.648	1	CLONAL	1	TRUE	1	0.21	2		508	277	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026248	36026248	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	22	1114	0	ENST00000358208.4:c.850G>A	p.Val284Met	p.V284M	ENST00000358208		284	Gtg/Atg	7/12	1	2	FACETS	0.491	0.379	0.62	0.491	0.379	0.62	SUBCLONAL	1	TRUE	1	0.21	2		1114	427	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739091	40739091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1178602063	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	20	695	0	ENST00000373198.4:c.3193C>T	p.His1065Tyr	p.H1065Y	ENST00000373198	NM_133170.3	1065	Cac/Tac	24/32	1	2	FACETS	0.477	0.364	0.61	0.477	0.364	0.61	SUBCLONAL	1	TRUE	1	0.21	2		695	399	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757455	40757455	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	31	670	0	ENST00000373198.4:c.2843T>A	p.Val948Glu	p.V948E	ENST00000373198	NM_133170.3	948	gTg/gAg	20/32	1	2	FACETS	0.839	0.679	1	0.839	0.679	1	CLONAL	1	TRUE	1	0.21	2		670	352	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553172	41553172	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	26	427	0	ENST00000263253.7:c.3262-1G>C		p.X1088_splice	ENST00000263253	NM_001429.3	1088			1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.21	2		427	219	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266888	41266888	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	39	459	0	ENST00000349496.5:c.559G>T	p.Ala187Ser	p.A187S	ENST00000349496	NM_001904.3	187	Gct/Tct	5/15	1	2	FACETS	0.78	0.652	0.921	1	0.958	1	CLONAL	2	TRUE	1	0.21	2		459	238	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960088	134960088	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	45	790	1	ENST00000398015.3:c.2445G>T	p.Trp815Cys	p.W815C	ENST00000398015	NM_004441.4	815	tgG/tgT	13/16	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.21	2		791	383	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430455	181430455	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	36	759	0	ENST00000325404.1:c.307A>T	p.Lys103Ter	p.K103*	ENST00000325404	NM_003106.3	103	Aag/Tag	1/1	1	2	FACETS	1	0.826	1	1	0.826	1	CLONAL	1	TRUE	1	0.21	2		759	342	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144131	55144131	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs377159519	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	44	572	0	ENST00000257290.5:c.1960C>A	p.His654Asn	p.H654N	ENST00000257290	NM_006206.4	654	Cat/Aat	14/23	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.21	2		572	392	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541406	187541406	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	23	360	0	ENST00000441802.2:c.6334A>G	p.Arg2112Gly	p.R2112G	ENST00000441802	NM_005245.3	2112	Aga/Gga	10/27	0.3	2	FACETS	1	0.797	1			1	CLONAL	1	TRUE	NA	0.21	2		360	215	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460569	149460569	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs749946644	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	39	752	0	ENST00000286301.3:c.68T>C	p.Ile23Thr	p.I23T	ENST00000286301	NM_005211.3	23	aTa/aCa	3/22	0.164885149755444	1	FACETS	0.908	0.754	1	0.908	0.754	1	CLONAL	1	TRUE	0	0.21	1		752	366	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515307	149515307	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	40	740	0	ENST00000261799.4:c.175C>A	p.Pro59Thr	p.P59T	ENST00000261799	NM_002609.3	59	Ccg/Acg	3/23	0.164885149755444	1	FACETS	0.977	0.814	1	0.977	0.814	1	CLONAL	1	TRUE	0	0.21	1		740	349	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680131	30680131	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	39	821	0	ENST00000376406.3:c.1588C>A	p.Pro530Thr	p.P530T	ENST00000376406	NM_014641.2	530	Ccg/Acg	5/15	0.164885149755444	3	FACETS	0.963	0.799	1	0.482	0.399	0.573	CLONAL	1	TRUE	1	0.21	3		821	426	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190320	32190320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	23	633	1	ENST00000375023.3:c.419G>T	p.Arg140Leu	p.R140L	ENST00000375023	NM_004557.3	140	cGc/cTc	3/30	0.3	2	FACETS	0.794	0.62	0.994			1	CLONAL	1	TRUE	NA	0.21	2		634	276	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641067	117641067	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	28	529	0	ENST00000368508.3:c.5904A>T	p.Leu1968Phe	p.L1968F	ENST00000368508	NM_002944.2	1968	ttA/ttT	36/43	0.111040347349096	0	FACETS	0.724	0.58	0.887			1	INDETERMINATE	1	TRUE	0	0.21	0		529	291	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468198	50468198	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	49	844	0	ENST00000331340.3:c.1433C>G	p.Thr478Ser	p.T478S	ENST00000331340	NM_006060.4	478	aCc/aGc	8/8	0.44603123772244	3	FACETS	1	0.934	1	0.595	0.505	0.695	CLONAL	1	TRUE	1	0.21	3		844	433	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917680	151917680	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	54	337	0	ENST00000262189.6:c.3640G>T	p.Val1214Leu	p.V1214L	ENST00000262189	NM_170606.2	1214	Gtg/Ttg	23/59	0.258220763327652	3	FACETS	1	0.895	1	1	0.971	1	CLONAL	3	TRUE	1	0.21	3		337	183	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007116	152007116	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	32	546	0	ENST00000262189.6:c.784G>T	p.Val262Leu	p.V262L	ENST00000262189	NM_170606.2	262	Gta/Tta	6/59	0.258220763327652	3	FACETS	0.842	0.684	1	0.421	0.342	0.511	CLONAL	1	TRUE	1	0.21	3		546	400	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279332	38279332	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	41	877	2	ENST00000425967.3:c.1157G>T	p.Trp386Leu	p.W386L	ENST00000425967	NM_001174067.1	386	tGg/tTg	9/19	1	2	FACETS	0.879	0.733	1	0.879	0.733	1	CLONAL	1	TRUE	1	0.21	2		879	444	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372026	55372026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1468771654	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	15	421	1	ENST00000297316.4:c.716C>T	p.Ala239Val	p.A239V	ENST00000297316	NM_022454.3	239	gCc/gTc	2/2	1	2	FACETS	0.707	0.518	0.933	0.707	0.518	0.933	CLONAL	1	TRUE	1	0.21	2		422	202	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982631	90982631	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	31	301	0	ENST00000265433.3:c.857A>C	p.Gln286Pro	p.Q286P	ENST00000265433	NM_002485.4	286	cAg/cCg	7/16	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.21	2		301	271	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141549469	141549470	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	28	499	0	ENST00000220592.5:c.2118_2119delinsTT	p.Val707Leu	p.V707L	ENST00000220592	NM_012154.3	706	gtGGtg/gtTTtg	16/19	1	2	FACETS	0.828	0.663	1	0.828	0.663	1	CLONAL	1	TRUE	1	0.21	2		499	322	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5078306	5078306	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	24	292	0	ENST00000381652.3:c.1993G>T	p.Glu665Ter	p.E665*	ENST00000381652	NM_004972.3	665	Gaa/Taa	16/25	0.164885149755444	1	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	0	0.21	1		292	169	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486172	8486172	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	19	469	0	ENST00000356435.5:c.2645C>A	p.Ala882Asp	p.A882D	ENST00000356435		882	gCt/gAt	17/35	0.164885149755444	1	FACETS	0.717	0.545	0.917	0.717	0.545	0.917	CLONAL	1	TRUE	0	0.21	1		469	226	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202445	123202445	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	21	255	0	ENST00000218089.9:c.2297G>C	p.Arg766Thr	p.R766T	ENST00000218089	NM_001042749.1	766	aGa/aCa	24/35	1	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	0	0.21	1		255	128	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	17	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.924	0.693	1	0.924	0.693	1	CLONAL	1	FALSE	1	0.216498542483783	2		334	170	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248324	59248325	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0050967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	37	197	0	ENST00000371222.2:c.418dup	p.Ala140GlyfsTer170	p.A140Gfs*170	ENST00000371222	NM_002228.3	140	gca/gGca	1/1	0.216498542483783	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	0	0.216498542483783	1		197	210	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057328	30057328	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	21	374	0	ENST00000338641.4:c.810+1del		p.E270fs	ENST00000338641	NM_000268.3	270	gaG/ga	8/16	1	2	FACETS	0.743	0.573	0.941	0.743	0.573	0.941	CLONAL	1	FALSE	1	0.216498542483783	2		374	261	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856623	111856623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	23	180	0	ENST00000341259.2:c.674G>A	p.Arg225His	p.R225H	ENST00000341259	NM_005475.2	225	cGc/cAc	2/8	1	2	FACETS	0.432	0.338	0.538	0.432	0.338	0.538	SUBCLONAL	1	TRUE	1	0.573030032056204	2		180	186	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835787	68835787	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	110	493	0	ENST00000261769.5:c.378del	p.His128IlefsTer87	p.H128Ifs*87	ENST00000261769	NM_004360.3	126	ccG/cc	3/16	0.573030032056204	1	FACETS	0.761	0.691	0.834	0.761	0.691	0.834	SUBCLONAL	1	TRUE	0	0.573030032056204	1		493	360	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259331	36259331	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	125	326	0	ENST00000300305.3:c.160G>A	p.Glu54Lys	p.E54K	ENST00000300305		54	Gag/Aag	3/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.573030032056204	2		326	380	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589588	67589593	+	protein_altering_variant	In_Frame_Del	DEL	GAATAT	GAATAT	AAA	novel	NA	P-0050968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	73	231	2	ENST00000274335.5:c.1351_1356delinsAAA	p.Glu451_Tyr452delinsLys	p.E451_Y452delinsK	ENST00000274335		451	GAATAT/AAA	10/15	1	2	FACETS	0.777	0.685	0.874	0.777	0.685	0.874	SUBCLONAL	1	TRUE	1	0.573030032056204	2		233	328	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772950	135772951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs118203724	NA	P-0050971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	115	447	1	ENST00000298552.3:c.2672dup	p.Asn891LysfsTer13	p.N891Kfs*13	ENST00000298552	NM_001162426.1	891	aac/aaAc	21/23	0.643288381897334	1	FACETS	0.695	0.633	0.759	0.695	0.633	0.759	SUBCLONAL	1	TRUE	0	0.643288381897334	1		448	349	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651931	36651932	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0050971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	286	830	0	ENST00000244741.5:c.55dup	p.Arg19ProfsTer17	p.R19Pfs*17	ENST00000244741	NM_000389.4	18	tgc/tgCc	2/3	0.643288381897334	1	FACETS	0.973	0.923	1	0.973	0.923	1	CLONAL	1	TRUE	0	0.643288381897334	1		830	620	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294970	1294971	+	missense_variant	Missense_Mutation	DNP	CG	CG	TT	novel	NA	P-0050971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	66	88	1	ENST00000310581.5:c.134_135delinsAA	p.Ala45Glu	p.A45E	ENST00000310581	NM_198253.2	45	gCG/gAA	1/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.643288381897334	2		89	160	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375216	118375217	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0050971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	58	419	1	ENST00000534358.1:c.8612_8613dup	p.Ser2873HisfsTer7	p.S2873Hfs*7	ENST00000534358	NM_005933.3	2870	cca/ccAGa	27/36	0.416302812586956	1	FACETS	0.321	0.277	0.369	0.321	0.277	0.369	SUBCLONAL	1	TRUE	0	0.643288381897334	1		420	381	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236679	236687	+	inframe_deletion	In_Frame_Del	DEL	CATGTGCCC	CATGTGCCC	-	novel	NA	P-0050971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	148	527	0	ENST00000264932.6:c.1397_1405del	p.Ala466_Leu469delinsVal	p.A466_L469delinsV	ENST00000264932	NM_004168.2	466	gCATGTGCCCtg/gtg	10/15	1	2	FACETS	0.789	0.724	0.857	0.789	0.724	0.857	SUBCLONAL	1	TRUE	1	0.643288381897334	2		527	583	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525049	187525049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	33	547	2	ENST00000441802.2:c.10631C>T	p.Ala3544Val	p.A3544V	ENST00000441802	NM_005245.3	3544	gCg/gTg	19/27	1	2	FACETS	0.246	0.2	0.298	0.246	0.2	0.298	SUBCLONAL	1	TRUE	1	0.635869889750746	2		549	422	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	47	765	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.461935705077732	2	FACETS	0.407	0.344	0.477	0.204	0.172	0.239	SUBCLONAL	1	TRUE	0	0.476824187577179	2		765	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	186	620	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.476824187577179	2	FACETS	0.916	0.856	0.976	0.916	0.856	0.976	CLONAL	2	TRUE	0	0.476824187577179	2		620	426	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742679	39742679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	103	476	0	ENST00000361337.2:c.1522C>T	p.Arg508Cys	p.R508C	ENST00000361337	NM_003286.2	508	Cgt/Tgt	15/21	0.264420142555068	5	FACETS	0.933	0.842	1	0.622	0.561	0.686	INDETERMINATE	2	TRUE	2	0.476824187577179	5		476	397	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148507497	148507497	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	52	326	0	ENST00000320356.2:c.1957C>G	p.Gln653Glu	p.Q653E	ENST00000320356	NM_004456.4	653	Caa/Gaa	17/20	0.470870553858897	5	FACETS	1	0.939	1	0.238	0.204	0.276	CLONAL	1	TRUE	0	0.476824187577179	5		326	314	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554512	63554512	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	43	811	0	ENST00000307078.5:c.227C>T	p.Thr76Ile	p.T76I	ENST00000307078	NM_004655.3	76	aCc/aTc	2/11	0.445080555555758	3	FACETS	0.472	0.395	0.558	0.236	0.197	0.279	SUBCLONAL	1	TRUE	1	0.476824187577179	3		811	473	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007689	45007690	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	63	410	0	ENST00000558401.1:c.137_138del	p.Tyr46CysfsTer10	p.Y46Cfs*10	ENST00000558401	NM_004048.2	46	TAt/t	2/4	0.461935705077732	2	FACETS	0.982	0.858	1	0.491	0.429	0.557	CLONAL	1	TRUE	0	0.476824187577179	2		410	269	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413129	139413131	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	118	1222	0	ENST00000277541.6:c.1011_1013del	p.Asp338del	p.D338del	ENST00000277541	NM_017617.3	337	gaTGAc/gac	6/34	0.448173286929949	3	FACETS	0.881	0.795	0.97	0.294	0.265	0.324	CLONAL	1	TRUE	0	0.476824187577179	3		1222	696	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26970433	26970433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	47	173	0	ENST00000381527.3:c.802G>A	p.Glu268Lys	p.E268K	ENST00000381527	NM_001260.1	268	Gaa/Aaa	8/13	0.476824187577179	4	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	2	0.476824187577179	4		173	123	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80160631	80160631	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	122	492	0	ENST00000265081.6:c.3001-1G>T		p.X1001_splice	ENST00000265081	NM_002439.4	1001			0.476824187577179	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.476824187577179	2		492	242	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368260	31368260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781313570	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	210	996	0	ENST00000328111.2:c.131C>T	p.Pro44Leu	p.P44L	ENST00000328111	NM_006892.3	44	cCg/cTg	2/23	0.264420142555068	5	FACETS	1	0.988	1	0.832	0.778	0.888	INDETERMINATE	2	TRUE	2	0.476824187577179	5		996	605	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858758	9858760	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs766019656	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	22	367	0	ENST00000330684.3:c.2641_2643del	p.Lys881del	p.K881del	ENST00000330684	NM_001134407.1	881	AAG/-	13/13	0.327430724231152	4	FACETS	0.514	0.399	0.647	0.257	0.199	0.324	SUBCLONAL	1	TRUE	2	0.476824187577179	4		367	265	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665360	138665360	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	49	1155	0	ENST00000330315.3:c.205G>C	p.Glu69Gln	p.E69Q	ENST00000330315	NM_023067.3	69	Gag/Cag	1/1	0.476824187577179	6	FACETS	0.464	0.391	0.544			1	SUBCLONAL	1	TRUE	NA	0.476824187577179	6		1155	866	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346570	81346570	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	68	330	0	ENST00000222390.5:c.1383G>T	p.Trp461Cys	p.W461C	ENST00000222390	NM_000601.4	461	tgG/tgT	11/18	0.476824187577179	5	FACETS	1	0.952	1			1	CLONAL	1	TRUE	NA	0.476824187577179	5		330	411	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650407	48650407	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	47	565	1	ENST00000376670.3:c.377G>A	p.Gly126Glu	p.G126E	ENST00000376670	NM_002049.3	126	gGa/gAa	3/6	0.383372258696948	2	FACETS	0.566	0.48	0.661			1	SUBCLONAL	1	TRUE	NA	0.476824187577179	2		566	348	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875028	151875028	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	180	252	0	ENST00000262189.6:c.7510C>T	p.Gln2504Ter	p.Q2504*	ENST00000262189	NM_170606.2	2504	Caa/Taa	38/59	0.470870553858897	5	FACETS	0.935	0.885	0.983	0.935	0.885	0.983	CLONAL	5	TRUE	0	0.476824187577179	5		252	277	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92244546	92244546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	31	474	0	ENST00000265734.4:c.889C>T	p.His297Tyr	p.H297Y	ENST00000265734	NM_001259.6	297	Cac/Tac	8/8	0.476824187577179	7	FACETS	0.557	0.449	0.679	0.139	0.112	0.17	SUBCLONAL	1	TRUE	3	0.476824187577179	7		474	512	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665213	138665213	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	48	1057	0	ENST00000330315.3:c.352G>T	p.Glu118Ter	p.E118*	ENST00000330315	NM_023067.3	118	Gag/Tag	1/1	0.476824187577179	6	FACETS	0.49	0.413	0.575			1	SUBCLONAL	1	TRUE	NA	0.476824187577179	6		1057	803	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102166	27102166	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	28	615	0	ENST00000324856.7:c.5092G>C	p.Asp1698His	p.D1698H	ENST00000324856	NM_006015.4	1698	Gac/Cac	19/20	0.461935705077732	2	FACETS	0.346	0.277	0.426	0.173	0.138	0.213	SUBCLONAL	1	TRUE	0	0.476824187577179	2		615	339	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163298659	163298659	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	94	553	0	ENST00000271452.3:c.299G>T	p.Arg100Leu	p.R100L	ENST00000271452	NM_145697.2	100	cGg/cTg	5/14	0.476824187577179	6	FACETS	1	0.904	1	0.504	0.452	0.559	CLONAL	2	TRUE	2	0.476824187577179	6		553	382	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981778	101981778	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200985869	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	180	878	1	ENST00000282441.5:c.199G>T	p.Ala67Ser	p.A67S	ENST00000282441	NM_001130145.2	67	Gcg/Tcg	1/9	0.461935705077732	2	FACETS	0.961	0.898	1	0.961	0.898	1	CLONAL	2	TRUE	0	0.476824187577179	2		879	393	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416132	49416132	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	67	457	0	ENST00000301067.7:c.16343G>C	p.Arg5448Pro	p.R5448P	ENST00000301067	NM_003482.3	5448	cGa/cCa	52/54	0.476824187577179	3	FACETS	0.994	0.87	1	0.497	0.435	0.564	CLONAL	1	TRUE	1	0.476824187577179	3		457	350	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421822	49421822	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	88	1198	0	ENST00000301067.7:c.14485G>T	p.Glu4829Ter	p.E4829*	ENST00000301067	NM_003482.3	4829	Gag/Tag	46/54	0.476824187577179	3	FACETS	0.704	0.624	0.79	0.352	0.312	0.395	SUBCLONAL	1	TRUE	1	0.476824187577179	3		1198	649	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445487	49445487	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	91	1080	0	ENST00000301067.7:c.1979C>G	p.Ser660Ter	p.S660*	ENST00000301067	NM_003482.3	660	tCa/tGa	10/54	0.476824187577179	3	FACETS	0.911	0.811	1	0.455	0.405	0.508	CLONAL	1	TRUE	1	0.476824187577179	3		1080	519	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120783957	120783957	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	196	1221	0	ENST00000257552.2:c.1028G>T	p.Gly343Val	p.G343V	ENST00000257552	NM_002442.3	343	gGc/gTc	13/15	0.333513748951137	3	FACETS	0.892	0.831	0.953	0.892	0.831	0.953	CLONAL	2	TRUE	1	0.476824187577179	3		1221	571	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907404	32907404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	27	297	0	ENST00000380152.3:c.1789G>A	p.Glu597Lys	p.E597K	ENST00000380152		597	Gaa/Aaa	10/27	0.476824187577179	4	FACETS	0.706	0.564	0.866	0.353	0.282	0.433	SUBCLONAL	1	TRUE	2	0.476824187577179	4		297	237	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913044	32913044	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	37	585	0	ENST00000380152.3:c.4552G>C	p.Glu1518Gln	p.E1518Q	ENST00000380152		1518	Gaa/Caa	11/27	0.476824187577179	4	FACETS	0.507	0.418	0.607	0.254	0.209	0.304	SUBCLONAL	1	TRUE	2	0.476824187577179	4		585	452	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913099	32913099	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	135	497	0	ENST00000380152.3:c.4607A>G	p.Lys1536Arg	p.K1536R	ENST00000380152		1536	aAg/aGg	11/27	0.476824187577179	4	FACETS	1	0.922	1	1	0.922	1	CLONAL	2	TRUE	2	0.476824187577179	4		497	416	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134642	2134642	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	133	1263	0	ENST00000219476.3:c.4419G>C	p.Lys1473Asn	p.K1473N	ENST00000219476	NM_000548.3	1473	aaG/aaC	34/42	0.327430724231152	4	FACETS	1	0.974	1	0.595	0.541	0.652	CLONAL	1	TRUE	2	0.476824187577179	4		1263	692	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670658	67670658	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	43	552	0	ENST00000264010.4:c.1903G>C	p.Glu635Gln	p.E635Q	ENST00000264010	NM_006565.3	635	Gag/Cag	11/12	0.455436835844467	4	FACETS	0.53	0.443	0.626	0.265	0.221	0.313	SUBCLONAL	1	TRUE	2	0.476824187577179	4		552	503	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805292	89805292	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	28	795	0	ENST00000389301.3:c.4258G>A	p.Glu1420Lys	p.E1420K	ENST00000389301	NM_000135.2	1420	Gag/Aag	42/43	0.455436835844467	4	FACETS	0.334	0.266	0.411	0.167	0.133	0.206	SUBCLONAL	1	TRUE	2	0.476824187577179	4		795	520	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653166	29653166	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	58	387	0	ENST00000356175.3:c.5101del	p.Glu1701AsnfsTer12	p.E1701Nfs*12	ENST00000356175	NM_000267.3	1701	Gaa/aa	36/57	0.476824187577179	4	FACETS	0.95	0.82	1	0.475	0.41	0.546	CLONAL	1	TRUE	2	0.476824187577179	4		387	378	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78820288	78820288	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567946390	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	226	995	0	ENST00000306801.3:c.1228G>A	p.Ala410Thr	p.A410T	ENST00000306801	NM_020761.2	410	Gcc/Acc	11/34	0.445080555555758	3	FACETS	0.964	0.904	1	0.964	0.904	1	CLONAL	2	TRUE	1	0.476824187577179	3		995	609	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223314	36223314	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	38	1455	0	ENST00000222270.7:c.5864C>A	p.Ser1955Ter	p.S1955*	ENST00000222270	NM_014727.1	1955	tCa/tAa	28/37	0.291215558278983	4	FACETS	0.311	0.256	0.372	0.155	0.128	0.186	SUBCLONAL	1	TRUE	2	0.476824187577179	4		1455	758	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30954216	30954216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	48	386	0	ENST00000375687.4:c.87G>A	p.Met29Ile	p.M29I	ENST00000375687	NM_015338.5	29	atG/atA	2/13	0.264420142555068	5	FACETS	1	0.944	1	0.414	0.352	0.481	INDETERMINATE	1	TRUE	2	0.476824187577179	5		386	278	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644676	134644676	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	28	542	0	ENST00000398015.3:c.77G>C	p.Arg26Thr	p.R26T	ENST00000398015	NM_004441.4	26	aGa/aCa	2/16	0.325725076307822	6	FACETS	0.474	0.378	0.584			1	SUBCLONAL	1	TRUE	NA	0.476824187577179	6		542	484	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584556	189584556	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	63	418	0	ENST00000264731.3:c.852G>C	p.Gln284His	p.Q284H	ENST00000264731	NM_003722.4	284	caG/caC	6/14	0.476824187577179	9	FACETS	1	0.938	1	0.192	0.165	0.22	CLONAL	1	TRUE	3	0.476824187577179	9		418	613	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749460	41749460	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1553898048	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	158	621	0	ENST00000226382.2:c.335A>T	p.Glu112Val	p.E112V	ENST00000226382	NM_003924.3	112	gAg/gTg	2/3	0.457766205537662	2	FACETS	0.898	0.834	0.962	0.898	0.834	0.962	CLONAL	2	TRUE	0	0.476824187577179	2		621	369	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184149	56184149	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	15	336	0	ENST00000399503.3:c.4354G>A	p.Glu1452Lys	p.E1452K	ENST00000399503	NM_005921.1	1452	Gaa/Aaa	19/20	0.476824187577179	2	FACETS	0.31	0.227	0.409	0.155	0.113	0.205	SUBCLONAL	1	TRUE	0	0.476824187577179	2		336	203	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64289961	64289961	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	18	291	0	ENST00000370651.3:c.405-1G>C		p.X135_splice	ENST00000370651	NM_003463.4	135			0.476824187577179	4	FACETS	0.377	0.283	0.487	0.188	0.141	0.244	SUBCLONAL	1	TRUE	2	0.476824187577179	4		291	296	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38184335	38184335	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1232441188	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	26	482	0	ENST00000317025.8:c.1621G>A	p.Asp541Asn	p.D541N	ENST00000317025	NM_023034.1	541	Gac/Aac	7/24	0.445080555555758	3	FACETS	0.463	0.367	0.572	0.231	0.183	0.286	SUBCLONAL	1	TRUE	1	0.476824187577179	3		482	292	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38196124	38196124	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs1410767463	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	46	513	0	ENST00000317025.8:c.677G>C	p.Arg226Thr	p.R226T	ENST00000317025	NM_023034.1	226	aGa/aCa	3/24	0.445080555555758	3	FACETS	0.81	0.686	0.945	0.405	0.343	0.473	CLONAL	1	TRUE	1	0.476824187577179	3		513	295	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971055	21971066	+	inframe_deletion	In_Frame_Del	DEL	CCCGGCCCGGTG	CCCGGCCCGGTG	-	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	230	480	0	ENST00000304494.5:c.292_303del	p.His98_Gly101del	p.H98_G101del	ENST00000304494	NM_000077.4	98	CACCGGGCCGGG/-	2/3	0.476824187577179	3	FACETS	0.884	0.844	0.922	1	0.991	1	CLONAL	4	TRUE	0	0.476824187577179	3		480	338	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342605	87342605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	80	532	0	ENST00000277120.3:c.890C>T	p.Ser297Leu	p.S297L	ENST00000277120		297	tCa/tTa	9/19	0.476824187577179	2	FACETS	1	0.957	1	0.579	0.515	0.645	CLONAL	1	TRUE	0	0.476824187577179	2		532	290	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0050974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	52	355	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.257421264913843	3	FACETS	1	0.942	1	0.771	0.67	0.877	CLONAL	2	TRUE	0	0.336593733563809	3		355	156	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870966	12870966	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	132	310	0	ENST00000228872.4:c.193C>T	p.Gln65Ter	p.Q65*	ENST00000228872	NM_004064.3	65	Cag/Tag	1/3	0.336593733563809	14	FACETS	1	0.93	1			1	CLONAL	5	TRUE	NA	0.336593733563809	14		310	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0050974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	171	798	2	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	0.257421264913843	3	FACETS	0.853	0.792	0.915	0.853	0.792	0.915	CLONAL	3	TRUE	0	0.336593733563809	3		800	464	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0050974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	18	178	0	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	0.336593733563809	2	FACETS	0.972	0.76	1	0.972	0.76	1	CLONAL	2	TRUE	0	0.336593733563809	2		178	55	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721027	176721027	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	64	521	0	ENST00000439151.2:c.6658G>A	p.Glu2220Lys	p.E2220K	ENST00000439151	NM_022455.4	2220	Gag/Aag	23/23	0.305548931613508	2	FACETS	0.925	0.804	1	0.463	0.402	0.528	CLONAL	1	TRUE	0	0.336593733563809	2		521	411	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440543	49440543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	82	731	1	ENST00000301067.7:c.4267C>T	p.Arg1423Cys	p.R1423C	ENST00000301067	NM_003482.3	1423	Cgt/Tgt	15/54	0.257421264913843	3	FACETS	1	0.965	1	0.412	0.365	0.463	CLONAL	1	TRUE	0	0.336593733563809	3		732	460	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192740	94192740	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	10	348	0	ENST00000323929.3:c.1334A>T	p.Gln445Leu	p.Q445L	ENST00000323929	NM_005591.3	445	cAg/cTg	13/20	1	2	FACETS	0.716	0.491	0.991	0.716	0.491	0.991	CLONAL	1	TRUE	1	0.336593733563809	2		348	83	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362489	118362489	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	43	340	0	ENST00000534358.1:c.4850C>T	p.Pro1617Leu	p.P1617L	ENST00000534358	NM_005933.3	1617	cCa/cTa	15/36	1	2	FACETS	0.998	0.841	1	0.998	0.841	1	CLONAL	1	TRUE	1	0.336593733563809	2		340	256	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741220	40741221	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0050974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	232	788	2	ENST00000392038.2:c.1212_1213delinsTT	p.Met404_Glu405delinsIleTer	p.M404_E405delinsI*	ENST00000392038	NM_001626.4	404	atGGag/atTTag	12/14	0.130640977950222	4	FACETS	0.91	0.853	0.968	1	0.991	1	INDETERMINATE	3	TRUE	2	0.336593733563809	4		790	675	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526456	31526456	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	141	819	0	ENST00000344624.3:c.584G>T	p.Ser195Ile	p.S195I	ENST00000344624		195	aGt/aTt	2/33	0.295206462939142	5	FACETS	1	0.978	1	0.801	0.733	0.87	CLONAL	2	TRUE	2	0.336593733563809	5		819	525	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816608	32816608	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	84	719	1	ENST00000354258.4:c.1567T>G	p.Ser523Ala	p.S523A	ENST00000354258	NM_000593.5	523	Tcc/Gcc	7/11	0.103980828746843	4	FACETS	1	0.97	1	0.646	0.572	0.725	INDETERMINATE	1	TRUE	2	0.336593733563809	4		720	516	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816791	32816791	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs774377990	NA	P-0050974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	98	630	0	ENST00000354258.4:c.1533G>C	p.Gln511His	p.Q511H	ENST00000354258	NM_000593.5	511	caG/caC	6/11	0.103980828746843	4	FACETS	0.772	0.691	0.857	0.772	0.691	0.857	INDETERMINATE	2	TRUE	2	0.336593733563809	4		630	504	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039404	47039404	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	83	727	4	ENST00000377604.3:c.1027C>A	p.Arg343Ser	p.R343S	ENST00000377604	NM_001204468.1	343	Cgc/Agc	10/24	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.336593733563809	2		731	464	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763848	76763848	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	43	470	0	ENST00000373344.5:c.7460C>A	p.Ser2487Tyr	p.S2487Y	ENST00000373344	NM_000489.3	2487	tCc/tAc	35/35	0.336593733563809	1	FACETS	0.84	0.708	0.984	0.84	0.708	0.984	CLONAL	1	TRUE	0	0.336593733563809	1		470	253	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944403	76944403	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	15	453	0	ENST00000373344.5:c.502A>T	p.Ile168Phe	p.I168F	ENST00000373344	NM_000489.3	168	Att/Ttt	7/35	0.336593733563809	1	FACETS	0.68	0.503	0.887	0.68	0.503	0.887	SUBCLONAL	1	TRUE	0	0.336593733563809	1		453	109	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	49	276	0				ENST00000310581	NM_198253.2	-/1132			0.103043249935957	3	FACETS	0.896	0.762	1	0.896	0.762	1	CLONAL	2	TRUE	1	0.16	3		276	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0050975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	83	633	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.883	0.777	0.998	0.883	0.777	0.998	CLONAL	1	TRUE	1	0.16	2		633	1175	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0050975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	96	559	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	0.805	0.717	0.899	1	0.982	1	CLONAL	2	TRUE	1	0.16	2		559	745	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431339	49431339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	59	810	0	ENST00000301067.7:c.9800C>T	p.Ser3267Leu	p.S3267L	ENST00000301067	NM_003482.3	3267	tCa/tTa	34/54	1	2	FACETS	0.684	0.586	0.791	0.684	0.586	0.791	SUBCLONAL	1	TRUE	1	0.16	2		810	1079	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136286	202136286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	44	669	1	ENST00000358485.4:c.530G>A	p.Arg177Lys	p.R177K	ENST00000358485	NM_001080125.1	177	aGg/aAg	3/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.16	NA		670	818	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090646	71090646	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	25	497	0	ENST00000318789.4:c.702A>T	p.Glu234Asp	p.E234D	ENST00000318789	NM_032682.5	234	gaA/gaT	11/21	1	2	FACETS	0.631	0.496	0.787	0.631	0.496	0.787	SUBCLONAL	1	TRUE	1	0.16	2		497	495	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968335	134968335	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0050975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	60	748	0	ENST00000398015.3:c.2846+2T>C		p.X949_splice	ENST00000398015	NM_004441.4	949			1	2	FACETS	0.933	0.802	1	0.933	0.802	1	CLONAL	1	TRUE	1	0.16	2		748	804	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275777	38275777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs923019674	NA	P-0050975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	62	884	2	ENST00000425967.3:c.1492G>A	p.Glu498Lys	p.E498K	ENST00000425967	NM_001174067.1	498	Gaa/Aaa	11/19	1	2	FACETS	0.71	0.611	0.819	0.71	0.611	0.819	SUBCLONAL	1	TRUE	1	0.16	2		886	1091	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	139	517	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.909	0.831	0.99	0.909	0.831	0.99	CLONAL	1	TRUE	1	0.543345691732456	2		517	563	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	15	518	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.137	0.099	0.182	0.137	0.099	0.182	SUBCLONAL	1	TRUE	1	0.543345691732456	2		518	404	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	119	404	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.618	0.558	0.681	0.618	0.558	0.681	SUBCLONAL	1	TRUE	1	0.543345691732456	2		404	709	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	86	339	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	1	2	FACETS	0.761	0.677	0.85	0.761	0.677	0.85	SUBCLONAL	1	TRUE	1	0.543345691732456	2		339	416	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	142	740	4	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.64	0.583	0.699	0.64	0.583	0.699	SUBCLONAL	1	TRUE	1	0.543345691732456	2		744	817	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308383	15308383	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	51	879	4	ENST00000263388.2:c.125del	p.Pro42LeufsTer194	p.P42Lfs*194	ENST00000263388	NM_000435.2	42	cCt/ct	2/33	1	2	FACETS	0.286	0.242	0.334	0.286	0.242	0.334	SUBCLONAL	1	TRUE	1	0.543345691732456	2		883	657	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	157	616	1	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	1	2	FACETS	0.917	0.844	0.994	0.917	0.844	0.994	CLONAL	1	TRUE	1	0.543345691732456	2		617	630	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850705	63850705	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs201178069	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	67	328	0	ENST00000279873.7:c.1489del	p.Ile497Ter	p.I497*	ENST00000279873	NM_032199.2	495	Aaa/aa	10/10	1	2	FACETS	0.572	0.499	0.651	0.572	0.499	0.651	SUBCLONAL	1	TRUE	1	0.543345691732456	2		328	431	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	213	317	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.543345691732456	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.543345691732456	2		317	384	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	73	1027	7	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	1	2	FACETS	0.336	0.293	0.382	0.336	0.293	0.382	SUBCLONAL	1	TRUE	1	0.543345691732456	2		1034	800	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	134	1011	4	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.626	0.569	0.686	0.626	0.569	0.686	SUBCLONAL	1	TRUE	1	0.543345691732456	2		1015	788	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358978	81358978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374484762	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	148	508	0	ENST00000222390.5:c.983G>A	p.Arg328His	p.R328H	ENST00000222390	NM_000601.4	328	cGt/cAt	8/18	1	2	FACETS	0.87	0.798	0.946	0.87	0.798	0.946	CLONAL	1	TRUE	1	0.543345691732456	2		508	626	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130244	2130244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45473098	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	166	998	0	ENST00000219476.3:c.3476G>A	p.Arg1159Gln	p.R1159Q	ENST00000219476	NM_000548.3	1159	cGg/cAg	30/42	1	2	FACETS	0.781	0.719	0.846	0.781	0.719	0.846	SUBCLONAL	1	TRUE	1	0.543345691732456	2		998	782	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	103	777	1	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.65	0.583	0.721	0.65	0.583	0.721	SUBCLONAL	1	TRUE	1	0.543345691732456	2		778	583	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952138	178952138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	55	287	0	ENST00000263967.3:c.3193C>T	p.His1065Tyr	p.H1065Y	ENST00000263967	NM_006218.2	1065	Cat/Tat	21/21	1	2	FACETS	0.715	0.617	0.821	0.715	0.617	0.821	SUBCLONAL	1	TRUE	1	0.543345691732456	2		287	283	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	95	266	0	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	0.543345691732456	2	FACETS	0.872	0.782	0.967	0.436	0.391	0.484	CLONAL	1	TRUE	0	0.543345691732456	2		266	401	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	100	376	4	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.829	0.745	0.917	0.829	0.745	0.917	CLONAL	1	TRUE	1	0.543345691732456	2		380	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	25	647	3	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	1	2	FACETS	0.158	0.124	0.198	0.158	0.124	0.198	SUBCLONAL	1	TRUE	1	0.543345691732456	2		650	581	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149799	202149799	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	117	603	0	ENST00000358485.4:c.1245del	p.Phe415LeufsTer26	p.F415Lfs*26	ENST00000358485	NM_001080125.1	414	Ttt/tt	8/9	1	2	FACETS	0.729	0.659	0.802	0.729	0.659	0.802	SUBCLONAL	1	TRUE	1	0.543345691732456	2		603	591	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209298	133209298	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060500809	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	135	973	1	ENST00000320574.5:c.6088del	p.Ala2030ProfsTer18	p.A2030Pfs*18	ENST00000320574	NM_006231.2	2030	Gcc/cc	44/49	1	2	FACETS	0.687	0.625	0.752	0.687	0.625	0.752	SUBCLONAL	1	TRUE	1	0.543345691732456	2		974	723	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043407	180043407	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	135	824	1	ENST00000261937.6:c.3179G>T	p.Arg1060Leu	p.R1060L	ENST00000261937	NM_182925.4	1060	cGg/cTg	23/30	0.456120077818826	1	FACETS	0.503	0.458	0.551	0.503	0.458	0.551	SUBCLONAL	1	TRUE	0	0.543345691732456	1		825	719	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661663	227661664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761880048	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	128	725	20	ENST00000305123.5:c.1791dup	p.His598AlafsTer13	p.H598Afs*13	ENST00000305123	NM_005544.2	597	-/G	1/2	1	2	FACETS	0.992	0.905	1	0.992	0.905	1	CLONAL	1	TRUE	1	0.543345691732456	2		745	475	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822586	72822586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	115	629	2	ENST00000268489.5:c.9589del	p.Gln3197SerfsTer44	p.Q3197Sfs*44	ENST00000268489	NM_006885.3	3197	Cag/ag	10/10	1	2	FACETS	0.757	0.684	0.834	0.757	0.684	0.834	SUBCLONAL	1	TRUE	1	0.543345691732456	2		631	559	SUCCESS
APC	324	MSKCC	GRCh37	5	112164664	112164664	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1060503259	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	62	230	0	ENST00000257430.4:c.1742del	p.Lys581ArgfsTer9	p.K581Rfs*9	ENST00000257430	NM_000038.5	580	Aaa/aa	14/16	1	2	FACETS	0.683	0.594	0.779	0.683	0.594	0.779	SUBCLONAL	1	TRUE	1	0.543345691732456	2		230	334	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552143	29552144	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1555613558	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	63	267	0	ENST00000356175.3:c.1882dup	p.Tyr628LeufsTer6	p.Y628Lfs*6	ENST00000356175	NM_000267.3	626	ctt/cTtt	17/57	1	2	FACETS	0.808	0.705	0.918	0.808	0.705	0.918	CLONAL	1	TRUE	1	0.543345691732456	2		267	287	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486050	29486050	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1438566555	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	98	371	0	ENST00000356175.3:c.233del	p.Asn78IlefsTer7	p.N78Ifs*7	ENST00000356175	NM_000267.3	76	gAa/ga	3/57	1	2	FACETS	0.796	0.714	0.883	0.796	0.714	0.883	SUBCLONAL	1	TRUE	1	0.543345691732456	2		371	453	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861952	57861952	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777289743	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	108	626	2	ENST00000228682.2:c.1253G>A	p.Arg418Gln	p.R418Q	ENST00000228682	NM_005269.2	418	cGg/cAg	10/12	1	2	FACETS	0.849	0.767	0.936	0.849	0.767	0.936	CLONAL	1	TRUE	1	0.543345691732456	2		628	468	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420661	49420661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555185875	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	38	676	0	ENST00000301067.7:c.15088C>T	p.Arg5030Cys	p.R5030C	ENST00000301067	NM_003482.3	5030	Cgt/Tgt	48/54	1	2	FACETS	0.26	0.214	0.311	0.26	0.214	0.311	SUBCLONAL	1	TRUE	1	0.543345691732456	2		676	539	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368388	225368388	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1366667901	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	106	362	0	ENST00000264414.4:c.1358del	p.Asn453ThrfsTer2	p.N453Tfs*2	ENST00000264414	NM_003590.4	453	aAc/ac	9/16	1	2	FACETS	0.832	0.75	0.918	0.832	0.75	0.918	CLONAL	1	TRUE	1	0.543345691732456	2		362	469	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621972	1621972	+	splice_region_variant,intron_variant	Splice_Region	DEL	G	G	-	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	127	986	4	ENST00000344749.5:c.823-3del		p.X275_splice	ENST00000344749	NM_001136139.2	275			1	2	FACETS	0.724	0.657	0.793	0.724	0.657	0.793	SUBCLONAL	1	TRUE	1	0.543345691732456	2		990	646	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786650	3786650	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	160	601	1	ENST00000262367.5:c.4560+1G>A		p.X1520_splice	ENST00000262367	NM_004380.2	1520			1	2	FACETS	0.967	0.891	1	0.967	0.891	1	CLONAL	1	TRUE	1	0.543345691732456	2		602	609	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	120	951	4	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	1	2	FACETS	0.579	0.523	0.638	0.579	0.523	0.638	SUBCLONAL	1	TRUE	1	0.543345691732456	2		955	763	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29579995	29579996	+	intron_variant	Intron	INS	-	-	A	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	88	359	0	ENST00000356175.3:c.4110+3865dup		p.*1370*	ENST00000356175	NM_000267.3	1384/2839			1	2	FACETS	0.622	0.552	0.695	0.622	0.552	0.695	SUBCLONAL	1	TRUE	1	0.543345691732456	2		359	521	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754077	42754077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1381343253	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	132	607	3	ENST00000222329.4:c.275G>A	p.Arg92His	p.R92H	ENST00000222329	NM_006494.2	92	cGc/cAc	3/4	1	2	FACETS	0.885	0.807	0.966	0.885	0.807	0.966	CLONAL	1	TRUE	1	0.543345691732456	2		610	549	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524568	103524568	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	69	232	0	ENST00000355739.4:c.2705del	p.Asn902IlefsTer4	p.N902Ifs*4	ENST00000355739	NM_000123.3	900	cAa/ca	13/15	1	2	FACETS	0.958	0.844	1	0.958	0.844	1	CLONAL	1	TRUE	1	0.543345691732456	2		232	265	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420068	152420068	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	97	522	0	ENST00000206249.3:c.1759del	p.Glu587ArgfsTer20	p.E587Rfs*20	ENST00000206249	NM_000125.3	585	acG/ac	8/8	1	2	FACETS	0.735	0.658	0.816	0.735	0.658	0.816	SUBCLONAL	1	TRUE	1	0.543345691732456	2		522	486	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478548	99478548	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	75	345	0	ENST00000268035.6:c.3190C>T	p.Arg1064Ter	p.R1064*	ENST00000268035	NM_000875.3	1064	Cga/Tga	17/21	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.543345691732456	2		345	274	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817720	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	103	398	0	ENST00000262367.5:c.3250dup	p.Ile1084AsnfsTer3	p.I1084Nfs*3	ENST00000262367	NM_004380.2	1084	atc/aAtc		1	2	FACETS	0.8	0.719	0.884	0.8	0.719	0.884	SUBCLONAL	1	TRUE	1	0.543345691732456	2		398	474	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956141	175956141	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	255	432	0	ENST00000367669.3:c.2071C>T	p.Arg691Ter	p.R691*	ENST00000367669	NM_022457.5	691	Cga/Tga	18/20	0.42027600213928	3	FACETS	0.804	0.756	0.853	0.804	0.756	0.853	CLONAL	2	TRUE	1	0.543345691732456	3		432	742	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038550	47038550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	158	894	0	ENST00000377604.3:c.712G>A	p.Val238Met	p.V238M	ENST00000377604	NM_001204468.1	238	Gtg/Atg	8/24	1	2	FACETS	0.784	0.72	0.851	0.784	0.72	0.851	SUBCLONAL	1	TRUE	1	0.543345691732456	2		894	742	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989044	41989044	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	96	506	1	ENST00000219905.7:c.1840del	p.Arg614GlufsTer7	p.R614Efs*7	ENST00000219905	NM_001164273.1	612	ggA/gg	3/24	1	2	FACETS	0.672	0.6	0.747	0.672	0.6	0.747	SUBCLONAL	1	TRUE	1	0.543345691732456	2		507	526	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793313	139793313	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	174	770	1	ENST00000247668.2:c.121C>A	p.Leu41Ile	p.L41I	ENST00000247668	NM_021138.3	41	Ctc/Atc	2/11	1	2	FACETS	0.868	0.801	0.937	0.868	0.801	0.937	CLONAL	1	TRUE	1	0.543345691732456	2		771	738	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133770	2133770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767495365	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	50	900	3	ENST00000219476.3:c.3958G>A	p.Val1320Ile	p.V1320I	ENST00000219476	NM_000548.3	1320	Gtt/Att	33/42	1	2	FACETS	0.28	0.237	0.327	0.28	0.237	0.327	SUBCLONAL	1	TRUE	1	0.543345691732456	2		903	658	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061649	38061649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	13	174	0	ENST00000250448.2:c.340G>A	p.Gly114Ser	p.G114S	ENST00000250448	NM_004496.3	114	Ggc/Agc	2/2	1	2	FACETS	0.285	0.203	0.383	0.285	0.203	0.383	SUBCLONAL	1	TRUE	1	0.543345691732456	2		174	168	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069382	30069382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	160	765	2	ENST00000338641.4:c.1247C>T	p.Ala416Val	p.A416V	ENST00000338641	NM_000268.3	416	gCg/gTg	12/16	1	2	FACETS	0.945	0.87	1	0.945	0.87	1	CLONAL	1	TRUE	1	0.543345691732456	2		767	623	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511582	38511582	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	131	859	0	ENST00000254066.5:c.1080G>T	p.Lys360Asn	p.K360N	ENST00000254066	NM_000964.3	360	aaG/aaT	8/9	1	2	FACETS	0.701	0.637	0.768	0.701	0.637	0.768	SUBCLONAL	1	TRUE	1	0.543345691732456	2		859	688	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937171	36937171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	138	940	1	ENST00000361632.4:c.1148C>T	p.Ala383Val	p.A383V	ENST00000361632		383	gCc/gTc	9/16	1	2	FACETS	0.662	0.603	0.724	0.662	0.603	0.724	SUBCLONAL	1	TRUE	1	0.543345691732456	2		941	767	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549728	226549728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775722001	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	211	433	1	ENST00000366794.5:c.2905G>A	p.Val969Ile	p.V969I	ENST00000366794	NM_001618.3	969	Gtt/Att	22/23	0.42027600213928	3	FACETS	0.872	0.817	0.929	0.872	0.817	0.929	CLONAL	2	TRUE	1	0.543345691732456	3		434	566	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138914	64138914	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747042462	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	61	620	0	ENST00000334205.4:c.2281G>C	p.Ala761Pro	p.A761P	ENST00000334205	NM_003942.2	761	Gcc/Ccc	17/17	1	2	FACETS	0.522	0.452	0.598	0.522	0.452	0.598	SUBCLONAL	1	TRUE	1	0.543345691732456	2		620	430	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115428	115115428	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	39	576	0	ENST00000257566.3:c.898G>A	p.Ala300Thr	p.A300T	ENST00000257566	NM_016569.3	300	Gca/Aca	5/8	1	2	FACETS	0.191	0.158	0.229	0.191	0.158	0.229	SUBCLONAL	1	TRUE	1	0.543345691732456	2		576	751	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004270	29004270	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	83	324	0	ENST00000282397.4:c.1023G>C	p.Gln341His	p.Q341H	ENST00000282397	NM_002019.4	341	caG/caC	8/30	1	2	FACETS	0.667	0.591	0.748	0.667	0.591	0.748	SUBCLONAL	1	TRUE	1	0.543345691732456	2		324	458	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527956	103527956	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	109	385	1	ENST00000355739.4:c.3268del	p.Glu1090ArgfsTer21	p.E1090Rfs*21	ENST00000355739	NM_000123.3	1088	ttG/tt	15/15	1	2	FACETS	0.935	0.846	1	0.935	0.846	1	CLONAL	1	TRUE	1	0.543345691732456	2		386	429	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133039	30133039	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	92	449	0	ENST00000331968.5:c.562T>C	p.Cys188Arg	p.C188R	ENST00000331968	NM_002742.2	188	Tgt/Cgt	4/18	1	2	FACETS	0.649	0.578	0.724	0.649	0.578	0.724	SUBCLONAL	1	TRUE	1	0.543345691732456	2		449	522	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358608	67358608	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	124	578	0	ENST00000327367.4:c.116T>C	p.Val39Ala	p.V39A	ENST00000327367	NM_005902.3	39	gTc/gCc	1/9	1	2	FACETS	0.878	0.798	0.961	0.878	0.798	0.961	CLONAL	1	TRUE	1	0.543345691732456	2		578	520	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322636	30322636	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	124	544	0	ENST00000322652.5:c.1649A>G	p.Glu550Gly	p.E550G	ENST00000322652	NM_015355.2	550	gAa/gGa	14/16	1	2	FACETS	0.792	0.719	0.869	0.792	0.719	0.869	SUBCLONAL	1	TRUE	1	0.543345691732456	2		544	576	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299079	15299079	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1284132838	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	122	718	0	ENST00000263388.2:c.1459C>T	p.Arg487Ter	p.R487*	ENST00000263388	NM_000435.2	487	Cga/Tga	9/33	1	2	FACETS	0.713	0.646	0.783	0.713	0.646	0.783	SUBCLONAL	1	TRUE	1	0.543345691732456	2		718	630	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18972886	18972886	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	151	760	1	ENST00000262803.5:c.2525T>C	p.Val842Ala	p.V842A	ENST00000262803	NM_002911.3	842	gTg/gCg	18/24	1	2	FACETS	0.823	0.755	0.895	0.823	0.755	0.895	CLONAL	1	TRUE	1	0.543345691732456	2		761	675	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143324	30143324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	116	580	0	ENST00000389048.3:c.202G>A	p.Ala68Thr	p.A68T	ENST00000389048	NM_004304.4	68	Gcc/Acc	1/29	1	2	FACETS	0.794	0.718	0.873	0.794	0.718	0.873	SUBCLONAL	1	TRUE	1	0.543345691732456	2		580	538	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272432	21272432	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	127	887	0	ENST00000354336.3:c.213del	p.Phe71LeufsTer80	p.F71Lfs*80	ENST00000354336	NM_005207.3	70	cgT/cg	1/3	1	2	FACETS	0.569	0.515	0.625	0.569	0.515	0.625	SUBCLONAL	1	TRUE	1	0.543345691732456	2		887	822	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226927	142226927	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	124	424	0	ENST00000350721.4:c.4877A>G	p.Tyr1626Cys	p.Y1626C	ENST00000350721	NM_001184.3	1626	tAt/tGt	28/47	1	2	FACETS	0.748	0.679	0.821	0.748	0.679	0.821	SUBCLONAL	1	TRUE	1	0.543345691732456	2		424	610	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146501	185146501	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	24	482	0	ENST00000265026.3:c.132G>T	p.Glu44Asp	p.E44D	ENST00000265026	NM_004721.4	44	gaG/gaT	2/14	1	2	FACETS	0.19	0.148	0.238	0.19	0.148	0.238	SUBCLONAL	1	TRUE	1	0.543345691732456	2		482	465	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106182986	106182986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	94	304	0	ENST00000380013.4:c.4025C>T	p.Pro1342Leu	p.P1342L	ENST00000380013	NM_001127208.2	1342	cCt/cTt	8/11	1	2	FACETS	0.943	0.846	1	0.943	0.846	1	CLONAL	1	TRUE	1	0.543345691732456	2		304	367	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636806	176636806	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	99	426	0	ENST00000439151.2:c.1406A>G	p.Asp469Gly	p.D469G	ENST00000439151	NM_022455.4	469	gAc/gGc	5/23	NA	2	FACETS	0.686	0.615	0.762			1	INDETERMINATE	1	TRUE	NA	0.543345691732456	2		426	531	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637528	176637528	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	84	566	0	ENST00000439151.2:c.2128G>T	p.Asp710Tyr	p.D710Y	ENST00000439151	NM_022455.4	710	Gac/Tac	5/23	NA	2	FACETS	0.502	0.444	0.564			1	INDETERMINATE	1	TRUE	NA	0.543345691732456	2		566	616	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803118	32803118	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	76	540	0	ENST00000374899.4:c.758T>C	p.Leu253Pro	p.L253P	ENST00000374899	NM_018833.2	253	cTg/cCg	5/12	1	2	FACETS	0.541	0.475	0.611	0.541	0.475	0.611	SUBCLONAL	1	TRUE	1	0.543345691732456	2		540	517	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805595	32805595	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	141	918	0	ENST00000374899.4:c.416G>A	p.Trp139Ter	p.W139*	ENST00000374899	NM_018833.2	139	tGg/tAg	2/12	1	2	FACETS	0.61	0.555	0.667	0.61	0.555	0.667	SUBCLONAL	1	TRUE	1	0.543345691732456	2		918	851	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129315	152129315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	149	723	0	ENST00000206249.3:c.268G>A	p.Gly90Ser	p.G90S	ENST00000206249	NM_000125.3	90	Ggc/Agc	1/8	1	2	FACETS	0.89	0.817	0.967	0.89	0.817	0.967	CLONAL	1	TRUE	1	0.543345691732456	2		723	616	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026907	6026907	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749826312	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	62	210	1	ENST00000265849.7:c.1489G>A	p.Gly497Ser	p.G497S	ENST00000265849	NM_000535.5	497	Ggc/Agc	11/15	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.543345691732456	2		211	193	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851526	151851526	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	58	253	0	ENST00000262189.6:c.11965C>G	p.Gln3989Glu	p.Q3989E	ENST00000262189	NM_170606.2	3989	Cag/Gag	47/59	1	2	FACETS	0.827	0.718	0.944	0.827	0.718	0.944	CLONAL	1	TRUE	1	0.543345691732456	2		253	258	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040612	47040612	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	58	486	0	ENST00000377604.3:c.1249-2A>G		p.X417_splice	ENST00000377604	NM_001204468.1	417			1	2	FACETS	0.61	0.527	0.7	0.61	0.527	0.7	SUBCLONAL	1	TRUE	1	0.543345691732456	2		486	350	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239907	53239907	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	146	688	0	ENST00000375401.3:c.1534del	p.Cys512AlafsTer37	p.C512Afs*37	ENST00000375401	NM_004187.3	512	Tgc/gc	11/26	1	2	FACETS	0.787	0.72	0.857	0.787	0.72	0.857	SUBCLONAL	1	TRUE	1	0.543345691732456	2		688	683	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	37	276	0				ENST00000310581	NM_198253.2	-/1132			0.343044908422876	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.343044908422876	1		276	139	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870260	44870260	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	152	159	0	ENST00000377967.4:c.439C>T	p.Gln147Ter	p.Q147*	ENST00000377967	NM_021140.2	147	Cag/Tag	5/29	0.343044908422876	2	FACETS	0.991	0.925	1			1	CLONAL	3	TRUE	NA	0.343044908422876	2		159	298	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0051000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	193	896	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.223735904982469	3	FACETS	1	0.94	1	0.675	0.627	0.724	CLONAL	2	TRUE	0	0.343044908422876	3		896	651	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575116	48575116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	46	289	0	ENST00000342988.3:c.310C>T	p.Leu104Phe	p.L104F	ENST00000342988	NM_005359.5	104	Ctt/Ttt	3/12	0.271742124731676	3	FACETS	0.806	0.68	0.944	0.403	0.34	0.472	CLONAL	1	TRUE	1	0.343044908422876	3		289	390	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724508	112724508	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	43	452	0	ENST00000369452.4:c.392A>C	p.Tyr131Ser	p.Y131S	ENST00000369452	NM_007373.3	131	tAc/tCc	2/9	0.139222408034947	3	FACETS	0.686	0.575	0.809	0.229	0.191	0.27	INDETERMINATE	1	TRUE	0	0.343044908422876	3		452	428	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219472	5219472	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	31	451	1	ENST00000357368.4:c.3772G>T	p.Ala1258Ser	p.A1258S	ENST00000357368	NM_002850.3	1258	Gca/Tca	23/38	0.271742124731676	3	FACETS	0.501	0.404	0.609	0.25	0.202	0.305	SUBCLONAL	1	TRUE	1	0.343044908422876	3		452	423	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346664	225346664	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	150	359	0	ENST00000264414.4:c.1974A>G	p.Ile658Met	p.I658M	ENST00000264414	NM_003590.4	658	atA/atG	14/16	1	2	FACETS	0.97	0.894	1	1	0.992	1	CLONAL	2	TRUE	1	0.343044908422876	2		359	451	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1906067	1906067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	55	565	0	ENST00000382891.5:c.722C>T	p.Ser241Phe	p.S241F	ENST00000382891	NM_133335.3	241	tCt/tTt	3/22	1	2	FACETS	0.478	0.408	0.554	0.478	0.408	0.554	SUBCLONAL	1	TRUE	1	0.343044908422876	2		565	671	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035181	30035181	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	43	432	0	ENST00000338641.4:c.343C>T	p.Gln115Ter	p.Q115*	ENST00000338641	NM_000268.3	115	Caa/Taa	3/16	0.140577333234047	0	FACETS	0.952	0.814	1			1	CLONAL	4	FALSE	0	0.140577333234047	0		432	138	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359061	81359061	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	12	465	0	ENST00000222390.5:c.900G>C	p.Leu300Phe	p.L300F	ENST00000222390	NM_000601.4	300	ttG/ttC	8/18	0.0895831659824626	4	FACETS	1	0.812	1	0.612	0.432	0.833	CLONAL	1	FALSE	2	0.140577333234047	4		465	159	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0051003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	110	577	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.179475134598839	2		577	876	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564527	55564527	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	55	466	0	ENST00000288135.5:c.415A>G	p.Thr139Ala	p.T139A	ENST00000288135	NM_000222.2	139	Aca/Gca	3/21	0.174750616576826	1	FACETS	0.924	0.79	1	0.924	0.79	1	CLONAL	1	TRUE	0	0.179475134598839	1		466	604	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652959	29652959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876659922	NA	P-0051003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	41	427	0	ENST00000356175.3:c.4894C>T	p.Arg1632Cys	p.R1632C	ENST00000356175	NM_000267.3	1632	Cgc/Tgc	36/57	1	2	FACETS	0.796	0.662	0.945	0.796	0.662	0.945	CLONAL	1	TRUE	1	0.179475134598839	2		427	574	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602326	10602326	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	140	771	0	ENST00000171111.5:c.1252del	p.Val418TrpfsTer40	p.V418Wfs*40	ENST00000171111	NM_203500.1	418	Gtg/tg	3/6	0.179475134598839	2	FACETS	0.769	0.7	0.843	0.769	0.7	0.843	SUBCLONAL	2	TRUE	0	0.179475134598839	2		771	1014	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138407738	138407738	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	33	397	0	ENST00000289153.2:c.2115C>A	p.His705Gln	p.H705Q	ENST00000289153	NM_006219.2	705	caC/caA	14/22	1	2	FACETS	0.649	0.527	0.786	0.649	0.527	0.786	SUBCLONAL	1	TRUE	1	0.179475134598839	2		397	567	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149511625	149511625	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	85	546	0	ENST00000261799.4:c.1160A>C	p.Lys387Thr	p.K387T	ENST00000261799	NM_002609.3	387	aAg/aCg	8/23	0.174750616576826	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.179475134598839	1		546	686	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509033	106509033	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	57	496	0	ENST00000359195.3:c.1027G>C	p.Gly343Arg	p.G343R	ENST00000359195	NM_002649.2	343	Ggc/Cgc	2/11	1	2	FACETS	0.905	0.775	1	0.905	0.775	1	CLONAL	1	TRUE	1	0.179475134598839	2		496	702	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977949	134977949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56186270	NA	P-0051005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	87	539	0	ENST00000398015.3:c.2942C>T	p.Thr981Met	p.T981M	ENST00000398015	NM_004441.4	981	aCg/aTg	16/16	1	2	FACETS	0.809	0.719	0.905	1	0.981	1	CLONAL	2	TRUE	1	0.216804006192755	2		539	496	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432435	49432435	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	80	748	0	ENST00000301067.7:c.8704C>T	p.Gln2902Ter	p.Q2902*	ENST00000301067	NM_003482.3	2902	Cag/Tag	34/54	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.216804006192755	2		748	584	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456650	138456650	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs750830394	NA	P-0051005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	73	542	0	ENST00000289153.2:c.700A>G	p.Ile234Val	p.I234V	ENST00000289153	NM_006219.2	234	Att/Gtt	4/22	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.216804006192755	2		542	518	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845654	63845654	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	17	254	0	ENST00000279873.7:c.1393G>A	p.Ala465Thr	p.A465T	ENST00000279873	NM_032199.2	465	Gca/Aca	9/10	0.168539098385934	2	FACETS	0.67	0.501	0.871	0.335	0.25	0.436	SUBCLONAL	1	TRUE	0	0.216804006192755	2		254	234	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457823	69457823	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	32	402	1	ENST00000227507.2:c.223G>T	p.Glu75Ter	p.E75*	ENST00000227507	NM_053056.2	75	Gag/Tag	2/5	0.168539098385934	2	FACETS	0.853	0.694	1	0.427	0.347	0.517	CLONAL	1	TRUE	0	0.216804006192755	2		403	346	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432335	49432335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	87	792	1	ENST00000301067.7:c.8804C>T	p.Ser2935Leu	p.S2935L	ENST00000301067	NM_003482.3	2935	tCa/tTa	34/54	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.216804006192755	2		793	621	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432354	49432354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	87	768	0	ENST00000301067.7:c.8785C>T	p.Leu2929Phe	p.L2929F	ENST00000301067	NM_003482.3	2929	Ctt/Ttt	34/54	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.216804006192755	2		768	601	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432359	49432359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	87	795	0	ENST00000301067.7:c.8780C>T	p.Ser2927Leu	p.S2927L	ENST00000301067	NM_003482.3	2927	tCa/tTa	34/54	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.216804006192755	2		795	597	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432703	49432704	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCTG	novel	NA	P-0051005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	45	840	0	ENST00000301067.7:c.8431_8435dup	p.Gln2812HisfsTer41	p.Q2812Hfs*41	ENST00000301067	NM_003482.3	2812	cag/caCAGCAg	34/54	1	2	FACETS	0.568	0.476	0.67	0.568	0.476	0.67	SUBCLONAL	1	TRUE	1	0.216804006192755	2		840	731	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89862382	89862382	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	34	651	1	ENST00000389301.3:c.938C>A	p.Thr313Lys	p.T313K	ENST00000389301	NM_000135.2	313	aCa/aAa	11/43	NA	3	FACETS	0.578	0.471	0.699			1	INDETERMINATE	1	TRUE	NA	0.216804006192755	3		652	601	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0051006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	373	734	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.966	0.921	1	0.966	0.921	1	CLONAL	1	TRUE	1	0.8719617833862	2		735	886	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	153	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.967	0.897	1	0.967	0.897	1	CLONAL	1	TRUE	1	0.8719617833862	2		276	363	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5055739	5055739	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0051006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	152	310	0	ENST00000381652.3:c.1007C>G	p.Ser336Ter	p.S336*	ENST00000381652	NM_004972.3	336	tCa/tGa	8/25	0.8719617833862	1	FACETS	0.959	0.911	1	0.959	0.911	1	CLONAL	1	TRUE	0	0.8719617833862	1		310	205	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188181	108188181	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1565503182	NA	P-0051006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	95	284	0	ENST00000278616.4:c.6280G>T	p.Glu2094Ter	p.E2094*	ENST00000278616	NM_000051.3	2094	Gaa/Taa	43/63	1	2	FACETS	0.512	0.458	0.568	0.512	0.458	0.568	SUBCLONAL	1	TRUE	1	0.8719617833862	2		284	426	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870319	155870319	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	82	495	0	ENST00000368323.3:c.520G>T	p.Val174Phe	p.V174F	ENST00000368323	NM_006912.5	174	Gtt/Ttt	6/6	1	2	FACETS	0.246	0.216	0.278	0.246	0.216	0.278	SUBCLONAL	1	TRUE	1	0.8719617833862	2		495	765	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984412	201984413	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0051006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	359	558	0	ENST00000359651.3:c.1079dup	p.Trp361LeufsTer110	p.W361Lfs*110	ENST00000359651		359	-/G	8/8	0.837355351202621	1	FACETS	0.972	0.94	1	0.972	0.94	1	CLONAL	1	TRUE	0	0.8719617833862	1		558	478	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093424	30093424	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	218	333	0	ENST00000331968.5:c.1839C>G	p.Ile613Met	p.I613M	ENST00000331968	NM_002742.2	613	atC/atG	13/18	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.8719617833862	2		333	476	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217258	7217259	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CTGTCAGCTGCCATGAGGGTGC	novel	NA	P-0051006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	197	502	0	ENST00000380728.2:c.425_446dup	p.Ala150HisfsTer6	p.A150Hfs*6	ENST00000380728		149	aga/agGCACCCTCATGGCAGCTGACAGa	6/11	0.8719617833862	1	FACETS	0.61	0.572	0.647	0.61	0.572	0.647	SUBCLONAL	1	TRUE	0	0.8719617833862	1		502	418	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188344	142188344	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	29	402	0	ENST00000350721.4:c.6387T>A	p.His2129Gln	p.H2129Q	ENST00000350721	NM_001184.3	2129	caT/caA	38/47	1	2	FACETS	0.134	0.107	0.165	0.134	0.107	0.165	SUBCLONAL	1	TRUE	1	0.8719617833862	2		402	496	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947180	178947180	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	139	276	1	ENST00000263967.3:c.2616C>A	p.Phe872Leu	p.F872L	ENST00000263967	NM_006218.2	872	ttC/ttA	18/21	1	2	FACETS	0.805	0.741	0.871	0.805	0.741	0.871	CLONAL	1	TRUE	1	0.8719617833862	2		277	396	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0051007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	187	355	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.518195224039486	3	FACETS	0.929	0.866	0.993	0.929	0.866	0.993	CLONAL	2	TRUE	1	0.518195224039486	3		355	489	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276908	123276908	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs387906676	NA	P-0051007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	84	371	0	ENST00000358487.5:c.1009G>C	p.Ala337Pro	p.A337P	ENST00000358487	NM_000141.4	337	Gct/Cct	8/18	1	2	FACETS	0.815	0.724	0.911	0.815	0.724	0.911	CLONAL	1	TRUE	1	0.518195224039486	2		371	398	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562739	21562739	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	163	471	1	ENST00000382592.4:c.1180G>A	p.Val394Met	p.V394M	ENST00000382592	NM_014572.2	394	Gtg/Atg	4/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.518195224039486	2		472	591	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221275	1221275	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	154	647	1	ENST00000326873.7:c.798del	p.Asn266LysfsTer21	p.N266Kfs*21	ENST00000326873	NM_000455.4	266	aaC/aa	6/10	0.518195224039486	1	FACETS	0.925	0.853	0.999	0.925	0.853	0.999	CLONAL	1	TRUE	0	0.518195224039486	1		648	476	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626772	14626772	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1423328946	NA	P-0051007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	148	391	0	ENST00000254322.2:c.1003G>C	p.Glu335Gln	p.E335Q	ENST00000254322	NM_006145.1	335	Gag/Cag	3/3	0.518195224039486	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.518195224039486	1		391	397	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505471	25505471	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	148	612	0	ENST00000264709.3:c.287G>T	p.Arg96Leu	p.R96L	ENST00000264709	NM_175629.2	96	cGg/cTg	4/23	1	2	FACETS	0.927	0.85	1	0.927	0.85	1	CLONAL	1	TRUE	1	0.518195224039486	2		612	616	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31390189	31390189	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0051007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	123	362	1	ENST00000328111.2:c.2146-2A>T		p.X716_splice	ENST00000328111	NM_006892.3	716			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.518195224039486	2		363	425	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37628954	37628954	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	185	588	0	ENST00000249071.6:c.112G>C	p.Asp38His	p.D38H	ENST00000249071	NM_002872.4	38	Gac/Cac	3/7	1	2	FACETS	0.969	0.897	1	0.969	0.897	1	CLONAL	1	TRUE	1	0.518195224039486	2		588	737	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157896	106157896	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	97	311	0	ENST00000380013.4:c.2797C>T	p.Gln933Ter	p.Q933*	ENST00000380013	NM_001127208.2	933	Cag/Tag	3/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.518195224039486	2		311	355	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969984	161969984	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs894633561	NA	P-0051007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	159	551	0	ENST00000366898.1:c.985G>T	p.Gly329Cys	p.G329C	ENST00000366898	NM_004562.2	329	Ggc/Tgc	9/12	1	2	FACETS	0.966	0.889	1	0.966	0.889	1	CLONAL	1	TRUE	1	0.518195224039486	2		551	635	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891209	101891209	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	75	344	0	ENST00000374994.4:c.170C>G	p.Ser57Cys	p.S57C	ENST00000374994	NM_004612.2	57	tCt/tGt	2/9	0.518195224039486	1	FACETS	0.879	0.781	0.981	0.879	0.781	0.981	CLONAL	1	TRUE	0	0.518195224039486	1		344	244	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164957	123164957	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	56	237	0	ENST00000218089.9:c.270G>T	p.Met90Ile	p.M90I	ENST00000218089	NM_001042749.1	90	atG/atT	5/35	1	2	FACETS	0.72	0.622	0.827	0.72	0.622	0.827	SUBCLONAL	1	TRUE	1	0.518195224039486	2		237	300	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036014	180036014	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761503019	NA	P-0051009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	1216	676	0	ENST00000261937.6:c.3847G>A	p.Glu1283Lys	p.E1283K	ENST00000261937	NM_182925.4	1283	Gag/Aag	29/30	0.3	11	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	11		676	1798	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750566	57750568	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	rs764901947	NA	P-0051009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	32	362	0	ENST00000274289.3:c.1900_1902del	p.Ile634del	p.I634del	ENST00000274289	NM_006622.3	634	ATC/-	14/14	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		362	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0051010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	388	513	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.410194759045155	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.417070362341261	2		516	895	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539563	187539563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748950954	NA	P-0051010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	105	377	0	ENST00000441802.2:c.8177G>A	p.Arg2726Gln	p.R2726Q	ENST00000441802	NM_005245.3	2726	cGa/cAa	10/27	0.417070362341261	1	FACETS	0.972	0.877	1	0.972	0.877	1	CLONAL	1	TRUE	0	0.417070362341261	1		377	410	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461088	120461088	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	112	445	0	ENST00000256646.2:c.5870A>G	p.Glu1957Gly	p.E1957G	ENST00000256646	NM_024408.3	1957	gAg/gGg	32/34	1	2	FACETS	0.862	0.777	0.952	0.862	0.777	0.952	CLONAL	1	TRUE	1	0.417070362341261	2		445	623	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0051011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	22	422	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		422	386	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	348	513	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.986	1	1	0.997	1	CLONAL	2	TRUE	1	0.429714594555381	2		516	745	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519226	187519226	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200611830	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	275	489	0	ENST00000441802.2:c.12157G>A	p.Val4053Ile	p.V4053I	ENST00000441802	NM_005245.3	4053	Gtc/Atc	23/27	1	2	FACETS	1	0.979	1	1	0.996	1	CLONAL	2	TRUE	1	0.429714594555381	2		489	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	280	615	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.952	1	1	0.996	1	CLONAL	2	TRUE	1	0.429714594555381	2		617	648	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	110	256	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.941	0.86	1	1	0.989	1	CLONAL	2	TRUE	1	0.429714594555381	2		256	272	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911760	26911760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	72	356	0	ENST00000381527.3:c.185C>T	p.Ser62Leu	p.S62L	ENST00000381527	NM_001260.1	62	tCg/tTg	2/13	0.429714594555381	1	FACETS	0.812	0.715	0.915	0.812	0.715	0.915	CLONAL	1	TRUE	0	0.429714594555381	1		356	324	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132438	11132438	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794284	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	40	709	0	ENST00000358026.2:c.2654G>A	p.Arg885His	p.R885H	ENST00000358026	NM_001128849.1	885	cGc/cAc	19/36	1	2	FACETS	0.277	0.229	0.33	0.277	0.229	0.33	SUBCLONAL	1	TRUE	1	0.429714594555381	2		709	673	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311619	15311621	+	inframe_deletion	In_Frame_Del	DEL	AGC	AGC	-	rs746497955	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	10	170	0	ENST00000263388.2:c.96_98del	p.Leu33del	p.L33del	ENST00000263388	NM_000435.2	32	ctGCTa/cta	1/33	1	2	FACETS	0.252	0.17	0.354	0.252	0.17	0.354	SUBCLONAL	1	TRUE	1	0.429714594555381	2		170	185	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267698	198267698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	194	390	1	ENST00000335508.6:c.1781G>A	p.Arg594Gln	p.R594Q	ENST00000335508	NM_012433.2	594	cGa/cAa	13/25	1	2	FACETS	0.997	0.933	1	1	0.994	1	CLONAL	2	TRUE	1	0.429714594555381	2		391	453	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279443	1279443	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	34	832	1	ENST00000310581.5:c.2093G>A	p.Arg698Gln	p.R698Q	ENST00000310581	NM_198253.2	698	cGg/cAg	5/16	0.429714594555381	1	FACETS	0.199	0.162	0.241	0.199	0.162	0.241	SUBCLONAL	1	TRUE	0	0.429714594555381	1		833	624	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002659	37002659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1385943435	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	261	506	0	ENST00000358127.4:c.590G>A	p.Arg197His	p.R197H	ENST00000358127	NM_001280556.1	197	cGc/cAc	5/10	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.429714594555381	2		506	517	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410452	139410453	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs864622059	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	348	764	0	ENST00000277541.6:c.1649dup	p.Tyr550Ter	p.Y550*	ENST00000277541	NM_017617.3	550	tac/taAc	10/34	1	2	FACETS	1	0.978	1	1	0.997	1	CLONAL	2	TRUE	1	0.429714594555381	2		764	776	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793008	33793010	+	inframe_deletion	In_Frame_Del	DEL	CGC	CGC	-	rs780345232	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	10	66	0	ENST00000498907.2:c.311_313del	p.Gly104del	p.G104del	ENST00000498907	NM_004364.3	104	gGCGac/gac	1/1	1	2	FACETS	0.5	0.342	0.695	0.5	0.342	0.695	SUBCLONAL	1	TRUE	1	0.429714594555381	2		66	93	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115600	108115600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772821016	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	184	453	0	ENST00000278616.4:c.748C>T	p.Arg250Ter	p.R250*	ENST00000278616	NM_000051.3	250	Cga/Tga	7/63	1	2	FACETS	0.969	0.904	1	1	0.993	1	CLONAL	2	TRUE	1	0.429714594555381	2		453	442	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118821	61118821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146326268	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	138	183	0	ENST00000295025.8:c.14C>T	p.Ala5Val	p.A5V	ENST00000295025	NM_002908.2	5	gCg/gTg	2/11	0.429714594555381	2	FACETS	0.969	0.908	1	1	0.99	1	CLONAL	3	TRUE	0	0.429714594555381	2		183	221	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661500	227661500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757021553	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	143	693	1	ENST00000305123.5:c.1955G>A	p.Arg652His	p.R652H	ENST00000305123	NM_005544.2	652	cGc/cAc	1/2	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.429714594555381	2		694	645	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390735	139390736	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	44	793	0	ENST00000277541.6:c.7455dup	p.Ser2486LeufsTer21	p.S2486Lfs*21	ENST00000277541	NM_017617.3	2485	-/C	34/34	1	2	FACETS	0.237	0.198	0.281	0.237	0.198	0.281	SUBCLONAL	1	TRUE	1	0.429714594555381	2		793	864	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412303	139412303	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs869025494	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	62	715	1	ENST00000277541.6:c.1342C>T	p.Arg448Ter	p.R448*	ENST00000277541	NM_017617.3	448	Cga/Tga	8/34	1	2	FACETS	0.365	0.314	0.42	0.365	0.314	0.42	SUBCLONAL	1	TRUE	1	0.429714594555381	2		716	791	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470498	25470498	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747448117	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	54	656	0	ENST00000264709.3:c.976C>T	p.Arg326Cys	p.R326C	ENST00000264709	NM_175629.2	326	Cgc/Tgc	8/23	0.429714594555381	2	FACETS	0.352	0.3	0.41	0.176	0.15	0.205	SUBCLONAL	1	TRUE	0	0.429714594555381	2		656	713	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413100	139413100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201236538	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	52	742	1	ENST00000277541.6:c.1042G>A	p.Ala348Thr	p.A348T	ENST00000277541	NM_017617.3	348	Gcc/Acc	6/34	1	2	FACETS	0.318	0.269	0.371	0.318	0.269	0.371	SUBCLONAL	1	TRUE	1	0.429714594555381	2		743	762	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396482	139396482	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	35	721	0	ENST00000277541.6:c.5443del	p.Asp1815ThrfsTer72	p.D1815Tfs*72	ENST00000277541	NM_017617.3	1815	Gac/ac	29/34	1	2	FACETS	0.257	0.209	0.31	0.257	0.209	0.31	SUBCLONAL	1	TRUE	1	0.429714594555381	2		721	635	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874316	76874316	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	112	494	0	ENST00000373344.5:c.5406del	p.Lys1802AsnfsTer10	p.K1802Nfs*10	ENST00000373344	NM_000489.3	1802	aaA/aa	21/35	0.375158805846018	0	FACETS	0.78	0.708	0.855			1	SUBCLONAL	1	TRUE	0	0.429714594555381	0		494	381	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095644	178095644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763240080	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	91	442	0	ENST00000397062.3:c.1687G>A	p.Glu563Lys	p.E563K	ENST00000397062	NM_006164.4	563	Gaa/Aaa	5/5	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.429714594555381	2		442	388	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263999	104264000	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	29	336	1	ENST00000369902.3:c.95dup	p.Leu34ThrfsTer14	p.L34Tfs*14	ENST00000369902	NM_016169.3	30	-/C	1/12	1	2	FACETS	0.34	0.273	0.417	0.34	0.273	0.417	SUBCLONAL	1	TRUE	1	0.429714594555381	2		337	397	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932028	39932029	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	35	630	0	ENST00000378444.4:c.2570_2571del	p.Glu857GlyfsTer7	p.E857Gfs*7	ENST00000378444	NM_001123385.1	857	gAG/g	4/15	0.429714594555381	0	FACETS	0.232	0.19	0.279			1	SUBCLONAL	1	TRUE	0	0.429714594555381	0		630	400	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266717	18266717	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765334654	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	47	675	0	ENST00000222254.8:c.28C>T	p.Arg10Cys	p.R10C	ENST00000222254	NM_005027.3	10	Cgc/Tgc	2/16	1	2	FACETS	0.345	0.29	0.405	0.345	0.29	0.405	SUBCLONAL	1	TRUE	1	0.429714594555381	2		675	634	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403498	139403498	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756840659	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	103	756	0	ENST00000277541.6:c.2995G>A	p.Val999Met	p.V999M	ENST00000277541	NM_017617.3	999	Gtg/Atg	19/34	1	2	FACETS	0.639	0.572	0.711	0.639	0.572	0.711	SUBCLONAL	1	TRUE	1	0.429714594555381	2		756	750	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275708	41275708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886039332	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	44	488	0	ENST00000349496.5:c.1603C>T	p.Arg535Ter	p.R535*	ENST00000349496	NM_001904.3	535	Cga/Tga	10/15	1	2	FACETS	0.347	0.29	0.409	0.347	0.29	0.409	SUBCLONAL	1	TRUE	1	0.429714594555381	2		488	591	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122652	7122652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs926877336	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	255	567	1	ENST00000302850.5:c.3502G>A	p.Ala1168Thr	p.A1168T	ENST00000302850	NM_000208.2	1168	Gcc/Acc	19/22	1	2	FACETS	1	0.962	1	1	0.995	1	CLONAL	2	TRUE	1	0.429714594555381	2		568	580	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938263	36938263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138558210	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	41	711	0	ENST00000361632.4:c.698G>A	p.Arg233Gln	p.R233Q	ENST00000361632		233	cGg/cAg	6/16	1	2	FACETS	0.267	0.222	0.318	0.267	0.222	0.318	SUBCLONAL	1	TRUE	1	0.429714594555381	2		711	714	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599919	10599919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375390113	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	295	642	0	ENST00000171111.5:c.1657C>T	p.Arg553Trp	p.R553W	ENST00000171111	NM_203500.1	553	Cgg/Tgg	5/6	1	2	FACETS	0.982	0.931	1	1	0.996	1	CLONAL	2	TRUE	1	0.429714594555381	2		642	699	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484634	57484634	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	43	478	0	ENST00000371085.3:c.718G>A	p.Asp240Asn	p.D240N	ENST00000371085	NM_000516.4	240	Gat/Aat	9/13	1	2	FACETS	0.331	0.276	0.392	0.331	0.276	0.392	SUBCLONAL	1	TRUE	1	0.429714594555381	2		478	605	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214058	36214058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1385766471	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	52	788	2	ENST00000222270.7:c.2884C>T	p.Arg962Cys	p.R962C	ENST00000222270	NM_014727.1	962	Cgc/Tgc	6/37	1	2	FACETS	0.312	0.265	0.364	0.312	0.265	0.364	SUBCLONAL	1	TRUE	1	0.429714594555381	2		790	776	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166206	32166206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773724911	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	161	573	2	ENST00000375023.3:c.4748G>A	p.Arg1583His	p.R1583H	ENST00000375023	NM_004557.3	1583	cGt/cAt	26/30	0.429714594555381	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.429714594555381	1		575	570	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424741	49424741	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783692	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	45	560	1	ENST00000301067.7:c.13606C>T	p.Arg4536Ter	p.R4536*	ENST00000301067	NM_003482.3	4536	Cga/Tga	40/54	0.129667002596078	3	FACETS	0.336	0.281	0.396	0.168	0.14	0.198	INDETERMINATE	1	TRUE	1	0.429714594555381	3		561	758	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211853	36211853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs527331134	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	62	680	4	ENST00000222270.7:c.1604G>A	p.Arg535His	p.R535H	ENST00000222270	NM_014727.1	535	cGc/cAc	3/37	1	2	FACETS	0.394	0.34	0.454	0.394	0.34	0.454	SUBCLONAL	1	TRUE	1	0.429714594555381	2		684	732	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435852	110435852	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	28	524	0	ENST00000375856.3:c.2549C>T	p.Ala850Val	p.A850V	ENST00000375856	NM_003749.2	850	gCg/gTg	1/2	0.429714594555381	1	FACETS	0.269	0.214	0.33	0.269	0.214	0.33	SUBCLONAL	1	TRUE	0	0.429714594555381	1		524	381	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658568	206658568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199623162	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	33	472	2	ENST00000367120.3:c.1541C>T	p.Thr514Met	p.T514M	ENST00000367120	NM_014002.3	514	aCg/aTg	15/22	1	2	FACETS	0.34	0.276	0.411	0.34	0.276	0.411	SUBCLONAL	1	TRUE	1	0.429714594555381	2		474	452	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205499	61205499	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	31	421	0	ENST00000301761.2:c.284A>C	p.Gln95Pro	p.Q95P	ENST00000301761	NM_017841.2	95	cAg/cCg	3/4	1	2	FACETS	0.285	0.23	0.348	0.285	0.23	0.348	SUBCLONAL	1	TRUE	1	0.429714594555381	2		421	506	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349006	89349006	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs186068075	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	97	678	1	ENST00000301030.4:c.3944C>T	p.Pro1315Leu	p.P1315L	ENST00000301030	NM_001256183.1	1315	cCg/cTg	9/13	NA	2	FACETS	0.702	0.627	0.782			1	INDETERMINATE	1	TRUE	NA	0.429714594555381	2		679	643	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1646419	1646419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747413868	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	29	584	1	ENST00000344749.5:c.80C>T	p.Pro27Leu	p.P27L	ENST00000344749	NM_001136139.2	27	cCg/cTg	3/19	1	2	FACETS	0.237	0.19	0.292	0.237	0.19	0.292	SUBCLONAL	1	TRUE	1	0.429714594555381	2		585	569	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226209	2226209	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781060698	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	289	810	2	ENST00000398665.3:c.3689C>T	p.Ala1230Val	p.A1230V	ENST00000398665	NM_032482.2	1230	gCg/gTg	27/28	1	2	FACETS	0.985	0.933	1	1	0.996	1	CLONAL	2	TRUE	1	0.429714594555381	2		812	683	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966023	18966023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	224	585	1	ENST00000262803.5:c.1516G>A	p.Val506Ile	p.V506I	ENST00000262803	NM_002911.3	506	Gtc/Atc	11/24	1	2	FACETS	0.982	0.923	1	1	0.995	1	CLONAL	2	TRUE	1	0.429714594555381	2		586	531	SUCCESS
AXL	558	MSKCC	GRCh37	19	41737126	41737126	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759570308	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	166	687	0	ENST00000301178.4:c.706C>T	p.Arg236Cys	p.R236C	ENST00000301178	NM_021913.4	236	Cgc/Tgc	6/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.429714594555381	2		687	686	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657007	47657008	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAAGATTGTTACCGACTCT	novel	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	176	370	0	ENST00000233146.2:c.1204_1222dup	p.Tyr408SerfsTer15	p.Y408Sfs*15	ENST00000233146	NM_000251.2	401	-/CAAGATTGTTACCGACTCT	7/16	0.429714594555381	2	FACETS	0.982	0.916	1	0.982	0.916	1	CLONAL	2	TRUE	0	0.429714594555381	2		370	417	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030883	36030883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1252138081	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	52	578	0	ENST00000358208.4:c.1162C>T	p.Arg388Trp	p.R388W	ENST00000358208		388	Cgg/Tgg	10/12	1	2	FACETS	0.401	0.341	0.467	0.401	0.341	0.467	SUBCLONAL	1	TRUE	1	0.429714594555381	2		578	603	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177927	142177927	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754253403	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	24	354	0	ENST00000350721.4:c.7376G>A	p.Arg2459His	p.R2459H	ENST00000350721	NM_001184.3	2459	cGt/cAt	44/47	1	2	FACETS	0.284	0.222	0.356	0.284	0.222	0.356	SUBCLONAL	1	TRUE	1	0.429714594555381	2		354	393	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629340	187629340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769413470	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	45	601	0	ENST00000441802.2:c.1642C>T	p.Arg548Cys	p.R548C	ENST00000441802	NM_005245.3	548	Cgc/Tgc	2/27	1	2	FACETS	0.335	0.28	0.395	0.335	0.28	0.395	SUBCLONAL	1	TRUE	1	0.429714594555381	2		601	626	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004505	150004505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201128649	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	96	561	0	ENST00000253339.5:c.1720G>A	p.Glu574Lys	p.E574K	ENST00000253339		574	Gag/Aag	3/7	1	2	FACETS	0.688	0.614	0.768	0.688	0.614	0.768	SUBCLONAL	1	TRUE	1	0.429714594555381	2		561	649	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923040	39923040	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs961359571	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	118	564	0	ENST00000378444.4:c.3668C>T	p.Ser1223Leu	p.S1223L	ENST00000378444	NM_001123385.1	1223	tCg/tTg	8/15	0.429714594555381	0	FACETS	0.789	0.718	0.862			1	SUBCLONAL	1	TRUE	0	0.429714594555381	0		564	397	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041011	47041011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556779561	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	70	752	2	ENST00000377604.3:c.1541C>T	p.Ala514Val	p.A514V	ENST00000377604	NM_001204468.1	514	gCg/gTg	14/24	0.429714594555381	0	FACETS	0.444	0.389	0.504			1	SUBCLONAL	1	TRUE	0	0.429714594555381	0		754	418	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041648	47041648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1191525682	NA	P-0051016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	38	615	1	ENST00000377604.3:c.1873G>A	p.Gly625Arg	p.G625R	ENST00000377604	NM_001204468.1	625	Gga/Aga	17/24	0.429714594555381	0	FACETS	0.292	0.241	0.347			1	SUBCLONAL	1	TRUE	0	0.429714594555381	0		616	346	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098954	178098954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553488015	NA	P-0051017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	90	330	0	ENST00000397062.3:c.91G>A	p.Gly31Arg	p.G31R	ENST00000397062	NM_006164.4	31	Gga/Aga	2/5	0.641370778606193	4	FACETS	0.844	0.752	0.942	0.281	0.25	0.314	CLONAL	1	TRUE	1	0.802568228584008	4		330	479	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300846	137300846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	211	776	0	ENST00000481739.1:c.491G>A	p.Arg164His	p.R164H	ENST00000481739	NM_002957.4	164	cGc/cAc	4/10	1	2	FACETS	0.858	0.802	0.915	0.858	0.802	0.915	CLONAL	1	TRUE	1	0.802568228584008	2		776	613	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374756	149374756	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	165	479	0	ENST00000360632.3:c.338T>C	p.Leu113Pro	p.L113P	ENST00000360632	NM_015472.4	113	cTc/cCc	2/7	0.475113557164325	3	FACETS	1	0.984	1	0.61	0.565	0.656	INDETERMINATE	1	TRUE	1	0.802568228584008	3		479	472	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776372	76776372	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0051018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	173	173	0	ENST00000373344.5:c.7094C>G	p.Ser2365Ter	p.S2365*	ENST00000373344	NM_000489.3	2365	tCa/tGa	34/35	0.499662964953965	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.918650521729205	2		173	369	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971026	21971026	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	401	468	0	ENST00000304494.5:c.332del	p.Gly111AlafsTer35	p.G111Afs*35	ENST00000304494	NM_000077.4	111	gGc/gc	2/3	0.904825571106256	2	FACETS	0.968	0.948	0.986	0.968	0.948	0.986	CLONAL	2	TRUE	0	0.918650521729205	2		468	451	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717719	89717720	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs780264945	NA	P-0051018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	366	382	1	ENST00000371953.3:c.750_751del	p.Cys250TrpfsTer2	p.C250Wfs*2	ENST00000371953	NM_000314.4	248	ccTGtg/cctg	7/9	0.918650521729205	2	FACETS	0.942	0.919	0.963	0.942	0.919	0.963	CLONAL	2	TRUE	0	0.918650521729205	2		383	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579312	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0051018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	375	612	0	ENST00000269305.4:c.375_375+1delinsTT		p.X125_splice	ENST00000269305	NM_001126112.2	125		4/11	0.913542193172882	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.918650521729205	2		612	405	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057868	27057868	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	228	646	0	ENST00000324856.7:c.1576C>G	p.Pro526Ala	p.P526A	ENST00000324856	NM_006015.4	526	Cca/Gca	3/20	0.462071096057373	4	FACETS	1	0.985	1	0.394	0.368	0.421	INDETERMINATE	1	TRUE	1	0.918650521729205	4		646	805	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203607	108203607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	152	225	0	ENST00000278616.4:c.7907C>T	p.Thr2636Ile	p.T2636I	ENST00000278616	NM_000051.3	2636	aCt/aTt	53/63	0.500452400027206	4	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.918650521729205	4		225	480	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619912	21619912	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1339022400	NA	P-0051018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	209	516	0	ENST00000382592.4:c.254T>C	p.Leu85Ser	p.L85S	ENST00000382592	NM_014572.2	85	tTg/tCg	2/8	1	2	FACETS	0.946	0.888	1	0.946	0.888	1	CLONAL	1	TRUE	1	0.918650521729205	2		516	481	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602478	10602478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	315	861	0	ENST00000171111.5:c.1100G>A	p.Gly367Asp	p.G367D	ENST00000171111	NM_203500.1	367	gGc/gAc	3/6	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.918650521729205	2		861	648	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728800	190728800	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	186	314	0	ENST00000441310.2:c.2188C>A	p.Leu730Ile	p.L730I	ENST00000441310	NM_000534.4	730	Ctc/Atc	10/13	0.918650521729205	3	FACETS	0.879	0.815	0.945	0.44	0.407	0.473	CLONAL	1	TRUE	1	0.918650521729205	3		314	672	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164704	32164704	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	240	596	1	ENST00000375023.3:c.5198G>A	p.Trp1733Ter	p.W1733*	ENST00000375023	NM_004557.3	1733	tGg/tAg	28/30	0.870284773484411	3	FACETS	1	0.977	1	0.541	0.507	0.575	CLONAL	1	TRUE	1	0.918650521729205	3		597	705	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93953257	93953257	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	184	271	0	ENST00000369303.4:c.2884G>T	p.Asp962Tyr	p.D962Y	ENST00000369303	NM_004440.3	962	Gat/Tat	17/17	NA	2	FACETS	0.779	0.725	0.835			1	INDETERMINATE	1	TRUE	NA	0.918650521729205	2		271	514	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637121	93637121	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	377	430	0	ENST00000375746.1:c.1171C>G	p.Gln391Glu	p.Q391E	ENST00000375746	NM_001174167.1	391	Caa/Gaa	9/14	0.913542193172882	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.918650521729205	2		430	398	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156716	20156721	+	inframe_deletion	In_Frame_Del	DEL	CTGCGT	CTGCGT	-	novel	NA	P-0051018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	171	154	0	ENST00000379607.5:c.36_41del	p.Arg13_Arg14del	p.R13_R14del	ENST00000379607	NM_001412.3	12	agACGCAGg/agg	2/7	0.499662964953965	2	FACETS	0.947	0.883	1			1	INDETERMINATE	1	TRUE	NA	0.918650521729205	2		154	393	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228216	53228216	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	484	344	0	ENST00000375401.3:c.2186T>C	p.Val729Ala	p.V729A	ENST00000375401	NM_004187.3	729	gTc/gCc	15/26	0.499662964953965	2	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.918650521729205	2		344	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912656	NA	P-0051019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	34	563	0	ENST00000269305.4:c.734G>C	p.Gly245Ala	p.G245A	ENST00000269305	NM_001126112.2	245	gGc/gCc	7/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		563	606	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972575	32972575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80359251	NA	P-0051019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	37	484	0	ENST00000380152.3:c.9925G>A	p.Glu3309Lys	p.E3309K	ENST00000380152		3309	Gaa/Aaa	27/27	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		484	379	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348967	70348967	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	34	545	0	ENST00000374080.3:c.3479G>T	p.Cys1160Phe	p.C1160F	ENST00000374080		1160	tGt/tTt	25/45	0.221594007163505	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		545	440	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0051020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	342	513	0	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	0.606788552299732	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.611864904795865	2		513	548	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679334	29679346	+	frameshift_variant	Frame_Shift_Del	DEL	CCACCTATCCAAC	CCACCTATCCAAC	-	novel	NA	P-0051020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	244	377	0	ENST00000356175.3:c.7454_7466del	p.Ala2485ValfsTer13	p.A2485Vfs*13	ENST00000356175	NM_000267.3	2485	gCCACCTATCCAACt/gt	50/57	0.606788552299732	2	FACETS	0.985	0.937	1	0.985	0.937	1	CLONAL	2	TRUE	0	0.611864904795865	2		377	405	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0051026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	77	479	1	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.203404347479426	2		480	744	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417887	32417887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1564972874	NA	P-0051026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	74	527	1	ENST00000332351.3:c.1165C>T	p.Arg389Cys	p.R389C	ENST00000332351	NM_024426.4	389	Cgc/Tgc	7/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.203404347479426	2		528	620	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578260	7578260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204041	NA	P-0051026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	78	592	0	ENST00000269305.4:c.589G>A	p.Val197Met	p.V197M	ENST00000269305	NM_001126112.2	197	Gtg/Atg	6/11	NA	2	FACETS	1	0.952	1			1	INDETERMINATE	1	TRUE	NA	0.203404347479426	2		592	658	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349508	89349508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143417087	NA	P-0051026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	70	649	0	ENST00000301030.4:c.3442G>A	p.Gly1148Ser	p.G1148S	ENST00000301030	NM_001256183.1	1148	Ggc/Agc	9/13	1	2	FACETS	0.967	0.842	1	0.967	0.842	1	CLONAL	1	TRUE	1	0.203404347479426	2		649	712	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245993	46245993	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	59	300	0	ENST00000334344.6:c.4087del	p.Asp1363IlefsTer10	p.D1363Ifs*10	ENST00000334344	NM_152641.2	1363	Gat/at	15/21	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.203404347479426	2		300	550	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099319	4099319	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	78	722	0	ENST00000262948.5:c.799A>G	p.Ile267Val	p.I267V	ENST00000262948	NM_030662.3	267	Atc/Gtc	7/11	1	2	FACETS	0.976	0.856	1	0.976	0.856	1	CLONAL	1	TRUE	1	0.203404347479426	2		722	786	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155638	106155638	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	60	357	0	ENST00000380013.4:c.539A>C	p.Gln180Pro	p.Q180P	ENST00000380013	NM_001127208.2	180	cAg/cCg	3/11	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.203404347479426	2		357	586	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0051027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	169	571	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.464752348076387	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.464752348076387	1		571	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0051028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	82	567	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.817	0.721	0.921	0.817	0.721	0.921	CLONAL	1	TRUE	1	0.309178034229786	2		567	649	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0051028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	70	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.1774573340364	0	FACETS	0.734	0.643	0.832			1	INDETERMINATE	1	TRUE	0	0.309178034229786	0		436	426	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591865	48591865	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0051028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	64	500	0	ENST00000342988.3:c.1028C>G	p.Ser343Ter	p.S343*	ENST00000342988	NM_005359.5	343	tCa/tGa	9/12	0.309178034229786	1	FACETS	0.916	0.797	1	0.916	0.797	1	CLONAL	1	TRUE	0	0.309178034229786	1		500	382	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497949	25497949	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	80	630	0	ENST00000264709.3:c.500G>A	p.Arg167Gln	p.R167Q	ENST00000264709	NM_175629.2	167	cGg/cAg	6/23	1	2	FACETS	0.786	0.692	0.887	0.786	0.692	0.887	SUBCLONAL	1	TRUE	1	0.309178034229786	2		630	658	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028638	12028638	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	71	399	0	ENST00000353533.5:c.841C>T	p.Arg281Ter	p.R281*	ENST00000353533	NM_003010.3	281	Cga/Tga	8/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.309178034229786	2		399	371	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495616	56495616	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	42	565	0	ENST00000267101.3:c.3806G>A	p.Gly1269Glu	p.G1269E	ENST00000267101	NM_001982.3	1269	gGa/gAa	28/28	0.309178034229786	5	FACETS	0.484	0.403	0.575			1	SUBCLONAL	1	TRUE	NA	0.309178034229786	5		565	821	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0051030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	175	362	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.382544394835987	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	1	0.382544394835987	4		362	368	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	114	397	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.298613859472097	4	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	2	0.382544394835987	4		397	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574030	7574030	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	172	523	0	ENST00000269305.4:c.997del	p.Arg333ValfsTer12	p.R333Vfs*12	ENST00000269305	NM_001126112.2	333	Cgt/gt	10/11	0.382544394835987	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.382544394835987	2		523	360	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602335	10602335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	137	741	0	ENST00000171111.5:c.1243C>T	p.Arg415Cys	p.R415C	ENST00000171111	NM_203500.1	415	Cgc/Tgc	3/6	0.382544394835987	1	FACETS	0.823	0.758	0.889	1	0.99	1	CLONAL	2	TRUE	0	0.382544394835987	1		741	352	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845564	63845564	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	45	235	0	ENST00000279873.7:c.1306del	p.Thr436GlnfsTer43	p.T436Qfs*43	ENST00000279873	NM_032199.2	435	Aaa/aa	9/10	0.189180719645982	4	FACETS	1	0.94	1	0.621	0.525	0.724	INDETERMINATE	1	TRUE	2	0.382544394835987	4		235	262	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183705	10183706	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0051031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	203	565	0	ENST00000256474.2:c.176dup	p.Arg60AlafsTer72	p.R60Afs*72	ENST00000256474	NM_000551.3	58	-/C	1/3	0.582850661722033	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.582850661722033	1		565	470	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696268	52696268	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	105	398	0	ENST00000394830.3:c.409G>C	p.Ala137Pro	p.A137P	ENST00000394830	NM_018313.4	137	Gct/Cct	5/30	0.582850661722033	1	FACETS	0.896	0.815	0.979	0.896	0.815	0.979	CLONAL	1	TRUE	0	0.582850661722033	1		398	285	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177011	56177014	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	-	novel	NA	P-0051032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	32	339	0	ENST00000399503.3:c.2286_2289del	p.Arg763CysfsTer35	p.R763Cfs*35	ENST00000399503	NM_005921.1	761	ATAGat/at	13/20	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	FALSE	1	0.496789753672882	2		339	91	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003747	45003747	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs1057519877	NA	P-0051033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	60	553	0	ENST00000558401.1:c.3G>A	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	atG/atA	1/4	0.473539612362535	2	FACETS	0.532	0.46	0.611	0.266	0.23	0.306	SUBCLONAL	1	TRUE	0	0.546979588685727	2		553	412	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031885	26031885	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	78	375	0	ENST00000244661.2:c.404G>C	p.Arg135Thr	p.R135T	ENST00000244661	NM_003537.3	135	aGa/aCa	1/1	0.499876936788473	2	FACETS	0.689	0.608	0.775	0.344	0.304	0.388	SUBCLONAL	1	TRUE	0	0.546979588685727	2		375	414	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747137	40747137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752831315	NA	P-0051033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	210	436	2	ENST00000373198.4:c.2945C>T	p.Pro982Leu	p.P982L	ENST00000373198	NM_133170.3	982	cCg/cTg	22/32	0.546979588685727	2	FACETS	1	0.99	1	0.668	0.624	0.712	CLONAL	1	TRUE	0	0.546979588685727	2		438	575	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857275	9857275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426934537	NA	P-0051033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	236	489	0	ENST00000330684.3:c.4126C>T	p.Arg1376Cys	p.R1376C	ENST00000330684	NM_001134407.1	1376	Cgc/Tgc	13/13	0.172696519411201	5	FACETS	0.952	0.891	1	0.635	0.594	0.677	INDETERMINATE	2	TRUE	2	0.546979588685727	5		489	825	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906964	32906964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	97	239	0	ENST00000380152.3:c.1349C>T	p.Ser450Phe	p.S450F	ENST00000380152		450	tCt/tTt	10/27	0.345453898741006	5	FACETS	1	0.908	1			1	CLONAL	1	TRUE	NA	0.546979588685727	5		239	634	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972595	32972596	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0051033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	50	304	0	ENST00000380152.3:c.9946_9947del	p.Glu3316ThrfsTer10	p.E3316Tfs*10	ENST00000380152		3315	aaAGaa/aaaa	27/27	0.345453898741006	5	FACETS	0.473	0.401	0.554			1	SUBCLONAL	1	TRUE	NA	0.546979588685727	5		304	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577118	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs1567547933	NA	P-0051033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	501	547	0	ENST00000269305.4:c.820_821del	p.Val274LeufsTer31	p.V274Lfs*31	ENST00000269305	NM_001126112.2	274	GTt/t	8/11	0.478362470425986	3	FACETS	0.889	0.858	0.92	0.889	0.858	0.92	CLONAL	3	TRUE	0	0.546979588685727	3		547	875	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142913	7142913	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	173	706	0	ENST00000302850.5:c.2456G>C	p.Arg819Pro	p.R819P	ENST00000302850	NM_000208.2	819	cGc/cCc	12/22	0.495322071125985	2	FACETS	0.904	0.834	0.976	0.452	0.417	0.488	CLONAL	1	TRUE	0	0.546979588685727	2		706	700	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793537	42793537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	200	703	0	ENST00000575354.2:c.1339G>A	p.Glu447Lys	p.E447K	ENST00000575354	NM_015125.3	447	Gaa/Aaa	8/20	0.490855616532885	3	FACETS	0.931	0.863	1	0.31	0.287	0.334	CLONAL	1	TRUE	0	0.546979588685727	3		703	1000	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019229	31019229	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	115	422	0	ENST00000375687.4:c.824C>A	p.Ala275Asp	p.A275D	ENST00000375687	NM_015338.5	275	gCc/gAc	9/13	0.349524762799094	4	FACETS	0.819	0.738	0.905			1	CLONAL	1	TRUE	NA	0.546979588685727	4		422	794	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0051037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	93	484	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.12618106847582	4	FACETS	0.91	0.812	1	0.91	0.812	1	INDETERMINATE	2	TRUE	2	0.24	4		484	528	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717615	89717615	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909227	NA	P-0051037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	62	341	0	ENST00000371953.3:c.640C>T	p.Gln214Ter	p.Q214*	ENST00000371953	NM_000314.4	214	Cag/Tag	7/9	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.24	2		341	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579536	7579536	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567556930	NA	P-0051037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	122	705	1	ENST00000269305.4:c.151G>T	p.Glu51Ter	p.E51*	ENST00000269305	NM_001126112.2	51	Gaa/Taa	4/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.24	2		706	872	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874261	155874261	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs483352822	NA	P-0051037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	42	516	0	ENST00000368323.3:c.270G>T	p.Met90Ile	p.M90I	ENST00000368323	NM_006912.5	90	atG/atT	5/6	1	2	FACETS	0.48	0.4	0.57	0.48	0.4	0.57	SUBCLONAL	1	TRUE	1	0.24	2		516	729	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958295	11958295	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	44	335	0	ENST00000353533.5:c.205C>T	p.Gln69Ter	p.Q69*	ENST00000353533	NM_003010.3	69	Caa/Taa	2/11	1	2	FACETS	0.861	0.73	1	1	0.968	1	CLONAL	2	TRUE	1	0.24	2		335	213	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857203	9857203	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	88	487	0	ENST00000330684.3:c.4198T>C	p.Tyr1400His	p.Y1400H	ENST00000330684	NM_001134407.1	1400	Tat/Cat	13/13	0.111541083181131	3	FACETS	1	0.903	1	0.511	0.452	0.575	INDETERMINATE	1	TRUE	1	0.24	3		487	803	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602854	10602854	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	141	777	0	ENST00000171111.5:c.724G>A	p.Glu242Lys	p.E242K	ENST00000171111	NM_203500.1	242	Gag/Aag	3/6	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.24	2		777	1095	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36934859	36934859	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0051037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	26	335	0	ENST00000361632.4:c.1475-1G>T		p.X492_splice	ENST00000361632		492			1	2	FACETS	0.543	0.43	0.673	0.543	0.43	0.673	SUBCLONAL	1	TRUE	1	0.24	2		335	399	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89862344	89862344	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs758641682	NA	P-0051037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	100	510	0	ENST00000389301.3:c.976C>G	p.Gln326Glu	p.Q326E	ENST00000389301	NM_000135.2	326	Cag/Gag	11/43	0.111541083181131	3	FACETS	1	0.945	1	0.546	0.487	0.609	INDETERMINATE	1	TRUE	1	0.24	3		510	854	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588809	29588809	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	69	329	0	ENST00000356175.3:c.4595C>T	p.Pro1532Leu	p.P1532L	ENST00000356175	NM_000267.3	1532	cCt/cTt	34/57	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.24	2		329	454	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024357	31024357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	40	557	0	ENST00000375687.4:c.3842C>T	p.Ser1281Phe	p.S1281F	ENST00000375687	NM_015338.5	1281	tCc/tTc	13/13	1	2	FACETS	0.435	0.36	0.518	0.435	0.36	0.518	SUBCLONAL	1	TRUE	1	0.24	2		557	767	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540337	187540337	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	91	482	1	ENST00000441802.2:c.7403C>T	p.Ser2468Phe	p.S2468F	ENST00000441802	NM_005245.3	2468	tCt/tTt	10/27	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.24	2		483	569	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100725	8100726	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1564399278	NA	P-0051039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	202	481	0	ENST00000346208.3:c.701dup	p.Ser237GlnfsTer66	p.S237Qfs*66	ENST00000346208		233	-/T	3/6	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.63631107406593	2		481	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578260	7578266	+	frameshift_variant	Frame_Shift_Del	DEL	CTCGGAT	CTCGGAT	-	novel	NA	P-0051039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	209	467	0	ENST00000269305.4:c.583_589del	p.Ile195TrpfsTer50	p.I195Wfs*50	ENST00000269305	NM_001126112.2	195	ATCCGAGtg/tg	6/11	0.63631107406593	1	FACETS	0.97	0.911	1	0.97	0.911	1	CLONAL	1	TRUE	0	0.63631107406593	1		467	462	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138452214	138452214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	174	314	0	ENST00000289153.2:c.1039G>A	p.Glu347Lys	p.E347K	ENST00000289153	NM_006219.2	347	Gaa/Aaa	6/22	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.63631107406593	2		314	504	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294082	1294082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1478454852	NA	P-0051039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	184	703	0	ENST00000310581.5:c.919C>T	p.Pro307Ser	p.P307S	ENST00000310581	NM_198253.2	307	Ccc/Tcc	2/16	0.49700573684631	1	FACETS	0.446	0.412	0.482	0.446	0.412	0.482	SUBCLONAL	1	TRUE	0	0.63631107406593	1		703	884	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797150	42797150	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	162	831	0	ENST00000575354.2:c.3512G>A	p.Arg1171Gln	p.R1171Q	ENST00000575354	NM_015125.3	1171	cGg/cAg	15/20	0.120515338191673	4	FACETS	1	0.977	1	1	0.977	1	INDETERMINATE	2	TRUE	2	0.277809686464896	4		831	640	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120890	94120890	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0051042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	14	333	0	ENST00000369303.4:c.163-2A>C		p.X55_splice	ENST00000369303	NM_004440.3	55			0.277809686464896	2	FACETS	0.395	0.285	0.528	0.198	0.142	0.264	SUBCLONAL	1	TRUE	0	0.277809686464896	2		333	255	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43806175	43806175	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs777235976	NA	P-0051043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	193	217	0	ENST00000372470.3:c.971C>A	p.Pro324His	p.P324H	ENST00000372470	NM_005373.2	324	cCc/cAc	6/12	0.437186218559737	2	FACETS	0.883	0.826	0.94	0.883	0.826	0.94	CLONAL	2	TRUE	0	0.492407248467228	2		217	444	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166386	118166387	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0051043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	90	237	0	ENST00000369448.3:c.902_903dup	p.Ser302GlufsTer8	p.S302Efs*8	ENST00000369448	NM_017709.3	299	gaa/gaAGa	2/2	0.496647774334829	4	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	2	0.492407248467228	4		237	260	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435588	18435588	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	29	148	0	ENST00000266497.5:c.573G>T	p.Glu191Asp	p.E191D	ENST00000266497		191	gaG/gaT	1/31	0.492407248467228	6	FACETS	0.779	0.634	0.94	0.39	0.317	0.47	CLONAL	2	TRUE	2	0.492407248467228	6		148	150	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926888	112926888	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507546	NA	P-0051043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	89	572	0	ENST00000351677.2:c.1508G>T	p.Gly503Val	p.G503V	ENST00000351677	NM_002834.3	503	gGg/gTg	13/16	0.382623826309442	3	FACETS	1	0.979	1	0.711	0.637	0.788	CLONAL	1	TRUE	1	0.492407248467228	3		572	317	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781823	3781823	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs372308925	NA	P-0051043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	164	322	0	ENST00000262367.5:c.4844A>G	p.Asn1615Ser	p.N1615S	ENST00000262367	NM_004380.2	1615	aAt/aGt	29/31	0.447013230854145	4	FACETS	0.853	0.787	0.921	0.853	0.787	0.921	CLONAL	2	TRUE	2	0.492407248467228	4		322	583	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862866	9862866	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	191	392	0	ENST00000330684.3:c.2437G>T	p.Asp813Tyr	p.D813Y	ENST00000330684	NM_001134407.1	813	Gac/Tac	12/13	0.447013230854145	4	FACETS	0.893	0.83	0.959	0.893	0.83	0.959	CLONAL	2	TRUE	2	0.492407248467228	4		392	648	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614926	23614926	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1249960937	NA	P-0051043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	133	226	0	ENST00000261584.4:c.3415A>T	p.Ile1139Phe	p.I1139F	ENST00000261584	NM_024675.3	1139	Att/Ttt	13/13	0.447013230854145	4	FACETS	0.942	0.863	1	0.942	0.863	1	CLONAL	2	TRUE	2	0.492407248467228	4		226	428	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348652	89348652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1487348306	NA	P-0051043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	39	295	1	ENST00000301030.4:c.4298C>T	p.Ser1433Phe	p.S1433F	ENST00000301030	NM_001256183.1	1433	tCc/tTc	9/13	0.447013230854145	4	FACETS	0.721	0.599	0.855	0.36	0.299	0.428	SUBCLONAL	1	TRUE	2	0.492407248467228	4		296	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	235	319	0	ENST00000269305.4:c.734del	p.Gly245AlafsTer2	p.G245Afs*2	ENST00000269305	NM_001126112.2	245	gGc/gc	7/11	0.440395750388805	2	FACETS	0.897	0.845	0.949	0.897	0.845	0.949	CLONAL	2	TRUE	0	0.492407248467228	2		319	532	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39690038	39690038	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	71	98	0	ENST00000361337.2:c.63del	p.His22IlefsTer81	p.H22Ifs*81	ENST00000361337	NM_003286.2	21	tcT/tc	3/21	0.37284718455925	6	FACETS	0.917	0.815	1	0.688	0.611	0.768	CLONAL	3	TRUE	2	0.492407248467228	6		98	208	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967173	134967173	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370164002	NA	P-0051043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	78	249	0	ENST00000398015.3:c.2512G>A	p.Glu838Lys	p.E838K	ENST00000398015	NM_004441.4	838	Gag/Aag	14/16	0.496647774334829	4	FACETS	0.731	0.642	0.826	0.244	0.214	0.276	SUBCLONAL	1	TRUE	1	0.492407248467228	4		249	647	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599258	55599258	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	34	210	0	ENST00000288135.5:c.2384C>T	p.Ala795Val	p.A795V	ENST00000288135	NM_000222.2	795	gCc/gTc	17/21	0.399330561466014	2	FACETS	1	0.926	1	0.606	0.506	0.712	CLONAL	1	TRUE	0	0.492407248467228	2		210	114	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293797	1293797	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	438	519	0	ENST00000310581.5:c.1204C>A	p.Gln402Lys	p.Q402K	ENST00000310581	NM_198253.2	402	Cag/Aag	2/16	0.43790826377974	5	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	2	0.492407248467228	5		519	978	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486247	8486247	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	37	233	0	ENST00000356435.5:c.2570G>C	p.Arg857Pro	p.R857P	ENST00000356435		857	cGt/cCt	17/35	0.496647774334829	1	FACETS	0.532	0.442	0.63	0.532	0.442	0.63	SUBCLONAL	1	TRUE	0	0.492407248467228	1		233	213	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974721	21974721	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	58	233	0	ENST00000304494.5:c.106del	p.Ala36ArgfsTer17	p.A36Rfs*17	ENST00000304494	NM_000077.4	36	Gcg/cg	1/3	0.496647774334829	1	FACETS	0.728	0.632	0.829	0.728	0.632	0.829	SUBCLONAL	1	TRUE	0	0.492407248467228	1		233	244	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	112	276	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		276	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0051048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	70	603	2	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.199506625674902	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	0	0.212271466551803	1		605	560	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913558	32913559	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359479	NA	P-0051048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	80	350	1	ENST00000380152.3:c.5073dup	p.Trp1692MetfsTer3	p.W1692Mfs*3	ENST00000380152		1689	gca/gcAa	11/27	0.212271466551803	2	FACETS	1	0.977	1	0.745	0.657	0.838	CLONAL	1	TRUE	0	0.212271466551803	2		351	506	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665820	29665824	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TAAGG	TAAGG	-	novel	NA	P-0051048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	17	159	0	ENST00000356175.3:c.6858_6858+4del		p.X2286_splice	ENST00000356175	NM_000267.3	2286		45/57	0.0624213193827043	3	FACETS	0.647	0.483	0.841	0.323	0.241	0.421	INDETERMINATE	1	TRUE	1	0.212271466551803	3		159	274	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729874	30729887	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGAAGTAAAAGATT	AGAAGTAAAAGATT	CAA	novel	NA	P-0051048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	26	305	1	ENST00000295754.5:c.1397-2_1408delinsCAA		p.X466_splice	ENST00000295754	NM_003242.5	466		6/7	0.0624213193827043	3	FACETS	0.619	0.489	0.767	0.309	0.244	0.384	INDETERMINATE	1	TRUE	1	0.212271466551803	3		306	438	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910382	29910382	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	96	828	0	ENST00000376809.5:c.52G>C	p.Ala18Pro	p.A18P	ENST00000376809	NM_002116.7	18	Gcc/Ccc	1/8	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.212271466551803	2		828	874	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971209	21971209	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1554654224	NA	P-0051048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	57	416	2	ENST00000304494.5:c.151-2A>G		p.X51_splice	ENST00000304494	NM_000077.4	51			0.212271466551803	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.212271466551803	1		418	432	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0051050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	102	396	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.278244996520766	3	FACETS	0.975	0.886	1			1	INDETERMINATE	2	TRUE	NA	0.476233614049331	3		396	272	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0051050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	66	394	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.476233614049331	2		394	273	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609655	81609655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	137	485	0	ENST00000298171.2:c.1253G>A	p.Arg418Lys	p.R418K	ENST00000298171	NM_000369.2	418	aGa/aAa	10/10	1	2	FACETS	0.905	0.825	0.987	0.905	0.825	0.987	CLONAL	1	TRUE	1	0.476233614049331	2		485	636	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630683	158630683	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146610930	NA	P-0051050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	59	233	0	ENST00000263640.3:c.560C>T	p.Ser187Leu	p.S187L	ENST00000263640	NM_001105.4	187	tCg/tTg	6/11	0.306232012782679	1	FACETS	0.949	0.829	1	0.949	0.829	1	CLONAL	1	TRUE	0	0.476233614049331	1		233	199	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268959	55268959	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148019583	NA	P-0051050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	187	523	0	ENST00000275493.2:c.3025G>A	p.Asp1009Asn	p.D1009N	ENST00000275493	NM_005228.3	1009	Gac/Aac	25/28	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.476233614049331	2		523	763	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455143	50455143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	90	366	0	ENST00000331340.3:c.690G>A	p.Met230Ile	p.M230I	ENST00000331340	NM_006060.4	230	atG/atA	6/8	1	2	FACETS	0.863	0.77	0.961	0.863	0.77	0.961	CLONAL	1	TRUE	1	0.476233614049331	2		366	438	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16248769	16248769	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	75	339	0	ENST00000375759.3:c.1775A>G	p.Gln592Arg	p.Q592R	ENST00000375759	NM_015001.2	592	cAg/cGg	10/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.476233614049331	2		339	262	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198888	67198889	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0051050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	125	479	2	ENST00000312629.5:c.359_360delinsAA	p.Arg120Gln	p.R120Q	ENST00000312629	NM_003952.2	120	cGG/cAA	5/15	1	2	FACETS	0.851	0.772	0.933	0.851	0.772	0.933	CLONAL	1	TRUE	1	0.476233614049331	2		481	617	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254005	133254006	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0051050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	103	414	1	ENST00000320574.5:c.744_745delinsTT	p.Arg249Ter	p.R249*	ENST00000320574	NM_006231.2	248	taCCga/taTTga	8/49	1	2	FACETS	0.979	0.881	1	0.979	0.881	1	CLONAL	1	TRUE	1	0.476233614049331	2		415	442	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679174	88679174	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	149	415	1	ENST00000360948.2:c.863A>G	p.Asn288Ser	p.N288S	ENST00000360948	NM_001012338.2	288	aAc/aGc	8/19	1	2	FACETS	0.926	0.848	1	0.926	0.848	1	CLONAL	1	TRUE	1	0.476233614049331	2		416	676	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348098	89348098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	82	578	0	ENST00000301030.4:c.4852C>T	p.Pro1618Ser	p.P1618S	ENST00000301030	NM_001256183.1	1618	Ccc/Tcc	9/13	0.413192758069741	1	FACETS	0.343	0.302	0.388	0.343	0.302	0.388	SUBCLONAL	1	TRUE	0	0.476233614049331	1		578	764	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374888	45374888	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	24	459	0	ENST00000262160.6:c.955G>C	p.Val319Leu	p.V319L	ENST00000262160	NM_005901.5	319	Gtt/Ctt	8/11	1	2	FACETS	0.253	0.197	0.316	0.253	0.197	0.316	SUBCLONAL	1	TRUE	1	0.476233614049331	2		459	399	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11018775	11018777	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0051050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	126	679	0	ENST00000327064.4:c.408_410del	p.Phe137del	p.F137del	ENST00000327064	NM_199141.1	136	gTGTtc/gtc	3/16	1	2	FACETS	0.632	0.572	0.695	0.632	0.572	0.695	SUBCLONAL	1	TRUE	1	0.476233614049331	2		679	837	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216178	36216178	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	262	668	0	ENST00000222270.7:c.3586G>T	p.Val1196Leu	p.V1196L	ENST00000222270	NM_014727.1	1196	Gtg/Ttg	11/37	0.476233614049331	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.476233614049331	1		668	694	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719020	190719020	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	42	223	0	ENST00000441310.2:c.1022C>G	p.Pro341Arg	p.P341R	ENST00000441310	NM_000534.4	341	cCt/cGt	9/13	0.306232012782679	1	FACETS	0.878	0.747	1	0.878	0.747	1	CLONAL	1	TRUE	0	0.476233614049331	1		223	153	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643793	52643802	+	frameshift_variant	Frame_Shift_Del	DEL	TTTAATAGTC	TTTAATAGTC	-	novel	NA	P-0051050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	92	484	0	ENST00000394830.3:c.2094_2103del	p.Thr699SerfsTer12	p.T699Sfs*12	ENST00000394830	NM_018313.4	698	ctGACTATTAAA/ct	17/30	0.476233614049331	1	FACETS	0.846	0.758	0.937	0.846	0.758	0.937	CLONAL	1	TRUE	0	0.476233614049331	1		484	348	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920241	1920241	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	147	553	0	ENST00000382891.5:c.1301G>A	p.Gly434Glu	p.G434E	ENST00000382891	NM_133335.3	434	gGa/gAa	5/22	1	2	FACETS	0.888	0.813	0.967	0.888	0.813	0.967	CLONAL	1	TRUE	1	0.476233614049331	2		553	695	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14026281	14026281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	63	319	0	ENST00000405192.2:c.163G>A	p.Glu55Lys	p.E55K	ENST00000405192	NM_001163147.1	55	Gaa/Aaa	4/12	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.476233614049331	2		319	258	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0051054-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	236	595	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.321966877987407	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.321966877987407	3		596	817	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0051054-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	208	487	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.321966877987407	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	2	0.321966877987407	4		487	815	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039368	47039369	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0051054-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	137	267	0	ENST00000377604.3:c.992dup	p.Arg332AlafsTer49	p.R332Afs*49	ENST00000377604	NM_001204468.1	331	gtg/gTtg	10/24	1	1	FACETS	0.904	0.831	0.979	1	0.99	1	CLONAL	2	TRUE	0	0.321966877987407	1		267	395	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494163	140494163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051054-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	103	428	0	ENST00000288602.6:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000288602	NM_004333.4	362	cGa/cAa	8/18	0.321966877987407	4	FACETS	0.913	0.816	1	0.457	0.408	0.509	CLONAL	1	TRUE	2	0.321966877987407	4		428	926	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1064795203	NA	P-0051054-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	98	505	0	ENST00000269305.4:c.532C>A	p.His178Asn	p.H178N	ENST00000269305	NM_001126112.2	178	Cac/Aac	5/11	0.321966877987407	3	FACETS	0.758	0.675	0.847	0.379	0.337	0.424	SUBCLONAL	1	TRUE	1	0.321966877987407	3		505	932	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655200	45655200	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051054-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	79	391	0	ENST00000407780.3:c.652G>C	p.Glu218Gln	p.E218Q	ENST00000407780	NM_001283052.1	218	Gag/Cag	4/7	0.165708424576998	5	FACETS	0.938	0.824	1	0.313	0.274	0.354	INDETERMINATE	1	TRUE	2	0.321966877987407	5		391	776	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575366	64575366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051054-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	94	398	0	ENST00000312049.6:c.651G>T	p.Glu217Asp	p.E217D	ENST00000312049	NM_130799.2	217	gaG/gaT	3/10	0.321966877987407	5	FACETS	0.888	0.789	0.995	0.296	0.263	0.332	CLONAL	1	TRUE	2	0.321966877987407	5		398	975	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923112	48923112	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051054-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	53	214	0	ENST00000267163.4:c.560C>G	p.Ser187Cys	p.S187C	ENST00000267163	NM_000321.2	187	tCt/tGt	6/27	0.321966877987407	2	FACETS	0.89	0.762	1	0.445	0.381	0.515	CLONAL	1	TRUE	0	0.321966877987407	2		214	370	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831455	89831455	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051054-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	77	358	0	ENST00000389301.3:c.2621G>C	p.Arg874Thr	p.R874T	ENST00000389301	NM_000135.2	874	aGa/aCa	28/43	0.321966877987407	5	FACETS	0.789	0.691	0.895	0.197	0.172	0.224	SUBCLONAL	1	TRUE	1	0.321966877987407	5		358	899	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265109	46265109	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051054-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	63	280	0	ENST00000371998.3:c.1979C>G	p.Ser660Cys	p.S660C	ENST00000371998		660	tCc/tGc	12/23	0.321966877987407	6	FACETS	0.902	0.779	1	0.226	0.194	0.259	CLONAL	1	TRUE	2	0.321966877987407	6		280	713	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034435	123034435	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051054-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	59	132	0	ENST00000355640.3:c.1192C>G	p.Gln398Glu	p.Q398E	ENST00000355640		398	Cag/Gag	6/7	1	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.321966877987407	1		132	261	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295377	1295377	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0051054-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	56	155	0				ENST00000310581	NM_198253.2	-/1132			0.321966877987407	7	FACETS	0.791	0.68	0.911	0.316	0.272	0.365	CLONAL	2	TRUE	2	0.321966877987407	7		155	397	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578530	7578530	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs267605077	NA	P-0051217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	146	181	0	ENST00000269305.4:c.400T>C	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	Ttt/Ctt	5/11	0.254468266799698	3	FACETS	0.994	0.914	1	0.663	0.609	0.718	CLONAL	2	FALSE	0	0.355973843065228	3		181	486	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180957	108180957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	57	34	0	ENST00000278616.4:c.5833G>A	p.Ala1945Thr	p.A1945T	ENST00000278616	NM_000051.3	1945	Gct/Act	39/63	0.355973843065228	6	FACETS	1	0.904	1			1	CLONAL	2	FALSE	NA	0.355973843065228	6		34	260	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642766	3642766	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs771002901	NA	P-0051217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	79	178	0	ENST00000294008.3:c.2261A>G	p.Tyr754Cys	p.Y754C	ENST00000294008	NM_032444.2	754	tAt/tGt	11/15	0.252298755921037	4	FACETS	1	0.94	1			1	CLONAL	1	FALSE	NA	0.355973843065228	4		178	543	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190742041	190742041	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1219791878	NA	P-0051217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	50	96	0	ENST00000441310.2:c.2678C>G	p.Ser893Ter	p.S893*	ENST00000441310	NM_000534.4	893	tCa/tGa	13/13	0.355973843065228	8	FACETS	0.791	0.674	0.92			1	CLONAL	2	FALSE	NA	0.355973843065228	8		96	367	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188297	10188298	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0051217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	84	88	0	ENST00000256474.2:c.443_444del	p.Phe148CysfsTer25	p.F148Cfs*25	ENST00000256474	NM_000551.3	147	aTT/a	2/3	0.226340612714037	4	FACETS	0.869	0.774	0.971	0.58	0.516	0.647	CLONAL	2	FALSE	1	0.355973843065228	4		88	368	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651336	52651336	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	92	93	0	ENST00000394830.3:c.1760T>A	p.Ile587Lys	p.I587K	ENST00000394830	NM_018313.4	587	aTa/aAa	15/30	0.226340612714037	4	FACETS	1	0.954	1	0.739	0.664	0.818	CLONAL	2	FALSE	1	0.355973843065228	4		93	316	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503997	186503997	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	45	33	0	ENST00000323963.5:c.562A>C	p.Met188Leu	p.M188L	ENST00000323963		188	Atg/Ctg	6/11	0.315623541636404	4	FACETS	1	0.953	1	0.678	0.574	0.79	CLONAL	1	FALSE	2	0.355973843065228	4		33	253	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786937	135786937	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	44	99	0	ENST00000298552.3:c.932del	p.Pro311LeufsTer7	p.P311Lfs*7	ENST00000298552	NM_001162426.1	311	cCt/ct	10/23	0.355973843065228	1	FACETS	0.716	0.604	0.838	0.716	0.604	0.838	SUBCLONAL	1	FALSE	0	0.355973843065228	1		99	284	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874311	76874311	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	56	107	0	ENST00000373344.5:c.5411C>G	p.Ala1804Gly	p.A1804G	ENST00000373344	NM_000489.3	1804	gCt/gGt	21/35	NA	2	FACETS	1	0.896	1			1	INDETERMINATE	1	FALSE	NA	0.355973843065228	2		107	301	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260171	16260171	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	143	792	1	ENST00000375759.3:c.7436A>T	p.Lys2479Met	p.K2479M	ENST00000375759	NM_015001.2	2479	aAg/aTg	11/15	1	2	FACETS	0.992	0.908	1	0.992	0.908	1	CLONAL	1	TRUE	1	0.456749060122668	2		793	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579464	7579485	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCCACGGGGGGAGCAGCCTC	GGGCCACGGGGGGAGCAGCCTC	-	novel	NA	P-0051218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	394	1326	1	ENST00000269305.4:c.202_223del	p.Glu68LeufsTer48	p.E68Lfs*48	ENST00000269305	NM_001126112.2	68	GAGGCTGCTCCCCCCGTGGCCCct/ct	4/11	0.419568658834078	2	FACETS	0.975	0.931	1	0.975	0.931	1	CLONAL	2	TRUE	0	0.456749060122668	2		1327	885	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0051243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	94	626	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	1	2	FACETS	0.825	0.733	0.924	0.825	0.733	0.924	CLONAL	1	TRUE	1	0.253111858232528	2		626	900	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962899	2962899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3735134	NA	P-0051243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	51	677	1	ENST00000396946.4:c.2009C>T	p.Thr670Met	p.T670M	ENST00000396946	NM_032415.4	670	aCg/aTg	16/25	1	2	FACETS	0.443	0.375	0.518	0.443	0.375	0.518	SUBCLONAL	1	TRUE	1	0.253111858232528	2		678	909	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798418	32798418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776413811	NA	P-0051243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	91	551	0	ENST00000374899.4:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000374899	NM_018833.2	480	Cgc/Tgc	8/12	1	2	FACETS	0.842	0.747	0.944	0.842	0.747	0.944	CLONAL	1	TRUE	1	0.253111858232528	2		551	854	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	464	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.708155953339174	4	FACETS	0.994	0.97	1	0.994	0.97	1	CLONAL	4	TRUE	0	0.708155953339174	4		334	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0051265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	474	475	1	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.68309107217992	2	FACETS	0.96	0.93	0.99	0.96	0.93	0.99	CLONAL	2	TRUE	0	0.708155953339174	2		476	697	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144898	47144898	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	100	390	0	ENST00000409792.3:c.4855C>T	p.Gln1619Ter	p.Q1619*	ENST00000409792	NM_014159.6	1619	Caa/Taa	7/21	0.666189534178459	2	FACETS	0.984	0.892	1	0.492	0.446	0.54	CLONAL	1	TRUE	0	0.708155953339174	2		390	287	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	144	276	0				ENST00000310581	NM_198253.2	-/1132			0.448921892382349	4	FACETS	0.843	0.776	0.913	0.843	0.776	0.913	CLONAL	2	TRUE	2	0.641228003303554	4		276	437	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	62	268	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.641228003303554	2		268	193	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	534	760	2	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	0.620616299007253	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.641228003303554	2		762	789	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222757	5222757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779903263	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	392	603	0	ENST00000357368.4:c.3046C>T	p.Arg1016Trp	p.R1016W	ENST00000357368	NM_002850.3	1016	Cgg/Tgg	18/38	0.630147647259205	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.641228003303554	2		603	594	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670708	134670708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	138	460	0	ENST00000398015.3:c.619C>T	p.Pro207Ser	p.P207S	ENST00000398015	NM_004441.4	207	Cca/Tca	3/16	0.603500744041289	3	FACETS	1	0.925	1	0.507	0.463	0.552	CLONAL	1	TRUE	1	0.641228003303554	3		460	561	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043904	180043904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56082504	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	282	518	0	ENST00000261937.6:c.3092G>A	p.Arg1031Gln	p.R1031Q	ENST00000261937	NM_182925.4	1031	cGa/cAa	22/30	0.448921892382349	4	FACETS	0.873	0.823	0.923	0.873	0.823	0.923	CLONAL	2	TRUE	2	0.641228003303554	4		518	827	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	137	280	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	0.641228003303554	3	FACETS	0.879	0.812	0.947	0.879	0.812	0.947	CLONAL	2	TRUE	1	0.641228003303554	3		280	321	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015115	37015115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	427	570	0	ENST00000358127.4:c.289G>A	p.Glu97Lys	p.E97K	ENST00000358127	NM_001280556.1	97	Gaa/Aaa	3/10	0.623774591561855	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.641228003303554	3		570	811	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965706	93965706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	11	404	1	ENST00000369303.4:c.2222G>A	p.Gly741Glu	p.G741E	ENST00000369303	NM_004440.3	741	gGa/gAa	13/17	0.319209975074241	3	FACETS	0.214	0.147	0.296	0.071	0.049	0.099	INDETERMINATE	1	TRUE	0	0.641228003303554	3		405	212	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417634	139417634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749786734	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	392	826	0	ENST00000277541.6:c.410C>T	p.Ser137Leu	p.S137L	ENST00000277541	NM_017617.3	137	tCg/tTg	4/34	0.623774591561855	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.641228003303554	3		826	791	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967209	93967209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	93	303	0	ENST00000369303.4:c.2143G>A	p.Glu715Lys	p.E715K	ENST00000369303	NM_004440.3	715	Gaa/Aaa	12/17	0.319209975074241	3	FACETS	1	0.961	1	0.726	0.664	0.787	INDETERMINATE	2	TRUE	0	0.641228003303554	3		303	176	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027128	49027128	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs794727199	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	46	237	0	ENST00000267163.4:c.1696-1G>A		p.X566_splice	ENST00000267163	NM_000321.2	566			0.641228003303554	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.641228003303554	1		237	86	SUCCESS
APC	324	MSKCC	GRCh37	5	112173476	112173476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	111	267	0	ENST00000257430.4:c.2185C>T	p.Leu729Phe	p.L729F	ENST00000257430	NM_000038.5	729	Ctc/Ttc	16/16	0.448921892382349	4	FACETS	0.922	0.841	1	0.922	0.841	1	CLONAL	2	TRUE	2	0.641228003303554	4		267	308	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240686	55240686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	371	598	0	ENST00000275493.2:c.1930C>T	p.Pro644Ser	p.P644S	ENST00000275493	NM_005228.3	644	Ccg/Tcg	17/28	0.641228003303554	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.641228003303554	3		598	734	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993714	72993714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266350809	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	177	589	0	ENST00000268489.5:c.331G>A	p.Glu111Lys	p.E111K	ENST00000268489	NM_006885.3	111	Gag/Aag	2/10	0.641228003303554	3	FACETS	1	0.984	1	0.617	0.571	0.664	CLONAL	1	TRUE	1	0.641228003303554	3		589	591	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857436	9857436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	214	410	0	ENST00000330684.3:c.3965G>A	p.Gly1322Glu	p.G1322E	ENST00000330684	NM_001134407.1	1322	gGa/gAa	13/13	0.641228003303554	3	FACETS	0.934	0.878	0.99	0.934	0.878	0.99	CLONAL	2	TRUE	1	0.641228003303554	3		410	472	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	100	361	0	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	0.641228003303554	3	FACETS	0.997	0.897	1	0.499	0.448	0.551	CLONAL	1	TRUE	1	0.641228003303554	3		361	413	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4387932	4387932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	293	435	0	ENST00000261254.3:c.418G>A	p.Glu140Lys	p.E140K	ENST00000261254	NM_001759.3	140	Gaa/Aaa	3/5	0.641228003303554	3	FACETS	0.999	0.949	1	0.999	0.949	1	CLONAL	2	TRUE	1	0.641228003303554	3		435	604	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790000	40790000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159843	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	239	489	0	ENST00000373198.4:c.2731G>A	p.Glu911Lys	p.E911K	ENST00000373198	NM_133170.3	911	Gaa/Aaa	18/32	0.641228003303554	3	FACETS	0.927	0.874	0.98	0.927	0.874	0.98	CLONAL	2	TRUE	1	0.641228003303554	3		489	531	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1953914	1953914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	242	844	0	ENST00000382891.5:c.2093C>T	p.Ser698Phe	p.S698F	ENST00000382891	NM_133335.3	698	tCc/tTc	11/22	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.641228003303554	2		844	686	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950498	38950498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	71	342	0	ENST00000357387.3:c.3452C>T	p.Ser1151Phe	p.S1151F	ENST00000357387	NM_152756.3	1151	tCc/tTc	31/38	0.448921892382349	4	FACETS	1	0.977	1	0.748	0.662	0.838	CLONAL	1	TRUE	2	0.641228003303554	4		342	243	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729363	41729363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	299	583	0	ENST00000242208.4:c.1166C>T	p.Ser389Leu	p.S389L	ENST00000242208	NM_002192.2	389	tCg/tTg	3/3	0.641228003303554	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.641228003303554	3		583	612	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212110	36212110	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	265	392	0	ENST00000222270.7:c.1861C>T	p.Pro621Ser	p.P621S	ENST00000222270	NM_014727.1	621	Cct/Tct	3/37	0.630147647259205	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.641228003303554	2		392	381	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771873	135771873	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	179	565	0	ENST00000298552.3:c.3244C>T	p.Pro1082Ser	p.P1082S	ENST00000298552	NM_001162426.1	1082	Ccc/Tcc	23/23	0.623774591561855	3	FACETS	1	0.952	1	0.519	0.48	0.56	CLONAL	1	TRUE	1	0.641228003303554	3		565	710	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378654	25378654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	101	351	0	ENST00000311936.3:c.344G>A	p.Gly115Glu	p.G115E	ENST00000311936	NM_004985.3	115	gGa/gAa	4/5	0.641228003303554	3	FACETS	0.954	0.872	1	0.954	0.872	1	CLONAL	2	TRUE	1	0.641228003303554	3		351	218	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547841	41547841	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	96	437	0	ENST00000263253.7:c.2822C>T	p.Ser941Phe	p.S941F	ENST00000263253	NM_001429.3	941	tCc/tTc	15/31	0.641228003303554	3	FACETS	0.809	0.723	0.899	0.404	0.361	0.45	CLONAL	1	TRUE	1	0.641228003303554	3		437	489	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933563	39933563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	346	375	0	ENST00000378444.4:c.1036C>T	p.Pro346Ser	p.P346S	ENST00000378444	NM_001123385.1	346	Ccc/Tcc	4/15	0.582657548692706	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.641228003303554	2		375	452	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261452	16261452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	176	654	0	ENST00000375759.3:c.8717G>A	p.Arg2906Lys	p.R2906K	ENST00000375759	NM_015001.2	2906	aGg/aAg	11/15	0.641228003303554	3	FACETS	1	0.967	1	0.541	0.5	0.583	CLONAL	1	TRUE	1	0.641228003303554	3		654	670	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458931	120458931	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	149	619	1	ENST00000256646.2:c.6414G>T	p.Lys2138Asn	p.K2138N	ENST00000256646	NM_024408.3	2138	aaG/aaT	34/34	0.641228003303554	3	FACETS	0.937	0.859	1	0.468	0.429	0.509	CLONAL	1	TRUE	1	0.641228003303554	3		620	655	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450914	70450914	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	132	455	0	ENST00000373644.4:c.5754G>T	p.Met1918Ile	p.M1918I	ENST00000373644	NM_030625.2	1918	atG/atT	12/12	1	2	FACETS	0.915	0.837	0.995	0.915	0.837	0.995	CLONAL	1	TRUE	1	0.641228003303554	2		455	450	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946229	71946229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	367	712	0	ENST00000298229.2:c.2485G>A	p.Asp829Asn	p.D829N	ENST00000298229	NM_001567.3	829	Gat/Aat	22/28	0.641228003303554	3	FACETS	1	0.993	1	0.649	0.616	0.683	CLONAL	1	TRUE	1	0.641228003303554	3		712	1164	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209304	133209304	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	197	741	0	ENST00000320574.5:c.6082A>G	p.Arg2028Gly	p.R2028G	ENST00000320574	NM_006231.2	2028	Agg/Ggg	44/49	0.623774591561855	3	FACETS	1	0.933	1	0.503	0.466	0.541	CLONAL	1	TRUE	1	0.641228003303554	3		741	807	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346781	91346781	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	175	357	0	ENST00000355112.3:c.3389T>A	p.Ile1130Lys	p.I1130K	ENST00000355112	NM_000057.2	1130	aTa/aAa	18/22	0.469592941563737	4	FACETS	0.966	0.909	1	0.966	0.909	1	CLONAL	3	TRUE	1	0.641228003303554	4		357	309	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640194	3640194	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	168	810	0	ENST00000294008.3:c.3445G>A	p.Asp1149Asn	p.D1149N	ENST00000294008	NM_032444.2	1149	Gat/Aat	12/15	0.641228003303554	3	FACETS	1	0.928	1	0.504	0.464	0.545	CLONAL	1	TRUE	1	0.641228003303554	3		810	687	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979644	7979644	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	284	515	0	ENST00000319144.4:c.1381G>A	p.Glu461Lys	p.E461K	ENST00000319144	NM_001139.2	461	Gaa/Aaa	11/15	0.620616299007253	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.641228003303554	2		515	442	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627767	37627767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1381636441	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	355	647	1	ENST00000447079.4:c.1682C>T	p.Pro561Leu	p.P561L	ENST00000447079	NM_015083.1	561	cCa/cTa	2/14	0.641228003303554	3	FACETS	0.953	0.909	0.997	0.953	0.909	0.997	CLONAL	2	TRUE	1	0.641228003303554	3		648	767	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426803	212426803	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	103	316	0	ENST00000342788.4:c.2312T>C	p.Ile771Thr	p.I771T	ENST00000342788	NM_005235.2	771	aTc/aCc	20/28	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.641228003303554	2		316	314	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662220	227662220	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	170	702	0	ENST00000305123.5:c.1235C>G	p.Ser412Cys	p.S412C	ENST00000305123	NM_005544.2	412	tCt/tGt	1/2	1	2	FACETS	0.89	0.822	0.959	0.89	0.822	0.959	CLONAL	1	TRUE	1	0.641228003303554	2		702	596	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268320	46268320	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs901894203	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	174	268	0	ENST00000371998.3:c.2708-1G>A		p.X903_splice	ENST00000371998		903			0.641228003303554	3	FACETS	0.946	0.883	1	0.946	0.883	1	CLONAL	2	TRUE	1	0.641228003303554	3		268	379	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866309	42866309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1037177177	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	373	646	1	ENST00000398585.3:c.323C>T	p.Ser108Phe	p.S108F	ENST00000398585	NM_001135099.1	108	tCc/tTc	3/14	0.641228003303554	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.641228003303554	3		647	744	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670384	134670384	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	102	399	0	ENST00000398015.3:c.295C>T	p.Leu99Phe	p.L99F	ENST00000398015	NM_004441.4	99	Ctc/Ttc	3/16	0.603500744041289	3	FACETS	1	0.919	1	0.511	0.46	0.564	CLONAL	1	TRUE	1	0.641228003303554	3		399	411	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968235	134968236	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	250	624	0	ENST00000398015.3:c.2748_2749delinsAA	p.Asp917Asn	p.D917N	ENST00000398015	NM_004441.4	916	gtGGat/gtAAat	15/16	0.603500744041289	3	FACETS	0.848	0.8	0.897	0.848	0.8	0.897	CLONAL	2	TRUE	1	0.641228003303554	3		624	607	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807641	1807641	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	285	819	0	ENST00000260795.2:c.1810G>A	p.Gly604Ser	p.G604S	ENST00000260795		604	Ggc/Agc	12/17	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.641228003303554	2		819	711	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141011	55141011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs992063980	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	69	314	0	ENST00000257290.5:c.1657C>T	p.Pro553Ser	p.P553S	ENST00000257290	NM_006206.4	553	Ccg/Tcg	12/23	1	2	FACETS	0.92	0.812	1	0.92	0.812	1	CLONAL	1	TRUE	1	0.641228003303554	2		314	234	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164878	106164878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1296610391	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	181	445	0	ENST00000380013.4:c.3746C>T	p.Thr1249Ile	p.T1249I	ENST00000380013	NM_001127208.2	1249	aCc/aTc	6/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.641228003303554	2		445	514	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876307	35876307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778406	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	186	513	0	ENST00000303115.3:c.1099C>T	p.Leu367Phe	p.L367F	ENST00000303115	NM_002185.3	367	Ctc/Ttc	8/8	0.448921892382349	4	FACETS	0.893	0.831	0.957	0.893	0.831	0.957	CLONAL	2	TRUE	2	0.641228003303554	4		513	533	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171997	32171997	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	192	522	1	ENST00000375023.3:c.3035A>T	p.Asp1012Val	p.D1012V	ENST00000375023	NM_004557.3	1012	gAc/gTc	19/30	0.641228003303554	5	FACETS	1	0.989	1	0.355	0.329	0.383	CLONAL	1	TRUE	1	0.641228003303554	5		523	827	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983329	149983329	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs754312046	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	195	474	0	ENST00000253339.5:c.2929C>G	p.Leu977Val	p.L977V	ENST00000253339		977	Ctc/Gtc	7/7	0.620616299007253	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.641228003303554	2		474	297	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968281	2968281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	175	795	1	ENST00000396946.4:c.1705G>A	p.Gly569Arg	p.G569R	ENST00000396946	NM_032415.4	569	Gga/Aga	13/25	0.641228003303554	3	FACETS	0.892	0.823	0.964	0.446	0.411	0.482	CLONAL	1	TRUE	1	0.641228003303554	3		796	808	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266409	55266409	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	77	376	0	ENST00000275493.2:c.2702-1G>A		p.X901_splice	ENST00000275493	NM_005228.3	901			0.641228003303554	3	FACETS	0.952	0.843	1	0.476	0.421	0.534	CLONAL	1	TRUE	1	0.641228003303554	3		376	333	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965647	90965647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1286743873	NA	P-0051266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	87	308	0	ENST00000265433.3:c.1670C>T	p.Ala557Val	p.A557V	ENST00000265433	NM_002485.4	557	gCc/gTc	11/16	0.603500744041289	3	FACETS	0.861	0.779	0.945	0.861	0.779	0.945	CLONAL	2	TRUE	1	0.641228003303554	3		308	208	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0051270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	181	366	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.69703601351388	2		366	515	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0051270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	190	265	0	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	1	2	FACETS	0.974	0.906	1	0.974	0.906	1	CLONAL	1	TRUE	1	0.69703601351388	2		265	560	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0051270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	557	332	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.69703601351388	2		332	720	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642495	117642495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs9489124	NA	P-0051270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	325	492	0	ENST00000368508.3:c.5704G>A	p.Glu1902Lys	p.E1902K	ENST00000368508	NM_002944.2	1902	Gaa/Aaa	35/43	1	2	FACETS	0.947	0.896	0.998	0.947	0.896	0.998	CLONAL	1	TRUE	1	0.69703601351388	2		492	985	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244982	123244982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	330	499	0	ENST00000358487.5:c.2122C>T	p.Pro708Ser	p.P708S	ENST00000358487	NM_000141.4	708	Ccc/Tcc	16/18	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.69703601351388	2		499	889	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730938	40730938	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0051270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	240	395	0	ENST00000373198.4:c.3598-1G>A		p.X1200_splice	ENST00000373198	NM_133170.3	1200			NA	2	FACETS	0.97	0.91	1			1	INDETERMINATE	1	TRUE	NA	0.69703601351388	2		395	710	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326496	62326496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	452	757	0	ENST00000360203.5:c.3421C>T	p.Pro1141Ser	p.P1141S	ENST00000360203	NM_001283009.1	1141	Ccg/Tcg	33/35	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.69703601351388	2		757	1249	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189349307	189349307	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0051270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	149	215	0	ENST00000264731.3:c.3G>A	p.Met1?	p.M1?	ENST00000264731	NM_003722.4	1	atG/atA	1/14	1	2	FACETS	0.942	0.868	1	0.942	0.868	1	CLONAL	1	TRUE	1	0.69703601351388	2		215	454	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553117	106553117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750485966	NA	P-0051270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	288	509	0	ENST00000369096.4:c.1082C>T	p.Ser361Phe	p.S361F	ENST00000369096	NM_001198.3	361	tCc/tTc	5/7	1	2	FACETS	0.972	0.917	1	0.972	0.917	1	CLONAL	1	TRUE	1	0.69703601351388	2		509	850	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367243	50367243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	172	286	0	ENST00000331340.3:c.50G>A	p.Ser17Asn	p.S17N	ENST00000331340	NM_006060.4	17	aGc/aAc	3/8	1	2	FACETS	0.863	0.798	0.929	0.863	0.798	0.929	CLONAL	1	TRUE	1	0.69703601351388	2		286	572	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133234459	133234459	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs139603739	NA	P-0051270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	247	360	1	ENST00000320574.5:c.3373C>T	p.Arg1125Ter	p.R1125*	ENST00000320574	NM_006231.2	1125	Cga/Tga	27/49	1	2	FACETS	0.951	0.893	1	0.951	0.893	1	CLONAL	1	TRUE	1	0.69703601351388	2		361	745	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245323	133245323	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	423	576	1	ENST00000320574.5:c.1924C>T	p.Pro642Ser	p.P642S	ENST00000320574	NM_006231.2	642	Ccc/Tcc	18/49	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.69703601351388	2		577	1121	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614510	38614510	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	231	329	0	ENST00000299084.4:c.276G>A	p.Trp92Ter	p.W92*	ENST00000299084	NM_152594.2	92	tgG/tgA	3/7	1	2	FACETS	0.98	0.919	1	0.98	0.919	1	CLONAL	1	TRUE	1	0.69703601351388	2		329	676	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134265	2134265	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	343	642	1	ENST00000219476.3:c.4042C>T	p.His1348Tyr	p.H1348Y	ENST00000219476	NM_000548.3	1348	Cac/Tac	34/42	1	2	FACETS	0.866	0.82	0.913	0.866	0.82	0.913	CLONAL	1	TRUE	1	0.69703601351388	2		643	1137	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992751	72992751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	206	588	0	ENST00000268489.5:c.1294G>A	p.Glu432Lys	p.E432K	ENST00000268489	NM_006885.3	432	Gag/Aag	2/10	0.190172799840305	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.69703601351388	0		588	755	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215544	5215545	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0051270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	386	736	1	ENST00000357368.4:c.4158_4159delinsAA	p.Ala1387Thr	p.A1387T	ENST00000357368	NM_002850.3	1386	aaGGcc/aaAAcc	27/38	1	2	FACETS	0.952	0.905	0.999	0.952	0.905	0.999	CLONAL	1	TRUE	1	0.69703601351388	2		737	1164	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231614	5231614	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	130	174	0	ENST00000357368.4:c.1862C>T	p.Pro621Leu	p.P621L	ENST00000357368	NM_002850.3	621	cCc/cTc	14/38	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.69703601351388	2		174	301	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243938	5243938	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	334	498	1	ENST00000357368.4:c.1544C>T	p.Pro515Leu	p.P515L	ENST00000357368	NM_002850.3	515	cCc/cTc	11/38	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.69703601351388	2		499	883	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17389784	17389785	+	missense_variant	Missense_Mutation	DNP	CT	CT	TC	novel	NA	P-0051270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	396	837	0	ENST00000359435.4:c.917_918delinsTC	p.Pro306Leu	p.P306L	ENST00000359435	NM_001033549.1	306	cCT/cTC	9/9	1	2	FACETS	0.912	0.867	0.957	0.912	0.867	0.957	CLONAL	1	TRUE	1	0.69703601351388	2		837	1246	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693882	47693883	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0051270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	142	227	1	ENST00000233146.2:c.1596_1597delinsTT	p.Leu533Phe	p.L533F	ENST00000233146	NM_000251.2	532	gtCCtt/gtTTtt	10/16	1	2	FACETS	0.867	0.796	0.94	0.867	0.796	0.94	CLONAL	1	TRUE	1	0.69703601351388	2		228	470	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31939785	31939785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs761774914	NA	P-0051270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	387	634	0	ENST00000375333.2:c.12G>A	p.Trp4Ter	p.W4*	ENST00000375333	NM_032454.1	4	tgG/tgA	1/8	1	2	FACETS	0.977	0.93	1	0.977	0.93	1	CLONAL	1	TRUE	1	0.69703601351388	2		634	1136	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948553	31948553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	20	8	0	ENST00000375333.2:c.1036C>T	p.Leu346Phe	p.L346F	ENST00000375333	NM_032454.1	346	Ctc/Ttc	7/8	1	2	FACETS	0.897	0.748	1	1	0.951	1	CLONAL	2	TRUE	1	0.69703601351388	2		8	32	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55260493	55260493	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	272	409	0	ENST00000275493.2:c.2660T>C	p.Leu887Ser	p.L887S	ENST00000275493	NM_005228.3	887	tTa/tCa	22/28	1	2	FACETS	0.983	0.926	1	0.983	0.926	1	CLONAL	1	TRUE	1	0.69703601351388	2		409	794	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523696	148523696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	161	238	0	ENST00000320356.2:c.757C>T	p.Pro253Ser	p.P253S	ENST00000320356	NM_004456.4	253	Cca/Tca	8/20	1	2	FACETS	0.911	0.842	0.982	0.911	0.842	0.982	CLONAL	1	TRUE	1	0.69703601351388	2		238	507	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157933	27157933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	619	428	0	ENST00000380036.4:c.157G>A	p.Glu53Lys	p.E53K	ENST00000380036	NM_000459.3	53	Gag/Aag	2/23	0.688781201677475	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.69703601351388	2		428	853	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110251315	110251315	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	265	506	0	ENST00000374672.4:c.22T>C	p.Ser8Pro	p.S8P	ENST00000374672	NM_004235.4	8	Tct/Cct	2/5	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.69703601351388	2		506	709	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106129	27106129	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	92	454	0	ENST00000324856.7:c.5740A>G	p.Met1914Val	p.M1914V	ENST00000324856	NM_006015.4	1914	Atg/Gtg	20/20	0.317299254843032	6	FACETS	1	0.972	1	0.322	0.287	0.36	INDETERMINATE	1	TRUE	2	0.665306134659853	6		454	500	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499744	18499744	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	71	298	0	ENST00000266497.5:c.1599C>A	p.His533Gln	p.H533Q	ENST00000266497		533	caC/caA	10/31	0.509269260935997	5	FACETS	0.976	0.855	1	0.325	0.285	0.369	CLONAL	1	TRUE	2	0.665306134659853	5		298	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574027	7574069	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CACGGATCTGCAGCAACAGAGGAGGGGGAGAAGTAAGTATATA	CACGGATCTGCAGCAACAGAGGAGGGGGAGAAGTAAGTATATA	-	novel	NA	P-0051300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	249	483	1	ENST00000269305.4:c.994-36_1000del		p.X332_splice	ENST00000269305	NM_001126112.2	332		10/11	0.53074044013408	4	FACETS	0.853	0.808	0.898	0.64	0.606	0.674	CLONAL	3	TRUE	0	0.665306134659853	4		484	487	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590486	67590499	+	frameshift_variant	Frame_Shift_Del	DEL	CAATGAGAAAGAAA	CAATGAGAAAGAAA	TTT	novel	NA	P-0051300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	73	200	1	ENST00000274335.5:c.1548_1561delinsTTT	p.Asn517PhefsTer7	p.N517Ffs*7	ENST00000274335		516	ggCAATGAGAAAGAAAta/ggTTTta	11/15	0.5175524699807	3	FACETS	1	0.972	1	0.445	0.396	0.497	CLONAL	1	TRUE	0	0.665306134659853	3		201	219	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100387	8100389	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0051307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	41	709	0	ENST00000346208.3:c.361_363del	p.Ser121del	p.S121del	ENST00000346208		121	TCC/-	3/6	1	2	FACETS	0.504	0.418	0.6	0.504	0.418	0.6	SUBCLONAL	1	TRUE	1	0.21	2		709	775	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741423	17741423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	59	556	0	ENST00000250003.3:c.94G>A	p.Asp32Asn	p.D32N	ENST00000250003	NM_002478.4	32	Gac/Aac	1/3	1	2	FACETS	0.83	0.713	0.957	0.83	0.713	0.957	CLONAL	1	TRUE	1	0.21	2		556	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882005	NA	P-0051307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	79	532	0	ENST00000269305.4:c.713G>C	p.Cys238Ser	p.C238S	ENST00000269305	NM_001126112.2	238	tGt/tCt	7/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.21	2		532	615	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0051307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	77	734	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.21	2		735	716	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39233650	39233650	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	34	375	0	ENST00000402219.2:c.2694G>C	p.Lys898Asn	p.K898N	ENST00000402219	NM_005633.3	898	aaG/aaC	17/23	1	2	FACETS	0.863	0.706	1	0.863	0.706	1	CLONAL	1	TRUE	1	0.21	2		375	375	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231774	36231774	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1569061768	NA	P-0051307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	59	558	0	ENST00000300305.3:c.610C>T	p.Arg204Ter	p.R204*	ENST00000300305		204	Cga/Tga	5/8	1	2	FACETS	0.653	0.561	0.755	0.653	0.561	0.755	SUBCLONAL	1	TRUE	1	0.21	2		558	860	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	45	276	0				ENST00000310581	NM_198253.2	-/1132			0.167240949949946	4	FACETS	0.96	0.813	1	0.96	0.813	1	CLONAL	2	TRUE	2	0.21	4		276	270	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032069	26032069	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	84	546	0	ENST00000244661.2:c.220G>C	p.Glu74Gln	p.E74Q	ENST00000244661	NM_003537.3	74	Gaa/Caa	1/1	0.3	5	FACETS	1	0.922	1			1	CLONAL	1	TRUE	NA	0.21	5		546	991	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30682881	30682881	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	65	517	0	ENST00000376406.3:c.72G>T	p.Leu24Phe	p.L24F	ENST00000376406	NM_014641.2	24	ttG/ttT	2/15	0.3	4	FACETS	0.897	0.776	1	0.449	0.388	0.515	CLONAL	1	TRUE	2	0.21	4		517	835	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781467	135781467	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203537	NA	P-0051307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	61	493	0	ENST00000298552.3:c.1498C>T	p.Arg500Ter	p.R500*	ENST00000298552	NM_001162426.1	500	Cga/Tga	15/23	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.21	2		493	535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0051308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	57	532	2	ENST00000269305.4:c.97-1G>A		p.X33_splice	ENST00000269305	NM_001126112.2	33			1	2	FACETS	0.437	0.374	0.506	0.437	0.374	0.506	SUBCLONAL	1	TRUE	1	0.369358061864134	2		534	706	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs763804037	NA	P-0051308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	34	394	0	ENST00000304494.5:c.143C>G	p.Pro48Arg	p.P48R	ENST00000304494	NM_000077.4	48	cCg/cGg	1/3	0.202663041927309	1	FACETS	0.303	0.247	0.366	0.303	0.247	0.366	INDETERMINATE	1	TRUE	0	0.369358061864134	1		394	496	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518119	69518119	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	54	577	0	ENST00000294312.3:c.246del	p.Lys83ArgfsTer63	p.K83Rfs*63	ENST00000294312	NM_005117.2	82	atC/at	2/3	1	2	FACETS	0.425	0.362	0.494	0.425	0.362	0.494	SUBCLONAL	1	TRUE	1	0.369358061864134	2		577	688	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183695	10183695	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	48	552	0	ENST00000256474.2:c.164del	p.Glu55GlyfsTer12	p.E55Gfs*12	ENST00000256474	NM_000551.3	55	gAg/gg	1/3	1	2	FACETS	0.376	0.317	0.441	0.376	0.317	0.441	SUBCLONAL	1	TRUE	1	0.369358061864134	2		552	691	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176710894	176710894	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	28	495	0	ENST00000439151.2:c.6116G>A	p.Arg2039His	p.R2039H	ENST00000439151	NM_022455.4	2039	cGt/cAt	20/23	0.253323103763114	1	FACETS	0.847	0.68	1	0.847	0.68	1	CLONAL	1	TRUE	0	0.253323103763114	1		495	228	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412663	139412663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	38	819	0	ENST00000277541.6:c.1181G>A	p.Gly394Asp	p.G394D	ENST00000277541	NM_017617.3	394	gGc/gAc	7/34	0.253323103763114	1	FACETS	0.916	0.761	1	0.916	0.761	1	CLONAL	1	TRUE	0	0.253323103763114	1		819	286	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120469199	120469199	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	16	561	0	ENST00000256646.2:c.3928C>T	p.Gln1310Ter	p.Q1310*	ENST00000256646	NM_024408.3	1310	Cag/Tag	24/34	1	2	FACETS	0.501	0.371	0.657	0.501	0.371	0.657	SUBCLONAL	1	TRUE	1	0.253323103763114	2		561	252	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412744	139412744	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	17	606	0	ENST00000277541.6:c.1100G>A	p.Gly367Asp	p.G367D	ENST00000277541	NM_017617.3	367	gGt/gAt	7/34	0.253323103763114	1	FACETS	0.446	0.333	0.58	0.446	0.333	0.58	SUBCLONAL	1	TRUE	0	0.253323103763114	1		606	263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0051311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	241	692	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.405639067525018	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.405639067525018	1		692	877	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743923	46743923	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28910278	NA	P-0051311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	143	535	0	ENST00000371975.4:c.2213G>A	p.Arg738His	p.R738H	ENST00000371975	NM_003579.3	738	cGt/cAt	18/18	1	2	FACETS	0.951	0.869	1	0.951	0.869	1	CLONAL	1	TRUE	1	0.405639067525018	2		535	741	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499772	8499772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773166856	NA	P-0051311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	52	485	0	ENST00000356435.5:c.2197C>T	p.Arg733Cys	p.R733C	ENST00000356435		733	Cgc/Tgc	14/35	0.175504755023117	1	FACETS	0.269	0.228	0.313	0.269	0.228	0.313	INDETERMINATE	1	TRUE	0	0.405639067525018	1		485	761	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422737	49422839	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAAGACTGAATGAGAAAGAGGAATTTGTGTAACACTTGGCCGCCTCTCCCCCAGCTTCGGACAACCCAGGTGAACTGGGCCTGGCCCACATCCAGAGTAGCAC	GAAGACTGAATGAGAAAGAGGAATTTGTGTAACACTTGGCCGCCTCTCCCCCAGCTTCGGACAACCCAGGTGAACTGGGCCTGGCCCACATCCAGAGTAGCAC	-	novel	NA	P-0051311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	228	471	0	ENST00000301067.7:c.14251+5_14256del		p.X4751_splice	ENST00000301067	NM_003482.3	4751		45/54	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.405639067525018	2		471	856	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	27	276	0				ENST00000310581	NM_198253.2	-/1132			0.359452902036579	3	FACETS	0.913	0.742	1	0.457	0.371	0.551	INDETERMINATE	1	TRUE	1	0.74439541421429	3		276	109	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47684731	47684731	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	39	306	1	ENST00000347630.2:c.718C>T	p.Arg240Ter	p.R240*	ENST00000347630	NM_001007230.1	240	Cga/Tga	9/11	0.74439541421429	3	FACETS	0.304	0.252	0.362			1	SUBCLONAL	1	TRUE	NA	0.74439541421429	3		307	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0051312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	176	536	0	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	0.689992422221467	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.74439541421429	1		536	275	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211089	55211089	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs746631025	NA	P-0051312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	147	476	0	ENST00000275493.2:c.332T>C	p.Met111Thr	p.M111T	ENST00000275493	NM_005228.3	111	aTg/aCg	3/28	0.550676596457302	4	FACETS	0.757	0.697	0.819	0.757	0.697	0.819	SUBCLONAL	2	TRUE	2	0.74439541421429	4		476	455	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370756	225370756	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	63	411	0	ENST00000264414.4:c.1123G>C	p.Glu375Gln	p.E375Q	ENST00000264414	NM_003590.4	375	Gag/Cag	8/16	0.376067488247934	3	FACETS	0.702	0.611	0.799	0.351	0.305	0.4	INDETERMINATE	1	TRUE	1	0.74439541421429	3		411	331	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951141	48951141	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	218	338	0	ENST00000267163.4:c.1303G>T	p.Gly435Ter	p.G435*	ENST00000267163	NM_000321.2	435	Gga/Tga	13/27	0.73368203522728	2	FACETS	0.989	0.947	1	0.989	0.947	1	CLONAL	2	TRUE	0	0.74439541421429	2		338	296	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533330	29533330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	43	286	0	ENST00000356175.3:c.1333G>A	p.Glu445Lys	p.E445K	ENST00000356175	NM_000267.3	445	Gaa/Aaa	12/57	0.74439541421429	3	FACETS	0.447	0.375	0.526			1	SUBCLONAL	1	TRUE	NA	0.74439541421429	3		286	355	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980745	40980745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	20	389	0	ENST00000373198.4:c.1741C>T	p.Arg581Trp	p.R581W	ENST00000373198	NM_133170.3	581	Cgg/Tgg	10/32	0.74439541421429	3	FACETS	0.196	0.149	0.25	0.098	0.074	0.125	SUBCLONAL	1	TRUE	1	0.74439541421429	3		389	377	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957441	175957441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	32	344	0	ENST00000367669.3:c.1955G>A	p.Gly652Glu	p.G652E	ENST00000367669	NM_022457.5	652	gGa/gAa	17/20	0.74439541421429	4	FACETS	0.344	0.279	0.418	0.115	0.093	0.14	SUBCLONAL	1	TRUE	1	0.74439541421429	4		344	436	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222604	69222604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	52	437	0	ENST00000462284.1:c.577G>A	p.Asp193Asn	p.D193N	ENST00000462284	NM_002392.5	193	Gat/Aat	8/11	0.69910349732835	2	FACETS	0.445	0.381	0.514	0.222	0.19	0.257	SUBCLONAL	1	TRUE	0	0.74439541421429	2		437	314	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226573320	226573320	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374381502	NA	P-0051312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	43	489	1	ENST00000366794.5:c.896C>T	p.Ser299Leu	p.S299L	ENST00000366794	NM_001618.3	299	tCg/tTg	7/23	0.568122247375496	6	FACETS	0.483	0.404	0.572	0.121	0.101	0.143	SUBCLONAL	1	TRUE	2	0.74439541421429	6		490	595	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202762	108202762	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1555124747	NA	P-0051312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	30	260	0	ENST00000278616.4:c.7786G>A	p.Glu2596Lys	p.E2596K	ENST00000278616	NM_000051.3	2596	Gag/Aag	52/63	0.352791581949342	2	FACETS	0.388	0.314	0.469	0.194	0.157	0.235	INDETERMINATE	1	TRUE	0	0.74439541421429	2		260	208	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246093226	246093226	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	43	423	0	ENST00000388985.4:c.545C>T	p.Ser182Phe	p.S182F	ENST00000388985		182	tCt/tTt	6/12	0.568122247375496	6	FACETS	0.582	0.487	0.688	0.146	0.121	0.172	SUBCLONAL	1	TRUE	2	0.74439541421429	6		423	494	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88635782	88635782	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	77	324	0	ENST00000372037.3:c.7C>T	p.Gln3Ter	p.Q3*	ENST00000372037	NM_004329.2	3	Cag/Tag	3/13	0.74439541421429	1	FACETS	0.969	0.883	1	0.969	0.883	1	CLONAL	1	TRUE	0	0.74439541421429	1		324	134	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104269059	104269059	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1040654062	NA	P-0051312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	60	373	1	ENST00000369902.3:c.316G>A	p.Glu106Lys	p.E106K	ENST00000369902	NM_016169.3	106	Gag/Aag	2/12	0.74439541421429	1	FACETS	0.46	0.402	0.522	0.46	0.402	0.522	SUBCLONAL	1	TRUE	0	0.74439541421429	1		374	220	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945419	71945419	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	65	550	0	ENST00000298229.2:c.2307C>G	p.Phe769Leu	p.F769L	ENST00000298229	NM_001567.3	769	ttC/ttG	20/28	0.352791581949342	2	FACETS	0.528	0.46	0.599	0.264	0.23	0.3	INDETERMINATE	1	TRUE	0	0.74439541421429	2		550	331	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216575	108216575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876659505	NA	P-0051312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	38	320	0	ENST00000278616.4:c.8524C>T	p.Pro2842Ser	p.P2842S	ENST00000278616	NM_000051.3	2842	Cca/Tca	58/63	0.352791581949342	2	FACETS	0.363	0.302	0.432	0.182	0.151	0.216	INDETERMINATE	1	TRUE	0	0.74439541421429	2		320	281	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243012	105243012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	66	635	0	ENST00000349310.3:c.271G>A	p.Glu91Lys	p.E91K	ENST00000349310	NM_001014432.1	91	Gag/Aag	5/15	1	2	FACETS	0.556	0.486	0.63	0.556	0.486	0.63	SUBCLONAL	1	TRUE	1	0.74439541421429	2		635	319	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40379590	40379590	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	255	644	0	ENST00000293328.3:c.242T>G	p.Phe81Cys	p.F81C	ENST00000293328	NM_012448.3	81	tTt/tGt	3/19	0.73368203522728	2	FACETS	1	0.993	1	0.678	0.643	0.714	CLONAL	1	TRUE	0	0.74439541421429	2		644	505	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40871197	40871197	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	64	408	0	ENST00000428826.2:c.693C>G	p.Phe231Leu	p.F231L	ENST00000428826		231	ttC/ttG	8/21	0.73368203522728	2	FACETS	0.431	0.374	0.492	0.215	0.187	0.246	SUBCLONAL	1	TRUE	0	0.74439541421429	2		408	399	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281614	15281614	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	73	544	0	ENST00000263388.2:c.4759G>C	p.Asp1587His	p.D1587H	ENST00000263388	NM_000435.2	1587	Gac/Cac	26/33	0.352791581949342	2	FACETS	0.515	0.453	0.581	0.257	0.226	0.291	INDETERMINATE	1	TRUE	0	0.74439541421429	2		544	381	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965407	25965407	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	181	610	0	ENST00000435504.4:c.3799C>T	p.Gln1267Ter	p.Q1267*	ENST00000435504		1267	Cag/Tag	13/13	0.376067488247934	3	FACETS	0.83	0.776	0.884	0.83	0.776	0.884	INDETERMINATE	2	TRUE	1	0.74439541421429	3		610	402	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967296	25967296	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	158	344	0	ENST00000435504.4:c.1910C>G	p.Ser637Cys	p.S637C	ENST00000435504		637	tCt/tGt	13/13	0.376067488247934	3	FACETS	0.867	0.807	0.927	0.867	0.807	0.927	INDETERMINATE	2	TRUE	1	0.74439541421429	3		344	336	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39239429	39239429	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	141	478	1	ENST00000402219.2:c.2228C>T	p.Ala743Val	p.A743V	ENST00000402219	NM_005633.3	743	gCa/gTa	14/23	0.376067488247934	3	FACETS	0.783	0.724	0.843	0.783	0.724	0.843	INDETERMINATE	2	TRUE	1	0.74439541421429	3		479	332	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098883	47098883	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	73	558	1	ENST00000409792.3:c.6391C>T	p.Gln2131Ter	p.Q2131*	ENST00000409792	NM_014159.6	2131	Caa/Taa	15/21	0.612731579611586	4	FACETS	0.5	0.437	0.568	0.167	0.145	0.19	SUBCLONAL	1	TRUE	1	0.74439541421429	4		559	684	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607225	189607225	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	109	617	0	ENST00000264731.3:c.1604C>G	p.Ser535Cys	p.S535C	ENST00000264731	NM_003722.4	535	tCc/tGc	12/14	0.578993733529641	3	FACETS	0.818	0.739	0.902	0.409	0.369	0.451	CLONAL	1	TRUE	1	0.74439541421429	3		617	491	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584645	187584645	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	51	433	0	ENST00000441802.2:c.3388G>C	p.Glu1130Gln	p.E1130Q	ENST00000441802	NM_005245.3	1130	Gag/Cag	3/27	0.325660721106441	2	FACETS	0.479	0.41	0.554	0.24	0.205	0.277	INDETERMINATE	1	TRUE	0	0.74439541421429	2		433	286	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873699	35873699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	105	358	0	ENST00000303115.3:c.655G>A	p.Glu219Lys	p.E219K	ENST00000303115	NM_002185.3	219	Gaa/Aaa	5/8	0.540968166029263	4	FACETS	1	0.983	1	0.717	0.649	0.788	CLONAL	1	TRUE	2	0.74439541421429	4		358	343	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564809	86564809	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0051312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	43	563	0	ENST00000274376.6:c.539+2T>A		p.X180_splice	ENST00000274376	NM_002890.2	180			0.359452902036579	3	FACETS	0.434	0.364	0.512	0.217	0.182	0.256	INDETERMINATE	1	TRUE	1	0.74439541421429	3		563	365	SUCCESS
APC	324	MSKCC	GRCh37	5	112178445	112178445	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	24	327	0	ENST00000257430.4:c.7154C>A	p.Ser2385Tyr	p.S2385Y	ENST00000257430	NM_000038.5	2385	tCc/tAc	16/16	0.359452902036579	3	FACETS	0.386	0.304	0.481	0.193	0.152	0.241	INDETERMINATE	1	TRUE	1	0.74439541421429	3		327	229	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647566	117647566	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0051312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	34	412	0	ENST00000368508.3:c.5378C>G	p.Ser1793Ter	p.S1793*	ENST00000368508	NM_002944.2	1793	tCa/tGa	33/43	0.73368203522728	2	FACETS	0.274	0.224	0.329	0.137	0.112	0.165	SUBCLONAL	1	TRUE	0	0.74439541421429	2		412	334	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912346	97912346	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	46	376	0	ENST00000289081.3:c.545C>G	p.Ser182Cys	p.S182C	ENST00000289081	NM_000136.2	182	tCc/tGc	7/15	0.74439541421429	2	FACETS	0.377	0.318	0.441	0.188	0.159	0.221	SUBCLONAL	1	TRUE	0	0.74439541421429	2		376	328	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0051313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	124	355	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.207063967214246	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.207063967214246	3		355	550	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0051313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	95	604	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.207063967214246	2		604	772	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601375	28601375	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	46	328	0	ENST00000241453.7:c.2057C>A	p.Pro686Gln	p.P686Q	ENST00000241453	NM_004119.2	686	cCa/cAa	17/24	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.207063967214246	2		328	375	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964082	28964082	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs370849583	NA	P-0051313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	45	418	0	ENST00000282397.4:c.1820A>C	p.Gln607Pro	p.Q607P	ENST00000282397	NM_002019.4	607	cAa/cCa	13/30	1	2	FACETS	0.831	0.698	0.978	0.831	0.698	0.978	CLONAL	1	TRUE	1	0.207063967214246	2		418	523	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439512	220439512	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	78	708	0	ENST00000243786.2:c.365G>T	p.Arg122Leu	p.R122L	ENST00000243786	NM_002191.3	122	cGc/cTc	2/2	0.207063967214246	3	FACETS	0.953	0.836	1	0.477	0.418	0.54	CLONAL	1	TRUE	1	0.207063967214246	3		708	872	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188374	32188374	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	54	596	0	ENST00000375023.3:c.967C>G	p.Pro323Ala	p.P323A	ENST00000375023	NM_004557.3	323	Ccc/Gcc	6/30	1	2	FACETS	0.772	0.658	0.896	0.772	0.658	0.896	SUBCLONAL	1	TRUE	1	0.207063967214246	2		596	676	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015704	112015704	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	47	495	0	ENST00000368678.4:c.1138C>G	p.Arg380Gly	p.R380G	ENST00000368678		380	Cgc/Ggc	11/13	1	2	FACETS	0.718	0.605	0.844	0.718	0.605	0.844	SUBCLONAL	1	TRUE	1	0.207063967214246	2		495	632	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138201325	138201325	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	56	442	0	ENST00000237289.4:c.2024A>G	p.Gln675Arg	p.Q675R	ENST00000237289	NM_001270507.1	675	cAg/cGg	8/9	1	2	FACETS	0.841	0.72	0.974	0.841	0.72	0.974	CLONAL	1	TRUE	1	0.207063967214246	2		442	643	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491370	2491370	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	242	724	0	ENST00000355716.4:c.413G>A	p.Cys138Tyr	p.C138Y	ENST00000355716	NM_003820.2	138	tGc/tAc	4/8	1	2	FACETS	0.863	0.81	0.917	0.863	0.81	0.917	CLONAL	1	TRUE	1	0.792248269446828	2		724	708	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257768	16257768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	200	454	0	ENST00000375759.3:c.5033C>T	p.Thr1678Ile	p.T1678I	ENST00000375759	NM_015001.2	1678	aCc/aTc	11/15	1	2	FACETS	0.951	0.888	1	0.951	0.888	1	CLONAL	1	TRUE	1	0.792248269446828	2		454	531	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	240	566	0	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	1	2	FACETS	0.832	0.781	0.885	0.832	0.781	0.885	CLONAL	1	TRUE	1	0.792248269446828	2		566	728	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	203	630	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.856	0.798	0.914	0.856	0.798	0.914	CLONAL	1	TRUE	1	0.792248269446828	2		630	599	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303726	65303726	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	258	481	0	ENST00000342505.4:c.3029T>C	p.Leu1010Pro	p.L1010P	ENST00000342505	NM_002227.2	1010	cTt/cCt	22/25	1	2	FACETS	0.987	0.93	1	0.987	0.93	1	CLONAL	1	TRUE	1	0.792248269446828	2		481	660	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	147	524	2	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.723	0.665	0.784	0.723	0.665	0.784	SUBCLONAL	1	TRUE	1	0.792248269446828	2		526	513	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85742014	85742014	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1229802365	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	208	530	0	ENST00000370580.1:c.22C>A	p.Leu8Ile	p.L8I	ENST00000370580	NM_003921.4	8	Ctc/Atc	1/3	1	2	FACETS	0.746	0.695	0.798	0.746	0.695	0.798	SUBCLONAL	1	TRUE	1	0.792248269446828	2		530	704	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685315	89685315	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1554897280	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	312	194	0	ENST00000371953.3:c.209+1G>T		p.X70_splice	ENST00000371953	NM_000314.4	70			0.792248269446828	3	FACETS	0.996	0.969	1	0.996	0.969	1	CLONAL	3	TRUE	0	0.792248269446828	3		194	368	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156675	2156675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1230176657	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	239	640	0	ENST00000434045.2:c.247C>T	p.Arg83Cys	p.R83C	ENST00000434045	NM_001127598.1	83	Cgc/Tgc	3/5	1	2	FACETS	0.921	0.865	0.978	0.921	0.865	0.978	CLONAL	1	TRUE	1	0.792248269446828	2		640	655	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	246	651	0	ENST00000227507.2:c.859C>T	p.Pro287Ser	p.P287S	ENST00000227507	NM_053056.2	287	Ccc/Tcc	5/5	1	2	FACETS	0.942	0.886	0.999	0.942	0.886	0.999	CLONAL	1	TRUE	1	0.792248269446828	2		651	659	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114817	108114817	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786204543	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	226	443	0	ENST00000278616.4:c.640del	p.Ser214ProfsTer16	p.S214Pfs*16	ENST00000278616	NM_000051.3	212	Ttt/tt	6/63	1	2	FACETS	0.913	0.856	0.971	0.913	0.856	0.971	CLONAL	1	TRUE	1	0.792248269446828	2		443	625	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	207	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.792248269446828	2		334	518	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445437	49445437	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	297	663	0	ENST00000301067.7:c.2029del	p.Glu677SerfsTer253	p.E677Sfs*253	ENST00000301067	NM_003482.3	677	Gag/ag	10/54	1	2	FACETS	0.992	0.939	1	0.992	0.939	1	CLONAL	1	TRUE	1	0.792248269446828	2		663	756	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865076	57865076	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462976482	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	230	630	0	ENST00000228682.2:c.2557del	p.Gln853SerfsTer93	p.Q853Sfs*93	ENST00000228682	NM_005269.2	851	taC/ta	12/12	1	2	FACETS	0.786	0.735	0.837	0.786	0.735	0.837	SUBCLONAL	1	TRUE	1	0.792248269446828	2		630	739	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435300	110435302	+	inframe_deletion	In_Frame_Del	DEL	GGT	GGT	-	rs765493638	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	46	133	0	ENST00000375856.3:c.3099_3101del	p.Pro1036del	p.P1036del	ENST00000375856	NM_003749.2	1033	ccACCg/ccg	1/2	NA	2	FACETS	0.683	0.585	0.788			1	INDETERMINATE	1	TRUE	NA	0.792248269446828	2		133	170	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779293	3779293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	245	541	1	ENST00000262367.5:c.5755G>A	p.Ala1919Thr	p.A1919T	ENST00000262367	NM_004380.2	1919	Gct/Act	31/31	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.792248269446828	2		542	608	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512393	38512393	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1403898124	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	186	376	0	ENST00000254066.5:c.1304G>A	p.Gly435Asp	p.G435D	ENST00000254066	NM_000964.3	435	gGt/gAt	9/9	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.792248269446828	2		376	415	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	189	894	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.673	0.624	0.724	0.673	0.624	0.724	SUBCLONAL	1	TRUE	1	0.792248269446828	2		899	709	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621968	1621968	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	280	632	0	ENST00000344749.5:c.824G>A	p.Gly275Asp	p.G275D	ENST00000344749	NM_001136139.2	275	gGc/gAc	11/19	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.792248269446828	2		632	677	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349754	15349754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	222	634	0	ENST00000263377.2:c.3820C>T	p.Arg1274Trp	p.R1274W	ENST00000263377	NM_058243.2	1274	Cgg/Tgg	19/20	1	2	FACETS	0.981	0.921	1	0.981	0.921	1	CLONAL	1	TRUE	1	0.792248269446828	2		634	571	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091793	29091793	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs758677815	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	157	424	0	ENST00000328354.6:c.1164del	p.Thr389ProfsTer25	p.T389Pfs*25	ENST00000328354	NM_007194.3	388	ccC/cc	11/15	1	2	FACETS	0.788	0.727	0.851	0.788	0.727	0.851	SUBCLONAL	1	TRUE	1	0.792248269446828	2		424	503	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936096	178936096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	227	408	0	ENST00000263967.3:c.1638G>C	p.Gln546His	p.Q546H	ENST00000263967	NM_006218.2	546	caG/caC	10/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.792248269446828	2		408	520	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278818	1278818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs939537185	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	260	604	0	ENST00000310581.5:c.2224C>T	p.Arg742Cys	p.R742C	ENST00000310581	NM_198253.2	742	Cgt/Tgt	6/16	1	2	FACETS	0.944	0.89	1	0.944	0.89	1	CLONAL	1	TRUE	1	0.792248269446828	2		604	695	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950799	38950799	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	98	253	0	ENST00000357387.3:c.3151C>G	p.Arg1051Gly	p.R1051G	ENST00000357387	NM_152756.3	1051	Cgg/Ggg	31/38	1	2	FACETS	0.952	0.863	1	0.952	0.863	1	CLONAL	1	TRUE	1	0.792248269446828	2		253	260	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161221	56161221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781300314	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	196	401	0	ENST00000399503.3:c.1090C>T	p.Arg364Trp	p.R364W	ENST00000399503	NM_005921.1	364	Cgg/Tgg	5/20	1	2	FACETS	0.836	0.779	0.894	0.836	0.779	0.894	CLONAL	1	TRUE	1	0.792248269446828	2		401	592	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178257	56178258	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	131	287	0	ENST00000399503.3:c.3236dup	p.Asn1079LysfsTer2	p.N1079Kfs*2	ENST00000399503	NM_005921.1	1077	tca/tcAa	14/20	1	2	FACETS	0.846	0.775	0.918	0.846	0.775	0.918	CLONAL	1	TRUE	1	0.792248269446828	2		287	391	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	213	530	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.756	0.705	0.808	0.756	0.705	0.808	SUBCLONAL	1	TRUE	1	0.792248269446828	2		533	711	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694717	176694717	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	167	337	0	ENST00000439151.2:c.5301C>G	p.Tyr1767Ter	p.Y1767*	ENST00000439151	NM_022455.4	1767	taC/taG	15/23	1	2	FACETS	0.985	0.915	1	0.985	0.915	1	CLONAL	1	TRUE	1	0.792248269446828	2		337	428	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720928	176720928	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784209	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	230	422	0	ENST00000439151.2:c.6559C>T	p.Arg2187Ter	p.R2187*	ENST00000439151	NM_022455.4	2187	Cga/Tga	23/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.792248269446828	2		422	505	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394896	394896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	155	434	0	ENST00000380956.4:c.292C>T	p.Arg98Trp	p.R98W	ENST00000380956	NM_001195286.1	98	Cgg/Tgg	3/9	1	2	FACETS	0.766	0.706	0.828	0.766	0.706	0.828	SUBCLONAL	1	TRUE	1	0.792248269446828	2		434	511	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402570	20402570	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1374278196	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	128	280	0	ENST00000346618.3:c.107G>A	p.Arg36Lys	p.R36K	ENST00000346618	NM_001949.4	36	aGg/aAg	1/7	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.792248269446828	2		280	315	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161970022	161970022	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	191	503	0	ENST00000366898.1:c.947A>G	p.Gln316Arg	p.Q316R	ENST00000366898	NM_004562.2	316	cAg/cGg	9/12	1	2	FACETS	0.821	0.764	0.88	0.821	0.764	0.88	CLONAL	1	TRUE	1	0.792248269446828	2		503	587	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136839	69136839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780008732	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	160	343	0	ENST00000288368.4:c.4753C>T	p.Arg1585Trp	p.R1585W	ENST00000288368	NM_024870.2	1585	Cgg/Tgg	39/40	1	2	FACETS	0.914	0.846	0.983	0.914	0.846	0.983	CLONAL	1	TRUE	1	0.792248269446828	2		343	442	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965666	90965666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	172	336	3	ENST00000265433.3:c.1651del	p.Arg551GlyfsTer8	p.R551Gfs*8	ENST00000265433	NM_002485.4	551	Agg/gg	11/16	1	2	FACETS	0.976	0.907	1	0.976	0.907	1	CLONAL	1	TRUE	1	0.792248269446828	2		339	445	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27228229	27228229	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757379347	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	499	444	1	ENST00000380036.4:c.3226C>T	p.Arg1076Trp	p.R1076W	ENST00000380036	NM_000459.3	1076	Cgg/Tgg	22/23	0.791329398965329	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.792248269446828	3		445	865	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785964	135785964	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs118203506	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	223	525	1	ENST00000298552.3:c.1257del	p.Arg420GlyfsTer20	p.R420Gfs*20	ENST00000298552	NM_001162426.1	419	ccC/cc	12/23	0.792248269446828	1	FACETS	0.823	0.779	0.867	0.823	0.779	0.867	CLONAL	1	TRUE	0	0.792248269446828	1		526	413	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15818058	15818058	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	165	323	0	ENST00000307771.7:c.185A>C	p.Lys62Thr	p.K62T	ENST00000307771	NM_005089.3	62	aAg/aCg	3/11	1	2	FACETS	0.854	0.79	0.918	0.854	0.79	0.918	CLONAL	1	TRUE	1	0.792248269446828	2		323	488	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0051325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	49	390	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.485649296475127	2		390	138	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0051325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	61	517	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.977	0.852	1	0.977	0.852	1	CLONAL	1	TRUE	1	0.485649296475127	2		517	257	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266069	41266110	+	inframe_deletion	In_Frame_Del	DEL	TAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCA	TAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCA	-	novel	NA	P-0051325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	104	257	0	ENST00000349496.5:c.67_108del	p.His24_Ser37del	p.H24_S37del	ENST00000349496	NM_001904.3	22	gtTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCAt/gtt	3/15	0.47973229980248	2	FACETS	0.83	0.756	0.905	0.83	0.756	0.905	CLONAL	2	TRUE	0	0.485649296475127	2		257	258	SUCCESS
APC	324	MSKCC	GRCh37	5	112174580	112174580	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	161	249	0	ENST00000257430.4:c.3289G>T	p.Glu1097Ter	p.E1097*	ENST00000257430	NM_000038.5	1097	Gaa/Taa	16/16	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.604736440453993	2		249	402	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0051327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	50	219	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	NA	2	FACETS	0.707	0.606	0.815			1	INDETERMINATE	1	TRUE	NA	0.604736440453993	2		219	234	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953040	2953040	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141751925	NA	P-0051327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	40	657	3	ENST00000396946.4:c.2900G>A	p.Arg967His	p.R967H	ENST00000396946	NM_032415.4	967	cGc/cAc	22/25	1	2	FACETS	0.223	0.185	0.266	0.223	0.185	0.266	SUBCLONAL	1	TRUE	1	0.604736440453993	2		660	593	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784120	9784120	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	147	585	0	ENST00000377346.4:c.2688C>A	p.Ser896Arg	p.S896R	ENST00000377346	NM_005026.3	896	agC/agA	21/24	0.428892120041268	1	FACETS	0.854	0.789	0.921	0.854	0.789	0.921	CLONAL	1	TRUE	0	0.604736440453993	1		585	397	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574019	7574020	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0051327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	230	518	0	ENST00000269305.4:c.1007_1008del	p.Glu336AlafsTer10	p.E336Afs*10	ENST00000269305	NM_001126112.2	336	gAG/g	10/11	0.604736440453993	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.604736440453993	1		518	421	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340304	116340304	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	16	240	0	ENST00000397752.3:c.1166T>A	p.Phe389Tyr	p.F389Y	ENST00000397752	NM_000245.2	389	tTt/tAt	2/21	1	2	FACETS	0.184	0.135	0.242	0.184	0.135	0.242	SUBCLONAL	1	TRUE	1	0.604736440453993	2		240	288	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040969	47040969	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	95	729	0	ENST00000377604.3:c.1499A>T	p.Gln500Leu	p.Q500L	ENST00000377604	NM_001204468.1	500	cAg/cTg	14/24	0.604736440453993	3	FACETS	0.5	0.445	0.559	0.25	0.222	0.28	SUBCLONAL	1	TRUE	1	0.604736440453993	3		729	818	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480549	123480550	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0051327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	311	593	0	ENST00000371139.4:c.57_58delinsAA	p.Leu20Met	p.L20M	ENST00000371139	NM_001114937.2	19	ctCCtg/ctAAtg	1/4	0.604736440453993	3	FACETS	0.975	0.926	1	0.975	0.926	1	CLONAL	2	TRUE	1	0.604736440453993	3		593	687	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0051329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	126	513	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.971	0.878	1	0.971	0.878	1	CLONAL	1	TRUE	1	0.286592159596399	2		516	906	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821643	72821645	+	inframe_deletion	In_Frame_Del	DEL	CCG	CCG	-	rs762513291	NA	P-0051329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	14	57	0	ENST00000268489.5:c.10530_10532del	p.Gly3512del	p.G3512del	ENST00000268489	NM_006885.3	3510	ggCGGt/ggt	10/10	1	2	FACETS	0.607	0.44	0.806	0.607	0.44	0.806	SUBCLONAL	1	TRUE	1	0.286592159596399	2		57	161	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584761	48584761	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0051329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	117	423	1	ENST00000342988.3:c.839T>A	p.Leu280Ter	p.L280*	ENST00000342988	NM_005359.5	280	tTg/tAg	7/12	0.22938187600498	1	FACETS	0.919	0.829	1	0.919	0.829	1	CLONAL	1	TRUE	0	0.286592159596399	1		424	761	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246837	10246837	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	131	605	0	ENST00000340748.4:c.4568T>A	p.Phe1523Tyr	p.F1523Y	ENST00000340748		1523	tTc/tAc	37/40	1	2	FACETS	0.806	0.73	0.887	0.806	0.73	0.887	CLONAL	1	TRUE	1	0.286592159596399	2		605	1134	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579361	7579361	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1064796722	NA	P-0051332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	68	606	0	ENST00000269305.4:c.326T>C	p.Phe109Ser	p.F109S	ENST00000269305	NM_001126112.2	109	tTc/tCc	4/11	1	2	FACETS	0.603	0.524	0.69	0.603	0.524	0.69	SUBCLONAL	1	TRUE	1	0.27	2		606	835	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17947956	17947956	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1040476469	NA	P-0051332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	55	584	1	ENST00000458235.1:c.1768G>A	p.Val590Met	p.V590M	ENST00000458235	NM_000215.3	590	Gtg/Atg	13/24	1	2	FACETS	0.504	0.43	0.586	0.504	0.43	0.586	SUBCLONAL	1	TRUE	1	0.27	2		585	808	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961021	15961021	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	47	352	0	ENST00000268712.3:c.6199del	p.Gln2067LysfsTer27	p.Q2067Kfs*27	ENST00000268712	NM_006311.3	2067	Caa/aa	40/46	1	2	FACETS	0.683	0.576	0.8	0.683	0.576	0.8	SUBCLONAL	1	TRUE	1	0.27	2		352	510	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579592	7579592	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs879254212	NA	P-0051333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	417	474	0	ENST00000269305.4:c.97-2A>G		p.X33_splice	ENST00000269305	NM_001126112.2	33			1	2	FACETS	0.986	0.957	1	1	0.997	1	CLONAL	2	TRUE	1	0.770255856419784	2		474	549	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056218	26056218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs527943061	NA	P-0051333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	193	405	0	ENST00000343677.2:c.439C>T	p.Pro147Ser	p.P147S	ENST00000343677	NM_005319.3	147	Ccg/Tcg	1/1	1	2	FACETS	0.985	0.919	1	0.985	0.919	1	CLONAL	1	TRUE	1	0.770255856419784	2		405	509	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	47	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.37	2		276	242	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	244	476	1	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.30030140050354	2	FACETS	0.865	0.812	0.92	0.865	0.812	0.92	CLONAL	2	TRUE	0	0.37	2		477	762	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595990	43595990	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs547308774	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	92	542	0	ENST00000355710.3:c.157G>A	p.Val53Ile	p.V53I	ENST00000355710	NM_020975.4	53	Gtc/Atc	2/20	1	2	FACETS	0.811	0.722	0.906	0.811	0.722	0.906	CLONAL	1	TRUE	1	0.37	2		542	613	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638344	117638344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1484038087	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	58	374	0	ENST00000368508.3:c.6097G>A	p.Asp2033Asn	p.D2033N	ENST00000368508	NM_002944.2	2033	Gac/Aac	38/43	1	2	FACETS	0.814	0.702	0.935	0.814	0.702	0.935	CLONAL	1	TRUE	1	0.37	2		374	385	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982072	93982072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1334631229	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	77	419	1	ENST00000369303.4:c.1393G>A	p.Glu465Lys	p.E465K	ENST00000369303	NM_004440.3	465	Gaa/Aaa	6/17	1	2	FACETS	0.797	0.701	0.9	0.797	0.701	0.9	SUBCLONAL	1	TRUE	1	0.37	2		420	522	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341925	8341925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	93	323	0	ENST00000356435.5:c.4715G>A	p.Arg1572Lys	p.R1572K	ENST00000356435		1572	aGa/aAa	29/35	0.304190171560939	3	FACETS	0.879	0.789	0.972	0.879	0.789	0.972	CLONAL	2	TRUE	1	0.37	3		323	339	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120377	94120377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	46	276	0	ENST00000369303.4:c.674C>T	p.Ser225Phe	p.S225F	ENST00000369303	NM_004440.3	225	tCc/tTc	3/17	1	2	FACETS	0.749	0.633	0.875	0.749	0.633	0.875	SUBCLONAL	1	TRUE	1	0.37	2		276	332	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321292	1321292	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	80	446	0	ENST00000400841.2:c.463C>T	p.Pro155Ser	p.P155S	ENST00000400841		155	Ccc/Tcc	4/6	0.242868795147678	2	FACETS	0.94	0.831	1			1	CLONAL	1	TRUE	NA	0.37	2		446	460	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210696	36210697	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	75	529	0	ENST00000222270.7:c.447_448delinsTT	p.Arg150Ter	p.R150*	ENST00000222270	NM_014727.1	149	ccCCga/ccTTga	3/37	1	2	FACETS	0.715	0.627	0.809	0.715	0.627	0.809	SUBCLONAL	1	TRUE	1	0.37	2		529	567	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224171	36224171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779883307	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	87	466	0	ENST00000222270.7:c.6721G>A	p.Gly2241Ser	p.G2241S	ENST00000222270	NM_014727.1	2241	Ggc/Agc	28/37	1	2	FACETS	0.904	0.803	1	0.904	0.803	1	CLONAL	1	TRUE	1	0.37	2		466	520	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797167	42797167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	119	658	0	ENST00000575354.2:c.3529C>T	p.Pro1177Ser	p.P1177S	ENST00000575354	NM_015125.3	1177	Ccc/Tcc	15/20	1	2	FACETS	0.936	0.846	1	0.936	0.846	1	CLONAL	1	TRUE	1	0.37	2		658	687	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347143	347143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367788267	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	131	637	0	ENST00000262320.3:c.1868C>T	p.Ser623Leu	p.S623L	ENST00000262320	NM_003502.3	623	tCg/tTg	7/11	1	2	FACETS	0.928	0.843	1	0.928	0.843	1	CLONAL	1	TRUE	1	0.37	2		637	763	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793420	18793420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267603404	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	21	380	1	ENST00000266497.5:c.4117C>T	p.Pro1373Ser	p.P1373S	ENST00000266497		1373	Ccc/Tcc	30/31	0.304190171560939	1	FACETS	0.294	0.226	0.373	0.294	0.226	0.373	SUBCLONAL	1	TRUE	0	0.37	1		381	315	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981789	70981789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs889703632	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	129	626	0	ENST00000276594.2:c.307C>T	p.Pro103Ser	p.P103S	ENST00000276594	NM_024504.3	103	Cca/Tca	2/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.37	2		626	579	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748896	41748896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs545871181	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	124	479	2	ENST00000301178.4:c.1421G>A	p.Arg474Gln	p.R474Q	ENST00000301178	NM_021913.4	474	cGg/cAg	11/20	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.37	2		481	651	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138667	55138667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	89	348	0	ENST00000257290.5:c.1344G>A	p.Met448Ile	p.M448I	ENST00000257290	NM_006206.4	448	atG/atA	9/23	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.37	2		348	434	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873233	71873233	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	104	355	0	ENST00000357731.5:c.961G>A	p.Gly321Arg	p.G321R	ENST00000357731	NM_173808.2	321	Gga/Aga	7/7	0.135079786173323	3	FACETS	0.759	0.684	0.837	0.759	0.684	0.837	INDETERMINATE	2	TRUE	1	0.37	3		355	439	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372069	45372069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	59	396	0	ENST00000262160.6:c.1100G>A	p.Gly367Asp	p.G367D	ENST00000262160	NM_005901.5	367	gGc/gAc	9/11	1	2	FACETS	0.807	0.697	0.926	0.807	0.697	0.926	CLONAL	1	TRUE	1	0.37	2		396	395	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1959686	1959686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772239992	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	51	291	0	ENST00000382891.5:c.2908C>T	p.Arg970Cys	p.R970C	ENST00000382891	NM_133335.3	970	Cgt/Tgt	16/22	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.37	2		291	268	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080566	5080566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	33	281	1	ENST00000381652.3:c.2317C>T	p.Pro773Ser	p.P773S	ENST00000381652	NM_004972.3	773	Cct/Tct	18/25	0.304190171560939	3	FACETS	0.87	0.713	1	0.435	0.356	0.523	CLONAL	1	TRUE	1	0.37	3		282	243	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256859	16256859	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	162	508	0	ENST00000375759.3:c.4124C>T	p.Pro1375Leu	p.P1375L	ENST00000375759	NM_015001.2	1375	cCt/cTt	11/15	0.135079786173323	3	FACETS	1	0.989	1	0.75	0.69	0.812	INDETERMINATE	1	TRUE	1	0.37	3		508	692	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925336	114925336	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	73	444	0	ENST00000543371.1:c.1414T>C	p.Tyr472His	p.Y472H	ENST00000543371	NM_001198531.1	472	Tac/Cac	14/14	1	2	FACETS	0.775	0.679	0.878	0.775	0.679	0.878	SUBCLONAL	1	TRUE	1	0.37	2		444	509	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925496	114925497	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	104	502	0	ENST00000543371.1:c.1574_1575delinsTT	p.Pro525Leu	p.P525L	ENST00000543371	NM_001198531.1	525	cCC/cTT	14/14	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.37	2		502	548	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103427	77103427	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	51	354	0	ENST00000356341.3:c.139G>C	p.Glu47Gln	p.E47Q	ENST00000356341	NM_002576.4	47	Gag/Cag	2/15	0.304190171560939	1	FACETS	0.575	0.49	0.667	0.575	0.49	0.667	SUBCLONAL	1	TRUE	0	0.37	1		354	391	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156052	119156052	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs996627039	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	91	472	0	ENST00000264033.4:c.1717C>T	p.Pro573Ser	p.P573S	ENST00000264033	NM_005188.3	573	Ccc/Tcc	11/16	0.304190171560939	1	FACETS	0.759	0.676	0.848	0.759	0.676	0.848	SUBCLONAL	1	TRUE	0	0.37	1		472	528	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230629	46230629	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	36	368	0	ENST00000334344.6:c.878T>A	p.Leu293Ter	p.L293*	ENST00000334344	NM_152641.2	293	tTg/tAg	8/21	NA	2	FACETS	0.572	0.471	0.685			1	INDETERMINATE	1	TRUE	NA	0.37	2		368	340	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434964	49434964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	62	559	0	ENST00000301067.7:c.6589C>T	p.Pro2197Ser	p.P2197S	ENST00000301067	NM_003482.3	2197	Ccc/Tcc	31/54	NA	2	FACETS	0.661	0.572	0.758			1	INDETERMINATE	1	TRUE	NA	0.37	2		559	507	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99192827	99192827	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	112	393	0	ENST00000268035.6:c.17G>A	p.Gly6Glu	p.G6E	ENST00000268035	NM_000875.3	6	gGa/gAa	1/21	0.135079786173323	3	FACETS	1	0.948	1	0.541	0.487	0.598	INDETERMINATE	1	TRUE	1	0.37	3		393	663	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779241	3779241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	85	458	0	ENST00000262367.5:c.5807G>A	p.Gly1936Glu	p.G1936E	ENST00000262367	NM_004380.2	1936	gGg/gAg	31/31	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.37	2		458	415	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829923	72829923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	74	525	1	ENST00000268489.5:c.6658G>A	p.Glu2220Lys	p.E2220K	ENST00000268489	NM_006885.3	2220	Gag/Aag	9/10	1	2	FACETS	0.679	0.595	0.77	0.679	0.595	0.77	SUBCLONAL	1	TRUE	1	0.37	2		526	589	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528061	29528062	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	35	88	0	ENST00000356175.3:c.1074dup	p.Asn359Ter	p.N359*	ENST00000356175	NM_000267.3	357	ctt/cTtt	10/57	0.30030140050354	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	2	TRUE	0	0.37	2		88	89	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687175	37687175	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	185	464	0	ENST00000447079.4:c.4079C>T	p.Pro1360Leu	p.P1360L	ENST00000447079	NM_015083.1	1360	cCa/cTa	14/14	0.30030140050354	2	FACETS	0.888	0.825	0.952	0.888	0.825	0.952	CLONAL	2	TRUE	0	0.37	2		464	563	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440646	56440646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	145	500	0	ENST00000407977.2:c.572C>T	p.Pro191Leu	p.P191L	ENST00000407977		191	cCc/cTc	5/10	0.30030140050354	2	FACETS	1	0.986	1	0.692	0.635	0.752	CLONAL	1	TRUE	0	0.37	2		500	566	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222215	5222215	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	100	472	0	ENST00000357368.4:c.3120C>G	p.Phe1040Leu	p.F1040L	ENST00000357368	NM_002850.3	1040	ttC/ttG	19/38	1	2	FACETS	0.967	0.866	1	0.967	0.866	1	CLONAL	1	TRUE	1	0.37	2		472	559	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224571	36224571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	97	629	0	ENST00000222270.7:c.7033G>A	p.Gly2345Arg	p.G2345R	ENST00000222270	NM_014727.1	2345	Ggg/Agg	29/37	1	2	FACETS	0.8	0.714	0.892	0.8	0.714	0.892	SUBCLONAL	1	TRUE	1	0.37	2		629	655	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867005	45867005	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	79	456	0	ENST00000391945.4:c.1114C>T	p.Leu372Phe	p.L372F	ENST00000391945	NM_000400.3	372	Ctc/Ttc	11/23	1	2	FACETS	0.92	0.812	1	0.92	0.812	1	CLONAL	1	TRUE	1	0.37	2		456	464	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936660	49936661	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	59	549	1	ENST00000296474.3:c.1266_1267delinsTT	p.Arg423Cys	p.R423C	ENST00000296474	NM_002447.2	422	tgCCgc/tgTTgc	2/20	1	2	FACETS	0.509	0.438	0.588	0.509	0.438	0.588	SUBCLONAL	1	TRUE	1	0.37	2		550	626	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015159	71015160	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	34	313	0	ENST00000318789.4:c.1770_1771delinsAA	p.Met590_Gly591delinsIleArg	p.M590_G591delinsIR	ENST00000318789	NM_032682.5	590	atGGga/atAAga	20/21	1	2	FACETS	0.501	0.41	0.603	0.501	0.41	0.603	SUBCLONAL	1	TRUE	1	0.37	2		313	367	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521636	89521636	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	57	378	0	ENST00000336596.2:c.2713C>T	p.Gln905Ter	p.Q905*	ENST00000336596	NM_005233.5	905	Caa/Taa	16/17	1	2	FACETS	0.634	0.545	0.731	0.634	0.545	0.731	SUBCLONAL	1	TRUE	1	0.37	2		378	486	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268470	142268470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	44	390	0	ENST00000350721.4:c.3022C>T	p.Pro1008Ser	p.P1008S	ENST00000350721	NM_001184.3	1008	Cct/Tct	15/47	1	2	FACETS	0.706	0.594	0.828	0.706	0.594	0.828	SUBCLONAL	1	TRUE	1	0.37	2		390	337	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443324	187443324	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	85	311	0	ENST00000232014.4:c.1802C>T	p.Pro601Leu	p.P601L	ENST00000232014	NM_001130845.1	601	cCc/cTc	8/10	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.37	2		311	445	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1959741	1959741	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	61	279	0	ENST00000382891.5:c.2963C>T	p.Pro988Leu	p.P988L	ENST00000382891	NM_133335.3	988	cCc/cTc	16/22	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.37	2		279	313	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538238	187538238	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	60	497	0	ENST00000441802.2:c.8996C>T	p.Thr2999Ile	p.T2999I	ENST00000441802	NM_005245.3	2999	aCt/aTt	11/27	1	2	FACETS	0.726	0.627	0.833	0.726	0.627	0.833	SUBCLONAL	1	TRUE	1	0.37	2		497	447	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064817	80064817	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	25	261	0	ENST00000265081.6:c.2248C>T	p.Gln750Ter	p.Q750*	ENST00000265081	NM_002439.4	750	Cag/Tag	15/24	1	2	FACETS	0.866	0.69	1	0.866	0.69	1	CLONAL	1	TRUE	1	0.37	2		261	156	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672243	30672243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	117	565	0	ENST00000376406.3:c.4717C>T	p.Pro1573Ser	p.P1573S	ENST00000376406	NM_014641.2	1573	Cct/Tct	10/15	1	2	FACETS	0.982	0.887	1	0.982	0.887	1	CLONAL	1	TRUE	1	0.37	2		565	644	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026525	6026525	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	87	516	0	ENST00000265849.7:c.1871C>T	p.Ser624Phe	p.S624F	ENST00000265849	NM_000535.5	624	tCt/tTt	11/15	0.135079786173323	3	FACETS	1	0.901	1	0.508	0.451	0.57	INDETERMINATE	1	TRUE	1	0.37	3		516	548	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374392	81374392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	59	339	0	ENST00000222390.5:c.670G>A	p.Asp224Asn	p.D224N	ENST00000222390	NM_000601.4	224	Gat/Aat	6/18	0.135079786173323	3	FACETS	0.822	0.708	0.944	0.411	0.354	0.472	INDETERMINATE	1	TRUE	1	0.37	3		339	460	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509453	106509453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	137	485	1	ENST00000359195.3:c.1447C>T	p.His483Tyr	p.H483Y	ENST00000359195	NM_002649.2	483	Cac/Tac	2/11	0.135079786173323	3	FACETS	1	0.979	1	0.626	0.57	0.684	INDETERMINATE	1	TRUE	1	0.37	3		486	701	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945114	151945114	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	22	248	1	ENST00000262189.6:c.2405C>T	p.Ser802Leu	p.S802L	ENST00000262189	NM_170606.2	802	tCa/tTa	14/59	0.135079786173323	3	FACETS	0.641	0.498	0.804	0.32	0.249	0.402	INDETERMINATE	1	TRUE	1	0.37	3		249	220	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69000008	69000008	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868463537	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	118	482	0	ENST00000288368.4:c.2077G>A	p.Gly693Arg	p.G693R	ENST00000288368	NM_024870.2	693	Gga/Aga	19/40	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.37	2		482	557	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981893	70981893	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1440556377	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	95	598	0	ENST00000276594.2:c.203C>T	p.Pro68Leu	p.P68L	ENST00000276594	NM_024504.3	68	cCc/cTc	2/8	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.37	2		598	509	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549345	5549346	+	stop_gained	Nonsense_Mutation	DNP	GA	GA	AT	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	36	368	1	ENST00000397747.3:c.372_373delinsAT	p.Lys125Ter	p.K125*	ENST00000397747	NM_025239.3	124	agGAaa/agATaa	4/7	0.304190171560939	3	FACETS	0.562	0.462	0.674	0.281	0.231	0.337	SUBCLONAL	1	TRUE	1	0.37	3		369	410	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606496	93606496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	35	650	1	ENST00000375746.1:c.316C>T	p.Pro106Ser	p.P106S	ENST00000375746	NM_001174167.1	106	Ccc/Tcc	2/14	0.304190171560939	1	FACETS	0.247	0.202	0.298	0.247	0.202	0.298	SUBCLONAL	1	TRUE	0	0.37	1		651	624	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797334	135797335	+	missense_variant	Missense_Mutation	DNP	GG	GG	CA	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	52	241	1	ENST00000298552.3:c.534_535delinsTG	p.His179Asp	p.H179D	ENST00000298552	NM_001162426.1	178	gtCCat/gtTGat	7/23	0.304190171560939	1	FACETS	0.744	0.637	0.859	0.744	0.637	0.859	SUBCLONAL	1	TRUE	0	0.37	1		242	308	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137326008	137326009	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0051334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	69	547	2	ENST00000481739.1:c.1196_1197delinsTT	p.Ser399Phe	p.S399F	ENST00000481739	NM_002957.4	399	tCC/tTT	9/10	0.304190171560939	1	FACETS	0.56	0.488	0.637	0.56	0.488	0.637	SUBCLONAL	1	TRUE	0	0.37	1		549	543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0051341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	101	633	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.569493091107578	1	FACETS	0.987	0.903	1	0.987	0.903	1	CLONAL	1	TRUE	0	0.640851590717133	1		633	217	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0051341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	129	297	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.640851590717133	4	FACETS	0.834	0.764	0.907	0.556	0.509	0.605	CLONAL	2	TRUE	1	0.640851590717133	4		297	396	SUCCESS
APC	324	MSKCC	GRCh37	5	112176017	112176017	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554086134	NA	P-0051341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	15	255	0	ENST00000257430.4:c.4726G>T	p.Glu1576Ter	p.E1576*	ENST00000257430	NM_000038.5	1576	Gaa/Taa	16/16	0.236496778348245	3	FACETS	0.624	0.463	0.813	0.208	0.154	0.271	INDETERMINATE	1	TRUE	0	0.640851590717133	3		255	99	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093363	30093363	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	19	356	0	ENST00000331968.5:c.1900C>G	p.Leu634Val	p.L634V	ENST00000331968	NM_002742.2	634	Cta/Gta	13/18	0.280044262376342	4	FACETS	0.396	0.3	0.507	0.099	0.075	0.127	INDETERMINATE	1	TRUE	0	0.640851590717133	4		356	246	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539014	187539014	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	17	431	0	ENST00000441802.2:c.8726C>A	p.Thr2909Asn	p.T2909N	ENST00000441802	NM_005245.3	2909	aCc/aAc	10/27	0.150049519193788	3	FACETS	0.279	0.208	0.363	0.093	0.069	0.121	INDETERMINATE	1	TRUE	0	0.640851590717133	3		431	251	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692802	89692802	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	14	200	0	ENST00000371953.3:c.286C>A	p.Pro96Thr	p.P96T	ENST00000371953	NM_000314.4	96	Cca/Aca	5/9	0.283284435321517	1	FACETS	0.182	0.131	0.243	0.182	0.131	0.243	INDETERMINATE	1	TRUE	0	0.52851994120696	1		200	214	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919223	48919223	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1566186840	NA	P-0051342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	26	131	0	ENST00000267163.4:c.388A>T	p.Lys130Ter	p.K130*	ENST00000267163	NM_000321.2	130	Aaa/Taa	4/27	0.471635663111187	1	FACETS	0.916	0.749	1	0.916	0.749	1	CLONAL	1	TRUE	0	0.52851994120696	1		131	79	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0051342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	345	511	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.498483775191955	2	FACETS	0.841	0.801	0.882	0.841	0.801	0.882	CLONAL	2	TRUE	0	0.52851994120696	2		511	776	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412892	49412892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	155	436	0	ENST00000418115.1:c.131C>T	p.Ala44Val	p.A44V	ENST00000418115	NM_001664.2	44	gCa/gTa	2/5	0.338090897034168	1	FACETS	0.814	0.75	0.88	0.814	0.75	0.88	CLONAL	1	TRUE	0	0.52851994120696	1		436	530	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670645	134670645	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	130	486	0	ENST00000398015.3:c.556C>G	p.Leu186Val	p.L186V	ENST00000398015	NM_004441.4	186	Ctt/Gtt	3/16	0.456306903053524	1	FACETS	0.662	0.603	0.723	0.662	0.603	0.723	SUBCLONAL	1	TRUE	0	0.52851994120696	1		486	547	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933146	39933146	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	159	555	0	ENST00000378444.4:c.1453G>T	p.Glu485Ter	p.E485*	ENST00000378444	NM_001123385.1	485	Gaa/Taa	4/15	0.0853287572991994	5	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.52851994120696	5		555	916	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	226	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.450721882890227	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	2	0.560014683764932	4		334	616	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs371769427	NA	P-0051343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	138	298	1	ENST00000291552.4:c.101C>A	p.Ser34Tyr	p.S34Y	ENST00000291552	NM_006758.2	34	tCt/tAt	2/8	0.493504178605512	4	FACETS	0.922	0.847	0.999	0.922	0.847	0.999	CLONAL	2	TRUE	2	0.560014683764932	4		299	417	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	447	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.403598087213228	5	FACETS	1	0.99	1	1	0.99	1	CLONAL	4	TRUE	1	0.403598087213228	5		334	818	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866689	37866689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149210045	NA	P-0051345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1188	232	984	0	ENST00000269571.5:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269571		286	Gag/Aag	7/27	1	2	FACETS	0.81	0.753	0.868	0.81	0.753	0.868	CLONAL	1	TRUE	1	0.403598087213228	2		984	1420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0051345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	231	814	0	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.395420641503013	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.403598087213228	1		814	884	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0051346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	96	407	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.162877256617003	3	FACETS	0.922	0.821	1	0.922	0.821	1	CLONAL	2	TRUE	1	0.14	3		407	796	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0051346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	79	668	0	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	1	2	FACETS	0.942	0.826	1	0.942	0.826	1	CLONAL	1	TRUE	1	0.14	2		668	1198	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206608	108206608	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782317	NA	P-0051346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	46	297	0	ENST00000278616.4:c.8188C>A	p.Gln2730Lys	p.Q2730K	ENST00000278616	NM_000051.3	2730	Cag/Aag	56/63	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.14	2		297	630	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736204	204736204	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	34	287	0	ENST00000302823.3:c.561C>A	p.Ser187Arg	p.S187R	ENST00000302823	NM_005214.4	187	agC/agA	3/4	1	2	FACETS	0.886	0.723	1	0.886	0.723	1	CLONAL	1	TRUE	1	0.14	2		287	548	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410941	31410941	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	303	628	0	ENST00000344624.3:c.3579G>T	p.Glu1193Asp	p.E1193D	ENST00000344624		1193	gaG/gaT	28/33	1	2	FACETS	0.982	0.931	1	0.982	0.931	1	CLONAL	1	TRUE	1	0.845718744966919	2		628	730	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0051352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	101	637	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.215525883235368	2		637	791	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629328	187629328	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	44	532	1	ENST00000441802.2:c.1654G>T	p.Glu552Ter	p.E552*	ENST00000441802	NM_005245.3	552	Gaa/Taa	2/27	0.184068122276642	0	FACETS	0.43	0.359	0.508			1	SUBCLONAL	1	TRUE	0	0.215525883235368	0		533	745	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101352	27101352	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	114	695	0	ENST00000324856.7:c.4634G>A	p.Trp1545Ter	p.W1545*	ENST00000324856	NM_006015.4	1545	tGg/tAg	18/20	0.18344091526057	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.215525883235368	1		695	868	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166466	118166466	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	34	378	0	ENST00000369448.3:c.976C>A	p.Arg326Ser	p.R326S	ENST00000369448	NM_017709.3	326	Cgc/Agc	2/2	0.18344091526057	1	FACETS	0.491	0.4	0.594	0.491	0.4	0.594	SUBCLONAL	1	TRUE	0	0.215525883235368	1		378	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0051353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	310	547	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.308923731129311	3	FACETS	0.941	0.898	0.984	0.941	0.898	0.984	CLONAL	3	TRUE	0	0.476993501731304	3		547	570	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0051353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	61	283	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.476993501731304	2		283	252	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881392	37881392	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	1006	595	0	ENST00000269571.5:c.2584A>G	p.Thr862Ala	p.T862A	ENST00000269571		862	Aca/Gca	21/27	0.476993501731304	9	FACETS	0.99	0.967	1			1	CLONAL	7	TRUE	NA	0.476993501731304	9		595	1625	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795341	39795341	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1028107759	NA	P-0051353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	118	482	1	ENST00000288319.7:c.379G>A	p.Val127Met	p.V127M	ENST00000288319	NM_182918.3	127	Gtg/Atg	3/10	0.476993501731304	3	FACETS	1	0.985	1	0.485	0.441	0.531	CLONAL	1	TRUE	0	0.476993501731304	3		483	421	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743942	40743942	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868489194	NA	P-0051353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	267	512	0	ENST00000373198.4:c.3053G>A	p.Arg1018Gln	p.R1018Q	ENST00000373198	NM_133170.3	1018	cGa/cAa	23/32	0.457867123616648	5	FACETS	0.996	0.941	1	0.996	0.941	1	CLONAL	3	TRUE	2	0.476993501731304	5		512	643	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556077	29556077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	120	217	0	ENST00000356175.3:c.2444G>A	p.Arg815Lys	p.R815K	ENST00000356175	NM_000267.3	815	aGg/aAg	21/57	0.476993501731304	7	FACETS	1	0.977	1			1	CLONAL	2	TRUE	NA	0.476993501731304	7		217	449	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020768	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs926053251	NA	P-0051355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	313	513	0	ENST00000358127.4:c.77T>G	p.Val26Gly	p.V26G	ENST00000358127	NM_001280556.1	26	gTt/gGt	2/10	0.939562587145269	6	FACETS	0.979	0.925	1			1	CLONAL	2	FALSE	NA	0.939562587145269	6		513	980	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36653546	36653546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1489071647	NA	P-0051355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	272	564	0	ENST00000244741.5:c.464G>A	p.Arg155His	p.R155H	ENST00000244741	NM_000389.4	155	cGc/cAc	3/3	0.807998891785948	4	FACETS	0.856	0.809	0.903	0.856	0.809	0.903	CLONAL	2	FALSE	2	0.939562587145269	4		564	656	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0051356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	156	518	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.546942420762449	4	FACETS	0.935	0.863	1	0.935	0.863	1	CLONAL	2	TRUE	2	0.546942420762449	4		518	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579366	7579366	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0051356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	372	592	0	ENST00000269305.4:c.321C>G	p.Tyr107Ter	p.Y107*	ENST00000269305	NM_001126112.2	107	taC/taG	4/11	0.523102086140502	3	FACETS	0.996	0.958	1	0.996	0.958	1	CLONAL	3	TRUE	0	0.546942420762449	3		592	580	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627654	37627654	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	151	511	1	ENST00000447079.4:c.1569G>T	p.Lys523Asn	p.K523N	ENST00000447079	NM_015083.1	523	aaG/aaT	2/14	0.470155262278321	5	FACETS	1	0.968	1			1	CLONAL	1	TRUE	NA	0.546942420762449	5		512	896	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288306	21288306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	135	483	0	ENST00000354336.3:c.551C>T	p.Ser184Phe	p.S184F	ENST00000354336	NM_005207.3	184	tCc/tTc	2/3	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.546942420762449	2		483	464	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11273609	11273609	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532979867	NA	P-0051356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	104	289	0	ENST00000361445.4:c.3132G>A	p.Met1044Ile	p.M1044I	ENST00000361445	NM_004958.3	1044	atG/atA	21/58	0.546942420762449	2	FACETS	1	0.975	1	0.611	0.554	0.67	CLONAL	1	TRUE	0	0.546942420762449	2		289	311	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0051357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	64	467	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.467746488433869	2	FACETS	0.79	0.703	0.879	0.79	0.703	0.879	SUBCLONAL	2	FALSE	0	0.550773107199347	2		467	147	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645735	215645735	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854016	NA	P-0051357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	17	476	0	ENST00000260947.4:c.863C>T	p.Ser288Phe	p.S288F	ENST00000260947	NM_000465.2	288	tCt/tTt	4/11	0.431582190042652	3	FACETS	0.551	0.414	0.71	0.275	0.207	0.355	SUBCLONAL	1	FALSE	1	0.550773107199347	3		476	143	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578268	+	missense_variant	Missense_Mutation	TNP	TAA	TAA	GAT	novel	NA	P-0051358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	147	502	0	ENST00000269305.4:c.581_583delinsATC	p.Leu194_Ile195delinsHisLeu	p.L194_I195delinsHL	ENST00000269305	NM_001126112.2	194	cTTAtc/cATCtc	6/11	0.449319522987109	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.449319522987109	1		502	474	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145612	11145612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	51	502	0	ENST00000358026.2:c.3974G>A	p.Arg1325His	p.R1325H	ENST00000358026	NM_001128849.1	1325	cGc/cAc	29/36	0.449319522987109	1	FACETS	0.392	0.333	0.456	0.392	0.333	0.456	SUBCLONAL	1	TRUE	0	0.449319522987109	1		502	449	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18276985	18276985	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	89	401	0	ENST00000222254.8:c.1432C>T	p.Arg478Cys	p.R478C	ENST00000222254	NM_005027.3	478	Cgt/Tgt	12/16	0.348903758155088	1	FACETS	0.782	0.698	0.87	0.782	0.698	0.87	SUBCLONAL	1	TRUE	0	0.449319522987109	1		401	393	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277992	41277992	+	splice_donor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0051358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	97	299	0	ENST00000349496.5:c.1954+2del		p.X652_splice	ENST00000349496	NM_001904.3	652			0.320070290278982	3	FACETS	1	0.962	1	0.58	0.519	0.643	CLONAL	1	TRUE	1	0.449319522987109	3		299	456	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439300	52439303	+	frameshift_variant	Frame_Shift_Del	DEL	CTCT	CTCT	-	novel	NA	P-0051358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	125	502	0	ENST00000460680.1:c.939_942del	p.Glu314ArgfsTer20	p.E314Rfs*20	ENST00000460680	NM_004656.3	313	gcAGAG/gc	11/17	0.320070290278982	3	FACETS	0.958	0.869	1	0.479	0.434	0.527	CLONAL	1	TRUE	1	0.449319522987109	3		502	711	SUCCESS
APC	324	MSKCC	GRCh37	5	112174112	112174112	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	69	225	1	ENST00000257430.4:c.2821G>T	p.Glu941Ter	p.E941*	ENST00000257430	NM_000038.5	941	Gaa/Taa	16/16	0.449319522987109	1	FACETS	0.857	0.754	0.965	0.857	0.754	0.965	CLONAL	1	TRUE	0	0.449319522987109	1		226	278	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64290027	64290027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1423373632	NA	P-0051358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	95	342	0	ENST00000370651.3:c.470G>A	p.Arg157Gln	p.R157Q	ENST00000370651	NM_003463.4	157	cGg/cAg	6/6	0.17296515003505	3	FACETS	0.834	0.744	0.93	0.417	0.372	0.465	INDETERMINATE	1	TRUE	1	0.449319522987109	3		342	621	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962929	2962929	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147006022	NA	P-0051358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	166	707	0	ENST00000396946.4:c.1979G>A	p.Arg660Gln	p.R660Q	ENST00000396946	NM_032415.4	660	cGg/cAg	16/25	NA	2	FACETS	0.958	0.882	1			1	INDETERMINATE	1	TRUE	NA	0.449319522987109	2		707	771	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524357	148524357	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	58	184	0	ENST00000320356.2:c.627T>G	p.Asp209Glu	p.D209E	ENST00000320356	NM_004456.4	209	gaT/gaG	7/20	0.348903758155088	1	FACETS	0.91	0.792	1	0.91	0.792	1	CLONAL	1	TRUE	0	0.449319522987109	1		184	220	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624242	89624243	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs121913290	NA	P-0051360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	59	157	0	ENST00000371953.3:c.17_18del	p.Lys6ArgfsTer4	p.K6Rfs*4	ENST00000371953	NM_000314.4	6	AAa/a	1/9	0.658230030799905	1	FACETS	0.955	0.848	1	0.955	0.848	1	CLONAL	1	TRUE	0	0.658230030799905	1		157	126	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0051360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	256	529	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	0.658230030799905	8	FACETS	0.918	0.866	0.971			1	CLONAL	4	TRUE	NA	0.658230030799905	8		529	630	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350784	89350785	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0051360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	12	546	0	ENST00000301030.4:c.2165_2166del	p.Lys722ArgfsTer19	p.K722Rfs*19	ENST00000301030	NM_001256183.1	722	aAA/a	9/13	0.658230030799905	1	FACETS	0.252	0.179	0.34	0.252	0.179	0.34	SUBCLONAL	1	TRUE	0	0.658230030799905	1		546	97	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276749	15276749	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	17	614	0	ENST00000263388.2:c.5516G>C	p.Gly1839Ala	p.G1839A	ENST00000263388	NM_000435.2	1839	gGc/gCc	30/33	0.658230030799905	1	FACETS	0.248	0.186	0.319	0.248	0.186	0.319	SUBCLONAL	1	TRUE	0	0.658230030799905	1		614	140	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86676360	86676360	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	113	346	0	ENST00000274376.6:c.2638T>C	p.Ser880Pro	p.S880P	ENST00000274376	NM_002890.2	880	Tct/Cct	20/25	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.706391549654763	2		346	294	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	138	630	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.889	0.811	0.972	1	0.989	1	CLONAL	2	TRUE	1	0.218256505321047	2		630	711	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	128	696	1	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.883	0.802	0.968	1	0.989	1	CLONAL	2	TRUE	1	0.218256505321047	2		697	664	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	60	489	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.831	0.72	0.949	1	0.974	1	CLONAL	2	TRUE	1	0.218256505321047	2		489	331	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	92	594	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	1	2	FACETS	0.999	0.893	1	1	0.986	1	CLONAL	2	TRUE	1	0.218256505321047	2		594	422	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	94	554	1	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	1	2	FACETS	0.76	0.677	0.847	1	0.981	1	SUBCLONAL	2	TRUE	1	0.218256505321047	2		555	567	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	73	362	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.899	0.791	1	1	0.981	1	CLONAL	2	TRUE	1	0.218256505321047	2		362	372	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	49	468	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	0.85	0.726	0.985	1	0.97	1	CLONAL	2	TRUE	1	0.218256505321047	2		468	264	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	21	359	2	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.218256505321047	2		361	165	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057936	27057937	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1415146710	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	170	765	1	ENST00000324856.7:c.1650dup	p.Tyr551LeufsTer72	p.Y551Lfs*72	ENST00000324856	NM_006015.4	548	-/C	3/20	1	2	FACETS	0.938	0.864	1	1	0.992	1	CLONAL	2	TRUE	1	0.218256505321047	2		766	830	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	156	731	4	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.88	0.807	0.957	1	0.99	1	CLONAL	2	TRUE	1	0.218256505321047	2		735	812	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	83	404	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.911	1	1	0.989	1	CLONAL	3	TRUE	1	0.218256505321047	2		404	249	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021276	31021277	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886042532	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	91	670	1	ENST00000375687.4:c.1281dup	p.Gln428ThrfsTer10	p.Q428Tfs*10	ENST00000375687	NM_015338.5	425	-/A	12/13	1	2	FACETS	0.885	0.789	0.987	1	0.984	1	CLONAL	2	TRUE	1	0.218256505321047	2		671	471	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	144	819	2	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	1	0.941	1	1	0.991	1	CLONAL	2	TRUE	1	0.218256505321047	2		821	637	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938230	76938230	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	39	645	2	ENST00000373344.5:c.2518del	p.Arg840GlufsTer29	p.R840Efs*29	ENST00000373344	NM_000489.3	840	Aga/ga	9/35	0.218256505321047	1	FACETS	0.977	0.822	1	1	0.968	1	CLONAL	2	TRUE	0	0.218256505321047	1		647	163	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056856	102056856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	39	447	0	ENST00000282441.5:c.796C>T	p.Arg266Cys	p.R266C	ENST00000282441	NM_001130145.2	266	Cgt/Tgt	4/9	1	2	FACETS	1	0.884	1	1	0.97	1	CLONAL	2	TRUE	1	0.218256505321047	2		447	168	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940402	49940402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760399844	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	165	934	2	ENST00000296474.3:c.641G>A	p.Arg214His	p.R214H	ENST00000296474	NM_002447.2	214	cGc/cAc	1/20	1	2	FACETS	0.95	0.873	1	1	0.992	1	CLONAL	2	TRUE	1	0.218256505321047	2		936	796	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655413	45655413	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	180	772	1	ENST00000407780.3:c.439del	p.His147ThrfsTer15	p.H147Tfs*15	ENST00000407780	NM_001283052.1	147	Cac/ac	4/7	NA	2	FACETS	1	0.957	1			1	INDETERMINATE	2	TRUE	NA	0.218256505321047	2		773	784	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656840	45656840	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	163	688	3	ENST00000407780.3:c.316del	p.Gln106ArgfsTer11	p.Q106Rfs*11	ENST00000407780	NM_001283052.1	106	Cag/ag	3/7	NA	2	FACETS	0.997	0.917	1			1	INDETERMINATE	2	TRUE	NA	0.218256505321047	2		691	749	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279834	46279836	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	rs767107142	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	61	590	0	ENST00000371998.3:c.3762_3764del	p.Gln1276del	p.Q1276del	ENST00000371998		1254	CAA/-	20/23	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.218256505321047	2		590	517	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	327	943	5	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.988	0.939	1	1	0.997	1	CLONAL	4	TRUE	1	0.218256505321047	2		948	758	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	152	847	1	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	0.16192475266016	4	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	2	0.218256505321047	4		848	832	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352366	70352366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	98	659	0	ENST00000374080.3:c.4393C>T	p.Arg1465Cys	p.R1465C	ENST00000374080		1465	Cgt/Tgt	31/45	0.218256505321047	1	FACETS	0.924	0.829	1	1	0.986	1	CLONAL	2	TRUE	0	0.218256505321047	1		659	433	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	127	748	4	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	0.218256505321047	5	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	3	0.218256505321047	5		752	756	SUCCESS
APC	324	MSKCC	GRCh37	5	112177150	112177150	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	23	479	0	ENST00000257430.4:c.5862del	p.Phe1954LeufsTer16	p.F1954Lfs*16	ENST00000257430	NM_000038.5	1953	aaT/aa	16/16	1	2	FACETS	0.901	0.713	1	1	0.943	1	CLONAL	2	TRUE	1	0.218256505321047	2		479	117	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288789	15288789	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	95	257	0	ENST00000263388.2:c.3950del	p.Pro1317GlnfsTer103	p.P1317Qfs*103	ENST00000263388	NM_000435.2	1317	cCa/ca	24/33	1	2	FACETS	1	0.923	1	1	0.987	1	CLONAL	2	TRUE	1	0.218256505321047	2		257	420	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141557684	141557684	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1382352330	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	158	893	0	ENST00000220592.5:c.1631C>T	p.Thr544Met	p.T544M	ENST00000220592	NM_012154.3	544	aCg/aTg	13/19	0.218256505321047	1	FACETS	0.819	0.752	0.89	1	0.99	1	CLONAL	2	TRUE	0	0.218256505321047	1		893	787	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541507	187541507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758885671	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	61	421	0	ENST00000441802.2:c.6233C>T	p.Ala2078Val	p.A2078V	ENST00000441802	NM_005245.3	2078	gCg/gTg	10/27	1	2	FACETS	1	0.89	1	1	0.98	1	CLONAL	2	TRUE	1	0.218256505321047	2		421	273	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80169100	80169100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545543643	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	29	479	0	ENST00000265081.6:c.3296C>T	p.Thr1099Met	p.T1099M	ENST00000265081	NM_002439.4	1099	aCg/aTg	23/24	1	2	FACETS	0.868	0.714	1	1	0.966	1	CLONAL	3	TRUE	1	0.218256505321047	2		479	102	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957496	175957496	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1326454203	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	36	507	0	ENST00000367669.3:c.1900C>T	p.Arg634Cys	p.R634C	ENST00000367669	NM_022457.5	634	Cgt/Tgt	17/20	0.218256505321047	5	FACETS	0.811	0.67	0.967	0.405	0.335	0.484	CLONAL	2	TRUE	1	0.218256505321047	5		507	270	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863053	56863054	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	23	550	0	ENST00000519728.1:c.327dup	p.Glu110ArgfsTer40	p.E110Rfs*40	ENST00000519728	NM_002350.3	107	aca/acAa	5/13	0.218256505321047	1	FACETS	1	0.812	1	1	0.812	1	CLONAL	1	TRUE	0	0.218256505321047	1		550	181	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749509	41749509	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	149	663	1	ENST00000226382.2:c.286C>T	p.Arg96Cys	p.R96C	ENST00000226382	NM_003924.3	96	Cgc/Tgc	2/3	1	2	FACETS	1	0.976	1	1	0.992	1	CLONAL	2	TRUE	1	0.218256505321047	2		664	586	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426725	47426725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773318953	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	162	805	1	ENST00000377045.4:c.970G>A	p.Val324Met	p.V324M	ENST00000377045	NM_001654.4	324	Gtg/Atg	10/16	0.218256505321047	1	FACETS	0.852	0.783	0.924	1	0.991	1	CLONAL	2	TRUE	0	0.218256505321047	1		806	776	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979269	40979269	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	61	534	0	ENST00000373198.4:c.1864A>T	p.Ser622Cys	p.S622C	ENST00000373198	NM_133170.3	622	Agt/Tgt	11/32	1	2	FACETS	0.794	0.689	0.907	1	0.973	1	CLONAL	2	TRUE	1	0.218256505321047	2		534	352	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731124	162731124	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs183287339	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	71	660	0	ENST00000367921.3:c.979G>A	p.Val327Ile	p.V327I	ENST00000367921	NM_006182.2	327	Gtc/Atc	9/18	0.218256505321047	5	FACETS	1	0.96	1	0.316	0.275	0.36	CLONAL	1	TRUE	1	0.218256505321047	5		660	683	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927650	131927650	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	29	383	0	ENST00000265335.6:c.1722del	p.Lys574AsnfsTer24	p.K574Nfs*24	ENST00000265335		573	Aaa/aa	11/25	1	2	FACETS	0.929	0.756	1	1	0.955	1	CLONAL	2	TRUE	1	0.218256505321047	2		383	143	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710794	117710794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146130970	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	49	433	0	ENST00000368508.3:c.1478G>A	p.Arg493His	p.R493H	ENST00000368508	NM_002944.2	493	cGc/cAc	12/43	0.208442041654085	0	FACETS	0.82	0.703	0.946			1	CLONAL	2	TRUE	0	0.218256505321047	0		433	214	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879618	37879618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567911318	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	171	848	0	ENST00000269571.5:c.1993G>A	p.Val665Met	p.V665M	ENST00000269571		665	Gtg/Atg	17/27	1	2	FACETS	0.959	0.883	1	1	0.992	1	CLONAL	2	TRUE	1	0.218256505321047	2		848	817	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563390	87563390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1273745094	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	110	617	0	ENST00000277120.3:c.1778C>T	p.Ala593Val	p.A593V	ENST00000277120		593	gCc/gTc	16/19	0.218256505321047	1	FACETS	1	0.938	1	1	0.989	1	CLONAL	2	TRUE	0	0.218256505321047	1		617	428	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256357	16256357	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146795560	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	64	758	1	ENST00000375759.3:c.3622G>A	p.Val1208Ile	p.V1208I	ENST00000375759	NM_015001.2	1208	Gtt/Att	11/15	1	2	FACETS	0.878	0.765	0.998	1	0.978	1	CLONAL	2	TRUE	1	0.218256505321047	2		759	334	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262351	16262351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1284524934	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	68	477	0	ENST00000375759.3:c.9616G>A	p.Val3206Ile	p.V3206I	ENST00000375759	NM_015001.2	3206	Gtc/Atc	11/15	1	2	FACETS	0.847	0.741	0.96	1	0.978	1	CLONAL	2	TRUE	1	0.218256505321047	2		477	368	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838369	156838369	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1471711796	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	176	907	0	ENST00000524377.1:c.647A>G	p.Gln216Arg	p.Q216R	ENST00000524377	NM_002529.3	216	cAg/cGg	6/17	0.218256505321047	5	FACETS	0.876	0.805	0.95	0.438	0.402	0.475	CLONAL	2	TRUE	1	0.218256505321047	5		907	1222	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567742	226567742	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	119	678	1	ENST00000366794.5:c.1424C>T	p.Ala475Val	p.A475V	ENST00000366794	NM_001618.3	475	gCg/gTg	10/23	0.218256505321047	5	FACETS	0.928	0.838	1	0.464	0.419	0.512	CLONAL	2	TRUE	1	0.218256505321047	5		679	780	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717645	89717646	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	53	604	0	ENST00000371953.3:c.674_675del	p.Tyr225PhefsTer17	p.Y225Ffs*17	ENST00000371953	NM_000314.4	224	ATa/a	7/9	1	2	FACETS	1	0.911	1	1	0.978	1	CLONAL	2	TRUE	1	0.218256505321047	2		604	226	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137020	64137020	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	161	760	0	ENST00000334205.4:c.1531C>A	p.Arg511Ser	p.R511S	ENST00000334205	NM_003942.2	511	Cgc/Agc	13/17	1	2	FACETS	1	0.965	1	1	0.992	1	CLONAL	2	TRUE	1	0.218256505321047	2		760	678	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170444	119170444	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	73	484	0	ENST00000264033.4:c.2674C>A	p.Leu892Ile	p.L892I	ENST00000264033	NM_005188.3	892	Ctc/Atc	16/16	1	2	FACETS	1	0.902	1	1	0.983	1	CLONAL	2	TRUE	1	0.218256505321047	2		484	326	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394818	394818	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	48	481	0	ENST00000399788.2:c.4877T>C	p.Val1626Ala	p.V1626A	ENST00000399788	NM_001042603.1	1626	gTa/gCa	28/28	0.208337735084908	1	FACETS	1	0.902	1	1	0.976	1	CLONAL	2	TRUE	0	0.218256505321047	1		481	184	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427590	427590	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	16	480	0	ENST00000399788.2:c.2579C>T	p.Ala860Val	p.A860V	ENST00000399788	NM_001042603.1	860	gCt/gTt	19/28	0.208337735084908	1	FACETS	0.634	0.47	0.829	0.634	0.47	0.829	SUBCLONAL	1	TRUE	0	0.218256505321047	1		480	206	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21630798	21630798	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	21	561	0	ENST00000421138.2:c.806del	p.Leu269CysfsTer37	p.L269Cfs*37	ENST00000421138		269	tTg/tg	8/16	1	2	FACETS	1	0.784	1	1	0.784	1	CLONAL	1	TRUE	1	0.218256505321047	2		561	190	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431256	49431256	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	114	793	0	ENST00000301067.7:c.9883A>G	p.Met3295Val	p.M3295V	ENST00000301067	NM_003482.3	3295	Atg/Gtg	34/54	0.218256505321047	5	FACETS	0.869	0.785	0.956	1	0.979	1	CLONAL	3	TRUE	3	0.218256505321047	5		793	532	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434333	49434333	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	191	887	0	ENST00000301067.7:c.7220C>A	p.Pro2407His	p.P2407H	ENST00000301067	NM_003482.3	2407	cCt/cAt	31/54	0.218256505321047	5	FACETS	0.878	0.813	0.946	1	0.987	1	CLONAL	3	TRUE	3	0.218256505321047	5		887	882	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562184	21562184	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	131	990	0	ENST00000382592.4:c.1735C>A	p.Pro579Thr	p.P579T	ENST00000382592	NM_014572.2	579	Ccc/Acc	4/8	0.218256505321047	1	FACETS	0.821	0.747	0.899	1	0.988	1	CLONAL	2	TRUE	0	0.218256505321047	1		990	651	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465439	99465439	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	42	560	0	ENST00000268035.6:c.2264G>T	p.Arg755Met	p.R755M	ENST00000268035	NM_000875.3	755	aGg/aTg	11/21	1	2	FACETS	0.842	0.703	0.996	0.842	0.703	0.996	CLONAL	1	TRUE	1	0.218256505321047	2		560	457	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396543	396543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	151	840	0	ENST00000262320.3:c.483G>T	p.Lys161Asn	p.K161N	ENST00000262320	NM_003502.3	161	aaG/aaT	2/11	1	2	FACETS	1	0.93	1	1	0.992	1	CLONAL	2	TRUE	1	0.218256505321047	2		840	681	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779608	3779608	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs747252584	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	194	1010	1	ENST00000262367.5:c.5440G>T	p.Gly1814Trp	p.G1814W	ENST00000262367	NM_004380.2	1814	Ggg/Tgg	31/31	1	2	FACETS	1	0.945	1	1	0.993	1	CLONAL	2	TRUE	1	0.218256505321047	2		1011	868	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81927384	81927384	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	140	666	0	ENST00000359376.3:c.1057T>G	p.Cys353Gly	p.C353G	ENST00000359376	NM_002661.3	353	Tgt/Ggt	12/33	1	2	FACETS	0.914	0.834	0.997	1	0.99	1	CLONAL	2	TRUE	1	0.218256505321047	2		666	702	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346662	89346662	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	127	659	0	ENST00000301030.4:c.6288del	p.Leu2098TrpfsTer77	p.L2098Wfs*77	ENST00000301030	NM_001256183.1	2096	ggG/gg	9/13	1	2	FACETS	0.878	0.801	0.957	1	0.992	1	CLONAL	3	TRUE	1	0.218256505321047	2		659	442	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351566	89351569	+	frameshift_variant	Frame_Shift_Del	DEL	TTTC	TTTC	-	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	106	784	0	ENST00000301030.4:c.1381_1384del	p.Glu461GlnfsTer48	p.E461Qfs*48	ENST00000301030	NM_001256183.1	461	GAAAca/ca	9/13	1	2	FACETS	0.874	0.786	0.966	1	0.986	1	CLONAL	2	TRUE	1	0.218256505321047	2		784	556	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973646	15973646	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779429826	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	86	608	0	ENST00000268712.3:c.4346C>T	p.Thr1449Met	p.T1449M	ENST00000268712	NM_006311.3	1449	aCg/aTg	31/46	1	2	FACETS	0.806	0.715	0.902	1	0.981	1	CLONAL	2	TRUE	1	0.218256505321047	2		608	489	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512435	38512435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1190379367	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	166	863	1	ENST00000254066.5:c.1346G>A	p.Ser449Asn	p.S449N	ENST00000254066	NM_000964.3	449	aGc/aAc	9/9	1	2	FACETS	0.909	0.835	0.985	1	0.991	1	CLONAL	2	TRUE	1	0.218256505321047	2		864	837	SUCCESS
YES1	7525	MSKCC	GRCh37	18	742999	743000	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	32	522	0	ENST00000314574.4:c.978dup	p.Leu327IlefsTer4	p.L327Ifs*4	ENST00000314574	NM_005433.3	326	-/A	8/12	1	2	FACETS	0.899	0.739	1	1	0.958	1	CLONAL	2	TRUE	1	0.218256505321047	2		522	163	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220376	1220376	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	127	763	1	ENST00000326873.7:c.469T>C	p.Phe157Leu	p.F157L	ENST00000326873	NM_000455.4	157	Ttc/Ctc	4/10	1	2	FACETS	0.905	0.822	0.992	1	0.989	1	CLONAL	2	TRUE	1	0.218256505321047	2		764	643	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095992	11095992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	170	798	3	ENST00000358026.2:c.266G>A	p.Arg89His	p.R89H	ENST00000358026	NM_001128849.1	89	cGc/cAc	3/36	1	2	FACETS	1	0.953	1	1	0.993	1	CLONAL	2	TRUE	1	0.218256505321047	2		801	744	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349751	15349751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	58	864	1	ENST00000263377.2:c.3823G>A	p.Ala1275Thr	p.A1275T	ENST00000263377	NM_058243.2	1275	Gcc/Acc	19/20	1	2	FACETS	0.722	0.619	0.835	0.722	0.619	0.835	SUBCLONAL	1	TRUE	1	0.218256505321047	2		865	736	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18943193	18943193	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1315599115	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	21	40	0	ENST00000262803.5:c.175G>C	p.Ala59Pro	p.A59P	ENST00000262803	NM_002911.3	59	Gcg/Ccg	1/24	1	2	FACETS	1	0.886	1	1	0.951	1	CLONAL	2	TRUE	1	0.218256505321047	2		40	80	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705482	47705482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	22	506	0	ENST00000233146.2:c.2282G>A	p.Gly761Glu	p.G761E	ENST00000233146	NM_000251.2	761	gGg/gAg	14/16	1	2	FACETS	0.769	0.604	0.957	1	0.927	1	CLONAL	2	TRUE	1	0.218256505321047	2		506	131	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627289	37627289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	63	958	1	ENST00000249071.6:c.430G>A	p.Ala144Thr	p.A144T	ENST00000249071	NM_002872.4	144	Gca/Aca	5/7	1	2	FACETS	0.638	0.55	0.734	0.638	0.55	0.734	SUBCLONAL	1	TRUE	1	0.218256505321047	2		959	905	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417925	138417925	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	44	388	0	ENST00000289153.2:c.1594A>G	p.Lys532Glu	p.K532E	ENST00000289153	NM_006219.2	532	Aaa/Gaa	11/22	1	2	FACETS	0.878	0.75	1	1	0.977	1	CLONAL	3	TRUE	1	0.218256505321047	2		388	153	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451340	187451340	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	81	444	0	ENST00000232014.4:c.142del	p.Thr48ArgfsTer18	p.T48Rfs*18	ENST00000232014	NM_001130845.1	48	Acg/cg	3/10	1	2	FACETS	0.888	0.786	0.996	1	0.982	1	CLONAL	2	TRUE	1	0.218256505321047	2		444	418	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521066	187521066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572074365	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	106	514	0	ENST00000441802.2:c.12089C>T	p.Pro4030Leu	p.P4030L	ENST00000441802	NM_005245.3	4030	cCg/cTg	22/27	1	2	FACETS	1	0.972	1	1	0.99	1	CLONAL	2	TRUE	1	0.218256505321047	2		514	403	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410882	31410882	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs899896220	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	144	681	1	ENST00000344624.3:c.3638G>A	p.Arg1213His	p.R1213H	ENST00000344624		1213	cGc/cAc	28/33	1	2	FACETS	1	0.926	1	1	0.991	1	CLONAL	2	TRUE	1	0.218256505321047	2		682	651	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526231	31526231	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	178	878	0	ENST00000344624.3:c.809A>G	p.Asp270Gly	p.D270G	ENST00000344624		270	gAc/gGc	2/33	1	2	FACETS	1	0.98	1	1	0.993	1	CLONAL	2	TRUE	1	0.218256505321047	2		878	697	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250428	26250428	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	128	637	2	ENST00000446824.2:c.406G>A	p.Ala136Thr	p.A136T	ENST00000446824	NM_021018.2	136	Gca/Aca	1/1	0.218256505321047	7	FACETS	0.917	0.833	1	0.459	0.416	0.503	CLONAL	3	TRUE	1	0.218256505321047	7		639	659	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681034	30681034	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	93	652	0	ENST00000376406.3:c.685G>A	p.Ala229Thr	p.A229T	ENST00000376406	NM_014641.2	229	Gcc/Acc	5/15	0.16192475266016	4	FACETS	0.951	0.848	1	0.951	0.848	1	CLONAL	2	TRUE	2	0.218256505321047	4		652	546	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800220	32800220	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	86	530	0	ENST00000374899.4:c.1162C>T	p.Gln388Ter	p.Q388*	ENST00000374899	NM_018833.2	388	Cag/Tag	7/12	0.16192475266016	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	2	0.218256505321047	4		530	413	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715401	117715402	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1392239785	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	12	417	0	ENST00000368508.3:c.1087dup	p.Tyr363LeufsTer25	p.Y363Lfs*25	ENST00000368508	NM_002944.2	363	tac/tTac	10/43	0.208442041654085	0	FACETS	0.803	0.57	1			1	CLONAL	1	TRUE	0	0.218256505321047	0		417	107	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004417	150004417	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	54	629	0	ENST00000253339.5:c.1808G>T	p.Gly603Val	p.G603V	ENST00000253339		603	gGg/gTg	3/7	0.16192475266016	4	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	2	0.218256505321047	4		629	250	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222640	157222641	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	168	665	0	ENST00000346085.5:c.1909_1910del	p.Arg637ValfsTer15	p.R637Vfs*15	ENST00000346085	NM_020732.3	636	cAG/c	4/20	0.16192475266016	4	FACETS	0.844	0.777	0.913	1	0.984	1	CLONAL	3	TRUE	2	0.218256505321047	4		665	741	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527961	157527961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	141	698	0	ENST00000346085.5:c.5686C>T	p.Pro1896Ser	p.P1896S	ENST00000346085	NM_020732.3	1896	Ccc/Tcc	20/20	0.16192475266016	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.218256505321047	4		698	639	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595297	141595297	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	138	838	1	ENST00000220592.5:c.136G>T	p.Glu46Ter	p.E46*	ENST00000220592	NM_012154.3	46	Gaa/Taa	2/19	0.218256505321047	1	FACETS	0.978	0.894	1	1	0.991	1	CLONAL	2	TRUE	0	0.218256505321047	1		839	576	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760445	133760445	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	158	783	0	ENST00000318560.5:c.2768C>T	p.Ala923Val	p.A923V	ENST00000318560	NM_005157.4	923	gCc/gTc	11/11	0.218256505321047	1	FACETS	1	0.965	1	1	0.992	1	CLONAL	2	TRUE	0	0.218256505321047	1		783	595	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343068	70343068	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	85	597	0	ENST00000374080.3:c.1609G>T	p.Glu537Ter	p.E537*	ENST00000374080		537	Gag/Tag	11/45	0.218256505321047	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.218256505321047	1		597	536	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360492	70360492	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	99	707	0	ENST00000374080.3:c.6052del	p.His2018ThrfsTer9	p.H2018Tfs*9	ENST00000374080		2018	Cac/ac	42/45	0.218256505321047	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.218256505321047	1		707	594	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0051367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	78	401	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.317338376316368	4	FACETS	1	0.931	1	0.54	0.476	0.609	CLONAL	1	TRUE	2	0.435488458571129	4		401	476	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0051367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	149	270	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.418783449476708	2	FACETS	0.948	0.878	1	0.948	0.878	1	CLONAL	2	TRUE	0	0.435488458571129	2		270	361	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905962	50905962	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371612922	NA	P-0051367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	173	739	1	ENST00000440232.2:c.934G>A	p.Val312Met	p.V312M	ENST00000440232	NM_002691.3	312	Gtg/Atg	8/27	0.435488458571129	4	FACETS	0.905	0.831	0.983	0.302	0.277	0.328	CLONAL	1	TRUE	1	0.435488458571129	4		740	1260	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114833	108114837	+	frameshift_variant	Frame_Shift_Del	DEL	TTCAG	TTCAG	-	novel	NA	P-0051367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	88	408	0	ENST00000278616.4:c.651_655del	p.Ile217MetfsTer35	p.I217Mfs*35	ENST00000278616	NM_000051.3	217	aTTCAG/a	6/63	1	2	FACETS	0.823	0.732	0.92	0.823	0.732	0.92	CLONAL	1	TRUE	1	0.435488458571129	2		408	491	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134403	30134403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781519812	NA	P-0051367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	325	577	0	ENST00000263025.4:c.128C>T	p.Thr43Met	p.T43M	ENST00000263025	NM_002746.2	43	aCg/aTg	1/9	0.435488458571129	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.435488458571129	3		577	872	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828485	72828485	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	57	583	0	ENST00000268489.5:c.8096G>C	p.Gly2699Ala	p.G2699A	ENST00000268489	NM_006885.3	2699	gGa/gCa	9/10	0.311215565727416	3	FACETS	0.418	0.358	0.484	0.209	0.179	0.242	SUBCLONAL	1	TRUE	1	0.435488458571129	3		583	762	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80083398	80083398	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	121	488	0	ENST00000265081.6:c.2450A>C	p.His817Pro	p.H817P	ENST00000265081	NM_002439.4	817	cAt/cCt	18/24	0.418783449476708	2	FACETS	0.893	0.809	0.982	0.447	0.404	0.491	CLONAL	1	TRUE	0	0.435488458571129	2		488	622	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931846	68931846	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	166	532	0	ENST00000288368.4:c.276A>C	p.Glu92Asp	p.E92D	ENST00000288368	NM_024870.2	92	gaA/gaC	3/40	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.435488458571129	2		532	756	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950454	68950454	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	108	415	0	ENST00000288368.4:c.766T>C	p.Ser256Pro	p.S256P	ENST00000288368	NM_024870.2	256	Tct/Cct	7/40	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.435488458571129	2		415	477	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	66	530	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.396737842463047	1	FACETS	0.525	0.457	0.599	0.525	0.457	0.599	SUBCLONAL	1	TRUE	0	0.435675165306778	1		533	451	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	45	696	1	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.234	0.196	0.277	0.234	0.196	0.277	SUBCLONAL	1	TRUE	1	0.435675165306778	2		697	881	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	212	731	4	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.968	0.9	1	0.968	0.9	1	CLONAL	1	TRUE	1	0.435675165306778	2		735	1005	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	189	531	2	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	0.341099675713657	1	FACETS	0.965	0.895	1	0.965	0.895	1	CLONAL	1	TRUE	0	0.435675165306778	1		533	703	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	88	359	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.435675165306778	2		359	317	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	12	265	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.341099675713657	1	FACETS	0.268	0.188	0.364	0.268	0.188	0.364	SUBCLONAL	1	TRUE	0	0.435675165306778	1		265	161	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106336	27106337	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	88	537	0	ENST00000324856.7:c.5952_5953del	p.Ser1985GlnfsTer13	p.S1985Qfs*13	ENST00000324856	NM_006015.4	1983	TGt/t	20/20	0.341099675713657	1	FACETS	0.457	0.405	0.513	0.457	0.405	0.513	SUBCLONAL	1	TRUE	0	0.435675165306778	1		537	691	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	62	498	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	0.435675165306778	1	FACETS	0.495	0.428	0.567	0.495	0.428	0.567	SUBCLONAL	1	TRUE	0	0.435675165306778	1		498	450	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308382	15308383	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs749829137	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	147	581	0	ENST00000263388.2:c.125dup	p.Cys43LeufsTer32	p.C43Lfs*32	ENST00000263388	NM_000435.2	42	cct/ccCt	2/33	1	2	FACETS	0.835	0.763	0.911	0.835	0.763	0.911	CLONAL	1	TRUE	1	0.435675165306778	2		581	808	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451784	29451784	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs772809305	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	68	450	3	ENST00000389048.3:c.2781del	p.Cys928AlafsTer11	p.C928Afs*11	ENST00000389048	NM_004304.4	927	ggG/gg	16/29	1	2	FACETS	0.534	0.464	0.608	0.534	0.464	0.608	SUBCLONAL	1	TRUE	1	0.435675165306778	2		453	585	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	179	565	0	ENST00000397062.3:c.246A>T	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaT	2/5	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.435675165306778	2		565	750	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	66	469	1	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	0.482	0.418	0.552	0.482	0.418	0.552	SUBCLONAL	1	TRUE	1	0.435675165306778	2		470	628	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944382	131944382	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs748536322	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	39	265	3	ENST00000265335.6:c.2801del	p.Asn934IlefsTer6	p.N934Ifs*6	ENST00000265335		932	Aaa/aa	17/25	0.396737842463047	1	FACETS	0.819	0.688	0.96	0.819	0.688	0.96	CLONAL	1	TRUE	0	0.435675165306778	1		268	171	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678572	88678572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1161765368	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	79	446	0	ENST00000360948.2:c.964G>A	p.Glu322Lys	p.E322K	ENST00000360948	NM_001012338.2	322	Gag/Aag	9/19	0.396737842463047	1	FACETS	0.506	0.445	0.57	0.506	0.445	0.57	SUBCLONAL	1	TRUE	0	0.435675165306778	1		446	561	SUCCESS
APC	324	MSKCC	GRCh37	5	112176023	112176024	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs863225359	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	30	334	0	ENST00000257430.4:c.4733_4734del	p.Cys1578TyrfsTer12	p.C1578Yfs*12	ENST00000257430	NM_000038.5	1578	TGt/t	16/16	0.396737842463047	1	FACETS	0.39	0.315	0.475	0.39	0.315	0.475	SUBCLONAL	1	TRUE	0	0.435675165306778	1		334	276	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353939	15353947	+	inframe_deletion	In_Frame_Del	DEL	GGGGTGGTG	GGGGTGGTG	-	rs758265124	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	85	313	11	ENST00000263377.2:c.2933_2941del	p.Pro978_Pro980del	p.P978_P980del	ENST00000263377	NM_058243.2	978	cCACCACCCCag/cag	14/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.435675165306778	2		324	355	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716329	52716329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863225094	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	209	607	0	ENST00000322088.6:c.773G>A	p.Arg258His	p.R258H	ENST00000322088	NM_014225.5	258	cGc/cAc	6/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.435675165306778	2		607	857	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348561	56348561	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	28	329	0	ENST00000348428.3:c.374del	p.Pro125GlnfsTer3	p.P125Qfs*3	ENST00000348428	NM_006785.3	123	agC/ag	2/17	0.396737842463047	1	FACETS	0.34	0.272	0.417	0.34	0.272	0.417	SUBCLONAL	1	TRUE	0	0.435675165306778	1		329	296	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911141	29911141	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	73	668	0	ENST00000376809.5:c.440A>G	p.Tyr147Cys	p.Y147C	ENST00000376809	NM_002116.7	147	tAc/tGc	3/8	0.173788438846734	2	FACETS	0.505	0.441	0.573	0.252	0.22	0.287	INDETERMINATE	1	TRUE	0	0.435675165306778	2		668	664	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	105	801	0	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.503	0.45	0.56	0.503	0.45	0.56	SUBCLONAL	1	TRUE	1	0.435675165306778	2		801	958	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795066	42795066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537583557	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	93	752	1	ENST00000575354.2:c.2146C>T	p.Arg716Trp	p.R716W	ENST00000575354	NM_015125.3	716	Cgg/Tgg	10/20	1	2	FACETS	0.477	0.423	0.535	0.477	0.423	0.535	SUBCLONAL	1	TRUE	1	0.435675165306778	2		753	895	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300040	137300040	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	101	623	0	ENST00000481739.1:c.331del	p.Leu111TrpfsTer57	p.L111Wfs*57	ENST00000481739	NM_002957.4	109	Ccc/cc	3/10	0.396737842463047	1	FACETS	0.458	0.409	0.51	0.458	0.409	0.51	SUBCLONAL	1	TRUE	0	0.435675165306778	1		623	792	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213358	36213359	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	81	758	0	ENST00000222270.7:c.2561_2562del	p.Glu854AlafsTer34	p.E854Afs*34	ENST00000222270	NM_014727.1	852	aAG/a	4/37	1	2	FACETS	0.361	0.317	0.409	0.361	0.317	0.409	SUBCLONAL	1	TRUE	1	0.435675165306778	2		758	1030	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434959	49434959	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555192751	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	167	613	0	ENST00000301067.7:c.6594del	p.Tyr2199IlefsTer65	p.Y2199Ifs*65	ENST00000301067	NM_003482.3	2198	ccC/cc	31/54	1	2	FACETS	0.921	0.847	0.998	0.921	0.847	0.998	CLONAL	1	TRUE	1	0.435675165306778	2		613	832	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830807	72830807	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	194	543	0	ENST00000268489.5:c.5774del	p.Gly1925ValfsTer72	p.G1925Vfs*72	ENST00000268489	NM_006885.3	1925	gGt/gt	9/10	0.435675165306778	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.435675165306778	1		543	638	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916646	178916646	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	62	352	0	ENST00000263967.3:c.33G>T	p.Trp11Cys	p.W11C	ENST00000263967	NM_006218.2	11	tgG/tgT	2/21	1	2	FACETS	0.887	0.771	1	0.887	0.771	1	CLONAL	1	TRUE	1	0.435675165306778	2		352	321	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233757	133233759	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1555225139	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	168	466	0	ENST00000320574.5:c.3545_3547del	p.Lys1182del	p.K1182del	ENST00000320574	NM_006231.2	1182	aAGAtc/atc	29/49	1	2	FACETS	0.976	0.899	1	0.976	0.899	1	CLONAL	1	TRUE	1	0.435675165306778	2		466	790	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267470	7267470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1240458376	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	162	490	0	ENST00000302850.5:c.538G>A	p.Glu180Lys	p.E180K	ENST00000302850	NM_000208.2	180	Gag/Aag	2/22	1	2	FACETS	0.973	0.895	1	0.973	0.895	1	CLONAL	1	TRUE	1	0.435675165306778	2		490	764	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748375	43748375	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	158	655	1	ENST00000382044.4:c.2431G>T	p.Glu811Ter	p.E811*	ENST00000382044	NM_001141980.1	811	Gaa/Taa	12/28	0.396737842463047	1	FACETS	0.874	0.804	0.947	0.874	0.804	0.947	CLONAL	1	TRUE	0	0.435675165306778	1		656	649	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572612	141572612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	384	610	0	ENST00000220592.5:c.458G>A	p.Ser153Asn	p.S153N	ENST00000220592	NM_012154.3	153	aGc/aAc	4/19	0.434594612060847	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.435675165306778	3		610	952	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157924	106157924	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	78	372	0	ENST00000380013.4:c.2825C>T	p.Pro942Leu	p.P942L	ENST00000380013	NM_001127208.2	942	cCc/cTc	3/11	1	2	FACETS	0.875	0.773	0.984	0.875	0.773	0.984	CLONAL	1	TRUE	1	0.435675165306778	2		372	409	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762168	43762168	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	85	646	2	ENST00000382044.4:c.1277del	p.Pro426LeufsTer65	p.P426Lfs*65	ENST00000382044	NM_001141980.1	426	cCt/ct	11/28	0.396737842463047	1	FACETS	0.421	0.372	0.474	0.421	0.372	0.474	SUBCLONAL	1	TRUE	0	0.435675165306778	1		648	725	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253416	226253416	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	16	101	0	ENST00000366813.1:c.188T>A	p.Ile63Asn	p.I63N	ENST00000366813		63	aTt/aAt	2/3	0.231459434365782	3	FACETS	0.542	0.403	0.707	0.181	0.134	0.236	INDETERMINATE	1	TRUE	0	0.435675165306778	3		101	165	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720677	89720677	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	55	333	0	ENST00000371953.3:c.828del	p.Asn276LysfsTer15	p.N276Kfs*15	ENST00000371953	NM_000314.4	276	aaT/aa	8/9	0.341099675713657	1	FACETS	0.833	0.721	0.953	0.833	0.721	0.953	CLONAL	1	TRUE	0	0.435675165306778	1		333	237	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588129	69588129	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	208	599	0	ENST00000168712.1:c.569G>T	p.Gly190Val	p.G190V	ENST00000168712	NM_002007.2	190	gGg/gTg	3/3	0.396737842463047	1	FACETS	0.921	0.857	0.987	0.921	0.857	0.987	CLONAL	1	TRUE	0	0.435675165306778	1		599	811	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114808	108114808	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	38	431	0	ENST00000278616.4:c.629del	p.Leu210TrpfsTer20	p.L210Wfs*20	ENST00000278616	NM_000051.3	209	Ttt/tt	6/63	0.396737842463047	1	FACETS	0.407	0.337	0.485	0.407	0.337	0.485	SUBCLONAL	1	TRUE	0	0.435675165306778	1		431	335	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784045	120784045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763290869	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	217	747	1	ENST00000257552.2:c.940G>A	p.Gly314Ser	p.G314S	ENST00000257552	NM_002442.3	314	Ggc/Agc	13/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.435675165306778	2		748	959	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912783	32912783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	30	380	0	ENST00000380152.3:c.4291G>A	p.Ala1431Thr	p.A1431T	ENST00000380152		1431	Gca/Aca	11/27	1	2	FACETS	0.522	0.422	0.634	0.522	0.422	0.634	SUBCLONAL	1	TRUE	1	0.435675165306778	2		380	264	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346323	73346323	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	58	381	0	ENST00000377767.4:c.1477C>T	p.Arg493Ter	p.R493*	ENST00000377767	NM_014953.3	493	Cga/Tga	10/21	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.435675165306778	2		381	254	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060795	38060795	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	254	810	0	ENST00000250448.2:c.1194C>A	p.His398Gln	p.H398Q	ENST00000250448	NM_004496.3	398	caC/caA	2/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.435675165306778	2		810	1086	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639759	3639759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749975141	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	192	694	0	ENST00000294008.3:c.3880G>A	p.Ala1294Thr	p.A1294T	ENST00000294008	NM_032444.2	1294	Gcc/Acc	12/15	1	2	FACETS	0.932	0.862	1	0.932	0.862	1	CLONAL	1	TRUE	1	0.435675165306778	2		694	946	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554284	63554284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	172	630	1	ENST00000307078.5:c.455C>T	p.Ala152Val	p.A152V	ENST00000307078	NM_004655.3	152	gCc/gTc	2/11	1	2	FACETS	0.961	0.885	1	0.961	0.885	1	CLONAL	1	TRUE	1	0.435675165306778	2		631	822	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2185892	2185892	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	180	527	0	ENST00000398665.3:c.164T>C	p.Met55Thr	p.M55T	ENST00000398665	NM_032482.2	55	aTg/aCg	3/28	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.435675165306778	2		527	799	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229316	36229316	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	190	590	0	ENST00000222270.7:c.8006A>T	p.Gln2669Leu	p.Q2669L	ENST00000222270	NM_014727.1	2669	cAg/cTg	37/37	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.435675165306778	2		590	843	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626981	158626982	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	127	367	0	ENST00000263640.3:c.688dup	p.Glu230GlyfsTer12	p.E230Gfs*12	ENST00000263640	NM_001105.4	230	gag/gGag	7/11	1	2	FACETS	0.914	0.83	1	0.914	0.83	1	CLONAL	1	TRUE	1	0.435675165306778	2		367	638	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163623	47163623	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	16	387	0	ENST00000409792.3:c.2503A>G	p.Ile835Val	p.I835V	ENST00000409792	NM_014159.6	835	Ata/Gta	3/21	1	2	FACETS	0.302	0.223	0.396	0.302	0.223	0.396	SUBCLONAL	1	TRUE	1	0.435675165306778	2		387	243	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099743	157099743	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	36	166	0	ENST00000346085.5:c.680T>G	p.Val227Gly	p.V227G	ENST00000346085	NM_020732.3	227	gTc/gGc	1/20	0.341099675713657	1	FACETS	0.813	0.678	0.959	0.813	0.678	0.959	CLONAL	1	TRUE	0	0.435675165306778	1		166	159	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172287	38172287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	245	380	0	ENST00000317025.8:c.2120G>A	p.Cys707Tyr	p.C707Y	ENST00000317025	NM_023034.1	707	tGt/tAt	12/24	0.434594612060847	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	1	0.435675165306778	3		380	675	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98247974	98247974	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	154	383	0	ENST00000331920.6:c.577T>C	p.Tyr193His	p.Y193H	ENST00000331920	NM_000264.3	193	Tac/Cac	3/24	0.396737842463047	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.435675165306778	1		383	542	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006863	47006863	+	5_prime_UTR_variant	5'UTR	SNP	C	C	T	rs1406919407	NA	P-0051368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	199	641	1	ENST00000377604.3:c.-18C>T		p.*6*	ENST00000377604	NM_001204468.1	-/852		2/24	0.435675165306778	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.435675165306778	1		642	705	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412884	49412884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	63	599	0	ENST00000418115.1:c.139G>A	p.Glu47Lys	p.E47K	ENST00000418115	NM_001664.2	47	Gag/Aag	2/5	0.173306508108882	3	FACETS	0.781	0.677	0.892	0.26	0.225	0.298	INDETERMINATE	1	FALSE	0	0.455449649866383	3		599	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	192	734	0	ENST00000269305.4:c.313G>T	p.Gly105Cys	p.G105C	ENST00000269305	NM_001126112.2	105	Ggc/Tgc	4/11	0.299974928718245	3	FACETS	1	0.988	1	0.818	0.766	0.87	CLONAL	2	FALSE	0	0.455449649866383	3		734	422	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851706	134851706	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1164993873	NA	P-0051369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	42	685	0	ENST00000398015.3:c.1112C>T	p.Ser371Phe	p.S371F	ENST00000398015	NM_004441.4	371	tCc/tTc	5/16	1	2	FACETS	0.443	0.37	0.524	0.443	0.37	0.524	SUBCLONAL	1	FALSE	1	0.455449649866383	2		685	416	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882954	89882954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1311396994	NA	P-0051369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	21	174	1	ENST00000389301.3:c.70G>A	p.Glu24Lys	p.E24K	ENST00000389301	NM_000135.2	24	Gag/Aag	1/43	0.455449649866383	1	FACETS	0.421	0.327	0.53	0.421	0.327	0.53	SUBCLONAL	1	FALSE	0	0.455449649866383	1		175	169	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967269	134967269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749666684	NA	P-0051369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	124	646	0	ENST00000398015.3:c.2608C>T	p.Arg870Trp	p.R870W	ENST00000398015	NM_004441.4	870	Cgg/Tgg	14/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.455449649866383	2		646	471	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444684	49444684	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	41	794	0	ENST00000301067.7:c.2782C>T	p.Gln928Ter	p.Q928*	ENST00000301067	NM_003482.3	928	Cag/Tag	10/54	0.395895161797131	4	FACETS	0.501	0.417	0.595	0.167	0.139	0.199	SUBCLONAL	1	FALSE	1	0.455449649866383	4		794	523	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0051369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	88	366	0				ENST00000310581	NM_198253.2	-/1132			0.455449649866383	1	FACETS	0.765	0.694	0.837	1	0.984	1	SUBCLONAL	2	FALSE	0	0.455449649866383	1		366	195	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448439	49448439	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	36	700	0	ENST00000301067.7:c.272G>A	p.Trp91Ter	p.W91*	ENST00000301067	NM_003482.3	91	tGg/tAg	3/54	0.395895161797131	4	FACETS	0.437	0.359	0.526	0.146	0.119	0.176	SUBCLONAL	1	FALSE	1	0.455449649866383	4		700	526	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223254	5223254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1407721470	NA	P-0051369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	103	698	0	ENST00000357368.4:c.2549C>T	p.Ala850Val	p.A850V	ENST00000357368	NM_002850.3	850	gCa/gTa	18/38	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.455449649866383	2		698	381	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163820	72163820	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0051369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	49	342	1	ENST00000357731.5:c.538A>T	p.Lys180Ter	p.K180*	ENST00000357731	NM_173808.2	180	Aaa/Taa	4/7	0.164583866037746	3	FACETS	0.761	0.647	0.886	0.254	0.215	0.296	INDETERMINATE	1	FALSE	0	0.455449649866383	3		343	347	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78435635	78435635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	86	531	0	ENST00000370768.2:c.185G>A	p.Gly62Glu	p.G62E	ENST00000370768	NM_003902.3	62	gGa/gAa	2/20	0.164583866037746	3	FACETS	0.704	0.623	0.79	0.235	0.207	0.264	INDETERMINATE	1	FALSE	0	0.455449649866383	3		531	659	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992236	11992236	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0051369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	37	413	0	ENST00000396373.4:c.326C>G	p.Ser109Ter	p.S109*	ENST00000396373	NM_001987.4	109	tCa/tGa	3/8	0.455449649866383	3	FACETS	0.521	0.43	0.622			1	SUBCLONAL	1	FALSE	NA	0.455449649866383	3		413	383	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930681	32930681	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555286279	NA	P-0051369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	62	515	0	ENST00000380152.3:c.7552C>G	p.Leu2518Val	p.L2518V	ENST00000380152		2518	Ctg/Gtg	15/27	0.455449649866383	3	FACETS	0.645	0.558	0.74	0.323	0.279	0.37	SUBCLONAL	1	FALSE	1	0.455449649866383	3		515	518	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820720	3820720	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	123	816	0	ENST00000262367.5:c.2731C>T	p.Gln911Ter	p.Q911*	ENST00000262367	NM_004380.2	911	Caa/Taa	14/31	0.455449649866383	1	FACETS	0.939	0.856	1	0.939	0.856	1	CLONAL	1	FALSE	0	0.455449649866383	1		816	444	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862942	9862942	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	13	437	0	ENST00000330684.3:c.2361G>C	p.Glu787Asp	p.E787D	ENST00000330684	NM_001134407.1	787	gaG/gaC	12/13	0.455449649866383	1	FACETS	0.178	0.127	0.241	0.178	0.127	0.241	SUBCLONAL	1	FALSE	0	0.455449649866383	1		437	247	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805061	89805061	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587778322	NA	P-0051369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	111	676	0	ENST00000389301.3:c.4316G>C	p.Arg1439Thr	p.R1439T	ENST00000389301	NM_000135.2	1439	aGa/aCa	43/43	0.455449649866383	1	FACETS	0.84	0.76	0.924	0.84	0.76	0.924	CLONAL	1	FALSE	0	0.455449649866383	1		676	448	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89862426	89862426	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	48	570	1	ENST00000389301.3:c.894G>T	p.Trp298Cys	p.W298C	ENST00000389301	NM_000135.2	298	tgG/tgT	11/43	0.455449649866383	1	FACETS	0.421	0.356	0.491	0.421	0.356	0.491	SUBCLONAL	1	FALSE	0	0.455449649866383	1		571	387	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7168032	7168032	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	92	594	0	ENST00000302850.5:c.1557C>A	p.Tyr519Ter	p.Y519*	ENST00000302850	NM_000208.2	519	taC/taA	7/22	1	2	FACETS	0.81	0.722	0.902	0.81	0.722	0.902	CLONAL	1	FALSE	1	0.455449649866383	2		594	499	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254594	10254594	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	92	588	0	ENST00000340748.4:c.2916C>G	p.His972Gln	p.H972Q	ENST00000340748		972	caC/caG	28/40	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	1	0.455449649866383	2		588	376	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262190	10262190	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	33	693	0	ENST00000340748.4:c.2101G>A	p.Asp701Asn	p.D701N	ENST00000340748		701	Gac/Aac	23/40	1	2	FACETS	0.346	0.281	0.418	0.346	0.281	0.418	SUBCLONAL	1	FALSE	1	0.455449649866383	2		693	419	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62293873	62293873	+	intron_variant	Intron	SNP	C	C	G	rs80224512	NA	P-0051369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	126	662	0	ENST00000360203.5:c.396-26C>G		p.*132*	ENST00000360203	NM_001283009.1	148/1243			0.17983931311979	5	FACETS	1	0.983	1	0.275	0.249	0.302	INDETERMINATE	1	FALSE	0	0.455449649866383	5		662	678	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513680	41513680	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0051369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	69	686	0	ENST00000263253.7:c.584C>G	p.Ser195Ter	p.S195*	ENST00000263253	NM_001429.3	195	tCa/tGa	2/31	0.455449649866383	1	FACETS	0.505	0.441	0.574	0.505	0.441	0.574	SUBCLONAL	1	FALSE	0	0.455449649866383	1		686	463	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412903	49412903	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	68	605	0	ENST00000418115.1:c.120G>C	p.Glu40Asp	p.E40D	ENST00000418115	NM_001664.2	40	gaG/gaC	2/5	0.173306508108882	3	FACETS	0.759	0.662	0.864	0.253	0.22	0.288	INDETERMINATE	1	FALSE	0	0.455449649866383	3		605	483	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873066	134873066	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	138	610	0	ENST00000398015.3:c.1370C>A	p.Pro457Gln	p.P457Q	ENST00000398015	NM_004441.4	457	cCg/cAg	6/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.455449649866383	2		610	460	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185169163	185169163	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879126131	NA	P-0051369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	69	463	0	ENST00000265026.3:c.1258G>A	p.Glu420Lys	p.E420K	ENST00000265026	NM_004721.4	420	Gaa/Aaa	7/14	0.151453888487687	5	FACETS	0.948	0.827	1	0.316	0.275	0.36	INDETERMINATE	1	FALSE	2	0.455449649866383	5		463	538	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55991415	55991415	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	52	727	0	ENST00000263923.4:c.46G>A	p.Glu16Lys	p.E16K	ENST00000263923	NM_002253.2	16	Gag/Aag	1/30	0.103054853125025	5	FACETS	0.717	0.61	0.834	0.179	0.152	0.209	INDETERMINATE	1	FALSE	1	0.455449649866383	5		727	536	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138613	37138613	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	51	642	1	ENST00000373509.5:c.147C>A	p.Phe49Leu	p.F49L	ENST00000373509	NM_002648.3	49	ttC/ttA	2/6	1	2	FACETS	0.479	0.407	0.557	0.479	0.407	0.557	SUBCLONAL	1	FALSE	1	0.455449649866383	2		643	468	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0051370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	101	674	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.26	2		674	607	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958789	55958789	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	59	507	0	ENST00000263923.4:c.3064C>T	p.Arg1022Ter	p.R1022*	ENST00000263923	NM_002253.2	1022	Cga/Tga	22/30	0.121052749630867	1	FACETS	0.704	0.606	0.811	0.704	0.606	0.811	INDETERMINATE	1	TRUE	0	0.26	1		507	561	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420108	49420108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123729	NA	P-0051370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	37	650	0	ENST00000301067.7:c.15641G>A	p.Arg5214His	p.R5214H	ENST00000301067	NM_003482.3	5214	cGc/cAc	48/54	0.233852358677214	3	FACETS	0.549	0.451	0.658	0.274	0.225	0.329	SUBCLONAL	1	TRUE	1	0.26	3		650	586	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983120	201983121	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0051370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	75	640	0	ENST00000359651.3:c.970_971dup	p.Met324IlefsTer2	p.M324Ifs*2	ENST00000359651		323	-/AT	7/8	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.26	2		640	561	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983043	201983043	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	77	754	0	ENST00000359651.3:c.892C>G	p.Arg298Gly	p.R298G	ENST00000359651		298	Cgg/Ggg	7/8	1	2	FACETS	0.952	0.836	1	0.952	0.836	1	CLONAL	1	TRUE	1	0.26	2		754	622	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947606	48947606	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	42	293	0	ENST00000267163.4:c.1196del	p.Asn399IlefsTer2	p.N399Ifs*2	ENST00000267163	NM_000321.2	398	gAa/ga	12/27	1	2	FACETS	0.744	0.622	0.88	0.744	0.622	0.88	SUBCLONAL	1	TRUE	1	0.26	2		293	434	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777886	27777886	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	62	549	0	ENST00000369163.2:c.35C>A	p.Thr12Asn	p.T12N	ENST00000369163	NM_003536.2	12	aCc/aAc	1/1	0.3	5	FACETS	0.988	0.853	1			1	CLONAL	1	TRUE	NA	0.26	5		549	671	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938568	44938568	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	58	227	0	ENST00000377967.4:c.3116A>G	p.Gln1039Arg	p.Q1039R	ENST00000377967	NM_021140.2	1039	cAg/cGg	20/29	0.3	2	FACETS	1	0.969	1	0.736	0.637	0.843	CLONAL	1	TRUE	0	0.26	2		227	303	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202470	123202470	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	62	178	0	ENST00000218089.9:c.2323del	p.Tyr775ThrfsTer2	p.Y775Tfs*2	ENST00000218089	NM_001042749.1	774	caT/ca	24/35	0.3	2	FACETS	0.852	0.742	0.968	0.852	0.742	0.968	CLONAL	2	TRUE	0	0.26	2		178	280	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	90	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.165573465017915	0	FACETS	0.456	0.408	0.507			1	INDETERMINATE	1	TRUE	0	0.520950284256914	0		334	363	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0051372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	83	436	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.885	0.787	0.989	0.885	0.787	0.989	CLONAL	1	TRUE	1	0.520950284256914	2		436	360	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023108	27023108	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	64	90	0	ENST00000324856.7:c.214G>T	p.Glu72Ter	p.E72*	ENST00000324856	NM_006015.4	72	Gag/Tag	1/20	0.520950284256914	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.520950284256914	2		90	114	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258970	153258970	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	54	333	0	ENST00000281708.4:c.845C>A	p.Ser282Ter	p.S282*	ENST00000281708	NM_033632.3	282	tCa/tAa	5/12	1	2	FACETS	0.983	0.851	1	0.983	0.851	1	CLONAL	1	TRUE	1	0.520950284256914	2		333	211	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879622	151879622	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	99	354	0	ENST00000262189.6:c.5323C>T	p.Gln1775Ter	p.Q1775*	ENST00000262189	NM_170606.2	1775	Cag/Tag	36/59	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.520950284256914	2		354	350	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118896	115118896	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	285	397	0	ENST00000257566.3:c.445T>A	p.Tyr149Asn	p.Y149N	ENST00000257566	NM_016569.3	149	Tac/Aac	2/8	0.520950284256914	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.520950284256914	2		397	455	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907097	101907097	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	67	473	0	ENST00000374994.4:c.1057G>A	p.Gly353Arg	p.G353R	ENST00000374994	NM_004612.2	353	Gga/Aga	6/9	1	2	FACETS	0.752	0.658	0.853	0.752	0.658	0.853	SUBCLONAL	1	TRUE	1	0.520950284256914	2		473	342	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274910	41274910	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	135	559	0	ENST00000349496.5:c.1160A>T	p.Asn387Ile	p.N387I	ENST00000349496	NM_001904.3	387	aAt/aTt	8/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.520950284256914	2		559	473	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106730	2106730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397515011	NA	P-0051372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	145	738	0	ENST00000219476.3:c.734G>A	p.Arg245His	p.R245H	ENST00000219476	NM_000548.3	245	cGc/cAc	8/42	1	2	FACETS	0.922	0.844	1	0.922	0.844	1	CLONAL	1	TRUE	1	0.520950284256914	2		738	604	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420204	49420204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	166	642	0	ENST00000301067.7:c.15545G>A	p.Gly5182Asp	p.G5182D	ENST00000301067	NM_003482.3	5182	gGc/gAc	48/54	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.520950284256914	2		642	545	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008509	70008509	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	127	385	0	ENST00000394351.3:c.796G>T	p.Glu266Ter	p.E266*	ENST00000394351	NM_000248.3	266	Gaa/Taa	8/9	0.520950284256914	3	FACETS	0.864	0.784	0.949	0.432	0.392	0.475	CLONAL	1	TRUE	1	0.520950284256914	3		385	711	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152426	56152426	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0051372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	62	220	0	ENST00000399503.3:c.483-1G>A		p.X161_splice	ENST00000399503	NM_005921.1	161			1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.520950284256914	2		220	226	SUCCESS
APC	324	MSKCC	GRCh37	5	112175770	112175785	+	frameshift_variant	Frame_Shift_Del	DEL	GGAAAGTACTCCAGAT	GGAAAGTACTCCAGAT	-	novel	NA	P-0051372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	78	384	0	ENST00000257430.4:c.4482_4497del	p.Glu1494AspfsTer8	p.E1494Dfs*8	ENST00000257430	NM_000038.5	1493	acGGAAAGTACTCCAGAT/ac	16/16	1	2	FACETS	0.865	0.766	0.97	0.865	0.766	0.97	CLONAL	1	TRUE	1	0.520950284256914	2		384	346	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934334	68934334	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1423317895	NA	P-0051372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	81	558	0	ENST00000288368.4:c.400C>A	p.Leu134Ile	p.L134I	ENST00000288368	NM_024870.2	134	Ctt/Att	4/40	0.24473784568068	2	FACETS	0.653	0.577	0.734	0.327	0.288	0.367	INDETERMINATE	1	TRUE	0	0.520950284256914	2		558	476	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891346	101891346	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	129	506	0	ENST00000374994.4:c.307C>T	p.Gln103Ter	p.Q103*	ENST00000374994	NM_004612.2	103	Cag/Tag	2/9	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.520950284256914	2		506	476	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0051373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	601	627	3	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.866051223397563	6	FACETS	1	0.98	1	1	0.98	1	CLONAL	4	TRUE	2	0.866051223397563	6		630	937	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212011	142212011	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	97	491	0	ENST00000350721.4:c.6041C>T	p.Ala2014Val	p.A2014V	ENST00000350721	NM_001184.3	2014	gCt/gTt	35/47	0.866051223397563	3	FACETS	0.887	0.798	0.98	0.443	0.399	0.49	CLONAL	1	TRUE	1	0.866051223397563	3		491	362	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045961	26045986	+	frameshift_variant	Frame_Shift_Del	DEL	CCAATCTGTGCGCTATTCACGCTAAA	CCAATCTGTGCGCTATTCACGCTAAA	ACAT	novel	NA	P-0051373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	125	670	2	ENST00000540144.1:c.323_348delinsACAT	p.Thr108AsnfsTer?	p.T108Nfs*?	ENST00000540144	NM_003531.2	108	aCCAATCTGTGCGCTATTCACGCTAAA/aACAT	1/1	0.541982273826068	4	FACETS	1	0.912	1	0.334	0.304	0.366	CLONAL	1	TRUE	1	0.866051223397563	4		672	537	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202430	138202430	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	141	643	0	ENST00000237289.4:c.2347T>A	p.Phe783Ile	p.F783I	ENST00000237289	NM_001270507.1	783	Ttt/Att	9/9	0.866051223397563	3	FACETS	0.744	0.68	0.811	0.372	0.34	0.406	SUBCLONAL	1	TRUE	1	0.866051223397563	3		643	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0051374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	195	633	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.481250962788972	1	FACETS	0.907	0.844	0.972	0.907	0.844	0.972	CLONAL	1	TRUE	0	0.516699964755316	1		633	617	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0051374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	87	398	1	ENST00000311936.3:c.34_35delinsTT	p.Gly12Phe	p.G12F	ENST00000311936	NM_004985.3	12	GGt/TTt	2/5	0.265703119034031	0	FACETS	0.522	0.467	0.579			1	INDETERMINATE	1	TRUE	0	0.516699964755316	0		399	312	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347846	70347846	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	166	627	1	ENST00000374080.3:c.3085C>T	p.Pro1029Ser	p.P1029S	ENST00000374080		1029	Cct/Tct	22/45	0.139708767352858	0	FACETS	0.436	0.401	0.472			1	INDETERMINATE	1	TRUE	0	0.516699964755316	0		628	712	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206898	36206898	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	10	287	0	ENST00000300305.3:c.614G>C	p.Arg205Thr	p.R205T	ENST00000300305		205	aGa/aCa	6/8	1	2	FACETS	0.101	0.068	0.143	0.101	0.068	0.143	SUBCLONAL	1	TRUE	1	0.516699964755316	2		287	384	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988452	41988452	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0051374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	153	477	0	ENST00000219905.7:c.1244C>G	p.Ser415Ter	p.S415*	ENST00000219905	NM_001164273.1	415	tCa/tGa	3/24	0.516699964755316	1	FACETS	0.898	0.828	0.971	0.898	0.828	0.971	CLONAL	1	TRUE	0	0.516699964755316	1		477	489	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934174	39934174	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	148	664	0	ENST00000378444.4:c.425C>A	p.Pro142Gln	p.P142Q	ENST00000378444	NM_001123385.1	142	cCa/cAa	4/15	NA	2	FACETS	0.749	0.685	0.816			1	INDETERMINATE	1	TRUE	NA	0.516699964755316	2		664	765	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684350	29684350	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	108	584	0	ENST00000356175.3:c.7870G>T	p.Glu2624Ter	p.E2624*	ENST00000356175	NM_000267.3	2624	Gag/Tag	53/57	0.516699964755316	3	FACETS	0.971	0.874	1	0.485	0.437	0.536	CLONAL	1	TRUE	1	0.516699964755316	3		584	542	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732415	74732415	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	152	452	0	ENST00000359995.5:c.494C>A	p.Ser165Tyr	p.S165Y	ENST00000359995	NM_001195427.1	165	tCc/tAc	2/3	0.516699964755316	3	FACETS	0.921	0.843	1	0.46	0.421	0.501	CLONAL	1	TRUE	1	0.516699964755316	3		452	804	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422505	225422505	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	79	424	0	ENST00000264414.4:c.135G>C	p.Gln45His	p.Q45H	ENST00000264414	NM_003590.4	45	caG/caC	2/16	1	2	FACETS	0.835	0.74	0.937	0.835	0.74	0.937	CLONAL	1	TRUE	1	0.516699964755316	2		424	366	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934222	49934222	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	207	691	0	ENST00000296474.3:c.2285G>A	p.Trp762Ter	p.W762*	ENST00000296474	NM_002447.2	762	tGg/tAg	8/20	1	2	FACETS	0.948	0.881	1	0.948	0.881	1	CLONAL	1	TRUE	1	0.516699964755316	2		691	845	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515664	31515664	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	96	408	1	ENST00000344624.3:c.955G>T	p.Gly319Cys	p.G319C	ENST00000344624		319	Ggt/Tgt	4/33	1	2	FACETS	0.883	0.791	0.979	0.883	0.791	0.979	CLONAL	1	TRUE	1	0.516699964755316	2		409	421	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184743	32184743	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	163	591	0	ENST00000375023.3:c.1840C>A	p.Leu614Ile	p.L614I	ENST00000375023	NM_004557.3	614	Ctc/Atc	11/30	0.173251479398011	3	FACETS	1	0.973	1	0.566	0.521	0.613	INDETERMINATE	1	TRUE	1	0.516699964755316	3		591	701	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38139056	38139056	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	152	468	0	ENST00000317025.8:c.3547G>C	p.Glu1183Gln	p.E1183Q	ENST00000317025	NM_023034.1	1183	Gaa/Caa	20/24	0.285063764472549	3	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.516699964755316	3		468	561	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146196	38146196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	290	612	0	ENST00000317025.8:c.3310G>A	p.Asp1104Asn	p.D1104N	ENST00000317025	NM_023034.1	1104	Gat/Aat	19/24	0.285063764472549	3	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.516699964755316	3		612	1096	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	183	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.875	0.815	0.936	0.875	0.815	0.936	CLONAL	1	TRUE	1	0.860725619843534	2		276	486	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0051375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	79	401	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.854	0.765	0.945	0.854	0.765	0.945	CLONAL	1	TRUE	1	0.860725619843534	2		401	215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0051375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	320	558	1	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.813313792887075	1	FACETS	0.894	0.859	0.927	0.894	0.859	0.927	CLONAL	1	TRUE	0	0.860725619843534	1		559	474	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55603410	55603410	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	305	339	0	ENST00000288135.5:c.2766G>T	p.Gln922His	p.Q922H	ENST00000288135	NM_000222.2	922	caG/caT	20/21	0.81518173397593	2	FACETS	0.909	0.879	0.937	0.909	0.879	0.937	CLONAL	2	TRUE	0	0.860725619843534	2		339	390	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725559	162725560	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AT	novel	NA	P-0051375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	122	323	0	ENST00000367921.3:c.671_671+1delinsAT		p.X224_splice	ENST00000367921	NM_006182.2	224		7/18	0.8115344468956	3	FACETS	0.826	0.751	0.904	0.413	0.375	0.452	CLONAL	1	TRUE	1	0.860725619843534	3		323	491	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246027122	246027122	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	270	485	0	ENST00000388985.4:c.880G>A	p.Glu294Lys	p.E294K	ENST00000388985		294	Gaa/Aaa	9/12	0.813792770079417	5	FACETS	0.985	0.921	1	0.246	0.23	0.263	CLONAL	1	TRUE	1	0.860725619843534	5		485	1460	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41247903	41247904	+	missense_variant	Missense_Mutation	DNP	TT	TT	AA	novel	NA	P-0051375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	217	443	0	ENST00000357654.3:c.629_630inv	p.Gln210Leu	p.Q210L	ENST00000357654	NM_007294.3	210	cAA/cTT	9/23	1	2	FACETS	0.993	0.932	1	0.993	0.932	1	CLONAL	1	TRUE	1	0.860725619843534	2		443	508	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940174	31940174	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	1251	719	1	ENST00000375333.2:c.316A>G	p.Ile106Val	p.I106V	ENST00000375333	NM_032454.1	106	Ata/Gta	2/8	0.860725619843534	3	FACETS	0.969	0.956	0.98	0.969	0.956	0.98	CLONAL	3	TRUE	0	0.860725619843534	3		720	1431	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0051376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	77	465	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.415851135441508	3	FACETS	0.941	0.829	1	0.471	0.414	0.531	CLONAL	1	TRUE	1	0.423638733259563	3		465	468	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0051376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	84	339	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	1	2	FACETS	0.967	0.859	1	0.967	0.859	1	CLONAL	1	TRUE	1	0.423638733259563	2		339	410	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0051376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	107	337	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.423638733259563	2		337	442	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0051376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	101	394	2	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.423638733259563	2		396	475	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624242	89624242	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	83	190	0	ENST00000371953.3:c.18del	p.Glu7ArgfsTer17	p.E7Rfs*17	ENST00000371953	NM_000314.4	6	Aaa/aa	1/9	0.415851135441508	3	FACETS	0.954	0.854	1	0.954	0.854	1	CLONAL	2	TRUE	1	0.423638733259563	3		190	249	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231785	36231785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	138	564	0	ENST00000300305.3:c.599C>T	p.Pro200Leu	p.P200L	ENST00000300305		200	cCc/cTc	5/8	1	2	FACETS	0.91	0.829	0.994	0.91	0.829	0.994	CLONAL	1	TRUE	1	0.423638733259563	2		564	716	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0051378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	452	852	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.633938673311979	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.633938673311979	2		852	699	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121052	3121052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777133920	NA	P-0051378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	243	802	0	ENST00000078429.4:c.955G>A	p.Asp319Asn	p.D319N	ENST00000078429	NM_002067.2	319	Gac/Aac	7/7	0.633938673311979	1	FACETS	0.99	0.935	1	0.99	0.935	1	CLONAL	1	TRUE	0	0.633938673311979	1		802	529	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223179	5223179	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	126	844	0	ENST00000357368.4:c.2624C>A	p.Ser875Ter	p.S875*	ENST00000357368	NM_002850.3	875	tCg/tAg	18/38	0.633938673311979	1	FACETS	0.493	0.448	0.54	0.493	0.448	0.54	SUBCLONAL	1	TRUE	0	0.633938673311979	1		844	551	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044351	128044351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200098409	NA	P-0051378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	230	617	0	ENST00000285398.2:c.1270G>A	p.Glu424Lys	p.E424K	ENST00000285398	NM_000122.1	424	Gag/Aag	8/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.633938673311979	2		617	669	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971191	21971211	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGCCCATCATCATGACCTGC	CTGCCCATCATCATGACCTGC	-	novel	NA	P-0051378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	200	576	0	ENST00000304494.5:c.151-4_167del		p.X51_splice	ENST00000304494	NM_000077.4	51		2/3	0.633938673311979	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.633938673311979	1		576	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0051379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	332	668	0	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	0.665392525400323	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.665392525400323	1		668	568	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913384	NA	P-0051379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	308	592	0	ENST00000304494.5:c.262G>T	p.Glu88Ter	p.E88*	ENST00000304494	NM_000077.4	88	Gag/Tag	2/3	0.665392525400323	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.665392525400323	1		592	512	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015039	37015039	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	481	528	0	ENST00000358127.4:c.365G>T	p.Arg122Leu	p.R122L	ENST00000358127	NM_001280556.1	122	cGg/cTg	3/10	1	2	FACETS	0.77	0.74	0.799	1	0.997	1	SUBCLONAL	2	TRUE	1	0.665392525400323	2		528	939	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864757	57864757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138157845	NA	P-0051380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	304	653	1	ENST00000228682.2:c.2234C>T	p.Ala745Val	p.A745V	ENST00000228682	NM_005269.2	745	gCg/gTg	12/12	0.519999120273113	3	FACETS	0.935	0.885	0.985	0.935	0.885	0.985	CLONAL	2	TRUE	1	0.519999120273113	3		654	788	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0051406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	31	380	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.544	0.439	0.663	0.544	0.439	0.663	SUBCLONAL	1	TRUE	1	0.228249691394509	2		380	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	127	546	0	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	0.158965819632189	2	FACETS	1	0.983	1	0.706	0.64	0.776	CLONAL	1	TRUE	0	0.228249691394509	2		546	788	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	54	273	0	ENST00000257430.4:c.4199C>A	p.Ser1400Ter	p.S1400*	ENST00000257430	NM_000038.5	1400	tCg/tAg	16/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.228249691394509	2		273	358	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244067	153244071	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTT	AGCTT	-	novel	NA	P-0051406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	45	344	0	ENST00000281708.4:c.2086_2090del	p.Lys696AlafsTer6	p.K696Afs*6	ENST00000281708	NM_033632.3	696	AAGCTg/g	12/12	1	2	FACETS	0.798	0.671	0.939	0.798	0.671	0.939	CLONAL	1	TRUE	1	0.228249691394509	2		344	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0051407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	499	872	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.942577647076544	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.942577647076544	1		872	535	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626755	28626755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750445891	NA	P-0051407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	284	369	0	ENST00000241453.7:c.541G>A	p.Ala181Thr	p.A181T	ENST00000241453	NM_004119.2	181	Gcc/Acc	5/24	0.942577647076544	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.942577647076544	1		369	314	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992762	68992762	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	246	424	0	ENST00000288368.4:c.1727A>T	p.His576Leu	p.H576L	ENST00000288368	NM_024870.2	576	cAt/cTt	16/40	1	2	FACETS	0.947	0.894	1	0.947	0.894	1	CLONAL	1	TRUE	1	0.942577647076544	2		424	551	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153709	55153709	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0051407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	332	389	0	ENST00000257290.5:c.2674+1G>T		p.X892_splice	ENST00000257290	NM_006206.4	892			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.942577647076544	2		389	679	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537208	80537208	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	236	310	0	ENST00000286548.4:c.190G>T	p.Gly64Trp	p.G64W	ENST00000286548	NM_002072.3	64	Ggg/Tgg	2/7	0.942577647076544	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.942577647076544	1		310	252	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204512046	204512046	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	182	224	0	ENST00000367182.3:c.646G>T	p.Gly216Cys	p.G216C	ENST00000367182	NM_001278516.1	216	Ggc/Tgc	8/11	1	2	FACETS	0.965	0.903	1	0.965	0.903	1	CLONAL	1	TRUE	1	0.942577647076544	2		224	400	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098364	108098364	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	48	257	0	ENST00000278616.4:c.13C>G	p.Leu5Val	p.L5V	ENST00000278616	NM_000051.3	5	Ctt/Gtt	2/63	1	2	FACETS	0.212	0.179	0.249	0.212	0.179	0.249	SUBCLONAL	1	TRUE	1	0.942577647076544	2		257	480	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646294	3646294	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	499	619	0	ENST00000294008.3:c.1784G>C	p.Cys595Ser	p.C595S	ENST00000294008	NM_032444.2	595	tGt/tCt	8/15	0.942577647076544	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.942577647076544	1		619	546	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288083	21288083	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs200265850	NA	P-0051407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	247	253	0	ENST00000354336.3:c.328A>G	p.Met110Val	p.M110V	ENST00000354336	NM_005207.3	110	Atg/Gtg	2/3	0.942577647076544	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.942577647076544	1		253	263	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37637630	37637630	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	394	548	0	ENST00000249071.6:c.104C>A	p.Thr35Asn	p.T35N	ENST00000249071	NM_002872.4	35	aCc/aAc	2/7	0.942577647076544	1	FACETS	0.998	0.977	1	0.998	0.977	1	CLONAL	1	TRUE	0	0.942577647076544	1		548	443	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129601	47129601	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0051407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	263	249	1	ENST00000409792.3:c.5277+2T>A		p.X1759_splice	ENST00000409792	NM_014159.6	1759			0.942577647076544	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.942577647076544	1		250	284	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401173	139401173	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	457	574	0	ENST00000277541.6:c.3896A>C	p.His1299Pro	p.H1299P	ENST00000277541	NM_017617.3	1299	cAc/cCc	23/34	0.942577647076544	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.942577647076544	1		574	493	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170525	11170525	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	173	667	0	ENST00000358026.2:c.4828G>T	p.Glu1610Ter	p.E1610*	ENST00000358026	NM_001128849.1	1610	Gag/Tag	34/36	1	2	FACETS	0.888	0.82	0.958	0.888	0.82	0.958	CLONAL	1	TRUE	1	0.56	2		667	696	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250272	39250272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397517147	NA	P-0051409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	146	583	0	ENST00000402219.2:c.1297G>A	p.Glu433Lys	p.E433K	ENST00000402219	NM_005633.3	433	Gag/Aag	10/23	1	2	FACETS	0.875	0.802	0.951	0.875	0.802	0.951	CLONAL	1	TRUE	1	0.56	2		583	596	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696704	47696704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	121	313	0	ENST00000347630.2:c.244G>A	p.Asp82Asn	p.D82N	ENST00000347630	NM_001007230.1	82	Gat/Aat	5/11	1	2	FACETS	0.939	0.854	1	0.939	0.854	1	CLONAL	1	TRUE	1	0.56	2		313	460	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144867	11144868	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0051409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	140	439	0	ENST00000358026.2:c.3943_3944del	p.Leu1315ValfsTer45	p.L1315Vfs*45	ENST00000358026	NM_001128849.1	1314	gaTCtg/gatg	28/36	1	2	FACETS	0.938	0.859	1	0.938	0.859	1	CLONAL	1	TRUE	1	0.56	2		439	533	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290897	15290897	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	161	705	0	ENST00000263388.2:c.3313G>A	p.Gly1105Ser	p.G1105S	ENST00000263388	NM_000435.2	1105	Ggc/Agc	20/33	1	2	FACETS	0.763	0.701	0.827	0.763	0.701	0.827	SUBCLONAL	1	TRUE	1	0.56	2		705	754	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0051410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	162	355	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.279274020656638	2	FACETS	0.886	0.816	0.959	0.886	0.816	0.959	CLONAL	2	TRUE	0	0.28	2		355	653	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555526101	NA	P-0051410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	174	643	0	ENST00000269305.4:c.497C>G	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tGa	5/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.28	2		643	1034	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183788	10183788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882034	NA	P-0051410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	195	543	2	ENST00000256474.2:c.257C>T	p.Pro86Leu	p.P86L	ENST00000256474	NM_000551.3	86	cCc/cTc	1/3	0.159181389843181	3	FACETS	1	0.985	1	0.628	0.58	0.678	INDETERMINATE	1	TRUE	1	0.28	3		545	1264	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845885	156845885	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	180	730	0	ENST00000524377.1:c.1515C>G	p.Ile505Met	p.I505M	ENST00000524377	NM_002529.3	505	atC/atG	13/17	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.28	2		730	1284	SUCCESS
APC	324	MSKCC	GRCh37	5	112176254	112176254	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs759441332	NA	P-0051410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	41	355	0	ENST00000257430.4:c.4963A>G	p.Thr1655Ala	p.T1655A	ENST00000257430	NM_000038.5	1655	Aca/Gca	16/16	1	2	FACETS	0.476	0.396	0.566	0.476	0.396	0.566	SUBCLONAL	1	TRUE	1	0.28	2		355	615	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044906	47044907	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0051410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	163	412	0	ENST00000377604.3:c.2237dup	p.Glu748Ter	p.E748*	ENST00000377604	NM_001204468.1	744	-/G	20/24	0.166355369693859	2	FACETS	0.857	0.789	0.928			1	INDETERMINATE	2	TRUE	NA	0.28	2		412	679	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115269008	115269008	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0051410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	39	241	0	ENST00000438362.2:c.1603-1G>T		p.X535_splice	ENST00000438362	NM_001242891.1	535			1	2	FACETS	0.615	0.51	0.732	0.615	0.51	0.732	SUBCLONAL	1	TRUE	1	0.28	2		241	453	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571907	64571907	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1457	113	827	0	ENST00000312049.6:c.1732C>A	p.Gln578Lys	p.Q578K	ENST00000312049	NM_130799.2	578	Caa/Aaa	10/10	1	2	FACETS	0.514	0.461	0.571	0.514	0.461	0.571	SUBCLONAL	1	TRUE	1	0.28	2		827	1570	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029002	14029002	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0051410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	35	188	0	ENST00000311895.7:c.1214-1G>T		p.X405_splice	ENST00000311895	NM_005236.2	405			1	2	FACETS	0.906	0.746	1	0.906	0.746	1	CLONAL	1	TRUE	1	0.28	2		188	276	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842333	68842333	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	81	337	0	ENST00000261769.5:c.394G>C	p.Val132Leu	p.V132L	ENST00000261769	NM_004360.3	132	Gtt/Ctt	4/16	0.159181389843181	3	FACETS	0.889	0.783	1	0.444	0.391	0.502	INDETERMINATE	1	TRUE	1	0.28	3		337	742	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830088	72830088	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	56	557	0	ENST00000268489.5:c.6493G>C	p.Asp2165His	p.D2165H	ENST00000268489	NM_006885.3	2165	Gac/Cac	9/10	0.159181389843181	3	FACETS	0.425	0.363	0.494	0.212	0.181	0.247	INDETERMINATE	1	TRUE	1	0.28	3		557	1073	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830278	72830278	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1456428565	NA	P-0051410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	31	368	0	ENST00000268489.5:c.6303G>A	p.Met2101Ile	p.M2101I	ENST00000268489	NM_006885.3	2101	atG/atA	9/10	0.159181389843181	3	FACETS	0.416	0.335	0.508	0.208	0.167	0.254	INDETERMINATE	1	TRUE	1	0.28	3		368	607	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830823	72830823	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	58	557	0	ENST00000268489.5:c.5758G>C	p.Glu1920Gln	p.E1920Q	ENST00000268489	NM_006885.3	1920	Gag/Cag	9/10	0.159181389843181	3	FACETS	0.444	0.38	0.514	0.222	0.19	0.257	INDETERMINATE	1	TRUE	1	0.28	3		557	1064	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441443	40441443	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	56	416	0	ENST00000345506.4:c.14T>G	p.Ile5Ser	p.I5S	ENST00000345506	NM_003152.3	5	aTc/aGc	3/20	1	2	FACETS	0.476	0.407	0.552	0.476	0.407	0.552	SUBCLONAL	1	TRUE	1	0.28	2		416	840	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603113	48603113	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	44	382	0	ENST00000342988.3:c.1414C>T	p.Pro472Ser	p.P472S	ENST00000342988	NM_005359.5	472	Cca/Tca	11/12	1	2	FACETS	0.412	0.344	0.487	0.412	0.344	0.487	SUBCLONAL	1	TRUE	1	0.28	2		382	763	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213367	36213368	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0051410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	152	745	0	ENST00000222270.7:c.2564_2565delinsTT	p.Arg855Leu	p.R855L	ENST00000222270	NM_014727.1	855	cGG/cTT	4/37	0.161662538815562	2	FACETS	0.913	0.833	0.997	0.457	0.416	0.499	INDETERMINATE	1	TRUE	0	0.28	2		745	1189	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467194	25467194	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	55	459	1	ENST00000264709.3:c.1681G>A	p.Glu561Lys	p.E561K	ENST00000264709	NM_175629.2	561	Gag/Aag	15/23	0.262804919188684	1	FACETS	0.521	0.445	0.604	0.521	0.445	0.604	SUBCLONAL	1	TRUE	0	0.28	1		460	649	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721197	39721197	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	54	370	0	ENST00000361337.2:c.700C>G	p.Leu234Val	p.L234V	ENST00000361337	NM_003286.2	234	Ctt/Gtt	9/21	1	2	FACETS	0.531	0.453	0.618	0.531	0.453	0.618	SUBCLONAL	1	TRUE	1	0.28	2		370	726	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158202	47158202	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0051410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	106	352	1	ENST00000409792.3:c.4497T>A	p.Cys1499Ter	p.C1499*	ENST00000409792	NM_014159.6	1499	tgT/tgA	4/21	0.159181389843181	3	FACETS	1	0.964	1	0.585	0.524	0.649	INDETERMINATE	1	TRUE	1	0.28	3		353	738	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467548	66467548	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	65	304	0	ENST00000273854.3:c.721G>C	p.Ala241Pro	p.A241P	ENST00000273854	NM_004439.5	241	Gct/Cct	3/18	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.28	2		304	456	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517826	187517826	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	73	274	1	ENST00000441802.2:c.12868G>T	p.Glu4290Ter	p.E4290*	ENST00000441802	NM_005245.3	4290	Gag/Tag	25/27	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.28	2		275	469	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818324	170818324	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	144	474	0	ENST00000296930.5:c.154G>A	p.Gly52Ser	p.G52S	ENST00000296930	NM_002520.6	52	Ggt/Agt	3/11	0.159181389843181	3	FACETS	1	0.964	1	0.556	0.506	0.609	INDETERMINATE	1	TRUE	1	0.28	3		474	1054	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370846	55370846	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775715316	NA	P-0051410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	130	413	0	ENST00000297316.4:c.148G>A	p.Ala50Thr	p.A50T	ENST00000297316	NM_022454.3	50	Gcg/Acg	1/2	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.28	2		413	826	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0051410-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	112	430	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.431976816672816	3	FACETS	0.839	0.764	0.916	0.839	0.764	0.916	CLONAL	2	TRUE	1	0.52714140427144	3		430	320	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041101	180041101	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051410-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	50	717	1	ENST00000261937.6:c.3298T>C	p.Phe1100Leu	p.F1100L	ENST00000261937	NM_182925.4	1100	Ttt/Ctt	24/30	0.248583412894733	0	FACETS	0.325	0.277	0.376			1	INDETERMINATE	1	TRUE	0	0.52714140427144	0		718	276	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197116	26197116	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051410-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	395	576	0	ENST00000356476.2:c.363G>T	p.Met121Ile	p.M121I	ENST00000356476		121	atG/atT	1/1	0.52714140427144	9	FACETS	0.961	0.919	1			1	CLONAL	5	TRUE	NA	0.52714140427144	9		576	887	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526613	106526613	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051410-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	29	300	0	ENST00000359195.3:c.2906T>C	p.Leu969Pro	p.L969P	ENST00000359195	NM_002649.2	969	cTt/cCt	10/11	0.264192963520853	3	FACETS	1	0.944	1	0.488	0.402	0.58	INDETERMINATE	1	TRUE	0	0.52714140427144	3		300	95	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636729	8636729	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051410-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	28	267	0	ENST00000356435.5:c.180A>T	p.Lys60Asn	p.K60N	ENST00000356435		60	aaA/aaT	2/35	0.52714140427144	1	FACETS	0.611	0.496	0.737	0.611	0.496	0.737	SUBCLONAL	1	TRUE	0	0.52714140427144	1		267	128	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0051411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	443	396	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.568539471392907	4	FACETS	0.919	0.883	0.954	0.919	0.883	0.954	CLONAL	3	TRUE	1	0.648953377037796	4		396	817	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971176	21971177	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0051411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	193	373	4	ENST00000304494.5:c.181dup	p.Glu61GlyfsTer59	p.E61Gfs*59	ENST00000304494	NM_000077.4	61	gag/gGag	2/3	0.648953377037796	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.648953377037796	1		377	383	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851502	151851502	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	35	382	0	ENST00000262189.6:c.11989A>G	p.Thr3997Ala	p.T3997A	ENST00000262189	NM_170606.2	3997	Act/Gct	47/59	0.185358766598054	4	FACETS	0.91	0.746	1	0.455	0.373	0.547	CLONAL	1	TRUE	2	0.20513128581614	4		382	452	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343021	118343021	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	30	239	0	ENST00000534358.1:c.1147G>A	p.Ala383Thr	p.A383T	ENST00000534358	NM_005933.3	383	Gct/Act	3/36	0.20513128581614	3	FACETS	1	0.832	1	0.517	0.417	0.629	CLONAL	1	TRUE	1	0.20513128581614	3		239	312	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40497645	40497645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	136	505	0	ENST00000264657.5:c.304G>A	p.Ala102Thr	p.A102T	ENST00000264657	NM_139276.2	102	Gcc/Acc	4/24	0.20513128581614	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	0	0.20513128581614	2		505	634	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430900	181430901	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0051412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	66	768	0	ENST00000325404.1:c.758dup	p.Val254CysfsTer56	p.V254Cfs*56	ENST00000325404	NM_003106.3	251	agc/agCc	1/1	0.20513128581614	3	FACETS	0.917	0.794	1	0.458	0.397	0.525	CLONAL	1	TRUE	1	0.20513128581614	3		768	774	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0051413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	51	366	0				ENST00000310581	NM_198253.2	-/1132			0.278270488055766	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.278270488055766	1		366	252	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397800	49397800	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	203	363	0	ENST00000418115.1:c.424G>A	p.Glu142Lys	p.E142K	ENST00000418115	NM_001664.2	142	Gaa/Aaa	5/5	0.27076049739267	3	FACETS	0.908	0.847	0.971	0.908	0.847	0.971	CLONAL	3	TRUE	0	0.278270488055766	3		363	610	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0051413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	186	559	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.241065941435359	3	FACETS	0.999	0.937	1			1	CLONAL	4	TRUE	NA	0.278270488055766	3		559	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0051413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	130	678	4	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.278270488055766	2		682	675	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577543	7577543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1019340046	NA	P-0051413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	110	525	0	ENST00000269305.4:c.738G>A	p.Met246Ile	p.M246I	ENST00000269305	NM_001126112.2	246	atG/atA	7/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.278270488055766	2		525	567	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821155	72821155	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	91	536	0	ENST00000268489.5:c.11020G>C	p.Gly3674Arg	p.G3674R	ENST00000268489	NM_006885.3	3674	Gga/Cga	10/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.278270488055766	2		536	524	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149776	202149776	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	71	499	2	ENST00000358485.4:c.1217C>T	p.Ser406Phe	p.S406F	ENST00000358485	NM_001080125.1	406	tCc/tTc	8/9	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.278270488055766	2		501	374	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659203	86659203	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	36	164	0	ENST00000274376.6:c.1492G>C	p.Glu498Gln	p.E498Q	ENST00000274376	NM_002890.2	498	Gag/Cag	11/25	0.0620645555648913	3	FACETS	1	0.937	1	0.658	0.545	0.782	INDETERMINATE	1	TRUE	1	0.278270488055766	3		164	224	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911061	29911061	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs199474481	NA	P-0051413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	117	671	0	ENST00000376809.5:c.360G>C	p.Gln120His	p.Q120H	ENST00000376809	NM_002116.7	120	caG/caC	3/8	1	2	FACETS	0.774	0.701	0.851	1	0.985	1	SUBCLONAL	2	TRUE	1	0.278270488055766	2		671	543	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652311	48652311	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	76	788	0	ENST00000376670.3:c.982G>T	p.Glu328Ter	p.E328*	ENST00000376670	NM_002049.3	328	Gaa/Taa	6/6	0.278270488055766	1	FACETS	0.946	0.832	1	0.946	0.832	1	CLONAL	1	TRUE	0	0.278270488055766	1		788	497	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098935	178098935	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	78	256	0	ENST00000397062.3:c.110T>C	p.Phe37Ser	p.F37S	ENST00000397062	NM_006164.4	37	tTt/tCt	2/5	1	2	FACETS	0.964	0.859	1	1	0.987	1	CLONAL	3	TRUE	1	0.209842268285227	2		256	257	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244986	46244996	+	frameshift_variant	Frame_Shift_Del	DEL	AAGTACAAGTT	AAGTACAAGTT	-	novel	NA	P-0051418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	74	410	0	ENST00000334344.6:c.3080_3090del	p.Gln1027ProfsTer26	p.Q1027Pfs*26	ENST00000334344	NM_152641.2	1027	cAAGTACAAGTT/c	15/21	1	2	FACETS	0.765	0.672	0.865	1	0.976	1	SUBCLONAL	2	TRUE	1	0.209842268285227	2		410	461	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0051420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	339	546	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	0.323700852966845	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.323700852966845	3		546	1042	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119562107	119562107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139402886	NA	P-0051420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	25	279	0	ENST00000316626.5:c.1229C>T	p.Ala410Val	p.A410V	ENST00000316626		410	gCg/gTg	11/12	1	2	FACETS	0.788	0.625	0.973	0.788	0.625	0.973	CLONAL	1	TRUE	1	0.323700852966845	2		279	196	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910297	50910297	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	256	640	0	ENST00000440232.2:c.1552C>G	p.Leu518Val	p.L518V	ENST00000440232	NM_002691.3	518	Ctg/Gtg	13/27	0.323700852966845	2	FACETS	0.836	0.788	0.884	1	0.991	1	CLONAL	3	TRUE	0	0.323700852966845	2		640	631	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31472280	31472280	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	31	499	0	ENST00000344624.3:c.2131A>G	p.Lys711Glu	p.K711E	ENST00000344624		711	Aaa/Gaa	14/33	1	2	FACETS	0.859	0.699	1	0.859	0.699	1	CLONAL	1	TRUE	1	0.323700852966845	2		499	223	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410538	63410538	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	151	318	0	ENST00000330258.3:c.2629G>C	p.Gly877Arg	p.G877R	ENST00000330258	NM_152424.3	877	Ggc/Cgc	2/2	0.317469287218354	2	FACETS	1	0.947	1			1	CLONAL	4	TRUE	NA	0.323700852966845	2		318	232	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	70	276	0				ENST00000310581	NM_198253.2	-/1132			0.177338018089525	6	FACETS	0.805	0.702	0.917	0.322	0.28	0.367	CLONAL	2	TRUE	1	0.177338018089525	6		276	664	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0051421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	95	614	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.177338018089525	2		614	908	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0051421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	52	788	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	1	2	FACETS	0.687	0.583	0.801	0.687	0.583	0.801	SUBCLONAL	1	TRUE	1	0.177338018089525	2		788	854	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421528	32421528	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	48	486	0	ENST00000332351.3:c.1064G>A	p.Arg355Lys	p.R355K	ENST00000332351	NM_024426.4	355	aGa/aAa	6/10	0.123025440750645	1	FACETS	0.6	0.506	0.705	0.6	0.506	0.705	SUBCLONAL	1	TRUE	0	0.177338018089525	1		486	822	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038526	47038526	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	43	304	0	ENST00000377604.3:c.688C>T	p.Arg230Ter	p.R230*	ENST00000377604	NM_001204468.1	230	Cga/Tga	8/24	1	1	FACETS	0.993	0.832	1	0.993	0.832	1	CLONAL	1	TRUE	0	0.177338018089525	1		304	445	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027133	49027133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853292	NA	P-0051421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	84	528	0	ENST00000267163.4:c.1700C>T	p.Ser567Leu	p.S567L	ENST00000267163	NM_000321.2	567	tCa/tTa	18/27	0.177338018089525	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	2	TRUE	0	0.177338018089525	2		528	458	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139121	37139121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	46	536	0	ENST00000373509.5:c.461C>T	p.Ala154Val	p.A154V	ENST00000373509	NM_002648.3	154	gCc/gTc	4/6	0.177338018089525	3	FACETS	0.726	0.61	0.855	0.363	0.305	0.428	SUBCLONAL	1	TRUE	1	0.177338018089525	3		536	778	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870853	12870853	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	55	227	0	ENST00000228872.4:c.80C>A	p.Ser27Ter	p.S27*	ENST00000228872	NM_004064.3	27	tCg/tAg	1/3	1	2	FACETS	0.926	0.796	1	1	0.975	1	CLONAL	2	TRUE	1	0.177338018089525	2		227	335	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100919	27100919	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	74	578	0	ENST00000324856.7:c.4201C>T	p.Gln1401Ter	p.Q1401*	ENST00000324856	NM_006015.4	1401	Cag/Tag	18/20	1	2	FACETS	0.977	0.854	1	0.977	0.854	1	CLONAL	1	TRUE	1	0.177338018089525	2		578	854	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969444	44969444	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	65	273	0	ENST00000377967.4:c.4126G>T	p.Glu1376Ter	p.E1376*	ENST00000377967	NM_021140.2	1376	Gaa/Taa	28/29	1	1	FACETS	0.829	0.722	0.944	1	0.976	1	CLONAL	2	TRUE	0	0.177338018089525	1		273	403	SUCCESS
APC	324	MSKCC	GRCh37	5	112173918	112173918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373428732	NA	P-0051421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	26	326	0	ENST00000257430.4:c.2627G>A	p.Arg876Gln	p.R876Q	ENST00000257430	NM_000038.5	876	cGa/cAa	16/16	1	2	FACETS	0.594	0.469	0.737	0.594	0.469	0.737	SUBCLONAL	1	TRUE	1	0.177338018089525	2		326	494	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060766	38060766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1285104042	NA	P-0051421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1162	73	862	0	ENST00000250448.2:c.1223C>T	p.Ser408Phe	p.S408F	ENST00000250448	NM_004496.3	408	tCc/tTc	2/2	1	2	FACETS	0.667	0.581	0.76	0.667	0.581	0.76	SUBCLONAL	1	TRUE	1	0.177338018089525	2		862	1235	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060990	38060990	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	34	380	0	ENST00000250448.2:c.999G>C	p.Gln333His	p.Q333H	ENST00000250448	NM_004496.3	333	caG/caC	2/2	1	2	FACETS	0.691	0.563	0.835	0.691	0.563	0.835	SUBCLONAL	1	TRUE	1	0.177338018089525	2		380	555	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157543	106157543	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	27	302	1	ENST00000380013.4:c.2444G>T	p.Arg815Ile	p.R815I	ENST00000380013	NM_001127208.2	815	aGa/aTa	3/11	0.123025440750645	1	FACETS	0.601	0.477	0.742	0.601	0.477	0.742	SUBCLONAL	1	TRUE	0	0.177338018089525	1		303	462	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738284	145738284	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	55	800	2	ENST00000428558.2:c.2701G>T	p.Glu901Ter	p.E901*	ENST00000428558	NM_004260.3	901	Gag/Tag	16/22	1	2	FACETS	0.575	0.49	0.669	0.575	0.49	0.669	SUBCLONAL	1	TRUE	1	0.177338018089525	2		802	1078	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528747	8528747	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	97	428	0	ENST00000356435.5:c.385G>C	p.Asp129His	p.D129H	ENST00000356435		129	Gac/Cac	4/35	1	2	FACETS	0.838	0.748	0.933	1	0.984	1	CLONAL	2	TRUE	1	0.177338018089525	2		428	653	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411789	63411789	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	73	413	1	ENST00000330258.3:c.1378C>T	p.Gln460Ter	p.Q460*	ENST00000330258	NM_152424.3	460	Cag/Tag	2/2	1	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.177338018089525	1		414	532	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611929	100611929	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	39	255	0	ENST00000308731.7:c.1192G>C	p.Asp398His	p.D398H	ENST00000308731	NM_000061.2	398	Gat/Cat	14/19	1	1	FACETS	0.95	0.788	1	0.95	0.788	1	CLONAL	1	TRUE	0	0.177338018089525	1		255	422	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0051422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	168	383	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.520253328628789	3	FACETS	1	0.987	1	0.81	0.759	0.86	CLONAL	2	TRUE	0	0.569672771407455	3		383	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0051422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	403	600	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.569672771407455	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.569672771407455	2		600	686	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911143	40911143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370795038	NA	P-0051422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	80	407	1	ENST00000373198.4:c.2162G>A	p.Arg721His	p.R721H	ENST00000373198	NM_133170.3	721	cGt/cAt	13/32	0.569672771407455	8	FACETS	0.646	0.567	0.732	0.129	0.113	0.147	SUBCLONAL	1	TRUE	3	0.569672771407455	8		408	1177	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564515	55564515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754738766	NA	P-0051422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	129	437	0	ENST00000288135.5:c.403C>T	p.Arg135Cys	p.R135C	ENST00000288135	NM_000222.2	135	Cgc/Tgc	3/21	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.569672771407455	2		437	415	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911568	32911568	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	50	327	0	ENST00000380152.3:c.3076A>G	p.Lys1026Glu	p.K1026E	ENST00000380152		1026	Aag/Gag	11/27	0.569672771407455	6	FACETS	0.535	0.453	0.626	0.134	0.113	0.157	SUBCLONAL	1	TRUE	2	0.569672771407455	6		327	702	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0051423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	485	788	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.753656633869656	2	FACETS	0.989	0.961	1	0.989	0.961	1	CLONAL	2	TRUE	0	0.753656633869656	2		788	651	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0051423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	232	551	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.753656633869656	2		551	600	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934364	39934364	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1462787258	NA	P-0051423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	210	468	0	ENST00000378444.4:c.235C>T	p.Arg79Trp	p.R79W	ENST00000378444	NM_001123385.1	79	Cgg/Tgg	4/15	NA	2	FACETS	0.974	0.911	1			1	INDETERMINATE	1	TRUE	NA	0.753656633869656	2		468	572	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729290	41729290	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	149	358	0	ENST00000242208.4:c.1239G>C	p.Lys413Asn	p.K413N	ENST00000242208	NM_002192.2	413	aaG/aaC	3/3	0.745309046168205	3	FACETS	0.935	0.859	1	0.468	0.429	0.508	CLONAL	1	TRUE	1	0.753656633869656	3		358	582	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120796850	120796850	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424495218	NA	P-0051424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	111	512	0	ENST00000257552.2:c.409G>A	p.Asp137Asn	p.D137N	ENST00000257552	NM_002442.3	137	Gac/Aac	7/15	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.28	2		512	789	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392616	118392616	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	33	323	0	ENST00000534358.1:c.11648T>C	p.Ile3883Thr	p.I3883T	ENST00000534358	NM_005933.3	3883	aTt/aCt	36/36	1	2	FACETS	0.372	0.302	0.451	0.372	0.302	0.451	SUBCLONAL	1	TRUE	1	0.28	2		323	634	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	35	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.979	0.801	1	0.979	0.801	1	CLONAL	1	TRUE	1	0.13	2		334	550	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0051425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	39	513	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.817	0.676	0.977	0.817	0.676	0.977	CLONAL	1	TRUE	1	0.13	2		516	734	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484269	8484269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	41	432	0	ENST00000356435.5:c.3263G>A	p.Arg1088His	p.R1088H	ENST00000356435		1088	cGt/cAt	19/35	1	2	FACETS	0.904	0.751	1	0.904	0.751	1	CLONAL	1	TRUE	1	0.13	2		432	698	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218083	36218084	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0051425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	30	359	0	ENST00000222270.7:c.4031dup	p.Cys1344TrpfsTer3	p.C1344Wfs*3	ENST00000222270	NM_014727.1	1344	tgc/tGgc	15/37	1	2	FACETS	1	0.808	1	1	0.808	1	CLONAL	1	TRUE	1	0.13	2		359	460	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0051426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	301	627	3	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.837686497843462	2		630	700	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161680	56161680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	176	337	1	ENST00000399503.3:c.1177C>T	p.His393Tyr	p.H393Y	ENST00000399503	NM_005921.1	393	Cac/Tac	6/20	1	2	FACETS	0.975	0.908	1	0.975	0.908	1	CLONAL	1	TRUE	1	0.837686497843462	2		338	431	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149437108	149437108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1240901881	NA	P-0051426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	314	655	0	ENST00000286301.3:c.2180G>A	p.Arg727Lys	p.R727K	ENST00000286301	NM_005211.3	727	aGg/aAg	16/22	0.199773679800011	1	FACETS	0.561	0.532	0.591	0.561	0.532	0.591	INDETERMINATE	1	TRUE	0	0.837686497843462	1		655	776	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0051427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	120	390	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.505	0.458	0.555	0.505	0.458	0.555	SUBCLONAL	1	TRUE	1	0.874389289205142	2		390	543	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115701	8115701	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs112417755	NA	P-0051427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	45	174	0	ENST00000346208.3:c.1048-1G>C		p.X350_splice	ENST00000346208		350			1	2	FACETS	0.383	0.324	0.447	0.383	0.324	0.447	SUBCLONAL	1	TRUE	1	0.874389289205142	2		174	269	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639905	93639905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201438493	NA	P-0051427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	58	200	1	ENST00000375746.1:c.1234G>A	p.Ala412Thr	p.A412T	ENST00000375746	NM_001174167.1	412	Gct/Act	10/14	1	2	FACETS	0.506	0.439	0.578	0.506	0.439	0.578	SUBCLONAL	1	TRUE	1	0.874389289205142	2		201	262	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070660	67070660	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0051427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	43	102	0	ENST00000412916.2:c.282+2T>C		p.X94_splice	ENST00000412916		94			0.461874931564437	1	FACETS	0.299	0.253	0.348	0.299	0.253	0.348	INDETERMINATE	1	TRUE	0	0.874389289205142	1		102	185	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0051428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	92	355	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.269886037703619	3	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	FALSE	1	0.269886037703619	3		355	360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520000	NA	P-0051428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	275	740	1	ENST00000269305.4:c.452C>A	p.Pro151His	p.P151H	ENST00000269305	NM_001126112.2	151	cCc/cAc	5/11	0.269886037703619	4	FACETS	0.981	0.924	1	0.981	0.924	1	CLONAL	3	FALSE	1	0.269886037703619	4		741	879	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056021	26056021	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs987043105	NA	P-0051428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	27	236	0	ENST00000343677.2:c.636G>C	p.Lys212Asn	p.K212N	ENST00000343677	NM_005319.3	212	aaG/aaC	1/1	0.269886037703619	8	FACETS	0.734	0.583	0.908			1	CLONAL	1	FALSE	NA	0.269886037703619	8		236	493	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412627	139412627	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	63	598	0	ENST00000277541.6:c.1217del	p.Gly406AlafsTer225	p.G406Afs*225	ENST00000277541	NM_017617.3	406	gGc/gc	7/34	0.269886037703619	3	FACETS	0.736	0.636	0.845	0.368	0.318	0.423	SUBCLONAL	1	FALSE	1	0.269886037703619	3		598	720	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895658	28895658	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	63	440	0	ENST00000282397.4:c.3116G>A	p.Cys1039Tyr	p.C1039Y	ENST00000282397	NM_002019.4	1039	tGt/tAt	23/30	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	FALSE	1	0.269886037703619	2		440	435	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804244	43804244	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	67	376	1	ENST00000372470.3:c.244C>A	p.Gln82Lys	p.Q82K	ENST00000372470	NM_005373.2	82	Cag/Aag	3/12	0.269886037703619	3	FACETS	1	0.923	1	0.543	0.472	0.619	CLONAL	1	FALSE	1	0.269886037703619	3		377	519	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533790	533790	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs755322824	NA	P-0051428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	43	612	0	ENST00000451590.1:c.266C>G	p.Ser89Cys	p.S89C	ENST00000451590	NM_001130442.1	89	tCt/tGt	3/5	0.160946051438311	2	FACETS	0.485	0.405	0.574	0.243	0.202	0.287	INDETERMINATE	1	FALSE	0	0.269886037703619	2		612	657	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38631957	38631957	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1357395650	NA	P-0051428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	29	480	0	ENST00000299084.4:c.443C>A	p.Ser148Tyr	p.S148Y	ENST00000299084	NM_152594.2	148	tCc/tAc	5/7	0.269886037703619	3	FACETS	0.792	0.637	0.967	0.264	0.212	0.323	CLONAL	1	FALSE	0	0.269886037703619	3		480	308	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347891	347891	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	171	802	0	ENST00000262320.3:c.1615G>T	p.Val539Phe	p.V539F	ENST00000262320	NM_003502.3	539	Gtc/Ttc	6/11	0.269886037703619	3	FACETS	0.842	0.775	0.912			1	CLONAL	2	FALSE	NA	0.269886037703619	3		802	854	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122329	2122329	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	114	624	0	ENST00000219476.3:c.2185A>T	p.Ser729Cys	p.S729C	ENST00000219476	NM_000548.3	729	Agt/Tgt	20/42	0.269886037703619	3	FACETS	1	0.979	1			1	CLONAL	1	FALSE	NA	0.269886037703619	3		624	721	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641160	3641160	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	69	862	0	ENST00000294008.3:c.2479G>C	p.Glu827Gln	p.E827Q	ENST00000294008	NM_032444.2	827	Gag/Cag	12/15	0.269886037703619	3	FACETS	0.577	0.501	0.66			1	SUBCLONAL	1	FALSE	NA	0.269886037703619	3		862	1006	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644745	67644745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	38	366	0	ENST00000264010.4:c.10G>A	p.Asp4Asn	p.D4N	ENST00000264010	NM_006565.3	4	Gat/Aat	3/12	0.267347559511895	3	FACETS	0.73	0.603	0.871			1	SUBCLONAL	1	FALSE	NA	0.269886037703619	3		366	438	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119998	70119998	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs777735151	NA	P-0051428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	27	176	0	ENST00000245479.2:c.1000G>T	p.Val334Leu	p.V334L	ENST00000245479	NM_000346.3	334	Gtg/Ttg	3/3	0.224321272117446	5	FACETS	1	0.927	1	0.464	0.371	0.568	CLONAL	1	FALSE	2	0.269886037703619	5		176	202	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130373	11130373	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	56	507	1	ENST00000358026.2:c.2612C>A	p.Ala871Asp	p.A871D	ENST00000358026	NM_001128849.1	871	gCc/gAc	18/36	0.269886037703619	3	FACETS	0.901	0.772	1	0.3	0.257	0.347	CLONAL	1	FALSE	0	0.269886037703619	3		508	523	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967066	18967066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760602224	NA	P-0051428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	63	624	0	ENST00000262803.5:c.1781G>A	p.Arg594Gln	p.R594Q	ENST00000262803	NM_002911.3	594	cGg/cAg	13/24	0.267347559511895	3	FACETS	0.785	0.678	0.901			1	CLONAL	1	FALSE	NA	0.269886037703619	3		624	675	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721116	61721116	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	29	442	0	ENST00000401558.2:c.1158C>G	p.Phe386Leu	p.F386L	ENST00000401558	NM_003400.3	386	ttC/ttG	12/25	0.269886037703619	5	FACETS	0.637	0.51	0.781	0.212	0.17	0.261	SUBCLONAL	1	FALSE	2	0.269886037703619	5		442	474	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149592	202149592	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1274560305	NA	P-0051428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	32	394	0	ENST00000358485.4:c.1033G>C	p.Asp345His	p.D345H	ENST00000358485	NM_001080125.1	345	Gac/Cac	8/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.269886037703619	NA		394	443	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281204	142281204	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	24	316	0	ENST00000350721.4:c.1040G>T	p.Cys347Phe	p.C347F	ENST00000350721	NM_001184.3	347	tGc/tTc	4/47	0.269886037703619	4	FACETS	0.624	0.489	0.78	0.312	0.244	0.39	SUBCLONAL	1	FALSE	2	0.269886037703619	4		316	362	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186507037	186507037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	40	205	0	ENST00000323963.5:c.1203G>A	p.Met401Ile	p.M401I	ENST00000323963		401	atG/atA	11/11	0.269886037703619	4	FACETS	1	0.934	1	0.627	0.524	0.742	CLONAL	1	FALSE	2	0.269886037703619	4		205	300	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155797	106155797	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	21	334	0	ENST00000380013.4:c.698A>G	p.Tyr233Cys	p.Y233C	ENST00000380013	NM_001127208.2	233	tAt/tGt	3/11	0.182383873108369	2	FACETS	0.424	0.326	0.539	0.212	0.163	0.27	SUBCLONAL	1	FALSE	0	0.269886037703619	2		334	367	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517834	187517834	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs757371939	NA	P-0051428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	62	319	0	ENST00000441802.2:c.12860T>A	p.Phe4287Tyr	p.F4287Y	ENST00000441802	NM_005245.3	4287	tTt/tAt	25/27	0.182383873108369	2	FACETS	1	0.96	1	0.647	0.562	0.739	CLONAL	1	FALSE	0	0.269886037703619	2		319	355	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949114	151949114	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	44	388	0	ENST00000262189.6:c.1531G>C	p.Glu511Gln	p.E511Q	ENST00000262189	NM_170606.2	511	Gag/Cag	11/59	0.269886037703619	4	FACETS	0.926	0.778	1	0.309	0.259	0.364	CLONAL	1	FALSE	1	0.269886037703619	4		388	447	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978516	70978516	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	44	438	0	ENST00000276594.2:c.1137C>A	p.Ser379Arg	p.S379R	ENST00000276594	NM_024504.3	379	agC/agA	5/8	1	2	FACETS	0.726	0.609	0.855	0.726	0.609	0.855	SUBCLONAL	1	FALSE	1	0.269886037703619	2		438	449	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738398	145738398	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	42	649	0	ENST00000428558.2:c.2587G>C	p.Glu863Gln	p.E863Q	ENST00000428558	NM_004260.3	863	Gag/Cag	16/22	0.22804948638412	4	FACETS	0.529	0.44	0.628	0.265	0.22	0.314	SUBCLONAL	1	FALSE	2	0.269886037703619	4		649	747	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738496	145738496	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	53	600	0	ENST00000428558.2:c.2489G>C	p.Arg830Thr	p.R830T	ENST00000428558	NM_004260.3	830	aGa/aCa	16/22	0.22804948638412	4	FACETS	0.69	0.587	0.803	0.345	0.293	0.402	SUBCLONAL	1	FALSE	2	0.269886037703619	4		600	723	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484327	8484327	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	18	385	0	ENST00000356435.5:c.3205C>A	p.Gln1069Lys	p.Q1069K	ENST00000356435		1069	Cag/Aag	19/35	1	2	FACETS	0.389	0.292	0.503	0.389	0.292	0.503	SUBCLONAL	1	FALSE	1	0.269886037703619	2		385	343	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404411	139404411	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	46	565	0	ENST00000277541.6:c.2743C>T	p.Pro915Ser	p.P915S	ENST00000277541	NM_017617.3	915	Ccg/Tcg	18/34	0.269886037703619	3	FACETS	0.575	0.483	0.677	0.287	0.241	0.339	SUBCLONAL	1	FALSE	1	0.269886037703619	3		565	673	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	181	276	0				ENST00000310581	NM_198253.2	-/1132			0.691337298840093	4	FACETS	0.952	0.888	1	0.952	0.888	1	CLONAL	2	TRUE	2	0.75217287704312	4		276	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0051433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	564	674	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.75217287704312	3	FACETS	1	0.995	1			1	CLONAL	3	TRUE	NA	0.75217287704312	3		674	653	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391377	139391377	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752505638	NA	P-0051433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	408	776	1	ENST00000277541.6:c.6814C>T	p.Arg2272Cys	p.R2272C	ENST00000277541	NM_017617.3	2272	Cgt/Tgt	34/34	0.75217287704312	4	FACETS	1	0.987	1	0.718	0.687	0.75	CLONAL	2	TRUE	1	0.75217287704312	4		777	882	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057979	27057979	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	171	629	0	ENST00000324856.7:c.1687C>T	p.Gln563Ter	p.Q563*	ENST00000324856	NM_006015.4	563	Cag/Tag	3/20	0.75217287704312	6	FACETS	0.904	0.829	0.982			1	CLONAL	1	TRUE	NA	0.75217287704312	6		629	1260	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048638	6048638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	188	568	0	ENST00000265849.7:c.13G>A	p.Glu5Lys	p.E5K	ENST00000265849	NM_000535.5	5	Gag/Aag	1/15	0.749869805439384	5	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.75217287704312	5		568	857	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0051433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	13	391	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	0.746322427965849	3	FACETS	0.11	0.078	0.15	0.055	0.039	0.075	SUBCLONAL	1	TRUE	1	0.75217287704312	3		391	432	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039133	49039133	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0051433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	174	162	0	ENST00000267163.4:c.2212-1G>C		p.X738_splice	ENST00000267163	NM_000321.2	738			0.75217287704312	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	4	TRUE	0	0.75217287704312	4		162	191	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075394	8075394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	88	233	0	ENST00000377482.5:c.176C>T	p.Ser59Phe	p.S59F	ENST00000377482	NM_018948.3	59	tCt/tTt	3/4	0.747332664627923	3	FACETS	1	0.903	1	0.505	0.452	0.56	CLONAL	1	TRUE	1	0.75217287704312	3		233	319	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099471	27099471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	122	395	1	ENST00000324856.7:c.3708G>A	p.Met1236Ile	p.M1236I	ENST00000324856	NM_006015.4	1236	atG/atA	14/20	0.75217287704312	6	FACETS	1	0.918	1			1	CLONAL	1	TRUE	NA	0.75217287704312	6		396	799	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78938126	78938126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	144	619	0	ENST00000306801.3:c.4004G>A	p.Arg1335Lys	p.R1335K	ENST00000306801	NM_020761.2	1335	aGa/aAa	34/34	0.75217287704312	3	FACETS	0.916	0.839	0.996	0.458	0.419	0.498	CLONAL	1	TRUE	1	0.75217287704312	3		619	575	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39935760	39935760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745470688	NA	P-0051433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	172	514	0	ENST00000378444.4:c.112G>A	p.Ala38Thr	p.A38T	ENST00000378444	NM_001123385.1	38	Gct/Act	3/15	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.75217287704312	2		514	432	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264034	16264034	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	248	803	2	ENST00000375759.3:c.10403C>T	p.Pro3468Leu	p.P3468L	ENST00000375759	NM_015001.2	3468	cCa/cTa	12/15	0.747332664627923	3	FACETS	1	0.938	1	0.501	0.469	0.534	CLONAL	1	TRUE	1	0.75217287704312	3		805	906	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124541	108124541	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs1040176168	NA	P-0051433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	103	220	0	ENST00000278616.4:c.1899T>G	p.Cys633Trp	p.C633W	ENST00000278616	NM_000051.3	633	tgT/tgG	13/63	0.75217287704312	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.75217287704312	2		220	115	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428002	49428002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	406	659	0	ENST00000301067.7:c.10588G>A	p.Glu3530Lys	p.E3530K	ENST00000301067	NM_003482.3	3530	Gag/Aag	38/54	0.75217287704312	3	FACETS	1	0.984	1			1	CLONAL	2	TRUE	NA	0.75217287704312	3		659	711	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883653	37883653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	465	752	1	ENST00000269571.5:c.3265G>A	p.Asp1089Asn	p.D1089N	ENST00000269571		1089	Gac/Aac	26/27	0.75217287704312	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.75217287704312	3		753	817	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353845	40353845	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	156	493	0	ENST00000293328.3:c.2275C>G	p.Leu759Val	p.L759V	ENST00000293328	NM_012448.3	759	Ctg/Gtg	19/19	0.75217287704312	3	FACETS	0.909	0.836	0.985	0.454	0.418	0.493	CLONAL	1	TRUE	1	0.75217287704312	3		493	628	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245994	41245994	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	163	603	0	ENST00000357654.3:c.1554C>G	p.Ile518Met	p.I518M	ENST00000357654	NM_007294.3	518	atC/atG	10/23	0.75217287704312	3	FACETS	1	0.974	1	0.563	0.52	0.607	CLONAL	1	TRUE	1	0.75217287704312	3		603	530	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246239	41246239	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	129	485	0	ENST00000357654.3:c.1309C>G	p.His437Asp	p.H437D	ENST00000357654	NM_007294.3	437	Cat/Gat	10/23	0.75217287704312	3	FACETS	1	0.915	1	0.501	0.457	0.547	CLONAL	1	TRUE	1	0.75217287704312	3		485	471	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47710066	47710066	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	40	203	0	ENST00000233146.2:c.2783C>T	p.Ser928Leu	p.S928L	ENST00000233146	NM_000251.2	928	tCa/tTa	16/16	0.256355435447109	3	FACETS	1	0.945	1	0.631	0.538	0.728	INDETERMINATE	1	TRUE	1	0.75217287704312	3		203	116	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873009	134873009	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	172	556	0	ENST00000398015.3:c.1313C>T	p.Pro438Leu	p.P438L	ENST00000398015	NM_004441.4	438	cCc/cTc	6/16	0.75217287704312	3	FACETS	1	0.937	1	0.508	0.469	0.547	CLONAL	1	TRUE	1	0.75217287704312	3		556	620	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226814	142226814	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	40	353	0	ENST00000350721.4:c.4990G>A	p.Glu1664Lys	p.E1664K	ENST00000350721	NM_001184.3	1664	Gaa/Aaa	28/47	0.75217287704312	3	FACETS	0.335	0.278	0.398	0.167	0.139	0.199	SUBCLONAL	1	TRUE	1	0.75217287704312	3		353	437	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542468	187542468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	134	466	0	ENST00000441802.2:c.5272G>A	p.Glu1758Lys	p.E1758K	ENST00000441802	NM_005245.3	1758	Gag/Aag	10/27	0.746322427965849	3	FACETS	1	0.917	1	0.501	0.458	0.546	CLONAL	1	TRUE	1	0.75217287704312	3		466	489	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848544	151848544	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200004824	NA	P-0051433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	66	301	0	ENST00000262189.6:c.12649C>A	p.Leu4217Met	p.L4217M	ENST00000262189	NM_170606.2	4217	Ctg/Atg	50/59	0.75217287704312	5	FACETS	0.753	0.655	0.859	0.251	0.218	0.287	SUBCLONAL	1	TRUE	2	0.75217287704312	5		301	496	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848595	151848595	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	69	346	0	ENST00000262189.6:c.12598C>A	p.His4200Asn	p.H4200N	ENST00000262189	NM_170606.2	4200	Cat/Aat	50/59	0.75217287704312	5	FACETS	0.784	0.684	0.891	0.261	0.228	0.297	SUBCLONAL	1	TRUE	2	0.75217287704312	5		346	498	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151850011	151850011	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	80	292	0	ENST00000262189.6:c.12305C>A	p.Ser4102Tyr	p.S4102Y	ENST00000262189	NM_170606.2	4102	tCc/tAc	49/59	0.75217287704312	5	FACETS	0.896	0.791	1	0.299	0.263	0.337	CLONAL	1	TRUE	2	0.75217287704312	5		292	505	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965699	90965699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554558393	NA	P-0051433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	52	315	0	ENST00000265433.3:c.1618C>T	p.His540Tyr	p.H540Y	ENST00000265433	NM_002485.4	540	Cat/Tat	11/16	0.75217287704312	9	FACETS	0.832	0.707	0.968	0.104	0.088	0.121	CLONAL	1	TRUE	1	0.75217287704312	9		315	604	SUCCESS
AR	367	MSKCC	GRCh37	X	66766201	66766201	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	147	434	0	ENST00000374690.3:c.1213C>T	p.Gln405Ter	p.Q405*	ENST00000374690	NM_000044.3	405	Cag/Tag	1/8	0.747332664627923	3	FACETS	1	0.973	1	0.567	0.522	0.614	CLONAL	1	TRUE	1	0.75217287704312	3		434	474	SUCCESS
AR	367	MSKCC	GRCh37	X	66766408	66766408	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	27	119	0	ENST00000374690.3:c.1420G>T	p.Glu474Ter	p.E474*	ENST00000374690	NM_000044.3	474	Gag/Tag	1/8	0.747332664627923	3	FACETS	1	0.829	1	0.509	0.415	0.611	CLONAL	1	TRUE	1	0.75217287704312	3		119	97	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034475	123034475	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	177	442	0	ENST00000355640.3:c.1232T>C	p.Val411Ala	p.V411A	ENST00000355640		411	gTt/gCt	6/7	0.75217287704312	3	FACETS	0.82	0.766	0.874	0.82	0.766	0.874	CLONAL	2	TRUE	1	0.75217287704312	3		442	395	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	21	630	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	0.322326338414995	4	FACETS	0.413	0.317	0.525	0.207	0.158	0.263	SUBCLONAL	1	TRUE	2	0.322326338414995	4		630	417	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114817	108114817	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786204543	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	45	443	0	ENST00000278616.4:c.640del	p.Ser214ProfsTer16	p.S214Pfs*16	ENST00000278616	NM_000051.3	212	Ttt/tt	6/63	1	2	FACETS	0.844	0.712	0.988	0.844	0.712	0.988	CLONAL	1	TRUE	1	0.322326338414995	2		443	331	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	50	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.322326338414995	2		334	279	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	65	518	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.322326338414995	4	FACETS	1	0.885	1	1	0.885	1	CLONAL	2	TRUE	2	0.322326338414995	4		518	264	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	19	270	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.991	0.762	1	0.991	0.762	1	CLONAL	1	TRUE	1	0.322326338414995	2		270	119	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	101	765	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.169657093028411	4	FACETS	1	0.948	1	0.55	0.492	0.613	INDETERMINATE	1	TRUE	2	0.322326338414995	4		765	753	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231449	5231449	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	68	656	3	ENST00000357368.4:c.2027del	p.Pro676ArgfsTer134	p.P676Rfs*134	ENST00000357368	NM_002850.3	676	cCg/cg	14/38	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.322326338414995	2		659	319	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	56	525	1	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.322326338414995	3	FACETS	1	0.948	1	0.609	0.525	0.701	CLONAL	1	TRUE	1	0.322326338414995	3		526	331	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188165	11188165	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1277403206	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	29	426	0	ENST00000361445.4:c.5929A>G	p.Thr1977Ala	p.T1977A	ENST00000361445	NM_004958.3	1977	Aca/Gca	43/58	0.315944396350017	1	FACETS	0.665	0.537	0.809	0.665	0.537	0.809	SUBCLONAL	1	TRUE	0	0.322326338414995	1		426	227	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248061	59248061	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	18	387	0	ENST00000371222.2:c.682del	p.Glu228SerfsTer33	p.E228Sfs*33	ENST00000371222	NM_002228.3	228	Gag/ag	1/1	0.322326338414995	4	FACETS	0.533	0.401	0.689	0.267	0.2	0.345	SUBCLONAL	1	TRUE	2	0.322326338414995	4		387	277	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834552	156834552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540521894	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	38	723	0	ENST00000524377.1:c.320C>T	p.Ala107Val	p.A107V	ENST00000524377	NM_002529.3	107	gCg/gTg	3/17	1	2	FACETS	0.756	0.627	0.898	0.756	0.627	0.898	SUBCLONAL	1	TRUE	1	0.322326338414995	2		723	312	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193110997	193110997	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	24	216	0	ENST00000367435.3:c.530T>C	p.Met177Thr	p.M177T	ENST00000367435	NM_024529.4	177	aTg/aCg	7/17	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.322326338414995	2		216	118	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117069	193117069	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	41	311	0	ENST00000367435.3:c.802C>T	p.Arg268Ter	p.R268*	ENST00000367435	NM_024529.4	268	Cga/Tga	8/17	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.322326338414995	2		311	231	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683208	88683209	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	20	389	0	ENST00000372037.3:c.1426_1427dup	p.Lys477SerfsTer22	p.K477Sfs*22	ENST00000372037	NM_004329.2	473	gtt/gtTGt	12/13	1	2	FACETS	0.73	0.562	0.924	0.73	0.562	0.924	CLONAL	1	TRUE	1	0.322326338414995	2		389	170	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307238	118307238	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	18	203	1	ENST00000534358.1:c.11G>A	p.Ser4Asn	p.S4N	ENST00000534358	NM_005933.3	4	aGc/aAc	1/36	1	2	FACETS	0.479	0.361	0.618	0.479	0.361	0.618	SUBCLONAL	1	TRUE	1	0.322326338414995	2		204	233	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	25	465	1	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	0.248405777865223	5	FACETS	0.645	0.508	0.802	0.215	0.169	0.268	SUBCLONAL	1	TRUE	2	0.322326338414995	5		466	357	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911131	32911131	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	19	406	0	ENST00000380152.3:c.2639A>G	p.Glu880Gly	p.E880G	ENST00000380152		880	gAa/gGa	11/27	0.322326338414995	5	FACETS	0.655	0.498	0.84	0.218	0.166	0.28	SUBCLONAL	1	TRUE	2	0.322326338414995	5		406	267	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437427	110437427	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	50	375	0	ENST00000375856.3:c.974A>G	p.His325Arg	p.H325R	ENST00000375856	NM_003749.2	325	cAc/cGc	1/2	0.322326338414995	5	FACETS	0.77	0.657	0.892	0.513	0.438	0.595	SUBCLONAL	2	TRUE	2	0.322326338414995	5		375	299	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591625	38591642	+	inframe_deletion	In_Frame_Del	DEL	TGGTGGATGGTTACCACT	TGGTGGATGGTTACCACT	-	novel	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	36	467	0	ENST00000299084.4:c.87_104del	p.Trp31_Gly36del	p.W31_G36del	ENST00000299084	NM_152594.2	28	agTGGTGGATGGTTACCACTt/agt	2/7	0.169657093028411	4	FACETS	0.909	0.749	1	0.454	0.374	0.544	INDETERMINATE	1	TRUE	2	0.322326338414995	4		467	325	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129408	30129408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200652640	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	27	575	0	ENST00000263025.4:c.620C>T	p.Thr207Met	p.T207M	ENST00000263025	NM_002746.2	207	aCg/aTg	4/9	1	2	FACETS	0.327	0.259	0.404	0.327	0.259	0.404	SUBCLONAL	1	TRUE	1	0.322326338414995	2		575	513	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822585	72822586	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs764626362	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	27	513	2	ENST00000268489.5:c.9589dup	p.Gln3197ProfsTer42	p.Q3197Pfs*42	ENST00000268489	NM_006885.3	3197	cag/cCag	10/10	1	2	FACETS	0.886	0.711	1	0.886	0.711	1	CLONAL	1	TRUE	1	0.322326338414995	2		515	189	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	62	561	2	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	0.322326338414995	3	FACETS	1	0.919	1	1	0.919	1	CLONAL	2	TRUE	1	0.322326338414995	3		563	210	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55693397	55693397	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	84	629	0	ENST00000284073.2:c.604G>T	p.Gly202Ter	p.G202*	ENST00000284073	NM_138962.2	202	Gga/Tga	9/14	0.322326338414995	3	FACETS	1	0.971	1	0.656	0.582	0.735	CLONAL	1	TRUE	1	0.322326338414995	3		629	461	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533939	63533940	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs771001164	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	34	341	0	ENST00000307078.5:c.1214_1215del	p.Glu405GlyfsTer56	p.E405Gfs*56	ENST00000307078	NM_004655.3	405	gAG/g	6/11	0.322326338414995	3	FACETS	0.942	0.774	1	0.471	0.387	0.565	CLONAL	1	TRUE	1	0.322326338414995	3		341	260	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272337	15272337	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs771517374	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	73	739	3	ENST00000263388.2:c.6102del	p.Gly2035ValfsTer50	p.G2035Vfs*50	ENST00000263388	NM_000435.2	2034	ccC/cc	33/33	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.322326338414995	2		742	316	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378304	15378305	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	37	415	0	ENST00000263377.2:c.481dup	p.Ile161AsnfsTer3	p.I161Nfs*3	ENST00000263377	NM_058243.2	161	ata/aAta	4/20	1	2	FACETS	0.893	0.741	1	0.893	0.741	1	CLONAL	1	TRUE	1	0.322326338414995	2		415	257	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794441	42794441	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	72	888	4	ENST00000575354.2:c.1526del	p.Pro509HisfsTer14	p.P509Hfs*14	ENST00000575354	NM_015125.3	507	cgC/cg	10/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.322326338414995	2		892	392	SUCCESS
ALK	238	MSKCC	GRCh37	2	29430109	29430109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173246434	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	33	502	1	ENST00000389048.3:c.3866C>T	p.Ala1289Val	p.A1289V	ENST00000389048	NM_004304.4	1289	gCc/gTc	26/29	0.168545904689205	1	FACETS	0.855	0.702	1	0.855	0.702	1	INDETERMINATE	1	TRUE	0	0.322326338414995	1		503	201	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543652	29543652	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	19	593	0	ENST00000389048.3:c.1511G>T	p.Arg504Met	p.R504M	ENST00000389048	NM_004304.4	504	aGg/aTg	7/29	0.168545904689205	1	FACETS	0.351	0.266	0.45	0.351	0.266	0.45	INDETERMINATE	1	TRUE	0	0.322326338414995	1		593	282	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250247	39250247	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs727504295	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	21	681	0	ENST00000402219.2:c.1322G>A	p.Cys441Tyr	p.C441Y	ENST00000402219	NM_005633.3	441	tGt/tAt	10/23	0.168545904689205	1	FACETS	0.276	0.212	0.351	0.276	0.212	0.351	INDETERMINATE	1	TRUE	0	0.322326338414995	1		681	396	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37045935	37045935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750781	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	63	462	0	ENST00000231790.2:c.350C>T	p.Thr117Met	p.T117M	ENST00000231790	NM_000249.3	117	aCg/aTg	4/19	0.271390343723821	4	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	2	0.322326338414995	4		462	228	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623220	52623220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs771983602	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	43	343	0	ENST00000394830.3:c.2831A>G	p.His944Arg	p.H944R	ENST00000394830	NM_018313.4	944	cAt/cGt	19/30	0.168545904689205	1	FACETS	0.925	0.78	1	0.925	0.78	1	INDETERMINATE	1	TRUE	0	0.322326338414995	1		343	242	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748155	41748155	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1228610109	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	14	331	0	ENST00000226382.2:c.614C>A	p.Thr205Asn	p.T205N	ENST00000226382	NM_003924.3	205	aCc/aAc	3/3	0.168545904689205	1	FACETS	0.645	0.471	0.851	0.645	0.471	0.851	INDETERMINATE	1	TRUE	0	0.322326338414995	1		331	113	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55987301	55987301	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	60	437	0	ENST00000263923.4:c.124A>G	p.Thr42Ala	p.T42A	ENST00000263923	NM_002253.2	42	Aca/Gca	2/30	0.168545904689205	1	FACETS	1	0.93	1	1	0.93	1	INDETERMINATE	1	TRUE	0	0.322326338414995	1		437	281	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557259	187557259	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	10	518	0	ENST00000441802.2:c.4103T>G	p.Met1368Arg	p.M1368R	ENST00000441802	NM_005245.3	1368	aTg/aGg	6/27	0.322326338414995	1	FACETS	0.263	0.178	0.37	0.263	0.178	0.37	SUBCLONAL	1	TRUE	0	0.322326338414995	1		518	198	SUCCESS
APC	324	MSKCC	GRCh37	5	112177863	112177864	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	14	265	0	ENST00000257430.4:c.6579dup	p.Val2194SerfsTer3	p.V2194Sfs*3	ENST00000257430	NM_000038.5	2191	gga/ggAa	16/16	1	2	FACETS	0.439	0.317	0.585	0.439	0.317	0.585	SUBCLONAL	1	TRUE	1	0.322326338414995	2		265	198	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046674	180046674	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	31	799	1	ENST00000261937.6:c.2638A>G	p.Met880Val	p.M880V	ENST00000261937	NM_182925.4	880	Atg/Gtg	18/30	0.2931052400815	0	FACETS	0.655	0.534	0.789			1	SUBCLONAL	1	TRUE	0	0.322326338414995	0		800	199	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29913009	29913009	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	76	518	0	ENST00000376809.5:c.1046-2A>G		p.X349_splice	ENST00000376809	NM_002116.7	349			0.129104609940151	4	FACETS	0.942	0.833	1	0.942	0.833	1	INDETERMINATE	2	TRUE	2	0.322326338414995	4		518	331	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798150	32798150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	73	613	0	ENST00000374899.4:c.1529G>A	p.Ser510Asn	p.S510N	ENST00000374899	NM_018833.2	510	aGc/aAc	9/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.322326338414995	2		613	344	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982744	90982744	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	22	294	0	ENST00000265433.3:c.744A>C	p.Glu248Asp	p.E248D	ENST00000265433	NM_002485.4	248	gaA/gaC	7/16	0.248405777865223	5	FACETS	0.708	0.549	0.892	0.236	0.183	0.298	SUBCLONAL	1	TRUE	2	0.322326338414995	5		294	286	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937657	44937657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	26	191	1	ENST00000377967.4:c.2845C>T	p.Arg949Cys	p.R949C	ENST00000377967	NM_021140.2	949	Cgt/Tgt	19/29	1	1	FACETS	0.694	0.553	0.853	0.694	0.553	0.853	SUBCLONAL	1	TRUE	0	0.322326338414995	1		192	195	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411576	63411576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	39	367	0	ENST00000330258.3:c.1591C>T	p.Arg531Ter	p.R531*	ENST00000330258	NM_152424.3	531	Cga/Tga	2/2	1	1	FACETS	0.94	0.801	1	1	0.97	1	CLONAL	2	TRUE	0	0.322326338414995	1		367	108	SUCCESS
APC	324	MSKCC	GRCh37	5	112157646	112157647	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0051435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	279	414	0	ENST00000257430.4:c.1369dup	p.Ser457PhefsTer3	p.S457Ffs*3	ENST00000257430	NM_000038.5	456	ctt/cTtt	11/16	0.764033102948384	1	FACETS	0.956	0.914	0.996	0.956	0.914	0.996	CLONAL	1	TRUE	0	0.800899050618972	1		414	437	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	103	530	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.839	0.751	0.931	0.839	0.751	0.931	CLONAL	1	TRUE	1	0.37270838384884	2		533	659	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	228	531	2	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	0.308873486221327	2	FACETS	0.995	0.933	1	0.995	0.933	1	CLONAL	2	TRUE	0	0.37270838384884	2		533	615	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945064	31945064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61745042	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	154	609	1	ENST00000340398.3:c.37G>A	p.Gly13Ser	p.G13S	ENST00000340398	NM_001013699.2	13	Ggt/Agt	1/1	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.37270838384884	2		610	779	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	84	453	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	1	2	FACETS	0.882	0.781	0.989	0.882	0.781	0.989	CLONAL	1	TRUE	1	0.37270838384884	2		453	511	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	67	377	3	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	0.37270838384884	2	FACETS	0.821	0.716	0.934	0.41	0.358	0.467	CLONAL	1	TRUE	0	0.37270838384884	2		380	438	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	102	765	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.37270838384884	2		765	535	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661664	227661664	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs761880048	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	191	482	10	ENST00000305123.5:c.1791del	p.His598ThrfsTer38	p.H598Tfs*38	ENST00000305123	NM_005544.2	597	ggG/gg	1/2	0.37270838384884	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.37270838384884	2		492	506	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	213	281	4	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	0.262620955975117	4	FACETS	0.897	0.839	0.956	0.897	0.839	0.956	CLONAL	3	TRUE	1	0.37270838384884	4		285	583	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	292	634	1	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	0.37270838384884	2	FACETS	0.936	0.884	0.989	0.936	0.884	0.989	CLONAL	2	TRUE	0	0.37270838384884	2		635	837	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044500	12044500	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367662793	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	82	300	0	ENST00000353533.5:c.1123G>A	p.Val375Ile	p.V375I	ENST00000353533	NM_003010.3	375	Gtt/Att	11/11	1	2	FACETS	0.891	0.788	1	0.891	0.788	1	CLONAL	1	TRUE	1	0.37270838384884	2		300	494	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781193	135781193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768985094	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	100	521	1	ENST00000298552.3:c.1772C>T	p.Pro591Leu	p.P591L	ENST00000298552	NM_001162426.1	591	cCg/cTg	15/23	0.37270838384884	2	FACETS	0.797	0.713	0.887	0.399	0.356	0.444	SUBCLONAL	1	TRUE	0	0.37270838384884	2		522	673	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105676	27105678	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs753766136	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	147	323	3	ENST00000324856.7:c.5299_5301del	p.Glu1767del	p.E1767del	ENST00000324856	NM_006015.4	1763	GAA/-	20/20	0.308873486221327	2	FACETS	0.867	0.798	0.938	0.867	0.798	0.938	CLONAL	2	TRUE	0	0.37270838384884	2		326	455	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210691	5210691	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	114	507	0	ENST00000357368.4:c.5360G>A	p.Arg1787Gln	p.R1787Q	ENST00000357368	NM_002850.3	1787	cGg/cAg	34/38	0.37270838384884	2	FACETS	0.88	0.793	0.972	0.44	0.396	0.486	CLONAL	1	TRUE	0	0.37270838384884	2		507	695	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341730	8341730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41281783	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	114	442	0	ENST00000356435.5:c.4910C>T	p.Thr1637Met	p.T1637M	ENST00000356435		1637	aCg/aTg	29/35	0.37270838384884	2	FACETS	0.959	0.865	1	0.479	0.432	0.529	CLONAL	1	TRUE	0	0.37270838384884	2		442	638	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828024	72828024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200701402	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	200	599	0	ENST00000268489.5:c.8557G>A	p.Ala2853Thr	p.A2853T	ENST00000268489	NM_006885.3	2853	Gca/Aca	9/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.37270838384884	2		599	987	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110791	2110791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45517148	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	144	591	0	ENST00000219476.3:c.1096G>A	p.Glu366Lys	p.E366K	ENST00000219476	NM_000548.3	366	Gaa/Aaa	11/42	1	2	FACETS	0.977	0.892	1	0.977	0.892	1	CLONAL	1	TRUE	1	0.37270838384884	2		591	791	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228145	36228145	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	312	543	0	ENST00000222270.7:c.7531C>T	p.Arg2511Trp	p.R2511W	ENST00000222270	NM_014727.1	2511	Cgg/Tgg	33/37	0.37270838384884	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.37270838384884	2		543	769	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458270	12458270	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	96	423	0	ENST00000287820.6:c.892del	p.Leu298CysfsTer38	p.L298Cfs*38	ENST00000287820	NM_015869.4	296	aCc/ac	6/7	1	2	FACETS	0.819	0.731	0.913	0.819	0.731	0.913	CLONAL	1	TRUE	1	0.37270838384884	2		423	629	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205850	128205850	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	93	288	0	ENST00000341105.2:c.25C>T	p.Arg9Cys	p.R9C	ENST00000341105	NM_032638.4	9	Cgc/Tgc	2/6	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.37270838384884	2		288	410	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211504	36211504	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	61	428	0	ENST00000222270.7:c.1259del	p.Pro420LeufsTer55	p.P420Lfs*55	ENST00000222270	NM_014727.1	419	Ccc/cc	3/37	0.37270838384884	2	FACETS	0.603	0.52	0.692	0.301	0.26	0.346	SUBCLONAL	1	TRUE	0	0.37270838384884	2		428	543	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129421	152129421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	81	338	0	ENST00000206249.3:c.374G>A	p.Gly125Asp	p.G125D	ENST00000206249	NM_000125.3	125	gGc/gAc	1/8	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.37270838384884	2		338	424	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421039	49421039	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123721	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	86	386	0	ENST00000301067.7:c.14710C>T	p.Arg4904Ter	p.R4904*	ENST00000301067	NM_003482.3	4904	Cga/Tga	48/54	1	2	FACETS	0.832	0.737	0.932	0.832	0.737	0.932	CLONAL	1	TRUE	1	0.37270838384884	2		386	555	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128201209	128201209	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1369730858	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	139	580	1	ENST00000265960.3:c.1526C>T	p.Thr509Met	p.T509M	ENST00000265960	NM_001006617.1	509	aCg/aTg	12/12	0.37270838384884	2	FACETS	0.929	0.846	1	0.464	0.423	0.508	CLONAL	1	TRUE	0	0.37270838384884	2		581	803	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953633	32953633	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359732	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	46	320	0	ENST00000380152.3:c.8940del	p.Glu2981LysfsTer7	p.E2981Kfs*7	ENST00000380152		2978	tcA/tc	22/27	0.262620955975117	4	FACETS	0.635	0.534	0.746	0.212	0.178	0.249	SUBCLONAL	1	TRUE	1	0.37270838384884	4		320	534	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231449	5231449	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	151	656	3	ENST00000357368.4:c.2027del	p.Pro676ArgfsTer134	p.P676Rfs*134	ENST00000357368	NM_002850.3	676	cCg/cg	14/38	0.37270838384884	2	FACETS	1	0.941	1	0.517	0.473	0.563	CLONAL	1	TRUE	0	0.37270838384884	2		659	783	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912134	50912134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781327088	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	156	597	1	ENST00000440232.2:c.1868G>A	p.Arg623Gln	p.R623Q	ENST00000440232	NM_002691.3	623	cGg/cAg	15/27	0.37270838384884	2	FACETS	1	0.956	1	0.533	0.489	0.58	CLONAL	1	TRUE	0	0.37270838384884	2		598	785	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280332	1280332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194223999	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	182	662	1	ENST00000310581.5:c.1891C>T	p.Arg631Trp	p.R631W	ENST00000310581	NM_198253.2	631	Cgg/Tgg	4/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.37270838384884	2		663	907	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911154	29911155	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	96	455	0	ENST00000376809.5:c.453_454del	p.Asn151LysfsTer25	p.N151Kfs*25	ENST00000376809	NM_002116.7	151	aaCGag/aaag	3/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.37270838384884	2		455	463	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98247992	98247992	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554702047	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	99	346	0	ENST00000331920.6:c.559C>T	p.Arg187Cys	p.R187C	ENST00000331920	NM_000264.3	187	Cgt/Tgt	3/24	0.37270838384884	2	FACETS	0.989	0.886	1	0.495	0.443	0.549	CLONAL	1	TRUE	0	0.37270838384884	2		346	537	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652330	206652330	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	394	585	1	ENST00000367120.3:c.1042del	p.Arg348AspfsTer32	p.R348Dfs*32	ENST00000367120	NM_014002.3	346	gCc/gc	10/22	0.37270838384884	3	FACETS	0.924	0.882	0.966	0.924	0.882	0.966	CLONAL	3	TRUE	0	0.37270838384884	3		586	905	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670328	134670328	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559321367	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	78	387	0	ENST00000398015.3:c.239G>A	p.Arg80Gln	p.R80Q	ENST00000398015	NM_004441.4	80	cGg/cAg	3/16	1	2	FACETS	0.904	0.797	1	0.904	0.797	1	CLONAL	1	TRUE	1	0.37270838384884	2		387	463	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4387948	4387948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219347646	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	102	434	0	ENST00000261254.3:c.434G>A	p.Gly145Glu	p.G145E	ENST00000261254	NM_001759.3	145	gGg/gAg	3/5	1	2	FACETS	0.854	0.765	0.948	0.854	0.765	0.948	CLONAL	1	TRUE	1	0.37270838384884	2		434	641	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443884	49443884	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs892437631	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	43	592	1	ENST00000301067.7:c.3487G>A	p.Val1163Met	p.V1163M	ENST00000301067	NM_003482.3	1163	Gtg/Atg	11/54	1	2	FACETS	0.284	0.237	0.337	0.284	0.237	0.337	SUBCLONAL	1	TRUE	1	0.37270838384884	2		593	812	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490333	29490333	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691119	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	125	368	0	ENST00000356175.3:c.421del	p.Val141PhefsTer24	p.V141Ffs*24	ENST00000356175	NM_000267.3	140	Ggg/gg	4/57	1	2	FACETS	0.958	0.869	1	0.958	0.869	1	CLONAL	1	TRUE	1	0.37270838384884	2		368	700	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55729496	55729496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747741239	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	173	570	1	ENST00000284073.2:c.764C>T	p.Ala255Val	p.A255V	ENST00000284073	NM_138962.2	255	gCg/gTg	11/14	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.37270838384884	2		571	855	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383299	42383299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371599562	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	128	497	1	ENST00000221972.3:c.319C>T	p.Arg107Trp	p.R107W	ENST00000221972	NM_021601.3	107	Cgg/Tgg	2/5	0.37270838384884	2	FACETS	1	0.966	1	0.564	0.512	0.618	CLONAL	1	TRUE	0	0.37270838384884	2		498	609	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683486	182683486	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs200589493	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	85	448	0	ENST00000292782.4:c.59A>G	p.Gln20Arg	p.Q20R	ENST00000292782	NM_020640.2	20	cAa/cGa	2/7	1	2	FACETS	0.793	0.702	0.89	0.793	0.702	0.89	SUBCLONAL	1	TRUE	1	0.37270838384884	2		448	575	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164004	106164004	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	66	300	0	ENST00000380013.4:c.3514G>T	p.Gly1172Cys	p.G1172C	ENST00000380013	NM_001127208.2	1172	Ggt/Tgt	5/11	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.37270838384884	2		300	345	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137522074	137522074	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	70	248	0	ENST00000367739.4:c.805del	p.Tyr269IlefsTer8	p.Y269Ifs*8	ENST00000367739	NM_000416.2	269	Tat/at	6/7	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.37270838384884	2		248	333	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864754	68864754	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	92	419	2	ENST00000288368.4:c.125T>C	p.Leu42Pro	p.L42P	ENST00000288368	NM_024870.2	42	cTg/cCg	1/40	1	2	FACETS	0.834	0.742	0.931	0.834	0.742	0.931	CLONAL	1	TRUE	1	0.37270838384884	2		421	592	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969342	44969342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	67	182	0	ENST00000377967.4:c.4024C>T	p.Leu1342Phe	p.L1342F	ENST00000377967	NM_021140.2	1342	Ctt/Ttt	28/29	1	1	FACETS	0.77	0.682	0.861	1	0.977	1	SUBCLONAL	2	TRUE	0	0.37270838384884	1		182	190	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690842	89690842	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1554897879	NA	P-0051437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	63	265	0	ENST00000371953.3:c.249C>A	p.Cys83Ter	p.C83*	ENST00000371953	NM_000314.4	83	tgC/tgA	4/9	0.202514398184755	4	FACETS	0.84	0.732	0.954	0.84	0.732	0.954	INDETERMINATE	2	TRUE	2	0.342610111632364	4		265	294	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692848	89692848	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	35	159	0	ENST00000371953.3:c.332G>A	p.Trp111Ter	p.W111*	ENST00000371953	NM_000314.4	111	tGg/tAg	5/9	0.202514398184755	4	FACETS	1	0.874	1	1	0.874	1	INDETERMINATE	2	TRUE	2	0.342610111632364	4		159	130	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183821	10183845	+	frameshift_variant	Frame_Shift_Del	DEL	CCTACCCAACGCTGCCGCCTGGCAC	CCTACCCAACGCTGCCGCCTGGCAC	GTTGGGTAG	novel	NA	P-0051437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	130	593	2	ENST00000256474.2:c.290_314delinsGTTGGGTAG	p.Pro97ArgfsTer57	p.P97Rfs*57	ENST00000256474	NM_000551.3	97	cCCTACCCAACGCTGCCGCCTGGCACg/cGTTGGGTAGg	1/3	0.342610111632364	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.342610111632364	2		595	350	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0051438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	83	384	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.264384721129357	4	FACETS	0.876	0.782	0.975	1	0.973	1	CLONAL	3	TRUE	2	0.264384721129357	4		384	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0051438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	99	567	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA	2	FACETS	0.993	0.894	1			1	INDETERMINATE	2	TRUE	NA	0.264384721129357	2		567	377	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604778	48604778	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767383	NA	P-0051438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	64	285	1	ENST00000342988.3:c.1600C>T	p.Gln534Ter	p.Q534*	ENST00000342988	NM_005359.5	534	Cag/Tag	12/12	0.264384721129357	4	FACETS	0.962	0.847	1	0.962	0.847	1	CLONAL	3	TRUE	1	0.264384721129357	4		286	212	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971127	21971128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTGG	novel	NA	P-0051438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	39	333	0	ENST00000304494.5:c.227_230dup	p.Leu78HisfsTer43	p.L78Hfs*43	ENST00000304494	NM_000077.4	77	act/acCCACt	2/3	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.264384721129357	2		333	235	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193565	99193565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	169	513	0	ENST00000074304.5:c.2760G>A	p.Met920Ile	p.M920I	ENST00000074304	NM_001134224.1	920	atG/atA	25/26	0.643631052839764	3	FACETS	0.931	0.858	1	0.465	0.429	0.503	CLONAL	1	TRUE	1	0.731599192839768	3		513	678	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578412	7578414	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0051447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	459	944	0	ENST00000269305.4:c.516_518del	p.Val173del	p.V173del	ENST00000269305	NM_001126112.2	172	gtTGTg/gtg	5/11	0.380109331150384	3	FACETS	0.835	0.802	0.869	0.835	0.802	0.869	CLONAL	3	TRUE	0	0.477135710993124	3		944	951	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745177	41745177	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	149	762	1	ENST00000301178.4:c.1243G>A	p.Gly415Arg	p.G415R	ENST00000301178	NM_021913.4	415	Gga/Aga	9/20	0.136062214119484	5	FACETS	1	0.978	1	0.406	0.371	0.443	INDETERMINATE	1	TRUE	2	0.477135710993124	5		763	880	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660629	227660629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	38	720	0	ENST00000305123.5:c.2826G>A	p.Met942Ile	p.M942I	ENST00000305123	NM_005544.2	942	atG/atA	1/2	1	2	FACETS	0.361	0.298	0.433	0.361	0.298	0.433	SUBCLONAL	1	TRUE	1	0.32057042164218	2		720	656	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0051448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	24	341	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.342	0.267	0.428	0.342	0.267	0.428	SUBCLONAL	1	TRUE	1	0.32057042164218	2		341	438	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324514	31324517	+	frameshift_variant	Frame_Shift_Del	DEL	GTCA	GTCA	-	novel	NA	P-0051448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	143	1110	0	ENST00000412585.2:c.291_294del	p.Asp98GlufsTer52	p.D98Efs*52	ENST00000412585	NM_005514.6	97	acTGAC/ac	2/8	0.32057042164218	1	FACETS	0.968	0.883	1	0.968	0.883	1	CLONAL	1	TRUE	0	0.32057042164218	1		1110	774	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016267	150016267	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	94	433	0	ENST00000253339.5:c.439C>T	p.Arg147Ter	p.R147*	ENST00000253339		147	Cga/Tga	2/7	0.32057042164218	1	FACETS	0.875	0.78	0.975	0.875	0.78	0.975	CLONAL	1	TRUE	0	0.32057042164218	1		433	563	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023151	27023179	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	-	novel	NA	P-0051449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	101	29	0	ENST00000324856.7:c.267_295del	p.Ser90ProfsTer11	p.S90Pfs*11	ENST00000324856	NM_006015.4	86	gGCGGAGCCGGCAGCGGCGGCGGGCCCGGC/g	1/20	0.139855724714782	3	FACETS	1	0.933	1	1	0.933	1	INDETERMINATE	3	TRUE	0	0.479886648682966	3		29	172	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448389	49448389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1233258179	NA	P-0051449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	87	731	1	ENST00000301067.7:c.322G>A	p.Ala108Thr	p.A108T	ENST00000301067	NM_003482.3	108	Gca/Aca	3/54	0.442868579419642	3	FACETS	0.706	0.625	0.792	0.353	0.312	0.396	SUBCLONAL	1	TRUE	1	0.479886648682966	3		732	637	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480661	50480661	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	63	236	0	ENST00000394963.4:c.531G>T	p.Lys177Asn	p.K177N	ENST00000394963	NM_003076.4	177	aaG/aaT	4/13	0.442868579419642	3	FACETS	0.878	0.763	1	0.439	0.381	0.501	CLONAL	1	TRUE	1	0.479886648682966	3		236	371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	273	617	0	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	0.479886648682966	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.479886648682966	1		617	579	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223012	5223012	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	95	588	0	ENST00000357368.4:c.2791C>G	p.His931Asp	p.H931D	ENST00000357368	NM_002850.3	931	Cac/Gac	18/38	1	2	FACETS	0.945	0.847	1	0.945	0.847	1	CLONAL	1	TRUE	1	0.479886648682966	2		588	419	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122742	7122742	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	103	703	2	ENST00000302850.5:c.3412C>T	p.Gln1138Ter	p.Q1138*	ENST00000302850	NM_000208.2	1138	Cag/Tag	19/22	1	2	FACETS	0.728	0.653	0.807	0.728	0.653	0.807	SUBCLONAL	1	TRUE	1	0.479886648682966	2		705	590	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907659	111907659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	32	363	0	ENST00000393256.3:c.433G>A	p.Glu145Lys	p.E145K	ENST00000393256	NM_006538.4	145	Gag/Aag	3/4	1	2	FACETS	0.291	0.235	0.353	0.291	0.235	0.353	SUBCLONAL	1	TRUE	1	0.479886648682966	2		363	459	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295714	212295714	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	97	463	0	ENST00000342788.4:c.2599C>G	p.Leu867Val	p.L867V	ENST00000342788	NM_005235.2	867	Ctc/Gtc	21/28	1	2	FACETS	0.879	0.787	0.975	0.879	0.787	0.975	CLONAL	1	TRUE	1	0.479886648682966	2		463	460	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982139	38982139	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0051449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	36	259	0	ENST00000357387.3:c.584-1G>C		p.X195_splice	ENST00000357387	NM_152756.3	195			0.479886648682966	3	FACETS	0.416	0.342	0.499	0.208	0.171	0.25	SUBCLONAL	1	TRUE	1	0.479886648682966	3		259	447	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325418	1325418	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	43	511	0	ENST00000400841.2:c.257T>A	p.Leu86Gln	p.L86Q	ENST00000400841		86	cTa/cAa	3/6	1	1	FACETS	0.422	0.354	0.496	0.422	0.354	0.496	SUBCLONAL	1	TRUE	0	0.479886648682966	1		511	323	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436327	110436327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs980704170	NA	P-0051451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	23	241	0	ENST00000375856.3:c.2074C>T	p.Pro692Ser	p.P692S	ENST00000375856	NM_003749.2	692	Ccc/Tcc	1/2	1	2	FACETS	0.457	0.357	0.572	0.457	0.357	0.572	SUBCLONAL	1	TRUE	1	0.362160003841307	2		241	278	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183763	10183776	+	frameshift_variant	Frame_Shift_Del	DEL	AATCGCAGTCCGCG	AATCGCAGTCCGCG	-	novel	NA	P-0051451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	130	606	0	ENST00000256474.2:c.232_245del	p.Asn78ArgfsTer49	p.N78Rfs*49	ENST00000256474	NM_000551.3	78	AATCGCAGTCCGCGc/c	1/3	0.362160003841307	1	FACETS	0.996	0.907	1	0.996	0.907	1	CLONAL	1	TRUE	0	0.362160003841307	1		606	590	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52685827	52685827	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0051451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	65	312	0	ENST00000394830.3:c.646-1G>A		p.X216_splice	ENST00000394830	NM_018313.4	216			0.362160003841307	1	FACETS	0.805	0.702	0.916	0.805	0.702	0.916	CLONAL	1	TRUE	0	0.362160003841307	1		312	365	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0051453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	297	474	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.6095251603239	3	FACETS	0.882	0.836	0.927	0.882	0.836	0.927	CLONAL	2	TRUE	1	0.679910795411566	3		474	664	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921620	39921620	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	174	235	0	ENST00000378444.4:c.4200del	p.Pro1401ArgfsTer83	p.P1401Rfs*83	ENST00000378444	NM_001123385.1	1400	cgG/cg	10/15	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.679910795411566	1		235	293	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0051454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	10	390	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.589894030400858	4	FACETS	0.118	0.079	0.168	0.059	0.039	0.084	SUBCLONAL	1	TRUE	2	0.820040123191712	4		390	375	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0051454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	42	219	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.606	0.514	0.705	0.606	0.514	0.705	SUBCLONAL	1	TRUE	1	0.820040123191712	2		219	169	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0051454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	360	633	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.584432027826449	2	FACETS	0.753	0.723	0.782	0.753	0.723	0.782	SUBCLONAL	2	TRUE	0	0.820040123191712	2		633	583	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11177096	11177096	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878855328	NA	P-0051454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	61	339	0	ENST00000361445.4:c.6981G>A	p.Met2327Ile	p.M2327I	ENST00000361445	NM_004958.3	2327	atG/atA	50/58	0.619055675256425	2	FACETS	0.404	0.35	0.462	0.202	0.175	0.231	SUBCLONAL	1	TRUE	0	0.820040123191712	2		339	368	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0051454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	53	383	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.818	0.712	0.929	0.818	0.712	0.929	CLONAL	1	TRUE	1	0.820040123191712	2		383	158	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118924	70118926	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0051454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	377	706	0	ENST00000245479.2:c.499_501del	p.Lys167del	p.K167del	ENST00000245479	NM_000346.3	166	AAG/-	2/3	0.589894030400858	4	FACETS	0.786	0.748	0.825	0.786	0.748	0.825	SUBCLONAL	2	TRUE	2	0.820040123191712	4		706	1064	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851931	128851931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749061719	NA	P-0051454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	387	714	3	ENST00000249373.3:c.2003G>A	p.Arg668His	p.R668H	ENST00000249373	NM_005631.4	668	cGc/cAc	12/12	0.589894030400858	4	FACETS	0.865	0.824	0.906	0.865	0.824	0.906	CLONAL	2	TRUE	2	0.820040123191712	4		717	993	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014105	70014105	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	36	416	0	ENST00000394351.3:c.966G>C	p.Glu322Asp	p.E322D	ENST00000394351	NM_000248.3	322	gaG/gaC	9/9	0.641981579572567	3	FACETS	0.238	0.195	0.286	0.119	0.097	0.143	SUBCLONAL	1	TRUE	1	0.820040123191712	3		416	520	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	39	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.412323298235873	2		276	174	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961559	18961559	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	107	542	0	ENST00000262803.5:c.692C>T	p.Pro231Leu	p.P231L	ENST00000262803	NM_002911.3	231	cCg/cTg	5/24	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.412323298235873	2		542	506	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42384976	42384976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782417731	NA	P-0051455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	111	566	2	ENST00000221972.3:c.610C>T	p.Arg204Trp	p.R204W	ENST00000221972	NM_021601.3	204	Cgg/Tgg	5/5	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.412323298235873	2		568	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs28934577	NA	P-0051456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	308	633	0	ENST00000269305.4:c.770T>A	p.Leu257Gln	p.L257Q	ENST00000269305	NM_001126112.2	257	cTg/cAg	7/11	0.278119927985977	2	FACETS	0.975	0.923	1	0.975	0.923	1	CLONAL	2	TRUE	0	0.397517939072427	2		633	795	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573277	41573278	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0051457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	139	741	1	ENST00000263253.7:c.5564dup	p.Thr1856AsnfsTer27	p.T1856Nfs*27	ENST00000263253	NM_001429.3	1854	-/C	31/31	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		742	734	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	49	517	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.22	2		517	332	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	37	404	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.678	0.559	0.812	0.678	0.559	0.812	SUBCLONAL	1	TRUE	1	0.22	2		404	496	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	41	265	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	1	0.85	1	1	0.97	1	CLONAL	2	TRUE	1	0.22	2		265	185	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	57	613	1	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.22	2		614	506	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512290	120512290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782230202	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	55	537	0	ENST00000256646.2:c.952C>T	p.Arg318Cys	p.R318C	ENST00000256646	NM_024408.3	318	Cgc/Tgc	6/34	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.22	2		537	478	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436102	49436102	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	25	451	0	ENST00000301067.7:c.5879del	p.Gly1960AlafsTer87	p.G1960Afs*87	ENST00000301067	NM_003482.3	1960	gGc/gc	28/54	1	2	FACETS	0.931	0.737	1	0.931	0.737	1	CLONAL	1	TRUE	1	0.22	2		451	244	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69230503	69230505	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	19	302	0	ENST00000462284.1:c.897_899del	p.Glu299del	p.E299del	ENST00000462284	NM_002392.5	298	GAA/-	10/11	1	2	FACETS	0.617	0.468	0.791	0.617	0.468	0.791	SUBCLONAL	1	TRUE	1	0.22	2		302	280	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254166	133254166	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs371882716	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	33	449	1	ENST00000320574.5:c.718G>A	p.Val240Met	p.V240M	ENST00000320574	NM_006231.2	240	Gtg/Atg	7/49	1	2	FACETS	0.701	0.571	0.848	0.701	0.571	0.848	SUBCLONAL	1	TRUE	1	0.22	2		450	428	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435253	110435253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771232244	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	20	160	0	ENST00000375856.3:c.3148G>A	p.Val1050Ile	p.V1050I	ENST00000375856	NM_003749.2	1050	Gtt/Att	1/2	1	2	FACETS	0.713	0.546	0.908	0.713	0.546	0.908	CLONAL	1	TRUE	1	0.22	2		160	255	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566220	95566220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767112987	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	27	514	0	ENST00000393063.1:c.4103G>A	p.Arg1368His	p.R1368H	ENST00000393063	NM_030621.3	1368	cGc/cAc	23/28	1	2	FACETS	0.536	0.426	0.662	0.536	0.426	0.662	SUBCLONAL	1	TRUE	1	0.22	2		514	458	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701263	43701263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1157211964	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	56	444	1	ENST00000382044.4:c.5432C>T	p.Ala1811Val	p.A1811V	ENST00000382044	NM_001141980.1	1811	gCg/gTg	26/28	1	2	FACETS	0.926	0.793	1	0.926	0.793	1	CLONAL	1	TRUE	1	0.22	2		445	550	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639131	3639131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370637700	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	68	808	0	ENST00000294008.3:c.4508C>T	p.Pro1503Leu	p.P1503L	ENST00000294008	NM_032444.2	1503	cCg/cTg	12/15	1	2	FACETS	0.914	0.795	1	0.914	0.795	1	CLONAL	1	TRUE	1	0.22	2		808	676	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650710	67650710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243010179	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	63	496	0	ENST00000264010.4:c.1015C>T	p.Arg339Trp	p.R339W	ENST00000264010	NM_006565.3	339	Cgg/Tgg	5/12	1	2	FACETS	0.822	0.71	0.943	0.822	0.71	0.943	CLONAL	1	TRUE	1	0.22	2		496	697	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849480	68849480	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	57	581	0	ENST00000261769.5:c.1386del	p.Phe462LeufsTer19	p.F462Lfs*19	ENST00000261769	NM_004360.3	461	ccT/cc	10/16	1	2	FACETS	0.858	0.736	0.991	0.858	0.736	0.991	CLONAL	1	TRUE	1	0.22	2		581	604	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246532	41246532	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357569	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	54	559	1	ENST00000357654.3:c.1016del	p.Lys339ArgfsTer2	p.K339Rfs*2	ENST00000357654	NM_007294.3	339	aAg/ag	10/23	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.22	2		560	460	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099271	4099271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs185999703	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	38	834	0	ENST00000262948.5:c.847G>A	p.Val283Met	p.V283M	ENST00000262948	NM_030662.3	283	Gtg/Atg	7/11	1	2	FACETS	0.539	0.444	0.645	0.539	0.444	0.645	SUBCLONAL	1	TRUE	1	0.22	2		834	641	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384974	17384974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765161255	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	50	829	0	ENST00000359435.4:c.524C>T	p.Thr175Met	p.T175M	ENST00000359435	NM_001033549.1	175	aCg/aTg	5/9	1	2	FACETS	0.563	0.476	0.659	0.563	0.476	0.659	SUBCLONAL	1	TRUE	1	0.22	2		829	807	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212138	36212138	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1258696516	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	16	389	0	ENST00000222270.7:c.1893del	p.Ser632ProfsTer28	p.S632Pfs*28	ENST00000222270	NM_014727.1	630	gCc/gc	3/37	1	2	FACETS	0.535	0.395	0.702	0.535	0.395	0.702	SUBCLONAL	1	TRUE	1	0.22	2		389	272	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505345	25505345	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1310158529	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	31	723	0	ENST00000264709.3:c.413C>T	p.Thr138Ile	p.T138I	ENST00000264709	NM_175629.2	138	aCc/aTc	4/23	1	2	FACETS	0.598	0.483	0.729	0.598	0.483	0.729	SUBCLONAL	1	TRUE	1	0.22	2		723	471	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068421	26068421	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	28	274	0	ENST00000435504.4:c.69del	p.Lys23AsnfsTer7	p.K23Nfs*7	ENST00000435504		23	aaA/aa	2/13	1	2	FACETS	0.964	0.773	1	0.964	0.773	1	CLONAL	1	TRUE	1	0.22	2		274	264	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635687	47635693	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CATATAA	CATATAA	TATTT	novel	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	42	296	0	ENST00000233146.2:c.359_365delinsTATTT	p.Ala120ValfsTer12	p.A120Vfs*12	ENST00000233146	NM_000251.2	120	gCATATAAg/gTATTTg	2/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.22	2		296	288	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61729409	61729409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749929742	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	36	329	0	ENST00000401558.2:c.338C>T	p.Thr113Met	p.T113M	ENST00000401558	NM_003400.3	113	aCg/aTg	5/25	1	2	FACETS	0.963	0.793	1	0.963	0.793	1	CLONAL	1	TRUE	1	0.22	2		329	340	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62312043	62312043	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762108489	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	47	845	0	ENST00000360203.5:c.1162G>A	p.Gly388Arg	p.G388R	ENST00000360203	NM_001283009.1	388	Gga/Aga	14/35	1	2	FACETS	0.539	0.454	0.635	0.539	0.454	0.635	SUBCLONAL	1	TRUE	1	0.22	2		845	792	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725013	49725013	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145300894	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	47	629	0	ENST00000449682.2:c.331C>T	p.Arg111Cys	p.R111C	ENST00000449682	NM_020998.3	111	Cgc/Tgc	3/18	1	2	FACETS	0.812	0.685	0.952	0.812	0.685	0.952	CLONAL	1	TRUE	1	0.22	2		629	526	SUCCESS
ATR	545	MSKCC	GRCh37	3	142222265	142222265	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	23	315	0	ENST00000350721.4:c.5227A>G	p.Met1743Val	p.M1743V	ENST00000350721	NM_001184.3	1743	Atg/Gtg	30/47	1	2	FACETS	0.67	0.523	0.841	0.67	0.523	0.841	SUBCLONAL	1	TRUE	1	0.22	2		315	312	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936096	178936096	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519940	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	26	471	0	ENST00000263967.3:c.1638G>T	p.Gln546His	p.Q546H	ENST00000263967	NM_006218.2	546	caG/caT	10/21	1	2	FACETS	0.605	0.478	0.749	0.605	0.478	0.749	SUBCLONAL	1	TRUE	1	0.22	2		471	391	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984863	55984866	+	frameshift_variant	Frame_Shift_Del	DEL	GTGA	GTGA	-	novel	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	66	462	0	ENST00000263923.4:c.263_266del	p.Leu88GlnfsTer5	p.L88Qfs*5	ENST00000263923	NM_002253.2	88	cTCACa/ca	3/30	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.22	2		462	500	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271297	1271297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	55	540	1	ENST00000310581.5:c.2405G>A	p.Ser802Asn	p.S802N	ENST00000310581	NM_198253.2	802	aGc/aAc	8/16	1	2	FACETS	0.88	0.753	1	0.88	0.753	1	CLONAL	1	TRUE	1	0.22	2		541	568	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637294	176637294	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	50	507	0	ENST00000439151.2:c.1894C>T	p.Arg632Ter	p.R632*	ENST00000439151	NM_022455.4	632	Cga/Tga	5/23	1	2	FACETS	0.928	0.788	1	0.928	0.788	1	CLONAL	1	TRUE	1	0.22	2		507	490	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687004	176687004	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	24	346	0	ENST00000439151.2:c.4981T>G	p.Cys1661Gly	p.C1661G	ENST00000439151	NM_022455.4	1661	Tgt/Ggt	14/23	1	2	FACETS	0.511	0.4	0.64	0.511	0.4	0.64	SUBCLONAL	1	TRUE	1	0.22	2		346	427	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048760	180048760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754245879	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	64	826	0	ENST00000261937.6:c.1802C>T	p.Ala601Val	p.A601V	ENST00000261937	NM_182925.4	601	gCg/gTg	13/30	1	2	FACETS	0.751	0.649	0.862	0.751	0.649	0.862	SUBCLONAL	1	TRUE	1	0.22	2		826	775	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522131	157522131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780970034	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	54	590	1	ENST00000346085.5:c.4403G>A	p.Arg1468His	p.R1468H	ENST00000346085	NM_020732.3	1468	cGc/cAc	18/20	1	2	FACETS	0.992	0.848	1	0.992	0.848	1	CLONAL	1	TRUE	1	0.22	2		591	495	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970919	70970919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1563439440	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	82	593	1	ENST00000276594.2:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000276594	NM_024504.3	448	Cgg/Tgg	6/8	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.22	2		594	586	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030454	47030454	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	90	813	0	ENST00000377604.3:c.229G>A	p.Glu77Lys	p.E77K	ENST00000377604	NM_001204468.1	77	Gag/Aag	4/24	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.22	2		813	714	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422384	47422384	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	26	475	1	ENST00000377045.4:c.23del	p.Pro8LeufsTer26	p.P8Lfs*26	ENST00000377045	NM_001654.4	6	ggC/gg	2/16	1	2	FACETS	0.561	0.444	0.696	0.561	0.444	0.696	SUBCLONAL	1	TRUE	1	0.22	2		476	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0051459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	213	978	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	0.193347070140549	2	FACETS	0.963	0.894	1	0.963	0.894	1	CLONAL	2	TRUE	0	0.211279809378364	2		978	1047	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913471	NA	P-0051459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	424	695	0	ENST00000269571.5:c.2329G>C	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ctg	20/27	0.211279809378364	3	FACETS	0.919	0.877	0.962			1	CLONAL	4	TRUE	NA	0.211279809378364	3		695	1207	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872556	35872556	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	49	369	0	ENST00000216797.5:c.347A>G	p.His116Arg	p.H116R	ENST00000216797	NM_020529.2	116	cAc/cGc	3/6	0.211279809378364	1	FACETS	0.694	0.587	0.811	0.694	0.587	0.811	SUBCLONAL	1	TRUE	0	0.211279809378364	1		369	598	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193530	99193530	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	102	687	0	ENST00000074304.5:c.2725G>T	p.Glu909Ter	p.E909*	ENST00000074304	NM_001134224.1	909	Gag/Tag	25/26	1	2	FACETS	0.98	0.875	1	0.98	0.875	1	CLONAL	1	TRUE	1	0.211279809378364	2		687	985	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32439169	32439169	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1739	120	381	0	ENST00000332351.3:c.904G>A	p.Glu302Lys	p.E302K	ENST00000332351	NM_024426.4	302	Gaa/Aaa	4/10	0.211279809378364	17	FACETS	0.79	0.71	0.875			1	SUBCLONAL	2	TRUE	NA	0.211279809378364	17		381	1859	SUCCESS
BLM	641	MSKCC	GRCh37	15	91337567	91337567	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	26	182	0	ENST00000355112.3:c.3190G>A	p.Asp1064Asn	p.D1064N	ENST00000355112	NM_000057.2	1064	Gat/Aat	16/22	0.211279809378364	4	FACETS	0.742	0.587	0.919	0.247	0.195	0.307	CLONAL	1	TRUE	1	0.211279809378364	4		182	402	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781832	3781832	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs764431514	NA	P-0051459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	80	589	0	ENST00000262367.5:c.4835A>G	p.Asn1612Ser	p.N1612S	ENST00000262367	NM_004380.2	1612	aAc/aGc	29/31	0.197655060901426	3	FACETS	0.804	0.705	0.91	0.402	0.352	0.455	CLONAL	1	TRUE	1	0.211279809378364	3		589	1042	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227019	2227019	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	25	444	0	ENST00000398665.3:c.4499C>G	p.Ser1500Cys	p.S1500C	ENST00000398665	NM_032482.2	1500	tCt/tGt	27/28	1	2	FACETS	0.481	0.378	0.6	0.481	0.378	0.6	SUBCLONAL	1	FALSE	1	0.208759752179582	2		444	498	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717676	89717676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909235	NA	P-0051460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	31	383	0	ENST00000371953.3:c.701G>A	p.Arg234Gln	p.R234Q	ENST00000371953	NM_000314.4	234	cGg/cAg	7/9	0.0857208232195927	3	FACETS	0.668	0.539	0.814	0.334	0.269	0.407	INDETERMINATE	1	FALSE	1	0.208759752179582	3		383	491	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618851	37618851	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	35	446	0	ENST00000447079.4:c.527C>A	p.Ser176Ter	p.S176*	ENST00000447079	NM_015083.1	176	tCa/tAa	1/14	0.208759752179582	2	FACETS	0.607	0.497	0.732	0.304	0.248	0.366	SUBCLONAL	1	FALSE	0	0.208759752179582	2		446	552	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0051461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	17	366	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.84	1	1	0.84	1	CLONAL	1	TRUE	1	0.15	2		366	193	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0051461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	36	396	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.15	2		396	369	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686238	117686238	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs772772410	NA	P-0051461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	16	231	0	ENST00000368508.3:c.3103C>T	p.Arg1035Ter	p.R1035*	ENST00000368508	NM_002944.2	1035	Cga/Tga	20/43	1	2	FACETS	0.731	0.54	0.959	0.731	0.54	0.959	CLONAL	1	TRUE	1	0.15	2		231	292	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943349	17943349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759015510	NA	P-0051461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	28	541	0	ENST00000458235.1:c.2659C>T	p.Arg887Cys	p.R887C	ENST00000458235	NM_000215.3	887	Cgt/Tgt	19/24	1	2	FACETS	0.699	0.557	0.861	0.699	0.557	0.861	SUBCLONAL	1	TRUE	1	0.15	2		541	534	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675103	40675103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	40	729	2	ENST00000249776.8:c.67G>A	p.Asp23Asn	p.D23N	ENST00000249776	NM_033286.3	23	Gat/Aat	1/9	1	2	FACETS	0.787	0.652	0.937	0.787	0.652	0.937	CLONAL	1	TRUE	1	0.15	2		731	678	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615568	100615568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	29	403	0	ENST00000308731.7:c.764G>A	p.Arg255Gln	p.R255Q	ENST00000308731	NM_000061.2	255	cGa/cAa	8/19	1	2	FACETS	1	0.816	1	1	0.816	1	CLONAL	1	TRUE	1	0.15	2		403	380	SUCCESS
AR	367	MSKCC	GRCh37	X	66942767	66942767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	29	354	0	ENST00000374690.3:c.2548C>T	p.Pro850Ser	p.P850S	ENST00000374690	NM_000044.3	850	Ccc/Tcc	7/8	1	2	FACETS	0.877	0.703	1	0.877	0.703	1	CLONAL	1	TRUE	1	0.15	2		354	441	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248672	212248672	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780519461	NA	P-0051461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	28	344	0	ENST00000342788.4:c.3595G>A	p.Glu1199Lys	p.E1199K	ENST00000342788	NM_005235.2	1199	Gag/Aag	28/28	1	2	FACETS	0.938	0.75	1	0.938	0.75	1	CLONAL	1	TRUE	1	0.15	2		344	398	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362004	118362004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	19	242	0	ENST00000534358.1:c.4790C>T	p.Ser1597Phe	p.S1597F	ENST00000534358	NM_005933.3	1597	tCc/tTc	14/36	1	2	FACETS	0.741	0.562	0.952	0.741	0.562	0.952	CLONAL	1	TRUE	1	0.15	2		242	342	SUCCESS
BLM	641	MSKCC	GRCh37	15	91337531	91337531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	26	285	0	ENST00000355112.3:c.3154C>T	p.Pro1052Ser	p.P1052S	ENST00000355112	NM_000057.2	1052	Cct/Tct	16/22	1	2	FACETS	0.929	0.736	1	0.929	0.736	1	CLONAL	1	TRUE	1	0.15	2		285	373	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121250	29121250	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	39	540	1	ENST00000328354.6:c.425A>T	p.Lys142Ile	p.K142I	ENST00000328354	NM_007194.3	142	aAa/aTa	3/15	1	2	FACETS	0.802	0.664	0.958	0.802	0.664	0.958	CLONAL	1	TRUE	1	0.15	2		541	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573983	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0051464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	162	514	0	ENST00000269305.4:c.1044_1045delinsTT	p.Leu348_Glu349delinsPheTer	p.L348_E349delinsF*	ENST00000269305	NM_001126112.2	348	ttGGaa/ttTTaa	10/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.360269099702573	2		514	789	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951091	48951094	+	frameshift_variant	Frame_Shift_Del	DEL	GAGT	GAGT	-	novel	NA	P-0051464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	28	223	0	ENST00000267163.4:c.1255_1258del	p.Val419ArgfsTer3	p.V419Rfs*3	ENST00000267163	NM_000321.2	418	aGAGTg/ag	13/27	0.35203846811718	1	FACETS	0.855	0.692	1	0.855	0.692	1	CLONAL	1	TRUE	0	0.360269099702573	1		223	149	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132922	30132922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	84	298	0	ENST00000331968.5:c.679C>T	p.Pro227Ser	p.P227S	ENST00000331968	NM_002742.2	227	Cct/Tct	4/18	1	2	FACETS	0.773	0.684	0.869	0.773	0.684	0.869	SUBCLONAL	1	TRUE	1	0.360269099702573	2		298	603	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467432	66467432	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	26	203	0	ENST00000273854.3:c.837A>T	p.Glu279Asp	p.E279D	ENST00000273854	NM_004439.5	279	gaA/gaT	3/18	0.299419635253766	1	FACETS	0.342	0.271	0.424	0.342	0.271	0.424	SUBCLONAL	1	TRUE	0	0.360269099702573	1		203	346	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681660	30681660	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748179039	NA	P-0051464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	127	391	1	ENST00000376406.3:c.437C>T	p.Thr146Ile	p.T146I	ENST00000376406	NM_014641.2	146	aCa/aTa	3/15	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.360269099702573	2		392	672	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	56	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.82618155343325	2		276	131	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0051465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	274	674	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.82618155343325	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.82618155343325	1		674	372	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739111	46739111	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs372225086	NA	P-0051465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	132	462	0	ENST00000371975.4:c.1460C>G	p.Ser487Cys	p.S487C	ENST00000371975	NM_003579.3	487	tCt/tGt	13/18	1	2	FACETS	0.852	0.782	0.924	0.852	0.782	0.924	CLONAL	1	TRUE	1	0.82618155343325	2		462	375	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796353	42796353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	315	809	0	ENST00000575354.2:c.3002C>T	p.Ser1001Phe	p.S1001F	ENST00000575354	NM_015125.3	1001	tCc/tTc	12/20	NA	2	FACETS	1	0.963	1			1	INDETERMINATE	1	TRUE	NA	0.82618155343325	2		809	749	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094386	27094386	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	149	437	1	ENST00000324856.7:c.3094G>T	p.Glu1032Ter	p.E1032*	ENST00000324856	NM_006015.4	1032	Gag/Tag	11/20	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.82618155343325	2		438	350	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162722894	162722894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1340393535	NA	P-0051465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	55	459	0	ENST00000367921.3:c.92G>A	p.Arg31His	p.R31H	ENST00000367921	NM_006182.2	31	cGc/cAc	4/18	1	2	FACETS	0.374	0.321	0.431	0.374	0.321	0.431	SUBCLONAL	1	TRUE	1	0.82618155343325	2		459	356	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094472	27094472	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	130	385	0	ENST00000324856.7:c.3180G>C	p.Glu1060Asp	p.E1060D	ENST00000324856	NM_006015.4	1060	gaG/gaC	11/20	1	2	FACETS	0.98	0.903	1	0.98	0.903	1	CLONAL	1	TRUE	1	0.82618155343325	2		385	321	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142914	7142914	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555738952	NA	P-0051465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	72	653	0	ENST00000302850.5:c.2455C>G	p.Arg819Gly	p.R819G	ENST00000302850	NM_000208.2	819	Cgc/Ggc	12/22	1	2	FACETS	0.268	0.234	0.305	0.268	0.234	0.305	SUBCLONAL	1	TRUE	1	0.82618155343325	2		653	650	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31393175	31393175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764716011	NA	P-0051465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	86	333	0	ENST00000328111.2:c.2263G>A	p.Glu755Lys	p.E755K	ENST00000328111	NM_006892.3	755	Gag/Aag	21/23	1	2	FACETS	0.959	0.865	1	0.959	0.865	1	CLONAL	1	TRUE	1	0.82618155343325	2		333	217	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524491	44524491	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	58	201	0	ENST00000291552.4:c.66C>G	p.Phe22Leu	p.F22L	ENST00000291552	NM_006758.2	22	ttC/ttG	2/8	NA	2	FACETS	1	0.885	1			1	INDETERMINATE	1	TRUE	NA	0.82618155343325	2		201	140	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41558748	41558757	+	frameshift_variant	Frame_Shift_Del	DEL	TTCCAAGAGA	TTCCAAGAGA	-	novel	NA	P-0051465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	19	183	0	ENST00000263253.7:c.3693_3702del	p.Phe1231LeufsTer43	p.F1231Lfs*43	ENST00000263253	NM_001429.3	1231	ttTTCCAAGAGA/tt	21/31	0.480765197051385	1	FACETS	0.16	0.122	0.204	0.16	0.122	0.204	INDETERMINATE	1	TRUE	0	0.82618155343325	1		183	169	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0051466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	121	467	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.43302675000827	1	FACETS	0.849	0.77	0.93	0.849	0.77	0.93	CLONAL	1	TRUE	0	0.43302675000827	1		467	516	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217283	11217283	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	87	477	0	ENST00000361445.4:c.4395G>C	p.Lys1465Asn	p.K1465N	ENST00000361445	NM_004958.3	1465	aaG/aaC	30/58	0.271053702303009	1	FACETS	0.435	0.385	0.489	0.435	0.385	0.489	SUBCLONAL	1	TRUE	0	0.43302675000827	1		477	723	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711922	89711922	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	119	374	0	ENST00000371953.3:c.540C>A	p.Tyr180Ter	p.Y180*	ENST00000371953	NM_000314.4	180	taC/taA	6/9	0.43302675000827	1	FACETS	0.985	0.896	1	0.985	0.896	1	CLONAL	1	TRUE	0	0.43302675000827	1		374	437	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557347	29557348	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTAATGATGGCAAGGAGAGATGACCTCTCATTTTGCC	novel	NA	P-0051466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	39	190	0	ENST00000356175.3:c.3061_3097dup	p.Gln1033ArgfsTer8	p.Q1033Rfs*8	ENST00000356175	NM_000267.3	1020	-/GTAATGATGGCAAGGAGAGATGACCTCTCATTTTGCC	23/57	0.43302675000827	1	FACETS	0.466	0.387	0.552	0.466	0.387	0.552	SUBCLONAL	1	TRUE	0	0.43302675000827	1		190	303	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696659	47696659	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	81	324	0	ENST00000347630.2:c.289G>A	p.Glu97Lys	p.E97K	ENST00000347630	NM_001007230.1	97	Gaa/Aaa	5/11	0.43302675000827	1	FACETS	0.606	0.535	0.681	0.606	0.535	0.681	SUBCLONAL	1	TRUE	0	0.43302675000827	1		324	484	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495450	149495450	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	110	772	0	ENST00000261799.4:c.3197C>G	p.Pro1066Arg	p.P1066R	ENST00000261799	NM_002609.3	1066	cCc/cGc	23/23	1	2	FACETS	0.511	0.458	0.567	0.511	0.458	0.567	SUBCLONAL	1	TRUE	1	0.43302675000827	2		772	994	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0051467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	265	633	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	0.167757393378429	3	FACETS	0.769	0.724	0.815	0.769	0.724	0.815	INDETERMINATE	2	TRUE	1	0.584138745915478	3		633	762	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061317	38061317	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	146	471	0	ENST00000250448.2:c.672C>A	p.Phe224Leu	p.F224L	ENST00000250448	NM_004496.3	224	ttC/ttA	2/2	1	2	FACETS	0.888	0.814	0.964	0.888	0.814	0.964	CLONAL	1	TRUE	1	0.584138745915478	2		471	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578452	7578453	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCGCGGACGCGGGTGCCGGG	novel	NA	P-0051467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	47	672	0	ENST00000269305.4:c.457_477dup	p.Pro153_Ala159dup	p.P153_A159dup	ENST00000269305	NM_001126112.2	153	-/CCCGGCACCCGCGTCCGCGCC	5/11	0.560025993250253	1	FACETS	0.235	0.198	0.276	0.235	0.198	0.276	SUBCLONAL	1	TRUE	0	0.584138745915478	1		672	484	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845843	151845843	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	124	537	0	ENST00000262189.6:c.13169T>C	p.Leu4390Pro	p.L4390P	ENST00000262189	NM_170606.2	4390	cTt/cCt	52/59	0.115383461944587	3	FACETS	1	0.976	1	0.605	0.551	0.662	INDETERMINATE	1	TRUE	1	0.584138745915478	3		537	453	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0051468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	44	268	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.305388026518291	2		268	269	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23635360	23635360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769009609	NA	P-0051468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	65	360	1	ENST00000261584.4:c.2804C>T	p.Ala935Val	p.A935V	ENST00000261584	NM_024675.3	935	gCt/gTt	8/13	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.305388026518291	2		361	371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579698	7579700	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ACC	ACC	-	novel	NA	P-0051468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	39	338	0	ENST00000269305.4:c.96_96+2del		p.X32_splice	ENST00000269305	NM_001126112.2	32		3/11	0.305388026518291	1	FACETS	0.958	0.8	1	0.958	0.8	1	CLONAL	1	TRUE	0	0.305388026518291	1		338	226	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0051468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	64	221	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.305388026518291	3	FACETS	0.905	0.792	1	0.905	0.792	1	CLONAL	2	TRUE	1	0.305388026518291	3		221	267	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618630	37618630	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	GAT	novel	NA	P-0051468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	195	424	0	ENST00000447079.4:c.306delinsGAT	p.Asp103MetfsTer22	p.D103Mfs*22	ENST00000447079	NM_015083.1	102	tcA/tcGAT	1/14	0.213175153500822	3	FACETS	1	0.971	1			1	CLONAL	3	TRUE	NA	0.305388026518291	3		424	460	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289247	33289247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1455644209	NA	P-0051469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	184	487	0	ENST00000374542.5:c.305C>T	p.Ser102Leu	p.S102L	ENST00000374542	NM_001141970.1	102	tCg/tTg	3/8	0.693315725538786	1	FACETS	0.991	0.931	1	0.991	0.931	1	CLONAL	1	TRUE	0	0.693315725538786	1		487	350	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041125	42041125	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	288	375	0	ENST00000219905.7:c.5503G>A	p.Gly1835Arg	p.G1835R	ENST00000219905	NM_001164273.1	1835	Ggg/Agg	16/24	0.543867869171938	6	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	FALSE	3	0.850748158019661	6		375	575	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982440	25982440	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	184	295	0	ENST00000435504.4:c.850C>G	p.Arg284Gly	p.R284G	ENST00000435504		284	Cga/Gga	9/13	0.543867869171938	6	FACETS	0.881	0.823	0.941	0.881	0.823	0.941	CLONAL	3	FALSE	3	0.850748158019661	6		295	442	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29090017	29090019	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CAC	CAC	AA	novel	NA	P-0051470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	103	154	1	ENST00000328354.6:c.1461+1_1461+3delinsTT		p.X487_splice	ENST00000328354	NM_007194.3	487			0.850748158019661	3	FACETS	0.928	0.855	1	0.619	0.57	0.667	CLONAL	2	FALSE	0	0.850748158019661	3		155	186	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971370	13971370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748346103	NA	P-0051470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	170	266	0	ENST00000405192.2:c.559C>T	p.Arg187Cys	p.R187C	ENST00000405192	NM_001163147.1	187	Cgc/Tgc	8/12	0.543867869171938	6	FACETS	0.928	0.865	0.991	0.928	0.865	0.991	CLONAL	3	FALSE	3	0.850748158019661	6		266	388	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376040	8376040	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	39	215	0	ENST00000356435.5:c.4557G>T	p.Trp1519Cys	p.W1519C	ENST00000356435		1519	tgG/tgT	28/35	0.620585227742725	6	FACETS	0.643	0.534	0.765	0.214	0.178	0.255	SUBCLONAL	1	FALSE	3	0.850748158019661	6		215	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579505	7579506	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CTGGACCTGGGTCTTCAGTGAACCATTGTTCAATATCGTCCGGGGA	novel	NA	P-0051471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	175	650	0	ENST00000269305.4:c.136_181dup	p.Asp61ValfsTer6	p.D61Vfs*6	ENST00000269305	NM_001126112.2	61	gat/gTCCCCGGACGATATTGAACAATGGTTCACTGAAGACCCAGGTCCAGat	4/11	0.253772575344685	3	FACETS	0.922	0.848	0.999	0.307	0.282	0.333	INDETERMINATE	1	TRUE	0	0.441540983515196	3		650	1050	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652885	29652885	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0051471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	117	206	0	ENST00000356175.3:c.4820T>G	p.Leu1607Ter	p.L1607*	ENST00000356175	NM_000267.3	1607	tTa/tGa	36/57	0.393789043873839	2	FACETS	0.957	0.878	1	0.957	0.878	1	CLONAL	2	TRUE	0	0.441540983515196	2		206	277	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814227	76814227	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	123	294	1	ENST00000373344.5:c.6417G>T	p.Trp2139Cys	p.W2139C	ENST00000373344	NM_000489.3	2139	tgG/tgT	29/35	0.441540983515196	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.441540983515196	1		295	301	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0051472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	52	518	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.929	0.797	1	0.929	0.797	1	CLONAL	1	TRUE	1	0.4	2		518	280	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877869	151877887	+	frameshift_variant	Frame_Shift_Del	DEL	ACAGGTCCAGGAAGTTGGG	ACAGGTCCAGGAAGTTGGG	-	novel	NA	P-0051472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	43	336	0	ENST00000262189.6:c.7058_7076del	p.Ser2353CysfsTer6	p.S2353Cfs*6	ENST00000262189	NM_170606.2	2353	tCCCAACTTCCTGGACCTGTg/tg	36/59	1	2	FACETS	0.911	0.769	1	0.911	0.769	1	CLONAL	1	TRUE	1	0.4	2		336	236	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259162	36259164	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	novel	NA	P-0051472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	60	481	0	ENST00000300305.3:c.327_329del	p.Asn109del	p.N109del	ENST00000300305		109	aaCAAg/aag	3/8	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.4	2		481	286	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876920	151876920	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	25	243	0	ENST00000262189.6:c.7441del	p.Arg2481AspfsTer34	p.R2481Dfs*34	ENST00000262189	NM_170606.2	2481	Aga/ga	37/59	1	2	FACETS	0.977	0.781	1	0.977	0.781	1	CLONAL	1	TRUE	1	0.4	2		243	128	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0051476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	77	355	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.33562028896831	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.370697713996689	1		355	293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0051476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	70	547	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.33562028896831	1	FACETS	0.805	0.706	0.912	0.805	0.706	0.912	CLONAL	1	TRUE	0	0.370697713996689	1		547	382	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0051476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	51	518	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.819	0.699	0.949	0.819	0.699	0.949	CLONAL	1	TRUE	1	0.370697713996689	2		518	336	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0051476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	79	380	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.370697713996689	2		380	373	SUCCESS
APC	324	MSKCC	GRCh37	5	112175756	112175756	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	70	312	0	ENST00000257430.4:c.4466del	p.Leu1489TyrfsTer18	p.L1489Yfs*18	ENST00000257430	NM_000038.5	1489	Tta/ta	16/16	0.370697713996689	2	FACETS	1	0.974	1	0.715	0.631	0.804	CLONAL	1	TRUE	0	0.370697713996689	2		312	264	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906330	50906330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370734242	NA	P-0051476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	92	782	1	ENST00000440232.2:c.991C>T	p.Arg331Trp	p.R331W	ENST00000440232	NM_002691.3	331	Cgg/Tgg	9/27	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.370697713996689	2		783	460	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982401	201982402	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0051476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	117	669	0	ENST00000359651.3:c.782_783del	p.Leu261ArgfsTer39	p.L261Rfs*39	ENST00000359651		260	tgTCtc/tgtc	6/8	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.370697713996689	2		669	602	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119291	3119293	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0051476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	108	693	0	ENST00000078429.4:c.826_828del	p.Lys276del	p.K276del	ENST00000078429	NM_002067.2	275	AAG/-	6/7	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.370697713996689	2		693	468	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	86	276	0				ENST00000310581	NM_198253.2	-/1132			0.173170506901922	1	FACETS	0.721	0.648	0.797	0.721	0.648	0.797	INDETERMINATE	1	TRUE	0	0.649500853444689	1		276	248	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653796	89653809	+	frameshift_variant	Frame_Shift_Del	DEL	ATTATTGCTATGGG	ATTATTGCTATGGG	-	novel	NA	P-0051477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	108	83	0	ENST00000371953.3:c.97_110del	p.Ile33SerfsTer6	p.I33Sfs*6	ENST00000371953	NM_000314.4	32	ATTATTGCTATGGGa/a	2/9	0.649500853444689	1	FACETS	0.936	0.857	1	0.936	0.857	1	CLONAL	1	TRUE	0	0.649500853444689	1		83	240	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941629	48941629	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1131690860	NA	P-0051477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	82	33	0	ENST00000267163.4:c.940-1G>T		p.X314_splice	ENST00000267163	NM_000321.2	314			0.649500853444689	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.649500853444689	1		33	156	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574007	7574011	+	frameshift_variant	Frame_Shift_Del	DEL	CATCT	CATCT	-	novel	NA	P-0051477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	249	560	0	ENST00000269305.4:c.1016_1020del	p.Glu339ValfsTer6	p.E339Vfs*6	ENST00000269305	NM_001126112.2	339	gAGATG/g	10/11	1	2	FACETS	0.932	0.874	0.991	0.932	0.874	0.991	CLONAL	1	TRUE	1	0.649500853444689	2		560	823	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579355	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519997	NA	P-0051477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	337	713	0	ENST00000269305.4:c.332T>C	p.Leu111Pro	p.L111P	ENST00000269305	NM_001126112.2	111	cTg/cCg	4/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.649500853444689	2		713	978	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098913	47098917	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	GTTCC	GTTCC	TCAAACAACT	novel	NA	P-0051477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	306	388	0	ENST00000409792.3:c.6357_6361delinsAGTTGTTTGA	p.Glu2120ValfsTer3	p.E2120Vfs*3	ENST00000409792	NM_014159.6	2119	gaGGAACgc/gaAGTTGTTTGAgc	15/21	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	1	TRUE	NA	0.649500853444689	2		388	914	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564069	139564069	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	175	852	0	ENST00000308874.7:c.209G>A	p.Arg70Lys	p.R70K	ENST00000308874		70	aGg/aAg	5/10	0.11467744907177	4	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.667224528165647	4		852	696	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103828	47103828	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs976581260	NA	P-0051479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	115	443	0	ENST00000409792.3:c.6118C>T	p.Arg2040Ter	p.R2040*	ENST00000409792	NM_014159.6	2040	Cga/Tga	14/21	0.620033590443227	1	FACETS	0.951	0.873	1	0.951	0.873	1	CLONAL	1	TRUE	0	0.620033590443227	1		443	269	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226432	41226432	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	215	718	0	ENST00000357654.3:c.4591G>T	p.Val1531Phe	p.V1531F	ENST00000357654	NM_007294.3	1531	Gtt/Ttt	14/23	1	2	FACETS	0.951	0.888	1	0.951	0.888	1	CLONAL	1	TRUE	1	0.620033590443227	2		718	729	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105646	11105646	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	320	564	0	ENST00000358026.2:c.1563del	p.Ile522SerfsTer91	p.I522Sfs*91	ENST00000358026	NM_001128849.1	521	cGg/cg	9/36	0.716252160834535	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.716252160834535	1		564	568	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0051481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	22	518	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	1	0.12	2		518	327	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0051481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	21	466	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	1	2	FACETS	0.959	0.738	1	0.959	0.738	1	CLONAL	1	TRUE	1	0.12	2		466	365	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0051481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	16	320	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.549	0.404	0.723	0.549	0.404	0.723	SUBCLONAL	1	TRUE	1	0.12	2		320	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782197	NA	P-0051483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	949	808	0	ENST00000269305.4:c.434T>C	p.Leu145Pro	p.L145P	ENST00000269305	NM_001126112.2	145	cTg/cCg	5/11	0.748260552201757	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.748260552201757	2		808	1219	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054514	42054514	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	146	373	0	ENST00000219905.7:c.7698G>T	p.Arg2566Ser	p.R2566S	ENST00000219905	NM_001164273.1	2566	agG/agT	22/24	0.694749514244216	2	FACETS	1	0.972	1	0.551	0.51	0.593	CLONAL	1	TRUE	0	0.748260552201757	2		373	354	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16001742	16001742	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0051483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	88	446	0	ENST00000268712.3:c.2759T>G	p.Leu920Ter	p.L920*	ENST00000268712	NM_006311.3	920	tTa/tGa	21/46	0.748260552201757	2	FACETS	0.399	0.353	0.447	0.199	0.176	0.224	SUBCLONAL	1	TRUE	0	0.748260552201757	2		446	590	SUCCESS
REL	5966	MSKCC	GRCh37	2	61121671	61121671	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	156	255	0	ENST00000295025.8:c.293G>C	p.Arg98Thr	p.R98T	ENST00000295025	NM_002908.2	98	aGa/aCa	3/11	0.43306595778607	5	FACETS	1	0.969	1			1	INDETERMINATE	2	TRUE	NA	0.748260552201757	5		255	408	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15833899	15833899	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0051483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	37	65	0	ENST00000307771.7:c.657T>A	p.Tyr219Ter	p.Y219*	ENST00000307771	NM_005089.3	219	taT/taA	8/11	0.748260552201757	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.748260552201757	1		65	49	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830751	72830751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761415382	NA	P-0051484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	429	541	0	ENST00000268489.5:c.5830G>A	p.Ala1944Thr	p.A1944T	ENST00000268489	NM_006885.3	1944	Gcc/Acc	9/10	0.919941335660773	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.919941335660773	1		541	477	SUCCESS
AR	367	MSKCC	GRCh37	X	66765876	66765876	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	667	480	0	ENST00000374690.3:c.888C>G	p.Asp296Glu	p.D296E	ENST00000374690	NM_000044.3	296	gaC/gaG	1/8	1	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.919941335660773	1		480	706	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190632	11190632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371177430	NA	P-0051484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	540	688	0	ENST00000361445.4:c.5567C>T	p.Thr1856Ile	p.T1856I	ENST00000361445	NM_004958.3	1856	aCc/aTc	39/58	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.919941335660773	2		688	1138	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375975	118375975	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	299	501	0	ENST00000534358.1:c.9368del	p.Ser3123Ter	p.S3123*	ENST00000534358	NM_005933.3	3123	tCa/ta	27/36	0.919941335660773	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.919941335660773	1		501	326	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117585	70117585	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	91	624	0	ENST00000245479.2:c.53T>A	p.Leu18Gln	p.L18Q	ENST00000245479	NM_000346.3	18	cTg/cAg	1/3	1	2	FACETS	0.206	0.182	0.232	0.206	0.182	0.232	SUBCLONAL	1	TRUE	1	0.919941335660773	2		624	959	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	93	276	0				ENST00000310581	NM_198253.2	-/1132			0.267040591681085	4	FACETS	0.935	0.843	1	0.935	0.843	1	CLONAL	3	TRUE	1	0.317908777421006	4		276	275	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578491	7578491	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1567553924	NA	P-0051486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	393	772	0	ENST00000269305.4:c.439del	p.Val147LeufsTer23	p.V147Lfs*23	ENST00000269305	NM_001126112.2	147	Gtt/tt	5/11	0.300786764157908	3	FACETS	0.988	0.942	1	0.988	0.942	1	CLONAL	3	TRUE	0	0.317908777421006	3		772	967	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3114968	3114968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	96	642	1	ENST00000078429.4:c.503C>T	p.Ala168Val	p.A168V	ENST00000078429	NM_002067.2	168	gCc/gTc	4/7	0.100070486519637	5	FACETS	1	0.917	1	0.259	0.23	0.29	INDETERMINATE	1	TRUE	1	0.317908777421006	5		643	861	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977658	2977658	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	172	607	0	ENST00000396946.4:c.1026G>T	p.Glu342Asp	p.E342D	ENST00000396946	NM_032415.4	342	gaG/gaT	8/25	0.173191175603851	5	FACETS	1	0.934	1	0.677	0.624	0.732	INDETERMINATE	2	TRUE	2	0.317908777421006	5		607	787	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249701	110249701	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	204	775	0	ENST00000374672.4:c.974T>G	p.Leu325Arg	p.L325R	ENST00000374672	NM_004235.4	325	cTg/cGg	3/5	0.173191175603851	5	FACETS	1	0.933	1	0.671	0.622	0.721	INDETERMINATE	2	TRUE	2	0.317908777421006	5		775	942	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0051487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	176	401	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.331123774608537	4	FACETS	1	0.977	1	0.794	0.752	0.834	INDETERMINATE	3	TRUE	0	0.728491685429568	4		401	263	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140449202	140449202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	43	249	0	ENST00000288602.6:c.1877G>A	p.Arg626Lys	p.R626K	ENST00000288602	NM_004333.4	626	aGa/aAa	16/18	0.728491685429568	3	FACETS	0.753	0.636	0.879	0.376	0.318	0.44	SUBCLONAL	1	TRUE	1	0.728491685429568	3		249	214	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0051488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	96	366	0				ENST00000310581	NM_198253.2	-/1132			0.616832633434446	1	FACETS	0.875	0.796	0.955	0.875	0.796	0.955	CLONAL	1	TRUE	0	0.657612615319231	1		366	224	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0051488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	606	627	3	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.43440176925073	6	FACETS	1	0.995	1			1	CLONAL	4	TRUE	NA	0.657612615319231	6		630	958	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224541	108224541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56887719	NA	P-0051488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	87	292	0	ENST00000278616.4:c.8720C>T	p.Pro2907Leu	p.P2907L	ENST00000278616	NM_000051.3	2907	cCt/cTt	60/63	0.616832633434446	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.657612615319231	1		292	174	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636465	21636465	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	105	394	0	ENST00000421138.2:c.545C>T	p.Ser182Phe	p.S182F	ENST00000421138		182	tCc/tTc	7/16	0.209554943806519	0	FACETS	0.283	0.255	0.311			1	INDETERMINATE	1	TRUE	0	0.657612615319231	0		394	387	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105240287	105240287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs551254461	NA	P-0051488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	227	850	0	ENST00000349310.3:c.664C>T	p.Arg222Cys	p.R222C	ENST00000349310	NM_001014432.1	222	Cgc/Tgc	9/15	1	2	FACETS	0.954	0.892	1	0.954	0.892	1	CLONAL	1	TRUE	1	0.657612615319231	2		850	724	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271676	15271676	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	165	1114	0	ENST00000263388.2:c.6763T>A	p.Trp2255Arg	p.W2255R	ENST00000263388	NM_000435.2	2255	Tgg/Agg	33/33	0.562217531780581	1	FACETS	0.632	0.584	0.681	0.632	0.584	0.681	SUBCLONAL	1	TRUE	0	0.657612615319231	1		1114	533	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281539	15281539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	166	671	0	ENST00000263388.2:c.4834G>A	p.Gly1612Arg	p.G1612R	ENST00000263388	NM_000435.2	1612	Gga/Aga	26/33	0.562217531780581	1	FACETS	0.702	0.65	0.755	0.702	0.65	0.755	SUBCLONAL	1	TRUE	0	0.657612615319231	1		671	483	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937694	17937694	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	50	697	0	ENST00000458235.1:c.3233G>A	p.Trp1078Ter	p.W1078*	ENST00000458235	NM_000215.3	1078	tGg/tAg	24/24	0.562217531780581	1	FACETS	0.231	0.196	0.269	0.231	0.196	0.269	SUBCLONAL	1	TRUE	0	0.657612615319231	1		697	442	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762856	40762856	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770250877	NA	P-0051488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	173	731	0	ENST00000392038.2:c.152C>T	p.Pro51Leu	p.P51L	ENST00000392038	NM_001626.4	51	cCc/cTc	3/14	1	2	FACETS	0.858	0.794	0.925	0.858	0.794	0.925	CLONAL	1	TRUE	1	0.657612615319231	2		731	613	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906810	50906810	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	224	861	0	ENST00000440232.2:c.1198A>T	p.Asn400Tyr	p.N400Y	ENST00000440232	NM_002691.3	400	Aac/Tac	10/27	1	2	FACETS	0.973	0.91	1	0.973	0.91	1	CLONAL	1	TRUE	1	0.657612615319231	2		861	700	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735501	40735501	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	148	701	1	ENST00000373198.4:c.3372G>T	p.Glu1124Asp	p.E1124D	ENST00000373198	NM_133170.3	1124	gaG/gaT	25/32	0.21266441668277	1	FACETS	0.587	0.539	0.636	0.587	0.539	0.636	INDETERMINATE	1	TRUE	0	0.657612615319231	1		702	515	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656804	45656804	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	170	688	1	ENST00000407780.3:c.352C>T	p.Gln118Ter	p.Q118*	ENST00000407780	NM_001283052.1	118	Caa/Taa	3/7	1	2	FACETS	0.898	0.83	0.967	0.898	0.83	0.967	CLONAL	1	TRUE	1	0.657612615319231	2		689	576	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177945	56177945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	116	427	1	ENST00000399503.3:c.2918C>T	p.Ser973Phe	p.S973F	ENST00000399503	NM_005921.1	973	tCt/tTt	14/20	0.616832633434446	1	FACETS	0.929	0.854	1	0.929	0.854	1	CLONAL	1	TRUE	0	0.657612615319231	1		428	255	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502190	157502190	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs387907144	NA	P-0051488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	165	537	0	ENST00000346085.5:c.3223C>T	p.Arg1075Ter	p.R1075*	ENST00000346085	NM_020732.3	1075	Cga/Tga	12/20	0.616832633434446	1	FACETS	0.994	0.928	1	0.994	0.928	1	CLONAL	1	TRUE	0	0.657612615319231	1		537	339	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339968	116339968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	81	371	0	ENST00000397752.3:c.830G>A	p.Arg277Lys	p.R277K	ENST00000397752	NM_000245.2	277	aGa/aAa	2/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.657612615319231	2		371	228	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971143	21971144	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0051488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	209	460	0	ENST00000304494.5:c.214dup	p.Cys72LeufsTer48	p.C72Lfs*48	ENST00000304494	NM_000077.4	72	tgc/tTgc	2/3	0.657612615319231	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.657612615319231	1		460	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0051491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	114	430	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.362688026412636	2	FACETS	0.961	0.882	1	0.961	0.882	1	CLONAL	2	TRUE	0	0.470898310852812	2		430	252	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980402	55980402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1357848255	NA	P-0051491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	35	304	0	ENST00000263923.4:c.689C>T	p.Pro230Leu	p.P230L	ENST00000263923	NM_002253.2	230	cCg/cTg	6/30	0.381333127919485	3	FACETS	1	0.953	1	0.741	0.62	0.87	CLONAL	1	TRUE	1	0.470898310852812	3		304	124	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953634	38953634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146765449	NA	P-0051491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	28	204	0	ENST00000357387.3:c.2719C>T	p.Arg907Cys	p.R907C	ENST00000357387	NM_152756.3	907	Cgt/Tgt	28/38	0.205617791934187	5	FACETS	0.846	0.688	1	0.564	0.459	0.679	INDETERMINATE	2	TRUE	2	0.470898310852812	5		204	120	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273066	18273066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	336	804	2	ENST00000222254.8:c.956G>A	p.Gly319Glu	p.G319E	ENST00000222254	NM_005027.3	319	gGa/gAa	8/16	0.470898310852812	5	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	2	0.470898310852812	5		806	742	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641409	23641409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749602688	NA	P-0051491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	51	701	0	ENST00000261584.4:c.2066C>T	p.Ser689Leu	p.S689L	ENST00000261584	NM_024675.3	689	tCg/tTg	5/13	0.38705492586635	3	FACETS	1	0.893	1	0.35	0.3	0.404	CLONAL	1	TRUE	0	0.470898310852812	3		701	255	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245092	41245092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	42	667	1	ENST00000357654.3:c.2456C>T	p.Ser819Phe	p.S819F	ENST00000357654	NM_007294.3	819	tCc/tTc	10/23	0.336365391446386	4	FACETS	0.869	0.729	1	0.434	0.364	0.512	CLONAL	1	TRUE	2	0.470898310852812	4		668	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0051494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	309	349	0	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	1	2	FACETS	0.913	0.865	0.961	0.913	0.865	0.961	CLONAL	1	TRUE	1	0.856040324396634	2		349	791	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476815	140476815	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	213	278	0	ENST00000288602.6:c.1591T>C	p.Trp531Arg	p.W531R	ENST00000288602	NM_004333.4	531	Tgg/Cgg	13/18	0.809567285686393	3	FACETS	0.946	0.882	1	0.473	0.441	0.506	CLONAL	1	TRUE	1	0.856040324396634	3		278	751	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981260	201981261	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0051494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	392	389	0	ENST00000359651.3:c.341_342dup	p.Gly115LeufsTer41	p.G115Lfs*41	ENST00000359651		113	-/TT	2/8	1	2	FACETS	0.92	0.877	0.963	0.92	0.877	0.963	CLONAL	1	TRUE	1	0.856040324396634	2		389	996	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577136	7577137	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCGTC	novel	NA	P-0051494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	294	350	0	ENST00000269305.4:c.797_801dup	p.Asn268AspfsTer79	p.N268Dfs*79	ENST00000269305	NM_001126112.2	267	-/GACGG	8/11	1	2	FACETS	0.903	0.854	0.952	0.903	0.854	0.952	CLONAL	1	TRUE	1	0.856040324396634	2		350	761	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266086	41266249	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAG	AGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAG	-	novel	NA	P-0051494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	68	195	0	ENST00000349496.5:c.86_241+8del		p.X29_splice	ENST00000349496	NM_001904.3	29		3/15	1	2	FACETS	0.516	0.452	0.583	0.516	0.452	0.583	SUBCLONAL	1	TRUE	1	0.856040324396634	2		195	308	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278090	41278092	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	novel	NA	P-0051494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	187	208	2	ENST00000349496.5:c.1970_1972del	p.Ala657del	p.A657del	ENST00000349496	NM_001904.3	656	GCT/-	13/15	1	2	FACETS	0.918	0.856	0.98	0.918	0.856	0.98	CLONAL	1	TRUE	1	0.856040324396634	2		210	476	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	28	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.154622794320398	1	FACETS	0.628	0.502	0.771	0.628	0.502	0.771	SUBCLONAL	1	TRUE	0	0.22	1		334	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0051495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	71	912	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.3	1	FACETS	0.707	0.616	0.805	0.707	0.616	0.805	SUBCLONAL	1	TRUE	0	0.22	1		914	813	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030426	49030426	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0051495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	77	186	0	ENST00000267163.4:c.1901C>G	p.Ser634Ter	p.S634*	ENST00000267163	NM_000321.2	634	tCa/tGa	19/27	1	2	FACETS	0.843	0.744	0.949	1	0.98	1	CLONAL	2	TRUE	1	0.22	2		186	415	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604701	48604701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555687572	NA	P-0051495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	31	256	0	ENST00000342988.3:c.1523G>A	p.Gly508Asp	p.G508D	ENST00000342988	NM_005359.5	508	gGc/gAc	12/12	0.112714075963081	0	FACETS	0.424	0.342	0.517			1	INDETERMINATE	1	TRUE	0	0.22	0		256	518	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784089	120784089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265704785	NA	P-0051495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	109	493	0	ENST00000257552.2:c.896C>T	p.Ser299Leu	p.S299L	ENST00000257552	NM_002442.3	299	tCg/tTg	13/15	0.154622794320398	1	FACETS	0.846	0.758	0.94	0.846	0.758	0.94	CLONAL	1	TRUE	0	0.22	1		493	1042	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0051496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	57	567	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.16	2		567	636	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0051496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	8	507	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.606	0.39	0.885	0.606	0.39	0.885	SUBCLONAL	1	TRUE	1	0.16	2		507	165	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	176	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.973	1	1	0.995	1	CLONAL	3	TRUE	1	0.261004345119669	2		276	414	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0051506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	298	378	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	1	0.985	1	1	0.997	1	CLONAL	3	TRUE	1	0.261004345119669	2		378	694	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913233	NA	P-0051506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	599	718	1	ENST00000451590.1:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000451590	NM_001130442.1	61	cAg/cTg	3/5	1	2	FACETS	1	0.993	1	1	0.998	1	CLONAL	3	TRUE	1	0.261004345119669	2		719	1375	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467780	50467780	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760454379	NA	P-0051506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	71	601	1	ENST00000331340.3:c.1015G>A	p.Glu339Lys	p.E339K	ENST00000331340	NM_006060.4	339	Gag/Aag	8/8	1	2	FACETS	0.51	0.444	0.583	0.51	0.444	0.583	SUBCLONAL	1	TRUE	1	0.261004345119669	2		602	1066	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856356	45856356	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1328	97	790	0	ENST00000391945.4:c.1816G>C	p.Glu606Gln	p.E606Q	ENST00000391945	NM_000400.3	606	Gag/Cag	19/23	1	2	FACETS	0.522	0.463	0.584	0.522	0.463	0.584	SUBCLONAL	1	TRUE	1	0.261004345119669	2		790	1425	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184592	11184592	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs774204282	NA	P-0051506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	416	562	0	ENST00000361445.4:c.6625C>G	p.Leu2209Val	p.L2209V	ENST00000361445	NM_004958.3	2209	Ctg/Gtg	47/58	1	2	FACETS	1	0.97	1	1	0.997	1	CLONAL	3	TRUE	1	0.261004345119669	2		562	1042	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099954	27099954	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	100	731	1	ENST00000324856.7:c.3833A>T	p.His1278Leu	p.H1278L	ENST00000324856	NM_006015.4	1278	cAc/cTc	15/20	1	2	FACETS	0.611	0.544	0.683	0.611	0.544	0.683	SUBCLONAL	1	TRUE	1	0.261004345119669	2		732	1254	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670760	134670760	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	421	541	0	ENST00000398015.3:c.671C>G	p.Thr224Arg	p.T224R	ENST00000398015	NM_004441.4	224	aCa/aGa	3/16	1	2	FACETS	1	0.983	1	1	0.997	1	CLONAL	3	TRUE	1	0.261004345119669	2		541	1020	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0051507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	635	614	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.633213792483711	2	FACETS	0.976	0.947	1	0.976	0.947	1	CLONAL	2	TRUE	0	0.635477026438513	2		614	1024	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098815	178098815	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	560	580	0	ENST00000397062.3:c.230A>T	p.Asp77Val	p.D77V	ENST00000397062	NM_006164.4	77	gAt/gTt	2/5	NA	2	FACETS	0.781	0.753	0.809			1	INDETERMINATE	2	TRUE	NA	0.635477026438513	2		580	1128	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955391	48955391	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	84	244	0	ENST00000267163.4:c.1507del	p.Ser503LeufsTer16	p.S503Lfs*16	ENST00000267163	NM_000321.2	503	Tct/ct	17/27	0.635477026438513	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.635477026438513	1		244	150	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3929872	3929872	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	68	439	0	ENST00000262367.5:c.46A>G	p.Lys16Glu	p.K16E	ENST00000262367	NM_004380.2	16	Aaa/Gaa	1/31	0.635477026438513	1	FACETS	0.302	0.263	0.344	0.302	0.263	0.344	SUBCLONAL	1	TRUE	0	0.635477026438513	1		439	483	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537227	41537227	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0051507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	61	392	0	ENST00000263253.7:c.2053+1G>C		p.X685_splice	ENST00000263253	NM_001429.3	685			0.553074157770063	1	FACETS	0.268	0.231	0.308	0.268	0.231	0.308	SUBCLONAL	1	TRUE	0	0.635477026438513	1		392	489	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0051508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	43	390	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.833	0.698	0.981	0.833	0.698	0.981	CLONAL	1	TRUE	1	0.268214351910588	2		390	385	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466432	120466432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194257253	NA	P-0051508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	111	598	0	ENST00000256646.2:c.4687C>T	p.Arg1563Cys	p.R1563C	ENST00000256646	NM_024408.3	1563	Cgc/Tgc	26/34	0.268214351910588	2	FACETS	1	0.911	1	0.507	0.456	0.562	CLONAL	1	TRUE	0	0.268214351910588	2		598	816	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845152	128845152	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	125	754	0	ENST00000249373.3:c.646C>T	p.Gln216Ter	p.Q216*	ENST00000249373	NM_005631.4	216	Cag/Tag	3/12	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.268214351910588	2		754	892	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981225	201981225	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	378	867	0	ENST00000359651.3:c.304C>G	p.Leu102Val	p.L102V	ENST00000359651		102	Ctc/Gtc	2/8	0.268214351910588	5	FACETS	0.961	0.912	1	0.961	0.912	1	CLONAL	3	TRUE	2	0.268214351910588	5		867	1371	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727399	66727399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	44	469	1	ENST00000307102.5:c.115G>A	p.Glu39Lys	p.E39K	ENST00000307102	NM_002755.3	39	Gag/Aag	2/11	0.237357139798288	3	FACETS	0.525	0.439	0.62	0.262	0.219	0.31	SUBCLONAL	1	TRUE	1	0.268214351910588	3		470	709	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219344	1219344	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	222	672	0	ENST00000326873.7:c.396C>G	p.Cys132Trp	p.C132W	ENST00000326873	NM_000455.4	132	tgC/tgG	3/10	0.22152797404298	2	FACETS	0.852	0.793	0.912	0.852	0.793	0.912	CLONAL	2	TRUE	0	0.268214351910588	2		672	972	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911449	134911449	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	38	523	0	ENST00000398015.3:c.1914G>C	p.Leu638Phe	p.L638F	ENST00000398015	NM_004441.4	638	ttG/ttC	11/16	1	2	FACETS	0.484	0.399	0.578	0.484	0.399	0.578	SUBCLONAL	1	TRUE	1	0.268214351910588	2		523	586	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138409911	138409911	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	58	432	0	ENST00000289153.2:c.1967T>C	p.Leu656Pro	p.L656P	ENST00000289153	NM_006219.2	656	cTc/cCc	13/22	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.268214351910588	2		432	428	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158364	106158364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	30	330	0	ENST00000380013.4:c.3265G>A	p.Glu1089Lys	p.E1089K	ENST00000380013	NM_001127208.2	1089	Gaa/Aaa	3/11	1	2	FACETS	0.68	0.549	0.828	0.68	0.549	0.828	SUBCLONAL	1	TRUE	1	0.268214351910588	2		330	329	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851351	151851351	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0051508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	55	421	0	ENST00000262189.6:c.12139+1G>A		p.X4047_splice	ENST00000262189	NM_170606.2	4047			1	2	FACETS	0.856	0.733	0.99	0.856	0.733	0.99	CLONAL	1	TRUE	1	0.268214351910588	2		421	479	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864419	151864419	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	48	362	0	ENST00000262189.6:c.9562C>T	p.Gln3188Ter	p.Q3188*	ENST00000262189	NM_170606.2	3188	Caa/Taa	42/59	1	2	FACETS	0.749	0.633	0.876	0.749	0.633	0.876	SUBCLONAL	1	TRUE	1	0.268214351910588	2		362	478	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0051509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	19	366	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.748	0.579	0.937	0.748	0.579	0.937	CLONAL	1	TRUE	1	0.57766762392941	2		366	88	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0051509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	79	525	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.533795408802276	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.57766762392941	2		525	127	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432409	49432412	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	novel	NA	P-0051509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	86	907	0	ENST00000301067.7:c.8727_8730del	p.Ser2910ArgfsTer32	p.S2910Rfs*32	ENST00000301067	NM_003482.3	2909	gtAAGT/gt	34/54	0.57766762392941	6	FACETS	1	0.976	1	0.351	0.312	0.393	CLONAL	1	TRUE	2	0.57766762392941	6		907	457	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151947968	151947968	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	56	526	1	ENST00000262189.6:c.1705C>T	p.Gln569Ter	p.Q569*	ENST00000262189	NM_170606.2	569	Cag/Tag	12/59	0.295210662565121	6	FACETS	0.937	0.813	1	0.468	0.406	0.535	INDETERMINATE	2	TRUE	2	0.57766762392941	6		527	223	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199501	16199501	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	70	430	0	ENST00000375759.3:c.274G>C	p.Asp92His	p.D92H	ENST00000375759	NM_015001.2	92	Gat/Cat	2/15	0.57766762392941	5	FACETS	1	0.955	1	0.577	0.513	0.644	CLONAL	2	TRUE	1	0.57766762392941	5		430	196	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154769	2154769	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1457247306	NA	P-0051509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	52	986	0	ENST00000434045.2:c.452C>T	p.Ser151Leu	p.S151L	ENST00000434045	NM_001127598.1	151	tCg/tTg	4/5	0.241775449609395	3	FACETS	1	0.964	1	0.686	0.595	0.782	INDETERMINATE	1	TRUE	1	0.57766762392941	3		986	169	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431850	49431850	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	162	873	0	ENST00000301067.7:c.9289G>T	p.Glu3097Ter	p.E3097*	ENST00000301067	NM_003482.3	3097	Gag/Tag	34/54	0.57766762392941	6	FACETS	1	0.974	1	0.823	0.766	0.881	CLONAL	3	TRUE	2	0.57766762392941	6		873	367	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433575	49433575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	230	1080	0	ENST00000301067.7:c.7978G>A	p.Glu2660Lys	p.E2660K	ENST00000301067	NM_003482.3	2660	Gaa/Aaa	31/54	0.57766762392941	6	FACETS	0.925	0.873	0.976	0.925	0.873	0.976	CLONAL	4	TRUE	2	0.57766762392941	6		1080	464	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788600	3788600	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	177	492	0	ENST00000262367.5:c.4354G>T	p.Glu1452Ter	p.E1452*	ENST00000262367	NM_004380.2	1452	Gag/Tag	26/31	0.520266259568256	4	FACETS	0.991	0.943	1	0.991	0.943	1	CLONAL	4	TRUE	0	0.57766762392941	4		492	244	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845343	151845345	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0051509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	73	653	0	ENST00000262189.6:c.13667_13669del	p.His4556_Thr4557delinsPro	p.H4556_T4557delinsP	ENST00000262189	NM_170606.2	4556	cACAca/cca	52/59	0.295210662565121	6	FACETS	0.922	0.822	1	0.691	0.616	0.768	INDETERMINATE	3	TRUE	2	0.57766762392941	6		653	197	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196806	123196806	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	130	264	0	ENST00000218089.9:c.1693G>T	p.Glu565Ter	p.E565*	ENST00000218089	NM_001042749.1	565	Gag/Tag	18/35	0.57766762392941	2	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.57766762392941	2		264	188	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0051510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	87	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.351337423739071	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.351337423739071	1		436	391	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342425	70342425	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	140	630	0	ENST00000374080.3:c.1316G>A	p.Trp439Ter	p.W439*	ENST00000374080		439	tGg/tAg	9/45	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.351337423739071	2		630	736	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0051552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	49	380	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.242291805126184	0	FACETS	0.847	0.723	0.981			1	CLONAL	1	TRUE	0	0.3	0		380	270	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	126	799	0	ENST00000269305.4:c.398T>G	p.Met133Arg	p.M133R	ENST00000269305	NM_001126112.2	133	aTg/aGg	5/11	1	2	FACETS	0.946	0.856	1	0.946	0.856	1	CLONAL	1	TRUE	1	0.3	2		799	888	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549515	187549515	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs577375480	NA	P-0051552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	95	440	0	ENST00000441802.2:c.4603C>T	p.Arg1535Ter	p.R1535*	ENST00000441802	NM_005245.3	1535	Cga/Tga	9/27	0.141693232019707	3	FACETS	0.756	0.676	0.84	0.756	0.676	0.84	INDETERMINATE	2	TRUE	1	0.3	3		440	482	SUCCESS
APC	324	MSKCC	GRCh37	5	112162945	112162945	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs1114167599	NA	P-0051552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	34	344	0	ENST00000257430.4:c.1548+1G>C		p.X516_splice	ENST00000257430	NM_000038.5	516			1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.3	2		344	157	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0051553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	37	457	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	1	2	FACETS	0.913	0.751	1	0.913	0.751	1	CLONAL	1	TRUE	1	0.14	2		457	579	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859199	151859200	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	novel	NA	P-0051553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	26	341	0	ENST00000262189.6:c.11460+2dup		p.X3820_splice	ENST00000262189	NM_170606.2	3820			1	2	FACETS	1	0.821	1	1	0.821	1	CLONAL	1	TRUE	1	0.14	2		341	357	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938417	44938418	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0051553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	28	201	0	ENST00000377967.4:c.2965_2966insG	p.Leu989CysfsTer5	p.L989Cfs*5	ENST00000377967	NM_021140.2	989	ttg/tGtg	20/29	0.3	2	FACETS	0.901	0.724	1	0.901	0.724	1	CLONAL	2	TRUE	0	0.14	2		201	222	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396699	30396699	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs572057574	NA	P-0051554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	14	0	0	ENST00000331968.5:c.20T>C	p.Leu7Pro	p.L7P	ENST00000331968	NM_002742.2	7	cTg/cCg	1/18	1	2	FACETS	0.847	0.665	1	1	0.923	1	CLONAL	2	TRUE	1	0.636061535643769	2		0	26	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46736337	46736381	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CCCATGAATTCAAGAAGCATTTTGAATTGCCAATTTTGAAGGGTC	CCCATGAATTCAAGAAGCATTTTGAATTGCCAATTTTGAAGGGTC	TGTTTAGGGACTGTGTTTA	novel	NA	P-0051554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	41	436	0	ENST00000371975.4:c.1049_1093delinsTGTTTAGGGACTGTGTTTA	p.Ala350ValfsTer7	p.A350Vfs*7	ENST00000371975	NM_003579.3	350	gCCCATGAATTCAAGAAGCATTTTGAATTGCCAATTTTGAAGGGTCga/gTGTTTAGGGACTGTGTTTAga	10/18	0.368275458945382	4	FACETS	0.79	0.662	0.93	0.395	0.331	0.465	INDETERMINATE	1	TRUE	2	0.636061535643769	4		436	267	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0051555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	20	270	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.562	0.43	0.717	0.562	0.43	0.717	SUBCLONAL	1	TRUE	1	0.244399210056781	2		270	291	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696644	47696644	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519964	NA	P-0051555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	57	481	0	ENST00000347630.2:c.304T>G	p.Phe102Val	p.F102V	ENST00000347630	NM_001007230.1	102	Ttc/Gtc	5/11	1	2	FACETS	0.856	0.735	0.988	0.856	0.735	0.988	CLONAL	1	TRUE	1	0.244399210056781	2		481	545	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0051557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	21	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.167438379352646	2		436	196	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900873	3900873	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	31	617	0	ENST00000262367.5:c.223C>T	p.Arg75Ter	p.R75*	ENST00000262367	NM_004380.2	75	Cga/Tga	2/31	1	2	FACETS	0.781	0.635	0.944	1	0.946	1	CLONAL	2	TRUE	1	0.167438379352646	2		617	237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0051557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	43	436	0	ENST00000269305.4:c.375+1G>C		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.167438379352646	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	2	TRUE	0	0.167438379352646	2		436	224	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602359	28602359	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	15	509	0	ENST00000241453.7:c.2009G>A	p.Ser670Asn	p.S670N	ENST00000241453	NM_004119.2	670	aGc/aAc	16/24	1	2	FACETS	0.737	0.539	0.975	0.737	0.539	0.975	CLONAL	1	TRUE	1	0.167438379352646	2		509	243	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	54	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.24702658094256	3	FACETS	0.798	0.681	0.925	0.399	0.34	0.463	CLONAL	1	TRUE	1	0.258767240862717	3		334	591	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508737	148508737	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	70	434	0	ENST00000320356.2:c.1927A>G	p.Ile643Val	p.I643V	ENST00000320356	NM_004456.4	643	Atc/Gtc	16/20	0.258767240862717	1	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	0	0.258767240862717	1		434	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577572	7577572	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882004	NA	P-0051570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	21	527	0	ENST00000269305.4:c.709A>G	p.Met237Val	p.M237V	ENST00000269305	NM_001126112.2	237	Atg/Gtg	7/11	1	2	FACETS	0.213	0.163	0.272	0.213	0.163	0.272	SUBCLONAL	1	TRUE	1	0.258767240862717	2		527	763	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932556	39932557	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0051570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	139	337	0	ENST00000378444.4:c.2042dup	p.His682SerfsTer58	p.H682Sfs*58	ENST00000378444	NM_001123385.1	681	cct/ccCt	4/15	1	1	FACETS	1	0.924	1	1	0.991	1	CLONAL	2	TRUE	0	0.258767240862717	1		337	464	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	45	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.842	0.708	0.99	0.842	0.708	0.99	CLONAL	1	TRUE	1	0.22	2		276	486	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0051573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	100	355	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.22	2		355	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0051573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	148	600	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.22	2		600	1046	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732911	30732911	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0051573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	49	262	0	ENST00000295754.5:c.1525-1G>T		p.X509_splice	ENST00000295754	NM_003242.5	509			1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.22	2		262	366	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520152	9520152	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	69	448	0	ENST00000353224.5:c.2117C>A	p.Pro706Gln	p.P706Q	ENST00000353224	NM_177990.2	706	cCg/cAg	10/10	1	2	FACETS	0.849	0.738	0.968	0.849	0.738	0.968	CLONAL	1	TRUE	1	0.22	2		448	739	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044988	47044988	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	126	296	0	ENST00000377604.3:c.2314G>T	p.Glu772Ter	p.E772*	ENST00000377604	NM_001204468.1	772	Gag/Tag	20/24	1	1	FACETS	0.934	0.849	1	1	0.989	1	CLONAL	2	TRUE	0	0.22	1		296	546	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469994	157469994	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1002364077	NA	P-0051573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	36	524	0	ENST00000346085.5:c.2788G>T	p.Gly930Ter	p.G930*	ENST00000346085	NM_020732.3	930	Gga/Tga	9/20	1	2	FACETS	0.464	0.38	0.558	0.464	0.38	0.558	SUBCLONAL	1	TRUE	1	0.22	2		524	706	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342996	70342996	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	103	289	0	ENST00000374080.3:c.1537A>G	p.Ser513Gly	p.S513G	ENST00000374080		513	Agc/Ggc	11/45	1	1	FACETS	0.789	0.709	0.874	1	0.984	1	SUBCLONAL	2	TRUE	0	0.22	1		289	528	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5225803	5225803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	70	622	0	ENST00000357368.4:c.2429C>T	p.Ala810Val	p.A810V	ENST00000357368	NM_002850.3	810	gCc/gTc	17/38	1	2	FACETS	0.769	0.67	0.878	0.769	0.67	0.878	SUBCLONAL	1	TRUE	1	0.22	2		622	827	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539018	187539018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374444088	NA	P-0051576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	88	460	0	ENST00000441802.2:c.8722G>A	p.Val2908Ile	p.V2908I	ENST00000441802	NM_005245.3	2908	Gtc/Atc	10/27	NA	2	FACETS	0.856	0.76	0.958			1	INDETERMINATE	1	TRUE	NA	0.355186342121489	2		460	579	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs80338963	NA	P-0051576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	183	397	0	ENST00000342988.3:c.1081C>G	p.Arg361Gly	p.R361G	ENST00000342988	NM_005359.5	361	Cgc/Ggc	9/12	0.355186342121489	2	FACETS	0.997	0.927	1	0.997	0.927	1	CLONAL	2	TRUE	0	0.355186342121489	2		397	517	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43783886	43783886	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	92	568	0	ENST00000382044.4:c.352C>T	p.Gln118Ter	p.Q118*	ENST00000382044	NM_001141980.1	118	Cag/Tag	4/28	0.342113228192206	3	FACETS	0.806	0.716	0.902	0.403	0.358	0.451	CLONAL	1	TRUE	1	0.355186342121489	3		568	757	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37876048	37876109	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCTGGATGACAAGGGCTGCCCCGCCGAGCAGAGAGCCAGGTTGGCCTGGACCCCAGGATGT	ACCTGGATGACAAGGGCTGCCCCGCCGAGCAGAGAGCCAGGTTGGCCTGGACCCCAGGATGT	-	novel	NA	P-0051576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	97	560	1	ENST00000269571.5:c.1910_1946+25del		p.X637_splice	ENST00000269571		637		16/27	0.355186342121489	6	FACETS	0.827	0.735	0.925			1	CLONAL	1	TRUE	NA	0.355186342121489	6		561	1130	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27192485	27192485	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0051576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	72	368	0	ENST00000380036.4:c.1490-2A>G		p.X497_splice	ENST00000380036	NM_000459.3	497			0.355186342121489	2	FACETS	0.843	0.738	0.955	0.421	0.369	0.478	CLONAL	1	TRUE	0	0.355186342121489	2		368	481	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	143	276	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.781293736057471	NA		276	346	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59934505	59934508	+	frameshift_variant	Frame_Shift_Del	DEL	TTGT	TTGT	-	rs763009188	NA	P-0051579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	161	452	0	ENST00000259008.2:c.290_293del	p.Asn97MetfsTer3	p.N97Mfs*3	ENST00000259008	NM_032043.2	97	aACAAt/at	4/20	1	2	FACETS	0.963	0.893	1	0.963	0.893	1	CLONAL	1	TRUE	1	0.781293736057471	2		452	428	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696432	47696432	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519968	NA	P-0051586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	84	525	0	ENST00000347630.2:c.391T>G	p.Trp131Gly	p.W131G	ENST00000347630	NM_001007230.1	131	Tgg/Ggg	6/11	1	2	FACETS	0.488	0.43	0.549	0.488	0.43	0.549	SUBCLONAL	1	TRUE	1	0.49	2		525	703	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72863738	72863738	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	100	576	0	ENST00000268489.5:c.3469G>T	p.Glu1157Ter	p.E1157*	ENST00000268489	NM_006885.3	1157	Gaa/Taa	5/10	1	2	FACETS	0.568	0.507	0.632	0.568	0.507	0.632	SUBCLONAL	1	TRUE	1	0.49	2		576	719	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	71	424	0	ENST00000347630.2:c.305T>C	p.Phe102Ser	p.F102S	ENST00000347630	NM_001007230.1	102	tTc/tCc	5/11	1	2	FACETS	0.788	0.688	0.897	0.788	0.688	0.897	SUBCLONAL	1	FALSE	1	0.270049474947611	2		424	667	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137320989	137320989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	74	637	2	ENST00000481739.1:c.946C>T	p.Arg316Cys	p.R316C	ENST00000481739	NM_002957.4	316	Cgc/Tgc	7/10	1	2	FACETS	0.656	0.573	0.745	0.656	0.573	0.745	SUBCLONAL	1	FALSE	1	0.270049474947611	2		639	836	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	85	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.985	0.878	1	0.985	0.878	1	CLONAL	1	TRUE	1	0.518461028838723	2		334	333	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0051588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	78	390	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.896	0.793	1	0.896	0.793	1	CLONAL	1	TRUE	1	0.518461028838723	2		390	336	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998544	100998544	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs775749546	NA	P-0051588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	131	355	0	ENST00000325455.5:c.1258G>C	p.Gly420Arg	p.G420R	ENST00000325455	NM_001202474.3	420	Ggg/Cgg	1/8	1	2	FACETS	0.64	0.581	0.702	0.64	0.581	0.702	SUBCLONAL	1	TRUE	1	0.518461028838723	2		355	790	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0051588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	245	643	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.518461028838723	2		643	909	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118859	70118859	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0051588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	379	414	0	ENST00000245479.2:c.432-1G>A		p.X144_splice	ENST00000245479	NM_000346.3	144			0.501860347808115	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.518461028838723	2		414	686	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150030	202150030	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs931648756	NA	P-0051588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	67	480	0	ENST00000358485.4:c.1471C>T	p.Arg491Ter	p.R491*	ENST00000358485	NM_001080125.1	491	Cga/Tga	8/9	1	2	FACETS	0.267	0.231	0.306	0.267	0.231	0.306	SUBCLONAL	1	TRUE	1	0.518461028838723	2		480	967	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713544	30713546	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0051588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	165	497	0	ENST00000295754.5:c.871_873del	p.Lys291del	p.K291del	ENST00000295754	NM_003242.5	290	gAGAag/gag	4/7	1	2	FACETS	0.957	0.882	1	0.957	0.882	1	CLONAL	1	TRUE	1	0.518461028838723	2		497	665	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	110	540	2	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	1	2	FACETS	0.847	0.765	0.933	0.847	0.765	0.933	CLONAL	1	TRUE	1	0.518461028838723	2		542	501	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247367	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	95	308	0	ENST00000281708.4:c.1435C>T	p.Arg479Ter	p.R479*	ENST00000281708	NM_033632.3	479	Cga/Tga	10/12	1	2	FACETS	0.8	0.716	0.889	0.8	0.716	0.889	SUBCLONAL	1	TRUE	1	0.518461028838723	2		308	458	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0051588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	106	341	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	1	2	FACETS	0.877	0.791	0.968	0.877	0.791	0.968	CLONAL	1	TRUE	1	0.518461028838723	2		341	466	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047710	180047710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144822344	NA	P-0051588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	232	511	0	ENST00000261937.6:c.2305G>A	p.Glu769Lys	p.E769K	ENST00000261937	NM_182925.4	769	Gag/Aag	16/30	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.518461028838723	2		511	876	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225112	53225112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	249	254	0	ENST00000375401.3:c.3106G>A	p.Val1036Ile	p.V1036I	ENST00000375401	NM_004187.3	1036	Gtt/Att	20/26	1	1	FACETS	0.799	0.759	0.839	1	0.995	1	SUBCLONAL	2	TRUE	0	0.518461028838723	1		254	445	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0051592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	174	401	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		401	470	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220707	1220707	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	179	338	0	ENST00000326873.7:c.725G>T	p.Gly242Val	p.G242V	ENST00000326873	NM_000455.4	242	gGg/gTg	5/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		338	372	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351481	89351481	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	203	477	0	ENST00000301030.4:c.1469A>T	p.Glu490Val	p.E490V	ENST00000301030	NM_001256183.1	490	gAg/gTg	9/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		477	654	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214708	5214708	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	214	476	0	ENST00000357368.4:c.4358A>C	p.Asp1453Ala	p.D1453A	ENST00000357368	NM_002850.3	1453	gAc/gCc	29/38	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		476	431	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0051593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	34	449	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	0.495	0.403	0.598	0.495	0.403	0.598	SUBCLONAL	1	TRUE	1	0.263318416481721	2		449	522	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572597	141572597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376660302	NA	P-0051593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	150	571	0	ENST00000220592.5:c.473C>T	p.Thr158Met	p.T158M	ENST00000220592	NM_012154.3	158	aCg/aTg	4/19	0.15266111150767	3	FACETS	1	0.978	1	0.611	0.557	0.667	INDETERMINATE	1	TRUE	1	0.263318416481721	3		571	1055	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726574	46726574	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145410495	NA	P-0051593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	73	478	0	ENST00000371975.4:c.653C>T	p.Ser218Leu	p.S218L	ENST00000371975	NM_003579.3	218	tCg/tTg	7/18	1	2	FACETS	0.614	0.536	0.699	0.614	0.536	0.699	SUBCLONAL	1	TRUE	1	0.263318416481721	2		478	903	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991700	72991711	+	inframe_deletion	In_Frame_Del	DEL	GCCGCCGCCGCA	GCCGCCGCCGCA	-	novel	NA	P-0051593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	66	538	0	ENST00000268489.5:c.2334_2345del	p.Ala781_Ala784del	p.A781_A784del	ENST00000268489	NM_006885.3	778	gcTGCGGCGGCGGCg/gcg	2/10	1	2	FACETS	0.958	0.833	1	0.958	0.833	1	CLONAL	1	TRUE	1	0.263318416481721	2		538	523	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50481245	50481287	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTAGAAGGACGGCTCCTGGAGGATGTGAGTTCAAGGTCCACAA	GTAGAAGGACGGCTCCTGGAGGATGTGAGTTCAAGGTCCACAA	-	novel	NA	P-0051593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	45	418	0	ENST00000394963.4:c.631_654+19del		p.X211_splice	ENST00000394963	NM_003076.4	211		5/13	1	2	FACETS	0.411	0.344	0.486	0.411	0.344	0.486	SUBCLONAL	1	TRUE	1	0.263318416481721	2		418	831	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916841	48916841	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1271889879	NA	P-0051593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	30	399	0	ENST00000267163.4:c.371T>C	p.Ile124Thr	p.I124T	ENST00000267163	NM_000321.2	124	aTa/aCa	3/27	1	2	FACETS	0.519	0.418	0.634	0.519	0.418	0.634	SUBCLONAL	1	TRUE	1	0.263318416481721	2		399	439	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356369	66356369	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	38	447	1	ENST00000273854.3:c.1128A>T	p.Glu376Asp	p.E376D	ENST00000273854	NM_004439.5	376	gaA/gaT	5/18	1	2	FACETS	0.395	0.325	0.473	0.395	0.325	0.473	SUBCLONAL	1	TRUE	1	0.263318416481721	2		448	731	SUCCESS
APC	324	MSKCC	GRCh37	5	112175629	112175629	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	50	345	0	ENST00000257430.4:c.4338del	p.Gln1447LysfsTer26	p.Q1447Kfs*26	ENST00000257430	NM_000038.5	1446	gcT/gc	16/16	1	2	FACETS	0.624	0.528	0.728	0.624	0.528	0.728	SUBCLONAL	1	TRUE	1	0.263318416481721	2		345	609	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0051599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	43	322	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.857	0.717	1	0.857	0.717	1	CLONAL	1	TRUE	1	0.2	2		322	502	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266112	41266112	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913228	NA	P-0051599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	51	383	0	ENST00000349496.5:c.109T>G	p.Ser37Ala	p.S37A	ENST00000349496	NM_001904.3	37	Tct/Gct	3/15	1	2	FACETS	0.946	0.804	1	0.946	0.804	1	CLONAL	1	TRUE	1	0.2	2		383	539	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281176	15281176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	78	664	1	ENST00000263388.2:c.5080C>T	p.Arg1694Trp	p.R1694W	ENST00000263388	NM_000435.2	1694	Cgg/Tgg	27/33	1	2	FACETS	0.885	0.776	1	0.885	0.776	1	CLONAL	1	TRUE	1	0.2	2		665	881	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260713	16260713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1390995788	NA	P-0051599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	85	584	1	ENST00000375759.3:c.7978G>A	p.Val2660Ile	p.V2660I	ENST00000375759	NM_015001.2	2660	Gtc/Atc	11/15	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.2	2		585	784	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71947009	71947009	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	69	692	1	ENST00000298229.2:c.2860del	p.Glu954ArgfsTer4	p.E954Rfs*4	ENST00000298229	NM_001567.3	953	cGg/cg	25/28	1	2	FACETS	0.958	0.834	1	0.958	0.834	1	CLONAL	1	TRUE	1	0.2	2		693	720	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196137	108196137	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	25	445	0	ENST00000278616.4:c.6673G>C	p.Ala2225Pro	p.A2225P	ENST00000278616	NM_000051.3	2225	Gct/Cct	46/63	1	2	FACETS	0.386	0.303	0.48	0.386	0.303	0.48	SUBCLONAL	1	TRUE	1	0.33	2		445	393	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0051601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	216	569	1	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	1	2	FACETS	0.931	0.869	0.993	0.931	0.869	0.993	CLONAL	1	TRUE	1	0.683668118690407	2		570	679	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	53	276	0				ENST00000310581	NM_198253.2	-/1132			0.241331145728554	4	FACETS	1	0.969	1	0.75	0.649	0.856	INDETERMINATE	1	TRUE	2	0.587393637386273	4		276	191	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876658468	NA	P-0051602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	288	546	0	ENST00000269305.4:c.577C>G	p.His193Asp	p.H193D	ENST00000269305	NM_001126112.2	193	Cat/Gat	6/11	0.587393637386273	3	FACETS	0.959	0.919	0.998	0.959	0.919	0.998	CLONAL	3	TRUE	0	0.587393637386273	3		546	441	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870260	44870260	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	190	159	0	ENST00000377967.4:c.439C>T	p.Gln147Ter	p.Q147*	ENST00000377967	NM_021140.2	147	Cag/Tag	5/29	0.403088741352463	2	FACETS	0.859	0.821	0.895			1	CLONAL	3	TRUE	NA	0.587393637386273	2		159	251	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403452	139403452	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1393225618	NA	P-0051602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	229	664	0	ENST00000277541.6:c.3041C>T	p.Thr1014Met	p.T1014M	ENST00000277541	NM_017617.3	1014	aCg/aTg	19/34	0.587393637386273	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.587393637386273	2		664	358	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023212	27023215	+	frameshift_variant	Frame_Shift_Del	DEL	CGCG	CGCG	-	novel	NA	P-0051602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	83	131	0	ENST00000324856.7:c.318_321del	p.Asn106LysfsTer7	p.N106Kfs*7	ENST00000324856	NM_006015.4	106	aaCGCG/aa	1/20	0.258929972856506	5	FACETS	0.898	0.82	0.975			1	INDETERMINATE	4	TRUE	NA	0.587393637386273	5		131	148	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55478762	55478762	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	157	455	0	ENST00000284073.2:c.335T>C	p.Ile112Thr	p.I112T	ENST00000284073	NM_138962.2	112	aTa/aCa	6/14	0.241331145728554	4	FACETS	0.852	0.786	0.92	0.852	0.786	0.92	INDETERMINATE	2	TRUE	2	0.587393637386273	4		455	498	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210566	5210566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773706905	NA	P-0051602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	232	616	0	ENST00000357368.4:c.5401C>T	p.Arg1801Cys	p.R1801C	ENST00000357368	NM_002850.3	1801	Cgc/Tgc	35/38	0.195596677615318	3	FACETS	1	0.989	1	0.781	0.739	0.823	INDETERMINATE	2	TRUE	0	0.587393637386273	3		616	436	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858039	45858039	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	45	654	0	ENST00000391945.4:c.1614C>A	p.Phe538Leu	p.F538L	ENST00000391945	NM_000400.3	538	ttC/ttA	17/23	0.587393637386273	3	FACETS	0.319	0.267	0.376	0.106	0.089	0.126	SUBCLONAL	1	TRUE	0	0.587393637386273	3		654	622	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917728	29917728	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	148	610	0	ENST00000389048.3:c.940G>C	p.Glu314Gln	p.E314Q	ENST00000389048	NM_004304.4	314	Gag/Cag	3/29	0.478276008149022	3	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.587393637386273	3		610	448	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89478271	89478271	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	23	380	0	ENST00000336596.2:c.2090T>A	p.Ile697Asn	p.I697N	ENST00000336596	NM_005233.5	697	aTt/aAt	12/17	0.314918942794494	2	FACETS	0.196	0.152	0.247	0.098	0.076	0.124	INDETERMINATE	1	TRUE	0	0.587393637386273	2		380	399	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670690	86670697	+	frameshift_variant	Frame_Shift_Del	DEL	AACTCTTA	AACTCTTA	-	novel	NA	P-0051602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	15	266	0	ENST00000274376.6:c.1968_1975del	p.Ile656MetfsTer2	p.I656Mfs*2	ENST00000274376	NM_002890.2	656	atAACTCTTAgt/atgt	15/25	0.560300162413683	2	FACETS	0.18	0.131	0.239	0.09	0.065	0.12	SUBCLONAL	1	TRUE	0	0.587393637386273	2		266	283	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864525	56864525	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	73	447	0	ENST00000519728.1:c.488G>T	p.Gly163Val	p.G163V	ENST00000519728	NM_002350.3	163	gGa/gTa	7/13	0.587393637386273	4	FACETS	0.689	0.603	0.781			1	SUBCLONAL	1	TRUE	NA	0.587393637386273	4		447	573	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742478	145742478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	179	591	0	ENST00000428558.2:c.310G>A	p.Asp104Asn	p.D104N	ENST00000428558	NM_004260.3	104	Gac/Aac	4/22	0.45497026694362	5	FACETS	0.952	0.883	1	0.635	0.588	0.683	CLONAL	2	TRUE	2	0.587393637386273	5		591	602	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228065	53228065	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	91	289	0	ENST00000375401.3:c.2249G>C	p.Arg750Pro	p.R750P	ENST00000375401	NM_004187.3	750	cGg/cCg	16/26	0.403088741352463	2	FACETS	1	0.952	1			1	CLONAL	1	TRUE	NA	0.587393637386273	2		289	282	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0051605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	146	559	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.43143186050127	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.43143186050127	1		559	474	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0051605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	281	441	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.43143186050127	2		441	951	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577576	7577578	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	novel	NA	P-0051605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	231	430	1	ENST00000269305.4:c.703_705del	p.Asn235del	p.N235del	ENST00000269305	NM_001126112.2	235	AAC/-	7/11	0.419298138085159	1	FACETS	0.975	0.911	1	0.975	0.911	1	CLONAL	1	TRUE	0	0.43143186050127	1		431	861	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441262	52441262	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	157	407	0	ENST00000460680.1:c.508T>G	p.Phe170Val	p.F170V	ENST00000460680	NM_004656.3	170	Ttt/Gtt	7/17	0.419298138085159	1	FACETS	0.9	0.828	0.976	0.9	0.828	0.976	CLONAL	1	TRUE	0	0.43143186050127	1		407	634	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0051605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	101	205	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.43143186050127	2		205	442	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380265	25380265	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	292	386	0	ENST00000311936.3:c.193A>T	p.Ser65Cys	p.S65C	ENST00000311936	NM_004985.3	65	Agt/Tgt	3/5	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.43143186050127	2		386	958	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966688	36966688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137870876	NA	P-0051606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	47	465	1	ENST00000358127.4:c.638C>T	p.Ser213Leu	p.S213L	ENST00000358127	NM_001280556.1	213	tCg/tTg	6/10	0.196272944106271	1	FACETS	0.786	0.663	0.921	0.786	0.663	0.921	CLONAL	1	TRUE	0	0.22	1		466	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0051606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	97	703	0	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.22	2		703	751	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492623	56492623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	78	465	0	ENST00000267101.3:c.2773G>A	p.Glu925Lys	p.E925K	ENST00000267101	NM_001982.3	925	Gag/Aag	23/28	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.22	2		465	664	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137740	64137740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	103	721	1	ENST00000334205.4:c.1841G>A	p.Gly614Asp	p.G614D	ENST00000334205	NM_003942.2	614	gGc/gAc	15/17	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.22	2		722	690	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973811	15973811	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	62	505	0	ENST00000268712.3:c.4181C>A	p.Ser1394Ter	p.S1394*	ENST00000268712	NM_006311.3	1394	tCa/tAa	31/46	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.22	2		505	537	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224493	108224493	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs748192003	NA	P-0051634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	19	219	0	ENST00000278616.4:c.8672G>A	p.Gly2891Asp	p.G2891D	ENST00000278616	NM_000051.3	2891	gGt/gAt	60/63	1	2	FACETS	1	0.813	1	1	0.813	1	CLONAL	1	TRUE	1	0.211348716195023	2		219	167	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0051635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	188	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.391523098573924	3	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.445343928612164	3		436	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577123	7577123	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876660333	NA	P-0051635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	204	553	0	ENST00000269305.4:c.815T>A	p.Val272Glu	p.V272E	ENST00000269305	NM_001126112.2	272	gTg/gAg	8/11	0.423597659009451	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.445343928612164	2		553	446	SUCCESS
APC	324	MSKCC	GRCh37	5	112175761	112175761	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	63	272	0	ENST00000257430.4:c.4473del	p.Phe1491LeufsTer16	p.F1491Lfs*16	ENST00000257430	NM_000038.5	1490	caT/ca	16/16	0.289589908561598	5	FACETS	1	0.911	1	0.699	0.613	0.79	CLONAL	2	TRUE	2	0.445343928612164	5		272	225	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464920	120464920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1233590749	NA	P-0051635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	71	420	0	ENST00000256646.2:c.5152C>T	p.Arg1718Cys	p.R1718C	ENST00000256646	NM_024408.3	1718	Cgc/Tgc	28/34	0.344497383222244	2	FACETS	0.893	0.785	1	0.447	0.392	0.505	CLONAL	1	TRUE	0	0.445343928612164	2		420	357	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748456	43748456	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	49	600	1	ENST00000382044.4:c.2350G>T	p.Glu784Ter	p.E784*	ENST00000382044	NM_001141980.1	784	Gag/Tag	12/28	0.178662612160844	3	FACETS	0.747	0.635	0.87	0.249	0.211	0.29	INDETERMINATE	1	TRUE	0	0.445343928612164	3		601	360	SUCCESS
APC	324	MSKCC	GRCh37	5	112164576	112164576	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1554082100	NA	P-0051635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	85	267	0	ENST00000257430.4:c.1652del	p.Leu551CysfsTer7	p.L551Cfs*7	ENST00000257430	NM_000038.5	550	aaT/aa	14/16	0.289589908561598	5	FACETS	0.983	0.877	1	0.655	0.584	0.729	CLONAL	2	TRUE	2	0.445343928612164	5		267	324	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	75	276	0				ENST00000310581	NM_198253.2	-/1132			0.140260949898138	3	FACETS	0.739	0.646	0.839	0.37	0.323	0.42	INDETERMINATE	1	TRUE	1	0.268611173782623	3		276	857	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637062	93637062	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369986984	NA	P-0051636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	55	483	0	ENST00000375746.1:c.1112C>T	p.Thr371Met	p.T371M	ENST00000375746	NM_001174167.1	371	aCg/aTg	9/14	1	2	FACETS	0.567	0.484	0.658	0.567	0.484	0.658	SUBCLONAL	1	TRUE	1	0.268611173782623	2		483	722	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7126627	7126627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	54	565	0	ENST00000302850.5:c.2981C>T	p.Ser994Phe	p.S994F	ENST00000302850	NM_000208.2	994	tCt/tTt	16/22	1	2	FACETS	0.48	0.409	0.559	0.48	0.409	0.559	SUBCLONAL	1	TRUE	1	0.268611173782623	2		565	837	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851443	63851443	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	71	485	0	ENST00000279873.7:c.2221A>T	p.Thr741Ser	p.T741S	ENST00000279873	NM_032199.2	741	Act/Tct	10/10	1	2	FACETS	0.705	0.614	0.803	0.705	0.614	0.803	SUBCLONAL	1	TRUE	1	0.268611173782623	2		485	750	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875650	56875650	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	62	466	0	ENST00000308159.5:c.2254A>G	p.Thr752Ala	p.T752A	ENST00000308159	NM_014669.4	752	Acc/Gcc	21/22	1	2	FACETS	0.596	0.513	0.685	0.596	0.513	0.685	SUBCLONAL	1	TRUE	1	0.268611173782623	2		466	775	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89809287	89809287	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	90	590	0	ENST00000389301.3:c.3686C>A	p.Ala1229Glu	p.A1229E	ENST00000389301	NM_000135.2	1229	gCa/gAa	37/43	1	2	FACETS	0.706	0.625	0.793	0.706	0.625	0.793	SUBCLONAL	1	TRUE	1	0.268611173782623	2		590	949	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577137	7577145	+	inframe_deletion	In_Frame_Del	DEL	CCGTCCCAG	CCGTCCCAG	-	novel	NA	P-0051636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	140	531	0	ENST00000269305.4:c.793_801del	p.Leu265_Arg267del	p.L265_R267del	ENST00000269305	NM_001126112.2	265	CTGGGACGG/-	8/11	0.211536379426244	3	FACETS	1	0.984	1	0.682	0.621	0.746	CLONAL	1	TRUE	1	0.268611173782623	3		531	867	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872351	45872352	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0051636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	56	702	2	ENST00000391945.4:c.159_160delinsCT	p.Leu53_Ala54delinsPheSer	p.L53_A54delinsFS	ENST00000391945	NM_000400.3	53	ttGGcc/ttCTcc	3/23	1	2	FACETS	0.387	0.33	0.449	0.387	0.33	0.449	SUBCLONAL	1	TRUE	1	0.268611173782623	2		704	1078	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035104	30035104	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	37	401	0	ENST00000338641.4:c.266A>G	p.Glu89Gly	p.E89G	ENST00000338641	NM_000268.3	89	gAa/gGa	3/16	1	2	FACETS	0.385	0.316	0.463	0.385	0.316	0.463	SUBCLONAL	1	TRUE	1	0.268611173782623	2		401	715	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177570	56177570	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	61	376	0	ENST00000399503.3:c.2543A>G	p.His848Arg	p.H848R	ENST00000399503	NM_005921.1	848	cAc/cGc	14/20	0.258250800418975	3	FACETS	0.875	0.755	1	0.437	0.377	0.503	CLONAL	1	TRUE	1	0.268611173782623	3		376	589	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0051637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	142	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.306630608063114	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	FALSE	1	0.306131940421483	3		436	495	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0051637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	79	425	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.306131940421483	2		425	410	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	62	536	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.529	0.456	0.608	0.529	0.456	0.608	SUBCLONAL	1	FALSE	1	0.306131940421483	2		536	766	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182641	38182641	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs387907272	NA	P-0051637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	20	265	0	ENST00000396334.3:c.794T>C	p.Leu265Pro	p.L265P	ENST00000396334	NM_002468.4	265	cTg/cCg	5/5	1	2	FACETS	0.358	0.273	0.458	0.358	0.273	0.458	SUBCLONAL	1	FALSE	1	0.306131940421483	2		265	365	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714390	117714390	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1433758459	NA	P-0051637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	58	287	0	ENST00000368508.3:c.1259A>G	p.Asn420Ser	p.N420S	ENST00000368508	NM_002944.2	420	aAt/aGt	11/43	1	2	FACETS	0.879	0.757	1	0.879	0.757	1	CLONAL	1	FALSE	1	0.306131940421483	2		287	431	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0051638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	129	518	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.331101108766733	3	FACETS	0.934	0.852	1	0.934	0.852	1	CLONAL	2	TRUE	1	0.331101108766733	3		518	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0051638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	94	558	1	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.331101108766733	1	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	0	0.331101108766733	1		559	466	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0051638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	1086	525	1	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.331101108766733	16	FACETS	0.967	0.946	0.987			1	CLONAL	14	TRUE	NA	0.331101108766733	16		526	1608	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103346	2103346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777459404	NA	P-0051638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	89	537	0	ENST00000219476.3:c.229G>A	p.Ala77Thr	p.A77T	ENST00000219476	NM_000548.3	77	Gca/Aca	4/42	0.331101108766733	3	FACETS	1	0.948	1	0.558	0.496	0.625	CLONAL	1	TRUE	1	0.331101108766733	3		537	561	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526792	31526792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149389256	NA	P-0051638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	92	604	2	ENST00000344624.3:c.248C>T	p.Pro83Leu	p.P83L	ENST00000344624		83	cCa/cTa	2/33	0.331101108766733	3	FACETS	0.925	0.822	1	0.463	0.411	0.518	CLONAL	1	TRUE	1	0.331101108766733	3		606	700	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245357	53245357	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	128	502	0	ENST00000375401.3:c.680T>C	p.Ile227Thr	p.I227T	ENST00000375401	NM_004187.3	227	aTt/aCt	6/26	0.222596108930014	4	FACETS	0.817	0.742	0.895	0.817	0.742	0.895	CLONAL	2	TRUE	2	0.331101108766733	4		502	630	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339201	65339201	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747503301	NA	P-0051638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	43	343	0	ENST00000342505.4:c.335A>G	p.Tyr112Cys	p.Y112C	ENST00000342505	NM_002227.2	112	tAt/tGt	5/25	1	2	FACETS	0.755	0.634	0.888	0.755	0.634	0.888	SUBCLONAL	1	TRUE	1	0.331101108766733	2		343	344	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244175	46244175	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	51	316	0	ENST00000334344.6:c.2269G>A	p.Val757Met	p.V757M	ENST00000334344	NM_152641.2	757	Gtg/Atg	15/21	0.331101108766733	3	FACETS	0.898	0.765	1	0.449	0.382	0.521	CLONAL	1	TRUE	1	0.331101108766733	3		316	400	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118710	115118712	+	inframe_deletion	In_Frame_Del	DEL	TGG	TGG	-	novel	NA	P-0051638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	91	412	0	ENST00000257566.3:c.629_631del	p.Thr210del	p.T210del	ENST00000257566	NM_016569.3	210	aCCAac/aac	2/8	0.295606001754942	3	FACETS	1	0.942	1	0.547	0.486	0.611	CLONAL	1	TRUE	1	0.331101108766733	3		412	586	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061168	38061169	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0051638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	226	255	0	ENST00000250448.2:c.820dup	p.Ala274GlyfsTer19	p.A274Gfs*19	ENST00000250448	NM_004496.3	274	gcc/gGcc	2/2	0.331101108766733	5	FACETS	1	0.97	1			1	CLONAL	4	TRUE	NA	0.331101108766733	5		255	489	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905767	50905767	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	81	621	0	ENST00000440232.2:c.815A>C	p.Lys272Thr	p.K272T	ENST00000440232	NM_002691.3	272	aAa/aCa	7/27	1	2	FACETS	0.852	0.752	0.96	0.852	0.752	0.96	CLONAL	1	TRUE	1	0.331101108766733	2		621	574	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160186	22160186	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	35	308	0	ENST00000215832.6:c.445G>C	p.Asp149His	p.D149H	ENST00000215832	NM_002745.4	149	Gac/Cac	3/9	0.295606001754942	3	FACETS	0.542	0.444	0.652	0.271	0.222	0.326	SUBCLONAL	1	TRUE	1	0.331101108766733	3		308	455	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515150	31515150	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	101	684	0	ENST00000344624.3:c.1235G>A	p.Trp412Ter	p.W412*	ENST00000344624		412	tGg/tAg	5/33	0.331101108766733	3	FACETS	0.9	0.804	1	0.45	0.402	0.501	CLONAL	1	TRUE	1	0.331101108766733	3		684	790	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459229	99459851	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTCCTCTTCTCAGTTAATCGTGAAGTGGAACCCTCCCTCTCTGCCCAACGGCAACCTGAGTTACTACATTGTGCGCTGGCAGCGGCAGCCTCAGGACGGCTACCTTTACCGGCACAATTACTGCTCCAAAGGTAAGGGTGCAGCAGCGGCCTGGACGGAGGGTGTGACCGTTCATTCCTGTGGTTGTAATGTGCCTGAGCCCTAATATTACACGTATCAGACAACAGTGTAGTTCTCCATTGGAAACCAGCTATCTTCTGGTTTTTTTTTTTTTTTTTTGAGACAGAGTCTCACTCTGTTGCCCAGGCTGGAGTGCAGTGGCACGATCATGGCTCACTGCAATTTCTGCCTCCCAGGTTCAAGCATTTCTCATTCCCCAGCATTCCGAGTAGCTGGGATTACAGGCATGCACCACCATGCCCAGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGCCCAGGCTGGTCTGAAACTCCTAACCTCAGGTGATTTGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTATAGCCTTGAGCCACCACATCTGGCCGAGACCAGCTATCTTCTTGATTAAAGGTACTGAGAGCTATTATTTTTCCTTACAAGCATGT	ACTCCTCTTCTCAGTTAATCGTGAAGTGGAACCCTCCCTCTCTGCCCAACGGCAACCTGAGTTACTACATTGTGCGCTGGCAGCGGCAGCCTCAGGACGGCTACCTTTACCGGCACAATTACTGCTCCAAAGGTAAGGGTGCAGCAGCGGCCTGGACGGAGGGTGTGACCGTTCATTCCTGTGGTTGTAATGTGCCTGAGCCCTAATATTACACGTATCAGACAACAGTGTAGTTCTCCATTGGAAACCAGCTATCTTCTGGTTTTTTTTTTTTTTTTTTGAGACAGAGTCTCACTCTGTTGCCCAGGCTGGAGTGCAGTGGCACGATCATGGCTCACTGCAATTTCTGCCTCCCAGGTTCAAGCATTTCTCATTCCCCAGCATTCCGAGTAGCTGGGATTACAGGCATGCACCACCATGCCCAGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGCCCAGGCTGGTCTGAAACTCCTAACCTCAGGTGATTTGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTATAGCCTTGAGCCACCACATCTGGCCGAGACCAGCTATCTTCTTGATTAAAGGTACTGAGAGCTATTATTTTTCCTTACAAGCATGT	-	novel	NA	P-0051640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	74	535	0	ENST00000268035.6:c.1866_1997-49del		p.X622_splice	ENST00000268035	NM_000875.3	622		9/21	NA	2	FACETS	0.233	0.203	0.266			1	INDETERMINATE	1	TRUE	NA	0.599217622405781	2		535	1058	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296425	15296425	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	393	722	0	ENST00000263388.2:c.2017G>T	p.Val673Leu	p.V673L	ENST00000263388	NM_000435.2	673	Gtg/Ttg	13/33	0.3907182966094	1	FACETS	0.87	0.829	0.912	0.87	0.829	0.912	CLONAL	1	TRUE	0	0.599217622405781	1		722	1056	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004574	150004601	+	frameshift_variant	Frame_Shift_Del	DEL	TTGGAGCTTCAGCAACAGGTGGCATCAC	TTGGAGCTTCAGCAACAGGTGGCATCAC	-	novel	NA	P-0051640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	303	610	0	ENST00000253339.5:c.1624_1651del	p.Val542ThrfsTer97	p.V542Tfs*97	ENST00000253339		542	GTGATGCCACCTGTTGCTGAAGCTCCAAac/ac	3/7	0.599217622405781	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.599217622405781	1		610	699	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	262	276	0				ENST00000310581	NM_198253.2	-/1132			0.666557347423969	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.692674702534469	3		276	484	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0051641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	475	839	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.692674702534469	2	FACETS	0.997	0.966	1	0.997	0.966	1	CLONAL	2	TRUE	0	0.692674702534469	2		839	688	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097751	27097751	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	472	556	2	ENST00000324856.7:c.3344del	p.Pro1115GlnfsTer46	p.P1115Qfs*46	ENST00000324856	NM_006015.4	1114	Ccc/cc	12/20	0.66922879642313	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	2	0.692674702534469	4		558	1004	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953760	48953760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913302	NA	P-0051641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	136	207	0	ENST00000267163.4:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000267163	NM_000321.2	455	Cga/Tga	14/27	0.666779309948433	2	FACETS	0.888	0.832	0.944	0.888	0.832	0.944	CLONAL	2	TRUE	0	0.692674702534469	2		207	221	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348800	89348800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776994699	NA	P-0051641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	342	988	1	ENST00000301030.4:c.4150G>A	p.Gly1384Ser	p.G1384S	ENST00000301030	NM_001256183.1	1384	Ggt/Agt	9/13	0.68008527123104	3	FACETS	1	0.977	1	0.53	0.501	0.56	CLONAL	1	TRUE	1	0.692674702534469	3		989	1254	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3795309	3795309	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs559939930	NA	P-0051641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	332	480	0	ENST00000262367.5:c.3883G>T	p.Val1295Phe	p.V1295F	ENST00000262367	NM_004380.2	1295	Gtt/Ttt	22/31	0.68008527123104	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.692674702534469	3		480	641	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074213	8074213	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs765025014	NA	P-0051641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	172	462	0	ENST00000377482.5:c.446G>C	p.Gly149Ala	p.G149A	ENST00000377482	NM_018948.3	149	gGt/gCt	4/4	NA	2	FACETS	0.855	0.791	0.921			1	INDETERMINATE	1	TRUE	NA	0.692674702534469	2		462	581	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828084	243828084	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	183	325	0	ENST00000263826.5:c.274C>G	p.Pro92Ala	p.P92A	ENST00000263826	NM_005465.4	92	Cca/Gca	3/13	0.375195698352436	3	FACETS	0.849	0.793	0.905	0.849	0.793	0.905	INDETERMINATE	2	TRUE	1	0.692674702534469	3		325	419	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77043839	77043839	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	448	703	0	ENST00000356341.3:c.1487A>G	p.Asp496Gly	p.D496G	ENST00000356341	NM_002576.4	496	gAc/gGc	14/15	0.68008527123104	3	FACETS	0.986	0.947	1	0.986	0.947	1	CLONAL	2	TRUE	1	0.692674702534469	3		703	883	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444878	49444878	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs747921601	NA	P-0051641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	501	783	0	ENST00000301067.7:c.2588G>T	p.Arg863Leu	p.R863L	ENST00000301067	NM_003482.3	863	cGg/cTg	10/54	0.692674702534469	2	FACETS	0.941	0.911	0.97	0.941	0.911	0.97	CLONAL	2	TRUE	0	0.692674702534469	2		783	769	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862760	9862760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779911797	NA	P-0051641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	176	566	1	ENST00000330684.3:c.2543G>A	p.Cys848Tyr	p.C848Y	ENST00000330684	NM_001134407.1	848	tGt/tAt	12/13	0.68008527123104	3	FACETS	0.937	0.866	1	0.469	0.433	0.506	CLONAL	1	TRUE	1	0.692674702534469	3		567	730	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122785	7122785	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0051641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	181	593	0	ENST00000302850.5:c.3370-1G>C		p.X1124_splice	ENST00000302850	NM_000208.2	1124			0.328274032213799	2	FACETS	0.945	0.878	1	0.473	0.439	0.507	INDETERMINATE	1	TRUE	0	0.692674702534469	2		593	553	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394872	394872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	126	451	0	ENST00000380956.4:c.268C>T	p.Pro90Ser	p.P90S	ENST00000380956	NM_001195286.1	90	Cct/Tct	3/9	0.666557347423969	3	FACETS	0.527	0.477	0.581	0.264	0.238	0.291	SUBCLONAL	1	TRUE	1	0.692674702534469	3		451	929	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56860179	56860180	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0051641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	143	502	0	ENST00000519728.1:c.181_182delinsAA	p.Pro61Lys	p.P61K	ENST00000519728	NM_002350.3	61	CCa/AAa	4/13	0.344522726979553	5	FACETS	1	0.976	1	0.396	0.361	0.432	INDETERMINATE	1	TRUE	2	0.692674702534469	5		502	709	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250289	110250289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	423	789	2	ENST00000374672.4:c.386C>T	p.Ser129Leu	p.S129L	ENST00000374672	NM_004235.4	129	tCa/tTa	3/5	0.692674702534469	2	FACETS	1	0.996	1	0.694	0.665	0.723	CLONAL	1	TRUE	0	0.692674702534469	2		791	880	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	56	330	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	0.230378968555365	5	FACETS	0.897	0.777	1	0.897	0.777	1	CLONAL	3	TRUE	2	0.230378968555365	5		330	243	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18958624	18958624	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	64	579	0	ENST00000262803.5:c.443G>C	p.Arg148Pro	p.R148P	ENST00000262803	NM_002911.3	148	cGt/cCt	3/24	0.153307808119737	3	FACETS	0.876	0.758	1	0.438	0.379	0.503	CLONAL	1	TRUE	1	0.230378968555365	3		579	707	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430709	181430709	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	89	694	0	ENST00000325404.1:c.561T>A	p.Asn187Lys	p.N187K	ENST00000325404	NM_003106.3	187	aaT/aaA	1/1	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.230378968555365	2		694	686	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967713	90967713	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	13	331	0	ENST00000265433.3:c.1195G>C	p.Asp399His	p.D399H	ENST00000265433	NM_002485.4	399	Gat/Cat	10/16	0.230378968555365	5	FACETS	0.723	0.516	0.975	0.145	0.103	0.195	CLONAL	1	TRUE	0	0.230378968555365	5		331	210	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967740	90967740	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	11	302	0	ENST00000265433.3:c.1168G>C	p.Glu390Gln	p.E390Q	ENST00000265433	NM_002485.4	390	Gaa/Caa	10/16	0.230378968555365	5	FACETS	0.756	0.523	1	0.151	0.104	0.209	CLONAL	1	TRUE	0	0.230378968555365	5		302	170	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0051644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	359	513	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.593522411267171	2	FACETS	0.959	0.919	0.998	0.959	0.919	0.998	CLONAL	2	TRUE	0	0.593522411267171	2		516	631	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023294	27023295	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	T	novel	NA	P-0051644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	66	59	0	ENST00000324856.7:c.400_401delinsT	p.Ala134CysfsTer98	p.A134Cfs*98	ENST00000324856	NM_006015.4	134	GCg/Tg	1/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.593522411267171	2		59	182	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024599	31024599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	147	275	0	ENST00000375687.4:c.4084G>A	p.Ala1362Thr	p.A1362T	ENST00000375687	NM_015338.5	1362	Gcc/Acc	13/13	0.593522411267171	7	FACETS	0.967	0.881	1	0.161	0.146	0.177	CLONAL	1	TRUE	1	0.593522411267171	7		275	1272	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953616	38953616	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	65	120	0	ENST00000357387.3:c.2737G>C	p.Asp913His	p.D913H	ENST00000357387	NM_152756.3	913	Gat/Cat	28/38	0.328296174040325	5	FACETS	1	0.883	1	0.338	0.294	0.386	INDETERMINATE	1	TRUE	2	0.593522411267171	5		120	408	SUCCESS
APC	324	MSKCC	GRCh37	5	112162839	112162839	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	196	180	0	ENST00000257430.4:c.1444del	p.Asp482ThrfsTer16	p.D482Tfs*16	ENST00000257430	NM_000038.5	481	gtG/gt	12/16	0.328296174040325	5	FACETS	1	0.979	1	0.747	0.697	0.799	INDETERMINATE	2	TRUE	2	0.593522411267171	5		180	557	SUCCESS
APC	324	MSKCC	GRCh37	5	112175357	112175358	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0051644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	144	109	0	ENST00000257430.4:c.4067dup	p.Gly1357ArgfsTer18	p.G1357Rfs*18	ENST00000257430	NM_000038.5	1356	tca/tCca	16/16	0.328296174040325	5	FACETS	1	0.97	1	0.74	0.682	0.8	INDETERMINATE	2	TRUE	2	0.593522411267171	5		109	413	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894974	101894974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745324433	NA	P-0051644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	89	118	0	ENST00000374994.4:c.527C>T	p.Thr176Met	p.T176M	ENST00000374994	NM_004612.2	176	aCg/aTg	3/9	0.589150207424829	3	FACETS	1	0.902	1	0.505	0.451	0.562	CLONAL	1	TRUE	1	0.593522411267171	3		118	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0051645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	68	633	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.14	2		633	790	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0051645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	27	449	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	0.758	0.602	0.937	0.758	0.602	0.937	CLONAL	1	TRUE	1	0.14	2		449	509	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0051645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	50	474	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.916	0.775	1	0.916	0.775	1	CLONAL	1	TRUE	1	0.14	2		474	780	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0051645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	20	259	0	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	1	2	FACETS	0.762	0.582	0.973	0.762	0.582	0.973	CLONAL	1	TRUE	1	0.14	2		259	375	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252170	226252170	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	12	169	0	ENST00000366813.1:c.118C>A	p.His40Asn	p.H40N	ENST00000366813		40	Cat/Aat	1/3	1	2	FACETS	0.72	0.506	0.985	0.72	0.506	0.985	CLONAL	1	TRUE	1	0.14	2		169	238	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591901	48591901	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	41	446	0	ENST00000342988.3:c.1064A>T	p.Asp355Val	p.D355V	ENST00000342988	NM_005359.5	355	gAc/gTc	9/12	1	2	FACETS	0.989	0.823	1	0.989	0.823	1	CLONAL	1	TRUE	1	0.14	2		446	592	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412045	116412045	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0051648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	256	653	0	ENST00000397752.3:c.3028+2T>C		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.317933044374556	2	FACETS	0.975	0.916	1	0.975	0.916	1	CLONAL	2	TRUE	0	0.331503394673161	2		653	792	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891166	101891166	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	49	330	0	ENST00000374994.4:c.127A>G	p.Lys43Glu	p.K43E	ENST00000374994	NM_004612.2	43	Aaa/Gaa	2/9	1	2	FACETS	0.944	0.804	1	0.944	0.804	1	CLONAL	1	TRUE	1	0.331503394673161	2		330	313	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136016	64136016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	157	614	1	ENST00000334205.4:c.1277G>A	p.Arg426His	p.R426H	ENST00000334205	NM_003942.2	426	cGc/cAc	11/17	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.317615329774078	2		615	831	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0051649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	91	595	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.317615329774078	1	FACETS	0.761	0.677	0.852	0.761	0.677	0.852	SUBCLONAL	1	TRUE	0	0.317615329774078	1		596	633	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262073	10262073	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0051649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	73	441	0	ENST00000340748.4:c.2217+1G>C		p.X739_splice	ENST00000340748		739			1	2	FACETS	0.867	0.76	0.983	0.867	0.76	0.983	CLONAL	1	TRUE	1	0.317615329774078	2		441	530	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620470	52620470	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	37	464	0	ENST00000394830.3:c.3283C>T	p.Arg1095Ter	p.R1095*	ENST00000394830	NM_018313.4	1095	Cga/Tga	21/30	1	2	FACETS	0.384	0.316	0.461	0.384	0.316	0.461	SUBCLONAL	1	TRUE	1	0.317615329774078	2		464	607	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532891	187532891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	79	345	0	ENST00000441802.2:c.9502G>A	p.Ala3168Thr	p.A3168T	ENST00000441802	NM_005245.3	3168	Gct/Act	14/27	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.317615329774078	2		345	451	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962378	2962378	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1275601330	NA	P-0051649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	77	600	0	ENST00000396946.4:c.2159G>A	p.Arg720Gln	p.R720Q	ENST00000396946	NM_032415.4	720	cGa/cAa	17/25	0.308072674337158	3	FACETS	0.716	0.628	0.811	0.358	0.314	0.406	SUBCLONAL	1	TRUE	1	0.317615329774078	3		600	785	SUCCESS
APC	324	MSKCC	GRCh37	5	112175385	112175399	+	frameshift_variant	Frame_Shift_Del	DEL	GTGCTCAGACACCCA	GTGCTCAGACACCCA	T	novel	NA	P-0051649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	87	247	0	ENST00000257430.4:c.4094_4108delinsT	p.Gly1365ValfsTer5	p.G1365Vfs*5	ENST00000257430	NM_000038.5	1365	gGTGCTCAGACACCCAaa/gTaa	16/16	0.303930449679339	2	FACETS	0.872	0.78	0.968	0.872	0.78	0.968	CLONAL	2	TRUE	0	0.317615329774078	2		247	314	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0051650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	175	436	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.869	0.801	0.939	0.869	0.801	0.939	CLONAL	1	TRUE	1	0.50928253538616	2		436	791	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076799	72076799	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	113	444	0	ENST00000357731.5:c.698G>C	p.Gly233Ala	p.G233A	ENST00000357731	NM_173808.2	233	gGc/gCc	5/7	1	2	FACETS	0.551	0.495	0.609	0.551	0.495	0.609	SUBCLONAL	1	TRUE	1	0.50928253538616	2		444	806	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928656	49928656	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	339	686	0	ENST00000296474.3:c.3618C>A	p.His1206Gln	p.H1206Q	ENST00000296474	NM_002447.2	1206	caC/caA	17/20	0.50928253538616	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.50928253538616	1		686	939	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942026	44942027	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0051650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	162	379	0	ENST00000377967.4:c.3277dup	p.Asp1093GlyfsTer10	p.D1093Gfs*10	ENST00000377967	NM_021140.2	1092	-/G	22/29	0.50928253538616	1	FACETS	0.968	0.895	1	0.968	0.895	1	CLONAL	1	TRUE	0	0.50928253538616	1		379	490	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120467992	120467992	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	187	704	0	ENST00000256646.2:c.4447C>G	p.Leu1483Val	p.L1483V	ENST00000256646	NM_024408.3	1483	Ctg/Gtg	25/34	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.332595937612332	2		704	1023	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600433	43600433	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1182941467	NA	P-0051651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	123	585	1	ENST00000355710.3:c.659G>T	p.Ser220Ile	p.S220I	ENST00000355710	NM_020975.4	220	aGc/aTc	4/20	1	2	FACETS	0.972	0.879	1	0.972	0.879	1	CLONAL	1	TRUE	1	0.332595937612332	2		586	761	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0051651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	18	501	2	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.19	0.142	0.247	0.19	0.142	0.247	SUBCLONAL	1	TRUE	1	0.332595937612332	2		503	569	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912140	114912140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	90	528	0	ENST00000543371.1:c.1210C>T	p.Arg404Trp	p.R404W	ENST00000543371	NM_001198531.1	404	Cgg/Tgg	11/14	1	2	FACETS	0.816	0.725	0.914	0.816	0.725	0.914	CLONAL	1	TRUE	1	0.332595937612332	2		528	663	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21623931	21623931	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0051651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	20	134	0	ENST00000421138.2:c.1769T>G	p.Val590Gly	p.V590G	ENST00000421138		590	gTg/gGg	15/16	1	2	FACETS	0.738	0.568	0.933	0.738	0.568	0.933	CLONAL	1	TRUE	1	0.332595937612332	2		134	163	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578490	7578490	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1453167097	NA	P-0051651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	234	868	0	ENST00000269305.4:c.440T>G	p.Val147Gly	p.V147G	ENST00000269305	NM_001126112.2	147	gTt/gGt	5/11	0.332595937612332	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.332595937612332	1		868	936	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622362	1622362	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770464889	NA	P-0051651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	192	820	1	ENST00000344749.5:c.602C>T	p.Pro201Leu	p.P201L	ENST00000344749	NM_001136139.2	201	cCg/cTg	9/19	0.332595937612332	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.332595937612332	1		821	893	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311700	30311700	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0051651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	63	478	0	ENST00000262643.3:c.554A>T	p.Lys185Ile	p.K185I	ENST00000262643	NM_001238.2	185	aAa/aTa	7/12	1	2	FACETS	0.693	0.599	0.794	0.693	0.599	0.794	SUBCLONAL	1	TRUE	1	0.332595937612332	2		478	547	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918231	50918231	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760898812	NA	P-0051651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	66	723	1	ENST00000440232.2:c.2548C>T	p.Arg850Cys	p.R850C	ENST00000440232	NM_002691.3	850	Cgc/Tgc	20/27	1	2	FACETS	0.48	0.416	0.551	0.48	0.416	0.551	SUBCLONAL	1	TRUE	1	0.332595937612332	2		724	826	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664562	138664562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	55	151	0	ENST00000330315.3:c.1003C>T	p.Pro335Ser	p.P335S	ENST00000330315	NM_023067.3	335	Ccc/Tcc	1/1	0.181375348277664	3	FACETS	0.784	0.678	0.898	0.784	0.678	0.898	INDETERMINATE	2	TRUE	1	0.332595937612332	3		151	246	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976837	55976837	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs770118276	NA	P-0051651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	289	533	2	ENST00000263923.4:c.1075C>A	p.Pro359Thr	p.P359T	ENST00000263923	NM_002253.2	359	Ccc/Acc	8/30	0.332595937612332	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.332595937612332	3		535	890	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467918	66467918	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	62	366	0	ENST00000273854.3:c.351G>T	p.Trp117Cys	p.W117C	ENST00000273854	NM_004439.5	117	tgG/tgT	3/18	0.103598737184682	3	FACETS	0.856	0.74	0.981			1	INDETERMINATE	1	TRUE	NA	0.332595937612332	3		366	508	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508759	31508759	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	146	699	0	ENST00000344624.3:c.1556A>G	p.His519Arg	p.H519R	ENST00000344624		519	cAt/cGt	7/33	0.181375348277664	3	FACETS	0.933	0.85	1	0.466	0.425	0.51	INDETERMINATE	1	TRUE	1	0.332595937612332	3		699	1098	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502294	157502294	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	99	466	0	ENST00000346085.5:c.3327G>T	p.Glu1109Asp	p.E1109D	ENST00000346085	NM_020732.3	1109	gaG/gaT	12/20	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.332595937612332	2		466	571	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335645	81335645	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs766769838	NA	P-0051651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	71	545	0	ENST00000222390.5:c.1715A>G	p.Tyr572Cys	p.Y572C	ENST00000222390	NM_000601.4	572	tAt/tGt	15/18	1	2	FACETS	0.652	0.569	0.742	0.652	0.569	0.742	SUBCLONAL	1	TRUE	1	0.332595937612332	2		545	655	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859452	151859452	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	85	510	0	ENST00000262189.6:c.11210A>T	p.Glu3737Val	p.E3737V	ENST00000262189	NM_170606.2	3737	gAg/gTg	43/59	1	2	FACETS	0.759	0.671	0.854	0.759	0.671	0.854	SUBCLONAL	1	TRUE	1	0.332595937612332	2		510	673	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909649	76909649	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	98	262	0	ENST00000373344.5:c.4256A>G	p.Tyr1419Cys	p.Y1419C	ENST00000373344	NM_000489.3	1419	tAt/tGt	14/35	1	1	FACETS	0.941	0.853	1	1	0.988	1	CLONAL	2	TRUE	0	0.332595937612332	1		262	261	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449743	8449744	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	T	novel	NA	P-0051651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	115	547	0	ENST00000356435.5:c.3969_3970delinsA	p.Asn1325ThrfsTer25	p.N1325Tfs*25	ENST00000356435		1323	cgCCtt/cgAtt	23/35	0.332595937612332	1	FACETS	0.939	0.848	1	0.939	0.848	1	CLONAL	1	TRUE	0	0.332595937612332	1		547	614	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0051652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	108	390	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.923	0.833	1	0.923	0.833	1	CLONAL	1	TRUE	1	0.491652160816755	2		390	476	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0051652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	176	465	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.491652160816755	2	FACETS	0.927	0.866	0.989	0.927	0.866	0.989	CLONAL	2	TRUE	0	0.491652160816755	2		465	386	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0051652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	76	310	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	0.719	0.633	0.81	0.719	0.633	0.81	SUBCLONAL	1	TRUE	1	0.491652160816755	2		310	430	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881489	48881490	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs587778862	NA	P-0051652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	53	367	0	ENST00000267163.4:c.219_220del	p.Arg73SerfsTer36	p.R73Sfs*36	ENST00000267163	NM_000321.2	71	AGa/a	2/27	1	2	FACETS	0.611	0.523	0.706	0.611	0.523	0.706	SUBCLONAL	1	TRUE	1	0.491652160816755	2		367	353	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0051652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	67	293	0	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			1	2	FACETS	0.828	0.725	0.939	0.828	0.725	0.939	CLONAL	1	TRUE	1	0.491652160816755	2		293	329	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101278	27101278	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	109	620	0	ENST00000324856.7:c.4563del	p.Ala1522ProfsTer5	p.A1522Pfs*5	ENST00000324856	NM_006015.4	1520	ggC/gg	18/20	1	2	FACETS	0.729	0.656	0.806	0.729	0.656	0.806	SUBCLONAL	1	TRUE	1	0.491652160816755	2		620	608	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939260	71939260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	49	762	0	ENST00000298229.2:c.209G>A	p.Arg70His	p.R70H	ENST00000298229	NM_001567.3	70	cGc/cAc	2/28	1	2	FACETS	0.264	0.223	0.31	0.264	0.223	0.31	SUBCLONAL	1	TRUE	1	0.491652160816755	2		762	754	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644826	67644826	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	145	474	0	ENST00000264010.4:c.95del	p.Gly32AlafsTer30	p.G32Afs*30	ENST00000264010	NM_006565.3	31	Ggg/gg	3/12	0.491652160816755	1	FACETS	0.813	0.746	0.883	0.813	0.746	0.883	CLONAL	1	TRUE	0	0.491652160816755	1		474	547	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716328	52716328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1343613316	NA	P-0051652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	191	582	3	ENST00000322088.6:c.772C>T	p.Arg258Cys	p.R258C	ENST00000322088	NM_014225.5	258	Cgc/Tgc	6/15	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.491652160816755	2		585	765	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323309	31323309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	67	209	0	ENST00000412585.2:c.680G>A	p.Cys227Tyr	p.C227Y	ENST00000412585	NM_005514.6	227	tGc/tAc	4/8	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.491652160816755	2		209	215	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112565	115112565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1214834962	NA	P-0051652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	245	685	2	ENST00000257566.3:c.1175C>T	p.Ala392Val	p.A392V	ENST00000257566	NM_016569.3	392	gCg/gTg	7/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.491652160816755	2		687	880	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073432	8073432	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs779337445	NA	P-0051652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	112	477	0	ENST00000377482.5:c.1227A>T	p.Lys409Asn	p.K409N	ENST00000377482	NM_018948.3	409	aaA/aaT	4/4	1	2	FACETS	0.812	0.733	0.895	0.812	0.733	0.895	CLONAL	1	TRUE	1	0.491652160816755	2		477	561	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215923	36215923	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	153	791	0	ENST00000222270.7:c.3465del	p.Asn1156MetfsTer26	p.N1156Mfs*26	ENST00000222270	NM_014727.1	1155	Ccc/cc	10/37	1	2	FACETS	0.678	0.62	0.739	0.678	0.62	0.739	SUBCLONAL	1	TRUE	1	0.491652160816755	2		791	918	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593613	55593613	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913521	NA	P-0051670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	98	259	0	ENST00000288135.5:c.1679T>A	p.Val560Asp	p.V560D	ENST00000288135	NM_000222.2	560	gTt/gAt	11/21	1	2	FACETS	0.748	0.673	0.826	0.748	0.673	0.826	SUBCLONAL	1	TRUE	1	0.712283553835395	2		259	368	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713601	30713601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202168735	NA	P-0051670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	122	391	0	ENST00000295754.5:c.926C>T	p.Thr309Met	p.T309M	ENST00000295754	NM_003242.5	309	aCg/aTg	4/7	1	2	FACETS	0.73	0.664	0.799	0.73	0.664	0.799	SUBCLONAL	1	TRUE	1	0.712283553835395	2		391	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578429	7578429	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1567553148	NA	P-0051672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	501	638	0	ENST00000269305.4:c.501del	p.Gln167HisfsTer3	p.Q167Hfs*3	ENST00000269305	NM_001126112.2	167	caG/ca	5/11	0.872753002874277	1	FACETS	0.983	0.957	1	0.983	0.957	1	CLONAL	1	TRUE	0	0.872753002874277	1		638	658	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215817	133215817	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	153	483	0	ENST00000320574.5:c.5446A>C	p.Asn1816His	p.N1816H	ENST00000320574	NM_006231.2	1816	Aac/Cac	40/49	1	2	FACETS	0.492	0.451	0.535	0.492	0.451	0.535	SUBCLONAL	1	TRUE	1	0.872753002874277	2		483	713	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952562	17952564	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	novel	NA	P-0051672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	308	507	0	ENST00000458235.1:c.869_871del	p.Gln290del	p.Q290del	ENST00000458235	NM_000215.3	290	cAGCcc/ccc	7/24	1	2	FACETS	0.848	0.803	0.894	0.848	0.803	0.894	CLONAL	1	TRUE	1	0.872753002874277	2		507	832	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890133	76890138	+	inframe_deletion	In_Frame_Del	DEL	ACCTGG	ACCTGG	-	novel	NA	P-0051672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	69	349	0	ENST00000373344.5:c.4756_4761del	p.Pro1586_Gly1587del	p.P1586_G1587del	ENST00000373344	NM_000489.3	1586	CCAGGT/-	17/35	0.872753002874277	1	FACETS	0.958	0.886	1	0.958	0.886	1	CLONAL	1	TRUE	0	0.872753002874277	1		349	93	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262221	115262221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	56	320	0	ENST00000438362.2:c.2333C>T	p.Ala778Val	p.A778V	ENST00000438362	NM_001242891.1	778	gCc/gTc	18/20	NA	2	FACETS	0.685	0.587	0.793			1	INDETERMINATE	1	TRUE	NA	0.276046247525213	2		320	592	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191513	10191513	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1205346910	NA	P-0051673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	85	403	0	ENST00000256474.2:c.506del	p.Leu169GlnfsTer33	p.L169Qfs*33	ENST00000256474	NM_000551.3	169	cTa/ca	3/3	0.275238136823659	1	FACETS	0.875	0.774	0.982	0.875	0.774	0.982	CLONAL	1	TRUE	0	0.276046247525213	1		403	607	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47088076	47088076	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	97	431	0	ENST00000409792.3:c.6999del	p.Gln2334AsnfsTer19	p.Q2334Nfs*19	ENST00000409792	NM_014159.6	2333	ggG/gg	16/21	0.275238136823659	1	FACETS	0.921	0.822	1	0.921	0.822	1	CLONAL	1	TRUE	0	0.276046247525213	1		431	658	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441216	52441216	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553645794	NA	P-0051673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	74	353	0	ENST00000460680.1:c.554G>A	p.Gly185Glu	p.G185E	ENST00000460680	NM_004656.3	185	gGg/gAg	7/17	0.275238136823659	1	FACETS	0.994	0.873	1	0.994	0.873	1	CLONAL	1	TRUE	0	0.276046247525213	1		353	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0051675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	122	567	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.947	0.858	1	0.947	0.858	1	CLONAL	1	TRUE	1	0.37	2		567	696	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0051675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	21	422	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.35	0.269	0.445	0.35	0.269	0.445	SUBCLONAL	1	TRUE	1	0.37	2		422	324	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257240	16257240	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	32	524	0	ENST00000375759.3:c.4505C>T	p.Thr1502Ile	p.T1502I	ENST00000375759	NM_015001.2	1502	aCt/aTt	11/15	1	2	FACETS	0.338	0.273	0.411	0.338	0.273	0.411	SUBCLONAL	1	TRUE	1	0.37	2		524	512	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678616	88678616	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	18	391	0	ENST00000360948.2:c.920T>C	p.Val307Ala	p.V307A	ENST00000360948	NM_001012338.2	307	gTg/gCg	9/19	1	2	FACETS	0.274	0.206	0.355	0.274	0.206	0.355	SUBCLONAL	1	TRUE	1	0.37	2		391	355	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177081	56177081	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	13	254	0	ENST00000399503.3:c.2351C>G	p.Ala784Gly	p.A784G	ENST00000399503	NM_005921.1	784	gCt/gGt	13/20	1	2	FACETS	0.278	0.198	0.376	0.278	0.198	0.376	SUBCLONAL	1	TRUE	1	0.37	2		254	253	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675682	30675682	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	42	732	0	ENST00000376406.3:c.2674G>T	p.Val892Leu	p.V892L	ENST00000376406	NM_014641.2	892	Gta/Tta	8/15	1	2	FACETS	0.282	0.234	0.335	0.282	0.234	0.335	SUBCLONAL	1	TRUE	1	0.37	2		732	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0051676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	111	430	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.767	0.692	0.845	0.767	0.692	0.845	SUBCLONAL	1	TRUE	1	0.571173430445098	2		430	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	85	581	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	1	2	FACETS	0.717	0.637	0.802	0.717	0.637	0.802	SUBCLONAL	1	TRUE	1	0.571173430445098	2		581	415	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933781	39933781	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	181	276	0	ENST00000378444.4:c.818C>T	p.Ser273Phe	p.S273F	ENST00000378444	NM_001123385.1	273	tCc/tTc	4/15	0.55453550338514	2	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.571173430445098	2		276	498	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983275	149983275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	134	446	0	ENST00000253339.5:c.2983C>T	p.Arg995Cys	p.R995C	ENST00000253339		995	Cgc/Tgc	7/7	0.31843745793538	3	FACETS	0.859	0.791	0.929	0.573	0.527	0.62	INDETERMINATE	2	TRUE	0	0.571173430445098	3		446	351	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0051676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	88	786	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	1	2	FACETS	0.529	0.47	0.593	0.529	0.47	0.593	SUBCLONAL	1	TRUE	1	0.571173430445098	2		786	582	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426771	212426771	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879060634	NA	P-0051676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	99	414	0	ENST00000342788.4:c.2344C>T	p.Arg782Trp	p.R782W	ENST00000342788	NM_005235.2	782	Cgg/Tgg	20/28	0.419444412429526	3	FACETS	0.874	0.783	0.97	0.437	0.391	0.485	CLONAL	1	TRUE	1	0.571173430445098	3		414	510	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262016	16262016	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	37	402	0	ENST00000375759.3:c.9281C>T	p.Ser3094Phe	p.S3094F	ENST00000375759	NM_015001.2	3094	tCc/tTc	11/15	0.262507491781933	2	FACETS	0.255	0.209	0.305	0.127	0.104	0.153	INDETERMINATE	1	TRUE	0	0.571173430445098	2		402	509	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264129	16264129	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1309232938	NA	P-0051676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	37	523	0	ENST00000375759.3:c.10498C>G	p.Gln3500Glu	p.Q3500E	ENST00000375759	NM_015001.2	3500	Caa/Gaa	12/15	0.262507491781933	2	FACETS	0.22	0.18	0.264	0.11	0.09	0.132	INDETERMINATE	1	TRUE	0	0.571173430445098	2		523	590	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363575	40363576	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0051676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	65	435	1	ENST00000397332.2:c.653_654delinsTT	p.Thr218Ile	p.T218I	ENST00000397332	NM_001033082.2	218	aCC/aTT	3/3	0.262507491781933	2	FACETS	0.362	0.313	0.414	0.181	0.156	0.207	INDETERMINATE	1	TRUE	0	0.571173430445098	2		436	629	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287503	46287503	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0051676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	120	295	0	ENST00000334344.6:c.5362A>T	p.Arg1788Ter	p.R1788*	ENST00000334344	NM_152641.2	1788	Aga/Tga	20/21	0.372711561730598	4	FACETS	0.877	0.808	0.945	0.658	0.606	0.709	CLONAL	3	TRUE	0	0.571173430445098	4		295	251	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448521	49448521	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761525910	NA	P-0051676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	162	473	1	ENST00000301067.7:c.190C>T	p.Arg64Trp	p.R64W	ENST00000301067	NM_003482.3	64	Cgg/Tgg	3/54	0.372711561730598	4	FACETS	1	0.974	1	0.286	0.262	0.31	CLONAL	1	TRUE	0	0.571173430445098	4		474	780	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028714	42028714	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1029483306	NA	P-0051676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	40	443	0	ENST00000219905.7:c.4252G>C	p.Asp1418His	p.D1418H	ENST00000219905	NM_001164273.1	1418	Gat/Cat	13/24	1	2	FACETS	0.388	0.323	0.46	0.388	0.323	0.46	SUBCLONAL	1	TRUE	1	0.571173430445098	2		443	361	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006624	62006624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	130	563	0	ENST00000392795.3:c.655G>A	p.Val219Met	p.V219M	ENST00000392795	NM_001039933.1	219	Gtg/Atg	6/6	1	2	FACETS	0.799	0.727	0.873	0.799	0.727	0.873	SUBCLONAL	1	TRUE	1	0.571173430445098	2		563	570	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416544	29416544	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	166	546	0	ENST00000389048.3:c.4409C>A	p.Ala1470Asp	p.A1470D	ENST00000389048	NM_004304.4	1470	gCc/gAc	29/29	0.419444412429526	3	FACETS	0.972	0.894	1	0.486	0.447	0.526	CLONAL	1	TRUE	1	0.571173430445098	3		546	769	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718965	190718965	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	22	209	0	ENST00000441310.2:c.967G>A	p.Glu323Lys	p.E323K	ENST00000441310	NM_000534.4	323	Gaa/Aaa	9/13	0.419444412429526	3	FACETS	0.854	0.672	1	0.427	0.336	0.529	CLONAL	1	TRUE	1	0.571173430445098	3		209	116	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403191	213403191	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	112	384	0	ENST00000342788.4:c.64C>A	p.Pro22Thr	p.P22T	ENST00000342788	NM_005235.2	22	Ccc/Acc	1/28	0.419444412429526	3	FACETS	0.803	0.724	0.886	0.401	0.362	0.443	CLONAL	1	TRUE	1	0.571173430445098	3		384	628	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266530	41266531	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0051676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	109	371	0	ENST00000349496.5:c.327_328delinsTT	p.Pro110Ser	p.P110S	ENST00000349496	NM_001904.3	109	atCCca/atTTca	4/15	0.456834220170144	3	FACETS	1	0.98	1	0.663	0.601	0.727	CLONAL	1	TRUE	1	0.571173430445098	3		371	370	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413710	138413711	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0051676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	154	387	1	ENST00000289153.2:c.1809_1810delinsTT	p.Arg604Trp	p.R604W	ENST00000289153	NM_006219.2	603	ccCCgg/ccTTgg	12/22	0.456834220170144	3	FACETS	1	0.984	1	0.643	0.592	0.696	CLONAL	1	TRUE	1	0.571173430445098	3		388	539	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271239	153271239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265788422	NA	P-0051676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	48	199	0	ENST00000281708.4:c.539C>T	p.Ser180Phe	p.S180F	ENST00000281708	NM_033632.3	180	tCt/tTt	3/12	0.441636679555876	2	FACETS	1	0.914	1	0.542	0.467	0.621	CLONAL	1	TRUE	0	0.571173430445098	2		199	155	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521112	187521113	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0051676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	219	424	2	ENST00000441802.2:c.12042_12043delinsAA	p.Glu4015Lys	p.E4015K	ENST00000441802	NM_005245.3	4014	acGGaa/acAAaa	22/27	0.441636679555876	2	FACETS	0.784	0.737	0.831	0.784	0.737	0.831	SUBCLONAL	2	TRUE	0	0.571173430445098	2		426	489	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630913	187630914	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0051676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	240	377	0	ENST00000441802.2:c.68dup	p.Ser24GlnfsTer5	p.S24Qfs*5	ENST00000441802	NM_005245.3	23	ggc/ggGc	2/27	0.441636679555876	2	FACETS	0.76	0.716	0.804	0.76	0.716	0.804	SUBCLONAL	2	TRUE	0	0.571173430445098	2		377	553	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405823	157405823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	87	319	0	ENST00000346085.5:c.2065C>T	p.Pro689Ser	p.P689S	ENST00000346085	NM_020732.3	689	Ccc/Tcc	6/20	0.31843745793538	3	FACETS	0.886	0.788	0.99	0.295	0.262	0.33	INDETERMINATE	1	TRUE	0	0.571173430445098	3		319	442	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412358	139412358	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	583	597	0	ENST00000277541.6:c.1287C>G	p.Cys429Trp	p.C429W	ENST00000277541	NM_017617.3	429	tgC/tgG	8/34	0.571173430445098	3	FACETS	0.952	0.923	0.98	0.952	0.923	0.98	CLONAL	3	TRUE	0	0.571173430445098	3		597	919	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356431	70356431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	319	270	0	ENST00000374080.3:c.5326C>T	p.Pro1776Ser	p.P1776S	ENST00000374080		1776	Cca/Tca	37/45	0.55453550338514	2	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.571173430445098	2		270	474	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845262	151845262	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747850540	NA	P-0051679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	66	327	1	ENST00000262189.6:c.13750C>T	p.Arg4584Trp	p.R4584W	ENST00000262189	NM_170606.2	4584	Cgg/Tgg	52/59	1	2	FACETS	0.778	0.682	0.879	0.778	0.682	0.879	SUBCLONAL	1	TRUE	1	0.617102281394573	2		328	275	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106617	27106617	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	158	472	1	ENST00000324856.7:c.6228C>A	p.Tyr2076Ter	p.Y2076*	ENST00000324856	NM_006015.4	2076	taC/taA	20/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.617102281394573	2		473	468	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419919	152419920	+	missense_variant	Missense_Mutation	DNP	CT	CT	AA	novel	NA	P-0051679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	145	430	1	ENST00000206249.3:c.1606_1607delinsAA	p.Leu536Asn	p.L536N	ENST00000206249	NM_000125.3	536	CTc/AAc	8/8	0.123505938612199	4	FACETS	0.913	0.842	0.987	0.913	0.842	0.987	INDETERMINATE	2	TRUE	2	0.617102281394573	4		431	416	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148928	119148928	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	297	468	0	ENST00000264033.4:c.1148T>G	p.Ile383Arg	p.I383R	ENST00000264033	NM_005188.3	383	aTa/aGa	8/16	0.740672530252024	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.761088303907319	2		468	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578440	7578440	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs879254249	NA	P-0051696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	363	846	0	ENST00000269305.4:c.490A>G	p.Lys164Glu	p.K164E	ENST00000269305	NM_001126112.2	164	Aag/Gag	5/11	0.635694503123265	2	FACETS	0.885	0.853	0.916	0.885	0.853	0.916	CLONAL	2	TRUE	0	0.761088303907319	2		846	539	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531733	46531733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	83	322	0	ENST00000262741.5:c.614C>T	p.Thr205Ile	p.T205I	ENST00000262741	NM_003629.3	205	aCa/aTa	5/10	0.625397219695106	3	FACETS	0.921	0.82	1	0.46	0.41	0.514	CLONAL	1	TRUE	1	0.761088303907319	3		322	327	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843589	156843589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1213393905	NA	P-0051696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	192	896	0	ENST00000524377.1:c.1015G>A	p.Glu339Lys	p.E339K	ENST00000524377	NM_002529.3	339	Gag/Aag	8/17	0.487678621214674	4	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.761088303907319	4		896	743	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921728	111921728	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs972594463	NA	P-0051696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	93	300	0	ENST00000393256.3:c.517C>G	p.Gln173Glu	p.Q173E	ENST00000393256	NM_006538.4	173	Caa/Gaa	4/4	0.488189099361639	3	FACETS	0.998	0.896	1	0.499	0.448	0.553	CLONAL	1	TRUE	1	0.761088303907319	3		300	338	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0051697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	40	391	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.893	1	1	0.972	1	CLONAL	2	FALSE	1	0.277709094091009	2		391	135	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372518	55372518	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	292	895	0	ENST00000297316.4:c.1208G>T	p.Ser403Ile	p.S403I	ENST00000297316	NM_022454.3	403	aGc/aTc	2/2	1	2	FACETS	1	0.983	1	1	0.996	1	CLONAL	2	FALSE	1	0.277709094091009	2		895	952	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106805	27106805	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1302295523	NA	P-0051697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	144	648	1	ENST00000324856.7:c.6416C>A	p.Pro2139His	p.P2139H	ENST00000324856	NM_006015.4	2139	cCc/cAc	20/20	1	2	FACETS	1	0.92	1	1	0.991	1	CLONAL	2	FALSE	1	0.277709094091009	2		649	517	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371798	55371819	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCGGCCGCGCTGGGCCCCGA	AGGCGGCCGCGCTGGGCCCCGA	-	novel	NA	P-0051697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	143	136	0	ENST00000297316.4:c.488_509del	p.Gln163ArgfsTer217	p.Q163Rfs*217	ENST00000297316	NM_022454.3	163	cAGGCGGCCGCGCTGGGCCCCGAg/cg	2/2	1	2	FACETS	1	0.972	1	1	0.994	1	CLONAL	3	FALSE	1	0.277709094091009	2		136	312	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089678	27089678	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	163	673	0	ENST00000324856.7:c.2635del	p.Val879LeufsTer12	p.V879Lfs*12	ENST00000324856	NM_006015.4	878	caG/ca	8/20	1	2	FACETS	0.806	0.742	0.873	1	0.99	1	CLONAL	2	FALSE	1	0.277709094091009	2		673	728	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717650	89717651	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0051697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	169	459	0	ENST00000371953.3:c.675_676del	p.Ser226LeufsTer16	p.S226Lfs*16	ENST00000371953	NM_000314.4	225	taTTcc/tacc	7/9	0.277709094091009	1	FACETS	1	0.958	1	1	0.995	1	CLONAL	4	FALSE	0	0.277709094091009	1		459	258	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0051698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	191	518	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.841941072359027	2		518	436	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0051698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	144	355	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA	2	FACETS	1	0.954	1			1	INDETERMINATE	1	TRUE	NA	0.841941072359027	2		355	329	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572033	64572033	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	418	640	0	ENST00000312049.6:c.1606C>T	p.Gln536Ter	p.Q536*	ENST00000312049	NM_130799.2	536	Cag/Tag	10/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.841941072359027	2		640	976	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578349	212578349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1484791833	NA	P-0051698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	235	340	0	ENST00000342788.4:c.908C>T	p.Ser303Phe	p.S303F	ENST00000342788	NM_005235.2	303	tCt/tTt	8/28	0.812883928713167	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.841941072359027	3		340	378	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870849	12870849	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	142	225	0	ENST00000228872.4:c.78del	p.Ser27ArgfsTer15	p.S27Rfs*15	ENST00000228872	NM_004064.3	26	Ccc/cc	1/3	1	2	FACETS	0.961	0.888	1	0.961	0.888	1	CLONAL	1	TRUE	1	0.841941072359027	2		225	351	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133862	41133862	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0051698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	180	396	0	ENST00000379561.5:c.1766G>C	p.Arg589Thr	p.R589T	ENST00000379561	NM_002015.3	589	aGa/aCa	2/3	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.841941072359027	2		396	395	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23652442	23652442	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0051698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	411	737	0	ENST00000261584.4:c.37G>T	p.Glu13Ter	p.E13*	ENST00000261584	NM_024675.3	13	Gag/Tag	1/13	0.812883928713167	3	FACETS	1	0.96	1	0.505	0.48	0.53	CLONAL	1	TRUE	1	0.841941072359027	3		737	1373	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856073	151856073	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	257	393	0	ENST00000262189.6:c.11545C>T	p.Gln3849Ter	p.Q3849*	ENST00000262189	NM_170606.2	3849	Cag/Tag	44/59	0.800185521324418	3	FACETS	0.993	0.932	1	0.496	0.466	0.528	CLONAL	1	TRUE	1	0.841941072359027	3		393	874	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937480	76937480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	81	427	0	ENST00000373344.5:c.3268G>A	p.Glu1090Lys	p.E1090K	ENST00000373344	NM_000489.3	1090	Gag/Aag	9/35	0.305598708737345	1	FACETS	0.451	0.403	0.501	0.451	0.403	0.501	INDETERMINATE	1	TRUE	0	0.841941072359027	1		427	247	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123025146	123025146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs967223819	NA	P-0051698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	97	333	0	ENST00000355640.3:c.1036C>T	p.His346Tyr	p.H346Y	ENST00000355640		346	Cat/Tat	4/7	0.305598708737345	1	FACETS	0.604	0.55	0.659	0.604	0.55	0.659	INDETERMINATE	1	TRUE	0	0.841941072359027	1		333	221	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123026588	123026588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	152	379	0	ENST00000355640.3:c.1064C>T	p.Thr355Ile	p.T355I	ENST00000355640		355	aCt/aTt	5/7	0.305598708737345	1	FACETS	0.521	0.482	0.561	0.521	0.482	0.561	INDETERMINATE	1	TRUE	0	0.841941072359027	1		379	401	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549493	21549493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	27	326	0	ENST00000382592.4:c.2783G>T	p.Trp928Leu	p.W928L	ENST00000382592	NM_014572.2	928	tGg/tTg	8/8	1	2	FACETS	0.132	0.105	0.164	0.132	0.105	0.164	SUBCLONAL	1	TRUE	1	0.805789422092857	2		326	506	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938578	76938579	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0051699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	133	322	0	ENST00000373344.5:c.2169_2170del	p.Glu723AspfsTer9	p.E723Dfs*9	ENST00000373344	NM_000489.3	723	gaGAct/gact	9/35	1	2	FACETS	0.988	0.91	1	0.988	0.91	1	CLONAL	1	TRUE	1	0.805789422092857	2		322	334	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0051701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	130	487	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.215934428116181	3	FACETS	0.876	0.8	0.955	0.876	0.8	0.955	INDETERMINATE	2	TRUE	1	0.375779664230796	3		487	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578525	7578525	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519976	NA	P-0051702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	229	918	0	ENST00000269305.4:c.405C>G	p.Cys135Trp	p.C135W	ENST00000269305	NM_001126112.2	135	tgC/tgG	5/11	0.430803490584793	1	FACETS	0.698	0.651	0.747	0.698	0.651	0.747	SUBCLONAL	1	TRUE	0	0.49947064447805	1		918	985	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656299	18656299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	71	478	0	ENST00000266497.5:c.2978C>T	p.Thr993Ile	p.T993I	ENST00000266497		993	aCa/aTa	21/31	0.396488247038695	3	FACETS	0.764	0.669	0.866			1	SUBCLONAL	1	TRUE	NA	0.49947064447805	3		478	465	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443517	49443517	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0051702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	48	620	0	ENST00000301067.7:c.3854A>T	p.Glu1285Val	p.E1285V	ENST00000301067	NM_003482.3	1285	gAg/gTg	11/54	NA	2	FACETS	0.228	0.192	0.268			1	INDETERMINATE	1	TRUE	NA	0.49947064447805	2		620	842	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213976	2213976	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	211	703	2	ENST00000326181.6:c.55C>T	p.Leu19Phe	p.L19F	ENST00000326181	NM_032271.2	19	Ctt/Ttt	2/21	0.228017873894879	3	FACETS	0.925	0.858	0.995	0.463	0.429	0.498	INDETERMINATE	1	TRUE	1	0.49947064447805	3		705	1141	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285312	212285312	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0051702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	50	340	0	ENST00000342788.4:c.2989A>C	p.Ser997Arg	p.S997R	ENST00000342788	NM_005235.2	997	Agt/Cgt	25/28	0.44658238025607	1	FACETS	0.598	0.512	0.691	0.598	0.512	0.691	SUBCLONAL	1	TRUE	0	0.49947064447805	1		340	251	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71050197	71050197	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	56	302	0	ENST00000318789.4:c.988G>A	p.Glu330Lys	p.E330K	ENST00000318789	NM_032682.5	330	Gag/Aag	13/21	1	2	FACETS	0.684	0.589	0.786	0.684	0.589	0.786	SUBCLONAL	1	TRUE	1	0.49947064447805	2		302	328	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576352	67576357	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTAGAA	GTAGAA	-	novel	NA	P-0051702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	42	222	0	ENST00000274335.5:c.635-1_639del		p.X212_splice	ENST00000274335		212		5/15	1	2	FACETS	0.94	0.795	1	0.94	0.795	1	CLONAL	1	TRUE	1	0.49947064447805	2		222	179	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021004	26021004	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1268	205	633	0	ENST00000357647.3:c.287C>A	p.Ala96Glu	p.A96E	ENST00000357647	NM_003529.2	96	gCg/gAg	1/1	0.49947064447805	6	FACETS	1	0.974	1	0.278	0.257	0.301	CLONAL	1	TRUE	2	0.49947064447805	6		633	1473	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426063	47426063	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	224	850	0	ENST00000377045.4:c.583G>C	p.Glu195Gln	p.E195Q	ENST00000377045	NM_001654.4	195	Gag/Cag	7/16	0.48616727888638	1	FACETS	0.749	0.699	0.802	0.749	0.699	0.802	SUBCLONAL	1	TRUE	0	0.49947064447805	1		850	898	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010443	48010443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201684	NA	P-0051715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	137	514	0	ENST00000234420.5:c.71C>T	p.Ser24Leu	p.S24L	ENST00000234420	NM_000179.2	24	tCg/tTg	1/10	0.267898583547896	3	FACETS	1	0.916	1	0.502	0.458	0.547	INDETERMINATE	1	TRUE	1	0.609215925761756	3		514	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578391	7578392	+	inframe_insertion	In_Frame_Ins	INS	-	-	CATGGTGGGGGCAGCGCC	novel	NA	P-0051715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	288	697	0	ENST00000269305.4:c.521_538dup	p.His179_Glu180insGlyArgCysProHisHis	p.H179_E180insGRCPHH	ENST00000269305	NM_001126112.2	180	gag/gGGCGCTGCCCCCACCATGag	5/11	0.609215925761756	3	FACETS	0.803	0.759	0.848	0.535	0.506	0.565	CLONAL	2	TRUE	0	0.609215925761756	3		697	768	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186501404	186501404	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764605841	NA	P-0051716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	63	312	0	ENST00000323963.5:c.5C>G	p.Ser2Cys	p.S2C	ENST00000323963		2	tCt/tGt	1/11	1	2	FACETS	0.937	0.815	1	0.937	0.815	1	CLONAL	1	TRUE	1	0.355639743040348	2		312	378	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557424	21557430	+	frameshift_variant	Frame_Shift_Del	DEL	GAGTTTA	GAGTTTA	-	novel	NA	P-0051716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	115	576	0	ENST00000382592.4:c.2415_2421del	p.Lys806GlnfsTer47	p.K806Qfs*47	ENST00000382592	NM_014572.2	805	atTAAACTC/at	5/8	0.355639743040348	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.355639743040348	1		576	510	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	150	517	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.197175249828532	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.27	3		517	550	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	41	801	0	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.402	0.333	0.478	0.402	0.333	0.478	SUBCLONAL	1	TRUE	1	0.27	2		801	756	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670328	134670328	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559321367	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	122	387	0	ENST00000398015.3:c.239G>A	p.Arg80Gln	p.R80Q	ENST00000398015	NM_004441.4	80	cGg/cAg	3/16	0.3	1	FACETS	1	0.94	1	1	0.99	1	CLONAL	2	TRUE	0	0.27	1		387	377	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	76	292	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.885	0.783	0.993	1	0.982	1	CLONAL	2	TRUE	1	0.27	2		292	318	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	121	293	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.846	0.774	0.921	1	0.991	1	CLONAL	3	TRUE	1	0.27	2		293	353	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222593	69222593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194693256	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	29	356	0	ENST00000462284.1:c.566G>A	p.Arg189His	p.R189H	ENST00000462284	NM_002392.5	189	cGc/cAc	8/11	0.197175249828532	3	FACETS	0.434	0.347	0.533	0.217	0.173	0.267	SUBCLONAL	1	TRUE	1	0.27	3		356	562	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118885	70118885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	70	651	1	ENST00000245479.2:c.457C>T	p.Pro153Ser	p.P153S	ENST00000245479	NM_000346.3	153	Ccc/Tcc	2/3	1	2	FACETS	0.874	0.763	0.995	0.874	0.763	0.995	CLONAL	1	TRUE	1	0.27	2		652	593	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209110082	209110082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148190775	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	79	458	0	ENST00000345146.2:c.481G>A	p.Gly161Arg	p.G161R	ENST00000345146	NM_005896.2	161	Gga/Aga	5/10	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.27	2		458	550	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411246	63411246	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	196	702	0	ENST00000330258.3:c.1921C>T	p.Arg641Ter	p.R641*	ENST00000330258	NM_152424.3	641	Cga/Tga	2/2	1	2	FACETS	1	0.984	1	1	0.994	1	CLONAL	2	TRUE	1	0.27	2		702	608	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545061	41545061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs544338126	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	67	418	0	ENST00000263253.7:c.2261G>A	p.Arg754His	p.R754H	ENST00000263253	NM_001429.3	754	cGt/cAt	13/31	1	2	FACETS	0.859	0.747	0.98	0.859	0.747	0.98	CLONAL	1	TRUE	1	0.27	2		418	578	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715685	30715685	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	76	280	0	ENST00000295754.5:c.1343A>G	p.Tyr448Cys	p.Y448C	ENST00000295754	NM_003242.5	448	tAc/tGc	5/7	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.27	2		280	386	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909698	50909698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	220	743	0	ENST00000440232.2:c.1418C>T	p.Thr473Met	p.T473M	ENST00000440232	NM_002691.3	473	aCg/aTg	12/27	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.27	2		743	682	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778821	3778821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	228	771	0	ENST00000262367.5:c.6227C>T	p.Ser2076Leu	p.S2076L	ENST00000262367	NM_004380.2	2076	tCg/tTg	31/31	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.27	2		771	711	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458869	120458869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755184344	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	43	608	0	ENST00000256646.2:c.6476C>T	p.Thr2159Met	p.T2159M	ENST00000256646	NM_024408.3	2159	aCg/aTg	34/34	1	2	FACETS	0.546	0.456	0.646	0.546	0.456	0.646	SUBCLONAL	1	TRUE	1	0.27	2		608	583	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445500	49445500	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs886042284	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	70	653	0	ENST00000301067.7:c.1966del	p.Leu656CysfsTer274	p.L656Cfs*274	ENST00000301067	NM_003482.3	656	Ctg/tg	10/54	0.197175249828532	3	FACETS	0.885	0.771	1	0.442	0.385	0.504	CLONAL	1	TRUE	1	0.27	3		653	665	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523731	176523731	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	53	607	1	ENST00000292408.4:c.2147del	p.Pro716GlnfsTer6	p.P716Qfs*6	ENST00000292408	NM_213647.1	714	tgC/tg	16/18	1	2	FACETS	0.7	0.597	0.813	0.7	0.597	0.813	SUBCLONAL	1	TRUE	1	0.27	2		608	561	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56801430	56801430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881932	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	113	394	0	ENST00000337432.4:c.934C>T	p.Arg312Trp	p.R312W	ENST00000337432	NM_058216.2	312	Cgg/Tgg	7/9	1	2	FACETS	0.859	0.777	0.945	1	0.987	1	CLONAL	2	TRUE	1	0.27	2		394	487	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223190	36223190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs949745356	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	257	854	0	ENST00000222270.7:c.5740C>T	p.Arg1914Cys	p.R1914C	ENST00000222270	NM_014727.1	1914	Cgt/Tgt	28/37	1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	1	0.27	2		854	802	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223614	36223614	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	64	860	2	ENST00000222270.7:c.6169del	p.Arg2057AlafsTer34	p.R2057Afs*34	ENST00000222270	NM_014727.1	2055	gCc/gc	28/37	1	2	FACETS	0.603	0.521	0.692	0.603	0.521	0.692	SUBCLONAL	1	TRUE	1	0.27	2		862	786	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163309259	163309260	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	40	295	0	ENST00000271452.3:c.604dup	p.Thr202AsnfsTer24	p.T202Nfs*24	ENST00000271452	NM_145697.2	200	caa/cAaa	8/14	1	2	FACETS	0.739	0.615	0.877	0.739	0.615	0.877	SUBCLONAL	1	TRUE	1	0.27	2		295	401	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924823	49924823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772336656	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	78	780	1	ENST00000296474.3:c.4120C>T	p.Arg1374Cys	p.R1374C	ENST00000296474	NM_002447.2	1374	Cgt/Tgt	20/20	1	2	FACETS	0.73	0.641	0.827	0.73	0.641	0.827	SUBCLONAL	1	TRUE	1	0.27	2		781	791	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849900	151849900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773458258	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	93	330	0	ENST00000262189.6:c.12416G>A	p.Arg4139Gln	p.R4139Q	ENST00000262189	NM_170606.2	4139	cGa/cAa	49/59	1	2	FACETS	0.797	0.713	0.886	1	0.983	1	SUBCLONAL	2	TRUE	1	0.27	2		330	432	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141562	11141562	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	78	636	0	ENST00000358026.2:c.3539C>A	p.Pro1180His	p.P1180H	ENST00000358026	NM_001128849.1	1180	cCt/cAt	25/36	1	2	FACETS	0.896	0.787	1	0.896	0.787	1	CLONAL	1	TRUE	1	0.27	2		636	645	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325150	39325150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	59	504	0	ENST00000373001.3:c.169G>A	p.Ala57Thr	p.A57T	ENST00000373001	NM_022157.3	57	Gct/Act	1/7	1	2	FACETS	0.733	0.631	0.845	0.733	0.631	0.845	SUBCLONAL	1	TRUE	1	0.27	2		504	596	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95556891	95556891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	86	327	1	ENST00000393063.1:c.5713G>A	p.Ala1905Thr	p.A1905T	ENST00000393063	NM_030621.3	1905	Gca/Aca	28/28	1	2	FACETS	0.815	0.725	0.909	1	0.982	1	CLONAL	2	TRUE	1	0.27	2		328	391	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435674	56435674	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	163	649	0	ENST00000407977.2:c.1463del	p.Gln488ArgfsTer14	p.Q488Rfs*14	ENST00000407977		488	cAg/cg	9/10	1	2	FACETS	1	0.934	1	1	0.992	1	CLONAL	2	TRUE	1	0.27	2		649	595	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727912	78727912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	103	474	1	ENST00000306801.3:c.757C>T	p.Pro253Ser	p.P253S	ENST00000306801	NM_020761.2	253	Ccc/Tcc	6/34	1	2	FACETS	0.828	0.745	0.915	1	0.985	1	CLONAL	2	TRUE	1	0.27	2		475	461	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226253	2226253	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	67	882	0	ENST00000398665.3:c.3733T>C	p.Phe1245Leu	p.F1245L	ENST00000398665	NM_032482.2	1245	Ttc/Ctc	27/28	1	2	FACETS	0.619	0.537	0.708	0.619	0.537	0.708	SUBCLONAL	1	TRUE	1	0.27	2		882	802	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967038	18967038	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	173	568	0	ENST00000262803.5:c.1756del	p.Glu586SerfsTer13	p.E586Sfs*13	ENST00000262803	NM_002911.3	585	Ggg/gg	13/24	1	2	FACETS	1	0.947	1	1	0.993	1	CLONAL	2	TRUE	1	0.27	2		568	622	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967071	18967071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1165210352	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	245	650	0	ENST00000262803.5:c.1786C>T	p.Arg596Trp	p.R596W	ENST00000262803	NM_002911.3	596	Cgg/Tgg	13/24	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	1	0.27	2		650	748	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702337	47702337	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs267607982	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	157	351	0	ENST00000233146.2:c.1933C>T	p.Gln645Ter	p.Q645*	ENST00000233146	NM_000251.2	645	Caa/Taa	12/16	0.3	0	FACETS	0.827	0.77	0.885			1	CLONAL	3	TRUE	0	0.27	0		351	342	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631562	119631562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	107	262	0	ENST00000316626.5:c.704C>T	p.Thr235Ile	p.T235I	ENST00000316626		235	aCc/aTc	6/12	1	2	FACETS	1	0.96	1	1	0.989	1	CLONAL	2	TRUE	1	0.27	2		262	357	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253746	153253746	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	19	254	0	ENST00000281708.4:c.985+2T>C		p.X329_splice	ENST00000281708	NM_033632.3	329			1	2	FACETS	0.402	0.305	0.517	0.402	0.305	0.517	SUBCLONAL	1	TRUE	1	0.27	2		254	350	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190819	32190819	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	96	772	0	ENST00000375023.3:c.118A>G	p.Thr40Ala	p.T40A	ENST00000375023	NM_004557.3	40	Acc/Gcc	2/30	1	2	FACETS	0.844	0.751	0.943	0.844	0.751	0.943	CLONAL	1	TRUE	1	0.27	2		772	843	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138197252	138197252	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0051718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	27	318	0	ENST00000237289.4:c.754T>C	p.Tyr252His	p.Y252H	ENST00000237289	NM_001270507.1	252	Tat/Cat	5/9	1	2	FACETS	0.483	0.384	0.597	0.483	0.384	0.597	SUBCLONAL	1	TRUE	1	0.27	2		318	414	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0051719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	240	334	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.360472215768611	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	3	TRUE	0	0.365474332546206	3		334	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0051719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	266	732	0	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	0.332649867214473	2	FACETS	0.81	0.761	0.861	0.81	0.761	0.861	CLONAL	2	TRUE	0	0.365474332546206	2		732	898	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0051723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	433	600	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.538497162296207	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.530447878929843	3		600	608	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958126	2958126	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs763435728	NA	P-0051723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	35	1161	1	ENST00000396946.4:c.2606G>A	p.Arg869Gln	p.R869Q	ENST00000396946	NM_032415.4	869	cGg/cAg	19/25	0.538497162296207	0	FACETS	0.115	0.094	0.139			1	SUBCLONAL	1	TRUE	0	0.530447878929843	0		1162	537	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48921983	48921984	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0051723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	161	245	0	ENST00000267163.4:c.526_527del	p.Gln176ThrfsTer8	p.Q176Tfs*8	ENST00000267163	NM_000321.2	175	ACa/a	5/27	0.487034415155942	3	FACETS	1	0.987	1	0.829	0.775	0.882	CLONAL	2	TRUE	0	0.530447878929843	3		245	309	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0051724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	99	276	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.70327151858474	2		276	261	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779172	135779172	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203631	NA	P-0051724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	49	493	0	ENST00000298552.3:c.2074C>T	p.Arg692Ter	p.R692*	ENST00000298552	NM_001162426.1	692	Cga/Tga	17/23	0.70327151858474	1	FACETS	0.262	0.222	0.305	0.262	0.222	0.305	SUBCLONAL	1	TRUE	0	0.70327151858474	1		493	345	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056209	27056210	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0051724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	163	751	0	ENST00000324856.7:c.1206dup	p.Gln403AlafsTer220	p.Q403Afs*220	ENST00000324856	NM_006015.4	402	tcg/tcGg	2/20	1	2	FACETS	0.716	0.66	0.775	0.716	0.66	0.775	SUBCLONAL	1	TRUE	1	0.70327151858474	2		751	647	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781075	135781075	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	96	683	0	ENST00000298552.3:c.1890del	p.Ala631GlnfsTer22	p.A631Qfs*22	ENST00000298552	NM_001162426.1	630	aaA/aa	15/23	0.70327151858474	1	FACETS	0.553	0.498	0.61	0.553	0.498	0.61	SUBCLONAL	1	TRUE	0	0.70327151858474	1		683	320	SUCCESS
APC	324	MSKCC	GRCh37	5	112175182	112175182	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0051725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	22	100	0	ENST00000257430.4:c.3892del	p.Ser1298LeufsTer7	p.S1298Lfs*7	ENST00000257430	NM_000038.5	1297	gaT/ga	16/16	0.375395102293873	3	FACETS	1	0.785	1	0.501	0.392	0.624	CLONAL	1	FALSE	1	0.375395102293873	3		100	139	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0051725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	22	96	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	0.375395102293873	3	FACETS	0.703	0.548	0.881	0.352	0.274	0.441	SUBCLONAL	1	FALSE	1	0.375395102293873	3		96	198	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120124	70120124	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0051725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	68	178	0	ENST00000245479.2:c.1126C>T	p.Gln376Ter	p.Q376*	ENST00000245479	NM_000346.3	376	Cag/Tag	3/3	0.375395102293873	2	FACETS	0.888	0.798	0.978	1	0.975	1	CLONAL	3	FALSE	0	0.375395102293873	2		178	136	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63816875	63816875	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0051725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	34	96	0	ENST00000279873.7:c.847-1G>A		p.X283_splice	ENST00000279873	NM_032199.2	283			0.375395102293873	3	FACETS	0.982	0.809	1	0.491	0.404	0.587	CLONAL	1	FALSE	1	0.375395102293873	3		96	219	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141455	11141458	+	frameshift_variant	Frame_Shift_Del	DEL	GCCC	GCCC	-	novel	NA	P-0051725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	142	642	0	ENST00000358026.2:c.3433_3436del	p.Pro1145AlafsTer18	p.P1145Afs*18	ENST00000358026	NM_001128849.1	1144	gaGCCC/ga	25/36	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	FALSE	1	0.375395102293873	2		642	718	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234301	39234304	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0051725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	44	54	0	ENST00000402219.2:c.2541_2544del	p.Arg848Ter	p.R848*	ENST00000402219	NM_005633.3	847	gaAAGA/ga	16/23	0.295451001194296	4	FACETS	1	0.92	1			1	CLONAL	1	FALSE	NA	0.375395102293873	4		54	280	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726040	61726040	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1051821670	NA	P-0051725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	31	75	0	ENST00000401558.2:c.599A>G	p.Asn200Ser	p.N200S	ENST00000401558	NM_003400.3	200	aAt/aGt	8/25	0.295451001194296	4	FACETS	0.923	0.751	1			1	CLONAL	1	FALSE	NA	0.375395102293873	4		75	246	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155046	55155046	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	53	435	0	ENST00000257290.5:c.2755G>C	p.Asp919His	p.D919H	ENST00000257290	NM_006206.4	919	Gac/Cac	20/23	0.189001426975295	0	FACETS	0.639	0.549	0.736			1	INDETERMINATE	1	FALSE	0	0.375395102293873	0		435	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0051727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	29	478	0	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	1	2	FACETS	0.833	0.672	1	0.833	0.672	1	CLONAL	1	TRUE	1	0.293696666770626	2		478	237	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307414	118307416	+	inframe_deletion	In_Frame_Del	DEL	GCG	GCG	-	rs781936420	NA	P-0051727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	11	23	0	ENST00000534358.1:c.200_202del	p.Ala67del	p.A67del	ENST00000534358	NM_005933.3	63	GCG/-	1/36	1	2	FACETS	1	0.763	1	1	0.763	1	CLONAL	1	TRUE	1	0.293696666770626	2		23	68	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894230	NA	P-0051728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	151	503	0	ENST00000451590.1:c.35G>A	p.Gly12Asp	p.G12D	ENST00000451590	NM_001130442.1	12	gGc/gAc	2/5	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.507367784242182	2		503	573	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332882	153332882	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0051729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	82	201	0	ENST00000281708.4:c.74C>G	p.Ser25Ter	p.S25*	ENST00000281708	NM_033632.3	25	tCa/tGa	2/12	1	2	FACETS	0.921	0.817	1	0.921	0.817	1	CLONAL	1	TRUE	1	0.448530480674917	2		201	397	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637539	52637540	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0051730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	90	297	0	ENST00000394830.3:c.2776dup	p.Arg926LysfsTer4	p.R926Kfs*4	ENST00000394830	NM_018313.4	926	aga/aAga	18/30	0.45152504162329	2	FACETS	0.788	0.71	0.868	0.788	0.71	0.868	SUBCLONAL	2	TRUE	0	0.45152504162329	2		297	253	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183734	10183735	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0051730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	96	511	0	ENST00000256474.2:c.204dup	p.Arg69AlafsTer63	p.R69Afs*63	ENST00000256474	NM_000551.3	68	tcg/tcGg	1/3	0.45152504162329	2	FACETS	0.782	0.707	0.859	0.782	0.707	0.859	SUBCLONAL	2	TRUE	0	0.45152504162329	2		511	272	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7150535	7150535	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0051730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	118	495	0	ENST00000302850.5:c.2240C>A	p.Ser747Tyr	p.S747Y	ENST00000302850	NM_000208.2	747	tCt/tAt	11/22	0.0849322595269474	6	FACETS	1	0.941	1	0.699	0.635	0.767	INDETERMINATE	2	TRUE	3	0.45152504162329	6		495	474	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210113	55210113	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0051730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	137	356	0	ENST00000275493.2:c.223G>C	p.Asp75His	p.D75H	ENST00000275493	NM_005228.3	75	Gat/Cat	2/28	0.12578925679445	6	FACETS	0.928	0.852	1	0.928	0.852	1	INDETERMINATE	3	TRUE	3	0.45152504162329	6		356	415	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407966	139407966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0051730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	69	555	0	ENST00000277541.6:c.2231G>A	p.Gly744Glu	p.G744E	ENST00000277541	NM_017617.3	744	gGg/gAg	14/34	1	2	FACETS	0.873	0.765	0.988	0.873	0.765	0.988	CLONAL	1	TRUE	1	0.45152504162329	2		555	350	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223633	53223634	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0051730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	165	313	0	ENST00000375401.3:c.3725dup	p.Leu1243ProfsTer57	p.L1243Pfs*57	ENST00000375401	NM_004187.3	1242	ttc/ttTc	23/26	0.45152504162329	3	FACETS	1	0.976	1			1	CLONAL	3	TRUE	NA	0.45152504162329	3		313	278	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0000259-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	57	534	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.995	0.853	1	0.995	0.853	1	CLONAL	1	TRUE	1	0.17	2		534	674	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86667940	86667940	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000259-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	27	251	0	ENST00000274376.6:c.1704G>A	p.Trp568Ter	p.W568*	ENST00000274376	NM_002890.2	568	tgG/tgA	13/25	1	2	FACETS	0.792	0.63	0.978	0.792	0.63	0.978	CLONAL	1	TRUE	1	0.17	2		251	401	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131926973	131926973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554098400	NA	P-0000259-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	20	139	0	ENST00000265335.6:c.1510G>A	p.Val504Ile	p.V504I	ENST00000265335		504	Gta/Ata	10/25	1	2	FACETS	0.72	0.55	0.918	0.72	0.55	0.918	CLONAL	1	TRUE	1	0.17	2		139	327	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934920	9934920	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	146	393	0	ENST00000330684.3:c.1370A>T	p.Lys457Met	p.K457M	ENST00000330684	NM_001134407.1	457	aAg/aTg	6/13	NA	2	FACETS	1	0.963	1			1	INDETERMINATE	1	TRUE	NA	0.90212401640345	2		393	306	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624421	140624421	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	162	253	0	ENST00000288602.6:c.83G>C	p.Gly28Ala	p.G28A	ENST00000288602	NM_004333.4	28	gGc/gCc	1/18	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.90212401640345	NA		253	728	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003787-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	451	624	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.750205214197131	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.750205214197131	3		624	824	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0003787-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	170	273	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.750205214197131	4	FACETS	0.994	0.926	1	0.994	0.926	1	CLONAL	2	TRUE	2	0.750205214197131	4		273	399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578493	7578493	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1206165503	NA	P-0003787-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	642	949	0	ENST00000269305.4:c.437G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tGg/tAg	5/11	NA	2	FACETS	0.997	0.973	1			1	INDETERMINATE	2	TRUE	NA	0.750205214197131	2		949	858	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155369	99155369	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs954252241	NA	P-0003787-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	303	367	0	ENST00000074304.5:c.595G>A	p.Asp199Asn	p.D199N	ENST00000074304	NM_001134224.1	199	Gat/Aat	9/26	0.365711517034789	6	FACETS	1	0.96	1	1	0.96	1	INDETERMINATE	3	TRUE	3	0.750205214197131	6		367	665	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982743	7982743	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764382022	NA	P-0003787-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	480	790	0	ENST00000319144.4:c.1042G>C	p.Glu348Gln	p.E348Q	ENST00000319144	NM_001139.2	348	Gag/Cag	8/15	0.750205214197131	4	FACETS	0.942	0.902	0.982	0.942	0.902	0.982	CLONAL	2	TRUE	2	0.750205214197131	4		790	1189	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266702	18266702	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003787-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	581	835	1	ENST00000222254.8:c.13G>A	p.Glu5Lys	p.E5K	ENST00000222254	NM_005027.3	5	Gag/Aag	2/16	0.739924048494873	4	FACETS	0.979	0.943	1	0.979	0.943	1	CLONAL	2	TRUE	2	0.750205214197131	4		836	1384	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037866	49037866	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs587778860	NA	P-0003787-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	182	270	0	ENST00000267163.4:c.2107-1G>A		p.X703_splice	ENST00000267163	NM_000321.2	703			NA	2	FACETS	1	0.975	1			1	INDETERMINATE	2	TRUE	NA	0.750205214197131	2		270	236	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268930	55268930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149248025	NA	P-0003787-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	58	658	2	ENST00000275493.2:c.2996G>A	p.Arg999His	p.R999H	ENST00000275493	NM_005228.3	999	cGt/cAt	25/28	0.365711517034789	6	FACETS	0.346	0.296	0.401	0.115	0.098	0.134	INDETERMINATE	1	TRUE	3	0.750205214197131	6		660	1117	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1331525	1331525	+	start_lost	Translation_Start_Site	SNP	C	C	G	novel	NA	P-0003787-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	397	538	0	ENST00000400841.2:c.3G>C	p.Met1?	p.M1?	ENST00000400841		1	atG/atC	1/6	0.739924048494873	4	FACETS	0.986	0.942	1	0.986	0.942	1	CLONAL	2	TRUE	2	0.750205214197131	4		538	939	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005141-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	25	468	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.799	0.631	0.992	0.799	0.631	0.992	CLONAL	1	TRUE	1	0.21	2		468	298	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851785	134851785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005141-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	37	619	0	ENST00000398015.3:c.1191G>A	p.Trp397Ter	p.W397*	ENST00000398015	NM_004441.4	397	tgG/tgA	5/16	1	2	FACETS	0.558	0.459	0.67	0.558	0.459	0.67	SUBCLONAL	1	TRUE	1	0.21	2		619	631	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0005141-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	16	220	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	1	2	FACETS	0.856	0.635	1	0.856	0.635	1	CLONAL	1	TRUE	1	0.21	2		220	178	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161387	185161387	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005141-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	31	415	0	ENST00000265026.3:c.814C>T	p.Leu272Phe	p.L272F	ENST00000265026	NM_004721.4	272	Ctc/Ttc	4/14	1	2	FACETS	0.546	0.44	0.666	0.546	0.44	0.666	SUBCLONAL	1	TRUE	1	0.21	2		415	541	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46608752	46608752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005141-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	138	659	0	ENST00000263734.3:c.2063G>A	p.Gly688Glu	p.G688E	ENST00000263734	NM_001430.4	688	gGg/gAg	13/16	0.211350483954808	3	FACETS	0.949	0.865	1	0.949	0.865	1	CLONAL	2	TRUE	1	0.21	3		659	765	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082488	16082488	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752749374	NA	P-0005141-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	50	604	0	ENST00000281043.3:c.302G>A	p.Gly101Glu	p.G101E	ENST00000281043	NM_005378.4	101	gGa/gAa	2/3	0.211350483954808	3	FACETS	0.777	0.658	0.908	0.389	0.329	0.454	CLONAL	1	TRUE	1	0.21	3		604	677	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182680	38182680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005141-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	35	437	0	ENST00000396334.3:c.833C>T	p.Pro278Leu	p.P278L	ENST00000396334	NM_002468.4	278	cCc/cTc	5/5	1	2	FACETS	0.679	0.556	0.817	0.679	0.556	0.817	SUBCLONAL	1	TRUE	1	0.21	2		437	491	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226589977	226589977	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005141-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	51	545	0	ENST00000366794.5:c.224C>T	p.Ser75Phe	p.S75F	ENST00000366794	NM_001618.3	75	tCt/tTt	2/23	0.195176333765468	4	FACETS	0.734	0.622	0.857	0.367	0.311	0.429	SUBCLONAL	1	TRUE	2	0.21	4		545	801	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154272	2154272	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005141-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	53	722	0	ENST00000434045.2:c.656C>T	p.Thr219Ile	p.T219I	ENST00000434045	NM_001127598.1	219	aCc/aTc	5/5	1	2	FACETS	0.697	0.593	0.811	0.697	0.593	0.811	SUBCLONAL	1	TRUE	1	0.21	2		722	724	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244422	46244422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005141-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	29	417	0	ENST00000334344.6:c.2516G>A	p.Gly839Asp	p.G839D	ENST00000334344	NM_152641.2	839	gGt/gAt	15/21	1	2	FACETS	0.514	0.412	0.632	0.514	0.412	0.632	SUBCLONAL	1	TRUE	1	0.21	2		417	537	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685512	29685512	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005141-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	18	272	0	ENST00000356175.3:c.7922A>G	p.Asp2641Gly	p.D2641G	ENST00000356175	NM_000267.3	2641	gAc/gGc	54/57	1	2	FACETS	0.621	0.468	0.802	0.621	0.468	0.802	SUBCLONAL	1	TRUE	1	0.21	2		272	276	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207572	2207572	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0005141-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	41	501	0	ENST00000398665.3:c.857-1G>A		p.X286_splice	ENST00000398665	NM_032482.2	286			1	2	FACETS	0.685	0.57	0.814	0.685	0.57	0.814	SUBCLONAL	1	TRUE	1	0.21	2		501	570	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211733	36211733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005141-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	56	639	0	ENST00000222270.7:c.1484C>T	p.Pro495Leu	p.P495L	ENST00000222270	NM_014727.1	495	cCc/cTc	3/37	1	2	FACETS	0.848	0.726	0.981	0.848	0.726	0.981	CLONAL	1	TRUE	1	0.21	2		639	629	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46611722	46611722	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005141-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	62	684	1	ENST00000263734.3:c.2536G>A	p.Val846Met	p.V846M	ENST00000263734	NM_001430.4	846	Gtg/Atg	16/16	0.211350483954808	3	FACETS	0.806	0.694	0.927	0.403	0.347	0.464	CLONAL	1	TRUE	1	0.21	3		685	810	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693797	47693797	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1191742655	NA	P-0005141-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	20	228	0	ENST00000233146.2:c.1511G>A	p.Gly504Asp	p.G504D	ENST00000233146	NM_000251.2	504	gGc/gAc	10/16	0.211350483954808	3	FACETS	0.768	0.588	0.979	0.384	0.294	0.49	CLONAL	1	TRUE	1	0.21	3		228	274	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728955	190728955	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0005141-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	23	239	0	ENST00000441310.2:c.2342+1G>A		p.X781_splice	ENST00000441310	NM_000534.4	781			0.211350483954808	3	FACETS	0.764	0.596	0.958	0.382	0.298	0.479	CLONAL	1	TRUE	1	0.21	3		239	317	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074302	30074302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005141-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	40	332	0	ENST00000338641.4:c.1564G>A	p.Glu522Lys	p.E522K	ENST00000338641	NM_000268.3	522	Gag/Aag	14/16	0.170339769767849	2	FACETS	0.96	0.799	1	0.48	0.399	0.569	CLONAL	1	TRUE	0	0.21	2		332	397	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37038124	37038124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63751109	NA	P-0005141-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	33	149	0	ENST00000231790.2:c.131C>T	p.Ser44Phe	p.S44F	ENST00000231790	NM_000249.3	44	tCc/tTc	2/19	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.21	2		149	235	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37081776	37081776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781270312	NA	P-0005141-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	38	282	0	ENST00000231790.2:c.1658C>T	p.Thr553Ile	p.T553I	ENST00000231790	NM_000249.3	553	aCc/aTc	14/19	1	2	FACETS	0.84	0.694	1	0.84	0.694	1	CLONAL	1	TRUE	1	0.21	2		282	431	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268730	41268730	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005141-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	15	277	0	ENST00000349496.5:c.968C>T	p.Ala323Val	p.A323V	ENST00000349496	NM_001904.3	323	gCt/gTt	7/15	1	2	FACETS	0.494	0.361	0.655	0.494	0.361	0.655	SUBCLONAL	1	TRUE	1	0.21	2		277	289	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114614	73114614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005141-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	19	282	0	ENST00000356692.5:c.995C>T	p.Ala332Val	p.A332V	ENST00000356692		332	gCc/gTc	9/9	1	2	FACETS	0.576	0.437	0.74	0.576	0.437	0.74	SUBCLONAL	1	TRUE	1	0.21	2		282	314	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750806	128750806	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005141-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	43	620	0	ENST00000377970.2:c.343G>A	p.Glu115Lys	p.E115K	ENST00000377970	NM_002467.4	115	Gag/Aag	2/3	1	2	FACETS	0.713	0.596	0.844	0.713	0.596	0.844	SUBCLONAL	1	TRUE	1	0.21	2		620	574	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341847	8341847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005141-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	33	462	1	ENST00000356435.5:c.4793C>T	p.Thr1598Ile	p.T1598I	ENST00000356435		1598	aCa/aTa	29/35	NA	2	FACETS	0.619	0.503	0.749			1	INDETERMINATE	1	TRUE	NA	0.21	2		463	508	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268776	98268776	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005141-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	29	425	0	ENST00000331920.6:c.307G>A	p.Val103Ile	p.V103I	ENST00000331920	NM_000264.3	103	Gtt/Att	2/24	1	2	FACETS	0.495	0.396	0.608	0.495	0.396	0.608	SUBCLONAL	1	TRUE	1	0.21	2		425	558	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0005749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	147	352	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	0.926	0.857	0.996	0.926	0.857	0.996	CLONAL	1	TRUE	1	0.877345316198301	2		352	362	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913492	NA	P-0005749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	115	339	0	ENST00000286548.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000286548	NM_002072.3	209	cAa/cTa	5/7	1	2	FACETS	0.96	0.88	1	0.96	0.88	1	CLONAL	1	TRUE	1	0.877345316198301	2		339	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0005873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	72	725	31	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.216269393292649	1	FACETS	0.704	0.614	0.802	0.704	0.614	0.802	SUBCLONAL	1	TRUE	0	0.216269393292649	1		756	843	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708054	117708054	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	31	338	0	ENST00000368508.3:c.2123C>T	p.Ser708Leu	p.S708L	ENST00000368508	NM_002944.2	708	tCa/tTa	14/43	0.216269393292649	1	FACETS	0.759	0.615	0.921	0.759	0.615	0.921	CLONAL	1	TRUE	0	0.216269393292649	1		338	337	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174386	11174386	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	50	796	0	ENST00000361445.4:c.7289G>T	p.Arg2430Met	p.R2430M	ENST00000361445	NM_004958.3	2430	aGg/aTg	53/58	NA	2	FACETS	0.583	0.493	0.682			1	INDETERMINATE	1	TRUE	NA	0.216269393292649	2		796	793	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281837	39281837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374761537	NA	P-0005873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	26	270	0	ENST00000402219.2:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000402219	NM_005633.3	213	cGa/cAa	5/23	1	2	FACETS	0.508	0.402	0.631	0.508	0.402	0.631	SUBCLONAL	1	TRUE	1	0.216269393292649	2		270	473	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798295	45798295	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	148	995	0	ENST00000450313.1:c.641G>T	p.Gly214Val	p.G214V	ENST00000450313	NM_012222.2	214	gGc/gTc	8/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.216269393292649	2		995	1001	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411902	116411902	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0005873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	126	879	0	ENST00000397752.3:c.2888-1G>C		p.X963_splice	ENST00000397752	NM_000245.2	963			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.216269393292649	2		879	863	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248007	59248007	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1355452123	NA	P-0005873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	63	871	0	ENST00000371222.2:c.736G>C	p.Asp246His	p.D246H	ENST00000371222	NM_002228.3	246	Gac/Cac	1/1	1	2	FACETS	0.601	0.518	0.692	0.601	0.518	0.692	SUBCLONAL	1	TRUE	1	0.216269393292649	2		871	969	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969962	81969962	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	64	577	0	ENST00000359376.3:c.3031G>T	p.Ala1011Ser	p.A1011S	ENST00000359376	NM_002661.3	1011	Gca/Tca	27/33	1	2	FACETS	0.988	0.856	1	0.988	0.856	1	CLONAL	1	TRUE	1	0.216269393292649	2		577	599	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434901	56434901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	53	1000	1	ENST00000407977.2:c.2236G>A	p.Glu746Lys	p.E746K	ENST00000407977		746	Gaa/Aaa	9/10	1	2	FACETS	0.508	0.431	0.592	0.508	0.431	0.592	SUBCLONAL	1	TRUE	1	0.216269393292649	2		1001	965	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262283	46262283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	75	473	0	ENST00000371998.3:c.867G>A	p.Met289Ile	p.M289I	ENST00000371998		289	atG/atA	9/23	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.216269393292649	2		473	614	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045021	47045021	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	144	1137	0	ENST00000377604.3:c.2347del	p.Leu783SerfsTer19	p.L783Sfs*19	ENST00000377604	NM_001204468.1	783	Ctc/tc	20/24	0.216269393292649	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.216269393292649	1		1137	1117	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008574-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	380	624	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.736579809985688	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.736579809985688	1		624	630	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115284219	115284219	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008574-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	279	604	0	ENST00000438362.2:c.67T>G	p.Leu23Val	p.L23V	ENST00000438362	NM_001242891.1	23	Tta/Gta	2/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.736579809985688	2		604	741	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667443	241667443	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008574-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	243	483	0	ENST00000366560.3:c.1007T>A	p.Met336Lys	p.M336K	ENST00000366560	NM_000143.3	336	aTg/aAg	7/10	0.726716656933346	3	FACETS	1	0.959	1	0.516	0.483	0.55	CLONAL	1	TRUE	1	0.736579809985688	3		483	875	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435559	18435559	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008574-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	138	338	0	ENST00000266497.5:c.544T>C	p.Phe182Leu	p.F182L	ENST00000266497		182	Ttc/Ctc	1/31	1	2	FACETS	0.986	0.908	1	0.986	0.908	1	CLONAL	1	TRUE	1	0.736579809985688	2		338	380	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353770	40353770	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008574-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	379	732	3	ENST00000293328.3:c.2350C>A	p.His784Asn	p.H784N	ENST00000293328	NM_012448.3	784	Cac/Aac	19/19	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.736579809985688	2		735	1021	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637845	39637845	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0008574-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	186	444	0	ENST00000262039.4:c.2264-2A>C		p.X755_splice	ENST00000262039	NM_002647.2	755			1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.736579809985688	2		444	500	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248543	212248543	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008574-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	348	705	0	ENST00000342788.4:c.3724T>A	p.Tyr1242Asn	p.Y1242N	ENST00000342788	NM_005235.2	1242	Tac/Aac	28/28	1	2	FACETS	0.949	0.9	0.998	0.949	0.9	0.998	CLONAL	1	TRUE	1	0.736579809985688	2		705	996	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508244	106508244	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008574-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	272	653	0	ENST00000359195.3:c.238G>C	p.Glu80Gln	p.E80Q	ENST00000359195	NM_002649.2	80	Gag/Cag	2/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.736579809985688	2		653	714	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978659	70978660	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0008574-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	286	729	0	ENST00000276594.2:c.993_994delinsAA	p.Arg332Ser	p.R332S	ENST00000276594	NM_024504.3	331	gcCCgc/gcAAgc	5/8	1	2	FACETS	0.844	0.795	0.894	0.844	0.795	0.894	CLONAL	1	TRUE	1	0.736579809985688	2		729	920	SUCCESS
AR	367	MSKCC	GRCh37	X	66943552	66943552	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137852578	NA	P-0010523-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	132	215	0	ENST00000374690.3:c.2632A>G	p.Thr878Ala	p.T878A	ENST00000374690	NM_000044.3	878	Act/Gct	8/8	1	1	FACETS	0.846	0.775	0.918	1	0.989	1	CLONAL	2	TRUE	0	0.323076647173152	1		215	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579556	7579557	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0010523-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	169	644	0	ENST00000269305.4:c.130_131del	p.Met44AlafsTer7	p.M44Afs*7	ENST00000269305	NM_001126112.2	44	ATg/g	4/11	0.298747405620461	1	FACETS	0.918	0.843	0.995	0.918	0.843	0.995	CLONAL	1	TRUE	0	0.323076647173152	1		644	956	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	264	468	0				ENST00000310581	NM_198253.2	-/1132			0.366643601797647	6	FACETS	0.915	0.868	0.963	0.915	0.868	0.963	CLONAL	4	TRUE	2	0.584684209622973	6		468	535	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0013150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	798	606	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	0.406302944598362	4	FACETS	1	0.993	1			1	CLONAL	4	TRUE	NA	0.584684209622973	4		606	1049	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132542	11132542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	408	708	0	ENST00000358026.2:c.2758G>A	p.Glu920Lys	p.E920K	ENST00000358026	NM_001128849.1	920	Gag/Aag	19/36	0.478823315262988	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	2	0.584684209622973	4		708	990	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820697	3820703	+	frameshift_variant	Frame_Shift_Del	DEL	GACTGTA	GACTGTA	-	novel	NA	P-0013150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	419	815	0	ENST00000262367.5:c.2748_2754del	p.Thr917ArgfsTer8	p.T917Rfs*8	ENST00000262367	NM_004380.2	916	ccTACAGTC/cc	14/31	0.584684209622973	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.584684209622973	3		815	886	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099864	27099864	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	382	554	0	ENST00000324856.7:c.3743C>A	p.Ser1248Ter	p.S1248*	ENST00000324856	NM_006015.4	1248	tCa/tAa	15/20	0.366643601797647	6	FACETS	0.956	0.916	0.997	0.956	0.916	0.997	CLONAL	4	TRUE	2	0.584684209622973	6		554	741	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833925	44833925	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013150-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	292	246	0	ENST00000377967.4:c.349C>G	p.Gln117Glu	p.Q117E	ENST00000377967	NM_021140.2	117	Cag/Gag	4/29	0.494732449605116	2	FACETS	0.925	0.896	0.952			1	CLONAL	3	TRUE	NA	0.584684209622973	2		246	360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587782529	NA	P-0013978-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	111	669	0	ENST00000269305.4:c.1009C>G	p.Arg337Gly	p.R337G	ENST00000269305	NM_001126112.2	337	Cgc/Ggc	10/11	0.467818244146729	2	FACETS	1	0.979	1	0.64	0.58	0.701	CLONAL	1	FALSE	0	0.467818244146729	2		669	371	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354008	15354008	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014653-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	32	286	0	ENST00000263377.2:c.2872del	p.Leu958CysfsTer110	p.L958Cfs*110	ENST00000263377	NM_058243.2	958	Ctg/tg	14/20	0.217269147533771	5	FACETS	1	0.902	1			1	INDETERMINATE	2	TRUE	NA	0.479900668647828	5		286	102	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691039	NA	P-0014653-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	210	673	1	ENST00000269305.4:c.919+1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.217086817899093	3	FACETS	0.857	0.807	0.907			1	INDETERMINATE	3	TRUE	NA	0.479900668647828	3		674	422	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934384	81934384	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014653-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	28	466	0	ENST00000359376.3:c.1361A>T	p.Lys454Met	p.K454M	ENST00000359376	NM_002661.3	454	aAg/aTg	14/33	0.225181738472289	2	FACETS	0.753	0.609	0.913	0.376	0.304	0.457	INDETERMINATE	1	TRUE	0	0.479900668647828	2		466	155	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0015363-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	660	690	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.574370639829811	3	FACETS	0.859	0.835	0.882	0.859	0.835	0.882	CLONAL	3	TRUE	0	0.670833287412427	3		690	1020	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0015363-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	560	592	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.582546215357906	2	FACETS	0.852	0.823	0.88	0.852	0.823	0.88	CLONAL	2	TRUE	0	0.670833287412427	2		592	980	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259554	55259554	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs397517134	NA	P-0015363-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	645	688	0	ENST00000275493.2:c.2612C>G	p.Ala871Gly	p.A871G	ENST00000275493	NM_005228.3	871	gCa/gGa	21/28	0.574370639829811	3	FACETS	0.861	0.837	0.885	0.861	0.837	0.885	CLONAL	3	TRUE	0	0.670833287412427	3		688	994	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931791	68931791	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015363-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	279	401	0	ENST00000288368.4:c.221T>A	p.Phe74Tyr	p.F74Y	ENST00000288368	NM_024870.2	74	tTc/tAc	3/40	0.545310575532744	2	FACETS	1	0.994	1	0.732	0.695	0.77	CLONAL	1	TRUE	0	0.670833287412427	2		401	568	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243668580	243668580	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016055-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	84	670	0	ENST00000263826.5:c.1411T>C	p.Phe471Leu	p.F471L	ENST00000263826	NM_005465.4	471	Ttt/Ctt	13/13	0.283711170295224	3	FACETS	1	0.893	1			1	CLONAL	1	TRUE	NA	0.401599385594981	3		670	498	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94163103	94163103	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016055-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	71	691	0	ENST00000323929.3:c.2044A>G	p.Lys682Glu	p.K682E	ENST00000323929	NM_005591.3	682	Aaa/Gaa	19/20	0.401599385594981	3	FACETS	0.817	0.714	0.927	0.408	0.357	0.464	CLONAL	1	TRUE	1	0.401599385594981	3		691	520	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670501	134670501	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016055-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	72	1106	0	ENST00000398015.3:c.412G>C	p.Asp138His	p.D138H	ENST00000398015	NM_004441.4	138	Gac/Cac	3/16	0.401599385594981	3	FACETS	0.473	0.412	0.539	0.158	0.137	0.18	SUBCLONAL	1	TRUE	0	0.401599385594981	3		1106	910	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593609	55593611	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	rs121913685	NA	P-0017531-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	1317	477	0	ENST00000288135.5:c.1679_1681del	p.Val560del	p.V560del	ENST00000288135	NM_000222.2	559	GTT/-	11/21	0.818955078076152	6	FACETS	1	0.997	1			1	CLONAL	6	TRUE	NA	0.818955078076152	6		477	1395	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456341	32456341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017717-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	51	769	0	ENST00000332351.3:c.551C>T	p.Pro184Leu	p.P184L	ENST00000332351	NM_024426.4	184	cCg/cTg	1/10	0.593591067894182	3	FACETS	0.426	0.362	0.496	0.213	0.181	0.248	SUBCLONAL	1	TRUE	1	0.593591067894182	3		769	523	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858288	9858288	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017717-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	84	510	0	ENST00000330684.3:c.3113C>G	p.Thr1038Arg	p.T1038R	ENST00000330684	NM_001134407.1	1038	aCa/aGa	13/13	1	2	FACETS	0.979	0.875	1	0.979	0.875	1	CLONAL	1	TRUE	1	0.593591067894182	2		510	289	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859555	151859555	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017717-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	439	591	2	ENST00000262189.6:c.11107G>T	p.Glu3703Ter	p.E3703*	ENST00000262189	NM_170606.2	3703	Gaa/Taa	43/59	0.516930026883712	6	FACETS	1	0.993	1	0.899	0.872	0.925	CLONAL	5	TRUE	0	0.593591067894182	6		593	600	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098955	+	protein_altering_variant	In_Frame_Ins	INS	CCA	CCA	TTGGAGGCAAGATAT	novel	NA	P-0017717-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	84	328	0	ENST00000397062.3:c.90_92delinsATATCTTGCCTCCAA	p.Gly31delinsTyrLeuAlaSerLys	p.G31delinsYLASK	ENST00000397062	NM_006164.4	30	ctTGGa/ctATATCTTGCCTCCAAa	2/5	0.530409888342736	3	FACETS	0.834	0.751	0.92	0.556	0.5	0.613	CLONAL	2	TRUE	0	0.593591067894182	3		328	220	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0017717-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	64	797	0	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	0.234180790902139	4	FACETS	0.577	0.499	0.66	0.288	0.249	0.33	INDETERMINATE	1	TRUE	2	0.593591067894182	4		797	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0018771-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	142	754	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	1	2	FACETS	0.678	0.617	0.742	0.678	0.617	0.742	SUBCLONAL	1	TRUE	1	0.418642163707911	2		754	1001	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974744	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAGCAGCGCCCGCA	CCTCCAGCAGCGCCCGCA	-	novel	NA	P-0018771-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	23	286	0	ENST00000304494.5:c.83_100del	p.Val28_Glu33del	p.V28_E33del	ENST00000304494	NM_000077.4	28	gTGCGGGCGCTGCTGGAGGcg/gcg	1/3	1	2	FACETS	0.277	0.215	0.348	0.277	0.215	0.348	SUBCLONAL	1	TRUE	1	0.418642163707911	2		286	397	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437600	56437600	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018771-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	56	369	0	ENST00000407977.2:c.862A>T	p.Ile288Phe	p.I288F	ENST00000407977		288	Att/Ttt	8/10	1	2	FACETS	0.45	0.385	0.521	0.45	0.385	0.521	SUBCLONAL	1	TRUE	1	0.418642163707911	2		369	594	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217855	7217858	+	frameshift_variant	Frame_Shift_Del	DEL	CTTC	CTTC	-	novel	NA	P-0018771-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	103	526	0	ENST00000380728.2:c.153_156del	p.Lys53ArgfsTer9	p.K53Rfs*9	ENST00000380728		51	agGAAG/ag	3/11	1	2	FACETS	0.624	0.558	0.694	0.624	0.558	0.694	SUBCLONAL	1	TRUE	1	0.418642163707911	2		526	789	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522081	157522082	+	missense_variant	Missense_Mutation	DNP	GC	GC	TA	novel	NA	P-0018771-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	54	550	1	ENST00000346085.5:c.4353_4354delinsTA	p.Leu1452Met	p.L1452M	ENST00000346085	NM_020732.3	1451	ccGCtg/ccTAtg	18/20	1	2	FACETS	0.396	0.338	0.46	0.396	0.338	0.46	SUBCLONAL	1	TRUE	1	0.418642163707911	2		551	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0019607-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	333	454	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.435749947939904	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.435749947939904	2		455	743	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128989	64128989	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019607-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	156	870	0	ENST00000334205.4:c.619G>A	p.Glu207Lys	p.E207K	ENST00000334205	NM_003942.2	207	Gaa/Aaa	6/17	0.435749947939904	4	FACETS	0.861	0.787	0.939	0.43	0.393	0.47	CLONAL	1	TRUE	2	0.435749947939904	4		870	1194	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412045	116412045	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0019607-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	411	674	0	ENST00000397752.3:c.3028+2T>G		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.435749947939904	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.435749947939904	2		674	869	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0020342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	29	476	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.671030569582396	3	FACETS	0.954	0.78	1	0.477	0.39	0.572	CLONAL	1	FALSE	1	0.671030569582396	3		476	121	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405978	49405978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	22	361	0	ENST00000418115.1:c.160G>A	p.Glu54Lys	p.E54K	ENST00000418115	NM_001664.2	54	Gag/Aag	3/5	0.577567345895449	5	FACETS	0.765	0.607	0.938	0.51	0.405	0.626	CLONAL	2	FALSE	2	0.671030569582396	5		361	86	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117321	115117321	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	29	221	0	ENST00000257566.3:c.853C>G	p.Gln285Glu	p.Q285E	ENST00000257566	NM_016569.3	285	Cag/Gag	4/8	0.671030569582396	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	FALSE	0	0.671030569582396	2		221	39	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161703	47161703	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs774624204	NA	P-0020342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	7	0	0	ENST00000409792.3:c.4423C>G	p.Leu1475Val	p.L1475V	ENST00000409792	NM_014159.6	1475	Ctt/Gtt	3/21	0.577567345895449	5	FACETS	0.734	0.465	1	0.245	0.155	0.359	CLONAL	1	FALSE	2	0.671030569582396	5		0	57	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721420	176721420	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020342-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	31	397	0	ENST00000439151.2:c.7051G>A	p.Glu2351Lys	p.E2351K	ENST00000439151	NM_022455.4	2351	Gaa/Aaa	23/23	0.313046164041541	5	FACETS	0.883	0.731	1	0.589	0.487	0.697	INDETERMINATE	2	FALSE	2	0.671030569582396	5		397	105	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438481	52438482	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCGGA	novel	NA	P-0023612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	186	596	0	ENST00000460680.1:c.1237_1238insTCCGA	p.Asn413IlefsTer19	p.N413Ifs*19	ENST00000460680	NM_004656.3	413	aac/aTCCGAac	12/17	0.673547048524921	1	FACETS	0.954	0.894	1	0.954	0.894	1	CLONAL	1	TRUE	0	0.673547048524921	1		596	384	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449820	149449820	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	348	1029	0	ENST00000286301.3:c.1244G>C	p.Gly415Ala	p.G415A	ENST00000286301	NM_005211.3	415	gGc/gCc	9/22	0.673547048524921	2	FACETS	1	0.971	1	0.517	0.49	0.544	CLONAL	1	TRUE	0	0.673547048524921	2		1029	1000	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480360	89480360	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	13	288	0	ENST00000336596.2:c.2197G>A	p.Gly733Ser	p.G733S	ENST00000336596	NM_005233.5	733	Ggc/Agc	13/17	0.673547048524921	1	FACETS	0.141	0.1	0.19	0.141	0.1	0.19	SUBCLONAL	1	TRUE	0	0.673547048524921	1		288	182	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0024083-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	403	454	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.500670034828637	4	FACETS	1	0.993	1	0.853	0.821	0.885	CLONAL	3	TRUE	0	0.552142317008816	4		454	664	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0024083-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	194	608	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.469953058131987	2	FACETS	0.756	0.707	0.805	0.756	0.707	0.805	SUBCLONAL	2	TRUE	0	0.552142317008816	2		608	465	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936091	71936091	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024083-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	61	104	0	ENST00000298229.2:c.63G>A	p.Trp21Ter	p.W21*	ENST00000298229	NM_001567.3	21	tgG/tgA	1/28	0.342570485808393	4	FACETS	0.907	0.797	1	0.907	0.797	1	CLONAL	2	TRUE	2	0.552142317008816	4		104	189	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149793	202149793	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs773127303	NA	P-0024083-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	145	505	0	ENST00000358485.4:c.1234A>G	p.Lys412Glu	p.K412E	ENST00000358485	NM_001080125.1	412	Aaa/Gaa	8/9	0.282933827596347	5	FACETS	1	0.98	1	0.414	0.378	0.452	INDETERMINATE	1	TRUE	2	0.552142317008816	5		505	773	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606986	47606986	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024083-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	163	339	0	ENST00000263735.4:c.736C>G	p.Gln246Glu	p.Q246E	ENST00000263735	NM_002354.2	246	Caa/Gaa	7/9	0.552142317008816	5	FACETS	0.842	0.776	0.911	0.421	0.388	0.456	CLONAL	2	TRUE	1	0.552142317008816	5		339	641	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186507023	186507023	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024083-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	73	202	0	ENST00000323963.5:c.1189G>T	p.Glu397Ter	p.E397*	ENST00000323963		397	Gag/Tag	11/11	0.425271743453706	4	FACETS	0.834	0.74	0.933	0.417	0.37	0.467	CLONAL	2	TRUE	0	0.552142317008816	4		202	246	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324193	31324193	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1476918609	NA	P-0024083-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	215	404	0	ENST00000412585.2:c.370G>A	p.Gly124Ser	p.G124S	ENST00000412585	NM_005514.6	124	Ggc/Agc	3/8	0.342570485808393	4	FACETS	1	0.978	1	1	0.994	1	CLONAL	3	TRUE	2	0.552142317008816	4		404	379	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0025689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	34	361	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.547	0.446	0.661	0.547	0.446	0.661	SUBCLONAL	1	TRUE	1	0.21	2		361	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520000	NA	P-0025689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	36	607	0	ENST00000269305.4:c.452C>A	p.Pro151His	p.P151H	ENST00000269305	NM_001126112.2	151	cCc/cAc	5/11	1	2	FACETS	0.59	0.484	0.709	0.59	0.484	0.709	SUBCLONAL	1	TRUE	1	0.21	2		607	581	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097814	27097814	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0025689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	14	262	0	ENST00000324856.7:c.3404del	p.Pro1135LeufsTer26	p.P1135Lfs*26	ENST00000324856	NM_006015.4	1135	Cct/ct	12/20	1	2	FACETS	0.492	0.355	0.658	0.492	0.355	0.658	SUBCLONAL	1	TRUE	1	0.21	2		262	271	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439935	56439960	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCAGCACCGAAGCCAGGATGATCA	GCGCAGCACCGAAGCCAGGATGATCA	TCG	novel	NA	P-0025689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	55	617	3	ENST00000407977.2:c.632_657delinsCGA	p.Val211AlafsTer40	p.V211Afs*40	ENST00000407977		211	gTGATCATCCTGGCTTCGGTGCTGCGC/gCGA	6/10	1	2	FACETS	0.998	0.854	1	0.998	0.854	1	CLONAL	1	TRUE	1	0.21	2		620	525	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120851	94120851	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs889062730	NA	P-0025689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	40	433	0	ENST00000369303.4:c.200C>T	p.Pro67Leu	p.P67L	ENST00000369303	NM_004440.3	67	cCg/cTg	3/17	1	2	FACETS	0.711	0.59	0.846	0.711	0.59	0.846	SUBCLONAL	1	TRUE	1	0.21	2		433	536	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971167	21971186	+	frameshift_variant	Frame_Shift_Del	DEL	AGCAGCAGCTCCGCCACTCG	AGCAGCAGCTCCGCCACTCG	CGCAGCC	novel	NA	P-0025689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	26	359	2	ENST00000304494.5:c.172_191delinsGGCTGCG	p.Arg58GlyfsTer84	p.R58Gfs*84	ENST00000304494	NM_000077.4	58	CGAGTGGCGGAGCTGCTGCTg/GGCTGCGg	2/3	1	2	FACETS	0.963	0.766	1	0.963	0.766	1	CLONAL	1	TRUE	1	0.21	2		361	257	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578541	7578541	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027054-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	628	656	0	ENST00000269305.4:c.389T>A	p.Leu130His	p.L130H	ENST00000269305	NM_001126112.2	130	cTc/cAc	5/11	0.88610214846233	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.88610214846233	1		656	731	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875981	76875984	+	frameshift_variant	Frame_Shift_Del	DEL	ACAA	ACAA	-	novel	NA	P-0027054-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	271	255	0	ENST00000373344.5:c.5151_5154del	p.Cys1718MetfsTer6	p.C1718Mfs*6	ENST00000373344	NM_000489.3	1717	gtTTGT/gt	20/35	0.88610214846233	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.88610214846233	1		255	336	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923159	48923159	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027054-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	179	201	0	ENST00000267163.4:c.607+1del		p.G203fs	ENST00000267163	NM_000321.2	203	Ggg/gg	6/27	0.88610214846233	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.88610214846233	1		201	221	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692817	89692819	+	inframe_deletion	In_Frame_Del	DEL	ATC	ATC	-	novel	NA	P-0027054-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	166	193	0	ENST00000371953.3:c.302_304del	p.Ile101del	p.I101del	ENST00000371953	NM_000314.4	101	ATC/-	5/9	0.88610214846233	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.88610214846233	1		193	208	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185570	27185570	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027054-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	498	478	0	ENST00000380036.4:c.1270T>A	p.Cys424Ser	p.C424S	ENST00000380036	NM_000459.3	424	Tgc/Agc	9/23	0.88610214846233	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.88610214846233	1		478	579	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0027467-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	134	223	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.402064049907145	4	FACETS	0.958	0.876	1	0.958	0.876	1	CLONAL	2	TRUE	2	0.402064049907145	4		223	488	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937769	76937770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027467-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	228	324	0	ENST00000373344.5:c.2978dup	p.Lys994GlufsTer6	p.K994Efs*6	ENST00000373344	NM_000489.3	993	aag/aaAg	9/35	0.327079727878718	2	FACETS	0.894	0.846	0.941			1	CLONAL	3	TRUE	NA	0.402064049907145	2		324	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0027467-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	728	805	1	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.402064049907145	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	4	TRUE	0	0.402064049907145	4		806	1246	SUCCESS
ATR	545	MSKCC	GRCh37	3	142241628	142241628	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027467-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	180	539	0	ENST00000350721.4:c.4208del	p.Ala1403ValfsTer52	p.A1403Vfs*52	ENST00000350721	NM_001184.3	1403	gCt/gt	23/47	0.368434085371189	5	FACETS	0.808	0.746	0.873	0.539	0.497	0.582	CLONAL	2	TRUE	2	0.402064049907145	5		539	888	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133565	55133565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027467-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3443	396	650	0	ENST00000257290.5:c.869G>A	p.Cys290Tyr	p.C290Y	ENST00000257290	NM_006206.4	290	tGt/tAt	6/23	0.402064049907145	30	FACETS	1	0.987	1			1	CLONAL	3	TRUE	NA	0.402064049907145	30		650	3839	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0028255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	60	662	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.17	2		662	669	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0028255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	65	537	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	0.87	0.752	0.998	0.87	0.752	0.998	CLONAL	1	TRUE	1	0.17	2		537	879	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058090	27058104	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCGCAGGTAAGATAT	CCGCAGGTAAGATAT	-	novel	NA	P-0028255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	35	356	0	ENST00000324856.7:c.1800_1803+11del		p.X600_splice	ENST00000324856	NM_006015.4	600		3/20	1	2	FACETS	0.86	0.704	1	0.86	0.704	1	CLONAL	1	TRUE	1	0.17	2		356	479	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247338	153247338	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	49	338	0	ENST00000281708.4:c.1464del	p.Ile488MetfsTer10	p.I488Mfs*10	ENST00000281708	NM_033632.3	488	atT/at	10/12	1	2	FACETS	0.838	0.708	0.981	0.838	0.708	0.981	CLONAL	1	TRUE	1	0.17	2		338	688	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	28	413	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	1	0.224174111370727	2		413	182	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0029281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	68	662	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.957	0.832	1	0.957	0.832	1	CLONAL	1	FALSE	1	0.224174111370727	2		662	634	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970912	21971408	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCGCGGCATCTATGCGGGCATGGTTACTGCCTCTGGTGCCCCCCGCAGCCGCGCGCAGGTACCGTGCGACATCGCGATGGCCCAGCTCCTCAGCCAGGTCCACGGGCAGACGGCCCCAGGCATCGCGCACGTCCAGCCGCGCCCCGGCCCGGTGCAGCACCACCAGCGTGTCCAGGAAGCCCTCCCGGGCAGCGTCGTGCACGGGTCGGGTGAGAGTGGCGGGGTCGGCGCAGTTGGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCTGCCCATCATCATGACCTGCCAGAGAGAACAGAATGGTCAGAGCCAGGGTGGGGGCCGGCATGACGGAAAGGAAGCTTGTGTAGAGCCCCCTCACCGCCAAGCAGACCCCCACACAAGCCCCAGGTGTCTAATTACCCCTACATTTGCTTCCAGTTTCCAATTTCCTTCTTGAGTTCTCTATCCATTCTTCAGTACACAATGAATTCCATTATATCC	TCCGCGGCATCTATGCGGGCATGGTTACTGCCTCTGGTGCCCCCCGCAGCCGCGCGCAGGTACCGTGCGACATCGCGATGGCCCAGCTCCTCAGCCAGGTCCACGGGCAGACGGCCCCAGGCATCGCGCACGTCCAGCCGCGCCCCGGCCCGGTGCAGCACCACCAGCGTGTCCAGGAAGCCCTCCCGGGCAGCGTCGTGCACGGGTCGGGTGAGAGTGGCGGGGTCGGCGCAGTTGGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCTGCCCATCATCATGACCTGCCAGAGAGAACAGAATGGTCAGAGCCAGGGTGGGGGCCGGCATGACGGAAAGGAAGCTTGTGTAGAGCCCCCTCACCGCCAAGCAGACCCCCACACAAGCCCCAGGTGTCTAATTACCCCTACATTTGCTTCCAGTTTCCAATTTCCTTCTTGAGTTCTCTATCCATTCTTCAGTACACAATGAATTCCATTATATCC	-	novel	NA	P-0029281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	61	736	0	ENST00000304494.5:c.151-201_446del		p.X51_splice	ENST00000304494	NM_000077.4	51		2/3	1	2	FACETS	0.945	0.815	1	0.945	0.815	1	CLONAL	1	FALSE	1	0.224174111370727	2		736	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0029428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	544	568	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.530293226609815	3	FACETS	0.877	0.848	0.905	0.877	0.848	0.905	CLONAL	3	TRUE	0	0.59598852593385	3		568	901	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243926	41243926	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0029428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	408	495	1	ENST00000357654.3:c.3622A>T	p.Lys1208Ter	p.K1208*	ENST00000357654	NM_007294.3	1208	Aaa/Taa	10/23	0.530293226609815	3	FACETS	0.878	0.845	0.91	0.878	0.845	0.91	CLONAL	3	TRUE	0	0.59598852593385	3		496	675	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521562	46521562	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	272	427	0	ENST00000262741.5:c.846G>C	p.Lys282Asn	p.K282N	ENST00000262741	NM_003629.3	282	aaG/aaC	7/10	0.59598852593385	4	FACETS	0.903	0.85	0.956			1	CLONAL	2	TRUE	NA	0.59598852593385	4		427	807	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565503	41565507	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATAGG	ATAGG	-	novel	NA	P-0029428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	104	211	1	ENST00000263253.7:c.4173-3_4174del		p.X1391_splice	ENST00000263253	NM_001429.3	1391		26/31	0.59598852593385	4	FACETS	0.89	0.807	0.975	0.89	0.807	0.975	CLONAL	2	TRUE	2	0.59598852593385	4		212	313	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492937	8492937	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1373453870	NA	P-0029428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	285	504	0	ENST00000356435.5:c.2392C>G	p.Leu798Val	p.L798V	ENST00000356435		798	Ctc/Gtc	16/35	0.549907621996381	6	FACETS	0.895	0.841	0.951	0.448	0.42	0.476	CLONAL	2	TRUE	2	0.59598852593385	6		504	1171	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0030048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	56	382	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.154146052695564	1	FACETS	0.986	0.849	1	1	0.977	1	CLONAL	2	TRUE	0	0.154146052695564	1		382	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0030048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	123	568	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.154146052695564	1	FACETS	0.844	0.765	0.925	1	0.991	1	CLONAL	3	TRUE	0	0.154146052695564	1		568	582	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	77	476	3	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	0.127069801572003	3	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	1	0.154146052695564	3		479	482	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0030048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	48	328	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.154146052695564	0	FACETS	1	0.872	1			1	CLONAL	2	TRUE	0	0.154146052695564	0		328	257	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	109	515	2	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	0.127069801572003	3	FACETS	0.989	0.888	1	0.989	0.888	1	CLONAL	2	TRUE	1	0.154146052695564	3		517	770	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015230	128015230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs189511674	NA	P-0030048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	68	419	1	ENST00000285398.2:c.2291C>T	p.Ser764Leu	p.S764L	ENST00000285398	NM_000122.1	764	tCg/tTg	15/15	1	2	FACETS	0.939	0.819	1	1	0.98	1	CLONAL	2	TRUE	1	0.154146052695564	2		420	470	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882050	36882050	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs780753361	NA	P-0030048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	100	742	5	ENST00000358127.4:c.963del	p.Ala322LeufsTer11	p.A322Lfs*11	ENST00000358127	NM_001280556.1	321	ccC/cc	8/10	1	2	FACETS	0.973	0.87	1	1	0.987	1	CLONAL	2	TRUE	1	0.154146052695564	2		747	667	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637539	52637540	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	39	283	0	ENST00000394830.3:c.2776dup	p.Arg926LysfsTer4	p.R926Kfs*4	ENST00000394830	NM_018313.4	926	aga/aAga	18/30	0.152305660310789	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	2	TRUE	0	0.154146052695564	2		283	251	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505443	157505443	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554231830	NA	P-0030048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	20	331	0	ENST00000346085.5:c.3428del	p.Lys1143SerfsTer68	p.K1143Sfs*68	ENST00000346085	NM_020732.3	1142	Aaa/aa	13/20	0.152305660310789	2	FACETS	0.667	0.509	0.853	0.334	0.254	0.427	SUBCLONAL	1	TRUE	0	0.154146052695564	2		331	389	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891687	28891687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	88	503	0	ENST00000282397.4:c.3334C>T	p.Arg1112Cys	p.R1112C	ENST00000282397	NM_002019.4	1112	Cgc/Tgc	25/30	1	2	FACETS	0.855	0.761	0.955	1	0.988	1	CLONAL	3	TRUE	1	0.154146052695564	2		503	445	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483963	212483963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	34	310	0	ENST00000342788.4:c.2240C>T	p.Pro747Leu	p.P747L	ENST00000342788	NM_005235.2	747	cCt/cTt	19/28	1	2	FACETS	1	0.847	1	1	0.964	1	CLONAL	2	TRUE	1	0.154146052695564	2		310	214	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321073	137321073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768721235	NA	P-0030048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	62	507	2	ENST00000481739.1:c.1030G>A	p.Ala344Thr	p.A344T	ENST00000481739	NM_002957.4	344	Gcc/Acc	7/10	1	2	FACETS	0.951	0.824	1	1	0.978	1	CLONAL	2	TRUE	1	0.154146052695564	2		509	423	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156918	89156920	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	rs768142526	NA	P-0030048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	60	415	0	ENST00000336596.2:c.27_29del	p.Leu11del	p.L11del	ENST00000336596	NM_005233.5	7	aTCCtc/atc	1/17	1	2	FACETS	0.893	0.771	1	1	0.976	1	CLONAL	2	TRUE	1	0.154146052695564	2		415	436	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310518	65310518	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1307956862	NA	P-0030048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	79	462	1	ENST00000342505.4:c.2170C>T	p.Arg724Cys	p.R724C	ENST00000342505	NM_002227.2	724	Cgt/Tgt	16/25	0.127069801572003	3	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	1	0.154146052695564	3		463	491	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612809	228612809	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773691912	NA	P-0030048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	94	716	1	ENST00000366696.1:c.218G>A	p.Arg73His	p.R73H	ENST00000366696	NM_003493.2	73	cGc/cAc	1/1	0.127069801572003	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.154146052695564	3		717	540	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495355	149495355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600485	NA	P-0030048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	77	605	0	ENST00000261799.4:c.3292C>T	p.Arg1098Trp	p.R1098W	ENST00000261799	NM_002609.3	1098	Cgg/Tgg	23/23	1	2	FACETS	1	0.917	1	1	0.984	1	CLONAL	2	TRUE	1	0.154146052695564	2		605	475	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048561	180048562	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	80	631	0	ENST00000261937.6:c.2000dup	p.Lys668GlufsTer104	p.K668Efs*104	ENST00000261937	NM_182925.4	667	aag/aaAg	13/30	1	2	FACETS	0.878	0.778	0.985	1	0.987	1	CLONAL	3	TRUE	1	0.154146052695564	2		631	394	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056155	26056155	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	60	341	0	ENST00000343677.2:c.502A>G	p.Lys168Glu	p.K168E	ENST00000343677	NM_005319.3	168	Aag/Gag	1/1	0.152305660310789	2	FACETS	0.963	0.833	1	0.963	0.833	1	CLONAL	2	TRUE	0	0.154146052695564	2		341	404	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439613	140439614	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0030048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	57	295	0	ENST00000288602.6:c.2125dup	p.Gln709ProfsTer7	p.Q709Pfs*7	ENST00000288602	NM_004333.4	709	caa/cCaa	17/18	1	2	FACETS	1	0.893	1	1	0.978	1	CLONAL	2	TRUE	1	0.154146052695564	2		295	355	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561430	141561430	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	144	455	1	ENST00000220592.5:c.1375del	p.Gln459SerfsTer9	p.Q459Sfs*9	ENST00000220592	NM_012154.3	459	Cag/ag	11/19	0.127069801572003	3	FACETS	0.903	0.828	0.981	1	0.99	1	CLONAL	4	TRUE	1	0.154146052695564	3		456	557	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471057	8471057	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	31	252	0	ENST00000356435.5:c.3442A>G	p.Lys1148Glu	p.K1148E	ENST00000356435		1148	Aag/Gag	20/35	1	2	FACETS	0.779	0.633	0.943	1	0.946	1	CLONAL	2	TRUE	1	0.154146052695564	2		252	258	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262762	16262762	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0030048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	14	227	0	ENST00000375759.3:c.10026+1G>A		p.X3342_splice	ENST00000375759	NM_015001.2	3342			0.127069801572003	3	FACETS	0.699	0.504	0.934	0.349	0.252	0.467	SUBCLONAL	1	TRUE	1	0.154146052695564	3		227	280	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143240	30143240	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057065255	NA	P-0030048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	24	686	0	ENST00000389048.3:c.286G>A	p.Ala96Thr	p.A96T	ENST00000389048	NM_004304.4	96	Gcc/Acc	1/29	1	2	FACETS	0.703	0.55	0.88	0.703	0.55	0.88	SUBCLONAL	1	TRUE	1	0.154146052695564	2		686	443	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170015100	170015100	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	22	373	0	ENST00000295797.4:c.1506G>T	p.Lys502Asn	p.K502N	ENST00000295797	NM_002740.5	502	aaG/aaT	16/18	1	2	FACETS	0.673	0.521	0.851	0.673	0.521	0.851	SUBCLONAL	1	TRUE	1	0.154146052695564	2		373	424	SUCCESS
APC	324	MSKCC	GRCh37	5	112173592	112173592	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030048-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	12	223	0	ENST00000257430.4:c.2301G>T	p.Gln767His	p.Q767H	ENST00000257430	NM_000038.5	767	caG/caT	16/16	1	2	FACETS	0.79	0.556	1	0.79	0.556	1	CLONAL	1	TRUE	1	0.154146052695564	2		223	197	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720649	89720649	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs587782455	NA	P-0030465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	60	350	2	ENST00000371953.3:c.802-2A>T		p.X268_splice	ENST00000371953	NM_000314.4	268			0.403877667052318	1	FACETS	0.941	0.82	1	0.941	0.82	1	CLONAL	1	TRUE	0	0.403877667052318	1		352	252	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720649	89720649	+	splice_acceptor_variant	Splice_Site	DEL	A	A	-	rs886047397	NA	P-0030465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	14	352	0	ENST00000371953.3:c.802-2del		p.X268_splice	ENST00000371953	NM_000314.4	268			0.403877667052318	1	FACETS	0.22	0.158	0.294	0.22	0.158	0.294	SUBCLONAL	1	TRUE	0	0.403877667052318	1		352	252	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577146	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0030465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	106	611	0	ENST00000269305.4:c.792_794del	p.Leu265del	p.L265del	ENST00000269305	NM_001126112.2	264	ctACTg/ctg	8/11	1	2	FACETS	0.788	0.707	0.874	0.788	0.707	0.874	SUBCLONAL	1	TRUE	1	0.403877667052318	2		611	666	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577144	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	120	611	0	ENST00000269305.4:c.794T>G	p.Leu265Arg	p.L265R	ENST00000269305	NM_001126112.2	265	cTg/cGg	8/11	1	2	FACETS	0.892	0.807	0.982	0.892	0.807	0.982	CLONAL	1	TRUE	1	0.403877667052318	2		611	666	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442932	49442932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886049484	NA	P-0030465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	151	700	1	ENST00000301067.7:c.3976C>T	p.Arg1326Trp	p.R1326W	ENST00000301067	NM_003482.3	1326	Cgg/Tgg	12/54	1	2	FACETS	0.955	0.874	1	0.955	0.874	1	CLONAL	1	TRUE	1	0.403877667052318	2		701	783	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456452	32456452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	128	726	0	ENST00000332351.3:c.440G>A	p.Gly147Asp	p.G147D	ENST00000332351	NM_024426.4	147	gGc/gAc	1/10	1	2	FACETS	0.978	0.889	1	0.978	0.889	1	CLONAL	1	TRUE	1	0.403877667052318	2		726	648	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696422	47696422	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	103	475	0	ENST00000347630.2:c.401A>C	p.Lys134Thr	p.K134T	ENST00000347630	NM_001007230.1	134	aAg/aCg	6/11	1	2	FACETS	0.856	0.768	0.949	0.856	0.768	0.949	CLONAL	1	TRUE	1	0.403877667052318	2		475	596	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0030833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	76	413	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.816	0.716	0.922	0.816	0.716	0.922	CLONAL	1	TRUE	1	0.323590872374584	2		413	576	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726951	46726951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141226335	NA	P-0030833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	69	394	0	ENST00000371975.4:c.785G>A	p.Arg262His	p.R262H	ENST00000371975	NM_003579.3	262	cGt/cAt	8/18	1	2	FACETS	0.806	0.703	0.917	0.806	0.703	0.917	CLONAL	1	TRUE	1	0.323590872374584	2		394	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579366	7579366	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	138	715	0	ENST00000269305.4:c.321del	p.Tyr107Ter	p.Y107*	ENST00000269305	NM_001126112.2	107	taC/ta	4/11	0.323590872374584	1	FACETS	0.915	0.834	1	0.915	0.834	1	CLONAL	1	TRUE	0	0.323590872374584	1		715	781	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492920	56492920	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	48	222	0	ENST00000407977.2:c.19del	p.Leu7CysfsTer11	p.L7Cfs*11	ENST00000407977		7	Ctg/tg	2/10	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.323590872374584	2		222	235	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851767	63851767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031015-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	158	500	0	ENST00000279873.7:c.2545C>T	p.His849Tyr	p.H849Y	ENST00000279873	NM_032199.2	849	Cat/Tat	10/10	1	2	FACETS	0.844	0.783	0.905	1	0.991	1	CLONAL	2	TRUE	1	0.491349086979841	2		500	381	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217653	7217654	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0031015-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	23	363	0	ENST00000380728.2:c.273_274del	p.Lys92SerfsTer4	p.K92Sfs*4	ENST00000380728		91	aaGAaa/aaaa	4/11	0.491349086979841	1	FACETS	0.308	0.241	0.386	0.308	0.241	0.386	SUBCLONAL	1	TRUE	0	0.491349086979841	1		363	229	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038879	12038879	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031137-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	47	404	0	ENST00000396373.4:c.1172A>G	p.Tyr391Cys	p.Y391C	ENST00000396373	NM_001987.4	391	tAt/tGt	7/8	0.440044758097738	3	FACETS	0.582	0.491	0.681	0.291	0.245	0.341	SUBCLONAL	1	FALSE	1	0.440044758097738	3		404	448	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729084	66729100	+	protein_altering_variant	In_Frame_Del	DEL	CTAATTCATCTGGAGAT	CTAATTCATCTGGAGAT	GAGAG	novel	NA	P-0031137-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	197	658	2	ENST00000307102.5:c.292_308delinsGAGAG	p.Leu98_Ile103delinsGluSer	p.L98_I103delinsES	ENST00000307102	NM_002755.3	98	CTAATTCATCTGGAGATc/GAGAGc	3/11	0.381210943453599	2	FACETS	0.795	0.741	0.85	0.795	0.741	0.85	SUBCLONAL	2	FALSE	0	0.440044758097738	2		660	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578525	7578525	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519976	NA	P-0031137-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	275	910	0	ENST00000269305.4:c.405C>G	p.Cys135Trp	p.C135W	ENST00000269305	NM_001126112.2	135	tgC/tgG	5/11	NA	2	FACETS	0.839	0.791	0.887			1	INDETERMINATE	2	FALSE	NA	0.440044758097738	2		910	745	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841814	151841814	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031137-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	208	339	0	ENST00000262189.6:c.14327del	p.Ala4776AspfsTer34	p.A4776Dfs*34	ENST00000262189	NM_170606.2	4776	gCa/ga	55/59	0.440044758097738	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	FALSE	1	0.440044758097738	4		339	433	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033244-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	89	626	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.265350936169392	1	FACETS	0.793	0.704	0.887	0.793	0.704	0.887	SUBCLONAL	1	TRUE	0	0.331470544400166	1		626	565	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807889	1807889	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs78311289	NA	P-0033709-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	377	926	0	ENST00000260795.2:c.1948A>G	p.Lys650Glu	p.K650E	ENST00000260795		650	Aag/Gag	13/17	1	2	FACETS	0.976	0.927	1	0.976	0.927	1	CLONAL	1	TRUE	1	0.616769886124351	2		926	1252	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120787	115120787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033709-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	355	625	0	ENST00000257566.3:c.219G>T	p.Glu73Asp	p.E73D	ENST00000257566	NM_016569.3	73	gaG/gaT	1/8	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.616769886124351	2		625	1004	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442667	442667	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033709-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	236	462	0	ENST00000399788.2:c.1639G>C	p.Glu547Gln	p.E547Q	ENST00000399788	NM_001042603.1	547	Gag/Cag	12/28	NA	2	FACETS	0.99	0.927	1			1	INDETERMINATE	1	TRUE	NA	0.616769886124351	2		462	773	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609887	117609887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749542060	NA	P-0033709-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	180	425	0	ENST00000368508.3:c.6812G>A	p.Gly2271Glu	p.G2271E	ENST00000368508	NM_002944.2	2271	gGg/gAg	43/43	0.616769886124351	1	FACETS	0.994	0.929	1	0.994	0.929	1	CLONAL	1	TRUE	0	0.616769886124351	1		425	406	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41242998	41242998	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs80357071	NA	P-0033709-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	116	420	0	ENST00000357654.3:c.4148C>G	p.Ser1383Ter	p.S1383*	ENST00000357654	NM_007294.3	1383	tCa/tGa	11/23	1	2	FACETS	0.548	0.495	0.605	0.548	0.495	0.605	SUBCLONAL	1	TRUE	1	0.616769886124351	2		420	686	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	33	468	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.818	1	1	0.818	1	CLONAL	1	TRUE	1	0.14	2		468	469	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519938	NA	P-0035076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	29	312	0	ENST00000263967.3:c.1034A>C	p.Asn345Thr	p.N345T	ENST00000263967	NM_006218.2	345	aAt/aCt	5/21	1	2	FACETS	0.714	0.572	0.877	0.714	0.572	0.877	SUBCLONAL	1	TRUE	1	0.14	2		312	580	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442078	52442078	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0035076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	61	612	0	ENST00000460680.1:c.271del	p.Cys91ValfsTer7	p.C91Vfs*7	ENST00000460680	NM_004656.3	91	Tgt/gt	5/17	1	2	FACETS	0.912	0.784	1	0.912	0.784	1	CLONAL	1	TRUE	1	0.14	2		612	956	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0035340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	523	1017	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.721947392796973	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.721947392796973	2		1017	680	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221322	1221322	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	485	758	0	ENST00000326873.7:c.845T>G	p.Leu282Arg	p.L282R	ENST00000326873	NM_000455.4	282	cTc/cGc	6/10	0.721947392796973	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.721947392796973	2		758	632	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494637	2494637	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	401	844	1	ENST00000355716.4:c.777G>T	p.Gln259His	p.Q259H	ENST00000355716	NM_003820.2	259	caG/caT	8/8	0.721947392796973	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.721947392796973	2		845	518	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431922	49431922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	536	813	2	ENST00000301067.7:c.9217G>A	p.Val3073Ile	p.V3073I	ENST00000301067	NM_003482.3	3073	Gta/Ata	34/54	0.721947392796973	5	FACETS	1	0.975	1			1	CLONAL	3	TRUE	NA	0.721947392796973	5		815	1017	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112464	115112464	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	620	788	1	ENST00000257566.3:c.1276G>T	p.Gly426Trp	p.G426W	ENST00000257566	NM_016569.3	426	Ggg/Tgg	7/8	0.721947392796973	3	FACETS	0.932	0.909	0.955	1	0.998	1	CLONAL	3	TRUE	1	0.721947392796973	3		789	836	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251135	251135	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	130	222	0	ENST00000264932.6:c.1580G>T	p.Arg527Leu	p.R527L	ENST00000264932	NM_004168.2	527	cGt/cTt	12/15	0.721947392796973	5	FACETS	0.893	0.825	0.961	0.893	0.825	0.961	CLONAL	3	TRUE	2	0.721947392796973	5		222	280	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141568600	141568600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	233	722	1	ENST00000220592.5:c.862C>T	p.Pro288Ser	p.P288S	ENST00000220592	NM_012154.3	288	Ccc/Tcc	7/19	0.721947392796973	3	FACETS	1	0.961	1	0.519	0.485	0.554	CLONAL	1	TRUE	1	0.721947392796973	3		723	846	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435625	18435625	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	64	225	0	ENST00000266497.5:c.610T>A	p.Ser204Thr	p.S204T	ENST00000266497		204	Tct/Act	1/31	0.721947392796973	12	FACETS	0.825	0.712	0.948			1	CLONAL	1	TRUE	NA	0.721947392796973	12		225	991	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28901669	28901669	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	90	348	0	ENST00000282397.4:c.2726T>A	p.Val909Asp	p.V909D	ENST00000282397	NM_002019.4	909	gTt/gAt	20/30	0.721947392796973	3	FACETS	0.93	0.832	1	0.465	0.416	0.517	CLONAL	1	TRUE	1	0.721947392796973	3		348	365	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270181	198270181	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	107	278	1	ENST00000335508.6:c.1255G>T	p.Ala419Ser	p.A419S	ENST00000335508	NM_012433.2	419	Gct/Tct	10/25	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.721947392796973	2		279	259	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138624	55138624	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	170	490	0	ENST00000257290.5:c.1301G>T	p.Arg434Met	p.R434M	ENST00000257290	NM_006206.4	434	aGg/aTg	9/23	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.721947392796973	2		490	455	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973882	131973883	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0035340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	96	305	0	ENST00000265335.6:c.3585_3586delinsCT	p.Leu1195_Asp1196delinsPheTyr	p.L1195_D1196delinsFY	ENST00000265335		1195	ttGGat/ttCTat	23/25	1	2	FACETS	0.95	0.858	1	0.95	0.858	1	CLONAL	1	TRUE	1	0.721947392796973	2		305	280	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534566	140534566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	117	347	0	ENST00000288602.6:c.347C>T	p.Ser116Leu	p.S116L	ENST00000288602	NM_004333.4	116	tCa/tTa	3/18	0.721947392796973	3	FACETS	1	0.935	1	0.518	0.47	0.567	CLONAL	1	TRUE	1	0.721947392796973	3		347	426	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0035511-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	96	225	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	1	2	FACETS	0.787	0.705	0.874	1	0.983	1	SUBCLONAL	2	TRUE	1	0.271503969174358	2		225	449	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175945	176175945	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370981350	NA	P-0035511-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	51	149	1	ENST00000367669.3:c.170G>A	p.Gly57Asp	p.G57D	ENST00000367669	NM_022457.5	57	gGc/gAc	1/20	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.271503969174358	2		150	370	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574565	64574565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060499973	NA	P-0035511-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	59	666	0	ENST00000312049.6:c.830C>T	p.Pro277Leu	p.P277L	ENST00000312049	NM_130799.2	277	cCc/cTc	6/10	1	2	FACETS	0.856	0.737	0.984	0.856	0.737	0.984	CLONAL	1	TRUE	1	0.271503969174358	2		666	508	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180535	94180535	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035511-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	45	372	0	ENST00000323929.3:c.1633C>T	p.Leu545Phe	p.L545F	ENST00000323929	NM_005591.3	545	Ctt/Ttt	15/20	0.271503969174358	1	FACETS	0.858	0.724	1	0.858	0.724	1	CLONAL	1	TRUE	0	0.271503969174358	1		372	334	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348011	89348011	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035511-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	74	767	0	ENST00000301030.4:c.4939C>T	p.Pro1647Ser	p.P1647S	ENST00000301030	NM_001256183.1	1647	Cct/Tct	9/13	0.214494266854928	1	FACETS	0.754	0.66	0.855	0.754	0.66	0.855	SUBCLONAL	1	TRUE	0	0.271503969174358	1		767	625	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796963	78796963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035511-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	116	476	0	ENST00000306801.3:c.1076C>T	p.Ser359Leu	p.S359L	ENST00000306801	NM_020761.2	359	tCg/tTg	9/34	0.210705624229709	2	FACETS	0.937	0.85	1	0.937	0.85	1	CLONAL	2	TRUE	0	0.271503969174358	2		476	456	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636966	158636967	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AT	novel	NA	P-0035511-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	24	471	0	ENST00000263640.3:c.213_214delinsAT	p.Phe71_Gln72delinsLeuTer	p.F71_Q72delinsL*	ENST00000263640	NM_001105.4	71	ttCCag/ttATag	4/11	0.140307156295006	4	FACETS	0.513	0.402	0.642	0.257	0.201	0.322	INDETERMINATE	1	TRUE	2	0.271503969174358	4		471	438	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733280	40733280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370508724	NA	P-0035511-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	55	483	0	ENST00000373198.4:c.3526C>T	p.Arg1176Cys	p.R1176C	ENST00000373198	NM_133170.3	1176	Cgt/Tgt	26/32	0.157837762660902	5	FACETS	1	0.912	1	0.364	0.311	0.422	INDETERMINATE	1	TRUE	2	0.271503969174358	5		483	522	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0035511-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	10	238	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	0.15509323513799	3	FACETS	0.395	0.267	0.555	0.197	0.133	0.278	INDETERMINATE	1	TRUE	1	0.271503969174358	3		238	212	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197387	26197387	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1344624542	NA	P-0035511-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	68	407	0	ENST00000356476.2:c.92C>T	p.Pro31Leu	p.P31L	ENST00000356476		31	cCa/cTa	1/1	0.271503969174358	3	FACETS	0.991	0.863	1	0.496	0.431	0.565	CLONAL	1	TRUE	1	0.271503969174358	3		407	574	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188355	32188355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035511-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	104	673	0	ENST00000375023.3:c.986G>A	p.Gly329Glu	p.G329E	ENST00000375023	NM_004557.3	329	gGg/gAg	6/30	0.15509323513799	3	FACETS	1	0.968	1	0.603	0.54	0.67	INDETERMINATE	1	TRUE	1	0.271503969174358	3		673	721	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229226	55229227	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0035511-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	89	556	0	ENST00000275493.2:c.1533_1534delinsTT	p.Pro512Ser	p.P512S	ENST00000275493	NM_005228.3	511	tcCCcc/tcTTcc	13/28	0.271503969174358	3	FACETS	1	0.972	1	0.658	0.584	0.736	CLONAL	1	TRUE	1	0.271503969174358	3		556	566	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740573	145740573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573164516	NA	P-0035511-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	123	808	0	ENST00000428558.2:c.1444C>T	p.Arg482Cys	p.R482C	ENST00000428558	NM_004260.3	482	Cgc/Tgc	8/22	0.15509323513799	3	FACETS	1	0.962	1	0.564	0.51	0.622	INDETERMINATE	1	TRUE	1	0.271503969174358	3		808	912	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126432	5126432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035511-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	28	259	0	ENST00000381652.3:c.3277G>A	p.Gly1093Arg	p.G1093R	ENST00000381652	NM_004972.3	1093	Gga/Aga	24/25	NA	2	FACETS	1	0.874	1			1	INDETERMINATE	1	TRUE	NA	0.271503969174358	2		259	185	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0035511-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	14	308	1				ENST00000310581	NM_198253.2	-/1132			0.271503969174358	1	FACETS	0.256	0.184	0.343	0.256	0.184	0.343	SUBCLONAL	1	TRUE	0	0.271503969174358	1		309	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0035624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	281	590	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.629703029761802	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.629703029761802	2		591	439	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	636	413	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.629703029761802	6	FACETS	1	0.986	1			1	CLONAL	5	TRUE	NA	0.629703029761802	6		413	897	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106862	27106863	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	429	706	0	ENST00000324856.7:c.6476dup	p.Asn2160GlufsTer65	p.N2160Efs*65	ENST00000324856	NM_006015.4	2158	cga/cgAa	20/20	0.629703029761802	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	0	0.629703029761802	3		706	587	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416920	416920	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	106	499	0	ENST00000399788.2:c.3630C>G	p.Phe1210Leu	p.F1210L	ENST00000399788	NM_001042603.1	1210	ttC/ttG	23/28	0.627946030956702	3	FACETS	0.871	0.785	0.963	0.436	0.392	0.482	CLONAL	1	TRUE	1	0.629703029761802	3		499	508	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562882	176562882	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs757338956	NA	P-0035624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	131	537	0	ENST00000439151.2:c.778C>G	p.Leu260Val	p.L260V	ENST00000439151	NM_022455.4	260	Cta/Gta	2/23	0.616671505751779	4	FACETS	0.954	0.867	1	0.318	0.289	0.349	CLONAL	1	TRUE	1	0.629703029761802	4		537	711	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0035649-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	29	618	0	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.416380890926124	1	FACETS	0.231	0.185	0.283	0.231	0.185	0.283	SUBCLONAL	1	TRUE	0	0.416380890926124	1		618	478	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0035649-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	50	626	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.416380890926124	1	FACETS	0.498	0.423	0.579	0.498	0.423	0.579	SUBCLONAL	1	TRUE	0	0.416380890926124	1		626	382	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1331464	1331464	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035649-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	49	514	0	ENST00000400841.2:c.64G>T	p.Gly22Trp	p.G22W	ENST00000400841		22	Ggg/Tgg	1/6	0.416380890926124	1	FACETS	0.366	0.31	0.428	0.366	0.31	0.428	SUBCLONAL	1	TRUE	0	0.416380890926124	1		514	509	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938097	76938100	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0035649-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	56	542	0	ENST00000373344.5:c.2648_2651del	p.Gln883ArgfsTer21	p.Q883Rfs*21	ENST00000373344	NM_000489.3	883	cAAGAg/cg	9/35	0.416380890926124	1	FACETS	0.48	0.412	0.554	0.48	0.412	0.554	SUBCLONAL	1	TRUE	0	0.416380890926124	1		542	444	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249017	55249018	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCA	rs1554350381	NA	P-0036307-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	96	598	0	ENST00000275493.2:c.2317_2319dup	p.His773dup	p.H773dup	ENST00000275493	NM_005228.3	773	ccc/ccCCAc	20/28	0.315947958034095	5	FACETS	1	0.959	1	0.291	0.259	0.325	CLONAL	1	TRUE	1	0.315947958034095	5		598	770	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0036748-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	79	364	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.157973595453206	1	FACETS	0.817	0.723	0.917	0.817	0.723	0.917	INDETERMINATE	1	TRUE	0	0.398843673781895	1		364	388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0036748-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	200	663	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.398843673781895	2		663	867	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345809	152345809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036748-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	55	411	0	ENST00000359321.1:c.761C>T	p.Ser254Leu	p.S254L	ENST00000359321	NM_005431.1	254	tCa/tTa	3/3	0.398843673781895	1	FACETS	0.48	0.411	0.555	0.48	0.411	0.555	SUBCLONAL	1	TRUE	0	0.398843673781895	1		411	460	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460351	149460351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1318254419	NA	P-0036748-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	141	540	2	ENST00000286301.3:c.286G>A	p.Ala96Thr	p.A96T	ENST00000286301	NM_005211.3	96	Gcc/Acc	3/22	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.398843673781895	2		542	548	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683357	88683357	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201040	NA	P-0036748-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	195	603	0	ENST00000372037.3:c.1480C>T	p.Arg494Ter	p.R494*	ENST00000372037	NM_004329.2	494	Cga/Tga	13/13	0.34951764797493	2	FACETS	0.781	0.727	0.837	0.781	0.727	0.837	SUBCLONAL	2	TRUE	0	0.398843673781895	2		603	626	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875632	35875632	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036748-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	128	371	0	ENST00000303115.3:c.819G>A	p.Trp273Ter	p.W273*	ENST00000303115	NM_002185.3	273	tgG/tgA	7/8	0.398843673781895	3	FACETS	0.764	0.696	0.834	0.764	0.696	0.834	SUBCLONAL	2	TRUE	1	0.398843673781895	3		371	504	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603007	48603007	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0036748-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	76	288	0	ENST00000342988.3:c.1309-1G>C		p.X437_splice	ENST00000342988	NM_005359.5	437			0.325277860570714	1	FACETS	0.956	0.846	1	0.956	0.846	1	CLONAL	1	TRUE	0	0.398843673781895	1		288	319	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036748-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	144	400	0	ENST00000371953.3:c.511C>A	p.Gln171Lys	p.Q171K	ENST00000371953	NM_000314.4	171	Cag/Aag	6/9	0.34951764797493	2	FACETS	0.844	0.777	0.912	0.844	0.777	0.912	CLONAL	2	TRUE	0	0.398843673781895	2		400	428	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500432	99500432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356080771	NA	P-0036748-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	202	736	1	ENST00000268035.6:c.3865G>A	p.Glu1289Lys	p.E1289K	ENST00000268035	NM_000875.3	1289	Gag/Aag	21/21	0.398843673781895	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.398843673781895	1		737	708	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440934	56440935	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0036748-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	240	655	0	ENST00000407977.2:c.402dup	p.Ser135GlnfsTer6	p.S135Qfs*6	ENST00000407977		134	-/C	4/10	0.398843673781895	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.398843673781895	1		655	753	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0037923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	36	361	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.82	0.676	0.981	0.82	0.676	0.981	CLONAL	1	TRUE	1	0.258168363835979	2		361	340	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54959348	54959348	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	25	332	0	ENST00000312783.6:c.352C>T	p.Gln118Ter	p.Q118*	ENST00000312783	NM_198436.1	118	Cag/Tag	5/10	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.258168363835979	2		332	157	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028094	69028094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1409727717	NA	P-0037923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	89	447	1	ENST00000288368.4:c.3253G>A	p.Val1085Ile	p.V1085I	ENST00000288368	NM_024870.2	1085	Gta/Ata	26/40	1	2	FACETS	1	0.949	1	1	0.987	1	CLONAL	2	TRUE	1	0.258168363835979	2		448	314	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971026	21971300	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCCAGGCATCGCGCACGTCCAGCCGCGCCCCGGCCCGGTGCAGCACCACCAGCGTGTCCAGGAAGCCCTCCCGGGCAGCGTCGTGCACGGGTCGGGTGAGAGTGGCGGGGTCGGCGCAGTTGGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCTGCCCATCATCATGACCTGCCAGAGAGAACAGAATGGTCAGAGCCAGGGTGGGGGCCGGCATGACGGAAAGGAAGCTTGTGTAGAGCCCCCTCACCGCCAAGCAGACCC	CCCCAGGCATCGCGCACGTCCAGCCGCGCCCCGGCCCGGTGCAGCACCACCAGCGTGTCCAGGAAGCCCTCCCGGGCAGCGTCGTGCACGGGTCGGGTGAGAGTGGCGGGGTCGGCGCAGTTGGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCTGCCCATCATCATGACCTGCCAGAGAGAACAGAATGGTCAGAGCCAGGGTGGGGGCCGGCATGACGGAAAGGAAGCTTGTGTAGAGCCCCCTCACCGCCAAGCAGACCC	-	novel	NA	P-0037923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	132	607	0	ENST00000304494.5:c.151-93_332del		p.X51_splice	ENST00000304494	NM_000077.4	51		2/3	0.258168363835979	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.258168363835979	1		607	674	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647504	23647510	+	frameshift_variant	Frame_Shift_Del	DEL	TGTTCTT	TGTTCTT	-	novel	NA	P-0037923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	65	475	0	ENST00000261584.4:c.357_363del	p.Arg120MetfsTer55	p.R120Mfs*55	ENST00000261584	NM_024675.3	119	caAAGAACA/ca	4/13	0.258168363835979	3	FACETS	1	0.961	1	0.431	0.374	0.491	CLONAL	1	TRUE	0	0.258168363835979	3		475	440	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0038062-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	158	534	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.58222840118366	3	FACETS	0.914	0.851	0.977	0.914	0.851	0.977	CLONAL	2	TRUE	1	0.671331342631969	3		534	344	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038062-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	477	914	2	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.558105104002907	2	FACETS	0.896	0.865	0.927	0.896	0.865	0.927	CLONAL	2	TRUE	0	0.671331342631969	2		916	793	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0038062-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	432	503	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.671331342631969	4	FACETS	0.922	0.895	0.949	0.922	0.895	0.949	CLONAL	4	TRUE	0	0.671331342631969	4		503	583	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120842	115120843	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0038062-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	369	654	0	ENST00000257566.3:c.163_164del	p.Ser55AlafsTer55	p.S55Afs*55	ENST00000257566	NM_016569.3	55	TCg/g	1/8	0.597426851136401	5	FACETS	1	0.993	1	0.818	0.779	0.857	CLONAL	2	TRUE	2	0.671331342631969	5		654	899	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803501	32803501	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs142794316	NA	P-0038062-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1422	101	885	3	ENST00000374899.4:c.658C>T	p.Arg220Ter	p.R220*	ENST00000374899	NM_018833.2	220	Cga/Tga	4/12	0.655617182017617	4	FACETS	0.33	0.294	0.369	0.11	0.098	0.123	SUBCLONAL	1	TRUE	1	0.671331342631969	4		888	1523	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821287	32821287	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038062-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	287	949	0	ENST00000354258.4:c.307A>G	p.Ile103Val	p.I103V	ENST00000354258	NM_000593.5	103	Ata/Gta	1/11	0.655617182017617	4	FACETS	0.941	0.882	1	0.314	0.294	0.334	CLONAL	1	TRUE	1	0.671331342631969	4		949	1519	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0039687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	236	364	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.414075087460951	5	FACETS	0.934	0.879	0.99	0.934	0.879	0.99	CLONAL	3	TRUE	2	0.51132966622019	5		364	582	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0039687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	152	328	0				ENST00000310581	NM_198253.2	-/1132			0.477748059640398	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.51132966622019	3		328	316	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484261	57484261	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	65	401	0	ENST00000371085.3:c.575C>T	p.Pro192Leu	p.P192L	ENST00000371085	NM_000516.4	192	cCg/cTg	7/13	0.51132966622019	7	FACETS	0.646	0.558	0.741	0.129	0.111	0.149	SUBCLONAL	1	TRUE	2	0.51132966622019	7		401	897	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807365	3807365	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	154	350	0	ENST00000262367.5:c.3622C>T	p.Pro1208Ser	p.P1208S	ENST00000262367	NM_004380.2	1208	Cca/Tca	19/31	0.477748059640398	3	FACETS	0.907	0.839	0.976	0.907	0.839	0.976	CLONAL	2	TRUE	1	0.51132966622019	3		350	417	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725524	117725524	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1388562198	NA	P-0039687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	79	397	1	ENST00000368508.3:c.357G>A	p.Trp119Ter	p.W119*	ENST00000368508	NM_002944.2	119	tgG/tgA	5/43	1	2	FACETS	0.863	0.765	0.967	0.863	0.765	0.967	CLONAL	1	TRUE	1	0.51132966622019	2		398	358	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033249	69033249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs114811202	NA	P-0039687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	81	479	0	ENST00000288368.4:c.3689G>A	p.Arg1230Gln	p.R1230Q	ENST00000288368	NM_024870.2	1230	cGg/cAg	30/40	0.235869936672631	4	FACETS	0.596	0.524	0.673	0.149	0.131	0.169	INDETERMINATE	1	TRUE	0	0.51132966622019	4		479	804	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280034	18280034	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs202137312	NA	P-0039687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	73	397	0	ENST00000222254.8:c.2117A>G	p.Asp706Gly	p.D706G	ENST00000222254	NM_005027.3	706	gAc/gGc	16/16	0.359321928509561	4	FACETS	0.99	0.869	1	0.495	0.434	0.56	CLONAL	1	TRUE	2	0.51132966622019	4		397	436	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879061	151879061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs965807663	NA	P-0039687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	211	485	0	ENST00000262189.6:c.5884C>T	p.Pro1962Ser	p.P1962S	ENST00000262189	NM_170606.2	1962	Ccc/Tcc	36/59	0.414075087460951	5	FACETS	0.989	0.922	1	0.66	0.615	0.706	CLONAL	2	TRUE	2	0.51132966622019	5		485	737	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40678643	40678643	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	107	491	1	ENST00000249776.8:c.385G>A	p.Gly129Arg	p.G129R	ENST00000249776	NM_033286.3	129	Gga/Aga	3/9	0.29448676082721	3	FACETS	0.957	0.862	1	0.479	0.431	0.529	INDETERMINATE	1	TRUE	1	0.51132966622019	3		492	549	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81979789	81979789	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781497956	NA	P-0039687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	76	389	0	ENST00000359376.3:c.3491C>T	p.Ser1164Phe	p.S1164F	ENST00000359376	NM_002661.3	1164	tCc/tTc	31/33	1	2	FACETS	0.826	0.729	0.928	0.826	0.729	0.928	CLONAL	1	TRUE	1	0.51132966622019	2		389	360	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696399	47696400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	120	443	0	ENST00000347630.2:c.423dup	p.Leu142SerfsTer4	p.L142Sfs*4	ENST00000347630	NM_001007230.1	141	-/T	6/11	0.490238819962065	4	FACETS	1	0.978	1	0.426	0.386	0.468	CLONAL	1	TRUE	1	0.51132966622019	4		443	555	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705287	52705287	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	108	404	1	ENST00000322088.6:c.169G>A	p.Asp57Asn	p.D57N	ENST00000322088	NM_014225.5	57	Gat/Aat	2/15	0.432106008762397	3	FACETS	1	0.971	1	0.599	0.541	0.659	CLONAL	1	TRUE	1	0.51132966622019	3		405	443	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306658	41306658	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	333	732	1	ENST00000373198.4:c.1001G>T	p.Trp334Leu	p.W334L	ENST00000373198	NM_133170.3	334	tGg/tTg	7/32	0.51132966622019	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.51132966622019	3		733	711	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876232	35876232	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	85	475	0	ENST00000303115.3:c.1024G>A	p.Gly342Arg	p.G342R	ENST00000303115	NM_002185.3	342	Ggg/Agg	8/8	0.51132966622019	4	FACETS	0.86	0.762	0.966	0.287	0.254	0.322	CLONAL	1	TRUE	1	0.51132966622019	4		475	584	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971133	21971147	+	inframe_deletion	In_Frame_Del	DEL	GGGGTCGGCGCAGTT	GGGGTCGGCGCAGTT	-	novel	NA	P-0039687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	172	489	0	ENST00000304494.5:c.211_225del	p.Asn71_Pro75del	p.N71_P75del	ENST00000304494	NM_000077.4	71	AACTGCGCCGACCCC/-	2/3	0.51132966622019	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.51132966622019	1		489	398	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410667	63410667	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868452636	NA	P-0039687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	231	725	0	ENST00000330258.3:c.2500C>T	p.Leu834Phe	p.L834F	ENST00000330258	NM_152424.3	834	Ctt/Ttt	2/2	0.477748059640398	3	FACETS	0.766	0.716	0.816	0.766	0.716	0.816	SUBCLONAL	2	TRUE	1	0.51132966622019	3		725	741	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859845	151859845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	104	305	0	ENST00000262189.6:c.10817G>A	p.Arg3606Lys	p.R3606K	ENST00000262189	NM_170606.2	3606	aGa/aAa	43/59	0.414075087460951	5	FACETS	0.866	0.781	0.955	0.577	0.52	0.637	CLONAL	2	TRUE	2	0.51132966622019	5		305	415	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244406	5244406	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039860-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	619	945	1	ENST00000357368.4:c.1076C>A	p.Pro359His	p.P359H	ENST00000357368	NM_002850.3	359	cCt/cAt	11/38	0.288772439101273	4	FACETS	1	0.986	1	1	0.998	1	CLONAL	4	TRUE	2	0.291570142331026	4		946	1317	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828051	3828051	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039860-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	186	695	0	ENST00000262367.5:c.2074C>A	p.Pro692Thr	p.P692T	ENST00000262367	NM_004380.2	692	Ccc/Acc	10/31	0.291570142331026	1	FACETS	0.944	0.878	1	1	0.993	1	CLONAL	2	TRUE	0	0.291570142331026	1		695	577	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31466297	31466297	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039860-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	227	447	0	ENST00000344624.3:c.2458C>T	p.Gln820Ter	p.Q820*	ENST00000344624		820	Cag/Tag	16/33	0.291570142331026	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.291570142331026	2		447	717	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244406	5244406	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	45	945	1	ENST00000357368.4:c.1076C>A	p.Pro359His	p.P359H	ENST00000357368	NM_002850.3	359	cCt/cAt	11/38	0.192127157817817	4	FACETS	0.984	0.864	1	1	0.979	1	CLONAL	5	TRUE	2	0.266260741688916	4		946	87	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828051	3828051	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	23	695	0	ENST00000262367.5:c.2074C>A	p.Pro692Thr	p.P692T	ENST00000262367	NM_004380.2	692	Ccc/Acc	10/31	0.266260741688916	0	FACETS	0.813	0.666	0.963			1	CLONAL	3	TRUE	0	0.266260741688916	0		695	52	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31466297	31466297	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039860-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	20	447	0	ENST00000344624.3:c.2458C>T	p.Gln820Ter	p.Q820*	ENST00000344624		820	Cag/Tag	16/33	0.265998157329955	2	FACETS	1	0.835	1	1	0.835	1	CLONAL	2	TRUE	0	0.266260741688916	2		447	70	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040655-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	389	788	0	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.698782136319997	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.698782136319997	2		788	520	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0040655-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	203	325	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.698782136319997	3	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	1	0.698782136319997	3		325	391	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959073	28959073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761475937	NA	P-0040655-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	98	302	0	ENST00000282397.4:c.2065G>A	p.Glu689Lys	p.E689K	ENST00000282397	NM_002019.4	689	Gag/Aag	14/30	NA	2	FACETS	1	0.956	1			1	INDETERMINATE	1	TRUE	NA	0.698782136319997	2		302	257	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145589	11145589	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0040655-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	343	591	0	ENST00000358026.2:c.3952-1G>A		p.X1318_splice	ENST00000358026	NM_001128849.1	1318			0.698782136319997	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.698782136319997	2		591	456	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254728	46254728	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040655-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	172	204	0	ENST00000334344.6:c.4918A>G	p.Lys1640Glu	p.K1640E	ENST00000334344	NM_152641.2	1640	Aaa/Gaa	16/21	0.698782136319997	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.698782136319997	3		204	275	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112580	115112581	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0040655-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	288	734	1	ENST00000257566.3:c.1159_1160delinsAA	p.Pro387Asn	p.P387N	ENST00000257566	NM_016569.3	387	CCc/AAc	7/8	0.698782136319997	3	FACETS	0.933	0.886	0.98	0.933	0.886	0.98	CLONAL	2	TRUE	1	0.698782136319997	3		735	596	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748889	41748889	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040655-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	118	559	0	ENST00000301178.4:c.1414G>T	p.Val472Phe	p.V472F	ENST00000301178	NM_021913.4	472	Gtc/Ttc	11/20	0.215561623047419	3	FACETS	0.881	0.799	0.968	0.294	0.266	0.323	INDETERMINATE	1	TRUE	0	0.698782136319997	3		559	517	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964388	70964388	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040655-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	264	355	1	ENST00000276594.2:c.1640C>A	p.Ser547Ter	p.S547*	ENST00000276594	NM_024504.3	547	tCa/tAa	8/8	0.698782136319997	8	FACETS	1	0.974	1	0.429	0.402	0.457	CLONAL	2	TRUE	3	0.698782136319997	8		356	1091	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039883	47039883	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040655-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	309	719	1	ENST00000377604.3:c.1226C>A	p.Ala409Glu	p.A409E	ENST00000377604	NM_001204468.1	409	gCg/gAg	12/24	0.172787212516592	6	FACETS	0.997	0.946	1	0.997	0.946	1	INDETERMINATE	3	TRUE	3	0.698782136319997	6		720	709	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988182	85988182	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0040655-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	60	190	0	ENST00000263360.6:c.1125+2T>C		p.X375_splice	ENST00000263360	NM_003797.3	375			0.539474571613451	4	FACETS	0.81	0.702	0.927	0.405	0.351	0.464	CLONAL	1	TRUE	2	0.698782136319997	4		190	360	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239294	105239294	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040655-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	155	707	0	ENST00000349310.3:c.1093G>T	p.Glu365Ter	p.E365*	ENST00000349310	NM_001014432.1	365	Gag/Tag	12/15	0.698782136319997	3	FACETS	1	0.967	1	0.546	0.503	0.591	CLONAL	1	TRUE	1	0.698782136319997	3		707	548	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660280	227660280	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040655-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	258	633	0	ENST00000305123.5:c.3175C>A	p.Leu1059Met	p.L1059M	ENST00000305123	NM_005544.2	1059	Ctg/Atg	1/2	0.509244547884185	3	FACETS	0.931	0.882	0.981			1	CLONAL	2	TRUE	NA	0.698782136319997	3		633	535	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098556	47098562	+	frameshift_variant	Frame_Shift_Del	DEL	ACTGGGA	ACTGGGA	-	novel	NA	P-0040655-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	130	480	0	ENST00000409792.3:c.6712_6718del	p.Ser2238MetfsTer8	p.S2238Mfs*8	ENST00000409792	NM_014159.6	2238	TCCCAGTat/at	15/21	0.174346621679383	3	FACETS	0.758	0.698	0.82			1	INDETERMINATE	2	TRUE	NA	0.698782136319997	3		480	331	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879391	56879391	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040655-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	135	513	0	ENST00000519728.1:c.908T>C	p.Val303Ala	p.V303A	ENST00000519728	NM_002350.3	303	gTg/gCg	9/13	0.469335102531689	4	FACETS	0.835	0.759	0.914			1	CLONAL	1	TRUE	NA	0.698782136319997	4		513	786	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729248	41729248	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0040655-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	55	267	0	ENST00000242208.4:c.1281G>C	p.Ter427TyrextTer29	p.*427Yext*29	ENST00000242208	NM_002192.2	427	taG/taC	3/3	0.698782136319997	3	FACETS	0.725	0.625	0.833	0.362	0.312	0.417	SUBCLONAL	1	TRUE	1	0.698782136319997	3		267	293	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041365-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	50	468	0				ENST00000310581	NM_198253.2	-/1132			0.36379695573263	10	FACETS	1	0.957	1	0.155	0.131	0.181	CLONAL	1	TRUE	1	0.36379695573263	10		468	484	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402765	139402765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1386494518	NA	P-0041365-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	157	928	1	ENST00000277541.6:c.3244C>T	p.Arg1082Cys	p.R1082C	ENST00000277541	NM_017617.3	1082	Cgc/Tgc	20/34	0.227895140577212	3	FACETS	1	0.987	1	0.702	0.644	0.762	CLONAL	1	TRUE	1	0.36379695573263	3		929	727	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651879	36651879	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0041365-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	227	614	0	ENST00000244741.5:c.1A>G	p.Met1?	p.M1?	ENST00000244741	NM_000389.4	1	Atg/Gtg	2/3	0.145162496613189	6	FACETS	1	0.984	1	1	0.984	1	INDETERMINATE	3	TRUE	3	0.36379695573263	6		614	628	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977883	131977883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561655417	NA	P-0041365-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	49	319	0	ENST00000265335.6:c.3766C>T	p.Arg1256Cys	p.R1256C	ENST00000265335		1256	Cgc/Tgc	25/25	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.36379695573263	2		319	264	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201854	67201854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041365-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	80	638	0	ENST00000312629.5:c.1054G>C	p.Glu352Gln	p.E352Q	ENST00000312629	NM_003952.2	352	Gag/Cag	13/15	0.0975074368635152	4	FACETS	1	0.947	1	0.567	0.5	0.638	INDETERMINATE	1	TRUE	2	0.36379695573263	4		638	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0041365-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	354	610	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.126834021100824	4	FACETS	0.981	0.944	1			1	INDETERMINATE	5	TRUE	NA	0.36379695573263	4		610	541	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486587	56486587	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041365-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	217	535	0	ENST00000267101.3:c.1166C>T	p.Thr389Ile	p.T389I	ENST00000267101	NM_001982.3	389	aCa/aTa	10/28	0.126186279168817	6	FACETS	1	0.983	1	1	0.983	1	INDETERMINATE	3	TRUE	3	0.36379695573263	6		535	601	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878077	48878114	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCCACCGCCGCCGCTGCCGCCGCGGAACCCCCGGCA	CCGCCACCGCCGCCGCTGCCGCCGCGGAACCCCCGGCA	-	novel	NA	P-0041365-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	150	116	1	ENST00000267163.4:c.34_71del	p.Thr12AlafsTer6	p.T12Afs*6	ENST00000267163	NM_000321.2	10	gCCGCCACCGCCGCCGCTGCCGCCGCGGAACCCCCGGCA/g	1/27	0.153336456841387	3	FACETS	0.956	0.896	1	1	0.993	1	INDETERMINATE	4	TRUE	1	0.36379695573263	3		117	255	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266691	18266692	+	frameshift_variant,start_lost	Frame_Shift_Ins	INS	-	-	GGCG	novel	NA	P-0041365-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	101	647	0	ENST00000222254.8:c.6_9dup	p.Pro4_?3	p.P4_?3	ENST00000222254	NM_005027.3	1	atg/atGGCGg	2/16	0.0975074368635152	4	FACETS	1	0.907	1	0.508	0.454	0.566	INDETERMINATE	1	TRUE	2	0.36379695573263	4		647	745	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878869	117878869	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041365-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	58	330	0	ENST00000297338.2:c.100G>C	p.Glu34Gln	p.E34Q	ENST00000297338	NM_006265.2	34	Gag/Cag	2/14	0.309430020087253	5	FACETS	1	0.902	1	0.353	0.304	0.407	CLONAL	1	TRUE	2	0.36379695573263	5		330	465	SUCCESS
APC	324	MSKCC	GRCh37	5	112178867	112178867	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041365-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	19	295	0	ENST00000257430.4:c.7576C>A	p.His2526Asn	p.H2526N	ENST00000257430	NM_000038.5	2526	Cat/Aat	16/16	0.36379695573263	3	FACETS	0.385	0.291	0.494	0.192	0.145	0.247	SUBCLONAL	1	TRUE	1	0.36379695573263	3		295	321	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486309	8486309	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041365-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	22	259	0	ENST00000356435.5:c.2508G>T	p.Met836Ile	p.M836I	ENST00000356435		836	atG/atT	17/35	0.227895140577212	3	FACETS	0.537	0.417	0.676	0.269	0.208	0.338	SUBCLONAL	1	TRUE	1	0.36379695573263	3		259	266	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0041987-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	89	240	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.136066651442326	3	FACETS	0.879	0.784	0.979	0.586	0.523	0.653	INDETERMINATE	2	TRUE	0	0.284096394933498	3		240	407	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041987-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	58	468	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.991	0.854	1	0.991	0.854	1	CLONAL	1	TRUE	1	0.284096394933498	2		468	412	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0041987-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	271	822	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.0829951178275252	4	FACETS	1	0.964	1			1	INDETERMINATE	3	TRUE	NA	0.284096394933498	4		822	792	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577600	7577600	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041987-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	209	489	0	ENST00000269305.4:c.681del	p.Asp228ThrfsTer19	p.D228Tfs*19	ENST00000269305	NM_001126112.2	227	tcT/tc	7/11	0.274555000712386	2	FACETS	0.95	0.885	1	0.95	0.885	1	CLONAL	2	TRUE	0	0.284096394933498	2		489	774	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652056	36652056	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041987-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	116	974	0	ENST00000244741.5:c.178G>T	p.Glu60Ter	p.E60*	ENST00000244741	NM_000389.4	60	Gag/Tag	2/3	0.169789527278472	3	FACETS	0.855	0.769	0.946	0.427	0.384	0.473	INDETERMINATE	1	TRUE	1	0.284096394933498	3		974	1091	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30954259	30954259	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0041987-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	56	327	0	ENST00000375687.4:c.130A>T	p.Lys44Ter	p.K44*	ENST00000375687	NM_015338.5	44	Aag/Tag	2/13	0.270562666843831	4	FACETS	1	0.884	1	0.345	0.296	0.399	CLONAL	1	TRUE	1	0.284096394933498	4		327	489	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383280	31383280	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778547539	NA	P-0041987-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	358	496	0	ENST00000328111.2:c.1192C>T	p.Arg398Cys	p.R398C	ENST00000328111	NM_006892.3	398	Cgc/Tgc	11/23	0.270562666843831	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	1	0.284096394933498	4		496	1008	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922830	44922831	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0041987-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	177	458	0	ENST00000377967.4:c.1692_1693dup	p.Gln565ArgfsTer29	p.Q565Rfs*29	ENST00000377967	NM_021140.2	564	ggg/ggGCg	16/29	0.284096394933498	1	FACETS	0.797	0.737	0.859	1	0.991	1	SUBCLONAL	2	TRUE	0	0.284096394933498	1		458	671	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11194430	11194430	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041987-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	133	526	0	ENST00000361445.4:c.5224G>A	p.Glu1742Lys	p.E1742K	ENST00000361445	NM_004958.3	1742	Gaa/Aaa	37/58	0.284096394933498	3	FACETS	1	0.982	1	0.667	0.606	0.731	CLONAL	1	TRUE	1	0.284096394933498	3		526	802	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539855	187539855	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041987-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	8	0	0	ENST00000441802.2:c.7885G>C	p.Ala2629Pro	p.A2629P	ENST00000441802	NM_005245.3	2629	Gcc/Ccc	10/27	0.284096394933498	3	FACETS	0.121	0.077	0.178	0.06	0.038	0.089	SUBCLONAL	1	TRUE	1	0.284096394933498	3		0	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0042583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	167	454	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.119289210204863	0	FACETS	0.95	0.876	1			1	CLONAL	4	FALSE	0	0.119289210204863	0		455	649	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0042745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	56	364	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.24	2		364	466	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732285	74732285	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	50	401	0	ENST00000359995.5:c.624T>G	p.Ser208Arg	p.S208R	ENST00000359995	NM_001195427.1	208	agT/agG	2/3	1	2	FACETS	0.621	0.526	0.726	0.621	0.526	0.726	SUBCLONAL	1	TRUE	1	0.24	2		401	671	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190045	123190045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042745-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	33	462	0	ENST00000218089.9:c.1264C>T	p.Arg422Trp	p.R422W	ENST00000218089	NM_001042749.1	422	Cgg/Tgg	14/35	1	2	FACETS	0.493	0.4	0.597	0.493	0.4	0.597	SUBCLONAL	1	TRUE	1	0.24	2		462	558	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043366-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	23	468	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		468	267	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922749	44922750	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	205	201	0	ENST00000377967.4:c.1611dup	p.Val538SerfsTer15	p.V538Sfs*15	ENST00000377967	NM_021140.2	537	tca/tcAa	16/29	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.681657854426422	1		201	341	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099449	27099671	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATAAGGATCCTTATGGCAGCATGAGGAAAGGTGACTGATCTGATTGCTATTTGAACTTGTGCTCGTAAAGACAGGGCCAGTGAAATGGGGGGAAATCTTGAGAATGGCTCAGGGTTCTTGTGGAGCCATCCTCTGAGATAATGCATTTCCTGCCCTAACTACCCCTCTTCATCCTTACCTCCTTTCTTGTCTTCTCCTTGGCTTCACCTTGTCATCCCTTAAT	ATAAGGATCCTTATGGCAGCATGAGGAAAGGTGACTGATCTGATTGCTATTTGAACTTGTGCTCGTAAAGACAGGGCCAGTGAAATGGGGGGAAATCTTGAGAATGGCTCAGGGTTCTTGTGGAGCCATCCTCTGAGATAATGCATTTCCTGCCCTAACTACCCCTCTTCATCCTTACCTCCTTTCTTGTCTTCTCCTTGGCTTCACCTTGTCATCCCTTAAT	-	novel	NA	P-0043713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	187	536	0	ENST00000324856.7:c.3687_3716-165del		p.X1229_splice	ENST00000324856	NM_006015.4	1229		14/20	0.656443118672163	1	FACETS	0.83	0.775	0.884	0.83	0.775	0.884	CLONAL	1	TRUE	0	0.681657854426422	1		536	436	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440044	49440044	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1234276911	NA	P-0043713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	346	677	1	ENST00000301067.7:c.4582C>T	p.Arg1528Trp	p.R1528W	ENST00000301067	NM_003482.3	1528	Cgg/Tgg	16/54	1	2	FACETS	0.988	0.937	1	0.988	0.937	1	CLONAL	1	TRUE	1	0.681657854426422	2		678	1027	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26046047	26046056	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	TAAGTCTGCC	TAAGTCTGCC	GA	novel	NA	P-0043713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	149	357	1	ENST00000540144.1:c.409_*7delinsGA		p.*137*	ENST00000540144	NM_003531.2	137		1/1	1	2	FACETS	0.987	0.91	1	0.987	0.91	1	CLONAL	1	TRUE	1	0.681657854426422	2		358	443	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0044480-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	1126	577	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.247844973412408	29	FACETS	1	0.983	1	0.892	0.874	0.91	CLONAL	24	TRUE	2	0.247844973412408	29		577	1639	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430891	181430891	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044480-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	67	745	0	ENST00000325404.1:c.743C>G	p.Ala248Gly	p.A248G	ENST00000325404	NM_003106.3	248	gCc/gGc	1/1	0.221317095197737	3	FACETS	0.872	0.757	0.996	0.436	0.378	0.498	CLONAL	1	TRUE	1	0.247844973412408	3		745	697	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044934	47044935	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCGACTGGCAGAAGCTGGCCTGTCTGCTCTG	novel	NA	P-0044480-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	98	399	0	ENST00000377604.3:c.2266_2296dup	p.Arg766LeufsTer34	p.R766Lfs*34	ENST00000377604	NM_001204468.1	754	acc/aCCGACTGGCAGAAGCTGGCCTGTCTGCTCTGcc	20/24	0.247844973412408	2	FACETS	0.807	0.723	0.896			1	CLONAL	2	TRUE	NA	0.247844973412408	2		399	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0044940-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	640	744	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	1	2	FACETS	1	0.992	1	1	0.998	1	CLONAL	2	TRUE	1	0.840063152878178	2		744	747	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121913370	NA	P-0044940-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	141	231	0	ENST00000288602.6:c.1742A>G	p.Asn581Ser	p.N581S	ENST00000288602	NM_004333.4	581	aAt/aGt	15/18	0.186146210728336	3	FACETS	1	0.989	1	0.74	0.685	0.796	INDETERMINATE	1	TRUE	1	0.840063152878178	3		231	322	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033998	48033998	+	stop_lost	Nonstop_Mutation	SNP	A	A	C	novel	NA	P-0044940-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	204	257	0	ENST00000234420.5:c.4082A>C	p.Ter1361SerextTer29	p.*1361Sext*29	ENST00000234420	NM_000179.2	1361	tAg/tCg	10/10	0.454192807030649	4	FACETS	1	0.982	1	0.39	0.362	0.418	INDETERMINATE	1	TRUE	1	0.840063152878178	4		257	764	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878049	48878049	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0044940-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	215	295	0	ENST00000267163.4:c.1A>G	p.Met1?	p.M1?	ENST00000267163	NM_000321.2	1	Atg/Gtg	1/27	0.817741639865566	2	FACETS	0.981	0.946	1	0.981	0.946	1	CLONAL	2	TRUE	0	0.840063152878178	2		295	261	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14317380	14317380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044940-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	419	286	0	ENST00000256196.4:c.130G>A	p.Asp44Asn	p.D44N	ENST00000256196		44	Gat/Aat	2/6	0.813107107628335	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.840063152878178	2		286	486	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003207	42003207	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs779115860	NA	P-0044940-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	264	474	0	ENST00000219905.7:c.2744A>T	p.Tyr915Phe	p.Y915F	ENST00000219905	NM_001164273.1	915	tAt/tTt	8/24	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.840063152878178	2		474	618	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953097	81953097	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044940-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	126	291	0	ENST00000359376.3:c.2063G>C	p.Gly688Ala	p.G688A	ENST00000359376	NM_002661.3	688	gGc/gCc	20/33	0.813107107628335	2	FACETS	1	0.974	1	0.564	0.521	0.607	CLONAL	1	TRUE	0	0.840063152878178	2		291	266	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41554499	41554499	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044940-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	392	424	0	ENST00000263253.7:c.3585G>T	p.Gln1195His	p.Q1195H	ENST00000263253	NM_001429.3	1195	caG/caT	19/31	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	2	TRUE	NA	0.840063152878178	2		424	459	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55570029	55570029	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044940-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	164	262	0	ENST00000288135.5:c.896C>A	p.Ala299Glu	p.A299E	ENST00000288135	NM_000222.2	299	gCa/gAa	5/21	0.322231474133201	1	FACETS	0.562	0.522	0.602	0.562	0.522	0.602	INDETERMINATE	1	TRUE	0	0.840063152878178	1		262	403	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335634	81335634	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044940-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	253	346	0	ENST00000222390.5:c.1726G>T	p.Gly576Ter	p.G576*	ENST00000222390	NM_000601.4	576	Gga/Tga	15/18	0.186146210728336	3	FACETS	0.756	0.714	0.798	0.756	0.714	0.798	INDETERMINATE	2	TRUE	1	0.840063152878178	3		346	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0044951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	52	504	0	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			1	2	FACETS	0.707	0.601	0.824	0.707	0.601	0.824	SUBCLONAL	1	TRUE	1	0.21	2		504	700	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878785	151878785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	58	436	0	ENST00000262189.6:c.6160C>T	p.Gln2054Ter	p.Q2054*	ENST00000262189	NM_170606.2	2054	Cag/Tag	36/59	1	2	FACETS	0.922	0.792	1	0.922	0.792	1	CLONAL	1	TRUE	1	0.21	2		436	599	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982411	201982411	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	86	755	0	ENST00000359651.3:c.790A>G	p.Lys264Glu	p.K264E	ENST00000359651		264	Aag/Gag	6/8	1	2	FACETS	0.823	0.726	0.927	0.823	0.726	0.927	CLONAL	1	TRUE	1	0.21	2		755	995	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577560	7577560	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520002	NA	P-0045231-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	184	470	0	ENST00000269305.4:c.721T>G	p.Ser241Ala	p.S241A	ENST00000269305	NM_001126112.2	241	Tcc/Gcc	7/11	0.306579938187469	2	FACETS	0.917	0.851	0.984	0.917	0.851	0.984	CLONAL	2	TRUE	0	0.341907216347397	2		470	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934578	NA	P-0045525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	31	659	0	ENST00000269305.4:c.524G>T	p.Arg175Leu	p.R175L	ENST00000269305	NM_001126112.2	175	cGc/cTc	5/11	0.757095219195936	1	FACETS	0.081	0.064	0.099	0.081	0.064	0.099	SUBCLONAL	1	TRUE	0	0.757095219195936	1		659	632	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0046000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	175	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.270830315265956	6	FACETS	1	0.936	1	1	0.936	1	CLONAL	4	TRUE	2	0.270830315265956	6		327	494	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572986	7572986	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555524156	NA	P-0046000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	97	430	0	ENST00000269305.4:c.1123C>T	p.Gln375Ter	p.Q375*	ENST00000269305	NM_001126112.2	375	Cag/Tag	11/11	0.207906683235001	2	FACETS	0.799	0.717	0.887	0.799	0.717	0.887	SUBCLONAL	2	TRUE	0	0.270830315265956	2		430	448	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023612	27023634	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTCCGGCGCGGCGGCGGCTGC	GGCTCCGGCGCGGCGGCGGCTGC	-	novel	NA	P-0046000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	169	194	0	ENST00000324856.7:c.718_740del	p.Gly240ArgfsTer152	p.G240Rfs*152	ENST00000324856	NM_006015.4	240	GGCTCCGGCGCGGCGGCGGCTGCc/c	1/20	0.263248028241457	5	FACETS	0.914	0.852	0.977	1	0.991	1	CLONAL	5	TRUE	2	0.270830315265956	5		194	384	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105866	27105867	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0046000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	130	425	0	ENST00000324856.7:c.5478dup	p.Cys1827LeufsTer4	p.C1827Lfs*4	ENST00000324856	NM_006015.4	1826	gac/gaCc	20/20	0.263248028241457	5	FACETS	1	0.91	1	0.668	0.607	0.732	CLONAL	2	TRUE	2	0.270830315265956	5		425	674	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645180	67645180	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	81	510	0	ENST00000264010.4:c.445G>T	p.Glu149Ter	p.E149*	ENST00000264010	NM_006565.3	149	Gaa/Taa	3/12	0.270830315265956	3	FACETS	1	0.92	1	0.528	0.465	0.595	CLONAL	1	TRUE	1	0.270830315265956	3		510	643	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137390	202137390	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	75	222	0	ENST00000358485.4:c.618G>T	p.Glu206Asp	p.E206D	ENST00000358485	NM_001080125.1	206	gaG/gaT	4/9	0.263248028241457	5	FACETS	1	0.937	1	0.731	0.645	0.823	CLONAL	2	TRUE	2	0.270830315265956	5		222	355	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054993	176054993	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046209-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	110	446	0	ENST00000367669.3:c.1060G>C	p.Ala354Pro	p.A354P	ENST00000367669	NM_022457.5	354	Gca/Cca	10/20	0.293489411823497	3	FACETS	1	0.981	1	0.694	0.626	0.767	CLONAL	1	TRUE	1	0.316339547208705	3		446	580	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78797023	78797023	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046209-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	87	411	0	ENST00000306801.3:c.1136G>A	p.Trp379Ter	p.W379*	ENST00000306801	NM_020761.2	379	tGg/tAg	9/34	0.293489411823497	3	FACETS	1	0.964	1	0.608	0.539	0.681	CLONAL	1	TRUE	1	0.316339547208705	3		411	524	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626117	12626118	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046209-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	104	336	0	ENST00000251849.4:c.1842_1843insT	p.Lys615Ter	p.K615*	ENST00000251849	NM_002880.3	614	-/T	17/17	0.126280697390768	5	FACETS	0.936	0.841	1	0.624	0.561	0.69	INDETERMINATE	2	TRUE	2	0.316339547208705	5		336	518	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411886	116411896	+	splice_region_variant,intron_variant	Splice_Region	DEL	TTTCTCTCTGT	TTTCTCTCTGT	-	novel	NA	P-0046209-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	1717	595	0	ENST00000397752.3:c.2888-14_2888-4del		p.X963_splice	ENST00000397752	NM_000245.2	963			0.316339547208705	16	FACETS	0.97	0.956	0.984			1	CLONAL	16	TRUE	NA	0.316339547208705	16		595	2248	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040652	47040653	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0046209-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	142	348	0	ENST00000377604.3:c.1287_1288delinsTT	p.Glu429_Glu430delinsAspTer	p.E429_E430delinsD*	ENST00000377604	NM_001204468.1	429	gaGGag/gaTTag	13/24	0.0587637190018828	2	FACETS	0.956	0.886	1			1	INDETERMINATE	3	TRUE	NA	0.316339547208705	2		348	313	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094381	27094382	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0046717-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	258	423	0	ENST00000324856.7:c.3089_3090del	p.Phe1030TyrfsTer2	p.F1030Yfs*2	ENST00000324856	NM_006015.4	1030	tTC/t	11/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.850225826374461	2		423	574	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133921	38133921	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046717-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	388	633	0	ENST00000317025.8:c.3965A>G	p.Asp1322Gly	p.D1322G	ENST00000317025	NM_023034.1	1322	gAt/gGt	23/24	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.850225826374461	2		633	895	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046776-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	276	624	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		624	616	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0046776-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	74	369	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		369	316	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217299	7217316	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGGGCTCCCTAGAAAGG	CAGGGCTCCCTAGAAAGG	-	novel	NA	P-0046776-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	204	481	0	ENST00000380728.2:c.398-9_406del		p.X133_splice	ENST00000380728		133		6/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		481	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573959	7573995	+	frameshift_variant	Frame_Shift_Del	DEL	CCCAGCCTGGGCATCCTTGAGTTCCAAGGCCTCATTC	CCCAGCCTGGGCATCCTTGAGTTCCAAGGCCTCATTC	-	novel	NA	P-0046776-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	191	600	1	ENST00000269305.4:c.1032_1068del	p.Asn345ArgfsTer13	p.N345Rfs*13	ENST00000269305	NM_001126112.2	344	ctGAATGAGGCCTTGGAACTCAAGGATGCCCAGGCTGGG/ct	10/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		601	395	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143044517	143044517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046776-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	109	359	0	ENST00000262992.4:c.1945G>A	p.Asp649Asn	p.D649N	ENST00000262992	NM_001101669.1	649	Gac/Aac	18/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		359	284	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827226	72827226	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046776-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	121	507	1	ENST00000268489.5:c.9355C>A	p.Gln3119Lys	p.Q3119K	ENST00000268489	NM_006885.3	3119	Cag/Aag	9/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		508	406	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	251	597	2	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	0.660852529206332	3	FACETS	0.922	0.862	0.984			1	CLONAL	1	TRUE	NA	0.664191304325523	3		599	1092	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046873-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	252	633	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	1	2	FACETS	0.907	0.851	0.964	0.907	0.851	0.964	CLONAL	1	TRUE	1	0.664191304325523	2		633	837	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	114	364	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.307636945892787	1	FACETS	0.942	0.86	1	0.942	0.86	1	INDETERMINATE	1	TRUE	0	0.556302985409278	1		364	314	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	54	534	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.307636945892787	1	FACETS	0.389	0.334	0.45	0.389	0.334	0.45	INDETERMINATE	1	TRUE	0	0.556302985409278	1		534	360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	221	454	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.556302985409278	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.556302985409278	1		454	528	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435798	110435798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1240854451	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	137	357	0	ENST00000375856.3:c.2603C>T	p.Ser868Leu	p.S868L	ENST00000375856	NM_003749.2	868	tCg/tTg	1/2	0.297019900450919	1	FACETS	0.589	0.537	0.642	0.589	0.537	0.642	INDETERMINATE	1	TRUE	0	0.556302985409278	1		357	604	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41021830	41021830	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1555429629	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	64	406	0	ENST00000267868.3:c.772G>A	p.Glu258Lys	p.E258K	ENST00000267868	NM_002875.4	258	Gag/Aag	8/10	0.277191795183665	1	FACETS	0.319	0.277	0.366	0.319	0.277	0.366	INDETERMINATE	1	TRUE	0	0.556302985409278	1		406	520	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675622	86675622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	66	175	0	ENST00000274376.6:c.2558C>T	p.Ser853Leu	p.S853L	ENST00000274376	NM_002890.2	853	tCa/tTa	19/25	0.297019900450919	1	FACETS	0.812	0.716	0.912	0.812	0.716	0.912	INDETERMINATE	1	TRUE	0	0.556302985409278	1		175	211	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023696	27023696	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	231	464	0	ENST00000324856.7:c.802C>T	p.Gln268Ter	p.Q268*	ENST00000324856	NM_006015.4	268	Cag/Tag	1/20	0.307636945892787	1	FACETS	0.564	0.525	0.604	0.564	0.525	0.604	INDETERMINATE	1	TRUE	0	0.556302985409278	1		464	1063	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231415	5231415	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	163	676	0	ENST00000357368.4:c.2061G>C	p.Glu687Asp	p.E687D	ENST00000357368	NM_002850.3	687	gaG/gaC	14/38	0.353845878539246	0	FACETS	0.316	0.29	0.343			1	SUBCLONAL	1	TRUE	0	0.556302985409278	0		676	824	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873648	35873648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867618621	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	186	256	0	ENST00000303115.3:c.604G>A	p.Glu202Lys	p.E202K	ENST00000303115	NM_002185.3	202	Gag/Aag	5/8	0.556302985409278	3	FACETS	0.982	0.918	1	0.982	0.918	1	CLONAL	2	TRUE	1	0.556302985409278	3		256	435	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422086	81422086	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	110	473	0	ENST00000298171.2:c.62G>A	p.Gly21Glu	p.G21E	ENST00000298171	NM_000369.2	21	gGa/gAa	1/10	0.507046900792285	2	FACETS	0.578	0.52	0.64	0.289	0.26	0.32	SUBCLONAL	1	TRUE	0	0.556302985409278	2		473	684	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877476	89877476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	103	477	0	ENST00000389301.3:c.287C>T	p.Ser96Phe	p.S96F	ENST00000389301	NM_000135.2	96	tCt/tTt	4/43	0.556302985409278	1	FACETS	0.556	0.5	0.615	0.556	0.5	0.615	SUBCLONAL	1	TRUE	0	0.556302985409278	1		477	481	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090508	5090508	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	25	193	0	ENST00000381652.3:c.2824C>T	p.Gln942Ter	p.Q942*	ENST00000381652	NM_004972.3	942	Caa/Taa	21/25	0.361634344609596	1	FACETS	0.375	0.298	0.462	0.375	0.298	0.462	SUBCLONAL	1	TRUE	0	0.556302985409278	1		193	173	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250274	110250274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777396288	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	260	747	0	ENST00000374672.4:c.401C>T	p.Ser134Leu	p.S134L	ENST00000374672	NM_004235.4	134	tCg/tTg	3/5	0.361634344609596	1	FACETS	0.506	0.473	0.54	0.506	0.473	0.54	SUBCLONAL	1	TRUE	0	0.556302985409278	1		747	1333	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100919	27100919	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	112	537	0	ENST00000324856.7:c.4201C>T	p.Gln1401Ter	p.Q1401*	ENST00000324856	NM_006015.4	1401	Cag/Tag	18/20	0.307636945892787	1	FACETS	0.407	0.366	0.45	0.407	0.366	0.45	INDETERMINATE	1	TRUE	0	0.556302985409278	1		537	714	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976373	18976373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746427790	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	240	744	1	ENST00000262803.5:c.3023G>A	p.Arg1008Gln	p.R1008Q	ENST00000262803	NM_002911.3	1008	cGa/cAa	22/24	0.302626024934074	0	FACETS	0.403	0.377	0.431			1	INDETERMINATE	1	TRUE	0	0.556302985409278	0		745	949	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163282	32163282	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	1419	827	0	ENST00000375023.3:c.5944C>T	p.Gln1982Ter	p.Q1982*	ENST00000375023	NM_004557.3	1982	Caa/Taa	30/30	0.4395878125447	5	FACETS	1	0.99	1	0.813	0.797	0.83	CLONAL	4	TRUE	0	0.556302985409278	5		827	2301	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150013	202150013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	103	460	0	ENST00000358485.4:c.1454G>A	p.Cys485Tyr	p.C485Y	ENST00000358485	NM_001080125.1	485	tGc/tAc	8/9	0.297019900450919	1	FACETS	0.409	0.367	0.455	0.409	0.367	0.455	INDETERMINATE	1	TRUE	0	0.556302985409278	1		460	653	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913836	32913836	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs80358757	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	30	277	0	ENST00000380152.3:c.5344C>T	p.Gln1782Ter	p.Q1782*	ENST00000380152		1782	Caa/Taa	11/27	0.297019900450919	1	FACETS	0.313	0.253	0.38	0.313	0.253	0.38	INDETERMINATE	1	TRUE	0	0.556302985409278	1		277	249	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473705	67473705	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	176	534	1	ENST00000327367.4:c.785A>G	p.Asp262Gly	p.D262G	ENST00000327367	NM_005902.3	262	gAc/gGc	6/9	0.277191795183665	1	FACETS	0.584	0.539	0.631	0.584	0.539	0.631	INDETERMINATE	1	TRUE	0	0.556302985409278	1		535	782	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658359	206658359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	98	513	0	ENST00000367120.3:c.1453G>A	p.Glu485Lys	p.E485K	ENST00000367120	NM_014002.3	485	Gag/Aag	14/22	0.297019900450919	1	FACETS	0.38	0.339	0.424	0.38	0.339	0.424	INDETERMINATE	1	TRUE	0	0.556302985409278	1		513	669	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94910935	94910935	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	203	381	0	ENST00000536441.1:c.1195A>C	p.Thr399Pro	p.T399P	ENST00000536441	NM_144665.3	399	Acc/Ccc	8/10	0.292695338649706	3	FACETS	0.864	0.807	0.921	0.864	0.807	0.921	INDETERMINATE	2	TRUE	1	0.556302985409278	3		381	540	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118353162	118353162	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	95	269	0	ENST00000534358.1:c.4038A>C	p.Lys1346Asn	p.K1346N	ENST00000534358	NM_005933.3	1346	aaA/aaC	8/36	0.292695338649706	3	FACETS	0.887	0.793	0.987	0.444	0.396	0.494	INDETERMINATE	1	TRUE	1	0.556302985409278	3		269	492	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499754	18499754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	53	239	0	ENST00000266497.5:c.1609G>A	p.Glu537Lys	p.E537K	ENST00000266497		537	Gaa/Aaa	10/31	0.490992435263775	4	FACETS	0.503	0.428	0.584	0.168	0.142	0.195	SUBCLONAL	1	TRUE	1	0.556302985409278	4		239	590	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865566	57865566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	158	643	1	ENST00000228682.2:c.3043G>A	p.Glu1015Lys	p.E1015K	ENST00000228682	NM_005269.2	1015	Gag/Aag	12/12	0.202952102955657	2	FACETS	0.624	0.572	0.679	0.312	0.286	0.34	INDETERMINATE	1	TRUE	0	0.556302985409278	2		644	910	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254014	133254014	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	77	381	0	ENST00000320574.5:c.736G>A	p.Val246Ile	p.V246I	ENST00000320574	NM_006231.2	246	Gtc/Atc	8/49	0.361634344609596	1	FACETS	0.4	0.352	0.452	0.4	0.352	0.452	SUBCLONAL	1	TRUE	0	0.556302985409278	1		381	499	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40678641	40678641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	68	430	0	ENST00000249776.8:c.383C>T	p.Ser128Leu	p.S128L	ENST00000249776	NM_033286.3	128	tCa/tTa	3/9	0.277191795183665	1	FACETS	0.309	0.268	0.352	0.309	0.268	0.352	INDETERMINATE	1	TRUE	0	0.556302985409278	1		430	572	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041857	42041857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	130	345	0	ENST00000219905.7:c.6052G>A	p.Glu2018Lys	p.E2018K	ENST00000219905	NM_001164273.1	2018	Gaa/Aaa	17/24	0.277191795183665	1	FACETS	0.713	0.651	0.778	0.713	0.651	0.778	INDETERMINATE	1	TRUE	0	0.556302985409278	1		345	473	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40460303	40460303	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	85	527	3	ENST00000345506.4:c.2014G>A	p.Asp672Asn	p.D672N	ENST00000345506	NM_003152.3	672	Gac/Aac	17/20	1	2	FACETS	0.377	0.332	0.424	0.377	0.332	0.424	SUBCLONAL	1	TRUE	1	0.556302985409278	2		530	811	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435458	56435458	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	285	619	1	ENST00000407977.2:c.1679A>C	p.Lys560Thr	p.K560T	ENST00000407977		560	aAg/aCg	9/10	0.292695338649706	3	FACETS	1	0.99	1	0.619	0.582	0.657	INDETERMINATE	1	TRUE	1	0.556302985409278	3		620	1058	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291182	10291182	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753670606	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	133	467	0	ENST00000340748.4:c.289C>T	p.His97Tyr	p.H97Y	ENST00000340748		97	Cat/Tat	4/40	0.353845878539246	0	FACETS	0.365	0.332	0.398			1	SUBCLONAL	1	TRUE	0	0.556302985409278	0		467	582	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095023	11095023	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	209	939	0	ENST00000358026.2:c.196C>G	p.Gln66Glu	p.Q66E	ENST00000358026	NM_001128849.1	66	Cag/Gag	2/36	0.353845878539246	0	FACETS	0.339	0.314	0.364			1	SUBCLONAL	1	TRUE	0	0.556302985409278	0		939	984	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139099	50139099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	329	276	1	ENST00000246792.3:c.464C>T	p.Ser155Leu	p.S155L	ENST00000246792	NM_006270.3	155	tCa/tTa	5/6	0.253300609735914	3	FACETS	1	0.993	1	0.811	0.775	0.848	INDETERMINATE	2	TRUE	0	0.556302985409278	3		277	621	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147569	61147569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	15	49	0	ENST00000295025.8:c.974C>T	p.Ser325Leu	p.S325L	ENST00000295025	NM_002908.2	325	tCa/tTa	9/11	1	2	FACETS	0.749	0.56	0.965	0.749	0.56	0.965	CLONAL	1	TRUE	1	0.556302985409278	2		49	72	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084050	47084050	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	65	342	0	ENST00000409792.3:c.7238+1G>T		p.X2413_splice	ENST00000409792	NM_014159.6	2413			0.307636945892787	1	FACETS	0.36	0.312	0.411	0.36	0.312	0.411	INDETERMINATE	1	TRUE	0	0.556302985409278	1		342	469	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164321	47164321	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	69	224	0	ENST00000409792.3:c.1805del	p.Met602ArgfsTer20	p.M602Rfs*20	ENST00000409792	NM_014159.6	602	aTg/ag	3/21	0.307636945892787	1	FACETS	0.722	0.637	0.812	0.722	0.637	0.812	INDETERMINATE	1	TRUE	0	0.556302985409278	1		224	248	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397719	49397719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	271	440	0	ENST00000418115.1:c.505G>A	p.Glu169Lys	p.E169K	ENST00000418115	NM_001664.2	169	Gag/Aag	5/5	0.307636945892787	1	FACETS	0.982	0.927	1	0.982	0.927	1	INDETERMINATE	1	TRUE	0	0.556302985409278	1		440	716	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932639	49932639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747839672	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	145	597	1	ENST00000296474.3:c.3232G>A	p.Glu1078Lys	p.E1078K	ENST00000296474	NM_002447.2	1078	Gag/Aag	14/20	0.307636945892787	1	FACETS	0.401	0.365	0.438	0.401	0.365	0.438	INDETERMINATE	1	TRUE	0	0.556302985409278	1		598	939	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643384	52643384	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	66	314	0	ENST00000394830.3:c.2512G>A	p.Asp838Asn	p.D838N	ENST00000394830	NM_018313.4	838	Gat/Aat	17/30	0.307636945892787	1	FACETS	0.468	0.408	0.532	0.468	0.408	0.532	INDETERMINATE	1	TRUE	0	0.556302985409278	1		314	366	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72891467	72891467	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	69	384	0	ENST00000325599.8:c.295A>C	p.Lys99Gln	p.K99Q	ENST00000325599	NM_018130.2	99	Aaa/Caa	3/11	0.307636945892787	1	FACETS	0.349	0.304	0.397	0.349	0.304	0.397	INDETERMINATE	1	TRUE	0	0.556302985409278	1		384	513	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189585651	189585651	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	139	382	0	ENST00000264731.3:c.912C>A	p.Tyr304Ter	p.Y304*	ENST00000264731	NM_003722.4	304	taC/taA	7/14	0.476814299816262	1	FACETS	0.876	0.805	0.948	0.876	0.805	0.948	CLONAL	1	TRUE	0	0.556302985409278	1		382	412	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287398	33287398	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	120	452	0	ENST00000374542.5:c.1699T>G	p.Phe567Val	p.F567V	ENST00000374542	NM_001141970.1	567	Ttt/Gtt	6/8	0.219104027150794	6	FACETS	0.891	0.803	0.984			1	INDETERMINATE	1	TRUE	NA	0.556302985409278	6		452	1023	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072564	5072564	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	97	296	0	ENST00000381652.3:c.1714C>T	p.Gln572Ter	p.Q572*	ENST00000381652	NM_004972.3	572	Caa/Taa	13/25	0.361634344609596	1	FACETS	0.782	0.705	0.862	0.782	0.705	0.862	SUBCLONAL	1	TRUE	0	0.556302985409278	1		296	322	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93627348	93627348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752623158	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	141	335	0	ENST00000375746.1:c.815G>A	p.Gly272Asp	p.G272D	ENST00000375746	NM_001174167.1	272	gGc/gAc	6/14	0.361634344609596	1	FACETS	0.811	0.745	0.879	0.811	0.745	0.879	CLONAL	1	TRUE	0	0.556302985409278	1		335	451	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395225	139395225	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1330630388	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	365	765	0	ENST00000277541.6:c.5713G>A	p.Asp1905Asn	p.D1905N	ENST00000277541	NM_017617.3	1905	Gac/Aac	31/34	0.361634344609596	1	FACETS	0.931	0.885	0.978	0.931	0.885	0.978	CLONAL	1	TRUE	0	0.556302985409278	1		765	1017	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938092	76938092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047193-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	65	407	0	ENST00000373344.5:c.2656G>A	p.Glu886Lys	p.E886K	ENST00000373344	NM_000489.3	886	Gag/Aag	9/35	1	2	FACETS	0.415	0.36	0.475	0.415	0.36	0.475	SUBCLONAL	1	TRUE	1	0.556302985409278	2		407	563	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0047201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	161	413	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.269480346874325	5	FACETS	1	0.982	1			1	CLONAL	2	FALSE	NA	0.269480346874325	5		413	682	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	270	468	0				ENST00000310581	NM_198253.2	-/1132			0.578447973517026	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.647238640081388	4		468	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	781	1017	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.647238640081388	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.647238640081388	2		1017	1078	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435317	56435317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200066146	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	159	912	0	ENST00000407977.2:c.1820C>T	p.Ser607Leu	p.S607L	ENST00000407977		607	tCg/tTg	9/10	0.399340499638201	5	FACETS	0.715	0.653	0.779	0.238	0.217	0.26	SUBCLONAL	1	TRUE	2	0.647238640081388	5		912	1355	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260544	10260544	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1201583942	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	87	588	0	ENST00000340748.4:c.2318C>T	p.Pro773Leu	p.P773L	ENST00000340748		773	cCg/cTg	24/40	0.399340499638201	5	FACETS	0.546	0.482	0.614	0.182	0.16	0.205	SUBCLONAL	1	TRUE	2	0.647238640081388	5		588	971	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437616	110437616	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1425	137	895	0	ENST00000375856.3:c.785C>T	p.Ser262Leu	p.S262L	ENST00000375856	NM_003749.2	262	tCg/tTg	1/2	0.586037636152974	4	FACETS	0.446	0.404	0.491			1	SUBCLONAL	1	TRUE	NA	0.647238640081388	4		895	1562	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481600	56481600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1176464861	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	289	764	1	ENST00000267101.3:c.635C>T	p.Pro212Leu	p.P212L	ENST00000267101	NM_001982.3	212	cCt/cTt	6/28	0.364771753460767	2	FACETS	1	0.989	1	0.591	0.558	0.623	INDETERMINATE	1	TRUE	0	0.647238640081388	2		765	756	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023303	27023303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	81	251	1	ENST00000324856.7:c.409C>T	p.His137Tyr	p.H137Y	ENST00000324856	NM_006015.4	137	Cac/Tac	1/20	0.543428227074014	3	FACETS	0.785	0.695	0.881	0.262	0.231	0.294	SUBCLONAL	1	TRUE	0	0.647238640081388	3		252	422	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573200	41573200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	154	907	2	ENST00000263253.7:c.5485C>T	p.Arg1829Cys	p.R1829C	ENST00000263253	NM_001429.3	1829	Cgc/Tgc	31/31	0.647238640081388	1	FACETS	0.473	0.433	0.513	0.473	0.433	0.513	SUBCLONAL	1	TRUE	0	0.647238640081388	1		909	681	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378633	25378633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	107	429	0	ENST00000311936.3:c.365C>T	p.Ser122Phe	p.S122F	ENST00000311936	NM_004985.3	122	tCt/tTt	4/5	0.355014287385109	4	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.647238640081388	4		429	420	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622495	158622495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316254232	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	89	488	0	ENST00000263640.3:c.1004G>A	p.Arg335Gln	p.R335Q	ENST00000263640	NM_001105.4	335	cGa/cAa	8/11	0.364771753460767	2	FACETS	0.538	0.478	0.602	0.269	0.239	0.301	INDETERMINATE	1	TRUE	0	0.647238640081388	2		488	511	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872475	35872475	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	649	611	0	ENST00000216797.5:c.428G>C	p.Arg143Pro	p.R143P	ENST00000216797	NM_020529.2	143	cGa/cCa	3/6	0.647238640081388	6	FACETS	0.87	0.837	0.902			1	CLONAL	3	TRUE	NA	0.647238640081388	6		611	1764	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961321	54961321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs2230743	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	146	597	0	ENST00000312783.6:c.311C>T	p.Ser104Leu	p.S104L	ENST00000312783	NM_198436.1	104	tCg/tTg	4/10	0.647238640081388	5	FACETS	0.772	0.703	0.844	0.257	0.234	0.282	SUBCLONAL	1	TRUE	2	0.647238640081388	5		597	1152	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156155	106156155	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	102	340	0	ENST00000380013.4:c.1056C>G	p.Phe352Leu	p.F352L	ENST00000380013	NM_001127208.2	352	ttC/ttG	3/11	0.647238640081388	3	FACETS	1	0.915	1	0.339	0.305	0.375	CLONAL	1	TRUE	0	0.647238640081388	3		340	410	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687129	37687129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	334	596	1	ENST00000447079.4:c.4033G>A	p.Glu1345Lys	p.E1345K	ENST00000447079	NM_015083.1	1345	Gaa/Aaa	14/14	0.399340499638201	5	FACETS	1	0.961	1	0.678	0.642	0.714	CLONAL	2	TRUE	2	0.647238640081388	5		597	1000	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435981	56435981	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777370175	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	108	629	1	ENST00000407977.2:c.1156C>T	p.Arg386Trp	p.R386W	ENST00000407977		386	Cgg/Tgg	9/10	0.399340499638201	5	FACETS	0.716	0.642	0.796	0.239	0.214	0.266	SUBCLONAL	1	TRUE	2	0.647238640081388	5		630	918	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056617	26056617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751385999	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	112	289	0	ENST00000343677.2:c.40C>T	p.Pro14Ser	p.P14S	ENST00000343677	NM_005319.3	14	Cct/Tct	1/1	0.545376588727023	4	FACETS	1	0.979	1	0.648	0.586	0.712	CLONAL	1	TRUE	2	0.647238640081388	4		289	440	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097629	27097629	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	207	579	1	ENST00000324856.7:c.3218G>A	p.Trp1073Ter	p.W1073*	ENST00000324856	NM_006015.4	1073	tGg/tAg	12/20	0.543428227074014	3	FACETS	1	0.959	1	0.348	0.323	0.373	CLONAL	1	TRUE	0	0.647238640081388	3		580	811	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430411	78430411	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	74	422	0	ENST00000370768.2:c.757G>C	p.Glu253Gln	p.E253Q	ENST00000370768	NM_003902.3	253	Gag/Cag	10/20	0.543428227074014	3	FACETS	0.609	0.534	0.689	0.203	0.178	0.23	SUBCLONAL	1	TRUE	0	0.647238640081388	3		422	497	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681100	30681100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765107298	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	100	485	0	ENST00000376406.3:c.619G>A	p.Gly207Ser	p.G207S	ENST00000376406	NM_014641.2	207	Ggc/Agc	5/15	0.545376588727023	4	FACETS	0.664	0.593	0.74	0.332	0.296	0.37	SUBCLONAL	1	TRUE	2	0.647238640081388	4		485	766	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281576	142281576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	78	510	0	ENST00000350721.4:c.668G>A	p.Arg223Lys	p.R223K	ENST00000350721	NM_001184.3	223	aGa/aAa	4/47	0.647238640081388	4	FACETS	0.483	0.424	0.547	0.161	0.141	0.183	SUBCLONAL	1	TRUE	1	0.647238640081388	4		510	822	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57567440	57567440	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	124	681	1	ENST00000316660.6:c.31C>A	p.Gln11Lys	p.Q11K	ENST00000316660	NM_021127.2	11	Caa/Aaa	1/2	0.647238640081388	3	FACETS	0.6	0.543	0.661	0.3	0.271	0.331	SUBCLONAL	1	TRUE	1	0.647238640081388	3		682	845	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051676	13051676	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	93	589	0	ENST00000316448.5:c.935G>A	p.Gly312Asp	p.G312D	ENST00000316448	NM_004343.3	312	gGc/gAc	7/9	0.224694893004168	5	FACETS	0.565	0.501	0.634	0.188	0.167	0.212	INDETERMINATE	1	TRUE	2	0.647238640081388	5		589	1002	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741153	145741153	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs548957135	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	126	637	2	ENST00000428558.2:c.1253G>A	p.Arg418Gln	p.R418Q	ENST00000428558	NM_004260.3	418	cGg/cAg	6/22	NA	2	FACETS	0.578	0.524	0.634			1	INDETERMINATE	1	TRUE	NA	0.647238640081388	2		639	674	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007560	62007560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	311	884	1	ENST00000392795.3:c.307G>A	p.Glu103Lys	p.E103K	ENST00000392795	NM_001039933.1	103	Gaa/Aaa	3/6	0.343671003650649	3	FACETS	1	0.987	1	0.384	0.362	0.406	INDETERMINATE	1	TRUE	0	0.647238640081388	3		885	1105	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517446	157517446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761133847	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	179	498	0	ENST00000346085.5:c.4010G>A	p.Arg1337Gln	p.R1337Q	ENST00000346085	NM_020732.3	1337	cGa/cAa	16/20	0.343671003650649	3	FACETS	1	0.982	1	0.396	0.366	0.426	INDETERMINATE	1	TRUE	0	0.647238640081388	3		498	617	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778967	9778967	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	311	678	0	ENST00000377346.4:c.1236G>C	p.Lys412Asn	p.K412N	ENST00000377346	NM_005026.3	412	aaG/aaC	9/24	0.47324302550283	3	FACETS	0.767	0.727	0.808	0.511	0.484	0.539	SUBCLONAL	2	TRUE	0	0.647238640081388	3		678	829	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101657	27101657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1201	175	1018	2	ENST00000324856.7:c.4939G>A	p.Glu1647Lys	p.E1647K	ENST00000324856	NM_006015.4	1647	Gaa/Aaa	18/20	0.543428227074014	3	FACETS	0.52	0.477	0.565	0.173	0.159	0.189	SUBCLONAL	1	TRUE	0	0.647238640081388	3		1020	1376	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429310	78429310	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	97	525	0	ENST00000370768.2:c.1132G>C	p.Glu378Gln	p.E378Q	ENST00000370768	NM_003902.3	378	Gaa/Caa	13/20	0.543428227074014	3	FACETS	0.586	0.523	0.653	0.195	0.174	0.218	SUBCLONAL	1	TRUE	0	0.647238640081388	3		525	677	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166069	118166069	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	57	369	0	ENST00000369448.3:c.579C>G	p.Phe193Leu	p.F193L	ENST00000369448	NM_017709.3	193	ttC/ttG	2/2	0.647238640081388	3	FACETS	0.469	0.403	0.541	0.235	0.201	0.271	SUBCLONAL	1	TRUE	1	0.647238640081388	3		369	497	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243392	46243392	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	39	276	0	ENST00000334344.6:c.1745G>C	p.Arg582Thr	p.R582T	ENST00000334344	NM_152641.2	582	aGa/aCa	14/21	0.644992184366886	3	FACETS	0.43	0.357	0.511	0.215	0.178	0.256	SUBCLONAL	1	TRUE	1	0.647238640081388	3		276	371	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222565	69222565	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	65	338	0	ENST00000462284.1:c.538G>T	p.Glu180Ter	p.E180*	ENST00000462284	NM_002392.5	180	Gaa/Taa	8/11	0.364771753460767	2	FACETS	0.674	0.589	0.764	0.337	0.294	0.382	INDETERMINATE	1	TRUE	0	0.647238640081388	2		338	298	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123880945	123880945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	68	402	0	ENST00000330479.4:c.563G>A	p.Arg188Gln	p.R188Q	ENST00000330479	NM_020382.3	188	cGa/cAa	5/9	0.364771753460767	2	FACETS	0.524	0.458	0.595	0.262	0.229	0.298	INDETERMINATE	1	TRUE	0	0.647238640081388	2		402	401	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871605	35871605	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	56	330	0	ENST00000216797.5:c.901G>T	p.Asp301Tyr	p.D301Y	ENST00000216797	NM_020529.2	301	Gac/Tac	5/6	0.647238640081388	6	FACETS	0.498	0.426	0.578			1	SUBCLONAL	1	TRUE	NA	0.647238640081388	6		330	797	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847234	68847234	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	81	491	0	ENST00000261769.5:c.1156G>C	p.Glu386Gln	p.E386Q	ENST00000261769	NM_004360.3	386	Gag/Cag	9/16	0.647238640081388	3	FACETS	0.404	0.355	0.457	0.202	0.177	0.229	SUBCLONAL	1	TRUE	1	0.647238640081388	3		491	820	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243029	41243029	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	214	568	0	ENST00000357654.3:c.4117G>C	p.Glu1373Gln	p.E1373Q	ENST00000357654	NM_007294.3	1373	Gag/Cag	11/23	0.399340499638201	5	FACETS	0.795	0.74	0.851	0.53	0.493	0.567	SUBCLONAL	2	TRUE	2	0.647238640081388	5		568	820	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619361	1619361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1417	188	1093	0	ENST00000344749.5:c.1280C>T	p.Ser427Leu	p.S427L	ENST00000344749	NM_001136139.2	427	tCa/tTa	15/19	0.224694893004168	5	FACETS	0.713	0.657	0.773	0.238	0.219	0.258	INDETERMINATE	1	TRUE	2	0.647238640081388	5		1093	1605	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099368	4099368	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1327	319	1051	0	ENST00000262948.5:c.750C>G	p.Ile250Met	p.I250M	ENST00000262948	NM_030662.3	250	atC/atG	7/11	0.224694893004168	5	FACETS	1	0.988	1	0.393	0.37	0.418	INDETERMINATE	1	TRUE	2	0.647238640081388	5		1051	1646	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627527	14627527	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	103	612	0	ENST00000254322.2:c.543G>C	p.Lys181Asn	p.K181N	ENST00000254322	NM_006145.1	181	aaG/aaC	2/3	0.224694893004168	5	FACETS	0.791	0.708	0.88	0.264	0.236	0.294	INDETERMINATE	1	TRUE	2	0.647238640081388	5		612	793	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218104	36218104	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	175	486	0	ENST00000222270.7:c.4051G>A	p.Glu1351Lys	p.E1351K	ENST00000222270	NM_014727.1	1351	Gag/Aag	15/37	0.233215065988785	4	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.647238640081388	4		486	700	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856583	45856583	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1427879797	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1722	243	673	0	ENST00000391945.4:c.1675G>C	p.Glu559Gln	p.E559Q	ENST00000391945	NM_000400.3	559	Gag/Cag	18/23	0.647238640081388	7	FACETS	1	0.931	1			1	CLONAL	1	TRUE	NA	0.647238640081388	7		673	1965	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085891	16085891	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	105	612	0	ENST00000281043.3:c.1067C>G	p.Pro356Arg	p.P356R	ENST00000281043	NM_005378.4	356	cCa/cGa	3/3	NA	2	FACETS	0.513	0.461	0.569			1	INDETERMINATE	1	TRUE	NA	0.647238640081388	2		612	632	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419862	41419862	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	147	586	0	ENST00000373198.4:c.459C>G	p.Ile153Met	p.I153M	ENST00000373198	NM_133170.3	153	atC/atG	3/32	0.586037636152974	4	FACETS	0.779	0.711	0.851			1	SUBCLONAL	1	TRUE	NA	0.647238640081388	4		586	960	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268387	46268387	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	142	361	0	ENST00000371998.3:c.2774C>G	p.Ser925Ter	p.S925*	ENST00000371998		925	tCa/tGa	15/23	0.647238640081388	5	FACETS	0.989	0.902	1	0.33	0.3	0.361	CLONAL	1	TRUE	2	0.647238640081388	5		361	874	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57470738	57470738	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	38	279	0	ENST00000371085.3:c.211G>A	p.Glu71Lys	p.E71K	ENST00000371085	NM_000516.4	71	Gag/Aag	2/13	0.647238640081388	5	FACETS	0.353	0.291	0.422	0.118	0.097	0.141	SUBCLONAL	1	TRUE	2	0.647238640081388	5		279	656	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545825	41545825	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	37	676	2	ENST00000263253.7:c.2440G>A	p.Gly814Arg	p.G814R	ENST00000263253	NM_001429.3	814	Ggg/Agg	14/31	0.647238640081388	1	FACETS	0.117	0.096	0.141	0.117	0.096	0.141	SUBCLONAL	1	TRUE	0	0.647238640081388	1		678	661	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548327	41548327	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	139	385	0	ENST00000263253.7:c.3115C>G	p.Pro1039Ala	p.P1039A	ENST00000263253	NM_001429.3	1039	Ccg/Gcg	16/31	0.647238640081388	1	FACETS	0.854	0.789	0.921	0.854	0.789	0.921	CLONAL	1	TRUE	0	0.647238640081388	1		385	340	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41560115	41560115	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs773553894	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	58	371	0	ENST00000263253.7:c.3787G>C	p.Glu1263Gln	p.E1263Q	ENST00000263253	NM_001429.3	1263	Gag/Cag	22/31	0.647238640081388	1	FACETS	0.364	0.314	0.418	0.364	0.314	0.418	SUBCLONAL	1	TRUE	0	0.647238640081388	1		371	333	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421306	12421306	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	111	626	0	ENST00000287820.6:c.186C>G	p.Ile62Met	p.I62M	ENST00000287820	NM_015869.4	62	atC/atG	2/7	0.399340499638201	5	FACETS	0.585	0.524	0.649	0.195	0.174	0.217	SUBCLONAL	1	TRUE	2	0.647238640081388	5		626	1156	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266052	41266052	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	57	248	0	ENST00000349496.5:c.49G>C	p.Asp17His	p.D17H	ENST00000349496	NM_001904.3	17	Gac/Cac	3/15	0.399340499638201	5	FACETS	0.751	0.646	0.866	0.25	0.215	0.289	SUBCLONAL	1	TRUE	2	0.647238640081388	5		248	462	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670741	134670741	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	111	648	0	ENST00000398015.3:c.652C>G	p.Leu218Val	p.L218V	ENST00000398015	NM_004441.4	218	Ctg/Gtg	3/16	0.647238640081388	4	FACETS	0.476	0.426	0.528	0.159	0.142	0.176	SUBCLONAL	1	TRUE	1	0.647238640081388	4		648	1188	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665159	138665159	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1224	141	752	0	ENST00000330315.3:c.406G>C	p.Asp136His	p.D136H	ENST00000330315	NM_023067.3	136	Gac/Cac	1/1	0.647238640081388	4	FACETS	0.526	0.477	0.577	0.175	0.159	0.193	SUBCLONAL	1	TRUE	1	0.647238640081388	4		752	1365	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136912	55136912	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	149	331	0	ENST00000257290.5:c.1234C>G	p.Gln412Glu	p.Q412E	ENST00000257290	NM_006206.4	412	Caa/Gaa	8/23	0.647238640081388	3	FACETS	1	0.958	1	0.534	0.49	0.579	CLONAL	1	TRUE	1	0.647238640081388	3		331	571	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594190	55594190	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	58	348	0	ENST00000288135.5:c.1893G>C	p.Leu631Phe	p.L631F	ENST00000288135	NM_000222.2	631	ttG/ttC	13/21	0.647238640081388	5	FACETS	0.415	0.355	0.48			1	SUBCLONAL	1	TRUE	NA	0.647238640081388	5		348	852	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528306	157528306	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554237841	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	296	808	0	ENST00000346085.5:c.6031G>T	p.Glu2011Ter	p.E2011*	ENST00000346085	NM_020732.3	2011	Gag/Tag	20/20	0.343671003650649	3	FACETS	1	0.99	1	0.412	0.388	0.436	INDETERMINATE	1	TRUE	0	0.647238640081388	3		808	980	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395496	116395496	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs769073123	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	170	466	0	ENST00000397752.3:c.1789G>C	p.Asp597His	p.D597H	ENST00000397752	NM_000245.2	597	Gat/Cat	6/21	0.647238640081388	3	FACETS	1	0.985	1	0.625	0.578	0.673	CLONAL	1	TRUE	1	0.647238640081388	3		466	556	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869557	117869557	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	53	367	0	ENST00000297338.2:c.637G>C	p.Asp213His	p.D213H	ENST00000297338	NM_006265.2	213	Gat/Cat	6/14	0.355014287385109	4	FACETS	0.602	0.514	0.698			1	INDETERMINATE	1	TRUE	NA	0.647238640081388	4		367	448	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750538	128750538	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	150	692	1	ENST00000377970.2:c.75G>T	p.Arg25Ser	p.R25S	ENST00000377970	NM_002467.4	25	agG/agT	2/3	0.355014287385109	4	FACETS	0.75	0.685	0.819			1	INDETERMINATE	1	TRUE	NA	0.647238640081388	4		693	1018	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5029853	5029853	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	47	515	0	ENST00000381652.3:c.297C>G	p.Asn99Lys	p.N99K	ENST00000381652	NM_004972.3	99	aaC/aaG	4/25	1	2	FACETS	0.38	0.321	0.445	0.38	0.321	0.445	SUBCLONAL	1	TRUE	1	0.647238640081388	2		515	382	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53254035	53254035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	135	795	0	ENST00000375401.3:c.37G>A	p.Glu13Lys	p.E13K	ENST00000375401	NM_004187.3	13	Gag/Aag	1/26	0.41127087879351	3	FACETS	0.567	0.514	0.622			1	SUBCLONAL	1	TRUE	NA	0.647238640081388	3		795	974	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0047246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	360	590	1	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.703439888805411	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.717798815510302	1		591	630	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402607	20402608	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCCGCT	rs758546976	NA	P-0047246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	80	343	0	ENST00000346618.3:c.150_155dup	p.Ala52_Ala53dup	p.A52_A53dup	ENST00000346618	NM_001949.4	52	-/GCCGCT	1/7	0.706145563419432	1	FACETS	0.399	0.354	0.447	0.399	0.354	0.447	SUBCLONAL	1	TRUE	0	0.717798815510302	1		343	358	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869695	117869695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	168	269	0	ENST00000297338.2:c.499G>A	p.Asp167Asn	p.D167N	ENST00000297338	NM_006265.2	167	Gat/Aat	6/14	0.717798815510302	3	FACETS	0.89	0.82	0.962	0.445	0.41	0.481	CLONAL	1	TRUE	1	0.717798815510302	3		269	715	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047421-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	83	468	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.972	1			1	INDETERMINATE	1	TRUE	NA	0.308987695604566	2		468	405	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670597	134670597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1330628001	NA	P-0047421-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	157	760	1	ENST00000398015.3:c.508C>T	p.Arg170Trp	p.R170W	ENST00000398015	NM_004441.4	170	Cgg/Tgg	3/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.308987695604566	2		761	969	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286812	212286812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047421-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	43	428	0	ENST00000342788.4:c.2884G>A	p.Asp962Asn	p.D962N	ENST00000342788	NM_005235.2	962	Gac/Aac	24/28	1	2	FACETS	0.661	0.554	0.78	0.661	0.554	0.78	SUBCLONAL	1	TRUE	1	0.308987695604566	2		428	421	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056294	27056294	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047421-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	183	570	1	ENST00000324856.7:c.1292del	p.Pro431ArgfsTer2	p.P431Rfs*2	ENST00000324856	NM_006015.4	430	taC/ta	2/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.308987695604566	2		571	791	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938499	44938505	+	frameshift_variant	Frame_Shift_Del	DEL	GAACAAA	GAACAAA	-	novel	NA	P-0047421-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	112	278	0	ENST00000377967.4:c.3050_3056del	p.Thr1017LysfsTer29	p.T1017Kfs*29	ENST00000377967	NM_021140.2	1016	gGAACAAAg/gg	20/29	0.0814953712175952	2	FACETS	1	0.971	1			1	INDETERMINATE	2	TRUE	NA	0.308987695604566	2		278	314	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123629	108123629	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs148191382	NA	P-0047421-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	40	377	0	ENST00000278616.4:c.1888G>C	p.Val630Leu	p.V630L	ENST00000278616	NM_000051.3	630	Gtg/Ctg	12/63	0.232875001097038	2	FACETS	0.624	0.519	0.741	0.312	0.259	0.371	SUBCLONAL	1	TRUE	0	0.308987695604566	2		377	415	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536671	120536671	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047421-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	94	707	0	ENST00000229340.5:c.421C>T	p.Gln141Ter	p.Q141*	ENST00000229340	NM_006861.6	141	Cag/Tag	5/6	1	2	FACETS	0.59	0.523	0.661	0.59	0.523	0.661	SUBCLONAL	1	TRUE	1	0.308987695604566	2		707	1032	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0047477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	130	372	2	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		374	754	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106355	27106355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773909963	NA	P-0047477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	223	299	0	ENST00000324856.7:c.5966G>A	p.Arg1989Gln	p.R1989Q	ENST00000324856	NM_006015.4	1989	cGa/cAa	20/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		299	488	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604673	48604673	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060500738	NA	P-0047477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	124	353	0	ENST00000342988.3:c.1495T>C	p.Cys499Arg	p.C499R	ENST00000342988	NM_005359.5	499	Tgc/Cgc	12/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		353	311	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577501	7577501	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	rs1427471466	NA	P-0047477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	225	305	0	ENST00000269305.4:c.780del	p.Ser261ValfsTer84	p.S261Vfs*84	ENST00000269305	NM_001126112.2	260	tcC/tc	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		305	626	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446321	70446321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	99	455	0	ENST00000373644.4:c.5261C>T	p.Ser1754Phe	p.S1754F	ENST00000373644	NM_030625.2	1754	tCt/tTt	11/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		455	512	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0047477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	178	469	0	ENST00000304494.5:c.151-1G>A		p.X51_splice	ENST00000304494	NM_000077.4	51			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		469	409	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715789	18715789	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	59	284	0	ENST00000266497.5:c.3620G>C	p.Arg1207Thr	p.R1207T	ENST00000266497		1207	aGa/aCa	25/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		284	248	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415906	49415906	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	149	276	0	ENST00000301067.7:c.16441T>C	p.Cys5481Arg	p.C5481R	ENST00000301067	NM_003482.3	5481	Tgt/Cgt	53/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		276	509	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56809865	56809865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567817363	NA	P-0047477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	52	350	0	ENST00000337432.4:c.986C>T	p.Ser329Leu	p.S329L	ENST00000337432	NM_058216.2	329	tCa/tTa	8/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		350	420	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537128	80537129	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	128	654	0	ENST00000286548.4:c.269dup	p.Met90IlefsTer15	p.M90Ifs*15	ENST00000286548	NM_002072.3	90	atg/atTg	2/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		654	520	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146978	38146980	+	missense_variant	Missense_Mutation	TNP	CTT	CTT	GTA	novel	NA	P-0047477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	236	488	0	ENST00000317025.8:c.3162_3164delinsTAC	p.Gln1054_Arg1055delinsHisThr	p.Q1054_R1055delinsHT	ENST00000317025	NM_023034.1	1054	caAAGa/caTACa	18/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		488	987	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061115	38061115	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1016447126	NA	P-0047497-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	137	234	0	ENST00000250448.2:c.874G>A	p.Glu292Lys	p.E292K	ENST00000250448	NM_004496.3	292	Gag/Aag	2/2	0.633943202045478	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.633943202045478	1		234	239	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129643	2129652	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCGGGATC	GCCCGGGATC	AT	novel	NA	P-0047497-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	397	954	3	ENST00000219476.3:c.3370_3379delinsAT	p.Ala1124MetfsTer41	p.A1124Mfs*41	ENST00000219476	NM_000548.3	1124	GCCCGGGATCgg/ATgg	29/42	0.596993213418774	3	FACETS	1	0.981	1	0.534	0.506	0.562	CLONAL	1	TRUE	1	0.633943202045478	3		957	1545	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	343	825	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.962	1	1	0.997	1	CLONAL	4	TRUE	1	0.219175889903349	2		829	773	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	209	454	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.993	0.932	1	1	0.996	1	CLONAL	4	TRUE	1	0.219175889903349	2		459	480	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	213	388	4	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	1	0.978	1	1	0.996	1	CLONAL	4	TRUE	1	0.219175889903349	2		392	450	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	193	366	1	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	0.929	0.868	0.99	1	0.995	1	CLONAL	4	TRUE	1	0.219175889903349	2		367	474	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	142	396	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.0144374057828971	3	FACETS	1	0.97	1	1	0.992	1	INDETERMINATE	4	TRUE	1	0.219175889903349	3		396	329	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920469	134920469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	301	574	5	ENST00000398015.3:c.2284G>A	p.Asp762Asn	p.D762N	ENST00000398015	NM_004441.4	762	Gac/Aac	12/16	1	2	FACETS	1	0.961	1	1	0.997	1	CLONAL	4	TRUE	1	0.219175889903349	2		579	677	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088787	27088788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	310	500	0	ENST00000324856.7:c.2402dup	p.Gln802SerfsTer15	p.Q802Sfs*15	ENST00000324856	NM_006015.4	799	cag/caGg	7/20	1	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	4	TRUE	1	0.219175889903349	2		500	630	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	94	274	0	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	1	2	FACETS	0.966	0.877	1	1	0.991	1	CLONAL	4	TRUE	1	0.219175889903349	2		274	222	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	318	729	1	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	1	0.976	1	1	0.997	1	CLONAL	4	TRUE	1	0.219175889903349	2		730	695	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	335	842	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	1	0.972	1	1	0.997	1	CLONAL	4	TRUE	1	0.219175889903349	2		843	743	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	129	357	15	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	1	0.954	1	1	0.993	1	CLONAL	4	TRUE	1	0.219175889903349	2		372	281	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940012	76940012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs122445105	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	217	271	0	ENST00000373344.5:c.736C>T	p.Arg246Cys	p.R246C	ENST00000373344	NM_000489.3	246	Cgc/Tgc	9/35	1	1	FACETS	0.954	0.933	0.972	1	0.996	1	CLONAL	8	TRUE	0	0.219175889903349	1		271	231	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189085	32189085	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762851866	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	239	487	3	ENST00000375023.3:c.469C>T	p.Arg157Trp	p.R157W	ENST00000375023	NM_004557.3	157	Cgg/Tgg	4/30	1	2	FACETS	0.94	0.885	0.996	1	0.996	1	CLONAL	4	TRUE	1	0.219175889903349	2		490	580	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154241	2154242	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755455183	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	268	763	4	ENST00000434045.2:c.686dup	p.Glu230ArgfsTer50	p.E230Rfs*50	ENST00000434045	NM_001127598.1	229	cca/ccCa	5/5	1	2	FACETS	1	0.971	1	1	0.996	1	CLONAL	3	TRUE	1	0.219175889903349	2		767	778	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945008	31945008	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	388	697	2	ENST00000340398.3:c.93del	p.Ser32LeufsTer5	p.S32Lfs*5	ENST00000340398	NM_001013699.2	31	ccC/cc	1/1	1	2	FACETS	1	0.977	1	1	0.997	1	CLONAL	4	TRUE	1	0.219175889903349	2		699	856	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930730	32930730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs74047012	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	230	460	0	ENST00000380152.3:c.7601C>T	p.Ala2534Val	p.A2534V	ENST00000380152		2534	gCg/gTg	15/27	1	2	FACETS	1	0.961	1	1	0.996	1	CLONAL	4	TRUE	1	0.219175889903349	2		460	512	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	289	655	4	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.94	0.89	0.991	1	0.997	1	CLONAL	4	TRUE	1	0.219175889903349	2		659	701	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280036	18280036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	246	345	2	ENST00000222254.8:c.2119G>A	p.Ala707Thr	p.A707T	ENST00000222254	NM_005027.3	707	Gcg/Acg	16/16	1	2	FACETS	1	0.977	1	1	0.996	1	CLONAL	4	TRUE	1	0.219175889903349	2		347	528	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968144	18968144	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	341	667	0	ENST00000262803.5:c.1984G>A	p.Asp662Asn	p.D662N	ENST00000262803	NM_002911.3	662	Gac/Aac	15/24	1	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	4	TRUE	1	0.219175889903349	2		667	699	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042709	42042711	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs1159823543	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	128	475	1	ENST00000219905.7:c.6909_6911del	p.Glu2303del	p.E2303del	ENST00000219905	NM_001164273.1	2302	GAA/-	17/24	1	2	FACETS	1	0.974	1	1	0.993	1	CLONAL	3	TRUE	1	0.219175889903349	2		476	339	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733022	74733022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	330	497	2	ENST00000359995.5:c.221C>T	p.Ala74Val	p.A74V	ENST00000359995	NM_001195427.1	74	gCc/gTc	1/3	1	2	FACETS	1	0.981	1	1	0.997	1	CLONAL	4	TRUE	1	0.219175889903349	2		499	712	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120557	2120557	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	412	773	0	ENST00000219476.3:c.1817T>C	p.Ile606Thr	p.I606T	ENST00000219476	NM_000548.3	606	aTc/aCc	17/42	1	2	FACETS	1	0.979	1	1	0.998	1	CLONAL	4	TRUE	1	0.219175889903349	2		773	906	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222816	5222816	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775778266	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	355	606	0	ENST00000357368.4:c.2987C>T	p.Thr996Met	p.T996M	ENST00000357368	NM_002850.3	996	aCg/aTg	18/38	1	2	FACETS	1	0.981	1	1	0.997	1	CLONAL	4	TRUE	1	0.219175889903349	2		606	770	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169036	32169036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745902446	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	51	672	1	ENST00000375023.3:c.3997C>T	p.Arg1333Cys	p.R1333C	ENST00000375023	NM_004557.3	1333	Cgt/Tgt	22/30	1	2	FACETS	0.652	0.553	0.761	0.652	0.553	0.761	SUBCLONAL	1	TRUE	1	0.219175889903349	2		673	714	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677912	117677912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765109582	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	33	416	0	ENST00000368508.3:c.4021G>A	p.Ala1341Thr	p.A1341T	ENST00000368508	NM_002944.2	1341	Gct/Act	25/43	1	2	FACETS	0.799	0.651	0.965	0.799	0.651	0.965	CLONAL	1	TRUE	1	0.219175889903349	2		416	377	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856274	111856274	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	95	50	2	ENST00000341259.2:c.325G>A	p.Gly109Ser	p.G109S	ENST00000341259	NM_005475.2	109	Ggc/Agc	2/8	1	2	FACETS	1	0.964	1	1	0.992	1	CLONAL	5	TRUE	1	0.219175889903349	2		52	160	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574584	41574584	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	358	643	2	ENST00000263253.7:c.6869A>G	p.Gln2290Arg	p.Q2290R	ENST00000263253	NM_001429.3	2290	cAg/cGg	31/31	1	2	FACETS	0.914	0.869	0.958	1	0.997	1	CLONAL	4	TRUE	1	0.219175889903349	2		645	894	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023765	27023765	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	130	281	2	ENST00000324856.7:c.871G>C	p.Ala291Pro	p.A291P	ENST00000324856	NM_006015.4	291	Gcc/Ccc	1/20	1	2	FACETS	1	0.97	1	1	0.993	1	CLONAL	3	TRUE	1	0.219175889903349	2		283	353	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803902	43803902	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs368753117	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	311	462	0	ENST00000372470.3:c.212G>A	p.Arg71Gln	p.R71Q	ENST00000372470	NM_005373.2	71	cGg/cAg	2/12	1	2	FACETS	0.914	0.87	0.958	1	0.997	1	CLONAL	5	TRUE	1	0.219175889903349	2		462	621	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438235	49438236	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	326	548	1	ENST00000301067.7:c.5033_5034del	p.Lys1678ArgfsTer12	p.K1678Rfs*12	ENST00000301067	NM_003482.3	1678	aAA/a	20/54	1	2	FACETS	0.984	0.935	1	1	0.997	1	CLONAL	4	TRUE	1	0.219175889903349	2		549	756	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384783	17384783	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772589405	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	317	608	2	ENST00000359435.4:c.415G>A	p.Asp139Asn	p.D139N	ENST00000359435	NM_001033549.1	139	Gac/Aac	4/9	1	2	FACETS	1	0.96	1	1	0.997	1	CLONAL	4	TRUE	1	0.219175889903349	2		610	715	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439680	220439680	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	338	859	0	ENST00000243786.2:c.533T>C	p.Val178Ala	p.V178A	ENST00000243786	NM_002191.3	178	gTg/gCg	2/2	1	2	FACETS	0.989	0.941	1	1	0.997	1	CLONAL	4	TRUE	1	0.219175889903349	2		859	780	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542762	187542762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	154	479	0	ENST00000441802.2:c.4978G>A	p.Ala1660Thr	p.A1660T	ENST00000441802	NM_005245.3	1660	Gct/Act	10/27	0.0144374057828971	3	FACETS	0.917	0.853	0.982	1	0.993	1	INDETERMINATE	5	TRUE	1	0.219175889903349	3		479	340	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402523	20402523	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770338281	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	331	396	2	ENST00000346618.3:c.64del	p.Ala22ArgfsTer18	p.A22Rfs*18	ENST00000346618	NM_001949.4	20	gaG/ga	1/7	0.183607815140053	3	FACETS	1	0.955	1	1	0.997	1	CLONAL	5	TRUE	1	0.219175889903349	3		398	669	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729357	41729357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	253	570	1	ENST00000242208.4:c.1172G>A	p.Cys391Tyr	p.C391Y	ENST00000242208	NM_002192.2	391	tGt/tAt	3/3	1	2	FACETS	0.962	0.908	1	1	0.996	1	CLONAL	4	TRUE	1	0.219175889903349	2		571	600	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8525033	8525033	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047668-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	154	324	0	ENST00000356435.5:c.571G>A	p.Ala191Thr	p.A191T	ENST00000356435		191	Gcc/Acc	7/35	1	2	FACETS	0.913	0.851	0.974	1	0.994	1	CLONAL	5	TRUE	1	0.219175889903349	2		324	308	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0047744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	25	251	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.286	0.224	0.357	0.286	0.224	0.357	SUBCLONAL	1	TRUE	1	0.32	2		251	547	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0047744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	75	643	1	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	1	2	FACETS	0.441	0.385	0.502	0.441	0.385	0.502	SUBCLONAL	1	TRUE	1	0.32	2		644	1063	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412958	49412958	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	79	615	1	ENST00000418115.1:c.65T>G	p.Leu22Arg	p.L22R	ENST00000418115	NM_001664.2	22	cTc/cGc	2/5	1	2	FACETS	0.442	0.388	0.502	0.442	0.388	0.502	SUBCLONAL	1	TRUE	1	0.32	2		616	1116	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002915	69002915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1393555535	NA	P-0047744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	66	302	0	ENST00000288368.4:c.2215G>A	p.Val739Ile	p.V739I	ENST00000288368	NM_024870.2	739	Gtt/Att	20/40	0.235459725781089	3	FACETS	0.848	0.737	0.969	0.424	0.368	0.485	CLONAL	1	TRUE	1	0.32	3		302	564	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130426	29130426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750596499	NA	P-0047744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	122	575	2	ENST00000328354.6:c.284G>A	p.Arg95Gln	p.R95Q	ENST00000328354	NM_007194.3	95	cGa/cAa	2/15	1	2	FACETS	0.763	0.689	0.842	0.763	0.689	0.842	SUBCLONAL	1	TRUE	1	0.32	2		577	999	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845735	68845746	+	inframe_deletion	In_Frame_Del	DEL	TGTGGTCACCAC	TGTGGTCACCAC	-	novel	NA	P-0047744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	59	407	0	ENST00000261769.5:c.983_994del	p.Val328_Thr331del	p.V328_T331del	ENST00000261769	NM_004360.3	327	agTGTGGTCACCACt/agt	7/16	1	2	FACETS	0.551	0.474	0.636	0.551	0.474	0.636	SUBCLONAL	1	TRUE	1	0.32	2		407	669	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578488	7578490	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	novel	NA	P-0047744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1327	113	875	1	ENST00000269305.4:c.440_442del	p.Val147del	p.V147del	ENST00000269305	NM_001126112.2	147	gTTGat/gat	5/11	1	2	FACETS	0.49	0.439	0.545	0.49	0.439	0.545	SUBCLONAL	1	TRUE	1	0.32	2		876	1440	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162736	47162736	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	43	394	1	ENST00000409792.3:c.3390G>T	p.Lys1130Asn	p.K1130N	ENST00000409792	NM_014159.6	1130	aaG/aaT	3/21	1	2	FACETS	0.429	0.358	0.508	0.429	0.358	0.508	SUBCLONAL	1	TRUE	1	0.32	2		395	626	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224466	53224466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	80	332	0	ENST00000375401.3:c.3247G>A	p.Glu1083Lys	p.E1083K	ENST00000375401	NM_004187.3	1083	Gag/Aag	21/26	0.114616559844702	2	FACETS	0.882	0.777	0.994			1	INDETERMINATE	1	TRUE	NA	0.32	2		332	567	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048148-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	37	505	0	ENST00000397752.3:c.3028G>A	p.Asp1010Asn	p.D1010N	ENST00000397752	NM_000245.2	1010	Gat/Aat	14/21	1	2	FACETS	0.794	0.656	0.947	1	0.955	1	CLONAL	2	TRUE	1	0.14	2		505	333	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36014578	36014578	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0048148-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	30	410	2	ENST00000358208.4:c.350+1G>A		p.X117_splice	ENST00000358208		117			1	2	FACETS	0.722	0.58	0.883	0.722	0.58	0.883	SUBCLONAL	1	TRUE	1	0.14	2		412	594	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70971074	70971074	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048148-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	23	399	0	ENST00000276594.2:c.1187C>A	p.Ser396Tyr	p.S396Y	ENST00000276594	NM_024504.3	396	tCt/tAt	6/8	1	2	FACETS	0.842	0.656	1	0.842	0.656	1	CLONAL	1	TRUE	1	0.14	2		399	390	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0048300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	109	282	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	0.209861277259491	5	FACETS	0.968	0.879	1	0.645	0.586	0.707	INDETERMINATE	2	TRUE	2	0.67	5		282	337	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0048300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	117	307	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.209861277259491	5	FACETS	0.975	0.889	1	0.65	0.593	0.71	INDETERMINATE	2	TRUE	2	0.67	5		307	359	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	129	488	0	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	0.209861277259491	5	FACETS	1	0.974	1	0.397	0.36	0.435	INDETERMINATE	1	TRUE	2	0.67	5		488	649	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411246	63411246	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	163	293	0	ENST00000330258.3:c.1921C>T	p.Arg641Ter	p.R641*	ENST00000330258	NM_152424.3	641	Cga/Tga	2/2	0.3	2	FACETS	0.977	0.923	1	0.977	0.923	1	INDETERMINATE	2	TRUE	0	0.67	2		293	249	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778007	135778007	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	185	436	0	ENST00000298552.3:c.2376G>T	p.Gln792His	p.Q792H	ENST00000298552	NM_001162426.1	792	caG/caT	18/23	0.209861277259491	3	FACETS	1	0.988	1	0.662	0.615	0.71	INDETERMINATE	1	TRUE	1	0.67	3		436	557	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23635397	23635397	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs767165391	NA	P-0048300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	171	343	0	ENST00000261584.4:c.2767G>T	p.Val923Phe	p.V923F	ENST00000261584	NM_024675.3	923	Gtt/Ttt	8/13	0.209861277259491	4	FACETS	0.851	0.789	0.914	0.851	0.789	0.914	INDETERMINATE	2	TRUE	2	0.67	4		343	501	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0048333-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	92	457	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.335904042162689	3	FACETS	1	0.974	1	0.652	0.582	0.724	CLONAL	1	TRUE	1	0.408768521730264	3		457	416	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0048333-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	88	294	0	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	NA	2	FACETS	1	0.942	1			1	INDETERMINATE	1	TRUE	NA	0.408768521730264	2		294	396	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591825	48591825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767342	NA	P-0048333-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	157	401	0	ENST00000342988.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000342988	NM_005359.5	330	Gaa/Aaa	9/12	0.408768521730264	2	FACETS	0.965	0.895	1	0.965	0.895	1	CLONAL	2	TRUE	0	0.408768521730264	2		401	398	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539018	187539018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374444088	NA	P-0048333-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	151	432	1	ENST00000441802.2:c.8722G>A	p.Val2908Ile	p.V2908I	ENST00000441802	NM_005245.3	2908	Gtc/Atc	10/27	0.219420913945378	4	FACETS	0.987	0.908	1			1	INDETERMINATE	2	TRUE	NA	0.408768521730264	4		433	527	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562641	29562641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854562	NA	P-0048433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	59	428	0	ENST00000356175.3:c.3721C>T	p.Arg1241Ter	p.R1241*	ENST00000356175	NM_000267.3	1241	Cga/Tga	28/57	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.372740341049848	2		428	281	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653151	29653151	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	49	411	0	ENST00000356175.3:c.5086G>T	p.Glu1696Ter	p.E1696*	ENST00000356175	NM_000267.3	1696	Gag/Tag	36/57	1	2	FACETS	0.809	0.688	0.94	0.809	0.688	0.94	CLONAL	1	TRUE	1	0.372740341049848	2		411	325	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151628	55151628	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	61	674	1	ENST00000257290.5:c.2414G>T	p.Gly805Val	p.G805V	ENST00000257290	NM_006206.4	805	gGa/gTa	17/23	0.363339802927255	1	FACETS	0.748	0.649	0.855	0.748	0.649	0.855	SUBCLONAL	1	TRUE	0	0.372740341049848	1		675	356	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615635	100615635	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	69	342	0	ENST00000308731.7:c.697C>A	p.Leu233Ile	p.L233I	ENST00000308731	NM_000061.2	233	Cta/Ata	8/19	1	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.372740341049848	1		342	223	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494642	2494642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	101	984	0	ENST00000355716.4:c.782C>T	p.Pro261Leu	p.P261L	ENST00000355716	NM_003820.2	261	cCt/cTt	8/8	0.372740341049848	1	FACETS	0.746	0.668	0.828	0.746	0.668	0.828	SUBCLONAL	1	TRUE	0	0.372740341049848	1		984	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579356	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAC	novel	NA	P-0048433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	129	989	0	ENST00000269305.4:c.329_331dup	p.Arg110dup	p.R110dup	ENST00000269305	NM_001126112.2	110	ctg/cGTCtg	4/11	0.372740341049848	1	FACETS	0.869	0.79	0.952	0.869	0.79	0.952	CLONAL	1	TRUE	0	0.372740341049848	1		989	648	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39607470	39607470	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	28	279	0	ENST00000262039.4:c.1548G>T	p.Met516Ile	p.M516I	ENST00000262039	NM_002647.2	516	atG/atT	14/25	0.363339802927255	1	FACETS	0.736	0.595	0.894	0.736	0.595	0.894	SUBCLONAL	1	TRUE	0	0.372740341049848	1		279	166	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600426	10600427	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0048433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	132	998	1	ENST00000171111.5:c.1428_1429delinsTT	p.Gly477Cys	p.G477C	ENST00000171111	NM_203500.1	476	ggGGgc/ggTTgc	4/6	0.372740341049848	1	FACETS	0.826	0.751	0.904	0.826	0.751	0.904	CLONAL	1	TRUE	0	0.372740341049848	1		999	698	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662376	227662376	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	95	1046	0	ENST00000305123.5:c.1079G>T	p.Arg360Leu	p.R360L	ENST00000305123	NM_005544.2	360	cGg/cTg	1/2	0.363339802927255	1	FACETS	0.632	0.563	0.706	0.632	0.563	0.706	SUBCLONAL	1	TRUE	0	0.372740341049848	1		1046	656	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264942	46264942	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	96	391	0	ENST00000371998.3:c.1812G>T	p.Glu604Asp	p.E604D	ENST00000371998		604	gaG/gaT	12/23	0.372740341049848	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.372740341049848	1		391	333	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067362	37067362	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	72	480	0	ENST00000231790.2:c.1273A>T	p.Arg425Trp	p.R425W	ENST00000231790	NM_000249.3	425	Agg/Tgg	12/19	1	2	FACETS	0.847	0.743	0.959	0.847	0.743	0.959	CLONAL	1	TRUE	1	0.372740341049848	2		480	456	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129936	55129936	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	53	631	0	ENST00000257290.5:c.470C>A	p.Thr157Asn	p.T157N	ENST00000257290	NM_006206.4	157	aCt/aAt	4/23	0.363339802927255	1	FACETS	0.503	0.429	0.583	0.503	0.429	0.583	SUBCLONAL	1	TRUE	0	0.372740341049848	1		631	460	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176715820	176715820	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	94	390	0	ENST00000439151.2:c.6152G>A	p.Gly2051Asp	p.G2051D	ENST00000439151	NM_022455.4	2051	gGc/gAc	21/23	0.372740341049848	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.372740341049848	1		390	277	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407554	407554	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	43	430	0	ENST00000380956.4:c.1312G>T	p.Glu438Ter	p.E438*	ENST00000380956	NM_001195286.1	438	Gaa/Taa	9/9	0.372740341049848	1	FACETS	0.865	0.731	1	0.865	0.731	1	CLONAL	1	TRUE	0	0.372740341049848	1		430	217	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434475	140434476	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0048433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	40	457	0	ENST00000288602.6:c.2222_2223del	p.Glu741GlyfsTer3	p.E741Gfs*3	ENST00000288602	NM_004333.4	741	gAG/g	18/18	1	2	FACETS	0.439	0.364	0.522	0.439	0.364	0.522	SUBCLONAL	1	TRUE	1	0.372740341049848	2		457	489	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600426	10600426	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	132	994	1	ENST00000171111.5:c.1429G>T	p.Gly477Cys	p.G477C	ENST00000171111	NM_203500.1	477	Ggc/Tgc	4/6	0.372740341049848	1	FACETS	0.826	0.751	0.904	0.826	0.751	0.904	CLONAL	1	TRUE	0	0.372740341049848	1		995	698	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310572	65310572	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	15	363	0	ENST00000342505.4:c.2116G>A	p.Glu706Lys	p.E706K	ENST00000342505	NM_002227.2	706	Gag/Aag	16/25	0.591216454930173	1	FACETS	0.151	0.11	0.2	0.151	0.11	0.2	SUBCLONAL	1	TRUE	0	0.591216454930173	1		363	237	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0048653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	86	175	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.530351722851198	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.530351722851198	1		175	196	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374865	45374865	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	210	367	0	ENST00000262160.6:c.978A>C	p.Glu326Asp	p.E326D	ENST00000262160	NM_005901.5	326	gaA/gaC	8/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.530351722851198	2		367	622	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	218	626	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.745594654450506	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.745594654450506	1		626	356	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510610	38510610	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	280	721	0	ENST00000254066.5:c.864C>A	p.Asp288Glu	p.D288E	ENST00000254066	NM_000964.3	288	gaC/gaA	7/9	0.745594654450506	4	FACETS	0.972	0.911	1	0.486	0.455	0.517	CLONAL	1	TRUE	2	0.745594654450506	4		721	1349	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509377	46509377	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	218	568	0	ENST00000262741.5:c.1354del	p.Val452PhefsTer39	p.V452Ffs*39	ENST00000262741	NM_003629.3	452	Gtt/tt	10/10	0.745594654450506	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.745594654450506	1		568	366	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2089944	2089944	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	269	731	1	ENST00000219066.1:c.920C>A	p.Pro307Gln	p.P307Q	ENST00000219066	NM_002528.5	307	cCg/cAg	6/6	1	2	FACETS	0.946	0.891	1	0.946	0.891	1	CLONAL	1	TRUE	1	0.745594654450506	2		732	763	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713714	52713714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1289736713	NA	P-0048711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	147	371	0	ENST00000394830.3:c.14G>A	p.Arg5Lys	p.R5K	ENST00000394830	NM_018313.4	5	aGa/aAa	2/30	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.745594654450506	2		371	364	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176590	56176591	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0048711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	142	336	0	ENST00000399503.3:c.2141dup	p.Gly715ArgfsTer21	p.G715Rfs*21	ENST00000399503	NM_005921.1	714	gca/gCca	12/20	1	2	FACETS	0.927	0.853	1	0.927	0.853	1	CLONAL	1	TRUE	1	0.745594654450506	2		336	411	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0049080-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	143	756	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	0.380712016008001	1	FACETS	1	0.94	1	1	0.992	1	CLONAL	2	TRUE	0	0.380712016008001	1		756	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0049080-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	39	646	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.348877663609644	1	FACETS	0.855	0.717	1	0.855	0.717	1	CLONAL	1	TRUE	0	0.380712016008001	1		646	194	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572857	41572858	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGA	novel	NA	P-0049080-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	22	530	0	ENST00000263253.7:c.5144_5147dup	p.Ser1716ArgfsTer168	p.S1716Rfs*168	ENST00000263253	NM_001429.3	1714	-/GAGA	31/31	0.223682677562451	1	FACETS	0.403	0.313	0.507	0.403	0.313	0.507	INDETERMINATE	1	TRUE	0	0.380712016008001	1		530	232	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418727	49418727	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049080-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	28	355	0	ENST00000301067.7:c.15787del	p.Val5263CysfsTer12	p.V5263Cfs*12	ENST00000301067	NM_003482.3	5263	Gtg/tg	49/54	0.323888659668253	3	FACETS	0.656	0.526	0.803	0.328	0.263	0.402	SUBCLONAL	1	TRUE	1	0.380712016008001	3		355	267	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974744	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAGCAGCGCCCGCA	CCTCCAGCAGCGCCCGCA	-	novel	NA	P-0049091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	325	286	0	ENST00000304494.5:c.83_100del	p.Val28_Glu33del	p.V28_E33del	ENST00000304494	NM_000077.4	28	gTGCGGGCGCTGCTGGAGGcg/gcg	1/3	0.593263340610811	3	FACETS	0.966	0.929	1	0.966	0.929	1	CLONAL	3	TRUE	0	0.593263340610811	3		286	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0049091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	440	631	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.586919790595795	4	FACETS	0.991	0.947	1	0.991	0.947	1	CLONAL	2	TRUE	2	0.593263340610811	4		631	1192	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578266	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs942158624	NA	P-0049091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	471	641	0	ENST00000269305.4:c.583A>T	p.Ile195Phe	p.I195F	ENST00000269305	NM_001126112.2	195	Atc/Ttc	6/11	0.586919790595795	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.593263340610811	4		641	1217	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842439	68842439	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs864622655	NA	P-0049091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	209	521	4	ENST00000261769.5:c.504del	p.Gly169AlafsTer46	p.G169Afs*46	ENST00000261769	NM_004360.3	167	gAa/ga	4/16	0.593263340610811	3	FACETS	0.998	0.928	1	0.499	0.464	0.536	CLONAL	1	TRUE	1	0.593263340610811	3		525	915	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106489	27106489	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	469	633	0	ENST00000324856.7:c.6100G>T	p.Glu2034Ter	p.E2034*	ENST00000324856	NM_006015.4	2034	Gag/Tag	20/20	0.593263340610811	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.593263340610811	2		633	776	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610364	10610364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	565	697	2	ENST00000171111.5:c.346C>T	p.Arg116Trp	p.R116W	ENST00000171111	NM_203500.1	116	Cgg/Tgg	2/6	0.593263340610811	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.593263340610811	2		699	922	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098895	178098900	+	inframe_deletion	In_Frame_Del	DEL	TTTTTC	TTTTTC	-	novel	NA	P-0049091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	361	451	0	ENST00000397062.3:c.145_150del	p.Glu49_Lys50del	p.E49_K50del	ENST00000397062	NM_006164.4	49	GAAAAA/-	2/5	0.561941832505865	3	FACETS	0.854	0.819	0.888	0.854	0.819	0.888	CLONAL	3	TRUE	0	0.593263340610811	3		451	616	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225365186	225365186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	276	347	0	ENST00000264414.4:c.1504G>A	p.Asp502Asn	p.D502N	ENST00000264414	NM_003590.4	502	Gat/Aat	11/16	0.561941832505865	3	FACETS	0.918	0.878	0.958	0.918	0.878	0.958	CLONAL	3	TRUE	0	0.593263340610811	3		347	438	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376772	31376772	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	1101	518	0	ENST00000328111.2:c.767C>G	p.Ser256Cys	p.S256C	ENST00000328111	NM_006892.3	256	tCt/tGt	7/23	0.593263340610811	7	FACETS	0.975	0.955	0.994	0.975	0.955	0.994	CLONAL	6	TRUE	1	0.593263340610811	7		518	1576	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265450	46265450	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	93	270	0	ENST00000371998.3:c.2320A>G	p.Ile774Val	p.I774V	ENST00000371998		774	Att/Gtt	12/23	0.593263340610811	3	FACETS	1	0.898	1			1	CLONAL	1	TRUE	NA	0.593263340610811	3		270	405	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162773	47162774	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0049091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	289	366	1	ENST00000409792.3:c.3352_3353delinsTT	p.Glu1118Leu	p.E1118L	ENST00000409792	NM_014159.6	1118	GAa/TTa	3/21	0.593263340610811	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.593263340610811	2		367	480	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151216560	151216560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	52	146	0	ENST00000262187.5:c.38G>A	p.Gly13Asp	p.G13D	ENST00000262187	NM_005614.3	13	gGc/gAc	1/8	0.593263340610811	3	FACETS	0.827	0.709	0.953	0.413	0.354	0.477	CLONAL	1	TRUE	1	0.593263340610811	3		146	275	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132931	30132933	+	frameshift_variant	Frame_Shift_Del	DEL	TAG	TAG	C	novel	NA	P-0049091-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	136	515	0	ENST00000331968.5:c.668_670delinsG	p.Ser223CysfsTer5	p.S223Cfs*5	ENST00000331968	NM_002742.2	223	tCTAca/tGca	4/18	0.593263340610811	3	FACETS	0.86	0.784	0.94	0.43	0.392	0.47	CLONAL	1	TRUE	1	0.593263340610811	3		515	691	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	186	476	3	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.361113832997902	2		479	867	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	206	646	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.361113832997902	2		646	960	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188150	11188150	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	128	463	0	ENST00000361445.4:c.5944T>C	p.Ser1982Pro	p.S1982P	ENST00000361445	NM_004958.3	1982	Tct/Cct	43/58	1	2	FACETS	0.915	0.829	1	0.915	0.829	1	CLONAL	1	TRUE	1	0.361113832997902	2		463	775	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255503	16255503	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	118	473	0	ENST00000375759.3:c.2768A>T	p.Glu923Val	p.E923V	ENST00000375759	NM_015001.2	923	gAg/gTg	11/15	1	2	FACETS	0.939	0.848	1	0.939	0.848	1	CLONAL	1	TRUE	1	0.361113832997902	2		473	696	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094413	27094416	+	frameshift_variant	Frame_Shift_Del	DEL	CTGC	CTGC	-	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	145	524	0	ENST00000324856.7:c.3125_3128del	p.Pro1042LeufsTer16	p.P1042Lfs*16	ENST00000324856	NM_006015.4	1041	CTGCct/ct	11/20	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.361113832997902	2		524	770	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097713	27097713	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1023884503	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	163	565	0	ENST00000324856.7:c.3302A>G	p.Tyr1101Cys	p.Y1101C	ENST00000324856	NM_006015.4	1101	tAt/tGt	12/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.361113832997902	2		565	848	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322735	39322735	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	98	468	0	ENST00000373001.3:c.257C>A	p.Ser86Ter	p.S86*	ENST00000373001	NM_022157.3	86	tCa/tAa	2/7	1	2	FACETS	0.84	0.75	0.935	0.84	0.75	0.935	CLONAL	1	TRUE	1	0.361113832997902	2		468	646	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309857	65309857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	127	527	0	ENST00000342505.4:c.2293G>A	p.Glu765Lys	p.E765K	ENST00000342505	NM_002227.2	765	Gag/Aag	17/25	1	2	FACETS	0.919	0.833	1	0.919	0.833	1	CLONAL	1	TRUE	1	0.361113832997902	2		527	765	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458737	120458737	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	131	544	0	ENST00000256646.2:c.6608A>G	p.Asn2203Ser	p.N2203S	ENST00000256646	NM_024408.3	2203	aAc/aGc	34/34	1	2	FACETS	0.924	0.839	1	0.924	0.839	1	CLONAL	1	TRUE	1	0.361113832997902	2		544	785	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193172941	193172941	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149875598	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	92	444	0	ENST00000367435.3:c.989G>A	p.Arg330Gln	p.R330Q	ENST00000367435	NM_024529.4	330	cGg/cAg	11/17	1	2	FACETS	0.903	0.805	1	0.903	0.805	1	CLONAL	1	TRUE	1	0.361113832997902	2		444	564	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742934	17742934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	172	710	0	ENST00000250003.3:c.842G>A	p.Arg281His	p.R281H	ENST00000250003	NM_002478.4	281	cGc/cAc	3/3	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.361113832997902	2		710	934	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924716	94924716	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	152	613	0	ENST00000536441.1:c.194A>C	p.Glu65Ala	p.E65A	ENST00000536441	NM_144665.3	65	gAa/gCa	3/10	1	2	FACETS	0.963	0.881	1	0.963	0.881	1	CLONAL	1	TRUE	1	0.361113832997902	2		613	874	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909926	100909926	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs756031764	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	83	427	0	ENST00000325455.5:c.2723T>C	p.Met908Thr	p.M908T	ENST00000325455	NM_001202474.3	908	aTg/aCg	8/8	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.361113832997902	2		427	451	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998714	100998714	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	153	779	0	ENST00000325455.5:c.1088A>G	p.Tyr363Cys	p.Y363C	ENST00000325455	NM_001202474.3	363	tAc/tGc	1/8	1	2	FACETS	0.938	0.858	1	0.938	0.858	1	CLONAL	1	TRUE	1	0.361113832997902	2		779	903	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102033242	102033242	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs148057981	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	155	577	0	ENST00000282441.5:c.628A>G	p.Met210Val	p.M210V	ENST00000282441	NM_001130145.2	210	Atg/Gtg	3/9	1	2	FACETS	0.961	0.88	1	0.961	0.88	1	CLONAL	1	TRUE	1	0.361113832997902	2		577	893	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122646	108122646	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754524029	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	90	458	0	ENST00000278616.4:c.1690T>C	p.Cys564Arg	p.C564R	ENST00000278616	NM_000051.3	564	Tgt/Cgt	11/63	1	2	FACETS	0.89	0.792	0.995	0.89	0.792	0.995	CLONAL	1	TRUE	1	0.361113832997902	2		458	560	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534726	18534726	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	105	436	0	ENST00000266497.5:c.1784T>C	p.Phe595Ser	p.F595S	ENST00000266497		595	tTc/tCc	12/31	1	2	FACETS	0.864	0.775	0.958	0.864	0.775	0.958	CLONAL	1	TRUE	1	0.361113832997902	2		436	673	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431874	49431874	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	166	716	2	ENST00000301067.7:c.9265del	p.Val3089TrpfsTer30	p.V3089Wfs*30	ENST00000301067	NM_003482.3	3089	Gtg/tg	34/54	1	2	FACETS	0.921	0.846	1	0.921	0.846	1	CLONAL	1	TRUE	1	0.361113832997902	2		718	998	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	140	720	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	1	2	FACETS	0.968	0.882	1	0.968	0.882	1	CLONAL	1	TRUE	1	0.361113832997902	2		720	801	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864218	57864218	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	166	552	2	ENST00000228682.2:c.1700del	p.Pro567LeufsTer46	p.P567Lfs*46	ENST00000228682	NM_005269.2	565	ttC/tt	12/12	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.361113832997902	2		554	913	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891040	112891040	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	86	336	0	ENST00000351677.2:c.374T>C	p.Leu125Ser	p.L125S	ENST00000351677	NM_002834.3	125	tTa/tCa	4/16	1	2	FACETS	0.927	0.822	1	0.927	0.822	1	CLONAL	1	TRUE	1	0.361113832997902	2		336	514	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112433	115112433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	155	612	0	ENST00000257566.3:c.1307G>A	p.Arg436His	p.R436H	ENST00000257566	NM_016569.3	436	cGc/cAc	7/8	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.361113832997902	2		612	790	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912672	32912672	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	106	469	0	ENST00000380152.3:c.4180A>G	p.Lys1394Glu	p.K1394E	ENST00000380152		1394	Aaa/Gaa	11/27	0.353948593809438	3	FACETS	1	0.912	1	0.509	0.456	0.564	CLONAL	1	TRUE	1	0.361113832997902	3		469	681	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930601	32930601	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs185012573	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	105	405	0	ENST00000380152.3:c.7472A>G	p.Gln2491Arg	p.Q2491R	ENST00000380152		2491	cAg/cGg	15/27	0.353948593809438	3	FACETS	1	0.957	1	0.561	0.503	0.622	CLONAL	1	TRUE	1	0.361113832997902	3		405	612	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32931885	32931885	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	69	324	0	ENST00000380152.3:c.7624A>G	p.Thr2542Ala	p.T2542A	ENST00000380152		2542	Acg/Gcg	16/27	0.353948593809438	3	FACETS	0.966	0.844	1	0.483	0.422	0.549	CLONAL	1	TRUE	1	0.361113832997902	3		324	467	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953754	48953754	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	59	263	0	ENST00000267163.4:c.1357T>C	p.Tyr453His	p.Y453H	ENST00000267163	NM_000321.2	453	Tat/Cat	14/27	0.353948593809438	3	FACETS	0.95	0.82	1	0.475	0.41	0.546	CLONAL	1	TRUE	1	0.361113832997902	3		263	406	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355952	73355952	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	143	538	0	ENST00000377767.4:c.19T>C	p.Phe7Leu	p.F7L	ENST00000377767	NM_014953.3	7	Ttc/Ctc	1/21	0.353948593809438	3	FACETS	0.901	0.82	0.986	0.45	0.41	0.493	CLONAL	1	TRUE	1	0.361113832997902	3		538	1038	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518693	103518693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142438319	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	109	382	0	ENST00000355739.4:c.2281G>A	p.Ala761Thr	p.A761T	ENST00000355739	NM_000123.3	761	Gct/Act	10/15	0.353948593809438	3	FACETS	1	0.956	1	0.556	0.5	0.615	CLONAL	1	TRUE	1	0.361113832997902	3		382	641	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434851	110434851	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	141	595	0	ENST00000375856.3:c.3550A>G	p.Lys1184Glu	p.K1184E	ENST00000375856	NM_003749.2	1184	Aaa/Gaa	1/2	0.353948593809438	3	FACETS	0.914	0.831	1	0.457	0.415	0.5	CLONAL	1	TRUE	1	0.361113832997902	3		595	1009	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436083	110436083	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	205	787	0	ENST00000375856.3:c.2318A>G	p.Asp773Gly	p.D773G	ENST00000375856	NM_003749.2	773	gAc/gGc	1/2	0.353948593809438	3	FACETS	1	0.938	1	0.507	0.469	0.547	CLONAL	1	TRUE	1	0.361113832997902	3		787	1321	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986841	36986841	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	40	184	0	ENST00000354822.5:c.848A>G	p.Gln283Arg	p.Q283R	ENST00000354822	NM_001079668.2	283	cAg/cGg	3/3	1	2	FACETS	0.743	0.62	0.879	0.743	0.62	0.879	SUBCLONAL	1	TRUE	1	0.361113832997902	2		184	298	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988375	36988375	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	99	287	0	ENST00000354822.5:c.278C>T	p.Ala93Val	p.A93V	ENST00000354822	NM_001079668.2	93	gCc/gTc	2/3	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.361113832997902	2		287	434	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95593072	95593072	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	111	394	1	ENST00000393063.1:c.748C>T	p.Pro250Ser	p.P250S	ENST00000393063	NM_030621.3	250	Cca/Tca	8/28	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.361113832997902	2		395	605	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40998394	40998394	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	115	537	0	ENST00000267868.3:c.245T>C	p.Val82Ala	p.V82A	ENST00000267868	NM_002875.4	82	gTt/gCt	4/10	1	2	FACETS	0.887	0.8	0.979	0.887	0.8	0.979	CLONAL	1	TRUE	1	0.361113832997902	2		537	718	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99452050	99452050	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	93	407	0	ENST00000268035.6:c.1384A>G	p.Met462Val	p.M462V	ENST00000268035	NM_000875.3	462	Atg/Gtg	6/21	1	2	FACETS	0.815	0.725	0.91	0.815	0.725	0.91	CLONAL	1	TRUE	1	0.361113832997902	2		407	632	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478620	99478620	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	108	482	0	ENST00000268035.6:c.3262A>G	p.Lys1088Glu	p.K1088E	ENST00000268035	NM_000875.3	1088	Aaa/Gaa	17/21	1	2	FACETS	0.824	0.74	0.913	0.824	0.74	0.913	CLONAL	1	TRUE	1	0.361113832997902	2		482	726	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99491900	99491900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368518102	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	157	650	2	ENST00000268035.6:c.3685G>A	p.Gly1229Ser	p.G1229S	ENST00000268035	NM_000875.3	1229	Ggc/Agc	20/21	1	2	FACETS	0.942	0.863	1	0.942	0.863	1	CLONAL	1	TRUE	1	0.361113832997902	2		652	923	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779383	3779383	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	218	753	0	ENST00000262367.5:c.5665C>T	p.Pro1889Ser	p.P1889S	ENST00000262367	NM_004380.2	1889	Ccg/Tcg	31/31	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.361113832997902	2		753	1074	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789591	3789591	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	97	412	0	ENST00000262367.5:c.4268del	p.Pro1423LeufsTer36	p.P1423Lfs*36	ENST00000262367	NM_004380.2	1423	cCt/ct	25/31	1	2	FACETS	0.861	0.769	0.959	0.861	0.769	0.959	CLONAL	1	TRUE	1	0.361113832997902	2		412	624	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934831	9934831	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	102	454	0	ENST00000330684.3:c.1459A>G	p.Lys487Glu	p.K487E	ENST00000330684	NM_001134407.1	487	Aag/Gag	6/13	1	2	FACETS	0.856	0.766	0.951	0.856	0.766	0.951	CLONAL	1	TRUE	1	0.361113832997902	2		454	660	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349298	11349298	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	111	406	0	ENST00000332029.2:c.38T>C	p.Val13Ala	p.V13A	ENST00000332029	NM_003745.1	13	gTc/gCc	2/2	1	2	FACETS	0.939	0.845	1	0.939	0.845	1	CLONAL	1	TRUE	1	0.361113832997902	2		406	655	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041722	14041722	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	119	487	0	ENST00000311895.7:c.2269C>A	p.Leu757Ile	p.L757I	ENST00000311895	NM_005236.2	757	Ctt/Att	11/11	1	2	FACETS	0.946	0.855	1	0.946	0.855	1	CLONAL	1	TRUE	1	0.361113832997902	2		487	697	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67646013	67646014	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs1470210640	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	126	426	2	ENST00000264010.4:c.950_951del	p.Thr317ArgfsTer91	p.T317Rfs*91	ENST00000264010	NM_006565.3	314	aAC/a	4/12	1	2	FACETS	0.902	0.817	0.991	0.902	0.817	0.991	CLONAL	1	TRUE	1	0.361113832997902	2		428	774	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772234	68772234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	89	787	1	ENST00000261769.5:c.83G>A	p.Cys28Tyr	p.C28Y	ENST00000261769	NM_004360.3	28	tGc/tAc	2/16	1	2	FACETS	0.426	0.376	0.479	0.426	0.376	0.479	SUBCLONAL	1	TRUE	1	0.361113832997902	2		788	1157	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828060	72828060	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	159	662	0	ENST00000268489.5:c.8521G>T	p.Ala2841Ser	p.A2841S	ENST00000268489	NM_006885.3	2841	Gca/Tca	9/10	1	2	FACETS	0.976	0.895	1	0.976	0.895	1	CLONAL	1	TRUE	1	0.361113832997902	2		662	902	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845895	72845895	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	116	529	0	ENST00000268489.5:c.3572C>G	p.Ala1191Gly	p.A1191G	ENST00000268489	NM_006885.3	1191	gCa/gGa	6/10	1	2	FACETS	0.864	0.779	0.953	0.864	0.779	0.953	CLONAL	1	TRUE	1	0.361113832997902	2		529	744	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991685	72991685	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	59	385	0	ENST00000268489.5:c.2360G>C	p.Ser787Thr	p.S787T	ENST00000268489	NM_006885.3	787	aGt/aCt	2/10	1	2	FACETS	0.681	0.587	0.783	0.681	0.587	0.783	SUBCLONAL	1	TRUE	1	0.361113832997902	2		385	480	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	81	398	0	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.758	0.668	0.854	0.758	0.668	0.854	SUBCLONAL	1	TRUE	1	0.361113832997902	2		398	592	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992059	72992059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	157	689	0	ENST00000268489.5:c.1986G>A	p.Met662Ile	p.M662I	ENST00000268489	NM_006885.3	662	atG/atA	2/10	1	2	FACETS	0.977	0.895	1	0.977	0.895	1	CLONAL	1	TRUE	1	0.361113832997902	2		689	890	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337275	89337275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	120	513	0	ENST00000301030.4:c.7756C>T	p.Gln2586Ter	p.Q2586*	ENST00000301030	NM_001256183.1	2586	Cag/Tag	12/13	1	2	FACETS	0.907	0.819	0.999	0.907	0.819	0.999	CLONAL	1	TRUE	1	0.361113832997902	2		513	733	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347878	89347878	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763039848	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	162	635	0	ENST00000301030.4:c.5072C>T	p.Ala1691Val	p.A1691V	ENST00000301030	NM_001256183.1	1691	gCg/gTg	9/13	1	2	FACETS	0.969	0.889	1	0.969	0.889	1	CLONAL	1	TRUE	1	0.361113832997902	2		635	926	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349246	89349246	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	149	695	0	ENST00000301030.4:c.3704A>G	p.Lys1235Arg	p.K1235R	ENST00000301030	NM_001256183.1	1235	aAa/aGa	9/13	1	2	FACETS	0.834	0.762	0.911	0.834	0.762	0.911	CLONAL	1	TRUE	1	0.361113832997902	2		695	989	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350237	89350237	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	176	634	0	ENST00000301030.4:c.2713T>C	p.Phe905Leu	p.F905L	ENST00000301030	NM_001256183.1	905	Ttc/Ctc	9/13	1	2	FACETS	0.977	0.899	1	0.977	0.899	1	CLONAL	1	TRUE	1	0.361113832997902	2		634	998	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572927	7572927	+	stop_lost	Nonstop_Mutation	SNP	T	T	C	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	151	469	0	ENST00000269305.4:c.1182A>G	p.Ter394TrpextTer9	p.*394Wext*9	ENST00000269305	NM_001126112.2	394	tgA/tgG	11/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.361113832997902	2		469	769	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	151	519	0	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.361113832997902	2		519	832	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245789	41245789	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	114	565	0	ENST00000357654.3:c.1759A>G	p.Ile587Val	p.I587V	ENST00000357654	NM_007294.3	587	Ata/Gta	10/23	1	2	FACETS	0.817	0.735	0.903	0.817	0.735	0.903	CLONAL	1	TRUE	1	0.361113832997902	2		565	773	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696673	47696673	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	125	478	0	ENST00000347630.2:c.275G>T	p.Ser92Ile	p.S92I	ENST00000347630	NM_001007230.1	92	aGc/aTc	5/11	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.361113832997902	2		478	687	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435074	56435074	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	195	752	0	ENST00000407977.2:c.2063T>C	p.Val688Ala	p.V688A	ENST00000407977		688	gTg/gCg	9/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.361113832997902	2		752	982	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780626	56780626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760911964	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	124	552	0	ENST00000337432.4:c.641G>A	p.Arg214His	p.R214H	ENST00000337432	NM_058216.2	214	cGt/cAt	4/9	1	2	FACETS	0.969	0.877	1	0.969	0.877	1	CLONAL	1	TRUE	1	0.361113832997902	2		552	709	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885827	59885827	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs587781655	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	84	354	0	ENST00000259008.2:c.918+1G>A		p.X306_splice	ENST00000259008	NM_032043.2	306			1	2	FACETS	0.94	0.833	1	0.94	0.833	1	CLONAL	1	TRUE	1	0.361113832997902	2		354	495	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59886038	59886038	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	129	545	0	ENST00000259008.2:c.708T>A	p.Asp236Glu	p.D236E	ENST00000259008	NM_032043.2	236	gaT/gaA	7/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.361113832997902	2		545	608	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375007	45375007	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	98	407	0	ENST00000262160.6:c.836A>G	p.Tyr279Cys	p.Y279C	ENST00000262160	NM_005901.5	279	tAt/tGt	8/11	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.361113832997902	2		407	506	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573505	48573506	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	77	327	0	ENST00000342988.3:c.94_95del	p.Ser32Ter	p.S32*	ENST00000342988	NM_005359.5	30	gGA/g	2/12	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.361113832997902	2		327	404	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575109	48575109	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	81	352	0	ENST00000342988.3:c.303G>A	p.Trp101Ter	p.W101*	ENST00000342988	NM_005359.5	101	tgG/tgA	3/12	1	2	FACETS	0.908	0.803	1	0.908	0.803	1	CLONAL	1	TRUE	1	0.361113832997902	2		352	494	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985848	60985848	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	110	458	0	ENST00000333681.4:c.52T>C	p.Tyr18His	p.Y18H	ENST00000333681		18	Tac/Cac	2/3	1	2	FACETS	0.845	0.76	0.935	0.845	0.76	0.935	CLONAL	1	TRUE	1	0.361113832997902	2		458	721	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	213	687	0	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.361113832997902	2		687	1121	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221230	5221230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767809989	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	161	728	0	ENST00000357368.4:c.3236G>A	p.Gly1079Asp	p.G1079D	ENST00000357368	NM_002850.3	1079	gGc/gAc	20/38	1	2	FACETS	0.958	0.878	1	0.958	0.878	1	CLONAL	1	TRUE	1	0.361113832997902	2		728	931	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254565	10254565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	160	545	0	ENST00000340748.4:c.2945G>A	p.Gly982Asp	p.G982D	ENST00000340748		982	gGc/gAc	28/40	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.361113832997902	2		545	796	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602815	10602815	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	228	803	0	ENST00000171111.5:c.763T>C	p.Tyr255His	p.Y255H	ENST00000171111	NM_203500.1	255	Tac/Cac	3/6	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.361113832997902	2		803	1239	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097228	11097228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201600949	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	209	705	1	ENST00000358026.2:c.719C>T	p.Pro240Leu	p.P240L	ENST00000358026	NM_001128849.1	240	cCg/cTg	4/36	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.361113832997902	2		706	1055	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101982	11101982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	206	832	1	ENST00000358026.2:c.1402C>T	p.Arg468Cys	p.R468C	ENST00000358026	NM_001128849.1	468	Cgc/Tgc	8/36	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.361113832997902	2		833	1134	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132578	11132578	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	252	773	0	ENST00000358026.2:c.2794A>G	p.Ile932Val	p.I932V	ENST00000358026	NM_001128849.1	932	Atc/Gtc	19/36	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.361113832997902	2		773	1136	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350307	15350307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs562849437	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	178	619	1	ENST00000263377.2:c.3472G>A	p.Gly1158Arg	p.G1158R	ENST00000263377	NM_058243.2	1158	Ggg/Agg	17/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.361113832997902	2		620	880	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792311	33792311	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760372994	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	211	785	2	ENST00000498907.2:c.1010C>T	p.Thr337Met	p.T337M	ENST00000498907	NM_004364.3	337	aCg/aTg	1/1	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.361113832997902	2		787	1095	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210440	36210440	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	157	568	0	ENST00000222270.7:c.433C>T	p.Arg145Ter	p.R145*	ENST00000222270	NM_014727.1	145	Cga/Tga	2/37	1	2	FACETS	0.969	0.888	1	0.969	0.888	1	CLONAL	1	TRUE	1	0.361113832997902	2		568	897	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	200	771	4	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	1	2	FACETS	0.973	0.901	1	0.973	0.901	1	CLONAL	1	TRUE	1	0.361113832997902	2		775	1138	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214058	36214058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1385766471	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	208	821	0	ENST00000222270.7:c.2884C>T	p.Arg962Cys	p.R962C	ENST00000222270	NM_014727.1	962	Cgc/Tgc	6/37	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.361113832997902	2		821	1134	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221655	36221655	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	178	777	1	ENST00000222270.7:c.5324G>A	p.Trp1775Ter	p.W1775*	ENST00000222270	NM_014727.1	1775	tGg/tAg	26/37	1	2	FACETS	0.888	0.817	0.962	0.888	0.817	0.962	CLONAL	1	TRUE	1	0.361113832997902	2		778	1110	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752723	42752723	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1410725157	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	167	740	0	ENST00000222329.4:c.1541G>A	p.Arg514His	p.R514H	ENST00000222329	NM_006494.2	514	cGt/cAt	4/4	1	2	FACETS	0.936	0.86	1	0.936	0.86	1	CLONAL	1	TRUE	1	0.361113832997902	2		740	988	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794013	42794013	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs373688363	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	166	725	0	ENST00000575354.2:c.1374C>A	p.Phe458Leu	p.F458L	ENST00000575354	NM_015125.3	458	ttC/ttA	9/20	1	2	FACETS	0.971	0.892	1	0.971	0.892	1	CLONAL	1	TRUE	1	0.361113832997902	2		725	947	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	91	311	1	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.361113832997902	2		312	445	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	173	846	6	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	0.361113832997902	2	FACETS	0.868	0.798	0.941	0.434	0.399	0.471	CLONAL	1	TRUE	0	0.361113832997902	2		852	1104	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976459	25976459	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	95	432	0	ENST00000435504.4:c.1086G>T	p.Lys362Asn	p.K362N	ENST00000435504		362	aaG/aaT	11/13	0.361113832997902	2	FACETS	0.917	0.818	1	0.458	0.409	0.511	CLONAL	1	TRUE	0	0.361113832997902	2		432	574	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	161	692	4	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	0.361113832997902	2	FACETS	0.842	0.771	0.916	0.421	0.385	0.458	CLONAL	1	TRUE	0	0.361113832997902	2		696	1059	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663043	227663043	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs376142568	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	125	590	0	ENST00000305123.5:c.412G>T	p.Gly138Cys	p.G138C	ENST00000305123	NM_005544.2	138	Ggc/Tgc	1/2	0.361113832997902	2	FACETS	0.804	0.727	0.885	0.402	0.363	0.443	CLONAL	1	TRUE	0	0.361113832997902	2		590	861	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022443	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	rs750318549	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	85	331	1	ENST00000375687.4:c.1933_1934del	p.Gly645TrpfsTer12	p.G645Wfs*12	ENST00000375687	NM_015338.5	643	GGg/g	13/13	1	2	FACETS	0.997	0.885	1	0.997	0.885	1	CLONAL	1	TRUE	1	0.361113832997902	2		332	472	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31369180	31369180	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	124	555	0	ENST00000328111.2:c.164T>C	p.Leu55Pro	p.L55P	ENST00000328111	NM_006892.3	55	cTc/cCc	3/23	1	2	FACETS	0.916	0.829	1	0.916	0.829	1	CLONAL	1	TRUE	1	0.361113832997902	2		555	750	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031642	36031642	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	199	864	0	ENST00000358208.4:c.1473del	p.Glu492SerfsTer152	p.E492Sfs*152	ENST00000358208		491	Ccc/cc	12/12	1	2	FACETS	0.923	0.854	0.995	0.923	0.854	0.995	CLONAL	1	TRUE	1	0.361113832997902	2		864	1194	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741464	39741464	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	101	387	1	ENST00000361337.2:c.1356del	p.Lys452AsnfsTer19	p.K452Nfs*19	ENST00000361337	NM_003286.2	451	Aaa/aa	14/21	1	2	FACETS	0.923	0.827	1	0.923	0.827	1	CLONAL	1	TRUE	1	0.361113832997902	2		388	606	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	111	577	3	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	0.324368532263062	1	FACETS	0.656	0.59	0.726	0.656	0.59	0.726	SUBCLONAL	1	TRUE	0	0.361113832997902	1		580	768	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39870285	39870285	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	60	319	0	ENST00000288319.7:c.18+2T>C		p.X6_splice	ENST00000288319	NM_182918.3	6			1	2	FACETS	0.667	0.576	0.767	0.667	0.576	0.767	SUBCLONAL	1	TRUE	1	0.361113832997902	2		319	498	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277261	41277261	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	97	354	0	ENST00000349496.5:c.1730T>G	p.Leu577Arg	p.L577R	ENST00000349496	NM_001904.3	577	cTt/cGt	11/15	1	2	FACETS	0.991	0.886	1	0.991	0.886	1	CLONAL	1	TRUE	1	0.361113832997902	2		354	542	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125581	47125581	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	112	354	0	ENST00000409792.3:c.5689A>G	p.Thr1897Ala	p.T1897A	ENST00000409792	NM_014159.6	1897	Acc/Gcc	12/21	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.361113832997902	2		354	563	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165213	47165213	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	73	371	0	ENST00000409792.3:c.913del	p.Thr305GlnfsTer35	p.T305Qfs*35	ENST00000409792	NM_014159.6	305	Aca/ca	3/21	1	2	FACETS	0.83	0.728	0.94	0.83	0.728	0.94	CLONAL	1	TRUE	1	0.361113832997902	2		371	487	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936403	49936403	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	185	724	0	ENST00000296474.3:c.1445A>G	p.Tyr482Cys	p.Y482C	ENST00000296474	NM_002447.2	482	tAc/tGc	3/20	1	2	FACETS	0.997	0.92	1	0.997	0.92	1	CLONAL	1	TRUE	1	0.361113832997902	2		724	1028	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440300	52440300	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	158	638	0	ENST00000460680.1:c.752A>G	p.Asn251Ser	p.N251S	ENST00000460680	NM_004656.3	251	aAc/aGc	9/17	1	2	FACETS	0.918	0.841	0.999	0.918	0.841	0.999	CLONAL	1	TRUE	1	0.361113832997902	2		638	953	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440912	52440912	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1205668341	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	192	625	1	ENST00000460680.1:c.592del	p.Glu198ArgfsTer33	p.E198Rfs*33	ENST00000460680	NM_004656.3	198	Gag/ag	8/17	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.361113832997902	2		626	985	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462329	89462329	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	55	469	0	ENST00000336596.2:c.1801A>T	p.Thr601Ser	p.T601S	ENST00000336596	NM_005233.5	601	Aca/Tca	10/17	1	2	FACETS	0.527	0.451	0.611	0.527	0.451	0.611	SUBCLONAL	1	TRUE	1	0.361113832997902	2		469	578	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664951	138664951	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	85	281	0	ENST00000330315.3:c.614C>T	p.Pro205Leu	p.P205L	ENST00000330315	NM_023067.3	205	cCg/cTg	1/1	1	2	FACETS	0.997	0.885	1	0.997	0.885	1	CLONAL	1	TRUE	1	0.361113832997902	2		281	472	SUCCESS
ATR	545	MSKCC	GRCh37	3	142185167	142185167	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs145119827	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	90	395	0	ENST00000350721.4:c.6896T>C	p.Met2299Thr	p.M2299T	ENST00000350721	NM_001184.3	2299	aTg/aCg	40/47	1	2	FACETS	0.981	0.874	1	0.981	0.874	1	CLONAL	1	TRUE	1	0.361113832997902	2		395	508	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215357	142215357	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs201445100	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	109	330	0	ENST00000350721.4:c.5744A>G	p.Asp1915Gly	p.D1915G	ENST00000350721	NM_001184.3	1915	gAt/gGt	34/47	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.361113832997902	2		330	526	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281435	142281435	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	133	577	1	ENST00000350721.4:c.809del	p.Phe270SerfsTer8	p.F270Sfs*8	ENST00000350721	NM_001184.3	270	tTc/tc	4/47	1	2	FACETS	0.967	0.879	1	0.967	0.879	1	CLONAL	1	TRUE	1	0.361113832997902	2		578	762	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916644	178916644	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	96	384	0	ENST00000263967.3:c.31T>C	p.Trp11Arg	p.W11R	ENST00000263967	NM_006218.2	11	Tgg/Cgg	2/21	1	2	FACETS	0.974	0.87	1	0.974	0.87	1	CLONAL	1	TRUE	1	0.361113832997902	2		384	546	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916662	178916662	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	98	380	0	ENST00000263967.3:c.49C>T	p.Pro17Ser	p.P17S	ENST00000263967	NM_006218.2	17	Ccc/Tcc	2/21	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.361113832997902	2		380	519	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	98	473	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.891	0.797	0.992	0.891	0.797	0.992	CLONAL	1	TRUE	1	0.361113832997902	2		473	609	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186507027	186507027	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	50	234	0	ENST00000323963.5:c.1193A>C	p.Glu398Ala	p.E398A	ENST00000323963		398	gAg/gCg	11/11	1	2	FACETS	0.706	0.601	0.822	0.706	0.601	0.822	SUBCLONAL	1	TRUE	1	0.361113832997902	2		234	392	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129923	55129923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	174	544	1	ENST00000257290.5:c.457A>G	p.Thr153Ala	p.T153A	ENST00000257290	NM_006206.4	153	Act/Gct	4/23	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.361113832997902	2		545	777	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157385	106157385	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	86	349	0	ENST00000380013.4:c.2290del	p.Gln764LysfsTer49	p.Q764Kfs*49	ENST00000380013	NM_001127208.2	762	caC/ca	3/11	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.361113832997902	2		349	476	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524815	187524815	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778212581	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	166	639	0	ENST00000441802.2:c.10865C>T	p.Thr3622Met	p.T3622M	ENST00000441802	NM_005245.3	3622	aCg/aTg	19/27	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.361113832997902	2		639	837	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525548	187525548	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	127	441	0	ENST00000441802.2:c.10531T>C	p.Tyr3511His	p.Y3511H	ENST00000441802	NM_005245.3	3511	Tac/Cac	18/27	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.361113832997902	2		441	603	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532709	187532710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	90	499	0	ENST00000441802.2:c.9683dup	p.Val3229CysfsTer3	p.V3229Cfs*3	ENST00000441802	NM_005245.3	3228	cct/ccCt	14/27	1	2	FACETS	0.695	0.617	0.779	0.695	0.617	0.779	SUBCLONAL	1	TRUE	1	0.361113832997902	2		499	717	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947473	38947473	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	61	275	0	ENST00000357387.3:c.4207C>A	p.Leu1403Met	p.L1403M	ENST00000357387	NM_152756.3	1403	Ctg/Atg	32/38	1	2	FACETS	0.868	0.752	0.994	0.868	0.752	0.994	CLONAL	1	TRUE	1	0.361113832997902	2		275	389	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80024769	80024769	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1323813414	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	61	395	0	ENST00000265081.6:c.1553T>C	p.Met518Thr	p.M518T	ENST00000265081	NM_002439.4	518	aTg/aCg	10/24	1	2	FACETS	0.757	0.655	0.868	0.757	0.655	0.868	SUBCLONAL	1	TRUE	1	0.361113832997902	2		395	446	SUCCESS
APC	324	MSKCC	GRCh37	5	112162877	112162877	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1554081691	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	93	473	0	ENST00000257430.4:c.1481G>C	p.Ser494Thr	p.S494T	ENST00000257430	NM_000038.5	494	aGt/aCt	12/16	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.361113832997902	2		473	511	SUCCESS
APC	324	MSKCC	GRCh37	5	112173956	112173957	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	95	362	0	ENST00000257430.4:c.2666_2667del	p.Lys889SerfsTer22	p.K889Sfs*22	ENST00000257430	NM_000038.5	889	AAa/a	16/16	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.361113832997902	2		362	520	SUCCESS
APC	324	MSKCC	GRCh37	5	112174146	112174146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776560257	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	80	328	0	ENST00000257430.4:c.2855C>T	p.Ala952Val	p.A952V	ENST00000257430	NM_000038.5	952	gCc/gTc	16/16	1	2	FACETS	0.97	0.857	1	0.97	0.857	1	CLONAL	1	TRUE	1	0.361113832997902	2		328	457	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	77	330	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.902	0.794	1	0.902	0.794	1	CLONAL	1	TRUE	1	0.361113832997902	2		330	473	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523104	176523104	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	197	747	0	ENST00000292408.4:c.1868A>G	p.Asp623Gly	p.D623G	ENST00000292408	NM_213647.1	623	gAc/gGc	14/18	1	2	FACETS	0.95	0.879	1	0.95	0.879	1	CLONAL	1	TRUE	1	0.361113832997902	2		747	1148	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707830	176707830	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	57	255	0	ENST00000439151.2:c.5891del	p.Lys1964ArgfsTer5	p.K1964Rfs*5	ENST00000439151	NM_022455.4	1963	Aaa/aa	18/23	1	2	FACETS	0.683	0.587	0.788	0.683	0.587	0.788	SUBCLONAL	1	TRUE	1	0.361113832997902	2		255	462	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048601	180048601	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	208	865	0	ENST00000261937.6:c.1961A>G	p.Glu654Gly	p.E654G	ENST00000261937	NM_182925.4	654	gAa/gGa	13/30	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.361113832997902	2		865	1117	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057749	180057749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs574248675	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	161	674	1	ENST00000261937.6:c.206C>T	p.Ala69Val	p.A69V	ENST00000261937	NM_182925.4	69	gCc/gTc	3/30	1	2	FACETS	0.954	0.874	1	0.954	0.874	1	CLONAL	1	TRUE	1	0.361113832997902	2		675	935	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056065	26056065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752256145	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	146	399	2	ENST00000343677.2:c.592G>A	p.Ala198Thr	p.A198T	ENST00000343677	NM_005319.3	198	Gct/Act	1/1	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.361113832997902	2		401	680	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056208	26056208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780220505	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	170	523	0	ENST00000343677.2:c.449G>A	p.Ser150Asn	p.S150N	ENST00000343677	NM_005319.3	150	aGc/aAc	1/1	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.361113832997902	2		523	827	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056237	26056245	+	inframe_deletion	In_Frame_Del	DEL	CTTCTTGGG	CTTCTTGGG	-	rs749190253	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	122	539	0	ENST00000343677.2:c.412_420del	p.Pro138_Lys140del	p.P138_K140del	ENST00000343677	NM_005319.3	138	CCCAAGAAG/-	1/1	1	2	FACETS	0.762	0.688	0.84	0.762	0.688	0.84	SUBCLONAL	1	TRUE	1	0.361113832997902	2		539	887	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858446	27858446	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	181	575	0	ENST00000359303.2:c.125A>G	p.Tyr42Cys	p.Y42C	ENST00000359303	NM_003535.2	42	tAc/tGc	1/1	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.361113832997902	2		575	858	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323170	31323172	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	190	648	0	ENST00000412585.2:c.817_819del	p.Val273del	p.V273del	ENST00000412585	NM_005514.6	273	GTG/-	4/8	1	2	FACETS	0.98	0.905	1	0.98	0.905	1	CLONAL	1	TRUE	1	0.361113832997902	2		648	1074	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527319	137527319	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	141	698	0	ENST00000367739.4:c.327del	p.Glu110AsnfsTer33	p.E110Nfs*33	ENST00000367739	NM_000416.2	109	aaA/aa	3/7	1	2	FACETS	0.922	0.84	1	0.922	0.84	1	CLONAL	1	TRUE	1	0.361113832997902	2		698	847	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157454317	157454317	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554301256	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	110	460	0	ENST00000346085.5:c.2527C>T	p.Gln843Ter	p.Q843*	ENST00000346085	NM_020732.3	843	Cag/Tag	8/20	1	2	FACETS	0.933	0.84	1	0.933	0.84	1	CLONAL	1	TRUE	1	0.361113832997902	2		460	653	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340247	116340247	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	75	342	0	ENST00000397752.3:c.1109T>C	p.Val370Ala	p.V370A	ENST00000397752	NM_000245.2	370	gTc/gCc	2/21	0.354290279225575	3	FACETS	0.828	0.726	0.938	0.414	0.363	0.469	CLONAL	1	TRUE	1	0.361113832997902	3		342	592	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874149	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	114	470	0	ENST00000262189.6:c.8389_8390del	p.Lys2797GlyfsTer11	p.K2797Gfs*11	ENST00000262189	NM_170606.2	2797	AAg/g	38/59	0.354290279225575	3	FACETS	0.996	0.898	1	0.498	0.449	0.551	CLONAL	1	TRUE	1	0.361113832997902	3		470	748	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132732	152132732	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	114	303	0	ENST00000262189.6:c.140del	p.Pro47LeufsTer58	p.P47Lfs*58	ENST00000262189	NM_170606.2	47	cCt/ct	1/59	0.354290279225575	3	FACETS	1	0.981	1	0.684	0.618	0.753	CLONAL	1	TRUE	1	0.361113832997902	3		303	545	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345810	152345810	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	105	442	0	ENST00000359321.1:c.760T>C	p.Ser254Pro	p.S254P	ENST00000359321	NM_005431.1	254	Tca/Cca	3/3	0.354290279225575	3	FACETS	0.919	0.824	1	0.46	0.412	0.51	CLONAL	1	TRUE	1	0.361113832997902	3		442	747	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38137193	38137193	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	98	475	0	ENST00000317025.8:c.3625A>G	p.Ile1209Val	p.I1209V	ENST00000317025	NM_023034.1	1209	Ata/Gta	21/24	0.354290279225575	3	FACETS	0.798	0.711	0.89	0.399	0.355	0.445	SUBCLONAL	1	TRUE	1	0.361113832997902	3		475	803	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162940	38162940	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1300563598	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	118	458	0	ENST00000317025.8:c.2266A>G	p.Lys756Glu	p.K756E	ENST00000317025	NM_023034.1	756	Aaa/Gaa	13/24	0.354290279225575	3	FACETS	0.859	0.774	0.949	0.43	0.387	0.475	CLONAL	1	TRUE	1	0.361113832997902	3		458	898	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271295	38271295	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	161	784	0	ENST00000425967.3:c.2413G>A	p.Asp805Asn	p.D805N	ENST00000425967	NM_001174067.1	805	Gac/Aac	19/19	0.354290279225575	3	FACETS	0.844	0.772	0.92	0.422	0.386	0.46	CLONAL	1	TRUE	1	0.361113832997902	3		784	1247	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863256	56863256	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs368483911	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	131	594	0	ENST00000519728.1:c.400A>G	p.Ile134Val	p.I134V	ENST00000519728	NM_002350.3	134	Ata/Gta	6/13	0.354290279225575	3	FACETS	0.911	0.826	1	0.456	0.413	0.501	CLONAL	1	TRUE	1	0.361113832997902	3		594	940	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748399150	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	179	573	4	ENST00000220592.5:c.1806del	p.Ala603ProfsTer92	p.A603Pfs*92	ENST00000220592	NM_012154.3	602	ccC/cc	14/19	0.354290279225575	3	FACETS	0.911	0.838	0.987	0.455	0.419	0.494	CLONAL	1	TRUE	1	0.361113832997902	3		577	1285	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8338935	8338935	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	107	397	0	ENST00000356435.5:c.5366T>C	p.Val1789Ala	p.V1789A	ENST00000356435		1789	gTc/gCc	32/35	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.361113832997902	2		397	559	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341154	8341154	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	79	463	0	ENST00000356435.5:c.5062C>A	p.Leu1688Met	p.L1688M	ENST00000356435		1688	Ctg/Atg	30/35	1	2	FACETS	0.861	0.759	0.97	0.861	0.759	0.97	CLONAL	1	TRUE	1	0.361113832997902	2		463	508	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500844	8500845	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	106	470	0	ENST00000356435.5:c.2037dup	p.Trp680MetfsTer3	p.W680Mfs*3	ENST00000356435		679	-/A	13/35	1	2	FACETS	0.836	0.75	0.927	0.836	0.75	0.927	CLONAL	1	TRUE	1	0.361113832997902	2		470	702	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970964	21970964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	183	634	0	ENST00000304494.5:c.394G>A	p.Ala132Thr	p.A132T	ENST00000304494	NM_000077.4	132	Gcg/Acg	2/3	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.361113832997902	2		634	996	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864000	97864000	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	128	421	0	ENST00000289081.3:c.1666A>G	p.Thr556Ala	p.T556A	ENST00000289081	NM_000136.2	556	Act/Gct	15/15	1	2	FACETS	0.996	0.904	1	0.996	0.904	1	CLONAL	1	TRUE	1	0.361113832997902	2		421	712	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270593	98270595	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs756897237	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	11	60	0	ENST00000331920.6:c.49_51del	p.Gly17del	p.G17del	ENST00000331920	NM_000264.3	17	GGC/-	1/24	1	2	FACETS	0.655	0.457	0.895	0.655	0.457	0.895	SUBCLONAL	1	TRUE	1	0.361113832997902	2		60	93	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249830	110249830	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	205	755	0	ENST00000374672.4:c.845T>A	p.Val282Asp	p.V282D	ENST00000374672	NM_004235.4	282	gTc/gAc	3/5	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.361113832997902	2		755	1045	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128206830	128206831	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	110	488	0	ENST00000265960.3:c.1392dup	p.His465ThrfsTer5	p.H465Tfs*5	ENST00000265960	NM_001006617.1	464	-/A	11/12	1	2	FACETS	0.926	0.833	1	0.926	0.833	1	CLONAL	1	TRUE	1	0.361113832997902	2		488	658	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391455	139391455	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	244	801	0	ENST00000277541.6:c.6736C>T	p.His2246Tyr	p.H2246Y	ENST00000277541	NM_017617.3	2246	Cac/Tac	34/34	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.361113832997902	2		801	1214	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410085	139410085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775217381	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	225	925	2	ENST00000277541.6:c.1753G>A	p.Ala585Thr	p.A585T	ENST00000277541	NM_017617.3	585	Gcc/Acc	11/34	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.361113832997902	2		927	1209	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341574	70341574	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	208	336	0	ENST00000374080.3:c.1009C>A	p.Pro337Thr	p.P337T	ENST00000374080		337	Cca/Aca	7/45	1	1	FACETS	0.844	0.79	0.9	1	0.993	1	CLONAL	2	TRUE	0	0.361113832997902	1		336	559	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939499	76939499	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	114	318	0	ENST00000373344.5:c.1249T>C	p.Phe417Leu	p.F417L	ENST00000373344	NM_000489.3	417	Ttt/Ctt	9/35	1	1	FACETS	0.756	0.689	0.826	1	0.986	1	SUBCLONAL	2	TRUE	0	0.361113832997902	1		318	342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0049244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	311	592	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	NA	2	FACETS	0.913	0.87	0.956			1	INDETERMINATE	2	TRUE	NA	0.569701277786853	2		592	598	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707939	47707939	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1553370404	NA	P-0049244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	92	417	0	ENST00000233146.2:c.2563C>T	p.Gln855Ter	p.Q855*	ENST00000233146	NM_000251.2	855	Cag/Tag	15/16	0.569984427758584	3	FACETS	0.889	0.793	0.989	0.444	0.396	0.495	CLONAL	1	TRUE	1	0.569701277786853	3		417	467	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431900	49431900	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	149	751	0	ENST00000301067.7:c.9239C>G	p.Ala3080Gly	p.A3080G	ENST00000301067	NM_003482.3	3080	gCt/gGt	34/54	0.569984427758584	4	FACETS	0.863	0.788	0.942			1	CLONAL	1	TRUE	NA	0.569701277786853	4		751	951	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56873500	56873500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	94	407	0	ENST00000308159.5:c.2204G>A	p.Arg735Lys	p.R735K	ENST00000308159	NM_014669.4	735	aGa/aAa	20/22	NA	2	FACETS	0.821	0.735	0.911			1	INDETERMINATE	1	TRUE	NA	0.569701277786853	2		407	402	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793643	42794610	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGCCCCTTTGTTTTCTTTTCCACTTGGTTTATGGTTGCATGTGGCCAGTTCAGGCCCTGCCGAGTAAATCCAGCCCTGCCCTCAGGAAGCCCCCAGCCCTGCAGGAAATCTGGAGGACAGGGGGCATGACCAGATCTTCAGGTGCAGTGTTAGGGGCTCTGTCCTGCAGGCTCATAGGCTCCTGCACTGGGCAGTGGGCACTGGGCATGTGGGCACAGCCCTGGGCTGAGGAGTAGCCTTCCTGGACAGCACTCCCTGCCGGTTTGGAGCAGAGCTGAGATCCAGGCTCCAGACTGTTTCTCCTGGGTCCCCCTGCATCTAGCCCCCTCCCCATACTGTTCCCTCCACTCCCTCAGCTGACGATGGCTTCGGCACCACTGACATTGATCTCAAGTGCAAGGAGCGGGTGACCGACAGCGAGAGTGGGGACAGCTCTGGGGAGGACCCAGAGGGCAACAAGGTGAGGGCTTGGGTCACGGTGCTGTCCCATCACACTCCCTCCTAAGCCATGGGAATGTCTGTTTCTCCCGGGCTTGAGAGAGGGGGAGATTAAGGTCCAGAGAGGGCAAGCTGCTTGCCCCGTGGGGAGTTGGGTCATAGTCAGGATGAATTGAGGCCTTCAGCTGGCAGGGGTGCAGCCCTAGGCTGGCCTGGCTGACAGGCTGGATGGGCATGGCTAGGGGGCTGCTATCGAGGTGTCGGAGTGTCCTGACCTGGGGTGTCTCCCTTCCTTTCATGCAGGGCTTTGGTCGGAAGGTGTTTTCACCTGTGATCCGTTCCTCCTTTACCCACTGCCGCCCCCCACTGGACCCTGAGCCCCCAGGGCCCCCGGATCCTCCTGTAGCCTTTGGCAAAGGCTATGGTTCCGCCCCATCCTCCTCTGCGTCCTCGCCTGCTTCCTCCTCAGCCTCGGCAGCCACCTCCTTCTCACTGGGCTCAGGAACCTTCAAGGCCCAGGAGTCTGGTC	AGGCCCCTTTGTTTTCTTTTCCACTTGGTTTATGGTTGCATGTGGCCAGTTCAGGCCCTGCCGAGTAAATCCAGCCCTGCCCTCAGGAAGCCCCCAGCCCTGCAGGAAATCTGGAGGACAGGGGGCATGACCAGATCTTCAGGTGCAGTGTTAGGGGCTCTGTCCTGCAGGCTCATAGGCTCCTGCACTGGGCAGTGGGCACTGGGCATGTGGGCACAGCCCTGGGCTGAGGAGTAGCCTTCCTGGACAGCACTCCCTGCCGGTTTGGAGCAGAGCTGAGATCCAGGCTCCAGACTGTTTCTCCTGGGTCCCCCTGCATCTAGCCCCCTCCCCATACTGTTCCCTCCACTCCCTCAGCTGACGATGGCTTCGGCACCACTGACATTGATCTCAAGTGCAAGGAGCGGGTGACCGACAGCGAGAGTGGGGACAGCTCTGGGGAGGACCCAGAGGGCAACAAGGTGAGGGCTTGGGTCACGGTGCTGTCCCATCACACTCCCTCCTAAGCCATGGGAATGTCTGTTTCTCCCGGGCTTGAGAGAGGGGGAGATTAAGGTCCAGAGAGGGCAAGCTGCTTGCCCCGTGGGGAGTTGGGTCATAGTCAGGATGAATTGAGGCCTTCAGCTGGCAGGGGTGCAGCCCTAGGCTGGCCTGGCTGACAGGCTGGATGGGCATGGCTAGGGGGCTGCTATCGAGGTGTCGGAGTGTCCTGACCTGGGGTGTCTCCCTTCCTTTCATGCAGGGCTTTGGTCGGAAGGTGTTTTCACCTGTGATCCGTTCCTCCTTTACCCACTGCCGCCCCCCACTGGACCCTGAGCCCCCAGGGCCCCCGGATCCTCCTGTAGCCTTTGGCAAAGGCTATGGTTCCGCCCCATCCTCCTCTGCGTCCTCGCCTGCTTCCTCCTCAGCCTCGGCAGCCACCTCCTTCTCACTGGGCTCAGGAACCTTCAAGGCCCAGGAGTCTGGTC	-	novel	NA	P-0049244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	136	385	0	ENST00000575354.2:c.1360+88_1693del		p.X454_splice	ENST00000575354	NM_015125.3	454		9-10/20	0.495474299469879	3	FACETS	1	0.986	1	0.699	0.641	0.759	CLONAL	1	TRUE	1	0.569701277786853	3		385	439	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131155	55131155	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	113	464	0	ENST00000257290.5:c.698T>C	p.Val233Ala	p.V233A	ENST00000257290	NM_006206.4	233	gTc/gCc	5/23	1	2	FACETS	0.938	0.85	1	0.938	0.85	1	CLONAL	1	TRUE	1	0.569701277786853	2		464	423	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0049301-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	181	382	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.283995445587335	4	FACETS	0.915	0.849	0.984	0.915	0.849	0.984	CLONAL	3	TRUE	1	0.283995445587335	4		382	596	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0049301-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	135	567	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.283995445587335	2		567	708	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876366	35876366	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049301-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	133	594	0	ENST00000303115.3:c.1158G>T	p.Arg386Ser	p.R386S	ENST00000303115	NM_002185.3	386	agG/agT	8/8	0.146683785704286	4	FACETS	1	0.984	1	0.713	0.648	0.782	INDETERMINATE	1	TRUE	2	0.283995445587335	4		594	843	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409357	31409357	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049301-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	56	428	0	ENST00000344624.3:c.3750A>T	p.Lys1250Asn	p.K1250N	ENST00000344624		1250	aaA/aaT	29/33	0.146683785704286	4	FACETS	0.843	0.721	0.975	0.421	0.36	0.488	INDETERMINATE	1	TRUE	2	0.283995445587335	4		428	601	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632106	1632106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138963927	NA	P-0049301-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	46	721	0	ENST00000344749.5:c.229G>A	p.Glu77Lys	p.E77K	ENST00000344749	NM_001136139.2	77	Gag/Aag	5/19	0.283995445587335	1	FACETS	0.393	0.33	0.462	0.393	0.33	0.462	SUBCLONAL	1	TRUE	0	0.283995445587335	1		721	708	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152237	11152237	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0049301-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	100	407	0	ENST00000358026.2:c.4520+1G>A		p.X1507_splice	ENST00000358026	NM_001128849.1	1507			0.283995445587335	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.283995445587335	1		407	481	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210953	133210953	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049301-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	43	508	0	ENST00000320574.5:c.5823G>C	p.Gln1941His	p.Q1941H	ENST00000320574	NM_006231.2	1941	caG/caC	43/49	0.270423639592221	1	FACETS	0.422	0.352	0.499	0.422	0.352	0.499	SUBCLONAL	1	TRUE	0	0.283995445587335	1		508	616	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106110	27106110	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049301-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	23	0	0	ENST00000324856.7:c.5721C>G	p.Ile1907Met	p.I1907M	ENST00000324856	NM_006015.4	1907	atC/atG	20/20	1	2	FACETS	0.237	0.184	0.299	0.237	0.184	0.299	SUBCLONAL	1	TRUE	1	0.283995445587335	2		0	683	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654814	29654814	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049301-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	51	327	0	ENST00000356175.3:c.5503A>G	p.Asn1835Asp	p.N1835D	ENST00000356175	NM_000267.3	1835	Aat/Gat	37/57	1	2	FACETS	0.891	0.759	1	0.891	0.759	1	CLONAL	1	TRUE	1	0.283995445587335	2		327	403	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636341	87636341	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049301-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	74	582	0	ENST00000277120.3:c.2506A>T	p.Ile836Phe	p.I836F	ENST00000277120		836	Att/Ttt	19/19	1	2	FACETS	0.721	0.63	0.818	0.721	0.63	0.818	SUBCLONAL	1	TRUE	1	0.283995445587335	2		582	723	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216486	108216486	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1565563280	NA	P-0049301-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	17	223	0	ENST00000278616.4:c.8435C>G	p.Ser2812Cys	p.S2812C	ENST00000278616	NM_000051.3	2812	tCt/tGt	58/63	0.146683785704286	4	FACETS	0.561	0.419	0.73	0.281	0.209	0.365	INDETERMINATE	1	TRUE	2	0.283995445587335	4		223	274	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493448	56493448	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049301-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	34	432	0	ENST00000267101.3:c.2856G>C	p.Glu952Asp	p.E952D	ENST00000267101	NM_001982.3	952	gaG/gaC	24/28	0.195889508387638	2	FACETS	0.446	0.364	0.539	0.223	0.182	0.27	SUBCLONAL	1	TRUE	0	0.283995445587335	2		432	537	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69203064	69203064	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049301-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	32	400	1	ENST00000462284.1:c.91G>A	p.Glu31Lys	p.E31K	ENST00000462284	NM_002392.5	31	Gag/Aag	2/11	0.270423639592221	1	FACETS	0.412	0.334	0.501	0.412	0.334	0.501	SUBCLONAL	1	TRUE	0	0.283995445587335	1		401	469	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467215	99467215	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049301-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	85	392	0	ENST00000268035.6:c.2596G>C	p.Glu866Gln	p.E866Q	ENST00000268035	NM_000875.3	866	Gaa/Caa	12/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.283995445587335	2		392	443	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076922	41076922	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049301-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	58	510	2	ENST00000373198.4:c.1498G>T	p.Glu500Ter	p.E500*	ENST00000373198	NM_133170.3	500	Gag/Tag	9/32	0.132910230448398	3	FACETS	0.646	0.554	0.747	0.215	0.184	0.249	INDETERMINATE	1	TRUE	0	0.283995445587335	3		512	722	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261573	142261573	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049301-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	44	274	0	ENST00000350721.4:c.3384G>T	p.Leu1128Phe	p.L1128F	ENST00000350721	NM_001184.3	1128	ttG/ttT	17/47	1	2	FACETS	0.835	0.702	0.982	0.835	0.702	0.982	CLONAL	1	TRUE	1	0.283995445587335	2		274	371	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460500	8460500	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049301-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	72	463	2	ENST00000356435.5:c.3786T>A	p.Asp1262Glu	p.D1262E	ENST00000356435		1262	gaT/gaA	22/35	0.283995445587335	1	FACETS	0.845	0.739	0.958	0.845	0.739	0.958	CLONAL	1	TRUE	0	0.283995445587335	1		465	515	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317516	1317516	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1361857498	NA	P-0049301-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	34	380	0	ENST00000400841.2:c.549C>G	p.Phe183Leu	p.F183L	ENST00000400841		183	ttC/ttG	5/6	0.283995445587335	2	FACETS	0.376	0.306	0.455			1	SUBCLONAL	1	TRUE	NA	0.283995445587335	2		380	637	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222959	53222959	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049301-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	53	325	0	ENST00000375401.3:c.4113G>C	p.Lys1371Asn	p.K1371N	ENST00000375401	NM_004187.3	1371	aaG/aaC	24/26	1	1	FACETS	0.799	0.683	0.925	0.799	0.683	0.925	CLONAL	1	TRUE	0	0.283995445587335	1		325	401	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0049304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	107	534	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.407654648043039	9	FACETS	1	0.954	1	1	0.954	1	CLONAL	6	TRUE	3	0.407654648043039	9		534	202	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0049304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	204	698	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.34956138385707	2	FACETS	0.812	0.758	0.868	0.812	0.758	0.868	CLONAL	2	TRUE	0	0.407654648043039	2		698	616	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057835	27057835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	234	707	0	ENST00000324856.7:c.1543C>T	p.Gln515Ter	p.Q515*	ENST00000324856	NM_006015.4	515	Cag/Tag	3/20	0.212518190779301	3	FACETS	0.945	0.886	1	0.63	0.59	0.671	INDETERMINATE	2	TRUE	0	0.407654648043039	3		707	731	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054620	13054620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	148	498	0	ENST00000316448.5:c.1147G>A	p.Glu383Lys	p.E383K	ENST00000316448	NM_004343.3	383	Gag/Aag	9/9	0.331796492985515	5	FACETS	0.982	0.9	1	0.654	0.6	0.711	CLONAL	2	TRUE	2	0.407654648043039	5		498	596	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977233	85977233	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	11	270	0	ENST00000263360.6:c.835G>C	p.Asp279His	p.D279H	ENST00000263360	NM_003797.3	279	Gat/Cat	8/12	0.2746794404536	4	FACETS	0.987	0.692	1	0.493	0.346	0.67	CLONAL	1	TRUE	2	0.407654648043039	4		270	77	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622490	158622490	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	66	399	0	ENST00000263640.3:c.1009T>A	p.Leu337Ile	p.L337I	ENST00000263640	NM_001105.4	337	Tta/Ata	8/11	0.2746794404536	4	FACETS	0.958	0.842	1	0.958	0.842	1	CLONAL	2	TRUE	2	0.407654648043039	4		399	238	SUCCESS
APC	324	MSKCC	GRCh37	5	112176947	112176947	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587781400	NA	P-0049304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	14	293	0	ENST00000257430.4:c.5656G>C	p.Glu1886Gln	p.E1886Q	ENST00000257430	NM_000038.5	1886	Gaa/Caa	16/16	0.2746794404536	4	FACETS	0.686	0.499	0.909	0.343	0.249	0.455	SUBCLONAL	1	TRUE	2	0.407654648043039	4		293	141	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	173	687	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.337760848113064	2	FACETS	0.996	0.924	1	0.996	0.924	1	CLONAL	2	FALSE	0	0.337760848113064	2		687	514	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207064	1207065	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1131690917	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	124	934	0	ENST00000326873.7:c.157dup	p.Asp53GlyfsTer110	p.D53Gfs*110	ENST00000326873	NM_000455.4	51	atg/atGg	1/10	0.337760848113064	1	FACETS	0.981	0.89	1	0.981	0.89	1	CLONAL	1	FALSE	0	0.337760848113064	1		934	622	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974677	21974677	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1057519882	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	105	558	0	ENST00000304494.5:c.150G>T	p.Gln50His	p.Q50H	ENST00000304494	NM_000077.4	50	caG/caT	1/3	0.337760848113064	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	0	0.337760848113064	1		558	446	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528612	8528612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	52	479	0	ENST00000356435.5:c.520C>T	p.Arg174Cys	p.R174C	ENST00000356435		174	Cgt/Tgt	4/35	0.337760848113064	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	FALSE	0	0.337760848113064	1		479	237	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427690	72427690	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	83	438	1	ENST00000477973.2:c.800G>T	p.Arg267Leu	p.R267L	ENST00000477973	NM_012234.5	267	cGc/cTc	4/4	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.337760848113064	2		439	392	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219187	94219187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1023372148	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	58	512	0	ENST00000323929.3:c.217C>T	p.His73Tyr	p.H73Y	ENST00000323929	NM_005591.3	73	Cat/Tat	4/20	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	FALSE	1	0.337760848113064	2		512	311	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311604	15311605	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	61	311	0	ENST00000263388.2:c.112dup	p.Ala38GlyfsTer37	p.A38Gfs*37	ENST00000263388	NM_000435.2	38	gct/gGct	1/33	0.337760848113064	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	0	0.337760848113064	1		311	223	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435493	110435493	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	61	739	0	ENST00000375856.3:c.2908C>T	p.Arg970Trp	p.R970W	ENST00000375856	NM_003749.2	970	Cgg/Tgg	1/2	0.276980792840827	1	FACETS	0.62	0.536	0.712	0.62	0.536	0.712	SUBCLONAL	1	FALSE	0	0.337760848113064	1		739	484	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046674	42046674	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	77	499	0	ENST00000219905.7:c.7048G>T	p.Val2350Leu	p.V2350L	ENST00000219905	NM_001164273.1	2350	Gtg/Ttg	18/24	0.337760848113064	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	0	0.337760848113064	1		499	344	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248708	212248708	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	50	445	0	ENST00000342788.4:c.3559G>T	p.Glu1187Ter	p.E1187*	ENST00000342788	NM_005235.2	1187	Gaa/Taa	28/28	1	2	FACETS	0.8	0.681	0.93	0.8	0.681	0.93	CLONAL	1	FALSE	1	0.337760848113064	2		445	370	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420273	88420273	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	70	542	0	ENST00000360948.2:c.2413G>T	p.Gly805Trp	p.G805W	ENST00000360948	NM_001012338.2	805	Ggg/Tgg	19/19	1	2	FACETS	0.752	0.657	0.855	0.752	0.657	0.855	SUBCLONAL	1	FALSE	1	0.337760848113064	2		542	551	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448542	89448542	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	51	491	0	ENST00000336596.2:c.1506C>A	p.Asp502Glu	p.D502E	ENST00000336596	NM_005233.5	502	gaC/gaA	7/17	1	2	FACETS	0.728	0.62	0.845	0.728	0.62	0.845	SUBCLONAL	1	FALSE	1	0.337760848113064	2		491	415	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727424	66727424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	95	478	0	ENST00000307102.5:c.140G>T	p.Arg47Leu	p.R47L	ENST00000307102	NM_002755.3	47	cGa/cTa	2/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.337760848113064	2		478	459	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483921	88483921	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	81	753	0	ENST00000360948.2:c.1649del	p.Gly550GlufsTer22	p.G550Efs*22	ENST00000360948	NM_001012338.2	550	gGa/ga	14/19	1	2	FACETS	0.698	0.615	0.787	0.698	0.615	0.787	SUBCLONAL	1	FALSE	1	0.337760848113064	2		753	687	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251954	153251954	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	22	511	0	ENST00000281708.4:c.1052G>T	p.Trp351Leu	p.W351L	ENST00000281708	NM_033632.3	351	tGg/tTg	7/12	1	2	FACETS	0.532	0.413	0.669	0.532	0.413	0.669	SUBCLONAL	1	FALSE	1	0.337760848113064	2		511	245	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176153781	176153781	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	35	443	0	ENST00000367669.3:c.455G>C	p.Gly152Ala	p.G152A	ENST00000367669	NM_022457.5	152	gGc/gCc	2/20	1	2	FACETS	0.882	0.728	1	0.882	0.728	1	CLONAL	1	FALSE	1	0.337760848113064	2		443	235	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206661275	206661275	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	46	790	0	ENST00000367120.3:c.1641G>T	p.Leu547Phe	p.L547F	ENST00000367120	NM_014002.3	547	ttG/ttT	16/22	1	2	FACETS	0.525	0.442	0.617	0.525	0.442	0.617	SUBCLONAL	1	FALSE	1	0.337760848113064	2		790	519	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601894	43601894	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs77702891	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	74	890	3	ENST00000355710.3:c.938G>T	p.Arg313Leu	p.R313L	ENST00000355710	NM_020975.4	313	cGg/cTg	5/20	1	2	FACETS	0.618	0.541	0.702	0.618	0.541	0.702	SUBCLONAL	1	FALSE	1	0.337760848113064	2		893	709	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70412331	70412331	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	57	339	0	ENST00000373644.4:c.4441G>C	p.Gly1481Arg	p.G1481R	ENST00000373644	NM_030625.2	1481	Ggg/Cgg	6/12	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	1	0.337760848113064	2		339	272	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724594	112724594	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	35	562	0	ENST00000369452.4:c.478A>T	p.Ser160Cys	p.S160C	ENST00000369452	NM_007373.3	160	Agt/Tgt	2/9	1	2	FACETS	0.478	0.391	0.574	0.478	0.391	0.574	SUBCLONAL	1	FALSE	1	0.337760848113064	2		562	434	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4388030	4388030	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	134	537	0	ENST00000261254.3:c.516G>T	p.Glu172Asp	p.E172D	ENST00000261254	NM_001759.3	172	gaG/gaT	3/5	0.317523523441727	2	FACETS	0.83	0.759	0.903	0.83	0.759	0.903	CLONAL	2	FALSE	0	0.337760848113064	2		537	478	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445113	49445113	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	30	806	0	ENST00000301067.7:c.2353G>C	p.Glu785Gln	p.E785Q	ENST00000301067	NM_003482.3	785	Gag/Cag	10/54	0.317523523441727	2	FACETS	0.309	0.248	0.378	0.154	0.124	0.189	SUBCLONAL	1	FALSE	0	0.337760848113064	2		806	575	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877366	28877366	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	53	587	0	ENST00000282397.4:c.3955G>C	p.Ala1319Pro	p.A1319P	ENST00000282397	NM_002019.4	1319	Gcg/Ccg	30/30	0.276980792840827	1	FACETS	0.612	0.523	0.709	0.612	0.523	0.709	SUBCLONAL	1	FALSE	0	0.337760848113064	1		587	426	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29002026	29002026	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	34	393	0	ENST00000282397.4:c.1139C>A	p.Ser380Tyr	p.S380Y	ENST00000282397	NM_002019.4	380	tCt/tAt	9/30	0.276980792840827	1	FACETS	0.636	0.522	0.763	0.636	0.522	0.763	SUBCLONAL	1	FALSE	0	0.337760848113064	1		393	263	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892276	9892276	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	33	539	0	ENST00000330684.3:c.2214G>T	p.Lys738Asn	p.K738N	ENST00000330684	NM_001134407.1	738	aaG/aaT	11/13	1	2	FACETS	0.587	0.479	0.708	0.587	0.479	0.708	SUBCLONAL	1	FALSE	1	0.337760848113064	2		539	333	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993712	72993712	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	54	793	0	ENST00000268489.5:c.333G>C	p.Glu111Asp	p.E111D	ENST00000268489	NM_006885.3	111	gaG/gaC	2/10	1	2	FACETS	0.686	0.587	0.795	0.686	0.587	0.795	SUBCLONAL	1	FALSE	1	0.337760848113064	2		793	466	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976226	7976226	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	81	760	0	ENST00000319144.4:c.1969G>T	p.Ala657Ser	p.A657S	ENST00000319144	NM_001139.2	657	Gcc/Tcc	15/15	0.337760848113064	2	FACETS	0.93	0.821	1	0.465	0.41	0.523	CLONAL	1	FALSE	0	0.337760848113064	2		760	516	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876593	59876593	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	51	510	0	ENST00000259008.2:c.1208G>C	p.Arg403Pro	p.R403P	ENST00000259008	NM_032043.2	403	cGg/cCg	9/20	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	FALSE	1	0.337760848113064	2		510	296	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885991	59885991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567838124	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	51	581	0	ENST00000259008.2:c.755C>T	p.Thr252Ile	p.T252I	ENST00000259008	NM_032043.2	252	aCa/aTa	7/20	1	2	FACETS	0.712	0.607	0.828	0.712	0.607	0.828	SUBCLONAL	1	FALSE	1	0.337760848113064	2		581	424	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353835	15353835	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	55	377	0	ENST00000263377.2:c.3045G>T	p.Gln1015His	p.Q1015H	ENST00000263377	NM_058243.2	1015	caG/caT	14/20	0.337760848113064	1	FACETS	0.977	0.843	1	0.977	0.843	1	CLONAL	1	FALSE	0	0.337760848113064	1		377	277	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796531	42796531	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	129	1131	1	ENST00000575354.2:c.3088A>T	p.Thr1030Ser	p.T1030S	ENST00000575354	NM_015125.3	1030	Acc/Tcc	13/20	0.273868894806863	3	FACETS	1	0.941	1	0.525	0.476	0.577	CLONAL	1	FALSE	1	0.337760848113064	3		1132	850	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497913	25497913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	58	845	0	ENST00000264709.3:c.536G>A	p.Ser179Asn	p.S179N	ENST00000264709	NM_175629.2	179	aGc/aAc	6/23	1	2	FACETS	0.605	0.519	0.698	0.605	0.519	0.698	SUBCLONAL	1	FALSE	1	0.337760848113064	2		845	568	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754868	29754868	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	82	601	0	ENST00000389048.3:c.1067A>T	p.Gln356Leu	p.Q356L	ENST00000389048	NM_004304.4	356	cAg/cTg	4/29	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	1	0.337760848113064	2		601	437	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248555	212248555	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	36	625	0	ENST00000342788.4:c.3712G>T	p.Asp1238Tyr	p.D1238Y	ENST00000342788	NM_005235.2	1238	Gac/Tac	28/28	1	2	FACETS	0.426	0.35	0.512	0.426	0.35	0.512	SUBCLONAL	1	FALSE	1	0.337760848113064	2		625	500	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251686	212251686	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	44	485	0	ENST00000342788.4:c.3373A>T	p.Thr1125Ser	p.T1125S	ENST00000342788	NM_005235.2	1125	Acc/Tcc	27/28	1	2	FACETS	0.639	0.536	0.751	0.639	0.536	0.751	SUBCLONAL	1	FALSE	1	0.337760848113064	2		485	408	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295744	212295744	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	81	587	1	ENST00000342788.4:c.2569G>T	p.Val857Leu	p.V857L	ENST00000342788	NM_005235.2	857	Gtg/Ttg	21/28	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.337760848113064	2		588	379	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989504	212989504	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	68	394	0	ENST00000342788.4:c.207G>T	p.Glu69Asp	p.E69D	ENST00000342788	NM_005235.2	69	gaG/gaT	2/28	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	1	0.337760848113064	2		394	368	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561440	9561440	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	32	550	0	ENST00000353224.5:c.342C>A	p.Ser114Arg	p.S114R	ENST00000353224	NM_177990.2	114	agC/agA	4/10	1	2	FACETS	0.414	0.335	0.502	0.414	0.335	0.502	SUBCLONAL	1	FALSE	1	0.337760848113064	2		550	458	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748598	40748598	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1295515790	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	70	450	0	ENST00000373198.4:c.2918C>T	p.Pro973Leu	p.P973L	ENST00000373198	NM_133170.3	973	cCt/cTt	21/32	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	FALSE	1	0.337760848113064	2		450	401	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46276031	46276031	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	85	557	0	ENST00000371998.3:c.3467G>T	p.Arg1156Leu	p.R1156L	ENST00000371998		1156	cGa/cTa	18/23	1	2	FACETS	0.955	0.846	1	0.955	0.846	1	CLONAL	1	FALSE	1	0.337760848113064	2		557	527	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713909	30713909	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	64	597	0	ENST00000295754.5:c.1234G>T	p.Asp412Tyr	p.D412Y	ENST00000295754	NM_003242.5	412	Gac/Tac	4/7	1	2	FACETS	0.894	0.777	1	0.894	0.777	1	CLONAL	1	FALSE	1	0.337760848113064	2		597	424	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69998201	69998201	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	64	396	0	ENST00000394351.3:c.442-1G>C		p.X148_splice	ENST00000394351	NM_000248.3	148			1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	FALSE	1	0.337760848113064	2		396	378	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851562	134851562	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	58	554	0	ENST00000398015.3:c.968C>G	p.Pro323Arg	p.P323R	ENST00000398015	NM_004441.4	323	cCa/cGa	5/16	1	2	FACETS	0.791	0.682	0.91	0.791	0.682	0.91	CLONAL	1	FALSE	1	0.337760848113064	2		554	434	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133615	55133615	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs371882159	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	46	488	0	ENST00000257290.5:c.919A>G	p.Ile307Val	p.I307V	ENST00000257290	NM_006206.4	307	Att/Gtt	6/23	1	2	FACETS	0.774	0.654	0.905	0.774	0.654	0.905	CLONAL	1	FALSE	1	0.337760848113064	2		488	352	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156535	55156535	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	60	653	1	ENST00000257290.5:c.2936G>T	p.Arg979Leu	p.R979L	ENST00000257290	NM_006206.4	979	cGc/cTc	22/23	1	2	FACETS	0.767	0.662	0.881	0.767	0.662	0.881	SUBCLONAL	1	FALSE	1	0.337760848113064	2		654	463	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155771	106155771	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	27	442	0	ENST00000380013.4:c.672A>T	p.Glu224Asp	p.E224D	ENST00000380013	NM_001127208.2	224	gaA/gaT	3/11	1	2	FACETS	0.486	0.387	0.599	0.486	0.387	0.599	SUBCLONAL	1	FALSE	1	0.337760848113064	2		442	329	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539114	187539114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	51	505	0	ENST00000441802.2:c.8626G>A	p.Asp2876Asn	p.D2876N	ENST00000441802	NM_005245.3	2876	Gac/Aac	10/27	1	2	FACETS	0.709	0.604	0.824	0.709	0.604	0.824	SUBCLONAL	1	FALSE	1	0.337760848113064	2		505	426	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584750	187584750	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	41	322	0	ENST00000441802.2:c.3283G>T	p.Asp1095Tyr	p.D1095Y	ENST00000441802	NM_005245.3	1095	Gat/Tat	3/27	1	2	FACETS	0.956	0.802	1	0.956	0.802	1	CLONAL	1	FALSE	1	0.337760848113064	2		322	254	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629885	187629885	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	57	718	0	ENST00000441802.2:c.1097A>T	p.Lys366Met	p.K366M	ENST00000441802	NM_005245.3	366	aAg/aTg	2/27	1	2	FACETS	0.678	0.582	0.782	0.678	0.582	0.782	SUBCLONAL	1	FALSE	1	0.337760848113064	2		718	498	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522329	176522329	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	96	637	0	ENST00000292408.4:c.1520-2A>T		p.X507_splice	ENST00000292408	NM_213647.1	507			0.337760848113064	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	0	0.337760848113064	1		637	422	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225581	26225581	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	100	792	0	ENST00000360408.1:c.199C>A	p.Pro67Thr	p.P67T	ENST00000360408	NM_003532.2	67	Ccg/Acg	1/1	1	2	FACETS	0.995	0.891	1	0.995	0.891	1	CLONAL	1	FALSE	1	0.337760848113064	2		792	595	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187453	32187453	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	124	898	0	ENST00000375023.3:c.1426C>A	p.His476Asn	p.H476N	ENST00000375023	NM_004557.3	476	Cac/Aac	8/30	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.337760848113064	2		898	601	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188578	32188578	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	75	895	0	ENST00000375023.3:c.877G>T	p.Asp293Tyr	p.D293Y	ENST00000375023	NM_004557.3	293	Gat/Tat	5/30	1	2	FACETS	0.802	0.703	0.907	0.802	0.703	0.907	CLONAL	1	FALSE	1	0.337760848113064	2		895	554	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017516	112017516	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	47	398	0	ENST00000368678.4:c.997G>T	p.Glu333Ter	p.E333*	ENST00000368678		333	Gag/Tag	9/13	1	2	FACETS	0.786	0.666	0.918	0.786	0.666	0.918	CLONAL	1	FALSE	1	0.337760848113064	2		398	354	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677917	117677917	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	70	428	0	ENST00000368508.3:c.4016C>T	p.Ala1339Val	p.A1339V	ENST00000368508	NM_002944.2	1339	gCa/gTa	25/43	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	FALSE	1	0.337760848113064	2		428	361	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381534	81381534	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	40	315	0	ENST00000222390.5:c.527A>G	p.Tyr176Cys	p.Y176C	ENST00000222390	NM_000601.4	176	tAc/tGc	5/18	1	2	FACETS	0.846	0.707	0.999	0.846	0.707	0.999	CLONAL	1	FALSE	1	0.337760848113064	2		315	280	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381577	81381577	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	28	226	0	ENST00000222390.5:c.484T>G	p.Phe162Val	p.F162V	ENST00000222390	NM_000601.4	162	Ttt/Gtt	5/18	1	2	FACETS	0.837	0.674	1	0.837	0.674	1	CLONAL	1	FALSE	1	0.337760848113064	2		226	198	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388078	81388078	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	38	435	0	ENST00000222390.5:c.297C>A	p.Phe99Leu	p.F99L	ENST00000222390	NM_000601.4	99	ttC/ttA	3/18	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	FALSE	1	0.337760848113064	2		435	204	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523596	148523596	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	44	289	0	ENST00000320356.2:c.857G>C	p.Cys286Ser	p.C286S	ENST00000320356	NM_004456.4	286	tGt/tCt	8/20	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	FALSE	1	0.337760848113064	2		289	245	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956805	68956805	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	40	642	0	ENST00000288368.4:c.923A>G	p.Glu308Gly	p.E308G	ENST00000288368	NM_024870.2	308	gAg/gGg	8/40	0.276980792840827	1	FACETS	0.49	0.407	0.581	0.49	0.407	0.581	SUBCLONAL	1	FALSE	0	0.337760848113064	1		642	402	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636715	8636715	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	41	331	0	ENST00000356435.5:c.194G>C	p.Ser65Thr	p.S65T	ENST00000356435		65	aGc/aCc	2/35	0.337760848113064	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	FALSE	0	0.337760848113064	1		331	176	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339164	87339164	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs772111782	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	37	422	0	ENST00000277120.3:c.746C>A	p.Ser249Tyr	p.S249Y	ENST00000277120		249	tCc/tAc	8/19	0.337760848113064	1	FACETS	0.624	0.516	0.743	0.624	0.516	0.743	SUBCLONAL	1	FALSE	0	0.337760848113064	1		422	292	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128201269	128201269	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	61	762	0	ENST00000265960.3:c.1466G>T	p.Arg489Leu	p.R489L	ENST00000265960	NM_001006617.1	489	cGa/cTa	12/12	0.337760848113064	1	FACETS	0.657	0.568	0.753	0.657	0.568	0.753	SUBCLONAL	1	FALSE	0	0.337760848113064	1		762	457	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399852	139399852	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	109	1101	0	ENST00000277541.6:c.4496A>G	p.Tyr1499Cys	p.Y1499C	ENST00000277541	NM_017617.3	1499	tAc/tGc	25/34	0.337760848113064	1	FACETS	0.893	0.803	0.987	0.893	0.803	0.987	CLONAL	1	FALSE	0	0.337760848113064	1		1101	601	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152853832	152853832	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	26	59	1	ENST00000406277.2:c.732G>T	p.Glu244Asp	p.E244D	ENST00000406277	NM_152274.4	244	gaG/gaT	7/7	1	1	FACETS	1	0.912	1	1	0.963	1	CLONAL	2	FALSE	0	0.337760848113064	1		60	55	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562517	21562519	+	missense_variant	Missense_Mutation	TNP	CGG	CGG	AGC	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	11	79	0	ENST00000382592.4:c.1400_1402delinsGCT	p.Pro467_Ala468delinsArgSer	p.P467_A468delinsRS	ENST00000382592	NM_014572.2	467	cCCGcg/cGCTcg	4/8	0.276980792840827	1	FACETS	0.859	0.606	1	0.859	0.606	1	CLONAL	1	FALSE	0	0.337760848113064	1		79	63	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807432	36807434	+	missense_variant	Missense_Mutation	TNP	CGC	CGC	AGA	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	57	914	0	ENST00000373129.3:c.1230_1232delinsTCT	p.Arg411Leu	p.R411L	ENST00000373129	NM_032017.1	410	gtGCGa/gtTCTa	12/12	1	2	FACETS	0.563	0.483	0.651	0.563	0.483	0.651	SUBCLONAL	1	FALSE	1	0.337760848113064	2		914	599	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636926	158636927	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	A	novel	NA	P-0049308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	26	527	0	ENST00000263640.3:c.253_254delinsT	p.Pro85CysfsTer47	p.P85Cfs*47	ENST00000263640	NM_001105.4	85	CCg/Tg	4/11	1	2	FACETS	0.367	0.29	0.455	0.367	0.29	0.455	SUBCLONAL	1	FALSE	1	0.337760848113064	2		527	420	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522623	176522623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773674820	NA	P-0049352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	35	656	0	ENST00000292408.4:c.1720C>T	p.Pro574Ser	p.P574S	ENST00000292408	NM_213647.1	574	Ccc/Tcc	13/18	0.696879832502075	1	FACETS	0.109	0.089	0.132	0.109	0.089	0.132	SUBCLONAL	1	TRUE	0	0.696879832502075	1		656	601	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68292250	68292250	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	268	311	0	ENST00000487270.1:c.154C>G	p.Leu52Val	p.L52V	ENST00000487270	NM_133509.3	52	Ctt/Gtt	3/11	0.124883451184618	5	FACETS	1	0.971	1	0.698	0.658	0.739	INDETERMINATE	2	TRUE	2	0.696879832502075	5		311	751	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578459	7578460	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	455	637	0	ENST00000269305.4:c.470_471insG	p.Arg158ProfsTer23	p.R158Pfs*23	ENST00000269305	NM_001126112.2	157	gtc/gtGc	5/11	0.696879832502075	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.696879832502075	1		637	765	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957776	1957776	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	47	439	0	ENST00000382891.5:c.2742G>C	p.Glu914Asp	p.E914D	ENST00000382891	NM_133335.3	914	gaG/gaC	15/22	0.592760311408612	1	FACETS	0.131	0.11	0.155	0.131	0.11	0.155	SUBCLONAL	1	TRUE	0	0.696879832502075	1		439	670	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467712	66467712	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	206	256	0	ENST00000273854.3:c.557T>C	p.Leu186Pro	p.L186P	ENST00000273854	NM_004439.5	186	cTt/cCt	3/18	0.696879832502075	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.696879832502075	1		256	357	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0049357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	108	454	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.27132273056572	1	FACETS	0.94	0.844	1	0.94	0.844	1	CLONAL	1	TRUE	0	0.27132273056572	1		455	732	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402834	20402836	+	inframe_deletion	In_Frame_Del	DEL	GCG	GCG	-	rs746263274	NA	P-0049357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	10	47	1	ENST00000346618.3:c.385_387del	p.Gly129del	p.G129del	ENST00000346618	NM_001949.4	124	aGCGgc/agc	1/7	0.27132273056572	1	FACETS	0.873	0.6	1	0.873	0.6	1	CLONAL	1	TRUE	0	0.27132273056572	1		48	73	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228613023	228613023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	45	436	0	ENST00000366696.1:c.4G>A	p.Ala2Thr	p.A2T	ENST00000366696	NM_003493.2	2	Gcc/Acc	1/1	0.27132273056572	1	FACETS	0.538	0.452	0.633	0.538	0.452	0.633	SUBCLONAL	1	TRUE	0	0.27132273056572	1		436	533	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045772	26045786	+	inframe_deletion	In_Frame_Del	DEL	GCACCGTGGCCTTGC	GCACCGTGGCCTTGC	-	novel	NA	P-0049357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	94	482	0	ENST00000540144.1:c.136_150del	p.Thr46_Arg50del	p.T46_R50del	ENST00000540144	NM_003531.2	45	gGCACCGTGGCCTTGCgc/ggc	1/1	0.116921031265415	3	FACETS	1	0.955	1	0.571	0.508	0.638	INDETERMINATE	1	TRUE	1	0.27132273056572	3		482	689	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896345	151896365	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTGAATAATTCTACATACCG	TGTGAATAATTCTACATACCG	-	novel	NA	P-0049357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	131	242	0	ENST00000262189.6:c.4272_4273+19del		p.X1424_splice	ENST00000262189	NM_170606.2	1424		27/59	0.177976704771356	5	FACETS	1	0.953	1	0.717	0.652	0.784	CLONAL	2	TRUE	2	0.27132273056572	5		242	632	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	104	364	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.49	2		364	367	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870231	44870231	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	68	275	0	ENST00000377967.4:c.410G>T	p.Gly137Val	p.G137V	ENST00000377967	NM_021140.2	137	gGt/gTt	5/29	1	2	FACETS	0.901	0.791	1	0.901	0.791	1	CLONAL	1	TRUE	1	0.49	2		275	308	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119910	70119910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1297203260	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	118	469	0	ENST00000245479.2:c.916del	p.Val306CysfsTer77	p.V306Cfs*77	ENST00000245479	NM_000346.3	304	ccG/cc	3/3	0.492192066338985	2	FACETS	1	0.938	1	0.521	0.473	0.571	CLONAL	1	TRUE	0	0.49	2		469	462	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	61	205	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.808	0.703	0.922	0.808	0.703	0.922	CLONAL	1	TRUE	1	0.49	2		205	308	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	68	364	1	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	1	2	FACETS	0.941	0.826	1	0.941	0.826	1	CLONAL	1	TRUE	1	0.49	2		365	295	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	102	475	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.767	0.688	0.85	0.767	0.688	0.85	SUBCLONAL	1	TRUE	1	0.49	2		475	543	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993708	72993708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs62640010	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	130	565	0	ENST00000268489.5:c.337G>A	p.Ala113Thr	p.A113T	ENST00000268489	NM_006885.3	113	Gcc/Acc	2/10	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.49	2		565	495	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467637	50467637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1262982300	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	75	370	0	ENST00000331340.3:c.872C>T	p.Thr291Met	p.T291M	ENST00000331340	NM_006060.4	291	aCg/aTg	8/8	1	2	FACETS	0.911	0.805	1	0.911	0.805	1	CLONAL	1	TRUE	1	0.49	2		370	336	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	99	377	4	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	0.935	0.84	1	0.935	0.84	1	CLONAL	1	TRUE	1	0.49	2		381	432	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	153	643	3	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.49	2		646	616	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655381	67655381	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	111	381	0	ENST00000264010.4:c.1244G>A	p.Arg415Gln	p.R415Q	ENST00000264010	NM_006565.3	415	cGg/cAg	7/12	1	2	FACETS	0.93	0.841	1	0.93	0.841	1	CLONAL	1	TRUE	1	0.49	2		381	487	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998898	11998898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	55	155	1	ENST00000353533.5:c.400C>T	p.Arg134Trp	p.R134W	ENST00000353533	NM_003010.3	134	Cgg/Tgg	4/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.49	2		156	198	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	97	399	1	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.857	0.768	0.951	0.857	0.768	0.951	CLONAL	1	TRUE	1	0.49	2		400	462	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	119	375	3	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.49	2		378	468	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097625	11097625	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	162	734	1	ENST00000358026.2:c.810del	p.Met272CysfsTer31	p.M272Cfs*31	ENST00000358026	NM_001128849.1	269	Ccc/cc	5/36	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.49	2		735	640	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270529	98270530	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs751977093	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	74	282	0	ENST00000331920.6:c.114dup	p.Leu39AlafsTer51	p.L39Afs*51	ENST00000331920	NM_000264.3	38	-/G	1/24	1	2	FACETS	0.981	0.866	1	0.981	0.866	1	CLONAL	1	TRUE	1	0.49	2		282	308	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019143	31019144	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	113	350	0	ENST00000375687.4:c.742dup	p.Glu248GlyfsTer6	p.E248Gfs*6	ENST00000375687	NM_015338.5	246	-/G	9/13	1	2	FACETS	0.896	0.81	0.986	0.896	0.81	0.986	CLONAL	1	TRUE	1	0.49	2		350	515	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	220	763	9	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.49	2		772	606	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	148	542	3	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	1	2	FACETS	0.987	0.905	1	0.987	0.905	1	CLONAL	1	TRUE	1	0.49	2		545	612	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	136	910	4	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	0.89	0.811	0.971	0.89	0.811	0.971	CLONAL	1	TRUE	1	0.49	2		914	624	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658481	3658481	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140876043	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	142	445	0	ENST00000294008.3:c.485C>T	p.Thr162Met	p.T162M	ENST00000294008	NM_032444.2	162	aCg/aTg	2/15	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.49	2		445	566	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131409	17131409	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	179	603	2	ENST00000285071.4:c.43G>T	p.Gly15Cys	p.G15C	ENST00000285071	NM_144997.5	15	Ggc/Tgc	4/14	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.49	2		605	666	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352560	89352560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768058427	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	141	496	0	ENST00000301030.4:c.779C>T	p.Pro260Leu	p.P260L	ENST00000301030	NM_001256183.1	260	cCg/cTg	8/13	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.49	2		496	560	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47685282	47685282	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767942932	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	81	285	0	ENST00000347630.2:c.668C>T	p.Pro223Leu	p.P223L	ENST00000347630	NM_001007230.1	223	cCg/cTg	8/11	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.49	2		285	311	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688707	47688707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779385564	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	143	346	0	ENST00000347630.2:c.593G>A	p.Arg198Gln	p.R198Q	ENST00000347630	NM_001007230.1	198	cGg/cAg	7/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.49	2		346	531	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448526	49448526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371342351	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	106	477	0	ENST00000301067.7:c.185C>T	p.Pro62Leu	p.P62L	ENST00000301067	NM_003482.3	62	cCg/cTg	3/54	1	2	FACETS	0.83	0.747	0.918	0.83	0.747	0.918	CLONAL	1	TRUE	1	0.49	2		477	521	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814798	139814798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201857326	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	149	577	0	ENST00000247668.2:c.791C>T	p.Ala264Val	p.A264V	ENST00000247668	NM_021138.3	264	gCg/gTg	8/11	1	2	FACETS	0.928	0.851	1	0.928	0.851	1	CLONAL	1	TRUE	1	0.49	2		577	655	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332463	153332463	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	85	203	0	ENST00000281708.4:c.493del	p.Thr165GlnfsTer4	p.T165Qfs*4	ENST00000281708	NM_033632.3	165	Aca/ca	2/12	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.49	2		203	333	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967285	25967285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	113	319	0	ENST00000435504.4:c.1921C>T	p.Arg641Cys	p.R641C	ENST00000435504		641	Cgt/Tgt	13/13	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.49	2		319	444	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781167	135781167	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	43	502	0	ENST00000298552.3:c.1798C>T	p.Gln600Ter	p.Q600*	ENST00000298552	NM_001162426.1	600	Cag/Tag	15/23	1	2	FACETS	0.331	0.277	0.392	0.331	0.277	0.392	SUBCLONAL	1	TRUE	1	0.49	2		502	530	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941889	71941889	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	160	580	0	ENST00000298229.2:c.1247C>A	p.Ser416Tyr	p.S416Y	ENST00000298229	NM_001567.3	416	tCc/tAc	11/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.49	2		580	581	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748317	43748317	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	131	467	0	ENST00000382044.4:c.2489C>A	p.Pro830His	p.P830H	ENST00000382044	NM_001141980.1	830	cCt/cAt	12/28	1	2	FACETS	0.85	0.774	0.93	0.85	0.774	0.93	CLONAL	1	TRUE	1	0.49	2		467	629	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354455	40354455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752593400	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	132	645	0	ENST00000293328.3:c.2140G>A	p.Ala714Thr	p.A714T	ENST00000293328	NM_012448.3	714	Gca/Aca	18/19	1	2	FACETS	0.915	0.833	1	0.915	0.833	1	CLONAL	1	TRUE	1	0.49	2		645	589	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492743	56492743	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	319	473	0	ENST00000407977.2:c.196del	p.Glu66LysfsTer10	p.E66Kfs*10	ENST00000407977		66	Gaa/aa	2/10	0.492192066338985	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.49	2		473	581	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955121	17955122	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	159	669	0	ENST00000458235.1:c.105dup	p.Gly36ArgfsTer16	p.G36Rfs*16	ENST00000458235	NM_000215.3	35	-/C	2/24	1	2	FACETS	0.942	0.866	1	0.942	0.866	1	CLONAL	1	TRUE	1	0.49	2		669	689	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271878	18271878	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1208639269	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	158	562	1	ENST00000222254.8:c.481G>A	p.Asp161Asn	p.D161N	ENST00000222254	NM_005027.3	161	Gac/Aac	5/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.49	2		563	573	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643393	52643393	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750354025	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	122	279	0	ENST00000394830.3:c.2503C>T	p.Arg835Cys	p.R835C	ENST00000394830	NM_018313.4	835	Cgt/Tgt	17/30	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.49	2		279	408	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446152	187446152	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	135	470	1	ENST00000232014.4:c.1536C>A	p.Ser512Arg	p.S512R	ENST00000232014	NM_001130845.1	512	agC/agA	6/10	1	2	FACETS	0.974	0.889	1	0.974	0.889	1	CLONAL	1	TRUE	1	0.49	2		471	566	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143044528	143044528	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	95	329	0	ENST00000262992.4:c.1934C>T	p.Thr645Ile	p.T645I	ENST00000262992	NM_001101669.1	645	aCa/aTa	18/24	1	2	FACETS	0.939	0.841	1	0.939	0.841	1	CLONAL	1	TRUE	1	0.49	2		329	413	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685285	86685285	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	82	194	0	ENST00000274376.6:c.3001A>T	p.Ile1001Phe	p.I1001F	ENST00000274376	NM_002890.2	1001	Att/Ttt	24/25	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.49	2		194	324	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056527	26056527	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs200279816	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	21	298	0	ENST00000343677.2:c.130A>G	p.Ile44Val	p.I44V	ENST00000343677	NM_005319.3	44	Atc/Gtc	1/1	1	2	FACETS	0.258	0.198	0.328	0.258	0.198	0.328	SUBCLONAL	1	TRUE	1	0.49	2		298	332	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170103	32170103	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	117	685	0	ENST00000375023.3:c.3505del	p.Arg1169GlyfsTer135	p.R1169Gfs*135	ENST00000375023	NM_004557.3	1169	Cgg/gg	21/30	1	2	FACETS	0.796	0.72	0.876	0.796	0.72	0.876	SUBCLONAL	1	TRUE	1	0.49	2		685	600	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803531	32803531	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1372620501	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	157	569	0	ENST00000374899.4:c.628C>T	p.Arg210Ter	p.R210*	ENST00000374899	NM_018833.2	210	Cga/Tga	4/12	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.49	2		569	588	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017549	112017549	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	114	310	0	ENST00000368678.4:c.964A>G	p.Lys322Glu	p.K322E	ENST00000368678		322	Aag/Gag	9/13	1	2	FACETS	0.986	0.893	1	0.986	0.893	1	CLONAL	1	TRUE	1	0.49	2		310	472	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864657	68864657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	69	257	1	ENST00000288368.4:c.28C>T	p.Arg10Cys	p.R10C	ENST00000288368	NM_024870.2	10	Cgc/Tgc	1/40	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.49	2		258	260	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923181	39923181	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	105	374	0	ENST00000378444.4:c.3527C>T	p.Thr1176Ile	p.T1176I	ENST00000378444	NM_001123385.1	1176	aCa/aTa	8/15	1	2	FACETS	0.95	0.856	1	0.95	0.856	1	CLONAL	1	TRUE	1	0.49	2		374	451	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0049364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	34	443	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.19	2		443	278	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0049364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	28	361	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.837	0.676	1	1	0.947	1	CLONAL	2	TRUE	1	0.19	2		361	176	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0049364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	26	328	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.19	2		328	218	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249348	110249348	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	68	866	1	ENST00000374672.4:c.1225A>C	p.Lys409Gln	p.K409Q	ENST00000374672	NM_004235.4	409	Aag/Cag	4/5	1	2	FACETS	0.879	0.768	0.998	1	0.979	1	CLONAL	2	TRUE	1	0.19	2		867	407	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038526	47038526	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	43	807	1	ENST00000377604.3:c.688C>T	p.Arg230Ter	p.R230*	ENST00000377604	NM_001204468.1	230	Cga/Tga	8/24	0.128830943592058	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.19	1		808	359	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448323	56448323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	103	807	1	ENST00000407977.2:c.324G>T	p.Lys108Asn	p.K108N	ENST00000407977		108	aaG/aaT	3/10	0.254556444579793	2	FACETS	0.974	0.88	1	1	0.983	1	CLONAL	3	TRUE	0	0.19	2		808	371	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453990	140453990	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	12	183	0	ENST00000288602.6:c.1738A>G	p.Asn580Asp	p.N580D	ENST00000288602	NM_004333.4	580	Aat/Gat	14/18	1	2	FACETS	1	0.737	1	1	0.737	1	CLONAL	1	TRUE	1	0.19	2		183	121	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0049426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	18	240	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.905	0.685	1	0.905	0.685	1	CLONAL	1	TRUE	1	0.23	2		240	173	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0049426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	16	223	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.23	2		223	110	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395570	116395570	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1013431413	NA	P-0049426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	11	410	0	ENST00000397752.3:c.1862+1G>A		p.X621_splice	ENST00000397752	NM_000245.2	621			1	2	FACETS	0.664	0.461	0.915	0.664	0.461	0.915	SUBCLONAL	1	TRUE	1	0.23	2		410	144	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0049426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	89	328	0				ENST00000310581	NM_198253.2	-/1132			0.110975671628674	3	FACETS	1	0.966	1	1	0.966	1	INDETERMINATE	2	TRUE	1	0.23	3		328	360	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625598	1625598	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs905918880	NA	P-0049426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	120	935	1	ENST00000344749.5:c.476G>A	p.Arg159Gln	p.R159Q	ENST00000344749	NM_001136139.2	159	cGg/cAg	7/19	1	2	FACETS	0.785	0.71	0.863	1	0.986	1	SUBCLONAL	2	TRUE	1	0.23	2		936	665	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419987	41419987	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376239850	NA	P-0049454-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	20	622	0	ENST00000373198.4:c.334C>T	p.Arg112Cys	p.R112C	ENST00000373198	NM_133170.3	112	Cgt/Tgt	3/32	0.208628023279053	1	FACETS	0.4	0.306	0.509	0.4	0.306	0.509	SUBCLONAL	1	FALSE	0	0.336905878042553	1		622	247	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0049545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	192	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.743643335044454	2		327	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0049545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	367	582	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.730653543763896	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	0	0.743643335044454	1		582	598	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0049545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	243	328	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.743643335044454	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	0	0.743643335044454	1		328	410	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959240	2959240	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148354898	NA	P-0049545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	271	451	0	ENST00000396946.4:c.2276G>A	p.Arg759Gln	p.R759Q	ENST00000396946	NM_032415.4	759	cGg/cAg	18/25	1	2	FACETS	0.889	0.837	0.942	0.889	0.837	0.942	CLONAL	1	FALSE	1	0.743643335044454	2		451	820	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50815323	50815323	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0049545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	81	429	0	ENST00000398568.2:c.1675+1G>C		p.X559_splice	ENST00000398568	NM_001042412.1	559			1	2	FACETS	0.342	0.301	0.386	0.342	0.301	0.386	SUBCLONAL	1	FALSE	1	0.743643335044454	2		429	637	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277955	41277955	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	168	321	0	ENST00000349496.5:c.1919T>A	p.Leu640Gln	p.L640Q	ENST00000349496	NM_001904.3	640	cTg/cAg	12/15	1	2	FACETS	0.961	0.892	1	0.961	0.892	1	CLONAL	1	FALSE	1	0.743643335044454	2		321	470	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127933461	127933461	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0049545-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	208	317	0	ENST00000373547.4:c.76-2A>T		p.X26_splice	ENST00000373547	NM_002721.4	26			1	2	FACETS	0.995	0.931	1	0.995	0.931	1	CLONAL	1	FALSE	1	0.743643335044454	2		317	562	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577564	7577564	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	64	660	0	ENST00000269305.4:c.717C>A	p.Asn239Lys	p.N239K	ENST00000269305	NM_001126112.2	239	aaC/aaA	7/11	0.284169326000486	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.284169326000486	1		660	357	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732469	74732469	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	106	313	0	ENST00000359995.5:c.440C>G	p.Ser147Trp	p.S147W	ENST00000359995	NM_001195427.1	147	tCg/tGg	2/3	0.250105952917902	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.284169326000486	3		313	385	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534285	534285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894226	NA	P-0049593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	55	651	0	ENST00000451590.1:c.38G>A	p.Gly13Asp	p.G13D	ENST00000451590	NM_001130442.1	13	gGt/gAt	2/5	0.284169326000486	1	FACETS	0.837	0.718	0.965	0.837	0.718	0.965	CLONAL	1	TRUE	0	0.284169326000486	1		651	397	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626680	12626680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751232720	NA	P-0049593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	69	538	0	ENST00000251849.4:c.1609G>A	p.Val537Ile	p.V537I	ENST00000251849	NM_002880.3	537	Gta/Ata	15/17	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.284169326000486	2		538	402	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468517	89468517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372257039	NA	P-0049593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	21	294	0	ENST00000336596.2:c.2051G>A	p.Arg684Gln	p.R684Q	ENST00000336596	NM_005233.5	684	cGa/cAa	11/17	1	2	FACETS	0.786	0.609	0.99	0.786	0.609	0.99	CLONAL	1	TRUE	1	0.284169326000486	2		294	188	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665042	29665042	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1060500356	NA	P-0049593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	39	452	0	ENST00000356175.3:c.6642-1G>A		p.X2214_splice	ENST00000356175	NM_000267.3	2214			0.284169326000486	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	0	0.284169326000486	1		452	210	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62323143	62323143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	67	629	0	ENST00000360203.5:c.2605G>A	p.Glu869Lys	p.E869K	ENST00000360203	NM_001283009.1	869	Gaa/Aaa	28/35	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.284169326000486	2		629	437	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248570	212248571	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0049593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	25	498	2	ENST00000342788.4:c.3696_3697delinsTT	p.Lys1232_Ala1233delinsAsnSer	p.K1232_A1233delinsNS	ENST00000342788	NM_005235.2	1232	aaGGcc/aaTTcc	28/28	1	2	FACETS	0.569	0.449	0.707	0.569	0.449	0.707	SUBCLONAL	1	TRUE	1	0.284169326000486	2		500	309	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0049650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	2451	577	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.539254278857041	22	FACETS	1	0.995	1			1	CLONAL	18	TRUE	NA	0.539254278857041	22		577	3189	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0049650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	440	725	31	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.538321570760692	2	FACETS	0.907	0.87	0.943	0.907	0.87	0.943	CLONAL	2	TRUE	0	0.539254278857041	2		756	900	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033844	49033844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853294	NA	P-0049650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	67	474	1	ENST00000267163.4:c.1981C>T	p.Arg661Trp	p.R661W	ENST00000267163	NM_000321.2	661	Cgg/Tgg	20/27	0.530234650359009	1	FACETS	0.693	0.609	0.781	0.693	0.609	0.781	SUBCLONAL	1	TRUE	0	0.539254278857041	1		475	262	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321140	62321140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	484	1000	0	ENST00000360203.5:c.2063C>T	p.Ser688Phe	p.S688F	ENST00000360203	NM_001283009.1	688	tCc/tTc	24/35	0.132499354205948	6	FACETS	0.893	0.855	0.933	0.893	0.855	0.933	INDETERMINATE	3	TRUE	3	0.539254278857041	6		1000	1392	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248124	98248124	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049650-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	241	486	0	ENST00000331920.6:c.427A>C	p.Thr143Pro	p.T143P	ENST00000331920	NM_000264.3	143	Act/Cct	3/24	0.539254278857041	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.539254278857041	1		486	506	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188196	10188196	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0049673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	125	410	1	ENST00000256474.2:c.341-2A>T		p.X114_splice	ENST00000256474	NM_000551.3	114			0.351536189039778	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.351536189039778	1		411	491	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929179	32929179	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	98	405	0	ENST00000380152.3:c.7189A>G	p.Ile2397Val	p.I2397V	ENST00000380152		2397	Att/Gtt	14/27	1	2	FACETS	0.996	0.891	1	0.996	0.891	1	CLONAL	1	TRUE	1	0.351536189039778	2		405	560	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098957	47098957	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	124	447	0	ENST00000409792.3:c.6317del	p.Lys2106ArgfsTer41	p.K2106Rfs*41	ENST00000409792	NM_014159.6	2106	aAg/ag	15/21	0.351536189039778	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.351536189039778	1		447	466	SUCCESS
ATR	545	MSKCC	GRCh37	3	142222223	142222223	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	84	348	0	ENST00000350721.4:c.5269A>T	p.Asn1757Tyr	p.N1757Y	ENST00000350721	NM_001184.3	1757	Aat/Tat	30/47	1	2	FACETS	0.987	0.875	1	0.987	0.875	1	CLONAL	1	TRUE	1	0.351536189039778	2		348	484	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38156976	38156976	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	66	415	0	ENST00000317025.8:c.2744A>C	p.Lys915Thr	p.K915T	ENST00000317025	NM_023034.1	915	aAg/aCg	15/24	1	2	FACETS	0.871	0.759	0.992	0.871	0.759	0.992	CLONAL	1	TRUE	1	0.351536189039778	2		415	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0049675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	259	582	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.258729506799964	2	FACETS	0.813	0.762	0.865	0.813	0.762	0.865	CLONAL	2	TRUE	0	0.330150036512732	2		582	965	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414967	78414967	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1442633263	NA	P-0049675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	44	365	0	ENST00000370768.2:c.1799C>T	p.Pro600Leu	p.P600L	ENST00000370768	NM_003902.3	600	cCg/cTg	19/20	0.20267459981411	3	FACETS	0.518	0.434	0.612	0.259	0.217	0.306	SUBCLONAL	1	TRUE	1	0.330150036512732	3		365	599	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459122	120459122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150516342	NA	P-0049675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	67	683	1	ENST00000256646.2:c.6223G>A	p.Val2075Met	p.V2075M	ENST00000256646	NM_024408.3	2075	Gtg/Atg	34/34	0.20267459981411	3	FACETS	0.518	0.449	0.593	0.259	0.224	0.297	SUBCLONAL	1	TRUE	1	0.330150036512732	3		684	913	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893415	32893415	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	109	320	0	ENST00000380152.3:c.269T>G	p.Leu90Arg	p.L90R	ENST00000380152		90	cTg/cGg	3/27	0.156073923714512	4	FACETS	0.905	0.817	0.998	0.905	0.817	0.998	INDETERMINATE	2	TRUE	2	0.330150036512732	4		320	485	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0049701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	67	364	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.886	0.772	1	0.886	0.772	1	CLONAL	1	TRUE	1	0.320331006891243	2		364	472	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135800990	135800990	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049701-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	86	409	0	ENST00000298552.3:c.347T>C	p.Leu116Ser	p.L116S	ENST00000298552	NM_001162426.1	116	tTa/tCa	5/23	0.320331006891243	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.320331006891243	1		409	408	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577522	7577522	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567549129	NA	P-0049777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	54	621	0	ENST00000269305.4:c.759del	p.Ile254SerfsTer91	p.I254Sfs*91	ENST00000269305	NM_001126112.2	253	acC/ac	7/11	1	2	FACETS	0.638	0.543	0.742	0.638	0.543	0.742	SUBCLONAL	1	TRUE	1	0.2	2		621	847	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911672	32911672	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	45	315	0	ENST00000380152.3:c.3180C>A	p.Ser1060Arg	p.S1060R	ENST00000380152		1060	agC/agA	11/27	1	2	FACETS	0.857	0.72	1	0.857	0.72	1	CLONAL	1	TRUE	1	0.2	2		315	525	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731448	47731448	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1158415172	NA	P-0049777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	14	137	1	ENST00000449228.1:c.344C>T	p.Ser115Phe	p.S115F	ENST00000449228	NM_001127240.2	115	tCc/tTc	2/4	1	2	FACETS	0.603	0.436	0.806	0.603	0.436	0.806	SUBCLONAL	1	TRUE	1	0.2	2		138	232	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0049801-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	93	332	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.776	0.693	0.864	0.776	0.693	0.864	SUBCLONAL	1	TRUE	1	0.502240141065819	2		332	477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577512	7577512	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049801-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	531	561	0	ENST00000269305.4:c.769C>G	p.Leu257Val	p.L257V	ENST00000269305	NM_001126112.2	257	Ctg/Gtg	7/11	0.502240141065819	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.502240141065819	2		561	1042	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100397	157100399	+	inframe_deletion	In_Frame_Del	DEL	CGC	CGC	-	rs572236007	NA	P-0049801-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	10	102	0	ENST00000346085.5:c.1348_1350del	p.Pro450del	p.P450del	ENST00000346085	NM_020732.3	445	gCGCcg/gcg	1/20	1	2	FACETS	0.237	0.16	0.333	0.237	0.16	0.333	SUBCLONAL	1	TRUE	1	0.502240141065819	2		102	168	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282583	1282583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1311034283	NA	P-0049801-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	60	576	0	ENST00000310581.5:c.1730G>A	p.Arg577Gln	p.R577Q	ENST00000310581	NM_198253.2	577	cGg/cAg	3/16	1	2	FACETS	0.239	0.205	0.276	0.239	0.205	0.276	SUBCLONAL	1	TRUE	1	0.502240141065819	2		576	1000	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939783	76939783	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0049801-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	204	277	0	ENST00000373344.5:c.965C>G	p.Ser322Ter	p.S322*	ENST00000373344	NM_000489.3	322	tCa/tGa	9/35	1	1	FACETS	0.759	0.714	0.803	1	0.993	1	SUBCLONAL	2	TRUE	0	0.502240141065819	1		277	401	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049813-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	152	468	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.972	0.896	1	0.972	0.896	1	CLONAL	1	TRUE	1	0.672910299146334	2		468	465	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049813-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	421	413	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.60159853806497	2	FACETS	0.981	0.947	1	0.981	0.947	1	CLONAL	2	TRUE	0	0.672910299146334	2		413	638	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058033	27058033	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049813-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	216	441	0	ENST00000324856.7:c.1741C>T	p.Gln581Ter	p.Q581*	ENST00000324856	NM_006015.4	581	Cag/Tag	3/20	1	2	FACETS	0.911	0.85	0.973	0.911	0.85	0.973	CLONAL	1	TRUE	1	0.672910299146334	2		441	705	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646021	215646021	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049813-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	221	452	0	ENST00000260947.4:c.577G>C	p.Glu193Gln	p.E193Q	ENST00000260947	NM_000465.2	193	Gag/Cag	4/11	0.672910299146334	1	FACETS	0.939	0.885	0.994	0.939	0.885	0.994	CLONAL	1	TRUE	0	0.672910299146334	1		452	464	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295195	1295195	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0049813-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	156	277	3				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.672910299146334	2		280	456	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431358	49431358	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049813-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	268	593	0	ENST00000301067.7:c.9781C>T	p.Gln3261Ter	p.Q3261*	ENST00000301067	NM_003482.3	3261	Cag/Tag	34/54	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.672910299146334	2		593	734	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087885	27087904	+	frameshift_variant	Frame_Shift_Del	DEL	GCCACCTCGGCCACCCAGTG	GCCACCTCGGCCACCCAGTG	-	novel	NA	P-0049813-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	314	554	0	ENST00000324856.7:c.2176_2195del	p.Pro726ValfsTer84	p.P726Vfs*84	ENST00000324856	NM_006015.4	724	atGCCACCTCGGCCACCCAGTGgc/atgc	6/20	1	2	FACETS	0.987	0.933	1	0.987	0.933	1	CLONAL	1	TRUE	1	0.672910299146334	2		554	946	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900498	3900498	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783509	NA	P-0049813-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	365	799	0	ENST00000262367.5:c.598C>T	p.Gln200Ter	p.Q200*	ENST00000262367	NM_004380.2	200	Cag/Tag	2/31	1	2	FACETS	0.911	0.864	0.959	0.911	0.864	0.959	CLONAL	1	TRUE	1	0.672910299146334	2		799	1191	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156731	20156731	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049830-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	130	96	0	ENST00000379607.5:c.26G>C	p.Gly9Ala	p.G9A	ENST00000379607	NM_001412.3	9	gGt/gCt	2/7	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.578041862295177	1		96	227	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740867	58740867	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049833-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	176	487	0	ENST00000305921.3:c.1772G>C	p.Gly591Ala	p.G591A	ENST00000305921	NM_003620.3	591	gGa/gCa	6/6	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.569705527779763	2		487	584	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	25	468	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.77	0.609	0.954	0.77	0.609	0.954	CLONAL	1	TRUE	1	0.254591792643821	2		468	255	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0049840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	74	454	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.936	0.82	1	0.936	0.82	1	CLONAL	1	TRUE	1	0.254591792643821	2		455	621	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446284	70446284	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	37	411	0	ENST00000373644.4:c.5230del	p.Arg1744GlufsTer18	p.R1744Efs*18	ENST00000373644	NM_030625.2	1742	Aaa/aa	11/12	1	2	FACETS	0.533	0.439	0.639	0.533	0.439	0.639	SUBCLONAL	1	TRUE	1	0.254591792643821	2		411	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0049840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	49	482	0	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	1	2	FACETS	0.685	0.58	0.801	0.685	0.58	0.801	SUBCLONAL	1	TRUE	1	0.254591792643821	2		482	562	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933397	100933397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	354	363	0	ENST00000325455.5:c.1993G>A	p.Glu665Lys	p.E665K	ENST00000325455	NM_001202474.3	665	Gaa/Aaa	4/8	0.254591792643821	3	FACETS	1	0.971	1	1	0.997	1	CLONAL	4	TRUE	1	0.254591792643821	3		363	765	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974703	21974703	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	40	376	0	ENST00000304494.5:c.124A>C	p.Asn42His	p.N42H	ENST00000304494	NM_000077.4	42	Aat/Cat	1/3	0.254591792643821	1	FACETS	0.844	0.704	0.999	0.844	0.704	0.999	CLONAL	1	TRUE	0	0.254591792643821	1		376	325	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933436	100933436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	248	284	0	ENST00000325455.5:c.1954G>A	p.Asp652Asn	p.D652N	ENST00000325455	NM_001202474.3	652	Gat/Aat	4/8	0.254591792643821	3	FACETS	1	0.97	1	1	0.995	1	CLONAL	4	TRUE	1	0.254591792643821	3		284	529	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933280	100933280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	424	423	0	ENST00000325455.5:c.2110G>A	p.Asp704Asn	p.D704N	ENST00000325455	NM_001202474.3	704	Gac/Aac	4/8	0.254591792643821	3	FACETS	1	0.986	1	1	0.997	1	CLONAL	4	TRUE	1	0.254591792643821	3		423	882	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933301	100933301	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	418	435	0	ENST00000325455.5:c.2089G>C	p.Asp697His	p.D697H	ENST00000325455	NM_001202474.3	697	Gat/Cat	4/8	0.254591792643821	3	FACETS	1	0.985	1	1	0.997	1	CLONAL	4	TRUE	1	0.254591792643821	3		435	872	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933427	100933427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	264	300	0	ENST00000325455.5:c.1963G>A	p.Ala655Thr	p.A655T	ENST00000325455	NM_001202474.3	655	Gct/Act	4/8	0.254591792643821	3	FACETS	1	0.972	1	1	0.996	1	CLONAL	4	TRUE	1	0.254591792643821	3		300	561	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933453	100933453	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs753321148	NA	P-0049840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	203	219	0	ENST00000325455.5:c.1937G>C	p.Arg646Thr	p.R646T	ENST00000325455	NM_001202474.3	646	aGa/aCa	4/8	0.254591792643821	3	FACETS	1	0.972	1	1	0.995	1	CLONAL	4	TRUE	1	0.254591792643821	3		219	425	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0049841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	96	364	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.368443403068335	2		364	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0049841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	103	361	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.368443403068335	1	FACETS	0.92	0.827	1	0.92	0.827	1	CLONAL	1	TRUE	0	0.368443403068335	1		361	496	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602493	10602493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	203	444	1	ENST00000171111.5:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000171111	NM_203500.1	362	cGg/cAg	3/6	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.368443403068335	2		445	748	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473779	67473779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906850	NA	P-0049841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	186	300	0	ENST00000327367.4:c.859C>T	p.Arg287Trp	p.R287W	ENST00000327367	NM_005902.3	287	Cgg/Tgg	6/9	0.345354488802939	2	FACETS	0.85	0.789	0.912	0.85	0.789	0.912	CLONAL	2	TRUE	0	0.368443403068335	2		300	594	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144880	47144880	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	80	256	0	ENST00000409792.3:c.4873C>T	p.Arg1625Cys	p.R1625C	ENST00000409792	NM_014159.6	1625	Cgt/Tgt	7/21	1	2	FACETS	0.857	0.756	0.964	0.857	0.756	0.964	CLONAL	1	TRUE	1	0.368443403068335	2		256	507	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749340	43749340	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	108	243	0	ENST00000382044.4:c.1466C>G	p.Ser489Cys	p.S489C	ENST00000382044	NM_001141980.1	489	tCt/tGt	12/28	0.345354488802939	2	FACETS	1	0.92	1	0.512	0.461	0.567	CLONAL	1	TRUE	0	0.368443403068335	2		243	572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	112	347	0	ENST00000269305.4:c.580C>A	p.Leu194Ile	p.L194I	ENST00000269305	NM_001126112.2	194	Ctt/Att	6/11	0.368443403068335	1	FACETS	0.95	0.858	1	0.95	0.858	1	CLONAL	1	TRUE	0	0.368443403068335	1		347	522	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484415	57484415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1267396058	NA	P-0049841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	67	246	0	ENST00000371085.3:c.596G>A	p.Arg199His	p.R199H	ENST00000371085	NM_000516.4	199	cGc/cAc	8/13	1	2	FACETS	0.674	0.586	0.768	0.674	0.586	0.768	SUBCLONAL	1	TRUE	1	0.368443403068335	2		246	540	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162966	47162967	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	63	211	0	ENST00000409792.3:c.3159dup	p.Thr1054TyrfsTer5	p.T1054Yfs*5	ENST00000409792	NM_014159.6	1053	-/T	3/21	1	2	FACETS	0.853	0.741	0.974	0.853	0.741	0.974	CLONAL	1	TRUE	1	0.368443403068335	2		211	401	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137522069	137522070	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0049841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	60	131	0	ENST00000367739.4:c.809_810del	p.Ile270LysfsTer4	p.I270Kfs*4	ENST00000367739	NM_000416.2	270	aTT/a	6/7	0.368443403068335	1	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	0	0.368443403068335	1		131	255	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007146	152007146	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	94	221	0	ENST00000262189.6:c.754C>A	p.His252Asn	p.H252N	ENST00000262189	NM_170606.2	252	Cat/Aat	6/59	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.368443403068335	2		221	490	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76777853	76777853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1135401774	NA	P-0049841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	132	222	0	ENST00000373344.5:c.6863G>A	p.Arg2288His	p.R2288H	ENST00000373344	NM_000489.3	2288	cGt/cAt	32/35	0.212368775995609	2	FACETS	1	0.985	1	0.7	0.639	0.763	INDETERMINATE	1	TRUE	0	0.368443403068335	2		222	512	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	22	468	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	1	0.9	1	1	0.955	1	CLONAL	2	TRUE	0	0.23	1		468	69	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589589	67589590	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATATAACACTCAGTTTCAAGAAAAAAGTCGAGAATATGATAG	novel	NA	P-0049842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	23	184	0	ENST00000274335.5:c.1355_1396dup	p.Tyr452_Arg465dup	p.Y452_R465dup	ENST00000274335		452	gaa/gaATATAACACTCAGTTTCAAGAAAAAAGTCGAGAATATGATAGa	10/15	0.3	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.23	1		184	125	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945441	151945441	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	37	597	0	ENST00000262189.6:c.2078C>G	p.Thr693Ser	p.T693S	ENST00000262189	NM_170606.2	693	aCt/aGt	14/59	1	2	FACETS	0.177	0.145	0.213	0.177	0.145	0.213	SUBCLONAL	1	TRUE	1	0.668803527486443	2		597	625	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0049845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	8	225	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	0.222755267397164	3	FACETS	0.2	0.128	0.294	0.1	0.064	0.147	SUBCLONAL	1	TRUE	1	0.222755267397164	3		225	400	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363148	40363148	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	36	433	0	ENST00000397332.2:c.1081C>T	p.Gln361Ter	p.Q361*	ENST00000397332	NM_001033082.2	361	Caa/Taa	3/3	0.222755267397164	3	FACETS	0.774	0.636	0.929	0.387	0.318	0.465	CLONAL	1	TRUE	1	0.222755267397164	3		433	464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0049846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	293	550	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.556133036280794	2	FACETS	0.95	0.905	0.996	0.95	0.905	0.996	CLONAL	2	TRUE	0	0.555504356613871	2		550	555	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386409	31386409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572676072	NA	P-0049846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	339	592	1	ENST00000328111.2:c.1634G>A	p.Arg545His	p.R545H	ENST00000328111	NM_006892.3	545	cGc/cAc	15/23	0.434766355992837	4	FACETS	0.967	0.917	1	0.967	0.917	1	CLONAL	2	TRUE	2	0.555504356613871	4		593	982	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589684	69589684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	43	113	0	ENST00000168712.1:c.169C>T	p.Arg57Cys	p.R57C	ENST00000168712	NM_002007.2	57	Cgc/Tgc	1/3	0.555504356613871	5	FACETS	0.825	0.693	0.971	0.275	0.231	0.324	CLONAL	1	TRUE	2	0.555504356613871	5		113	344	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912745	100912745	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	83	344	0	ENST00000325455.5:c.2577G>C	p.Arg859Ser	p.R859S	ENST00000325455	NM_001202474.3	859	agG/agC	7/8	0.556133036280794	3	FACETS	0.95	0.843	1	0.475	0.421	0.532	CLONAL	1	TRUE	1	0.555504356613871	3		344	402	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647427	23647428	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGAA	novel	NA	P-0049846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	246	388	0	ENST00000261584.4:c.439_440insTTCT	p.Arg147IlefsTer22	p.R147Ifs*22	ENST00000261584	NM_024675.3	147	aga/aTTCTga	4/13	0.556133036280794	3	FACETS	0.982	0.926	1	0.982	0.926	1	CLONAL	2	TRUE	1	0.555504356613871	3		388	576	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945523	17945523	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	245	436	0	ENST00000458235.1:c.2207A>C	p.Gln736Pro	p.Q736P	ENST00000458235	NM_000215.3	736	cAa/cCa	17/24	0.434766355992837	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	2	0.555504356613871	4		436	660	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209712	98209712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	335	647	0	ENST00000331920.6:c.3826C>T	p.His1276Tyr	p.H1276Y	ENST00000331920	NM_000264.3	1276	Cat/Tat	23/24	0.434766355992837	4	FACETS	0.938	0.889	0.988	0.938	0.889	0.988	CLONAL	2	TRUE	2	0.555504356613871	4		647	1000	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573991	7573991	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567542019	NA	P-0049847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	753	618	0	ENST00000269305.4:c.1036G>T	p.Glu346Ter	p.E346*	ENST00000269305	NM_001126112.2	346	Gag/Tag	10/11	0.666624515306152	3	FACETS	0.971	0.949	0.993	0.971	0.949	0.993	CLONAL	3	TRUE	0	0.666624515306152	3		618	1034	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745588	162745588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754868982	NA	P-0049847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	115	348	0	ENST00000367921.3:c.2003G>A	p.Arg668His	p.R668H	ENST00000367921	NM_006182.2	668	cGc/cAc	15/18	0.666624515306152	3	FACETS	0.922	0.835	1	0.461	0.417	0.507	CLONAL	1	TRUE	1	0.666624515306152	3		348	499	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573432	48573432	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1376500870	NA	P-0049847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	63	189	0	ENST00000342988.3:c.16A>G	p.Ile6Val	p.I6V	ENST00000342988	NM_005359.5	6	Att/Gtt	2/12	0.666624515306152	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.666624515306152	3		189	113	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604211	189604211	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	140	328	0	ENST00000264731.3:c.1378G>C	p.Gly460Arg	p.G460R	ENST00000264731	NM_003722.4	460	Ggt/Cgt	11/14	0.57293357229377	4	FACETS	0.943	0.86	1	0.472	0.43	0.515	CLONAL	1	TRUE	2	0.666624515306152	4		328	742	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417641	139417641	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0049847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	500	684	0	ENST00000277541.6:c.404-1G>A		p.X135_splice	ENST00000277541	NM_017617.3	135			0.666624515306152	2	FACETS	0.999	0.968	1	0.999	0.968	1	CLONAL	2	TRUE	0	0.666624515306152	2		684	751	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578213	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs864309495	NA	P-0049848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	438	473	0	ENST00000269305.4:c.636del	p.Arg213AspfsTer34	p.R213Dfs*34	ENST00000269305	NM_001126112.2	212	ttT/tt	6/11	1	2	FACETS	1	0.996	1	1	0.998	1	CLONAL	2	TRUE	1	0.702291909466316	2		473	540	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023501	31023501	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	412	338	0	ENST00000375687.4:c.2986G>T	p.Gly996Cys	p.G996C	ENST00000375687	NM_015338.5	996	Ggt/Tgt	13/13	0.705323612070609	4	FACETS	0.888	0.853	0.923			1	CLONAL	3	TRUE	NA	0.702291909466316	4		338	750	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49449079	49449079	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	179	376	0	ENST00000301067.7:c.29A>T	p.Asp10Val	p.D10V	ENST00000301067	NM_003482.3	10	gAt/gTt	1/54	0.705323612070609	3	FACETS	1	0.962	1			1	CLONAL	1	TRUE	NA	0.702291909466316	3		376	649	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914091	32914091	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	109	290	0	ENST00000380152.3:c.5599A>C	p.Thr1867Pro	p.T1867P	ENST00000380152		1867	Aca/Cca	11/27	0.705323612070609	3	FACETS	1	0.965	1	0.379	0.343	0.416	CLONAL	1	TRUE	0	0.702291909466316	3		290	369	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212703	36212703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	234	460	0	ENST00000222270.7:c.2454G>A	p.Met818Ile	p.M818I	ENST00000222270	NM_014727.1	818	atG/atA	3/37	0.705323612070609	4	FACETS	1	0.986	1	0.404	0.377	0.431	CLONAL	1	TRUE	1	0.702291909466316	4		460	937	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794973	242794973	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	238	794	1	ENST00000334409.5:c.236T>C	p.Leu79Pro	p.L79P	ENST00000334409	NM_005018.2	79	cTg/cCg	2/5	0.502578883492106	4	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.702291909466316	4		795	1067	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0049849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	25	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.159230926419137	1	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	0	0.159230926419137	1		327	254	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0049849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	25	264	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.949	0.748	1	0.949	0.748	1	CLONAL	1	TRUE	1	0.159230926419137	2		264	331	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	22	239	0	ENST00000257430.4:c.4199C>A	p.Ser1400Ter	p.S1400*	ENST00000257430	NM_000038.5	1400	tCg/tAg	16/16	1	2	FACETS	1	0.796	1	1	0.796	1	CLONAL	1	TRUE	1	0.159230926419137	2		239	269	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236087	108236087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781894	NA	P-0049849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	19	350	0	ENST00000278616.4:c.9023G>A	p.Arg3008His	p.R3008H	ENST00000278616	NM_000051.3	3008	cGt/cAt	63/63	1	2	FACETS	0.617	0.467	0.793	0.617	0.467	0.793	SUBCLONAL	1	TRUE	1	0.159230926419137	2		350	387	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990400	81990400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370547009	NA	P-0049849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	27	417	0	ENST00000359376.3:c.3671G>A	p.Arg1224His	p.R1224H	ENST00000359376	NM_002661.3	1224	cGc/cAc	32/33	1	2	FACETS	0.742	0.59	0.917	0.742	0.59	0.917	CLONAL	1	TRUE	1	0.159230926419137	2		417	457	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554681	63554681	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	44	502	0	ENST00000307078.5:c.58G>T	p.Asp20Tyr	p.D20Y	ENST00000307078	NM_004655.3	20	Gat/Tat	2/11	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.159230926419137	2		502	531	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437568	110437568	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	58	608	0	ENST00000375856.3:c.833T>C	p.Val278Ala	p.V278A	ENST00000375856	NM_003749.2	278	gTg/gCg	1/2	0.159230926419137	3	FACETS	1	0.932	1	0.573	0.492	0.662	CLONAL	1	TRUE	1	0.159230926419137	3		608	686	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222757	53222758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	154	346	0	ENST00000375401.3:c.4178dup	p.Ala1394GlyfsTer22	p.A1394Gfs*22	ENST00000375401	NM_004187.3	1393	gag/gaAg	25/26	1	1	FACETS	1	0.982	1	1	0.993	1	CLONAL	2	TRUE	0	0.264424555409718	1		346	420	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147543	47147543	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	224	296	0	ENST00000409792.3:c.4783G>T	p.Glu1595Ter	p.E1595*	ENST00000409792	NM_014159.6	1595	Gag/Tag	6/21	NA	2	FACETS	0.881	0.83	0.932			1	INDETERMINATE	2	TRUE	NA	0.533290352527987	2		296	477	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442489	52442489	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1060503750	NA	P-0049861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	251	314	0	ENST00000460680.1:c.255+1G>A		p.X85_splice	ENST00000460680	NM_004656.3	85			NA	2	FACETS	0.91	0.861	0.959			1	INDETERMINATE	2	TRUE	NA	0.533290352527987	2		314	517	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0049862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	288	328	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.847859844653942	2		328	598	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0049862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	952	443	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.763200838801549	3	FACETS	0.975	0.961	0.989			1	CLONAL	3	TRUE	NA	0.847859844653942	3		443	1093	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517766	176517766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370322847	NA	P-0049862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	385	631	0	ENST00000292408.4:c.376G>A	p.Asp126Asn	p.D126N	ENST00000292408	NM_213647.1	126	Gat/Aat	4/18	1	2	FACETS	0.954	0.91	0.999	0.954	0.91	0.999	CLONAL	1	TRUE	1	0.847859844653942	2		631	952	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214713	36214714	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0049862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	355	581	0	ENST00000222270.7:c.3145dup	p.Ala1049GlyfsTer39	p.A1049Gfs*39	ENST00000222270	NM_014727.1	1047	cgg/cGgg	8/37	1	2	FACETS	0.891	0.847	0.936	0.891	0.847	0.936	CLONAL	1	TRUE	1	0.847859844653942	2		581	940	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206921	102206921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	147	201	0	ENST00000263464.3:c.1549G>A	p.Ala517Thr	p.A517T	ENST00000263464	NM_001165.4	517	Gct/Act	7/9	1	2	FACETS	0.863	0.796	0.93	0.863	0.796	0.93	CLONAL	1	TRUE	1	0.847859844653942	2		201	402	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40468851	40468851	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	318	410	0	ENST00000264657.5:c.2213G>A	p.Gly738Glu	p.G738E	ENST00000264657	NM_139276.2	738	gGa/gAa	23/24	1	2	FACETS	0.935	0.887	0.984	0.935	0.887	0.984	CLONAL	1	TRUE	1	0.847859844653942	2		410	802	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288889	15288889	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	230	215	0	ENST00000263388.2:c.3850C>T	p.Pro1284Ser	p.P1284S	ENST00000263388	NM_000435.2	1284	Ccg/Tcg	24/33	1	2	FACETS	0.999	0.94	1	0.999	0.94	1	CLONAL	1	TRUE	1	0.847859844653942	2		215	543	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939104	131939105	+	missense_variant	Missense_Mutation	DNP	CT	CT	TA	novel	NA	P-0049862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	208	335	1	ENST00000265335.6:c.2320_2321delinsTA	p.Leu774Tyr	p.L774Y	ENST00000265335		774	CTc/TAc	14/25	1	2	FACETS	0.871	0.815	0.929	0.871	0.815	0.929	CLONAL	1	TRUE	1	0.847859844653942	2		336	563	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979511	2979511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	332	395	0	ENST00000396946.4:c.736G>A	p.Glu246Lys	p.E246K	ENST00000396946	NM_032415.4	246	Gag/Aag	6/25	0.134598536488983	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.847859844653942	0		395	772	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295133	15295133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	489	655	0	ENST00000263388.2:c.2539G>A	p.Asp847Asn	p.D847N	ENST00000263388	NM_000435.2	847	Gat/Aat	16/33	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.847859844653942	2		655	1104	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0049865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	34	337	1	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		338	447	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223839	2223839	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0049865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	57	754	0	ENST00000326181.6:c.1135+2T>G		p.X379_splice	ENST00000326181	NM_032271.2	379			1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		754	730	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0049866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	42	240	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.616	0.515	0.728	0.616	0.515	0.728	SUBCLONAL	1	TRUE	1	0.32	2		240	426	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	89	468	0				ENST00000310581	NM_198253.2	-/1132			0.301913613980546	3	FACETS	1	0.973	1	0.661	0.588	0.738	CLONAL	1	TRUE	1	0.32	3		468	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	150	480	0	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	0.301913613980546	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.32	1		480	702	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182032	38182032	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	71	401	0	ENST00000396334.3:c.656C>G	p.Ser219Cys	p.S219C	ENST00000396334	NM_002468.4	219	tCt/tGt	3/5	1	2	FACETS	0.61	0.531	0.694	0.61	0.531	0.694	SUBCLONAL	1	TRUE	1	0.32	2		401	728	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121909	2121909	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760489473	NA	P-0049866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	196	872	0	ENST00000219476.3:c.2071C>T	p.Arg691Cys	p.R691C	ENST00000219476	NM_000548.3	691	Cgc/Tgc	19/42	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.32	2		872	1083	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942703	44942703	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0049866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	86	275	0	ENST00000377967.4:c.3285-2A>T		p.X1095_splice	ENST00000377967	NM_021140.2	1095			0.25344157717926	1	FACETS	0.965	0.857	1	0.965	0.857	1	CLONAL	1	TRUE	0	0.32	1		275	468	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982157	201982157	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	150	581	0	ENST00000359651.3:c.684del	p.Ser229AlafsTer25	p.S229Afs*25	ENST00000359651		227	ttC/tt	5/8	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.32	2		581	901	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524812	187524812	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs184690159	NA	P-0049866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	204	496	1	ENST00000441802.2:c.10868C>T	p.Thr3623Met	p.T3623M	ENST00000441802	NM_005245.3	3623	aCg/aTg	19/27	0.230193793640102	2	FACETS	0.828	0.77	0.888	0.828	0.77	0.888	CLONAL	2	TRUE	0	0.32	2		497	770	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981085	201981086	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0049866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	105	420	0	ENST00000359651.3:c.165_166insGG	p.Lys56GlyfsTer100	p.K56Gfs*100	ENST00000359651		55	gag/gaGGg	2/8	1	2	FACETS	0.931	0.835	1	0.931	0.835	1	CLONAL	1	TRUE	1	0.32	2		420	705	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545842	41545842	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0049866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	137	474	0	ENST00000263253.7:c.2457T>A	p.Cys819Ter	p.C819*	ENST00000263253	NM_001429.3	819	tgT/tgA	14/31	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.32	2		474	798	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286922	33286922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	187	621	0	ENST00000374542.5:c.2015C>T	p.Pro672Leu	p.P672L	ENST00000374542	NM_001141970.1	672	cCc/cTc	7/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.32	2		621	953	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577543	7577543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1019340046	NA	P-0049867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	28	579	0	ENST00000269305.4:c.738G>A	p.Met246Ile	p.M246I	ENST00000269305	NM_001126112.2	246	atG/atA	7/11	1	2	FACETS	0.427	0.339	0.527	0.427	0.339	0.527	SUBCLONAL	1	TRUE	1	0.13	2		579	1010	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112287	115112287	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	25	177	1	ENST00000257566.3:c.1453C>T	p.Gln485Ter	p.Q485*	ENST00000257566	NM_016569.3	485	Cag/Tag	7/8	1	2	FACETS	1	0.807	1	1	0.807	1	CLONAL	1	TRUE	1	0.13	2		178	375	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935620	13935620	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	41	332	0	ENST00000405192.2:c.1236G>C	p.Lys412Asn	p.K412N	ENST00000405192	NM_001163147.1	412	aaG/aaC	12/12	1	2	FACETS	0.932	0.774	1	0.932	0.774	1	CLONAL	1	TRUE	1	0.13	2		332	677	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427687	49427687	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	12	532	0	ENST00000301067.7:c.10801C>T	p.Gln3601Ter	p.Q3601*	ENST00000301067	NM_003482.3	3601	Caa/Taa	39/54	0.378583241868291	4	FACETS	0.448	0.315	0.611	0.224	0.157	0.306	SUBCLONAL	1	FALSE	2	0.378583241868291	4		532	195	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572371	41572371	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	17	551	0	ENST00000263253.7:c.4900G>C	p.Ala1634Pro	p.A1634P	ENST00000263253	NM_001429.3	1634	Gca/Cca	30/31	0.283499681779069	3	FACETS	0.516	0.386	0.669	0.258	0.193	0.335	SUBCLONAL	1	FALSE	1	0.378583241868291	3		551	207	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0049869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	43	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.387015442589843	3	FACETS	0.946	0.799	1	0.473	0.399	0.553	CLONAL	1	TRUE	1	0.479573342698184	3		327	235	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575209	48575209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767326	NA	P-0049869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	23	210	0	ENST00000342988.3:c.403C>T	p.Arg135Ter	p.R135*	ENST00000342988	NM_005359.5	135	Cga/Tga	3/12	0.479573342698184	1	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	0	0.479573342698184	1		210	66	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443530	49443530	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	110	606	0	ENST00000301067.7:c.3841G>T	p.Gly1281Ter	p.G1281*	ENST00000301067	NM_003482.3	1281	Gga/Tga	11/54	0.411639005153155	1	FACETS	0.901	0.817	0.989	0.901	0.817	0.989	CLONAL	1	TRUE	0	0.479573342698184	1		606	387	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2215893	2215893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370203279	NA	P-0049869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	162	654	0	ENST00000326181.6:c.95C>T	p.Thr32Met	p.T32M	ENST00000326181	NM_032271.2	32	aCg/aTg	3/21	0.479573342698184	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.479573342698184	1		654	469	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900152	101900152	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049869-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	28	185	0	ENST00000374994.4:c.586C>G	p.Leu196Val	p.L196V	ENST00000374994	NM_004612.2	196	Ctt/Gtt	4/9	0.479573342698184	3	FACETS	1	0.825	1	0.51	0.413	0.617	CLONAL	1	TRUE	1	0.479573342698184	3		185	142	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0049870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	18	328	0				ENST00000310581	NM_198253.2	-/1132			0.3	0	FACETS	0.798	0.605	1			1	CLONAL	2	TRUE	0	0.13	0		328	151	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0049870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	45	604	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.217940440504328	3	FACETS	1	0.903	1	0.554	0.465	0.654	CLONAL	1	TRUE	1	0.13	3		604	665	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100436	8100436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1220437638	NA	P-0049870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	36	819	1	ENST00000346208.3:c.410C>T	p.Ser137Leu	p.S137L	ENST00000346208		137	tCg/tTg	3/6	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.13	2		820	484	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928929	44928929	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	22	184	0	ENST00000377967.4:c.2029C>T	p.Gln677Ter	p.Q677*	ENST00000377967	NM_021140.2	677	Cag/Tag	17/29	0.3	2	FACETS	1	0.921	1	0.749	0.582	0.94	CLONAL	1	TRUE	0	0.13	2		184	226	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740498	58740498	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs375975790	NA	P-0049870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	32	401	0	ENST00000305921.3:c.1403C>G	p.Ser468Ter	p.S468*	ENST00000305921	NM_003620.3	468	tCa/tGa	6/6	0.159932512786081	1	FACETS	0.921	0.746	1	0.921	0.746	1	CLONAL	1	TRUE	0	0.13	1		401	500	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059213	27059213	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	35	387	0	ENST00000324856.7:c.1850C>A	p.Ser617Ter	p.S617*	ENST00000324856	NM_006015.4	617	tCa/tAa	4/20	0.3	5	FACETS	1	0.857	1			1	CLONAL	1	TRUE	NA	0.13	5		387	609	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828936	72828936	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	19	558	0	ENST00000268489.5:c.7645C>T	p.Gln2549Ter	p.Q2549*	ENST00000268489	NM_006885.3	2549	Cag/Tag	9/10	1	2	FACETS	0.852	0.646	1	0.852	0.646	1	CLONAL	1	TRUE	1	0.13	2		558	343	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224744	123224744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	13	172	0	ENST00000218089.9:c.3508G>A	p.Glu1170Lys	p.E1170K	ENST00000218089	NM_001042749.1	1170	Gaa/Aaa	32/35	1	1	FACETS	0.776	0.553	1	0.776	0.553	1	CLONAL	1	TRUE	0	0.13	1		172	241	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224751	123224751	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	17	176	0	ENST00000218089.9:c.3515G>T	p.Arg1172Met	p.R1172M	ENST00000218089	NM_001042749.1	1172	aGg/aTg	32/35	1	1	FACETS	0.982	0.734	1	0.982	0.734	1	CLONAL	1	TRUE	0	0.13	1		176	249	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0049872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	18	427	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	1	2	FACETS	0.285	0.214	0.369	0.285	0.214	0.369	SUBCLONAL	1	FALSE	1	0.377836024930308	2		427	334	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730011	41730011	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	22	579	0	ENST00000242208.4:c.518T>C	p.Ile173Thr	p.I173T	ENST00000242208	NM_002192.2	173	aTc/aCc	3/3	1	2	FACETS	0.451	0.35	0.568	0.451	0.35	0.568	SUBCLONAL	1	FALSE	1	0.377836024930308	2		579	258	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680583	241680583	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	106	366	0	ENST00000366560.3:c.166del	p.Thr56ProfsTer5	p.T56Pfs*5	ENST00000366560	NM_000143.3	56	Acc/cc	2/10	0.71543508738986	1	FACETS	0.986	0.91	1	0.986	0.91	1	CLONAL	1	TRUE	0	0.71543508738986	1		366	193	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	74	413	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.293477768622809	2		413	366	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0049874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	271	927	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	NA	2	FACETS	0.87	0.816	0.924			1	INDETERMINATE	2	TRUE	NA	0.293477768622809	2		927	1062	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974695	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1554656253	NA	P-0049874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	142	764	0	ENST00000304494.5:c.132C>G	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	taC/taG	1/3	0.293477768622809	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.293477768622809	1		764	810	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034417	47034417	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0049874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	148	1011	0	ENST00000377604.3:c.503-1G>A		p.X168_splice	ENST00000377604	NM_001204468.1	168			1	2	FACETS	0.916	0.835	1	0.916	0.835	1	CLONAL	1	TRUE	1	0.293477768622809	2		1011	1101	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728724	39728724	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	44	299	0	ENST00000361337.2:c.1004T>G	p.Leu335Arg	p.L335R	ENST00000361337	NM_003286.2	335	cTg/cGg	12/21	1	2	FACETS	0.92	0.775	1	0.92	0.775	1	CLONAL	1	TRUE	1	0.293477768622809	2		299	326	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936075	49936076	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049874-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	134	1372	0	ENST00000296474.3:c.1594dup	p.Thr532AsnfsTer39	p.T532Nfs*39	ENST00000296474	NM_002447.2	532	acc/aAcc	4/20	1	2	FACETS	0.753	0.682	0.828	0.753	0.682	0.828	SUBCLONAL	1	TRUE	1	0.293477768622809	2		1372	1213	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	412	468	0				ENST00000310581	NM_198253.2	-/1132			0.270950683970881	5	FACETS	1	0.992	1	1	0.992	1	INDETERMINATE	3	TRUE	2	0.533283306237755	5		468	820	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870988	12870988	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	152	439	0	ENST00000228872.4:c.215G>T	p.Gly72Val	p.G72V	ENST00000228872	NM_004064.3	72	gGc/gTc	1/3	0.533283306237755	5	FACETS	0.983	0.947	1	1	0.994	1	CLONAL	6	TRUE	2	0.533283306237755	5		439	174	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871758	12871758	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0049875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	65	160	0	ENST00000228872.4:c.476-1G>C		p.X159_splice	ENST00000228872	NM_004064.3	159			0.533283306237755	5	FACETS	1	0.933	1	1	0.979	1	CLONAL	4	TRUE	2	0.533283306237755	5		160	106	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125006	46125006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	28	250	0	ENST00000334344.6:c.193G>A	p.Glu65Lys	p.E65K	ENST00000334344	NM_152641.2	65	Gag/Aag	3/21	0.269799518279308	4	FACETS	0.875	0.751	0.993	1	0.963	1	INDETERMINATE	4	TRUE	2	0.533283306237755	4		250	46	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934164	48934164	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1	25	326	0	ENST00000267163.4:c.619C>T	p.Gln207Ter	p.Q207*	ENST00000267163	NM_000321.2	207	Caa/Taa	7/27	0.533283306237755	1	FACETS		NA	1	1	0.972	1	NA	3	TRUE	0	0.533283306237755	1		326	26	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647697	3647697	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0049875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	124	708	0	ENST00000294008.3:c.1367-1G>C		p.X456_splice	ENST00000294008	NM_032444.2	456			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.533283306237755	2		708	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780071	NA	P-0049875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	138	751	0	ENST00000269305.4:c.580C>T	p.Leu194Phe	p.L194F	ENST00000269305	NM_001126112.2	194	Ctt/Ttt	6/11	0.533283306237755	1	FACETS	1	0.992	1	1	0.994	1	CLONAL	2	TRUE	0	0.533283306237755	1		751	153	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872213	45872213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	365	785	0	ENST00000391945.4:c.221C>T	p.Ser74Leu	p.S74L	ENST00000391945	NM_000400.3	74	tCa/tTa	4/23	0.495000945284226	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	1	0.533283306237755	4		785	637	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206728	36206728	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	211	673	0	ENST00000300305.3:c.784C>T	p.Gln262Ter	p.Q262*	ENST00000300305		262	Cag/Tag	6/8	0.248491502538007	3	FACETS	0.781	0.729	0.834	0.781	0.729	0.834	INDETERMINATE	2	TRUE	1	0.533283306237755	3		673	642	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582198	52582198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	174	404	0	ENST00000394830.3:c.4630C>T	p.His1544Tyr	p.H1544Y	ENST00000394830	NM_018313.4	1544	Cac/Tac	30/30	0.326493472913709	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.533283306237755	2		404	294	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73047300	73047302	+	missense_variant	Missense_Mutation	TNP	GAG	GAG	AAA	novel	NA	P-0049875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	100	508	0	ENST00000356692.5:c.107_109delinsAAA	p.Gly36_Glu37delinsGluLys	p.G36_E37delinsEK	ENST00000356692		36	gGAGaa/gAAAaa	2/9	0.326493472913709	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.533283306237755	2		508	155	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149375069	149375069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs921827996	NA	P-0049875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	374	932	0	ENST00000360632.3:c.25C>T	p.Pro9Ser	p.P9S	ENST00000360632	NM_015472.4	9	Ccg/Tcg	2/7	0.326493472913709	2	FACETS	0.932	0.883	0.982	0.466	0.441	0.491	CLONAL	1	TRUE	0	0.533283306237755	2		932	1505	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908786	101908786	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	24	343	0	ENST00000374994.4:c.1150C>G	p.Leu384Val	p.L384V	ENST00000374994	NM_004612.2	384	Ctc/Gtc	7/9	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.533283306237755	2		343	61	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039325	47039325	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	520	427	0	ENST00000377604.3:c.949del	p.Leu317TrpfsTer18	p.L317Wfs*18	ENST00000377604	NM_001204468.1	316	atC/at	10/24	0.528154491637752	2	FACETS	1	0.995	1			1	CLONAL	3	TRUE	NA	0.533283306237755	2		427	609	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534285	534285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894226	NA	P-0049876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	110	651	0	ENST00000451590.1:c.38G>A	p.Gly13Asp	p.G13D	ENST00000451590	NM_001130442.1	13	gGt/gAt	2/5	1	2	FACETS	1	0.943	1	1	0.991	1	CLONAL	3	FALSE	1	0.148431409453649	2		651	465	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692917	89692917	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	50	494	0	ENST00000371953.3:c.401T>A	p.Met134Lys	p.M134K	ENST00000371953	NM_000314.4	134	aTg/aAg	5/9	0.148431409453649	3	FACETS	0.834	0.709	0.971	0.556	0.472	0.647	CLONAL	2	FALSE	0	0.148431409453649	3		494	434	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670145	29670145	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	76	349	2	ENST00000356175.3:c.7121del	p.Leu2374Ter	p.L2374*	ENST00000356175	NM_000267.3	2373	cTt/ct	47/57	1	2	FACETS	0.898	0.793	1	1	0.986	1	CLONAL	3	FALSE	1	0.148431409453649	2		351	380	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	50	468	0				ENST00000310581	NM_198253.2	-/1132			0.287365127457806	1	FACETS	0.799	0.703	0.897	0.799	0.703	0.897	INDETERMINATE	1	TRUE	0	0.742137180483684	1		468	106	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0049877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	67	223	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.742137180483684	2		223	162	SUCCESS
ATM	472	MSKCC	GRCh37	11	108168020	108168020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752459491	NA	P-0049877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	70	238	1	ENST00000278616.4:c.4916C>T	p.Pro1639Leu	p.P1639L	ENST00000278616	NM_000051.3	1639	cCg/cTg	33/63	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.742137180483684	2		239	126	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528051	157528051	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554237658	NA	P-0049877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	82	580	0	ENST00000346085.5:c.5776C>T	p.Arg1926Ter	p.R1926*	ENST00000346085	NM_020732.3	1926	Cga/Tga	20/20	0.157736781288867	4	FACETS	1	0.973	1	0.657	0.586	0.732	INDETERMINATE	1	TRUE	2	0.742137180483684	4		580	293	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412283	139412285	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	novel	NA	P-0049877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	70	982	0	ENST00000277541.6:c.1360_1362del	p.Asn454del	p.N454del	ENST00000277541	NM_017617.3	454	AAC/-	8/34	1	2	FACETS	0.621	0.546	0.7	0.621	0.546	0.7	SUBCLONAL	1	TRUE	1	0.742137180483684	2		982	304	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144054	11144056	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0049877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	51	848	0	ENST00000358026.2:c.3638_3640del	p.Lys1213del	p.K1213del	ENST00000358026	NM_001128849.1	1212	gAGAag/gag	26/36	0.287365127457806	1	FACETS	0.329	0.281	0.38	0.329	0.281	0.38	INDETERMINATE	1	TRUE	0	0.742137180483684	1		848	263	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	206	468	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		468	534	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981086	55981086	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	272	447	0	ENST00000263923.4:c.613A>G	p.Asn205Asp	p.N205D	ENST00000263923	NM_002253.2	205	Aat/Gat	5/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		447	458	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845679	151845679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	366	554	1	ENST00000262189.6:c.13333G>A	p.Gly4445Ser	p.G4445S	ENST00000262189	NM_170606.2	4445	Ggt/Agt	52/59	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		555	997	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133065	30133065	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	116	322	0	ENST00000331968.5:c.536G>A	p.Gly179Glu	p.G179E	ENST00000331968	NM_002742.2	179	gGg/gAg	4/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		322	619	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288730	11288730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758634485	NA	P-0049878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	336	475	0	ENST00000361445.4:c.3025C>T	p.Arg1009Trp	p.R1009W	ENST00000361445	NM_004958.3	1009	Cgg/Tgg	19/58	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		475	550	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107090	27107093	+	frameshift_variant	Frame_Shift_Del	DEL	CTGC	CTGC	-	novel	NA	P-0049878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	170	514	0	ENST00000324856.7:c.6702_6705del	p.Ala2237CysfsTer29	p.A2237Cfs*29	ENST00000324856	NM_006015.4	2234	gCTGCc/gc	20/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		514	584	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63699990	63699990	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	100	277	0	ENST00000279873.7:c.325C>G	p.Leu109Val	p.L109V	ENST00000279873	NM_032199.2	109	Ctg/Gtg	3/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		277	521	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929007	32929007	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	274	380	0	ENST00000380152.3:c.7018del	p.Glu2340AsnfsTer27	p.E2340Nfs*27	ENST00000380152		2339	aaG/aa	14/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		380	742	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396591	396591	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0049878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	422	690	0	ENST00000262320.3:c.435C>G	p.Tyr145Ter	p.Y145*	ENST00000262320	NM_003502.3	145	taC/taG	2/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		690	705	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881311	37881311	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	459	731	0	ENST00000269571.5:c.2503T>C	p.Tyr835His	p.Y835H	ENST00000269571		835	Tac/Cac	21/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		731	1267	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138376607	138376607	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	295	438	0	ENST00000289153.2:c.2867del	p.Val956GlyfsTer36	p.V956Gfs*36	ENST00000289153	NM_006219.2	956	gTg/gg	20/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		438	808	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268688	98268704	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CCTTCCACCCACAGCTC	CCTTCCACCCACAGCTC	-	novel	NA	P-0049878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	201	357	0	ENST00000331920.6:c.379_394+1del		p.X127_splice	ENST00000331920	NM_000264.3	127		2/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		357	624	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023845	27023864	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCGGGCCCCAGGACGGGG	TGGCGGGCCCCAGGACGGGG	CGT	novel	NA	P-0049878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	113	383	2	ENST00000324856.7:c.951_970delinsCGT	p.Gly318ValfsTer76	p.G318Vfs*76	ENST00000324856	NM_006015.4	317	agTGGCGGGCCCCAGGACGGGGgc/agCGTgc	1/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		385	378	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0049881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	154	604	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	0.925	0.846	1	0.925	0.846	1	CLONAL	1	TRUE	1	0.369256454278537	2		604	902	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0049886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	294	590	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.0939960543378621	6	FACETS	1	0.986	1			1	INDETERMINATE	3	TRUE	NA	0.587001334187301	6		591	654	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808295	99808295	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	91	260	0	ENST00000280892.6:c.394C>T	p.Arg132Ter	p.R132*	ENST00000280892	NM_001130678.1	132	Cga/Tga	5/7	0.562831878163287	4	FACETS	0.812	0.729	0.898	0.812	0.729	0.898	CLONAL	2	TRUE	2	0.587001334187301	4		260	303	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730095	41730095	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	93	380	0	ENST00000242208.4:c.434G>A	p.Ser145Asn	p.S145N	ENST00000242208	NM_002192.2	145	aGt/aAt	3/3	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.382020217775981	2		380	472	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978928	25978953	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAATTCATTGTTAAGGGCTGAGCC	AAGAATTCATTGTTAAGGGCTGAGCC	-	novel	NA	P-0049888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	55	363	0	ENST00000435504.4:c.970_995del	p.Gly324HisfsTer15	p.G324Hfs*15	ENST00000435504		324	GGCTCAGCCCTTAACAATGAATTCTTc/c	10/13	0.382020217775981	1	FACETS	0.608	0.522	0.702	0.608	0.522	0.702	SUBCLONAL	1	TRUE	0	0.382020217775981	1		363	383	SUCCESS
REL	5966	MSKCC	GRCh37	2	61148975	61148975	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	64	308	0	ENST00000295025.8:c.1165C>A	p.Pro389Thr	p.P389T	ENST00000295025	NM_002908.2	389	Ccc/Acc	11/11	0.382020217775981	1	FACETS	0.913	0.797	1	0.913	0.797	1	CLONAL	1	TRUE	0	0.382020217775981	1		308	297	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0049889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	67	534	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.146062786309291	5	FACETS	1	0.962	1	0.434	0.378	0.496	INDETERMINATE	1	TRUE	2	0.268559033281572	5		534	537	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0049889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	81	458	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.231713714449234	3	FACETS	0.873	0.774	0.978	0.873	0.774	0.978	CLONAL	2	TRUE	1	0.268559033281572	3		460	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578448	7578448	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1064795691	NA	P-0049889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	417	803	3	ENST00000269305.4:c.482C>A	p.Ala161Asp	p.A161D	ENST00000269305	NM_001126112.2	161	gCc/gAc	5/11	0.154689323900883	3	FACETS	0.993	0.946	1	0.993	0.946	1	INDETERMINATE	3	TRUE	0	0.268559033281572	3		806	1183	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625090	69625090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554980287	NA	P-0049889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	49	711	0	ENST00000334134.2:c.703G>A	p.Glu235Lys	p.E235K	ENST00000334134	NM_005247.2	235	Gag/Aag	3/3	0.236649613881096	2	FACETS	0.653	0.552	0.763	0.326	0.276	0.382	SUBCLONAL	1	TRUE	0	0.268559033281572	2		711	559	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437836	110437836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	108	442	1	ENST00000375856.3:c.565C>T	p.Pro189Ser	p.P189S	ENST00000375856	NM_003749.2	189	Ccc/Tcc	1/2	0.146062786309291	5	FACETS	0.95	0.855	1	0.633	0.57	0.7	INDETERMINATE	2	TRUE	2	0.268559033281572	5		443	594	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589681	69589681	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	14	209	0	ENST00000168712.1:c.172C>G	p.Leu58Val	p.L58V	ENST00000168712	NM_002007.2	58	Ctg/Gtg	1/3	0.236649613881096	2	FACETS	0.552	0.4	0.735	0.276	0.2	0.368	SUBCLONAL	1	TRUE	0	0.268559033281572	2		209	189	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151181	202151181	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs1354563506	NA	P-0049889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	27	197	0	ENST00000358485.4:c.1482-1G>C		p.X494_splice	ENST00000358485	NM_001080125.1	494			0.2474293679104	5	FACETS	1	0.807	1	0.253	0.201	0.311	CLONAL	1	TRUE	1	0.268559033281572	5		197	279	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222823	36222823	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	111	812	0	ENST00000222270.7:c.5452G>T	p.Glu1818Ter	p.E1818*	ENST00000222270	NM_014727.1	1818	Gag/Tag	27/37	0.0915934342664528	4	FACETS	0.975	0.874	1	0.487	0.437	0.541	INDETERMINATE	1	TRUE	2	0.268559033281572	4		812	1076	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125513771	125513771	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	105	425	0	ENST00000428830.2:c.899T>G	p.Phe300Cys	p.F300C	ENST00000428830	NM_001114121.2	300	tTc/tGc	9/14	0.236649613881096	2	FACETS	0.985	0.889	1	0.985	0.889	1	CLONAL	2	TRUE	0	0.268559033281572	2		425	397	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138507	11138507	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	77	620	0	ENST00000358026.2:c.3263T>A	p.Ile1088Asn	p.I1088N	ENST00000358026	NM_001128849.1	1088	aTt/aAt	24/36	0.0915934342664528	4	FACETS	0.823	0.721	0.933	0.411	0.36	0.467	INDETERMINATE	1	TRUE	2	0.268559033281572	4		620	884	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288454	15288454	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	141	513	0	ENST00000263388.2:c.4285G>A	p.Glu1429Lys	p.E1429K	ENST00000263388	NM_000435.2	1429	Gag/Aag	24/33	0.0915934342664528	4	FACETS	1	0.962	1	1	0.962	1	INDETERMINATE	2	TRUE	2	0.268559033281572	4		513	609	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99179930	99179930	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	77	627	0	ENST00000074304.5:c.1873G>A	p.Glu625Lys	p.E625K	ENST00000074304	NM_001134224.1	625	Gaa/Aaa	19/26	0.268559033281572	5	FACETS	0.785	0.687	0.891			1	SUBCLONAL	1	TRUE	NA	0.268559033281572	5		627	1025	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570103	212570103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	39	338	0	ENST00000342788.4:c.1138G>A	p.Ala380Thr	p.A380T	ENST00000342788	NM_005235.2	380	Gca/Aca	10/28	0.2474293679104	5	FACETS	0.837	0.693	0.997	0.209	0.173	0.25	CLONAL	1	TRUE	1	0.268559033281572	5		338	487	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466842	57466842	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	53	360	0	ENST00000371085.3:c.61G>C	p.Glu21Gln	p.E21Q	ENST00000371085	NM_000516.4	21	Gag/Cag	1/13	0.268559033281572	5	FACETS	0.825	0.703	0.96	0.206	0.175	0.24	CLONAL	1	TRUE	1	0.268559033281572	5		360	671	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162636	47162636	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	33	397	0	ENST00000409792.3:c.3490C>G	p.Gln1164Glu	p.Q1164E	ENST00000409792	NM_014159.6	1164	Cag/Gag	3/21	0.146062786309291	5	FACETS	0.748	0.609	0.905	0.249	0.203	0.302	INDETERMINATE	1	TRUE	2	0.268559033281572	5		397	461	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371749	116371749	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	75	316	0	ENST00000397752.3:c.1228G>A	p.Glu410Lys	p.E410K	ENST00000397752	NM_000245.2	410	Gaa/Aaa	3/21	0.268559033281572	5	FACETS	0.761	0.668	0.86	0.38	0.334	0.43	SUBCLONAL	2	TRUE	1	0.268559033281572	5		316	515	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0049890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	98	223	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.339453323032199	4	FACETS	1	0.971	1	1	0.987	1	CLONAL	3	TRUE	2	0.339453323032199	4		223	222	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0049890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	163	656	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	1	2	FACETS	1	0.981	1	1	0.993	1	CLONAL	2	TRUE	1	0.339453323032199	2		656	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0049890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	211	737	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	1	2	FACETS	1	0.977	1	1	0.994	1	CLONAL	2	TRUE	1	0.339453323032199	2		737	568	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909629	76909629	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs919106518	NA	P-0049890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	110	193	0	ENST00000373344.5:c.4276C>T	p.Arg1426Ter	p.R1426*	ENST00000373344	NM_000489.3	1426	Cga/Tga	14/35	0.329248457912007	2	FACETS	0.976	0.911	1			1	CLONAL	4	TRUE	NA	0.339453323032199	2		193	166	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0049891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	57	364	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.331186311031721	1	FACETS	0.484	0.417	0.557	0.484	0.417	0.557	SUBCLONAL	1	TRUE	0	0.465439196778196	1		364	388	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086133	16086133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	67	567	0	ENST00000281043.3:c.1309G>A	p.Glu437Lys	p.E437K	ENST00000281043	NM_005378.4	437	Gag/Aag	3/3	0.394746514259228	1	FACETS	0.488	0.425	0.555	0.488	0.425	0.555	SUBCLONAL	1	TRUE	0	0.465439196778196	1		567	453	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557610	21557610	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	81	672	1	ENST00000382592.4:c.2235G>A	p.Met745Ile	p.M745I	ENST00000382592	NM_014572.2	745	atG/atA	5/8	0.394746514259228	1	FACETS	0.528	0.466	0.594	0.528	0.466	0.594	SUBCLONAL	1	TRUE	0	0.465439196778196	1		673	506	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864302	151864302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	95	422	0	ENST00000262189.6:c.9679C>T	p.Pro3227Ser	p.P3227S	ENST00000262189	NM_170606.2	3227	Cca/Tca	42/59	0.331186311031721	1	FACETS	0.637	0.569	0.708	0.637	0.569	0.708	SUBCLONAL	1	TRUE	0	0.465439196778196	1		422	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0049892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	32	805	1	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.262169797354394	1	FACETS	0.291	0.235	0.355	0.291	0.235	0.355	SUBCLONAL	1	TRUE	0	0.262169797354394	1		806	728	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0049892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	74	646	0	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	0.262169797354394	1	FACETS	0.871	0.764	0.987	0.871	0.764	0.987	CLONAL	1	TRUE	0	0.262169797354394	1		646	563	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140165	50140165	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	96	666	0	ENST00000246792.3:c.260A>T	p.Gln87Leu	p.Q87L	ENST00000246792	NM_006270.3	87	cAg/cTg	3/6	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.262169797354394	2		666	553	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044971	47044971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	121	450	2	ENST00000377604.3:c.2297G>A	p.Arg766His	p.R766H	ENST00000377604	NM_001204468.1	766	cGc/cAc	20/24	1	1	FACETS	0.955	0.87	1	1	0.989	1	CLONAL	2	TRUE	0	0.262169797354394	1		452	420	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849858	156849858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	113	620	1	ENST00000524377.1:c.2114C>T	p.Thr705Ile	p.T705I	ENST00000524377	NM_002529.3	705	aCc/aTc	16/17	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.262169797354394	2		621	602	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557563	95557563	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747510783	NA	P-0049892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	41	332	0	ENST00000393063.1:c.5504A>G	p.Tyr1835Cys	p.Y1835C	ENST00000393063	NM_030621.3	1835	tAt/tGt	26/28	1	2	FACETS	0.788	0.657	0.933	0.788	0.657	0.933	CLONAL	1	TRUE	1	0.262169797354394	2		332	397	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223666	53223667	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0049892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	102	429	0	ENST00000375401.3:c.3692dup	p.Leu1232ThrfsTer68	p.L1232Tfs*68	ENST00000375401	NM_004187.3	1231	cca/ccCa	23/26	1	1	FACETS	0.916	0.827	1	1	0.987	1	CLONAL	2	TRUE	0	0.262169797354394	1		429	369	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933462	36933477	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCCCCAGCCTGGCT	TGGCCCCAGCCTGGCT	CCA	novel	NA	P-0049892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	99	853	2	ENST00000361632.4:c.1810_1825delinsTGG	p.Ser604TrpfsTer9	p.S604Wfs*9	ENST00000361632		604	AGCCAGGCTGGGGCCAcc/TGGcc	13/16	1	2	FACETS	0.944	0.842	1	0.944	0.842	1	CLONAL	1	TRUE	1	0.262169797354394	2		855	800	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074249	30074258	+	frameshift_variant	Frame_Shift_Del	DEL	GCCTGTCTTT	GCCTGTCTTT	-	novel	NA	P-0049893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	103	493	0	ENST00000338641.4:c.1511_1520del	p.Ser504ThrfsTer8	p.S504Tfs*8	ENST00000338641	NM_000268.3	504	aGCCTGTCTTTc/ac	14/16	0.366834257364501	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.366834257364501	1		493	424	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0049894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	57	394	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.226079543134569	2		394	463	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857311	68857312	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	34	330	0	ENST00000261769.5:c.1947dup	p.Ile650TyrfsTer13	p.I650Yfs*13	ENST00000261769	NM_004360.3	649	tct/tcTt	13/16	0.226079543134569	1	FACETS	0.839	0.687	1	0.839	0.687	1	CLONAL	1	TRUE	0	0.226079543134569	1		330	318	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100610	67100610	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	46	356	0	ENST00000412916.2:c.308T>C	p.Leu103Pro	p.L103P	ENST00000412916		103	cTg/cCg	4/6	0.226079543134569	1	FACETS	0.731	0.615	0.858	0.731	0.615	0.858	SUBCLONAL	1	TRUE	0	0.226079543134569	1		356	494	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55087029	55087029	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1028735720	NA	P-0049894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	44	343	0	ENST00000275493.2:c.59C>G	p.Pro20Arg	p.P20R	ENST00000275493	NM_005228.3	20	cCg/cGg	1/28	1	2	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	TRUE	1	0.226079543134569	2		343	387	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0049895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	290	756	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		756	966	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0049896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	33	331	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.15608785326452	3	FACETS	0.951	0.782	1	0.476	0.391	0.569	INDETERMINATE	1	FALSE	1	0.419807439029978	3		331	200	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88677026	88677026	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	17	227	0	ENST00000372037.3:c.811T>G	p.Trp271Gly	p.W271G	ENST00000372037	NM_004329.2	271	Tgg/Ggg	9/13	0.133994106894218	4	FACETS	0.871	0.669	1	0.871	0.669	1	INDETERMINATE	2	FALSE	2	0.419807439029978	4		227	66	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16021261	16021261	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	19	324	0	ENST00000268712.3:c.1996T>C	p.Tyr666His	p.Y666H	ENST00000268712	NM_006311.3	666	Tat/Cat	18/46	0.419807439029978	1	FACETS	0.385	0.293	0.491	0.385	0.293	0.491	SUBCLONAL	1	FALSE	0	0.419807439029978	1		324	186	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247573	53247573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	106	192	0	ENST00000375401.3:c.236C>T	p.Thr79Met	p.T79M	ENST00000375401	NM_004187.3	79	aCg/aTg	3/26	1	1	FACETS	0.939	0.855	1	0.939	0.855	1	CLONAL	1	TRUE	0	0.570158780468386	1		192	283	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593597	55593611	+	inframe_deletion	In_Frame_Del	DEL	GTACAGTGGAAGGTT	GTACAGTGGAAGGTT	-	novel	NA	P-0049899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	44	284	0	ENST00000288135.5:c.1665_1679del	p.Gln556_Val560del	p.Q556_V560del	ENST00000288135	NM_000222.2	555	GTACAGTGGAAGGTT/-	11/21	0.51110298113635	1	FACETS	0.832	0.711	0.961	0.832	0.711	0.961	CLONAL	1	TRUE	0	0.51110298113635	1		284	154	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268766	41268766	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	50	387	0	ENST00000349496.5:c.1004A>T	p.Lys335Ile	p.K335I	ENST00000349496	NM_001904.3	335	aAa/aTa	7/15	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.347841473331121	2		387	262	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042125	42042125	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	55	411	0	ENST00000219905.7:c.6324del	p.Lys2108AsnfsTer5	p.K2108Nfs*5	ENST00000219905	NM_001164273.1	2107	cAa/ca	17/24	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.347841473331121	2		411	260	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505480	157505480	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	50	370	0	ENST00000346085.5:c.3461G>C	p.Cys1154Ser	p.C1154S	ENST00000346085	NM_020732.3	1154	tGc/tCc	13/20	0.250566659290657	3	FACETS	1	0.962	1	0.712	0.61	0.821	CLONAL	1	TRUE	1	0.347841473331121	3		370	237	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349953	70349953	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	80	396	0	ENST00000374080.3:c.3936G>C	p.Leu1312Phe	p.L1312F	ENST00000374080		1312	ttG/ttC	28/45	0.172195367367727	2	FACETS	1	0.944	1			1	INDETERMINATE	2	TRUE	NA	0.347841473331121	2		396	213	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	150	468	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.916	0.846	0.987	0.916	0.846	0.987	CLONAL	1	TRUE	1	0.796787400091891	2		468	411	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0049902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	228	475	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.796787400091891	1	FACETS	0.995	0.949	1	0.995	0.949	1	CLONAL	1	TRUE	0	0.796787400091891	1		475	346	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512176	120512176	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782349821	NA	P-0049902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	256	505	1	ENST00000256646.2:c.1066C>T	p.Arg356Cys	p.R356C	ENST00000256646	NM_024408.3	356	Cgt/Tgt	6/34	1	2	FACETS	0.956	0.901	1	0.956	0.901	1	CLONAL	1	TRUE	1	0.796787400091891	2		506	672	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117383	7117383	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	341	711	0	ENST00000302850.5:c.3833A>G	p.Lys1278Arg	p.K1278R	ENST00000302850	NM_000208.2	1278	aAg/aGg	22/22	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.796787400091891	2		711	838	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847399	68847399	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0049903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	71	348	1	ENST00000261769.5:c.1320+1G>T		p.X440_splice	ENST00000261769	NM_004360.3	440			1	2	FACETS	0.967	0.845	1	0.967	0.845	1	CLONAL	1	TRUE	1	0.27	2		349	544	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0049903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	44	298	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	0.229988073188087	3	FACETS	0.699	0.586	0.825	0.35	0.293	0.413	SUBCLONAL	1	TRUE	1	0.27	3		298	529	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0049903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	21	360	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	1	2	FACETS	0.294	0.225	0.375	0.294	0.225	0.375	SUBCLONAL	1	TRUE	1	0.27	2		360	529	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855984	68855984	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121964877	NA	P-0049903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	98	481	0	ENST00000261769.5:c.1792C>T	p.Arg598Ter	p.R598*	ENST00000261769	NM_004360.3	598	Cga/Tga	12/16	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.27	2		481	703	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715678	30715678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039551	NA	P-0049903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	45	289	0	ENST00000295754.5:c.1336G>A	p.Asp446Asn	p.D446N	ENST00000295754	NM_003242.5	446	Gat/Aat	5/7	1	2	FACETS	0.995	0.84	1	0.995	0.84	1	CLONAL	1	TRUE	1	0.27	2		289	335	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438296	56438296	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1334858429	NA	P-0049903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	144	655	0	ENST00000407977.2:c.697C>T	p.Gln233Ter	p.Q233*	ENST00000407977		233	Cag/Tag	7/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.27	2		655	825	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405962	49405962	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	106	499	0	ENST00000418115.1:c.176A>G	p.Asp59Gly	p.D59G	ENST00000418115	NM_001664.2	59	gAc/gGc	3/5	1	2	FACETS	0.883	0.791	0.981	0.883	0.791	0.981	CLONAL	1	TRUE	1	0.27	2		499	889	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0049904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	36	303	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	0.404416270808305	1	FACETS	0.267	0.219	0.321	0.267	0.219	0.321	SUBCLONAL	1	TRUE	0	0.484094595267489	1		303	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913343	NA	P-0049904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	180	597	0	ENST00000269305.4:c.817C>A	p.Arg273Ser	p.R273S	ENST00000269305	NM_001126112.2	273	Cgt/Agt	8/11	0.484094595267489	1	FACETS	0.849	0.786	0.914	0.849	0.786	0.914	CLONAL	1	TRUE	0	0.484094595267489	1		597	664	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0049904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	476	344	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.484094595267489	5	FACETS	0.908	0.877	0.937	0.908	0.877	0.937	CLONAL	5	TRUE	0	0.484094595267489	5		344	748	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971138	21971138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760640852	NA	P-0049904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	235	606	0	ENST00000304494.5:c.220G>A	p.Asp74Asn	p.D74N	ENST00000304494	NM_000077.4	74	Gac/Aac	2/3	0.484094595267489	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.484094595267489	1		606	621	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971423	15971423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	36	449	0	ENST00000268712.3:c.4526C>T	p.Ser1509Phe	p.S1509F	ENST00000268712	NM_006311.3	1509	tCt/tTt	32/46	0.484094595267489	1	FACETS	0.23	0.188	0.276	0.23	0.188	0.276	SUBCLONAL	1	TRUE	0	0.484094595267489	1		449	491	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778367	3778368	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0049904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	38	917	0	ENST00000262367.5:c.6680_6681delinsTT	p.Gly2227Val	p.G2227V	ENST00000262367	NM_004380.2	2227	gGG/gTT	31/31	0.484094595267489	1	FACETS	0.158	0.129	0.189	0.158	0.129	0.189	SUBCLONAL	1	TRUE	0	0.484094595267489	1		917	755	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788648	3788648	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	22	343	0	ENST00000262367.5:c.4306A>T	p.Ser1436Cys	p.S1436C	ENST00000262367	NM_004380.2	1436	Agt/Tgt	26/31	0.484094595267489	1	FACETS	0.168	0.13	0.213	0.168	0.13	0.213	SUBCLONAL	1	TRUE	0	0.484094595267489	1		343	410	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346184	89346184	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	105	554	0	ENST00000301030.4:c.6766C>T	p.Gln2256Ter	p.Q2256*	ENST00000301030	NM_001256183.1	2256	Cag/Tag	9/13	1	2	FACETS	0.793	0.713	0.878	0.793	0.713	0.878	SUBCLONAL	1	TRUE	1	0.484094595267489	2		554	547	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543656	9543656	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	147	417	0	ENST00000353224.5:c.1498G>T	p.Asp500Tyr	p.D500Y	ENST00000353224	NM_177990.2	500	Gat/Tat	6/10	1	2	FACETS	0.98	0.898	1	0.98	0.898	1	CLONAL	1	TRUE	1	0.484094595267489	2		417	620	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324185	62324185	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	212	749	0	ENST00000360203.5:c.2680G>T	p.Asp894Tyr	p.D894Y	ENST00000360203	NM_001283009.1	894	Gac/Tac	29/35	1	2	FACETS	0.894	0.83	0.959	0.894	0.83	0.959	CLONAL	1	TRUE	1	0.484094595267489	2		749	980	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532546	187532546	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0049904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	329	294	2	ENST00000441802.2:c.9847A>T	p.Lys3283Ter	p.K3283*	ENST00000441802	NM_005245.3	3283	Aaa/Taa	14/27	0.484094595267489	3	FACETS	0.912	0.871	0.953			1	CLONAL	3	TRUE	NA	0.484094595267489	3		296	617	SUCCESS
AR	367	MSKCC	GRCh37	X	66765475	66765475	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	230	415	0	ENST00000374690.3:c.487A>C	p.Thr163Pro	p.T163P	ENST00000374690	NM_000044.3	163	Acg/Ccg	1/8	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.484094595267489	1		415	501	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0049904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	201	719	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.397008251508224	3	FACETS	0.926	0.857	0.999	0.463	0.428	0.5	CLONAL	1	TRUE	1	0.397008251508224	3		719	1310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	rs786202799	NA	P-0049904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	471	794	0	ENST00000269305.4:c.376-2A>T		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.397008251508224	3	FACETS	0.895	0.855	0.937	0.895	0.855	0.937	CLONAL	2	TRUE	1	0.397008251508224	3		794	1588	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549491	187549491	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs888946039	NA	P-0049904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	177	432	1	ENST00000441802.2:c.4627C>T	p.Arg1543Cys	p.R1543C	ENST00000441802	NM_005245.3	1543	Cgc/Tgc	9/27	0.397008251508224	3	FACETS	0.801	0.741	0.863	0.801	0.741	0.863	CLONAL	2	TRUE	1	0.397008251508224	3		433	667	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820994	36820994	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145487256	NA	P-0049904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1258	219	777	0	ENST00000373129.3:c.383G>A	p.Arg128Gln	p.R128Q	ENST00000373129	NM_032017.1	128	cGg/cAg	6/12	0.397008251508224	3	FACETS	0.895	0.83	0.963	0.448	0.415	0.482	CLONAL	1	TRUE	1	0.397008251508224	3		777	1477	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443607	49443607	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1231	191	787	0	ENST00000301067.7:c.3764G>C	p.Gly1255Ala	p.G1255A	ENST00000301067	NM_003482.3	1255	gGc/gCc	11/54	0.397008251508224	4	FACETS	0.945	0.872	1	0.473	0.436	0.511	CLONAL	1	TRUE	2	0.397008251508224	4		787	1422	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967820	93967820	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	30	339	0	ENST00000369303.4:c.2107A>G	p.Arg703Gly	p.R703G	ENST00000369303	NM_004440.3	703	Aga/Gga	11/17	0.397008251508224	5	FACETS	0.849	0.694	1			1	CLONAL	2	TRUE	NA	0.397008251508224	5		339	142	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334980	81334980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	11	445	0	ENST00000222390.5:c.1847G>A	p.Gly616Asp	p.G616D	ENST00000222390	NM_000601.4	616	gGc/gAc	16/18	0.397008251508224	3	FACETS	1	0.709	1	0.503	0.354	0.68	CLONAL	1	TRUE	1	0.397008251508224	3		445	66	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128322008	128322008	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs142318505	NA	P-0049904-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	130	653	0	ENST00000265960.3:c.752A>G	p.Asn251Ser	p.N251S	ENST00000265960	NM_001006617.1	251	aAt/aGt	6/12	0.397008251508224	3	FACETS	0.883	0.8	0.97	0.294	0.266	0.324	CLONAL	1	TRUE	0	0.397008251508224	3		653	889	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	480	413	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.503840819040989	6	FACETS	0.908	0.875	0.94	1	0.994	1	CLONAL	5	TRUE	2	0.503840819040989	6		413	843	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0049911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	305	753	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.503840819040989	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.503840819040989	2		753	589	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577145	7577150	+	inframe_deletion	In_Frame_Del	DEL	GTAGAT	GTAGAT	-	novel	NA	P-0049912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	112	512	0	ENST00000269305.4:c.788_793del	p.Asn263_Leu265delinsMet	p.N263_L265delinsM	ENST00000269305	NM_001126112.2	263	aATCTACtg/atg	8/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.31	2		512	602	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667870	37667870	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	128	413	0	ENST00000447079.4:c.2755G>T	p.Val919Phe	p.V919F	ENST00000447079	NM_015083.1	919	Gtt/Ttt	8/14	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.31	2		413	555	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857674	59857674	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1064794907	NA	P-0049912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	17	356	0	ENST00000259008.2:c.1883G>T	p.Gly628Val	p.G628V	ENST00000259008	NM_032043.2	628	gGt/gTt	13/20	0.3	1	FACETS	0.275	0.205	0.359	0.275	0.205	0.359	SUBCLONAL	1	TRUE	0	0.31	1		356	337	SUCCESS
APC	324	MSKCC	GRCh37	5	112174826	112174827	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0049912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	20	272	0	ENST00000257430.4:c.3537_3538del	p.Tyr1179Ter	p.Y1179*	ENST00000257430	NM_000038.5	1179	TAt/t	16/16	1	2	FACETS	0.45	0.344	0.573	0.45	0.344	0.573	SUBCLONAL	1	TRUE	1	0.31	2		272	287	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0049913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	74	662	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.969	0.848	1	0.969	0.848	1	CLONAL	1	TRUE	1	0.214503821529079	2		662	712	SUCCESS
APC	324	MSKCC	GRCh37	5	112174096	112174096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs137854575	NA	P-0049913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	24	337	0	ENST00000257430.4:c.2805C>A	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	taC/taA	16/16	1	2	FACETS	0.623	0.488	0.779	0.623	0.488	0.779	SUBCLONAL	1	TRUE	1	0.214503821529079	2		337	359	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101186	27101186	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	61	882	1	ENST00000324856.7:c.4468G>T	p.Glu1490Ter	p.E1490*	ENST00000324856	NM_006015.4	1490	Gag/Tag	18/20	1	2	FACETS	0.769	0.662	0.885	0.769	0.662	0.885	SUBCLONAL	1	TRUE	1	0.214503821529079	2		883	740	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482868	67482888	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	GTCTTAGAGACATCAAGTATG	GTCTTAGAGACATCAAGTATG	-	novel	NA	P-0049913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	35	584	1	ENST00000327367.4:c.1274_*16del		p.*425*	ENST00000327367	NM_005902.3	424		9/9	1	2	FACETS	0.62	0.508	0.747	0.62	0.508	0.747	SUBCLONAL	1	TRUE	1	0.214503821529079	2		585	526	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878127	48878127	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1276653645	NA	P-0049914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	130	224	0	ENST00000267163.4:c.83del	p.Pro28LeufsTer37	p.P28Lfs*37	ENST00000267163	NM_000321.2	27	Ccc/cc	1/27	0.654687148002882	2	FACETS	0.946	0.888	1	0.946	0.888	1	CLONAL	2	TRUE	0	0.712347380586594	2		224	193	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163587	32163587	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1191585262	NA	P-0049914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	54	649	0	ENST00000375023.3:c.5639G>C	p.Arg1880Pro	p.R1880P	ENST00000375023	NM_004557.3	1880	cGg/cCg	30/30	0.712347380586594	3	FACETS	0.209	0.177	0.243	0.07	0.059	0.081	SUBCLONAL	1	TRUE	0	0.712347380586594	3		649	985	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522604	106522604	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	244	485	0	ENST00000359195.3:c.2581G>T	p.Asp861Tyr	p.D861Y	ENST00000359195	NM_002649.2	861	Gat/Tat	7/11	0.652672232597601	4	FACETS	0.895	0.842	0.95	0.895	0.842	0.95	CLONAL	2	TRUE	2	0.712347380586594	4		485	655	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544135	18544135	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	219	465	1	ENST00000266497.5:c.1952A>T	p.Lys651Met	p.K651M	ENST00000266497		651	aAg/aTg	13/31	0.712347380586594	5	FACETS	0.874	0.816	0.933	0.582	0.544	0.622	CLONAL	2	TRUE	2	0.712347380586594	5		466	728	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888160	81888160	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	418	515	0	ENST00000359376.3:c.305C>A	p.Thr102Asn	p.T102N	ENST00000359376	NM_002661.3	102	aCt/aAt	3/33	0.694918611785566	2	FACETS	0.945	0.913	0.976	0.945	0.913	0.976	CLONAL	2	TRUE	0	0.712347380586594	2		515	621	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38148166	38148166	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	185	518	0	ENST00000317025.8:c.2945G>A	p.Arg982Lys	p.R982K	ENST00000317025	NM_023034.1	982	aGg/aAg	17/24	0.712347380586594	4	FACETS	0.746	0.688	0.807	0.249	0.229	0.269	SUBCLONAL	1	TRUE	1	0.712347380586594	4		518	1192	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412978	63412978	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs750745643	NA	P-0049914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	67	819	0	ENST00000330258.3:c.189G>T	p.Lys63Asn	p.K63N	ENST00000330258	NM_152424.3	63	aaG/aaT	2/2	NA	2	FACETS	0.189	0.163	0.217			1	INDETERMINATE	1	TRUE	NA	0.712347380586594	2		819	995	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938705	76938705	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0049914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	59	636	2	ENST00000373344.5:c.2043T>A	p.Cys681Ter	p.C681*	ENST00000373344	NM_000489.3	681	tgT/tgA	9/35	0.46408816799386	4	FACETS	0.317	0.271	0.366			1	SUBCLONAL	1	TRUE	NA	0.712347380586594	4		638	896	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	31	468	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.46	0.371	0.561	0.46	0.371	0.561	SUBCLONAL	1	FALSE	1	0.230101161897282	2		468	586	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0049916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	49	534	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.581	0.491	0.681	0.581	0.491	0.681	SUBCLONAL	1	FALSE	1	0.230101161897282	2		534	733	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966768	44966768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	29	295	0	ENST00000377967.4:c.3992G>A	p.Cys1331Tyr	p.C1331Y	ENST00000377967	NM_021140.2	1331	tGt/tAt	27/29	1	1	FACETS	0.539	0.432	0.66	0.539	0.432	0.66	SUBCLONAL	1	FALSE	0	0.230101161897282	1		295	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0049916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	72	744	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	1	2	FACETS	0.579	0.504	0.66	0.579	0.504	0.66	SUBCLONAL	1	FALSE	1	0.230101161897282	2		744	1081	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034471	47034471	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	35	399	0	ENST00000377604.3:c.556C>T	p.Arg186Ter	p.R186*	ENST00000377604	NM_001204468.1	186	Cga/Tga	6/24	1	1	FACETS	0.547	0.448	0.659	0.547	0.448	0.659	SUBCLONAL	1	FALSE	0	0.230101161897282	1		399	492	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981167	201981168	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	102	865	0	ENST00000359651.3:c.248dup	p.Asn83LysfsTer9	p.N83Kfs*9	ENST00000359651		82	-/A	2/8	1	2	FACETS	0.749	0.668	0.836	0.749	0.668	0.836	SUBCLONAL	1	FALSE	1	0.230101161897282	2		865	1183	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873782	151873782	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0049916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	38	541	0	ENST00000262189.6:c.8756C>G	p.Ser2919Ter	p.S2919*	ENST00000262189	NM_170606.2	2919	tCa/tGa	38/59	1	2	FACETS	0.452	0.373	0.542	0.452	0.373	0.542	SUBCLONAL	1	FALSE	1	0.230101161897282	2		541	730	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15984016	15984016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	37	382	0	ENST00000268712.3:c.3203C>T	p.Ser1068Phe	p.S1068F	ENST00000268712	NM_006311.3	1068	tCt/tTt	24/46	1	2	FACETS	0.615	0.506	0.737	0.615	0.506	0.737	SUBCLONAL	1	FALSE	1	0.230101161897282	2		382	523	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926543	59926543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	49	701	0	ENST00000259008.2:c.454G>A	p.Asp152Asn	p.D152N	ENST00000259008	NM_032043.2	152	Gat/Aat	5/20	1	2	FACETS	0.48	0.405	0.563	0.48	0.405	0.563	SUBCLONAL	1	FALSE	1	0.230101161897282	2		701	887	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169993035	169993035	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs370513574	NA	P-0049916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	39	250	0	ENST00000295797.4:c.665C>G	p.Ser222Ter	p.S222*	ENST00000295797	NM_002740.5	222	tCa/tGa	8/18	1	2	FACETS	0.572	0.473	0.682	0.572	0.473	0.682	SUBCLONAL	1	FALSE	1	0.230101161897282	2		250	593	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201834	152201834	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	27	430	0	ENST00000206249.3:c.688G>A	p.Asp230Asn	p.D230N	ENST00000206249	NM_000125.3	230	Gat/Aat	3/8	1	2	FACETS	0.448	0.355	0.554	0.448	0.355	0.554	SUBCLONAL	1	FALSE	1	0.230101161897282	2		430	524	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054832	5054832	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	41	386	0	ENST00000381652.3:c.884G>A	p.Gly295Glu	p.G295E	ENST00000381652	NM_004972.3	295	gGa/gAa	7/25	1	2	FACETS	0.615	0.512	0.731	0.615	0.512	0.731	SUBCLONAL	1	FALSE	1	0.230101161897282	2		386	579	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5465525	5465525	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	25	264	0	ENST00000381577.3:c.709G>C	p.Glu237Gln	p.E237Q	ENST00000381577	NM_014143.3	237	Gaa/Caa	5/7	1	2	FACETS	0.607	0.478	0.755	0.607	0.478	0.755	SUBCLONAL	1	FALSE	1	0.230101161897282	2		264	358	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0049917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	203	888	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.445153861184191	1	FACETS	0.866	0.804	0.929	0.866	0.804	0.929	CLONAL	1	TRUE	0	0.445153861184191	1		888	819	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169376	11169376	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	133	500	0	ENST00000361445.4:c.7499T>A	p.Ile2500Asn	p.I2500N	ENST00000361445	NM_004958.3	2500	aTt/aAt	56/58	0.388930721635356	1	FACETS	0.98	0.896	1	0.98	0.896	1	CLONAL	1	TRUE	0	0.445153861184191	1		500	474	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480459	89480459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	92	388	1	ENST00000336596.2:c.2296G>A	p.Gly766Arg	p.G766R	ENST00000336596	NM_005233.5	766	Gga/Aga	13/17	0.180801313857575	3	FACETS	1	0.953	1	0.549	0.495	0.605	INDETERMINATE	1	TRUE	1	0.914247488606431	3		389	267	SUCCESS
APC	324	MSKCC	GRCh37	5	112175411	112175411	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	124	263	0	ENST00000257430.4:c.4120G>T	p.Glu1374Ter	p.E1374*	ENST00000257430	NM_000038.5	1374	Gaa/Taa	16/16	0.384540349850762	2	FACETS	0.863	0.791	0.936	0.863	0.791	0.936	CLONAL	2	TRUE	0	0.434322559319255	2		263	331	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119875	70119875	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	209	669	0	ENST00000245479.2:c.877G>T	p.Glu293Ter	p.E293*	ENST00000245479	NM_000346.3	293	Gag/Tag	3/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.434322559319255	2		669	843	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670155	29670155	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0049919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	80	314	0	ENST00000356175.3:c.7126+2T>C		p.X2376_splice	ENST00000356175	NM_000267.3	2376			0.434322559319255	1	FACETS	0.856	0.76	0.957	0.856	0.76	0.957	CLONAL	1	TRUE	0	0.434322559319255	1		314	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577152	7577167	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCACTACTCAGGATA	ACCACTACTCAGGATA	TCT	novel	NA	P-0049919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	127	512	2	ENST00000269305.4:c.783-12_786delinsAGA		p.X261_splice	ENST00000269305	NM_001126112.2	261		8/11	0.434322559319255	1	FACETS	0.826	0.752	0.904	0.826	0.752	0.904	CLONAL	1	TRUE	0	0.434322559319255	1		514	554	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0049920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	127	364	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.54329789865406	3	FACETS	0.804	0.729	0.883	0.402	0.364	0.442	CLONAL	1	TRUE	1	0.54329789865406	3		364	739	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0049920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2170	253	849	2	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.54329789865406	7	FACETS	0.906	0.844	0.972			1	CLONAL	1	TRUE	NA	0.54329789865406	7		851	2423	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624263	89624266	+	frameshift_variant	Frame_Shift_Del	DEL	AAAA	AAAA	-	novel	NA	P-0049920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	123	269	0	ENST00000371953.3:c.37_40del	p.Lys13GlyfsTer10	p.K13Gfs*10	ENST00000371953	NM_000314.4	13	AAAAgg/gg	1/9	0.54329789865406	1	FACETS	0.967	0.886	1	0.967	0.886	1	CLONAL	1	TRUE	0	0.54329789865406	1		269	341	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38632085	38632085	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	179	378	0	ENST00000299084.4:c.571C>T	p.Gln191Ter	p.Q191*	ENST00000299084	NM_152594.2	191	Caa/Taa	5/7	1	2	FACETS	0.973	0.901	1	0.973	0.901	1	CLONAL	1	TRUE	1	0.54329789865406	2		378	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0049921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	275	927	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.651004817145242	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.651004817145242	1		927	556	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832811	3832811	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555484797	NA	P-0049921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	368	636	1	ENST00000262367.5:c.1447C>T	p.Arg483Ter	p.R483*	ENST00000262367	NM_004380.2	483	Cga/Tga	6/31	0.553665732614382	4	FACETS	0.87	0.826	0.914	0.58	0.551	0.609	CLONAL	2	TRUE	1	0.651004817145242	4		637	1073	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186838	11186838	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	53	405	0	ENST00000361445.4:c.6367C>G	p.Leu2123Val	p.L2123V	ENST00000361445	NM_004958.3	2123	Ctg/Gtg	46/58	0.651004817145242	3	FACETS	0.456	0.389	0.529	0.152	0.129	0.177	SUBCLONAL	1	TRUE	0	0.651004817145242	3		405	473	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609988	43609988	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	134	832	0	ENST00000355710.3:c.1940T>A	p.Ile647Asn	p.I647N	ENST00000355710	NM_020975.4	647	aTc/aAc	11/20	0.579086053876914	3	FACETS	0.45	0.407	0.495	0.225	0.203	0.248	SUBCLONAL	1	TRUE	1	0.651004817145242	3		832	1213	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434611	99434611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1481088368	NA	P-0049921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	204	587	1	ENST00000268035.6:c.698C>T	p.Pro233Leu	p.P233L	ENST00000268035	NM_000875.3	233	cCc/cTc	3/21	0.579086053876914	3	FACETS	0.963	0.894	1	0.481	0.447	0.517	CLONAL	1	TRUE	1	0.651004817145242	3		588	863	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609730	46609730	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	80	675	0	ENST00000263734.3:c.2454G>T	p.Lys818Asn	p.K818N	ENST00000263734	NM_001430.4	818	aaG/aaT	15/16	0.651004817145242	3	FACETS	0.29	0.254	0.329	0.145	0.127	0.165	SUBCLONAL	1	TRUE	1	0.651004817145242	3		675	1124	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675490	30675879	+	inframe_deletion	In_Frame_Del	DEL	GGCTCCCTCCCTCTGGCTCCCCTCTCTGTGTATCTCTCTCCAGGATCACTTTGGGCACCTTCTCTTCTAACTCGGCTGGATCGCACTCTCTGTTTGCTACTGGTCTCTCTACTTCTCTCTCAAATGCTTTGCTTGGAAGGGTCTGCTTCTGTACTTGTTTCTCTTGTATTTCCTCAGATGTCTCAATTTCTACCTTCAAACTCTCCCTATCTCTTTCAGGACTTGCACTTTCCCCATTTTTGTCAGATTCTTGTCTCTGGGTGTCTCTAGCTAACAACTGTTTTTGTTCTCTGTCCTGTTTCCCCTTGGTTAATTCTTCCTCTCCTGTCACATCTGTCTGTCTTTCTGGTAGCAGTTTCTCAGTTTCTCTCTCCAATGGCCCTCTCTCAG	GGCTCCCTCCCTCTGGCTCCCCTCTCTGTGTATCTCTCTCCAGGATCACTTTGGGCACCTTCTCTTCTAACTCGGCTGGATCGCACTCTCTGTTTGCTACTGGTCTCTCTACTTCTCTCTCAAATGCTTTGCTTGGAAGGGTCTGCTTCTGTACTTGTTTCTCTTGTATTTCCTCAGATGTCTCAATTTCTACCTTCAAACTCTCCCTATCTCTTTCAGGACTTGCACTTTCCCCATTTTTGTCAGATTCTTGTCTCTGGGTGTCTCTAGCTAACAACTGTTTTTGTTCTCTGTCCTGTTTCCCCTTGGTTAATTCTTCCTCTCCTGTCACATCTGTCTGTCTTTCTGGTAGCAGTTTCTCAGTTTCTCTCTCCAATGGCCCTCTCTCAG	-	novel	NA	P-0049921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	92	759	0	ENST00000376406.3:c.2477_2866del	p.Pro826_Ser955del	p.P826_S955del	ENST00000376406	NM_014641.2	826	cCTGAGAGAGGGCCATTGGAGAGAGAAACTGAGAAACTGCTACCAGAAAGACAGACAGATGTGACAGGAGAGGAAGAATTAACCAAGGGGAAACAGGACAGAGAACAAAAACAGTTGTTAGCTAGAGACACCCAGAGACAAGAATCTGACAAAAATGGGGAAAGTGCAAGTCCTGAAAGAGATAGGGAGAGTTTGAAGGTAGAAATTGAGACATCTGAGGAAATACAAGAGAAACAAGTACAGAAGCAGACCCTTCCAAGCAAAGCATTTGAGAGAGAAGTAGAGAGACCAGTAGCAAACAGAGAGTGCGATCCAGCCGAGTTAGAAGAGAAGGTGCCCAAAGTGATCCTGGAGAGAGATACACAGAGAGGGGAGCCAGAGGGAGGGAGCCag/cag	8/15	0.624545115719809	3	FACETS	0.375	0.332	0.42	0.187	0.166	0.21	SUBCLONAL	1	TRUE	1	0.651004817145242	3		759	1000	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850933	128850933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	294	532	0	ENST00000249373.3:c.1780G>A	p.Val594Met	p.V594M	ENST00000249373	NM_005631.4	594	Gtg/Atg	10/12	0.651004817145242	3	FACETS	1	0.991	1	0.627	0.591	0.663	CLONAL	1	TRUE	1	0.651004817145242	3		532	955	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879430	151879430	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	81	565	0	ENST00000262189.6:c.5515A>T	p.Thr1839Ser	p.T1839S	ENST00000262189	NM_170606.2	1839	Acg/Tcg	36/59	0.449125525849965	6	FACETS	0.527	0.463	0.597	0.132	0.115	0.15	SUBCLONAL	1	TRUE	2	0.651004817145242	6		565	1086	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741496	145741496	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1470222070	NA	P-0049921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	1624	838	0	ENST00000428558.2:c.1007C>T	p.Thr336Ile	p.T336I	ENST00000428558	NM_004260.3	336	aCa/aTa	5/22	0.651004817145242	7	FACETS	0.988	0.973	1	0.988	0.973	1	CLONAL	6	TRUE	1	0.651004817145242	7		838	2211	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0049924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	85	656	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	1	2	FACETS	0.917	0.809	1	0.917	0.809	1	CLONAL	1	TRUE	1	0.2	2		656	927	SUCCESS
APC	324	MSKCC	GRCh37	5	112175199	112175199	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	17	258	0	ENST00000257430.4:c.3910del	p.Ile1304Ter	p.I1304*	ENST00000257430	NM_000038.5	1303	cAa/ca	16/16	1	2	FACETS	0.612	0.456	0.796	0.612	0.456	0.796	SUBCLONAL	1	TRUE	1	0.2	2		258	278	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	610	682	6	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.899933117877424	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.899933117877424	1		688	724	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954192	48954192	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	181	173	2	ENST00000267163.4:c.1393G>T	p.Glu465Ter	p.E465*	ENST00000267163	NM_000321.2	465	Gaa/Taa	15/27	0.899933117877424	2	FACETS	0.944	0.91	0.975	0.944	0.91	0.975	CLONAL	2	TRUE	0	0.899933117877424	2		175	213	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057235	180057235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148392893	NA	P-0049926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	432	674	8	ENST00000261937.6:c.503C>T	p.Thr168Met	p.T168M	ENST00000261937	NM_182925.4	168	aCg/aTg	4/30	0.899933117877424	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.899933117877424	1		682	510	SUCCESS
APC	324	MSKCC	GRCh37	5	112177660	112177660	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	257	388	1	ENST00000257430.4:c.6371del	p.Leu2124TyrfsTer15	p.L2124Yfs*15	ENST00000257430	NM_000038.5	2123	tgT/tg	16/16	0.899933117877424	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.899933117877424	1		389	304	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105875	27105876	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	154	551	0	ENST00000324856.7:c.5487dup	p.Lys1830Ter	p.K1830*	ENST00000324856	NM_006015.4	1829	gat/gaTt	20/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.418848956508979	2		551	706	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252733	10252733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	129	712	2	ENST00000340748.4:c.3232G>A	p.Gly1078Ser	p.G1078S	ENST00000340748		1078	Ggc/Agc	29/40	0.418848956508979	5	FACETS	0.795	0.719	0.876	0.199	0.179	0.219	SUBCLONAL	1	TRUE	1	0.418848956508979	5		714	1261	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11114018	11114018	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	127	556	0	ENST00000358026.2:c.1946A>G	p.Tyr649Cys	p.Y649C	ENST00000358026	NM_001128849.1	649	tAt/tGt	13/36	0.418848956508979	5	FACETS	0.937	0.847	1	0.234	0.211	0.258	CLONAL	1	TRUE	1	0.418848956508979	5		556	1054	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127191	22127191	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	444	540	0	ENST00000215832.6:c.937C>G	p.Leu313Val	p.L313V	ENST00000215832	NM_002745.4	313	Ctg/Gtg	7/9	0.418848956508979	1	FACETS	0.844	0.808	0.88	1	0.997	1	CLONAL	2	TRUE	0	0.418848956508979	1		540	993	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0049928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	104	321	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.470713603067563	2		321	400	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150335	108150335	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	110	243	0	ENST00000278616.4:c.3402G>A	p.Met1134Ile	p.M1134I	ENST00000278616	NM_000051.3	1134	atG/atA	23/63	0.387522888272821	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	1	0.470713603067563	3		243	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0049929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	204	662	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.320893677145028	2	FACETS	0.847	0.789	0.907	0.847	0.789	0.907	CLONAL	2	TRUE	0	0.361050008124851	2		662	667	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59793411	59793411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375082407	NA	P-0049929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	32	397	0	ENST00000259008.2:c.2393G>A	p.Arg798Gln	p.R798Q	ENST00000259008	NM_032043.2	798	cGa/cAa	17/20	0.130456385309479	3	FACETS	0.524	0.426	0.636	0.175	0.142	0.212	INDETERMINATE	1	TRUE	0	0.361050008124851	3		397	399	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878863	151878863	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1563288201	NA	P-0049929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	281	519	0	ENST00000262189.6:c.6082C>T	p.Arg2028Ter	p.R2028*	ENST00000262189	NM_170606.2	2028	Cga/Tga	36/59	0.23505451500974	4	FACETS	0.937	0.884	0.99			1	CLONAL	3	TRUE	NA	0.361050008124851	4		519	754	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212103	36212104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	142	625	3	ENST00000222270.7:c.1859dup	p.Pro621SerfsTer55	p.P621Sfs*55	ENST00000222270	NM_014727.1	618	-/C	3/37	0.200736954707465	4	FACETS	1	0.982	1	0.654	0.596	0.714	INDETERMINATE	1	TRUE	2	0.361050008124851	4		628	819	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590683	189590683	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	130	408	0	ENST00000264731.3:c.1248G>C	p.Lys416Asn	p.K416N	ENST00000264731	NM_003722.4	416	aaG/aaC	10/14	0.368448760380061	4	FACETS	1	0.985	1	0.734	0.667	0.804	CLONAL	1	TRUE	2	0.361050008124851	4		408	668	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184787	32184787	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	33	562	0	ENST00000375023.3:c.1796C>A	p.Pro599His	p.P599H	ENST00000375023	NM_004557.3	599	cCc/cAc	11/30	0.23483755731727	3	FACETS	0.356	0.289	0.432	0.178	0.144	0.216	SUBCLONAL	1	TRUE	1	0.361050008124851	3		562	606	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974741	21974741	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	58	322	0	ENST00000304494.5:c.86G>C	p.Arg29Pro	p.R29P	ENST00000304494	NM_000077.4	29	cGg/cCg	1/3	0.368448760380061	1	FACETS	0.93	0.806	1	0.93	0.806	1	CLONAL	1	TRUE	0	0.361050008124851	1		322	283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0049930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	187	687	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.912	0.843	0.983	1	0.994	1	CLONAL	3	TRUE	1	0.159942375312565	2		688	855	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971035	21971035	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	38	502	1	ENST00000304494.5:c.323A>G	p.Asp108Gly	p.D108G	ENST00000304494	NM_000077.4	108	gAt/gGt	2/3	0.159942375312565	1	FACETS	0.917	0.757	1	0.917	0.757	1	CLONAL	1	TRUE	0	0.159942375312565	1		503	477	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627549	14627550	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1251025883	NA	P-0049930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	51	586	0	ENST00000254322.2:c.520dup	p.Glu174GlyfsTer61	p.E174Gfs*61	ENST00000254322	NM_006145.1	174	gag/gGag	2/3	1	2	FACETS	0.92	0.781	1	0.92	0.781	1	CLONAL	1	TRUE	1	0.159942375312565	2		586	693	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965421	68965421	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs777847032	NA	P-0049930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	50	733	0	ENST00000288368.4:c.1033A>T	p.Thr345Ser	p.T345S	ENST00000288368	NM_024870.2	345	Aca/Tca	9/40	0.159942375312565	6	FACETS	0.873	0.738	1			1	CLONAL	1	TRUE	NA	0.159942375312565	6		733	945	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	266	825	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.761	0.716	0.807	0.761	0.716	0.807	SUBCLONAL	1	TRUE	1	0.837212429980799	2		829	835	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	110	454	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.428	0.385	0.473	0.428	0.385	0.473	SUBCLONAL	1	TRUE	1	0.837212429980799	2		459	614	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	26	398	0	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.128	0.101	0.16	0.128	0.101	0.16	SUBCLONAL	1	TRUE	1	0.837212429980799	2		398	484	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	125	399	1	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.551	0.501	0.603	0.551	0.501	0.603	SUBCLONAL	1	TRUE	1	0.837212429980799	2		400	542	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	469	461	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.837212429980799	2	FACETS	0.976	0.952	0.999	0.976	0.952	0.999	CLONAL	2	TRUE	0	0.837212429980799	2		461	574	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	112	352	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.528	0.477	0.581	0.528	0.477	0.581	SUBCLONAL	1	TRUE	1	0.837212429980799	2		352	507	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	282	472	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.988	0.935	1	0.988	0.935	1	CLONAL	1	TRUE	1	0.837212429980799	2		472	682	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	105	424	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.414	0.371	0.459	0.414	0.371	0.459	SUBCLONAL	1	TRUE	1	0.837212429980799	2		424	606	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	120	359	2	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	1	2	FACETS	0.637	0.579	0.697	0.637	0.579	0.697	SUBCLONAL	1	TRUE	1	0.837212429980799	2		361	450	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945696	17945696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3213409	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	176	755	0	ENST00000458235.1:c.2164G>A	p.Val722Ile	p.V722I	ENST00000458235	NM_000215.3	722	Gtc/Atc	16/24	1	2	FACETS	0.472	0.435	0.511	0.472	0.435	0.511	SUBCLONAL	1	TRUE	1	0.837212429980799	2		755	890	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519134	103519135	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	36	454	0	ENST00000355739.4:c.2478dup	p.Asn827Ter	p.N827*	ENST00000355739	NM_000123.3	824	-/T	11/15	1	2	FACETS	0.145	0.119	0.175	0.145	0.119	0.175	SUBCLONAL	1	TRUE	1	0.837212429980799	2		454	592	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	150	826	4	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	0.389	0.355	0.424	0.389	0.355	0.424	SUBCLONAL	1	TRUE	1	0.837212429980799	2		830	922	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	91	521	2	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	0.358	0.318	0.4	0.358	0.318	0.4	SUBCLONAL	1	TRUE	1	0.837212429980799	2		523	608	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303305	15303305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762164861	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	159	832	1	ENST00000263388.2:c.223C>T	p.Arg75Trp	p.R75W	ENST00000263388	NM_000435.2	75	Cgg/Tgg	3/33	1	2	FACETS	0.376	0.344	0.409	0.376	0.344	0.409	SUBCLONAL	1	TRUE	1	0.837212429980799	2		833	1011	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	126	522	1	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	1	2	FACETS	0.456	0.414	0.501	0.456	0.414	0.501	SUBCLONAL	1	TRUE	1	0.837212429980799	2		523	660	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794441	42794441	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	171	895	2	ENST00000575354.2:c.1526del	p.Pro509HisfsTer14	p.P509Hfs*14	ENST00000575354	NM_015125.3	507	cgC/cg	10/20	1	2	FACETS	0.392	0.36	0.426	0.392	0.36	0.426	SUBCLONAL	1	TRUE	1	0.837212429980799	2		897	1041	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72861878	72861878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201983708	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	81	538	0	ENST00000325599.8:c.1004G>A	p.Arg335His	p.R335H	ENST00000325599	NM_018130.2	335	cGc/cAc	9/11	1	2	FACETS	0.32	0.282	0.361	0.32	0.282	0.361	SUBCLONAL	1	TRUE	1	0.837212429980799	2		538	604	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156719	20156719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	228	328	0	ENST00000379607.5:c.38G>A	p.Arg13His	p.R13H	ENST00000379607	NM_001412.3	13	cGc/cAc	2/7	1	2	FACETS	0.848	0.795	0.902	0.848	0.795	0.902	CLONAL	1	TRUE	1	0.837212429980799	2		328	642	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372092	55372093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	78	456	0	ENST00000297316.4:c.788dup	p.Glu264GlyfsTer101	p.E264Gfs*101	ENST00000297316	NM_022454.3	261	ggc/ggCc	2/2	1	2	FACETS	0.345	0.303	0.39	0.345	0.303	0.39	SUBCLONAL	1	TRUE	1	0.837212429980799	2		456	540	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621893	1621893	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371336835	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	104	824	0	ENST00000344749.5:c.899C>T	p.Thr300Met	p.T300M	ENST00000344749	NM_001136139.2	300	aCg/aTg	11/19	1	2	FACETS	0.325	0.29	0.361	0.325	0.29	0.361	SUBCLONAL	1	TRUE	1	0.837212429980799	2		824	765	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573977	41573977	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201569846	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	181	580	1	ENST00000263253.7:c.6262C>T	p.Arg2088Trp	p.R2088W	ENST00000263253	NM_001429.3	2088	Cgg/Tgg	31/31	1	2	FACETS	0.634	0.587	0.683	0.634	0.587	0.683	SUBCLONAL	1	TRUE	1	0.837212429980799	2		581	682	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647685	2647685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	308	632	0	ENST00000342085.4:c.1588G>A	p.Gly530Arg	p.G530R	ENST00000342085	NM_002613.4	530	Ggg/Agg	14/14	1	2	FACETS	0.988	0.937	1	0.988	0.937	1	CLONAL	1	TRUE	1	0.837212429980799	2		632	745	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555273	226555273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781122492	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	183	544	0	ENST00000366794.5:c.2314G>A	p.Glu772Lys	p.E772K	ENST00000366794	NM_001618.3	772	Gag/Aag	17/23	0.837212429980799	4	FACETS	0.635	0.584	0.688	0.212	0.194	0.23	SUBCLONAL	1	TRUE	1	0.837212429980799	4		544	1265	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248737	212248737	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	38	321	0	ENST00000342788.4:c.3530del	p.Asn1177MetfsTer27	p.N1177Mfs*27	ENST00000342788	NM_005235.2	1177	aAt/at	28/28	1	2	FACETS	0.226	0.187	0.27	0.226	0.187	0.27	SUBCLONAL	1	TRUE	1	0.837212429980799	2		321	402	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	58	717	12	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	0.206	0.176	0.238	0.206	0.176	0.238	SUBCLONAL	1	TRUE	1	0.837212429980799	2		729	674	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088712	27088712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754046530	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	120	708	0	ENST00000324856.7:c.2321G>A	p.Arg774His	p.R774H	ENST00000324856	NM_006015.4	774	cGt/cAt	7/20	1	2	FACETS	0.35	0.316	0.387	0.35	0.316	0.387	SUBCLONAL	1	TRUE	1	0.837212429980799	2		708	818	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106421	27106421	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	113	645	0	ENST00000324856.7:c.6032T>C	p.Leu2011Pro	p.L2011P	ENST00000324856	NM_006015.4	2011	cTg/cCg	20/20	1	2	FACETS	0.391	0.352	0.432	0.391	0.352	0.432	SUBCLONAL	1	TRUE	1	0.837212429980799	2		645	691	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466025	69466026	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGA	novel	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	121	824	0	ENST00000227507.2:c.866_868dup	p.Asp289dup	p.D289dup	ENST00000227507	NM_053056.2	289	acc/acCGAc	5/5	1	2	FACETS	0.322	0.291	0.356	0.322	0.291	0.356	SUBCLONAL	1	TRUE	1	0.837212429980799	2		824	897	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119750	70119751	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	192	739	0	ENST00000245479.2:c.754dup	p.Leu252ProfsTer44	p.L252Pfs*44	ENST00000245479	NM_000346.3	251	gac/gaCc	3/3	1	2	FACETS	0.577	0.534	0.621	0.577	0.534	0.621	SUBCLONAL	1	TRUE	1	0.837212429980799	2		739	795	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281237	142281237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754554657	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	93	475	0	ENST00000350721.4:c.1007G>A	p.Arg336Gln	p.R336Q	ENST00000350721	NM_001184.3	336	cGg/cAg	4/47	1	2	FACETS	0.461	0.411	0.513	0.461	0.411	0.513	SUBCLONAL	1	TRUE	1	0.837212429980799	2		475	482	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639760	3639760	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	260	852	1	ENST00000294008.3:c.3879G>T	p.Arg1293Ser	p.R1293S	ENST00000294008	NM_032444.2	1293	agG/agT	12/15	1	2	FACETS	0.632	0.593	0.673	0.632	0.593	0.673	SUBCLONAL	1	TRUE	1	0.837212429980799	2		853	982	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518228	187518228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199692977	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	86	412	0	ENST00000441802.2:c.12466G>A	p.Glu4156Lys	p.E4156K	ENST00000441802	NM_005245.3	4156	Gag/Aag	25/27	1	2	FACETS	0.456	0.405	0.51	0.456	0.405	0.51	SUBCLONAL	1	TRUE	1	0.837212429980799	2		412	451	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506213	120506213	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	54	330	0	ENST00000256646.2:c.1899C>A	p.Cys633Ter	p.C633*	ENST00000256646	NM_024408.3	633	tgC/tgA	11/34	1	2	FACETS	0.305	0.261	0.353	0.305	0.261	0.353	SUBCLONAL	1	TRUE	1	0.837212429980799	2		330	423	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246091244	246091244	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1476109987	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	104	450	2	ENST00000388985.4:c.691G>A	p.Val231Met	p.V231M	ENST00000388985		231	Gtg/Atg	7/12	0.837212429980799	4	FACETS	0.373	0.333	0.416	0.124	0.111	0.139	SUBCLONAL	1	TRUE	1	0.837212429980799	4		452	1224	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596063	43596063	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs570176656	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	53	687	1	ENST00000355710.3:c.230G>A	p.Arg77His	p.R77H	ENST00000355710	NM_020975.4	77	cGc/cAc	2/20	1	2	FACETS	0.168	0.142	0.196	0.168	0.142	0.196	SUBCLONAL	1	TRUE	1	0.837212429980799	2		688	755	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63700158	63700158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	50	208	1	ENST00000279873.7:c.493G>A	p.Ala165Thr	p.A165T	ENST00000279873	NM_032199.2	165	Gca/Aca	3/10	1	2	FACETS	0.438	0.374	0.506	0.438	0.374	0.506	SUBCLONAL	1	TRUE	1	0.837212429980799	2		209	273	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759925	63759925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	79	362	2	ENST00000279873.7:c.578G>A	p.Arg193His	p.R193H	ENST00000279873	NM_032199.2	193	cGc/cAc	4/10	1	2	FACETS	0.418	0.368	0.47	0.418	0.368	0.47	SUBCLONAL	1	TRUE	1	0.837212429980799	2		364	452	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332808	70332808	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	47	620	0	ENST00000373644.4:c.713G>T	p.Gly238Val	p.G238V	ENST00000373644	NM_030625.2	238	gGt/gTt	2/12	1	2	FACETS	0.161	0.135	0.19	0.161	0.135	0.19	SUBCLONAL	1	TRUE	1	0.837212429980799	2		620	697	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279676	123279677	+	missense_variant	Missense_Mutation	DNP	CG	CG	AC	novel	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	161	431	0	ENST00000358487.5:c.755_756delinsGT	p.Ser252Cys	p.S252C	ENST00000358487	NM_000141.4	252	tCG/tGT	7/18	1	2	FACETS	0.624	0.575	0.675	0.624	0.575	0.675	SUBCLONAL	1	TRUE	1	0.837212429980799	2		431	616	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203804	94203804	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	40	197	0	ENST00000323929.3:c.850G>A	p.Val284Ile	p.V284I	ENST00000323929	NM_005591.3	284	Gtt/Att	9/20	1	2	FACETS	0.455	0.382	0.535	0.455	0.382	0.535	SUBCLONAL	1	TRUE	1	0.837212429980799	2		197	210	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28901661	28901661	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	136	370	0	ENST00000282397.4:c.2734T>A	p.Cys912Ser	p.C912S	ENST00000282397	NM_002019.4	912	Tgc/Agc	20/30	1	2	FACETS	0.662	0.605	0.72	0.662	0.605	0.72	SUBCLONAL	1	TRUE	1	0.837212429980799	2		370	491	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434974	56434974	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	127	755	0	ENST00000407977.2:c.2163T>A	p.Asn721Lys	p.N721K	ENST00000407977		721	aaT/aaA	9/10	1	2	FACETS	0.357	0.323	0.392	0.357	0.323	0.392	SUBCLONAL	1	TRUE	1	0.837212429980799	2		755	851	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632103	1632103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1331208832	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	123	712	0	ENST00000344749.5:c.232G>A	p.Gly78Ser	p.G78S	ENST00000344749	NM_001136139.2	78	Ggc/Agc	5/19	1	2	FACETS	0.389	0.351	0.428	0.389	0.351	0.428	SUBCLONAL	1	TRUE	1	0.837212429980799	2		712	756	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303256	15303256	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	162	909	1	ENST00000263388.2:c.272G>A	p.Gly91Asp	p.G91D	ENST00000263388	NM_000435.2	91	gGt/gAt	3/33	1	2	FACETS	0.372	0.341	0.405	0.372	0.341	0.405	SUBCLONAL	1	TRUE	1	0.837212429980799	2		910	1040	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349961	15349961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1473772530	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	48	798	0	ENST00000263377.2:c.3691G>A	p.Ala1231Thr	p.A1231T	ENST00000263377	NM_058243.2	1231	Gct/Act	18/20	1	2	FACETS	0.15	0.126	0.176	0.15	0.126	0.176	SUBCLONAL	1	TRUE	1	0.837212429980799	2		798	766	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218495	36218495	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754398149	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	178	732	0	ENST00000222270.7:c.4274T>C	p.Val1425Ala	p.V1425A	ENST00000222270	NM_014727.1	1425	gTg/gCg	16/37	1	2	FACETS	0.638	0.591	0.688	0.638	0.591	0.688	SUBCLONAL	1	TRUE	1	0.837212429980799	2		732	666	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033451	48033451	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	75	382	0	ENST00000234420.5:c.3755T>C	p.Leu1252Ser	p.L1252S	ENST00000234420	NM_000179.2	1252	tTa/tCa	8/10	1	2	FACETS	0.351	0.308	0.397	0.351	0.308	0.397	SUBCLONAL	1	TRUE	1	0.837212429980799	2		382	510	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150007	202150007	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	186	578	0	ENST00000358485.4:c.1448C>T	p.Ser483Leu	p.S483L	ENST00000358485	NM_001080125.1	483	tCa/tTa	8/9	1	2	FACETS	0.605	0.56	0.651	0.605	0.56	0.651	SUBCLONAL	1	TRUE	1	0.837212429980799	2		578	735	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62322226	62322226	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376930232	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	42	830	0	ENST00000360203.5:c.2482C>T	p.Arg828Trp	p.R828W	ENST00000360203	NM_001283009.1	828	Cgg/Tgg	27/35	1	2	FACETS	0.124	0.103	0.148	0.124	0.103	0.148	SUBCLONAL	1	TRUE	1	0.837212429980799	2		830	806	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467724	66467725	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	65	405	0	ENST00000273854.3:c.544dup	p.Ser182LysfsTer6	p.S182Kfs*6	ENST00000273854	NM_004439.5	182	agc/aAgc	3/18	0.127935939773193	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.837212429980799	0		405	420	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542324	187542324	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	65	359	0	ENST00000441802.2:c.5416T>G	p.Leu1806Val	p.L1806V	ENST00000441802	NM_005245.3	1806	Ttg/Gtg	10/27	1	2	FACETS	0.445	0.388	0.506	0.445	0.388	0.506	SUBCLONAL	1	TRUE	1	0.837212429980799	2		359	349	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294898	1294898	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	17	107	0	ENST00000310581.5:c.207del	p.Ser70ProfsTer8	p.S70Pfs*8	ENST00000310581	NM_198253.2	69	ccC/cc	1/16	1	2	FACETS	0.508	0.387	0.644	0.508	0.387	0.644	SUBCLONAL	1	TRUE	1	0.837212429980799	2		107	80	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183066	32183066	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	262	877	0	ENST00000375023.3:c.1958A>G	p.Asp653Gly	p.D653G	ENST00000375023	NM_004557.3	653	gAt/gGt	12/30	1	2	FACETS	0.662	0.621	0.704	0.662	0.621	0.704	SUBCLONAL	1	TRUE	1	0.837212429980799	2		877	945	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955481	90955481	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	107	409	0	ENST00000265433.3:c.2184G>T	p.Glu728Asp	p.E728D	ENST00000265433	NM_002485.4	728	gaG/gaT	14/16	1	2	FACETS	0.614	0.555	0.676	0.614	0.555	0.676	SUBCLONAL	1	TRUE	1	0.837212429980799	2		409	416	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753897	133753897	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	159	610	0	ENST00000318560.5:c.1366T>A	p.Tyr456Asn	p.Y456N	ENST00000318560	NM_005157.4	456	Tac/Aac	8/11	1	2	FACETS	0.537	0.493	0.583	0.537	0.493	0.583	SUBCLONAL	1	TRUE	1	0.837212429980799	2		610	707	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222815	53222815	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1556833062	NA	P-0049931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	228	809	0	ENST00000375401.3:c.4121T>G	p.Leu1374Arg	p.L1374R	ENST00000375401	NM_004187.3	1374	cTg/cGg	25/26	1	2	FACETS	0.553	0.515	0.592	0.553	0.515	0.592	SUBCLONAL	1	TRUE	1	0.837212429980799	2		809	985	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0049932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	90	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.263782644056121	4	FACETS	0.875	0.785	0.97	0.875	0.785	0.97	INDETERMINATE	2	TRUE	2	0.486779339002821	4		327	314	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041366	42041366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	205	596	1	ENST00000219905.7:c.5561C>T	p.Ser1854Phe	p.S1854F	ENST00000219905	NM_001164273.1	1854	tCt/tTt	17/24	1	2	FACETS	0.894	0.839	0.95	1	0.994	1	CLONAL	2	TRUE	1	0.486779339002821	2		597	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577123	7577123	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876660333	NA	P-0049932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	183	665	0	ENST00000269305.4:c.815T>G	p.Val272Gly	p.V272G	ENST00000269305	NM_001126112.2	272	gTg/gGg	8/11	0.487078650795202	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.486779339002821	1		665	512	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220400	1220400	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1359582062	NA	P-0049932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	172	740	0	ENST00000326873.7:c.493G>T	p.Glu165Ter	p.E165*	ENST00000326873	NM_000455.4	165	Gag/Tag	4/10	0.487078650795202	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.486779339002821	1		740	459	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086017	16086017	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	55	594	1	ENST00000281043.3:c.1193G>T	p.Arg398Leu	p.R398L	ENST00000281043	NM_005378.4	398	cGg/cTg	3/3	0.192570137896898	2	FACETS	0.492	0.422	0.569	0.246	0.211	0.285	INDETERMINATE	1	TRUE	0	0.486779339002821	2		595	459	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500825	149500825	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	108	660	0	ENST00000261799.4:c.2405A>T	p.Asp802Val	p.D802V	ENST00000261799	NM_002609.3	802	gAc/gTc	17/23	1	2	FACETS	0.756	0.68	0.836	0.756	0.68	0.836	SUBCLONAL	1	TRUE	1	0.486779339002821	2		660	587	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048231	180048231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201884197	NA	P-0049932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	45	827	0	ENST00000261937.6:c.2042C>T	p.Thr681Met	p.T681M	ENST00000261937	NM_182925.4	681	aCg/aTg	14/30	1	2	FACETS	0.327	0.274	0.385	0.327	0.274	0.385	SUBCLONAL	1	TRUE	1	0.486779339002821	2		827	566	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508517	106508517	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	68	305	0	ENST00000359195.3:c.511G>T	p.Asp171Tyr	p.D171Y	ENST00000359195	NM_002649.2	171	Gat/Tat	2/11	0.191233411253056	4	FACETS	1	0.968	1	0.67	0.588	0.757	INDETERMINATE	1	TRUE	2	0.486779339002821	4		305	310	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370775	55370775	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	98	516	0	ENST00000297316.4:c.77G>T	p.Gly26Val	p.G26V	ENST00000297316	NM_022454.3	26	gGg/gTg	1/2	0.216919425756134	3	FACETS	1	0.902	1	0.504	0.451	0.559	INDETERMINATE	1	TRUE	1	0.486779339002821	3		516	497	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389329	8389329	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049932-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	122	558	0	ENST00000356435.5:c.4289G>T	p.Gly1430Val	p.G1430V	ENST00000356435		1430	gGa/gTa	26/35	NA	2	FACETS	0.766	0.702	0.832			1	INDETERMINATE	2	TRUE	NA	0.486779339002821	2		558	327	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692981	89692982	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0049933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	29	285	0	ENST00000371953.3:c.469dup	p.Glu157GlyfsTer23	p.E157Gfs*23	ENST00000371953	NM_000314.4	155	-/G	5/9	NA	2	FACETS	0.251	0.2	0.308			1	INDETERMINATE	1	TRUE	NA	0.416351388287056	2		285	556	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820785	3820785	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0049933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	267	973	0	ENST00000262367.5:c.2666C>G	p.Ser889Ter	p.S889*	ENST00000262367	NM_004380.2	889	tCa/tGa	14/31	0.403367823242224	1	FACETS	0.868	0.813	0.924	0.868	0.813	0.924	CLONAL	1	TRUE	0	0.416351388287056	1		973	1170	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998922	100998922	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	194	703	0	ENST00000325455.5:c.880T>A	p.Ser294Thr	p.S294T	ENST00000325455	NM_001202474.3	294	Tcc/Acc	1/8	0.297528022786836	1	FACETS	0.878	0.814	0.945	0.878	0.814	0.945	CLONAL	1	TRUE	0	0.416351388287056	1		703	840	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578586	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TGTAGGAAGAGGAAGGAGACAGAGTTGAAAG	TGTAGGAAGAGGAAGGAGACAGAGTTGAAAG	-	novel	NA	P-0049933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	371	737	0	ENST00000269305.4:c.376-32_376-2del		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.386605429738419	2	FACETS	0.81	0.77	0.851	0.81	0.77	0.851	CLONAL	2	TRUE	0	0.416351388287056	2		737	1100	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500548	149500548	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049933-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	186	743	0	ENST00000261799.4:c.2489G>C	p.Arg830Thr	p.R830T	ENST00000261799	NM_002609.3	830	aGg/aCg	18/23	0.403367823242224	1	FACETS	0.857	0.792	0.923	0.857	0.792	0.923	CLONAL	1	TRUE	0	0.416351388287056	1		743	826	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593607	55593612	+	inframe_deletion	In_Frame_Del	DEL	AGGTTG	AGGTTG	-	novel	NA	P-0049934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	55	188	0	ENST00000288135.5:c.1673_1678del	p.Lys558_Val560delinsIle	p.K558_V560delinsI	ENST00000288135	NM_000222.2	558	aAGGTTGtt/att	11/21	1	2	FACETS	0.686	0.587	0.796	0.686	0.587	0.796	SUBCLONAL	1	TRUE	1	0.25	2		188	641	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647606	3647606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558236399	NA	P-0049934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	58	896	3	ENST00000294008.3:c.1457G>A	p.Arg486His	p.R486H	ENST00000294008	NM_032444.2	486	cGt/cAt	7/15	0.121828053786488	1	FACETS	0.371	0.318	0.43	0.371	0.318	0.43	INDETERMINATE	1	TRUE	0	0.25	1		899	1093	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0049936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	217	435	2	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.5	2		437	709	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	216	442	0	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.5	2		442	732	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947457	38947457	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757156639	NA	P-0049938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	58	289	1	ENST00000357387.3:c.4223C>T	p.Ser1408Leu	p.S1408L	ENST00000357387	NM_152756.3	1408	tCa/tTa	32/38	0.406746255801347	7	FACETS	0.926	0.795	1	0.185	0.159	0.214	CLONAL	1	TRUE	2	0.406746255801347	7		290	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578496	7578496	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782197	NA	P-0049938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	480	849	0	ENST00000269305.4:c.434T>C	p.Leu145Pro	p.L145P	ENST00000269305	NM_001126112.2	145	cTg/cCg	5/11	0.406746255801347	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	TRUE	0	0.406746255801347	3		849	940	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020477	14020477	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145402255	NA	P-0049938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	143	338	0	ENST00000311895.7:c.448C>T	p.Arg150Cys	p.R150C	ENST00000311895	NM_005236.2	150	Cgc/Tgc	3/11	0.319077804272209	5	FACETS	1	0.975	1	0.772	0.708	0.837	CLONAL	2	TRUE	2	0.406746255801347	5		338	489	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272515	15272515	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	255	623	0	ENST00000263388.2:c.5924C>A	p.Pro1975His	p.P1975H	ENST00000263388	NM_000435.2	1975	cCc/cAc	33/33	0.38550687172467	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.406746255801347	2		623	595	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400020	49400020	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	85	508	0	ENST00000418115.1:c.317del	p.Phe106SerfsTer26	p.F106Sfs*26	ENST00000418115	NM_001664.2	106	tTc/tc	4/5	0.38550687172467	2	FACETS	0.802	0.711	0.899	0.401	0.355	0.45	CLONAL	1	TRUE	0	0.406746255801347	2		508	521	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898707	134898707	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	91	275	0	ENST00000398015.3:c.1765C>G	p.Pro589Ala	p.P589A	ENST00000398015	NM_004441.4	589	Cca/Gca	10/16	0.391951085678975	4	FACETS	0.795	0.71	0.883	0.795	0.71	0.883	SUBCLONAL	2	TRUE	2	0.406746255801347	4		275	396	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974768	21974769	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0049938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	140	268	0	ENST00000304494.5:c.58_59delinsAA	p.Ala20Lys	p.A20K	ENST00000304494	NM_000077.4	20	GCg/AAg	1/3	0.38550687172467	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.406746255801347	2		268	330	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0049939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	64	263	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	0.170427768178133	3	FACETS	0.796	0.69	0.911	0.398	0.345	0.456	INDETERMINATE	1	TRUE	1	0.331073356149716	3		263	566	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205741	108205741	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555127125	NA	P-0049939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	52	262	0	ENST00000278616.4:c.8056T>C	p.Phe2686Leu	p.F2686L	ENST00000278616	NM_000051.3	2686	Ttt/Ctt	55/63	0.311038395435183	1	FACETS	0.649	0.554	0.752	0.649	0.554	0.752	SUBCLONAL	1	TRUE	0	0.331073356149716	1		262	404	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493713	56493713	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	128	454	0	ENST00000267101.3:c.3029A>T	p.Asp1010Val	p.D1010V	ENST00000267101	NM_001982.3	1010	gAc/gTc	25/28	0.170427768178133	3	FACETS	1	0.974	1	0.6	0.544	0.659	INDETERMINATE	1	TRUE	1	0.331073356149716	3		454	751	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234282	39234282	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	67	327	0	ENST00000402219.2:c.2563A>C	p.Ile855Leu	p.I855L	ENST00000402219	NM_005633.3	855	Att/Ctt	16/23	0.331073356149716	7	FACETS	0.597	0.516	0.684			1	SUBCLONAL	1	TRUE	NA	0.331073356149716	7		327	1240	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0049953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	125	328	0				ENST00000310581	NM_198253.2	-/1132			0.326782853383759	3	FACETS	0.852	0.782	0.924	1	0.982	1	CLONAL	3	TRUE	1	0.351474919953948	3		328	327	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0049953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	49	302	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.351474919953948	4	FACETS	0.88	0.747	1			1	CLONAL	1	TRUE	NA	0.351474919953948	4		302	428	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226589917	226589917	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	70	489	1	ENST00000366794.5:c.284C>A	p.Thr95Lys	p.T95K	ENST00000366794	NM_001618.3	95	aCa/aAa	2/23	0.351474919953948	4	FACETS	0.874	0.762	0.995	0.218	0.19	0.249	CLONAL	1	TRUE	0	0.351474919953948	4		490	616	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129464	64129465	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0049953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	119	968	0	ENST00000334205.4:c.896_897delinsTT	p.Pro299Leu	p.P299L	ENST00000334205	NM_003942.2	299	cCC/cTT	8/17	1	2	FACETS	0.864	0.78	0.952	0.864	0.78	0.952	CLONAL	1	TRUE	1	0.351474919953948	2		968	784	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335563	73335563	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	58	274	0	ENST00000377767.4:c.2608G>A	p.Glu870Lys	p.E870K	ENST00000377767	NM_014953.3	870	Gaa/Aaa	19/21	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.351474919953948	2		274	327	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0049958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	287	328	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.785486835040813	2		328	633	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0049958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	397	822	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.896	0.853	0.94	0.896	0.853	0.94	CLONAL	1	TRUE	1	0.785486835040813	2		822	1128	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949016	44949016	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	440	233	0	ENST00000377967.4:c.3577T>C	p.Trp1193Arg	p.W1193R	ENST00000377967	NM_021140.2	1193	Tgg/Cgg	25/29	0.714708266155495	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.785486835040813	2		233	496	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044473	47044473	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	699	349	0	ENST00000377604.3:c.1970G>C	p.Arg657Pro	p.R657P	ENST00000377604	NM_001204468.1	657	cGc/cCc	18/24	0.714708266155495	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.785486835040813	2		349	814	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101401	27101402	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	247	620	1	ENST00000324856.7:c.4689dup	p.Met1564HisfsTer8	p.M1564Hfs*8	ENST00000324856	NM_006015.4	1561	-/C	18/20	1	2	FACETS	0.813	0.762	0.864	0.813	0.762	0.864	CLONAL	1	TRUE	1	0.785486835040813	2		621	774	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0049960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	146	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.399739988761713	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.399739988761713	3		327	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0049960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	209	789	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	NA	2	FACETS	1	0.96	1			1	INDETERMINATE	2	TRUE	NA	0.399739988761713	2		789	507	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455075	50455075	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	21	403	0	ENST00000331340.3:c.622C>T	p.Arg208Ter	p.R208*	ENST00000331340	NM_006060.4	208	Cga/Tga	6/8	0.399739988761713	1	FACETS	0.306	0.235	0.387	0.306	0.235	0.387	SUBCLONAL	1	TRUE	0	0.399739988761713	1		403	275	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066713	77066713	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs201726311	NA	P-0049960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	25	260	0	ENST00000356341.3:c.772C>T	p.Arg258Ter	p.R258*	ENST00000356341	NM_002576.4	258	Cga/Tga	7/15	0.166153055182051	2	FACETS	0.532	0.421	0.659	0.266	0.21	0.33	INDETERMINATE	1	TRUE	0	0.399739988761713	2		260	235	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250808	99250808	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	28	484	0	ENST00000268035.6:c.112G>C	p.Asp38His	p.D38H	ENST00000268035	NM_000875.3	38	Gac/Cac	2/21	0.216275424262974	1	FACETS	0.385	0.308	0.472	0.385	0.308	0.472	INDETERMINATE	1	TRUE	0	0.399739988761713	1		484	291	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224152	39224152	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	60	403	0	ENST00000402219.2:c.2992G>T	p.Gly998Ter	p.G998*	ENST00000402219	NM_005633.3	998	Gga/Tga	19/23	1	2	FACETS	0.975	0.846	1	0.975	0.846	1	CLONAL	1	TRUE	1	0.399739988761713	2		403	308	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735455	40735455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1209632836	NA	P-0049960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	91	770	0	ENST00000373198.4:c.3418G>A	p.Ala1140Thr	p.A1140T	ENST00000373198	NM_133170.3	1140	Gcc/Acc	25/32	0.338993377564264	4	FACETS	0.971	0.863	1	0.486	0.431	0.544	CLONAL	1	TRUE	2	0.399739988761713	4		770	656	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	240533	240533	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	11	17	0	ENST00000264932.6:c.1493A>C	p.Lys498Thr	p.K498T	ENST00000264932	NM_004168.2	498	aAa/aCa	11/15	1	2	FACETS	0.917	0.698	1	1	0.924	1	CLONAL	3	TRUE	1	0.399739988761713	2		17	20	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069619	69069619	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	44	542	0	ENST00000288368.4:c.4294C>T	p.Gln1432Ter	p.Q1432*	ENST00000288368	NM_024870.2	1432	Cag/Tag	35/40	0.303410449627844	1	FACETS	0.89	0.755	1	0.89	0.755	1	CLONAL	1	TRUE	0	0.399739988761713	1		542	198	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0049963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	84	887	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	0.387289966690238	3	FACETS	0.834	0.752	0.918	1	0.973	1	CLONAL	3	TRUE	1	0.387289966690238	3		887	207	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878115	48878115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	10	259	0	ENST00000267163.4:c.68del	p.Pro23ArgfsTer42	p.P23Rfs*42	ENST00000267163	NM_000321.2	23	Ccg/cg	1/27	0.306995958663751	3	FACETS	0.545	0.372	0.761	0.182	0.124	0.254	SUBCLONAL	1	TRUE	0	0.387289966690238	3		259	113	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450399	50450399	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	44	520	0	ENST00000331340.3:c.583C>A	p.His195Asn	p.H195N	ENST00000331340	NM_006060.4	195	Cac/Aac	5/8	0.38309106600509	4	FACETS	1	0.862	1	1	0.862	1	CLONAL	2	TRUE	2	0.387289966690238	4		520	156	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0049976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	250	534	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.281411930910062	6	FACETS	1	0.977	1	0.715	0.673	0.758	CLONAL	4	TRUE	0	0.281411930910062	6		534	647	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775231	73775231	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1375	81	771	2	ENST00000254810.4:c.25C>A	p.Arg9Ser	p.R9S	ENST00000254810	NM_005324.3	9	Cgt/Agt	2/4	0.281411930910062	7	FACETS	0.674	0.591	0.763	0.096	0.084	0.109	SUBCLONAL	1	TRUE	0	0.281411930910062	7		773	1456	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552264	29552264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	71	491	0	ENST00000356175.3:c.1997C>T	p.Ser666Phe	p.S666F	ENST00000356175	NM_000267.3	666	tCt/tTt	17/57	0.281411930910062	4	FACETS	1	0.952	1	0.297	0.259	0.337	CLONAL	1	TRUE	0	0.281411930910062	4		491	545	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66777472	66777472	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	221	833	0	ENST00000307102.5:c.838G>T	p.Glu280Ter	p.E280*	ENST00000307102	NM_002755.3	280	Gaa/Taa	7/11	0.281411930910062	3	FACETS	0.945	0.88	1	0.945	0.88	1	CLONAL	2	TRUE	1	0.281411930910062	3		833	948	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579851	7579851	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	396	831	0	ENST00000269305.4:c.62del	p.Asp21AlafsTer23	p.D21Afs*23	ENST00000269305	NM_001126112.2	21	gAc/gc	2/11	0.225662496166016	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.281411930910062	3		831	987	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348484	56348484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	89	410	0	ENST00000348428.3:c.292G>A	p.Glu98Lys	p.E98K	ENST00000348428	NM_006785.3	98	Gaa/Aaa	2/17	0.104060894292596	4	FACETS	0.763	0.678	0.853	0.763	0.678	0.853	INDETERMINATE	2	TRUE	2	0.281411930910062	4		410	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0049977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	156	687	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.805	0.738	0.875	0.805	0.738	0.875	CLONAL	1	TRUE	1	0.490741636078201	2		688	790	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020768	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs926053251	NA	P-0049977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	57	544	0	ENST00000358127.4:c.77T>G	p.Val26Gly	p.V26G	ENST00000358127	NM_001280556.1	26	gTt/gGt	2/10	0.165123428763823	2	FACETS	0.283	0.242	0.328	0.142	0.121	0.164	INDETERMINATE	1	TRUE	0	0.490741636078201	2		544	820	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248998	55248999	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCAGCG	rs727504263	NA	P-0049977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	438	634	0	ENST00000275493.2:c.2300_2308dup	p.Ala767_Val769dup	p.A767_V769dup	ENST00000275493	NM_005228.3	767	atg/aTGGCCAGCGtg	20/28	0.305712900516557	6	FACETS	1	0.982	1	0.79	0.755	0.825	CLONAL	3	TRUE	2	0.490741636078201	6		634	1120	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	154	771	1	ENST00000269305.4:c.548C>A	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tAa	5/11	1	2	FACETS	0.79	0.724	0.86	0.79	0.724	0.86	SUBCLONAL	1	TRUE	1	0.490741636078201	2		772	794	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564979	226564979	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	258	444	0	ENST00000366794.5:c.1771del	p.Arg591ValfsTer5	p.R591Vfs*5	ENST00000366794	NM_001618.3	591	Cgt/gt	13/23	0.305712900516557	6	FACETS	1	0.982	1	0.561	0.526	0.597	CLONAL	2	TRUE	2	0.490741636078201	6		444	928	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105258972	105258972	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1192	93	912	0	ENST00000349310.3:c.9C>A	p.Asp3Glu	p.D3E	ENST00000349310	NM_001014432.1	3	gaC/gaA	3/15	0.227020953076	5	FACETS	0.512	0.454	0.575	0.171	0.151	0.192	INDETERMINATE	1	TRUE	2	0.490741636078201	5		912	1285	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0049978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	60	454	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.733	0.631	0.845	0.733	0.631	0.845	SUBCLONAL	1	FALSE	1	0.240679791204372	2		455	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0049978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	27	686	2	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	1	2	FACETS	0.373	0.295	0.462	0.373	0.295	0.462	SUBCLONAL	1	FALSE	1	0.240679791204372	2		688	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0049979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	589	656	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	NA	2	FACETS	0.981	0.946	1			1	INDETERMINATE	2	TRUE	NA	0.497631027457634	2		656	1207	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89871709	89871709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144560850	NA	P-0049979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1212	212	740	3	ENST00000389301.3:c.688G>A	p.Val230Ile	p.V230I	ENST00000389301	NM_000135.2	230	Gtc/Atc	7/43	0.498055320183835	3	FACETS	0.747	0.692	0.805	0.374	0.346	0.403	SUBCLONAL	1	TRUE	1	0.497631027457634	3		743	1424	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900946	114900946	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	342	611	0	ENST00000543371.1:c.556A>G	p.Asn186Asp	p.N186D	ENST00000543371	NM_001198531.1	186	Aac/Gac	6/14	0.425792394470152	2	FACETS	0.903	0.86	0.946	0.903	0.86	0.946	CLONAL	2	TRUE	0	0.497631027457634	2		611	761	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28886129	28886129	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0049979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	273	492	0	ENST00000282397.4:c.3492+1G>T		p.X1164_splice	ENST00000282397	NM_002019.4	1164			0.398957720234021	3	FACETS	1	0.989	1	0.77	0.73	0.811	CLONAL	2	TRUE	0	0.497631027457634	3		492	593	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537954	212537954	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	287	544	0	ENST00000342788.4:c.1651A>G	p.Ile551Val	p.I551V	ENST00000342788	NM_005235.2	551	Atc/Gtc	14/28	0.463571187252796	2	FACETS	0.936	0.888	0.984	0.936	0.888	0.984	CLONAL	2	TRUE	0	0.497631027457634	2		544	616	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564652	55564652	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	219	651	2	ENST00000288135.5:c.540T>A	p.His180Gln	p.H180Q	ENST00000288135	NM_000222.2	180	caT/caA	3/21	0.498055320183835	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.497631027457634	1		653	632	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270451	98270451	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	559	726	0	ENST00000331920.6:c.193A>C	p.Ile65Leu	p.I65L	ENST00000331920	NM_000264.3	65	Att/Ctt	1/24	0.498055320183835	3	FACETS	0.885	0.849	0.921	0.885	0.849	0.921	CLONAL	2	TRUE	1	0.497631027457634	3		726	1585	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	236	413	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.929	0.87	0.989	0.929	0.87	0.989	CLONAL	1	TRUE	1	0.673257823226185	2		413	755	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967173	134967173	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370164002	NA	P-0049980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	193	428	0	ENST00000398015.3:c.2512G>A	p.Glu838Lys	p.E838K	ENST00000398015	NM_004441.4	838	Gag/Aag	14/16	1	2	FACETS	0.906	0.842	0.971	0.906	0.842	0.971	CLONAL	1	TRUE	1	0.673257823226185	2		428	633	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178257	56178258	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	146	266	0	ENST00000399503.3:c.3236dup	p.Asn1079LysfsTer2	p.N1079Kfs*2	ENST00000399503	NM_005921.1	1077	tca/tcAa	14/20	1	2	FACETS	0.815	0.748	0.885	0.815	0.748	0.885	CLONAL	1	TRUE	1	0.673257823226185	2		266	532	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0049981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	68	349	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.29611190854695	1	FACETS	0.817	0.712	0.929	0.817	0.712	0.929	CLONAL	1	TRUE	0	0.29	1		349	491	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575209	48575209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767326	NA	P-0049981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	44	210	0	ENST00000342988.3:c.403C>T	p.Arg135Ter	p.R135*	ENST00000342988	NM_005359.5	135	Cga/Tga	3/12	0.29611190854695	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.29	1		210	232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578206	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs886039484	NA	P-0049981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	139	854	0	ENST00000269305.4:c.643A>G	p.Ser215Gly	p.S215G	ENST00000269305	NM_001126112.2	215	Agt/Ggt	6/11	0.29611190854695	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.29	1		854	768	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133523	55133523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142492533	NA	P-0049981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	85	591	1	ENST00000257290.5:c.827C>T	p.Thr276Met	p.T276M	ENST00000257290	NM_006206.4	276	aCg/aTg	6/23	1	2	FACETS	0.847	0.749	0.952	0.847	0.749	0.952	CLONAL	1	TRUE	1	0.29	2		592	692	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245865	46245865	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0049981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	48	412	0	ENST00000334344.6:c.3959C>G	p.Ser1320Ter	p.S1320*	ENST00000334344	NM_152641.2	1320	tCa/tGa	15/21	0.247967274763154	3	FACETS	1	0.933	1	0.592	0.503	0.689	CLONAL	1	TRUE	1	0.29	3		412	320	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732942	30732942	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	135	395	1	ENST00000295754.5:c.1555G>A	p.Glu519Lys	p.E519K	ENST00000295754	NM_003242.5	519	Gag/Aag	7/7	0.470893738256056	1	FACETS	0.996	0.913	1	0.996	0.913	1	CLONAL	1	TRUE	0	0.470893738256056	1		396	440	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007146	152007146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	141	402	0	ENST00000262189.6:c.754C>T	p.His252Tyr	p.H252Y	ENST00000262189	NM_170606.2	252	Cat/Tat	6/59	1	2	FACETS	0.789	0.72	0.862	0.789	0.72	0.862	SUBCLONAL	1	TRUE	1	0.470893738256056	2		402	759	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347947	347947	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763210434	NA	P-0049982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	461	1161	1	ENST00000262320.3:c.1559C>T	p.Ser520Leu	p.S520L	ENST00000262320	NM_003502.3	520	tCa/tTa	6/11	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.470893738256056	2		1162	1610	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197197	106197197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754174059	NA	P-0049982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	147	404	0	ENST00000380013.4:c.5530G>A	p.Asp1844Asn	p.D1844N	ENST00000380013	NM_001127208.2	1844	Gat/Aat	11/11	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.470893738256056	2		404	600	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323241	31323241	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	292	812	0	ENST00000412585.2:c.748C>A	p.Gln250Lys	p.Q250K	ENST00000412585	NM_005514.6	250	Cag/Aag	4/8	0.470893738256056	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.470893738256056	1		812	923	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864407	151864407	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	114	442	0	ENST00000262189.6:c.9574C>G	p.Gln3192Glu	p.Q3192E	ENST00000262189	NM_170606.2	3192	Caa/Gaa	42/59	1	2	FACETS	0.7	0.631	0.773	0.7	0.631	0.773	SUBCLONAL	1	TRUE	1	0.470893738256056	2		442	692	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223431	53223431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	257	879	0	ENST00000375401.3:c.3928G>A	p.Glu1310Lys	p.E1310K	ENST00000375401	NM_004187.3	1310	Gag/Aag	23/26	0.280779690126344	1	FACETS	0.682	0.638	0.728	0.682	0.638	0.728	INDETERMINATE	1	TRUE	0	0.470893738256056	1		879	1224	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574002	7574002	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs375338359	NA	P-0049983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	153	903	0	ENST00000269305.4:c.1025G>C	p.Arg342Pro	p.R342P	ENST00000269305	NM_001126112.2	342	cGa/cCa	10/11	0.288877459139551	1	FACETS	0.798	0.731	0.868	0.798	0.731	0.868	SUBCLONAL	1	TRUE	0	0.405025744081572	1		903	755	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870931	12870931	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	82	447	0	ENST00000228872.4:c.158A>T	p.Glu53Val	p.E53V	ENST00000228872	NM_004064.3	53	gAa/gTa	1/3	0.405025744081572	6	FACETS	0.944	0.832	1	0.236	0.208	0.267	CLONAL	1	TRUE	2	0.405025744081572	6		447	776	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7163108	7163109	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGTG	novel	NA	P-0049983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	132	816	0	ENST00000302850.5:c.1960_1963dup	p.Tyr655SerfsTer14	p.Y655Sfs*14	ENST00000302850	NM_000208.2	655	tac/tCACTac	9/22	NA	2	FACETS	0.684	0.62	0.751			1	INDETERMINATE	1	TRUE	NA	0.405025744081572	2		816	953	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963121	38963121	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	35	257	0	ENST00000357387.3:c.1423T>A	p.Cys475Ser	p.C475S	ENST00000357387	NM_152756.3	475	Tgt/Agt	17/38	0.334631471371396	4	FACETS	0.93	0.767	1	0.465	0.383	0.556	CLONAL	1	TRUE	2	0.405025744081572	4		257	261	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009366	69009366	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	146	665	0	ENST00000288368.4:c.2483C>G	p.Thr828Arg	p.T828R	ENST00000288368	NM_024870.2	828	aCa/aGa	22/40	0.388293415722944	4	FACETS	1	0.976	1	0.594	0.542	0.649	CLONAL	1	TRUE	2	0.405025744081572	4		665	852	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	57	364	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.160866537336066	3	FACETS	0.75	0.645	0.864	0.75	0.645	0.864	SUBCLONAL	2	TRUE	1	0.19	3		364	438	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	77	390	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.19	2		392	651	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	162	825	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.92	0.844	0.999	1	0.991	1	CLONAL	2	TRUE	1	0.19	2		829	927	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	104	454	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.974	0.875	1	1	0.987	1	CLONAL	2	TRUE	1	0.19	2		459	562	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324139	31324139	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs151341241	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	275	697	1	ENST00000412585.2:c.424T>C	p.Tyr142His	p.Y142H	ENST00000412585	NM_005514.6	142	Tac/Cac	3/8	0.160866537336066	3	FACETS	0.893	0.841	0.947	1	0.995	1	CLONAL	4	TRUE	1	0.19	3		698	887	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	89	388	4	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	1	0.891	1	1	0.986	1	CLONAL	2	TRUE	1	0.19	2		392	468	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214058	36214058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1385766471	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	240	821	0	ENST00000222270.7:c.2884C>T	p.Arg962Cys	p.R962C	ENST00000222270	NM_014727.1	962	Cgc/Tgc	6/37	1	2	FACETS	1	0.966	1	1	0.995	1	CLONAL	2	TRUE	1	0.19	2		821	1195	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	93	846	6	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	1	2	FACETS	0.832	0.737	0.933	0.832	0.737	0.933	CLONAL	1	TRUE	1	0.19	2		852	1177	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	118	461	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.942	0.852	1	1	0.988	1	CLONAL	2	TRUE	1	0.19	2		461	659	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429978	78429978	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	61	241	0	ENST00000370768.2:c.901del	p.Ile301TyrfsTer22	p.I301Yfs*22	ENST00000370768	NM_003902.3	301	Ata/ta	11/20	1	2	FACETS	0.912	0.791	1	1	0.977	1	CLONAL	2	TRUE	1	0.19	2		241	352	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434367	121434367	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	85	654	3	ENST00000257555.6:c.1136del	p.Pro379LeufsTer5	p.P379Lfs*5	ENST00000257555		377	ctC/ct	6/10	0.3	3	FACETS	0.887	0.781	1	0.443	0.39	0.5	CLONAL	1	TRUE	1	0.19	3		657	1105	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943641	9943641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	129	547	0	ENST00000330684.3:c.1300G>A	p.Val434Met	p.V434M	ENST00000330684	NM_001134407.1	434	Gtg/Atg	5/13	1	2	FACETS	0.94	0.854	1	1	0.989	1	CLONAL	2	TRUE	1	0.19	2		547	722	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070349	37070349	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs63750855	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	83	369	0	ENST00000231790.2:c.1489del	p.Arg497GlyfsTer11	p.R497Gfs*11	ENST00000231790	NM_000249.3	495	aCc/ac	13/19	1	2	FACETS	0.877	0.777	0.984	1	0.982	1	CLONAL	2	TRUE	1	0.19	2		369	498	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406317	406318	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	60	441	0	ENST00000399788.2:c.4123dup	p.Cys1375LeufsTer2	p.C1375Lfs*2	ENST00000399788	NM_001042603.1	1375	tgt/tTgt	25/28	0.127386113520568	3	FACETS	1	0.866	1			1	CLONAL	1	TRUE	NA	0.19	3		441	687	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907692	111907692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775080943	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	47	313	0	ENST00000393256.3:c.466G>A	p.Gly156Arg	p.G156R	ENST00000393256	NM_006538.4	156	Gga/Aga	3/4	1	2	FACETS	0.885	0.746	1	0.885	0.746	1	CLONAL	1	TRUE	1	0.19	2		313	559	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533905	63533905	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	131	627	0	ENST00000307078.5:c.1249del	p.Ala417ArgfsTer41	p.A417Rfs*41	ENST00000307078	NM_004655.3	417	Gcg/cg	6/11	1	2	FACETS	0.916	0.832	1	1	0.989	1	CLONAL	2	TRUE	1	0.19	2		627	753	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	110	273	0	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	0.160866537336066	3	FACETS	0.921	0.832	1	1	0.981	1	CLONAL	3	TRUE	1	0.19	3		273	459	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354008	15354008	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	25	286	0	ENST00000263377.2:c.2872del	p.Leu958CysfsTer110	p.L958Cfs*110	ENST00000263377	NM_058243.2	958	Ctg/tg	14/20	1	2	FACETS	0.914	0.722	1	0.914	0.722	1	CLONAL	1	TRUE	1	0.19	2		286	288	SUCCESS
ATR	545	MSKCC	GRCh37	3	142257448	142257448	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs974313531	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	72	280	0	ENST00000350721.4:c.3601C>T	p.Arg1201Cys	p.R1201C	ENST00000350721	NM_001184.3	1201	Cgc/Tgc	19/47	1	2	FACETS	0.839	0.74	0.944	1	0.985	1	CLONAL	3	TRUE	1	0.19	2		280	301	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562747	29562747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137854556	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	65	352	1	ENST00000356175.3:c.3827G>A	p.Arg1276Gln	p.R1276Q	ENST00000356175	NM_000267.3	1276	cGa/cAa	28/57	1	2	FACETS	0.864	0.752	0.984	1	0.977	1	CLONAL	2	TRUE	1	0.19	2		353	396	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007332	143007332	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	57	290	0	ENST00000262992.4:c.2452del	p.Arg818GlufsTer4	p.R818Efs*4	ENST00000262992	NM_001101669.1	818	Aga/ga	22/24	1	2	FACETS	0.923	0.797	1	1	0.976	1	CLONAL	2	TRUE	1	0.19	2		290	325	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	175	800	8	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	0.867	0.798	0.94	1	0.991	1	CLONAL	2	TRUE	1	0.19	2		808	1062	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	220	740	9	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	2	TRUE	NA	0.19	2		749	1091	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890149	76890150	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	38	429	2	ENST00000373344.5:c.4744dup	p.Thr1582AsnfsTer19	p.T1582Nfs*19	ENST00000373344	NM_000489.3	1582	aca/aAca	17/35	1	2	FACETS	0.755	0.623	0.902	0.755	0.623	0.902	CLONAL	1	TRUE	1	0.19	2		431	530	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455144	50455144	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	99	369	0	ENST00000331340.3:c.691G>A	p.Gly231Ser	p.G231S	ENST00000331340	NM_006060.4	231	Ggc/Agc	6/8	0.160866537336066	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.19	3		369	474	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	105	428	1	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	1	0.952	1	1	0.989	1	CLONAL	2	TRUE	1	0.19	2		429	504	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	56	239	0	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	1	2	FACETS	0.88	0.758	1	1	0.974	1	CLONAL	2	TRUE	1	0.19	2		239	335	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017578	112017578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	59	396	1	ENST00000368678.4:c.935C>T	p.Ala312Val	p.A312V	ENST00000368678		312	gCg/gTg	9/13	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.19	2		397	605	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931452	131931453	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	77	336	0	ENST00000265335.6:c.2164_2165del	p.Lys722GlyfsTer5	p.K722Gfs*5	ENST00000265335		719	ctAAaa/ctaa	13/25	1	2	FACETS	0.988	0.872	1	1	0.983	1	CLONAL	2	TRUE	1	0.19	2		336	410	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149799	202149799	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	44	484	0	ENST00000358485.4:c.1245del	p.Phe415LeufsTer26	p.F415Lfs*26	ENST00000358485	NM_001080125.1	414	Ttt/tt	8/9	1	2	FACETS	0.723	0.605	0.853	0.723	0.605	0.853	SUBCLONAL	1	TRUE	1	0.19	2		484	641	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	106	488	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.975	0.877	1	1	0.987	1	CLONAL	2	TRUE	1	0.19	2		488	572	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820836	36820836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1452017656	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	126	476	0	ENST00000373129.3:c.541G>A	p.Val181Met	p.V181M	ENST00000373129	NM_032017.1	181	Gtg/Atg	6/12	1	2	FACETS	0.991	0.899	1	1	0.99	1	CLONAL	2	TRUE	1	0.19	2		476	669	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116262	209116263	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs754375602	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	28	216	0	ENST00000345146.2:c.13dup	p.Ile5AsnfsTer13	p.I5Nfs*13	ENST00000345146	NM_005896.2	5	atc/aAtc	3/10	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.19	2		216	218	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383944	84383944	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	42	401	1	ENST00000321945.7:c.908del	p.Asn303IlefsTer17	p.N303Ifs*17	ENST00000321945	NM_139076.2	303	aAt/at	9/9	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.19	2		402	407	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221206	5221206	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200191658	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	170	731	0	ENST00000357368.4:c.3260C>T	p.Thr1087Met	p.T1087M	ENST00000357368	NM_002850.3	1087	aCg/aTg	20/38	1	2	FACETS	0.905	0.831	0.981	1	0.991	1	CLONAL	2	TRUE	1	0.19	2		731	989	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426645	47426645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	59	646	0	ENST00000377045.4:c.890G>A	p.Arg297Gln	p.R297Q	ENST00000377045	NM_001654.4	297	cGg/cAg	10/16	1	2	FACETS	0.92	0.791	1	0.92	0.791	1	CLONAL	1	TRUE	1	0.19	2		646	675	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524567	103524568	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs759551120	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	45	277	0	ENST00000355739.4:c.2705dup	p.Asn902LysfsTer7	p.N902Kfs*7	ENST00000355739	NM_000123.3	900	caa/cAaa	13/15	0.127386113520568	3	FACETS	0.986	0.835	1			1	CLONAL	2	TRUE	NA	0.19	3		277	263	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333105	70333105	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755974529	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	166	561	3	ENST00000373644.4:c.1010C>T	p.Ala337Val	p.A337V	ENST00000373644	NM_030625.2	337	gCg/gTg	2/12	1	2	FACETS	1	0.973	1	1	0.993	1	CLONAL	2	TRUE	1	0.19	2		564	775	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	205	399	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.981	1	1	0.995	1	CLONAL	3	TRUE	1	0.19	2		403	631	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	202	903	1	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.917	0.848	0.987	1	0.993	1	CLONAL	2	TRUE	1	0.19	2		904	1160	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164163	108164164	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs864622164	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	27	176	0	ENST00000278616.4:c.4741dup	p.Ile1581AsnfsTer5	p.I1581Nfs*5	ENST00000278616	NM_000051.3	1579	caa/cAaa	31/63	0.160866537336066	3	FACETS	1	0.912	1	0.643	0.514	0.789	CLONAL	1	TRUE	1	0.19	3		176	242	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434182	12434182	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776687	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	35	373	1	ENST00000287820.6:c.556del	p.Ser186ValfsTer47	p.S186Vfs*47	ENST00000287820	NM_015869.4	184	Aaa/aa	4/7	1	2	FACETS	0.757	0.619	0.911	0.757	0.619	0.911	CLONAL	1	TRUE	1	0.19	2		374	487	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21553849	21553849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868208801	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	136	401	0	ENST00000382592.4:c.2753C>T	p.Pro918Leu	p.P918L	ENST00000382592	NM_014572.2	918	cCc/cTc	7/8	1	2	FACETS	0.956	0.87	1	1	0.99	1	CLONAL	2	TRUE	1	0.19	2		401	749	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435833	56435834	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	121	567	0	ENST00000407977.2:c.1303_1304insA	p.Leu435HisfsTer8	p.L435Hfs*8	ENST00000407977		435	cta/cAta	9/10	1	2	FACETS	0.892	0.807	0.982	1	0.988	1	CLONAL	2	TRUE	1	0.19	2		567	714	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	59	683	1	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	0.3	3	FACETS	0.876	0.753	1	0.438	0.376	0.506	CLONAL	1	TRUE	1	0.19	3		684	776	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629776	187629776	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	49	486	0	ENST00000441802.2:c.1206del	p.Phe402LeufsTer12	p.F402Lfs*12	ENST00000441802	NM_005245.3	402	ttT/tt	2/27	1	2	FACETS	0.97	0.821	1	0.97	0.821	1	CLONAL	1	TRUE	1	0.19	2		486	532	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323133	31323133	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	200	764	2	ENST00000412585.2:c.856C>T	p.Gln286Ter	p.Q286*	ENST00000412585	NM_005514.6	286	Cag/Tag	4/8	0.160866537336066	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.19	3		766	1002	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435199	49435199	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	184	708	2	ENST00000301067.7:c.6354del	p.Ala2119LeufsTer25	p.A2119Lfs*25	ENST00000301067	NM_003482.3	2118	ccC/cc	31/54	0.3	3	FACETS	0.885	0.818	0.954	1	0.987	1	CLONAL	3	TRUE	1	0.19	3		710	799	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158026	27158026	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	123	531	0	ENST00000380036.4:c.255del	p.Val86LeufsTer31	p.V86Lfs*31	ENST00000380036	NM_000459.3	84	Aaa/aa	2/23	1	2	FACETS	0.882	0.798	0.97	1	0.988	1	CLONAL	2	TRUE	1	0.19	2		531	734	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279760	46279760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757419594	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	90	420	1	ENST00000371998.3:c.3686G>A	p.Arg1229His	p.R1229H	ENST00000371998		1229	cGc/cAc	20/23	1	2	FACETS	0.796	0.707	0.89	1	0.981	1	SUBCLONAL	2	TRUE	1	0.19	2		421	595	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798457	32798457	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	182	751	0	ENST00000374899.4:c.1399del	p.Val467LeufsTer2	p.V467Lfs*2	ENST00000374899	NM_018833.2	467	Gtt/tt	8/12	0.160866537336066	3	FACETS	0.902	0.831	0.976	0.902	0.831	0.976	CLONAL	2	TRUE	1	0.19	3		751	1163	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180035975	180035975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138599624	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	149	639	2	ENST00000261937.6:c.3886G>A	p.Gly1296Ser	p.G1296S	ENST00000261937	NM_182925.4	1296	Ggc/Agc	29/30	1	2	FACETS	0.855	0.781	0.933	1	0.989	1	CLONAL	2	TRUE	1	0.19	2		641	917	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216188	36216189	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	173	773	0	ENST00000222270.7:c.3602dup	p.Met1202AspfsTer22	p.M1202Dfs*22	ENST00000222270	NM_014727.1	1199	ggc/ggCc	11/37	1	2	FACETS	0.885	0.814	0.959	1	0.991	1	CLONAL	2	TRUE	1	0.19	2		773	1029	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795483	42795483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751769419	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	158	708	0	ENST00000575354.2:c.2563G>A	p.Gly855Ser	p.G855S	ENST00000575354	NM_015125.3	855	Ggc/Agc	10/20	1	2	FACETS	0.935	0.857	1	1	0.991	1	CLONAL	2	TRUE	1	0.19	2		708	889	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068421	26068421	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	47	267	0	ENST00000435504.4:c.69del	p.Lys23AsnfsTer7	p.K23Nfs*7	ENST00000435504		23	aaA/aa	2/13	1	2	FACETS	0.883	0.75	1	1	0.97	1	CLONAL	2	TRUE	1	0.19	2		267	280	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420309	88420309	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs878997142	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	93	377	0	ENST00000360948.2:c.2377C>T	p.Arg793Ter	p.R793*	ENST00000360948	NM_001012338.2	793	Cga/Tga	19/19	0.3	1	FACETS	0.816	0.727	0.91	1	0.983	1	CLONAL	2	TRUE	0	0.19	1		377	543	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422091	81422091	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	133	538	0	ENST00000298171.2:c.67G>T	p.Gly23Trp	p.G23W	ENST00000298171	NM_000369.2	23	Ggg/Tgg	1/10	1	2	FACETS	0.94	0.854	1	1	0.99	1	CLONAL	2	TRUE	1	0.19	2		538	745	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050701	69050701	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	51	331	1	ENST00000288368.4:c.4036G>A	p.Glu1346Lys	p.E1346K	ENST00000288368	NM_024870.2	1346	Gaa/Aaa	33/40	1	2	FACETS	0.789	0.674	0.915	1	0.967	1	CLONAL	2	TRUE	1	0.19	2		332	340	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783767	50783767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375455772	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	93	455	0	ENST00000398568.2:c.158G>A	p.Arg53His	p.R53H	ENST00000398568	NM_001042412.1	53	cGt/cAt	3/18	1	2	FACETS	1	0.895	1	1	0.986	1	CLONAL	2	TRUE	1	0.19	2		455	488	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566484	139566484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	168	911	1	ENST00000308874.7:c.743G>A	p.Gly248Asp	p.G248D	ENST00000308874		248	gGc/gAc	9/10	NA	2	FACETS	0.853	0.783	0.926			1	INDETERMINATE	2	TRUE	NA	0.19	2		912	1037	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665362	138665362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	121	822	0	ENST00000330315.3:c.203G>A	p.Arg68His	p.R68H	ENST00000330315	NM_023067.3	68	cGc/cAc	1/1	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.19	2		822	1149	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370763	55370763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757830070	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	174	558	2	ENST00000297316.4:c.65C>T	p.Ala22Val	p.A22V	ENST00000297316	NM_022454.3	22	gCg/gTg	1/2	1	2	FACETS	1	0.951	1	1	0.993	1	CLONAL	2	TRUE	1	0.19	2		560	877	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246297	46246297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770601353	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	43	310	1	ENST00000334344.6:c.4391G>A	p.Arg1464His	p.R1464H	ENST00000334344	NM_152641.2	1464	cGc/cAc	15/21	0.3	3	FACETS	1	0.908	1	0.563	0.472	0.665	CLONAL	1	TRUE	1	0.19	3		311	440	SUCCESS
AR	367	MSKCC	GRCh37	X	66905905	66905905	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886041128	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	72	351	0	ENST00000374690.3:c.1822C>T	p.Arg608Ter	p.R608*	ENST00000374690	NM_000044.3	608	Cga/Tga	3/8	1	2	FACETS	1	0.931	1	1	0.984	1	CLONAL	2	TRUE	1	0.19	2		351	349	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557981	187557981	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	90	382	0	ENST00000441802.2:c.3730C>T	p.Gln1244Ter	p.Q1244*	ENST00000441802	NM_005245.3	1244	Cag/Tag	5/27	1	2	FACETS	1	0.942	1	1	0.987	1	CLONAL	2	TRUE	1	0.19	2		382	436	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800223	32800223	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	152	426	0	ENST00000374899.4:c.1159del	p.Val387CysfsTer4	p.V387Cfs*4	ENST00000374899	NM_018833.2	387	Gtg/tg	7/12	0.160866537336066	3	FACETS	0.931	0.855	1	1	0.987	1	CLONAL	3	TRUE	1	0.19	3		426	627	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981891	70981892	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	95	807	0	ENST00000276594.2:c.204dup	p.Phe69LeufsTer59	p.F69Lfs*59	ENST00000276594	NM_024504.3	68	-/C	2/8	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.19	2		807	961	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598802	28598802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	97	729	0	ENST00000253063.3:c.362C>T	p.Ala121Val	p.A121V	ENST00000253063	NM_031459.4	121	gCc/gTc	4/10	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.19	2		729	932	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546409	46546410	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	82	302	0	ENST00000262741.5:c.119dup	p.Pro41AlafsTer3	p.P41Afs*3	ENST00000262741	NM_003629.3	40	aag/aaAg	2/10	1	2	FACETS	1	0.945	1	1	0.986	1	CLONAL	2	TRUE	1	0.19	2		302	389	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150549952	150549952	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	53	187	0	ENST00000369026.2:c.952T>C	p.Phe318Leu	p.F318L	ENST00000369026	NM_021960.4	318	Ttc/Ctc	3/3	1	2	FACETS	0.816	0.699	0.942	1	0.97	1	CLONAL	2	TRUE	1	0.19	2		187	342	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609963	43609963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777122776	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	207	782	0	ENST00000355710.3:c.1915G>A	p.Ala639Thr	p.A639T	ENST00000355710	NM_020975.4	639	Gca/Aca	11/20	1	2	FACETS	0.968	0.897	1	1	0.993	1	CLONAL	2	TRUE	1	0.19	2		782	1126	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114901006	114901006	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	176	551	0	ENST00000543371.1:c.616T>C	p.Tyr206His	p.Y206H	ENST00000543371	NM_001198531.1	206	Tac/Cac	6/14	1	2	FACETS	1	0.948	1	1	0.993	1	CLONAL	2	TRUE	1	0.19	2		551	894	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127679	64127679	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	283	889	2	ENST00000334205.4:c.172G>A	p.Ala58Thr	p.A58T	ENST00000334205	NM_003942.2	58	Gcg/Acg	3/17	0.160866537336066	3	FACETS	0.834	0.782	0.887	1	0.99	1	CLONAL	3	TRUE	1	0.19	3		891	1304	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196045	108196045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1476384636	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	40	280	0	ENST00000278616.4:c.6581C>T	p.Thr2194Ile	p.T2194I	ENST00000278616	NM_000051.3	2194	aCa/aTa	46/63	0.160866537336066	3	FACETS	0.823	0.688	0.972	0.823	0.688	0.972	CLONAL	2	TRUE	1	0.19	3		280	280	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499604	18499604	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	84	409	0	ENST00000266497.5:c.1459T>C	p.Ser487Pro	p.S487P	ENST00000266497		487	Tcc/Ccc	10/31	0.3	3	FACETS	0.953	0.844	1	0.953	0.844	1	CLONAL	2	TRUE	1	0.19	3		409	508	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222558	69222558	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	54	282	0	ENST00000462284.1:c.531T>A	p.Asn177Lys	p.N177K	ENST00000462284	NM_002392.5	177	aaT/aaA	8/11	0.3	3	FACETS	0.879	0.754	1	0.879	0.754	1	CLONAL	2	TRUE	1	0.19	3		282	354	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233090	69233090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs577942747	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	124	276	0	ENST00000462284.1:c.955C>T	p.Pro319Ser	p.P319S	ENST00000462284	NM_002392.5	319	Ccc/Tcc	11/11	0.3	3	FACETS	1	0.959	1	1	0.988	1	CLONAL	3	TRUE	1	0.19	3		276	437	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120785317	120785317	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	240	591	1	ENST00000257552.2:c.791C>T	p.Ala264Val	p.A264V	ENST00000257552	NM_002442.3	264	gCc/gTc	12/15	0.3	3	FACETS	1	0.974	1	1	0.993	1	CLONAL	3	TRUE	1	0.19	3		592	858	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437633	110437635	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	157	748	1	ENST00000375856.3:c.766_768del	p.Phe256del	p.F256del	ENST00000375856	NM_003749.2	256	TTC/-	1/2	0.127386113520568	3	FACETS	0.798	0.73	0.87			1	SUBCLONAL	2	TRUE	NA	0.19	3		749	1134	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041581	42041581	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	62	494	0	ENST00000219905.7:c.5776T>G	p.Ser1926Ala	p.S1926A	ENST00000219905	NM_001164273.1	1926	Tca/Gca	17/24	0.3	1	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	0	0.19	1		494	560	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041584	42041584	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	119	498	0	ENST00000219905.7:c.5779G>T	p.Gly1927Ter	p.G1927*	ENST00000219905	NM_001164273.1	1927	Gga/Tga	17/24	0.3	1	FACETS	1	0.912	1	1	0.989	1	CLONAL	2	TRUE	0	0.19	1		498	563	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857030	9857030	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	19	227	0	ENST00000330684.3:c.4371G>A	p.Met1457Ile	p.M1457I	ENST00000330684	NM_001134407.1	1457	atG/atA	13/13	1	2	FACETS	0.901	0.686	1	0.901	0.686	1	CLONAL	1	TRUE	1	0.19	2		227	222	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81941374	81941374	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	102	423	0	ENST00000359376.3:c.1552C>G	p.Pro518Ala	p.P518A	ENST00000359376	NM_002661.3	518	Ccc/Gcc	16/33	1	2	FACETS	0.98	0.879	1	1	0.987	1	CLONAL	2	TRUE	1	0.19	2		423	548	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831393	89831393	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755207440	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	81	608	0	ENST00000389301.3:c.2683C>T	p.Pro895Ser	p.P895S	ENST00000389301	NM_000135.2	895	Ccc/Tcc	28/43	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.19	2		608	829	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210795	2210795	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371162200	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	66	596	0	ENST00000398665.3:c.1292C>T	p.Thr431Ile	p.T431I	ENST00000398665	NM_032482.2	431	aCt/aTt	14/28	1	2	FACETS	0.852	0.738	0.976	0.852	0.738	0.976	CLONAL	1	TRUE	1	0.19	2		596	815	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303200	15303200	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	188	888	0	ENST00000263388.2:c.328C>A	p.Arg110Ser	p.R110S	ENST00000263388	NM_000435.2	110	Cgt/Agt	3/33	1	2	FACETS	0.834	0.769	0.901	1	0.991	1	CLONAL	2	TRUE	1	0.19	2		888	1187	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383083	42383083	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	57	296	0	ENST00000221972.3:c.103A>G	p.Met35Val	p.M35V	ENST00000221972	NM_021601.3	35	Atg/Gtg	2/5	1	2	FACETS	0.833	0.718	0.958	1	0.973	1	CLONAL	2	TRUE	1	0.19	2		296	360	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907684	111907684	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	51	323	1	ENST00000393256.3:c.458G>T	p.Arg153Leu	p.R153L	ENST00000393256	NM_006538.4	153	cGg/cTg	3/4	1	2	FACETS	0.907	0.77	1	0.907	0.77	1	CLONAL	1	TRUE	1	0.19	2		324	592	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713379	40713379	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	133	730	0	ENST00000373198.4:c.4136T>A	p.Leu1379Gln	p.L1379Q	ENST00000373198	NM_133170.3	1379	cTg/cAg	30/32	1	2	FACETS	0.793	0.72	0.87	1	0.987	1	SUBCLONAL	2	TRUE	1	0.19	2		730	883	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114184	73114184	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	72	353	0	ENST00000356692.5:c.820G>T	p.Gly274Ter	p.G274*	ENST00000356692		274	Gga/Tga	8/9	1	2	FACETS	0.846	0.742	0.958	1	0.979	1	CLONAL	2	TRUE	1	0.19	2		353	448	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480493	89480493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs34437982	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	61	233	0	ENST00000336596.2:c.2330C>T	p.Ala777Val	p.A777V	ENST00000336596	NM_005233.5	777	gCt/gTt	13/17	1	2	FACETS	0.899	0.78	1	1	0.977	1	CLONAL	2	TRUE	1	0.19	2		233	357	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749546	41749546	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	123	496	0	ENST00000226382.2:c.249del	p.Tyr83Ter	p.Y83*	ENST00000226382	NM_003924.3	83	taC/ta	2/3	1	2	FACETS	0.921	0.834	1	1	0.988	1	CLONAL	2	TRUE	1	0.19	2		496	703	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213911	66213911	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	17	304	0	ENST00000273854.3:c.2519T>A	p.Ile840Asn	p.I840N	ENST00000273854	NM_004439.5	840	aTt/aAt	15/18	1	2	FACETS	0.615	0.459	0.801	0.615	0.459	0.801	SUBCLONAL	1	TRUE	1	0.19	2		304	291	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525088	187525088	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	39	372	0	ENST00000441802.2:c.10592T>C	p.Ile3531Thr	p.I3531T	ENST00000441802	NM_005245.3	3531	aTt/aCt	19/27	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.19	2		372	380	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	218507	218507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	59	203	1	ENST00000264932.6:c.37G>A	p.Ala13Thr	p.A13T	ENST00000264932	NM_004168.2	13	Gct/Act	1/15	1	2	FACETS	1	0.884	1	1	0.979	1	CLONAL	2	TRUE	1	0.19	2		204	304	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500876	149500876	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	131	530	0	ENST00000261799.4:c.2354G>T	p.Arg785Met	p.R785M	ENST00000261799	NM_002609.3	785	aGg/aTg	17/23	1	2	FACETS	0.924	0.84	1	1	0.989	1	CLONAL	2	TRUE	1	0.19	2		530	746	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041151	112041151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1294520439	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	73	483	0	ENST00000368678.4:c.104C>T	p.Thr35Ile	p.T35I	ENST00000368678		35	aCc/aTc	3/13	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.19	2		483	708	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340337	116340337	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	57	203	0	ENST00000397752.3:c.1199G>T	p.Arg400Met	p.R400M	ENST00000397752	NM_000245.2	400	aGg/aTg	2/21	0.160866537336066	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.19	3		203	263	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359930	87359930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	27	275	0	ENST00000277120.3:c.1238G>A	p.Arg413Lys	p.R413K	ENST00000277120		413	aGa/aAa	11/19	1	2	FACETS	0.636	0.505	0.786	0.636	0.505	0.786	SUBCLONAL	1	TRUE	1	0.19	2		275	447	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139818373	139818373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754210099	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	225	729	1	ENST00000247668.2:c.1208G>A	p.Arg403Gln	p.R403Q	ENST00000247668	NM_021138.3	403	cGa/cAa	10/11	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	2	TRUE	NA	0.19	2		730	1069	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841030	15841030	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	64	625	0	ENST00000307771.7:c.1114G>A	p.Asp372Asn	p.D372N	ENST00000307771	NM_005089.3	372	Gac/Aac	11/11	1	2	FACETS	0.791	0.683	0.908	0.791	0.683	0.908	CLONAL	1	TRUE	1	0.19	2		625	852	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205159	123205161	+	inframe_deletion	In_Frame_Del	DEL	ATA	ATA	-	novel	NA	P-0049984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	20	313	0	ENST00000218089.9:c.2525_2527del	p.Asn842del	p.N842del	ENST00000218089	NM_001042749.1	840	gATAat/gat	25/35	1	2	FACETS	0.627	0.479	0.8	0.627	0.479	0.8	SUBCLONAL	1	TRUE	1	0.19	2		313	336	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0049986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	15	842	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		843	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0049987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	456	626	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.554499045164074	2	FACETS	0.913	0.878	0.947	0.913	0.878	0.947	CLONAL	2	TRUE	0	0.60196344566026	2		626	830	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413909	139413909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376104770	NA	P-0049987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1484	196	882	0	ENST00000277541.6:c.851C>T	p.Pro284Leu	p.P284L	ENST00000277541	NM_017617.3	284	cCg/cTg	5/34	0.302263677431416	5	FACETS	0.738	0.68	0.798			1	INDETERMINATE	1	TRUE	NA	0.60196344566026	5		882	1680	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107152	27107152	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	484	662	0	ENST00000324856.7:c.6763G>T	p.Glu2255Ter	p.E2255*	ENST00000324856	NM_006015.4	2255	Gaa/Taa	20/20	NA	2	FACETS	0.907	0.874	0.941			1	INDETERMINATE	2	TRUE	NA	0.60196344566026	2		662	886	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218623	98218623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778629	NA	P-0049987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	103	582	0	ENST00000331920.6:c.3241G>A	p.Val1081Met	p.V1081M	ENST00000331920	NM_000264.3	1081	Gtg/Atg	19/24	0.206581232423245	3	FACETS	0.502	0.448	0.559	0.167	0.149	0.187	INDETERMINATE	1	TRUE	0	0.60196344566026	3		582	887	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11270881	11270881	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	74	348	0	ENST00000361445.4:c.3644G>C	p.Arg1215Thr	p.R1215T	ENST00000361445	NM_004958.3	1215	aGa/aCa	24/58	0.548941089640416	3	FACETS	0.579	0.508	0.656	0.193	0.169	0.219	SUBCLONAL	1	TRUE	0	0.60196344566026	3		348	552	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261115	16261115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1055178218	NA	P-0049987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	92	641	2	ENST00000375759.3:c.8380G>A	p.Asp2794Asn	p.D2794N	ENST00000375759	NM_015001.2	2794	Gac/Aac	11/15	0.548941089640416	3	FACETS	0.43	0.381	0.483	0.143	0.127	0.161	SUBCLONAL	1	TRUE	0	0.60196344566026	3		643	924	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69103958	69103958	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1563581001	NA	P-0049987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	328	468	0	ENST00000288368.4:c.4348G>A	p.Ala1450Thr	p.A1450T	ENST00000288368	NM_024870.2	1450	Gca/Aca	36/40	0.364996938327472	5	FACETS	0.897	0.852	0.941	0.897	0.852	0.941	CLONAL	3	TRUE	2	0.60196344566026	5		468	771	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929092	44929092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	132	531	0	ENST00000377967.4:c.2192G>A	p.Ser731Asn	p.S731N	ENST00000377967	NM_021140.2	731	aGc/aAc	17/29	0.33739749081959	4	FACETS	0.67	0.607	0.736			1	INDETERMINATE	1	TRUE	NA	0.60196344566026	4		531	1049	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	212	468	0				ENST00000310581	NM_198253.2	-/1132			0.468296936715596	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	1	0.482760480311133	4		468	400	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0049988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	160	558	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	1	2	FACETS	0.985	0.906	1	0.985	0.906	1	CLONAL	1	TRUE	1	0.482760480311133	2		558	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0049988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	132	155	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	1	2	FACETS	0.982	0.895	1	0.982	0.895	1	CLONAL	1	TRUE	1	0.482760480311133	2		155	557	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119789	70119789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778047936	NA	P-0049988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	30	161	0	ENST00000245479.2:c.791G>A	p.Arg264Lys	p.R264K	ENST00000245479	NM_000346.3	264	aGa/aAa	3/3	0.482760480311133	2	FACETS	0.22	0.177	0.27	0.11	0.088	0.135	SUBCLONAL	1	TRUE	0	0.482760480311133	2		161	564	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271150	38271150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758677681	NA	P-0049988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	127	158	0	ENST00000425967.3:c.2558G>A	p.Arg853His	p.R853H	ENST00000425967	NM_001174067.1	853	cGc/cAc	19/19	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.482760480311133	2		158	428	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786039	3786039	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	126	123	0	ENST00000262367.5:c.4726G>T	p.Glu1576Ter	p.E1576*	ENST00000262367	NM_004380.2	1576	Gag/Tag	28/31	0.388028919571151	1	FACETS	0.816	0.744	0.892	0.816	0.744	0.892	CLONAL	1	TRUE	0	0.482760480311133	1		123	485	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520447	176520447	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	65	217	0	ENST00000292408.4:c.1292C>G	p.Ser431Cys	p.S431C	ENST00000292408	NM_213647.1	431	tCc/tGc	10/18	1	2	FACETS	0.387	0.335	0.444	0.387	0.335	0.444	SUBCLONAL	1	TRUE	1	0.482760480311133	2		217	695	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652247	36652251	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGG	AGGGG	-	novel	NA	P-0049988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	177	182	0	ENST00000244741.5:c.371_375del	p.Gly124AlafsTer3	p.G124Afs*3	ENST00000244741	NM_000389.4	123	tcAGGGGag/tcag	2/3	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.482760480311133	2		182	713	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528564	157528564	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	75	162	0	ENST00000346085.5:c.6289G>T	p.Asp2097Tyr	p.D2097Y	ENST00000346085	NM_020732.3	2097	Gac/Tac	20/20	1	2	FACETS	0.602	0.529	0.681	0.602	0.529	0.681	SUBCLONAL	1	TRUE	1	0.482760480311133	2		162	516	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531882	41531882	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs771622894	NA	P-0049989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	12	510	0	ENST00000263253.7:c.1594A>G	p.Met532Val	p.M532V	ENST00000263253	NM_001429.3	532	Atg/Gtg	7/31	NA	2	FACETS	0.24	0.169	0.326			1	INDETERMINATE	1	TRUE	NA	0.729025150937287	2		510	137	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904831	101904831	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	187	333	0	ENST00000374994.4:c.819G>C	p.Trp273Cys	p.W273C	ENST00000374994	NM_004612.2	273	tgG/tgC	5/9	0.651471206863434	2	FACETS	0.983	0.931	1	0.983	0.931	1	CLONAL	2	FALSE	0	0.651471206863434	2		333	292	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0049991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	28	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.765	0.61	0.943	0.765	0.61	0.943	CLONAL	1	TRUE	1	0.13	2		327	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578196	7578196	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	35	702	0	ENST00000269305.4:c.653T>A	p.Val218Glu	p.V218E	ENST00000269305	NM_001126112.2	218	gTg/gAg	6/11	1	2	FACETS	0.975	0.798	1	0.975	0.798	1	CLONAL	1	TRUE	1	0.13	2		702	552	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608282	28608282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773466203	NA	P-0049991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	27	551	0	ENST00000241453.7:c.1774G>A	p.Val592Ile	p.V592I	ENST00000241453	NM_004119.2	592	Gtt/Att	14/24	1	2	FACETS	0.791	0.628	0.979	0.791	0.628	0.979	CLONAL	1	TRUE	1	0.13	2		551	525	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0049992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	50	349	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.0958897335996178	4	FACETS	0.714	0.605	0.835	0.357	0.302	0.418	INDETERMINATE	1	TRUE	2	0.28	4		349	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0049992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	83	681	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	NA	2	FACETS	0.975	0.861	1			1	INDETERMINATE	1	TRUE	NA	0.28	2		681	608	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0049992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	66	264	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.250716633747277	3	FACETS	0.79	0.69	0.897	0.79	0.69	0.897	SUBCLONAL	2	TRUE	1	0.28	3		264	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912654	NA	P-0049992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	164	998	0	ENST00000269305.4:c.469G>A	p.Val157Ile	p.V157I	ENST00000269305	NM_001126112.2	157	Gtc/Atc	5/11	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.28	2		998	864	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606678	29606678	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs188859061	NA	P-0049992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	29	632	2	ENST00000389048.3:c.1202G>A	p.Arg401Gln	p.R401Q	ENST00000389048	NM_004304.4	401	cGa/cAa	5/29	1	2	FACETS	0.413	0.331	0.508	0.413	0.331	0.508	SUBCLONAL	1	TRUE	1	0.28	2		634	501	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468083	50468083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775617502	NA	P-0049992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	65	653	1	ENST00000331340.3:c.1318G>A	p.Ala440Thr	p.A440T	ENST00000331340	NM_006060.4	440	Gcc/Acc	8/8	0.250716633747277	3	FACETS	0.961	0.834	1	0.48	0.417	0.549	CLONAL	1	TRUE	1	0.28	3		654	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520000	NA	P-0049993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	581	607	0	ENST00000269305.4:c.452C>A	p.Pro151His	p.P151H	ENST00000269305	NM_001126112.2	151	cCc/cAc	5/11	0.495991201504773	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.502628380803223	2		607	1147	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628433	86628437	+	frameshift_variant	Frame_Shift_Del	DEL	TTACT	TTACT	-	novel	NA	P-0049993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	81	274	0	ENST00000274376.6:c.806_810del	p.Leu269ProfsTer11	p.L269Pfs*11	ENST00000274376	NM_002890.2	268	TTACTt/t	3/25	NA	2	FACETS	1	0.921	1			1	INDETERMINATE	1	TRUE	NA	0.502628380803223	2		274	309	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149982980	149982980	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	151	431	0	ENST00000253339.5:c.3278A>T	p.Tyr1093Phe	p.Y1093F	ENST00000253339		1093	tAt/tTt	7/7	0.477226976193926	3	FACETS	0.974	0.892	1	0.325	0.297	0.354	CLONAL	1	TRUE	0	0.502628380803223	3		431	772	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559387	141559387	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	175	767	0	ENST00000220592.5:c.1414G>C	p.Glu472Gln	p.E472Q	ENST00000220592	NM_012154.3	472	Gag/Cag	12/19	0.495991201504773	2	FACETS	0.818	0.754	0.885	0.409	0.377	0.443	CLONAL	1	TRUE	0	0.502628380803223	2		767	851	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0049994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	589	454	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.687358607747642	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.687358607747642	2		455	757	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161990392	161990392	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	128	398	0	ENST00000366898.1:c.928G>T	p.Glu310Ter	p.E310*	ENST00000366898	NM_004562.2	310	Gag/Tag	8/12	0.687358607747642	3	FACETS	0.961	0.875	1	0.48	0.437	0.525	CLONAL	1	TRUE	1	0.687358607747642	3		398	521	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965531	90965531	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	101	301	0	ENST00000265433.3:c.1786G>T	p.Asp596Tyr	p.D596Y	ENST00000265433	NM_002485.4	596	Gat/Tat	11/16	0.624293374404769	3	FACETS	0.99	0.891	1	0.495	0.445	0.547	CLONAL	1	TRUE	1	0.687358607747642	3		301	399	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0049996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	470	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.651047768459062	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.651047768459062	3		327	624	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	58	468	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.651047768459062	2		468	174	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764146326	NA	P-0049996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	189	652	0	ENST00000269305.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000269305	NM_001126112.2	281	Gac/Aac	8/11	0.651047768459062	1	FACETS	0.977	0.915	1	0.977	0.915	1	CLONAL	1	TRUE	0	0.651047768459062	1		652	401	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586425	189586425	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	136	399	0	ENST00000264731.3:c.1049G>C	p.Arg350Thr	p.R350T	ENST00000264731	NM_003722.4	350	aGa/aCa	8/14	0.651047768459062	3	FACETS	0.942	0.86	1	0.471	0.43	0.514	CLONAL	1	TRUE	1	0.651047768459062	3		399	588	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423503	88423503	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	135	486	0	ENST00000360948.2:c.2332G>A	p.Glu778Lys	p.E778K	ENST00000360948	NM_001012338.2	778	Gag/Aag	18/19	1	2	FACETS	0.915	0.839	0.995	0.915	0.839	0.995	CLONAL	1	TRUE	1	0.651047768459062	2		486	453	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910756	29910756	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	172	718	0	ENST00000376809.5:c.296G>C	p.Arg99Pro	p.R99P	ENST00000376809	NM_002116.7	99	cGa/cCa	2/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.651047768459062	2		718	457	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039904	47039904	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	344	342	0	ENST00000377604.3:c.1247A>G	p.Gln416Arg	p.Q416R	ENST00000377604	NM_001204468.1	416	cAg/cGg	12/24	0.527385095637	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.651047768459062	2		342	449	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206684	108206684	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	128	259	0	ENST00000278616.4:c.8264A>G	p.Tyr2755Cys	p.Y2755C	ENST00000278616	NM_000051.3	2755	tAt/tGt	56/63	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.651047768459062	2		259	384	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947457	38947457	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757156639	NA	P-0049996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	97	289	1	ENST00000357387.3:c.4223C>T	p.Ser1408Leu	p.S1408L	ENST00000357387	NM_152756.3	1408	tCa/tTa	32/38	1	2	FACETS	0.879	0.792	0.97	0.879	0.792	0.97	CLONAL	1	TRUE	1	0.651047768459062	2		290	339	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073521	8073521	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1319362763	NA	P-0049996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	26	348	0	ENST00000377482.5:c.1138C>G	p.Leu380Val	p.L380V	ENST00000377482	NM_018948.3	380	Ctg/Gtg	4/4	NA	2	FACETS	0.166	0.131	0.206			1	INDETERMINATE	1	TRUE	NA	0.651047768459062	2		348	481	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36823872	36823872	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	130	462	0	ENST00000373129.3:c.310G>C	p.Asp104His	p.D104H	ENST00000373129	NM_032017.1	104	Gat/Cat	5/12	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.651047768459062	2		462	394	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273024	115273024	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	203	451	0	ENST00000438362.2:c.1349G>C	p.Arg450Thr	p.R450T	ENST00000438362	NM_001242891.1	450	aGa/aCa	12/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.651047768459062	2		451	562	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864729	57864729	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	187	744	0	ENST00000228682.2:c.2206G>A	p.Glu736Lys	p.E736K	ENST00000228682	NM_005269.2	736	Gaa/Aaa	12/12	0.639896999004487	2	FACETS	0.937	0.87	1	0.469	0.435	0.503	CLONAL	1	TRUE	0	0.651047768459062	2		744	613	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991356	72991356	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs373464063	NA	P-0049996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	153	603	1	ENST00000268489.5:c.2689G>T	p.Gly897Trp	p.G897W	ENST00000268489	NM_006885.3	897	Ggg/Tgg	2/10	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.651047768459062	2		604	459	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246296	41246296	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	182	508	0	ENST00000357654.3:c.1252G>C	p.Glu418Gln	p.E418Q	ENST00000357654	NM_007294.3	418	Gag/Cag	10/23	0.651047768459062	3	FACETS	1	0.957	1	0.524	0.485	0.565	CLONAL	1	TRUE	1	0.651047768459062	3		508	707	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096189	71096189	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	121	284	1	ENST00000318789.4:c.568C>T	p.Gln190Ter	p.Q190*	ENST00000318789	NM_032682.5	190	Cag/Tag	10/21	1	2	FACETS	0.973	0.888	1	0.973	0.888	1	CLONAL	1	TRUE	1	0.651047768459062	2		285	382	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480319	89480319	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	61	235	0	ENST00000336596.2:c.2156C>A	p.Thr719Asn	p.T719N	ENST00000336596	NM_005233.5	719	aCt/aAt	13/17	1	2	FACETS	0.759	0.662	0.861	0.759	0.662	0.861	SUBCLONAL	1	TRUE	1	0.651047768459062	2		235	247	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510151	149510151	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	257	694	0	ENST00000261799.4:c.1318G>C	p.Gly440Arg	p.G440R	ENST00000261799	NM_002609.3	440	Ggc/Cgc	9/23	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.651047768459062	2		694	679	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945043	151945044	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0049996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	56	421	0	ENST00000262189.6:c.2475_2476delinsTT	p.Met825_Gly826delinsIleCys	p.M825_G826delinsIC	ENST00000262189	NM_170606.2	825	atGGgt/atTTgt	14/59	0.651047768459062	3	FACETS	0.452	0.387	0.522	0.226	0.193	0.261	SUBCLONAL	1	TRUE	1	0.651047768459062	3		421	505	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395252	139395252	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	32	817	0	ENST00000277541.6:c.5686G>C	p.Glu1896Gln	p.E1896Q	ENST00000277541	NM_017617.3	1896	Gag/Cag	31/34	0.651047768459062	2	FACETS	0.158	0.127	0.192	0.079	0.063	0.096	SUBCLONAL	1	TRUE	0	0.651047768459062	2		817	624	SUCCESS
AR	367	MSKCC	GRCh37	X	66905936	66905936	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	125	177	0	ENST00000374690.3:c.1853G>T	p.Arg618Leu	p.R618L	ENST00000374690	NM_000044.3	618	cGg/cTg	3/8	0.527385095637	2	FACETS	1	0.955	1			1	CLONAL	1	TRUE	NA	0.651047768459062	2		177	360	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245219	46245219	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	103	400	0	ENST00000334344.6:c.3313C>T	p.Gln1105Ter	p.Q1105*	ENST00000334344	NM_152641.2	1105	Caa/Taa	15/21	0.252643671367376	2	FACETS	1	0.954	1	0.554	0.498	0.614	CLONAL	1	TRUE	0	0.359473369614975	2		400	517	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0049998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	30	453	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.27	0.218	0.329	0.27	0.218	0.329	SUBCLONAL	1	TRUE	1	0.87385711193634	2		453	254	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807974	3807974	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	570	461	0	ENST00000262367.5:c.3445G>T	p.Glu1149Ter	p.E1149*	ENST00000262367	NM_004380.2	1149	Gag/Tag	18/31	0.87385711193634	2	FACETS	0.976	0.957	0.995	0.976	0.957	0.995	CLONAL	2	TRUE	0	0.87385711193634	2		461	668	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0049999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	86	240	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.212327834580634	3	FACETS	0.884	0.784	0.99	0.884	0.784	0.99	CLONAL	2	TRUE	1	0.212327834580634	3		240	507	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	92	468	0				ENST00000310581	NM_198253.2	-/1132			0.212327834580634	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	1	0.212327834580634	3		468	429	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0049999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	146	606	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.212327834580634	2		606	1131	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708093	117708093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	52	315	0	ENST00000368508.3:c.2084G>A	p.Gly695Asp	p.G695D	ENST00000368508	NM_002944.2	695	gGc/gAc	14/43	1	2	FACETS	0.846	0.72	0.984	0.846	0.72	0.984	CLONAL	1	TRUE	1	0.212327834580634	2		315	579	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426893	6426893	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	90	299	0	ENST00000356142.4:c.86C>G	p.Pro29Arg	p.P29R	ENST00000356142	NM_018890.3	29	cCt/cGt	2/7	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.212327834580634	2		299	690	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76812962	76812962	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1557059602	NA	P-0050000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	107	342	0	ENST00000373344.5:c.6659C>T	p.Ser2220Leu	p.S2220L	ENST00000373344	NM_000489.3	2220	tCa/tTa	30/35	0.184646982542477	4	FACETS	1	0.922	1	1	0.922	1	CLONAL	2	TRUE	2	0.209446492515005	4		342	600	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936074	178936074	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913285	NA	P-0050001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	241	366	0	ENST00000263967.3:c.1616C>G	p.Pro539Arg	p.P539R	ENST00000263967	NM_006218.2	539	cCt/cGt	10/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.740871175503063	2		366	607	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111554	8111554	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	312	520	0	ENST00000346208.3:c.1040T>G	p.Leu347Arg	p.L347R	ENST00000346208		347	cTt/cGt	5/6	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.740871175503063	2		520	785	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921555	178921555	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	198	291	0	ENST00000263967.3:c.1037T>G	p.Val346Gly	p.V346G	ENST00000263967	NM_006218.2	346	gTa/gGa	5/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.740871175503063	2		291	511	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027164	49027165	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GACCGAGA	novel	NA	P-0050001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	193	280	0	ENST00000267163.4:c.1732_1739dup	p.Gly581ThrfsTer33	p.G581Tfs*33	ENST00000267163	NM_000321.2	577	-/GACCGAGA	18/27	0.740871175503063	1	FACETS	0.794	0.745	0.844	0.794	0.745	0.844	SUBCLONAL	1	TRUE	0	0.740871175503063	1		280	413	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0050002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	61	294	0	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	1	2	FACETS	0.753	0.652	0.862	0.753	0.652	0.862	SUBCLONAL	1	TRUE	1	0.392216413485823	2		294	413	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653835	89653835	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	35	354	0	ENST00000371953.3:c.133del	p.Val45TyrfsTer9	p.V45Yfs*9	ENST00000371953	NM_000314.4	45	Gta/ta	2/9	0.387032963422963	3	FACETS	0.719	0.591	0.861	0.359	0.295	0.431	SUBCLONAL	1	TRUE	1	0.392216413485823	3		354	297	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023308	27023309	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0050002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	41	127	0	ENST00000324856.7:c.414_415del	p.Ala139ArgfsTer260	p.A139Rfs*260	ENST00000324856	NM_006015.4	138	tcAGcc/tccc	1/20	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.392216413485823	2		127	192	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692991	89692992	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0050002-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	132	384	0	ENST00000371953.3:c.477dup	p.Thr160AspfsTer20	p.T160Dfs*20	ENST00000371953	NM_000314.4	159	agg/aGgg	5/9	0.387032963422963	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.392216413485823	3		384	345	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0050003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	346	625	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.359419737244674	3	FACETS	1	0.99	1	0.761	0.725	0.797	CLONAL	2	TRUE	0	0.497467163988848	3		625	761	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0050003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	783	511	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.497467163988848	7	FACETS	0.949	0.921	0.977	0.949	0.921	0.977	CLONAL	5	TRUE	2	0.497467163988848	7		511	1489	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0050003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	137	331	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	0.387537305310329	3	FACETS	0.782	0.717	0.848	0.521	0.478	0.566	SUBCLONAL	2	TRUE	0	0.497467163988848	3		331	440	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683691	162683691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	173	547	0	ENST00000366898.1:c.278G>A	p.Gly93Glu	p.G93E	ENST00000366898	NM_004562.2	93	gGa/gAa	3/12	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.497467163988848	2		547	633	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602541	10602541	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	352	812	0	ENST00000171111.5:c.1037A>G	p.Asn346Ser	p.N346S	ENST00000171111	NM_203500.1	346	aAc/aGc	3/6	0.475848742016485	2	FACETS	0.841	0.801	0.882	0.841	0.801	0.882	CLONAL	2	TRUE	0	0.497467163988848	2		812	841	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	117	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.296881620989861	2		327	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579328	7579328	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	126	648	0	ENST00000269305.4:c.359A>G	p.Lys120Arg	p.K120R	ENST00000269305	NM_001126112.2	120	aAg/aGg	4/11	0.296881620989861	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.296881620989861	1		648	703	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0050005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	54	332	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.904	0.784	1	0.904	0.784	1	CLONAL	1	TRUE	1	0.606158098143044	2		332	197	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575116	48575116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	28	263	0	ENST00000342988.3:c.310C>T	p.Leu104Phe	p.L104F	ENST00000342988	NM_005359.5	104	Ctt/Ttt	3/12	0.603944040005927	1	FACETS	0.294	0.236	0.359	0.294	0.236	0.359	SUBCLONAL	1	TRUE	0	0.606158098143044	1		263	219	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121531	108121531	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779815	NA	P-0050005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	89	429	1	ENST00000278616.4:c.1339C>T	p.Arg447Ter	p.R447*	ENST00000278616	NM_000051.3	447	Cga/Tga	10/63	0.606158098143044	1	FACETS	0.871	0.786	0.958	0.871	0.786	0.958	CLONAL	1	TRUE	0	0.606158098143044	1		430	235	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073827	8073828	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATCGGAGTTAG	novel	NA	P-0050005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	59	321	0	ENST00000377482.5:c.821_831dup	p.Glu278LeufsTer21	p.E278Lfs*21	ENST00000377482	NM_018948.3	277	-/CTAACTCCGAT	4/4	0.606158098143044	1	FACETS	0.714	0.625	0.807	0.714	0.625	0.807	SUBCLONAL	1	TRUE	0	0.606158098143044	1		321	190	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527844	157527844	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	116	410	0	ENST00000346085.5:c.5569A>C	p.Lys1857Gln	p.K1857Q	ENST00000346085	NM_020732.3	1857	Aaa/Caa	20/20	0.606158098143044	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.606158098143044	1		410	239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0050006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	414	522	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.367476437951978	3	FACETS	0.965	0.924	1	0.965	0.924	1	CLONAL	3	TRUE	0	0.367476437951978	3		522	921	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0050006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	282	421	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.367476437951978	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	TRUE	0	0.367476437951978	3		421	578	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5286129	5286129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	302	727	11	ENST00000357368.4:c.23G>A	p.Gly8Asp	p.G8D	ENST00000357368	NM_002850.3	8	gGc/gAc	2/38	0.154799010112931	2	FACETS	0.83	0.783	0.878	0.83	0.783	0.878	INDETERMINATE	2	TRUE	0	0.367476437951978	2		738	990	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763406	41763406	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	73	502	1	ENST00000301178.4:c.2205C>A	p.Phe735Leu	p.F735L	ENST00000301178	NM_021913.4	735	ttC/ttA	19/20	0.154799010112931	2	FACETS	0.606	0.529	0.688	0.303	0.264	0.344	INDETERMINATE	1	TRUE	0	0.367476437951978	2		503	656	SUCCESS
APC	324	MSKCC	GRCh37	5	112175138	112175138	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	87	211	0	ENST00000257430.4:c.3847del	p.Ala1283LeufsTer5	p.A1283Lfs*5	ENST00000257430	NM_000038.5	1283	Gct/ct	16/16	0.367476437951978	2	FACETS	0.825	0.739	0.914	0.825	0.739	0.914	CLONAL	2	TRUE	0	0.367476437951978	2		211	287	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918691	44918691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	44	448	0	ENST00000377967.4:c.1174G>A	p.Ala392Thr	p.A392T	ENST00000377967	NM_021140.2	392	Gca/Aca	12/29	0.154799010112931	2	FACETS	0.409	0.342	0.483	0.204	0.171	0.242	INDETERMINATE	1	TRUE	0	0.367476437951978	2		448	586	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	208	413	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.508011296235981	3	FACETS	0.9	0.842	0.959	0.9	0.842	0.959	CLONAL	2	TRUE	1	0.52478480720629	3		413	556	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0050007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	209	730	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.884	0.822	0.949	0.884	0.822	0.949	CLONAL	1	TRUE	1	0.52478480720629	2		730	901	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252866	36252866	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs759068561	NA	P-0050007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	37	291	0	ENST00000300305.3:c.496C>T	p.Arg166Ter	p.R166*	ENST00000300305		166	Cga/Tga	4/8	0.52478480720629	2	FACETS	0.338	0.279	0.405	0.169	0.139	0.203	SUBCLONAL	1	TRUE	0	0.52478480720629	2		291	417	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120016	70120016	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1339655148	NA	P-0050007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	94	123	0	ENST00000245479.2:c.1018C>T	p.Gln340Ter	p.Q340*	ENST00000245479	NM_000346.3	340	Cag/Tag	3/3	0.289928598742348	2	FACETS	0.905	0.825	0.985	0.905	0.825	0.985	INDETERMINATE	2	TRUE	0	0.52478480720629	2		123	198	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411678	63411678	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	427	706	0	ENST00000330258.3:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000330258	NM_152424.3	497	Cga/Tga	2/2	0.283758325064196	5	FACETS	1	0.988	1	0.734	0.7	0.77	INDETERMINATE	2	TRUE	2	0.52478480720629	5		706	1320	SUCCESS
APC	324	MSKCC	GRCh37	5	112175577	112175577	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	199	293	0	ENST00000257430.4:c.4288del	p.Thr1430ProfsTer43	p.T1430Pfs*43	ENST00000257430	NM_000038.5	1429	cAa/ca	16/16	0.52478480720629	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.52478480720629	2		293	373	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426415	49426415	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	148	792	0	ENST00000301067.7:c.12073G>A	p.Glu4025Lys	p.E4025K	ENST00000301067	NM_003482.3	4025	Gaa/Aaa	39/54	0.508011296235981	3	FACETS	0.566	0.515	0.619	0.283	0.257	0.31	SUBCLONAL	1	TRUE	1	0.52478480720629	3		792	1259	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149452	61149452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	126	293	0	ENST00000295025.8:c.1642G>A	p.Ala548Thr	p.A548T	ENST00000295025	NM_002908.2	548	Gcc/Acc	11/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.52478480720629	2		293	440	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106650	27106651	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTC	novel	NA	P-0050007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	419	571	0	ENST00000324856.7:c.6264_6266dup	p.Leu2089dup	p.L2089dup	ENST00000324856	NM_006015.4	2089	-/CTC	20/20	0.470960259816967	2	FACETS	0.988	0.948	1	0.988	0.948	1	CLONAL	2	TRUE	0	0.52478480720629	2		571	808	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982104	201982104	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	244	727	0	ENST00000359651.3:c.628T>G	p.Ser210Ala	p.S210A	ENST00000359651		210	Tca/Gca	5/8	1	2	FACETS	0.91	0.85	0.971	0.91	0.85	0.971	CLONAL	1	TRUE	1	0.52478480720629	2		727	1022	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200902	67200902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755385727	NA	P-0050007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	239	630	0	ENST00000312629.5:c.890G>A	p.Arg297Gln	p.R297Q	ENST00000312629	NM_003952.2	297	cGg/cAg	10/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.52478480720629	2		630	850	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119969	70120021	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCGGCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAGGCG	CCGCGGCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAGGCG	-	novel	NA	P-0050007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	32	350	0	ENST00000245479.2:c.975_1027del	p.Ser330AlafsTer230	p.S330Afs*230	ENST00000245479	NM_000346.3	324	aCCGCGGCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAGGCG/a	3/3	0.289928598742348	2	FACETS	0.267	0.217	0.325	0.134	0.108	0.163	INDETERMINATE	1	TRUE	0	0.52478480720629	2		350	456	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272520	15272520	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	194	545	0	ENST00000263388.2:c.5919G>T	p.Glu1973Asp	p.E1973D	ENST00000263388	NM_000435.2	1973	gaG/gaT	33/33	1	2	FACETS	0.998	0.926	1	0.998	0.926	1	CLONAL	1	TRUE	1	0.52478480720629	2		545	741	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612866	228612866	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138699472	NA	P-0050008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	282	727	1	ENST00000366696.1:c.161G>A	p.Arg54His	p.R54H	ENST00000366696	NM_003493.2	54	cGc/cAc	1/1	0.401351881493548	3	FACETS	0.791	0.744	0.84	0.528	0.496	0.56	SUBCLONAL	2	TRUE	0	0.401881399061075	3		728	1065	SUCCESS
APC	324	MSKCC	GRCh37	5	112175069	112175069	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	24	157	0	ENST00000257430.4:c.3778C>T	p.Gln1260Ter	p.Q1260*	ENST00000257430	NM_000038.5	1260	Cag/Tag	16/16	0.39636631281802	2	FACETS	1	0.928	1	0.703	0.565	0.851	CLONAL	1	TRUE	0	0.401881399061075	2		157	85	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647222	2647222	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	132	458	0	ENST00000342085.4:c.1500G>T	p.Trp500Cys	p.W500C	ENST00000342085	NM_002613.4	500	tgG/tgT	13/14	0.197095225567238	4	FACETS	0.949	0.867	1			1	INDETERMINATE	2	TRUE	NA	0.401881399061075	4		458	485	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349016	89349016	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	82	610	0	ENST00000301030.4:c.3934G>C	p.Gly1312Arg	p.G1312R	ENST00000301030	NM_001256183.1	1312	Ggg/Cgg	9/13	0.10924096321106	3	FACETS	0.528	0.464	0.597	0.264	0.232	0.299	INDETERMINATE	1	TRUE	1	0.401881399061075	3		610	928	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973779	15973785	+	frameshift_variant	Frame_Shift_Del	DEL	ATTTGAC	ATTTGAC	-	novel	NA	P-0050008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	116	410	1	ENST00000268712.3:c.4207_4213del	p.Val1403ProfsTer2	p.V1403Pfs*2	ENST00000268712	NM_006311.3	1403	GTCAAATcc/cc	31/46	0.337560577883484	3	FACETS	0.891	0.811	0.975	0.594	0.54	0.65	CLONAL	2	TRUE	0	0.401881399061075	3		411	389	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528178	29528178	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0050008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	14	399	0	ENST00000356175.3:c.1185+1G>T		p.X395_splice	ENST00000356175	NM_000267.3	395			0.337560577883484	3	FACETS	0.382	0.276	0.51	0.127	0.092	0.17	SUBCLONAL	1	TRUE	0	0.401881399061075	3		399	219	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971124	21971125	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0050009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	228	523	0	ENST00000304494.5:c.233_234del	p.Leu78HisfsTer41	p.L78Hfs*41	ENST00000304494	NM_000077.4	78	cTC/c	2/3	0.644559362945422	1	FACETS	0.965	0.909	1	0.965	0.909	1	CLONAL	1	TRUE	0	0.644559362945422	1		523	497	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0050012-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	41	175	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.764551155175258	1	FACETS	0.417	0.353	0.485	0.417	0.353	0.485	SUBCLONAL	1	TRUE	0	0.764551155175258	1		175	159	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578397	7578398	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0050012-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	325	714	0	ENST00000269305.4:c.532dup	p.His178ProfsTer3	p.H178Pfs*3	ENST00000269305	NM_001126112.2	178	cac/cCac	5/11	0.764551155175258	1	FACETS	0.679	0.644	0.713	0.679	0.644	0.713	SUBCLONAL	1	TRUE	0	0.764551155175258	1		714	774	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934155	48934155	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050012-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	71	249	0	ENST00000267163.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000267163	NM_000321.2	204	Gaa/Taa	7/27	0.764551155175258	1	FACETS	0.62	0.553	0.689	0.62	0.553	0.689	SUBCLONAL	1	TRUE	0	0.764551155175258	1		249	185	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294075	1294075	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050012-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1197	127	822	0	ENST00000310581.5:c.926C>G	p.Ser309Cys	p.S309C	ENST00000310581	NM_198253.2	309	tCc/tGc	2/16	0.463546176110414	1	FACETS	0.155	0.14	0.171	0.155	0.14	0.171	SUBCLONAL	1	TRUE	0	0.764551155175258	1		822	1324	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050015-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	275	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.419923632133684	3	FACETS	0.906	0.852	0.96	0.906	0.852	0.96	CLONAL	2	TRUE	1	0.419923632133684	3		327	875	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578439	7578439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050015-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	235	1026	0	ENST00000269305.4:c.491del	p.Lys164SerfsTer6	p.K164Sfs*6	ENST00000269305	NM_001126112.2	164	aAg/ag	5/11	0.419923632133684	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.419923632133684	1		1026	826	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737142	145737142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61755067	NA	P-0050015-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	261	1095	1	ENST00000428558.2:c.3424G>A	p.Asp1142Asn	p.D1142N	ENST00000428558	NM_004260.3	1142	Gac/Aac	21/22	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.419923632133684	2		1096	1200	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050015-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	108	609	0	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	0.419923632133684	1	FACETS	0.84	0.757	0.926	0.84	0.757	0.926	CLONAL	1	TRUE	0	0.419923632133684	1		609	484	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050021-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	37	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.856	0.709	1	0.856	0.709	1	CLONAL	1	TRUE	1	0.307591648459394	2		327	281	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144146	11144146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050021-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	39	505	1	ENST00000358026.2:c.3727C>T	p.Arg1243Trp	p.R1243W	ENST00000358026	NM_001128849.1	1243	Cgg/Tgg	26/36	0.307591648459394	1	FACETS	0.451	0.373	0.537	0.451	0.373	0.537	SUBCLONAL	1	TRUE	0	0.307591648459394	1		506	476	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468056	50468056	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050021-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	56	524	0	ENST00000331340.3:c.1291G>T	p.Glu431Ter	p.E431*	ENST00000331340	NM_006060.4	431	Gag/Tag	8/8	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.307591648459394	2		524	328	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599889	10599889	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050021-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	127	593	2	ENST00000171111.5:c.1687C>T	p.Gln563Ter	p.Q563*	ENST00000171111	NM_203500.1	563	Cag/Tag	5/6	0.307591648459394	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.307591648459394	1		595	579	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411949	116412050	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCATTTGGATAGGCTTGTAAGTGCCCGAAGTGTAAGCCCAACTACAGAAATGGTTTCAAATGAATCTGTAGACTACCGAGCTACTTTTCCAGAAGGTATATT	TCATTTGGATAGGCTTGTAAGTGCCCGAAGTGTAAGCCCAACTACAGAAATGGTTTCAAATGAATCTGTAGACTACCGAGCTACTTTTCCAGAAGGTATATT	-	novel	NA	P-0050024-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	277	581	0	ENST00000397752.3:c.2937_3028+10del		p.X979_splice	ENST00000397752	NM_000245.2	979		14/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		581	941	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	196	468	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.805	0.752	0.859	1	0.992	1	CLONAL	2	TRUE	1	0.474682909933918	2		468	513	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0050035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	317	443	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.474682909933918	1	FACETS	0.807	0.769	0.845	1	0.996	1	CLONAL	2	TRUE	0	0.474682909933918	1		443	631	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9928064	9928064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1476673300	NA	P-0050035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	134	323	0	ENST00000330684.3:c.1675G>A	p.Val559Met	p.V559M	ENST00000330684	NM_001134407.1	559	Gtg/Atg	8/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.474682909933918	2		323	411	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0050055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	252	486	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.38028687221631	7	FACETS	1	0.984	1			1	CLONAL	5	TRUE	NA	0.38028687221631	7		486	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs483352695	NA	P-0050055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	60	758	1	ENST00000269305.4:c.736A>T	p.Met246Leu	p.M246L	ENST00000269305	NM_001126112.2	246	Atg/Ttg	7/11	0.365570027331685	1	FACETS	0.913	0.793	1	0.913	0.793	1	CLONAL	1	TRUE	0	0.38028687221631	1		759	280	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394879	394879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	21	535	0	ENST00000380956.4:c.275C>T	p.Thr92Ile	p.T92I	ENST00000380956	NM_001195286.1	92	aCc/aTc	3/9	0.243410423558715	1	FACETS	0.33	0.254	0.418	0.33	0.254	0.418	SUBCLONAL	1	TRUE	0	0.38028687221631	1		535	271	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944603	32944603	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	32	558	0	ENST00000380152.3:c.8396G>T	p.Arg2799Ile	p.R2799I	ENST00000380152		2799	aGa/aTa	19/27	0.38028687221631	1	FACETS	0.847	0.696	1	0.847	0.696	1	CLONAL	1	TRUE	0	0.38028687221631	1		558	161	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041683	42041683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	38	499	0	ENST00000219905.7:c.5878C>T	p.Leu1960Phe	p.L1960F	ENST00000219905	NM_001164273.1	1960	Ctt/Ttt	17/24	1	2	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	TRUE	1	0.38028687221631	2		499	199	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303014	15303014	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555729510	NA	P-0050055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	56	1031	0	ENST00000263388.2:c.436T>C	p.Cys146Arg	p.C146R	ENST00000263388	NM_000435.2	146	Tgc/Cgc	4/33	0.372337389516218	1	FACETS	0.986	0.854	1	0.986	0.854	1	CLONAL	1	TRUE	0	0.38028687221631	1		1031	242	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620644	52620644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781632065	NA	P-0050055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	33	438	0	ENST00000394830.3:c.3109C>T	p.Arg1037Trp	p.R1037W	ENST00000394830	NM_018313.4	1037	Cgg/Tgg	21/30	0.342368715057973	1	FACETS	0.79	0.65	0.943	0.79	0.65	0.943	CLONAL	1	TRUE	0	0.38028687221631	1		438	178	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146605	55146605	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0050055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	13	540	0	ENST00000257290.5:c.2279C>G	p.Ser760Ter	p.S760*	ENST00000257290	NM_006206.4	760	tCa/tGa	16/23	0.16671624712982	1	FACETS	0.336	0.24	0.451	0.336	0.24	0.451	INDETERMINATE	1	TRUE	0	0.38028687221631	1		540	165	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467613	66467613	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	42	371	0	ENST00000273854.3:c.656C>T	p.Ala219Val	p.A219V	ENST00000273854	NM_004439.5	219	gCt/gTt	3/18	0.16671624712982	1	FACETS	0.962	0.814	1	0.962	0.814	1	INDETERMINATE	1	TRUE	0	0.38028687221631	1		371	186	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683704	162683704	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0050055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	34	679	0	ENST00000366898.1:c.265A>T	p.Arg89Ter	p.R89*	ENST00000366898	NM_004562.2	89	Aga/Tga	3/12	1	2	FACETS	0.704	0.578	0.844	0.704	0.578	0.844	SUBCLONAL	1	TRUE	1	0.38028687221631	2		679	254	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0050056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	222	240	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.240866999411468	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	0	0.276630139111741	3		240	544	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	122	468	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.926	1	1	0.99	1	CLONAL	2	TRUE	1	0.276630139111741	2		468	433	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874903	151874912	+	frameshift_variant	Frame_Shift_Del	DEL	GCTCTGTGGT	GCTCTGTGGT	-	novel	NA	P-0050056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	45	382	0	ENST00000262189.6:c.7626_7635del	p.Pro2543CysfsTer16	p.P2543Cfs*16	ENST00000262189	NM_170606.2	2542	tcACCACAGAGC/tc	38/59	0.276630139111741	6	FACETS	0.672	0.563	0.793	0.134	0.112	0.159	SUBCLONAL	1	TRUE	1	0.276630139111741	6		382	752	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	237	361	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.69592848976708	3	FACETS	0.985	0.92	1	0.493	0.46	0.526	CLONAL	1	FALSE	1	0.69592848976708	3		361	932	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	458	729	1	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	0.677897821812521	2	FACETS	0.926	0.894	0.956	0.926	0.894	0.956	CLONAL	2	FALSE	0	0.69592848976708	2		730	711	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974677	21974677	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1057519882	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	306	558	0	ENST00000304494.5:c.150G>T	p.Gln50His	p.Q50H	ENST00000304494	NM_000077.4	50	caG/caT	1/3	0.69592848976708	5	FACETS	0.805	0.758	0.852	0.536	0.505	0.568	CLONAL	2	FALSE	2	0.69592848976708	5		558	1117	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524567	103524568	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs759551120	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	56	277	0	ENST00000355739.4:c.2705dup	p.Asn902LysfsTer7	p.N902Kfs*7	ENST00000355739	NM_000123.3	900	caa/cAaa	13/15	0.670000385452896	3	FACETS	0.767	0.662	0.879	0.383	0.331	0.44	SUBCLONAL	1	FALSE	1	0.69592848976708	3		277	283	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6036958	6036958	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	265	450	0	ENST00000265849.7:c.802del	p.Tyr268ThrfsTer39	p.Y268Tfs*39	ENST00000265849	NM_000535.5	268	Tac/ac	7/15	0.62156804761792	4	FACETS	0.915	0.862	0.968	0.915	0.862	0.968	CLONAL	2	FALSE	2	0.69592848976708	4		450	706	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	151	599	5	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	0.418627622987074	4	FACETS	0.92	0.842	1	0.46	0.421	0.501	CLONAL	1	FALSE	2	0.69592848976708	4		604	800	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823918	3823918	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	274	659	0	ENST00000262367.5:c.2297C>T	p.Pro766Leu	p.P766L	ENST00000262367	NM_004380.2	766	cCt/cTt	13/31	0.418627622987074	4	FACETS	0.769	0.724	0.815	0.769	0.724	0.815	SUBCLONAL	2	FALSE	2	0.69592848976708	4		659	868	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40743901	40743901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761347839	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	413	691	1	ENST00000392038.2:c.806G>A	p.Arg269Gln	p.R269Q	ENST00000392038	NM_001626.4	269	cGg/cAg	9/14	0.332674397538555	5	FACETS	0.904	0.865	0.942	0.904	0.865	0.942	INDETERMINATE	3	FALSE	2	0.69592848976708	5		692	895	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	271	704	2	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	0.425888344671004	4	FACETS	1	0.992	1	0.673	0.632	0.715	CLONAL	1	FALSE	2	0.69592848976708	4		706	981	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	425	983	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.425888344671004	4	FACETS	0.878	0.837	0.919	0.878	0.837	0.919	CLONAL	2	FALSE	2	0.69592848976708	4		983	1180	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633289	12633291	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	287	464	0	ENST00000251849.4:c.1109_1111del	p.Gly370del	p.G370del	ENST00000251849	NM_002880.3	370	gGAGat/gat	11/17	0.69592848976708	2	FACETS	0.933	0.894	0.971	0.933	0.894	0.971	CLONAL	2	FALSE	0	0.69592848976708	2		464	442	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243108	105243108	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	461	761	1	ENST00000349310.3:c.176-1G>A		p.X59_splice	ENST00000349310	NM_001014432.1	59			0.635215692833294	3	FACETS	0.937	0.9	0.974	0.937	0.9	0.974	CLONAL	2	FALSE	1	0.69592848976708	3		762	953	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657658	37657658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	179	425	1	ENST00000447079.4:c.2575G>A	p.Asp859Asn	p.D859N	ENST00000447079	NM_015083.1	859	Gat/Aat	6/14	0.418627622987074	4	FACETS	0.761	0.706	0.818	0.761	0.706	0.818	SUBCLONAL	2	FALSE	2	0.69592848976708	4		426	573	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505403	125505404	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1565368022	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	74	322	0	ENST00000428830.2:c.700dup	p.Ile234AsnfsTer11	p.I234Nfs*11	ENST00000428830	NM_001114121.2	231	-/A	7/14	0.332674397538555	5	FACETS	0.842	0.739	0.953	0.281	0.246	0.318	INDETERMINATE	1	FALSE	2	0.69592848976708	5		322	516	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78831591	78831591	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	366	592	0	ENST00000306801.3:c.1400C>T	p.Ala467Val	p.A467V	ENST00000306801	NM_020761.2	467	gCc/gTc	13/34	0.491112042646236	4	FACETS	1	0.993	1	0.795	0.76	0.83	CLONAL	2	FALSE	1	0.69592848976708	4		592	748	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204623	128204623	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	164	786	0	ENST00000341105.2:c.818del	p.Gly273AspfsTer53	p.G273Dfs*53	ENST00000341105	NM_032638.4	273	gGa/ga	3/6	0.62156804761792	4	FACETS	0.63	0.577	0.686	0.315	0.288	0.343	SUBCLONAL	1	FALSE	2	0.69592848976708	4		786	1268	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928960	49928960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766187988	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	272	826	1	ENST00000296474.3:c.3406C>T	p.Arg1136Cys	p.R1136C	ENST00000296474	NM_002447.2	1136	Cgt/Tgt	16/20	0.69592848976708	2	FACETS	1	0.976	1	0.532	0.501	0.563	CLONAL	1	FALSE	0	0.69592848976708	2		827	735	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106004	8106004	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	159	491	3	ENST00000346208.3:c.824G>A	p.Arg275Gln	p.R275Q	ENST00000346208		275	cGg/cAg	4/6	0.418627622987074	4	FACETS	1	0.926	1	0.505	0.463	0.548	CLONAL	1	FALSE	2	0.69592848976708	4		494	768	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109321766	109321766	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	186	579	0	ENST00000436639.2:c.657del	p.Lys219AsnfsTer5	p.K219Nfs*5	ENST00000436639	NM_014454.2	219	aaA/aa	4/10	0.560379032017236	4	FACETS	1	0.943	1	0.512	0.473	0.553	CLONAL	1	FALSE	2	0.69592848976708	4		579	885	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218658	98218658	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	375	552	1	ENST00000331920.6:c.3206G>A	p.Gly1069Asp	p.G1069D	ENST00000331920	NM_000264.3	1069	gGc/gAc	19/24	0.69592848976708	2	FACETS	0.998	0.963	1	0.998	0.963	1	CLONAL	2	FALSE	0	0.69592848976708	2		553	540	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874227	151874227	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	229	394	0	ENST00000262189.6:c.8311del	p.Ser2771AlafsTer7	p.S2771Afs*7	ENST00000262189	NM_170606.2	2771	Agc/gc	38/59	0.62156804761792	4	FACETS	0.899	0.843	0.955	0.899	0.843	0.955	CLONAL	2	FALSE	2	0.69592848976708	4		394	621	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494696	2494696	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369340704	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	369	752	1	ENST00000355716.4:c.836G>A	p.Arg279Lys	p.R279K	ENST00000355716	NM_003820.2	279	aGg/aAg	8/8	0.69592848976708	4	FACETS	0.84	0.799	0.883			1	CLONAL	2	FALSE	NA	0.69592848976708	4		753	1070	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506293	120506294	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	280	534	1	ENST00000256646.2:c.1818_1819delinsTT	p.Gln607Ter	p.Q607*	ENST00000256646	NM_024408.3	606	gaCCag/gaTTag	11/34	0.69592848976708	4	FACETS	0.89	0.84	0.94	0.89	0.84	0.94	CLONAL	2	FALSE	2	0.69592848976708	4		535	767	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729596	162729596	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	135	452	0	ENST00000367921.3:c.682G>A	p.Gly228Arg	p.G228R	ENST00000367921	NM_006182.2	228	Ggg/Agg	8/18	0.418627622987074	4	FACETS	1	0.972	1	0.576	0.526	0.629	CLONAL	1	FALSE	2	0.69592848976708	4		452	571	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648231	206648232	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	308	581	0	ENST00000367120.3:c.252_253delinsAT	p.Val85Leu	p.V85L	ENST00000367120	NM_014002.3	84	ctGGtg/ctATtg	5/22	0.418627622987074	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	FALSE	2	0.69592848976708	4		581	708	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202504	67202504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	380	835	0	ENST00000312629.5:c.1313G>A	p.Ser438Asn	p.S438N	ENST00000312629	NM_003952.2	438	aGc/aAc	15/15	0.332674397538555	5	FACETS	1	0.959	1	0.673	0.64	0.706	INDETERMINATE	2	FALSE	2	0.69592848976708	5		835	1106	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426895	49426896	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	289	659	1	ENST00000301067.7:c.11592_11593delinsTT	p.Gln3865Ter	p.Q3865*	ENST00000301067	NM_003482.3	3864	caCCaa/caTTaa	39/54	0.425888344671004	4	FACETS	0.923	0.873	0.974	0.923	0.873	0.974	CLONAL	2	FALSE	2	0.69592848976708	4		660	763	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914143	32914143	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs886040602	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	255	475	0	ENST00000380152.3:c.5653del	p.Cys1885AlafsTer24	p.C1885Afs*24	ENST00000380152		1884	aTt/at	11/27	0.670000385452896	3	FACETS	0.937	0.887	0.987	0.937	0.887	0.987	CLONAL	2	FALSE	1	0.69592848976708	3		475	527	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337635	73337635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	149	272	0	ENST00000377767.4:c.2081C>T	p.Pro694Leu	p.P694L	ENST00000377767	NM_014953.3	694	cCa/cTa	16/21	0.670000385452896	3	FACETS	0.896	0.833	0.96	0.896	0.833	0.96	CLONAL	2	FALSE	1	0.69592848976708	3		272	322	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738588	43738588	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	219	442	0	ENST00000382044.4:c.3037G>C	p.Glu1013Gln	p.E1013Q	ENST00000382044	NM_001141980.1	1013	Gaa/Caa	14/28	0.560379032017236	4	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	FALSE	2	0.69592848976708	4		442	531	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652293	3652293	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	330	661	0	ENST00000294008.3:c.776C>T	p.Pro259Leu	p.P259L	ENST00000294008	NM_032444.2	259	cCc/cTc	4/15	0.418627622987074	4	FACETS	0.937	0.889	0.986	0.937	0.889	0.986	CLONAL	2	FALSE	2	0.69592848976708	4		661	858	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819280	3819281	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	295	636	3	ENST00000262367.5:c.2954_2955delinsTT	p.Ser985Phe	p.S985F	ENST00000262367	NM_004380.2	985	tCC/tTT	15/31	0.418627622987074	4	FACETS	0.866	0.818	0.915	0.866	0.818	0.915	CLONAL	2	FALSE	2	0.69592848976708	4		639	830	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756640	756641	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	279	486	1	ENST00000314574.4:c.187_188delinsAA	p.Gly63Lys	p.G63K	ENST00000314574	NM_005433.3	63	GGa/AAa	2/12	0.635215692833294	3	FACETS	0.829	0.784	0.874	0.829	0.784	0.874	CLONAL	2	FALSE	1	0.69592848976708	3		487	652	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621181	1621182	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	502	843	0	ENST00000344749.5:c.964_965delinsAA	p.Gly322Lys	p.G322K	ENST00000344749	NM_001136139.2	322	GGg/AAg	12/19	0.677897821812521	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	FALSE	0	0.69592848976708	2		843	721	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099259	4099259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	476	799	2	ENST00000262948.5:c.859G>A	p.Glu287Lys	p.E287K	ENST00000262948	NM_030662.3	287	Gaa/Aaa	7/11	0.677897821812521	2	FACETS	0.974	0.944	1	0.974	0.944	1	CLONAL	2	FALSE	0	0.69592848976708	2		801	702	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215674170	215674170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	466	771	1	ENST00000260947.4:c.124G>A	p.Asp42Asn	p.D42N	ENST00000260947	NM_000465.2	42	Gac/Aac	1/11	0.252411099167656	4	FACETS	1	0.994	1	1	0.994	1	INDETERMINATE	2	FALSE	2	0.69592848976708	4		772	958	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485413	57485413	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	112	396	0	ENST00000371085.3:c.995C>A	p.Pro332Gln	p.P332Q	ENST00000371085	NM_000516.4	332	cCa/cAa	12/13	0.69592848976708	4	FACETS	0.917	0.827	1	0.459	0.413	0.506	CLONAL	1	FALSE	2	0.69592848976708	4		396	595	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656888	45656888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566695508	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	431	705	1	ENST00000407780.3:c.268G>A	p.Gly90Ser	p.G90S	ENST00000407780	NM_001283052.1	90	Ggc/Agc	3/7	0.62156804761792	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	FALSE	2	0.69592848976708	4		706	1022	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572978	41572978	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	453	773	0	ENST00000263253.7:c.5263C>G	p.Leu1755Val	p.L1755V	ENST00000263253	NM_001429.3	1755	Ctg/Gtg	31/31	0.61169482011413	4	FACETS	0.918	0.878	0.959			1	CLONAL	2	FALSE	NA	0.69592848976708	4		773	1202	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37038200	37038201	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	115	224	0	ENST00000231790.2:c.207_207+1delinsAA		p.X69_splice	ENST00000231790	NM_000249.3	69		2/19	0.69592848976708	2	FACETS	0.893	0.832	0.953	0.893	0.832	0.953	CLONAL	2	FALSE	0	0.69592848976708	2		224	185	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169985777	169985777	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	283	502	0	ENST00000295797.4:c.439C>T	p.Arg147Cys	p.R147C	ENST00000295797	NM_002740.5	147	Cgt/Tgt	5/18	0.62156804761792	4	FACETS	0.97	0.917	1	0.97	0.917	1	CLONAL	2	FALSE	2	0.69592848976708	4		502	711	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612078	189612080	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs1294809942	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	141	661	0	ENST00000264731.3:c.1834_1836del	p.Ser612del	p.S612del	ENST00000264731	NM_003722.4	610	ttCTCc/ttc	14/14	0.62156804761792	4	FACETS	0.761	0.693	0.833	0.381	0.346	0.417	SUBCLONAL	1	FALSE	2	0.69592848976708	4		661	903	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161429	55161429	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	114	476	0	ENST00000257290.5:c.3260G>T	p.Ser1087Ile	p.S1087I	ENST00000257290	NM_006206.4	1087	aGc/aTc	23/23	0.687169970132708	2	FACETS	0.86	0.781	0.941	0.43	0.39	0.471	CLONAL	1	FALSE	0	0.69592848976708	2		476	381	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958890	38958891	+	stop_gained	Nonsense_Mutation	DNP	CT	CT	TA	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	82	264	0	ENST00000357387.3:c.2221_2222delinsTA	p.Arg741Ter	p.R741*	ENST00000357387	NM_152756.3	741	AGa/TAa	23/38	0.418680929408217	3	FACETS	1	0.929	1	0.528	0.47	0.588	CLONAL	1	FALSE	1	0.69592848976708	3		264	301	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31947194	31947194	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	149	525	0	ENST00000375333.2:c.679C>A	p.Leu227Ile	p.L227I	ENST00000375333	NM_032454.1	227	Ctc/Atc	5/8	0.69592848976708	4	FACETS	0.826	0.755	0.901	0.413	0.377	0.451	CLONAL	1	FALSE	2	0.69592848976708	4		525	879	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288809	33288810	+	stop_gained	Nonsense_Mutation	DNP	AG	AG	TA	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	334	548	1	ENST00000374542.5:c.742_743delinsTA	p.Leu248Ter	p.L248*	ENST00000374542	NM_001141970.1	248	CTg/TAg	3/8	0.69592848976708	4	FACETS	0.904	0.858	0.951	0.904	0.858	0.951	CLONAL	2	FALSE	2	0.69592848976708	4		549	900	SUCCESS
AR	367	MSKCC	GRCh37	X	66766580	66766580	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	456	789	0	ENST00000374690.3:c.1592A>G	p.Tyr531Cys	p.Y531C	ENST00000374690	NM_000044.3	531	tAc/tGc	1/8	0.677897821812521	2	FACETS	0.997	0.966	1	0.997	0.966	1	CLONAL	2	FALSE	0	0.69592848976708	2		789	657	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383709	15383709	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0050058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	151	718	1	ENST00000263377.2:c.202A>T	p.Arg68Ter	p.R68*	ENST00000263377	NM_058243.2	68	Aga/Tga	2/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.310568363565856	2		719	928	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188226	10188227	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0050058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	108	587	0	ENST00000256474.2:c.369_370del	p.His125ArgfsTer6	p.H125Rfs*6	ENST00000256474	NM_000551.3	123	ggGAca/ggca	2/3	0.310568363565856	1	FACETS	0.861	0.774	0.954	0.861	0.774	0.954	CLONAL	1	TRUE	0	0.310568363565856	1		587	682	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668805	52668806	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TGACTCTCCCTCTTCA	novel	NA	P-0050058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	36	303	0	ENST00000394830.3:c.1098_1113dup	p.Glu372Ter	p.E372*	ENST00000394830	NM_018313.4	371	-/TGAAGAGGGAGAGTCA	12/30	0.310568363565856	1	FACETS	0.538	0.443	0.644	0.538	0.443	0.644	SUBCLONAL	1	TRUE	0	0.310568363565856	1		303	364	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183117	32183117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751471446	NA	P-0050058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	165	895	2	ENST00000375023.3:c.1907C>T	p.Pro636Leu	p.P636L	ENST00000375023	NM_004557.3	636	cCc/cTc	12/30	1	2	FACETS	0.974	0.893	1	0.974	0.893	1	CLONAL	1	TRUE	1	0.310568363565856	2		897	1091	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802587	135802587	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0050058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	50	278	0	ENST00000298552.3:c.210+1G>C		p.X70_splice	ENST00000298552	NM_001162426.1	70			1	2	FACETS	0.811	0.69	0.943	0.811	0.69	0.943	CLONAL	1	TRUE	1	0.310568363565856	2		278	397	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0050059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	443	590	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.589005585291243	3	FACETS	0.897	0.866	0.926	0.897	0.866	0.926	CLONAL	3	TRUE	0	0.644264355908424	3		591	676	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672399	30672399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754933032	NA	P-0050059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	133	540	0	ENST00000376406.3:c.4561C>T	p.Arg1521Trp	p.R1521W	ENST00000376406	NM_014641.2	1521	Cgg/Tgg	10/15	0.644264355908424	8	FACETS	0.895	0.81	0.985	0.149	0.135	0.165	CLONAL	1	TRUE	2	0.644264355908424	8		540	1353	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226573267	226573267	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1392242492	NA	P-0050059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	86	613	0	ENST00000366794.5:c.949G>C	p.Ala317Pro	p.A317P	ENST00000366794	NM_001618.3	317	Gcc/Ccc	7/23	0.20215476128021	6	FACETS	0.733	0.648	0.825	0.244	0.216	0.275	INDETERMINATE	1	TRUE	3	0.644264355908424	6		613	833	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924877	49924877	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1425433681	NA	P-0050061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	134	907	0	ENST00000296474.3:c.4066C>G	p.Leu1356Val	p.L1356V	ENST00000296474	NM_002447.2	1356	Ctg/Gtg	20/20	1	2	FACETS	0.674	0.611	0.741	0.674	0.611	0.741	SUBCLONAL	1	FALSE	1	0.368695880178777	2		907	1078	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727894	78727894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778029024	NA	P-0050063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	317	674	1	ENST00000306801.3:c.739G>A	p.Glu247Lys	p.E247K	ENST00000306801	NM_020761.2	247	Gag/Aag	6/34	0.690968706612278	4	FACETS	1	0.988	1	0.582	0.548	0.617	CLONAL	1	TRUE	2	0.690968706612278	4		675	1333	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11210275	11210275	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	94	478	1	ENST00000361445.4:c.4478T>C	p.Leu1493Pro	p.L1493P	ENST00000361445	NM_004958.3	1493	cTc/cCc	31/58	1	2	FACETS	0.433	0.385	0.483	0.433	0.385	0.483	SUBCLONAL	1	TRUE	1	0.690968706612278	2		479	629	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958612	175958612	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	128	328	0	ENST00000367669.3:c.1733A>G	p.His578Arg	p.H578R	ENST00000367669	NM_022457.5	578	cAc/cGc	16/20	0.681830811942025	4	FACETS	0.917	0.833	1	0.306	0.277	0.336	CLONAL	1	TRUE	1	0.690968706612278	4		328	683	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983992	7983992	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769882996	NA	P-0050064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	55	333	1	ENST00000319144.4:c.634G>A	p.Val212Ile	p.V212I	ENST00000319144	NM_001139.2	212	Gtc/Atc	5/15	0.528636899691013	5	FACETS	1	0.967	1	0.358	0.31	0.409	CLONAL	1	FALSE	1	0.760523462084805	5		334	216	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574002	7574006	+	frameshift_variant	Frame_Shift_Del	DEL	CGGAA	CGGAA	-	novel	NA	P-0050064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	345	725	0	ENST00000269305.4:c.1021_1025del	p.Phe341ArgfsTer4	p.F341Rfs*4	ENST00000269305	NM_001126112.2	341	TTCCGa/a	10/11	0.528636899691013	5	FACETS	0.916	0.89	0.941	1	0.995	1	CLONAL	5	FALSE	1	0.760523462084805	5		725	424	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933301	39933302	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0050064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	244	914	0	ENST00000378444.4:c.1297dup	p.Thr433AsnfsTer7	p.T433Nfs*7	ENST00000378444	NM_001123385.1	433	acc/aAcc	4/15	0.219040584469394	3	FACETS	1	0.975	1	0.695	0.66	0.729	INDETERMINATE	2	FALSE	0	0.760523462084805	3		914	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0050065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	317	646	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.132461211348667	3	FACETS	1	0.991	1	0.616	0.582	0.652	INDETERMINATE	1	TRUE	1	0.59	3		646	1129	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579310	7579310	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1555526469	NA	P-0050065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	281	558	0	ENST00000269305.4:c.375+2T>C		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.132461211348667	3	FACETS	1	0.992	1	0.682	0.642	0.723	INDETERMINATE	1	TRUE	1	0.59	3		558	904	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996771	73996771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753990511	NA	P-0050065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	334	431	0	ENST00000318443.5:c.1327C>T	p.Pro443Ser	p.P443S	ENST00000318443	NM_001024736.1	443	Ccc/Tcc	6/10	0.167507474640756	2	FACETS	1	0.995	1	0.736	0.7	0.772	INDETERMINATE	1	TRUE	0	0.59	2		431	769	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652195	36652195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1279	102	751	3	ENST00000244741.5:c.317C>T	p.Ala106Val	p.A106V	ENST00000244741	NM_000389.4	106	gCa/gTa	2/3	0.132461211348667	3	FACETS	0.324	0.289	0.362	0.162	0.144	0.181	INDETERMINATE	1	TRUE	1	0.59	3		754	1381	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971049	21971060	+	inframe_deletion	In_Frame_Del	DEL	CCGCGCCCCGGC	CCGCGCCCCGGC	-	novel	NA	P-0050065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	227	575	0	ENST00000304494.5:c.298_309del	p.Ala100_Arg103del	p.A100_R103del	ENST00000304494	NM_000077.4	100	GCCGGGGCGCGG/-	2/3	0.205828751753499	0	FACETS	0.384	0.358	0.41			1	INDETERMINATE	1	TRUE	0	0.59	0		575	822	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974700	21974701	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0050065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	184	466	0	ENST00000304494.5:c.126_127del	p.Asn42LysfsTer77	p.N42Kfs*77	ENST00000304494	NM_000077.4	42	aaTAgt/aagt	1/3	0.205828751753499	0	FACETS	0.35	0.324	0.378			1	INDETERMINATE	1	TRUE	0	0.59	0		466	730	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	28	270	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	FALSE	1	0.168372270684249	2		270	309	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	135	528	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	0.875	0.798	0.955	1	0.992	1	CLONAL	3	FALSE	1	0.168372270684249	2		528	611	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	22	274	0	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	1	2	FACETS	0.722	0.559	0.911	0.722	0.559	0.911	CLONAL	1	FALSE	1	0.168372270684249	2		274	362	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	107	352	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.973	1	1	0.99	1	CLONAL	2	FALSE	1	0.168372270684249	2		352	517	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	150	730	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	1	0.963	1	1	0.992	1	CLONAL	2	FALSE	1	0.168372270684249	2		730	812	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	156	750	1	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	1	2	FACETS	1	0.966	1	1	0.992	1	CLONAL	2	FALSE	1	0.168372270684249	2		751	839	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	87	294	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	1	0.904	1	1	0.985	1	CLONAL	2	FALSE	1	0.168372270684249	2		294	507	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021817	71021817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs797045586	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	48	219	0	ENST00000318789.4:c.1541G>A	p.Arg514His	p.R514H	ENST00000318789	NM_032682.5	514	cGt/cAt	18/21	1	2	FACETS	1	0.866	1	1	0.974	1	CLONAL	2	FALSE	1	0.168372270684249	2		219	280	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130120	143130120	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	106	438	0	ENST00000262992.4:c.896del	p.Asn299MetfsTer10	p.N299Mfs*10	ENST00000262992	NM_001101669.1	299	aAt/at	11/24	1	2	FACETS	1	0.963	1	1	0.989	1	CLONAL	2	FALSE	1	0.168372270684249	2		438	546	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	120	495	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.921	1	1	0.989	1	CLONAL	2	FALSE	1	0.168372270684249	2		495	698	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136984	64136984	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157020356	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	81	682	2	ENST00000334205.4:c.1495C>T	p.Arg499Trp	p.R499W	ENST00000334205	NM_003942.2	499	Cgg/Tgg	13/17	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	1	0.168372270684249	2		684	854	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069059	5069060	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	50	266	0	ENST00000381652.3:c.1370dup	p.Asn457LysfsTer2	p.N457Kfs*2	ENST00000381652	NM_004972.3	455	aca/acAa	11/25	1	2	FACETS	0.958	0.817	1	1	0.974	1	CLONAL	2	FALSE	1	0.168372270684249	2		266	310	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843495	3843495	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	127	513	0	ENST00000262367.5:c.1108C>T	p.Arg370Ter	p.R370*	ENST00000262367	NM_004380.2	370	Cga/Tga	4/31	1	2	FACETS	1	0.961	1	1	0.99	1	CLONAL	2	FALSE	1	0.168372270684249	2		513	679	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262742	16262742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769028117	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	98	362	1	ENST00000375759.3:c.10007G>A	p.Arg3336Gln	p.R3336Q	ENST00000375759	NM_015001.2	3336	cGg/cAg	11/15	1	2	FACETS	1	0.957	1	1	0.988	1	CLONAL	2	FALSE	1	0.168372270684249	2		363	513	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533760	63533760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764640447	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	157	624	0	ENST00000307078.5:c.1394G>A	p.Arg465His	p.R465H	ENST00000307078	NM_004655.3	465	cGc/cAc	6/11	1	2	FACETS	1	0.977	1	1	0.993	1	CLONAL	2	FALSE	1	0.168372270684249	2		624	792	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249230	10249230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779967013	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	130	620	0	ENST00000340748.4:c.3952G>A	p.Ala1318Thr	p.A1318T	ENST00000340748		1318	Gcg/Acg	34/40	1	2	FACETS	1	0.955	1	1	0.991	1	CLONAL	2	FALSE	1	0.168372270684249	2		620	713	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405827	157405827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373508866	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	108	461	0	ENST00000346085.5:c.2069C>T	p.Thr690Met	p.T690M	ENST00000346085	NM_020732.3	690	aCg/aTg	6/20	1	2	FACETS	0.866	0.781	0.955	1	0.99	1	CLONAL	3	FALSE	1	0.168372270684249	2		461	494	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877349	40877349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747289224	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	119	466	0	ENST00000373198.4:c.2347G>A	p.Val783Met	p.V783M	ENST00000373198	NM_133170.3	783	Gtg/Atg	15/32	1	2	FACETS	0.86	0.779	0.944	1	0.991	1	CLONAL	3	FALSE	1	0.168372270684249	2		466	548	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856469	111856469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	119	413	1	ENST00000341259.2:c.520G>A	p.Ala174Thr	p.A174T	ENST00000341259	NM_005475.2	174	Gcc/Acc	2/8	1	2	FACETS	0.95	0.862	1	1	0.991	1	CLONAL	3	FALSE	1	0.168372270684249	2		414	496	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207633	2207633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752264656	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	194	680	1	ENST00000398665.3:c.917C>T	p.Thr306Met	p.T306M	ENST00000398665	NM_032482.2	306	aCg/aTg	11/28	1	2	FACETS	1	0.985	1	1	0.994	1	CLONAL	2	FALSE	1	0.168372270684249	2		681	930	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797268	32797268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770111657	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	171	745	1	ENST00000374899.4:c.1841G>A	p.Arg614His	p.R614H	ENST00000374899	NM_018833.2	614	cGt/cAt	11/12	1	2	FACETS	1	0.966	1	1	0.993	1	CLONAL	2	FALSE	1	0.168372270684249	2		746	931	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275302	115275302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	151	508	0	ENST00000438362.2:c.1111C>T	p.Arg371Cys	p.R371C	ENST00000438362	NM_001242891.1	371	Cgt/Tgt	10/20	1	2	FACETS	1	0.981	1	1	0.993	1	CLONAL	2	FALSE	1	0.168372270684249	2		508	721	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273278	55273278	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369585356	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	128	470	0	ENST00000275493.2:c.3601G>A	p.Ala1201Thr	p.A1201T	ENST00000275493	NM_005228.3	1201	Gcg/Acg	28/28	1	2	FACETS	0.86	0.783	0.942	1	0.991	1	CLONAL	3	FALSE	1	0.168372270684249	2		470	589	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462783	69462783	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1222442441	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	132	610	0	ENST00000227507.2:c.596C>T	p.Pro199Leu	p.P199L	ENST00000227507	NM_053056.2	199	cCg/cTg	4/5	1	2	FACETS	1	0.976	1	1	0.991	1	CLONAL	2	FALSE	1	0.168372270684249	2		610	646	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741394	145741394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377494266	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	244	865	0	ENST00000428558.2:c.1109G>A	p.Arg370His	p.R370H	ENST00000428558	NM_004260.3	370	cGt/cAt	5/22	1	2	FACETS	0.884	0.826	0.944	1	0.995	1	CLONAL	3	FALSE	1	0.168372270684249	2		865	1093	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003191	42003191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs761227360	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	142	465	0	ENST00000219905.7:c.2728C>T	p.Arg910Ter	p.R910*	ENST00000219905	NM_001164273.1	910	Cga/Tga	8/24	1	2	FACETS	1	0.98	1	1	0.992	1	CLONAL	2	FALSE	1	0.168372270684249	2		465	680	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528658	157528658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777278111	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	147	556	0	ENST00000346085.5:c.6383G>A	p.Arg2128Gln	p.R2128Q	ENST00000346085	NM_020732.3	2128	cGa/cAa	20/20	1	2	FACETS	1	0.979	1	1	0.992	1	CLONAL	2	FALSE	1	0.168372270684249	2		556	717	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019410	42019410	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs528009988	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	146	438	0	ENST00000219905.7:c.3463C>T	p.Arg1155Ter	p.R1155*	ENST00000219905	NM_001164273.1	1155	Cga/Tga	10/24	1	2	FACETS	0.942	0.863	1	1	0.993	1	CLONAL	3	FALSE	1	0.168372270684249	2		438	614	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350234	89350234	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	173	671	0	ENST00000301030.4:c.2716C>T	p.Arg906Ter	p.R906*	ENST00000301030	NM_001256183.1	906	Cga/Tga	9/13	1	2	FACETS	1	0.979	1	1	0.993	1	CLONAL	2	FALSE	1	0.168372270684249	2		671	873	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687121	176687121	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784137	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	110	441	0	ENST00000439151.2:c.5098C>T	p.Arg1700Ter	p.R1700*	ENST00000439151	NM_022455.4	1700	Cga/Tga	14/23	1	2	FACETS	1	0.939	1	1	0.989	1	CLONAL	2	FALSE	1	0.168372270684249	2		441	617	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120469232	120469232	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs371580595	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	120	398	0	ENST00000256646.2:c.3895C>T	p.Arg1299Trp	p.R1299W	ENST00000256646	NM_024408.3	1299	Cgg/Tgg	24/34	1	2	FACETS	1	0.973	1	1	0.99	1	CLONAL	2	FALSE	1	0.168372270684249	2		398	594	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494872	56494872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112651994	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	137	522	1	ENST00000267101.3:c.3229C>T	p.Arg1077Trp	p.R1077W	ENST00000267101	NM_001982.3	1077	Cgg/Tgg	27/28	1	2	FACETS	1	0.972	1	1	0.991	1	CLONAL	2	FALSE	1	0.168372270684249	2		523	700	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418643	49418643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs936142615	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	145	549	0	ENST00000301067.7:c.15871G>A	p.Glu5291Lys	p.E5291K	ENST00000301067	NM_003482.3	5291	Gag/Aag	49/54	1	2	FACETS	1	0.973	1	1	0.992	1	CLONAL	2	FALSE	1	0.168372270684249	2		549	741	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104636	69104636	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757884988	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	143	581	0	ENST00000288368.4:c.4480C>T	p.Arg1494Cys	p.R1494C	ENST00000288368	NM_024870.2	1494	Cgc/Tgc	37/40	1	2	FACETS	1	0.954	1	1	0.991	1	CLONAL	2	FALSE	1	0.168372270684249	2		581	793	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988217	36988217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	149	459	0	ENST00000354822.5:c.436G>A	p.Ala146Thr	p.A146T	ENST00000354822	NM_001079668.2	146	Gcc/Acc	2/3	1	2	FACETS	1	0.918	1	1	0.993	1	CLONAL	3	FALSE	1	0.168372270684249	2		459	590	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602911	55602911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753419764	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	108	377	1	ENST00000288135.5:c.2621C>T	p.Pro874Leu	p.P874L	ENST00000288135	NM_000222.2	874	cCg/cTg	19/21	1	2	FACETS	0.837	0.754	0.924	1	0.99	1	CLONAL	3	FALSE	1	0.168372270684249	2		378	511	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828497	72828497	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	175	588	0	ENST00000268489.5:c.8084G>A	p.Arg2695Gln	p.R2695Q	ENST00000268489	NM_006885.3	2695	cGg/cAg	9/10	1	2	FACETS	1	0.984	1	1	0.993	1	CLONAL	2	FALSE	1	0.168372270684249	2		588	832	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957482	1957482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1422388271	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	161	625	0	ENST00000382891.5:c.2581G>A	p.Glu861Lys	p.E861K	ENST00000382891	NM_133335.3	861	Gag/Aag	14/22	1	2	FACETS	1	0.98	1	1	0.993	1	CLONAL	2	FALSE	1	0.168372270684249	2		625	788	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589892	212589892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	131	502	1	ENST00000342788.4:c.650G>A	p.Cys217Tyr	p.C217Y	ENST00000342788	NM_005235.2	217	tGt/tAt	6/28	1	2	FACETS	1	0.977	1	1	0.991	1	CLONAL	2	FALSE	1	0.168372270684249	2		503	631	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662351	67662351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	131	512	1	ENST00000264010.4:c.1597C>T	p.Arg533Cys	p.R533C	ENST00000264010	NM_006565.3	533	Cgc/Tgc	9/12	1	2	FACETS	1	0.969	1	1	0.991	1	CLONAL	2	FALSE	1	0.168372270684249	2		513	677	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212423	5212423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768007031	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	162	762	0	ENST00000357368.4:c.4694C>T	p.Thr1565Met	p.T1565M	ENST00000357368	NM_002850.3	1565	aCg/aTg	31/38	1	2	FACETS	1	0.97	1	1	0.992	1	CLONAL	2	FALSE	1	0.168372270684249	2		762	859	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841268	15841268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	127	426	1	ENST00000307771.7:c.1352G>A	p.Arg451His	p.R451H	ENST00000307771	NM_005089.3	451	cGc/cAc	11/11	1	2	FACETS	0.945	0.86	1	1	0.992	1	CLONAL	3	FALSE	1	0.168372270684249	2		427	532	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31947213	31947213	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs570620120	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	118	589	1	ENST00000375333.2:c.698G>A	p.Arg233Gln	p.R233Q	ENST00000375333	NM_032454.1	233	cGa/cAa	5/8	1	2	FACETS	1	0.92	1	1	0.989	1	CLONAL	2	FALSE	1	0.168372270684249	2		590	687	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212615400	212615400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769311799	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	118	423	1	ENST00000342788.4:c.586C>T	p.Arg196Cys	p.R196C	ENST00000342788	NM_005235.2	196	Cgt/Tgt	5/28	1	2	FACETS	1	0.972	1	1	0.99	1	CLONAL	2	FALSE	1	0.168372270684249	2		424	585	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511680	46511680	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	144	434	0	ENST00000262741.5:c.1097T>C	p.Val366Ala	p.V366A	ENST00000262741	NM_003629.3	366	gTa/gCa	9/10	1	2	FACETS	0.902	0.825	0.982	1	0.993	1	CLONAL	3	FALSE	1	0.168372270684249	2		434	632	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332696	65332696	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	82	387	0	ENST00000342505.4:c.843C>G	p.Tyr281Ter	p.Y281*	ENST00000342505	NM_002227.2	281	taC/taG	7/25	1	2	FACETS	0.904	0.798	1	1	0.982	1	CLONAL	2	FALSE	1	0.168372270684249	2		387	539	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612884	228612884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756376731	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	174	637	0	ENST00000366696.1:c.143C>T	p.Ala48Val	p.A48V	ENST00000366696	NM_003493.2	48	gCg/gTg	1/1	1	2	FACETS	0.86	0.793	0.93	1	0.994	1	CLONAL	3	FALSE	1	0.168372270684249	2		637	801	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201491	67201491	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766984944	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	170	742	1	ENST00000312629.5:c.932G>A	p.Arg311Gln	p.R311Q	ENST00000312629	NM_003952.2	311	cGg/cAg	11/15	1	2	FACETS	1	0.956	1	1	0.992	1	CLONAL	2	FALSE	1	0.168372270684249	2		743	954	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201672	67201672	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	132	673	0	ENST00000312629.5:c.973C>A	p.His325Asn	p.H325N	ENST00000312629	NM_003952.2	325	Cat/Aat	12/15	1	2	FACETS	1	0.932	1	1	0.99	1	CLONAL	2	FALSE	1	0.168372270684249	2		673	760	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416684	416684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372350658	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	101	363	0	ENST00000399788.2:c.3866G>A	p.Arg1289Gln	p.R1289Q	ENST00000399788	NM_001042603.1	1289	cGa/cAa	23/28	1	2	FACETS	1	0.968	1	1	0.989	1	CLONAL	2	FALSE	1	0.168372270684249	2		363	502	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211656	46211656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	53	229	0	ENST00000334344.6:c.622G>A	p.Gly208Arg	p.G208R	ENST00000334344	NM_152641.2	208	Ggg/Agg	5/21	1	2	FACETS	1	0.919	1	1	0.978	1	CLONAL	2	FALSE	1	0.168372270684249	2		229	285	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445893	49445893	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	215	809	0	ENST00000301067.7:c.1573G>T	p.Glu525Ter	p.E525*	ENST00000301067	NM_003482.3	525	Gag/Tag	10/54	1	2	FACETS	0.878	0.816	0.941	1	0.995	1	CLONAL	3	FALSE	1	0.168372270684249	2		809	970	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209313	133209313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs995579204	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	178	721	0	ENST00000320574.5:c.6073G>A	p.Val2025Met	p.V2025M	ENST00000320574	NM_006231.2	2025	Gtg/Atg	44/49	1	2	FACETS	0.958	0.885	1	1	0.994	1	CLONAL	3	FALSE	1	0.168372270684249	2		721	736	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602373	28602373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	127	417	1	ENST00000241453.7:c.1995G>A	p.Met665Ile	p.M665I	ENST00000241453	NM_004119.2	665	atG/atA	16/24	1	2	FACETS	1	0.976	1	1	0.991	1	CLONAL	2	FALSE	1	0.168372270684249	2		418	619	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68878231	68878231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	74	307	0	ENST00000487270.1:c.944C>T	p.Ser315Leu	p.S315L	ENST00000487270	NM_133509.3	315	tCa/tTa	9/11	1	2	FACETS	1	0.895	1	1	0.983	1	CLONAL	2	FALSE	1	0.168372270684249	2		307	431	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712857	43712857	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1388529096	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	141	636	0	ENST00000382044.4:c.4327C>T	p.Arg1443Cys	p.R1443C	ENST00000382044	NM_001141980.1	1443	Cgt/Tgt	21/28	1	2	FACETS	1	0.946	1	1	0.991	1	CLONAL	2	FALSE	1	0.168372270684249	2		636	797	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14015970	14015970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768270013	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	79	314	0	ENST00000311895.7:c.290G>A	p.Arg97His	p.R97H	ENST00000311895	NM_005236.2	97	cGc/cAc	2/11	1	2	FACETS	1	0.93	1	1	0.985	1	CLONAL	2	FALSE	1	0.168372270684249	2		314	437	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133215	30133215	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	155	619	0	ENST00000263025.4:c.283T>G	p.Phe95Val	p.F95V	ENST00000263025	NM_002746.2	95	Ttc/Gtc	2/9	1	2	FACETS	0.862	0.791	0.936	1	0.993	1	CLONAL	3	FALSE	1	0.168372270684249	2		619	712	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654631	67654631	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	136	476	0	ENST00000264010.4:c.1118A>G	p.His373Arg	p.H373R	ENST00000264010	NM_006565.3	373	cAt/cGt	6/12	1	2	FACETS	1	0.968	1	1	0.991	1	CLONAL	2	FALSE	1	0.168372270684249	2		476	710	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337293	89337293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1335837964	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	150	420	0	ENST00000301030.4:c.7738G>A	p.Asp2580Asn	p.D2580N	ENST00000301030	NM_001256183.1	2580	Gac/Aac	12/13	1	2	FACETS	0.893	0.819	0.971	1	0.993	1	CLONAL	3	FALSE	1	0.168372270684249	2		420	665	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687255	37687255	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	135	552	1	ENST00000447079.4:c.4159A>G	p.Ser1387Gly	p.S1387G	ENST00000447079	NM_015083.1	1387	Agc/Ggc	14/14	1	2	FACETS	1	0.968	1	1	0.991	1	CLONAL	2	FALSE	1	0.168372270684249	2		553	706	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66524000	66524000	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	29	197	0	ENST00000358598.2:c.728G>A	p.Arg243Gln	p.R243Q	ENST00000358598	NM_212471.2	243	cGg/cAg	8/11	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	1	0.168372270684249	2		197	247	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1623951	1623951	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs374988827	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	146	558	1	ENST00000344749.5:c.548C>T	p.Ser183Leu	p.S183L	ENST00000344749	NM_001136139.2	183	tCg/tTg	8/19	1	2	FACETS	1	0.978	1	1	0.992	1	CLONAL	2	FALSE	1	0.168372270684249	2		559	713	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257875	19257875	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	213	844	0	ENST00000162023.5:c.511C>T	p.Arg171Ter	p.R171*	ENST00000162023		171	Cga/Tga	9/13	1	2	FACETS	0.949	0.883	1	1	0.995	1	CLONAL	3	FALSE	1	0.168372270684249	2		844	889	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224559	36224559	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	71	788	0	ENST00000222270.7:c.7024del	p.Glu2342SerfsTer97	p.E2342Sfs*97	ENST00000222270	NM_014727.1	2341	Ggg/gg	29/37	1	2	FACETS	0.854	0.744	0.975	0.854	0.744	0.975	CLONAL	1	FALSE	1	0.168372270684249	2		788	987	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026498	48026498	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	106	406	0	ENST00000234420.5:c.1376C>A	p.Ser459Tyr	p.S459Y	ENST00000234420	NM_000179.2	459	tCt/tAt	4/10	1	2	FACETS	1	0.961	1	1	0.989	1	CLONAL	2	FALSE	1	0.168372270684249	2		406	553	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033699	48033715	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCTTGCTAATCTCCC	AGGCTTGCTAATCTCCC	-	novel	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	68	366	0	ENST00000234420.5:c.3912_3928del	p.Leu1305GlyfsTer8	p.L1305Gfs*8	ENST00000234420	NM_000179.2	1304	AGGCTTGCTAATCTCCCa/a	9/10	1	2	FACETS	0.941	0.822	1	1	0.98	1	CLONAL	2	FALSE	1	0.168372270684249	2		366	429	SUCCESS
ATR	545	MSKCC	GRCh37	3	142180907	142180907	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751772547	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	49	277	0	ENST00000350721.4:c.7067G>A	p.Arg2356His	p.R2356H	ENST00000350721	NM_001184.3	2356	cGt/cAt	42/47	1	2	FACETS	1	0.905	1	1	0.976	1	CLONAL	2	FALSE	1	0.168372270684249	2		277	269	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917489	178917489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754044428	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	69	298	0	ENST00000263967.3:c.364G>A	p.Gly122Ser	p.G122S	ENST00000263967	NM_006218.2	122	Ggc/Agc	3/21	1	2	FACETS	1	0.959	1	1	0.984	1	CLONAL	2	FALSE	1	0.168372270684249	2		298	334	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861040	35861040	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	26	405	0	ENST00000303115.3:c.169T>C	p.Cys57Arg	p.C57R	ENST00000303115	NM_002185.3	57	Tgt/Cgt	2/8	1	2	FACETS	0.63	0.498	0.782	0.63	0.498	0.782	SUBCLONAL	1	FALSE	1	0.168372270684249	2		405	490	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939105	76939105	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782088332	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	29	420	2	ENST00000373344.5:c.1643G>A	p.Gly548Asp	p.G548D	ENST00000373344	NM_000489.3	548	gGc/gAc	9/35	1	2	FACETS	0.598	0.479	0.735	0.598	0.479	0.735	SUBCLONAL	1	FALSE	1	0.168372270684249	2		422	576	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195105	123195105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	134	418	0	ENST00000218089.9:c.1448G>A	p.Ser483Asn	p.S483N	ENST00000218089	NM_001042749.1	483	aGc/aAc	16/35	1	2	FACETS	0.907	0.827	0.99	1	0.992	1	CLONAL	3	FALSE	1	0.168372270684249	2		418	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0050067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	538	710	1	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.866219122763201	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.866219122763201	1		711	642	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615652	43615652	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0050071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	151	494	0	ENST00000355710.3:c.2730+1G>A		p.X910_splice	ENST00000355710	NM_020975.4	910			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		494	540	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426974	70426974	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	147	307	0	ENST00000373644.4:c.4634A>G	p.Asn1545Ser	p.N1545S	ENST00000373644	NM_030625.2	1545	aAt/aGt	7/12	0.212720588377869	3	FACETS	0.997	0.913	1	0.665	0.608	0.724	CLONAL	2	TRUE	0	0.241896406807543	3		307	683	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772950	135772951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs118203724	NA	P-0050072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	87	306	0	ENST00000298552.3:c.2672dup	p.Asn891LysfsTer13	p.N891Kfs*13	ENST00000298552	NM_001162426.1	891	aac/aaAc	21/23	0.167171297202963	2	FACETS	1	0.949	1	0.565	0.5	0.633	CLONAL	1	TRUE	0	0.241896406807543	2		306	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0050072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	131	674	1	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.167171297202963	2	FACETS	1	0.979	1	0.634	0.575	0.696	CLONAL	1	TRUE	0	0.241896406807543	2		675	854	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334828	81334828	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs769585774	NA	P-0050072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	110	329	0	ENST00000222390.5:c.1888C>T	p.Arg630Ter	p.R630*	ENST00000222390	NM_000601.4	630	Cga/Tga	17/18	0.241896406807543	3	FACETS	1	0.982	1	0.479	0.43	0.53	CLONAL	1	TRUE	0	0.241896406807543	3		329	710	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632419	3632419	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs757727147	NA	P-0050072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	100	629	0	ENST00000294008.3:c.5429C>G	p.Thr1810Ser	p.T1810S	ENST00000294008	NM_032444.2	1810	aCt/aGt	15/15	0.241896406807543	3	FACETS	0.743	0.662	0.831	0.372	0.331	0.416	SUBCLONAL	1	TRUE	1	0.241896406807543	3		629	1247	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161284200	161284200	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs781337432	NA	P-0050072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	72	390	0	ENST00000367975.2:c.5C>G	p.Ala2Gly	p.A2G	ENST00000367975	NM_003001.3	2	gCt/gGt	1/6	0.171193084762099	4	FACETS	0.788	0.687	0.898	0.394	0.343	0.449	SUBCLONAL	1	TRUE	2	0.241896406807543	4		390	938	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028780	42028780	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	79	434	0	ENST00000219905.7:c.4318G>C	p.Val1440Leu	p.V1440L	ENST00000219905	NM_001164273.1	1440	Gtg/Ctg	13/24	1	2	FACETS	0.848	0.745	0.959	0.848	0.745	0.959	CLONAL	1	TRUE	1	0.241896406807543	2		434	770	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16022796	16022796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	105	300	0	ENST00000268712.3:c.1856C>T	p.Ser619Phe	p.S619F	ENST00000268712	NM_006311.3	619	tCt/tTt	17/46	0.167171297202963	2	FACETS	0.751	0.675	0.832	0.751	0.675	0.832	SUBCLONAL	2	TRUE	0	0.241896406807543	2		300	578	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42790949	42790949	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	61	505	0	ENST00000575354.2:c.94G>C	p.Val32Leu	p.V32L	ENST00000575354	NM_015125.3	32	Gtg/Ctg	2/20	1	2	FACETS	0.5	0.43	0.577	0.5	0.43	0.577	SUBCLONAL	1	TRUE	1	0.241896406807543	2		505	1009	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38153387	38153387	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1374124695	NA	P-0050072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	262	435	0	ENST00000317025.8:c.2842A>G	p.Asn948Asp	p.N948D	ENST00000317025	NM_023034.1	948	Aat/Gat	16/24	0.195811496089227	5	FACETS	1	0.988	1	0.825	0.772	0.879	CLONAL	2	TRUE	2	0.241896406807543	5		435	1193	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	290	468	0				ENST00000310581	NM_198253.2	-/1132			0.826418600344021	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.826418600344021	3		468	478	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0050073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	706	582	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.826418600344021	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.826418600344021	2		582	835	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120554403	120554403	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	45	117	0	ENST00000229340.5:c.52G>A	p.Gly18Ser	p.G18S	ENST00000229340	NM_006861.6	18	Ggt/Agt	1/6	0.331521329746943	1	FACETS	0.46	0.395	0.528	0.46	0.395	0.528	INDETERMINATE	1	TRUE	0	0.826418600344021	1		117	139	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498304	29498304	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	55	687	0	ENST00000389048.3:c.1876G>C	p.Asp626His	p.D626H	ENST00000389048	NM_004304.4	626	Gac/Cac	10/29	1	2	FACETS	0.179	0.152	0.208	0.179	0.152	0.208	SUBCLONAL	1	TRUE	1	0.826418600344021	2		687	744	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81340827	81340827	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	100	229	0	ENST00000222390.5:c.1414G>C	p.Asp472His	p.D472H	ENST00000222390	NM_000601.4	472	Gat/Cat	12/18	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.826418600344021	2		229	233	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0050074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	99	829	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	0.367404177971062	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.367404177971062	1		829	394	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs775623976	NA	P-0050074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	61	393	0	ENST00000335508.6:c.1873C>G	p.Arg625Gly	p.R625G	ENST00000335508	NM_012433.2	625	Cgt/Ggt	14/25	1	2	FACETS	0.925	0.802	1	0.925	0.802	1	CLONAL	1	TRUE	1	0.367404177971062	2		393	359	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620611	52620613	+	inframe_deletion	In_Frame_Del	DEL	TTT	TTT	-	novel	NA	P-0050074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	81	570	0	ENST00000394830.3:c.3140_3142del	p.Lys1047del	p.K1047del	ENST00000394830	NM_018313.4	1047	aAAAtt/att	21/30	0.367404177971062	1	FACETS	0.925	0.82	1	0.925	0.82	1	CLONAL	1	TRUE	0	0.367404177971062	1		570	389	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335697	81335697	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	76	525	0	ENST00000222390.5:c.1663G>T	p.Gly555Ter	p.G555*	ENST00000222390	NM_000601.4	555	Gga/Tga	15/18	0.378387080679133	3	FACETS	0.844	0.741	0.954	0.422	0.37	0.477	CLONAL	1	TRUE	1	0.378387080679133	3		525	566	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829040	128829042	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	rs570242755	NA	P-0050075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	10	71	0	ENST00000249373.3:c.67_69del	p.Leu23del	p.L23del	ENST00000249373	NM_005631.4	16	ggGCTg/ggg	1/12	0.378387080679133	3	FACETS	0.469	0.319	0.656	0.235	0.159	0.328	SUBCLONAL	1	TRUE	1	0.378387080679133	3		71	134	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186791	11186791	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	131	624	1	ENST00000361445.4:c.6414G>T	p.Leu2138Phe	p.L2138F	ENST00000361445	NM_004958.3	2138	ttG/ttT	46/58	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.378387080679133	2		625	669	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041387	42041388	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs767351416	NA	P-0050075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	135	717	1	ENST00000219905.7:c.5585_5586del	p.Ser1862CysfsTer30	p.S1862Cfs*30	ENST00000219905	NM_001164273.1	1861	tTC/t	17/24	0.378387080679133	1	FACETS	0.976	0.89	1	0.976	0.89	1	CLONAL	1	TRUE	0	0.378387080679133	1		718	593	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026119	48026119	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs886056143	NA	P-0050075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	96	531	0	ENST00000234420.5:c.997A>G	p.Thr333Ala	p.T333A	ENST00000234420	NM_000179.2	333	Acc/Gcc	4/10	1	2	FACETS	0.952	0.851	1	0.952	0.851	1	CLONAL	1	TRUE	1	0.378387080679133	2		531	533	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188310	10188311	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0050075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	119	583	0	ENST00000256474.2:c.456_457del	p.Leu153AlafsTer20	p.L153Afs*20	ENST00000256474	NM_000551.3	151	atCAca/atca	2/3	0.378387080679133	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.378387080679133	1		583	464	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52675986	52675986	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	135	698	0	ENST00000394830.3:c.1071del	p.Asp358MetfsTer4	p.D358Mfs*4	ENST00000394830	NM_018313.4	357	gaA/ga	11/30	0.378387080679133	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.378387080679133	1		698	501	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0050076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	289	328	0				ENST00000310581	NM_198253.2	-/1132			0.530836311881435	3	FACETS	0.957	0.914	0.999	1	0.995	1	CLONAL	3	FALSE	1	0.530836311881435	3		328	480	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559842	29559842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	170	386	0	ENST00000356175.3:c.3439C>T	p.Leu1147Phe	p.L1147F	ENST00000356175	NM_000267.3	1147	Ctt/Ttt	26/57	0.477332641714286	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	FALSE	2	0.530836311881435	4		386	405	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317572	1317572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	99	367	0	ENST00000400841.2:c.493G>A	p.Glu165Lys	p.E165K	ENST00000400841		165	Gaa/Aaa	5/6	0.530836311881435	2	FACETS	1	0.984	1			1	CLONAL	1	FALSE	NA	0.530836311881435	2		367	251	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0050076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	227	442	1	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.530836311881435	9	FACETS	1	0.983	1	1	0.983	1	CLONAL	7	FALSE	2	0.530836311881435	9		443	329	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692896	89692896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123322	NA	P-0050076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	82	403	0	ENST00000371953.3:c.380G>A	p.Gly127Glu	p.G127E	ENST00000371953	NM_000314.4	127	gGa/gAa	5/9	0.530836311881435	2	FACETS	0.945	0.881	1	1	0.986	1	CLONAL	3	FALSE	0	0.530836311881435	2		403	109	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436012	116436012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369312680	NA	P-0050076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	185	717	1	ENST00000397752.3:c.4007G>A	p.Arg1336Gln	p.R1336Q	ENST00000397752	NM_000245.2	1336	cGg/cAg	21/21	0.530836311881435	9	FACETS	0.998	0.93	1	0.57	0.531	0.61	CLONAL	4	FALSE	2	0.530836311881435	9		718	499	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093455	30093455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776034417	NA	P-0050076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	12	322	0	ENST00000331968.5:c.1808G>A	p.Arg603His	p.R603H	ENST00000331968	NM_002742.2	603	cGt/cAt	13/18	0.477332641714286	4	FACETS	0.624	0.442	0.843	0.312	0.221	0.422	SUBCLONAL	1	FALSE	2	0.530836311881435	4		322	111	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953820	55953820	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	141	648	0	ENST00000263923.4:c.3616G>A	p.Glu1206Lys	p.E1206K	ENST00000263923	NM_002253.2	1206	Gaa/Aaa	27/30	0.530836311881435	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	FALSE	1	0.530836311881435	3		648	280	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437443	110437443	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753666571	NA	P-0050076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	416	499	0	ENST00000375856.3:c.958C>T	p.Pro320Ser	p.P320S	ENST00000375856	NM_003749.2	320	Ccc/Tcc	1/2	0.503243786437655	5	FACETS	1	0.96	1	1	0.96	1	CLONAL	3	FALSE	2	0.530836311881435	5		499	935	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021061	26021061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	276	627	2	ENST00000357647.3:c.344C>T	p.Ala115Val	p.A115V	ENST00000357647	NM_003529.2	115	gCc/gTc	1/1	0.530836311881435	6	FACETS	1	0.957	1	1	0.957	1	CLONAL	3	FALSE	3	0.530836311881435	6		629	704	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422928	12422928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765206131	NA	P-0050076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	45	658	0	ENST00000287820.6:c.418C>T	p.Arg140Cys	p.R140C	ENST00000287820	NM_015869.4	140	Cgt/Tgt	3/7	0.530836311881435	3	FACETS	0.851	0.721	0.993	0.426	0.36	0.497	CLONAL	1	FALSE	1	0.530836311881435	3		658	252	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944292	206944292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	298	630	1	ENST00000423557.1:c.338G>A	p.Gly113Glu	p.G113E	ENST00000423557	NM_000572.2	113	gGg/gAg	3/5	0.530836311881435	5	FACETS	1	0.987	1	0.76	0.717	0.803	CLONAL	2	FALSE	2	0.530836311881435	5		631	885	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032572	47032572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	448	405	1	ENST00000377604.3:c.478C>T	p.Arg160Trp	p.R160W	ENST00000377604	NM_001204468.1	160	Cgg/Tgg	5/24	0.530836311881435	2	FACETS	1	0.997	1			1	CLONAL	3	FALSE	NA	0.530836311881435	2		406	500	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928517	69928517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	135	722	0	ENST00000352241.4:c.337C>T	p.Pro113Ser	p.P113S	ENST00000352241	NM_198159.2	113	Ccg/Tcg	2/10	0.530836311881435	3	FACETS	1	0.976	1	0.596	0.544	0.65	CLONAL	1	FALSE	1	0.530836311881435	3		722	540	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176118171	176118171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	52	363	0	ENST00000367669.3:c.802C>T	p.Leu268Phe	p.L268F	ENST00000367669	NM_022457.5	268	Ctc/Ttc	6/20	0.530836311881435	5	FACETS	0.989	0.856	1	0.659	0.571	0.752	CLONAL	2	FALSE	2	0.530836311881435	5		363	178	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195468	102195468	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	90	546	0	ENST00000263464.3:c.228G>A	p.Trp76Ter	p.W76*	ENST00000263464	NM_001165.4	76	tgG/tgA	2/9	0.530836311881435	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	FALSE	2	0.530836311881435	4		546	223	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377307	118377307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782271033	NA	P-0050076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	137	418	0	ENST00000534358.1:c.10700C>T	p.Ser3567Phe	p.S3567F	ENST00000534358	NM_005933.3	3567	tCt/tTt	27/36	0.530836311881435	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	FALSE	2	0.530836311881435	4		418	338	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060608	38060608	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	316	890	0	ENST00000250448.2:c.1381C>T	p.Gln461Ter	p.Q461*	ENST00000250448	NM_004496.3	461	Caa/Taa	2/2	0.477332641714286	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	FALSE	2	0.530836311881435	4		890	801	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217003	7217003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	221	686	0	ENST00000380728.2:c.518G>A	p.Gly173Glu	p.G173E	ENST00000380728		173	gGg/gAg	7/11	0.530836311881435	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	FALSE	0	0.530836311881435	3		686	334	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928469	69928469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	146	761	0	ENST00000352241.4:c.289G>A	p.Ala97Thr	p.A97T	ENST00000352241	NM_198159.2	97	Gcc/Acc	2/10	0.530836311881435	3	FACETS	1	0.972	1	0.571	0.523	0.62	CLONAL	1	FALSE	1	0.530836311881435	3		761	610	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013732	170013732	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	58	462	0	ENST00000295797.4:c.1451C>T	p.Ser484Phe	p.S484F	ENST00000295797	NM_002740.5	484	tCt/tTt	15/18	0.530836311881435	3	FACETS	1	0.942	1	0.579	0.503	0.659	CLONAL	1	FALSE	1	0.530836311881435	3		462	239	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582025	189582025	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	34	448	0	ENST00000264731.3:c.584C>T	p.Ser195Phe	p.S195F	ENST00000264731	NM_003722.4	195	tCc/tTc	5/14	0.530836311881435	3	FACETS	1	0.953	1	0.744	0.623	0.872	CLONAL	1	FALSE	1	0.530836311881435	3		448	109	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670602	30670602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	302	670	0	ENST00000376406.3:c.5918C>T	p.Pro1973Leu	p.P1973L	ENST00000376406	NM_014641.2	1973	cCt/cTt	13/15	0.530836311881435	6	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	FALSE	3	0.530836311881435	6		670	672	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109309847	109309847	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757187967	NA	P-0050076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	61	533	0	ENST00000436639.2:c.1468C>T	p.Arg490Cys	p.R490C	ENST00000436639	NM_014454.2	490	Cgt/Tgt	9/10	0.530836311881435	6	FACETS	0.863	0.759	0.972	0.863	0.759	0.972	CLONAL	3	FALSE	3	0.530836311881435	6		533	183	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426893	6426893	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	151	554	0	ENST00000356142.4:c.86C>A	p.Pro29His	p.P29H	ENST00000356142	NM_018890.3	29	cCt/cAt	2/7	0.530836311881435	3	FACETS	0.983	0.942	1	1	0.992	1	CLONAL	4	FALSE	0	0.530836311881435	3		554	183	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945021	151945021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756918375	NA	P-0050076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	20	90	0	ENST00000262189.6:c.2498G>A	p.Arg833Lys	p.R833K	ENST00000262189	NM_170606.2	833	aGa/aAa	14/59	0.530836311881435	9	FACETS	1	0.858	1	0.167	0.128	0.212	CLONAL	1	FALSE	2	0.530836311881435	9		90	184	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145043	58145043	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	424	632	0	ENST00000257904.6:c.301A>G	p.Arg101Gly	p.R101G	ENST00000257904	NM_000075.3	101	Agg/Ggg	3/8	0.610866960062232	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.610866960062232	3		632	839	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0050085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	114	608	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.357247913026261	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.357247913026261	1		608	498	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031973	26031973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	81	533	0	ENST00000244661.2:c.316G>A	p.Glu106Lys	p.E106K	ENST00000244661	NM_003537.3	106	Gag/Aag	1/1	1	2	FACETS	0.959	0.848	1	0.959	0.848	1	CLONAL	1	TRUE	1	0.357247913026261	2		533	473	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127933378	127933378	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	38	533	0	ENST00000373547.4:c.157G>A	p.Asp53Asn	p.D53N	ENST00000373547	NM_002721.4	53	Gat/Aat	2/7	0.357247913026261	1	FACETS	0.418	0.346	0.499	0.418	0.346	0.499	SUBCLONAL	1	TRUE	0	0.357247913026261	1		533	418	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425229	49425229	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375999143	NA	P-0050085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	143	847	0	ENST00000301067.7:c.13259G>A	p.Arg4420Gln	p.R4420Q	ENST00000301067	NM_003482.3	4420	cGg/cAg	39/54	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.357247913026261	2		847	696	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944833	31944833	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1212962780	NA	P-0050085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	82	671	1	ENST00000340398.3:c.268G>A	p.Gly90Ser	p.G90S	ENST00000340398	NM_001013699.2	90	Ggt/Agt	1/1	0.357247913026261	1	FACETS	0.564	0.498	0.636	0.564	0.498	0.636	SUBCLONAL	1	TRUE	0	0.357247913026261	1		672	668	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347904	128347904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	60	757	1	ENST00000265960.3:c.601G>T	p.Ala201Ser	p.A201S	ENST00000265960	NM_001006617.1	201	Gcc/Tcc	5/12	0.357247913026261	1	FACETS	0.434	0.374	0.501	0.434	0.374	0.501	SUBCLONAL	1	TRUE	0	0.357247913026261	1		758	635	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0050087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	175	328	0				ENST00000310581	NM_198253.2	-/1132			0.445170344989728	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.453843672968062	2		328	367	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0050087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	538	442	1	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.362862589426371	4	FACETS	1	0.995	1	0.87	0.84	0.901	CLONAL	3	TRUE	0	0.453843672968062	4		443	990	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757428	40757428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763638227	NA	P-0050087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	255	793	0	ENST00000373198.4:c.2870C>T	p.Pro957Leu	p.P957L	ENST00000373198	NM_133170.3	957	cCg/cTg	20/32	0.314783050144013	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.453843672968062	1		793	814	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908122	41908122	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3218089	NA	P-0050087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	382	825	0	ENST00000372991.4:c.400C>T	p.Pro134Ser	p.P134S	ENST00000372991	NM_001760.3	134	Ccc/Tcc	2/5	0.243793455347706	2	FACETS	0.765	0.728	0.803	0.765	0.728	0.803	INDETERMINATE	2	TRUE	0	0.453843672968062	2		825	1100	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274198	10274198	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1337036703	NA	P-0050087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	209	695	0	ENST00000330684.3:c.71G>A	p.Ser24Asn	p.S24N	ENST00000330684	NM_001134407.1	24	aGc/aAc	2/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.453843672968062	2		695	822	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948653	71948653	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147991973	NA	P-0050087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	327	1043	0	ENST00000298229.2:c.3365C>T	p.Ser1122Leu	p.S1122L	ENST00000298229	NM_001567.3	1122	tCg/tTg	26/28	0.258190933166387	1	FACETS	1	0.957	1	1	0.957	1	INDETERMINATE	1	TRUE	0	0.453843672968062	1		1043	1099	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30095735	30095735	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	208	416	0	ENST00000331968.5:c.1753C>T	p.Pro585Ser	p.P585S	ENST00000331968	NM_002742.2	585	Cct/Tct	12/18	0.258190933166387	1	FACETS	1	0.963	1	1	0.963	1	INDETERMINATE	1	TRUE	0	0.453843672968062	1		416	675	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834541	156834542	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0050087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	542	971	2	ENST00000524377.1:c.309_310delinsTT	p.Arg104Cys	p.R104C	ENST00000524377	NM_002529.3	103	ctCCgt/ctTTgt	3/17	0.453843672968062	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.453843672968062	3		973	1397	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597582	28597582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	302	602	0	ENST00000241453.7:c.2323G>A	p.Glu775Lys	p.E775K	ENST00000241453	NM_004119.2	775	Gaa/Aaa	19/24	0.162427845921068	3	FACETS	0.827	0.78	0.875	0.827	0.78	0.875	INDETERMINATE	2	TRUE	1	0.453843672968062	3		602	987	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100919	41100919	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	185	712	0	ENST00000373198.4:c.1437G>T	p.Gln479His	p.Q479H	ENST00000373198	NM_133170.3	479	caG/caT	8/32	0.314783050144013	1	FACETS	0.844	0.781	0.909	0.844	0.781	0.909	CLONAL	1	TRUE	0	0.453843672968062	1		712	747	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419946	41419946	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	46	767	0	ENST00000373198.4:c.375G>T	p.Lys125Asn	p.K125N	ENST00000373198	NM_133170.3	125	aaG/aaT	3/32	0.314783050144013	1	FACETS	0.177	0.149	0.21	0.177	0.149	0.21	SUBCLONAL	1	TRUE	0	0.453843672968062	1		767	883	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419968	41419968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	127	760	1	ENST00000373198.4:c.353G>A	p.Gly118Glu	p.G118E	ENST00000373198	NM_133170.3	118	gGg/gAg	3/32	0.314783050144013	1	FACETS	0.507	0.459	0.558	0.507	0.459	0.558	SUBCLONAL	1	TRUE	0	0.453843672968062	1		761	853	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790768	89790768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	148	967	1	ENST00000336032.3:c.155C>T	p.Pro52Leu	p.P52L	ENST00000336032	NM_006813.2	52	cCc/cTc	1/2	0.314783050144013	1	FACETS	0.471	0.429	0.515	0.471	0.429	0.515	SUBCLONAL	1	TRUE	0	0.453843672968062	1		968	1071	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662708	117662708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531832845	NA	P-0050087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	189	501	0	ENST00000368508.3:c.4757G>A	p.Gly1586Glu	p.G1586E	ENST00000368508	NM_002944.2	1586	gGa/gAa	29/43	0.314783050144013	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.453843672968062	1		501	639	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230898	53230898	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	288	927	0	ENST00000375401.3:c.1895A>T	p.His632Leu	p.H632L	ENST00000375401	NM_004187.3	632	cAc/cTc	14/26	0.314783050144013	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.453843672968062	1		927	979	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0050088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	171	633	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	0.628414511460739	3	FACETS	1	0.962	1	0.534	0.493	0.576	CLONAL	1	TRUE	1	0.628414511460739	3		633	670	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107012	27107012	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	148	615	0	ENST00000324856.7:c.6623T>A	p.Phe2208Tyr	p.F2208Y	ENST00000324856	NM_006015.4	2208	tTc/tAc	20/20	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.628414511460739	2		615	458	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427431	49427431	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	213	702	0	ENST00000301067.7:c.11057C>G	p.Ser3686Cys	p.S3686C	ENST00000301067	NM_003482.3	3686	tCt/tGt	39/54	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.628414511460739	2		702	620	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448194	49448194	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	180	550	0	ENST00000301067.7:c.406T>C	p.Cys136Arg	p.C136R	ENST00000301067	NM_003482.3	136	Tgc/Cgc	4/54	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.628414511460739	2		550	486	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218321	133218321	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	65	674	0	ENST00000320574.5:c.5290del	p.Ala1764ProfsTer6	p.A1764Pfs*6	ENST00000320574	NM_006231.2	1764	Gcc/cc	39/49	0.628414511460739	3	FACETS	0.371	0.321	0.426	0.186	0.16	0.213	SUBCLONAL	1	TRUE	1	0.628414511460739	3		674	732	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984725	72984725	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	179	697	0	ENST00000268489.5:c.2859C>A	p.Phe953Leu	p.F953L	ENST00000268489	NM_006885.3	953	ttC/ttA	3/10	0.493725571913038	4	FACETS	0.888	0.818	0.961	0.444	0.409	0.481	CLONAL	1	TRUE	2	0.628414511460739	4		697	1045	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099397	4099397	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1305191745	NA	P-0050088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	206	705	0	ENST00000262948.5:c.721G>C	p.Gly241Arg	p.G241R	ENST00000262948	NM_030662.3	241	Ggc/Cgc	7/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.628414511460739	2		705	642	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224504	36224504	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	170	763	0	ENST00000222270.7:c.6966C>A	p.Ser2322Arg	p.S2322R	ENST00000222270	NM_014727.1	2322	agC/agA	29/37	0.628414511460739	3	FACETS	0.771	0.709	0.836	0.386	0.354	0.418	SUBCLONAL	1	TRUE	1	0.628414511460739	3		763	922	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584583	52584583	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	191	622	0	ENST00000394830.3:c.4430del	p.Pro1477LeufsTer12	p.P1477Lfs*12	ENST00000394830	NM_018313.4	1477	cCt/ct	29/30	1	2	FACETS	0.941	0.872	1	0.941	0.872	1	CLONAL	1	TRUE	1	0.532172107572545	2		622	763	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50830354	50830354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121908390	NA	P-0050089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	168	483	1	ENST00000398568.2:c.2797C>T	p.Arg933Ter	p.R933*	ENST00000398568	NM_001042412.1	933	Cga/Tga	18/18	0.532172107572545	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.532172107572545	1		484	438	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222359	39222359	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	222	577	0	ENST00000402219.2:c.3251G>C	p.Arg1084Thr	p.R1084T	ENST00000402219	NM_005633.3	1084	aGa/aCa	20/23	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.532172107572545	2		577	813	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119702	108119703	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs1555069617	NA	P-0050096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	16	182	1	ENST00000278616.4:c.1109dup	p.Tyr370Ter	p.Y370*	ENST00000278616	NM_000051.3	370	tac/tAac	9/63	1	2	FACETS	0.339	0.251	0.446	0.339	0.251	0.446	SUBCLONAL	1	TRUE	1	0.345387179478628	2		183	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913343	NA	P-0050097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	239	597	0	ENST00000269305.4:c.817C>A	p.Arg273Ser	p.R273S	ENST00000269305	NM_001126112.2	273	Cgt/Agt	8/11	0.0771771953961493	9	FACETS	0.961	0.898	1	1	0.994	1	CLONAL	9	TRUE	4	0.0771771953961493	9		597	910	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	274	718	0	ENST00000269305.4:c.383del	p.Pro128LeufsTer42	p.P128Lfs*42	ENST00000269305	NM_001126112.2	128	cCt/ct	5/11	0.0771771953961493	9	FACETS	0.945	0.888	1	1	0.994	1	CLONAL	9	TRUE	4	0.0771771953961493	9		718	1060	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952073	178952073	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519937	NA	P-0050097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	173	414	0	ENST00000263967.3:c.3128T>C	p.Met1043Thr	p.M1043T	ENST00000263967	NM_006218.2	1043	aTg/aCg	21/21	0.0771771953961493	10	FACETS	0.998	0.926	1	1	0.993	1	CLONAL	12	TRUE	4	0.0771771953961493	10		414	490	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866987936	NA	P-0050097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	89	293	0	ENST00000281708.4:c.1436G>T	p.Arg479Leu	p.R479L	ENST00000281708	NM_033632.3	479	cGa/cTa	10/12	0.0771771953961493	9	FACETS	0.982	0.877	1	1	0.982	1	CLONAL	8	TRUE	4	0.0771771953961493	9		293	373	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696404	47696404	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	225	541	0	ENST00000347630.2:c.419A>G	p.Asp140Gly	p.D140G	ENST00000347630	NM_001007230.1	140	gAt/gGt	6/11	0.0771771953961493	8	FACETS	1	0.948	1	1	0.995	1	CLONAL	9	TRUE	4	0.0771771953961493	8		541	784	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0050098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	37	534	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.298	0.245	0.358	0.298	0.245	0.358	SUBCLONAL	1	TRUE	1	0.409644044780127	2		534	606	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0050098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	97	328	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.409644044780127	1	FACETS	0.897	0.804	0.993	0.897	0.804	0.993	CLONAL	1	TRUE	0	0.409644044780127	1		328	420	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0050098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	151	421	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.409644044780127	2		421	605	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	202	507	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.409644044780127	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.409644044780127	1		507	681	SUCCESS
APC	324	MSKCC	GRCh37	5	112155042	112155042	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs863225310	NA	P-0050098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	91	360	0	ENST00000257430.4:c.1312+1G>A		p.X438_splice	ENST00000257430	NM_000038.5	438			0.409644044780127	1	FACETS	0.942	0.843	1	0.942	0.843	1	CLONAL	1	TRUE	0	0.409644044780127	1		360	375	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625281	69625281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35983315	NA	P-0050098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	139	754	2	ENST00000334134.2:c.512G>A	p.Arg171His	p.R171H	ENST00000334134	NM_005247.2	171	cGc/cAc	3/3	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.409644044780127	2		756	677	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798320	45798320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	155	700	1	ENST00000450313.1:c.616G>A	p.Glu206Lys	p.E206K	ENST00000450313	NM_012222.2	206	Gag/Aag	8/16	1	2	FACETS	0.966	0.886	1	0.966	0.886	1	CLONAL	1	TRUE	1	0.409644044780127	2		701	783	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911638	114911639	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0050099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	94	448	0	ENST00000543371.1:c.1157_1158dup	p.Arg387GlyfsTer105	p.R387Gfs*105	ENST00000543371	NM_001198531.1	386	cgg/cGGgg	10/14	1	2	FACETS	0.814	0.725	0.908	0.814	0.725	0.908	CLONAL	1	TRUE	1	0.388919981195938	2		448	594	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391340	139391341	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCTGGTGCCAGAGGCCAC	novel	NA	P-0050099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	123	916	0	ENST00000277541.6:c.6832_6850dup	p.Thr2284SerfsTer76	p.T2284Sfs*76	ENST00000277541	NM_017617.3	2284	acc/aGTGGCCTCTGGCACCAGCAcc	34/34	1	2	FACETS	0.66	0.596	0.727	0.66	0.596	0.727	SUBCLONAL	1	TRUE	1	0.388919981195938	2		916	959	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396746	139396746	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	161	730	0	ENST00000277541.6:c.5362G>C	p.Gly1788Arg	p.G1788R	ENST00000277541	NM_017617.3	1788	Ggc/Cgc	28/34	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.388919981195938	2		730	806	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812205	43812205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866559375	NA	P-0050100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	253	532	0	ENST00000372470.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000372470	NM_005373.2	357	cGa/cAa	7/12	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.679124448433234	2		532	665	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326765	62326765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778286683	NA	P-0050100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	48	899	0	ENST00000360203.5:c.3584C>T	p.Ala1195Val	p.A1195V	ENST00000360203	NM_001283009.1	1195	gCg/gTg	34/35	0.539258565051322	2	FACETS	0.15	0.126	0.177	0.075	0.063	0.089	SUBCLONAL	1	TRUE	0	0.679124448433234	2		899	941	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643679	38643680	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs878855228	NA	P-0050100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	251	575	0	ENST00000299084.4:c.1151_1152del	p.Glu384GlyfsTer5	p.E384Gfs*5	ENST00000299084	NM_152594.2	383	tcAGag/tcag	7/7	1	2	FACETS	0.986	0.926	1	0.986	0.926	1	CLONAL	1	TRUE	1	0.679124448433234	2		575	750	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660547	227660547	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1447919275	NA	P-0050100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	295	726	1	ENST00000305123.5:c.2908C>T	p.Pro970Ser	p.P970S	ENST00000305123	NM_005544.2	970	Ccc/Tcc	1/2	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.679124448433234	2		727	788	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749432	41749432	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	206	536	0	ENST00000226382.2:c.363C>G	p.His121Gln	p.H121Q	ENST00000226382	NM_003924.3	121	caC/caG	2/3	1	2	FACETS	0.982	0.916	1	0.982	0.916	1	CLONAL	1	TRUE	1	0.679124448433234	2		536	618	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	202	454	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.97	1	1	0.996	1	CLONAL	10	TRUE	1	0.11	2		459	353	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	225	797	0	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	1	2	FACETS	0.945	0.881	1	1	0.996	1	CLONAL	5	TRUE	1	0.11	2		797	866	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154241	2154242	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755455183	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	143	763	4	ENST00000434045.2:c.686dup	p.Glu230ArgfsTer50	p.E230Rfs*50	ENST00000434045	NM_001127598.1	229	cca/ccCa	5/5	0.191592967111506	3	FACETS	1	0.937	1	1	0.991	1	CLONAL	4	TRUE	1	0.11	3		767	666	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	204	846	6	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	1	2	FACETS	0.992	0.923	1	1	0.995	1	CLONAL	5	TRUE	1	0.11	2		852	748	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	255	983	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.191592967111506	3	FACETS	0.955	0.896	1	1	0.996	1	CLONAL	6	TRUE	1	0.11	3		983	854	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	243	548	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	1	2	FACETS	1	0.94	1	1	0.996	1	CLONAL	6	TRUE	1	0.11	2		548	735	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004217	150004217	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1431439182	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	36	114	1	ENST00000253339.5:c.2008C>T	p.Arg670Trp	p.R670W	ENST00000253339		670	Cgg/Tgg	3/7	0.191592967111506	3	FACETS	0.966	0.808	1	1	0.971	1	CLONAL	5	TRUE	1	0.11	3		115	143	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	76	435	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	1	0.912	1	1	0.988	1	CLONAL	4	TRUE	1	0.11	2		436	333	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451784	29451784	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs772809305	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	99	419	0	ENST00000389048.3:c.2781del	p.Cys928AlafsTer11	p.C928Afs*11	ENST00000389048	NM_004304.4	927	ggG/gg	16/29	1	2	FACETS	1	0.924	1	1	0.991	1	CLONAL	4	TRUE	1	0.11	2		419	435	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106696	27106696	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	203	598	1	ENST00000324856.7:c.6310del	p.Ser2104ProfsTer31	p.S2104Pfs*31	ENST00000324856	NM_006015.4	2103	Ttt/tt	20/20	1	2	FACETS	0.98	0.912	1	1	0.995	1	CLONAL	5	TRUE	1	0.11	2		599	753	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923086	39923087	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	253	614	0	ENST00000378444.4:c.3621dup	p.Gln1208ThrfsTer8	p.Q1208Tfs*8	ENST00000378444	NM_001123385.1	1207	-/A	8/15	0.110426755222827	0	FACETS	0.899	0.845	0.954			1	CLONAL	6	TRUE	0	0.11	0		614	759	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	203	702	2	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	1	2	FACETS	0.929	0.866	0.994	1	0.996	1	CLONAL	6	TRUE	1	0.11	2		704	662	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831357	72831358	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTG	rs34918837	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	53	467	0	ENST00000268489.5:c.5221_5223dup	p.Gln1741dup	p.Q1741dup	ENST00000268489	NM_006885.3	1741	-/CAA	9/10	1	2	FACETS	0.892	0.767	1	1	0.983	1	CLONAL	4	TRUE	1	0.11	2		467	270	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760024	133760024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	218	730	0	ENST00000318560.5:c.2352del	p.Arg785GlyfsTer3	p.R785Gfs*3	ENST00000318560	NM_005157.4	783	Ccc/cc	11/11	0.161348313056309	1	FACETS	1	0.935	1	1	0.996	1	CLONAL	5	TRUE	0	0.11	1		730	748	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187558039	187558039	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	62	281	0	ENST00000441802.2:c.3672del	p.Lys1225AsnfsTer9	p.K1225Nfs*9	ENST00000441802	NM_005245.3	1224	ccC/cc	5/27	0.191592967111506	3	FACETS	0.939	0.824	1	1	0.984	1	CLONAL	6	TRUE	1	0.11	3		281	211	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986830	36986830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	144	162	0	ENST00000354822.5:c.859C>T	p.Arg287Cys	p.R287C	ENST00000354822	NM_001079668.2	287	Cgc/Tgc	3/3	1	2	FACETS	1	0.951	1	1	0.994	1	CLONAL	6	TRUE	1	0.11	2		162	418	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610521	81610521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568577739	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	109	414	0	ENST00000298171.2:c.2119C>T	p.Arg707Trp	p.R707W	ENST00000298171	NM_000369.2	707	Cgg/Tgg	10/10	1	2	FACETS	0.918	0.832	1	1	0.992	1	CLONAL	6	TRUE	1	0.11	2		414	360	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933013	39933013	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	241	805	1	ENST00000378444.4:c.1586del	p.Asn529ThrfsTer60	p.N529Tfs*60	ENST00000378444	NM_001123385.1	529	aAc/ac	4/15	0.110426755222827	0	FACETS	0.951	0.891	1			1	CLONAL	5	TRUE	0	0.11	0		806	820	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119007	3119007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769503200	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	230	744	1	ENST00000078429.4:c.691G>A	p.Ala231Thr	p.A231T	ENST00000078429	NM_002067.2	231	Gcc/Acc	5/7	1	2	FACETS	0.989	0.926	1	1	0.996	1	CLONAL	6	TRUE	1	0.11	2		745	705	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497299	149497299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142762235	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	213	719	2	ENST00000261799.4:c.3019G>A	p.Val1007Ile	p.V1007I	ENST00000261799	NM_002609.3	1007	Gtc/Atc	22/23	1	2	FACETS	1	0.96	1	1	0.996	1	CLONAL	6	TRUE	1	0.11	2		721	623	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11297959	11297959	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1468487695	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	237	601	1	ENST00000361445.4:c.2149C>T	p.Arg717Ter	p.R717*	ENST00000361445	NM_004958.3	717	Cga/Tga	13/58	0.161348313056309	1	FACETS	0.917	0.859	0.976	1	0.996	1	CLONAL	6	TRUE	0	0.11	1		602	740	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324892	31324892	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs765875917	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	43	567	0	ENST00000412585.2:c.44del	p.Ala15GlyfsTer5	p.A15Gfs*5	ENST00000412585	NM_005514.6	15	gCg/gg	1/8	0.191592967111506	3	FACETS	1	0.941	1	0.648	0.542	0.767	CLONAL	1	TRUE	1	0.11	3		567	636	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	124	345	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	0.191592967111506	3	FACETS	0.928	0.847	1	1	0.992	1	CLONAL	6	TRUE	1	0.11	3		345	427	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800902	120800903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748469666	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	266	718	3	ENST00000257552.2:c.345dup	p.Leu116AlafsTer15	p.L116Afs*15	ENST00000257552	NM_002442.3	115	-/G	6/15	0.202552145800344	0	FACETS	0.978	0.919	1			1	CLONAL	5	TRUE	0	0.11	0		721	880	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735408	204735408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	148	470	0	ENST00000302823.3:c.209G>A	p.Arg70Gln	p.R70Q	ENST00000302823	NM_005214.4	70	cGg/cAg	2/4	1	2	FACETS	1	0.924	1	1	0.994	1	CLONAL	5	TRUE	1	0.11	2		470	535	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390435	56390435	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757096789	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	66	183	0	ENST00000348428.3:c.1174C>T	p.Arg392Cys	p.R392C	ENST00000348428	NM_006785.3	392	Cgt/Tgt	10/17	1	2	FACETS	1	0.917	1	1	0.987	1	CLONAL	5	TRUE	1	0.11	2		183	228	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860097	152860097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201043377	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	193	664	0	ENST00000406277.2:c.331C>T	p.Arg111Cys	p.R111C	ENST00000406277	NM_152274.4	111	Cgc/Tgc	5/7	0.110426755222827		FACETS		0.847	0.984				CLONAL	4	TRUE	0	0.11	0		664	854	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288789	15288789	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	90	131	0	ENST00000263388.2:c.3950del	p.Pro1317GlnfsTer103	p.P1317Qfs*103	ENST00000263388	NM_000435.2	1317	cCa/ca	24/33	1	2	FACETS	0.971	0.873	1	1	0.991	1	CLONAL	6	TRUE	1	0.11	2		131	281	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230604	46230604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	77	347	2	ENST00000334344.6:c.853C>T	p.Arg285Trp	p.R285W	ENST00000334344	NM_152641.2	285	Cgg/Tgg	8/21	0.191592967111506	3	FACETS	1	0.9	1	1	0.986	1	CLONAL	5	TRUE	1	0.11	3		349	291	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518231	8518231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750058892	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	107	388	0	ENST00000356435.5:c.1160C>T	p.Ser387Leu	p.S387L	ENST00000356435		387	tCg/tTg	10/35	0.161348313056309	1	FACETS	0.923	0.837	1	1	0.992	1	CLONAL	6	TRUE	0	0.11	1		388	332	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794637	42794637	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	222	797	1	ENST00000575354.2:c.1721del	p.Pro574HisfsTer154	p.P574Hfs*154	ENST00000575354	NM_015125.3	573	Ccc/cc	10/20	1	2	FACETS	0.952	0.89	1	1	0.996	1	CLONAL	6	TRUE	1	0.11	2		798	707	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372287	55372288	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1170462661	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	172	555	0	ENST00000297316.4:c.983dup	p.Gly331ArgfsTer34	p.G331Rfs*34	ENST00000297316	NM_022454.3	326	cac/caCc	2/2	0.110426755222827	0	FACETS	0.956	0.885	1			1	CLONAL	5	TRUE	0	0.11	0		555	582	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111145	193111146	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	rs760591174	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	83	236	0	ENST00000367435.3:c.687_688dup	p.Val230GlufsTer28	p.V230Efs*28	ENST00000367435	NM_024529.4	226	-/AG	7/17	1	2	FACETS	1	0.9	1	1	0.99	1	CLONAL	5	TRUE	1	0.11	2		236	299	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022180	5022180	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs773146013	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	72	311	0	ENST00000381652.3:c.193G>C	p.Glu65Gln	p.E65Q	ENST00000381652	NM_004972.3	65	Gaa/Caa	3/25	0.161348313056309	1	FACETS	1	0.924	1	1	0.988	1	CLONAL	4	TRUE	0	0.11	1		311	291	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964076	28964077	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	98	365	0	ENST00000282397.4:c.1825dup	p.Met609AsnfsTer5	p.M609Nfs*5	ENST00000282397	NM_002019.4	609	atg/aAtg	13/30	1	2	FACETS	0.961	0.868	1	1	0.991	1	CLONAL	6	TRUE	1	0.11	2		365	309	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199670	11199670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766533620	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	149	615	1	ENST00000361445.4:c.4918C>T	p.Arg1640Trp	p.R1640W	ENST00000361445	NM_004958.3	1640	Cgg/Tgg	35/58	0.161348313056309	1	FACETS	1	0.962	1	1	0.994	1	CLONAL	4	TRUE	0	0.11	1		616	591	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009254	69009254	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs757509439	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	50	283	0	ENST00000288368.4:c.2371G>A	p.Val791Ile	p.V791I	ENST00000288368	NM_024870.2	791	Gtt/Att	22/40	0.110426755222827	0	FACETS	0.969	0.837	1			1	CLONAL	5	TRUE	0	0.11	0		283	167	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36931961	36931961	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	197	652	0	ENST00000361632.4:c.2508C>A	p.Phe836Leu	p.F836L	ENST00000361632		836	ttC/ttA	16/16	1	2	FACETS	1	0.971	1	1	0.995	1	CLONAL	5	TRUE	1	0.11	2		652	662	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438210	49438211	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1555194303	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	193	538	1	ENST00000301067.7:c.5058dup	p.Arg1687ThrfsTer4	p.R1687Tfs*4	ENST00000301067	NM_003482.3	1686	-/A	20/54	0.191592967111506	3	FACETS	1	0.93	1	1	0.994	1	CLONAL	5	TRUE	1	0.11	3		539	739	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419977	152419977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778554662	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	189	625	0	ENST00000206249.3:c.1664G>A	p.Arg555His	p.R555H	ENST00000206249	NM_000125.3	555	cGt/cAt	8/8	0.191592967111506	3	FACETS	0.935	0.868	1	1	0.994	1	CLONAL	6	TRUE	1	0.11	3		625	646	SUCCESS
ATM	472	MSKCC	GRCh37	11	108159797	108159797	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	35	67	0	ENST00000278616.4:c.4207del	p.Ser1403AlafsTer3	p.S1403Afs*3	ENST00000278616	NM_000051.3	1401	ttA/tt	28/63	0.191592967111506	3	FACETS	1	0.853	1	1	0.975	1	CLONAL	7	TRUE	1	0.11	3		67	95	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806150	1806150	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	277	779	0	ENST00000260795.2:c.1169T>C	p.Val390Ala	p.V390A	ENST00000260795		390	gTg/gCg	8/17	NA	2	FACETS	0.961	0.907	1			1	INDETERMINATE	7	TRUE	NA	0.11	2		779	749	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514027	125514027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761313560	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	97	445	0	ENST00000428830.2:c.965G>A	p.Arg322His	p.R322H	ENST00000428830	NM_001114121.2	322	cGc/cAc	10/14	0.191592967111506	3	FACETS	1	0.946	1	1	0.988	1	CLONAL	4	TRUE	1	0.11	3		445	428	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778920	9778920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571644641	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	264	675	1	ENST00000377346.4:c.1189G>A	p.Val397Met	p.V397M	ENST00000377346	NM_005026.3	397	Gtg/Atg	9/24	0.161348313056309	1	FACETS	1	0.974	1	1	0.996	1	CLONAL	5	TRUE	0	0.11	1		676	853	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202881	16202881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	180	541	0	ENST00000375759.3:c.589C>T	p.His197Tyr	p.H197Y	ENST00000375759	NM_015001.2	197	Cat/Tat	3/15	0.3	5	FACETS	0.984	0.911	1			1	CLONAL	6	TRUE	NA	0.11	5		541	646	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057979	27057979	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	203	632	0	ENST00000324856.7:c.1687C>G	p.Gln563Glu	p.Q563E	ENST00000324856	NM_006015.4	563	Cag/Gag	3/20	1	2	FACETS	0.945	0.879	1	1	0.995	1	CLONAL	5	TRUE	1	0.11	2		632	781	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28586425	28586425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	201	560	0	ENST00000253063.3:c.67G>A	p.Val23Ile	p.V23I	ENST00000253063	NM_031459.4	23	Gtc/Atc	1/10	1	2	FACETS	0.967	0.901	1	1	0.996	1	CLONAL	6	TRUE	1	0.11	2		560	630	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305284	65305284	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	78	459	0	ENST00000342505.4:c.2842+2T>C		p.X948_splice	ENST00000342505	NM_002227.2	948			1	2	FACETS	0.999	0.884	1	1	0.988	1	CLONAL	4	TRUE	1	0.11	2		459	355	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100555	8100555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	171	843	0	ENST00000346208.3:c.529C>T	p.Arg177Trp	p.R177W	ENST00000346208		177	Cgg/Tgg	3/6	1	2	FACETS	0.938	0.866	1	1	0.995	1	CLONAL	5	TRUE	1	0.11	2		843	663	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717667	89717667	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	160	446	0	ENST00000371953.3:c.692C>A	p.Pro231His	p.P231H	ENST00000371953	NM_000314.4	231	cCc/cAc	7/9	1	2	FACETS	0.994	0.918	1	1	0.995	1	CLONAL	6	TRUE	1	0.11	2		446	488	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211663	46211663	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	42	158	0	ENST00000334344.6:c.629T>C	p.Phe210Ser	p.F210S	ENST00000334344	NM_152641.2	210	tTt/tCt	5/21	0.191592967111506	3	FACETS	0.926	0.784	1	1	0.974	1	CLONAL	5	TRUE	1	0.11	3		158	174	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230549	46230549	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	65	275	0	ENST00000334344.6:c.798G>A	p.Trp266Ter	p.W266*	ENST00000334344	NM_152641.2	266	tgG/tgA	8/21	0.191592967111506	3	FACETS	1	0.889	1	1	0.985	1	CLONAL	6	TRUE	1	0.11	3		275	206	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986700	36986700	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs994624549	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	42	32	0	ENST00000354822.5:c.989C>T	p.Ala330Val	p.A330V	ENST00000354822	NM_001079668.2	330	gCg/gTg	3/3	1	2	FACETS	1	0.887	1	1	0.982	1	CLONAL	8	TRUE	1	0.11	2		32	93	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476337	88476337	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	156	602	1	ENST00000360948.2:c.1795C>T	p.His599Tyr	p.H599Y	ENST00000360948	NM_001012338.2	599	Cac/Tac	15/19	1	2	FACETS	0.957	0.88	1	1	0.994	1	CLONAL	5	TRUE	1	0.11	2		603	593	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644529	3644529	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	288	755	0	ENST00000294008.3:c.2085del	p.Gln696ArgfsTer26	p.Q696Rfs*26	ENST00000294008	NM_032444.2	695	ttT/tt	10/15	1	2	FACETS	1	0.956	1	1	0.997	1	CLONAL	6	TRUE	1	0.11	2		755	860	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15938168	15938168	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775915024	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	135	407	0	ENST00000268712.3:c.7046G>A	p.Arg2349Gln	p.R2349Q	ENST00000268712	NM_006311.3	2349	cGg/cAg	45/46	1	2	FACETS	1	0.946	1	1	0.994	1	CLONAL	5	TRUE	1	0.11	2		407	470	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533349	29533349	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747466938	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	82	280	0	ENST00000356175.3:c.1352T>C	p.Val451Ala	p.V451A	ENST00000356175	NM_000267.3	451	gTg/gCg	12/57	1	2	FACETS	0.927	0.828	1	1	0.99	1	CLONAL	6	TRUE	1	0.11	2		280	268	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2164188	2164188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1432450655	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	120	397	0	ENST00000398665.3:c.5G>A	p.Gly2Glu	p.G2E	ENST00000398665	NM_032482.2	2	gGg/gAg	1/28	1	2	FACETS	0.928	0.844	1	1	0.993	1	CLONAL	5	TRUE	1	0.11	2		397	470	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299803	15299803	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370186772	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	202	717	1	ENST00000263388.2:c.1375G>A	p.Ala459Thr	p.A459T	ENST00000263388	NM_000435.2	459	Gca/Aca	8/33	1	2	FACETS	1	0.974	1	1	0.996	1	CLONAL	5	TRUE	1	0.11	2		718	672	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794105	42794105	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	123	394	0	ENST00000575354.2:c.1464+2T>C		p.X488_splice	ENST00000575354	NM_015125.3	488			1	2	FACETS	1	0.927	1	1	0.993	1	CLONAL	6	TRUE	1	0.11	2		394	367	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038187	128038187	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	179	479	0	ENST00000285398.2:c.1363C>T	p.Leu455Phe	p.L455F	ENST00000285398	NM_000122.1	455	Ctc/Ttc	9/15	1	2	FACETS	1	0.955	1	1	0.995	1	CLONAL	5	TRUE	1	0.11	2		479	625	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468538	89468538	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	52	189	0	ENST00000336596.2:c.2072A>C	p.Lys691Thr	p.K691T	ENST00000336596	NM_005233.5	691	aAa/aCa	11/17	1	2	FACETS	0.95	0.821	1	1	0.984	1	CLONAL	5	TRUE	1	0.11	2		189	199	SUCCESS
APC	324	MSKCC	GRCh37	5	112162944	112162944	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	46	151	0	ENST00000257430.4:c.1548G>T	p.Lys516Asn	p.K516N	ENST00000257430	NM_000038.5	516	aaG/aaT	12/16	1	2	FACETS	0.917	0.788	1	1	0.982	1	CLONAL	6	TRUE	1	0.11	2		151	152	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	62	345	0	ENST00000412585.2:c.626C>A	p.Pro209Gln	p.P209Q	ENST00000412585	NM_005514.6	209	cCa/cAa	4/8	0.191592967111506	3	FACETS	0.928	0.805	1	1	0.966	1	CLONAL	3	TRUE	1	0.11	3		345	427	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902197	151902197	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	96	320	0	ENST00000262189.6:c.3955G>T	p.Asp1319Tyr	p.D1319Y	ENST00000262189	NM_170606.2	1319	Gat/Tat	25/59	1	2	FACETS	1	0.934	1	1	0.991	1	CLONAL	5	TRUE	1	0.11	2		320	333	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540168	23540168	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	186	293	1	ENST00000380871.4:c.235G>T	p.Gly79Trp	p.G79W	ENST00000380871	NM_006167.3	79	Ggg/Tgg	1/2	0.110426755222827	0	FACETS	0.989	0.922	1			1	CLONAL	6	TRUE	0	0.11	0		294	507	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740808	145740808	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1342271031	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	287	829	0	ENST00000428558.2:c.1292A>G	p.Glu431Gly	p.E431G	ENST00000428558	NM_004260.3	431	gAg/gGg	7/22	0.3	6	FACETS	1	0.981	1	0.888	0.833	0.944	CLONAL	4	TRUE	1	0.11	6		829	1434	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022138	5022138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	77	338	0	ENST00000381652.3:c.151G>A	p.Glu51Lys	p.E51K	ENST00000381652	NM_004972.3	51	Gag/Aag	3/25	0.161348313056309	1	FACETS	1	0.89	1	1	0.988	1	CLONAL	4	TRUE	0	0.11	1		338	329	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606554	93606554	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	177	695	0	ENST00000375746.1:c.377del	p.Asn126ThrfsTer7	p.N126Tfs*7	ENST00000375746	NM_001174167.1	125	gAa/ga	2/14	0.161348313056309	1	FACETS	1	0.97	1	1	0.995	1	CLONAL	5	TRUE	0	0.11	1		695	560	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321019	137321019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	248	718	0	ENST00000481739.1:c.976C>A	p.Leu326Met	p.L326M	ENST00000481739	NM_002957.4	326	Ctg/Atg	7/10	0.161348313056309	1	FACETS	0.955	0.896	1	1	0.996	1	CLONAL	6	TRUE	0	0.11	1		718	744	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424294	47424295	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	135	587	0	ENST00000377045.4:c.303dup	p.Val102CysfsTer12	p.V102Cfs*12	ENST00000377045	NM_001654.4	100	aat/aaTt	4/16	0.110426755222827	0	FACETS	0.86	0.784	0.94			1	CLONAL	4	TRUE	0	0.11	0		587	635	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210274	123210274	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	65	231	0	ENST00000218089.9:c.2626G>A	p.Val876Met	p.V876M	ENST00000218089	NM_001042749.1	876	Gtg/Atg	26/35	0.110426755222827	0	FACETS	0.942	0.825	1			1	CLONAL	4	TRUE	0	0.11	0		231	279	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	141	468	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.626523070552088	2		468	416	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712017	89712017	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs1114167622	NA	P-0050109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	69	192	0	ENST00000371953.3:c.634+1G>C		p.X212_splice	ENST00000371953	NM_000314.4	212			0.626523070552088	1	FACETS	0.784	0.696	0.875	0.784	0.696	0.875	SUBCLONAL	1	TRUE	0	0.626523070552088	1		192	193	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074115	8074115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	136	340	0	ENST00000377482.5:c.544del	p.Leu182PhefsTer2	p.L182Ffs*2	ENST00000377482	NM_018948.3	182	Ctt/tt	4/4	1	2	FACETS	0.948	0.869	1	0.948	0.869	1	CLONAL	1	TRUE	1	0.626523070552088	2		340	458	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161963	47161966	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0050109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	120	340	0	ENST00000409792.3:c.4160_4163del	p.Lys1387IlefsTer6	p.K1387Ifs*6	ENST00000409792	NM_014159.6	1387	aAAGAt/at	3/21	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.626523070552088	2		340	377	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372475	55372475	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	95	887	1	ENST00000297316.4:c.1165C>A	p.Pro389Thr	p.P389T	ENST00000297316	NM_022454.3	389	Ccc/Acc	2/2	1	2	FACETS	0.288	0.255	0.323	0.288	0.255	0.323	SUBCLONAL	1	TRUE	1	0.626523070552088	2		888	1053	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593613	55593613	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913521	NA	P-0050110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	274	368	0	ENST00000288135.5:c.1679T>A	p.Val560Asp	p.V560D	ENST00000288135	NM_000222.2	560	gTt/gAt	11/21	1	2	FACETS	0.942	0.891	0.994	0.942	0.891	0.994	CLONAL	1	TRUE	1	0.893625125937627	2		368	651	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280672	115280672	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	271	431	0	ENST00000438362.2:c.359C>A	p.Ser120Ter	p.S120*	ENST00000438362	NM_001242891.1	120	tCa/tAa	4/20	0.893625125937627	1	FACETS	0.956	0.922	0.988	0.956	0.922	0.988	CLONAL	1	TRUE	0	0.893625125937627	1		431	351	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602900	55602900	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0050110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	290	342	2	ENST00000288135.5:c.2610T>G	p.Tyr870Ter	p.Y870*	ENST00000288135	NM_000222.2	870	taT/taG	19/21	1	2	FACETS	0.922	0.873	0.972	0.922	0.873	0.972	CLONAL	1	TRUE	1	0.893625125937627	2		344	704	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	161	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.14207060552326	6	FACETS	0.968	0.897	1	0.968	0.897	1	INDETERMINATE	3	FALSE	3	0.540393369928366	6		327	427	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	54	763	9	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	0.296555987602214	3	FACETS	0.531	0.454	0.615	0.266	0.227	0.308	INDETERMINATE	1	FALSE	1	0.540393369928366	3		772	478	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	178	352	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	0.540393369928366	1	FACETS	0.907	0.86	0.953	1	0.994	1	CLONAL	2	FALSE	0	0.540393369928366	1		352	265	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	20	273	0	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	1	2	FACETS	0.307	0.235	0.391	0.307	0.235	0.391	SUBCLONAL	1	FALSE	1	0.540393369928366	2		273	241	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	76	495	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.629	0.554	0.71	0.629	0.554	0.71	SUBCLONAL	1	FALSE	1	0.540393369928366	2		495	447	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	12	548	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	1	2	FACETS	0.083	0.057	0.114	0.083	0.057	0.114	SUBCLONAL	1	FALSE	1	0.540393369928366	2		548	537	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	158	483	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.104407568437152	4	FACETS	1	0.968	1	1	0.968	1	INDETERMINATE	2	FALSE	2	0.540393369928366	4		483	417	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910661	32910662	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs276174819	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	15	317	0	ENST00000380152.3:c.2175dup	p.Val726SerfsTer25	p.V726Sfs*25	ENST00000380152		723	-/A	11/27	1	2	FACETS	0.193	0.14	0.256	0.193	0.14	0.256	SUBCLONAL	1	FALSE	1	0.540393369928366	2		317	288	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952142	178952142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253171657	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	16	212	0	ENST00000263967.3:c.3197C>T	p.Ala1066Val	p.A1066V	ENST00000263967	NM_006218.2	1066	gCa/gTa	21/21	1	2	FACETS	0.281	0.208	0.367	0.281	0.208	0.367	SUBCLONAL	1	FALSE	1	0.540393369928366	2		212	211	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	15	429	2	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	0.330793678382884	1	FACETS	0.167	0.122	0.222	0.167	0.122	0.222	SUBCLONAL	1	FALSE	0	0.540393369928366	1		431	242	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900984	114900984	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778855667	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	58	472	0	ENST00000543371.1:c.598del	p.Leu200SerfsTer25	p.L200Sfs*25	ENST00000543371	NM_001198531.1	198	caC/ca	6/14	0.104407568437152	4	FACETS	0.903	0.78	1	0.452	0.39	0.519	INDETERMINATE	1	FALSE	2	0.540393369928366	4		472	366	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196880	108196880	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	90	333	1	ENST00000278616.4:c.6908del	p.Lys2303ArgfsTer7	p.K2303Rfs*7	ENST00000278616	NM_000051.3	2301	gcA/gc	47/63	0.296555987602214	3	FACETS	1	0.972	1	0.628	0.562	0.696	INDETERMINATE	1	FALSE	1	0.540393369928366	3		334	337	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862138	68862139	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	178	469	0	ENST00000261769.5:c.2231dup	p.Glu745ArgfsTer3	p.E745Rfs*3	ENST00000261769	NM_004360.3	742	-/C	14/16	0.540393369928366	3	FACETS	1	0.986	1			1	CLONAL	1	FALSE	NA	0.540393369928366	3		469	645	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412627	139412627	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	279	680	0	ENST00000277541.6:c.1217del	p.Gly406AlafsTer225	p.G406Afs*225	ENST00000277541	NM_017617.3	406	gGc/gc	7/34	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	FALSE	1	0.540393369928366	2		680	717	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500832	8500832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756198535	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	26	420	1	ENST00000356435.5:c.2050C>T	p.Arg684Trp	p.R684W	ENST00000356435		684	Cgg/Tgg	13/35	0.2755521465391	0	FACETS	0.14	0.111	0.174			1	INDETERMINATE	1	FALSE	0	0.540393369928366	0		421	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540654	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	185	637	1	ENST00000269305.4:c.329G>A	p.Arg110His	p.R110H	ENST00000269305	NM_001126112.2	110	cGt/cAt	4/11	0.0586219176985199	3	FACETS	1	0.984	1			1	INDETERMINATE	1	FALSE	NA	0.540393369928366	3		638	712	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030658	47030658	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs782679832	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	21	582	0	ENST00000377604.3:c.432+1G>A		p.X144_splice	ENST00000377604	NM_001204468.1	144			0.480911755194625	0	FACETS	0.116	0.089	0.147			1	SUBCLONAL	1	FALSE	0	0.540393369928366	0		582	308	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371799	55371820	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCCGCGCTGGGCCCCGAG	GGCGGCCGCGCTGGGCCCCGAG	-	novel	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	208	219	0	ENST00000297316.4:c.499_520del	p.Leu167TrpfsTer213	p.L167Wfs*213	ENST00000297316	NM_022454.3	163	caGGCGGCCGCGCTGGGCCCCGAG/ca	2/2	0.132979751955119	6	FACETS	1	0.979	1			1	INDETERMINATE	4	FALSE	NA	0.540393369928366	6		219	373	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466003	69466038	+	inframe_deletion	In_Frame_Del	DEL	GTGGACCTGGCTTGCACACCCACCGACGTGCGGGAC	GTGGACCTGGCTTGCACACCCACCGACGTGCGGGAC	-	novel	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	101	657	0	ENST00000227507.2:c.847_882del	p.Leu283_Asp294del	p.L283_D294del	ENST00000227507	NM_053056.2	281	GTGGACCTGGCTTGCACACCCACCGACGTGCGGGAC/-	5/5	0.296555987602214	3	FACETS	1	0.936	1	0.528	0.474	0.584	INDETERMINATE	1	FALSE	1	0.540393369928366	3		657	450	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937657	44937657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	58	299	2	ENST00000377967.4:c.2845C>T	p.Arg949Cys	p.R949C	ENST00000377967	NM_021140.2	949	Cgt/Tgt	19/29	1	2	FACETS	0.778	0.674	0.889	0.778	0.674	0.889	SUBCLONAL	1	FALSE	1	0.540393369928366	2		301	276	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	179	678	3	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.540393369928366	2		681	587	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227036	53227036	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	31	402	2	ENST00000375401.3:c.2539C>T	p.Gln847Ter	p.Q847*	ENST00000375401	NM_004187.3	847	Cag/Tag	18/26	0.480911755194625	0	FACETS	0.152	0.123	0.185			1	SUBCLONAL	1	FALSE	0	0.540393369928366	0		404	347	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395053	139395053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1484525055	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	53	623	1	ENST00000277541.6:c.5885G>A	p.Arg1962His	p.R1962H	ENST00000277541	NM_017617.3	1962	cGc/cAc	31/34	1	2	FACETS	0.303	0.258	0.353	0.303	0.258	0.353	SUBCLONAL	1	FALSE	1	0.540393369928366	2		624	647	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907687	111907687	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373945451	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	146	348	0	ENST00000393256.3:c.461G>A	p.Arg154His	p.R154H	ENST00000393256	NM_006538.4	154	cGt/cAt	3/4	0.441559532542996	5	FACETS	1	0.943	1			1	CLONAL	2	FALSE	NA	0.540393369928366	5		348	474	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941274	71941274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754842505	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	35	712	1	ENST00000298229.2:c.1049G>A	p.Arg350Gln	p.R350Q	ENST00000298229	NM_001567.3	350	cGg/cAg	9/28	0.296555987602214	3	FACETS	0.244	0.199	0.295	0.122	0.099	0.148	INDETERMINATE	1	FALSE	1	0.540393369928366	3		713	673	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286764	212286764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	42	346	0	ENST00000342788.4:c.2932G>A	p.Ala978Thr	p.A978T	ENST00000342788	NM_005235.2	978	Gct/Act	24/28	1	2	FACETS	0.429	0.359	0.507	0.429	0.359	0.507	SUBCLONAL	1	FALSE	1	0.540393369928366	2		346	362	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216184	36216184	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	106	637	2	ENST00000222270.7:c.3596del	p.Gly1199AlafsTer156	p.G1199Afs*156	ENST00000222270	NM_014727.1	1198	Ggg/gg	11/37	1	2	FACETS	0.737	0.663	0.815	0.737	0.663	0.815	SUBCLONAL	1	FALSE	1	0.540393369928366	2		639	532	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258894	16258894	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	54	513	0	ENST00000375759.3:c.6164del	p.Pro2055LeufsTer9	p.P2055Lfs*9	ENST00000375759	NM_015001.2	2053	aaC/aa	11/15	0.540393369928366	5	FACETS	0.552	0.47	0.641	0.184	0.156	0.214	SUBCLONAL	1	FALSE	2	0.540393369928366	5		513	656	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057717	180057717	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	39	674	2	ENST00000261937.6:c.238del	p.Val80TrpfsTer53	p.V80Wfs*53	ENST00000261937	NM_182925.4	80	Gtg/tg	3/30	0.480911755194625	0	FACETS	0.161	0.133	0.191			1	SUBCLONAL	1	FALSE	0	0.540393369928366	0		676	413	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250692	26250692	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	31	560	0	ENST00000446824.2:c.142G>A	p.Ala48Thr	p.A48T	ENST00000446824	NM_021018.2	48	Gcc/Acc	1/1	0.133469850063088	6	FACETS	0.408	0.329	0.498	0.136	0.109	0.166	INDETERMINATE	1	FALSE	3	0.540393369928366	6		560	585	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713882	30713882	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886038960	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	43	545	0	ENST00000295754.5:c.1207C>T	p.Arg403Cys	p.R403C	ENST00000295754	NM_003242.5	403	Cgt/Tgt	4/7	0.540393369928366	2	FACETS	0.331	0.277	0.391	0.165	0.138	0.196	SUBCLONAL	1	FALSE	0	0.540393369928366	2		545	481	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332883	65332883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764523308	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	11	190	0	ENST00000342505.4:c.656G>A	p.Arg219Gln	p.R219Q	ENST00000342505	NM_002227.2	219	cGa/cAa	7/25	0.540393369928366	1	FACETS	0.198	0.137	0.273	0.198	0.137	0.273	SUBCLONAL	1	FALSE	0	0.540393369928366	1		190	150	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246490641	246490641	+	splice_acceptor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	41	228	1	ENST00000388985.4:c.395-2del		p.X132_splice	ENST00000388985		132			1	2	FACETS	0.807	0.681	0.944	0.807	0.681	0.944	CLONAL	1	FALSE	1	0.540393369928366	2		229	188	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074348	8074349	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	427	306	1	ENST00000377482.5:c.310_311del	p.Gly104ThrfsTer3	p.G104Tfs*3	ENST00000377482	NM_018948.3	104	GGa/a	4/4	0.540393369928366	2	FACETS	1	0.993	1	1	0.997	1	CLONAL	3	FALSE	0	0.540393369928366	2		307	502	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105581	27105581	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	513	440	0	ENST00000324856.7:c.5192T>G	p.Leu1731Ter	p.L1731*	ENST00000324856	NM_006015.4	1731	tTa/tGa	20/20	0.540393369928366	5	FACETS	0.973	0.953	0.991	1	0.998	1	CLONAL	6	FALSE	2	0.540393369928366	5		440	589	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36824372	36824372	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	129	488	0	ENST00000373129.3:c.164G>T	p.Arg55Met	p.R55M	ENST00000373129	NM_032017.1	55	aGg/aTg	4/12	0.540393369928366	1	FACETS	0.537	0.488	0.588	0.537	0.488	0.588	SUBCLONAL	1	FALSE	0	0.540393369928366	1		488	649	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666385	206666385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199747005	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	152	575	0	ENST00000367120.3:c.1865G>A	p.Arg622His	p.R622H	ENST00000367120	NM_014002.3	622	cGc/cAc	19/22	1		FACETS		0.962	1				CLONAL	1	FALSE	1	0.540393369928366	2		575	523	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061129	38061129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	20	250	0	ENST00000250448.2:c.860C>T	p.Ala287Val	p.A287V	ENST00000250448	NM_004496.3	287	gCc/gTc	2/2	1	2	FACETS	0.428	0.329	0.542	0.428	0.329	0.542	SUBCLONAL	1	FALSE	1	0.540393369928366	2		250	173	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627232	12627232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs546131178	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	54	382	2	ENST00000251849.4:c.1484G>A	p.Arg495His	p.R495H	ENST00000251849	NM_002880.3	495	cGc/cAc	14/17	0.540393369928366	2	FACETS	0.452	0.387	0.523	0.226	0.193	0.262	SUBCLONAL	1	FALSE	0	0.540393369928366	2		384	442	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917498	178917499	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	41	261	0	ENST00000263967.3:c.378_379del	p.Cys126Ter	p.C126*	ENST00000263967	NM_006218.2	125	GTg/g	3/21	1	2	FACETS	0.609	0.511	0.717	0.609	0.511	0.717	SUBCLONAL	1	FALSE	1	0.540393369928366	2		261	249	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748252	41748252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	73	514	0	ENST00000226382.2:c.517G>A	p.Gly173Ser	p.G173S	ENST00000226382	NM_003924.3	173	Ggc/Agc	3/3	1	2	FACETS	0.677	0.595	0.765	0.677	0.595	0.765	SUBCLONAL	1	FALSE	1	0.540393369928366	2		514	399	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131976374	131976374	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	91	394	0	ENST00000265335.6:c.3629C>A	p.Ser1210Ter	p.S1210*	ENST00000265335		1210	tCa/tAa	24/25	1	2	FACETS	0.893	0.799	0.992	0.893	0.799	0.992	CLONAL	1	FALSE	1	0.540393369928366	2		394	377	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288803	33288803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	114	395	0	ENST00000374542.5:c.749G>A	p.Gly250Asp	p.G250D	ENST00000374542	NM_001141970.1	250	gGc/gAc	3/8	1	2	FACETS	0.745	0.673	0.821	0.745	0.673	0.821	SUBCLONAL	1	FALSE	1	0.540393369928366	2		395	566	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138386	37138386	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	36	422	0	ENST00000373509.5:c.35T>C	p.Leu12Pro	p.L12P	ENST00000373509	NM_002648.3	12	cTg/cCg	1/6	1	2	FACETS	0.292	0.24	0.351	0.292	0.24	0.351	SUBCLONAL	1	FALSE	1	0.540393369928366	2		422	456	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117632241	117632241	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	17	393	0	ENST00000368508.3:c.6175C>A	p.Leu2059Met	p.L2059M	ENST00000368508	NM_002944.2	2059	Ctg/Atg	39/43	0.530470916762237	1	FACETS	0.215	0.16	0.279	0.215	0.16	0.279	SUBCLONAL	1	FALSE	0	0.540393369928366	1		393	214	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450351	50450351	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	72	530	0	ENST00000331340.3:c.535A>G	p.Asn179Asp	p.N179D	ENST00000331340	NM_006060.4	179	Aac/Gac	5/8	0.460599782829971	1	FACETS	0.748	0.661	0.839	0.748	0.661	0.839	SUBCLONAL	1	FALSE	0	0.540393369928366	1		530	260	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539564	187539564	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	88	379	1	ENST00000441802.2:c.8176C>T	p.Arg2726Ter	p.R2726*	ENST00000441802	NM_005245.3	2726	Cga/Tga	10/27	0.454501703952715	3	FACETS	1	0.901	1	0.507	0.451	0.566	CLONAL	1	TRUE	1	0.454501703952715	3		380	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579356	7579356	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	335	666	1	ENST00000269305.4:c.331C>A	p.Leu111Met	p.L111M	ENST00000269305	NM_001126112.2	111	Ctg/Atg	4/11	0.454501703952715	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.454501703952715	2		667	689	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935418	36935418	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	192	687	2	ENST00000361632.4:c.1309G>T	p.Ala437Ser	p.A437S	ENST00000361632		437	Gcc/Tcc	10/16	0.454501703952715	2	FACETS	1	0.976	1	0.56	0.519	0.602	CLONAL	1	TRUE	0	0.454501703952715	2		689	755	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780289	9780289	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1550	217	490	0	ENST00000377346.4:c.1459G>T	p.Ala487Ser	p.A487S	ENST00000377346	NM_005026.3	487	Gcc/Tcc	11/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.224324426726513	2		490	1767	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512329	149512329	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1577	791	508	0	ENST00000261799.4:c.1111A>G	p.Asn371Asp	p.N371D	ENST00000261799	NM_002609.3	371	Aac/Gac	7/23	1	2	FACETS	0.993	0.959	1	1	0.998	1	CLONAL	3	TRUE	1	0.224324426726513	2		508	2368	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	83	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.421293584415129	5	FACETS	1	0.959	1	0.842	0.76	0.924	CLONAL	3	TRUE	1	0.421293584415129	5		327	191	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134566	2134566	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	141	841	0	ENST00000219476.3:c.4343G>C	p.Ser1448Thr	p.S1448T	ENST00000219476	NM_000548.3	1448	aGc/aCc	34/42	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.421293584415129	2		841	640	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	78	326	0	ENST00000335508.6:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000335508	NM_012433.2	902	Gaa/Aaa	18/25	1	2	FACETS	0.926	0.817	1	0.926	0.817	1	CLONAL	1	TRUE	1	0.378734637302756	2		326	445	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992136	11992136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	163	499	0	ENST00000396373.4:c.226G>A	p.Glu76Lys	p.E76K	ENST00000396373	NM_001987.4	76	Gag/Aag	3/8	0.296652529467087	3	FACETS	0.757	0.697	0.82	0.757	0.697	0.82	SUBCLONAL	2	TRUE	1	0.378734637302756	3		499	676	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	115	224	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	1	1	FACETS	0.764	0.698	0.833	1	0.986	1	SUBCLONAL	2	TRUE	0	0.378734637302756	1		224	322	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005093	150005093	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	108	446	0	ENST00000253339.5:c.1132C>G	p.Leu378Val	p.L378V	ENST00000253339		378	Ctg/Gtg	3/7	1	2	FACETS	0.992	0.893	1	0.992	0.893	1	CLONAL	1	TRUE	1	0.378734637302756	2		446	575	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651138	206651138	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	88	761	0	ENST00000367120.3:c.748C>T	p.Gln250Ter	p.Q250*	ENST00000367120	NM_014002.3	250	Cag/Tag	8/22	1	2	FACETS	0.473	0.418	0.532	0.473	0.418	0.532	SUBCLONAL	1	TRUE	1	0.378734637302756	2		761	983	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856345	45856345	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	176	646	1	ENST00000391945.4:c.1827C>A	p.Asp609Glu	p.D609E	ENST00000391945	NM_000400.3	609	gaC/gaA	19/23	1	2	FACETS	0.966	0.89	1	0.966	0.89	1	CLONAL	1	TRUE	1	0.378734637302756	2		647	962	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47600619	47600619	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	89	340	0	ENST00000263735.4:c.94T>C	p.Tyr32His	p.Y32H	ENST00000263735	NM_002354.2	32	Tac/Cac	2/9	1	2	FACETS	0.892	0.793	0.997	0.892	0.793	0.997	CLONAL	1	TRUE	1	0.378734637302756	2		340	527	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125431	47125431	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1340757729	NA	P-0050117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	87	433	0	ENST00000409792.3:c.5839A>G	p.Ser1947Gly	p.S1947G	ENST00000409792	NM_014159.6	1947	Agt/Ggt	12/21	0.378734637302756	1	FACETS	0.872	0.776	0.974	0.872	0.776	0.974	CLONAL	1	TRUE	0	0.378734637302756	1		433	427	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156393	106156393	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	63	348	0	ENST00000380013.4:c.1294G>A	p.Glu432Lys	p.E432K	ENST00000380013	NM_001127208.2	432	Gaa/Aaa	3/11	1	2	FACETS	0.813	0.706	0.929	0.813	0.706	0.929	CLONAL	1	TRUE	1	0.378734637302756	2		348	409	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149452871	149452871	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	122	516	0	ENST00000286301.3:c.1075A>T	p.Thr359Ser	p.T359S	ENST00000286301	NM_005211.3	359	Aca/Tca	7/22	0.378734637302756	1	FACETS	0.944	0.857	1	0.944	0.857	1	CLONAL	1	TRUE	0	0.378734637302756	1		516	553	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519547	137519547	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	84	393	0	ENST00000367739.4:c.1091A>G	p.Asp364Gly	p.D364G	ENST00000367739	NM_000416.2	364	gAc/gGc	7/7	1	2	FACETS	0.871	0.772	0.977	0.871	0.772	0.977	CLONAL	1	TRUE	1	0.378734637302756	2		393	509	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0050119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	148	394	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.749559064334708	3	FACETS	0.933	0.856	1	0.466	0.428	0.507	CLONAL	1	TRUE	1	0.749559064334708	3		394	582	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0050119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	182	303	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	0.979	0.911	1	0.979	0.911	1	CLONAL	1	TRUE	1	0.749559064334708	2		303	496	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962846	2962846	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	304	734	1	ENST00000396946.4:c.2062C>T	p.Arg688Ter	p.R688*	ENST00000396946	NM_032415.4	688	Cga/Tga	16/25	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.749559064334708	2		735	745	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711350	114711350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243981730	NA	P-0050119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	119	260	0	ENST00000543371.1:c.365C>T	p.Ser122Leu	p.S122L	ENST00000543371	NM_001198531.1	122	tCg/tTg	3/14	1	2	FACETS	0.959	0.877	1	0.959	0.877	1	CLONAL	1	TRUE	1	0.749559064334708	2		260	331	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005006	150005006	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	204	429	0	ENST00000253339.5:c.1219C>T	p.Gln407Ter	p.Q407*	ENST00000253339		407	Cag/Tag	3/7	0.749559064334708	1	FACETS	0.986	0.934	1	0.986	0.934	1	CLONAL	1	TRUE	0	0.749559064334708	1		429	345	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099199	4099199	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1469141139	NA	P-0050119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	176	606	1	ENST00000262948.5:c.919G>A	p.Gly307Ser	p.G307S	ENST00000262948	NM_030662.3	307	Ggt/Agt	7/11	1	2	FACETS	0.774	0.716	0.833	0.774	0.716	0.833	SUBCLONAL	1	TRUE	1	0.749559064334708	2		607	607	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665424	176665424	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	217	439	0	ENST00000439151.2:c.4108del	p.Gln1370SerfsTer2	p.Q1370Sfs*2	ENST00000439151	NM_022455.4	1370	Cag/ag	7/23	0.157417284702819	3	FACETS	1	0.99	1	0.663	0.621	0.707	INDETERMINATE	1	TRUE	1	0.749559064334708	3		439	600	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176700678	176700678	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	192	360	0	ENST00000439151.2:c.5515C>T	p.Gln1839Ter	p.Q1839*	ENST00000439151	NM_022455.4	1839	Cag/Tag	17/23	0.157417284702819	3	FACETS	1	0.989	1	0.672	0.627	0.718	INDETERMINATE	1	TRUE	1	0.749559064334708	3		360	524	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004798	150004798	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	191	485	0	ENST00000253339.5:c.1427C>G	p.Ser476Cys	p.S476C	ENST00000253339		476	tCt/tGt	3/7	0.749559064334708	1	FACETS	0.91	0.857	0.963	0.91	0.857	0.963	CLONAL	1	TRUE	0	0.749559064334708	1		485	350	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878769	151878770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATCC	novel	NA	P-0050119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	154	441	0	ENST00000262189.6:c.6172_6175dup	p.Ser2059TrpfsTer13	p.S2059Wfs*13	ENST00000262189	NM_170606.2	2059	tca/tGGATca	36/59	0.583774240277882	1	FACETS	0.803	0.748	0.858	0.803	0.748	0.858	CLONAL	1	TRUE	0	0.749559064334708	1		441	320	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344150	70344150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	240	592	0	ENST00000374080.3:c.1886C>T	p.Pro629Leu	p.P629L	ENST00000374080		629	cCt/cTt	13/45	0.324409391592342	1	FACETS	0.627	0.589	0.665	0.627	0.589	0.665	INDETERMINATE	1	TRUE	0	0.749559064334708	1		592	639	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356480	70356480	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1322748106	NA	P-0050119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	262	637	3	ENST00000374080.3:c.5375G>A	p.Arg1792His	p.R1792H	ENST00000374080		1792	cGc/cAc	37/45	0.324409391592342	1	FACETS	0.635	0.599	0.672	0.635	0.599	0.672	INDETERMINATE	1	TRUE	0	0.749559064334708	1		640	688	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0050120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	28	215	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.607	0.485	0.744	0.607	0.485	0.744	SUBCLONAL	1	TRUE	1	0.289407383565794	2		215	319	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0050120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	95	349	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.801	0.717	0.888	1	0.983	1	CLONAL	2	TRUE	1	0.289407383565794	2		349	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	108	1029	0	ENST00000269305.4:c.313G>T	p.Gly105Cys	p.G105C	ENST00000269305	NM_001126112.2	105	Ggc/Tgc	4/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.289407383565794	2		1029	604	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430792	181430792	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	44	1046	0	ENST00000325404.1:c.644C>A	p.Thr215Asn	p.T215N	ENST00000325404	NM_003106.3	215	aCc/aAc	1/1	1	2	FACETS	0.486	0.406	0.574	0.486	0.406	0.574	SUBCLONAL	1	TRUE	1	0.289407383565794	2		1046	626	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102882	71102882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	41	540	0	ENST00000318789.4:c.325C>T	p.Pro109Ser	p.P109S	ENST00000318789	NM_032682.5	109	Ccc/Tcc	8/21	1	2	FACETS	0.756	0.631	0.894	0.756	0.631	0.894	SUBCLONAL	1	TRUE	1	0.289407383565794	2		540	375	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877393	40877393	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	48	764	0	ENST00000373198.4:c.2303G>T	p.Gly768Val	p.G768V	ENST00000373198	NM_133170.3	768	gGc/gTc	15/32	1	2	FACETS	0.584	0.493	0.684	0.584	0.493	0.684	SUBCLONAL	1	TRUE	1	0.289407383565794	2		764	568	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426736	49426771	+	inframe_deletion	In_Frame_Del	DEL	GCTGCTGCTGCTGCTGAAGTTGCTGTTGCTGTTGCA	GCTGCTGCTGCTGCTGAAGTTGCTGTTGCTGTTGCA	-	rs1415174573	NA	P-0050120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	17	389	0	ENST00000301067.7:c.11717_11752del	p.Leu3906_Gln3917del	p.L3906_Q3917del	ENST00000301067	NM_003482.3	3906	cTGCAACAGCAACAGCAACTTCAGCAGCAGCAGCAGCag/cag	39/54	1	2	FACETS	0.443	0.331	0.577	0.443	0.331	0.577	SUBCLONAL	1	TRUE	1	0.289407383565794	2		389	265	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863392	57863392	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759027001	NA	P-0050120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	91	1030	2	ENST00000228682.2:c.1487G>A	p.Arg496His	p.R496H	ENST00000228682	NM_005269.2	496	cGc/cAc	11/12	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.289407383565794	2		1032	591	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777132	9777132	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	54	1032	0	ENST00000377346.4:c.896C>A	p.Pro299Gln	p.P299Q	ENST00000377346	NM_005026.3	299	cCg/cAg	7/24	1	2	FACETS	0.573	0.489	0.666	0.573	0.489	0.666	SUBCLONAL	1	TRUE	1	0.289407383565794	2		1032	651	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056188	27056188	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1204236291	NA	P-0050120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	40	716	0	ENST00000324856.7:c.1184A>G	p.Tyr395Cys	p.Y395C	ENST00000324856	NM_006015.4	395	tAt/tGt	2/20	1	2	FACETS	0.562	0.467	0.668	0.562	0.467	0.668	SUBCLONAL	1	TRUE	1	0.289407383565794	2		716	492	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132092	176132092	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	51	504	0	ENST00000367669.3:c.675G>C	p.Trp225Cys	p.W225C	ENST00000367669	NM_022457.5	225	tgG/tgC	5/20	0.167456828814397	3	FACETS	1	0.879	1	0.517	0.441	0.601	INDETERMINATE	1	TRUE	1	0.289407383565794	3		504	390	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683388	88683388	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	61	556	0	ENST00000372037.3:c.1511G>T	p.Trp504Leu	p.W504L	ENST00000372037	NM_004329.2	504	tGg/tTg	13/13	1	2	FACETS	0.969	0.838	1	0.969	0.838	1	CLONAL	1	TRUE	1	0.289407383565794	2		556	435	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719911	18719911	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	19	474	0	ENST00000266497.5:c.3808A>T	p.Thr1270Ser	p.T1270S	ENST00000266497		1270	Aca/Tca	27/31	1	2	FACETS	0.377	0.286	0.485	0.377	0.286	0.485	SUBCLONAL	1	TRUE	1	0.289407383565794	2		474	348	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434545	121434545	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	94	986	0	ENST00000257555.6:c.1309G>T	p.Gly437Cys	p.G437C	ENST00000257555		437	Ggc/Tgc	6/10	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.289407383565794	2		986	617	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443580	29443580	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	96	828	0	ENST00000389048.3:c.3637C>A	p.Pro1213Thr	p.P1213T	ENST00000389048	NM_004304.4	1213	Cct/Act	23/29	0.287104403529269	1	FACETS	0.935	0.834	1	0.935	0.834	1	CLONAL	1	TRUE	0	0.289407383565794	1		828	607	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646161	215646161	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	40	547	0	ENST00000260947.4:c.437G>T	p.Trp146Leu	p.W146L	ENST00000260947	NM_000465.2	146	tGg/tTg	4/11	1	2	FACETS	0.691	0.575	0.82	0.691	0.575	0.82	SUBCLONAL	1	TRUE	1	0.289407383565794	2		547	400	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388641	31388642	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0050120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	62	694	0	ENST00000328111.2:c.1908dup	p.Glu637Ter	p.E637*	ENST00000328111	NM_006892.3	636	att/aTtt	18/23	1	2	FACETS	0.976	0.846	1	0.976	0.846	1	CLONAL	1	TRUE	1	0.289407383565794	2		694	439	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259271	89259271	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	26	503	0	ENST00000336596.2:c.415C>A	p.Gln139Lys	p.Q139K	ENST00000336596	NM_005233.5	139	Cag/Aag	3/17	0.146284941615375	0	FACETS	0.398	0.315	0.492			1	INDETERMINATE	1	TRUE	0	0.289407383565794	0		503	321	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317572	1317572	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	20	323	1	ENST00000400841.2:c.493G>T	p.Glu165Ter	p.E165*	ENST00000400841		165	Gaa/Taa	5/6	1	2	FACETS	0.532	0.407	0.677	0.532	0.407	0.677	SUBCLONAL	1	TRUE	1	0.289407383565794	2		324	260	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888785	76888785	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	29	580	0	ENST00000373344.5:c.5044G>C	p.Gly1682Arg	p.G1682R	ENST00000373344	NM_000489.3	1682	Ggc/Cgc	19/35	1	2	FACETS	0.491	0.394	0.602	0.491	0.394	0.602	SUBCLONAL	1	TRUE	1	0.289407383565794	2		580	408	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952065	76952065	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	15	393	0	ENST00000373344.5:c.370G>C	p.Gly124Arg	p.G124R	ENST00000373344	NM_000489.3	124	Ggt/Cgt	5/35	1	2	FACETS	0.355	0.259	0.471	0.355	0.259	0.471	SUBCLONAL	1	TRUE	1	0.289407383565794	2		393	292	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	63	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.891	0.772	1	0.891	0.772	1	CLONAL	1	TRUE	1	0.278818555771903	2		327	507	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0050121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	19	394	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.408	0.309	0.524	0.408	0.309	0.524	SUBCLONAL	1	TRUE	1	0.278818555771903	2		394	334	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0050121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	105	720	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	0.184960614803251	3	FACETS	1	0.974	1	0.637	0.571	0.706	CLONAL	1	TRUE	1	0.278818555771903	3		720	674	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686907	37686907	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	39	507	0	ENST00000447079.4:c.3811G>A	p.Gly1271Arg	p.G1271R	ENST00000447079	NM_015083.1	1271	Gga/Aga	14/14	0.187587005178623	2	FACETS	0.396	0.327	0.473	0.198	0.163	0.237	SUBCLONAL	1	TRUE	0	0.28	2		507	704	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130300	11130300	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	112	717	1	ENST00000358026.2:c.2539C>T	p.Gln847Ter	p.Q847*	ENST00000358026	NM_001128849.1	847	Cag/Tag	18/36	1	2	FACETS	0.821	0.738	0.91	0.821	0.738	0.91	CLONAL	1	TRUE	1	0.28	2		718	974	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092955	29092955	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	45	494	0	ENST00000328354.6:c.1029T>G	p.Ile343Met	p.I343M	ENST00000328354	NM_007194.3	343	atT/atG	10/15	1	2	FACETS	0.714	0.601	0.84	0.714	0.601	0.84	SUBCLONAL	1	TRUE	1	0.28	2		494	450	SUCCESS
APC	324	MSKCC	GRCh37	5	112175852	112175852	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	139	291	0	ENST00000257430.4:c.4561G>T	p.Glu1521Ter	p.E1521*	ENST00000257430	NM_000038.5	1521	Gaa/Taa	16/16	0.691008963162754	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.691008963162754	1		291	259	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321210	65321220	+	frameshift_variant	Frame_Shift_Del	DEL	AGCAGCGTTTT	AGCAGCGTTTT	-	novel	NA	P-0050123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	155	557	0	ENST00000342505.4:c.1620_1630del	p.Lys541ProfsTer15	p.K541Pfs*15	ENST00000342505	NM_002227.2	540	ctAAAACGCTGCTgc/ctgc	11/25	0.225659441829162	1	FACETS	0.485	0.445	0.525	0.485	0.445	0.525	INDETERMINATE	1	TRUE	0	0.691008963162754	1		557	606	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906938	32906938	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	201	478	0	ENST00000380152.3:c.1324del	p.Ser442GlnfsTer18	p.S442Qfs*18	ENST00000380152		441	acT/ac	10/27	0.691008963162754	1	FACETS	0.979	0.922	1	0.979	0.922	1	CLONAL	1	TRUE	0	0.691008963162754	1		478	389	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434569	99434569	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	305	688	0	ENST00000268035.6:c.656G>A	p.Cys219Tyr	p.C219Y	ENST00000268035	NM_000875.3	219	tGt/tAt	3/21	0.691008963162754	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.691008963162754	1		688	577	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867697	45867697	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	203	826	1	ENST00000391945.4:c.703G>A	p.Glu235Lys	p.E235K	ENST00000391945	NM_000400.3	235	Gag/Aag	8/23	0.266960965104524	1	FACETS	0.423	0.392	0.455	0.423	0.392	0.455	INDETERMINATE	1	TRUE	0	0.691008963162754	1		827	909	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446992	187446992	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	371	747	0	ENST00000232014.4:c.1201G>A	p.Gly401Ser	p.G401S	ENST00000232014	NM_001130845.1	401	Ggc/Agc	5/10	0.671205078954493	3	FACETS	1	0.98	1	0.356	0.337	0.375	CLONAL	1	TRUE	0	0.691008963162754	3		747	1353	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549185	87549185	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs778882958	NA	P-0050123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	237	525	0	ENST00000277120.3:c.1742A>G	p.Asp581Gly	p.D581G	ENST00000277120		581	gAc/gGc	15/19	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.691008963162754	2		525	621	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0050124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	33	332	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.97	0.791	1	0.97	0.791	1	CLONAL	1	TRUE	1	0.19	2		332	358	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498374	89498374	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs779836309	NA	P-0050124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	17	203	0	ENST00000336596.2:c.2347-1G>A		p.X783_splice	ENST00000336596	NM_005233.5	783			1	2	FACETS	0.788	0.589	1	0.788	0.589	1	CLONAL	1	TRUE	1	0.19	2		203	227	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223522	55223522	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0050125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	313	827	0	ENST00000275493.2:c.890-1G>T		p.X297_splice	ENST00000275493	NM_005228.3	297			0.219237311042723	3	FACETS	1	0.986	1	0.566	0.534	0.599	INDETERMINATE	1	TRUE	1	0.676623119646743	3		827	1093	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249007	+	missense_variant	Missense_Mutation	TNP	GCG	GCG	TCT	novel	NA	P-0050125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	331	814	1	ENST00000275493.2:c.2303_2305delinsTCT	p.Ser768_Val769delinsIleLeu	p.S768_V769delinsIL	ENST00000275493	NM_005228.3	768	aGCGtg/aTCTtg	20/28	0.219237311042723	3	FACETS	0.756	0.717	0.795	0.756	0.717	0.795	INDETERMINATE	2	TRUE	1	0.676623119646743	3		815	866	SUCCESS
AR	367	MSKCC	GRCh37	X	66765076	66765076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761416673	NA	P-0050125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	97	887	1	ENST00000374690.3:c.88G>A	p.Val30Met	p.V30M	ENST00000374690	NM_000044.3	30	Gtg/Atg	1/8	0.676623119646743	3	FACETS	0.299	0.265	0.335	0.149	0.132	0.168	SUBCLONAL	1	TRUE	1	0.676623119646743	3		888	1284	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173601	108173601	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	28	397	0	ENST00000278616.4:c.5341G>C	p.Asp1781His	p.D1781H	ENST00000278616	NM_000051.3	1781	Gac/Cac	36/63	0.656467187470663	2	FACETS	0.267	0.213	0.328	0.133	0.106	0.164	SUBCLONAL	1	TRUE	0	0.676623119646743	2		397	310	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248454	212248454	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	62	476	0	ENST00000342788.4:c.3813T>A	p.Asn1271Lys	p.N1271K	ENST00000342788	NM_005235.2	1271	aaT/aaA	28/28	0.676623119646743	1	FACETS	0.374	0.325	0.427	0.374	0.325	0.427	SUBCLONAL	1	TRUE	0	0.676623119646743	1		476	324	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670099	29670099	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	344	624	0	ENST00000356175.3:c.7072G>T	p.Gly2358Ter	p.G2358*	ENST00000356175	NM_000267.3	2358	Gga/Tga	47/57	0.611976625544727	2	FACETS	0.866	0.83	0.902	0.866	0.83	0.902	CLONAL	2	TRUE	0	0.676623119646743	2		624	587	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572489	41572489	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	394	1072	0	ENST00000263253.7:c.5018G>A	p.Cys1673Tyr	p.C1673Y	ENST00000263253	NM_001429.3	1673	tGc/tAc	30/31	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.676623119646743	2		1072	1111	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056748	180056748	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	428	1137	1	ENST00000261937.6:c.764G>T	p.Trp255Leu	p.W255L	ENST00000261937	NM_182925.4	255	tGg/tTg	6/30	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	1	TRUE	NA	0.676623119646743	2		1138	991	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511280	157511280	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	79	661	0	ENST00000346085.5:c.3798G>A	p.Met1266Ile	p.M1266I	ENST00000346085	NM_020732.3	1266	atG/atA	15/20	NA	2	FACETS	0.312	0.274	0.353			1	INDETERMINATE	1	TRUE	NA	0.676623119646743	2		661	748	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579474	7579475	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	A	novel	NA	P-0050125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	252	922	3	ENST00000269305.4:c.212_213delinsT	p.Pro71LeufsTer52	p.P71Lfs*52	ENST00000269305	NM_001126112.2	71	cCC/cT	4/11	0.676623119646743	1	FACETS	0.837	0.79	0.884	0.837	0.79	0.884	CLONAL	1	TRUE	0	0.676623119646743	1		925	589	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430757	47430758	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	A	novel	NA	P-0050125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	279	1001	0	ENST00000377045.4:c.1722_1723delinsA	p.Lys576ArgfsTer?	p.K576Rfs*?	ENST00000377045	NM_001654.4	574	ctCCcc/ctAcc	16/16	NA	2	FACETS	0.958	0.902	1			1	INDETERMINATE	1	TRUE	NA	0.676623119646743	2		1001	861	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0121469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	349	349	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.673215266859058	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	NA	0	0.673215266859058	2		349	499	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0050127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	71	328	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.993	0.872	1	0.993	0.872	1	CLONAL	1	TRUE	1	0.383265886530138	2		328	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0050127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	97	568	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.6	0.535	0.671	0.6	0.535	0.671	SUBCLONAL	1	TRUE	1	0.383265886530138	2		568	843	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0050127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	3335	849	2	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.383265886530138	19	FACETS	1	0.998	1			1	CLONAL	17	TRUE	NA	0.383265886530138	19		851	4255	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591247	67591249	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GGT	GGT	-	rs1131692243	NA	P-0050127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	91	385	0	ENST00000274335.5:c.1748_1750del		p.X583_splice	ENST00000274335		583		13/15	1	2	FACETS	0.911	0.812	1	0.911	0.812	1	CLONAL	1	TRUE	1	0.383265886530138	2		385	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519990	NA	P-0050127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	91	606	0	ENST00000269305.4:c.796G>C	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Cga	8/11	1	2	FACETS	0.63	0.559	0.706	0.63	0.559	0.706	SUBCLONAL	1	TRUE	1	0.383265886530138	2		606	754	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206908	162206908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1233588284	NA	P-0050127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	87	454	0	ENST00000366898.1:c.767G>A	p.Arg256His	p.R256H	ENST00000366898	NM_004562.2	256	cGc/cAc	7/12	1	2	FACETS	0.845	0.75	0.947	0.845	0.75	0.947	CLONAL	1	TRUE	1	0.383265886530138	2		454	537	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592283	29592283	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	32	263	0	ENST00000356175.3:c.4698G>T	p.Leu1566Phe	p.L1566F	ENST00000356175	NM_000267.3	1566	ttG/ttT	35/57	0.185937840663776	3	FACETS	0.569	0.462	0.689			1	INDETERMINATE	1	TRUE	NA	0.383265886530138	3		263	350	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72891494	72891494	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs761065004	NA	P-0050127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	139	489	0	ENST00000325599.8:c.268A>G	p.Met90Val	p.M90V	ENST00000325599	NM_018130.2	90	Atg/Gtg	3/11	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.383265886530138	2		489	724	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557322	29557331	+	frameshift_variant	Frame_Shift_Del	DEL	AAACGAAACT	AAACGAAACT	-	novel	NA	P-0050127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	24	335	0	ENST00000356175.3:c.3035_3044del	p.Lys1012SerfsTer4	p.K1012Sfs*4	ENST00000356175	NM_000267.3	1012	aAAACGAAACTg/ag	23/57	0.185937840663776	3	FACETS	0.342	0.267	0.428			1	INDETERMINATE	1	TRUE	NA	0.383265886530138	3		335	437	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0050131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	120	461	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.482	0.436	0.53	0.482	0.436	0.53	SUBCLONAL	1	TRUE	1	0.765508831017123	2		461	651	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262206	115262206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769519003	NA	P-0050131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	105	374	1	ENST00000438362.2:c.2348G>A	p.Arg783Gln	p.R783Q	ENST00000438362	NM_001242891.1	783	cGa/cAa	18/20	1	2	FACETS	0.469	0.421	0.52	0.469	0.421	0.52	SUBCLONAL	1	TRUE	1	0.765508831017123	2		375	585	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73995386	73995386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs184115783	NA	P-0050131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	130	421	2	ENST00000318443.5:c.692C>T	p.Ala231Val	p.A231V	ENST00000318443	NM_001024736.1	231	gCg/gTg	4/10	1	2	FACETS	0.535	0.486	0.586	0.535	0.486	0.586	SUBCLONAL	1	TRUE	1	0.765508831017123	2		423	635	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871880	12871880	+	stop_lost	Nonstop_Mutation	SNP	A	A	C	rs1565420117	NA	P-0050131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	60	182	0	ENST00000228872.4:c.597A>C	p.Ter199TyrextTer60	p.*199Yext*60	ENST00000228872	NM_004064.3	199	taA/taC	2/3	1	2	FACETS	0.45	0.39	0.515	0.45	0.39	0.515	SUBCLONAL	1	TRUE	1	0.765508831017123	2		182	348	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859909	151859918	+	frameshift_variant	Frame_Shift_Del	DEL	ATCCCGGATA	ATCCCGGATA	-	novel	NA	P-0050131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	113	424	0	ENST00000262189.6:c.10744_10753del	p.Tyr3582GlnfsTer12	p.Y3582Qfs*12	ENST00000262189	NM_170606.2	3582	TATCCGGGATca/ca	43/59	1	2	FACETS	0.474	0.427	0.523	0.474	0.427	0.523	SUBCLONAL	1	TRUE	1	0.765508831017123	2		424	623	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0050132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	105	223	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.963	0.875	1	0.963	0.875	1	CLONAL	1	TRUE	1	0.744153956315149	2		223	293	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0050132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	101	451	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.987	0.896	1	0.987	0.896	1	CLONAL	1	TRUE	1	0.744153956315149	2		451	275	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0050132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	567	566	1	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	0.744153956315149	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.744153956315149	2		567	747	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413070	139413072	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0050132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	48	628	0	ENST00000277541.6:c.1070_1072del	p.Phe357del	p.F357del	ENST00000277541	NM_017617.3	357	tTCTac/tac	6/34	0.435180754787573	1	FACETS	0.154	0.13	0.181	0.154	0.13	0.181	INDETERMINATE	1	TRUE	0	0.744153956315149	1		628	525	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807399	36807399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	69	652	0	ENST00000373129.3:c.1265C>T	p.Ser422Phe	p.S422F	ENST00000373129	NM_032017.1	422	tCc/tTc	12/12	1	2	FACETS	0.234	0.203	0.267	0.234	0.203	0.267	SUBCLONAL	1	TRUE	1	0.744153956315149	2		652	794	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393353	139393355	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	TGT	TGT	-	rs1057518096	NA	P-0050132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	192	588	0	ENST00000277541.6:c.6176_6178del	p.Asn2059del	p.N2059del	ENST00000277541	NM_017617.3	2059	aACAgg/agg	33/34	0.435180754787573	1	FACETS	0.562	0.523	0.601	0.562	0.523	0.601	INDETERMINATE	1	TRUE	0	0.744153956315149	1		588	577	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907613	76907613	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	203	229	0	ENST00000373344.5:c.4548del	p.Lys1516AsnfsTer2	p.K1516Nfs*2	ENST00000373344	NM_000489.3	1516	aaA/aa	15/35	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.744153956315149	1		229	287	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115252348	115252348	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	85	245	0	ENST00000369535.4:c.292G>C	p.Glu98Gln	p.E98Q	ENST00000369535	NM_002524.4	98	Gag/Cag	4/7	0.400546923054944	3	FACETS	1	0.973	1	0.663	0.59	0.741	CLONAL	1	TRUE	1	0.400546923054944	3		245	384	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609054	43609054	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746901176	NA	P-0050133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	209	644	2	ENST00000355710.3:c.1810G>A	p.Ala604Thr	p.A604T	ENST00000355710	NM_020975.4	604	Gct/Act	10/20	0.165625736113795	3	FACETS	1	0.99	1	0.715	0.664	0.767	INDETERMINATE	1	TRUE	1	0.400546923054944	3		646	876	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224493	108224493	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs748192003	NA	P-0050133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	66	240	0	ENST00000278616.4:c.8672G>T	p.Gly2891Val	p.G2891V	ENST00000278616	NM_000051.3	2891	gGt/gTt	60/63	0.165625736113795	3	FACETS	1	0.969	1	0.689	0.604	0.78	INDETERMINATE	1	TRUE	1	0.400546923054944	3		240	287	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443611	49443612	+	stop_gained	Nonsense_Mutation	DNP	CA	CA	AC	novel	NA	P-0050133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	492	647	0	ENST00000301067.7:c.3759_3760delinsGT	p.Asp1253_Glu1254delinsGluTer	p.D1253_E1254delinsE*	ENST00000301067	NM_003482.3	1253	gaTGag/gaGTag	11/54	0.210147597791495	6	FACETS	1	0.967	1	0.672	0.645	0.699	INDETERMINATE	4	TRUE	0	0.400546923054944	6		647	1097	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484291	50484291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253128772	NA	P-0050133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	466	600	0	ENST00000394963.4:c.1051C>T	p.Arg351Cys	p.R351C	ENST00000394963	NM_003076.4	351	Cgt/Tgt	9/13	0.210147597791495	6	FACETS	0.998	0.957	1	0.665	0.638	0.693	INDETERMINATE	4	TRUE	0	0.400546923054944	6		600	1050	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578440	7578440	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0050133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	369	618	0	ENST00000269305.4:c.490A>T	p.Lys164Ter	p.K164*	ENST00000269305	NM_001126112.2	164	Aag/Tag	5/11	0.338095212669985	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.400546923054944	2		618	911	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627319	37627319	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142798057	NA	P-0050133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	280	500	2	ENST00000447079.4:c.1234G>A	p.Ala412Thr	p.A412T	ENST00000447079	NM_015083.1	412	Gca/Aca	2/14	0.348221475491605	4	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	2	0.400546923054944	4		502	970	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7119553	7119553	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	279	515	0	ENST00000302850.5:c.3701A>C	p.Glu1234Ala	p.E1234A	ENST00000302850	NM_000208.2	1234	gAa/gCa	21/22	0.400546923054944	3	FACETS	0.996	0.939	1	0.996	0.939	1	CLONAL	2	TRUE	1	0.400546923054944	3		515	839	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314606	30314606	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	135	526	0	ENST00000262643.3:c.1155G>T	p.Arg385Ser	p.R385S	ENST00000262643	NM_001238.2	385	agG/agT	12/12	0.400546923054944	3	FACETS	0.965	0.878	1	0.483	0.439	0.529	CLONAL	1	TRUE	1	0.400546923054944	3		526	838	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259156	89259156	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1294076209	NA	P-0050133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	134	365	0	ENST00000336596.2:c.300G>T	p.Lys100Asn	p.K100N	ENST00000336596	NM_005233.5	100	aaG/aaT	3/17	0.366863530003457	2	FACETS	0.894	0.822	0.969	0.894	0.822	0.969	CLONAL	2	TRUE	0	0.400546923054944	2		365	374	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439282	149439282	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	312	509	0	ENST00000286301.3:c.2113G>T	p.Glu705Ter	p.E705*	ENST00000286301	NM_005211.3	705	Gag/Tag	15/22	0.393380381864185	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.400546923054944	2		509	763	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38178589	38178589	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0050133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	160	378	0	ENST00000317025.8:c.1809+1G>T		p.X603_splice	ENST00000317025	NM_023034.1	603			0.393380381864185	2	FACETS	0.947	0.877	1	0.947	0.877	1	CLONAL	2	TRUE	0	0.400546923054944	2		378	422	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050683	69050683	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	76	389	0	ENST00000288368.4:c.4018G>T	p.Val1340Phe	p.V1340F	ENST00000288368	NM_024870.2	1340	Gtt/Ttt	33/40	0.195323713667049	5	FACETS	1	0.904	1	0.682	0.604	0.764	INDETERMINATE	2	TRUE	2	0.400546923054944	5		389	297	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974799	21974799	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	192	244	0	ENST00000304494.5:c.28G>T	p.Glu10Ter	p.E10*	ENST00000304494	NM_000077.4	10	Gag/Tag	1/3	0.400546923054944	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.400546923054944	2		244	404	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781056	135781056	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	282	640	0	ENST00000298552.3:c.1909G>T	p.Glu637Ter	p.E637*	ENST00000298552	NM_001162426.1	637	Gaa/Taa	15/23	0.400546923054944	2	FACETS	0.976	0.923	1	0.976	0.923	1	CLONAL	2	TRUE	0	0.400546923054944	2		640	721	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778861	76778861	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	74	429	0	ENST00000373344.5:c.6718C>G	p.Leu2240Val	p.L2240V	ENST00000373344	NM_000489.3	2240	Ctc/Gtc	31/35	1	2	FACETS	0.884	0.777	0.998	0.884	0.777	0.998	CLONAL	1	TRUE	1	0.400546923054944	2		429	418	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0050134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	98	423	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	1	2	FACETS	0.49	0.438	0.545	0.49	0.438	0.545	SUBCLONAL	1	TRUE	1	0.655674371557128	2		423	610	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	104	503	1	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	1	2	FACETS	0.5	0.449	0.555	0.5	0.449	0.555	SUBCLONAL	1	TRUE	1	0.655674371557128	2		504	634	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115692	8115710	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTTGTTTAGATTAACAGA	CTTTGTTTAGATTAACAGA	-	novel	NA	P-0050134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	35	195	0	ENST00000346208.3:c.1048-9_1057del		p.X350_splice	ENST00000346208		350		6/6	1	2	FACETS	0.441	0.364	0.527	0.441	0.364	0.527	SUBCLONAL	1	TRUE	1	0.655674371557128	2		195	242	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100583	67100583	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0050134-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	135	378	0	ENST00000412916.2:c.283-2A>T		p.X95_splice	ENST00000412916		95			0.423642294483903	1	FACETS	0.621	0.568	0.674	0.621	0.568	0.674	SUBCLONAL	1	TRUE	0	0.655674371557128	1		378	446	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	39	468	0				ENST00000310581	NM_198253.2	-/1132			0.221656904541791	1	FACETS	0.545	0.452	0.648	0.545	0.452	0.648	SUBCLONAL	1	TRUE	0	0.312859621768758	1		468	386	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727138	40727138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375402843	NA	P-0050136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	77	530	1	ENST00000373198.4:c.3826G>A	p.Val1276Met	p.V1276M	ENST00000373198	NM_133170.3	1276	Gtg/Atg	28/32	0.312859621768758	1	FACETS	0.651	0.571	0.736	0.651	0.571	0.736	SUBCLONAL	1	TRUE	0	0.312859621768758	1		531	638	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720679	89720679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123329	NA	P-0050136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	15	127	0	ENST00000371953.3:c.830C>T	p.Thr277Ile	p.T277I	ENST00000371953	NM_000314.4	277	aCa/aTa	8/9	0.264073403123895	1	FACETS	0.999	0.744	1	0.999	0.744	1	CLONAL	1	TRUE	0	0.312859621768758	1		127	81	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0050138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	120	302	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.505446622334689	3	FACETS	0.994	0.913	1	0.994	0.913	1	CLONAL	2	TRUE	1	0.552501170442942	3		302	279	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495360	149495360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs114435947	NA	P-0050138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	74	763	0	ENST00000261799.4:c.3287C>T	p.Ala1096Val	p.A1096V	ENST00000261799	NM_002609.3	1096	gCg/gTg	23/23	0.505446622334689	3	FACETS	0.907	0.799	1	0.453	0.399	0.511	CLONAL	1	TRUE	1	0.552501170442942	3		763	377	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	37	469	0	ENST00000401558.2:c.2246G>C	p.Arg749Pro	p.R749P	ENST00000401558	NM_003400.3	749	cGa/cCa	19/25	0.446731506845897	3	FACETS	0.939	0.784	1	0.47	0.392	0.555	CLONAL	1	TRUE	1	0.552501170442942	3		469	182	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264052	16264052	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	109	891	0	ENST00000375759.3:c.10421C>T	p.Pro3474Leu	p.P3474L	ENST00000375759	NM_015001.2	3474	cCa/cTa	12/15	1	2	FACETS	0.969	0.877	1	0.969	0.877	1	CLONAL	1	TRUE	1	0.552501170442942	2		891	407	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231102	46231102	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0050138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	31	302	0	ENST00000334344.6:c.1024-2A>G		p.X342_splice	ENST00000334344	NM_152641.2	342			1	2	FACETS	0.753	0.618	0.902	0.753	0.618	0.902	CLONAL	1	TRUE	1	0.552501170442942	2		302	149	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0050139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	250	674	1	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.479601465081512	2	FACETS	0.789	0.745	0.834	0.789	0.745	0.834	SUBCLONAL	2	TRUE	0	0.553847310895333	2		675	572	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023909	27023923	+	inframe_deletion	In_Frame_Del	DEL	GCTGCGGCGGCGGCA	GCTGCGGCGGCGGCA	-	rs751352361	NA	P-0050139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	33	184	0	ENST00000324856.7:c.1029_1043del	p.Ala345_Ala349del	p.A345_A349del	ENST00000324856	NM_006015.4	339	GCTGCGGCGGCGGCA/-	1/20	0.479601465081512	2	FACETS	0.705	0.581	0.841	0.353	0.29	0.421	SUBCLONAL	1	TRUE	0	0.553847310895333	2		184	169	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956236	175956236	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	27	270	0	ENST00000367669.3:c.1976G>C	p.Ser659Thr	p.S659T	ENST00000367669	NM_022457.5	659	aGt/aCt	18/20	0.553847310895333	3	FACETS	0.284	0.226	0.351	0.095	0.075	0.117	SUBCLONAL	1	TRUE	0	0.553847310895333	3		270	438	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121160	3121160	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	69	628	0	ENST00000078429.4:c.1063G>C	p.Glu355Gln	p.E355Q	ENST00000078429	NM_002067.2	355	Gag/Cag	7/7	0.43757936135254	3	FACETS	0.455	0.396	0.519	0.228	0.198	0.26	SUBCLONAL	1	TRUE	1	0.553847310895333	3		628	699	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	172	379	0	ENST00000397062.3:c.92G>T	p.Gly31Val	p.G31V	ENST00000397062	NM_006164.4	31	gGa/gTa	2/5	0.283059700547083	5	FACETS	1	0.98	1			1	INDETERMINATE	2	TRUE	NA	0.553847310895333	5		379	491	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	223633	223633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395903862	NA	P-0050139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	149	438	1	ENST00000264932.6:c.100C>T	p.His34Tyr	p.H34Y	ENST00000264932	NM_004168.2	34	Cac/Tac	2/15	0.553847310895333	4	FACETS	0.972	0.888	1	0.486	0.444	0.53	CLONAL	1	TRUE	2	0.553847310895333	4		439	860	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224491	224491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	21	101	0	ENST00000264932.6:c.167C>T	p.Pro56Leu	p.P56L	ENST00000264932	NM_004168.2	56	cCa/cTa	3/15	0.553847310895333	4	FACETS	0.786	0.611	0.985	0.393	0.305	0.493	CLONAL	1	TRUE	2	0.553847310895333	4		101	150	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221936	98221936	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1064794260	NA	P-0050139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	442	608	0	ENST00000331920.6:c.2833C>T	p.Arg945Ter	p.R945*	ENST00000331920	NM_000264.3	945	Cga/Tga	17/24	0.553847310895333	3	FACETS	0.945	0.911	0.978	0.945	0.911	0.978	CLONAL	3	TRUE	0	0.553847310895333	3		608	719	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489566	56489566	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	107	560	0	ENST00000267101.3:c.2031G>C	p.Met677Ile	p.M677I	ENST00000267101	NM_001982.3	677	atG/atC	17/28	0.40983453546144	2	FACETS	0.785	0.705	0.87	0.393	0.352	0.435	SUBCLONAL	1	TRUE	0	0.40983453546144	2		560	665	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577577	7577577	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	279	603	0	ENST00000269305.4:c.704del	p.Asn235ThrfsTer12	p.N235Tfs*12	ENST00000269305	NM_001126112.2	235	aAc/ac	7/11	0.408524952812138	2	FACETS	0.947	0.894	1	0.947	0.894	1	CLONAL	2	TRUE	0	0.40983453546144	2		603	719	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126112	2126112	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs45470695	NA	P-0050140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	140	757	0	ENST00000219476.3:c.2683A>G	p.Met895Val	p.M895V	ENST00000219476	NM_000548.3	895	Atg/Gtg	24/42	0.40983453546144	2	FACETS	0.752	0.685	0.823	0.376	0.342	0.412	SUBCLONAL	1	TRUE	0	0.40983453546144	2		757	908	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42840447	42840447	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	118	556	0	ENST00000398585.3:c.1301T>C	p.Leu434Pro	p.L434P	ENST00000398585	NM_001135099.1	434	cTg/cCg	12/14	0.370526485860603	4	FACETS	0.858	0.773	0.948	0.286	0.257	0.316	CLONAL	1	TRUE	1	0.40983453546144	4		556	946	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285743	87285743	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	166	686	0	ENST00000277120.3:c.80G>T	p.Arg27Met	p.R27M	ENST00000277120		27	aGg/aTg	2/19	0.1266321789183	5	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.40983453546144	5		686	923	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0050141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4879	149	361	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.59915109982303	18	FACETS	0.573	0.52	0.63			1	SUBCLONAL	1	TRUE	NA	0.59915109982303	18		361	5028	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0050141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	665	558	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.599711069912887	2	FACETS	0.859	0.84	0.878	1	0.998	1	CLONAL	3	TRUE	0	0.59915109982303	2		558	861	SUCCESS
APC	324	MSKCC	GRCh37	5	112175879	112175880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	97	288	0	ENST00000257430.4:c.4592dup	p.Asn1531LysfsTer2	p.N1531Kfs*2	ENST00000257430	NM_000038.5	1530	gaa/gAaa	16/16	0.59915109982303	1	FACETS	0.654	0.588	0.722	0.654	0.588	0.722	SUBCLONAL	1	TRUE	0	0.59915109982303	1		288	347	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945532	151945532	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	107	361	0	ENST00000262189.6:c.1987C>T	p.Gln663Ter	p.Q663*	ENST00000262189	NM_170606.2	663	Cag/Tag	14/59	0.599711069912887	1	FACETS	0.607	0.549	0.668	0.607	0.549	0.668	SUBCLONAL	1	TRUE	0	0.59915109982303	1		361	412	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974420	18974420	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs189120195	NA	P-0050141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	158	385	0	ENST00000262803.5:c.2774C>T	p.Pro925Leu	p.P925L	ENST00000262803	NM_002911.3	925	cCg/cTg	19/24	0.192999034137414	1	FACETS	0.522	0.479	0.566	0.522	0.479	0.566	INDETERMINATE	1	TRUE	0	0.59915109982303	1		385	708	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481696	56481696	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	264	648	0	ENST00000267101.3:c.731T>C	p.Phe244Ser	p.F244S	ENST00000267101	NM_001982.3	244	tTt/tCt	6/28	0.358237944255317	1	FACETS	0.615	0.577	0.655	0.615	0.577	0.655	INDETERMINATE	1	TRUE	0	0.59915109982303	1		648	1003	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087486	27087567	+	frameshift_variant	Frame_Shift_Del	DEL	CTCACCTGCCTGGCATCCGAGGCCCTTCCCCGTCCCCTGTTGGCTCTCCCGCCAGTGTTGCTCAGTCTCGCTCAGGACCACT	CTCACCTGCCTGGCATCCGAGGCCCTTCCCCGTCCCCTGTTGGCTCTCCCGCCAGTGTTGCTCAGTCTCGCTCAGGACCACT	-	novel	NA	P-0050141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	68	606	0	ENST00000324856.7:c.2063_2144del	p.His688ArgfsTer27	p.H688Rfs*27	ENST00000324856	NM_006015.4	687	cCTCACCTGCCTGGCATCCGAGGCCCTTCCCCGTCCCCTGTTGGCTCTCCCGCCAGTGTTGCTCAGTCTCGCTCAGGACCACTc/cc	5/20	0.192999034137414	1	FACETS	0.152	0.132	0.175	0.152	0.132	0.175	INDETERMINATE	1	TRUE	0	0.59915109982303	1		606	1044	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532567	63532567	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	198	692	0	ENST00000307078.5:c.2012del	p.Arg671ProfsTer18	p.R671Pfs*18	ENST00000307078	NM_004655.3	671	cGc/cc	8/11	1	2	FACETS	0.607	0.561	0.654	0.607	0.561	0.654	SUBCLONAL	1	TRUE	1	0.59915109982303	2		692	1089	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251713	212251713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	247	396	3	ENST00000342788.4:c.3346G>A	p.Ala1116Thr	p.A1116T	ENST00000342788	NM_005235.2	1116	Gca/Aca	27/28	0.494604739204548	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.59915109982303	1		399	536	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352400	143352400	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	174	550	0	ENST00000262992.4:c.13G>C	p.Glu5Gln	p.E5Q	ENST00000262992	NM_001101669.1	5	Gag/Cag	2/24	0.192999034137414	1	FACETS	0.463	0.427	0.502	0.463	0.427	0.502	INDETERMINATE	1	TRUE	0	0.59915109982303	1		550	878	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86658369	86658369	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	30	122	0	ENST00000274376.6:c.1334A>G	p.Asp445Gly	p.D445G	ENST00000274376	NM_002890.2	445	gAt/gGt	10/25	0.59915109982303	1	FACETS	0.309	0.25	0.375	0.309	0.25	0.375	SUBCLONAL	1	TRUE	0	0.59915109982303	1		122	227	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69039652	69039652	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	52	352	0	ENST00000288368.4:c.3764C>T	p.Ser1255Leu	p.S1255L	ENST00000288368	NM_024870.2	1255	tCa/tTa	31/40	0.26338599072929	1	FACETS	0.232	0.197	0.27	0.232	0.197	0.27	INDETERMINATE	1	TRUE	0	0.59915109982303	1		352	525	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93636990	93636990	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	144	452	0	ENST00000375746.1:c.1040T>A	p.Val347Glu	p.V347E	ENST00000375746	NM_001174167.1	347	gTg/gAg	9/14	1	2	FACETS	0.669	0.611	0.729	0.669	0.611	0.729	SUBCLONAL	1	TRUE	1	0.59915109982303	2		452	719	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0050142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	420	486	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.34418992904629	6	FACETS	1	0.992	1	0.856	0.821	0.892	INDETERMINATE	3	TRUE	2	0.715748225926097	6		486	833	SUCCESS
FH	2271	MSKCC	GRCh37	1	241671958	241671958	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	152	494	0	ENST00000366560.3:c.683T>G	p.Ile228Ser	p.I228S	ENST00000366560	NM_000143.3	228	aTc/aGc	5/10	0.715748225926097	6	FACETS	0.803	0.732	0.877	0.268	0.244	0.293	CLONAL	1	TRUE	3	0.715748225926097	6		494	1286	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573009	41573019	+	frameshift_variant	Frame_Shift_Del	DEL	TGCAGCATACC	TGCAGCATACC	G	novel	NA	P-0050142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	530	772	0	ENST00000263253.7:c.5294_5304delinsG	p.Val1765GlyfsTer40	p.V1765Gfs*40	ENST00000263253	NM_001429.3	1765	gTGCAGCATACC/gG	31/31	0.715748225926097	2	FACETS	0.982	0.954	1	0.982	0.954	1	CLONAL	2	TRUE	0	0.715748225926097	2		772	754	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260899	16260899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	117	559	0	ENST00000375759.3:c.8164C>T	p.Pro2722Ser	p.P2722S	ENST00000375759	NM_015001.2	2722	Cca/Tca	11/15	0.201925779965772	2	FACETS	0.666	0.604	0.73	0.333	0.302	0.365	INDETERMINATE	1	TRUE	0	0.752609243940504	2		559	467	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027707	152027707	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	37	532	0	ENST00000262189.6:c.368T>G	p.Val123Gly	p.V123G	ENST00000262189	NM_170606.2	123	gTt/gGt	3/59	1	2	FACETS	0.246	0.202	0.294	0.246	0.202	0.294	SUBCLONAL	1	TRUE	1	0.752609243940504	2		532	400	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260899	16260899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050144-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	111	559	0	ENST00000375759.3:c.8164C>T	p.Pro2722Ser	p.P2722S	ENST00000375759	NM_015001.2	2722	Cca/Tca	11/15	NA	2	FACETS	0.425	0.382	0.47			1	INDETERMINATE	1	TRUE	NA	0.790718436329835	2		559	661	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645274	67645274	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050144-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	111	514	0	ENST00000264010.4:c.539A>C	p.Gln180Pro	p.Q180P	ENST00000264010	NM_006565.3	180	cAa/cCa	3/12	0.396246106758983	4	FACETS	0.601	0.54	0.666			1	INDETERMINATE	1	TRUE	NA	0.790718436329835	4		514	836	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032356	10032356	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763500409	NA	P-0050145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	78	97	0	ENST00000330684.3:c.467C>T	p.Thr156Met	p.T156M	ENST00000330684	NM_001134407.1	156	aCg/aTg	3/13	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.365368721000686	2		97	366	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632654	3632654	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	57	188	2	ENST00000294008.3:c.5194G>T	p.Gly1732Cys	p.G1732C	ENST00000294008	NM_032444.2	1732	Ggt/Tgt	15/15	1	2	FACETS	0.511	0.438	0.59	0.511	0.438	0.59	SUBCLONAL	1	TRUE	1	0.365368721000686	2		190	611	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620542	52620542	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	94	117	0	ENST00000394830.3:c.3211del	p.Arg1071AlafsTer63	p.R1071Afs*63	ENST00000394830	NM_018313.4	1071	Cgc/gc	21/30	0.365368721000686	1	FACETS	0.85	0.759	0.945	0.85	0.759	0.945	CLONAL	1	TRUE	0	0.365368721000686	1		117	495	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224718	123224718	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	21	88	0	ENST00000218089.9:c.3482G>A	p.Trp1161Ter	p.W1161*	ENST00000218089	NM_001042749.1	1161	tGg/tAg	32/35	0.264500507780619	1	FACETS	0.366	0.282	0.463	0.366	0.282	0.463	SUBCLONAL	1	TRUE	0	0.365368721000686	1		88	257	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202713	16202713	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	137	401	0	ENST00000375759.3:c.421G>T	p.Glu141Ter	p.E141*	ENST00000375759	NM_015001.2	141	Gag/Tag	3/15	0.738967416488648	1	FACETS	0.947	0.882	1	0.947	0.882	1	CLONAL	1	TRUE	0	0.738967416488648	1		401	247	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107739	30107739	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778680785	NA	P-0050146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	127	524	0	ENST00000331968.5:c.941C>T	p.Pro314Leu	p.P314L	ENST00000331968	NM_002742.2	314	cCg/cTg	6/18	1	2	FACETS	0.774	0.707	0.844	0.774	0.707	0.844	SUBCLONAL	1	TRUE	1	0.738967416488648	2		524	444	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675494	40675516	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCTGCGCTGAGCGGCGGCCAG	CCTCTGCGCTGAGCGGCGGCCAG	-	novel	NA	P-0050146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	78	742	0	ENST00000249776.8:c.277_299del	p.Ser93GlyfsTer10	p.S93Gfs*10	ENST00000249776	NM_033286.3	92	cCCTCTGCGCTGAGCGGCGGCCAG/c	2/9	1	2	FACETS	0.199	0.174	0.226	0.199	0.174	0.226	SUBCLONAL	1	TRUE	1	0.738967416488648	2		742	1059	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0050148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	551	1004	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	0.368519913567722	4	FACETS	0.939	0.905	0.972	0.939	0.905	0.972	CLONAL	4	TRUE	0	0.368948255395116	4		1004	1089	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794903	242794903	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	152	947	0	ENST00000334409.5:c.306C>A	p.Asn102Lys	p.N102K	ENST00000334409	NM_005018.2	102	aaC/aaA	2/5	0.368948255395116	3	FACETS	0.938	0.856	1	0.469	0.428	0.512	CLONAL	1	TRUE	1	0.368948255395116	3		947	1041	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565857	55565857	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	83	584	0	ENST00000288135.5:c.681A>T	p.Glu227Asp	p.E227D	ENST00000288135	NM_000222.2	227	gaA/gaT	4/21	0.368948255395116	3	FACETS	0.663	0.584	0.747	0.331	0.292	0.374	SUBCLONAL	1	TRUE	1	0.368948255395116	3		584	804	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	134	476	3	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.585746749422621	2		479	454	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	173	740	9	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	1	2	FACETS	0.95	0.878	1	0.95	0.878	1	CLONAL	1	TRUE	1	0.585746749422621	2		749	622	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	77	683	1	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	1	2	FACETS	0.573	0.504	0.646	0.573	0.504	0.646	SUBCLONAL	1	TRUE	1	0.585746749422621	2		684	459	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	211	983	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.585746749422621	2		983	682	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	114	483	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.585746749422621	2		483	384	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	119	334	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.585746749422621	2		334	377	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821594	72821596	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs374416547	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	15	124	1	ENST00000268489.5:c.10579_10581del	p.Gly3527del	p.G3527del	ENST00000268489	NM_006885.3	3527	GGC/-	10/10	1	2	FACETS	0.483	0.357	0.63	0.483	0.357	0.63	SUBCLONAL	1	TRUE	1	0.585746749422621	2		125	106	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838347	156838347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1376334182	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	244	1055	1	ENST00000524377.1:c.625G>A	p.Asp209Asn	p.D209N	ENST00000524377	NM_002529.3	209	Gac/Aac	6/17	0.585746749422621	4	FACETS	1	0.973	1	0.36	0.336	0.385	CLONAL	1	TRUE	1	0.585746749422621	4		1056	1223	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	92	351	5	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	1	2	FACETS	0.97	0.871	1	0.97	0.871	1	CLONAL	1	TRUE	1	0.585746749422621	2		356	324	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272497	15272497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771678721	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	166	843	0	ENST00000263388.2:c.5942G>A	p.Arg1981His	p.R1981H	ENST00000263388	NM_000435.2	1981	cGc/cAc	33/33	1	2	FACETS	0.897	0.827	0.969	0.897	0.827	0.969	CLONAL	1	TRUE	1	0.585746749422621	2		843	632	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913250	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	116	402	0	ENST00000369535.4:c.34G>T	p.Gly12Cys	p.G12C	ENST00000369535	NM_002524.4	12	Ggt/Tgt	2/7	1	2	FACETS	0.988	0.898	1	0.988	0.898	1	CLONAL	1	TRUE	1	0.585746749422621	2		402	401	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796882	42796883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761345552	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	42	1057	1	ENST00000575354.2:c.3347dup	p.Ser1117LysfsTer34	p.S1117Kfs*34	ENST00000575354	NM_015125.3	1114	gcc/gCcc	14/20	1	2	FACETS	0.187	0.155	0.223	0.187	0.155	0.223	SUBCLONAL	1	TRUE	1	0.585746749422621	2		1058	766	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514780	44514780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769567889	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	37	507	2	ENST00000291552.4:c.467G>A	p.Arg156His	p.R156H	ENST00000291552	NM_006758.2	156	cGt/cAt	6/8	1	2	FACETS	0.22	0.181	0.264	0.22	0.181	0.264	SUBCLONAL	1	TRUE	1	0.585746749422621	2		509	574	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350023	15350023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1489035830	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	192	949	2	ENST00000263377.2:c.3629C>T	p.Pro1210Leu	p.P1210L	ENST00000263377	NM_058243.2	1210	cCg/cTg	18/20	1	2	FACETS	0.876	0.813	0.942	0.876	0.813	0.942	CLONAL	1	TRUE	1	0.585746749422621	2		951	748	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654646	67654646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	164	572	0	ENST00000264010.4:c.1133C>T	p.Pro378Leu	p.P378L	ENST00000264010	NM_006565.3	378	cCg/cTg	6/12	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.585746749422621	2		572	543	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39706276	39706276	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	75	258	0	ENST00000361337.2:c.334A>G	p.Ser112Gly	p.S112G	ENST00000361337	NM_003286.2	112	Agt/Ggt	5/21	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.585746749422621	2		258	229	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228795	36228795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1193546654	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	190	862	1	ENST00000222270.7:c.7694G>A	p.Arg2565His	p.R2565H	ENST00000222270	NM_014727.1	2565	cGt/cAt	35/37	1	2	FACETS	0.924	0.857	0.993	0.924	0.857	0.993	CLONAL	1	TRUE	1	0.585746749422621	2		863	702	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162078	47162078	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	119	395	0	ENST00000409792.3:c.4048del	p.Ser1350GlnfsTer23	p.S1350Qfs*23	ENST00000409792	NM_014159.6	1350	Tca/ca	3/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.585746749422621	2		395	352	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982165	201982165	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	174	795	2	ENST00000359651.3:c.688+1G>A		p.X230_splice	ENST00000359651		230			0.585746749422621	4	FACETS	0.956	0.88	1	0.319	0.293	0.346	CLONAL	1	TRUE	1	0.585746749422621	4		797	985	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946961	71946961	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	195	1002	0	ENST00000298229.2:c.2810A>C	p.Lys937Thr	p.K937T	ENST00000298229	NM_001567.3	937	aAa/aCa	25/28	1	2	FACETS	0.946	0.878	1	0.946	0.878	1	CLONAL	1	TRUE	1	0.585746749422621	2		1002	704	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160366	108160366	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	74	291	0	ENST00000278616.4:c.4274A>G	p.Gln1425Arg	p.Q1425R	ENST00000278616	NM_000051.3	1425	cAa/cGa	29/63	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.585746749422621	2		291	225	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230387	46230389	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	novel	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	92	345	0	ENST00000334344.6:c.722_724del	p.Val241del	p.V241del	ENST00000334344	NM_152641.2	241	GTT/-	7/21	1	2	FACETS	0.87	0.78	0.965	0.87	0.78	0.965	CLONAL	1	TRUE	1	0.585746749422621	2		345	361	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831273	72831273	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	141	573	0	ENST00000268489.5:c.5308C>T	p.Gln1770Ter	p.Q1770*	ENST00000268489	NM_006885.3	1770	Cag/Tag	9/10	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.585746749422621	2		573	469	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627595	37627595	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	122	536	0	ENST00000447079.4:c.1510A>G	p.Lys504Glu	p.K504E	ENST00000447079	NM_015083.1	504	Aaa/Gaa	2/14	1	2	FACETS	0.949	0.864	1	0.949	0.864	1	CLONAL	1	TRUE	1	0.585746749422621	2		536	439	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745803	745803	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	113	597	0	ENST00000314574.4:c.629A>G	p.Lys210Arg	p.K210R	ENST00000314574	NM_005433.3	210	aAa/aGa	6/12	1	2	FACETS	0.984	0.894	1	0.984	0.894	1	CLONAL	1	TRUE	1	0.585746749422621	2		597	392	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765784	41765784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	120	546	0	ENST00000301178.4:c.2660C>T	p.Ala887Val	p.A887V	ENST00000301178	NM_021913.4	887	gCc/gTc	20/20	1	2	FACETS	0.98	0.892	1	0.98	0.892	1	CLONAL	1	TRUE	1	0.585746749422621	2		546	418	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030816	48030816	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	76	278	0	ENST00000234420.5:c.3430A>T	p.Met1144Leu	p.M1144L	ENST00000234420	NM_000179.2	1144	Atg/Ttg	5/10	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.585746749422621	2		278	241	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267681	198267681	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	87	346	0	ENST00000335508.6:c.1798T>G	p.Leu600Val	p.L600V	ENST00000335508	NM_012433.2	600	Ttg/Gtg	13/25	1	2	FACETS	0.98	0.878	1	0.98	0.878	1	CLONAL	1	TRUE	1	0.585746749422621	2		346	303	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023637	31023637	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	170	643	1	ENST00000375687.4:c.3125del	p.Pro1042HisfsTer5	p.P1042Hfs*5	ENST00000375687	NM_015338.5	1041	gCc/gc	13/13	1	2	FACETS	0.991	0.916	1	0.991	0.916	1	CLONAL	1	TRUE	1	0.585746749422621	2		644	586	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125773	47125773	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	42	319	1	ENST00000409792.3:c.5497G>A	p.Ala1833Thr	p.A1833T	ENST00000409792	NM_014159.6	1833	Gct/Act	12/21	1	2	FACETS	0.389	0.325	0.459	0.389	0.325	0.459	SUBCLONAL	1	TRUE	1	0.585746749422621	2		320	369	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664945	138664945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	107	277	0	ENST00000330315.3:c.620C>T	p.Pro207Leu	p.P207L	ENST00000330315	NM_023067.3	207	cCg/cTg	1/1	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.585746749422621	2		277	333	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281818	142281818	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	122	462	0	ENST00000350721.4:c.426del	p.Phe142LeufsTer23	p.F142Lfs*23	ENST00000350721	NM_001184.3	142	ttT/tt	4/47	1	2	FACETS	0.992	0.904	1	0.992	0.904	1	CLONAL	1	TRUE	1	0.585746749422621	2		462	420	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249391	153249391	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	104	510	0	ENST00000281708.4:c.1387A>G	p.Thr463Ala	p.T463A	ENST00000281708	NM_033632.3	463	Act/Gct	9/12	1	2	FACETS	0.89	0.803	0.981	0.89	0.803	0.981	CLONAL	1	TRUE	1	0.585746749422621	2		510	399	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589580	67589609	+	inframe_deletion	In_Frame_Del	DEL	AATTACATGAATATAACACTCAGTTTCAAG	AATTACATGAATATAACACTCAGTTTCAAG	-	novel	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	35	229	0	ENST00000274335.5:c.1345_1374del	p.Leu449_Glu458del	p.L449_E458del	ENST00000274335		448	aAATTACATGAATATAACACTCAGTTTCAAGaa/aaa	10/15	1	2	FACETS	0.716	0.594	0.848	0.716	0.594	0.848	SUBCLONAL	1	TRUE	1	0.585746749422621	2		229	167	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672299	86672299	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	130	410	0	ENST00000274376.6:c.2101A>G	p.Ile701Val	p.I701V	ENST00000274376	NM_002890.2	701	Att/Gtt	16/25	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.585746749422621	2		410	387	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056113	26056113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	137	514	0	ENST00000343677.2:c.544C>T	p.Pro182Ser	p.P182S	ENST00000343677	NM_005319.3	182	Ccc/Tcc	1/1	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.585746749422621	2		514	437	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056362	26056362	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	110	441	0	ENST00000343677.2:c.295A>G	p.Thr99Ala	p.T99A	ENST00000343677	NM_005319.3	99	Acc/Gcc	1/1	1	2	FACETS	0.971	0.88	1	0.971	0.88	1	CLONAL	1	TRUE	1	0.585746749422621	2		441	387	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704655	117704655	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	100	317	0	ENST00000368508.3:c.2321T>C	p.Val774Ala	p.V774A	ENST00000368508	NM_002944.2	774	gTg/gCg	16/43	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.585746749422621	2		317	280	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55270294	55270294	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	209	816	2	ENST00000275493.2:c.3247G>T	p.Asp1083Tyr	p.D1083Y	ENST00000275493	NM_005228.3	1083	Gac/Tac	27/28	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.585746749422621	2		818	673	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508686	106508686	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	152	556	0	ENST00000359195.3:c.680G>T	p.Ser227Ile	p.S227I	ENST00000359195	NM_002649.2	227	aGc/aTc	2/11	1	2	FACETS	0.951	0.874	1	0.951	0.874	1	CLONAL	1	TRUE	1	0.585746749422621	2		556	546	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250140	110250141	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	166	893	0	ENST00000374672.4:c.534dup	p.Pro179SerfsTer78	p.P179Sfs*78	ENST00000374672	NM_004235.4	178	-/T	3/5	1	2	FACETS	0.898	0.829	0.97	0.898	0.829	0.97	CLONAL	1	TRUE	1	0.585746749422621	2		893	631	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127951954	127951954	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs747498656	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	188	804	0	ENST00000373547.4:c.44T>C	p.Leu15Pro	p.L15P	ENST00000373547	NM_002721.4	15	cTg/cCg	1/7	1	2	FACETS	0.992	0.921	1	0.992	0.921	1	CLONAL	1	TRUE	1	0.585746749422621	2		804	647	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939100	76939100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs201284965	NA	P-0050149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	126	546	0	ENST00000373344.5:c.1648A>G	p.Ser550Gly	p.S550G	ENST00000373344	NM_000489.3	550	Agt/Ggt	9/35	1	2	FACETS	0.883	0.805	0.965	0.883	0.805	0.965	CLONAL	1	TRUE	1	0.585746749422621	2		546	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0050150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	34	361	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	0.665	0.541	0.806	0.665	0.541	0.806	SUBCLONAL	1	TRUE	1	0.11	2		361	929	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0050150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	21	355	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	1	2	FACETS	0.703	0.54	0.895	0.703	0.54	0.895	SUBCLONAL	1	TRUE	1	0.11	2		355	543	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868209	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0050150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	27	679	0	ENST00000269571.5:c.929_930delinsAT	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCC/tAT	8/27	1	2	FACETS	0.512	0.406	0.636	0.512	0.406	0.636	SUBCLONAL	1	TRUE	1	0.11	2		679	958	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	53	468	0				ENST00000310581	NM_198253.2	-/1132			0.277474896754748	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.717322054069725	0		468	143	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0050151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	95	364	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.907	0.818	0.999	0.907	0.818	0.999	CLONAL	1	TRUE	1	0.717322054069725	2		364	292	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0050151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	198	435	2	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.717322054069725	2		437	526	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0050153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	29	484	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.211539195472769	1	FACETS	0.409	0.327	0.503	0.409	0.327	0.503	SUBCLONAL	1	TRUE	0	0.211539195472769	1		484	599	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0050154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	164	396	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.998	0.928	1	0.998	0.928	1	CLONAL	1	TRUE	1	0.856047703467025	2		396	384	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275399	142275399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202162034	NA	P-0050154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	116	265	0	ENST00000350721.4:c.1904G>A	p.Arg635Gln	p.R635Q	ENST00000350721	NM_001184.3	635	cGa/cAa	9/47	0.764752161053195	4	FACETS	1	0.906	1	0.333	0.302	0.367	CLONAL	1	TRUE	1	0.856047703467025	4		265	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	1097	629	0	ENST00000269305.4:c.569del	p.Pro190LeufsTer57	p.P190Lfs*57	ENST00000269305	NM_001126112.2	190	cCt/ct	6/11	0.841041512734746	5	FACETS	0.981	0.97	0.991	0.981	0.97	0.991	CLONAL	5	TRUE	0	0.856047703467025	5		629	1194	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936018	44936018	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	219	493	0	ENST00000377967.4:c.2779C>G	p.Pro927Ala	p.P927A	ENST00000377967	NM_021140.2	927	Cca/Gca	18/29	0.731248109835828	6	FACETS	1	0.967	1			1	CLONAL	1	TRUE	NA	0.856047703467025	6		493	1296	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696634	47696638	+	missense_variant	Missense_Mutation	ONP	GAGAA	GAGAA	AAGAT	novel	NA	P-0050165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	31	395	0	ENST00000347630.2:c.310_314delinsATCTT	p.Phe104_Ser105delinsIlePhe	p.F104_S105delinsIF	ENST00000347630	NM_001007230.1	104	TTCTCc/ATCTTc	5/11	1	2	FACETS	0.839	0.682	1	1	0.951	1	CLONAL	2	TRUE	1	0.16	2		395	231	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602314	10602314	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	437	834	0	ENST00000171111.5:c.1264G>C	p.Asp422His	p.D422H	ENST00000171111	NM_203500.1	422	Gat/Cat	3/6	0.454130612299419	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.454130612299419	1		834	1219	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261167	16261167	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	165	556	1	ENST00000375759.3:c.8432C>A	p.Ser2811Tyr	p.S2811Y	ENST00000375759	NM_015001.2	2811	tCt/tAt	11/15	1	2	FACETS	0.896	0.824	0.971	0.896	0.824	0.971	CLONAL	1	TRUE	1	0.454130612299419	2		557	811	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579508	7579514	+	frameshift_variant	Frame_Shift_Del	DEL	GGACCTG	GGACCTG	-	novel	NA	P-0050166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	465	808	0	ENST00000269305.4:c.173_179del	p.Pro58GlnfsTer63	p.P58Qfs*63	ENST00000269305	NM_001126112.2	58	cCAGGTCCa/ca	4/11	0.305476135641449	2	FACETS	0.895	0.857	0.933	0.895	0.857	0.933	CLONAL	2	TRUE	0	0.454130612299419	2		808	1144	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965461	15965486	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGTTCCATTGGTTCCTTGGAAAAC	CTGGTTCCATTGGTTCCTTGGAAAAC	-	novel	NA	P-0050166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	55	397	0	ENST00000268712.3:c.5320_5345del	p.Val1774CysfsTer61	p.V1774Cfs*61	ENST00000268712	NM_006311.3	1774	GTTTTCCAAGGAACCAATGGAACCAGt/t	36/46	0.305476135641449	2	FACETS	0.455	0.389	0.527	0.228	0.194	0.264	SUBCLONAL	1	TRUE	0	0.454130612299419	2		397	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0050167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	243	596	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.293355989826938	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	FALSE	0	0.293355989826938	2		596	756	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881462	48881462	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	45	172	0	ENST00000267163.4:c.184C>T	p.Gln62Ter	p.Q62*	ENST00000267163	NM_000321.2	62	Cag/Tag	2/27	0.293355989826938	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	2	FALSE	0	0.293355989826938	2		172	151	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989697	68989697	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	45	445	0	ENST00000288368.4:c.1635G>T	p.Met545Ile	p.M545I	ENST00000288368	NM_024870.2	545	atG/atT	15/40	0.137698944148871	4	FACETS	0.613	0.514	0.723	0.307	0.257	0.362	INDETERMINATE	1	FALSE	2	0.293355989826938	4		445	647	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77051780	77051780	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	197	393	0	ENST00000356341.3:c.1027G>T	p.Val343Phe	p.V343F	ENST00000356341	NM_002576.4	343	Gtt/Ttt	11/15	0.235586612733531	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	FALSE	2	0.293355989826938	4		393	826	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102080266	102080266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	88	373	0	ENST00000282441.5:c.1003C>T	p.Pro335Ser	p.P335S	ENST00000282441	NM_001130145.2	335	Ccc/Tcc	6/9	0.235586612733531	4	FACETS	0.789	0.701	0.881	0.789	0.701	0.881	SUBCLONAL	2	FALSE	2	0.293355989826938	4		373	492	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602339	28602339	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	199	397	0	ENST00000241453.7:c.2029C>A	p.Leu677Met	p.L677M	ENST00000241453	NM_004119.2	677	Ctg/Atg	16/24	0.293355989826938	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	FALSE	0	0.293355989826938	2		397	598	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646222	215646222	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	47	245	0	ENST00000260947.4:c.376G>T	p.Asp126Tyr	p.D126Y	ENST00000260947	NM_000465.2	126	Gat/Tat	4/11	0.180601323231504	3	FACETS	0.962	0.823	1	0.962	0.823	1	CLONAL	2	FALSE	1	0.293355989826938	3		245	191	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846100	128846100	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	258	664	0	ENST00000249373.3:c.1030A>G	p.Lys344Glu	p.K344E	ENST00000249373	NM_005631.4	344	Aaa/Gaa	5/12	0.235586612733531	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	FALSE	2	0.293355989826938	4		664	1078	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636818	8636818	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	119	360	0	ENST00000356435.5:c.91G>C	p.Val31Leu	p.V31L	ENST00000356435		31	Gtt/Ctt	2/35	0.133175598051157	5	FACETS	0.899	0.813	0.989	0.599	0.542	0.66	INDETERMINATE	2	FALSE	2	0.293355989826938	5		360	650	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411938	63411938	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	219	316	0	ENST00000330258.3:c.1229G>T	p.Trp410Leu	p.W410L	ENST00000330258	NM_152424.3	410	tGg/tTg	2/2	0.208686999043758	2	FACETS	1	0.977	1			1	CLONAL	3	FALSE	NA	0.293355989826938	2		316	464	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	18	413	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.447	0.337	0.578	0.447	0.337	0.578	SUBCLONAL	1	TRUE	1	0.287504372998609	2		413	280	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974695	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	138	366	0	ENST00000304494.5:c.132C>A	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	taC/taA	1/3	0.287504372998609	1	FACETS	0.763	0.697	0.83	1	0.988	1	SUBCLONAL	2	TRUE	0	0.287504372998609	1		366	539	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782329	NA	P-0050168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	175	571	0	ENST00000269305.4:c.746G>C	p.Arg249Thr	p.R249T	ENST00000269305	NM_001126112.2	249	aGg/aCg	7/11	0.201814833224873	2	FACETS	1	0.989	1	0.746	0.688	0.806	CLONAL	1	TRUE	0	0.287504372998609	2		571	816	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604715	48604715	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	40	341	0	ENST00000342988.3:c.1537T>C	p.Tyr513His	p.Y513H	ENST00000342988	NM_005359.5	513	Tac/Cac	12/12	0.287504372998609	1	FACETS	0.603	0.502	0.716	0.603	0.502	0.716	SUBCLONAL	1	TRUE	0	0.287504372998609	1		341	395	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608963	100608963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	34	424	0	ENST00000308731.7:c.1645G>A	p.Asp549Asn	p.D549N	ENST00000308731	NM_000061.2	549	Gat/Aat	17/19	1	2	FACETS	0.429	0.35	0.519	0.429	0.35	0.519	SUBCLONAL	1	TRUE	1	0.287504372998609	2		424	551	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106852	27106853	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCAG	novel	NA	P-0050168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	125	531	0	ENST00000324856.7:c.6465_6468dup	p.Asp2157GlnfsTer2	p.D2157Qfs*2	ENST00000324856	NM_006015.4	2155	ctc/cTCAGtc	20/20	0.201814833224873	2	FACETS	1	0.981	1	0.669	0.607	0.734	CLONAL	1	TRUE	0	0.287504372998609	2		531	650	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778179	27778179	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	64	629	0	ENST00000369163.2:c.328C>A	p.Leu110Met	p.L110M	ENST00000369163	NM_003536.2	110	Ctg/Atg	1/1	0.183978196933134	5	FACETS	0.751	0.648	0.862	0.25	0.216	0.288	SUBCLONAL	1	TRUE	2	0.287504372998609	5		629	849	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0050169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	18	753	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.105	0.078	0.137	0.105	0.078	0.137	SUBCLONAL	1	TRUE	1	0.456910860263952	2		753	748	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165207	47165207	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	48	294	0	ENST00000409792.3:c.919del	p.Ser307LeufsTer33	p.S307Lfs*33	ENST00000409792	NM_014159.6	307	Tct/ct	3/21	1	2	FACETS	0.84	0.717	0.974	0.84	0.717	0.974	CLONAL	1	TRUE	1	0.456910860263952	2		294	250	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980462	1980462	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs752348506	NA	P-0050170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	274	824	0	ENST00000382891.5:c.3924G>C	p.Gln1308His	p.Q1308H	ENST00000382891	NM_133335.3	1308	caG/caC	22/22	1	2	FACETS	0.711	0.668	0.755	0.711	0.668	0.755	SUBCLONAL	1	TRUE	1	0.778862278424214	2		824	990	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994159	21994159	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	69	717	0	ENST00000579755.1:c.172C>T	p.Gln58Ter	p.Q58*	ENST00000579755		58	Cag/Tag	1/3	1		FACETS		0.154	0.204				SUBCLONAL	1	TRUE	1	0.778862278424214	2		717	994	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	231	476	3	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.72434090815412	2		479	550	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434367	121434367	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	223	654	3	ENST00000257555.6:c.1136del	p.Pro379LeufsTer5	p.P379Lfs*5	ENST00000257555		377	ctC/ct	6/10	1	2	FACETS	0.961	0.9	1	0.961	0.9	1	CLONAL	1	TRUE	1	0.72434090815412	2		657	641	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158026	27158026	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	197	531	0	ENST00000380036.4:c.255del	p.Val86LeufsTer31	p.V86Lfs*31	ENST00000380036	NM_000459.3	84	Aaa/aa	2/23	1	2	FACETS	0.872	0.811	0.933	0.872	0.811	0.933	CLONAL	1	TRUE	1	0.72434090815412	2		531	624	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	141	435	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.998	0.92	1	0.998	0.92	1	CLONAL	1	TRUE	1	0.72434090815412	2		436	390	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254978	16254978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770472402	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	156	328	0	ENST00000375759.3:c.2243C>T	p.Pro748Leu	p.P748L	ENST00000375759	NM_015001.2	748	cCg/cTg	11/15	1	2	FACETS	0.977	0.903	1	0.977	0.903	1	CLONAL	1	TRUE	1	0.72434090815412	2		328	441	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106532	27106532	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	297	654	0	ENST00000324856.7:c.6143G>A	p.Trp2048Ter	p.W2048*	ENST00000324856	NM_006015.4	2048	tGg/tAg	20/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.72434090815412	2		654	758	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746143	162746143	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	102	232	0	ENST00000367921.3:c.2266T>C	p.Trp756Arg	p.W756R	ENST00000367921	NM_006182.2	756	Tgg/Cgg	16/18	0.658819696861222	3	FACETS	0.909	0.818	1	0.455	0.409	0.502	CLONAL	1	TRUE	1	0.72434090815412	3		232	422	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851924	63851924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199637139	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	225	444	0	ENST00000279873.7:c.2702C>T	p.Thr901Met	p.T901M	ENST00000279873	NM_032199.2	901	aCg/aTg	10/10	0.72434090815412	2	FACETS	1	0.977	1	0.54	0.507	0.574	CLONAL	1	TRUE	0	0.72434090815412	2		444	575	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690843	89690843	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1554897880	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	259	277	0	ENST00000371953.3:c.250A>T	p.Arg84Ter	p.R84*	ENST00000371953	NM_000314.4	84	Aga/Tga	4/9	0.72434090815412	2	FACETS	0.985	0.945	1	0.985	0.945	1	CLONAL	2	TRUE	0	0.72434090815412	2		277	363	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466026	69466043	+	inframe_deletion	In_Frame_Del	DEL	CGACGTGCGGGACGTGGA	CGACGTGCGGGACGTGGA	-	novel	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	190	732	1	ENST00000227507.2:c.865_882del	p.Asp289_Asp294del	p.D289_D294del	ENST00000227507	NM_053056.2	288	acCGACGTGCGGGACGTGGAc/acc	5/5	1	2	FACETS	0.815	0.757	0.874	0.815	0.757	0.874	CLONAL	1	TRUE	1	0.72434090815412	2		733	644	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942199	71942200	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	216	566	0	ENST00000298229.2:c.1465dup	p.Leu489ProfsTer63	p.L489Pfs*63	ENST00000298229	NM_001567.3	488	ggc/ggCc	12/28	1	2	FACETS	0.938	0.877	1	0.938	0.877	1	CLONAL	1	TRUE	1	0.72434090815412	2		566	636	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943918	71943918	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	234	608	0	ENST00000298229.2:c.1852-1G>A		p.X618_splice	ENST00000298229	NM_001567.3	618			1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.72434090815412	2		608	645	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100581	102100581	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	213	404	0	ENST00000282441.5:c.1425G>T	p.Gln475His	p.Q475H	ENST00000282441	NM_001130145.2	475	caG/caT	9/9	1	2	FACETS	0.974	0.911	1	0.974	0.911	1	CLONAL	1	TRUE	1	0.72434090815412	2		404	604	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416121	49416121	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	167	358	0	ENST00000301067.7:c.16354A>G	p.Met5452Val	p.M5452V	ENST00000301067	NM_003482.3	5452	Atg/Gtg	52/54	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.72434090815412	2		358	458	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434247	49434247	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	312	743	0	ENST00000301067.7:c.7306del	p.Cys2436AlafsTer49	p.C2436Afs*49	ENST00000301067	NM_003482.3	2436	Tgc/gc	31/54	1	2	FACETS	0.938	0.888	0.99	0.938	0.888	0.99	CLONAL	1	TRUE	1	0.72434090815412	2		743	918	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435237	49435237	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	218	647	0	ENST00000301067.7:c.6316A>G	p.Ile2106Val	p.I2106V	ENST00000301067	NM_003482.3	2106	Att/Gtt	31/54	1	2	FACETS	0.939	0.878	1	0.939	0.878	1	CLONAL	1	TRUE	1	0.72434090815412	2		647	641	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994850	73994850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141119771	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	32	93	0	ENST00000318443.5:c.334G>A	p.Val112Met	p.V112M	ENST00000318443	NM_001024736.1	112	Gtg/Atg	3/10	1	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	TRUE	1	0.72434090815412	2		93	88	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650728	67650729	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	283	459	1	ENST00000264010.4:c.1034dup	p.His345GlnfsTer64	p.H345Qfs*64	ENST00000264010	NM_006565.3	345	cac/cAac	5/12	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.72434090815412	2		460	764	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935726	15935726	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs138200388	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	212	372	0	ENST00000268712.3:c.7207T>C	p.Cys2403Arg	p.C2403R	ENST00000268712	NM_006311.3	2403	Tgt/Cgt	46/46	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.72434090815412	2		372	551	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370236	40370236	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs761761205	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	163	768	3	ENST00000293328.3:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000293328	NM_012448.3	368	Cag/ag	9/19	1	2	FACETS	0.626	0.576	0.678	0.626	0.576	0.678	SUBCLONAL	1	TRUE	1	0.72434090815412	2		771	719	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214046	36214046	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	297	709	1	ENST00000222270.7:c.2872G>A	p.Gly958Ser	p.G958S	ENST00000222270	NM_014727.1	958	Ggc/Agc	6/37	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.72434090815412	2		710	788	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380445	31380445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	217	509	0	ENST00000328111.2:c.935G>A	p.Arg312Gln	p.R312Q	ENST00000328111	NM_006892.3	312	cGa/cAa	9/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.72434090815412	2		509	539	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927403	49927403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263755936	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	290	624	0	ENST00000296474.3:c.3901G>A	p.Ala1301Thr	p.A1301T	ENST00000296474	NM_002447.2	1301	Gcc/Acc	19/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.72434090815412	2		624	675	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374293	138374293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	233	404	0	ENST00000289153.2:c.3151G>A	p.Glu1051Lys	p.E1051K	ENST00000289153	NM_006219.2	1051	Gaa/Aaa	22/22	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.72434090815412	2		404	586	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361248	66361248	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	99	246	0	ENST00000273854.3:c.924del	p.Phe309SerfsTer113	p.F309Sfs*113	ENST00000273854	NM_004439.5	308	ggG/gg	4/18	1	2	FACETS	0.844	0.762	0.929	0.844	0.762	0.929	CLONAL	1	TRUE	1	0.72434090815412	2		246	324	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519486	176519486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776720644	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	299	754	1	ENST00000292408.4:c.892G>A	p.Gly298Ser	p.G298S	ENST00000292408	NM_213647.1	298	Ggt/Agt	7/18	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.72434090815412	2		755	802	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100302	157100302	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1417035592	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	101	229	0	ENST00000346085.5:c.1243del	p.Ala415ProfsTer15	p.A415Pfs*15	ENST00000346085	NM_020732.3	413	tcG/tc	1/20	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.72434090815412	2		229	276	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100576	157100577	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	130	317	0	ENST00000346085.5:c.1518dup	p.Gly507ArgfsTer28	p.G507Rfs*28	ENST00000346085	NM_020732.3	505	acc/aCcc	1/20	1	2	FACETS	0.957	0.878	1	0.957	0.878	1	CLONAL	1	TRUE	1	0.72434090815412	2		317	375	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	215	503	2	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.933	0.873	0.996	0.933	0.873	0.996	CLONAL	1	TRUE	1	0.72434090815412	2		505	636	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042170	6042170	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1562689635	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	205	497	0	ENST00000265849.7:c.451del	p.Arg151AlafsTer50	p.R151Afs*50	ENST00000265849	NM_000535.5	151	Cgc/gc	5/15	1	2	FACETS	0.973	0.908	1	0.973	0.908	1	CLONAL	1	TRUE	1	0.72434090815412	2		497	582	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	230	731	2	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	1	2	FACETS	0.822	0.768	0.876	0.822	0.768	0.876	CLONAL	1	TRUE	1	0.72434090815412	2		733	773	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	230	825	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.72434090815412	2		825	575	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	241	554	5	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.72434090815412	2		559	661	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802538	139802538	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756632275	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	258	648	1	ENST00000247668.2:c.383G>A	p.Arg128His	p.R128H	ENST00000247668	NM_021138.3	128	cGc/cAc	5/11	1	2	FACETS	0.919	0.864	0.975	0.919	0.864	0.975	CLONAL	1	TRUE	1	0.72434090815412	2		649	775	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933593	39933594	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0050171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	172	510	0	ENST00000378444.4:c.1005dup	p.Ser336LeufsTer45	p.S336Lfs*45	ENST00000378444	NM_001123385.1	335	-/C	4/15	1	2	FACETS	0.808	0.747	0.87	0.808	0.747	0.87	CLONAL	1	TRUE	1	0.72434090815412	2		510	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579355	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519997	NA	P-0050172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	137	739	0	ENST00000269305.4:c.332T>A	p.Leu111Gln	p.L111Q	ENST00000269305	NM_001126112.2	111	cTg/cAg	4/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.189935510356871	2		739	1287	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0050172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	70	411	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.189935510356871	5	FACETS	1	0.958	1	0.415	0.361	0.474	CLONAL	1	TRUE	2	0.189935510356871	5		411	760	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0050173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	195	590	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.515238784127325	3	FACETS	0.84	0.777	0.906	0.28	0.259	0.302	CLONAL	1	TRUE	0	0.563007434165748	3		591	1057	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829040	128829042	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	rs570242755	NA	P-0050173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	10	71	0	ENST00000249373.3:c.67_69del	p.Leu23del	p.L23del	ENST00000249373	NM_005631.4	16	ggGCTg/ggg	1/12	0.507506429849639	3	FACETS	0.288	0.195	0.404	0.096	0.065	0.135	SUBCLONAL	1	TRUE	0	0.563007434165748	3		71	158	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579346	7579348	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs764486868	NA	P-0050173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	637	773	0	ENST00000269305.4:c.339_341del	p.Phe113del	p.F113del	ENST00000269305	NM_001126112.2	113	ttCTTg/ttg	4/11	0.515238784127325	3	FACETS	0.88	0.853	0.907	0.88	0.853	0.907	CLONAL	3	TRUE	0	0.563007434165748	3		773	1098	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259640	11259640	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	368	508	0	ENST00000361445.4:c.4065G>C	p.Gln1355His	p.Q1355H	ENST00000361445	NM_004958.3	1355	caG/caC	27/58	0.527161767660499	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.563007434165748	2		508	629	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530136	212530136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	208	357	0	ENST00000342788.4:c.1783G>A	p.Asp595Asn	p.D595N	ENST00000342788	NM_005235.2	595	Gat/Aat	15/28	0.527161767660499	2	FACETS	0.851	0.801	0.902	0.851	0.801	0.902	CLONAL	2	TRUE	0	0.563007434165748	2		357	434	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	256	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.54	2		327	647	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	137	468	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.805	0.744	0.867	1	0.99	1	CLONAL	2	TRUE	1	0.54	2		468	315	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0050174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	145	215	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.54	2		215	430	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432409	49432412	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	novel	NA	P-0050174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	333	690	0	ENST00000301067.7:c.8727_8730del	p.Ser2910ArgfsTer32	p.S2910Rfs*32	ENST00000301067	NM_003482.3	2909	gtAAGT/gt	34/54	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.54	2		690	920	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878020	151878020	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	237	343	0	ENST00000262189.6:c.6925C>T	p.Gln2309Ter	p.Q2309*	ENST00000262189	NM_170606.2	2309	Cag/Tag	36/59	0.3	3	FACETS	1	0.973	1	1	0.973	1	INDETERMINATE	2	TRUE	1	0.54	3		343	529	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878332	151878332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	323	452	0	ENST00000262189.6:c.6613C>T	p.His2205Tyr	p.H2205Y	ENST00000262189	NM_170606.2	2205	Cat/Tat	36/59	0.3	3	FACETS	0.988	0.938	1	0.988	0.938	1	INDETERMINATE	2	TRUE	1	0.54	3		452	769	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982141	201982142	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0050174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	358	684	0	ENST00000359651.3:c.666dup	p.Asp223Ter	p.D223*	ENST00000359651		222	act/acTt	5/8	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.54	2		684	971	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431915	49431916	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	327	650	0	ENST00000301067.7:c.9223dup	p.Ser3075PhefsTer3	p.S3075Ffs*3	ENST00000301067	NM_003482.3	3075	tcg/tTcg	34/54	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.54	2		650	893	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808012	3808013	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0050174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	236	422	0	ENST00000262367.5:c.3406_3407del	p.Ser1136HisfsTer32	p.S1136Hfs*32	ENST00000262367	NM_004380.2	1136	TCc/c	18/31	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.54	2		422	636	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860636	3860636	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0050174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	94	473	0	ENST00000262367.5:c.943A>T	p.Lys315Ter	p.K315*	ENST00000262367	NM_004380.2	315	Aag/Tag	3/31	1	2	FACETS	0.416	0.369	0.466	0.416	0.369	0.466	SUBCLONAL	1	TRUE	1	0.54	2		473	837	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862194	68862194	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659664	NA	P-0050174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	227	399	0	ENST00000261769.5:c.2282G>C	p.Gly761Ala	p.G761A	ENST00000261769	NM_004360.3	761	gGa/gCa	14/16	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.54	2		399	620	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965117	81965117	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	181	426	0	ENST00000359376.3:c.2597G>T	p.Gly866Val	p.G866V	ENST00000359376	NM_002661.3	866	gGa/gTa	25/33	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.54	2		426	565	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523067	25523067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	310	614	0	ENST00000264709.3:c.118G>A	p.Glu40Lys	p.E40K	ENST00000264709	NM_175629.2	40	Gag/Aag	3/23	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.54	2		614	875	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878088	151878088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749125377	NA	P-0050174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	276	384	0	ENST00000262189.6:c.6857C>T	p.Thr2286Ile	p.T2286I	ENST00000262189	NM_170606.2	2286	aCa/aTa	36/59	0.3	3	FACETS	1	0.983	1	1	0.983	1	INDETERMINATE	2	TRUE	1	0.54	3		384	598	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878094	151878094	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0050174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	286	384	0	ENST00000262189.6:c.6851C>G	p.Ser2284Ter	p.S2284*	ENST00000262189	NM_170606.2	2284	tCa/tGa	36/59	0.3	3	FACETS	1	0.985	1	1	0.985	1	INDETERMINATE	2	TRUE	1	0.54	3		384	614	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878287	151878287	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	307	448	0	ENST00000262189.6:c.6658C>G	p.Gln2220Glu	p.Q2220E	ENST00000262189	NM_170606.2	2220	Cag/Gag	36/59	0.3	3	FACETS	0.965	0.915	1	0.965	0.915	1	INDETERMINATE	2	TRUE	1	0.54	3		448	748	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878301	151878301	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	309	457	0	ENST00000262189.6:c.6644del	p.Ser2215LeufsTer24	p.S2215Lfs*24	ENST00000262189	NM_170606.2	2215	tCt/tt	36/59	0.3	3	FACETS	0.973	0.923	1	0.973	0.923	1	INDETERMINATE	2	TRUE	1	0.54	3		457	747	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879484	151879484	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	324	374	0	ENST00000262189.6:c.5461C>G	p.Pro1821Ala	p.P1821A	ENST00000262189	NM_170606.2	1821	Cct/Gct	36/59	0.3	3	FACETS	1	0.988	1	1	0.988	1	INDETERMINATE	2	TRUE	1	0.54	3		374	687	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151932972	151932972	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	20	37	0	ENST00000262189.6:c.2699del	p.Gly900AspfsTer13	p.G900Dfs*13	ENST00000262189	NM_170606.2	900	gGa/ga	16/59	0.3	3	FACETS	1	0.911	1	0.682	0.537	0.839	INDETERMINATE	1	TRUE	1	0.54	3		37	69	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966698	44966698	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	258	202	0	ENST00000377967.4:c.3922G>T	p.Glu1308Ter	p.E1308*	ENST00000377967	NM_021140.2	1308	Gaa/Taa	27/29	1	1	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	0	0.54	1		202	324	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	285	413	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.712915128590688	3	FACETS	0.917	0.871	0.964	0.917	0.871	0.964	CLONAL	2	TRUE	1	0.728085616741933	3		413	582	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0050175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	758	582	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.72327266568779	2	FACETS	0.975	0.952	0.998	0.975	0.952	0.998	CLONAL	2	TRUE	0	0.728085616741933	2		582	1068	SUCCESS
APC	324	MSKCC	GRCh37	5	112175235	112175235	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	97	207	0	ENST00000257430.4:c.3944C>A	p.Ser1315Ter	p.S1315*	ENST00000257430	NM_000038.5	1315	tCa/tAa	16/16	1	2	FACETS	0.994	0.9	1	0.994	0.9	1	CLONAL	1	TRUE	1	0.728085616741933	2		207	268	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250883	153250883	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	127	293	0	ENST00000281708.4:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000281708	NM_033632.3	393	Cga/Tga	8/12	1	2	FACETS	0.951	0.871	1	0.951	0.871	1	CLONAL	1	TRUE	1	0.728085616741933	2		293	367	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755782	57755782	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	244	450	0	ENST00000274289.3:c.5A>G	p.Glu2Gly	p.E2G	ENST00000274289	NM_006622.3	2	gAg/gGg	1/14	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.728085616741933	2		450	670	SUCCESS
APC	324	MSKCC	GRCh37	5	112174018	112174019	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	132	239	0	ENST00000257430.4:c.2728dup	p.Thr910AsnfsTer2	p.T910Nfs*2	ENST00000257430	NM_000038.5	909	-/A	16/16	1	2	FACETS	0.952	0.873	1	0.952	0.873	1	CLONAL	1	TRUE	1	0.728085616741933	2		239	381	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0050177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	15	394	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.754	1	1	0.754	1	CLONAL	1	TRUE	1	0.275219400798802	2		394	107	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	50	617	0	ENST00000269305.4:c.672G>C	p.Glu224Asp	p.E224D	ENST00000269305	NM_001126112.2	224	gaG/gaC	6/11	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.275219400798802	2		617	311	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687037	176687037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	92	403	0	ENST00000439151.2:c.5014G>A	p.Asp1672Asn	p.D1672N	ENST00000439151	NM_022455.4	1672	Gac/Aac	14/23	0.275219400798802	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	0	0.275219400798802	2		403	320	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972864	55972864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866807777	NA	P-0050183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	17	319	0	ENST00000263923.4:c.1526G>A	p.Gly509Glu	p.G509E	ENST00000263923	NM_002253.2	509	gGa/gAa	11/30	1	2	FACETS	0.552	0.411	0.719	0.552	0.411	0.719	SUBCLONAL	1	TRUE	1	0.2	2		319	308	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261229	16261229	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	52	615	0	ENST00000375759.3:c.8494G>T	p.Ala2832Ser	p.A2832S	ENST00000375759	NM_015001.2	2832	Gcc/Tcc	11/15	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.2	2		615	508	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748501	162748502	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0050183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	22	333	1	ENST00000367921.3:c.2415_2416delinsTT	p.Arg806Ter	p.R806*	ENST00000367921	NM_006182.2	805	ttCCga/ttTTga	17/18	1	2	FACETS	0.71	0.55	0.895	0.71	0.55	0.895	SUBCLONAL	1	TRUE	1	0.2	2		334	310	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906520	32906520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80359158	NA	P-0050183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	23	305	0	ENST00000380152.3:c.905C>T	p.Thr302Ile	p.T302I	ENST00000380152		302	aCc/aTc	10/27	1	2	FACETS	0.667	0.52	0.837	0.667	0.52	0.837	SUBCLONAL	1	TRUE	1	0.2	2		305	345	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130331	2130332	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0050183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	47	858	1	ENST00000219476.3:c.3563_3564delinsTT	p.Pro1188Leu	p.P1188L	ENST00000219476	NM_000548.3	1188	cCC/cTT	30/42	1	2	FACETS	0.785	0.661	0.921	0.785	0.661	0.921	CLONAL	1	TRUE	1	0.2	2		859	599	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924993	49924993	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	48	568	0	ENST00000296474.3:c.3950A>C	p.Tyr1317Ser	p.Y1317S	ENST00000296474	NM_002447.2	1317	tAc/tCc	20/20	1	2	FACETS	0.996	0.842	1	0.996	0.842	1	CLONAL	1	TRUE	1	0.2	2		568	482	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73112883	73112883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	18	266	0	ENST00000356692.5:c.479C>T	p.Pro160Leu	p.P160L	ENST00000356692		160	cCa/cTa	6/9	1	2	FACETS	0.632	0.475	0.816	0.632	0.475	0.816	SUBCLONAL	1	TRUE	1	0.2	2		266	285	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650822	93650822	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	31	348	0	ENST00000375746.1:c.1748C>T	p.Ala583Val	p.A583V	ENST00000375746	NM_001174167.1	583	gCt/gTt	13/14	1	2	FACETS	0.914	0.741	1	0.914	0.741	1	CLONAL	1	TRUE	1	0.2	2		348	339	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0050185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	12	220	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	1	2	FACETS	0.824	0.579	1	0.824	0.579	1	CLONAL	1	TRUE	1	0.14	2		220	208	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0050185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	21	495	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.472	0.362	0.602	0.472	0.362	0.602	SUBCLONAL	1	TRUE	1	0.14	2		495	635	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0050185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	35	942	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	0.452	0.369	0.547	0.452	0.369	0.547	SUBCLONAL	1	TRUE	1	0.14	2		942	1106	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717715	89717716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587782341	NA	P-0050185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	52	402	1	ENST00000371953.3:c.741dup	p.Pro248ThrfsTer5	p.P248Tfs*5	ENST00000371953	NM_000314.4	247	tta/ttAa	7/9	1	2	FACETS	0.758	0.646	0.881	1	0.965	1	SUBCLONAL	2	TRUE	1	0.14	2		403	490	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274746	123274746	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs387906677	NA	P-0050185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	48	493	0	ENST00000358487.5:c.1172T>G	p.Met391Arg	p.M391R	ENST00000358487	NM_000141.4	391	aTg/aGg	9/18	1	2	FACETS	0.901	0.76	1	0.901	0.76	1	CLONAL	1	TRUE	1	0.14	2		493	761	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023253	27023274	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCCGGCGGCGGCGGTGGCGG	CGCCCGGCGGCGGCGGTGGCGG	-	novel	NA	P-0050185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	23	189	0	ENST00000324856.7:c.360_381del	p.Pro121AlafsTer104	p.P121Afs*104	ENST00000324856	NM_006015.4	120	cCGCCCGGCGGCGGCGGTGGCGGc/cc	1/20	1	2	FACETS	1	0.819	1	1	0.819	1	CLONAL	1	TRUE	1	0.14	2		189	311	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645933	67645933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	46	524	0	ENST00000264010.4:c.862del	p.His288ThrfsTer22	p.H288Tfs*22	ENST00000264010	NM_006565.3	287	agC/ag	4/12	1	2	FACETS	0.743	0.623	0.875	0.743	0.623	0.875	SUBCLONAL	1	TRUE	1	0.14	2		524	885	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0050186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	120	542	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.293441643073452	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.293441643073452	1		542	556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0050186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	175	825	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.293441643073452	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.293441643073452	1		825	919	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056421	180056421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	54	638	0	ENST00000261937.6:c.823C>T	p.Arg275Trp	p.R275W	ENST00000261937	NM_182925.4	275	Cgg/Tgg	7/30	1	2	FACETS	0.764	0.653	0.884	0.764	0.653	0.884	SUBCLONAL	1	TRUE	1	0.293441643073452	2		638	482	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420011	41420011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773011187	NA	P-0050186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	61	599	1	ENST00000373198.4:c.310G>A	p.Asp104Asn	p.D104N	ENST00000373198	NM_133170.3	104	Gac/Aac	3/32	1	2	FACETS	0.672	0.579	0.772	0.672	0.579	0.772	SUBCLONAL	1	TRUE	1	0.293441643073452	2		600	619	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492756	56492757	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0050186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	109	523	0	ENST00000407977.2:c.182_183del	p.Leu61GlnfsTer13	p.L61Qfs*13	ENST00000407977		61	cTG/c	2/10	0.293441643073452	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.293441643073452	1		523	617	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609362	39609362	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	90	314	0	ENST00000262039.4:c.1664T>G	p.Leu555Arg	p.L555R	ENST00000262039	NM_002647.2	555	cTa/cGa	15/25	0.293441643073452	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.293441643073452	1		314	484	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398283	25398285	+	missense_variant	Missense_Mutation	TNP	ACC	ACC	CCG	novel	NA	P-0050186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	79	376	0	ENST00000311936.3:c.34_36delinsCGG	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	GGT/CGG	2/5	1	2	FACETS	0.953	0.839	1	0.953	0.839	1	CLONAL	1	TRUE	1	0.293441643073452	2		376	565	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	69	626	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.605	0.526	0.691	0.605	0.526	0.691	SUBCLONAL	1	FALSE	1	0.260676075455833	2		626	875	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101402	27101402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	34	464	0	ENST00000324856.7:c.4689del	p.Met1564Ter	p.M1564*	ENST00000324856	NM_006015.4	1562	Ccc/cc	18/20	1	2	FACETS	0.444	0.361	0.536	0.444	0.361	0.536	SUBCLONAL	1	FALSE	1	0.260676075455833	2		464	588	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0050187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	9	273	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.552	0.367	0.786	0.552	0.367	0.786	SUBCLONAL	1	FALSE	1	0.260676075455833	2		273	125	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717769	89717770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	48	316	0	ENST00000371953.3:c.800dup	p.Asp268GlyfsTer30	p.D268Gfs*30	ENST00000371953	NM_000314.4	265	cta/ctAa	7/9	0.239184574851719	2	FACETS	0.78	0.666	0.903	0.78	0.666	0.903	CLONAL	2	FALSE	0	0.260676075455833	2		316	236	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0050187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	68	632	0	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	1	2	FACETS	0.758	0.659	0.866	0.758	0.659	0.866	SUBCLONAL	1	FALSE	1	0.260676075455833	2		632	688	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs371769427	NA	P-0050187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	28	280	0	ENST00000291552.4:c.101C>A	p.Ser34Tyr	p.S34Y	ENST00000291552	NM_006758.2	34	tCt/tAt	2/8	1	2	FACETS	0.623	0.498	0.765	0.623	0.498	0.765	SUBCLONAL	1	FALSE	1	0.260676075455833	2		280	345	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224440	39224440	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs727505016	NA	P-0050187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	16	545	0	ENST00000402219.2:c.2918A>T	p.Gln973Leu	p.Q973L	ENST00000402219	NM_005633.3	973	cAg/cTg	18/23	1	2	FACETS	0.44	0.325	0.578	0.44	0.325	0.578	SUBCLONAL	1	FALSE	1	0.260676075455833	2		545	279	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696730	47696730	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	73	331	0	ENST00000347630.2:c.218C>G	p.Pro73Arg	p.P73R	ENST00000347630	NM_001007230.1	73	cCc/cGc	5/11	0.260676075455833	1	FACETS	0.837	0.739	0.94	1	0.98	1	CLONAL	2	FALSE	0	0.260676075455833	1		331	291	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101474	27101475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCAGCCCTGCTCCCCTGCC	novel	NA	P-0050187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	103	754	0	ENST00000324856.7:c.4759_4777dup	p.Arg1593GlnfsTer16	p.R1593Qfs*16	ENST00000324856	NM_006015.4	1586	tcc/tCCAGCCCTGCTCCCCTGCCcc	18/20	1	2	FACETS	0.741	0.662	0.826	0.741	0.662	0.826	SUBCLONAL	1	FALSE	1	0.260676075455833	2		754	1066	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763912	76763912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782540364	NA	P-0050187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	66	606	1	ENST00000373344.5:c.7396G>A	p.Gly2466Ser	p.G2466S	ENST00000373344	NM_000489.3	2466	Ggt/Agt	35/35	1	2	FACETS	0.703	0.61	0.805	0.703	0.61	0.805	SUBCLONAL	1	FALSE	1	0.260676075455833	2		607	720	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781056	135781056	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	171	640	0	ENST00000298552.3:c.1909G>T	p.Glu637Ter	p.E637*	ENST00000298552	NM_001162426.1	637	Gaa/Taa	15/23	0.419280824813047	2	FACETS	0.869	0.807	0.931	0.869	0.807	0.931	CLONAL	2	TRUE	0	0.434525490651792	2		640	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs967461896	NA	P-0050188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	251	763	0	ENST00000269305.4:c.526T>A	p.Cys176Ser	p.C176S	ENST00000269305	NM_001126112.2	176	Tgc/Agc	5/11	0.310898880805827	3	FACETS	1	0.978	1	0.718	0.676	0.761	CLONAL	2	TRUE	0	0.434525490651792	3		763	653	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980792	40980792	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs552058956	NA	P-0050188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	44	551	0	ENST00000373198.4:c.1694C>A	p.Thr565Asn	p.T565N	ENST00000373198	NM_133170.3	565	aCc/aAc	10/32	NA	2	FACETS	0.49	0.412	0.577			1	INDETERMINATE	1	TRUE	NA	0.434525490651792	2		551	413	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966655	44966655	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	20	259	1	ENST00000377967.4:c.3879G>T	p.Lys1293Asn	p.K1293N	ENST00000377967	NM_021140.2	1293	aaG/aaT	27/29	0.167823871922238	3	FACETS	0.958	0.743	1			1	INDETERMINATE	1	TRUE	NA	0.434525490651792	3		260	117	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211452	46211452	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1346120756	NA	P-0050188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	39	156	0	ENST00000334344.6:c.419-1G>T		p.X140_splice	ENST00000334344	NM_152641.2	140			0.330924946908516	5	FACETS	1	0.881	1	0.701	0.592	0.817	CLONAL	2	TRUE	2	0.434525490651792	5		156	141	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954168	48954197	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTTAAATTATCTGTTTCAGGAAGAAGAA	TTTTTAAATTATCTGTTTCAGGAAGAAGAA	-	novel	NA	P-0050188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	16	162	0	ENST00000267163.4:c.1390-21_1398del		p.X464_splice	ENST00000267163	NM_000321.2	464		15/27	NA	2	FACETS	0.8	0.601	1			1	INDETERMINATE	1	TRUE	NA	0.434525490651792	2		162	92	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392042	81392042	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	61	298	0	ENST00000222390.5:c.235G>T	p.Gly79Ter	p.G79*	ENST00000222390	NM_000601.4	79	Gga/Tga	2/18	0.434525490651792	4	FACETS	1	0.899	1	1	0.899	1	CLONAL	2	TRUE	2	0.434525490651792	4		298	196	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0050189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	84	240	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.989	0.883	1	1	0.988	1	CLONAL	3	TRUE	1	0.19	2		240	298	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0050189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	123	251	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.966	1	1	0.992	1	CLONAL	3	TRUE	1	0.19	2		251	387	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936103	178936103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519699	NA	P-0050189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	145	420	0	ENST00000263967.3:c.1645G>A	p.Asp549Asn	p.D549N	ENST00000263967	NM_006218.2	549	Gat/Aat	10/21	1	2	FACETS	1	0.963	1	1	0.993	1	CLONAL	3	TRUE	1	0.19	2		420	470	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023183	27023183	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	62	117	0	ENST00000324856.7:c.289G>T	p.Glu97Ter	p.E97*	ENST00000324856	NM_006015.4	97	Gag/Tag	1/20	1	2	FACETS	1	0.921	1	1	0.986	1	CLONAL	4	TRUE	1	0.19	2		117	155	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0050189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	263	563	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	0.3	2	FACETS	0.937	0.895	0.979			1	CLONAL	7	TRUE	NA	0.19	2		563	422	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803165	1803165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1031160906	NA	P-0050189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	303	991	1	ENST00000260795.2:c.517C>T	p.Arg173Cys	p.R173C	ENST00000260795		173	Cgc/Tgc	4/17	1	2	FACETS	0.884	0.835	0.934	1	0.997	1	CLONAL	4	TRUE	1	0.19	2		992	902	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339326	70339327	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	GCTT	novel	NA	P-0050189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	162	443	0	ENST00000374080.3:c.204_204+1insCTTG	p.Ile69LeufsTer17	p.I69Lfs*17	ENST00000374080		68	aag/aaGCTTg	2/45	1	2	FACETS	1	0.966	1	1	0.994	1	CLONAL	3	TRUE	1	0.19	2		443	526	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0050193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	157	581	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.81	2		581	380	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431319	49431319	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	117	631	0	ENST00000301067.7:c.9820C>T	p.Gln3274Ter	p.Q3274*	ENST00000301067	NM_003482.3	3274	Cag/Tag	34/54	0.182904674428621	3	FACETS	1	0.985	1	0.697	0.639	0.757	INDETERMINATE	1	TRUE	1	0.81	3		631	291	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433053	49433062	+	frameshift_variant	Frame_Shift_Del	DEL	GAGAGTCGGT	GAGAGTCGGT	-	novel	NA	P-0050193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	153	881	0	ENST00000301067.7:c.8309_8318del	p.Asp2770AlafsTer14	p.D2770Afs*14	ENST00000301067	NM_003482.3	2770	gACCGACTCTCc/gc	33/54	0.182904674428621	3	FACETS	1	0.985	1	0.636	0.588	0.686	INDETERMINATE	1	TRUE	1	0.81	3		881	417	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048714	180048714	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	111	866	1	ENST00000261937.6:c.1848C>A	p.Phe616Leu	p.F616L	ENST00000261937	NM_182925.4	616	ttC/ttA	13/30	1	2	FACETS	0.993	0.908	1	0.993	0.908	1	CLONAL	1	TRUE	1	0.81	2		867	276	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184086	123184086	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	87	194	0	ENST00000218089.9:c.944G>A	p.Trp315Ter	p.W315*	ENST00000218089	NM_001042749.1	315	tGg/tAg	11/35	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.81	1		194	103	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2194560	2194560	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	42	484	0	ENST00000398665.3:c.635A>G	p.Lys212Arg	p.K212R	ENST00000398665	NM_032482.2	212	aAg/aGg	7/28	0.203042557358057	0	FACETS	0.248	0.207	0.293			1	INDETERMINATE	1	TRUE	0	0.459947487235113	0		484	398	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	111	468	0				ENST00000310581	NM_198253.2	-/1132			0.593447206653083	3	FACETS	0.89	0.817	0.965	0.89	0.817	0.965	CLONAL	2	TRUE	1	0.678867635980751	3		468	246	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0050195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	223	822	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.678867635980751	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.678867635980751	3		822	417	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880257	37880257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	179	427	0	ENST00000269571.5:c.2301C>G	p.Ile767Met	p.I767M	ENST00000269571		767	atC/atG	19/27	0.18567381973225	3	FACETS	0.987	0.925	1	0.658	0.616	0.699	INDETERMINATE	2	TRUE	0	0.678867635980751	3		427	358	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947852	178947852	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	48	255	0	ENST00000263967.3:c.2727C>A	p.Phe909Leu	p.F909L	ENST00000263967	NM_006218.2	909	ttC/ttA	19/21	0.593447206653083	3	FACETS	0.877	0.75	1	0.438	0.375	0.507	CLONAL	1	TRUE	1	0.678867635980751	3		255	216	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808930	1808930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371433215	NA	P-0050195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	335	894	0	ENST00000260795.2:c.2362G>A	p.Val788Met	p.V788M	ENST00000260795		788	Gtg/Atg	17/17	0.678867635980751	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.678867635980751	3		894	567	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884145	37884145	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	163	795	0	ENST00000269571.5:c.3616C>T	p.Gln1206Ter	p.Q1206*	ENST00000269571		1206	Cag/Tag	27/27	0.18567381973225	3	FACETS	0.966	0.889	1	0.322	0.296	0.349	INDETERMINATE	1	TRUE	0	0.678867635980751	3		795	666	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11181402	11181402	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	128	701	0	ENST00000361445.4:c.6834G>C	p.Leu2278Phe	p.L2278F	ENST00000361445	NM_004958.3	2278	ttG/ttC	49/58	0.593447206653083	3	FACETS	0.863	0.785	0.945	0.432	0.392	0.473	CLONAL	1	TRUE	1	0.678867635980751	3		701	585	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422224	422224	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	110	394	0	ENST00000399788.2:c.3034C>T	p.Gln1012Ter	p.Q1012*	ENST00000399788	NM_001042603.1	1012	Cag/Tag	20/28	0.509018688562744	1	FACETS	0.817	0.747	0.888	0.817	0.747	0.888	CLONAL	1	TRUE	0	0.678867635980751	1		394	262	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11181374	11181374	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	131	719	0	ENST00000361445.4:c.6862G>C	p.Glu2288Gln	p.E2288Q	ENST00000361445	NM_004958.3	2288	Gag/Cag	49/58	0.593447206653083	3	FACETS	0.859	0.782	0.939	0.429	0.391	0.47	CLONAL	1	TRUE	1	0.678867635980751	3		719	602	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938406	44938406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	39	359	0	ENST00000377967.4:c.2954C>T	p.Ser985Phe	p.S985F	ENST00000377967	NM_021140.2	985	tCt/tTt	20/29	0.18567381973225	3	FACETS	0.681	0.569	0.803	0.227	0.189	0.268	INDETERMINATE	1	TRUE	0	0.678867635980751	3		359	226	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925378	114925378	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	305	685	0	ENST00000543371.1:c.1456G>T	p.Asp486Tyr	p.D486Y	ENST00000543371	NM_001198531.1	486	Gat/Tat	14/14	0.675616709669002	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.678867635980751	2		685	427	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609722	117609722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1430294646	NA	P-0050195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	80	451	0	ENST00000368508.3:c.6977C>T	p.Ser2326Phe	p.S2326F	ENST00000368508	NM_002944.2	2326	tCt/tTt	43/43	1	2	FACETS	0.95	0.849	1	0.95	0.849	1	CLONAL	1	TRUE	1	0.678867635980751	2		451	248	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158432	108158432	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	74	369	0	ENST00000278616.4:c.4099G>C	p.Asp1367His	p.D1367H	ENST00000278616	NM_000051.3	1367	Gac/Cac	27/63	1	2	FACETS	0.858	0.761	0.96	0.858	0.761	0.96	CLONAL	1	TRUE	1	0.678867635980751	2		369	254	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654583	29654583	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	91	257	0	ENST00000356175.3:c.5272C>G	p.Leu1758Val	p.L1758V	ENST00000356175	NM_000267.3	1758	Cta/Gta	37/57	0.18567381973225	3	FACETS	0.95	0.865	1	0.633	0.577	0.69	INDETERMINATE	2	TRUE	0	0.678867635980751	3		257	189	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219785	36219785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	149	776	0	ENST00000222270.7:c.4682C>T	p.Ser1561Leu	p.S1561L	ENST00000222270	NM_014727.1	1561	tCa/tTa	20/37	0.678867635980751	3	FACETS	0.992	0.91	1	0.496	0.455	0.538	CLONAL	1	TRUE	1	0.678867635980751	3		776	593	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743889	40743889	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	163	552	0	ENST00000373198.4:c.3106G>T	p.Glu1036Ter	p.E1036*	ENST00000373198	NM_133170.3	1036	Gaa/Taa	23/32	0.349497265902519	3	FACETS	1	0.987	1	0.669	0.619	0.72	INDETERMINATE	1	TRUE	1	0.678867635980751	3		552	481	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026116	71026116	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057524152	NA	P-0050195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	115	352	0	ENST00000318789.4:c.1506C>G	p.Phe502Leu	p.F502L	ENST00000318789	NM_032682.5	502	ttC/ttG	17/21	0.593447206653083	3	FACETS	0.89	0.805	0.978	0.445	0.402	0.489	CLONAL	1	TRUE	1	0.678867635980751	3		352	510	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43746206	43746206	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	125	548	2	ENST00000523873.1:c.325A>G	p.Ile109Val	p.I109V	ENST00000523873		109	Atc/Gtc	4/8	1	2	FACETS	0.935	0.854	1	0.935	0.854	1	CLONAL	1	TRUE	1	0.678867635980751	2		550	394	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945129	44945130	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0050195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	100	334	1	ENST00000377967.4:c.3455dup	p.Cys1153LeufsTer4	p.C1153Lfs*4	ENST00000377967	NM_021140.2	1151	-/T	24/29	0.18567381973225	3	FACETS	0.94	0.859	1	0.626	0.573	0.68	INDETERMINATE	2	TRUE	0	0.678867635980751	3		335	210	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211906	123211906	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	116	303	0	ENST00000218089.9:c.2773C>T	p.Gln925Ter	p.Q925*	ENST00000218089	NM_001042749.1	925	Cag/Tag	27/35	0.18567381973225	3	FACETS	1	0.978	1	0.767	0.712	0.821	INDETERMINATE	2	TRUE	0	0.678867635980751	3		303	199	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	110	452	3	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	0.470940423163202	1	FACETS	0.727	0.657	0.801	0.727	0.657	0.801	SUBCLONAL	1	FALSE	0	0.470940423163202	1		455	491	SUCCESS
AR	367	MSKCC	GRCh37	X	66943552	66943552	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137852578	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	130	215	0	ENST00000374690.3:c.2632A>G	p.Thr878Ala	p.T878A	ENST00000374690	NM_000044.3	878	Act/Gct	8/8	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	0	0.470940423163202	1		215	309	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	193	608	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.453992579199631	1	FACETS	0.885	0.822	0.95	0.885	0.822	0.95	CLONAL	1	FALSE	0	0.470940423163202	1		608	708	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	113	910	4	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	0.453992579199631	1	FACETS	0.392	0.352	0.434	0.392	0.352	0.434	SUBCLONAL	1	FALSE	0	0.470940423163202	1		914	937	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	188	359	2	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	0.453992579199631	1	FACETS	0.779	0.73	0.827	1	0.992	1	SUBCLONAL	2	FALSE	0	0.470940423163202	1		361	392	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	358	399	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.938	0.895	0.983	1	0.996	1	CLONAL	2	FALSE	1	0.470940423163202	2		403	810	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801767	3801767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567282647	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	154	607	0	ENST00000262367.5:c.3739G>A	p.Glu1247Lys	p.E1247K	ENST00000262367	NM_004380.2	1247	Gag/Aag	20/31	1	2	FACETS	0.857	0.786	0.932	0.857	0.786	0.932	CLONAL	1	FALSE	1	0.470940423163202	2		607	763	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673750	176673750	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	125	422	0	ENST00000439151.2:c.4455del	p.Val1486Ter	p.V1486*	ENST00000439151	NM_022455.4	1484	Aaa/aa	10/23	0.470940423163202	3	FACETS	0.91	0.824	0.999	0.455	0.412	0.5	CLONAL	1	FALSE	1	0.470940423163202	3		422	721	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353819	15353819	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	106	454	2	ENST00000263377.2:c.3061del	p.His1021IlefsTer47	p.H1021Ifs*47	ENST00000263377	NM_058243.2	1021	Cat/at	14/20	1	2	FACETS	0.782	0.702	0.865	0.782	0.702	0.865	SUBCLONAL	1	FALSE	1	0.470940423163202	2		456	576	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418405	139418405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1286309175	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	538	1014	0	ENST00000277541.6:c.167G>A	p.Arg56Gln	p.R56Q	ENST00000277541	NM_017617.3	56	cGa/cAa	3/34	0.470940423163202	4	FACETS	0.942	0.902	0.983	0.628	0.601	0.656	CLONAL	2	FALSE	1	0.470940423163202	4		1014	1783	SUCCESS
AR	367	MSKCC	GRCh37	X	66931504	66931504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1340026226	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	204	321	0	ENST00000374690.3:c.2146G>A	p.Val716Met	p.V716M	ENST00000374690	NM_000044.3	716	Gtg/Atg	4/8	1	1	FACETS	0.751	0.705	0.797	1	0.993	1	SUBCLONAL	2	FALSE	0	0.470940423163202	1		321	441	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096044	11096044	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	272	987	0	ENST00000358026.2:c.321del	p.Pro109ArgfsTer194	p.P109Rfs*194	ENST00000358026	NM_001128849.1	106	atG/at	3/36	1	2	FACETS	0.947	0.888	1	0.947	0.888	1	CLONAL	1	FALSE	1	0.470940423163202	2		987	1220	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542110	187542110	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	121	439	1	ENST00000441802.2:c.5630del	p.Pro1877LeufsTer20	p.P1877Lfs*20	ENST00000441802	NM_005245.3	1877	cCt/ct	10/27	0.470940423163202	1	FACETS	0.933	0.85	1	0.933	0.85	1	CLONAL	1	FALSE	0	0.470940423163202	1		440	421	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499363	89499363	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1317589623	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	278	459	2	ENST00000336596.2:c.2538del	p.Met847TrpfsTer10	p.M847Wfs*10	ENST00000336596	NM_005233.5	845	Ccc/cc	15/17	0.453992579199631	1	FACETS	0.95	0.906	0.994	1	0.996	1	CLONAL	2	FALSE	0	0.470940423163202	1		461	475	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253418	226253418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	71	78	0	ENST00000366813.1:c.190C>T	p.Arg64Cys	p.R64C	ENST00000366813		64	Cgc/Tgc	2/3	1	2	FACETS	0.954	0.856	1	1	0.984	1	CLONAL	2	FALSE	1	0.470940423163202	2		78	158	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716329	52716329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863225094	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	22	722	0	ENST00000322088.6:c.773G>A	p.Arg258His	p.R258H	ENST00000322088	NM_014225.5	258	cGc/cAc	6/15	NA	2	FACETS	0.1	0.077	0.127			1	INDETERMINATE	1	FALSE	NA	0.470940423163202	2		722	936	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107136	27107137	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	384	637	0	ENST00000324856.7:c.6749_6750del	p.Glu2250ValfsTer27	p.E2250Vfs*27	ENST00000324856	NM_006015.4	2249	tcAGag/tcag	20/20	0.453992579199631	1	FACETS	0.946	0.909	0.983	1	0.997	1	CLONAL	2	FALSE	0	0.470940423163202	1		637	659	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551083	41551083	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	317	560	0	ENST00000263253.7:c.3227G>A	p.Arg1076His	p.R1076H	ENST00000263253	NM_001429.3	1076	cGt/cAt	17/31	1	2	FACETS	0.916	0.87	0.962	1	0.996	1	CLONAL	2	FALSE	1	0.470940423163202	2		560	735	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271224	26271224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	123	568	0	ENST00000305910.3:c.389G>A	p.Arg130His	p.R130H	ENST00000305910	NM_003534.2	130	cGc/cAc	1/1	0.3993904231093	1	FACETS	0.834	0.758	0.912	0.834	0.758	0.912	CLONAL	1	FALSE	0	0.470940423163202	1		568	479	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239899	105239899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768606668	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	206	745	3	ENST00000349310.3:c.721C>T	p.Arg241Trp	p.R241W	ENST00000349310	NM_001014432.1	241	Cgg/Tgg	10/15	1	2	FACETS	0.886	0.822	0.953	0.886	0.822	0.953	CLONAL	1	FALSE	1	0.470940423163202	2		748	987	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	533	1082	0	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.899	0.864	0.934	1	0.997	1	CLONAL	2	FALSE	1	0.470940423163202	2		1082	1259	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300040	137300040	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1247	458	990	0	ENST00000481739.1:c.331del	p.Leu111TrpfsTer57	p.L111Wfs*57	ENST00000481739	NM_002957.4	109	Ccc/cc	3/10	0.470940423163202	4	FACETS	0.839	0.799	0.879	0.559	0.533	0.586	CLONAL	2	FALSE	1	0.470940423163202	4		990	1705	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614463	38614463	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	128	424	0	ENST00000299084.4:c.234del	p.Asp79ThrfsTer42	p.D79Tfs*42	ENST00000299084	NM_152594.2	77	Aaa/aa	3/7	0.453992579199631	1	FACETS	0.999	0.913	1	0.999	0.913	1	CLONAL	1	FALSE	0	0.470940423163202	1		424	416	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468307	120468307	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	223	681	0	ENST00000256646.2:c.4132T>C	p.Cys1378Arg	p.C1378R	ENST00000256646	NM_024408.3	1378	Tgt/Cgt	25/34	0.453992579199631	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	0	0.470940423163202	1		681	655	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561376	9561376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774715756	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	282	585	0	ENST00000353224.5:c.406G>A	p.Asp136Asn	p.D136N	ENST00000353224	NM_177990.2	136	Gat/Aat	4/10	0.453992579199631	1	FACETS	1	0.97	1	1	0.996	1	CLONAL	2	FALSE	0	0.470940423163202	1		585	450	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223858	36223858	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	272	1110	6	ENST00000222270.7:c.6413del	p.Pro2138ArgfsTer15	p.P2138Rfs*15	ENST00000222270	NM_014727.1	2136	ctC/ct	28/37	1	2	FACETS	0.883	0.827	0.941	0.883	0.827	0.941	CLONAL	1	FALSE	1	0.470940423163202	2		1116	1308	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412297	139412297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	508	1036	0	ENST00000277541.6:c.1348G>A	p.Glu450Lys	p.E450K	ENST00000277541	NM_017617.3	450	Gag/Aag	8/34	0.470940423163202	4	FACETS	0.933	0.892	0.974	0.622	0.594	0.65	CLONAL	2	FALSE	1	0.470940423163202	4		1036	1701	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118365075	118365075	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs886041896	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	142	458	0	ENST00000534358.1:c.5251A>T	p.Lys1751Ter	p.K1751*	ENST00000534358	NM_005933.3	1751	Aaa/Taa	17/36	0.453992579199631	1	FACETS	0.955	0.876	1	0.955	0.876	1	CLONAL	1	FALSE	0	0.470940423163202	1		458	483	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	263	471	16	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	0.44518964169368	1	FACETS	0.845	0.802	0.888	1	0.995	1	CLONAL	2	FALSE	0	0.470940423163202	1		487	505	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453399	40453399	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs759027671	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	313	938	12	ENST00000345506.4:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000345506	NM_003152.3	366	Ccc/cc	10/20	0.453992579199631	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	0	0.470940423163202	1		950	905	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402268	402268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs539682097	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	64	589	0	ENST00000399788.2:c.4523G>A	p.Arg1508Gln	p.R1508Q	ENST00000399788	NM_001042603.1	1508	cGg/cAg	27/28	1	2	FACETS	0.314	0.271	0.361	0.314	0.271	0.361	SUBCLONAL	1	FALSE	1	0.470940423163202	2		589	865	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157790	106157790	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	92	303	0	ENST00000380013.4:c.2691G>T	p.Gln897His	p.Q897H	ENST00000380013	NM_001127208.2	897	caG/caT	3/11	0.470940423163202	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	0	0.470940423163202	1		303	278	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223485	53223485	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782288948	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	449	398	0	ENST00000375401.3:c.3874G>A	p.Ala1292Thr	p.A1292T	ENST00000375401	NM_004187.3	1292	Gcc/Acc	23/26	1	1	FACETS	1	0.99	1	1	0.998	1	CLONAL	3	FALSE	0	0.470940423163202	1		398	482	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968244	2968244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161484391	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	244	927	0	ENST00000396946.4:c.1742C>T	p.Ala581Val	p.A581V	ENST00000396946	NM_032415.4	581	gCg/gTg	13/25	1	2	FACETS	0.966	0.902	1	0.966	0.902	1	CLONAL	1	FALSE	1	0.470940423163202	2		927	1073	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2180739	2180741	+	inframe_deletion	In_Frame_Del	DEL	ATC	ATC	-	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	191	716	0	ENST00000398665.3:c.112_114del	p.Ile38del	p.I38del	ENST00000398665	NM_032482.2	37	ATC/-	2/28	1	2	FACETS	0.903	0.836	0.973	0.903	0.836	0.973	CLONAL	1	FALSE	1	0.470940423163202	2		716	898	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307276	65307279	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	88	337	0	ENST00000342505.4:c.2409_2412del	p.Glu803AspfsTer10	p.E803Dfs*10	ENST00000342505	NM_002227.2	803	gaGAGA/ga	18/25	0.453992579199631	1	FACETS	0.85	0.76	0.945	0.85	0.76	0.945	CLONAL	1	FALSE	0	0.470940423163202	1		337	336	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348796	11348796	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	83	330	0	ENST00000332029.2:c.540G>C	p.Gln180His	p.Q180H	ENST00000332029	NM_003745.1	180	caG/caC	2/2	1	2	FACETS	0.92	0.818	1	0.92	0.818	1	CLONAL	1	FALSE	1	0.470940423163202	2		330	383	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961631	18961631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339234477	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	84	800	2	ENST00000262803.5:c.764G>A	p.Arg255His	p.R255H	ENST00000262803	NM_002911.3	255	cGc/cAc	5/24	1	2	FACETS	0.349	0.307	0.395	0.349	0.307	0.395	SUBCLONAL	1	FALSE	1	0.470940423163202	2		802	1021	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294672	1294672	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1554043093	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	57	614	4	ENST00000310581.5:c.329del	p.Gly110AlafsTer18	p.G110Afs*18	ENST00000310581	NM_198253.2	110	gGc/gc	2/16	0.145676297175008	3	FACETS	0.321	0.274	0.373	0.107	0.091	0.125	INDETERMINATE	1	FALSE	0	0.470940423163202	3		618	931	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980496	1980496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151213547	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	228	877	0	ENST00000382891.5:c.3958C>T	p.Arg1320Trp	p.R1320W	ENST00000382891	NM_133335.3	1320	Cgg/Tgg	22/22	1	2	FACETS	0.874	0.814	0.936	0.874	0.814	0.936	CLONAL	1	FALSE	1	0.470940423163202	2		877	1108	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786008	135786008	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1225	229	711	1	ENST00000298552.3:c.1213G>A	p.Asp405Asn	p.D405N	ENST00000298552	NM_001162426.1	405	Gac/Aac	12/23	0.466399330690306	4	FACETS	0.984	0.914	1	0.328	0.304	0.352	CLONAL	1	FALSE	1	0.470940423163202	4		712	1454	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807188	1807188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1560437651	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	460	932	1	ENST00000260795.2:c.1519G>A	p.Val507Met	p.V507M	ENST00000260795		507	Gtg/Atg	10/17	1	2	FACETS	0.884	0.847	0.922	1	0.997	1	CLONAL	2	FALSE	1	0.470940423163202	2		933	1105	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202706	16202707	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	121	404	0	ENST00000375759.3:c.416dup	p.Asn139LysfsTer7	p.N139Kfs*7	ENST00000375759	NM_015001.2	138	-/A	3/15	0.453992579199631	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	0	0.470940423163202	1		404	362	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176118198	176118198	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	63	224	0	ENST00000367669.3:c.775G>T	p.Ala259Ser	p.A259S	ENST00000367669	NM_022457.5	259	Gcc/Tcc	6/20	1	2	FACETS	0.904	0.788	1	0.904	0.788	1	CLONAL	1	FALSE	1	0.470940423163202	2		224	296	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600417	43600417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	365	645	0	ENST00000355710.3:c.643C>T	p.Arg215Cys	p.R215C	ENST00000355710	NM_020975.4	215	Cgc/Tgc	4/20	0.470940423163202	1	FACETS	0.941	0.902	0.978	1	0.997	1	CLONAL	2	FALSE	0	0.470940423163202	1		645	630	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279612	123279612	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1488169619	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	188	652	1	ENST00000358487.5:c.820G>A	p.Val274Ile	p.V274I	ENST00000358487	NM_000141.4	274	Gta/Ata	7/18	0.470940423163202	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	0	0.470940423163202	1		653	593	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404783	404783	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290342440	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	78	505	0	ENST00000399788.2:c.4411G>A	p.Ala1471Thr	p.A1471T	ENST00000399788	NM_001042603.1	1471	Gcc/Acc	26/28	1	2	FACETS	0.497	0.437	0.562	0.497	0.437	0.562	SUBCLONAL	1	FALSE	1	0.470940423163202	2		505	666	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406282	406282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	265	542	0	ENST00000399788.2:c.4159G>A	p.Val1387Met	p.V1387M	ENST00000399788	NM_001042603.1	1387	Gtg/Atg	25/28	1	2	FACETS	0.844	0.796	0.892	1	0.995	1	CLONAL	2	FALSE	1	0.470940423163202	2		542	667	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427686	49427691	+	inframe_deletion	In_Frame_Del	DEL	TGCTGC	TGCTGC	-	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	194	707	0	ENST00000301067.7:c.10797_10802del	p.Gln3611_Gln3612del	p.Q3611_Q3612del	ENST00000301067	NM_003482.3	3599	caGCAGCAa/caa	39/54	0.453992579199631	1	FACETS	0.897	0.833	0.963	0.897	0.833	0.963	CLONAL	1	FALSE	0	0.470940423163202	1		707	702	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562352	21562352	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	242	842	0	ENST00000382592.4:c.1567C>A	p.Leu523Met	p.L523M	ENST00000382592	NM_014572.2	523	Ctg/Atg	4/8	0.470940423163202	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	0	0.470940423163202	1		842	738	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563029	21563029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770778568	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	257	917	0	ENST00000382592.4:c.890C>T	p.Pro297Leu	p.P297L	ENST00000382592	NM_014572.2	297	cCg/cTg	4/8	0.470940423163202	1	FACETS	0.961	0.902	1	0.961	0.902	1	CLONAL	1	FALSE	0	0.470940423163202	1		917	868	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900640	32900640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358747	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	114	435	0	ENST00000380152.3:c.521G>A	p.Arg174His	p.R174H	ENST00000380152		174	cGt/cAt	7/27	0.470940423163202	1	FACETS	0.947	0.86	1	0.947	0.86	1	CLONAL	1	FALSE	0	0.470940423163202	1		435	391	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914138	32914138	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	117	477	1	ENST00000380152.3:c.5650del	p.Ile1884PhefsTer25	p.I1884Ffs*25	ENST00000380152		1882	tcA/tc	11/27	0.470940423163202	1	FACETS	0.984	0.896	1	0.984	0.896	1	CLONAL	1	FALSE	0	0.470940423163202	1		478	386	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987126	36987127	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	524	849	0	ENST00000354822.5:c.562dup	p.Ser188LysfsTer251	p.S188Kfs*251	ENST00000354822	NM_001079668.2	188	agc/aAgc	3/3	1	2	FACETS	0.979	0.942	1	1	0.997	1	CLONAL	2	FALSE	1	0.470940423163202	2		849	1136	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034864	42034864	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	144	532	0	ENST00000219905.7:c.4706G>A	p.Ser1569Asn	p.S1569N	ENST00000219905	NM_001164273.1	1569	aGt/aAt	15/24	0.453992579199631	1	FACETS	0.853	0.782	0.927	0.853	0.782	0.927	CLONAL	1	FALSE	0	0.470940423163202	1		532	548	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244081	41244081	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	62	550	0	ENST00000357654.3:c.3467A>G	p.Asp1156Gly	p.D1156G	ENST00000357654	NM_007294.3	1156	gAt/gGt	10/23	0.453992579199631	1	FACETS	0.375	0.324	0.43	0.375	0.324	0.43	SUBCLONAL	1	FALSE	0	0.470940423163202	1		550	537	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400718	56400718	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	40	346	0	ENST00000348428.3:c.1312A>C	p.Asn438His	p.N438H	ENST00000348428	NM_006785.3	438	Aat/Cat	11/17	1	2	FACETS	0.331	0.275	0.394	0.331	0.275	0.394	SUBCLONAL	1	FALSE	1	0.470940423163202	2		346	513	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110605	4110605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756646033	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	448	847	0	ENST00000262948.5:c.352G>A	p.Glu118Lys	p.E118K	ENST00000262948	NM_030662.3	118	Gag/Aag	3/11	1	2	FACETS	0.965	0.925	1	1	0.997	1	CLONAL	2	FALSE	1	0.470940423163202	2		847	986	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223254	5223254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1407721470	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	237	939	1	ENST00000357368.4:c.2549C>T	p.Ala850Val	p.A850V	ENST00000357368	NM_002850.3	850	gCa/gTa	18/38	1	2	FACETS	0.908	0.847	0.971	0.908	0.847	0.971	CLONAL	1	FALSE	1	0.470940423163202	2		940	1109	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143085	30143085	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	483	950	0	ENST00000389048.3:c.441G>T	p.Glu147Asp	p.E147D	ENST00000389048	NM_004304.4	147	gaG/gaT	1/29	1	2	FACETS	0.934	0.896	0.972	1	0.997	1	CLONAL	2	FALSE	1	0.470940423163202	2		950	1098	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719800	190719800	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	61	286	0	ENST00000441310.2:c.1802C>T	p.Ala601Val	p.A601V	ENST00000441310	NM_000534.4	601	gCa/gTa	9/13	1	2	FACETS	0.989	0.862	1	0.989	0.862	1	CLONAL	1	FALSE	1	0.470940423163202	2		286	262	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538275	9538275	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	277	460	1	ENST00000353224.5:c.1723C>A	p.Leu575Ile	p.L575I	ENST00000353224	NM_177990.2	575	Ctc/Atc	7/10	0.453992579199631	1	FACETS	0.921	0.878	0.965	1	0.996	1	CLONAL	2	FALSE	0	0.470940423163202	1		461	488	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319054	62319054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	542	1102	0	ENST00000360203.5:c.1412G>A	p.Gly471Asp	p.G471D	ENST00000360203	NM_001283009.1	471	gGc/gAc	17/35	0.470940423163202	1	FACETS	0.95	0.919	0.982	1	0.998	1	CLONAL	2	FALSE	0	0.470940423163202	1		1102	926	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574058	41574058	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	63	647	0	ENST00000263253.7:c.6343C>T	p.Pro2115Ser	p.P2115S	ENST00000263253	NM_001429.3	2115	Cca/Tca	31/31	1	2	FACETS	0.313	0.27	0.36	0.313	0.27	0.36	SUBCLONAL	1	FALSE	1	0.470940423163202	2		647	854	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266951	41266951	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	120	493	2	ENST00000349496.5:c.622G>A	p.Val208Ile	p.V208I	ENST00000349496	NM_001904.3	208	Gta/Ata	5/15	0.453992579199631	1	FACETS	0.778	0.706	0.853	0.778	0.706	0.853	SUBCLONAL	1	FALSE	0	0.470940423163202	1		495	501	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72893531	72893531	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	23	511	0	ENST00000325599.8:c.187G>T	p.Gly63Trp	p.G63W	ENST00000325599	NM_018130.2	63	Ggg/Tgg	2/11	0.453992579199631	1	FACETS	0.164	0.128	0.207	0.164	0.128	0.207	SUBCLONAL	1	FALSE	0	0.470940423163202	1		511	454	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119634960	119634960	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	72	299	0	ENST00000316626.5:c.539G>A	p.Arg180Gln	p.R180Q	ENST00000316626		180	cGg/cAg	5/12	0.453992579199631	1	FACETS	0.74	0.652	0.833	0.74	0.652	0.833	SUBCLONAL	1	FALSE	0	0.470940423163202	1		299	316	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435666	149435667	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	84	790	0	ENST00000286301.3:c.2476_2477del	p.Ser826HisfsTer3	p.S826Hfs*3	ENST00000286301	NM_005211.3	826	AGc/c	19/22	NA	2	FACETS	0.381	0.335	0.43			1	INDETERMINATE	1	FALSE	NA	0.470940423163202	2		790	937	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271596	26271596	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	195	388	0	ENST00000305910.3:c.17A>G	p.Gln6Arg	p.Q6R	ENST00000305910	NM_003534.2	6	cAg/cGg	1/1	0.3993904231093	1	FACETS	0.918	0.866	0.969	1	0.994	1	CLONAL	2	FALSE	0	0.470940423163202	1		388	345	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680389	30680389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	231	611	2	ENST00000376406.3:c.1330C>T	p.Arg444Ter	p.R444*	ENST00000376406	NM_014641.2	444	Cga/Tga	5/15	0.453992579199631	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	0	0.470940423163202	1		613	665	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169923	32169923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	257	966	0	ENST00000375023.3:c.3685T>C	p.Cys1229Arg	p.C1229R	ENST00000375023	NM_004557.3	1229	Tgc/Cgc	21/30	0.453992579199631	1	FACETS	0.905	0.849	0.963	0.905	0.849	0.963	CLONAL	1	FALSE	0	0.470940423163202	1		966	922	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92244576	92244576	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	106	394	0	ENST00000265734.4:c.859A>G	p.Lys287Glu	p.K287E	ENST00000265734	NM_001259.6	287	Aaa/Gaa	8/8	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	1	0.470940423163202	2		394	433	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880172	151880172	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	27	442	0	ENST00000262189.6:c.5152del	p.Arg1718GlyfsTer23	p.R1718Gfs*23	ENST00000262189	NM_170606.2	1718	Agg/gg	35/59	0.44518964169368	1	FACETS	0.178	0.141	0.22	0.178	0.141	0.22	SUBCLONAL	1	FALSE	0	0.470940423163202	1		442	493	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194806	29194806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276207916	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	275	981	1	ENST00000240100.2:c.922G>A	p.Glu308Lys	p.E308K	ENST00000240100	NM_001394.6	308	Gag/Aag	4/4	1	2	FACETS	0.992	0.931	1	0.992	0.931	1	CLONAL	1	FALSE	1	0.470940423163202	2		982	1177	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740834	145740834	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	83	837	0	ENST00000428558.2:c.1266G>T	p.Glu422Asp	p.E422D	ENST00000428558	NM_004260.3	422	gaG/gaT	7/22	1	2	FACETS	0.342	0.301	0.386	0.342	0.301	0.386	SUBCLONAL	1	FALSE	1	0.470940423163202	2		837	1031	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970979	21970979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	104	762	0	ENST00000304494.5:c.379G>A	p.Ala127Thr	p.A127T	ENST00000304494	NM_000077.4	127	Gca/Aca	2/3	1	2	FACETS	0.42	0.375	0.468	0.42	0.375	0.468	SUBCLONAL	1	FALSE	1	0.470940423163202	2		762	1052	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239064	98239064	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554698260	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	97	458	0	ENST00000331920.6:c.1579C>T	p.Gln527Ter	p.Q527*	ENST00000331920	NM_000264.3	527	Cag/Tag	11/24	0.466399330690306	4	FACETS	0.752	0.67	0.839	0.251	0.223	0.28	SUBCLONAL	1	FALSE	1	0.470940423163202	4		458	806	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611079	100611079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	416	419	0	ENST00000308731.7:c.1527G>A	p.Met509Ile	p.M509I	ENST00000308731	NM_000061.2	509	atG/atA	15/19	1	1	FACETS	0.985	0.967	1	1	0.998	1	CLONAL	3	FALSE	0	0.470940423163202	1		419	457	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0050197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	85	352	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	0.868	0.769	0.973	0.868	0.769	0.973	CLONAL	1	TRUE	1	0.381018314076474	2		352	514	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758823	41758823	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	68	712	0	ENST00000301178.4:c.1877G>C	p.Gly626Ala	p.G626A	ENST00000301178	NM_021913.4	626	gGa/gCa	16/20	1	2	FACETS	0.357	0.309	0.409	0.357	0.309	0.409	SUBCLONAL	1	TRUE	1	0.381018314076474	2		712	1000	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426247	49426247	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1041469623	NA	P-0050197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	96	909	0	ENST00000301067.7:c.12241C>T	p.Gln4081Ter	p.Q4081*	ENST00000301067	NM_003482.3	4081	Cag/Tag	39/54	1	2	FACETS	0.42	0.373	0.471	0.42	0.373	0.471	SUBCLONAL	1	TRUE	1	0.381018314076474	2		909	1200	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250997	99250997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	77	519	0	ENST00000268035.6:c.301C>T	p.Pro101Ser	p.P101S	ENST00000268035	NM_000875.3	101	Ccc/Tcc	2/21	1	2	FACETS	0.497	0.436	0.564	0.497	0.436	0.564	SUBCLONAL	1	TRUE	1	0.381018314076474	2		519	813	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384826	17384826	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750288594	NA	P-0050197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	234	697	0	ENST00000359435.4:c.458C>T	p.Thr153Met	p.T153M	ENST00000359435	NM_001033549.1	153	aCg/aTg	4/9	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.381018314076474	2		697	1066	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356362	70356362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	46	633	0	ENST00000374080.3:c.5257G>A	p.Ala1753Thr	p.A1753T	ENST00000374080		1753	Gct/Act	37/45	0.359713167915279	1	FACETS	0.255	0.214	0.3	0.255	0.214	0.3	SUBCLONAL	1	TRUE	0	0.381018314076474	1		633	767	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0050198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	13	534	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.092	0.065	0.126	0.092	0.065	0.126	SUBCLONAL	1	TRUE	1	0.47215950376915	2		534	597	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238113	133238113	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	52	399	0	ENST00000320574.5:c.2864G>A	p.Arg955Lys	p.R955K	ENST00000320574	NM_006231.2	955	aGg/aAg	24/49	1	2	FACETS	0.729	0.625	0.842	0.729	0.625	0.842	SUBCLONAL	1	TRUE	1	0.47215950376915	2		399	302	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023107	33023107	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	85	527	0	ENST00000300177.4:c.216G>C	p.Glu72Asp	p.E72D	ENST00000300177	NM_001191322.1	72	gaG/gaC	2/2	1	2	FACETS	0.885	0.787	0.988	0.885	0.787	0.988	CLONAL	1	TRUE	1	0.47215950376915	2		527	407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578371	7578371	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs776167460	NA	P-0050198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	17	649	0	ENST00000269305.4:c.559G>A	p.Gly187Ser	p.G187S	ENST00000269305	NM_001126112.2	187	Ggt/Agt	5/11	0.45797707551097	1	FACETS	0.141	0.105	0.185	0.141	0.105	0.185	SUBCLONAL	1	TRUE	0	0.47215950376915	1		649	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	25	788	0	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.45797707551097	1	FACETS	0.141	0.11	0.176	0.141	0.11	0.176	SUBCLONAL	1	TRUE	0	0.47215950376915	1		788	574	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31495469	31495469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	95	465	0	ENST00000344624.3:c.1679C>T	p.Pro560Leu	p.P560L	ENST00000344624		560	cCc/cTc	9/33	1	2	FACETS	0.72	0.642	0.802	0.72	0.642	0.802	SUBCLONAL	1	TRUE	1	0.47215950376915	2		465	559	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242481	+	inframe_deletion	In_Frame_Del	DEL	AATTAAGAGAAGCAA	AATTAAGAGAAGCAA	-	rs121913425	NA	P-0050198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	103	439	0	ENST00000275493.2:c.2237_2251del	p.Glu746_Thr751delinsAla	p.E746_T751delinsA	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAAca/gca	19/28	0.266453077423258	5	FACETS	1	0.982	1	0.493	0.443	0.546	INDETERMINATE	1	TRUE	2	0.47215950376915	5		439	504	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006898	47006898	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1556762493	NA	P-0050198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	179	719	0	ENST00000377604.3:c.17+1G>T		p.X6_splice	ENST00000377604	NM_001204468.1	6			NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.47215950376915	2		719	566	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100069	27100070	+	splice_acceptor_variant	Splice_Site	DNP	AG	AG	TT	novel	NA	P-0050198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	37	699	0	ENST00000324856.7:c.3867-2_3867-1delinsTT		p.X1289_splice	ENST00000324856	NM_006015.4	1289			1	2	FACETS	0.288	0.236	0.345	0.288	0.236	0.345	SUBCLONAL	1	TRUE	1	0.47215950376915	2		699	545	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	29	413	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.197	0.158	0.242	0.197	0.158	0.242	SUBCLONAL	1	TRUE	1	0.66	2		413	446	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs28934577	NA	P-0050199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	48	626	0	ENST00000269305.4:c.770T>G	p.Leu257Arg	p.L257R	ENST00000269305	NM_001126112.2	257	cTg/cGg	7/11	1	2	FACETS	0.246	0.207	0.288	0.246	0.207	0.288	SUBCLONAL	1	TRUE	1	0.66	2		626	592	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231286	46231286	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	22	327	0	ENST00000334344.6:c.1126G>T	p.Glu376Ter	p.E376*	ENST00000334344	NM_152641.2	376	Gaa/Taa	10/21	1	2	FACETS	0.255	0.198	0.322	0.255	0.198	0.322	SUBCLONAL	1	TRUE	1	0.66	2		327	261	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494933	56494933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	50	600	0	ENST00000267101.3:c.3290C>T	p.Ser1097Leu	p.S1097L	ENST00000267101	NM_001982.3	1097	tCa/tTa	27/28	1	2	FACETS	0.255	0.216	0.298	0.255	0.216	0.298	SUBCLONAL	1	TRUE	1	0.66	2		600	595	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782233	56782233	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	50	538	0	ENST00000308159.5:c.74A>G	p.Glu25Gly	p.E25G	ENST00000308159	NM_014669.4	25	gAg/gGg	2/22	1	2	FACETS	0.288	0.244	0.336	0.288	0.244	0.336	SUBCLONAL	1	TRUE	1	0.66	2		538	526	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648394	30648395	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0050199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	29	564	0	ENST00000295754.5:c.23dup	p.Leu9ProfsTer25	p.L9Pfs*25	ENST00000295754	NM_003242.5	7	agg/aGgg	1/7	1	2	FACETS	0.209	0.167	0.256	0.209	0.167	0.256	SUBCLONAL	1	TRUE	1	0.66	2		564	421	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188200	10188200	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	184	433	0	ENST00000256474.2:c.343C>A	p.His115Asn	p.H115N	ENST00000256474	NM_000551.3	115	Cac/Aac	2/3	0.628480145320433	1	FACETS	0.989	0.925	1	0.989	0.925	1	CLONAL	1	TRUE	0	0.628480145320433	1		433	406	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597493	52597493	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	89	320	0	ENST00000394830.3:c.3817C>T	p.Gln1273Ter	p.Q1273*	ENST00000394830	NM_018313.4	1273	Cag/Tag	25/30	0.628480145320433	1	FACETS	0.891	0.806	0.978	0.891	0.806	0.978	CLONAL	1	TRUE	0	0.628480145320433	1		320	218	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197269	106197269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780808372	NA	P-0050200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	136	295	0	ENST00000380013.4:c.5602C>T	p.His1868Tyr	p.H1868Y	ENST00000380013	NM_001127208.2	1868	Cat/Tat	11/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.628480145320433	2		295	393	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156557	106156560	+	frameshift_variant	Frame_Shift_Del	DEL	CAGG	CAGG	-	novel	NA	P-0050200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	106	282	0	ENST00000380013.4:c.1458_1461del	p.Asn486LysfsTer10	p.N486Kfs*10	ENST00000380013	NM_001127208.2	486	aaCAGG/aa	3/11	1	2	FACETS	0.874	0.79	0.961	0.874	0.79	0.961	CLONAL	1	TRUE	1	0.628480145320433	2		282	386	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	234	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.234798534121117	4	FACETS	1	0.966	1			1	CLONAL	4	TRUE	NA	0.264901127511709	4		327	539	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494603	2494603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	110	562	2	ENST00000355716.4:c.743C>T	p.Ala248Val	p.A248V	ENST00000355716	NM_003820.2	248	gCa/gTa	8/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.264901127511709	2		564	674	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	94	468	0				ENST00000310581	NM_198253.2	-/1132			0.272607909355693	1	FACETS	0.645	0.579	0.713	0.645	0.579	0.713	INDETERMINATE	1	TRUE	0	0.616784797709892	1		468	327	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0050202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	196	822	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.345620533006609	1	FACETS	0.802	0.748	0.857	0.802	0.748	0.857	INDETERMINATE	1	TRUE	0	0.616784797709892	1		822	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0050202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	221	604	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.937	0.875	1	0.937	0.875	1	CLONAL	1	TRUE	1	0.616784797709892	2		604	765	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856020	68856020	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	108	526	0	ENST00000261769.5:c.1828C>T	p.Gln610Ter	p.Q610*	ENST00000261769	NM_004360.3	610	Cag/Tag	12/16	0.272607909355693	1	FACETS	0.473	0.426	0.522	0.473	0.426	0.522	INDETERMINATE	1	TRUE	0	0.616784797709892	1		526	512	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720803	89720804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs786204892	NA	P-0050202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	97	220	0	ENST00000371953.3:c.955dup	p.Thr319AsnfsTer6	p.T319Nfs*6	ENST00000371953	NM_000314.4	318	-/A	8/9	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.616784797709892	2		220	218	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436599	49436599	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886041405	NA	P-0050202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	217	691	0	ENST00000301067.7:c.5707C>T	p.Arg1903Ter	p.R1903*	ENST00000301067	NM_003482.3	1903	Cga/Tga	26/54	1	2	FACETS	0.891	0.83	0.953	0.891	0.83	0.953	CLONAL	1	TRUE	1	0.616784797709892	2		691	790	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790170	40790170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373191879	NA	P-0050202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	125	423	0	ENST00000373198.4:c.2561G>A	p.Arg854His	p.R854H	ENST00000373198	NM_133170.3	854	cGc/cAc	18/32	1	2	FACETS	0.897	0.817	0.979	0.897	0.817	0.979	CLONAL	1	TRUE	1	0.616784797709892	2		423	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577553	7577554	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCAGGAACTGTTACACATGTAGT	novel	NA	P-0050202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	132	567	0	ENST00000269305.4:c.704_727dup	p.Asn235_Cys242dup	p.N235_C242dup	ENST00000269305	NM_001126112.2	235	atg/aACTACATGTGTAACAGTTCCTGCAtg	7/11	1	2	FACETS	0.614	0.558	0.673	0.614	0.558	0.673	SUBCLONAL	1	TRUE	1	0.616784797709892	2		567	697	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808914	1808925	+	inframe_deletion	In_Frame_Del	DEL	CTCAGGGGACGA	CTCAGGGGACGA	-	novel	NA	P-0050202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	246	848	0	ENST00000260795.2:c.2349_2360del	p.Gly784_Ser787del	p.G784_S787del	ENST00000260795		782	tcCTCAGGGGACGAc/tcc	17/17	0.345620533006609	1	FACETS	0.837	0.787	0.888	0.837	0.787	0.888	INDETERMINATE	1	TRUE	0	0.616784797709892	1		848	659	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509679	106509679	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	179	481	0	ENST00000359195.3:c.1673T>A	p.Ile558Asn	p.I558N	ENST00000359195	NM_002649.2	558	aTc/aAc	2/11	0.202554085181532	3	FACETS	1	0.987	1	0.658	0.61	0.707	INDETERMINATE	1	TRUE	1	0.616784797709892	3		481	577	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328427	137328428	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATA	novel	NA	P-0050202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	263	902	0	ENST00000481739.1:c.1356_1357insATA	p.Met452_Glu453insIle	p.M452_E453insI	ENST00000481739	NM_002957.4	452	-/ATA	10/10	0.616784797709892	1	FACETS	0.998	0.944	1	0.998	0.944	1	CLONAL	1	TRUE	0	0.616784797709892	1		902	591	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629147	14629149	+	missense_variant	Missense_Mutation	TNP	GTA	GTA	CTG	novel	NA	P-0050202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	145	434	0	ENST00000254322.2:c.13_15delinsCAG	p.Tyr5Gln	p.Y5Q	ENST00000254322	NM_006145.1	5	TAC/CAG	1/3	1	2	FACETS	0.942	0.865	1	0.942	0.865	1	CLONAL	1	TRUE	1	0.616784797709892	2		434	499	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0050205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	87	349	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		349	562	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	65	468	0				ENST00000310581	NM_198253.2	-/1132			0.260461351533174	3	FACETS	0.783	0.683	0.891	0.783	0.683	0.891	SUBCLONAL	2	FALSE	1	0.260461351533174	3		468	360	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912174	29912174	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	rs199474643	NA	P-0050206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	27	188	0	ENST00000376809.5:c.895G>T	p.Glu299Ter	p.E299*	ENST00000376809	NM_002116.7	299	Gag/Tag	4/8	1	2	FACETS	0.864	0.69	1	0.864	0.69	1	CLONAL	1	FALSE	1	0.260461351533174	2		188	240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	174	738	0	ENST00000269305.4:c.476C>A	p.Ala159Asp	p.A159D	ENST00000269305	NM_001126112.2	159	gCc/gAc	5/11	0.260461351533174	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	0	0.260461351533174	1		738	813	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855787	45855787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	88	707	0	ENST00000391945.4:c.2023G>T	p.Gly675Cys	p.G675C	ENST00000391945	NM_000400.3	675	Ggc/Tgc	21/23	0.183564711368032	1	FACETS	0.881	0.781	0.988	0.881	0.781	0.988	CLONAL	1	FALSE	0	0.260461351533174	1		707	667	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40742005	40742005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	126	636	0	ENST00000392038.2:c.967G>A	p.Glu323Lys	p.E323K	ENST00000392038	NM_001626.4	323	Gag/Aag	11/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.260461351533174	2		636	737	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197474	26197474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	47	309	1	ENST00000356476.2:c.5C>T	p.Ala2Val	p.A2V	ENST00000356476		2	gCt/gTt	1/1	1	2	FACETS	0.889	0.752	1	0.889	0.752	1	CLONAL	1	FALSE	1	0.260461351533174	2		310	406	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258257	16258257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	58	527	0	ENST00000375759.3:c.5522C>G	p.Thr1841Arg	p.T1841R	ENST00000375759	NM_015001.2	1841	aCa/aGa	11/15	1	2	FACETS	0.694	0.595	0.801	0.694	0.595	0.801	SUBCLONAL	1	FALSE	1	0.260461351533174	2		527	642	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342482	118342482	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	89	196	0	ENST00000534358.1:c.608A>C	p.Glu203Ala	p.E203A	ENST00000534358	NM_005933.3	203	gAg/gCg	3/36	0.260461351533174	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	FALSE	0	0.260461351533174	2		196	305	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863199	57863275	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCATCTTCTCCACAGAAGCCACAGCCAAGCCCTGGGGCCCAGTCATCCTGCAGCAGTGACCACTCCCCGGCAGGGAG	TCATCTTCTCCACAGAAGCCACAGCCAAGCCCTGGGGCCCAGTCATCCTGCAGCAGTGACCACTCCCCGGCAGGGAG	-	novel	NA	P-0050206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	57	386	0	ENST00000228682.2:c.1309-14_1371del		p.X437_splice	ENST00000228682	NM_005269.2	437		11/12	1	2	FACETS	0.862	0.74	0.994	0.862	0.74	0.994	CLONAL	1	FALSE	1	0.260461351533174	2		386	508	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103510629	103510629	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1458700366	NA	P-0050206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	40	246	0	ENST00000355739.4:c.533A>G	p.Glu178Gly	p.E178G	ENST00000355739	NM_000123.3	178	gAg/gGg	6/15	1	2	FACETS	0.828	0.689	0.981	0.828	0.689	0.981	CLONAL	1	FALSE	1	0.260461351533174	2		246	371	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47607056	47607056	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs764624596	NA	P-0050206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	68	463	0	ENST00000263735.4:c.806T>C	p.Ile269Thr	p.I269T	ENST00000263735	NM_002354.2	269	aTt/aCt	7/9	1	2	FACETS	0.835	0.727	0.953	0.835	0.727	0.953	CLONAL	1	FALSE	1	0.260461351533174	2		463	625	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165062	47165062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	58	278	0	ENST00000409792.3:c.1064C>T	p.Ser355Leu	p.S355L	ENST00000409792	NM_014159.6	355	tCa/tTa	3/21	1	2	FACETS	0.975	0.839	1	0.975	0.839	1	CLONAL	1	FALSE	1	0.260461351533174	2		278	457	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439194	52439194	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	85	701	2	ENST00000460680.1:c.1048C>A	p.Pro350Thr	p.P350T	ENST00000460680	NM_004656.3	350	Ccc/Acc	11/17	1	2	FACETS	0.825	0.729	0.929	0.825	0.729	0.929	CLONAL	1	FALSE	1	0.260461351533174	2		703	791	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253741	153253755	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCTTACCCTCTTCT	ACCTTACCCTCTTCT	-	novel	NA	P-0050206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	38	270	0	ENST00000281708.4:c.978_985+7del		p.X326_splice	ENST00000281708	NM_033632.3	326		6/12	1	2	FACETS	0.724	0.599	0.863	0.724	0.599	0.863	SUBCLONAL	1	FALSE	1	0.260461351533174	2		270	403	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253760	153253780	+	inframe_deletion	In_Frame_Del	DEL	ATTTCTCTCTCCAGAGAAGGT	ATTTCTCTCTCCAGAGAAGGT	-	novel	NA	P-0050206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	45	303	0	ENST00000281708.4:c.953_973del	p.Asn318_Cys325delinsSer	p.N318_C325delinsS	ENST00000281708	NM_033632.3	318	aACCTTCTCTGGAGAGAGAAATgc/agc	6/12	1	2	FACETS	0.731	0.614	0.859	0.731	0.614	0.859	SUBCLONAL	1	FALSE	1	0.260461351533174	2		303	473	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	231007	231007	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	108	675	0	ENST00000264932.6:c.787T>C	p.Tyr263His	p.Y263H	ENST00000264932	NM_004168.2	263	Tac/Cac	7/15	1	2	FACETS	0.946	0.848	1	0.946	0.848	1	CLONAL	1	FALSE	1	0.260461351533174	2		675	877	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858285	27858285	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	105	612	2	ENST00000359303.2:c.286G>T	p.Ala96Ser	p.A96S	ENST00000359303	NM_003535.2	96	Gcg/Tcg	1/1	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	FALSE	1	0.260461351533174	2		614	789	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033970	49033970	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0050207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	722	359	0	ENST00000267163.4:c.2106+1G>T		p.X702_splice	ENST00000267163	NM_000321.2	702			0.729936889090353	6	FACETS	0.93	0.914	0.945	0.93	0.914	0.945	CLONAL	6	TRUE	0	0.814420904673398	6		359	835	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984893	101984893	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs747656585	NA	P-0050207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	293	518	0	ENST00000282441.5:c.340A>T	p.Thr114Ser	p.T114S	ENST00000282441	NM_001130145.2	114	Act/Tct	2/9	0.647909116300082	4	FACETS	0.95	0.9	1	0.95	0.9	1	CLONAL	2	TRUE	2	0.814420904673398	4		518	687	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100481	102100481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	271	477	0	ENST00000282441.5:c.1325C>T	p.Pro442Leu	p.P442L	ENST00000282441	NM_001130145.2	442	cCa/cTa	9/9	0.647909116300082	4	FACETS	0.883	0.833	0.933	0.883	0.833	0.933	CLONAL	2	TRUE	2	0.814420904673398	4		477	684	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427272	427272	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	260	478	0	ENST00000399788.2:c.2897G>T	p.Arg966Ile	p.R966I	ENST00000399788	NM_001042603.1	966	aGa/aTa	19/28	0.745107841316588	3	FACETS	0.886	0.84	0.932	0.886	0.84	0.932	CLONAL	2	TRUE	1	0.814420904673398	3		478	507	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563083	21563092	+	frameshift_variant	Frame_Shift_Del	DEL	GTCTTGCTCT	GTCTTGCTCT	-	novel	NA	P-0050207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	685	945	0	ENST00000382592.4:c.827_836del	p.Gln276ArgfsTer154	p.Q276Rfs*154	ENST00000382592	NM_014572.2	276	cAGAGCAAGACg/cg	4/8	0.729936889090353	6	FACETS	0.969	0.936	1	0.484	0.468	0.501	CLONAL	3	TRUE	0	0.814420904673398	6		945	1522	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738705	43738705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	354	602	0	ENST00000382044.4:c.2920G>A	p.Gly974Arg	p.G974R	ENST00000382044	NM_001141980.1	974	Ggg/Agg	14/28	0.708690496677534	2	FACETS	0.907	0.877	0.936	0.907	0.877	0.936	CLONAL	2	TRUE	0	0.814420904673398	2		602	479	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343542	343542	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	189	821	1	ENST00000262320.3:c.2132G>T	p.Arg711Leu	p.R711L	ENST00000262320	NM_003502.3	711	cGc/cTc	8/11	0.814420904673398	3	FACETS	0.915	0.848	0.983	0.457	0.424	0.492	CLONAL	1	TRUE	1	0.814420904673398	3		822	714	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490313	29490313	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	301	499	0	ENST00000356175.3:c.398A>G	p.Glu133Gly	p.E133G	ENST00000356175	NM_000267.3	133	gAa/gGa	4/57	0.703367111179908	4	FACETS	0.925	0.877	0.974	0.462	0.438	0.487	CLONAL	2	TRUE	0	0.814420904673398	4		499	725	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791163	42791163	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	395	866	0	ENST00000575354.2:c.223G>C	p.Ala75Pro	p.A75P	ENST00000575354	NM_015125.3	75	Gct/Cct	3/20	0.647909116300082	4	FACETS	0.937	0.895	0.98	0.937	0.895	0.98	CLONAL	2	TRUE	2	0.814420904673398	4		866	939	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576821	212576821	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	128	455	0	ENST00000342788.4:c.1078A>G	p.Thr360Ala	p.T360A	ENST00000342788	NM_005235.2	360	Acc/Gcc	9/28	0.760606171131519	3	FACETS	0.918	0.837	1	0.459	0.418	0.501	CLONAL	1	TRUE	1	0.814420904673398	3		455	482	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161408	55161408	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	137	457	0	ENST00000257290.5:c.3239C>G	p.Ser1080Cys	p.S1080C	ENST00000257290	NM_006206.4	1080	tCt/tGt	23/23	0.802775169180507	3	FACETS	0.85	0.777	0.926	0.425	0.388	0.463	CLONAL	1	TRUE	1	0.814420904673398	3		457	557	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710887	117710887	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	162	449	1	ENST00000368508.3:c.1385C>A	p.Pro462Gln	p.P462Q	ENST00000368508	NM_002944.2	462	cCa/cAa	12/43	0.745107841316588	3	FACETS	1	0.981	1	0.589	0.545	0.635	CLONAL	1	TRUE	1	0.814420904673398	3		450	475	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266491	55266491	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	183	582	0	ENST00000275493.2:c.2783A>T	p.Glu928Val	p.E928V	ENST00000275493	NM_005228.3	928	gAg/gTg	23/28	0.745107841316588	3	FACETS	0.973	0.902	1	0.486	0.451	0.523	CLONAL	1	TRUE	1	0.814420904673398	3		582	650	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021726	69021726	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	348	462	0	ENST00000288368.4:c.3014A>T	p.Gln1005Leu	p.Q1005L	ENST00000288368	NM_024870.2	1005	cAg/cTg	25/40	0.647909116300082	4	FACETS	0.967	0.92	1	0.967	0.92	1	CLONAL	2	TRUE	2	0.814420904673398	4		462	802	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579579	7579580	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	A	novel	NA	P-0050207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	645	709	0	ENST00000269305.4:c.107_108delinsT	p.Pro36LeufsTer8	p.P36Lfs*8	ENST00000269305	NM_001126112.2	36	cCG/cT	4/11	0.703367111179908	4	FACETS	0.924	0.905	0.941	0.924	0.905	0.941	CLONAL	4	TRUE	0	0.814420904673398	4		709	778	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378351	225378351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	102	204	1	ENST00000264414.4:c.544G>A	p.Ala182Thr	p.A182T	ENST00000264414	NM_003590.4	182	Gca/Aca	5/16	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.594052302058009	2		205	338	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825602	50825602	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0050208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	129	316	0	ENST00000398568.2:c.2232+1G>T		p.X744_splice	ENST00000398568	NM_001042412.1	744			0.594052302058009	1	FACETS	0.877	0.806	0.951	0.877	0.806	0.951	CLONAL	1	TRUE	0	0.594052302058009	1		316	348	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880997	37880998	+	protein_altering_variant	In_Frame_Ins	INS	-	-	TAT	novel	NA	P-0050208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	663	787	0	ENST00000269571.5:c.2326_2327insTAT	p.Gly776delinsValCys	p.G776delinsVC	ENST00000269571		776	ggt/gTATgt	20/27	0.594052302058009	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.594052302058009	3		787	1443	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577330	64577333	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	rs587776841	NA	P-0050209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	287	568	0	ENST00000312049.6:c.249_252del	p.Ile85SerfsTer33	p.I85Sfs*33	ENST00000312049	NM_130799.2	83	ctGTCT/ct	2/10	0.726607141122695	1	FACETS	0.96	0.914	1	0.96	0.914	1	CLONAL	1	TRUE	0	0.726607141122695	1		568	524	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73047270	73047270	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	143	356	0	ENST00000356692.5:c.77A>G	p.Asp26Gly	p.D26G	ENST00000356692		26	gAt/gGt	2/9	0.726607141122695	1	FACETS	0.822	0.762	0.881	0.822	0.762	0.881	CLONAL	1	TRUE	0	0.726607141122695	1		356	305	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888797	76888797	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	210	260	0	ENST00000373344.5:c.5032G>T	p.Val1678Phe	p.V1678F	ENST00000373344	NM_000489.3	1678	Gtt/Ttt	19/35	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.726607141122695	1		260	291	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0050212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	184	481	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.404366610540217	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.404366610540217	1		481	677	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098957	178098957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	52	238	0	ENST00000397062.3:c.88C>T	p.Leu30Phe	p.L30F	ENST00000397062	NM_006164.4	30	Ctt/Ttt	2/5	1	2	FACETS	0.641	0.547	0.744	0.641	0.547	0.744	SUBCLONAL	1	TRUE	1	0.404366610540217	2		238	401	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222001	1222001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	170	643	1	ENST00000326873.7:c.916C>T	p.His306Tyr	p.H306Y	ENST00000326873	NM_000455.4	306	Cac/Tac	7/10	0.404366610540217	1	FACETS	0.886	0.817	0.958	0.886	0.817	0.958	CLONAL	1	TRUE	0	0.404366610540217	1		644	757	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628610	90628610	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	188	726	0	ENST00000330062.3:c.977C>T	p.Ser326Phe	p.S326F	ENST00000330062	NM_002168.2	326	tCc/tTc	8/11	1	2	FACETS	0.908	0.839	0.98	0.908	0.839	0.98	CLONAL	1	TRUE	1	0.404366610540217	2		726	1024	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352535	118352535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	98	449	0	ENST00000534358.1:c.3740C>T	p.Ser1247Leu	p.S1247L	ENST00000534358	NM_005933.3	1247	tCa/tTa	7/36	0.389266591863815	3	FACETS	0.687	0.612	0.767			1	SUBCLONAL	1	TRUE	NA	0.404366610540217	3		449	848	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944592	40944592	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	70	329	0	ENST00000373198.4:c.1910G>C	p.Arg637Pro	p.R637P	ENST00000373198	NM_133170.3	637	cGg/cCg	12/32	0.151340408825815	0	FACETS	0.517	0.453	0.586			1	INDETERMINATE	1	TRUE	0	0.404366610540217	0		329	399	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431650	6431650	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050214-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	92	528	0	ENST00000356142.4:c.203G>C	p.Arg68Pro	p.R68P	ENST00000356142	NM_018890.3	68	cGc/cCc	3/7	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.227414819650862	2		528	713	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579408	7579460	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTG	CAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTG	-	rs1555526610	NA	P-0050215-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	486	716	0	ENST00000269305.4:c.227_279del	p.Ala76ValfsTer55	p.A76Vfs*55	ENST00000269305	NM_001126112.2	76	gCACCAGCAGCTCCTACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTG/g	4/11	0.760668741132415	2	FACETS	0.945	0.917	0.972	0.945	0.917	0.972	CLONAL	2	TRUE	0	0.760668741132415	2		716	676	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144114	11144114	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050215-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	268	698	0	ENST00000358026.2:c.3695G>A	p.Gly1232Asp	p.G1232D	ENST00000358026	NM_001128849.1	1232	gGc/gAc	26/36	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.760668741132415	2		698	693	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879582	37879604	+	missense_variant	Missense_Mutation	ONP	TCCATCATCTCTGCGGTGGTTGG	TCCATCATCTCTGCGGTGGTTGG	ACCAGCAGAATGCCAACCACCGC	novel	NA	P-0050215-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	480	641	0	ENST00000269571.5:c.1957_1979delinsACCAGCAGAATGCCAACCACCGC	p.Ser653_Gly660delinsThrSerArgMetProThrThrAla	p.S653_G660delinsTSRMPTTA	ENST00000269571		653	TCCATCATCTCTGCGGTGGTTGGc/ACCAGCAGAATGCCAACCACCGCc	17/27	0.760668741132415	8	FACETS	0.97	0.931	1			1	CLONAL	4	TRUE	NA	0.760668741132415	8		641	1067	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134254	11134254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050215-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	214	630	0	ENST00000358026.2:c.2920C>T	p.Pro974Ser	p.P974S	ENST00000358026	NM_001128849.1	974	Ccc/Tcc	20/36	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.760668741132415	2		630	559	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0050216-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	857	457	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.416748107311528	12	FACETS	0.973	0.947	0.998	0.796	0.775	0.817	CLONAL	9	TRUE	1	0.416748107311528	12		457	1449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0050216-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	259	913	0	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.394266769042121	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.416748107311528	1		913	875	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302894	15302894	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050216-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	229	1070	0	ENST00000263388.2:c.556C>A	p.Pro186Thr	p.P186T	ENST00000263388	NM_000435.2	186	Cca/Aca	4/33	0.394266769042121	1	FACETS	0.991	0.925	1	0.991	0.925	1	CLONAL	1	TRUE	0	0.416748107311528	1		1070	878	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211897	36211897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050216-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	225	887	0	ENST00000222270.7:c.1648G>A	p.Asp550Asn	p.D550N	ENST00000222270	NM_014727.1	550	Gac/Aac	3/37	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.416748107311528	2		887	1023	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911560	131911560	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050216-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	217	390	0	ENST00000265335.6:c.305G>T	p.Cys102Phe	p.C102F	ENST00000265335		102	tGt/tTt	3/25	0.379407435911585	3	FACETS	0.881	0.823	0.941	0.881	0.823	0.941	CLONAL	2	TRUE	1	0.416748107311528	3		390	714	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524762	137524768	+	protein_altering_variant	In_Frame_Del	DEL	CTAACTG	CTAACTG	T	novel	NA	P-0050216-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	105	416	0	ENST00000367739.4:c.601_607delinsA	p.Gln201_Ala203delinsThr	p.Q201_A203delinsT	ENST00000367739	NM_000416.2	201	CAGTTAGcg/Acg	5/7	0.379407435911585	3	FACETS	0.838	0.751	0.93	0.419	0.375	0.465	CLONAL	1	TRUE	1	0.416748107311528	3		416	727	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0050227-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2291	142	542	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.749313986609082	8	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.13	8		542	2433	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712598	52712598	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	43	380	0	ENST00000394830.3:c.154G>T	p.Glu52Ter	p.E52*	ENST00000394830	NM_018313.4	52	Gaa/Taa	3/30	0.239445094731089	1	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	0	0.239445094731089	1		380	313	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183708	10183717	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCCCGTG	GCGGCCCGTG	-	novel	NA	P-0050228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	130	926	0	ENST00000256474.2:c.177_186del	p.Arg60CysfsTer4	p.R60Cfs*4	ENST00000256474	NM_000551.3	59	ccGCGGCCCGTG/cc	1/3	0.239445094731089	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.239445094731089	1		926	643	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	43	468	0				ENST00000310581	NM_198253.2	-/1132			0.478502485811213	1	FACETS	0.668	0.566	0.778	0.668	0.566	0.778	SUBCLONAL	1	TRUE	0	0.498346914076361	1		468	194	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0050229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	134	280	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	NA	2	FACETS	0.872	0.794	0.952			1	INDETERMINATE	1	TRUE	NA	0.498346914076361	2		280	617	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864656	37864656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs950730453	NA	P-0050229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	141	575	1	ENST00000269571.5:c.308G>A	p.Arg103Gln	p.R103Q	ENST00000269571		103	cGa/cAa	3/27	0.216186762330994	4	FACETS	1	0.981	1	0.632	0.577	0.689	INDETERMINATE	1	TRUE	2	0.498346914076361	4		576	671	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374334	15374334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201883209	NA	P-0050229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	49	184	0	ENST00000263377.2:c.1238G>A	p.Arg413His	p.R413H	ENST00000263377	NM_058243.2	413	cGt/cAt	7/20	1	2	FACETS	0.361	0.306	0.423	0.361	0.306	0.423	SUBCLONAL	1	TRUE	1	0.498346914076361	2		184	544	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226354	41226354	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs80356906	NA	P-0050229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	37	123	0	ENST00000357654.3:c.4669G>T	p.Asp1557Tyr	p.D1557Y	ENST00000357654	NM_007294.3	1557	Gat/Tat	14/23	1	2	FACETS	0.306	0.251	0.366	0.306	0.251	0.366	SUBCLONAL	1	TRUE	1	0.498346914076361	2		123	486	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20152125	20152125	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	31	45	0	ENST00000379607.5:c.205G>T	p.Val69Phe	p.V69F	ENST00000379607	NM_001412.3	69	Gtt/Ttt	4/7	1	1	FACETS	0.404	0.329	0.489	0.404	0.329	0.489	SUBCLONAL	1	TRUE	0	0.498346914076361	1		45	231	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966653	44966654	+	splice_acceptor_variant	Splice_Site	INS	-	-	G	novel	NA	P-0050229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	43	42	0	ENST00000377967.4:c.3879dup		p.X1293_splice	ENST00000377967	NM_021140.2	1293			1	1	FACETS	0.919	0.785	1	0.919	0.785	1	CLONAL	1	TRUE	0	0.498346914076361	1		42	141	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0050230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	178	411	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.491980196156959	3	FACETS	0.777	0.72	0.836	0.777	0.72	0.836	SUBCLONAL	2	TRUE	1	0.491980196156959	3		411	580	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0050230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	20	280	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.211	0.161	0.27	0.211	0.161	0.27	SUBCLONAL	1	TRUE	1	0.491980196156959	2		280	385	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642470	117642470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765146445	NA	P-0050230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	85	588	0	ENST00000368508.3:c.5729G>A	p.Arg1910Gln	p.R1910Q	ENST00000368508	NM_002944.2	1910	cGa/cAa	35/43	1	2	FACETS	0.42	0.371	0.474	0.42	0.371	0.474	SUBCLONAL	1	TRUE	1	0.491980196156959	2		588	822	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134306	11134306	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	142	507	0	ENST00000358026.2:c.2972A>C	p.Lys991Thr	p.K991T	ENST00000358026	NM_001128849.1	991	aAg/aCg	20/36	0.491980196156959	1	FACETS	0.847	0.776	0.92	0.847	0.776	0.92	CLONAL	1	TRUE	0	0.491980196156959	1		507	514	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625302	69625302	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782573423	NA	P-0050230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	199	886	2	ENST00000334134.2:c.491G>A	p.Arg164His	p.R164H	ENST00000334134	NM_005247.2	164	cGc/cAc	3/3	1	2	FACETS	0.951	0.882	1	0.951	0.882	1	CLONAL	1	TRUE	1	0.491980196156959	2		888	851	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244882	41244882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769712441	NA	P-0050230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	120	467	0	ENST00000357654.3:c.2666C>T	p.Ser889Phe	p.S889F	ENST00000357654	NM_007294.3	889	tCt/tTt	10/23	1	2	FACETS	0.825	0.748	0.907	0.825	0.748	0.907	CLONAL	1	TRUE	1	0.491980196156959	2		467	591	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152079	11152080	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0050230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	39	500	0	ENST00000358026.2:c.4367dup	p.Thr1457AspfsTer30	p.T1457Dfs*30	ENST00000358026	NM_001128849.1	1455	acc/aCcc	31/36	0.491980196156959	1	FACETS	0.244	0.202	0.291	0.244	0.202	0.291	SUBCLONAL	1	TRUE	0	0.491980196156959	1		500	490	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881440	37881440	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	99	733	0	ENST00000269571.5:c.2632C>T	p.His878Tyr	p.H878Y	ENST00000269571		878	Cat/Tat	21/27	0.314414514399528	3	FACETS	1	0.954	1	0.728	0.659	0.8	CLONAL	2	TRUE	0	0.361379210341734	3		733	296	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579321	7579322	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs587780067	NA	P-0050231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	79	726	0	ENST00000269305.4:c.365_366del	p.Val122AspfsTer26	p.V122Dfs*26	ENST00000269305	NM_001126112.2	122	gTG/g	4/11	0.361379210341734	3	FACETS	0.967	0.861	1	0.967	0.861	1	CLONAL	2	TRUE	1	0.361379210341734	3		726	267	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786752	3786752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519207	NA	P-0050231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	59	624	3	ENST00000262367.5:c.4459C>T	p.His1487Tyr	p.H1487Y	ENST00000262367	NM_004380.2	1487	Cac/Tac	27/31	1	2	FACETS	0.793	0.692	0.898	1	0.974	1	SUBCLONAL	2	TRUE	1	0.361379210341734	2		627	206	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418693	49418964	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATGGCAGCCACAGGCTCAATGATGCGATTCCACACGGCTAAGAAGCAGGGAAGAGAGCAGTCCTCAGAGGCAACTTCTGCTCACTGACCTCCAGTCCCTAACCCCAATCCAGAACTGCAGTTTTCTGAGGCCTTCAAGCCTCCCTATCATGAAGTTGTGTTGGTCTTCCAGATCCTCTCTTGGCCTCCTAGTCTCACTCTCTCTTAAGAAGCAGGAGGTTTCCAACCCCAAGGGGTCATCACAGAGCCTTGAGATACAAACCCAGGGCCCAG	ATGGCAGCCACAGGCTCAATGATGCGATTCCACACGGCTAAGAAGCAGGGAAGAGAGCAGTCCTCAGAGGCAACTTCTGCTCACTGACCTCCAGTCCCTAACCCCAATCCAGAACTGCAGTTTTCTGAGGCCTTCAAGCCTCCCTATCATGAAGTTGTGTTGGTCTTCCAGATCCTCTCTTGGCCTCCTAGTCTCACTCTCTCTTAAGAAGCAGGAGGTTTCCAACCCCAAGGGGTCATCACAGAGCCTTGAGATACAAACCCAGGGCCCAG	-	novel	NA	P-0050231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	24	611	0	ENST00000301067.7:c.15785-235_15821del		p.X5262_splice	ENST00000301067	NM_003482.3	5262		49/54	0.361379210341734	6	FACETS	0.5	0.391	0.626	0.167	0.13	0.209	SUBCLONAL	1	TRUE	3	0.361379210341734	6		611	458	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0050233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	259	443	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.552935674796727	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.552935674796727	2		443	449	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308312	15308313	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GG	GG	CA	novel	NA	P-0050233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	158	703	1	ENST00000263388.2:c.195_196delinsTG	p.Leu66Val	p.L66V	ENST00000263388	NM_000435.2	65	tgCCtg/tgTGtg	2/33	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.552935674796727	2		704	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578467	7578467	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	468	997	0	ENST00000269305.4:c.463A>C	p.Thr155Pro	p.T155P	ENST00000269305	NM_001126112.2	155	Acc/Ccc	5/11	0.688826186017555	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.688826186017555	1		997	856	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17359587	17359587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1454196953	NA	P-0050234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	232	399	1	ENST00000375499.3:c.254C>T	p.Ser85Phe	p.S85F	ENST00000375499	NM_003000.2	85	tCt/tTt	3/8	1	2	FACETS	0.979	0.918	1	0.979	0.918	1	CLONAL	1	TRUE	1	0.688826186017555	2		400	688	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746114	162746114	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771259035	NA	P-0050234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	160	347	0	ENST00000367921.3:c.2237G>A	p.Arg746Gln	p.R746Q	ENST00000367921	NM_006182.2	746	cGg/cAg	16/18	0.688826186017555	3	FACETS	0.988	0.91	1	0.494	0.455	0.535	CLONAL	1	TRUE	1	0.688826186017555	3		347	632	SUCCESS
BLM	641	MSKCC	GRCh37	15	91306237	91306237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201458487	NA	P-0050234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	160	317	1	ENST00000355112.3:c.1924G>A	p.Glu642Lys	p.E642K	ENST00000355112	NM_000057.2	642	Gag/Aag	8/22	0.688826186017555	3	FACETS	0.903	0.83	0.978	0.451	0.415	0.489	CLONAL	1	TRUE	1	0.688826186017555	3		318	692	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099250	4099250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	556	1060	0	ENST00000262948.5:c.868G>A	p.Glu290Lys	p.E290K	ENST00000262948	NM_030662.3	290	Gag/Aag	7/11	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.688826186017555	2		1060	1375	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172322	7172322	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757322264	NA	P-0050234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	286	461	1	ENST00000302850.5:c.1247G>A	p.Arg416Gln	p.R416Q	ENST00000302850	NM_000208.2	416	cGa/cAa	5/22	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.688826186017555	2		462	754	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520159	9520159	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	241	537	1	ENST00000353224.5:c.2110G>T	p.Gly704Cys	p.G704C	ENST00000353224	NM_177990.2	704	Ggt/Tgt	10/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.688826186017555	2		538	690	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713664	52713664	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	261	524	0	ENST00000394830.3:c.64G>T	p.Gly22Trp	p.G22W	ENST00000394830	NM_018313.4	22	Ggg/Tgg	2/30	0.688826186017555	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.688826186017555	1		524	461	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114032	73114032	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	28	76	0	ENST00000356692.5:c.669del	p.Ser224GlnfsTer2	p.S224Qfs*2	ENST00000356692		223	tCc/tc	8/9	0.688826186017555	1	FACETS	0.919	0.773	1	0.919	0.773	1	CLONAL	1	TRUE	0	0.688826186017555	1		76	58	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249456	153249456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	125	526	0	ENST00000281708.4:c.1322G>A	p.Arg441Gln	p.R441Q	ENST00000281708	NM_033632.3	441	cGg/cAg	9/12	0.47294090807176	3	FACETS	1	0.932	1	0.516	0.468	0.567	CLONAL	1	TRUE	1	0.471137038936026	3		526	635	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872411	35872414	+	frameshift_variant	Frame_Shift_Del	DEL	AGTC	AGTC	-	novel	NA	P-0050235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	428	863	0	ENST00000216797.5:c.489_492del	p.Thr164SerfsTer12	p.T164Sfs*12	ENST00000216797	NM_020529.2	163	ctGACT/ct	3/6	0.463255013182767	2	FACETS	0.865	0.827	0.904	0.865	0.827	0.904	CLONAL	2	TRUE	0	0.471137038936026	2		863	1050	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843455	3843455	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	118	590	0	ENST00000262367.5:c.1148C>G	p.Pro383Arg	p.P383R	ENST00000262367	NM_004380.2	383	cCg/cGg	4/31	1	2	FACETS	0.756	0.683	0.832	0.756	0.683	0.832	SUBCLONAL	1	TRUE	1	0.471137038936026	2		590	663	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413042	139413042	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0050235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	511	739	0	ENST00000277541.6:c.1099+1G>A		p.X367_splice	ENST00000277541	NM_017617.3	367			0.47294090807176	3	FACETS	0.958	0.923	0.992	0.958	0.923	0.992	CLONAL	3	TRUE	0	0.471137038936026	3		739	933	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0050236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	222	611	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.245028052065377	2	FACETS	0.891	0.833	0.95	0.891	0.833	0.95	CLONAL	2	FALSE	0	0.357935891714193	2		611	696	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464577	25464577	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs748440577	NA	P-0050236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	201	626	0	ENST00000264709.3:c.1937-1G>A		p.X646_splice	ENST00000264709	NM_175629.2	646			0.165765386249177	3	FACETS	0.815	0.757	0.875	0.815	0.757	0.875	INDETERMINATE	2	FALSE	1	0.357935891714193	3		626	812	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526492	66526492	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	146	379	0	ENST00000358598.2:c.1048C>G	p.Leu350Val	p.L350V	ENST00000358598	NM_212471.2	350	Ctg/Gtg	11/11	0.276730353020396	2	FACETS	1	0.986	1	0.701	0.642	0.762	CLONAL	1	FALSE	0	0.357935891714193	2		379	582	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199888	128199888	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	131	540	0	ENST00000341105.2:c.1417T>G	p.Ser473Ala	p.S473A	ENST00000341105	NM_032638.4	473	Tcc/Gcc	6/6	0.125635712575151	4	FACETS	1	0.96	1	0.554	0.502	0.609	INDETERMINATE	1	FALSE	2	0.357935891714193	4		540	897	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0050237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	20	443	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.644	0.49	0.825	0.644	0.49	0.825	SUBCLONAL	1	TRUE	1	0.11	2		443	565	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0050237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	30	421	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.0911099718129403	3	FACETS	0.887	0.712	1	0.443	0.356	0.543	CLONAL	1	TRUE	1	0.11	3		421	649	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218045	108218045	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782451	NA	P-0050237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	27	330	0	ENST00000278616.4:c.8624A>G	p.Asn2875Ser	p.N2875S	ENST00000278616	NM_000051.3	2875	aAt/aGt	59/63	1	2	FACETS	0.951	0.755	1	0.951	0.755	1	CLONAL	1	TRUE	1	0.11	2		330	516	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	81	468	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.622977678527574	2		468	241	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143993	11143993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568509370	NA	P-0050239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	190	628	0	ENST00000358026.2:c.3574C>T	p.Arg1192Cys	p.R1192C	ENST00000358026	NM_001128849.1	1192	Cgc/Tgc	26/36	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.622977678527574	2		628	490	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0050239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	206	824	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.622977678527574	2		824	609	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981767	201981767	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0050239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	204	793	0	ENST00000359651.3:c.479-1G>A		p.X160_splice	ENST00000359651		160			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.622977678527574	2		793	583	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163381	108163381	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	80	450	0	ENST00000278616.4:c.4472T>G	p.Phe1491Cys	p.F1491C	ENST00000278616	NM_000051.3	1491	tTc/tGc	30/63	1	2	FACETS	0.941	0.839	1	0.941	0.839	1	CLONAL	1	TRUE	1	0.622977678527574	2		450	273	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447020	49447021	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0050239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	106	492	0	ENST00000301067.7:c.923_924del	p.Glu308GlyfsTer33	p.E308Gfs*33	ENST00000301067	NM_003482.3	308	gAG/g	7/54	1	2	FACETS	0.978	0.886	1	0.978	0.886	1	CLONAL	1	TRUE	1	0.622977678527574	2		492	348	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711182	61711182	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs768499033	NA	P-0050239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	119	469	0	ENST00000401558.2:c.2567A>G	p.Asn856Ser	p.N856S	ENST00000401558	NM_003400.3	856	aAt/aGt	21/25	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.622977678527574	2		469	308	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499401	89499401	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767812508	NA	P-0050239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	75	437	0	ENST00000336596.2:c.2571G>A	p.Met857Ile	p.M857I	ENST00000336596	NM_005233.5	857	atG/atA	15/17	1	2	FACETS	0.533	0.468	0.601	0.533	0.468	0.601	SUBCLONAL	1	TRUE	1	0.622977678527574	2		437	452	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206653	27206653	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	122	489	0	ENST00000380036.4:c.2438C>A	p.Pro813His	p.P813H	ENST00000380036	NM_000459.3	813	cCt/cAt	15/23	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.622977678527574	2		489	374	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0050240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	44	498	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	0.874	0.735	1	0.874	0.735	1	CLONAL	1	TRUE	1	0.27	2		498	373	SUCCESS
APC	324	MSKCC	GRCh37	5	112175903	112175903	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	10	212	0	ENST00000257430.4:c.4612G>T	p.Glu1538Ter	p.E1538*	ENST00000257430	NM_000038.5	1538	Gaa/Taa	16/16	1	2	FACETS	0.602	0.41	0.841	0.602	0.41	0.841	SUBCLONAL	1	TRUE	1	0.27	2		212	123	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845140	128845140	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	110	927	0	ENST00000249373.3:c.634G>C	p.Gly212Arg	p.G212R	ENST00000249373	NM_005631.4	212	Ggc/Cgc	3/12	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.27	2		927	778	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242482	+	protein_altering_variant	In_Frame_Del	DEL	GGAATTAAGAGAAGCAAC	GGAATTAAGAGAAGCAAC	AAT	novel	NA	P-0050241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	139	369	1	ENST00000275493.2:c.2235_2252delinsAAT	p.Glu746_Thr751delinsIle	p.E746_T751delinsI	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCAACa/aaAATa	19/28	0.261850095198255	5	FACETS	1	0.928	1	0.678	0.619	0.739	CLONAL	2	TRUE	2	0.337541466218357	5		370	610	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921347	178921347	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	84	300	0	ENST00000263967.3:c.829A>C	p.Ile277Leu	p.I277L	ENST00000263967	NM_006218.2	277	Ata/Cta	5/21	1	2	FACETS	0.857	0.758	0.962	0.857	0.758	0.962	CLONAL	1	TRUE	1	0.337541466218357	2		300	581	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817859	3817859	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	29	506	0	ENST00000262367.5:c.3112A>G	p.Ile1038Val	p.I1038V	ENST00000262367	NM_004380.2	1038	Ata/Gta	16/31	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		506	501	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444452	50444452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	121	345	0	ENST00000331340.3:c.382G>A	p.Gly128Arg	p.G128R	ENST00000331340	NM_006060.4	128	Ggg/Agg	4/8	0.452565880190626	3	FACETS	1	0.948	1	0.534	0.484	0.587	CLONAL	1	TRUE	1	0.452422425608478	3		345	614	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0050244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	230	666	1	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	0.452565880190626	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.452422425608478	1		667	759	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729271	41729271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749989847	NA	P-0050244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	205	354	0	ENST00000242208.4:c.1258G>A	p.Val420Met	p.V420M	ENST00000242208	NM_002192.2	420	Gtg/Atg	3/3	0.372642600270404	4	FACETS	0.962	0.896	1			1	CLONAL	2	TRUE	NA	0.452422425608478	4		354	684	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682997	241682997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	198	647	0	ENST00000366560.3:c.26C>T	p.Ala9Val	p.A9V	ENST00000366560	NM_000143.3	9	gCg/gTg	1/10	0.354001431276551	3	FACETS	1	0.94	1	0.509	0.471	0.548	CLONAL	1	TRUE	1	0.452422425608478	3		647	1055	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066841	30066841	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	331	473	1	ENST00000331968.5:c.2290C>A	p.Leu764Ile	p.L764I	ENST00000331968	NM_002742.2	764	Cta/Ata	16/18	0.452422425608478	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.452422425608478	2		474	707	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0050247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	300	662	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.619870681278672	1	FACETS	0.857	0.812	0.904	0.857	0.812	0.904	CLONAL	1	TRUE	0	0.619870681278672	1		662	779	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983863	2983863	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	208	667	0	ENST00000396946.4:c.667C>T	p.Arg223Ter	p.R223*	ENST00000396946	NM_032415.4	223	Cga/Tga	5/25	1	2	FACETS	0.803	0.746	0.861	0.803	0.746	0.861	CLONAL	1	TRUE	1	0.619870681278672	2		667	836	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965935	25965935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749408482	NA	P-0050247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	150	678	1	ENST00000435504.4:c.3271G>A	p.Ala1091Thr	p.A1091T	ENST00000435504		1091	Gct/Act	13/13	1	2	FACETS	0.792	0.727	0.86	0.792	0.727	0.86	SUBCLONAL	1	TRUE	1	0.619870681278672	2		679	611	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423598	88423598	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	123	538	0	ENST00000360948.2:c.2237A>C	p.Lys746Thr	p.K746T	ENST00000360948	NM_001012338.2	746	aAg/aCg	18/19	1	2	FACETS	0.88	0.801	0.962	0.88	0.801	0.962	CLONAL	1	TRUE	1	0.619870681278672	2		538	451	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849649	68849649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	128	549	0	ENST00000261769.5:c.1552G>T	p.Glu518Ter	p.E518*	ENST00000261769	NM_004360.3	518	Gaa/Taa	10/16	1	2	FACETS	0.845	0.77	0.922	0.845	0.77	0.922	CLONAL	1	TRUE	1	0.619870681278672	2		549	489	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844178	68844178	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	179	614	0	ENST00000261769.5:c.766A>C	p.Asn256His	p.N256H	ENST00000261769	NM_004360.3	256	Aat/Cat	6/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.619870681278672	2		614	539	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577157	7577157	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0050248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	67	518	0	ENST00000269305.4:c.783-2A>C		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.17	2		518	602	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665158	29665158	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0050248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	53	371	0	ENST00000356175.3:c.6756+1G>T		p.X2252_splice	ENST00000356175	NM_000267.3	2252			1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.17	2		371	569	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672363	86672367	+	frameshift_variant	Frame_Shift_Del	DEL	AGTAC	AGTAC	-	novel	NA	P-0050248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	30	255	0	ENST00000274376.6:c.2168_2172del	p.Tyr723Ter	p.Y723*	ENST00000274376	NM_002890.2	722	gAGTAC/g	16/25	1	2	FACETS	0.838	0.675	1	0.838	0.675	1	CLONAL	1	TRUE	1	0.17	2		255	421	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170180	32170180	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	50	911	0	ENST00000375023.3:c.3428A>T	p.Asn1143Ile	p.N1143I	ENST00000375023	NM_004557.3	1143	aAt/aTt	21/30	1	2	FACETS	0.675	0.571	0.791	0.675	0.571	0.791	SUBCLONAL	1	TRUE	1	0.17	2		911	871	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480607	123480607	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	44	576	0	ENST00000371139.4:c.115G>T	p.Gly39Cys	p.G39C	ENST00000371139	NM_001114937.2	39	Ggc/Tgc	1/4	1	2	FACETS	0.82	0.687	0.969	0.82	0.687	0.969	CLONAL	1	TRUE	1	0.17	2		576	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0050250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	40	662	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.57	0.472	0.68	0.57	0.472	0.68	SUBCLONAL	1	TRUE	1	0.16	2		662	877	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0050250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	49	411	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.218148578828332	3	FACETS	1	0.921	1	0.571	0.483	0.668	CLONAL	1	TRUE	1	0.16	3		411	579	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577064	7577064	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0050250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	59	700	0	ENST00000269305.4:c.874A>T	p.Lys292Ter	p.K292*	ENST00000269305	NM_001126112.2	292	Aaa/Taa	8/11	1	2	FACETS	0.828	0.71	0.956	0.828	0.71	0.956	CLONAL	1	TRUE	1	0.16	2		700	891	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247872	59247872	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	61	816	0	ENST00000371222.2:c.871A>C	p.Asn291His	p.N291H	ENST00000371222	NM_002228.3	291	Aac/Cac	1/1	1	2	FACETS	0.681	0.586	0.786	0.681	0.586	0.786	SUBCLONAL	1	TRUE	1	0.16	2		816	1119	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0050251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	50	530	0	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	1	2	FACETS	0.77	0.654	0.897	0.77	0.654	0.897	SUBCLONAL	1	TRUE	1	0.284303247403439	2		530	457	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513377	41513377	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1392142896	NA	P-0050251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	67	543	0	ENST00000263253.7:c.281A>G	p.Asn94Ser	p.N94S	ENST00000263253	NM_001429.3	94	aAt/aGt	2/31	1	2	FACETS	0.899	0.783	1	0.899	0.783	1	CLONAL	1	TRUE	1	0.284303247403439	2		543	524	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411858	116411894	+	intron_variant	Intron	DEL	ATGATAGCCGTCTTTAACAAGCTCTTTCTTTCTCTCT	ATGATAGCCGTCTTTAACAAGCTCTTTCTTTCTCTCT	-	novel	NA	P-0050251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	168	704	0	ENST00000397752.3:c.2888-45_2888-9del		p.*963*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.284303247403439	2		704	803	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2493180	2493180	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0050252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1289	345	591	0	ENST00000355716.4:c.620C>G	p.Ser207Ter	p.S207*	ENST00000355716	NM_003820.2	207	tCa/tGa	6/8	0.166514771964175	5	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.679264002869155	5		591	1634	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871305	35871754	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGCGGAGCTCTGCCAAGCTACCGGGATGGGGAGGCCACTACTGGAAATAACTCTTGGACTCCATTCTCCATAGCCCAAATATAATGAACTTTACAGGCTGAGAGAGTTTGCCTTTAATGCTTCTCTTTAAAAAAAGAGGGGGGGCAGGTACATTCTTGGGATACTGGTTATGCACAGAAATTTGAGAGACTCATTATGTAGATACCCCTCTGATAAGGAGCAGCTCTAGGGGCCTGGGAGGGTGAAGGGAATGGCACCTCATTAGTTAGAGCGCCGAAGGAGTTCACAGACTCACCTCGTCCTCTGTGAACTCCGTGAACTCTGACTCTGTGTCATAGCTCTCCTCATCCTCACTCTCTGGCAGCATCTGAAGGTTTTCTAGTGTCAGCTGGCCCAGCTGCTGCTGTATCCGGGTGCTTGGGCGGCCCCAGGTGAGCTGGTAGGGAGAAT	AGCGGAGCTCTGCCAAGCTACCGGGATGGGGAGGCCACTACTGGAAATAACTCTTGGACTCCATTCTCCATAGCCCAAATATAATGAACTTTACAGGCTGAGAGAGTTTGCCTTTAATGCTTCTCTTTAAAAAAAGAGGGGGGGCAGGTACATTCTTGGGATACTGGTTATGCACAGAAATTTGAGAGACTCATTATGTAGATACCCCTCTGATAAGGAGCAGCTCTAGGGGCCTGGGAGGGTGAAGGGAATGGCACCTCATTAGTTAGAGCGCCGAAGGAGTTCACAGACTCACCTCGTCCTCTGTGAACTCCGTGAACTCTGACTCTGTGTCATAGCTCTCCTCATCCTCACTCTCTGGCAGCATCTGAAGGTTTTCTAGTGTCAGCTGGCCCAGCTGCTGCTGTATCCGGGTGCTTGGGCGGCCCCAGGTGAGCTGGTAGGGAGAAT	-	novel	NA	P-0050252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	110	206	0	ENST00000216797.5:c.752_907-39del		p.X251_splice	ENST00000216797	NM_020529.2	251		5/6	0.624700153766666	1	FACETS	0.581	0.527	0.637	0.581	0.527	0.637	SUBCLONAL	1	TRUE	0	0.679264002869155	1		206	368	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454587	99454587	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	121	399	0	ENST00000268035.6:c.1506G>C	p.Lys502Asn	p.K502N	ENST00000268035	NM_000875.3	502	aaG/aaC	7/21	NA	2	FACETS	0.348	0.313	0.384			1	INDETERMINATE	1	TRUE	NA	0.679264002869155	2		399	1025	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2132476	2132476	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1527	91	826	0	ENST00000219476.3:c.3854G>C	p.Gly1285Ala	p.G1285A	ENST00000219476	NM_000548.3	1285	gGa/gCa	32/42	1	2	FACETS	0.166	0.146	0.187	0.166	0.146	0.187	SUBCLONAL	1	TRUE	1	0.679264002869155	2		826	1618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0050252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	373	636	0	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	0.611084860331332	1	FACETS	0.785	0.748	0.823	0.785	0.748	0.823	SUBCLONAL	1	TRUE	0	0.679264002869155	1		636	924	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976603	7976603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	172	644	0	ENST00000319144.4:c.1789G>A	p.Ala597Thr	p.A597T	ENST00000319144	NM_001139.2	597	Gcg/Acg	14/15	0.611084860331332	1	FACETS	0.357	0.328	0.387	0.357	0.328	0.387	SUBCLONAL	1	TRUE	0	0.679264002869155	1		644	936	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63531751	63531751	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	79	510	0	ENST00000307078.5:c.2230C>G	p.Pro744Ala	p.P744A	ENST00000307078	NM_004655.3	744	Cca/Gca	9/11	1	2	FACETS	0.257	0.225	0.292	0.257	0.225	0.292	SUBCLONAL	1	TRUE	1	0.679264002869155	2		510	904	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096304	178096304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	247	365	0	ENST00000397062.3:c.1027G>A	p.Asp343Asn	p.D343N	ENST00000397062	NM_006164.4	343	Gac/Aac	5/5	0.556608620753622	1	FACETS	0.798	0.752	0.844	0.798	0.752	0.844	SUBCLONAL	1	TRUE	0	0.679264002869155	1		365	602	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31393166	31393166	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	83	279	0	ENST00000328111.2:c.2254G>A	p.Asp752Asn	p.D752N	ENST00000328111	NM_006892.3	752	Gat/Aat	21/23	1	2	FACETS	0.328	0.289	0.369	0.328	0.289	0.369	SUBCLONAL	1	TRUE	1	0.679264002869155	2		279	746	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067839	30067839	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	104	391	0	ENST00000338641.4:c.1024G>C	p.Glu342Gln	p.E342Q	ENST00000338641	NM_000268.3	342	Gag/Cag	11/16	1	2	FACETS	0.387	0.346	0.43	0.387	0.346	0.43	SUBCLONAL	1	TRUE	1	0.679264002869155	2		391	792	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048640	6048640	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs745361721	NA	P-0050252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	292	624	0	ENST00000265849.7:c.11C>G	p.Ala4Gly	p.A4G	ENST00000265849	NM_000535.5	4	gCt/gGt	1/15	1	2	FACETS	0.608	0.571	0.646	0.608	0.571	0.646	SUBCLONAL	1	TRUE	1	0.679264002869155	2		624	1414	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934250	39934250	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	48	570	1	ENST00000378444.4:c.349del	p.Glu117LysfsTer44	p.E117Kfs*44	ENST00000378444	NM_001123385.1	117	Gaa/aa	4/15	0.3526792222312	1	FACETS	0.098	0.082	0.115	0.098	0.082	0.115	INDETERMINATE	1	TRUE	0	0.679264002869155	1		571	957	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041600	47041601	+	missense_variant	Missense_Mutation	DNP	GA	GA	CC	novel	NA	P-0050252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	228	622	0	ENST00000377604.3:c.1825_1826delinsCC	p.Asp609Pro	p.D609P	ENST00000377604	NM_001204468.1	609	GAt/CCt	17/24	NA	2	FACETS	0.511	0.474	0.548			1	INDETERMINATE	1	TRUE	NA	0.679264002869155	2		622	1315	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174395	11174395	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1085307113	NA	P-0050253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	127	586	0	ENST00000361445.4:c.7280T>A	p.Leu2427Gln	p.L2427Q	ENST00000361445	NM_004958.3	2427	cTg/cAg	53/58	0.508761886564249	1	FACETS	0.681	0.619	0.745	0.681	0.619	0.745	SUBCLONAL	1	TRUE	0	0.509953065125378	1		586	545	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971180	21971180	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	284	495	0	ENST00000304494.5:c.178del	p.Ala60ArgfsTer86	p.A60Rfs*86	ENST00000304494	NM_000077.4	60	Gcg/cg	2/3	0.497813847051816	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.509953065125378	2		495	528	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589632	67589643	+	inframe_deletion	In_Frame_Del	DEL	ATTATATGAAGA	ATTATATGAAGA	-	novel	NA	P-0050253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	56	181	0	ENST00000274335.5:c.1397_1408del	p.Leu466_Glu469del	p.L466_E469del	ENST00000274335		465	agATTATATGAAGAa/aga	10/15	1	2	FACETS	0.676	0.582	0.777	0.676	0.582	0.777	SUBCLONAL	1	TRUE	1	0.509953065125378	2		181	325	SUCCESS
APC	324	MSKCC	GRCh37	5	112175476	112175476	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	71	357	0	ENST00000257430.4:c.4188del	p.Phe1396LeufsTer19	p.F1396Lfs*19	ENST00000257430	NM_000038.5	1395	agT/ag	16/16	0.3115130651688	2	FACETS	0.958	0.848	1	0.958	0.848	1	CLONAL	2	TRUE	0	0.3115130651688	2		357	238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587782289	NA	P-0050254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	198	623	0	ENST00000269305.4:c.706T>A	p.Tyr236Asn	p.Y236N	ENST00000269305	NM_001126112.2	236	Tac/Aac	7/11	0.3115130651688	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.3115130651688	2		623	612	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150552004	150552004	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0050254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	61	567	0	ENST00000369026.2:c.3G>A	p.Met1?	p.M1?	ENST00000369026	NM_021960.4	1	atG/atA	1/3	0.226823188011451	4	FACETS	0.865	0.746	0.994	0.432	0.373	0.497	CLONAL	1	TRUE	2	0.3115130651688	4		567	594	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473704	67473704	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1201995588	NA	P-0050254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	147	704	0	ENST00000327367.4:c.784G>T	p.Asp262Tyr	p.D262Y	ENST00000327367	NM_005902.3	262	Gac/Tac	6/9	0.3115130651688	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	0	0.3115130651688	2		704	470	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251773	212251773	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	44	398	0	ENST00000342788.4:c.3286G>A	p.Gly1096Ser	p.G1096S	ENST00000342788	NM_005235.2	1096	Ggt/Agt	27/28	0.263975901692052	3	FACETS	1	0.88	1	0.527	0.444	0.618	CLONAL	1	TRUE	1	0.3115130651688	3		398	310	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128848652	128848652	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	67	803	0	ENST00000249373.3:c.1317G>C	p.Glu439Asp	p.E439D	ENST00000249373	NM_005631.4	439	gaG/gaC	7/12	0.3115130651688	5	FACETS	0.768	0.666	0.879	0.192	0.166	0.22	SUBCLONAL	1	TRUE	1	0.3115130651688	5		803	822	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981217	201981217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	195	1074	0	ENST00000359651.3:c.296G>A	p.Gly99Asp	p.G99D	ENST00000359651		99	gGc/gAc	2/8	0.301639955992095	2	FACETS	0.93	0.864	0.998	0.93	0.864	0.998	CLONAL	2	TRUE	0	0.3115130651688	2		1074	673	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183793	10183793	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1553619431	NA	P-0050255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	271	866	0	ENST00000256474.2:c.262T>C	p.Trp88Arg	p.W88R	ENST00000256474	NM_000551.3	88	Tgg/Cgg	1/3	0.188471432609368	3	FACETS	0.849	0.799	0.9	0.849	0.799	0.9	CLONAL	3	TRUE	0	0.287857046755747	3		866	846	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332684	153332684	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	27	376	0	ENST00000281708.4:c.272C>G	p.Ser91Cys	p.S91C	ENST00000281708	NM_033632.3	91	tCc/tGc	2/12	1	2	FACETS	0.525	0.418	0.648	0.525	0.418	0.648	SUBCLONAL	1	TRUE	1	0.287857046755747	2		376	357	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928358	69928358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774545277	NA	P-0050255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	189	500	0	ENST00000352241.4:c.178C>T	p.Arg60Cys	p.R60C	ENST00000352241	NM_198159.2	60	Cgc/Tgc	2/10	0.188471432609368	3	FACETS	0.926	0.862	0.991	0.926	0.862	0.991	CLONAL	3	TRUE	0	0.287857046755747	3		500	541	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822421	72822421	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	57	889	0	ENST00000268489.5:c.9754G>A	p.Glu3252Lys	p.E3252K	ENST00000268489	NM_006885.3	3252	Gaa/Aaa	10/10	1	2	FACETS	0.469	0.401	0.543	0.469	0.401	0.543	SUBCLONAL	1	TRUE	1	0.287857046755747	2		889	845	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967122	25967122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	37	507	0	ENST00000435504.4:c.2084C>T	p.Pro695Leu	p.P695L	ENST00000435504		695	cCa/cTa	13/13	1	2	FACETS	0.491	0.404	0.588	0.491	0.404	0.588	SUBCLONAL	1	TRUE	1	0.287857046755747	2		507	524	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656894	45656894	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	40	620	0	ENST00000407780.3:c.262C>G	p.Pro88Ala	p.P88A	ENST00000407780	NM_001283052.1	88	Ccg/Gcg	3/7	1	2	FACETS	0.358	0.296	0.427	0.358	0.296	0.427	SUBCLONAL	1	TRUE	1	0.287857046755747	2		620	777	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440365	52440376	+	inframe_deletion	In_Frame_Del	DEL	GTTGAAGCGGAT	GTTGAAGCGGAT	-	novel	NA	P-0050255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	197	607	0	ENST00000460680.1:c.676_687del	p.Ile226_Asn229del	p.I226_N229del	ENST00000460680	NM_004656.3	226	ATCCGCTTCAAC/-	9/17	0.188471432609368	3	FACETS	1	0.978	1	0.749	0.696	0.803	CLONAL	2	TRUE	0	0.287857046755747	3		607	697	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0050256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	124	364	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		364	557	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242481	+	inframe_deletion	In_Frame_Del	DEL	AATTAAGAGAAGCAA	AATTAAGAGAAGCAA	-	rs121913425	NA	P-0050257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	129	439	0	ENST00000275493.2:c.2237_2251del	p.Glu746_Thr751delinsAla	p.E746_T751delinsA	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAAca/gca	19/28	0.304200674707515	3	FACETS	1	0.983	1	0.67	0.611	0.733	CLONAL	1	TRUE	1	0.433565842239056	3		439	540	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0050257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	55	705	2	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.304200674707515	3	FACETS	0.363	0.309	0.422	0.181	0.154	0.211	SUBCLONAL	1	TRUE	1	0.433565842239056	3		707	851	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0050258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	143	534	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.212371004940703	4	FACETS	0.791	0.722	0.862	0.791	0.722	0.862	INDETERMINATE	2	TRUE	2	0.36685377360093	4		534	674	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155700	56155701	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1338345984	NA	P-0050258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	110	396	0	ENST00000399503.3:c.793_794del	p.Glu265IlefsTer35	p.E265Ifs*35	ENST00000399503	NM_005921.1	264	tcAGaa/tcaa	3/20	0.36685377360093	4	FACETS	0.836	0.755	0.922	0.836	0.755	0.922	CLONAL	2	TRUE	2	0.36685377360093	4		396	490	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	100	413	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.272267586385841	3	FACETS	1	0.981	1	0.719	0.645	0.796	CLONAL	1	TRUE	1	0.356464106902657	3		413	460	SUCCESS
APC	324	MSKCC	GRCh37	5	112116486	112116486	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1554072547	NA	P-0050259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	21	236	0	ENST00000257430.4:c.532-1G>A		p.X178_splice	ENST00000257430	NM_000038.5	178			1	2	FACETS	0.76	0.59	0.954	0.76	0.59	0.954	CLONAL	1	TRUE	1	0.356464106902657	2		236	155	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271456	38271456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs527606454	NA	P-0050259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	52	1027	3	ENST00000425967.3:c.2365G>A	p.Val789Met	p.V789M	ENST00000425967	NM_001174067.1	789	Gtg/Atg	18/19	1	2	FACETS	0.341	0.289	0.398	0.341	0.289	0.398	SUBCLONAL	1	TRUE	1	0.356464106902657	2		1030	856	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	281	468	0				ENST00000310581	NM_198253.2	-/1132			0.567453437125498	3	FACETS	0.937	0.888	0.988	0.937	0.888	0.988	CLONAL	2	TRUE	1	0.598154139992555	3		468	651	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729153	66729153	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519856	NA	P-0050260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	251	771	0	ENST00000307102.5:c.361T>A	p.Cys121Ser	p.C121S	ENST00000307102	NM_002755.3	121	Tgc/Agc	3/11	1	2	FACETS	0.863	0.808	0.92	0.863	0.808	0.92	CLONAL	1	TRUE	1	0.598154139992555	2		771	972	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696644	47696644	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519964	NA	P-0050261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	127	464	0	ENST00000347630.2:c.304T>G	p.Phe102Val	p.F102V	ENST00000347630	NM_001007230.1	102	Ttc/Gtc	5/11	1	2	FACETS	0.821	0.745	0.9	0.821	0.745	0.9	CLONAL	1	TRUE	1	0.467451780599572	2		464	662	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935496	13935497	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0050261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	128	352	0	ENST00000405192.2:c.1359_1360del	p.Tyr454LeufsTer62	p.Y454Lfs*62	ENST00000405192	NM_001163147.1	453	gtGTat/gtat	12/12	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.467451780599572	2		352	520	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129632	47129632	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	107	427	0	ENST00000409792.3:c.5248C>T	p.Gln1750Ter	p.Q1750*	ENST00000409792	NM_014159.6	1750	Cag/Tag	10/21	0.42136388736635	3	FACETS	0.909	0.818	1	0.455	0.409	0.503	CLONAL	1	TRUE	1	0.491919981763645	3		427	596	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098859	47098859	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	375	808	2	ENST00000409792.3:c.6415C>T	p.Gln2139Ter	p.Q2139*	ENST00000409792	NM_014159.6	2139	Caa/Taa	15/21	0.42136388736635	3	FACETS	0.905	0.86	0.949	0.905	0.86	0.949	CLONAL	2	TRUE	1	0.491919981763645	3		810	1050	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0050264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	134	307	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.475610543384598	2		307	538	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0050264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	319	349	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.119679831545829	3	FACETS	1	0.979	1			1	INDETERMINATE	2	TRUE	NA	0.475610543384598	3		349	783	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0050264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	143	316	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.475610543384598	2		316	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578281	7578281	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660254	NA	P-0050264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	260	649	0	ENST00000269305.4:c.568C>A	p.Pro190Thr	p.P190T	ENST00000269305	NM_001126112.2	190	Cct/Act	6/11	0.475610543384598	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.475610543384598	1		649	802	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	225	468	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.932	0.875	0.989	0.932	0.875	0.989	CLONAL	1	TRUE	1	0.85927349284682	2		468	562	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233044	55233046	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0050265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	19322	487	0	ENST00000275493.2:c.1794_1796del	p.Val599del	p.V599del	ENST00000275493	NM_005228.3	598	ggAGTc/ggc	15/28	0.85927349284682	23	FACETS	1	0.999	1	0.973	0.971	0.975	CLONAL	22	TRUE	0	0.85927349284682	23		487	20146	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589591	67589594	+	protein_altering_variant	In_Frame_Del	DEL	TATA	TATA	C	novel	NA	P-0050265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	66	210	0	ENST00000274335.5:c.1354_1357delinsC	p.Tyr452_Asn453delinsHis	p.Y452_N453delinsH	ENST00000274335		452	TATAac/Cac	10/15	1	2	FACETS	0.456	0.398	0.517	0.456	0.398	0.517	SUBCLONAL	1	TRUE	1	0.85927349284682	2		210	337	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	181	364	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.201159998524542	4	FACETS	0.986	0.919	1	1	0.993	1	CLONAL	6	TRUE	1	0.15	4		364	469	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	116	442	10	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	0.266975754630391	4	FACETS	0.979	0.889	1	1	0.98	1	CLONAL	4	TRUE	1	0.15	4		452	454	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	79	927	0	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	0.0746800087261446	3	FACETS	1	0.961	1	0.621	0.545	0.704	INDETERMINATE	1	TRUE	1	0.15	3		927	911	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	188	753	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.935	0.864	1	1	0.994	1	CLONAL	3	TRUE	1	0.15	2		753	894	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	20	364	1	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	0.0746800087261446	3	FACETS	0.922	0.705	1	0.461	0.352	0.588	INDETERMINATE	1	TRUE	1	0.15	3		365	311	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	129	399	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.0746800087261446	3	FACETS	1	0.964	1	1	0.988	1	INDETERMINATE	3	TRUE	1	0.15	3		403	553	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	184	435	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	0.3	2	FACETS	0.967	0.903	1	1	0.995	1	CLONAL	6	TRUE	0	0.15	2		436	423	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	179	825	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	1	0.946	1	1	0.994	1	CLONAL	3	TRUE	1	0.15	2		825	773	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	394	1088	1	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	0.201159998524542	4	FACETS	0.931	0.886	0.975	1	0.996	1	CLONAL	6	TRUE	1	0.15	4		1089	1082	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	113	427	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	0.0746800087261446	3	FACETS	0.922	0.836	1	1	0.988	1	INDETERMINATE	4	TRUE	1	0.15	3		427	439	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497754	120497754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782066959	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	172	608	0	ENST00000256646.2:c.2128G>A	p.Glu710Lys	p.E710K	ENST00000256646	NM_024408.3	710	Gag/Aag	13/34	1	2	FACETS	1	0.943	1	1	0.995	1	CLONAL	4	TRUE	1	0.15	2		608	561	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524714	187524714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs192691397	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	79	815	1	ENST00000441802.2:c.10966G>A	p.Val3656Ile	p.V3656I	ENST00000441802	NM_005245.3	3656	Gtt/Att	19/27	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.15	2		816	1003	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	29	362	1	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	0.201159998524542	4	FACETS	0.844	0.676	1	0.281	0.225	0.346	CLONAL	1	TRUE	1	0.15	4		363	527	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226423	2226423	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	362	1257	1	ENST00000398665.3:c.3907del	p.Ala1303LeufsTer24	p.A1303Lfs*24	ENST00000398665	NM_032482.2	1301	tcG/tc	27/28	0.0131298494985721	3	FACETS	0.959	0.908	1	1	0.996	1	INDETERMINATE	4	TRUE	1	0.15	3		1258	1353	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641389	18641389	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1229278001	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	14	261	0	ENST00000266497.5:c.2393del	p.Asn798MetfsTer16	p.N798Mfs*16	ENST00000266497		796	ctA/ct	17/31	0.0131298494985721	3	FACETS	0.876	0.634	1	0.438	0.317	0.585	INDETERMINATE	1	TRUE	1	0.15	3		261	229	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579584	7579585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	221	764	0	ENST00000269305.4:c.102dup	p.Pro36AlafsTer7	p.P36Afs*7	ENST00000269305	NM_001126112.2	34	-/C	4/11	1	2	FACETS	0.914	0.853	0.977	1	0.996	1	CLONAL	4	TRUE	1	0.15	2		764	806	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799098	42799098	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	81	1170	1	ENST00000575354.2:c.4586del	p.Pro1529LeufsTer91	p.P1529Lfs*91	ENST00000575354	NM_015125.3	1528	Ccc/cc	20/20	0.0131298494985721	3	FACETS	0.907	0.796	1	0.454	0.398	0.514	INDETERMINATE	1	TRUE	1	0.15	3		1171	1280	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245587	41245587	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357522	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	49	645	1	ENST00000357654.3:c.1961del	p.Lys654SerfsTer47	p.K654Sfs*47	ENST00000357654	NM_007294.3	654	aAg/ag	10/23	1	2	FACETS	0.954	0.806	1	0.954	0.806	1	CLONAL	1	TRUE	1	0.15	2		646	685	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661836	227661836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs577407654	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	78	970	0	ENST00000305123.5:c.1619C>T	p.Pro540Leu	p.P540L	ENST00000305123	NM_005544.2	540	cCg/cTg	1/2	0.0131298494985721	3	FACETS	1	0.931	1	0.547	0.479	0.62	INDETERMINATE	1	TRUE	1	0.15	3		970	1022	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007688	45007688	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	97	413	1	ENST00000558401.1:c.135C>A	p.Cys45Ter	p.C45*	ENST00000558401	NM_004048.2	45	tgC/tgA	2/4	0.0746800087261446	3	FACETS	1	0.958	1	1	0.985	1	INDETERMINATE	3	TRUE	1	0.15	3		414	410	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310208	91310208	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs747341586	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	25	273	0	ENST00000355112.3:c.2268del	p.Asp757ThrfsTer4	p.D757Tfs*4	ENST00000355112	NM_000057.2	754	tcA/tc	10/22	0.0746800087261446	3	FACETS	1	0.88	1	0.589	0.465	0.732	INDETERMINATE	1	TRUE	1	0.15	3		273	304	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793677	89793677	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	19	435	2	ENST00000336032.3:c.752del	p.Lys251SerfsTer14	p.K251Sfs*14	ENST00000336032	NM_006813.2	249	gAa/ga	2/2	0.0131298494985721	3	FACETS	0.771	0.585	0.992	0.386	0.292	0.496	INDETERMINATE	1	TRUE	1	0.15	3		437	353	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481454	20481455	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	37	313	0	ENST00000346618.3:c.529dup	p.Thr177AsnfsTer4	p.T177Nfs*4	ENST00000346618	NM_001949.4	175	gaa/gAaa	3/7	0.0131298494985721	3	FACETS	1	0.913	1	0.592	0.488	0.708	INDETERMINATE	1	TRUE	1	0.15	3		313	448	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163554	32163554	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	185	955	2	ENST00000375023.3:c.5672del	p.Gly1891AlafsTer13	p.G1891Afs*13	ENST00000375023	NM_004557.3	1891	gGc/gc	30/30	0.0131298494985721	3	FACETS	1	0.936	1	1	0.993	1	INDETERMINATE	4	TRUE	1	0.15	3		957	656	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138563	37138563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775870535	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	239	893	1	ENST00000373509.5:c.97C>T	p.Pro33Ser	p.P33S	ENST00000373509	NM_002648.3	33	Ccc/Tcc	2/6	0.0131298494985721	3	FACETS	1	0.954	1	1	0.995	1	INDETERMINATE	4	TRUE	1	0.15	3		894	837	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460504	8460504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148300682	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	187	532	0	ENST00000356435.5:c.3782C>T	p.Thr1261Met	p.T1261M	ENST00000356435		1261	aCg/aTg	22/35	1	2	FACETS	1	0.978	1	1	0.995	1	CLONAL	3	TRUE	1	0.15	2		532	726	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829075	128829075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1247591045	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	25	92	0	ENST00000249373.3:c.88del	p.Ala30ArgfsTer25	p.A30Rfs*25	ENST00000249373	NM_005631.4	28	cGg/cg	1/12	0.201159998524542	4	FACETS	1	0.873	1	0.761	0.605	0.936	CLONAL	2	TRUE	1	0.15	4		92	168	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739894	41739894	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	155	569	0	ENST00000242208.4:c.79G>A	p.Glu27Lys	p.E27K	ENST00000242208	NM_002192.2	27	Gag/Aag	2/3	0.201159998524542	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	1	0.15	4		569	702	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226049	2226049	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	69	982	1	ENST00000326181.6:c.1747-1G>T		p.X583_splice	ENST00000326181	NM_032271.2	583			1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.15	2		983	845	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760430	133760430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372727500	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	88	957	2	ENST00000318560.5:c.2753C>T	p.Pro918Leu	p.P918L	ENST00000318560	NM_005157.4	918	cCg/cTg	11/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.15	2		959	886	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517874	187517874	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs983524169	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	50	511	1	ENST00000441802.2:c.12820G>A	p.Glu4274Lys	p.E4274K	ENST00000441802	NM_005245.3	4274	Gaa/Aaa	25/27	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.15	2		512	558	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243975	5243975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1488811231	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	71	828	0	ENST00000357368.4:c.1507G>A	p.Ala503Thr	p.A503T	ENST00000357368	NM_002850.3	503	Gcc/Acc	11/38	0.0131298494985721	3	FACETS	0.992	0.863	1	0.496	0.431	0.566	INDETERMINATE	1	TRUE	1	0.15	3		828	1026	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132814	152132815	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	149	749	0	ENST00000262189.6:c.57dup	p.Glu20ArgfsTer39	p.E20Rfs*39	ENST00000262189	NM_170606.2	19	-/C	1/59	0.201159998524542	4	FACETS	1	0.955	1	0.716	0.653	0.782	CLONAL	2	TRUE	1	0.15	4		749	1064	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554306	81554306	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908865	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	29	370	0	ENST00000298171.2:c.326G>A	p.Arg109Gln	p.R109Q	ENST00000298171	NM_000369.2	109	cGg/cAg	4/10	1	2	FACETS	0.731	0.585	0.897	0.731	0.585	0.897	SUBCLONAL	1	TRUE	1	0.15	2		370	529	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912485	50912485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	62	899	1	ENST00000440232.2:c.1999C>T	p.Arg667Trp	p.R667W	ENST00000440232	NM_002691.3	667	Cgg/Tgg	16/27	0.0131298494985721	3	FACETS	0.945	0.814	1	0.473	0.407	0.545	INDETERMINATE	1	TRUE	1	0.15	3		900	940	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126085	2126085	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs999523698	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	153	947	0	ENST00000219476.3:c.2656G>T	p.Val886Leu	p.V886L	ENST00000219476	NM_000548.3	886	Gtg/Ttg	24/42	1	2	FACETS	1	0.979	1	1	0.992	1	CLONAL	2	TRUE	1	0.15	2		947	834	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867714	45867714	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763125782	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	304	1025	0	ENST00000391945.4:c.686C>T	p.Ala229Val	p.A229V	ENST00000391945	NM_000400.3	229	gCc/gTc	8/23	0.0131298494985721	3	FACETS	0.909	0.856	0.963	1	0.995	1	INDETERMINATE	4	TRUE	1	0.15	3		1025	1199	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190704	11190704	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	322	945	1	ENST00000361445.4:c.5495C>T	p.Ala1832Val	p.A1832V	ENST00000361445	NM_004958.3	1832	gCc/gTc	39/58	1	2	FACETS	1	0.968	1	1	0.997	1	CLONAL	4	TRUE	1	0.15	2		946	1038	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254653	16254653	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	40	524	0	ENST00000375759.3:c.1918G>T	p.Gly640Cys	p.G640C	ENST00000375759	NM_015001.2	640	Ggc/Tgc	11/15	1	2	FACETS	0.907	0.753	1	0.907	0.753	1	CLONAL	1	TRUE	1	0.15	2		524	588	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156620	2156620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	78	838	0	ENST00000434045.2:c.302G>A	p.Cys101Tyr	p.C101Y	ENST00000434045	NM_001127598.1	101	tGt/tAt	3/5	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.15	2		838	892	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435197	18435197	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	22	399	0	ENST00000266497.5:c.182A>G	p.Asn61Ser	p.N61S	ENST00000266497		61	aAc/aGc	1/31	0.0131298494985721	3	FACETS	0.967	0.75	1	0.484	0.375	0.61	INDETERMINATE	1	TRUE	1	0.15	3		399	326	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230704	46230704	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	24	385	0	ENST00000334344.6:c.953T>C	p.Leu318Pro	p.L318P	ENST00000334344	NM_152641.2	318	cTt/cCt	8/21	0.0131298494985721	3	FACETS	1	0.795	1	0.507	0.398	0.634	INDETERMINATE	1	TRUE	1	0.15	3		385	339	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426580	49426580	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	106	994	0	ENST00000301067.7:c.11908C>A	p.Gln3970Lys	p.Q3970K	ENST00000301067	NM_003482.3	3970	Cag/Aag	39/54	0.0131298494985721	3	FACETS	1	0.96	1	0.578	0.516	0.644	INDETERMINATE	1	TRUE	1	0.15	3		994	1314	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240999	133240999	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	212	791	1	ENST00000320574.5:c.2518G>A	p.Ala840Thr	p.A840T	ENST00000320574	NM_006231.2	840	Gcc/Acc	22/49	0.0131298494985721	3	FACETS	1	0.969	1	1	0.992	1	INDETERMINATE	3	TRUE	1	0.15	3		792	943	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107748	30107748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775384193	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	152	621	0	ENST00000331968.5:c.932G>A	p.Arg311His	p.R311H	ENST00000331968	NM_002742.2	311	cGt/cAt	6/18	1	2	FACETS	1	0.972	1	1	0.994	1	CLONAL	3	TRUE	1	0.15	2		621	597	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862910	9862910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	35	659	0	ENST00000330684.3:c.2393G>A	p.Gly798Glu	p.G798E	ENST00000330684	NM_001134407.1	798	gGg/gAg	12/13	1	2	FACETS	0.68	0.556	0.821	0.68	0.556	0.821	SUBCLONAL	1	TRUE	1	0.15	2		659	686	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462592	40462592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1029737475	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	83	751	0	ENST00000345506.4:c.2290G>A	p.Val764Met	p.V764M	ENST00000345506	NM_003152.3	764	Gtg/Atg	20/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.15	2		751	815	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870591	40870591	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	205	841	0	ENST00000428826.2:c.812del	p.Pro271LeufsTer97	p.P271Lfs*97	ENST00000428826		271	cCt/ct	9/21	1	2	FACETS	0.917	0.85	0.985	1	0.995	1	CLONAL	3	TRUE	1	0.15	2		841	994	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78617573	78617573	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	115	422	0	ENST00000306801.3:c.311C>T	p.Ala104Val	p.A104V	ENST00000306801	NM_020761.2	104	gCa/gTa	3/34	1	2	FACETS	0.923	0.834	1	1	0.991	1	CLONAL	3	TRUE	1	0.15	2		422	554	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2202721	2202721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	199	823	0	ENST00000398665.3:c.730G>A	p.Ala244Thr	p.A244T	ENST00000398665	NM_032482.2	244	Gcc/Acc	9/28	0.0131298494985721	3	FACETS	1	0.972	1	1	0.992	1	INDETERMINATE	3	TRUE	1	0.15	3		823	870	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627759	14627759	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	198	827	0	ENST00000254322.2:c.311A>G	p.Glu104Gly	p.E104G	ENST00000254322	NM_006145.1	104	gAg/gGg	2/3	0.0131298494985721	3	FACETS	0.885	0.821	0.95	1	0.993	1	INDETERMINATE	4	TRUE	1	0.15	3		827	802	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221508	36221508	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	127	994	1	ENST00000222270.7:c.5267T>A	p.Ile1756Asn	p.I1756N	ENST00000222270	NM_014727.1	1756	aTt/aAt	25/37	0.0131298494985721	3	FACETS	0.91	0.823	1	0.91	0.823	1	INDETERMINATE	2	TRUE	1	0.15	3		995	1000	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753602	42753602	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	59	1078	3	ENST00000222329.4:c.662del	p.Pro221ArgfsTer50	p.P221Rfs*50	ENST00000222329	NM_006494.2	221	cCg/cg	4/4	0.0131298494985721	3	FACETS	0.751	0.644	0.869	0.376	0.322	0.435	INDETERMINATE	1	TRUE	1	0.15	3		1081	1126	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446266	29446266	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	217	754	0	ENST00000389048.3:c.3301A>G	p.Lys1101Glu	p.K1101E	ENST00000389048	NM_004304.4	1101	Aag/Gag	20/29	0.0131298494985721	3	FACETS	1	0.981	1	1	0.993	1	INDETERMINATE	3	TRUE	1	0.15	3		754	908	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46597036	46597036	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	49	537	0	ENST00000263734.3:c.850C>A	p.Leu284Ile	p.L284I	ENST00000263734	NM_001430.4	284	Cta/Ata	7/16	0.0131298494985721	3	FACETS	0.87	0.735	1	0.435	0.367	0.51	INDETERMINATE	1	TRUE	1	0.15	3		537	807	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027538	48027538	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	26	361	0	ENST00000234420.5:c.2416T>C	p.Ser806Pro	p.S806P	ENST00000234420	NM_000179.2	806	Tcc/Ccc	4/10	0.0131298494985721	3	FACETS	0.978	0.775	1	0.489	0.387	0.606	INDETERMINATE	1	TRUE	1	0.15	3		361	381	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466844	57466844	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	44	382	0	ENST00000371085.3:c.63G>T	p.Glu21Asp	p.E21D	ENST00000371085	NM_000516.4	21	gaG/gaT	1/13	0.0131298494985721	3	FACETS	1	0.838	1	0.501	0.419	0.591	INDETERMINATE	1	TRUE	1	0.15	3		382	630	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799574	72799574	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	184	574	0	ENST00000325599.8:c.1595T>C	p.Leu532Pro	p.L532P	ENST00000325599	NM_018130.2	532	cTt/cCt	11/11	1	2	FACETS	0.954	0.884	1	1	0.995	1	CLONAL	4	TRUE	1	0.15	2		574	643	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861058	35861058	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	102	414	0	ENST00000303115.3:c.187G>T	p.Asp63Tyr	p.D63Y	ENST00000303115	NM_002185.3	63	Gat/Tat	2/8	0.0746800087261446	3	FACETS	1	0.951	1	1	0.985	1	INDETERMINATE	3	TRUE	1	0.15	3		414	445	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874644	35874644	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	92	433	0	ENST00000303115.3:c.800G>T	p.Arg267Met	p.R267M	ENST00000303115	NM_002185.3	267	aGg/aTg	6/8	0.0746800087261446	3	FACETS	0.877	0.785	0.973	1	0.985	1	INDETERMINATE	4	TRUE	1	0.15	3		433	376	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158577	26158577	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	56	703	0	ENST00000289316.2:c.180G>T	p.Met60Ile	p.M60I	ENST00000289316	NM_138720.2	60	atG/atT	1/2	0.0131298494985721	3	FACETS	1	0.937	1	0.588	0.503	0.682	INDETERMINATE	1	TRUE	1	0.15	3		703	682	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652194	36652194	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs947512082	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	276	928	0	ENST00000244741.5:c.316G>A	p.Ala106Thr	p.A106T	ENST00000244741	NM_000389.4	106	Gca/Aca	2/3	0.0131298494985721	3	FACETS	0.99	0.931	1	1	0.995	1	INDETERMINATE	4	TRUE	1	0.15	3		928	999	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983033	111983033	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	259	799	0	ENST00000368678.4:c.1514A>G	p.Glu505Gly	p.E505G	ENST00000368678		505	gAa/gGa	13/13	0.0131298494985721	3	FACETS	0.966	0.906	1	1	0.995	1	INDETERMINATE	4	TRUE	1	0.15	3		799	961	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983103	111983103	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	61	687	0	ENST00000368678.4:c.1444A>G	p.Met482Val	p.M482V	ENST00000368678		482	Atg/Gtg	13/13	0.0131298494985721	3	FACETS	1	0.915	1	0.544	0.468	0.627	INDETERMINATE	1	TRUE	1	0.15	3		687	804	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444309	50444309	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	116	370	0	ENST00000331340.3:c.239A>G	p.Glu80Gly	p.E80G	ENST00000331340	NM_006060.4	80	gAg/gGg	4/8	0.201159998524542	4	FACETS	1	0.949	1	1	0.949	1	CLONAL	3	TRUE	1	0.15	4		370	552	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69012046	69012046	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	152	552	0	ENST00000288368.4:c.2683C>A	p.His895Asn	p.H895N	ENST00000288368	NM_024870.2	895	Cac/Aac	23/40	0.0746800087261446	3	FACETS	1	0.936	1	1	0.992	1	INDETERMINATE	4	TRUE	1	0.15	3		552	534	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325642	87325642	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	110	586	0	ENST00000277120.3:c.519T>A	p.Asp173Glu	p.D173E	ENST00000277120		173	gaT/gaA	6/19	1	2	FACETS	0.984	0.888	1	1	0.991	1	CLONAL	3	TRUE	1	0.15	2		586	497	SUCCESS
AR	367	MSKCC	GRCh37	X	66765440	66765440	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	221	998	0	ENST00000374690.3:c.452C>T	p.Ala151Val	p.A151V	ENST00000374690	NM_000044.3	151	gCa/gTa	1/8	0.0746800087261446	3	FACETS	0.898	0.837	0.961	1	0.993	1	INDETERMINATE	4	TRUE	1	0.15	3		998	882	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937662	76937662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	22	494	1	ENST00000373344.5:c.3086C>A	p.Pro1029His	p.P1029H	ENST00000373344	NM_000489.3	1029	cCt/cAt	9/35	0.0746800087261446	3	FACETS	0.848	0.656	1	0.424	0.328	0.535	INDETERMINATE	1	TRUE	1	0.15	3		495	372	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	79	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.539	0.477	0.605	0.539	0.477	0.605	SUBCLONAL	1	TRUE	1	0.763406805830226	2		327	384	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0050269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	68	283	1	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.489	0.428	0.555	0.489	0.428	0.555	SUBCLONAL	1	TRUE	1	0.763406805830226	2		284	364	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0050269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	113	583	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.496	0.447	0.547	0.496	0.447	0.547	SUBCLONAL	1	TRUE	1	0.763406805830226	2		583	597	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	75	235	0	ENST00000397062.3:c.92G>A	p.Gly31Glu	p.G31E	ENST00000397062	NM_006164.4	31	gGa/gAa	2/5	1	2	FACETS	0.655	0.579	0.735	0.655	0.579	0.735	SUBCLONAL	1	TRUE	1	0.763406805830226	2		235	300	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0050269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	50	217	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	0.475	0.405	0.549	0.475	0.405	0.549	SUBCLONAL	1	TRUE	1	0.763406805830226	2		217	276	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696462	47696462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	79	355	0	ENST00000347630.2:c.361C>T	p.Arg121Trp	p.R121W	ENST00000347630	NM_001007230.1	121	Cgg/Tgg	6/11	1	2	FACETS	0.517	0.457	0.581	0.517	0.457	0.581	SUBCLONAL	1	TRUE	1	0.763406805830226	2		355	400	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717678	89717679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAGAC	novel	NA	P-0050269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	75	379	0	ENST00000371953.3:c.707_711dup	p.Phe238ThrfsTer20	p.F238Tfs*20	ENST00000371953	NM_000314.4	235	gaa/gAAGACaa	7/9	1	2	FACETS	0.449	0.394	0.506	0.449	0.394	0.506	SUBCLONAL	1	TRUE	1	0.763406805830226	2		379	438	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663437	67663437	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0050269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	44	222	0	ENST00000264010.4:c.1837+1G>C		p.X613_splice	ENST00000264010	NM_006565.3	613			1	2	FACETS	0.393	0.331	0.461	0.393	0.331	0.461	SUBCLONAL	1	TRUE	1	0.763406805830226	2		222	293	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589614	67589635	+	protein_altering_variant	In_Frame_Del	DEL	AAGTCGAGAATATGATAGATTA	AAGTCGAGAATATGATAGATTA	T	novel	NA	P-0050269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	10	177	0	ENST00000274335.5:c.1377_1398delinsT	p.Lys459_Leu466delinsAsn	p.K459_L466delinsN	ENST00000274335		459	aaAAGTCGAGAATATGATAGATTA/aaT	10/15	1	2	FACETS	0.15	0.101	0.211	0.15	0.101	0.211	SUBCLONAL	1	TRUE	1	0.763406805830226	2		177	175	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0050270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	16	325	2	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.283418889913837	1	FACETS	0.682	0.508	0.887	0.682	0.508	0.887	SUBCLONAL	1	TRUE	0	0.283418889913837	1		327	142	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913499	NA	P-0050270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	30	211	0	ENST00000345146.2:c.394C>A	p.Arg132Ser	p.R132S	ENST00000345146	NM_005896.2	132	Cgt/Agt	4/10	0.1814210020428	4	FACETS	1	0.844	1			1	CLONAL	1	TRUE	NA	0.283418889913837	4		211	259	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79968135	79968135	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	55	471	0	ENST00000265081.6:c.865A>G	p.Arg289Gly	p.R289G	ENST00000265081	NM_002439.4	289	Aga/Gga	5/24	0.283418889913837	3	FACETS	1	0.869	1	0.507	0.434	0.586	CLONAL	1	TRUE	1	0.283418889913837	3		471	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0050271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	596	481	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.899702056578723	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.899702056578723	2		481	640	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	289	429	0	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.899702056578723	2		429	618	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664899	29664899	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs1060500376	NA	P-0050271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	454	262	0	ENST00000356175.3:c.6641+1G>C		p.X2214_splice	ENST00000356175	NM_000267.3	2214			0.899702056578723	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.899702056578723	2		262	489	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	171	277	0	ENST00000256196.4:c.68G>A	p.Gly23Asp	p.G23D	ENST00000256196		23	gGc/gAc	1/6	1	2	FACETS	0.888	0.826	0.951	0.888	0.826	0.951	CLONAL	1	TRUE	1	0.899702056578723	2		277	428	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428962	47428962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	276	593	0	ENST00000377045.4:c.1325C>T	p.Thr442Met	p.T442M	ENST00000377045	NM_001654.4	442	aCg/aTg	13/16	1	2	FACETS	0.883	0.834	0.932	0.883	0.834	0.932	CLONAL	1	TRUE	1	0.899702056578723	2		593	695	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518169	187518169	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	222	333	0	ENST00000441802.2:c.12525G>T	p.Trp4175Cys	p.W4175C	ENST00000441802	NM_005245.3	4175	tgG/tgT	25/27	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.899702056578723	2		333	474	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	198	413	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.345634990210905	5	FACETS	0.96	0.898	1	0.96	0.898	1	CLONAL	3	TRUE	2	0.486164780678866	5		413	489	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0050272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	109	401	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.486164780678866	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.486164780678866	1		401	261	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579269	7579474	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCATTGAAGTCTCATGGAAGCCAGCCCCTCAGGGCAACTGACCGTGCAAGTCACAGACTTGGCTGTCCCAGAATGCAAGAAGCCCAGACGGAAACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGGACAGAAGATGACAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTGCAGGGGCCACGGGG	GGCATTGAAGTCTCATGGAAGCCAGCCCCTCAGGGCAACTGACCGTGCAAGTCACAGACTTGGCTGTCCCAGAATGCAAGAAGCCCAGACGGAAACCGTAGCTGCCCTGGTAGGTTTTCTGGGAAGGGACAGAAGATGACAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTGCAGGGGCCACGGGG	-	novel	NA	P-0050272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	210	381	0	ENST00000269305.4:c.213_375+43del		p.X71_splice	ENST00000269305	NM_001126112.2	71		4/11	0.486164780678866	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.486164780678866	2		381	358	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0050273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	36	583	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.75	0.615	0.901	0.75	0.615	0.901	CLONAL	1	TRUE	1	0.17	2		583	565	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0050273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	101	836	1	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.17	2		837	833	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624275	89624275	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204910	NA	P-0050273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	27	353	1	ENST00000371953.3:c.49C>T	p.Gln17Ter	p.Q17*	ENST00000371953	NM_000314.4	17	Caa/Taa	1/9	1	2	FACETS	0.666	0.529	0.823	0.666	0.529	0.823	SUBCLONAL	1	TRUE	1	0.17	2		354	477	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199469672	NA	P-0050273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	24	580	1	ENST00000374080.3:c.131G>T	p.Gly44Val	p.G44V	ENST00000374080		44	gGt/gTt	2/45	1	2	FACETS	0.385	0.3	0.484	0.385	0.3	0.484	SUBCLONAL	1	TRUE	1	0.17	2		581	733	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023753	27023753	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1383675220	NA	P-0050273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	29	523	1	ENST00000324856.7:c.862del	p.Gln288SerfsTer75	p.Q288Sfs*75	ENST00000324856	NM_006015.4	287	Ccc/cc	1/20	1	2	FACETS	0.635	0.509	0.78	0.635	0.509	0.78	SUBCLONAL	1	TRUE	1	0.17	2		524	537	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15952245	15952245	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	62	636	0	ENST00000268712.3:c.6450C>G	p.Ile2150Met	p.I2150M	ENST00000268712	NM_006311.3	2150	atC/atG	41/46	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.17	2		636	719	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120460314	120460314	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	60	503	0	ENST00000256646.2:c.6001G>T	p.Ala2001Ser	p.A2001S	ENST00000256646	NM_024408.3	2001	Gcc/Tcc	33/34	1	2	FACETS	0.645	0.555	0.744	0.645	0.555	0.744	SUBCLONAL	1	TRUE	1	0.28	2		503	664	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115941	8115942	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0050274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	78	411	0	ENST00000346208.3:c.1289_1290dup	p.Gly431LeufsTer45	p.G431Lfs*45	ENST00000346208		429	-/TT	6/6	1	2	FACETS	0.906	0.797	1	0.906	0.797	1	CLONAL	1	TRUE	1	0.28	2		411	615	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863224683	NA	P-0050275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	397	715	0	ENST00000269305.4:c.388C>G	p.Leu130Val	p.L130V	ENST00000269305	NM_001126112.2	130	Ctc/Gtc	5/11	0.44633832479221	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.44633832479221	2		715	850	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0050275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	634	401	2	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.44633832479221	5	FACETS	1	0.991	1			1	CLONAL	4	TRUE	NA	0.44633832479221	5		403	1121	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0050275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	389	296	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.441714430394675	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.44633832479221	2		296	866	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0050275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	309	364	0	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	0.44633832479221	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	0	0.44633832479221	3		364	548	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46724370	46724370	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs138566817	NA	P-0050275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	76	409	0	ENST00000371975.4:c.223C>T	p.Arg75Ter	p.R75*	ENST00000371975	NM_003579.3	75	Cga/Tga	4/18	0.44633832479221	3	FACETS	0.801	0.704	0.905	0.267	0.234	0.302	CLONAL	1	TRUE	0	0.44633832479221	3		409	520	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315354	30315354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1480541649	NA	P-0050275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	93	306	0	ENST00000322652.5:c.1039G>A	p.Glu347Lys	p.E347K	ENST00000322652	NM_015355.2	347	Gaa/Aaa	10/16	0.44633832479221	4	FACETS	1	0.949	1	0.556	0.496	0.62	CLONAL	1	TRUE	2	0.44633832479221	4		306	542	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404607	70404609	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0050275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	193	400	1	ENST00000373644.4:c.2122_2124del	p.Glu708del	p.E708del	ENST00000373644	NM_030625.2	707	gtGGAg/gtg	4/12	0.44633832479221	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.44633832479221	3		401	490	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622618	158622618	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	175	349	0	ENST00000263640.3:c.881A>G	p.Tyr294Cys	p.Y294C	ENST00000263640	NM_001105.4	294	tAt/tGt	8/11	0.44633832479221	4	FACETS	0.921	0.852	0.991	0.921	0.852	0.991	CLONAL	2	TRUE	2	0.44633832479221	4		349	616	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394875	394875	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	158	393	0	ENST00000380956.4:c.271C>T	p.Pro91Ser	p.P91S	ENST00000380956	NM_001195286.1	91	Ccc/Tcc	3/9	0.44633832479221	4	FACETS	0.777	0.714	0.842	0.777	0.714	0.842	SUBCLONAL	2	TRUE	2	0.44633832479221	4		393	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0050276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	27	646	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.306	0.242	0.379	0.306	0.242	0.379	SUBCLONAL	1	FALSE	1	0.254764674582784	2		646	693	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0050276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	19	335	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.425	0.322	0.546	0.425	0.322	0.546	SUBCLONAL	1	FALSE	1	0.254764674582784	2		335	351	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968867	15968867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772605440	NA	P-0050276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	51	506	1	ENST00000268712.3:c.4883G>A	p.Arg1628His	p.R1628H	ENST00000268712	NM_006311.3	1628	cGt/cAt	33/46	1	2	FACETS	0.615	0.522	0.718	0.615	0.522	0.718	SUBCLONAL	1	FALSE	1	0.254764674582784	2		507	651	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0050276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	43	455	0	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	1	2	FACETS	0.635	0.53	0.75	0.635	0.53	0.75	SUBCLONAL	1	FALSE	1	0.254764674582784	2		455	532	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881329	37881329	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	54	732	0	ENST00000269571.5:c.2521C>A	p.Leu841Ile	p.L841I	ENST00000269571		841	Ctc/Atc	21/27	1	2	FACETS	0.546	0.465	0.634	0.546	0.465	0.634	SUBCLONAL	1	FALSE	1	0.254764674582784	2		732	777	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981283	201981284	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0050276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	52	794	0	ENST00000359651.3:c.363_364dup	p.His122ProfsTer34	p.H122Pfs*34	ENST00000359651		121	ctc/ctCCc	2/8	1	2	FACETS	0.517	0.439	0.604	0.517	0.439	0.604	SUBCLONAL	1	FALSE	1	0.254764674582784	2		794	789	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488281	56488281	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	47	560	0	ENST00000267101.3:c.1800C>G	p.Ile600Met	p.I600M	ENST00000267101	NM_001982.3	600	atC/atG	15/28	1	2	FACETS	0.546	0.459	0.641	0.546	0.459	0.641	SUBCLONAL	1	FALSE	1	0.254764674582784	2		560	676	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584817	48584817	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	37	383	0	ENST00000342988.3:c.895G>T	p.Gly299Ter	p.G299*	ENST00000342988	NM_005359.5	299	Gga/Tga	7/12	0.254764674582784	1	FACETS	0.515	0.424	0.617	0.515	0.424	0.617	SUBCLONAL	1	FALSE	0	0.254764674582784	1		383	492	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207097	1207131	+	frameshift_variant	Frame_Shift_Del	DEL	AGGTGAAGGAGGTGCTGGACTCGGAGACGCTGTGC	AGGTGAAGGAGGTGCTGGACTCGGAGACGCTGTGC	-	novel	NA	P-0050276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	93	812	0	ENST00000326873.7:c.188_222del	p.Val63GlufsTer88	p.V63Efs*88	ENST00000326873	NM_000455.4	62	aAGGTGAAGGAGGTGCTGGACTCGGAGACGCTGTGC/a	1/10	0.254764674582784	1	FACETS	0.813	0.722	0.909	0.813	0.722	0.909	CLONAL	1	FALSE	0	0.254764674582784	1		812	784	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855837	45855837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762141272	NA	P-0050276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	92	896	0	ENST00000391945.4:c.1973G>A	p.Arg658His	p.R658H	ENST00000391945	NM_000400.3	658	cGc/cAc	21/23	1	2	FACETS	0.811	0.719	0.909	0.811	0.719	0.909	CLONAL	1	FALSE	1	0.254764674582784	2		896	891	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0050277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	345	927	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.690146043790761	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.690146043790761	1		927	626	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0050277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	186	424	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	0.928	0.862	0.995	0.928	0.862	0.995	CLONAL	1	TRUE	1	0.690146043790761	2		424	581	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562657	29562660	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs1064794276	NA	P-0050277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	213	403	0	ENST00000356175.3:c.3739_3742del	p.Phe1247IlefsTer18	p.F1247Ifs*18	ENST00000356175	NM_000267.3	1246	cTGTTt/ct	28/57	0.690146043790761	1	FACETS	0.972	0.917	1	0.972	0.917	1	CLONAL	1	TRUE	0	0.690146043790761	1		403	416	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911639	114911639	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	111	376	0	ENST00000543371.1:c.1157G>A	p.Arg386Gln	p.R386Q	ENST00000543371	NM_001198531.1	386	cGg/cAg	10/14	1	2	FACETS	0.485	0.437	0.536	0.485	0.437	0.536	SUBCLONAL	1	TRUE	1	0.690146043790761	2		376	663	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436695	110436695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	61	852	0	ENST00000375856.3:c.1706G>A	p.Arg569Gln	p.R569Q	ENST00000375856	NM_003749.2	569	cGa/cAa	1/2	0.413458344543794	1	FACETS	0.127	0.109	0.146	0.127	0.109	0.146	INDETERMINATE	1	TRUE	0	0.690146043790761	1		852	914	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510601	38510603	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0050277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	329	680	0	ENST00000254066.5:c.857_859del	p.Phe286del	p.F286del	ENST00000254066	NM_000964.3	285	acCTTc/acc	7/9	0.690146043790761	1	FACETS	0.985	0.94	1	0.985	0.94	1	CLONAL	1	TRUE	0	0.690146043790761	1		680	634	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619918	21619918	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	106	553	0	ENST00000382592.4:c.248C>T	p.Ser83Phe	p.S83F	ENST00000382592	NM_014572.2	83	tCc/tTc	2/8	0.413458344543794	1	FACETS	0.323	0.29	0.359	0.323	0.29	0.359	INDETERMINATE	1	TRUE	0	0.690146043790761	1		553	622	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682919	241682919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs942065027	NA	P-0050277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	157	568	0	ENST00000366560.3:c.104C>T	p.Ser35Leu	p.S35L	ENST00000366560	NM_000143.3	35	tCg/tTg	1/10	0.446214550447232	3	FACETS	0.632	0.579	0.688	0.316	0.289	0.344	SUBCLONAL	1	TRUE	1	0.690146043790761	3		568	968	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450931	70450931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	124	431	0	ENST00000373644.4:c.5771C>T	p.Ser1924Phe	p.S1924F	ENST00000373644	NM_030625.2	1924	tCt/tTt	12/12	1	2	FACETS	0.548	0.496	0.602	0.548	0.496	0.602	SUBCLONAL	1	TRUE	1	0.690146043790761	2		431	656	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233271	46233271	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	106	303	0	ENST00000334344.6:c.1490C>G	p.Ser497Cys	p.S497C	ENST00000334344	NM_152641.2	497	tCt/tGt	11/21	1	2	FACETS	0.538	0.483	0.595	0.538	0.483	0.595	SUBCLONAL	1	TRUE	1	0.690146043790761	2		303	571	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432147	49432147	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	131	762	0	ENST00000301067.7:c.8992G>C	p.Asp2998His	p.D2998H	ENST00000301067	NM_003482.3	2998	Gat/Cat	34/54	1	2	FACETS	0.36	0.326	0.396	0.36	0.326	0.396	SUBCLONAL	1	TRUE	1	0.690146043790761	2		762	1054	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070567	67070568	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0050277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	122	198	0	ENST00000412916.2:c.192_193del	p.Leu66ProfsTer16	p.L66Pfs*16	ENST00000412916		64	cTG/c	3/6	0.690146043790761	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.690146043790761	1		198	229	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068373	16068373	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	15	20	0	ENST00000268712.3:c.538G>C	p.Glu180Gln	p.E180Q	ENST00000268712	NM_006311.3	180	Gag/Cag	5/46	0.690146043790761	1	FACETS	0.918	0.72	1	0.918	0.72	1	CLONAL	1	TRUE	0	0.690146043790761	1		20	31	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121151	11121151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	133	773	0	ENST00000358026.2:c.2218G>A	p.Glu740Lys	p.E740K	ENST00000358026	NM_001128849.1	740	Gag/Aag	15/36	0.205872182258126	1	FACETS	0.25	0.226	0.275	0.25	0.226	0.275	INDETERMINATE	1	TRUE	0	0.690146043790761	1		773	1011	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950374	38950374	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	79	335	0	ENST00000357387.3:c.3576G>C	p.Glu1192Asp	p.E1192D	ENST00000357387	NM_152756.3	1192	gaG/gaC	31/38	0.205872182258126	1	FACETS	0.296	0.26	0.333	0.296	0.26	0.333	INDETERMINATE	1	TRUE	0	0.690146043790761	1		335	507	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170911	56170911	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	26	309	0	ENST00000399503.3:c.1739G>C	p.Arg580Thr	p.R580T	ENST00000399503	NM_005921.1	580	aGa/aCa	10/20	0.690146043790761	1	FACETS	0.138	0.109	0.172	0.138	0.109	0.172	SUBCLONAL	1	TRUE	0	0.690146043790761	1		309	357	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56171004	56171004	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	30	337	0	ENST00000399503.3:c.1832G>C	p.Gly611Ala	p.G611A	ENST00000399503	NM_005921.1	611	gGa/gCa	10/20	0.690146043790761	1	FACETS	0.149	0.12	0.182	0.149	0.12	0.182	SUBCLONAL	1	TRUE	0	0.690146043790761	1		337	382	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174888	56174889	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0050277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	192	419	0	ENST00000399503.3:c.2049dup	p.Val684CysfsTer13	p.V684Cfs*13	ENST00000399503	NM_005921.1	683	gtt/gTtt	11/20	0.690146043790761	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.690146043790761	1		419	356	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522357	176522357	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs34158682	NA	P-0050277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	178	682	1	ENST00000292408.4:c.1546G>T	p.Asp516Tyr	p.D516Y	ENST00000292408	NM_213647.1	516	Gac/Tac	12/18	0.690146043790761	1	FACETS	0.506	0.468	0.546	0.506	0.468	0.546	SUBCLONAL	1	TRUE	0	0.690146043790761	1		683	667	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202444	138202444	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	151	655	0	ENST00000237289.4:c.2361G>C	p.Gln787His	p.Q787H	ENST00000237289	NM_001270507.1	787	caG/caC	9/9	1	2	FACETS	0.499	0.456	0.544	0.499	0.456	0.544	SUBCLONAL	1	TRUE	1	0.690146043790761	2		655	877	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0050278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	20	349	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.529	0.403	0.677	0.529	0.403	0.677	SUBCLONAL	1	TRUE	1	0.13	2		349	582	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498206	498206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	34	399	0	ENST00000399788.2:c.52G>A	p.Glu18Lys	p.E18K	ENST00000399788	NM_001042603.1	18	Gag/Aag	1/28	1	2	FACETS	0.914	0.746	1	0.914	0.746	1	CLONAL	1	TRUE	1	0.13	2		399	572	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502455	186502455	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	25	263	0	ENST00000323963.5:c.178C>T	p.Gln60Ter	p.Q60*	ENST00000323963		60	Cag/Tag	3/11	1	2	FACETS	0.872	0.686	1	0.872	0.686	1	CLONAL	1	TRUE	1	0.13	2		263	441	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665743	29665743	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	167	194	0	ENST00000356175.3:c.6778G>T	p.Gly2260Ter	p.G2260*	ENST00000356175	NM_000267.3	2260	Gga/Tga	45/57	0.607349425535042	2	FACETS	0.946	0.891	1	0.946	0.891	1	CLONAL	2	TRUE	0	0.639564642793485	2		194	276	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	17	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	1	0.21	2		327	137	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0050280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	61	296	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	0.892	0.769	1	0.892	0.769	1	CLONAL	1	TRUE	1	0.21	2		296	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0050280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	74	319	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	1	2	FACETS	0.929	0.812	1	0.929	0.812	1	CLONAL	1	TRUE	1	0.21	2		319	759	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555687605	NA	P-0050280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	11	75	0	ENST00000342988.3:c.1610A>G	p.Asp537Gly	p.D537G	ENST00000342988	NM_005359.5	537	gAc/gGc	12/12	0.3	2	FACETS	0.595	0.412	0.822			1	SUBCLONAL	1	TRUE	NA	0.21	2		75	176	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160638	56160639	+	missense_variant	Missense_Mutation	DNP	AA	AA	CC	novel	NA	P-0050280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	12	80	0	ENST00000399503.3:c.912_913delinsCC	p.Asn305His	p.N305H	ENST00000399503	NM_005921.1	304	acAAac/acCCac	4/20	1	2	FACETS	0.486	0.341	0.665	0.486	0.341	0.665	SUBCLONAL	1	TRUE	1	0.21	2		80	235	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188174	11188174	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	165	381	0	ENST00000361445.4:c.5920T>C	p.Tyr1974His	p.Y1974H	ENST00000361445	NM_004958.3	1974	Tac/Cac	43/58	0.607645353077926	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.621667847414366	1		381	346	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36945081	36945081	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	238	599	0	ENST00000361632.4:c.17del	p.Asn6ThrfsTer4	p.N6Tfs*4	ENST00000361632		6	aAc/ac	2/16	1	2	FACETS	0.898	0.84	0.957	0.898	0.84	0.957	CLONAL	1	TRUE	1	0.621667847414366	2		599	853	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332716	65332716	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	49	325	0	ENST00000342505.4:c.823G>T	p.Glu275Ter	p.E275*	ENST00000342505	NM_002227.2	275	Gaa/Taa	7/25	1	2	FACETS	0.765	0.656	0.882	0.765	0.656	0.882	SUBCLONAL	1	TRUE	1	0.621667847414366	2		325	206	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650177	206650177	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	210	492	0	ENST00000367120.3:c.697A>G	p.Ile233Val	p.I233V	ENST00000367120	NM_014002.3	233	Atc/Gtc	7/22	1	2	FACETS	0.946	0.882	1	0.946	0.882	1	CLONAL	1	TRUE	1	0.621667847414366	2		492	714	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	55	413	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.906	0.777	1	0.906	0.777	1	CLONAL	1	TRUE	1	0.282274940883918	2		413	430	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0050283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	62	618	1	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.258393100786936	1	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	0	0.282274940883918	1		619	369	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366483	118366483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782730461	NA	P-0050283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	35	390	3	ENST00000534358.1:c.5432G>A	p.Arg1811Gln	p.R1811Q	ENST00000534358	NM_005933.3	1811	cGa/cAa	19/36	1	2	FACETS	0.727	0.597	0.872	0.727	0.597	0.872	SUBCLONAL	1	TRUE	1	0.282274940883918	2		393	341	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376700	118376700	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	111	383	0	ENST00000534358.1:c.10093G>C	p.Val3365Leu	p.V3365L	ENST00000534358	NM_005933.3	3365	Gtc/Ctc	27/36	1	2	FACETS	0.612	0.552	0.676	0.612	0.552	0.676	SUBCLONAL	1	TRUE	1	0.629713085541255	2		383	576	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183758	10183759	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0050284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	326	809	0	ENST00000256474.2:c.228_229del	p.Phe76LeufsTer55	p.F76Lfs*55	ENST00000256474	NM_000551.3	76	tTC/t	1/3	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.629713085541255	2		809	1031	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807348	1807348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	223	719	0	ENST00000260795.2:c.1597G>A	p.Gly533Arg	p.G533R	ENST00000260795		533	Ggg/Agg	11/17	1	2	FACETS	0.757	0.706	0.811	0.757	0.706	0.811	SUBCLONAL	1	TRUE	1	0.629713085541255	2		719	935	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158416	106158416	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	115	192	0	ENST00000380013.4:c.3317A>G	p.Glu1106Gly	p.E1106G	ENST00000380013	NM_001127208.2	1106	gAg/gGg	3/11	1	2	FACETS	0.966	0.879	1	0.966	0.879	1	CLONAL	1	TRUE	1	0.629713085541255	2		192	378	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0050286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	132	690	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.118850303644134	4	FACETS	1	0.961	1	1	0.961	1	INDETERMINATE	2	TRUE	2	0.242621432058864	4		690	615	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260269	10260269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	84	608	0	ENST00000340748.4:c.2398G>A	p.Gly800Arg	p.G800R	ENST00000340748		800	Ggg/Agg	25/40	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.242621432058864	2		608	593	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998136	169998136	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	67	386	0	ENST00000295797.4:c.827C>G	p.Thr276Arg	p.T276R	ENST00000295797	NM_002740.5	276	aCa/aGa	9/18	1	2	FACETS	0.966	0.84	1	0.966	0.84	1	CLONAL	1	TRUE	1	0.242621432058864	2		386	572	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034418	47034421	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GTCA	GTCA	-	novel	NA	P-0050286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	64	656	0	ENST00000377604.3:c.504_507del	p.Gln169AlafsTer96	p.Q169Afs*96	ENST00000377604	NM_001204468.1	168	gGTCAg/gg	6/24	1	2	FACETS	0.783	0.677	0.897	0.783	0.677	0.897	SUBCLONAL	1	TRUE	1	0.242621432058864	2		656	674	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0050287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	147	454	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.380371557048065	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.380371557048065	1		455	573	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0050287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	342	461	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.112866718731368	5	FACETS	1	0.98	1			1	INDETERMINATE	4	TRUE	NA	0.380371557048065	5		461	674	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535430	66535430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	101	818	0	ENST00000273854.3:c.31C>T	p.Arg11Cys	p.R11C	ENST00000273854	NM_004439.5	11	Cgc/Tgc	1/18	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.380371557048065	2		818	501	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242651	46242651	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	49	284	0	ENST00000334344.6:c.1613G>C	p.Cys538Ser	p.C538S	ENST00000334344	NM_152641.2	538	tGt/tCt	13/21	0.380371557048065	1	FACETS	0.77	0.657	0.892	0.77	0.657	0.892	SUBCLONAL	1	TRUE	0	0.380371557048065	1		284	271	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188272	10188273	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs869025649	NA	P-0050288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	119	535	0	ENST00000256474.2:c.419_420del	p.Leu140GlnfsTer3	p.L140Qfs*3	ENST00000256474	NM_000551.3	139	TCt/t	2/3	0.378250787629777	1	FACETS	0.963	0.873	1	0.963	0.873	1	CLONAL	1	TRUE	0	0.378250787629777	1		535	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0050289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	310	657	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.818570648691454	1	FACETS	0.917	0.879	0.954	0.917	0.879	0.954	CLONAL	1	TRUE	0	0.818570648691454	1		657	488	SUCCESS
AR	367	MSKCC	GRCh37	X	66943552	66943552	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137852578	NA	P-0050289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	134	215	0	ENST00000374690.3:c.2632A>G	p.Thr878Ala	p.T878A	ENST00000374690	NM_000044.3	878	Act/Gct	8/8	1	1	FACETS	0.608	0.561	0.656	0.608	0.561	0.656	SUBCLONAL	1	TRUE	0	0.818570648691454	1		215	318	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0050290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	34	394	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.972	0.796	1	0.972	0.796	1	CLONAL	1	TRUE	1	0.22	2		394	318	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0050290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	36	563	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	1	2	FACETS	0.998	0.823	1	0.998	0.823	1	CLONAL	1	TRUE	1	0.22	2		563	328	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106556	27106556	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	60	912	1	ENST00000324856.7:c.6167T>A	p.Leu2056His	p.L2056H	ENST00000324856	NM_006015.4	2056	cTc/cAc	20/20	1	2	FACETS	0.867	0.747	0.998	0.867	0.747	0.998	CLONAL	1	TRUE	1	0.22	2		913	629	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653805	89653805	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659443	NA	P-0050290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	16	398	0	ENST00000371953.3:c.103A>G	p.Met35Val	p.M35V	ENST00000371953	NM_000314.4	35	Atg/Gtg	2/9	1	2	FACETS	0.717	0.531	0.937	0.717	0.531	0.937	CLONAL	1	TRUE	1	0.22	2		398	203	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692887	89692887	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	16	356	0	ENST00000371953.3:c.371G>T	p.Cys124Phe	p.C124F	ENST00000371953	NM_000314.4	124	tGt/tTt	5/9	1	2	FACETS	0.529	0.391	0.694	0.529	0.391	0.694	SUBCLONAL	1	TRUE	1	0.22	2		356	275	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3795277	3795277	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1555475352	NA	P-0050290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	21	471	0	ENST00000262367.5:c.3914+1G>T		p.X1305_splice	ENST00000262367	NM_004380.2	1305			1	2	FACETS	0.593	0.456	0.752	0.593	0.456	0.752	SUBCLONAL	1	TRUE	1	0.22	2		471	322	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0050290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	35	264	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.0866836386982495	3	FACETS	1	0.88	1	0.547	0.449	0.656	INDETERMINATE	1	TRUE	1	0.22	3		264	323	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542188	187542188	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	36	480	0	ENST00000441802.2:c.5552A>C	p.Asp1851Ala	p.D1851A	ENST00000441802	NM_005245.3	1851	gAc/gCc	10/27	0.57569357909538	3	FACETS	0.282	0.231	0.339	0.141	0.115	0.17	SUBCLONAL	1	FALSE	1	0.57569357909538	3		480	572	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374298	138374298	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	160	417	0	ENST00000289153.2:c.3146T>G	p.Leu1049Arg	p.L1049R	ENST00000289153	NM_006219.2	1049	cTc/cGc	22/22	0.276460895973447	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	FALSE	0	0.3	2		417	487	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753764	42753764	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	205	742	0	ENST00000222329.4:c.500del	p.Ser167TyrfsTer104	p.S167Yfs*104	ENST00000222329	NM_006494.2	167	tCa/ta	4/4	1	2	FACETS	0.756	0.702	0.812	1	0.991	1	SUBCLONAL	2	FALSE	1	0.3	2		742	904	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960013	134960013	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	170	478	0	ENST00000398015.3:c.2370G>T	p.Trp790Cys	p.W790C	ENST00000398015	NM_004441.4	790	tgG/tgT	13/16	0.276460895973447	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	FALSE	0	0.3	2		478	523	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629410	187629410	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1236982918	NA	P-0050309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	85	543	0	ENST00000441802.2:c.1572C>G	p.Asn524Lys	p.N524K	ENST00000441802	NM_005245.3	524	aaC/aaG	2/27	1	2	FACETS	0.915	0.81	1	0.915	0.81	1	CLONAL	1	FALSE	1	0.3	2		543	619	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	48	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.899	0.762	1	0.899	0.762	1	CLONAL	1	TRUE	1	0.256007430177707	2		327	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0050310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	60	662	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.256007430177707	2		662	420	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	124	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.477887121885797	2		327	504	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560804	9560804	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	49	381	0	ENST00000353224.5:c.978G>A	p.Met326Ile	p.M326I	ENST00000353224	NM_177990.2	326	atG/atA	4/10	1	2	FACETS	0.394	0.333	0.46	0.394	0.333	0.46	SUBCLONAL	1	TRUE	1	0.477887121885797	2		381	521	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	81	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.253954836712373	4	FACETS	0.863	0.768	0.963	0.863	0.768	0.963	CLONAL	3	TRUE	1	0.253954836712373	4		327	309	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0050312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	99	633	0	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.253954836712373	2	FACETS	0.884	0.794	0.979	0.884	0.794	0.979	CLONAL	2	TRUE	0	0.253954836712373	2		633	441	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63661984	63661985	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0050312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	41	391	0	ENST00000279873.7:c.88_89insT	p.Glu30ValfsTer45	p.E30Vfs*45	ENST00000279873	NM_032199.2	30	gaa/gTaa	2/10	0.253954836712373	5	FACETS	1	0.909	1	0.38	0.317	0.45	CLONAL	1	TRUE	2	0.253954836712373	5		391	391	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435912	56435912	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	92	635	0	ENST00000407977.2:c.1225del	p.Gln409SerfsTer10	p.Q409Sfs*10	ENST00000407977		409	Cag/ag	9/10	0.226499714383288	4	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	2	0.253954836712373	4		635	430	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652798	212652798	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	11	403	0	ENST00000342788.4:c.508C>A	p.Pro170Thr	p.P170T	ENST00000342788	NM_005235.2	170	Cca/Aca	4/28	0.226499714383288	4	FACETS	0.527	0.364	0.73	0.264	0.182	0.365	SUBCLONAL	1	TRUE	2	0.253954836712373	4		403	206	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970969	21970969	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	177	566	0	ENST00000304494.5:c.389T>G	p.Leu130Arg	p.L130R	ENST00000304494	NM_000077.4	130	cTg/cGg	2/3	0.231368449595117	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	0	0.253954836712373	3		566	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0050313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	133	522	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.824436815685031	1	FACETS	0.797	0.742	0.851	0.797	0.742	0.851	SUBCLONAL	1	TRUE	0	0.824436815685031	1		522	238	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011144	12011144	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	113	393	0	ENST00000353533.5:c.551C>A	p.Ser184Ter	p.S184*	ENST00000353533	NM_003010.3	184	tCg/tAg	5/11	0.824436815685031	1	FACETS	0.76	0.702	0.818	0.76	0.702	0.818	SUBCLONAL	1	TRUE	0	0.824436815685031	1		393	212	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880997	37880998	+	protein_altering_variant	In_Frame_Ins	INS	-	-	TCT	rs397516979	NA	P-0050313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	921	591	0	ENST00000269571.5:c.2326_2327insTCT	p.Gly776delinsValCys	p.G776delinsVC	ENST00000269571		776	ggt/gTCTgt	20/27	0.824436815685031	3	FACETS	0.974	0.959	0.988			1	CLONAL	3	TRUE	NA	0.824436815685031	3		591	1080	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138897	64138898	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGT	novel	NA	P-0050313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	100	557	0	ENST00000334205.4:c.2267_2269dup	p.Val756dup	p.V756dup	ENST00000334205	NM_003942.2	756	ccc/ccCGTc	17/17	0.486250087219628	1	FACETS	0.416	0.375	0.458	0.416	0.375	0.458	INDETERMINATE	1	TRUE	0	0.824436815685031	1		557	343	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914700	32914700	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	141	436	0	ENST00000380152.3:c.6208G>C	p.Glu2070Gln	p.E2070Q	ENST00000380152		2070	Gaa/Caa	11/27	1	2	FACETS	0.557	0.509	0.607	0.557	0.509	0.607	SUBCLONAL	1	TRUE	1	0.824436815685031	2		436	614	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727523	88727523	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	73	406	0	ENST00000360948.2:c.256G>C	p.Glu86Gln	p.E86Q	ENST00000360948	NM_001012338.2	86	Gag/Cag	3/19	0.824436815685031	1	FACETS	0.445	0.395	0.497	0.445	0.395	0.497	SUBCLONAL	1	TRUE	0	0.824436815685031	1		406	234	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182252	38182252	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	227	459	0	ENST00000396334.3:c.688C>A	p.Arg230Ser	p.R230S	ENST00000396334	NM_002468.4	230	Cgc/Agc	4/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.824436815685031	2		459	497	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0050315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	23	369	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.634	0.494	0.795	0.634	0.494	0.795	SUBCLONAL	1	TRUE	1	0.22467559825452	2		369	323	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	39	488	0	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	1	2	FACETS	0.782	0.648	0.931	0.782	0.648	0.931	CLONAL	1	TRUE	1	0.22467559825452	2		488	444	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0050315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	55	421	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.180689556917027	3	FACETS	1	0.962	1	0.696	0.598	0.804	CLONAL	1	TRUE	1	0.22467559825452	3		421	391	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0050315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	26	264	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.793	0.629	0.979	0.793	0.629	0.979	CLONAL	1	TRUE	1	0.22467559825452	2		264	292	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989385	7989385	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200663524	NA	P-0050315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	30	750	1	ENST00000319144.4:c.301G>A	p.Ala101Thr	p.A101T	ENST00000319144	NM_001139.2	101	Gcc/Acc	2/15	1	2	FACETS	0.611	0.492	0.747	0.611	0.492	0.747	SUBCLONAL	1	TRUE	1	0.22467559825452	2		751	437	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374887	45374887	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	28	456	0	ENST00000262160.6:c.956T>C	p.Val319Ala	p.V319A	ENST00000262160	NM_005901.5	319	gTt/gCt	8/11	0.22467559825452	1	FACETS	0.588	0.47	0.723	0.588	0.47	0.723	SUBCLONAL	1	TRUE	0	0.22467559825452	1		456	376	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831308	3831308	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0050315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	27	289	0	ENST00000262367.5:c.1574-1G>A		p.X525_splice	ENST00000262367	NM_004380.2	525			1	2	FACETS	0.791	0.63	0.973	0.791	0.63	0.973	CLONAL	1	TRUE	1	0.22467559825452	2		289	304	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509128	66509128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1439062174	NA	P-0050315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	42	286	0	ENST00000273854.3:c.199C>T	p.Arg67Cys	p.R67C	ENST00000273854	NM_004439.5	67	Cgc/Tgc	2/18	0.22467559825452	0	FACETS	0.895	0.75	1			1	CLONAL	1	TRUE	0	0.22467559825452	0		286	324	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172446	108172446	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1060501669	NA	P-0050315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	38	380	0	ENST00000278616.4:c.5249G>A	p.Trp1750Ter	p.W1750*	ENST00000278616	NM_000051.3	1750	tGg/tAg	35/63	1	2	FACETS	0.734	0.606	0.876	0.734	0.606	0.876	SUBCLONAL	1	TRUE	1	0.22467559825452	2		380	461	SUCCESS
APC	324	MSKCC	GRCh37	5	112174989	112174990	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAGT	novel	NA	P-0050315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	40	216	0	ENST00000257430.4:c.3699_3702dup	p.Ser1235LysfsTer6	p.S1235Kfs*6	ENST00000257430	NM_000038.5	1233	cca/ccAAGTa	16/16	1	2	FACETS	0.868	0.729	1	1	0.965	1	CLONAL	2	TRUE	1	0.22467559825452	2		216	205	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	267	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.349004519493718	3	FACETS	0.864	0.815	0.913	1	0.992	1	CLONAL	3	FALSE	1	0.360269513587362	3		327	675	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482926	140482927	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs777474487	NA	P-0050316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	93	434	3	ENST00000288602.6:c.1208dup	p.Ala404CysfsTer9	p.A404Cfs*9	ENST00000288602	NM_004333.4	403	cct/ccCt	10/18	1	2	FACETS	0.719	0.639	0.804	0.719	0.639	0.804	SUBCLONAL	1	FALSE	1	0.360269513587362	2		437	718	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057792	27057792	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0050316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	306	577	0	ENST00000324856.7:c.1500T>A	p.Tyr500Ter	p.Y500*	ENST00000324856	NM_006015.4	500	taT/taA	3/20	0.320735256188052	1	FACETS	0.902	0.855	0.95	1	0.996	1	CLONAL	2	FALSE	0	0.360269513587362	1		577	772	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988415	36988415	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	46	349	1	ENST00000354822.5:c.238A>G	p.Thr80Ala	p.T80A	ENST00000354822	NM_001079668.2	80	Aca/Gca	2/3	1	2	FACETS	0.536	0.452	0.63	0.536	0.452	0.63	SUBCLONAL	1	FALSE	1	0.360269513587362	2		350	476	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456375	40456375	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	395	466	0	ENST00000345506.4:c.1185G>C	p.Glu395Asp	p.E395D	ENST00000345506	NM_003152.3	395	gaG/gaC	11/20	0.349004519493718	3	FACETS	0.964	0.921	1	1	0.996	1	CLONAL	3	FALSE	1	0.360269513587362	3		466	895	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	60	413	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.18	2		413	460	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0050317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	63	763	9	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.972	0.84	1	0.972	0.84	1	CLONAL	1	TRUE	1	0.18	2		772	720	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692892	89692892	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554898129	NA	P-0050317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	23	292	0	ENST00000371953.3:c.376G>T	p.Ala126Ser	p.A126S	ENST00000371953	NM_000314.4	126	Gct/Tct	5/9	1	2	FACETS	0.94	0.734	1	0.94	0.734	1	CLONAL	1	TRUE	1	0.18	2		292	272	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466026	69466028	+	inframe_deletion	In_Frame_Del	DEL	CGA	CGA	-	novel	NA	P-0050317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	76	699	0	ENST00000227507.2:c.866_868del	p.Asp289del	p.D289del	ENST00000227507	NM_053056.2	288	acCGAc/acc	5/5	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.18	2		699	793	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720805	89720806	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0050317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	25	171	0	ENST00000371953.3:c.959dup	p.Leu320PhefsTer5	p.L320Ffs*5	ENST00000371953	NM_000314.4	319	act/acTt	8/9	1	2	FACETS	1	0.795	1	1	0.795	1	CLONAL	1	TRUE	1	0.18	2		171	276	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107092	27107093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0050317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	127	458	0	ENST00000324856.7:c.6706dup	p.Arg2236ProfsTer42	p.R2236Pfs*42	ENST00000324856	NM_006015.4	2235	gcc/gCcc	20/20	1	2	FACETS	1	0.951	1	1	0.99	1	CLONAL	2	TRUE	1	0.18	2		458	657	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782307	56782307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765922828	NA	P-0050317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	50	499	2	ENST00000308159.5:c.148C>T	p.Arg50Cys	p.R50C	ENST00000308159	NM_014669.4	50	Cgc/Tgc	2/22	1	2	FACETS	0.803	0.68	0.938	0.803	0.68	0.938	CLONAL	1	TRUE	1	0.18	2		501	692	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101364	27101364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	53	671	1	ENST00000324856.7:c.4646G>A	p.Gly1549Asp	p.G1549D	ENST00000324856	NM_006015.4	1549	gGc/gAc	18/20	1	2	FACETS	0.865	0.736	1	0.865	0.736	1	CLONAL	1	TRUE	1	0.18	2		672	681	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938144	36938144	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	46	697	3	ENST00000361632.4:c.817C>T	p.Gln273Ter	p.Q273*	ENST00000361632		273	Cag/Tag	6/16	1	2	FACETS	0.645	0.542	0.76	0.645	0.542	0.76	SUBCLONAL	1	TRUE	1	0.18	2		700	792	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94906469	94906469	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	25	314	0	ENST00000536441.1:c.1429C>T	p.Gln477Ter	p.Q477*	ENST00000536441	NM_144665.3	477	Caa/Taa	10/10	1	2	FACETS	0.6	0.472	0.748	0.6	0.472	0.748	SUBCLONAL	1	TRUE	1	0.18	2		314	463	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249316	133249316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs116263919	NA	P-0050317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	48	622	1	ENST00000320574.5:c.1583C>T	p.Thr528Met	p.T528M	ENST00000320574	NM_006231.2	528	aCg/aTg	15/49	1	2	FACETS	0.711	0.6	0.835	0.711	0.6	0.835	SUBCLONAL	1	TRUE	1	0.18	2		623	750	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639991	3639991	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	42	644	0	ENST00000294008.3:c.3648G>C	p.Gln1216His	p.Q1216H	ENST00000294008	NM_032444.2	1216	caG/caC	12/15	1	2	FACETS	0.686	0.572	0.814	0.686	0.572	0.814	SUBCLONAL	1	TRUE	1	0.18	2		644	680	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026043	14026043	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs758884625	NA	P-0050317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	26	249	0	ENST00000311895.7:c.1003A>G	p.Met335Val	p.M335V	ENST00000311895	NM_005236.2	335	Atg/Gtg	6/11	1	2	FACETS	0.698	0.552	0.865	0.698	0.552	0.865	SUBCLONAL	1	TRUE	1	0.18	2		249	414	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59924477	59924495	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGTTTATCTTTTCCAGT	GGAGTTTATCTTTTCCAGT	-	novel	NA	P-0050317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	24	257	0	ENST00000259008.2:c.594_612del	p.Leu199PhefsTer69	p.L199Ffs*69	ENST00000259008	NM_032043.2	198	ccACTGGAAAAGATAAACTCC/cc	6/20	1	2	FACETS	0.677	0.53	0.846	0.677	0.53	0.846	SUBCLONAL	1	TRUE	1	0.18	2		257	394	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213284	39213284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	44	550	0	ENST00000402219.2:c.3683G>A	p.Ser1228Asn	p.S1228N	ENST00000402219	NM_005633.3	1228	aGc/aAc	23/23	1	2	FACETS	0.681	0.57	0.805	0.681	0.57	0.805	SUBCLONAL	1	TRUE	1	0.18	2		550	718	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251990	153251990	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	39	381	0	ENST00000281708.4:c.1016G>T	p.Arg339Ile	p.R339I	ENST00000281708	NM_033632.3	339	aGa/aTa	7/12	1	2	FACETS	0.98	0.813	1	0.98	0.813	1	CLONAL	1	TRUE	1	0.18	2		381	442	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064704	80064705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs751236312	NA	P-0050317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	42	335	0	ENST00000265081.6:c.2141dup	p.Arg715GlufsTer4	p.R715Efs*4	ENST00000265081	NM_002439.4	712	ata/atAa	15/24	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.18	2		335	432	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100645	8100645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1218595084	NA	P-0050340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	18	774	0	ENST00000346208.3:c.619G>A	p.Ala207Thr	p.A207T	ENST00000346208		207	Gcc/Acc	3/6	0.157617631146334	3	FACETS	1	0.858	1	1	0.858	1	CLONAL	2	FALSE	1	0.176191194029144	3		774	94	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs730882001	NA	P-0050340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	59	724	1	ENST00000269305.4:c.493C>A	p.Gln165Lys	p.Q165K	ENST00000269305	NM_001126112.2	165	Cag/Aag	5/11	0.160758739512566	0	FACETS	0.836	0.748	0.923			1	CLONAL	6	FALSE	0	0.176191194029144	0		725	110	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249196	10249196	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	35	820	0	ENST00000340748.4:c.3986A>C	p.Glu1329Ala	p.E1329A	ENST00000340748		1329	gAg/gCg	34/40	0.176191194029144	6	FACETS	0.986	0.829	1	0.822	0.691	0.96	CLONAL	5	FALSE	0	0.176191194029144	6		820	109	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0050340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	23	283	1	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	1	0.858	1	1	0.964	1	CLONAL	4	FALSE	1	0.176191194029144	2		284	61	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98241342	98241342	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1060502297	NA	P-0050340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	32	706	0	ENST00000331920.6:c.1155del	p.Asn386ThrfsTer46	p.N386Tfs*46	ENST00000331920	NM_000264.3	385	atC/at	8/24	0.176191194029144	1	FACETS	0.966	0.843	1	1	0.977	1	CLONAL	7	FALSE	0	0.176191194029144	1		706	49	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938589	44938589	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0050340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	16	502	0	ENST00000377967.4:c.3137C>G	p.Ser1046Ter	p.S1046*	ENST00000377967	NM_021140.2	1046	tCa/tGa	20/29	0.122703572571848	0	FACETS	0.978	0.751	1			1	CLONAL	3	FALSE	0	0.176191194029144	0		502	51	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748399150	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	187	573	4	ENST00000220592.5:c.1806del	p.Ala603ProfsTer92	p.A603Pfs*92	ENST00000220592	NM_012154.3	602	ccC/cc	14/19	0.24108211725797	4	FACETS	1	0.981	1	0.598	0.551	0.647	CLONAL	1	TRUE	2	0.31	4		577	1321	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	116	399	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.939	0.846	1	0.939	0.846	1	CLONAL	1	TRUE	1	0.31	2		403	797	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288789	15288789	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	22	131	0	ENST00000263388.2:c.3950del	p.Pro1317GlnfsTer103	p.P1317Qfs*103	ENST00000263388	NM_000435.2	1317	cCa/ca	24/33	1	2	FACETS	0.706	0.55	0.885	0.706	0.55	0.885	SUBCLONAL	1	TRUE	1	0.31	2		131	201	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	114	503	2	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.862	0.776	0.954	0.862	0.776	0.954	CLONAL	1	TRUE	1	0.31	2		505	853	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755128667	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	134	652	3	ENST00000407977.2:c.1976dup	p.Pro660SerfsTer87	p.P660Sfs*87	ENST00000407977		659	ggt/ggGt	9/10	1	2	FACETS	0.779	0.706	0.856	0.779	0.706	0.856	SUBCLONAL	1	TRUE	1	0.31	2		655	1110	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	132	673	4	ENST00000324856.7:c.4555del	p.Gln1519ArgfsTer8	p.Q1519Rfs*8	ENST00000324856	NM_006015.4	1517	gCc/gc	18/20	1	2	FACETS	0.884	0.802	0.971	0.884	0.802	0.971	CLONAL	1	TRUE	1	0.31	2		677	963	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	162	683	5	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.31	2		688	1036	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460401	149460401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	121	567	0	ENST00000286301.3:c.236C>T	p.Thr79Met	p.T79M	ENST00000286301	NM_005211.3	79	aCg/aTg	3/22	1	2	FACETS	0.891	0.805	0.983	0.891	0.805	0.983	CLONAL	1	TRUE	1	0.31	2		567	876	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099403	157099429	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAGCAACAG	CAGCAGCAGCAGCAGCAGCAGCAACAG	-	rs910569810	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	48	281	0	ENST00000346085.5:c.360_386del	p.Gln123_Gln131del	p.Q123_Q131del	ENST00000346085	NM_020732.3	114	CAGCAGCAGCAGCAGCAGCAGCAACAG/-	1/20	1	2	FACETS	0.657	0.556	0.769	0.657	0.556	0.769	SUBCLONAL	1	TRUE	1	0.31	2		281	471	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98222053	98222053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	71	353	0	ENST00000331920.6:c.2716C>T	p.Arg906Cys	p.R906C	ENST00000331920	NM_000264.3	906	Cgt/Tgt	17/24	1	2	FACETS	0.812	0.71	0.923	0.812	0.71	0.923	CLONAL	1	TRUE	1	0.31	2		353	564	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442788	187442788	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	115	510	0	ENST00000232014.4:c.1918C>T	p.Arg640Trp	p.R640W	ENST00000232014	NM_001130845.1	640	Cgg/Tgg	9/10	0.222566632982799	3	FACETS	0.923	0.831	1	0.462	0.415	0.511	CLONAL	1	TRUE	1	0.31	3		510	928	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981721	101981721	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555075353	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	54	221	0	ENST00000282441.5:c.147del	p.Ala50ProfsTer24	p.A50Pfs*24	ENST00000282441	NM_001130145.2	48	Ccc/cc	1/9	1	2	FACETS	0.981	0.842	1	0.981	0.842	1	CLONAL	1	TRUE	1	0.31	2		221	355	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427975	49427975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	88	542	0	ENST00000301067.7:c.10615C>T	p.Arg3539Trp	p.R3539W	ENST00000301067	NM_003482.3	3539	Cgg/Tgg	38/54	1	2	FACETS	0.603	0.533	0.678	0.603	0.533	0.678	SUBCLONAL	1	TRUE	1	0.31	2		542	942	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864800	117864800	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs905123790	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	71	342	0	ENST00000297338.2:c.1309C>T	p.Arg437Cys	p.R437C	ENST00000297338	NM_006265.2	437	Cgt/Tgt	10/14	0.24108211725797	4	FACETS	0.778	0.678	0.887	0.389	0.339	0.444	SUBCLONAL	1	TRUE	2	0.31	4		342	771	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594061	55594061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs891140054	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	68	376	0	ENST00000288135.5:c.1847C>T	p.Ala616Val	p.A616V	ENST00000288135	NM_000222.2	616	gCg/gTg	12/21	1	2	FACETS	0.704	0.613	0.803	0.704	0.613	0.803	SUBCLONAL	1	TRUE	1	0.31	2		376	623	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042725	42042725	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	96	417	0	ENST00000219905.7:c.6920A>G	p.Asp2307Gly	p.D2307G	ENST00000219905	NM_001164273.1	2307	gAt/gGt	17/24	1	2	FACETS	0.909	0.811	1	0.909	0.811	1	CLONAL	1	TRUE	1	0.31	2		417	681	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723037	49723037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767971831	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	25	254	0	ENST00000449682.2:c.1379G>A	p.Arg460Gln	p.R460Q	ENST00000449682	NM_020998.3	460	cGa/cAa	11/18	0.222566632982799	3	FACETS	0.386	0.304	0.482	0.193	0.152	0.241	SUBCLONAL	1	TRUE	1	0.31	3		254	482	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38139034	38139034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201914561	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	81	403	0	ENST00000317025.8:c.3569G>A	p.Arg1190Gln	p.R1190Q	ENST00000317025	NM_023034.1	1190	cGa/cAa	20/24	0.24108211725797	4	FACETS	0.812	0.714	0.917	0.406	0.357	0.459	CLONAL	1	TRUE	2	0.31	4		403	843	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148504766	148504766	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	95	450	1	ENST00000320356.2:c.2228G>A	p.Gly743Asp	p.G743D	ENST00000320356	NM_004456.4	743	gGc/gAc	20/20	1	2	FACETS	0.832	0.74	0.929	0.832	0.74	0.929	CLONAL	1	TRUE	1	0.31	2		451	737	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162828	38162828	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754800291	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	101	482	2	ENST00000317025.8:c.2378G>A	p.Arg793His	p.R793H	ENST00000317025	NM_023034.1	793	cGc/cAc	13/24	0.24108211725797	4	FACETS	0.875	0.78	0.975	0.437	0.39	0.488	CLONAL	1	TRUE	2	0.31	4		484	976	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073916	8073918	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	95	393	0	ENST00000377482.5:c.741_743del	p.Arg248del	p.R248del	ENST00000377482	NM_018948.3	247	agAAGg/agg	4/4	1	2	FACETS	0.929	0.828	1	0.929	0.828	1	CLONAL	1	TRUE	1	0.31	2		393	660	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456515	32456515	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	40	110	0	ENST00000332351.3:c.377C>T	p.Pro126Leu	p.P126L	ENST00000332351	NM_024426.4	126	cCg/cTg	1/10	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.31	2		110	197	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998641	100998641	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	109	546	0	ENST00000325455.5:c.1161A>G	p.Ile387Met	p.I387M	ENST00000325455	NM_001202474.3	387	atA/atG	1/8	1	2	FACETS	0.827	0.742	0.918	0.827	0.742	0.918	CLONAL	1	TRUE	1	0.31	2		546	850	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134175	41134175	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs765624020	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	69	375	0	ENST00000379561.5:c.1453G>C	p.Ala485Pro	p.A485P	ENST00000379561	NM_002015.3	485	Gcc/Ccc	2/3	1	2	FACETS	0.782	0.682	0.891	0.782	0.682	0.891	SUBCLONAL	1	TRUE	1	0.31	2		375	569	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43769903	43769903	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	68	388	0	ENST00000382044.4:c.843del	p.Glu282AsnfsTer141	p.E282Nfs*141	ENST00000382044	NM_001141980.1	281	aaA/aa	8/28	1	2	FACETS	0.602	0.523	0.687	0.602	0.523	0.687	SUBCLONAL	1	TRUE	1	0.31	2		388	729	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223966	2223966	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	68	633	0	ENST00000326181.6:c.1180G>T	p.Gly394Cys	p.G394C	ENST00000326181	NM_032271.2	394	Ggc/Tgc	13/21	1	2	FACETS	0.439	0.381	0.503	0.439	0.381	0.503	SUBCLONAL	1	TRUE	1	0.31	2		633	999	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341322	89341322	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	56	258	0	ENST00000301030.4:c.7613A>G	p.His2538Arg	p.H2538R	ENST00000301030	NM_001256183.1	2538	cAc/cGc	11/13	1	2	FACETS	0.836	0.718	0.965	0.836	0.718	0.965	CLONAL	1	TRUE	1	0.31	2		258	432	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10267180	10267180	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	33	373	0	ENST00000340748.4:c.1238A>G	p.Tyr413Cys	p.Y413C	ENST00000340748		413	tAc/tGc	17/40	1	2	FACETS	0.333	0.27	0.404	0.333	0.27	0.404	SUBCLONAL	1	TRUE	1	0.31	2		373	640	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47600986	47600986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749805135	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	121	475	0	ENST00000263735.4:c.224G>A	p.Gly75Asp	p.G75D	ENST00000263735	NM_002354.2	75	gGc/gAc	3/9	1	2	FACETS	0.921	0.831	1	0.921	0.831	1	CLONAL	1	TRUE	1	0.31	2		475	848	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945248	54945248	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	31	388	0	ENST00000312783.6:c.1178G>A	p.Cys393Tyr	p.C393Y	ENST00000312783	NM_198436.1	393	tGc/tAc	10/10	1	2	FACETS	0.351	0.283	0.429	0.351	0.283	0.429	SUBCLONAL	1	TRUE	1	0.31	2		388	569	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641671	12641671	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	114	456	0	ENST00000251849.4:c.970A>T	p.Thr324Ser	p.T324S	ENST00000251849	NM_002880.3	324	Acc/Tcc	9/17	0.222566632982799	3	FACETS	0.898	0.807	0.994	0.449	0.403	0.497	CLONAL	1	TRUE	1	0.31	3		456	946	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71064806	71064806	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	38	263	0	ENST00000318789.4:c.870-2A>G		p.X290_splice	ENST00000318789	NM_032682.5	290			0.222566632982799	3	FACETS	0.553	0.457	0.661	0.277	0.228	0.331	SUBCLONAL	1	TRUE	1	0.31	3		263	512	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799548	72799548	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	111	456	0	ENST00000325599.8:c.1621G>T	p.Glu541Ter	p.E541*	ENST00000325599	NM_018130.2	541	Gag/Tag	11/11	0.222566632982799	3	FACETS	1	0.9	1	0.501	0.45	0.555	CLONAL	1	TRUE	1	0.31	3		456	826	SUCCESS
ATR	545	MSKCC	GRCh37	3	142297515	142297515	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	115	637	0	ENST00000350721.4:c.32T>C	p.Met11Thr	p.M11T	ENST00000350721	NM_001184.3	11	aTg/aCg	1/47	0.222566632982799	3	FACETS	0.78	0.701	0.864	0.39	0.35	0.432	SUBCLONAL	1	TRUE	1	0.31	3		637	1099	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513205	149513205	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	82	572	0	ENST00000261799.4:c.878T>C	p.Val293Ala	p.V293A	ENST00000261799	NM_002609.3	293	gTg/gCg	6/23	1	2	FACETS	0.543	0.477	0.613	0.543	0.477	0.613	SUBCLONAL	1	TRUE	1	0.31	2		572	975	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968193	68968193	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	76	501	0	ENST00000288368.4:c.1222A>T	p.Lys408Ter	p.K408*	ENST00000288368	NM_024870.2	408	Aaa/Taa	10/40	0.24108211725797	4	FACETS	0.612	0.535	0.695	0.306	0.267	0.348	SUBCLONAL	1	TRUE	2	0.31	4		501	1050	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864799	117864799	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765264685	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	83	341	0	ENST00000297338.2:c.1310G>A	p.Arg437His	p.R437H	ENST00000297338	NM_006265.2	437	cGt/cAt	10/14	0.24108211725797	4	FACETS	0.911	0.803	1	0.456	0.401	0.514	CLONAL	1	TRUE	2	0.31	4		341	770	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393702	139393702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764422420	NA	P-0050349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	129	673	1	ENST00000277541.6:c.5944C>T	p.Arg1982Trp	p.R1982W	ENST00000277541	NM_017617.3	1982	Cgg/Tgg	32/34	1	2	FACETS	0.793	0.718	0.873	0.793	0.718	0.873	SUBCLONAL	1	TRUE	1	0.31	2		674	1049	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0050351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	349	657	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.818	0.775	0.861	0.818	0.775	0.861	CLONAL	1	TRUE	1	0.806185491216324	2		657	1059	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0050351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	730	625	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.806185491216324	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.806185491216324	2		625	888	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22412941	22412941	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	72	159	0	ENST00000344548.3:c.188A>T	p.Asp63Val	p.D63V	ENST00000344548	NM_001039802.1	63	gAt/gTt	5/7	1	2	FACETS	0.805	0.714	0.899	0.805	0.714	0.899	CLONAL	1	TRUE	1	0.806185491216324	2		159	222	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636830	2636834	+	frameshift_variant	Frame_Shift_Del	DEL	GACTT	GACTT	-	novel	NA	P-0050351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	353	626	0	ENST00000342085.4:c.1279_1283del	p.Asp427ThrfsTer6	p.D427Tfs*6	ENST00000342085	NM_002613.4	427	GACTTa/a	11/14	0.194410762178372	5	FACETS	0.775	0.733	0.817	0.31	0.293	0.327	INDETERMINATE	2	TRUE	0	0.806185491216324	5		626	1249	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117587	4117587	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	53	459	1	ENST00000262948.5:c.133G>A	p.Glu45Lys	p.E45K	ENST00000262948	NM_030662.3	45	Gaa/Aaa	2/11	0.806185491216324	2	FACETS	0.183	0.155	0.213	0.092	0.077	0.107	SUBCLONAL	1	TRUE	0	0.806185491216324	2		460	718	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277557	142277557	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	96	393	0	ENST00000350721.4:c.1794G>T	p.Trp598Cys	p.W598C	ENST00000350721	NM_001184.3	598	tgG/tgT	8/47	0.455686002819866	5	FACETS	0.713	0.635	0.796	0.238	0.211	0.266	INDETERMINATE	1	TRUE	2	0.806185491216324	5		393	738	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349900	70349900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863223706	NA	P-0050352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	119	139	0	ENST00000374080.3:c.3883C>T	p.Arg1295Cys	p.R1295C	ENST00000374080		1295	Cgt/Tgt	28/45	1	1	FACETS	0.953	0.871	1	1	0.99	1	CLONAL	2	TRUE	0	0.313313677942527	1		139	336	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0050354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	14	302	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.22	0.158	0.296	0.22	0.158	0.296	SUBCLONAL	1	FALSE	1	0.264136422546768	2		302	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0050354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	127	550	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.264136422546768	2		550	849	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230552	46230564	+	frameshift_variant	Frame_Shift_Del	DEL	GTCTTTATTTCAT	GTCTTTATTTCAT	-	novel	NA	P-0050354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	55	318	0	ENST00000334344.6:c.801_813del	p.Glu267AspfsTer21	p.E267Dfs*21	ENST00000334344	NM_152641.2	267	gaGTCTTTATTTCAT/ga	8/21	0.264136422546768	3	FACETS	0.984	0.843	1	0.492	0.421	0.569	CLONAL	1	FALSE	1	0.264136422546768	3		318	479	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670149	29670149	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs777872719	NA	P-0050354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	44	266	0	ENST00000356175.3:c.7125del	p.Tyr2377ThrfsTer20	p.Y2377Tfs*20	ENST00000356175	NM_000267.3	2374	ttA/tt	47/57	1	2	FACETS	0.803	0.674	0.945	0.803	0.674	0.945	CLONAL	1	FALSE	1	0.264136422546768	2		266	415	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210850	2210851	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0050354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	53	403	0	ENST00000398665.3:c.1347_1348insTG	p.Gln450CysfsTer40	p.Q450Cfs*40	ENST00000398665	NM_032482.2	449	-/TG	14/28	0.264136422546768	1	FACETS	0.746	0.637	0.865	0.746	0.637	0.865	SUBCLONAL	1	FALSE	0	0.264136422546768	1		403	467	SUCCESS
APC	324	MSKCC	GRCh37	5	112174510	112174513	+	frameshift_variant	Frame_Shift_Del	DEL	AACT	AACT	-	novel	NA	P-0050354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	35	337	0	ENST00000257430.4:c.3219_3222del	p.Thr1074IlefsTer51	p.T1074Ifs*51	ENST00000257430	NM_000038.5	1073	acAACT/ac	16/16	1	2	FACETS	0.72	0.591	0.865	0.72	0.591	0.865	SUBCLONAL	1	FALSE	1	0.264136422546768	2		337	368	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851499	128851499	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	58	556	0	ENST00000249373.3:c.1824T>A	p.Asn608Lys	p.N608K	ENST00000249373	NM_005631.4	608	aaT/aaA	11/12	0.0607306336737687	4	FACETS	0.808	0.693	0.933	0.404	0.346	0.467	INDETERMINATE	1	FALSE	2	0.264136422546768	4		556	687	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141498	11141498	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	49	700	2	ENST00000358026.2:c.3475G>T	p.Gly1159Trp	p.G1159W	ENST00000358026	NM_001128849.1	1159	Ggg/Tgg	25/36	1	2	FACETS	0.867	0.734	1	0.867	0.734	1	CLONAL	1	TRUE	1	0.19	2		702	595	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158239	47158242	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TTCT	TTCT	-	rs1553699115	NA	P-0050355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	13	293	0	ENST00000409792.3:c.4457_4460del	p.Lys1486ArgfsTer28	p.K1486Rfs*28	ENST00000409792	NM_014159.6	1486	aAGAAg/ag	4/21	1	2	FACETS	0.671	0.479	0.904	0.671	0.479	0.904	SUBCLONAL	1	TRUE	1	0.19	2		293	204	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575658	55575658	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	34	459	0	ENST00000288135.5:c.1184C>A	p.Ser395Tyr	p.S395Y	ENST00000288135	NM_000222.2	395	tCc/tAc	7/21	1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	1	0.19	2		459	340	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106245	27106258	+	frameshift_variant	Frame_Shift_Del	DEL	CAAGATCCTAGAGG	CAAGATCCTAGAGG	-	novel	NA	P-0050355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	41	548	0	ENST00000324856.7:c.5856_5869del	p.Lys1953ArgfsTer5	p.K1953Rfs*5	ENST00000324856	NM_006015.4	1952	atCAAGATCCTAGAGGac/atac	20/20	1	2	FACETS	0.832	0.692	0.987	0.832	0.692	0.987	CLONAL	1	TRUE	1	0.19	2		548	519	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160412	108160416	+	frameshift_variant	Frame_Shift_Del	DEL	AATAT	AATAT	-	novel	NA	P-0050355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	28	382	0	ENST00000278616.4:c.4321_4325del	p.Ile1441SerfsTer5	p.I1441Sfs*5	ENST00000278616	NM_000051.3	1440	aaAATATat/aaat	29/63	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.19	2		382	262	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191470	10191472	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GTG	GTG	T	novel	NA	P-0050355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	24	367	0	ENST00000256474.2:c.464-1_465delinsT		p.X155_splice	ENST00000256474	NM_000551.3	155		3/3	1	2	FACETS	0.72	0.564	0.899	0.72	0.564	0.899	SUBCLONAL	1	TRUE	1	0.19	2		367	351	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0050356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	104	382	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.262056617479624	1	FACETS	0.911	0.816	1	0.911	0.816	1	CLONAL	1	TRUE	0	0.270256687898936	1		382	731	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579529	7579529	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658483	NA	P-0050356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	149	754	0	ENST00000269305.4:c.158G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tGg/tAg	4/11	0.270256687898936	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.270256687898936	1		754	797	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0050356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	93	323	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	0.270256687898936	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.270256687898936	1		323	512	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219970	5219970	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs116545788	NA	P-0050356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	84	687	1	ENST00000357368.4:c.3745G>A	p.Val1249Met	p.V1249M	ENST00000357368	NM_002850.3	1249	Gtg/Atg	22/38	0.270256687898936	1	FACETS	0.71	0.627	0.8	0.71	0.627	0.8	SUBCLONAL	1	TRUE	0	0.270256687898936	1		688	757	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411447	63411447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754938624	NA	P-0050356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	69	749	1	ENST00000330258.3:c.1720C>T	p.Arg574Trp	p.R574W	ENST00000330258	NM_152424.3	574	Cgg/Tgg	2/2	0.262056617479624	1	FACETS	0.568	0.493	0.648	0.568	0.493	0.648	SUBCLONAL	1	TRUE	0	0.270256687898936	1		750	778	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288635	33288635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138014437	NA	P-0050356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	59	505	0	ENST00000374542.5:c.917G>A	p.Arg306Gln	p.R306Q	ENST00000374542	NM_001141970.1	306	cGa/cAa	3/8	1	2	FACETS	0.685	0.589	0.79	0.685	0.589	0.79	SUBCLONAL	1	TRUE	1	0.270256687898936	2		505	637	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0050387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	49	537	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.17	2		537	525	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934576	NA	P-0050387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	71	606	0	ENST00000269305.4:c.818G>C	p.Arg273Pro	p.R273P	ENST00000269305	NM_001126112.2	273	cGt/cCt	8/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.17	2		606	687	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444435	50444435	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	37	298	1	ENST00000331340.3:c.365G>T	p.Cys122Phe	p.C122F	ENST00000331340	NM_006060.4	122	tGt/tTt	4/8	1	2	FACETS	0.938	0.773	1	0.938	0.773	1	CLONAL	1	TRUE	1	0.17	2		299	464	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410344	63410344	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	61	696	0	ENST00000330258.3:c.2823C>A	p.Ser941Arg	p.S941R	ENST00000330258	NM_152424.3	941	agC/agA	2/2	1	2	FACETS	0.778	0.67	0.897	0.778	0.67	0.897	SUBCLONAL	1	TRUE	1	0.17	2		696	922	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651978	36651979	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0050389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	412	745	0	ENST00000244741.5:c.102_103del	p.Cys34Ter	p.C34*	ENST00000244741	NM_000389.4	34	TGt/t	2/3	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.824592731041869	2		745	952	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360845	118360846	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0050389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	23	263	0	ENST00000534358.1:c.4578dup	p.Cys1527LeufsTer8	p.C1527Lfs*8	ENST00000534358	NM_005933.3	1526	atc/atCc	13/36	1	2	FACETS	0.15	0.117	0.189	0.15	0.117	0.189	SUBCLONAL	1	TRUE	1	0.824592731041869	2		263	371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0050392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	152	725	31	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.164268805585391	2	FACETS	0.942	0.863	1	0.942	0.863	1	CLONAL	2	TRUE	0	0.231559082457667	2		756	697	SUCCESS
APC	324	MSKCC	GRCh37	5	112173251	112173251	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	12	175	0	ENST00000257430.4:c.1960C>T	p.Gln654Ter	p.Q654*	ENST00000257430	NM_000038.5	654	Caa/Taa	16/16	1	2	FACETS	0.997	0.707	1	0.997	0.707	1	CLONAL	1	TRUE	1	0.231559082457667	2		175	104	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0050393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	20	809	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.305805229843295	3	FACETS	0.214	0.163	0.275	0.107	0.081	0.138	SUBCLONAL	1	TRUE	1	0.305805229843295	3		809	704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0050393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	34	590	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.305805229843295	3	FACETS	0.42	0.342	0.508	0.21	0.171	0.254	SUBCLONAL	1	TRUE	1	0.305805229843295	3		591	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0050393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	26	608	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.305805229843295	3	FACETS	0.383	0.302	0.476	0.191	0.151	0.238	SUBCLONAL	1	TRUE	1	0.305805229843295	3		608	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578509	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0050393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	258	810	0	ENST00000269305.4:c.421_422insA	p.Cys141Ter	p.C141*	ENST00000269305	NM_001126112.2	141	tgc/tAgc	5/11	0.305805229843295	3	FACETS	0.921	0.867	0.976	1	0.992	1	CLONAL	3	TRUE	1	0.305805229843295	3		810	704	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385239	41385239	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377294483	NA	P-0050394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	275	666	1	ENST00000373198.4:c.722G>A	p.Arg241His	p.R241H	ENST00000373198	NM_133170.3	241	cGt/cAt	6/32	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.785122155342092	2		667	697	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439308	52439334	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CATCTGAGACAGGGCAAGAACACAGGC	CATCTGAGACAGGGCAAGAACACAGGC	A	novel	NA	P-0050394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	196	587	0	ENST00000460680.1:c.932-24_934delinsT		p.X311_splice	ENST00000460680	NM_004656.3	311		11/17	0.785122155342092	1	FACETS	0.982	0.931	1	0.982	0.931	1	CLONAL	1	TRUE	0	0.785122155342092	1		587	309	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0050395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	173	534	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.955	0.891	1	0.955	0.891	1	CLONAL	1	TRUE	1	0.924055113378499	2		534	392	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0050395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	96	225	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.924055113378499	1	FACETS	0.873	0.818	0.924	0.873	0.818	0.924	CLONAL	1	TRUE	0	0.924055113378499	1		225	128	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0050395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	168	458	2	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.878	0.817	0.941	0.878	0.817	0.941	CLONAL	1	TRUE	1	0.924055113378499	2		460	414	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997825	149997826	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0050395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	266	486	0	ENST00000253339.5:c.2641dup	p.Asp881GlyfsTer40	p.D881Gfs*40	ENST00000253339		881	gat/gGat	5/7	1	2	FACETS	0.92	0.869	0.971	0.92	0.869	0.971	CLONAL	1	TRUE	1	0.924055113378499	2		486	626	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066739	5066739	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1340580425	NA	P-0050395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	165	323	0	ENST00000381652.3:c.1276C>T	p.Arg426Ter	p.R426*	ENST00000381652	NM_004972.3	426	Cga/Tga	10/25	0.924055113378499	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.924055113378499	1		323	179	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271294	26271294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	309	543	0	ENST00000305910.3:c.319G>A	p.Asp107Asn	p.D107N	ENST00000305910	NM_003534.2	107	Gat/Aat	1/1	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.924055113378499	2		543	638	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379676	17379676	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	264	578	0	ENST00000359435.4:c.61G>T	p.Ala21Ser	p.A21S	ENST00000359435	NM_001033549.1	21	Gca/Tca	2/9	1	2	FACETS	0.635	0.596	0.675	0.635	0.596	0.675	SUBCLONAL	1	TRUE	1	0.924055113378499	2		578	900	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268151	153268151	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	249	310	0	ENST00000281708.4:c.657del	p.Gln220AsnfsTer19	p.Q220Nfs*19	ENST00000281708	NM_033632.3	219	ggG/gg	4/12	1	2	FACETS	0.941	0.888	0.994	0.941	0.888	0.994	CLONAL	1	TRUE	1	0.924055113378499	2		310	573	SUCCESS
APC	324	MSKCC	GRCh37	5	112174323	112174323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	159	261	0	ENST00000257430.4:c.3032C>A	p.Ala1011Glu	p.A1011E	ENST00000257430	NM_000038.5	1011	gCa/gAa	16/16	0.924055113378499	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.924055113378499	1		261	183	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0050397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	153	382	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.275278476011917	3	FACETS	0.89	0.82	0.962	0.89	0.82	0.962	CLONAL	2	TRUE	1	0.409206625575373	3		382	506	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604790	48604790	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1568211615	NA	P-0050397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	35	400	0	ENST00000342988.3:c.1612G>T	p.Glu538Ter	p.E538*	ENST00000342988	NM_005359.5	538	Gaa/Taa	12/12	0.295865672662204	2	FACETS	0.636	0.524	0.761	0.318	0.262	0.381	SUBCLONAL	1	TRUE	0	0.409206625575373	2		400	269	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0050397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	75	261	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	0.250969111541	3	FACETS	0.833	0.739	0.932	0.833	0.739	0.932	CLONAL	2	TRUE	1	0.409206625575373	3		261	265	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577137	7577137	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	208	602	0	ENST00000269305.4:c.801del	p.Asn268ThrfsTer77	p.N268Tfs*77	ENST00000269305	NM_001126112.2	267	cgG/cg	8/11	0.409206625575373	2	FACETS	0.968	0.907	1	0.968	0.907	1	CLONAL	2	TRUE	0	0.409206625575373	2		602	525	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530157	212530157	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050397-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	36	422	0	ENST00000342788.4:c.1762A>C	p.Asn588His	p.N588H	ENST00000342788	NM_005235.2	588	Aac/Cac	15/28	0.374186264872096	3	FACETS	0.481	0.395	0.577	0.24	0.197	0.289	SUBCLONAL	1	TRUE	1	0.409206625575373	3		422	441	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	162	308	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.956	0.886	1	0.956	0.886	1	CLONAL	1	TRUE	1	0.807301599087199	2		309	420	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32439138	32439138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564987636	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	241	404	0	ENST00000332351.3:c.935G>A	p.Gly312Glu	p.G312E	ENST00000332351	NM_024426.4	312	gGa/gAa	4/10	1	2	FACETS	0.872	0.818	0.926	0.872	0.818	0.926	CLONAL	1	TRUE	1	0.807301599087199	2		404	685	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041073	29041073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	236	416	0	ENST00000282397.4:c.355G>A	p.Glu119Lys	p.E119K	ENST00000282397	NM_002019.4	119	Gaa/Aaa	3/30	1	2	FACETS	0.951	0.893	1	0.951	0.893	1	CLONAL	1	TRUE	1	0.807301599087199	2		416	615	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391000	89391000	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	283	467	0	ENST00000336596.2:c.1066G>A	p.Asp356Asn	p.D356N	ENST00000336596	NM_005233.5	356	Gat/Aat	5/17	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.807301599087199	2		467	692	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877381	89877381	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763338641	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	300	579	0	ENST00000389301.3:c.382C>T	p.Pro128Ser	p.P128S	ENST00000389301	NM_000135.2	128	Cca/Tca	4/43	1	2	FACETS	0.974	0.922	1	0.974	0.922	1	CLONAL	1	TRUE	1	0.807301599087199	2		579	763	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561352	9561352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773981325	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	271	441	0	ENST00000353224.5:c.430G>A	p.Glu144Lys	p.E144K	ENST00000353224	NM_177990.2	144	Gaa/Aaa	4/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.807301599087199	2		441	609	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468275	50468275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	328	571	0	ENST00000331340.3:c.1510G>A	p.Glu504Lys	p.E504K	ENST00000331340	NM_006060.4	504	Gag/Aag	8/8	1	2	FACETS	0.973	0.924	1	0.973	0.924	1	CLONAL	1	TRUE	1	0.807301599087199	2		571	835	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480352	89480352	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	204	253	0	ENST00000336596.2:c.2189T>G	p.Ile730Arg	p.I730R	ENST00000336596	NM_005233.5	730	aTa/aGa	13/17	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.807301599087199	2		253	455	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245204	46245204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	269	454	0	ENST00000334344.6:c.3298C>T	p.Gln1100Ter	p.Q1100*	ENST00000334344	NM_152641.2	1100	Cag/Tag	15/21	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.807301599087199	2		454	651	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1539	411	715	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	0.807301599087199	4	FACETS	0.944	0.895	0.993	0.315	0.298	0.332	CLONAL	1	TRUE	1	0.807301599087199	4		715	1950	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972936	68972936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	421	364	0	ENST00000288368.4:c.1261G>A	p.Glu421Lys	p.E421K	ENST00000288368	NM_024870.2	421	Gaa/Aaa	11/40	0.63350273602523	3	FACETS	0.948	0.911	0.985	0.948	0.911	0.985	CLONAL	2	TRUE	1	0.807301599087199	3		364	772	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258970	153258970	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	156	238	0	ENST00000281708.4:c.845C>T	p.Ser282Leu	p.S282L	ENST00000281708	NM_033632.3	282	tCa/tTa	5/12	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.807301599087199	2		238	366	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553668	106553668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1261004652	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	268	470	1	ENST00000369096.4:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000369096	NM_001198.3	545	Gaa/Aaa	5/7	0.807301599087199	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.807301599087199	1		471	380	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7174711	7174711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	249	478	0	ENST00000302850.5:c.1006C>T	p.Pro336Ser	p.P336S	ENST00000302850	NM_000208.2	336	Ccc/Tcc	4/22	1	2	FACETS	0.937	0.882	0.994	0.937	0.882	0.994	CLONAL	1	TRUE	1	0.807301599087199	2		478	658	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843718	156843718	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs569895276	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	1119	719	0	ENST00000524377.1:c.1144C>T	p.Pro382Ser	p.P382S	ENST00000524377	NM_002529.3	382	Cct/Tct	8/17	0.691908092601182	4	FACETS	0.981	0.96	1			1	CLONAL	3	TRUE	NA	0.807301599087199	4		719	1702	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243238	123243238	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs868056281	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	370	602	1	ENST00000358487.5:c.2275C>T	p.Arg759Ter	p.R759*	ENST00000358487	NM_000141.4	759	Cga/Tga	17/18	0.807301599087199	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.807301599087199	1		603	526	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426786	212426786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866491191	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	218	408	1	ENST00000342788.4:c.2329C>T	p.His777Tyr	p.H777Y	ENST00000342788	NM_005235.2	777	Cat/Tat	20/28	1	2	FACETS	0.971	0.911	1	0.971	0.911	1	CLONAL	1	TRUE	1	0.807301599087199	2		409	556	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612128	43612128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	230	378	0	ENST00000355710.3:c.2233C>T	p.His745Tyr	p.H745Y	ENST00000355710	NM_020975.4	745	Cat/Tat	12/20	0.781219018859442	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.807301599087199	1		378	329	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627355	37627355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs910521882	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	1323	713	3	ENST00000249071.6:c.364G>A	p.Asp122Asn	p.D122N	ENST00000249071	NM_002872.4	122	Gac/Aac	5/7	0.761917317488214	4	FACETS	1	0.99	1			1	CLONAL	3	TRUE	NA	0.807301599087199	4		716	1947	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780833	9780833	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	356	672	0	ENST00000377346.4:c.1555G>A	p.Gly519Arg	p.G519R	ENST00000377346	NM_005026.3	519	Ggg/Agg	13/24	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.807301599087199	2		672	880	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257843	16257843	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750957886	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	311	456	0	ENST00000375759.3:c.5108C>T	p.Pro1703Leu	p.P1703L	ENST00000375759	NM_015001.2	1703	cCc/cTc	11/15	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.807301599087199	2		456	658	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22413291	22413291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	76	59	0	ENST00000344548.3:c.418G>A	p.Glu140Lys	p.E140K	ENST00000344548	NM_001039802.1	140	Gag/Aag	6/7	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.807301599087199	2		59	141	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731106	162731106	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	225	449	0	ENST00000367921.3:c.961C>T	p.Pro321Ser	p.P321S	ENST00000367921	NM_006182.2	321	Ccc/Tcc	9/18	0.19287149198174	6	FACETS	0.795	0.741	0.85			1	INDETERMINATE	2	TRUE	NA	0.807301599087199	6		449	917	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406379	70406379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	285	558	0	ENST00000373644.4:c.3893C>T	p.Pro1298Leu	p.P1298L	ENST00000373644	NM_030625.2	1298	cCt/cTt	4/12	NA	2	FACETS	0.856	0.807	0.905			1	INDETERMINATE	1	TRUE	NA	0.807301599087199	2		558	825	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865683	57865683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	402	630	0	ENST00000228682.2:c.3160G>A	p.Asp1054Asn	p.D1054N	ENST00000228682	NM_005269.2	1054	Gat/Aat	12/12	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.807301599087199	2		630	882	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14022028	14022028	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	293	409	0	ENST00000311895.7:c.728A>C	p.His243Pro	p.H243P	ENST00000311895	NM_005236.2	243	cAt/cCt	4/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.807301599087199	2		409	712	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346486	89346486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	368	668	0	ENST00000301030.4:c.6464C>T	p.Pro2155Leu	p.P2155L	ENST00000301030	NM_001256183.1	2155	cCc/cTc	9/13	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.807301599087199	2		668	864	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990705	7990705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140795969	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	389	630	1	ENST00000319144.4:c.56G>A	p.Arg19Gln	p.R19Q	ENST00000319144	NM_001139.2	19	cGg/cAg	1/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.807301599087199	2		631	886	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627164	37627164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	181	360	0	ENST00000447079.4:c.1079C>T	p.Pro360Leu	p.P360L	ENST00000447079	NM_015083.1	360	cCt/cTt	2/14	1	2	FACETS	0.872	0.811	0.935	0.872	0.811	0.935	CLONAL	1	TRUE	1	0.807301599087199	2		360	514	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222346	2222346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	384	746	0	ENST00000398665.3:c.3178C>T	p.Pro1060Ser	p.P1060S	ENST00000398665	NM_032482.2	1060	Ccc/Tcc	24/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.807301599087199	2		746	920	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241985	39241985	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	189	236	0	ENST00000402219.2:c.1861C>T	p.Pro621Ser	p.P621S	ENST00000402219	NM_005633.3	621	Ccc/Tcc	11/23	1	2	FACETS	0.994	0.928	1	0.994	0.928	1	CLONAL	1	TRUE	1	0.807301599087199	2		236	471	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212289012	212289012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	185	315	0	ENST00000342788.4:c.2734G>A	p.Glu912Lys	p.E912K	ENST00000342788	NM_005235.2	912	Gaa/Aaa	23/28	1	2	FACETS	0.917	0.854	0.981	0.917	0.854	0.981	CLONAL	1	TRUE	1	0.807301599087199	2		315	500	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980813	40980813	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	257	462	1	ENST00000373198.4:c.1673C>T	p.Pro558Leu	p.P558L	ENST00000373198	NM_133170.3	558	cCa/cTa	10/32	0.807301599087199	3	FACETS	0.966	0.906	1	0.483	0.453	0.514	CLONAL	1	TRUE	1	0.807301599087199	3		463	925	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513337	44513338	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	259	543	1	ENST00000291552.4:c.597_598delinsTT	p.Arg200Trp	p.R200W	ENST00000291552	NM_006758.2	199	tcCCgg/tcTTgg	8/8	1	2	FACETS	0.864	0.813	0.916	0.864	0.813	0.916	CLONAL	1	TRUE	1	0.807301599087199	2		544	743	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164826	47164826	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	231	289	0	ENST00000409792.3:c.1300T>C	p.Tyr434His	p.Y434H	ENST00000409792	NM_014159.6	434	Tac/Cac	3/21	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.807301599087199	2		289	556	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933987	49933987	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	305	615	0	ENST00000296474.3:c.2425G>A	p.Ala809Thr	p.A809T	ENST00000296474	NM_002447.2	809	Gca/Aca	9/20	1	2	FACETS	0.903	0.854	0.952	0.903	0.854	0.952	CLONAL	1	TRUE	1	0.807301599087199	2		615	837	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152053	55152053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	290	493	1	ENST00000257290.5:c.2485G>A	p.Gly829Arg	p.G829R	ENST00000257290	NM_006206.4	829	Gga/Aga	18/23	1	2	FACETS	0.968	0.916	1	0.968	0.916	1	CLONAL	1	TRUE	1	0.807301599087199	2		494	742	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156118	106156118	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	227	364	0	ENST00000380013.4:c.1019T>A	p.Ile340Asn	p.I340N	ENST00000380013	NM_001127208.2	340	aTc/aAc	3/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.807301599087199	2		364	547	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948488	31948488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	140	176	0	ENST00000375333.2:c.971C>T	p.Ser324Leu	p.S324L	ENST00000375333	NM_032454.1	324	tCa/tTa	7/8	0.807301599087199	4	FACETS	1	0.972	1	0.383	0.35	0.417	CLONAL	1	TRUE	1	0.807301599087199	4		176	546	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444473	50444473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	160	294	0	ENST00000331340.3:c.403C>T	p.His135Tyr	p.H135Y	ENST00000331340	NM_006060.4	135	Cac/Tac	4/8	1	2	FACETS	0.905	0.838	0.973	0.905	0.838	0.973	CLONAL	1	TRUE	1	0.807301599087199	2		294	438	SUCCESS
MET	4233	MSKCC	GRCh37	7	116417467	116417467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	424	274	0	ENST00000397752.3:c.3284G>A	p.Gly1095Glu	p.G1095E	ENST00000397752	NM_000245.2	1095	gGg/gAg	16/21	0.807301599087199	3	FACETS	0.982	0.944	1	0.982	0.944	1	CLONAL	2	TRUE	1	0.807301599087199	3		274	751	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540117	23540117	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	156	253	1	ENST00000380871.4:c.286G>A	p.Glu96Lys	p.E96K	ENST00000380871	NM_006167.3	96	Gaa/Aaa	1/2	0.807301599087199	1	FACETS	0.998	0.943	1	0.998	0.943	1	CLONAL	1	TRUE	0	0.807301599087199	1		254	231	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534771	5534771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	253	338	0	ENST00000397747.3:c.82G>A	p.Glu28Lys	p.E28K	ENST00000397747	NM_025239.3	28	Gaa/Aaa	3/7	0.807301599087199	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.807301599087199	1		338	371	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650849	93650849	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	241	470	0	ENST00000375746.1:c.1775G>A	p.Gly592Glu	p.G592E	ENST00000375746	NM_001174167.1	592	gGg/gAg	13/14	1	2	FACETS	0.888	0.835	0.943	0.888	0.835	0.943	CLONAL	1	TRUE	1	0.807301599087199	2		470	672	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477839	140477855	+	protein_altering_variant	In_Frame_Del	DEL	GGTGCTGTCACATTCAA	GGTGCTGTCACATTCAA	AG	novel	NA	P-0050399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	395	436	2	ENST00000288602.6:c.1453_1469delinsCT	p.Asn486_Pro490del	p.N486_P490del	ENST00000288602	NM_004333.4	485	TTGAATGTGACAGCACCt/CTt	12/18	0.807301599087199	3	FACETS	1	0.996	1	0.733	0.7	0.767	CLONAL	1	TRUE	1	0.807301599087199	3		438	937	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0050400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	599	662	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.707197102166464	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.707768146437751	3		662	748	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061214	38061231	+	inframe_deletion	In_Frame_Del	DEL	AGCAGCCGTTCTCGAACA	AGCAGCCGTTCTCGAACA	-	novel	NA	P-0050401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	209	681	0	ENST00000250448.2:c.758_775del	p.Met253_Tyr259delinsAsn	p.M253_Y259delinsN	ENST00000250448	NM_004496.3	253	aTGTTCGAGAACGGCTGCTac/aac	2/2	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.49466438801586	2		681	607	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17120412	17120412	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	121	626	0	ENST00000285071.4:c.1147C>G	p.Leu383Val	p.L383V	ENST00000285071	NM_144997.5	383	Ctc/Gtc	10/14	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.49466438801586	2		626	488	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372701	81372701	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	120	400	0	ENST00000222390.5:c.833C>G	p.Thr278Ser	p.T278S	ENST00000222390	NM_000601.4	278	aCc/aGc	7/18	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.49466438801586	2		400	484	SUCCESS
APC	324	MSKCC	GRCh37	5	112175879	112175886	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAATGA	GAAAATGA	T	novel	NA	P-0050401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	77	267	0	ENST00000257430.4:c.4588_4595delinsT	p.Glu1530SerfsTer33	p.E1530Sfs*33	ENST00000257430	NM_000038.5	1530	GAAAATGAc/Tc	16/16	0.426603030851824	1	FACETS	0.945	0.841	1	0.945	0.841	1	CLONAL	1	TRUE	0	0.49466438801586	1		267	248	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0050402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	93	328	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.431804139362548	2		328	424	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0050402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	209	822	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA	2	FACETS	1	0.95	1			1	INDETERMINATE	1	TRUE	NA	0.431804139362548	2		822	942	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0050402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	176	604	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.431804139362548	1	FACETS	0.883	0.815	0.953	0.883	0.815	0.953	CLONAL	1	TRUE	0	0.431804139362548	1		604	724	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199824	108199824	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1018140779	NA	P-0050402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	69	367	0	ENST00000278616.4:c.7166C>T	p.Ser2389Leu	p.S2389L	ENST00000278616	NM_000051.3	2389	tCa/tTa	49/63	1	2	FACETS	0.776	0.678	0.88	0.776	0.678	0.88	SUBCLONAL	1	TRUE	1	0.431804139362548	2		367	412	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421078	49421078	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	136	568	0	ENST00000301067.7:c.14671C>T	p.Gln4891Ter	p.Q4891*	ENST00000301067	NM_003482.3	4891	Cag/Tag	48/54	1	2	FACETS	0.949	0.865	1	0.949	0.865	1	CLONAL	1	TRUE	1	0.431804139362548	2		568	664	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443467	49443467	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	161	612	1	ENST00000301067.7:c.3904C>T	p.Gln1302Ter	p.Q1302*	ENST00000301067	NM_003482.3	1302	Cag/Tag	11/54	1	2	FACETS	0.986	0.906	1	0.986	0.906	1	CLONAL	1	TRUE	1	0.431804139362548	2		613	756	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378358	15378358	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	82	266	0	ENST00000263377.2:c.428G>C	p.Gly143Ala	p.G143A	ENST00000263377	NM_058243.2	143	gGa/gCa	4/20	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.431804139362548	2		266	371	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082767	16082767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	41	143	0	ENST00000281043.3:c.581C>T	p.Pro194Leu	p.P194L	ENST00000281043	NM_005378.4	194	cCc/cTc	2/3	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.431804139362548	2		143	167	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86676403	86676403	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	58	271	0	ENST00000274376.6:c.2681G>C	p.Arg894Thr	p.R894T	ENST00000274376	NM_002890.2	894	aGa/aCa	20/25	1	2	FACETS	0.819	0.708	0.939	0.819	0.708	0.939	CLONAL	1	TRUE	1	0.431804139362548	2		271	328	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509517	106509517	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	484	687	0	ENST00000359195.3:c.1511C>G	p.Ser504Cys	p.S504C	ENST00000359195	NM_002649.2	504	tCt/tGt	2/11	0.431804139362548	3	FACETS	0.937	0.901	0.973	1	0.996	1	CLONAL	3	TRUE	1	0.431804139362548	3		687	970	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860722	151860722	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	428	546	1	ENST00000262189.6:c.9940C>T	p.Gln3314Ter	p.Q3314*	ENST00000262189	NM_170606.2	3314	Cag/Tag	43/59	0.410838799553942	3	FACETS	0.959	0.92	0.997	0.959	0.92	0.997	CLONAL	3	TRUE	0	0.431804139362548	3		547	838	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945136	151945136	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	12	193	0	ENST00000262189.6:c.2383G>C	p.Asp795His	p.D795H	ENST00000262189	NM_170606.2	795	Gac/Cac	14/59	NA	2	FACETS	0.26	0.182	0.355			1	INDETERMINATE	1	TRUE	NA	0.431804139362548	2		193	214	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0050403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	851	476	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.270081180667067	7	FACETS	1	0.991	1			1	CLONAL	6	TRUE	NA	0.270081180667067	7		476	1675	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440904	56440904	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1458799446	NA	P-0050403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	43	625	0	ENST00000407977.2:c.433C>T	p.Arg145Ter	p.R145*	ENST00000407977		145	Cga/Tga	4/10	1	2	FACETS	0.384	0.32	0.455	0.384	0.32	0.455	SUBCLONAL	1	TRUE	1	0.270081180667067	2		625	829	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847399	68847399	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0050403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	101	348	1	ENST00000261769.5:c.1320+1G>T		p.X440_splice	ENST00000261769	NM_004360.3	440			0.270081180667067	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.270081180667067	1		349	565	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061205	38061205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	32	517	0	ENST00000250448.2:c.784C>T	p.Arg262Cys	p.R262C	ENST00000250448	NM_004496.3	262	Cgc/Tgc	2/2	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.17	2		517	337	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627418	37627419	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0050404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	20	487	0	ENST00000447079.4:c.1336_1337del	p.Lys446ValfsTer15	p.K446Vfs*15	ENST00000447079	NM_015083.1	445	AAa/a	2/14	1	2	FACETS	0.875	0.67	1	0.875	0.67	1	CLONAL	1	TRUE	1	0.17	2		487	269	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646846	37646847	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGAAGGAACAGAGGACACGTCACTTACTCACAGACCTTCCTCTCCCTCCAGAGCTCCCTGGTG	novel	NA	P-0050404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	22	362	0	ENST00000447079.4:c.1973_2036dup	p.Asp679GlufsTer42	p.D679Efs*42	ENST00000447079	NM_015083.1	656	-/GAGAAGGAACAGAGGACACGTCACTTACTCACAGACCTTCCTCTCCCTCCAGAGCTCCCTGGTG	3/14	1	2	FACETS	0.768	0.595	0.969	0.768	0.595	0.969	CLONAL	1	TRUE	1	0.17	2		362	337	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942571	17942571	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	41	695	0	ENST00000458235.1:c.2717C>A	p.Pro906His	p.P906H	ENST00000458235	NM_000215.3	906	cCc/cAc	20/24	1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	TRUE	1	0.17	2		695	476	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	107	468	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.915	0.829	1	0.915	0.829	1	CLONAL	1	TRUE	1	0.657151690181319	2		468	356	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	274	756	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	1	2	FACETS	0.963	0.906	1	0.963	0.906	1	CLONAL	1	TRUE	1	0.657151690181319	2		756	866	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	310	582	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	1	2	FACETS	0.987	0.933	1	0.987	0.933	1	CLONAL	1	TRUE	1	0.657151690181319	2		582	956	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561396	9561396	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1262495622	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	170	380	0	ENST00000353224.5:c.386C>T	p.Ser129Phe	p.S129F	ENST00000353224	NM_177990.2	129	tCc/tTc	4/10	1	2	FACETS	0.932	0.863	1	0.932	0.863	1	CLONAL	1	TRUE	1	0.657151690181319	2		380	555	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601310	28601310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	140	315	0	ENST00000241453.7:c.2122G>A	p.Glu708Lys	p.E708K	ENST00000241453	NM_004119.2	708	Gaa/Aaa	17/24	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.657151690181319	2		315	420	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508281	106508281	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778832310	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	209	399	0	ENST00000359195.3:c.275G>A	p.Gly92Glu	p.G92E	ENST00000359195	NM_002649.2	92	gGa/gAa	2/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.657151690181319	2		399	608	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857436	9857436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	174	416	0	ENST00000330684.3:c.3965G>A	p.Gly1322Glu	p.G1322E	ENST00000330684	NM_001134407.1	1322	gGa/gAa	13/13	0.657151690181319	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.657151690181319	1		416	315	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312683	91312683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759330541	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	97	221	2	ENST00000355112.3:c.2422C>T	p.Arg808Cys	p.R808C	ENST00000355112	NM_000057.2	808	Cgt/Tgt	12/22	1	2	FACETS	0.848	0.764	0.937	0.848	0.764	0.937	CLONAL	1	TRUE	1	0.657151690181319	2		223	348	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414251	32414251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121907910	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	150	329	0	ENST00000332351.3:c.1300C>T	p.Arg434Cys	p.R434C	ENST00000332351	NM_024426.4	434	Cgt/Tgt	8/10	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.657151690181319	2		329	449	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934002	49934002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	228	610	0	ENST00000296474.3:c.2410C>T	p.His804Tyr	p.H804Y	ENST00000296474	NM_002447.2	804	Cat/Tat	9/20	1	2	FACETS	0.991	0.928	1	0.991	0.928	1	CLONAL	1	TRUE	1	0.657151690181319	2		610	700	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346895	89346895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1165374364	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	164	417	0	ENST00000301030.4:c.6055C>T	p.Pro2019Ser	p.P2019S	ENST00000301030	NM_001256183.1	2019	Ccc/Tcc	9/13	0.657151690181319	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.657151690181319	1		417	287	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909674	50909674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199700312	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	288	693	0	ENST00000440232.2:c.1394G>A	p.Arg465Gln	p.R465Q	ENST00000440232	NM_002691.3	465	cGg/cAg	12/27	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.657151690181319	2		693	847	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964374	70964374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766779014	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	174	350	0	ENST00000276594.2:c.1654G>A	p.Gly552Arg	p.G552R	ENST00000276594	NM_024504.3	552	Ggg/Agg	8/8	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.657151690181319	2		350	520	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93953241	93953241	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267601169	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	99	322	0	ENST00000369303.4:c.2900G>A	p.Gly967Glu	p.G967E	ENST00000369303	NM_004440.3	967	gGg/gAg	17/17	0.595838307675417	1	FACETS	0.72	0.652	0.79	0.72	0.652	0.79	SUBCLONAL	1	TRUE	0	0.657151690181319	1		322	281	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517766	176517766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370322847	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	218	631	0	ENST00000292408.4:c.376G>A	p.Asp126Asn	p.D126N	ENST00000292408	NM_213647.1	126	Gat/Aat	4/18	1	2	FACETS	0.999	0.934	1	0.999	0.934	1	CLONAL	1	TRUE	1	0.657151690181319	2		631	664	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276875	15276875	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	253	602	0	ENST00000263388.2:c.5390C>T	p.Ser1797Phe	p.S1797F	ENST00000263388	NM_000435.2	1797	tCc/tTc	30/33	1	2	FACETS	0.994	0.933	1	0.994	0.933	1	CLONAL	1	TRUE	1	0.657151690181319	2		602	775	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715746	18715746	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1191317818	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	119	263	0	ENST00000266497.5:c.3577C>T	p.Pro1193Ser	p.P1193S	ENST00000266497		1193	Cct/Tct	25/31	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.657151690181319	2		263	329	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911247	32911247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs431825298	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	109	392	0	ENST00000380152.3:c.2755G>A	p.Glu919Lys	p.E919K	ENST00000380152		919	Gaa/Aaa	11/27	1	2	FACETS	0.906	0.822	0.994	0.906	0.822	0.994	CLONAL	1	TRUE	1	0.657151690181319	2		392	366	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980726	40980726	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	161	288	0	ENST00000373198.4:c.1760C>T	p.Ser587Leu	p.S587L	ENST00000373198	NM_133170.3	587	tCa/tTa	10/32	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.657151690181319	2		288	410	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525576	137525576	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	120	342	0	ENST00000367739.4:c.439C>T	p.His147Tyr	p.H147Y	ENST00000367739	NM_000416.2	147	Cac/Tac	4/7	0.595838307675417	1	FACETS	0.778	0.713	0.845	0.778	0.713	0.845	SUBCLONAL	1	TRUE	0	0.657151690181319	1		342	315	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655271	45655271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56105929	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	323	613	0	ENST00000407780.3:c.581G>A	p.Arg194Gln	p.R194Q	ENST00000407780	NM_001283052.1	194	cGg/cAg	4/7	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.657151690181319	2		613	890	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669301	241669301	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	140	281	0	ENST00000366560.3:c.904+2T>C		p.X302_splice	ENST00000366560	NM_000143.3	302			1	2	FACETS	0.971	0.892	1	0.971	0.892	1	CLONAL	1	TRUE	1	0.657151690181319	2		281	439	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138917	64138918	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	286	676	0	ENST00000334205.4:c.2284_2285delinsTT	p.Pro762Phe	p.P762F	ENST00000334205	NM_003942.2	762	CCc/TTc	17/17	1	2	FACETS	0.982	0.926	1	0.982	0.926	1	CLONAL	1	TRUE	1	0.657151690181319	2		676	886	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372504	118372504	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	200	397	0	ENST00000534358.1:c.6437C>T	p.Pro2146Leu	p.P2146L	ENST00000534358	NM_005933.3	2146	cCc/cTc	26/36	1	2	FACETS	0.882	0.821	0.945	0.882	0.821	0.945	CLONAL	1	TRUE	1	0.657151690181319	2		397	690	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435159	49435160	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	205	507	1	ENST00000301067.7:c.6393_6394delinsTT	p.Pro2132Ser	p.P2132S	ENST00000301067	NM_003482.3	2131	acCCcc/acTTcc	31/54	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.657151690181319	2		508	600	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112499	115112499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	307	652	0	ENST00000257566.3:c.1241C>T	p.Ala414Val	p.A414V	ENST00000257566	NM_016569.3	414	gCt/gTt	7/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.657151690181319	2		652	842	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30095714	30095714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519635	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	121	275	0	ENST00000331968.5:c.1774G>A	p.Gly592Arg	p.G592R	ENST00000331968	NM_002742.2	592	Gga/Aga	12/18	1	2	FACETS	0.982	0.896	1	0.982	0.896	1	CLONAL	1	TRUE	1	0.657151690181319	2		275	375	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643661	38643662	+	stop_gained	Nonsense_Mutation	DNP	TC	TC	AA	novel	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	190	454	0	ENST00000299084.4:c.1131_1132delinsAA	p.Tyr377_His378delinsTer	p.Y377_H378delins*	ENST00000299084	NM_152594.2	377	taTCat/taAAat	7/7	1	2	FACETS	0.937	0.871	1	0.937	0.871	1	CLONAL	1	TRUE	1	0.657151690181319	2		454	617	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170016889	170016889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	145	321	0	ENST00000295797.4:c.1694C>T	p.Pro565Leu	p.P565L	ENST00000295797	NM_002740.5	565	cCa/cTa	17/18	1	2	FACETS	0.953	0.877	1	0.953	0.877	1	CLONAL	1	TRUE	1	0.657151690181319	2		321	463	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294392	1294392	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	278	699	1	ENST00000310581.5:c.609G>A	p.Trp203Ter	p.W203*	ENST00000310581	NM_198253.2	203	tgG/tgA	2/16	1	2	FACETS	0.967	0.911	1	0.967	0.911	1	CLONAL	1	TRUE	1	0.657151690181319	2		700	875	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665497	176665497	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	160	330	0	ENST00000439151.2:c.4181T>G	p.Val1394Gly	p.V1394G	ENST00000439151	NM_022455.4	1394	gTt/gGt	7/23	1	2	FACETS	0.97	0.896	1	0.97	0.896	1	CLONAL	1	TRUE	1	0.657151690181319	2		330	502	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665505	176665505	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	148	320	0	ENST00000439151.2:c.4189C>G	p.Pro1397Ala	p.P1397A	ENST00000439151	NM_022455.4	1397	Cca/Gca	7/23	1	2	FACETS	0.916	0.842	0.991	0.916	0.842	0.991	CLONAL	1	TRUE	1	0.657151690181319	2		320	492	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120390	94120390	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	16	254	0	ENST00000369303.4:c.661G>A	p.Gly221Ser	p.G221S	ENST00000369303	NM_004440.3	221	Ggt/Agt	3/17	0.595838307675417	1	FACETS	0.128	0.094	0.169	0.128	0.094	0.169	SUBCLONAL	1	TRUE	0	0.657151690181319	1		254	255	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55219048	55219048	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	199	388	0	ENST00000275493.2:c.621C>G	p.Cys207Trp	p.C207W	ENST00000275493	NM_005228.3	207	tgC/tgG	5/28	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.657151690181319	2		388	579	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180252	27180252	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	205	370	0	ENST00000380036.4:c.916T>C	p.Phe306Leu	p.F306L	ENST00000380036	NM_000459.3	306	Ttt/Ctt	7/23	0.657151690181319	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.657151690181319	1		370	371	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321387	1321387	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	142	331	0	ENST00000400841.2:c.368del	p.Lys123SerfsTer3	p.K123Sfs*3	ENST00000400841		123	aAg/ag	4/6	1	1	FACETS	0.55	0.503	0.597	0.55	0.503	0.597	SUBCLONAL	1	TRUE	0	0.657151690181319	1		331	528	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0050406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	129	534	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.612	0.557	0.67	0.612	0.557	0.67	SUBCLONAL	1	TRUE	1	0.73136153420491	2		534	576	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692794	89692794	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121909238	NA	P-0050406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	43	265	0	ENST00000371953.3:c.278A>G	p.His93Arg	p.H93R	ENST00000371953	NM_000314.4	93	cAt/cGt	5/9	1	2	FACETS	0.316	0.265	0.373	0.316	0.265	0.373	SUBCLONAL	1	TRUE	1	0.73136153420491	2		265	372	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46240692	46240695	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	-	novel	NA	P-0050406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	62	267	0	ENST00000334344.6:c.1556_1559del	p.Asp519ValfsTer9	p.D519Vfs*9	ENST00000334344	NM_152641.2	518	ATAGat/at	12/21	1	2	FACETS	0.378	0.327	0.434	0.378	0.327	0.434	SUBCLONAL	1	TRUE	1	0.73136153420491	2		267	448	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0050406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	78	242	0	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	1	2	FACETS	0.54	0.477	0.607	0.54	0.477	0.607	SUBCLONAL	1	TRUE	1	0.73136153420491	2		242	395	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857758	78857758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs962629512	NA	P-0050406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	146	570	0	ENST00000306801.3:c.1828G>A	p.Asp610Asn	p.D610N	ENST00000306801	NM_020761.2	610	Gac/Aac	16/34	1	2	FACETS	0.664	0.609	0.722	0.664	0.609	0.722	SUBCLONAL	1	TRUE	1	0.73136153420491	2		570	601	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148516713	148516713	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	23	275	0	ENST00000320356.2:c.974G>T	p.Cys325Phe	p.C325F	ENST00000320356	NM_004456.4	325	tGt/tTt	9/20	1	2	FACETS	0.147	0.114	0.186	0.147	0.114	0.186	SUBCLONAL	1	TRUE	1	0.73136153420491	2		275	427	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572171	64572171	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	263	705	0	ENST00000312049.6:c.1468G>T	p.Glu490Ter	p.E490*	ENST00000312049	NM_130799.2	490	Gag/Tag	10/10	0.52780594162968	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.52780594162968	1		705	682	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0050409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	385	461	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.626465361015861	4	FACETS	0.976	0.936	1	0.976	0.936	1	CLONAL	3	TRUE	1	0.626465361015861	4		461	683	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0050409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	138	510	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.626465361015861	3	FACETS	1	0.937	1	0.515	0.47	0.561	CLONAL	1	TRUE	1	0.626465361015861	3		510	562	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561052	9561052	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760823835	NA	P-0050409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	100	397	0	ENST00000353224.5:c.730G>A	p.Gly244Arg	p.G244R	ENST00000353224	NM_177990.2	244	Ggg/Agg	4/10	0.626465361015861	4	FACETS	0.939	0.841	1	0.469	0.42	0.521	CLONAL	1	TRUE	2	0.626465361015861	4		397	553	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231788	36231788	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	300	651	0	ENST00000300305.3:c.596G>A	p.Gly199Glu	p.G199E	ENST00000300305		199	gGg/gAg	5/8	0.613944483669106	2	FACETS	0.965	0.923	1	0.965	0.923	1	CLONAL	2	TRUE	0	0.626465361015861	2		651	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0050410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	224	568	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.332903431030246	2	FACETS	0.958	0.898	1	0.958	0.898	1	CLONAL	2	TRUE	0	0.384623314101514	2		568	608	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914815	32914815	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35029074	NA	P-0050410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	30	349	0	ENST00000380152.3:c.6323G>A	p.Arg2108His	p.R2108H	ENST00000380152		2108	cGt/cAt	11/27	0.384623314101514	1	FACETS	0.417	0.337	0.508	0.417	0.337	0.508	SUBCLONAL	1	TRUE	0	0.384623314101514	1		349	302	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18496273	18496273	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	13	183	0	ENST00000266497.5:c.1408A>T	p.Ser470Cys	p.S470C	ENST00000266497		470	Agt/Tgt	9/31	0.177329633481697	3	FACETS	0.324	0.23	0.437	0.108	0.076	0.146	INDETERMINATE	1	TRUE	0	0.384623314101514	3		183	249	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058588	69058588	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0050410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	20	413	0	ENST00000288368.4:c.4231+1G>C		p.X1411_splice	ENST00000288368	NM_024870.2	1411			0.384623314101514	1	FACETS	0.215	0.164	0.276	0.215	0.164	0.276	SUBCLONAL	1	TRUE	0	0.384623314101514	1		413	390	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412646	63412646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	32	540	0	ENST00000330258.3:c.521G>A	p.Ser174Asn	p.S174N	ENST00000330258	NM_152424.3	174	aGc/aAc	2/2	0.384623314101514	0	FACETS	0.293	0.237	0.355			1	SUBCLONAL	1	TRUE	0	0.384623314101514	0		540	350	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0050411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	243	510	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.781619270666674	3	FACETS	1	0.993	1	0.739	0.696	0.783	CLONAL	1	FALSE	1	0.781619270666674	3		510	585	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0050411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	72	366	1	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	0.687433716826851	5	FACETS	0.824	0.721	0.933	0.275	0.24	0.311	CLONAL	1	FALSE	2	0.781619270666674	5		367	486	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178085	56178085	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	144	300	0	ENST00000399503.3:c.3058C>T	p.Gln1020Ter	p.Q1020*	ENST00000399503	NM_005921.1	1020	Caa/Taa	14/20	0.781619270666674	4	FACETS	0.795	0.732	0.859	0.795	0.732	0.859	SUBCLONAL	2	FALSE	2	0.781619270666674	4		300	413	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945131	151945131	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	24	268	0	ENST00000262189.6:c.2388G>A	p.Met796Ile	p.M796I	ENST00000262189	NM_170606.2	796	atG/atA	14/59	0.781619270666674	5	FACETS	0.442	0.347	0.551	0.147	0.115	0.184	SUBCLONAL	1	FALSE	2	0.781619270666674	5		268	302	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711963	89711963	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1554900622	NA	P-0050411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	199	330	0	ENST00000371953.3:c.581T>A	p.Leu194Ter	p.L194*	ENST00000371953	NM_000314.4	194	tTg/tAg	6/9	0.649416555412356	2	FACETS	0.84	0.798	0.881	0.84	0.798	0.881	CLONAL	2	FALSE	0	0.781619270666674	2		330	303	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146112	38146112	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5642	324	547	0	ENST00000317025.8:c.3394G>C	p.Asp1132His	p.D1132H	ENST00000317025	NM_023034.1	1132	Gat/Cat	19/24	0.781619270666674	27	FACETS	1	0.993	1			1	CLONAL	1	FALSE	NA	0.781619270666674	27		547	5966	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97879632	97879632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050411-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	208	455	1	ENST00000289081.3:c.1037C>T	p.Pro346Leu	p.P346L	ENST00000289081	NM_000136.2	346	cCa/cTa	11/15	0.722973140087892	3	FACETS	0.881	0.83	0.933	0.881	0.83	0.933	CLONAL	2	FALSE	1	0.781619270666674	3		456	420	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667835	37667835	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	110	447	0	ENST00000447079.4:c.2720T>C	p.Leu907Pro	p.L907P	ENST00000447079	NM_015083.1	907	cTg/cCg	8/14	0.367465713035008	1	FACETS	0.983	0.889	1	0.983	0.889	1	CLONAL	1	TRUE	0	0.420914573122615	1		447	420	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0050416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	40	344	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	1	2	FACETS	0.871	0.727	1	0.871	0.727	1	CLONAL	1	TRUE	1	0.302066652435312	2		344	304	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608224	28608224	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	42	512	0	ENST00000241453.7:c.1832A>T	p.Glu611Val	p.E611V	ENST00000241453	NM_004119.2	611	gAg/gTg	14/24	1	2	FACETS	0.664	0.555	0.784	0.664	0.555	0.784	SUBCLONAL	1	TRUE	1	0.302066652435312	2		512	419	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0050417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	82	534	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.25	2		534	567	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0050417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	44	255	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.85	0.714	1	0.85	0.714	1	CLONAL	1	TRUE	1	0.25	2		255	414	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844139	68844139	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	89	482	0	ENST00000261769.5:c.727G>A	p.Glu243Lys	p.E243K	ENST00000261769	NM_004360.3	243	Gag/Aag	6/16	0.297218402616118	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.25	1		482	512	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426267	49426268	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0050417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	104	649	1	ENST00000301067.7:c.12220_12221del	p.Gln4074ThrfsTer32	p.Q4074Tfs*32	ENST00000301067	NM_003482.3	4074	CAa/a	39/54	1	2	FACETS	0.952	0.852	1	0.952	0.852	1	CLONAL	1	TRUE	1	0.25	2		650	874	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0050419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	93	294	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.586929903317923	2		294	317	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	76	507	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.478046189317919	1	FACETS	0.299	0.262	0.339	0.299	0.262	0.339	SUBCLONAL	1	TRUE	0	0.586929903317923	1		507	612	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	259	483	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.586929903317923	2		483	843	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863224499	NA	P-0050419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	190	490	0	ENST00000269305.4:c.672+1G>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.478046189317919	1	FACETS	0.798	0.743	0.855	0.798	0.743	0.855	SUBCLONAL	1	TRUE	0	0.586929903317923	1		490	573	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481412	140481412	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913353	NA	P-0050419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	86	246	0	ENST00000288602.6:c.1396G>C	p.Gly466Arg	p.G466R	ENST00000288602	NM_004333.4	466	Gga/Cga	11/18	1	2	FACETS	0.924	0.826	1	0.924	0.826	1	CLONAL	1	TRUE	1	0.586929903317923	2		246	317	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821821	72821821	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	217	410	0	ENST00000268489.5:c.10354del	p.Leu3452SerfsTer33	p.L3452Sfs*33	ENST00000268489	NM_006885.3	3452	Ctc/tc	10/10	0.586929903317923	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.586929903317923	1		410	493	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074093	8074094	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	62	266	0	ENST00000377482.5:c.565dup	p.Ser189PhefsTer2	p.S189Ffs*2	ENST00000377482	NM_018948.3	189	tct/tTct	4/4	0.292681828317485	0	FACETS	0.342	0.299	0.389			1	INDETERMINATE	1	TRUE	0	0.586929903317923	0		266	255	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	58	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.254846179111362	2	FACETS	0.771	0.668	0.883	0.771	0.668	0.883	SUBCLONAL	2	TRUE	0	0.254846179111362	2		327	295	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0050420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	111	927	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.254846179111362	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.254846179111362	1		927	674	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604764	48604765	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs377767376	NA	P-0050420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	54	336	0	ENST00000342988.3:c.1587dup	p.His530ThrfsTer47	p.H530Tfs*47	ENST00000342988	NM_005359.5	529	tta/ttAa	12/12	0.254846179111362	1	FACETS	0.943	0.808	1	0.943	0.808	1	CLONAL	1	TRUE	0	0.254846179111362	1		336	392	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257158	16257158	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	38	377	0	ENST00000375759.3:c.4423C>T	p.Arg1475Ter	p.R1475*	ENST00000375759	NM_015001.2	1475	Cga/Tga	11/15	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.254846179111362	2		377	219	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909291	41909291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778979671	NA	P-0050420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	121	590	0	ENST00000372991.4:c.97C>T	p.Arg33Cys	p.R33C	ENST00000372991	NM_001760.3	33	Cgc/Tgc	1/5	0.0962697712608038	3	FACETS	1	0.971	1	0.599	0.541	0.661	INDETERMINATE	1	TRUE	1	0.254846179111362	3		590	893	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726595	41726595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1260076571	NA	P-0050420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	123	612	1	ENST00000301178.4:c.140C>T	p.Ala47Val	p.A47V	ENST00000301178	NM_021913.4	47	gCc/gTc	2/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.254846179111362	2		613	744	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	135	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.648894394550139	2		327	412	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0050424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	44	175	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.848	0.723	0.98	0.848	0.723	0.98	CLONAL	1	TRUE	1	0.648894394550139	2		175	160	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0050424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	225	662	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.648894394550139	1	FACETS	0.95	0.895	1	0.95	0.895	1	CLONAL	1	TRUE	0	0.648894394550139	1		662	493	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713506	30713506	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	191	474	0	ENST00000295754.5:c.831G>C	p.Lys277Asn	p.K277N	ENST00000295754	NM_003242.5	277	aaG/aaC	4/7	1	2	FACETS	0.939	0.873	1	0.939	0.873	1	CLONAL	1	TRUE	1	0.648894394550139	2		474	627	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717699	89717699	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554825210	NA	P-0050424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	134	372	0	ENST00000371953.3:c.724G>T	p.Glu242Ter	p.E242*	ENST00000371953	NM_000314.4	242	Gag/Tag	7/9	1	2	FACETS	0.912	0.835	0.991	0.912	0.835	0.991	CLONAL	1	TRUE	1	0.648894394550139	2		372	453	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098803	178098803	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	179	570	0	ENST00000397062.3:c.242G>C	p.Gly81Ala	p.G81A	ENST00000397062	NM_006164.4	81	gGt/gCt	2/5	1	2	FACETS	0.78	0.722	0.841	0.78	0.722	0.841	SUBCLONAL	1	TRUE	1	0.648894394550139	2		570	707	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818417	43818417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759895996	NA	P-0050424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	161	471	0	ENST00000372470.3:c.1882C>T	p.Pro628Ser	p.P628S	ENST00000372470	NM_005373.2	628	Cca/Tca	12/12	1	2	FACETS	0.86	0.793	0.929	0.86	0.793	0.929	CLONAL	1	TRUE	1	0.648894394550139	2		471	577	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860087	57860087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	132	575	1	ENST00000228682.2:c.827C>T	p.Ser276Phe	p.S276F	ENST00000228682	NM_005269.2	276	tCc/tTc	8/12	1	2	FACETS	0.477	0.433	0.524	0.477	0.433	0.524	SUBCLONAL	1	TRUE	1	0.648894394550139	2		576	853	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461579	138461579	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	144	390	0	ENST00000289153.2:c.442T>C	p.Phe148Leu	p.F148L	ENST00000289153	NM_006219.2	148	Ttt/Ctt	3/22	1	2	FACETS	0.959	0.881	1	0.959	0.881	1	CLONAL	1	TRUE	1	0.648894394550139	2		390	463	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589024	67589028	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TAAGG	TAAGG	-	novel	NA	P-0050424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	63	229	0	ENST00000274335.5:c.1118+1_1118+5del		p.X373_splice	ENST00000274335		373		8/15	1	2	FACETS	0.981	0.863	1	0.981	0.863	1	CLONAL	1	TRUE	1	0.648894394550139	2		229	198	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589597	67589647	+	inframe_deletion	In_Frame_Del	DEL	ACTCAGTTTCAAGAAAAAAGTCGAGAATATGATAGATTATATGAAGAATAT	ACTCAGTTTCAAGAAAAAAGTCGAGAATATGATAGATTATATGAAGAATAT	-	novel	NA	P-0050424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	35	254	0	ENST00000274335.5:c.1362_1412del	p.Gln455_Thr471del	p.Q455_T471del	ENST00000274335		454	ACTCAGTTTCAAGAAAAAAGTCGAGAATATGATAGATTATATGAAGAATAT/-	10/15	1	2	FACETS	0.455	0.375	0.543	0.455	0.375	0.543	SUBCLONAL	1	TRUE	1	0.648894394550139	2		254	237	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641059	117641059	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	147	420	0	ENST00000368508.3:c.5912G>C	p.Gly1971Ala	p.G1971A	ENST00000368508	NM_002944.2	1971	gGa/gCa	36/43	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.648894394550139	2		420	452	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	18	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.594	0.445	0.771	0.594	0.445	0.771	SUBCLONAL	1	TRUE	1	0.11	2		327	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs17849781	NA	P-0050425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	24	585	0	ENST00000269305.4:c.832C>A	p.Pro278Thr	p.P278T	ENST00000269305	NM_001126112.2	278	Cct/Act	8/11	1	2	FACETS	0.713	0.557	0.894	0.713	0.557	0.894	SUBCLONAL	1	TRUE	1	0.11	2		585	612	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138191	64138191	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	27	567	0	ENST00000334205.4:c.2114C>A	p.Thr705Asn	p.T705N	ENST00000334205	NM_003942.2	705	aCc/aAc	16/17	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.11	2		567	452	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877344	28877344	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	147	379	0	ENST00000282397.4:c.3977A>G	p.Asp1326Gly	p.D1326G	ENST00000282397	NM_002019.4	1326	gAc/gGc	30/30	1	2	FACETS	0.92	0.844	0.999	0.92	0.844	0.999	CLONAL	1	TRUE	1	0.570498175706783	2		379	560	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794793	242794793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759141096	NA	P-0050426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	144	353	0	ENST00000334409.5:c.416G>A	p.Arg139Gln	p.R139Q	ENST00000334409	NM_005018.2	139	cGg/cAg	2/5	1	2	FACETS	0.94	0.862	1	0.94	0.862	1	CLONAL	1	TRUE	1	0.570498175706783	2		353	537	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799940	72799940	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1224175056	NA	P-0050426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	73	360	0	ENST00000325599.8:c.1229T>G	p.Leu410Arg	p.L410R	ENST00000325599	NM_018130.2	410	cTt/cGt	11/11	1	2	FACETS	0.606	0.532	0.685	0.606	0.532	0.685	SUBCLONAL	1	TRUE	1	0.570498175706783	2		360	422	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925370	131925370	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	58	183	0	ENST00000265335.6:c.1293G>T	p.Glu431Asp	p.E431D	ENST00000265335		431	gaG/gaT	9/25	1	2	FACETS	0.908	0.79	1	0.908	0.79	1	CLONAL	1	TRUE	1	0.570498175706783	2		183	224	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538910	23538910	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	24	455	0	ENST00000380871.4:c.529T>C	p.Tyr177His	p.Y177H	ENST00000380871	NM_006167.3	177	Tat/Cat	2/2	0.570498175706783	1	FACETS	0.127	0.099	0.159	0.127	0.099	0.159	SUBCLONAL	1	TRUE	0	0.570498175706783	1		455	474	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	18	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.82	1	1	0.82	1	CLONAL	1	TRUE	1	0.11	2		327	294	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0050428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	17	443	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.641	0.477	0.838	0.641	0.477	0.838	SUBCLONAL	1	TRUE	1	0.11	2		443	482	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0050428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	15	534	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.931	0.68	1	0.931	0.68	1	CLONAL	1	TRUE	1	0.11	2		534	293	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	115	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.462109232995038	3	FACETS	0.901	0.821	0.983	0.901	0.821	0.983	CLONAL	2	TRUE	1	0.462109232995038	3		327	340	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0050429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	37	394	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.386262305748839	2	FACETS	0.875	0.73	1	0.438	0.365	0.517	CLONAL	1	TRUE	0	0.462109232995038	2		394	183	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0050429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	55	222	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	1	2	FACETS	0.799	0.688	0.918	0.799	0.688	0.918	CLONAL	1	TRUE	1	0.462109232995038	2		222	298	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577555	7577555	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs375874539	NA	P-0050429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	206	491	0	ENST00000269305.4:c.726C>G	p.Cys242Trp	p.C242W	ENST00000269305	NM_001126112.2	242	tgC/tgG	7/11	0.462109232995038	2	FACETS	0.984	0.924	1	0.984	0.924	1	CLONAL	2	TRUE	0	0.462109232995038	2		491	453	SUCCESS
APC	324	MSKCC	GRCh37	5	112116517	112116517	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs869312753	NA	P-0050429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	25	308	0	ENST00000257430.4:c.562C>T	p.Gln188Ter	p.Q188*	ENST00000257430	NM_000038.5	188	Caa/Taa	6/16	1	2	FACETS	0.608	0.483	0.749	0.608	0.483	0.749	SUBCLONAL	1	TRUE	1	0.462109232995038	2		308	178	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219008	36219008	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	149	495	0	ENST00000222270.7:c.4507T>G	p.Ser1503Ala	p.S1503A	ENST00000222270	NM_014727.1	1503	Tct/Gct	19/37	0.462109232995038	3	FACETS	1	0.978	1	0.596	0.546	0.648	CLONAL	1	TRUE	1	0.462109232995038	3		495	666	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447463	187447463	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529677174	NA	P-0050429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	226	498	0	ENST00000232014.4:c.730C>T	p.Arg244Trp	p.R244W	ENST00000232014	NM_001130845.1	244	Cgg/Tgg	5/10	0.386262305748839	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.462109232995038	2		498	451	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749464	41749464	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	124	444	0	ENST00000226382.2:c.331A>C	p.Lys111Gln	p.K111Q	ENST00000226382	NM_003924.3	111	Aaa/Caa	2/3	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.462109232995038	2		444	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0050430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	311	454	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.867353460961912	1	FACETS	0.967	0.933	1	0.967	0.933	1	CLONAL	1	TRUE	0	0.867353460961912	1		455	420	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0050431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	176	461	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.755376333688202	2	FACETS	1	0.94	1	0.505	0.47	0.541	CLONAL	1	TRUE	0	0.755376333688202	2		461	461	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471047	8471047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201751722	NA	P-0050431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	238	374	0	ENST00000356435.5:c.3452G>A	p.Arg1151His	p.R1151H	ENST00000356435		1151	cGc/cAc	20/35	0.755376333688202	4	FACETS	0.895	0.841	0.949	0.597	0.561	0.633	CLONAL	2	TRUE	1	0.755376333688202	4		374	618	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508682	106508682	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760803722	NA	P-0050431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	415	542	1	ENST00000359195.3:c.676C>T	p.Arg226Cys	p.R226C	ENST00000359195	NM_002649.2	226	Cgc/Tgc	2/11	0.755376333688202	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.755376333688202	2		543	518	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376665	8376665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753080783	NA	P-0050431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	150	501	0	ENST00000356435.5:c.4448C>T	p.Thr1483Met	p.T1483M	ENST00000356435		1483	aCg/aTg	27/35	0.755376333688202	4	FACETS	0.789	0.721	0.86	0.263	0.24	0.287	SUBCLONAL	1	TRUE	1	0.755376333688202	4		501	884	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137522066	137522066	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	103	329	0	ENST00000367739.4:c.813G>C	p.Lys271Asn	p.K271N	ENST00000367739	NM_000416.2	271	aaG/aaC	6/7	0.755376333688202	1	FACETS	0.998	0.924	1	0.998	0.924	1	CLONAL	1	TRUE	0	0.755376333688202	1		329	170	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293846	1293847	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0050431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	155	717	2	ENST00000310581.5:c.1154_1155delinsAA	p.Arg385Gln	p.R385Q	ENST00000310581	NM_198253.2	385	cGC/cAA	2/16	0.755376333688202	4	FACETS	0.755	0.691	0.822	0.252	0.23	0.274	SUBCLONAL	1	TRUE	1	0.755376333688202	4		719	954	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137522061	137522062	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0050431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	88	334	0	ENST00000367739.4:c.817dup	p.Ile273AsnfsTer2	p.I273Nfs*2	ENST00000367739	NM_000416.2	273	att/aAtt	6/7	0.755376333688202	1	FACETS	0.824	0.75	0.897	0.824	0.75	0.897	CLONAL	1	TRUE	0	0.755376333688202	1		334	176	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395188	139395200	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTGGTAGATGA	CCCTGGTAGATGA	-	novel	NA	P-0050431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	201	648	0	ENST00000277541.6:c.5738_5750del	p.Phe1913SerfsTer64	p.F1913Sfs*64	ENST00000277541	NM_017617.3	1913	tTCATCTACCAGGGc/tc	31/34	0.755376333688202	3	FACETS	0.96	0.892	1	0.48	0.446	0.515	CLONAL	1	TRUE	1	0.755376333688202	3		648	764	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121913370	NA	P-0050432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	52	231	0	ENST00000288602.6:c.1742A>G	p.Asn581Ser	p.N581S	ENST00000288602	NM_004333.4	581	aAt/aGt	15/18	0.277996178863266	3	FACETS	0.966	0.824	1	0.483	0.412	0.561	CLONAL	1	TRUE	1	0.283978193942136	3		231	433	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136162	11136162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	202	485	0	ENST00000358026.2:c.3146C>T	p.Pro1049Leu	p.P1049L	ENST00000358026	NM_001128849.1	1049	cCc/cTc	22/36	0.283978193942136	2	FACETS	0.941	0.875	1	0.941	0.875	1	CLONAL	2	TRUE	0	0.283978193942136	2		485	756	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	271	505	0	ENST00000326873.7:c.667G>T	p.Glu223Ter	p.E223*	ENST00000326873	NM_000455.4	223	Gag/Tag	5/10	0.283978193942136	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.283978193942136	2		505	899	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067836	30067836	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315499	NA	P-0050432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	158	387	1	ENST00000338641.4:c.1021C>T	p.Arg341Ter	p.R341*	ENST00000338641	NM_000268.3	341	Cga/Tga	11/16	0.283978193942136	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	0	0.283978193942136	2		388	544	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252856	36252856	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	147	326	1	ENST00000300305.3:c.506G>C	p.Arg169Thr	p.R169T	ENST00000300305		169	aGa/aCa	4/8	0.283978193942136	2	FACETS	0.964	0.885	1	0.964	0.885	1	CLONAL	2	TRUE	0	0.283978193942136	2		327	537	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254840	16254840	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	95	544	0	ENST00000375759.3:c.2105G>C	p.Arg702Pro	p.R702P	ENST00000375759	NM_015001.2	702	cGa/cCa	11/15	1	2	FACETS	0.904	0.805	1	0.904	0.805	1	CLONAL	1	TRUE	1	0.283978193942136	2		544	740	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18747227	18747436	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTCACACAAAAGTTTAGTTTAACTTAATGGTAAGATGATAGCACTGACTTAATTAACCTTTCTAATATACTTTCTCTCTATTTGTAGAATCTATAACAGGTATCTATTTTAAAATGATATATATGGCAATTTTATGTAATAATGAATAGCAGTAACAAATATAAGAAATAAAGAAATATTATGTTTCATTTTGTTTTTCAGAGTGATTGT	GTCACACAAAAGTTTAGTTTAACTTAATGGTAAGATGATAGCACTGACTTAATTAACCTTTCTAATATACTTTCTCTCTATTTGTAGAATCTATAACAGGTATCTATTTTAAAATGATATATATGGCAATTTTATGTAATAATGAATAGCAGTAACAAATATAAGAAATAAAGAAATATTATGTTTCATTTTGTTTTTCAGAGTGATTGT	-	novel	NA	P-0050432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	54	24	0	ENST00000266497.5:c.3889-199_3899del		p.X1297_splice	ENST00000266497		1297		28/31	1	2	FACETS	0.916	0.827	1	1	0.986	1	CLONAL	5	TRUE	1	0.283978193942136	2		24	83	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663428	67663428	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	56	265	0	ENST00000264010.4:c.1829C>G	p.Ser610Cys	p.S610C	ENST00000264010	NM_006565.3	610	tCt/tGt	10/12	1	2	FACETS	0.888	0.763	1	0.888	0.763	1	CLONAL	1	TRUE	1	0.283978193942136	2		265	444	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2199889	2199889	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	259	494	0	ENST00000398665.3:c.658del	p.Arg220GlufsTer21	p.R220Efs*21	ENST00000398665	NM_032482.2	220	Aga/ga	8/28	0.283978193942136	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.283978193942136	2		494	845	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266791	198266791	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	116	370	0	ENST00000335508.6:c.2141A>G	p.Glu714Gly	p.E714G	ENST00000335508	NM_012433.2	714	gAa/gGa	15/25	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.283978193942136	2		370	685	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0050433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	35	510	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.482512703955936	3	FACETS	0.234	0.191	0.283	0.078	0.063	0.095	SUBCLONAL	1	TRUE	0	0.562605476659287	3		510	681	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100175	27100176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0050433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	79	455	0	ENST00000324856.7:c.3977dup	p.Gln1327AlafsTer11	p.Q1327Afs*11	ENST00000324856	NM_006015.4	1324	tac/taCc	16/20	1	2	FACETS	0.814	0.721	0.912	0.814	0.721	0.912	CLONAL	1	TRUE	1	0.562605476659287	2		455	345	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578541	7578541	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	205	694	0	ENST00000269305.4:c.389T>G	p.Leu130Arg	p.L130R	ENST00000269305	NM_001126112.2	130	cTc/cGc	5/11	0.559617995838674	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.562605476659287	1		694	461	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061215	38061235	+	inframe_deletion	In_Frame_Del	DEL	GCAGCCGTTCTCGAACATGTT	GCAGCCGTTCTCGAACATGTT	-	novel	NA	P-0050434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	87	402	0	ENST00000250448.2:c.754_774del	p.Asn252_Cys258del	p.N252_C258del	ENST00000250448	NM_004496.3	252	AACATGTTCGAGAACGGCTGC/-	2/2	1	2	FACETS	0.845	0.75	0.947	0.845	0.75	0.947	CLONAL	1	TRUE	1	0.350674602463473	2		402	587	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38148105	38148105	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	195	502	0	ENST00000317025.8:c.3006C>A	p.Phe1002Leu	p.F1002L	ENST00000317025	NM_023034.1	1002	ttC/ttA	17/24	0.234590991751703	3	FACETS	0.934	0.867	1	0.934	0.867	1	CLONAL	2	TRUE	1	0.350674602463473	3		502	700	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	206	468	0				ENST00000310581	NM_198253.2	-/1132			0.737684149565896	6	FACETS	1	0.963	1	0.524	0.489	0.561	CLONAL	2	TRUE	2	0.737684149565896	6		468	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0050435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	314	482	0	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	0.737684149565896	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.737684149565896	2		482	403	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0050435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	427	303	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	0.70262284303441	5	FACETS	0.966	0.934	0.998	0.966	0.934	0.998	CLONAL	4	TRUE	1	0.737684149565896	5		303	631	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0050435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	341	581	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	NA	2	FACETS	0.979	0.945	1			1	INDETERMINATE	2	TRUE	NA	0.737684149565896	2		581	472	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864656	37864656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs950730453	NA	P-0050435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	379	575	1	ENST00000269571.5:c.308G>A	p.Arg103Gln	p.R103Q	ENST00000269571		103	cGa/cAa	3/27	0.520993216591871	4	FACETS	1	0.973	1			1	CLONAL	2	TRUE	NA	0.737684149565896	4		576	869	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781386	135781386	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203549	NA	P-0050435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	331	533	1	ENST00000298552.3:c.1579C>T	p.Gln527Ter	p.Q527*	ENST00000298552	NM_001162426.1	527	Cag/Tag	15/23	0.737684149565896	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.737684149565896	2		534	423	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031919	26031919	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1270004025	NA	P-0050435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	109	333	0	ENST00000244661.2:c.370G>C	p.Asp124His	p.D124H	ENST00000244661	NM_003537.3	124	Gac/Cac	1/1	0.457826718196404	4	FACETS	1	0.91	1	0.504	0.455	0.557	CLONAL	1	TRUE	2	0.737684149565896	4		333	509	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871992	45871992	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	228	534	0	ENST00000391945.4:c.256G>C	p.Glu86Gln	p.E86Q	ENST00000391945	NM_000400.3	86	Gag/Cag	5/23	0.351253460399095	4	FACETS	1	0.977	1	1	0.977	1	INDETERMINATE	2	TRUE	2	0.737684149565896	4		534	501	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545177	41545177	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	304	470	0	ENST00000263253.7:c.2377C>T	p.Gln793Ter	p.Q793*	ENST00000263253	NM_001429.3	793	Caa/Taa	13/31	0.722315644677225	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.737684149565896	2		470	398	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446415	49446415	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	348	560	0	ENST00000301067.7:c.1190del	p.Lys397ArgfsTer5	p.K397Rfs*5	ENST00000301067	NM_003482.3	397	aAg/ag	9/54	0.671259695804236	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.737684149565896	4		560	762	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018160	48018160	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	366	566	0	ENST00000234420.5:c.355T>C	p.Phe119Leu	p.F119L	ENST00000234420	NM_000179.2	119	Ttc/Ctc	2/10	0.737684149565896	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.737684149565896	4		566	835	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309691	30309691	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	98	576	0	ENST00000307677.4:c.331C>G	p.Gln111Glu	p.Q111E	ENST00000307677	NM_138578.1	111	Cag/Gag	2/3	0.671259695804236	4	FACETS	0.566	0.505	0.632	0.283	0.252	0.316	SUBCLONAL	1	TRUE	2	0.737684149565896	4		576	815	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458209	12458209	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	215	432	0	ENST00000287820.6:c.826G>C	p.Val276Leu	p.V276L	ENST00000287820	NM_015869.4	276	Gtt/Ctt	6/7	0.535713089928032	6	FACETS	0.961	0.896	1			1	CLONAL	2	TRUE	NA	0.737684149565896	6		432	751	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598157	55598157	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	43	316	0	ENST00000288135.5:c.2354C>A	p.Ser785Tyr	p.S785Y	ENST00000288135	NM_000222.2	785	tCc/tAc	16/21	0.32098558370636	3	FACETS	0.437	0.367	0.515	0.146	0.122	0.172	INDETERMINATE	1	TRUE	0	0.737684149565896	3		316	365	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911478	131911478	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658433	NA	P-0050435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	240	342	0	ENST00000265335.6:c.223G>A	p.Glu75Lys	p.E75K	ENST00000265335		75	Gaa/Aaa	3/25	0.737684149565896	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.737684149565896	2		342	302	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911567	131911567	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	264	423	0	ENST00000265335.6:c.312G>C	p.Gln104His	p.Q104H	ENST00000265335		104	caG/caC	3/25	0.737684149565896	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.737684149565896	2		423	344	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324070	31324089	+	frameshift_variant	Frame_Shift_Del	DEL	GAGCCGCCGTGTCCGCGGCG	GAGCCGCCGTGTCCGCGGCG	-	novel	NA	P-0050435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	239	439	0	ENST00000412585.2:c.474_493del	p.Ala159AspfsTer11	p.A159Dfs*11	ENST00000412585	NM_005514.6	158	acCGCCGCGGACACGGCGGCTCag/acag	3/8	0.457826718196404	4	FACETS	0.856	0.804	0.909	0.856	0.804	0.909	CLONAL	2	TRUE	2	0.737684149565896	4		439	658	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813067	76813067	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	156	590	0	ENST00000373344.5:c.6554T>C	p.Leu2185Pro	p.L2185P	ENST00000373344	NM_000489.3	2185	cTg/cCg	30/35	0.737684149565896	3	FACETS	1	0.948	1	0.519	0.477	0.561	CLONAL	1	TRUE	1	0.737684149565896	3		590	558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882005	NA	P-0050438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	22	610	0	ENST00000269305.4:c.713G>C	p.Cys238Ser	p.C238S	ENST00000269305	NM_001126112.2	238	tGt/tCt	7/11	1	2	FACETS	0.551	0.425	0.698	0.551	0.425	0.698	SUBCLONAL	1	TRUE	1	0.13	2		610	614	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	67	705	0	ENST00000267101.3:c.273G>A	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atA	3/28	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.13	2		705	741	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787845	135787845	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1564490210	NA	P-0050438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	19	397	0	ENST00000298552.3:c.738-1G>A		p.X246_splice	ENST00000298552	NM_001162426.1	246			1	2	FACETS	0.814	0.617	1	0.814	0.617	1	CLONAL	1	TRUE	1	0.13	2		397	359	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295176	1295176	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1475402448	NA	P-0050438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	19	302	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.937	0.711	1	0.937	0.711	1	CLONAL	1	TRUE	1	0.13	2		302	312	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324010	31324010	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs41558016	NA	P-0050438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	34	570	0	ENST00000412585.2:c.553G>T	p.Glu185Ter	p.E185*	ENST00000412585	NM_005514.6	185	Gag/Tag	3/8	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.13	2		570	498	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324096	31324096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs281864626	NA	P-0050438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	24	471	0	ENST00000412585.2:c.467C>T	p.Ser156Phe	p.S156F	ENST00000412585	NM_005514.6	156	tCc/tTc	3/8	1	2	FACETS	0.907	0.71	1	0.907	0.71	1	CLONAL	1	TRUE	1	0.13	2		471	407	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0050441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	203	532	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.0841318626411217	5	FACETS	0.936	0.876	0.997	1	0.988	1	INDETERMINATE	4	FALSE	2	0.307690424344946	5		532	515	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522624	176522624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	159	627	0	ENST00000292408.4:c.1721C>T	p.Pro574Leu	p.P574L	ENST00000292408	NM_213647.1	574	cCc/cTc	13/18	0.290788392461806	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.328469058692713	3		627	455	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061102	38061103	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0050445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	66	339	0	ENST00000250448.2:c.886dup	p.Asp296GlyfsTer7	p.D296Gfs*7	ENST00000250448	NM_004496.3	296	gac/gGac	2/2	0.26117826858062	3	FACETS	1	0.956	1	0.408	0.356	0.464	CLONAL	1	TRUE	0	0.328469058692713	3		339	382	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43785234	43785234	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0050445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	119	536	0	ENST00000382044.4:c.7+1G>C		p.X3_splice	ENST00000382044	NM_001141980.1	3			1	2	FACETS	1	0.972	1	1	0.991	1	CLONAL	2	TRUE	1	0.328469058692713	2		536	315	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0050446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	101	240	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.201526516000424	4	FACETS	0.94	0.85	1	0.94	0.85	1	CLONAL	4	TRUE	0	0.205613409359467	4		240	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0050446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	75	662	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.862	0.754	0.979	0.862	0.754	0.979	CLONAL	1	TRUE	1	0.205613409359467	2		662	846	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0050446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	84	657	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.961	0.848	1	0.961	0.848	1	CLONAL	1	TRUE	1	0.205613409359467	2		657	850	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254787	16254787	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	55	483	1	ENST00000375759.3:c.2052G>T	p.Arg684Ser	p.R684S	ENST00000375759	NM_015001.2	684	agG/agT	11/15	0.156954188530037	3	FACETS	0.855	0.73	0.992	0.428	0.365	0.496	CLONAL	1	TRUE	1	0.205613409359467	3		484	690	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577106	+	inframe_insertion	In_Frame_Ins	INS	-	-	GACAGGCACAAACAC	novel	NA	P-0050446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	55	530	0	ENST00000269305.4:c.818_832dup	p.Arg273_Cys277dup	p.R273_C277dup	ENST00000269305	NM_001126112.2	273	cct/cGTGTTTGTGCCTGTCct	8/11	1	2	FACETS	0.548	0.467	0.637	0.548	0.467	0.637	SUBCLONAL	1	TRUE	1	0.205613409359467	2		530	976	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28934873	NA	P-0050447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	365	484	0	ENST00000269305.4:c.398T>C	p.Met133Thr	p.M133T	ENST00000269305	NM_001126112.2	133	aTg/aCg	5/11	0.546362440497735	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.546362440497735	1		484	756	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007182	62007182	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147194821	NA	P-0050447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	161	502	0	ENST00000392795.3:c.500C>T	p.Thr167Met	p.T167M	ENST00000392795	NM_001039933.1	167	aCg/aTg	4/6	0.546362440497735	1	FACETS	0.671	0.618	0.727	0.671	0.618	0.727	SUBCLONAL	1	TRUE	0	0.546362440497735	1		502	638	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395913	395913	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	186	359	0	ENST00000380956.4:c.470C>A	p.Pro157His	p.P157H	ENST00000380956	NM_001195286.1	157	cCt/cAt	4/9	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.546362440497735	2		359	563	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405157	70405157	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	177	414	0	ENST00000373644.4:c.2671G>A	p.Val891Met	p.V891M	ENST00000373644	NM_030625.2	891	Gtg/Atg	4/12	0.546362440497735	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.546362440497735	1		414	413	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446395	49446395	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs777479385	NA	P-0050447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	197	454	0	ENST00000301067.7:c.1210A>G	p.Met404Val	p.M404V	ENST00000301067	NM_003482.3	404	Atg/Gtg	9/54	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.546362440497735	2		454	679	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941738	48941738	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	67	189	0	ENST00000267163.4:c.1048A>T	p.Ser350Cys	p.S350C	ENST00000267163	NM_000321.2	350	Agt/Tgt	10/27	0.546362440497735	1	FACETS	0.964	0.854	1	0.964	0.854	1	CLONAL	1	TRUE	0	0.546362440497735	1		189	185	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129086	2130108	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCGTGGCCCAGGCTGACGATAGCCTGAAAAACCTCCACCTGGAGCTCACGGAAACCTGTCTGGACATGATGGCTCGATACGTCTTCTCCAACTTCACGGCTGTCCCGAAGAGGTCCAGGCGGCACTACAGGGCTGGGCGGGCCTGCGGGAGCTCCACGGGCAAGCTGGGTTTCACGCTCCCTGTCTTCTAGGTCTCCTGTGGGCGAGTTCCTCCTAGCGGGTGGCAGGACCAAAACCTGGCTGGTTGGGAACAAGCTTGTCACTGTGACGACAAGCGTGGGAACCGGGACCCGGTCGTTACTAGGCCTGGACTCGGGGGAGCTGCAGTCCGGCCCGGAGTCGAGGTGACTGCACCTTCCTTTCCTCCGCGCCTGCCAGCCTCGACACCGGCTGTCCCGAGCCCAGGCCCACGTGGCACCCTCGTACCAGCCTGGGGACTAAGTCCACCCTGTGCGTGGGATTCTCTTCTCAGCTCCAGCCCCGGGGTGCATGTGAGACAGACCAAGGAGGCGCCGGCCAAGCTGGAGTCCCAGGCTGGGCAGCAGGTGTCCCGTGGGGCCCGGGATCGGGTCCGTTCCATGTCGGGTGAGCCTTGGCCCCAGCCACCTCCACACAGGCACCGGGGCTCCCTCAGTTGCTGCTGGTCCCAGTGTTCAGGAAGGCCCCGAGCCCAGGGGCCGGGGTGGCTGGCTTCAGGCCCGGCCCACGTCCTGACTCTGGGGTGAGCCTTCCACAGCTCACCCCAGAGCCGTGGAGTGGTGGAGTGTGGCCCGCTTGCTGCAGAGGGGCCTGCTCTGGGTGCTGGTGTTTCCTGCGGGTTTTCAGCTCGGCTCAGTCCTGGAGCCCTTCTCTGCTCCAGCGAGCCGTGGTCTGACTGCAGGACAGGTTCTGGGTCCCTCCCTGTGGCCCTGGGTTCACTGAGGCCAGCACTGTGGTGGGCCGTGCCCCAAGGGCAGAGCTGCCACCGTCTCTGGCTGCCTGTGGCACTAGCTTGCCAGGCTCGGGGGGAGCATTCAGCTTGAG	CCGTGGCCCAGGCTGACGATAGCCTGAAAAACCTCCACCTGGAGCTCACGGAAACCTGTCTGGACATGATGGCTCGATACGTCTTCTCCAACTTCACGGCTGTCCCGAAGAGGTCCAGGCGGCACTACAGGGCTGGGCGGGCCTGCGGGAGCTCCACGGGCAAGCTGGGTTTCACGCTCCCTGTCTTCTAGGTCTCCTGTGGGCGAGTTCCTCCTAGCGGGTGGCAGGACCAAAACCTGGCTGGTTGGGAACAAGCTTGTCACTGTGACGACAAGCGTGGGAACCGGGACCCGGTCGTTACTAGGCCTGGACTCGGGGGAGCTGCAGTCCGGCCCGGAGTCGAGGTGACTGCACCTTCCTTTCCTCCGCGCCTGCCAGCCTCGACACCGGCTGTCCCGAGCCCAGGCCCACGTGGCACCCTCGTACCAGCCTGGGGACTAAGTCCACCCTGTGCGTGGGATTCTCTTCTCAGCTCCAGCCCCGGGGTGCATGTGAGACAGACCAAGGAGGCGCCGGCCAAGCTGGAGTCCCAGGCTGGGCAGCAGGTGTCCCGTGGGGCCCGGGATCGGGTCCGTTCCATGTCGGGTGAGCCTTGGCCCCAGCCACCTCCACACAGGCACCGGGGCTCCCTCAGTTGCTGCTGGTCCCAGTGTTCAGGAAGGCCCCGAGCCCAGGGGCCGGGGTGGCTGGCTTCAGGCCCGGCCCACGTCCTGACTCTGGGGTGAGCCTTCCACAGCTCACCCCAGAGCCGTGGAGTGGTGGAGTGTGGCCCGCTTGCTGCAGAGGGGCCTGCTCTGGGTGCTGGTGTTTCCTGCGGGTTTTCAGCTCGGCTCAGTCCTGGAGCCCTTCTCTGCTCCAGCGAGCCGTGGTCTGACTGCAGGACAGGTTCTGGGTCCCTCCCTGTGGCCCTGGGTTCACTGAGGCCAGCACTGTGGTGGGCCGTGCCCCAAGGGCAGAGCTGCCACCGTCTCTGGCTGCCTGTGGCACTAGCTTGCCAGGCTCGGGGGGAGCATTCAGCTTGAG	-	novel	NA	P-0050447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	174	477	1	ENST00000219476.3:c.3020_3398-58del		p.X1007_splice	ENST00000219476	NM_000548.3	1007		27-29/42	0.546362440497735	1	FACETS	0.897	0.832	0.964	0.897	0.832	0.964	CLONAL	1	TRUE	0	0.546362440497735	1		478	516	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113833	11113833	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	184	464	0	ENST00000358026.2:c.1943+1del		p.P647fs	ENST00000358026	NM_001128849.1	647	ccG/cc	12/36	0.546362440497735	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.546362440497735	1		464	483	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52725439	52725439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	198	456	0	ENST00000322088.6:c.1606G>A	p.Val536Ile	p.V536I	ENST00000322088	NM_014225.5	536	Gtc/Atc	13/15	0.546362440497735	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.546362440497735	1		456	508	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99154420	99154420	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	166	399	1	ENST00000074304.5:c.562G>A	p.Asp188Asn	p.D188N	ENST00000074304	NM_001134224.1	188	Gac/Aac	8/26	1	2	FACETS	0.932	0.859	1	0.932	0.859	1	CLONAL	1	TRUE	1	0.546362440497735	2		400	652	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129733	47129733	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	117	244	0	ENST00000409792.3:c.5147A>G	p.Asp1716Gly	p.D1716G	ENST00000409792	NM_014159.6	1716	gAt/gGt	10/21	0.546362440497735	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.546362440497735	1		244	284	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31947204	31947204	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	228	401	0	ENST00000375333.2:c.689G>T	p.Cys230Phe	p.C230F	ENST00000375333	NM_032454.1	230	tGt/tTt	5/8	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.546362440497735	2		401	630	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468113	50468113	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	162	403	0	ENST00000331340.3:c.1348C>A	p.Arg450Ser	p.R450S	ENST00000331340	NM_006060.4	450	Cgc/Agc	8/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.546362440497735	2		403	548	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371752	116371753	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0050447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	178	295	0	ENST00000397752.3:c.1235_1236del	p.Arg412ProfsTer2	p.R412Pfs*2	ENST00000397752	NM_000245.2	411	GCg/g	3/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.546362440497735	2		295	535	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410433	63410433	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	192	513	0	ENST00000330258.3:c.2734G>T	p.Val912Phe	p.V912F	ENST00000330258	NM_152424.3	912	Gtc/Ttc	2/2	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.546362440497735	2		513	661	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	88	468	0				ENST00000310581	NM_198253.2	-/1132			0.135194152833314	4	FACETS	0.775	0.688	0.868	0.775	0.688	0.868	INDETERMINATE	2	TRUE	2	0.258887437926145	4		468	552	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0050448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	78	316	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	0.208185143149143	3	FACETS	1	0.975	1	0.481	0.424	0.542	CLONAL	1	TRUE	0	0.258887437926145	3		316	472	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793008	33793010	+	inframe_deletion	In_Frame_Del	DEL	CGC	CGC	-	rs780345232	NA	P-0050448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	12	101	0	ENST00000498907.2:c.311_313del	p.Gly104del	p.G104del	ENST00000498907	NM_004364.3	104	gGCGac/gac	1/1	0.135194152833314	4	FACETS	0.753	0.531	1	0.376	0.265	0.512	INDETERMINATE	1	TRUE	2	0.258887437926145	4		101	155	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160646	56160646	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343464548	NA	P-0050448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	93	338	0	ENST00000399503.3:c.920G>A	p.Arg307His	p.R307H	ENST00000399503	NM_005921.1	307	cGt/cAt	4/20	0.135194152833314	4	FACETS	0.816	0.728	0.91	0.816	0.728	0.91	INDETERMINATE	2	TRUE	2	0.258887437926145	4		338	554	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115277060	115277061	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	novel	NA	P-0050448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	114	419	0	ENST00000438362.2:c.720+2dup		p.X240_splice	ENST00000438362	NM_001242891.1	240			0.258887437926145	4	FACETS	0.906	0.822	0.993	0.906	0.822	0.993	CLONAL	3	TRUE	1	0.258887437926145	4		419	408	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098943	178098975	+	inframe_deletion	In_Frame_Del	DEL	TCGACTTACTCCAAGATCTATATCTTGCCTCCA	TCGACTTACTCCAAGATCTATATCTTGCCTCCA	-	novel	NA	P-0050448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	66	294	0	ENST00000397062.3:c.70_102del	p.Trp24_Arg34del	p.W24_R34del	ENST00000397062	NM_006164.4	24	TGGAGGCAAGATATAGATCTTGGAGTAAGTCGA/-	2/5	0.258887437926145	3	FACETS	0.802	0.7	0.911	0.802	0.7	0.911	CLONAL	2	TRUE	1	0.258887437926145	3		294	359	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	22	413	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.932	0.726	1	0.932	0.726	1	CLONAL	1	FALSE	1	0.245979597099254	2		413	192	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0050449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	36	582	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.245979597099254	1	FACETS	0.586	0.482	0.703	0.586	0.482	0.703	SUBCLONAL	1	FALSE	0	0.245979597099254	1		582	438	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426708	47426708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777175765	NA	P-0050449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	26	639	2	ENST00000377045.4:c.953C>T	p.Thr318Met	p.T318M	ENST00000377045	NM_001654.4	318	aCg/aTg	10/16	1	2	FACETS	0.45	0.355	0.558	0.45	0.355	0.558	SUBCLONAL	1	FALSE	1	0.245979597099254	2		641	470	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043381	180043381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760077499	NA	P-0050449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	22	514	2	ENST00000261937.6:c.3205G>A	p.Val1069Ile	p.V1069I	ENST00000261937	NM_182925.4	1069	Gtc/Atc	23/30	1	2	FACETS	0.501	0.388	0.633	0.501	0.388	0.633	SUBCLONAL	1	FALSE	1	0.245979597099254	2		516	357	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433354	138433354	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1007545037	NA	P-0050449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	10	444	1	ENST00000289153.2:c.1258A>G	p.Ile420Val	p.I420V	ENST00000289153	NM_006219.2	420	Att/Gtt	7/22	1	2	FACETS	0.511	0.347	0.717	0.511	0.347	0.717	SUBCLONAL	1	FALSE	1	0.245979597099254	2		445	159	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971040	21971041	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	31	467	0	ENST00000304494.5:c.317dup	p.Arg107AlafsTer13	p.R107Afs*13	ENST00000304494	NM_000077.4	106	gtg/gtTg	2/3	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	FALSE	1	0.245979597099254	2		467	210	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663821	29663823	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	novel	NA	P-0050450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	69	483	0	ENST00000356175.3:c.6256_6258del	p.Val2086del	p.V2086del	ENST00000356175	NM_000267.3	2085	GTT/-	41/57	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.255229095145142	2		483	533	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	32	468	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.731	0.593	0.887	0.731	0.593	0.887	SUBCLONAL	1	TRUE	1	0.19	2		468	461	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0050451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	32	534	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.776	0.63	0.942	0.776	0.63	0.942	CLONAL	1	TRUE	1	0.19	2		534	434	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0050451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	42	382	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.19	2		382	408	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051596	30051596	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	50	342	0	ENST00000338641.4:c.530A>G	p.Tyr177Cys	p.Y177C	ENST00000338641	NM_000268.3	177	tAt/tGt	6/16	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.19	2		342	500	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922884	44922884	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	34	223	0	ENST00000377967.4:c.1745del	p.Ser582Ter	p.S582*	ENST00000377967	NM_021140.2	582	tCa/ta	16/29	1	1	FACETS	0.936	0.766	1	0.936	0.766	1	CLONAL	1	TRUE	0	0.19	1		223	346	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861153	57861153	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	159	462	0	ENST00000228682.2:c.950A>T	p.Asn317Ile	p.N317I	ENST00000228682	NM_005269.2	317	aAc/aTc	9/12	1	2	FACETS	0.808	0.742	0.877	0.808	0.742	0.877	CLONAL	1	TRUE	1	0.518287316381166	2		462	759	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0050452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	401	596	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.505860793098084	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.518287316381166	2		596	722	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684326	29684328	+	frameshift_variant	Frame_Shift_Del	DEL	CGA	CGA	GT	novel	NA	P-0050452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	106	413	1	ENST00000356175.3:c.7846_7848delinsGT	p.Arg2616ValfsTer7	p.R2616Vfs*7	ENST00000356175	NM_000267.3	2616	CGA/GT	53/57	0.518287316381166	1	FACETS	0.773	0.699	0.851	0.773	0.699	0.851	SUBCLONAL	1	TRUE	0	0.518287316381166	1		414	392	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481781	40481781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781724933	NA	P-0050452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	114	316	0	ENST00000264657.5:c.1123G>A	p.Val375Ile	p.V375I	ENST00000264657	NM_139276.2	375	Gtt/Att	12/24	0.518287316381166	1	FACETS	0.791	0.718	0.867	0.791	0.718	0.867	SUBCLONAL	1	TRUE	0	0.518287316381166	1		316	412	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141463	11141463	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	190	526	0	ENST00000358026.2:c.3440C>G	p.Ser1147Cys	p.S1147C	ENST00000358026	NM_001128849.1	1147	tCt/tGt	25/36	0.518287316381166	2	FACETS	0.918	0.85	0.988	0.459	0.425	0.494	CLONAL	1	TRUE	0	0.518287316381166	2		526	799	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152077	11152077	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	181	457	0	ENST00000358026.2:c.4361C>G	p.Ser1454Cys	p.S1454C	ENST00000358026	NM_001128849.1	1454	tCc/tGc	31/36	0.518287316381166	2	FACETS	0.953	0.881	1	0.476	0.44	0.514	CLONAL	1	TRUE	0	0.518287316381166	2		457	733	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187384	38187384	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	159	361	0	ENST00000317025.8:c.1093C>T	p.Arg365Cys	p.R365C	ENST00000317025	NM_023034.1	365	Cgt/Tgt	6/24	0.417407444038551	3	FACETS	1	0.97	1	0.557	0.511	0.604	CLONAL	1	TRUE	1	0.518287316381166	3		361	694	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737428	145737428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768802673	NA	P-0050452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	178	552	1	ENST00000428558.2:c.3259C>T	p.Pro1087Ser	p.P1087S	ENST00000428558	NM_004260.3	1087	Ccc/Tcc	20/22	0.518287316381166	4	FACETS	0.886	0.815	0.96	0.443	0.407	0.48	CLONAL	1	TRUE	2	0.518287316381166	4		553	1177	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044988	47044988	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	217	554	0	ENST00000377604.3:c.2314G>C	p.Glu772Gln	p.E772Q	ENST00000377604	NM_001204468.1	772	Gag/Cag	20/24	1	2	FACETS	0.944	0.879	1	0.944	0.879	1	CLONAL	1	TRUE	1	0.518287316381166	2		554	887	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926888	112926888	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397507546	NA	P-0050454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	99	476	0	ENST00000351677.2:c.1508G>C	p.Gly503Ala	p.G503A	ENST00000351677	NM_002834.3	503	gGg/gCg	13/16	0.780572852428315	4	FACETS	1	0.954	1			1	CLONAL	1	TRUE	NA	0.922790010370706	4		476	373	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268177	153268177	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	192	268	0	ENST00000281708.4:c.631G>T	p.Asp211Tyr	p.D211Y	ENST00000281708	NM_033632.3	211	Gac/Tac	4/12	0.922790010370706	2	FACETS	1	0.977	1	0.542	0.509	0.575	CLONAL	1	TRUE	0	0.922790010370706	2		268	384	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115284234	115284234	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	219	467	0	ENST00000438362.2:c.52C>A	p.Pro18Thr	p.P18T	ENST00000438362	NM_001242891.1	18	Cct/Act	2/20	0.825194438161353	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.922790010370706	1		467	243	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281980	49281980	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	422	547	1	ENST00000282018.3:c.1027G>T	p.Glu343Ter	p.E343*	ENST00000282018	NM_020377.2	343	Gaa/Taa	1/1	0.922790010370706	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.922790010370706	2		548	444	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129011	30129011	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	38	558	0	ENST00000263025.4:c.755A>G	p.Asp252Gly	p.D252G	ENST00000263025	NM_002746.2	252	gAt/gGt	5/9	0.327932230708657	4	FACETS	0.297	0.245	0.355	0.149	0.122	0.178	INDETERMINATE	1	TRUE	2	0.922790010370706	4		558	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578452	7578452	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	417	587	0	ENST00000269305.4:c.478del	p.Met160TrpfsTer10	p.M160Wfs*10	ENST00000269305	NM_001126112.2	160	Atg/tg	5/11	0.922790010370706	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.922790010370706	1		587	460	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795270	42795270	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	203	549	0	ENST00000575354.2:c.2350G>T	p.Gly784Trp	p.G784W	ENST00000575354	NM_015125.3	784	Ggg/Tgg	10/20	0.921540658960101	4	FACETS	0.865	0.81	0.92			1	CLONAL	2	TRUE	NA	0.922790010370706	4		549	489	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430960	181430960	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	173	612	0	ENST00000325404.1:c.812G>C	p.Arg271Pro	p.R271P	ENST00000325404	NM_003106.3	271	cGg/cCg	1/1	0.802249183528531	3	FACETS	0.801	0.75	0.852	0.801	0.75	0.852	CLONAL	2	TRUE	1	0.922790010370706	3		612	342	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184086	56184086	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	19	410	0	ENST00000399503.3:c.4291G>A	p.Asp1431Asn	p.D1431N	ENST00000399503	NM_005921.1	1431	Gat/Aat	19/20	0.922790010370706	3	FACETS	0.174	0.131	0.224	0.087	0.065	0.112	SUBCLONAL	1	TRUE	1	0.922790010370706	3		410	346	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752612	128752650	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGGAGTGATTTCTATTTCCTTTCTTAAAGAGGAGGAAC	AAGGAGTGATTTCTATTTCCTTTCTTAAAGAGGAGGAAC	-	novel	NA	P-0050454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	56	165	0	ENST00000377970.2:c.803-27_814del		p.X268_splice	ENST00000377970	NM_002467.4	268		3/3	0.922790010370706	5	FACETS	1	0.905	1			1	CLONAL	1	TRUE	NA	0.922790010370706	5		165	273	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344193	70344193	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	181	351	0	ENST00000374080.3:c.1929C>A	p.Asp643Glu	p.D643E	ENST00000374080		643	gaC/gaA	13/45	0.922790010370706	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.922790010370706	1		351	190	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	700	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.821798053445181	8	FACETS	0.997	0.986	1	0.997	0.986	1	CLONAL	8	TRUE	0	0.821798053445181	8		327	740	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0050455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	608	393	2	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.821798053445181	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.821798053445181	3		395	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0050455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	619	625	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.821798053445181	3	FACETS	0.981	0.963	0.999	0.981	0.963	0.999	CLONAL	3	TRUE	0	0.821798053445181	3		625	722	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141534	11141534	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	432	556	0	ENST00000358026.2:c.3511G>A	p.Val1171Met	p.V1171M	ENST00000358026	NM_001128849.1	1171	Gtg/Atg	25/36	0.808551384553671	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.821798053445181	2		556	523	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038822	47038822	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	282	659	0	ENST00000377604.3:c.829C>T	p.Gln277Ter	p.Q277*	ENST00000377604	NM_001204468.1	277	Cag/Tag	9/24	0.821798053445181	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.821798053445181	1		659	371	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514445	103514445	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	73	285	0	ENST00000355739.4:c.946G>T	p.Gly316Cys	p.G316C	ENST00000355739	NM_000123.3	316	Ggc/Tgc	8/15	0.821798053445181	1	FACETS	0.879	0.803	0.954	0.879	0.803	0.954	CLONAL	1	TRUE	0	0.821798053445181	1		285	119	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999315	100999315	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs772284923	NA	P-0050455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	471	725	0	ENST00000325455.5:c.487C>A	p.Pro163Thr	p.P163T	ENST00000325455	NM_001202474.3	163	Ccg/Acg	1/8	0.744537607381386	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.821798053445181	3		725	806	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858573	57858573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776244778	NA	P-0050455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	695	597	1	ENST00000228682.2:c.311G>A	p.Ser104Asn	p.S104N	ENST00000228682	NM_005269.2	104	aGc/aAc	4/12	0.821798053445181	6	FACETS	0.875	0.845	0.906			1	CLONAL	3	TRUE	NA	0.821798053445181	6		598	1703	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118382	17118382	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	427	547	0	ENST00000285071.4:c.1455G>C	p.Lys485Asn	p.K485N	ENST00000285071	NM_144997.5	485	aaG/aaC	13/14	0.821798053445181	3	FACETS	0.987	0.949	1	0.658	0.633	0.683	CLONAL	2	TRUE	0	0.821798053445181	3		547	743	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793212	33793212	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	163	122	0	ENST00000498907.2:c.109G>T	p.Ala37Ser	p.A37S	ENST00000498907	NM_004364.3	37	Gcg/Tcg	1/1	0.789828525100518	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.821798053445181	4		122	323	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458245	12458245	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	317	483	0	ENST00000287820.6:c.862G>T	p.Asp288Tyr	p.D288Y	ENST00000287820	NM_015869.4	288	Gat/Tat	6/7	0.374556560753902	6	FACETS	0.951	0.904	0.998	0.951	0.904	0.998	INDETERMINATE	3	TRUE	3	0.821798053445181	6		483	715	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205840	128205840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1263269900	NA	P-0050455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	148	448	1	ENST00000341105.2:c.35C>T	p.Ala12Val	p.A12V	ENST00000341105	NM_032638.4	12	gCg/gTg	2/6	0.821798053445181	3	FACETS	0.86	0.789	0.934	0.43	0.394	0.467	CLONAL	1	TRUE	1	0.821798053445181	3		449	591	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519261	187519261	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	320	439	0	ENST00000441802.2:c.12122G>T	p.Ser4041Ile	p.S4041I	ENST00000441802	NM_005245.3	4041	aGt/aTt	23/27	0.780017724389361	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.821798053445181	3		439	525	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020787	26020787	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	183	320	0	ENST00000357647.3:c.70A>G	p.Lys24Glu	p.K24E	ENST00000357647	NM_003529.2	24	Aag/Gag	1/1	0.821798053445181	5	FACETS	0.836	0.775	0.897	0.557	0.517	0.598	CLONAL	2	TRUE	2	0.821798053445181	5		320	595	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169230	32169230	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	447	603	0	ENST00000375023.3:c.3803G>T	p.Cys1268Phe	p.C1268F	ENST00000375023	NM_004557.3	1268	tGt/tTt	22/30	0.821798053445181	3	FACETS	0.984	0.947	1	0.984	0.947	1	CLONAL	2	TRUE	1	0.821798053445181	3		603	780	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969162	93969162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	109	377	0	ENST00000369303.4:c.1834G>A	p.Glu612Lys	p.E612K	ENST00000369303	NM_004440.3	612	Gaa/Aaa	10/17	1	2	FACETS	0.887	0.808	0.968	0.887	0.808	0.968	CLONAL	1	TRUE	1	0.821798053445181	2		377	299	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729865	41729865	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	172	482	0	ENST00000242208.4:c.664C>A	p.Pro222Thr	p.P222T	ENST00000242208	NM_002192.2	222	Cct/Act	3/3	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.821798053445181	2		482	407	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	48	468	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.203778384492095	2		468	439	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023491	27023492	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0050456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	66	438	0	ENST00000324856.7:c.598dup	p.Gln200ProfsTer200	p.Q200Pfs*200	ENST00000324856	NM_006015.4	199	-/C	1/20	1	2	FACETS	0.971	0.843	1	0.971	0.843	1	CLONAL	1	TRUE	1	0.203778384492095	2		438	667	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579507	7580166	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	TGGACCTGGGTCTTCAGTGAACCATTGTTCAATATCGTCCGGGGACAGCATCAAATCATCCATTGCTTGGGACGGCAAGGGGGACTGTAGATGGGTGAAAAGAGCAGTCAGAGGACCAGGTCCTCAGCCCCCCAGCCCCCCAGCCCTCCAGGTCCCCAGCCCTCCAGGTCCCCAGCCCAACCCTTGTCCTTACCAGAACGTTGTTTTCAGGAAGTCTGAAAGACAAGAGCAGAAAGTCAGTCCCATGGAATTTTCGCTTCCCACAGGTCTCTGCTAGGGGGCTGGGGTTGGGGTGGGGGTGGTGGGCCTGCCCTTCCAATGGATCCACTCACAGTTTCCATAGGTCTGAAAATGTTTCCTGACTCAGAGGGGGCTCGACGCTAGGATCTGACTGCGGCTCCTCCATGGCAGTGACCCGGAAGGCAGTCTGGCTGCTGCAAGAGGAAAAGTGGGGATCCAGCATGAGACACTTCCAACCCTGGGTCACCTGGGCCTGCAGAGAAGGAACCCCCTCCCCCAACACCATGCCAGTGTCTGAGACAGCTCGGCTTCCTGTGGAGCAGGAAAAGAATGGCTGCTTCACATTCTCTCTTCCAATGTTTCACCACAACCCAAGCACTCCTGCCCCACCCCTCACCAGCCATGCACTTCTTTGAGGAA	TGGACCTGGGTCTTCAGTGAACCATTGTTCAATATCGTCCGGGGACAGCATCAAATCATCCATTGCTTGGGACGGCAAGGGGGACTGTAGATGGGTGAAAAGAGCAGTCAGAGGACCAGGTCCTCAGCCCCCCAGCCCCCCAGCCCTCCAGGTCCCCAGCCCTCCAGGTCCCCAGCCCAACCCTTGTCCTTACCAGAACGTTGTTTTCAGGAAGTCTGAAAGACAAGAGCAGAAAGTCAGTCCCATGGAATTTTCGCTTCCCACAGGTCTCTGCTAGGGGGCTGGGGTTGGGGTGGGGGTGGTGGGCCTGCCCTTCCAATGGATCCACTCACAGTTTCCATAGGTCTGAAAATGTTTCCTGACTCAGAGGGGGCTCGACGCTAGGATCTGACTGCGGCTCCTCCATGGCAGTGACCCGGAAGGCAGTCTGGCTGCTGCAAGAGGAAAAGTGGGGATCCAGCATGAGACACTTCCAACCCTGGGTCACCTGGGCCTGCAGAGAAGGAACCCCCTCCCCCAACACCATGCCAGTGTCTGAGACAGCTCGGCTTCCTGTGGAGCAGGAAAAGAATGGCTGCTTCACATTCTCTCTTCCAATGTTTCACCACAACCCAAGCACTCCTGCCCCACCCCTCACCAGCCATGCACTTCTTTGAGGAA	-	novel	NA	P-0050456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	60	597	0	ENST00000269305.4:c.-28-226_180del		p.X10_splice	ENST00000269305	NM_001126112.2	10		2-4/11	1	2	FACETS	0.752	0.647	0.867	0.752	0.647	0.867	SUBCLONAL	1	TRUE	1	0.203778384492095	2		597	783	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519927	NA	P-0050456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	70	300	0	ENST00000263967.3:c.1625A>C	p.Glu542Ala	p.E542A	ENST00000263967	NM_006218.2	542	gAa/gCa	10/21	1	2	FACETS	0.753	0.659	0.855	1	0.974	1	SUBCLONAL	2	TRUE	1	0.203778384492095	2		300	456	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106923	27106940	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCCTGGCAGCTCGTGC	CAGCCTGGCAGCTCGTGC	G	novel	NA	P-0050456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	61	492	0	ENST00000324856.7:c.6534_6551delinsG	p.Asp2178GlufsTer41	p.D2178Efs*41	ENST00000324856	NM_006015.4	2178	gaCAGCCTGGCAGCTCGTGCc/gaGc	20/20	1	2	FACETS	0.904	0.78	1	0.904	0.78	1	CLONAL	1	TRUE	1	0.203778384492095	2		492	662	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593602	55593606	+	protein_altering_variant	In_Frame_Del	DEL	GTGGA	GTGGA	AC	novel	NA	P-0050457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	187	329	0	ENST00000288135.5:c.1668_1672delinsAC	p.Trp557_Lys558delinsGln	p.W557_K558delinsQ	ENST00000288135	NM_000222.2	556	caGTGGAag/caACag	11/21	1	2	FACETS	0.847	0.788	0.908	0.847	0.788	0.908	CLONAL	1	TRUE	1	0.795469213942529	2		329	555	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930399	39930399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1433397184	NA	P-0050457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	124	230	0	ENST00000378444.4:c.3065G>A	p.Arg1022His	p.R1022H	ENST00000378444	NM_001123385.1	1022	cGc/cAc	6/15	1	2	FACETS	0.983	0.903	1	0.983	0.903	1	CLONAL	1	TRUE	1	0.795469213942529	2		230	317	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	164	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.580353888544618	4	FACETS	1	0.989	1	0.734	0.678	0.792	CLONAL	1	TRUE	2	0.661590154309655	4		327	561	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812538	43812538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772102737	NA	P-0050486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	170	666	0	ENST00000372470.3:c.1241C>T	p.Ser414Leu	p.S414L	ENST00000372470	NM_005373.2	414	tCg/tTg	8/12	0.507455178391479	3	FACETS	0.827	0.761	0.895	0.413	0.38	0.448	CLONAL	1	TRUE	1	0.661590154309655	3		666	827	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276477	115276477	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	73	513	0	ENST00000438362.2:c.851G>A	p.Gly284Asp	p.G284D	ENST00000438362	NM_001242891.1	284	gGt/gAt	9/20	0.507455178391479	3	FACETS	0.864	0.761	0.973	0.432	0.38	0.487	CLONAL	1	TRUE	1	0.661590154309655	3		513	340	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145430	58145430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894340	NA	P-0050486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	220	489	1	ENST00000257904.6:c.71G>A	p.Arg24His	p.R24H	ENST00000257904	NM_000075.3	24	cGt/cAt	2/8	0.580353888544618	4	FACETS	1	0.991	1	0.72	0.672	0.77	CLONAL	1	TRUE	2	0.661590154309655	4		490	767	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562747	21562747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747638434	NA	P-0050486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	1212	706	1	ENST00000382592.4:c.1172G>A	p.Arg391His	p.R391H	ENST00000382592	NM_014572.2	391	cGc/cAc	4/8	0.661590154309655	8	FACETS	1	0.995	1	0.887	0.868	0.907	CLONAL	5	TRUE	2	0.661590154309655	8		707	2054	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577600	7577601	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0050486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	228	539	0	ENST00000269305.4:c.680_681del	p.Ser227Ter	p.S227*	ENST00000269305	NM_001126112.2	227	tCT/t	7/11	0.500213949488749	2	FACETS	1	0.992	1	0.695	0.655	0.735	CLONAL	1	TRUE	0	0.661590154309655	2		539	496	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118858	70118858	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0050486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	150	572	0	ENST00000245479.2:c.432-2A>T		p.X144_splice	ENST00000245479	NM_000346.3	144			0.538597614131593	3	FACETS	0.994	0.912	1	0.497	0.456	0.54	CLONAL	1	TRUE	1	0.661590154309655	3		572	607	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	27	270	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	0.507455178391479	3	FACETS	0.829	0.67	1	0.415	0.335	0.503	CLONAL	1	TRUE	1	0.661590154309655	3		270	131	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876218	35876218	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	101	521	0	ENST00000303115.3:c.1010A>C	p.Lys337Thr	p.K337T	ENST00000303115	NM_002185.3	337	aAg/aCg	8/8	0.44337634519545	4	FACETS	0.851	0.762	0.945	0.426	0.381	0.473	CLONAL	1	TRUE	2	0.661590154309655	4		521	596	SUCCESS
APC	324	MSKCC	GRCh37	5	112175328	112175328	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	207	259	1	ENST00000257430.4:c.4037C>A	p.Ser1346Ter	p.S1346*	ENST00000257430	NM_000038.5	1346	tCa/tAa	16/16	0.661590154309655	3	FACETS	0.876	0.832	0.918	0.876	0.832	0.918	CLONAL	3	TRUE	0	0.661590154309655	3		260	317	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641128	117641128	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140237260	NA	P-0050486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	121	581	0	ENST00000368508.3:c.5843G>A	p.Arg1948His	p.R1948H	ENST00000368508	NM_002944.2	1948	cGt/cAt	36/43	0.661590154309655	4	FACETS	0.763	0.689	0.84	0.254	0.229	0.28	SUBCLONAL	1	TRUE	1	0.661590154309655	4		581	797	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508647	106508647	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	244	606	0	ENST00000359195.3:c.641A>G	p.Lys214Arg	p.K214R	ENST00000359195	NM_002649.2	214	aAg/aGg	2/11	0.44337634519545	4	FACETS	0.87	0.817	0.924	0.87	0.817	0.924	CLONAL	2	TRUE	2	0.661590154309655	4		606	704	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030633	47030639	+	frameshift_variant	Frame_Shift_Del	DEL	GCCACAG	GCCACAG	-	novel	NA	P-0050486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	330	386	0	ENST00000377604.3:c.410_416del	p.Pro137GlnfsTer23	p.P137Qfs*23	ENST00000377604	NM_001204468.1	136	ctGCCACAG/ct	4/24	0.661590154309655	2	FACETS	0.98	0.941	1			1	CLONAL	2	TRUE	NA	0.661590154309655	2		386	509	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426737	47426737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200106543	NA	P-0050486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	346	399	0	ENST00000377045.4:c.982C>T	p.Arg328Trp	p.R328W	ENST00000377045	NM_001654.4	328	Cgg/Tgg	10/16	0.661590154309655	2	FACETS	1	0.964	1			1	CLONAL	2	TRUE	NA	0.661590154309655	2		399	522	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133025	30133025	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	45	500	0	ENST00000331968.5:c.576A>G	p.Ile192Met	p.I192M	ENST00000331968	NM_002742.2	192	atA/atG	4/18	1	2	FACETS	0.195	0.163	0.23	0.195	0.163	0.23	SUBCLONAL	1	TRUE	1	0.787093809338138	2		500	587	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66679695	66679695	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	44	591	0	ENST00000307102.5:c.10A>G	p.Lys4Glu	p.K4E	ENST00000307102	NM_002755.3	4	Aag/Gag	1/11	1	2	FACETS	0.182	0.152	0.215	0.182	0.152	0.215	SUBCLONAL	1	TRUE	1	0.787093809338138	2		591	615	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614904	23614904	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	59	587	0	ENST00000261584.4:c.3437del	p.Gln1146ArgfsTer17	p.Q1146Rfs*17	ENST00000261584	NM_024675.3	1146	cAg/cg	13/13	1	2	FACETS	0.273	0.234	0.314	0.273	0.234	0.314	SUBCLONAL	1	TRUE	1	0.787093809338138	2		587	550	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579349	7579349	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	261	892	0	ENST00000269305.4:c.338T>C	p.Phe113Ser	p.F113S	ENST00000269305	NM_001126112.2	113	tTc/tCc	4/11	0.64361768376995	1	FACETS	0.624	0.588	0.659	0.624	0.588	0.659	SUBCLONAL	1	TRUE	0	0.787093809338138	1		892	645	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740510	58740510	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	43	585	0	ENST00000305921.3:c.1415A>G	p.Glu472Gly	p.E472G	ENST00000305921	NM_003620.3	472	gAa/gGa	6/6	1	2	FACETS	0.205	0.171	0.243	0.205	0.171	0.243	SUBCLONAL	1	TRUE	1	0.787093809338138	2		585	533	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306679	41306679	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	69	859	0	ENST00000373198.4:c.980A>G	p.Tyr327Cys	p.Y327C	ENST00000373198	NM_133170.3	327	tAt/tGt	7/32	1	2	FACETS	0.228	0.198	0.26	0.228	0.198	0.26	SUBCLONAL	1	TRUE	1	0.787093809338138	2		859	770	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151834002	151834002	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs748426014	NA	P-0050487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	224	544	0	ENST00000262189.6:c.14651A>G	p.Tyr4884Cys	p.Y4884C	ENST00000262189	NM_170606.2	4884	tAt/tGt	59/59	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.787093809338138	2		544	543	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412440	80412440	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	34	350	0	ENST00000286548.4:c.601T>C	p.Phe201Leu	p.F201L	ENST00000286548	NM_002072.3	201	Ttc/Ctc	4/7	1	2	FACETS	0.24	0.196	0.289	0.24	0.196	0.289	SUBCLONAL	1	TRUE	1	0.787093809338138	2		350	360	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396734	139396734	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	56	990	1	ENST00000277541.6:c.5374G>T	p.Val1792Leu	p.V1792L	ENST00000277541	NM_017617.3	1792	Gtg/Ttg	28/34	1	2	FACETS	0.162	0.138	0.188	0.162	0.138	0.188	SUBCLONAL	1	TRUE	1	0.787093809338138	2		991	881	SUCCESS
APC	324	MSKCC	GRCh37	5	112174438	112174438	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs863225340	NA	P-0050488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	27	247	0	ENST00000257430.4:c.3147G>A	p.Trp1049Ter	p.W1049*	ENST00000257430	NM_000038.5	1049	tgG/tgA	16/16	0.356311421040093	3	FACETS	0.93	0.746	1	0.465	0.373	0.569	CLONAL	1	TRUE	1	0.356311421040093	3		247	192	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579355	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519997	NA	P-0050488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	580	739	0	ENST00000269305.4:c.332T>A	p.Leu111Gln	p.L111Q	ENST00000269305	NM_001126112.2	111	cTg/cAg	4/11	0.356311421040093	2	FACETS	1	0.975	1	1	0.997	1	CLONAL	3	TRUE	0	0.356311421040093	2		739	1074	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570404	87570404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	157	753	1	ENST00000277120.3:c.2144G>A	p.Arg715Gln	p.R715Q	ENST00000277120		715	cGg/cAg	17/19	0.356311421040093	3	FACETS	1	0.946	1	0.522	0.478	0.569	CLONAL	1	TRUE	1	0.356311421040093	3		754	994	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372007	55372007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1601	131	554	0	ENST00000297316.4:c.697G>A	p.Asp233Asn	p.D233N	ENST00000297316	NM_022454.3	233	Gac/Aac	2/2	0.356311421040093	8	FACETS	0.878	0.794	0.968	0.146	0.132	0.162	CLONAL	1	TRUE	2	0.356311421040093	8		554	1732	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983995	2983995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	289	658	1	ENST00000396946.4:c.535C>T	p.Arg179Trp	p.R179W	ENST00000396946	NM_032415.4	179	Cgg/Tgg	5/25	0.288856591651764	4	FACETS	0.972	0.914	1	0.972	0.914	1	CLONAL	2	TRUE	2	0.356311421040093	4		659	1132	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609958	81609958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780018604	NA	P-0050488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	71	419	0	ENST00000298171.2:c.1556G>A	p.Arg519His	p.R519H	ENST00000298171	NM_000369.2	519	cGc/cAc	10/10	0.356311421040093	3	FACETS	0.8	0.699	0.909	0.4	0.349	0.455	CLONAL	1	TRUE	1	0.356311421040093	3		419	587	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338650	70338650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	286	640	1	ENST00000374080.3:c.46C>T	p.Arg16Trp	p.R16W	ENST00000374080		16	Cgg/Tgg	1/45	0.226475311692766	4	FACETS	0.967	0.909	1	0.967	0.909	1	CLONAL	2	TRUE	2	0.356311421040093	4		641	1126	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178129262	178129262	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	239	378	0	ENST00000397062.3:c.43C>G	p.Gln15Glu	p.Q15E	ENST00000397062	NM_006164.4	15	Cag/Gag	1/5	0.356311421040093	3	FACETS	0.999	0.936	1	0.999	0.936	1	CLONAL	2	TRUE	1	0.356311421040093	3		378	791	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434174	12434174	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	67	460	0	ENST00000287820.6:c.542G>C	p.Arg181Pro	p.R181P	ENST00000287820	NM_015869.4	181	cGg/cCg	4/7	0.356311421040093	3	FACETS	1	0.905	1	0.522	0.456	0.594	CLONAL	1	TRUE	1	0.356311421040093	3		460	424	SUCCESS
APC	324	MSKCC	GRCh37	5	112174770	112174771	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	76	250	0	ENST00000257430.4:c.3482dup	p.Asn1161LysfsTer3	p.N1161Kfs*3	ENST00000257430	NM_000038.5	1160	aca/acAa	16/16	0.356311421040093	3	FACETS	0.967	0.859	1	0.967	0.859	1	CLONAL	2	TRUE	1	0.356311421040093	3		250	260	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	120	468	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.343060741063749	2		468	591	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0050490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	77	528	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	0.48	0.42	0.545	0.48	0.42	0.545	SUBCLONAL	1	TRUE	1	0.343060741063749	2		528	935	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0050490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	115	950	2	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.588	0.528	0.652	0.588	0.528	0.652	SUBCLONAL	1	TRUE	1	0.343060741063749	2		952	1140	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651995	36651995	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	67	1105	0	ENST00000244741.5:c.119del	p.Gly40AlafsTer108	p.G40Afs*108	ENST00000244741	NM_000389.4	39	gcG/gc	2/3	1	2	FACETS	0.306	0.265	0.351	0.306	0.265	0.351	SUBCLONAL	1	TRUE	1	0.343060741063749	2		1105	1276	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983121	201983122	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0050490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	204	853	0	ENST00000359651.3:c.971dup	p.Met324IlefsTer147	p.M324Ifs*147	ENST00000359651		324	atg/aTtg	7/8	0.102431621161338	4	FACETS	0.778	0.721	0.837	0.778	0.721	0.837	INDETERMINATE	2	TRUE	2	0.343060741063749	4		853	1027	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349778	15349778	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199833114	NA	P-0050490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1383	89	1193	2	ENST00000263377.2:c.3796G>A	p.Glu1266Lys	p.E1266K	ENST00000263377	NM_058243.2	1266	Gag/Aag	19/20	0.343060741063749	3	FACETS	0.413	0.364	0.465	0.206	0.182	0.233	SUBCLONAL	1	TRUE	1	0.343060741063749	3		1195	1472	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788617	3788617	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	67	586	0	ENST00000262367.5:c.4337del	p.Arg1446ProfsTer13	p.R1446Pfs*13	ENST00000262367	NM_004380.2	1446	cGc/cc	26/31	1	2	FACETS	0.557	0.484	0.637	0.557	0.484	0.637	SUBCLONAL	1	TRUE	1	0.343060741063749	2		586	701	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512384	38512384	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774473938	NA	P-0050490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	37	622	0	ENST00000254066.5:c.1295G>A	p.Arg432Gln	p.R432Q	ENST00000254066	NM_000964.3	432	cGg/cAg	9/9	1	2	FACETS	0.293	0.241	0.353	0.293	0.241	0.353	SUBCLONAL	1	TRUE	1	0.343060741063749	2		622	735	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982983	201982986	+	frameshift_variant	Frame_Shift_Del	DEL	TTCA	TTCA	-	novel	NA	P-0050490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	221	1082	0	ENST00000359651.3:c.833_836del	p.Phe278SerfsTer15	p.F278Sfs*15	ENST00000359651		278	TTCAtc/tc	7/8	0.102431621161338	4	FACETS	1	0.99	1	0.713	0.663	0.766	INDETERMINATE	1	TRUE	2	0.343060741063749	4		1082	1213	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983017	201983018	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CG	novel	NA	P-0050490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	234	1108	0	ENST00000359651.3:c.867_868dup	p.Glu290AlafsTer5	p.E290Afs*5	ENST00000359651		289	aac/aaCGc	7/8	0.102431621161338	4	FACETS	1	0.992	1	0.743	0.692	0.796	INDETERMINATE	1	TRUE	2	0.343060741063749	4		1108	1233	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447788	49447788	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0050490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	75	760	2	ENST00000301067.7:c.646G>T	p.Glu216Ter	p.E216*	ENST00000301067	NM_003482.3	216	Gag/Tag	5/54	1	2	FACETS	0.529	0.462	0.6	0.529	0.462	0.6	SUBCLONAL	1	TRUE	1	0.343060741063749	2		762	827	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246344	41246344	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	186	687	0	ENST00000357654.3:c.1204G>A	p.Glu402Lys	p.E402K	ENST00000357654	NM_007294.3	402	Gag/Aag	10/23	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.343060741063749	2		687	861	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11027128	11027128	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199572188	NA	P-0050490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3553	259	1152	2	ENST00000327064.4:c.893C>T	p.Thr298Met	p.T298M	ENST00000327064	NM_199141.1	298	aCg/aTg	7/16	0.343060741063749	14	FACETS	1	0.986	1	0.093	0.086	0.1	CLONAL	1	TRUE	1	0.343060741063749	14		1154	3812	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349745	15349745	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1379	101	1222	0	ENST00000263377.2:c.3829G>C	p.Glu1277Gln	p.E1277Q	ENST00000263377	NM_058243.2	1277	Gag/Cag	19/20	0.343060741063749	3	FACETS	0.466	0.415	0.521	0.233	0.207	0.261	SUBCLONAL	1	TRUE	1	0.343060741063749	3		1222	1480	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350501	15350501	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1263	83	1124	0	ENST00000263377.2:c.3414G>C	p.Glu1138Asp	p.E1138D	ENST00000263377	NM_058243.2	1138	gaG/gaC	16/20	0.343060741063749	3	FACETS	0.421	0.37	0.476	0.211	0.185	0.238	SUBCLONAL	1	TRUE	1	0.343060741063749	3		1124	1346	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982503	25982503	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	45	320	0	ENST00000435504.4:c.787A>G	p.Arg263Gly	p.R263G	ENST00000435504		263	Aga/Gga	9/13	1	2	FACETS	0.664	0.559	0.78	0.664	0.559	0.78	SUBCLONAL	1	TRUE	1	0.343060741063749	2		320	395	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436407	52436407	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	107	999	1	ENST00000460680.1:c.2087T>A	p.Ile696Asn	p.I696N	ENST00000460680	NM_004656.3	696	aTc/aAc	17/17	NA	2	FACETS	0.55	0.491	0.612			1	INDETERMINATE	1	TRUE	NA	0.343060741063749	2		1000	1135	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798466	32798466	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	72	955	3	ENST00000374899.4:c.1390C>A	p.Leu464Met	p.L464M	ENST00000374899	NM_018833.2	464	Ctg/Atg	8/12	1	2	FACETS	0.369	0.321	0.422	0.369	0.321	0.422	SUBCLONAL	1	TRUE	1	0.343060741063749	2		958	1136	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137320984	137320984	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	417	1152	0	ENST00000481739.1:c.941C>G	p.Ser314Cys	p.S314C	ENST00000481739	NM_002957.4	314	tCc/tGc	7/10	0.343060741063749	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.343060741063749	2		1152	1213	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0050491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	578	662	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.691985601582402	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	FALSE	0	0.691985601582402	1		662	797	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0050491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	127	382	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.175151490760309	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.691985601582402	0		382	385	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982096	93982096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1484017296	NA	P-0050491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	217	545	2	ENST00000369303.4:c.1369C>T	p.Arg457Trp	p.R457W	ENST00000369303	NM_004440.3	457	Cgg/Tgg	6/17	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	1	0.691985601582402	2		547	617	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966768	44966768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	127	295	0	ENST00000377967.4:c.3992G>A	p.Cys1331Tyr	p.C1331Y	ENST00000377967	NM_021140.2	1331	tGt/tAt	27/29	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	0	0.691985601582402	1		295	190	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612188	189612188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774550896	NA	P-0050491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	243	591	1	ENST00000264731.3:c.1940G>A	p.Arg647His	p.R647H	ENST00000264731	NM_003722.4	647	cGc/cAc	14/14	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	FALSE	1	0.691985601582402	2		592	700	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456430	29456430	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0050491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	180	607	0	ENST00000389048.3:c.2487+1G>T		p.X829_splice	ENST00000389048	NM_004304.4	829			0.183682651465146	2	FACETS	0.767	0.71	0.826	0.384	0.355	0.413	INDETERMINATE	1	FALSE	0	0.691985601582402	2		607	678	SUCCESS
APC	324	MSKCC	GRCh37	5	112175884	112175885	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0050491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	89	284	0	ENST00000257430.4:c.4593_4594insTG	p.Asp1532TrpfsTer34	p.D1532Wfs*34	ENST00000257430	NM_000038.5	1531	-/TG	16/16	0.691985601582402	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	0	0.691985601582402	1		284	147	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	22	468	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.973	0.756	1	0.973	0.756	1	CLONAL	1	TRUE	1	0.17	2		468	266	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0050492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	46	390	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.903	0.76	1	0.903	0.76	1	CLONAL	1	TRUE	1	0.17	2		392	599	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0050492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	71	583	2	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.174048445820379	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.17	1		585	634	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970901	21970901	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs45476696	NA	P-0050492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	61	708	0	ENST00000304494.5:c.457G>A	p.Asp153Asn	p.D153N	ENST00000304494	NM_000077.4	153	Gac/Aac	2/3	1	2	FACETS	0.946	0.814	1	0.946	0.814	1	CLONAL	1	TRUE	1	0.17	2		708	759	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553478	29553478	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781807	NA	P-0050492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	81	520	2	ENST00000356175.3:c.2033del	p.Pro678ArgfsTer10	p.P678Rfs*10	ENST00000356175	NM_000267.3	676	aCc/ac	18/57	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.17	2		522	653	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42790944	42790944	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367972487	NA	P-0050492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	49	700	1	ENST00000575354.2:c.89G>A	p.Arg30His	p.R30H	ENST00000575354	NM_015125.3	30	cGc/cAc	2/20	1	2	FACETS	0.999	0.846	1	0.999	0.846	1	CLONAL	1	TRUE	1	0.17	2		701	577	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474041	29474041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs78723472	NA	P-0050492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	48	785	0	ENST00000389048.3:c.2134G>A	p.Val712Met	p.V712M	ENST00000389048	NM_004304.4	712	Gtg/Atg	12/29	1	2	FACETS	0.852	0.719	0.999	0.852	0.719	0.999	CLONAL	1	TRUE	1	0.17	2		785	663	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564697	86564698	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs766715946	NA	P-0050492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	45	702	0	ENST00000274376.6:c.434dup	p.Leu146PhefsTer12	p.L146Ffs*12	ENST00000274376	NM_002890.2	143	-/C	1/25	1	2	FACETS	0.858	0.72	1	0.858	0.72	1	CLONAL	1	TRUE	1	0.17	2		702	617	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244076	46244076	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	30	415	0	ENST00000334344.6:c.2173del	p.Gln725ArgfsTer33	p.Q725Rfs*33	ENST00000334344	NM_152641.2	724	Ccc/cc	15/21	1	2	FACETS	0.791	0.637	0.967	0.791	0.637	0.967	CLONAL	1	TRUE	1	0.17	2		415	446	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510134	120510134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	44	471	1	ENST00000256646.2:c.1375G>A	p.Glu459Lys	p.E459K	ENST00000256646	NM_024408.3	459	Gag/Aag	8/34	1	2	FACETS	0.964	0.808	1	0.964	0.808	1	CLONAL	1	TRUE	1	0.17	2		472	537	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422068	81422068	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	26	518	0	ENST00000298171.2:c.44T>C	p.Leu15Pro	p.L15P	ENST00000298171	NM_000369.2	15	cTg/cCg	1/10	1	2	FACETS	0.713	0.564	0.884	0.713	0.564	0.884	SUBCLONAL	1	TRUE	1	0.17	2		518	429	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645372	67645372	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1220590499	NA	P-0050492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	29	355	1	ENST00000264010.4:c.637C>T	p.Arg213Cys	p.R213C	ENST00000264010	NM_006565.3	213	Cgt/Tgt	3/12	1	2	FACETS	0.774	0.62	0.948	0.774	0.62	0.948	CLONAL	1	TRUE	1	0.17	2		356	441	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053545	37053545	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0050492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	42	520	0	ENST00000231790.2:c.632C>G	p.Ser211Ter	p.S211*	ENST00000231790	NM_000249.3	211	tCa/tGa	8/19	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.17	2		520	467	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524452	187524452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	45	486	0	ENST00000441802.2:c.11228G>A	p.Cys3743Tyr	p.C3743Y	ENST00000441802	NM_005245.3	3743	tGc/tAc	19/27	1	2	FACETS	0.961	0.807	1	0.961	0.807	1	CLONAL	1	TRUE	1	0.17	2		486	551	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730371	133730371	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs774952482	NA	P-0050493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	89	461	0	ENST00000318560.5:c.437A>G	p.Asn146Ser	p.N146S	ENST00000318560	NM_005157.4	146	aAt/aGt	3/11	0.516539969222248	1	FACETS	0.363	0.322	0.407	0.363	0.322	0.407	SUBCLONAL	1	TRUE	0	0.516539969222248	1		461	704	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372393	118372393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	102	328	1	ENST00000534358.1:c.6326C>T	p.Ser2109Leu	p.S2109L	ENST00000534358	NM_005933.3	2109	tCa/tTa	26/36	0.516539969222248	1	FACETS	0.594	0.534	0.658	0.594	0.534	0.658	SUBCLONAL	1	TRUE	0	0.516539969222248	1		329	493	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264098	16264098	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	358	685	0	ENST00000375759.3:c.10467C>G	p.His3489Gln	p.H3489Q	ENST00000375759	NM_015001.2	3489	caC/caG	12/15	0.516539969222248	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.516539969222248	1		685	821	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595973	43595973	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	89	724	1	ENST00000355710.3:c.140G>T	p.Gly47Val	p.G47V	ENST00000355710	NM_020975.4	47	gGc/gTc	2/20	1	2	FACETS	0.356	0.314	0.4	0.356	0.314	0.4	SUBCLONAL	1	TRUE	1	0.516539969222248	2		725	969	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646805	23646806	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	GATTTCTCTGTTTGATTTTGTTCTTTTAAGTTTTGGTTTTCATT	novel	NA	P-0050493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	140	498	0	ENST00000261584.4:c.1018_1061dup	p.Leu355MetfsTer6	p.L355Mfs*6	ENST00000261584	NM_024675.3	354	tct/tcAATGAAAACCAAAACTTAAAAGAACAAAATCAAACAGAGAAATCt	4/13	1	2	FACETS	0.534	0.485	0.585	0.534	0.485	0.585	SUBCLONAL	1	TRUE	1	0.516539969222248	2		498	1015	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162954	38162954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	101	388	0	ENST00000317025.8:c.2252C>T	p.Pro751Leu	p.P751L	ENST00000317025	NM_023034.1	751	cCa/cTa	13/24	NA	2	FACETS	0.598	0.535	0.665			1	INDETERMINATE	1	TRUE	NA	0.516539969222248	2		388	654	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0050494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	58	240	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.914	0.787	1	0.914	0.787	1	CLONAL	1	TRUE	1	0.262102114495121	2		240	484	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061192	38061192	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs879940115	NA	P-0050494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	72	497	0	ENST00000250448.2:c.797T>A	p.Phe266Tyr	p.F266Y	ENST00000250448	NM_004496.3	266	tTc/tAc	2/2	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.262102114495121	2		497	525	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063688	67063698	+	protein_altering_variant	In_Frame_Del	DEL	ACGCCTGCCGC	ACGCCTGCCGC	GA	novel	NA	P-0050494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	45	355	3	ENST00000412916.2:c.137_147delinsGA	p.Asn46_Cys48del	p.N46_C48del	ENST00000412916		46	aACGCCTGCCGC/aGA	2/6	0.262102114495121	1	FACETS	0.75	0.631	0.88	0.75	0.631	0.88	SUBCLONAL	1	TRUE	0	0.262102114495121	1		358	398	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857460	68857460	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121964874	NA	P-0050494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	76	542	0	ENST00000261769.5:c.2095C>T	p.Gln699Ter	p.Q699*	ENST00000261769	NM_004360.3	699	Cag/Tag	13/16	0.262102114495121	1	FACETS	0.964	0.847	1	0.964	0.847	1	CLONAL	1	TRUE	0	0.262102114495121	1		542	523	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs397517201	NA	P-0050494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	80	383	0	ENST00000263967.3:c.1637A>T	p.Gln546Leu	p.Q546L	ENST00000263967	NM_006218.2	546	cAg/cTg	10/21	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.262102114495121	2		383	536	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	60	468	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.886	0.77	1	1	0.977	1	CLONAL	2	TRUE	1	0.246278599052249	2		468	275	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0050495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	218	604	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.20760671425189	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	3	TRUE	0	0.246278599052249	3		604	631	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431634	6431634	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	76	356	0	ENST00000356142.4:c.187G>C	p.Asp63His	p.D63H	ENST00000356142	NM_018890.3	63	Gat/Cat	3/7	0.23495599014289	4	FACETS	1	0.906	1	1	0.906	1	CLONAL	2	TRUE	2	0.246278599052249	4		356	373	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195794	102195794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	27	429	0	ENST00000263464.3:c.554C>T	p.Ser185Leu	p.S185L	ENST00000263464	NM_001165.4	185	tCg/tTg	2/9	0.246278599052249	3	FACETS	0.504	0.4	0.623	0.252	0.2	0.312	SUBCLONAL	1	TRUE	1	0.246278599052249	3		429	489	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420670	49420670	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs797045659	NA	P-0050495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	152	644	0	ENST00000301067.7:c.15079C>T	p.Arg5027Ter	p.R5027*	ENST00000301067	NM_003482.3	5027	Cga/Tga	48/54	0.246278599052249	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	1	0.246278599052249	3		644	659	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885731	23885731	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	87	870	0	ENST00000374561.5:c.187C>T	p.Gln63Ter	p.Q63*	ENST00000374561	NM_002167.4	63	Cag/Tag	1/3	0.246278599052249	3	FACETS	0.972	0.86	1	0.486	0.43	0.547	CLONAL	1	TRUE	1	0.246278599052249	3		870	816	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830454	72830454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1386537099	NA	P-0050495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	56	307	0	ENST00000268489.5:c.6127C>T	p.Pro2043Ser	p.P2043S	ENST00000268489	NM_006885.3	2043	Ccc/Tcc	9/10	0.169136621149985	4	FACETS	1	0.914	1	1	0.914	1	CLONAL	2	TRUE	2	0.246278599052249	4		307	263	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626892	158626892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	87	483	0	ENST00000263640.3:c.778G>A	p.Glu260Lys	p.E260K	ENST00000263640	NM_001105.4	260	Gaa/Aaa	7/11	0.23495599014289	4	FACETS	0.897	0.797	1	0.897	0.797	1	CLONAL	2	TRUE	2	0.246278599052249	4		483	491	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259651	11259651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	127	554	0	ENST00000361445.4:c.4054G>A	p.Glu1352Lys	p.E1352K	ENST00000361445	NM_004958.3	1352	Gaa/Aaa	27/58	0.246278599052249	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	1	0.246278599052249	3		554	546	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944947	31944947	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	76	408	0	ENST00000340398.3:c.154C>G	p.Arg52Gly	p.R52G	ENST00000340398	NM_001013699.2	52	Cgt/Ggt	1/1	0.246278599052249	3	FACETS	0.86	0.758	0.968	0.86	0.758	0.968	CLONAL	2	TRUE	1	0.246278599052249	3		408	403	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81902822	81902822	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	85	467	0	ENST00000359376.3:c.483C>G	p.Ile161Met	p.I161M	ENST00000359376	NM_002661.3	161	atC/atG	6/33	0.169136621149985	4	FACETS	0.838	0.743	0.94	0.838	0.743	0.94	CLONAL	2	TRUE	2	0.246278599052249	4		467	513	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641537	47641537	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0050495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	33	346	0	ENST00000233146.2:c.922A>T	p.Arg308Ter	p.R308*	ENST00000233146	NM_000251.2	308	Aga/Tga	5/16	0.23495599014289	4	FACETS	0.817	0.665	0.987	0.408	0.332	0.494	CLONAL	1	TRUE	2	0.246278599052249	4		346	409	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162062	22162062	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	44	504	0	ENST00000215832.6:c.193T>C	p.Cys65Arg	p.C65R	ENST00000215832	NM_002745.4	65	Tgc/Cgc	2/9	NA	2	FACETS	0.748	0.627	0.881			1	INDETERMINATE	1	TRUE	NA	0.246278599052249	2		504	478	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902311	151902311	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0050495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	32	165	0	ENST00000262189.6:c.3842-1G>A		p.X1281_splice	ENST00000262189	NM_170606.2	1281			0.184872720266713	5	FACETS	0.927	0.759	1	0.618	0.506	0.742	CLONAL	2	TRUE	2	0.246278599052249	5		165	192	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0050496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	178	443	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.711558781310509	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	FALSE	2	0.711558781310509	4		443	410	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0050498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	94	240	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.59	2		240	318	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	90	468	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.829	0.741	0.921	0.829	0.741	0.921	CLONAL	1	TRUE	1	0.59	2		468	368	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0050498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	128	364	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.109996740496304	3	FACETS	1	0.984	1	0.674	0.616	0.734	INDETERMINATE	1	TRUE	1	0.59	3		364	417	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	532731	532731	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	247	783	0	ENST00000451590.1:c.475T>G	p.Leu159Val	p.L159V	ENST00000451590	NM_001130442.1	159	Ttg/Gtg	5/5	1	2	FACETS	0.978	0.917	1	0.978	0.917	1	CLONAL	1	TRUE	1	0.59	2		783	856	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808953	3808953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	187	470	0	ENST00000262367.5:c.3271C>T	p.Arg1091Cys	p.R1091C	ENST00000262367	NM_004380.2	1091	Cgc/Tgc	17/31	1	2	FACETS	0.992	0.921	1	0.992	0.921	1	CLONAL	1	TRUE	1	0.59	2		470	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0050499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	273	658	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	0.342918550549837	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	3	TRUE	0	0.440678240618491	3		658	500	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8252045	8252045	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs770912955	NA	P-0050499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	273	686	0	ENST00000335790.3:c.32C>G	p.Pro11Arg	p.P11R	ENST00000335790	NM_002315.2	11	cCg/cGg	2/4	0.342918550549837	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.440678240618491	3		686	463	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	139	468	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.918	0.842	0.997	0.918	0.842	0.997	CLONAL	1	TRUE	1	0.64	2		468	473	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	147	394	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.855	0.785	0.928	0.855	0.785	0.928	CLONAL	1	TRUE	1	0.64	2		394	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	69	361	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	0.226	0.196	0.259	0.226	0.196	0.259	SUBCLONAL	1	TRUE	1	0.64	2		361	954	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	230	668	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	1	2	FACETS	0.924	0.864	0.985	0.924	0.864	0.985	CLONAL	1	TRUE	1	0.64	2		668	778	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	186	303	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	0.975	0.906	1	0.975	0.906	1	CLONAL	1	TRUE	1	0.64	2		303	596	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870231	44870231	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	244	275	0	ENST00000377967.4:c.410G>T	p.Gly137Val	p.G137V	ENST00000377967	NM_021140.2	137	gGt/gTt	5/29	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.64	1		275	399	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030637	47030637	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	398	496	0	ENST00000377604.3:c.412C>T	p.Gln138Ter	p.Q138*	ENST00000377604	NM_001204468.1	138	Cag/Tag	4/24	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.64	1		496	618	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728500	190728500	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs139932286	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	153	387	1	ENST00000441310.2:c.1888C>T	p.Arg630Ter	p.R630*	ENST00000441310	NM_000534.4	630	Cga/Tga	10/13	1	2	FACETS	0.839	0.771	0.909	0.839	0.771	0.909	CLONAL	1	TRUE	1	0.64	2		388	570	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061887	38061887	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	324	941	0	ENST00000250448.2:c.102G>A	p.Met34Ile	p.M34I	ENST00000250448	NM_004496.3	34	atG/atA	2/2	1	2	FACETS	0.902	0.853	0.953	0.902	0.853	0.953	CLONAL	1	TRUE	1	0.64	2		941	1122	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308081	30308081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762615251	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	264	701	0	ENST00000262643.3:c.218C>T	p.Ser73Phe	p.S73F	ENST00000262643	NM_001238.2	73	tCc/tTc	5/12	1	2	FACETS	0.994	0.935	1	0.994	0.935	1	CLONAL	1	TRUE	1	0.64	2		701	830	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346352	73346352	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	178	429	0	ENST00000377767.4:c.1448G>T	p.Cys483Phe	p.C483F	ENST00000377767	NM_014953.3	483	tGt/tTt	10/21	1	2	FACETS	0.941	0.872	1	0.941	0.872	1	CLONAL	1	TRUE	1	0.64	2		429	591	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243948	41243948	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs56214134	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	85	675	0	ENST00000357654.3:c.3600G>C	p.Gln1200His	p.Q1200H	ENST00000357654	NM_007294.3	1200	caG/caC	10/23	1	2	FACETS	0.299	0.264	0.337	0.299	0.264	0.337	SUBCLONAL	1	TRUE	1	0.64	2		675	888	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143370	30143370	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	273	893	0	ENST00000389048.3:c.156G>C	p.Lys52Asn	p.K52N	ENST00000389048	NM_004304.4	52	aaG/aaC	1/29	1	2	FACETS	0.854	0.802	0.907	0.854	0.802	0.907	CLONAL	1	TRUE	1	0.64	2		893	999	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197104	106197104	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1315434367	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	197	481	1	ENST00000380013.4:c.5437C>T	p.Gln1813Ter	p.Q1813*	ENST00000380013	NM_001127208.2	1813	Caa/Taa	11/11	1	2	FACETS	0.949	0.883	1	0.949	0.883	1	CLONAL	1	TRUE	1	0.64	2		482	649	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405847	70405847	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs368453444	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	251	540	0	ENST00000373644.4:c.3361G>T	p.Gly1121Cys	p.G1121C	ENST00000373644	NM_030625.2	1121	Ggc/Tgc	4/12	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.64	2		540	746	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710993	114710993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	199	530	1	ENST00000543371.1:c.217G>A	p.Glu73Lys	p.E73K	ENST00000543371	NM_001198531.1	73	Gaa/Aaa	2/14	1	2	FACETS	0.923	0.858	0.989	0.923	0.858	0.989	CLONAL	1	TRUE	1	0.64	2		531	674	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375404	118375404	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	177	422	0	ENST00000534358.1:c.8797G>C	p.Asp2933His	p.D2933H	ENST00000534358	NM_005933.3	2933	Gat/Cat	27/36	1	2	FACETS	0.954	0.884	1	0.954	0.884	1	CLONAL	1	TRUE	1	0.64	2		422	580	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415915	49415915	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	216	571	0	ENST00000301067.7:c.16432G>A	p.Ala5478Thr	p.A5478T	ENST00000301067	NM_003482.3	5478	Gcc/Acc	53/54	1	2	FACETS	0.978	0.914	1	0.978	0.914	1	CLONAL	1	TRUE	1	0.64	2		571	690	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432554	49432554	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	326	943	0	ENST00000301067.7:c.8585C>G	p.Pro2862Arg	p.P2862R	ENST00000301067	NM_003482.3	2862	cCa/cGa	34/54	1	2	FACETS	0.952	0.9	1	0.952	0.9	1	CLONAL	1	TRUE	1	0.64	2		943	1070	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95578573	95578573	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	143	371	0	ENST00000393063.1:c.2052G>A	p.Met684Ile	p.M684I	ENST00000393063	NM_030621.3	684	atG/atA	14/28	1	2	FACETS	0.848	0.777	0.921	0.848	0.777	0.921	CLONAL	1	TRUE	1	0.64	2		371	527	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007755	45007755	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs767825635	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	207	501	0	ENST00000558401.1:c.202A>G	p.Lys68Glu	p.K68E	ENST00000558401	NM_004048.2	68	Aaa/Gaa	2/4	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.64	2		501	617	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639575	3639575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	345	1105	0	ENST00000294008.3:c.4064C>T	p.Ser1355Phe	p.S1355F	ENST00000294008	NM_032444.2	1355	tCt/tTt	12/15	1	2	FACETS	0.954	0.904	1	0.954	0.904	1	CLONAL	1	TRUE	1	0.64	2		1105	1130	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639621	3639621	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	397	1088	0	ENST00000294008.3:c.4018C>A	p.His1340Asn	p.H1340N	ENST00000294008	NM_032444.2	1340	Cac/Aac	12/15	1	2	FACETS	0.972	0.924	1	0.972	0.924	1	CLONAL	1	TRUE	1	0.64	2		1088	1277	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37876071	37876109	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCCGAGCAGAGAGCCAGGTTGGCCTGGACCCCAGGATGT	GCCGAGCAGAGAGCCAGGTTGGCCTGGACCCCAGGATGT	-	novel	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	180	864	0	ENST00000269571.5:c.1930_1946+22del		p.X644_splice	ENST00000269571		644		16/27	1	2	FACETS	0.653	0.602	0.705	0.653	0.602	0.705	SUBCLONAL	1	TRUE	1	0.64	2		864	862	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244082	41244082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793302	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	63	619	0	ENST00000357654.3:c.3466G>A	p.Asp1156Asn	p.D1156N	ENST00000357654	NM_007294.3	1156	Gat/Aat	10/23	1	2	FACETS	0.234	0.201	0.269	0.234	0.201	0.269	SUBCLONAL	1	TRUE	1	0.64	2		619	843	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244294	41244294	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	76	709	0	ENST00000357654.3:c.3254G>C	p.Arg1085Thr	p.R1085T	ENST00000357654	NM_007294.3	1085	aGa/aCa	10/23	1	2	FACETS	0.25	0.218	0.284	0.25	0.218	0.284	SUBCLONAL	1	TRUE	1	0.64	2		709	951	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244436	41244436	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	62	616	0	ENST00000357654.3:c.3112G>C	p.Glu1038Gln	p.E1038Q	ENST00000357654	NM_007294.3	1038	Gaa/Caa	10/23	1	2	FACETS	0.251	0.216	0.289	0.251	0.216	0.289	SUBCLONAL	1	TRUE	1	0.64	2		616	772	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272278	18272278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	12	40	0	ENST00000222254.8:c.788C>T	p.Ser263Leu	p.S263L	ENST00000222254	NM_005027.3	263	tCg/tTg	6/16	1	2	FACETS	0.708	0.511	0.933	0.708	0.511	0.933	CLONAL	1	TRUE	1	0.64	2		40	53	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	326	953	0	ENST00000391945.4:c.713A>C	p.Asn238Thr	p.N238T	ENST00000391945	NM_000400.3	238	aAc/aCc	8/23	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.64	2		953	988	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738314	190738314	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	162	418	0	ENST00000441310.2:c.2566G>A	p.Ala856Thr	p.A856T	ENST00000441310	NM_000534.4	856	Gct/Act	12/13	1	2	FACETS	0.893	0.824	0.964	0.893	0.824	0.964	CLONAL	1	TRUE	1	0.64	2		418	567	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660564	227660564	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	316	904	2	ENST00000305123.5:c.2891G>A	p.Arg964Lys	p.R964K	ENST00000305123	NM_005544.2	964	aGa/aAa	1/2	1	2	FACETS	0.961	0.908	1	0.961	0.908	1	CLONAL	1	TRUE	1	0.64	2		906	1028	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940747	49940747	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	256	940	0	ENST00000296474.3:c.296C>G	p.Pro99Arg	p.P99R	ENST00000296474	NM_002447.2	99	cCt/cGt	1/20	1	2	FACETS	0.827	0.775	0.881	0.827	0.775	0.881	CLONAL	1	TRUE	1	0.64	2		940	967	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440366	52440366	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	295	831	0	ENST00000460680.1:c.686A>T	p.Asn229Ile	p.N229I	ENST00000460680	NM_004656.3	229	aAc/aTc	9/17	1	2	FACETS	0.964	0.909	1	0.964	0.909	1	CLONAL	1	TRUE	1	0.64	2		831	956	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751931	57751931	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	61	606	0	ENST00000274289.3:c.1306G>C	p.Glu436Gln	p.E436Q	ENST00000274289	NM_006622.3	436	Gaa/Caa	10/14	1	2	FACETS	0.214	0.184	0.248	0.214	0.184	0.248	SUBCLONAL	1	TRUE	1	0.64	2		606	889	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522624	67522624	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	183	485	0	ENST00000274335.5:c.121G>T	p.Gly41Ter	p.G41*	ENST00000274335		41	Gga/Tga	1/15	1	2	FACETS	0.945	0.877	1	0.945	0.877	1	CLONAL	1	TRUE	1	0.64	2		485	605	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884860	151884860	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	235	532	0	ENST00000262189.6:c.4733del	p.Pro1578HisfsTer87	p.P1578Hfs*87	ENST00000262189	NM_170606.2	1578	cCa/ca	32/59	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.64	2		532	733	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942704	44942704	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	197	239	0	ENST00000377967.4:c.3285-1G>C		p.X1095_splice	ENST00000377967	NM_021140.2	1095			1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.64	1		239	323	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223338	53223338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	308	393	2	ENST00000375401.3:c.4021G>A	p.Gly1341Ser	p.G1341S	ENST00000375401	NM_004187.3	1341	Ggc/Agc	23/26	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.64	1		395	480	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	110	468	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.963	0.878	1	0.963	0.878	1	CLONAL	1	TRUE	1	0.774586463680376	2		468	295	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624301	89624301	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	19	664	0	ENST00000371953.3:c.75G>C	p.Leu25Phe	p.L25F	ENST00000371953	NM_000314.4	25	ttG/ttC	1/9	0.774586463680376	1	FACETS	0.095	0.071	0.122	0.095	0.071	0.122	SUBCLONAL	1	TRUE	0	0.774586463680376	1		664	318	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436103	51436104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	179	509	0	ENST00000262662.1:c.64dup	p.Thr22AsnfsTer2	p.T22Nfs*2	ENST00000262662		21	-/A	3/4	0.774586463680376	1	FACETS	0.976	0.922	1	0.976	0.922	1	CLONAL	1	TRUE	0	0.774586463680376	1		509	290	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551658	150551658	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	305	653	0	ENST00000369026.2:c.349G>C	p.Asp117His	p.D117H	ENST00000369026	NM_021960.4	117	Gac/Cac	1/3	0.774586463680376	1	FACETS	0.937	0.896	0.977	0.937	0.896	0.977	CLONAL	1	TRUE	0	0.774586463680376	1		653	515	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0050502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	164	223	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.66892733539306	2		223	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0050502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	589	657	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	NA	2	FACETS		NA	1			1	INDETERMINATE	3	TRUE	NA	0.66892733539306	2		657	620	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888848	76888848	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	96	459	1	ENST00000373344.5:c.4981C>T	p.Arg1661Cys	p.R1661C	ENST00000373344	NM_000489.3	1661	Cgt/Tgt	19/35	1	2	FACETS	0.443	0.395	0.494	0.443	0.395	0.494	SUBCLONAL	1	TRUE	1	0.66892733539306	2		460	648	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608309	28608309	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767430269	NA	P-0050502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	55	536	0	ENST00000241453.7:c.1747G>A	p.Gly583Ser	p.G583S	ENST00000241453	NM_004119.2	583	Ggc/Agc	14/24	0.213603749555089	1	FACETS	0.198	0.169	0.23	0.198	0.169	0.23	INDETERMINATE	1	TRUE	0	0.66892733539306	1		536	553	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119673	108119673	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs775767808	NA	P-0050502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	34	190	0	ENST00000278616.4:c.1079A>T	p.Asp360Val	p.D360V	ENST00000278616	NM_000051.3	360	gAt/gTt	9/63	1	2	FACETS	0.345	0.282	0.414	0.345	0.282	0.414	SUBCLONAL	1	TRUE	1	0.66892733539306	2		190	295	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30946584	30946584	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	98	212	0	ENST00000375687.4:c.6G>C	p.Lys2Asn	p.K2N	ENST00000375687	NM_015338.5	2	aaG/aaC	1/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.66892733539306	2		212	214	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888728	76888729	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	293	466	0	ENST00000373344.5:c.5100dup	p.Lys1701Ter	p.K1701*	ENST00000373344	NM_000489.3	1700	-/T	19/35	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.66892733539306	2		466	655	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685281	89685281	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060500116	NA	P-0050503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	188	275	0	ENST00000371953.3:c.176C>G	p.Ser59Ter	p.S59*	ENST00000371953	NM_000314.4	59	tCa/tGa	3/9	0.859449323675563	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.859449323675563	1		275	236	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411625	63411625	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	377	807	0	ENST00000330258.3:c.1542C>A	p.Ser514Arg	p.S514R	ENST00000330258	NM_152424.3	514	agC/agA	2/2	0.859449323675563	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.859449323675563	1		807	489	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577119	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	387	748	0	ENST00000269305.4:c.819dup	p.Val274CysfsTer32	p.V274Cfs*32	ENST00000269305	NM_001126112.2	273	-/T	8/11	0.85701973458571	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.859449323675563	1		748	470	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484803	57484803	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	323	634	0	ENST00000371085.3:c.783C>G	p.Asn261Lys	p.N261K	ENST00000371085	NM_000516.4	261	aaC/aaG	10/13	0.143855193584711	3	FACETS	0.768	0.73	0.805	0.768	0.73	0.805	INDETERMINATE	2	TRUE	1	0.859449323675563	3		634	700	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99806181	99806181	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	322	321	0	ENST00000280892.6:c.491A>C	p.Asp164Ala	p.D164A	ENST00000280892	NM_001130678.1	164	gAc/gCc	6/7	0.173182527323415	6	FACETS	0.911	0.872	0.95			1	INDETERMINATE	4	TRUE	NA	0.859449323675563	6		321	559	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	67	364	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.934	1	1	0.983	1	CLONAL	2	TRUE	1	0.18882047919322	2		364	321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	117	582	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.929	0.839	1	1	0.988	1	CLONAL	2	TRUE	1	0.18882047919322	2		582	667	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1023835002	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	129	558	0	ENST00000558401.1:c.1A>G	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Gtg	1/4	1	2	FACETS	1	0.977	1	1	0.991	1	CLONAL	2	TRUE	1	0.18882047919322	2		558	561	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	282	825	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.982	1	1	0.997	1	CLONAL	4	TRUE	1	0.18882047919322	2		829	686	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779211	3779211	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783507	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	58	457	0	ENST00000262367.5:c.5837del	p.Pro1946HisfsTer30	p.P1946Hfs*30	ENST00000262367	NM_004380.2	1946	cCa/ca	31/31	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.18882047919322	2		457	432	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	78	452	3	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.984	0.868	1	1	0.983	1	CLONAL	2	TRUE	1	0.18882047919322	2		455	420	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631413	117631413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750308356	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	50	314	2	ENST00000368508.3:c.6265G>A	p.Val2089Met	p.V2089M	ENST00000368508	NM_002944.2	2089	Gtg/Atg	40/43	0.18882047919322	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.18882047919322	1		316	321	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	66	362	5	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	1	0.921	1	1	0.982	1	CLONAL	2	TRUE	1	0.18882047919322	2		367	326	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149710	202149710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	145	566	1	ENST00000358485.4:c.1151G>A	p.Gly384Asp	p.G384D	ENST00000358485	NM_001080125.1	384	gGc/gAc	8/9	1	2	FACETS	0.85	0.779	0.925	1	0.992	1	CLONAL	3	TRUE	1	0.18882047919322	2		567	602	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644679	134644679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773064927	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	103	467	0	ENST00000398015.3:c.80C>T	p.Thr27Met	p.T27M	ENST00000398015	NM_004441.4	27	aCg/aTg	2/16	1	2	FACETS	1	0.951	1	1	0.988	1	CLONAL	2	TRUE	1	0.18882047919322	2		467	498	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	148	700	0	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	1	0.97	1	1	0.992	1	CLONAL	2	TRUE	1	0.18882047919322	2		700	695	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007824	45007825	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	76	392	0	ENST00000558401.1:c.276dup	p.Thr93HisfsTer2	p.T93Hfs*2	ENST00000558401	NM_004048.2	91	acc/aCcc	2/4	1	2	FACETS	0.892	0.786	1	1	0.981	1	CLONAL	2	TRUE	1	0.18882047919322	2		392	451	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	75	442	10	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	1	0.936	1	1	0.984	1	CLONAL	2	TRUE	1	0.18882047919322	2		452	363	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	75	454	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.893	0.785	1	1	0.981	1	CLONAL	2	TRUE	1	0.18882047919322	2		459	445	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	90	927	0	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	0.18882047919322	1	FACETS	0.833	0.742	0.931	1	0.983	1	CLONAL	2	TRUE	0	0.18882047919322	1		927	518	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139625	202139626	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	76	352	0	ENST00000358485.4:c.790dup	p.Val264GlyfsTer13	p.V264Gfs*13	ENST00000358485	NM_001080125.1	262	-/G	6/9	1	2	FACETS	1	0.921	1	1	0.984	1	CLONAL	2	TRUE	1	0.18882047919322	2		352	381	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	83	455	2	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	1	0.92	1	1	0.985	1	CLONAL	2	TRUE	1	0.18882047919322	2		457	420	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733513	85733513	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs387906350	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	109	425	2	ENST00000370580.1:c.499del	p.Ser167LeufsTer6	p.S167Lfs*6	ENST00000370580	NM_003921.4	167	Tct/ct	3/3	1	2	FACETS	0.871	0.787	0.958	1	0.99	1	CLONAL	3	TRUE	1	0.18882047919322	2		427	442	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868176	45868176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559154781	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	173	831	3	ENST00000391945.4:c.514G>A	p.Ala172Thr	p.A172T	ENST00000391945	NM_000400.3	172	Gct/Act	7/23	1	2	FACETS	0.842	0.777	0.91	1	0.994	1	CLONAL	3	TRUE	1	0.18882047919322	2		834	725	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449779	149449779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776196303	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	127	678	0	ENST00000286301.3:c.1285G>A	p.Val429Met	p.V429M	ENST00000286301	NM_005211.3	429	Gtg/Atg	9/22	1	2	FACETS	1	0.925	1	1	0.99	1	CLONAL	2	TRUE	1	0.18882047919322	2		678	659	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119910	70119910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1297203260	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	104	469	0	ENST00000245479.2:c.916del	p.Val306CysfsTer77	p.V306Cfs*77	ENST00000245479	NM_000346.3	304	ccG/cc	3/3	1	2	FACETS	1	0.95	1	1	0.988	1	CLONAL	2	TRUE	1	0.18882047919322	2		469	505	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822586	72822586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	82	539	1	ENST00000268489.5:c.9589del	p.Gln3197SerfsTer44	p.Q3197Sfs*44	ENST00000268489	NM_006885.3	3197	Cag/ag	10/10	1	2	FACETS	0.812	0.717	0.912	1	0.98	1	CLONAL	2	TRUE	1	0.18882047919322	2		540	535	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs753143066	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	93	548	4	ENST00000295797.4:c.826dup	p.Thr276AsnfsTer16	p.T276Nfs*16	ENST00000295797	NM_002740.5	273	tta/ttAa	9/18	1	2	FACETS	0.915	0.816	1	1	0.985	1	CLONAL	2	TRUE	1	0.18882047919322	2		552	538	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016675	12016675	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	55	341	0	ENST00000353533.5:c.811G>A	p.Ala271Thr	p.A271T	ENST00000353533	NM_003010.3	271	Gca/Aca	7/11	1	2	FACETS	0.802	0.689	0.925	1	0.97	1	CLONAL	2	TRUE	1	0.18882047919322	2		341	363	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	80	506	3	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	0.168882849266853	1	FACETS	0.775	0.684	0.872	1	0.978	1	SUBCLONAL	2	TRUE	0	0.18882047919322	1		509	495	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43730536	43730536	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	92	418	0	ENST00000382044.4:c.3177del	p.Thr1060ProfsTer36	p.T1060Pfs*36	ENST00000382044	NM_001141980.1	1059	ccC/cc	16/28	1	2	FACETS	1	0.952	1	1	0.987	1	CLONAL	2	TRUE	1	0.18882047919322	2		418	436	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860842	151860842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781376139	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	100	445	1	ENST00000262189.6:c.9820G>A	p.Ala3274Thr	p.A3274T	ENST00000262189	NM_170606.2	3274	Gca/Aca	43/59	1	2	FACETS	1	0.939	1	1	0.988	1	CLONAL	2	TRUE	1	0.18882047919322	2		446	497	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388044	81388045	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1186073562	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	42	389	1	ENST00000222390.5:c.330dup	p.Glu111ArgfsTer5	p.E111Rfs*5	ENST00000222390	NM_000601.4	110	-/A	3/18	1	2	FACETS	0.815	0.684	0.958	1	0.963	1	CLONAL	2	TRUE	1	0.18882047919322	2		390	273	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783668	50783668	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	70	492	0	ENST00000398568.2:c.64del	p.Tyr22ThrfsTer25	p.Y22Tfs*25	ENST00000398568	NM_001042412.1	20	aTt/at	3/18	1	2	FACETS	0.774	0.676	0.879	1	0.975	1	SUBCLONAL	2	TRUE	1	0.18882047919322	2		492	479	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738808	145738808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367570292	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	116	1028	0	ENST00000428558.2:c.2257C>T	p.Arg753Trp	p.R753W	ENST00000428558	NM_004260.3	753	Cgg/Tgg	14/22	0.18882047919322	3	FACETS	0.754	0.679	0.833	0.502	0.452	0.556	SUBCLONAL	2	TRUE	0	0.18882047919322	3		1028	892	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162916	38162916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1030084373	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	98	527	1	ENST00000317025.8:c.2290C>T	p.Arg764Cys	p.R764C	ENST00000317025	NM_023034.1	764	Cgt/Tgt	13/24	0.18882047919322	3	FACETS	0.867	0.774	0.966	0.578	0.516	0.644	CLONAL	2	TRUE	0	0.18882047919322	3		528	655	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523642	41523642	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1386169409	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	164	579	0	ENST00000263253.7:c.1058G>A	p.Arg353His	p.R353H	ENST00000263253	NM_001429.3	353	cGc/cAc	4/31	1	2	FACETS	0.847	0.779	0.916	1	0.993	1	CLONAL	3	TRUE	1	0.18882047919322	2		579	684	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324139	31324139	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs151341241	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	75	697	1	ENST00000412585.2:c.424T>C	p.Tyr142His	p.Y142H	ENST00000412585	NM_005514.6	142	Tac/Cac	3/8	1	2	FACETS	0.773	0.679	0.874	1	0.977	1	SUBCLONAL	2	TRUE	1	0.18882047919322	2		698	514	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247355	71247355	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	119	548	1	ENST00000318789.4:c.178C>T	p.Gln60Ter	p.Q60*	ENST00000318789	NM_032682.5	60	Cag/Tag	6/21	1	2	FACETS	1	0.961	1	1	0.99	1	CLONAL	2	TRUE	1	0.18882047919322	2		549	565	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229375	36229375	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	107	616	0	ENST00000222270.7:c.8065G>A	p.Asp2689Asn	p.D2689N	ENST00000222270	NM_014727.1	2689	Gac/Aac	37/37	1	2	FACETS	0.941	0.846	1	1	0.987	1	CLONAL	2	TRUE	1	0.18882047919322	2		616	602	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932791	39932791	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	160	710	0	ENST00000378444.4:c.1808C>G	p.Ala603Gly	p.A603G	ENST00000378444	NM_001123385.1	603	gCc/gGc	4/15	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	2	TRUE	NA	0.18882047919322	2		710	723	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991664	72991664	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760236892	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	90	495	0	ENST00000268489.5:c.2381C>T	p.Ser794Leu	p.S794L	ENST00000268489	NM_006885.3	794	tCg/tTg	2/10	1	2	FACETS	0.926	0.824	1	1	0.985	1	CLONAL	2	TRUE	1	0.18882047919322	2		495	515	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430666	181430666	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	138	761	0	ENST00000325404.1:c.518T>C	p.Met173Thr	p.M173T	ENST00000325404	NM_003106.3	173	aTg/aCg	1/1	1	2	FACETS	1	0.975	1	1	0.992	1	CLONAL	2	TRUE	1	0.18882047919322	2		761	620	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023607	27023613	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCGGG	CTCCGGG	-	novel	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	104	435	0	ENST00000324856.7:c.719_725del	p.Gly240AlafsTer121	p.G240Afs*121	ENST00000324856	NM_006015.4	238	aCTCCGGGc/ac	1/20	0.123323723047876	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	1	0.18882047919322	3		435	550	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612800	228612800	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	138	727	0	ENST00000366696.1:c.227C>A	p.Ala76Asp	p.A76D	ENST00000366696	NM_003493.2	76	gCt/gAt	1/1	1	2	FACETS	1	0.971	1	1	0.992	1	CLONAL	2	TRUE	1	0.18882047919322	2		727	636	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246197	46246197	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	91	362	0	ENST00000334344.6:c.4291A>G	p.Ile1431Val	p.I1431V	ENST00000334344	NM_152641.2	1431	Ata/Gta	15/21	1	2	FACETS	1	0.96	1	1	0.987	1	CLONAL	2	TRUE	1	0.18882047919322	2		362	416	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424448	49424449	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	130	737	0	ENST00000301067.7:c.13774_13775insT	p.Arg4592MetfsTer14	p.R4592Mfs*14	ENST00000301067	NM_003482.3	4592	agg/aTgg	41/54	1	2	FACETS	1	0.932	1	1	0.99	1	CLONAL	2	TRUE	1	0.18882047919322	2		737	668	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433772	49433772	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1346171688	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	170	947	0	ENST00000301067.7:c.7781T>C	p.Leu2594Pro	p.L2594P	ENST00000301067	NM_003482.3	2594	cTg/cCg	31/54	1	2	FACETS	1	0.976	1	1	0.993	1	CLONAL	2	TRUE	1	0.18882047919322	2		947	784	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447286	49447286	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	131	633	0	ENST00000301067.7:c.812del	p.Pro271LeufsTer33	p.P271Lfs*33	ENST00000301067	NM_003482.3	271	cCt/ct	6/54	1	2	FACETS	1	0.936	1	1	0.99	1	CLONAL	2	TRUE	1	0.18882047919322	2		633	670	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061168	38061168	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	114	397	0	ENST00000250448.2:c.821C>G	p.Ala274Gly	p.A274G	ENST00000250448	NM_004496.3	274	gCc/gGc	2/2	1	2	FACETS	0.919	0.833	1	1	0.991	1	CLONAL	3	TRUE	1	0.18882047919322	2		397	438	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95579439	95579439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	44	294	0	ENST00000393063.1:c.2030C>T	p.Ala677Val	p.A677V	ENST00000393063	NM_030621.3	677	gCc/gTc	13/28	1	2	FACETS	0.983	0.832	1	1	0.971	1	CLONAL	2	TRUE	1	0.18882047919322	2		294	237	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105237115	105237115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	129	562	0	ENST00000349310.3:c.1330G>A	p.Ala444Thr	p.A444T	ENST00000349310	NM_001014432.1	444	Gcc/Acc	14/15	1	2	FACETS	1	0.945	1	1	0.99	1	CLONAL	2	TRUE	1	0.18882047919322	2		562	647	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15978884	15978884	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	148	498	0	ENST00000268712.3:c.3634T>C	p.Tyr1212His	p.Y1212H	ENST00000268712	NM_006311.3	1212	Tat/Cat	27/46	1	2	FACETS	0.922	0.846	1	1	0.993	1	CLONAL	3	TRUE	1	0.18882047919322	2		498	567	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7163055	7163055	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	102	494	0	ENST00000302850.5:c.2017T>C	p.Tyr673His	p.Y673H	ENST00000302850	NM_000208.2	673	Tat/Cat	9/22	1	2	FACETS	1	0.925	1	1	0.988	1	CLONAL	2	TRUE	1	0.18882047919322	2		494	521	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032387	11032387	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	124	820	2	ENST00000327064.4:c.1781C>T	p.Ala594Val	p.A594V	ENST00000327064	NM_199141.1	594	gCg/gTg	16/16	1	2	FACETS	0.886	0.802	0.974	1	0.988	1	CLONAL	2	TRUE	1	0.18882047919322	2		822	741	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169467	11169467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985886104	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	134	628	0	ENST00000358026.2:c.4633C>T	p.Arg1545Cys	p.R1545C	ENST00000358026	NM_001128849.1	1545	Cgc/Tgc	33/36	1	2	FACETS	1	0.976	1	1	0.992	1	CLONAL	2	TRUE	1	0.18882047919322	2		628	589	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256806	19256806	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	136	739	1	ENST00000162023.5:c.907G>A	p.Gly303Ser	p.G303S	ENST00000162023		303	Ggt/Agt	13/13	1	2	FACETS	1	0.962	1	1	0.991	1	CLONAL	2	TRUE	1	0.18882047919322	2		740	655	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41818293	41818293	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	26	66	0	ENST00000373198.4:c.81C>A	p.Ser27Arg	p.S27R	ENST00000373198	NM_133170.3	27	agC/agA	1/32	1	2	FACETS	0.977	0.793	1	1	0.964	1	CLONAL	3	TRUE	1	0.18882047919322	2		66	94	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428465	72428497	+	inframe_deletion	In_Frame_Del	DEL	TTCTCTTTGTCCTGCTTTTCAACTTTCTCCTTC	TTCTCTTTGTCCTGCTTTTCAACTTTCTCCTTC	-	novel	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	71	431	0	ENST00000477973.2:c.505_537del	p.Lys170_Lys180del	p.K170_K180del	ENST00000477973	NM_012234.5	169	aaGAAGGAGAAAGTTGAAAAGCAGGACAAAGAGAAa/aaa	2/4	1	2	FACETS	0.872	0.764	0.988	1	0.979	1	CLONAL	2	TRUE	1	0.18882047919322	2		431	431	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957534	1957534	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	165	702	1	ENST00000382891.5:c.2633T>C	p.Leu878Pro	p.L878P	ENST00000382891	NM_133335.3	878	cTg/cCg	14/22	1	2	FACETS	0.858	0.79	0.928	1	0.993	1	CLONAL	3	TRUE	1	0.18882047919322	2		703	679	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361231	66361232	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	48	330	0	ENST00000273854.3:c.940_941delinsAT	p.Pro314Ile	p.P314I	ENST00000273854	NM_004439.5	314	CCt/ATt	4/18	0.18882047919322	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.18882047919322	1		330	335	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196366	106196366	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	55	374	0	ENST00000380013.4:c.4699A>G	p.Asn1567Asp	p.N1567D	ENST00000380013	NM_001127208.2	1567	Aat/Gat	11/11	1	2	FACETS	0.825	0.709	0.951	1	0.972	1	CLONAL	2	TRUE	1	0.18882047919322	2		374	353	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38972017	38972017	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	33	313	0	ENST00000357387.3:c.934C>A	p.Leu312Ile	p.L312I	ENST00000357387	NM_152756.3	312	Cta/Ata	11/38	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.18882047919322	2		313	235	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852185	128852185	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	156	805	1	ENST00000249373.3:c.2257C>T	p.Pro753Ser	p.P753S	ENST00000249373	NM_005631.4	753	Ccg/Tcg	12/12	1	2	FACETS	1	0.957	1	1	0.992	1	CLONAL	2	TRUE	1	0.18882047919322	2		806	773	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127916205	127916206	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	85	466	0	ENST00000373547.4:c.438dup	p.Asp147Ter	p.D147*	ENST00000373547	NM_002721.4	146	-/T	5/7	1	2	FACETS	1	0.901	1	1	0.985	1	CLONAL	2	TRUE	1	0.18882047919322	2		466	443	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356386	70356386	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	81	597	1	ENST00000374080.3:c.5285del	p.Lys1762ArgfsTer53	p.K1762Rfs*53	ENST00000374080		1761	Aaa/aa	37/45	0.18882047919322	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.18882047919322	1		598	557	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183797	10183797	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs5030807	NA	P-0050510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	486	683	0	ENST00000256474.2:c.266T>C	p.Leu89Pro	p.L89P	ENST00000256474	NM_000551.3	89	cTc/cCc	1/3	0.672529518581435	1	FACETS	0.991	0.953	1	0.991	0.953	1	CLONAL	1	TRUE	0	0.672529518581435	1		683	968	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103900	209103902	+	inframe_deletion	In_Frame_Del	DEL	TTA	TTA	-	novel	NA	P-0050510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	253	383	0	ENST00000345146.2:c.1047_1049del	p.Asn349del	p.N349del	ENST00000345146	NM_005896.2	349	aaTAAa/aaa	9/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.672529518581435	2		383	737	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582105	52582106	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0050510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	162	242	0	ENST00000394830.3:c.4722_4723del	p.Gln1575SerfsTer20	p.Q1575Sfs*20	ENST00000394830	NM_018313.4	1574	cgCCaa/cgaa	30/30	0.672529518581435	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.672529518581435	1		242	306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0050511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	131	454	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	NA	2	FACETS	0.938	0.859	1			1	INDETERMINATE	2	TRUE	NA	0.326244961527713	2		455	428	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0050511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	115	382	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.326244961527713	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.326244961527713	3		382	371	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0050511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	35	215	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.745	0.613	0.892	0.745	0.613	0.892	SUBCLONAL	1	TRUE	1	0.326244961527713	2		215	288	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631102	69631102	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121917704	NA	P-0050511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	136	620	0	ENST00000334134.2:c.310C>T	p.Arg104Ter	p.R104*	ENST00000334134	NM_005247.2	104	Cga/Tga	2/3	0.326244961527713	3	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	1	0.326244961527713	3		620	464	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023842	27023842	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0050511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	88	416	0	ENST00000324856.7:c.948C>G	p.Tyr316Ter	p.Y316*	ENST00000324856	NM_006015.4	316	taC/taG	1/20	0.326244961527713	3	FACETS	0.902	0.806	1	0.902	0.806	1	CLONAL	2	TRUE	1	0.326244961527713	3		416	348	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604778	48604778	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767383	NA	P-0050512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	402	408	1	ENST00000342988.3:c.1600C>T	p.Gln534Ter	p.Q534*	ENST00000342988	NM_005359.5	534	Cag/Tag	12/12	0.966399957062763	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.966399957062763	2		409	416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578552	7578552	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	726	770	1	ENST00000269305.4:c.378C>A	p.Tyr126Ter	p.Y126*	ENST00000269305	NM_001126112.2	126	taC/taA	5/11	0.962711258782052	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.966399957062763	2		771	745	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038508	47038508	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781804786	NA	P-0050512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	329	701	2	ENST00000377604.3:c.670G>A	p.Val224Ile	p.V224I	ENST00000377604	NM_001204468.1	224	Gtc/Atc	8/24	0.957083357047629	3	FACETS	0.916	0.867	0.967	0.458	0.433	0.484	CLONAL	1	TRUE	1	0.966399957062763	3		703	1102	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027153	49027153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	374	379	0	ENST00000267163.4:c.1722del	p.Lys574AsnfsTer37	p.K574Nfs*37	ENST00000267163	NM_000321.2	574	Aaa/aa	18/27	0.962711258782052	2	FACETS	0.985	0.97	0.997	0.985	0.97	0.997	CLONAL	2	TRUE	0	0.966399957062763	2		379	393	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0050513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	272	374	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.735028899663352	2		374	724	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038564	47038564	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0050513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	59	383	0	ENST00000377604.3:c.724+2T>C		p.X242_splice	ENST00000377604	NM_001204468.1	242			1	1	FACETS	0.162	0.139	0.187	0.162	0.139	0.187	SUBCLONAL	1	TRUE	0	0.735028899663352	1		383	627	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197576	106197576	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	94	332	0	ENST00000380013.4:c.5909C>G	p.Ser1970Cys	p.S1970C	ENST00000380013	NM_001127208.2	1970	tCt/tGt	11/11	0.735028899663352	3	FACETS	0.384	0.341	0.431	0.192	0.17	0.216	SUBCLONAL	1	TRUE	1	0.735028899663352	3		332	910	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	23	413	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.278923769870097	1	FACETS	0.604	0.472	0.755	0.604	0.472	0.755	SUBCLONAL	1	TRUE	0	0.278923769868596	1		413	235	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0050514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	182	753	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.278923769868596	2		753	1252	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879628	37879628	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1572	244	724	0	ENST00000269571.5:c.2003G>C	p.Gly668Ala	p.G668A	ENST00000269571		668	gGg/gCg	17/27	1	2	FACETS	0.963	0.897	1	0.963	0.897	1	CLONAL	1	TRUE	1	0.278923769868596	2		724	1816	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573556	48573556	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	17	250	0	ENST00000342988.3:c.140T>G	p.Leu47Arg	p.L47R	ENST00000342988	NM_005359.5	47	cTg/cGg	2/12	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.278923769868596	2		250	103	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803148	1803148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1569	94	871	3	ENST00000260795.2:c.500C>T	p.Pro167Leu	p.P167L	ENST00000260795		167	cCg/cTg	4/17	0.33030755984547	5	FACETS	0.512	0.453	0.575	0.171	0.151	0.192	SUBCLONAL	1	TRUE	2	0.33030755984547	5		874	1663	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	175	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.76151773878377	1	FACETS	0.978	0.933	1	0.978	0.933	1	CLONAL	1	TRUE	0	0.868652098513729	1		327	233	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0050517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	110	282	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.928	0.848	1	0.928	0.848	1	CLONAL	1	TRUE	1	0.868652098513729	2		282	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0050517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	270	576	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	0.868652098513729	1	FACETS	0.945	0.909	0.981	0.945	0.909	0.981	CLONAL	1	TRUE	0	0.868652098513729	1		576	372	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604787	48604787	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519741	NA	P-0050517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	153	414	0	ENST00000342988.3:c.1609G>T	p.Asp537Tyr	p.D537Y	ENST00000342988	NM_005359.5	537	Gac/Tac	12/12	0.868652098513729	1	FACETS	0.882	0.833	0.929	0.882	0.833	0.929	CLONAL	1	TRUE	0	0.868652098513729	1		414	226	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412095	63412095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852217	NA	P-0050517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	615	695	2	ENST00000330258.3:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000330258	NM_152424.3	358	Cga/Tga	2/2	0.702393761698446	4	FACETS	0.998	0.963	1	0.998	0.963	1	CLONAL	2	TRUE	2	0.868652098513729	4		697	1326	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584501	189584501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908849	NA	P-0050517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	123	357	0	ENST00000264731.3:c.797G>A	p.Arg266Gln	p.R266Q	ENST00000264731	NM_003722.4	266	cGa/cAa	6/14	1	2	FACETS	0.807	0.738	0.877	0.807	0.738	0.877	CLONAL	1	TRUE	1	0.868652098513729	2		357	351	SUCCESS
APC	324	MSKCC	GRCh37	5	112176020	112176020	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	110	262	0	ENST00000257430.4:c.4729G>T	p.Glu1577Ter	p.E1577*	ENST00000257430	NM_000038.5	1577	Gaa/Taa	16/16	1	2	FACETS	0.924	0.844	1	0.924	0.844	1	CLONAL	1	TRUE	1	0.868652098513729	2		262	274	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420273	49420273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1205083140	NA	P-0050517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	269	649	0	ENST00000301067.7:c.15476G>A	p.Arg5159Gln	p.R5159Q	ENST00000301067	NM_003482.3	5159	cGg/cAg	48/54	1	2	FACETS	0.909	0.859	0.961	0.909	0.859	0.961	CLONAL	1	TRUE	1	0.868652098513729	2		649	681	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111886044	111886044	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769682050	NA	P-0050517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	233	604	1	ENST00000341259.2:c.1666G>A	p.Glu556Lys	p.E556K	ENST00000341259	NM_005475.2	556	Gaa/Aaa	8/8	1	2	FACETS	0.93	0.874	0.986	0.93	0.874	0.986	CLONAL	1	TRUE	1	0.868652098513729	2		605	577	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491276	2491276	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372896541	NA	P-0050517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	328	824	0	ENST00000355716.4:c.319G>A	p.Ala107Thr	p.A107T	ENST00000355716	NM_003820.2	107	Gcg/Acg	4/8	1	2	FACETS	0.973	0.925	1	0.973	0.925	1	CLONAL	1	TRUE	1	0.868652098513729	2		824	776	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188183	11188183	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	127	395	0	ENST00000361445.4:c.5911G>C	p.Ala1971Pro	p.A1971P	ENST00000361445	NM_004958.3	1971	Gcc/Ccc	43/58	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.504143014475122	2		395	415	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259207	16259207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	140	486	0	ENST00000375759.3:c.6472C>T	p.Pro2158Ser	p.P2158S	ENST00000375759	NM_015001.2	2158	Ccg/Tcg	11/15	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.504143014475122	2		486	517	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200965	108200965	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	228	351	0	ENST00000278616.4:c.7332G>T	p.Glu2444Asp	p.E2444D	ENST00000278616	NM_000051.3	2444	gaG/gaT	50/63	0.504143014475122	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.504143014475122	3		351	511	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200991	108200991	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587781361	NA	P-0050521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	110	381	0	ENST00000278616.4:c.7358G>C	p.Arg2453Pro	p.R2453P	ENST00000278616	NM_000051.3	2453	cGt/cCt	50/63	0.504143014475122	3	FACETS	0.965	0.87	1	0.483	0.435	0.533	CLONAL	1	TRUE	1	0.504143014475122	3		381	566	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0050521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	256	537	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.504143014475122	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.504143014475122	2		537	497	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28644704	28644704	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	109	415	0	ENST00000241453.7:c.89T>A	p.Leu30Gln	p.L30Q	ENST00000241453	NM_004119.2	30	cTg/cAg	2/24	0.504143014475122	3	FACETS	0.918	0.826	1	0.459	0.413	0.507	CLONAL	1	TRUE	1	0.504143014475122	3		415	590	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042400	42042400	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	296	483	0	ENST00000219905.7:c.6595G>T	p.Glu2199Ter	p.E2199*	ENST00000219905	NM_001164273.1	2199	Gag/Tag	17/24	0.504143014475122	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.504143014475122	2		483	538	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39542529	39542529	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	88	365	0	ENST00000262039.4:c.333G>T	p.Trp111Cys	p.W111C	ENST00000262039	NM_002647.2	111	tgG/tgT	3/25	0.504143014475122	3	FACETS	0.754	0.669	0.844	0.377	0.334	0.422	SUBCLONAL	1	TRUE	1	0.504143014475122	3		365	580	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619130	1619130	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	165	668	0	ENST00000344749.5:c.1430G>T	p.Arg477Leu	p.R477L	ENST00000344749	NM_001136139.2	477	cGg/cTg	16/19	0.504143014475122	3	FACETS	0.945	0.868	1	0.473	0.434	0.513	CLONAL	1	TRUE	1	0.504143014475122	3		668	867	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118960	61118960	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	222	320	0	ENST00000295025.8:c.153G>T	p.Gln51His	p.Q51H	ENST00000295025	NM_002908.2	51	caG/caT	2/11	0.504143014475122	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	2	0.504143014475122	4		320	644	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265244	46265244	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	212	318	0	ENST00000371998.3:c.2114C>G	p.Ala705Gly	p.A705G	ENST00000371998		705	gCc/gGc	12/23	0.504143014475122	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	2	0.504143014475122	4		318	602	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928002	49928002	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	352	589	0	ENST00000296474.3:c.3726A>T	p.Gln1242His	p.Q1242H	ENST00000296474	NM_002447.2	1242	caA/caT	18/20	0.504143014475122	4	FACETS	0.996	0.945	1	0.996	0.945	1	CLONAL	2	TRUE	2	0.504143014475122	4		589	1054	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664514	138664514	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	246	356	0	ENST00000330315.3:c.1051C>G	p.Pro351Ala	p.P351A	ENST00000330315	NM_023067.3	351	Ccc/Gcc	1/1	0.504143014475122	4	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	2	0.504143014475122	4		356	732	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233143	66233143	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0050521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	245	360	0	ENST00000273854.3:c.1857-1G>T		p.X619_splice	ENST00000273854	NM_004439.5	619			0.504143014475122	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.504143014475122	4		360	700	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524519	187524519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	149	449	0	ENST00000441802.2:c.11161G>A	p.Asp3721Asn	p.D3721N	ENST00000441802	NM_005245.3	3721	Gac/Aac	19/27	0.504143014475122	4	FACETS	0.941	0.859	1	0.47	0.429	0.514	CLONAL	1	TRUE	2	0.504143014475122	4		449	945	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950030	38950030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1367871779	NA	P-0050521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	90	369	0	ENST00000357387.3:c.3920C>T	p.Ser1307Phe	p.S1307F	ENST00000357387	NM_152756.3	1307	tCt/tTt	31/38	0.504143014475122	7	FACETS	0.85	0.753	0.955	0.213	0.188	0.239	CLONAL	1	TRUE	3	0.504143014475122	7		369	949	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950351	38950351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369474390	NA	P-0050521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	230	348	0	ENST00000357387.3:c.3599G>A	p.Arg1200Gln	p.R1200Q	ENST00000357387	NM_152756.3	1200	cGa/cAa	31/38	0.504143014475122	7	FACETS	0.993	0.925	1	0.496	0.462	0.531	CLONAL	2	TRUE	3	0.504143014475122	7		348	1039	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190351	32190351	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	379	619	0	ENST00000375023.3:c.388A>T	p.Arg130Trp	p.R130W	ENST00000375023	NM_004557.3	130	Agg/Tgg	3/30	0.504143014475122	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.504143014475122	2		619	711	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044540	47044540	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	TT	novel	NA	P-0050521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	333	366	0	ENST00000377604.3:c.2037delinsTT	p.Arg680SerfsTer3	p.R680Sfs*3	ENST00000377604	NM_001204468.1	679	ctG/ctTT	18/24	0.488940093979854	2	FACETS	0.857	0.823	0.89			1	CLONAL	3	TRUE	NA	0.504143014475122	2		366	514	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0050522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	121	364	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.240582229005817	4	FACETS	0.881	0.801	0.965	0.881	0.801	0.965	CLONAL	2	TRUE	2	0.388238172893309	4		364	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0050522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	219	596	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.295654177294509	2	FACETS	0.871	0.814	0.928	0.871	0.814	0.928	CLONAL	2	TRUE	0	0.388238172893309	2		596	648	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004721	150004721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1034620976	NA	P-0050522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	132	422	0	ENST00000253339.5:c.1504C>T	p.Arg502Cys	p.R502C	ENST00000253339		502	Cgt/Tgt	3/7	0.364838894092335	5	FACETS	0.876	0.798	0.958	0.584	0.532	0.639	CLONAL	2	TRUE	2	0.388238172893309	5		422	614	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354431	354431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774250998	NA	P-0050522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	96	585	0	ENST00000262320.3:c.1127G>A	p.Arg376Gln	p.R376Q	ENST00000262320	NM_003502.3	376	cGg/cAg	5/11	0.388238172893309	3	FACETS	0.651	0.579	0.728	0.326	0.289	0.364	SUBCLONAL	1	TRUE	1	0.388238172893309	3		585	907	SUCCESS
ATR	545	MSKCC	GRCh37	3	142172007	142172007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762196224	NA	P-0050522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	100	428	2	ENST00000350721.4:c.7724C>T	p.Ala2575Val	p.A2575V	ENST00000350721	NM_001184.3	2575	gCg/gTg	46/47	0.199881620315218	3	FACETS	1	0.945	1	0.543	0.487	0.604	INDETERMINATE	1	TRUE	1	0.388238172893309	3		430	566	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023327	33023336	+	frameshift_variant	Frame_Shift_Del	DEL	CCCAAGAAAT	CCCAAGAAAT	-	novel	NA	P-0050522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	115	558	0	ENST00000300177.4:c.436_445del	p.Pro146SerfsTer4	p.P146Sfs*4	ENST00000300177	NM_001191322.1	146	CCCAAGAAATtc/tc	2/2	0.388238172893309	3	FACETS	0.783	0.704	0.866	0.391	0.352	0.433	SUBCLONAL	1	TRUE	1	0.388238172893309	3		558	904	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437567	56437568	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACAGTTACGATGGGTGG	novel	NA	P-0050522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	115	463	0	ENST00000407977.2:c.894_895insCCACCCATCGTAACTGT	p.Val299ProfsTer126	p.V299Pfs*126	ENST00000407977		298	-/CCACCCATCGTAACTGT	8/10	0.295654177294509	2	FACETS	1	0.934	1	0.521	0.471	0.574	CLONAL	1	TRUE	0	0.388238172893309	2		463	568	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646206	215646206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1163172447	NA	P-0050522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	77	283	0	ENST00000260947.4:c.392G>A	p.Ser131Asn	p.S131N	ENST00000260947	NM_000465.2	131	aGt/aAt	4/11	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.388238172893309	2		283	355	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796834	42796834	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	207	766	1	ENST00000575354.2:c.3292G>A	p.Gly1098Ser	p.G1098S	ENST00000575354	NM_015125.3	1098	Ggc/Agc	14/20	0.374159114532982	3	FACETS	1	0.991	1	0.726	0.674	0.779	CLONAL	1	TRUE	1	0.388238172893309	3		767	877	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0050523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	366	927	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.795330010643854	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.795330010643854	1		927	494	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851916	128851916	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	80	674	0	ENST00000249373.3:c.1988C>G	p.Pro663Arg	p.P663R	ENST00000249373	NM_005631.4	663	cCa/cGa	12/12	0.0929309096871805	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		674	462	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868076	56868076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141371158	NA	P-0050528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	53	495	0	ENST00000308159.5:c.1574G>A	p.Arg525Gln	p.R525Q	ENST00000308159	NM_014669.4	525	cGg/cAg	14/22	1	2	FACETS	0.584	0.497	0.679	0.584	0.497	0.679	SUBCLONAL	1	TRUE	1	0.268962362303397	2		495	675	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293898	1293898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1303	82	924	0	ENST00000310581.5:c.1103C>T	p.Ser368Phe	p.S368F	ENST00000310581	NM_198253.2	368	tCc/tTc	2/16	0.179548200624731	3	FACETS	0.499	0.438	0.565	0.25	0.219	0.283	SUBCLONAL	1	TRUE	1	0.268962362303397	3		924	1385	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50816307	50816307	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	37	341	0	ENST00000398568.2:c.1747A>G	p.Ile583Val	p.I583V	ENST00000398568	NM_001042412.1	583	Ata/Gta	10/18	1	2	FACETS	0.517	0.426	0.62	0.517	0.426	0.62	SUBCLONAL	1	TRUE	1	0.268962362303397	2		341	532	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125680	47125680	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	39	366	0	ENST00000409792.3:c.5590C>G	p.Leu1864Val	p.L1864V	ENST00000409792	NM_014159.6	1864	Ctg/Gtg	12/21	1	2	FACETS	0.492	0.407	0.588	0.492	0.407	0.588	SUBCLONAL	1	TRUE	1	0.268962362303397	2		366	589	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149498404	149498404	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	85	585	0	ENST00000261799.4:c.2810T>C	p.Met937Thr	p.M937T	ENST00000261799	NM_002609.3	937	aTg/aCg	21/23	1	2	FACETS	0.694	0.612	0.782	0.694	0.612	0.782	SUBCLONAL	1	TRUE	1	0.268962362303397	2		585	911	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056455	26056455	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs61751205	NA	P-0050528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	51	357	0	ENST00000343677.2:c.202G>T	p.Ala68Ser	p.A68S	ENST00000343677	NM_005319.3	68	Gcc/Tcc	1/1	1	2	FACETS	0.751	0.639	0.874	0.751	0.639	0.874	SUBCLONAL	1	TRUE	1	0.268962362303397	2		357	505	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	88	468	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.854	0.769	0.942	1	0.985	1	CLONAL	2	TRUE	1	0.410525305027297	2		468	251	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0050529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	144	534	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.225306058729866	3	FACETS	1	0.974	1	0.586	0.536	0.639	INDETERMINATE	1	TRUE	1	0.410525305027297	3		534	721	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28586389	28586389	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	126	433	1	ENST00000253063.3:c.31G>C	p.Glu11Gln	p.E11Q	ENST00000253063	NM_031459.4	11	Gag/Cag	1/10	1	2	FACETS	0.933	0.847	1	0.933	0.847	1	CLONAL	1	TRUE	1	0.410525305027297	2		434	658	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245912952	245912952	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	73	322	0	ENST00000388985.4:c.1200G>C	p.Met400Ile	p.M400I	ENST00000388985		400	atG/atC	12/12	1	2	FACETS	0.77	0.675	0.871	0.77	0.675	0.871	SUBCLONAL	1	TRUE	1	0.410525305027297	2		322	462	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112602	115112604	+	missense_variant	Missense_Mutation	TNP	CGG	CGG	TTT	novel	NA	P-0050529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	202	597	0	ENST00000257566.3:c.1136_1138delinsAAA	p.Ala379_Glu380delinsGluLys	p.A379_E380delinsEK	ENST00000257566	NM_016569.3	379	gCCGag/gAAAag	7/8	0.410525305027297	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.410525305027297	1		597	730	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947596	48947596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1566196458	NA	P-0050529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	113	347	0	ENST00000267163.4:c.1183C>T	p.Gln395Ter	p.Q395*	ENST00000267163	NM_000321.2	395	Caa/Taa	12/27	0.352120447069311	1	FACETS	0.955	0.865	1	0.955	0.865	1	CLONAL	1	TRUE	0	0.410525305027297	1		347	458	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652273	3652273	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	215	575	1	ENST00000294008.3:c.796G>C	p.Ala266Pro	p.A266P	ENST00000294008	NM_032444.2	266	Gct/Cct	4/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.410525305027297	2		576	923	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0050529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	227	571	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.410525305027297	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.410525305027297	1		571	732	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732314	74732314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267605064	NA	P-0050529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	135	347	1	ENST00000359995.5:c.595G>A	p.Glu199Lys	p.E199K	ENST00000359995	NM_001195427.1	199	Gaa/Aaa	2/3	0.410525305027297	3	FACETS	1	0.968	1	0.567	0.516	0.62	CLONAL	1	TRUE	1	0.410525305027297	3		348	699	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223667	36223667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	563	902	0	ENST00000222270.7:c.6217G>A	p.Glu2073Lys	p.E2073K	ENST00000222270	NM_014727.1	2073	Gag/Aag	28/37	0.389724553299984	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	2	0.410525305027297	4		902	1724	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234318	39234318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	154	230	0	ENST00000402219.2:c.2527G>A	p.Glu843Lys	p.E843K	ENST00000402219	NM_005633.3	843	Gaa/Aaa	16/23	0.225306058729866	3	FACETS	0.822	0.756	0.89	0.822	0.756	0.89	INDETERMINATE	2	TRUE	1	0.410525305027297	3		230	550	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149245662	149245662	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	319	491	0	ENST00000360632.3:c.866G>C	p.Arg289Thr	p.R289T	ENST00000360632	NM_015472.4	289	aGa/aCa	5/7	0.225306058729866	3	FACETS	0.908	0.858	0.958	0.908	0.858	0.958	INDETERMINATE	2	TRUE	1	0.410525305027297	3		491	1032	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170009729	170009729	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	107	199	0	ENST00000295797.4:c.1291G>T	p.Gly431Cys	p.G431C	ENST00000295797	NM_002740.5	431	Ggt/Tgt	13/18	0.225306058729866	3	FACETS	1	0.974	1	0.621	0.559	0.686	INDETERMINATE	1	TRUE	1	0.410525305027297	3		199	506	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170015122	170015122	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	229	458	0	ENST00000295797.4:c.1528C>G	p.Gln510Glu	p.Q510E	ENST00000295797	NM_002740.5	510	Caa/Gaa	16/18	0.225306058729866	3	FACETS	0.768	0.717	0.821	0.768	0.717	0.821	INDETERMINATE	2	TRUE	1	0.410525305027297	3		458	875	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151932982	151932982	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs772146328	NA	P-0050529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	30	38	0	ENST00000262189.6:c.2689C>T	p.Arg897Ter	p.R897*	ENST00000262189	NM_170606.2	897	Cga/Tga	16/59	0.188081714127695	3	FACETS	0.908	0.751	1	0.605	0.501	0.717	INDETERMINATE	2	TRUE	0	0.410525305027297	3		38	97	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275454	38275454	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	90	621	0	ENST00000425967.3:c.1579G>C	p.Glu527Gln	p.E527Q	ENST00000425967	NM_001174067.1	527	Gag/Cag	12/19	0.162559724560816	2	FACETS	0.474	0.419	0.532	0.237	0.209	0.266	INDETERMINATE	1	TRUE	0	0.410525305027297	2		621	926	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485981	8485981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	78	394	0	ENST00000356435.5:c.2836G>A	p.Glu946Lys	p.E946K	ENST00000356435		946	Gag/Aag	17/35	1	2	FACETS	0.626	0.55	0.707	0.626	0.55	0.707	SUBCLONAL	1	TRUE	1	0.410525305027297	2		394	607	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0050532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	59	175	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.190563775057426	4	FACETS	0.847	0.735	0.968	0.847	0.735	0.968	CLONAL	3	TRUE	1	0.190563775057426	4		175	290	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0050532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	48	255	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.992	0.839	1	0.992	0.839	1	CLONAL	1	TRUE	1	0.190563775057426	2		255	508	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0050532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	32	254	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	1	2	FACETS	0.713	0.578	0.866	0.713	0.578	0.866	SUBCLONAL	1	TRUE	1	0.190563775057426	2		254	471	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279674	123279674	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs77543610	NA	P-0050532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	227	383	0	ENST00000358487.5:c.758C>G	p.Pro253Arg	p.P253R	ENST00000358487	NM_000141.4	253	cCt/cGt	7/18	0.190563775057426	4	FACETS	0.929	0.869	0.991	1	0.988	1	CLONAL	4	TRUE	1	0.190563775057426	4		383	763	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591228	67591277	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAAAAGGTGTTCGGCAAAA	TTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAAAAGGTGTTCGGCAAAA	-	novel	NA	P-0050532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	42	278	0	ENST00000274335.5:c.1746-20_1775del		p.X582_splice	ENST00000274335		582		13/15	0.190563775057426	2	FACETS	1	0.901	1	0.555	0.464	0.656	CLONAL	1	TRUE	0	0.190563775057426	2		278	397	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0050533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	26	361	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.665	0.525	0.825	0.665	0.525	0.825	SUBCLONAL	1	TRUE	1	0.16	2		361	489	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579486	7579486	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0050533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	79	772	0	ENST00000269305.4:c.201del	p.Glu68ArgfsTer55	p.E68Rfs*55	ENST00000269305	NM_001126112.2	67	ccA/cc	4/11	1	2	FACETS	0.986	0.865	1	0.986	0.865	1	CLONAL	1	TRUE	1	0.16	2		772	1002	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686345	30686346	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0050533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	41	406	0	ENST00000295754.5:c.202_203dup	p.Met68IlefsTer2	p.M68Ifs*2	ENST00000295754	NM_003242.5	67	-/AT	2/7	1	2	FACETS	0.947	0.788	1	0.947	0.788	1	CLONAL	1	TRUE	1	0.16	2		406	541	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0050534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	116	240	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.290021006327838	4	FACETS	1	0.984	1	0.74	0.671	0.813	CLONAL	1	TRUE	2	0.468581562652152	4		240	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0050534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	186	753	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.299434667476463	2	FACETS	0.799	0.744	0.854	0.799	0.744	0.854	SUBCLONAL	2	TRUE	0	0.468581562652152	2		753	497	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716326	52716326	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	208	574	2	ENST00000322088.6:c.770G>T	p.Trp257Leu	p.W257L	ENST00000322088	NM_014225.5	257	tGg/tTg	6/15	0.243553805906216	4	FACETS	0.887	0.826	0.95	0.887	0.826	0.95	INDETERMINATE	2	TRUE	2	0.468581562652152	4		576	735	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543343	65543343	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	78	566	0	ENST00000358664.4:c.334C>A	p.Gln112Lys	p.Q112K	ENST00000358664	NM_002382.4	112	Cag/Aag	5/5	0.335035122969459	3	FACETS	0.694	0.61	0.784	0.347	0.305	0.392	SUBCLONAL	1	TRUE	1	0.468581562652152	3		566	592	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828341	72828342	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0050534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	75	571	0	ENST00000268489.5:c.8239_8240del	p.Leu2747ValfsTer8	p.L2747Vfs*8	ENST00000268489	NM_006885.3	2747	CTg/g	9/10	1	2	FACETS	0.678	0.596	0.766	0.678	0.596	0.766	SUBCLONAL	1	TRUE	1	0.468581562652152	2		571	472	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999449	100999450	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs777896116	NA	P-0050535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	269	725	0	ENST00000325455.5:c.352_353del	p.Leu118ValfsTer65	p.L118Vfs*65	ENST00000325455	NM_001202474.3	118	CTg/g	1/8	0.358327500405528	3	FACETS	1	0.991	1	0.663	0.622	0.705	CLONAL	1	TRUE	1	0.453781735179033	3		725	1097	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577070	7577070	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	AT	novel	NA	P-0050535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	568	553	0	ENST00000269305.4:c.868delinsAT	p.Arg290MetfsTer16	p.R290Mfs*16	ENST00000269305	NM_001126112.2	290	Cgc/ATgc	8/11	0.336219563628633	4	FACETS	1	0.993	1	0.831	0.802	0.86	CLONAL	3	TRUE	0	0.453781735179033	4		553	1095	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306583	41306583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs571224137	NA	P-0050535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	99	527	1	ENST00000373198.4:c.1076G>A	p.Arg359Gln	p.R359Q	ENST00000373198	NM_133170.3	359	cGa/cAa	7/32	0.453781735179033	1	FACETS	0.426	0.38	0.476	0.426	0.38	0.476	SUBCLONAL	1	TRUE	0	0.453781735179033	1		528	791	SUCCESS
ATR	545	MSKCC	GRCh37	3	142224086	142224086	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	97	362	0	ENST00000350721.4:c.5091G>C	p.Lys1697Asn	p.K1697N	ENST00000350721	NM_001184.3	1697	aaG/aaC	29/47	0.313898712946861	3	FACETS	0.891	0.796	0.991	0.297	0.265	0.331	CLONAL	1	TRUE	0	0.453781735179033	3		362	589	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541338	187541338	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0050535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	44	326	0	ENST00000441802.2:c.6402A>T	p.Glu2134Asp	p.E2134D	ENST00000441802	NM_005245.3	2134	gaA/gaT	10/27	0.453781735179033	1	FACETS	0.481	0.405	0.564	0.481	0.405	0.564	SUBCLONAL	1	TRUE	0	0.453781735179033	1		326	312	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137528128	137528128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	98	253	0	ENST00000367739.4:c.172G>A	p.Val58Ile	p.V58I	ENST00000367739	NM_000416.2	58	Gtt/Att	2/7	0.324459369340179	12	FACETS	0.848	0.757	0.943	0.283	0.252	0.315	CLONAL	3	TRUE	3	0.324459369340179	12		253	623	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579367	7579370	+	frameshift_variant	Frame_Shift_Del	DEL	TAGC	TAGC	-	novel	NA	P-0050537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	187	745	1	ENST00000269305.4:c.317_320del	p.Ser106ThrfsTer16	p.S106Tfs*16	ENST00000269305	NM_001126112.2	106	aGCTAc/ac	4/11	0.309903419989077	3	FACETS	0.87	0.811	0.931	0.87	0.811	0.931	CLONAL	3	TRUE	0	0.324459369340179	3		746	513	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967492	38967492	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	72	321	0	ENST00000357387.3:c.1098T>G	p.Asp366Glu	p.D366E	ENST00000357387	NM_152756.3	366	gaT/gaG	13/38	0.292386775721429	3	FACETS	1	0.949	1	0.581	0.509	0.658	CLONAL	1	TRUE	1	0.324459369340179	3		321	444	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591107	67591121	+	inframe_deletion	In_Frame_Del	DEL	AACCAGACCTTATCC	AACCAGACCTTATCC	-	novel	NA	P-0050537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	47	283	0	ENST00000274335.5:c.1701_1715del	p.Pro568_Gln572del	p.P568_Q572del	ENST00000274335		567	aAACCAGACCTTATCCag/aag	12/15	0.292386775721429	3	FACETS	1	0.937	1	0.603	0.512	0.702	CLONAL	1	TRUE	1	0.324459369340179	3		283	279	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056083	26056121	+	inframe_deletion	In_Frame_Del	DEL	CCTTAGCAGCACTTTTGGCAGCTTTCTTGGGCTTCGCAA	CCTTAGCAGCACTTTTGGCAGCTTTCTTGGGCTTCGCAA	-	novel	NA	P-0050537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	162	441	0	ENST00000343677.2:c.536_574del	p.Val179_Lys191del	p.V179_K191del	ENST00000343677	NM_005319.3	179	gTTGCGAAGCCCAAGAAAGCTGCCAAAAGTGCTGCTAAGGct/gct	1/1	0.324459369340179	7	FACETS	1	0.966	1	0.541	0.499	0.584	CLONAL	3	TRUE	1	0.324459369340179	7		441	557	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200026	123200027	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0050537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	44	276	1	ENST00000218089.9:c.2098_2099delinsTT	p.Ala700Phe	p.A700F	ENST00000218089	NM_001042749.1	700	GCc/TTc	22/35	0.128168032254888	5	FACETS	1	0.887	1			1	INDETERMINATE	1	TRUE	NA	0.324459369340179	5		277	377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0050540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	261	687	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	NA	2	FACETS	0.947	0.903	0.99			1	INDETERMINATE	2	TRUE	NA	0.63967416789905	2		688	431	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060846	38060864	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTGCCAAGCCGTGTGCC	GGGTGCCAAGCCGTGTGCC	-	novel	NA	P-0050540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	328	671	1	ENST00000250448.2:c.1125_1143del	p.Ala376ThrfsTer7	p.A376Tfs*7	ENST00000250448	NM_004496.3	375	ccGGCACACGGCTTGGCACCC/cc	2/2	0.469467598340946	3	FACETS	0.766	0.727	0.807	0.766	0.727	0.807	SUBCLONAL	2	TRUE	1	0.63967416789905	3		672	883	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78935274	78935274	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	106	621	1	ENST00000306801.3:c.3686G>A	p.Ser1229Asn	p.S1229N	ENST00000306801	NM_020761.2	1229	aGt/aAt	31/34	0.169773785634417	4	FACETS	0.821	0.737	0.91	0.41	0.368	0.455	INDETERMINATE	1	TRUE	2	0.63967416789905	4		622	662	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944257	206944257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	35	336	0	ENST00000423557.1:c.373C>T	p.Arg125Cys	p.R125C	ENST00000423557	NM_000572.2	125	Cgc/Tgc	3/5	0.101105163936176	3	FACETS	0.369	0.301	0.445	0.184	0.15	0.223	INDETERMINATE	1	TRUE	1	0.35	3		336	637	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752989	128752989	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	78	393	1	ENST00000377970.2:c.1150G>A	p.Glu384Lys	p.E384K	ENST00000377970	NM_002467.4	384	Gag/Aag	3/3	0.3	3	FACETS	0.702	0.616	0.794	0.351	0.308	0.397	SUBCLONAL	1	TRUE	1	0.35	3		394	746	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113761	11113761	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	59	558	0	ENST00000358026.2:c.1869G>C	p.Glu623Asp	p.E623D	ENST00000358026	NM_001128849.1	623	gaG/gaC	12/36	0.101105163936176	3	FACETS	0.391	0.335	0.453	0.196	0.167	0.227	INDETERMINATE	1	TRUE	1	0.35	3		558	1012	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178236	56178236	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778518101	NA	P-0050541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	29	288	0	ENST00000399503.3:c.3209C>A	p.Thr1070Lys	p.T1070K	ENST00000399503	NM_005921.1	1070	aCa/aAa	14/20	1	2	FACETS	0.396	0.318	0.486	0.396	0.318	0.486	SUBCLONAL	1	TRUE	1	0.35	2		288	418	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	121	468	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		468	327	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023405	27023405	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	109	416	1	ENST00000324856.7:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000324856	NM_006015.4	171	Caa/Taa	1/20	0.547895025749188	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.547895025749188	1		417	288	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774119	56774119	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1555594699	NA	P-0050544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	32	507	0	ENST00000337432.4:c.470T>G	p.Phe157Cys	p.F157C	ENST00000337432	NM_058216.2	157	tTt/tGt	3/9	1	2	FACETS	0.467	0.378	0.567	0.467	0.378	0.567	SUBCLONAL	1	TRUE	1	0.29	2		507	473	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974695	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	37	366	0	ENST00000304494.5:c.132C>A	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	taC/taA	1/3	1	2	FACETS	0.735	0.608	0.878	0.735	0.608	0.878	SUBCLONAL	1	TRUE	1	0.29	2		366	347	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0050546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	63	240	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.444	0.386	0.506	0.444	0.386	0.506	SUBCLONAL	1	TRUE	1	0.825164221615852	2		240	344	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0050546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	76	255	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.534	0.472	0.6	0.534	0.472	0.6	SUBCLONAL	1	TRUE	1	0.825164221615852	2		255	345	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176992	56176993	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0050546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	80	288	0	ENST00000399503.3:c.2263_2264del	p.Leu755TrpfsTer8	p.L755Wfs*8	ENST00000399503	NM_005921.1	754	ctTCtt/cttt	13/20	1	2	FACETS	0.384	0.339	0.432	0.384	0.339	0.432	SUBCLONAL	1	TRUE	1	0.825164221615852	2		288	505	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178461	56178461	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0050546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	69	300	0	ENST00000399503.3:c.3434del	p.Thr1145LysfsTer3	p.T1145Kfs*3	ENST00000399503	NM_005921.1	1145	aCa/aa	14/20	1	2	FACETS	0.479	0.42	0.542	0.479	0.42	0.542	SUBCLONAL	1	TRUE	1	0.825164221615852	2		300	349	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0050547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	235	328	0				ENST00000310581	NM_198253.2	-/1132			0.696952604775202	5	FACETS	1	0.969	1	0.701	0.658	0.745	CLONAL	2	TRUE	2	0.696952604775202	5		328	656	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879871	44879871	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	173	218	0	ENST00000377967.4:c.460C>T	p.Gln154Ter	p.Q154*	ENST00000377967	NM_021140.2	154	Cag/Tag	6/29	0.476341861670809	2	FACETS	0.937	0.886	0.986			1	CLONAL	2	TRUE	NA	0.696952604775202	2		218	265	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397742	49397742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552757	NA	P-0050547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	323	547	0	ENST00000418115.1:c.482C>T	p.Ala161Val	p.A161V	ENST00000418115	NM_001664.2	161	gCa/gTa	5/5	0.674548409184683	4	FACETS	0.887	0.84	0.934	0.887	0.84	0.934	CLONAL	2	TRUE	2	0.696952604775202	4		547	887	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564895	226564895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	392	458	0	ENST00000366794.5:c.1855G>A	p.Glu619Lys	p.E619K	ENST00000366794	NM_001618.3	619	Gaa/Aaa	13/23	0.596831793071194	4	FACETS	0.875	0.839	0.911	0.875	0.839	0.911	CLONAL	3	TRUE	1	0.696952604775202	4		458	727	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378579	25378579	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	74	437	0	ENST00000311936.3:c.419del	p.Pro140LeufsTer20	p.P140Lfs*20	ENST00000311936	NM_004985.3	140	cCt/ct	4/5	0.696952604775202	4	FACETS	0.702	0.616	0.795	0.176	0.154	0.199	SUBCLONAL	1	TRUE	0	0.696952604775202	4		437	513	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145605	24145605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	349	652	1	ENST00000263121.7:c.624G>A	p.Met208Ile	p.M208I	ENST00000263121	NM_003073.3	208	atG/atA	5/9	0.586561000802644	4	FACETS	0.952	0.905	0.999	0.952	0.905	0.999	CLONAL	2	TRUE	2	0.696952604775202	4		653	893	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151167676	151167676	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	270	324	0	ENST00000262187.5:c.443C>G	p.Ser148Cys	p.S148C	ENST00000262187	NM_005614.3	148	tCt/tGt	7/8	0.261205731877754	5	FACETS	1	0.974	1	1	0.974	1	INDETERMINATE	3	TRUE	2	0.696952604775202	5		324	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576851	7576851	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0050548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	204	621	0	ENST00000269305.4:c.993+2T>G		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.302911358351299	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.404790908143909	1		621	783	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539210	187539210	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	134	423	0	ENST00000441802.2:c.8530G>C	p.Val2844Leu	p.V2844L	ENST00000441802	NM_005245.3	2844	Gtt/Ctt	10/27	1	2	FACETS	0.981	0.893	1	0.981	0.893	1	CLONAL	1	TRUE	1	0.404790908143909	2		423	675	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0050549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	416	662	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.490657337665912	4	FACETS	0.879	0.845	0.912	1	0.994	1	CLONAL	4	TRUE	1	0.490657337665912	4		662	719	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs79184941	NA	P-0050549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	82	395	2	ENST00000358487.5:c.755C>T	p.Ser252Leu	p.S252L	ENST00000358487	NM_000141.4	252	tCg/tTg	7/18	0.444403484573596	3	FACETS	0.925	0.819	1	0.462	0.409	0.519	CLONAL	1	TRUE	1	0.490657337665912	3		397	450	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259012	153259013	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0050549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	71	272	0	ENST00000281708.4:c.802_803del	p.Met268AspfsTer18	p.M268Dfs*18	ENST00000281708	NM_033632.3	268	ATg/g	5/12	1	2	FACETS	0.76	0.667	0.859	0.76	0.667	0.859	SUBCLONAL	1	TRUE	1	0.490657337665912	2		272	381	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225674	26225674	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	152	769	0	ENST00000360408.1:c.292G>A	p.Glu98Lys	p.E98K	ENST00000360408	NM_003532.2	98	Gag/Aag	1/1	0.434880306429596	3	FACETS	0.968	0.886	1	0.323	0.295	0.352	CLONAL	1	TRUE	0	0.490657337665912	3		769	797	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759951	63759951	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs758963278	NA	P-0050549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	85	366	0	ENST00000279873.7:c.604C>G	p.Leu202Val	p.L202V	ENST00000279873	NM_032199.2	202	Cta/Gta	4/10	0.444403484573596	3	FACETS	0.972	0.863	1	0.486	0.431	0.544	CLONAL	1	TRUE	1	0.490657337665912	3		366	444	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50483683	50483683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	89	399	0	ENST00000394963.4:c.788C>T	p.Thr263Ile	p.T263I	ENST00000394963	NM_003076.4	263	aCt/aTt	7/13	0.365736506562012	1	FACETS	0.668	0.596	0.744	0.668	0.596	0.744	SUBCLONAL	1	TRUE	0	0.490657337665912	1		399	410	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628255	90628256	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0050549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	189	782	1	ENST00000330062.3:c.1155_1156delinsAA	p.Asp386Asn	p.D386N	ENST00000330062	NM_002168.2	385	ctGGat/ctAAat	9/11	0.195134024154671	3	FACETS	0.772	0.718	0.829	0.772	0.718	0.829	INDETERMINATE	2	TRUE	1	0.490657337665912	3		783	621	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349430	89349430	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	257	783	0	ENST00000301030.4:c.3520G>C	p.Glu1174Gln	p.E1174Q	ENST00000301030	NM_001256183.1	1174	Gag/Cag	9/13	0.102986415222246	6	FACETS	1	0.988	1	0.798	0.749	0.848	INDETERMINATE	2	TRUE	3	0.490657337665912	6		783	867	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359726	40359726	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	414	344	0	ENST00000293328.3:c.1927C>G	p.Leu643Val	p.L643V	ENST00000293328	NM_012448.3	643	Ctg/Gtg	16/19	0.490657337665912	3	FACETS	1	0.98	1			1	CLONAL	3	TRUE	NA	0.490657337665912	3		344	682	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164622	36164622	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	169	499	0	ENST00000300305.3:c.1253T>C	p.Met418Thr	p.M418T	ENST00000300305		418	aTg/aCg	8/8	0.43412183438788	2	FACETS	0.931	0.869	0.994	0.931	0.869	0.994	CLONAL	2	TRUE	0	0.490657337665912	2		499	370	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253832	153253832	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	89	293	0	ENST00000281708.4:c.901del	p.Leu301CysfsTer41	p.L301Cfs*41	ENST00000281708	NM_033632.3	301	Ctg/tg	6/12	1	2	FACETS	0.902	0.805	1	0.902	0.805	1	CLONAL	1	TRUE	1	0.490657337665912	2		293	402	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856043	151856043	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	105	497	0	ENST00000262189.6:c.11575G>C	p.Glu3859Gln	p.E3859Q	ENST00000262189	NM_170606.2	3859	Gag/Cag	44/59	0.463550825297133	3	FACETS	0.72	0.645	0.8	0.36	0.322	0.4	SUBCLONAL	1	TRUE	1	0.490657337665912	3		497	740	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74868218	74868228	+	frameshift_variant	Frame_Shift_Del	DEL	CATCAGATGAT	CATCAGATGAT	-	novel	NA	P-0050549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	24	174	0	ENST00000284811.8:c.66_76del	p.Ile22MetfsTer3	p.I22Mfs*3	ENST00000284811		22	atATCATCTGATGgc/atgc	3/4	0.102986415222246	6	FACETS	0.7	0.55	0.872	0.233	0.183	0.291	INDETERMINATE	1	TRUE	3	0.490657337665912	6		174	277	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0050565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	529	656	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.740776825230052	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	FALSE	0	0.740776825230052	2		656	699	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609710	28609710	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs202109868	NA	P-0050565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	465	836	0	ENST00000241453.7:c.1519A>G	p.Ile507Val	p.I507V	ENST00000241453	NM_004119.2	507	Ata/Gta	12/24	0.73393512566647	2	FACETS	0.964	0.935	0.992	0.964	0.935	0.992	CLONAL	2	FALSE	0	0.740776825230052	2		836	651	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789696	3789696	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs761058155	NA	P-0050565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	188	615	0	ENST00000262367.5:c.4163C>G	p.Ser1388Cys	p.S1388C	ENST00000262367	NM_004380.2	1388	tCt/tGt	25/31	1	2	FACETS	0.935	0.87	1	0.935	0.87	1	CLONAL	1	FALSE	1	0.740776825230052	2		615	543	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205277	38205277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775297532	NA	P-0050565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	3810	1112	4	ENST00000317025.8:c.413C>T	p.Ser138Leu	p.S138L	ENST00000317025	NM_023034.1	138	tCg/tTg	2/24	0.740776825230052	15	FACETS	0.982	0.974	0.991			1	CLONAL	13	FALSE	NA	0.740776825230052	15		1116	4684	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939531	71939531	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755641145	NA	P-0050565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	303	884	0	ENST00000298229.2:c.386G>A	p.Arg129Gln	p.R129Q	ENST00000298229	NM_001567.3	129	cGg/cAg	3/28	0.740776825230052	4	FACETS	1	0.97	1	0.524	0.493	0.557	CLONAL	1	FALSE	2	0.740776825230052	4		884	1358	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148635	119148915	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTCATTGGAACCCATTGACTAGATTAGTGAATTTGTGTGTATGTGGTTTCACTTTAAACCCTGGAGCTTAAAATAGGACCCAGACTAGATGCTTTCTGGTTTAATAAAAAATAAACCACTGTTGTGACATTTTTATATAAGCAAAATTTGTATAGGAAACAAGTCTTCACTTTTTCTGTTAACATTTATAATTGCAGTTATTTATTCAACTAATAGTCTTTTAATTTTTTTTAATCAAAGGAACAATATGAATTATACTGTGAGATGGGCTCCACATTCC	ATTCATTGGAACCCATTGACTAGATTAGTGAATTTGTGTGTATGTGGTTTCACTTTAAACCCTGGAGCTTAAAATAGGACCCAGACTAGATGCTTTCTGGTTTAATAAAAAATAAACCACTGTTGTGACATTTTTATATAAGCAAAATTTGTATAGGAAACAAGTCTTCACTTTTTCTGTTAACATTTATAATTGCAGTTATTTATTCAACTAATAGTCTTTTAATTTTTTTTAATCAAAGGAACAATATGAATTATACTGTGAGATGGGCTCCACATTCC	-	novel	NA	P-0050565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	44	155	0	ENST00000264033.4:c.1095+82_1136del		p.X365_splice	ENST00000264033	NM_005188.3	365		8/16	0.740776825230052	4	FACETS	0.766	0.647	0.896	0.383	0.323	0.448	SUBCLONAL	1	FALSE	2	0.740776825230052	4		155	270	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788659	3788659	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	173	534	1	ENST00000262367.5:c.4295C>G	p.Ser1432Cys	p.S1432C	ENST00000262367	NM_004380.2	1432	tCt/tGt	26/31	1	2	FACETS	0.86	0.797	0.925	0.86	0.797	0.925	CLONAL	1	FALSE	1	0.740776825230052	2		535	543	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789702	3789702	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	183	592	0	ENST00000262367.5:c.4157C>T	p.Ser1386Phe	p.S1386F	ENST00000262367	NM_004380.2	1386	tCt/tTt	25/31	1	2	FACETS	0.936	0.87	1	0.936	0.87	1	CLONAL	1	FALSE	1	0.740776825230052	2		592	528	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155275	185155275	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	720	569	0	ENST00000265026.3:c.516G>T	p.Gln172His	p.Q172H	ENST00000265026	NM_004721.4	172	caG/caT	3/14	0.740776825230052	6	FACETS	1	0.995	1	1	0.995	1	CLONAL	4	FALSE	2	0.740776825230052	6		569	1096	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800534	32800534	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	391	915	2	ENST00000374899.4:c.1013G>T	p.Gly338Val	p.G338V	ENST00000374899	NM_018833.2	338	gGg/gTg	6/12	0.321110092982241	5	FACETS	1	0.993	1	0.798	0.761	0.835	INDETERMINATE	2	FALSE	2	0.740776825230052	5		917	931	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92244563	92244563	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	124	496	0	ENST00000265734.4:c.872C>G	p.Ala291Gly	p.A291G	ENST00000265734	NM_001259.6	291	gCc/gGc	8/8	0.532871022427272	6	FACETS	1	0.912	1	0.336	0.304	0.37	CLONAL	1	FALSE	3	0.740776825230052	6		496	824	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275885	38275885	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2530	362	629	1	ENST00000425967.3:c.1384G>T	p.Ala462Ser	p.A462S	ENST00000425967	NM_001174067.1	462	Gct/Tct	11/19	0.740776825230052	15	FACETS	0.983	0.926	1			1	CLONAL	2	FALSE	NA	0.740776825230052	15		630	2892	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0050566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	385	240	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.562795915979774	3	FACETS	0.917	0.882	0.952	1	0.996	1	CLONAL	3	FALSE	1	0.561706745748239	3		240	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0050566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	740	662	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	3	FALSE	NA	0.561706745748239	2		662	870	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624229	89624229	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0050566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	12	190	0	ENST00000371953.3:c.3G>A	p.Met1?	p.M1?	ENST00000371953	NM_000314.4	1	atG/atA	1/9	0.258593526768917	0	FACETS	0.136	0.095	0.185			1	INDETERMINATE	1	FALSE	0	0.561706745748239	0		190	138	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624270	89624270	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs398123324	NA	P-0050566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	40	439	0	ENST00000371953.3:c.44G>C	p.Arg15Thr	p.R15T	ENST00000371953	NM_000314.4	15	aGa/aCa	1/9	0.258593526768917	0	FACETS	0.185	0.154	0.22			1	INDETERMINATE	1	FALSE	0	0.561706745748239	0		439	337	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653674	89653781	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	ATAGTGGGGAAAACTTTCTTTTCATAACTAGCTAATGTTTTAAAAAGTATTCTTTTAGTTTGATTGCTGCATATTTCAGATATTTCTTTCCTTAACTAAAGTACTCAG	ATAGTGGGGAAAACTTTCTTTTCATAACTAGCTAATGTTTTAAAAAGTATTCTTTTAGTTTGATTGCTGCATATTTCAGATATTTCTTTCCTTAACTAAAGTACTCAG	-	novel	NA	P-0050566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	10	139	0	ENST00000371953.3:c.80-105_82del		p.X27_splice	ENST00000371953	NM_000314.4	27			0.258593526768917	0	FACETS	0.119	0.081	0.167			1	INDETERMINATE	1	FALSE	0	0.561706745748239	0		139	131	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919281	48919281	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs587778870	NA	P-0050566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	39	246	0	ENST00000267163.4:c.446C>G	p.Ser149Ter	p.S149*	ENST00000267163	NM_000321.2	149	tCa/tGa	4/27	0.561706745748239	1	FACETS	0.344	0.286	0.408	0.344	0.286	0.408	SUBCLONAL	1	FALSE	0	0.561706745748239	1		246	290	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566125	95566125	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	33	363	0	ENST00000393063.1:c.4198G>C	p.Asp1400His	p.D1400H	ENST00000393063	NM_030621.3	1400	Gat/Cat	23/28	1	2	FACETS	0.289	0.235	0.35	0.289	0.235	0.35	SUBCLONAL	1	FALSE	1	0.561706745748239	2		363	406	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347179	347179	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	109	691	0	ENST00000262320.3:c.1832C>A	p.Ser611Ter	p.S611*	ENST00000262320	NM_003502.3	611	tCg/tAg	7/11	0.562795915979774	1	FACETS	0.559	0.504	0.617	0.559	0.504	0.617	SUBCLONAL	1	FALSE	0	0.561706745748239	1		691	499	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786117	3786117	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	29	783	0	ENST00000262367.5:c.4648G>C	p.Glu1550Gln	p.E1550Q	ENST00000262367	NM_004380.2	1550	Gaa/Caa	28/31	0.562795915979774	1	FACETS	0.141	0.112	0.173	0.141	0.112	0.173	SUBCLONAL	1	FALSE	0	0.561706745748239	1		783	527	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136252	202136252	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	77	602	0	ENST00000358485.4:c.496C>G	p.Gln166Glu	p.Q166E	ENST00000358485	NM_001080125.1	166	Cag/Gag	3/9	0.1848949399309	6	FACETS	0.566	0.495	0.642			1	INDETERMINATE	1	FALSE	NA	0.561706745748239	6		602	1029	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983016	149983016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326200282	NA	P-0050566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	80	690	0	ENST00000253339.5:c.3242G>A	p.Arg1081Gln	p.R1081Q	ENST00000253339		1081	cGa/cAa	7/7	1	2	FACETS	0.409	0.36	0.462	0.409	0.36	0.462	SUBCLONAL	1	FALSE	1	0.561706745748239	2		690	696	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415027	116415027	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	136	642	0	ENST00000397752.3:c.3121G>A	p.Asp1041Asn	p.D1041N	ENST00000397752	NM_000245.2	1041	Gat/Aat	15/21	0.562795915979774	3	FACETS	0.684	0.621	0.75			1	SUBCLONAL	1	FALSE	NA	0.561706745748239	3		642	907	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	143	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.437914866445512	3	FACETS	0.838	0.778	0.899	1	0.985	1	CLONAL	3	TRUE	1	0.460274494623814	3		327	304	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262661	16262661	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	197	416	0	ENST00000375759.3:c.9926G>T	p.Gly3309Val	p.G3309V	ENST00000375759	NM_015001.2	3309	gGc/gTc	11/15	0.453995186414395	4	FACETS	0.938	0.873	1	0.938	0.873	1	CLONAL	2	TRUE	2	0.460274494623814	4		416	666	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28605733	28605733	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0050568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	256	642	0	ENST00000253063.3:c.1337A>T	p.His446Leu	p.H446L	ENST00000253063	NM_031459.4	446	cAc/cTc	9/10	0.453995186414395	4	FACETS	0.992	0.931	1	0.992	0.931	1	CLONAL	2	TRUE	2	0.460274494623814	4		642	819	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161298233	161298233	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	307	481	0	ENST00000367975.2:c.125G>C	p.Trp42Ser	p.W42S	ENST00000367975	NM_003001.3	42	tGg/tCg	3/6	0.460274494623814	6	FACETS	1	0.963	1	1	0.963	1	CLONAL	4	TRUE	2	0.460274494623814	6		481	631	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195544	102195544	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs922637067	NA	P-0050568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	162	548	0	ENST00000263464.3:c.304G>T	p.Val102Phe	p.V102F	ENST00000263464	NM_001165.4	102	Gtt/Ttt	2/9	0.460274494623814	3	FACETS	0.844	0.78	0.91	0.844	0.78	0.91	CLONAL	2	TRUE	1	0.460274494623814	3		548	513	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641068	23641068	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	126	733	1	ENST00000261584.4:c.2407G>T	p.Asp803Tyr	p.D803Y	ENST00000261584	NM_024675.3	803	Gac/Tac	5/13	0.460274494623814	4	FACETS	0.812	0.734	0.894	0.271	0.244	0.298	CLONAL	1	TRUE	1	0.460274494623814	4		734	985	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028689	12028689	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0050568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	114	448	0	ENST00000353533.5:c.891+1G>A		p.X297_splice	ENST00000353533	NM_003010.3	297			0.460274494623814	3	FACETS	0.828	0.753	0.905	0.828	0.753	0.905	CLONAL	2	TRUE	1	0.460274494623814	3		448	368	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221266	1221266	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	444	730	0	ENST00000326873.7:c.789del	p.Leu263PhefsTer24	p.L263Ffs*24	ENST00000326873	NM_000455.4	263	ttG/tt	6/10	0.447422875775656	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	0	0.460274494623814	3		730	775	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602334	10602334	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	461	660	0	ENST00000171111.5:c.1244G>T	p.Arg415Leu	p.R415L	ENST00000171111	NM_203500.1	415	cGc/cTc	3/6	0.447422875775656	3	FACETS	0.973	0.937	1	0.973	0.937	1	CLONAL	3	TRUE	0	0.460274494623814	3		660	844	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143044483	143044484	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	A	novel	NA	P-0050568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	75	480	0	ENST00000262992.4:c.1978_1979delinsT	p.Gly660CysfsTer2	p.G660Cfs*2	ENST00000262992	NM_001101669.1	660	GGg/Tg	18/24	0.432039786401744	4	FACETS	0.878	0.779	0.982	0.878	0.779	0.982	CLONAL	2	TRUE	2	0.460274494623814	4		480	271	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435639	149435639	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0050568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	258	649	0	ENST00000286301.3:c.2504A>G	p.Gln835Arg	p.Q835R	ENST00000286301	NM_005211.3	835	cAg/cGg	19/22	0.412481264271496	5	FACETS	0.969	0.908	1	0.646	0.605	0.688	CLONAL	2	TRUE	2	0.460274494623814	5		649	978	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518172	8518172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	205	518	0	ENST00000356435.5:c.1219C>T	p.Pro407Ser	p.P407S	ENST00000356435		407	Cct/Tct	10/35	0.328166942462263	4	FACETS	0.928	0.864	0.993	0.928	0.864	0.993	CLONAL	2	TRUE	2	0.460274494623814	4		518	701	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349204	70349204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	125	717	1	ENST00000374080.3:c.3616C>T	p.His1206Tyr	p.H1206Y	ENST00000374080		1206	Cac/Tac	26/45	0.460274494623814	3	FACETS	0.864	0.783	0.95	0.432	0.391	0.475	CLONAL	1	TRUE	1	0.460274494623814	3		718	773	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041266	47041266	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0050569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	552	711	0	ENST00000377604.3:c.1693+1G>A		p.X565_splice	ENST00000377604	NM_001204468.1	565			NA	2	FACETS	0.699	0.67	0.728			1	INDETERMINATE	1	TRUE	NA	0.979012896252797	2		711	1613	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845580	151845580	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1287135873	NA	P-0050569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	2342	652	0	ENST00000262189.6:c.13432C>T	p.Arg4478Ter	p.R4478*	ENST00000262189	NM_170606.2	4478	Cga/Tga	52/59	0.979012896252797	2	FACETS	1	0.999	1	1	0.999	1	CLONAL	2	TRUE	0	0.979012896252797	2		652	2377	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534307	187534307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375308616	NA	P-0050569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	260	594	0	ENST00000441802.2:c.9419C>T	p.Pro3140Leu	p.P3140L	ENST00000441802	NM_005245.3	3140	cCg/cTg	13/27	0.755711437745914	1	FACETS	0.208	0.194	0.222	0.208	0.194	0.222	SUBCLONAL	1	TRUE	0	0.979012896252797	1		594	1304	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125033	46125034	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	492	307	0	ENST00000334344.6:c.222dup	p.Glu75ArgfsTer10	p.E75Rfs*10	ENST00000334344	NM_152641.2	74	gaa/gAaa	3/21	0.613719588470358	1	FACETS	0.712	0.69	0.733	0.712	0.69	0.733	SUBCLONAL	1	TRUE	0	0.979012896252797	1		307	721	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41197711	41197711	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs80357322	NA	P-0050569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	1253	651	0	ENST00000357654.3:c.5576C>G	p.Pro1859Arg	p.P1859R	ENST00000357654	NM_007294.3	1859	cCc/cGc	23/23	0.488648261367229	1	FACETS	0.703	0.689	0.717	0.703	0.689	0.717	INDETERMINATE	1	TRUE	0	0.979012896252797	1		651	1858	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118943	61118943	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	806	530	0	ENST00000295025.8:c.136A>G	p.Thr46Ala	p.T46A	ENST00000295025	NM_002908.2	46	Aca/Gca	2/11	0.580297881117124	1	FACETS	0.67	0.653	0.687	0.67	0.653	0.687	INDETERMINATE	1	TRUE	0	0.979012896252797	1		530	1254	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903800	41903800	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	443	652	0	ENST00000372991.4:c.757G>A	p.Glu253Lys	p.E253K	ENST00000372991	NM_001760.3	253	Gag/Aag	5/5	0.580297881117124	1	FACETS	0.348	0.331	0.364	0.348	0.331	0.364	INDETERMINATE	1	TRUE	0	0.979012896252797	1		652	1329	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741238	145741238	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0050569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	832	668	0	ENST00000428558.2:c.1168T>C	p.Phe390Leu	p.F390L	ENST00000428558	NM_004260.3	390	Ttt/Ctt	6/22	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.979012896252797	2		668	1664	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0050618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	212	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.486446619919803	6	FACETS	1	0.977	1	1	0.977	1	CLONAL	4	TRUE	2	0.486446619919803	6		327	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0050618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	213	809	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.39253939208395	3	FACETS	0.95	0.898	1	0.95	0.898	1	CLONAL	3	TRUE	0	0.486446619919803	3		809	382	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022913	27022938	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGCCGCCGCCAGCAGCCTGGGCAA	CCCGCCGCCGCCAGCAGCCTGGGCAA	-	rs797045262	NA	P-0050618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	27	24	0	ENST00000324856.7:c.31_56del	p.Ser11AlafsTer91	p.S11Afs*91	ENST00000324856	NM_006015.4	7	CCCGCCGCCGCCAGCAGCCTGGGCAAc/c	1/20	0.486446619919803	4	FACETS	1	0.922	1	1	0.922	1	CLONAL	2	TRUE	2	0.486446619919803	4		24	67	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772211	68772220	+	frameshift_variant	Frame_Shift_Del	DEL	GCTCTGCCAG	GCTCTGCCAG	CA	novel	NA	P-0050619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	153	659	2	ENST00000261769.5:c.60_69delinsCA	p.Trp20CysfsTer11	p.W20Cfs*11	ENST00000261769	NM_004360.3	20	tgGCTCTGCCAG/tgCA	2/16	0.43777701265467	1	FACETS	0.924	0.849	1	0.924	0.849	1	CLONAL	1	TRUE	0	0.43777701265467	1		661	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0050619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	203	590	1	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.43777701265467	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.43777701265467	1		591	700	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0050619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	139	240	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.43777701265467	3	FACETS	0.96	0.883	1	0.96	0.883	1	CLONAL	2	TRUE	1	0.43777701265467	3		240	403	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	63	468	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.331349067385676	2		468	340	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217230	11217230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205165	NA	P-0050620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	107	581	0	ENST00000361445.4:c.4448G>A	p.Cys1483Tyr	p.C1483Y	ENST00000361445	NM_004958.3	1483	tGc/tAc	30/58	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.331349067385676	2		581	603	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11018787	11018787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	140	863	1	ENST00000327064.4:c.419G>A	p.Arg140Gln	p.R140Q	ENST00000327064	NM_199141.1	140	cGg/cAg	3/16	1	2	FACETS	0.998	0.909	1	0.998	0.909	1	CLONAL	1	TRUE	1	0.331349067385676	2		864	847	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653173	29653174	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0050620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	108	334	0	ENST00000356175.3:c.5109_5110del	p.Lys1704ThrfsTer31	p.K1704Tfs*31	ENST00000356175	NM_000267.3	1703	cAG/c	36/57	0.331349067385676	2	FACETS	0.991	0.9	1	0.991	0.9	1	CLONAL	2	TRUE	0	0.331349067385676	2		334	329	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1327763	1327763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	110	604	0	ENST00000400841.2:c.118G>A	p.Glu40Lys	p.E40K	ENST00000400841		40	Gaa/Aaa	2/6	0.193554989501217	2	FACETS	0.988	0.889	1			1	INDETERMINATE	1	TRUE	NA	0.331349067385676	2		604	672	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	99	468	0				ENST00000310581	NM_198253.2	-/1132			0.225246818178937	5	FACETS	0.869	0.78	0.963	0.869	0.78	0.963	CLONAL	3	TRUE	2	0.225246818178937	5		468	451	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056211	27056211	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs878853088	NA	P-0050621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	149	565	0	ENST00000324856.7:c.1207C>T	p.Gln403Ter	p.Q403*	ENST00000324856	NM_006015.4	403	Cag/Tag	2/20	0.197682782535498	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	1	0.225246818178937	3		565	696	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226573238	226573238	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	215	593	0	ENST00000366794.5:c.978G>C	p.Gln326His	p.Q326H	ENST00000366794	NM_001618.3	326	caG/caC	7/23	0.225246818178937	3	FACETS	0.847	0.789	0.907	1	0.988	1	CLONAL	3	TRUE	1	0.225246818178937	3		593	836	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0050621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	154	430	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.225246818178937	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.225246818178937	2		430	567	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438192	49438192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	256	636	0	ENST00000301067.7:c.5077C>T	p.Arg1693Trp	p.R1693W	ENST00000301067	NM_003482.3	1693	Cgg/Tgg	20/54	0.225246818178937	4	FACETS	0.855	0.8	0.911	1	0.99	1	CLONAL	3	TRUE	2	0.225246818178937	4		636	1086	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439847	49439847	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs886041406	NA	P-0050621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	164	676	0	ENST00000301067.7:c.4693+1G>T		p.X1565_splice	ENST00000301067	NM_003482.3	1565			0.225246818178937	4	FACETS	0.929	0.853	1	0.929	0.853	1	CLONAL	2	TRUE	2	0.225246818178937	4		676	960	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303921	91303921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777845306	NA	P-0050621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	87	594	0	ENST00000355112.3:c.1318G>A	p.Glu440Lys	p.E440K	ENST00000355112	NM_000057.2	440	Gag/Aag	7/22	0.197682782535498	3	FACETS	1	0.954	1	0.578	0.511	0.649	CLONAL	1	TRUE	1	0.225246818178937	3		594	744	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50827522	50827522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	118	472	1	ENST00000398568.2:c.2407C>T	p.Pro803Ser	p.P803S	ENST00000398568	NM_001042412.1	803	Ccg/Tcg	16/18	0.225246818178937	3	FACETS	0.822	0.742	0.906	0.822	0.742	0.906	CLONAL	2	TRUE	1	0.225246818178937	3		473	709	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0050621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	197	481	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.184684033242747	3	FACETS	0.854	0.792	0.917			1	CLONAL	3	TRUE	NA	0.225246818178937	3		481	760	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584772	48584772	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	111	480	0	ENST00000342988.3:c.850C>T	p.Gln284Ter	p.Q284*	ENST00000342988	NM_005359.5	284	Caa/Taa	7/12	0.205360136486349	2	FACETS	0.821	0.74	0.907	0.821	0.74	0.907	CLONAL	2	TRUE	0	0.225246818178937	2		480	600	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796616	42796616	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0050621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	93	659	0	ENST00000575354.2:c.3173C>T	p.Ser1058Leu	p.S1058L	ENST00000575354	NM_015125.3	1058	tCa/tTa	13/20	0.197682782535498	3	FACETS	1	0.947	1	0.557	0.494	0.623	CLONAL	1	TRUE	1	0.225246818178937	3		659	825	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919628	96919628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	136	617	0	ENST00000258439.3:c.635C>T	p.Ser212Leu	p.S212L	ENST00000258439	NM_001193304.2	212	tCa/tTa	4/4	0.165154055538356	4	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	2	0.225246818178937	4		617	724	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193769	106193769	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0050621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	40	316	0	ENST00000380013.4:c.4231G>T	p.Glu1411Ter	p.E1411*	ENST00000380013	NM_001127208.2	1411	Gag/Tag	10/11	0.197682782535498	3	FACETS	1	0.86	1	0.519	0.432	0.615	CLONAL	1	TRUE	1	0.225246818178937	3		316	381	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878563	151878563	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0050621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	227	628	1	ENST00000262189.6:c.6382C>T	p.Gln2128Ter	p.Q2128*	ENST00000262189	NM_170606.2	2128	Cag/Tag	36/59	0.20549765494249	3	FACETS	0.943	0.881	1	0.943	0.881	1	CLONAL	3	TRUE	0	0.225246818178937	3		629	793	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27192562	27192562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138894008	NA	P-0050621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	83	555	1	ENST00000380036.4:c.1565G>A	p.Arg522His	p.R522H	ENST00000380036	NM_000459.3	522	cGt/cAt	11/23	0.225246818178937	3	FACETS	1	0.954	1	0.582	0.513	0.655	CLONAL	1	TRUE	1	0.225246818178937	3		556	705	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0050622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	134	468	0				ENST00000310581	NM_198253.2	-/1132			0.25510575778541	3	FACETS	0.846	0.773	0.921	0.846	0.773	0.921	CLONAL	2	TRUE	1	0.373805052629685	3		468	503	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913403	NA	P-0050622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	13	327	0	ENST00000349496.5:c.110C>A	p.Ser37Tyr	p.S37Y	ENST00000349496	NM_001904.3	37	tCt/tAt	3/15	1	2	FACETS	0.149	0.105	0.202	0.149	0.105	0.202	SUBCLONAL	1	TRUE	1	0.373805052629685	2		327	468	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785546	50785546	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	114	662	0	ENST00000398568.2:c.536G>T	p.Gly179Val	p.G179V	ENST00000398568	NM_001042412.1	179	gGg/gTg	4/18	1	2	FACETS	0.798	0.719	0.882	0.798	0.719	0.882	SUBCLONAL	1	TRUE	1	0.373805052629685	2		662	764	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579489	7579489	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	118	875	1	ENST00000269305.4:c.198G>T	p.Met66Ile	p.M66I	ENST00000269305	NM_001126112.2	66	atG/atT	4/11	1	2	FACETS	0.629	0.566	0.695	0.629	0.566	0.695	SUBCLONAL	1	TRUE	1	0.373805052629685	2		876	1004	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411874	116411899	+	splice_region_variant,intron_variant	Splice_Region	DEL	ACAAGCTCTTTCTTTCTCTCTGTTTT	ACAAGCTCTTTCTTTCTCTCTGTTTT	-	novel	NA	P-0050622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	175	1035	1	ENST00000397752.3:c.2888-28_2888-3del		p.X963_splice	ENST00000397752	NM_000245.2	963			1	2	FACETS	0.837	0.77	0.908	0.837	0.77	0.908	CLONAL	1	TRUE	1	0.373805052629685	2		1036	1118	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850894	128850905	+	inframe_deletion	In_Frame_Del	DEL	CAGAACCCAGGC	CAGAACCCAGGC	-	novel	NA	P-0050623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	108	625	0	ENST00000249373.3:c.1744_1755del	p.Asn582_Gln585del	p.N582_Q585del	ENST00000249373	NM_005631.4	581	CAGAACCCAGGC/-	10/12	0.535843232091779	2	FACETS	0.783	0.706	0.864	0.392	0.353	0.432	SUBCLONAL	1	TRUE	0	0.560412218556818	2		625	492	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723457	52723457	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	129	590	5	ENST00000322088.6:c.1318G>C	p.Asp440His	p.D440H	ENST00000322088	NM_014225.5	440	Gat/Cat	11/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.418410580015624	2		595	549	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919935	50919935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1044937882	NA	P-0050624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	170	787	7	ENST00000440232.2:c.3022C>T	p.Arg1008Cys	p.R1008C	ENST00000440232	NM_002691.3	1008	Cgc/Tgc	24/27	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.418410580015624	2		794	782	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0050624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	387	826	15	ENST00000269305.4:c.503A>C	p.His168Pro	p.H168P	ENST00000269305	NM_001126112.2	168	cAc/cCc	5/11	0.418410580015624	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.418410580015624	2		841	881	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31405830	31405830	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0050624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	33	255	1	ENST00000344624.3:c.3948T>G	p.Ser1316Arg	p.S1316R	ENST00000344624		1316	agT/agG	32/33	0.409340302152546	5	FACETS	0.859	0.702	1	0.286	0.234	0.345	CLONAL	1	TRUE	2	0.418410580015624	5		256	299	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166282	7166282	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	108	721	0	ENST00000302850.5:c.1744G>T	p.Gly582Cys	p.G582C	ENST00000302850	NM_000208.2	582	Ggt/Tgt	8/22	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.24	2		721	753	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844205	68844205	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs876659503	NA	P-0050625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	93	691	2	ENST00000261769.5:c.793G>T	p.Glu265Ter	p.E265*	ENST00000261769	NM_004360.3	265	Gag/Tag	6/16	0.304554591358494	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.24	1		693	640	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241694	55241694	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	67	631	0	ENST00000275493.2:c.2142G>C	p.Lys714Asn	p.K714N	ENST00000275493	NM_005228.3	714	aaG/aaC	18/28	1	2	FACETS	0.828	0.719	0.947	0.828	0.719	0.947	CLONAL	1	TRUE	1	0.24	2		631	674	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29099515	29099515	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876659553	NA	P-0050634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	61	385	0	ENST00000328354.6:c.886G>T	p.Asp296Tyr	p.D296Y	ENST00000328354	NM_007194.3	296	Gat/Tat	8/15	1	2	FACETS	0.581	0.504	0.663	0.581	0.504	0.663	SUBCLONAL	1	TRUE	1	0.61258382709953	2		385	343	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941053	36941053	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	83	806	0	ENST00000361632.4:c.286C>G	p.Gln96Glu	p.Q96E	ENST00000361632		96	Cag/Gag	3/16	1	2	FACETS	0.93	0.823	1	0.93	0.823	1	CLONAL	1	TRUE	1	0.347983446641817	2		806	513	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203684	94203684	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0050635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	56	356	0	ENST00000323929.3:c.970G>C	p.Asp324His	p.D324H	ENST00000323929	NM_005591.3	324	Gat/Cat	9/20	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.347983446641817	2		356	287	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347625	118347625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	99	674	1	ENST00000534358.1:c.3262G>A	p.Asp1088Asn	p.D1088N	ENST00000534358	NM_005933.3	1088	Gat/Aat	4/36	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.347983446641817	2		675	563	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117376	115117382	+	frameshift_variant	Frame_Shift_Del	DEL	ACTATAA	ACTATAA	-	novel	NA	P-0050635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	51	461	0	ENST00000257566.3:c.792_798del	p.Tyr265HisfsTer15	p.Y265Hfs*15	ENST00000257566	NM_016569.3	264	ccTTATAGT/cc	4/8	1	2	FACETS	0.964	0.825	1	0.964	0.825	1	CLONAL	1	TRUE	1	0.347983446641817	2		461	304	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028154	48028154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1387534158	NA	P-0050635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	99	420	0	ENST00000234420.5:c.3032T>C	p.Ile1011Thr	p.I1011T	ENST00000234420	NM_000179.2	1011	aTt/aCt	4/10	0.327739403767517	3	FACETS	0.923	0.831	1	0.923	0.831	1	CLONAL	2	TRUE	1	0.347983446641817	3		420	362	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309661	30309661	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	83	753	0	ENST00000307677.4:c.361C>G	p.Gln121Glu	p.Q121E	ENST00000307677	NM_138578.1	121	Cag/Gag	2/3	0.327739403767517	3	FACETS	0.895	0.79	1	0.447	0.395	0.503	CLONAL	1	TRUE	1	0.347983446641817	3		753	626	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928060	178928086	+	inframe_deletion	In_Frame_Del	DEL	GCCAGTACCTCATGGATTAGAAGATTT	GCCAGTACCTCATGGATTAGAAGATTT	-	novel	NA	P-0050635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	36	598	0	ENST00000263967.3:c.1340_1366del	p.Pro447_Leu455del	p.P447_L455del	ENST00000263967	NM_006218.2	446	tgGCCAGTACCTCATGGATTAGAAGATTTg/tgg	8/21	1	2	FACETS	0.441	0.362	0.53	0.441	0.362	0.53	SUBCLONAL	1	TRUE	1	0.347983446641817	2		598	469	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38943054	38943054	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	29	431	0	ENST00000357387.3:c.4933C>G	p.Gln1645Glu	p.Q1645E	ENST00000357387	NM_152756.3	1645	Caa/Gaa	37/38	0.340485209142261	3	FACETS	0.553	0.444	0.676	0.276	0.222	0.338	SUBCLONAL	1	TRUE	1	0.347983446641817	3		431	354	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161270	56161270	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0050635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	112	409	0	ENST00000399503.3:c.1139T>A	p.Leu380Ter	p.L380*	ENST00000399503	NM_005921.1	380	tTa/tAa	5/20	0.340485209142261	3	FACETS	0.976	0.886	1	0.976	0.886	1	CLONAL	2	TRUE	1	0.347983446641817	3		409	387	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032057	26032057	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561919033	NA	P-0050635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	64	561	0	ENST00000244661.2:c.232G>A	p.Asp78Asn	p.D78N	ENST00000244661	NM_003537.3	78	Gac/Aac	1/1	0.340485209142261	3	FACETS	0.86	0.746	0.984	0.43	0.373	0.492	CLONAL	1	TRUE	1	0.347983446641817	3		561	502	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891599	151891602	+	frameshift_variant	Frame_Shift_Del	DEL	TGAT	TGAT	-	novel	NA	P-0050635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	54	422	0	ENST00000262189.6:c.4430_4433del	p.Asn1477ArgfsTer6	p.N1477Rfs*6	ENST00000262189	NM_170606.2	1477	aATCAg/ag	29/59	1	2	FACETS	0.828	0.71	0.956	0.828	0.71	0.956	CLONAL	1	TRUE	1	0.347983446641817	2		422	375	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158047	27158047	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs758187604	NA	P-0050635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	178	737	0	ENST00000380036.4:c.271G>C	p.Glu91Gln	p.E91Q	ENST00000380036	NM_000459.3	91	Gaa/Caa	2/23	0.327739403767517	3	FACETS	0.913	0.844	0.983	0.913	0.844	0.983	CLONAL	2	TRUE	1	0.347983446641817	3		737	658	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030463	47030463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781862400	NA	P-0050635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	100	857	0	ENST00000377604.3:c.238C>T	p.Arg80Cys	p.R80C	ENST00000377604	NM_001204468.1	80	Cgt/Tgt	4/24	1	2	FACETS	0.996	0.892	1	0.996	0.892	1	CLONAL	1	TRUE	1	0.347983446641817	2		857	577	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813064	76813064	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0050635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	94	700	0	ENST00000373344.5:c.6557C>G	p.Ser2186Cys	p.S2186C	ENST00000373344	NM_000489.3	2186	tCt/tGt	30/35	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.347983446641817	2		700	495	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145430	58145430	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894340	NA	P-0050638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	98	567	0	ENST00000257904.6:c.71G>T	p.Arg24Leu	p.R24L	ENST00000257904	NM_000075.3	24	cGt/cTt	2/8	0.0852111294557765	4	FACETS	1	0.971	1	0.634	0.565	0.707	INDETERMINATE	1	TRUE	2	0.25627533637547	4		567	758	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0050638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	92	596	0	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	1	2	FACETS	0.727	0.645	0.816	0.727	0.645	0.816	SUBCLONAL	1	TRUE	1	0.25627533637547	2		596	987	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0050638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	223	832	0	ENST00000397752.3:c.3028+1del		p.D1010fs	ENST00000397752	NM_000245.2	1010	Gat/at	14/21	0.178980811327152	2	FACETS	0.848	0.789	0.909	0.848	0.789	0.909	CLONAL	2	TRUE	0	0.25627533637547	2		832	1026	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155093	108155093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622654	NA	P-0050638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	60	565	0	ENST00000278616.4:c.3886C>T	p.Pro1296Ser	p.P1296S	ENST00000278616	NM_000051.3	1296	Cct/Tct	26/63	1	2	FACETS	0.773	0.665	0.889	0.773	0.665	0.889	SUBCLONAL	1	TRUE	1	0.25627533637547	2		565	606	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40498636	40498636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0050638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	53	565	1	ENST00000264657.5:c.224C>T	p.Ser75Leu	p.S75L	ENST00000264657	NM_139276.2	75	tCg/tTg	3/24	0.193228967768019	3	FACETS	0.573	0.487	0.668	0.287	0.243	0.334	SUBCLONAL	1	TRUE	1	0.25627533637547	3		566	814	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528097	29528097	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0050638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	38	376	0	ENST00000356175.3:c.1105C>T	p.Gln369Ter	p.Q369*	ENST00000356175	NM_000267.3	369	Cag/Tag	10/57	0.193228967768019	3	FACETS	0.742	0.613	0.885	0.371	0.306	0.443	SUBCLONAL	1	TRUE	1	0.25627533637547	3		376	451	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710622	114710622	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1282664682	NA	P-0050638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	54	489	1	ENST00000543371.1:c.107C>T	p.Ser36Leu	p.S36L	ENST00000543371	NM_001198531.1	36	tCg/tTg	1/14	1	2	FACETS	0.642	0.548	0.746	0.642	0.548	0.746	SUBCLONAL	1	TRUE	1	0.25627533637547	2		490	656	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618767	37618767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs957118817	NA	P-0050638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	63	617	1	ENST00000447079.4:c.443C>T	p.Ser148Leu	p.S148L	ENST00000447079	NM_015083.1	148	tCg/tTg	1/14	0.193228967768019	3	FACETS	0.646	0.557	0.742	0.323	0.278	0.371	SUBCLONAL	1	TRUE	1	0.25627533637547	3		618	859	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40447653	40447653	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0050638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	75	662	0	ENST00000345506.4:c.392G>T	p.Gly131Val	p.G131V	ENST00000345506	NM_003152.3	131	gGg/gTg	6/20	0.193228967768019	3	FACETS	0.841	0.736	0.955	0.421	0.368	0.478	CLONAL	1	TRUE	1	0.25627533637547	3		662	785	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993691	90993691	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0050638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	50	365	0	ENST00000265433.3:c.232G>T	p.Val78Phe	p.V78F	ENST00000265433	NM_002485.4	78	Gtt/Ttt	3/16	1	2	FACETS	0.795	0.675	0.926	0.795	0.675	0.926	CLONAL	1	TRUE	1	0.25627533637547	2		365	491	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5557747	5557747	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0050638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	47	431	0	ENST00000397747.3:c.761C>G	p.Ser254Ter	p.S254*	ENST00000397747	NM_025239.3	254	tCa/tGa	5/7	NA	2	FACETS	0.797	0.673	0.934			1	INDETERMINATE	1	TRUE	NA	0.25627533637547	2		431	460	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0050639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	129	240	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.272192562244684	3	FACETS	0.864	0.791	0.94	1	0.982	1	CLONAL	3	TRUE	1	0.271641663588105	3		240	416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0050639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	47	881	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	1	2	FACETS	0.407	0.342	0.479	0.407	0.342	0.479	SUBCLONAL	1	TRUE	1	0.271641663588105	2		881	851	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922694	44922694	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397514628	NA	P-0050639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	57	398	0	ENST00000377967.4:c.1555C>T	p.Arg519Ter	p.R519*	ENST00000377967	NM_021140.2	519	Cga/Tga	16/29	NA	2	FACETS	1	0.946	1			1	INDETERMINATE	1	TRUE	NA	0.271641663588105	2		398	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578501	7578502	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0050639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	151	925	0	ENST00000269305.4:c.428_429del	p.Val143AlafsTer5	p.V143Afs*5	ENST00000269305	NM_001126112.2	143	gTG/g	5/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.271641663588105	2		925	906	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549451	5549451	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146333130	NA	P-0050639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	40	809	0	ENST00000397747.3:c.478G>A	p.Val160Ile	p.V160I	ENST00000397747	NM_025239.3	160	Gtt/Att	4/7	0.272192562244684	2	FACETS	0.421	0.348	0.502	0.21	0.174	0.251	SUBCLONAL	1	TRUE	0	0.271641663588105	2		809	700	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579715	7579715	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0050639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	69	641	0	ENST00000269305.4:c.81del	p.Glu28LysfsTer16	p.E28Kfs*16	ENST00000269305	NM_001126112.2	27	ccT/cc	3/11	1	2	FACETS	0.898	0.782	1	0.898	0.782	1	CLONAL	1	TRUE	1	0.271641663588105	2		641	566	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652925	29652926	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTAG	novel	NA	P-0050639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	26	432	0	ENST00000356175.3:c.4861_4864dup	p.Val1622GlyfsTer10	p.V1622Gfs*10	ENST00000356175	NM_000267.3	1620	-/GTAG	36/57	1	2	FACETS	0.454	0.359	0.563	0.454	0.359	0.563	SUBCLONAL	1	TRUE	1	0.271641663588105	2		432	422	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805798	43805798	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0050640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	80	885	0	ENST00000372470.3:c.853+1G>A		p.X285_splice	ENST00000372470	NM_005373.2	285			0.411972865216344	6	FACETS	1	0.963	1			1	CLONAL	1	TRUE	NA	0.411972865216344	6		885	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577137	7577138	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0050640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	204	946	0	ENST00000269305.4:c.800_801del	p.Arg267GlnfsTer4	p.R267Qfs*4	ENST00000269305	NM_001126112.2	267	cGG/c	8/11	0.434323516134472	3	FACETS	0.965	0.9	1	0.965	0.9	1	CLONAL	2	TRUE	1	0.411972865216344	3		946	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0050642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	225	590	1	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.509123789367193	1	FACETS	0.908	0.849	0.968	0.908	0.849	0.968	CLONAL	1	TRUE	0	0.509123789367193	1		591	726	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0050642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	257	413	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.509123789367193	3	FACETS	0.919	0.866	0.973			1	CLONAL	2	TRUE	NA	0.509123789367193	3		413	689	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058536	69058536	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753703	NA	P-0050642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	114	723	1	ENST00000288368.4:c.4180C>T	p.Arg1394Trp	p.R1394W	ENST00000288368	NM_024870.2	1394	Cgg/Tgg	34/40	1	2	FACETS	0.883	0.799	0.971	0.883	0.799	0.971	CLONAL	1	TRUE	1	0.509123789367193	2		724	507	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097687	27097688	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0050642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	377	729	0	ENST00000324856.7:c.3281dup	p.Gln1095AlafsTer10	p.Q1095Afs*10	ENST00000324856	NM_006015.4	1092	-/A	12/20	0.509123789367193	2	FACETS	0.903	0.862	0.944	0.903	0.862	0.944	CLONAL	2	TRUE	0	0.509123789367193	2		729	820	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	24	782	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.279802923406438	2	FACETS	0.529	0.415	0.661	0.265	0.207	0.331	SUBCLONAL	1	FALSE	0	0.279802923406438	2		787	324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	30	616	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.279802923406438	3	FACETS	0.781	0.631	0.951	0.39	0.315	0.476	CLONAL	1	FALSE	1	0.279802923406438	3		618	313	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	15	368	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	0.279802923406438	6	FACETS	0.653	0.478	0.864	0.131	0.095	0.173	SUBCLONAL	1	FALSE	1	0.279802923406438	6		368	256	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	35	250	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	0.129534084846795	4	FACETS	1	0.842	1	1	0.842	1	INDETERMINATE	2	FALSE	2	0.279802923406438	4		250	158	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	64	533	0	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.279802923406438	2		533	348	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	32	400	2	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.129534084846795	4	FACETS	0.787	0.645	0.944	0.787	0.645	0.944	INDETERMINATE	2	FALSE	2	0.279802923406438	4		402	186	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490980	56490980	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs931676601	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	32	481	0	ENST00000267101.3:c.2426A>G	p.Gln809Arg	p.Q809R	ENST00000267101	NM_001982.3	809	cAg/cGg	20/28	0.279802923406438	5	FACETS	0.806	0.654	0.977	0.403	0.327	0.489	CLONAL	1	FALSE	3	0.279802923406438	5		481	403	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	66	261	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	0.227727042238375	4	FACETS	0.835	0.734	0.941	1	0.962	1	CLONAL	3	FALSE	2	0.279802923406438	4		261	241	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	27	189	0	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	0.227727042238375	4	FACETS	0.767	0.617	0.935	0.767	0.617	0.935	CLONAL	2	FALSE	2	0.279802923406438	4		189	161	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	9	331	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.315	0.208	0.452	0.315	0.208	0.452	SUBCLONAL	1	FALSE	1	0.279802923406438	2		331	204	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968322	2968323	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762770988	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	20	573	3	ENST00000396946.4:c.1663dup	p.Arg555ProfsTer38	p.R555Pfs*38	ENST00000396946	NM_032415.4	555	cgg/cCgg	13/25	0.279802923406438	0	FACETS	0.585	0.45	0.741			1	SUBCLONAL	1	FALSE	0	0.279802923406438	0		576	176	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346884	73346884	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	44	224	1	ENST00000377767.4:c.1333del	p.Ser445HisfsTer20	p.S445Hfs*20	ENST00000377767	NM_014953.3	445	Tca/ca	9/21	0.279802923406438	3	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	FALSE	1	0.279802923406438	3		225	155	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	13	218	1	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	1	2	FACETS	0.563	0.403	0.757	0.563	0.403	0.757	SUBCLONAL	1	FALSE	1	0.279802923406438	2		219	165	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692981	89692982	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	67	388	0	ENST00000371953.3:c.469dup	p.Glu157GlyfsTer23	p.E157Gfs*23	ENST00000371953	NM_000314.4	155	-/G	5/9	0.129534084846795	4	FACETS	0.97	0.849	1	0.97	0.849	1	INDETERMINATE	2	FALSE	2	0.279802923406438	4		388	316	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739581	145739581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375100228	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	22	704	0	ENST00000428558.2:c.1870G>A	p.Val624Ile	p.V624I	ENST00000428558	NM_004260.3	624	Gtc/Atc	11/22	0.227727042238375	4	FACETS	0.559	0.433	0.706	0.28	0.216	0.353	SUBCLONAL	1	FALSE	2	0.279802923406438	4		704	360	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132522	11132522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778175819	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	22	687	0	ENST00000358026.2:c.2738C>T	p.Pro913Leu	p.P913L	ENST00000358026	NM_001128849.1	913	cCg/cTg	19/36	1	2	FACETS	0.576	0.447	0.725	0.576	0.447	0.725	SUBCLONAL	1	FALSE	1	0.279802923406438	2		687	273	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007824	45007825	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	19	0	0	ENST00000558401.1:c.276dup	p.Thr93HisfsTer2	p.T93Hfs*2	ENST00000558401	NM_004048.2	91	acc/aCcc	2/4	1	2	FACETS	0.284	0.215	0.366	0.284	0.215	0.366	SUBCLONAL	1	FALSE	1	0.279802923406438	2		0	478	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47601139	47601139	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	154	360	0	ENST00000263735.4:c.377G>A	p.Arg126Lys	p.R126K	ENST00000263735	NM_002354.2	126	aGa/aAa	3/9	0.129534084846795	4	FACETS	1	0.972	1	1	0.991	1	INDETERMINATE	3	FALSE	2	0.279802923406438	4		360	424	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215250	142215250	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs758234545	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	85	365	0	ENST00000350721.4:c.5851C>T	p.Arg1951Ter	p.R1951*	ENST00000350721	NM_001184.3	1951	Cga/Tga	34/47	0.129534084846795	4	FACETS	0.858	0.767	0.954	1	0.973	1	INDETERMINATE	3	FALSE	2	0.279802923406438	4		365	302	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178095	56178095	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374455781	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	37	212	0	ENST00000399503.3:c.3068G>A	p.Arg1023His	p.R1023H	ENST00000399503	NM_005921.1	1023	cGc/cAc	14/20	0.227727042238375	4	FACETS	1	0.917	1	1	0.917	1	CLONAL	2	FALSE	2	0.279802923406438	4		212	146	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858432	27858432	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	104	473	0	ENST00000359303.2:c.139G>C	p.Val47Leu	p.V47L	ENST00000359303	NM_003535.2	47	Gtg/Ctg	1/1	0.279802923406438	14	FACETS	0.953	0.859	1	0.397	0.358	0.438	CLONAL	5	FALSE	2	0.279802923406438	14		473	418	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691128	18691128	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	29	302	0	ENST00000266497.5:c.3239A>G	p.Tyr1080Cys	p.Y1080C	ENST00000266497		1080	tAc/tGc	23/31	0.110347323197656	0	FACETS	0.633	0.517	0.758			1	INDETERMINATE	2	FALSE	0	0.279802923406438	0		302	118	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985596	60985596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761696930	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	14	350	0	ENST00000333681.4:c.304G>A	p.Asp102Asn	p.D102N	ENST00000333681		102	Gac/Aac	2/3	1	2	FACETS	0.529	0.383	0.705	0.529	0.383	0.705	SUBCLONAL	1	FALSE	1	0.279802923406438	2		350	189	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251552	10251552	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375976847	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	51	578	0	ENST00000340748.4:c.3380C>T	p.Pro1127Leu	p.P1127L	ENST00000340748		1127	cCg/cTg	31/40	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.279802923406438	2		578	279	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253807	30253807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1447088802	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	104	460	2	ENST00000307677.4:c.647C>T	p.Thr216Met	p.T216M	ENST00000307677	NM_138578.1	216	aCg/aTg	3/3	0.253929475772495	4	FACETS	0.927	0.834	1	0.618	0.556	0.684	CLONAL	2	FALSE	1	0.279802923406438	4		462	513	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656849	45656849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199766847	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	106	486	1	ENST00000407780.3:c.307G>A	p.Val103Ile	p.V103I	ENST00000407780	NM_001283052.1	103	Gtc/Atc	3/7	NA	2	FACETS	1	0.942	1			1	INDETERMINATE	2	FALSE	NA	0.279802923406438	2		487	359	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933883	39933883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	53	623	0	ENST00000378444.4:c.716C>T	p.Thr239Ile	p.T239I	ENST00000378444	NM_001123385.1	239	aCc/aTc	4/15	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	FALSE	NA	0.279802923406438	2		623	264	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76931785	76931785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	30	270	0	ENST00000373344.5:c.3745G>A	p.Ala1249Thr	p.A1249T	ENST00000373344	NM_000489.3	1249	Gcc/Acc	10/35	0.258745903525615	0	FACETS	0.669	0.542	0.811			1	SUBCLONAL	1	FALSE	0	0.279802923406438	0		270	231	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830902	72830903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	26	391	0	ENST00000268489.5:c.5677_5678dup	p.Asp1894GlyfsTer21	p.D1894Gfs*21	ENST00000268489	NM_006885.3	1893	agg/agAGg	9/10	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	FALSE	1	0.279802923406438	2		391	145	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492828	56492829	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	269	379	0	ENST00000407977.2:c.110_111del	p.Glu37ValfsTer2	p.E37Vfs*2	ENST00000407977		37	gAG/g	2/10	0.279802923406438	2	FACETS	1	0.985	1	1	0.996	1	CLONAL	4	FALSE	0	0.279802923406438	2		379	447	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100727	8100728	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs771019738	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	26	597	3	ENST00000346208.3:c.708dup	p.Ser237GlnfsTer66	p.S237Qfs*66	ENST00000346208		234	ttc/ttCc	3/6	0.229693828162928	0	FACETS	0.744	0.594	0.912			1	CLONAL	1	FALSE	0	0.279802923406438	0		600	180	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150022	202150022	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	39	431	0	ENST00000358485.4:c.1463T>C	p.Leu488Pro	p.L488P	ENST00000358485	NM_001080125.1	488	cTg/cCg	8/9	0.129534084846795	4	FACETS	1	0.893	1	0.551	0.458	0.653	INDETERMINATE	1	FALSE	2	0.279802923406438	4		431	324	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781901	3781903	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs751071525	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	22	416	0	ENST00000262367.5:c.4764_4766del	p.Lys1588del	p.K1588del	ENST00000262367	NM_004380.2	1588	aaGAAc/aac	29/31	1	2	FACETS	0.767	0.597	0.962	0.767	0.597	0.962	CLONAL	1	FALSE	1	0.279802923406438	2		416	205	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739743	145739743	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373178405	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	67	571	0	ENST00000428558.2:c.1708C>T	p.Arg570Trp	p.R570W	ENST00000428558	NM_004260.3	570	Cgg/Tgg	11/22	0.227727042238375	4	FACETS	0.834	0.734	0.939	1	0.962	1	CLONAL	3	FALSE	2	0.279802923406438	4		571	245	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231350	5231350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370338775	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	32	570	0	ENST00000357368.4:c.2126C>T	p.Ser709Leu	p.S709L	ENST00000357368	NM_002850.3	709	tCg/tTg	14/38	0.279802923406438	0	FACETS	0.881	0.722	1			1	CLONAL	1	FALSE	0	0.279802923406438	0		570	187	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398220	25398220	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	44	279	0	ENST00000311936.3:c.99T>G	p.Asp33Glu	p.D33E	ENST00000311936	NM_004985.3	33	gaT/gaG	2/5	0.110347323197656	0	FACETS	0.989	0.837	1			1	INDETERMINATE	1	FALSE	0	0.279802923406438	0		279	229	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480133	20480133	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	16	301	0	ENST00000346618.3:c.454del	p.Thr152ProfsTer43	p.T152Pfs*43	ENST00000346618	NM_001949.4	150	ttA/tt	2/7	NA	2	FACETS	0.563	0.417	0.737			1	INDETERMINATE	1	FALSE	NA	0.279802923406438	2		301	203	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504349	149504349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139554380	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	31	597	2	ENST00000261799.4:c.1853C>T	p.Thr618Met	p.T618M	ENST00000261799	NM_002609.3	618	aCg/aTg	13/23	1	2	FACETS	0.772	0.626	0.936	0.772	0.626	0.936	CLONAL	1	FALSE	1	0.279802923406438	2		599	287	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885144	111885145	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs892433462	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	15	720	2	ENST00000341259.2:c.1038dup	p.Leu347AlafsTer38	p.L347Afs*38	ENST00000341259	NM_005475.2	344	-/G	6/8	1	2	FACETS	0.403	0.294	0.534	0.403	0.294	0.534	SUBCLONAL	1	FALSE	1	0.279802923406438	2		722	266	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992721	68992721	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs764112302	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	28	392	3	ENST00000288368.4:c.1693del	p.Ser565ArgfsTer10	p.S565Rfs*10	ENST00000288368	NM_024870.2	562	cgT/cg	16/40	0.279802923406438	0	FACETS	0.93	0.752	1			1	CLONAL	1	FALSE	0	0.279802923406438	0		395	155	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402522	139402522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1336014812	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	59	737	0	ENST00000277541.6:c.3395G>A	p.Arg1132His	p.R1132H	ENST00000277541	NM_017617.3	1132	cGc/cAc	21/34	0.110347323197656	0	FACETS	1	0.923	1			1	INDETERMINATE	1	FALSE	0	0.279802923406438	0		737	278	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	20	499	1	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	0.279802923406438	3	FACETS	0.69	0.529	0.878	0.345	0.264	0.439	SUBCLONAL	1	FALSE	1	0.279802923406438	3		500	236	SUCCESS
APC	324	MSKCC	GRCh37	5	112175773	112175773	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	23	211	0	ENST00000257430.4:c.4482A>C	p.Glu1494Asp	p.E1494D	ENST00000257430	NM_000038.5	1494	gaA/gaC	16/16	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	FALSE	1	0.279802923406438	2		211	136	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526755	31526755	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	43	460	0	ENST00000344624.3:c.285del	p.Cys96AlafsTer12	p.C96Afs*12	ENST00000344624		95	ccC/cc	2/33	0.229693828162928	0	FACETS	0.975	0.824	1			1	CLONAL	1	FALSE	0	0.279802923406438	0		460	227	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632465	3632465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762619200	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	15	761	0	ENST00000294008.3:c.5383C>T	p.Arg1795Cys	p.R1795C	ENST00000294008	NM_032444.2	1795	Cgc/Tgc	15/15	1	2	FACETS	0.462	0.338	0.611	0.462	0.338	0.611	SUBCLONAL	1	FALSE	1	0.279802923406438	2		761	232	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433960	49433960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	60	729	0	ENST00000301067.7:c.7593del	p.Ser2532LeufsTer11	p.S2532Lfs*11	ENST00000301067	NM_003482.3	2531	ccC/cc	31/54	0.279802923406438	5	FACETS	0.757	0.655	0.868	0.757	0.655	0.868	SUBCLONAL	2	FALSE	3	0.279802923406438	5		729	402	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321727	62321729	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs771771098	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	79	597	0	ENST00000360203.5:c.2351_2353del	p.Phe784del	p.F784del	ENST00000360203	NM_001283009.1	782	ccCTTc/ccc	26/35	0.267250303745935	4	FACETS	0.854	0.755	0.96	0.569	0.503	0.64	CLONAL	2	FALSE	1	0.279802923406438	4		597	423	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307913	11307913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557482604	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	32	431	0	ENST00000361445.4:c.1079G>A	p.Arg360Gln	p.R360Q	ENST00000361445	NM_004958.3	360	cGg/cAg	7/58	0.110347323197656	0	FACETS	0.719	0.588	0.866			1	INDETERMINATE	1	FALSE	0	0.279802923406438	0		431	229	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816451	32816451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760636031	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	126	531	1	ENST00000354258.4:c.1724G>A	p.Arg575His	p.R575H	ENST00000354258	NM_000593.5	575	cGc/cAc	7/11	0.279802923406438	7	FACETS	0.971	0.88	1	0.324	0.293	0.356	CLONAL	2	FALSE	1	0.279802923406438	7		532	788	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470993	25470993	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs769015785	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	25	633	0	ENST00000264709.3:c.768del	p.Thr257LeufsTer59	p.T257Lfs*59	ENST00000264709	NM_175629.2	256	ccC/cc	7/23	1	2	FACETS	0.543	0.428	0.675	0.543	0.428	0.675	SUBCLONAL	1	FALSE	1	0.279802923406438	2		633	329	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200419	138200419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778025601	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	34	403	1	ENST00000237289.4:c.1837G>A	p.Val613Met	p.V613M	ENST00000237289	NM_001270507.1	613	Gtg/Atg	7/9	0.129534084846795	4	FACETS	0.72	0.588	0.868	0.36	0.294	0.434	INDETERMINATE	1	FALSE	2	0.279802923406438	4		404	432	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681100	30681100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765107298	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	29	325	0	ENST00000376406.3:c.619G>A	p.Gly207Ser	p.G207S	ENST00000376406	NM_014641.2	207	Ggc/Agc	5/15	0.279802923406438	6	FACETS	1	0.835	1	0.209	0.167	0.255	CLONAL	1	FALSE	1	0.279802923406438	6		325	310	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50821755	50821755	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	26	267	0	ENST00000398568.2:c.2095del	p.Ile699Ter	p.I699*	ENST00000398568	NM_001042412.1	697	ctA/ct	13/18	1	2	FACETS	1	0.802	1	1	0.802	1	CLONAL	1	FALSE	1	0.279802923406438	2		267	185	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981163	201981165	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	164	685	0	ENST00000359651.3:c.246_248del	p.Lys82del	p.K82del	ENST00000359651		81	gAGAag/gag	2/8	0.279802923406438	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	FALSE	1	0.279802923406438	3		685	543	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271703	38271703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1415925468	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	44	758	5	ENST00000425967.3:c.2246G>A	p.Arg749His	p.R749H	ENST00000425967	NM_001174067.1	749	cGc/cAc	17/19	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	FALSE	1	0.279802923406438	2		763	260	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279824	46279825	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAA	rs749655240	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	15	320	0	ENST00000371998.3:c.3752_3753insACA	p.Gln1276dup	p.Q1276dup	ENST00000371998		1276	-/CAA	20/23	0.267250303745935	4	FACETS	0.69	0.505	0.91	0.23	0.168	0.304	SUBCLONAL	1	FALSE	1	0.279802923406438	4		320	199	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713667	30713667	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1332138742	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	35	403	2	ENST00000295754.5:c.992G>A	p.Gly331Asp	p.G331D	ENST00000295754	NM_003242.5	331	gGc/gAc	4/7	0.227727042238375	4	FACETS	1	0.828	1	0.503	0.414	0.604	CLONAL	1	FALSE	2	0.279802923406438	4		405	318	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347402	89347402	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	25	696	0	ENST00000301030.4:c.5548T>C	p.Tyr1850His	p.Y1850H	ENST00000301030	NM_001256183.1	1850	Tac/Cac	9/13	1	2	FACETS	0.801	0.635	0.991	0.801	0.635	0.991	CLONAL	1	FALSE	1	0.279802923406438	2		696	223	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436596	110436596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1438903340	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	49	764	0	ENST00000375856.3:c.1805G>A	p.Arg602Gln	p.R602Q	ENST00000375856	NM_003749.2	602	cGg/cAg	1/2	0.279802923406438	3	FACETS	1	0.935	1	0.594	0.505	0.691	CLONAL	1	FALSE	1	0.279802923406438	3		764	336	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255793	16255793	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	30	276	0	ENST00000375759.3:c.3058C>A	p.Pro1020Thr	p.P1020T	ENST00000375759	NM_015001.2	1020	Cct/Act	11/15	0.268720229143182	4	FACETS	1	0.91	1			1	CLONAL	1	FALSE	NA	0.279802923406438	4		276	224	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138095	64138095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	18	708	0	ENST00000334205.4:c.2018G>A	p.Trp673Ter	p.W673*	ENST00000334205	NM_003942.2	673	tGg/tAg	16/17	0.279802923406438	3	FACETS	0.571	0.43	0.737	0.285	0.215	0.369	SUBCLONAL	1	FALSE	1	0.279802923406438	3		708	257	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945645	71945645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144781166	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	48	429	0	ENST00000298229.2:c.2401C>T	p.Arg801Cys	p.R801C	ENST00000298229	NM_001567.3	801	Cgc/Tgc	21/28	1	2	FACETS	0.762	0.651	0.882	1	0.965	1	SUBCLONAL	2	FALSE	1	0.279802923406438	2		429	225	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447781	49447781	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	62	427	0	ENST00000301067.7:c.653G>A	p.Ser218Asn	p.S218N	ENST00000301067	NM_003482.3	218	aGt/aAt	5/54	0.279802923406438	5	FACETS	0.942	0.819	1	0.942	0.819	1	CLONAL	2	FALSE	3	0.279802923406438	5		427	334	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222659	69222659	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	58	409	0	ENST00000462284.1:c.632T>C	p.Ile211Thr	p.I211T	ENST00000462284	NM_002392.5	211	aTa/aCa	8/11	0.279802923406438	5	FACETS	1	0.898	1	1	0.898	1	CLONAL	2	FALSE	3	0.279802923406438	5		409	282	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906700	32906700	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs561004600	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	29	318	0	ENST00000380152.3:c.1085A>T	p.Asp362Val	p.D362V	ENST00000380152		362	gAt/gTt	10/27	0.279802923406438	3	FACETS	1	0.869	1	0.55	0.444	0.668	CLONAL	1	FALSE	1	0.279802923406438	3		318	215	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134957	41134957	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	16	185	0	ENST00000379561.5:c.671T>C	p.Ile224Thr	p.I224T	ENST00000379561	NM_002015.3	224	aTt/aCt	2/3	0.279802923406438	3	FACETS	1	0.827	1	0.572	0.427	0.74	CLONAL	1	FALSE	1	0.279802923406438	3		185	114	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437430	110437430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1434568022	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	37	454	1	ENST00000375856.3:c.971G>A	p.Arg324His	p.R324H	ENST00000375856	NM_003749.2	324	cGc/cAc	1/2	0.279802923406438	3	FACETS	1	0.915	1	0.589	0.488	0.7	CLONAL	1	FALSE	1	0.279802923406438	3		455	256	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007897	45007897	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	38	202	0	ENST00000558401.1:c.346+1del		p.W115fs	ENST00000558401	NM_004048.2	115	tGg/tg	2/4	1	2	FACETS	0.693	0.573	0.826	0.693	0.573	0.826	SUBCLONAL	1	FALSE	1	0.279802923406438	2		202	392	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779002	3779002	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1189648750	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	26	586	0	ENST00000262367.5:c.6046A>T	p.Met2016Leu	p.M2016L	ENST00000262367	NM_004380.2	2016	Atg/Ttg	31/31	1	2	FACETS	0.889	0.709	1	0.889	0.709	1	CLONAL	1	FALSE	1	0.279802923406438	2		586	209	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89828381	89828381	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779851064	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	21	341	0	ENST00000389301.3:c.2828C>T	p.Ala943Val	p.A943V	ENST00000389301	NM_000135.2	943	gCt/gTt	29/43	1	2	FACETS	0.472	0.363	0.599	0.472	0.363	0.599	SUBCLONAL	1	FALSE	1	0.279802923406438	2		341	318	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627896	37627896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	26	409	0	ENST00000447079.4:c.1811C>T	p.Pro604Leu	p.P604L	ENST00000447079	NM_015083.1	604	cCt/cTt	2/14	0.279802923406438	3	FACETS	0.609	0.482	0.754	0.304	0.241	0.377	SUBCLONAL	1	FALSE	1	0.279802923406438	3		409	348	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622168	1622168	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	30	681	0	ENST00000344749.5:c.707del	p.Phe236SerfsTer48	p.F236Sfs*48	ENST00000344749	NM_001136139.2	236	tTc/tc	10/19	0.110347323197656	0	FACETS	0.531	0.429	0.646			1	INDETERMINATE	1	FALSE	0	0.279802923406438	0		681	291	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265675	10265675	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	21	472	0	ENST00000340748.4:c.1502T>C	p.Leu501Pro	p.L501P	ENST00000340748		501	cTg/cCg	19/40	1	2	FACETS	0.682	0.527	0.862	0.682	0.527	0.862	SUBCLONAL	1	FALSE	1	0.279802923406438	2		472	220	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118601	11118601	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	11	406	0	ENST00000358026.2:c.2025G>T	p.Gln675His	p.Q675H	ENST00000358026	NM_001128849.1	675	caG/caT	14/36	1	2	FACETS	0.401	0.277	0.555	0.401	0.277	0.555	SUBCLONAL	1	FALSE	1	0.279802923406438	2		406	196	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47601162	47601162	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	110	351	0	ENST00000263735.4:c.400A>T	p.Thr134Ser	p.T134S	ENST00000263735	NM_002354.2	134	Acc/Tcc	3/9	0.129534084846795	4	FACETS	1	0.96	1	1	0.96	1	INDETERMINATE	2	FALSE	2	0.279802923406438	4		351	451	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47602421	47602421	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	20	234	0	ENST00000263735.4:c.474T>A	p.Asp158Glu	p.D158E	ENST00000263735	NM_002354.2	158	gaT/gaA	4/9	0.129534084846795	4	FACETS	0.585	0.447	0.746	0.292	0.223	0.373	INDETERMINATE	1	FALSE	2	0.279802923406438	4		234	313	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536256	41536256	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	59	354	0	ENST00000263253.7:c.1873A>G	p.Asn625Asp	p.N625D	ENST00000263253	NM_001429.3	625	Aat/Gat	9/31	1	2	FACETS	0.817	0.71	0.931	1	0.974	1	CLONAL	2	FALSE	1	0.279802923406438	2		354	258	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428463	72428463	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	40	399	0	ENST00000477973.2:c.541C>A	p.Pro181Thr	p.P181T	ENST00000477973	NM_012234.5	181	Cct/Act	2/4	0.227727042238375	4	FACETS	0.779	0.652	0.917	0.779	0.652	0.917	CLONAL	2	FALSE	2	0.279802923406438	4		399	235	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428563	72428563	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	20	211	0	ENST00000477973.2:c.441T>A	p.Asn147Lys	p.N147K	ENST00000477973	NM_012234.5	147	aaT/aaA	2/4	0.227727042238375	4	FACETS	1	0.868	1	0.598	0.461	0.755	CLONAL	1	FALSE	2	0.279802923406438	4		211	153	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456730	138456730	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	17	242	0	ENST00000289153.2:c.622-2A>C		p.X208_splice	ENST00000289153	NM_006219.2	208			0.187945404607044	0	FACETS	0.576	0.433	0.743			1	SUBCLONAL	1	FALSE	0	0.279802923406438	0		242	152	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801083	1801083	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	28	832	0	ENST00000260795.2:c.212C>A	p.Pro71His	p.P71H	ENST00000260795		71	cCc/cAc	2/17	0.258745903525615	0	FACETS	0.621	0.499	0.759			1	SUBCLONAL	1	FALSE	0	0.279802923406438	0		832	232	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947539	38947539	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	19	142	0	ENST00000357387.3:c.4141A>G	p.Met1381Val	p.M1381V	ENST00000357387	NM_152756.3	1381	Atg/Gtg	32/38	0.227727042238375	4	FACETS	0.82	0.632	1	0.82	0.632	1	CLONAL	2	FALSE	2	0.279802923406438	4		142	106	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522780	67522780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264843487	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	52	141	0	ENST00000274335.5:c.277C>T	p.Arg93Trp	p.R93W	ENST00000274335		93	Cgg/Tgg	1/15	0.227727042238375	4	FACETS	0.971	0.835	1	0.971	0.835	1	CLONAL	2	FALSE	2	0.279802923406438	4		141	245	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163539	32163539	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	64	609	0	ENST00000375023.3:c.5687A>G	p.His1896Arg	p.H1896R	ENST00000375023	NM_004557.3	1896	cAt/cGt	30/30	0.279802923406438	6	FACETS	0.951	0.828	1	0.381	0.331	0.434	CLONAL	2	FALSE	1	0.279802923406438	6		609	375	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813534	32813534	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	46	399	0	ENST00000354258.4:c.2249A>C	p.Glu750Ala	p.E750A	ENST00000354258	NM_000593.5	750	gAg/gCg	11/11	0.279802923406438	7	FACETS	1	0.947	1	0.219	0.184	0.257	CLONAL	1	FALSE	1	0.279802923406438	7		399	426	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631428	117631428	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	24	229	0	ENST00000368508.3:c.6250A>T	p.Asn2084Tyr	p.N2084Y	ENST00000368508	NM_002944.2	2084	Aat/Tat	40/43	0.279802923406438	0	FACETS	1	0.877	1			1	CLONAL	1	FALSE	0	0.279802923406438	0		229	108	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419962	152419962	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs764597512	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	31	480	0	ENST00000206249.3:c.1649A>G	p.His550Arg	p.H550R	ENST00000206249	NM_000125.3	550	cAt/cGt	8/8	0.129534084846795	4	FACETS	0.999	0.81	1	0.499	0.405	0.605	INDETERMINATE	1	FALSE	2	0.279802923406438	4		480	284	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046445	69046445	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	32	469	0	ENST00000288368.4:c.3918G>C	p.Arg1306Ser	p.R1306S	ENST00000288368	NM_024870.2	1306	agG/agC	32/40	0.279802923406438	0	FACETS	0.695	0.567	0.837			1	SUBCLONAL	1	FALSE	0	0.279802923406438	0		469	237	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738370	145738371	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	22	736	0	ENST00000428558.2:c.2614_2615del	p.Arg872AlafsTer11	p.R872Afs*11	ENST00000428558	NM_004260.3	872	AGg/g	16/22	0.227727042238375	4	FACETS	0.541	0.419	0.683	0.271	0.209	0.342	SUBCLONAL	1	FALSE	2	0.279802923406438	4		736	372	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517959	8517959	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs999374680	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	24	280	0	ENST00000356435.5:c.1432A>G	p.Thr478Ala	p.T478A	ENST00000356435		478	Act/Gct	10/35	0.279802923406438	0	FACETS	0.864	0.685	1			1	CLONAL	1	FALSE	0	0.279802923406438	0		280	143	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412319	139412319	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	50	730	1	ENST00000277541.6:c.1326G>T	p.Gln442His	p.Q442H	ENST00000277541	NM_017617.3	442	caG/caT	8/34	0.110347323197656	0	FACETS	0.9	0.769	1			1	INDETERMINATE	1	FALSE	0	0.279802923406438	0		731	286	SUCCESS
AR	367	MSKCC	GRCh37	X	66765753	66765753	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	16	832	1	ENST00000374690.3:c.765G>T	p.Glu255Asp	p.E255D	ENST00000374690	NM_000044.3	255	gaG/gaT	1/8	0.258745903525615	0	FACETS	0.406	0.3	0.531			1	SUBCLONAL	1	FALSE	0	0.279802923406438	0		833	203	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352796	70352796	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	30	502	0	ENST00000374080.3:c.4517A>C	p.Gln1506Pro	p.Q1506P	ENST00000374080		1506	cAg/cCg	32/45	0.258745903525615	0	FACETS	0.581	0.469	0.706			1	SUBCLONAL	1	FALSE	0	0.279802923406438	0		502	266	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020031	123020031	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	25	519	0	ENST00000355640.3:c.519G>A	p.Trp173Ter	p.W173*	ENST00000355640		173	tgG/tgA	2/7	0.209300869442164	3	FACETS	0.623	0.491	0.774			1	SUBCLONAL	1	FALSE	NA	0.279802923406438	3		519	327	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152857993	152857993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782742456	NA	P-0004076-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	22	294	0	ENST00000406277.2:c.622G>A	p.Glu208Lys	p.E208K	ENST00000406277	NM_152274.4	208	Gag/Aag	6/7	0.279802923406438	0	FACETS	0.809	0.647	0.983			1	CLONAL	2	FALSE	0	0.279802923406438	0		294	70	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0005071-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	131	406	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.318071483314389	2	FACETS	0.946	0.866	1	0.946	0.866	1	CLONAL	2	TRUE	0	0.342928635100011	2		406	404	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0005071-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	103	268	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.318071483314389	2	FACETS	0.899	0.814	0.988	0.899	0.814	0.988	CLONAL	2	TRUE	0	0.342928635100011	2		268	334	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856529	111856529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005071-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	57	502	1	ENST00000341259.2:c.580G>A	p.Glu194Lys	p.E194K	ENST00000341259	NM_005475.2	194	Gag/Aag	2/8	0.323070450486912	3	FACETS	0.862	0.741	0.993	0.431	0.37	0.497	CLONAL	1	TRUE	1	0.342928635100011	3		503	452	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221846	55221846	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0005071-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	86	684	1	ENST00000275493.2:c.889+1G>A		p.X297_splice	ENST00000275493	NM_005228.3	297			0.179803459971396	5	FACETS	0.948	0.838	1	0.316	0.279	0.356	INDETERMINATE	1	TRUE	2	0.342928635100011	5		685	801	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679377	29679377	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005071-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	41	278	1	ENST00000356175.3:c.7497A>T	p.Lys2499Asn	p.K2499N	ENST00000356175	NM_000267.3	2499	aaA/aaT	50/57	0.342928635100011	4	FACETS	0.756	0.63	0.895	0.378	0.315	0.448	SUBCLONAL	1	TRUE	2	0.342928635100011	4		279	425	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	432	863	7	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	1	2	FACETS	0.858	0.82	0.896	0.858	0.82	0.896	CLONAL	1	TRUE	1	0.933968041391602	2		870	1078	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835781	68835781	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060501215	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	283	506	2	ENST00000261769.5:c.377del	p.Pro126ArgfsTer89	p.P126Rfs*89	ENST00000261769	NM_004360.3	124	cgC/cg	3/16	0.933968041391602	1	FACETS	0.875	0.845	0.905	0.875	0.845	0.905	CLONAL	1	TRUE	0	0.933968041391602	1		508	369	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	211	470	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.721	0.673	0.769	0.721	0.673	0.769	SUBCLONAL	1	TRUE	1	0.933968041391602	2		472	627	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	128	214	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.91768137708681	1	FACETS	0.835	0.788	0.879	0.835	0.788	0.879	CLONAL	1	TRUE	0	0.933968041391602	1		214	175	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244155	153244156	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	83	471	0	ENST00000281708.4:c.2001dup	p.Ser668GlufsTer26	p.S668Efs*26	ENST00000281708	NM_033632.3	667	-/G	12/12	NA	2	FACETS	0.238	0.209	0.268			1	INDETERMINATE	1	TRUE	NA	0.933968041391602	2		471	747	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061334	38061334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	423	674	0	ENST00000250448.2:c.655C>A	p.Arg219Ser	p.R219S	ENST00000250448	NM_004496.3	219	Cgc/Agc	2/2	1	2	FACETS	0.964	0.922	1	0.964	0.922	1	CLONAL	1	TRUE	1	0.933968041391602	2		674	940	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	251	202	0	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.933968041391602	1		202	271	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871052	12871053	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1555085575	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	52	368	0	ENST00000228872.4:c.285dup	p.Lys96GlnfsTer29	p.K96Qfs*29	ENST00000228872	NM_004064.3	93	-/C	1/3	1	2	FACETS	0.215	0.183	0.251	0.215	0.183	0.251	SUBCLONAL	1	TRUE	1	0.933968041391602	2		368	517	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931452	131931452	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507178	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	212	317	5	ENST00000265335.6:c.2165del	p.Lys722ArgfsTer14	p.K722Rfs*14	ENST00000265335		719	ctA/ct	13/25	1	2	FACETS	0.981	0.922	1	0.981	0.922	1	CLONAL	1	TRUE	1	0.933968041391602	2		322	463	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	236	403	0	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	0.933968041391602	1	FACETS	0.858	0.824	0.89	0.858	0.824	0.89	CLONAL	1	TRUE	0	0.933968041391602	1		403	314	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905546	50905546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144979965	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	145	995	2	ENST00000440232.2:c.674G>A	p.Arg225His	p.R225H	ENST00000440232	NM_002691.3	225	cGt/cAt	6/27	1	2	FACETS	0.242	0.22	0.265	0.242	0.22	0.265	SUBCLONAL	1	TRUE	1	0.933968041391602	2		997	1283	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864850	57864850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	396	698	0	ENST00000228682.2:c.2327C>T	p.Thr776Ile	p.T776I	ENST00000228682	NM_005269.2	776	aCc/aTc	12/12	1	2	FACETS	0.998	0.954	1	0.998	0.954	1	CLONAL	1	TRUE	1	0.933968041391602	2		698	850	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437288	220437288	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1190141661	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	557	959	2	ENST00000243786.2:c.197del	p.Gly66AlafsTer61	p.G66Afs*61	ENST00000243786	NM_002191.3	64	ctG/ct	1/2	1	2	FACETS	0.902	0.867	0.936	0.902	0.867	0.936	CLONAL	1	TRUE	1	0.933968041391602	2		961	1323	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	487	804	3	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	1	2	FACETS	0.908	0.871	0.945	0.908	0.871	0.945	CLONAL	1	TRUE	1	0.933968041391602	2		807	1149	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874147	151874148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs747256476	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	207	427	16	ENST00000262189.6:c.8390dup	p.Glu2798GlyfsTer11	p.E2798Gfs*11	ENST00000262189	NM_170606.2	2797	aag/aaAg	38/59	1	2	FACETS	0.708	0.661	0.757	0.708	0.661	0.757	SUBCLONAL	1	TRUE	1	0.933968041391602	2		443	626	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421039	49421039	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123721	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	303	436	0	ENST00000301067.7:c.14710C>T	p.Arg4904Ter	p.R4904*	ENST00000301067	NM_003482.3	4904	Cga/Tga	48/54	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.933968041391602	2		436	620	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644874	67644874	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	307	512	0	ENST00000264010.4:c.143del	p.Gly48ValfsTer14	p.G48Vfs*14	ENST00000264010	NM_006565.3	47	Ggg/gg	3/12	0.933968041391602	1	FACETS	0.927	0.899	0.954	0.927	0.899	0.954	CLONAL	1	TRUE	0	0.933968041391602	1		512	378	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030338	11030340	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	306	551	0	ENST00000327064.4:c.1091_1093del	p.Glu364del	p.E364del	ENST00000327064	NM_199141.1	363	aAAGaa/aaa	9/16	1	2	FACETS	0.883	0.837	0.929	0.883	0.837	0.929	CLONAL	1	TRUE	1	0.933968041391602	2		551	742	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445095	49445095	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	174	580	0	ENST00000301067.7:c.2371del	p.Gln791ArgfsTer139	p.Q791Rfs*139	ENST00000301067	NM_003482.3	791	Cag/ag	10/54	1	2	FACETS	0.448	0.413	0.485	0.448	0.413	0.485	SUBCLONAL	1	TRUE	1	0.933968041391602	2		580	831	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466824	57466826	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	209	252	0	ENST00000371085.3:c.46_48del	p.Glu16del	p.E16del	ENST00000371085	NM_000516.4	15	GAG/-	1/13	1	2	FACETS	0.946	0.888	1	0.946	0.888	1	CLONAL	1	TRUE	1	0.933968041391602	2		252	473	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222522	2222523	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs750035555	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	488	854	0	ENST00000326181.6:c.722dup	p.Leu242AlafsTer55	p.L242Afs*55	ENST00000326181	NM_032271.2	239	tgc/tgCc	9/21	1	2	FACETS	0.942	0.904	0.98	0.942	0.904	0.98	CLONAL	1	TRUE	1	0.933968041391602	2		854	1109	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260194	16260194	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1557761571	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	336	449	1	ENST00000375759.3:c.7464del	p.Ile2489SerfsTer10	p.I2489Sfs*10	ENST00000375759	NM_015001.2	2487	Ggg/gg	11/15	1	2	FACETS	0.995	0.948	1	0.995	0.948	1	CLONAL	1	TRUE	1	0.933968041391602	2		450	723	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743580	46743580	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs888235109	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	429	582	1	ENST00000371975.4:c.1961G>A	p.Arg654His	p.R654H	ENST00000371975	NM_003579.3	654	cGc/cAc	17/18	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.933968041391602	2		583	875	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39021178	39021178	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	209	321	0	ENST00000357387.3:c.158A>G	p.Asn53Ser	p.N53S	ENST00000357387	NM_152756.3	53	aAt/aGt	3/38	1	2	FACETS	0.948	0.89	1	0.948	0.89	1	CLONAL	1	TRUE	1	0.933968041391602	2		321	472	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217260	11217260	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	86	654	0	ENST00000361445.4:c.4418A>G	p.Asp1473Gly	p.D1473G	ENST00000361445	NM_004958.3	1473	gAc/gGc	30/58	1	2	FACETS	0.21	0.186	0.237	0.21	0.186	0.237	SUBCLONAL	1	TRUE	1	0.933968041391602	2		654	875	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265810	16265810	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	357	534	0	ENST00000375759.3:c.10883T>A	p.Ile3628Asn	p.I3628N	ENST00000375759	NM_015001.2	3628	aTc/aAc	15/15	1	2	FACETS	0.928	0.884	0.972	0.928	0.884	0.972	CLONAL	1	TRUE	1	0.933968041391602	2		534	824	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724139	112724140	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	182	335	0	ENST00000369452.4:c.26_27del	p.Lys9ArgfsTer3	p.K9Rfs*3	ENST00000369452	NM_007373.3	8	gAA/g	2/9	1	2	FACETS	0.955	0.893	1	0.955	0.893	1	CLONAL	1	TRUE	1	0.933968041391602	2		335	408	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571826	64571826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	209	799	0	ENST00000312049.6:c.1813C>T	p.Arg605Trp	p.R605W	ENST00000312049	NM_130799.2	605	Cgg/Tgg	10/10	1	2	FACETS	0.403	0.374	0.434	0.403	0.374	0.434	SUBCLONAL	1	TRUE	1	0.933968041391602	2		799	1110	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518464	69518464	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318349402	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	233	326	0	ENST00000294312.3:c.181C>T	p.Arg61Cys	p.R61C	ENST00000294312	NM_005117.2	61	Cgc/Tgc	1/3	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.933968041391602	2		326	492	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500318	99500318	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	421	628	0	ENST00000268035.6:c.3751T>C	p.Tyr1251His	p.Y1251H	ENST00000268035	NM_000875.3	1251	Tat/Cat	21/21	0.933968041391602	1	FACETS	0.959	0.936	0.981	0.959	0.936	0.981	CLONAL	1	TRUE	0	0.933968041391602	1		628	501	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857148	9857148	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	231	373	0	ENST00000330684.3:c.4253del	p.Gly1418AlafsTer28	p.G1418Afs*28	ENST00000330684	NM_001134407.1	1418	gGc/gc	13/13	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.933968041391602	2		373	473	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81968128	81968128	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	208	325	0	ENST00000359376.3:c.2834A>G	p.Asp945Gly	p.D945G	ENST00000359376	NM_002661.3	945	gAc/gGc	26/33	0.933968041391602	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.933968041391602	1		325	235	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245655	41245656	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	369	557	0	ENST00000357654.3:c.1892_1893del	p.Leu631GlnfsTer4	p.L631Qfs*4	ENST00000357654	NM_007294.3	631	cTA/c	10/23	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.933968041391602	2		557	790	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120181	70120181	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	299	399	0	ENST00000245479.2:c.1183A>G	p.Thr395Ala	p.T395A	ENST00000245479	NM_000346.3	395	Acg/Gcg	3/3	1	2	FACETS	0.95	0.901	0.999	0.95	0.901	0.999	CLONAL	1	TRUE	1	0.933968041391602	2		399	674	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50138906	50138906	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	499	841	0	ENST00000246792.3:c.584A>G	p.Glu195Gly	p.E195G	ENST00000246792	NM_006270.3	195	gAa/gGa	6/6	1	2	FACETS	0.937	0.899	0.974	0.937	0.899	0.974	CLONAL	1	TRUE	1	0.933968041391602	2		841	1141	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198299713	198299713	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1559283864	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	228	363	0	ENST00000335508.6:c.11T>A	p.Ile4Asn	p.I4N	ENST00000335508	NM_012433.2	4	aTc/aAc	1/25	1	2	FACETS	0.932	0.877	0.987	0.932	0.877	0.987	CLONAL	1	TRUE	1	0.933968041391602	2		363	524	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660037	227660037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763295813	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	405	618	0	ENST00000305123.5:c.3418C>T	p.Arg1140Cys	p.R1140C	ENST00000305123	NM_005544.2	1140	Cgc/Tgc	1/2	1	2	FACETS	0.983	0.941	1	0.983	0.941	1	CLONAL	1	TRUE	1	0.933968041391602	2		618	882	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663054	227663054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	357	574	0	ENST00000305123.5:c.401G>A	p.Gly134Asp	p.G134D	ENST00000305123	NM_005544.2	134	gGc/gAc	1/2	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.933968041391602	2		574	757	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375172	31375172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774138031	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	482	771	1	ENST00000328111.2:c.569G>A	p.Arg190His	p.R190H	ENST00000328111	NM_006892.3	190	cGc/cAc	6/23	1	2	FACETS	0.999	0.96	1	0.999	0.96	1	CLONAL	1	TRUE	1	0.933968041391602	2		772	1033	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157644	106157644	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	188	280	1	ENST00000380013.4:c.2545A>G	p.Thr849Ala	p.T849A	ENST00000380013	NM_001127208.2	849	Aca/Gca	3/11	1	2	FACETS	0.982	0.92	1	0.982	0.92	1	CLONAL	1	TRUE	1	0.933968041391602	2		281	410	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967467	38967467	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	42	333	0	ENST00000357387.3:c.1123A>C	p.Thr375Pro	p.T375P	ENST00000357387	NM_152756.3	375	Act/Cct	13/38	1	2	FACETS	0.175	0.146	0.208	0.175	0.146	0.208	SUBCLONAL	1	TRUE	1	0.933968041391602	2		333	513	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441323	149441325	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	novel	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	169	591	0	ENST00000286301.3:c.1714_1716del	p.Asn572del	p.N572del	ENST00000286301	NM_005211.3	572	AAC/-	12/22	1	2	FACETS	0.439	0.404	0.476	0.439	0.404	0.476	SUBCLONAL	1	TRUE	1	0.933968041391602	2		591	824	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679966	30679966	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	324	524	0	ENST00000376406.3:c.1753A>G	p.Thr585Ala	p.T585A	ENST00000376406	NM_014641.2	585	Acc/Gcc	5/15	1	2	FACETS	0.936	0.89	0.983	0.936	0.89	0.983	CLONAL	1	TRUE	1	0.933968041391602	2		524	741	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192365	138192365	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	18	169	0	ENST00000237289.4:c.1A>G	p.Met1?	p.M1?	ENST00000237289	NM_001270507.1	1	Atg/Gtg	2/9	1	2	FACETS	0.165	0.124	0.214	0.165	0.124	0.214	SUBCLONAL	1	TRUE	1	0.933968041391602	2		169	233	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016228	150016228	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	257	415	0	ENST00000253339.5:c.478A>G	p.Asn160Asp	p.N160D	ENST00000253339		160	Aat/Gat	2/7	1	2	FACETS	0.992	0.938	1	0.992	0.938	1	CLONAL	1	TRUE	1	0.933968041391602	2		415	555	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259449	55259449	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	326	429	0	ENST00000275493.2:c.2507G>T	p.Arg836Leu	p.R836L	ENST00000275493	NM_005228.3	836	cGc/cTc	21/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.933968041391602	2		429	670	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009350	69009350	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	337	454	0	ENST00000288368.4:c.2467T>C	p.Tyr823His	p.Y823H	ENST00000288368	NM_024870.2	823	Tat/Cat	22/40	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.933968041391602	2		454	667	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741488	145741488	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1060501384	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	502	843	2	ENST00000428558.2:c.1015del	p.Leu339CysfsTer20	p.L339Cfs*20	ENST00000428558	NM_004260.3	339	Ctg/tg	5/22	1	2	FACETS	0.875	0.839	0.911	0.875	0.839	0.911	CLONAL	1	TRUE	1	0.933968041391602	2		845	1229	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224172	98224172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	167	306	0	ENST00000331920.6:c.2669C>T	p.Thr890Ile	p.T890I	ENST00000331920	NM_000264.3	890	aCc/aTc	16/24	1	2	FACETS	0.805	0.748	0.864	0.805	0.748	0.864	CLONAL	1	TRUE	1	0.933968041391602	2		306	444	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759688	133759688	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008667-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	392	692	0	ENST00000318560.5:c.2011G>T	p.Gly671Ter	p.G671*	ENST00000318560	NM_005157.4	671	Gga/Tga	11/11	1	2	FACETS	0.96	0.918	1	0.96	0.918	1	CLONAL	1	TRUE	1	0.933968041391602	2		692	874	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010103-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	14	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.802	1	1	0.802	1	CLONAL	1	TRUE	1	0.22	2		148	113	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0010103-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	16	402	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.507	0.374	0.665	0.507	0.374	0.665	SUBCLONAL	1	TRUE	1	0.22	2		402	287	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461152	120461152	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010103-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	13	372	0	ENST00000256646.2:c.5806G>T	p.Asp1936Tyr	p.D1936Y	ENST00000256646	NM_024408.3	1936	Gat/Tat	32/34	1	2	FACETS	0.875	0.628	1	0.875	0.628	1	CLONAL	1	TRUE	1	0.22	2		372	135	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652088	36652098	+	frameshift_variant	Frame_Shift_Del	DEL	CCTTGGCCTGC	CCTTGGCCTGC	-	novel	NA	P-0010103-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	14	678	0	ENST00000244741.5:c.212_222del	p.Leu71GlnfsTer14	p.L71Qfs*14	ENST00000244741	NM_000389.4	70	ggCCTTGGCCTGCcc/ggcc	2/3	1	2	FACETS	0.461	0.333	0.617	0.461	0.333	0.617	SUBCLONAL	1	TRUE	1	0.22	2		678	276	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0010183-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	109	336	0	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	1	2	FACETS	0.409	0.368	0.452	0.409	0.368	0.452	SUBCLONAL	1	TRUE	1	0.938093106656345	2		336	568	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243905	46243905	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010183-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	215	287	0	ENST00000334344.6:c.1999A>C	p.Met667Leu	p.M667L	ENST00000334344	NM_152641.2	667	Atg/Ctg	15/21	1	2	FACETS	0.996	0.938	1	0.996	0.938	1	CLONAL	1	TRUE	1	0.938093106656345	2		287	460	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341502	89341502	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1466808569	NA	P-0010183-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	186	727	0	ENST00000301030.4:c.7568G>A	p.Arg2523Gln	p.R2523Q	ENST00000301030	NM_001256183.1	2523	cGg/cAg	10/13	1	2	FACETS	0.452	0.418	0.488	0.452	0.418	0.488	SUBCLONAL	1	TRUE	1	0.938093106656345	2		727	877	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593600	55593650	+	inframe_deletion	In_Frame_Del	DEL	CAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGAC	CAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGAC	-	novel	NA	P-0010183-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	159	302	0	ENST00000288135.5:c.1667_1717del	p.Gln556_Asp572del	p.Q556_D572del	ENST00000288135	NM_000222.2	556	CAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGAC/-	11/21	1	2	FACETS	0.876	0.813	0.94	0.876	0.813	0.94	CLONAL	1	TRUE	1	0.938093106656345	2		302	387	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112025282	112025282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370545141	NA	P-0010183-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	137	342	0	ENST00000368678.4:c.467G>A	p.Arg156Gln	p.R156Q	ENST00000368678		156	cGa/cAa	6/13	0.59120119215673	1	FACETS	0.322	0.295	0.351	0.322	0.295	0.351	SUBCLONAL	1	TRUE	0	0.938093106656345	1		342	481	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051386	13051386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1328636364	NA	P-0010183-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	131	376	0	ENST00000316448.5:c.734C>T	p.Pro245Leu	p.P245L	ENST00000316448	NM_004343.3	245	cCt/cTt	6/9	1	2	FACETS	0.501	0.457	0.548	0.501	0.457	0.548	SUBCLONAL	1	TRUE	1	0.938093106656345	2		376	557	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060846	38060864	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTGCCAAGCCGTGTGCC	GGGTGCCAAGCCGTGTGCC	-	novel	NA	P-0010315-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	237	588	0	ENST00000250448.2:c.1125_1143del	p.Ala376ThrfsTer7	p.A376Tfs*7	ENST00000250448	NM_004496.3	375	ccGGCACACGGCTTGGCACCC/cc	2/2	0.754768744992388	4	FACETS	0.976	0.91	1	0.488	0.455	0.522	CLONAL	1	TRUE	2	0.806696448692544	4		588	1088	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117711004	117711004	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs752178140	NA	P-0010315-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	64	202	0	ENST00000368508.3:c.1268T>C	p.Val423Ala	p.V423A	ENST00000368508	NM_002944.2	423	gTc/gCc	12/43	0.806696448692544	3	FACETS	0.96	0.842	1	0.32	0.28	0.361	CLONAL	1	TRUE	0	0.806696448692544	3		202	232	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280287	1280287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147521473	NA	P-0010315-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	257	668	0	ENST00000310581.5:c.1936C>T	p.Arg646Cys	p.R646C	ENST00000310581	NM_198253.2	646	Cgc/Tgc	4/16	0.806696448692544	3	FACETS	0.952	0.893	1	0.476	0.446	0.507	CLONAL	1	TRUE	1	0.806696448692544	3		668	939	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420968	49421397	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTGGCAGGAGAAGGTGCCAAGGGGGAAGGGGGCGGGGAGGGTTCTTCAGGAGGTGGGGCCGAGAGCTGTCGCACATCCAGATTGGAGACATTGTAGGTATAGCTGTGCTGAGTGGGTGGCTCTGGGGCGGGGCTCTCCTGTAGGAGGGTGCCCTGTATCATTAGTGCCAGCTCCTCATCTAACTAGCTCCCTCCTTCCCCTCACCCATATGCCACCCTCCCAAAAGGCCTCCACATTCTTTGCCCTAGACAGCCTCTTTTTTCTTTTCTTTTCTTTTTTTTTTGAGACACAGTCTTGCTCTGTTGCCCAGGCTGGATCCAGTGGCACAATCTTGGCTCACTGCAACCTCTGCCTCCTGGGTTCAAGGGATTCTCATGCCTCAGCCTTTCGAGTAGCTGGGATTACAGGCACGCACCATCACGCCTGGCT	ACTGGCAGGAGAAGGTGCCAAGGGGGAAGGGGGCGGGGAGGGTTCTTCAGGAGGTGGGGCCGAGAGCTGTCGCACATCCAGATTGGAGACATTGTAGGTATAGCTGTGCTGAGTGGGTGGCTCTGGGGCGGGGCTCTCCTGTAGGAGGGTGCCCTGTATCATTAGTGCCAGCTCCTCATCTAACTAGCTCCCTCCTTCCCCTCACCCATATGCCACCCTCCCAAAAGGCCTCCACATTCTTTGCCCTAGACAGCCTCTTTTTTCTTTTCTTTTCTTTTTTTTTTGAGACACAGTCTTGCTCTGTTGCCCAGGCTGGATCCAGTGGCACAATCTTGGCTCACTGCAACCTCTGCCTCCTGGGTTCAAGGGATTCTCATGCCTCAGCCTTTCGAGTAGCTGGGATTACAGGCACGCACCATCACGCCTGGCT	-	novel	NA	P-0010315-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	294	382	0	ENST00000301067.7:c.14643+189_14781del		p.X4881_splice	ENST00000301067	NM_003482.3	4881		48/54	0.778445696540805	3	FACETS	1	0.979	1	0.694	0.664	0.725	CLONAL	2	TRUE	0	0.806696448692544	3		382	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0012098-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	97	683	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.173442038644027	2		683	816	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878083	48878117	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCCGCCGCTGCCGCCGCGGAACCCCCGGCACCG	CCGCCGCCGCTGCCGCCGCGGAACCCCCGGCACCG	-	novel	NA	P-0012098-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	59	161	0	ENST00000267163.4:c.45_79del	p.Ala16ProfsTer3	p.A16Pfs*3	ENST00000267163	NM_000321.2	12	aCCGCCGCCGCTGCCGCCGCGGAACCCCCGGCACCG/a	1/27	0.149488998704227	1	FACETS	1	0.871	1	1	0.979	1	CLONAL	2	TRUE	0	0.173442038644027	1		161	309	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242482	+	protein_altering_variant	In_Frame_Del	DEL	GGAATTAAGAGAAGCAAC	GGAATTAAGAGAAGCAAC	AAT	novel	NA	P-0012098-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	184	289	1	ENST00000275493.2:c.2235_2252delinsAAT	p.Glu746_Thr751delinsIle	p.E746_T751delinsI	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCAACa/aaAATa	19/28	0.173442038644027	12	FACETS	0.984	0.912	1			1	CLONAL	6	TRUE	NA	0.173442038644027	12		290	671	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876392	35876392	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014052-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	26	534	0	ENST00000303115.3:c.1184A>G	p.Lys395Arg	p.K395R	ENST00000303115	NM_002185.3	395	aAg/aGg	8/8	1	2	FACETS	0.125	0.098	0.156	0.125	0.098	0.156	SUBCLONAL	1	TRUE	1	0.779946630605274	2		534	533	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121609	2121609	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs745414854	NA	P-0014052-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	311	734	1	ENST00000219476.3:c.1938C>A	p.Cys646Ter	p.C646*	ENST00000219476	NM_000548.3	646	tgC/tgA	18/42	1	2	FACETS	0.97	0.919	1	0.97	0.919	1	CLONAL	1	TRUE	1	0.779946630605274	2		735	822	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130349	2130349	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397515168	NA	P-0014052-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	350	779	0	ENST00000219476.3:c.3581G>A	p.Trp1194Ter	p.W1194*	ENST00000219476	NM_000548.3	1194	tGg/tAg	30/42	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.779946630605274	2		779	873	SUCCESS
AR	367	MSKCC	GRCh37	X	66765111	66765111	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014052-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	210	540	1	ENST00000374690.3:c.123C>A	p.His41Gln	p.H41Q	ENST00000374690	NM_000044.3	41	caC/caA	1/8	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.779946630605274	2		541	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782177	NA	P-0015099-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	306	558	0	ENST00000269305.4:c.644G>C	p.Ser215Thr	p.S215T	ENST00000269305	NM_001126112.2	215	aGt/aCt	6/11	0.809545153560883	2	FACETS	0.964	0.933	0.994	0.964	0.933	0.994	CLONAL	2	TRUE	0	0.809545153560883	2		558	392	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625281	69625281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35983315	NA	P-0015099-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	192	812	1	ENST00000334134.2:c.512G>A	p.Arg171His	p.R171H	ENST00000334134	NM_005247.2	171	cGc/cAc	3/3	0.726538876777946	3	FACETS	0.919	0.853	0.988	0.46	0.426	0.494	CLONAL	1	TRUE	1	0.809545153560883	3		813	725	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015099-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	434	528	2	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	0.580993829287731	6	FACETS	1	0.99	1	0.748	0.713	0.783	CLONAL	2	TRUE	3	0.809545153560883	6		530	1252	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653849	89653859	+	frameshift_variant	Frame_Shift_Del	DEL	TATTGATGATG	TATTGATGATG	-	novel	NA	P-0015099-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	102	304	0	ENST00000371953.3:c.149_159del	p.Ile50SerfsTer9	p.I50Sfs*9	ENST00000371953	NM_000314.4	49	aaTATTGATGATGta/aata	2/9	0.809545153560883	1	FACETS	0.937	0.87	1	0.937	0.87	1	CLONAL	1	TRUE	0	0.809545153560883	1		304	160	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396959	396959	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015099-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	211	680	0	ENST00000262320.3:c.67C>A	p.Pro23Thr	p.P23T	ENST00000262320	NM_003502.3	23	Ccc/Acc	2/11	0.439476268127665	5	FACETS	1	0.99	1	0.466	0.433	0.499	INDETERMINATE	1	TRUE	2	0.809545153560883	5		680	826	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042320	16042320	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0015099-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	188	268	0	ENST00000268712.3:c.1352+2T>C		p.X451_splice	ENST00000268712	NM_006311.3	451			0.809545153560883	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.809545153560883	2		268	226	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249826	39249826	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015099-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	192	405	0	ENST00000402219.2:c.1743C>G	p.Asp581Glu	p.D581E	ENST00000402219	NM_005633.3	581	gaC/gaG	10/23	0.809545153560883	2	FACETS	1	0.935	1	0.5	0.467	0.534	CLONAL	1	TRUE	0	0.809545153560883	2		405	474	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672836	86672836	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015099-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	61	218	0	ENST00000274376.6:c.2323G>C	p.Asp775His	p.D775H	ENST00000274376	NM_002890.2	775	Gac/Cac	17/25	0.56043118349776	3	FACETS	0.571	0.494	0.653	0.285	0.247	0.327	SUBCLONAL	1	TRUE	1	0.809545153560883	3		218	371	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953040	2953040	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141751925	NA	P-0015099-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	189	689	2	ENST00000396946.4:c.2900G>A	p.Arg967His	p.R967H	ENST00000396946	NM_032415.4	967	cGc/cAc	22/25	0.805646222888233	2	FACETS	1	0.981	1	0.561	0.525	0.597	CLONAL	1	TRUE	0	0.809545153560883	2		691	416	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657039	45657039	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015099-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	44	411	0	ENST00000407780.3:c.117C>G	p.Cys39Trp	p.C39W	ENST00000407780	NM_001283052.1	39	tgC/tgG	3/7	0.413414970446851	4	FACETS	0.37	0.31	0.437	0.185	0.155	0.219	INDETERMINATE	1	TRUE	2	0.809545153560883	4		411	531	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016240-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	118	148	0				ENST00000310581	NM_198253.2	-/1132			0.251478418198611	6	FACETS	0.986	0.905	1	1	0.98	1	CLONAL	5	TRUE	2	0.251478418198611	6		148	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0016240-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	28	334	0	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	0.251478418198611	3	FACETS	0.444	0.353	0.547	0.148	0.117	0.183	SUBCLONAL	1	TRUE	0	0.251478418198611	3		334	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0016240-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	136	363	1	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.251478418198611	3	FACETS	1	0.978	1	0.804	0.735	0.875	CLONAL	2	TRUE	0	0.251478418198611	3		364	505	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47004894	47004894	+	intron_variant	Intron	SNP	G	G	C	novel	NA	P-0016240-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	86	407	0	ENST00000377604.3:c.-126+10G>C		p.*42*	ENST00000377604	NM_001204468.1	-/163			1	2	FACETS	0.994	0.88	1	0.994	0.88	1	CLONAL	1	TRUE	1	0.251478418198611	2		407	688	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288493	15288493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016240-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	51	146	0	ENST00000263388.2:c.4246G>T	p.Asp1416Tyr	p.D1416Y	ENST00000263388	NM_000435.2	1416	Gac/Tac	24/33	0.251478418198611	1	FACETS	0.785	0.674	0.903	1	0.969	1	CLONAL	2	TRUE	0	0.251478418198611	1		146	226	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151615	55151615	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016240-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	76	400	0	ENST00000257290.5:c.2401C>T	p.Gln801Ter	p.Q801*	ENST00000257290	NM_006206.4	801	Caa/Taa	17/23	0.251478418198611	1	FACETS	0.91	0.799	1	0.91	0.799	1	CLONAL	1	TRUE	0	0.251478418198611	1		400	581	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78599549	78599549	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	127	406	0	ENST00000306801.3:c.221A>G	p.Asp74Gly	p.D74G	ENST00000306801	NM_020761.2	74	gAt/gGt	2/34	0.591960073943197	3	FACETS	1	0.955	1	0.536	0.489	0.584	CLONAL	1	TRUE	1	0.778197186176093	3		406	423	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100142	157100142	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	25	94	0	ENST00000346085.5:c.1079G>C	p.Gly360Ala	p.G360A	ENST00000346085	NM_020732.3	360	gGc/gCc	1/20	1	2	FACETS	0.824	0.669	0.989	0.824	0.669	0.989	CLONAL	1	TRUE	1	0.778197186176093	2		94	78	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145662	11145662	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770839933	NA	P-0018057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	90	722	0	ENST00000358026.2:c.4024G>A	p.Glu1342Lys	p.E1342K	ENST00000358026	NM_001128849.1	1342	Gag/Aag	29/36	0.739629718322184	4	FACETS	0.43	0.38	0.483	0.215	0.19	0.242	SUBCLONAL	1	TRUE	2	0.778197186176093	4		722	957	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285879	39285879	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs144757941	NA	P-0018057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	52	307	0	ENST00000402219.2:c.280A>G	p.Ile94Val	p.I94V	ENST00000402219	NM_005633.3	94	Att/Gtt	3/23	0.746748012163286	3	FACETS	0.587	0.503	0.679	0.294	0.251	0.34	SUBCLONAL	1	TRUE	1	0.778197186176093	3		307	316	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740245	162740245	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	41	345	0	ENST00000367921.3:c.1447G>T	p.Glu483Ter	p.E483*	ENST00000367921	NM_006182.2	483	Gag/Tag	12/18	0.778197186176093	3	FACETS	0.324	0.27	0.384	0.162	0.135	0.192	SUBCLONAL	1	TRUE	1	0.778197186176093	3		345	452	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144033	11144033	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	59	616	0	ENST00000358026.2:c.3614G>C	p.Cys1205Ser	p.C1205S	ENST00000358026	NM_001128849.1	1205	tGc/tCc	26/36	0.739629718322184	4	FACETS	0.324	0.278	0.374	0.162	0.139	0.187	SUBCLONAL	1	TRUE	2	0.778197186176093	4		616	833	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050688	30050688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	31	296	0	ENST00000338641.4:c.490G>A	p.Ala164Thr	p.A164T	ENST00000338641	NM_000268.3	164	Gcc/Acc	5/16	0.771734232019071	2	FACETS	0.291	0.236	0.353	0.145	0.118	0.177	SUBCLONAL	1	TRUE	0	0.778197186176093	2		296	274	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514415	149514415	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	47	498	0	ENST00000261799.4:c.529C>G	p.Arg177Gly	p.R177G	ENST00000261799	NM_002609.3	177	Cgt/Ggt	4/23	0.778197186176093	3	FACETS	0.284	0.239	0.334	0.095	0.079	0.112	SUBCLONAL	1	TRUE	0	0.778197186176093	3		498	590	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573495	48573530	+	protein_altering_variant	In_Frame_Del	DEL	AGACAAGGTGGAGAGAGTGAAACATTTGCAAAAAGA	AGACAAGGTGGAGAGAGTGAAACATTTGCAAAAAGA	TAT	novel	NA	P-0018057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	12	174	1	ENST00000342988.3:c.79_114delinsTAT	p.Arg27_Arg38delinsTyr	p.R27_R38delinsY	ENST00000342988	NM_005359.5	27	AGACAAGGTGGAGAGAGTGAAACATTTGCAAAAAGA/TAT	2/12	0.778197186176093	3	FACETS	0.204	0.143	0.279	0.102	0.071	0.14	SUBCLONAL	1	TRUE	1	0.778197186176093	3		175	210	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0018669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	71	214	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.925	0.82	1	0.925	0.82	1	CLONAL	1	TRUE	1	0.679511924275338	2		214	226	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0018669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	932	654	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	0.679511924275338	3	FACETS	0.942	0.922	0.962	1	0.998	1	CLONAL	3	TRUE	1	0.679511924275338	3		654	1300	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845101	128845101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201246258	NA	P-0018669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	404	818	1	ENST00000249373.3:c.595C>T	p.Arg199Trp	p.R199W	ENST00000249373	NM_005631.4	199	Cgg/Tgg	3/12	1	2	FACETS	0.957	0.91	1	0.957	0.91	1	CLONAL	1	TRUE	1	0.679511924275338	2		819	1243	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176329	24176329	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1568963596	NA	P-0018669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	809	785	1	ENST00000263121.7:c.1120C>T	p.Arg374Trp	p.R374W	ENST00000263121	NM_003073.3	374	Cgg/Tgg	9/9	0.67844354984026	2	FACETS	0.988	0.964	1	0.988	0.964	1	CLONAL	2	TRUE	0	0.679511924275338	2		786	1205	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920446	114920446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	380	389	0	ENST00000543371.1:c.1387del	p.Cys463AlafsTer28	p.C463Afs*28	ENST00000543371	NM_001198531.1	463	Tgc/gc	13/14	0.679511924275338	3	FACETS	0.982	0.939	1	0.982	0.939	1	CLONAL	2	TRUE	1	0.679511924275338	3		389	763	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217572	142217572	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	189	350	1	ENST00000350721.4:c.5425T>G	p.Leu1809Val	p.L1809V	ENST00000350721	NM_001184.3	1809	Tta/Gta	32/47	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.679511924275338	2		351	536	SUCCESS
APC	324	MSKCC	GRCh37	5	112116518	112116519	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATTGGAAT	novel	NA	P-0018669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	64	208	0	ENST00000257430.4:c.566_573dup	p.Glu192TrpfsTer16	p.E192Wfs*16	ENST00000257430	NM_000038.5	188	caa/caATTGGAATa	6/16	1	2	FACETS	0.753	0.66	0.852	0.753	0.66	0.852	SUBCLONAL	1	TRUE	1	0.679511924275338	2		208	250	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500945	8500945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	166	346	0	ENST00000356435.5:c.1937C>T	p.Ser646Phe	p.S646F	ENST00000356435		646	tCc/tTc	13/35	0.67844354984026	2	FACETS	1	0.935	1	0.505	0.467	0.543	CLONAL	1	TRUE	0	0.679511924275338	2		346	484	SUCCESS
ATM	472	MSKCC	GRCh37	11	108183192	108183192	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587782274	NA	P-0018669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	90	181	0	ENST00000278616.4:c.5973A>C	p.Glu1991Asp	p.E1991D	ENST00000278616	NM_000051.3	1991	gaA/gaC	40/63	0.679511924275338	3	FACETS	1	0.928	1	0.523	0.469	0.581	CLONAL	1	TRUE	1	0.679511924275338	3		181	339	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435380	18435380	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	123	254	0	ENST00000266497.5:c.365A>C	p.Lys122Thr	p.K122T	ENST00000266497		122	aAa/aCa	1/31	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.679511924275338	2		254	354	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	110	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.758700001764559	2		148	278	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0019056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	96	343	0	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	0.749425521679773	1	FACETS	0.982	0.906	1	0.982	0.906	1	CLONAL	1	TRUE	0	0.758700001764559	1		343	160	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591076	67591076	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	78	167	0	ENST00000274335.5:c.1669C>G	p.Arg557Gly	p.R557G	ENST00000274335		557	Cga/Gga	12/15	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.758700001764559	2		167	203	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577612	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTAG	CTAG	-	novel	NA	P-0019056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	171	377	0	ENST00000269305.4:c.673-4_673-1del		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.749425521679773	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.758700001764559	1		377	249	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244900	46244902	+	inframe_deletion	In_Frame_Del	DEL	ACC	ACC	-	novel	NA	P-0019056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	84	346	0	ENST00000334344.6:c.2997_2999del	p.Pro1001del	p.P1001del	ENST00000334344	NM_152641.2	998	ggACCa/gga	15/21	0.122505159076021	1	FACETS	0.323	0.286	0.361	0.323	0.286	0.361	INDETERMINATE	1	TRUE	0	0.758700001764559	1		346	426	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28963938	28963938	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	21	271	0	ENST00000282397.4:c.1964T>C	p.Ile655Thr	p.I655T	ENST00000282397	NM_002019.4	655	aTc/aCc	13/30	1	2	FACETS	0.163	0.125	0.207	0.163	0.125	0.207	SUBCLONAL	1	TRUE	1	0.758700001764559	2		271	340	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560979	9560979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	64	350	0	ENST00000353224.5:c.803C>T	p.Pro268Leu	p.P268L	ENST00000353224	NM_177990.2	268	cCa/cTa	4/10	0.758700001764559	3	FACETS	0.455	0.394	0.52	0.227	0.197	0.26	SUBCLONAL	1	TRUE	1	0.758700001764559	3		350	512	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31379500	31379500	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019056-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	31	332	0	ENST00000328111.2:c.907T>C	p.Tyr303His	p.Y303H	ENST00000328111	NM_006892.3	303	Tac/Cac	8/23	0.758700001764559	3	FACETS	0.218	0.176	0.266	0.109	0.088	0.133	SUBCLONAL	1	TRUE	1	0.758700001764559	3		332	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0019607-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	126	583	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.20006038694549	2		583	901	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412045	116412045	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0019607-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	77	730	0	ENST00000397752.3:c.3028+2T>G		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.180202226638009	1	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	0	0.20006038694549	1		730	675	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0021477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	150	230	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.989	0.919	1	0.989	0.919	1	CLONAL	1	TRUE	1	0.930372608404519	2		230	326	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107138	27107142	+	frameshift_variant	Frame_Shift_Del	DEL	AGTTT	AGTTT	-	novel	NA	P-0021477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	306	361	0	ENST00000324856.7:c.6750_6754del	p.Glu2250AspfsTer26	p.E2250Dfs*26	ENST00000324856	NM_006015.4	2250	gAGTTT/g	20/20	0.928270750363376	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.930372608404519	1		361	320	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095966	11095966	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	358	459	0	ENST00000358026.2:c.240T>G	p.His80Gln	p.H80Q	ENST00000358026	NM_001128849.1	80	caT/caG	3/36	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.930372608404519	2		459	719	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938435	44938435	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	285	156	0	ENST00000377967.4:c.2983G>T	p.Glu995Ter	p.E995*	ENST00000377967	NM_021140.2	995	Gaa/Taa	20/29	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.930372608404519	1		156	304	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003747	45003747	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs1057519877	NA	P-0021477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	266	298	0	ENST00000558401.1:c.3G>A	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	atG/atA	1/4	0.842750160129055	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.930372608404519	1		298	292	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0021477-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	96	230	0	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.878	0.794	0.964	1	0.99	1	CLONAL	3	TRUE	1	0.27	2		230	270	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107138	27107142	+	frameshift_variant	Frame_Shift_Del	DEL	AGTTT	AGTTT	-	novel	NA	P-0021477-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	288	361	0	ENST00000324856.7:c.6750_6754del	p.Glu2250AspfsTer26	p.E2250Dfs*26	ENST00000324856	NM_006015.4	2250	gAGTTT/g	20/20	0.3	0	FACETS	0.806	0.77	0.842			1	CLONAL	4	TRUE	0	0.27	0		361	483	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095966	11095966	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021477-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	396	459	0	ENST00000358026.2:c.240T>G	p.His80Gln	p.H80Q	ENST00000358026	NM_001128849.1	80	caT/caG	3/36	1	2	FACETS	1	0.993	1	1	0.997	1	CLONAL	2	TRUE	1	0.27	2		459	1183	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938435	44938435	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021477-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	199	156	0	ENST00000377967.4:c.2983G>T	p.Glu995Ter	p.E995*	ENST00000377967	NM_021140.2	995	Gaa/Taa	20/29	1	1	FACETS	1	0.988	1	1	0.996	1	CLONAL	4	TRUE	0	0.27	1		156	285	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41209084	41209084	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021477-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	66	591	0	ENST00000357654.3:c.5262A>T	p.Glu1754Asp	p.E1754D	ENST00000357654	NM_007294.3	1754	gaA/gaT	19/23	1	2	FACETS	0.55	0.476	0.63	0.55	0.476	0.63	SUBCLONAL	1	TRUE	1	0.27	2		591	889	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577524	7577524	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022143-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	287	608	0	ENST00000269305.4:c.757A>C	p.Thr253Pro	p.T253P	ENST00000269305	NM_001126112.2	253	Acc/Ccc	7/11	0.397381349201296	2	FACETS	0.984	0.932	1	0.984	0.932	1	CLONAL	2	TRUE	0	0.443392979917312	2		608	658	SUCCESS
APC	324	MSKCC	GRCh37	5	112176863	112176863	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1270783041	NA	P-0022143-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	47	336	0	ENST00000257430.4:c.5572C>T	p.Arg1858Ter	p.R1858*	ENST00000257430	NM_000038.5	1858	Cga/Tga	16/16	0.359144749876902	1	FACETS	0.571	0.485	0.665	0.571	0.485	0.665	SUBCLONAL	1	TRUE	0	0.443392979917312	1		336	289	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556727	41556727	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0022143-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	64	320	0	ENST00000263253.7:c.3671+1G>A		p.X1224_splice	ENST00000263253	NM_001429.3	1224			0.421167892397287	2	FACETS	0.78	0.679	0.889	0.39	0.339	0.445	SUBCLONAL	1	TRUE	0	0.443392979917312	2		320	370	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335690	81335690	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022143-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	162	433	0	ENST00000222390.5:c.1670G>T	p.Gly557Val	p.G557V	ENST00000222390	NM_000601.4	557	gGa/gTa	15/18	0.443392979917312	5	FACETS	0.832	0.765	0.902			1	CLONAL	2	TRUE	NA	0.443392979917312	5		433	731	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604648	48604649	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGTGTTG	novel	NA	P-0022143-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	56	353	0	ENST00000342988.3:c.1471_1477dup	p.Asp493GlyfsTer3	p.D493Gfs*3	ENST00000342988	NM_005359.5	490	-/GGTGTTG	12/12	0.423264924339234	1	FACETS	0.695	0.6	0.796	0.695	0.6	0.796	SUBCLONAL	1	TRUE	0	0.443392979917312	1		353	283	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349966	15349966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022143-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	148	768	1	ENST00000263377.2:c.3686G>A	p.Arg1229His	p.R1229H	ENST00000263377	NM_058243.2	1229	cGc/cAc	18/20	0.286036080005544	3	FACETS	0.969	0.885	1	0.484	0.442	0.528	CLONAL	1	TRUE	1	0.443392979917312	3		769	842	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192454	138192454	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1324617507	NA	P-0022143-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	84	328	0	ENST00000237289.4:c.90T>A	p.Phe30Leu	p.F30L	ENST00000237289	NM_001270507.1	30	ttT/ttA	2/9	0.443392979917312	3	FACETS	0.922	0.817	1	0.461	0.408	0.517	CLONAL	1	TRUE	1	0.443392979917312	3		328	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0022458-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	342	577	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.55762436913027	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.809239757448046	1		577	437	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628567	187628567	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022458-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	292	503	1	ENST00000441802.2:c.2415G>T	p.Trp805Cys	p.W805C	ENST00000441802	NM_005245.3	805	tgG/tgT	2/27	1	2	FACETS	0.96	0.908	1	0.96	0.908	1	CLONAL	1	TRUE	1	0.809239757448046	2		504	752	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030409	49030410	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0022458-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	380	310	0	ENST00000267163.4:c.1887_1888del	p.Glu629AspfsTer23	p.E629Dfs*23	ENST00000267163	NM_000321.2	628	gcAGag/gcag	19/27	0.807405982770651	2	FACETS	0.958	0.93	0.986	0.958	0.93	0.986	CLONAL	2	TRUE	0	0.809239757448046	2		310	490	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051656	13051656	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022458-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	279	430	0	ENST00000316448.5:c.915C>G	p.Ile305Met	p.I305M	ENST00000316448	NM_004343.3	305	atC/atG	7/9	0.805734705113724	3	FACETS	1	0.981	1	0.365	0.344	0.387	CLONAL	1	TRUE	0	0.809239757448046	3		430	884	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242478	+	protein_altering_variant	In_Frame_Del	DEL	ATTAAGAGAAG	ATTAAGAGAAG	CA	novel	NA	P-0022458-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	169	404	2	ENST00000275493.2:c.2238_2248delinsCA	p.Glu746_Ala750delinsAspThr	p.E746_A750delinsDT	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGca/gaCAca	19/28	0.809239757448046	3	FACETS	0.844	0.778	0.912	0.422	0.389	0.456	CLONAL	1	TRUE	1	0.809239757448046	3		406	695	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220339	98220339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772406487	NA	P-0022482-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	49	579	1	ENST00000331920.6:c.3124G>A	p.Val1042Met	p.V1042M	ENST00000331920	NM_000264.3	1042	Gtg/Atg	18/24	1	2	FACETS	0.827	0.702	0.965	0.827	0.702	0.965	CLONAL	1	TRUE	1	0.28	2		580	423	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262240	115262240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022482-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	73	514	1	ENST00000438362.2:c.2314C>T	p.Arg772Cys	p.R772C	ENST00000438362	NM_001242891.1	772	Cgc/Tgc	18/20	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.28	2		515	479	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22008901	22008901	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022482-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	77	956	0	ENST00000276925.6:c.52C>G	p.Leu18Val	p.L18V	ENST00000276925	NM_004936.3	18	Ctg/Gtg	1/2	1	2	FACETS	0.826	0.725	0.934	0.826	0.725	0.934	CLONAL	1	TRUE	1	0.28	2		956	666	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589623	67589634	+	inframe_deletion	In_Frame_Del	DEL	ATATGATAGATT	ATATGATAGATT	-	novel	NA	P-0022936-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	44	222	0	ENST00000274335.5:c.1392_1403del	p.Asp464_Tyr467del	p.D464_Y467del	ENST00000274335		462	gaATATGATAGATTa/gaa	10/15	0.52684675148418	1	FACETS	0.687	0.585	0.797	0.687	0.585	0.797	SUBCLONAL	1	TRUE	0	0.52684675148418	1		222	179	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0022936-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	455	619	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	NA	2	FACETS	0.936	0.898	0.973			1	INDETERMINATE	2	TRUE	NA	0.52684675148418	2		619	923	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932065	39932065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1009877078	NA	P-0022936-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	225	327	0	ENST00000378444.4:c.2534C>T	p.Ala845Val	p.A845V	ENST00000378444	NM_001123385.1	845	gCc/gTc	4/15	0.242254123432785	0	FACETS	0.818	0.77	0.866			1	INDETERMINATE	1	TRUE	NA	0.52684675148418	0		327	494	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230535	46230535	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022936-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	115	283	0	ENST00000334344.6:c.784G>A	p.Gly262Arg	p.G262R	ENST00000334344	NM_152641.2	262	Gga/Aga	8/21	1	2	FACETS	0.917	0.831	1	0.917	0.831	1	CLONAL	1	TRUE	1	0.52684675148418	2		283	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0023553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	369	485	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	NA	2	FACETS	0.981	0.948	1			1	INDETERMINATE	2	TRUE	NA	0.745070640688944	2		486	505	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528105	157528105	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1028186690	NA	P-0023553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	196	161	0	ENST00000346085.5:c.5830C>T	p.Arg1944Ter	p.R1944*	ENST00000346085	NM_020732.3	1944	Cga/Tga	20/20	0.136173860115905	3	FACETS	1	0.992	1	0.49	0.458	0.523	INDETERMINATE	1	TRUE	0	0.745070640688944	3		161	491	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955187	17955187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs896064879	NA	P-0023553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	418	257	0	ENST00000458235.1:c.40C>T	p.Arg14Cys	p.R14C	ENST00000458235	NM_000215.3	14	Cgt/Tgt	2/24	0.745070640688944	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.745070640688944	3		257	757	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555305	106555305	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	118	146	0	ENST00000369096.4:c.2422C>A	p.Leu808Ile	p.L808I	ENST00000369096	NM_001198.3	808	Cta/Ata	7/7	0.745070640688944	3	FACETS	0.885	0.803	0.971	0.443	0.401	0.486	CLONAL	1	TRUE	1	0.745070640688944	3		146	491	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663587	117663587	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	125	201	0	ENST00000368508.3:c.4645A>T	p.Ile1549Phe	p.I1549F	ENST00000368508	NM_002944.2	1549	Att/Ttt	28/43	0.745070640688944	3	FACETS	0.919	0.837	1	0.46	0.418	0.503	CLONAL	1	TRUE	1	0.745070640688944	3		201	501	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227986	55227986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769434273	NA	P-0023553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	94	125	0	ENST00000275493.2:c.1453G>A	p.Gly485Ser	p.G485S	ENST00000275493	NM_005228.3	485	Ggt/Agt	12/28	0.745070640688944	3	FACETS	0.9	0.806	0.997	0.45	0.403	0.499	CLONAL	1	TRUE	1	0.745070640688944	3		125	385	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136839	69136839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780008732	NA	P-0023553-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	111	107	0	ENST00000288368.4:c.4753C>T	p.Arg1585Trp	p.R1585W	ENST00000288368	NM_024870.2	1585	Cgg/Tgg	39/40	0.745070640688944	3	FACETS	0.978	0.886	1	0.489	0.443	0.537	CLONAL	1	TRUE	1	0.745070640688944	3		107	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0023553-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	266	485	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.295324741722048	1	FACETS	1	0.991	1	1	0.991	1	INDETERMINATE	1	TRUE	0	0.566430189086945	1		486	547	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528105	157528105	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1028186690	NA	P-0023553-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	192	161	0	ENST00000346085.5:c.5830C>T	p.Arg1944Ter	p.R1944*	ENST00000346085	NM_020732.3	1944	Cga/Tga	20/20	0.153440467501252	4	FACETS	0.953	0.888	1	0.953	0.888	1	INDETERMINATE	2	TRUE	2	0.566430189086945	4		161	557	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955187	17955187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs896064879	NA	P-0023553-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	317	257	0	ENST00000458235.1:c.40C>T	p.Arg14Cys	p.R14C	ENST00000458235	NM_000215.3	14	Cgt/Tgt	2/24	0.368699300330899	3	FACETS	0.822	0.778	0.866	0.822	0.778	0.866	CLONAL	2	TRUE	1	0.566430189086945	3		257	874	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663587	117663587	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023553-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	158	201	0	ENST00000368508.3:c.4645A>T	p.Ile1549Phe	p.I1549F	ENST00000368508	NM_002944.2	1549	Att/Ttt	28/43	0.153440467501252	4	FACETS	0.811	0.747	0.876	0.811	0.747	0.876	INDETERMINATE	2	TRUE	2	0.566430189086945	4		201	539	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227986	55227986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769434273	NA	P-0023553-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	136	125	0	ENST00000275493.2:c.1453G>A	p.Gly485Ser	p.G485S	ENST00000275493	NM_005228.3	485	Ggt/Agt	12/28	0.566430189086945	3	FACETS	0.794	0.73	0.86	0.794	0.73	0.86	SUBCLONAL	2	TRUE	1	0.566430189086945	3		125	388	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136839	69136839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780008732	NA	P-0023553-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	65	107	0	ENST00000288368.4:c.4753C>T	p.Arg1585Trp	p.R1585W	ENST00000288368	NM_024870.2	1585	Cgg/Tgg	39/40	0.214091916072386	4	FACETS	0.755	0.656	0.862	0.378	0.328	0.431	INDETERMINATE	1	TRUE	2	0.566430189086945	4		107	476	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604736	48604736	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023553-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	51	164	0	ENST00000342988.3:c.1558G>T	p.Glu520Ter	p.E520*	ENST00000342988	NM_005359.5	520	Gaa/Taa	12/12	1	2	FACETS	0.423	0.36	0.491	0.423	0.36	0.491	SUBCLONAL	1	TRUE	1	0.566430189086945	2		164	426	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386387	31386387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs987153673	NA	P-0023553-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	52	211	0	ENST00000328111.2:c.1612C>T	p.Arg538Cys	p.R538C	ENST00000328111	NM_006892.3	538	Cgc/Tgc	15/23	0.304126586003375	5	FACETS	0.361	0.306	0.422	0.12	0.102	0.141	INDETERMINATE	1	TRUE	2	0.566430189086945	5		211	941	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530116	212530116	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023553-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	55	127	0	ENST00000342788.4:c.1803C>A	p.Asn601Lys	p.N601K	ENST00000342788	NM_005235.2	601	aaC/aaA	15/28	0.153440467501252	4	FACETS	0.772	0.663	0.891	0.386	0.331	0.446	INDETERMINATE	1	TRUE	2	0.566430189086945	4		127	394	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439590	220439590	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023553-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	203	252	1	ENST00000243786.2:c.443C>G	p.Ser148Cys	p.S148C	ENST00000243786	NM_002191.3	148	tCt/tGt	2/2	0.153440467501252	4	FACETS	0.77	0.716	0.825	0.77	0.716	0.825	INDETERMINATE	2	TRUE	2	0.566430189086945	4		253	729	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986517	36986517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023553-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	78	220	0	ENST00000354822.5:c.1172C>T	p.Ser391Phe	p.S391F	ENST00000354822	NM_001079668.2	391	tCc/tTc	3/3	0.153440467501252	4	FACETS	0.594	0.522	0.672	0.297	0.261	0.336	INDETERMINATE	1	TRUE	2	0.566430189086945	4		220	726	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637749	52637749	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0023553-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	74	125	0	ENST00000394830.3:c.2568-1G>A		p.X856_splice	ENST00000394830	NM_018313.4	856			0.214091916072386	4	FACETS	1	0.889	1	0.505	0.444	0.57	INDETERMINATE	1	TRUE	2	0.566430189086945	4		125	405	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755689	57755689	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023553-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	54	148	0	ENST00000274289.3:c.98A>T	p.Lys33Met	p.K33M	ENST00000274289	NM_006622.3	33	aAg/aTg	1/14	0.214091916072386	4	FACETS	0.387	0.329	0.45	0.193	0.164	0.225	INDETERMINATE	1	TRUE	2	0.566430189086945	4		148	772	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910432	50910432	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0024088-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	100	567	0	ENST00000440232.2:c.1686+1G>T		p.X562_splice	ENST00000440232	NM_002691.3	562			0.146893404652943	3	FACETS	0.775	0.696	0.858			1	INDETERMINATE	1	TRUE	NA	0.784105648704356	3		567	458	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514027	125514027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761313560	NA	P-0024088-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	118	382	0	ENST00000428830.2:c.965G>A	p.Arg322His	p.R322H	ENST00000428830	NM_001114121.2	322	cGc/cAc	10/14	0.297463595395527	2	FACETS	1	0.937	1	0.514	0.471	0.557	INDETERMINATE	1	TRUE	0	0.784105648704356	2		382	293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577053	7577057	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCT	AGGCT	-	novel	NA	P-0024088-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	387	498	0	ENST00000269305.4:c.881_885del	p.Glu294AlafsTer10	p.E294Afs*10	ENST00000269305	NM_001126112.2	294	gAGCCT/g	8/11	0.79834999485833	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.784105648704356	1		498	423	SUCCESS
CALR	811	MSKCC	GRCh37	19	13049535	13049535	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024088-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	297	465	0	ENST00000316448.5:c.43del	p.Ala15ProfsTer83	p.A15Pfs*83	ENST00000316448	NM_004343.3	14	ctG/ct	1/9	0.79834999485833	2	FACETS	1	0.995	1	0.737	0.704	0.77	CLONAL	1	TRUE	0	0.784105648704356	2		465	514	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050694	30050694	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024088-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	185	272	0	ENST00000338641.4:c.496G>C	p.Glu166Gln	p.E166Q	ENST00000338641	NM_000268.3	166	Gag/Cag	5/16	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.784105648704356	2		272	390	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93973635	93973635	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0024088-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	118	276	0	ENST00000369303.4:c.1743-2A>T		p.X581_splice	ENST00000369303	NM_004440.3	581			0.104004209462505	5	FACETS	1	0.943	1			1	INDETERMINATE	3	TRUE	NA	0.784105648704356	5		276	214	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024797-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	83	148	0				ENST00000310581	NM_198253.2	-/1132			0.24579050006386	4	FACETS	0.866	0.771	0.965	0.866	0.771	0.965	CLONAL	3	FALSE	1	0.24579050006386	4		148	324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0024797-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	157	583	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.183915149230665	3	FACETS	1	0.982	1			1	CLONAL	2	FALSE	NA	0.24579050006386	3		583	586	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934194	48934194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024797-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	48	340	1	ENST00000267163.4:c.649C>T	p.Gln217Ter	p.Q217*	ENST00000267163	NM_000321.2	217	Cag/Tag	7/27	1	2	FACETS	0.955	0.809	1	0.955	0.809	1	CLONAL	1	FALSE	1	0.24579050006386	2		341	409	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438587	49438587	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024797-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	75	617	0	ENST00000301067.7:c.4903del	p.Gly1636AlafsTer86	p.G1636Afs*86	ENST00000301067	NM_003482.3	1635	Ctt/tt	19/54	1	2	FACETS	0.984	0.863	1	0.984	0.863	1	CLONAL	1	FALSE	1	0.24579050006386	2		617	620	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095002	11095002	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1315494799	NA	P-0024797-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	144	847	1	ENST00000358026.2:c.175C>T	p.Gln59Ter	p.Q59*	ENST00000358026	NM_001128849.1	59	Cag/Tag	2/36	0.24579050006386	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	FALSE	1	0.24579050006386	3		848	614	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263757	16263757	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024797-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	47	488	0	ENST00000375759.3:c.10126C>G	p.Gln3376Glu	p.Q3376E	ENST00000375759	NM_015001.2	3376	Cag/Gag	12/15	0.24579050006386	3	FACETS	0.806	0.68	0.945	0.403	0.34	0.473	CLONAL	1	FALSE	1	0.24579050006386	3		488	533	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775024	73775024	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024797-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	28	381	0	ENST00000254810.4:c.149G>C	p.Arg50Pro	p.R50P	ENST00000254810	NM_005324.3	50	cGa/cCa	3/4	0.24579050006386	3	FACETS	0.608	0.485	0.748	0.304	0.242	0.374	SUBCLONAL	1	FALSE	1	0.24579050006386	3		381	421	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216441	2216442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024797-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	51	722	0	ENST00000398665.3:c.2086dup	p.Cys696LeufsTer26	p.C696Lfs*26	ENST00000398665	NM_032482.2	695	-/T	20/28	0.24579050006386	2	FACETS	0.701	0.595	0.817	0.35	0.297	0.409	SUBCLONAL	1	FALSE	0	0.24579050006386	2		722	592	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022597	36022597	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024797-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	38	604	0	ENST00000358208.4:c.470C>A	p.Thr157Asn	p.T157N	ENST00000358208		157	aCc/aAc	5/12	0.24579050006386	3	FACETS	0.588	0.485	0.704	0.294	0.242	0.352	SUBCLONAL	1	FALSE	1	0.24579050006386	3		604	590	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191536	185191536	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	235	372	0	ENST00000265026.3:c.2417G>T	p.Arg806Met	p.R806M	ENST00000265026	NM_004721.4	806	aGg/aTg	11/14	0.654184142145889	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.654184142145889	3		372	455	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044496	47044496	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	222	524	0	ENST00000377604.3:c.1993C>G	p.Gln665Glu	p.Q665E	ENST00000377604	NM_001204468.1	665	Caa/Gaa	18/24	0.335562630328799	6	FACETS	0.893	0.837	0.949	0.893	0.837	0.949	INDETERMINATE	3	TRUE	3	0.654184142145889	6		524	585	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634755	158634755	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	78	277	0	ENST00000263640.3:c.431T>G	p.Val144Gly	p.V144G	ENST00000263640	NM_001105.4	144	gTt/gGt	5/11	1	2	FACETS	0.932	0.83	1	0.932	0.83	1	CLONAL	1	TRUE	1	0.654184142145889	2		277	256	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	62	336	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.305463341134168	1	FACETS	0.308	0.267	0.353	0.308	0.267	0.353	INDETERMINATE	1	TRUE	0	0.619837860235886	1		336	448	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	38	248	1				ENST00000310581	NM_198253.2	-/1132			0.371442838158786	1	FACETS	0.462	0.387	0.545	0.462	0.387	0.545	INDETERMINATE	1	TRUE	0	0.619837860235886	1		249	183	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945102	151945102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	35	350	0	ENST00000262189.6:c.2417C>T	p.Ser806Phe	p.S806F	ENST00000262189	NM_170606.2	806	tCc/tTc	14/59	1	2	FACETS	0.349	0.286	0.418	0.349	0.286	0.418	SUBCLONAL	1	TRUE	1	0.619837860235886	2		350	324	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	198	698	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.619837860235886	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.619837860235886	1		698	356	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541628	187541628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	66	329	0	ENST00000441802.2:c.6112C>T	p.Pro2038Ser	p.P2038S	ENST00000441802	NM_005245.3	2038	Ccc/Tcc	10/27	0.302613917882319	1	FACETS	0.343	0.299	0.391	0.343	0.299	0.391	INDETERMINATE	1	TRUE	0	0.619837860235886	1		329	428	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187102	11187102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	246	485	0	ENST00000361445.4:c.6316C>T	p.His2106Tyr	p.H2106Y	ENST00000361445	NM_004958.3	2106	Cat/Tat	45/58	0.329995862743379	1	FACETS	0.944	0.89	0.999	0.944	0.89	0.999	INDETERMINATE	1	TRUE	0	0.619837860235886	1		485	580	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885658	23885658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	107	573	1	ENST00000374561.5:c.260C>T	p.Pro87Leu	p.P87L	ENST00000374561	NM_002167.4	87	cCa/cTa	1/3	0.329995862743379	1	FACETS	0.408	0.367	0.452	0.408	0.367	0.452	INDETERMINATE	1	TRUE	0	0.619837860235886	1		574	584	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521597	46521597	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	114	396	1	ENST00000262741.5:c.811C>T	p.His271Tyr	p.H271Y	ENST00000262741	NM_003629.3	271	Cat/Tat	7/10	0.305463341134168	1	FACETS	0.445	0.401	0.49	0.445	0.401	0.49	INDETERMINATE	1	TRUE	0	0.619837860235886	1		397	571	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78421009	78421009	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	181	275	0	ENST00000370768.2:c.1711C>T	p.Gln571Ter	p.Q571*	ENST00000370768	NM_003902.3	571	Cag/Tag	18/20	0.305463341134168	1	FACETS	0.872	0.813	0.933	0.872	0.813	0.933	INDETERMINATE	1	TRUE	0	0.619837860235886	1		275	462	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166533	118166533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	78	408	0	ENST00000369448.3:c.1043C>T	p.Pro348Leu	p.P348L	ENST00000369448	NM_017709.3	348	cCc/cTc	2/2	0.305463341134168	1	FACETS	0.409	0.36	0.46	0.409	0.36	0.46	INDETERMINATE	1	TRUE	0	0.619837860235886	1		408	425	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120509023	120509023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782444829	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	238	441	0	ENST00000256646.2:c.1543C>T	p.Arg515Cys	p.R515C	ENST00000256646	NM_024408.3	515	Cgt/Tgt	9/34	0.305463341134168	1	FACETS	0.92	0.866	0.975	0.92	0.866	0.975	INDETERMINATE	1	TRUE	0	0.619837860235886	1		441	576	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731107	162731107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	336	528	1	ENST00000367921.3:c.962C>T	p.Pro321Leu	p.P321L	ENST00000367921	NM_006182.2	321	cCc/cTc	9/18	0.324854866550029	2	FACETS	0.823	0.785	0.86	0.823	0.785	0.86	INDETERMINATE	2	TRUE	0	0.619837860235886	2		529	659	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663812	241663812	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	42	164	0	ENST00000366560.3:c.1315C>T	p.Gln439Ter	p.Q439*	ENST00000366560	NM_000143.3	439	Cag/Tag	9/10	0.324854866550029	2	FACETS	0.542	0.456	0.636	0.271	0.228	0.318	INDETERMINATE	1	TRUE	0	0.619837860235886	2		164	250	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100474	8100474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	109	715	0	ENST00000346208.3:c.448C>T	p.Leu150Phe	p.L150F	ENST00000346208		150	Ctc/Ttc	3/6	0.332675110722324	1	FACETS	0.415	0.373	0.459	0.415	0.373	0.459	INDETERMINATE	1	TRUE	0	0.619837860235886	1		715	585	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606655	43606655	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	184	509	1	ENST00000355710.3:c.1264A>T	p.Ile422Phe	p.I422F	ENST00000355710	NM_020975.4	422	Atc/Ttc	7/20	0.332675110722324	1	FACETS	0.819	0.763	0.877	0.819	0.763	0.877	INDETERMINATE	1	TRUE	0	0.619837860235886	1		510	500	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606743	43606743	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774092678	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	124	682	2	ENST00000355710.3:c.1352C>T	p.Thr451Met	p.T451M	ENST00000355710	NM_020975.4	451	aCg/aTg	7/20	0.332675110722324	1	FACETS	0.42	0.381	0.462	0.42	0.381	0.462	INDETERMINATE	1	TRUE	0	0.619837860235886	1		684	657	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683183	88683183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	142	251	0	ENST00000372037.3:c.1393C>T	p.Pro465Ser	p.P465S	ENST00000372037	NM_004329.2	465	Ccg/Tcg	12/13	0.332675110722324	1	FACETS	1	0.93	1	1	0.93	1	INDETERMINATE	1	TRUE	0	0.619837860235886	1		251	315	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309747	104309747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	231	481	1	ENST00000369902.3:c.338C>T	p.Pro113Leu	p.P113L	ENST00000369902	NM_016169.3	113	cCt/cTt	3/12	0.332675110722324	1	FACETS	0.82	0.77	0.872	0.82	0.77	0.872	INDETERMINATE	1	TRUE	0	0.619837860235886	1		482	627	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310821	123310821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	113	526	1	ENST00000358487.5:c.607C>T	p.Arg203Cys	p.R203C	ENST00000358487	NM_000141.4	203	Cgc/Tgc	5/18	0.332675110722324	1	FACETS	0.443	0.4	0.488	0.443	0.4	0.488	INDETERMINATE	1	TRUE	0	0.619837860235886	1		527	568	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625285	69625285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782512706	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	92	687	0	ENST00000334134.2:c.508C>T	p.Arg170Cys	p.R170C	ENST00000334134	NM_005247.2	170	Cgc/Tgc	3/3	0.371442838158786	1	FACETS	0.385	0.343	0.43	0.385	0.343	0.43	INDETERMINATE	1	TRUE	0	0.619837860235886	1		687	532	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944134	71944134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1208152317	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	99	579	0	ENST00000298229.2:c.1967C>T	p.Ser656Phe	p.S656F	ENST00000298229	NM_001567.3	656	tCc/tTc	17/28	0.371442838158786	1	FACETS	0.43	0.385	0.477	0.43	0.385	0.477	INDETERMINATE	1	TRUE	0	0.619837860235886	1		579	513	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94224048	94224048	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	198	400	0	ENST00000323929.3:c.104A>G	p.Asp35Gly	p.D35G	ENST00000323929	NM_005591.3	35	gAt/gGt	3/20	0.305463341134168	1	FACETS	0.796	0.742	0.85	0.796	0.742	0.85	INDETERMINATE	1	TRUE	0	0.619837860235886	1		400	554	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363797	118363797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	196	418	0	ENST00000534358.1:c.5030C>T	p.Pro1677Leu	p.P1677L	ENST00000534358	NM_005933.3	1677	cCc/cTc	16/36	0.305463341134168	1	FACETS	0.88	0.822	0.938	0.88	0.822	0.938	INDETERMINATE	1	TRUE	0	0.619837860235886	1		418	496	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118382704	118382704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555050211	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	117	404	0	ENST00000534358.1:c.11110C>T	p.Arg3704Ter	p.R3704*	ENST00000534358	NM_005933.3	3704	Cga/Tga	31/36	0.305463341134168	1	FACETS	0.506	0.458	0.556	0.506	0.458	0.556	INDETERMINATE	1	TRUE	0	0.619837860235886	1		404	515	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170447	119170447	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368138875	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	105	392	0	ENST00000264033.4:c.2677C>T	p.Arg893Trp	p.R893W	ENST00000264033	NM_005188.3	893	Cgg/Tgg	16/16	0.305463341134168	1	FACETS	0.539	0.486	0.594	0.539	0.486	0.594	INDETERMINATE	1	TRUE	0	0.619837860235886	1		392	434	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398059	4398059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	222	502	0	ENST00000261254.3:c.623G>A	p.Gly208Glu	p.G208E	ENST00000261254	NM_001759.3	208	gGa/gAa	4/5	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.619837860235886	2		502	617	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435040	18435040	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	162	276	0	ENST00000266497.5:c.25C>T	p.Pro9Ser	p.P9S	ENST00000266497		9	Cca/Tca	1/31	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.619837860235886	2		276	441	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435253	18435253	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	128	304	0	ENST00000266497.5:c.238G>A	p.Glu80Lys	p.E80K	ENST00000266497		80	Gaa/Aaa	1/31	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.619837860235886	2		304	382	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573966	18573966	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1363775683	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	129	235	0	ENST00000266497.5:c.2284C>T	p.Gln762Ter	p.Q762*	ENST00000266497		762	Cag/Tag	15/31	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.619837860235886	2		235	415	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793421	18793421	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	196	373	0	ENST00000266497.5:c.4118C>T	p.Pro1373Leu	p.P1373L	ENST00000266497		1373	cCc/cTc	30/31	1	2	FACETS	0.97	0.902	1	0.97	0.902	1	CLONAL	1	TRUE	1	0.619837860235886	2		373	652	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243484	46243484	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	182	389	0	ENST00000334344.6:c.1837C>T	p.Gln613Ter	p.Q613*	ENST00000334344	NM_152641.2	613	Cag/Tag	14/21	1	2	FACETS	0.992	0.92	1	0.992	0.92	1	CLONAL	1	TRUE	1	0.619837860235886	2		389	592	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245184	46245184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	178	444	0	ENST00000334344.6:c.3278C>T	p.Pro1093Leu	p.P1093L	ENST00000334344	NM_152641.2	1093	cCt/cTt	15/21	1	2	FACETS	0.957	0.887	1	0.957	0.887	1	CLONAL	1	TRUE	1	0.619837860235886	2		444	600	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433554	49433554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	297	832	0	ENST00000301067.7:c.7999C>T	p.Pro2667Ser	p.P2667S	ENST00000301067	NM_003482.3	2667	Cca/Tca	31/54	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.619837860235886	2		832	894	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445448	49445448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	130	718	0	ENST00000301067.7:c.2018C>T	p.Pro673Leu	p.P673L	ENST00000301067	NM_003482.3	673	cCa/cTa	10/54	1	2	FACETS	0.477	0.432	0.524	0.477	0.432	0.524	SUBCLONAL	1	TRUE	1	0.619837860235886	2		718	880	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445746	49445746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	301	767	1	ENST00000301067.7:c.1720C>T	p.Pro574Ser	p.P574S	ENST00000301067	NM_003482.3	574	Cca/Tca	10/54	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.619837860235886	2		768	918	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120802555	120802555	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	89	493	0	ENST00000257552.2:c.271G>C	p.Asp91His	p.D91H	ENST00000257552	NM_002442.3	91	Gac/Cac	5/15	1	2	FACETS	0.444	0.394	0.497	0.444	0.394	0.497	SUBCLONAL	1	TRUE	1	0.619837860235886	2		493	647	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256148	133256149	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	189	472	1	ENST00000320574.5:c.512_513delinsTT	p.Ser171Phe	p.S171F	ENST00000320574	NM_006231.2	171	tCC/tTT	6/49	1	2	FACETS	0.93	0.863	0.998	0.93	0.863	0.998	CLONAL	1	TRUE	1	0.619837860235886	2		473	656	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896963	28896963	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868166954	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	165	422	0	ENST00000282397.4:c.2917G>A	p.Glu973Lys	p.E973K	ENST00000282397	NM_002019.4	973	Gaa/Aaa	21/30	0.619837860235886	1	FACETS	0.867	0.805	0.93	0.867	0.805	0.93	CLONAL	1	TRUE	0	0.619837860235886	1		422	424	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28980009	28980009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866351272	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	167	379	0	ENST00000282397.4:c.1459G>A	p.Glu487Lys	p.E487K	ENST00000282397	NM_002019.4	487	Gaa/Aaa	11/30	0.619837860235886	1	FACETS	0.961	0.895	1	0.961	0.895	1	CLONAL	1	TRUE	0	0.619837860235886	1		379	387	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504557	103504557	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	167	357	1	ENST00000355739.4:c.178C>T	p.His60Tyr	p.H60Y	ENST00000355739	NM_000123.3	60	Cat/Tat	2/15	0.619837860235886	1	FACETS	0.973	0.907	1	0.973	0.907	1	CLONAL	1	TRUE	0	0.619837860235886	1		358	382	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609925	81609925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772490052	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	166	421	1	ENST00000298171.2:c.1523C>T	p.Ser508Leu	p.S508L	ENST00000298171	NM_000369.2	508	tCg/tTg	10/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.619837860235886	2		422	494	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023055	33023055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	69	540	0	ENST00000300177.4:c.164C>T	p.Ser55Phe	p.S55F	ENST00000300177	NM_001191322.1	55	tCc/tTc	2/2	0.302613917882319	1	FACETS	0.316	0.276	0.36	0.316	0.276	0.36	INDETERMINATE	1	TRUE	0	0.619837860235886	1		540	486	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88428947	88428947	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1460807501	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	138	269	0	ENST00000360948.2:c.2153A>T	p.Asn718Ile	p.N718I	ENST00000360948	NM_001012338.2	718	aAt/aTt	17/19	0.302613917882319	1	FACETS	0.856	0.789	0.924	0.856	0.789	0.924	INDETERMINATE	1	TRUE	0	0.619837860235886	1		269	359	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679837	88679837	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	146	328	0	ENST00000360948.2:c.626T>C	p.Leu209Pro	p.L209P	ENST00000360948	NM_001012338.2	209	cTt/cCt	7/19	0.302613917882319	1	FACETS	0.825	0.762	0.89	0.825	0.762	0.89	INDETERMINATE	1	TRUE	0	0.619837860235886	1		328	394	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	360056	360056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	195	644	0	ENST00000262320.3:c.1033C>T	p.Pro345Ser	p.P345S	ENST00000262320	NM_003502.3	345	Cca/Tca	4/11	0.371442838158786	1	FACETS	0.824	0.769	0.88	0.824	0.769	0.88	INDETERMINATE	1	TRUE	0	0.619837860235886	1		644	527	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121834	2121835	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	101	794	1	ENST00000219476.3:c.1996_1997delinsTT	p.Pro666Phe	p.P666F	ENST00000219476	NM_000548.3	666	CCc/TTc	19/42	0.371442838158786	1	FACETS	0.393	0.352	0.437	0.393	0.352	0.437	INDETERMINATE	1	TRUE	0	0.619837860235886	1		795	572	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222315	2222315	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	230	721	0	ENST00000326181.6:c.599C>T	p.Pro200Leu	p.P200L	ENST00000326181	NM_032271.2	200	cCc/cTc	8/21	0.371442838158786	1	FACETS	0.936	0.881	0.992	0.936	0.881	0.992	INDETERMINATE	1	TRUE	0	0.619837860235886	1		721	547	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789595	3789595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	87	399	0	ENST00000262367.5:c.4264C>T	p.Pro1422Ser	p.P1422S	ENST00000262367	NM_004380.2	1422	Ccc/Tcc	25/31	0.371442838158786	1	FACETS	0.428	0.38	0.478	0.428	0.38	0.478	INDETERMINATE	1	TRUE	0	0.619837860235886	1		399	453	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857305	9857305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766598240	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	180	520	0	ENST00000330684.3:c.4096C>T	p.Pro1366Ser	p.P1366S	ENST00000330684	NM_001134407.1	1366	Cct/Tct	13/13	0.371442838158786	1	FACETS	0.833	0.775	0.892	0.833	0.775	0.892	INDETERMINATE	1	TRUE	0	0.619837860235886	1		520	481	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858202	9858202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	90	448	0	ENST00000330684.3:c.3199C>T	p.Arg1067Trp	p.R1067W	ENST00000330684	NM_001134407.1	1067	Cgg/Tgg	13/13	0.371442838158786	1	FACETS	0.435	0.387	0.485	0.435	0.387	0.485	INDETERMINATE	1	TRUE	0	0.619837860235886	1		448	461	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858359	9858359	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1306036000	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	143	365	0	ENST00000330684.3:c.3042G>A	p.Trp1014Ter	p.W1014*	ENST00000330684	NM_001134407.1	1014	tgG/tgA	13/13	0.371442838158786	1	FACETS	0.863	0.797	0.93	0.863	0.797	0.93	INDETERMINATE	1	TRUE	0	0.619837860235886	1		365	369	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858754	9858754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	137	305	0	ENST00000330684.3:c.2647C>T	p.Pro883Ser	p.P883S	ENST00000330684	NM_001134407.1	883	Cca/Tca	13/13	0.371442838158786	1	FACETS	0.968	0.895	1	0.968	0.895	1	INDETERMINATE	1	TRUE	0	0.619837860235886	1		305	315	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923328	9923328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	107	485	0	ENST00000330684.3:c.1959G>A	p.Met653Ile	p.M653I	ENST00000330684	NM_001134407.1	653	atG/atA	9/13	0.371442838158786	1	FACETS	0.433	0.39	0.479	0.433	0.39	0.479	INDETERMINATE	1	TRUE	0	0.619837860235886	1		485	550	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984954	9984954	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	110	387	0	ENST00000330684.3:c.1011T>A	p.Phe337Leu	p.F337L	ENST00000330684	NM_001134407.1	337	ttT/ttA	4/13	0.371442838158786	1	FACETS	0.518	0.468	0.57	0.518	0.468	0.57	INDETERMINATE	1	TRUE	0	0.619837860235886	1		387	473	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032006	10032006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	213	545	0	ENST00000330684.3:c.817C>T	p.Pro273Ser	p.P273S	ENST00000330684	NM_001134407.1	273	Cca/Tca	3/13	0.371442838158786	1	FACETS	0.859	0.805	0.914	0.859	0.805	0.914	INDETERMINATE	1	TRUE	0	0.619837860235886	1		545	552	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032293	10032293	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	188	485	0	ENST00000330684.3:c.530T>G	p.Phe177Cys	p.F177C	ENST00000330684	NM_001134407.1	177	tTc/tGc	3/13	0.371442838158786	1	FACETS	0.832	0.776	0.89	0.832	0.776	0.89	INDETERMINATE	1	TRUE	0	0.619837860235886	1		485	503	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641511	23641511	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	187	497	0	ENST00000261584.4:c.1964T>G	p.Phe655Cys	p.F655C	ENST00000261584	NM_024675.3	655	tTt/tGt	5/13	1	2	FACETS	0.893	0.828	0.959	0.893	0.828	0.959	CLONAL	1	TRUE	1	0.619837860235886	2		497	676	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044560	12044560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	199	424	0	ENST00000353533.5:c.1183C>T	p.Pro395Ser	p.P395S	ENST00000353533	NM_003010.3	395	Ccc/Tcc	11/11	0.619837860235886	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.619837860235886	1		424	427	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528079	29528079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	104	161	0	ENST00000356175.3:c.1087C>T	p.Pro363Ser	p.P363S	ENST00000356175	NM_000267.3	363	Cca/Tca	10/57	0.619837860235886	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.619837860235886	1		161	188	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528166	29528166	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	237	422	0	ENST00000356175.3:c.1174C>T	p.Gln392Ter	p.Q392*	ENST00000356175	NM_000267.3	392	Caa/Taa	10/57	0.619837860235886	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.619837860235886	1		422	496	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362264	40362264	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	202	425	0	ENST00000293328.3:c.1831C>T	p.Pro611Ser	p.P611S	ENST00000293328	NM_012448.3	611	Cca/Tca	15/19	0.619837860235886	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.619837860235886	1		425	433	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459505	40459505	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	203	489	1	ENST00000345506.4:c.1766G>A	p.Trp589Ter	p.W589*	ENST00000345506	NM_003152.3	589	tGg/tAg	15/20	0.619837860235886	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.619837860235886	1		490	438	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56801401	56801401	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	393	408	0	ENST00000337432.4:c.905G>A	p.Gly302Glu	p.G302E	ENST00000337432	NM_058216.2	302	gGg/gAg	7/9	0.619837860235886	3	FACETS	0.977	0.934	1	0.977	0.934	1	CLONAL	2	TRUE	1	0.619837860235886	3		408	850	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533791	63533791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779863826	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	96	640	0	ENST00000307078.5:c.1363C>T	p.Pro455Ser	p.P455S	ENST00000307078	NM_004655.3	455	Cca/Tca	6/11	0.619837860235886	3	FACETS	0.456	0.406	0.51	0.228	0.203	0.255	SUBCLONAL	1	TRUE	1	0.619837860235886	3		640	889	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191141	2191141	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	209	653	0	ENST00000398665.3:c.395C>T	p.Ser132Phe	p.S132F	ENST00000398665	NM_032482.2	132	tCc/tTc	5/28	1	2	FACETS	0.933	0.869	0.998	0.933	0.869	0.998	CLONAL	1	TRUE	1	0.619837860235886	2		653	723	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244400	5244400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs79388082	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	254	700	0	ENST00000357368.4:c.1082C>T	p.Ser361Phe	p.S361F	ENST00000357368	NM_002850.3	361	tCc/tTc	11/38	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.619837860235886	2		700	793	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170546	7170546	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	63	345	0	ENST00000302850.5:c.1483+2T>G		p.X495_splice	ENST00000302850	NM_000208.2	495			1	2	FACETS	0.516	0.448	0.589	0.516	0.448	0.589	SUBCLONAL	1	TRUE	1	0.619837860235886	2		345	394	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172397	7172397	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	191	436	0	ENST00000302850.5:c.1172T>A	p.Ile391Asn	p.I391N	ENST00000302850	NM_000208.2	391	aTt/aAt	5/22	1	2	FACETS	0.966	0.898	1	0.966	0.898	1	CLONAL	1	TRUE	1	0.619837860235886	2		436	638	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105610	11105610	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	253	581	0	ENST00000358026.2:c.1526C>T	p.Ala509Val	p.A509V	ENST00000358026	NM_001128849.1	509	gCc/gTc	9/36	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.619837860235886	2		581	753	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132633	11132633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217938288	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	269	739	0	ENST00000358026.2:c.2849C>T	p.Thr950Ile	p.T950I	ENST00000358026	NM_001128849.1	950	aCc/aTc	19/36	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.619837860235886	2		739	725	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271543	15271543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	262	761	0	ENST00000263388.2:c.6896C>T	p.Ser2299Phe	p.S2299F	ENST00000263388	NM_000435.2	2299	tCc/tTc	33/33	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.619837860235886	2		761	800	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271823	15271823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778006941	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	235	837	1	ENST00000263388.2:c.6616G>A	p.Glu2206Lys	p.E2206K	ENST00000263388	NM_000435.2	2206	Gag/Aag	33/33	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.619837860235886	2		838	727	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271975	15271975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs567953412	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	223	703	0	ENST00000263388.2:c.6464G>A	p.Gly2155Glu	p.G2155E	ENST00000263388	NM_000435.2	2155	gGa/gAa	33/33	1	2	FACETS	0.994	0.929	1	0.994	0.929	1	CLONAL	1	TRUE	1	0.619837860235886	2		703	724	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281227	15281227	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	219	747	0	ENST00000263388.2:c.5029C>T	p.Pro1677Ser	p.P1677S	ENST00000263388	NM_000435.2	1677	Cct/Tct	27/33	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.619837860235886	2		747	703	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289869	15289869	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	222	787	0	ENST00000263388.2:c.3685G>A	p.Gly1229Ser	p.G1229S	ENST00000263388	NM_000435.2	1229	Ggt/Agt	22/33	1	2	FACETS	0.935	0.873	0.999	0.935	0.873	0.999	CLONAL	1	TRUE	1	0.619837860235886	2		787	766	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291900	15291900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745954040	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	135	804	1	ENST00000263388.2:c.2866G>A	p.Gly956Arg	p.G956R	ENST00000263388	NM_000435.2	956	Gga/Aga	18/33	1	2	FACETS	0.561	0.51	0.614	0.561	0.51	0.614	SUBCLONAL	1	TRUE	1	0.619837860235886	2		805	777	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299836	15299836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	223	759	0	ENST00000263388.2:c.1342G>A	p.Asp448Asn	p.D448N	ENST00000263388	NM_000435.2	448	Gac/Aac	8/33	1	2	FACETS	0.926	0.865	0.989	0.926	0.865	0.989	CLONAL	1	TRUE	1	0.619837860235886	2		759	777	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353735	15353736	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	216	566	1	ENST00000263377.2:c.3144_3145delinsTT	p.His1049Tyr	p.H1049Y	ENST00000263377	NM_058243.2	1048	caCCac/caTTac	14/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.619837860235886	2		567	669	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354229	15354229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	210	731	0	ENST00000263377.2:c.2651C>T	p.Pro884Leu	p.P884L	ENST00000263377	NM_058243.2	884	cCc/cTc	14/20	1	2	FACETS	0.936	0.872	1	0.936	0.872	1	CLONAL	1	TRUE	1	0.619837860235886	2		731	724	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945794	17945794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	203	666	0	ENST00000458235.1:c.2066C>T	p.Pro689Leu	p.P689L	ENST00000458235	NM_000215.3	689	cCc/cTc	16/24	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.619837860235886	2		666	642	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953136	17953136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	157	605	1	ENST00000458235.1:c.850G>A	p.Gly284Arg	p.G284R	ENST00000458235	NM_000215.3	284	Gga/Aga	6/24	1	2	FACETS	0.909	0.838	0.984	0.909	0.838	0.984	CLONAL	1	TRUE	1	0.619837860235886	2		606	557	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953878	17953878	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs776089693	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	104	752	0	ENST00000458235.1:c.524G>C	p.Arg175Pro	p.R175P	ENST00000458235	NM_000215.3	175	cGa/cCa	5/24	1	2	FACETS	0.458	0.41	0.509	0.458	0.41	0.509	SUBCLONAL	1	TRUE	1	0.619837860235886	2		752	733	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273811	18273811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	239	584	0	ENST00000222254.8:c.1144C>T	p.His382Tyr	p.H382Y	ENST00000222254	NM_005027.3	382	Cac/Tac	10/16	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.619837860235886	2		584	762	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210703	36210703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200918556	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	230	683	1	ENST00000222270.7:c.454C>T	p.Arg152Trp	p.R152W	ENST00000222270	NM_014727.1	152	Cgg/Tgg	3/37	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.619837860235886	2		684	633	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220154	36220154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	177	638	0	ENST00000222270.7:c.4874C>T	p.Ser1625Phe	p.S1625F	ENST00000222270	NM_014727.1	1625	tCc/tTc	22/37	1	2	FACETS	0.946	0.876	1	0.946	0.876	1	CLONAL	1	TRUE	1	0.619837860235886	2		638	604	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222961	36222961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	243	745	1	ENST00000222270.7:c.5590C>T	p.Arg1864Ter	p.R1864*	ENST00000222270	NM_014727.1	1864	Cga/Tga	27/37	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.619837860235886	2		746	763	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794482	42794482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs958141258	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	248	716	1	ENST00000575354.2:c.1562C>T	p.Pro521Leu	p.P521L	ENST00000575354	NM_015125.3	521	cCt/cTt	10/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.619837860235886	2		717	767	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796328	42796329	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	215	692	0	ENST00000575354.2:c.2977_2978delinsTT	p.Pro993Phe	p.P993F	ENST00000575354	NM_015125.3	993	CCt/TTt	12/20	1	2	FACETS	0.974	0.909	1	0.974	0.909	1	CLONAL	1	TRUE	1	0.619837860235886	2		692	712	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262373	39262373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	109	415	0	ENST00000402219.2:c.1054C>T	p.His352Tyr	p.H352Y	ENST00000402219	NM_005633.3	352	Cat/Tat	8/23	0.302613917882319	1	FACETS	0.391	0.351	0.432	0.391	0.351	0.432	INDETERMINATE	1	TRUE	0	0.619837860235886	1		415	621	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606921	47606921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	182	284	0	ENST00000263735.4:c.671C>T	p.Ser224Phe	p.S224F	ENST00000263735	NM_002354.2	224	tCc/tTc	7/9	0.302613917882319	1	FACETS	0.862	0.803	0.922	0.862	0.803	0.922	INDETERMINATE	1	TRUE	0	0.619837860235886	1		284	470	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028246	48028246	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	190	358	0	ENST00000234420.5:c.3124A>G	p.Lys1042Glu	p.K1042E	ENST00000234420	NM_000179.2	1042	Aaa/Gaa	4/10	0.302613917882319	1	FACETS	0.928	0.867	0.989	0.928	0.867	0.989	INDETERMINATE	1	TRUE	0	0.619837860235886	1		358	456	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872836	136872836	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	63	379	0	ENST00000241393.3:c.662T>A	p.Ile221Asn	p.I221N	ENST00000241393	NM_003467.2	221	aTt/aAt	2/2	0.305463341134168	1	FACETS	0.358	0.311	0.409	0.358	0.311	0.409	INDETERMINATE	1	TRUE	0	0.619837860235886	1		379	392	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095622	178095622	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	88	426	0	ENST00000397062.3:c.1709A>G	p.Asp570Gly	p.D570G	ENST00000397062	NM_006164.4	570	gAt/gGt	5/5	0.305463341134168	1	FACETS	0.347	0.308	0.389	0.347	0.308	0.389	INDETERMINATE	1	TRUE	0	0.619837860235886	1		426	565	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728659	190728659	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	253	393	0	ENST00000441310.2:c.2047C>T	p.Gln683Ter	p.Q683*	ENST00000441310	NM_000534.4	683	Cag/Tag	10/13	0.305463341134168	1	FACETS	0.945	0.892	0.999	0.945	0.892	0.999	INDETERMINATE	1	TRUE	0	0.619837860235886	1		393	596	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735497	204735497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	213	453	0	ENST00000302823.3:c.298G>A	p.Asp100Asn	p.D100N	ENST00000302823	NM_005214.4	100	Gat/Aat	2/4	0.305463341134168	1	FACETS	0.885	0.829	0.941	0.885	0.829	0.941	INDETERMINATE	1	TRUE	0	0.619837860235886	1		453	536	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248614	212248614	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	109	413	1	ENST00000342788.4:c.3653A>T	p.Lys1218Ile	p.K1218I	ENST00000342788	NM_005235.2	1218	aAa/aTa	28/28	0.305463341134168	1	FACETS	0.445	0.4	0.491	0.445	0.4	0.491	INDETERMINATE	1	TRUE	0	0.619837860235886	1		414	546	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285204	212285204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867780056	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	77	377	0	ENST00000342788.4:c.3097C>T	p.Pro1033Ser	p.P1033S	ENST00000342788	NM_005235.2	1033	Ccc/Tcc	25/28	0.305463341134168	1	FACETS	0.334	0.293	0.377	0.334	0.293	0.377	INDETERMINATE	1	TRUE	0	0.619837860235886	1		377	514	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288996	212288996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	206	403	0	ENST00000342788.4:c.2750G>A	p.Gly917Glu	p.G917E	ENST00000342788	NM_005235.2	917	gGa/gAa	23/28	0.305463341134168	1	FACETS	0.875	0.819	0.932	0.875	0.819	0.932	INDETERMINATE	1	TRUE	0	0.619837860235886	1		403	524	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568867	212568868	+	missense_variant	Missense_Mutation	DNP	AA	AA	TG	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	181	413	1	ENST00000342788.4:c.1250_1251delinsCA	p.Phe417Ser	p.F417S	ENST00000342788	NM_005235.2	417	tTT/tCA	11/28	0.305463341134168	1	FACETS	0.685	0.636	0.736	0.685	0.636	0.736	INDETERMINATE	1	TRUE	0	0.619837860235886	1		414	588	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794434	242794434	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757671679	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	83	750	0	ENST00000334409.5:c.508G>A	p.Val170Met	p.V170M	ENST00000334409	NM_005018.2	170	Gtg/Atg	3/5	0.305463341134168	1	FACETS	0.314	0.277	0.354	0.314	0.277	0.354	INDETERMINATE	1	TRUE	0	0.619837860235886	1		750	588	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561090	9561090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	152	353	0	ENST00000353224.5:c.692C>T	p.Ser231Leu	p.S231L	ENST00000353224	NM_177990.2	231	tCa/tTa	4/10	NA	2	FACETS	1	0.954	1			1	INDETERMINATE	1	TRUE	NA	0.619837860235886	2		353	468	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561349	9561349	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	166	432	1	ENST00000353224.5:c.433A>T	p.Lys145Ter	p.K145*	ENST00000353224	NM_177990.2	145	Aag/Tag	4/10	NA	2	FACETS	1	0.937	1			1	INDETERMINATE	1	TRUE	NA	0.619837860235886	2		433	528	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024170	31024170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774688930	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	254	579	0	ENST00000375687.4:c.3655C>T	p.Pro1219Ser	p.P1219S	ENST00000375687	NM_015338.5	1219	Ccc/Tcc	13/13	0.619837860235886	3	FACETS	1	0.976	1	0.543	0.508	0.578	CLONAL	1	TRUE	1	0.619837860235886	3		579	989	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384651	31384651	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	190	544	0	ENST00000328111.2:c.1359del	p.Leu454SerfsTer136	p.L454Sfs*136	ENST00000328111	NM_006892.3	451	gaG/ga	13/23	0.619837860235886	3	FACETS	0.917	0.848	0.988	0.458	0.424	0.494	CLONAL	1	TRUE	1	0.619837860235886	3		544	876	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026144	36026144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	534	827	0	ENST00000358208.4:c.746C>T	p.Pro249Leu	p.P249L	ENST00000358208		249	cCc/cTc	7/12	0.619837860235886	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.619837860235886	3		827	1123	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748601	40748601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200545231	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	330	384	1	ENST00000373198.4:c.2915G>A	p.Arg972Gln	p.R972Q	ENST00000373198	NM_133170.3	972	cGa/cAa	21/32	0.619837860235886	3	FACETS	0.967	0.921	1	0.967	0.921	1	CLONAL	2	TRUE	1	0.619837860235886	3		385	721	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757459	40757460	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	400	545	2	ENST00000373198.4:c.2838_2839delinsTT	p.Arg947Trp	p.R947W	ENST00000373198	NM_133170.3	946	tcCCgg/tcTTgg	20/32	0.619837860235886	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.619837860235886	3		547	817	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827984	40827984	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1174893851	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	334	543	0	ENST00000373198.4:c.2444G>A	p.Arg815Lys	p.R815K	ENST00000373198	NM_133170.3	815	aGg/aAg	17/32	0.619837860235886	3	FACETS	0.962	0.916	1	0.962	0.916	1	CLONAL	2	TRUE	1	0.619837860235886	3		543	734	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899067	40899067	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	319	536	0	ENST00000373198.4:c.2203C>A	p.Pro735Thr	p.P735T	ENST00000373198	NM_133170.3	735	Ccg/Acg	14/32	0.619837860235886	3	FACETS	0.946	0.899	0.992	0.946	0.899	0.992	CLONAL	2	TRUE	1	0.619837860235886	3		536	713	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171607	36171607	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1569008655	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	127	333	0	ENST00000300305.3:c.958C>T	p.Arg320Ter	p.R320*	ENST00000300305		320	Cga/Tga	7/8	0.230162751595408	1	FACETS	0.628	0.573	0.685	0.628	0.573	0.685	INDETERMINATE	1	TRUE	0	0.619837860235886	1		333	450	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755685	39755685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	204	537	0	ENST00000288319.7:c.1080G>A	p.Met360Ile	p.M360I	ENST00000288319	NM_182918.3	360	atG/atA	10/10	0.230162751595408	1	FACETS	0.748	0.698	0.8	0.748	0.698	0.8	INDETERMINATE	1	TRUE	0	0.619837860235886	1		537	607	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795373	39795373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	241	624	0	ENST00000288319.7:c.347C>T	p.Pro116Leu	p.P116L	ENST00000288319	NM_182918.3	116	cCa/cTa	3/10	0.230162751595408	1	FACETS	0.708	0.664	0.753	0.708	0.664	0.753	INDETERMINATE	1	TRUE	0	0.619837860235886	1		624	758	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866495	42866495	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767591322	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	295	565	1	ENST00000398585.3:c.137C>T	p.Pro46Leu	p.P46L	ENST00000398585	NM_001135099.1	46	cCa/cTa	3/14	0.230162751595408	1	FACETS	0.772	0.729	0.815	0.772	0.729	0.815	INDETERMINATE	1	TRUE	0	0.619837860235886	1		566	851	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657086	45657086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	101	298	0	ENST00000407780.3:c.70G>A	p.Glu24Lys	p.E24K	ENST00000407780	NM_001283052.1	24	Gaa/Aaa	3/7	0.230162751595408	1	FACETS	0.684	0.618	0.752	0.684	0.618	0.752	INDETERMINATE	1	TRUE	0	0.619837860235886	1		298	329	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042498	37042498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	122	447	0	ENST00000231790.2:c.260C>T	p.Ser87Phe	p.S87F	ENST00000231790	NM_000249.3	87	tCc/tTc	3/19	0.305463341134168	1	FACETS	0.399	0.361	0.439	0.399	0.361	0.439	INDETERMINATE	1	TRUE	0	0.619837860235886	1		447	681	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180202	38180202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	76	547	0	ENST00000396334.3:c.50G>A	p.Gly17Glu	p.G17E	ENST00000396334	NM_002468.4	17	gGa/gAa	1/5	0.305463341134168	1	FACETS	0.345	0.303	0.39	0.345	0.303	0.39	INDETERMINATE	1	TRUE	0	0.619837860235886	1		547	490	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924970	49924970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	110	590	0	ENST00000296474.3:c.3973G>A	p.Glu1325Lys	p.E1325K	ENST00000296474	NM_002447.2	1325	Gag/Aag	20/20	0.305463341134168	1	FACETS	0.46	0.415	0.508	0.46	0.415	0.508	INDETERMINATE	1	TRUE	0	0.619837860235886	1		590	532	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259137	89259137	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	82	330	0	ENST00000336596.2:c.281A>T	p.Lys94Met	p.K94M	ENST00000336596	NM_005233.5	94	aAg/aTg	3/17	0.305463341134168	1	FACETS	0.421	0.372	0.472	0.421	0.372	0.472	INDETERMINATE	1	TRUE	0	0.619837860235886	1		330	434	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448615	89448615	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	252	482	1	ENST00000336596.2:c.1579G>A	p.Glu527Lys	p.E527K	ENST00000336596	NM_005233.5	527	Gaa/Aaa	7/17	0.305463341134168	1	FACETS	0.873	0.822	0.924	0.873	0.822	0.924	INDETERMINATE	1	TRUE	0	0.619837860235886	1		483	643	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468525	89468525	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	61	307	0	ENST00000336596.2:c.2059G>T	p.Gly687Ter	p.G687*	ENST00000336596	NM_005233.5	687	Gga/Tga	11/17	0.305463341134168	1	FACETS	0.333	0.288	0.381	0.333	0.288	0.381	INDETERMINATE	1	TRUE	0	0.619837860235886	1		307	408	SUCCESS
ATR	545	MSKCC	GRCh37	3	142241667	142241667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	194	320	0	ENST00000350721.4:c.4169C>T	p.Ser1390Leu	p.S1390L	ENST00000350721	NM_001184.3	1390	tCa/tTa	23/47	0.305463341134168	1	FACETS	0.935	0.875	0.996	0.935	0.875	0.996	INDETERMINATE	1	TRUE	0	0.619837860235886	1		320	462	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586382	189586382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867300924	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	122	310	0	ENST00000264731.3:c.1006G>A	p.Gly336Ser	p.G336S	ENST00000264731	NM_003722.4	336	Ggc/Agc	8/14	0.305463341134168	1	FACETS	0.73	0.667	0.795	0.73	0.667	0.795	INDETERMINATE	1	TRUE	0	0.619837860235886	1		310	372	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587144	189587144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140374868	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	97	349	0	ENST00000264731.3:c.1161G>A	p.Met387Ile	p.M387I	ENST00000264731	NM_003722.4	387	atG/atA	9/14	0.305463341134168	1	FACETS	0.418	0.374	0.465	0.418	0.374	0.465	INDETERMINATE	1	TRUE	0	0.619837860235886	1		349	517	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607131	189607131	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	217	552	0	ENST00000264731.3:c.1510C>T	p.Pro504Ser	p.P504S	ENST00000264731	NM_003722.4	504	Ccc/Tcc	12/14	0.305463341134168	1	FACETS	0.812	0.76	0.865	0.812	0.76	0.865	INDETERMINATE	1	TRUE	0	0.619837860235886	1		552	595	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607197	189607197	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1438616472	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	119	681	0	ENST00000264731.3:c.1576C>T	p.Pro526Ser	p.P526S	ENST00000264731	NM_003722.4	526	Cct/Tct	12/14	0.305463341134168	1	FACETS	0.449	0.406	0.494	0.449	0.406	0.494	INDETERMINATE	1	TRUE	0	0.619837860235886	1		681	590	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612106	189612106	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	223	549	0	ENST00000264731.3:c.1858C>G	p.Pro620Ala	p.P620A	ENST00000264731	NM_003722.4	620	Cca/Gca	14/14	0.305463341134168	1	FACETS	0.873	0.819	0.927	0.873	0.819	0.927	INDETERMINATE	1	TRUE	0	0.619837860235886	1		549	569	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806648	1806648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	212	782	0	ENST00000260795.2:c.1364C>T	p.Ser455Phe	p.S455F	ENST00000260795		455	tCc/tTc	9/17	0.302613917882319	1	FACETS	0.831	0.778	0.885	0.831	0.778	0.885	INDETERMINATE	1	TRUE	0	0.619837860235886	1		782	568	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750452	41750452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	98	529	0	ENST00000226382.2:c.176C>T	p.Ser59Phe	p.S59F	ENST00000226382	NM_003924.3	59	tCc/tTc	1/3	0.302613917882319	1	FACETS	0.466	0.418	0.517	0.466	0.418	0.517	INDETERMINATE	1	TRUE	0	0.619837860235886	1		529	468	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	216	424	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	0.302613917882319	1	FACETS	0.773	0.723	0.824	0.773	0.723	0.824	INDETERMINATE	1	TRUE	0	0.619837860235886	1		424	622	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356421	66356421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	129	299	0	ENST00000273854.3:c.1076C>T	p.Ser359Phe	p.S359F	ENST00000273854	NM_004439.5	359	tCt/tTt	5/18	0.302613917882319	1	FACETS	0.833	0.765	0.902	0.833	0.765	0.902	INDETERMINATE	1	TRUE	0	0.619837860235886	1		299	345	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157506	106157506	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs368508787	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	134	319	0	ENST00000380013.4:c.2407C>T	p.Gln803Ter	p.Q803*	ENST00000380013	NM_001127208.2	803	Caa/Taa	3/11	0.302613917882319	1	FACETS	0.831	0.764	0.899	0.831	0.764	0.899	INDETERMINATE	1	TRUE	0	0.619837860235886	1		319	359	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190815	106190815	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	122	430	0	ENST00000380013.4:c.4093G>C	p.Gly1365Arg	p.G1365R	ENST00000380013	NM_001127208.2	1365	Ggc/Cgc	9/11	0.302613917882319	1	FACETS	0.428	0.388	0.471	0.428	0.388	0.471	INDETERMINATE	1	TRUE	0	0.619837860235886	1		430	634	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247284	153247284	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	80	296	0	ENST00000281708.4:c.1518T>G	p.Cys506Trp	p.C506W	ENST00000281708	NM_033632.3	506	tgT/tgG	10/12	0.302613917882319	1	FACETS	0.36	0.317	0.405	0.36	0.317	0.405	INDETERMINATE	1	TRUE	0	0.619837860235886	1		296	495	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629514	187629514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769874804	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	128	494	0	ENST00000441802.2:c.1468C>T	p.Pro490Ser	p.P490S	ENST00000441802	NM_005245.3	490	Cct/Tct	2/27	0.302613917882319	1	FACETS	0.468	0.425	0.513	0.468	0.425	0.513	INDETERMINATE	1	TRUE	0	0.619837860235886	1		494	609	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282739	1282739	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	122	439	0	ENST00000310581.5:c.1574G>A	p.Gly525Glu	p.G525E	ENST00000310581	NM_198253.2	525	gGg/gAg	3/16	0.371442838158786	1	FACETS	0.757	0.692	0.824	0.757	0.692	0.824	INDETERMINATE	1	TRUE	0	0.619837860235886	1		439	359	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873672	35873672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	76	312	0	ENST00000303115.3:c.628G>A	p.Asp210Asn	p.D210N	ENST00000303115	NM_002185.3	210	Gat/Aat	5/8	0.371442838158786	1	FACETS	0.492	0.435	0.553	0.492	0.435	0.553	INDETERMINATE	1	TRUE	0	0.619837860235886	1		312	344	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950465	38950465	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	189	316	0	ENST00000357387.3:c.3485C>T	p.Ser1162Leu	p.S1162L	ENST00000357387	NM_152756.3	1162	tCa/tTa	31/38	0.175789378153813	2	FACETS	1	0.986	1	0.614	0.572	0.656	INDETERMINATE	1	TRUE	0	0.619837860235886	2		316	497	SUCCESS
APC	324	MSKCC	GRCh37	5	112177701	112177701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554087411	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	134	280	0	ENST00000257430.4:c.6410C>T	p.Ser2137Phe	p.S2137F	ENST00000257430	NM_000038.5	2137	tCc/tTc	16/16	0.329995862743379	1	FACETS	0.775	0.712	0.84	0.775	0.712	0.84	INDETERMINATE	1	TRUE	0	0.619837860235886	1		280	385	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449857	149449857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	111	718	1	ENST00000286301.3:c.1207G>A	p.Glu403Lys	p.E403K	ENST00000286301	NM_005211.3	403	Gag/Aag	9/22	0.329995862743379	1	FACETS	0.405	0.364	0.447	0.405	0.364	0.447	INDETERMINATE	1	TRUE	0	0.619837860235886	1		719	611	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459896	149459896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	208	544	0	ENST00000286301.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000286301	NM_005211.3	104	cCt/cTt	4/22	0.329995862743379	1	FACETS	0.864	0.809	0.92	0.864	0.809	0.92	INDETERMINATE	1	TRUE	0	0.619837860235886	1		544	536	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460492	149460492	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745585475	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	249	657	0	ENST00000286301.3:c.145G>A	p.Glu49Lys	p.E49K	ENST00000286301	NM_005211.3	49	Gaa/Aaa	3/22	0.329995862743379	1	FACETS	0.909	0.857	0.962	0.909	0.857	0.962	INDETERMINATE	1	TRUE	0	0.619837860235886	1		657	610	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495372	149495372	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146614144	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	103	648	0	ENST00000261799.4:c.3275C>T	p.Ser1092Leu	p.S1092L	ENST00000261799	NM_002609.3	1092	tCg/tTg	23/23	0.329995862743379	1	FACETS	0.408	0.366	0.453	0.408	0.366	0.453	INDETERMINATE	1	TRUE	0	0.619837860235886	1		648	562	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818753	170818753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	89	324	0	ENST00000296930.5:c.302G>A	p.Arg101Lys	p.R101K	ENST00000296930	NM_002520.6	101	aGg/aAg	4/11	0.329995862743379	1	FACETS	0.414	0.368	0.462	0.414	0.368	0.462	INDETERMINATE	1	TRUE	0	0.619837860235886	1		324	479	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520534	176520534	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	206	726	0	ENST00000292408.4:c.1379G>A	p.Trp460Ter	p.W460*	ENST00000292408	NM_213647.1	460	tGg/tAg	10/18	0.329995862743379	1	FACETS	0.776	0.725	0.829	0.776	0.725	0.829	INDETERMINATE	1	TRUE	0	0.619837860235886	1		726	591	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030382	180030382	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1382151235	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	182	630	0	ENST00000261937.6:c.3902G>A	p.Gly1301Glu	p.G1301E	ENST00000261937	NM_182925.4	1301	gGa/gAa	30/30	0.329995862743379	1	FACETS	0.705	0.654	0.757	0.705	0.654	0.757	INDETERMINATE	1	TRUE	0	0.619837860235886	1		630	575	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038386	180038386	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	204	712	0	ENST00000261937.6:c.3631C>T	p.Gln1211Ter	p.Q1211*	ENST00000261937	NM_182925.4	1211	Cag/Tag	27/30	0.329995862743379	1	FACETS	0.758	0.708	0.81	0.758	0.708	0.81	INDETERMINATE	1	TRUE	0	0.619837860235886	1		712	599	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180049814	180049814	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs757097428	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	209	595	0	ENST00000261937.6:c.1574A>G	p.Asn525Ser	p.N525S	ENST00000261937	NM_182925.4	525	aAt/aGt	12/30	0.329995862743379	1	FACETS	0.881	0.826	0.938	0.881	0.826	0.938	INDETERMINATE	1	TRUE	0	0.619837860235886	1		595	528	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056334	180056334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751948166	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	114	641	0	ENST00000261937.6:c.910G>A	p.Asp304Asn	p.D304N	ENST00000261937	NM_182925.4	304	Gac/Aac	7/30	0.329995862743379	1	FACETS	0.437	0.394	0.482	0.437	0.394	0.482	INDETERMINATE	1	TRUE	0	0.619837860235886	1		641	581	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057657	180057657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775457696	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	251	718	0	ENST00000261937.6:c.298G>A	p.Glu100Lys	p.E100K	ENST00000261937	NM_182925.4	100	Gag/Aag	3/30	0.329995862743379	1	FACETS	0.916	0.864	0.969	0.916	0.864	0.969	INDETERMINATE	1	TRUE	0	0.619837860235886	1		718	610	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187453	32187453	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	217	654	0	ENST00000375023.3:c.1426C>T	p.His476Tyr	p.H476Y	ENST00000375023	NM_004557.3	476	Cac/Tac	8/30	0.332675110722324	1	FACETS	0.793	0.743	0.845	0.793	0.743	0.845	INDETERMINATE	1	TRUE	0	0.619837860235886	1		654	609	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187527	32187527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	122	591	0	ENST00000375023.3:c.1352C>T	p.Ser451Phe	p.S451F	ENST00000375023	NM_004557.3	451	tCc/tTc	8/30	0.332675110722324	1	FACETS	0.422	0.382	0.464	0.422	0.382	0.464	INDETERMINATE	1	TRUE	0	0.619837860235886	1		591	643	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289095	33289095	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	267	625	1	ENST00000374542.5:c.457A>T	p.Asn153Tyr	p.N153Y	ENST00000374542	NM_001141970.1	153	Aat/Tat	3/8	0.332675110722324	1	FACETS	0.933	0.882	0.985	0.933	0.882	0.985	INDETERMINATE	1	TRUE	0	0.619837860235886	1		626	637	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967228	93967228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1247358846	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	72	242	0	ENST00000369303.4:c.2124G>A	p.Met708Ile	p.M708I	ENST00000369303	NM_004440.3	708	atG/atA	12/17	0.332675110722324	1	FACETS	0.416	0.366	0.471	0.416	0.366	0.471	INDETERMINATE	1	TRUE	0	0.619837860235886	1		242	385	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969189	93969189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868510824	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	56	332	0	ENST00000369303.4:c.1807C>T	p.Pro603Ser	p.P603S	ENST00000369303	NM_004440.3	603	Cca/Tca	10/17	0.332675110722324	1	FACETS	0.4	0.344	0.459	0.4	0.344	0.459	INDETERMINATE	1	TRUE	0	0.619837860235886	1		332	312	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066482	94066482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542602078	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	125	305	0	ENST00000369303.4:c.1277G>A	p.Arg426Gln	p.R426Q	ENST00000369303	NM_004440.3	426	cGa/cAa	5/17	0.332675110722324	1	FACETS	0.731	0.668	0.795	0.731	0.668	0.795	INDETERMINATE	1	TRUE	0	0.619837860235886	1		305	381	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120489	94120489	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	96	393	0	ENST00000369303.4:c.562G>A	p.Asp188Asn	p.D188N	ENST00000369303	NM_004440.3	188	Gat/Aat	3/17	0.332675110722324	1	FACETS	0.44	0.393	0.489	0.44	0.393	0.489	INDETERMINATE	1	TRUE	0	0.619837860235886	1		393	486	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94128966	94128966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	100	355	0	ENST00000369303.4:c.94G>A	p.Glu32Lys	p.E32K	ENST00000369303	NM_004440.3	32	Gaa/Aaa	1/17	0.332675110722324	1	FACETS	0.424	0.38	0.471	0.424	0.38	0.471	INDETERMINATE	1	TRUE	0	0.619837860235886	1		355	525	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106543511	106543511	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	139	248	0	ENST00000369096.4:c.313G>A	p.Glu105Lys	p.E105K	ENST00000369096	NM_001198.3	105	Gaa/Aaa	3/7	0.332675110722324	1	FACETS	0.792	0.728	0.856	0.792	0.728	0.856	INDETERMINATE	1	TRUE	0	0.619837860235886	1		248	391	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322511	109322511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769935193	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	250	376	0	ENST00000436639.2:c.526C>T	p.Arg176Cys	p.R176C	ENST00000436639	NM_014454.2	176	Cgt/Tgt	3/10	0.332675110722324	1	FACETS	0.852	0.802	0.903	0.852	0.802	0.903	INDETERMINATE	1	TRUE	0	0.619837860235886	1		376	653	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622245	117622245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	111	422	0	ENST00000368508.3:c.6625C>T	p.His2209Tyr	p.H2209Y	ENST00000368508	NM_002944.2	2209	Cat/Tat	42/43	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.619837860235886	NA		422	595	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687313	117687313	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	189	316	0	ENST00000368508.3:c.2738C>T	p.Thr913Ile	p.T913I	ENST00000368508	NM_002944.2	913	aCc/aTc	18/43	0.542387782897967	1	FACETS	0.923	0.862	0.984	0.923	0.862	0.984	CLONAL	1	TRUE	0	0.619837860235886	1		316	456	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704520	117704520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	198	363	0	ENST00000368508.3:c.2456C>T	p.Ser819Phe	p.S819F	ENST00000368508	NM_002944.2	819	tCc/tTc	16/43	0.542387782897967	1	FACETS	0.871	0.814	0.929	0.871	0.814	0.929	CLONAL	1	TRUE	0	0.619837860235886	1		363	506	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332814	152332814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	99	446	1	ENST00000206249.3:c.1120G>A	p.Asp374Asn	p.D374N	ENST00000206249	NM_000125.3	374	Gat/Aat	5/8	0.305463341134168	1	FACETS	0.365	0.326	0.406	0.365	0.326	0.406	INDETERMINATE	1	TRUE	0	0.619837860235886	1		447	604	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962363	2962363	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	105	635	0	ENST00000396946.4:c.2174G>C	p.Ser725Thr	p.S725T	ENST00000396946	NM_032415.4	725	aGt/aCt	17/25	1	2	FACETS	0.463	0.415	0.515	0.463	0.415	0.515	SUBCLONAL	1	TRUE	1	0.619837860235886	2		635	731	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985552	2985552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	203	473	0	ENST00000396946.4:c.259G>A	p.Gly87Ser	p.G87S	ENST00000396946	NM_032415.4	87	Ggc/Agc	4/25	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.619837860235886	2		473	597	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971178	13971178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs904139873	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	194	353	0	ENST00000405192.2:c.751C>T	p.Pro251Ser	p.P251S	ENST00000405192	NM_001163147.1	251	Ccc/Tcc	8/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.619837860235886	2		353	555	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729363	41729363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	214	520	0	ENST00000242208.4:c.1166C>T	p.Ser389Leu	p.S389L	ENST00000242208	NM_002192.2	389	tCg/tTg	3/3	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.619837860235886	2		520	661	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346583	81346583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	199	358	0	ENST00000222390.5:c.1370C>T	p.Pro457Leu	p.P457L	ENST00000222390	NM_000601.4	457	cCa/cTa	11/18	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.619837860235886	2		358	602	SUCCESS
MET	4233	MSKCC	GRCh37	7	116381023	116381023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	139	566	0	ENST00000397752.3:c.1645G>A	p.Glu549Lys	p.E549K	ENST00000397752	NM_000245.2	549	Gag/Aag	5/21	1	2	FACETS	0.489	0.444	0.535	0.489	0.444	0.535	SUBCLONAL	1	TRUE	1	0.619837860235886	2		566	918	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415003	116415003	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1294910019	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	256	488	0	ENST00000397752.3:c.3097C>T	p.Pro1033Ser	p.P1033S	ENST00000397752	NM_000245.2	1033	Ccc/Tcc	15/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.619837860235886	2		488	812	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435824	116435824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	239	455	0	ENST00000397752.3:c.3914C>T	p.Pro1305Leu	p.P1305L	ENST00000397752	NM_000245.2	1305	cCc/cTc	20/21	1	2	FACETS	0.968	0.906	1	0.968	0.906	1	CLONAL	1	TRUE	1	0.619837860235886	2		455	797	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879333	151879333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	168	376	0	ENST00000262189.6:c.5612C>T	p.Ala1871Val	p.A1871V	ENST00000262189	NM_170606.2	1871	gCt/gTt	36/59	1	2	FACETS	0.949	0.878	1	0.949	0.878	1	CLONAL	1	TRUE	1	0.619837860235886	2		376	571	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864738	68864738	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	142	430	2	ENST00000288368.4:c.109G>A	p.Asp37Asn	p.D37N	ENST00000288368	NM_024870.2	37	Gac/Aac	1/40	1	2	FACETS	0.935	0.858	1	0.935	0.858	1	CLONAL	1	TRUE	1	0.619837860235886	2		432	490	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931898	68931898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	211	447	0	ENST00000288368.4:c.328C>T	p.Leu110Phe	p.L110F	ENST00000288368	NM_024870.2	110	Ctt/Ttt	3/40	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.619837860235886	2		447	680	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968143	68968143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	230	481	1	ENST00000288368.4:c.1172G>A	p.Arg391Lys	p.R391K	ENST00000288368	NM_024870.2	391	aGa/aAa	10/40	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.619837860235886	2		482	699	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981348	68981348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	205	353	0	ENST00000288368.4:c.1420G>A	p.Glu474Lys	p.E474K	ENST00000288368	NM_024870.2	474	Gag/Aag	12/40	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.619837860235886	2		353	599	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995520	68995520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	237	494	0	ENST00000288368.4:c.1924G>A	p.Asp642Asn	p.D642N	ENST00000288368	NM_024870.2	642	Gac/Aac	18/40	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.619837860235886	2		494	761	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69000009	69000009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	240	470	0	ENST00000288368.4:c.2078G>A	p.Gly693Glu	p.G693E	ENST00000288368	NM_024870.2	693	gGa/gAa	19/40	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.619837860235886	2		470	741	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030850	69030850	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150128151	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	183	379	1	ENST00000288368.4:c.3392C>T	p.Ser1131Leu	p.S1131L	ENST00000288368	NM_024870.2	1131	tCg/tTg	27/40	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.619837860235886	2		380	584	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340386	8340386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	114	475	0	ENST00000356435.5:c.5210C>T	p.Ser1737Phe	p.S1737F	ENST00000356435		1737	tCc/tTc	31/35	0.302613917882319	1	FACETS	0.43	0.388	0.474	0.43	0.388	0.474	INDETERMINATE	1	TRUE	0	0.619837860235886	1		475	590	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449773	8449773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	134	484	0	ENST00000356435.5:c.3940C>T	p.His1314Tyr	p.H1314Y	ENST00000356435		1314	Cac/Tac	23/35	0.302613917882319	1	FACETS	0.419	0.381	0.459	0.419	0.381	0.459	INDETERMINATE	1	TRUE	0	0.619837860235886	1		484	712	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485918	8485919	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	147	407	1	ENST00000356435.5:c.2898_2899delinsAT	p.Pro967Ser	p.P967S	ENST00000356435		966	ctCCcg/ctATcg	17/35	0.302613917882319	1	FACETS	0.852	0.788	0.918	0.852	0.788	0.918	INDETERMINATE	1	TRUE	0	0.619837860235886	1		408	384	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27183606	27183606	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	156	357	0	ENST00000380036.4:c.1180C>T	p.His394Tyr	p.H394Y	ENST00000380036	NM_000459.3	394	Cat/Tat	8/23	0.619837860235886	1	FACETS	0.941	0.874	1	0.941	0.874	1	CLONAL	1	TRUE	0	0.619837860235886	1		357	369	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206694	27206694	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	188	412	0	ENST00000380036.4:c.2479C>T	p.Gln827Ter	p.Q827*	ENST00000380036	NM_000459.3	827	Caa/Taa	15/23	0.619837860235886	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.619837860235886	1		412	395	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624493	93624493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1276980680	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	55	384	0	ENST00000375746.1:c.584G>A	p.Arg195Gln	p.R195Q	ENST00000375746	NM_001174167.1	195	cGa/cAa	4/14	0.332675110722324	1	FACETS	0.361	0.31	0.416	0.361	0.31	0.416	INDETERMINATE	1	TRUE	0	0.619837860235886	1		384	339	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624598	93624599	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	90	515	0	ENST00000375746.1:c.692dup	p.Lys233GlufsTer15	p.K233Efs*15	ENST00000375746	NM_001174167.1	230	gag/gaGg	4/14	0.332675110722324	1	FACETS	0.405	0.36	0.452	0.405	0.36	0.452	INDETERMINATE	1	TRUE	0	0.619837860235886	1		515	495	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650798	93650798	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	41	330	0	ENST00000375746.1:c.1724G>A	p.Gly575Glu	p.G575E	ENST00000375746	NM_001174167.1	575	gGg/gAg	13/14	0.332675110722324	1	FACETS	0.263	0.219	0.311	0.263	0.219	0.311	INDETERMINATE	1	TRUE	0	0.619837860235886	1		330	347	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412267	139412267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1266989706	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	254	780	0	ENST00000277541.6:c.1378C>T	p.Pro460Ser	p.P460S	ENST00000277541	NM_017617.3	460	Ccg/Tcg	8/34	0.332675110722324	1	FACETS	0.817	0.769	0.866	0.817	0.769	0.866	INDETERMINATE	1	TRUE	0	0.619837860235886	1		780	692	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317433	1317433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	74	541	0	ENST00000400841.2:c.632G>A	p.Arg211Lys	p.R211K	ENST00000400841		211	aGa/aAa	5/6	1	1	FACETS	0.303	0.266	0.344	0.303	0.266	0.344	SUBCLONAL	1	TRUE	0	0.619837860235886	1		541	543	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220428	123220428	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025945-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	226	237	1	ENST00000218089.9:c.3085C>T	p.Gln1029Ter	p.Q1029*	ENST00000218089	NM_001042749.1	1029	Cag/Tag	30/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.619837860235886	1		238	359	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967900	93967900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373761211	NA	P-0026295-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	95	415	0	ENST00000369303.4:c.2027G>A	p.Arg676Lys	p.R676K	ENST00000369303	NM_004440.3	676	aGg/aAg	11/17	0.477642436102302	4	FACETS	0.879	0.783	0.98	0.293	0.261	0.327	CLONAL	1	TRUE	1	0.477642436102302	4		415	669	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836762	151836762	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026295-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	63	394	0	ENST00000262189.6:c.14458C>T	p.Gln4820Ter	p.Q4820*	ENST00000262189	NM_170606.2	4820	Cag/Tag	56/59	0.477642436102302	3	FACETS	0.787	0.683	0.9			1	SUBCLONAL	1	TRUE	NA	0.477642436102302	3		394	415	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796187	45796187	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs876659420	NA	P-0026295-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	70	394	0	ENST00000450313.1:c.1518+1G>T		p.X506_splice	ENST00000450313	NM_012222.2	506			1	2	FACETS	0.819	0.718	0.926	0.819	0.718	0.926	CLONAL	1	TRUE	1	0.477642436102302	2		394	358	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982339	201982339	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026295-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	149	736	0	ENST00000359651.3:c.718C>G	p.Pro240Ala	p.P240A	ENST00000359651		240	Ccc/Gcc	6/8	1	2	FACETS	0.947	0.868	1	0.947	0.868	1	CLONAL	1	TRUE	1	0.477642436102302	2		736	659	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982599	10982600	+	splice_donor_variant	Splice_Site	DEL	GT	GT	-	novel	NA	P-0026295-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	13	103	1	ENST00000327064.4:c.220+2_220+3del		p.X74_splice	ENST00000327064	NM_199141.1	74			1	2	FACETS	0.598	0.432	0.794	0.598	0.432	0.794	SUBCLONAL	1	TRUE	1	0.477642436102302	2		104	91	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278105	41278105	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026295-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	80	337	0	ENST00000349496.5:c.1981C>G	p.Arg661Gly	p.R661G	ENST00000349496	NM_001904.3	661	Cga/Gga	13/15	1	2	FACETS	0.928	0.823	1	0.928	0.823	1	CLONAL	1	TRUE	1	0.477642436102302	2		337	361	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436371	52436371	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026295-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	121	733	0	ENST00000460680.1:c.2123G>A	p.Arg708Gln	p.R708Q	ENST00000460680	NM_004656.3	708	cGg/cAg	17/17	1	2	FACETS	0.808	0.732	0.888	0.808	0.732	0.888	CLONAL	1	TRUE	1	0.477642436102302	2		733	627	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151882713	151882713	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs745593306	NA	P-0026295-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	88	185	0	ENST00000262189.6:c.5012G>A	p.Trp1671Ter	p.W1671*	ENST00000262189	NM_170606.2	1671	tGg/tAg	34/59	0.477642436102302	3	FACETS	0.92	0.829	1			1	CLONAL	2	TRUE	NA	0.477642436102302	3		185	248	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0026855-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	112	363	3	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.688	0.622	0.756	0.688	0.622	0.756	SUBCLONAL	1	TRUE	1	0.731965245916762	2		366	445	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs371769427	NA	P-0026855-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	113	295	0	ENST00000291552.4:c.101C>A	p.Ser34Tyr	p.S34Y	ENST00000291552	NM_006758.2	34	tCt/tAt	2/8	1	2	FACETS	0.924	0.842	1	0.924	0.842	1	CLONAL	1	TRUE	1	0.731965245916762	2		295	334	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118744	115118745	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAT	novel	NA	P-0026855-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	148	527	0	ENST00000257566.3:c.596_597insATC	p.Ser199dup	p.S199dup	ENST00000257566	NM_016569.3	199	tcc/tcATCc	2/8	0.412719465307993	5	FACETS	0.712	0.648	0.778	0.237	0.216	0.26	INDETERMINATE	1	TRUE	2	0.731965245916762	5		527	1192	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046524	30046524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026855-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	283	719	0	ENST00000331968.5:c.2659C>T	p.Pro887Ser	p.P887S	ENST00000331968	NM_002742.2	887	Cca/Tca	18/18	1	2	FACETS	0.951	0.897	1	0.951	0.897	1	CLONAL	1	TRUE	1	0.731965245916762	2		719	813	SUCCESS
APC	324	MSKCC	GRCh37	5	112176520	112176521	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554086550	NA	P-0026855-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	147	351	0	ENST00000257430.4:c.5234dup	p.Ile1746AspfsTer23	p.I1746Dfs*23	ENST00000257430	NM_000038.5	1743	-/A	16/16	0.731965245916762	1	FACETS	0.972	0.909	1	0.972	0.909	1	CLONAL	1	TRUE	0	0.731965245916762	1		351	262	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0027527-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	104	634	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.210522733867456	2		634	915	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637726	52637726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027918-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	244	447	0	ENST00000394830.3:c.2590G>A	p.Asp864Asn	p.D864N	ENST00000394830	NM_018313.4	864	Gat/Aat	18/30	0.957985226634418	4	FACETS	0.875	0.825	0.925	0.875	0.825	0.925	CLONAL	2	TRUE	2	0.957985226634418	4		447	570	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595518	55595519	+	missense_variant	Missense_Mutation	DNP	AC	AC	GA	novel	NA	P-0027918-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	192	371	0	ENST00000288135.5:c.2008_2009delinsGA	p.Thr670Glu	p.T670E	ENST00000288135	NM_000222.2	670	ACa/GAa	14/21	0.957985226634418	3	FACETS	0.898	0.848	0.948	0.898	0.848	0.948	CLONAL	2	TRUE	1	0.957985226634418	3		371	330	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860094	151860094	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027918-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	258	440	0	ENST00000262189.6:c.10568del	p.Pro3523LeufsTer10	p.P3523Lfs*10	ENST00000262189	NM_170606.2	3523	cCt/ct	43/59	0.957985226634418	4	FACETS	0.892	0.843	0.942	0.892	0.843	0.942	CLONAL	2	TRUE	2	0.957985226634418	4		440	591	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593604	55593620	+	stop_gained	Nonsense_Mutation	DEL	GGAAGGTTGTTGAGGAG	GGAAGGTTGTTGAGGAG	AGGGA	novel	NA	P-0027918-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	182	461	2	ENST00000288135.5:c.1670_1686delinsAGGGA	p.Trp557_Glu562delinsTer	p.W557_E562delins*	ENST00000288135	NM_000222.2	557	tGGAAGGTTGTTGAGGAG/tAGGGA	11/21	0.957985226634418	3	FACETS	1	0.99	1	0.694	0.649	0.739	CLONAL	1	TRUE	1	0.957985226634418	3		463	405	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0028096-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	13	408	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.111	0.078	0.151	0.111	0.078	0.151	SUBCLONAL	1	TRUE	1	0.361900215841003	2		408	649	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814713	139814713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753016580	NA	P-0028096-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	51	707	0	ENST00000247668.2:c.706G>A	p.Glu236Lys	p.E236K	ENST00000247668	NM_021138.3	236	Gag/Aag	8/11	1	2	FACETS	0.341	0.289	0.398	0.341	0.289	0.398	SUBCLONAL	1	TRUE	1	0.361900215841003	2		707	827	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406298	406298	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028096-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	65	690	0	ENST00000399788.2:c.4143C>G	p.Ile1381Met	p.I1381M	ENST00000399788	NM_001042603.1	1381	atC/atG	25/28	0.270377827228617	3	FACETS	0.469	0.405	0.538			1	SUBCLONAL	1	TRUE	NA	0.361900215841003	3		690	905	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412002	63412002	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0028096-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	162	388	0	ENST00000330258.3:c.1165G>T	p.Glu389Ter	p.E389*	ENST00000330258	NM_152424.3	389	Gaa/Taa	2/2	1	1	FACETS	0.952	0.885	1	1	0.993	1	CLONAL	2	TRUE	0	0.361900215841003	1		388	385	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221990	1221990	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028096-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	150	666	0	ENST00000326873.7:c.905A>C	p.Gln302Pro	p.Q302P	ENST00000326873	NM_000455.4	302	cAg/cCg	7/10	0.357291950217498	1	FACETS	0.954	0.873	1	0.954	0.873	1	CLONAL	1	TRUE	0	0.361900215841003	1		666	712	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602326	10602326	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028096-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	206	815	0	ENST00000171111.5:c.1252del	p.Val418TrpfsTer40	p.V418Wfs*40	ENST00000171111	NM_203500.1	418	Gtg/tg	3/6	0.357291950217498	1	FACETS	0.951	0.883	1	0.951	0.883	1	CLONAL	1	TRUE	0	0.361900215841003	1		815	980	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599283	28599283	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1372199272	NA	P-0028096-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	185	821	0	ENST00000253063.3:c.729G>C	p.Arg243Ser	p.R243S	ENST00000253063	NM_031459.4	243	agG/agC	5/10	1	2	FACETS	0.964	0.889	1	0.964	0.889	1	CLONAL	1	TRUE	1	0.361900215841003	2		821	1061	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483115	29483117	+	inframe_deletion	In_Frame_Del	DEL	ACT	ACT	-	novel	NA	P-0028096-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	38	524	0	ENST00000356175.3:c.179_181del	p.Thr60del	p.T60del	ENST00000356175	NM_000267.3	59	ACT/-	2/57	0.357291950217498	1	FACETS	0.334	0.276	0.399	0.334	0.276	0.399	SUBCLONAL	1	TRUE	0	0.361900215841003	1		524	515	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586066	29586066	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028096-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	27	498	0	ENST00000356175.3:c.4287del	p.Asn1430IlefsTer18	p.N1430Ifs*18	ENST00000356175	NM_000267.3	1429	gCc/gc	32/57	0.357291950217498	1	FACETS	0.342	0.272	0.422	0.342	0.272	0.422	SUBCLONAL	1	TRUE	0	0.361900215841003	1		498	357	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211097	2211097	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0028096-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	154	734	0	ENST00000398665.3:c.1352-1G>C		p.X451_splice	ENST00000398665	NM_032482.2	451			0.357291950217498	1	FACETS	0.817	0.748	0.889	0.817	0.748	0.889	CLONAL	1	TRUE	0	0.361900215841003	1		734	853	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577518	7577518	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519995	NA	P-0028391-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	21	635	0	ENST00000269305.4:c.763A>T	p.Ile255Phe	p.I255F	ENST00000269305	NM_001126112.2	255	Atc/Ttc	7/11	1	2	FACETS	0.686	0.527	0.873	0.686	0.527	0.873	SUBCLONAL	1	TRUE	1	0.12	2		635	510	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0028391-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	30	629	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	1	2	FACETS	0.996	0.801	1	0.996	0.801	1	CLONAL	1	TRUE	1	0.12	2		629	502	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0028391-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	32	721	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	1	2	FACETS	0.924	0.749	1	0.924	0.749	1	CLONAL	1	TRUE	1	0.12	2		721	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028838-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	206	584	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.318346495182663	3	FACETS	0.833	0.774	0.895	0.833	0.774	0.895	CLONAL	2	TRUE	1	0.318346495182663	3		584	900	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0028838-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	78	437	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.229276088103518	5	FACETS	1	0.909	1	0.347	0.305	0.393	CLONAL	1	TRUE	2	0.318346495182663	5		437	695	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720741	89720741	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs371387815	NA	P-0028838-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	18	168	0	ENST00000371953.3:c.892C>T	p.Gln298Ter	p.Q298*	ENST00000371953	NM_000314.4	298	Caa/Taa	8/9	0.318346495182663	3	FACETS	0.868	0.659	1	0.434	0.329	0.556	CLONAL	1	TRUE	1	0.318346495182663	3		168	151	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857494	9857494	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028838-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	42	428	0	ENST00000330684.3:c.3907G>C	p.Asp1303His	p.D1303H	ENST00000330684	NM_001134407.1	1303	Gac/Cac	13/13	0.229276088103518	5	FACETS	0.474	0.394	0.563	0.158	0.131	0.188	SUBCLONAL	1	TRUE	2	0.318346495182663	5		428	823	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713901	30713901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028838-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	118	505	0	ENST00000295754.5:c.1226C>T	p.Ser409Phe	p.S409F	ENST00000295754	NM_003242.5	409	tCt/tTt	4/7	0.318346495182663	3	FACETS	1	0.964	1	0.571	0.515	0.629	CLONAL	1	TRUE	1	0.318346495182663	3		505	753	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197580	27197580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028838-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	244	412	0	ENST00000380036.4:c.1892C>T	p.Ala631Val	p.A631V	ENST00000380036	NM_000459.3	631	gCt/gTt	12/23	0.318346495182663	4	FACETS	0.869	0.815	0.925	0.869	0.815	0.925	CLONAL	3	TRUE	1	0.318346495182663	4		412	775	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030048-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	75	419	0	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	0.235428992724367	10	FACETS	0.821	0.719	0.932			1	CLONAL	2	FALSE	NA	0.235428992724367	10		419	753	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0030048-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	120	581	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.235436604691724	4	FACETS	1	0.982	1	0.472	0.425	0.521	CLONAL	1	FALSE	1	0.235428992724367	4		581	890	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0030048-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	44	237	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.235428992724367	1	FACETS	0.686	0.575	0.808	0.686	0.575	0.808	SUBCLONAL	1	FALSE	0	0.235428992724367	1		237	481	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030048-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	100	828	2	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	0.235428992724367	10	FACETS	1	0.977	1			1	CLONAL	1	FALSE	NA	0.235428992724367	10		830	1188	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015230	128015230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs189511674	NA	P-0030048-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	29	604	3	ENST00000285398.2:c.2291C>T	p.Ser764Leu	p.S764L	ENST00000285398	NM_000122.1	764	tCg/tTg	15/15	0.235436604691724	0	FACETS	0.373	0.299	0.458			1	SUBCLONAL	1	FALSE	0	0.235428992724367	0		607	505	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0030048-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	70	437	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	NA	2	FACETS	0.696	0.606	0.795			1	INDETERMINATE	1	FALSE	NA	0.235428992724367	2		437	854	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882050	36882050	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs780753361	NA	P-0030048-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	51	817	3	ENST00000358127.4:c.963del	p.Ala322LeufsTer11	p.A322Lfs*11	ENST00000358127	NM_001280556.1	321	ccC/cc	8/10	0.187103048006052	0	FACETS	0.9	0.768	1			1	CLONAL	1	FALSE	0	0.235428992724367	0		820	368	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637539	52637540	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030048-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	42	465	0	ENST00000394830.3:c.2776dup	p.Arg926LysfsTer4	p.R926Kfs*4	ENST00000394830	NM_018313.4	926	aga/aAga	18/30	0.139111111334209	4	FACETS	1	0.85	1	0.509	0.425	0.602	INDETERMINATE	1	FALSE	2	0.235428992724367	4		465	433	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505443	157505443	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554231830	NA	P-0030048-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	61	525	0	ENST00000346085.5:c.3428del	p.Lys1143SerfsTer68	p.K1143Sfs*68	ENST00000346085	NM_020732.3	1142	Aaa/aa	13/20	0.235428992724367	5	FACETS	1	0.929	1	0.375	0.323	0.431	CLONAL	1	FALSE	2	0.235428992724367	5		525	624	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891687	28891687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030048-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	24	700	0	ENST00000282397.4:c.3334C>T	p.Arg1112Cys	p.R1112C	ENST00000282397	NM_002019.4	1112	Cgc/Tgc	25/30	0.210289944934498	0	FACETS	0.444	0.348	0.555			1	SUBCLONAL	1	FALSE	0	0.235428992724367	0		700	351	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483963	212483963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030048-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	22	522	2	ENST00000342788.4:c.2240C>T	p.Pro747Leu	p.P747L	ENST00000342788	NM_005235.2	747	cCt/cTt	19/28	1	2	FACETS	0.525	0.406	0.663	0.525	0.406	0.663	SUBCLONAL	1	FALSE	1	0.235428992724367	2		524	356	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117632201	117632201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779401784	NA	P-0030048-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	28	586	0	ENST00000368508.3:c.6215G>A	p.Arg2072Gln	p.R2072Q	ENST00000368508	NM_002944.2	2072	cGg/cAg	39/43	0.235436604691724	1	FACETS	0.56	0.447	0.688	0.56	0.447	0.688	SUBCLONAL	1	FALSE	0	0.235428992724367	1		586	375	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321073	137321073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768721235	NA	P-0030048-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	21	610	1	ENST00000481739.1:c.1030G>A	p.Ala344Thr	p.A344T	ENST00000481739	NM_002957.4	344	Gcc/Acc	7/10	0.139111111334209	4	FACETS	0.605	0.466	0.769	0.303	0.233	0.385	INDETERMINATE	1	FALSE	2	0.235428992724367	4		611	364	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156918	89156920	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	rs768142526	NA	P-0030048-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	23	648	0	ENST00000336596.2:c.27_29del	p.Leu11del	p.L11del	ENST00000336596	NM_005233.5	7	aTCCtc/atc	1/17	0.139111111334209	4	FACETS	0.592	0.46	0.744	0.296	0.23	0.372	INDETERMINATE	1	FALSE	2	0.235428992724367	4		648	408	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310518	65310518	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1307956862	NA	P-0030048-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	48	623	2	ENST00000342505.4:c.2170C>T	p.Arg724Cys	p.R724C	ENST00000342505	NM_002227.2	724	Cgt/Tgt	16/25	1	2	FACETS	0.75	0.633	0.878	0.75	0.633	0.878	SUBCLONAL	1	FALSE	1	0.235428992724367	2		625	544	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612809	228612809	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773691912	NA	P-0030048-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	50	724	1	ENST00000366696.1:c.218G>A	p.Arg73His	p.R73H	ENST00000366696	NM_003493.2	73	cGc/cAc	1/1	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	FALSE	1	0.235428992724367	2		725	400	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048561	180048562	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030048-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	27	803	0	ENST00000261937.6:c.2000dup	p.Lys668GlufsTer104	p.K668Efs*104	ENST00000261937	NM_182925.4	667	aag/aaAg	13/30	0.235428992724367	0	FACETS	0.682	0.545	0.838			1	SUBCLONAL	1	FALSE	0	0.235428992724367	0		803	257	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056155	26056155	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030048-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1247	83	579	0	ENST00000343677.2:c.502A>G	p.Lys168Glu	p.K168E	ENST00000343677	NM_005319.3	168	Aag/Gag	1/1	0.235428992724367	11	FACETS	1	0.933	1			1	CLONAL	1	FALSE	NA	0.235428992724367	11		579	1330	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439613	140439614	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0030048-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	21	621	0	ENST00000288602.6:c.2125dup	p.Gln709ProfsTer7	p.Q709Pfs*7	ENST00000288602	NM_004333.4	709	caa/cCaa	17/18	0.183367239995279	3	FACETS	0.585	0.45	0.742	0.292	0.225	0.371	SUBCLONAL	1	FALSE	1	0.235428992724367	3		621	341	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561430	141561430	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030048-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	69	560	0	ENST00000220592.5:c.1375del	p.Gln459SerfsTer9	p.Q459Sfs*9	ENST00000220592	NM_012154.3	459	Cag/ag	11/19	0.139111111334209	4	FACETS	1	0.961	1	0.637	0.556	0.726	INDETERMINATE	1	FALSE	2	0.235428992724367	4		560	568	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471057	8471057	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030048-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	28	428	0	ENST00000356435.5:c.3442A>G	p.Lys1148Glu	p.K1148E	ENST00000356435		1148	Aag/Gag	20/35	0.187103048006052	0	FACETS	0.598	0.479	0.734			1	SUBCLONAL	1	FALSE	0	0.235428992724367	0		428	304	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15826384	15826384	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030048-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	32	511	0	ENST00000307771.7:c.428C>T	p.Ala143Val	p.A143V	ENST00000307771	NM_005089.3	143	gCt/gTt	6/11	0.210289944934498	0	FACETS	0.437	0.354	0.53			1	SUBCLONAL	1	FALSE	0	0.235428992724367	0		511	476	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0030901-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	9	400	2	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.282	0.186	0.405	0.282	0.186	0.405	SUBCLONAL	1	TRUE	1	0.210792000015845	2		402	303	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41021015	41021015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030901-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	29	493	1	ENST00000267868.3:c.637G>A	p.Glu213Lys	p.E213K	ENST00000267868	NM_002875.4	213	Gaa/Aaa	7/10	0.127689354851518	3	FACETS	0.557	0.446	0.684			1	SUBCLONAL	1	TRUE	NA	0.210792000015845	3		494	546	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803818	43803818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147938568	NA	P-0031607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	343	516	0	ENST00000372470.3:c.128G>A	p.Arg43Gln	p.R43Q	ENST00000372470	NM_005373.2	43	cGa/cAa	2/12	0.137833820609963	5	FACETS	0.98	0.932	1			1	INDETERMINATE	3	TRUE	NA	0.476450007619337	5		516	840	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30946592	30946594	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs752094508	NA	P-0031607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	76	195	0	ENST00000375687.4:c.25_27del	p.Lys9del	p.K9del	ENST00000375687	NM_015338.5	5	cAGAag/cag	1/13	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.476450007619337	2		195	303	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640578	3640578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138344471	NA	P-0031607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	211	616	0	ENST00000294008.3:c.3061C>T	p.Arg1021Cys	p.R1021C	ENST00000294008	NM_032444.2	1021	Cgc/Tgc	12/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.476450007619337	2		616	836	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111521	8111545	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTCTGCAATGCCTGTGGGCTCTA	CTGTCTGCAATGCCTGTGGGCTCTA	-	novel	NA	P-0031607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	71	565	0	ENST00000346208.3:c.1009_1033del	p.Val337ThrfsTer10	p.V337Tfs*10	ENST00000346208		336	cCTGTCTGCAATGCCTGTGGGCTCTAc/cc	5/6	0.476450007619337	4	FACETS	0.392	0.341	0.448	0.131	0.113	0.15	SUBCLONAL	1	TRUE	1	0.476450007619337	4		565	1123	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459184	99459194	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTCTCCAGTT	CCTCTCCAGTT	-	novel	NA	P-0031607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	140	466	0	ENST00000268035.6:c.1829-6_1833del		p.X610_splice	ENST00000268035	NM_000875.3	610		9/21	1	2	FACETS	0.945	0.863	1	0.945	0.863	1	CLONAL	1	TRUE	1	0.476450007619337	2		466	622	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647395	23647402	+	frameshift_variant	Frame_Shift_Del	DEL	GTGAAATA	GTGAAATA	CTG	novel	NA	P-0031607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	136	479	1	ENST00000261584.4:c.465_472delinsCAG	p.Ile156ArgfsTer10	p.I156Rfs*10	ENST00000261584	NM_024675.3	155	ttTATTTCACag/ttCAGag	4/13	1	2	FACETS	0.902	0.822	0.985	0.902	0.822	0.985	CLONAL	1	TRUE	1	0.476450007619337	2		480	633	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31379438	31379438	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	132	413	0	ENST00000328111.2:c.845T>G	p.Leu282Arg	p.L282R	ENST00000328111	NM_006892.3	282	cTg/cGg	8/23	0.476450007619337	3	FACETS	0.983	0.894	1	0.491	0.447	0.538	CLONAL	1	TRUE	1	0.476450007619337	3		413	698	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332108	70332108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140156594	NA	P-0031716-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	9	0	0	ENST00000373644.4:c.13C>T	p.Arg5Cys	p.R5C	ENST00000373644	NM_030625.2	5	Cgc/Tgc	2/12	0.193098856061297	0	FACETS	0.775	0.517	1			1	CLONAL	1	FALSE	0	0.193098856061297	0		0	97	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443475	49443475	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266718915	NA	P-0031716-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	84	362	1	ENST00000301067.7:c.3896G>A	p.Arg1299His	p.R1299H	ENST00000301067	NM_003482.3	1299	cGc/cAc	11/54	0.193098856061297	0	FACETS	0.688	0.606	0.776			1	SUBCLONAL	1	FALSE	0	0.193098856061297	0		363	1021	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100590	67100590	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0031716-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	17	275	0	ENST00000412916.2:c.288T>A	p.Tyr96Ter	p.Y96*	ENST00000412916		96	taT/taA	4/6	1	2	FACETS	0.699	0.522	0.908	0.699	0.522	0.908	SUBCLONAL	1	FALSE	1	0.193098856061297	2		275	252	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969391	44969391	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031716-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	8	0	0	ENST00000377967.4:c.4073G>C	p.Cys1358Ser	p.C1358S	ENST00000377967	NM_021140.2	1358	tGc/tCc	28/29	0.193098856061297	0	FACETS	0.76	0.502	1			1	CLONAL	2	FALSE	NA	0.193098856061297	0		0	44	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649577	48649577	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031716-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	48	295	0	ENST00000376670.3:c.61C>A	p.Pro21Thr	p.P21T	ENST00000376670	NM_002049.3	21	Cct/Act	2/6	0.193098856061297	0	FACETS	0.922	0.781	1			1	CLONAL	1	FALSE	NA	0.193098856061297	0		295	435	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	111	248	1				ENST00000310581	NM_198253.2	-/1132			0.792984278743116	3	FACETS	0.958	0.868	1	0.479	0.434	0.526	CLONAL	1	TRUE	1	0.792984278743116	3		249	408	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217302	11217302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	52	796	2	ENST00000361445.4:c.4376C>T	p.Ala1459Val	p.A1459V	ENST00000361445	NM_004958.3	1459	gCc/gTc	30/58	1	2	FACETS	0.177	0.15	0.207	0.177	0.15	0.207	SUBCLONAL	1	TRUE	1	0.792984278743116	2		798	739	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303304	11303304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	78	657	0	ENST00000361445.4:c.1279G>A	p.Glu427Lys	p.E427K	ENST00000361445	NM_004958.3	427	Gag/Aag	9/58	1	2	FACETS	0.36	0.317	0.407	0.36	0.317	0.407	SUBCLONAL	1	TRUE	1	0.792984278743116	2		657	546	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199553	16199553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	174	476	1	ENST00000375759.3:c.326G>A	p.Gly109Glu	p.G109E	ENST00000375759	NM_015001.2	109	gGa/gAa	2/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.792984278743116	2		477	406	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089568	27089568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs923663579	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	286	790	0	ENST00000324856.7:c.2524C>T	p.His842Tyr	p.H842Y	ENST00000324856	NM_006015.4	842	Cat/Tat	8/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.792984278743116	2		790	715	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092830	27092830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	51	556	0	ENST00000324856.7:c.2851G>A	p.Gly951Ser	p.G951S	ENST00000324856	NM_006015.4	951	Ggt/Agt	9/20	1	2	FACETS	0.24	0.203	0.279	0.24	0.203	0.279	SUBCLONAL	1	TRUE	1	0.792984278743116	2		556	537	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105809	27105809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	41	505	0	ENST00000324856.7:c.5420G>A	p.Ser1807Asn	p.S1807N	ENST00000324856	NM_006015.4	1807	aGt/aAt	20/20	1	2	FACETS	0.239	0.199	0.283	0.239	0.199	0.283	SUBCLONAL	1	TRUE	1	0.792984278743116	2		505	433	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36814339	36814339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1467754610	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	238	679	0	ENST00000373129.3:c.701G>A	p.Arg234Lys	p.R234K	ENST00000373129	NM_032017.1	234	aGa/aAa	8/12	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.792984278743116	2		679	568	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521549	46521549	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	212	436	0	ENST00000262741.5:c.859G>A	p.Asp287Asn	p.D287N	ENST00000262741	NM_003629.3	287	Gac/Aac	7/10	1	2	FACETS	0.962	0.901	1	0.962	0.901	1	CLONAL	1	TRUE	1	0.792984278743116	2		436	556	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166125	118166125	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	170	360	0	ENST00000369448.3:c.635G>A	p.Gly212Glu	p.G212E	ENST00000369448	NM_017709.3	212	gGg/gAg	2/2	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.792984278743116	2		360	405	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120460314	120460314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	116	595	0	ENST00000256646.2:c.6001G>A	p.Ala2001Thr	p.A2001T	ENST00000256646	NM_024408.3	2001	Gcc/Acc	33/34	1	2	FACETS	0.509	0.46	0.56	0.509	0.46	0.56	SUBCLONAL	1	TRUE	1	0.792984278743116	2		595	575	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647801	206647801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782361671	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	188	492	0	ENST00000367120.3:c.215C>T	p.Ala72Val	p.A72V	ENST00000367120	NM_014002.3	72	gCg/gTg	4/22	1	2	FACETS	0.968	0.903	1	0.968	0.903	1	CLONAL	1	TRUE	1	0.792984278743116	2		492	490	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943732	71943732	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	51	810	1	ENST00000298229.2:c.1775C>T	p.Ala592Val	p.A592V	ENST00000298229	NM_001567.3	592	gCc/gTc	15/28	1	2	FACETS	0.173	0.146	0.203	0.173	0.146	0.203	SUBCLONAL	1	TRUE	1	0.792984278743116	2		811	743	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999752	100999752	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767664725	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	59	928	1	ENST00000325455.5:c.50G>A	p.Gly17Asp	p.G17D	ENST00000325455	NM_001202474.3	17	gGc/gAc	1/8	1	2	FACETS	0.219	0.188	0.254	0.219	0.188	0.254	SUBCLONAL	1	TRUE	1	0.792984278743116	2		929	678	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359410	118359410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	163	400	0	ENST00000534358.1:c.4414G>A	p.Glu1472Lys	p.E1472K	ENST00000534358	NM_005933.3	1472	Gaa/Aaa	11/36	1	2	FACETS	0.924	0.856	0.993	0.924	0.856	0.993	CLONAL	1	TRUE	1	0.792984278743116	2		400	445	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118365013	118365013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	23	278	0	ENST00000534358.1:c.5189G>A	p.Ser1730Asn	p.S1730N	ENST00000534358	NM_005933.3	1730	aGt/aAt	17/36	1	2	FACETS	0.183	0.142	0.23	0.183	0.142	0.23	SUBCLONAL	1	TRUE	1	0.792984278743116	2		278	317	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376836	118376836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	45	398	0	ENST00000534358.1:c.10229C>T	p.Pro3410Leu	p.P3410L	ENST00000534358	NM_005933.3	3410	cCa/cTa	27/36	1	2	FACETS	0.291	0.245	0.342	0.291	0.245	0.342	SUBCLONAL	1	TRUE	1	0.792984278743116	2		398	390	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409147	4409147	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587777622	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	38	550	0	ENST00000261254.3:c.842C>T	p.Pro281Leu	p.P281L	ENST00000261254	NM_001759.3	281	cCt/cTt	5/5	0.121709817175129	3	FACETS	0.255	0.211	0.306	0.128	0.105	0.153	INDETERMINATE	1	TRUE	1	0.792984278743116	3		550	524	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433979	49433979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	326	975	0	ENST00000301067.7:c.7574G>A	p.Gly2525Asp	p.G2525D	ENST00000301067	NM_003482.3	2525	gGt/gAt	31/54	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.792984278743116	2		975	782	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444013	49444013	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760063855	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	224	820	0	ENST00000301067.7:c.3358G>A	p.Glu1120Lys	p.E1120K	ENST00000301067	NM_003482.3	1120	Gaa/Aaa	11/54	1	2	FACETS	0.907	0.85	0.965	0.907	0.85	0.965	CLONAL	1	TRUE	1	0.792984278743116	2		820	623	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444354	49444354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	35	776	0	ENST00000301067.7:c.3017G>A	p.Gly1006Asp	p.G1006D	ENST00000301067	NM_003482.3	1006	gGc/gAc	11/54	1	2	FACETS	0.15	0.123	0.182	0.15	0.123	0.182	SUBCLONAL	1	TRUE	1	0.792984278743116	2		776	587	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859671	57859671	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1183121569	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	30	578	0	ENST00000228682.2:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000228682	NM_005269.2	242	tGc/tAc	7/12	1	2	FACETS	0.162	0.13	0.198	0.162	0.13	0.198	SUBCLONAL	1	TRUE	1	0.792984278743116	2		578	467	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865062	57865062	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	283	971	0	ENST00000228682.2:c.2539C>T	p.Leu847Phe	p.L847F	ENST00000228682	NM_005269.2	847	Ctc/Ttc	12/12	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.792984278743116	2		971	702	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888210	112888210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121918464	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	12	550	1	ENST00000351677.2:c.226G>A	p.Glu76Lys	p.E76K	ENST00000351677	NM_002834.3	76	Gag/Aag	3/16	1	2	FACETS	0.055	0.038	0.076	0.055	0.038	0.076	SUBCLONAL	1	TRUE	1	0.792984278743116	2		551	551	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915713	112915713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	53	451	0	ENST00000351677.2:c.986C>T	p.Ala329Val	p.A329V	ENST00000351677	NM_002834.3	329	gCc/gTc	9/16	1	2	FACETS	0.297	0.253	0.345	0.297	0.253	0.345	SUBCLONAL	1	TRUE	1	0.792984278743116	2		451	450	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220467	133220467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146711942	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	206	660	0	ENST00000320574.5:c.4246G>A	p.Ala1416Thr	p.A1416T	ENST00000320574	NM_006231.2	1416	Gct/Act	33/49	1	2	FACETS	0.902	0.843	0.962	0.902	0.843	0.962	CLONAL	1	TRUE	1	0.792984278743116	2		660	576	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245479	133245479	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	217	586	0	ENST00000320574.5:c.1841C>T	p.Pro614Leu	p.P614L	ENST00000320574	NM_006231.2	614	cCc/cTc	17/49	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.792984278743116	2		586	546	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254001	133254001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	28	470	0	ENST00000320574.5:c.749G>A	p.Gly250Glu	p.G250E	ENST00000320574	NM_006231.2	250	gGa/gAa	8/49	1	2	FACETS	0.131	0.104	0.162	0.131	0.104	0.162	SUBCLONAL	1	TRUE	1	0.792984278743116	2		470	538	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26971363	26971363	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	89	170	0	ENST00000381527.3:c.933+1G>A		p.X311_splice	ENST00000381527	NM_001260.1	311			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.792984278743116	2		170	203	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26974638	26974638	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	30	445	0	ENST00000381527.3:c.982C>T	p.Gln328Ter	p.Q328*	ENST00000381527	NM_001260.1	328	Cag/Tag	10/13	1	2	FACETS	0.152	0.122	0.186	0.152	0.122	0.186	SUBCLONAL	1	TRUE	1	0.792984278743116	2		445	499	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622445	28622445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	32	427	0	ENST00000241453.7:c.1172C>T	p.Pro391Leu	p.P391L	ENST00000241453	NM_004119.2	391	cCt/cTt	9/24	1	2	FACETS	0.153	0.123	0.186	0.153	0.123	0.186	SUBCLONAL	1	TRUE	1	0.792984278743116	2		427	528	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28885737	28885737	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	72	376	0	ENST00000282397.4:c.3625G>A	p.Asp1209Asn	p.D1209N	ENST00000282397	NM_002019.4	1209	Gat/Aat	27/30	1	2	FACETS	0.445	0.39	0.503	0.445	0.39	0.503	SUBCLONAL	1	TRUE	1	0.792984278743116	2		376	408	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931726	28931726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	155	428	1	ENST00000282397.4:c.2213G>A	p.Gly738Asp	p.G738D	ENST00000282397	NM_002019.4	738	gGc/gAc	15/30	1	2	FACETS	0.929	0.859	1	0.929	0.859	1	CLONAL	1	TRUE	1	0.792984278743116	2		429	421	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435504	110435504	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	141	663	1	ENST00000375856.3:c.2897G>A	p.Ser966Asn	p.S966N	ENST00000375856	NM_003749.2	966	aGc/aAc	1/2	1	2	FACETS	0.6	0.548	0.653	0.6	0.548	0.653	SUBCLONAL	1	TRUE	1	0.792984278743116	2		664	593	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435573	110435573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	242	573	0	ENST00000375856.3:c.2828C>T	p.Ala943Val	p.A943V	ENST00000375856	NM_003749.2	943	gCc/gTc	1/2	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.792984278743116	2		573	527	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437563	110437563	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	188	833	0	ENST00000375856.3:c.838G>A	p.Ala280Thr	p.A280T	ENST00000375856	NM_003749.2	280	Gcg/Acg	1/2	1	2	FACETS	0.642	0.594	0.69	0.642	0.594	0.69	SUBCLONAL	1	TRUE	1	0.792984278743116	2		833	739	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003213	42003213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	216	518	0	ENST00000219905.7:c.2750C>T	p.Ser917Phe	p.S917F	ENST00000219905	NM_001164273.1	917	tCc/tTc	8/24	1	2	FACETS	0.943	0.883	1	0.943	0.883	1	CLONAL	1	TRUE	1	0.792984278743116	2		518	578	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058409	42058409	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	172	443	0	ENST00000219905.7:c.8129G>A	p.Arg2710Lys	p.R2710K	ENST00000219905	NM_001164273.1	2710	aGa/aAa	24/24	1	2	FACETS	0.984	0.915	1	0.984	0.915	1	CLONAL	1	TRUE	1	0.792984278743116	2		443	441	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43699633	43699633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763713800	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	73	503	1	ENST00000382044.4:c.5882G>A	p.Arg1961Lys	p.R1961K	ENST00000382044	NM_001141980.1	1961	aGa/aAa	28/28	1	2	FACETS	0.322	0.282	0.366	0.322	0.282	0.366	SUBCLONAL	1	TRUE	1	0.792984278743116	2		504	571	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628613	90628613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	67	1014	1	ENST00000330062.3:c.974G>A	p.Gly325Asp	p.G325D	ENST00000330062	NM_002168.2	325	gGc/gAc	8/11	1	2	FACETS	0.247	0.214	0.282	0.247	0.214	0.282	SUBCLONAL	1	TRUE	1	0.792984278743116	2		1015	685	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225307	2225307	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	38	841	1	ENST00000326181.6:c.1392G>A	p.Trp464Ter	p.W464*	ENST00000326181	NM_032271.2	464	tgG/tgA	16/21	1	2	FACETS	0.159	0.131	0.191	0.159	0.131	0.191	SUBCLONAL	1	TRUE	1	0.792984278743116	2		842	603	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843573	3843573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	51	515	0	ENST00000262367.5:c.1030C>T	p.Pro344Ser	p.P344S	ENST00000262367	NM_004380.2	344	Ccc/Tcc	4/31	1	2	FACETS	0.219	0.186	0.256	0.219	0.186	0.256	SUBCLONAL	1	TRUE	1	0.792984278743116	2		515	587	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860687	3860687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	222	632	1	ENST00000262367.5:c.892G>A	p.Ala298Thr	p.A298T	ENST00000262367	NM_004380.2	298	Gcc/Acc	3/31	1	2	FACETS	0.962	0.902	1	0.962	0.902	1	CLONAL	1	TRUE	1	0.792984278743116	2		633	582	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844238	68844238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	59	495	0	ENST00000261769.5:c.826C>T	p.Leu276Phe	p.L276F	ENST00000261769	NM_004360.3	276	Ctt/Ttt	6/16	1	2	FACETS	0.332	0.286	0.382	0.332	0.286	0.382	SUBCLONAL	1	TRUE	1	0.792984278743116	2		495	448	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867206	68867206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	199	506	1	ENST00000261769.5:c.2453C>T	p.Ala818Val	p.A818V	ENST00000261769	NM_004360.3	818	gCt/gTt	16/16	1	2	FACETS	0.965	0.902	1	0.965	0.902	1	CLONAL	1	TRUE	1	0.792984278743116	2		507	520	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867352	68867352	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	186	509	0	ENST00000261769.5:c.2599A>G	p.Asn867Asp	p.N867D	ENST00000261769	NM_004360.3	867	Aat/Gat	16/16	1	2	FACETS	0.929	0.865	0.994	0.929	0.865	0.994	CLONAL	1	TRUE	1	0.792984278743116	2		509	505	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821656	72821656	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201978300	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	66	219	1	ENST00000268489.5:c.10519G>A	p.Gly3507Ser	p.G3507S	ENST00000268489	NM_006885.3	3507	Ggc/Agc	10/10	1	2	FACETS	0.858	0.759	0.961	0.858	0.759	0.961	CLONAL	1	TRUE	1	0.792984278743116	2		220	194	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992925	72992925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	56	852	0	ENST00000268489.5:c.1120G>A	p.Glu374Lys	p.E374K	ENST00000268489	NM_006885.3	374	Gaa/Aaa	2/10	1	2	FACETS	0.195	0.166	0.226	0.195	0.166	0.226	SUBCLONAL	1	TRUE	1	0.792984278743116	2		852	724	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805949	89805949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479443055	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	45	746	1	ENST00000389301.3:c.3947G>A	p.Gly1316Glu	p.G1316E	ENST00000389301	NM_000135.2	1316	gGg/gAg	40/43	1	2	FACETS	0.19	0.159	0.224	0.19	0.159	0.224	SUBCLONAL	1	TRUE	1	0.792984278743116	2		747	598	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028618	12028618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	29	309	0	ENST00000353533.5:c.821G>A	p.Arg274Lys	p.R274K	ENST00000353533	NM_003010.3	274	aGa/aAa	8/11	1	2	FACETS	0.193	0.155	0.237	0.193	0.155	0.237	SUBCLONAL	1	TRUE	1	0.792984278743116	2		309	379	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15938133	15938133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	29	340	0	ENST00000268712.3:c.7081G>A	p.Asp2361Asn	p.D2361N	ENST00000268712	NM_006311.3	2361	Gat/Aat	45/46	1	2	FACETS	0.203	0.163	0.249	0.203	0.163	0.249	SUBCLONAL	1	TRUE	1	0.792984278743116	2		340	360	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942884	15942884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	34	491	0	ENST00000268712.3:c.6818G>A	p.Gly2273Glu	p.G2273E	ENST00000268712	NM_006311.3	2273	gGa/gAa	44/46	1	2	FACETS	0.18	0.147	0.218	0.18	0.147	0.218	SUBCLONAL	1	TRUE	1	0.792984278743116	2		491	476	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974811	15974811	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	186	402	0	ENST00000268712.3:c.4064C>T	p.Pro1355Leu	p.P1355L	ENST00000268712	NM_006311.3	1355	cCa/cTa	30/46	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.792984278743116	2		402	438	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983373	15983373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200574326	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	132	300	0	ENST00000268712.3:c.3406G>A	p.Ala1136Thr	p.A1136T	ENST00000268712	NM_006311.3	1136	Gca/Aca	26/46	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.792984278743116	2		300	325	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37876088	37876088	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	43	708	1	ENST00000269571.5:c.1946+1G>A		p.X649_splice	ENST00000269571		649			1	2	FACETS	0.183	0.152	0.217	0.183	0.152	0.217	SUBCLONAL	1	TRUE	1	0.792984278743116	2		709	593	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40364021	40364021	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	57	685	0	ENST00000293328.3:c.1661C>T	p.Ser554Phe	p.S554F	ENST00000293328	NM_012448.3	554	tCc/tTc	13/19	1	2	FACETS	0.189	0.161	0.219	0.189	0.161	0.219	SUBCLONAL	1	TRUE	1	0.792984278743116	2		685	762	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485908	40485908	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	239	508	1	ENST00000264657.5:c.956+1G>A		p.X319_splice	ENST00000264657	NM_139276.2	319			1	2	FACETS	0.946	0.889	1	0.946	0.889	1	CLONAL	1	TRUE	1	0.792984278743116	2		509	637	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434828	56434828	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	222	725	1	ENST00000407977.2:c.2308+1G>A		p.X770_splice	ENST00000407977		770			1	2	FACETS	0.957	0.898	1	0.957	0.898	1	CLONAL	1	TRUE	1	0.792984278743116	2		726	585	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119705	70119705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	40	688	0	ENST00000245479.2:c.707C>T	p.Thr236Ile	p.T236I	ENST00000245479	NM_000346.3	236	aCc/aTc	3/3	1	2	FACETS	0.172	0.142	0.205	0.172	0.142	0.205	SUBCLONAL	1	TRUE	1	0.792984278743116	2		688	587	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896588	78896588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	42	828	0	ENST00000306801.3:c.2585C>T	p.Ala862Val	p.A862V	ENST00000306801	NM_020761.2	862	gCc/gTc	22/34	1	2	FACETS	0.15	0.124	0.178	0.15	0.124	0.178	SUBCLONAL	1	TRUE	1	0.792984278743116	2		828	707	SUCCESS
YES1	7525	MSKCC	GRCh37	18	751795	751795	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	161	335	0	ENST00000314574.4:c.281C>T	p.Thr94Ile	p.T94I	ENST00000314574	NM_005433.3	94	aCt/aTt	3/12	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.792984278743116	2		335	382	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57567426	57567426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758523123	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	40	801	0	ENST00000316660.6:c.17C>T	p.Ala6Val	p.A6V	ENST00000316660	NM_021127.2	6	gCg/gTg	1/2	1	2	FACETS	0.165	0.136	0.196	0.165	0.136	0.196	SUBCLONAL	1	TRUE	1	0.792984278743116	2		801	613	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250434	10250434	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	44	704	1	ENST00000340748.4:c.3818C>T	p.Ser1273Phe	p.S1273F	ENST00000340748		1273	tCc/tTc	33/40	1	2	FACETS	0.18	0.15	0.212	0.18	0.15	0.212	SUBCLONAL	1	TRUE	1	0.792984278743116	2		705	618	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10257084	10257084	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	265	684	1	ENST00000340748.4:c.2789G>A	p.Gly930Asp	p.G930D	ENST00000340748		930	gGc/gAc	27/40	1	2	FACETS	0.992	0.936	1	0.992	0.936	1	CLONAL	1	TRUE	1	0.792984278743116	2		685	674	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272273	15272273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs556851818	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	296	1008	0	ENST00000263388.2:c.6166G>A	p.Ala2056Thr	p.A2056T	ENST00000263388	NM_000435.2	2056	Gca/Aca	33/33	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.792984278743116	2		1008	680	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748819	41748819	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	41	823	0	ENST00000301178.4:c.1344G>A	p.Trp448Ter	p.W448*	ENST00000301178	NM_021913.4	448	tgG/tgA	11/20	1	2	FACETS	0.156	0.129	0.186	0.156	0.129	0.186	SUBCLONAL	1	TRUE	1	0.792984278743116	2		823	664	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082374	16082374	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	305	1040	0	ENST00000281043.3:c.188C>T	p.Pro63Leu	p.P63L	ENST00000281043	NM_005378.4	63	cCc/cTc	2/3	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.792984278743116	2		1040	730	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026605	48026605	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779212	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	137	397	0	ENST00000234420.5:c.1483C>T	p.Arg495Ter	p.R495*	ENST00000234420	NM_000179.2	495	Cga/Tga	4/10	1	2	FACETS	0.952	0.877	1	0.952	0.877	1	CLONAL	1	TRUE	1	0.792984278743116	2		397	363	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027580	48027581	+	missense_variant	Missense_Mutation	DNP	AG	AG	GA	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	110	284	0	ENST00000234420.5:c.2458_2459delinsGA	p.Arg820Glu	p.R820E	ENST00000234420	NM_000179.2	820	AGg/GAg	4/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.792984278743116	2		284	241	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248717	212248717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	101	395	0	ENST00000342788.4:c.3550G>A	p.Asp1184Asn	p.D1184N	ENST00000342788	NM_005235.2	1184	Gat/Aat	28/28	1	2	FACETS	0.696	0.628	0.767	0.696	0.628	0.767	SUBCLONAL	1	TRUE	1	0.792984278743116	2		395	366	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437133	220437133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	64	1069	0	ENST00000243786.2:c.37C>T	p.Pro13Ser	p.P13S	ENST00000243786	NM_002191.3	13	Cca/Tca	1/2	1	2	FACETS	0.204	0.176	0.234	0.204	0.176	0.234	SUBCLONAL	1	TRUE	1	0.792984278743116	2		1069	792	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371607	225371607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	35	425	1	ENST00000264414.4:c.997G>A	p.Gly333Arg	p.G333R	ENST00000264414	NM_003590.4	333	Gga/Aga	7/16	1	2	FACETS	0.197	0.161	0.237	0.197	0.161	0.237	SUBCLONAL	1	TRUE	1	0.792984278743116	2		426	448	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662574	227662574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	50	729	0	ENST00000305123.5:c.881C>T	p.Pro294Leu	p.P294L	ENST00000305123	NM_005544.2	294	cCc/cTc	1/2	1	2	FACETS	0.206	0.174	0.241	0.206	0.174	0.241	SUBCLONAL	1	TRUE	1	0.792984278743116	2		729	613	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386321	31386321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	137	891	1	ENST00000328111.2:c.1546G>A	p.Ala516Thr	p.A516T	ENST00000328111	NM_006892.3	516	Gcc/Acc	15/23	1	2	FACETS	0.487	0.444	0.533	0.487	0.444	0.533	SUBCLONAL	1	TRUE	1	0.792984278743116	2		892	709	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790167	40790167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	34	501	0	ENST00000373198.4:c.2564G>A	p.Gly855Glu	p.G855E	ENST00000373198	NM_133170.3	855	gGg/gAg	18/32	1	2	FACETS	0.197	0.16	0.238	0.197	0.16	0.238	SUBCLONAL	1	TRUE	1	0.792984278743116	2		501	436	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256692	46256692	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	26	414	1	ENST00000371998.3:c.748G>A	p.Ala250Thr	p.A250T	ENST00000371998		250	Gca/Aca	8/23	1	2	FACETS	0.139	0.109	0.172	0.139	0.109	0.172	SUBCLONAL	1	TRUE	1	0.792984278743116	2		415	473	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945540	54945540	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	96	794	0	ENST00000312783.6:c.1029+1G>A		p.X343_splice	ENST00000312783	NM_198436.1	343			1	2	FACETS	0.306	0.272	0.342	0.306	0.272	0.342	SUBCLONAL	1	TRUE	1	0.792984278743116	2		794	792	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62320486	62320486	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	223	751	1	ENST00000360203.5:c.1878+1G>A		p.X626_splice	ENST00000360203	NM_001283009.1	626			1	2	FACETS	0.937	0.879	0.997	0.937	0.879	0.997	CLONAL	1	TRUE	1	0.792984278743116	2		752	600	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513313	44513313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	63	581	1	ENST00000291552.4:c.622G>A	p.Asp208Asn	p.D208N	ENST00000291552	NM_006758.2	208	Gac/Aac	8/8	1	2	FACETS	0.244	0.21	0.28	0.244	0.21	0.28	SUBCLONAL	1	TRUE	1	0.792984278743116	2		582	652	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641710	12641710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770199768	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	128	556	0	ENST00000251849.4:c.931C>T	p.Pro311Ser	p.P311S	ENST00000251849	NM_002880.3	311	Ccc/Tcc	9/17	1	2	FACETS	0.57	0.519	0.624	0.57	0.519	0.624	SUBCLONAL	1	TRUE	1	0.792984278743116	2		556	566	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12647725	12647725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	19	316	0	ENST00000251849.4:c.655G>A	p.Glu219Lys	p.E219K	ENST00000251849	NM_002880.3	219	Gag/Aag	6/17	1	2	FACETS	0.132	0.099	0.17	0.132	0.099	0.17	SUBCLONAL	1	TRUE	1	0.792984278743116	2		316	364	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098627	47098627	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752976032	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	33	637	0	ENST00000409792.3:c.6647C>T	p.Pro2216Leu	p.P2216L	ENST00000409792	NM_014159.6	2216	cCc/cTc	15/21	1	2	FACETS	0.168	0.136	0.204	0.168	0.136	0.204	SUBCLONAL	1	TRUE	1	0.792984278743116	2		637	496	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940700	49940700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	45	827	0	ENST00000296474.3:c.343C>T	p.Pro115Ser	p.P115S	ENST00000296474	NM_002447.2	115	Ccc/Tcc	1/20	1	2	FACETS	0.19	0.159	0.224	0.19	0.159	0.224	SUBCLONAL	1	TRUE	1	0.792984278743116	2		827	598	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440903	52440903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	230	748	0	ENST00000460680.1:c.601G>A	p.Glu201Lys	p.E201K	ENST00000460680	NM_004656.3	201	Gag/Aag	8/17	1	2	FACETS	0.87	0.815	0.925	0.87	0.815	0.925	CLONAL	1	TRUE	1	0.792984278743116	2		748	667	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977951	134977951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754767477	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	37	524	2	ENST00000398015.3:c.2944G>A	p.Ala982Thr	p.A982T	ENST00000398015	NM_004441.4	982	Gca/Aca	16/16	1	2	FACETS	0.17	0.14	0.204	0.17	0.14	0.204	SUBCLONAL	1	TRUE	1	0.792984278743116	2		526	548	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916923	178916923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	51	428	0	ENST00000263967.3:c.310C>T	p.Pro104Ser	p.P104S	ENST00000263967	NM_006218.2	104	Cca/Tca	2/21	0.792984278743116	3	FACETS	0.24	0.203	0.281	0.12	0.101	0.141	SUBCLONAL	1	TRUE	1	0.792984278743116	3		428	748	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146596	185146596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	194	523	0	ENST00000265026.3:c.227C>T	p.Ser76Phe	p.S76F	ENST00000265026	NM_004721.4	76	tCc/tTc	2/14	0.792984278743116	3	FACETS	0.872	0.808	0.937	0.436	0.404	0.469	CLONAL	1	TRUE	1	0.792984278743116	3		523	784	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504970	186504970	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	149	372	0	ENST00000323963.5:c.826G>A	p.Ala276Thr	p.A276T	ENST00000323963		276	Gct/Act	8/11	0.792984278743116	3	FACETS	0.885	0.812	0.961	0.442	0.406	0.481	CLONAL	1	TRUE	1	0.792984278743116	3		372	593	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968108	55968108	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	42	474	0	ENST00000263923.4:c.2222G>A	p.Ser741Asn	p.S741N	ENST00000263923	NM_002253.2	741	aGt/aAt	15/30	1	2	FACETS	0.223	0.186	0.265	0.223	0.186	0.265	SUBCLONAL	1	TRUE	1	0.792984278743116	2		474	474	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156342	106156342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	16	313	0	ENST00000380013.4:c.1243G>A	p.Val415Ile	p.V415I	ENST00000380013	NM_001127208.2	415	Gtt/Att	3/11	1	2	FACETS	0.133	0.098	0.175	0.133	0.098	0.175	SUBCLONAL	1	TRUE	1	0.792984278743116	2		313	304	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157961	106157961	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	142	364	0	ENST00000380013.4:c.2862G>A	p.Trp954Ter	p.W954*	ENST00000380013	NM_001127208.2	954	tgG/tgA	3/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.792984278743116	2		364	323	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045812	143045812	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	51	506	0	ENST00000262992.4:c.1822C>T	p.Gln608Ter	p.Q608*	ENST00000262992	NM_001101669.1	608	Cag/Tag	17/24	1	2	FACETS	0.246	0.209	0.287	0.246	0.209	0.287	SUBCLONAL	1	TRUE	1	0.792984278743116	2		506	523	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	231073	231073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747045191	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	195	704	0	ENST00000264932.6:c.853C>T	p.Leu285Phe	p.L285F	ENST00000264932	NM_004168.2	285	Ctt/Ttt	7/15	0.792984278743116	3	FACETS	0.717	0.663	0.772	0.358	0.331	0.386	SUBCLONAL	1	TRUE	1	0.792984278743116	3		704	958	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952444	38952444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	126	285	0	ENST00000357387.3:c.2981G>A	p.Arg994Lys	p.R994K	ENST00000357387	NM_152756.3	994	aGg/aAg	30/38	0.792984278743116	3	FACETS	0.893	0.813	0.976	0.446	0.406	0.488	CLONAL	1	TRUE	1	0.792984278743116	3		285	497	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178368	56178368	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451626052	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	26	293	0	ENST00000399503.3:c.3341C>T	p.Thr1114Ile	p.T1114I	ENST00000399503	NM_005921.1	1114	aCc/aTc	14/20	0.792984278743116	3	FACETS	0.212	0.168	0.264	0.106	0.084	0.132	SUBCLONAL	1	TRUE	1	0.792984278743116	3		293	431	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131926947	131926947	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501967	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	24	180	0	ENST00000265335.6:c.1484G>A	p.Ser495Asn	p.S495N	ENST00000265335		495	aGc/aAc	10/25	0.792984278743116	3	FACETS	0.32	0.251	0.399	0.16	0.125	0.2	SUBCLONAL	1	TRUE	1	0.792984278743116	3		180	264	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510112	149510112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	574	720	0	ENST00000261799.4:c.1357G>A	p.Asp453Asn	p.D453N	ENST00000261799	NM_002609.3	453	Gac/Aac	9/23	0.792984278743116	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	1	0.792984278743116	3		720	903	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480119	20480119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1275994110	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	182	441	0	ENST00000346618.3:c.436C>T	p.Leu146Phe	p.L146F	ENST00000346618	NM_001949.4	146	Ctc/Ttc	2/7	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.792984278743116	2		441	459	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858182	27858182	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	33	560	3	ENST00000359303.2:c.389G>A	p.Arg130His	p.R130H	ENST00000359303	NM_003535.2	130	cGt/cAt	1/1	1	2	FACETS	0.162	0.132	0.197	0.162	0.132	0.197	SUBCLONAL	1	TRUE	1	0.792984278743116	2		563	513	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288759	33288759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	28	528	0	ENST00000374542.5:c.793C>T	p.Pro265Ser	p.P265S	ENST00000374542	NM_001141970.1	265	Cca/Tca	3/8	1	2	FACETS	0.163	0.13	0.201	0.163	0.13	0.201	SUBCLONAL	1	TRUE	1	0.792984278743116	2		528	433	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109313989	109313989	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	37	322	0	ENST00000436639.2:c.1233+1G>A		p.X411_splice	ENST00000436639	NM_014454.2	411			1	2	FACETS	0.237	0.195	0.283	0.237	0.195	0.283	SUBCLONAL	1	TRUE	1	0.792984278743116	2		322	394	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109321717	109321717	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	254	537	0	ENST00000436639.2:c.706C>T	p.Leu236Phe	p.L236F	ENST00000436639	NM_014454.2	236	Ctt/Ttt	4/10	1	2	FACETS	0.992	0.935	1	0.992	0.935	1	CLONAL	1	TRUE	1	0.792984278743116	2		537	646	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622176	117622176	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	43	301	0	ENST00000368508.3:c.6694G>A	p.Glu2232Lys	p.E2232K	ENST00000368508	NM_002944.2	2232	Gaa/Aaa	42/43	1	2	FACETS	0.326	0.273	0.383	0.326	0.273	0.383	SUBCLONAL	1	TRUE	1	0.792984278743116	2		301	333	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677923	117677923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	23	361	0	ENST00000368508.3:c.4010G>A	p.Ser1337Asn	p.S1337N	ENST00000368508	NM_002944.2	1337	aGt/aAt	25/43	1	2	FACETS	0.139	0.108	0.175	0.139	0.108	0.175	SUBCLONAL	1	TRUE	1	0.792984278743116	2		361	417	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137540398	137540398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1331566701	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	31	676	1	ENST00000367739.4:c.67G>A	p.Asp23Asn	p.D23N	ENST00000367739	NM_000416.2	23	Gat/Aat	1/7	1	2	FACETS	0.128	0.102	0.156	0.128	0.102	0.156	SUBCLONAL	1	TRUE	1	0.792984278743116	2		677	613	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522397	157522397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	36	721	0	ENST00000346085.5:c.4669G>A	p.Ala1557Thr	p.A1557T	ENST00000346085	NM_020732.3	1557	Gcg/Acg	18/20	1	2	FACETS	0.142	0.116	0.171	0.142	0.116	0.171	SUBCLONAL	1	TRUE	1	0.792984278743116	2		721	640	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527940	157527940	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	132	650	1	ENST00000346085.5:c.5665C>T	p.Pro1889Ser	p.P1889S	ENST00000346085	NM_020732.3	1889	Cct/Tct	20/20	1	2	FACETS	0.609	0.555	0.665	0.609	0.555	0.665	SUBCLONAL	1	TRUE	1	0.792984278743116	2		651	547	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683656	162683656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	42	629	0	ENST00000366898.1:c.313G>A	p.Val105Met	p.V105M	ENST00000366898	NM_004562.2	105	Gtg/Atg	3/12	1	2	FACETS	0.181	0.15	0.215	0.181	0.15	0.215	SUBCLONAL	1	TRUE	1	0.792984278743116	2		629	586	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55269032	55269032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	265	591	0	ENST00000275493.2:c.3098C>T	p.Pro1033Leu	p.P1033L	ENST00000275493	NM_005228.3	1033	cCc/cTc	25/28	0.792984278743116	3	FACETS	0.993	0.932	1	0.496	0.466	0.528	CLONAL	1	TRUE	1	0.792984278743116	3		591	940	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	254	493	0	ENST00000397752.3:c.3028+1G>A		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.792984278743116	3	FACETS	0.9	0.843	0.959	0.45	0.421	0.48	CLONAL	1	TRUE	1	0.792984278743116	3		493	994	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140549910	140549910	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	27	289	0	ENST00000288602.6:c.240+1G>A		p.X80_splice	ENST00000288602	NM_004333.4	80			0.792984278743116	3	FACETS	0.189	0.15	0.235	0.095	0.075	0.118	SUBCLONAL	1	TRUE	1	0.792984278743116	3		289	502	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859473	151859473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	216	490	0	ENST00000262189.6:c.11189G>A	p.Gly3730Asp	p.G3730D	ENST00000262189	NM_170606.2	3730	gGc/gAc	43/59	0.792984278743116	3	FACETS	1	0.952	1	0.513	0.478	0.548	CLONAL	1	TRUE	1	0.792984278743116	3		490	742	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859867	151859867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	31	356	0	ENST00000262189.6:c.10795G>A	p.Glu3599Lys	p.E3599K	ENST00000262189	NM_170606.2	3599	Gag/Aag	43/59	0.792984278743116	3	FACETS	0.228	0.184	0.279	0.114	0.092	0.14	SUBCLONAL	1	TRUE	1	0.792984278743116	3		356	478	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38135849	38135849	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	56	498	0	ENST00000317025.8:c.3842G>A	p.Ser1281Asn	p.S1281N	ENST00000317025	NM_023034.1	1281	aGt/aAt	22/24	1	2	FACETS	0.25	0.214	0.289	0.25	0.214	0.289	SUBCLONAL	1	TRUE	1	0.792984278743116	2		498	565	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271517	38271517	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	275	995	0	ENST00000425967.3:c.2304G>A	p.Trp768Ter	p.W768*	ENST00000425967	NM_001174067.1	768	tgG/tgA	18/19	1	2	FACETS	0.967	0.913	1	0.967	0.913	1	CLONAL	1	TRUE	1	0.792984278743116	2		995	717	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145743004	145743004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	22	203	0	ENST00000428558.2:c.100G>A	p.Ala34Thr	p.A34T	ENST00000428558	NM_004260.3	34	Gcg/Acg	2/22	1	2	FACETS	0.243	0.189	0.306	0.243	0.189	0.306	SUBCLONAL	1	TRUE	1	0.792984278743116	2		203	228	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404558	8404558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	74	222	0	ENST00000356435.5:c.4189G>A	p.Val1397Ile	p.V1397I	ENST00000356435		1397	Gtt/Att	25/35	1	2	FACETS	0.765	0.679	0.855	0.765	0.679	0.855	SUBCLONAL	1	TRUE	1	0.792984278743116	2		222	244	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8501020	8501020	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	139	289	0	ENST00000356435.5:c.1862C>T	p.Pro621Leu	p.P621L	ENST00000356435		621	cCa/cTa	13/35	1	2	FACETS	0.915	0.843	0.99	0.915	0.843	0.99	CLONAL	1	TRUE	1	0.792984278743116	2		289	383	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27209230	27209230	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	166	370	0	ENST00000380036.4:c.2686+1G>A		p.X896_splice	ENST00000380036	NM_000459.3	896			0.792984278743116	1	FACETS	0.972	0.917	1	0.972	0.917	1	CLONAL	1	TRUE	0	0.792984278743116	1		370	260	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015106	37015106	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1313118042	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	266	684	1	ENST00000358127.4:c.298G>T	p.Ala100Ser	p.A100S	ENST00000358127	NM_001280556.1	100	Gct/Tct	3/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.792984278743116	2		685	645	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636249	87636249	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	36	630	0	ENST00000277120.3:c.2414G>A	p.Cys805Tyr	p.C805Y	ENST00000277120		805	tGc/tAc	19/19	1	2	FACETS	0.166	0.136	0.2	0.166	0.136	0.2	SUBCLONAL	1	TRUE	1	0.792984278743116	2		630	546	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030445	47030445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs967857316	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	103	890	2	ENST00000377604.3:c.220C>T	p.Pro74Ser	p.P74S	ENST00000377604	NM_001204468.1	74	Ccg/Tcg	4/24	1	2	FACETS	0.404	0.362	0.449	0.404	0.362	0.449	SUBCLONAL	1	TRUE	1	0.792984278743116	2		892	643	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430825	47430825	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	77	812	1	ENST00000377045.4:c.1790G>A	p.Cys597Tyr	p.C597Y	ENST00000377045	NM_001654.4	597	tGc/tAc	16/16	1	2	FACETS	0.278	0.243	0.315	0.278	0.243	0.315	SUBCLONAL	1	TRUE	1	0.792984278743116	2		813	699	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225100	53225100	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs782246658	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	228	664	0	ENST00000375401.3:c.3118C>T	p.Gln1040Ter	p.Q1040*	ENST00000375401	NM_004187.3	1040	Caa/Taa	20/26	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.792984278743116	2		664	536	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225986	53225986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556837246	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	345	1070	0	ENST00000375401.3:c.2863G>A	p.Val955Ile	p.V955I	ENST00000375401	NM_004187.3	955	Gtc/Atc	19/26	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.792984278743116	2		1070	820	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411095	63411095	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1406658299	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	248	768	0	ENST00000330258.3:c.2072G>A	p.Ser691Asn	p.S691N	ENST00000330258	NM_152424.3	691	aGc/aAc	2/2	1	2	FACETS	0.976	0.919	1	0.976	0.919	1	CLONAL	1	TRUE	1	0.792984278743116	2		768	641	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412041	63412041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	41	694	1	ENST00000330258.3:c.1126G>A	p.Asp376Asn	p.D376N	ENST00000330258	NM_152424.3	376	Gat/Aat	2/2	1	2	FACETS	0.171	0.141	0.203	0.171	0.141	0.203	SUBCLONAL	1	TRUE	1	0.792984278743116	2		695	606	SUCCESS
AR	367	MSKCC	GRCh37	X	66863102	66863102	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381810275	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	81	586	0	ENST00000374690.3:c.1621G>A	p.Glu541Lys	p.E541K	ENST00000374690	NM_000044.3	541	Gag/Aag	2/8	1	2	FACETS	0.392	0.346	0.441	0.392	0.346	0.441	SUBCLONAL	1	TRUE	1	0.792984278743116	2		586	521	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338663	70338663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	199	773	1	ENST00000374080.3:c.59G>A	p.Gly20Glu	p.G20E	ENST00000374080		20	gGg/gAg	1/45	1	2	FACETS	0.961	0.898	1	0.961	0.898	1	CLONAL	1	TRUE	1	0.792984278743116	2		774	522	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356212	70356212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	51	881	1	ENST00000374080.3:c.5107G>A	p.Gly1703Ser	p.G1703S	ENST00000374080		1703	Ggc/Agc	37/45	1	2	FACETS	0.159	0.135	0.186	0.159	0.135	0.186	SUBCLONAL	1	TRUE	1	0.792984278743116	2		882	808	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019573	123019573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770762804	NA	P-0032299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	129	427	0	ENST00000355640.3:c.61G>A	p.Glu21Lys	p.E21K	ENST00000355640		21	Gaa/Aaa	2/7	1	2	FACETS	0.585	0.533	0.64	0.585	0.533	0.64	SUBCLONAL	1	TRUE	1	0.792984278743116	2		427	556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0034751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	253	591	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.256271179752356	2	FACETS	1	0.992	1	0.727	0.681	0.773	CLONAL	1	TRUE	0	0.386450947913716	2		593	901	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739064	40739064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780908301	NA	P-0034751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	90	645	2	ENST00000373198.4:c.3220G>A	p.Val1074Ile	p.V1074I	ENST00000373198	NM_133170.3	1074	Gtt/Att	24/32	0.267808176188604	3	FACETS	0.654	0.579	0.734	0.327	0.289	0.367	SUBCLONAL	1	TRUE	1	0.386450947913716	3		647	850	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864658	68864658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1418006656	NA	P-0034751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	42	312	0	ENST00000288368.4:c.29G>A	p.Arg10His	p.R10H	ENST00000288368	NM_024870.2	10	cGc/cAc	1/40	1	2	FACETS	0.562	0.47	0.663	0.562	0.47	0.663	SUBCLONAL	1	TRUE	1	0.386450947913716	2		312	387	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1266640	1266640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372868296	NA	P-0034751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	82	498	1	ENST00000310581.5:c.2593C>T	p.Arg865Cys	p.R865C	ENST00000310581	NM_198253.2	865	Cgt/Tgt	10/16	0.275486098161559	3	FACETS	0.789	0.696	0.888	0.394	0.348	0.444	SUBCLONAL	1	TRUE	1	0.386450947913716	3		499	642	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950049	44950049	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	148	270	0	ENST00000377967.4:c.3818T>G	p.Leu1273Arg	p.L1273R	ENST00000377967	NM_021140.2	1273	cTt/cGt	26/29	0.386450947913716	2	FACETS	1	0.973	1			1	CLONAL	2	TRUE	NA	0.386450947913716	2		270	346	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257265	16257265	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	72	559	0	ENST00000375759.3:c.4530T>A	p.Asp1510Glu	p.D1510E	ENST00000375759	NM_015001.2	1510	gaT/gaA	11/15	1	2	FACETS	0.54	0.471	0.614	0.54	0.471	0.614	SUBCLONAL	1	TRUE	1	0.386450947913716	2		559	690	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425078	49425078	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	139	937	0	ENST00000301067.7:c.13410G>C	p.Lys4470Asn	p.K4470N	ENST00000301067	NM_003482.3	4470	aaG/aaC	39/54	0.267808176188604	3	FACETS	0.808	0.734	0.886	0.404	0.367	0.443	CLONAL	1	TRUE	1	0.386450947913716	3		937	1062	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557447	21557447	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	204	566	0	ENST00000382592.4:c.2398G>A	p.Asp800Asn	p.D800N	ENST00000382592	NM_014572.2	800	Gat/Aat	5/8	0.267808176188604	3	FACETS	0.839	0.78	0.899	0.839	0.78	0.899	CLONAL	2	TRUE	1	0.386450947913716	3		566	751	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266534	55266534	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	75	543	0	ENST00000275493.2:c.2826T>A	p.Asp942Glu	p.D942E	ENST00000275493	NM_005228.3	942	gaT/gaA	23/28	0.267808176188604	3	FACETS	0.657	0.575	0.745	0.328	0.287	0.373	SUBCLONAL	1	TRUE	1	0.386450947913716	3		543	705	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38135870	38135870	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034751-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	151	572	0	ENST00000317025.8:c.3821A>G	p.His1274Arg	p.H1274R	ENST00000317025	NM_023034.1	1274	cAc/cGc	22/24	0.328461121123891	5	FACETS	1	0.974	1			1	CLONAL	1	TRUE	NA	0.386450947913716	5		572	1058	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578262	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs483352697	NA	P-0037105-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	258	771	0	ENST00000269305.4:c.587G>C	p.Arg196Pro	p.R196P	ENST00000269305	NM_001126112.2	196	cGa/cCa	6/11	0.228603494593072	2	FACETS	0.848	0.795	0.903	0.848	0.795	0.903	CLONAL	2	FALSE	0	0.3	2		771	1014	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979267	93979267	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1417829621	NA	P-0037105-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	31	357	0	ENST00000369303.4:c.1561G>T	p.Ala521Ser	p.A521S	ENST00000369303	NM_004440.3	521	Gct/Tct	7/17	0.3	3	FACETS	0.578	0.467	0.704	0.289	0.233	0.352	SUBCLONAL	1	FALSE	1	0.3	3		357	411	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120592	94120592	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037105-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	166	401	0	ENST00000369303.4:c.459A>T	p.Glu153Asp	p.E153D	ENST00000369303	NM_004440.3	153	gaA/gaT	3/17	0.3	3	FACETS	0.954	0.879	1	0.954	0.879	1	CLONAL	2	FALSE	1	0.3	3		401	667	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321780	62321780	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037105-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1162	101	491	0	ENST00000360203.5:c.2399A>G	p.Lys800Arg	p.K800R	ENST00000360203	NM_001283009.1	800	aAg/aGg	26/35	0.3	6	FACETS	0.853	0.76	0.953	0.213	0.19	0.239	CLONAL	1	FALSE	2	0.3	6		491	1263	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224552	53224552	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037105-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	122	399	0	ENST00000375401.3:c.3161T>C	p.Leu1054Pro	p.L1054P	ENST00000375401	NM_004187.3	1054	cTa/cCa	21/26	0.282457219109156	2	FACETS	1	0.97	1			1	CLONAL	1	FALSE	NA	0.3	2		399	693	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578196	7578196	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555525743	NA	P-0039511-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	818	749	0	ENST00000269305.4:c.653T>G	p.Val218Gly	p.V218G	ENST00000269305	NM_001126112.2	218	gTg/gGg	6/11	0.937255806074386	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.937255806074386	2		749	852	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7167980	7167980	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039511-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	279	537	0	ENST00000302850.5:c.1609G>A	p.Ala537Thr	p.A537T	ENST00000302850	NM_000208.2	537	Gcc/Acc	7/22	1	2	FACETS	0.992	0.941	1	0.992	0.941	1	CLONAL	1	TRUE	1	0.937255806074386	2		537	600	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0040984-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	45	397	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.271294760388575	1	FACETS	0.763	0.643	0.895	0.763	0.643	0.895	SUBCLONAL	1	FALSE	0	0.271294760388575	1		397	376	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207021	1207021	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913324	NA	P-0040984-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	143	867	2	ENST00000326873.7:c.109C>T	p.Gln37Ter	p.Q37*	ENST00000326873	NM_000455.4	37	Cag/Tag	1/10	0.271294760388575	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	0	0.271294760388575	1		869	820	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs869025608	NA	P-0040984-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	134	492	1	ENST00000307102.5:c.171G>T	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaT	2/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.271294760388575	2		493	747	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602698	10602698	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040984-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	209	1106	0	ENST00000171111.5:c.880G>T	p.Asp294Tyr	p.D294Y	ENST00000171111	NM_203500.1	294	Gac/Tac	3/6	0.271294760388575	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	0	0.271294760388575	1		1106	1163	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994779	73994779	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040984-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	303	983	0	ENST00000318443.5:c.263C>G	p.Ala88Gly	p.A88G	ENST00000318443	NM_001024736.1	88	gCc/gGc	3/10	1	2	FACETS	0.969	0.913	1	1	0.995	1	CLONAL	2	FALSE	1	0.271294760388575	2		983	1153	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762459	41762497	+	inframe_deletion	In_Frame_Del	DEL	CAAGTGGATTGCCATTGAGAGTCTAGCTGACCGTGTCTA	CAAGTGGATTGCCATTGAGAGTCTAGCTGACCGTGTCTA	-	novel	NA	P-0040984-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	35	607	0	ENST00000301178.4:c.2141_2179del	p.Lys714_Tyr726del	p.K714_Y726del	ENST00000301178	NM_021913.4	713	gtCAAGTGGATTGCCATTGAGAGTCTAGCTGACCGTGTCTAc/gtc	18/20	0.271294760388575	1	FACETS	0.329	0.269	0.397	0.329	0.269	0.397	SUBCLONAL	1	FALSE	0	0.271294760388575	1		607	678	SUCCESS
APC	324	MSKCC	GRCh37	5	112173673	112173673	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040984-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	24	342	0	ENST00000257430.4:c.2382T>A	p.Ser794Arg	p.S794R	ENST00000257430	NM_000038.5	794	agT/agA	16/16	0.271294760388575	1	FACETS	0.577	0.453	0.719	0.577	0.453	0.719	SUBCLONAL	1	FALSE	0	0.271294760388575	1		342	265	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0041583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	80	616	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.221313603671399	1	FACETS	0.973	0.857	1	0.973	0.857	1	CLONAL	1	TRUE	0	0.250687580236776	1		618	574	SUCCESS
AR	367	MSKCC	GRCh37	X	66765796	66765796	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	64	785	0	ENST00000374690.3:c.808G>T	p.Ala270Ser	p.A270S	ENST00000374690	NM_000044.3	270	Gcc/Tcc	1/8	0.121647689746598	0	FACETS	0.495	0.428	0.568			1	INDETERMINATE	1	TRUE	0	0.250687580236776	0		785	773	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161339	55161339	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	36	348	0	ENST00000257290.5:c.3170C>T	p.Ser1057Phe	p.S1057F	ENST00000257290	NM_006206.4	1057	tCc/tTc	23/23	1	2	FACETS	0.679	0.558	0.814	0.679	0.558	0.814	SUBCLONAL	1	TRUE	1	0.250687580236776	2		348	423	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022483	12022483	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	49	580	0	ENST00000396373.4:c.589G>T	p.Glu197Ter	p.E197*	ENST00000396373	NM_001987.4	197	Gag/Tag	5/8	0.214932385260591	1	FACETS	0.527	0.445	0.617	0.527	0.445	0.617	SUBCLONAL	1	TRUE	0	0.250687580236776	1		580	649	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223930	2223930	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	45	541	0	ENST00000326181.6:c.1144C>G	p.Pro382Ala	p.P382A	ENST00000326181	NM_032271.2	382	Cct/Gct	13/21	0.250687580236776	1	FACETS	0.539	0.452	0.635	0.539	0.452	0.635	SUBCLONAL	1	TRUE	0	0.250687580236776	1		541	583	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351692	89351692	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	107	504	0	ENST00000301030.4:c.1258G>C	p.Val420Leu	p.V420L	ENST00000301030	NM_001256183.1	420	Gtg/Ctg	9/13	0.250687580236776	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.250687580236776	1		504	636	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226455	41226455	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555581955	NA	P-0041583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	82	450	1	ENST00000357654.3:c.4568C>T	p.Pro1523Leu	p.P1523L	ENST00000357654	NM_007294.3	1523	cCa/cTa	14/23	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.250687580236776	2		451	565	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602727	10602727	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	108	688	0	ENST00000171111.5:c.851A>G	p.Gln284Arg	p.Q284R	ENST00000171111	NM_203500.1	284	cAg/cGg	3/6	0.250687580236776	1	FACETS	0.996	0.894	1	0.996	0.894	1	CLONAL	1	TRUE	0	0.250687580236776	1		688	757	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100069	11100069	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0041583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	99	602	0	ENST00000358026.2:c.1195A>T	p.Lys399Ter	p.K399*	ENST00000358026	NM_001128849.1	399	Aaa/Taa	7/36	0.250687580236776	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.250687580236776	1		602	625	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082874	16082874	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	5	0	0	ENST00000281043.3:c.688G>A	p.Gly230Arg	p.G230R	ENST00000281043	NM_005378.4	230	Ggg/Agg	2/3	1	2	FACETS	0.475	0.27	0.757	0.475	0.27	0.757	SUBCLONAL	1	TRUE	1	0.250687580236776	2		0	84	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937489	178937489	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	25	348	0	ENST00000263967.3:c.1877A>G	p.Asp626Gly	p.D626G	ENST00000263967	NM_006218.2	626	gAc/gGc	12/21	1	2	FACETS	0.567	0.446	0.705	0.567	0.446	0.705	SUBCLONAL	1	TRUE	1	0.250687580236776	2		348	352	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573428	55573428	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0041583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	20	225	0	ENST00000288135.5:c.1090A>T	p.Lys364Ter	p.K364*	ENST00000288135	NM_000222.2	364	Aag/Tag	6/21	1	2	FACETS	0.516	0.395	0.659	0.516	0.395	0.659	SUBCLONAL	1	TRUE	1	0.250687580236776	2		225	309	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189077	32189077	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	36	380	1	ENST00000375023.3:c.477C>G	p.Phe159Leu	p.F159L	ENST00000375023	NM_004557.3	159	ttC/ttG	4/30	1	2	FACETS	0.513	0.421	0.616	0.513	0.421	0.616	SUBCLONAL	1	TRUE	1	0.250687580236776	2		381	560	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224135	36224212	+	inframe_deletion	In_Frame_Del	DEL	CCCACCTCCTGGACTCTGCCCCCAGGCCCCCTCCTCGGCGTGCTGCCCGTGGTCGGAGTGGTCCGCCCTGCCCCGCCC	CCCACCTCCTGGACTCTGCCCCCAGGCCCCCTCCTCGGCGTGCTGCCCGTGGTCGGAGTGGTCCGCCCTGCCCCGCCC	-	novel	NA	P-0041583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	46	591	0	ENST00000222270.7:c.6687_6764del	p.Thr2230_Pro2255del	p.T2230_P2255del	ENST00000222270	NM_014727.1	2229	CCCACCTCCTGGACTCTGCCCCCAGGCCCCCTCCTCGGCGTGCTGCCCGTGGTCGGAGTGGTCCGCCCTGCCCCGCCC/-	28/37	0.227980751483549	0	FACETS	0.486	0.409	0.571			1	SUBCLONAL	1	TRUE	0	0.250687580236776	0		591	566	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041987-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	89	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.999	0.892	1	0.999	0.892	1	CLONAL	1	TRUE	1	0.476543283408878	2		148	374	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0041987-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	183	263	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.476543283408878	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.476543283408878	3		263	428	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0041987-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	465	402	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.151940725574496	6	FACETS	0.952	0.913	0.991			1	INDETERMINATE	4	TRUE	NA	0.476543283408878	6		402	1001	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577600	7577600	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041987-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	283	331	0	ENST00000269305.4:c.681del	p.Asp228ThrfsTer19	p.D228Tfs*19	ENST00000269305	NM_001126112.2	227	tcT/tc	7/11	NA	2	FACETS	1	0.96	1			1	INDETERMINATE	2	TRUE	NA	0.476543283408878	2		331	586	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652056	36652056	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041987-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	252	730	1	ENST00000244741.5:c.178G>T	p.Glu60Ter	p.E60*	ENST00000244741	NM_000389.4	60	Gag/Tag	2/3	0.404610702562629	5	FACETS	1	0.953	1	0.68	0.637	0.724	CLONAL	2	TRUE	2	0.476543283408878	5		731	889	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30954259	30954259	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0041987-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	82	202	0	ENST00000375687.4:c.130A>T	p.Lys44Ter	p.K44*	ENST00000375687	NM_015338.5	44	Aag/Tag	2/13	0.476543283408878	6	FACETS	0.91	0.802	1	0.182	0.16	0.206	CLONAL	1	TRUE	1	0.476543283408878	6		202	739	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383280	31383280	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778547539	NA	P-0041987-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	650	402	0	ENST00000328111.2:c.1192C>T	p.Arg398Cys	p.R398C	ENST00000328111	NM_006892.3	398	Cgc/Tgc	11/23	0.476543283408878	6	FACETS	0.969	0.939	0.998	0.969	0.939	0.998	CLONAL	5	TRUE	1	0.476543283408878	6		402	1100	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922830	44922831	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0041987-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	196	315	0	ENST00000377967.4:c.1692_1693dup	p.Gln565ArgfsTer29	p.Q565Rfs*29	ENST00000377967	NM_021140.2	564	ggg/ggGCg	16/29	0.228161701397844	1	FACETS	1	0.991	1	1	0.991	1	INDETERMINATE	1	TRUE	0	0.476543283408878	1		315	452	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11194430	11194430	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041987-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	135	385	0	ENST00000361445.4:c.5224G>A	p.Glu1742Lys	p.E1742K	ENST00000361445	NM_004958.3	1742	Gaa/Aaa	37/58	0.476543283408878	3	FACETS	0.984	0.896	1	0.492	0.448	0.538	CLONAL	1	TRUE	1	0.476543283408878	3		385	713	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539855	187539855	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041987-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	38	265	0	ENST00000441802.2:c.7885G>C	p.Ala2629Pro	p.A2629P	ENST00000441802	NM_005245.3	2629	Gcc/Ccc	10/27	0.238475029566374	2	FACETS	0.406	0.336	0.484	0.203	0.168	0.242	INDETERMINATE	1	TRUE	0	0.476543283408878	2		265	393	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0043625-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	124	423	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.81717548379319	2		423	221	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647077	23647077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043625-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	82	624	0	ENST00000261584.4:c.790C>T	p.His264Tyr	p.H264Y	ENST00000261584	NM_024675.3	264	Cac/Tac	4/13	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.81717548379319	2		624	193	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987179	36987193	+	inframe_deletion	In_Frame_Del	DEL	CATGCCGCTCATGTT	CATGCCGCTCATGTT	-	novel	NA	P-0043625-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	19	656	0	ENST00000354822.5:c.496_510del	p.Asn166_Met170del	p.N166_M170del	ENST00000354822	NM_001079668.2	166	AACATGAGCGGCATG/-	3/3	NA	2	FACETS	0.581	0.452	0.726			1	INDETERMINATE	1	TRUE	NA	0.81717548379319	2		656	80	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222648	69222668	+	inframe_deletion	In_Frame_Del	DEL	AATAAGGGAGATATGTTGTGA	AATAAGGGAGATATGTTGTGA	-	novel	NA	P-0043625-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	43	537	1	ENST00000462284.1:c.623_643del	p.Ile208_Glu214del	p.I208_E214del	ENST00000462284	NM_002392.5	207	gtAATAAGGGAGATATGTTGTGAa/gta	8/11	1	2	FACETS	0.948	0.817	1	0.948	0.817	1	CLONAL	1	TRUE	1	0.81717548379319	2		538	111	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892221	9892221	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043625-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	76	559	2	ENST00000330684.3:c.2269G>T	p.Ala757Ser	p.A757S	ENST00000330684	NM_001134407.1	757	Gcc/Tcc	11/13	1	2	FACETS	0.969	0.868	1	0.969	0.868	1	CLONAL	1	TRUE	1	0.81717548379319	2		561	192	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821927	59821927	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043625-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	67	380	0	ENST00000259008.2:c.2123G>T	p.Trp708Leu	p.W708L	ENST00000259008	NM_032043.2	708	tGg/tTg	15/20	0.105935191010561	1	FACETS	0.581	0.516	0.647	0.581	0.516	0.647	INDETERMINATE	1	TRUE	0	0.81717548379319	1		380	167	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599904	10599904	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043625-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	91	735	0	ENST00000171111.5:c.1672G>C	p.Gly558Arg	p.G558R	ENST00000171111	NM_203500.1	558	Ggg/Cgg	5/6	0.81717548379319	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.81717548379319	1		735	124	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285857	198285857	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043625-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	55	410	2	ENST00000335508.6:c.196G>T	p.Asp66Tyr	p.D66Y	ENST00000335508	NM_012433.2	66	Gat/Tat	3/25	1	2	FACETS	0.968	0.85	1	0.968	0.85	1	CLONAL	1	TRUE	1	0.81717548379319	2		412	139	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940450	13940450	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043625-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	61	352	1	ENST00000405192.2:c.1056G>T	p.Trp352Cys	p.W352C	ENST00000405192	NM_001163147.1	352	tgG/tgT	11/12	1	2	FACETS	0.939	0.829	1	0.939	0.829	1	CLONAL	1	TRUE	1	0.81717548379319	2		353	159	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729544	41729544	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043625-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	66	620	0	ENST00000242208.4:c.985A>G	p.Ser329Gly	p.S329G	ENST00000242208	NM_002192.2	329	Agt/Ggt	3/3	0.565142755852538	5	FACETS	1	0.956	1	0.768	0.684	0.854	CLONAL	2	TRUE	2	0.81717548379319	5		620	156	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970978	21970986	+	inframe_deletion	In_Frame_Del	DEL	GCGACATCG	GCGACATCG	-	novel	NA	P-0043625-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	28	625	0	ENST00000304494.5:c.372_380del	p.Asp125_Ala127del	p.D125_A127del	ENST00000304494	NM_000077.4	124	cgCGATGTCGCa/cga	2/3	0.81717548379319	1	FACETS	0.811	0.69	0.928	0.811	0.69	0.928	CLONAL	1	TRUE	0	0.81717548379319	1		625	50	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045137	47045137	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043625-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	76	321	0	ENST00000377604.3:c.2378G>T	p.Arg793Leu	p.R793L	ENST00000377604	NM_001204468.1	793	cGa/cTa	21/24	0.397235205576643	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	NA	0.81717548379319	0		321	95	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191506	10191506	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs5030820	NA	P-0043725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	243	536	1	ENST00000256474.2:c.499C>T	p.Arg167Trp	p.R167W	ENST00000256474	NM_000551.3	167	Cgg/Tgg	3/3	0.77796756433814	1	FACETS	0.976	0.93	1	0.976	0.93	1	CLONAL	1	TRUE	0	0.77796756433814	1		537	391	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1962801	1962801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772470710	NA	P-0043725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	140	533	1	ENST00000382891.5:c.3295G>A	p.Glu1099Lys	p.E1099K	ENST00000382891	NM_133335.3	1099	Gag/Aag	18/22	0.38571691002718	3	FACETS	0.563	0.512	0.616	0.281	0.256	0.308	INDETERMINATE	1	TRUE	1	0.77796756433814	3		534	888	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133035	30133035	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1469534185	NA	P-0043725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	246	476	0	ENST00000331968.5:c.566C>T	p.Ala189Val	p.A189V	ENST00000331968	NM_002742.2	189	gCa/gTa	4/18	1	2	FACETS	0.922	0.866	0.978	0.922	0.866	0.978	CLONAL	1	TRUE	1	0.77796756433814	2		476	686	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0044017-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	217	325	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.285584030621107	6	FACETS	0.924	0.863	0.986	0.693	0.647	0.74	CLONAL	3	TRUE	2	0.417876268549213	6		325	688	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0044017-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	383	986	1	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	0.397382857471423	2	FACETS	0.94	0.896	0.985	0.94	0.896	0.985	CLONAL	2	TRUE	0	0.417876268549213	2		987	975	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533586	533586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730880462	NA	P-0044017-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1275	210	1072	0	ENST00000451590.1:c.317C>T	p.Ser106Leu	p.S106L	ENST00000451590	NM_001130442.1	106	tCg/tTg	4/5	0.282262282208308	4	FACETS	0.96	0.888	1	0.48	0.444	0.517	CLONAL	1	TRUE	2	0.417876268549213	4		1072	1485	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984418	72984418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044017-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	131	924	0	ENST00000268489.5:c.3166C>T	p.Arg1056Trp	p.R1056W	ENST00000268489	NM_006885.3	1056	Cgg/Tgg	3/10	0.408457851034164	4	FACETS	0.879	0.797	0.966			1	CLONAL	1	TRUE	NA	0.417876268549213	4		924	1011	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056315	180056315	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044017-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	223	1116	0	ENST00000261937.6:c.929G>A	p.Cys310Tyr	p.C310Y	ENST00000261937	NM_182925.4	310	tGc/tAc	7/30	0.417876268549213	3	FACETS	1	0.954	1	0.517	0.48	0.555	CLONAL	1	TRUE	1	0.417876268549213	3		1116	1248	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026568	6026568	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044017-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1447	227	666	0	ENST00000265849.7:c.1828A>C	p.Lys610Gln	p.K610Q	ENST00000265849	NM_000535.5	610	Aaa/Caa	11/15	0.285584030621107	6	FACETS	1	0.983	1	0.298	0.276	0.32	CLONAL	1	TRUE	2	0.417876268549213	6		666	1674	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149238646	149238651	+	missense_variant	Missense_Mutation	ONP	GAAGAG	GAAGAG	TAAAAA	novel	NA	P-0044017-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	88	478	1	ENST00000360632.3:c.1144_1149delinsTTTTTA	p.Leu382_Phe383delinsPheLeu	p.L382_F383delinsFL	ENST00000360632	NM_015472.4	382	CTCTTC/TTTTTA	7/7	0.416136711310385	5	FACETS	0.554	0.489	0.624	0.138	0.122	0.156	SUBCLONAL	1	TRUE	1	0.417876268549213	5		479	1237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0046175-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	62	431	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		431	614	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041404	47041405	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0046398-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	331	693	0	ENST00000377604.3:c.1753dup	p.Gln585ProfsTer7	p.Q585Pfs*7	ENST00000377604	NM_001204468.1	583	gac/gaCc	16/24	1	2	FACETS	0.989	0.937	1	0.989	0.937	1	CLONAL	1	TRUE	1	0.71	2		693	943	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241964	72241965	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0046398-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	79	223	0	ENST00000357731.5:c.425_426del	p.Tyr142Ter	p.Y142*	ENST00000357731	NM_173808.2	142	tAT/t	3/7	1	2	FACETS	0.815	0.726	0.909	0.815	0.726	0.909	CLONAL	1	TRUE	1	0.71	2		223	273	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859477	151859477	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046398-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	187	433	0	ENST00000262189.6:c.11185C>T	p.Pro3729Ser	p.P3729S	ENST00000262189	NM_170606.2	3729	Cca/Tca	43/59	1	2	FACETS	0.941	0.875	1	0.941	0.875	1	CLONAL	1	TRUE	1	0.71	2		433	560	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942716	44942716	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046398-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	189	343	0	ENST00000377967.4:c.3296A>G	p.Gln1099Arg	p.Q1099R	ENST00000377967	NM_021140.2	1099	cAg/cGg	23/29	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.71	2		343	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0046749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	444	583	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.385524133140388	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.426857896980398	2		583	946	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533012	63533012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200201811	NA	P-0046749-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	172	651	1	ENST00000307078.5:c.1882C>T	p.Arg628Trp	p.R628W	ENST00000307078	NM_004655.3	628	Cgg/Tgg	7/11	0.391557020618143	2	FACETS	0.817	0.752	0.886	0.409	0.376	0.443	CLONAL	1	TRUE	0	0.426857896980398	2		652	986	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046815-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	75	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.831	0.736	0.929	0.831	0.736	0.929	CLONAL	1	TRUE	1	0.663901345504971	2		148	272	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0046815-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	157	350	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.663901345504971	3	FACETS	0.896	0.823	0.972	0.448	0.411	0.486	CLONAL	1	TRUE	1	0.663901345504971	3		350	703	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412262	63412262	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1235049855	NA	P-0046815-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	282	416	0	ENST00000330258.3:c.905A>G	p.Asn302Ser	p.N302S	ENST00000330258	NM_152424.3	302	aAt/aGt	2/2	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.663901345504971	1		416	400	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593522	48593523	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0046888-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	156	218	0	ENST00000342988.3:c.1273_1274delinsTT	p.Ala425Phe	p.A425F	ENST00000342988	NM_005359.5	425	GCt/TTt	10/12	0.77076579256334	1	FACETS	0.957	0.899	1	0.957	0.899	1	CLONAL	1	TRUE	0	0.77076579256334	1		218	260	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197306	26197306	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047191-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	98	690	0	ENST00000356476.2:c.173C>T	p.Ser58Leu	p.S58L	ENST00000356476		58	tCg/tTg	1/1	0.446363578165359	2	FACETS	0.473	0.422	0.528	0.237	0.211	0.264	SUBCLONAL	1	TRUE	0	0.554674564673448	2		690	747	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295181	1295181	+	upstream_gene_variant	5'Flank	SNP	G	G	C	novel	NA	P-0047191-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	81	335	0				ENST00000310581	NM_198253.2	-/1132			0.432429905296619	3	FACETS	0.85	0.752	0.954	0.425	0.376	0.477	CLONAL	1	TRUE	1	0.554674564673448	3		335	439	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584552	48584552	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0047191-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	264	593	0	ENST00000342988.3:c.725C>G	p.Ser242Ter	p.S242*	ENST00000342988	NM_005359.5	242	tCa/tGa	6/12	0.554674564673448	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.554674564673448	1		593	585	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412022	116412022	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047191-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	1139	767	0	ENST00000397752.3:c.3007T>A	p.Tyr1003Asn	p.Y1003N	ENST00000397752	NM_000245.2	1003	Tac/Aac	14/21	0.554674564673448	5	FACETS	1	0.995	1	1	0.995	1	CLONAL	5	TRUE	0	0.554674564673448	5		767	1462	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135804196	135804196	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749030456	NA	P-0047191-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	269	645	1	ENST00000298552.3:c.64C>T	p.Arg22Trp	p.R22W	ENST00000298552	NM_001162426.1	22	Cgg/Tgg	3/23	0.244331704848959	3	FACETS	1	0.993	1	0.496	0.466	0.526	INDETERMINATE	1	TRUE	0	0.554674564673448	3		646	833	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101985064	101985064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770456398	NA	P-0047191-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	2655	873	1	ENST00000282441.5:c.511G>A	p.Val171Ile	p.V171I	ENST00000282441	NM_001130145.2	171	Gta/Ata	2/9	0.554674564673448	13	FACETS	1	0.998	1			1	CLONAL	11	TRUE	NA	0.554674564673448	13		874	3409	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811697	102811697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1356336413	NA	P-0047191-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	201	695	0	ENST00000307046.8:c.487G>A	p.Glu163Lys	p.E163K	ENST00000307046	NM_001111285.1	163	Gag/Aag	4/4	0.371801235618022	3	FACETS	1	0.955	1	0.52	0.482	0.559	CLONAL	1	TRUE	1	0.554674564673448	3		695	890	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577608	7577609	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0047191-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	163	557	2	ENST00000269305.4:c.673-1_673delinsTT		p.X225_splice	ENST00000269305	NM_001126112.2	225		7/11	0.5138428299338	1	FACETS	0.878	0.812	0.945	0.878	0.812	0.945	CLONAL	1	TRUE	0	0.554674564673448	1		559	484	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37672024	37672024	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047191-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	65	549	0	ENST00000447079.4:c.2809C>G	p.Gln937Glu	p.Q937E	ENST00000447079	NM_015083.1	937	Caa/Gaa	9/14	0.554674564673448	3	FACETS	0.477	0.413	0.546	0.238	0.206	0.273	SUBCLONAL	1	TRUE	1	0.554674564673448	3		549	628	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47684640	47684640	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047191-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	49	605	0	ENST00000347630.2:c.809C>A	p.Ala270Asp	p.A270D	ENST00000347630	NM_001007230.1	270	gCt/gAt	9/11	0.554674564673448	3	FACETS	0.315	0.266	0.369	0.157	0.133	0.185	SUBCLONAL	1	TRUE	1	0.554674564673448	3		605	717	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183559	10183559	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047191-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	318	892	0	ENST00000256474.2:c.28G>C	p.Glu10Gln	p.E10Q	ENST00000256474	NM_000551.3	10	Gag/Cag	1/3	0.251448803572885	4	FACETS	1	0.988	1	0.589	0.554	0.624	INDETERMINATE	1	TRUE	2	0.554674564673448	4		892	1514	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251937	153251955	+	frameshift_variant	Frame_Shift_Del	DEL	TGATGTATGCACTTTTCCA	TGATGTATGCACTTTTCCA	-	novel	NA	P-0047191-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	89	547	0	ENST00000281708.4:c.1051_1069del	p.Trp351AspfsTer20	p.W351Dfs*20	ENST00000281708	NM_033632.3	351	TGGAAAAGTGCATACATCAga/ga	7/12	1	2	FACETS	0.896	0.801	0.996	0.896	0.801	0.996	CLONAL	1	TRUE	1	0.554674564673448	2		547	358	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0047288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	28	428	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.735	0.585	0.906	0.735	0.585	0.906	CLONAL	1	TRUE	1	0.12	2		428	635	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165674	118165674	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	24	280	0	ENST00000369448.3:c.184G>A	p.Ala62Thr	p.A62T	ENST00000369448	NM_017709.3	62	Gca/Aca	2/2	1	2	FACETS	0.913	0.715	1	0.913	0.715	1	CLONAL	1	TRUE	1	0.12	2		280	438	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987031	36987031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	29	361	0	ENST00000354822.5:c.658del	p.Glu220SerfsTer8	p.E220Sfs*8	ENST00000354822	NM_001079668.2	220	Gag/ag	3/3	1	2	FACETS	0.953	0.764	1	0.953	0.764	1	CLONAL	1	TRUE	1	0.12	2		361	507	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781800	3781800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1246776885	NA	P-0047288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	36	415	0	ENST00000262367.5:c.4867G>A	p.Ala1623Thr	p.A1623T	ENST00000262367	NM_004380.2	1623	Gcc/Acc	29/31	1	2	FACETS	0.855	0.701	1	0.855	0.701	1	CLONAL	1	TRUE	1	0.12	2		415	702	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022302	31022302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	31	320	0	ENST00000375687.4:c.1787G>T	p.Arg596Leu	p.R596L	ENST00000375687	NM_015338.5	596	cGg/cTg	13/13	1	2	FACETS	0.929	0.75	1	0.929	0.75	1	CLONAL	1	TRUE	1	0.12	2		320	556	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754920	57754920	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0047288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	18	165	0	ENST00000274289.3:c.271-1G>T		p.X91_splice	ENST00000274289	NM_006622.3	91			1	2	FACETS	0.852	0.641	1	0.852	0.641	1	CLONAL	1	TRUE	1	0.12	2		165	352	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915834	127915834	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	27	271	0	ENST00000373547.4:c.647T>C	p.Phe216Ser	p.F216S	ENST00000373547	NM_002721.4	216	tTt/tCt	6/7	1	2	FACETS	0.932	0.74	1	0.932	0.74	1	CLONAL	1	TRUE	1	0.12	2		271	483	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115416	115115416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	74	537	0	ENST00000257566.3:c.910C>T	p.Arg304Trp	p.R304W	ENST00000257566	NM_016569.3	304	Cgg/Tgg	5/8	0.734801076377093	3	FACETS	1	0.935	1	0.54	0.479	0.604	CLONAL	1	TRUE	1	0.734801076377093	3		537	255	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870612	40870612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	64	551	0	ENST00000428826.2:c.791C>T	p.Ser264Leu	p.S264L	ENST00000428826		264	tCa/tTa	9/21	0.734801076377093	2	FACETS	0.754	0.662	0.851	0.377	0.331	0.426	SUBCLONAL	1	TRUE	0	0.734801076377093	2		551	231	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578470	+	frameshift_variant	Frame_Shift_Del	DEL	ACGCGGGTGCC	ACGCGGGTGCC	GCG	novel	NA	P-0047352-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	186	948	2	ENST00000269305.4:c.460_470delinsCGC	p.Gly154ArgfsTer24	p.G154Rfs*24	ENST00000269305	NM_001126112.2	154	GGCACCCGCGTc/CGCc	5/11	NA	2	FACETS	0.898	0.851	0.943			1	INDETERMINATE	2	TRUE	NA	0.734801076377093	2		950	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0047416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	218	628	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.59147857202814	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.595764269833819	2		628	344	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	83	423	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.504792433625594	4	FACETS	1	0.925	1	1	0.925	1	CLONAL	2	TRUE	2	0.595764269833819	4		423	215	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0047416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	25	259	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.595764269833819	3	FACETS	0.858	0.686	1	0.429	0.343	0.524	CLONAL	1	TRUE	1	0.595764269833819	3		259	127	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119765	70119766	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0047416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	151	409	0	ENST00000245479.2:c.770_771dup	p.Pro258AlafsTer22	p.P258Afs*22	ENST00000245479	NM_000346.3	256	ggg/ggGCg	3/3	0.586538158809808	3	FACETS	0.985	0.915	1	0.985	0.915	1	CLONAL	2	TRUE	1	0.595764269833819	3		409	334	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955593	55955593	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs373654225	NA	P-0047416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	52	376	1	ENST00000263923.4:c.3352C>T	p.Arg1118Ter	p.R1118*	ENST00000263923	NM_002253.2	1118	Cga/Tga	25/30	0.595764269833819	3	FACETS	1	0.967	1	0.712	0.619	0.81	CLONAL	1	TRUE	1	0.595764269833819	3		377	159	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467877	66467877	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	10	300	0	ENST00000273854.3:c.392A>T	p.Lys131Ile	p.K131I	ENST00000273854	NM_004439.5	131	aAa/aTa	3/18	0.595764269833819	3	FACETS	0.3	0.204	0.421	0.15	0.102	0.211	SUBCLONAL	1	TRUE	1	0.595764269833819	3		300	145	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411944	63411948	+	frameshift_variant	Frame_Shift_Del	DEL	TATTC	TATTC	-	novel	NA	P-0047416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	123	604	0	ENST00000330258.3:c.1219_1223del	p.Glu407SerfsTer32	p.E407Sfs*32	ENST00000330258	NM_152424.3	407	GAATAt/t	2/2	0.595764269833819	3	FACETS	0.918	0.844	0.993	0.918	0.844	0.993	CLONAL	2	TRUE	1	0.595764269833819	3		604	292	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692794	89692794	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121909238	NA	P-0047475-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	20	266	0	ENST00000371953.3:c.278A>G	p.His93Arg	p.H93R	ENST00000371953	NM_000314.4	93	cAt/cGt	5/9	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.570668990675997	2		266	57	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266112	41266112	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913228	NA	P-0047475-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	18	247	0	ENST00000349496.5:c.109T>G	p.Ser37Ala	p.S37A	ENST00000349496	NM_001904.3	37	Tct/Gct	3/15	0.180349183063623	4	FACETS	1	0.86	1	0.59	0.453	0.744	INDETERMINATE	1	TRUE	2	0.570668990675997	4		247	84	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097627	27097627	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047475-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	31	359	0	ENST00000324856.7:c.3216A>C	p.Lys1072Asn	p.K1072N	ENST00000324856	NM_006015.4	1072	aaA/aaC	12/20	0.131869600303063	4	FACETS	0.783	0.648	0.928	0.783	0.648	0.928	INDETERMINATE	2	TRUE	2	0.570668990675997	4		359	109	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0047538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	652	402	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.855026063393682	3	FACETS	0.95	0.921	0.979	0.95	0.921	0.979	CLONAL	2	TRUE	1	0.855026063393682	3		402	1146	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	407	755	0	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	1	2	FACETS	0.936	0.894	0.979	0.936	0.894	0.979	CLONAL	1	TRUE	1	0.855026063393682	2		755	1017	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0047538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	26	243	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	0.715169709900513	1	FACETS	0.118	0.094	0.147	0.118	0.094	0.147	SUBCLONAL	1	TRUE	0	0.855026063393682	1		243	294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0047538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	376	616	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.855026063393682	2		616	855	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579585	7579585	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	253	499	0	ENST00000269305.4:c.102del	p.Leu35CysfsTer9	p.L35Cfs*9	ENST00000269305	NM_001126112.2	34	ccC/cc	4/11	1	2	FACETS	0.913	0.86	0.967	0.913	0.86	0.967	CLONAL	1	TRUE	1	0.855026063393682	2		499	648	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918553	44918553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	258	344	1	ENST00000377967.4:c.1036C>T	p.Gln346Ter	p.Q346*	ENST00000377967	NM_021140.2	346	Caa/Taa	12/29	0.855026063393682	1	FACETS	0.97	0.932	1	0.97	0.932	1	CLONAL	1	TRUE	0	0.855026063393682	1		345	356	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056214	27056214	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	677	518	1	ENST00000324856.7:c.1210C>T	p.Gln404Ter	p.Q404*	ENST00000324856	NM_006015.4	404	Caa/Taa	2/20	0.855026063393682	2	FACETS	0.988	0.97	1	0.988	0.97	1	CLONAL	2	TRUE	0	0.855026063393682	2		519	801	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287398	38287398	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778531708	NA	P-0047538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	309	611	0	ENST00000425967.3:c.259C>T	p.Arg87Cys	p.R87C	ENST00000425967	NM_001174067.1	87	Cgc/Tgc	4/19	1	2	FACETS	0.899	0.852	0.947	0.899	0.852	0.947	CLONAL	1	TRUE	1	0.855026063393682	2		611	804	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061593	38061622	+	inframe_deletion	In_Frame_Del	DEL	GGCCGCGTAGGGGCCCAGGCCATTCATGGA	GGCCGCGTAGGGGCCCAGGCCATTCATGGA	-	novel	NA	P-0047538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	109	281	0	ENST00000250448.2:c.367_396del	p.Ser123_Ala132del	p.S123_A132del	ENST00000250448	NM_004496.3	123	TCCATGAATGGCCTGGGCCCCTACGCGGCC/-	2/2	1	2	FACETS	0.697	0.632	0.764	0.697	0.632	0.764	SUBCLONAL	1	TRUE	1	0.855026063393682	2		281	366	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255035	16255035	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	192	287	0	ENST00000375759.3:c.2300G>C	p.Ser767Thr	p.S767T	ENST00000375759	NM_015001.2	767	aGc/aCc	11/15	0.855026063393682	2	FACETS	0.875	0.817	0.935	0.438	0.408	0.468	CLONAL	1	TRUE	0	0.855026063393682	2		287	513	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542273	187542273	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	22	266	0	ENST00000441802.2:c.5467G>A	p.Asp1823Asn	p.D1823N	ENST00000441802	NM_005245.3	1823	Gat/Aat	10/27	0.715169709900513	1	FACETS	0.131	0.101	0.165	0.131	0.101	0.165	SUBCLONAL	1	TRUE	0	0.855026063393682	1		266	225	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135277	2135277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047819-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	69	819	0	ENST00000219476.3:c.4616C>T	p.Ser1539Leu	p.S1539L	ENST00000219476	NM_000548.3	1539	tCa/tTa	36/42	1	2	FACETS	0.226	0.196	0.258	0.226	0.196	0.258	SUBCLONAL	1	TRUE	1	0.72	2		819	849	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913499	NA	P-0047839-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	19	180	0	ENST00000345146.2:c.394C>A	p.Arg132Ser	p.R132S	ENST00000345146	NM_005896.2	132	Cgt/Agt	4/10	0.29656817345846	1	FACETS	0.261	0.199	0.333	0.261	0.199	0.333	INDETERMINATE	1	TRUE	0	0.584970981677492	1		180	176	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0047839-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	101	376	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.584970981677492	2		376	343	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004224	29004224	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047839-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	83	246	0	ENST00000282397.4:c.1069A>G	p.Met357Val	p.M357V	ENST00000282397	NM_002019.4	357	Atg/Gtg	8/30	0.584970981677492	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.584970981677492	1		246	198	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274842	38274843	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCG	novel	NA	P-0047839-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	49	301	0	ENST00000425967.3:c.1737_1738insCGGG	p.Gly580ArgfsTer108	p.G580Rfs*108	ENST00000425967	NM_001174067.1	579	-/CGGG	13/19	0.349097066105058	3	FACETS	0.727	0.619	0.843	0.363	0.309	0.422	INDETERMINATE	1	TRUE	1	0.584970981677492	3		301	298	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442558	52442565	+	frameshift_variant	Frame_Shift_Del	DEL	AGACCTTT	AGACCTTT	-	novel	NA	P-0047839-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	67	343	0	ENST00000460680.1:c.180_187del	p.Lys61TyrfsTer5	p.K61Yfs*5	ENST00000460680	NM_004656.3	60	cgAAAGGTCTct/cgct	4/17	0.584970981677492	1	FACETS	0.75	0.662	0.842	0.75	0.662	0.842	SUBCLONAL	1	TRUE	0	0.584970981677492	1		343	216	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128206803	128206803	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047839-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	50	305	0	ENST00000265960.3:c.1420A>G	p.Thr474Ala	p.T474A	ENST00000265960	NM_001006617.1	474	Acc/Gcc	11/12	0.413373981900458	1	FACETS	0.484	0.414	0.559	0.484	0.414	0.559	SUBCLONAL	1	TRUE	0	0.584970981677492	1		305	250	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122863	2122874	+	frameshift_variant	Frame_Shift_Del	DEL	AGACACTGGAGC	AGACACTGGAGC	TT	novel	NA	P-0047839-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	86	483	2	ENST00000219476.3:c.2234_2245delinsTT	p.Lys745IlefsTer23	p.K745Ifs*23	ENST00000219476	NM_000548.3	745	aAGACACTGGAGCgg/aTTgg	21/42	0.584970981677492	1	FACETS	0.846	0.76	0.934	0.846	0.76	0.934	CLONAL	1	TRUE	0	0.584970981677492	1		485	246	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295247	1295247	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0047840-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	15	271	0				ENST00000310581	NM_198253.2	-/1132			0.198996544439688	7	FACETS	0.57	0.416	0.757	0.095	0.069	0.127	SUBCLONAL	1	TRUE	1	0.198996544439688	7		271	396	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097788	8097790	+	inframe_deletion	In_Frame_Del	DEL	GCA	GCA	-	novel	NA	P-0047840-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	62	543	0	ENST00000346208.3:c.170_172del	p.Gly57_Asn58delinsAsp	p.G57_N58delinsD	ENST00000346208		57	gGCAac/gac	2/6	1	2	FACETS	0.977	0.843	1	0.977	0.843	1	CLONAL	1	TRUE	1	0.198996544439688	2		543	638	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120546250	120546250	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047840-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	41	448	0	ENST00000229340.5:c.74T>C	p.Leu25Pro	p.L25P	ENST00000229340	NM_006861.6	25	cTg/cCg	2/6	1	2	FACETS	0.697	0.58	0.828	0.697	0.58	0.828	SUBCLONAL	1	TRUE	1	0.198996544439688	2		448	591	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199881	108199881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881315	NA	P-0047956-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	69	192	0	ENST00000278616.4:c.7223C>T	p.Ser2408Leu	p.S2408L	ENST00000278616	NM_000051.3	2408	tCg/tTg	49/63	1	2	FACETS	0.824	0.723	0.932	0.824	0.723	0.932	CLONAL	1	TRUE	1	0.498530366423782	2		192	336	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047989-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	74	148	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.972	0.86	1			1	INDETERMINATE	1	TRUE	NA	0.551962381698829	2		148	276	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588751	29588751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760703505	NA	P-0047989-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	35	195	0	ENST00000356175.3:c.4537C>T	p.Arg1513Ter	p.R1513*	ENST00000356175	NM_000267.3	1513	Cga/Tga	34/57	0.551962381698829	1	FACETS	0.439	0.363	0.523	0.439	0.363	0.523	SUBCLONAL	1	TRUE	0	0.551962381698829	1		195	209	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133371	38133371	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370007995	NA	P-0047989-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	133	337	0	ENST00000317025.8:c.4102G>A	p.Asp1368Asn	p.D1368N	ENST00000317025	NM_023034.1	1368	Gat/Aat	24/24	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.551962381698829	2		337	472	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0048090-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	203	506	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.934	0.871	0.997	0.934	0.871	0.997	CLONAL	1	TRUE	1	0.733311809338137	2		506	593	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048090-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	265	466	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.733311809338137	2		466	711	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111562	8111563	+	splice_donor_variant	Splice_Site	INS	-	-	TT	novel	NA	P-0048090-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	216	468	0	ENST00000346208.3:c.1047+2_1047+3insTT		p.X349_splice	ENST00000346208		349			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.733311809338137	2		468	566	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0048102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	624	698	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.406187511025856	1	FACETS	0.916	0.884	0.948	1	0.998	1	CLONAL	2	TRUE	0	0.406187511025856	1		698	1336	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341344	89341344	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	241	388	0	ENST00000301030.4:c.7591G>C	p.Glu2531Gln	p.E2531Q	ENST00000301030	NM_001256183.1	2531	Gag/Cag	11/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.406187511025856	2		388	1129	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106676	27106676	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0048102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	130	450	0	ENST00000324856.7:c.6287C>G	p.Ser2096Ter	p.S2096*	ENST00000324856	NM_006015.4	2096	tCa/tGa	20/20	0.356875655966677	3	FACETS	1	0.969	1	0.575	0.522	0.63	CLONAL	1	TRUE	1	0.406187511025856	3		450	670	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831181	72831181	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	91	352	0	ENST00000268489.5:c.5400C>G	p.Phe1800Leu	p.F1800L	ENST00000268489	NM_006885.3	1800	ttC/ttG	9/10	1	2	FACETS	0.818	0.728	0.913	0.818	0.728	0.913	CLONAL	1	TRUE	1	0.406187511025856	2		352	548	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582062	189582062	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	74	254	0	ENST00000264731.3:c.621G>C	p.Lys207Asn	p.K207N	ENST00000264731	NM_003722.4	207	aaG/aaC	5/14	0.406187511025856	5	FACETS	0.971	0.858	1	0.647	0.572	0.727	CLONAL	2	TRUE	2	0.406187511025856	5		254	302	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225365093	225365093	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs772779469	NA	P-0048102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	41	312	0	ENST00000264414.4:c.1597G>C	p.Glu533Gln	p.E533Q	ENST00000264414	NM_003590.4	533	Gag/Cag	11/16	0.307181804552898	3	FACETS	0.858	0.719	1	0.429	0.359	0.506	CLONAL	1	TRUE	1	0.406187511025856	3		312	283	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098536	108098536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	32	208	0	ENST00000278616.4:c.106G>A	p.Asp36Asn	p.D36N	ENST00000278616	NM_000051.3	36	Gat/Aat	3/63	0.231720460287193	5	FACETS	0.813	0.669	0.971	0.542	0.446	0.647	INDETERMINATE	2	TRUE	2	0.406187511025856	5		208	156	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098572	108098572	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	33	214	0	ENST00000278616.4:c.142G>C	p.Asp48His	p.D48H	ENST00000278616	NM_000051.3	48	Gat/Cat	3/63	0.231720460287193	5	FACETS	0.866	0.716	1	0.577	0.477	0.687	INDETERMINATE	2	TRUE	2	0.406187511025856	5		214	151	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122649	108122649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	30	295	0	ENST00000278616.4:c.1693G>T	p.Glu565Ter	p.E565*	ENST00000278616	NM_000051.3	565	Gaa/Taa	11/63	0.231720460287193	5	FACETS	0.849	0.694	1	0.566	0.463	0.679	INDETERMINATE	2	TRUE	2	0.406187511025856	5		295	140	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186749	108186749	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786204141	NA	P-0048102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	48	275	0	ENST00000278616.4:c.6107A>G	p.Tyr2036Cys	p.Y2036C	ENST00000278616	NM_000051.3	2036	tAt/tGt	42/63	0.231720460287193	5	FACETS	0.813	0.694	0.941	0.542	0.462	0.627	INDETERMINATE	2	TRUE	2	0.406187511025856	5		275	234	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031965	10031965	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	49	417	0	ENST00000330684.3:c.858C>A	p.Tyr286Ter	p.Y286*	ENST00000330684	NM_001134407.1	286	taC/taA	3/13	0.406187511025856	3	FACETS	0.626	0.53	0.73	0.313	0.265	0.365	SUBCLONAL	1	TRUE	1	0.406187511025856	3		417	464	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37865672	37865672	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	113	374	0	ENST00000269571.5:c.541C>G	p.Leu181Val	p.L181V	ENST00000269571		181	Ctc/Gtc	4/27	0.391122440750078	4	FACETS	0.879	0.79	0.973	0.44	0.395	0.487	CLONAL	1	TRUE	2	0.406187511025856	4		374	890	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215381	41215381	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	17	266	0	ENST00000357654.3:c.5162A>C	p.Gln1721Pro	p.Q1721P	ENST00000357654	NM_007294.3	1721	cAg/cCg	18/23	0.391122440750078	4	FACETS	0.654	0.49	0.846	0.327	0.245	0.423	SUBCLONAL	1	TRUE	2	0.406187511025856	4		266	180	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917042	50917042	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1555792660	NA	P-0048102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1943	436	600	0	ENST00000440232.2:c.2294T>G	p.Val765Gly	p.V765G	ENST00000440232	NM_002691.3	765	gTg/gGg	19/27	0.406187511025856	3	FACETS	1	0.984	1	0.543	0.515	0.571	CLONAL	1	TRUE	1	0.406187511025856	3		600	2379	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793347	242793347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1543	340	619	1	ENST00000334409.5:c.730G>A	p.Glu244Lys	p.E244K	ENST00000334409	NM_005018.2	244	Gag/Aag	5/5	0.307181804552898	3	FACETS	1	0.977	1	0.535	0.504	0.567	CLONAL	1	TRUE	1	0.406187511025856	3		620	1883	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775433	39775433	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	39	324	0	ENST00000288319.7:c.587G>C	p.Arg196Thr	p.R196T	ENST00000288319	NM_182918.3	196	aGa/aCa	4/10	0.165297135563787	5	FACETS	1	0.862	1	0.347	0.288	0.411	INDETERMINATE	1	TRUE	2	0.406187511025856	5		324	297	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074190	30074190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	30	250	0	ENST00000338641.4:c.1452G>A	p.Met484Ile	p.M484I	ENST00000338641	NM_000268.3	484	atG/atA	14/16	0.267939576852515	3	FACETS	0.863	0.7	1	0.288	0.233	0.348	CLONAL	1	TRUE	0	0.406187511025856	3		250	206	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361199	66361200	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0048102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	20	206	0	ENST00000273854.3:c.972_973del	p.His325GlnfsTer5	p.H325Qfs*5	ENST00000273854	NM_004439.5	324	ccTCac/ccac	4/18	0.406187511025856	3	FACETS	1	0.815	1	0.529	0.41	0.663	CLONAL	1	TRUE	1	0.406187511025856	3		206	112	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38975652	38975652	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	20	342	0	ENST00000357387.3:c.876C>G	p.Phe292Leu	p.F292L	ENST00000357387	NM_152756.3	292	ttC/ttG	10/38	0.307181804552898	3	FACETS	0.755	0.582	0.953	0.377	0.291	0.477	CLONAL	1	TRUE	1	0.406187511025856	3		342	157	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100172	157100172	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	50	61	0	ENST00000346085.5:c.1109C>G	p.Ser370Cys	p.S370C	ENST00000346085	NM_020732.3	370	tCc/tGc	1/20	0.390846147674219	3	FACETS	1	0.957	1	0.445	0.381	0.513	CLONAL	1	TRUE	0	0.406187511025856	3		61	222	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741693	145741693	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1333353971	NA	P-0048102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2274	351	526	0	ENST00000428558.2:c.810G>C	p.Glu270Asp	p.E270D	ENST00000428558	NM_004260.3	270	gaG/gaC	5/22	0.406187511025856	4	FACETS	0.926	0.872	0.981	0.463	0.436	0.491	CLONAL	1	TRUE	2	0.406187511025856	4		526	2625	SUCCESS
AR	367	MSKCC	GRCh37	X	66942759	66942760	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	17	337	0	ENST00000374690.3:c.2546dup	p.Asn849LysfsTer32	p.N849Kfs*32	ENST00000374690	NM_000044.3	847	aga/agAa	7/8	0.406187511025856	0	FACETS	0.401	0.302	0.515			1	SUBCLONAL	1	TRUE	0	0.406187511025856	0		337	124	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048165-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	86	148	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.881	0.792	0.973			1	INDETERMINATE	1	TRUE	NA	0.793498901284636	2		148	246	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0048165-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	316	616	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.793498901284636	2		618	760	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876449	35876449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2229232	NA	P-0048165-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	234	586	0	ENST00000303115.3:c.1241C>T	p.Thr414Met	p.T414M	ENST00000303115	NM_002185.3	414	aCg/aTg	8/8	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.793498901284636	2		586	589	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0048165-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16156	2479	419	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.793498901284636	34	FACETS	0.918	0.898	0.939	0.135	0.132	0.139	CLONAL	5	TRUE	0	0.793498901284636	34		419	18635	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74000724	74000724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048165-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	323	619	1	ENST00000318443.5:c.1414G>A	p.Gly472Arg	p.G472R	ENST00000318443	NM_001024736.1	472	Ggg/Agg	7/10	1	2	FACETS	0.946	0.896	0.995	0.946	0.896	0.995	CLONAL	1	TRUE	1	0.793498901284636	2		620	861	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0048167-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	119	485	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.271278329140674	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.271278329140674	1		485	610	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849852	156849852	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048167-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	155	504	0	ENST00000524377.1:c.2108A>C	p.Lys703Thr	p.K703T	ENST00000524377	NM_002529.3	703	aAg/aCg	16/17	0.271278329140674	3	FACETS	0.846	0.776	0.919	0.846	0.776	0.919	CLONAL	2	TRUE	1	0.271278329140674	3		504	767	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457304	67457304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223765	NA	P-0048167-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	114	658	0	ENST00000327367.4:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000327367	NM_005902.3	93	cGa/cAa	2/9	1	2	FACETS	0.938	0.844	1	0.938	0.844	1	CLONAL	1	TRUE	1	0.271278329140674	2		658	896	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263992	104263992	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758001170	NA	P-0048167-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	85	364	0	ENST00000369902.3:c.83C>T	p.Ser28Leu	p.S28L	ENST00000369902	NM_016169.3	28	tCg/tTg	1/12	0.271278329140674	3	FACETS	1	0.934	1	0.542	0.479	0.609	CLONAL	1	TRUE	1	0.271278329140674	3		364	657	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001578	150001578	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048167-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	42	284	0	ENST00000253339.5:c.2026G>C	p.Asp676His	p.D676H	ENST00000253339		676	Gat/Cat	4/7	0.271278329140674	3	FACETS	0.933	0.781	1	0.466	0.39	0.551	CLONAL	1	TRUE	1	0.271278329140674	3		284	377	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832810	3832810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048167-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	97	457	0	ENST00000262367.5:c.1448G>A	p.Arg483Gln	p.R483Q	ENST00000262367	NM_004380.2	483	cGa/cAa	6/31	0.267620638117722	4	FACETS	1	0.96	1	0.582	0.519	0.65	CLONAL	1	TRUE	2	0.271278329140674	4		457	781	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678589	88678589	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201426743	NA	P-0048167-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	56	348	2	ENST00000360948.2:c.947G>A	p.Arg316His	p.R316H	ENST00000360948	NM_001012338.2	316	cGc/cAc	9/19	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.271278329140674	2		350	404	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733594	85733594	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048167-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	69	389	0	ENST00000370580.1:c.418G>T	p.Glu140Ter	p.E140*	ENST00000370580	NM_003921.4	140	Gag/Tag	3/3	0.208774208396792	4	FACETS	1	0.88	1	0.505	0.44	0.576	CLONAL	1	TRUE	2	0.271278329140674	4		389	640	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11297908	11297908	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048167-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	56	417	0	ENST00000361445.4:c.2200C>G	p.Leu734Val	p.L734V	ENST00000361445	NM_004958.3	734	Ctc/Gtc	13/58	0.208774208396792	4	FACETS	0.821	0.703	0.951	0.411	0.351	0.476	CLONAL	1	TRUE	2	0.271278329140674	4		417	639	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134471	41134471	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0048167-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	70	402	0	ENST00000379561.5:c.1157C>G	p.Ser386Ter	p.S386*	ENST00000379561	NM_002015.3	386	tCa/tGa	2/3	0.271278329140674	2	FACETS	0.945	0.825	1	0.473	0.412	0.537	CLONAL	1	TRUE	0	0.271278329140674	2		402	546	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060869	38060869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048167-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	122	669	0	ENST00000250448.2:c.1120C>T	p.His374Tyr	p.H374Y	ENST00000250448	NM_004496.3	374	Cac/Tac	2/2	0.271278329140674	3	FACETS	0.914	0.824	1	0.305	0.274	0.337	CLONAL	1	TRUE	0	0.271278329140674	3		669	1118	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68758609	68758609	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048167-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	220	291	0	ENST00000487270.1:c.765G>C	p.Leu255Phe	p.L255F	ENST00000487270	NM_133509.3	255	ttG/ttC	8/11	0.271278329140674	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	0	0.271278329140674	3		291	582	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457623	67457623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048167-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	120	599	1	ENST00000327367.4:c.433G>A	p.Glu145Lys	p.E145K	ENST00000327367	NM_005902.3	145	Gag/Aag	3/9	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.271278329140674	2		600	782	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257883	19257883	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048167-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	395	837	0	ENST00000162023.5:c.503C>G	p.Ser168Cys	p.S168C	ENST00000162023		168	tCt/tGt	9/13	0.271278329140674	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	2	0.271278329140674	4		837	1485	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921500	178921500	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048167-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	57	369	0	ENST00000263967.3:c.982T>C	p.Trp328Arg	p.W328R	ENST00000263967	NM_006218.2	328	Tgg/Cgg	5/21	0.224035434666306	3	FACETS	1	0.886	1			1	CLONAL	1	TRUE	NA	0.271278329140674	3		369	461	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46738445	46738445	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048167-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	74	404	0	ENST00000371975.4:c.1346C>A	p.Ser449Tyr	p.S449Y	ENST00000371975	NM_003579.3	449	tCc/tAc	12/18	0.208774208396792	4	FACETS	0.878	0.767	0.997	0.439	0.383	0.499	CLONAL	1	TRUE	2	0.271278329140674	4		404	790	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782908	66782908	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048167-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	40	390	0	ENST00000307102.5:c.1137C>G	p.Ile379Met	p.I379M	ENST00000307102	NM_002755.3	379	atC/atG	11/11	1	2	FACETS	0.611	0.507	0.726	0.611	0.507	0.726	SUBCLONAL	1	TRUE	1	0.271278329140674	2		390	483	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793173	33793173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048167-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	51	267	0	ENST00000498907.2:c.148G>A	p.Glu50Lys	p.E50K	ENST00000498907	NM_004364.3	50	Gag/Aag	1/1	0.271278329140674	7	FACETS	0.945	0.802	1			1	CLONAL	1	TRUE	NA	0.271278329140674	7		267	668	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219761	36219761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048167-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1515	130	690	0	ENST00000222270.7:c.4658C>T	p.Ser1553Leu	p.S1553L	ENST00000222270	NM_014727.1	1553	tCa/tTa	20/37	0.271278329140674	7	FACETS	0.978	0.883	1			1	CLONAL	1	TRUE	NA	0.271278329140674	7		690	1645	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705266	52705266	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048167-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	70	409	1	ENST00000322088.6:c.148G>A	p.Glu50Lys	p.E50K	ENST00000322088	NM_014225.5	50	Gag/Aag	2/15	NA	2	FACETS	0.92	0.803	1			1	INDETERMINATE	1	TRUE	NA	0.271278329140674	2		410	561	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185056	99185056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048167-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	56	280	0	ENST00000074304.5:c.2458G>A	p.Glu820Lys	p.E820K	ENST00000074304	NM_001134224.1	820	Gaa/Aaa	23/26	0.271278329140674	3	FACETS	1	0.934	1	0.576	0.495	0.664	CLONAL	1	TRUE	1	0.271278329140674	3		280	407	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597398	52597398	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048167-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	74	420	0	ENST00000394830.3:c.3912G>T	p.Met1304Ile	p.M1304I	ENST00000394830	NM_018313.4	1304	atG/atT	25/30	0.271278329140674	2	FACETS	1	0.913	1	0.526	0.461	0.595	CLONAL	1	TRUE	0	0.271278329140674	2		420	519	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937012	178937012	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048167-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	50	371	0	ENST00000263967.3:c.1693C>G	p.Leu565Val	p.L565V	ENST00000263967	NM_006218.2	565	Cta/Gta	11/21	0.224035434666306	3	FACETS	0.869	0.737	1			1	CLONAL	1	TRUE	NA	0.271278329140674	3		371	482	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048225-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	90	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.503099884913014	2		148	328	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0048225-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	231	402	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.429676300721628	3	FACETS	0.875	0.82	0.93	0.875	0.82	0.93	CLONAL	2	TRUE	1	0.503099884913014	3		402	657	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0048225-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	210	506	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.503099884913014	3	FACETS	0.92	0.86	0.98	0.92	0.86	0.98	CLONAL	2	TRUE	1	0.503099884913014	3		506	568	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788617	3788617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519884	NA	P-0048225-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	111	395	0	ENST00000262367.5:c.4337G>A	p.Arg1446His	p.R1446H	ENST00000262367	NM_004380.2	1446	cGc/cAc	26/31	1	2	FACETS	0.914	0.826	1	0.914	0.826	1	CLONAL	1	TRUE	1	0.503099884913014	2		395	483	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425119	49425119	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048225-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	156	725	0	ENST00000301067.7:c.13369G>T	p.Glu4457Ter	p.E4457*	ENST00000301067	NM_003482.3	4457	Gaa/Taa	39/54	1	2	FACETS	0.901	0.828	0.978	0.901	0.828	0.978	CLONAL	1	TRUE	1	0.503099884913014	2		725	688	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988553	36988553	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048225-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	168	706	0	ENST00000354822.5:c.100A>T	p.Ser34Cys	p.S34C	ENST00000354822	NM_001079668.2	34	Agt/Tgt	2/3	0.503099884913014	3	FACETS	1	0.945	1	0.517	0.475	0.56	CLONAL	1	TRUE	1	0.503099884913014	3		706	809	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482843	67482927	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	CCCCAAGCATCCGCTGTTCCAGTGTGTCTTAGAGACATCAAGTATGGTAGGGGAGGGCAGGCTTGGGGAAAATGGCCATGCAGGA	CCCCAAGCATCCGCTGTTCCAGTGTGTCTTAGAGACATCAAGTATGGTAGGGGAGGGCAGGCTTGGGGAAAATGGCCATGCAGGA	-	novel	NA	P-0048225-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	94	515	0	ENST00000327367.4:c.1247_*53del		p.*416*	ENST00000327367	NM_005902.3	416		9/9	1	2	FACETS	0.723	0.645	0.805	0.723	0.645	0.805	SUBCLONAL	1	TRUE	1	0.503099884913014	2		515	517	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860773	45860773	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048225-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	140	610	0	ENST00000391945.4:c.1336C>G	p.Pro446Ala	p.P446A	ENST00000391945	NM_000400.3	446	Ccc/Gcc	14/23	1	2	FACETS	0.905	0.827	0.986	0.905	0.827	0.986	CLONAL	1	TRUE	1	0.503099884913014	2		610	615	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945154	44945154	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048225-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	117	247	0	ENST00000377967.4:c.3478G>C	p.Gly1160Arg	p.G1160R	ENST00000377967	NM_021140.2	1160	Ggc/Cgc	24/29	1	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.503099884913014	1		247	262	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179163	123179187	+	frameshift_variant	Frame_Shift_Del	DEL	TACAGGATTGTCTGACTCACAAGTC	TACAGGATTGTCTGACTCACAAGTC	-	novel	NA	P-0048225-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	80	241	0	ENST00000218089.9:c.612_636del	p.Thr205GlufsTer12	p.T205Efs*12	ENST00000218089	NM_001042749.1	204	ctTACAGGATTGTCTGACTCACAAGTC/ct	8/35	1	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.503099884913014	1		241	233	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599338	55599338	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	346	546	0	ENST00000288135.5:c.2464A>T	p.Asn822Tyr	p.N822Y	ENST00000288135	NM_000222.2	822	Aat/Tat	17/21	0.854985472089379	3	FACETS	0.966	0.927	1	0.966	0.927	1	CLONAL	2	TRUE	1	0.895491654405962	3		546	579	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955580	48955580	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587778857	NA	P-0048280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	119	340	0	ENST00000267163.4:c.1695+1G>A		p.X565_splice	ENST00000267163	NM_000321.2	565			0.893012268800143	1	FACETS	0.9	0.848	0.95	0.9	0.848	0.95	CLONAL	1	TRUE	0	0.895491654405962	1		340	163	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262321	115262322	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0048280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	305	498	0	ENST00000438362.2:c.2232_2233del	p.Phe746ProfsTer10	p.F746Pfs*10	ENST00000438362	NM_001242891.1	744	ctCTtt/cttt	18/20	0.895491654405962	1	FACETS	0.95	0.918	0.98	0.95	0.918	0.98	CLONAL	1	TRUE	0	0.895491654405962	1		498	396	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352676	118352676	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048280-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	784	537	0	ENST00000534358.1:c.3881C>A	p.Ser1294Ter	p.S1294*	ENST00000534358	NM_005933.3	1294	tCa/tAa	7/36	0.892354572528523	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.895491654405962	2		537	870	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40789994	40789994	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs746391800	NA	P-0048295-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	70	426	0	ENST00000373198.4:c.2737G>A	p.Glu913Lys	p.E913K	ENST00000373198	NM_133170.3	913	Gag/Aag	18/32	NA	2	FACETS	0.347	0.303	0.395			1	INDETERMINATE	1	TRUE	NA	0.753133745968484	2		426	535	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0048295-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	516	402	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.308321206906462	6	FACETS	1	0.994	1	0.736	0.713	0.758	INDETERMINATE	4	TRUE	0	0.753133745968484	6		402	778	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0048295-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	160	248	1				ENST00000310581	NM_198253.2	-/1132			0.1695352610879	5	FACETS	0.914	0.853	0.976	0.914	0.853	0.976	INDETERMINATE	3	TRUE	2	0.753133745968484	5		249	330	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793212	33793212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1404014711	NA	P-0048295-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	132	135	1	ENST00000498907.2:c.109G>A	p.Ala37Thr	p.A37T	ENST00000498907	NM_004364.3	37	Gcg/Acg	1/1	0.704673872054141	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.753133745968484	4		136	271	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492308	56492308	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1278635698	NA	P-0048295-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	494	471	0	ENST00000267101.3:c.2641G>A	p.Glu881Lys	p.E881K	ENST00000267101	NM_001982.3	881	Gag/Aag	22/28	0.753133745968484	7	FACETS	0.886	0.848	0.925	0.664	0.636	0.694	CLONAL	3	TRUE	3	0.753133745968484	7		471	1423	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0048299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	166	423	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.838872611781157	4	FACETS	0.97	0.904	1	0.97	0.904	1	CLONAL	2	TRUE	2	0.860091348528052	4		423	370	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0048299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	180	608	1	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.860091348528052	3	FACETS	0.962	0.892	1	0.481	0.446	0.518	CLONAL	1	TRUE	1	0.860091348528052	3		609	622	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0048299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	273	471	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.860091348528052	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.860091348528052	2		471	298	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0048299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	122	250	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.847678034082971	2	FACETS	0.946	0.899	0.987	0.946	0.899	0.987	CLONAL	2	TRUE	0	0.860091348528052	2		250	150	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589618	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519838	NA	P-0048299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	100	230	0	ENST00000274335.5:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000274335		461	Cga/Tga	10/15	0.847678034082971	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.860091348528052	2		230	115	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411937	63411937	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	340	639	0	ENST00000330258.3:c.1230G>A	p.Trp410Ter	p.W410*	ENST00000330258	NM_152424.3	410	tgG/tgA	2/2	0.860091348528052	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.860091348528052	3		639	556	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970924	70970924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1277239045	NA	P-0048299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	256	482	0	ENST00000276594.2:c.1337G>A	p.Arg446Gln	p.R446Q	ENST00000276594	NM_024504.3	446	cGg/cAg	6/8	0.860091348528052	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.860091348528052	3		482	407	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134513	41134513	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048299-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	218	393	0	ENST00000379561.5:c.1115A>G	p.Glu372Gly	p.E372G	ENST00000379561	NM_002015.3	372	gAa/gGa	2/3	0.860091348528052	9	FACETS	0.939	0.873	1	0.268	0.249	0.288	CLONAL	2	TRUE	2	0.860091348528052	9		393	1082	SUCCESS
APC	324	MSKCC	GRCh37	5	112111408	112111411	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	-	rs387906231	NA	P-0048384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	17	329	0	ENST00000257430.4:c.509_512del	p.Asp170ValfsTer4	p.D170Vfs*4	ENST00000257430	NM_000038.5	169	ATAGat/at	5/16	0.170328639512062	3	FACETS	1	0.794	1	0.529	0.399	0.679	INDETERMINATE	1	FALSE	1	0.321774999886895	3		329	116	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0048384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	12	247	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.170328639512062	3	FACETS	1	0.84	1	0.646	0.463	0.861	INDETERMINATE	1	FALSE	1	0.321774999886895	3		247	67	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0048384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	78	898	1	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.170328639512062	3	FACETS	1	0.909	1	0.519	0.457	0.586	INDETERMINATE	1	FALSE	1	0.321774999886895	3		899	542	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100117	157100119	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs797045268	NA	P-0048384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	12	76	0	ENST00000346085.5:c.1069_1071del	p.Gly357del	p.G357del	ENST00000346085	NM_020732.3	352	GGC/-	1/20	0.220494615614763	4	FACETS	0.454	0.319	0.621	0.227	0.159	0.311	SUBCLONAL	1	FALSE	2	0.321774999886895	4		76	217	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524624	103524624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377353991	NA	P-0048384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	12	423	2	ENST00000355739.4:c.2755C>T	p.Arg919Trp	p.R919W	ENST00000355739	NM_000123.3	919	Cgg/Tgg	13/15	0.321774999886895	4	FACETS	0.45	0.316	0.615	0.225	0.158	0.308	SUBCLONAL	1	FALSE	2	0.321774999886895	4		425	219	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912188	114912188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	41	521	2	ENST00000543371.1:c.1258C>T	p.Arg420Trp	p.R420W	ENST00000543371	NM_001198531.1	420	Cgg/Tgg	11/14	0.319138526092422	4	FACETS	0.757	0.631	0.897	0.378	0.315	0.449	SUBCLONAL	1	FALSE	2	0.321774999886895	4		523	445	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933619	39933619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs993034359	NA	P-0048384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	130	390	0	ENST00000378444.4:c.980G>A	p.Gly327Glu	p.G327E	ENST00000378444	NM_001123385.1	327	gGg/gAg	4/15	0.321774999886895	3	FACETS	1	0.97	1			1	CLONAL	3	FALSE	NA	0.321774999886895	3		390	284	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21626569	21626569	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199740132	NA	P-0048384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	10	398	0	ENST00000421138.2:c.1363C>T	p.Arg455Cys	p.R455C	ENST00000421138		455	Cgt/Tgt	13/16	0.319138526092422	4	FACETS	0.483	0.328	0.678	0.242	0.164	0.339	SUBCLONAL	1	FALSE	2	0.321774999886895	4		398	170	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164393	47164393	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0048384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	13	349	0	ENST00000409792.3:c.1733T>G	p.Leu578Ter	p.L578*	ENST00000409792	NM_014159.6	578	tTa/tGa	3/21	1	2	FACETS	1	0.783	1	1	0.783	1	CLONAL	1	FALSE	1	0.321774999886895	2		349	74	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120527	70120527	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0048386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	100	679	0	ENST00000245479.2:c.1529G>C	p.Ter510SerextTer49	p.*510Sext*49	ENST00000245479	NM_000346.3	510	tGa/tCa	3/3	0.293050244536951	1	FACETS	0.984	0.881	1	0.984	0.881	1	CLONAL	1	TRUE	0	0.293050244536951	1		679	592	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089676	27089676	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	82	668	0	ENST00000324856.7:c.2632C>T	p.Gln878Ter	p.Q878*	ENST00000324856	NM_006015.4	878	Cag/Tag	8/20	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.293050244536951	2		668	493	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092859	27092860	+	splice_donor_variant,intron_variant	Splice_Site	DNP	TA	TA	AT	novel	NA	P-0048386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	58	470	1	ENST00000324856.7:c.2878+2_2878+3delinsAT		p.X960_splice	ENST00000324856	NM_006015.4	960			1	2	FACETS	0.894	0.77	1	0.894	0.77	1	CLONAL	1	TRUE	1	0.293050244536951	2		471	443	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099030	27099030	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0048386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	73	598	0	ENST00000324856.7:c.3446C>G	p.Ser1149Ter	p.S1149*	ENST00000324856	NM_006015.4	1149	tCa/tGa	13/20	1	2	FACETS	0.977	0.856	1	0.977	0.856	1	CLONAL	1	TRUE	1	0.293050244536951	2		598	510	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306550	163306550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201079271	NA	P-0048386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	56	344	0	ENST00000271452.3:c.347G>A	p.Arg116Gln	p.R116Q	ENST00000271452	NM_145697.2	116	cGg/cAg	6/14	0.293050244536951	5	FACETS	1	0.869	1	0.338	0.29	0.391	CLONAL	1	TRUE	2	0.293050244536951	5		344	542	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720808	89720808	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	36	264	0	ENST00000371953.3:c.959T>C	p.Leu320Ser	p.L320S	ENST00000371953	NM_000314.4	320	tTa/tCa	8/9	1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	1	0.293050244536951	2		264	239	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120645	115120646	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0048386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	154	720	0	ENST00000257566.3:c.359_360dup	p.Thr121AlafsTer19	p.T121Afs*19	ENST00000257566	NM_016569.3	120	-/GC	1/8	0.293050244536951	1	FACETS	0.834	0.767	0.902	1	0.99	1	CLONAL	2	TRUE	0	0.293050244536951	1		720	538	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416800	121416800	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770695671	NA	P-0048386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	56	875	1	ENST00000257555.6:c.229G>A	p.Asp77Asn	p.D77N	ENST00000257555		77	Gat/Aat	1/10	0.293050244536951	1	FACETS	0.741	0.636	0.855	0.741	0.636	0.855	SUBCLONAL	1	TRUE	0	0.293050244536951	1		876	440	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954326	48954326	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	29	241	0	ENST00000267163.4:c.1447C>G	p.His483Asp	p.H483D	ENST00000267163	NM_000321.2	483	Cat/Gat	16/27	NA	2	FACETS	0.755	0.609	0.921			1	INDETERMINATE	1	TRUE	NA	0.293050244536951	2		241	262	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640317	3640317	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1237732471	NA	P-0048386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	65	831	1	ENST00000294008.3:c.3322G>C	p.Glu1108Gln	p.E1108Q	ENST00000294008	NM_032444.2	1108	Gag/Cag	12/15	1	2	FACETS	0.805	0.699	0.92	0.805	0.699	0.92	CLONAL	1	TRUE	1	0.293050244536951	2		832	551	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14021954	14021954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	27	494	0	ENST00000311895.7:c.654G>A	p.Met218Ile	p.M218I	ENST00000311895	NM_005236.2	218	atG/atA	4/11	1	2	FACETS	0.402	0.319	0.497	0.402	0.319	0.497	SUBCLONAL	1	TRUE	1	0.293050244536951	2		494	458	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862075	68862075	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0048386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	41	375	0	ENST00000261769.5:c.2165-2A>G		p.X722_splice	ENST00000261769	NM_004360.3	722			0.293050244536951	1	FACETS	0.995	0.835	1	0.995	0.835	1	CLONAL	1	TRUE	0	0.293050244536951	1		375	240	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172049	99172049	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	51	567	0	ENST00000074304.5:c.1615G>C	p.Glu539Gln	p.E539Q	ENST00000074304	NM_001134224.1	539	Gag/Cag	17/26	NA	3	FACETS	0.928	0.79	1	0.464	0.395	0.54	INDETERMINATE	1	TRUE	1	0.293050244536951	3		567	430	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702543	52702543	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	58	368	0	ENST00000394830.3:c.355C>G	p.Leu119Val	p.L119V	ENST00000394830	NM_018313.4	119	Ctt/Gtt	4/30	1	2	FACETS	0.921	0.793	1	0.921	0.793	1	CLONAL	1	TRUE	1	0.293050244536951	2		368	430	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630459	187630459	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	61	599	0	ENST00000441802.2:c.523G>A	p.Asp175Asn	p.D175N	ENST00000441802	NM_005245.3	175	Gat/Aat	2/27	1	2	FACETS	0.7	0.603	0.804	0.7	0.603	0.804	SUBCLONAL	1	TRUE	1	0.293050244536951	2		599	595	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249419	110249419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536679242	NA	P-0048386-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	124	936	1	ENST00000374672.4:c.1154G>A	p.Arg385Lys	p.R385K	ENST00000374672	NM_004235.4	385	aGa/aAa	4/5	1	2	FACETS	0.973	0.88	1	0.973	0.88	1	CLONAL	1	TRUE	1	0.293050244536951	2		937	870	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623655	43623655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048422-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	41	508	0	ENST00000355710.3:c.3283G>A	p.Val1095Ile	p.V1095I	ENST00000355710	NM_020975.4	1095	Gta/Ata	20/20	1	2	FACETS	0.146	0.121	0.174	0.146	0.121	0.174	SUBCLONAL	1	TRUE	1	0.719989328795828	2		508	780	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0048427-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	415	674	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.413252080219596	3	FACETS	0.957	0.917	0.997	0.957	0.917	0.997	CLONAL	3	TRUE	0	0.413252080219596	3		674	844	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909674	76909674	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048427-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	77	241	1	ENST00000373344.5:c.4231G>T	p.Glu1411Ter	p.E1411*	ENST00000373344	NM_000489.3	1411	Gag/Tag	14/35	0.389907272819885	1	FACETS	0.966	0.857	1	0.966	0.857	1	CLONAL	1	TRUE	0	0.413252080219596	1		242	306	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0048476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	255	343	0	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	0.854077677436256	1	FACETS	0.937	0.898	0.975	0.937	0.898	0.975	CLONAL	1	TRUE	0	0.854077677436256	1		343	365	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65323437	65323437	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1240783724	NA	P-0048476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	33	560	0	ENST00000342505.4:c.1360C>T	p.Arg454Trp	p.R454W	ENST00000342505	NM_002227.2	454	Cgg/Tgg	10/25	0.854077677436256	1	FACETS	0.073	0.059	0.089	0.073	0.059	0.089	SUBCLONAL	1	TRUE	0	0.854077677436256	1		560	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514495	NA	P-0048476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	675	805	1	ENST00000269305.4:c.542G>A	p.Arg181His	p.R181H	ENST00000269305	NM_001126112.2	181	cGc/cAc	5/11	0.854077677436256	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.854077677436256	1		806	891	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097200	11097205	+	inframe_deletion	In_Frame_Del	DEL	GGCCCT	GGCCCT	-	rs372601826	NA	P-0048476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	445	952	1	ENST00000358026.2:c.708_713del	p.Gly243_Pro244del	p.G243_P244del	ENST00000358026	NM_001128849.1	231	GGCCCT/-	4/36	1	2	FACETS	0.642	0.612	0.674	0.642	0.612	0.674	SUBCLONAL	1	TRUE	1	0.854077677436256	2		953	1622	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922973	44922973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	488	579	0	ENST00000377967.4:c.1834C>T	p.Arg612Ter	p.R612*	ENST00000377967	NM_021140.2	612	Cga/Tga	16/29	0.854077677436256	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.854077677436256	1		579	624	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138729528	NA	P-0048476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	716	870	0	ENST00000269305.4:c.523C>T	p.Arg175Cys	p.R175C	ENST00000269305	NM_001126112.2	175	Cgc/Tgc	5/11	0.854077677436256	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.854077677436256	1		870	951	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890150	76890150	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	386	503	1	ENST00000373344.5:c.4744del	p.Thr1582GlnfsTer24	p.T1582Qfs*24	ENST00000373344	NM_000489.3	1582	Aca/ca	17/35	0.854077677436256	1	FACETS	0.97	0.938	1	0.97	0.938	1	CLONAL	1	TRUE	0	0.854077677436256	1		504	534	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268793	98268793	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1554708751	NA	P-0048476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	400	515	0	ENST00000331920.6:c.290del	p.Asn97ThrfsTer20	p.N97Tfs*20	ENST00000331920	NM_000264.3	97	aAc/ac	2/24	1	2	FACETS	0.875	0.834	0.917	0.875	0.834	0.917	CLONAL	1	TRUE	1	0.854077677436256	2		515	1070	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4388007	4388007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775067994	NA	P-0048476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	483	589	0	ENST00000261254.3:c.493C>T	p.Arg165Cys	p.R165C	ENST00000261254	NM_001759.3	165	Cgc/Tgc	3/5	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.854077677436256	2		589	1115	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371948	55371948	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	527	632	0	ENST00000297316.4:c.638C>A	p.Pro213Gln	p.P213Q	ENST00000297316	NM_022454.3	213	cCg/cAg	2/2	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.854077677436256	2		632	1178	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383350	42383350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144006380	NA	P-0048476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	523	629	0	ENST00000221972.3:c.370C>T	p.Arg124Cys	p.R124C	ENST00000221972	NM_021601.3	124	Cgc/Tgc	2/5	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.854077677436256	2		629	1221	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555752	21555752	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200852337	NA	P-0048476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	576	781	0	ENST00000382592.4:c.2518G>A	p.Asp840Asn	p.D840N	ENST00000382592	NM_014572.2	840	Gac/Aac	6/8	0.854077677436256	1	FACETS	0.993	0.968	1	0.993	0.968	1	CLONAL	1	TRUE	0	0.854077677436256	1		781	778	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670882	134670882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200018500	NA	P-0048476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	356	448	0	ENST00000398015.3:c.793G>A	p.Val265Met	p.V265M	ENST00000398015	NM_004441.4	265	Gtg/Atg	3/16	0.854077677436256	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.854077677436256	1		448	460	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781225	9781225	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	81	831	0	ENST00000377346.4:c.1730T>C	p.Leu577Pro	p.L577P	ENST00000377346	NM_005026.3	577	cTg/cCg	14/24	0.854077677436256	1	FACETS	0.129	0.113	0.146	0.129	0.113	0.146	SUBCLONAL	1	TRUE	0	0.854077677436256	1		831	843	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	224	406	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.277966801620872	7	FACETS	1	0.977	1	1	0.977	1	CLONAL	4	TRUE	3	0.277966801620872	7		406	627	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	55	248	1				ENST00000310581	NM_198253.2	-/1132			0.278057000955104	4	FACETS	1	0.919	1	1	0.919	1	CLONAL	2	TRUE	2	0.277966801620872	4		249	232	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	1945	490	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.277966801620872	34	FACETS	1	0.991	1			1	CLONAL	33	TRUE	NA	0.277966801620872	34		490	2305	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175857	24175859	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs875989800	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	40	492	0	ENST00000263121.7:c.1091_1093del	p.Lys364del	p.K364del	ENST00000263121	NM_003073.3	362	gAGAag/gag	8/9	0.278057000955104	4	FACETS	0.836	0.695	0.993	0.418	0.347	0.497	CLONAL	1	TRUE	2	0.277966801620872	4		492	440	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	267	563	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.277966801620872	3	FACETS	0.918	0.868	0.968	1	0.991	1	CLONAL	4	TRUE	0	0.277966801620872	3		563	596	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438317	110438322	+	inframe_deletion	In_Frame_Del	DEL	GTTGTT	GTTGTT	-	rs532810290	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	19	173	0	ENST00000375856.3:c.79_84del	p.Asn27_Asn28del	p.N27_N28del	ENST00000375856	NM_003749.2	27	AACAAC/-	1/2	0.224506410675961	4	FACETS	0.84	0.64	1	0.42	0.32	0.537	CLONAL	1	TRUE	2	0.277966801620872	4		173	208	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	275	508	0	ENST00000269305.4:c.772G>C	p.Glu258Gln	p.E258Q	ENST00000269305	NM_001126112.2	258	Gaa/Caa	7/11	0.277966801620872	3	FACETS	1	0.985	1	1	0.994	1	CLONAL	4	TRUE	0	0.277966801620872	3		508	517	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222924	5222924	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	167	510	0	ENST00000357368.4:c.2879G>A	p.Gly960Glu	p.G960E	ENST00000357368	NM_002850.3	960	gGg/gAg	18/38	0.277966801620872	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	0	0.277966801620872	3		510	413	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478902	56478902	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	148	622	0	ENST00000267101.3:c.358A>G	p.Met120Val	p.M120V	ENST00000267101	NM_001982.3	120	Atg/Gtg	3/28	0.25961222822076	4	FACETS	0.918	0.84	1	0.918	0.84	1	CLONAL	2	TRUE	2	0.277966801620872	4		622	741	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1953841	1953841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	63	678	0	ENST00000382891.5:c.2020G>A	p.Glu674Lys	p.E674K	ENST00000382891	NM_133335.3	674	Gag/Aag	11/22	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.277966801620872	2		678	356	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37865697	37865697	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	1375	406	0	ENST00000269571.5:c.566C>G	p.Ser189Cys	p.S189C	ENST00000269571		189	tCt/tGt	4/27	0.277966801620872	34	FACETS	1	0.994	1			1	CLONAL	33	TRUE	NA	0.277966801620872	34		406	1612	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752830	128752830	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	38	252	0	ENST00000377970.2:c.991C>G	p.Arg331Gly	p.R331G	ENST00000377970	NM_002467.4	331	Cgg/Ggg	3/3	0.278057000955104	3	FACETS	1	0.909	1	0.575	0.477	0.682	CLONAL	1	TRUE	1	0.277966801620872	3		252	271	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235838	108235838	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	44	233	0	ENST00000278616.4:c.8880G>C	p.Trp2960Cys	p.W2960C	ENST00000278616	NM_000051.3	2960	tgG/tgC	62/63	0.246495761678159	3	FACETS	0.764	0.646	0.892	0.764	0.646	0.892	SUBCLONAL	2	TRUE	1	0.277966801620872	3		233	236	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445575	49445575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	102	713	1	ENST00000301067.7:c.1891G>A	p.Glu631Lys	p.E631K	ENST00000301067	NM_003482.3	631	Gag/Aag	10/54	0.25961222822076	4	FACETS	0.758	0.679	0.841	0.758	0.679	0.841	SUBCLONAL	2	TRUE	2	0.277966801620872	4		714	619	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952012	178952012	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	59	274	0	ENST00000263967.3:c.3067C>T	p.Arg1023Ter	p.R1023*	ENST00000263967	NM_006218.2	1023	Cga/Tga	21/21	0.277966801620872	7	FACETS	1	0.869	1	0.502	0.434	0.576	CLONAL	2	TRUE	3	0.277966801620872	7		274	358	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510733	120510733	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	151	480	0	ENST00000256646.2:c.1231G>C	p.Asp411His	p.D411H	ENST00000256646	NM_024408.3	411	Gac/Cac	7/34	0.25961222822076	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.277966801620872	4		480	558	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243668617	243668617	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	23	232	0	ENST00000263826.5:c.1374C>A	p.Asp458Glu	p.D458E	ENST00000263826	NM_005465.4	458	gaC/gaA	13/13	0.278057000955104	3	FACETS	0.633	0.494	0.793	0.316	0.247	0.397	SUBCLONAL	1	TRUE	1	0.277966801620872	3		232	298	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94908677	94908677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1437988813	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	54	367	0	ENST00000536441.1:c.1377C>G	p.Phe459Leu	p.F459L	ENST00000536441	NM_144665.3	459	ttC/ttG	9/10	0.246495761678159	3	FACETS	1	0.89	1	0.523	0.448	0.605	CLONAL	1	TRUE	1	0.277966801620872	3		367	423	SUCCESS
ATM	472	MSKCC	GRCh37	11	108126960	108126960	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs758864982	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	74	384	0	ENST00000278616.4:c.2143C>G	p.Leu715Val	p.L715V	ENST00000278616	NM_000051.3	715	Ctt/Gtt	14/63	0.246495761678159	3	FACETS	0.798	0.703	0.899	0.798	0.703	0.899	SUBCLONAL	2	TRUE	1	0.277966801620872	3		384	380	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118350908	118350908	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	54	254	0	ENST00000534358.1:c.3589C>G	p.Leu1197Val	p.L1197V	ENST00000534358	NM_005933.3	1197	Cta/Gta	6/36	0.246495761678159	3	FACETS	0.829	0.714	0.952	0.829	0.714	0.952	CLONAL	2	TRUE	1	0.277966801620872	3		254	267	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914629	32914629	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	85	370	0	ENST00000380152.3:c.6137C>G	p.Ser2046Ter	p.S2046*	ENST00000380152		2046	tCa/tGa	11/27	0.224506410675961	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	2	0.277966801620872	4		370	340	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914766	32914766	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587779365	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	87	299	0	ENST00000380152.3:c.6274C>G	p.Leu2092Val	p.L2092V	ENST00000380152		2092	Ctt/Gtt	11/27	0.224506410675961	4	FACETS	0.877	0.785	0.973	1	0.975	1	CLONAL	3	TRUE	2	0.277966801620872	4		299	304	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059296	42059296	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	35	287	0	ENST00000219905.7:c.9016C>T	p.Gln3006Ter	p.Q3006*	ENST00000219905	NM_001164273.1	3006	Cag/Tag	24/24	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.277966801620872	2		287	238	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	338160	338160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	83	610	1	ENST00000262320.3:c.2551G>A	p.Glu851Lys	p.E851K	ENST00000262320	NM_003502.3	851	Gag/Aag	11/11	1	2	FACETS	0.79	0.702	0.883	1	0.98	1	SUBCLONAL	2	TRUE	1	0.277966801620872	2		611	378	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47679235	47679235	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	46	319	0	ENST00000347630.2:c.972C>A	p.Phe324Leu	p.F324L	ENST00000347630	NM_001007230.1	324	ttC/ttA	10/11	0.278057000955104	3	FACETS	1	0.938	1	0.614	0.52	0.717	CLONAL	1	TRUE	1	0.277966801620872	3		319	307	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221766	36221766	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	205	641	0	ENST00000222270.7:c.5435C>G	p.Ser1812Ter	p.S1812*	ENST00000222270	NM_014727.1	1812	tCa/tGa	26/37	0.277966801620872	3	FACETS	1	0.941	1	1	0.941	1	CLONAL	3	TRUE	0	0.277966801620872	3		641	556	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082291	16082291	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs766296336	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	350	757	0	ENST00000281043.3:c.105C>G	p.Phe35Leu	p.F35L	ENST00000281043	NM_005378.4	35	ttC/ttG	2/3	0.277966801620872	5	FACETS	1	0.973	1	1	0.994	1	CLONAL	4	TRUE	2	0.277966801620872	5		757	863	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965584	25965584	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	48	461	0	ENST00000435504.4:c.3622G>C	p.Gly1208Arg	p.G1208R	ENST00000435504		1208	Ggt/Cgt	13/13	0.277966801620872	5	FACETS	0.715	0.604	0.839	0.238	0.201	0.28	SUBCLONAL	1	TRUE	2	0.277966801620872	5		461	684	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368432	225368432	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	114	254	0	ENST00000264414.4:c.1314G>T	p.Arg438Ser	p.R438S	ENST00000264414	NM_003590.4	438	agG/agT	9/16	0.224506410675961	4	FACETS	0.896	0.814	0.981	1	0.982	1	CLONAL	3	TRUE	2	0.277966801620872	4		254	390	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433336	138433336	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	30	335	0	ENST00000289153.2:c.1276C>G	p.Gln426Glu	p.Q426E	ENST00000289153	NM_006219.2	426	Cag/Gag	7/22	0.277966801620872	7	FACETS	0.689	0.554	0.843	0.172	0.138	0.211	SUBCLONAL	1	TRUE	3	0.277966801620872	7		335	531	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206840	162206840	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	92	328	0	ENST00000366898.1:c.835C>G	p.His279Asp	p.H279D	ENST00000366898	NM_004562.2	279	Cac/Gac	7/12	0.272745537534468	3	FACETS	1	0.895	1	0.667	0.597	0.74	CLONAL	2	TRUE	0	0.277966801620872	3		328	377	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335744	81335744	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	66	213	0	ENST00000222390.5:c.1617-1G>A		p.X539_splice	ENST00000222390	NM_000601.4	539			0.277966801620872	5	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	3	0.277966801620872	5		213	290	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358929	81358929	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	118	308	0	ENST00000222390.5:c.1032C>G	p.Phe344Leu	p.F344L	ENST00000222390	NM_000601.4	344	ttC/ttG	8/18	0.277966801620872	5	FACETS	0.899	0.817	0.985	1	0.982	1	CLONAL	3	TRUE	3	0.277966801620872	5		308	446	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820542	44820569	+	frameshift_variant	Frame_Shift_Del	DEL	ATGAATCTCTAATCTTAAAAGCTGAAGG	ATGAATCTCTAATCTTAAAAGCTGAAGG	-	novel	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	96	154	0	ENST00000377967.4:c.240_267del	p.Tyr80Ter	p.Y80*	ENST00000377967	NM_021140.2	80	tATGAATCTCTAATCTTAAAAGCTGAAGGa/ta	3/29	0.277966801620872	4	FACETS	1	0.961	1			1	CLONAL	4	TRUE	NA	0.277966801620872	4		154	201	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76764088	76764088	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557034949	NA	P-0048499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	104	197	0	ENST00000373344.5:c.7220G>A	p.Arg2407Gln	p.R2407Q	ENST00000373344	NM_000489.3	2407	cGa/cAa	35/35	0.278057000955104	2	FACETS	1	0.974	1			1	CLONAL	3	TRUE	NA	0.277966801620872	2		197	214	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0048569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	252	1067	2	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.181301334172503	2	FACETS	1	0.992	1	0.736	0.686	0.786	CLONAL	1	TRUE	0	0.237747784826562	2		1069	1441	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934155	48934155	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	34	290	0	ENST00000267163.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000267163	NM_000321.2	204	Gaa/Taa	7/27	1	2	FACETS	1	0.823	1	1	0.823	1	CLONAL	1	TRUE	1	0.237747784826562	2		290	285	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56477654	56477654	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	124	673	0	ENST00000267101.3:c.202A>G	p.Thr68Ala	p.T68A	ENST00000267101	NM_001982.3	68	Acg/Gcg	2/28	1	2	FACETS	0.931	0.841	1	0.931	0.841	1	CLONAL	1	TRUE	1	0.237747784826562	2		673	1120	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563357	21563360	+	frameshift_variant	Frame_Shift_Del	DEL	CGCT	CGCT	-	novel	NA	P-0048569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1511	110	1286	0	ENST00000382592.4:c.559_562del	p.Ser187ValfsTer52	p.S187Vfs*52	ENST00000382592	NM_014572.2	187	AGCGgt/gt	4/8	1	2	FACETS	0.571	0.511	0.635	0.571	0.511	0.635	SUBCLONAL	1	TRUE	1	0.237747784826562	2		1286	1621	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40364181	40364181	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	144	920	0	ENST00000293328.3:c.1501A>G	p.Lys501Glu	p.K501E	ENST00000293328	NM_012448.3	501	Aaa/Gaa	13/19	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.237747784826562	2		920	1133	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553204	41553204	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	39	469	0	ENST00000263253.7:c.3293A>T	p.Asp1098Val	p.D1098V	ENST00000263253	NM_001429.3	1098	gAt/gTt	18/31	1	2	FACETS	0.654	0.541	0.779	0.654	0.541	0.779	SUBCLONAL	1	TRUE	1	0.237747784826562	2		469	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0048587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	54	579	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.27	2		579	284	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507423	8507423	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	12	230	0	ENST00000356435.5:c.1555C>A	p.Pro519Thr	p.P519T	ENST00000356435		519	Cca/Aca	11/35	0.304708170052312	1	FACETS	0.754	0.535	1	0.754	0.535	1	CLONAL	1	TRUE	0	0.27	1		230	102	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974809	21974809	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	11	162	0	ENST00000304494.5:c.18del	p.Ser7AlafsTer19	p.S7Afs*19	ENST00000304494	NM_000077.4	6	ggG/gg	1/3	0.304708170052312	1	FACETS	1	0.788	1	1	0.788	1	CLONAL	1	TRUE	0	0.27	1		162	61	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141507	11141507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	17	569	0	ENST00000358026.2:c.3484G>A	p.Gly1162Ser	p.G1162S	ENST00000358026	NM_001128849.1	1162	Ggc/Agc	25/36	1	2	FACETS	0.605	0.453	0.785	0.605	0.453	0.785	SUBCLONAL	1	TRUE	1	0.27	2		569	208	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740806	58740806	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	30	380	0	ENST00000305921.3:c.1711C>T	p.Gln571Ter	p.Q571*	ENST00000305921	NM_003620.3	571	Cag/Tag	6/6	1	2	FACETS	1	0.815	1	1	0.815	1	CLONAL	1	TRUE	1	0.27	2		380	221	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281849	49281849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs560961886	NA	P-0048587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	13	496	0	ENST00000282018.3:c.896G>T	p.Cys299Phe	p.C299F	ENST00000282018	NM_020377.2	299	tGc/tTc	1/1	0.203643775488768	3	FACETS	0.632	0.452	0.85	0.316	0.226	0.425	SUBCLONAL	1	TRUE	1	0.27	3		496	173	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991265	41991265	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	17	345	0	ENST00000219905.7:c.2096A>C	p.Tyr699Ser	p.Y699S	ENST00000219905	NM_001164273.1	699	tAc/tCc	5/24	1	2	FACETS	0.845	0.635	1	0.845	0.635	1	CLONAL	1	TRUE	1	0.27	2		345	149	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200172	138200172	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	22	392	0	ENST00000237289.4:c.1590G>T	p.Arg530Ser	p.R530S	ENST00000237289	NM_001270507.1	530	agG/agT	7/9	0.161956638635629	4	FACETS	0.92	0.716	1	0.46	0.358	0.578	INDETERMINATE	1	TRUE	2	0.27	4		392	225	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969972	161969972	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	30	507	0	ENST00000366898.1:c.997C>G	p.Pro333Ala	p.P333A	ENST00000366898	NM_004562.2	333	Ccc/Gcc	9/12	0.161956638635629	4	FACETS	1	0.908	1	0.608	0.493	0.738	INDETERMINATE	1	TRUE	2	0.27	4		507	232	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426493	47426493	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	26	596	0	ENST00000377045.4:c.836G>T	p.Arg279Leu	p.R279L	ENST00000377045	NM_001654.4	279	cGc/cTc	9/16	1	2	FACETS	0.651	0.516	0.804	0.651	0.516	0.804	SUBCLONAL	1	TRUE	1	0.27	2		596	296	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0048713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	86	445	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.771	0.682	0.866	0.771	0.682	0.866	SUBCLONAL	1	TRUE	1	0.34	2		445	656	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0048713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	72	394	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.34	2		394	421	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106793	27106793	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	113	513	0	ENST00000324856.7:c.6404T>A	p.Ile2135Asn	p.I2135N	ENST00000324856	NM_006015.4	2135	aTt/aAt	20/20	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.34	2		513	654	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934190	39934190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146403660	NA	P-0048713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	130	624	0	ENST00000378444.4:c.409G>A	p.Val137Ile	p.V137I	ENST00000378444	NM_001123385.1	137	Gtc/Atc	4/15	1	2	FACETS	0.944	0.857	1	0.944	0.857	1	CLONAL	1	TRUE	1	0.34	2		624	810	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692980	89692980	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060500126	NA	P-0048713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	75	395	0	ENST00000371953.3:c.464A>G	p.Tyr155Cys	p.Y155C	ENST00000371953	NM_000314.4	155	tAt/tGt	5/9	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.34	2		395	434	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0048713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	86	363	0	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	1	2	FACETS	0.828	0.733	0.929	0.828	0.733	0.929	CLONAL	1	TRUE	1	0.34	2		363	611	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650711	67650711	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	111	488	0	ENST00000264010.4:c.1016G>C	p.Arg339Pro	p.R339P	ENST00000264010	NM_006565.3	339	cGg/cCg	5/12	1	2	FACETS	0.798	0.717	0.884	0.798	0.717	0.884	SUBCLONAL	1	TRUE	1	0.34	2		488	818	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757416	40757416	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	41	573	0	ENST00000373198.4:c.2882A>G	p.Tyr961Cys	p.Y961C	ENST00000373198	NM_133170.3	961	tAc/tGc	20/32	1	2	FACETS	0.357	0.296	0.424	0.357	0.296	0.424	SUBCLONAL	1	TRUE	1	0.34	2		573	676	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798109	42798109	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	99	551	0	ENST00000575354.2:c.4063T>C	p.Phe1355Leu	p.F1355L	ENST00000575354	NM_015125.3	1355	Ttc/Ctc	17/20	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.34	2		551	577	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591149	+	inframe_deletion	In_Frame_Del	DEL	GACGAGAGACCAATACTT	GACGAGAGACCAATACTT	-	novel	NA	P-0048713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	25	265	0	ENST00000274335.5:c.1727_1744del	p.Thr576_Leu581del	p.T576_L581del	ENST00000274335		575	aaGACGAGAGACCAATACTTg/aag	12/15	1	2	FACETS	0.521	0.412	0.647	0.521	0.412	0.647	SUBCLONAL	1	TRUE	1	0.34	2		265	282	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371697	55371698	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0048713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	74	494	0	ENST00000297316.4:c.388dup	p.Gln130ProfsTer32	p.Q130Pfs*32	ENST00000297316	NM_022454.3	129	-/C	2/2	1	2	FACETS	0.834	0.731	0.944	0.834	0.731	0.944	CLONAL	1	TRUE	1	0.34	2		494	522	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140165	50140165	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	153	664	1	ENST00000246792.3:c.260A>T	p.Gln87Leu	p.Q87L	ENST00000246792	NM_006270.3	87	cAg/cTg	3/6	1	2	FACETS	0.757	0.692	0.826	1	0.988	1	SUBCLONAL	2	TRUE	1	0.2	2		665	1010	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218035	108218035	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	26	247	0	ENST00000278616.4:c.8614C>A	p.His2872Asn	p.H2872N	ENST00000278616	NM_000051.3	2872	Cat/Aat	59/63	1	2	FACETS	0.825	0.655	1	0.825	0.655	1	CLONAL	1	TRUE	1	0.2	2		247	315	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045491	47045491	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	118	357	0	ENST00000377604.3:c.2458G>T	p.Glu820Ter	p.E820*	ENST00000377604	NM_001204468.1	820	Gaa/Taa	22/24	1	1	FACETS	0.991	0.898	1	1	0.989	1	CLONAL	2	TRUE	0	0.2	1		357	536	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342770	87342770	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	57	371	0	ENST00000277120.3:c.1055C>G	p.Thr352Ser	p.T352S	ENST00000277120		352	aCt/aGt	9/19	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.2	2		371	558	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913514	NA	P-0048771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	128	439	0	ENST00000288135.5:c.2466T>A	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaA	17/21	0.376265710542503	25	FACETS	0.914	0.829	1			1	CLONAL	5	TRUE	NA	0.376265710542503	25		439	793	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913514	NA	P-0048771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	266	439	0	ENST00000288135.5:c.2466T>G	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaG	17/21	0.376265710542503	25	FACETS	1	0.972	1			1	CLONAL	9	TRUE	NA	0.376265710542503	25		439	793	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4097336	4097336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377755503	NA	P-0048771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	10	559	0	ENST00000262948.5:c.925G>A	p.Gly309Arg	p.G309R	ENST00000262948	NM_030662.3	309	Ggg/Agg	8/11	1	2	FACETS	0.275	0.186	0.387	0.275	0.186	0.387	SUBCLONAL	1	TRUE	1	0.376265710542503	2		559	193	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959201	2959201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1466997751	NA	P-0048771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	67	738	1	ENST00000396946.4:c.2315C>T	p.Ser772Leu	p.S772L	ENST00000396946	NM_032415.4	772	tCg/tTg	18/25	0.333140393781897	1	FACETS	0.933	0.832	1	1	0.983	1	CLONAL	2	TRUE	0	0.376265710542503	1		739	155	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356404	66356404	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs372046653	NA	P-0048771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	41	368	0	ENST00000273854.3:c.1093A>G	p.Ile365Val	p.I365V	ENST00000273854	NM_004439.5	365	Atc/Gtc	5/18	1	2	FACETS	1	0.939	1	1	0.976	1	CLONAL	2	TRUE	1	0.376265710542503	2		368	93	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593608	55593629	+	protein_altering_variant	In_Frame_Del	DEL	GGTTGTTGAGGAGATAAATGGA	GGTTGTTGAGGAGATAAATGGA	T	novel	NA	P-0048771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	305	409	0	ENST00000288135.5:c.1674_1695delinsT	p.Lys558_Gly565delinsAsn	p.K558_G565delinsN	ENST00000288135	NM_000222.2	558	aaGGTTGTTGAGGAGATAAATGGA/aaT	11/21	0.376265710542503	25	FACETS	0.994	0.943	1			1	CLONAL	12	TRUE	NA	0.376265710542503	25		409	724	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0048855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	19	263	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.968	0.752	1	1	0.937	1	CLONAL	2	FALSE	1	0.242315366592349	2		263	81	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0048855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	8	292	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	0.242315366592349	4	FACETS	0.882	0.572	1	0.441	0.286	0.638	CLONAL	1	FALSE	2	0.242315366592349	4		292	93	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383225	4383225	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	16	413	0	ENST00000261254.3:c.19G>C	p.Glu7Gln	p.E7Q	ENST00000261254	NM_001759.3	7	Gag/Cag	1/5	0.242315366592349	4	FACETS	0.636	0.47	0.834	0.318	0.235	0.417	SUBCLONAL	1	FALSE	2	0.242315366592349	4		413	258	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567695	226567695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	21	527	0	ENST00000366794.5:c.1471G>A	p.Glu491Lys	p.E491K	ENST00000366794	NM_001618.3	491	Gaa/Aaa	10/23	0.242315366592349	5	FACETS	0.647	0.498	0.822	0.162	0.124	0.206	SUBCLONAL	1	FALSE	1	0.242315366592349	5		527	365	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89806408	89806408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	18	417	1	ENST00000389301.3:c.3928G>A	p.Glu1310Lys	p.E1310K	ENST00000389301	NM_000135.2	1310	Gag/Aag	39/43	0.198302056892427	3	FACETS	0.986	0.747	1	0.493	0.373	0.632	CLONAL	1	FALSE	1	0.242315366592349	3		418	169	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262203	10262203	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	21	463	0	ENST00000340748.4:c.2088G>T	p.Met696Ile	p.M696I	ENST00000340748		696	atG/atT	23/40	1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	FALSE	1	0.242315366592349	2		463	154	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228811	36228811	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	43	609	0	ENST00000222270.7:c.7710G>C	p.Lys2570Asn	p.K2570N	ENST00000222270	NM_014727.1	2570	aaG/aaC	35/37	0.242315366592349	6	FACETS	0.951	0.795	1	0.19	0.159	0.225	CLONAL	1	FALSE	1	0.242315366592349	6		609	554	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542247	141542247	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	22	352	0	ENST00000220592.5:c.2476G>C	p.Glu826Gln	p.E826Q	ENST00000220592	NM_012154.3	826	Gaa/Caa	19/19	0.198302056892427	3	FACETS	1	0.86	1	0.572	0.446	0.716	CLONAL	1	FALSE	1	0.242315366592349	3		352	178	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907666	76907666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	25	388	0	ENST00000373344.5:c.4495G>A	p.Glu1499Lys	p.E1499K	ENST00000373344	NM_000489.3	1499	Gaa/Aaa	15/35	0.185347346208722	4	FACETS	1	0.912	1	0.657	0.521	0.811	CLONAL	1	FALSE	2	0.242315366592349	4		388	195	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546113	29546113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	11	298	0	ENST00000356175.3:c.1618G>A	p.Glu540Lys	p.E540K	ENST00000356175	NM_000267.3	540	Gag/Aag	14/57	1	2	FACETS	0.704	0.489	0.968	0.704	0.489	0.968	CLONAL	1	FALSE	1	0.242315366592349	2		298	129	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551229	29551229	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	37	522	0	ENST00000389048.3:c.1401G>C	p.Glu467Asp	p.E467D	ENST00000389048	NM_004304.4	467	gaG/gaC	6/29	0.198302056892427	3	FACETS	0.981	0.811	1	0.491	0.405	0.586	CLONAL	1	FALSE	1	0.242315366592349	3		522	349	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212522516	212522546	+	frameshift_variant	Frame_Shift_Del	DEL	GGTAGTAAATGCAGTCATGACTAGTGGGACC	GGTAGTAAATGCAGTCATGACTAGTGGGACC	-	novel	NA	P-0048855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	14	298	0	ENST00000342788.4:c.1879_1909del	p.Gly627HisfsTer16	p.G627Hfs*16	ENST00000342788	NM_005235.2	627	GGTCCCACTAGTCATGACTGCATTTACTACCca/ca	16/28	0.198302056892427	3	FACETS	0.932	0.678	1	0.466	0.339	0.618	CLONAL	1	FALSE	1	0.242315366592349	3		298	139	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	77	148	0				ENST00000310581	NM_198253.2	-/1132			0.3	4	FACETS	1	0.92	1	1	0.987	1	CLONAL	7	TRUE	1	0.15	4		148	165	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0048856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	97	350	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.956	1	1	0.991	1	CLONAL	4	TRUE	1	0.15	2		350	293	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81971483	81971483	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	35	429	0	ENST00000359376.3:c.3173A>T	p.Lys1058Met	p.K1058M	ENST00000359376	NM_002661.3	1058	aAg/aTg	28/33	0.207232360720338	0	FACETS	1	0.869	1			1	CLONAL	1	TRUE	0	0.15	0		429	370	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530099	212530099	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1243222622	NA	P-0048856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	36	270	0	ENST00000342788.4:c.1820A>G	p.Tyr607Cys	p.Y607C	ENST00000342788	NM_005235.2	607	tAt/tGt	15/28	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.15	2		270	370	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513316	149513316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1351556504	NA	P-0048856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	85	385	0	ENST00000261799.4:c.767G>A	p.Arg256Gln	p.R256Q	ENST00000261799	NM_002609.3	256	cGg/cAg	6/23	1	2	FACETS	1	0.956	1	1	0.989	1	CLONAL	3	TRUE	1	0.15	2		385	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	269	768	7	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	0.751	0.715	0.786			1	INDETERMINATE	2	TRUE	NA	0.777134286878885	2		775	461	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	491	419	0	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	0.487593105885892	3	FACETS	0.968	0.945	0.991	0.968	0.945	0.991	CLONAL	3	TRUE	0	0.777134286878885	3		419	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	96	616	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	NA	2	FACETS	0.633	0.568	0.702			1	INDETERMINATE	1	TRUE	NA	0.777134286878885	2		618	390	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	36	347	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.510279575271351	1	FACETS	0.453	0.38	0.531	0.453	0.38	0.531	SUBCLONAL	1	TRUE	0	0.777134286878885	1		347	125	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	111	523	1	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.777134286878885	2		524	257	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775719	9775719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557659540	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	552	768	1	ENST00000377346.4:c.262C>T	p.Arg88Cys	p.R88C	ENST00000377346	NM_005026.3	88	Cgt/Tgt	4/24	0.487593105885892	3	FACETS	0.84	0.816	0.863	0.84	0.816	0.863	CLONAL	3	TRUE	0	0.777134286878885	3		769	783	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	142	361	12	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.777134286878885	2		373	363	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625281	69625281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35983315	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	167	812	1	ENST00000334134.2:c.512G>A	p.Arg171His	p.R171H	ENST00000334134	NM_005247.2	171	cGc/cAc	3/3	0.20030430344646	1	FACETS	0.655	0.61	0.702	0.655	0.61	0.702	INDETERMINATE	1	TRUE	0	0.777134286878885	1		813	401	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	121	343	2	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	0.510279575271351	1	FACETS	0.957	0.891	1	0.957	0.891	1	CLONAL	1	TRUE	0	0.777134286878885	1		345	199	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954198	48954198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123331	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	47	152	0	ENST00000267163.4:c.1399C>T	p.Arg467Ter	p.R467*	ENST00000267163	NM_000321.2	467	Cga/Tga	15/27	1	2	FACETS	0.938	0.812	1	0.938	0.812	1	CLONAL	1	TRUE	1	0.777134286878885	2		152	129	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243668558	243668558	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751275167	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	48	236	0	ENST00000263826.5:c.1433G>A	p.Arg478Gln	p.R478Q	ENST00000263826	NM_005465.4	478	cGa/cAa	13/13	0.487593105885892	3	FACETS	0.875	0.75	1	0.292	0.25	0.337	CLONAL	1	TRUE	0	0.777134286878885	3		236	196	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850705	63850705	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs201178069	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	63	282	0	ENST00000279873.7:c.1489del	p.Ile497Ter	p.I497*	ENST00000279873	NM_032199.2	495	Aaa/aa	10/10	1	2	FACETS	0.886	0.781	0.995	0.886	0.781	0.995	CLONAL	1	TRUE	1	0.777134286878885	2		282	183	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	202	287	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.487593105885892	3	FACETS	1	0.988	1	0.761	0.723	0.799	CLONAL	2	TRUE	0	0.777134286878885	3		287	316	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526486	66526486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772571340	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	139	353	0	ENST00000358598.2:c.1042G>A	p.Val348Ile	p.V348I	ENST00000358598	NM_212471.2	348	Gtt/Att	11/11	0.510279575271351	1	FACETS	0.559	0.515	0.605	0.559	0.515	0.605	SUBCLONAL	1	TRUE	0	0.777134286878885	1		353	391	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100414	157100414	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1438676618	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	30	33	1	ENST00000346085.5:c.1351T>C	p.Ser451Pro	p.S451P	ENST00000346085	NM_020732.3	451	Tcg/Ccg	1/20	0.777134286878885	3	FACETS	0.744	0.609	0.894	0.248	0.203	0.298	SUBCLONAL	1	TRUE	0	0.777134286878885	3		34	144	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285059	15285059	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs367543285	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	30	710	0	ENST00000263388.2:c.4556T>C	p.Leu1519Pro	p.L1519P	ENST00000263388	NM_000435.2	1519	cTg/cCg	25/33	0.446924173001363	1	FACETS	0.12	0.097	0.147	0.12	0.097	0.147	INDETERMINATE	1	TRUE	0	0.777134286878885	1		710	392	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640784	3640784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs78637028	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	196	631	0	ENST00000294008.3:c.2855C>T	p.Ala952Val	p.A952V	ENST00000294008	NM_032444.2	952	gCg/gTg	12/15	0.510279575271351	1	FACETS	0.967	0.915	1	0.967	0.915	1	CLONAL	1	TRUE	0	0.777134286878885	1		631	319	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161412	2161412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303250662	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	157	544	0	ENST00000434045.2:c.115C>T	p.Arg39Cys	p.R39C	ENST00000434045	NM_001127598.1	39	Cgc/Tgc	2/5	0.20030430344646	1	FACETS	0.696	0.647	0.745	0.696	0.647	0.745	INDETERMINATE	1	TRUE	0	0.777134286878885	1		544	355	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184568	11184568	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	333	433	0	ENST00000361445.4:c.6649C>T	p.Arg2217Trp	p.R2217W	ENST00000361445	NM_004958.3	2217	Cgg/Tgg	47/58	0.487593105885892	3	FACETS	0.895	0.866	0.924	0.895	0.866	0.924	CLONAL	3	TRUE	0	0.777134286878885	3		433	443	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859872	117859872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	62	205	2	ENST00000297338.2:c.1763C>T	p.Thr588Met	p.T588M	ENST00000297338	NM_006265.2	588	aCg/aTg	14/14	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.777134286878885	2		207	118	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791751	42791751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	109	568	2	ENST00000575354.2:c.637C>T	p.Arg213Trp	p.R213W	ENST00000575354	NM_015125.3	213	Cgg/Tgg	5/20	0.446924173001363	1	FACETS	0.398	0.36	0.438	0.398	0.36	0.438	INDETERMINATE	1	TRUE	0	0.777134286878885	1		570	431	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480468	89480468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	47	261	0	ENST00000336596.2:c.2305C>T	p.Arg769Cys	p.R769C	ENST00000336596	NM_005233.5	769	Cgt/Tgt	13/17	1	2	FACETS	0.903	0.78	1	0.903	0.78	1	CLONAL	1	TRUE	1	0.777134286878885	2		261	134	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80057379	80057379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764832633	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	18	267	0	ENST00000265081.6:c.1778G>A	p.Arg593Gln	p.R593Q	ENST00000265081	NM_002439.4	593	cGg/cAg	13/24	0.446924173001363	1	FACETS	0.257	0.196	0.328	0.257	0.196	0.328	INDETERMINATE	1	TRUE	0	0.777134286878885	1		267	110	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950138	38950138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573790456	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	42	366	1	ENST00000357387.3:c.3812C>T	p.Thr1271Met	p.T1271M	ENST00000357387	NM_152756.3	1271	aCg/aTg	31/38	0.446924173001363	1	FACETS	0.391	0.331	0.455	0.391	0.331	0.455	INDETERMINATE	1	TRUE	0	0.777134286878885	1		367	169	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268950	115268950	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs750855257	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	210	372	0	ENST00000438362.2:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000438362	NM_001242891.1	554	Cga/Tga	14/20	0.487593105885892	3	FACETS	0.854	0.816	0.89	0.854	0.816	0.89	CLONAL	3	TRUE	0	0.777134286878885	3		372	293	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939048	48939048	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	49	216	0	ENST00000267163.4:c.884del	p.Asn295IlefsTer6	p.N295Ifs*6	ENST00000267163	NM_000321.2	294	Aaa/aa	9/27	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.777134286878885	2		216	125	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960062	134960062	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774372100	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	131	497	0	ENST00000398015.3:c.2419G>A	p.Val807Ile	p.V807I	ENST00000398015	NM_004441.4	807	Gtt/Att	13/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.777134286878885	2		497	321	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996065	73996065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747735855	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	150	724	1	ENST00000318443.5:c.799C>T	p.Arg267Cys	p.R267C	ENST00000318443	NM_001024736.1	267	Cgc/Tgc	5/10	0.20030430344646	1	FACETS	0.492	0.453	0.532	0.492	0.453	0.532	INDETERMINATE	1	TRUE	0	0.777134286878885	1		725	480	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81891928	81891928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61755444	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	50	460	0	ENST00000359376.3:c.398C>T	p.Ala133Val	p.A133V	ENST00000359376	NM_002661.3	133	gCg/gTg	4/33	0.510279575271351	1	FACETS	0.389	0.335	0.448	0.389	0.335	0.448	SUBCLONAL	1	TRUE	0	0.777134286878885	1		460	202	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885568	111885568	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	304	675	0	ENST00000341259.2:c.1345G>A	p.Glu449Lys	p.E449K	ENST00000341259	NM_005475.2	449	Gag/Aag	7/8	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.777134286878885	2		675	603	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223278	2223278	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755925380	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	151	651	1	ENST00000326181.6:c.890G>A	p.Arg297His	p.R297H	ENST00000326181	NM_032271.2	297	cGc/cAc	10/21	0.510279575271351	1	FACETS	0.771	0.718	0.825	0.771	0.718	0.825	SUBCLONAL	1	TRUE	0	0.777134286878885	1		652	308	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112939997	112939997	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767712281	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	131	429	2	ENST00000351677.2:c.1649C>T	p.Ala550Val	p.A550V	ENST00000351677	NM_002834.3	550	gCg/gTg	14/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.777134286878885	2		431	285	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041048	29041048	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	53	277	0	ENST00000282397.4:c.380T>G	p.Phe127Cys	p.F127C	ENST00000282397	NM_002019.4	127	tTt/tGt	3/30	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.777134286878885	2		277	125	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434797	110434797	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	236	503	0	ENST00000375856.3:c.3604A>G	p.Thr1202Ala	p.T1202A	ENST00000375856	NM_003749.2	1202	Acc/Gcc	1/2	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.777134286878885	2		503	523	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66777514	66777514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1205783274	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	199	562	1	ENST00000307102.5:c.880G>A	p.Gly294Arg	p.G294R	ENST00000307102	NM_002755.3	294	Ggg/Agg	7/11	0.20030430344646	1	FACETS	0.616	0.576	0.657	0.616	0.576	0.657	INDETERMINATE	1	TRUE	0	0.777134286878885	1		563	508	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647124	2647124	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	90	295	0	ENST00000342085.4:c.1402G>T	p.Gly468Cys	p.G468C	ENST00000342085	NM_002613.4	468	Ggt/Tgt	13/14	0.510279575271351	1	FACETS	0.858	0.786	0.93	0.858	0.786	0.93	CLONAL	1	TRUE	0	0.777134286878885	1		295	165	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799672	3799672	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	32	246	0	ENST00000262367.5:c.3792G>T	p.Lys1264Asn	p.K1264N	ENST00000262367	NM_004380.2	1264	aaG/aaT	21/31	0.510279575271351	1	FACETS	0.48	0.399	0.566	0.48	0.399	0.566	SUBCLONAL	1	TRUE	0	0.777134286878885	1		246	105	SUCCESS
YES1	7525	MSKCC	GRCh37	18	747987	747987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202083013	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	83	412	0	ENST00000314574.4:c.403G>A	p.Ala135Thr	p.A135T	ENST00000314574	NM_005433.3	135	Gct/Act	4/12	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.777134286878885	2		412	203	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101019	4101019	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1166526430	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	75	513	0	ENST00000262948.5:c.703G>T	p.Ala235Ser	p.A235S	ENST00000262948	NM_030662.3	235	Gct/Tct	6/11	0.446924173001363	1	FACETS	0.417	0.369	0.467	0.417	0.369	0.467	INDETERMINATE	1	TRUE	0	0.777134286878885	1		513	283	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256749	19256749	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	179	571	0	ENST00000162023.5:c.964C>T	p.Arg322Cys	p.R322C	ENST00000162023		322	Cgc/Tgc	13/13	0.446924173001363	1	FACETS	0.886	0.833	0.937	0.886	0.833	0.937	INDETERMINATE	1	TRUE	0	0.777134286878885	1		571	318	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753785	42753785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	122	802	0	ENST00000222329.4:c.479G>A	p.Arg160His	p.R160H	ENST00000222329	NM_006494.2	160	cGc/cAc	4/4	0.446924173001363	1	FACETS	0.373	0.338	0.409	0.373	0.338	0.409	INDETERMINATE	1	TRUE	0	0.777134286878885	1		802	515	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41562607	41562607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs190692702	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	67	305	0	ENST00000263253.7:c.3811G>A	p.Val1271Ile	p.V1271I	ENST00000263253	NM_001429.3	1271	Gtc/Atc	23/31	0.446924173001363	1	FACETS	0.676	0.603	0.75	0.676	0.603	0.75	INDETERMINATE	1	TRUE	0	0.777134286878885	1		305	156	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165647	185165647	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	20	342	0	ENST00000265026.3:c.922A>C	p.Ser308Arg	p.S308R	ENST00000265026	NM_004721.4	308	Agt/Cgt	5/14	1	2	FACETS	0.174	0.133	0.223	0.174	0.133	0.223	SUBCLONAL	1	TRUE	1	0.777134286878885	2		342	295	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056491	26056491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770870852	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	237	251	0	ENST00000343677.2:c.166G>A	p.Gly56Arg	p.G56R	ENST00000343677	NM_005319.3	56	Gga/Aga	1/1	0.777134286878885	6	FACETS	0.984	0.935	1			1	CLONAL	4	TRUE	NA	0.777134286878885	6		251	396	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29913028	29913028	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	142	451	1	ENST00000376809.5:c.1063G>A	p.Gly355Ser	p.G355S	ENST00000376809	NM_002116.7	355	Ggc/Agc	7/8	0.584853199409122	4	FACETS	1	0.986	1	0.467	0.428	0.506	CLONAL	1	TRUE	1	0.777134286878885	4		452	464	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38137181	38137181	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465750290	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	74	391	1	ENST00000317025.8:c.3637G>A	p.Gly1213Ser	p.G1213S	ENST00000317025	NM_023034.1	1213	Ggc/Agc	21/24	1	2	FACETS	0.952	0.85	1	0.952	0.85	1	CLONAL	1	TRUE	1	0.777134286878885	2		392	200	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958368	90958369	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	39	265	0	ENST00000265433.3:c.2069dup	p.Val691GlyfsTer51	p.V691Gfs*51	ENST00000265433	NM_002485.4	690	aag/aaAg	13/16	1	2	FACETS	0.965	0.824	1	0.965	0.824	1	CLONAL	1	TRUE	1	0.777134286878885	2		265	104	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357080	70357080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	221	656	1	ENST00000374080.3:c.5595G>A	p.Met1865Ile	p.M1865I	ENST00000374080		1865	atG/atA	39/45	0.465067782542048	1	FACETS	0.83	0.784	0.876	0.83	0.784	0.876	INDETERMINATE	1	TRUE	0	0.777134286878885	1		657	419	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430041	78430041	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	17	162	0	ENST00000370768.2:c.838G>T	p.Val280Phe	p.V280F	ENST00000370768	NM_003902.3	280	Gtc/Ttc	11/20	0.487593105885892	3	FACETS	0.49	0.369	0.63	0.163	0.123	0.21	SUBCLONAL	1	TRUE	0	0.777134286878885	3		162	124	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027133	49027133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853292	NA	P-0048858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	43	204	0	ENST00000267163.4:c.1700C>T	p.Ser567Leu	p.S567L	ENST00000267163	NM_000321.2	567	tCa/tTa	18/27	0.301540253859732	4	FACETS	0.995	0.846	1	1	0.961	1	CLONAL	3	TRUE	2	0.21	4		204	166	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133799	55133799	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	17	337	0	ENST00000257290.5:c.1012G>C	p.Glu338Gln	p.E338Q	ENST00000257290	NM_006206.4	338	Gag/Cag	7/23	1	2	FACETS	0.782	0.585	1	0.782	0.585	1	CLONAL	1	TRUE	1	0.21	2		337	207	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165741	108165741	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	13	313	0	ENST00000278616.4:c.4864G>T	p.Glu1622Ter	p.E1622*	ENST00000278616	NM_000051.3	1622	Gaa/Taa	32/63	0.174564710253026	2	FACETS	0.917	0.658	1	0.459	0.329	0.614	CLONAL	1	TRUE	0	0.21	2		313	135	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431671	431671	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1409825935	NA	P-0048858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	17	390	0	ENST00000399788.2:c.2338C>G	p.Leu780Val	p.L780V	ENST00000399788	NM_001042603.1	780	Ctc/Gtc	17/28	0.301540253859732	5	FACETS	0.696	0.519	0.906			1	SUBCLONAL	1	TRUE	NA	0.21	5		390	306	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961518	41961518	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	22	345	0	ENST00000219905.7:c.426G>A	p.Trp142Ter	p.W142*	ENST00000219905	NM_001164273.1	142	tgG/tgA	2/24	1	2	FACETS	0.931	0.724	1	0.931	0.724	1	CLONAL	1	TRUE	1	0.21	2		345	225	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929161	32929161	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	19	375	0	ENST00000380152.3:c.7171G>T	p.Glu2391Ter	p.E2391*	ENST00000380152		2391	Gaa/Taa	14/27	0.301540253859732	4	FACETS	1	0.785	1	0.516	0.393	0.66	CLONAL	1	TRUE	2	0.21	4		375	212	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705502	47705502	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	15	278	0	ENST00000233146.2:c.2302G>C	p.Glu768Gln	p.E768Q	ENST00000233146	NM_000251.2	768	Gaa/Caa	14/16	1	2	FACETS	0.952	0.701	1	0.952	0.701	1	CLONAL	1	TRUE	1	0.21	2		278	150	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5070023	5070023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	20	201	0	ENST00000381652.3:c.1612C>T	p.His538Tyr	p.H538Y	ENST00000381652	NM_004972.3	538	Cac/Tac	12/25	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.21	2		201	165	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711891	89711891	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660507	NA	P-0048859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	47	343	0	ENST00000371953.3:c.509G>T	p.Ser170Ile	p.S170I	ENST00000371953	NM_000314.4	170	aGt/aTt	6/9	1	2	FACETS	0.732	0.618	0.858	0.732	0.618	0.858	SUBCLONAL	1	TRUE	1	0.253211415393059	2		343	507	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17354303	17354303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553177682	NA	P-0048859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	66	361	0	ENST00000375499.3:c.481G>A	p.Asp161Asn	p.D161N	ENST00000375499	NM_003000.2	161	Gat/Aat	5/8	1	2	FACETS	0.795	0.689	0.909	0.795	0.689	0.909	CLONAL	1	TRUE	1	0.253211415393059	2		361	656	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244829	46244829	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	70	378	0	ENST00000334344.6:c.2923T>C	p.Ser975Pro	p.S975P	ENST00000334344	NM_152641.2	975	Tca/Cca	15/21	1	2	FACETS	0.764	0.665	0.87	0.764	0.665	0.87	SUBCLONAL	1	TRUE	1	0.253211415393059	2		378	724	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271722	15271738	+	frameshift_variant	Frame_Shift_Del	DEL	GGGAACCCGCAGGAAGC	GGGAACCCGCAGGAAGC	-	novel	NA	P-0048859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	115	758	1	ENST00000263388.2:c.6701_6717del	p.Arg2234GlnfsTer2	p.R2234Qfs*2	ENST00000263388	NM_000435.2	2234	cGCTTCCTGCGGGTTCCC/c	33/33	1	2	FACETS	0.724	0.65	0.803	0.724	0.65	0.803	SUBCLONAL	1	TRUE	1	0.253211415393059	2		759	1254	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332072	81332072	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	32	169	1	ENST00000222390.5:c.2012G>T	p.Gly671Val	p.G671V	ENST00000222390	NM_000601.4	671	gGg/gTg	18/18	1	2	FACETS	1	0.822	1	1	0.822	1	CLONAL	1	TRUE	1	0.253211415393059	2		170	251	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046324	69046324	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	62	335	0	ENST00000288368.4:c.3797T>A	p.Val1266Asp	p.V1266D	ENST00000288368	NM_024870.2	1266	gTt/gAt	32/40	1	2	FACETS	0.897	0.775	1	0.897	0.775	1	CLONAL	1	TRUE	1	0.253211415393059	2		335	546	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	82	148	0				ENST00000310581	NM_198253.2	-/1132			0.383702375587985	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.383702375587985	1		148	295	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	81	406	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.876	0.774	0.984	0.876	0.774	0.984	CLONAL	1	TRUE	1	0.383702375587985	2		406	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0048861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	203	538	0	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.383702375587985	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.383702375587985	1		538	819	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111982953	111982953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	142	500	0	ENST00000368678.4:c.1594G>A	p.Glu532Lys	p.E532K	ENST00000368678		532	Gaa/Aaa	13/13	1	2	FACETS	0.867	0.79	0.947	0.867	0.79	0.947	CLONAL	1	TRUE	1	0.383702375587985	2		500	854	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11181374	11181374	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	174	584	0	ENST00000361445.4:c.6862G>C	p.Glu2288Gln	p.E2288Q	ENST00000361445	NM_004958.3	2288	Gag/Cag	49/58	0.293327375249287	1	FACETS	0.803	0.739	0.869	0.803	0.739	0.869	CLONAL	1	TRUE	0	0.383702375587985	1		584	913	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099380	27099380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	60	463	0	ENST00000324856.7:c.3617C>T	p.Thr1206Ile	p.T1206I	ENST00000324856	NM_006015.4	1206	aCt/aTt	14/20	0.293327375249287	1	FACETS	0.326	0.28	0.376	0.326	0.28	0.376	SUBCLONAL	1	TRUE	0	0.383702375587985	1		463	776	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36823966	36823966	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	81	532	0	ENST00000373129.3:c.216G>C	p.Glu72Asp	p.E72D	ENST00000373129	NM_032017.1	72	gaG/gaC	5/12	0.293327375249287	1	FACETS	0.398	0.35	0.45	0.398	0.35	0.45	SUBCLONAL	1	TRUE	0	0.383702375587985	1		532	858	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36824358	36824358	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	109	484	0	ENST00000373129.3:c.178G>C	p.Asp60His	p.D60H	ENST00000373129	NM_032017.1	60	Gat/Cat	4/12	0.293327375249287	1	FACETS	0.592	0.531	0.656	0.592	0.531	0.656	SUBCLONAL	1	TRUE	0	0.383702375587985	1		484	776	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458564	120458564	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	163	509	0	ENST00000256646.2:c.6781G>A	p.Glu2261Lys	p.E2261K	ENST00000256646	NM_024408.3	2261	Gag/Aag	34/34	1	2	FACETS	0.915	0.839	0.993	0.915	0.839	0.993	CLONAL	1	TRUE	1	0.383702375587985	2		509	929	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799225	88799225	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	80	516	0	ENST00000360948.2:c.160T>C	p.Phe54Leu	p.F54L	ENST00000360948	NM_001012338.2	54	Ttc/Ctc	2/19	0.293327375249287	1	FACETS	0.42	0.369	0.475	0.42	0.369	0.475	SUBCLONAL	1	TRUE	0	0.383702375587985	1		516	803	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788660	3788660	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	116	314	0	ENST00000262367.5:c.4294T>C	p.Ser1432Pro	p.S1432P	ENST00000262367	NM_004380.2	1432	Tct/Cct	26/31	0.228382907729602	1	FACETS	0.915	0.828	1	0.915	0.828	1	INDETERMINATE	1	TRUE	0	0.383702375587985	1		314	534	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244907	41244907	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397508988	NA	P-0048861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	130	395	0	ENST00000357654.3:c.2641G>A	p.Glu881Lys	p.E881K	ENST00000357654	NM_007294.3	881	Gaa/Aaa	10/23	1	2	FACETS	0.84	0.762	0.922	0.84	0.762	0.922	CLONAL	1	TRUE	1	0.383702375587985	2		395	807	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166342	7166342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	100	596	2	ENST00000302850.5:c.1684G>A	p.Asp562Asn	p.D562N	ENST00000302850	NM_000208.2	562	Gac/Aac	8/22	0.228382907729602	1	FACETS	0.443	0.395	0.495	0.443	0.395	0.495	INDETERMINATE	1	TRUE	0	0.383702375587985	1		598	950	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267787	7267787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	143	503	2	ENST00000302850.5:c.221G>T	p.Arg74Leu	p.R74L	ENST00000302850	NM_000208.2	74	cGa/cTa	2/22	0.228382907729602	1	FACETS	0.75	0.684	0.819	0.75	0.684	0.819	INDETERMINATE	1	TRUE	0	0.383702375587985	1		505	803	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267794	7267794	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	134	474	0	ENST00000302850.5:c.214G>T	p.Asp72Tyr	p.D72Y	ENST00000302850	NM_000208.2	72	Gat/Tat	2/22	0.228382907729602	1	FACETS	0.722	0.656	0.791	0.722	0.656	0.791	INDETERMINATE	1	TRUE	0	0.383702375587985	1		474	782	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267839	7267839	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	119	420	1	ENST00000302850.5:c.169G>T	p.Glu57Ter	p.E57*	ENST00000302850	NM_000208.2	57	Gaa/Taa	2/22	0.228382907729602	1	FACETS	0.753	0.68	0.829	0.753	0.68	0.829	INDETERMINATE	1	TRUE	0	0.383702375587985	1		421	666	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39240651	39240651	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	86	245	0	ENST00000402219.2:c.2117G>C	p.Arg706Thr	p.R706T	ENST00000402219	NM_005633.3	706	aGa/aCa	13/23	1	2	FACETS	0.907	0.805	1	0.907	0.805	1	CLONAL	1	TRUE	1	0.383702375587985	2		245	494	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272340	21272340	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	231	605	0	ENST00000354336.3:c.118G>A	p.Asp40Asn	p.D40N	ENST00000354336	NM_005207.3	40	Gat/Aat	1/3	0.383702375587985	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.383702375587985	1		605	960	SUCCESS
ATR	545	MSKCC	GRCh37	3	142254004	142254004	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	96	269	0	ENST00000350721.4:c.3863C>G	p.Ser1288Cys	p.S1288C	ENST00000350721	NM_001184.3	1288	tCt/tGt	21/47	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.383702375587985	2		269	500	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522558	67522558	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	63	157	0	ENST00000274335.5:c.55G>A	p.Glu19Lys	p.E19K	ENST00000274335		19	Gaa/Aaa	1/15	0.228382907729602	1	FACETS	0.783	0.681	0.892	0.783	0.681	0.892	INDETERMINATE	1	TRUE	0	0.383702375587985	1		157	339	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818365	170818365	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	54	216	0	ENST00000296930.5:c.195G>A	p.Met65Ile	p.M65I	ENST00000296930	NM_002520.6	65	atG/atA	3/11	0.182077769152452	2	FACETS	0.641	0.549	0.742	0.321	0.274	0.371	INDETERMINATE	1	TRUE	0	0.383702375587985	2		216	439	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163263	32163263	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	290	773	0	ENST00000375023.3:c.5963C>G	p.Pro1988Arg	p.P1988R	ENST00000375023	NM_004557.3	1988	cCa/cGa	30/30	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.383702375587985	2		773	1448	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977567	2977567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	211	557	1	ENST00000396946.4:c.1117G>A	p.Glu373Lys	p.E373K	ENST00000396946	NM_032415.4	373	Gag/Aag	8/25	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.383702375587985	2		558	1097	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340130	116340130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	51	207	0	ENST00000397752.3:c.992G>A	p.Arg331Lys	p.R331K	ENST00000397752	NM_000245.2	331	aGa/aAa	2/21	1	2	FACETS	0.687	0.586	0.797	0.687	0.586	0.797	SUBCLONAL	1	TRUE	1	0.383702375587985	2		207	387	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740422	145740422	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1395	186	806	0	ENST00000428558.2:c.1518del	p.Gly507AlafsTer51	p.G507Afs*51	ENST00000428558	NM_004260.3	506	gcC/gc	9/22	1	2	FACETS	0.613	0.564	0.665	0.613	0.564	0.665	SUBCLONAL	1	TRUE	1	0.383702375587985	2		806	1581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0048864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	60	470	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	NA	2	FACETS	0.845	0.728	0.972			1	INDETERMINATE	1	TRUE	NA	0.25	2		470	568	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129622	47129623	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	133	210	0	ENST00000409792.3:c.5257dup	p.Thr1753AsnfsTer36	p.T1753Nfs*36	ENST00000409792	NM_014159.6	1753	acc/aAcc	10/21	0.134006277221367	3	FACETS	0.978	0.891	1	0.652	0.594	0.713	INDETERMINATE	2	TRUE	0	0.25	3		210	612	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0048866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	146	431	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.936	0.858	1	0.936	0.858	1	CLONAL	1	TRUE	1	0.532190728499727	2		431	586	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0048866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	117	221	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	0.532190728499727	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.532190728499727	1		221	300	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098815	178098823	+	inframe_deletion	In_Frame_Del	DEL	TCTAGTTGT	TCTAGTTGT	-	novel	NA	P-0048866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	203	566	0	ENST00000397062.3:c.222_230del	p.Leu74_Asp77delinsPhe	p.L74_D77delinsF	ENST00000397062	NM_006164.4	74	ttACAACTAGAt/ttt	2/5	1	2	FACETS	0.981	0.912	1	0.981	0.912	1	CLONAL	1	TRUE	1	0.532190728499727	2		566	778	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603120	48603120	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0048866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	158	483	0	ENST00000342988.3:c.1421C>G	p.Ser474Ter	p.S474*	ENST00000342988	NM_005359.5	474	tCa/tGa	11/12	0.532190728499727	1	FACETS	0.935	0.864	1	0.935	0.864	1	CLONAL	1	TRUE	0	0.532190728499727	1		483	466	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944967	31944967	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	151	645	1	ENST00000340398.3:c.134C>A	p.Thr45Asn	p.T45N	ENST00000340398	NM_001013699.2	45	aCc/aAc	1/1	1	2	FACETS	0.785	0.719	0.854	0.785	0.719	0.854	SUBCLONAL	1	TRUE	1	0.532190728499727	2		646	723	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436567	110436567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775295986	NA	P-0048866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	243	1070	1	ENST00000375856.3:c.1834C>T	p.Leu612Phe	p.L612F	ENST00000375856	NM_003749.2	612	Ctc/Ttc	1/2	0.256418006539505	3	FACETS	1	0.965	1	0.526	0.491	0.562	INDETERMINATE	1	TRUE	1	0.532190728499727	3		1071	1100	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784585	43784585	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	89	500	0	ENST00000382044.4:c.89C>T	p.Ser30Phe	p.S30F	ENST00000382044	NM_001141980.1	30	tCt/tTt	2/28	0.370934425215419	1	FACETS	0.407	0.361	0.456	0.407	0.361	0.456	SUBCLONAL	1	TRUE	0	0.532190728499727	1		500	603	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784619	43784619	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	94	464	0	ENST00000382044.4:c.55C>G	p.Gln19Glu	p.Q19E	ENST00000382044	NM_001141980.1	19	Cag/Gag	2/28	0.370934425215419	1	FACETS	0.415	0.369	0.463	0.415	0.369	0.463	SUBCLONAL	1	TRUE	0	0.532190728499727	1		464	625	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021137	31021137	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	207	600	1	ENST00000375687.4:c.1136A>T	p.Glu379Val	p.E379V	ENST00000375687	NM_015338.5	379	gAg/gTg	12/13	1	2	FACETS	0.963	0.895	1	0.963	0.895	1	CLONAL	1	TRUE	1	0.532190728499727	2		601	808	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729954	41729954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	192	699	0	ENST00000242208.4:c.575C>T	p.Ala192Val	p.A192V	ENST00000242208	NM_002192.2	192	gCc/gTc	3/3	1	2	FACETS	0.97	0.899	1	0.97	0.899	1	CLONAL	1	TRUE	1	0.532190728499727	2		699	744	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040762	47040763	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048866-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	224	916	0	ENST00000377604.3:c.1398dup	p.Gly467TrpfsTer51	p.G467Wfs*51	ENST00000377604	NM_001204468.1	466	cct/ccTt	13/24	0.121523553338297	3	FACETS	1	0.957	1	0.518	0.482	0.556	INDETERMINATE	1	TRUE	1	0.532190728499727	3		916	1028	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0048868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	105	325	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.292667831388556	3	FACETS	0.758	0.682	0.838	0.758	0.682	0.838	SUBCLONAL	2	TRUE	1	0.32	3		325	502	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273962	10273962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	69	663	0	ENST00000330684.3:c.307G>A	p.Asp103Asn	p.D103N	ENST00000330684	NM_001134407.1	103	Gac/Aac	2/13	1	2	FACETS	0.546	0.474	0.623	0.546	0.474	0.623	SUBCLONAL	1	TRUE	1	0.32	2		663	790	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797221	135797221	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs118203417	NA	P-0048868-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	40	197	0	ENST00000298552.3:c.648del	p.Phe216LeufsTer8	p.F216Lfs*8	ENST00000298552	NM_001162426.1	216	ttT/tt	7/23	1	2	FACETS	0.916	0.765	1	0.916	0.765	1	CLONAL	1	TRUE	1	0.32	2		197	273	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0048874-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	1488	479	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.230979001231187	19	FACETS	0.998	0.983	1	1	0.997	1	CLONAL	20	TRUE	0	0.230979001231187	19		479	1913	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600393	10600393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048874-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	144	666	0	ENST00000171111.5:c.1462G>A	p.Glu488Lys	p.E488K	ENST00000171111	NM_203500.1	488	Gag/Aag	4/6	0.230979001231187	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.230979001231187	1		666	889	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157474	106157474	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0048874-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	66	287	0	ENST00000380013.4:c.2375C>G	p.Ser792Ter	p.S792*	ENST00000380013	NM_001127208.2	792	tCa/tGa	3/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.230979001231187	2		287	424	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817814	3817814	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200424021	NA	P-0048874-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	139	565	1	ENST00000262367.5:c.3157C>T	p.Pro1053Ser	p.P1053S	ENST00000262367	NM_004380.2	1053	Cct/Tct	16/31	0.230979001231187	4	FACETS	0.801	0.729	0.877	0.801	0.729	0.877	CLONAL	2	TRUE	2	0.230979001231187	4		566	925	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829714	72829714	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048874-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	84	605	0	ENST00000268489.5:c.6867G>T	p.Trp2289Cys	p.W2289C	ENST00000268489	NM_006885.3	2289	tgG/tgT	9/10	0.230979001231187	5	FACETS	0.892	0.785	1			1	CLONAL	1	TRUE	NA	0.230979001231187	5		605	1098	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967571	90967571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048874-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	69	335	0	ENST00000265433.3:c.1337C>T	p.Ala446Val	p.A446V	ENST00000265433	NM_002485.4	446	gCt/gTt	10/16	0.230979001231187	5	FACETS	1	0.965	1	0.334	0.291	0.381	CLONAL	1	TRUE	1	0.230979001231187	5		335	602	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008036	29008036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754160537	NA	P-0048875-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	36	356	0	ENST00000282397.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000282397	NM_002019.4	245	Ggc/Agc	6/30	0.372829855514976	1	FACETS	0.438	0.36	0.524	0.438	0.36	0.524	SUBCLONAL	1	TRUE	0	0.372829855514976	1		356	359	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499345	89499345	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048875-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	84	493	0	ENST00000336596.2:c.2515G>T	p.Glu839Ter	p.E839*	ENST00000336596	NM_005233.5	839	Gag/Tag	15/17	0.192959075901986	5	FACETS	1	0.97	1	0.435	0.384	0.488	INDETERMINATE	1	TRUE	2	0.372829855514976	5		493	539	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0048875-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	252	593	2	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	0.300113525783816	3	FACETS	1	0.972	1	0.706	0.663	0.75	CLONAL	2	TRUE	0	0.372829855514976	3		595	757	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945066	31945066	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048875-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	157	673	0	ENST00000340398.3:c.35C>A	p.Thr12Asn	p.T12N	ENST00000340398	NM_001013699.2	12	aCc/aAc	1/1	0.372829855514976	4	FACETS	1	0.957	1	0.358	0.327	0.39	CLONAL	1	TRUE	1	0.372829855514976	4		673	1078	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245300	41245300	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048875-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	198	601	0	ENST00000357654.3:c.2248C>A	p.Leu750Ile	p.L750I	ENST00000357654	NM_007294.3	750	Ctc/Atc	10/23	0.2246923663062	5	FACETS	1	0.964	1	0.708	0.657	0.76	CLONAL	2	TRUE	2	0.372829855514976	5		601	780	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974769	21974769	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs760065045	NA	P-0048875-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	217	268	0	ENST00000304494.5:c.58G>T	p.Ala20Ser	p.A20S	ENST00000304494	NM_000077.4	20	Gcg/Tcg	1/3	0.325532921478318	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	3	TRUE	0	0.372829855514976	3		268	449	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515100	31515100	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048875-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	64	539	0	ENST00000344624.3:c.1285C>G	p.Gln429Glu	p.Q429E	ENST00000344624		429	Cag/Gag	5/33	0.372829855514976	8	FACETS	0.576	0.497	0.663	0.096	0.082	0.111	SUBCLONAL	1	TRUE	2	0.372829855514976	8		539	1263	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55987320	55987320	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048875-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	53	448	0	ENST00000263923.4:c.105C>A	p.Ser35Arg	p.S35R	ENST00000263923	NM_002253.2	35	agC/agA	2/30	0.372829855514976	3	FACETS	0.772	0.659	0.894	0.386	0.329	0.447	SUBCLONAL	1	TRUE	1	0.372829855514976	3		448	437	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218695	98218696	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0048875-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	150	420	0	ENST00000331920.6:c.3169-1_3169delinsTT		p.X1057_splice	ENST00000331920	NM_000264.3	1057		19/24	0.352242886505183	2	FACETS	0.949	0.876	1	0.949	0.876	1	CLONAL	2	TRUE	0	0.372829855514976	2		420	424	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199749	108199749	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1555121919	NA	P-0048875-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	32	266	0	ENST00000278616.4:c.7091C>T	p.Ala2364Val	p.A2364V	ENST00000278616	NM_000051.3	2364	gCa/gTa	49/63	1	2	FACETS	0.795	0.65	0.956	0.795	0.65	0.956	CLONAL	1	TRUE	1	0.372829855514976	2		266	216	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741683	17741683	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048875-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	550	413	0	ENST00000250003.3:c.354G>T	p.Glu118Asp	p.E118D	ENST00000250003	NM_002478.4	118	gaG/gaT	1/3	0.372829855514976	6	FACETS	1	0.99	1			1	CLONAL	5	TRUE	NA	0.372829855514976	6		413	971	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117753474	117753474	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048875-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	50	617	2	ENST00000369458.3:c.4G>T	p.Ala2Ser	p.A2S	ENST00000369458	NM_024626.3	2	Gct/Tct	1/6	0.361112930961791	3	FACETS	0.521	0.441	0.608	0.26	0.22	0.304	SUBCLONAL	1	TRUE	1	0.372829855514976	3		619	611	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567636	226567636	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048875-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	297	672	0	ENST00000366794.5:c.1530G>T	p.Gln510His	p.Q510H	ENST00000366794	NM_001618.3	510	caG/caT	10/23	0.372829855514976	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.372829855514976	2		672	771	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999332	100999332	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048875-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	235	989	0	ENST00000325455.5:c.470C>A	p.Thr157Asn	p.T157N	ENST00000325455	NM_001202474.3	157	aCc/aAc	1/8	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.372829855514976	2		989	925	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658360	18658360	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048875-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	58	403	0	ENST00000266497.5:c.3165C>G	p.Phe1055Leu	p.F1055L	ENST00000266497		1055	ttC/ttG	22/31	0.372829855514976	4	FACETS	0.915	0.787	1	0.305	0.262	0.351	CLONAL	1	TRUE	1	0.372829855514976	4		403	467	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988558	36988558	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048875-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1481	176	692	0	ENST00000354822.5:c.95C>A	p.Ser32Ter	p.S32*	ENST00000354822	NM_001079668.2	32	tCg/tAg	2/3	0.372829855514976	9	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.372829855514976	9		692	1657	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95577713	95577713	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048875-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	67	402	0	ENST00000393063.1:c.2197G>C	p.Glu733Gln	p.E733Q	ENST00000393063	NM_030621.3	733	Gag/Cag	15/28	0.372829855514976	2	FACETS	0.85	0.741	0.966	0.425	0.37	0.483	CLONAL	1	TRUE	0	0.372829855514976	2		402	423	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14028139	14028139	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048875-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	113	462	0	ENST00000311895.7:c.1193G>C	p.Ser398Thr	p.S398T	ENST00000311895	NM_005236.2	398	aGt/aCt	7/11	0.352242886505183	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.372829855514976	2		462	288	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100905	41100905	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0048875-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	117	612	0	ENST00000373198.4:c.1450+1G>T		p.X484_splice	ENST00000373198	NM_133170.3	484			0.372829855514976	3	FACETS	0.967	0.872	1	0.484	0.436	0.534	CLONAL	1	TRUE	1	0.372829855514976	3		612	770	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590707	189590707	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048875-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	145	552	0	ENST00000264731.3:c.1272G>C	p.Met424Ile	p.M424I	ENST00000264731	NM_003722.4	424	atG/atC	10/14	0.192959075901986	5	FACETS	0.834	0.762	0.909	0.556	0.508	0.606	INDETERMINATE	2	TRUE	2	0.372829855514976	5		552	727	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561765	55561765	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048875-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	88	422	0	ENST00000288135.5:c.155A>T	p.Asp52Val	p.D52V	ENST00000288135	NM_000222.2	52	gAc/gTc	2/21	0.372829855514976	3	FACETS	1	0.894	1	0.504	0.447	0.564	CLONAL	1	TRUE	1	0.372829855514976	3		422	556	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972024	55972024	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048875-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	204	493	0	ENST00000263923.4:c.1620G>T	p.Glu540Asp	p.E540D	ENST00000263923	NM_002253.2	540	gaG/gaT	12/30	0.372829855514976	3	FACETS	0.999	0.931	1	0.999	0.931	1	CLONAL	2	TRUE	1	0.372829855514976	3		493	650	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106543541	106543541	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048875-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	69	323	0	ENST00000369096.4:c.343C>G	p.Pro115Ala	p.P115A	ENST00000369096	NM_001198.3	115	Ccc/Gcc	3/7	0.346389305019624	2	FACETS	1	0.972	1	0.693	0.61	0.78	CLONAL	1	TRUE	0	0.372829855514976	2		323	267	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462502	92462502	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1290397698	NA	P-0048875-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	99	678	1	ENST00000265734.4:c.136C>T	p.Arg46Trp	p.R46W	ENST00000265734	NM_001259.6	46	Cgg/Tgg	2/8	0.307926029388338	4	FACETS	0.759	0.676	0.847	0.19	0.169	0.212	SUBCLONAL	1	TRUE	0	0.372829855514976	4		679	961	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974763	21974768	+	inframe_deletion	In_Frame_Del	DEL	GGGCCG	GGGCCG	-	novel	NA	P-0048875-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	233	308	0	ENST00000304494.5:c.59_64del	p.Ala20_Arg22delinsGly	p.A20_R22delinsG	ENST00000304494	NM_000077.4	20	gCGGCCCgg/ggg	1/3	0.325532921478318	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	3	TRUE	0	0.372829855514976	3		308	482	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434776	128434776	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048875-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	120	614	0	ENST00000265960.3:c.78G>C	p.Met26Ile	p.M26I	ENST00000265960	NM_001006617.1	26	atG/atC	2/12	0.372829855514976	3	FACETS	1	0.921	1	0.34	0.307	0.375	CLONAL	1	TRUE	0	0.372829855514976	3		614	748	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974763	21974763	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048875-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	29	308	0	ENST00000304494.5:c.64C>T	p.Arg22Trp	p.R22W	ENST00000304494	NM_000077.4	22	Cgg/Tgg	1/3	0.325532921478318	3	FACETS	0.383	0.307	0.47	0.128	0.102	0.157	SUBCLONAL	1	TRUE	0	0.372829855514976	3		308	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577536	+	frameshift_variant	Frame_Shift_Del	DEL	CCT	CCT	TC	novel	NA	P-0048875-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	300	654	2	ENST00000269305.4:c.745_747delinsGA	p.Arg249AspfsTer96	p.R249Dfs*96	ENST00000269305	NM_001126112.2	249	AGG/GA	7/11	0.300113525783816	3	FACETS	1	0.991	1	0.821	0.777	0.866	CLONAL	2	TRUE	0	0.372829855514976	3		656	775	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713606	52713607	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0049011-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	44	572	0	ENST00000394830.3:c.121_122del	p.Leu41SerfsTer11	p.L41Sfs*11	ENST00000394830	NM_018313.4	41	CTt/t	2/30	0.150225926362195	1	FACETS	0.839	0.702	0.991	0.839	0.702	0.991	CLONAL	1	TRUE	0	0.150225926362195	1		572	646	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191547	10191547	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049011-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	107	711	0	ENST00000256474.2:c.540del	p.Ile180MetfsTer22	p.I180Mfs*22	ENST00000256474	NM_000551.3	180	atC/at	3/3	0.150225926362195	1	FACETS	1	0.905	1	1	0.988	1	CLONAL	2	TRUE	0	0.150225926362195	1		711	654	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604679	43604679	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0049011-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	76	634	1	ENST00000355710.3:c.1263+1G>A		p.X421_splice	ENST00000355710	NM_020975.4	421			1	2	FACETS	0.922	0.81	1	1	0.981	1	CLONAL	2	TRUE	1	0.150225926362195	2		635	549	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839702	42839702	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049011-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	110	796	0	ENST00000398585.3:c.1537A>G	p.Asn513Asp	p.N513D	ENST00000398585	NM_001135099.1	513	Aat/Gat	13/14	1	2	FACETS	0.967	0.869	1	1	0.988	1	CLONAL	2	TRUE	1	0.150225926362195	2		796	757	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495645	72495645	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0049012-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	55	199	0	ENST00000477973.2:c.423+2T>C		p.X141_splice	ENST00000477973	NM_012234.5	141			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		199	256	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0049026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	375	423	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.619613268550563	3	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.619613268550563	3		423	704	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533773	41533773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	23	348	2	ENST00000263253.7:c.1739G>A	p.Arg580Gln	p.R580Q	ENST00000263253	NM_001429.3	580	cGa/cAa	8/31	0.602496478133111	3	FACETS	0.224	0.174	0.281	0.112	0.087	0.141	SUBCLONAL	1	TRUE	1	0.619613268550563	3		350	435	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827961	40827961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757952832	NA	P-0049026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	94	392	0	ENST00000373198.4:c.2467G>A	p.Ala823Thr	p.A823T	ENST00000373198	NM_133170.3	823	Gcc/Acc	17/32	0.218287318573174	3	FACETS	0.818	0.731	0.91	0.273	0.243	0.304	INDETERMINATE	1	TRUE	0	0.619613268550563	3		392	486	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106557	108106557	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	105	232	0	ENST00000278616.4:c.492G>A	p.Trp164Ter	p.W164*	ENST00000278616	NM_000051.3	164	tgG/tgA	5/63	0.619613268550563	1	FACETS	0.932	0.851	1	0.932	0.851	1	CLONAL	1	TRUE	0	0.619613268550563	1		232	251	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866707	37866707	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	360	546	0	ENST00000269571.5:c.874G>T	p.Gly292Cys	p.G292C	ENST00000269571		292	Ggc/Tgc	7/27	0.602496478133111	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.619613268550563	3		546	749	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221950	1221950	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	548	714	0	ENST00000326873.7:c.865del	p.Met289CysfsTer47	p.M289Cfs*47	ENST00000326873	NM_000455.4	289	Atg/tg	7/10	0.615824955388837	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.619613268550563	2		714	779	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513276	106513276	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	152	242	0	ENST00000359195.3:c.2180C>T	p.Ala727Val	p.A727V	ENST00000359195	NM_002649.2	727	gCc/gTc	4/11	0.366166095522867	5	FACETS	1	0.971	1	0.736	0.679	0.793	INDETERMINATE	2	TRUE	2	0.619613268550563	5		242	429	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002922	69002922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	67	228	2	ENST00000288368.4:c.2222C>T	p.Ala741Val	p.A741V	ENST00000288368	NM_024870.2	741	gCc/gTc	20/40	0.595886270229106	3	FACETS	0.882	0.773	0.999	0.441	0.386	0.5	CLONAL	1	TRUE	1	0.619613268550563	3		230	321	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411673	63411673	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	299	638	0	ENST00000330258.3:c.1494C>G	p.Asp498Glu	p.D498E	ENST00000330258	NM_152424.3	498	gaC/gaG	2/2	0.329164608281611	4	FACETS	0.86	0.812	0.909			1	INDETERMINATE	2	TRUE	NA	0.619613268550563	4		638	909	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0049027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	122	591	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.949	0.86	1	1	0.989	1	CLONAL	2	TRUE	1	0.21256439754953	2		592	605	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0049027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	114	401	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	1	2	FACETS	0.873	0.788	0.963	1	0.987	1	CLONAL	2	TRUE	1	0.21256439754953	2		401	614	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866987936	NA	P-0049027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	36	220	0	ENST00000281708.4:c.1436G>T	p.Arg479Leu	p.R479L	ENST00000281708	NM_033632.3	479	cGa/cTa	10/12	0.179848859554807	1	FACETS	0.961	0.793	1	0.961	0.793	1	CLONAL	1	TRUE	0	0.21256439754953	1		220	315	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626736	12626736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149580968	NA	P-0049027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	79	399	0	ENST00000251849.4:c.1553G>A	p.Arg518Gln	p.R518Q	ENST00000251849	NM_002880.3	518	cGa/cAa	15/17	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.21256439754953	2		399	602	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032035	10032035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	83	479	0	ENST00000330684.3:c.788G>A	p.Gly263Glu	p.G263E	ENST00000330684	NM_001134407.1	263	gGg/gAg	3/13	0.21256439754953	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.21256439754953	1		479	632	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222293	2222293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763973302	NA	P-0049027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	56	763	2	ENST00000326181.6:c.577C>T	p.Arg193Trp	p.R193W	ENST00000326181	NM_032271.2	193	Cgg/Tgg	8/21	NA	2	FACETS	0.517	0.441	0.6			1	INDETERMINATE	1	TRUE	NA	0.21256439754953	2		765	1019	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181432	185181432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	27	343	0	ENST00000265026.3:c.1373G>A	p.Arg458His	p.R458H	ENST00000265026	NM_004721.4	458	cGc/cAc	8/14	1	2	FACETS	0.484	0.384	0.599	0.484	0.384	0.599	SUBCLONAL	1	TRUE	1	0.21256439754953	2		343	525	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801127	1801127	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	143	911	1	ENST00000260795.2:c.256C>A	p.Arg86Ser	p.R86S	ENST00000260795		86	Cgt/Agt	2/17	0.179848859554807	1	FACETS	0.971	0.883	1	0.971	0.883	1	CLONAL	1	TRUE	0	0.21256439754953	1		912	1239	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989690	68989690	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	42	423	0	ENST00000288368.4:c.1628G>T	p.Gly543Val	p.G543V	ENST00000288368	NM_024870.2	543	gGa/gTa	15/40	1	2	FACETS	0.678	0.565	0.803	0.678	0.565	0.803	SUBCLONAL	1	TRUE	1	0.21256439754953	2		423	583	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0049028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	163	250	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.817855450217628	2	FACETS	0.87	0.829	0.907	0.87	0.829	0.907	CLONAL	2	TRUE	0	0.884146533915564	2		250	212	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0049028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	371	441	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.780598638886379	2	FACETS	0.904	0.878	0.929	0.904	0.878	0.929	CLONAL	2	TRUE	0	0.884146533915564	2		441	464	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463575	25463575	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	359	453	0	ENST00000264709.3:c.2107C>G	p.Leu703Val	p.L703V	ENST00000264709	NM_175629.2	703	Ctg/Gtg	18/23	0.312923351632043	4	FACETS	0.977	0.932	1	0.977	0.932	1	INDETERMINATE	2	TRUE	2	0.884146533915564	4		453	783	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453987	140453987	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	99	209	0	ENST00000288602.6:c.1741A>T	p.Asn581Tyr	p.N581Y	ENST00000288602	NM_004333.4	581	Aat/Tat	14/18	0.21417927374952	6	FACETS	1	0.952	1			1	CLONAL	4	TRUE	NA	0.21417927374952	6		209	304	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843595	156843595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139875058	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	72	816	0	ENST00000524377.1:c.1021G>A	p.Val341Met	p.V341M	ENST00000524377	NM_002529.3	341	Gtg/Atg	8/17	0.21417927374952	3	FACETS	0.918	0.801	1	0.459	0.4	0.523	CLONAL	1	TRUE	1	0.21417927374952	3		816	811	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239245	105239245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	46	637	0	ENST00000349310.3:c.1142C>T	p.Ser381Leu	p.S381L	ENST00000349310	NM_001014432.1	381	tCa/tTa	12/15	0.182182799156686	3	FACETS	0.787	0.662	0.926	0.394	0.331	0.463	CLONAL	1	TRUE	1	0.21417927374952	3		637	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579575	7579575	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	98	670	1	ENST00000269305.4:c.112C>T	p.Gln38Ter	p.Q38*	ENST00000269305	NM_001126112.2	38	Caa/Taa	4/11	1	2	FACETS	0.862	0.771	0.957	1	0.985	1	CLONAL	2	TRUE	1	0.21417927374952	2		671	531	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993237	72993237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567606533	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	140	752	3	ENST00000268489.5:c.808G>A	p.Asp270Asn	p.D270N	ENST00000268489	NM_006885.3	270	Gat/Aat	2/10	0.168770313748264	4	FACETS	0.947	0.863	1	0.947	0.863	1	CLONAL	2	TRUE	2	0.21417927374952	4		755	838	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727843	78727843	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	140	661	0	ENST00000306801.3:c.688C>G	p.Gln230Glu	p.Q230E	ENST00000306801	NM_020761.2	230	Cag/Gag	6/34	0.168770313748264	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.21417927374952	4		661	729	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248561	8248561	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	58	795	0	ENST00000335790.3:c.326A>T	p.Tyr109Phe	p.Y109F	ENST00000335790	NM_002315.2	109	tAt/tTt	3/4	1	2	FACETS	0.785	0.673	0.907	0.785	0.673	0.907	CLONAL	1	TRUE	1	0.21417927374952	2		795	690	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426121	47426121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519786	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	331	417	0	ENST00000377045.4:c.641C>T	p.Ser214Phe	p.S214F	ENST00000377045	NM_001654.4	214	tCc/tTc	7/16	0.21417927374952	4	FACETS	1	0.987	1			1	CLONAL	6	TRUE	NA	0.21417927374952	4		417	580	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190956	185190956	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	71	742	0	ENST00000265026.3:c.1837G>A	p.Glu613Lys	p.E613K	ENST00000265026	NM_004721.4	613	Gaa/Aaa	11/14	0.168770313748264	4	FACETS	1	0.879	1	0.504	0.439	0.575	CLONAL	1	TRUE	2	0.21417927374952	4		742	798	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883998	37883998	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	96	810	0	ENST00000269571.5:c.3469C>G	p.Leu1157Val	p.L1157V	ENST00000269571		1157	Ctg/Gtg	27/27	0.168770313748264	4	FACETS	1	0.979	1	0.732	0.652	0.818	CLONAL	1	TRUE	2	0.21417927374952	4		810	743	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978330	2978330	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	155	713	0	ENST00000396946.4:c.1000G>C	p.Glu334Gln	p.E334Q	ENST00000396946	NM_032415.4	334	Gag/Cag	7/25	0.21417927374952	5	FACETS	0.847	0.776	0.92			1	CLONAL	3	TRUE	NA	0.21417927374952	5		713	753	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348371	89348371	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777979146	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	95	780	1	ENST00000301030.4:c.4579G>A	p.Asp1527Asn	p.D1527N	ENST00000301030	NM_001256183.1	1527	Gat/Aat	9/13	0.168770313748264	4	FACETS	1	0.979	1	0.734	0.653	0.82	CLONAL	1	TRUE	2	0.21417927374952	4		781	734	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602473	10602473	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	162	930	0	ENST00000171111.5:c.1105G>T	p.Val369Leu	p.V369L	ENST00000171111	NM_203500.1	369	Gtg/Ttg	3/6	0.18363892759477	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	0	0.21417927374952	2		930	749	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971098	21971098	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	103	516	0	ENST00000304494.5:c.260G>T	p.Arg87Leu	p.R87L	ENST00000304494	NM_000077.4	87	cGg/cTg	2/3	0.18363892759477	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	2	TRUE	0	0.21417927374952	2		516	467	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30103654	30103654	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs374628064	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	74	476	1	ENST00000331968.5:c.1284G>T	p.Trp428Cys	p.W428C	ENST00000331968	NM_002742.2	428	tgG/tgT	8/18	0.182182799156686	3	FACETS	0.753	0.661	0.852	0.753	0.661	0.852	SUBCLONAL	2	TRUE	1	0.21417927374952	3		477	508	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463296	25463296	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	127	477	0	ENST00000264709.3:c.2197G>C	p.Glu733Gln	p.E733Q	ENST00000264709	NM_175629.2	733	Gag/Cag	19/23	0.207199992732943	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.21417927374952	3		477	558	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299072	15299072	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs376728138	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	103	626	0	ENST00000263388.2:c.1466A>G	p.Asn489Ser	p.N489S	ENST00000263388	NM_000435.2	489	aAt/aGt	9/33	0.18363892759477	2	FACETS	0.876	0.786	0.97	0.876	0.786	0.97	CLONAL	2	TRUE	0	0.21417927374952	2		626	549	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478927	56478927	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	68	640	0	ENST00000267101.3:c.383G>T	p.Ser128Ile	p.S128I	ENST00000267101	NM_001982.3	128	aGc/aTc	3/28	0.182182799156686	3	FACETS	1	0.907	1	0.527	0.458	0.602	CLONAL	1	TRUE	1	0.21417927374952	3		640	667	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248683	212248683	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	97	433	0	ENST00000342788.4:c.3584C>G	p.Pro1195Arg	p.P1195R	ENST00000342788	NM_005235.2	1195	cCa/cGa	28/28	0.21417927374952	5	FACETS	0.901	0.807	0.999	0.901	0.807	0.999	CLONAL	3	TRUE	2	0.21417927374952	5		433	443	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969193	93969193	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	20	234	0	ENST00000369303.4:c.1803A>C	p.Lys601Asn	p.K601N	ENST00000369303	NM_004440.3	601	aaA/aaC	10/17	0.21417927374952	3	FACETS	0.811	0.621	1	0.405	0.31	0.516	CLONAL	1	TRUE	1	0.21417927374952	3		234	255	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012403	176012404	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AG	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	21	322	0	ENST00000367669.3:c.1531-1_1531delinsCT		p.X511_splice	ENST00000367669	NM_022457.5	511		14/20	0.21417927374952	3	FACETS	0.536	0.412	0.681	0.268	0.206	0.341	SUBCLONAL	1	TRUE	1	0.21417927374952	3		322	405	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648310	206648310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	60	641	0	ENST00000367120.3:c.331G>A	p.Glu111Lys	p.E111K	ENST00000367120	NM_014002.3	111	Gag/Aag	5/22	0.21417927374952	3	FACETS	0.954	0.822	1	0.477	0.411	0.55	CLONAL	1	TRUE	1	0.21417927374952	3		641	650	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192723	94192723	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	45	326	0	ENST00000323929.3:c.1351G>T	p.Glu451Ter	p.E451*	ENST00000323929	NM_005591.3	451	Gaa/Taa	13/20	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.21417927374952	2		326	380	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343490	118343490	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	39	372	1	ENST00000534358.1:c.1616G>T	p.Gly539Val	p.G539V	ENST00000534358	NM_005933.3	539	gGa/gTa	3/36	0.198924567515926	4	FACETS	0.983	0.815	1	0.491	0.407	0.585	CLONAL	1	TRUE	2	0.21417927374952	4		373	450	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81574742	81574742	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	24	302	0	ENST00000298171.2:c.638T>G	p.Leu213Arg	p.L213R	ENST00000298171	NM_000369.2	213	cTg/cGg	8/10	0.182182799156686	3	FACETS	0.745	0.584	0.93	0.373	0.292	0.465	CLONAL	1	TRUE	1	0.21417927374952	3		302	333	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571552	95571552	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	35	362	0	ENST00000393063.1:c.3125C>G	p.Pro1042Arg	p.P1042R	ENST00000393063	NM_030621.3	1042	cCa/cGa	21/28	0.182182799156686	3	FACETS	0.857	0.703	1	0.429	0.351	0.516	CLONAL	1	TRUE	1	0.21417927374952	3		362	422	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013741	12013741	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	69	241	0	ENST00000353533.5:c.683G>A	p.Arg228Lys	p.R228K	ENST00000353533	NM_003010.3	228	aGa/aAa	6/11	1	2	FACETS	0.928	0.814	1	1	0.98	1	CLONAL	2	TRUE	1	0.21417927374952	2		241	347	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422969	45422969	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	69	335	0	ENST00000262160.6:c.159G>C	p.Lys53Asn	p.K53N	ENST00000262160	NM_005901.5	53	aaG/aaC	2/11	0.21417927374952	3	FACETS	0.849	0.743	0.963	0.849	0.743	0.963	CLONAL	2	TRUE	1	0.21417927374952	3		335	420	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047360	128047360	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	76	391	0	ENST00000285398.2:c.562C>G	p.Leu188Val	p.L188V	ENST00000285398	NM_000122.1	188	Ctt/Gtt	5/15	0.168770313748264	4	FACETS	0.955	0.841	1	0.955	0.841	1	CLONAL	2	TRUE	2	0.21417927374952	4		391	451	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248588	212248588	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	57	477	0	ENST00000342788.4:c.3679C>G	p.Leu1227Val	p.L1227V	ENST00000342788	NM_005235.2	1227	Ctg/Gtg	28/28	0.21417927374952	5	FACETS	1	0.961	1	0.458	0.393	0.529	CLONAL	1	TRUE	2	0.21417927374952	5		477	512	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660301	227660301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	53	605	0	ENST00000305123.5:c.3154G>A	p.Glu1052Lys	p.E1052K	ENST00000305123	NM_005544.2	1052	Gag/Aag	1/2	0.21417927374952	5	FACETS	1	0.885	1	0.349	0.297	0.406	CLONAL	1	TRUE	2	0.21417927374952	5		605	625	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662074	227662074	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	227	678	0	ENST00000305123.5:c.1381G>C	p.Glu461Gln	p.E461Q	ENST00000305123	NM_005544.2	461	Gag/Cag	1/2	0.21417927374952	5	FACETS	0.963	0.901	1	1	0.989	1	CLONAL	4	TRUE	2	0.21417927374952	5		678	727	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546839	9546839	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	197	456	0	ENST00000353224.5:c.1183A>G	p.Ile395Val	p.I395V	ENST00000353224	NM_177990.2	395	Atc/Gtc	5/10	0.21417927374952	5	FACETS	0.933	0.871	0.996			1	CLONAL	5	TRUE	NA	0.21417927374952	5		456	521	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513603	41513603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	49	581	0	ENST00000263253.7:c.507G>A	p.Met169Ile	p.M169I	ENST00000263253	NM_001429.3	169	atG/atA	2/31	0.21417927374952	3	FACETS	0.926	0.784	1	0.463	0.392	0.541	CLONAL	1	TRUE	1	0.21417927374952	3		581	547	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623180	52623180	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	92	499	0	ENST00000394830.3:c.2871G>T	p.Met957Ile	p.M957I	ENST00000394830	NM_018313.4	957	atG/atT	19/30	0.212432154654316	2	FACETS	0.851	0.758	0.948	0.851	0.758	0.948	CLONAL	2	TRUE	0	0.21417927374952	2		499	505	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498450	89498450	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	28	299	0	ENST00000336596.2:c.2422T>A	p.Trp808Arg	p.W808R	ENST00000336596	NM_005233.5	808	Tgg/Agg	14/17	0.212432154654316	2	FACETS	0.849	0.68	1	0.424	0.34	0.521	CLONAL	1	TRUE	0	0.21417927374952	2		299	308	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911651	134911651	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	44	333	0	ENST00000398015.3:c.2116G>T	p.Asp706Tyr	p.D706Y	ENST00000398015	NM_004441.4	706	Gat/Tat	11/16	0.168770313748264	4	FACETS	0.821	0.692	0.962	0.821	0.692	0.962	CLONAL	2	TRUE	2	0.21417927374952	4		333	304	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127285	55127285	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	85	417	0	ENST00000257290.5:c.73C>G	p.Leu25Val	p.L25V	ENST00000257290	NM_006206.4	25	Ctt/Gtt	3/23	0.21417927374952	3	FACETS	0.979	0.869	1	0.979	0.869	1	CLONAL	2	TRUE	1	0.21417927374952	3		417	449	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956145	55956145	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	82	426	0	ENST00000263923.4:c.3170C>A	p.Pro1057Gln	p.P1057Q	ENST00000263923	NM_002253.2	1057	cCa/cAa	23/30	0.21417927374952	3	FACETS	1	0.977	1	0.737	0.651	0.829	CLONAL	1	TRUE	1	0.21417927374952	3		426	575	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532737	187532737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	41	401	0	ENST00000441802.2:c.9656C>T	p.Ser3219Leu	p.S3219L	ENST00000441802	NM_005245.3	3219	tCa/tTa	14/27	0.21417927374952	3	FACETS	0.814	0.677	0.965	0.407	0.338	0.483	CLONAL	1	TRUE	1	0.21417927374952	3		401	521	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630710	187630710	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	39	507	0	ENST00000441802.2:c.272G>C	p.Gly91Ala	p.G91A	ENST00000441802	NM_005245.3	91	gGa/gCa	2/27	0.21417927374952	3	FACETS	0.775	0.642	0.924	0.388	0.321	0.462	CLONAL	1	TRUE	1	0.21417927374952	3		507	520	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295226	1295226	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	110	251	0				ENST00000310581	NM_198253.2	-/1132			0.21417927374952	3	FACETS	1	0.96	1	1	0.987	1	CLONAL	3	TRUE	1	0.21417927374952	3		251	343	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522696	176522696	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	69	851	0	ENST00000292408.4:c.1793G>T	p.Arg598Leu	p.R598L	ENST00000292408	NM_213647.1	598	cGa/cTa	13/18	0.21417927374952	3	FACETS	1	0.883	1	0.508	0.442	0.58	CLONAL	1	TRUE	1	0.21417927374952	3		851	702	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394938	394938	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	76	446	0	ENST00000380956.4:c.334G>C	p.Glu112Gln	p.E112Q	ENST00000380956	NM_001195286.1	112	Gag/Cag	3/9	0.21417927374952	3	FACETS	1	0.969	1			1	CLONAL	1	TRUE	NA	0.21417927374952	3		446	587	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480092	20480092	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	83	351	0	ENST00000346618.3:c.409G>C	p.Glu137Gln	p.E137Q	ENST00000346618	NM_001949.4	137	Gag/Cag	2/7	0.21417927374952	5	FACETS	1	0.964	1	0.815	0.723	0.912	CLONAL	2	TRUE	2	0.21417927374952	5		351	419	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287890	33287890	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	151	466	0	ENST00000374542.5:c.1363G>C	p.Glu455Gln	p.E455Q	ENST00000374542	NM_001141970.1	455	Gag/Cag	5/8	0.21417927374952	5	FACETS	1	0.975	1	1	0.99	1	CLONAL	3	TRUE	3	0.21417927374952	5		466	541	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111995807	111995807	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	34	440	0	ENST00000368678.4:c.1291G>T	p.Ala431Ser	p.A431S	ENST00000368678		431	Gcc/Tcc	12/13	0.21417927374952	3	FACETS	0.808	0.66	0.974	0.404	0.33	0.487	CLONAL	1	TRUE	1	0.21417927374952	3		440	435	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285479	38285479	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	91	508	0	ENST00000425967.3:c.674del	p.Gly225AlafsTer23	p.G225Afs*23	ENST00000425967	NM_001174067.1	225	gGc/gc	6/19	0.18363892759477	2	FACETS	0.796	0.708	0.888	0.796	0.708	0.888	SUBCLONAL	2	TRUE	0	0.21417927374952	2		508	534	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965473	90965473	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	52	257	0	ENST00000265433.3:c.1844C>G	p.Ser615Cys	p.S615C	ENST00000265433	NM_002485.4	615	tCt/tGt	11/16	0.21417927374952	5	FACETS	1	0.916	1	0.732	0.628	0.845	CLONAL	2	TRUE	2	0.21417927374952	5		257	292	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755916	133755916	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	91	597	0	ENST00000318560.5:c.1543G>T	p.Val515Phe	p.V515F	ENST00000318560	NM_005157.4	515	Gtc/Ttc	10/11	0.18363892759477	2	FACETS	0.893	0.796	0.995	0.893	0.796	0.995	CLONAL	2	TRUE	0	0.21417927374952	2		597	476	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793591	89793591	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs757427555	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	57	280	0	ENST00000336032.3:c.660G>T	p.Leu220Phe	p.L220F	ENST00000336032	NM_006813.2	220	ttG/ttT	2/2	0.21417927374952	3	FACETS	0.915	0.79	1	0.915	0.79	1	CLONAL	2	TRUE	1	0.21417927374952	3		280	322	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012403	176012403	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	21	322	0	ENST00000367669.3:c.1531G>T	p.Glu511Ter	p.E511*	ENST00000367669	NM_022457.5	511	Gag/Tag	14/20	0.21417927374952	3	FACETS	0.536	0.412	0.681	0.268	0.206	0.341	SUBCLONAL	1	TRUE	1	0.21417927374952	3		322	405	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012404	176012404	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0049029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	21	306	0	ENST00000367669.3:c.1531-1G>C		p.X511_splice	ENST00000367669	NM_022457.5	511			0.21417927374952	3	FACETS	0.565	0.435	0.718	0.283	0.217	0.359	SUBCLONAL	1	TRUE	1	0.21417927374952	3		306	384	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0049030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	18	423	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.215564209967908	3	FACETS	1	0.791	1	0.52	0.397	0.662	CLONAL	1	FALSE	1	0.357759326345753	3		423	114	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936072	44936072	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1135401809	NA	P-0049030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	24	165	0	ENST00000377967.4:c.2832+1G>A		p.X944_splice	ENST00000377967	NM_021140.2	944			1	1	FACETS	0.984	0.808	1	1	0.955	1	CLONAL	2	FALSE	0	0.357759326345753	1		165	56	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974696	21974697	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	10	365	0	ENST00000304494.5:c.130dup	p.Tyr44LeufsTer76	p.Y44Lfs*76	ENST00000304494	NM_000077.4	44	tac/tTac	1/3	0.340715277047366	0	FACETS	0.552	0.381	0.759			1	SUBCLONAL	1	FALSE	0	0.357759326345753	0		365	65	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578220	7578220	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	14	496	0	ENST00000269305.4:c.629del	p.Asn210ThrfsTer37	p.N210Tfs*37	ENST00000269305	NM_001126112.2	210	aAc/ac	6/11	1	2	FACETS	0.824	0.604	1	0.824	0.604	1	CLONAL	1	FALSE	1	0.357759326345753	2		496	95	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0049031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	286	402	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.812246492181759	2		402	682	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199881	108199881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881315	NA	P-0049031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	24	192	0	ENST00000278616.4:c.7223C>T	p.Ser2408Leu	p.S2408L	ENST00000278616	NM_000051.3	2408	tCg/tTg	49/63	1	2	FACETS	0.213	0.167	0.265	0.213	0.167	0.265	SUBCLONAL	1	TRUE	1	0.812246492181759	2		192	278	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941643	48941643	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs886050271	NA	P-0049031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	29	157	0	ENST00000267163.4:c.953C>G	p.Ser318Cys	p.S318C	ENST00000267163	NM_000321.2	318	tCt/tGt	10/27	1	2	FACETS	0.254	0.204	0.31	0.254	0.204	0.31	SUBCLONAL	1	TRUE	1	0.812246492181759	2		157	281	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132428	11132428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	383	774	0	ENST00000358026.2:c.2644G>A	p.Glu882Lys	p.E882K	ENST00000358026	NM_001128849.1	882	Gaa/Aaa	19/36	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.812246492181759	2		774	926	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831357	72831358	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTG	rs34918837	NA	P-0049031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	107	353	0	ENST00000268489.5:c.5221_5223dup	p.Gln1741dup	p.Q1741dup	ENST00000268489	NM_006885.3	1741	-/CAA	9/10	1	2	FACETS	0.591	0.533	0.651	0.591	0.533	0.651	SUBCLONAL	1	TRUE	1	0.812246492181759	2		353	446	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151893043	151893043	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1406863036	NA	P-0049031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	49	305	0	ENST00000262189.6:c.4327G>A	p.Asp1443Asn	p.D1443N	ENST00000262189	NM_170606.2	1443	Gac/Aac	28/59	1	2	FACETS	0.309	0.262	0.361	0.309	0.262	0.361	SUBCLONAL	1	TRUE	1	0.812246492181759	2		305	390	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431797	49431798	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0049031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	69	665	0	ENST00000301067.7:c.9341_9342del	p.Val3114AlafsTer3	p.V3114Afs*3	ENST00000301067	NM_003482.3	3114	gTG/g	34/54	1	2	FACETS	0.211	0.183	0.241	0.211	0.183	0.241	SUBCLONAL	1	TRUE	1	0.812246492181759	2		665	807	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186618	108186618	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	30	256	0	ENST00000278616.4:c.6075G>T	p.Lys2025Asn	p.K2025N	ENST00000278616	NM_000051.3	2025	aaG/aaT	41/63	1	2	FACETS	0.206	0.166	0.251	0.206	0.166	0.251	SUBCLONAL	1	TRUE	1	0.812246492181759	2		256	359	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779809	3779810	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	382	708	0	ENST00000262367.5:c.5238dup	p.Leu1747AlafsTer5	p.L1747Afs*5	ENST00000262367	NM_004380.2	1746	-/G	31/31	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.812246492181759	2		708	885	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277897	41277898	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0049031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	164	298	0	ENST00000349496.5:c.1862_1863dup	p.Ala622LeufsTer20	p.A622Lfs*20	ENST00000349496	NM_001904.3	621	ctt/cTTtt	12/15	1	2	FACETS	0.964	0.895	1	0.964	0.895	1	CLONAL	1	TRUE	1	0.812246492181759	2		298	419	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455536	189455536	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	198	362	0	ENST00000264731.3:c.70G>C	p.Glu24Gln	p.E24Q	ENST00000264731	NM_003722.4	24	Gaa/Caa	2/14	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.812246492181759	2		362	466	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969329	44969329	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	139	141	0	ENST00000377967.4:c.4012del	p.Val1338PhefsTer18	p.V1338Ffs*18	ENST00000377967	NM_021140.2	1337	gaG/ga	28/29	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.812246492181759	1		141	179	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181278	123181279	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATGAAGCAGAACGGAATAAAATG	novel	NA	P-0049031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	73	118	0	ENST00000218089.9:c.745_767dup	p.Ile256MetfsTer8	p.I256Mfs*8	ENST00000218089	NM_001042749.1	248	tat/tATGAAGCAGAACGGAATAAAATGat	9/35	1	1	FACETS	0.596	0.533	0.661	0.596	0.533	0.661	SUBCLONAL	1	TRUE	0	0.812246492181759	1		118	179	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481417	140481417	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913348	NA	P-0049032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	32	284	0	ENST00000288602.6:c.1391G>T	p.Gly464Val	p.G464V	ENST00000288602	NM_004333.4	464	gGa/gTa	11/18	1	2	FACETS	0.659	0.534	0.8	0.659	0.534	0.8	SUBCLONAL	1	TRUE	1	0.218247346981777	2		284	445	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696405	47696405	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	35	374	0	ENST00000347630.2:c.418G>T	p.Asp140Tyr	p.D140Y	ENST00000347630	NM_001007230.1	140	Gat/Tat	6/11	0.218247346981777	3	FACETS	0.554	0.453	0.668	0.277	0.226	0.334	SUBCLONAL	1	TRUE	1	0.218247346981777	3		374	642	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372701	81372701	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	23	299	0	ENST00000222390.5:c.833C>A	p.Thr278Asn	p.T278N	ENST00000222390	NM_000601.4	278	aCc/aAc	7/18	1	2	FACETS	0.487	0.379	0.612	0.487	0.379	0.612	SUBCLONAL	1	TRUE	1	0.218247346981777	2		299	433	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409887	63409887	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	67	455	0	ENST00000330258.3:c.3280C>A	p.His1094Asn	p.H1094N	ENST00000330258	NM_152424.3	1094	Cac/Aac	2/2	1	2	FACETS	0.998	0.868	1	0.998	0.868	1	CLONAL	1	TRUE	1	0.218247346981777	2		455	615	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797129	45797129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	89	698	0	ENST00000450313.1:c.1286G>A	p.Gly429Glu	p.G429E	ENST00000450313	NM_012222.2	429	gGg/gAg	13/16	0.218247346981777	3	FACETS	0.785	0.694	0.883	0.262	0.231	0.295	SUBCLONAL	1	TRUE	0	0.218247346981777	3		698	1152	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115252290	115252290	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	139	307	0	ENST00000369535.4:c.350A>T	p.Lys117Met	p.K117M	ENST00000369535	NM_002524.4	117	aAg/aTg	4/7	0.218247346981777	3	FACETS	0.879	0.804	0.956	0.879	0.804	0.956	CLONAL	3	TRUE	0	0.218247346981777	3		307	536	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911911	94911911	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	83	359	0	ENST00000536441.1:c.1019G>T	p.Arg340Ile	p.R340I	ENST00000536441	NM_144665.3	340	aGa/aTa	7/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.218247346981777	2		359	594	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920707	100920707	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	68	337	1	ENST00000325455.5:c.2441G>T	p.Ser814Ile	p.S814I	ENST00000325455	NM_001202474.3	814	aGc/aTc	6/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.218247346981777	2		338	466	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576134	29576134	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	95	295	0	ENST00000356175.3:c.4107C>A	p.Tyr1369Ter	p.Y1369*	ENST00000356175	NM_000267.3	1369	taC/taA	30/57	0.218247346981777	3	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	1	0.218247346981777	3		295	444	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664963	138664963	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	78	230	0	ENST00000330315.3:c.602A>G	p.Asn201Ser	p.N201S	ENST00000330315	NM_023067.3	201	aAc/aGc	1/1	0.110500499504456	4	FACETS	1	0.956	1	1	0.956	1	INDETERMINATE	2	TRUE	2	0.218247346981777	4		230	372	SUCCESS
ATR	545	MSKCC	GRCh37	3	142222259	142222259	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	102	313	0	ENST00000350721.4:c.5233G>T	p.Gly1745Cys	p.G1745C	ENST00000350721	NM_001184.3	1745	Ggt/Tgt	30/47	0.110500499504456	4	FACETS	1	0.916	1	1	0.916	1	INDETERMINATE	2	TRUE	2	0.218247346981777	4		313	556	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1918615	1918615	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	75	312	0	ENST00000382891.5:c.778C>G	p.Arg260Gly	p.R260G	ENST00000382891	NM_133335.3	260	Cgc/Ggc	4/22	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.218247346981777	2		312	515	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55570008	55570008	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	39	263	0	ENST00000288135.5:c.875C>G	p.Ala292Gly	p.A292G	ENST00000288135	NM_000222.2	292	gCc/gGc	5/21	0.218247346981777	1	FACETS	0.892	0.741	1	0.892	0.741	1	CLONAL	1	TRUE	0	0.218247346981777	1		263	357	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067040	143067040	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs753099355	NA	P-0049032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	47	311	0	ENST00000262992.4:c.1673G>T	p.Gly558Val	p.G558V	ENST00000262992	NM_001101669.1	558	gGa/gTa	16/24	0.218247346981777	1	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	0	0.218247346981777	1		311	383	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754893	57754893	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	55	233	0	ENST00000274289.3:c.297G>A	p.Met99Ile	p.M99I	ENST00000274289	NM_006622.3	99	atG/atA	2/14	0.209000503594624	2	FACETS	1	0.962	1	0.698	0.6	0.805	CLONAL	1	TRUE	0	0.218247346981777	2		233	361	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984012	2984012	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	53	550	0	ENST00000396946.4:c.518T>A	p.Leu173Gln	p.L173Q	ENST00000396946	NM_032415.4	173	cTg/cAg	5/25	0.218247346981777	3	FACETS	0.658	0.559	0.766	0.329	0.279	0.383	SUBCLONAL	1	TRUE	1	0.218247346981777	3		550	819	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835937	151835937	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	29	313	0	ENST00000262189.6:c.14587G>C	p.Glu4863Gln	p.E4863Q	ENST00000262189	NM_170606.2	4863	Gag/Cag	58/59	1	2	FACETS	0.502	0.402	0.617	0.502	0.402	0.617	SUBCLONAL	1	TRUE	1	0.218247346981777	2		313	529	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759354	133759354	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0049032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	48	406	0	ENST00000318560.5:c.1679-2A>T		p.X560_splice	ENST00000318560	NM_005157.4	560			1	2	FACETS	0.687	0.58	0.806	0.687	0.58	0.806	SUBCLONAL	1	TRUE	1	0.218247346981777	2		406	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0049033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	412	655	1	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.685482727098079	1	FACETS	0.903	0.864	0.941	0.903	0.864	0.941	CLONAL	1	TRUE	0	0.687669198651672	1		656	871	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450847	70450847	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	272	376	0	ENST00000373644.4:c.5687C>A	p.Ala1896Asp	p.A1896D	ENST00000373644	NM_030625.2	1896	gCt/gAt	12/12	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.687669198651672	2		376	705	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231701	66231701	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	156	294	1	ENST00000273854.3:c.1999G>T	p.Ala667Ser	p.A667S	ENST00000273854	NM_004439.5	667	Gct/Tct	11/18	1	2	FACETS	0.917	0.846	0.99	0.917	0.846	0.99	CLONAL	1	TRUE	1	0.687669198651672	2		295	495	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0049034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	48	346	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.18	2		346	468	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844415	156844416	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0049034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	66	745	0	ENST00000524377.1:c.1251+1dup		p.-416fs	ENST00000524377	NM_002529.3	416	-/G	10/17	1	2	FACETS	0.744	0.644	0.853	0.744	0.644	0.853	SUBCLONAL	1	TRUE	1	0.18	2		745	986	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383313	4383313	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	85	637	0	ENST00000261254.3:c.107G>T	p.Arg36Leu	p.R36L	ENST00000261254	NM_001759.3	36	cGc/cTc	1/5	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.18	2		637	841	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345265	73345265	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	25	241	0	ENST00000377767.4:c.1624G>T	p.Glu542Ter	p.E542*	ENST00000377767	NM_014953.3	542	Gag/Tag	12/21	1	2	FACETS	0.782	0.617	0.973	0.782	0.617	0.973	CLONAL	1	TRUE	1	0.18	2		241	355	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0049034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	47	538	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	1	2	FACETS	0.724	0.61	0.851	0.724	0.61	0.851	SUBCLONAL	1	TRUE	1	0.18	2		538	721	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385182	41385182	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs367872006	NA	P-0049034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	121	648	0	ENST00000373198.4:c.779G>T	p.Arg260Leu	p.R260L	ENST00000373198	NM_133170.3	260	cGg/cTg	6/32	1	2	FACETS	0.813	0.734	0.896	1	0.986	1	CLONAL	2	TRUE	1	0.18	2		648	827	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259238	89259238	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	36	340	0	ENST00000336596.2:c.382G>T	p.Asp128Tyr	p.D128Y	ENST00000336596	NM_005233.5	128	Gat/Tat	3/17	1	2	FACETS	0.862	0.708	1	0.862	0.708	1	CLONAL	1	TRUE	1	0.18	2		340	464	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178941899	178941899	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	22	307	0	ENST00000263967.3:c.2218A>T	p.Arg740Trp	p.R740W	ENST00000263967	NM_006218.2	740	Agg/Tgg	15/21	1	2	FACETS	0.59	0.457	0.746	0.59	0.457	0.746	SUBCLONAL	1	TRUE	1	0.18	2		307	414	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372780	81372780	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	29	295	0	ENST00000222390.5:c.754del	p.Asp252ThrfsTer42	p.D252Tfs*42	ENST00000222390	NM_000601.4	252	Gac/ac	7/18	1	2	FACETS	0.704	0.564	0.863	0.704	0.564	0.863	SUBCLONAL	1	TRUE	1	0.18	2		295	458	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482873	140482873	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	43	455	0	ENST00000288602.6:c.1262G>C	p.Gly421Ala	p.G421A	ENST00000288602	NM_004333.4	421	gGa/gCa	10/18	1	2	FACETS	0.705	0.588	0.834	0.705	0.588	0.834	SUBCLONAL	1	TRUE	1	0.18	2		455	678	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879309	151879309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745965490	NA	P-0049034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	38	389	0	ENST00000262189.6:c.5636C>T	p.Pro1879Leu	p.P1879L	ENST00000262189	NM_170606.2	1879	cCg/cTg	36/59	1	2	FACETS	0.724	0.598	0.866	0.724	0.598	0.866	SUBCLONAL	1	TRUE	1	0.18	2		389	583	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965708	90965708	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	39	274	0	ENST00000265433.3:c.1609A>T	p.Ser537Cys	p.S537C	ENST00000265433	NM_002485.4	537	Agt/Tgt	11/16	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.18	2		274	401	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354281	70354281	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	76	750	0	ENST00000374080.3:c.4692C>G	p.Ile1564Met	p.I1564M	ENST00000374080		1564	atC/atG	34/45	1	2	FACETS	0.911	0.797	1	0.911	0.797	1	CLONAL	1	TRUE	1	0.18	2		750	927	SUCCESS
APC	324	MSKCC	GRCh37	5	112175530	112175530	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	164	229	0	ENST00000257430.4:c.4240del	p.Val1414Ter	p.V1414*	ENST00000257430	NM_000038.5	1413	atG/at	16/16	1	2	FACETS	0.973	0.907	1	0.973	0.907	1	CLONAL	1	TRUE	1	0.931008215560028	2		229	362	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0049036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	94	400	2	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.529044665537602	1	FACETS	0.683	0.629	0.736	0.683	0.629	0.736	INDETERMINATE	1	TRUE	0	0.931008215560028	1		402	158	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0049036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	240	426	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.931008215560028	2		426	510	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0049036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	70	239	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.946	0.847	1	0.946	0.847	1	CLONAL	1	TRUE	1	0.931008215560028	2		239	159	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578217	7578217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	391	511	0	ENST00000269305.4:c.632C>T	p.Thr211Ile	p.T211I	ENST00000269305	NM_001126112.2	211	aCt/aTt	6/11	0.931008215560028	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.931008215560028	1		511	442	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953890	17953890	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764890523	NA	P-0049036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	778	639	1	ENST00000458235.1:c.512C>T	p.Ala171Val	p.A171V	ENST00000458235	NM_000215.3	171	gCc/gTc	5/24	1	2	FACETS	0.993	0.962	1	0.993	0.962	1	CLONAL	1	TRUE	1	0.931008215560028	2		640	1683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0049037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	366	632	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.413544636094264	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.413544636094264	2		632	876	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100282	8100282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	153	686	0	ENST00000346208.3:c.256C>T	p.Arg86Cys	p.R86C	ENST00000346208		86	Cgc/Tgc	3/6	0.265769241605328	1	FACETS	0.846	0.776	0.919	0.846	0.776	0.919	CLONAL	1	TRUE	0	0.413544636094264	1		686	694	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0049037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	132	350	2	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.413544636094264	2	FACETS	0.902	0.829	0.976	0.902	0.829	0.976	CLONAL	2	TRUE	0	0.413544636094264	2		352	354	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845549	72845551	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs763986819	NA	P-0049037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	70	545	0	ENST00000268489.5:c.3789_3791del	p.Asn1263del	p.N1263del	ENST00000268489	NM_006885.3	1263	aaCAAg/aag	7/10	0.408490378044611	3	FACETS	0.382	0.332	0.436	0.191	0.166	0.218	SUBCLONAL	1	TRUE	1	0.413544636094264	3		545	1070	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436342	52436342	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1186981831	NA	P-0049037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	194	634	1	ENST00000460680.1:c.2152C>T	p.Arg718Trp	p.R718W	ENST00000460680	NM_004656.3	718	Cgg/Tgg	17/17	0.194826860394062	3	FACETS	1	0.962	1	0.532	0.491	0.573	INDETERMINATE	1	TRUE	1	0.413544636094264	3		635	1065	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746132	162746132	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	84	231	0	ENST00000367921.3:c.2255G>T	p.Arg752Leu	p.R752L	ENST00000367921	NM_006182.2	752	cGc/cTc	16/18	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.413544636094264	2		231	362	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316393	14316393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1160017680	NA	P-0049037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	121	363	0	ENST00000256196.4:c.212G>A	p.Gly71Glu	p.G71E	ENST00000256196		71	gGa/gAa	3/6	0.258232300291274	3	FACETS	1	0.958	1			1	CLONAL	1	TRUE	NA	0.413544636094264	3		363	641	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117934	70117935	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTCA	novel	NA	P-0049037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	306	413	0	ENST00000245479.2:c.403_406dup	p.Ser136ThrfsTer117	p.S136Tfs*117	ENST00000245479	NM_000346.3	134	-/CTCA	1/3	0.20480851822723	3	FACETS	1	0.991	1	0.796	0.754	0.838	INDETERMINATE	2	TRUE	0	0.413544636094264	3		413	748	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566703	212566703	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	31	217	0	ENST00000342788.4:c.1478C>G	p.Ala493Gly	p.A493G	ENST00000342788	NM_005235.2	493	gCt/gGt	12/28	NA	2	FACETS	0.421	0.341	0.512			1	INDETERMINATE	1	TRUE	NA	0.413544636094264	2		217	356	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403459	139403459	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776957107	NA	P-0049037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	141	831	0	ENST00000277541.6:c.3034G>A	p.Gly1012Ser	p.G1012S	ENST00000277541	NM_017617.3	1012	Ggc/Agc	19/34	0.210147911360788	2	FACETS	0.563	0.511	0.617	0.281	0.255	0.309	INDETERMINATE	1	TRUE	0	0.413544636094264	2		831	1212	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	22	431	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.3	1	FACETS	0.552	0.427	0.696	0.552	0.427	0.696	SUBCLONAL	1	TRUE	0	0.21	1		431	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934574	NA	P-0049038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	50	555	0	ENST00000269305.4:c.844C>G	p.Arg282Gly	p.R282G	ENST00000269305	NM_001126112.2	282	Cgg/Ggg	8/11	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.21	2		555	457	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637606	52637620	+	frameshift_variant	Frame_Shift_Del	DEL	TCTCCACATCATTAT	TCTCCACATCATTAT	AA	novel	NA	P-0049038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	26	394	1	ENST00000394830.3:c.2696_2710delinsTT	p.His899LeufsTer12	p.H899Lfs*12	ENST00000394830	NM_018313.4	899	cATAATGATGTGGAGAaa/cTTaa	18/30	1	2	FACETS	0.762	0.604	0.943	0.762	0.604	0.943	CLONAL	1	TRUE	1	0.21	2		395	325	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	13	431	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		431	559	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123159713	123159713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	78	275	0	ENST00000218089.9:c.68C>T	p.Ser23Phe	p.S23F	ENST00000218089	NM_001042749.1	23	tCt/tTt	4/35	0.761547285821516	1	FACETS	0.529	0.471	0.588	0.529	0.471	0.588	SUBCLONAL	1	TRUE	0	0.761547285821516	1		275	240	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041117	42041117	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747757361	NA	P-0049040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	71	370	0	ENST00000219905.7:c.5495G>C	p.Arg1832Pro	p.R1832P	ENST00000219905	NM_001164273.1	1832	cGg/cCg	16/24	0.386347775767846	3	FACETS	0.446	0.39	0.507	0.149	0.13	0.169	INDETERMINATE	1	TRUE	0	0.761547285821516	3		370	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578447	+	inframe_deletion	In_Frame_Del	DEL	GACTGCTTGTAGATG	GACTGCTTGTAGATG	-	novel	NA	P-0049040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	572	662	0	ENST00000269305.4:c.483_497del	p.Ile162_Ser166del	p.I162_S166del	ENST00000269305	NM_001126112.2	161	gcCATCTACAAGCAGTCa/gca	5/11	0.761547285821516	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.761547285821516	2		662	730	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680817	30680817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	75	420	0	ENST00000376406.3:c.902C>T	p.Thr301Ile	p.T301I	ENST00000376406	NM_014641.2	301	aCa/aTa	5/15	0.386347775767846	3	FACETS	0.511	0.449	0.578	0.17	0.149	0.193	INDETERMINATE	1	TRUE	0	0.761547285821516	3		420	532	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347666	89347666	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	129	512	0	ENST00000301030.4:c.5284G>T	p.Asp1762Tyr	p.D1762Y	ENST00000301030	NM_001256183.1	1762	Gac/Tac	9/13	1	2	FACETS	0.493	0.447	0.541	0.493	0.447	0.541	SUBCLONAL	1	TRUE	1	0.698090509995306	2		512	750	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349097	89349097	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	152	613	0	ENST00000301030.4:c.3853G>T	p.Glu1285Ter	p.E1285*	ENST00000301030	NM_001256183.1	1285	Gaa/Taa	9/13	1	2	FACETS	0.472	0.431	0.514	0.472	0.431	0.514	SUBCLONAL	1	TRUE	1	0.698090509995306	2		613	923	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	120	148	0				ENST00000310581	NM_198253.2	-/1132			0.553571880525064	3	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	1	0.553571880525064	3		148	273	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166231	118166231	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	36	291	0	ENST00000369448.3:c.741C>A	p.Tyr247Ter	p.Y247*	ENST00000369448	NM_017709.3	247	taC/taA	2/2	0.197505559612904	0	FACETS	0.241	0.199	0.287			1	INDETERMINATE	1	TRUE	0	0.553571880525064	0		291	241	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121773	108121773	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	39	300	0	ENST00000278616.4:c.1581T>G	p.Phe527Leu	p.F527L	ENST00000278616	NM_000051.3	527	ttT/ttG	10/63	0.281152264844033	2	FACETS	0.407	0.338	0.484	0.204	0.169	0.242	INDETERMINATE	1	TRUE	0	0.553571880525064	2		300	346	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0049045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	92	346	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.242686626471041	1	FACETS	0.49	0.436	0.548	0.49	0.436	0.548	INDETERMINATE	1	FALSE	0	0.461040629901295	1		346	627	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143269	24143269	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0049045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	227	588	0	ENST00000263121.7:c.500+1G>T		p.X167_splice	ENST00000263121	NM_003073.3	167			0.461040629901295	1	FACETS	0.973	0.909	1	0.973	0.909	1	CLONAL	1	FALSE	0	0.461040629901295	1		588	779	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922293	100922293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149186732	NA	P-0049045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	43	218	0	ENST00000325455.5:c.2219G>A	p.Arg740Gln	p.R740Q	ENST00000325455	NM_001202474.3	740	cGa/cAa	5/8	0.242686626471041	1	FACETS	0.377	0.316	0.444	0.377	0.316	0.444	INDETERMINATE	1	FALSE	0	0.461040629901295	1		218	381	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222987	1222987	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	177	424	0	ENST00000326873.7:c.924G>T	p.Trp308Cys	p.W308C	ENST00000326873	NM_000455.4	308	tgG/tgT	8/10	0.461040629901295	1	FACETS	0.962	0.891	1	0.962	0.891	1	CLONAL	1	FALSE	0	0.461040629901295	1		424	614	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117423	115117423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	99	257	0	ENST00000257566.3:c.751C>T	p.Arg251Trp	p.R251W	ENST00000257566	NM_016569.3	251	Cgg/Tgg	4/8	0.242686626471041	1	FACETS	0.705	0.632	0.781	0.705	0.632	0.781	INDETERMINATE	1	FALSE	0	0.461040629901295	1		257	469	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742476	17742476	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	221	583	0	ENST00000250003.3:c.658G>C	p.Ala220Pro	p.A220P	ENST00000250003	NM_002478.4	220	Gcc/Ccc	2/3	0.242686626471041	1	FACETS	0.855	0.797	0.915	0.855	0.797	0.915	INDETERMINATE	1	FALSE	0	0.461040629901295	1		583	863	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343835	118343835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782450420	NA	P-0049045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	173	391	0	ENST00000534358.1:c.1961C>T	p.Pro654Leu	p.P654L	ENST00000534358	NM_005933.3	654	cCt/cTt	3/36	0.461040629901295	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	FALSE	0	0.461040629901295	1		391	569	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877494	28877494	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	101	288	0	ENST00000282397.4:c.3827C>G	p.Thr1276Ser	p.T1276S	ENST00000282397	NM_002019.4	1276	aCc/aGc	30/30	0.461040629901295	1	FACETS	0.86	0.775	0.949	0.86	0.775	0.949	CLONAL	1	FALSE	0	0.461040629901295	1		288	392	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602421	10602421	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	285	690	0	ENST00000171111.5:c.1157del	p.Gly386AlafsTer14	p.G386Afs*14	ENST00000171111	NM_203500.1	386	gGc/gc	3/6	0.461040629901295	1	FACETS	0.968	0.911	1	0.968	0.911	1	CLONAL	1	FALSE	0	0.461040629901295	1		690	983	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312978	30312978	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	194	459	2	ENST00000262643.3:c.781G>T	p.Asp261Tyr	p.D261Y	ENST00000262643	NM_001238.2	261	Gac/Tac	9/12	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	1	0.461040629901295	2		461	822	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92300796	92300797	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0049045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	99	353	2	ENST00000265734.4:c.590_591delinsAA	p.Ala197Glu	p.A197E	ENST00000265734	NM_001259.6	197	gCC/gAA	5/8	1	2	FACETS	0.753	0.674	0.837	0.753	0.674	0.837	SUBCLONAL	1	FALSE	1	0.461040629901295	2		355	570	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499687	8499687	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	165	380	0	ENST00000356435.5:c.2282del	p.Gly761AlafsTer5	p.G761Afs*5	ENST00000356435		761	gGc/gc	14/35	0.461040629901295	1	FACETS	0.955	0.881	1	0.955	0.881	1	CLONAL	1	FALSE	0	0.461040629901295	1		380	577	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0049046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	600	698	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.61609897914732	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.61609897914732	3		698	819	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0049046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	162	572	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	1	2	FACETS	0.888	0.819	0.96	0.888	0.819	0.96	CLONAL	1	TRUE	1	0.61609897914732	2		572	592	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094309	193094309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748952219	NA	P-0049046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	64	300	0	ENST00000367435.3:c.199G>A	p.Val67Met	p.V67M	ENST00000367435	NM_024529.4	67	Gtg/Atg	2/17	0.61609897914732	3	FACETS	0.937	0.819	1	0.469	0.409	0.532	CLONAL	1	TRUE	1	0.61609897914732	3		300	290	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519920	NA	P-0049046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	58	190	0	ENST00000397062.3:c.85G>A	p.Asp29Asn	p.D29N	ENST00000397062	NM_006164.4	29	Gat/Aat	2/5	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.61609897914732	2		190	156	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	145	562	0	ENST00000269305.4:c.548C>A	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tAa	5/11	1	2	FACETS	0.877	0.804	0.952	0.877	0.804	0.952	CLONAL	1	TRUE	1	0.61609897914732	2		562	537	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0049048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	124	261	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.56	2		261	378	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913237	NA	P-0049048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	462	270	0	ENST00000369535.4:c.35G>T	p.Gly12Val	p.G12V	ENST00000369535	NM_002524.4	12	gGt/gTt	2/7	0.558060304911149	4	FACETS	1	0.978	1			1	CLONAL	3	TRUE	NA	0.56	4		270	839	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192470	138192470	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	145	221	0	ENST00000237289.4:c.106A>G	p.Ile36Val	p.I36V	ENST00000237289	NM_001270507.1	36	Atc/Gtc	2/9	0.558060304911149	1	FACETS	0.984	0.909	1	0.984	0.909	1	CLONAL	1	TRUE	0	0.56	1		221	379	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0049049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	83	325	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	0.931	0.825	1	1	0.983	1	CLONAL	2	TRUE	1	0.19	2		325	469	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552696	18552696	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1023238256	NA	P-0049049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	36	482	1	ENST00000266497.5:c.2107G>A	p.Glu703Lys	p.E703K	ENST00000266497		703	Gaa/Aaa	14/31	0.199776598519443	0	FACETS	0.706	0.58	0.846			1	SUBCLONAL	1	TRUE	0	0.19	0		483	435	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033971	49033971	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0049049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	18	251	0	ENST00000267163.4:c.2106+2T>G		p.X702_splice	ENST00000267163	NM_000321.2	702			1	2	FACETS	0.538	0.405	0.697	0.538	0.405	0.697	SUBCLONAL	1	TRUE	1	0.19	2		251	352	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399991	139399991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746144524	NA	P-0049049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	71	732	1	ENST00000277541.6:c.4357G>A	p.Glu1453Lys	p.E1453K	ENST00000277541	NM_017617.3	1453	Gag/Aag	25/34	1	2	FACETS	0.757	0.659	0.864	0.757	0.659	0.864	SUBCLONAL	1	TRUE	1	0.19	2		733	987	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138729528	NA	P-0049050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	171	598	1	ENST00000269305.4:c.523C>G	p.Arg175Gly	p.R175G	ENST00000269305	NM_001126112.2	175	Cgc/Ggc	5/11	0.212139352239917	2	FACETS	0.853	0.787	0.922	0.853	0.787	0.922	CLONAL	2	TRUE	0	0.275677918189927	2		599	727	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526700	106526700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	29	302	0	ENST00000359195.3:c.2993C>T	p.Ser998Phe	p.S998F	ENST00000359195	NM_002649.2	998	tCt/tTt	10/11	1	2	FACETS	0.573	0.46	0.702	0.573	0.46	0.702	SUBCLONAL	1	TRUE	1	0.275677918189927	2		302	367	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073887	8073888	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0049050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	55	272	0	ENST00000377482.5:c.770_771dup	p.Asn258LeufsTer6	p.N258Lfs*6	ENST00000377482	NM_018948.3	257	-/TT	4/4	0.263958034689877	2	FACETS	0.756	0.652	0.867	0.756	0.652	0.867	SUBCLONAL	2	TRUE	0	0.275677918189927	2		272	264	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057947	27057947	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	197	469	0	ENST00000324856.7:c.1655C>A	p.Ser552Ter	p.S552*	ENST00000324856	NM_006015.4	552	tCa/tAa	3/20	0.263958034689877	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.275677918189927	2		469	686	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864936	57864936	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	70	537	0	ENST00000228682.2:c.2413C>G	p.Arg805Gly	p.R805G	ENST00000228682	NM_005269.2	805	Cga/Gga	12/12	1	2	FACETS	0.8	0.697	0.911	0.8	0.697	0.911	CLONAL	1	TRUE	1	0.275677918189927	2		537	635	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28885841	28885841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	17	309	0	ENST00000282397.4:c.3521C>T	p.Ala1174Val	p.A1174V	ENST00000282397	NM_002019.4	1174	gCc/gTc	27/30	0.275677918189927	3	FACETS	0.499	0.372	0.65	0.25	0.186	0.325	SUBCLONAL	1	TRUE	1	0.275677918189927	3		309	281	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514571	103514581	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGAGGAGCT	GAAGAGGAGCT	-	novel	NA	P-0049050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	33	257	0	ENST00000355739.4:c.1073_1083del	p.Glu358GlyfsTer3	p.E358Gfs*3	ENST00000355739	NM_000123.3	358	GAAGAGGAGCTg/g	8/15	0.275677918189927	3	FACETS	0.882	0.72	1	0.441	0.36	0.531	CLONAL	1	TRUE	1	0.275677918189927	3		257	309	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225344	2225344	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	80	649	0	ENST00000326181.6:c.1429G>T	p.Ala477Ser	p.A477S	ENST00000326181	NM_032271.2	477	Gcc/Tcc	16/21	0.275677918189927	3	FACETS	0.691	0.607	0.782	0.345	0.303	0.391	SUBCLONAL	1	TRUE	1	0.275677918189927	3		649	956	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502271	157502271	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs387907141	NA	P-0049050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	110	435	0	ENST00000346085.5:c.3304C>T	p.Arg1102Ter	p.R1102*	ENST00000346085	NM_020732.3	1102	Cga/Tga	12/20	0.212139352239917	2	FACETS	0.767	0.692	0.846	0.767	0.692	0.846	SUBCLONAL	2	TRUE	0	0.275677918189927	2		435	520	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265906	41266360	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGC	ATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGC	-	novel	NA	P-0049056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	78	70	0	ENST00000349496.5:c.14-110_242-84del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		70	103	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0049057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	258	500	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.425099772482863	2	FACETS	0.863	0.82	0.905	1	0.993	1	CLONAL	3	TRUE	0	0.425099772482863	2		500	469	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821458	32821458	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs565646119	NA	P-0049057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	220	777	0	ENST00000354258.4:c.136G>T	p.Glu46Ter	p.E46*	ENST00000354258	NM_000593.5	46	Gag/Tag	1/11	0.299721524910937	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	2	0.425099772482863	4		777	696	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434458	140434458	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	71	279	0	ENST00000288602.6:c.2240C>T	p.Ala747Val	p.A747V	ENST00000288602	NM_004333.4	747	gCt/gTt	18/18	0.425099772482863	6	FACETS	0.929	0.811	1			1	CLONAL	1	TRUE	NA	0.425099772482863	6		279	665	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431167	49431170	+	frameshift_variant	Frame_Shift_Del	DEL	ACCT	ACCT	-	novel	NA	P-0049057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	547	641	0	ENST00000301067.7:c.9969_9972del	p.Gly3324CysfsTer5	p.G3324Cfs*5	ENST00000301067	NM_003482.3	3323	ccAGGT/cc	34/54	0.425099772482863	7	FACETS	1	0.978	1			1	CLONAL	6	TRUE	NA	0.425099772482863	7		641	874	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445677	49445681	+	frameshift_variant	Frame_Shift_Del	DEL	ATGCC	ATGCC	-	novel	NA	P-0049057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	118	716	0	ENST00000301067.7:c.1785_1789del	p.Glu595AspfsTer8	p.E595Dfs*8	ENST00000301067	NM_003482.3	595	gaGGCATct/gact	10/54	0.425099772482863	7	FACETS	1	0.915	1			1	CLONAL	1	TRUE	NA	0.425099772482863	7		716	1124	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734021	58734021	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	198	451	0	ENST00000305921.3:c.1079A>T	p.Gln360Leu	p.Q360L	ENST00000305921	NM_003620.3	360	cAg/cTg	5/6	0.425099772482863	3	FACETS	0.848	0.795	0.901	1	0.989	1	CLONAL	3	TRUE	1	0.425099772482863	3		451	444	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0049059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	51	221	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	0.488766037447131	3	FACETS	0.886	0.758	1	0.443	0.379	0.513	CLONAL	1	TRUE	1	0.488766037447131	3		221	293	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	84	148	0				ENST00000310581	NM_198253.2	-/1132			0.137602464005612	4	FACETS	1	0.902	1	1	0.902	1	INDETERMINATE	2	TRUE	2	0.234990977769118	4		148	434	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0049060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	128	442	0	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	1	2	FACETS	0.966	0.879	1	1	0.99	1	CLONAL	2	TRUE	1	0.234990977769118	2		442	564	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652017	36652017	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	75	790	1	ENST00000244741.5:c.139G>T	p.Glu47Ter	p.E47*	ENST00000244741	NM_000389.4	47	Gag/Tag	2/3	0.195003184053212	3	FACETS	1	0.877	1	0.501	0.438	0.568	CLONAL	1	TRUE	1	0.234990977769118	3		791	712	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843447	3843447	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783461	NA	P-0049060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	89	408	1	ENST00000262367.5:c.1156C>T	p.Arg386Ter	p.R386*	ENST00000262367	NM_004380.2	386	Cga/Tga	4/31	0.234990977769118	3	FACETS	0.98	0.873	1	0.98	0.873	1	CLONAL	2	TRUE	1	0.234990977769118	3		409	432	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652048	36652049	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	200	805	0	ENST00000244741.5:c.171dup	p.Pro58ThrfsTer5	p.P58Tfs*5	ENST00000244741	NM_000389.4	57	aca/acAa	2/3	0.195003184053212	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.234990977769118	3		805	763	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652074	36652074	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	64	791	0	ENST00000244741.5:c.196G>C	p.Glu66Gln	p.E66Q	ENST00000244741	NM_000389.4	66	Gag/Cag	2/3	0.195003184053212	3	FACETS	0.802	0.693	0.92	0.401	0.346	0.46	CLONAL	1	TRUE	1	0.234990977769118	3		791	759	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613418	100613418	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	80	216	0	ENST00000308731.7:c.982C>G	p.Gln328Glu	p.Q328E	ENST00000308731	NM_000061.2	328	Caa/Gaa	12/19	0.22490190410207	2	FACETS	0.92	0.829	1			1	CLONAL	4	TRUE	NA	0.234990977769118	2		216	185	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298785	46298785	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	154	276	0	ENST00000334344.6:c.5433del	p.Ala1812ProfsTer27	p.A1812Pfs*27	ENST00000334344	NM_152641.2	1811	cTt/ct	21/21	0.1931731050513	2	FACETS	1	0.982	1	0.601	0.556	0.648	INDETERMINATE	1	TRUE	0	0.617058499646969	2		276	415	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835591	68835591	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	248	363	2	ENST00000261769.5:c.182C>T	p.Thr61Ile	p.T61I	ENST00000261769	NM_004360.3	61	aCc/aTc	3/16	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.617058499646969	2		365	691	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	205	695	3	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.39174998025241	2		698	1035	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	137	467	6	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.946	0.862	1	0.946	0.862	1	CLONAL	1	TRUE	1	0.39174998025241	2		473	739	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	141	755	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.747	0.68	0.817	0.747	0.68	0.817	SUBCLONAL	1	TRUE	1	0.39174998025241	2		758	964	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	96	437	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.39174998025241	2		437	482	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	78	199	3	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.39174998025241	2		202	310	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	229	784	3	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.39174998025241	2		787	1060	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007825	45007825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	105	300	0	ENST00000558401.1:c.276del	p.Thr93LeufsTer10	p.T93Lfs*10	ENST00000558401	NM_004048.2	91	aCc/ac	2/4	1	2	FACETS	0.996	0.896	1	0.996	0.896	1	CLONAL	1	TRUE	1	0.39174998025241	2		300	538	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	89	263	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.39174998025241	2		263	447	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	95	424	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.882	0.787	0.982	0.882	0.787	0.982	CLONAL	1	TRUE	1	0.39174998025241	2		424	550	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	67	312	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	0.725	0.631	0.825	0.725	0.631	0.825	SUBCLONAL	1	TRUE	1	0.39174998025241	2		312	472	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	90	218	1	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.39174998025241	2		219	412	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	109	389	7	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	NA	2	FACETS	0.997	0.899	1			1	INDETERMINATE	1	TRUE	NA	0.39174998025241	2		396	558	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123837	46123837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	119	249	0	ENST00000334344.6:c.109del	p.Ile37SerfsTer21	p.I37Sfs*21	ENST00000334344	NM_152641.2	35	Aaa/aa	2/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.39174998025241	2		249	474	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	175	217	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.390840426774146	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.39174998025241	2		217	426	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979529	7979529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768784091	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	163	472	0	ENST00000319144.4:c.1496G>A	p.Arg499His	p.R499H	ENST00000319144	NM_001139.2	499	cGc/cAc	11/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.39174998025241	2		472	720	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851930	128851930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779777438	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	152	588	0	ENST00000249373.3:c.2002C>T	p.Arg668Cys	p.R668C	ENST00000249373	NM_005631.4	668	Cgc/Tgc	12/12	1	2	FACETS	0.915	0.837	0.997	0.915	0.837	0.997	CLONAL	1	TRUE	1	0.39174998025241	2		588	848	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979987	7979987	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746723399	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	175	514	1	ENST00000319144.4:c.1350del	p.Leu451SerfsTer16	p.L451Sfs*16	ENST00000319144	NM_001139.2	450	ggG/gg	10/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.39174998025241	2		515	791	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256768	19256769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1202792889	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	72	603	1	ENST00000162023.5:c.944dup	p.Val316SerfsTer6	p.V316Sfs*6	ENST00000162023		315	cca/ccCa	13/13	1	2	FACETS	0.501	0.437	0.57	0.501	0.437	0.57	SUBCLONAL	1	TRUE	1	0.39174998025241	2		604	734	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	54	462	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.276	0.235	0.322	0.276	0.235	0.322	SUBCLONAL	1	TRUE	1	0.39174998025241	2		462	999	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896573	78896573	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	188	649	0	ENST00000306801.3:c.2570C>T	p.Thr857Met	p.T857M	ENST00000306801	NM_020761.2	857	aCg/aTg	22/34	1	2	FACETS	0.971	0.897	1	0.971	0.897	1	CLONAL	1	TRUE	1	0.39174998025241	2		649	988	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097624	11097625	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1165714406	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	223	746	0	ENST00000358026.2:c.810dup	p.Gly271ArgfsTer16	p.G271Rfs*16	ENST00000358026	NM_001128849.1	268	-/C	5/36	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.39174998025241	2		746	1052	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117594	70117594	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	208	564	0	ENST00000245479.2:c.66del	p.Ser23AlafsTer38	p.S23Afs*38	ENST00000245479	NM_000346.3	21	gCc/gc	1/3	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.39174998025241	2		564	1024	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347484	91347484	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	131	370	1	ENST00000355112.3:c.3651del	p.Lys1217AsnfsTer62	p.K1217Nfs*62	ENST00000355112	NM_000057.2	1216	Aaa/aa	19/22	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.39174998025241	2		371	627	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145549	24145549	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	221	562	1	ENST00000263121.7:c.568C>T	p.Arg190Trp	p.R190W	ENST00000263121	NM_003073.3	190	Cgg/Tgg	5/9	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.39174998025241	2		563	913	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435128	110435129	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs772322568	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	116	633	0	ENST00000375856.3:c.3272dup	p.Lys1092GlufsTer233	p.K1092Efs*233	ENST00000375856	NM_003749.2	1091	ccg/ccCg	1/2	1	2	FACETS	0.558	0.502	0.618	0.558	0.502	0.618	SUBCLONAL	1	TRUE	1	0.39174998025241	2		633	1061	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639588	47639588	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63749897	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	81	277	0	ENST00000233146.2:c.687del	p.Ala230LeufsTer16	p.A230Lfs*16	ENST00000233146	NM_000251.2	227	agA/ag	4/16	1	2	FACETS	0.996	0.883	1	0.996	0.883	1	CLONAL	1	TRUE	1	0.39174998025241	2		277	415	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957465	175957465	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	95	282	0	ENST00000367669.3:c.1931del	p.Asn644ThrfsTer3	p.N644Tfs*3	ENST00000367669	NM_022457.5	644	aAc/ac	17/20	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.39174998025241	2		282	457	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675196	30675196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs551577509	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	133	428	0	ENST00000376406.3:c.3049G>A	p.Ala1017Thr	p.A1017T	ENST00000376406	NM_014641.2	1017	Gct/Act	9/15	1	2	FACETS	0.877	0.797	0.961	0.877	0.797	0.961	CLONAL	1	TRUE	1	0.39174998025241	2		428	774	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404587	8404587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	58	239	0	ENST00000356435.5:c.4160C>T	p.Ala1387Val	p.A1387V	ENST00000356435		1387	gCg/gTg	25/35	1	2	FACETS	0.906	0.783	1	0.906	0.783	1	CLONAL	1	TRUE	1	0.39174998025241	2		239	327	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279483	1279483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	226	794	2	ENST00000310581.5:c.2053G>A	p.Asp685Asn	p.D685N	ENST00000310581	NM_198253.2	685	Gat/Aat	5/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.39174998025241	2		796	1018	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200107	138200107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746331032	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	121	351	0	ENST00000237289.4:c.1525G>A	p.Ala509Thr	p.A509T	ENST00000237289	NM_001270507.1	509	Gcc/Acc	7/9	1	2	FACETS	0.911	0.824	1	0.911	0.824	1	CLONAL	1	TRUE	1	0.39174998025241	2		351	678	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231610	5231611	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	28	128	0	ENST00000357368.4:c.1865dup	p.Gln623SerfsTer4	p.Q623Sfs*4	ENST00000357368	NM_002850.3	622	cct/ccCt	14/38	1	2	FACETS	0.588	0.472	0.719	0.588	0.472	0.719	SUBCLONAL	1	TRUE	1	0.39174998025241	2		128	243	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210432	36210432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	118	451	0	ENST00000222270.7:c.425G>A	p.Arg142Gln	p.R142Q	ENST00000222270	NM_014727.1	142	cGa/cAa	2/37	1	2	FACETS	0.801	0.723	0.883	0.801	0.723	0.883	CLONAL	1	TRUE	1	0.39174998025241	2		451	752	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778302	3778302	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs794727551	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	223	686	0	ENST00000262367.5:c.6746G>A	p.Arg2249His	p.R2249H	ENST00000262367	NM_004380.2	2249	cGc/cAc	31/31	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.39174998025241	2		686	989	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905960	50905960	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	217	793	0	ENST00000440232.2:c.932G>T	p.Arg311Leu	p.R311L	ENST00000440232	NM_002691.3	311	cGc/cTc	8/27	1	2	FACETS	0.937	0.87	1	0.937	0.87	1	CLONAL	1	TRUE	1	0.39174998025241	2		793	1182	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874713	151874713	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	118	323	0	ENST00000262189.6:c.7825C>T	p.Arg2609Ter	p.R2609*	ENST00000262189	NM_170606.2	2609	Cga/Tga	38/59	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.39174998025241	2		323	597	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436815	110436815	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	203	730	0	ENST00000375856.3:c.1586del	p.Pro529ArgfsTer15	p.P529Rfs*15	ENST00000375856	NM_003749.2	529	cCg/cg	1/2	1	2	FACETS	0.921	0.853	0.992	0.921	0.853	0.992	CLONAL	1	TRUE	1	0.39174998025241	2		730	1125	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001085	150001085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	80	313	0	ENST00000253339.5:c.2519G>A	p.Gly840Asp	p.G840D	ENST00000253339		840	gGt/gAt	4/7	1	2	FACETS	0.825	0.728	0.928	0.825	0.728	0.928	CLONAL	1	TRUE	1	0.39174998025241	2		313	495	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602290	10602290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	246	621	0	ENST00000171111.5:c.1288G>A	p.Gly430Ser	p.G430S	ENST00000171111	NM_203500.1	430	Ggc/Agc	3/6	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.39174998025241	2		621	1078	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268792	98268793	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	151	379	0	ENST00000331920.6:c.290dup	p.Asn97LysfsTer43	p.N97Kfs*43	ENST00000331920	NM_000264.3	97	aac/aaAc	2/24	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.39174998025241	2		379	688	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925621	114925622	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	156	508	0	ENST00000543371.1:c.1704dup	p.Ser569LeufsTer40	p.S569Lfs*40	ENST00000543371	NM_001198531.1	567	gcc/gCcc	14/14	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.39174998025241	2		508	714	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245404	133245404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754616313	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	146	505	1	ENST00000320574.5:c.1916G>A	p.Arg639His	p.R639H	ENST00000320574	NM_006231.2	639	cGc/cAc	17/49	1	2	FACETS	0.999	0.913	1	0.999	0.913	1	CLONAL	1	TRUE	1	0.39174998025241	2		506	746	SUCCESS
APC	324	MSKCC	GRCh37	5	112164565	112164566	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1554082091	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	67	157	0	ENST00000257430.4:c.1643dup	p.Leu548PhefsTer12	p.L548Ffs*12	ENST00000257430	NM_000038.5	547	gtt/gTtt	14/16	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.39174998025241	2		157	308	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424442	49424443	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs797044740	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	155	562	2	ENST00000301067.7:c.13780dup	p.Ala4594GlyfsTer12	p.A4594Gfs*12	ENST00000301067	NM_003482.3	4594	gcc/gGcc	41/54	1	2	FACETS	0.916	0.839	0.997	0.916	0.839	0.997	CLONAL	1	TRUE	1	0.39174998025241	2		564	864	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201854	67201856	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	164	570	0	ENST00000312629.5:c.1059_1061del	p.Glu353del	p.E353del	ENST00000312629	NM_003952.2	352	GAG/-	13/15	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.39174998025241	2		570	836	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111995809	111995809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	72	332	0	ENST00000368678.4:c.1289C>T	p.Thr430Met	p.T430M	ENST00000368678		430	aCg/aTg	12/13	1	2	FACETS	0.667	0.583	0.757	0.667	0.583	0.757	SUBCLONAL	1	TRUE	1	0.39174998025241	2		332	551	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22412962	22412962	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	32	97	0	ENST00000344548.3:c.209T>C	p.Leu70Pro	p.L70P	ENST00000344548	NM_001039802.1	70	cTg/cCg	5/7	1	2	FACETS	0.918	0.753	1	0.918	0.753	1	CLONAL	1	TRUE	1	0.39174998025241	2		97	178	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982426	201982426	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	170	555	0	ENST00000359651.3:c.805G>T	p.Ala269Ser	p.A269S	ENST00000359651		269	Gcg/Tcg	6/8	1	2	FACETS	0.89	0.818	0.965	0.89	0.818	0.965	CLONAL	1	TRUE	1	0.39174998025241	2		555	975	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939438	71939438	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	211	746	0	ENST00000298229.2:c.293T>C	p.Leu98Pro	p.L98P	ENST00000298229	NM_001567.3	98	cTc/cCc	3/28	1	2	FACETS	0.908	0.842	0.977	0.908	0.842	0.977	CLONAL	1	TRUE	1	0.39174998025241	2		746	1186	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214057	108214057	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1174335574	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	74	221	0	ENST00000278616.4:c.8377C>T	p.Pro2793Ser	p.P2793S	ENST00000278616	NM_000051.3	2793	Cca/Tca	57/63	1	2	FACETS	0.933	0.821	1	0.933	0.821	1	CLONAL	1	TRUE	1	0.39174998025241	2		221	405	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125523706	125523706	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	58	245	1	ENST00000428830.2:c.1299G>T	p.Met433Ile	p.M433I	ENST00000428830	NM_001114121.2	433	atG/atT	12/14	1	2	FACETS	0.853	0.737	0.979	0.853	0.737	0.979	CLONAL	1	TRUE	1	0.39174998025241	2		246	347	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719935	18719935	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	81	342	0	ENST00000266497.5:c.3832A>G	p.Arg1278Gly	p.R1278G	ENST00000266497		1278	Aga/Gga	27/31	1	2	FACETS	0.791	0.698	0.889	0.791	0.698	0.889	SUBCLONAL	1	TRUE	1	0.39174998025241	2		342	523	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244305	46244306	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	100	247	0	ENST00000334344.6:c.2401_2402del	p.Met801ValfsTer39	p.M801Vfs*39	ENST00000334344	NM_152641.2	800	cAT/c	15/21	1	2	FACETS	0.987	0.885	1	0.987	0.885	1	CLONAL	1	TRUE	1	0.39174998025241	2		247	517	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244548	46244548	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	132	399	0	ENST00000334344.6:c.2642C>A	p.Ala881Asp	p.A881D	ENST00000334344	NM_152641.2	881	gCt/gAt	15/21	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.39174998025241	2		399	642	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912528	32912528	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	103	354	0	ENST00000380152.3:c.4036A>G	p.Thr1346Ala	p.T1346A	ENST00000380152		1346	Act/Gct	11/27	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.39174998025241	2		354	522	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436380	110436380	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	216	590	0	ENST00000375856.3:c.2021A>C	p.Asp674Ala	p.D674A	ENST00000375856	NM_003749.2	674	gAc/gCc	1/2	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.39174998025241	2		590	960	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068870	30068870	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	96	368	0	ENST00000331968.5:c.2059A>T	p.Ile687Phe	p.I687F	ENST00000331968	NM_002742.2	687	Att/Ttt	14/18	1	2	FACETS	0.906	0.81	1	0.906	0.81	1	CLONAL	1	TRUE	1	0.39174998025241	2		368	541	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108011	30108011	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	125	384	0	ENST00000331968.5:c.796A>G	p.Lys266Glu	p.K266E	ENST00000331968	NM_002742.2	266	Aaa/Gaa	5/18	1	2	FACETS	0.857	0.776	0.941	0.857	0.776	0.941	CLONAL	1	TRUE	1	0.39174998025241	2		384	745	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239857	105239857	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375395037	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	154	650	0	ENST00000349310.3:c.763G>A	p.Ala255Thr	p.A255T	ENST00000349310	NM_001014432.1	255	Gct/Act	10/15	1	2	FACETS	0.883	0.808	0.962	0.883	0.808	0.962	CLONAL	1	TRUE	1	0.39174998025241	2		650	890	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129568	2129568	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs137854162	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	227	723	0	ENST00000219476.3:c.3298del	p.Val1100CysfsTer3	p.V1100Cfs*3	ENST00000219476	NM_000548.3	1099	Ggg/gg	29/42	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.39174998025241	2		723	968	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136350	2136350	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	200	633	1	ENST00000219476.3:c.4819A>G	p.Thr1607Ala	p.T1607A	ENST00000219476	NM_000548.3	1607	Acc/Gcc	37/42	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.39174998025241	2		634	947	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89880960	89880960	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	121	382	0	ENST00000389301.3:c.251A>G	p.Glu84Gly	p.E84G	ENST00000389301	NM_000135.2	84	gAg/gGg	3/43	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.39174998025241	2		382	599	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40467815	40467815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	147	378	0	ENST00000264657.5:c.2261C>T	p.Ser754Phe	p.S754F	ENST00000264657	NM_139276.2	754	tCc/tTc	24/24	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.39174998025241	2		378	633	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870516	40870516	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	148	466	0	ENST00000428826.2:c.887C>T	p.Thr296Ile	p.T296I	ENST00000428826		296	aCa/aTa	9/21	1	2	FACETS	0.956	0.874	1	0.956	0.874	1	CLONAL	1	TRUE	1	0.39174998025241	2		466	790	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519943	66519943	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	75	322	0	ENST00000358598.2:c.426T>A	p.Asp142Glu	p.D142E	ENST00000358598	NM_212471.2	142	gaT/gaA	4/11	1	2	FACETS	0.728	0.639	0.823	0.728	0.639	0.823	SUBCLONAL	1	TRUE	1	0.39174998025241	2		322	526	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117695	70117695	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	275	657	1	ENST00000245479.2:c.163A>G	p.Lys55Glu	p.K55E	ENST00000245479	NM_000346.3	55	Aag/Gag	1/3	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.39174998025241	2		658	1113	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216659	2216659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1159206435	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	223	801	1	ENST00000398665.3:c.2303C>T	p.Ala768Val	p.A768V	ENST00000398665	NM_032482.2	768	gCa/gTa	20/28	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.39174998025241	2		802	1137	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226766	2226766	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1187883994	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	182	608	0	ENST00000398665.3:c.4246C>T	p.Arg1416Cys	p.R1416C	ENST00000398665	NM_032482.2	1416	Cgc/Tgc	27/28	1	2	FACETS	0.956	0.882	1	0.956	0.882	1	CLONAL	1	TRUE	1	0.39174998025241	2		608	972	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110595	4110595	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	160	605	0	ENST00000262948.5:c.362T>C	p.Val121Ala	p.V121A	ENST00000262948	NM_030662.3	121	gTc/gCc	3/11	1	2	FACETS	0.854	0.782	0.928	0.854	0.782	0.928	CLONAL	1	TRUE	1	0.39174998025241	2		605	957	SUCCESS
AXL	558	MSKCC	GRCh37	19	41725320	41725320	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	204	680	0	ENST00000301178.4:c.23T>C	p.Met8Thr	p.M8T	ENST00000301178	NM_021913.4	8	aTg/aCg	1/20	1	2	FACETS	0.995	0.922	1	0.995	0.922	1	CLONAL	1	TRUE	1	0.39174998025241	2		680	1047	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250035	39250035	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	103	405	0	ENST00000402219.2:c.1534C>T	p.His512Tyr	p.H512Y	ENST00000402219	NM_005633.3	512	Cat/Tat	10/23	1	2	FACETS	0.919	0.825	1	0.919	0.825	1	CLONAL	1	TRUE	1	0.39174998025241	2		405	572	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010599	48010599	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780672	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	177	474	0	ENST00000234420.5:c.227T>C	p.Leu76Pro	p.L76P	ENST00000234420	NM_000179.2	76	cTg/cCg	1/10	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.39174998025241	2		474	892	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021680	31021680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	124	398	0	ENST00000375687.4:c.1679C>T	p.Pro560Leu	p.P560L	ENST00000375687	NM_015338.5	560	cCa/cTa	12/13	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.39174998025241	2		398	629	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52685799	52685799	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	100	316	0	ENST00000394830.3:c.673A>G	p.Lys225Glu	p.K225E	ENST00000394830	NM_018313.4	225	Aag/Gag	7/30	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.39174998025241	2		316	501	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920365	134920365	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	130	368	0	ENST00000398015.3:c.2180G>A	p.Gly727Asp	p.G727D	ENST00000398015	NM_004441.4	727	gGc/gAc	12/16	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.39174998025241	2		368	631	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156630	55156630	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	143	458	0	ENST00000257290.5:c.3031A>G	p.Arg1011Gly	p.R1011G	ENST00000257290	NM_006206.4	1011	Aga/Gga	22/23	1	2	FACETS	0.902	0.823	0.985	0.902	0.823	0.985	CLONAL	1	TRUE	1	0.39174998025241	2		458	809	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911308	29911309	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	80	547	0	ENST00000376809.5:c.608dup	p.Gln204AlafsTer17	p.Q204Afs*17	ENST00000376809	NM_002116.7	203	ctg/cTtg	3/8	1	2	FACETS	0.514	0.451	0.581	0.514	0.451	0.581	SUBCLONAL	1	TRUE	1	0.39174998025241	2		547	795	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323131	31323131	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	177	532	0	ENST00000412585.2:c.858G>C	p.Gln286His	p.Q286H	ENST00000412585	NM_005514.6	286	caG/caC	4/8	1	2	FACETS	0.95	0.875	1	0.95	0.875	1	CLONAL	1	TRUE	1	0.39174998025241	2		532	951	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860398	151860398	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	126	405	0	ENST00000262189.6:c.10264C>T	p.Gln3422Ter	p.Q3422*	ENST00000262189	NM_170606.2	3422	Caa/Taa	43/59	1	2	FACETS	0.926	0.839	1	0.926	0.839	1	CLONAL	1	TRUE	1	0.39174998025241	2		405	695	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874227	151874227	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	71	288	0	ENST00000262189.6:c.8311del	p.Ser2771AlafsTer7	p.S2771Afs*7	ENST00000262189	NM_170606.2	2771	Agc/gc	38/59	1	2	FACETS	0.762	0.666	0.864	0.762	0.666	0.864	SUBCLONAL	1	TRUE	1	0.39174998025241	2		288	476	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128201187	128201189	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs769571755	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	112	538	0	ENST00000265960.3:c.1546_1548del	p.Glu516del	p.E516del	ENST00000265960	NM_001006617.1	516	GAG/-	12/12	1	2	FACETS	0.659	0.592	0.73	0.659	0.592	0.73	SUBCLONAL	1	TRUE	1	0.39174998025241	2		538	868	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412479	63412479	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	25	306	0	ENST00000330258.3:c.688A>T	p.Asn230Tyr	p.N230Y	ENST00000330258	NM_152424.3	230	Aac/Tac	2/2	1	1	FACETS	0.235	0.184	0.293	0.235	0.184	0.293	SUBCLONAL	1	TRUE	0	0.39174998025241	1		306	437	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0049066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	275	426	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.605417428323596	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.605417428323596	1		426	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0049066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	543	591	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.583027746058889	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.605417428323596	2		593	897	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396771	396771	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	236	589	0	ENST00000262320.3:c.255G>A	p.Trp85Ter	p.W85*	ENST00000262320	NM_003502.3	85	tgG/tgA	2/11	0.605417428323596	1	FACETS	0.985	0.928	1	0.985	0.928	1	CLONAL	1	TRUE	0	0.605417428323596	1		589	552	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867253	68867253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567517670	NA	P-0049066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	209	427	0	ENST00000261769.5:c.2500G>A	p.Asp834Asn	p.D834N	ENST00000261769	NM_004360.3	834	Gac/Aac	16/16	NA	2	FACETS	0.905	0.843	0.969			1	INDETERMINATE	1	TRUE	NA	0.605417428323596	2		427	763	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191298	185191298	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	39	529	0	ENST00000265026.3:c.2179G>A	p.Asp727Asn	p.D727N	ENST00000265026	NM_004721.4	727	Gac/Aac	11/14	1	2	FACETS	0.171	0.141	0.205	0.171	0.141	0.205	SUBCLONAL	1	TRUE	1	0.605417428323596	2		529	754	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967880	93967880	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	61	381	0	ENST00000369303.4:c.2047G>T	p.Ala683Ser	p.A683S	ENST00000369303	NM_004440.3	683	Gca/Tca	11/17	0.209708723589173	0	FACETS	0.198	0.171	0.227			1	INDETERMINATE	1	TRUE	0	0.605417428323596	0		381	401	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995502	68995502	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	140	370	1	ENST00000288368.4:c.1906A>T	p.Ile636Phe	p.I636F	ENST00000288368	NM_024870.2	636	Att/Ttt	18/40	1	2	FACETS	0.948	0.869	1	0.948	0.869	1	CLONAL	1	TRUE	1	0.605417428323596	2		371	488	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717656	89717657	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	136	440	0	ENST00000371953.3:c.683dup	p.Asn228LysfsTer15	p.N228Kfs*15	ENST00000371953	NM_000314.4	227	-/A	7/9	0.321040660672195	0	FACETS	0.684	0.625	0.746			1	SUBCLONAL	1	TRUE	0	0.419485921462716	0		440	550	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437571	56437572	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	157	561	0	ENST00000407977.2:c.890_891insG	p.Asn297LysfsTer146	p.N297Kfs*146	ENST00000407977		297	aac/aaGc	8/10	0.419485921462716	1	FACETS	0.77	0.707	0.837	0.77	0.707	0.837	SUBCLONAL	1	TRUE	0	0.419485921462716	1		561	768	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0049070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	123	350	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.406510739505913	3	FACETS	1	0.982	1	0.682	0.619	0.747	CLONAL	1	TRUE	1	0.406510739505913	3		350	534	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0049070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	47	214	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.406510739505913	2		214	187	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0049070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	18	506	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.158	0.118	0.205	0.158	0.118	0.205	SUBCLONAL	1	TRUE	1	0.406510739505913	2		506	562	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0049070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	74	350	2	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.406510739505913	2		352	361	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169377	11169377	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519916	NA	P-0049070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	42	449	1	ENST00000361445.4:c.7498A>T	p.Ile2500Phe	p.I2500F	ENST00000361445	NM_004958.3	2500	Att/Ttt	56/58	0.406510739505913	1	FACETS	0.364	0.304	0.431	0.364	0.304	0.431	SUBCLONAL	1	TRUE	0	0.406510739505913	1		450	452	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174395	11174395	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1085307113	NA	P-0049070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	177	536	0	ENST00000361445.4:c.7280T>A	p.Leu2427Gln	p.L2427Q	ENST00000361445	NM_004958.3	2427	cTg/cAg	53/58	0.406510739505913	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.406510739505913	1		536	631	SUCCESS
ATM	472	MSKCC	GRCh37	11	108128229	108128229	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1555075658	NA	P-0049070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	125	334	0	ENST00000278616.4:c.2272G>T	p.Glu758Ter	p.E758*	ENST00000278616	NM_000051.3	758	Gaa/Taa	15/63	0.406510739505913	1	FACETS	0.854	0.786	0.922	1	0.99	1	CLONAL	2	TRUE	0	0.406510739505913	1		334	287	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678518	88678518	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	67	453	0	ENST00000360948.2:c.1018C>A	p.Gln340Lys	p.Q340K	ENST00000360948	NM_001012338.2	340	Cag/Aag	9/19	0.406510739505913	1	FACETS	0.585	0.51	0.666	0.585	0.51	0.666	SUBCLONAL	1	TRUE	0	0.406510739505913	1		453	449	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593417	48593417	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	96	238	0	ENST00000342988.3:c.1168G>T	p.Glu390Ter	p.E390*	ENST00000342988	NM_005359.5	390	Gaa/Taa	10/12	0.406510739505913	1	FACETS	0.996	0.894	1	0.996	0.894	1	CLONAL	1	TRUE	0	0.406510739505913	1		238	378	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604784	48604784	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	22	319	0	ENST00000342988.3:c.1606C>A	p.Leu536Ile	p.L536I	ENST00000342988	NM_005359.5	536	Cta/Ata	12/12	0.406510739505913	1	FACETS	0.219	0.169	0.277	0.219	0.169	0.277	SUBCLONAL	1	TRUE	0	0.406510739505913	1		319	394	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743883	40743883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	106	484	2	ENST00000373198.4:c.3112G>A	p.Glu1038Lys	p.E1038K	ENST00000373198	NM_133170.3	1038	Gag/Aag	23/32	1	2	FACETS	0.805	0.723	0.892	0.805	0.723	0.892	CLONAL	1	TRUE	1	0.406510739505913	2		486	648	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119635021	119635021	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	26	152	0	ENST00000316626.5:c.478T>G	p.Leu160Val	p.L160V	ENST00000316626		160	Ttg/Gtg	5/12	1	2	FACETS	0.882	0.707	1	0.882	0.707	1	CLONAL	1	TRUE	1	0.406510739505913	2		152	145	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	28	302	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.851	0.684	1	0.851	0.684	1	CLONAL	1	TRUE	1	0.28	2		302	235	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	91	564	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.28	2		564	566	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247028	53247028	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	92	457	1	ENST00000375401.3:c.472G>A	p.Glu158Lys	p.E158K	ENST00000375401	NM_004187.3	158	Gaa/Aaa	4/26	0.202817456493915	1	FACETS	0.824	0.732	0.921	0.824	0.732	0.921	CLONAL	1	TRUE	0	0.28	1		458	686	SUCCESS
APC	324	MSKCC	GRCh37	5	112177901	112177901	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs752654519	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	20	216	0	ENST00000257430.4:c.6610C>T	p.Arg2204Ter	p.R2204*	ENST00000257430	NM_000038.5	2204	Cga/Tga	16/16	1	2	FACETS	0.585	0.449	0.745	0.585	0.449	0.745	SUBCLONAL	1	TRUE	1	0.28	2		216	244	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557837	187557837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs184443677	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	82	312	0	ENST00000441802.2:c.3874G>A	p.Glu1292Lys	p.E1292K	ENST00000441802	NM_005245.3	1292	Gaa/Aaa	5/27	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.28	2		312	479	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201008	108201008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881383	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	35	339	0	ENST00000278616.4:c.7375C>T	p.Arg2459Cys	p.R2459C	ENST00000278616	NM_000051.3	2459	Cgt/Tgt	50/63	1	2	FACETS	0.774	0.636	0.928	0.774	0.636	0.928	CLONAL	1	TRUE	1	0.28	2		339	323	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041527	14041527	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs756155469	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	53	293	0	ENST00000311895.7:c.2074C>T	p.Arg692Ter	p.R692*	ENST00000311895	NM_005236.2	692	Cga/Tga	11/11	1	2	FACETS	0.951	0.814	1	0.951	0.814	1	CLONAL	1	TRUE	1	0.28	2		293	398	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522657	67522657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	42	243	0	ENST00000274335.5:c.154G>T	p.Glu52Ter	p.E52*	ENST00000274335		52	Gaa/Taa	1/15	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.28	2		243	262	SUCCESS
APC	324	MSKCC	GRCh37	5	112175921	112175921	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	20	154	0	ENST00000257430.4:c.4630G>T	p.Glu1544Ter	p.E1544*	ENST00000257430	NM_000038.5	1544	Gaa/Taa	16/16	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.28	2		154	123	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	34	308	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.838	1	1	0.838	1	CLONAL	1	TRUE	1	0.28	2		308	238	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	17	229	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	1	2	FACETS	0.783	0.589	1	0.783	0.589	1	CLONAL	1	TRUE	1	0.28	2		229	155	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	69	363	0	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	1	2	FACETS	0.84	0.732	0.956	0.84	0.732	0.956	CLONAL	1	TRUE	1	0.28	2		363	587	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738509	145738509	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs386833851	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	92	521	1	ENST00000428558.2:c.2476C>T	p.Arg826Ter	p.R826*	ENST00000428558	NM_004260.3	826	Cga/Tga	16/22	1	2	FACETS	0.947	0.842	1	0.947	0.842	1	CLONAL	1	TRUE	1	0.28	2		522	694	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317111	87317111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	46	293	1	ENST00000277120.3:c.250G>A	p.Glu84Lys	p.E84K	ENST00000277120		84	Gaa/Aaa	3/19	1	2	FACETS	0.766	0.646	0.898	0.766	0.646	0.898	SUBCLONAL	1	TRUE	1	0.28	2		294	429	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215937	142215937	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs141429029	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	43	315	0	ENST00000350721.4:c.5656C>T	p.Arg1886Ter	p.R1886*	ENST00000350721	NM_001184.3	1886	Cga/Tga	33/47	1	2	FACETS	0.77	0.645	0.907	0.77	0.645	0.907	CLONAL	1	TRUE	1	0.28	2		315	399	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748309	41748309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs894529129	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	107	564	2	ENST00000226382.2:c.460C>T	p.Arg154Cys	p.R154C	ENST00000226382	NM_003924.3	154	Cgc/Tgc	3/3	1	2	FACETS	0.891	0.798	0.989	0.891	0.798	0.989	CLONAL	1	TRUE	1	0.28	2		566	858	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247367	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	34	180	0	ENST00000281708.4:c.1435C>T	p.Arg479Ter	p.R479*	ENST00000281708	NM_033632.3	479	Cga/Tga	10/12	1	2	FACETS	0.864	0.709	1	0.864	0.709	1	CLONAL	1	TRUE	1	0.28	2		180	281	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248749	212248749	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	13	209	0	ENST00000342788.4:c.3518C>A	p.Ser1173Tyr	p.S1173Y	ENST00000342788	NM_005235.2	1173	tCt/tAt	28/28	1	2	FACETS	0.494	0.353	0.665	0.494	0.353	0.665	SUBCLONAL	1	TRUE	1	0.28	2		209	188	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102874103	102874103	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	20	170	0	ENST00000307046.8:c.57C>A	p.Phe19Leu	p.F19L	ENST00000307046	NM_001111285.1	19	ttC/ttA	1/4	1	2	FACETS	0.789	0.607	1	0.789	0.607	1	CLONAL	1	TRUE	1	0.28	2		170	181	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911519	134911519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752762812	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	87	361	0	ENST00000398015.3:c.1984C>T	p.Arg662Cys	p.R662C	ENST00000398015	NM_004441.4	662	Cgt/Tgt	11/16	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.28	2		361	618	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891541	76891541	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	16	257	0	ENST00000373344.5:c.4564G>T	p.Glu1522Ter	p.E1522*	ENST00000373344	NM_000489.3	1522	Gaa/Taa	16/35	0.202817456493915	1	FACETS	0.461	0.342	0.604	0.461	0.342	0.604	SUBCLONAL	1	TRUE	0	0.28	1		257	213	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259071	153259071	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	14	136	0	ENST00000281708.4:c.744G>T	p.Glu248Asp	p.E248D	ENST00000281708	NM_033632.3	248	gaG/gaT	5/12	1	2	FACETS	0.699	0.508	0.927	0.699	0.508	0.927	SUBCLONAL	1	TRUE	1	0.28	2		136	143	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332915	153332915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200698994	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	35	216	1	ENST00000281708.4:c.41G>A	p.Arg14Gln	p.R14Q	ENST00000281708	NM_033632.3	14	cGa/cAa	2/12	1	2	FACETS	0.616	0.505	0.74	0.616	0.505	0.74	SUBCLONAL	1	TRUE	1	0.28	2		217	406	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267600319	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	35	200	0	ENST00000257430.4:c.4199C>T	p.Ser1400Leu	p.S1400L	ENST00000257430	NM_000038.5	1400	tCg/tTg	16/16	1	2	FACETS	0.781	0.642	0.936	0.781	0.642	0.936	CLONAL	1	TRUE	1	0.28	2		200	320	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141989	108141989	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	21	276	0	ENST00000278616.4:c.2933C>A	p.Ser978Tyr	p.S978Y	ENST00000278616	NM_000051.3	978	tCt/tAt	20/63	1	2	FACETS	0.833	0.646	1	0.833	0.646	1	CLONAL	1	TRUE	1	0.28	2		276	180	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851255	156851255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1480681042	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	75	503	0	ENST00000524377.1:c.2212G>A	p.Asp738Asn	p.D738N	ENST00000524377	NM_002529.3	738	Gac/Aac	17/17	1	2	FACETS	0.829	0.727	0.94	0.829	0.727	0.94	CLONAL	1	TRUE	1	0.28	2		503	646	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968610	55968610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374980446	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	59	413	0	ENST00000263923.4:c.2053G>A	p.Glu685Lys	p.E685K	ENST00000263923	NM_002253.2	685	Gaa/Aaa	14/30	1	2	FACETS	0.692	0.595	0.798	0.692	0.595	0.798	SUBCLONAL	1	TRUE	1	0.28	2		413	609	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	20	247	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.69	0.53	0.876	0.69	0.53	0.876	SUBCLONAL	1	TRUE	1	0.28	2		247	207	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098533	108098533	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs55861249	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	16	176	0	ENST00000278616.4:c.103C>T	p.Arg35Ter	p.R35*	ENST00000278616	NM_000051.3	35	Cga/Tga	3/63	1	2	FACETS	0.834	0.622	1	0.834	0.622	1	CLONAL	1	TRUE	1	0.28	2		176	137	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161380	55161380	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376544204	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	16	341	0	ENST00000257290.5:c.3211G>A	p.Asp1071Asn	p.D1071N	ENST00000257290	NM_006206.4	1071	Gac/Aac	23/23	1	2	FACETS	0.215	0.158	0.284	0.215	0.158	0.284	SUBCLONAL	1	TRUE	1	0.28	2		341	532	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849069	156849069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750168062	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	97	583	1	ENST00000524377.1:c.1961G>A	p.Arg654His	p.R654H	ENST00000524377	NM_002529.3	654	cGc/cAc	15/17	1	2	FACETS	0.88	0.785	0.983	0.88	0.785	0.983	CLONAL	1	TRUE	1	0.28	2		584	787	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624270	89624270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123324	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	40	245	0	ENST00000371953.3:c.44G>A	p.Arg15Lys	p.R15K	ENST00000371953	NM_000314.4	15	aGa/aAa	1/9	1	2	FACETS	0.928	0.774	1	0.928	0.774	1	CLONAL	1	TRUE	1	0.28	2		245	308	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29107974	29107974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121908702	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	33	331	0	ENST00000328354.6:c.715G>A	p.Glu239Lys	p.E239K	ENST00000328354	NM_007194.3	239	Gag/Aag	6/15	1	2	FACETS	0.755	0.617	0.911	0.755	0.617	0.911	CLONAL	1	TRUE	1	0.28	2		331	312	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347916	73347916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139907646	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	23	175	0	ENST00000377767.4:c.1145G>A	p.Arg382Gln	p.R382Q	ENST00000377767	NM_014953.3	382	cGa/cAa	8/21	1	2	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	TRUE	1	0.28	2		175	152	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225362541	225362541	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs767240461	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	42	315	0	ENST00000264414.4:c.1636C>T	p.Arg546Ter	p.R546*	ENST00000264414	NM_003590.4	546	Cga/Tga	12/16	1	2	FACETS	0.824	0.69	0.972	0.824	0.69	0.972	CLONAL	1	TRUE	1	0.28	2		315	364	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169935	32169935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142477287	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	122	576	1	ENST00000375023.3:c.3673C>T	p.Arg1225Trp	p.R1225W	ENST00000375023	NM_004557.3	1225	Cgg/Tgg	21/30	1	2	FACETS	0.995	0.899	1	0.995	0.899	1	CLONAL	1	TRUE	1	0.28	2		577	876	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352373	70352373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	55	358	1	ENST00000374080.3:c.4400G>A	p.Arg1467Gln	p.R1467Q	ENST00000374080		1467	cGa/cAa	31/45	0.202817456493915	1	FACETS	0.651	0.557	0.753	0.651	0.557	0.753	SUBCLONAL	1	TRUE	0	0.28	1		359	519	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166818	32166818	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1441415979	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	125	607	0	ENST00000375023.3:c.4420C>T	p.Arg1474Ter	p.R1474*	ENST00000375023	NM_004557.3	1474	Cga/Tga	24/30	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.28	2		607	845	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646884	23646884	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	46	352	0	ENST00000261584.4:c.983C>A	p.Ser328Tyr	p.S328Y	ENST00000261584	NM_024675.3	328	tCt/tAt	4/13	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.28	2		352	268	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556886	29556886	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	12	154	0	ENST00000356175.3:c.2884G>T	p.Glu962Ter	p.E962*	ENST00000356175	NM_000267.3	962	Gaa/Taa	22/57	1	2	FACETS	0.697	0.493	0.944	0.697	0.493	0.944	SUBCLONAL	1	TRUE	1	0.28	2		154	123	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845640	72845640	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148354034	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	104	471	0	ENST00000268489.5:c.3700G>A	p.Asp1234Asn	p.D1234N	ENST00000268489	NM_006885.3	1234	Gat/Aat	7/10	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.28	2		471	738	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631279	176631279	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	26	195	0	ENST00000439151.2:c.1222G>T	p.Gly408Ter	p.G408*	ENST00000439151	NM_022455.4	408	Gga/Tga	4/23	1	2	FACETS	0.897	0.715	1	0.897	0.715	1	CLONAL	1	TRUE	1	0.28	2		195	207	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685312	86685312	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	40	128	1	ENST00000274376.6:c.3028C>T	p.Arg1010Ter	p.R1010*	ENST00000274376	NM_002890.2	1010	Cga/Tga	24/25	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.28	2		129	272	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534356	187534356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770029391	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	81	409	0	ENST00000441802.2:c.9370G>A	p.Glu3124Lys	p.E3124K	ENST00000441802	NM_005245.3	3124	Gaa/Aaa	13/27	1	2	FACETS	0.911	0.803	1	0.911	0.803	1	CLONAL	1	TRUE	1	0.28	2		409	635	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449600	187449600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781532443	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	64	304	1	ENST00000232014.4:c.280C>T	p.Arg94Trp	p.R94W	ENST00000232014	NM_001130845.1	94	Cgg/Tgg	4/10	1	2	FACETS	0.981	0.852	1	0.981	0.852	1	CLONAL	1	TRUE	1	0.28	2		305	466	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682778	190682778	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	11	224	0	ENST00000441310.2:c.454C>A	p.Leu152Ile	p.L152I	ENST00000441310	NM_000534.4	152	Cta/Ata	5/13	1	2	FACETS	0.565	0.392	0.778	0.565	0.392	0.778	SUBCLONAL	1	TRUE	1	0.28	2		224	139	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99203950	99203950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755469992	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	20	260	0	ENST00000074304.5:c.2813G>A	p.Arg938Gln	p.R938Q	ENST00000074304	NM_001134224.1	938	cGa/cAa	26/26	1	2	FACETS	0.525	0.402	0.669	0.525	0.402	0.669	SUBCLONAL	1	TRUE	1	0.28	2		260	272	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182574	99182574	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	52	432	0	ENST00000074304.5:c.2377C>T	p.Arg793Ter	p.R793*	ENST00000074304	NM_001134224.1	793	Cga/Tga	22/26	1	2	FACETS	0.576	0.489	0.671	0.576	0.489	0.671	SUBCLONAL	1	TRUE	1	0.28	2		432	645	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751145	57751145	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	39	230	0	ENST00000274289.3:c.1722C>A	p.Tyr574Ter	p.Y574*	ENST00000274289	NM_006622.3	574	taC/taA	12/14	1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	TRUE	1	0.28	2		230	275	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720928	176720928	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784209	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	62	298	0	ENST00000439151.2:c.6559C>T	p.Arg2187Ter	p.R2187*	ENST00000439151	NM_022455.4	2187	Cga/Tga	23/23	1	2	FACETS	0.828	0.716	0.949	0.828	0.716	0.949	CLONAL	1	TRUE	1	0.28	2		298	535	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687431	117687431	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	30	276	0	ENST00000368508.3:c.2620G>T	p.Glu874Ter	p.E874*	ENST00000368508	NM_002944.2	874	Gaa/Taa	18/43	1	2	FACETS	0.739	0.597	0.899	0.739	0.597	0.899	SUBCLONAL	1	TRUE	1	0.28	2		276	290	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351980	89351980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	136	593	0	ENST00000301030.4:c.970G>A	p.Glu324Lys	p.E324K	ENST00000301030	NM_001256183.1	324	Gaa/Aaa	9/13	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.28	2		593	956	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541679	187541679	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs185406112	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	43	243	0	ENST00000441802.2:c.6061C>T	p.Arg2021Cys	p.R2021C	ENST00000441802	NM_005245.3	2021	Cgc/Tgc	10/27	1	2	FACETS	0.903	0.759	1	0.903	0.759	1	CLONAL	1	TRUE	1	0.28	2		243	340	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520141	9520141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560752200	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	50	329	1	ENST00000353224.5:c.2128G>A	p.Val710Ile	p.V710I	ENST00000353224	NM_177990.2	710	Gtc/Atc	10/10	1	2	FACETS	0.72	0.611	0.84	0.72	0.611	0.84	SUBCLONAL	1	TRUE	1	0.28	2		330	496	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692978	89692978	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	25	345	0	ENST00000371953.3:c.462C>A	p.Phe154Leu	p.F154L	ENST00000371953	NM_000314.4	154	ttC/ttA	5/9	1	2	FACETS	0.76	0.601	0.94	0.76	0.601	0.94	CLONAL	1	TRUE	1	0.28	2		345	235	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029461	14029461	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	39	253	0	ENST00000311895.7:c.1672C>A	p.Leu558Met	p.L558M	ENST00000311895	NM_005236.2	558	Ctg/Atg	8/11	1	2	FACETS	0.702	0.582	0.834	0.702	0.582	0.834	SUBCLONAL	1	TRUE	1	0.28	2		253	397	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850948	63850948	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	55	349	1	ENST00000279873.7:c.1726G>T	p.Glu576Ter	p.E576*	ENST00000279873	NM_032199.2	576	Gaa/Taa	10/10	1	2	FACETS	0.634	0.541	0.735	0.634	0.541	0.735	SUBCLONAL	1	TRUE	1	0.28	2		350	620	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471048	8471048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	15	300	2	ENST00000356435.5:c.3451C>T	p.Arg1151Cys	p.R1151C	ENST00000356435		1151	Cgc/Tgc	20/35	1	2	FACETS	0.387	0.282	0.512	0.387	0.282	0.512	SUBCLONAL	1	TRUE	1	0.28	2		302	277	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159157	143159157	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	17	150	0	ENST00000262992.4:c.696G>T	p.Lys232Asn	p.K232N	ENST00000262992	NM_001101669.1	232	aaG/aaT	10/24	1	2	FACETS	1	0.845	1	1	0.845	1	CLONAL	1	TRUE	1	0.28	2		150	104	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466940	18466940	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	27	264	0	ENST00000266497.5:c.1079C>A	p.Ser360Tyr	p.S360Y	ENST00000266497		360	tCt/tAt	5/31	1	2	FACETS	0.712	0.568	0.875	0.712	0.568	0.875	SUBCLONAL	1	TRUE	1	0.28	2		264	271	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197518	106197518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1043057789	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	43	235	0	ENST00000380013.4:c.5851C>T	p.Arg1951Trp	p.R1951W	ENST00000380013	NM_001127208.2	1951	Cgg/Tgg	11/11	1	2	FACETS	0.766	0.642	0.903	0.766	0.642	0.903	CLONAL	1	TRUE	1	0.28	2		235	401	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39542545	39542545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750067845	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	77	320	0	ENST00000262039.4:c.349G>A	p.Gly117Arg	p.G117R	ENST00000262039	NM_002647.2	117	Gga/Aga	3/25	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.28	2		320	529	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457176	25457176	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149095705	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	96	446	1	ENST00000264709.3:c.2711C>T	p.Pro904Leu	p.P904L	ENST00000264709	NM_175629.2	904	cCg/cTg	23/23	1	2	FACETS	0.843	0.751	0.942	0.843	0.751	0.942	CLONAL	1	TRUE	1	0.28	2		447	813	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376306	118376306	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	27	338	0	ENST00000534358.1:c.9699G>T	p.Lys3233Asn	p.K3233N	ENST00000534358	NM_005933.3	3233	aaG/aaT	27/36	1	2	FACETS	0.513	0.408	0.633	0.513	0.408	0.633	SUBCLONAL	1	TRUE	1	0.28	2		338	376	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830631	72830631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753599043	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	66	467	0	ENST00000268489.5:c.5950G>A	p.Glu1984Lys	p.E1984K	ENST00000268489	NM_006885.3	1984	Gag/Aag	9/10	1	2	FACETS	0.749	0.65	0.857	0.749	0.65	0.857	SUBCLONAL	1	TRUE	1	0.28	2		467	629	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128432165	128432165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1371596131	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	31	382	2	ENST00000265960.3:c.281G>A	p.Arg94Gln	p.R94Q	ENST00000265960	NM_001006617.1	94	cGa/cAa	3/12	1	2	FACETS	0.934	0.76	1	0.934	0.76	1	CLONAL	1	TRUE	1	0.28	2		384	237	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933464	100933464	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	35	183	0	ENST00000325455.5:c.1926C>A	p.Phe642Leu	p.F642L	ENST00000325455	NM_001202474.3	642	ttC/ttA	4/8	1	2	FACETS	0.988	0.815	1	0.988	0.815	1	CLONAL	1	TRUE	1	0.28	2		183	253	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127349	55127349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	71	387	0	ENST00000257290.5:c.137C>A	p.Ser46Tyr	p.S46Y	ENST00000257290	NM_006206.4	46	tCt/tAt	3/23	1	2	FACETS	0.931	0.813	1	0.931	0.813	1	CLONAL	1	TRUE	1	0.28	2		387	545	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748890	43748890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201785039	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	70	495	0	ENST00000382044.4:c.1916G>A	p.Arg639Gln	p.R639Q	ENST00000382044	NM_001141980.1	639	cGa/cAa	12/28	1	2	FACETS	0.778	0.678	0.885	0.778	0.678	0.885	SUBCLONAL	1	TRUE	1	0.28	2		495	643	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816896	32816896	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1159721335	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	53	307	1	ENST00000354258.4:c.1429-1G>T		p.X477_splice	ENST00000354258	NM_000593.5	477			1	2	FACETS	0.976	0.835	1	0.976	0.835	1	CLONAL	1	TRUE	1	0.28	2		308	388	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797230	45797230	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs587781628	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	77	540	0	ENST00000450313.1:c.1187-2A>G		p.X396_splice	ENST00000450313	NM_012222.2	396			1	2	FACETS	0.955	0.839	1	0.955	0.839	1	CLONAL	1	TRUE	1	0.28	2		540	576	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942079	71942079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139442327	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	79	588	0	ENST00000298229.2:c.1343C>T	p.Ser448Leu	p.S448L	ENST00000298229	NM_001567.3	448	tCg/tTg	12/28	1	2	FACETS	0.739	0.649	0.835	0.739	0.649	0.835	SUBCLONAL	1	TRUE	1	0.28	2		588	764	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948538	54948538	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	16	294	0	ENST00000312783.6:c.780G>T	p.Glu260Asp	p.E260D	ENST00000312783	NM_198436.1	260	gaG/gaT	8/10	1	2	FACETS	0.39	0.288	0.512	0.39	0.288	0.512	SUBCLONAL	1	TRUE	1	0.28	2		294	293	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749297	43749297	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs748115671	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	36	397	0	ENST00000382044.4:c.1509G>T	p.Lys503Asn	p.K503N	ENST00000382044	NM_001141980.1	503	aaG/aaT	12/28	1	2	FACETS	0.819	0.675	0.979	0.819	0.675	0.979	CLONAL	1	TRUE	1	0.28	2		397	314	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204742	94204742	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs750098871	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	23	244	0	ENST00000323929.3:c.843G>T	p.Lys281Asn	p.K281N	ENST00000323929	NM_005591.3	281	aaG/aaT	8/20	1	2	FACETS	1	0.824	1	1	0.824	1	CLONAL	1	TRUE	1	0.28	2		244	156	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815404	32815404	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	66	487	0	ENST00000354258.4:c.1969G>T	p.Glu657Ter	p.E657*	ENST00000354258	NM_000593.5	657	Gaa/Taa	9/11	1	2	FACETS	0.886	0.77	1	0.886	0.77	1	CLONAL	1	TRUE	1	0.28	2		487	532	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026224	48026224	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	32	245	0	ENST00000234420.5:c.1102G>T	p.Glu368Ter	p.E368*	ENST00000234420	NM_000179.2	368	Gaa/Taa	4/10	1	2	FACETS	0.791	0.644	0.955	0.791	0.644	0.955	CLONAL	1	TRUE	1	0.28	2		245	289	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341506	89341506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	90	568	0	ENST00000301030.4:c.7564G>A	p.Glu2522Lys	p.E2522K	ENST00000301030	NM_001256183.1	2522	Gag/Aag	10/13	1	2	FACETS	0.849	0.753	0.952	0.849	0.753	0.952	CLONAL	1	TRUE	1	0.28	2		568	757	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593483	215593483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139785364	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	48	251	0	ENST00000260947.4:c.2251C>T	p.Arg751Trp	p.R751W	ENST00000260947	NM_000465.2	751	Cgg/Tgg	11/11	1	2	FACETS	0.924	0.784	1	0.924	0.784	1	CLONAL	1	TRUE	1	0.28	2		251	371	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902586	1902586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1401743505	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	94	475	0	ENST00000382891.5:c.205G>A	p.Asp69Asn	p.D69N	ENST00000382891	NM_133335.3	69	Gac/Aac	2/22	1	2	FACETS	0.837	0.744	0.936	0.837	0.744	0.936	CLONAL	1	TRUE	1	0.28	2		475	802	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629679	187629679	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	63	378	0	ENST00000441802.2:c.1303G>T	p.Glu435Ter	p.E435*	ENST00000441802	NM_005245.3	435	Gaa/Taa	2/27	1	2	FACETS	0.93	0.806	1	0.93	0.806	1	CLONAL	1	TRUE	1	0.28	2		378	484	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170015104	170015104	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs762444412	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	43	385	0	ENST00000295797.4:c.1510C>T	p.Arg504Ter	p.R504*	ENST00000295797	NM_002740.5	504	Cga/Tga	16/18	1	2	FACETS	0.742	0.622	0.875	0.742	0.622	0.875	SUBCLONAL	1	TRUE	1	0.28	2		385	414	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419064	419064	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	37	310	0	ENST00000399788.2:c.3283G>T	p.Glu1095Ter	p.E1095*	ENST00000399788	NM_001042603.1	1095	Gaa/Taa	22/28	1	2	FACETS	0.861	0.712	1	0.861	0.712	1	CLONAL	1	TRUE	1	0.28	2		310	307	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995501	68995501	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1326956245	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	24	349	1	ENST00000288368.4:c.1905G>T	p.Lys635Asn	p.K635N	ENST00000288368	NM_024870.2	635	aaG/aaT	18/40	1	2	FACETS	0.67	0.526	0.834	0.67	0.526	0.834	SUBCLONAL	1	TRUE	1	0.28	2		350	256	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861584	152861584	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	72	580	0	ENST00000406277.2:c.168C>A	p.Phe56Leu	p.F56L	ENST00000406277	NM_152274.4	56	ttC/ttA	4/7	0.202817456493915		FACETS		0.592	0.77				SUBCLONAL	1	TRUE	0	0.28	1		580	653	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709561	176709561	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	20	224	0	ENST00000439151.2:c.5988C>A	p.Phe1996Leu	p.F1996L	ENST00000439151	NM_022455.4	1996	ttC/ttA	19/23	1	2	FACETS	0.91	0.701	1	0.91	0.701	1	CLONAL	1	TRUE	1	0.28	2		224	157	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182679086	182679086	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	13	263	0	ENST00000292782.4:c.448G>T	p.Glu150Ter	p.E150*	ENST00000292782	NM_020640.2	150	Gaa/Taa	4/7	1	2	FACETS	0.389	0.277	0.525	0.389	0.277	0.525	SUBCLONAL	1	TRUE	1	0.28	2		263	239	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391869	139391869	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780963597	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	116	755	0	ENST00000277541.6:c.6322G>A	p.Asp2108Asn	p.D2108N	ENST00000277541	NM_017617.3	2108	Gac/Aac	34/34	1	2	FACETS	0.965	0.869	1	0.965	0.869	1	CLONAL	1	TRUE	1	0.28	2		755	859	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054998	176054998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757438162	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	20	312	0	ENST00000367669.3:c.1055C>T	p.Thr352Met	p.T352M	ENST00000367669	NM_022457.5	352	aCg/aTg	10/20	1	2	FACETS	0.448	0.342	0.572	0.448	0.342	0.572	SUBCLONAL	1	TRUE	1	0.28	2		312	319	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022033	5022033	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1422678517	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	43	348	0	ENST00000381652.3:c.46A>G	p.Thr16Ala	p.T16A	ENST00000381652	NM_004972.3	16	Acc/Gcc	3/25	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.28	2		348	301	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955568	48955568	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	13	222	0	ENST00000267163.4:c.1684G>T	p.Ala562Ser	p.A562S	ENST00000267163	NM_000321.2	562	Gca/Tca	17/27	1	2	FACETS	0.619	0.443	0.831	0.619	0.443	0.831	SUBCLONAL	1	TRUE	1	0.28	2		222	150	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841862	151841862	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	42	220	0	ENST00000262189.6:c.14279C>T	p.Ser4760Leu	p.S4760L	ENST00000262189	NM_170606.2	4760	tCg/tTg	55/59	1	2	FACETS	0.909	0.762	1	0.909	0.762	1	CLONAL	1	TRUE	1	0.28	2		220	330	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347493	91347493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	51	385	0	ENST00000355112.3:c.3655C>A	p.Leu1219Ile	p.L1219I	ENST00000355112	NM_000057.2	1219	Ctt/Att	19/22	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.28	2		385	301	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970907	55970907	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	51	383	0	ENST00000263923.4:c.1890G>T	p.Lys630Asn	p.K630N	ENST00000263923	NM_002253.2	630	aaG/aaT	13/30	1	2	FACETS	0.857	0.73	0.996	0.857	0.73	0.996	CLONAL	1	TRUE	1	0.28	2		383	425	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829684	72829684	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	70	455	0	ENST00000268489.5:c.6897G>T	p.Lys2299Asn	p.K2299N	ENST00000268489	NM_006885.3	2299	aaG/aaT	9/10	1	2	FACETS	0.776	0.677	0.884	0.776	0.677	0.884	SUBCLONAL	1	TRUE	1	0.28	2		455	644	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115267948	115267948	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	22	227	0	ENST00000438362.2:c.1785C>A	p.Phe595Leu	p.F595L	ENST00000438362	NM_001242891.1	595	ttC/ttA	15/20	1	2	FACETS	0.485	0.376	0.612	0.485	0.376	0.612	SUBCLONAL	1	TRUE	1	0.28	2		227	324	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971145	13971145	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	38	215	0	ENST00000405192.2:c.784G>A	p.Asp262Asn	p.D262N	ENST00000405192	NM_001163147.1	262	Gat/Aat	8/12	1	2	FACETS	0.854	0.708	1	0.854	0.708	1	CLONAL	1	TRUE	1	0.28	2		215	318	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976421	18976421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1234132463	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	92	636	1	ENST00000262803.5:c.3071G>A	p.Arg1024His	p.R1024H	ENST00000262803	NM_002911.3	1024	cGc/cAc	22/24	1	2	FACETS	0.738	0.654	0.827	0.738	0.654	0.827	SUBCLONAL	1	TRUE	1	0.28	2		637	891	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159059	143159059	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	20	200	0	ENST00000262992.4:c.794C>A	p.Pro265His	p.P265H	ENST00000262992	NM_001101669.1	265	cCt/cAt	10/24	1	2	FACETS	0.887	0.684	1	0.887	0.684	1	CLONAL	1	TRUE	1	0.28	2		200	161	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912693	100912693	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	35	260	0	ENST00000325455.5:c.2629C>A	p.Leu877Ile	p.L877I	ENST00000325455	NM_001202474.3	877	Ctt/Att	7/8	1	2	FACETS	0.831	0.683	0.995	0.831	0.683	0.995	CLONAL	1	TRUE	1	0.28	2		260	301	SUCCESS
YES1	7525	MSKCC	GRCh37	18	739800	739800	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	35	265	0	ENST00000314574.4:c.1072G>A	p.Asp358Asn	p.D358N	ENST00000314574	NM_005433.3	358	Gat/Aat	9/12	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.28	2		265	199	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112942506	112942506	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	22	237	0	ENST00000351677.2:c.1720G>T	p.Glu574Ter	p.E574*	ENST00000351677	NM_002834.3	574	Gaa/Taa	15/16	1	2	FACETS	0.806	0.628	1	0.806	0.628	1	CLONAL	1	TRUE	1	0.28	2		237	195	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035031	42035031	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	63	418	0	ENST00000219905.7:c.4873G>T	p.Glu1625Ter	p.E1625*	ENST00000219905	NM_001164273.1	1625	Gaa/Taa	15/24	1	2	FACETS	0.836	0.724	0.958	0.836	0.724	0.958	CLONAL	1	TRUE	1	0.28	2		418	538	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255113	16255113	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	59	272	0	ENST00000375759.3:c.2378A>C	p.Lys793Thr	p.K793T	ENST00000375759	NM_015001.2	793	aAa/aCa	11/15	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.28	2		272	337	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255152	16255152	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	23	291	0	ENST00000375759.3:c.2417G>T	p.Arg806Ile	p.R806I	ENST00000375759	NM_015001.2	806	aGa/aTa	11/15	1	2	FACETS	0.416	0.324	0.523	0.416	0.324	0.523	SUBCLONAL	1	TRUE	1	0.28	2		291	395	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805073	43805073	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	66	492	0	ENST00000372470.3:c.523G>T	p.Asp175Tyr	p.D175Y	ENST00000372470	NM_005373.2	175	Gat/Tat	4/12	1	2	FACETS	0.749	0.65	0.857	0.749	0.65	0.857	SUBCLONAL	1	TRUE	1	0.28	2		492	629	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400936	72400936	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	28	215	0	ENST00000357731.5:c.235T>G	p.Phe79Val	p.F79V	ENST00000357731	NM_173808.2	79	Ttt/Gtt	2/7	1	2	FACETS	0.743	0.596	0.91	0.743	0.596	0.91	CLONAL	1	TRUE	1	0.28	2		215	269	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736581	85736581	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	18	120	0	ENST00000370580.1:c.66A>C	p.Glu22Asp	p.E22D	ENST00000370580	NM_003921.4	22	gaA/gaC	2/3	1	2	FACETS	1	0.818	1	1	0.818	1	CLONAL	1	TRUE	1	0.28	2		120	118	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724427	162724427	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	45	344	0	ENST00000367921.3:c.199G>T	p.Glu67Ter	p.E67*	ENST00000367921	NM_006182.2	67	Gaa/Taa	5/18	1	2	FACETS	0.727	0.612	0.855	0.727	0.612	0.855	SUBCLONAL	1	TRUE	1	0.28	2		344	442	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63816933	63816933	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	26	152	0	ENST00000279873.7:c.904A>C	p.Lys302Gln	p.K302Q	ENST00000279873	NM_032199.2	302	Aaa/Caa	6/10	1	2	FACETS	0.848	0.675	1	0.848	0.675	1	CLONAL	1	TRUE	1	0.28	2		152	219	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724495	112724495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	30	377	0	ENST00000369452.4:c.379G>A	p.Glu127Lys	p.E127K	ENST00000369452	NM_007373.3	127	Gaa/Aaa	2/9	1	2	FACETS	0.717	0.579	0.872	0.717	0.579	0.872	SUBCLONAL	1	TRUE	1	0.28	2		377	299	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575565	64575565	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	56	351	1	ENST00000312049.6:c.452A>C	p.Lys151Thr	p.K151T	ENST00000312049	NM_130799.2	151	aAa/aCa	3/10	1	2	FACETS	0.781	0.67	0.903	0.781	0.67	0.903	CLONAL	1	TRUE	1	0.28	2		352	512	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457887	69457887	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	102	413	0	ENST00000227507.2:c.287A>C	p.Lys96Thr	p.K96T	ENST00000227507	NM_053056.2	96	aAg/aCg	2/5	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.28	2		413	688	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924732	94924732	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	79	423	0	ENST00000536441.1:c.178A>C	p.Asn60His	p.N60H	ENST00000536441	NM_144665.3	60	Aac/Cac	3/10	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.28	2		423	517	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195625	102195625	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	32	287	0	ENST00000263464.3:c.385G>T	p.Glu129Ter	p.E129*	ENST00000263464	NM_001165.4	129	Gaa/Taa	2/9	1	2	FACETS	0.742	0.604	0.897	0.742	0.604	0.897	SUBCLONAL	1	TRUE	1	0.28	2		287	308	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201113	108201113	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	38	245	0	ENST00000278616.4:c.7480A>C	p.Asn2494His	p.N2494H	ENST00000278616	NM_000051.3	2494	Aat/Cat	50/63	1	2	FACETS	0.998	0.829	1	0.998	0.829	1	CLONAL	1	TRUE	1	0.28	2		245	272	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366528	118366528	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	43	292	0	ENST00000534358.1:c.5477T>G	p.Ile1826Ser	p.I1826S	ENST00000534358	NM_005933.3	1826	aTc/aGc	19/36	1	2	FACETS	0.687	0.575	0.811	0.687	0.575	0.811	SUBCLONAL	1	TRUE	1	0.28	2		292	447	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376047	118376047	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	56	343	0	ENST00000534358.1:c.9440C>A	p.Ser3147Tyr	p.S3147Y	ENST00000534358	NM_005933.3	3147	tCt/tAt	27/36	1	2	FACETS	0.985	0.847	1	0.985	0.847	1	CLONAL	1	TRUE	1	0.28	2		343	406	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125499310	125499310	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	21	335	0	ENST00000428830.2:c.379A>C	p.Thr127Pro	p.T127P	ENST00000428830	NM_001114121.2	127	Act/Cct	5/14	1	2	FACETS	0.798	0.618	1	0.798	0.618	1	CLONAL	1	TRUE	1	0.28	2		335	188	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438129	438129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	59	269	0	ENST00000399788.2:c.1840G>A	p.Glu614Lys	p.E614K	ENST00000399788	NM_001042603.1	614	Gag/Aag	14/28	1	2	FACETS	0.85	0.732	0.977	0.85	0.732	0.977	CLONAL	1	TRUE	1	0.28	2		269	496	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409087	4409087	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	71	248	0	ENST00000261254.3:c.782A>T	p.Tyr261Phe	p.Y261F	ENST00000261254	NM_001759.3	261	tAc/tTc	5/5	1	2	FACETS	0.899	0.786	1	0.899	0.786	1	CLONAL	1	TRUE	1	0.28	2		248	564	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21639480	21639480	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	12	189	0	ENST00000421138.2:c.434A>G	p.Glu145Gly	p.E145G	ENST00000421138		145	gAa/gGa	6/16	1	2	FACETS	0.519	0.366	0.707	0.519	0.366	0.707	SUBCLONAL	1	TRUE	1	0.28	2		189	165	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202762	133202762	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	95	454	0	ENST00000320574.5:c.6472T>C	p.Cys2158Arg	p.C2158R	ENST00000320574	NM_006231.2	2158	Tgc/Cgc	46/49	1	2	FACETS	0.992	0.884	1	0.992	0.884	1	CLONAL	1	TRUE	1	0.28	2		454	684	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133236088	133236088	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs765536104	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	76	295	0	ENST00000320574.5:c.3068A>G	p.Asn1023Ser	p.N1023S	ENST00000320574	NM_006231.2	1023	aAc/aGc	26/49	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.28	2		295	449	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28901649	28901649	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	33	286	0	ENST00000282397.4:c.2746A>C	p.Asn916His	p.N916H	ENST00000282397	NM_002019.4	916	Aat/Cat	20/30	1	2	FACETS	0.673	0.549	0.813	0.673	0.549	0.813	SUBCLONAL	1	TRUE	1	0.28	2		286	350	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911400	32911400	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	14	256	0	ENST00000380152.3:c.2908G>T	p.Asp970Tyr	p.D970Y	ENST00000380152		970	Gat/Tat	11/27	1	2	FACETS	0.621	0.451	0.825	0.621	0.451	0.825	SUBCLONAL	1	TRUE	1	0.28	2		256	161	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914700	32914700	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	22	315	0	ENST00000380152.3:c.6208G>T	p.Glu2070Ter	p.E2070*	ENST00000380152		2070	Gaa/Taa	11/27	1	2	FACETS	0.763	0.594	0.957	0.763	0.594	0.957	CLONAL	1	TRUE	1	0.28	2		315	206	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937596	32937596	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	64	348	0	ENST00000380152.3:c.8257C>A	p.Leu2753Ile	p.L2753I	ENST00000380152		2753	Ctt/Att	18/27	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.28	2		348	423	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281527	49281527	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	75	460	0	ENST00000282018.3:c.574C>A	p.Leu192Ile	p.L192I	ENST00000282018	NM_020377.2	192	Ctc/Atc	1/1	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.28	2		460	501	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81558880	81558880	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	38	271	0	ENST00000298171.2:c.473T>G	p.Ile158Ser	p.I158S	ENST00000298171	NM_000369.2	158	aTt/aGt	6/10	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.28	2		271	261	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81574731	81574731	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	25	153	0	ENST00000298171.2:c.627G>T	p.Lys209Asn	p.K209N	ENST00000298171	NM_000369.2	209	aaG/aaT	8/10	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.28	2		153	120	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059465	42059465	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	70	272	0	ENST00000219905.7:c.9185C>A	p.Ser3062Tyr	p.S3062Y	ENST00000219905	NM_001164273.1	3062	tCt/tAt	24/24	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.28	2		272	478	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680785	88680785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	81	456	0	ENST00000360948.2:c.472G>A	p.Glu158Lys	p.E158K	ENST00000360948	NM_001012338.2	158	Gag/Aag	6/19	1	2	FACETS	0.829	0.73	0.935	0.829	0.73	0.935	CLONAL	1	TRUE	1	0.28	2		456	698	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292926	91292926	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1488217859	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	42	336	0	ENST00000355112.3:c.428C>A	p.Ser143Tyr	p.S143Y	ENST00000355112	NM_000057.2	143	tCt/tAt	3/22	1	2	FACETS	0.997	0.836	1	0.997	0.836	1	CLONAL	1	TRUE	1	0.28	2		336	301	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644457	3644457	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	115	483	0	ENST00000294008.3:c.2157G>C	p.Gln719His	p.Q719H	ENST00000294008	NM_032444.2	719	caG/caC	10/15	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.28	2		483	801	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832863	3832863	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	56	314	0	ENST00000262367.5:c.1395G>T	p.Gln465His	p.Q465H	ENST00000262367	NM_004380.2	465	caG/caT	6/31	1	2	FACETS	0.907	0.779	1	0.907	0.779	1	CLONAL	1	TRUE	1	0.28	2		314	441	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020582	14020582	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs767437700	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	25	233	1	ENST00000311895.7:c.553C>A	p.Leu185Ile	p.L185I	ENST00000311895	NM_005236.2	185	Ctt/Att	3/11	1	2	FACETS	0.692	0.547	0.858	0.692	0.547	0.858	SUBCLONAL	1	TRUE	1	0.28	2		234	258	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56792557	56792557	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1487797109	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	61	314	0	ENST00000308159.5:c.287C>T	p.Thr96Ile	p.T96I	ENST00000308159	NM_014669.4	96	aCt/aTt	3/22	1	2	FACETS	0.878	0.759	1	0.878	0.759	1	CLONAL	1	TRUE	1	0.28	2		314	496	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828693	72828693	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145288413	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	94	409	0	ENST00000268489.5:c.7888G>A	p.Asp2630Asn	p.D2630N	ENST00000268489	NM_006885.3	2630	Gac/Aac	9/10	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.28	2		409	633	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838134	89838134	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	111	433	0	ENST00000389301.3:c.2103G>T	p.Lys701Asn	p.K701N	ENST00000389301	NM_000135.2	701	aaG/aaT	23/43	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.28	2		433	756	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968325	15968325	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	19	186	0	ENST00000268712.3:c.4960G>T	p.Asp1654Tyr	p.D1654Y	ENST00000268712	NM_006311.3	1654	Gac/Tac	34/46	1	2	FACETS	0.738	0.563	0.941	0.738	0.563	0.941	CLONAL	1	TRUE	1	0.28	2		186	184	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527456	29527456	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	28	304	0	ENST00000356175.3:c.905G>C	p.Ser302Thr	p.S302T	ENST00000356175	NM_000267.3	302	aGt/aCt	9/57	1	2	FACETS	0.576	0.461	0.708	0.576	0.461	0.708	SUBCLONAL	1	TRUE	1	0.28	2		304	347	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677228	29677228	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533110479	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	43	248	0	ENST00000356175.3:c.7286G>A	p.Arg2429Gln	p.R2429Q	ENST00000356175	NM_000267.3	2429	cGa/cAa	49/57	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.28	2		248	208	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618712	37618712	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	68	371	0	ENST00000447079.4:c.388A>C	p.Lys130Gln	p.K130Q	ENST00000447079	NM_015083.1	130	Aaa/Caa	1/14	1	2	FACETS	0.911	0.794	1	0.911	0.794	1	CLONAL	1	TRUE	1	0.28	2		371	533	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884184	37884184	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	89	469	0	ENST00000269571.5:c.3655A>G	p.Asn1219Asp	p.N1219D	ENST00000269571		1219	Aac/Gac	27/27	1	2	FACETS	0.898	0.796	1	0.898	0.796	1	CLONAL	1	TRUE	1	0.28	2		469	708	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770874	59770874	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	16	181	0	ENST00000259008.2:c.2493-1G>T		p.X831_splice	ENST00000259008	NM_032043.2	831			1	2	FACETS	0.866	0.646	1	0.866	0.646	1	CLONAL	1	TRUE	1	0.28	2		181	132	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530044	63530044	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	67	358	0	ENST00000307078.5:c.2391A>C	p.Lys797Asn	p.K797N	ENST00000307078	NM_004655.3	797	aaA/aaC	10/11	1	2	FACETS	0.858	0.746	0.978	0.858	0.746	0.978	CLONAL	1	TRUE	1	0.28	2		358	558	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117539	70117539	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	55	408	0	ENST00000245479.2:c.7C>A	p.Leu3Ile	p.L3I	ENST00000245479	NM_000346.3	3	Ctc/Atc	1/3	1	2	FACETS	0.699	0.598	0.81	0.699	0.598	0.81	SUBCLONAL	1	TRUE	1	0.28	2		408	562	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39613831	39613831	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	12	287	0	ENST00000262039.4:c.1749G>T	p.Met583Ile	p.M583I	ENST00000262039	NM_002647.2	583	atG/atT	16/25	1	2	FACETS	0.437	0.307	0.597	0.437	0.307	0.597	SUBCLONAL	1	TRUE	1	0.28	2		287	196	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39623727	39623727	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	26	231	0	ENST00000262039.4:c.2134A>C	p.Asn712His	p.N712H	ENST00000262039	NM_002647.2	712	Aat/Cat	20/25	1	2	FACETS	0.784	0.623	0.966	0.784	0.623	0.966	CLONAL	1	TRUE	1	0.28	2		231	237	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298769	15298769	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	143	647	0	ENST00000263388.2:c.1529A>C	p.Glu510Ala	p.E510A	ENST00000263388	NM_000435.2	510	gAa/gCa	10/33	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.28	2		647	933	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954666	17954666	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	120	603	0	ENST00000458235.1:c.228G>T	p.Glu76Asp	p.E76D	ENST00000458235	NM_000215.3	76	gaG/gaT	3/24	1	2	FACETS	0.959	0.865	1	0.959	0.865	1	CLONAL	1	TRUE	1	0.28	2		603	894	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266855	18266855	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	107	574	0	ENST00000222254.8:c.166T>C	p.Trp56Arg	p.W56R	ENST00000222254	NM_005027.3	56	Tgg/Cgg	2/16	1	2	FACETS	0.913	0.819	1	0.913	0.819	1	CLONAL	1	TRUE	1	0.28	2		574	837	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257155	19257155	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	81	423	2	ENST00000162023.5:c.808T>G	p.Leu270Val	p.L270V	ENST00000162023		270	Ttg/Gtg	12/13	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.28	2		425	513	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211396	36211396	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	62	410	0	ENST00000222270.7:c.1147G>T	p.Glu383Ter	p.E383*	ENST00000222270	NM_014727.1	383	Gaa/Taa	3/37	1	2	FACETS	0.808	0.699	0.927	0.808	0.699	0.927	CLONAL	1	TRUE	1	0.28	2		410	548	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748878	41748878	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	73	514	0	ENST00000301178.4:c.1403C>A	p.Ala468Asp	p.A468D	ENST00000301178	NM_021913.4	468	gCt/gAt	11/20	1	2	FACETS	0.677	0.591	0.77	0.677	0.591	0.77	SUBCLONAL	1	TRUE	1	0.28	2		514	770	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462607	29462607	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	78	584	0	ENST00000389048.3:c.2294T>C	p.Leu765Pro	p.L765P	ENST00000389048	NM_004304.4	765	cTg/cCg	13/29	1	2	FACETS	0.759	0.666	0.859	0.759	0.666	0.859	SUBCLONAL	1	TRUE	1	0.28	2		584	734	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047272	128047272	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	33	276	0	ENST00000285398.2:c.650A>G	p.Lys217Arg	p.K217R	ENST00000285398	NM_000122.1	217	aAa/aGa	5/15	1	2	FACETS	0.601	0.49	0.727	0.601	0.49	0.727	SUBCLONAL	1	TRUE	1	0.28	2		276	392	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017153	31017153	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	50	167	0	ENST00000375687.4:c.484A>C	p.Lys162Gln	p.K162Q	ENST00000375687	NM_015338.5	162	Aag/Cag	7/13	1	2	FACETS	0.833	0.708	0.969	0.833	0.708	0.969	CLONAL	1	TRUE	1	0.28	2		167	429	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400125	41400125	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	77	415	0	ENST00000373198.4:c.634C>A	p.Gln212Lys	p.Q212K	ENST00000373198	NM_133170.3	212	Cag/Aag	5/32	1	2	FACETS	0.912	0.801	1	0.912	0.801	1	CLONAL	1	TRUE	1	0.28	2		415	603	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259394	36259394	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	76	474	1	ENST00000300305.3:c.98-1G>T		p.X33_splice	ENST00000300305		33			1	2	FACETS	0.81	0.711	0.918	0.81	0.711	0.918	CLONAL	1	TRUE	1	0.28	2		475	670	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795347	39795347	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	73	416	0	ENST00000288319.7:c.373G>T	p.Val125Phe	p.V125F	ENST00000288319	NM_182918.3	125	Gtt/Ttt	3/10	1	2	FACETS	0.838	0.733	0.951	0.838	0.733	0.951	CLONAL	1	TRUE	1	0.28	2		416	622	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536201	41536201	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	60	399	0	ENST00000263253.7:c.1818A>C	p.Glu606Asp	p.E606D	ENST00000263253	NM_001429.3	606	gaA/gaC	9/31	1	2	FACETS	0.882	0.761	1	0.882	0.761	1	CLONAL	1	TRUE	1	0.28	2		399	486	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458242	12458242	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	46	277	0	ENST00000287820.6:c.859G>T	p.Glu287Ter	p.E287*	ENST00000287820	NM_015869.4	287	Gaa/Taa	6/7	1	2	FACETS	0.821	0.693	0.962	0.821	0.693	0.962	CLONAL	1	TRUE	1	0.28	2		277	400	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626709	12626709	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	49	346	0	ENST00000251849.4:c.1580T>C	p.Phe527Ser	p.F527S	ENST00000251849	NM_002880.3	527	tTc/tCc	15/17	1	2	FACETS	0.729	0.618	0.851	0.729	0.618	0.851	SUBCLONAL	1	TRUE	1	0.28	2		346	480	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162426	47162426	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	41	310	0	ENST00000409792.3:c.3700G>T	p.Glu1234Ter	p.E1234*	ENST00000409792	NM_014159.6	1234	Gaa/Taa	3/21	1	2	FACETS	0.933	0.78	1	0.933	0.78	1	CLONAL	1	TRUE	1	0.28	2		310	314	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162482	47162482	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	16	274	0	ENST00000409792.3:c.3644A>C	p.Lys1215Thr	p.K1215T	ENST00000409792	NM_014159.6	1215	aAg/aCg	3/21	1	2	FACETS	0.452	0.334	0.592	0.452	0.334	0.592	SUBCLONAL	1	TRUE	1	0.28	2		274	253	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259655	89259655	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	27	182	1	ENST00000336596.2:c.799G>T	p.Gly267Cys	p.G267C	ENST00000336596	NM_005233.5	267	Ggt/Tgt	3/17	1	2	FACETS	0.821	0.656	1	0.821	0.656	1	CLONAL	1	TRUE	1	0.28	2		183	235	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266616	142266616	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	25	266	0	ENST00000350721.4:c.3308G>T	p.Ser1103Ile	p.S1103I	ENST00000350721	NM_001184.3	1103	aGt/aTt	16/47	1	2	FACETS	0.7	0.554	0.868	0.7	0.554	0.868	SUBCLONAL	1	TRUE	1	0.28	2		266	255	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268428	142268428	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	25	285	0	ENST00000350721.4:c.3064A>C	p.Asn1022His	p.N1022H	ENST00000350721	NM_001184.3	1022	Aat/Cat	15/47	1	2	FACETS	0.757	0.599	0.937	0.757	0.599	0.937	CLONAL	1	TRUE	1	0.28	2		285	236	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278198	142278198	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	31	324	1	ENST00000350721.4:c.1627G>T	p.Val543Leu	p.V543L	ENST00000350721	NM_001184.3	543	Gtg/Ttg	7/47	1	2	FACETS	0.993	0.808	1	0.993	0.808	1	CLONAL	1	TRUE	1	0.28	2		325	223	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998123	169998123	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1335738205	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	61	418	0	ENST00000295797.4:c.814C>T	p.Arg272Ter	p.R272*	ENST00000295797	NM_002740.5	272	Cga/Tga	9/18	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.28	2		418	370	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178941923	178941923	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	34	295	0	ENST00000263967.3:c.2242C>A	p.Leu748Ile	p.L748I	ENST00000263967	NM_006218.2	748	Cta/Ata	15/21	1	2	FACETS	0.714	0.585	0.859	0.714	0.585	0.859	SUBCLONAL	1	TRUE	1	0.28	2		295	340	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185200153	185200153	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	44	327	0	ENST00000265026.3:c.2810A>C	p.Gln937Pro	p.Q937P	ENST00000265026	NM_004721.4	937	cAg/cCg	14/14	1	2	FACETS	0.651	0.546	0.767	0.651	0.546	0.767	SUBCLONAL	1	TRUE	1	0.28	2		327	483	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807302	1807302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	98	542	0	ENST00000260795.2:c.1551G>T	p.Lys517Asn	p.K517N	ENST00000260795		517	aaG/aaT	11/17	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.28	2		542	684	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1936949	1936949	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	67	388	0	ENST00000382891.5:c.1634C>A	p.Pro545His	p.P545H	ENST00000382891	NM_133335.3	545	cCc/cAc	7/22	1	2	FACETS	0.835	0.726	0.953	0.835	0.726	0.953	CLONAL	1	TRUE	1	0.28	2		388	573	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1953960	1953960	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	97	537	0	ENST00000382891.5:c.2137+2C>G		p.X713_splice	ENST00000382891	NM_133335.3	713			1	2	FACETS	0.91	0.812	1	0.91	0.812	1	CLONAL	1	TRUE	1	0.28	2		537	761	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133762	55133762	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	63	319	0	ENST00000257290.5:c.975A>T	p.Glu325Asp	p.E325D	ENST00000257290	NM_006206.4	325	gaA/gaT	7/23	1	2	FACETS	0.949	0.823	1	0.949	0.823	1	CLONAL	1	TRUE	1	0.28	2		319	474	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144528	55144528	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	33	299	0	ENST00000257290.5:c.2003-1G>A		p.X668_splice	ENST00000257290	NM_006206.4	668			1	2	FACETS	0.807	0.66	0.972	0.807	0.66	0.972	CLONAL	1	TRUE	1	0.28	2		299	292	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003209	143003209	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	58	279	0	ENST00000262992.4:c.2617A>G	p.Ile873Val	p.I873V	ENST00000262992	NM_001101669.1	873	Atc/Gtc	23/24	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.28	2		279	352	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007376	143007376	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	12	169	0	ENST00000262992.4:c.2408A>C	p.Lys803Thr	p.K803T	ENST00000262992	NM_001101669.1	803	aAa/aCa	22/24	1	2	FACETS	0.587	0.414	0.798	0.587	0.414	0.798	SUBCLONAL	1	TRUE	1	0.28	2		169	146	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244200	153244200	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	50	284	0	ENST00000281708.4:c.1957A>G	p.Thr653Ala	p.T653A	ENST00000281708	NM_033632.3	653	Acg/Gcg	12/12	1	2	FACETS	0.794	0.674	0.924	0.794	0.674	0.924	CLONAL	1	TRUE	1	0.28	2		284	450	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554912	187554912	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	60	315	0	ENST00000441802.2:c.4249C>A	p.Leu1417Ile	p.L1417I	ENST00000441802	NM_005245.3	1417	Ctt/Att	7/27	1	2	FACETS	0.938	0.81	1	0.938	0.81	1	CLONAL	1	TRUE	1	0.28	2		315	457	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753981	57753981	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	31	204	0	ENST00000274289.3:c.643G>T	p.Glu215Ter	p.E215*	ENST00000274289	NM_006622.3	215	Gaa/Taa	5/14	1	2	FACETS	0.733	0.595	0.889	0.733	0.595	0.889	SUBCLONAL	1	TRUE	1	0.28	2		204	302	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754280	57754280	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	51	300	0	ENST00000274289.3:c.571T>G	p.Ser191Ala	p.S191A	ENST00000274289	NM_006622.3	191	Tct/Gct	4/14	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.28	2		300	341	SUCCESS
APC	324	MSKCC	GRCh37	5	112111328	112111328	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	10	96	0	ENST00000257430.4:c.425C>A	p.Ser142Ter	p.S142*	ENST00000257430	NM_000038.5	142	tCa/tAa	5/16	1	2	FACETS	0.831	0.569	1	0.831	0.569	1	CLONAL	1	TRUE	1	0.28	2		96	86	SUCCESS
APC	324	MSKCC	GRCh37	5	112176050	112176050	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	28	225	0	ENST00000257430.4:c.4759T>A	p.Ser1587Thr	p.S1587T	ENST00000257430	NM_000038.5	1587	Tca/Aca	16/16	1	2	FACETS	0.769	0.617	0.941	0.769	0.617	0.941	CLONAL	1	TRUE	1	0.28	2		225	260	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927617	131927617	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	15	198	0	ENST00000265335.6:c.1684G>T	p.Glu562Ter	p.E562*	ENST00000265335		562	Gaa/Taa	11/25	1	2	FACETS	0.812	0.598	1	0.812	0.598	1	CLONAL	1	TRUE	1	0.28	2		198	132	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460454	149460454	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	113	517	0	ENST00000286301.3:c.183C>A	p.Tyr61Ter	p.Y61*	ENST00000286301	NM_005211.3	61	taC/taA	3/22	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.28	2		517	714	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819917	170819917	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	15	202	0	ENST00000296930.5:c.460-1G>T		p.X154_splice	ENST00000296930	NM_002520.6	154			1	2	FACETS	0.705	0.518	0.926	0.705	0.518	0.926	CLONAL	1	TRUE	1	0.28	2		202	152	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180076524	180076524	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	18	141	0	ENST00000261937.6:c.22T>C	p.Cys8Arg	p.C8R	ENST00000261937	NM_182925.4	8	Tgc/Cgc	1/30	1	2	FACETS	0.523	0.394	0.674	0.523	0.394	0.674	SUBCLONAL	1	TRUE	1	0.28	2		141	246	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671599	30671599	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	73	432	0	ENST00000376406.3:c.5361G>T	p.Gln1787His	p.Q1787H	ENST00000376406	NM_014641.2	1787	caG/caT	10/15	1	2	FACETS	0.761	0.665	0.865	0.761	0.665	0.865	SUBCLONAL	1	TRUE	1	0.28	2		432	685	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185829	32185829	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	88	555	0	ENST00000375023.3:c.1567C>A	p.Leu523Met	p.L523M	ENST00000375023	NM_004557.3	523	Ctg/Atg	9/30	1	2	FACETS	0.719	0.636	0.808	0.719	0.636	0.808	SUBCLONAL	1	TRUE	1	0.28	2		555	874	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797276	32797276	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	96	568	0	ENST00000374899.4:c.1833G>T	p.Gln611His	p.Q611H	ENST00000374899	NM_018833.2	611	caG/caT	11/12	1	2	FACETS	0.767	0.682	0.857	0.767	0.682	0.857	SUBCLONAL	1	TRUE	1	0.28	2		568	894	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286887	33286887	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	92	530	0	ENST00000374542.5:c.2050A>G	p.Thr684Ala	p.T684A	ENST00000374542	NM_001141970.1	684	Acg/Gcg	7/8	1	2	FACETS	0.842	0.748	0.943	0.842	0.748	0.943	CLONAL	1	TRUE	1	0.28	2		530	780	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196141	138196141	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	63	231	0	ENST00000237289.4:c.455T>G	p.Phe152Cys	p.F152C	ENST00000237289	NM_001270507.1	152	tTt/tGt	3/9	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.28	2		231	422	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099757	157099757	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	37	193	0	ENST00000346085.5:c.694A>C	p.Asn232His	p.N232H	ENST00000346085	NM_020732.3	232	Aat/Cat	1/20	1	2	FACETS	0.878	0.727	1	0.878	0.727	1	CLONAL	1	TRUE	1	0.28	2		193	301	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268989	55268989	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1562805765	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	107	425	1	ENST00000275493.2:c.3055C>A	p.Pro1019Thr	p.P1019T	ENST00000275493	NM_005228.3	1019	Cca/Aca	25/28	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.28	2		426	725	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350125	81350125	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	23	295	0	ENST00000222390.5:c.1207T>G	p.Leu403Val	p.L403V	ENST00000222390	NM_000601.4	403	Tta/Gta	10/18	1	2	FACETS	0.73	0.572	0.912	0.73	0.572	0.912	CLONAL	1	TRUE	1	0.28	2		295	225	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508329	106508329	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	45	331	0	ENST00000359195.3:c.323A>T	p.Glu108Val	p.E108V	ENST00000359195	NM_002649.2	108	gAg/gTg	2/11	1	2	FACETS	0.736	0.619	0.864	0.736	0.619	0.864	SUBCLONAL	1	TRUE	1	0.28	2		331	437	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397722	116397722	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	53	327	0	ENST00000397752.3:c.1996T>C	p.Tyr666His	p.Y666H	ENST00000397752	NM_000245.2	666	Tac/Cac	8/21	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.28	2		327	316	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540127	23540127	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	49	309	0	ENST00000380871.4:c.276G>T	p.Glu92Asp	p.E92D	ENST00000380871	NM_006167.3	92	gaG/gaT	1/2	1	2	FACETS	0.732	0.621	0.855	0.732	0.621	0.855	SUBCLONAL	1	TRUE	1	0.28	2		309	478	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56910937	56910937	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	94	368	0	ENST00000519728.1:c.1083G>T	p.Lys361Asn	p.K361N	ENST00000519728	NM_002350.3	361	aaG/aaT	11/13	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.28	2		368	628	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970918	70970918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1211840014	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	94	381	0	ENST00000276594.2:c.1343G>A	p.Arg448Gln	p.R448Q	ENST00000276594	NM_024504.3	448	cGg/cAg	6/8	1	2	FACETS	0.948	0.844	1	0.948	0.844	1	CLONAL	1	TRUE	1	0.28	2		381	708	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117875397	117875397	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	34	250	1	ENST00000297338.2:c.246C>A	p.Phe82Leu	p.F82L	ENST00000297338	NM_006265.2	82	ttC/ttA	3/14	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.28	2		251	216	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5557740	5557740	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	34	235	1	ENST00000397747.3:c.754T>C	p.Tyr252His	p.Y252H	ENST00000397747	NM_025239.3	252	Tat/Cat	5/7	1	2	FACETS	0.826	0.677	0.992	0.826	0.677	0.992	CLONAL	1	TRUE	1	0.28	2		236	294	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376091	8376091	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	29	153	0	ENST00000356435.5:c.4507-1G>T		p.X1503_splice	ENST00000356435		1503			1	2	FACETS	1	0.835	1	1	0.835	1	CLONAL	1	TRUE	1	0.28	2		153	200	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484375	8484375	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	25	196	0	ENST00000356435.5:c.3157C>A	p.Leu1053Ile	p.L1053I	ENST00000356435		1053	Ctt/Att	19/35	1	2	FACETS	0.888	0.705	1	0.888	0.705	1	CLONAL	1	TRUE	1	0.28	2		196	201	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500939	8500939	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	26	309	0	ENST00000356435.5:c.1943A>C	p.Lys648Thr	p.K648T	ENST00000356435		648	aAg/aCg	13/35	1	2	FACETS	0.493	0.39	0.61	0.493	0.39	0.61	SUBCLONAL	1	TRUE	1	0.28	2		309	377	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339247	87339247	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	29	331	0	ENST00000277120.3:c.829G>T	p.Asp277Tyr	p.D277Y	ENST00000277120		277	Gat/Tat	8/19	1	2	FACETS	0.49	0.393	0.6	0.49	0.393	0.6	SUBCLONAL	1	TRUE	1	0.28	2		331	423	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730365	133730365	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	76	387	0	ENST00000318560.5:c.431G>T	p.Gly144Val	p.G144V	ENST00000318560	NM_005157.4	144	gGg/gTg	3/11	1	2	FACETS	0.864	0.758	0.978	0.864	0.758	0.978	CLONAL	1	TRUE	1	0.28	2		387	628	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321058	137321058	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs757381591	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	81	534	0	ENST00000481739.1:c.1015A>G	p.Ser339Gly	p.S339G	ENST00000481739	NM_002957.4	339	Agc/Ggc	7/10	1	2	FACETS	0.841	0.741	0.948	0.841	0.741	0.948	CLONAL	1	TRUE	1	0.28	2		534	688	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349905	70349905	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	80	566	0	ENST00000374080.3:c.3888C>A	p.Cys1296Ter	p.C1296*	ENST00000374080		1296	tgC/tgA	28/45	0.202817456493915	1	FACETS	0.672	0.591	0.759	0.672	0.591	0.759	SUBCLONAL	1	TRUE	0	0.28	1		566	731	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354640	70354640	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	77	439	0	ENST00000374080.3:c.4805C>T	p.Ser1602Leu	p.S1602L	ENST00000374080		1602	tCg/tTg	35/45	0.202817456493915	1	FACETS	0.709	0.622	0.802	0.709	0.622	0.802	SUBCLONAL	1	TRUE	0	0.28	1		439	667	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938149	76938149	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	34	403	0	ENST00000373344.5:c.2599A>C	p.Asn867His	p.N867H	ENST00000373344	NM_000489.3	867	Aat/Cat	9/35	0.202817456493915	1	FACETS	0.607	0.497	0.731	0.607	0.497	0.731	SUBCLONAL	1	TRUE	0	0.28	1		403	344	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972659	76972659	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	38	320	0	ENST00000373344.5:c.82G>T	p.Glu28Ter	p.E28*	ENST00000373344	NM_000489.3	28	Gaa/Taa	2/35	0.202817456493915	1	FACETS	0.816	0.678	0.969	0.816	0.678	0.969	CLONAL	1	TRUE	0	0.28	1		320	286	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197893	123197893	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	10	225	0	ENST00000218089.9:c.2017C>A	p.Leu673Met	p.L673M	ENST00000218089	NM_001042749.1	673	Ctg/Atg	20/35	0.202817456493915	1	FACETS	0.391	0.265	0.549	0.391	0.265	0.549	SUBCLONAL	1	TRUE	0	0.28	1		225	157	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202434	123202434	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	12	230	0	ENST00000218089.9:c.2286G>T	p.Lys762Asn	p.K762N	ENST00000218089	NM_001042749.1	762	aaG/aaT	24/35	0.202817456493915	1	FACETS	0.485	0.342	0.659	0.485	0.342	0.659	SUBCLONAL	1	TRUE	0	0.28	1		230	152	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215241	123215241	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	23	237	0	ENST00000218089.9:c.2787A>C	p.Glu929Asp	p.E929D	ENST00000218089	NM_001042749.1	929	gaA/gaC	28/35	0.202817456493915	1	FACETS	0.803	0.631	0.999	0.803	0.631	0.999	CLONAL	1	TRUE	0	0.28	1		237	176	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0049074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	76	628	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.162462181549383	2		628	796	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0049074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	34	523	1	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	1	2	FACETS	0.498	0.405	0.603	0.498	0.405	0.603	SUBCLONAL	1	FALSE	1	0.162462181549383	2		524	841	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371806	55371806	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	28	290	0	ENST00000297316.4:c.496G>A	p.Ala166Thr	p.A166T	ENST00000297316	NM_022454.3	166	Gcg/Acg	2/2	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	FALSE	1	0.162462181549383	2		290	278	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78831654	78831654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780248757	NA	P-0049074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	97	788	1	ENST00000306801.3:c.1463G>A	p.Arg488Gln	p.R488Q	ENST00000306801	NM_020761.2	488	cGg/cAg	13/34	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.162462181549383	2		789	891	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577111	7577111	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs786202082	NA	P-0049075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	591	600	0	ENST00000269305.4:c.827C>G	p.Ala276Gly	p.A276G	ENST00000269305	NM_001126112.2	276	gCc/gGc	8/11	0.576021753316171	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	TRUE	0	0.576021753316171	3		600	877	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458911	120458911	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0049075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	84	594	0	ENST00000256646.2:c.6434C>G	p.Ser2145Ter	p.S2145*	ENST00000256646	NM_024408.3	2145	tCa/tGa	34/34	0.193902451517527	1	FACETS	0.444	0.393	0.497	0.444	0.393	0.497	INDETERMINATE	1	TRUE	0	0.576021753316171	1		594	468	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912001	32912007	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCATC	CCCCATC	-	novel	NA	P-0049075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	161	472	0	ENST00000380152.3:c.3509_3515del	p.Ala1170GlyfsTer5	p.A1170Gfs*5	ENST00000380152		1170	gCCCCATCg/gg	11/27	0.481485414842153	2	FACETS	1	0.99	1	0.72	0.669	0.772	CLONAL	1	TRUE	0	0.576021753316171	2		472	388	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636743	2636748	+	inframe_deletion	In_Frame_Del	DEL	TCAGCC	TCAGCC	-	novel	NA	P-0049075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	118	534	1	ENST00000342085.4:c.1194_1199del	p.Ala399_Ser400del	p.A399_S400del	ENST00000342085	NM_002613.4	398	TCAGCC/-	11/14	0.564243833071411	3	FACETS	0.775	0.7	0.854	0.387	0.35	0.427	SUBCLONAL	1	TRUE	1	0.576021753316171	3		535	681	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551239	29551239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	108	595	0	ENST00000389048.3:c.1391G>A	p.Gly464Glu	p.G464E	ENST00000389048	NM_004304.4	464	gGa/gAa	6/29	0.179209926060234	3	FACETS	0.872	0.785	0.963	0.291	0.261	0.321	INDETERMINATE	1	TRUE	0	0.576021753316171	3		595	554	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1918626	1918626	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	81	348	0	ENST00000382891.5:c.789C>G	p.His263Gln	p.H263Q	ENST00000382891	NM_133335.3	263	caC/caG	4/22	0.253220265829328	2	FACETS	0.558	0.493	0.628	0.279	0.246	0.314	INDETERMINATE	1	TRUE	0	0.576021753316171	2		348	504	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003247	143003247	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	96	387	0	ENST00000262992.4:c.2579T>C	p.Ile860Thr	p.I860T	ENST00000262992	NM_001101669.1	860	aTc/aCc	23/24	0.443712056915301	3	FACETS	0.86	0.77	0.956	0.43	0.385	0.478	CLONAL	1	TRUE	1	0.576021753316171	3		387	499	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739710	41739710	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	117	611	0	ENST00000242208.4:c.263G>C	p.Arg88Thr	p.R88T	ENST00000242208	NM_002192.2	88	aGa/aCa	2/3	0.179209926060234	3	FACETS	0.698	0.629	0.77	0.233	0.209	0.257	INDETERMINATE	1	TRUE	0	0.576021753316171	3		611	750	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0049076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	58	161	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	FALSE	1	0.355918917088111	2		161	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577518	7577518	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519995	NA	P-0049076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	167	635	0	ENST00000269305.4:c.763A>T	p.Ile255Phe	p.I255F	ENST00000269305	NM_001126112.2	255	Atc/Ttc	7/11	0.355918917088111	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	0	0.355918917088111	1		635	652	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001523	150001523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264217871	NA	P-0049076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	98	259	0	ENST00000253339.5:c.2081G>A	p.Arg694His	p.R694H	ENST00000253339		694	cGt/cAt	4/7	1	2	FACETS	0.954	0.853	1	0.954	0.853	1	CLONAL	1	FALSE	1	0.355918917088111	2		259	577	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250867	153250867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	79	220	0	ENST00000281708.4:c.1193C>T	p.Ser398Phe	p.S398F	ENST00000281708	NM_033632.3	398	tCt/tTt	8/12	0.355918917088111	1	FACETS	0.824	0.727	0.926	0.824	0.727	0.926	CLONAL	1	FALSE	0	0.355918917088111	1		220	443	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023141	27023143	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs1015322780	NA	P-0049077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	10	73	0	ENST00000324856.7:c.258_260del	p.Gly87del	p.G87del	ENST00000324856	NM_006015.4	83	GGC/-	1/20	1	2	FACETS	0.802	0.546	1	0.802	0.546	1	CLONAL	1	FALSE	1	0.190298672274099	2		73	131	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447263	49447263	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	208	588	1	ENST00000301067.7:c.835T>C	p.Cys279Arg	p.C279R	ENST00000301067	NM_003482.3	279	Tgc/Cgc	6/54	1	2	FACETS	0.987	0.928	1	1	0.996	1	CLONAL	5	FALSE	1	0.190298672274099	2		589	443	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351743	89351743	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	204	714	0	ENST00000301030.4:c.1207T>A	p.Ser403Thr	p.S403T	ENST00000301030	NM_001256183.1	403	Tcc/Acc	9/13	0.190298672274099	5	FACETS	0.98	0.912	1	0.784	0.73	0.84	CLONAL	4	FALSE	0	0.190298672274099	5		714	703	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933397	49933398	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0049077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	128	764	0	ENST00000296474.3:c.2791_2792dup	p.Leu931PhefsTer6	p.L931Ffs*6	ENST00000296474	NM_002447.2	931	ttg/ttTTg	11/20	0.190298672274099	8	FACETS	0.95	0.867	1	0.678	0.619	0.739	CLONAL	5	FALSE	1	0.190298672274099	8		764	445	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80149984	80149984	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	65	129	0	ENST00000265081.6:c.2849G>C	p.Ser950Thr	p.S950T	ENST00000265081	NM_002439.4	950	aGt/aCt	21/24	0.190298672274099	5	FACETS	0.976	0.863	1	1	0.978	1	CLONAL	5	FALSE	2	0.190298672274099	5		129	180	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0049079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	196	428	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.444882197061724	3	FACETS	0.987	0.921	1	0.987	0.921	1	CLONAL	2	TRUE	1	0.462002304540619	3		428	529	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913315	NA	P-0049079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	349	697	0	ENST00000326873.7:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000326873	NM_000455.4	194	Gac/Tac	4/10	0.462002304540619	2	FACETS	0.901	0.858	0.946	0.901	0.858	0.946	CLONAL	2	TRUE	0	0.462002304540619	2		697	838	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602878	10602878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	470	795	0	ENST00000171111.5:c.700C>T	p.Arg234Trp	p.R234W	ENST00000171111	NM_203500.1	234	Cgg/Tgg	3/6	0.462002304540619	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.462002304540619	2		795	938	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619203	43619203	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	149	558	0	ENST00000355710.3:c.2886C>A	p.Asn962Lys	p.N962K	ENST00000355710	NM_020975.4	962	aaC/aaA	17/20	0.429332139639779	4	FACETS	0.949	0.866	1	0.474	0.433	0.518	CLONAL	1	TRUE	2	0.462002304540619	4		558	994	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157183	106157183	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	68	337	0	ENST00000380013.4:c.2084T>A	p.Met695Lys	p.M695K	ENST00000380013	NM_001127208.2	695	aTg/aAg	3/11	0.444882197061724	3	FACETS	0.789	0.689	0.898	0.395	0.344	0.449	SUBCLONAL	1	TRUE	1	0.462002304540619	3		337	459	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069662	69069662	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	134	374	0	ENST00000288368.4:c.4337A>C	p.Gln1446Pro	p.Q1446P	ENST00000288368	NM_024870.2	1446	cAg/cCg	35/40	0.429332139639779	4	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	2	0.462002304540619	4		374	412	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0049079-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	193	428	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.368722443382546	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.39874927287128	3		428	545	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913315	NA	P-0049079-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	170	697	0	ENST00000326873.7:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000326873	NM_000455.4	194	Gac/Tac	4/10	0.39874927287128	2	FACETS	0.888	0.824	0.954	0.888	0.824	0.954	CLONAL	2	TRUE	0	0.39874927287128	2		697	480	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602878	10602878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049079-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	277	795	0	ENST00000171111.5:c.700C>T	p.Arg234Trp	p.R234W	ENST00000171111	NM_203500.1	234	Cgg/Tgg	3/6	0.39874927287128	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.39874927287128	2		795	681	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619203	43619203	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049079-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	88	558	0	ENST00000355710.3:c.2886C>A	p.Asn962Lys	p.N962K	ENST00000355710	NM_020975.4	962	aaC/aaA	17/20	0.337724050214638	4	FACETS	0.968	0.858	1	0.484	0.429	0.543	CLONAL	1	TRUE	2	0.39874927287128	4		558	638	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157183	106157183	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049079-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	73	337	0	ENST00000380013.4:c.2084T>A	p.Met695Lys	p.M695K	ENST00000380013	NM_001127208.2	695	aTg/aAg	3/11	0.340185669077881	3	FACETS	0.989	0.868	1	0.495	0.434	0.559	CLONAL	1	TRUE	1	0.39874927287128	3		337	444	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069662	69069662	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049079-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	180	374	0	ENST00000288368.4:c.4337A>C	p.Gln1446Pro	p.Q1446P	ENST00000288368	NM_024870.2	1446	cAg/cCg	35/40	0.31007138348547	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.39874927287128	4		374	564	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141426	11141426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049079-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	128	638	0	ENST00000358026.2:c.3403C>T	p.Arg1135Trp	p.R1135W	ENST00000358026	NM_001128849.1	1135	Cgg/Tgg	25/36	0.39874927287128	2	FACETS	1	0.969	1	0.571	0.52	0.625	CLONAL	1	TRUE	0	0.39874927287128	2		638	562	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0049080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	61	498	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.176985261337132	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	2	FALSE	0	0.176985261337132	2		498	342	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0049080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	164	621	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	0.176985261337132	2	FACETS	0.971	0.895	1	1	0.989	1	CLONAL	3	FALSE	0	0.176985261337132	2		621	636	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572857	41572858	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGA	novel	NA	P-0049080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	34	550	0	ENST00000263253.7:c.5144_5147dup	p.Ser1716ArgfsTer168	p.S1716Rfs*168	ENST00000263253	NM_001429.3	1714	-/GAGA	31/31	1	2	FACETS	0.933	0.762	1	0.933	0.762	1	CLONAL	1	FALSE	1	0.176985261337132	2		550	412	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0049087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	182	425	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.289539432929082	3	FACETS	0.813	0.75	0.877	0.542	0.5	0.585	CLONAL	2	TRUE	0	0.294349089886596	3		425	873	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577138	7577138	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587780075	NA	P-0049087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	394	516	0	ENST00000269305.4:c.800G>C	p.Arg267Pro	p.R267P	ENST00000269305	NM_001126112.2	267	cGg/cCg	8/11	0.289539432929082	3	FACETS	0.958	0.912	1	0.958	0.912	1	CLONAL	3	TRUE	0	0.294349089886596	3		516	1069	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62305428	62305428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201365106	NA	P-0049087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	452	588	5	ENST00000360203.5:c.901G>A	p.Ala301Thr	p.A301T	ENST00000360203	NM_001283009.1	301	Gcg/Acg	10/35	0.294349089886596	4	FACETS	0.909	0.867	0.951	0.909	0.867	0.951	CLONAL	3	TRUE	1	0.294349089886596	4		593	1458	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246092	46246092	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	57	267	0	ENST00000334344.6:c.4186C>T	p.Gln1396Ter	p.Q1396*	ENST00000334344	NM_152641.2	1396	Caa/Taa	15/21	0.244106489507659	3	FACETS	1	0.958	1	0.651	0.562	0.748	CLONAL	1	TRUE	1	0.294349089886596	3		267	341	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266793	18266793	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762238231	NA	P-0049087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	121	322	2	ENST00000222254.8:c.104G>A	p.Arg35Gln	p.R35Q	ENST00000222254	NM_005027.3	35	cGg/cAg	2/16	0.249328434005503	3	FACETS	1	0.961	1	0.374	0.338	0.413	CLONAL	1	TRUE	0	0.294349089886596	3		324	840	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512384	38512384	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774473938	NA	P-0049087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	301	290	1	ENST00000254066.5:c.1295G>A	p.Arg432Gln	p.R432Q	ENST00000254066	NM_000964.3	432	cGg/cAg	9/9	0.289539432929082	3	FACETS	0.915	0.869	0.961	1	0.992	1	CLONAL	4	TRUE	0	0.294349089886596	3		291	641	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426934	70426934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241056232	NA	P-0049087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	228	342	2	ENST00000373644.4:c.4594C>T	p.Arg1532Trp	p.R1532W	ENST00000373644	NM_030625.2	1532	Cgg/Tgg	7/12	0.249328434005503	3	FACETS	0.882	0.826	0.938	0.882	0.826	0.938	CLONAL	3	TRUE	0	0.294349089886596	3		344	672	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428192	49428192	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0049087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	240	555	0	ENST00000301067.7:c.10507+1G>C		p.X3503_splice	ENST00000301067	NM_003482.3	3503			0.244106489507659	3	FACETS	0.823	0.768	0.88	0.823	0.768	0.88	CLONAL	2	TRUE	1	0.294349089886596	3		555	1136	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0049088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	108	583	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.612435745581874	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.612435745581874	3		583	197	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0049088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	21	208	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.577923033395325	2	FACETS	0.836	0.687	0.985	0.836	0.687	0.985	CLONAL	2	TRUE	0	0.612435745581874	2		208	41	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0049088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	57	655	1	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.612435745581874	3	FACETS	1	0.935	1	0.563	0.489	0.641	CLONAL	1	TRUE	1	0.612435745581874	3		656	216	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14017099	14017099	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	30	220	0	ENST00000405192.2:c.188T>C	p.Val63Ala	p.V63A	ENST00000405192	NM_001163147.1	63	gTa/gCa	5/12	0.612435745581874	6	FACETS	1	0.882	1	0.545	0.45	0.646	CLONAL	2	TRUE	2	0.612435745581874	6		220	100	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469669	NA	P-0049089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	19	350	0	ENST00000374080.3:c.130G>A	p.Gly44Ser	p.G44S	ENST00000374080		44	Ggt/Agt	2/45	0.123933749524488	1	FACETS	0.654	0.496	0.84	0.654	0.496	0.84	SUBCLONAL	1	TRUE	0	0.16	1		350	334	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0049089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	13	293	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.671	0.479	0.907	0.671	0.479	0.907	SUBCLONAL	1	TRUE	1	0.16	2		293	242	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057947	27057948	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	40	336	0	ENST00000324856.7:c.1656dup	p.Gln553ThrfsTer70	p.Q553Tfs*70	ENST00000324856	NM_006015.4	552	tca/tcAa	3/20	1	2	FACETS	0.962	0.798	1	0.962	0.798	1	CLONAL	1	TRUE	1	0.16	2		336	520	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	166	431	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.371699229963118	3	FACETS	0.923	0.852	0.995	0.923	0.852	0.995	CLONAL	2	TRUE	1	0.371699229963118	3		431	574	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882019	NA	P-0049090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	178	658	0	ENST00000269305.4:c.455dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	ccg/ccCg	5/11	0.371699229963118	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.371699229963118	1		658	718	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440430	49440431	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0049090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	107	510	0	ENST00000301067.7:c.4379dup	p.Leu1461ThrfsTer30	p.L1461Tfs*30	ENST00000301067	NM_003482.3	1460	cca/ccCa	15/54	0.371699229963118	3	FACETS	0.799	0.716	0.887			1	SUBCLONAL	1	TRUE	NA	0.371699229963118	3		510	855	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851075	63851075	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	101	395	0	ENST00000279873.7:c.1853C>A	p.Ala618Asp	p.A618D	ENST00000279873	NM_032199.2	618	gCc/gAc	10/10	1	2	FACETS	0.872	0.781	0.969	0.872	0.781	0.969	CLONAL	1	TRUE	1	0.371699229963118	2		395	623	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037455	12037463	+	inframe_deletion	In_Frame_Del	DEL	CAAAGAATC	CAAAGAATC	-	novel	NA	P-0049090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	175	306	0	ENST00000396373.4:c.1090_1098del	p.Glu364_Lys366del	p.E364_K366del	ENST00000396373	NM_001987.4	362	gaCAAAGAATCc/gac	6/8	0.371699229963118	3	FACETS	0.898	0.83	0.967	0.898	0.83	0.967	CLONAL	2	TRUE	1	0.371699229963118	3		306	622	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422188	81422188	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	92	311	0	ENST00000298171.2:c.164A>G	p.Gln55Arg	p.Q55R	ENST00000298171	NM_000369.2	55	cAg/cGg	1/10	1	2	FACETS	0.971	0.865	1	0.971	0.865	1	CLONAL	1	TRUE	1	0.371699229963118	2		311	510	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89807275	89807275	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0049090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	68	242	0	ENST00000389301.3:c.3766-1G>A		p.X1256_splice	ENST00000389301	NM_000135.2	1256			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.371699229963118	2		242	315	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713385	40713385	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs180871064	NA	P-0049090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	162	463	1	ENST00000373198.4:c.4130G>A	p.Arg1377Gln	p.R1377Q	ENST00000373198	NM_133170.3	1377	cGa/cAa	30/32	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.371699229963118	2		464	766	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0049091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	442	511	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.809104558742806	2		511	1037	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578266	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs942158624	NA	P-0049091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	413	518	0	ENST00000269305.4:c.583A>T	p.Ile195Phe	p.I195F	ENST00000269305	NM_001126112.2	195	Atc/Ttc	6/11	1	2	FACETS	0.948	0.905	0.992	0.948	0.905	0.992	CLONAL	1	TRUE	1	0.809104558742806	2		518	1077	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974744	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAGCAGCGCCCGCA	CCTCCAGCAGCGCCCGCA	-	novel	NA	P-0049091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	558	310	0	ENST00000304494.5:c.83_100del	p.Val28_Glu33del	p.V28_E33del	ENST00000304494	NM_000077.4	28	gTGCGGGCGCTGCTGGAGGcg/gcg	1/3	0.785058625819406	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.809104558742806	1		310	789	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106489	27106489	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	437	491	1	ENST00000324856.7:c.6100G>T	p.Glu2034Ter	p.E2034*	ENST00000324856	NM_006015.4	2034	Gag/Tag	20/20	0.809104558742806	1	FACETS	0.985	0.952	1	0.985	0.952	1	CLONAL	1	TRUE	0	0.809104558742806	1		492	653	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610364	10610364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	678	683	1	ENST00000171111.5:c.346C>T	p.Arg116Trp	p.R116W	ENST00000171111	NM_203500.1	116	Cgg/Tgg	2/6	0.809104558742806	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.809104558742806	1		684	962	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098895	178098900	+	inframe_deletion	In_Frame_Del	DEL	TTTTTC	TTTTTC	-	novel	NA	P-0049091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	168	314	0	ENST00000397062.3:c.145_150del	p.Glu49_Lys50del	p.E49_K50del	ENST00000397062	NM_006164.4	49	GAAAAA/-	2/5	0.740252772711487	1	FACETS	0.706	0.66	0.753	0.706	0.66	0.753	SUBCLONAL	1	TRUE	0	0.809104558742806	1		314	350	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225365186	225365186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	352	225	0	ENST00000264414.4:c.1504G>A	p.Asp502Asn	p.D502N	ENST00000264414	NM_003590.4	502	Gat/Aat	11/16	0.740252772711487	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.809104558742806	1		225	515	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376772	31376772	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	485	483	0	ENST00000328111.2:c.767C>G	p.Ser256Cys	p.S256C	ENST00000328111	NM_006892.3	256	tCt/tGt	7/23	0.594470384170249	1	FACETS	0.775	0.746	0.804	0.775	0.746	0.804	SUBCLONAL	1	TRUE	0	0.809104558742806	1		483	921	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265450	46265450	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	35	219	0	ENST00000371998.3:c.2320A>G	p.Ile774Val	p.I774V	ENST00000371998		774	Att/Gtt	12/23	0.594470384170249	1	FACETS	0.221	0.182	0.264	0.221	0.182	0.264	SUBCLONAL	1	TRUE	0	0.809104558742806	1		219	233	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162773	47162774	+	missense_variant	Missense_Mutation	DNP	TC	TC	AA	novel	NA	P-0049091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	70	299	0	ENST00000409792.3:c.3352_3353delinsTT	p.Glu1118Leu	p.E1118L	ENST00000409792	NM_014159.6	1118	GAa/TTa	3/21	0.704119072560611	1	FACETS	0.498	0.441	0.556	0.498	0.441	0.556	SUBCLONAL	1	TRUE	0	0.809104558742806	1		299	207	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151216560	151216560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	190	136	0	ENST00000262187.5:c.38G>A	p.Gly13Asp	p.G13D	ENST00000262187	NM_005614.3	13	gGc/gAc	1/8	0.331296407738087	1	FACETS	0.403	0.374	0.433	0.403	0.374	0.433	INDETERMINATE	1	TRUE	0	0.809104558742806	1		136	694	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132931	30132933	+	frameshift_variant	Frame_Shift_Del	DEL	TAG	TAG	C	novel	NA	P-0049091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	423	426	0	ENST00000331968.5:c.668_670delinsG	p.Ser223CysfsTer5	p.S223Cfs*5	ENST00000331968	NM_002742.2	223	tCTAca/tGca	4/18	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.809104558742806	2		426	1043	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	72	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.985	0.875	1	0.985	0.875	1	CLONAL	1	TRUE	1	0.686387679412584	2		148	213	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0049092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	301	368	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.686387679412584	2	FACETS	1	0.993	1	0.654	0.62	0.687	CLONAL	1	TRUE	0	0.686387679412584	2		368	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579529	7579529	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658483	NA	P-0049092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	258	527	0	ENST00000269305.4:c.158G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tGg/tAg	4/11	0.686387679412584	2	FACETS	0.871	0.818	0.926	0.436	0.409	0.463	CLONAL	1	TRUE	0	0.686387679412584	2		527	863	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165212	47165213	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	45	238	0	ENST00000409792.3:c.913dup	p.Thr305AsnfsTer4	p.T305Nfs*4	ENST00000409792	NM_014159.6	305	aca/aAca	3/21	1	2	FACETS	0.341	0.287	0.401	0.341	0.287	0.401	SUBCLONAL	1	TRUE	1	0.686387679412584	2		238	384	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs149840192	NA	P-0049092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	86	591	1	ENST00000275493.2:c.866C>A	p.Ala289Asp	p.A289D	ENST00000275493	NM_005228.3	289	gCc/gAc	7/28	0.686387679412584	3	FACETS	0.341	0.3	0.384	0.17	0.15	0.192	SUBCLONAL	1	TRUE	1	0.686387679412584	3		592	988	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692775	89692775	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554898053	NA	P-0049092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	80	238	0	ENST00000371953.3:c.259C>T	p.Gln87Ter	p.Q87*	ENST00000371953	NM_000314.4	87	Caa/Taa	5/9	0.686387679412584	1	FACETS	0.519	0.462	0.579	0.519	0.462	0.579	SUBCLONAL	1	TRUE	0	0.686387679412584	1		238	295	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285086	15285086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	55	555	3	ENST00000263388.2:c.4529G>A	p.Arg1510His	p.R1510H	ENST00000263388	NM_000435.2	1510	cGc/cAc	25/33	1	2	FACETS	0.202	0.172	0.235	0.202	0.172	0.235	SUBCLONAL	1	TRUE	1	0.686387679412584	2		558	793	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030388	49030388	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	148	241	0	ENST00000267163.4:c.1863del	p.Val622Ter	p.V622*	ENST00000267163	NM_000321.2	621	cgT/cg	19/27	0.686387679412584	2	FACETS	1	0.95	1	0.52	0.479	0.561	CLONAL	1	TRUE	0	0.686387679412584	2		241	415	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274174	10274174	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	120	420	0	ENST00000330684.3:c.95C>A	p.Pro32His	p.P32H	ENST00000330684	NM_001134407.1	32	cCc/cAc	2/13	1	2	FACETS	0.597	0.54	0.656	0.597	0.54	0.656	SUBCLONAL	1	TRUE	1	0.686387679412584	2		420	586	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976144	18976144	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	167	695	1	ENST00000262803.5:c.2904del	p.Met968IlefsTer12	p.M968Ifs*12	ENST00000262803	NM_002911.3	968	atG/at	21/24	1	2	FACETS	0.53	0.487	0.575	0.53	0.487	0.575	SUBCLONAL	1	TRUE	1	0.686387679412584	2		696	918	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61720169	61720169	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	60	234	0	ENST00000401558.2:c.1265G>A	p.Ser422Asn	p.S422N	ENST00000401558	NM_003400.3	422	aGt/aAt	13/25	0.215126303531467	1	FACETS	0.279	0.241	0.321	0.279	0.241	0.321	INDETERMINATE	1	TRUE	0	0.686387679412584	1		234	411	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47088039	47088040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0049092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	137	430	0	ENST00000409792.3:c.7034_7035dup	p.Val2346TrpfsTer8	p.V2346Wfs*8	ENST00000409792	NM_014159.6	2345	-/TG	16/21	1	2	FACETS	0.604	0.551	0.66	0.604	0.551	0.66	SUBCLONAL	1	TRUE	1	0.686387679412584	2		430	661	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0049095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	111	248	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.765485554600876	2		249	251	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0049095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	94	209	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.948	0.857	1	0.948	0.857	1	CLONAL	1	TRUE	1	0.765485554600876	2		209	259	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791700	42791700	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	101	600	1	ENST00000575354.2:c.586G>T	p.Glu196Ter	p.E196*	ENST00000575354	NM_015125.3	196	Gag/Tag	5/20	0.765485554600876	1	FACETS	0.491	0.443	0.54	0.491	0.443	0.54	SUBCLONAL	1	TRUE	0	0.765485554600876	1		601	332	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114292	73114292	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	74	170	0	ENST00000356692.5:c.928G>T	p.Glu310Ter	p.E310*	ENST00000356692		310	Gag/Tag	8/9	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.765485554600876	2		170	184	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586506	189586506	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0049095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	29	263	0	ENST00000264731.3:c.1129+1G>T		p.X377_splice	ENST00000264731	NM_003722.4	377			1	2	FACETS	0.266	0.214	0.325	0.266	0.214	0.325	SUBCLONAL	1	TRUE	1	0.765485554600876	2		263	285	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0049096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	45	445	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.935	0.796	1	0.935	0.796	1	CLONAL	1	TRUE	1	0.483453773029413	2		445	199	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55693370	55693370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	70	543	1	ENST00000284073.2:c.577C>T	p.Pro193Ser	p.P193S	ENST00000284073	NM_138962.2	193	Cca/Tca	9/14	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.483453773029413	2		544	207	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923440	9923440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	46	438	0	ENST00000330684.3:c.1847C>T	p.Ser616Phe	p.S616F	ENST00000330684	NM_001134407.1	616	tCc/tTc	9/13	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.483453773029413	2		438	163	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745566	162745566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	49	345	0	ENST00000367921.3:c.1981G>A	p.Asp661Asn	p.D661N	ENST00000367921	NM_006182.2	661	Gat/Aat	15/18	0.483453773029413	3	FACETS	1	0.93	1	0.575	0.492	0.663	CLONAL	1	TRUE	1	0.483453773029413	3		345	219	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911343	32911343	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	53	361	0	ENST00000380152.3:c.2851C>T	p.Leu951Phe	p.L951F	ENST00000380152		951	Ctt/Ttt	11/27	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.483453773029413	2		361	154	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	40	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.714	0.603	0.833	0.714	0.603	0.833	SUBCLONAL	1	TRUE	1	0.727491429003209	2		148	154	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983460	90983460	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34767364	NA	P-0049097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	115	214	0	ENST00000265433.3:c.643C>T	p.Arg215Trp	p.R215W	ENST00000265433	NM_002485.4	215	Cgg/Tgg	6/16	1	2	FACETS	0.807	0.733	0.883	0.807	0.733	0.883	CLONAL	1	TRUE	1	0.727491429003209	2		214	392	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032401	10032401	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs78631453	NA	P-0049097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	97	248	0	ENST00000330684.3:c.422C>T	p.Thr141Met	p.T141M	ENST00000330684	NM_001134407.1	141	aCg/aTg	3/13	1	2	FACETS	0.866	0.781	0.953	0.866	0.781	0.953	CLONAL	1	TRUE	1	0.727491429003209	2		248	308	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129903	69129903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752113779	NA	P-0049097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	139	316	0	ENST00000288368.4:c.4657G>A	p.Gly1553Arg	p.G1553R	ENST00000288368	NM_024870.2	1553	Gga/Aga	38/40	1	2	FACETS	0.872	0.801	0.946	0.872	0.801	0.946	CLONAL	1	TRUE	1	0.727491429003209	2		316	438	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528428	29528428	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs876660782	NA	P-0049097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	124	213	0	ENST00000356175.3:c.1186-1G>C		p.X396_splice	ENST00000356175	NM_000267.3	396			0.651914232109071	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.727491429003209	1		213	213	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528124	29528124	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	149	326	0	ENST00000356175.3:c.1132G>A	p.Asp378Asn	p.D378N	ENST00000356175	NM_000267.3	378	Gac/Aac	10/57	0.651914232109071	1	FACETS	0.785	0.729	0.842	0.785	0.729	0.842	SUBCLONAL	1	TRUE	0	0.727491429003209	1		326	332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0049098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	13	768	7	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.671327912343599	1	FACETS	0.069	0.049	0.094	0.069	0.049	0.094	SUBCLONAL	1	TRUE	0	0.671327912343599	1		775	371	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	555	431	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.671327912343599	6	FACETS	1	0.992	1			1	CLONAL	4	TRUE	NA	0.671327912343599	6		431	900	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0049098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	26	423	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.671327912343599	6	FACETS	0.202	0.159	0.251			1	SUBCLONAL	1	TRUE	NA	0.671327912343599	6		423	900	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0049098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	16	322	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.671327912343599	0	FACETS		NA	1			1	NA	1	TRUE	0	0.671327912343599	0		322	95	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578529	7578529	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs780442292	NA	P-0049098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	249	663	0	ENST00000269305.4:c.401T>G	p.Phe134Cys	p.F134C	ENST00000269305	NM_001126112.2	134	tTt/tGt	5/11	0.671327912343599	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.671327912343599	1		663	491	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	245	570	0	ENST00000267101.3:c.310G>C	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ctg	3/28	0.173372788760723	6	FACETS	1	0.981	1			1	INDETERMINATE	2	TRUE	NA	0.671327912343599	6		570	769	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256591	16256591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	127	392	0	ENST00000375759.3:c.3856G>A	p.Gly1286Arg	p.G1286R	ENST00000375759	NM_015001.2	1286	Ggg/Agg	11/15	0.181884983079422	3	FACETS	1	0.965	1	0.555	0.506	0.606	INDETERMINATE	1	TRUE	1	0.671327912343599	3		392	455	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444287	49444288	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	187	642	0	ENST00000301067.7:c.3083_3084insA	p.Gln1029SerfsTer39	p.Q1029Sfs*39	ENST00000301067	NM_003482.3	1028	ctt/ctAt	11/54	0.216007242961185	3	FACETS	1	0.981	1	0.58	0.538	0.623	INDETERMINATE	1	TRUE	1	0.671327912343599	3		642	642	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0049099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	148	406	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.48829524469391	2		406	558	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696730	47696730	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	82	275	0	ENST00000347630.2:c.218C>G	p.Pro73Arg	p.P73R	ENST00000347630	NM_001007230.1	73	cCc/cGc	5/11	1	2	FACETS	0.807	0.716	0.905	0.807	0.716	0.905	CLONAL	1	TRUE	1	0.48829524469391	2		275	416	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157470057	157470057	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554226145	NA	P-0049099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	101	357	0	ENST00000346085.5:c.2851C>T	p.Gln951Ter	p.Q951*	ENST00000346085	NM_020732.3	951	Cag/Tag	9/20	1	2	FACETS	0.969	0.872	1	0.969	0.872	1	CLONAL	1	TRUE	1	0.48829524469391	2		357	427	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107082	27107088	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCGG	GCGGCGG	-	novel	NA	P-0049099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	393	421	1	ENST00000324856.7:c.6695_6701del	p.Arg2232LeufsTer33	p.R2232Lfs*33	ENST00000324856	NM_006015.4	2231	atGCGGCGG/at	20/20	0.48829524469391	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.48829524469391	2		422	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	266	628	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.46	2		628	1085	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	200	564	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	0.959	0.889	1	0.959	0.889	1	CLONAL	1	TRUE	1	0.46	2		564	907	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	121	549	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.948	0.86	1	0.948	0.86	1	CLONAL	1	TRUE	1	0.46	2		549	555	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	239	480	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.46	2		480	885	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857197	9857197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866121846	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	184	490	0	ENST00000330684.3:c.4204C>T	p.Arg1402Trp	p.R1402W	ENST00000330684	NM_001134407.1	1402	Cgg/Tgg	13/13	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.46	2		490	789	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650710	67650710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243010179	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	245	465	1	ENST00000264010.4:c.1015C>T	p.Arg339Trp	p.R339W	ENST00000264010	NM_006565.3	339	Cgg/Tgg	5/12	1	2	FACETS	0.965	0.901	1	0.965	0.901	1	CLONAL	1	TRUE	1	0.46	2		466	1104	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609382	39609382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463795009	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	141	307	0	ENST00000262039.4:c.1684G>A	p.Glu562Lys	p.E562K	ENST00000262039	NM_002647.2	562	Gaa/Aaa	15/25	1	2	FACETS	0.926	0.846	1	0.926	0.846	1	CLONAL	1	TRUE	1	0.46	2		307	662	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589618	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519838	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	59	230	0	ENST00000274335.5:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000274335		461	Cga/Tga	10/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.46	2		230	194	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027593	48027593	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	90	271	0	ENST00000234420.5:c.2471A>C	p.Lys824Thr	p.K824T	ENST00000234420	NM_000179.2	824	aAa/aCa	4/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.46	2		271	316	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770576	40770576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	133	412	0	ENST00000373198.4:c.2806C>T	p.Arg936Ter	p.R936*	ENST00000373198	NM_133170.3	936	Cga/Tga	19/32	1	2	FACETS	0.918	0.836	1	0.918	0.836	1	CLONAL	1	TRUE	1	0.46	2		412	630	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692940	89692940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746152219	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	96	500	0	ENST00000371953.3:c.424C>T	p.Arg142Trp	p.R142W	ENST00000371953	NM_000314.4	142	Cgg/Tgg	5/9	1	2	FACETS	0.842	0.753	0.935	0.842	0.753	0.935	CLONAL	1	TRUE	1	0.46	2		500	496	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128432165	128432165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1371596131	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	61	382	2	ENST00000265960.3:c.281G>A	p.Arg94Gln	p.R94Q	ENST00000265960	NM_001006617.1	94	cGa/cAa	3/12	1	2	FACETS	0.787	0.683	0.899	0.787	0.683	0.899	SUBCLONAL	1	TRUE	1	0.46	2		384	337	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780675	9780675	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	300	678	0	ENST00000377346.4:c.1477G>A	p.Glu493Lys	p.E493K	ENST00000377346	NM_005026.3	493	Gag/Aag	12/24	1	2	FACETS	0.949	0.892	1	0.949	0.892	1	CLONAL	1	TRUE	1	0.46	2		678	1375	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11293523	11293523	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	30	430	0	ENST00000361445.4:c.2353G>T	p.Asp785Tyr	p.D785Y	ENST00000361445	NM_004958.3	785	Gat/Tat	15/58	1	2	FACETS	0.243	0.195	0.298	0.243	0.195	0.298	SUBCLONAL	1	TRUE	1	0.46	2		430	536	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242715	16242715	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	143	515	0	ENST00000375759.3:c.1336G>T	p.Glu446Ter	p.E446*	ENST00000375759	NM_015001.2	446	Gaa/Taa	6/15	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.46	2		515	596	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254906	16254906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	186	466	0	ENST00000375759.3:c.2171G>A	p.Arg724Gln	p.R724Q	ENST00000375759	NM_015001.2	724	cGa/cAa	11/15	1	2	FACETS	0.905	0.836	0.976	0.905	0.836	0.976	CLONAL	1	TRUE	1	0.46	2		466	894	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256435	16256435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199763346	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	180	489	1	ENST00000375759.3:c.3700G>A	p.Asp1234Asn	p.D1234N	ENST00000375759	NM_015001.2	1234	Gat/Aat	11/15	1	2	FACETS	0.873	0.806	0.944	0.873	0.806	0.944	CLONAL	1	TRUE	1	0.46	2		490	896	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258696	16258696	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	230	491	0	ENST00000375759.3:c.5961G>T	p.Gln1987His	p.Q1987H	ENST00000375759	NM_015001.2	1987	caG/caT	11/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.46	2		491	930	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089596	27089596	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	230	748	0	ENST00000324856.7:c.2552G>A	p.Gly851Asp	p.G851D	ENST00000324856	NM_006015.4	851	gGc/gAc	8/20	1	2	FACETS	0.929	0.866	0.995	0.929	0.866	0.995	CLONAL	1	TRUE	1	0.46	2		748	1076	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107195	27107195	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	177	457	0	ENST00000324856.7:c.6806C>A	p.Ser2269Ter	p.S2269*	ENST00000324856	NM_006015.4	2269	tCa/tAa	20/20	1	2	FACETS	0.836	0.77	0.904	0.836	0.77	0.904	CLONAL	1	TRUE	1	0.46	2		457	921	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46733154	46733154	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	170	440	0	ENST00000371975.4:c.915G>T	p.Glu305Asp	p.E305D	ENST00000371975	NM_003579.3	305	gaG/gaT	9/18	1	2	FACETS	0.872	0.802	0.944	0.872	0.802	0.944	CLONAL	1	TRUE	1	0.46	2		440	848	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736474	85736474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	93	336	0	ENST00000370580.1:c.173G>A	p.Arg58Gln	p.R58Q	ENST00000370580	NM_003921.4	58	cGa/cAa	2/3	1	2	FACETS	0.97	0.868	1	0.97	0.868	1	CLONAL	1	TRUE	1	0.46	2		336	417	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736583	85736583	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	10	196	0	ENST00000370580.1:c.64G>T	p.Glu22Ter	p.E22*	ENST00000370580	NM_003921.4	22	Gaa/Taa	2/3	1	2	FACETS	0.224	0.151	0.315	0.224	0.151	0.315	SUBCLONAL	1	TRUE	1	0.46	2		196	194	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464431	120464431	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	91	370	0	ENST00000256646.2:c.5215A>C	p.Asn1739His	p.N1739H	ENST00000256646	NM_024408.3	1739	Aat/Cat	29/34	1	2	FACETS	0.912	0.814	1	0.912	0.814	1	CLONAL	1	TRUE	1	0.46	2		370	434	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162750010	162750010	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	130	378	1	ENST00000367921.3:c.2542C>A	p.Leu848Met	p.L848M	ENST00000367921	NM_006182.2	848	Ctg/Atg	18/18	1	2	FACETS	0.759	0.689	0.832	0.759	0.689	0.832	SUBCLONAL	1	TRUE	1	0.46	2		379	745	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957437	175957437	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	101	340	0	ENST00000367669.3:c.1959T>G	p.Asp653Glu	p.D653E	ENST00000367669	NM_022457.5	653	gaT/gaG	17/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.46	2		340	408	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111168	193111168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1452051467	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	59	255	1	ENST00000367435.3:c.701G>A	p.Arg234Gln	p.R234Q	ENST00000367435	NM_024529.4	234	cGa/cAa	7/17	1	2	FACETS	0.719	0.621	0.823	0.719	0.621	0.823	SUBCLONAL	1	TRUE	1	0.46	2		256	357	SUCCESS
FH	2271	MSKCC	GRCh37	1	241663787	241663787	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	38	376	0	ENST00000366560.3:c.1340A>G	p.Lys447Arg	p.K447R	ENST00000366560	NM_000143.3	447	aAg/aGg	9/10	1	2	FACETS	0.443	0.367	0.528	0.443	0.367	0.528	SUBCLONAL	1	TRUE	1	0.46	2		376	373	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716220	243716220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	97	448	0	ENST00000263826.5:c.974G>A	p.Arg325Gln	p.R325Q	ENST00000263826	NM_005465.4	325	cGa/cAa	10/13	1	2	FACETS	0.748	0.668	0.832	0.748	0.668	0.832	SUBCLONAL	1	TRUE	1	0.46	2		448	564	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800966	243800966	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	45	486	0	ENST00000263826.5:c.508A>C	p.Ser170Arg	p.S170R	ENST00000263826	NM_005465.4	170	Agt/Cgt	5/13	1	2	FACETS	0.565	0.477	0.663	0.565	0.477	0.663	SUBCLONAL	1	TRUE	1	0.46	2		486	346	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450766	70450766	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	145	483	0	ENST00000373644.4:c.5606C>A	p.Ser1869Ter	p.S1869*	ENST00000373644	NM_030625.2	1869	tCa/tAa	12/12	1	2	FACETS	0.824	0.753	0.899	0.824	0.753	0.899	CLONAL	1	TRUE	1	0.46	2		483	765	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624258	89624258	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	81	258	0	ENST00000371953.3:c.32G>T	p.Arg11Ile	p.R11I	ENST00000371953	NM_000314.4	11	aGa/aTa	1/9	1	2	FACETS	0.92	0.815	1	0.92	0.815	1	CLONAL	1	TRUE	1	0.46	2		258	383	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624296	89624296	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786201995	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	153	479	0	ENST00000371953.3:c.70G>T	p.Asp24Tyr	p.D24Y	ENST00000371953	NM_000314.4	24	Gac/Tac	1/9	1	2	FACETS	0.871	0.798	0.947	0.871	0.798	0.947	CLONAL	1	TRUE	1	0.46	2		479	764	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720870	89720870	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1554825652	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	119	330	1	ENST00000371953.3:c.1021T>G	p.Phe341Val	p.F341V	ENST00000371953	NM_000314.4	341	Ttt/Gtt	8/9	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.46	2		331	368	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154267	2154267	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	242	609	0	ENST00000434045.2:c.661G>T	p.Asp221Tyr	p.D221Y	ENST00000434045	NM_001127598.1	221	Gac/Tac	5/5	1	2	FACETS	0.975	0.911	1	0.975	0.911	1	CLONAL	1	TRUE	1	0.46	2		609	1079	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14317380	14317380	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	70	355	1	ENST00000256196.4:c.130G>T	p.Asp44Tyr	p.D44Y	ENST00000256196		44	Gat/Tat	2/6	1	2	FACETS	0.827	0.725	0.936	0.827	0.725	0.936	CLONAL	1	TRUE	1	0.46	2		356	368	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936075	71936075	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs905561373	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	35	67	0	ENST00000298229.2:c.47G>A	p.Ser16Asn	p.S16N	ENST00000298229	NM_001567.3	16	aGc/aAc	1/28	1	2	FACETS	0.885	0.734	1	0.885	0.734	1	CLONAL	1	TRUE	1	0.46	2		67	172	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94201000	94201000	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	102	365	0	ENST00000323929.3:c.1077G>T	p.Glu359Asp	p.E359D	ENST00000323929	NM_005591.3	359	gaG/gaT	10/20	1	2	FACETS	0.85	0.763	0.941	0.85	0.763	0.941	CLONAL	1	TRUE	1	0.46	2		365	522	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911954	94911954	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	97	467	1	ENST00000536441.1:c.976C>T	p.Arg326Ter	p.R326*	ENST00000536441	NM_144665.3	326	Cga/Tga	7/10	1	2	FACETS	0.866	0.775	0.962	0.866	0.775	0.962	CLONAL	1	TRUE	1	0.46	2		468	487	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924618	94924618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1400088899	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	67	598	0	ENST00000536441.1:c.292C>T	p.Arg98Cys	p.R98C	ENST00000536441	NM_144665.3	98	Cgc/Tgc	3/10	1	2	FACETS	0.316	0.273	0.362	0.316	0.273	0.362	SUBCLONAL	1	TRUE	1	0.46	2		598	923	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909938	100909938	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	131	398	0	ENST00000325455.5:c.2711A>C	p.Glu904Ala	p.E904A	ENST00000325455	NM_001202474.3	904	gAa/gCa	8/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.46	2		398	449	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920768	100920768	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	98	372	0	ENST00000325455.5:c.2380T>C	p.Phe794Leu	p.F794L	ENST00000325455	NM_001202474.3	794	Ttc/Ctc	6/8	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.46	2		372	369	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962527	100962527	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	140	479	0	ENST00000325455.5:c.1870C>A	p.Leu624Ile	p.L624I	ENST00000325455	NM_001202474.3	624	Ctt/Att	3/8	1	2	FACETS	0.799	0.728	0.873	0.799	0.728	0.873	SUBCLONAL	1	TRUE	1	0.46	2		479	762	SUCCESS
ATM	472	MSKCC	GRCh37	11	108137941	108137941	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	86	353	0	ENST00000278616.4:c.2510C>A	p.Ser837Ter	p.S837*	ENST00000278616	NM_000051.3	837	tCa/tAa	17/63	1	2	FACETS	0.905	0.805	1	0.905	0.805	1	CLONAL	1	TRUE	1	0.46	2		353	413	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376887	118376887	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	54	365	0	ENST00000534358.1:c.10280C>A	p.Ser3427Tyr	p.S3427Y	ENST00000534358	NM_005933.3	3427	tCt/tAt	27/36	1	2	FACETS	0.367	0.313	0.426	0.367	0.313	0.426	SUBCLONAL	1	TRUE	1	0.46	2		365	640	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392721	118392721	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	60	465	0	ENST00000534358.1:c.11753C>A	p.Ser3918Tyr	p.S3918Y	ENST00000534358	NM_005933.3	3918	tCt/tAt	36/36	1	2	FACETS	0.33	0.284	0.381	0.33	0.284	0.381	SUBCLONAL	1	TRUE	1	0.46	2		465	790	SUCCESS
CBL	867	MSKCC	GRCh37	11	119077317	119077317	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	289	656	1	ENST00000264033.4:c.190G>T	p.Asp64Tyr	p.D64Y	ENST00000264033	NM_005188.3	64	Gac/Tac	1/16	1	2	FACETS	0.917	0.861	0.975	0.917	0.861	0.975	CLONAL	1	TRUE	1	0.46	2		657	1370	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503175	125503175	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	74	281	0	ENST00000428830.2:c.542G>T	p.Arg181Ile	p.R181I	ENST00000428830	NM_001114121.2	181	aGa/aTa	6/14	1	2	FACETS	0.889	0.783	1	0.889	0.783	1	CLONAL	1	TRUE	1	0.46	2		281	362	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125507383	125507383	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	63	367	1	ENST00000428830.2:c.758G>T	p.Arg253Ile	p.R253I	ENST00000428830	NM_001114121.2	253	aGa/aTa	8/14	1	2	FACETS	0.78	0.679	0.889	0.78	0.679	0.889	SUBCLONAL	1	TRUE	1	0.46	2		368	351	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992214	11992214	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	186	374	0	ENST00000396373.4:c.304T>G	p.Phe102Val	p.F102V	ENST00000396373	NM_001987.4	102	Ttt/Gtt	3/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.46	2		374	735	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870930	12870930	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	144	355	1	ENST00000228872.4:c.157G>T	p.Glu53Ter	p.E53*	ENST00000228872	NM_004064.3	53	Gaa/Taa	1/3	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.46	2		356	558	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435370	18435370	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	49	285	0	ENST00000266497.5:c.355A>C	p.Asn119His	p.N119H	ENST00000266497		119	Aat/Cat	1/31	1	2	FACETS	0.683	0.581	0.793	0.683	0.581	0.793	SUBCLONAL	1	TRUE	1	0.46	2		285	312	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18477976	18477976	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	55	363	0	ENST00000266497.5:c.1216C>A	p.Leu406Ile	p.L406I	ENST00000266497		406	Ctc/Atc	7/31	1	2	FACETS	0.681	0.585	0.785	0.681	0.585	0.785	SUBCLONAL	1	TRUE	1	0.46	2		363	351	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800874	18800874	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	23	404	0	ENST00000266497.5:c.4250C>A	p.Thr1417Asn	p.T1417N	ENST00000266497		1417	aCt/aAt	31/31	1	2	FACETS	0.364	0.284	0.456	0.364	0.284	0.456	SUBCLONAL	1	TRUE	1	0.46	2		404	275	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50482348	50482348	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	153	391	0	ENST00000394963.4:c.699C>A	p.Phe233Leu	p.F233L	ENST00000394963	NM_003076.4	233	ttC/ttA	6/13	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.46	2		391	628	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487277	56487277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035001455	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	218	519	0	ENST00000267101.3:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000267101	NM_001982.3	475	Cgg/Tgg	12/28	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.46	2		519	893	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489500	56489500	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	187	410	0	ENST00000267101.3:c.1965T>G	p.Ile655Met	p.I655M	ENST00000267101	NM_001982.3	655	atT/atG	17/28	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.46	2		410	806	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145001	58145001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772938517	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	182	523	0	ENST00000257904.6:c.343G>A	p.Glu115Lys	p.E115K	ENST00000257904	NM_000075.3	115	Gaa/Aaa	3/8	1	2	FACETS	0.841	0.776	0.909	0.841	0.776	0.909	CLONAL	1	TRUE	1	0.46	2		523	941	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120818	115120818	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	170	475	1	ENST00000257566.3:c.188C>T	p.Pro63Leu	p.P63L	ENST00000257566	NM_016569.3	63	cCg/cTg	1/8	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.46	2		476	728	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622539	28622539	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	71	350	0	ENST00000241453.7:c.1078G>T	p.Glu360Ter	p.E360*	ENST00000241453	NM_004119.2	360	Gaa/Taa	9/24	1	2	FACETS	0.882	0.775	0.996	0.882	0.775	0.996	CLONAL	1	TRUE	1	0.46	2		350	350	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891728	28891728	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	177	463	0	ENST00000282397.4:c.3293C>A	p.Ser1098Tyr	p.S1098Y	ENST00000282397	NM_002019.4	1098	tCt/tAt	25/30	1	2	FACETS	0.964	0.89	1	0.964	0.89	1	CLONAL	1	TRUE	1	0.46	2		463	798	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893671	28893671	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	93	359	0	ENST00000282397.4:c.3175A>G	p.Thr1059Ala	p.T1059A	ENST00000282397	NM_002019.4	1059	Act/Gct	24/30	1	2	FACETS	0.721	0.642	0.804	0.721	0.642	0.804	SUBCLONAL	1	TRUE	1	0.46	2		359	561	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906847	32906847	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs79597821	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	128	530	0	ENST00000380152.3:c.1232T>C	p.Ile411Thr	p.I411T	ENST00000380152		411	aTa/aCa	10/27	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.46	2		530	545	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915295	32915295	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	85	567	0	ENST00000380152.3:c.6803G>T	p.Arg2268Ile	p.R2268I	ENST00000380152		2268	aGa/aTa	11/27	1	2	FACETS	0.816	0.724	0.913	0.816	0.724	0.913	CLONAL	1	TRUE	1	0.46	2		567	453	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915335	32915335	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	79	575	0	ENST00000380152.3:c.6841+2T>G		p.X2281_splice	ENST00000380152		2281			1	2	FACETS	0.72	0.635	0.81	0.72	0.635	0.81	SUBCLONAL	1	TRUE	1	0.46	2		575	477	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068968	30068968	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	46	482	0	ENST00000331968.5:c.1961G>T	p.Arg654Ile	p.R654I	ENST00000331968	NM_002742.2	654	aGa/aTa	14/18	1	2	FACETS	0.331	0.278	0.389	0.331	0.278	0.389	SUBCLONAL	1	TRUE	1	0.46	2		482	605	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30099971	30099971	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	113	432	0	ENST00000331968.5:c.1649T>C	p.Val550Ala	p.V550A	ENST00000331968	NM_002742.2	550	gTg/gCg	10/18	1	2	FACETS	0.714	0.643	0.789	0.714	0.643	0.789	SUBCLONAL	1	TRUE	1	0.46	2		432	688	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571417	95571417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs180918578	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	107	202	0	ENST00000393063.1:c.3260C>T	p.Ala1087Val	p.A1087V	ENST00000393063	NM_030621.3	1087	gCg/gTg	21/28	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.46	2		202	423	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95578573	95578573	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	59	270	0	ENST00000393063.1:c.2052G>T	p.Met684Ile	p.M684I	ENST00000393063	NM_030621.3	684	atG/atT	14/28	1	2	FACETS	0.825	0.715	0.943	0.825	0.715	0.943	CLONAL	1	TRUE	1	0.46	2		270	311	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239267	105239267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	290	640	0	ENST00000349310.3:c.1120C>T	p.Pro374Ser	p.P374S	ENST00000349310	NM_001014432.1	374	Ccc/Tcc	12/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.46	2		640	1173	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028735	42028735	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	182	575	0	ENST00000219905.7:c.4273A>G	p.Lys1425Glu	p.K1425E	ENST00000219905	NM_001164273.1	1425	Aaa/Gaa	13/24	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.46	2		575	739	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701940	43701940	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	53	137	1	ENST00000382044.4:c.5306-1G>T		p.X1769_splice	ENST00000382044	NM_001141980.1	1769			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.46	2		138	163	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748095	43748095	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs944474760	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	114	366	0	ENST00000382044.4:c.2711C>A	p.Ser904Tyr	p.S904Y	ENST00000382044	NM_001141980.1	904	tCt/tAt	12/28	1	2	FACETS	0.696	0.627	0.769	0.696	0.627	0.769	SUBCLONAL	1	TRUE	1	0.46	2		366	712	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678629	88678629	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	139	345	0	ENST00000360948.2:c.908-1G>T		p.X303_splice	ENST00000360948	NM_001012338.2	303			1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.46	2		345	596	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726712	88726712	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs765578547	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	152	406	0	ENST00000360948.2:c.332A>G	p.Lys111Arg	p.K111R	ENST00000360948	NM_001012338.2	111	aAg/aGg	4/19	1	2	FACETS	0.948	0.869	1	0.948	0.869	1	CLONAL	1	TRUE	1	0.46	2		406	697	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295027	91295027	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	48	245	0	ENST00000355112.3:c.810A>C	p.Glu270Asp	p.E270D	ENST00000355112	NM_000057.2	270	gaA/gaC	4/22	1	2	FACETS	0.859	0.733	0.995	0.859	0.733	0.995	CLONAL	1	TRUE	1	0.46	2		245	243	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789707	3789707	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	190	416	0	ENST00000262367.5:c.4152A>C	p.Glu1384Asp	p.E1384D	ENST00000262367	NM_004380.2	1384	gaA/gaC	25/31	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.46	2		416	769	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3901011	3901011	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs11644721	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	122	400	0	ENST00000262367.5:c.86-1G>T		p.X29_splice	ENST00000262367	NM_004380.2	29			1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.46	2		400	519	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923443	9923443	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	76	482	0	ENST00000330684.3:c.1844A>C	p.Asn615Thr	p.N615T	ENST00000330684	NM_001134407.1	615	aAc/aCc	9/13	1	2	FACETS	0.402	0.352	0.456	0.402	0.352	0.456	SUBCLONAL	1	TRUE	1	0.46	2		482	822	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032163	10032163	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	176	619	0	ENST00000330684.3:c.660G>T	p.Lys220Asn	p.K220N	ENST00000330684	NM_001134407.1	220	aaG/aaT	3/13	1	2	FACETS	0.839	0.773	0.908	0.839	0.773	0.908	CLONAL	1	TRUE	1	0.46	2		619	912	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50827519	50827519	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568978023	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	144	475	1	ENST00000398568.2:c.2404G>A	p.Asp802Asn	p.D802N	ENST00000398568	NM_001042412.1	802	Gat/Aat	16/18	1	2	FACETS	0.807	0.737	0.88	0.807	0.737	0.88	CLONAL	1	TRUE	1	0.46	2		476	776	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828246	50828246	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	68	390	1	ENST00000398568.2:c.2584C>A	p.Leu862Ile	p.L862I	ENST00000398568	NM_001042412.1	862	Ctc/Atc	17/18	1	2	FACETS	0.398	0.345	0.455	0.398	0.345	0.455	SUBCLONAL	1	TRUE	1	0.46	2		391	743	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828486	72828486	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	90	638	0	ENST00000268489.5:c.8095G>T	p.Gly2699Ter	p.G2699*	ENST00000268489	NM_006885.3	2699	Gga/Tga	9/10	1	2	FACETS	0.347	0.307	0.39	0.347	0.307	0.39	SUBCLONAL	1	TRUE	1	0.46	2		638	1128	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828699	72828699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762362472	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	205	592	0	ENST00000268489.5:c.7882G>A	p.Glu2628Lys	p.E2628K	ENST00000268489	NM_006885.3	2628	Gaa/Aaa	9/10	1	2	FACETS	0.973	0.903	1	0.973	0.903	1	CLONAL	1	TRUE	1	0.46	2		592	916	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830731	72830731	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	206	503	1	ENST00000268489.5:c.5850G>T	p.Glu1950Asp	p.E1950D	ENST00000268489	NM_006885.3	1950	gaG/gaT	9/10	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.46	2		504	883	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371704	89371704	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144947610	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	259	643	0	ENST00000301030.4:c.136G>A	p.Asp46Asn	p.D46N	ENST00000301030	NM_001256183.1	46	Gat/Aat	4/13	1	2	FACETS	0.935	0.875	0.997	0.935	0.875	0.997	CLONAL	1	TRUE	1	0.46	2		643	1204	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831335	89831335	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	87	541	0	ENST00000389301.3:c.2741G>T	p.Arg914Ile	p.R914I	ENST00000389301	NM_000135.2	914	aGa/aTa	28/43	1	2	FACETS	0.348	0.307	0.392	0.348	0.307	0.392	SUBCLONAL	1	TRUE	1	0.46	2		541	1087	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89874771	89874771	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	180	413	0	ENST00000389301.3:c.527C>A	p.Ser176Tyr	p.S176Y	ENST00000389301	NM_000135.2	176	tCt/tAt	6/43	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.46	2		413	743	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877394	89877394	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1162	69	584	0	ENST00000389301.3:c.369G>T	p.Gln123His	p.Q123H	ENST00000389301	NM_000135.2	123	caG/caT	4/43	1	2	FACETS	0.244	0.211	0.279	0.244	0.211	0.279	SUBCLONAL	1	TRUE	1	0.46	2		584	1231	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979527	7979527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064796312	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	192	538	2	ENST00000319144.4:c.1498G>A	p.Asp500Asn	p.D500N	ENST00000319144	NM_001139.2	500	Gat/Aat	11/15	1	2	FACETS	0.822	0.76	0.886	0.822	0.76	0.886	CLONAL	1	TRUE	1	0.46	2		540	1016	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983564	7983564	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	196	533	1	ENST00000319144.4:c.743C>A	p.Ser248Tyr	p.S248Y	ENST00000319144	NM_001139.2	248	tCt/tAt	6/15	1	2	FACETS	0.945	0.875	1	0.945	0.875	1	CLONAL	1	TRUE	1	0.46	2		534	902	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049724	16049724	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	107	465	0	ENST00000268712.3:c.1048C>T	p.Arg350Ter	p.R350*	ENST00000268712	NM_006311.3	350	Cga/Tga	10/46	1	2	FACETS	0.835	0.752	0.923	0.835	0.752	0.923	CLONAL	1	TRUE	1	0.46	2		465	557	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661915	29661915	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	94	452	0	ENST00000356175.3:c.5809C>T	p.Arg1937Cys	p.R1937C	ENST00000356175	NM_000267.3	1937	Cgt/Tgt	39/57	1	2	FACETS	0.973	0.871	1	0.973	0.871	1	CLONAL	1	TRUE	1	0.46	2		452	420	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618478	37618478	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	177	445	0	ENST00000447079.4:c.154G>T	p.Asp52Tyr	p.D52Y	ENST00000447079	NM_015083.1	52	Gac/Tac	1/14	1	2	FACETS	0.975	0.9	1	0.975	0.9	1	CLONAL	1	TRUE	1	0.46	2		445	789	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627378	37627378	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	170	588	0	ENST00000447079.4:c.1293G>T	p.Glu431Asp	p.E431D	ENST00000447079	NM_015083.1	431	gaG/gaT	2/14	1	2	FACETS	0.817	0.751	0.885	0.817	0.751	0.885	CLONAL	1	TRUE	1	0.46	2		588	905	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40500411	40500411	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	118	378	0	ENST00000264657.5:c.124G>A	p.Asp42Asn	p.D42N	ENST00000264657	NM_139276.2	42	Gat/Aat	2/24	1	2	FACETS	0.802	0.725	0.883	0.802	0.725	0.883	CLONAL	1	TRUE	1	0.46	2		378	640	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40855800	40855800	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1458266017	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	191	540	0	ENST00000428826.2:c.2056C>T	p.Arg686Ter	p.R686*	ENST00000428826		686	Cga/Tga	19/21	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.46	2		540	810	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696421	47696421	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	179	439	0	ENST00000347630.2:c.402G>T	p.Lys134Asn	p.K134N	ENST00000347630	NM_001007230.1	134	aaG/aaT	6/11	1	2	FACETS	0.972	0.897	1	0.972	0.897	1	CLONAL	1	TRUE	1	0.46	2		439	801	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55334482	55334482	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	28	187	0	ENST00000284073.2:c.86G>T	p.Ser29Ile	p.S29I	ENST00000284073	NM_138962.2	29	aGc/aTc	2/14	1	2	FACETS	0.37	0.296	0.454	0.37	0.296	0.454	SUBCLONAL	1	TRUE	1	0.46	2		187	329	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780619	56780619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137947462	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	107	561	1	ENST00000337432.4:c.634C>T	p.Arg212Cys	p.R212C	ENST00000337432	NM_058216.2	212	Cgc/Tgc	4/9	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.46	2		562	456	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740629	58740629	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	141	448	0	ENST00000305921.3:c.1534A>C	p.Asn512His	p.N512H	ENST00000305921	NM_003620.3	512	Aat/Cat	6/6	1	2	FACETS	0.986	0.901	1	0.986	0.901	1	CLONAL	1	TRUE	1	0.46	2		448	622	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861667	59861667	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	14	444	0	ENST00000259008.2:c.1592T>G	p.Phe531Cys	p.F531C	ENST00000259008	NM_032043.2	531	tTt/tGt	11/20	1	2	FACETS	0.224	0.161	0.3	0.224	0.161	0.3	SUBCLONAL	1	TRUE	1	0.46	2		444	272	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006671	62006671	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747523556	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	227	707	0	ENST00000392795.3:c.608A>G	p.Asp203Gly	p.D203G	ENST00000392795	NM_001039933.1	203	gAc/gGc	6/6	1	2	FACETS	0.905	0.843	0.97	0.905	0.843	0.97	CLONAL	1	TRUE	1	0.46	2		707	1090	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570518	39570518	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	16	216	0	ENST00000262039.4:c.714G>T	p.Lys238Asn	p.K238N	ENST00000262039	NM_002647.2	238	aaG/aaT	6/25	1	2	FACETS	0.417	0.309	0.543	0.417	0.309	0.543	SUBCLONAL	1	TRUE	1	0.46	2		216	167	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265139	5265139	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1353	128	829	2	ENST00000357368.4:c.448C>T	p.Arg150Trp	p.R150W	ENST00000357368	NM_002850.3	150	Cgg/Tgg	5/38	1	2	FACETS	0.376	0.339	0.415	0.376	0.339	0.415	SUBCLONAL	1	TRUE	1	0.46	2		831	1481	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172328	7172328	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	141	432	0	ENST00000302850.5:c.1241T>G	p.Leu414Arg	p.L414R	ENST00000302850	NM_000208.2	414	cTg/cGg	5/22	1	2	FACETS	0.786	0.717	0.859	0.786	0.717	0.859	SUBCLONAL	1	TRUE	1	0.46	2		432	780	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7293806	7293806	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	11	22	0	ENST00000302850.5:c.97G>T	p.Glu33Ter	p.E33*	ENST00000302850	NM_000208.2	33	Gag/Tag	1/22	1	2	FACETS	0.759	0.535	1	0.759	0.535	1	CLONAL	1	TRUE	1	0.46	2		22	63	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10257089	10257089	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	200	691	0	ENST00000340748.4:c.2784G>T	p.Lys928Asn	p.K928N	ENST00000340748		928	aaG/aaT	27/40	1	2	FACETS	0.716	0.662	0.772	0.716	0.662	0.772	SUBCLONAL	1	TRUE	1	0.46	2		691	1215	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945768	17945768	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	311	736	0	ENST00000458235.1:c.2092G>T	p.Glu698Ter	p.E698*	ENST00000458235	NM_000215.3	698	Gag/Tag	16/24	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.46	2		736	1307	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952355	17952355	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	348	812	0	ENST00000458235.1:c.985G>A	p.Glu329Lys	p.E329K	ENST00000458235	NM_000215.3	329	Gag/Aag	8/24	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.46	2		812	1401	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18943127	18943127	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	141	255	0	ENST00000262803.5:c.109G>T	p.Asp37Tyr	p.D37Y	ENST00000262803	NM_002911.3	37	Gac/Tac	1/24	1	2	FACETS	0.863	0.788	0.942	0.863	0.788	0.942	CLONAL	1	TRUE	1	0.46	2		255	710	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211360	36211360	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	253	603	1	ENST00000222270.7:c.1111G>T	p.Glu371Ter	p.E371*	ENST00000222270	NM_014727.1	371	Gaa/Taa	3/37	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.46	2		604	964	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748496	40748496	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1287	129	780	0	ENST00000392038.2:c.386A>C	p.Asp129Ala	p.D129A	ENST00000392038	NM_001626.4	129	gAc/gCc	5/14	1	2	FACETS	0.396	0.358	0.437	0.396	0.358	0.437	SUBCLONAL	1	TRUE	1	0.46	2		780	1416	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743888	41743888	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1326	116	737	0	ENST00000301178.4:c.823G>A	p.Glu275Lys	p.E275K	ENST00000301178	NM_021913.4	275	Gaa/Aaa	7/20	1	2	FACETS	0.35	0.314	0.388	0.35	0.314	0.388	SUBCLONAL	1	TRUE	1	0.46	2		737	1442	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754482	42754482	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	272	647	1	ENST00000222329.4:c.257+1G>A		p.X86_splice	ENST00000222329	NM_006494.2	86			1	2	FACETS	0.969	0.909	1	0.969	0.909	1	CLONAL	1	TRUE	1	0.46	2		648	1220	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795722	42795722	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1201	349	918	0	ENST00000575354.2:c.2711C>A	p.Ser904Tyr	p.S904Y	ENST00000575354	NM_015125.3	904	tCt/tAt	11/20	1	2	FACETS	0.979	0.925	1	0.979	0.925	1	CLONAL	1	TRUE	1	0.46	2		918	1550	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469557	25469557	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	333	780	0	ENST00000264709.3:c.1211A>G	p.Lys404Arg	p.K404R	ENST00000264709	NM_175629.2	404	aAg/aGg	10/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.46	2		780	1384	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498328	29498328	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	178	542	0	ENST00000389048.3:c.1852G>T	p.Gly618Ter	p.G618*	ENST00000389048	NM_004304.4	618	Gga/Tga	10/29	1	2	FACETS	0.85	0.784	0.92	0.85	0.784	0.92	CLONAL	1	TRUE	1	0.46	2		542	910	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607635	46607635	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	252	767	0	ENST00000263734.3:c.1824C>A	p.Phe608Leu	p.F608L	ENST00000263734	NM_001430.4	608	ttC/ttA	12/16	1	2	FACETS	0.86	0.803	0.919	0.86	0.803	0.919	CLONAL	1	TRUE	1	0.46	2		767	1274	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639589	47639589	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	88	336	0	ENST00000233146.2:c.682A>C	p.Lys228Gln	p.K228Q	ENST00000233146	NM_000251.2	228	Aaa/Caa	4/16	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.46	2		336	351	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641447	47641447	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	121	482	1	ENST00000233146.2:c.832G>T	p.Glu278Ter	p.E278*	ENST00000233146	NM_000251.2	278	Gaa/Taa	5/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.46	2		483	482	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702340	47702340	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	67	389	0	ENST00000233146.2:c.1936G>T	p.Asp646Tyr	p.D646Y	ENST00000233146	NM_000251.2	646	Gat/Tat	12/16	1	2	FACETS	0.646	0.563	0.735	0.646	0.563	0.735	SUBCLONAL	1	TRUE	1	0.46	2		389	451	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715891	61715891	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	124	371	0	ENST00000401558.2:c.2038A>C	p.Lys680Gln	p.K680Q	ENST00000401558	NM_003400.3	680	Aaa/Caa	18/25	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.46	2		371	496	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921737	111921737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1170116948	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	107	308	1	ENST00000393256.3:c.526G>A	p.Glu176Lys	p.E176K	ENST00000393256	NM_006538.4	176	Gaa/Aaa	4/4	0.17955123398274	4	FACETS	1	0.98	1	0.679	0.612	0.75	INDETERMINATE	1	TRUE	2	0.46	4		309	500	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038195	128038195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	173	450	0	ENST00000285398.2:c.1355G>A	p.Arg452Gln	p.R452Q	ENST00000285398	NM_000122.1	452	cGa/cAa	9/15	1	2	FACETS	0.953	0.879	1	0.953	0.879	1	CLONAL	1	TRUE	1	0.46	2		450	789	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728762	190728762	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1398879495	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	14	373	0	ENST00000441310.2:c.2150A>G	p.Asp717Gly	p.D717G	ENST00000441310	NM_000534.4	717	gAc/gGc	10/13	1	2	FACETS	0.239	0.172	0.319	0.239	0.172	0.319	SUBCLONAL	1	TRUE	1	0.46	2		373	255	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266762	198266762	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	144	437	0	ENST00000335508.6:c.2170T>G	p.Phe724Val	p.F724V	ENST00000335508	NM_012433.2	724	Ttt/Gtt	15/25	1	2	FACETS	0.994	0.909	1	0.994	0.909	1	CLONAL	1	TRUE	1	0.46	2		437	630	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202123015	202123015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	135	401	0	ENST00000358485.4:c.61G>A	p.Ala21Thr	p.A21T	ENST00000358485	NM_001080125.1	21	Gcc/Acc	1/9	1	2	FACETS	0.748	0.68	0.819	0.748	0.68	0.819	SUBCLONAL	1	TRUE	1	0.46	2		401	785	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285182	212285182	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	75	368	0	ENST00000342788.4:c.3119G>A	p.Arg1040Lys	p.R1040K	ENST00000342788	NM_005235.2	1040	aGa/aAa	25/28	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.46	2		368	312	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379426	225379426	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	72	496	0	ENST00000264414.4:c.442C>T	p.Arg148Ter	p.R148*	ENST00000264414	NM_003590.4	148	Cga/Tga	4/16	1	2	FACETS	0.851	0.748	0.96	0.851	0.748	0.96	CLONAL	1	TRUE	1	0.46	2		496	368	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659965	227659965	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	266	644	0	ENST00000305123.5:c.3490G>A	p.Ala1164Thr	p.A1164T	ENST00000305123	NM_005544.2	1164	Gcc/Acc	1/2	1	2	FACETS	0.975	0.914	1	0.975	0.914	1	CLONAL	1	TRUE	1	0.46	2		644	1186	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546847	9546847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	187	433	0	ENST00000353224.5:c.1175C>T	p.Ser392Leu	p.S392L	ENST00000353224	NM_177990.2	392	tCg/tTg	5/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.46	2		433	781	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016182	31016182	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs144437064	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	117	340	0	ENST00000375687.4:c.428G>T	p.Arg143Leu	p.R143L	ENST00000375687	NM_015338.5	143	cGa/cTa	6/13	1	2	FACETS	0.795	0.718	0.876	0.795	0.718	0.876	SUBCLONAL	1	TRUE	1	0.46	2		340	640	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024619	31024619	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	220	584	0	ENST00000375687.4:c.4104G>T	p.Lys1368Asn	p.K1368N	ENST00000375687	NM_015338.5	1368	aaG/aaT	13/13	1	2	FACETS	0.975	0.908	1	0.975	0.908	1	CLONAL	1	TRUE	1	0.46	2		584	981	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026110	36026110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1433113895	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1301	292	928	0	ENST00000358208.4:c.712G>A	p.Asp238Asn	p.D238N	ENST00000358208		238	Gat/Aat	7/12	1	2	FACETS	0.797	0.748	0.848	0.797	0.748	0.848	SUBCLONAL	1	TRUE	1	0.46	2		928	1593	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39709815	39709815	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	26	152	0	ENST00000361337.2:c.442A>G	p.Lys148Glu	p.K148E	ENST00000361337	NM_003286.2	148	Aaa/Gaa	7/21	1	2	FACETS	0.774	0.621	0.945	0.774	0.621	0.945	CLONAL	1	TRUE	1	0.46	2		152	146	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39709872	39709872	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	25	212	0	ENST00000361337.2:c.499G>T	p.Glu167Ter	p.E167*	ENST00000361337	NM_003286.2	167	Gaa/Taa	7/21	1	2	FACETS	0.438	0.346	0.543	0.438	0.346	0.543	SUBCLONAL	1	TRUE	1	0.46	2		212	248	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39746831	39746831	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	155	382	0	ENST00000361337.2:c.1845G>T	p.Lys615Asn	p.K615N	ENST00000361337	NM_003286.2	615	aaG/aaT	18/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.46	2		382	652	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750422	39750422	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	123	322	0	ENST00000361337.2:c.2037G>T	p.Lys679Asn	p.K679N	ENST00000361337	NM_003286.2	679	aaG/aaT	19/21	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.46	2		322	530	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944607	40944607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766880457	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	108	353	0	ENST00000373198.4:c.1895G>A	p.Arg632Gln	p.R632Q	ENST00000373198	NM_133170.3	632	cGa/cAa	12/32	1	2	FACETS	0.824	0.741	0.91	0.824	0.741	0.91	CLONAL	1	TRUE	1	0.46	2		353	570	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164601	36164601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	111	560	1	ENST00000300305.3:c.1274C>T	p.Pro425Leu	p.P425L	ENST00000300305		425	cCg/cTg	8/8	1	2	FACETS	0.42	0.377	0.467	0.42	0.377	0.467	SUBCLONAL	1	TRUE	1	0.46	2		561	1148	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42843782	42843782	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	152	454	0	ENST00000398585.3:c.1137G>T	p.Lys379Asn	p.K379N	ENST00000398585	NM_001135099.1	379	aaG/aaT	10/14	1	2	FACETS	0.863	0.79	0.939	0.863	0.79	0.939	CLONAL	1	TRUE	1	0.46	2		454	766	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547910	41547910	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1342949087	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	175	480	0	ENST00000263253.7:c.2891C>A	p.Ser964Tyr	p.S964Y	ENST00000263253	NM_001429.3	964	tCt/tAt	15/31	1	2	FACETS	0.97	0.895	1	0.97	0.895	1	CLONAL	1	TRUE	1	0.46	2		480	784	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713298	30713298	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	137	387	0	ENST00000295754.5:c.623A>C	p.Lys208Thr	p.K208T	ENST00000295754	NM_003242.5	208	aAg/aCg	4/7	1	2	FACETS	0.901	0.822	0.984	0.901	0.822	0.984	CLONAL	1	TRUE	1	0.46	2		387	661	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163670	47163670	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	59	318	0	ENST00000409792.3:c.2456T>A	p.Ile819Asn	p.I819N	ENST00000409792	NM_014159.6	819	aTt/aAt	3/21	1	2	FACETS	0.957	0.831	1	0.957	0.831	1	CLONAL	1	TRUE	1	0.46	2		318	268	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390948	89390948	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	104	376	1	ENST00000336596.2:c.1014G>T	p.Glu338Asp	p.E338D	ENST00000336596	NM_005233.5	338	gaG/gaT	5/17	1	2	FACETS	0.956	0.86	1	0.956	0.86	1	CLONAL	1	TRUE	1	0.46	2		377	473	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445094	89445094	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	43	330	0	ENST00000336596.2:c.1414G>T	p.Val472Phe	p.V472F	ENST00000336596	NM_005233.5	472	Gtc/Ttc	6/17	1	2	FACETS	0.389	0.326	0.46	0.389	0.326	0.46	SUBCLONAL	1	TRUE	1	0.46	2		330	480	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462305	89462305	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	104	410	0	ENST00000336596.2:c.1777C>A	p.Leu593Ile	p.L593I	ENST00000336596	NM_005233.5	593	Ctc/Atc	10/17	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.46	2		410	447	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178199	142178199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746049210	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	43	235	0	ENST00000350721.4:c.7219C>T	p.Arg2407Cys	p.R2407C	ENST00000350721	NM_001184.3	2407	Cgc/Tgc	43/47	1	2	FACETS	0.682	0.574	0.8	0.682	0.574	0.8	SUBCLONAL	1	TRUE	1	0.46	2		235	274	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238521	142238521	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	23	258	1	ENST00000350721.4:c.4372C>A	p.Leu1458Ile	p.L1458I	ENST00000350721	NM_001184.3	1458	Cta/Ata	24/47	1	2	FACETS	0.368	0.287	0.461	0.368	0.287	0.461	SUBCLONAL	1	TRUE	1	0.46	2		259	272	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937046	178937046	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	45	308	0	ENST00000263967.3:c.1727C>A	p.Ser576Tyr	p.S576Y	ENST00000263967	NM_006218.2	576	tCt/tAt	11/21	1	2	FACETS	0.773	0.655	0.902	0.773	0.655	0.902	CLONAL	1	TRUE	1	0.46	2		308	253	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161301	185161301	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	194	556	0	ENST00000265026.3:c.728A>C	p.Glu243Ala	p.E243A	ENST00000265026	NM_004721.4	243	gAg/gCg	4/14	1	2	FACETS	0.996	0.923	1	0.996	0.923	1	CLONAL	1	TRUE	1	0.46	2		556	847	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443345	187443345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	152	378	0	ENST00000232014.4:c.1781G>A	p.Arg594Gln	p.R594Q	ENST00000232014	NM_001130845.1	594	cGa/cAa	8/10	1	2	FACETS	0.904	0.828	0.983	0.904	0.828	0.983	CLONAL	1	TRUE	1	0.46	2		378	731	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447065	187447065	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	244	689	0	ENST00000232014.4:c.1128G>T	p.Lys376Asn	p.K376N	ENST00000232014	NM_001130845.1	376	aaG/aaT	5/10	1	2	FACETS	0.849	0.792	0.908	0.849	0.792	0.908	CLONAL	1	TRUE	1	0.46	2		689	1250	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612212	189612212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764601563	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	202	484	0	ENST00000264731.3:c.1964G>A	p.Arg655Gln	p.R655Q	ENST00000264731	NM_003722.4	655	cGa/cAa	14/14	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.46	2		484	818	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955122	1955122	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	275	619	0	ENST00000382891.5:c.2209A>C	p.Lys737Gln	p.K737Q	ENST00000382891	NM_133335.3	737	Aaa/Caa	12/22	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.46	2		619	1056	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467565	66467565	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	109	349	0	ENST00000273854.3:c.704C>A	p.Ser235Tyr	p.S235Y	ENST00000273854	NM_004439.5	235	tCt/tAt	3/18	1	2	FACETS	0.975	0.88	1	0.975	0.88	1	CLONAL	1	TRUE	1	0.46	2		349	486	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193796	106193796	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	58	329	0	ENST00000380013.4:c.4258T>G	p.Leu1420Val	p.L1420V	ENST00000380013	NM_001127208.2	1420	Tta/Gta	10/11	1	2	FACETS	0.464	0.398	0.535	0.464	0.398	0.535	SUBCLONAL	1	TRUE	1	0.46	2		329	544	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193806	106193806	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	97	337	0	ENST00000380013.4:c.4268T>C	p.Val1423Ala	p.V1423A	ENST00000380013	NM_001127208.2	1423	gTc/gCc	10/11	1	2	FACETS	0.71	0.634	0.79	0.71	0.634	0.79	SUBCLONAL	1	TRUE	1	0.46	2		337	594	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007335	143007335	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	101	315	0	ENST00000262992.4:c.2449A>C	p.Lys817Gln	p.K817Q	ENST00000262992	NM_001101669.1	817	Aaa/Caa	22/24	1	2	FACETS	0.98	0.881	1	0.98	0.881	1	CLONAL	1	TRUE	1	0.46	2		315	448	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532921	187532921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	72	270	1	ENST00000441802.2:c.9472C>T	p.Arg3158Trp	p.R3158W	ENST00000441802	NM_005245.3	3158	Cgg/Tgg	14/27	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.46	2		271	286	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540178	187540178	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	89	408	0	ENST00000441802.2:c.7562C>A	p.Ser2521Tyr	p.S2521Y	ENST00000441802	NM_005245.3	2521	tCt/tAt	10/27	1	2	FACETS	0.768	0.683	0.858	0.768	0.683	0.858	SUBCLONAL	1	TRUE	1	0.46	2		408	504	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630588	187630588	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	159	555	0	ENST00000441802.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000441802	NM_005245.3	132	Cga/Tga	2/27	1	2	FACETS	0.848	0.778	0.921	0.848	0.778	0.921	CLONAL	1	TRUE	1	0.46	2		555	815	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409261	31409261	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	130	449	0	ENST00000344624.3:c.3756C>A	p.Phe1252Leu	p.F1252L	ENST00000344624		1252	ttC/ttA	30/33	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.46	2		449	553	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950524	38950524	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	92	410	0	ENST00000357387.3:c.3426T>G	p.Asn1142Lys	p.N1142K	ENST00000357387	NM_152756.3	1142	aaT/aaG	31/38	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.46	2		410	366	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160589	56160589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761217931	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	102	293	0	ENST00000399503.3:c.863G>A	p.Arg288Gln	p.R288Q	ENST00000399503	NM_005921.1	288	cGa/cAa	4/20	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.46	2		293	435	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183253	56183253	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	148	478	0	ENST00000399503.3:c.4163A>C	p.Asp1388Ala	p.D1388A	ENST00000399503	NM_005921.1	1388	gAt/gCt	18/20	1	2	FACETS	0.786	0.718	0.857	0.786	0.718	0.857	SUBCLONAL	1	TRUE	1	0.46	2		478	819	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569227	67569227	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	63	305	0	ENST00000274335.5:c.344T>G	p.Leu115Arg	p.L115R	ENST00000274335		115	cTc/cGc	2/15	1	2	FACETS	0.424	0.366	0.487	0.424	0.366	0.487	SUBCLONAL	1	TRUE	1	0.46	2		305	646	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	59	223	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.46	2		223	246	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589211	67589211	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	52	314	0	ENST00000274335.5:c.1199C>A	p.Ser400Tyr	p.S400Y	ENST00000274335		400	tCt/tAt	9/15	1	2	FACETS	0.942	0.81	1	0.942	0.81	1	CLONAL	1	TRUE	1	0.46	2		314	240	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649005	86649005	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	43	275	0	ENST00000274376.6:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000274376	NM_002890.2	429	Gaa/Taa	9/25	1	2	FACETS	0.742	0.625	0.869	0.742	0.625	0.869	SUBCLONAL	1	TRUE	1	0.46	2		275	252	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86667948	86667948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	58	251	0	ENST00000274376.6:c.1712G>A	p.Gly571Asp	p.G571D	ENST00000274376	NM_002890.2	571	gGt/gAt	13/25	1	2	FACETS	0.733	0.633	0.841	0.733	0.633	0.841	SUBCLONAL	1	TRUE	1	0.46	2		251	344	SUCCESS
APC	324	MSKCC	GRCh37	5	112174086	112174086	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs878853432	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	58	283	0	ENST00000257430.4:c.2795C>A	p.Ser932Ter	p.S932*	ENST00000257430	NM_000038.5	932	tCa/tAa	16/16	1	2	FACETS	0.861	0.745	0.984	0.861	0.745	0.984	CLONAL	1	TRUE	1	0.46	2		283	293	SUCCESS
APC	324	MSKCC	GRCh37	5	112174959	112174959	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	38	217	0	ENST00000257430.4:c.3668C>A	p.Ser1223Tyr	p.S1223Y	ENST00000257430	NM_000038.5	1223	tCt/tAt	16/16	1	2	FACETS	0.531	0.441	0.632	0.531	0.441	0.632	SUBCLONAL	1	TRUE	1	0.46	2		217	311	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497322	149497322	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs987244289	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	216	617	0	ENST00000261799.4:c.2996G>A	p.Arg999Gln	p.R999Q	ENST00000261799	NM_002609.3	999	cGa/cAa	22/23	1	2	FACETS	0.896	0.833	0.962	0.896	0.833	0.962	CLONAL	1	TRUE	1	0.46	2		617	1048	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514319	149514319	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	136	391	0	ENST00000261799.4:c.625C>A	p.Leu209Ile	p.L209I	ENST00000261799	NM_002609.3	209	Ctc/Atc	4/23	1	2	FACETS	0.863	0.786	0.943	0.863	0.786	0.943	CLONAL	1	TRUE	1	0.46	2		391	685	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562435	176562435	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1201715787	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	227	592	0	ENST00000439151.2:c.331A>G	p.Ile111Val	p.I111V	ENST00000439151	NM_022455.4	111	Att/Gtt	2/23	1	2	FACETS	0.956	0.891	1	0.956	0.891	1	CLONAL	1	TRUE	1	0.46	2		592	1032	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721984	176721984	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	183	510	0	ENST00000439151.2:c.7615C>A	p.Leu2539Ile	p.L2539I	ENST00000439151	NM_022455.4	2539	Ctt/Att	23/23	1	2	FACETS	0.935	0.864	1	0.935	0.864	1	CLONAL	1	TRUE	1	0.46	2		510	851	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030365	180030365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1483772533	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1206	358	759	0	ENST00000261937.6:c.3919G>A	p.Ala1307Thr	p.A1307T	ENST00000261937	NM_182925.4	1307	Gct/Act	30/30	1	2	FACETS	0.995	0.941	1	0.995	0.941	1	CLONAL	1	TRUE	1	0.46	2		759	1564	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057229	180057229	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754692331	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	264	663	1	ENST00000261937.6:c.509G>A	p.Arg170His	p.R170H	ENST00000261937	NM_182925.4	170	cGc/cAc	4/30	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.46	2		664	1112	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323196	31323196	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	272	697	0	ENST00000412585.2:c.793T>G	p.Phe265Val	p.F265V	ENST00000412585	NM_005514.6	265	Ttc/Gtc	4/8	1	2	FACETS	0.987	0.926	1	0.987	0.926	1	CLONAL	1	TRUE	1	0.46	2		697	1198	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180262	32180262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	235	566	2	ENST00000375023.3:c.2669C>T	p.Ala890Val	p.A890V	ENST00000375023	NM_004557.3	890	gCa/gTa	17/30	1	2	FACETS	0.925	0.863	0.99	0.925	0.863	0.99	CLONAL	1	TRUE	1	0.46	2		568	1104	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800447	32800447	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1152	270	855	0	ENST00000374899.4:c.1100G>A	p.Trp367Ter	p.W367*	ENST00000374899	NM_018833.2	367	tGg/tAg	6/12	1	2	FACETS	0.826	0.773	0.88	0.826	0.773	0.88	CLONAL	1	TRUE	1	0.46	2		855	1422	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803530	32803530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	249	607	0	ENST00000374899.4:c.629G>A	p.Arg210Gln	p.R210Q	ENST00000374899	NM_018833.2	210	cGa/cAa	4/12	1	2	FACETS	0.927	0.866	0.99	0.927	0.866	0.99	CLONAL	1	TRUE	1	0.46	2		607	1168	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805714	32805714	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	213	731	0	ENST00000374899.4:c.297G>A	p.Trp99Ter	p.W99*	ENST00000374899	NM_018833.2	99	tgG/tgA	2/12	1	2	FACETS	0.762	0.707	0.82	0.762	0.707	0.82	SUBCLONAL	1	TRUE	1	0.46	2		731	1215	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286979	33286979	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	174	675	0	ENST00000374542.5:c.1958G>T	p.Arg653Met	p.R653M	ENST00000374542	NM_001141970.1	653	aGg/aTg	7/8	1	2	FACETS	0.786	0.724	0.852	0.786	0.724	0.852	SUBCLONAL	1	TRUE	1	0.46	2		675	962	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956553	93956553	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1035177735	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	92	332	0	ENST00000369303.4:c.2683C>T	p.Arg895Ter	p.R895*	ENST00000369303	NM_004440.3	895	Cga/Tga	15/17	1	2	FACETS	0.866	0.773	0.964	0.866	0.773	0.964	CLONAL	1	TRUE	1	0.46	2		332	462	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93973596	93973596	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	43	317	0	ENST00000369303.4:c.1780G>T	p.Glu594Ter	p.E594*	ENST00000369303	NM_004440.3	594	Gaa/Taa	9/17	1	2	FACETS	0.733	0.618	0.859	0.733	0.618	0.859	SUBCLONAL	1	TRUE	1	0.46	2		317	255	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709180	117709180	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1330973277	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	96	326	0	ENST00000368508.3:c.1777G>T	p.Asp593Tyr	p.D593Y	ENST00000368508	NM_002944.2	593	Gat/Tat	13/43	1	2	FACETS	0.96	0.86	1	0.96	0.86	1	CLONAL	1	TRUE	1	0.46	2		326	435	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715366	117715366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	66	327	0	ENST00000368508.3:c.1123G>T	p.Asp375Tyr	p.D375Y	ENST00000368508	NM_002944.2	375	Gat/Tat	10/43	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.46	2		327	255	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527439	137527439	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	45	241	0	ENST00000367739.4:c.207G>T	p.Lys69Asn	p.K69N	ENST00000367739	NM_000416.2	69	aaG/aaT	3/7	1	2	FACETS	0.993	0.845	1	0.993	0.845	1	CLONAL	1	TRUE	1	0.46	2		241	197	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137528108	137528108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1314592282	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	47	210	0	ENST00000367739.4:c.192G>T	p.Lys64Asn	p.K64N	ENST00000367739	NM_000416.2	64	aaG/aaT	2/7	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.46	2		210	184	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199821	138199821	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	179	510	2	ENST00000237289.4:c.1239G>T	p.Lys413Asn	p.K413N	ENST00000237289	NM_001270507.1	413	aaG/aaT	7/9	1	2	FACETS	0.869	0.801	0.939	0.869	0.801	0.939	CLONAL	1	TRUE	1	0.46	2		512	896	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265323	152265323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866869178	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	112	255	0	ENST00000206249.3:c.776G>A	p.Arg259Gln	p.R259Q	ENST00000206249	NM_000125.3	259	cGa/cAa	4/8	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.46	2		255	455	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419889	152419889	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs779686273	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	214	519	0	ENST00000206249.3:c.1576T>C	p.Tyr526His	p.Y526H	ENST00000206249	NM_000125.3	526	Tac/Cac	8/8	1	2	FACETS	0.99	0.92	1	0.99	0.92	1	CLONAL	1	TRUE	1	0.46	2		519	940	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100595	157100595	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs775035352	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	167	390	0	ENST00000346085.5:c.1532G>T	p.Gly511Val	p.G511V	ENST00000346085	NM_020732.3	511	gGc/gTc	1/20	1	2	FACETS	0.876	0.806	0.949	0.876	0.806	0.949	CLONAL	1	TRUE	1	0.46	2		390	829	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157488293	157488293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750810656	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	158	411	0	ENST00000346085.5:c.2999C>T	p.Ala1000Val	p.A1000V	ENST00000346085	NM_020732.3	1000	gCg/gTg	10/20	1	2	FACETS	0.977	0.898	1	0.977	0.898	1	CLONAL	1	TRUE	1	0.46	2		411	703	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026663	6026663	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs63750770	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	239	883	0	ENST00000265849.7:c.1733G>T	p.Arg578Leu	p.R578L	ENST00000265849	NM_000535.5	578	cGt/cTt	11/15	1	2	FACETS	0.786	0.732	0.842	0.786	0.732	0.842	SUBCLONAL	1	TRUE	1	0.46	2		883	1322	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940387	13940387	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	79	364	0	ENST00000405192.2:c.1119C>A	p.Tyr373Ter	p.Y373*	ENST00000405192	NM_001163147.1	373	taC/taA	11/12	1	2	FACETS	0.84	0.742	0.943	0.84	0.742	0.943	CLONAL	1	TRUE	1	0.46	2		364	409	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444417	50444417	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	129	297	0	ENST00000331340.3:c.347A>G	p.Lys116Arg	p.K116R	ENST00000331340	NM_006060.4	116	aAa/aGa	4/8	1	2	FACETS	0.851	0.773	0.933	0.851	0.773	0.933	CLONAL	1	TRUE	1	0.46	2		297	659	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350142	81350142	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	57	337	0	ENST00000222390.5:c.1190A>C	p.Lys397Thr	p.K397T	ENST00000222390	NM_000601.4	397	aAa/aCa	10/18	1	2	FACETS	0.849	0.734	0.972	0.849	0.734	0.972	CLONAL	1	TRUE	1	0.46	2		337	292	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381528	81381528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776090604	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	113	283	0	ENST00000222390.5:c.533G>A	p.Arg178Gln	p.R178Q	ENST00000222390	NM_000601.4	178	cGa/cAa	5/18	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.46	2		283	470	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545635	106545635	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	42	426	0	ENST00000359195.3:c.3112G>T	p.Gly1038Ter	p.G1038*	ENST00000359195	NM_002649.2	1038	Gga/Tga	11/11	1	2	FACETS	0.277	0.231	0.329	0.277	0.231	0.329	SUBCLONAL	1	TRUE	1	0.46	2		426	659	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395478	116395478	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45602940	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	120	436	0	ENST00000397752.3:c.1771C>T	p.Arg591Trp	p.R591W	ENST00000397752	NM_000245.2	591	Cgg/Tgg	6/21	1	2	FACETS	0.994	0.902	1	0.994	0.902	1	CLONAL	1	TRUE	1	0.46	2		436	525	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403236	116403236	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	95	510	0	ENST00000397752.3:c.2497C>A	p.Leu833Ile	p.L833I	ENST00000397752	NM_000245.2	833	Ctc/Atc	11/21	1	2	FACETS	0.853	0.763	0.949	0.853	0.763	0.949	CLONAL	1	TRUE	1	0.46	2		510	484	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412056	116412056	+	intron_variant	Intron	SNP	T	T	G	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	156	676	0	ENST00000397752.3:c.3028+13T>G		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.885	0.812	0.962	0.885	0.812	0.962	CLONAL	1	TRUE	1	0.46	2		676	766	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	105	392	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.46	2		392	435	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494187	140494187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1158980679	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	224	548	2	ENST00000288602.6:c.1061G>A	p.Arg354Gln	p.R354Q	ENST00000288602	NM_004333.4	354	cGa/cAa	8/18	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.46	2		550	937	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896493	151896493	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	48	302	1	ENST00000262189.6:c.4144A>C	p.Ser1382Arg	p.S1382R	ENST00000262189	NM_170606.2	1382	Agt/Cgt	27/59	1	2	FACETS	0.877	0.748	1	0.877	0.748	1	CLONAL	1	TRUE	1	0.46	2		303	238	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945053	151945053	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1381538083	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	39	557	0	ENST00000262189.6:c.2466A>T	p.Lys822Asn	p.K822N	ENST00000262189	NM_170606.2	822	aaA/aaT	14/59	1	2	FACETS	0.23	0.19	0.275	0.23	0.19	0.275	SUBCLONAL	1	TRUE	1	0.46	2		557	737	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945341	151945341	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs906216502	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	54	141	0	ENST00000262189.6:c.2178G>T	p.Gln726His	p.Q726H	ENST00000262189	NM_170606.2	726	caG/caT	14/59	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.46	2		141	188	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538897	23538897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1200957711	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	235	508	0	ENST00000380871.4:c.542G>A	p.Arg181Gln	p.R181Q	ENST00000380871	NM_006167.3	181	cGa/cAa	2/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.46	2		508	895	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282083	38282083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528376963	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	286	803	0	ENST00000425967.3:c.973G>A	p.Glu325Lys	p.E325K	ENST00000425967	NM_001174067.1	325	Gag/Aag	8/19	1	2	FACETS	0.954	0.896	1	0.954	0.896	1	CLONAL	1	TRUE	1	0.46	2		803	1303	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38315005	38315005	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	264	668	0	ENST00000425967.3:c.59G>T	p.Arg20Ile	p.R20I	ENST00000425967	NM_001174067.1	20	aGa/aTa	3/19	1	2	FACETS	0.965	0.903	1	0.965	0.903	1	CLONAL	1	TRUE	1	0.46	2		668	1190	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74858992	74858992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	121	218	0	ENST00000284811.8:c.212C>T	p.Ser71Leu	p.S71L	ENST00000284811		71	tCg/tTg	4/4	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.46	2		218	388	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080372	5080372	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	29	248	0	ENST00000381652.3:c.2275T>C	p.Ser759Pro	p.S759P	ENST00000381652	NM_004972.3	759	Tct/Cct	17/25	1	2	FACETS	0.712	0.577	0.863	0.712	0.577	0.863	SUBCLONAL	1	TRUE	1	0.46	2		248	177	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089723	5089723	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	24	206	0	ENST00000381652.3:c.2621A>G	p.Asn874Ser	p.N874S	ENST00000381652	NM_004972.3	874	aAc/aGc	20/25	1	2	FACETS	0.262	0.205	0.328	0.262	0.205	0.328	SUBCLONAL	1	TRUE	1	0.46	2		206	398	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5467855	5467855	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	34	339	0	ENST00000381577.3:c.866A>G	p.Glu289Gly	p.E289G	ENST00000381577	NM_014143.3	289	gAg/gGg	7/7	1	2	FACETS	0.402	0.328	0.484	0.402	0.328	0.484	SUBCLONAL	1	TRUE	1	0.46	2		339	368	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549476	5549476	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	243	734	1	ENST00000397747.3:c.503G>T	p.Arg168Met	p.R168M	ENST00000397747	NM_025239.3	168	aGg/aTg	4/7	1	2	FACETS	0.857	0.799	0.916	0.857	0.799	0.916	CLONAL	1	TRUE	1	0.46	2		735	1233	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549503	5549503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760268393	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	267	734	1	ENST00000397747.3:c.530C>T	p.Thr177Ile	p.T177I	ENST00000397747	NM_025239.3	177	aCc/aTc	4/7	1	2	FACETS	0.934	0.875	0.995	0.934	0.875	0.995	CLONAL	1	TRUE	1	0.46	2		735	1243	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319952	8319952	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	58	259	0	ENST00000356435.5:c.5549G>T	p.Arg1850Ile	p.R1850I	ENST00000356435		1850	aGa/aTa	34/35	1	2	FACETS	0.74	0.639	0.848	0.74	0.639	0.848	SUBCLONAL	1	TRUE	1	0.46	2		259	341	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340432	8340432	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	71	421	0	ENST00000356435.5:c.5164G>A	p.Ala1722Thr	p.A1722T	ENST00000356435		1722	Gca/Aca	31/35	1	2	FACETS	0.398	0.346	0.453	0.398	0.346	0.453	SUBCLONAL	1	TRUE	1	0.46	2		421	776	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570366	87570366	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	233	712	0	ENST00000277120.3:c.2106G>T	p.Glu702Asp	p.E702D	ENST00000277120		702	gaG/gaT	17/19	1	2	FACETS	0.79	0.735	0.846	0.79	0.735	0.846	SUBCLONAL	1	TRUE	1	0.46	2		712	1283	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98003008	98003008	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	57	308	0	ENST00000289081.3:c.268C>A	p.Leu90Ile	p.L90I	ENST00000289081	NM_000136.2	90	Cta/Ata	4/15	1	2	FACETS	0.972	0.842	1	0.972	0.842	1	CLONAL	1	TRUE	1	0.46	2		308	255	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212216	98212216	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	117	229	0	ENST00000331920.6:c.3456C>A	p.Phe1152Leu	p.F1152L	ENST00000331920	NM_000264.3	1152	ttC/ttA	21/24	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.46	2		229	459	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232137	98232137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1382474804	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	122	394	0	ENST00000331920.6:c.1805G>A	p.Arg602Gln	p.R602Q	ENST00000331920	NM_000264.3	602	cGa/cAa	13/24	1	2	FACETS	0.857	0.777	0.941	0.857	0.777	0.941	CLONAL	1	TRUE	1	0.46	2		394	619	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908876	101908876	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs387906697	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	85	455	0	ENST00000374994.4:c.1240C>T	p.Arg414Ter	p.R414*	ENST00000374994	NM_004612.2	414	Cga/Tga	7/9	1	2	FACETS	0.658	0.582	0.738	0.658	0.582	0.738	SUBCLONAL	1	TRUE	1	0.46	2		455	562	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347969	128347969	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	112	683	0	ENST00000265960.3:c.536T>C	p.Val179Ala	p.V179A	ENST00000265960	NM_001006617.1	179	gTc/gCc	5/12	1	2	FACETS	0.405	0.363	0.45	0.405	0.363	0.45	SUBCLONAL	1	TRUE	1	0.46	2		683	1203	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760714	133760714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755821709	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	348	859	0	ENST00000318560.5:c.3037C>T	p.Arg1013Trp	p.R1013W	ENST00000318560	NM_005157.4	1013	Cgg/Tgg	11/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.46	2		859	1483	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801123	135801123	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	36	248	0	ENST00000298552.3:c.214C>A	p.Leu72Ile	p.L72I	ENST00000298552	NM_001162426.1	72	Ctc/Atc	5/23	1	2	FACETS	0.408	0.335	0.488	0.408	0.335	0.488	SUBCLONAL	1	TRUE	1	0.46	2		248	384	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802587	135802587	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs118203348	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	101	225	0	ENST00000298552.3:c.210+1G>A		p.X70_splice	ENST00000298552	NM_001162426.1	70			1	2	FACETS	0.998	0.897	1	0.998	0.897	1	CLONAL	1	TRUE	1	0.46	2		225	440	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317433	1317433	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	177	503	0	ENST00000400841.2:c.632G>T	p.Arg211Ile	p.R211I	ENST00000400841		211	aGa/aTa	5/6	1	2	FACETS	0.815	0.751	0.882	0.815	0.751	0.882	CLONAL	1	TRUE	1	0.46	2		503	944	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916526	39916526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265777184	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	260	634	0	ENST00000378444.4:c.4477C>T	p.Arg1493Trp	p.R1493W	ENST00000378444	NM_001123385.1	1493	Cgg/Tgg	11/15	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.46	2		634	1123	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933977	39933977	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753212580	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	236	654	0	ENST00000378444.4:c.622G>A	p.Asp208Asn	p.D208N	ENST00000378444	NM_001123385.1	208	Gac/Aac	4/15	1	2	FACETS	0.911	0.85	0.975	0.911	0.85	0.975	CLONAL	1	TRUE	1	0.46	2		654	1126	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032591	47032591	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	254	686	0	ENST00000377604.3:c.497C>A	p.Ser166Tyr	p.S166Y	ENST00000377604	NM_001204468.1	166	tCt/tAt	5/24	1	2	FACETS	0.863	0.807	0.922	0.863	0.807	0.922	CLONAL	1	TRUE	1	0.46	2		686	1279	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039693	47039693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	276	710	0	ENST00000377604.3:c.1145C>T	p.Ala382Val	p.A382V	ENST00000377604	NM_001204468.1	382	gCc/gTc	11/24	1	2	FACETS	0.926	0.868	0.986	0.926	0.868	0.986	CLONAL	1	TRUE	1	0.46	2		710	1296	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650766	48650766	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	124	724	0	ENST00000376670.3:c.635C>A	p.Thr212Asn	p.T212N	ENST00000376670	NM_002049.3	212	aCt/aAt	4/6	1	2	FACETS	0.426	0.384	0.47	0.426	0.384	0.47	SUBCLONAL	1	TRUE	1	0.46	2		724	1267	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222632	53222632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782413552	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	273	743	2	ENST00000375401.3:c.4304G>A	p.Arg1435His	p.R1435H	ENST00000375401	NM_004187.3	1435	cGc/cAc	25/26	1	2	FACETS	0.908	0.851	0.967	0.908	0.851	0.967	CLONAL	1	TRUE	1	0.46	2		745	1307	SUCCESS
AR	367	MSKCC	GRCh37	X	66765901	66765901	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	268	856	1	ENST00000374690.3:c.913G>T	p.Asp305Tyr	p.D305Y	ENST00000374690	NM_000044.3	305	Gat/Tat	1/8	1	2	FACETS	0.87	0.815	0.928	0.87	0.815	0.928	CLONAL	1	TRUE	1	0.46	2		857	1339	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854951	76854951	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	118	631	2	ENST00000373344.5:c.5885C>A	p.Ser1962Tyr	p.S1962Y	ENST00000373344	NM_000489.3	1962	tCt/tAt	25/35	1	2	FACETS	0.739	0.668	0.815	0.739	0.668	0.815	SUBCLONAL	1	TRUE	1	0.46	2		633	694	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872196	76872196	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	51	348	0	ENST00000373344.5:c.5451G>T	p.Arg1817Ser	p.R1817S	ENST00000373344	NM_000489.3	1817	agG/agT	22/35	1	2	FACETS	0.88	0.755	1	0.88	0.755	1	CLONAL	1	TRUE	1	0.46	2		348	252	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907616	76907616	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	72	465	0	ENST00000373344.5:c.4545A>C	p.Glu1515Asp	p.E1515D	ENST00000373344	NM_000489.3	1515	gaA/gaC	15/35	1	2	FACETS	0.447	0.39	0.508	0.447	0.39	0.508	SUBCLONAL	1	TRUE	1	0.46	2		465	701	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912099	76912099	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	19	424	0	ENST00000373344.5:c.4165G>T	p.Val1389Phe	p.V1389F	ENST00000373344	NM_000489.3	1389	Gtt/Ttt	13/35	1	2	FACETS	0.237	0.18	0.305	0.237	0.18	0.305	SUBCLONAL	1	TRUE	1	0.46	2		424	348	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937319	76937319	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs782073789	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	23	427	0	ENST00000373344.5:c.3429G>T	p.Lys1143Asn	p.K1143N	ENST00000373344	NM_000489.3	1143	aaG/aaT	9/35	1	2	FACETS	0.376	0.293	0.471	0.376	0.293	0.471	SUBCLONAL	1	TRUE	1	0.46	2		427	266	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937611	76937611	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	44	349	0	ENST00000373344.5:c.3137G>T	p.Ser1046Ile	p.S1046I	ENST00000373344	NM_000489.3	1046	aGt/aTt	9/35	1	2	FACETS	0.92	0.78	1	0.92	0.78	1	CLONAL	1	TRUE	1	0.46	2		349	208	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937657	76937657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782781078	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	45	415	0	ENST00000373344.5:c.3091G>A	p.Gly1031Ser	p.G1031S	ENST00000373344	NM_000489.3	1031	Ggc/Agc	9/35	1	2	FACETS	0.641	0.542	0.751	0.641	0.542	0.751	SUBCLONAL	1	TRUE	1	0.46	2		415	305	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938337	76938337	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	69	526	0	ENST00000373344.5:c.2411C>A	p.Ser804Tyr	p.S804Y	ENST00000373344	NM_000489.3	804	tCt/tAt	9/35	1	2	FACETS	0.698	0.61	0.792	0.698	0.61	0.792	SUBCLONAL	1	TRUE	1	0.46	2		526	430	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76953113	76953113	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	46	443	0	ENST00000373344.5:c.200C>A	p.Ser67Tyr	p.S67Y	ENST00000373344	NM_000489.3	67	tCt/tAt	4/35	1	2	FACETS	0.563	0.476	0.659	0.563	0.476	0.659	SUBCLONAL	1	TRUE	1	0.46	2		443	355	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608965	100608965	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	162	425	0	ENST00000308731.7:c.1643A>C	p.Asp548Ala	p.D548A	ENST00000308731	NM_000061.2	548	gAt/gCt	17/19	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.46	2		425	704	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617210	100617210	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	196	548	0	ENST00000308731.7:c.539C>T	p.Ser180Phe	p.S180F	ENST00000308731	NM_000061.2	180	tCt/tTt	7/19	1	2	FACETS	0.923	0.855	0.994	0.923	0.855	0.994	CLONAL	1	TRUE	1	0.46	2		548	923	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630192	100630192	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	142	476	0	ENST00000308731.7:c.81G>T	p.Lys27Asn	p.K27N	ENST00000308731	NM_000061.2	27	aaG/aaT	2/19	1	2	FACETS	0.768	0.7	0.839	0.768	0.7	0.839	SUBCLONAL	1	TRUE	1	0.46	2		476	804	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020371	123020371	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	19	315	1	ENST00000355640.3:c.859G>T	p.Ala287Ser	p.A287S	ENST00000355640		287	Gct/Tct	2/7	1	2	FACETS	0.257	0.194	0.33	0.257	0.194	0.33	SUBCLONAL	1	TRUE	1	0.46	2		316	322	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181242	123181242	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	45	292	0	ENST00000218089.9:c.706A>C	p.Asn236His	p.N236H	ENST00000218089	NM_001042749.1	236	Aat/Cat	9/35	0.3	0	FACETS	0.489	0.415	0.569			1	SUBCLONAL	1	TRUE	0	0.46	0		292	216	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195662	123195662	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	85	421	0	ENST00000218089.9:c.1576C>A	p.Leu526Ile	p.L526I	ENST00000218089	NM_001042749.1	526	Ctt/Att	17/35	0.3	0	FACETS	0.463	0.411	0.518			1	SUBCLONAL	1	TRUE	0	0.46	0		421	431	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197023	123197023	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	67	508	0	ENST00000218089.9:c.1789T>A	p.Leu597Met	p.L597M	ENST00000218089	NM_001042749.1	597	Ttg/Atg	19/35	0.3	0	FACETS	0.406	0.355	0.462			1	SUBCLONAL	1	TRUE	0	0.46	0		508	387	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215244	123215244	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	57	346	0	ENST00000218089.9:c.2790G>T	p.Met930Ile	p.M930I	ENST00000218089	NM_001042749.1	930	atG/atT	28/35	0.3	0	FACETS	0.497	0.431	0.569			1	SUBCLONAL	1	TRUE	0	0.46	0		346	269	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227869	123227869	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	68	249	2	ENST00000218089.9:c.3580C>T	p.Arg1194Trp	p.R1194W	ENST00000218089	NM_001042749.1	1194	Cgg/Tgg	33/35	0.3	0	FACETS	0.574	0.505	0.648			1	SUBCLONAL	1	TRUE	0	0.46	0		251	278	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229238	123229238	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	72	321	0	ENST00000218089.9:c.3722G>T	p.Arg1241Ile	p.R1241I	ENST00000218089	NM_001042749.1	1241	aGa/aTa	34/35	0.3	0	FACETS	0.5	0.44	0.564			1	SUBCLONAL	1	TRUE	0	0.46	0		321	338	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0049126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	37	302	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.784	0.651	0.932	0.784	0.651	0.932	CLONAL	1	TRUE	1	0.374317900964543	2		302	252	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0049126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	105	305	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.374317900964543	2	FACETS	0.911	0.827	0.997	0.911	0.827	0.997	CLONAL	2	TRUE	0	0.374317900964543	2		305	308	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983060	201983060	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	145	605	0	ENST00000359651.3:c.909C>A	p.Phe303Leu	p.F303L	ENST00000359651		303	ttC/ttA	7/8	1	2	FACETS	0.992	0.906	1	0.992	0.906	1	CLONAL	1	TRUE	1	0.374317900964543	2		605	781	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198262739	198262739	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	40	348	0	ENST00000335508.6:c.3236A>G	p.Asn1079Ser	p.N1079S	ENST00000335508	NM_012433.2	1079	aAc/aGc	22/25	1	2	FACETS	0.629	0.524	0.745	0.629	0.524	0.745	SUBCLONAL	1	TRUE	1	0.374317900964543	2		348	340	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912343	32912343	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	27	284	0	ENST00000380152.3:c.3851G>T	p.Ser1284Ile	p.S1284I	ENST00000380152		1284	aGt/aTt	11/27	0.374317900964543	3	FACETS	0.852	0.683	1	0.426	0.341	0.522	CLONAL	1	TRUE	1	0.374317900964543	3		284	201	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0049130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	174	346	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.397260676350696	3	FACETS	0.957	0.888	1	0.957	0.888	1	CLONAL	2	TRUE	1	0.423746523937244	3		346	520	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220640	1220640	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690940	NA	P-0049130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	317	798	0	ENST00000326873.7:c.658C>T	p.Gln220Ter	p.Q220*	ENST00000326873	NM_000455.4	220	Cag/Tag	5/10	0.357590784147696	2	FACETS	0.867	0.821	0.913	0.867	0.821	0.913	CLONAL	2	TRUE	0	0.423746523937244	2		798	863	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200976	108200976	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1275267580	NA	P-0049130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	206	352	0	ENST00000278616.4:c.7343A>T	p.Asp2448Val	p.D2448V	ENST00000278616	NM_000051.3	2448	gAt/gTt	50/63	0.423746523937244	3	FACETS	0.869	0.816	0.922	0.869	0.816	0.922	CLONAL	3	TRUE	0	0.423746523937244	3		352	452	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314622	30314622	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	282	544	0	ENST00000262643.3:c.1171A>T	p.Ser391Cys	p.S391C	ENST00000262643	NM_001238.2	391	Agt/Tgt	12/12	0.382208819892814	3	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	1	0.423746523937244	3		544	803	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793446	242793446	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	182	488	0	ENST00000334409.5:c.631G>T	p.Glu211Ter	p.E211*	ENST00000334409	NM_005018.2	211	Gag/Tag	5/5	0.382208819892814	3	FACETS	0.755	0.699	0.813	0.755	0.699	0.813	SUBCLONAL	2	TRUE	1	0.423746523937244	3		488	689	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141111	55141111	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	163	401	0	ENST00000257290.5:c.1757G>C	p.Trp586Ser	p.W586S	ENST00000257290	NM_006206.4	586	tGg/tCg	12/23	0.417402638468936	3	FACETS	0.909	0.84	0.979	0.909	0.84	0.979	CLONAL	2	TRUE	1	0.423746523937244	3		401	513	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392026	81392026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049130-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	44	260	0	ENST00000222390.5:c.251G>T	p.Cys84Phe	p.C84F	ENST00000222390	NM_000601.4	84	tGc/tTc	2/18	0.382208819892814	3	FACETS	0.732	0.616	0.859	0.366	0.308	0.43	SUBCLONAL	1	TRUE	1	0.423746523937244	3		260	344	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	205	472	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.676745447012416	2		475	602	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	172	406	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.676745447012416	2		406	486	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	209	523	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.836	0.778	0.895	0.836	0.778	0.895	CLONAL	1	TRUE	1	0.676745447012416	2		523	739	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266476	198266477	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1394586762	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	95	288	0	ENST00000335508.6:c.2359dup	p.Ile787AsnfsTer21	p.I787Nfs*21	ENST00000335508	NM_012433.2	787	att/aAtt	16/25	1	2	FACETS	0.9	0.811	0.993	0.9	0.811	0.993	CLONAL	1	TRUE	1	0.676745447012416	2		288	312	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	366	389	7	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	NA	2	FACETS	0.976	0.94	1			1	INDETERMINATE	2	TRUE	NA	0.676745447012416	2		396	554	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781324	3781326	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs587783502	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	332	822	0	ENST00000262367.5:c.5039_5041del	p.Ser1680del	p.S1680del	ENST00000262367	NM_004380.2	1680	tCCTtg/ttg	30/31	1	2	FACETS	0.978	0.927	1	0.978	0.927	1	CLONAL	1	TRUE	1	0.676745447012416	2		822	1003	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438316	110438317	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	rs532810290	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	62	175	0	ENST00000375856.3:c.82_84dup	p.Asn28dup	p.N28dup	ENST00000375856	NM_003749.2	28	-/AAC	1/2	1	2	FACETS	0.562	0.489	0.641	0.562	0.489	0.641	SUBCLONAL	1	TRUE	1	0.676745447012416	2		175	326	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791719	42791719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	257	585	2	ENST00000575354.2:c.605G>A	p.Arg202Gln	p.R202Q	ENST00000575354	NM_015125.3	202	cGg/cAg	5/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.676745447012416	2		587	750	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937164	39937164	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	280	358	1	ENST00000378444.4:c.19del	p.Leu7CysfsTer9	p.L7Cfs*9	ENST00000378444	NM_001123385.1	7	Ctg/tg	2/15	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.676745447012416	1		359	464	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097703	27097703	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	269	507	0	ENST00000324856.7:c.3292C>T	p.Gln1098Ter	p.Q1098*	ENST00000324856	NM_006015.4	1098	Cag/Tag	12/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.676745447012416	2		507	763	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001438	29001438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1473309404	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	126	369	0	ENST00000282397.4:c.1294G>A	p.Glu432Lys	p.E432K	ENST00000282397	NM_002019.4	432	Gaa/Aaa	10/30	1	2	FACETS	0.91	0.832	0.992	0.91	0.832	0.992	CLONAL	1	TRUE	1	0.676745447012416	2		369	409	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492824	56492824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	269	495	0	ENST00000407977.2:c.115G>A	p.Glu39Lys	p.E39K	ENST00000407977		39	Gaa/Aaa	2/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.676745447012416	2		495	688	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910371	29910372	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	580	772	0	ENST00000376809.5:c.46dup	p.Ala16GlyfsTer83	p.A16Gfs*83	ENST00000376809	NM_002116.7	14	tcg/tcGg	1/8	0.676745447012416	2	FACETS	0.894	0.866	0.921	0.894	0.866	0.921	CLONAL	2	TRUE	0	0.676745447012416	2		772	959	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715678	30715678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039551	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	160	351	0	ENST00000295754.5:c.1336G>A	p.Asp446Asn	p.D446N	ENST00000295754	NM_003242.5	446	Gat/Aat	5/7	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.676745447012416	2		351	447	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245449	46245449	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	195	399	0	ENST00000334344.6:c.3546del	p.Phe1182LeufsTer6	p.F1182Lfs*6	ENST00000334344	NM_152641.2	1181	agT/ag	15/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.676745447012416	2		399	541	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101031	4101031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375843855	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	169	417	1	ENST00000262948.5:c.691C>T	p.Arg231Cys	p.R231C	ENST00000262948	NM_030662.3	231	Cgc/Tgc	6/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.676745447012416	2		418	485	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	242	559	1	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.676745447012416	2		560	682	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	307	633	6	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.676745447012416	2		639	893	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948208	71948209	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs749079348	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	299	695	1	ENST00000298229.2:c.2927dup	p.Pro977ThrfsTer7	p.P977Tfs*7	ENST00000298229	NM_001567.3	974	gcc/gCcc	26/28	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.676745447012416	2		696	877	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112326	115112326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1302202171	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	146	158	1	ENST00000257566.3:c.1414G>A	p.Ala472Thr	p.A472T	ENST00000257566	NM_016569.3	472	Gcg/Acg	7/8	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.676745447012416	2		159	302	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526250	31526250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201911246	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	280	694	3	ENST00000344624.3:c.790C>T	p.Arg264Trp	p.R264W	ENST00000344624		264	Cgg/Tgg	2/33	1	2	FACETS	0.915	0.862	0.97	0.915	0.862	0.97	CLONAL	1	TRUE	1	0.676745447012416	2		697	904	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988316	36988316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	181	440	0	ENST00000354822.5:c.337G>A	p.Val113Met	p.V113M	ENST00000354822	NM_001079668.2	113	Gtg/Atg	2/3	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.676745447012416	2		440	529	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508508	106508508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	119	356	0	ENST00000359195.3:c.502G>A	p.Val168Met	p.V168M	ENST00000359195	NM_002649.2	168	Gtg/Atg	2/11	1	2	FACETS	0.911	0.83	0.995	0.911	0.83	0.995	CLONAL	1	TRUE	1	0.676745447012416	2		356	386	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210892	36210893	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs764234724	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	309	775	2	ENST00000222270.7:c.649dup	p.Arg217ProfsTer35	p.R217Pfs*35	ENST00000222270	NM_014727.1	215	acc/aCcc	3/37	1	2	FACETS	0.882	0.833	0.933	0.882	0.833	0.933	CLONAL	1	TRUE	1	0.676745447012416	2		777	1035	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094450	27094450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779484265	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	216	511	1	ENST00000324856.7:c.3158G>A	p.Arg1053His	p.R1053H	ENST00000324856	NM_006015.4	1053	cGc/cAc	11/20	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.676745447012416	2		512	632	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859392	151859393	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	204	431	0	ENST00000262189.6:c.11269_11270del	p.Gln3757GlufsTer18	p.Q3757Efs*18	ENST00000262189	NM_170606.2	3757	CAg/g	43/59	1	2	FACETS	0.949	0.885	1	0.949	0.885	1	CLONAL	1	TRUE	1	0.676745447012416	2		431	635	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023542	27023542	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	221	416	0	ENST00000324856.7:c.651del	p.Asn218ThrfsTer14	p.N218Tfs*14	ENST00000324856	NM_006015.4	216	taC/ta	1/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.676745447012416	2		416	650	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112566	115112566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	300	676	2	ENST00000257566.3:c.1174G>A	p.Ala392Thr	p.A392T	ENST00000257566	NM_016569.3	392	Gcg/Acg	7/8	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.676745447012416	2		678	882	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425776	49425776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123714	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	314	702	0	ENST00000301067.7:c.12712C>T	p.Arg4238Cys	p.R4238C	ENST00000301067	NM_003482.3	4238	Cgc/Tgc	39/54	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.676745447012416	2		702	840	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217783	2217783	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	304	640	1	ENST00000398665.3:c.2557C>A	p.Arg853Ser	p.R853S	ENST00000398665	NM_032482.2	853	Cgc/Agc	22/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.676745447012416	2		641	833	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31431719	31431719	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	170	407	0	ENST00000344624.3:c.3109C>T	p.Arg1037Ter	p.R1037*	ENST00000344624		1037	Cga/Tga	23/33	1	2	FACETS	0.912	0.844	0.982	0.912	0.844	0.982	CLONAL	1	TRUE	1	0.676745447012416	2		407	551	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376247	15376248	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs780128218	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	85	360	0	ENST00000263377.2:c.766dup	p.Gln256ProfsTer46	p.Q256Pfs*46	ENST00000263377	NM_058243.2	256	cag/cCag	5/20	1	2	FACETS	0.524	0.465	0.587	0.524	0.465	0.587	SUBCLONAL	1	TRUE	1	0.676745447012416	2		360	479	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613079	52613079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	187	368	0	ENST00000394830.3:c.3449G>A	p.Arg1150His	p.R1150H	ENST00000394830	NM_018313.4	1150	cGt/cAt	22/30	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.676745447012416	2		368	529	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945217	32945217	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	120	361	0	ENST00000380152.3:c.8612A>T	p.Glu2871Val	p.E2871V	ENST00000380152		2871	gAg/gTg	20/27	1	2	FACETS	0.876	0.798	0.956	0.876	0.798	0.956	CLONAL	1	TRUE	1	0.676745447012416	2		361	405	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476713	140476713	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	102	297	0	ENST00000288602.6:c.1693G>A	p.Asp565Asn	p.D565N	ENST00000288602	NM_004333.4	565	Gat/Aat	13/18	1	2	FACETS	0.966	0.875	1	0.966	0.875	1	CLONAL	1	TRUE	1	0.676745447012416	2		297	312	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097620	8097620	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	74	208	0	ENST00000346208.3:c.2T>C	p.Met1?	p.M1?	ENST00000346208		1	aTg/aCg	2/6	1	2	FACETS	0.955	0.849	1	0.955	0.849	1	CLONAL	1	TRUE	1	0.676745447012416	2		208	229	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466018	69466018	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	309	756	0	ENST00000227507.2:c.856A>C	p.Thr286Pro	p.T286P	ENST00000227507	NM_053056.2	286	Aca/Cca	5/5	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.676745447012416	2		756	884	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226566957	226566957	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	207	451	0	ENST00000366794.5:c.1631A>G	p.His544Arg	p.H544R	ENST00000366794	NM_001618.3	544	cAt/cGt	12/23	1	2	FACETS	0.99	0.924	1	0.99	0.924	1	CLONAL	1	TRUE	1	0.676745447012416	2		451	618	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417838	32417838	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	182	517	0	ENST00000332351.3:c.1214T>C	p.Leu405Pro	p.L405P	ENST00000332351	NM_024426.4	405	cTg/cCg	7/10	1	2	FACETS	0.959	0.89	1	0.959	0.89	1	CLONAL	1	TRUE	1	0.676745447012416	2		517	561	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475204	475204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200673994	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	211	514	0	ENST00000399788.2:c.433C>T	p.Arg145Cys	p.R145C	ENST00000399788	NM_001042603.1	145	Cgc/Tgc	4/28	NA	2	FACETS	1	0.96	1			1	INDETERMINATE	1	TRUE	NA	0.676745447012416	2		514	602	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427936	49427937	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs763440821	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	272	675	1	ENST00000301067.7:c.10653dup	p.Ala3552SerfsTer4	p.A3552Sfs*4	ENST00000301067	NM_003482.3	3551	-/A	38/54	1	2	FACETS	0.888	0.835	0.942	0.888	0.835	0.942	CLONAL	1	TRUE	1	0.676745447012416	2		676	905	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874016	123874016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1383461329	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	45	35	0	ENST00000330479.4:c.47C>T	p.Ala16Val	p.A16V	ENST00000330479	NM_020382.3	16	gCg/gTg	2/9	1	2	FACETS	0.842	0.744	0.938	1	0.975	1	CLONAL	2	TRUE	1	0.676745447012416	2		35	79	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874019	123874019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	45	32	0	ENST00000330479.4:c.50C>A	p.Ala17Glu	p.A17E	ENST00000330479	NM_020382.3	17	gCg/gAg	2/9	1	2	FACETS	0.852	0.754	0.949	1	0.975	1	CLONAL	2	TRUE	1	0.676745447012416	2		32	78	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679772	88679772	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	214	537	0	ENST00000360948.2:c.691T>C	p.Cys231Arg	p.C231R	ENST00000360948	NM_001012338.2	231	Tgc/Cgc	7/19	1	2	FACETS	0.948	0.886	1	0.948	0.886	1	CLONAL	1	TRUE	1	0.676745447012416	2		537	667	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47685266	47685266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	135	425	1	ENST00000347630.2:c.684G>A	p.Met228Ile	p.M228I	ENST00000347630	NM_001007230.1	228	atG/atA	8/11	1	2	FACETS	0.867	0.794	0.943	0.867	0.794	0.943	CLONAL	1	TRUE	1	0.676745447012416	2		426	460	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752807	42752807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1354585974	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	383	741	2	ENST00000222329.4:c.1457G>A	p.Arg486Gln	p.R486Q	ENST00000222329	NM_006494.2	486	cGg/cAg	4/4	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.676745447012416	2		743	993	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551329	29551329	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1558675795	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	252	566	0	ENST00000389048.3:c.1301A>G	p.Lys434Arg	p.K434R	ENST00000389048	NM_004304.4	434	aAg/aGg	6/29	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.676745447012416	2		566	716	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872966	136872966	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	145	374	0	ENST00000241393.3:c.532A>G	p.Ser178Gly	p.S178G	ENST00000241393	NM_003467.2	178	Agt/Ggt	2/2	1	2	FACETS	0.95	0.874	1	0.95	0.874	1	CLONAL	1	TRUE	1	0.676745447012416	2		374	451	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165594	47165594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	214	488	0	ENST00000409792.3:c.532G>A	p.Ala178Thr	p.A178T	ENST00000409792	NM_014159.6	178	Gca/Aca	3/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.676745447012416	2		488	585	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140703	55140703	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	199	455	0	ENST00000257290.5:c.1564C>A	p.Arg522Ser	p.R522S	ENST00000257290	NM_006206.4	522	Cgt/Agt	11/23	1	2	FACETS	0.972	0.906	1	0.972	0.906	1	CLONAL	1	TRUE	1	0.676745447012416	2		455	605	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153666	55153666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	212	570	1	ENST00000257290.5:c.2632G>A	p.Val878Ile	p.V878I	ENST00000257290	NM_006206.4	878	Gtc/Atc	19/23	1	2	FACETS	0.954	0.89	1	0.954	0.89	1	CLONAL	1	TRUE	1	0.676745447012416	2		571	657	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953861	55953861	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	163	401	0	ENST00000263923.4:c.3575T>C	p.Leu1192Pro	p.L1192P	ENST00000263923	NM_002253.2	1192	cTc/cCc	27/30	1	2	FACETS	0.969	0.896	1	0.969	0.896	1	CLONAL	1	TRUE	1	0.676745447012416	2		401	497	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521170	187521170	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	245	547	0	ENST00000441802.2:c.11985C>A	p.Ser3995Arg	p.S3995R	ENST00000441802	NM_005245.3	3995	agC/agA	22/27	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.676745447012416	2		547	704	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532566	187532566	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	109	355	1	ENST00000441802.2:c.9827G>T	p.Gly3276Val	p.G3276V	ENST00000441802	NM_005245.3	3276	gGg/gTg	14/27	1	2	FACETS	0.991	0.901	1	0.991	0.901	1	CLONAL	1	TRUE	1	0.676745447012416	2		356	325	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225768	26225768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	448	494	1	ENST00000360408.1:c.386G>A	p.Arg129His	p.R129H	ENST00000360408	NM_003532.2	129	cGc/cAc	1/1	0.676745447012416	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.676745447012416	2		495	657	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324113	31324152	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGGCGATGTAATCCTTGCCGTCGTAGGCGTACTGGTCA	CAGGGCGATGTAATCCTTGCCGTCGTAGGCGTACTGGTCA	-	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	491	302	0	ENST00000412585.2:c.411_450del	p.His137GlnfsTer64	p.H137Qfs*64	ENST00000412585	NM_005514.6	137	caTGACCAGTACGCCTACGACGGCAAGGATTACATCGCCCTG/ca	3/8	0.676745447012416	2	FACETS	0.965	0.934	0.995	0.965	0.934	0.995	CLONAL	2	TRUE	0	0.676745447012416	2		302	752	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265484	152265484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs909211388	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	217	480	0	ENST00000206249.3:c.937G>A	p.Asp313Asn	p.D313N	ENST00000206249	NM_000125.3	313	Gac/Aac	4/8	1	2	FACETS	0.993	0.928	1	0.993	0.928	1	CLONAL	1	TRUE	1	0.676745447012416	2		480	646	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527356	157527356	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	140	392	0	ENST00000346085.5:c.5085del	p.Phe1695LeufsTer71	p.F1695Lfs*71	ENST00000346085	NM_020732.3	1694	aTt/at	20/20	1	2	FACETS	0.867	0.796	0.942	0.867	0.796	0.942	CLONAL	1	TRUE	1	0.676745447012416	2		392	477	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527540	157527541	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	164	441	0	ENST00000346085.5:c.5266_5267del	p.Glu1756LysfsTer3	p.E1756Kfs*3	ENST00000346085	NM_020732.3	1755	acAGaa/acaa	20/20	1	2	FACETS	0.894	0.826	0.964	0.894	0.826	0.964	CLONAL	1	TRUE	1	0.676745447012416	2		441	542	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946062	13946062	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	112	291	0	ENST00000405192.2:c.1034C>A	p.Pro345His	p.P345H	ENST00000405192	NM_001163147.1	345	cCt/cAt	10/12	1	2	FACETS	0.907	0.824	0.993	0.907	0.824	0.993	CLONAL	1	TRUE	1	0.676745447012416	2		291	365	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845618	151845618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	230	592	0	ENST00000262189.6:c.13394G>A	p.Cys4465Tyr	p.C4465Y	ENST00000262189	NM_170606.2	4465	tGt/tAt	52/59	1	2	FACETS	0.926	0.867	0.987	0.926	0.867	0.987	CLONAL	1	TRUE	1	0.676745447012416	2		592	734	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864765	68864765	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	382	415	1	ENST00000288368.4:c.136G>T	p.Val46Leu	p.V46L	ENST00000288368	NM_024870.2	46	Gtg/Ttg	1/40	0.676745447012416	3	FACETS	0.936	0.895	0.978	0.936	0.895	0.978	CLONAL	2	TRUE	1	0.676745447012416	3		416	807	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68993063	68993063	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	103	284	0	ENST00000288368.4:c.1868C>A	p.Ser623Tyr	p.S623Y	ENST00000288368	NM_024870.2	623	tCt/tAt	17/40	0.676745447012416	3	FACETS	0.972	0.876	1	0.486	0.438	0.537	CLONAL	1	TRUE	1	0.676745447012416	3		284	419	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740393	145740393	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762113412	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	360	753	1	ENST00000428558.2:c.1547C>T	p.Ala516Val	p.A516V	ENST00000428558	NM_004260.3	516	gCg/gTg	9/22	0.676745447012416	3	FACETS	1	0.961	1	0.509	0.482	0.537	CLONAL	1	TRUE	1	0.676745447012416	3		754	1398	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932962	39932962	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866627719	NA	P-0049131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	276	361	0	ENST00000378444.4:c.1637G>A	p.Arg546His	p.R546H	ENST00000378444	NM_001123385.1	546	cGc/cAc	4/15	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.676745447012416	1		361	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691039	NA	P-0049140-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	460	524	0	ENST00000269305.4:c.919+1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.419879559949754	2	FACETS	0.864	0.829	0.899	0.864	0.829	0.899	CLONAL	2	TRUE	0	0.549689045170533	2		524	969	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246490592	246490592	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049140-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	125	408	0	ENST00000388985.4:c.442G>C	p.Val148Leu	p.V148L	ENST00000388985		148	Gta/Cta	5/12	1	2	FACETS	0.944	0.859	1	0.944	0.859	1	CLONAL	1	TRUE	1	0.549689045170533	2		408	482	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31466312	31466312	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0049140-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	463	479	0	ENST00000344624.3:c.2443A>T	p.Lys815Ter	p.K815*	ENST00000344624		815	Aaa/Taa	16/33	0.549689045170533	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.549689045170533	3		479	947	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545641	106545641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049140-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	121	391	0	ENST00000359195.3:c.3118C>T	p.Pro1040Ser	p.P1040S	ENST00000359195	NM_002649.2	1040	Ccc/Tcc	11/11	1	2	FACETS	0.75	0.68	0.824	0.75	0.68	0.824	SUBCLONAL	1	TRUE	1	0.549689045170533	2		391	587	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423398	116423398	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049140-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	23	254	0	ENST00000397752.3:c.3673C>G	p.Leu1225Val	p.L1225V	ENST00000397752	NM_000245.2	1225	Ctt/Gtt	19/21	1	2	FACETS	0.221	0.172	0.278	0.221	0.172	0.278	SUBCLONAL	1	TRUE	1	0.549689045170533	2		254	378	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0049147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	444	599	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.133410927222843	5	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.583665387157824	5		599	1211	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118704	115118706	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0049147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	135	391	0	ENST00000257566.3:c.635_637del	p.Asn212del	p.N212del	ENST00000257566	NM_016569.3	212	aACAtt/att	2/8	1	2	FACETS	0.728	0.664	0.796	0.728	0.664	0.796	SUBCLONAL	1	TRUE	1	0.583665387157824	2		391	635	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056181	27056181	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	73	548	0	ENST00000324856.7:c.1177C>T	p.Gln393Ter	p.Q393*	ENST00000324856	NM_006015.4	393	Cag/Tag	2/20	1	2	FACETS	0.351	0.306	0.399	0.351	0.306	0.399	SUBCLONAL	1	TRUE	1	0.583665387157824	2		548	713	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047320	77047320	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	147	372	0	ENST00000356341.3:c.1224del	p.Phe408LeufsTer7	p.F408Lfs*7	ENST00000356341	NM_002576.4	408	ttT/tt	13/15	1	2	FACETS	0.896	0.827	0.966	0.896	0.827	0.966	CLONAL	1	TRUE	1	0.818453740847414	2		372	401	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0049183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	169	400	2	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.608224201530784	2		402	555	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100691	8100692	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	194	889	0	ENST00000346208.3:c.668dup	p.Pro224AlafsTer79	p.P224Afs*79	ENST00000346208		222	tac/taCc	3/6	1	2	FACETS	0.983	0.914	1	0.983	0.914	1	CLONAL	1	TRUE	1	0.608224201530784	2		889	649	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196845	108196845	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1479339581	NA	P-0049183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	133	448	0	ENST00000278616.4:c.6868G>A	p.Glu2290Lys	p.E2290K	ENST00000278616	NM_000051.3	2290	Gag/Aag	47/63	1	2	FACETS	0.873	0.798	0.951	0.873	0.798	0.951	CLONAL	1	TRUE	1	0.608224201530784	2		448	501	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120620	115120620	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	234	745	0	ENST00000257566.3:c.386G>C	p.Gly129Ala	p.G129A	ENST00000257566	NM_016569.3	129	gGa/gCa	1/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.608224201530784	2		745	696	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771344	68771344	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	126	484	3	ENST00000261769.5:c.26C>A	p.Ser9Ter	p.S9*	ENST00000261769	NM_004360.3	9	tCg/tAg	1/16	0.608224201530784	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.608224201530784	1		487	266	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683508	29683508	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0049183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	114	368	0	ENST00000356175.3:c.7583C>G	p.Ser2528Ter	p.S2528*	ENST00000356175	NM_000267.3	2528	tCa/tGa	51/57	0.608224201530784	1	FACETS	0.847	0.773	0.922	0.847	0.773	0.922	CLONAL	1	TRUE	0	0.608224201530784	1		368	308	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881007	37881007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775190312	NA	P-0049183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4708	359	885	0	ENST00000269571.5:c.2336C>T	p.Ser779Phe	p.S779F	ENST00000269571		779	tCc/tTc	20/27	0.608224201530784	20	FACETS	0.754	0.709	0.801			1	SUBCLONAL	2	TRUE	NA	0.608224201530784	20		885	5067	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554439	63554439	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2452	285	705	0	ENST00000307078.5:c.300G>C	p.Glu100Asp	p.E100D	ENST00000307078	NM_004655.3	100	gaG/gaC	2/11	0.608224201530784	12	FACETS	1	0.992	1			1	CLONAL	1	TRUE	NA	0.608224201530784	12		705	2737	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198263292	198263292	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	123	436	0	ENST00000335508.6:c.3027G>T	p.Met1009Ile	p.M1009I	ENST00000335508	NM_012433.2	1009	atG/atT	21/25	1	2	FACETS	0.819	0.744	0.896	0.819	0.744	0.896	CLONAL	1	TRUE	1	0.608224201530784	2		436	494	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27192559	27192559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766717660	NA	P-0049183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	142	577	1	ENST00000380036.4:c.1562G>A	p.Arg521His	p.R521H	ENST00000380036	NM_000459.3	521	cGt/cAt	11/23	1	2	FACETS	0.838	0.768	0.912	0.838	0.768	0.912	CLONAL	1	TRUE	1	0.608224201530784	2		578	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579533	7579533	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	150	691	0	ENST00000269305.4:c.154C>T	p.Gln52Ter	p.Q52*	ENST00000269305	NM_001126112.2	52	Caa/Taa	4/11	0.220558745849681	3	FACETS	1	0.984	1	0.436	0.399	0.474	INDETERMINATE	1	TRUE	0	0.39137929332284	3		691	701	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210419	36210419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs567944243	NA	P-0049184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	129	557	1	ENST00000222270.7:c.412C>T	p.Arg138Cys	p.R138C	ENST00000222270	NM_014727.1	138	Cgc/Tgc	2/37	NA	2	FACETS	1	0.918	1			1	INDETERMINATE	1	TRUE	NA	0.39137929332284	2		558	652	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912898	50912898	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	63	781	1	ENST00000440232.2:c.2129A>G	p.Lys710Arg	p.K710R	ENST00000440232	NM_002691.3	710	aAg/aGg	17/27	0.39137929332284	1	FACETS	0.464	0.401	0.532	0.464	0.401	0.532	SUBCLONAL	1	TRUE	0	0.39137929332284	1		782	558	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713458	40713458	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	108	595	0	ENST00000373198.4:c.4057C>T	p.His1353Tyr	p.H1353Y	ENST00000373198	NM_133170.3	1353	Cac/Tac	30/32	0.39137929332284	1	FACETS	0.915	0.826	1	0.915	0.826	1	CLONAL	1	TRUE	0	0.39137929332284	1		595	485	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176719148	176719148	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1425053571	NA	P-0049184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	35	210	0	ENST00000439151.2:c.6452A>G	p.Lys2151Arg	p.K2151R	ENST00000439151	NM_022455.4	2151	aAg/aGg	22/23	0.288562791634059	3	FACETS	0.54	0.443	0.649	0.27	0.221	0.325	SUBCLONAL	1	TRUE	1	0.39137929332284	3		210	396	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0049186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	39	423	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.18	2		423	306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	24	707	0	ENST00000269305.4:c.376T>C	p.Tyr126His	p.Y126H	ENST00000269305	NM_001126112.2	126	Tac/Cac	5/11	1	2	FACETS	0.552	0.432	0.692	0.552	0.432	0.692	SUBCLONAL	1	TRUE	1	0.18	2		707	483	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0049190-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	453	506	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.697326346390826	2		506	623	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061191	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049190-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	121	329	0	ENST00000250448.2:c.798C>G	p.Phe266Leu	p.F266L	ENST00000250448	NM_004496.3	266	ttC/ttG	2/2	1	2	FACETS	0.975	0.891	1	0.975	0.891	1	CLONAL	1	TRUE	1	0.697326346390826	2		329	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0049190-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	266	644	2	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	0.697326346390826	1	FACETS	0.943	0.895	0.991	0.943	0.895	0.991	CLONAL	1	TRUE	0	0.697326346390826	1		646	527	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120527	70120527	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0049190-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	591	679	0	ENST00000245479.2:c.1529G>C	p.Ter510SerextTer49	p.*510Sext*49	ENST00000245479	NM_000346.3	510	tGa/tCa	3/3	0.697326346390826	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.697326346390826	2		679	812	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926885	112926885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507544	NA	P-0049190-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	186	475	2	ENST00000351677.2:c.1505C>T	p.Ser502Leu	p.S502L	ENST00000351677	NM_002834.3	502	tCa/tTa	13/16	1	2	FACETS	0.984	0.916	1	0.984	0.916	1	CLONAL	1	TRUE	1	0.697326346390826	2		477	542	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857311	68857312	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049190-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	157	350	0	ENST00000261769.5:c.1947dup	p.Ile650TyrfsTer13	p.I650Yfs*13	ENST00000261769	NM_004360.3	649	tct/tcTt	13/16	0.697326346390826	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.697326346390826	1		350	288	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604787	48604787	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049190-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	175	356	0	ENST00000342988.3:c.1609G>C	p.Asp537His	p.D537H	ENST00000342988	NM_005359.5	537	Gac/Cac	12/12	0.697326346390826	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.697326346390826	1		356	318	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343545	343545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768565859	NA	P-0049190-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	279	657	4	ENST00000262320.3:c.2129C>T	p.Ala710Val	p.A710V	ENST00000262320	NM_003502.3	710	gCg/gTg	8/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.697326346390826	2		661	774	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652996	29652996	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1135402867	NA	P-0049190-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	184	391	1	ENST00000356175.3:c.4935del	p.Pro1646LeufsTer31	p.P1646Lfs*31	ENST00000356175	NM_000267.3	1644	gTt/gt	36/57	0.697326346390826	1	FACETS	0.985	0.926	1	0.985	0.926	1	CLONAL	1	TRUE	0	0.697326346390826	1		392	349	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223262	36223262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049190-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	390	877	2	ENST00000222270.7:c.5812C>T	p.Gln1938Ter	p.Q1938*	ENST00000222270	NM_014727.1	1938	Cag/Tag	28/37	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.697326346390826	2		879	957	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94163105	94163105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782166	NA	P-0049190-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	190	395	2	ENST00000323929.3:c.2042C>T	p.Ser681Leu	p.S681L	ENST00000323929	NM_005591.3	681	tCg/tTg	19/20	1	2	FACETS	0.845	0.785	0.907	0.845	0.785	0.907	CLONAL	1	TRUE	1	0.697326346390826	2		397	645	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147720	61147720	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049190-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	174	315	0	ENST00000295025.8:c.1030G>C	p.Glu344Gln	p.E344Q	ENST00000295025	NM_002908.2	344	Gag/Cag	10/11	1	2	FACETS	0.973	0.903	1	0.973	0.903	1	CLONAL	1	TRUE	1	0.697326346390826	2		315	513	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332564	65332564	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049190-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	156	273	0	ENST00000342505.4:c.975G>A	p.Trp325Ter	p.W325*	ENST00000342505	NM_002227.2	325	tgG/tgA	7/25	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.697326346390826	2		273	447	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656563	3656563	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs777059567	NA	P-0049190-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	348	612	0	ENST00000294008.3:c.672G>C	p.Leu224Phe	p.L224F	ENST00000294008	NM_032444.2	224	ttG/ttC	3/15	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.697326346390826	2		612	877	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272029	15272029	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049190-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	246	748	0	ENST00000263388.2:c.6410del	p.Leu2137ArgfsTer12	p.L2137Rfs*12	ENST00000263388	NM_000435.2	2137	cTg/cg	33/33	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.697326346390826	2		748	690	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919726	50919726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049190-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	246	845	1	ENST00000440232.2:c.2894C>T	p.Pro965Leu	p.P965L	ENST00000440232	NM_002691.3	965	cCc/cTc	23/27	1	2	FACETS	0.905	0.849	0.962	0.905	0.849	0.962	CLONAL	1	TRUE	1	0.697326346390826	2		846	780	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198283238	198283238	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049190-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	49	379	0	ENST00000335508.6:c.490G>C	p.Glu164Gln	p.E164Q	ENST00000335508	NM_012433.2	164	Gaa/Caa	5/25	1	2	FACETS	0.199	0.168	0.233	0.199	0.168	0.233	SUBCLONAL	1	TRUE	1	0.697326346390826	2		379	706	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37637671	37637671	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049190-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	266	668	0	ENST00000249071.6:c.63C>G	p.Ile21Met	p.I21M	ENST00000249071	NM_002872.4	21	atC/atG	2/7	1	2	FACETS	0.95	0.894	1	0.95	0.894	1	CLONAL	1	TRUE	1	0.697326346390826	2		668	803	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163667	47163667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049190-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	171	277	0	ENST00000409792.3:c.2459C>T	p.Ser820Phe	p.S820F	ENST00000409792	NM_014159.6	820	tCt/tTt	3/21	0.697326346390826	1	FACETS	0.971	0.91	1	0.971	0.91	1	CLONAL	1	TRUE	0	0.697326346390826	1		277	329	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191526	185191526	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049190-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	232	504	3	ENST00000265026.3:c.2407C>T	p.Arg803Ter	p.R803*	ENST00000265026	NM_004721.4	803	Cga/Tga	11/14	1	2	FACETS	0.977	0.916	1	0.977	0.916	1	CLONAL	1	TRUE	1	0.697326346390826	2		507	681	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1940177	1940177	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0049190-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	83	108	0	ENST00000382891.5:c.1675-1G>A		p.X559_splice	ENST00000382891	NM_133335.3	559			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.697326346390826	2		108	205	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467500	66467500	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049190-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	69	368	1	ENST00000273854.3:c.769G>C	p.Glu257Gln	p.E257Q	ENST00000273854	NM_004439.5	257	Gaa/Caa	3/18	1	2	FACETS	0.437	0.381	0.496	0.437	0.381	0.496	SUBCLONAL	1	TRUE	1	0.697326346390826	2		369	453	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672089	30672089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049190-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	257	605	1	ENST00000376406.3:c.4871C>T	p.Ser1624Phe	p.S1624F	ENST00000376406	NM_014641.2	1624	tCc/tTc	10/15	1	2	FACETS	0.937	0.88	0.994	0.937	0.88	0.994	CLONAL	1	TRUE	1	0.697326346390826	2		606	787	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166722	32166722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147749837	NA	P-0049190-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	339	630	1	ENST00000375023.3:c.4516G>A	p.Glu1506Lys	p.E1506K	ENST00000375023	NM_004557.3	1506	Gag/Aag	24/30	1	2	FACETS	0.99	0.939	1	0.99	0.939	1	CLONAL	1	TRUE	1	0.697326346390826	2		631	982	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763954	76763954	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049190-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	237	508	0	ENST00000373344.5:c.7354C>T	p.Gln2452Ter	p.Q2452*	ENST00000373344	NM_000489.3	2452	Cag/Tag	35/35	0.331394880317675	1	FACETS	0.731	0.687	0.775	0.731	0.687	0.775	INDETERMINATE	1	TRUE	0	0.697326346390826	1		508	606	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285051	15285052	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGG	novel	NA	P-0049190-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	250	651	0	ENST00000263388.2:c.4563_4564insCCG	p.Pro1521dup	p.P1521dup	ENST00000263388	NM_000435.2	1521	-/CCG	25/33	1	2	FACETS	0.969	0.91	1	0.969	0.91	1	CLONAL	1	TRUE	1	0.697326346390826	2		651	740	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	140	431	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.446396667701793	1	FACETS	0.523	0.479	0.568	0.523	0.479	0.568	SUBCLONAL	1	TRUE	0	0.700180229580515	1		431	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0049191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	271	632	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.674537623951519	1	FACETS	0.811	0.768	0.856	0.811	0.768	0.856	CLONAL	1	TRUE	0	0.700180229580515	1		632	620	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0049191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	168	247	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.653009534953898	2	FACETS	0.833	0.783	0.882	0.833	0.783	0.882	CLONAL	2	TRUE	0	0.700180229580515	2		247	288	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235925	108235925	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	77	364	0	ENST00000278616.4:c.8967A>C	p.Gln2989His	p.Q2989H	ENST00000278616	NM_000051.3	2989	caA/caC	62/63	0.462161774423397	1	FACETS	0.427	0.377	0.479	0.427	0.377	0.479	SUBCLONAL	1	TRUE	0	0.700180229580515	1		364	335	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827859	170827859	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	11	186	0	ENST00000296930.5:c.599C>T	p.Pro200Leu	p.P200L	ENST00000296930	NM_002520.6	200	cCa/cTa	8/11	0.653009534953898	2	FACETS	0.165	0.113	0.228	0.082	0.056	0.114	SUBCLONAL	1	TRUE	0	0.700180229580515	2		186	191	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0049192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	158	583	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.212240632674288	3	FACETS	0.861	0.789	0.937	0.861	0.789	0.937	CLONAL	2	TRUE	1	0.222352750638553	3		583	917	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0049192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	88	332	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.181916718598291	2	FACETS	0.796	0.708	0.89	0.796	0.708	0.89	SUBCLONAL	2	TRUE	0	0.222352750638553	2		332	497	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0049192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	64	267	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.181916718598291	2	FACETS	0.825	0.718	0.939	0.825	0.718	0.939	CLONAL	2	TRUE	0	0.222352750638553	2		267	349	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828881	26828881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	105	385	0	ENST00000381527.3:c.103G>A	p.Val35Ile	p.V35I	ENST00000381527	NM_001260.1	35	Gtc/Atc	1/13	0.0986849054216934	4	FACETS	0.84	0.753	0.932	0.84	0.753	0.932	INDETERMINATE	2	TRUE	2	0.222352750638553	4		385	687	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0049192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	102	828	1	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.212240632674288	3	FACETS	0.868	0.774	0.968	0.434	0.387	0.484	CLONAL	1	TRUE	1	0.222352750638553	3		829	1175	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980413	1980413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	107	785	1	ENST00000382891.5:c.3875C>T	p.Ser1292Leu	p.S1292L	ENST00000382891	NM_133335.3	1292	tCg/tTg	22/22	0.185485984759018	2	FACETS	0.954	0.854	1	0.477	0.427	0.53	CLONAL	1	TRUE	0	0.222352750638553	2		786	1009	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371732	55371732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049192-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	100	519	0	ENST00000297316.4:c.422G>A	p.Arg141Gln	p.R141Q	ENST00000297316	NM_022454.3	141	cGg/cAg	2/2	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.222352750638553	2		519	885	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0049193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	250	768	7	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.573665694252835	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.573665694252835	1		775	548	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0049193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	124	400	2	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.573665694252835	2		402	362	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0049193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	103	350	2	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.573665694252835	2		352	332	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912188	114912188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	198	521	2	ENST00000543371.1:c.1258C>T	p.Arg420Trp	p.R420W	ENST00000543371	NM_001198531.1	420	Cgg/Tgg	11/14	1	2	FACETS	0.952	0.885	1	0.952	0.885	1	CLONAL	1	TRUE	1	0.573665694252835	2		523	725	SUCCESS
APC	324	MSKCC	GRCh37	5	112175536	112175536	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	70	336	1	ENST00000257430.4:c.4245del	p.Ser1415ArgfsTer4	p.S1415Rfs*4	ENST00000257430	NM_000038.5	1415	agT/ag	16/16	1	2	FACETS	0.756	0.664	0.853	0.756	0.664	0.853	SUBCLONAL	1	TRUE	1	0.573665694252835	2		337	323	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934239	81934239	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	45	708	1	ENST00000359376.3:c.1216G>A	p.Glu406Lys	p.E406K	ENST00000359376	NM_002661.3	406	Gag/Aag	14/33	0.541988392424652	3	FACETS	0.236	0.197	0.279	0.079	0.065	0.093	SUBCLONAL	1	TRUE	0	0.573665694252835	3		709	855	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054630	5054630	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772744665	NA	P-0049193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	65	354	0	ENST00000381652.3:c.682C>T	p.Arg228Ter	p.R228*	ENST00000381652	NM_004972.3	228	Cga/Tga	7/25	1	2	FACETS	0.94	0.826	1	0.94	0.826	1	CLONAL	1	TRUE	1	0.573665694252835	2		354	241	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0049194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	24	634	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.287	0.224	0.36	0.287	0.224	0.36	SUBCLONAL	1	TRUE	1	0.33	2		634	506	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0049194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	68	591	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.3	1	FACETS	0.684	0.596	0.779	0.684	0.596	0.779	SUBCLONAL	1	TRUE	0	0.33	1		592	503	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562482	21562483	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGGCG	rs550642106	NA	P-0049194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	10	180	1	ENST00000382592.4:c.1431_1436dup	p.Pro479_Ala480dup	p.P479_A480dup	ENST00000382592	NM_014572.2	479	ccg/ccCGCCCCg	4/8	1	2	FACETS	0.314	0.212	0.442	0.314	0.212	0.442	SUBCLONAL	1	TRUE	1	0.33	2		181	193	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842471	68842471	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1131690808	NA	P-0049194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	72	628	0	ENST00000261769.5:c.531+1G>A		p.X177_splice	ENST00000261769	NM_004360.3	177			1	2	FACETS	0.826	0.723	0.937	0.826	0.723	0.937	CLONAL	1	TRUE	1	0.33	2		628	528	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857382	68857382	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	102	617	0	ENST00000261769.5:c.2017C>T	p.Gln673Ter	p.Q673*	ENST00000261769	NM_004360.3	673	Cag/Tag	13/16	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.33	2		617	591	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511206	148511206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	130	539	0	ENST00000320356.2:c.1696C>T	p.Arg566Cys	p.R566C	ENST00000320356	NM_004456.4	566	Cgc/Tgc	15/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.33	2		539	701	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822706	72822706	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	110	854	0	ENST00000268489.5:c.9469A>G	p.Thr3157Ala	p.T3157A	ENST00000268489	NM_006885.3	3157	Aca/Gca	10/10	1	2	FACETS	0.998	0.898	1	0.998	0.898	1	CLONAL	1	TRUE	1	0.33	2		854	668	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249513	153249513	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	93	578	0	ENST00000281708.4:c.1265del	p.Gly422ValfsTer8	p.G422Vfs*8	ENST00000281708	NM_033632.3	422	gGt/gt	9/12	1	2	FACETS	0.972	0.866	1	0.972	0.866	1	CLONAL	1	TRUE	1	0.33	2		578	580	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0049195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	71	629	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.2053882463693	4	FACETS	1	0.898	1	1	0.973	1	CLONAL	4	TRUE	1	0.2053882463693	4		629	206	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577490	7577503	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTCCTGACCTGGA	GCTCCTGACCTGGA	-	novel	NA	P-0049195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	24	541	0	ENST00000269305.4:c.778_782+9del		p.X260_splice	ENST00000269305	NM_001126112.2	260		7/11	0.2053882463693	1	FACETS	0.782	0.622	0.963	1	0.934	1	CLONAL	2	TRUE	0	0.2053882463693	1		541	134	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202122974	202122974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762986379	NA	P-0049195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	22	407	0	ENST00000358485.4:c.20C>T	p.Ala7Val	p.A7V	ENST00000358485	NM_001080125.1	7	gCc/gTc	1/9	0.2053882463693	3	FACETS	1	0.915	1	0.707	0.552	0.884	CLONAL	1	TRUE	1	0.2053882463693	3		407	167	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579536	7579536	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567556930	NA	P-0049196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	182	592	0	ENST00000269305.4:c.151G>T	p.Glu51Ter	p.E51*	ENST00000269305	NM_001126112.2	51	Gaa/Taa	4/11	0.17680292778147	3	FACETS	1	0.932	1	1	0.988	1	CLONAL	4	FALSE	0	0.17680292778147	3		592	558	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441974	6441974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	275	424	0	ENST00000356142.4:c.533C>T	p.Ala178Val	p.A178V	ENST00000356142	NM_018890.3	178	gCg/gTg	7/7	1	2	FACETS	1	0.981	1	1	0.997	1	CLONAL	4	FALSE	1	0.17680292778147	2		424	716	SUCCESS
FH	2271	MSKCC	GRCh37	1	241671937	241671937	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	50	480	0	ENST00000366560.3:c.704A>G	p.His235Arg	p.H235R	ENST00000366560	NM_000143.3	235	cAt/cGt	5/10	1	2	FACETS	0.918	0.795	1	1	0.982	1	CLONAL	4	FALSE	1	0.17680292778147	2		480	154	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0049197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	360	479	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.34201913600402	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	2	0.393693204031499	4		479	1078	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318823	163318823	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	118	332	0	ENST00000271452.3:c.1213A>T	p.Ile405Phe	p.I405F	ENST00000271452	NM_145697.2	405	Att/Ttt	13/14	0.393693204031499	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.393693204031499	1		332	405	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061866	38061874	+	inframe_deletion	In_Frame_Del	DEL	CATGGAGCC	CATGGAGCC	-	novel	NA	P-0049197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	215	659	1	ENST00000250448.2:c.115_123del	p.Gly39_Met41del	p.G39_M41del	ENST00000250448	NM_004496.3	39	GGCTCCATG/-	2/2	0.393693204031499	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.393693204031499	1		660	763	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031834	10031834	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367543120	NA	P-0049197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	222	548	1	ENST00000330684.3:c.989C>T	p.Pro330Leu	p.P330L	ENST00000330684	NM_001134407.1	330	cCg/cTg	3/13	0.159665469731535	4	FACETS	0.829	0.772	0.888	0.829	0.772	0.888	INDETERMINATE	2	TRUE	2	0.393693204031499	4		549	948	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579428	7579429	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0049197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	398	714	0	ENST00000269305.4:c.258_259del	p.Pro87SerfsTer61	p.P87Sfs*61	ENST00000269305	NM_001126112.2	86	gcACca/gcca	4/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.393693204031499	2		714	908	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790153	40790153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	124	585	1	ENST00000373198.4:c.2578C>T	p.Pro860Ser	p.P860S	ENST00000373198	NM_133170.3	860	Ccc/Tcc	18/32	NA	2	FACETS	0.784	0.71	0.863			1	INDETERMINATE	1	TRUE	NA	0.393693204031499	2		586	803	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041725	47041725	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049197-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	137	208	0	ENST00000377604.3:c.1950G>C	p.Gln650His	p.Q650H	ENST00000377604	NM_001204468.1	650	caG/caC	17/24	0.276869467184298	2	FACETS	1	0.943	1			1	CLONAL	2	TRUE	NA	0.393693204031499	2		208	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0049198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	176	605	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.489664148650146	1	FACETS	0.848	0.785	0.913	0.848	0.785	0.913	CLONAL	1	TRUE	0	0.498476688325182	1		606	625	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0049198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	153	423	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.204007355856604	5	FACETS	1	0.98	1	0.688	0.641	0.735	INDETERMINATE	3	TRUE	0	0.498476688325182	5		423	312	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0049198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	73	248	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.861	0.759	0.97	0.861	0.759	0.97	CLONAL	1	TRUE	1	0.498476688325182	2		249	340	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439906	56439906	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs763974538	NA	P-0049198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	131	477	0	ENST00000407977.2:c.686C>T	p.Pro229Leu	p.P229L	ENST00000407977		229	cCg/cTg	6/10	1	2	FACETS	0.867	0.79	0.949	0.867	0.79	0.949	CLONAL	1	TRUE	1	0.498476688325182	2		477	606	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231280	46231280	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0049198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	18	331	0	ENST00000334344.6:c.1121-1G>T		p.X374_splice	ENST00000334344	NM_152641.2	374			0.204007355856604	5	FACETS	0.679	0.513	0.872	0.136	0.102	0.175	INDETERMINATE	1	TRUE	0	0.498476688325182	5		331	186	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588696	28588696	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	rs774626768	NA	P-0049198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	59	300	0	ENST00000241453.7:c.2754-2A>C		p.X918_splice	ENST00000241453	NM_004119.2	918			0.498476688325182	1	FACETS	0.823	0.718	0.934	0.823	0.718	0.934	CLONAL	1	TRUE	0	0.498476688325182	1		300	216	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450326	50450326	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	113	651	0	ENST00000331340.3:c.510G>T	p.Glu170Asp	p.E170D	ENST00000331340	NM_006060.4	170	gaG/gaT	5/8	0.428688041807905	3	FACETS	0.767	0.691	0.848	0.384	0.345	0.424	SUBCLONAL	1	TRUE	1	0.498476688325182	3		651	738	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8339002	8339002	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	63	415	1	ENST00000356435.5:c.5299C>T	p.Gln1767Ter	p.Q1767*	ENST00000356435		1767	Cag/Tag	32/35	1	2	FACETS	0.808	0.704	0.919	0.808	0.704	0.919	CLONAL	1	TRUE	1	0.498476688325182	2		416	313	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802594	139802594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	212	735	1	ENST00000247668.2:c.439G>A	p.Glu147Lys	p.E147K	ENST00000247668	NM_021138.3	147	Gaa/Aaa	5/11	0.428688041807905	3	FACETS	1	0.972	1	0.543	0.505	0.583	CLONAL	1	TRUE	1	0.498476688325182	3		736	978	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0049200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	2184	423	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.744246287795969	12	FACETS	1	0.998	1			1	CLONAL	11	TRUE	NA	0.744246287795969	12		423	2437	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235931	108235931	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	266	348	0	ENST00000278616.4:c.8973C>A	p.Cys2991Ter	p.C2991*	ENST00000278616	NM_000051.3	2991	tgC/tgA	62/63	0.717942807345918	2	FACETS	0.979	0.941	1	0.979	0.941	1	CLONAL	2	TRUE	0	0.744246287795969	2		348	365	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828160	3828165	+	inframe_deletion	In_Frame_Del	DEL	TGCTAA	TGCTAA	-	novel	NA	P-0049200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	94	329	0	ENST00000262367.5:c.1960_1965del	p.Leu654_Ala655del	p.L654_A655del	ENST00000262367	NM_004380.2	654	TTAGCA/-	10/31	0.717942807345918	2	FACETS	0.775	0.697	0.856	0.387	0.348	0.428	SUBCLONAL	1	TRUE	0	0.744246287795969	2		329	326	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660513	67660585	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTGATGCTGTGTTTCATGAGCGCTATGCCCTCATCCAGCATCAGAAGTCACACAAGAATGAGAAGCGCTTT	CTGTGATGCTGTGTTTCATGAGCGCTATGCCCTCATCCAGCATCAGAAGTCACACAAGAATGAGAAGCGCTTT	-	novel	NA	P-0049200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	134	457	0	ENST00000264010.4:c.1413_1485del	p.Tyr471Ter	p.Y471*	ENST00000264010	NM_006565.3	471	taCTGTGATGCTGTGTTTCATGAGCGCTATGCCCTCATCCAGCATCAGAAGTCACACAAGAATGAGAAGCGCTTT/ta	8/12	0.705287737447286	2	FACETS	0.75	0.686	0.817	0.375	0.343	0.409	SUBCLONAL	1	TRUE	0	0.744246287795969	2		457	480	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219367	1219367	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	900	732	0	ENST00000326873.7:c.419T>G	p.Leu140Arg	p.L140R	ENST00000326873	NM_000455.4	140	cTg/cGg	3/10	0.731100748947029	3	FACETS	0.986	0.968	1			1	CLONAL	3	TRUE	NA	0.744246287795969	3		732	1122	SUCCESS
ATR	545	MSKCC	GRCh37	3	142232414	142232414	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	288	460	0	ENST00000350721.4:c.4570G>T	p.Val1524Leu	p.V1524L	ENST00000350721	NM_001184.3	1524	Gtg/Ttg	26/47	0.717942807345918	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.744246287795969	2		460	373	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964865	55964865	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	245	270	0	ENST00000263923.4:c.2372G>T	p.Arg791Leu	p.R791L	ENST00000263923	NM_002253.2	791	cGg/cTg	16/30	0.720559484534847	4	FACETS	0.983	0.927	1	0.983	0.927	1	CLONAL	2	TRUE	2	0.744246287795969	4		270	584	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64289237	64289961	+	splice_acceptor_variant,splice_donor_variant,intron_variant	Splice_Site	DEL	GTAAGTAATGGATTCTCTTTTCATTTGTACTCTCTTTCATTTCCTTGTTGAGTGTCAGTGAGTTTAATAGTCTAATAGCCCATTTAATCATTATGATTATTTTTTGAGATAGTATTAAAACCAGGAAATCAAGATCTTACATTCTTTTTTGCATTTCATGCAGTTGCTCATATTACTAAGATTCTAATCCAACAAGAGTTTTTGAATTATTGTTTTGCTTTAAATACTTGATTGAATATGTTGGTTATTTTGTATTTTTATTGAGGTATAATTAAGATACATTTAAAGATACAATAAAATGCACAGGTCTCCAAAGGAGACCAGTTGACAATAACAGCCAAATTAACCATCCAATACAACACATAGAATATTTTGAGTGCTGTAGAACATGCCTTTGTGGCTTTTGTAGTCATCTTCCCTGCTACCAGAGGCAACTTCTGACTTCACTATAAATTAGTTTTGTCTTTTCGTGGACTTACGTGTAAATGGATTTGTGAGTCGACTGTTGTAACCAATACTCAAACGAAGATATAAAGAAAATTAACTTTTTATGATTTTTTCCATTTACACTGATGTGCCTGTTCATATTCCTTTCTGCATCAGGTCACAGCCTAATTAATCAAAAGATAAATTGCCACAAGAGAGGTGATGGTTGTCTATAAGACACTAAATATTACTGTAGGGGGCTTTTGCCTTGTTTCATTTTTTTTTTTTTTTCCTCCCAG	GTAAGTAATGGATTCTCTTTTCATTTGTACTCTCTTTCATTTCCTTGTTGAGTGTCAGTGAGTTTAATAGTCTAATAGCCCATTTAATCATTATGATTATTTTTTGAGATAGTATTAAAACCAGGAAATCAAGATCTTACATTCTTTTTTGCATTTCATGCAGTTGCTCATATTACTAAGATTCTAATCCAACAAGAGTTTTTGAATTATTGTTTTGCTTTAAATACTTGATTGAATATGTTGGTTATTTTGTATTTTTATTGAGGTATAATTAAGATACATTTAAAGATACAATAAAATGCACAGGTCTCCAAAGGAGACCAGTTGACAATAACAGCCAAATTAACCATCCAATACAACACATAGAATATTTTGAGTGCTGTAGAACATGCCTTTGTGGCTTTTGTAGTCATCTTCCCTGCTACCAGAGGCAACTTCTGACTTCACTATAAATTAGTTTTGTCTTTTCGTGGACTTACGTGTAAATGGATTTGTGAGTCGACTGTTGTAACCAATACTCAAACGAAGATATAAAGAAAATTAACTTTTTATGATTTTTTCCATTTACACTGATGTGCCTGTTCATATTCCTTTCTGCATCAGGTCACAGCCTAATTAATCAAAAGATAAATTGCCACAAGAGAGGTGATGGTTGTCTATAAGACACTAAATATTACTGTAGGGGGCTTTTGCCTTGTTTCATTTTTTTTTTTTTTTCCTCCCAG	-	novel	NA	P-0049200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	39	316	0	ENST00000370651.3:c.404+1_405-1del		p.X135_splice	ENST00000370651	NM_003463.4	135			0.399767653401439	5	FACETS	0.438	0.363	0.523	0.146	0.121	0.175	INDETERMINATE	1	TRUE	2	0.744246287795969	5		316	506	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545662	106545662	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	312	498	0	ENST00000359195.3:c.3139G>C	p.Asp1047His	p.D1047H	ENST00000359195	NM_002649.2	1047	Gac/Cac	11/11	0.670579888207656	4	FACETS	0.874	0.827	0.921	0.874	0.827	0.921	CLONAL	2	TRUE	2	0.744246287795969	4		498	837	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	41	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.643	0.538	0.759	0.643	0.538	0.759	SUBCLONAL	1	TRUE	1	0.41154197858529	2		148	310	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	75	261	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.993	0.876	1	0.993	0.876	1	CLONAL	1	TRUE	1	0.41154197858529	2		261	367	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	23	740	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	0.121	0.093	0.153	0.121	0.093	0.153	SUBCLONAL	1	TRUE	1	0.41154197858529	2		740	927	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188823	32188823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs8192585	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	148	909	1	ENST00000375023.3:c.731C>T	p.Ser244Leu	p.S244L	ENST00000375023	NM_004557.3	244	tCg/tTg	4/30	0.355397206668602	3	FACETS	0.865	0.789	0.944	0.432	0.394	0.472	CLONAL	1	TRUE	1	0.41154197858529	3		910	1003	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289863	15289863	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201680145	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	159	918	0	ENST00000263388.2:c.3691C>T	p.Arg1231Cys	p.R1231C	ENST00000263388	NM_000435.2	1231	Cgt/Tgt	22/33	1	2	FACETS	0.788	0.721	0.857	0.788	0.721	0.857	SUBCLONAL	1	TRUE	1	0.41154197858529	2		918	981	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295825	212295825	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	105	386	0	ENST00000342788.4:c.2488G>A	p.Gly830Arg	p.G830R	ENST00000342788	NM_005235.2	830	Gga/Aga	21/28	1	2	FACETS	0.987	0.888	1	0.987	0.888	1	CLONAL	1	TRUE	1	0.41154197858529	2		386	517	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	83	326	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.41154197858529	1	FACETS	0.811	0.72	0.907	0.811	0.72	0.907	CLONAL	1	TRUE	0	0.41154197858529	1		326	395	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	73	375	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	1	2	FACETS	0.631	0.553	0.716	0.631	0.553	0.716	SUBCLONAL	1	TRUE	1	0.41154197858529	2		375	562	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729175	66729175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908596	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	173	688	0	ENST00000307102.5:c.383G>A	p.Gly128Asp	p.G128D	ENST00000307102	NM_002755.3	128	gGc/gAc	3/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.41154197858529	2		688	792	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508721	106508721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754275924	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	136	585	0	ENST00000359195.3:c.715G>A	p.Asp239Asn	p.D239N	ENST00000359195	NM_002649.2	239	Gac/Aac	2/11	1	2	FACETS	0.827	0.752	0.906	0.827	0.752	0.906	CLONAL	1	TRUE	1	0.41154197858529	2		585	799	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584747	187584747	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1358297166	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	94	294	1	ENST00000441802.2:c.3286C>T	p.Arg1096Ter	p.R1096*	ENST00000441802	NM_005245.3	1096	Cga/Tga	3/27	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.41154197858529	2		295	387	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987165	36987165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	147	843	0	ENST00000354822.5:c.524C>T	p.Ser175Leu	p.S175L	ENST00000354822	NM_001079668.2	175	tCg/tTg	3/3	1	2	FACETS	0.931	0.851	1	0.931	0.851	1	CLONAL	1	TRUE	1	0.41154197858529	2		843	767	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032867	30032867	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	80	288	0	ENST00000338641.4:c.240+2T>C		p.X80_splice	ENST00000338641	NM_000268.3	80			1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.41154197858529	2		288	366	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031889	26031889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	154	328	0	ENST00000244661.2:c.400G>A	p.Glu134Lys	p.E134K	ENST00000244661	NM_003537.3	134	Gaa/Aaa	1/1	0.355397206668602	3	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	1	0.41154197858529	3		328	439	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976618	55976618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1217850741	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	112	494	0	ENST00000263923.4:c.1207C>T	p.Pro403Ser	p.P403S	ENST00000263923	NM_002253.2	403	Ccc/Tcc	9/30	1	2	FACETS	0.894	0.806	0.986	0.894	0.806	0.986	CLONAL	1	TRUE	1	0.41154197858529	2		494	609	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073907	8073907	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	98	397	0	ENST00000377482.5:c.752C>T	p.Ser251Leu	p.S251L	ENST00000377482	NM_018948.3	251	tCg/tTg	4/4	1	2	FACETS	0.88	0.788	0.978	0.88	0.788	0.978	CLONAL	1	TRUE	1	0.41154197858529	2		397	541	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28600580	28600580	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	130	565	0	ENST00000253063.3:c.931G>A	p.Asp311Asn	p.D311N	ENST00000253063	NM_031459.4	311	Gac/Aac	7/10	1	2	FACETS	0.884	0.803	0.969	0.884	0.803	0.969	CLONAL	1	TRUE	1	0.41154197858529	2		565	715	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631162	69631162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	132	652	1	ENST00000334134.2:c.250G>A	p.Gly84Ser	p.G84S	ENST00000334134	NM_005247.2	84	Ggc/Agc	2/3	1	2	FACETS	0.938	0.853	1	0.938	0.853	1	CLONAL	1	TRUE	1	0.41154197858529	2		653	684	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601235	28601235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769857405	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	93	383	0	ENST00000241453.7:c.2197C>T	p.Pro733Ser	p.P733S	ENST00000241453	NM_004119.2	733	Cca/Tca	17/24	1	2	FACETS	0.85	0.758	0.947	0.85	0.758	0.947	CLONAL	1	TRUE	1	0.41154197858529	2		383	532	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959124	28959124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	105	425	1	ENST00000282397.4:c.2014G>A	p.Val672Met	p.V672M	ENST00000282397	NM_002019.4	672	Gtg/Atg	14/30	1	2	FACETS	0.954	0.858	1	0.954	0.858	1	CLONAL	1	TRUE	1	0.41154197858529	2		426	535	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986496	36986496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	149	672	1	ENST00000354822.5:c.1193G>A	p.Gly398Asp	p.G398D	ENST00000354822	NM_001079668.2	398	gGt/gAt	3/3	1	2	FACETS	0.975	0.892	1	0.975	0.892	1	CLONAL	1	TRUE	1	0.41154197858529	2		673	743	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670394	88670395	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	59	332	0	ENST00000360948.2:c.1291_1292delinsAA	p.Gly431Lys	p.G431K	ENST00000360948	NM_001012338.2	431	GGg/AAg	11/19	1	2	FACETS	0.755	0.652	0.865	0.755	0.652	0.865	SUBCLONAL	1	TRUE	1	0.41154197858529	2		332	380	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900667	3900668	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	120	673	1	ENST00000262367.5:c.428_429delinsTT	p.Pro143Leu	p.P143L	ENST00000262367	NM_004380.2	143	cCC/cTT	2/31	1	2	FACETS	0.808	0.73	0.89	0.808	0.73	0.89	CLONAL	1	TRUE	1	0.41154197858529	2		674	722	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646326	23646327	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	102	593	1	ENST00000261584.4:c.1540_1541delinsAA	p.Gly514Lys	p.G514K	ENST00000261584	NM_024675.3	514	GGa/AAa	4/13	1	2	FACETS	0.64	0.573	0.713	0.64	0.573	0.713	SUBCLONAL	1	TRUE	1	0.41154197858529	2		594	774	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251829	10251829	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	154	604	0	ENST00000340748.4:c.3298C>T	p.Pro1100Ser	p.P1100S	ENST00000340748		1100	Ccc/Tcc	30/40	1	2	FACETS	0.941	0.862	1	0.941	0.862	1	CLONAL	1	TRUE	1	0.41154197858529	2		604	795	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276716	15276716	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	163	871	1	ENST00000263388.2:c.5549C>T	p.Ala1850Val	p.A1850V	ENST00000263388	NM_000435.2	1850	gCc/gTc	30/33	1	2	FACETS	0.864	0.793	0.938	0.864	0.793	0.938	CLONAL	1	TRUE	1	0.41154197858529	2		872	917	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728566	190728566	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	110	439	0	ENST00000441310.2:c.1954A>G	p.Lys652Glu	p.K652E	ENST00000441310	NM_000534.4	652	Aaa/Gaa	10/13	1	2	FACETS	0.808	0.727	0.893	0.808	0.727	0.893	CLONAL	1	TRUE	1	0.41154197858529	2		439	662	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55962425	55962425	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	134	445	0	ENST00000263923.4:c.2699A>G	p.Asn900Ser	p.N900S	ENST00000263923	NM_002253.2	900	aAc/aGc	19/30	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.41154197858529	2		445	650	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38949856	38949856	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372076021	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	79	299	0	ENST00000357387.3:c.4094C>T	p.Thr1365Ile	p.T1365I	ENST00000357387	NM_152756.3	1365	aCc/aTc	31/38	1	2	FACETS	0.763	0.673	0.86	0.763	0.673	0.86	SUBCLONAL	1	TRUE	1	0.41154197858529	2		299	503	SUCCESS
APC	324	MSKCC	GRCh37	5	112178102	112178102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	98	392	0	ENST00000257430.4:c.6811C>T	p.Pro2271Ser	p.P2271S	ENST00000257430	NM_000038.5	2271	Cct/Tct	16/16	1	2	FACETS	0.958	0.858	1	0.958	0.858	1	CLONAL	1	TRUE	1	0.41154197858529	2		392	497	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032059	26032059	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	115	539	0	ENST00000244661.2:c.230A>C	p.Gln77Pro	p.Q77P	ENST00000244661	NM_003537.3	77	cAa/cCa	1/1	0.355397206668602	3	FACETS	0.905	0.815	0.999	0.452	0.407	0.5	CLONAL	1	TRUE	1	0.41154197858529	3		539	745	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028074	69028074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	125	501	0	ENST00000288368.4:c.3233G>A	p.Gly1078Glu	p.G1078E	ENST00000288368	NM_024870.2	1078	gGa/gAa	26/40	1	2	FACETS	0.889	0.806	0.977	0.889	0.806	0.977	CLONAL	1	TRUE	1	0.41154197858529	2		501	683	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47004907	47004907	+	intron_variant	Intron	SNP	G	G	A	novel	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	108	494	0	ENST00000377604.3:c.-126+23G>A		p.*42*	ENST00000377604	NM_001204468.1	-/852			1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.41154197858529	2		494	519	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613621	100613621	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	148	577	0	ENST00000308731.7:c.958T>C	p.Phe320Leu	p.F320L	ENST00000308731	NM_000061.2	320	Ttt/Ctt	11/19	1	2	FACETS	0.981	0.898	1	0.981	0.898	1	CLONAL	1	TRUE	1	0.41154197858529	2		577	733	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020167	123020167	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	144	635	0	ENST00000355640.3:c.655G>T	p.Glu219Ter	p.E219*	ENST00000355640		219	Gaa/Taa	2/7	1	2	FACETS	0.822	0.75	0.898	0.822	0.75	0.898	CLONAL	1	TRUE	1	0.41154197858529	2		635	851	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	72	628	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.438	0.382	0.499	0.438	0.382	0.499	SUBCLONAL	1	TRUE	1	0.43	2		628	764	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	67	424	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.474	0.412	0.542	0.474	0.412	0.542	SUBCLONAL	1	TRUE	1	0.43	2		424	657	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812335	212812335	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	38	207	0	ENST00000342788.4:c.241C>T	p.Arg81Ter	p.R81*	ENST00000342788	NM_005235.2	81	Cga/Tga	3/28	1	2	FACETS	0.583	0.484	0.693	0.583	0.484	0.693	SUBCLONAL	1	TRUE	1	0.43	2		207	303	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816451	32816451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760636031	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	115	531	1	ENST00000354258.4:c.1724G>A	p.Arg575His	p.R575H	ENST00000354258	NM_000593.5	575	cGc/cAc	7/11	1	2	FACETS	0.606	0.546	0.671	0.606	0.546	0.671	SUBCLONAL	1	TRUE	1	0.43	2		532	882	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075676	8075676	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	26	301	0	ENST00000377482.5:c.4T>C	p.Ser2Pro	p.S2P	ENST00000377482	NM_018948.3	2	Tca/Cca	2/4	1	2	FACETS	0.247	0.195	0.307	0.247	0.195	0.307	SUBCLONAL	1	TRUE	1	0.43	2		301	489	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776497	9776497	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	127	571	0	ENST00000377346.4:c.601-1G>A		p.X201_splice	ENST00000377346	NM_005026.3	201			1	2	FACETS	0.679	0.615	0.747	0.679	0.615	0.747	SUBCLONAL	1	TRUE	1	0.43	2		571	870	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587777894	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	16	449	0	ENST00000361445.4:c.6644C>A	p.Ser2215Tyr	p.S2215Y	ENST00000361445	NM_004958.3	2215	tCt/tAt	47/58	1	2	FACETS	0.104	0.076	0.138	0.104	0.076	0.138	SUBCLONAL	1	TRUE	1	0.43	2		449	715	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22417932	22417932	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	20	148	0	ENST00000344548.3:c.498G>T	p.Lys166Asn	p.K166N	ENST00000344548	NM_001039802.1	166	aaG/aaT	7/7	1	2	FACETS	0.354	0.271	0.451	0.354	0.271	0.451	SUBCLONAL	1	TRUE	1	0.43	2		148	263	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885723	23885723	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	140	627	0	ENST00000374561.5:c.195C>A	p.Ser65Arg	p.S65R	ENST00000374561	NM_002167.4	65	agC/agA	1/3	1	2	FACETS	0.649	0.59	0.711	0.649	0.59	0.711	SUBCLONAL	1	TRUE	1	0.43	2		627	1003	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106482	27106482	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	183	509	0	ENST00000324856.7:c.6093T>G	p.Tyr2031Ter	p.Y2031*	ENST00000324856	NM_006015.4	2031	taT/taG	20/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.43	2		509	773	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39321465	39321465	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	35	407	0	ENST00000373001.3:c.556G>T	p.Asp186Tyr	p.D186Y	ENST00000373001	NM_022157.3	186	Gat/Tat	3/7	1	2	FACETS	0.242	0.197	0.292	0.242	0.197	0.292	SUBCLONAL	1	TRUE	1	0.43	2		407	673	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796887	45796887	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	171	571	0	ENST00000450313.1:c.1443T>G	p.Phe481Leu	p.F481L	ENST00000450313	NM_012222.2	481	ttT/ttG	14/16	1	2	FACETS	0.912	0.839	0.988	0.912	0.839	0.988	CLONAL	1	TRUE	1	0.43	2		571	872	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301084	65301084	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	44	200	0	ENST00000342505.4:c.3364G>T	p.Asp1122Tyr	p.D1122Y	ENST00000342505	NM_002227.2	1122	Gat/Tat	24/25	1	2	FACETS	0.578	0.486	0.679	0.578	0.486	0.679	SUBCLONAL	1	TRUE	1	0.43	2		200	354	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550850	150550850	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	143	319	0	ENST00000369026.2:c.806C>A	p.Ser269Tyr	p.S269Y	ENST00000369026	NM_021960.4	269	tCt/tAt	2/3	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.43	2		319	651	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743290	162743290	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	41	247	0	ENST00000367921.3:c.1760A>C	p.Lys587Thr	p.K587T	ENST00000367921	NM_006182.2	587	aAa/aCa	14/18	1	2	FACETS	0.432	0.36	0.513	0.432	0.36	0.513	SUBCLONAL	1	TRUE	1	0.43	2		247	441	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306627	163306627	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	135	249	0	ENST00000271452.3:c.424C>A	p.Leu142Ile	p.L142I	ENST00000271452	NM_145697.2	142	Ctt/Att	6/14	1	2	FACETS	0.858	0.789	0.928	1	0.99	1	CLONAL	2	TRUE	1	0.43	2		249	366	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111132	193111132	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	72	311	0	ENST00000367435.3:c.665G>A	p.Arg222Gln	p.R222Q	ENST00000367435	NM_024529.4	222	cGa/cAa	7/17	1	2	FACETS	0.91	0.8	1	0.91	0.8	1	CLONAL	1	TRUE	1	0.43	2		311	368	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206665005	206665005	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	81	409	0	ENST00000367120.3:c.1758A>C	p.Lys586Asn	p.K586N	ENST00000367120	NM_014002.3	586	aaA/aaC	18/22	1	2	FACETS	0.566	0.498	0.638	0.566	0.498	0.638	SUBCLONAL	1	TRUE	1	0.43	2		409	666	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226589979	226589979	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs759516960	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	109	525	0	ENST00000366794.5:c.222C>A	p.Phe74Leu	p.F74L	ENST00000366794	NM_001618.3	74	ttC/ttA	2/23	1	2	FACETS	0.681	0.612	0.755	0.681	0.612	0.755	SUBCLONAL	1	TRUE	1	0.43	2		525	744	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828104	243828104	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	114	293	0	ENST00000263826.5:c.254G>T	p.Arg85Ile	p.R85I	ENST00000263826	NM_005465.4	85	aGa/aTa	3/13	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.43	2		293	508	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115837	8115837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200935603	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	43	501	0	ENST00000346208.3:c.1183G>A	p.Ala395Thr	p.A395T	ENST00000346208		395	Gcc/Acc	6/6	1	2	FACETS	0.298	0.248	0.353	0.298	0.248	0.353	SUBCLONAL	1	TRUE	1	0.43	2		501	672	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333990	70333990	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	58	238	0	ENST00000373644.4:c.1895C>A	p.Ser632Tyr	p.S632Y	ENST00000373644	NM_030625.2	632	tCt/tAt	2/12	1	2	FACETS	0.716	0.617	0.822	0.716	0.617	0.822	SUBCLONAL	1	TRUE	1	0.43	2		238	377	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106400	108106400	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	47	141	0	ENST00000278616.4:c.335C>A	p.Ala112Glu	p.A112E	ENST00000278616	NM_000051.3	112	gCa/gAa	5/63	1	2	FACETS	0.998	0.852	1	0.998	0.852	1	CLONAL	1	TRUE	1	0.43	2		141	219	SUCCESS
ATM	472	MSKCC	GRCh37	11	108181037	108181037	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	54	243	0	ENST00000278616.4:c.5913G>T	p.Glu1971Asp	p.E1971D	ENST00000278616	NM_000051.3	1971	gaG/gaT	39/63	1	2	FACETS	0.888	0.764	1	0.888	0.764	1	CLONAL	1	TRUE	1	0.43	2		243	283	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201008	108201008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881383	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	87	339	0	ENST00000278616.4:c.7375C>T	p.Arg2459Cys	p.R2459C	ENST00000278616	NM_000051.3	2459	Cgt/Tgt	50/63	1	2	FACETS	0.712	0.632	0.798	0.712	0.632	0.798	SUBCLONAL	1	TRUE	1	0.43	2		339	568	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203492	108203492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs138941496	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	21	193	0	ENST00000278616.4:c.7792C>T	p.Arg2598Ter	p.R2598*	ENST00000278616	NM_000051.3	2598	Cga/Tga	53/63	1	2	FACETS	0.312	0.24	0.396	0.312	0.24	0.396	SUBCLONAL	1	TRUE	1	0.43	2		193	313	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374685	118374685	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	69	261	0	ENST00000534358.1:c.8078C>A	p.Ser2693Tyr	p.S2693Y	ENST00000534358	NM_005933.3	2693	tCt/tAt	27/36	1	2	FACETS	0.607	0.529	0.69	0.607	0.529	0.69	SUBCLONAL	1	TRUE	1	0.43	2		261	529	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552721	18552721	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	152	487	0	ENST00000266497.5:c.2132C>T	p.Thr711Ile	p.T711I	ENST00000266497		711	aCc/aTc	14/31	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.43	2		487	626	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644588	21644588	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	81	376	1	ENST00000421138.2:c.79G>T	p.Glu27Ter	p.E27*	ENST00000421138		27	Gaa/Taa	4/16	1	2	FACETS	0.596	0.525	0.672	0.596	0.525	0.672	SUBCLONAL	1	TRUE	1	0.43	2		377	632	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	63	299	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.742	0.644	0.847	0.742	0.644	0.847	SUBCLONAL	1	TRUE	1	0.43	2		299	395	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125024	46125024	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	57	183	0	ENST00000334344.6:c.211G>T	p.Glu71Ter	p.E71*	ENST00000334344	NM_152641.2	71	Gaa/Taa	3/21	1	2	FACETS	0.823	0.711	0.945	0.823	0.711	0.945	CLONAL	1	TRUE	1	0.43	2		183	322	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50490648	50490648	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	44	402	2	ENST00000394963.4:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000394963	NM_003076.4	429	Gaa/Taa	11/13	1	2	FACETS	0.292	0.244	0.345	0.292	0.244	0.345	SUBCLONAL	1	TRUE	1	0.43	2		404	701	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481696	56481696	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	231	614	0	ENST00000267101.3:c.731T>G	p.Phe244Cys	p.F244C	ENST00000267101	NM_001982.3	244	tTt/tGt	6/28	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.43	2		614	913	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491010	56491010	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	103	495	0	ENST00000267101.3:c.2456C>T	p.Ala819Val	p.A819V	ENST00000267101	NM_001982.3	819	gCc/gTc	20/28	1	2	FACETS	0.649	0.581	0.722	0.649	0.581	0.722	SUBCLONAL	1	TRUE	1	0.43	2		495	738	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249857	133249857	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1565972665	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	145	392	0	ENST00000320574.5:c.1366G>C	p.Ala456Pro	p.A456P	ENST00000320574	NM_006231.2	456	Gcc/Ccc	14/49	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.43	2		392	511	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911760	26911760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	59	285	0	ENST00000381527.3:c.185C>T	p.Ser62Leu	p.S62L	ENST00000381527	NM_001260.1	62	tCg/tTg	2/13	1	2	FACETS	0.625	0.539	0.718	0.625	0.539	0.718	SUBCLONAL	1	TRUE	1	0.43	2		285	439	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953980	32953980	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	83	289	0	ENST00000380152.3:c.9047C>A	p.Ser3016Tyr	p.S3016Y	ENST00000380152		3016	tCt/tAt	23/27	1	2	FACETS	0.785	0.695	0.88	0.785	0.695	0.88	SUBCLONAL	1	TRUE	1	0.43	2		289	492	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941730	48941730	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	73	196	0	ENST00000267163.4:c.1040C>A	p.Ser347Tyr	p.S347Y	ENST00000267163	NM_000321.2	347	tCt/tAt	10/27	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.43	2		196	299	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504590	103504590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1400329743	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	83	278	0	ENST00000355739.4:c.211C>T	p.Arg71Cys	p.R71C	ENST00000355739	NM_000123.3	71	Cgt/Tgt	2/15	1	2	FACETS	0.995	0.884	1	0.995	0.884	1	CLONAL	1	TRUE	1	0.43	2		278	388	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103520572	103520572	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	47	219	0	ENST00000355739.4:c.2643C>A	p.Phe881Leu	p.F881L	ENST00000355739	NM_000123.3	881	ttC/ttA	12/15	1	2	FACETS	0.591	0.5	0.69	0.591	0.5	0.69	SUBCLONAL	1	TRUE	1	0.43	2		219	370	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436784	110436784	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	129	679	1	ENST00000375856.3:c.1617C>A	p.Phe539Leu	p.F539L	ENST00000375856	NM_003749.2	539	ttC/ttA	1/2	1	2	FACETS	0.662	0.6	0.728	0.662	0.6	0.728	SUBCLONAL	1	TRUE	1	0.43	2		680	906	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066879	30066879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	130	419	1	ENST00000331968.5:c.2252C>T	p.Ala751Val	p.A751V	ENST00000331968	NM_002742.2	751	gCt/gTt	16/18	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.43	2		420	601	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093456	30093456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1008608681	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	62	238	0	ENST00000331968.5:c.1807C>T	p.Arg603Cys	p.R603C	ENST00000331968	NM_002742.2	603	Cgt/Tgt	13/18	1	2	FACETS	0.841	0.731	0.959	0.841	0.731	0.959	CLONAL	1	TRUE	1	0.43	2		238	343	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107713	30107713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1160777726	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	81	410	0	ENST00000331968.5:c.967G>A	p.Glu323Lys	p.E323K	ENST00000331968	NM_002742.2	323	Gaa/Aaa	6/18	1	2	FACETS	0.575	0.507	0.649	0.575	0.507	0.649	SUBCLONAL	1	TRUE	1	0.43	2		410	655	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609467	81609467	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	81	347	0	ENST00000298171.2:c.1065C>A	p.Phe355Leu	p.F355L	ENST00000298171	NM_000369.2	355	ttC/ttA	10/10	1	2	FACETS	0.706	0.623	0.794	0.706	0.623	0.794	SUBCLONAL	1	TRUE	1	0.43	2		347	534	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570126	95570126	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	119	345	0	ENST00000393063.1:c.3607A>C	p.Asn1203His	p.N1203H	ENST00000393063	NM_030621.3	1203	Aat/Cat	22/28	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.43	2		345	480	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570342	95570342	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	116	260	0	ENST00000393063.1:c.3391A>G	p.Asn1131Asp	p.N1131D	ENST00000393063	NM_030621.3	1131	Aat/Gat	22/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.43	2		260	433	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574292	95574292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144649926	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	44	250	0	ENST00000393063.1:c.2575C>T	p.Arg859Trp	p.R859W	ENST00000393063	NM_030621.3	859	Cgg/Tgg	17/28	1	2	FACETS	0.555	0.466	0.652	0.555	0.466	0.652	SUBCLONAL	1	TRUE	1	0.43	2		250	369	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749343	43749343	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	171	423	0	ENST00000382044.4:c.1463C>A	p.Ser488Ter	p.S488*	ENST00000382044	NM_001141980.1	488	tCa/tAa	12/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.43	2		423	703	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43766897	43766897	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	54	248	0	ENST00000382044.4:c.1154G>A	p.Ser385Asn	p.S385N	ENST00000382044	NM_001141980.1	385	aGt/aAt	10/28	1	2	FACETS	0.639	0.547	0.739	0.639	0.547	0.739	SUBCLONAL	1	TRUE	1	0.43	2		248	393	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43766924	43766924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201580098	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	21	244	0	ENST00000382044.4:c.1127G>A	p.Arg376Gln	p.R376Q	ENST00000382044	NM_001141980.1	376	cGa/cAa	10/28	1	2	FACETS	0.267	0.205	0.339	0.267	0.205	0.339	SUBCLONAL	1	TRUE	1	0.43	2		244	366	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43769790	43769790	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	83	372	0	ENST00000382044.4:c.955+1G>A		p.X319_splice	ENST00000382044	NM_001141980.1	319			1	2	FACETS	0.648	0.572	0.728	0.648	0.572	0.728	SUBCLONAL	1	TRUE	1	0.43	2		372	596	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66735647	66735647	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	78	307	1	ENST00000307102.5:c.468G>T	p.Lys156Asn	p.K156N	ENST00000307102	NM_002755.3	156	aaG/aaT	4/11	1	2	FACETS	0.688	0.606	0.776	0.688	0.606	0.776	SUBCLONAL	1	TRUE	1	0.43	2		308	527	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312398	91312398	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	122	362	1	ENST00000355112.3:c.2343G>T	p.Glu781Asp	p.E781D	ENST00000355112	NM_000057.2	781	gaG/gaT	11/22	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.43	2		363	555	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640538	3640538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150453226	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	98	697	2	ENST00000294008.3:c.3101G>A	p.Arg1034His	p.R1034H	ENST00000294008	NM_032444.2	1034	cGc/cAc	12/15	1	2	FACETS	0.477	0.425	0.533	0.477	0.425	0.533	SUBCLONAL	1	TRUE	1	0.43	2		699	955	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041527	14041527	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs756155469	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	104	293	0	ENST00000311895.7:c.2074C>T	p.Arg692Ter	p.R692*	ENST00000311895	NM_005236.2	692	Cga/Tga	11/11	1	2	FACETS	0.805	0.722	0.892	0.805	0.722	0.892	CLONAL	1	TRUE	1	0.43	2		293	601	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041854	14041854	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	95	331	1	ENST00000311895.7:c.2401C>A	p.Leu801Ile	p.L801I	ENST00000311895	NM_005236.2	801	Ctc/Atc	11/11	1	2	FACETS	0.861	0.77	0.958	0.861	0.77	0.958	CLONAL	1	TRUE	1	0.43	2		332	513	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783688	50783688	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	128	384	1	ENST00000398568.2:c.79G>T	p.Glu27Ter	p.E27*	ENST00000398568	NM_001042412.1	27	Gaa/Taa	3/18	1	2	FACETS	0.953	0.866	1	0.953	0.866	1	CLONAL	1	TRUE	1	0.43	2		385	625	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857517	68857517	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876658591	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	142	379	0	ENST00000261769.5:c.2152C>A	p.Leu718Ile	p.L718I	ENST00000261769	NM_004360.3	718	Ctt/Att	13/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.43	2		379	610	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867274	68867274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377489352	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	86	454	2	ENST00000261769.5:c.2521G>A	p.Glu841Lys	p.E841K	ENST00000261769	NM_004360.3	841	Gaa/Aaa	16/16	1	2	FACETS	0.576	0.509	0.647	0.576	0.509	0.647	SUBCLONAL	1	TRUE	1	0.43	2		456	695	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81892729	81892729	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	101	265	0	ENST00000359376.3:c.440G>T	p.Arg147Ile	p.R147I	ENST00000359376	NM_002661.3	147	aGa/aTa	5/33	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.43	2		265	431	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040679	16040679	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	93	318	0	ENST00000268712.3:c.1455G>T	p.Glu485Asp	p.E485D	ENST00000268712	NM_006311.3	485	gaG/gaT	14/46	1	2	FACETS	0.963	0.861	1	0.963	0.861	1	CLONAL	1	TRUE	1	0.43	2		318	449	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089913	16089913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	122	319	0	ENST00000268712.3:c.197G>A	p.Arg66Gln	p.R66Q	ENST00000268712	NM_006311.3	66	cGa/cAa	3/46	1	2	FACETS	0.957	0.868	1	0.957	0.868	1	CLONAL	1	TRUE	1	0.43	2		319	593	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17117090	17117090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1402955238	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	187	494	1	ENST00000285071.4:c.1619G>A	p.Gly540Asp	p.G540D	ENST00000285071	NM_144997.5	540	gGt/gAt	14/14	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.43	2		495	799	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30302704	30302704	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	46	321	0	ENST00000322652.5:c.795G>T	p.Met265Ile	p.M265I	ENST00000322652	NM_015355.2	265	atG/atT	7/16	1	2	FACETS	0.395	0.333	0.465	0.395	0.333	0.465	SUBCLONAL	1	TRUE	1	0.43	2		321	541	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627887	37627887	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	136	450	0	ENST00000447079.4:c.1802C>A	p.Ser601Tyr	p.S601Y	ENST00000447079	NM_015083.1	601	tCt/tAt	2/14	1	2	FACETS	0.809	0.736	0.885	0.809	0.736	0.885	CLONAL	1	TRUE	1	0.43	2		450	782	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870068	40870068	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	110	286	0	ENST00000428826.2:c.949A>C	p.Asn317His	p.N317H	ENST00000428826		317	Aat/Cat	10/21	1	2	FACETS	0.986	0.889	1	0.986	0.889	1	CLONAL	1	TRUE	1	0.43	2		286	519	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41209086	41209086	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs80357432	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	83	487	1	ENST00000357654.3:c.5260G>T	p.Glu1754Ter	p.E1754*	ENST00000357654	NM_007294.3	1754	Gaa/Taa	19/23	1	2	FACETS	0.528	0.466	0.595	0.528	0.466	0.595	SUBCLONAL	1	TRUE	1	0.43	2		488	731	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245080	41245080	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876659731	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	142	496	0	ENST00000357654.3:c.2468G>T	p.Arg823Ile	p.R823I	ENST00000357654	NM_007294.3	823	aGa/aTa	10/23	1	2	FACETS	0.757	0.689	0.827	0.757	0.689	0.827	SUBCLONAL	1	TRUE	1	0.43	2		496	873	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59886057	59886057	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759031349	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	95	387	0	ENST00000259008.2:c.689C>T	p.Ser230Leu	p.S230L	ENST00000259008	NM_032043.2	230	tCg/tTg	7/20	1	2	FACETS	0.74	0.66	0.825	0.74	0.66	0.825	SUBCLONAL	1	TRUE	1	0.43	2		387	597	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212433	5212433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778163463	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	127	634	1	ENST00000357368.4:c.4684G>A	p.Glu1562Lys	p.E1562K	ENST00000357368	NM_002850.3	1562	Gaa/Aaa	31/38	1	2	FACETS	0.624	0.565	0.687	0.624	0.565	0.687	SUBCLONAL	1	TRUE	1	0.43	2		635	946	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267855	7267855	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	142	410	0	ENST00000302850.5:c.153G>T	p.Glu51Asp	p.E51D	ENST00000302850	NM_000208.2	51	gaG/gaT	2/22	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.43	2		410	628	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271691	15271691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	64	814	1	ENST00000263388.2:c.6748G>A	p.Glu2250Lys	p.E2250K	ENST00000263388	NM_000435.2	2250	Gaa/Aaa	33/33	1	2	FACETS	0.284	0.245	0.327	0.284	0.245	0.327	SUBCLONAL	1	TRUE	1	0.43	2		815	1047	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955169	17955169	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	230	659	0	ENST00000458235.1:c.58T>C	p.Ser20Pro	p.S20P	ENST00000458235	NM_000215.3	20	Tcc/Ccc	2/24	1	2	FACETS	0.985	0.918	1	0.985	0.918	1	CLONAL	1	TRUE	1	0.43	2		659	1086	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763500	41763500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	113	453	0	ENST00000301178.4:c.2299C>T	p.Arg767Cys	p.R767C	ENST00000301178	NM_021913.4	767	Cgc/Tgc	19/20	1	2	FACETS	0.777	0.701	0.859	0.777	0.701	0.859	SUBCLONAL	1	TRUE	1	0.43	2		453	676	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976426	25976426	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	87	348	0	ENST00000435504.4:c.1119C>A	p.Phe373Leu	p.F373L	ENST00000435504		373	ttC/ttA	11/13	1	2	FACETS	0.671	0.595	0.752	0.671	0.595	0.752	SUBCLONAL	1	TRUE	1	0.43	2		348	603	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143162	30143162	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1558549790	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	169	711	0	ENST00000389048.3:c.364A>G	p.Thr122Ala	p.T122A	ENST00000389048	NM_004304.4	122	Acg/Gcg	1/29	1	2	FACETS	0.924	0.85	1	0.924	0.85	1	CLONAL	1	TRUE	1	0.43	2		711	851	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635547	47635547	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	77	222	1	ENST00000233146.2:c.219G>T	p.Lys73Asn	p.K73N	ENST00000233146	NM_000251.2	73	aaG/aaT	2/16	1	2	FACETS	0.853	0.752	0.96	0.853	0.752	0.96	CLONAL	1	TRUE	1	0.43	2		223	420	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027593	48027593	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	69	271	0	ENST00000234420.5:c.2471A>C	p.Lys824Thr	p.K824T	ENST00000234420	NM_000179.2	824	aAa/aCa	4/10	1	2	FACETS	0.817	0.715	0.926	0.817	0.715	0.926	CLONAL	1	TRUE	1	0.43	2		271	393	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033767	48033767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141464646	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	18	225	0	ENST00000234420.5:c.3978G>A	p.Met1326Ile	p.M1326I	ENST00000234420	NM_000179.2	1326	atG/atA	9/10	1	2	FACETS	0.235	0.176	0.305	0.235	0.176	0.305	SUBCLONAL	1	TRUE	1	0.43	2		225	356	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	19	335	0	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	0.143	0.108	0.185	0.143	0.108	0.185	SUBCLONAL	1	TRUE	1	0.43	2		335	619	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193519	99193519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	235	639	0	ENST00000074304.5:c.2714C>T	p.Ser905Leu	p.S905L	ENST00000074304	NM_001134224.1	905	tCg/tTg	25/26	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.43	2		639	930	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095836	178095836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1328262363	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	84	333	0	ENST00000397062.3:c.1495C>T	p.Arg499Trp	p.R499W	ENST00000397062	NM_006164.4	499	Cgg/Tgg	5/5	1	2	FACETS	0.751	0.665	0.843	0.751	0.665	0.843	SUBCLONAL	1	TRUE	1	0.43	2		333	520	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131398	202131398	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	81	370	0	ENST00000358485.4:c.366G>T	p.Lys122Asn	p.K122N	ENST00000358485	NM_001080125.1	122	aaG/aaT	2/9	1	2	FACETS	0.61	0.537	0.687	0.61	0.537	0.687	SUBCLONAL	1	TRUE	1	0.43	2		370	618	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495199	212495199	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	99	322	0	ENST00000342788.4:c.2067C>A	p.Phe689Leu	p.F689L	ENST00000342788	NM_005235.2	689	ttC/ttA	17/28	1	2	FACETS	0.942	0.844	1	0.942	0.844	1	CLONAL	1	TRUE	1	0.43	2		322	489	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439839	220439839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761479412	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	55	745	2	ENST00000243786.2:c.692G>A	p.Arg231Gln	p.R231Q	ENST00000243786	NM_002191.3	231	cGa/cAa	2/2	1	2	FACETS	0.255	0.217	0.297	0.255	0.217	0.297	SUBCLONAL	1	TRUE	1	0.43	2		747	1004	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661596	227661596	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	145	682	0	ENST00000305123.5:c.1859C>T	p.Ala620Val	p.A620V	ENST00000305123	NM_005544.2	620	gCc/gTc	1/2	1	2	FACETS	0.731	0.667	0.799	0.731	0.667	0.799	SUBCLONAL	1	TRUE	1	0.43	2		682	922	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546937	9546937	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	39	443	0	ENST00000353224.5:c.1085G>T	p.Ser362Ile	p.S362I	ENST00000353224	NM_177990.2	362	aGc/aTc	5/10	1	2	FACETS	0.305	0.252	0.364	0.305	0.252	0.364	SUBCLONAL	1	TRUE	1	0.43	2		443	595	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561352	9561352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773981325	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	113	337	0	ENST00000353224.5:c.430G>A	p.Glu144Lys	p.E144K	ENST00000353224	NM_177990.2	144	Gaa/Aaa	4/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.43	2		337	493	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36028609	36028609	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	114	588	2	ENST00000358208.4:c.951G>T	p.Met317Ile	p.M317I	ENST00000358208		317	atG/atT	8/12	1	2	FACETS	0.67	0.603	0.741	0.67	0.603	0.741	SUBCLONAL	1	TRUE	1	0.43	2		590	791	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39725963	39725963	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	47	217	0	ENST00000361337.2:c.834C>A	p.Phe278Leu	p.F278L	ENST00000361337	NM_003286.2	278	ttC/ttA	10/21	1	2	FACETS	0.744	0.631	0.866	0.744	0.631	0.866	SUBCLONAL	1	TRUE	1	0.43	2		217	294	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728716	39728716	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	19	235	0	ENST00000361337.2:c.996A>C	p.Glu332Asp	p.E332D	ENST00000361337	NM_003286.2	332	gaA/gaC	12/21	1	2	FACETS	0.252	0.191	0.324	0.252	0.191	0.324	SUBCLONAL	1	TRUE	1	0.43	2		235	351	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747091	40747091	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	99	519	1	ENST00000373198.4:c.2991G>T	p.Glu997Asp	p.E997D	ENST00000373198	NM_133170.3	997	gaG/gaT	22/32	1	2	FACETS	0.676	0.604	0.753	0.676	0.604	0.753	SUBCLONAL	1	TRUE	1	0.43	2		520	681	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757468	40757468	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	38	507	0	ENST00000373198.4:c.2830G>A	p.Asp944Asn	p.D944N	ENST00000373198	NM_133170.3	944	Gac/Aac	20/32	1	2	FACETS	0.263	0.216	0.315	0.263	0.216	0.315	SUBCLONAL	1	TRUE	1	0.43	2		507	673	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770576	40770576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	111	412	0	ENST00000373198.4:c.2806C>T	p.Arg936Ter	p.R936*	ENST00000373198	NM_133170.3	936	Cga/Tga	19/32	1	2	FACETS	0.927	0.836	1	0.927	0.836	1	CLONAL	1	TRUE	1	0.43	2		412	557	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948603	54948603	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	53	282	0	ENST00000312783.6:c.715G>T	p.Glu239Ter	p.E239*	ENST00000312783	NM_198436.1	239	Gaa/Taa	8/10	1	2	FACETS	0.524	0.448	0.608	0.524	0.448	0.608	SUBCLONAL	1	TRUE	1	0.43	2		282	470	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514895	44514895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	131	281	0	ENST00000291552.4:c.352C>T	p.Arg118Cys	p.R118C	ENST00000291552	NM_006758.2	118	Cgc/Tgc	6/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.43	2		281	464	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22153317	22153317	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	115	379	0	ENST00000215832.6:c.593T>G	p.Ile198Ser	p.I198S	ENST00000215832	NM_002745.4	198	aTt/aGt	4/9	1	2	FACETS	0.9	0.813	0.992	0.9	0.813	0.992	CLONAL	1	TRUE	1	0.43	2		379	594	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050676	30050676	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150667239	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	81	342	0	ENST00000338641.4:c.478C>T	p.Arg160Trp	p.R160W	ENST00000338641	NM_000268.3	160	Cgg/Tgg	5/16	1	2	FACETS	0.711	0.628	0.8	0.711	0.628	0.8	SUBCLONAL	1	TRUE	1	0.43	2		342	530	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533773	41533773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	143	348	2	ENST00000263253.7:c.1739G>A	p.Arg580Gln	p.R580Q	ENST00000263253	NM_001429.3	580	cGa/cAa	8/31	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.43	2		350	610	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421225	12421225	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	114	411	0	ENST00000287820.6:c.105G>T	p.Glu35Asp	p.E35D	ENST00000287820	NM_015869.4	35	gaG/gaT	2/7	1	2	FACETS	0.858	0.774	0.946	0.858	0.774	0.946	CLONAL	1	TRUE	1	0.43	2		411	618	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275240	41275240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	68	360	0	ENST00000349496.5:c.1406G>A	p.Arg469His	p.R469H	ENST00000349496	NM_001904.3	469	cGt/cAt	9/15	1	2	FACETS	0.576	0.502	0.657	0.576	0.502	0.657	SUBCLONAL	1	TRUE	1	0.43	2		360	549	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799675	72799675	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	164	482	0	ENST00000325599.8:c.1494A>C	p.Glu498Asp	p.E498D	ENST00000325599	NM_018130.2	498	gaA/gaC	11/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.43	2		482	709	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390072	89390072	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765502894	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	65	221	0	ENST00000336596.2:c.821G>A	p.Arg274Gln	p.R274Q	ENST00000336596	NM_005233.5	274	cGa/cAa	4/17	1	2	FACETS	0.859	0.749	0.976	0.859	0.749	0.976	CLONAL	1	TRUE	1	0.43	2		221	352	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119721084	119721084	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	40	330	0	ENST00000316626.5:c.91G>A	p.Asp31Asn	p.D31N	ENST00000316626		31	Gac/Aac	2/12	1	2	FACETS	0.329	0.272	0.391	0.329	0.272	0.391	SUBCLONAL	1	TRUE	1	0.43	2		330	566	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177859	142177859	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	65	294	0	ENST00000350721.4:c.7444C>A	p.Leu2482Ile	p.L2482I	ENST00000350721	NM_001184.3	2482	Ctc/Atc	44/47	1	2	FACETS	0.663	0.576	0.756	0.663	0.576	0.756	SUBCLONAL	1	TRUE	1	0.43	2		294	456	SUCCESS
ATR	545	MSKCC	GRCh37	3	142180899	142180899	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	77	300	1	ENST00000350721.4:c.7075G>T	p.Glu2359Ter	p.E2359*	ENST00000350721	NM_001184.3	2359	Gaa/Taa	42/47	1	2	FACETS	0.984	0.87	1	0.984	0.87	1	CLONAL	1	TRUE	1	0.43	2		301	364	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268410	142268410	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	106	316	0	ENST00000350721.4:c.3082A>C	p.Ile1028Leu	p.I1028L	ENST00000350721	NM_001184.3	1028	Att/Ctt	15/47	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.43	2		316	465	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178942585	178942585	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	82	248	0	ENST00000263967.3:c.2392G>T	p.Glu798Ter	p.E798*	ENST00000263967	NM_006218.2	798	Gag/Tag	16/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.43	2		248	316	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155297	185155297	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	65	343	0	ENST00000265026.3:c.538G>T	p.Gly180Ter	p.G180*	ENST00000265026	NM_004721.4	180	Gga/Tga	3/14	1	2	FACETS	0.528	0.457	0.604	0.528	0.457	0.604	SUBCLONAL	1	TRUE	1	0.43	2		343	573	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447327	187447327	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776120197	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	153	483	0	ENST00000232014.4:c.866G>A	p.Arg289Gln	p.R289Q	ENST00000232014	NM_001130845.1	289	cGa/cAa	5/10	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.43	2		483	709	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447384	187447384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780987785	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	110	517	1	ENST00000232014.4:c.809G>A	p.Arg270Gln	p.R270Q	ENST00000232014	NM_001130845.1	270	cGa/cAa	5/10	1	2	FACETS	0.636	0.571	0.705	0.636	0.571	0.705	SUBCLONAL	1	TRUE	1	0.43	2		518	804	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587113	189587113	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs148052765	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	87	259	0	ENST00000264731.3:c.1130C>T	p.Pro377Leu	p.P377L	ENST00000264731	NM_003722.4	377	cCg/cTg	9/14	1	2	FACETS	0.968	0.862	1	0.968	0.862	1	CLONAL	1	TRUE	1	0.43	2		259	418	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976666	55976666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	70	476	0	ENST00000263923.4:c.1159G>A	p.Glu387Lys	p.E387K	ENST00000263923	NM_002253.2	387	Gaa/Aaa	9/30	1	2	FACETS	0.517	0.45	0.589	0.517	0.45	0.589	SUBCLONAL	1	TRUE	1	0.43	2		476	630	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213879	66213879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	32	352	1	ENST00000273854.3:c.2551G>A	p.Ala851Thr	p.A851T	ENST00000273854	NM_004439.5	851	Gct/Act	15/18	1	2	FACETS	0.283	0.229	0.344	0.283	0.229	0.344	SUBCLONAL	1	TRUE	1	0.43	2		353	526	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280017	66280017	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	49	161	0	ENST00000273854.3:c.1672G>T	p.Glu558Ter	p.E558*	ENST00000273854	NM_004439.5	558	Gaa/Taa	7/18	1	2	FACETS	0.86	0.734	0.996	0.86	0.734	0.996	CLONAL	1	TRUE	1	0.43	2		161	265	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286238	66286238	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1229443873	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	71	313	0	ENST00000273854.3:c.1448A>G	p.Asn483Ser	p.N483S	ENST00000273854	NM_004439.5	483	aAc/aGc	6/18	1	2	FACETS	0.917	0.806	1	0.917	0.806	1	CLONAL	1	TRUE	1	0.43	2		313	360	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249503	153249503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs767037353	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	72	407	0	ENST00000281708.4:c.1275G>A	p.Trp425Ter	p.W425*	ENST00000281708	NM_033632.3	425	tgG/tgA	9/12	1	2	FACETS	0.55	0.48	0.625	0.55	0.48	0.625	SUBCLONAL	1	TRUE	1	0.43	2		407	609	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253835	153253835	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	51	268	0	ENST00000281708.4:c.898G>T	p.Asp300Tyr	p.D300Y	ENST00000281708	NM_033632.3	300	Gac/Tac	6/12	1	2	FACETS	0.599	0.51	0.696	0.599	0.51	0.696	SUBCLONAL	1	TRUE	1	0.43	2		268	396	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332708	153332708	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	32	307	0	ENST00000281708.4:c.248G>T	p.Arg83Ile	p.R83I	ENST00000281708	NM_033632.3	83	aGa/aTa	2/12	1	2	FACETS	0.27	0.218	0.329	0.27	0.218	0.329	SUBCLONAL	1	TRUE	1	0.43	2		307	551	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31423030	31423030	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	105	381	1	ENST00000344624.3:c.3283C>T	p.Arg1095Ter	p.R1095*	ENST00000344624		1095	Cga/Tga	26/33	1	2	FACETS	0.92	0.827	1	0.92	0.827	1	CLONAL	1	TRUE	1	0.43	2		382	531	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871249	35871249	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	112	256	0	ENST00000303115.3:c.471G>T	p.Lys157Asn	p.K157N	ENST00000303115	NM_002185.3	157	aaG/aaT	4/8	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.43	2		256	463	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950420	38950420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	78	324	0	ENST00000357387.3:c.3530G>A	p.Ser1177Asn	p.S1177N	ENST00000357387	NM_152756.3	1177	aGc/aAc	31/38	1	2	FACETS	0.894	0.789	1	0.894	0.789	1	CLONAL	1	TRUE	1	0.43	2		324	406	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752845	57752845	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	61	314	0	ENST00000274289.3:c.1083G>T	p.Lys361Asn	p.K361N	ENST00000274289	NM_006622.3	361	aaG/aaT	8/14	1	2	FACETS	0.61	0.527	0.7	0.61	0.527	0.7	SUBCLONAL	1	TRUE	1	0.43	2		314	465	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522657	67522657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	21	243	0	ENST00000274335.5:c.154G>T	p.Glu52Ter	p.E52*	ENST00000274335		52	Gaa/Taa	1/15	1	2	FACETS	0.256	0.197	0.326	0.256	0.197	0.326	SUBCLONAL	1	TRUE	1	0.43	2		243	381	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79965931	79965931	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	101	343	0	ENST00000265081.6:c.595G>T	p.Asp199Tyr	p.D199Y	ENST00000265081	NM_002439.4	199	Gat/Tat	4/24	1	2	FACETS	0.893	0.801	0.99	0.893	0.801	0.99	CLONAL	1	TRUE	1	0.43	2		343	526	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80040402	80040402	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	135	337	2	ENST00000265081.6:c.1731G>T	p.Lys577Asn	p.K577N	ENST00000265081	NM_002439.4	577	aaG/aaT	12/24	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.43	2		339	576	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685313	86685313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886060844	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	48	185	0	ENST00000274376.6:c.3029G>A	p.Arg1010Gln	p.R1010Q	ENST00000274376	NM_002890.2	1010	cGa/cAa	24/25	1	2	FACETS	0.707	0.6	0.822	0.707	0.6	0.822	SUBCLONAL	1	TRUE	1	0.43	2		185	316	SUCCESS
APC	324	MSKCC	GRCh37	5	112174149	112174149	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	44	254	0	ENST00000257430.4:c.2858A>C	p.Lys953Thr	p.K953T	ENST00000257430	NM_000038.5	953	aAa/aCa	16/16	1	2	FACETS	0.514	0.432	0.605	0.514	0.432	0.605	SUBCLONAL	1	TRUE	1	0.43	2		254	398	SUCCESS
APC	324	MSKCC	GRCh37	5	112174793	112174793	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	74	192	0	ENST00000257430.4:c.3502G>T	p.Glu1168Ter	p.E1168*	ENST00000257430	NM_000038.5	1168	Gaa/Taa	16/16	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.43	2		192	331	SUCCESS
APC	324	MSKCC	GRCh37	5	112175457	112175457	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	68	273	0	ENST00000257430.4:c.4166C>A	p.Ser1389Tyr	p.S1389Y	ENST00000257430	NM_000038.5	1389	tCt/tAt	16/16	1	2	FACETS	0.795	0.694	0.902	0.795	0.694	0.902	CLONAL	1	TRUE	1	0.43	2		273	398	SUCCESS
APC	324	MSKCC	GRCh37	5	112175921	112175921	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	46	154	0	ENST00000257430.4:c.4630G>T	p.Glu1544Ter	p.E1544*	ENST00000257430	NM_000038.5	1544	Gaa/Taa	16/16	1	2	FACETS	0.801	0.68	0.934	0.801	0.68	0.934	CLONAL	1	TRUE	1	0.43	2		154	267	SUCCESS
APC	324	MSKCC	GRCh37	5	112176234	112176234	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	78	332	0	ENST00000257430.4:c.4943C>A	p.Pro1648His	p.P1648H	ENST00000257430	NM_000038.5	1648	cCt/cAt	16/16	1	2	FACETS	0.764	0.673	0.86	0.764	0.673	0.86	SUBCLONAL	1	TRUE	1	0.43	2		332	475	SUCCESS
APC	324	MSKCC	GRCh37	5	112177170	112177170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781546	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	63	254	0	ENST00000257430.4:c.5879C>T	p.Pro1960Leu	p.P1960L	ENST00000257430	NM_000038.5	1960	cCg/cTg	16/16	1	2	FACETS	0.685	0.594	0.782	0.685	0.594	0.782	SUBCLONAL	1	TRUE	1	0.43	2		254	428	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441098	149441098	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	178	497	0	ENST00000286301.3:c.1814G>T	p.Gly605Val	p.G605V	ENST00000286301	NM_005211.3	605	gGc/gTc	13/22	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.43	2		497	755	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637721	176637721	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	145	425	0	ENST00000439151.2:c.2321A>C	p.Asn774Thr	p.N774T	ENST00000439151	NM_022455.4	774	aAt/aCt	5/23	1	2	FACETS	0.95	0.868	1	0.95	0.868	1	CLONAL	1	TRUE	1	0.43	2		425	710	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638456	176638456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750354456	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	157	512	0	ENST00000439151.2:c.3056G>A	p.Arg1019His	p.R1019H	ENST00000439151	NM_022455.4	1019	cGc/cAc	5/23	1	2	FACETS	0.782	0.716	0.851	0.782	0.716	0.851	SUBCLONAL	1	TRUE	1	0.43	2		512	934	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176662922	176662922	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	75	233	2	ENST00000439151.2:c.3897G>T	p.Lys1299Asn	p.K1299N	ENST00000439151	NM_022455.4	1299	aaG/aaT	6/23	1	2	FACETS	0.809	0.712	0.913	0.809	0.712	0.913	CLONAL	1	TRUE	1	0.43	2		235	431	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665349	176665349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	131	333	0	ENST00000439151.2:c.4033C>A	p.Leu1345Ile	p.L1345I	ENST00000439151	NM_022455.4	1345	Ctt/Att	7/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.43	2		333	478	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041073	180041073	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	182	681	0	ENST00000261937.6:c.3326C>A	p.Ser1109Tyr	p.S1109Y	ENST00000261937	NM_182925.4	1109	tCt/tAt	24/30	1	2	FACETS	0.954	0.881	1	0.954	0.881	1	CLONAL	1	TRUE	1	0.43	2		681	887	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393155	393155	+	start_lost	Translation_Start_Site	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	81	386	0	ENST00000380956.4:c.3G>T	p.Met1?	p.M1?	ENST00000380956	NM_001195286.1	1	atG/atT	2/9	1	2	FACETS	0.657	0.58	0.74	0.657	0.58	0.74	SUBCLONAL	1	TRUE	1	0.43	2		386	573	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407458	407458	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	69	192	0	ENST00000380956.4:c.1216G>T	p.Glu406Ter	p.E406*	ENST00000380956	NM_001195286.1	406	Gaa/Taa	9/9	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.43	2		192	301	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675856	30675856	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	185	505	2	ENST00000376406.3:c.2500G>T	p.Glu834Ter	p.E834*	ENST00000376406	NM_014641.2	834	Gaa/Taa	8/15	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.43	2		507	829	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32814855	32814855	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	94	532	1	ENST00000354258.4:c.2210G>A	p.Ser737Asn	p.S737N	ENST00000354258	NM_000593.5	737	aGc/aAc	10/11	1	2	FACETS	0.475	0.421	0.532	0.475	0.421	0.532	SUBCLONAL	1	TRUE	1	0.43	2		533	921	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288234	33288234	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	43	482	0	ENST00000374542.5:c.1174A>C	p.Lys392Gln	p.K392Q	ENST00000374542	NM_001141970.1	392	Aaa/Caa	4/8	1	2	FACETS	0.29	0.242	0.344	0.29	0.242	0.344	SUBCLONAL	1	TRUE	1	0.43	2		482	689	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120612	94120612	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	62	322	0	ENST00000369303.4:c.439G>T	p.Asp147Tyr	p.D147Y	ENST00000369303	NM_004440.3	147	Gac/Tac	3/17	1	2	FACETS	0.597	0.517	0.684	0.597	0.517	0.684	SUBCLONAL	1	TRUE	1	0.43	2		322	483	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622241	117622241	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs148104006	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	28	355	0	ENST00000368508.3:c.6629G>T	p.Arg2210Ile	p.R2210I	ENST00000368508	NM_002944.2	2210	aGa/aTa	42/43	1	2	FACETS	0.268	0.213	0.33	0.268	0.213	0.33	SUBCLONAL	1	TRUE	1	0.43	2		355	486	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677962	117677962	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	72	355	0	ENST00000368508.3:c.3971G>T	p.Arg1324Met	p.R1324M	ENST00000368508	NM_002944.2	1324	aGg/aTg	25/43	1	2	FACETS	0.618	0.54	0.701	0.618	0.54	0.701	SUBCLONAL	1	TRUE	1	0.43	2		355	542	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678991	117678991	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	96	301	0	ENST00000368508.3:c.3830C>A	p.Ser1277Tyr	p.S1277Y	ENST00000368508	NM_002944.2	1277	tCt/tAt	24/43	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.43	2		301	424	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714464	117714464	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	76	256	1	ENST00000368508.3:c.1185G>T	p.Glu395Asp	p.E395D	ENST00000368508	NM_002944.2	395	gaG/gaT	11/43	1	2	FACETS	0.93	0.821	1	0.93	0.821	1	CLONAL	1	TRUE	1	0.43	2		257	380	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202424	138202424	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	186	560	0	ENST00000237289.4:c.2341G>A	p.Glu781Lys	p.E781K	ENST00000237289	NM_001270507.1	781	Gaa/Aaa	9/9	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.43	2		560	841	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984024	2984024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	41	512	0	ENST00000396946.4:c.506C>T	p.Thr169Met	p.T169M	ENST00000396946	NM_032415.4	169	aCg/aTg	5/25	1	2	FACETS	0.261	0.216	0.31	0.261	0.216	0.31	SUBCLONAL	1	TRUE	1	0.43	2		512	732	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509697	106509697	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	133	458	0	ENST00000359195.3:c.1691T>G	p.Leu564Arg	p.L564R	ENST00000359195	NM_002649.2	564	cTt/cGt	2/11	1	2	FACETS	0.919	0.837	1	0.919	0.837	1	CLONAL	1	TRUE	1	0.43	2		458	673	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526619	106526619	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	84	324	0	ENST00000359195.3:c.2912A>C	p.Asn971Thr	p.N971T	ENST00000359195	NM_002649.2	971	aAt/aCt	10/11	1	2	FACETS	0.713	0.631	0.8	0.713	0.631	0.8	SUBCLONAL	1	TRUE	1	0.43	2		324	548	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846366	128846366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765478037	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	99	550	3	ENST00000249373.3:c.1202C>T	p.Ala401Val	p.A401V	ENST00000249373	NM_005631.4	401	gCg/gTg	6/12	1	2	FACETS	0.581	0.519	0.648	0.581	0.519	0.648	SUBCLONAL	1	TRUE	1	0.43	2		553	792	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846374	128846374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1044964080	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	115	542	0	ENST00000249373.3:c.1210G>A	p.Val404Met	p.V404M	ENST00000249373	NM_005631.4	404	Gtg/Atg	6/12	1	2	FACETS	0.679	0.611	0.75	0.679	0.611	0.75	SUBCLONAL	1	TRUE	1	0.43	2		542	788	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523717	148523717	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	83	215	0	ENST00000320356.2:c.736G>T	p.Glu246Ter	p.E246*	ENST00000320356	NM_004456.4	246	Gaa/Taa	8/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.43	2		215	325	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148529736	148529736	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	46	204	0	ENST00000320356.2:c.353A>T	p.Gln118Leu	p.Q118L	ENST00000320356	NM_004456.4	118	cAg/cTg	4/20	1	2	FACETS	0.598	0.505	0.699	0.598	0.505	0.699	SUBCLONAL	1	TRUE	1	0.43	2		204	358	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945109	151945109	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	31	312	0	ENST00000262189.6:c.2410C>T	p.Leu804Phe	p.L804F	ENST00000262189	NM_170606.2	804	Ctt/Ttt	14/59	1	2	FACETS	0.384	0.311	0.468	0.384	0.311	0.468	SUBCLONAL	1	TRUE	1	0.43	2		312	375	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942848	68942848	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	161	494	0	ENST00000288368.4:c.660G>T	p.Lys220Asn	p.K220N	ENST00000288368	NM_024870.2	220	aaG/aaT	6/40	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.43	2		494	739	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069589	69069589	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	105	335	0	ENST00000288368.4:c.4264G>T	p.Asp1422Tyr	p.D1422Y	ENST00000288368	NM_024870.2	1422	Gac/Tac	35/40	1	2	FACETS	0.989	0.89	1	0.989	0.89	1	CLONAL	1	TRUE	1	0.43	2		335	494	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980517	70980517	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	131	503	0	ENST00000276594.2:c.860T>G	p.Val287Gly	p.V287G	ENST00000276594	NM_024504.3	287	gTg/gGg	4/8	1	2	FACETS	0.777	0.706	0.852	0.777	0.706	0.852	SUBCLONAL	1	TRUE	1	0.43	2		503	784	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955525	90955525	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730881864	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	27	357	0	ENST00000265433.3:c.2140C>T	p.Arg714Ter	p.R714*	ENST00000265433	NM_002485.4	714	Cga/Tga	14/16	1	2	FACETS	0.247	0.196	0.305	0.247	0.196	0.305	SUBCLONAL	1	TRUE	1	0.43	2		357	509	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117875450	117875450	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	43	361	0	ENST00000297338.2:c.193C>T	p.Arg65Ter	p.R65*	ENST00000297338	NM_006265.2	65	Cga/Tga	3/14	1	2	FACETS	0.429	0.359	0.507	0.429	0.359	0.507	SUBCLONAL	1	TRUE	1	0.43	2		361	466	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750980	128750980	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	86	453	0	ENST00000377970.2:c.517G>T	p.Asp173Tyr	p.D173Y	ENST00000377970	NM_002467.4	173	Gac/Tac	2/3	1	2	FACETS	0.648	0.574	0.728	0.648	0.574	0.728	SUBCLONAL	1	TRUE	1	0.43	2		453	617	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563491	87563491	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201553907	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	108	487	2	ENST00000277120.3:c.1879G>A	p.Asp627Asn	p.D627N	ENST00000277120		627	Gac/Aac	16/19	1	2	FACETS	0.721	0.647	0.798	0.721	0.647	0.798	SUBCLONAL	1	TRUE	1	0.43	2		489	697	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229562	98229562	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	65	358	3	ENST00000331920.6:c.2396C>A	p.Ser799Tyr	p.S799Y	ENST00000331920	NM_000264.3	799	tCt/tAt	15/24	1	2	FACETS	0.554	0.48	0.633	0.554	0.48	0.633	SUBCLONAL	1	TRUE	1	0.43	2		361	546	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933958	39933958	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	154	288	0	ENST00000378444.4:c.641C>A	p.Ser214Ter	p.S214*	ENST00000378444	NM_001123385.1	214	tCa/tAa	4/15	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.43	1		288	434	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250046	53250046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1569282235	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	46	216	0	ENST00000375401.3:c.203G>A	p.Arg68Gln	p.R68Q	ENST00000375401	NM_004187.3	68	cGa/cAa	2/26	1	1	FACETS	0.426	0.36	0.5	0.426	0.36	0.5	SUBCLONAL	1	TRUE	0	0.43	1		216	394	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342421	70342421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771266719	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	178	238	0	ENST00000374080.3:c.1312C>T	p.Arg438Cys	p.R438C	ENST00000374080		438	Cgc/Tgc	9/45	1	1	FACETS	0.761	0.71	0.813	1	0.991	1	SUBCLONAL	2	TRUE	0	0.43	1		238	427	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615614	100615614	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs128621191	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	58	214	0	ENST00000308731.7:c.718G>T	p.Glu240Ter	p.E240*	ENST00000308731	NM_000061.2	240	Gaa/Taa	8/19	1	1	FACETS	0.773	0.67	0.883	0.773	0.67	0.883	SUBCLONAL	1	TRUE	0	0.43	1		214	274	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217381	123217381	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	69	172	0	ENST00000218089.9:c.3035G>A	p.Arg1012Gln	p.R1012Q	ENST00000218089	NM_001042749.1	1012	cGa/cAa	29/35	1	1	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	0	0.43	1		172	249	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504025	123504025	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0049202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	52	143	0	ENST00000371139.4:c.202-1G>T		p.X68_splice	ENST00000371139	NM_001114937.2	68			1	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.43	1		143	156	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0049203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	228	599	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.37263440834777	3	FACETS	0.887	0.829	0.946			1	CLONAL	2	TRUE	NA	0.397760845742889	3		599	775	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346633	225346633	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	55	252	0	ENST00000264414.4:c.2005C>G	p.Leu669Val	p.L669V	ENST00000264414	NM_003590.4	669	Cta/Gta	14/16	1	2	FACETS	0.804	0.691	0.926	0.804	0.691	0.926	CLONAL	1	TRUE	1	0.397760845742889	2		252	344	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100696	67100697	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0049203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	64	383	2	ENST00000412916.2:c.394_395delinsTT	p.Ala132Phe	p.A132F	ENST00000412916		132	GCc/TTc	4/6	0.357307012807379	1	FACETS	0.693	0.603	0.79	0.693	0.603	0.79	SUBCLONAL	1	TRUE	0	0.397760845742889	1		385	372	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004544	16004627	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTTATGGAACGAGCCTCACCTCTGCCTCTCTGGCTCTCCATCCACATCCTCATCAGCGCTGCACGTGGCACTGGAATCATTGT	ACTTATGGAACGAGCCTCACCTCTGCCTCTCTGGCTCTCCATCCACATCCTCATCAGCGCTGCACGTGGCACTGGAATCATTGT	GATTGC	novel	NA	P-0049203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	58	413	4	ENST00000268712.3:c.2627_2690+20delinsGCAATC		p.X876_splice	ENST00000268712	NM_006311.3	876		20/46	0.357307012807379	1	FACETS	0.633	0.546	0.727	0.633	0.546	0.727	SUBCLONAL	1	TRUE	0	0.397760845742889	1		417	369	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	214	381	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	0.763500236200653	1	FACETS	0.813	0.767	0.859	0.813	0.767	0.859	CLONAL	1	TRUE	0	0.770401781164023	1		381	420	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260234	16260235	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTGG	novel	NA	P-0049204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	175	423	0	ENST00000375759.3:c.7500_7503dup	p.Ile2502ValfsTer26	p.I2502Vfs*26	ENST00000375759	NM_015001.2	2500	gag/gaGTGGg	11/15	0.763500236200653	1	FACETS	0.743	0.694	0.792	0.743	0.694	0.792	SUBCLONAL	1	TRUE	0	0.770401781164023	1		423	376	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041432	42041432	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	283	400	1	ENST00000219905.7:c.5627del	p.Ala1876GlufsTer2	p.A1876Efs*2	ENST00000219905	NM_001164273.1	1876	gCa/ga	17/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.770401781164023	2		401	669	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0049206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	1606	740	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	1	0.999	1			1	CLONAL	2	TRUE	1	0.752130980286795	2		740	1869	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246445	105246445	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	592	761	0	ENST00000349310.3:c.155T>G	p.Leu52Arg	p.L52R	ENST00000349310	NM_001014432.1	52	cTc/cGc	4/15	0.652821997606631	3	FACETS	0.93	0.898	0.963			1	CLONAL	2	TRUE	NA	0.752130980286795	3		761	1164	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88677009	88677009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793937	NA	P-0049206-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	41	88	0	ENST00000372037.3:c.794C>T	p.Thr265Ile	p.T265I	ENST00000372037	NM_004329.2	265	aCc/aTc	9/13	1	2	FACETS	0.973	0.834	1	0.973	0.834	1	CLONAL	1	TRUE	1	0.752130980286795	2		88	112	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0049221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	93	487	1	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	1	2	FACETS	0.982	0.872	1	0.982	0.872	1	CLONAL	1	TRUE	1	0.226089311144286	2		488	838	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432437	78432437	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0049221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	36	340	0	ENST00000370768.2:c.416-2A>G		p.X139_splice	ENST00000370768	NM_003902.3	139			1	2	FACETS	0.593	0.487	0.713	0.593	0.487	0.713	SUBCLONAL	1	TRUE	1	0.226089311144286	2		340	537	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864364	57864364	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	79	733	0	ENST00000228682.2:c.1841G>T	p.Gly614Val	p.G614V	ENST00000228682	NM_005269.2	614	gGt/gTt	12/12	1	2	FACETS	0.675	0.592	0.764	0.675	0.592	0.764	SUBCLONAL	1	TRUE	1	0.226089311144286	2		733	1036	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220442	1220442	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	120	681	0	ENST00000326873.7:c.536del	p.Pro179ArgfsTer108	p.P179Rfs*108	ENST00000326873	NM_000455.4	179	Ccg/cg	4/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.226089311144286	2		681	925	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599867	10599868	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0049221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	113	515	1	ENST00000171111.5:c.1708_1708+1delinsTT		p.X570_splice	ENST00000171111	NM_203500.1	570		5/6	1	2	FACETS	0.957	0.859	1	0.957	0.859	1	CLONAL	1	TRUE	1	0.226089311144286	2		516	1045	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873447	45873447	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	226	583	0	ENST00000391945.4:c.49A>T	p.Ile17Phe	p.I17F	ENST00000391945	NM_000400.3	17	Atc/Ttc	2/23	0.213485578140582	2	FACETS	0.92	0.857	0.986	0.92	0.857	0.986	CLONAL	2	TRUE	0	0.226089311144286	2		583	1086	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610705	52610706	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0049221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	30	324	0	ENST00000394830.3:c.3467_3468del	p.Lys1156SerfsTer24	p.K1156Sfs*24	ENST00000394830	NM_018313.4	1156	aAA/a	23/30	1	2	FACETS	0.677	0.545	0.826	0.677	0.545	0.826	SUBCLONAL	1	TRUE	1	0.226089311144286	2		324	392	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594027	55594027	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	46	319	0	ENST00000288135.5:c.1813G>C	p.Glu605Gln	p.E605Q	ENST00000288135	NM_000222.2	605	Gag/Cag	12/21	1	2	FACETS	0.528	0.443	0.622	0.528	0.443	0.622	SUBCLONAL	1	TRUE	1	0.226089311144286	2		319	771	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218809	66218809	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	21	242	0	ENST00000273854.3:c.2249T>A	p.Met750Lys	p.M750K	ENST00000273854	NM_004439.5	750	aTg/aAg	13/18	1	2	FACETS	0.615	0.474	0.78	0.615	0.474	0.78	SUBCLONAL	1	TRUE	1	0.226089311144286	2		242	302	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535287	66535287	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	70	521	0	ENST00000273854.3:c.174C>A	p.Ser58Arg	p.S58R	ENST00000273854	NM_004439.5	58	agC/agA	1/18	1	2	FACETS	0.793	0.69	0.904	0.793	0.69	0.904	CLONAL	1	TRUE	1	0.226089311144286	2		521	781	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80071512	80071512	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0049221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	30	241	0	ENST00000265081.6:c.2254-1G>A		p.X752_splice	ENST00000265081	NM_002439.4	752			1	2	FACETS	0.592	0.477	0.724	0.592	0.477	0.724	SUBCLONAL	1	TRUE	1	0.226089311144286	2		241	448	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041675	47041675	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	25	251	0	ENST00000377604.3:c.1900A>C	p.Lys634Gln	p.K634Q	ENST00000377604	NM_001204468.1	634	Aag/Cag	17/24	0.0806072726633502	2	FACETS	0.469	0.368	0.584			1	INDETERMINATE	1	TRUE	NA	0.226089311144286	2		251	472	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185838	32185838	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	261	751	0	ENST00000375023.3:c.1558G>C	p.Ala520Pro	p.A520P	ENST00000375023	NM_004557.3	520	Gct/Cct	9/30	1	2	FACETS	0.992	0.93	1	0.992	0.93	1	CLONAL	1	TRUE	1	0.491136836701186	2		751	1071	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627318	86627318	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0049226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	53	306	0	ENST00000274376.6:c.692+1G>T		p.X231_splice	ENST00000274376	NM_002890.2	231			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		306	264	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0049227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	112	579	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	1	2	FACETS	0.608	0.545	0.674	0.608	0.545	0.674	SUBCLONAL	1	TRUE	1	0.360963492566301	2		579	1021	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0049227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	92	248	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.360963492566301	2		249	387	SUCCESS
APC	324	MSKCC	GRCh37	5	112175876	112175876	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085992	NA	P-0049227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	76	205	0	ENST00000257430.4:c.4585C>T	p.Gln1529Ter	p.Q1529*	ENST00000257430	NM_000038.5	1529	Cag/Tag	16/16	0.360963492566301	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.360963492566301	1		205	299	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032138	26032138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	75	513	0	ENST00000244661.2:c.151G>A	p.Glu51Lys	p.E51K	ENST00000244661	NM_003537.3	51	Gag/Aag	1/1	0.244667781164523	3	FACETS	0.529	0.462	0.601	0.265	0.231	0.301	SUBCLONAL	1	TRUE	1	0.360963492566301	3		513	927	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0049227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	321	682	1	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.320818079988644	2	FACETS	0.915	0.866	0.965	0.915	0.866	0.965	CLONAL	2	TRUE	0	0.360963492566301	2		683	972	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627327	37627327	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	74	482	0	ENST00000447079.4:c.1242G>C	p.Lys414Asn	p.K414N	ENST00000447079	NM_015083.1	414	aaG/aaC	2/14	1	2	FACETS	0.53	0.464	0.603	0.53	0.464	0.603	SUBCLONAL	1	TRUE	1	0.360963492566301	2		482	773	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446372	70446372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	42	448	0	ENST00000373644.4:c.5312G>A	p.Arg1771Lys	p.R1771K	ENST00000373644	NM_030625.2	1771	aGg/aAg	11/12	1	2	FACETS	0.294	0.244	0.349	0.294	0.244	0.349	SUBCLONAL	1	TRUE	1	0.360963492566301	2		448	792	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371653	55371653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	269	628	0	ENST00000297316.4:c.343C>T	p.Arg115Trp	p.R115W	ENST00000297316	NM_022454.3	115	Cgg/Tgg	2/2	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.360963492566301	2		628	1093	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141557641	141557641	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	98	774	2	ENST00000220592.5:c.1674G>T	p.Gln558His	p.Q558H	ENST00000220592	NM_012154.3	558	caG/caT	13/19	1	2	FACETS	0.455	0.404	0.509	0.455	0.404	0.509	SUBCLONAL	1	TRUE	1	0.360963492566301	2		776	1194	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348830	118348830	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	101	280	0	ENST00000534358.1:c.3483C>G	p.Cys1161Trp	p.C1161W	ENST00000534358	NM_005933.3	1161	tgC/tgG	5/36	0.198991801345252	1	FACETS	1	0.94	1	1	0.94	1	INDETERMINATE	1	TRUE	0	0.360963492566301	1		280	431	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061430	38061431	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	152	489	0	ENST00000250448.2:c.558dup	p.Pro187AlafsTer40	p.P187Afs*40	ENST00000250448	NM_004496.3	186	-/G	2/2	0.320818079988644	2	FACETS	1	0.974	1	0.579	0.531	0.63	CLONAL	1	TRUE	0	0.360963492566301	2		489	727	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108211	8108211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779280853	NA	P-0049227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	92	568	0	ENST00000585124.1:c.1013C>T	p.Ser338Phe	p.S338F	ENST00000585124	NM_004217.3	338	tCt/tTt	9/9	0.198991801345252	1	FACETS	0.464	0.412	0.52	0.464	0.412	0.52	INDETERMINATE	1	TRUE	0	0.360963492566301	1		568	900	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508593	38508593	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	77	530	1	ENST00000254066.5:c.641C>T	p.Ser214Leu	p.S214L	ENST00000254066	NM_000964.3	214	tCa/tTa	6/9	1	2	FACETS	0.476	0.417	0.54	0.476	0.417	0.54	SUBCLONAL	1	TRUE	1	0.360963492566301	2		531	896	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661627	227661627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1308136701	NA	P-0049227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	211	680	0	ENST00000305123.5:c.1828G>A	p.Asp610Asn	p.D610N	ENST00000305123	NM_005544.2	610	Gat/Aat	1/2	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.360963492566301	2		680	1137	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032267	26032267	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	102	323	0	ENST00000244661.2:c.22G>T	p.Ala8Ser	p.A8S	ENST00000244661	NM_003537.3	8	Gct/Tct	1/1	0.244667781164523	3	FACETS	1	0.953	1	0.556	0.498	0.617	CLONAL	1	TRUE	1	0.360963492566301	3		323	600	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900133	151900134	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	189	273	0	ENST00000262189.6:c.3977dup	p.Leu1326PhefsTer7	p.L1326Ffs*7	ENST00000262189	NM_170606.2	1326	tta/ttTa	26/59	0.345634686798703	4	FACETS	0.842	0.784	0.902	1	0.987	1	CLONAL	3	TRUE	2	0.360963492566301	4		273	564	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	10	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.833	0.564	1	0.833	0.564	1	CLONAL	1	TRUE	1	0.12	2		148	200	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0049229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	38	445	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.918	0.757	1	0.918	0.757	1	CLONAL	1	TRUE	1	0.12	2		445	690	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176145075	176145075	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs770721170	NA	P-0049246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	144	332	0	ENST00000367669.3:c.536A>G	p.Asn179Ser	p.N179S	ENST00000367669	NM_022457.5	179	aAt/aGt	3/20	0.715960244114735	3	FACETS	1	0.954	1	0.53	0.486	0.575	CLONAL	1	TRUE	1	0.719292805668399	3		332	514	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220538	133220538	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs755971358	NA	P-0049246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	165	470	0	ENST00000320574.5:c.4175A>G	p.Asn1392Ser	p.N1392S	ENST00000320574	NM_006231.2	1392	aAc/aGc	33/49	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.719292805668399	2		470	415	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59886010	59886010	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs376893571	NA	P-0049246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	182	514	0	ENST00000259008.2:c.736A>G	p.Ile246Val	p.I246V	ENST00000259008	NM_032043.2	246	Ata/Gta	7/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.719292805668399	2		514	484	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39746876	39746877	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	92	201	0	ENST00000361337.2:c.1892dup	p.Asn631LysfsTer11	p.N631Kfs*11	ENST00000361337	NM_003286.2	630	-/A	18/21	NA	2	FACETS	1	0.927	1			1	INDETERMINATE	1	TRUE	NA	0.719292805668399	2		201	248	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0049247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	68	583	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.24	2		583	489	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632609	3632609	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201214017	NA	P-0049247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	34	648	0	ENST00000294008.3:c.5239G>A	p.Val1747Met	p.V1747M	ENST00000294008	NM_032444.2	1747	Gtg/Atg	15/15	0.273703669343467	3	FACETS	0.553	0.451	0.668	0.276	0.225	0.334	SUBCLONAL	1	TRUE	1	0.24	3		648	574	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054911	176054911	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0049247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	17	294	0	ENST00000367669.3:c.1141+1G>T		p.X381_splice	ENST00000367669	NM_022457.5	381			1	2	FACETS	0.951	0.715	1	0.951	0.715	1	CLONAL	1	TRUE	1	0.24	2		294	149	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007706	62007706	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	22	420	0	ENST00000392795.3:c.161T>A	p.Ile54Lys	p.I54K	ENST00000392795	NM_001039933.1	54	aTa/aAa	3/6	1	2	FACETS	0.797	0.62	1	0.797	0.62	1	CLONAL	1	TRUE	1	0.24	2		420	230	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0049248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	109	341	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.343115675201866	2		341	606	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627631	37627631	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0049248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	134	529	0	ENST00000447079.4:c.1546A>T	p.Lys516Ter	p.K516*	ENST00000447079	NM_015083.1	516	Aag/Tag	2/14	1	2	FACETS	0.919	0.835	1	0.919	0.835	1	CLONAL	1	TRUE	1	0.343115675201866	2		529	850	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657630	37657630	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0049248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	139	402	0	ENST00000447079.4:c.2547C>G	p.Tyr849Ter	p.Y849*	ENST00000447079	NM_015083.1	849	taC/taG	6/14	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.343115675201866	2		402	667	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59886096	59886096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	185	375	0	ENST00000259008.2:c.650G>A	p.Cys217Tyr	p.C217Y	ENST00000259008	NM_032043.2	217	tGc/tAc	7/20	0.343115675201866	8	FACETS	1	0.927	1			1	CLONAL	2	TRUE	NA	0.343115675201866	8		375	1088	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0049249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	49	346	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.176083579393112	1	FACETS	0.776	0.66	0.902	1	0.965	1	CLONAL	2	TRUE	0	0.176083579393112	1		346	327	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146592	185146592	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	52	408	0	ENST00000265026.3:c.223G>A	p.Asp75Asn	p.D75N	ENST00000265026	NM_004721.4	75	Gat/Aat	2/14	0.176083579393112	1	FACETS	0.988	0.841	1	0.988	0.841	1	CLONAL	1	TRUE	0	0.176083579393112	1		408	545	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207064	1207065	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1131690917	NA	P-0049249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	121	572	0	ENST00000326873.7:c.157dup	p.Asp53GlyfsTer110	p.D53Gfs*110	ENST00000326873	NM_000455.4	51	atg/atGg	1/10	0.176083579393112	1	FACETS	0.895	0.81	0.985	1	0.988	1	CLONAL	2	TRUE	0	0.176083579393112	1		572	700	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602746	10602746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	161	617	1	ENST00000171111.5:c.832C>T	p.Pro278Ser	p.P278S	ENST00000171111	NM_203500.1	278	Ccg/Tcg	3/6	0.176083579393112	1	FACETS	0.983	0.902	1	1	0.992	1	CLONAL	2	TRUE	0	0.176083579393112	1		618	848	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348059	89348059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1402377065	NA	P-0049249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	111	739	2	ENST00000301030.4:c.4891C>T	p.Arg1631Trp	p.R1631W	ENST00000301030	NM_001256183.1	1631	Cgg/Tgg	9/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.176083579393112	2		741	937	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431421	49431421	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	93	499	0	ENST00000301067.7:c.9718C>G	p.Leu3240Val	p.L3240V	ENST00000301067	NM_003482.3	3240	Ctg/Gtg	34/54	0.0746030415543244	4	FACETS	0.933	0.83	1	0.933	0.83	1	INDETERMINATE	2	TRUE	2	0.176083579393112	4		499	666	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73350141	73350141	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	32	330	0	ENST00000377767.4:c.744A>T	p.Gln248His	p.Q248H	ENST00000377767	NM_014953.3	248	caA/caT	5/21	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.176083579393112	2		330	287	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250861	10250861	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	105	594	0	ENST00000340748.4:c.3619C>A	p.Arg1207Ser	p.R1207S	ENST00000340748		1207	Cgc/Agc	32/40	0.176083579393112	1	FACETS	0.804	0.721	0.892	1	0.984	1	CLONAL	2	TRUE	0	0.176083579393112	1		594	676	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215332	123215332	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	37	405	0	ENST00000218089.9:c.2879del	p.Gly960AspfsTer5	p.G960Dfs*5	ENST00000218089	NM_001042749.1	960	Gga/ga	28/35	1	2	FACETS	0.998	0.823	1	0.998	0.823	1	CLONAL	1	TRUE	1	0.176083579393112	2		405	421	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	108	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.535240171368357	2		148	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0049250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	266	583	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.535240171368357	2		583	955	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0049250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	233	419	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.535240171368357	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.535240171368357	1		419	490	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033967	49033967	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1131690865	NA	P-0049250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	153	261	0	ENST00000267163.4:c.2104C>T	p.Gln702Ter	p.Q702*	ENST00000267163	NM_000321.2	702	Caa/Taa	20/27	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.535240171368357	2		261	390	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339219	70339256	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCAGGATGAACTGACGGCCTTGAATGTAAAACAAGGTT	TCAGGATGAACTGACGGCCTTGAATGTAAAACAAGGTT	-	novel	NA	P-0049250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	153	387	0	ENST00000374080.3:c.100-1_136del		p.X34_splice	ENST00000374080		34		2/45	1	2	FACETS	0.913	0.839	0.991	0.913	0.839	0.991	CLONAL	1	TRUE	1	0.535240171368357	2		387	626	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0049252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	84	616	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.236920562308791	1	FACETS	0.852	0.752	0.959	0.852	0.752	0.959	CLONAL	1	TRUE	0	0.236920562308791	1		618	734	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765523	41765523	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199709000	NA	P-0049252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	82	681	0	ENST00000301178.4:c.2399G>A	p.Arg800Gln	p.R800Q	ENST00000301178	NM_021913.4	800	cGg/cAg	20/20	0.174438077869332	3	FACETS	0.833	0.733	0.941	0.417	0.366	0.471	CLONAL	1	TRUE	1	0.236920562308791	3		681	929	SUCCESS
APC	324	MSKCC	GRCh37	5	112175174	112175174	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	58	188	0	ENST00000257430.4:c.3883G>T	p.Glu1295Ter	p.E1295*	ENST00000257430	NM_000038.5	1295	Gaa/Taa	16/16	0.195435128348932	2	FACETS	0.758	0.655	0.868	0.758	0.655	0.868	SUBCLONAL	2	TRUE	0	0.236920562308791	2		188	323	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295271	1295271	+	upstream_gene_variant	5'Flank	SNP	G	G	C	novel	NA	P-0049252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	49	269	0				ENST00000310581	NM_198253.2	-/1132			0.236920562308791	5	FACETS	0.888	0.752	1	0.222	0.188	0.26	CLONAL	1	TRUE	1	0.236920562308791	5		269	631	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69032483	69032483	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	101	477	0	ENST00000288368.4:c.3557A>G	p.Asp1186Gly	p.D1186G	ENST00000288368	NM_024870.2	1186	gAc/gGc	29/40	0.137879450490866	4	FACETS	1	0.975	1	0.661	0.59	0.736	INDETERMINATE	1	TRUE	2	0.236920562308791	4		477	798	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806092	1806092	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913484	NA	P-0049257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	38	659	2	ENST00000260795.2:c.1111A>T	p.Ser371Cys	p.S371C	ENST00000260795		371	Agt/Tgt	8/17	0.186403862400983	4	FACETS	0.85	0.706	1	0.85	0.706	1	CLONAL	2	TRUE	2	0.187620307303157	4		661	283	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0049257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	30	240	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.186403862400983	4	FACETS	0.867	0.703	1	0.867	0.703	1	CLONAL	2	TRUE	2	0.187620307303157	4		240	219	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0049257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	12	157	0				ENST00000310581	NM_198253.2	-/1132			0.187622815871198	0	FACETS	1	0.773	1			1	CLONAL	1	TRUE	0	0.187620307303157	0		157	94	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188098	108188098	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs1060501570	NA	P-0049257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	31	200	0	ENST00000278616.4:c.6199-2A>T		p.X2067_splice	ENST00000278616	NM_000051.3	2067			0.133249896037359	4	FACETS	0.926	0.754	1	0.926	0.754	1	CLONAL	2	TRUE	2	0.187620307303157	4		200	212	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106991	11106991	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	21	565	0	ENST00000358026.2:c.1696G>A	p.Glu566Lys	p.E566K	ENST00000358026	NM_001128849.1	566	Gag/Aag	10/36	1	2	FACETS	0.711	0.547	0.901	0.711	0.547	0.901	CLONAL	1	TRUE	1	0.187620307303157	2		565	315	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102870	71102870	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	30	319	0	ENST00000318789.4:c.337C>T	p.Gln113Ter	p.Q113*	ENST00000318789	NM_032682.5	113	Cag/Tag	8/21	0.186403862400983	4	FACETS	1	0.892	1	0.583	0.47	0.71	CLONAL	1	TRUE	2	0.187620307303157	4		319	326	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021837	69021837	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	23	381	0	ENST00000288368.4:c.3125T>C	p.Met1042Thr	p.M1042T	ENST00000288368	NM_024870.2	1042	aTg/aCg	25/40	0.133249896037359	4	FACETS	1	0.789	1	0.506	0.394	0.634	CLONAL	1	TRUE	2	0.187620307303157	4		381	288	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936019	44936020	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0049257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	49	410	0	ENST00000377967.4:c.2782_2783dup	p.Pro929ThrfsTer9	p.P929Tfs*9	ENST00000377967	NM_021140.2	927	cca/ccATa	18/29	0.187622815871198	1	FACETS	0.8	0.681	0.928	1	0.967	1	CLONAL	2	TRUE	0	0.187620307303157	1		410	296	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181347	123181347	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	10	177	0	ENST00000218089.9:c.811del	p.Arg271GlyfsTer11	p.R271Gfs*11	ENST00000218089	NM_001042749.1	271	Cgg/gg	9/35	0.187622815871198	1	FACETS	0.911	0.622	1	0.911	0.622	1	CLONAL	1	TRUE	0	0.187620307303157	1		177	106	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0049258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	213	485	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.393587590128068	2	FACETS	0.997	0.935	1	0.997	0.935	1	CLONAL	2	TRUE	0	0.403101460666804	2		486	530	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534473	187534473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	51	296	0	ENST00000441802.2:c.9253del	p.Asp3086IlefsTer30	p.D3086Ifs*30	ENST00000441802	NM_005245.3	3085	Ctt/tt	13/27	0.380213872619224	3	FACETS	0.77	0.656	0.894	0.385	0.328	0.447	SUBCLONAL	1	TRUE	1	0.403101460666804	3		296	395	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729911	30729911	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	77	278	0	ENST00000295754.5:c.1432G>T	p.Val478Leu	p.V478L	ENST00000295754	NM_003242.5	478	Gtg/Ttg	6/7	0.393587590128068	2	FACETS	1	0.905	1	0.513	0.453	0.577	CLONAL	1	TRUE	0	0.403101460666804	2		278	372	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119721008	119721008	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	100	432	0	ENST00000316626.5:c.167A>G	p.Tyr56Cys	p.Y56C	ENST00000316626		56	tAt/tGt	2/12	0.256880696107351	5	FACETS	1	0.956	1	0.378	0.338	0.421	CLONAL	1	TRUE	2	0.403101460666804	5		432	702	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1959740	1959740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	98	218	0	ENST00000382891.5:c.2962C>T	p.Pro988Ser	p.P988S	ENST00000382891	NM_133335.3	988	Ccc/Tcc	16/22	0.325502430372046	4	FACETS	0.95	0.855	1			1	CLONAL	2	TRUE	NA	0.403101460666804	4		218	359	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346085	152346085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	74	403	0	ENST00000359321.1:c.485G>A	p.Gly162Glu	p.G162E	ENST00000359321	NM_005431.1	162	gGa/gAa	3/3	0.393587590128068	2	FACETS	0.85	0.747	0.96	0.425	0.373	0.48	CLONAL	1	TRUE	0	0.403101460666804	2		403	432	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	97	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.730584356989407	2		148	262	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0049259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	937	402	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.730584356989407	6	FACETS	0.922	0.902	0.943			1	CLONAL	5	TRUE	NA	0.730584356989407	6		402	1369	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652097	36652098	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	297	661	0	ENST00000244741.5:c.222dup	p.Lys75GlnfsTer14	p.K75Qfs*14	ENST00000244741	NM_000389.4	73	-/C	2/3	1	2	FACETS	0.885	0.835	0.935	0.885	0.835	0.935	CLONAL	1	TRUE	1	0.730584356989407	2		661	919	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021828	71021828	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0049259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	82	157	0	ENST00000318789.4:c.1531-1G>C		p.X511_splice	ENST00000318789	NM_032682.5	511			1	2	FACETS	0.909	0.814	1	0.909	0.814	1	CLONAL	1	TRUE	1	0.730584356989407	2		157	247	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542407	187542407	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	94	343	0	ENST00000441802.2:c.5333C>T	p.Ala1778Val	p.A1778V	ENST00000441802	NM_005245.3	1778	gCc/gTc	10/27	1	2	FACETS	0.478	0.427	0.533	0.478	0.427	0.533	SUBCLONAL	1	TRUE	1	0.730584356989407	2		343	538	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984337	201984338	+	inframe_insertion,splice_region_variant	In_Frame_Ins	INS	-	-	TAC	novel	NA	P-0049259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	432	444	0	ENST00000359651.3:c.1009_1011dup	p.Tyr337dup	p.Y337dup	ENST00000359651		337	-/TAC	8/8	0.676053293270545	3	FACETS	0.895	0.858	0.932	0.895	0.858	0.932	CLONAL	2	TRUE	1	0.730584356989407	3		444	902	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797223	135797223	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	101	161	0	ENST00000298552.3:c.646T>A	p.Phe216Ile	p.F216I	ENST00000298552	NM_001162426.1	216	Ttt/Att	7/23	0.730584356989407	1	FACETS	0.943	0.868	1	0.943	0.868	1	CLONAL	1	TRUE	0	0.730584356989407	1		161	186	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922962	44922963	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	223	232	0	ENST00000377967.4:c.1825dup	p.Tyr609LeufsTer12	p.Y609Lfs*12	ENST00000377967	NM_021140.2	608	cct/ccTt	16/29	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.730584356989407	1		232	317	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651929	36651933	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCC	CTGCC	T	novel	NA	P-0049259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	234	516	0	ENST00000244741.5:c.51_55delinsT	p.Cys18AlafsTer12	p.C18Afs*12	ENST00000244741	NM_000389.4	17	gcCTGCCgc/gcTgc	2/3	1	2	FACETS	0.833	0.78	0.888	0.833	0.78	0.888	CLONAL	1	TRUE	1	0.730584356989407	2		516	769	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231773	36231773	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1569061762	NA	P-0049260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	9	465	0	ENST00000300305.3:c.611G>A	p.Arg204Gln	p.R204Q	ENST00000300305		204	cGa/cAa	5/8	0.270623313521899	3	FACETS	0.198	0.13	0.285	0.099	0.065	0.143	SUBCLONAL	1	FALSE	1	0.270623313521899	3		465	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0049260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	15	354	0	ENST00000269305.4:c.673-2A>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.270623313521899	3	FACETS	0.632	0.464	0.834	0.316	0.232	0.417	SUBCLONAL	1	FALSE	1	0.270623313521899	3		354	199	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs587781702	NA	P-0049260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	61	513	1	ENST00000269305.4:c.920-1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.270623313521899	3	FACETS	1	0.899	1	1	0.975	1	CLONAL	3	FALSE	1	0.270623313521899	3		514	167	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384762	17384762	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs544132311	NA	P-0049260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	51	586	2	ENST00000359435.4:c.394G>A	p.Val132Met	p.V132M	ENST00000359435	NM_001033549.1	132	Gtg/Atg	4/9	0.270623313521899	2	FACETS	1	0.938	1	0.594	0.508	0.688	CLONAL	1	FALSE	0	0.270623313521899	2		588	317	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37006472	37006472	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1300663454	NA	P-0049260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	17	238	0	ENST00000358127.4:c.473T>C	p.Ile158Thr	p.I158T	ENST00000358127	NM_001280556.1	158	aTa/aCa	4/10	0.233830329945431	2	FACETS	1	0.897	1	0.706	0.536	0.899	CLONAL	1	FALSE	0	0.270623313521899	2		238	89	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520158	9520158	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	37	379	0	ENST00000353224.5:c.2111G>T	p.Gly704Val	p.G704V	ENST00000353224	NM_177990.2	704	gGt/gTt	10/10	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	FALSE	1	0.270623313521899	2		379	230	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844801	156844801	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs764771898	NA	P-0049260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	70	516	0	ENST00000524377.1:c.1354+1G>A		p.X452_splice	ENST00000524377	NM_002529.3	452			0.270623313521899	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	FALSE	1	0.270623313521899	3		516	260	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438174	110438174	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	25	126	0	ENST00000375856.3:c.227A>C	p.Tyr76Ser	p.Y76S	ENST00000375856	NM_003749.2	76	tAc/tCc	1/2	0.233830329945431	2	FACETS	0.748	0.592	0.926	0.374	0.296	0.463	CLONAL	1	FALSE	0	0.270623313521899	2		126	247	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105623	30105623	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	24	534	2	ENST00000331968.5:c.1063G>T	p.Gly355Trp	p.G355W	ENST00000331968	NM_002742.2	355	Ggg/Tgg	7/18	1	2	FACETS	0.896	0.707	1	0.896	0.707	1	CLONAL	1	FALSE	1	0.270623313521899	2		536	198	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042316	42042350	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGAAAGATGGAGAAAACATCTGAAGGGCCCCTT	AGGGAAAGATGGAGAAAACATCTGAAGGGCCCCTT	-	novel	NA	P-0049260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	10	431	0	ENST00000219905.7:c.6512_6546del	p.Arg2171AsnfsTer12	p.R2171Nfs*12	ENST00000219905	NM_001164273.1	2171	AGGGAAAGATGGAGAAAACATCTGAAGGGCCCCTTa/a	17/24	1	2	FACETS	0.762	0.521	1	0.762	0.521	1	CLONAL	1	FALSE	1	0.270623313521899	2		431	97	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849659	68849659	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	18	419	0	ENST00000261769.5:c.1562T>C	p.Ile521Thr	p.I521T	ENST00000261769	NM_004360.3	521	aTa/aCa	10/16	0.270623313521899	2	FACETS	1	0.799	1	0.528	0.402	0.673	CLONAL	1	FALSE	0	0.270623313521899	2		419	126	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348482	56348482	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	14	300	0	ENST00000348428.3:c.290G>T	p.Gly97Val	p.G97V	ENST00000348428	NM_006785.3	97	gGt/gTt	2/17	0.233830329945431	2	FACETS	0.985	0.72	1	0.493	0.36	0.649	CLONAL	1	FALSE	0	0.270623313521899	2		300	105	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729983	47729983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1030972880	NA	P-0049260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	32	276	0	ENST00000449228.1:c.406G>A	p.Ala136Thr	p.A136T	ENST00000449228	NM_001127240.2	136	Gca/Aca	3/4	0.270623313521899	5	FACETS	1	0.838	1	0.344	0.28	0.417	CLONAL	1	FALSE	2	0.270623313521899	5		276	322	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281805	46281805	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	43	470	1	ENST00000371998.3:c.4252G>T	p.Gly1418Cys	p.G1418C	ENST00000371998		1418	Ggt/Tgt	22/23	1	2	FACETS	0.85	0.72	0.989	1	0.967	1	CLONAL	2	FALSE	1	0.270623313521899	2		471	187	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750450	57750450	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	23	445	1	ENST00000274289.3:c.2018T>C	p.Met673Thr	p.M673T	ENST00000274289	NM_006622.3	673	aTg/aCg	14/14	0.270623313521899	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	2	FALSE	0	0.270623313521899	2		446	75	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501336	140501336	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs180177034	NA	P-0049260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	30	241	0	ENST00000288602.6:c.736G>C	p.Ala246Pro	p.A246P	ENST00000288602	NM_004333.4	246	Gca/Cca	6/18	0.270623313521899	5	FACETS	0.928	0.764	1	0.928	0.764	1	CLONAL	3	FALSE	2	0.270623313521899	5		241	112	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911374	39911374	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs757009393	NA	P-0049260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	17	426	0	ENST00000378444.4:c.5256C>A	p.Asp1752Glu	p.D1752E	ENST00000378444	NM_001123385.1	1752	gaC/gaA	15/15	1	2	FACETS	0.849	0.638	1	0.849	0.638	1	CLONAL	1	FALSE	1	0.270623313521899	2		426	148	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0049261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	144	581	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.507080693328136	1	FACETS	0.968	0.891	1	0.968	0.891	1	CLONAL	1	TRUE	0	0.507080693328136	1		581	438	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653782	89653782	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	35	107	0	ENST00000371953.3:c.80A>T	p.Tyr27Phe	p.Y27F	ENST00000371953	NM_000314.4	27	tAt/tTt	2/9	0.488832335044016	1	FACETS	0.912	0.766	1	0.912	0.766	1	CLONAL	1	TRUE	0	0.507080693328136	1		107	113	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637618	23637618	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	96	397	0	ENST00000261584.4:c.2687C>G	p.Ser896Cys	p.S896C	ENST00000261584	NM_024675.3	896	tCt/tGt	7/13	1	2	FACETS	0.994	0.892	1	0.994	0.892	1	CLONAL	1	TRUE	1	0.507080693328136	2		397	381	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52661381	52661381	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	61	203	0	ENST00000394830.3:c.1449G>C	p.Lys483Asn	p.K483N	ENST00000394830	NM_018313.4	483	aaG/aaC	14/30	0.488832335044016	1	FACETS	0.889	0.779	1	0.889	0.779	1	CLONAL	1	TRUE	0	0.507080693328136	1		203	202	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0049262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	112	437	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.271298999176342	1	FACETS	0.767	0.696	0.84	0.767	0.696	0.84	INDETERMINATE	1	TRUE	0	0.557311259301656	1		437	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs864622237	NA	P-0049262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	187	488	0	ENST00000269305.4:c.700T>A	p.Tyr234Asn	p.Y234N	ENST00000269305	NM_001126112.2	234	Tac/Aac	7/11	0.557311259301656	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.557311259301656	1		488	433	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106155	27106257	+	frameshift_variant	Frame_Shift_Del	DEL	GACCGAGGATGGAGCTAAGAGTTCAGAGGCCATCAAGGAGAGCAGCAAGTTTCCATTTGGCATTAGCCCAGCACAGAGCCACCGGAACATCAAGATCCTAGAG	GACCGAGGATGGAGCTAAGAGTTCAGAGGCCATCAAGGAGAGCAGCAAGTTTCCATTTGGCATTAGCCCAGCACAGAGCCACCGGAACATCAAGATCCTAGAG	-	novel	NA	P-0049262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	143	381	0	ENST00000324856.7:c.5769_5871del	p.Glu1924AsnfsTer57	p.E1924Nfs*57	ENST00000324856	NM_006015.4	1922	ttGACCGAGGATGGAGCTAAGAGTTCAGAGGCCATCAAGGAGAGCAGCAAGTTTCCATTTGGCATTAGCCCAGCACAGAGCCACCGGAACATCAAGATCCTAGAG/tt	20/20	1	2	FACETS	0.907	0.83	0.986	0.907	0.83	0.986	CLONAL	1	TRUE	1	0.557311259301656	2		381	566	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031742	36031742	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	201	525	0	ENST00000358208.4:c.1571C>G	p.Thr524Arg	p.T524R	ENST00000358208		524	aCg/aGg	12/12	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.557311259301656	2		525	682	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	90	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.601102839259844	2		148	262	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0049263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	343	442	0	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	1	2	FACETS	1	0.973	1	1	0.997	1	CLONAL	2	TRUE	1	0.601102839259844	2		442	561	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533854	533854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	68	547	1	ENST00000451590.1:c.202C>T	p.Arg68Trp	p.R68W	ENST00000451590	NM_001130442.1	68	Cgg/Tgg	3/5	1	2	FACETS	0.276	0.239	0.315	0.276	0.239	0.315	SUBCLONAL	1	TRUE	1	0.601102839259844	2		548	821	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968298	18968298	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	191	590	0	ENST00000262803.5:c.2138C>T	p.Ser713Phe	p.S713F	ENST00000262803	NM_002911.3	713	tCc/tTc	15/24	1	2	FACETS	0.725	0.671	0.782	0.725	0.671	0.782	SUBCLONAL	1	TRUE	1	0.601102839259844	2		590	876	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042125	42042125	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	40	440	1	ENST00000219905.7:c.6324del	p.Lys2108AsnfsTer5	p.K2108Nfs*5	ENST00000219905	NM_001164273.1	2107	cAa/ca	17/24	1	2	FACETS	0.906	0.762	1	0.906	0.762	1	CLONAL	1	TRUE	1	0.48	2		441	184	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647458	117647458	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	39	426	1	ENST00000368508.3:c.5486G>T	p.Arg1829Ile	p.R1829I	ENST00000368508	NM_002944.2	1829	aGa/aTa	33/43	0.3	1	FACETS	0.782	0.658	0.914	0.782	0.658	0.914	CLONAL	1	TRUE	0	0.48	1		427	158	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0049268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	105	437	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.914	0.823	1	0.914	0.823	1	CLONAL	1	TRUE	1	0.509630145244545	2		437	451	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467437	66467437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749830045	NA	P-0049268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	76	303	0	ENST00000273854.3:c.832G>A	p.Ala278Thr	p.A278T	ENST00000273854	NM_004439.5	278	Gcc/Acc	3/18	1	2	FACETS	0.875	0.773	0.982	0.875	0.773	0.982	CLONAL	1	TRUE	1	0.509630145244545	2		303	341	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120236	70120239	+	frameshift_variant	Frame_Shift_Del	DEL	ACTC	ACTC	TGA	novel	NA	P-0049268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	221	577	1	ENST00000245479.2:c.1238_1241delinsTGA	p.His413LeufsTer57	p.H413Lfs*57	ENST00000245479	NM_000346.3	413	cACTCg/cTGAg	3/3	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.509630145244545	2		578	782	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	233	576	0	ENST00000269305.4:c.527del	p.Cys176SerfsTer71	p.C176Sfs*71	ENST00000269305	NM_001126112.2	176	tGc/tc	5/11	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.509630145244545	2		576	737	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848602	151848602	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	120	336	0	ENST00000262189.6:c.12591G>A	p.Trp4197Ter	p.W4197*	ENST00000262189	NM_170606.2	4197	tgG/tgA	50/59	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.509630145244545	2		336	432	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572924	41572924	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	84	622	0	ENST00000263253.7:c.5209C>T	p.Arg1737Cys	p.R1737C	ENST00000263253	NM_001429.3	1737	Cgc/Tgc	31/31	0.176092032650415	3	FACETS	1	0.967	1	0.638	0.563	0.718	CLONAL	1	FALSE	1	0.185474382991448	3		622	776	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18747445	18747446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1206682126	NA	P-0049269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	34	318	0	ENST00000266497.5:c.3911dup	p.Leu1305ProfsTer3	p.L1305Pfs*3	ENST00000266497		1302	-/T	28/31	0.119765936689371	4	FACETS	0.767	0.625	0.926	0.383	0.312	0.463	CLONAL	1	FALSE	2	0.185474382991448	4		318	567	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607460	46607460	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772885274	NA	P-0049269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	176	736	2	ENST00000263734.3:c.1649G>A	p.Arg550Gln	p.R550Q	ENST00000263734	NM_001430.4	550	cGg/cAg	12/16	0.11180403838009	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	FALSE	2	0.185474382991448	4		738	1067	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733266	40733266	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	79	563	0	ENST00000373198.4:c.3540C>A	p.Tyr1180Ter	p.Y1180*	ENST00000373198	NM_133170.3	1180	taC/taA	26/32	0.185474382991448	4	FACETS	0.972	0.853	1	0.243	0.213	0.276	CLONAL	1	FALSE	0	0.185474382991448	4		563	1039	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149429	61149429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	42	419	0	ENST00000295025.8:c.1619C>T	p.Ser540Phe	p.S540F	ENST00000295025	NM_002908.2	540	tCc/tTc	11/11	1	2	FACETS	0.532	0.444	0.63	0.532	0.444	0.63	SUBCLONAL	1	TRUE	1	0.328943301405574	2		419	480	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249013	55249014	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACCCCC	novel	NA	P-0049271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	63	508	0	ENST00000275493.2:c.2314_2319dup	p.Pro772_His773dup	p.P772_H773dup	ENST00000275493	NM_005228.3	772	aac/aACCCCCac	20/28	0.875923150360237	3	FACETS	0.293	0.253	0.337	0.147	0.126	0.169	SUBCLONAL	1	FALSE	1	0.875923150360237	3		508	705	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118405	17118405	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0049271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	48	641	0	ENST00000285071.4:c.1433-1G>C		p.X478_splice	ENST00000285071	NM_144997.5	478			0.850480682319453	2	FACETS	0.163	0.137	0.192	0.082	0.068	0.096	SUBCLONAL	1	FALSE	0	0.875923150360237	2		641	671	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249013	55249014	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACCCCC	novel	NA	P-0049271-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	455	508	0	ENST00000275493.2:c.2314_2319dup	p.Pro772_His773dup	p.P772_H773dup	ENST00000275493	NM_005228.3	772	aac/aACCCCCac	20/28	0.580770372509013	3	FACETS	0.924	0.885	0.964	0.924	0.885	0.964	CLONAL	2	TRUE	1	0.58049615028148	3		508	1094	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118405	17118405	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0049271-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	435	641	0	ENST00000285071.4:c.1433-1G>C		p.X478_splice	ENST00000285071	NM_144997.5	478			NA	2	FACETS	0.983	0.946	1			1	INDETERMINATE	2	TRUE	NA	0.58049615028148	2		641	762	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0049271-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	240	587	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.58049615028148	2		587	770	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057936	27057937	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1415146710	NA	P-0049271-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	63	581	0	ENST00000324856.7:c.1650dup	p.Tyr551LeufsTer72	p.Y551Lfs*72	ENST00000324856	NM_006015.4	548	-/C	3/20	0.307957323886956	3	FACETS	0.298	0.257	0.343	0.099	0.085	0.115	INDETERMINATE	1	TRUE	0	0.58049615028148	3		581	940	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0049271-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	105	321	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.921	0.831	1	0.921	0.831	1	CLONAL	1	TRUE	1	0.58049615028148	2		321	393	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998223	100998223	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1253782670	NA	P-0049271-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	79	295	0	ENST00000325455.5:c.1579G>T	p.Ala527Ser	p.A527S	ENST00000325455	NM_001202474.3	527	Gcc/Tcc	1/8	0.580770372509013	3	FACETS	0.601	0.529	0.678	0.301	0.264	0.339	SUBCLONAL	1	TRUE	1	0.58049615028148	3		295	584	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218015	108218015	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049271-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	33	318	0	ENST00000278616.4:c.8594T>A	p.Ile2865Lys	p.I2865K	ENST00000278616	NM_000051.3	2865	aTa/aAa	59/63	0.580770372509013	3	FACETS	0.406	0.331	0.491	0.203	0.165	0.246	SUBCLONAL	1	TRUE	1	0.58049615028148	3		318	361	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799372	88799372	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049271-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	219	333	0	ENST00000360948.2:c.13C>G	p.Leu5Val	p.L5V	ENST00000360948	NM_001012338.2	5	Ctt/Gtt	2/19	0.561363038192029	2	FACETS	0.948	0.897	0.999	0.948	0.897	0.999	CLONAL	2	TRUE	0	0.58049615028148	2		333	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578258	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0049271-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	424	637	0	ENST00000269305.4:c.590_591dup	p.Glu198TrpfsTer50	p.E198Wfs*50	ENST00000269305	NM_001126112.2	197	-/TG	6/11	NA	2	FACETS	0.927	0.89	0.963			1	INDETERMINATE	2	TRUE	NA	0.58049615028148	2		637	788	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553142	106553142	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049271-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	114	475	0	ENST00000369096.4:c.1107G>T	p.Glu369Asp	p.E369D	ENST00000369096	NM_001198.3	369	gaG/gaT	5/7	0.269003992467618	2	FACETS	0.59	0.532	0.651	0.295	0.266	0.326	INDETERMINATE	1	TRUE	0	0.58049615028148	2		475	666	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161990408	161990408	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049271-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	69	402	0	ENST00000366898.1:c.912C>A	p.Phe304Leu	p.F304L	ENST00000366898	NM_004562.2	304	ttC/ttA	8/12	0.269003992467618	2	FACETS	0.452	0.394	0.514	0.226	0.197	0.257	INDETERMINATE	1	TRUE	0	0.58049615028148	2		402	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0049272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	320	485	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.404765254198219	3	FACETS	0.982	0.93	1	0.982	0.93	1	CLONAL	2	TRUE	1	0.442010479968218	3		486	900	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0049272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	245	417	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.233537118340995	3	FACETS	1	0.976	1	0.714	0.672	0.757	INDETERMINATE	2	TRUE	0	0.442010479968218	3		417	632	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100830	27100830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	113	443	0	ENST00000324856.7:c.4112G>A	p.Arg1371Gln	p.R1371Q	ENST00000324856	NM_006015.4	1371	cGg/cAg	18/20	1	2	FACETS	0.947	0.855	1	0.947	0.855	1	CLONAL	1	TRUE	1	0.442010479968218	2		443	540	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114901008	114901008	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	258	503	0	ENST00000543371.1:c.618del	p.Tyr206Ter	p.Y206*	ENST00000543371	NM_001198531.1	206	taC/ta	6/14	0.404765254198219	3	FACETS	0.885	0.832	0.94	0.885	0.832	0.94	CLONAL	2	TRUE	1	0.442010479968218	3		503	805	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456300	99456300	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	151	313	0	ENST00000268035.6:c.1617T>A	p.Asp539Glu	p.D539E	ENST00000268035	NM_000875.3	539	gaT/gaA	8/21	NA	2	FACETS	0.928	0.86	0.998			1	INDETERMINATE	2	TRUE	NA	0.442010479968218	2		313	368	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128016893	128016893	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	112	459	0	ENST00000285398.2:c.2196A>T	p.Glu732Asp	p.E732D	ENST00000285398	NM_000122.1	732	gaA/gaT	14/15	0.404765254198219	3	FACETS	0.913	0.822	1	0.456	0.411	0.504	CLONAL	1	TRUE	1	0.442010479968218	3		459	678	SUCCESS
APC	324	MSKCC	GRCh37	5	112175438	112175439	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	130	268	0	ENST00000257430.4:c.4148dup	p.Met1383IlefsTer3	p.M1383Ifs*3	ENST00000257430	NM_000038.5	1383	atg/aTtg	16/16	0.416439359135794	2	FACETS	0.843	0.774	0.913	0.843	0.774	0.913	CLONAL	2	TRUE	0	0.442010479968218	2		268	349	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287206	33287206	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	184	512	0	ENST00000374542.5:c.1891A>C	p.Lys631Gln	p.K631Q	ENST00000374542	NM_001141970.1	631	Aaa/Caa	6/8	0.442320945325088	3	FACETS	1	0.979	1	0.58	0.535	0.626	CLONAL	1	TRUE	1	0.442010479968218	3		512	877	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922202	39922202	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	186	483	0	ENST00000378444.4:c.3970del	p.Ile1324LeufsTer45	p.I1324Lfs*45	ENST00000378444	NM_001123385.1	1324	Att/tt	9/15	0.442320945325088	3	FACETS	1	0.975	1	0.565	0.521	0.609	CLONAL	1	TRUE	1	0.442010479968218	3		483	910	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0049273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	225	583	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.455318334193148	1	FACETS	0.806	0.754	0.86	0.806	0.754	0.86	CLONAL	1	TRUE	0	0.549780318572648	1		583	736	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0049273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	250	849	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	1	2	FACETS	0.678	0.633	0.725	0.678	0.633	0.725	SUBCLONAL	1	TRUE	1	0.549780318572648	2		849	1341	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536295	106536295	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367888338	NA	P-0049273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	137	423	0	ENST00000369096.4:c.262C>T	p.Leu88Phe	p.L88F	ENST00000369096	NM_001198.3	88	Ctt/Ttt	2/7	1	2	FACETS	0.769	0.701	0.84	0.769	0.701	0.84	SUBCLONAL	1	TRUE	1	0.549780318572648	2		423	648	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	68	302	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.35	2		302	374	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906944	32906944	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs73169186	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	54	478	0	ENST00000380152.3:c.1329G>T	p.Glu443Asp	p.E443D	ENST00000380152		443	gaG/gaT	10/27	1	2	FACETS	0.877	0.752	1	0.877	0.752	1	CLONAL	1	TRUE	1	0.35	2		478	352	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	97	424	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.85	0.759	0.947	0.85	0.759	0.947	CLONAL	1	TRUE	1	0.35	2		424	652	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	104	480	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.989	0.887	1	0.989	0.887	1	CLONAL	1	TRUE	1	0.35	2		480	601	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249847	133249847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	66	452	0	ENST00000320574.5:c.1376C>T	p.Ser459Phe	p.S459F	ENST00000320574	NM_006231.2	459	tCt/tTt	14/49	1	2	FACETS	0.754	0.656	0.86	0.754	0.656	0.86	SUBCLONAL	1	TRUE	1	0.35	2		452	500	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685307	89685307	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123317	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	42	224	0	ENST00000371953.3:c.202T>C	p.Tyr68His	p.Y68H	ENST00000371953	NM_000314.4	68	Tac/Cac	3/9	1	2	FACETS	0.772	0.647	0.909	0.772	0.647	0.909	CLONAL	1	TRUE	1	0.35	2		224	311	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210733	5210733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779302415	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	142	702	0	ENST00000357368.4:c.5318C>T	p.Ser1773Leu	p.S1773L	ENST00000357368	NM_002850.3	1773	tCg/tTg	34/38	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.35	2		702	801	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150031	202150031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167464002	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	107	567	0	ENST00000358485.4:c.1472G>A	p.Arg491Gln	p.R491Q	ENST00000358485	NM_001080125.1	491	cGa/cAa	8/9	1	2	FACETS	0.935	0.84	1	0.935	0.84	1	CLONAL	1	TRUE	1	0.35	2		567	654	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430668	80430668	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	50	487	0	ENST00000286548.4:c.340C>T	p.Arg114Ter	p.R114*	ENST00000286548	NM_002072.3	114	Cga/Tga	3/7	1	2	FACETS	0.68	0.578	0.792	0.68	0.578	0.792	SUBCLONAL	1	TRUE	1	0.35	2		487	420	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289660	33289660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758327720	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	110	579	0	ENST00000374542.5:c.43G>A	p.Glu15Lys	p.E15K	ENST00000374542	NM_001141970.1	15	Gaa/Aaa	2/8	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.35	2		579	560	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405915	70405915	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1430579993	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	89	551	0	ENST00000373644.4:c.3429G>T	p.Lys1143Asn	p.K1143N	ENST00000373644	NM_030625.2	1143	aaG/aaT	4/12	1	2	FACETS	0.933	0.829	1	0.933	0.829	1	CLONAL	1	TRUE	1	0.35	2		551	545	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692940	89692940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746152219	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	97	500	0	ENST00000371953.3:c.424C>T	p.Arg142Trp	p.R142W	ENST00000371953	NM_000314.4	142	Cgg/Tgg	5/9	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.35	2		500	447	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164385	47164385	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	47	308	1	ENST00000409792.3:c.1741G>T	p.Glu581Ter	p.E581*	ENST00000409792	NM_014159.6	581	Gaa/Taa	3/21	1	2	FACETS	0.79	0.669	0.922	0.79	0.669	0.922	CLONAL	1	TRUE	1	0.35	2		309	340	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633825	86633825	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	47	296	0	ENST00000274376.6:c.934G>T	p.Glu312Ter	p.E312*	ENST00000274376	NM_002890.2	312	Gaa/Taa	5/25	1	2	FACETS	0.883	0.75	1	0.883	0.75	1	CLONAL	1	TRUE	1	0.35	2		296	304	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215302	123215302	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	82	500	0	ENST00000218089.9:c.2848G>T	p.Glu950Ter	p.E950*	ENST00000218089	NM_001042749.1	950	Gaa/Taa	28/35	1	2	FACETS	0.882	0.78	0.992	0.882	0.78	0.992	CLONAL	1	TRUE	1	0.35	2		500	531	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720871	89720871	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	47	329	0	ENST00000371953.3:c.1022T>G	p.Phe341Cys	p.F341C	ENST00000371953	NM_000314.4	341	tTt/tGt	8/9	1	2	FACETS	0.795	0.673	0.927	0.795	0.673	0.927	CLONAL	1	TRUE	1	0.35	2		329	338	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001395	150001395	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	82	543	0	ENST00000253339.5:c.2209C>T	p.Arg737Ter	p.R737*	ENST00000253339		737	Cga/Tga	4/7	1	2	FACETS	0.956	0.846	1	0.956	0.846	1	CLONAL	1	TRUE	1	0.35	2		543	490	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020225	123020225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	89	646	0	ENST00000355640.3:c.713G>A	p.Arg238Gln	p.R238Q	ENST00000355640		238	cGa/cAa	2/7	1	2	FACETS	0.788	0.7	0.883	0.788	0.7	0.883	SUBCLONAL	1	TRUE	1	0.35	2		646	645	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641885	12641885	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	44	341	0	ENST00000251849.4:c.862+2T>C		p.X288_splice	ENST00000251849	NM_002880.3	288			1	2	FACETS	0.672	0.565	0.79	0.672	0.565	0.79	SUBCLONAL	1	TRUE	1	0.35	2		341	374	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851930	128851930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779777438	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	123	588	0	ENST00000249373.3:c.2002C>T	p.Arg668Cys	p.R668C	ENST00000249373	NM_005631.4	668	Cgc/Tgc	12/12	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.35	2		588	676	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099325	27099325	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	94	557	0	ENST00000324856.7:c.3562C>T	p.Gln1188Ter	p.Q1188*	ENST00000324856	NM_006015.4	1188	Cag/Tag	14/20	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.35	2		557	535	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682712	86682712	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	24	232	0	ENST00000274376.6:c.2917G>T	p.Glu973Ter	p.E973*	ENST00000274376	NM_002890.2	973	Gaa/Taa	23/25	1	2	FACETS	0.693	0.546	0.859	0.693	0.546	0.859	SUBCLONAL	1	TRUE	1	0.35	2		232	198	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094812	143094812	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	47	412	0	ENST00000262992.4:c.1332G>T	p.Lys444Asn	p.K444N	ENST00000262992	NM_001101669.1	444	aaG/aaT	14/24	1	2	FACETS	0.788	0.667	0.919	0.788	0.667	0.919	CLONAL	1	TRUE	1	0.35	2		412	341	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858200	27858200	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	72	564	0	ENST00000359303.2:c.371A>G	p.Asp124Gly	p.D124G	ENST00000359303	NM_003535.2	124	gAc/gGc	1/1	1	2	FACETS	0.8	0.701	0.908	0.8	0.701	0.908	CLONAL	1	TRUE	1	0.35	2		564	514	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444297	49444297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746163543	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	162	848	1	ENST00000301067.7:c.3074C>T	p.Ser1025Leu	p.S1025L	ENST00000301067	NM_003482.3	1025	tCg/tTg	11/54	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.35	2		849	838	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939558	76939558	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	84	598	0	ENST00000373344.5:c.1190C>A	p.Ser397Tyr	p.S397Y	ENST00000373344	NM_000489.3	397	tCt/tAt	9/35	1	2	FACETS	0.85	0.752	0.954	0.85	0.752	0.954	CLONAL	1	TRUE	1	0.35	2		598	565	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150022982	150022982	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	91	533	0	ENST00000253339.5:c.281C>A	p.Ser94Tyr	p.S94Y	ENST00000253339		94	tCt/tAt	1/7	1	2	FACETS	0.937	0.834	1	0.937	0.834	1	CLONAL	1	TRUE	1	0.35	2		533	555	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696405	47696405	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	110	374	0	ENST00000347630.2:c.418G>T	p.Asp140Tyr	p.D140Y	ENST00000347630	NM_001007230.1	140	Gat/Tat	6/11	1	2	FACETS	0.879	0.79	0.973	0.879	0.79	0.973	CLONAL	1	TRUE	1	0.35	2		374	715	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942524	17942524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763951351	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	89	716	0	ENST00000458235.1:c.2764G>A	p.Asp922Asn	p.D922N	ENST00000458235	NM_000215.3	922	Gat/Aat	20/24	1	2	FACETS	0.727	0.644	0.815	0.727	0.644	0.815	SUBCLONAL	1	TRUE	1	0.35	2		716	700	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865440	57865440	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	126	705	0	ENST00000228682.2:c.2917A>C	p.Asn973His	p.N973H	ENST00000228682	NM_005269.2	973	Aat/Cat	12/12	1	2	FACETS	0.925	0.838	1	0.925	0.838	1	CLONAL	1	TRUE	1	0.35	2		705	778	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575540	67575540	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	74	341	0	ENST00000274335.5:c.613G>T	p.Glu205Ter	p.E205*	ENST00000274335		205	Gaa/Taa	4/15	1	2	FACETS	0.868	0.762	0.982	0.868	0.762	0.982	CLONAL	1	TRUE	1	0.35	2		341	487	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058509	72058509	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs546160294	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	76	434	0	ENST00000357731.5:c.931C>A	p.Pro311Thr	p.P311T	ENST00000357731	NM_173808.2	311	Cct/Act	6/7	1	2	FACETS	0.746	0.655	0.844	0.746	0.655	0.844	SUBCLONAL	1	TRUE	1	0.35	2		434	582	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115279431	115279431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758243111	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	66	482	0	ENST00000438362.2:c.586G>A	p.Val196Ile	p.V196I	ENST00000438362	NM_001242891.1	196	Gtt/Att	6/20	1	2	FACETS	0.695	0.603	0.793	0.695	0.603	0.793	SUBCLONAL	1	TRUE	1	0.35	2		482	543	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117054	193117054	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	86	349	0	ENST00000367435.3:c.787C>G	p.Arg263Gly	p.R263G	ENST00000367435	NM_024529.4	263	Cgt/Ggt	8/17	1	2	FACETS	0.907	0.804	1	0.907	0.804	1	CLONAL	1	TRUE	1	0.35	2		349	542	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132794	64132794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	95	600	0	ENST00000334205.4:c.928G>A	p.Ala310Thr	p.A310T	ENST00000334205	NM_003942.2	310	Gct/Act	9/17	1	2	FACETS	0.93	0.829	1	0.93	0.829	1	CLONAL	1	TRUE	1	0.35	2		600	584	SUCCESS
EED	8726	MSKCC	GRCh37	11	85967544	85967544	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	48	291	0	ENST00000263360.6:c.542A>C	p.Gln181Pro	p.Q181P	ENST00000263360	NM_003797.3	181	cAg/cCg	5/12	1	2	FACETS	0.839	0.712	0.977	0.839	0.712	0.977	CLONAL	1	TRUE	1	0.35	2		291	327	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435161	18435161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	60	382	0	ENST00000266497.5:c.146G>A	p.Gly49Asp	p.G49D	ENST00000266497		49	gGc/gAc	1/31	1	2	FACETS	0.905	0.783	1	0.905	0.783	1	CLONAL	1	TRUE	1	0.35	2		382	379	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719966	18719966	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	63	435	0	ENST00000266497.5:c.3863T>G	p.Leu1288Ter	p.L1288*	ENST00000266497		1288	tTa/tGa	27/31	1	2	FACETS	0.826	0.716	0.944	0.826	0.716	0.944	CLONAL	1	TRUE	1	0.35	2		435	436	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515243	103515243	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	69	383	0	ENST00000355739.4:c.1744A>C	p.Ser582Arg	p.S582R	ENST00000355739	NM_000123.3	582	Agt/Cgt	8/15	1	2	FACETS	0.95	0.831	1	0.95	0.831	1	CLONAL	1	TRUE	1	0.35	2		383	415	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830958	72830959	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	103	516	0	ENST00000268489.5:c.5622_5623del	p.Glu1875LysfsTer53	p.E1875Kfs*53	ENST00000268489	NM_006885.3	1874	ccCGaa/ccaa	9/10	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.35	2		516	558	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256953	41256953	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	83	508	0	ENST00000357654.3:c.233G>T	p.Arg78Ile	p.R78I	ENST00000357654	NM_007294.3	78	aGa/aTa	5/23	1	2	FACETS	0.883	0.781	0.992	0.883	0.781	0.992	CLONAL	1	TRUE	1	0.35	2		508	537	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39593454	39593454	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	43	308	0	ENST00000262039.4:c.1219A>C	p.Asn407His	p.N407H	ENST00000262039	NM_002647.2	407	Aat/Cat	11/25	1	2	FACETS	0.788	0.662	0.925	0.788	0.662	0.925	CLONAL	1	TRUE	1	0.35	2		308	312	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46587803	46587803	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	65	462	2	ENST00000263734.3:c.481G>T	p.Asp161Tyr	p.D161Y	ENST00000263734	NM_001430.4	161	Gac/Tac	5/16	1	2	FACETS	0.775	0.674	0.885	0.775	0.674	0.885	SUBCLONAL	1	TRUE	1	0.35	2		464	479	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839676	42839676	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	94	652	0	ENST00000398585.3:c.1563T>G	p.Ile521Met	p.I521M	ENST00000398585	NM_001135099.1	521	atT/atG	13/14	1	2	FACETS	0.797	0.71	0.89	0.797	0.71	0.89	SUBCLONAL	1	TRUE	1	0.35	2		652	674	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799700	72799700	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1300888445	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	50	588	0	ENST00000325599.8:c.1469C>A	p.Ser490Tyr	p.S490Y	ENST00000325599	NM_018130.2	490	tCt/tAt	11/11	1	2	FACETS	0.43	0.364	0.503	0.43	0.364	0.503	SUBCLONAL	1	TRUE	1	0.35	2		588	664	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592154	55592154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371078350	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	101	567	0	ENST00000288135.5:c.1478C>T	p.Ala493Val	p.A493V	ENST00000288135	NM_000222.2	493	gCt/gTt	9/21	1	2	FACETS	0.811	0.725	0.902	0.811	0.725	0.902	CLONAL	1	TRUE	1	0.35	2		567	712	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467595	66467595	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	47	393	0	ENST00000273854.3:c.674C>A	p.Ser225Tyr	p.S225Y	ENST00000273854	NM_004439.5	225	tCt/tAt	3/18	1	2	FACETS	0.662	0.559	0.774	0.662	0.559	0.774	SUBCLONAL	1	TRUE	1	0.35	2		393	406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0049275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	180	487	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	0.759450683662474	1	FACETS	0.692	0.645	0.738	0.692	0.645	0.738	SUBCLONAL	1	TRUE	0	0.75957995107931	1		487	425	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601310	28601310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	145	397	0	ENST00000241453.7:c.2122G>A	p.Glu708Lys	p.E708K	ENST00000241453	NM_004119.2	708	Gaa/Aaa	17/24	1	2	FACETS	0.58	0.531	0.632	0.58	0.531	0.632	SUBCLONAL	1	TRUE	1	0.75957995107931	2		397	658	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717768	89717769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	184	298	0	ENST00000371953.3:c.794dup	p.Asp268GlyfsTer30	p.D268Gfs*30	ENST00000371953	NM_000314.4	265	cta/cTta	7/9	0.75957995107931	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.75957995107931	1		298	271	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416372	49416372	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0049275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	53	335	0	ENST00000301067.7:c.16338+1G>A		p.X5446_splice	ENST00000301067	NM_003482.3	5446			1	2	FACETS	0.264	0.225	0.307	0.264	0.225	0.307	SUBCLONAL	1	TRUE	1	0.75957995107931	2		335	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579406	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	GGGAAGGGACAGAAGATG	GGGAAGGGACAGAAGATG	-	novel	NA	P-0049275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	54	601	0	ENST00000269305.4:c.281_298del	p.Ser94_Gln100delinsTer	p.S94_Q100delins*	ENST00000269305	NM_001126112.2	94	tCATCTTCTGTCCCTTCCCag/tag	4/11	0.759450683662474	1	FACETS	0.168	0.143	0.195	0.168	0.143	0.195	SUBCLONAL	1	TRUE	0	0.75957995107931	1		601	524	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755599	39755599	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	34	453	0	ENST00000288319.7:c.1166A>T	p.Lys389Met	p.K389M	ENST00000288319	NM_182918.3	389	aAg/aTg	10/10	1	2	FACETS	0.148	0.12	0.18	0.148	0.12	0.18	SUBCLONAL	1	TRUE	1	0.75957995107931	2		453	604	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589622	67589623	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATATGATAGATT	novel	NA	P-0049275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	101	261	0	ENST00000274335.5:c.1392_1403dup	p.Asp464_Tyr467dup	p.D464_Y467dup	ENST00000274335		464	gaa/gaATATGATAGATTa	10/15	1	2	FACETS	0.739	0.666	0.814	0.739	0.666	0.814	SUBCLONAL	1	TRUE	1	0.75957995107931	2		261	360	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123505225	123505226	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0049275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	83	332	0	ENST00000371139.4:c.371_372delinsAT	p.Cys124Tyr	p.C124Y	ENST00000371139	NM_001114937.2	124	tGC/tAT	4/4	1	2	FACETS	0.545	0.484	0.61	0.545	0.484	0.61	SUBCLONAL	1	TRUE	1	0.75957995107931	2		332	401	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578502	7578502	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	290	826	0	ENST00000269305.4:c.428T>C	p.Val143Ala	p.V143A	ENST00000269305	NM_001126112.2	143	gTg/gCg	5/11	0.587766273704404	1	FACETS	0.899	0.85	0.949	0.899	0.85	0.949	CLONAL	1	TRUE	0	0.602015871462695	1		826	749	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873345	151873345	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	148	346	0	ENST00000262189.6:c.9193G>T	p.Glu3065Ter	p.E3065*	ENST00000262189	NM_170606.2	3065	Gaa/Taa	38/59	1	2	FACETS	0.981	0.902	1	0.981	0.902	1	CLONAL	1	TRUE	1	0.602015871462695	2		346	501	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89883020	89883020	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	43	177	0	ENST00000389301.3:c.4T>C	p.Ser2Pro	p.S2P	ENST00000389301	NM_000135.2	2	Tcc/Ccc	1/43	1	2	FACETS	0.612	0.517	0.715	0.612	0.517	0.715	SUBCLONAL	1	TRUE	1	0.62188309076215	2		177	226	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0049285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	51	628	2	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	1	2	FACETS	0.987	0.838	1	0.987	0.838	1	CLONAL	1	TRUE	1	0.16	2		630	646	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0049285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	48	431	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.16	2		431	518	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109873	115109873	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	30	568	0	ENST00000257566.3:c.2005C>A	p.Pro669Thr	p.P669T	ENST00000257566	NM_016569.3	669	Ccc/Acc	8/8	1	2	FACETS	0.752	0.605	0.919	0.752	0.605	0.919	CLONAL	1	TRUE	1	0.16	2		568	499	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117745	115117745	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	28	325	0	ENST00000257566.3:c.690G>C	p.Trp230Cys	p.W230C	ENST00000257566	NM_016569.3	230	tgG/tgC	3/8	1	2	FACETS	0.641	0.511	0.79	0.641	0.511	0.79	SUBCLONAL	1	TRUE	1	0.16	2		325	546	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602835	10602835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	81	791	0	ENST00000171111.5:c.743C>T	p.Ala248Val	p.A248V	ENST00000171111	NM_203500.1	248	gCc/gTc	3/6	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.16	2		791	981	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267498	198267498	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1438613366	NA	P-0049285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	30	381	0	ENST00000335508.6:c.1859T>C	p.Met620Thr	p.M620T	ENST00000335508	NM_012433.2	620	aTg/aCg	14/25	1	2	FACETS	0.746	0.6	0.912	0.746	0.6	0.912	CLONAL	1	TRUE	1	0.16	2		381	503	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039405	47039405	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	57	628	0	ENST00000377604.3:c.1028G>C	p.Arg343Pro	p.R343P	ENST00000377604	NM_001204468.1	343	cGc/cCc	10/24	0.136228207439583	1	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	0	0.16	1		628	640	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	61	347	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.19	2		347	605	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	33	304	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.888	0.724	1	0.888	0.724	1	CLONAL	1	TRUE	1	0.19	2		305	391	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	73	504	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.975	0.852	1	0.975	0.852	1	CLONAL	1	TRUE	1	0.19	2		504	788	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	42	316	0	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.19	2		316	408	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	82	615	1	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.19	2		616	784	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	77	666	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.862	0.755	0.978	0.862	0.755	0.978	CLONAL	1	TRUE	1	0.19	2		666	940	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150022976	150022976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373625760	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	59	456	0	ENST00000253339.5:c.287G>A	p.Arg96Gln	p.R96Q	ENST00000253339		96	cGg/cAg	1/7	1	2	FACETS	0.967	0.832	1	0.967	0.832	1	CLONAL	1	TRUE	1	0.19	2		456	642	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610439	10610439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202181679	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	71	730	0	ENST00000171111.5:c.271G>A	p.Ala91Thr	p.A91T	ENST00000171111	NM_203500.1	91	Gcc/Acc	2/6	1	2	FACETS	0.825	0.718	0.941	0.825	0.718	0.941	CLONAL	1	TRUE	1	0.19	2		730	906	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661945	29661945	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854552	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	67	501	1	ENST00000356175.3:c.5839C>T	p.Arg1947Ter	p.R1947*	ENST00000356175	NM_000267.3	1947	Cga/Tga	39/57	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.19	2		502	618	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429797	78429797	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	53	361	0	ENST00000370768.2:c.991C>T	p.Arg331Ter	p.R331*	ENST00000370768	NM_003902.3	331	Cga/Tga	12/20	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.19	2		361	550	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141632	202141632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764461240	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	33	373	0	ENST00000358485.4:c.920G>A	p.Arg307Gln	p.R307Q	ENST00000358485	NM_001080125.1	307	cGg/cAg	7/9	1	2	FACETS	0.635	0.516	0.77	0.635	0.516	0.77	SUBCLONAL	1	TRUE	1	0.19	2		373	547	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557837	187557837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs184443677	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	49	312	0	ENST00000441802.2:c.3874G>A	p.Glu1292Lys	p.E1292K	ENST00000441802	NM_005245.3	1292	Gaa/Aaa	5/27	1	2	FACETS	0.744	0.629	0.872	0.744	0.629	0.872	SUBCLONAL	1	TRUE	1	0.19	2		312	693	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236086	108236086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782292	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	29	451	0	ENST00000278616.4:c.9022C>T	p.Arg3008Cys	p.R3008C	ENST00000278616	NM_000051.3	3008	Cgt/Tgt	63/63	1	2	FACETS	0.458	0.366	0.563	0.458	0.366	0.563	SUBCLONAL	1	TRUE	1	0.19	2		451	667	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654553	29654553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876657714	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	31	255	0	ENST00000356175.3:c.5242C>T	p.Arg1748Ter	p.R1748*	ENST00000356175	NM_000267.3	1748	Cga/Tga	37/57	1	2	FACETS	0.841	0.68	1	0.841	0.68	1	CLONAL	1	TRUE	1	0.19	2		255	388	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913784	32913784	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	44	416	0	ENST00000380152.3:c.5297del	p.Asn1766IlefsTer11	p.N1766Ifs*11	ENST00000380152		1764	tcA/tc	11/27	1	2	FACETS	0.818	0.686	0.966	0.818	0.686	0.966	CLONAL	1	TRUE	1	0.19	2		416	566	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573224	41573224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1439243688	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	52	694	1	ENST00000263253.7:c.5509C>T	p.Arg1837Trp	p.R1837W	ENST00000263253	NM_001429.3	1837	Cgg/Tgg	31/31	1	2	FACETS	0.608	0.515	0.709	0.608	0.515	0.709	SUBCLONAL	1	TRUE	1	0.19	2		695	901	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248859	133248859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149296223	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	78	580	0	ENST00000320574.5:c.1736G>A	p.Arg579His	p.R579H	ENST00000320574	NM_006231.2	579	cGc/cAc	16/49	1	2	FACETS	0.834	0.731	0.945	0.834	0.731	0.945	CLONAL	1	TRUE	1	0.19	2		580	985	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958789	55958789	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	63	525	0	ENST00000263923.4:c.3064C>T	p.Arg1022Ter	p.R1022*	ENST00000263923	NM_002253.2	1022	Cga/Tga	22/30	1	2	FACETS	0.858	0.741	0.986	0.858	0.741	0.986	CLONAL	1	TRUE	1	0.19	2		525	773	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511155	148511155	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	72	445	0	ENST00000320356.2:c.1747C>T	p.Arg583Ter	p.R583*	ENST00000320356	NM_004456.4	583	Cga/Tga	15/20	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.19	2		445	743	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38631981	38631981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1255149646	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	61	587	5	ENST00000299084.4:c.471del	p.Gln158SerfsTer16	p.Q158Sfs*16	ENST00000299084	NM_152594.2	156	cTt/ct	5/7	1	2	FACETS	0.915	0.788	1	0.915	0.788	1	CLONAL	1	TRUE	1	0.19	2		592	702	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80150077	80150077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761465174	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	58	540	0	ENST00000265081.6:c.2942C>T	p.Thr981Met	p.T981M	ENST00000265081	NM_002439.4	981	aCg/aTg	21/24	1	2	FACETS	0.89	0.764	1	0.89	0.764	1	CLONAL	1	TRUE	1	0.19	2		540	686	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326204	62326204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780364760	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	57	672	2	ENST00000360203.5:c.3220G>A	p.Ala1074Thr	p.A1074T	ENST00000360203	NM_001283009.1	1074	Gcg/Acg	32/35	1	2	FACETS	0.67	0.573	0.776	0.67	0.573	0.776	SUBCLONAL	1	TRUE	1	0.19	2		674	896	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970916	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	75	555	0	ENST00000265081.6:c.1147_1148del	p.Lys383GlyfsTer20	p.K383Gfs*20	ENST00000265081	NM_002439.4	381	AAa/a	7/24	1	2	FACETS	0.987	0.864	1	0.987	0.864	1	CLONAL	1	TRUE	1	0.19	2		555	800	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041261	29041262	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	31	383	0	ENST00000282397.4:c.166dup	p.Glu56GlyfsTer5	p.E56Gfs*5	ENST00000282397	NM_002019.4	56	gaa/gGaa	3/30	1	2	FACETS	0.641	0.518	0.781	0.641	0.518	0.781	SUBCLONAL	1	TRUE	1	0.19	2		383	509	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645252	67645252	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	76	557	0	ENST00000264010.4:c.517G>T	p.Gly173Ter	p.G173*	ENST00000264010	NM_006565.3	173	Gga/Tga	3/12	1	2	FACETS	0.926	0.811	1	0.926	0.811	1	CLONAL	1	TRUE	1	0.19	2		557	864	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215833	98215833	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147025073	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	55	540	0	ENST00000331920.6:c.3376G>A	p.Val1126Ile	p.V1126I	ENST00000331920	NM_000264.3	1126	Gtc/Atc	20/24	1	2	FACETS	0.664	0.566	0.771	0.664	0.566	0.771	SUBCLONAL	1	TRUE	1	0.19	2		540	872	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001523	150001523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264217871	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	48	259	0	ENST00000253339.5:c.2081G>A	p.Arg694His	p.R694H	ENST00000253339		694	cGt/cAt	4/7	1	2	FACETS	0.834	0.704	0.977	0.834	0.704	0.977	CLONAL	1	TRUE	1	0.19	2		259	606	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615023	43615023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779996040	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	47	615	0	ENST00000355710.3:c.2437C>T	p.Arg813Trp	p.R813W	ENST00000355710	NM_020975.4	813	Cgg/Tgg	14/20	1	2	FACETS	0.712	0.599	0.836	0.712	0.599	0.836	SUBCLONAL	1	TRUE	1	0.19	2		615	695	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224339	36224340	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	55	755	1	ENST00000222270.7:c.6895dup	p.Arg2299ProfsTer4	p.R2299Pfs*4	ENST00000222270	NM_014727.1	2297	gcc/gCcc	28/37	1	2	FACETS	0.566	0.483	0.659	0.566	0.483	0.659	SUBCLONAL	1	TRUE	1	0.19	2		756	1022	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224183	36224183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771130237	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	76	585	0	ENST00000222270.7:c.6733G>A	p.Val2245Met	p.V2245M	ENST00000222270	NM_014727.1	2245	Gtg/Atg	28/37	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.19	2		585	764	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564686	86564686	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	57	671	0	ENST00000274376.6:c.422del	p.Pro141LeufsTer33	p.P141Lfs*33	ENST00000274376	NM_002890.2	140	Ccc/cc	1/25	1	2	FACETS	0.709	0.607	0.822	0.709	0.607	0.822	SUBCLONAL	1	TRUE	1	0.19	2		671	846	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032847	48032847	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	56	369	0	ENST00000234420.5:c.3646+1G>A		p.X1216_splice	ENST00000234420	NM_000179.2	1216			1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.19	2		369	567	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100282	8100282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	61	686	0	ENST00000346208.3:c.256C>T	p.Arg86Cys	p.R86C	ENST00000346208		86	Cgc/Tgc	3/6	1	2	FACETS	0.754	0.649	0.869	0.754	0.649	0.869	SUBCLONAL	1	TRUE	1	0.19	2		686	852	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798154	45798154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377639760	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	62	618	0	ENST00000450313.1:c.697G>A	p.Gly233Ser	p.G233S	ENST00000450313	NM_012222.2	233	Ggt/Agt	9/16	1	2	FACETS	0.714	0.615	0.822	0.714	0.615	0.822	SUBCLONAL	1	TRUE	1	0.19	2		618	914	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692768	89692768	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs786204926	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	52	409	1	ENST00000371953.3:c.254-2A>G		p.X85_splice	ENST00000371953	NM_000314.4	85			1	2	FACETS	0.981	0.835	1	0.981	0.835	1	CLONAL	1	TRUE	1	0.19	2		410	558	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8252007	8252007	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	76	660	0	ENST00000335790.3:c.70T>C	p.Cys24Arg	p.C24R	ENST00000335790	NM_002315.2	24	Tgt/Cgt	2/4	1	2	FACETS	0.883	0.773	1	0.883	0.773	1	CLONAL	1	TRUE	1	0.19	2		660	906	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196644	67196644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1342021737	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	67	561	0	ENST00000312629.5:c.173G>A	p.Gly58Asp	p.G58D	ENST00000312629	NM_003952.2	58	gGc/gAc	3/15	1	2	FACETS	0.945	0.821	1	0.945	0.821	1	CLONAL	1	TRUE	1	0.19	2		561	746	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480085	50480085	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	54	591	0	ENST00000394963.4:c.319C>T	p.Gln107Ter	p.Q107*	ENST00000394963	NM_003076.4	107	Cag/Tag	2/13	1	2	FACETS	0.734	0.626	0.854	0.734	0.626	0.854	SUBCLONAL	1	TRUE	1	0.19	2		591	774	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039362	49039362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	46	554	0	ENST00000267163.4:c.2347C>T	p.Pro783Ser	p.P783S	ENST00000267163	NM_000321.2	783	Cct/Tct	23/27	1	2	FACETS	0.618	0.519	0.729	0.618	0.519	0.729	SUBCLONAL	1	TRUE	1	0.19	2		554	783	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713260	43713260	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	102	739	0	ENST00000382044.4:c.4213C>T	p.Arg1405Ter	p.R1405*	ENST00000382044	NM_001141980.1	1405	Cga/Tga	20/28	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.19	2		739	1070	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222906	5222906	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs915133073	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	65	574	0	ENST00000357368.4:c.2897C>T	p.Thr966Met	p.T966M	ENST00000357368	NM_002850.3	966	aCg/aTg	18/38	1	2	FACETS	0.885	0.766	1	0.885	0.766	1	CLONAL	1	TRUE	1	0.19	2		574	773	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265001	10265001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146467216	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	56	390	0	ENST00000340748.4:c.1939G>A	p.Ala647Thr	p.A647T	ENST00000340748		647	Gcc/Acc	21/40	1	2	FACETS	0.939	0.804	1	0.939	0.804	1	CLONAL	1	TRUE	1	0.19	2		390	628	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366128	15366128	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772651117	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	57	455	2	ENST00000263377.2:c.2027G>A	p.Arg676Gln	p.R676Q	ENST00000263377	NM_058243.2	676	cGg/cAg	10/20	1	2	FACETS	0.855	0.732	0.989	0.855	0.732	0.989	CLONAL	1	TRUE	1	0.19	2		457	702	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256722	19256722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752132456	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	60	660	2	ENST00000162023.5:c.991G>A	p.Gly331Ser	p.G331S	ENST00000162023		331	Ggc/Agc	13/13	1	2	FACETS	0.827	0.711	0.953	0.827	0.711	0.953	CLONAL	1	TRUE	1	0.19	2		662	764	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741486	39741486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1313664473	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	46	373	0	ENST00000361337.2:c.1373G>A	p.Arg458Gln	p.R458Q	ENST00000361337	NM_003286.2	458	cGg/cAg	14/21	1	2	FACETS	0.687	0.577	0.809	0.687	0.577	0.809	SUBCLONAL	1	TRUE	1	0.19	2		373	705	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927417	49927417	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	54	654	0	ENST00000296474.3:c.3887T>C	p.Leu1296Pro	p.L1296P	ENST00000296474	NM_002447.2	1296	cTt/cCt	19/20	1	2	FACETS	0.57	0.485	0.664	0.57	0.485	0.664	SUBCLONAL	1	TRUE	1	0.19	2		654	997	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670049	86670049	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	60	371	0	ENST00000274376.6:c.1846T>C	p.Cys616Arg	p.C616R	ENST00000274376	NM_002890.2	616	Tgt/Cgt	14/25	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.19	2		371	554	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149436861	149436861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs281860271	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	44	528	4	ENST00000286301.3:c.2308G>A	p.Ala770Thr	p.A770T	ENST00000286301	NM_005211.3	770	Gct/Act	17/22	1	2	FACETS	0.696	0.583	0.823	0.696	0.583	0.823	SUBCLONAL	1	TRUE	1	0.19	2		532	665	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839711	27839711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747419710	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	50	470	0	ENST00000328488.2:c.383C>T	p.Ala128Val	p.A128V	ENST00000328488	NM_003533.2	128	gCg/gTg	1/1	1	2	FACETS	0.813	0.689	0.95	0.813	0.689	0.95	CLONAL	1	TRUE	1	0.19	2		470	647	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552769	106552770	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	58	465	0	ENST00000369096.4:c.740_741del	p.Glu247ValfsTer23	p.E247Vfs*23	ENST00000369096	NM_001198.3	245	aAG/a	5/7	1	2	FACETS	0.826	0.709	0.955	0.826	0.709	0.955	CLONAL	1	TRUE	1	0.19	2		465	739	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960177	151960177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773970643	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	49	328	0	ENST00000262189.6:c.1223C>T	p.Thr408Met	p.T408M	ENST00000262189	NM_170606.2	408	aCg/aTg	9/59	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.19	2		328	422	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218659	98218659	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	49	367	0	ENST00000331920.6:c.3205G>A	p.Gly1069Ser	p.G1069S	ENST00000331920	NM_000264.3	1069	Ggc/Agc	19/24	1	2	FACETS	0.84	0.711	0.983	0.84	0.711	0.983	CLONAL	1	TRUE	1	0.19	2		367	614	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922958	44922958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762821553	NA	P-0049291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	70	530	0	ENST00000377967.4:c.1819G>A	p.Val607Met	p.V607M	ENST00000377967	NM_021140.2	607	Gtg/Atg	16/29	1	2	FACETS	0.859	0.747	0.98	0.859	0.747	0.98	CLONAL	1	TRUE	1	0.19	2		530	858	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0049292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	832	683	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.554381341041573	4	FACETS	0.95	0.928	0.971	0.95	0.928	0.971	CLONAL	4	TRUE	0	0.597443283862208	4		683	1171	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399155	139399155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749490844	NA	P-0049292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	232	715	0	ENST00000277541.6:c.4988G>A	p.Arg1663Gln	p.R1663Q	ENST00000277541	NM_017617.3	1663	cGg/cAg	26/34	0.50121298017881	3	FACETS	1	0.981	1	0.567	0.529	0.605	CLONAL	1	TRUE	1	0.597443283862208	3		715	890	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945093	31945093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	176	523	0	ENST00000340398.3:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000340398	NM_001013699.2	3	cGa/cAa	1/1	0.597443283862208	5	FACETS	0.882	0.81	0.957			1	CLONAL	1	TRUE	NA	0.597443283862208	5		523	1267	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271600	26271600	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs770969115	NA	P-0049292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	93	336	0	ENST00000305910.3:c.13A>G	p.Lys5Glu	p.K5E	ENST00000305910	NM_003534.2	5	Aag/Gag	1/1	0.548550526921648	4	FACETS	0.83	0.739	0.927	0.277	0.246	0.309	CLONAL	1	TRUE	1	0.597443283862208	4		336	599	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524967	8524967	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	115	353	0	ENST00000356435.5:c.637G>C	p.Ala213Pro	p.A213P	ENST00000356435		213	Gcg/Ccg	7/35	0.548835204091451	5	FACETS	0.827	0.744	0.914	0.207	0.186	0.229	CLONAL	1	TRUE	1	0.597443283862208	5		353	883	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80343447	80343447	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	227	326	0	ENST00000286548.4:c.872A>G	p.Tyr291Cys	p.Y291C	ENST00000286548	NM_002072.3	291	tAc/tGc	6/7	0.50121298017881	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.597443283862208	3		326	486	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0049294-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	89	424	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.553467537315831	3	FACETS	0.364	0.322	0.409	0.182	0.161	0.205	SUBCLONAL	1	TRUE	1	0.865513012819252	3		424	810	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0049294-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	67	353	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	0.553467537315831	3	FACETS	0.373	0.324	0.427	0.187	0.162	0.214	SUBCLONAL	1	TRUE	1	0.865513012819252	3		353	594	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874314	76874314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049294-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	141	240	0	ENST00000373344.5:c.5408G>A	p.Arg1803His	p.R1803H	ENST00000373344	NM_000489.3	1803	cGt/cAt	21/35	0.865513012819252	0	FACETS		NA	1			1	NA	1	TRUE	NA	0.865513012819252	0		240	174	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281360	49281360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201503697	NA	P-0049294-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	81	641	0	ENST00000282018.3:c.407G>A	p.Arg136His	p.R136H	ENST00000282018	NM_020377.2	136	cGt/cAt	1/1	1	2	FACETS	0.188	0.165	0.213	0.188	0.165	0.213	SUBCLONAL	1	TRUE	1	0.865513012819252	2		641	997	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0049305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	229	610	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.29841260075556	2	FACETS	0.977	0.914	1	0.977	0.914	1	CLONAL	2	TRUE	0	0.31	2		610	756	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248573	8248573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780757257	NA	P-0049305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	93	754	1	ENST00000335790.3:c.314G>A	p.Arg105Gln	p.R105Q	ENST00000335790	NM_002315.2	105	cGg/cAg	3/4	0.215237502741862	1	FACETS	0.545	0.483	0.61	0.545	0.483	0.61	SUBCLONAL	1	TRUE	0	0.31	1		755	931	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120732	94120732	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	134	403	0	ENST00000369303.4:c.319A>T	p.Arg107Trp	p.R107W	ENST00000369303	NM_004440.3	107	Agg/Tgg	3/17	NA	2	FACETS	1	0.929	1			1	INDETERMINATE	2	TRUE	NA	0.31	2		403	426	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220463	1220464	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	296	827	0	ENST00000326873.7:c.558dup	p.Gly187ArgfsTer79	p.G187Rfs*79	ENST00000326873	NM_000455.4	186	acc/aCcc	4/10	0.302755211552765	2	FACETS	0.982	0.926	1	0.982	0.926	1	CLONAL	2	TRUE	0	0.31	2		827	972	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589779	55589779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1560414379	NA	P-0049305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	130	339	0	ENST00000288135.5:c.1261C>T	p.Leu421Phe	p.L421F	ENST00000288135	NM_000222.2	421	Ctc/Ttc	8/21	0.302755211552765	1	FACETS	0.862	0.789	0.937	1	0.989	1	CLONAL	2	TRUE	0	0.31	1		339	411	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600015	10600015	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	331	759	0	ENST00000171111.5:c.1561G>C	p.Ala521Pro	p.A521P	ENST00000171111	NM_203500.1	521	Gct/Cct	5/6	0.302755211552765	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.31	2		759	981	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834536	156834536	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	232	779	1	ENST00000524377.1:c.304G>T	p.Gly102Cys	p.G102C	ENST00000524377	NM_002529.3	102	Ggt/Tgt	3/17	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.31	2		780	1030	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498388	89498388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	75	181	0	ENST00000336596.2:c.2360C>T	p.Pro787Leu	p.P787L	ENST00000336596	NM_005233.5	787	cCa/cTa	14/17	0.190715873328129	2	FACETS	0.972	0.863	1	0.972	0.863	1	CLONAL	2	TRUE	0	0.31	2		181	249	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967332	134967332	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	45	381	0	ENST00000398015.3:c.2671G>T	p.Val891Leu	p.V891L	ENST00000398015	NM_004441.4	891	Gtg/Ttg	14/16	0.176399836007844	3	FACETS	0.603	0.506	0.71	0.201	0.168	0.237	INDETERMINATE	1	TRUE	0	0.31	3		381	556	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149375020	149375020	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	108	862	0	ENST00000360632.3:c.74A>T	p.Asp25Val	p.D25V	ENST00000360632	NM_015472.4	25	gAc/gTc	2/7	0.176399836007844	3	FACETS	0.67	0.6	0.745	0.223	0.2	0.249	INDETERMINATE	1	TRUE	0	0.31	3		862	1201	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143066998	143066998	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1561280492	NA	P-0049305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	93	289	0	ENST00000262992.4:c.1715C>G	p.Pro572Arg	p.P572R	ENST00000262992	NM_001101669.1	572	cCa/cGa	16/24	0.29841260075556	2	FACETS	0.929	0.835	1	0.929	0.835	1	CLONAL	2	TRUE	0	0.31	2		289	323	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38978707	38978707	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	72	315	0	ENST00000357387.3:c.799G>T	p.Asp267Tyr	p.D267Y	ENST00000357387	NM_152756.3	267	Gat/Tat	9/38	0.168716481265988	5	FACETS	0.773	0.678	0.875	0.516	0.452	0.584	INDETERMINATE	2	TRUE	2	0.31	5		315	440	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564587	86564587	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138308013	NA	P-0049305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	100	691	0	ENST00000274376.6:c.319G>C	p.Val107Leu	p.V107L	ENST00000274376	NM_002890.2	107	Gtt/Ctt	1/25	0.215237502741862	1	FACETS	0.725	0.647	0.807	0.725	0.647	0.807	SUBCLONAL	1	TRUE	0	0.31	1		691	752	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951932	2951932	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0049305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	201	465	0	ENST00000396946.4:c.3020-2A>T		p.X1007_splice	ENST00000396946	NM_032415.4	1007			0.302755211552765	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.31	3		465	720	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0049318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	21	248	1				ENST00000310581	NM_198253.2	-/1132			0.33092549975505	0	FACETS	0.707	0.565	0.858			1	SUBCLONAL	2	TRUE	0	0.327569160819194	0		249	61	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971153	21971153	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913383	NA	P-0049318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	104	463	0	ENST00000304494.5:c.205G>T	p.Glu69Ter	p.E69*	ENST00000304494	NM_000077.4	69	Gag/Tag	2/3	1	2	FACETS	0.962	0.893	1	1	0.992	1	CLONAL	4	TRUE	1	0.327569160819194	2		463	165	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	13	617	1	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.33092549975505	1	FACETS	0.402	0.288	0.541	0.402	0.288	0.541	SUBCLONAL	1	TRUE	0	0.327569160819194	1		618	165	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0049318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	20	502	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.33092549975505	1	FACETS	0.672	0.518	0.848	0.672	0.518	0.848	SUBCLONAL	1	TRUE	0	0.327569160819194	1		502	152	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539150	187539150	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs774570875	NA	P-0049318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	61	416	0	ENST00000441802.2:c.8590A>G	p.Met2864Val	p.M2864V	ENST00000441802	NM_005245.3	2864	Atg/Gtg	10/27	1	2	FACETS	1	0.909	1	1	0.981	1	CLONAL	2	TRUE	1	0.327569160819194	2		416	179	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	94	485	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.341114283209991	1	FACETS	0.943	0.842	1	0.943	0.842	1	CLONAL	1	FALSE	0	0.341114283209991	1		486	485	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	35	148	0				ENST00000310581	NM_198253.2	-/1132			0.251353068939468	1	FACETS	0.747	0.616	0.89	0.747	0.616	0.89	SUBCLONAL	1	FALSE	0	0.341114283209991	1		148	228	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141026	55141026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765680542	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	66	288	1	ENST00000257290.5:c.1672C>T	p.Arg558Cys	p.R558C	ENST00000257290	NM_006206.4	558	Cgc/Tgc	12/23	0.341114283209991	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	FALSE	0	0.341114283209991	1		289	302	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	92	508	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.251353068939468	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	0	0.341114283209991	1		508	353	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805071	43805071	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	126	566	0	ENST00000372470.3:c.521G>A	p.Arg174Lys	p.R174K	ENST00000372470	NM_005373.2	174	aGa/aAa	4/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.341114283209991	2		566	568	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175916375	175916375	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	32	203	0	ENST00000367669.3:c.2134G>A	p.Glu712Lys	p.E712K	ENST00000367669	NM_022457.5	712	Gag/Aag	19/20	0.251353068939468	1	FACETS	0.528	0.429	0.638	0.528	0.429	0.638	SUBCLONAL	1	FALSE	0	0.341114283209991	1		203	295	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206667325	206667325	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1553391465	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	115	570	0	ENST00000367120.3:c.2117+1G>A		p.X706_splice	ENST00000367120	NM_014002.3	706			0.251353068939468	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	FALSE	0	0.341114283209991	1		570	536	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612095	43612095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	69	455	1	ENST00000355710.3:c.2200G>A	p.Glu734Lys	p.E734K	ENST00000355710	NM_020975.4	734	Gaa/Aaa	12/20	0.251353068939468	1	FACETS	0.77	0.673	0.874	0.77	0.673	0.874	SUBCLONAL	1	FALSE	0	0.341114283209991	1		456	436	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405925	70405925	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	81	387	0	ENST00000373644.4:c.3439C>T	p.Gln1147Ter	p.Q1147*	ENST00000373644	NM_030625.2	1147	Cag/Tag	4/12	0.251353068939468	1	FACETS	0.906	0.801	1	0.906	0.801	1	CLONAL	1	FALSE	0	0.341114283209991	1		387	435	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316076	14316076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782490571	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	77	212	0	ENST00000256196.4:c.349C>T	p.Arg117Cys	p.R117C	ENST00000256196		117	Cgt/Tgt	4/6	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.341114283209991	2		212	356	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417841	32417841	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	103	428	0	ENST00000332351.3:c.1211A>G	p.Lys404Arg	p.K404R	ENST00000332351	NM_024426.4	404	aAg/aGg	7/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.341114283209991	2		428	484	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138885	64138886	+	missense_variant	Missense_Mutation	DNP	CG	CG	TT	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	79	523	2	ENST00000334205.4:c.2252_2253delinsTT	p.Pro751Leu	p.P751L	ENST00000334205	NM_003942.2	751	cCG/cTT	17/17	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	FALSE	1	0.341114283209991	2		525	449	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201675	67201675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	126	622	0	ENST00000312629.5:c.976C>T	p.Pro326Ser	p.P326S	ENST00000312629	NM_003952.2	326	Ccc/Tcc	12/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.341114283209991	2		622	574	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939807	71939807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	111	603	0	ENST00000298229.2:c.434C>T	p.Ser145Phe	p.S145F	ENST00000298229	NM_001567.3	145	tCt/tTt	4/28	1	2	FACETS	0.954	0.859	1	0.954	0.859	1	CLONAL	1	FALSE	1	0.341114283209991	2		603	682	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142524	119142524	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	85	356	1	ENST00000264033.4:c.523C>T	p.Gln175Ter	p.Q175*	ENST00000264033	NM_005188.3	175	Cag/Tag	3/16	1	2	FACETS	0.968	0.858	1	0.968	0.858	1	CLONAL	1	FALSE	1	0.341114283209991	2		357	515	SUCCESS
CBL	867	MSKCC	GRCh37	11	119146792	119146792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	114	365	0	ENST00000264033.4:c.955C>T	p.Pro319Ser	p.P319S	ENST00000264033	NM_005188.3	319	Cct/Tct	6/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.341114283209991	2		365	493	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149244	119149244	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	127	432	0	ENST00000264033.4:c.1252T>A	p.Phe418Ile	p.F418I	ENST00000264033	NM_005188.3	418	Ttc/Atc	9/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.341114283209991	2		432	573	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552630	18552630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200787716	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	55	390	0	ENST00000266497.5:c.2041C>T	p.Arg681Cys	p.R681C	ENST00000266497		681	Cgc/Tgc	14/31	0.167884352623218	0	FACETS	0.539	0.463	0.622			1	INDETERMINATE	1	FALSE	0	0.341114283209991	0		390	394	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650671	18650671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	33	306	0	ENST00000266497.5:c.2882G>A	p.Gly961Glu	p.G961E	ENST00000266497		961	gGa/gAa	20/31	0.167884352623218	0	FACETS	0.502	0.411	0.603			1	INDETERMINATE	1	FALSE	0	0.341114283209991	0		306	254	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18747504	18747504	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1299386474	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	64	272	1	ENST00000266497.5:c.3964+1G>A		p.X1322_splice	ENST00000266497		1322			0.167884352623218	0	FACETS	0.838	0.732	0.951			1	INDETERMINATE	1	FALSE	0	0.341114283209991	0		273	295	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245159	46245159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	52	398	0	ENST00000334344.6:c.3253C>T	p.Pro1085Ser	p.P1085S	ENST00000334344	NM_152641.2	1085	Cct/Tct	15/21	0.167884352623218	0	FACETS	0.522	0.445	0.605			1	INDETERMINATE	1	FALSE	0	0.341114283209991	0		398	385	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120806044	120806044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	74	541	0	ENST00000257552.2:c.133G>A	p.Glu45Lys	p.E45K	ENST00000257552	NM_002442.3	45	Gag/Aag	3/15	0.167884352623218	0	FACETS	0.617	0.542	0.698			1	INDETERMINATE	1	FALSE	0	0.341114283209991	0		541	463	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609704	28609704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	74	488	0	ENST00000241453.7:c.1525G>A	p.Gly509Arg	p.G509R	ENST00000241453	NM_004119.2	509	Ggg/Agg	12/24	0.341114283209991	1	FACETS	0.697	0.612	0.789	0.697	0.612	0.789	SUBCLONAL	1	FALSE	0	0.341114283209991	1		488	516	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012369	29012369	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	80	410	0	ENST00000282397.4:c.502A>G	p.Thr168Ala	p.T168A	ENST00000282397	NM_002019.4	168	Act/Gct	4/30	0.341114283209991	1	FACETS	0.766	0.676	0.862	0.766	0.676	0.862	SUBCLONAL	1	FALSE	0	0.341114283209991	1		410	508	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913021	32913021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	69	364	0	ENST00000380152.3:c.4529C>T	p.Pro1510Leu	p.P1510L	ENST00000380152		1510	cCc/cTc	11/27	1	2	FACETS	0.852	0.744	0.968	0.852	0.744	0.968	CLONAL	1	FALSE	1	0.341114283209991	2		364	475	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134628	41134628	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759316607	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	57	384	0	ENST00000379561.5:c.1000G>A	p.Glu334Lys	p.E334K	ENST00000379561	NM_002015.3	334	Gaa/Aaa	2/3	1	2	FACETS	0.846	0.728	0.973	0.846	0.728	0.973	CLONAL	1	FALSE	1	0.341114283209991	2		384	395	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335543	73335543	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	40	291	0	ENST00000377767.4:c.2628A>C	p.Glu876Asp	p.E876D	ENST00000377767	NM_014953.3	876	gaA/gaC	19/21	0.341114283209991	1	FACETS	0.599	0.499	0.709	0.599	0.499	0.709	SUBCLONAL	1	FALSE	0	0.341114283209991	1		291	325	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675046	40675046	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	122	527	1	ENST00000249776.8:c.10C>T	p.Pro4Ser	p.P4S	ENST00000249776	NM_033286.3	4	Ccc/Tcc	1/9	0.322129067575458	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	0	0.341114283209991	1		528	513	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059323	42059323	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	36	375	0	ENST00000219905.7:c.9043G>A	p.Ala3015Thr	p.A3015T	ENST00000219905	NM_001164273.1	3015	Gca/Aca	24/24	0.322129067575458	1	FACETS	0.437	0.359	0.523	0.437	0.359	0.523	SUBCLONAL	1	FALSE	0	0.341114283209991	1		375	401	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312765	91312765	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	59	346	0	ENST00000355112.3:c.2504C>A	p.Pro835His	p.P835H	ENST00000355112	NM_000057.2	835	cCc/cAc	12/22	0.322129067575458	1	FACETS	0.54	0.465	0.622	0.54	0.465	0.622	SUBCLONAL	1	FALSE	0	0.341114283209991	1		346	531	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396431	396431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	84	557	0	ENST00000262320.3:c.595C>T	p.Pro199Ser	p.P199S	ENST00000262320	NM_003502.3	199	Ccc/Tcc	2/11	0.167884352623218	0	FACETS	0.569	0.504	0.64			1	INDETERMINATE	1	FALSE	0	0.341114283209991	0		557	570	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644491	3644506	+	frameshift_variant	Frame_Shift_Del	DEL	AACTTGTGGGCGTAAA	AACTTGTGGGCGTAAA	-	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	75	674	0	ENST00000294008.3:c.2108_2123del	p.Leu703ProfsTer14	p.L703Pfs*14	ENST00000294008	NM_032444.2	703	cTTTACGCCCACAAGTTc/cc	10/15	0.167884352623218	0	FACETS	0.473	0.414	0.536			1	INDETERMINATE	1	FALSE	0	0.341114283209991	0		674	613	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857429	9857429	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	54	389	0	ENST00000330684.3:c.3972T>G	p.Phe1324Leu	p.F1324L	ENST00000330684	NM_001134407.1	1324	ttT/ttG	13/13	0.167884352623218	0	FACETS	0.615	0.528	0.71			1	INDETERMINATE	1	FALSE	0	0.341114283209991	0		389	339	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858487	9858487	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	42	436	0	ENST00000330684.3:c.2914A>G	p.Lys972Glu	p.K972E	ENST00000330684	NM_001134407.1	972	Aag/Gag	13/13	0.167884352623218	0	FACETS	0.447	0.374	0.528			1	INDETERMINATE	1	FALSE	0	0.341114283209991	0		436	363	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341269	89341269	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	40	313	0	ENST00000301030.4:c.7666A>C	p.Thr2556Pro	p.T2556P	ENST00000301030	NM_001256183.1	2556	Acg/Ccg	11/13	0.167884352623218	0	FACETS	0.652	0.546	0.768			1	INDETERMINATE	1	FALSE	0	0.341114283209991	0		313	237	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16056664	16056664	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs762815933	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	63	233	0	ENST00000268712.3:c.778A>G	p.Lys260Glu	p.K260E	ENST00000268712	NM_006311.3	260	Aaa/Gaa	7/46	0.341114283209991	1	FACETS	0.96	0.837	1	0.96	0.837	1	CLONAL	1	FALSE	0	0.341114283209991	1		233	319	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652988	29652988	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	62	358	0	ENST00000356175.3:c.4923G>A	p.Trp1641Ter	p.W1641*	ENST00000356175	NM_000267.3	1641	tgG/tgA	36/57	0.341114283209991	1	FACETS	0.876	0.762	1	0.876	0.762	1	CLONAL	1	FALSE	0	0.341114283209991	1		358	344	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435158	56435159	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	139	655	1	ENST00000407977.2:c.1978_1979delinsTT	p.Pro660Phe	p.P660F	ENST00000407977		660	CCc/TTc	9/10	0.250635999023753	4	FACETS	1	0.984	1	0.455	0.415	0.498	CLONAL	1	FALSE	1	0.341114283209991	4		656	800	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761145	59761145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878855154	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	141	419	0	ENST00000259008.2:c.3262C>T	p.His1088Tyr	p.H1088Y	ENST00000259008	NM_032043.2	1088	Cat/Tat	20/20	0.250635999023753	4	FACETS	1	0.985	1	0.471	0.429	0.515	CLONAL	1	FALSE	1	0.341114283209991	4		419	785	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007190	62007190	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	142	589	0	ENST00000392795.3:c.492G>A	p.Met164Ile	p.M164I	ENST00000392795	NM_001039933.1	164	atG/atA	4/6	0.250635999023753	4	FACETS	1	0.985	1	0.466	0.425	0.51	CLONAL	1	FALSE	1	0.341114283209991	4		589	798	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62009602	62009602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	149	587	1	ENST00000392795.3:c.20C>T	p.Ser7Phe	p.S7F	ENST00000392795	NM_001039933.1	7	tCt/tTt	1/6	0.250635999023753	4	FACETS	1	0.984	1	0.45	0.411	0.491	CLONAL	1	FALSE	1	0.341114283209991	4		588	867	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532532	63532533	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	141	722	1	ENST00000307078.5:c.2046_2047delinsTT	p.Pro683Ser	p.P683S	ENST00000307078	NM_004655.3	682	gaCCct/gaTTct	8/11	0.250635999023753	4	FACETS	1	0.982	1	0.434	0.395	0.475	CLONAL	1	FALSE	1	0.341114283209991	4		723	851	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545749	63545749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772279739	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	111	328	1	ENST00000307078.5:c.845C>T	p.Pro282Leu	p.P282L	ENST00000307078	NM_004655.3	282	cCt/cTt	3/11	0.250635999023753	4	FACETS	1	0.983	1	0.487	0.438	0.537	CLONAL	1	FALSE	1	0.341114283209991	4		329	598	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78765296	78765296	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	84	328	0	ENST00000306801.3:c.877G>A	p.Asp293Asn	p.D293N	ENST00000306801	NM_020761.2	293	Gat/Aat	7/34	0.250635999023753	4	FACETS	1	0.931	1	0.358	0.316	0.403	CLONAL	1	FALSE	1	0.341114283209991	4		328	615	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896617	78896617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	76	579	0	ENST00000306801.3:c.2614C>T	p.His872Tyr	p.H872Y	ENST00000306801	NM_020761.2	872	Cac/Tac	22/34	0.250635999023753	4	FACETS	0.907	0.795	1	0.302	0.265	0.343	CLONAL	1	FALSE	1	0.341114283209991	4		579	659	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2180755	2180755	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	125	515	0	ENST00000398665.3:c.125G>A	p.Arg42Gln	p.R42Q	ENST00000398665	NM_032482.2	42	cGa/cAa	2/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.341114283209991	2		515	675	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099207	4099207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	79	587	0	ENST00000262948.5:c.911C>T	p.Pro304Leu	p.P304L	ENST00000262948	NM_030662.3	304	cCc/cTc	7/11	1	2	FACETS	0.826	0.727	0.931	0.826	0.727	0.931	CLONAL	1	FALSE	1	0.341114283209991	2		587	561	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7141740	7141740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	121	554	1	ENST00000302850.5:c.2630C>T	p.Pro877Leu	p.P877L	ENST00000302850	NM_000208.2	877	cCc/cTc	13/22	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.341114283209991	2		555	640	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142914	7142914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	126	612	0	ENST00000302850.5:c.2455C>T	p.Arg819Cys	p.R819C	ENST00000302850	NM_000208.2	819	Cgc/Tgc	12/22	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	1	0.341114283209991	2		612	705	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172349	7172349	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	116	402	1	ENST00000302850.5:c.1220C>T	p.Ser407Phe	p.S407F	ENST00000302850	NM_000208.2	407	tCc/tTc	5/22	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.341114283209991	2		403	544	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11018819	11018819	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	162	599	0	ENST00000327064.4:c.451C>T	p.Gln151Ter	p.Q151*	ENST00000327064	NM_199141.1	151	Cag/Tag	3/16	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.341114283209991	2		599	686	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032084	11032084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	107	677	0	ENST00000327064.4:c.1649G>A	p.Arg550Gln	p.R550Q	ENST00000327064	NM_199141.1	550	cGg/cAg	15/16	1	2	FACETS	0.964	0.866	1	0.964	0.866	1	CLONAL	1	FALSE	1	0.341114283209991	2		677	651	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276875	15276875	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	97	560	0	ENST00000263388.2:c.5390C>T	p.Ser1797Phe	p.S1797F	ENST00000263388	NM_000435.2	1797	tCc/tTc	30/33	1	2	FACETS	0.893	0.797	0.995	0.893	0.797	0.995	CLONAL	1	FALSE	1	0.341114283209991	2		560	637	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210709	36210709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780868475	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	113	596	0	ENST00000222270.7:c.460C>T	p.Arg154Cys	p.R154C	ENST00000222270	NM_014727.1	154	Cgc/Tgc	3/37	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	FALSE	1	0.341114283209991	2		596	662	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212187	36212188	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	76	433	2	ENST00000222270.7:c.1938_1939delinsTT	p.Leu647Phe	p.L647F	ENST00000222270	NM_014727.1	646	ctCCtt/ctTTtt	3/37	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	FALSE	1	0.341114283209991	2		435	435	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213968	36213968	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	137	715	0	ENST00000222270.7:c.2794C>A	p.Pro932Thr	p.P932T	ENST00000222270	NM_014727.1	932	Cct/Act	6/37	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	FALSE	1	0.341114283209991	2		715	798	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224124	36224124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276663757	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	82	532	1	ENST00000222270.7:c.6674C>T	p.Ser2225Phe	p.S2225F	ENST00000222270	NM_014727.1	2225	tCc/tTc	28/37	1	2	FACETS	0.991	0.877	1	0.991	0.877	1	CLONAL	1	FALSE	1	0.341114283209991	2		533	485	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224142	36224142	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	105	618	1	ENST00000222270.7:c.6692C>T	p.Ser2231Phe	p.S2231F	ENST00000222270	NM_014727.1	2231	tCc/tTc	28/37	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.341114283209991	2		619	520	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919030	50919030	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	104	714	0	ENST00000440232.2:c.2767C>T	p.Pro923Ser	p.P923S	ENST00000440232	NM_002691.3	923	Ccc/Tcc	22/27	1	2	FACETS	0.973	0.872	1	0.973	0.872	1	CLONAL	1	FALSE	1	0.341114283209991	2		714	627	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978944	25978944	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	92	332	0	ENST00000435504.4:c.979C>T	p.Leu327Phe	p.L327F	ENST00000435504		327	Ctt/Ttt	10/13	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	FALSE	1	0.341114283209991	2		332	518	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015050	27015050	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	100	386	0	ENST00000335756.4:c.152T>C	p.Ile51Thr	p.I51T	ENST00000335756	NM_001809.3	51	aTc/aCc	2/5	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.341114283209991	2		386	494	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519775	29519775	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	110	501	0	ENST00000389048.3:c.1796C>T	p.Pro599Leu	p.P599L	ENST00000389048	NM_004304.4	599	cCt/cTt	9/29	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.341114283209991	2		501	513	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921740	111921740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	71	278	0	ENST00000393256.3:c.529G>A	p.Asp177Asn	p.D177N	ENST00000393256	NM_006538.4	177	Gac/Aac	4/4	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	FALSE	1	0.341114283209991	2		278	416	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566827	212566827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202247795	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	43	263	0	ENST00000342788.4:c.1354G>A	p.Glu452Lys	p.E452K	ENST00000342788	NM_005235.2	452	Gaa/Aaa	12/28	1	2	FACETS	0.733	0.615	0.862	0.733	0.615	0.862	SUBCLONAL	1	FALSE	1	0.341114283209991	2		263	344	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576877	212576877	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148183215	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	66	330	0	ENST00000342788.4:c.1022C>T	p.Ser341Leu	p.S341L	ENST00000342788	NM_005235.2	341	tCa/tTa	9/28	1	2	FACETS	0.868	0.755	0.988	0.868	0.755	0.988	CLONAL	1	FALSE	1	0.341114283209991	2		330	446	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812299	212812299	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	47	222	0	ENST00000342788.4:c.277C>T	p.Gln93Ter	p.Q93*	ENST00000342788	NM_005235.2	93	Cag/Tag	3/28	1	2	FACETS	0.765	0.648	0.894	0.765	0.648	0.894	SUBCLONAL	1	FALSE	1	0.341114283209991	2		222	360	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440144	220440144	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	166	644	0	ENST00000243786.2:c.997G>C	p.Gly333Arg	p.G333R	ENST00000243786	NM_002191.3	333	Ggg/Cgg	2/2	1	2	FACETS	0.764	0.704	0.825	1	0.99	1	SUBCLONAL	2	FALSE	1	0.341114283209991	2		644	637	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624933	9624933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	60	397	0	ENST00000353224.5:c.44C>T	p.Ser15Phe	p.S15F	ENST00000353224	NM_177990.2	15	tCc/tTc	3/10	1	2	FACETS	0.842	0.727	0.965	0.842	0.727	0.965	CLONAL	1	FALSE	1	0.341114283209991	2		397	418	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050356	37050356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	80	280	0	ENST00000231790.2:c.505C>T	p.Pro169Ser	p.P169S	ENST00000231790	NM_000249.3	169	Cca/Tca	6/19	1	2	FACETS	0.923	0.815	1	0.923	0.815	1	CLONAL	1	FALSE	1	0.341114283209991	2		280	508	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935108	49935108	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760946033	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	80	534	0	ENST00000296474.3:c.1891C>T	p.Arg631Trp	p.R631W	ENST00000296474	NM_002447.2	631	Cgg/Tgg	6/20	1	2	FACETS	0.907	0.801	1	0.907	0.801	1	CLONAL	1	FALSE	1	0.341114283209991	2		534	517	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939815	49939815	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	151	612	0	ENST00000296474.3:c.1228C>T	p.Pro410Ser	p.P410S	ENST00000296474	NM_002447.2	410	Ccg/Tcg	1/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.341114283209991	2		612	653	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247418	71247418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752297898	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	128	489	2	ENST00000318789.4:c.115G>A	p.Gly39Arg	p.G39R	ENST00000318789	NM_032682.5	39	Gga/Aga	6/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.341114283209991	2		491	619	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670282	134670282	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748807854	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	113	386	1	ENST00000398015.3:c.193G>A	p.Glu65Lys	p.E65K	ENST00000398015	NM_004441.4	65	Gag/Aag	3/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.341114283209991	2		387	508	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683510	182683510	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	88	376	0	ENST00000292782.4:c.35T>C	p.Val12Ala	p.V12A	ENST00000292782	NM_020640.2	12	gTt/gCt	2/7	1	2	FACETS	0.697	0.617	0.783	0.697	0.617	0.783	SUBCLONAL	1	FALSE	1	0.341114283209991	2		376	740	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167830	185167830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	104	325	0	ENST00000265026.3:c.1153C>T	p.Leu385Phe	p.L385F	ENST00000265026	NM_004721.4	385	Ctt/Ttt	6/14	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.341114283209991	2		325	419	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136873	55136873	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	26	327	0	ENST00000257290.5:c.1195G>A	p.Glu399Lys	p.E399K	ENST00000257290	NM_006206.4	399	Gaa/Aaa	8/23	0.341114283209991	1	FACETS	0.318	0.251	0.394	0.318	0.251	0.394	SUBCLONAL	1	FALSE	0	0.341114283209991	1		327	398	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139775	55139775	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777341485	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	117	513	0	ENST00000257290.5:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000257290	NM_006206.4	479	cGa/cAa	10/23	0.341114283209991	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	0	0.341114283209991	1		513	476	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31401661	31401661	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	98	304	1	ENST00000344624.3:c.4003C>T	p.Pro1335Ser	p.P1335S	ENST00000344624		1335	Ccc/Tcc	33/33	0.251353068939468	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	0	0.341114283209991	1		305	402	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873745	35873745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	37	244	0	ENST00000303115.3:c.701G>A	p.Ser234Asn	p.S234N	ENST00000303115	NM_002185.3	234	aGc/aAc	5/8	0.251353068939468	1	FACETS	0.569	0.471	0.679	0.569	0.471	0.679	SUBCLONAL	1	FALSE	0	0.341114283209991	1		244	316	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178545	56178545	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	33	230	0	ENST00000399503.3:c.3518A>G	p.His1173Arg	p.H1173R	ENST00000399503	NM_005921.1	1173	cAt/cGt	14/20	0.251353068939468	1	FACETS	0.567	0.463	0.683	0.567	0.463	0.683	SUBCLONAL	1	FALSE	0	0.341114283209991	1		230	283	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819792	170819792	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs934166729	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	92	303	0	ENST00000296930.5:c.431C>T	p.Ala144Val	p.A144V	ENST00000296930	NM_002520.6	144	gCc/gTc	5/11	0.251353068939468	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	FALSE	0	0.341114283209991	1		303	407	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032003	26032004	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	56	381	1	ENST00000244661.2:c.285_286delinsAA	p.Ala96Thr	p.A96T	ENST00000244661	NM_003537.3	95	gaGGct/gaAAct	1/1	0.341114283209991	2	FACETS	0.771	0.662	0.889	0.385	0.331	0.445	SUBCLONAL	1	FALSE	0	0.341114283209991	2		382	426	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679714	30679714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	124	535	0	ENST00000376406.3:c.2005C>T	p.Pro669Ser	p.P669S	ENST00000376406	NM_014641.2	669	Ccc/Tcc	5/15	0.341114283209991	2	FACETS	1	0.979	1	0.639	0.58	0.7	CLONAL	1	FALSE	0	0.341114283209991	2		535	569	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322271	31322271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	85	299	0	ENST00000412585.2:c.1078C>T	p.Leu360Phe	p.L360F	ENST00000412585	NM_005514.6	360	Ctc/Ttc	7/8	0.341114283209991	2	FACETS	1	0.969	1	0.628	0.558	0.701	CLONAL	1	FALSE	0	0.341114283209991	2		299	397	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554932	106554933	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	57	436	0	ENST00000369096.4:c.2049_2050delinsAA	p.Glu684Lys	p.E684K	ENST00000369096	NM_001198.3	683	cgGGag/cgAAag	7/7	0.167884352623218	0	FACETS	0.464	0.398	0.535			1	INDETERMINATE	1	FALSE	0	0.341114283209991	0		436	475	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958220	2958220	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	131	502	0	ENST00000396946.4:c.2512G>A	p.Ala838Thr	p.A838T	ENST00000396946	NM_032415.4	838	Gcc/Acc	19/25	0.341114283209991	3	FACETS	0.892	0.814	0.973	0.595	0.543	0.649	CLONAL	2	FALSE	0	0.341114283209991	3		502	504	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346284	152346284	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778698188	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	149	406	0	ENST00000359321.1:c.286C>T	p.Leu96Phe	p.L96F	ENST00000359321	NM_005431.1	96	Ctt/Ttt	3/3	0.106953495614928	3	FACETS	0.771	0.707	0.838	0.771	0.707	0.838	INDETERMINATE	2	FALSE	1	0.341114283209991	3		406	663	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285938	38285938	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913473	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	24	399	0	ENST00000425967.3:c.473C>T	p.Ser158Leu	p.S158L	ENST00000425967	NM_001174067.1	158	tCg/tTg	5/19	NA	2	FACETS	0.326	0.255	0.408			1	INDETERMINATE	1	FALSE	NA	0.341114283209991	2		399	432	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859789	117859789	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	50	271	0	ENST00000297338.2:c.1846C>T	p.Pro616Ser	p.P616S	ENST00000297338	NM_006265.2	616	Ccg/Tcg	14/14	0.341114283209991	1	FACETS	0.755	0.644	0.876	0.755	0.644	0.876	SUBCLONAL	1	FALSE	0	0.341114283209991	1		271	322	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319902	8319902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	62	264	0	ENST00000356435.5:c.5599G>A	p.Glu1867Lys	p.E1867K	ENST00000356435		1867	Gaa/Aaa	34/35	0.341114283209991	3	FACETS	0.685	0.592	0.787			1	SUBCLONAL	1	FALSE	NA	0.341114283209991	3		264	621	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331724	8331724	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763525789	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	333	397	0	ENST00000356435.5:c.5392C>T	p.Arg1798Ter	p.R1798*	ENST00000356435		1798	Cga/Tga	33/35	0.341114283209991	3	FACETS	1	0.991	1			1	CLONAL	3	FALSE	NA	0.341114283209991	3		397	663	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485307	8485307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	67	341	0	ENST00000356435.5:c.3073C>T	p.His1025Tyr	p.H1025Y	ENST00000356435		1025	Cat/Tat	18/35	0.341114283209991	3	FACETS	0.689	0.599	0.788			1	SUBCLONAL	1	FALSE	NA	0.341114283209991	3		341	667	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486041	8486041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	58	436	0	ENST00000356435.5:c.2776C>T	p.His926Tyr	p.H926Y	ENST00000356435		926	Cac/Tac	17/35	0.341114283209991	3	FACETS	0.618	0.53	0.714			1	SUBCLONAL	1	FALSE	NA	0.341114283209991	3		436	644	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500808	8500808	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376837190	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	83	381	0	ENST00000356435.5:c.2074G>A	p.Asp692Asn	p.D692N	ENST00000356435		692	Gat/Aat	13/35	0.341114283209991	3	FACETS	0.854	0.754	0.961			1	CLONAL	1	FALSE	NA	0.341114283209991	3		381	667	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518042	8518042	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	44	371	0	ENST00000356435.5:c.1349G>A	p.Gly450Glu	p.G450E	ENST00000356435		450	gGa/gAa	10/35	0.341114283209991	3	FACETS	0.499	0.418	0.589			1	SUBCLONAL	1	FALSE	NA	0.341114283209991	3		371	605	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518223	8518223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	43	355	0	ENST00000356435.5:c.1168G>A	p.Glu390Lys	p.E390K	ENST00000356435		390	Gaa/Aaa	10/35	0.341114283209991	3	FACETS	0.535	0.447	0.632			1	SUBCLONAL	1	FALSE	NA	0.341114283209991	3		355	552	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524996	8524996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	79	318	0	ENST00000356435.5:c.608G>A	p.Gly203Glu	p.G203E	ENST00000356435		203	gGa/gAa	7/35	0.341114283209991	3	FACETS	0.877	0.772	0.99			1	CLONAL	1	FALSE	NA	0.341114283209991	3		318	618	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563452	87563452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	92	452	0	ENST00000277120.3:c.1840G>A	p.Glu614Lys	p.E614K	ENST00000277120		614	Gag/Aag	16/19	0.251353068939468	1	FACETS	0.774	0.689	0.864	0.774	0.689	0.864	SUBCLONAL	1	FALSE	0	0.341114283209991	1		452	578	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93626926	93626926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	61	353	0	ENST00000375746.1:c.773C>T	p.Pro258Leu	p.P258L	ENST00000375746	NM_001174167.1	258	cCa/cTa	5/14	0.251353068939468	1	FACETS	0.626	0.541	0.718	0.626	0.541	0.718	SUBCLONAL	1	FALSE	0	0.341114283209991	1		353	474	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771828	135771828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779599439	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	78	537	0	ENST00000298552.3:c.3289C>T	p.Arg1097Cys	p.R1097C	ENST00000298552	NM_001162426.1	1097	Cgt/Tgt	23/23	0.251353068939468	1	FACETS	0.668	0.588	0.754	0.668	0.588	0.754	SUBCLONAL	1	FALSE	0	0.341114283209991	1		537	568	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351933	70351933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	142	288	0	ENST00000374080.3:c.4130C>T	p.Ser1377Phe	p.S1377F	ENST00000374080		1377	tCc/tTc	30/45	0.140529085062222	2	FACETS	0.854	0.791	0.918			1	INDETERMINATE	3	FALSE	NA	0.341114283209991	2		288	325	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938923	76938923	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	145	246	0	ENST00000373344.5:c.1825C>T	p.Pro609Ser	p.P609S	ENST00000373344	NM_000489.3	609	Cca/Tca	9/35	0.140529085062222	2	FACETS	1	0.98	1			1	INDETERMINATE	2	FALSE	NA	0.341114283209991	2		246	362	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611786	100611786	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	110	180	0	ENST00000308731.7:c.1335A>C	p.Glu445Asp	p.E445D	ENST00000308731	NM_000061.2	445	gaA/gaC	14/19	0.140529085062222	2	FACETS	0.86	0.788	0.933			1	INDETERMINATE	3	FALSE	NA	0.341114283209991	2		180	250	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533581	63533581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	402	824	1	ENST00000307078.5:c.1573C>T	p.Pro525Ser	p.P525S	ENST00000307078	NM_004655.3	525	Ccc/Tcc	6/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.71815122112754	2		825	1023	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750437	41750437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	222	557	0	ENST00000226382.2:c.191C>T	p.Ser64Phe	p.S64F	ENST00000226382	NM_003924.3	64	tCc/tTc	1/3	1	2	FACETS	0.891	0.833	0.95	0.891	0.833	0.95	CLONAL	1	TRUE	1	0.71815122112754	2		557	694	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678055	117678055	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	132	337	0	ENST00000368508.3:c.3878C>T	p.Ser1293Phe	p.S1293F	ENST00000368508	NM_002944.2	1293	tCc/tTc	25/43	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.71815122112754	2		337	348	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331980	81331980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1383506132	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	103	343	0	ENST00000222390.5:c.2104C>T	p.Arg702Cys	p.R702C	ENST00000222390	NM_000601.4	702	Cgt/Tgt	18/18	1	2	FACETS	0.829	0.75	0.912	0.829	0.75	0.912	CLONAL	1	TRUE	1	0.71815122112754	2		343	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577559	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	553	580	1	ENST00000269305.4:c.722_723delinsTT	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCC/tTT	7/11	1	2	FACETS	1	0.994	1	1	0.998	1	CLONAL	2	TRUE	1	0.71815122112754	2		581	719	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925411	114925411	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	258	563	0	ENST00000543371.1:c.1489C>T	p.Pro497Ser	p.P497S	ENST00000543371	NM_001198531.1	497	Ccg/Tcg	14/14	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.71815122112754	2		563	697	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281333	142281333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764261046	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	232	560	0	ENST00000350721.4:c.911C>T	p.Pro304Leu	p.P304L	ENST00000350721	NM_001184.3	304	cCc/cTc	4/47	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.71815122112754	2		560	600	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508628	106508628	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	226	606	1	ENST00000359195.3:c.622C>T	p.Pro208Ser	p.P208S	ENST00000359195	NM_002649.2	208	Ccg/Tcg	2/11	1	2	FACETS	0.976	0.914	1	0.976	0.914	1	CLONAL	1	TRUE	1	0.71815122112754	2		607	645	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961097	55961097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	274	627	0	ENST00000263923.4:c.2843G>A	p.Gly948Glu	p.G948E	ENST00000263923	NM_002253.2	948	gGg/gAg	21/30	1	2	FACETS	0.971	0.915	1	0.971	0.915	1	CLONAL	1	TRUE	1	0.71815122112754	2		627	786	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415701	152415701	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1455484428	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	222	570	0	ENST00000206249.3:c.1551G>A	p.Met517Ile	p.M517I	ENST00000206249	NM_000125.3	517	atG/atA	7/8	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.71815122112754	2		570	618	SUCCESS
APC	324	MSKCC	GRCh37	5	112173365	112173365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561574669	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	127	338	0	ENST00000257430.4:c.2074C>T	p.Pro692Ser	p.P692S	ENST00000257430	NM_000038.5	692	Cct/Tct	16/16	1	2	FACETS	0.921	0.843	1	0.921	0.843	1	CLONAL	1	TRUE	1	0.71815122112754	2		338	384	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156744	2156744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	245	712	1	ENST00000434045.2:c.178C>T	p.Pro60Ser	p.P60S	ENST00000434045	NM_001127598.1	60	Cca/Tca	3/5	1	2	FACETS	0.975	0.916	1	0.975	0.916	1	CLONAL	1	TRUE	1	0.71815122112754	2		713	700	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81979779	81979779	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	192	460	0	ENST00000359376.3:c.3482-1G>A		p.X1161_splice	ENST00000359376	NM_002661.3	1161			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.71815122112754	2		460	500	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543890	41543891	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	189	552	0	ENST00000263253.7:c.2181_2182delinsTT	p.Arg728Trp	p.R728W	ENST00000263253	NM_001429.3	727	ccCCgg/ccTTgg	12/31	1	2	FACETS	0.775	0.719	0.833	0.775	0.719	0.833	SUBCLONAL	1	TRUE	1	0.71815122112754	2		552	679	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867528	78867528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759154872	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	368	647	0	ENST00000306801.3:c.2264C>T	p.Ser755Phe	p.S755F	ENST00000306801	NM_020761.2	755	tCc/tTc	20/34	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.71815122112754	2		647	889	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042065	42042065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755927787	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	220	563	0	ENST00000219905.7:c.6260G>A	p.Arg2087Lys	p.R2087K	ENST00000219905	NM_001164273.1	2087	aGg/aAg	17/24	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.71815122112754	2		563	574	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524325	148524325	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs537373788	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	116	426	0	ENST00000320356.2:c.659C>T	p.Ser220Phe	p.S220F	ENST00000320356	NM_004456.4	220	tCt/tTt	7/20	1	2	FACETS	0.931	0.849	1	0.931	0.849	1	CLONAL	1	TRUE	1	0.71815122112754	2		426	347	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463556	25463556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	276	638	0	ENST00000264709.3:c.2126C>T	p.Pro709Leu	p.P709L	ENST00000264709	NM_175629.2	709	cCc/cTc	18/23	1	2	FACETS	0.964	0.909	1	0.964	0.909	1	CLONAL	1	TRUE	1	0.71815122112754	2		638	797	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459224	120459224	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	261	522	1	ENST00000256646.2:c.6121C>T	p.His2041Tyr	p.H2041Y	ENST00000256646	NM_024408.3	2041	Cat/Tat	34/34	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.71815122112754	2		523	704	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876520	35876520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	207	609	0	ENST00000303115.3:c.1312C>T	p.Leu438Phe	p.L438F	ENST00000303115	NM_002185.3	438	Ctt/Ttt	8/8	1	2	FACETS	0.967	0.903	1	0.967	0.903	1	CLONAL	1	TRUE	1	0.71815122112754	2		609	596	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257642	16257642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	237	506	1	ENST00000375759.3:c.4907C>T	p.Ser1636Phe	p.S1636F	ENST00000375759	NM_015001.2	1636	tCc/tTc	11/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.71815122112754	2		507	636	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112760193	112760193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	159	431	0	ENST00000369452.4:c.862C>T	p.Arg288Cys	p.R288C	ENST00000369452	NM_007373.3	288	Cgt/Tgt	4/9	1	2	FACETS	0.963	0.89	1	0.963	0.89	1	CLONAL	1	TRUE	1	0.71815122112754	2		431	460	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795056	45795056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	47	619	0	ENST00000450313.1:c.1572G>A	p.Met524Ile	p.M524I	ENST00000450313	NM_012222.2	524	atG/atA	16/16	1	2	FACETS	0.172	0.144	0.202	0.172	0.144	0.202	SUBCLONAL	1	TRUE	1	0.71815122112754	2		619	762	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998534	100998534	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	283	677	0	ENST00000325455.5:c.1268C>T	p.Pro423Leu	p.P423L	ENST00000325455	NM_001202474.3	423	cCc/cTc	1/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.71815122112754	2		677	736	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435663	18435663	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs539395234	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	103	319	0	ENST00000266497.5:c.648G>T	p.Met216Ile	p.M216I	ENST00000266497		216	atG/atT	1/31	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.71815122112754	2		319	267	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202785	133202785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	280	768	0	ENST00000320574.5:c.6449C>T	p.Ser2150Phe	p.S2150F	ENST00000320574	NM_006231.2	2150	tCc/tTc	46/49	1	2	FACETS	0.907	0.854	0.96	0.907	0.854	0.96	CLONAL	1	TRUE	1	0.71815122112754	2		768	860	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008313	29008313	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	140	351	0	ENST00000282397.4:c.558G>A	p.Trp186Ter	p.W186*	ENST00000282397	NM_002019.4	186	tgG/tgA	5/30	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.71815122112754	2		351	378	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900239	32900240	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	21	367	1	ENST00000380152.3:c.427_428delinsTT	p.Pro143Phe	p.P143F	ENST00000380152		143	CCt/TTt	5/27	1	2	FACETS	0.15	0.115	0.191	0.15	0.115	0.191	SUBCLONAL	1	TRUE	1	0.71815122112754	2		368	389	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281288	49281288	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	265	711	0	ENST00000282018.3:c.335G>A	p.Arg112Lys	p.R112K	ENST00000282018	NM_020377.2	112	aGg/aAg	1/1	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.71815122112754	2		711	738	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465498	99465498	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	227	540	0	ENST00000268035.6:c.2323T>C	p.Tyr775His	p.Y775H	ENST00000268035	NM_000875.3	775	Tac/Cac	11/21	1	2	FACETS	0.994	0.932	1	0.994	0.932	1	CLONAL	1	TRUE	1	0.71815122112754	2		540	636	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396432	396433	+	stop_gained	Nonsense_Mutation	INS	-	-	TAGGTGTTT	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	302	733	1	ENST00000262320.3:c.585_593dup	p.Thr197_Tyr198insTer	p.T197_Y198ins*	ENST00000262320	NM_003502.3	198	tat/taAAACACCTAt	2/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.71815122112754	2		734	829	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858666	9858666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	202	569	0	ENST00000330684.3:c.2735C>T	p.Ser912Phe	p.S912F	ENST00000330684	NM_001134407.1	912	tCc/tTc	13/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.71815122112754	2		569	536	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679306	29679306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1336098547	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	184	424	0	ENST00000356175.3:c.7426C>T	p.Pro2476Ser	p.P2476S	ENST00000356175	NM_000267.3	2476	Ccc/Tcc	50/57	1	2	FACETS	0.956	0.889	1	0.956	0.889	1	CLONAL	1	TRUE	1	0.71815122112754	2		424	536	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136111	11136111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	276	678	0	ENST00000358026.2:c.3095C>T	p.Thr1032Ile	p.T1032I	ENST00000358026	NM_001128849.1	1032	aCc/aTc	22/36	1	2	FACETS	0.996	0.939	1	0.996	0.939	1	CLONAL	1	TRUE	1	0.71815122112754	2		678	772	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945524	17945524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	196	614	0	ENST00000458235.1:c.2206C>T	p.Gln736Ter	p.Q736*	ENST00000458235	NM_000215.3	736	Caa/Taa	17/24	1	2	FACETS	0.963	0.897	1	0.963	0.897	1	CLONAL	1	TRUE	1	0.71815122112754	2		614	567	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082361	16082362	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	340	890	1	ENST00000281043.3:c.175_176delinsTT	p.Pro59Phe	p.P59F	ENST00000281043	NM_005378.4	59	CCc/TTc	2/3	1	2	FACETS	0.976	0.926	1	0.976	0.926	1	CLONAL	1	TRUE	1	0.71815122112754	2		891	970	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966138	25966138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	264	570	0	ENST00000435504.4:c.3068C>T	p.Thr1023Ile	p.T1023I	ENST00000435504		1023	aCc/aTc	13/13	1	2	FACETS	0.991	0.933	1	0.991	0.933	1	CLONAL	1	TRUE	1	0.71815122112754	2		570	742	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46608751	46608752	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	299	792	1	ENST00000263734.3:c.2062_2063delinsAA	p.Gly688Lys	p.G688K	ENST00000263734	NM_001430.4	688	GGg/AAg	13/16	1	2	FACETS	0.935	0.883	0.987	0.935	0.883	0.987	CLONAL	1	TRUE	1	0.71815122112754	2		793	891	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212615382	212615382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	177	427	0	ENST00000342788.4:c.604G>A	p.Glu202Lys	p.E202K	ENST00000342788	NM_005235.2	202	Gaa/Aaa	5/28	1	2	FACETS	0.887	0.822	0.953	0.887	0.822	0.953	CLONAL	1	TRUE	1	0.71815122112754	2		427	556	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019178	31019178	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	259	584	0	ENST00000375687.4:c.773T>A	p.Ile258Asn	p.I258N	ENST00000375687	NM_015338.5	258	aTt/aAt	9/13	1	2	FACETS	0.998	0.939	1	0.998	0.939	1	CLONAL	1	TRUE	1	0.71815122112754	2		584	723	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023952	31023952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757040754	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	312	678	0	ENST00000375687.4:c.3437C>T	p.Ser1146Leu	p.S1146L	ENST00000375687	NM_015338.5	1146	tCg/tTg	13/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.71815122112754	2		678	799	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710644	40710644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144244064	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	249	524	1	ENST00000373198.4:c.4207C>T	p.Arg1403Cys	p.R1403C	ENST00000373198	NM_133170.3	1403	Cgt/Tgt	31/32	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.71815122112754	2		525	666	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280281	1280282	+	missense_variant	Missense_Mutation	DNP	CT	CT	TG	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	320	786	0	ENST00000310581.5:c.1941_1942delinsCA	p.Arg647_Glu648delinsSerLys	p.R647_E648delinsSK	ENST00000310581	NM_198253.2	647	agAGaa/agCAaa	4/16	1	2	FACETS	0.954	0.903	1	0.954	0.903	1	CLONAL	1	TRUE	1	0.71815122112754	2		786	934	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950766	38950766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	95	285	0	ENST00000357387.3:c.3184C>T	p.Leu1062Phe	p.L1062F	ENST00000357387	NM_152756.3	1062	Ctt/Ttt	31/38	1	2	FACETS	0.995	0.899	1	0.995	0.899	1	CLONAL	1	TRUE	1	0.71815122112754	2		285	266	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068045	94068045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	135	350	0	ENST00000369303.4:c.917G>A	p.Gly306Asp	p.G306D	ENST00000369303	NM_004440.3	306	gGc/gAc	4/17	1	2	FACETS	0.897	0.823	0.974	0.897	0.823	0.974	CLONAL	1	TRUE	1	0.71815122112754	2		350	419	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426911	6426911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	169	468	0	ENST00000356142.4:c.104C>T	p.Thr35Ile	p.T35I	ENST00000356142	NM_018890.3	35	aCt/aTt	2/7	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.71815122112754	2		468	451	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55231511	55231511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1294381114	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	253	594	0	ENST00000275493.2:c.1717G>A	p.Gly573Arg	p.G573R	ENST00000275493	NM_005228.3	573	Gga/Aga	14/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.71815122112754	2		594	639	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873740	151873741	+	stop_gained	Nonsense_Mutation	DNP	CT	CT	TA	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	252	601	1	ENST00000262189.6:c.8797_8798delinsTA	p.Arg2933Ter	p.R2933*	ENST00000262189	NM_170606.2	2933	AGg/TAg	38/59	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.71815122112754	2		602	699	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342640	87342640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1192714938	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	37	496	0	ENST00000277120.3:c.925G>A	p.Gly309Ser	p.G309S	ENST00000277120		309	Ggc/Agc	9/19	0.715454039935821	2	FACETS	0.16	0.131	0.192	0.08	0.065	0.096	SUBCLONAL	1	TRUE	0	0.71815122112754	2		496	645	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239985	98239985	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	461	524	0	ENST00000331920.6:c.1348-1G>A		p.X450_splice	ENST00000331920	NM_000264.3	450			0.715454039935821	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.71815122112754	2		524	606	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933686	39933686	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	316	323	0	ENST00000378444.4:c.913C>T	p.Pro305Ser	p.P305S	ENST00000378444	NM_001123385.1	305	Cct/Tct	4/15	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.71815122112754	1		323	423	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295253	+	upstream_gene_variant	5'Flank	ONP	GAGG	GAGG	AGAA	novel	NA	P-0049328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	237	367	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.71815122112754	2		367	463	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0049353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	124	423	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.561862636880892	2		423	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0049353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	117	514	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.561862636880892	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.561862636880892	1		514	296	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs80338963	NA	P-0049353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	14	414	0	ENST00000342988.3:c.1081C>A	p.Arg361Ser	p.R361S	ENST00000342988	NM_005359.5	361	Cgc/Agc	9/12	0.468647603085562	0	FACETS	0.115	0.083	0.153			1	SUBCLONAL	1	TRUE	0	0.561862636880892	0		414	190	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	104	448	0	ENST00000304494.5:c.143C>A	p.Pro48Gln	p.P48Q	ENST00000304494	NM_000077.4	48	cCg/cAg	1/3	0.387351806641253	1	FACETS	0.822	0.744	0.901	0.822	0.744	0.901	CLONAL	1	TRUE	0	0.561862636880892	1		448	324	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375490	40375490	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	31	616	0	ENST00000293328.3:c.460G>T	p.Val154Phe	p.V154F	ENST00000293328	NM_012448.3	154	Gtc/Ttc	5/19	1	2	FACETS	0.235	0.19	0.287	0.235	0.19	0.287	SUBCLONAL	1	TRUE	1	0.561862636880892	2		616	469	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971185	21971207	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CGGGCGCTGCCCATCATCATGAC	CGGGCGCTGCCCATCATCATGAC	-	novel	NA	P-0049353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	76	519	0	ENST00000304494.5:c.151_173del	p.Val51SerfsTer61	p.V51Sfs*61	ENST00000304494	NM_000077.4	51	GTCATGATGATGGGCAGCGCCCGa/a	2/3	0.387351806641253	1	FACETS	0.646	0.572	0.724	0.646	0.572	0.724	SUBCLONAL	1	TRUE	0	0.561862636880892	1		519	301	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682895	241682895	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	231	487	0	ENST00000366560.3:c.128G>T	p.Arg43Leu	p.R43L	ENST00000366560	NM_000143.3	43	cGa/cTa	1/10	0.273806419683187	5	FACETS	1	0.966	1	0.699	0.654	0.744	INDETERMINATE	2	TRUE	2	0.587259107527344	5		487	706	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347792	347793	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0049354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	428	942	0	ENST00000262320.3:c.1712_1713dup	p.Gly572MetfsTer134	p.G572Mfs*134	ENST00000262320	NM_003502.3	571	-/AT	6/11	0.587259107527344	2	FACETS	0.873	0.838	0.908	0.873	0.838	0.908	CLONAL	2	TRUE	0	0.587259107527344	2		942	835	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021258	31021258	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	72	596	0	ENST00000375687.4:c.1257A>T	p.Arg419Ser	p.R419S	ENST00000375687	NM_015338.5	419	agA/agT	12/13	0.395790381057807	5	FACETS	0.6	0.523	0.683	0.2	0.174	0.228	SUBCLONAL	1	TRUE	2	0.587259107527344	5		596	769	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004720	150004720	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	126	414	0	ENST00000253339.5:c.1505G>T	p.Arg502Leu	p.R502L	ENST00000253339		502	cGt/cTt	3/7	0.485451173143173	3	FACETS	0.819	0.751	0.888	0.819	0.751	0.888	CLONAL	2	TRUE	1	0.587259107527344	3		414	339	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934287	68934287	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	78	115	0	ENST00000288368.4:c.353T>C	p.Ile118Thr	p.I118T	ENST00000288368	NM_024870.2	118	aTc/aCc	4/40	0.587259107527344	6	FACETS	0.938	0.832	1	0.469	0.416	0.525	CLONAL	2	TRUE	2	0.587259107527344	6		115	308	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967557	90967557	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	150	185	0	ENST00000265433.3:c.1351C>A	p.Gln451Lys	p.Q451K	ENST00000265433	NM_002485.4	451	Cag/Aag	10/16	0.587259107527344	6	FACETS	0.971	0.906	1	0.971	0.906	1	CLONAL	4	TRUE	2	0.587259107527344	6		185	286	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128268598	128268598	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749606853	NA	P-0049355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	108	566	2	ENST00000265960.3:c.1057C>T	p.Arg353Cys	p.R353C	ENST00000265960	NM_001006617.1	353	Cgc/Tgc	8/12	1	2	FACETS	0.689	0.618	0.764	0.689	0.618	0.764	SUBCLONAL	1	TRUE	1	0.382002995135041	2		568	821	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202872	16202872	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	150	453	0	ENST00000375759.3:c.580T>C	p.Phe194Leu	p.F194L	ENST00000375759	NM_015001.2	194	Ttt/Ctt	3/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.382002995135041	2		453	689	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650948	37650948	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0049355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	103	276	1	ENST00000447079.4:c.2419+1G>C		p.X807_splice	ENST00000447079	NM_015083.1	807			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.382002995135041	2		277	501	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902793	1902793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	148	552	4	ENST00000382891.5:c.412C>T	p.Leu138Phe	p.L138F	ENST00000382891	NM_133335.3	138	Ctc/Ttc	2/22	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.382002995135041	2		556	718	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900122	151900122	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1246539243	NA	P-0049355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	125	244	2	ENST00000262189.6:c.3989T>C	p.Leu1330Ser	p.L1330S	ENST00000262189	NM_170606.2	1330	tTa/tCa	26/59	0.207004425847773	3	FACETS	0.826	0.752	0.902	0.826	0.752	0.902	INDETERMINATE	2	TRUE	1	0.382002995135041	3		246	472	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133178	38133178	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	237	399	3	ENST00000317025.8:c.4295G>T	p.Gly1432Val	p.G1432V	ENST00000317025	NM_023034.1	1432	gGa/gTa	24/24	0.282329263337541	3	FACETS	0.97	0.908	1	0.97	0.908	1	CLONAL	2	TRUE	1	0.382002995135041	3		402	762	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849631	68849631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659244	NA	P-0049356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	243	502	0	ENST00000261769.5:c.1534G>A	p.Glu512Lys	p.E512K	ENST00000261769	NM_004360.3	512	Gag/Aag	10/16	1	2	FACETS	0.496	0.463	0.531	0.496	0.463	0.531	SUBCLONAL	1	TRUE	1	0.829072164580452	2		502	1181	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564540	86564560	+	inframe_deletion	In_Frame_Del	DEL	CTGCTGCTGGCGTAGCTGGTG	CTGCTGCTGGCGTAGCTGGTG	-	rs745572583	NA	P-0049356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	278	650	3	ENST00000274376.6:c.285_305del	p.Ala100_Ala106del	p.A100_A106del	ENST00000274376	NM_002890.2	91	aCTGCTGCTGGCGTAGCTGGTGct/act	1/25	1	2	FACETS	0.595	0.558	0.632	0.595	0.558	0.632	SUBCLONAL	1	TRUE	1	0.829072164580452	2		653	1128	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970872	21970989	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTACAAATTCTCAGATCATCAGTCCTCACCTGAGGGACCTTCCGCGGCATCTATGCGGGCATGGTTACTGCCTCTGGTGCCCCCCGCAGCCGCGCGCAGGTACCGTGCGACATCGCGA	GTACAAATTCTCAGATCATCAGTCCTCACCTGAGGGACCTTCCGCGGCATCTATGCGGGCATGGTTACTGCCTCTGGTGCCCCCCGCAGCCGCGCGCAGGTACCGTGCGACATCGCGA	-	novel	NA	P-0049356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	265	475	0	ENST00000304494.5:c.369_457+29del		p.X123_splice	ENST00000304494	NM_000077.4	123		2/3	0.829072164580452	1	FACETS	0.862	0.823	0.901	0.862	0.823	0.901	CLONAL	1	TRUE	0	0.829072164580452	1		475	434	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188215	10188215	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs869025642	NA	P-0049358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	66	380	0	ENST00000256474.2:c.358A>G	p.Arg120Gly	p.R120G	ENST00000256474	NM_000551.3	120	Aga/Gga	2/3	0.371922533042881	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.371922533042881	1		380	208	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441262	52441262	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	35	465	0	ENST00000460680.1:c.508T>A	p.Phe170Ile	p.F170I	ENST00000460680	NM_004656.3	170	Ttt/Att	7/17	0.371922533042881	1	FACETS	0.549	0.452	0.657	0.549	0.452	0.657	SUBCLONAL	1	TRUE	0	0.371922533042881	1		465	279	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52649366	52649372	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CTCAGCT	CTCAGCT	-	novel	NA	P-0049358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	16	378	0	ENST00000394830.3:c.1919_1924+1del		p.X640_splice	ENST00000394830	NM_018313.4	640		16/30	0.371922533042881	1	FACETS	0.556	0.415	0.721	0.556	0.415	0.721	SUBCLONAL	1	TRUE	0	0.371922533042881	1		378	126	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578497	7578498	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	T	novel	NA	P-0049358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	73	731	0	ENST00000269305.4:c.432_433delinsA	p.Leu145CysfsTer25	p.L145Cfs*25	ENST00000269305	NM_001126112.2	144	caGCtg/caAtg	5/11	0.371922533042881	3	FACETS	1	0.968	1	0.659	0.58	0.743	CLONAL	1	TRUE	1	0.371922533042881	3		731	353	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631839	90631839	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519906	NA	P-0049360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	133	556	0	ENST00000330062.3:c.514A>T	p.Arg172Trp	p.R172W	ENST00000330062	NM_002168.2	172	Agg/Tgg	4/11	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.420917462752927	2		556	628	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023247	27023265	+	frameshift_variant	Frame_Shift_Del	DEL	CGGAGCCGCCCGGCGGCGG	CGGAGCCGCCCGGCGGCGG	-	novel	NA	P-0049360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	12	169	0	ENST00000324856.7:c.356_374del	p.Glu119ValfsTer107	p.E119Vfs*107	ENST00000324856	NM_006015.4	118	aCGGAGCCGCCCGGCGGCGGc/ac	1/20	0.420917462752927	1	FACETS	0.23	0.161	0.314	0.23	0.161	0.314	SUBCLONAL	1	TRUE	0	0.420917462752927	1		169	196	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65311315	65311315	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	61	262	0	ENST00000342505.4:c.1996G>A	p.Val666Met	p.V666M	ENST00000342505	NM_002227.2	666	Gtg/Atg	15/25	1	2	FACETS	0.796	0.69	0.91	0.796	0.69	0.91	CLONAL	1	TRUE	1	0.420917462752927	2		262	364	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61712954	61712954	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	36	205	0	ENST00000401558.2:c.2457A>G	p.Ile819Met	p.I819M	ENST00000401558	NM_003400.3	819	atA/atG	20/25	1	2	FACETS	0.328	0.269	0.394	0.328	0.269	0.394	SUBCLONAL	1	TRUE	1	0.420917462752927	2		205	522	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442075	52442075	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	108	479	0	ENST00000460680.1:c.274G>A	p.Ala92Thr	p.A92T	ENST00000460680	NM_004656.3	92	Gca/Aca	5/17	0.420917462752927	1	FACETS	0.887	0.8	0.977	0.887	0.8	0.977	CLONAL	1	TRUE	0	0.420917462752927	1		479	457	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	141	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.480050908006215	2		148	442	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0049361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	112	209	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.480050908006215	2		209	320	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0049362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	140	581	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.779	0.708	0.854	1	0.987	1	SUBCLONAL	2	TRUE	1	0.17	2		581	1057	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119634952	119634952	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	23	233	0	ENST00000316626.5:c.547A>G	p.Lys183Glu	p.K183E	ENST00000316626		183	Aaa/Gaa	5/12	1	2	FACETS	0.588	0.458	0.74	0.588	0.458	0.74	SUBCLONAL	1	TRUE	1	0.17	2		233	460	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056175	26056175	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs61742489	NA	P-0049362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	41	432	0	ENST00000343677.2:c.482C>G	p.Pro161Arg	p.P161R	ENST00000343677	NM_005319.3	161	cCg/cGg	1/1	1	2	FACETS	0.653	0.542	0.776	0.653	0.542	0.776	SUBCLONAL	1	TRUE	1	0.17	2		432	739	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992997	68992997	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	36	309	0	ENST00000288368.4:c.1802G>T	p.Gly601Val	p.G601V	ENST00000288368	NM_024870.2	601	gGc/gTc	17/40	1	2	FACETS	0.835	0.686	1	0.835	0.686	1	CLONAL	1	TRUE	1	0.17	2		309	507	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685307	89685307	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123317	NA	P-0049363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	75	224	0	ENST00000371953.3:c.202T>C	p.Tyr68His	p.Y68H	ENST00000371953	NM_000314.4	68	Tac/Cac	3/9	0.444758984765169	2	FACETS	1	0.977	1	0.696	0.623	0.771	CLONAL	1	TRUE	0	0.572890953437202	2		224	188	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422239	422248	+	frameshift_variant	Frame_Shift_Del	DEL	TAGCGGTCCA	TAGCGGTCCA	-	novel	NA	P-0049363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	27	420	0	ENST00000399788.2:c.3010_3019del	p.Trp1004LysfsTer41	p.W1004Kfs*41	ENST00000399788	NM_001042603.1	1004	TGGACCGCTAaa/aa	20/28	1	2	FACETS	0.536	0.43	0.654	0.536	0.43	0.654	SUBCLONAL	1	TRUE	1	0.572890953437202	2		420	176	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577047	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0049363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	52	598	0	ENST00000269305.4:c.890_891dup	p.Glu298ThrfsTer48	p.E298Tfs*48	ENST00000269305	NM_001126112.2	297	-/AC	8/11	0.567728136426867	1	FACETS	0.712	0.616	0.813	0.712	0.616	0.813	SUBCLONAL	1	TRUE	0	0.572890953437202	1		598	182	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	180	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.923	0.861	0.986	0.923	0.861	0.986	CLONAL	1	TRUE	1	0.900416643584116	2		148	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0049365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	833	604	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	1	2	FACETS	1	0.995	1	1	0.999	1	CLONAL	2	TRUE	1	0.900416643584116	2		604	910	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245404	153245404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	328	405	0	ENST00000281708.4:c.1787C>T	p.Ser596Phe	p.S596F	ENST00000281708	NM_033632.3	596	tCt/tTt	11/12	1	2	FACETS	0.866	0.822	0.911	0.866	0.822	0.911	CLONAL	1	TRUE	1	0.900416643584116	2		405	841	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919244	48919244	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913296	NA	P-0049365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	53	68	0	ENST00000267163.4:c.409G>T	p.Glu137Ter	p.E137*	ENST00000267163	NM_000321.2	137	Gaa/Taa	4/27	0.900416643584116	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.900416643584116	1		68	61	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0049365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	339	243	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.900416643584116	2		243	724	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872380	45872380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	492	711	1	ENST00000391945.4:c.131C>T	p.Ser44Leu	p.S44L	ENST00000391945	NM_000400.3	44	tCa/tTa	3/23	1	2	FACETS	0.993	0.953	1	0.993	0.953	1	CLONAL	1	TRUE	1	0.900416643584116	2		712	1101	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445116	49445116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	421	676	0	ENST00000301067.7:c.2350G>A	p.Glu784Lys	p.E784K	ENST00000301067	NM_003482.3	784	Gag/Aag	10/54	1	2	FACETS	0.952	0.911	0.994	0.952	0.911	0.994	CLONAL	1	TRUE	1	0.900416643584116	2		676	982	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223202	2223202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	462	643	2	ENST00000326181.6:c.814C>T	p.Gln272Ter	p.Q272*	ENST00000326181	NM_032271.2	272	Cag/Tag	10/21	0.375492406983918	1	FACETS	0.661	0.636	0.686	0.661	0.636	0.686	INDETERMINATE	1	TRUE	0	0.900416643584116	1		645	854	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445170	49445170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	481	777	0	ENST00000301067.7:c.2296G>A	p.Glu766Lys	p.E766K	ENST00000301067	NM_003482.3	766	Gag/Aag	10/54	1	2	FACETS	0.97	0.93	1	0.97	0.93	1	CLONAL	1	TRUE	1	0.900416643584116	2		777	1102	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445140	49445140	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	463	733	0	ENST00000301067.7:c.2326G>T	p.Glu776Ter	p.E776*	ENST00000301067	NM_003482.3	776	Gag/Tag	10/54	1	2	FACETS	0.969	0.929	1	0.969	0.929	1	CLONAL	1	TRUE	1	0.900416643584116	2		733	1061	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262016	16262016	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	334	575	0	ENST00000375759.3:c.9281C>T	p.Ser3094Phe	p.S3094F	ENST00000375759	NM_015001.2	3094	tCc/tTc	11/15	1	2	FACETS	0.919	0.874	0.965	0.919	0.874	0.965	CLONAL	1	TRUE	1	0.900416643584116	2		575	807	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424385	49424385	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	373	536	0	ENST00000301067.7:c.13838A>G	p.Lys4613Arg	p.K4613R	ENST00000301067	NM_003482.3	4613	aAg/aGg	41/54	1	2	FACETS	0.927	0.883	0.971	0.927	0.883	0.971	CLONAL	1	TRUE	1	0.900416643584116	2		536	894	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445971	49445971	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	572	833	0	ENST00000301067.7:c.1495G>C	p.Glu499Gln	p.E499Q	ENST00000301067	NM_003482.3	499	Gag/Cag	10/54	1	2	FACETS	0.99	0.954	1	0.99	0.954	1	CLONAL	1	TRUE	1	0.900416643584116	2		833	1283	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667847	37667847	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	323	479	0	ENST00000447079.4:c.2733del	p.Glu911AspfsTer7	p.E911Dfs*7	ENST00000447079	NM_015083.1	911	gAa/ga	8/14	1	2	FACETS	0.946	0.899	0.994	0.946	0.899	0.994	CLONAL	1	TRUE	1	0.900416643584116	2		479	758	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44527592	44527592	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	252	442	0	ENST00000291552.4:c.13C>G	p.Leu5Val	p.L5V	ENST00000291552	NM_006758.2	5	Ctg/Gtg	1/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.900416643584116	2		442	532	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568540	41568540	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	266	329	0	ENST00000263253.7:c.4490G>T	p.Ser1497Ile	p.S1497I	ENST00000263253	NM_001429.3	1497	aGt/aTt	28/31	0.900416643584116	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.900416643584116	1		329	315	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652025	36652025	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	257	778	0	ENST00000244741.5:c.147G>C	p.Trp49Cys	p.W49C	ENST00000244741	NM_000389.4	49	tgG/tgC	2/3	0.492996892298203	1	FACETS	0.337	0.316	0.359	0.337	0.316	0.359	INDETERMINATE	1	TRUE	0	0.900416643584116	1		778	931	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652319	36652319	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	165	565	0	ENST00000244741.5:c.441G>T	p.Met147Ile	p.M147I	ENST00000244741	NM_000389.4	147	atG/atT	2/3	0.492996892298203	1	FACETS	0.3	0.276	0.325	0.3	0.276	0.325	INDETERMINATE	1	TRUE	0	0.900416643584116	1		565	671	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272085	38272085	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	432	651	0	ENST00000425967.3:c.2133G>C	p.Gln711His	p.Q711H	ENST00000425967	NM_001174067.1	711	caG/caC	16/19	0.375492406983918	1	FACETS	0.645	0.619	0.67	0.645	0.619	0.67	INDETERMINATE	1	TRUE	0	0.900416643584116	1		651	818	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168743	32168743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	202	661	0	ENST00000375023.3:c.4180C>T	p.Pro1394Ser	p.P1394S	ENST00000375023	NM_004557.3	1394	Cct/Tct	23/30	0.335033420208626	2	FACETS	0.661	0.614	0.709	0.33	0.307	0.355	INDETERMINATE	1	TRUE	0	0.820762581529313	2		661	745	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168689	32168689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	237	645	0	ENST00000375023.3:c.4234C>T	p.Leu1412Phe	p.L1412F	ENST00000375023	NM_004557.3	1412	Ctt/Ttt	23/30	0.335033420208626	2	FACETS	0.722	0.676	0.769	0.361	0.338	0.385	INDETERMINATE	1	TRUE	0	0.820762581529313	2		645	800	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168725	32168726	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0049366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	169	663	1	ENST00000375023.3:c.4197_4198delinsTT	p.Arg1400Cys	p.R1400C	ENST00000375023	NM_004557.3	1399	tcCCgc/tcTTgc	23/30	0.335033420208626	2	FACETS	0.576	0.531	0.623	0.288	0.265	0.312	INDETERMINATE	1	TRUE	0	0.820762581529313	2		664	715	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168620	32168627	+	missense_variant	Missense_Mutation	ONP	GAGGGTGG	GAGGGTGG	AAAGGTAA	novel	NA	P-0049366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	188	567	0	ENST00000375023.3:c.4296_4303delinsTTACCTTT	p.His1433_His1435delinsTyrLeuTyr	p.H1433_H1435delinsYLY	ENST00000375023	NM_004557.3	1432	gtCCACCCTCat/gtTTACCTTTat	23/30	0.335033420208626	2	FACETS	0.643	0.595	0.691	0.321	0.297	0.346	INDETERMINATE	1	TRUE	0	0.820762581529313	2		567	713	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168717	32168719	+	missense_variant	Missense_Mutation	TNP	GGG	GGG	AGA	novel	NA	P-0049366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	169	638	0	ENST00000375023.3:c.4204_4206delinsTCT	p.Pro1402Ser	p.P1402S	ENST00000375023	NM_004557.3	1402	CCC/TCT	23/30	0.335033420208626	2	FACETS	0.569	0.524	0.615	0.284	0.262	0.308	INDETERMINATE	1	TRUE	0	0.820762581529313	2		638	724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0049367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	143	485	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.405279379050222	3	FACETS	0.577	0.524	0.633	0.192	0.174	0.211	SUBCLONAL	1	TRUE	0	0.444738427398066	3		486	1362	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0049367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	543	248	1				ENST00000310581	NM_198253.2	-/1132			0.444738427398066	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	4	TRUE	0	0.444738427398066	4		249	794	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519893	NA	P-0049367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	307	595	0	ENST00000267101.3:c.310G>T	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ttg	3/28	0.327829383121004	3	FACETS	1	0.989	1	0.602	0.567	0.639	CLONAL	1	TRUE	1	0.444738427398066	3		595	1401	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0049367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	121	229	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.444738427398066	2		229	509	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922321	178922321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	129	324	0	ENST00000263967.3:c.1090G>A	p.Gly364Arg	p.G364R	ENST00000263967	NM_006218.2	364	Gga/Aga	6/21	0.327829383121004	3	FACETS	1	0.949	1	0.532	0.483	0.584	CLONAL	1	TRUE	1	0.444738427398066	3		324	666	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953785	48953785	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0049367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	141	167	0	ENST00000267163.4:c.1388C>G	p.Ser463Ter	p.S463*	ENST00000267163	NM_000321.2	463	tCa/tGa	14/27	0.299982346438434	4	FACETS	0.96	0.881	1	0.96	0.881	1	CLONAL	2	TRUE	2	0.444738427398066	4		167	477	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101829	11101829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	337	535	0	ENST00000358026.2:c.1249C>T	p.Arg417Cys	p.R417C	ENST00000358026	NM_001128849.1	417	Cgc/Tgc	8/36	0.327829383121004	3	FACETS	1	0.993	1	0.657	0.62	0.695	CLONAL	1	TRUE	1	0.444738427398066	3		535	1410	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519933	66519933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	164	416	1	ENST00000358598.2:c.416C>T	p.Ser139Leu	p.S139L	ENST00000358598	NM_212471.2	139	tCa/tTa	4/11	0.327829383121004	3	FACETS	1	0.972	1	0.562	0.516	0.61	CLONAL	1	TRUE	1	0.444738427398066	3		417	802	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030434	49030434	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778833	NA	P-0049367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	234	348	0	ENST00000267163.4:c.1909C>T	p.Gln637Ter	p.Q637*	ENST00000267163	NM_000321.2	637	Cag/Tag	19/27	0.299982346438434	4	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	2	0.444738427398066	4		348	758	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0049367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	472	554	0	ENST00000269305.4:c.920-2A>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.405279379050222	3	FACETS	1	0.987	1	0.715	0.684	0.746	CLONAL	2	TRUE	0	0.444738427398066	3		554	1210	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519895	NA	P-0049367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	176	402	0	ENST00000281708.4:c.1394G>T	p.Arg465Leu	p.R465L	ENST00000281708	NM_033632.3	465	cGt/cTt	9/12	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.444738427398066	2		402	644	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857958	9857958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140536516	NA	P-0049367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	229	481	0	ENST00000330684.3:c.3443C>T	p.Pro1148Leu	p.P1148L	ENST00000330684	NM_001134407.1	1148	cCg/cTg	13/13	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.444738427398066	2		481	983	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760711	59760711	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	266	345	0	ENST00000259008.2:c.3696G>C	p.Lys1232Asn	p.K1232N	ENST00000259008	NM_032043.2	1232	aaG/aaC	20/20	0.327829383121004	3	FACETS	0.858	0.807	0.911	0.858	0.807	0.911	CLONAL	2	TRUE	1	0.444738427398066	3		345	852	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992753	72992753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	138	628	0	ENST00000268489.5:c.1292C>T	p.Ser431Leu	p.S431L	ENST00000268489	NM_006885.3	431	tCa/tTa	2/10	1	2	FACETS	0.568	0.516	0.623	0.568	0.516	0.623	SUBCLONAL	1	TRUE	1	0.444738427398066	2		628	1092	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699358	117699358	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	390	491	0	ENST00000369458.3:c.283G>A	p.Glu95Lys	p.E95K	ENST00000369458	NM_024626.3	95	Gaa/Aaa	3/6	0.327829383121004	3	FACETS	0.978	0.931	1	0.978	0.931	1	CLONAL	2	TRUE	1	0.444738427398066	3		491	1096	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870322	155870322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	337	496	0	ENST00000368323.3:c.517G>A	p.Asp173Asn	p.D173N	ENST00000368323	NM_006912.5	173	Gat/Aat	6/6	0.327829383121004	3	FACETS	0.937	0.889	0.987	0.937	0.889	0.987	CLONAL	2	TRUE	1	0.444738427398066	3		496	988	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870355	155870355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	356	465	0	ENST00000368323.3:c.484G>A	p.Glu162Lys	p.E162K	ENST00000368323	NM_006912.5	162	Gag/Aag	6/6	0.327829383121004	3	FACETS	0.983	0.934	1	0.983	0.934	1	CLONAL	2	TRUE	1	0.444738427398066	3		465	995	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982968	201982969	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	369	653	0	ENST00000359651.3:c.820dup	p.His274ProfsTer27	p.H274Pfs*27	ENST00000359651		273	acc/aCcc	7/8	0.327829383121004	3	FACETS	1	0.994	1	0.691	0.655	0.729	CLONAL	1	TRUE	1	0.444738427398066	3		653	1467	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425895	49425895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750441480	NA	P-0049367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	375	747	0	ENST00000301067.7:c.12593G>A	p.Arg4198Gln	p.R4198Q	ENST00000301067	NM_003482.3	4198	cGa/cAa	39/54	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.444738427398066	2		747	1326	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245293	133245293	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	154	667	0	ENST00000320574.5:c.1954G>C	p.Ala652Pro	p.A652P	ENST00000320574	NM_006231.2	652	Gct/Cct	18/49	0.299794432292738	2	FACETS	0.518	0.472	0.566	0.259	0.236	0.283	SUBCLONAL	1	TRUE	0	0.444738427398066	2		667	1337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578507	7578508	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0049367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1627	214	707	1	ENST00000269305.4:c.422_423delinsTT	p.Cys141Phe	p.C141F	ENST00000269305	NM_001126112.2	141	tGC/tTT	5/11	0.405279379050222	3	FACETS	0.639	0.591	0.689	0.213	0.197	0.23	SUBCLONAL	1	TRUE	0	0.444738427398066	3		708	1841	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760845	59760845	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	297	447	0	ENST00000259008.2:c.3562G>T	p.Glu1188Ter	p.E1188*	ENST00000259008	NM_032043.2	1188	Gag/Tag	20/20	0.327829383121004	3	FACETS	0.913	0.862	0.965	0.913	0.862	0.965	CLONAL	2	TRUE	1	0.444738427398066	3		447	894	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761103	59761103	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	324	486	0	ENST00000259008.2:c.3304G>C	p.Asp1102His	p.D1102H	ENST00000259008	NM_032043.2	1102	Gac/Cac	20/20	0.327829383121004	3	FACETS	0.941	0.891	0.992	0.941	0.891	0.992	CLONAL	2	TRUE	1	0.444738427398066	3		486	946	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761139	59761139	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	323	483	0	ENST00000259008.2:c.3268G>C	p.Glu1090Gln	p.E1090Q	ENST00000259008	NM_032043.2	1090	Gaa/Caa	20/20	0.327829383121004	3	FACETS	0.938	0.888	0.989	0.938	0.888	0.989	CLONAL	2	TRUE	1	0.444738427398066	3		483	946	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211489	36211489	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1398096625	NA	P-0049367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	68	432	0	ENST00000222270.7:c.1240C>T	p.Pro414Ser	p.P414S	ENST00000222270	NM_014727.1	414	Cct/Tct	3/37	0.327829383121004	3	FACETS	0.426	0.37	0.488	0.213	0.185	0.244	SUBCLONAL	1	TRUE	1	0.444738427398066	3		432	877	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220981	36220981	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	298	527	0	ENST00000222270.7:c.5031C>G	p.Asp1677Glu	p.D1677E	ENST00000222270	NM_014727.1	1677	gaC/gaG	23/37	0.327829383121004	3	FACETS	1	0.992	1	0.665	0.625	0.705	CLONAL	1	TRUE	1	0.444738427398066	3		527	1232	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918303	44918304	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0049367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	247	187	0	ENST00000377967.4:c.929_930del	p.Ser310TyrfsTer2	p.S310Yfs*2	ENST00000377967	NM_021140.2	310	TCt/t	11/29	0.358772369269142	2	FACETS	0.903	0.86	0.946			1	CLONAL	3	TRUE	NA	0.444738427398066	2		187	410	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200052	123200062	+	frameshift_variant	Frame_Shift_Del	DEL	ATTTGCTTGTA	ATTTGCTTGTA	-	novel	NA	P-0049367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	210	172	0	ENST00000218089.9:c.2127_2137del	p.Phe709LeufsTer15	p.F709Lfs*15	ENST00000218089	NM_001042749.1	708	ttATTTGCTTGTAat/ttat	22/35	0.358772369269142	2	FACETS	0.954	0.906	1			1	CLONAL	3	TRUE	NA	0.444738427398066	2		172	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0049368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	183	583	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	NA	2	FACETS	0.757	0.699	0.817			1	INDETERMINATE	2	TRUE	NA	0.292705952717463	2		583	826	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477837	140477851	+	inframe_deletion	In_Frame_Del	DEL	TAGGTGCTGTCACAT	TAGGTGCTGTCACAT	-	novel	NA	P-0049368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	94	442	0	ENST00000288602.6:c.1457_1471del	p.Asn486_Pro490del	p.N486_P490del	ENST00000288602	NM_004333.4	486	aATGTGACAGCACCTAca/aca	12/18	1	2	FACETS	0.942	0.838	1	0.942	0.838	1	CLONAL	1	TRUE	1	0.292705952717463	2		442	682	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459852	149459852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	58	784	1	ENST00000286301.3:c.355G>A	p.Glu119Lys	p.E119K	ENST00000286301	NM_005211.3	119	Gag/Aag	4/22	1	2	FACETS	0.429	0.368	0.497	0.429	0.368	0.497	SUBCLONAL	1	TRUE	1	0.292705952717463	2		785	923	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130450	29130464	+	inframe_deletion	In_Frame_Del	DEL	TCCTCAGGTTCTTGG	TCCTCAGGTTCTTGG	-	rs587780181	NA	P-0049368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	62	604	0	ENST00000328354.6:c.246_260del	p.Asp82_Glu86del	p.D82_E86del	ENST00000328354	NM_007194.3	82	gaCCAAGAACCTGAGGAg/gag	2/15	0.170666109498788	2	FACETS	0.597	0.515	0.686	0.298	0.257	0.343	INDETERMINATE	1	TRUE	0	0.292705952717463	2		604	710	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115974	8115975	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0049369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	234	316	0	ENST00000346208.3:c.1321_1322del	p.Ala441HisfsTer65	p.A441Hfs*65	ENST00000346208		440	acCGcc/accc	6/6	1	2	FACETS	0.759	0.713	0.804	1	0.993	1	SUBCLONAL	2	TRUE	1	0.531835818283033	2		316	580	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250861	10250861	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779029407	NA	P-0049369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	182	590	0	ENST00000340748.4:c.3619C>T	p.Arg1207Cys	p.R1207C	ENST00000340748		1207	Cgc/Tgc	32/40	0.385949619030271	0	FACETS	0.537	0.498	0.577			1	SUBCLONAL	1	TRUE	0	0.531835818283033	0		590	597	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62293939	62293939	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1420390084	NA	P-0049369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1329	328	668	0	ENST00000360203.5:c.436A>C	p.Ile146Leu	p.I146L	ENST00000360203	NM_001283009.1	146	Atc/Ctc	5/35	0.468821262599274	5	FACETS	1	0.992	1			1	CLONAL	1	TRUE	NA	0.531835818283033	5		668	1657	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275114	41275114	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	93	309	0	ENST00000349496.5:c.1280T>C	p.Leu427Pro	p.L427P	ENST00000349496	NM_001904.3	427	cTc/cCc	9/15	0.326456748775658	1	FACETS	0.608	0.544	0.676	0.608	0.544	0.676	SUBCLONAL	1	TRUE	0	0.531835818283033	1		309	422	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	44	431	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.15	2		431	547	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0049370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	39	578	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	1	2	FACETS	0.78	0.645	0.931	0.78	0.645	0.931	CLONAL	1	TRUE	1	0.15	2		578	667	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472523	88472523	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1419472052	NA	P-0049370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	74	568	0	ENST00000360948.2:c.2032C>T	p.Arg678Ter	p.R678*	ENST00000360948	NM_001012338.2	678	Cga/Tga	16/19	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.15	2		568	836	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873491	45873491	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0049370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	36	508	0	ENST00000391945.4:c.6-1G>T		p.X2_splice	ENST00000391945	NM_000400.3	2			1	2	FACETS	0.812	0.666	0.976	0.812	0.666	0.976	CLONAL	1	TRUE	1	0.15	2		508	591	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466908	57466910	+	inframe_deletion	In_Frame_Del	DEL	CTG	CTG	-	rs774711025	NA	P-0049370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	14	191	0	ENST00000371085.3:c.136_138del	p.Leu46del	p.L46del	ENST00000371085	NM_000516.4	43	CTG/-	1/13	1	2	FACETS	0.686	0.495	0.918	0.686	0.495	0.918	SUBCLONAL	1	TRUE	1	0.15	2		191	272	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126085	2126085	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs999523698	NA	P-0049370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	60	582	0	ENST00000219476.3:c.2656G>T	p.Val886Leu	p.V886L	ENST00000219476	NM_000548.3	886	Gtg/Ttg	24/42	1	2	FACETS	0.939	0.807	1	0.939	0.807	1	CLONAL	1	TRUE	1	0.15	2		582	852	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217867	2217867	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	46	690	1	ENST00000398665.3:c.2641G>T	p.Val881Phe	p.V881F	ENST00000398665	NM_032482.2	881	Gtc/Ttc	22/28	1	2	FACETS	0.691	0.58	0.814	0.691	0.58	0.814	SUBCLONAL	1	TRUE	1	0.15	2		691	888	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239961	98239961	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	42	429	0	ENST00000331920.6:c.1371G>T	p.Met457Ile	p.M457I	ENST00000331920	NM_000264.3	457	atG/atT	10/24	1	2	FACETS	0.841	0.701	0.997	0.841	0.701	0.997	CLONAL	1	TRUE	1	0.15	2		429	666	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	110	424	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.706	0.636	0.78	0.706	0.636	0.78	SUBCLONAL	1	TRUE	1	0.53	2		424	588	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	131	549	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.852	0.776	0.932	0.852	0.776	0.932	CLONAL	1	TRUE	1	0.53	2		549	580	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247028	53247028	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	179	457	1	ENST00000375401.3:c.472G>A	p.Glu158Lys	p.E158K	ENST00000375401	NM_004187.3	158	Gaa/Aaa	4/26	1	2	FACETS	0.805	0.743	0.87	0.805	0.743	0.87	CLONAL	1	TRUE	1	0.53	2		458	839	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306676	41306676	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754008236	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	163	729	0	ENST00000373198.4:c.983G>A	p.Arg328His	p.R328H	ENST00000373198	NM_133170.3	328	cGc/cAc	7/32	1	2	FACETS	0.897	0.825	0.971	0.897	0.825	0.971	CLONAL	1	TRUE	1	0.53	2		729	686	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087961	27087961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	159	485	0	ENST00000324856.7:c.2248C>T	p.Arg750Ter	p.R750*	ENST00000324856	NM_006015.4	750	Cga/Tga	6/20	1	2	FACETS	0.946	0.871	1	0.946	0.871	1	CLONAL	1	TRUE	1	0.53	2		485	634	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	159	480	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.84	0.772	0.911	0.84	0.772	0.911	CLONAL	1	TRUE	1	0.53	2		480	714	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748596	40748596	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754546663	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	119	441	0	ENST00000373198.4:c.2920C>T	p.Arg974Trp	p.R974W	ENST00000373198	NM_133170.3	974	Cgg/Tgg	21/32	1	2	FACETS	0.877	0.795	0.962	0.877	0.795	0.962	CLONAL	1	TRUE	1	0.53	2		441	512	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692835	89692835	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs57374291	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	59	124	0	ENST00000371953.3:c.319G>T	p.Asp107Tyr	p.D107Y	ENST00000371953	NM_000314.4	107	Gat/Tat	5/9	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.53	2		124	171	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677876	47677876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	114	531	1	ENST00000347630.2:c.989C>T	p.Ser330Leu	p.S330L	ENST00000347630	NM_001007230.1	330	tCg/tTg	11/11	1	2	FACETS	0.772	0.698	0.851	0.772	0.698	0.851	SUBCLONAL	1	TRUE	1	0.53	2		532	557	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258036	123258036	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519045	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	140	455	0	ENST00000358487.5:c.1645A>C	p.Asn549His	p.N549H	ENST00000358487	NM_000141.4	549	Aat/Cat	12/18	1	2	FACETS	0.9	0.823	0.98	0.9	0.823	0.98	CLONAL	1	TRUE	1	0.53	2		455	587	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812335	212812335	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	61	207	0	ENST00000342788.4:c.241C>T	p.Arg81Ter	p.R81*	ENST00000342788	NM_005235.2	81	Cga/Tga	3/28	1	2	FACETS	0.84	0.732	0.956	0.84	0.732	0.956	CLONAL	1	TRUE	1	0.53	2		207	274	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698180	47698180	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63751411	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	23	214	0	ENST00000233146.2:c.1738G>T	p.Glu580Ter	p.E580*	ENST00000233146	NM_000251.2	580	Gaa/Taa	11/16	1	2	FACETS	0.223	0.173	0.28	0.223	0.173	0.28	SUBCLONAL	1	TRUE	1	0.53	2		214	390	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396589	396589	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	194	680	1	ENST00000262320.3:c.437G>A	p.Arg146Gln	p.R146Q	ENST00000262320	NM_003502.3	146	cGa/cAa	2/11	1	2	FACETS	0.987	0.916	1	0.987	0.916	1	CLONAL	1	TRUE	1	0.53	2		681	742	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249847	133249847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	141	452	0	ENST00000320574.5:c.1376C>T	p.Ser459Phe	p.S459F	ENST00000320574	NM_006231.2	459	tCt/tTt	14/49	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.53	2		452	529	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546725	9546725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210292896	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	94	450	0	ENST00000353224.5:c.1297C>T	p.Arg433Trp	p.R433W	ENST00000353224	NM_177990.2	433	Cgg/Tgg	5/10	1	2	FACETS	0.691	0.617	0.77	0.691	0.617	0.77	SUBCLONAL	1	TRUE	1	0.53	2		450	513	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630626	158630626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912678	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	34	327	1	ENST00000263640.3:c.617G>A	p.Arg206His	p.R206H	ENST00000263640	NM_001105.4	206	cGc/cAc	6/11	1	2	FACETS	0.352	0.288	0.425	0.352	0.288	0.425	SUBCLONAL	1	TRUE	1	0.53	2		328	364	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856190	111856190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	44	458	1	ENST00000341259.2:c.241G>A	p.Asp81Asn	p.D81N	ENST00000341259	NM_005475.2	81	Gac/Aac	2/8	1	2	FACETS	0.309	0.258	0.364	0.309	0.258	0.364	SUBCLONAL	1	TRUE	1	0.53	2		459	538	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674234	86674234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	95	297	0	ENST00000274376.6:c.2366G>A	p.Arg789Gln	p.R789Q	ENST00000274376	NM_002890.2	789	cGa/cAa	18/25	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.53	2		297	356	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591086	67591086	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	9	277	0	ENST00000274335.5:c.1679A>G	p.Asp560Gly	p.D560G	ENST00000274335		560	gAc/gGc	12/15	1	2	FACETS	0.091	0.06	0.131	0.091	0.06	0.131	SUBCLONAL	1	TRUE	1	0.53	2		277	373	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459558	50459558	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	98	262	0	ENST00000331340.3:c.847C>A	p.Leu283Ile	p.L283I	ENST00000331340	NM_006060.4	283	Ctt/Att	7/8	1	2	FACETS	0.922	0.829	1	0.922	0.829	1	CLONAL	1	TRUE	1	0.53	2		262	401	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715350	117715350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	70	285	0	ENST00000368508.3:c.1139G>A	p.Arg380Lys	p.R380K	ENST00000368508	NM_002944.2	380	aGa/aAa	10/43	1	2	FACETS	0.82	0.721	0.926	0.82	0.721	0.926	CLONAL	1	TRUE	1	0.53	2		285	322	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874214	155874214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	84	545	0	ENST00000368323.3:c.317G>A	p.Arg106Gln	p.R106Q	ENST00000368323	NM_006912.5	106	cGa/cAa	5/6	1	2	FACETS	0.452	0.399	0.509	0.452	0.399	0.509	SUBCLONAL	1	TRUE	1	0.53	2		545	701	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88672088	88672088	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	54	176	0	ENST00000372037.3:c.622G>T	p.Asp208Tyr	p.D208Y	ENST00000372037	NM_004329.2	208	Gac/Tac	8/13	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.53	2		176	178	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210688	36210688	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	177	627	0	ENST00000222270.7:c.439C>T	p.Arg147Ter	p.R147*	ENST00000222270	NM_014727.1	147	Cga/Tga	3/37	1	2	FACETS	0.84	0.775	0.907	0.84	0.775	0.907	CLONAL	1	TRUE	1	0.53	2		627	795	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740529	58740529	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs146477590	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	120	467	2	ENST00000305921.3:c.1434C>A	p.Cys478Ter	p.C478*	ENST00000305921	NM_003620.3	478	tgC/tgA	6/6	1	2	FACETS	0.84	0.762	0.922	0.84	0.762	0.922	CLONAL	1	TRUE	1	0.53	2		469	539	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776309	76776309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	162	594	0	ENST00000373344.5:c.7157G>A	p.Arg2386Gln	p.R2386Q	ENST00000373344	NM_000489.3	2386	cGa/cAa	34/35	1	2	FACETS	0.97	0.894	1	0.97	0.894	1	CLONAL	1	TRUE	1	0.53	2		594	630	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515591	31515591	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	109	362	1	ENST00000344624.3:c.1028C>A	p.Ser343Tyr	p.S343Y	ENST00000344624		343	tCt/tAt	4/33	1	2	FACETS	0.885	0.799	0.974	0.885	0.799	0.974	CLONAL	1	TRUE	1	0.53	2		363	465	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041214	29041214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758936491	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	33	551	0	ENST00000282397.4:c.214G>A	p.Glu72Lys	p.E72K	ENST00000282397	NM_002019.4	72	Gaa/Aaa	3/30	1	2	FACETS	0.199	0.161	0.242	0.199	0.161	0.242	SUBCLONAL	1	TRUE	1	0.53	2		551	626	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906949	32906949	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202373	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	109	381	0	ENST00000380152.3:c.1334C>A	p.Ser445Tyr	p.S445Y	ENST00000380152		445	tCt/tAt	10/27	1	2	FACETS	0.975	0.882	1	0.975	0.882	1	CLONAL	1	TRUE	1	0.53	2		381	422	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784902	9784902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs551657853	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	164	748	3	ENST00000377346.4:c.2905C>T	p.Arg969Cys	p.R969C	ENST00000377346	NM_005026.3	969	Cgc/Tgc	23/24	1	2	FACETS	0.728	0.669	0.79	0.728	0.669	0.79	SUBCLONAL	1	TRUE	1	0.53	2		751	850	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938995	76938995	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs886044898	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	157	456	0	ENST00000373344.5:c.1753G>T	p.Glu585Ter	p.E585*	ENST00000373344	NM_000489.3	585	Gaa/Taa	9/35	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.53	2		456	583	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692947	89692947	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	144	487	0	ENST00000371953.3:c.431A>C	p.Lys144Thr	p.K144T	ENST00000371953	NM_000314.4	144	aAa/aCa	5/9	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.53	2		487	517	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592288	29592288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs185660700	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	14	244	1	ENST00000356175.3:c.4703C>T	p.Thr1568Met	p.T1568M	ENST00000356175	NM_000267.3	1568	aCg/aTg	35/57	1	2	FACETS	0.189	0.136	0.253	0.189	0.136	0.253	SUBCLONAL	1	TRUE	1	0.53	2		245	280	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089719	27089719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1286907978	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	191	754	0	ENST00000324856.7:c.2675G>A	p.Arg892Gln	p.R892Q	ENST00000324856	NM_006015.4	892	cGg/cAg	8/20	1	2	FACETS	0.896	0.83	0.965	0.896	0.83	0.965	CLONAL	1	TRUE	1	0.53	2		754	804	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943716	9943716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1351978664	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	81	646	1	ENST00000330684.3:c.1225G>A	p.Val409Ile	p.V409I	ENST00000330684	NM_001134407.1	409	Gtc/Atc	5/13	1	2	FACETS	0.436	0.384	0.492	0.436	0.384	0.492	SUBCLONAL	1	TRUE	1	0.53	2		647	701	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176484	123176484	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	106	306	0	ENST00000218089.9:c.451G>T	p.Glu151Ter	p.E151*	ENST00000218089	NM_001042749.1	151	Gaa/Taa	7/35	1	2	FACETS	0.889	0.802	0.98	0.889	0.802	0.98	CLONAL	1	TRUE	1	0.53	2		306	450	SUCCESS
AR	367	MSKCC	GRCh37	X	66942713	66942713	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	91	514	0	ENST00000374690.3:c.2494C>T	p.Arg832Ter	p.R832*	ENST00000374690	NM_000044.3	832	Cga/Tga	7/8	1	2	FACETS	0.536	0.476	0.599	0.536	0.476	0.599	SUBCLONAL	1	TRUE	1	0.53	2		514	641	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830924	156830924	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	148	665	0	ENST00000524377.1:c.198G>T	p.Glu66Asp	p.E66D	ENST00000524377	NM_002529.3	66	gaG/gaT	1/17	1	2	FACETS	0.796	0.728	0.866	0.796	0.728	0.866	SUBCLONAL	1	TRUE	1	0.53	2		665	702	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831540	72831540	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	204	657	0	ENST00000268489.5:c.5041A>C	p.Ser1681Arg	p.S1681R	ENST00000268489	NM_006885.3	1681	Agc/Cgc	9/10	1	2	FACETS	0.982	0.913	1	0.982	0.913	1	CLONAL	1	TRUE	1	0.53	2		657	784	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993100	72993100	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	211	691	0	ENST00000268489.5:c.945A>C	p.Lys315Asn	p.K315N	ENST00000268489	NM_006885.3	315	aaA/aaC	2/10	1	2	FACETS	0.842	0.782	0.903	0.842	0.782	0.903	CLONAL	1	TRUE	1	0.53	2		691	946	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62323153	62323153	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751636582	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	39	543	0	ENST00000360203.5:c.2615G>A	p.Arg872Gln	p.R872Q	ENST00000360203	NM_001283009.1	872	cGa/cAa	28/35	1	2	FACETS	0.2	0.165	0.239	0.2	0.165	0.239	SUBCLONAL	1	TRUE	1	0.53	2		543	737	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643488	52643488	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	142	430	0	ENST00000394830.3:c.2408C>A	p.Ser803Tyr	p.S803Y	ENST00000394830	NM_018313.4	803	tCt/tAt	17/30	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.53	2		430	512	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138452210	138452210	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	159	394	3	ENST00000289153.2:c.1043C>T	p.Thr348Ile	p.T348I	ENST00000289153	NM_006219.2	348	aCt/aTt	6/22	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.53	2		397	576	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675598	86675598	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	102	265	0	ENST00000274376.6:c.2534T>G	p.Leu845Ter	p.L845*	ENST00000274376	NM_002890.2	845	tTa/tGa	19/25	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.53	2		265	357	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055989	180055989	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	155	687	0	ENST00000261937.6:c.996C>A	p.Phe332Leu	p.F332L	ENST00000261937	NM_182925.4	332	ttC/ttA	8/30	1	2	FACETS	0.762	0.698	0.828	0.762	0.698	0.828	SUBCLONAL	1	TRUE	1	0.53	2		687	768	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816567	32816567	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	186	646	0	ENST00000354258.4:c.1608G>T	p.Glu536Asp	p.E536D	ENST00000354258	NM_000593.5	536	gaG/gaT	7/11	1	2	FACETS	0.78	0.721	0.841	0.78	0.721	0.841	SUBCLONAL	1	TRUE	1	0.53	2		646	900	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860080	151860080	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	108	392	0	ENST00000262189.6:c.10582A>C	p.Asn3528His	p.N3528H	ENST00000262189	NM_170606.2	3528	Aat/Cat	43/59	1	2	FACETS	0.975	0.881	1	0.975	0.881	1	CLONAL	1	TRUE	1	0.53	2		392	418	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141569559	141569559	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	147	475	0	ENST00000220592.5:c.725G>T	p.Ser242Ile	p.S242I	ENST00000220592	NM_012154.3	242	aGt/aTt	6/19	1	2	FACETS	0.869	0.796	0.945	0.869	0.796	0.945	CLONAL	1	TRUE	1	0.53	2		475	638	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424384	47424384	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	136	595	0	ENST00000377045.4:c.304G>A	p.Val102Ile	p.V102I	ENST00000377045	NM_001654.4	102	Gta/Ata	5/16	1	2	FACETS	0.728	0.663	0.796	0.728	0.663	0.796	SUBCLONAL	1	TRUE	1	0.53	2		595	705	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874434	76874434	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	80	250	0	ENST00000373344.5:c.5288A>C	p.Asn1763Thr	p.N1763T	ENST00000373344	NM_000489.3	1763	aAt/aCt	21/35	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.53	2		250	295	SUCCESS
ATR	545	MSKCC	GRCh37	3	142168330	142168330	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	97	415	0	ENST00000350721.4:c.7876G>T	p.Glu2626Ter	p.E2626*	ENST00000350721	NM_001184.3	2626	Gaa/Taa	47/47	1	2	FACETS	0.826	0.741	0.916	0.826	0.741	0.916	CLONAL	1	TRUE	1	0.53	2		415	443	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31504699	31504699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1032572786	NA	P-0049372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	181	390	1	ENST00000344624.3:c.1631G>A	p.Arg544His	p.R544H	ENST00000344624		544	cGc/cAc	8/33	0.223889046341402	3	FACETS	0.806	0.743	0.872	0.806	0.743	0.872	CLONAL	2	TRUE	1	0.24	3		391	1048	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0049372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	218	543	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.217886522737558	2	FACETS	0.918	0.854	0.985	0.918	0.854	0.985	CLONAL	2	TRUE	0	0.24	2		543	989	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279534	1279534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1368095577	NA	P-0049372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1386	75	685	0	ENST00000310581.5:c.2002G>A	p.Glu668Lys	p.E668K	ENST00000310581	NM_198253.2	668	Gag/Aag	5/16	0.223889046341402	3	FACETS	0.479	0.418	0.546	0.24	0.209	0.273	SUBCLONAL	1	TRUE	1	0.24	3		685	1461	SUCCESS
APC	324	MSKCC	GRCh37	5	112175328	112175328	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	72	196	0	ENST00000257430.4:c.4037C>A	p.Ser1346Ter	p.S1346*	ENST00000257430	NM_000038.5	1346	tCa/tAa	16/16	0.217886522737558	2	FACETS	1	0.974	1	0.739	0.649	0.835	CLONAL	1	TRUE	0	0.24	2		196	406	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0049373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	17	406	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.696789090719415	3	FACETS	0.263	0.196	0.342	0.132	0.098	0.171	SUBCLONAL	1	TRUE	1	0.696789090719415	3		406	250	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0049373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	38	400	2	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.696789090719415	3	FACETS	0.66	0.55	0.78	0.33	0.275	0.39	SUBCLONAL	1	TRUE	1	0.696789090719415	3		402	223	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545939	41545939	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	250	599	1	ENST00000263253.7:c.2554C>T	p.Gln852Ter	p.Q852*	ENST00000263253	NM_001429.3	852	Cag/Tag	14/31	1	2	FACETS	0.838	0.786	0.892	0.838	0.786	0.892	CLONAL	1	TRUE	1	0.696789090719415	2		600	856	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878785	151878785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	171	400	0	ENST00000262189.6:c.6160C>T	p.Gln2054Ter	p.Q2054*	ENST00000262189	NM_170606.2	2054	Cag/Tag	36/59	1	2	FACETS	0.886	0.82	0.954	0.886	0.82	0.954	CLONAL	1	TRUE	1	0.696789090719415	2		400	554	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878332	151878332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	204	503	0	ENST00000262189.6:c.6613C>T	p.His2205Tyr	p.H2205Y	ENST00000262189	NM_170606.2	2205	Cat/Tat	36/59	1	2	FACETS	0.937	0.874	1	0.937	0.874	1	CLONAL	1	TRUE	1	0.696789090719415	2		503	625	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445068	49445068	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	179	527	0	ENST00000301067.7:c.2398C>T	p.Gln800Ter	p.Q800*	ENST00000301067	NM_003482.3	800	Cag/Tag	10/54	1	2	FACETS	0.624	0.576	0.674	0.624	0.576	0.674	SUBCLONAL	1	TRUE	1	0.696789090719415	2		527	823	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140871	37140871	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	252	561	0	ENST00000373509.5:c.707T>C	p.Val236Ala	p.V236A	ENST00000373509	NM_002648.3	236	gTg/gCg	5/6	1	2	FACETS	0.769	0.72	0.819	0.769	0.72	0.819	SUBCLONAL	1	TRUE	1	0.696789090719415	2		561	941	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896546	151896546	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0049373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	66	178	0	ENST00000262189.6:c.4093-2A>G		p.X1365_splice	ENST00000262189	NM_170606.2	1365			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.696789090719415	2		178	161	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915891	127915891	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0049373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	193	481	0	ENST00000373547.4:c.590C>G	p.Ser197Ter	p.S197*	ENST00000373547	NM_002721.4	197	tCa/tGa	6/7	1	2	FACETS	0.945	0.88	1	0.945	0.88	1	CLONAL	1	TRUE	1	0.696789090719415	2		481	586	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0049374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	184	217	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.0858168253783171	3	FACETS	1	0.983	1	0.597	0.554	0.64	INDETERMINATE	1	TRUE	1	0.76	3		217	560	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215817	133215817	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	116	455	0	ENST00000320574.5:c.5446A>C	p.Asn1816His	p.N1816H	ENST00000320574	NM_006231.2	1816	Aac/Cac	40/49	1	2	FACETS	0.507	0.458	0.559	0.507	0.458	0.559	SUBCLONAL	1	TRUE	1	0.76	2		455	602	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322971	31322971	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs41273028	NA	P-0049374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	312	629	1	ENST00000412585.2:c.925G>T	p.Val309Leu	p.V309L	ENST00000412585	NM_005514.6	309	Gtg/Ttg	5/8	1	2	FACETS	0.993	0.94	1	0.993	0.94	1	CLONAL	1	TRUE	1	0.76	2		630	827	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590777	95590778	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0049375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	154	275	0	ENST00000393063.1:c.1131_1132del	p.Ile378GlnfsTer10	p.I378Qfs*10	ENST00000393063	NM_030621.3	377	gtAAtc/gttc	9/28	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.591006685298893	2		275	520	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069458	30069458	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	149	495	0	ENST00000338641.4:c.1323del	p.Glu442ArgfsTer13	p.E442Rfs*13	ENST00000338641	NM_000268.3	441	gcT/gc	12/16	0.591006685298893	1	FACETS	0.817	0.753	0.882	0.817	0.753	0.882	CLONAL	1	TRUE	0	0.591006685298893	1		495	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0049377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	201	485	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.334511484755695	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	FALSE	0	0.334511484755695	2		486	573	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0049377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	201	423	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.334511484755695	5	FACETS	1	0.96	1	0.779	0.727	0.833	CLONAL	3	FALSE	1	0.334511484755695	5		423	579	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927457	178927457	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	103	331	1	ENST00000263967.3:c.1220G>T	p.Cys407Phe	p.C407F	ENST00000263967	NM_006218.2	407	tGc/tTc	7/21	0.0926196372747308	6	FACETS	0.948	0.851	1	0.632	0.567	0.7	INDETERMINATE	2	FALSE	3	0.334511484755695	6		332	542	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0049378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	28	346	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.334048957773365	3	FACETS	0.296	0.236	0.366	0.148	0.118	0.183	SUBCLONAL	1	FALSE	1	0.339101874332474	3		346	652	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481417	140481417	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913348	NA	P-0049378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	29	284	0	ENST00000288602.6:c.1391G>T	p.Gly464Val	p.G464V	ENST00000288602	NM_004333.4	464	gGa/gTa	11/18	1	2	FACETS	0.365	0.292	0.448	0.365	0.292	0.448	SUBCLONAL	1	FALSE	1	0.339101874332474	2		284	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0049379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	16	442	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.211892427621623	3	FACETS	0.242	0.178	0.32	0.121	0.089	0.16	SUBCLONAL	1	TRUE	1	0.212500201849424	3		442	687	SUCCESS
AR	367	MSKCC	GRCh37	X	66765403	66765403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1264061748	NA	P-0049379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	49	277	0	ENST00000374690.3:c.415G>A	p.Val139Met	p.V139M	ENST00000374690	NM_000044.3	139	Gtg/Atg	1/8	1	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.212500201849424	1		277	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs1202793339	NA	P-0049379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	85	551	0	ENST00000269305.4:c.560-1G>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.211892427621623	3	FACETS	1	0.977	1	0.739	0.654	0.829	CLONAL	1	TRUE	1	0.212500201849424	3		551	599	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632794	23632794	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	34	330	0	ENST00000261584.4:c.3002A>G	p.Lys1001Arg	p.K1001R	ENST00000261584	NM_024675.3	1001	aAa/aGa	10/13	1	2	FACETS	0.699	0.571	0.843	0.699	0.571	0.843	SUBCLONAL	1	TRUE	1	0.212500201849424	2		330	458	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550479	29550479	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	21	196	0	ENST00000356175.3:c.1739A>G	p.Tyr580Cys	p.Y580C	ENST00000356175	NM_000267.3	580	tAc/tGc	16/57	0.211892427621623	3	FACETS	0.671	0.516	0.851	0.335	0.258	0.426	SUBCLONAL	1	TRUE	1	0.212500201849424	3		196	326	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651895	36651895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	48	526	1	ENST00000244741.5:c.17G>A	p.Gly6Glu	p.G6E	ENST00000244741	NM_000389.4	6	gGg/gAg	2/3	1	2	FACETS	0.644	0.544	0.756	0.644	0.544	0.756	SUBCLONAL	1	TRUE	1	0.212500201849424	2		527	701	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0049380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	40	768	7	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		775	258	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544161	18544161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs954230255	NA	P-0049380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	18	279	1	ENST00000266497.5:c.1978C>T	p.Leu660Phe	p.L660F	ENST00000266497		660	Ctt/Ttt	13/31	0.331571450851854	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		280	220	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859568	151859568	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	45	401	1	ENST00000262189.6:c.11094del	p.Tyr3699MetfsTer6	p.Y3699Mfs*6	ENST00000262189	NM_170606.2	3698	acG/ac	43/59	0.187102635793417	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		402	238	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	339	431	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.265197545418606	4	FACETS	1	0.985	1	1	0.995	1	CLONAL	4	FALSE	1	0.265197545418606	4		431	748	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0049381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	303	533	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.265197545418606	0	FACETS	0.95	0.905	0.995			1	CLONAL	3	FALSE	0	0.265197545418606	0		533	589	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573587	48573587	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	66	98	0	ENST00000342988.3:c.171A>C	p.Leu57Phe	p.L57F	ENST00000342988	NM_005359.5	57	ttA/ttC	2/12	0.265197545418606	0	FACETS	0.737	0.648	0.832			1	SUBCLONAL	2	FALSE	0	0.265197545418606	0		98	248	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584562	48584566	+	frameshift_variant	Frame_Shift_Del	DEL	GCCAG	GCCAG	-	novel	NA	P-0049381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	31	391	0	ENST00000342988.3:c.736_740del	p.Pro246ThrfsTer16	p.P246Tfs*16	ENST00000342988	NM_005359.5	245	caGCCAGga/caga	6/12	0.265197545418606	0	FACETS	0.442	0.357	0.537			1	SUBCLONAL	1	FALSE	0	0.265197545418606	0		391	389	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910647	29910647	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199474387	NA	P-0049381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1653	444	1297	1	ENST00000376809.5:c.187G>T	p.Asp63Tyr	p.D63Y	ENST00000376809	NM_002116.7	63	Gac/Tac	2/8	1	2	FACETS	0.798	0.759	0.839	1	0.996	1	SUBCLONAL	2	FALSE	1	0.265197545418606	2		1298	2097	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0049382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	38	248	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.865	0.716	1	0.865	0.716	1	CLONAL	1	TRUE	1	0.23	2		249	382	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0049382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	137	493	0	ENST00000397752.3:c.3028+1G>A		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.3	3	FACETS	0.975	0.889	1	0.975	0.889	1	CLONAL	2	TRUE	1	0.23	3		493	681	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862850	9862850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751455326	NA	P-0049382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	49	498	0	ENST00000330684.3:c.2453C>T	p.Ala818Val	p.A818V	ENST00000330684	NM_001134407.1	818	gCg/gTg	12/13	1	2	FACETS	0.677	0.573	0.793	0.677	0.573	0.793	SUBCLONAL	1	TRUE	1	0.23	2		498	629	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897289	78897289	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0049382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	50	533	0	ENST00000306801.3:c.2625-1G>C		p.X875_splice	ENST00000306801	NM_020761.2	875			1	2	FACETS	0.58	0.491	0.679	0.58	0.491	0.679	SUBCLONAL	1	TRUE	1	0.23	2		533	749	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0049383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	598	441	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.85856135643736	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.85856135643736	2		441	690	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950724	79950725	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCGCAGCGC	rs1554066076	NA	P-0049384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	15	91	1	ENST00000265081.6:c.181_189dup	p.Ala61_Pro63dup	p.A61_P63dup	ENST00000265081	NM_002439.4	61	gcc/gCCGCAGCGCcc	1/24	1	2	FACETS	0.148	0.108	0.196	0.148	0.108	0.196	SUBCLONAL	1	TRUE	1	0.792140234102322	2		92	256	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50816282	50816282	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	183	220	4	ENST00000398568.2:c.1726del	p.Met576TrpfsTer8	p.M576Wfs*8	ENST00000398568	NM_001042412.1	574	ccA/cc	10/18	0.792140234102322	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.792140234102322	1		224	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0049385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	110	405	1	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.160836348495428	2	FACETS	0.859	0.773	0.951	0.859	0.773	0.951	CLONAL	2	TRUE	0	0.178006094421574	2		406	719	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0049385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	195	490	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.178006094421574	4	FACETS	1	0.949	1			1	CLONAL	3	TRUE	NA	0.178006094421574	4		490	835	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0049385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	158	286	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	0.178006094421574	3	FACETS	1	0.981	1	0.827	0.759	0.898	CLONAL	2	TRUE	0	0.178006094421574	3		286	779	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052629	42052629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	53	323	2	ENST00000219905.7:c.7300C>T	p.Arg2434Trp	p.R2434W	ENST00000219905	NM_001164273.1	2434	Cgg/Tgg	20/24	1	2	FACETS	0.999	0.852	1	0.999	0.852	1	CLONAL	1	TRUE	1	0.178006094421574	2		325	596	SUCCESS
APC	324	MSKCC	GRCh37	5	112179260	112179260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769433536	NA	P-0049385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	31	265	0	ENST00000257430.4:c.7969G>A	p.Val2657Ile	p.V2657I	ENST00000257430	NM_000038.5	2657	Gtt/Att	16/16	1	2	FACETS	0.825	0.667	1	0.825	0.667	1	CLONAL	1	TRUE	1	0.178006094421574	2		265	422	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711891	89711891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	301	236	0	ENST00000371953.3:c.509G>A	p.Ser170Asn	p.S170N	ENST00000371953	NM_000314.4	170	aGt/aAt	6/9	0.546104527028145	2	FACETS	0.97	0.925	1	0.97	0.925	1	CLONAL	2	TRUE	0	0.546104527028145	2		236	568	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435327	110435327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1450582670	NA	P-0049386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	39	300	1	ENST00000375856.3:c.3074C>T	p.Pro1025Leu	p.P1025L	ENST00000375856	NM_003749.2	1025	cCg/cTg	1/2	0.546104527028145	2	FACETS	0.398	0.33	0.473	0.199	0.165	0.237	SUBCLONAL	1	TRUE	0	0.546104527028145	2		301	359	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121524	2121524	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	43	464	1	ENST00000219476.3:c.1853T>C	p.Leu618Pro	p.L618P	ENST00000219476	NM_000548.3	618	cTg/cCg	18/42	0.546104527028145	2	FACETS	0.239	0.2	0.284	0.12	0.1	0.142	SUBCLONAL	1	TRUE	0	0.546104527028145	2		465	658	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589011	67589042	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TATACTCTTACACTAAGGTAAGCCAGGGAATA	TATACTCTTACACTAAGGTAAGCCAGGGAATA	-	novel	NA	P-0049386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	25	137	0	ENST00000274335.5:c.1104_1118+17del		p.X368_splice	ENST00000274335		368		8/15	0.546104527028145	2	FACETS	0.281	0.221	0.349	0.14	0.11	0.175	SUBCLONAL	1	TRUE	0	0.546104527028145	2		137	326	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0049387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	220	479	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.230384010270099	7	FACETS	0.879	0.819	0.941	0.879	0.819	0.941	CLONAL	4	TRUE	3	0.230384010270099	7		479	856	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259442	55259442	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397517127	NA	P-0049387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	196	332	0	ENST00000275493.2:c.2500G>T	p.Val834Leu	p.V834L	ENST00000275493	NM_005228.3	834	Gtg/Ttg	21/28	0.230384010270099	7	FACETS	0.902	0.838	0.969	0.902	0.838	0.969	CLONAL	4	TRUE	3	0.230384010270099	7		332	743	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783245	9783245	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756497515	NA	P-0049387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	41	433	1	ENST00000377346.4:c.2489G>A	p.Arg830His	p.R830H	ENST00000377346	NM_005026.3	830	cGt/cAt	20/24	1	2	FACETS	0.611	0.508	0.725	0.611	0.508	0.725	SUBCLONAL	1	TRUE	1	0.230384010270099	2		434	583	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040923	47040923	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	70	588	0	ENST00000377604.3:c.1453G>T	p.Glu485Ter	p.E485*	ENST00000377604	NM_001204468.1	485	Gag/Tag	14/24	0.230384010270099	1	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	0	0.230384010270099	1		588	524	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192121	108192121	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	103	325	0	ENST00000278616.4:c.6547del	p.Glu2183LysfsTer52	p.E2183Kfs*52	ENST00000278616	NM_000051.3	2182	ctG/ct	45/63	0.145397196547867	2	FACETS	0.77	0.69	0.853	0.77	0.69	0.853	SUBCLONAL	2	TRUE	0	0.230384010270099	2		325	581	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761237	59761237	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	68	329	0	ENST00000259008.2:c.3170A>T	p.Asn1057Ile	p.N1057I	ENST00000259008	NM_032043.2	1057	aAt/aTt	20/20	0.189543973120563	3	FACETS	1	0.875	1	0.503	0.437	0.575	CLONAL	1	TRUE	1	0.230384010270099	3		329	654	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361201	66361201	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	57	224	0	ENST00000273854.3:c.971C>A	p.Pro324His	p.P324H	ENST00000273854	NM_004439.5	324	cCt/cAt	4/18	0.230384010270099	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.230384010270099	1		224	401	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188086	151188099	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TCAATGAGGATTTC	TCAATGAGGATTTC	-	novel	NA	P-0049387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	54	185	0	ENST00000262187.5:c.54_67del	p.Lys19AspfsTer5	p.K19Dfs*5	ENST00000262187	NM_005614.3	18	ggGAAATCCTCATTGAcg/ggcg	2/8	0.230384010270099	3	FACETS	0.956	0.816	1	0.478	0.408	0.554	CLONAL	1	TRUE	1	0.230384010270099	3		185	547	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0049388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	219	579	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.245328558435269	2	FACETS	0.985	0.918	1	0.985	0.918	1	CLONAL	2	TRUE	0	0.245328558435269	2		579	906	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0049388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	93	426	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.245328558435269	2		426	716	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244155	153244156	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	114	471	0	ENST00000281708.4:c.2001dup	p.Ser668GlufsTer26	p.S668Efs*26	ENST00000281708	NM_033632.3	667	-/G	12/12	0.245328558435269	2	FACETS	1	0.976	1	0.637	0.573	0.703	CLONAL	1	TRUE	0	0.245328558435269	2		471	730	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141035	55141035	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	98	307	0	ENST00000257290.5:c.1681G>C	p.Val561Leu	p.V561L	ENST00000257290	NM_006206.4	561	Gtc/Ctc	12/23	0.245328558435269	1	FACETS	0.779	0.699	0.863	1	0.983	1	SUBCLONAL	2	TRUE	0	0.245328558435269	1		307	450	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011128	12011128	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	102	230	0	ENST00000353533.5:c.535G>T	p.Glu179Ter	p.E179*	ENST00000353533	NM_003010.3	179	Gaa/Taa	5/11	0.245328558435269	2	FACETS	0.96	0.864	1	0.96	0.864	1	CLONAL	2	TRUE	0	0.245328558435269	2		230	433	SUCCESS
APC	324	MSKCC	GRCh37	5	112175313	112175314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs863225351	NA	P-0049388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	98	221	0	ENST00000257430.4:c.4025dup	p.Leu1342PhefsTer12	p.L1342Ffs*12	ENST00000257430	NM_000038.5	1341	agt/agTt	16/16	0.245328558435269	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.245328558435269	2		221	342	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	51	431	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.842	0.716	0.98	0.842	0.716	0.98	CLONAL	1	TRUE	1	0.251831642057095	2		431	481	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0049389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	55	400	2	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.251831642057095	2		402	412	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0049389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	38	227	0	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	1	2	FACETS	0.896	0.742	1	0.896	0.742	1	CLONAL	1	TRUE	1	0.251831642057095	2		227	337	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295801	212295801	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1423325504	NA	P-0049389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	60	349	0	ENST00000342788.4:c.2512C>T	p.Arg838Ter	p.R838*	ENST00000342788	NM_005235.2	838	Cga/Tga	21/28	0.251831642057095	1	FACETS	0.793	0.684	0.912	0.793	0.684	0.912	CLONAL	1	TRUE	0	0.251831642057095	1		349	525	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119808	70119808	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	227	557	0	ENST00000245479.2:c.811del	p.Arg271AlafsTer8	p.R271Afs*8	ENST00000245479	NM_000346.3	270	ttC/tt	3/3	0.251831642057095	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.251831642057095	2		557	845	SUCCESS
APC	324	MSKCC	GRCh37	5	112173801	112173801	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs79512956	NA	P-0049389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	58	232	0	ENST00000257430.4:c.2510C>G	p.Ser837Ter	p.S837*	ENST00000257430	NM_000038.5	837	tCa/tGa	16/16	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.251831642057095	2		232	449	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604674	48604674	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	78	312	1	ENST00000342988.3:c.1496G>A	p.Cys499Tyr	p.C499Y	ENST00000342988	NM_005359.5	499	tGc/tAc	12/12	0.251831642057095	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.251831642057095	1		313	499	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0049391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	170	350	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.452846178721082	2		350	649	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88635803	88635803	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	52	236	0	ENST00000372037.3:c.28T>A	p.Leu10Ile	p.L10I	ENST00000372037	NM_004329.2	10	Tta/Ata	3/13	0.273699557530431	1	FACETS	0.339	0.288	0.394	0.339	0.288	0.394	SUBCLONAL	1	TRUE	0	0.452846178721082	1		236	524	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0049404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	138	437	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.392835319026278	3	FACETS	0.92	0.844	0.998	0.92	0.844	0.998	CLONAL	2	TRUE	1	0.40312741316624	3		437	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0049404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	167	583	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.40312741316624	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.40312741316624	1		583	573	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0049404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	36	247	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.835	0.692	0.991	0.835	0.692	0.991	CLONAL	1	TRUE	1	0.40312741316624	2		247	214	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245513	153245513	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	153	293	0	ENST00000281708.4:c.1678G>C	p.Asp560His	p.D560H	ENST00000281708	NM_033632.3	560	Gat/Cat	11/12	1	2	FACETS	0.978	0.906	1	1	0.992	1	CLONAL	2	TRUE	1	0.40312741316624	2		293	388	SUCCESS
APC	324	MSKCC	GRCh37	5	112173730	112173730	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	59	261	0	ENST00000257430.4:c.2442del	p.Phe814LeufsTer6	p.F814Lfs*6	ENST00000257430	NM_000038.5	813	aaT/aa	16/16	1	2	FACETS	0.941	0.815	1	0.941	0.815	1	CLONAL	1	TRUE	1	0.40312741316624	2		261	311	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212056	5212056	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1314953096	NA	P-0049404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	184	624	0	ENST00000357368.4:c.4975C>T	p.Arg1659Cys	p.R1659C	ENST00000357368	NM_002850.3	1659	Cgc/Tgc	32/38	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.40312741316624	2		624	883	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	94	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.831	0.749	0.916	0.831	0.749	0.916	CLONAL	1	TRUE	1	0.769719081749233	2		148	294	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159748	20159748	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	196	544	0	ENST00000379607.5:c.11A>G	p.Asn4Ser	p.N4S	ENST00000379607	NM_001412.3	4	aAt/aGt	1/7	1	2	FACETS	0.987	0.922	1	0.987	0.922	1	CLONAL	1	TRUE	1	0.769719081749233	2		544	516	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845580	151845580	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1287135873	NA	P-0049405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	194	509	3	ENST00000262189.6:c.13432C>T	p.Arg4478Ter	p.R4478*	ENST00000262189	NM_170606.2	4478	Cga/Tga	52/59	1	2	FACETS	0.908	0.847	0.971	0.908	0.847	0.971	CLONAL	1	TRUE	1	0.769719081749233	2		512	555	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141569579	141569582	+	frameshift_variant	Frame_Shift_Del	DEL	ACAA	ACAA	-	novel	NA	P-0049405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	30	335	0	ENST00000220592.5:c.702_705del	p.Cys235LysfsTer15	p.C235Kfs*15	ENST00000220592	NM_012154.3	234	gtTTGT/gt	6/19	1	2	FACETS	0.188	0.151	0.23	0.188	0.151	0.23	SUBCLONAL	1	TRUE	1	0.769719081749233	2		335	414	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360679	70360679	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	67	179	0	ENST00000374080.3:c.6239G>A	p.Arg2080Gln	p.R2080Q	ENST00000374080		2080	cGg/cAg	42/45	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.769719081749233	2		179	170	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0049407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	380	485	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.513047557666831	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.763391150350317	1		486	559	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0049407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	175	301	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	0.29681199462126	4	FACETS	1	0.973	1	1	0.973	1	INDETERMINATE	2	TRUE	2	0.763391150350317	4		301	375	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570332	87570332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	117	674	1	ENST00000277120.3:c.2072G>A	p.Arg691His	p.R691H	ENST00000277120		691	cGc/cAc	17/19	1	2	FACETS	0.407	0.366	0.449	0.407	0.366	0.449	SUBCLONAL	1	TRUE	1	0.763391150350317	2		675	754	SUCCESS
APC	324	MSKCC	GRCh37	5	112175198	112175199	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	84	137	0	ENST00000257430.4:c.3910dup	p.Ile1304AsnfsTer11	p.I1304Nfs*11	ENST00000257430	NM_000038.5	1303	caa/cAaa	16/16	0.29681199462126	4	FACETS	0.915	0.825	1	0.915	0.825	1	INDETERMINATE	2	TRUE	2	0.763391150350317	4		137	212	SUCCESS
APC	324	MSKCC	GRCh37	5	112173393	112173394	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs587783030	NA	P-0049407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	125	220	0	ENST00000257430.4:c.2107dup	p.Ala703GlyfsTer3	p.A703Gfs*3	ENST00000257430	NM_000038.5	701	atg/atGg	16/16	0.29681199462126	4	FACETS	0.764	0.699	0.831	0.764	0.699	0.831	INDETERMINATE	2	TRUE	2	0.763391150350317	4		220	378	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932591	39932591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148886271	NA	P-0049407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	465	338	0	ENST00000378444.4:c.2008C>T	p.Pro670Ser	p.P670S	ENST00000378444	NM_001123385.1	670	Ccc/Tcc	4/15	0.763391150350317	3	FACETS	1	0.996	1			1	CLONAL	1	TRUE	NA	0.763391150350317	3		338	1130	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061232	38061234	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0049408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	174	563	0	ENST00000250448.2:c.755_757del	p.Asn252del	p.N252del	ENST00000250448	NM_004496.3	252	aACAtg/atg	2/2	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.38447710579701	2		563	684	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0049409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	16	423	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.899	0.676	1	1	0.919	1	CLONAL	2	TRUE	1	0.2	2		423	89	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882005	NA	P-0049409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	36	484	0	ENST00000269305.4:c.713G>C	p.Cys238Ser	p.C238S	ENST00000269305	NM_001126112.2	238	tGt/tCt	7/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.2	2		484	259	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2949769	2949769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376446854	NA	P-0049409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	77	613	1	ENST00000396946.4:c.3175G>A	p.Gly1059Ser	p.G1059S	ENST00000396946	NM_032415.4	1059	Ggc/Agc	24/25	1	2	FACETS	1	0.937	1	1	0.985	1	CLONAL	2	TRUE	1	0.2	2		614	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0049412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	162	500	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.463366499223788	2	FACETS	0.956	0.891	1	0.956	0.891	1	CLONAL	2	TRUE	0	0.474591729875797	2		500	357	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023775	27023775	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	51	330	0	ENST00000324856.7:c.883del	p.Leu295SerfsTer68	p.L295Sfs*68	ENST00000324856	NM_006015.4	294	aCc/ac	1/20	1	2	FACETS	0.746	0.639	0.863	0.746	0.639	0.863	SUBCLONAL	1	TRUE	1	0.474591729875797	2		330	288	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0049413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	205	490	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.310413619562939	3	FACETS	0.871	0.81	0.933	0.871	0.81	0.933	CLONAL	2	TRUE	1	0.389022646130147	3		490	723	SUCCESS
APC	324	MSKCC	GRCh37	5	112177901	112177901	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs752654519	NA	P-0049413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	79	216	0	ENST00000257430.4:c.6610C>T	p.Arg2204Ter	p.R2204*	ENST00000257430	NM_000038.5	2204	Cga/Tga	16/16	0.33705935162547	2	FACETS	0.8	0.713	0.89	0.8	0.713	0.89	SUBCLONAL	2	TRUE	0	0.389022646130147	2		216	254	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685271	89685278	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TTTTTGGA	TTTTTGGA	-	novel	NA	P-0049413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	45	87	0	ENST00000371953.3:c.168_175del	p.Leu57LysfsTer3	p.L57Kfs*3	ENST00000371953	NM_000314.4	56	TTTTTGGAt/t	3/9	0.368593598262787	2	FACETS	0.782	0.67	0.899	0.782	0.67	0.899	SUBCLONAL	2	TRUE	0	0.389022646130147	2		87	148	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435007	110435007	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	117	619	2	ENST00000375856.3:c.3394G>A	p.Gly1132Ser	p.G1132S	ENST00000375856	NM_003749.2	1132	Ggc/Agc	1/2	1	2	FACETS	0.758	0.683	0.836	0.758	0.683	0.836	SUBCLONAL	1	TRUE	1	0.389022646130147	2		621	794	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220591	1220600	+	frameshift_variant	Frame_Shift_Del	DEL	GTTCGCGGCG	GTTCGCGGCG	-	novel	NA	P-0049413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	259	699	0	ENST00000326873.7:c.610_619del	p.Phe204ThrfsTer80	p.F204Tfs*80	ENST00000326873	NM_000455.4	203	ccGTTCGCGGCG/cc	5/10	0.35902733275736	2	FACETS	0.917	0.863	0.972	0.917	0.863	0.972	CLONAL	2	TRUE	0	0.389022646130147	2		699	726	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226559	2226570	+	inframe_deletion	In_Frame_Del	DEL	CTGAGCTCCCCG	CTGAGCTCCCCG	-	novel	NA	P-0049413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	276	783	0	ENST00000398665.3:c.4046_4057del	p.Ser1349_Ser1352del	p.S1349_S1352del	ENST00000398665	NM_032482.2	1347	CTGAGCTCCCCG/-	27/28	0.35902733275736	2	FACETS	0.815	0.768	0.864	0.815	0.768	0.864	CLONAL	2	TRUE	0	0.389022646130147	2		783	870	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137521932	137522029	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCTACTTTAAAAACATAATTTAAGAAACTATCAAAAAAGGTTCAAGTTAACTTTTTAGTGTATATAAAAAAATTAAATACATTACCAAGGACTTGGG	TTCTACTTTAAAAACATAATTTAAGAAACTATCAAAAAAGGTTCAAGTTAACTTTTTAGTGTATATAAAAAAATTAAATACATTACCAAGGACTTGGG	-	novel	NA	P-0049413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	32	40	0	ENST00000367739.4:c.850_861+86del		p.X284_splice	ENST00000367739	NM_000416.2	284		6/7	0.360095343218789	4	FACETS	0.952	0.816	1	0.952	0.816	1	CLONAL	4	TRUE	0	0.389022646130147	4		40	60	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0049414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	426	476	3	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.617237412418306	2	FACETS	0.968	0.933	1	0.968	0.933	1	CLONAL	2	TRUE	0	0.631348485106771	2		479	697	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912580	NA	P-0049414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	30	248	0	ENST00000342988.3:c.1157G>A	p.Gly386Asp	p.G386D	ENST00000342988	NM_005359.5	386	gGt/gAt	10/12	0.631348485106771	1	FACETS	0.252	0.204	0.306	0.252	0.204	0.306	SUBCLONAL	1	TRUE	0	0.631348485106771	1		248	258	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0049414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	372	762	2	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.631348485106771	2		764	1100	SUCCESS
APC	324	MSKCC	GRCh37	5	112151251	112151252	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs397515735	NA	P-0049414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	96	309	0	ENST00000257430.4:c.896_897del	p.Ser299CysfsTer27	p.S299Cfs*27	ENST00000257430	NM_000038.5	298	caCTct/cact	9/16	1	2	FACETS	0.74	0.664	0.82	0.74	0.664	0.82	SUBCLONAL	1	TRUE	1	0.631348485106771	2		309	411	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884875	134884875	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368240835	NA	P-0049414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	369	449	0	ENST00000398015.3:c.1651G>A	p.Val551Met	p.V551M	ENST00000398015	NM_004441.4	551	Gtg/Atg	8/16	0.631348485106771	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.631348485106771	1		449	592	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55962508	55962512	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCTA	TTCTA	-	novel	NA	P-0049414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	132	339	0	ENST00000263923.4:c.2615-3_2616del		p.X872_splice	ENST00000263923	NM_002253.2	872		19/30	1	2	FACETS	0.984	0.901	1	0.984	0.901	1	CLONAL	1	TRUE	1	0.631348485106771	2		339	425	SUCCESS
APC	324	MSKCC	GRCh37	5	112164640	112164640	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	129	243	0	ENST00000257430.4:c.1715del	p.Leu572Ter	p.L572*	ENST00000257430	NM_000038.5	572	Ttg/tg	14/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.631348485106771	2		243	366	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922891	39922891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	205	237	1	ENST00000378444.4:c.3817G>A	p.Glu1273Lys	p.E1273K	ENST00000378444	NM_001123385.1	1273	Gag/Aag	8/15	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.631348485106771	1		238	317	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582032	95582032	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1312425649	NA	P-0049415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	138	307	0	ENST00000393063.1:c.1879A>G	p.Ile627Val	p.I627V	ENST00000393063	NM_030621.3	627	Atc/Gtc	12/28	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.83925716194107	2		307	323	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	29	431	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.675	0.542	0.826	0.675	0.542	0.826	SUBCLONAL	1	TRUE	1	0.232340049430684	2		431	370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578530	7578530	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	554	632	0	ENST00000269305.4:c.400T>G	p.Phe134Val	p.F134V	ENST00000269305	NM_001126112.2	134	Ttt/Gtt	5/11	0.747006979147456	3	FACETS	0.972	0.951	0.993	0.972	0.951	0.993	CLONAL	3	FALSE	0	0.786184474302636	3		632	673	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0049418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	148	424	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.959	1	1	0.993	1	CLONAL	3	FALSE	1	0.154847762338213	2		424	593	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182158	11182158	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	107	499	0	ENST00000361445.4:c.6688T>G	p.Leu2230Val	p.L2230V	ENST00000361445	NM_004958.3	2230	Tta/Gta	48/58	0.154847762338213	0	FACETS	1	0.958	1			1	CLONAL	2	FALSE	0	0.154847762338213	0		499	521	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295166	1295168	+	upstream_gene_variant	5'Flank	TNP	CTC	CTC	ATG	novel	NA	P-0049418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	25	191	0				ENST00000310581	NM_198253.2	-/1132			0.154847762338213	0	FACETS	0.853	0.679	1			1	CLONAL	2	FALSE	0	0.154847762338213	0		191	160	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249391	153249391	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	120	348	0	ENST00000281708.4:c.1387A>C	p.Thr463Pro	p.T463P	ENST00000281708	NM_033632.3	463	Act/Cct	9/12	0.154847762338213	0	FACETS	0.97	0.882	1			1	CLONAL	3	FALSE	0	0.154847762338213	0		348	450	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429013	47429013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	123	223	0	ENST00000377045.4:c.1376G>A	p.Gly459Glu	p.G459E	ENST00000377045	NM_001654.4	459	gGg/gAg	13/16	1	1	FACETS	1	0.956	1	1	0.993	1	CLONAL	5	FALSE	0	0.154847762338213	1		223	277	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849663	68849663	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587780113	NA	P-0049419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	37	363	0	ENST00000261769.5:c.1565+1G>A		p.X522_splice	ENST00000261769	NM_004360.3	522			0.581813358744107	1	FACETS	0.949	0.808	1	0.949	0.808	1	CLONAL	1	FALSE	0	0.581813358744107	1		363	95	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577508	7577508	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060501201	NA	P-0049419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	48	491	0	ENST00000269305.4:c.773A>G	p.Glu258Gly	p.E258G	ENST00000269305	NM_001126112.2	258	gAa/gGa	7/11	0.581813358744107	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	0	0.581813358744107	1		491	103	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061517	38061517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771653601	NA	P-0049419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	38	405	0	ENST00000250448.2:c.472G>A	p.Asp158Asn	p.D158N	ENST00000250448	NM_004496.3	158	Gac/Aac	2/2	1	2	FACETS	0.68	0.569	0.802	0.68	0.569	0.802	SUBCLONAL	1	FALSE	1	0.581813358744107	2		405	192	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981798	70981798	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	48	729	0	ENST00000276594.2:c.298C>T	p.Pro100Ser	p.P100S	ENST00000276594	NM_024504.3	100	Ccg/Tcg	2/8	1	2	FACETS	0.943	0.81	1	0.943	0.81	1	CLONAL	1	FALSE	1	0.581813358744107	2		729	175	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888769	76888769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	36	365	0	ENST00000373344.5:c.5060G>A	p.Arg1687Lys	p.R1687K	ENST00000373344	NM_000489.3	1687	aGa/aAa	19/35	0.118797466459559	0	FACETS	0.386	0.323	0.454			1	INDETERMINATE	1	FALSE	0	0.581813358744107	0		365	134	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22405036	22405036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	22	95	0	ENST00000344548.3:c.65C>T	p.Ser22Phe	p.S22F	ENST00000344548	NM_001039802.1	22	tCc/tTc	3/7	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	FALSE	1	0.581813358744107	2		95	68	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471773	120471773	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	65	364	0	ENST00000256646.2:c.3718C>T	p.Gln1240Ter	p.Q1240*	ENST00000256646	NM_024408.3	1240	Cag/Tag	23/34	1	2	FACETS	0.931	0.818	1	0.931	0.818	1	CLONAL	1	FALSE	1	0.581813358744107	2		364	240	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226568832	226568832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	57	515	0	ENST00000366794.5:c.1237G>A	p.Glu413Lys	p.E413K	ENST00000366794	NM_001618.3	413	Gag/Aag	9/23	0.360173445420959	5	FACETS	1	0.945	1	0.298	0.257	0.342	CLONAL	1	FALSE	1	0.581813358744107	5		515	308	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624302	89624302	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876661010	NA	P-0049419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	50	373	0	ENST00000371953.3:c.76A>C	p.Thr26Pro	p.T26P	ENST00000371953	NM_000314.4	26	Acc/Ccc	1/9	0.118797466459559	0	FACETS	0.415	0.358	0.476			1	INDETERMINATE	1	FALSE	0	0.581813358744107	0		373	173	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046677	42046677	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	45	320	0	ENST00000219905.7:c.7051G>C	p.Asp2351His	p.D2351H	ENST00000219905	NM_001164273.1	2351	Gac/Cac	18/24	0.581813358744107	1	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	FALSE	0	0.581813358744107	1		320	106	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046697	42046697	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	45	341	0	ENST00000219905.7:c.7071G>C	p.Glu2357Asp	p.E2357D	ENST00000219905	NM_001164273.1	2357	gaG/gaC	18/24	0.581813358744107	1	FACETS	0.971	0.84	1	0.971	0.84	1	CLONAL	1	FALSE	0	0.581813358744107	1		341	113	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350303	89350303	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1135401804	NA	P-0049419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	39	606	1	ENST00000301030.4:c.2647G>T	p.Glu883Ter	p.E883*	ENST00000301030	NM_001256183.1	883	Gag/Tag	9/13	0.581813358744107	1	FACETS	0.749	0.634	0.87	0.749	0.634	0.87	SUBCLONAL	1	FALSE	0	0.581813358744107	1		607	127	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169991102	169991102	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	27	323	0	ENST00000295797.4:c.620C>A	p.Ser207Tyr	p.S207Y	ENST00000295797	NM_002740.5	207	tCc/tAc	7/18	0.581813358744107	3	FACETS	0.545	0.436	0.668	0.272	0.218	0.334	SUBCLONAL	1	FALSE	1	0.581813358744107	3		323	220	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612277	189612277	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs772579873	NA	P-0049419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	42	274	1	ENST00000264731.3:c.2029G>C	p.Glu677Gln	p.E677Q	ENST00000264731	NM_003722.4	677	Gag/Cag	14/14	0.581813358744107	3	FACETS	0.755	0.635	0.885	0.377	0.317	0.443	SUBCLONAL	1	FALSE	1	0.581813358744107	3		275	247	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178452	56178452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	27	236	0	ENST00000399503.3:c.3425C>T	p.Ser1142Leu	p.S1142L	ENST00000399503	NM_005921.1	1142	tCa/tTa	14/20	0.222354802852532	5	FACETS	1	0.869	1	0.369	0.297	0.45	INDETERMINATE	1	FALSE	2	0.581813358744107	5		236	157	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184158	56184158	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	19	248	0	ENST00000399503.3:c.4363T>A	p.Ser1455Thr	p.S1455T	ENST00000399503	NM_005921.1	1455	Tcc/Acc	19/20	0.222354802852532	5	FACETS	0.963	0.739	1	0.321	0.246	0.407	INDETERMINATE	1	FALSE	2	0.581813358744107	5		248	127	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715857	117715857	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	42	238	0	ENST00000368508.3:c.901C>G	p.Leu301Val	p.L301V	ENST00000368508	NM_002944.2	301	Cta/Gta	9/43	0.471394889250973	3	FACETS	1	0.949	1	0.431	0.367	0.5	CLONAL	1	FALSE	0	0.581813358744107	3		238	144	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739913	41739913	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	47	272	0	ENST00000242208.4:c.60T>G	p.Ser20Arg	p.S20R	ENST00000242208	NM_002192.2	20	agT/agG	2/3	0.222354802852532	5	FACETS	1	0.874	1	0.677	0.583	0.776	INDETERMINATE	2	FALSE	2	0.581813358744107	5		272	149	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512011	148512011	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	29	242	0	ENST00000320356.2:c.1667C>T	p.Ser556Leu	p.S556L	ENST00000320356	NM_004456.4	556	tCa/tTa	14/20	1	2	FACETS	0.697	0.567	0.84	0.697	0.567	0.84	SUBCLONAL	1	FALSE	1	0.581813358744107	2		242	143	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911388	39911388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	39	398	0	ENST00000378444.4:c.5242G>A	p.Asp1748Asn	p.D1748N	ENST00000378444	NM_001123385.1	1748	Gat/Aat	15/15	0.118797466459559	0	FACETS	0.33	0.277	0.387			1	INDETERMINATE	1	FALSE	0	0.581813358744107	0		398	170	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0049420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	154	599	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.382947143925508	3	FACETS	1	0.922	1	0.504	0.461	0.55	CLONAL	1	TRUE	1	0.38	3		599	956	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061261	38061261	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	344	557	0	ENST00000250448.2:c.728A>G	p.Tyr243Cys	p.Y243C	ENST00000250448	NM_004496.3	243	tAc/tGc	2/2	0.382947143925508	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.38	3		557	887	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120820	115120821	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	232	489	0	ENST00000257566.3:c.185dup	p.Pro63AlafsTer48	p.P63Afs*48	ENST00000257566	NM_016569.3	62	aag/aaAg	1/8	0.382947143925508	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.38	3		489	661	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061238	38061238	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	137	503	0	ENST00000250448.2:c.751G>T	p.Gly251Cys	p.G251C	ENST00000250448	NM_004496.3	251	Ggc/Tgc	2/2	0.382947143925508	3	FACETS	1	0.935	1	0.517	0.47	0.566	CLONAL	1	TRUE	1	0.38	3		503	830	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291073	10291073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773200699	NA	P-0049420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	125	489	0	ENST00000340748.4:c.398C>T	p.Ser133Phe	p.S133F	ENST00000340748		133	tCc/tTc	4/40	0.382947143925508	3	FACETS	1	0.915	1	0.506	0.458	0.556	CLONAL	1	TRUE	1	0.38	3		489	774	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148516768	148516768	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	31	151	0	ENST00000320356.2:c.919A>T	p.Thr307Ser	p.T307S	ENST00000320356	NM_004456.4	307	Aca/Tca	9/20	0.382947143925508	4	FACETS	0.571	0.462	0.695	0.286	0.231	0.348	SUBCLONAL	1	TRUE	2	0.38	4		151	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576888	7576888	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0049421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	378	541	0	ENST00000269305.4:c.958A>T	p.Lys320Ter	p.K320*	ENST00000269305	NM_001126112.2	320	Aag/Tag	9/11	0.301159836647151	5	FACETS	1	0.99	1			1	CLONAL	5	TRUE	NA	0.33	5		541	629	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965427	18965427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	99	392	1	ENST00000262803.5:c.1174G>A	p.Ala392Thr	p.A392T	ENST00000262803	NM_002911.3	392	Gcc/Acc	9/24	0.248474076778427	3	FACETS	0.876	0.788	0.968	0.876	0.788	0.968	CLONAL	2	TRUE	1	0.33	3		393	399	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342841	118342841	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	23	212	0	ENST00000534358.1:c.967G>C	p.Glu323Gln	p.E323Q	ENST00000534358	NM_005933.3	323	Gaa/Caa	3/36	0.301159836647151	2	FACETS	0.722	0.566	0.9	0.361	0.283	0.45	SUBCLONAL	1	TRUE	0	0.33	2		212	193	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871617	35871617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	44	251	1	ENST00000216797.5:c.889G>A	p.Glu297Lys	p.E297K	ENST00000216797	NM_020529.2	297	Gag/Aag	5/6	0.288802921463713	4	FACETS	1	0.945	1	0.43	0.363	0.503	CLONAL	1	TRUE	1	0.33	4		252	275	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993339	72993339	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	121	711	0	ENST00000268489.5:c.706G>T	p.Val236Leu	p.V236L	ENST00000268489	NM_006885.3	236	Gtg/Ttg	2/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.33	2		711	601	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756721	756722	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0049421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	41	366	2	ENST00000314574.4:c.106_107delinsAA	p.Pro36Asn	p.P36N	ENST00000314574	NM_005433.3	36	CCc/AAc	2/12	0.301159836647151	5	FACETS	0.713	0.593	0.846	0.238	0.197	0.282	SUBCLONAL	1	TRUE	2	0.33	5		368	521	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944410	40944410	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs777227473	NA	P-0049421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	40	455	0	ENST00000373198.4:c.2092C>G	p.Leu698Val	p.L698V	ENST00000373198	NM_133170.3	698	Ctg/Gtg	12/32	NA	2	FACETS	0.623	0.519	0.739			1	INDETERMINATE	1	TRUE	NA	0.33	2		455	389	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607261	189607261	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	86	608	1	ENST00000264731.3:c.1640G>A	p.Cys547Tyr	p.C547Y	ENST00000264731	NM_003722.4	547	tGc/tAc	12/14	0.301159836647151	3	FACETS	1	0.937	1	0.543	0.481	0.609	CLONAL	1	TRUE	1	0.33	3		609	559	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279562	123279562	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121918499	NA	P-0049422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	49	492	0	ENST00000358487.5:c.870G>C	p.Trp290Cys	p.W290C	ENST00000358487	NM_000141.4	290	tgG/tgC	7/18	0.679177146051635	3	FACETS	0.288	0.243	0.337	0.144	0.121	0.169	SUBCLONAL	1	FALSE	1	0.679177146051635	3		492	672	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061558	38061558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745367241	NA	P-0049422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	76	362	1	ENST00000250448.2:c.431C>T	p.Ala144Val	p.A144V	ENST00000250448	NM_004496.3	144	gCg/gTg	2/2	0.679177146051635	4	FACETS	0.753	0.662	0.85	0.377	0.331	0.425	SUBCLONAL	1	FALSE	2	0.679177146051635	4		363	499	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257135	198257135	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0049422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	132	342	0	ENST00000335508.6:c.3807C>G	p.Tyr1269Ter	p.Y1269*	ENST00000335508	NM_012433.2	1269	taC/taG	25/25	0.632875946999282	4	FACETS	0.777	0.712	0.844	0.777	0.712	0.844	SUBCLONAL	2	FALSE	2	0.679177146051635	4		342	420	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087893	27087893	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	500	545	0	ENST00000324856.7:c.2181del	p.Pro728HisfsTer14	p.P728Hfs*14	ENST00000324856	NM_006015.4	727	cGg/cg	6/20	0.753541141527908	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.753541141527908	2		545	597	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518419	69518419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	112	143	1	ENST00000294312.3:c.226G>A	p.Ala76Thr	p.A76T	ENST00000294312	NM_005117.2	76	Gcg/Acg	1/3	0.581034896426613	3	FACETS	0.93	0.857	1	0.93	0.857	1	CLONAL	2	TRUE	1	0.753541141527908	3		144	220	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486062	29486062	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs4795581	NA	P-0049423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	192	231	0	ENST00000356175.3:c.239A>T	p.Tyr80Phe	p.Y80F	ENST00000356175	NM_000267.3	80	tAt/tTt	3/57	0.753541141527908	4	FACETS	0.971	0.908	1	0.648	0.605	0.69	CLONAL	2	TRUE	1	0.753541141527908	4		231	460	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858190	40858190	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	551	647	0	ENST00000428826.2:c.1674C>A	p.Phe558Leu	p.F558L	ENST00000428826		558	ttC/ttA	16/21	0.658283934938186	4	FACETS	0.986	0.955	1	0.986	0.955	1	CLONAL	3	TRUE	1	0.753541141527908	4		647	867	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573597	48573597	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1064794204	NA	P-0049423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	110	258	1	ENST00000342988.3:c.181A>G	p.Ile61Val	p.I61V	ENST00000342988	NM_005359.5	61	Ata/Gta	2/12	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.753541141527908	2		259	274	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600380	10600380	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	525	842	1	ENST00000171111.5:c.1475C>G	p.Pro492Arg	p.P492R	ENST00000171111	NM_203500.1	492	cCa/cGa	4/6	0.753541141527908	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.753541141527908	2		843	666	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132532	11132532	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	517	930	1	ENST00000358026.2:c.2748C>A	p.Asn916Lys	p.N916K	ENST00000358026	NM_001128849.1	916	aaC/aaA	19/36	0.753541141527908	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.753541141527908	2		931	645	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795142	42795142	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	562	992	1	ENST00000575354.2:c.2222C>T	p.Ala741Val	p.A741V	ENST00000575354	NM_015125.3	741	gCc/gTc	10/20	0.733921286257188	5	FACETS	1	0.989	1	0.72	0.691	0.748	CLONAL	2	TRUE	2	0.753541141527908	5		993	1472	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131293	202131293	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	138	396	0	ENST00000358485.4:c.261C>G	p.Asp87Glu	p.D87E	ENST00000358485	NM_001080125.1	87	gaC/gaG	2/9	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.753541141527908	2		396	330	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136840	55136840	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	233	326	0	ENST00000257290.5:c.1162G>T	p.Asp388Tyr	p.D388Y	ENST00000257290	NM_006206.4	388	Gac/Tac	8/23	0.753541141527908	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.753541141527908	2		326	291	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020749	26020749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	124	282	0	ENST00000357647.3:c.32C>T	p.Ser11Phe	p.S11F	ENST00000357647	NM_003529.2	11	tCt/tTt	1/1	0.556447458568246	4	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.753541141527908	4		282	477	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0049424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	229	402	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.913	0.854	0.973	0.913	0.854	0.973	CLONAL	1	TRUE	1	0.681872805127032	2		402	736	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0049424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	117	248	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.948	0.864	1	0.948	0.864	1	CLONAL	1	TRUE	1	0.681872805127032	2		249	362	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981167	201981168	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	175	798	0	ENST00000359651.3:c.248dup	p.Asn83LysfsTer9	p.N83Kfs*9	ENST00000359651		82	-/A	2/8	1	2	FACETS	0.554	0.51	0.599	0.554	0.51	0.599	SUBCLONAL	1	TRUE	1	0.681872805127032	2		798	927	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845334	151845334	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	211	507	0	ENST00000262189.6:c.13678C>T	p.Gln4560Ter	p.Q4560*	ENST00000262189	NM_170606.2	4560	Cag/Tag	52/59	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.681872805127032	2		507	595	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446346	49446346	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0049424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	198	492	0	ENST00000301067.7:c.1258+1G>A		p.X420_splice	ENST00000301067	NM_003482.3	420			1	2	FACETS	0.981	0.914	1	0.981	0.914	1	CLONAL	1	TRUE	1	0.681872805127032	2		492	592	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873995	151874001	+	frameshift_variant	Frame_Shift_Del	DEL	TTATCTT	TTATCTT	-	novel	NA	P-0049424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	162	355	0	ENST00000262189.6:c.8537_8543del	p.Lys2846MetfsTer15	p.K2846Mfs*15	ENST00000262189	NM_170606.2	2846	aAAGATAAt/at	38/59	1	2	FACETS	0.947	0.875	1	0.947	0.875	1	CLONAL	1	TRUE	1	0.681872805127032	2		355	502	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215239	123215239	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	122	119	0	ENST00000218089.9:c.2785G>A	p.Glu929Lys	p.E929K	ENST00000218089	NM_001042749.1	929	Gaa/Aaa	28/35	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.681872805127032	1		119	181	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0049425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	467	677	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	NA	2	FACETS	0.983	0.947	1			1	INDETERMINATE	2	TRUE	NA	0.58729721573253	2		677	809	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570885	226570885	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0049425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	39	278	0	ENST00000366794.5:c.1012-1G>T		p.X338_splice	ENST00000366794	NM_001618.3	338			0.299774816324829	4	FACETS	0.462	0.383	0.551	0.231	0.191	0.276	INDETERMINATE	1	TRUE	2	0.58729721573253	4		278	456	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872356	35872430	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CATTGTAGTTGGTAGCCTTCAGGATGGAGTGGAGGTGCGGGGTGGTGCAGGACTGAGTCAGGACTCCCACGCTGG	CATTGTAGTTGGTAGCCTTCAGGATGGAGTGGAGGTGCGGGGTGGTGCAGGACTGAGTCAGGACTCCCACGCTGG	-	novel	NA	P-0049425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	187	447	0	ENST00000216797.5:c.473_547del	p.Ala158_Asn182del	p.A158_N182del	ENST00000216797	NM_020529.2	158	gCCAGCGTGGGAGTCCTGACTCAGTCCTGCACCACCCCGCACCTCCACTCCATCCTGAAGGCTACCAACTACAATGgc/ggc	3/6	0.58729721573253	2	FACETS	1	0.991	1	0.709	0.662	0.757	CLONAL	1	TRUE	0	0.58729721573253	2		447	449	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46596966	46596966	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	81	287	0	ENST00000263734.3:c.780A>C	p.Arg260Ser	p.R260S	ENST00000263734	NM_001430.4	260	agA/agC	7/16	0.166313678199078	6	FACETS	1	0.965	1	0.416	0.367	0.467	INDETERMINATE	1	TRUE	3	0.58729721573253	6		287	481	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0049427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	153	202	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.438440459178076	3	FACETS	1	0.979	1	0.588	0.543	0.635	INDETERMINATE	1	TRUE	1	0.810033215652025	3		202	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579468	7579472	+	frameshift_variant	Frame_Shift_Del	DEL	CACGG	CACGG	-	novel	NA	P-0049427-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	350	640	0	ENST00000269305.4:c.215_219del	p.Pro72ArgfsTer75	p.P72Rfs*75	ENST00000269305	NM_001126112.2	72	cCCGTG/c	4/11	0.748436401591118	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.810033215652025	1		640	458	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0049428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	30	248	1				ENST00000310581	NM_198253.2	-/1132			0.213539141448782	1	FACETS	0.691	0.557	0.843	0.691	0.557	0.843	SUBCLONAL	1	TRUE	0	0.213539141448782	1		249	363	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917054	50917054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049428-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	51	563	0	ENST00000440232.2:c.2306C>T	p.Ala769Val	p.A769V	ENST00000440232	NM_002691.3	769	gCt/gTt	19/27	0.127144360884849	3	FACETS	0.532	0.451	0.623	0.266	0.225	0.312	INDETERMINATE	1	TRUE	1	0.213539141448782	3		563	993	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	140	354	0	ENST00000347630.2:c.397T>C	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	Ttc/Ctc	6/11	0.1723352393075	5	FACETS	1	0.944	1	0.695	0.636	0.757	INDETERMINATE	2	TRUE	2	0.359526317639698	5		354	575	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876425	35876425	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	212	482	0	ENST00000303115.3:c.1217T>G	p.Leu406Arg	p.L406R	ENST00000303115	NM_002185.3	406	cTt/cGt	8/8	0.359526317639698	5	FACETS	1	0.979	1	0.749	0.697	0.802	CLONAL	2	TRUE	2	0.359526317639698	5		482	808	SUCCESS
APC	324	MSKCC	GRCh37	5	112176740	112176740	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	43	193	1	ENST00000257430.4:c.5453del	p.Asn1818IlefsTer45	p.N1818Ifs*45	ENST00000257430	NM_000038.5	1817	Aaa/aa	16/16	0.360184197199159	1	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	0	0.359526317639698	1		194	185	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879923	44879923	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0049429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	113	205	0	ENST00000377967.4:c.512T>G	p.Leu171Ter	p.L171*	ENST00000377967	NM_021140.2	171	tTa/tGa	6/29	0.360184197199159	2	FACETS	0.821	0.745	0.899			1	CLONAL	2	TRUE	NA	0.359526317639698	2		205	383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	17	614	0	ENST00000269305.4:c.166G>A	p.Glu56Lys	p.E56K	ENST00000269305	NM_001126112.2	56	Gaa/Aaa	4/11	0.685301980959263	0	FACETS		NA	1			1	NA	1	TRUE	0	0.716048118876028	0		614	268	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289844	15289844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	334	778	0	ENST00000263388.2:c.3710G>A	p.Gly1237Asp	p.G1237D	ENST00000263388	NM_000435.2	1237	gGc/gAc	22/33	0.646601518313807	3	FACETS	0.883	0.834	0.934	0.442	0.417	0.467	CLONAL	1	TRUE	1	0.716048118876028	3		778	1434	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960120	134960120	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	161	434	0	ENST00000398015.3:c.2477G>T	p.Trp826Leu	p.W826L	ENST00000398015	NM_004441.4	826	tGg/tTg	13/16	NA	2	FACETS	0.847	0.782	0.914			1	INDETERMINATE	1	TRUE	NA	0.716048118876028	2		434	531	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974758	21974779	+	frameshift_variant	Frame_Shift_Del	DEL	ACCCCGGGCCGCGGCCGTGGCC	ACCCCGGGCCGCGGCCGTGGCC	-	novel	NA	P-0049430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	336	316	0	ENST00000304494.5:c.48_69del	p.Ala17GlyfsTer2	p.A17Gfs*2	ENST00000304494	NM_000077.4	16	ctGGCCACGGCCGCGGCCCGGGGT/ct	1/3	0.710466167479567	2	FACETS	0.974	0.938	1	0.974	0.938	1	CLONAL	2	TRUE	0	0.716048118876028	2		316	482	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907639	76907652	+	frameshift_variant	Frame_Shift_Del	DEL	CAATACGTTTTCGT	CAATACGTTTTCGT	-	novel	NA	P-0049430-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	235	371	0	ENST00000373344.5:c.4509_4522del	p.Arg1503SerfsTer2	p.R1503Sfs*2	ENST00000373344	NM_000489.3	1503	agACGAAAACGTATTGct/agct	15/35	0.50386718663263	3	FACETS	0.816	0.769	0.864			1	CLONAL	2	TRUE	NA	0.716048118876028	3		371	546	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	157	148	0				ENST00000310581	NM_198253.2	-/1132			0.151788028751752	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.943937407563236	0		148	359	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0049431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	49	616	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.13	0.11	0.153	0.13	0.11	0.153	SUBCLONAL	1	TRUE	1	0.943937407563236	2		618	796	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0049431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	456	385	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.943937407563236	2		385	956	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501195	NA	P-0049431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	121	577	0	ENST00000269305.4:c.313G>A	p.Gly105Ser	p.G105S	ENST00000269305	NM_001126112.2	105	Ggc/Agc	4/11	1	2	FACETS	0.279	0.251	0.308	0.279	0.251	0.308	SUBCLONAL	1	TRUE	1	0.943937407563236	2		577	919	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520008	NA	P-0049431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	35	489	0	ENST00000269305.4:c.613T>C	p.Tyr205His	p.Y205H	ENST00000269305	NM_001126112.2	205	Tat/Cat	6/11	1	2	FACETS	0.099	0.08	0.12	0.099	0.08	0.12	SUBCLONAL	1	TRUE	1	0.943937407563236	2		489	751	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923091	48923091	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0049431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	52	147	0	ENST00000267163.4:c.540-1G>T		p.X180_splice	ENST00000267163	NM_000321.2	180			0.943937407563236	1	FACETS	0.923	0.855	0.981	0.923	0.855	0.981	CLONAL	1	TRUE	0	0.943937407563236	1		147	63	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239889	41239889	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	229	231	0	ENST00000379561.5:c.461C>A	p.Ser154Ter	p.S154*	ENST00000379561	NM_002015.3	154	tCg/tAg	1/3	0.209578787225338	1	FACETS	0.508	0.479	0.538	0.508	0.479	0.538	INDETERMINATE	1	TRUE	0	0.943937407563236	1		231	504	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070628	67070638	+	frameshift_variant	Frame_Shift_Del	DEL	GTATGTCGACT	GTATGTCGACT	-	novel	NA	P-0049431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	84	115	0	ENST00000412916.2:c.252_262del	p.Glu84AspfsTer28	p.E84Dfs*28	ENST00000412916		84	gaGTATGTCGACTta/gata	3/6	0.943937407563236	1	FACETS	0.949	0.898	0.994	0.949	0.898	0.994	CLONAL	1	TRUE	0	0.943937407563236	1		115	99	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070651	67070651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765529526	NA	P-0049431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	69	101	0	ENST00000412916.2:c.275C>T	p.Ala92Val	p.A92V	ENST00000412916		92	gCa/gTa	3/6	0.943937407563236	1	FACETS	0.93	0.871	0.98	0.93	0.871	0.98	CLONAL	1	TRUE	0	0.943937407563236	1		101	83	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650648	67650648	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	12	216	0	ENST00000264010.4:c.953G>C	p.Gly318Ala	p.G318A	ENST00000264010	NM_006565.3	318	gGt/gCt	5/12	0.943937407563236	1	FACETS	0.065	0.045	0.089	0.065	0.045	0.089	SUBCLONAL	1	TRUE	0	0.943937407563236	1		216	208	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687586	29687586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	32	336	0	ENST00000356175.3:c.8179G>A	p.Glu2727Lys	p.E2727K	ENST00000356175	NM_000267.3	2727	Gaa/Aaa	56/57	1	2	FACETS	0.703	0.569	0.855	0.703	0.569	0.855	SUBCLONAL	1	TRUE	1	0.16	2		336	569	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65569055	65569055	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0049432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	33	377	0	ENST00000358664.4:c.3G>A	p.Met1?	p.M1?	ENST00000358664	NM_002382.4	1	atG/atA	1/5	1	2	FACETS	0.711	0.578	0.862	0.711	0.578	0.862	SUBCLONAL	1	TRUE	1	0.16	2		377	580	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624274	89624274	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs587782187	NA	P-0049432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	23	315	0	ENST00000371953.3:c.48T>G	p.Tyr16Ter	p.Y16*	ENST00000371953	NM_000314.4	16	taT/taG	1/9	1	2	FACETS	0.68	0.529	0.855	0.68	0.529	0.855	SUBCLONAL	1	TRUE	1	0.16	2		315	423	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593264	67593264	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0049432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	29	172	0	ENST00000274335.5:c.2010T>A	p.Cys670Ter	p.C670*	ENST00000274335		670	tgT/tgA	15/15	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.16	2		172	302	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	125	431	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.261714723963809	4	FACETS	1	0.985	1	0.483	0.44	0.528	INDETERMINATE	1	TRUE	1	0.570508114330595	4		431	475	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0049433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	143	406	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.989	0.907	1	0.989	0.907	1	CLONAL	1	TRUE	1	0.570508114330595	2		406	507	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0049433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	128	347	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.212067478226863	3	FACETS	0.767	0.703	0.833	0.767	0.703	0.833	INDETERMINATE	2	TRUE	1	0.570508114330595	3		347	376	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504590	103504590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1400329743	NA	P-0049433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	133	278	0	ENST00000355739.4:c.211C>T	p.Arg71Cys	p.R71C	ENST00000355739	NM_000123.3	71	Cgt/Tgt	2/15	0.531581782655186	4	FACETS	0.857	0.785	0.932	0.572	0.523	0.621	CLONAL	2	TRUE	1	0.570508114330595	4		278	427	SUCCESS
APC	324	MSKCC	GRCh37	5	112175162	112175162	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561588104	NA	P-0049433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	121	159	0	ENST00000257430.4:c.3871C>T	p.Gln1291Ter	p.Q1291*	ENST00000257430	NM_000038.5	1291	Cag/Tag	16/16	0.550159523187368	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	0	0.570508114330595	3		159	173	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925316	114925317	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs745872748	NA	P-0049433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	158	385	9	ENST00000543371.1:c.1403dup	p.Cys469ValfsTer8	p.C469Vfs*8	ENST00000543371	NM_001198531.1	465	aga/agAa	14/14	1	2	FACETS	0.761	0.707	0.815	1	0.99	1	SUBCLONAL	2	TRUE	1	0.570508114330595	2		394	364	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858992	243858992	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	32	293	0	ENST00000263826.5:c.73A>G	p.Arg25Gly	p.R25G	ENST00000263826	NM_005465.4	25	Aga/Gga	2/13	0.570508114330595	3	FACETS	0.34	0.276	0.413	0.17	0.138	0.207	SUBCLONAL	1	TRUE	1	0.570508114330595	3		293	424	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584468	39584468	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253032956	NA	P-0049433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	86	292	0	ENST00000262039.4:c.1133G>A	p.Arg378His	p.R378H	ENST00000262039	NM_002647.2	378	cGt/cAt	10/25	0.26203799056525	1	FACETS	0.826	0.741	0.913	0.826	0.741	0.913	INDETERMINATE	1	TRUE	0	0.570508114330595	1		292	261	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332919	153332919	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs781123562	NA	P-0049433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	93	261	0	ENST00000281708.4:c.37C>T	p.Arg13Ter	p.R13*	ENST00000281708	NM_033632.3	13	Cga/Tga	2/12	0.212067478226863	3	FACETS	1	0.97	1	0.613	0.55	0.678	INDETERMINATE	1	TRUE	1	0.570508114330595	3		261	342	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43806114	43806115	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	69	532	2	ENST00000372470.3:c.911dup	p.Gln305AlafsTer6	p.Q305Afs*6	ENST00000372470	NM_005373.2	304	cag/cAag	6/12	1	2	FACETS	0.456	0.397	0.519	0.456	0.397	0.519	SUBCLONAL	1	TRUE	1	0.570508114330595	2		534	531	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845537	63845537	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	66	225	0	ENST00000279873.7:c.1276G>C	p.Glu426Gln	p.E426Q	ENST00000279873	NM_032199.2	426	Gag/Cag	9/10	1	2	FACETS	0.96	0.844	1	0.96	0.844	1	CLONAL	1	TRUE	1	0.570508114330595	2		225	241	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136205	64136205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	203	887	2	ENST00000334205.4:c.1364C>T	p.Ala455Val	p.A455V	ENST00000334205	NM_003942.2	455	gCt/gTt	12/17	1	2	FACETS	0.968	0.901	1	0.968	0.901	1	CLONAL	1	TRUE	1	0.570508114330595	2		889	735	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912729	100912729	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	91	366	0	ENST00000325455.5:c.2593T>G	p.Ser865Ala	p.S865A	ENST00000325455	NM_001202474.3	865	Tcg/Gcg	7/8	1	2	FACETS	0.848	0.759	0.942	0.848	0.759	0.942	CLONAL	1	TRUE	1	0.570508114330595	2		366	376	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195825	102195825	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	96	332	0	ENST00000263464.3:c.585C>A	p.Tyr195Ter	p.Y195*	ENST00000263464	NM_001165.4	195	taC/taA	2/9	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.570508114330595	2		332	304	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910860	32910860	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	40	301	0	ENST00000380152.3:c.2368G>C	p.Glu790Gln	p.E790Q	ENST00000380152		790	Gaa/Caa	11/27	0.261714723963809	4	FACETS	0.501	0.416	0.595	0.167	0.138	0.199	INDETERMINATE	1	TRUE	1	0.570508114330595	4		301	440	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609679	81609679	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	113	466	0	ENST00000298171.2:c.1277T>A	p.Leu426Gln	p.L426Q	ENST00000298171	NM_000369.2	426	cTg/cAg	10/10	1	2	FACETS	0.973	0.883	1	0.973	0.883	1	CLONAL	1	TRUE	1	0.570508114330595	2		466	407	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991880	72991880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	224	608	0	ENST00000268489.5:c.2165G>A	p.Gly722Asp	p.G722D	ENST00000268489	NM_006885.3	722	gGt/gAt	2/10	0.454046834137037	3	FACETS	0.77	0.721	0.821	0.77	0.721	0.821	SUBCLONAL	2	TRUE	1	0.570508114330595	3		608	655	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033436	48033440	+	frameshift_variant	Frame_Shift_Del	DEL	CTCAC	CTCAC	-	novel	NA	P-0049433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	34	389	0	ENST00000234420.5:c.3740_3744del	p.Thr1247IlefsTer26	p.T1247Ifs*26	ENST00000234420	NM_000179.2	1247	aCTCAC/a	8/10	0.302081643074223	3	FACETS	0.368	0.301	0.444	0.184	0.15	0.222	INDETERMINATE	1	TRUE	1	0.570508114330595	3		389	416	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022943	31022943	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	62	465	0	ENST00000375687.4:c.2428G>A	p.Asp810Asn	p.D810N	ENST00000375687	NM_015338.5	810	Gac/Aac	13/13	0.212067478226863	3	FACETS	0.587	0.508	0.672	0.293	0.254	0.336	INDETERMINATE	1	TRUE	1	0.570508114330595	3		465	476	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799550	72799550	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	70	473	0	ENST00000325599.8:c.1619A>C	p.Glu540Ala	p.E540A	ENST00000325599	NM_018130.2	540	gAg/gCg	11/11	1	2	FACETS	0.51	0.446	0.579	0.51	0.446	0.579	SUBCLONAL	1	TRUE	1	0.570508114330595	2		473	481	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133465	55133465	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	125	312	0	ENST00000257290.5:c.769G>C	p.Gly257Arg	p.G257R	ENST00000257290	NM_006206.4	257	Ggc/Cgc	6/23	0.212067478226863	3	FACETS	0.763	0.698	0.83	0.763	0.698	0.83	INDETERMINATE	2	TRUE	1	0.570508114330595	3		312	369	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90995054	90995054	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	130	293	0	ENST00000265433.3:c.67G>C	p.Glu23Gln	p.E23Q	ENST00000265433	NM_002485.4	23	Gag/Cag	2/16	0.454046834137037	3	FACETS	0.771	0.707	0.837	0.771	0.707	0.837	SUBCLONAL	2	TRUE	1	0.570508114330595	3		293	380	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128748843	128748844	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	42	347	0	ENST00000377970.2:c.5dup	p.Asp2GlufsTer20	p.D2Efs*20	ENST00000377970	NM_002467.4	2	gat/gAat	1/3	0.570508114330595	3	FACETS	0.358	0.299	0.425	0.179	0.149	0.213	SUBCLONAL	1	TRUE	1	0.570508114330595	3		347	528	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994182	21994182	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	105	753	0	ENST00000579755.1:c.149T>A	p.Leu50Gln	p.L50Q	ENST00000579755		50	cTg/cAg	1/3	0.296441951281058		FACETS		0.431	0.535				INDETERMINATE	1	TRUE	0	0.570508114330595	2		753	764	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0049434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	18	346	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.545	0.409	0.707	0.545	0.409	0.707	SUBCLONAL	1	TRUE	1	0.14	2		346	472	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484339	8484339	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	30	264	0	ENST00000356435.5:c.3193G>T	p.Gly1065Cys	p.G1065C	ENST00000356435		1065	Ggc/Tgc	19/35	1	2	FACETS	1	0.831	1	1	0.831	1	CLONAL	1	TRUE	1	0.14	2		264	414	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600471	10600471	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	54	568	2	ENST00000171111.5:c.1384G>T	p.Gly462Trp	p.G462W	ENST00000171111	NM_203500.1	462	Ggg/Tgg	4/6	0.138997328818493	1	FACETS	0.922	0.786	1	0.922	0.786	1	CLONAL	1	TRUE	0	0.14	1		570	778	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220433	1220433	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	73	873	1	ENST00000326873.7:c.526G>T	p.Asp176Tyr	p.D176Y	ENST00000326873	NM_000455.4	176	Gac/Tac	4/10	0.138997328818493	1	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	0	0.14	1		874	931	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878185	48878185	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	50	210	0	ENST00000267163.4:c.137G>A	p.Arg46Lys	p.R46K	ENST00000267163	NM_000321.2	46	aGg/aAg	1/27	1	2	FACETS	1	0.898	1	1	0.976	1	CLONAL	2	TRUE	1	0.14	2		210	334	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136147	11136147	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	52	652	0	ENST00000358026.2:c.3131A>G	p.Lys1044Arg	p.K1044R	ENST00000358026	NM_001128849.1	1044	aAg/aGg	22/36	0.138997328818493	1	FACETS	0.861	0.732	1	0.861	0.732	1	CLONAL	1	TRUE	0	0.14	1		652	802	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349964	15349964	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	63	835	0	ENST00000263377.2:c.3688G>T	p.Ala1230Ser	p.A1230S	ENST00000263377	NM_058243.2	1230	Gcc/Tcc	18/20	0.138997328818493	1	FACETS	0.885	0.763	1	0.885	0.763	1	CLONAL	1	TRUE	0	0.14	1		835	946	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129605	47129605	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	26	258	0	ENST00000409792.3:c.5275C>T	p.Gln1759Ter	p.Q1759*	ENST00000409792	NM_014159.6	1759	Cag/Tag	10/21	1	2	FACETS	0.99	0.784	1	0.99	0.784	1	CLONAL	1	TRUE	1	0.14	2		258	375	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0049438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	67	616	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	0.118964488386859	3	FACETS	1	0.888	1	0.511	0.445	0.582	INDETERMINATE	1	FALSE	1	0.320365338879035	3		616	475	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913558	32913559	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359479	NA	P-0049438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	64	461	0	ENST00000380152.3:c.5073dup	p.Trp1692MetfsTer3	p.W1692Mfs*3	ENST00000380152		1689	gca/gcAa	11/27	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.320365338879035	2		461	311	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268760	41268760	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	36	453	0	ENST00000349496.5:c.998A>T	p.Tyr333Phe	p.Y333F	ENST00000349496	NM_001904.3	333	tAc/tTc	7/15	0.188744318064878	4	FACETS	0.813	0.669	0.973	0.271	0.223	0.325	INDETERMINATE	1	FALSE	1	0.320365338879035	4		453	365	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40476846	40476846	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0049438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	28	509	1	ENST00000264657.5:c.1483A>T	p.Lys495Ter	p.K495*	ENST00000264657	NM_139276.2	495	Aag/Tag	17/24	1	2	FACETS	0.419	0.335	0.516	0.419	0.335	0.516	SUBCLONAL	1	FALSE	1	0.320365338879035	2		510	417	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279961	18279961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	35	718	1	ENST00000222254.8:c.2044C>T	p.Pro682Ser	p.P682S	ENST00000222254	NM_005027.3	682	Ccc/Tcc	16/16	1	2	FACETS	0.435	0.356	0.524	0.435	0.356	0.524	SUBCLONAL	1	FALSE	1	0.320365338879035	2		719	502	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0049455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	227	385	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.48	2		385	652	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	99	431	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.898	0.803	0.998	0.898	0.803	0.998	CLONAL	1	TRUE	1	0.377040029004992	2		431	585	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0049460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	97	591	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.907	0.811	1	0.907	0.811	1	CLONAL	1	TRUE	1	0.377040029004992	2		592	567	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912580	NA	P-0049460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	77	248	0	ENST00000342988.3:c.1157G>A	p.Gly386Asp	p.G386D	ENST00000342988	NM_005359.5	386	gGt/gAt	10/12	0.377040029004992	1	FACETS	0.863	0.762	0.97	0.863	0.762	0.97	CLONAL	1	TRUE	0	0.377040029004992	1		248	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876658468	NA	P-0049460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	135	512	0	ENST00000269305.4:c.577C>G	p.His193Asp	p.H193D	ENST00000269305	NM_001126112.2	193	Cat/Gat	6/11	0.377040029004992	1	FACETS	0.993	0.906	1	0.993	0.906	1	CLONAL	1	TRUE	0	0.377040029004992	1		512	585	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100041	157100055	+	inframe_deletion	In_Frame_Del	DEL	AGGAGGAGCAGGAGC	AGGAGGAGCAGGAGC	-	rs773423003	NA	P-0049460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	11	41	1	ENST00000346085.5:c.993_1007del	p.Gly333_Gly337del	p.G333_G337del	ENST00000346085	NM_020732.3	326	ggAGGAGGAGCAGGAGCa/gga	1/20	1	2	FACETS	0.729	0.511	0.992	0.729	0.511	0.992	CLONAL	1	TRUE	1	0.377040029004992	2		42	80	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971060	21971060	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	94	342	0	ENST00000304494.5:c.298del	p.Ala100ProfsTer46	p.A100Pfs*46	ENST00000304494	NM_000077.4	100	Gcc/cc	2/3	1	2	FACETS	0.873	0.779	0.974	0.873	0.779	0.974	CLONAL	1	TRUE	1	0.377040029004992	2		342	571	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045114	47045114	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0049460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	130	263	0	ENST00000377604.3:c.2356-1G>A		p.X786_splice	ENST00000377604	NM_001204468.1	786			1	1	FACETS	0.786	0.722	0.852	1	0.988	1	SUBCLONAL	2	TRUE	0	0.377040029004992	1		263	356	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs730881677	NA	P-0049460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	81	276	0	ENST00000304494.5:c.151-1G>C		p.X51_splice	ENST00000304494	NM_000077.4	51			1	2	FACETS	0.91	0.805	1	0.91	0.805	1	CLONAL	1	TRUE	1	0.377040029004992	2		276	472	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049461-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	66	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.956	0.852	1	0.956	0.852	1	CLONAL	1	TRUE	1	0.885076634155913	2		148	156	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0049461-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	30	406	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.942	0.79	1	0.942	0.79	1	CLONAL	1	TRUE	1	0.885076634155913	2		406	72	SUCCESS
BTK	695	MSKCC	GRCh37	X	100629540	100629540	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049461-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	92	473	0	ENST00000308731.7:c.224C>G	p.Pro75Arg	p.P75R	ENST00000308731	NM_000061.2	75	cCa/cGa	3/19	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.885076634155913	2		473	173	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	277	499	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.963	1	1	0.997	1	CLONAL	4	TRUE	1	0.246608939466582	2		499	552	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	46	523	1	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	1	2	FACETS	0.488	0.409	0.575	0.488	0.409	0.575	SUBCLONAL	1	TRUE	1	0.246608939466582	2		524	765	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346884	73346884	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	139	224	1	ENST00000377767.4:c.1333del	p.Ser445HisfsTer20	p.S445Hfs*20	ENST00000377767	NM_014953.3	445	Tca/ca	9/21	1	2	FACETS	1	0.975	1	1	0.993	1	CLONAL	3	TRUE	1	0.246608939466582	2		225	332	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	21	504	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.22	0.168	0.281	0.22	0.168	0.281	SUBCLONAL	1	TRUE	1	0.246608939466582	2		504	773	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236086	108236086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782292	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	62	451	0	ENST00000278616.4:c.9022C>T	p.Arg3008Cys	p.R3008C	ENST00000278616	NM_000051.3	3008	Cgt/Tgt	63/63	1	2	FACETS	0.887	0.766	1	0.887	0.766	1	CLONAL	1	TRUE	1	0.246608939466582	2		451	567	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647657	3647657	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs774532876	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	182	666	4	ENST00000294008.3:c.1406del	p.Pro469HisfsTer4	p.P469Hfs*4	ENST00000294008	NM_032444.2	469	cCa/ca	7/15	1	2	FACETS	0.98	0.906	1	1	0.993	1	CLONAL	2	TRUE	1	0.246608939466582	2		670	753	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487554	38487554	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	286	619	0	ENST00000254066.5:c.89del	p.Pro30LeufsTer12	p.P30Lfs*12	ENST00000254066	NM_000964.3	28	ttC/tt	2/9	1	2	FACETS	1	0.988	1	1	0.997	1	CLONAL	3	TRUE	1	0.246608939466582	2		619	670	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	245	405	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	1	2	FACETS	0.999	0.945	1	1	0.996	1	CLONAL	4	TRUE	1	0.246608939466582	2		405	497	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089706	27089706	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	322	657	1	ENST00000324856.7:c.2666del	p.Gly889AlafsTer2	p.G889Afs*2	ENST00000324856	NM_006015.4	888	Ggg/gg	8/20	1	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	3	TRUE	1	0.246608939466582	2		658	762	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	19	371	1	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	1	2	FACETS	0.353	0.267	0.454	0.353	0.267	0.454	SUBCLONAL	1	TRUE	1	0.246608939466582	2		372	437	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	280	719	30	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	1	0.983	1	1	0.996	1	CLONAL	3	TRUE	1	0.246608939466582	2		749	689	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	265	720	1	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	0.246608939466582	1	FACETS	0.891	0.84	0.943	1	0.996	1	CLONAL	3	TRUE	0	0.246608939466582	1		721	705	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274794	123274794	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913478	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	70	466	0	ENST00000358487.5:c.1124A>G	p.Tyr375Cys	p.Y375C	ENST00000358487	NM_000141.4	375	tAc/tGc	9/18	1	2	FACETS	0.875	0.763	0.996	0.875	0.763	0.996	CLONAL	1	TRUE	1	0.246608939466582	2		466	649	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	323	361	12	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	0.922	0.877	0.968	1	0.997	1	CLONAL	4	TRUE	1	0.246608939466582	2		373	710	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346158	89346158	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs878855327	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	122	421	0	ENST00000301030.4:c.6792del	p.Ala2265ProfsTer72	p.A2265Pfs*72	ENST00000301030	NM_001256183.1	2264	ccC/cc	9/13	1	2	FACETS	1	0.953	1	1	0.992	1	CLONAL	3	TRUE	1	0.246608939466582	2		421	312	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245024	133245024	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs752846614	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	349	712	0	ENST00000320574.5:c.2091del	p.Leu698CysfsTer94	p.L698Cfs*94	ENST00000320574	NM_006231.2	697	ccC/cc	19/49	1	2	FACETS	1	0.99	1	1	0.997	1	CLONAL	3	TRUE	1	0.246608939466582	2		712	819	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411071	63411071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750971248	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	268	655	0	ENST00000330258.3:c.2096G>A	p.Arg699His	p.R699H	ENST00000330258	NM_152424.3	699	cGt/cAt	2/2	1	2	FACETS	0.947	0.897	0.997	1	0.996	1	CLONAL	4	TRUE	1	0.246608939466582	2		655	574	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916726	178916726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772110575	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	25	379	0	ENST00000263967.3:c.113G>A	p.Arg38His	p.R38H	ENST00000263967	NM_006218.2	38	cGt/cAt	2/21	1	2	FACETS	0.466	0.367	0.581	0.466	0.367	0.581	SUBCLONAL	1	TRUE	1	0.246608939466582	2		379	435	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048626	180048626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748514089	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	304	816	0	ENST00000261937.6:c.1936G>A	p.Glu646Lys	p.E646K	ENST00000261937	NM_182925.4	646	Gag/Aag	13/30	1	2	FACETS	0.935	0.889	0.982	1	0.997	1	CLONAL	4	TRUE	1	0.246608939466582	2		816	659	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69458697	69458697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1373641771	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	276	520	0	ENST00000227507.2:c.512C>T	p.Ala171Val	p.A171V	ENST00000227507	NM_053056.2	171	gCg/gTg	3/5	1	2	FACETS	0.905	0.857	0.954	1	0.996	1	CLONAL	4	TRUE	1	0.246608939466582	2		520	618	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692892	89692892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554898129	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	189	331	0	ENST00000371953.3:c.376G>A	p.Ala126Thr	p.A126T	ENST00000371953	NM_000314.4	126	Gct/Act	5/9	1	2	FACETS	0.93	0.871	0.989	1	0.995	1	CLONAL	4	TRUE	1	0.246608939466582	2		331	412	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107231	193107231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	132	236	0	ENST00000367435.3:c.440G>A	p.Arg147His	p.R147H	ENST00000367435	NM_024529.4	147	cGc/cAc	6/17	0.246608939466582	5	FACETS	1	0.979	1	0.622	0.567	0.68	CLONAL	2	TRUE	1	0.246608939466582	5		236	589	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829585	72829585	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	277	562	0	ENST00000268489.5:c.6996del	p.Lys2332AsnfsTer44	p.K2332Nfs*44	ENST00000268489	NM_006885.3	2332	aaA/aa	9/10	0.0507150118097059	3	FACETS	0.95	0.899	1			1	INDETERMINATE	4	TRUE	NA	0.246608939466582	3		562	664	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	43	657	0	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.469	0.391	0.555	0.469	0.391	0.555	SUBCLONAL	1	TRUE	1	0.246608939466582	2		657	744	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78435627	78435627	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs759271820	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	238	399	1	ENST00000370768.2:c.193del	p.Arg65AspfsTer3	p.R65Dfs*3	ENST00000370768	NM_003902.3	65	Aga/ga	2/20	1	2	FACETS	1	0.972	1	1	0.996	1	CLONAL	3	TRUE	1	0.246608939466582	2		400	610	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	281	655	6	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	3	TRUE	1	0.246608939466582	2		661	656	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793317	139793317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755436517	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	370	723	1	ENST00000247668.2:c.125G>A	p.Arg42His	p.R42H	ENST00000247668	NM_021138.3	42	cGc/cAc	2/11	1	2	FACETS	0.958	0.915	1	1	0.997	1	CLONAL	4	TRUE	1	0.246608939466582	2		724	783	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18964097	18964097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770535477	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	203	542	0	ENST00000262803.5:c.1094G>A	p.Arg365Gln	p.R365Q	ENST00000262803	NM_002911.3	365	cGg/cAg	8/24	0.246608939466582	1	FACETS	0.997	0.927	1	1	0.994	1	CLONAL	2	TRUE	0	0.246608939466582	1		542	724	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427984	49427984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	283	584	0	ENST00000301067.7:c.10606C>T	p.Arg3536Cys	p.R3536C	ENST00000301067	NM_003482.3	3536	Cgc/Tgc	38/54	1	2	FACETS	0.911	0.863	0.959	1	0.997	1	CLONAL	4	TRUE	1	0.246608939466582	2		584	630	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024682	11024682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	249	492	0	ENST00000327064.4:c.799C>T	p.Arg267Cys	p.R267C	ENST00000327064	NM_199141.1	267	Cgc/Tgc	6/16	0.246608939466582	1	FACETS	0.891	0.843	0.938	1	0.996	1	CLONAL	4	TRUE	0	0.246608939466582	1		492	497	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227659	36227659	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	69	547	0	ENST00000222270.7:c.7228A>G	p.Thr2410Ala	p.T2410A	ENST00000222270	NM_014727.1	2410	Act/Gct	31/37	0.246608939466582	1	FACETS	0.775	0.675	0.883	0.775	0.675	0.883	SUBCLONAL	1	TRUE	0	0.246608939466582	1		547	633	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798600	45798600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	308	683	0	ENST00000450313.1:c.494C>T	p.Ala165Val	p.A165V	ENST00000450313	NM_012222.2	165	gCt/gTt	6/16	1	2	FACETS	0.881	0.836	0.926	1	0.997	1	CLONAL	4	TRUE	1	0.246608939466582	2		683	709	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712007	89712007	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1564838034	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	139	202	0	ENST00000371953.3:c.626del	p.Gly209GlufsTer12	p.G209Efs*12	ENST00000371953	NM_000314.4	209	Gga/ga	6/9	1	2	FACETS	0.909	0.842	0.977	1	0.993	1	CLONAL	4	TRUE	1	0.246608939466582	2		202	310	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64126710	64126710	+	frameshift_variant,start_lost	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	121	250	1	ENST00000334205.4:c.7del	p.Asp3?	p.D3?	ENST00000334205	NM_003942.2	1	atG/at	1/17	1	2	FACETS	0.933	0.859	1	1	0.993	1	CLONAL	4	TRUE	1	0.246608939466582	2		251	263	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589331	28589331	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1478647878	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	255	356	0	ENST00000241453.7:c.2716T>C	p.Phe906Leu	p.F906L	ENST00000241453	NM_004119.2	906	Ttt/Ctt	22/24	1	2	FACETS	0.956	0.904	1	1	0.996	1	CLONAL	4	TRUE	1	0.246608939466582	2		356	541	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831217	72831218	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	281	507	0	ENST00000268489.5:c.5363dup	p.Gln1789AlafsTer18	p.Q1789Afs*18	ENST00000268489	NM_006885.3	1788	ctg/ctTg	9/10	0.0507150118097059	3	FACETS	1	0.983	1			1	INDETERMINATE	4	TRUE	NA	0.246608939466582	3		507	592	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89806459	89806459	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1015729981	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	66	499	0	ENST00000389301.3:c.3877G>A	p.Glu1293Lys	p.E1293K	ENST00000389301	NM_000135.2	1293	Gag/Aag	39/43	1	2	FACETS	0.766	0.664	0.876	0.766	0.664	0.876	SUBCLONAL	1	TRUE	1	0.246608939466582	2		499	699	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526149	63526149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759355821	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	328	559	0	ENST00000307078.5:c.2477C>T	p.Thr826Met	p.T826M	ENST00000307078	NM_004655.3	826	aCg/aTg	11/11	1	2	FACETS	1	0.987	1	1	0.997	1	CLONAL	3	TRUE	1	0.246608939466582	2		559	795	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354058	15354058	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	26	613	0	ENST00000263377.2:c.2822del	p.Pro941LeufsTer8	p.P941Lfs*8	ENST00000263377	NM_058243.2	941	cCt/ct	14/20	0.246608939466582	1	FACETS	0.388	0.307	0.482	0.388	0.307	0.482	SUBCLONAL	1	TRUE	0	0.246608939466582	1		613	476	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796588	42796588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1360243390	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	284	722	0	ENST00000575354.2:c.3145G>A	p.Gly1049Ser	p.G1049S	ENST00000575354	NM_015125.3	1049	Ggc/Agc	13/20	0.246608939466582	1	FACETS	1	0.982	1	1	0.996	1	CLONAL	3	TRUE	0	0.246608939466582	1		722	626	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387107	31387107	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	324	557	0	ENST00000328111.2:c.1732C>A	p.Leu578Met	p.L578M	ENST00000328111	NM_006892.3	578	Ctg/Atg	16/23	0.246608939466582	1	FACETS	1	0.985	1	1	0.997	1	CLONAL	3	TRUE	0	0.246608939466582	1		557	708	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389099	31389101	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	35	455	0	ENST00000328111.2:c.2017_2019del	p.Phe673del	p.F673del	ENST00000328111	NM_006892.3	671	cTCTtc/ctc	19/23	0.246608939466582	1	FACETS	0.466	0.381	0.562	0.466	0.381	0.562	SUBCLONAL	1	TRUE	0	0.246608939466582	1		455	534	SUCCESS
ATR	545	MSKCC	GRCh37	3	142168286	142168286	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	46	340	0	ENST00000350721.4:c.7920G>T	p.Trp2640Cys	p.W2640C	ENST00000350721	NM_001184.3	2640	tgG/tgT	47/47	1	2	FACETS	0.947	0.799	1	0.947	0.799	1	CLONAL	1	TRUE	1	0.246608939466582	2		340	394	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753923	57753923	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	274	386	0	ENST00000274289.3:c.701A>G	p.Glu234Gly	p.E234G	ENST00000274289	NM_006622.3	234	gAa/gGa	5/14	NA	3	FACETS	0.998	0.945	1	1	0.996	1	INDETERMINATE	4	TRUE	1	0.246608939466582	3		386	625	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641031	117641031	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	54	307	0	ENST00000368508.3:c.5940G>T	p.Lys1980Asn	p.K1980N	ENST00000368508	NM_002944.2	1980	aaG/aaT	36/43	1	2	FACETS	0.956	0.818	1	0.956	0.818	1	CLONAL	1	TRUE	1	0.246608939466582	2		307	458	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151216558	151216558	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	25	182	0	ENST00000262187.5:c.40T>C	p.Tyr14His	p.Y14H	ENST00000262187	NM_005614.3	14	Tac/Cac	1/8	0.246608939466582	6	FACETS	1	0.861	1	0.224	0.177	0.278	CLONAL	1	TRUE	1	0.246608939466582	6		182	270	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	495096	495096	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	63	339	0	ENST00000399788.2:c.210C>A	p.Phe70Leu	p.F70L	ENST00000399788	NM_001042603.1	70	ttC/ttA	2/28	0.249320319757856	4	FACETS	1	0.931	1	0.549	0.48	0.622	CLONAL	2	TRUE	0	0.288735534749628	4		339	256	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579583	7579584	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0049475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	57	505	0	ENST00000269305.4:c.103_104del	p.Leu35AlafsTer7	p.L35Afs*7	ENST00000269305	NM_001126112.2	35	TTg/g	4/11	0.226103455926874	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	0	0.288735534749628	2		505	181	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0049476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	243	616	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.528701379356541	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.528701379356541	1		618	629	SUCCESS
APC	324	MSKCC	GRCh37	5	112170777	112170780	+	frameshift_variant	Frame_Shift_Del	DEL	CAGA	CAGA	-	rs878853420	NA	P-0049476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	152	494	0	ENST00000257430.4:c.1875_1878del	p.Asn627LeufsTer2	p.N627Lfs*2	ENST00000257430	NM_000038.5	625	CAGAca/ca	15/16	1	2	FACETS	0.831	0.762	0.903	0.831	0.762	0.903	CLONAL	1	TRUE	1	0.528701379356541	2		494	692	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30047522	30047522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	112	330	0	ENST00000331968.5:c.2479C>T	p.Arg827Cys	p.R827C	ENST00000331968	NM_002742.2	827	Cgc/Tgc	17/18	0.528701379356541	1	FACETS	0.854	0.776	0.935	0.854	0.776	0.935	CLONAL	1	TRUE	0	0.528701379356541	1		330	365	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591913	48591913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	24	406	0	ENST00000342988.3:c.1076G>A	p.Gly359Glu	p.G359E	ENST00000342988	NM_005359.5	359	gGa/gAa	9/12	0.528701379356541	1	FACETS	0.147	0.114	0.184	0.147	0.114	0.184	SUBCLONAL	1	TRUE	0	0.528701379356541	1		406	455	SUCCESS
APC	324	MSKCC	GRCh37	5	112162943	112162946	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	INS	AGGT	AGGT	TGTTTTTATAAC	novel	NA	P-0049476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	77	261	0	ENST00000257430.4:c.1547_1548+2delinsTGTTTTTATAAC		p.X516_splice	ENST00000257430	NM_000038.5	516		12/16	1	2	FACETS	0.823	0.728	0.924	0.823	0.728	0.924	CLONAL	1	TRUE	1	0.528701379356541	2		261	354	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0049477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	77	202	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.30208086871919	1	FACETS	0.875	0.772	0.986	0.875	0.772	0.986	CLONAL	1	TRUE	0	0.332592793803258	1		202	441	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248998	55248999	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCAGCG	rs727504263	NA	P-0049477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	93	569	0	ENST00000275493.2:c.2300_2308dup	p.Ala767_Val769dup	p.A767_V769dup	ENST00000275493	NM_005228.3	767	atg/aTGGCCAGCGtg	20/28	1	2	FACETS	0.708	0.629	0.792	0.708	0.629	0.792	SUBCLONAL	1	TRUE	1	0.332592793803258	2		569	790	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983190	149983190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	77	430	1	ENST00000253339.5:c.3068C>T	p.Ser1023Phe	p.S1023F	ENST00000253339		1023	tCt/tTt	7/7	1	2	FACETS	0.817	0.718	0.923	0.817	0.718	0.923	CLONAL	1	TRUE	1	0.332592793803258	2		431	567	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346028	73346028	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	34	266	0	ENST00000377767.4:c.1510G>T	p.Val504Phe	p.V504F	ENST00000377767	NM_014953.3	504	Gtt/Ttt	11/21	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.332592793803258	2		266	195	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937813	76937813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	56	447	1	ENST00000373344.5:c.2935G>A	p.Glu979Lys	p.E979K	ENST00000373344	NM_000489.3	979	Gaa/Aaa	9/35	0.171648681824542	2	FACETS	0.738	0.634	0.852	0.369	0.317	0.426	INDETERMINATE	1	TRUE	0	0.332592793803258	2		448	456	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	344	479	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.347295356615708	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.347295356615708	3		479	1151	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	202	490	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.347295356615708	2		490	1102	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	204	723	1	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	0.347295356615708	1	FACETS	0.984	0.912	1	0.984	0.912	1	CLONAL	1	TRUE	0	0.347295356615708	1		724	987	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641555	47641555	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1114167845	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	77	216	0	ENST00000233146.2:c.940C>T	p.Gln314Ter	p.Q314*	ENST00000233146	NM_000251.2	314	Cag/Tag	5/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.347295356615708	2		216	386	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468236	50468236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	192	707	0	ENST00000331340.3:c.1471G>A	p.Glu491Lys	p.E491K	ENST00000331340	NM_006060.4	491	Gag/Aag	8/8	0.347295356615708	3	FACETS	0.954	0.88	1	0.477	0.44	0.516	CLONAL	1	TRUE	1	0.347295356615708	3		707	1360	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955394	48955394	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886043247	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	84	277	0	ENST00000267163.4:c.1510C>T	p.Gln504Ter	p.Q504*	ENST00000267163	NM_000321.2	504	Cag/Tag	17/27	0.347295356615708	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.347295356615708	1		277	371	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063313	67063313	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	64	179	0	ENST00000412916.2:c.3G>A	p.Met1?	p.M1?	ENST00000412916		1	atG/atA	1/6	0.347295356615708	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.347295356615708	1		179	282	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781092	135781092	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	156	593	0	ENST00000298552.3:c.1873G>T	p.Glu625Ter	p.E625*	ENST00000298552	NM_001162426.1	625	Gag/Tag	15/23	0.337772905473213	2	FACETS	0.947	0.866	1	0.473	0.433	0.516	CLONAL	1	TRUE	0	0.347295356615708	2		593	949	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324477	31324477	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs151341205	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	36	353	0	ENST00000412585.2:c.331C>T	p.Gln111Ter	p.Q111*	ENST00000412585	NM_005514.6	111	Cag/Tag	2/8	0.347295356615708	1	FACETS	0.414	0.34	0.496	0.414	0.34	0.496	SUBCLONAL	1	TRUE	0	0.347295356615708	1		353	414	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113100	209113100	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	93	266	0	ENST00000345146.2:c.407G>T	p.Gly136Val	p.G136V	ENST00000345146	NM_005896.2	136	gGg/gTg	4/10	0.347295356615708	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.347295356615708	1		266	379	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719424	190719424	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	110	314	0	ENST00000441310.2:c.1426G>C	p.Asp476His	p.D476H	ENST00000441310	NM_000534.4	476	Gat/Cat	9/13	0.347295356615708	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.347295356615708	1		314	432	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543909	41543909	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	147	612	0	ENST00000263253.7:c.2200C>T	p.Gln734Ter	p.Q734*	ENST00000263253	NM_001429.3	734	Cag/Tag	12/31	0.347295356615708	1	FACETS	0.889	0.812	0.969	0.889	0.812	0.969	CLONAL	1	TRUE	0	0.347295356615708	1		612	787	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69143584	69143584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142298071	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	93	372	0	ENST00000288368.4:c.4792G>A	p.Glu1598Lys	p.E1598K	ENST00000288368	NM_024870.2	1598	Gag/Aag	40/40	1	2	FACETS	0.821	0.731	0.918	0.821	0.731	0.918	CLONAL	1	TRUE	1	0.347295356615708	2		372	652	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	401990	401990	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	160	491	0	ENST00000399788.2:c.4801G>C	p.Glu1601Gln	p.E1601Q	ENST00000399788	NM_001042603.1	1601	Gag/Cag	27/28	0.347295356615708	3	FACETS	1	0.96	1	0.54	0.494	0.587	CLONAL	1	TRUE	1	0.347295356615708	3		491	1002	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884812	111884812	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374278232	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	151	529	0	ENST00000341259.2:c.901G>A	p.Glu301Lys	p.E301K	ENST00000341259	NM_005475.2	301	Gag/Aag	4/8	1	2	FACETS	0.994	0.909	1	0.994	0.909	1	CLONAL	1	TRUE	1	0.347295356615708	2		529	875	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235903	133235903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1482283883	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	257	687	0	ENST00000320574.5:c.3253G>A	p.Glu1085Lys	p.E1085K	ENST00000320574	NM_006231.2	1085	Gag/Aag	26/49	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.347295356615708	2		687	1090	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555623	21555623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	67	657	0	ENST00000382592.4:c.2647G>A	p.Glu883Lys	p.E883K	ENST00000382592	NM_014572.2	883	Gag/Aag	6/8	1	2	FACETS	0.37	0.32	0.424	0.37	0.32	0.424	SUBCLONAL	1	TRUE	1	0.347295356615708	2		657	1044	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40460253	40460253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	199	671	0	ENST00000345506.4:c.1964C>T	p.Ser655Phe	p.S655F	ENST00000345506	NM_003152.3	655	tCc/tTc	17/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.347295356615708	2		671	995	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40880956	40880956	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	103	425	0	ENST00000428826.2:c.4G>A	p.Glu2Lys	p.E2K	ENST00000428826		2	Gaa/Aaa	3/21	1	2	FACETS	0.752	0.672	0.836	0.752	0.672	0.836	SUBCLONAL	1	TRUE	1	0.347295356615708	2		425	789	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220688	1220688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	206	784	0	ENST00000326873.7:c.706G>A	p.Val236Met	p.V236M	ENST00000326873	NM_000455.4	236	Gtg/Atg	5/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.347295356615708	2		784	1118	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621158	1621158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1250135870	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	253	930	1	ENST00000344749.5:c.988G>A	p.Asp330Asn	p.D330N	ENST00000344749	NM_001136139.2	330	Gat/Aat	12/19	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.347295356615708	2		931	1350	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445412	29445412	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	170	686	0	ENST00000389048.3:c.3421G>T	p.Asp1141Tyr	p.D1141Y	ENST00000389048	NM_004304.4	1141	Gac/Tac	21/29	1	2	FACETS	0.89	0.817	0.966	0.89	0.817	0.966	CLONAL	1	TRUE	1	0.347295356615708	2		686	1100	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873041	136873041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	207	454	0	ENST00000241393.3:c.457G>A	p.Glu153Lys	p.E153K	ENST00000241393	NM_003467.2	153	Gaa/Aaa	2/2	0.347295356615708	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.347295356615708	1		454	721	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386432	31386432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	209	713	0	ENST00000328111.2:c.1657G>A	p.Asp553Asn	p.D553N	ENST00000328111	NM_006892.3	553	Gac/Aac	15/23	0.347295356615708	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.347295356615708	1		713	992	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52677318	52677318	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	150	566	1	ENST00000394830.3:c.941C>T	p.Ser314Leu	p.S314L	ENST00000394830	NM_018313.4	314	tCa/tTa	10/30	0.347295356615708	1	FACETS	0.92	0.842	1	0.92	0.842	1	CLONAL	1	TRUE	0	0.347295356615708	1		567	776	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204977	128204977	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	219	754	0	ENST00000341105.2:c.464C>T	p.Ser155Leu	p.S155L	ENST00000341105	NM_032638.4	155	tCa/tTa	3/6	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.347295356615708	2		754	1176	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260159	149260162	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	novel	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	145	530	0	ENST00000360632.3:c.731_734del	p.Arg244LysfsTer11	p.R244Kfs*11	ENST00000360632	NM_015472.4	244	aGAGAa/aa	4/7	1	2	FACETS	0.896	0.817	0.979	0.896	0.817	0.979	CLONAL	1	TRUE	1	0.347295356615708	2		530	932	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584533	189584533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	143	399	0	ENST00000264731.3:c.829G>A	p.Glu277Lys	p.E277K	ENST00000264731	NM_003722.4	277	Gaa/Aaa	6/14	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.347295356615708	2		399	763	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067083	143067083	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	124	494	0	ENST00000262992.4:c.1630G>T	p.Glu544Ter	p.E544*	ENST00000262992	NM_001101669.1	544	Gaa/Taa	16/24	0.347295356615708	1	FACETS	0.99	0.899	1	0.99	0.899	1	CLONAL	1	TRUE	0	0.347295356615708	1		494	596	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233636	233636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1337704280	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	42	134	0	ENST00000264932.6:c.940G>A	p.Glu314Lys	p.E314K	ENST00000264932	NM_004168.2	314	Gag/Aag	8/15	1	2	FACETS	0.889	0.747	1	0.889	0.747	1	CLONAL	1	TRUE	1	0.347295356615708	2		134	272	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055955	180055955	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	189	761	0	ENST00000261937.6:c.1030G>C	p.Glu344Gln	p.E344Q	ENST00000261937	NM_182925.4	344	Gag/Cag	8/30	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.347295356615708	2		761	1074	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323241	31323241	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	136	657	0	ENST00000412585.2:c.748C>G	p.Gln250Glu	p.Q250E	ENST00000412585	NM_005514.6	250	Cag/Gag	4/8	0.347295356615708	1	FACETS	0.74	0.672	0.81	0.74	0.672	0.81	SUBCLONAL	1	TRUE	0	0.347295356615708	1		657	875	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971133	13971133	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	75	327	0	ENST00000405192.2:c.796G>C	p.Asp266His	p.D266H	ENST00000405192	NM_001163147.1	266	Gac/Cac	8/12	0.347295356615708	3	FACETS	0.805	0.705	0.912	0.402	0.352	0.456	CLONAL	1	TRUE	1	0.347295356615708	3		327	630	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878742	151878742	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	135	444	0	ENST00000262189.6:c.6203C>G	p.Ser2068Cys	p.S2068C	ENST00000262189	NM_170606.2	2068	tCt/tGt	36/59	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.347295356615708	2		444	725	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169596	27169596	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	158	693	1	ENST00000380036.4:c.597C>A	p.Phe199Leu	p.F199L	ENST00000380036	NM_000459.3	199	ttC/ttA	4/23	0.347295356615708	1	FACETS	0.852	0.781	0.927	0.852	0.781	0.927	CLONAL	1	TRUE	0	0.347295356615708	1		694	882	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760004	133760004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	250	789	0	ENST00000318560.5:c.2327C>T	p.Thr776Ile	p.T776I	ENST00000318560	NM_005157.4	776	aCc/aTc	11/11	0.337772905473213	2	FACETS	1	0.984	1	0.583	0.545	0.623	CLONAL	1	TRUE	0	0.347295356615708	2		789	1234	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148692	20148692	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	123	195	0	ENST00000379607.5:c.371G>C	p.Gly124Ala	p.G124A	ENST00000379607	NM_001412.3	124	gGa/gCa	6/7	1	1	FACETS	0.808	0.739	0.88	1	0.988	1	CLONAL	2	TRUE	0	0.347295356615708	1		195	362	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0049481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	56	571	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.177614768554333	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	FALSE	0	0.269093805430839	1		571	312	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0049481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	64	428	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.257221554391068	3	FACETS	0.789	0.687	0.898	0.789	0.687	0.898	SUBCLONAL	2	FALSE	1	0.269093805430839	3		428	342	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528105	157528105	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1028186690	NA	P-0049481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	74	161	0	ENST00000346085.5:c.5830C>T	p.Arg1944Ter	p.R1944*	ENST00000346085	NM_020732.3	1944	Cga/Tga	20/20	0.269093805430839	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	0	0.269093805430839	1		161	355	SUCCESS
AR	367	MSKCC	GRCh37	X	66863151	66863151	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	10	251	0	ENST00000374690.3:c.1670A>G	p.Gln557Arg	p.Q557R	ENST00000374690	NM_000044.3	557	cAg/cGg	2/8	0.162537341142158	0	FACETS	0.365	0.247	0.511			1	SUBCLONAL	1	FALSE	NA	0.269093805430839	0		251	149	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217678	7217678	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	54	407	0	ENST00000380728.2:c.249G>C	p.Lys83Asn	p.K83N	ENST00000380728		83	aaG/aaC	4/11	0.177614768554333	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	0	0.269093805430839	1		407	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912660	NA	P-0049482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	448	602	0	ENST00000269305.4:c.839G>T	p.Arg280Ile	p.R280I	ENST00000269305	NM_001126112.2	280	aGa/aTa	8/11	0.879510544000042	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.884445614928486	1		602	515	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943448	17943448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370332355	NA	P-0049482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	506	747	0	ENST00000458235.1:c.2560G>A	p.Val854Met	p.V854M	ENST00000458235	NM_000215.3	854	Gtg/Atg	19/24	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.884445614928486	2		747	1048	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	1067	632	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.672441592636743	4	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	1	0.672441592636743	4		632	1620	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578432	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	350	793	0	ENST00000269305.4:c.498dup	p.Gln167ThrfsTer14	p.Q167Tfs*14	ENST00000269305	NM_001126112.2	166	-/A	5/11	0.672441592636743	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.672441592636743	1		793	640	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	107	431	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.303590604030563	3	FACETS	0.86	0.776	0.948			1	CLONAL	2	TRUE	NA	0.32	3		431	451	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294328	1294328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	52	644	0	ENST00000310581.5:c.673G>A	p.Gly225Arg	p.G225R	ENST00000310581	NM_198253.2	225	Ggg/Agg	2/16	0.303590604030563	3	FACETS	0.929	0.793	1	0.464	0.396	0.539	CLONAL	1	TRUE	1	0.32	3		644	406	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098973	178098973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	30	299	0	ENST00000397062.3:c.72G>C	p.Trp24Cys	p.W24C	ENST00000397062	NM_006164.4	24	tgG/tgC	2/5	0.200145464796246	3	FACETS	0.891	0.722	1	0.446	0.361	0.541	CLONAL	1	TRUE	1	0.32	3		299	244	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564743	86564743	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	29	701	0	ENST00000274376.6:c.475C>G	p.Leu159Val	p.L159V	ENST00000274376	NM_002890.2	159	Ctg/Gtg	1/25	0.200145464796246	3	FACETS	0.422	0.338	0.518	0.211	0.169	0.259	SUBCLONAL	1	TRUE	1	0.32	3		701	498	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455262	29455262	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	53	741	0	ENST00000389048.3:c.2540G>A	p.Arg847Lys	p.R847K	ENST00000389048	NM_004304.4	847	aGg/aAg	15/29	0.200145464796246	3	FACETS	0.917	0.784	1	0.459	0.392	0.531	CLONAL	1	TRUE	1	0.32	3		741	419	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740354	46740354	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs778442529	NA	P-0049484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	71	569	0	ENST00000371975.4:c.1834C>G	p.Gln612Glu	p.Q612E	ENST00000371975	NM_003579.3	612	Caa/Gaa	16/18	0.275439436281684	2	FACETS	1	0.908	1	0.522	0.457	0.591	CLONAL	1	TRUE	0	0.32	2		569	425	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692835	89692835	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	27	152	0	ENST00000371953.3:c.319G>C	p.Asp107His	p.D107H	ENST00000371953	NM_000314.4	107	Gat/Cat	5/9	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.32	2		152	120	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925522	114925522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	60	663	0	ENST00000543371.1:c.1600C>T	p.Pro534Ser	p.P534S	ENST00000543371	NM_001198531.1	534	Ccg/Tcg	14/14	0.301265103221861	1	FACETS	0.943	0.818	1	0.943	0.818	1	CLONAL	1	TRUE	0	0.32	1		663	334	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858649	57858649	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	41	493	0	ENST00000228682.2:c.387G>C	p.Met129Ile	p.M129I	ENST00000228682	NM_005269.2	129	atG/atC	4/12	0.267760246996541	4	FACETS	0.881	0.735	1	0.294	0.245	0.348	CLONAL	1	TRUE	1	0.32	4		493	384	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774200	66774200	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	75	948	0	ENST00000307102.5:c.676A>T	p.Thr226Ser	p.T226S	ENST00000307102	NM_002755.3	226	Aca/Tca	6/11	0.28021238159699	1	FACETS	0.849	0.746	0.958	0.849	0.746	0.958	CLONAL	1	TRUE	0	0.32	1		948	464	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119729	70119729	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	26	413	0	ENST00000245479.2:c.731A>T	p.Asp244Val	p.D244V	ENST00000245479	NM_000346.3	244	gAc/gTc	3/3	0.303590604030563	3	FACETS	0.6	0.476	0.742	0.3	0.238	0.371	SUBCLONAL	1	TRUE	1	0.32	3		413	314	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219694	36219694	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	64	825	0	ENST00000222270.7:c.4591G>T	p.Val1531Leu	p.V1531L	ENST00000222270	NM_014727.1	1531	Gtg/Ttg	20/37	NA	2	FACETS	0.857	0.743	0.979			1	INDETERMINATE	1	TRUE	NA	0.32	2		825	467	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62294181	62294181	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0049484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	74	583	0	ENST00000360203.5:c.478-1G>T		p.X160_splice	ENST00000360203	NM_001283009.1	160			1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.32	2		583	403	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39763581	39763581	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	21	375	0	ENST00000288319.7:c.871G>A	p.Asp291Asn	p.D291N	ENST00000288319	NM_182918.3	291	Gat/Aat	8/10	1	2	FACETS	0.432	0.332	0.547	0.432	0.332	0.547	SUBCLONAL	1	TRUE	1	0.32	2		375	304	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547924	41547924	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	63	517	0	ENST00000263253.7:c.2905G>C	p.Glu969Gln	p.E969Q	ENST00000263253	NM_001429.3	969	Gag/Cag	15/31	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.32	2		517	387	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278148	41278148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	91	534	0	ENST00000349496.5:c.2024C>T	p.Ser675Leu	p.S675L	ENST00000349496	NM_001904.3	675	tCa/tTa	13/15	0.273811010020467	2	FACETS	1	0.98	1	0.735	0.657	0.817	CLONAL	1	TRUE	0	0.32	2		534	387	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	18	323	0	ENST00000257430.4:c.4057G>C	p.Glu1353Gln	p.E1353Q	ENST00000257430	NM_000038.5	1353	Gaa/Caa	16/16	0.200145464796246	3	FACETS	0.469	0.353	0.606	0.235	0.176	0.303	SUBCLONAL	1	TRUE	1	0.32	3		323	278	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	187	782	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.938	0.867	1	0.938	0.867	1	CLONAL	1	TRUE	1	0.419488892245621	2		787	950	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	66	695	3	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.308	0.266	0.353	0.308	0.266	0.353	SUBCLONAL	1	TRUE	1	0.419488892245621	2		698	1022	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	90	406	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.964	0.86	1	0.964	0.86	1	CLONAL	1	TRUE	1	0.419488892245621	2		406	445	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912858	50912858	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1306540639	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	199	918	1	ENST00000440232.2:c.2089G>A	p.Ala697Thr	p.A697T	ENST00000440232	NM_002691.3	697	Gcc/Acc	17/27	1	2	FACETS	0.874	0.809	0.942	0.874	0.809	0.942	CLONAL	1	TRUE	1	0.419488892245621	2		919	1085	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274794	123274794	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913478	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	92	466	0	ENST00000358487.5:c.1124A>G	p.Tyr375Cys	p.Y375C	ENST00000358487	NM_000141.4	375	tAc/tGc	9/18	1	2	FACETS	0.615	0.547	0.688	0.615	0.547	0.688	SUBCLONAL	1	TRUE	1	0.419488892245621	2		466	713	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	29	271	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	0.456	0.367	0.558	0.456	0.367	0.558	SUBCLONAL	1	TRUE	1	0.419488892245621	2		271	303	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022913	27022938	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGCCGCCGCCAGCAGCCTGGGCAA	CCCGCCGCCGCCAGCAGCCTGGGCAA	-	rs797045262	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	11	42	0	ENST00000324856.7:c.31_56del	p.Ser11AlafsTer91	p.S11Afs*91	ENST00000324856	NM_006015.4	7	CCCGCCGCCGCCAGCAGCCTGGGCAAc/c	1/20	1	2	FACETS	0.61	0.426	0.831	0.61	0.426	0.831	SUBCLONAL	1	TRUE	1	0.419488892245621	2		42	86	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	84	538	2	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	0.529	0.467	0.596	0.529	0.467	0.596	SUBCLONAL	1	TRUE	1	0.419488892245621	2		540	757	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	97	359	0	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	1	2	FACETS	0.916	0.82	1	0.916	0.82	1	CLONAL	1	TRUE	1	0.419488892245621	2		359	505	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	84	530	0	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	1	2	FACETS	0.565	0.499	0.636	0.565	0.499	0.636	SUBCLONAL	1	TRUE	1	0.419488892245621	2		530	709	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86667971	86667971	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770599456	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	52	301	0	ENST00000274376.6:c.1735C>T	p.Arg579Trp	p.R579W	ENST00000274376	NM_002890.2	579	Cgg/Tgg	13/25	1	2	FACETS	0.668	0.571	0.774	0.668	0.571	0.774	SUBCLONAL	1	TRUE	1	0.419488892245621	2		301	371	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685307	89685307	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123317	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	23	224	0	ENST00000371953.3:c.202T>C	p.Tyr68His	p.Y68H	ENST00000371953	NM_000314.4	68	Tac/Cac	3/9	1	2	FACETS	0.322	0.25	0.404	0.322	0.25	0.404	SUBCLONAL	1	TRUE	1	0.419488892245621	2		224	341	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs121913292	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	101	400	0	ENST00000371953.3:c.389del	p.Arg130GlnfsTer4	p.R130Qfs*4	ENST00000371953	NM_000314.4	130	cGa/ca	5/9	1	2	FACETS	0.965	0.866	1	0.965	0.866	1	CLONAL	1	TRUE	1	0.419488892245621	2		400	499	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223109	41223109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567775064	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	89	527	0	ENST00000357654.3:c.4822G>A	p.Ala1608Thr	p.A1608T	ENST00000357654	NM_007294.3	1608	Gca/Aca	15/23	1	2	FACETS	0.503	0.445	0.565	0.503	0.445	0.565	SUBCLONAL	1	TRUE	1	0.419488892245621	2		527	844	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905055	50905055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	63	641	2	ENST00000440232.2:c.342del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	113	Ggg/gg	4/27	1	2	FACETS	0.353	0.305	0.407	0.353	0.305	0.407	SUBCLONAL	1	TRUE	1	0.419488892245621	2		643	850	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759623	133759623	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	84	781	0	ENST00000318560.5:c.1950del	p.Leu651TrpfsTer43	p.L651Wfs*43	ENST00000318560	NM_005157.4	649	aCc/ac	11/11	1	2	FACETS	0.411	0.362	0.464	0.411	0.362	0.464	SUBCLONAL	1	TRUE	1	0.419488892245621	2		781	975	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5225777	5225777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751437578	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	66	691	1	ENST00000357368.4:c.2455G>A	p.Ala819Thr	p.A819T	ENST00000357368	NM_002850.3	819	Gct/Act	17/38	1	2	FACETS	0.315	0.272	0.362	0.315	0.272	0.362	SUBCLONAL	1	TRUE	1	0.419488892245621	2		692	999	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40500444	40500444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	46	459	0	ENST00000264657.5:c.91C>T	p.Arg31Trp	p.R31W	ENST00000264657	NM_139276.2	31	Cgg/Tgg	2/24	1	2	FACETS	0.305	0.256	0.359	0.305	0.256	0.359	SUBCLONAL	1	TRUE	1	0.419488892245621	2		459	719	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270529	98270530	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs751977093	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	24	282	1	ENST00000331920.6:c.114dup	p.Leu39AlafsTer51	p.L39Afs*51	ENST00000331920	NM_000264.3	38	-/G	1/24	1	2	FACETS	0.296	0.231	0.37	0.296	0.231	0.37	SUBCLONAL	1	TRUE	1	0.419488892245621	2		283	387	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307280	65307283	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	60	328	0	ENST00000342505.4:c.2405_2408del	p.Lys802ArgfsTer11	p.K802Rfs*11	ENST00000342505	NM_002227.2	802	aAAGAg/ag	18/25	1	2	FACETS	0.591	0.51	0.679	0.591	0.51	0.679	SUBCLONAL	1	TRUE	1	0.419488892245621	2		328	484	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969087	93969087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1270476760	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	19	266	0	ENST00000369303.4:c.1909C>T	p.Arg637Cys	p.R637C	ENST00000369303	NM_004440.3	637	Cgt/Tgt	10/17	1	2	FACETS	0.254	0.193	0.327	0.254	0.193	0.327	SUBCLONAL	1	TRUE	1	0.419488892245621	2		266	356	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508557	106508557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	59	452	0	ENST00000359195.3:c.551G>A	p.Arg184His	p.R184H	ENST00000359195	NM_002649.2	184	cGc/cAc	2/11	1	2	FACETS	0.569	0.49	0.655	0.569	0.49	0.655	SUBCLONAL	1	TRUE	1	0.419488892245621	2		452	494	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	123	732	3	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	0.596	0.538	0.657	0.596	0.538	0.657	SUBCLONAL	1	TRUE	1	0.419488892245621	2		735	984	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214398	36214398	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs868041281	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	99	516	1	ENST00000222270.7:c.3057del	p.Gly1020AlafsTer4	p.G1020Afs*4	ENST00000222270	NM_014727.1	1018	Aaa/aa	7/37	1	2	FACETS	0.543	0.484	0.606	0.543	0.484	0.606	SUBCLONAL	1	TRUE	1	0.419488892245621	2		517	869	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420108	49420108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123729	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	47	582	0	ENST00000301067.7:c.15641G>A	p.Arg5214His	p.R5214H	ENST00000301067	NM_003482.3	5214	cGc/cAc	48/54	1	2	FACETS	0.294	0.247	0.346	0.294	0.247	0.346	SUBCLONAL	1	TRUE	1	0.419488892245621	2		582	761	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176353	24176353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	102	760	0	ENST00000263121.7:c.1144G>A	p.Ala382Thr	p.A382T	ENST00000263121	NM_003073.3	382	Gcc/Acc	9/9	1	2	FACETS	0.517	0.462	0.577	0.517	0.462	0.577	SUBCLONAL	1	TRUE	1	0.419488892245621	2		760	940	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798457	32798457	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	109	689	2	ENST00000374899.4:c.1399del	p.Val467LeufsTer2	p.V467Lfs*2	ENST00000374899	NM_018833.2	467	Gtt/tt	8/12	1	2	FACETS	0.499	0.447	0.554	0.499	0.447	0.554	SUBCLONAL	1	TRUE	1	0.419488892245621	2		691	1042	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967091	18967092	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1384543747	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	86	728	0	ENST00000262803.5:c.1814_1815del	p.Glu605AlafsTer17	p.E605Afs*17	ENST00000262803	NM_002911.3	602	gcAGag/gcag	13/24	1	2	FACETS	0.426	0.376	0.48	0.426	0.376	0.48	SUBCLONAL	1	TRUE	1	0.419488892245621	2		728	962	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450105	32450105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1190263054	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	78	673	1	ENST00000332351.3:c.707C>T	p.Ala236Val	p.A236V	ENST00000332351	NM_024426.4	236	gCg/gTg	2/10	1	2	FACETS	0.392	0.344	0.445	0.392	0.344	0.445	SUBCLONAL	1	TRUE	1	0.419488892245621	2		674	948	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210785	36210785	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771353672	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	107	840	0	ENST00000222270.7:c.536G>A	p.Arg179Gln	p.R179Q	ENST00000222270	NM_014727.1	179	cGg/cAg	3/37	1	2	FACETS	0.48	0.429	0.534	0.48	0.429	0.534	SUBCLONAL	1	TRUE	1	0.419488892245621	2		840	1063	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100369	27100369	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs770710220	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	178	556	0	ENST00000324856.7:c.4081A>G	p.Met1361Val	p.M1361V	ENST00000324856	NM_006015.4	1361	Atg/Gtg	17/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.419488892245621	2		556	760	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487629	56487629	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779911233	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	72	612	0	ENST00000267101.3:c.1562G>A	p.Arg521Gln	p.R521Q	ENST00000267101	NM_001982.3	521	cGa/cAa	13/28	1	2	FACETS	0.467	0.407	0.531	0.467	0.407	0.531	SUBCLONAL	1	TRUE	1	0.419488892245621	2		612	735	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157730	106157732	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs750024433	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	70	301	0	ENST00000380013.4:c.2636_2638del	p.Leu879del	p.L879del	ENST00000380013	NM_001127208.2	877	gaTCTt/gat	3/11	1	2	FACETS	0.885	0.776	1	0.885	0.776	1	CLONAL	1	TRUE	1	0.419488892245621	2		301	377	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701200	43701200	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	80	537	0	ENST00000382044.4:c.5495C>T	p.Ser1832Phe	p.S1832F	ENST00000382044	NM_001141980.1	1832	tCt/tTt	26/28	1	2	FACETS	0.518	0.455	0.585	0.518	0.455	0.585	SUBCLONAL	1	TRUE	1	0.419488892245621	2		537	737	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981483	70981483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	132	748	0	ENST00000276594.2:c.613G>A	p.Val205Ile	p.V205I	ENST00000276594	NM_024504.3	205	Gtt/Att	2/8	1	2	FACETS	0.58	0.525	0.638	0.58	0.525	0.638	SUBCLONAL	1	TRUE	1	0.419488892245621	2		748	1085	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643738	38643738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772476060	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	52	615	2	ENST00000299084.4:c.1208G>A	p.Arg403Gln	p.R403Q	ENST00000299084	NM_152594.2	403	cGa/cAa	7/7	1	2	FACETS	0.265	0.225	0.31	0.265	0.225	0.31	SUBCLONAL	1	TRUE	1	0.419488892245621	2		617	935	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845564	63845564	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	51	313	0	ENST00000279873.7:c.1306del	p.Thr436GlnfsTer43	p.T436Qfs*43	ENST00000279873	NM_032199.2	435	Aaa/aa	9/10	1	2	FACETS	0.632	0.538	0.733	0.632	0.538	0.733	SUBCLONAL	1	TRUE	1	0.419488892245621	2		313	385	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506308	120506308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140311741	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	65	469	1	ENST00000256646.2:c.1804G>A	p.Ala602Thr	p.A602T	ENST00000256646	NM_024408.3	602	Gcc/Acc	11/34	1	2	FACETS	0.445	0.385	0.51	0.445	0.385	0.51	SUBCLONAL	1	TRUE	1	0.419488892245621	2		470	696	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510151	120510151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	132	512	0	ENST00000256646.2:c.1358G>A	p.Cys453Tyr	p.C453Y	ENST00000256646	NM_024408.3	453	tGt/tAt	8/34	1	2	FACETS	0.853	0.775	0.934	0.853	0.775	0.934	CLONAL	1	TRUE	1	0.419488892245621	2		512	738	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518085	69518085	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	61	746	0	ENST00000294312.3:c.280G>T	p.Gly94Cys	p.G94C	ENST00000294312	NM_005117.2	94	Ggc/Tgc	2/3	1	2	FACETS	0.316	0.272	0.365	0.316	0.272	0.365	SUBCLONAL	1	TRUE	1	0.419488892245621	2		746	920	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102033255	102033255	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	49	521	0	ENST00000282441.5:c.641C>G	p.Ala214Gly	p.A214G	ENST00000282441	NM_001130145.2	214	gCc/gGc	3/9	1	2	FACETS	0.264	0.223	0.31	0.264	0.223	0.31	SUBCLONAL	1	TRUE	1	0.419488892245621	2		521	885	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394683	394683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	68	535	0	ENST00000399788.2:c.5012C>T	p.Pro1671Leu	p.P1671L	ENST00000399788	NM_001042603.1	1671	cCa/cTa	28/28	1	2	FACETS	0.412	0.358	0.472	0.412	0.358	0.472	SUBCLONAL	1	TRUE	1	0.419488892245621	2		535	786	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557650	21557650	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	49	620	0	ENST00000382592.4:c.2195A>G	p.Tyr732Cys	p.Y732C	ENST00000382592	NM_014572.2	732	tAc/tGc	5/8	1	2	FACETS	0.306	0.258	0.359	0.306	0.258	0.359	SUBCLONAL	1	TRUE	1	0.419488892245621	2		620	764	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061583	38061583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	59	278	0	ENST00000250448.2:c.406C>T	p.Pro136Ser	p.P136S	ENST00000250448	NM_004496.3	136	Ccg/Tcg	2/2	1	2	FACETS	0.837	0.724	0.958	0.837	0.724	0.958	CLONAL	1	TRUE	1	0.419488892245621	2		278	336	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572033	95572033	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	43	445	0	ENST00000393063.1:c.3075A>C	p.Glu1025Asp	p.E1025D	ENST00000393063	NM_030621.3	1025	gaA/gaC	20/28	1	2	FACETS	0.336	0.28	0.397	0.336	0.28	0.397	SUBCLONAL	1	TRUE	1	0.419488892245621	2		445	611	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705433	43705433	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs756168682	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	48	651	0	ENST00000382044.4:c.5189A>G	p.Asn1730Ser	p.N1730S	ENST00000382044	NM_001141980.1	1730	aAc/aGc	24/28	1	2	FACETS	0.258	0.217	0.304	0.258	0.217	0.304	SUBCLONAL	1	TRUE	1	0.419488892245621	2		651	886	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778902	3778902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756453838	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	78	687	0	ENST00000262367.5:c.6146C>T	p.Ala2049Val	p.A2049V	ENST00000262367	NM_004380.2	2049	gCt/gTt	31/31	1	2	FACETS	0.484	0.424	0.547	0.484	0.424	0.547	SUBCLONAL	1	TRUE	1	0.419488892245621	2		687	769	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325729	30325729	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1286252124	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	46	314	0	ENST00000322652.5:c.1927T>C	p.Tyr643His	p.Y643H	ENST00000322652	NM_015355.2	643	Tat/Cat	16/16	1	2	FACETS	0.77	0.652	0.897	0.77	0.652	0.897	SUBCLONAL	1	TRUE	1	0.419488892245621	2		314	285	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375417	15375417	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	55	689	0	ENST00000263377.2:c.1010A>G	p.Asp337Gly	p.D337G	ENST00000263377	NM_058243.2	337	gAc/gGc	6/20	1	2	FACETS	0.28	0.238	0.325	0.28	0.238	0.325	SUBCLONAL	1	TRUE	1	0.419488892245621	2		689	938	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213553	36213553	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	144	924	1	ENST00000222270.7:c.2655G>T	p.Met885Ile	p.M885I	ENST00000222270	NM_014727.1	885	atG/atT	5/37	1	2	FACETS	0.588	0.535	0.644	0.588	0.535	0.644	SUBCLONAL	1	TRUE	1	0.419488892245621	2		925	1167	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214112	36214112	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	92	787	0	ENST00000222270.7:c.2938T>A	p.Ser980Thr	p.S980T	ENST00000222270	NM_014727.1	980	Tcc/Acc	6/37	1	2	FACETS	0.354	0.313	0.398	0.354	0.313	0.398	SUBCLONAL	1	TRUE	1	0.419488892245621	2		787	1239	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229244	36229244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	64	706	0	ENST00000222270.7:c.7934G>A	p.Gly2645Asp	p.G2645D	ENST00000222270	NM_014727.1	2645	gGc/gAc	37/37	1	2	FACETS	0.323	0.278	0.371	0.323	0.278	0.371	SUBCLONAL	1	TRUE	1	0.419488892245621	2		706	946	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965846	25965846	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	95	585	0	ENST00000435504.4:c.3360G>T	p.Met1120Ile	p.M1120I	ENST00000435504		1120	atG/atT	13/13	1	2	FACETS	0.525	0.467	0.587	0.525	0.467	0.587	SUBCLONAL	1	TRUE	1	0.419488892245621	2		585	863	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661479	227661479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1185619711	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	49	700	0	ENST00000305123.5:c.1976C>T	p.Pro659Leu	p.P659L	ENST00000305123	NM_005544.2	659	cCc/cTc	1/2	1	2	FACETS	0.302	0.255	0.354	0.302	0.255	0.354	SUBCLONAL	1	TRUE	1	0.419488892245621	2		700	774	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795075	242795075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	67	783	1	ENST00000334409.5:c.134C>T	p.Thr45Ile	p.T45I	ENST00000334409	NM_005018.2	45	aCc/aTc	2/5	1	2	FACETS	0.335	0.29	0.384	0.335	0.29	0.384	SUBCLONAL	1	TRUE	1	0.419488892245621	2		784	953	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019139	31019139	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs763582989	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	70	412	1	ENST00000375687.4:c.734A>T	p.Asn245Ile	p.N245I	ENST00000375687	NM_015338.5	245	aAc/aTc	9/13	1	2	FACETS	0.526	0.458	0.599	0.526	0.458	0.599	SUBCLONAL	1	TRUE	1	0.419488892245621	2		413	635	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42870105	42870105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	168	583	0	ENST00000398585.3:c.67C>T	p.His23Tyr	p.H23Y	ENST00000398585	NM_001135099.1	23	Cat/Tat	2/14	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.419488892245621	2		583	766	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199922	128199922	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	81	636	1	ENST00000341105.2:c.1383del	p.Ser462ProfsTer15	p.S462Pfs*15	ENST00000341105	NM_032638.4	461	ccC/cc	6/6	1	2	FACETS	0.485	0.427	0.548	0.485	0.427	0.548	SUBCLONAL	1	TRUE	1	0.419488892245621	2		637	796	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430510	181430515	+	inframe_deletion	In_Frame_Del	DEL	AGAAGG	AGAAGG	-	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	63	453	0	ENST00000325404.1:c.363_368del	p.Lys121_Asp123delinsAsn	p.K121_D123delinsN	ENST00000325404	NM_003106.3	121	aAGAAGGat/aat	1/1	1	2	FACETS	0.442	0.381	0.507	0.442	0.381	0.507	SUBCLONAL	1	TRUE	1	0.419488892245621	2		453	680	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468161	31468161	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	31	440	0	ENST00000344624.3:c.2251T>G	p.Ser751Ala	p.S751A	ENST00000344624		751	Tct/Gct	15/33	1	2	FACETS	0.263	0.212	0.322	0.263	0.212	0.322	SUBCLONAL	1	TRUE	1	0.419488892245621	2		440	561	SUCCESS
APC	324	MSKCC	GRCh37	5	112176906	112176906	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs748389037	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	31	392	0	ENST00000257430.4:c.5615T>A	p.Val1872Asp	p.V1872D	ENST00000257430	NM_000038.5	1872	gTt/gAt	16/16	1	2	FACETS	0.359	0.29	0.437	0.359	0.29	0.437	SUBCLONAL	1	TRUE	1	0.419488892245621	2		392	412	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805399	32805399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	81	575	0	ENST00000374899.4:c.523C>T	p.Arg175Cys	p.R175C	ENST00000374899	NM_018833.2	175	Cgt/Tgt	3/12	1	2	FACETS	0.426	0.374	0.481	0.426	0.374	0.481	SUBCLONAL	1	TRUE	1	0.419488892245621	2		575	907	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729789	41729789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	31	405	0	ENST00000242208.4:c.740G>A	p.Cys247Tyr	p.C247Y	ENST00000242208	NM_002192.2	247	tGc/tAc	3/3	1	2	FACETS	0.294	0.237	0.359	0.294	0.237	0.359	SUBCLONAL	1	TRUE	1	0.419488892245621	2		405	502	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462496	92462496	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	42	645	0	ENST00000265734.4:c.142C>T	p.Gln48Ter	p.Q48*	ENST00000265734	NM_001259.6	48	Cag/Tag	2/8	1	2	FACETS	0.27	0.224	0.32	0.27	0.224	0.32	SUBCLONAL	1	TRUE	1	0.419488892245621	2		645	743	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513324	106513324	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	26	321	0	ENST00000359195.3:c.2232del	p.Val745SerfsTer47	p.V745Sfs*47	ENST00000359195	NM_002649.2	743	cAa/ca	4/11	1	2	FACETS	0.25	0.197	0.311	0.25	0.197	0.311	SUBCLONAL	1	TRUE	1	0.419488892245621	2		321	496	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5463086	5463086	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	38	328	0	ENST00000381577.3:c.647C>A	p.Pro216His	p.P216H	ENST00000381577	NM_014143.3	216	cCt/cAt	4/7	1	2	FACETS	0.443	0.366	0.528	0.443	0.366	0.528	SUBCLONAL	1	TRUE	1	0.419488892245621	2		328	409	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390602	139390602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	125	811	0	ENST00000277541.6:c.7589C>T	p.Ser2530Phe	p.S2530F	ENST00000277541	NM_017617.3	2530	tCc/tTc	34/34	1	2	FACETS	0.584	0.527	0.643	0.584	0.527	0.643	SUBCLONAL	1	TRUE	1	0.419488892245621	2		811	1021	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466030	69466041	+	protein_altering_variant	In_Frame_Del	DEL	GTGCGGGACGTG	GTGCGGGACGTG	CCGCACGTC	novel	NA	P-0049485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	146	735	3	ENST00000227507.2:c.868_879delinsCCGCACGTC	p.Val290_Asp292delinsProHis	p.V290_D292delinsPH	ENST00000227507	NM_053056.2	290	GTGCGGGACGTG/CCGCACGTC	5/5	1	2	FACETS	0.779	0.71	0.85	0.779	0.71	0.85	SUBCLONAL	1	TRUE	1	0.419488892245621	2		738	894	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0049486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	81	437	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.313593181765469	2		437	485	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0049486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	120	409	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.313593181765469	2		415	586	SUCCESS
APC	324	MSKCC	GRCh37	5	112175760	112175761	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs398123122	NA	P-0049486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	78	311	0	ENST00000257430.4:c.4473dup	p.Ala1492CysfsTer22	p.A1492Cfs*22	ENST00000257430	NM_000038.5	1490	cat/caTt	16/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.313593181765469	2		311	398	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0049486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	71	263	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.313593181765469	2		263	439	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0049486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	103	523	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.848	0.758	0.942	0.848	0.758	0.942	CLONAL	1	TRUE	1	0.313593181765469	2		523	775	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0049486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	101	591	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.313593181765469	2		592	641	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200073	128200073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374457534	NA	P-0049486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	228	679	1	ENST00000341105.2:c.1232C>T	p.Ala411Val	p.A411V	ENST00000341105	NM_032638.4	411	gCg/gTg	6/6	1	2	FACETS	0.757	0.706	0.81	1	0.992	1	SUBCLONAL	2	TRUE	1	0.313593181765469	2		680	960	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0049486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	78	350	2	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.313593181765469	2		352	436	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032767	48032768	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1057517764	NA	P-0049486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	73	265	0	ENST00000234420.5:c.3573dup	p.Val1192CysfsTer2	p.V1192Cfs*2	ENST00000234420	NM_000179.2	1189	-/T	7/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.313593181765469	2		265	345	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105938	27105938	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs750044693	NA	P-0049486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	130	568	0	ENST00000324856.7:c.5549A>G	p.Asp1850Gly	p.D1850G	ENST00000324856	NM_006015.4	1850	gAc/gGc	20/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.313593181765469	2		568	761	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512377	38512377	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555574293	NA	P-0049486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	84	479	0	ENST00000254066.5:c.1293del	p.Arg432GlyfsTer211	p.R432Gfs*211	ENST00000254066	NM_000964.3	430	Ggg/gg	9/9	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.313593181765469	2		479	509	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970914	79970915	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587776701	NA	P-0049486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	194	452	10	ENST00000265081.6:c.1148dup	p.Asn385GlnfsTer19	p.N385Qfs*19	ENST00000265081	NM_002439.4	380	-/A	7/24	1	2	FACETS	0.973	0.905	1	1	0.993	1	CLONAL	2	TRUE	1	0.313593181765469	2		462	636	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098540	11098540	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	192	564	0	ENST00000358026.2:c.1062del	p.Ile355SerfsTer56	p.I355Sfs*56	ENST00000358026	NM_001128849.1	353	aCc/ac	6/36	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.313593181765469	2		564	850	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180035975	180035975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138599624	NA	P-0049486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	96	619	3	ENST00000261937.6:c.3886G>A	p.Gly1296Ser	p.G1296S	ENST00000261937	NM_182925.4	1296	Ggc/Agc	29/30	1	2	FACETS	0.661	0.588	0.739	0.661	0.588	0.739	SUBCLONAL	1	TRUE	1	0.313593181765469	2		622	926	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874011	123874016	+	inframe_deletion	In_Frame_Del	DEL	GGCGGC	GGCGGC	-	rs780061449	NA	P-0049486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	14	50	0	ENST00000330479.4:c.59_64del	p.Ala20_Ala21del	p.A20_A21del	ENST00000330479	NM_020382.3	14	gaGGCGGCg/gag	2/9	1	2	FACETS	0.902	0.66	1	0.902	0.66	1	CLONAL	1	TRUE	1	0.313593181765469	2		50	99	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260447	16260447	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	136	483	0	ENST00000375759.3:c.7715del	p.Pro2572ArgfsTer11	p.P2572Rfs*11	ENST00000375759	NM_015001.2	2571	gCc/gc	11/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.313593181765469	2		483	680	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143021	58143021	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778188	NA	P-0049486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	194	726	2	ENST00000257904.6:c.763C>T	p.Arg255Cys	p.R255C	ENST00000257904	NM_000075.3	255	Cgc/Tgc	7/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.313593181765469	2		728	1018	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738156	133738156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756003964	NA	P-0049486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	34	465	1	ENST00000318560.5:c.556G>A	p.Val186Ile	p.V186I	ENST00000318560	NM_005157.4	186	Gtc/Atc	4/11	1	2	FACETS	0.338	0.275	0.409	0.338	0.275	0.409	SUBCLONAL	1	TRUE	1	0.313593181765469	2		466	642	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21639508	21639508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138278747	NA	P-0049486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	64	208	0	ENST00000421138.2:c.406G>A	p.Val136Ile	p.V136I	ENST00000421138		136	Gtc/Atc	6/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.313593181765469	2		208	288	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420598	49420598	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	198	741	0	ENST00000301067.7:c.15151A>G	p.Asn5051Asp	p.N5051D	ENST00000301067	NM_003482.3	5051	Aac/Gac	48/54	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.313593181765469	2		741	907	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233794	133233794	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	50	563	0	ENST00000320574.5:c.3510del	p.Lys1170AsnfsTer49	p.K1170Nfs*49	ENST00000320574	NM_006231.2	1170	aaA/aa	29/49	1	2	FACETS	0.375	0.317	0.439	0.375	0.317	0.439	SUBCLONAL	1	TRUE	1	0.313593181765469	2		563	850	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953950	32953950	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	86	341	0	ENST00000380152.3:c.9017A>G	p.Tyr3006Cys	p.Y3006C	ENST00000380152		3006	tAc/tGc	23/27	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.313593181765469	2		341	434	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986709	36986709	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	15	34	0	ENST00000354822.5:c.980C>T	p.Ala327Val	p.A327V	ENST00000354822	NM_001079668.2	327	gCg/gTg	3/3	1	2	FACETS	1	0.832	1	1	0.832	1	CLONAL	1	TRUE	1	0.313593181765469	2		34	82	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658880	3658880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149117119	NA	P-0049486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	146	523	1	ENST00000294008.3:c.86G>A	p.Arg29His	p.R29H	ENST00000294008	NM_032444.2	29	cGc/cAc	2/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.313593181765469	2		524	715	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56857718	56857718	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1288227780	NA	P-0049486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	40	453	0	ENST00000308159.5:c.754A>G	p.Met252Val	p.M252V	ENST00000308159	NM_014669.4	252	Atg/Gtg	8/22	1	2	FACETS	0.357	0.296	0.426	0.357	0.296	0.426	SUBCLONAL	1	TRUE	1	0.313593181765469	2		453	714	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40468878	40468879	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0049486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	55	415	1	ENST00000264657.5:c.2185dup	p.Arg729ProfsTer12	p.R729Pfs*12	ENST00000264657	NM_139276.2	729	cgc/cCgc	23/24	1	2	FACETS	0.5	0.427	0.58	0.5	0.427	0.58	SUBCLONAL	1	TRUE	1	0.313593181765469	2		416	702	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222759	5222759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751272492	NA	P-0049486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	195	639	1	ENST00000357368.4:c.3044G>A	p.Arg1015His	p.R1015H	ENST00000357368	NM_002850.3	1015	cGc/cAc	18/38	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.313593181765469	2		640	879	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574884	41574884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	51	616	1	ENST00000263253.7:c.7169C>T	p.Ala2390Val	p.A2390V	ENST00000263253	NM_001429.3	2390	gCc/gTc	31/31	1	2	FACETS	0.336	0.284	0.393	0.336	0.284	0.393	SUBCLONAL	1	TRUE	1	0.313593181765469	2		617	969	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280754	41280755	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0049486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	143	515	0	ENST00000349496.5:c.2271dup	p.His758AlafsTer13	p.H758Afs*13	ENST00000349496	NM_001904.3	756	ctg/ctGg	15/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.313593181765469	2		515	670	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559291	141559291	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	49	734	0	ENST00000220592.5:c.1510A>G	p.Met504Val	p.M504V	ENST00000220592	NM_012154.3	504	Atg/Gtg	12/19	1	2	FACETS	0.326	0.275	0.383	0.326	0.275	0.383	SUBCLONAL	1	TRUE	1	0.313593181765469	2		734	958	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133710882	133710882	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	53	341	0	ENST00000318560.5:c.49C>A	p.Leu17Met	p.L17M	ENST00000318560	NM_005157.4	17	Ctg/Atg	1/11	1	2	FACETS	0.526	0.448	0.611	0.526	0.448	0.611	SUBCLONAL	1	TRUE	1	0.313593181765469	2		341	643	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409962	63409962	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	42	575	0	ENST00000330258.3:c.3205C>A	p.Pro1069Thr	p.P1069T	ENST00000330258	NM_152424.3	1069	Ccc/Acc	2/2	1	2	FACETS	0.403	0.336	0.479	0.403	0.336	0.479	SUBCLONAL	1	TRUE	1	0.313593181765469	2		575	664	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845236	89845236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775917892	NA	P-0049487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	253	497	0	ENST00000389301.3:c.1799G>A	p.Arg600His	p.R600H	ENST00000389301	NM_000135.2	600	cGt/cAt	20/43	1	2	FACETS	0.973	0.913	1	0.973	0.913	1	CLONAL	1	TRUE	1	0.622625437378313	2		497	835	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309824	104309824	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	194	434	0	ENST00000369902.3:c.415G>T	p.Glu139Ter	p.E139*	ENST00000369902	NM_016169.3	139	Gag/Tag	3/12	1	2	FACETS	0.88	0.817	0.945	0.88	0.817	0.945	CLONAL	1	TRUE	1	0.622625437378313	2		434	708	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436671	52436692	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GTCCTTCTCTGGTCATCAATCT	GTCCTTCTCTGGTCATCAATCT	-	novel	NA	P-0049487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	275	686	0	ENST00000460680.1:c.1984-2_2003del		p.X662_splice	ENST00000460680	NM_004656.3	662		16/17	1	2	FACETS	0.897	0.843	0.952	0.897	0.843	0.952	CLONAL	1	TRUE	1	0.622625437378313	2		686	985	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436808	52436812	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTT	CTCTT	-	novel	NA	P-0049487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	286	645	0	ENST00000460680.1:c.1966_1970del	p.Lys656GlufsTer6	p.K656Efs*6	ENST00000460680	NM_004656.3	656	AAGAGg/g	15/17	1	2	FACETS	0.95	0.895	1	0.95	0.895	1	CLONAL	1	TRUE	1	0.622625437378313	2		645	967	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14027740	14027740	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	162	337	0	ENST00000405192.2:c.104T>A	p.Ile35Asn	p.I35N	ENST00000405192	NM_001163147.1	35	aTt/aAt	3/12	1	2	FACETS	0.802	0.738	0.868	0.802	0.738	0.868	CLONAL	1	TRUE	1	0.622625437378313	2		337	649	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751247	128751247	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	191	425	0	ENST00000377970.2:c.784A>T	p.Thr262Ser	p.T262S	ENST00000377970	NM_002467.4	262	Acc/Tcc	2/3	1	2	FACETS	0.977	0.908	1	0.977	0.908	1	CLONAL	1	TRUE	1	0.622625437378313	2		425	628	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0049488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	996	325	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.608067405420784	10	FACETS	0.98	0.959	1	0.98	0.959	1	CLONAL	8	FALSE	2	0.608067405420784	10		325	1434	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916759	48916759	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	170	395	3	ENST00000267163.4:c.289G>T	p.Glu97Ter	p.E97*	ENST00000267163	NM_000321.2	97	Gaa/Taa	3/27	0.578307792163174	3	FACETS	1	0.988	1	0.818	0.769	0.867	CLONAL	2	FALSE	0	0.608067405420784	3		398	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0049488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	465	578	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.600495488482576	2	FACETS	0.996	0.961	1	0.996	0.961	1	CLONAL	2	FALSE	0	0.608067405420784	2		578	768	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518000	8518000	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	222	383	0	ENST00000356435.5:c.1391A>G	p.Asn464Ser	p.N464S	ENST00000356435		464	aAc/aGc	10/35	0.60811360300368	4	FACETS	0.799	0.746	0.853	0.799	0.746	0.853	SUBCLONAL	2	FALSE	2	0.608067405420784	4		383	735	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0049490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	632	591	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.563082884229585	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.563082884229585	2		593	1067	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0049490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	294	259	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.563082884229585	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.563082884229585	2		259	473	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5260818	5260818	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs747842113	NA	P-0049490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	241	575	0	ENST00000357368.4:c.593G>C	p.Arg198Pro	p.R198P	ENST00000357368	NM_002850.3	198	cGa/cCa	7/38	0.563082884229585	3	FACETS	0.969	0.904	1	0.485	0.452	0.518	CLONAL	1	TRUE	1	0.563082884229585	3		575	1132	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411291	63411291	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1408150272	NA	P-0049490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	603	306	1	ENST00000330258.3:c.1876C>T	p.Arg626Ter	p.R626*	ENST00000330258	NM_152424.3	626	Cga/Tga	2/2	0.513225514204978	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.563082884229585	2		307	871	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480350	56480350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147905731	NA	P-0049490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	206	463	0	ENST00000267101.3:c.457G>A	p.Asp153Asn	p.D153N	ENST00000267101	NM_001982.3	153	Gat/Aat	4/28	1	2	FACETS	0.924	0.859	0.991	0.924	0.859	0.991	CLONAL	1	TRUE	1	0.563082884229585	2		463	792	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245512	153245512	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	664	311	0	ENST00000281708.4:c.1679A>G	p.Asp560Gly	p.D560G	ENST00000281708	NM_033632.3	560	gAt/gGt	11/12	0.430554630184089	6	FACETS	0.943	0.916	0.969			1	CLONAL	5	TRUE	NA	0.563082884229585	6		311	1064	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874022	123874022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1164517572	NA	P-0049490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	21	52	0	ENST00000330479.4:c.53C>T	p.Ala18Val	p.A18V	ENST00000330479	NM_020382.3	18	gCg/gTg	2/9	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.563082884229585	2		52	60	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350815	15350815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	73	514	0	ENST00000263377.2:c.3188C>T	p.Pro1063Leu	p.P1063L	ENST00000263377	NM_058243.2	1063	cCc/cTc	15/20	0.563082884229585	3	FACETS	0.266	0.231	0.303	0.133	0.115	0.152	SUBCLONAL	1	TRUE	1	0.563082884229585	3		514	1251	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0049498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	39	437	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.377751414315669	5	FACETS	0.86	0.724	1	0.573	0.483	0.67	CLONAL	2	TRUE	2	0.521880722833631	5		437	155	SUCCESS
APC	324	MSKCC	GRCh37	5	112175706	112175706	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	14	355	0	ENST00000257430.4:c.4415del	p.Val1472GlufsTer35	p.V1472Efs*35	ENST00000257430	NM_000038.5	1472	gTa/ga	16/16	0.410312065160376	3	FACETS	0.846	0.622	1	0.423	0.311	0.553	CLONAL	1	TRUE	1	0.521880722833631	3		355	80	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0049498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	45	332	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.829	0.72	0.94	1	0.972	1	CLONAL	2	TRUE	1	0.521880722833631	2		332	104	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577594	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0049498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	101	508	0	ENST00000269305.4:c.687T>A	p.Cys229Ter	p.C229*	ENST00000269305	NM_001126112.2	229	tgT/tgA	7/11	0.502753631923611	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.521880722833631	2		508	177	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119751	70119752	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0049498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	172	450	0	ENST00000245479.2:c.754_755dup	p.Lys253Ter	p.K253*	ENST00000245479	NM_000346.3	251	-/CT	3/3	0.377751414315669	5	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	TRUE	2	0.521880722833631	5		450	367	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851273	156851273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763591781	NA	P-0049498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	111	698	0	ENST00000524377.1:c.2230C>T	p.Arg744Cys	p.R744C	ENST00000524377	NM_002529.3	744	Cgt/Tgt	17/17	0.123259725669329	5	FACETS	1	0.963	1	0.814	0.748	0.88	INDETERMINATE	3	TRUE	1	0.521880722833631	5		698	233	SUCCESS
APC	324	MSKCC	GRCh37	5	112174481	112174481	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1462312032	NA	P-0049498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	16	280	0	ENST00000257430.4:c.3190G>T	p.Glu1064Ter	p.E1064*	ENST00000257430	NM_000038.5	1064	Gag/Tag	16/16	0.410312065160376	3	FACETS	1	0.891	1	0.678	0.518	0.856	CLONAL	1	TRUE	1	0.521880722833631	3		280	57	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0049499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	303	591	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.623950162784946	1	FACETS	0.997	0.947	1	0.997	0.947	1	CLONAL	1	TRUE	0	0.623950162784946	1		593	670	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385068	31385068	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	57	689	0	ENST00000328111.2:c.1453C>T	p.Arg485Ter	p.R485*	ENST00000328111	NM_006892.3	485	Cga/Tga	14/23	1	2	FACETS	0.175	0.149	0.203	0.175	0.149	0.203	SUBCLONAL	1	TRUE	1	0.623950162784946	2		689	1047	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127911968	127911968	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768855518	NA	P-0049499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	141	344	0	ENST00000373547.4:c.902C>T	p.Thr301Met	p.T301M	ENST00000373547	NM_002721.4	301	aCg/aTg	7/7	1	2	FACETS	0.859	0.787	0.934	0.859	0.787	0.934	CLONAL	1	TRUE	1	0.623950162784946	2		344	526	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405110	139405110	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773185855	NA	P-0049499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	348	789	0	ENST00000277541.6:c.2735G>A	p.Arg912Gln	p.R912Q	ENST00000277541	NM_017617.3	912	cGg/cAg	17/34	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.623950162784946	2		789	1114	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0049500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	172	421	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	0.230895982690585	3	FACETS	1	0.986	1	0.672	0.619	0.728	CLONAL	1	TRUE	1	0.338937424319469	3		421	883	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346309	89346309	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1180020342	NA	P-0049500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	153	468	0	ENST00000301030.4:c.6641A>G	p.Asp2214Gly	p.D2214G	ENST00000301030	NM_001256183.1	2214	gAc/gGc	9/13	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.338937424319469	2		468	875	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0049501-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	19	423	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.522	0.395	0.672	0.522	0.395	0.672	SUBCLONAL	1	TRUE	1	0.16	2		423	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863224499	NA	P-0049501-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	47	751	0	ENST00000269305.4:c.672+1G>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			1	2	FACETS	0.84	0.708	0.988	0.84	0.708	0.988	CLONAL	1	TRUE	1	0.16	2		751	699	SUCCESS
BTK	695	MSKCC	GRCh37	X	100614317	100614317	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049501-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	32	586	0	ENST00000308731.7:c.858G>T	p.Met286Ile	p.M286I	ENST00000308731	NM_000061.2	286	atG/atT	10/19	1	2	FACETS	0.688	0.557	0.837	0.688	0.557	0.837	SUBCLONAL	1	TRUE	1	0.16	2		586	581	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0049502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	150	248	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.612796113172763	2		249	407	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978321	2978321	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs138920531	NA	P-0049502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	228	654	0	ENST00000396946.4:c.1009C>T	p.Arg337Ter	p.R337*	ENST00000396946	NM_032415.4	337	Cga/Tga	7/25	0.612796113172763	3	FACETS	0.887	0.826	0.95	0.443	0.413	0.475	CLONAL	1	TRUE	1	0.612796113172763	3		654	1096	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665757	29665757	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs772295894	NA	P-0049502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	21	261	0	ENST00000356175.3:c.6792C>A	p.Tyr2264Ter	p.Y2264*	ENST00000356175	NM_000267.3	2264	taC/taA	45/57	0.488539469576326	1	FACETS	0.126	0.097	0.161	0.126	0.097	0.161	SUBCLONAL	1	TRUE	0	0.612796113172763	1		261	377	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435374	18435374	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	149	265	0	ENST00000266497.5:c.359C>G	p.Thr120Arg	p.T120R	ENST00000266497		120	aCg/aGg	1/31	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.612796113172763	2		265	481	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0049503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	32	350	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.662	0.536	0.804	0.662	0.536	0.804	SUBCLONAL	1	TRUE	1	0.19	2		350	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0049503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	69	628	0	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	1	2	FACETS	0.824	0.716	0.942	0.824	0.716	0.942	CLONAL	1	TRUE	1	0.19	2		628	881	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252855	36252856	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	34	264	0	ENST00000300305.3:c.506dup	p.Gly170ArgfsTer43	p.G170Rfs*43	ENST00000300305		169	aga/agGa	4/8	1	2	FACETS	0.692	0.565	0.836	0.692	0.565	0.836	SUBCLONAL	1	TRUE	1	0.19	2		264	517	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143059	30143059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	73	651	0	ENST00000389048.3:c.467G>A	p.Gly156Glu	p.G156E	ENST00000389048	NM_004304.4	156	gGg/gAg	1/29	1	2	FACETS	0.868	0.758	0.988	0.868	0.758	0.988	CLONAL	1	TRUE	1	0.19	2		651	885	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428502	72428502	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049503-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	69	395	0	ENST00000477973.2:c.502G>C	p.Glu168Gln	p.E168Q	ENST00000477973	NM_012234.5	168	Gag/Cag	2/4	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.19	2		395	564	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0049504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	45	347	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.131769709547647	2		347	484	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0049504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	83	426	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.978	0.864	1	1	0.984	1	CLONAL	2	TRUE	1	0.131769709547647	2		426	644	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0049504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	26	267	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.131769709547647	2		267	332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0049504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	65	652	5	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.131769709547647	2		657	809	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0049504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	40	187	3	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			0.122306524549313	4	FACETS	1	0.879	1	1	0.879	1	CLONAL	2	TRUE	2	0.131769709547647	4		190	322	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845890	156845890	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750477154	NA	P-0049504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	108	578	6	ENST00000524377.1:c.1520G>A	p.Arg507His	p.R507H	ENST00000524377	NM_002529.3	507	cGc/cAc	13/17	1	2	FACETS	0.977	0.876	1	1	0.987	1	CLONAL	2	TRUE	1	0.131769709547647	2		584	839	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713341	40713341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1305277749	NA	P-0049504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	42	530	2	ENST00000373198.4:c.4174C>T	p.Arg1392Cys	p.R1392C	ENST00000373198	NM_133170.3	1392	Cgt/Tgt	30/32	1	2	FACETS	0.935	0.779	1	0.935	0.779	1	CLONAL	1	TRUE	1	0.131769709547647	2		532	682	SUCCESS
APC	324	MSKCC	GRCh37	5	112170705	112170705	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	37	354	3	ENST00000257430.4:c.1801G>T	p.Glu601Ter	p.E601*	ENST00000257430	NM_000038.5	601	Gag/Tag	15/16	1	2	FACETS	0.984	0.81	1	0.984	0.81	1	CLONAL	1	TRUE	1	0.131769709547647	2		357	571	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233582	69233582	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs777525974	NA	P-0049504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	24	249	0	ENST00000462284.1:c.1447G>T	p.Val483Leu	p.V483L	ENST00000462284	NM_002392.5	483	Gta/Tta	11/11	1	2	FACETS	0.878	0.687	1	0.878	0.687	1	CLONAL	1	TRUE	1	0.131769709547647	2		249	415	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749110	43749110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763646261	NA	P-0049504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	50	501	0	ENST00000382044.4:c.1696C>T	p.Pro566Ser	p.P566S	ENST00000382044	NM_001141980.1	566	Cct/Tct	12/28	1	2	FACETS	0.992	0.84	1	0.992	0.84	1	CLONAL	1	TRUE	1	0.131769709547647	2		501	765	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921447	178921447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	35	360	1	ENST00000263967.3:c.929G>A	p.Arg310His	p.R310H	ENST00000263967	NM_006218.2	310	cGc/cAc	5/21	1	2	FACETS	1	0.82	1	1	0.82	1	CLONAL	1	TRUE	1	0.131769709547647	2		361	530	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294178	1294178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758074759	NA	P-0049504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	58	660	3	ENST00000310581.5:c.823C>T	p.Pro275Ser	p.P275S	ENST00000310581	NM_198253.2	275	Cct/Tct	2/16	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.131769709547647	2		663	771	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	47	148	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		148	285	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0049505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	167	556	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		556	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	637	620	0	ENST00000269305.4:c.542G>C	p.Arg181Pro	p.R181P	ENST00000269305	NM_001126112.2	181	cGc/cCc	5/11	0.533696849070298	2	FACETS	0.835	0.812	0.858	1	0.997	1	CLONAL	3	TRUE	0	0.533696849070298	2		620	953	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317081	87317081	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201490630	NA	P-0049510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	206	399	0	ENST00000277120.3:c.220G>A	p.Ala74Thr	p.A74T	ENST00000277120		74	Gca/Aca	3/19	0.533696849070298	2	FACETS	0.846	0.795	0.899	0.846	0.795	0.899	CLONAL	2	TRUE	0	0.533696849070298	2		399	456	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62325788	62325788	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs116053476	NA	P-0049510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	634	640	0	ENST00000360203.5:c.3056A>G	p.Gln1019Arg	p.Q1019R	ENST00000360203	NM_001283009.1	1019	cAa/cGa	31/35	0.180513292513507	5	FACETS	1	0.995	1	0.852	0.824	0.881	INDETERMINATE	3	TRUE	1	0.533696849070298	5		640	1255	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998957	100998957	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	279	604	0	ENST00000325455.5:c.845T>G	p.Leu282Arg	p.L282R	ENST00000325455	NM_001202474.3	282	cTg/cGg	1/8	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.533696849070298	2		604	812	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906973	32906973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	86	386	0	ENST00000380152.3:c.1358C>T	p.Pro453Leu	p.P453L	ENST00000380152		453	cCa/cTa	10/27	0.492300681437814	2	FACETS	1	0.976	1	0.66	0.594	0.729	CLONAL	1	TRUE	0	0.533696849070298	2		386	244	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251007	99251007	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	197	547	0	ENST00000268035.6:c.311C>G	p.Thr104Arg	p.T104R	ENST00000268035	NM_000875.3	104	aCg/aGg	2/21	1	2	FACETS	0.994	0.923	1	0.994	0.923	1	CLONAL	1	TRUE	1	0.533696849070298	2		547	743	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566840	212566840	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	53	276	0	ENST00000342788.4:c.1341C>G	p.Phe447Leu	p.F447L	ENST00000342788	NM_005235.2	447	ttC/ttG	12/28	0.533696849070298	2	FACETS	0.492	0.42	0.569	0.246	0.21	0.285	SUBCLONAL	1	TRUE	0	0.533696849070298	2		276	404	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956820	68956820	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	90	481	0	ENST00000288368.4:c.938G>A	p.Gly313Asp	p.G313D	ENST00000288368	NM_024870.2	313	gGc/gAc	8/40	0.180513292513507	5	FACETS	0.958	0.851	1	0.239	0.212	0.268	INDETERMINATE	1	TRUE	1	0.533696849070298	5		481	634	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0049512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	84	437	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.954	0.848	1	0.954	0.848	1	CLONAL	1	TRUE	1	0.456343807893631	2		437	386	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443402	187443402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1262719853	NA	P-0049512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	100	354	0	ENST00000232014.4:c.1724G>A	p.Arg575His	p.R575H	ENST00000232014	NM_001130845.1	575	cGt/cAt	8/10	1	2	FACETS	0.959	0.861	1	0.959	0.861	1	CLONAL	1	TRUE	1	0.456343807893631	2		354	457	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838148	89838148	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376888740	NA	P-0049512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	178	551	3	ENST00000389301.3:c.2089G>A	p.Val697Ile	p.V697I	ENST00000389301	NM_000135.2	697	Gtt/Att	23/43	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.456343807893631	2		554	728	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265322	152265322	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	87	333	1	ENST00000206249.3:c.775C>T	p.Arg259Ter	p.R259*	ENST00000206249	NM_000125.3	259	Cga/Tga	4/8	0.444812121421212	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.456343807893631	1		334	279	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347377	89347377	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367980842	NA	P-0049512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	189	658	2	ENST00000301030.4:c.5573C>T	p.Pro1858Leu	p.P1858L	ENST00000301030	NM_001256183.1	1858	cCg/cTg	9/13	1	2	FACETS	0.921	0.852	0.993	0.921	0.852	0.993	CLONAL	1	TRUE	1	0.456343807893631	2		660	899	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508191	38508192	+	stop_gained,inframe_insertion	Nonsense_Mutation	INS	-	-	AGT	novel	NA	P-0049512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	158	571	1	ENST00000254066.5:c.501_502insTAG	p.Lys167_Glu168insTer	p.K167_E168ins*	ENST00000254066	NM_000964.3	167	aag/aAGTag	5/9	1	2	FACETS	0.934	0.858	1	0.934	0.858	1	CLONAL	1	TRUE	1	0.456343807893631	2		572	741	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591959	48591970	+	inframe_deletion	In_Frame_Del	DEL	AGCCATTGAGAG	AGCCATTGAGAG	-	novel	NA	P-0049512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	65	321	0	ENST00000342988.3:c.1125_1136del	p.Ile376_Ala379del	p.I376_A379del	ENST00000342988	NM_005359.5	374	gaAGCCATTGAGAGa/gaa	9/12	0.456343807893631	1	FACETS	0.777	0.68	0.88	0.777	0.68	0.88	SUBCLONAL	1	TRUE	0	0.456343807893631	1		321	283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0049513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	49	583	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.752	0.635	0.882	0.752	0.635	0.882	SUBCLONAL	1	TRUE	1	0.16	2		583	814	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0049513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	62	263	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.16	2		263	565	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679547	86679547	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	32	347	0	ENST00000274376.6:c.2708G>T	p.Arg903Leu	p.R903L	ENST00000274376	NM_002890.2	903	cGa/cTa	21/25	1	2	FACETS	0.899	0.729	1	0.899	0.729	1	CLONAL	1	TRUE	1	0.16	2		347	445	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0049513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	24	594	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.327	0.255	0.411	0.327	0.255	0.411	SUBCLONAL	1	TRUE	1	0.16	2		594	918	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998919	11998919	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	106	247	0	ENST00000353533.5:c.421G>C	p.Glu141Gln	p.E141Q	ENST00000353533	NM_003010.3	141	Gaa/Caa	4/11	NA	2	FACETS	0.989	0.903	1			1	INDETERMINATE	1	TRUE	NA	0.837299068147553	2		247	256	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589663	67589663	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587777709	NA	P-0049515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	99	198	2	ENST00000274335.5:c.1425+1G>A		p.X475_splice	ENST00000274335		475			0.544342254295452	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.544342254295452	1		200	203	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628716	21628716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755679996	NA	P-0049515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	121	321	4	ENST00000421138.2:c.992C>T	p.Thr331Met	p.T331M	ENST00000421138		331	aCg/aTg	10/16	NA	2	FACETS	1	0.921	1			1	INDETERMINATE	1	TRUE	NA	0.544342254295452	2		325	439	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137439	202137440	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0049515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	162	307	2	ENST00000358485.4:c.669_670del	p.Ala224ProfsTer14	p.A224Pfs*14	ENST00000358485	NM_001080125.1	223	TGt/t	4/9	0.100043358892799	4	FACETS	0.805	0.742	0.869	0.805	0.742	0.869	INDETERMINATE	2	TRUE	2	0.544342254295452	4		309	571	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940778	49940778	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1273800589	NA	P-0049515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	260	538	0	ENST00000296474.3:c.265C>T	p.Gln89Ter	p.Q89*	ENST00000296474	NM_002447.2	89	Cag/Tag	1/20	0.100043358892799	4	FACETS	0.852	0.8	0.905	0.852	0.8	0.905	INDETERMINATE	2	TRUE	2	0.544342254295452	4		538	866	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293868	1293868	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	278	690	1	ENST00000310581.5:c.1133G>C	p.Arg378Thr	p.R378T	ENST00000310581	NM_198253.2	378	aGg/aCg	2/16	0.544342254295452	3	FACETS	1	0.975	1	0.537	0.503	0.571	CLONAL	1	TRUE	1	0.544342254295452	3		691	1211	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0049516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	305	533	0	ENST00000269305.4:c.375+1G>T		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.641015029633752	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.636234243427155	2		533	462	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753098	42753098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs923763445	NA	P-0049516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	227	711	1	ENST00000222329.4:c.1166G>A	p.Arg389Gln	p.R389Q	ENST00000222329	NM_006494.2	389	cGg/cAg	4/4	0.445937456499994	3	FACETS	1	0.958	1			1	CLONAL	1	TRUE	NA	0.636234243427155	3		712	908	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115284147	115284148	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CA	CA	AG	novel	NA	P-0049516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	123	323	0	ENST00000438362.2:c.138_138+1delinsCT		p.X46_splice	ENST00000438362	NM_001242891.1	46		2/20	0.641015029633752	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.636234243427155	1		323	229	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968138	68968138	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	16	444	0	ENST00000288368.4:c.1167G>T	p.Met389Ile	p.M389I	ENST00000288368	NM_024870.2	389	atG/atT	10/40	0.641015029633752	1	FACETS	0.127	0.093	0.166	0.127	0.093	0.166	SUBCLONAL	1	TRUE	0	0.636234243427155	1		444	271	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	92	431	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.271233554744055	2	FACETS	0.864	0.774	0.958	0.864	0.774	0.958	CLONAL	2	TRUE	0	0.292457602747823	2		431	364	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0049518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	126	308	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.292457602747823	3	FACETS	0.862	0.788	0.937	0.862	0.788	0.937	CLONAL	3	TRUE	0	0.292457602747823	3		308	382	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0049518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	47	349	2	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.635	0.536	0.745	0.635	0.536	0.745	SUBCLONAL	1	TRUE	1	0.292457602747823	2		351	506	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100968	27100968	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	82	515	0	ENST00000324856.7:c.4251del	p.Ala1418LeufsTer63	p.A1418Lfs*63	ENST00000324856	NM_006015.4	1417	cAa/ca	18/20	1	2	FACETS	0.77	0.679	0.868	0.77	0.679	0.868	SUBCLONAL	1	TRUE	1	0.292457602747823	2		515	728	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136259	2136264	+	inframe_deletion	In_Frame_Del	DEL	GGGCCT	GGGCCT	-	novel	NA	P-0049518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	103	627	0	ENST00000219476.3:c.4733_4738del	p.Leu1578_Gly1579del	p.L1578_G1579del	ENST00000219476	NM_000548.3	1576	acGGGCCTg/acg	37/42	1	2	FACETS	0.863	0.772	0.96	0.863	0.772	0.96	CLONAL	1	TRUE	1	0.292457602747823	2		627	816	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591091	67591092	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTAT	novel	NA	P-0049518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	42	218	0	ENST00000274335.5:c.1686_1689dup	p.Asn564TyrfsTer5	p.N564Yfs*5	ENST00000274335		562	cgt/cGTATgt	12/15	1	2	FACETS	0.85	0.712	1	0.85	0.712	1	CLONAL	1	TRUE	1	0.292457602747823	2		218	338	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588970	67588985	+	protein_altering_variant	In_Frame_Del	DEL	CCTTTTTGGTACGAGA	CCTTTTTGGTACGAGA	T	novel	NA	P-0049518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	19	206	0	ENST00000274335.5:c.1061_1076delinsT	p.Thr354_Asp359delinsIle	p.T354_D359delinsI	ENST00000274335		354	aCCTTTTTGGTACGAGAt/aTt	8/15	1	2	FACETS	0.58	0.441	0.742	0.58	0.441	0.742	SUBCLONAL	1	TRUE	1	0.292457602747823	2		206	224	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0049519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	584	533	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.392531927420217	5	FACETS	0.966	0.935	0.996	0.966	0.935	0.996	CLONAL	5	TRUE	0	0.392531927420217	5		533	979	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434122	12434122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1170672782	NA	P-0049519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	253	333	0	ENST00000287820.6:c.490C>T	p.Arg164Trp	p.R164W	ENST00000287820	NM_015869.4	164	Cgg/Tgg	4/7	0.392531927420217	3	FACETS	0.994	0.941	1	0.994	0.941	1	CLONAL	3	TRUE	0	0.392531927420217	3		333	517	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37061882	37061882	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	114	507	0	ENST00000231790.2:c.966C>G	p.Ile322Met	p.I322M	ENST00000231790	NM_000249.3	322	atC/atG	11/19	0.392531927420217	3	FACETS	0.938	0.845	1	0.313	0.281	0.346	CLONAL	1	TRUE	0	0.392531927420217	3		507	741	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415054	116415071	+	inframe_deletion	In_Frame_Del	DEL	ACTGTCCACATTGACCTC	ACTGTCCACATTGACCTC	-	novel	NA	P-0049519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	164	525	0	ENST00000397752.3:c.3149_3166del	p.Thr1050_Leu1055del	p.T1050_L1055del	ENST00000397752	NM_000245.2	1050	ACTGTCCACATTGACCTC/-	15/21	0.283479065735182	4	FACETS	0.816	0.751	0.884	0.544	0.5	0.589	CLONAL	2	TRUE	1	0.392531927420217	4		525	713	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0049520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	35	616	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.431	0.352	0.52	0.431	0.352	0.52	SUBCLONAL	1	TRUE	1	0.21	2		618	774	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0049521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	276	626	2	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	0.54114358001443	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.54114358001443	1		628	669	SUCCESS
APC	324	MSKCC	GRCh37	5	112175068	112175069	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0049521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	62	203	0	ENST00000257430.4:c.3778_3779del	p.Gln1260AspfsTer15	p.Q1260Dfs*15	ENST00000257430	NM_000038.5	1259	atACag/atag	16/16	1	2	FACETS	0.796	0.693	0.905	0.796	0.693	0.905	CLONAL	1	TRUE	1	0.54114358001443	2		203	288	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371775	118371775	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782301554	NA	P-0049521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	155	285	0	ENST00000534358.1:c.6232C>T	p.Arg2078Cys	p.R2078C	ENST00000534358	NM_005933.3	2078	Cgt/Tgt	25/36	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.54114358001443	2		285	526	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100181	27100182	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCA	rs374564889	NA	P-0049521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	92	406	0	ENST00000324856.7:c.3999_4001dup	p.Gln1334dup	p.Q1334dup	ENST00000324856	NM_006015.4	1334	ccg/ccGCAg	16/20	1	2	FACETS	0.572	0.509	0.639	0.572	0.509	0.639	SUBCLONAL	1	TRUE	1	0.54114358001443	2		406	594	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285554	38285554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1413642890	NA	P-0049521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	377	436	3	ENST00000425967.3:c.599C>T	p.Pro200Leu	p.P200L	ENST00000425967	NM_001174067.1	200	cCg/cTg	6/19	0.54114358001443	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.54114358001443	3		439	883	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448270	56448270	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0049521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	224	501	0	ENST00000407977.2:c.375+2T>G		p.X125_splice	ENST00000407977		125			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.54114358001443	2		501	735	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573512	48573520	+	inframe_deletion	In_Frame_Del	DEL	TGAAACATT	TGAAACATT	-	novel	NA	P-0049521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	75	259	0	ENST00000342988.3:c.98_106del	p.Glu33_Phe35del	p.E33_F35del	ENST00000342988	NM_005359.5	32	agTGAAACATTt/agt	2/12	0.54114358001443	1	FACETS	0.887	0.79	0.988	0.887	0.79	0.988	CLONAL	1	TRUE	0	0.54114358001443	1		259	228	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0049522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	60	591	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.16	2		593	718	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11177107	11177107	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	183	401	0	ENST00000361445.4:c.6970T>G	p.Leu2324Val	p.L2324V	ENST00000361445	NM_004958.3	2324	Tta/Gta	50/58	1	2	FACETS	0.988	0.918	1	0.988	0.918	1	CLONAL	1	TRUE	1	0.635202030328054	2		401	583	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946944	71946944	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	274	738	1	ENST00000298229.2:c.2793A>T	p.Leu931Phe	p.L931F	ENST00000298229	NM_001567.3	931	ttA/ttT	25/28	0.21090025721416	6	FACETS	0.87	0.816	0.925	0.29	0.272	0.309	INDETERMINATE	2	TRUE	0	0.635202030328054	6		739	1126	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061383	38061442	+	inframe_deletion	In_Frame_Del	DEL	GTCCATGATCCACTGGTAGATCTCGCTCAGCGTGAGCATCTTGCTGGGCGCCTGCTGGAT	GTCCATGATCCACTGGTAGATCTCGCTCAGCGTGAGCATCTTGCTGGGCGCCTGCTGGAT	-	novel	NA	P-0049523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	211	505	1	ENST00000250448.2:c.547_606del	p.Ile183_Asp202del	p.I183_D202del	ENST00000250448	NM_004496.3	183	ATCCAGCAGGCGCCCAGCAAGATGCTCACGCTGAGCGAGATCTACCAGTGGATCATGGAC/-	2/2	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.635202030328054	2		506	631	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576874	212576874	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	170	370	0	ENST00000342788.4:c.1025T>C	p.Leu342Ser	p.L342S	ENST00000342788	NM_005235.2	342	tTg/tCg	9/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.635202030328054	2		370	476	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0049524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	117	502	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	0.777	0.702	0.855	0.777	0.702	0.855	SUBCLONAL	1	TRUE	1	0.500462003098074	2		502	602	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952169	76952172	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	novel	NA	P-0049524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	125	237	0	ENST00000373344.5:c.263_266del	p.Lys88MetfsTer2	p.K88Mfs*2	ENST00000373344	NM_000489.3	88	aAGTAt/at	5/35	1	1	FACETS	0.758	0.702	0.815	1	0.989	1	SUBCLONAL	2	TRUE	0	0.500462003098074	1		237	247	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061178	38061195	+	inframe_deletion	In_Frame_Del	DEL	GCTTCTCGCACTTGAAGC	GCTTCTCGCACTTGAAGC	-	novel	NA	P-0049525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	95	368	0	ENST00000250448.2:c.794_811del	p.Arg265_Lys270del	p.R265_K270del	ENST00000250448	NM_004496.3	265	cGCTTCAAGTGCGAGAAGCag/cag	2/2	0.270961265836413	3	FACETS	0.848	0.775	0.922	1	0.979	1	INDETERMINATE	3	FALSE	1	0.476607957000326	3		368	194	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828497	72828504	+	frameshift_variant	Frame_Shift_Del	DEL	CGAGCTCG	CGAGCTCG	-	novel	NA	P-0049525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	45	715	0	ENST00000268489.5:c.8077_8084del	p.Arg2693GlyfsTer32	p.R2693Gfs*32	ENST00000268489	NM_006885.3	2693	CGAGCTCGg/g	9/10	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	FALSE	1	0.476607957000326	2		715	187	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4	531	637	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.929591819759924	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.929591819759924	2		637	535	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175996761	175996761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	480	442	0	ENST00000367669.3:c.1676G>T	p.Cys559Phe	p.C559F	ENST00000367669	NM_022457.5	559	tGc/tTc	15/20	0.929591819759924	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	1	0.929591819759924	4		442	661	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955571	48955571	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs139500527	NA	P-0049526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	183	372	0	ENST00000267163.4:c.1687T>G	p.Trp563Gly	p.W563G	ENST00000267163	NM_000321.2	563	Tgg/Ggg	17/27	0.929591819759924	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.929591819759924	2		372	188	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374915	45374915	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	391	514	1	ENST00000262160.6:c.928A>T	p.Arg310Trp	p.R310W	ENST00000262160	NM_005901.5	310	Agg/Tgg	8/11	0.587874969893462	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.929591819759924	4		515	784	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280041	66280041	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	216	295	0	ENST00000273854.3:c.1648G>T	p.Val550Phe	p.V550F	ENST00000273854	NM_004439.5	550	Gtc/Ttc	7/18	0.372112153400501	2	FACETS	1	0.994	1	0.719	0.685	0.753	INDETERMINATE	1	TRUE	0	0.929591819759924	2		295	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587780070	NA	P-0049527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	76	653	1	ENST00000269305.4:c.535C>A	p.His179Asn	p.H179N	ENST00000269305	NM_001126112.2	179	Cat/Aat	5/11	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.14	2		654	936	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432581	78432581	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	39	465	0	ENST00000370768.2:c.402A>G	p.Ile134Met	p.I134M	ENST00000370768	NM_003902.3	134	atA/atG	6/20	1	2	FACETS	0.815	0.673	0.973	0.815	0.673	0.973	CLONAL	1	TRUE	1	0.14	2		465	684	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683223	88683223	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	38	341	0	ENST00000372037.3:c.1433G>C	p.Arg478Pro	p.R478P	ENST00000372037	NM_004329.2	478	cGt/cCt	12/13	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.14	2		341	478	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	100	431	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.258859552024669	1	FACETS	0.832	0.749	0.92	1	0.985	1	CLONAL	2	TRUE	0	0.258859552024669	1		431	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0049528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	118	632	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.258859552024669	2		632	799	SUCCESS
APC	324	MSKCC	GRCh37	5	112175761	112175761	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	105	380	0	ENST00000257430.4:c.4473del	p.Phe1491LeufsTer16	p.F1491Lfs*16	ENST00000257430	NM_000038.5	1490	caT/ca	16/16	0.163826236491895	3	FACETS	0.929	0.836	1	0.929	0.836	1	CLONAL	2	TRUE	1	0.258859552024669	3		380	493	SUCCESS
APC	324	MSKCC	GRCh37	5	112175706	112175706	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	66	355	0	ENST00000257430.4:c.4415del	p.Val1472GlufsTer35	p.V1472Efs*35	ENST00000257430	NM_000038.5	1472	gTa/ga	16/16	0.163826236491895	3	FACETS	1	0.905	1	0.525	0.456	0.6	CLONAL	1	TRUE	1	0.258859552024669	3		355	548	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153252021	153252021	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0049528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	35	396	0	ENST00000281708.4:c.986-1G>A		p.X329_splice	ENST00000281708	NM_033632.3	329			1	2	FACETS	0.89	0.732	1	0.89	0.732	1	CLONAL	1	TRUE	1	0.258859552024669	2		396	304	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249457	153249457	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	79	506	0	ENST00000281708.4:c.1321C>G	p.Arg441Gly	p.R441G	ENST00000281708	NM_033632.3	441	Cgg/Ggg	9/12	1	2	FACETS	0.997	0.878	1	0.997	0.878	1	CLONAL	1	TRUE	1	0.258859552024669	2		506	612	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777056	9777056	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	123	706	0	ENST00000377346.4:c.820C>A	p.Leu274Met	p.L274M	ENST00000377346	NM_005026.3	274	Ctg/Atg	7/24	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.258859552024669	2		706	924	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300123	15300123	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1568360640	NA	P-0049528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	158	753	0	ENST00000263388.2:c.1153G>C	p.Gly385Arg	p.G385R	ENST00000263388	NM_000435.2	385	Ggt/Cgt	7/33	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.258859552024669	2		753	1040	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913517	NA	P-0049529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	302	419	0	ENST00000288135.5:c.1676T>A	p.Val559Asp	p.V559D	ENST00000288135	NM_000222.2	559	gTt/gAt	11/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.946371854441665	2		419	611	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812259	212812259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs991337964	NA	P-0049529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	208	311	0	ENST00000342788.4:c.317G>A	p.Arg106His	p.R106H	ENST00000342788	NM_005235.2	106	cGt/cAt	3/28	1	2	FACETS	0.973	0.914	1	0.973	0.914	1	CLONAL	1	TRUE	1	0.946371854441665	2		311	452	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390435	56390435	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757096789	NA	P-0049530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	21	289	0	ENST00000348428.3:c.1174C>T	p.Arg392Cys	p.R392C	ENST00000348428	NM_006785.3	392	Cgt/Tgt	10/17	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		289	416	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0049532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	13	350	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.609930292894776	4	FACETS	0.125	0.088	0.17	0.042	0.029	0.057	SUBCLONAL	1	TRUE	1	0.781405712850162	4		350	475	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579355	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519997	NA	P-0049532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	378	693	0	ENST00000269305.4:c.332T>C	p.Leu111Pro	p.L111P	ENST00000269305	NM_001126112.2	111	cTg/cCg	4/11	0.718217804000664	3	FACETS	0.853	0.824	0.88	0.853	0.824	0.88	CLONAL	3	TRUE	0	0.781405712850162	3		693	526	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342671	70342671	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	63	512	0	ENST00000374080.3:c.1432G>C	p.Asp478His	p.D478H	ENST00000374080		478	Gac/Cac	10/45	0.686856573515844	2	FACETS	0.394	0.342	0.451	0.197	0.171	0.226	SUBCLONAL	1	TRUE	0	0.781405712850162	2		512	409	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254920	16254920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764181934	NA	P-0049532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	31	509	1	ENST00000375759.3:c.2185G>A	p.Val729Ile	p.V729I	ENST00000375759	NM_015001.2	729	Gtt/Att	11/15	0.472735625200112	5	FACETS	0.319	0.257	0.389			1	SUBCLONAL	1	TRUE	NA	0.781405712850162	5		510	541	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885884	23885884	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs765906626	NA	P-0049532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	114	486	0	ENST00000374561.5:c.34G>C	p.Glu12Gln	p.E12Q	ENST00000374561	NM_002167.4	12	Gag/Cag	1/3	0.726321511709036	3	FACETS	1	0.971	1	0.386	0.352	0.422	CLONAL	1	TRUE	0	0.781405712850162	3		486	350	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490386	29490386	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	27	382	0	ENST00000356175.3:c.471T>G	p.Ile157Met	p.I157M	ENST00000356175	NM_000267.3	157	atT/atG	4/57	0.657977592317252	3	FACETS	0.184	0.146	0.228	0.061	0.048	0.076	SUBCLONAL	1	TRUE	0	0.781405712850162	3		382	522	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157454171	157454171	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	107	423	0	ENST00000346085.5:c.2381C>G	p.Ala794Gly	p.A794G	ENST00000346085	NM_020732.3	794	gCa/gGa	8/20	0.263798918996336	4	FACETS	0.85	0.774	0.928	0.85	0.774	0.928	INDETERMINATE	2	TRUE	2	0.781405712850162	4		423	287	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0049533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	33	263	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.764	0.621	0.927	0.764	0.621	0.927	CLONAL	1	TRUE	1	0.14	2		263	617	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177011	56177014	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	-	novel	NA	P-0049533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	29	358	0	ENST00000399503.3:c.2286_2289del	p.Arg763CysfsTer35	p.R763Cfs*35	ENST00000399503	NM_005921.1	761	ATAGat/at	13/20	1	2	FACETS	0.788	0.631	0.967	0.788	0.631	0.967	CLONAL	1	TRUE	1	0.14	2		358	526	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061191	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	33	329	0	ENST00000250448.2:c.798C>G	p.Phe266Leu	p.F266L	ENST00000250448	NM_004496.3	266	ttC/ttG	2/2	1	2	FACETS	0.821	0.667	0.995	0.821	0.667	0.995	CLONAL	1	TRUE	1	0.14	2		329	574	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206578	108206578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659942	NA	P-0049533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	31	317	0	ENST00000278616.4:c.8158G>A	p.Asp2720Asn	p.D2720N	ENST00000278616	NM_000051.3	2720	Gat/Aat	56/63	1	2	FACETS	0.986	0.797	1	0.986	0.797	1	CLONAL	1	TRUE	1	0.14	2		317	449	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023895	27023895	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	14	169	0	ENST00000324856.7:c.1001C>A	p.Ser334Ter	p.S334*	ENST00000324856	NM_006015.4	334	tCg/tAg	1/20	1	2	FACETS	0.778	0.562	1	0.778	0.562	1	CLONAL	1	TRUE	1	0.14	2		169	257	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188980	32188980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	89	742	0	ENST00000375023.3:c.574G>A	p.Glu192Lys	p.E192K	ENST00000375023	NM_004557.3	192	Gaa/Aaa	4/30	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.14	2		742	1146	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160564	56160564	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	27	212	1	ENST00000399503.3:c.838C>T	p.Gln280Ter	p.Q280*	ENST00000399503	NM_005921.1	280	Cag/Tag	4/20	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.14	2		213	348	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104269035	104269035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	56	538	0	ENST00000369902.3:c.292C>T	p.Leu98Phe	p.L98F	ENST00000369902	NM_016169.3	98	Ctc/Ttc	2/12	1	2	FACETS	0.935	0.799	1	0.935	0.799	1	CLONAL	1	TRUE	1	0.14	2		538	856	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831312	72831312	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	41	391	0	ENST00000268489.5:c.5269C>T	p.Gln1757Ter	p.Q1757*	ENST00000268489	NM_006885.3	1757	Cag/Tag	9/10	1	2	FACETS	0.905	0.753	1	0.905	0.753	1	CLONAL	1	TRUE	1	0.14	2		391	647	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953288	17953288	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	75	785	0	ENST00000458235.1:c.698C>T	p.Ser233Leu	p.S233L	ENST00000458235	NM_000215.3	233	tCg/tTg	6/24	1	2	FACETS	0.933	0.815	1	0.933	0.815	1	CLONAL	1	TRUE	1	0.14	2		785	1148	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6045556	6045556	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786202669	NA	P-0049533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	24	221	0	ENST00000265849.7:c.130G>C	p.Glu44Gln	p.E44Q	ENST00000265849	NM_000535.5	44	Gaa/Caa	2/15	1	2	FACETS	0.788	0.617	0.986	0.788	0.617	0.986	CLONAL	1	TRUE	1	0.14	2		221	435	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613387	100613387	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	56	524	0	ENST00000308731.7:c.1013C>G	p.Ser338Cys	p.S338C	ENST00000308731	NM_000061.2	338	tCc/tGc	12/19	1	2	FACETS	0.986	0.843	1	0.986	0.843	1	CLONAL	1	TRUE	1	0.14	2		524	811	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498282	29498282	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	21	434	0	ENST00000389048.3:c.1898A>G	p.Asp633Gly	p.D633G	ENST00000389048	NM_004304.4	633	gAc/gGc	10/29	0.374754903406337	0	FACETS	0.274	0.211	0.347			1	SUBCLONAL	1	FALSE	0	0.375693091920837	0		434	255	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0049538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	136	768	7	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.59369433895915	1	FACETS	0.971	0.897	1	0.971	0.897	1	CLONAL	1	TRUE	0	0.604899562730435	1		775	323	SUCCESS
APC	324	MSKCC	GRCh37	5	112111408	112111411	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	-	rs387906231	NA	P-0049538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	127	329	0	ENST00000257430.4:c.509_512del	p.Asp170ValfsTer4	p.D170Vfs*4	ENST00000257430	NM_000038.5	169	ATAGat/at	5/16	0.241538978902613	3	FACETS	0.882	0.811	0.954	0.588	0.541	0.636	INDETERMINATE	2	TRUE	0	0.604899562730435	3		329	310	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161807896	161807896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761213043	NA	P-0049538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	19	354	0	ENST00000366898.1:c.1097G>A	p.Arg366Gln	p.R366Q	ENST00000366898	NM_004562.2	366	cGg/cAg	10/12	0.204548532696958	2	FACETS	0.268	0.204	0.344	0.134	0.102	0.172	INDETERMINATE	1	TRUE	0	0.604899562730435	2		354	234	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0049538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	22	236	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.241538978902613	3	FACETS	0.496	0.386	0.622	0.165	0.128	0.208	INDETERMINATE	1	TRUE	0	0.604899562730435	3		236	191	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979623	55979623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764358120	NA	P-0049538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	108	428	0	ENST00000263923.4:c.824G>A	p.Arg275Gln	p.R275Q	ENST00000263923	NM_002253.2	275	cGa/cAa	7/30	0.272506817755645	0	FACETS	0.448	0.407	0.49			1	INDETERMINATE	1	TRUE	0	0.604899562730435	0		428	315	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263979	104263979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	35	234	1	ENST00000369902.3:c.70C>T	p.Pro24Ser	p.P24S	ENST00000369902	NM_016169.3	24	Ccg/Tcg	1/12	0.204548532696958	2	FACETS	0.456	0.375	0.545	0.228	0.187	0.273	INDETERMINATE	1	TRUE	0	0.604899562730435	2		235	254	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326461	62326461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	63	946	1	ENST00000360203.5:c.3386C>T	p.Ser1129Leu	p.S1129L	ENST00000360203	NM_001283009.1	1129	tCa/tTa	33/35	0.251946571848354	5	FACETS	0.665	0.575	0.763	0.222	0.191	0.255	INDETERMINATE	1	TRUE	2	0.604899562730435	5		947	597	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324051	31324051	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs41551018	NA	P-0049538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	83	487	2	ENST00000412585.2:c.512G>A	p.Trp171Ter	p.W171*	ENST00000412585	NM_005514.6	171	tGg/tAg	3/8	0.204548532696958	2	FACETS	1	0.96	1	0.574	0.515	0.635	INDETERMINATE	1	TRUE	0	0.604899562730435	2		489	239	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523554	148523554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs897885462	NA	P-0049538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	37	237	0	ENST00000320356.2:c.899G>A	p.Cys300Tyr	p.C300Y	ENST00000320356	NM_004456.4	300	tGc/tAc	8/20	1	2	FACETS	0.463	0.384	0.551	0.463	0.384	0.551	SUBCLONAL	1	TRUE	1	0.604899562730435	2		237	264	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0049539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	238	406	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.370091197063256	4	FACETS	1	0.957	1	0.765	0.72	0.81	CLONAL	3	TRUE	0	0.370091197063256	4		406	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579355	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	513	814	4	ENST00000269305.4:c.332del	p.Leu111ArgfsTer12	p.L111Rfs*12	ENST00000269305	NM_001126112.2	111	cTg/cg	4/11	0.370091197063256	4	FACETS	0.979	0.943	1	0.979	0.943	1	CLONAL	4	TRUE	0	0.370091197063256	4		818	970	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279932	18279932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1423694208	NA	P-0049539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	131	780	2	ENST00000222254.8:c.2015G>A	p.Arg672His	p.R672H	ENST00000222254	NM_005027.3	672	cGc/cAc	16/16	0.370091197063256	9	FACETS	1	0.984	1	0.206	0.186	0.227	CLONAL	1	TRUE	2	0.370091197063256	9		782	1125	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220126	5220126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781134304	NA	P-0049539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	245	765	5	ENST00000357368.4:c.3589C>T	p.Arg1197Trp	p.R1197W	ENST00000357368	NM_002850.3	1197	Cgg/Tgg	22/38	0.366591754428293	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.370091197063256	2		770	646	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940384	49940384	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs749581478	NA	P-0049539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	143	878	0	ENST00000296474.3:c.659G>C	p.Arg220Pro	p.R220P	ENST00000296474	NM_002447.2	220	cGt/cCt	1/20	0.370091197063256	3	FACETS	0.927	0.844	1	0.309	0.281	0.338	CLONAL	1	TRUE	0	0.370091197063256	3		878	988	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69103973	69103973	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	202	410	0	ENST00000288368.4:c.4363A>G	p.Lys1455Glu	p.K1455E	ENST00000288368	NM_024870.2	1455	Aag/Gag	36/40	0.370091197063256	8	FACETS	1	0.977	1	0.322	0.298	0.347	CLONAL	2	TRUE	1	0.370091197063256	8		410	1021	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222441	53222441	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	121	940	0	ENST00000375401.3:c.4391A>C	p.Asp1464Ala	p.D1464A	ENST00000375401	NM_004187.3	1464	gAt/gCt	26/26	0.370091197063256	3	FACETS	0.868	0.783	0.957			1	CLONAL	1	TRUE	NA	0.370091197063256	3		940	893	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56409145	56409145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1308397244	NA	P-0049541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	174	326	0	ENST00000348428.3:c.1652G>A	p.Arg551Gln	p.R551Q	ENST00000348428	NM_006785.3	551	cGa/cAa	14/17	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.945206663839104	2		326	357	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644827	67644827	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs990055512	NA	P-0049541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	200	458	0	ENST00000264010.4:c.92G>A	p.Gly31Glu	p.G31E	ENST00000264010	NM_006565.3	31	gGg/gAg	3/12	0.945206663839104	2	FACETS	1	0.95	1	0.506	0.475	0.537	CLONAL	1	TRUE	0	0.945206663839104	2		458	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579360	7579363	+	frameshift_variant	Frame_Shift_Del	DEL	GAAA	GAAA	-	novel	NA	P-0049541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	611	615	1	ENST00000269305.4:c.324_327del	p.Phe109ValfsTer13	p.F109Vfs*13	ENST00000269305	NM_001126112.2	108	ggTTTC/gg	4/11	0.945206663839104	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.945206663839104	2		616	626	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	40	431	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.358	0.297	0.427	0.358	0.297	0.427	SUBCLONAL	1	TRUE	1	0.31	2		431	720	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820554	44820554	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	35	419	0	ENST00000377967.4:c.251del	p.Ile84ThrfsTer2	p.I84Tfs*2	ENST00000377967	NM_021140.2	84	aTc/ac	3/29	NA	2	FACETS	0.35	0.286	0.422			1	INDETERMINATE	1	TRUE	NA	0.31	2		419	645	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913351	NA	P-0049543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	69	298	0	ENST00000288602.6:c.1397G>C	p.Gly466Ala	p.G466A	ENST00000288602	NM_004333.4	466	gGa/gCa	11/18	0.396416278580229	3	FACETS	0.565	0.492	0.643	0.282	0.246	0.322	SUBCLONAL	1	FALSE	1	0.537453440686822	3		298	577	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543946	41543946	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs766548877	NA	P-0049543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	410	505	0	ENST00000263253.7:c.2237A>G	p.Asn746Ser	p.N746S	ENST00000263253	NM_001429.3	746	aAc/aGc	12/31	0.510374859168708	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	FALSE	2	0.537453440686822	4		505	998	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573987	7574023	+	frameshift_variant	Frame_Shift_Del	DEL	GCCTCATTCAGCTCTCGGAACATCTCGAAGCGCTCAC	GCCTCATTCAGCTCTCGGAACATCTCGAAGCGCTCAC	-	novel	NA	P-0049543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	202	656	0	ENST00000269305.4:c.1004_1040del	p.Arg335ProfsTer23	p.R335Pfs*23	ENST00000269305	NM_001126112.2	335	cGTGAGCGCTTCGAGATGTTCCGAGAGCTGAATGAGGCc/cc	10/11	0.545706786370554	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	0	0.537453440686822	1		656	382	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120028	70120028	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	10	39	0	ENST00000245479.2:c.1030C>G	p.Pro344Ala	p.P344A	ENST00000245479	NM_000346.3	344	Cca/Gca	3/3	0.545706786370554	3	FACETS	0.964	0.671	1	0.482	0.335	0.654	CLONAL	1	FALSE	1	0.537453440686822	3		39	49	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955900	55955900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763851452	NA	P-0049543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	65	405	0	ENST00000263923.4:c.3262G>A	p.Val1088Ile	p.V1088I	ENST00000263923	NM_002253.2	1088	Gtc/Atc	24/30	0.490168602271159	4	FACETS	0.462	0.4	0.53	0.154	0.133	0.177	SUBCLONAL	1	FALSE	1	0.537453440686822	4		405	805	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10305513	10305545	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCAGCGAGATGGCCGGGACGGCCAGTGTGGG	GGGCAGCGAGATGGCCGGGACGGCCAGTGTGGG	A	novel	NA	P-0049543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	289	385	0	ENST00000340748.4:c.31_63delinsT	p.Pro11Ter	p.P11*	ENST00000340748		11	CCCACACTGGCCGTCCCGGCCATCTCGCTGCCC/T	1/40	0.293237800592414	5	FACETS	0.898	0.855	0.94	1	0.992	1	INDETERMINATE	4	FALSE	2	0.537453440686822	5		385	541	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0049552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	72	346	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.228496474755199	3	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	1	0.228496474755199	3		346	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0049552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	50	559	0	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	1	2	FACETS	0.99	0.841	1	0.99	0.841	1	CLONAL	1	TRUE	1	0.228496474755199	2		559	442	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70355083	70355083	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	64	624	1	ENST00000374080.3:c.5005G>T	p.Asp1669Tyr	p.D1669Y	ENST00000374080		1669	Gat/Tat	36/45	0.184152804844709	1	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	0	0.228496474755199	1		625	492	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115753	108115753	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	11	129	0	ENST00000278616.4:c.901G>C	p.Gly301Arg	p.G301R	ENST00000278616	NM_000051.3	301	Ggt/Cgt	7/63	0.228496474755199	3	FACETS	0.984	0.686	1	0.492	0.343	0.675	CLONAL	1	TRUE	1	0.228496474755199	3		129	109	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155388	99155388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465343631	NA	P-0049552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	20	375	1	ENST00000074304.5:c.614C>T	p.Ala205Val	p.A205V	ENST00000074304	NM_001134224.1	205	gCg/gTg	9/26	0.215095949084268	2	FACETS	0.612	0.468	0.78	0.306	0.234	0.39	SUBCLONAL	1	TRUE	0	0.228496474755199	2		376	286	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737831	145737831	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs778030723	NA	P-0049552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	97	762	0	ENST00000428558.2:c.2999T>C	p.Leu1000Pro	p.L1000P	ENST00000428558	NM_004260.3	1000	cTg/cCg	18/22	0.228496474755199	3	FACETS	0.798	0.713	0.888	0.798	0.713	0.888	SUBCLONAL	2	TRUE	1	0.228496474755199	3		762	593	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	195	431	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.249022440104542	3	FACETS	0.901	0.838	0.965	0.901	0.838	0.965	CLONAL	2	TRUE	1	0.411024657072974	3		431	635	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0049553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	207	746	1	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	0.411024657072974	1	FACETS	0.909	0.845	0.976	0.909	0.845	0.976	CLONAL	1	TRUE	0	0.411024657072974	1		747	880	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998985	11998985	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	66	271	0	ENST00000353533.5:c.487C>T	p.Gln163Ter	p.Q163*	ENST00000353533	NM_003010.3	163	Cag/Tag	4/11	0.411024657072974	1	FACETS	0.828	0.725	0.939	0.828	0.725	0.939	CLONAL	1	TRUE	0	0.411024657072974	1		271	308	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0049554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	177	248	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.932946910989247	2		249	334	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692830	89692830	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	105	133	0	ENST00000371953.3:c.314G>T	p.Cys105Phe	p.C105F	ENST00000371953	NM_000314.4	105	tGt/tTt	5/9	0.932946910989247	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.932946910989247	1		133	118	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845489	151845490	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0049555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	19	554	0	ENST00000262189.6:c.13522_13523del	p.Pro4508LysfsTer5	p.P4508Kfs*5	ENST00000262189	NM_170606.2	4508	CCa/a	52/59	0.321358311039419	4	FACETS	1	0.875	1	0.403	0.313	0.503	INDETERMINATE	1	TRUE	1	0.634789758400315	4		554	81	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	257	714	0	ENST00000269305.4:c.380C>A	p.Ser127Tyr	p.S127Y	ENST00000269305	NM_001126112.2	127	tCc/tAc	5/11	0.216462415118238	2	FACETS	0.984	0.921	1	0.984	0.921	1	CLONAL	2	TRUE	0	0.217939313372546	2		714	1198	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807399	36807399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	131	751	1	ENST00000373129.3:c.1265C>T	p.Ser422Phe	p.S422F	ENST00000373129	NM_032017.1	422	tCc/tTc	12/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.217939313372546	2		752	1043	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982309	201982309	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0049556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	113	668	0	ENST00000359651.3:c.689-1G>A		p.X230_splice	ENST00000359651		230			1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.217939313372546	2		668	904	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953653	32953653	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0049556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	43	271	0	ENST00000380152.3:c.8953+1G>C		p.X2985_splice	ENST00000380152		2985			0.217939313372546	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.217939313372546	1		271	273	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422724	49422725	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	98	529	0	ENST00000301067.7:c.14268dup	p.Pro4757ThrfsTer25	p.P4757Tfs*25	ENST00000301067	NM_003482.3	4756	-/A	45/54	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.217939313372546	2		529	728	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751549	57751549	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1449761842	NA	P-0049556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	31	297	0	ENST00000274289.3:c.1442G>T	p.Gly481Val	p.G481V	ENST00000274289	NM_006622.3	481	gGa/gTa	11/14	0.217939313372546	1	FACETS	0.599	0.484	0.729	0.599	0.484	0.729	SUBCLONAL	1	TRUE	0	0.217939313372546	1		297	423	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310478	65310491	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	AGCTTGATGAATGG	AGCTTGATGAATGG	TCACTCACC	novel	NA	P-0049556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	81	444	0	ENST00000342505.4:c.2197_2210delinsGGTGAGTGA	p.Pro733GlyfsTer3	p.P733Gfs*3	ENST00000342505	NM_002227.2	733	CCATTCATCAAGCTc/GGTGAGTGAc	16/25	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.217939313372546	2		444	742	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0049557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	15	423	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.885	0.651	1	0.885	0.651	1	CLONAL	1	TRUE	1	0.22	2		423	154	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603041	48603041	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767361	NA	P-0049557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	27	259	0	ENST00000342988.3:c.1342C>T	p.Gln448Ter	p.Q448*	ENST00000342988	NM_005359.5	448	Cag/Tag	11/12	1	2	FACETS	0.864	0.689	1	0.864	0.689	1	CLONAL	1	TRUE	1	0.22	2		259	284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	36	566	0	ENST00000269305.4:c.641del	p.His214LeufsTer33	p.H214Lfs*33	ENST00000269305	NM_001126112.2	214	cAt/ct	6/11	1	2	FACETS	0.763	0.627	0.915	0.763	0.627	0.915	CLONAL	1	TRUE	1	0.22	2		566	429	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273231	18273231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1260910794	NA	P-0049557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	39	517	1	ENST00000222254.8:c.1024G>A	p.Glu342Lys	p.E342K	ENST00000222254	NM_005027.3	342	Gag/Aag	9/16	1	2	FACETS	0.779	0.646	0.928	0.779	0.646	0.928	CLONAL	1	TRUE	1	0.22	2		518	455	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652353	48652353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1340713003	NA	P-0049557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	16	426	0	ENST00000376670.3:c.1024G>A	p.Gly342Ser	p.G342S	ENST00000376670	NM_002049.3	342	Ggt/Agt	6/6	1	1	FACETS	0.518	0.383	0.679	0.518	0.383	0.679	SUBCLONAL	1	TRUE	0	0.22	1		426	250	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424685	49424686	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0049557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	36	575	0	ENST00000301067.7:c.13661_13662del	p.Gln4554ProfsTer20	p.Q4554Pfs*20	ENST00000301067	NM_003482.3	4554	cAG/c	40/54	1	2	FACETS	0.683	0.561	0.82	0.683	0.561	0.82	SUBCLONAL	1	TRUE	1	0.22	2		575	479	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125476	47125476	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	26	357	0	ENST00000409792.3:c.5794C>T	p.Gln1932Ter	p.Q1932*	ENST00000409792	NM_014159.6	1932	Cag/Tag	12/21	1	2	FACETS	0.783	0.621	0.967	0.783	0.621	0.967	CLONAL	1	TRUE	1	0.22	2		357	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0049558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	138	591	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.106108606373215	5	FACETS	0.861	0.785	0.94	0.645	0.589	0.705	INDETERMINATE	3	FALSE	1	0.210983778017657	5		593	667	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0049558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	152	325	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.210983778017657	6	FACETS	1	0.973	1	0.895	0.825	0.966	CLONAL	4	FALSE	1	0.210983778017657	6		325	458	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349957	15349957	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	103	731	0	ENST00000263377.2:c.3695G>C	p.Arg1232Pro	p.R1232P	ENST00000263377	NM_058243.2	1232	cGg/cCg	18/20	0.196266614901337	3	FACETS	0.896	0.804	0.994	0.896	0.804	0.994	CLONAL	2	FALSE	1	0.210983778017657	3		731	602	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0049559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	526	479	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.853652012876576	5	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	2	0.853652012876576	5		479	895	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0049559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	672	552	0	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	0.853652012876576	4	FACETS	0.989	0.974	1	0.989	0.974	1	CLONAL	4	TRUE	0	0.853652012876576	4		552	738	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551603	150551603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	127	525	2	ENST00000369026.2:c.404G>A	p.Gly135Glu	p.G135E	ENST00000369026	NM_021960.4	135	gGg/gAg	1/3	0.853652012876576	10	FACETS	1	0.932	1			1	CLONAL	1	TRUE	NA	0.853652012876576	10		527	1264	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955482	48955482	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	398	310	0	ENST00000267163.4:c.1600del	p.Ser534ValfsTer9	p.S534Vfs*9	ENST00000267163	NM_000321.2	533	gAa/ga	17/27	0.853652012876576	3	FACETS	0.994	0.974	1	0.994	0.974	1	CLONAL	3	TRUE	0	0.853652012876576	3		310	446	SUCCESS
ATR	545	MSKCC	GRCh37	3	142222219	142222219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	612	301	1	ENST00000350721.4:c.5273G>A	p.Gly1758Glu	p.G1758E	ENST00000350721	NM_001184.3	1758	gGa/gAa	30/47	0.853652012876576	8	FACETS	0.941	0.911	0.971	0.941	0.911	0.971	CLONAL	5	TRUE	3	0.853652012876576	8		302	1085	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214320	55214320	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	165	551	1	ENST00000275493.2:c.446G>T	p.Arg149Leu	p.R149L	ENST00000275493	NM_005228.3	149	cGg/cTg	4/28	0.853652012876576	6	FACETS	1	0.943	1	0.259	0.237	0.281	CLONAL	1	TRUE	2	0.853652012876576	6		552	1012	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs786201838	NA	P-0049560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	316	600	1	ENST00000269305.4:c.578A>T	p.His193Leu	p.H193L	ENST00000269305	NM_001126112.2	193	cAt/cTt	6/11	0.822648770960852	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.822648770960852	1		601	443	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627654	14627654	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs774560970	NA	P-0049560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1330	296	545	3	ENST00000254322.2:c.416G>T	p.Gly139Val	p.G139V	ENST00000254322	NM_006145.1	139	gGt/gTt	2/3	0.79542813277212	3	FACETS	0.625	0.586	0.664	0.312	0.293	0.332	SUBCLONAL	1	TRUE	1	0.822648770960852	3		548	1626	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056100	26056100	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	206	337	0	ENST00000343677.2:c.557C>A	p.Ala186Asp	p.A186D	ENST00000343677	NM_005319.3	186	gCc/gAc	1/1	0.822648770960852	1	FACETS	0.986	0.94	1	0.986	0.94	1	CLONAL	1	TRUE	0	0.822648770960852	1		337	299	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0049562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	149	423	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.183191210313256	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.772963376244642	0		423	522	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0049562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	101	344	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.402397394101834	2	FACETS	0.488	0.438	0.542	0.244	0.219	0.271	INDETERMINATE	1	TRUE	0	0.772963376244642	2		344	535	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0049562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	427	642	1	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	0.76331567457535	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.772963376244642	1		643	665	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346094	152346094	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367696886	NA	P-0049562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	168	457	0	ENST00000359321.1:c.476G>A	p.Arg159His	p.R159H	ENST00000359321	NM_005431.1	159	cGc/cAc	3/3	0.505014702006092	3	FACETS	0.608	0.558	0.66	0.304	0.279	0.33	SUBCLONAL	1	TRUE	1	0.772963376244642	3		457	991	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104356917	104356917	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs749533220	NA	P-0049562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	197	504	0	ENST00000369902.3:c.777C>G	p.Ile259Met	p.I259M	ENST00000369902	NM_016169.3	259	atC/atG	7/12	0.297187138480847	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.772963376244642	0		504	642	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336214	73336214	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	65	247	0	ENST00000377767.4:c.2189C>A	p.Ser730Tyr	p.S730Y	ENST00000377767	NM_014953.3	730	tCt/tAt	17/21	0.334245598186304	1	FACETS	0.303	0.264	0.344	0.303	0.264	0.344	INDETERMINATE	1	TRUE	0	0.772963376244642	1		247	341	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222937	36222937	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	248	867	0	ENST00000222270.7:c.5566G>T	p.Ala1856Ser	p.A1856S	ENST00000222270	NM_014727.1	1856	Gcc/Tcc	27/37	1	2	FACETS	0.453	0.423	0.485	0.453	0.423	0.485	SUBCLONAL	1	TRUE	1	0.772963376244642	2		867	1415	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	238	782	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.859	0.805	0.915	1	0.994	1	CLONAL	2	TRUE	1	0.368228868908838	2		787	752	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563311	21563311	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs77919685	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	179	764	0	ENST00000382592.4:c.608C>T	p.Ala203Val	p.A203V	ENST00000382592	NM_014572.2	203	gCg/gTg	4/8	0.267033698533631	4	FACETS	1	0.944	1	0.344	0.316	0.374	CLONAL	1	TRUE	1	0.368228868908838	4		764	1288	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967171	25967171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372578149	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	70	324	2	ENST00000435504.4:c.2035G>A	p.Ala679Thr	p.A679T	ENST00000435504		679	Gca/Aca	13/13	1	2	FACETS	0.907	0.794	1	0.907	0.794	1	CLONAL	1	TRUE	1	0.368228868908838	2		326	419	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	126	374	3	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.954	0.865	1	0.954	0.865	1	CLONAL	1	TRUE	1	0.368228868908838	2		377	717	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	81	399	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	1	2	FACETS	0.753	0.664	0.848	0.753	0.664	0.848	SUBCLONAL	1	TRUE	1	0.368228868908838	2		399	584	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	112	680	3	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.368228868908838	2		683	575	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131402	17131402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398124537	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	137	522	0	ENST00000285071.4:c.50G>A	p.Arg17His	p.R17H	ENST00000285071	NM_144997.5	17	cGc/cAc	4/14	1	2	FACETS	0.83	0.755	0.91	0.83	0.755	0.91	CLONAL	1	TRUE	1	0.368228868908838	2		522	896	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023327	27023327	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	35	149	0	ENST00000324856.7:c.437del	p.Pro146GlnfsTer86	p.P146Qfs*86	ENST00000324856	NM_006015.4	145	Ccc/cc	1/20	1	2	FACETS	0.602	0.494	0.721	0.602	0.494	0.721	SUBCLONAL	1	TRUE	1	0.368228868908838	2		149	316	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	49	199	3	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.368228868908838	2		202	239	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478633	57478633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1131691999	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	79	321	1	ENST00000371085.3:c.305C>T	p.Ala102Val	p.A102V	ENST00000371085	NM_000516.4	102	gCg/gTg	4/13	0.353823278473965	3	FACETS	0.707	0.621	0.799	0.353	0.31	0.4	SUBCLONAL	1	TRUE	1	0.368228868908838	3		322	719	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387080	31387080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1007955291	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	130	504	2	ENST00000328111.2:c.1705G>A	p.Ala569Thr	p.A569T	ENST00000328111	NM_006892.3	569	Gca/Aca	16/23	0.353823278473965	3	FACETS	0.813	0.736	0.894	0.406	0.368	0.447	CLONAL	1	TRUE	1	0.368228868908838	3		506	1029	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	186	784	3	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	1	2	FACETS	0.979	0.903	1	0.979	0.903	1	CLONAL	1	TRUE	1	0.368228868908838	2		787	1032	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780068	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	190	682	0	ENST00000269305.4:c.472C>T	p.Arg158Cys	p.R158C	ENST00000269305	NM_001126112.2	158	Cgc/Tgc	5/11	1	2	FACETS	0.92	0.849	0.993	0.92	0.849	0.993	CLONAL	1	TRUE	1	0.368228868908838	2		682	1122	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	85	795	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.739	0.653	0.83	0.739	0.653	0.83	SUBCLONAL	1	TRUE	1	0.368228868908838	2		795	625	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937904	36937904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1386293956	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	152	714	2	ENST00000361632.4:c.932G>A	p.Arg311His	p.R311H	ENST00000361632		311	cGc/cAc	7/16	1	2	FACETS	0.842	0.769	0.918	0.842	0.769	0.918	CLONAL	1	TRUE	1	0.368228868908838	2		716	981	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	75	409	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.945	0.832	1	0.945	0.832	1	CLONAL	1	TRUE	1	0.368228868908838	2		415	431	SUCCESS
AR	367	MSKCC	GRCh37	X	66766199	66766199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1035114992	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	103	424	1	ENST00000374690.3:c.1211C>T	p.Ala404Val	p.A404V	ENST00000374690	NM_000044.3	404	gCg/gTg	1/8	0.368228868908838	1	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	0	0.368228868908838	1		425	455	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513282	44513287	+	inframe_deletion	In_Frame_Del	DEL	CCACCG	CCACCG	-	rs745888281	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	119	424	2	ENST00000291552.4:c.648_653del	p.Gly222_Gly223del	p.G222_G223del	ENST00000291552	NM_006758.2	216	ggCGGTGGt/ggt	8/8	1	2	FACETS	0.737	0.665	0.814	0.737	0.665	0.814	SUBCLONAL	1	TRUE	1	0.368228868908838	2		426	877	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007825	45007825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	57	300	0	ENST00000558401.1:c.276del	p.Thr93LeufsTer10	p.T93Lfs*10	ENST00000558401	NM_004048.2	91	aCc/ac	2/4	1	2	FACETS	0.961	0.83	1	0.961	0.83	1	CLONAL	1	TRUE	1	0.368228868908838	2		300	322	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390736	139390736	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	172	706	1	ENST00000277541.6:c.7455del	p.Ser2486ArgfsTer103	p.S2486Rfs*103	ENST00000277541	NM_017617.3	2485	ccC/cc	34/34	1	2	FACETS	0.865	0.795	0.938	0.865	0.795	0.938	CLONAL	1	TRUE	1	0.368228868908838	2		707	1080	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509528	106509528	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	84	452	0	ENST00000359195.3:c.1522C>A	p.Pro508Thr	p.P508T	ENST00000359195	NM_002649.2	508	Cca/Aca	2/11	1	2	FACETS	0.888	0.786	0.996	0.888	0.786	0.996	CLONAL	1	TRUE	1	0.368228868908838	2		452	514	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439925	56439925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755478993	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	136	484	0	ENST00000407977.2:c.667C>T	p.Arg223Cys	p.R223C	ENST00000407977		223	Cgc/Tgc	6/10	1	2	FACETS	0.857	0.779	0.939	0.857	0.779	0.939	CLONAL	1	TRUE	1	0.368228868908838	2		484	862	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906603	32906603	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359777	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	37	242	0	ENST00000380152.3:c.994del	p.Ile332PhefsTer17	p.I332Ffs*17	ENST00000380152		330	Aaa/aa	10/27	0.267033698533631	4	FACETS	1	0.888	1	0.365	0.303	0.434	CLONAL	1	TRUE	1	0.368228868908838	4		242	251	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513331	44513331	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	166	432	1	ENST00000291552.4:c.604C>T	p.Arg202Cys	p.R202C	ENST00000291552	NM_006758.2	202	Cgt/Tgt	8/8	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.368228868908838	2		433	861	SUCCESS
RET	5979	MSKCC	GRCh37	10	43572762	43572762	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	80	211	0	ENST00000355710.3:c.56T>C	p.Leu19Pro	p.L19P	ENST00000355710	NM_020975.4	19	cTg/cCg	1/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.368228868908838	2		211	372	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	75	361	1	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.93	0.818	1	0.93	0.818	1	CLONAL	1	TRUE	1	0.368228868908838	2		362	438	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196143	108196143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564652222	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	47	300	0	ENST00000278616.4:c.6679C>T	p.Arg2227Cys	p.R2227C	ENST00000278616	NM_000051.3	2227	Cgc/Tgc	46/63	1	2	FACETS	0.749	0.634	0.874	0.749	0.634	0.874	SUBCLONAL	1	TRUE	1	0.368228868908838	2		300	341	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869534	102869534	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775312813	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	95	366	1	ENST00000307046.8:c.107C>T	p.Ala36Val	p.A36V	ENST00000307046	NM_001111285.1	36	gCg/gTg	2/4	1	2	FACETS	0.866	0.772	0.965	0.866	0.772	0.965	CLONAL	1	TRUE	1	0.368228868908838	2		367	596	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858811	78858811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1440436634	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	141	501	0	ENST00000306801.3:c.1846C>T	p.Arg616Cys	p.R616C	ENST00000306801	NM_020761.2	616	Cgc/Tgc	17/34	1	2	FACETS	0.948	0.864	1	0.948	0.864	1	CLONAL	1	TRUE	1	0.368228868908838	2		501	808	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46215214	46215214	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1433103583	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	31	146	0	ENST00000334344.6:c.652del	p.Ser218ProfsTer74	p.S218Pfs*74	ENST00000334344	NM_152641.2	217	Ttt/tt	6/21	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.368228868908838	2		146	151	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524621	103524621	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	28	297	0	ENST00000355739.4:c.2752T>A	p.Leu918Ile	p.L918I	ENST00000355739	NM_000123.3	918	Tta/Ata	13/15	0.267033698533631	4	FACETS	0.41	0.327	0.506	0.137	0.109	0.169	SUBCLONAL	1	TRUE	1	0.368228868908838	4		297	507	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522693	67522693	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	24	168	0	ENST00000274335.5:c.193del	p.Glu65LysfsTer10	p.E65Kfs*10	ENST00000274335		64	Ggg/gg	1/15	1	2	FACETS	0.467	0.367	0.582	0.467	0.367	0.582	SUBCLONAL	1	TRUE	1	0.368228868908838	2		168	279	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948098	178948098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	35	185	0	ENST00000263967.3:c.2870C>T	p.Thr957Ile	p.T957I	ENST00000263967	NM_006218.2	957	aCa/aTa	20/21	1	2	FACETS	0.823	0.679	0.982	0.823	0.679	0.982	CLONAL	1	TRUE	1	0.368228868908838	2		185	231	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	155	597	1	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	1	2	FACETS	0.901	0.825	0.981	0.901	0.825	0.981	CLONAL	1	TRUE	1	0.368228868908838	2		598	934	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645975	215645975	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs587780033	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	88	270	0	ENST00000260947.4:c.623del	p.Lys208ArgfsTer4	p.K208Rfs*4	ENST00000260947	NM_000465.2	208	aAg/ag	4/11	0.353823278473965	3	FACETS	0.913	0.818	1	0.913	0.818	1	CLONAL	2	TRUE	1	0.368228868908838	3		270	310	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133981	38133981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	79	372	0	ENST00000317025.8:c.3905del	p.Asn1302MetfsTer4	p.N1302Mfs*4	ENST00000317025	NM_023034.1	1302	aAt/at	23/24	1	2	FACETS	0.862	0.76	0.97	0.862	0.76	0.97	CLONAL	1	TRUE	1	0.368228868908838	2		372	498	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641202	3641202	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770020510	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	77	633	0	ENST00000294008.3:c.2437G>A	p.Glu813Lys	p.E813K	ENST00000294008	NM_032444.2	813	Gag/Aag	12/15	1	2	FACETS	0.406	0.356	0.461	0.406	0.356	0.461	SUBCLONAL	1	TRUE	1	0.368228868908838	2		633	1029	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712018	89712018	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs727504114	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	25	167	0	ENST00000371953.3:c.634+2T>C		p.X212_splice	ENST00000371953	NM_000314.4	212			1	2	FACETS	0.917	0.732	1	0.917	0.732	1	CLONAL	1	TRUE	1	0.368228868908838	2		167	148	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434005	49434005	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	139	859	1	ENST00000301067.7:c.7548del	p.Asn2517IlefsTer26	p.N2517Ifs*26	ENST00000301067	NM_003482.3	2516	ccC/cc	31/54	1	2	FACETS	0.831	0.756	0.91	0.831	0.756	0.91	CLONAL	1	TRUE	1	0.368228868908838	2		860	908	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685289	89685289	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554897267	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	23	159	0	ENST00000371953.3:c.188del	p.Asn63ThrfsTer36	p.N63Tfs*36	ENST00000371953	NM_000314.4	62	Aaa/aa	3/9	1	2	FACETS	0.796	0.626	0.988	0.796	0.626	0.988	CLONAL	1	TRUE	1	0.368228868908838	2		159	157	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607691	46607692	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	135	630	0	ENST00000263734.3:c.1886_1887del	p.Ser629PhefsTer86	p.S629Ffs*86	ENST00000263734	NM_001430.4	627	cCT/c	12/16	1	2	FACETS	0.882	0.802	0.967	0.882	0.802	0.967	CLONAL	1	TRUE	1	0.368228868908838	2		630	831	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831345	89831346	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs878853663	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	116	459	4	ENST00000389301.3:c.2730_2731del	p.Trp911AspfsTer31	p.W911Dfs*31	ENST00000389301	NM_000135.2	910	ctCTgg/ctgg	28/43	1	2	FACETS	0.918	0.829	1	0.918	0.829	1	CLONAL	1	TRUE	1	0.368228868908838	2		463	686	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289501	33289501	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1359646835	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	129	519	0	ENST00000374542.5:c.202G>A	p.Glu68Lys	p.E68K	ENST00000374542	NM_001141970.1	68	Gaa/Aaa	2/8	0.353823278473965	3	FACETS	0.845	0.765	0.929	0.422	0.382	0.465	CLONAL	1	TRUE	1	0.368228868908838	3		519	982	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170998	56170998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766159820	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	44	234	1	ENST00000399503.3:c.1826G>A	p.Ser609Asn	p.S609N	ENST00000399503	NM_005921.1	609	aGc/aAc	10/20	1	2	FACETS	0.629	0.529	0.739	0.629	0.529	0.739	SUBCLONAL	1	TRUE	1	0.368228868908838	2		235	380	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989699	15989699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs557813338	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	116	275	1	ENST00000268712.3:c.3074C>T	p.Pro1025Leu	p.P1025L	ENST00000268712	NM_006311.3	1025	cCg/cTg	23/46	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.368228868908838	2		276	603	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911766	26911766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	33	258	0	ENST00000381527.3:c.191G>A	p.Cys64Tyr	p.C64Y	ENST00000381527	NM_001260.1	64	tGt/tAt	2/13	0.267033698533631	4	FACETS	0.652	0.532	0.788	0.217	0.177	0.263	SUBCLONAL	1	TRUE	1	0.368228868908838	4		258	376	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268763	41268763	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	70	300	0	ENST00000349496.5:c.1005del	p.Lys335AsnfsTer10	p.K335Nfs*10	ENST00000349496	NM_001904.3	334	gAa/ga	7/15	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.368228868908838	2		300	330	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224198	36224198	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1351767688	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	107	566	1	ENST00000222270.7:c.6748C>T	p.Arg2250Cys	p.R2250C	ENST00000222270	NM_014727.1	2250	Cgc/Tgc	28/37	1	2	FACETS	0.856	0.769	0.948	0.856	0.769	0.948	CLONAL	1	TRUE	1	0.368228868908838	2		567	679	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660270	227660270	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	105	577	1	ENST00000305123.5:c.3185del	p.Gly1062AlafsTer8	p.G1062Afs*8	ENST00000305123	NM_005544.2	1062	gGc/gc	1/2	0.353823278473965	3	FACETS	0.897	0.804	0.996	0.448	0.402	0.498	CLONAL	1	TRUE	1	0.368228868908838	3		578	753	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906610	32906610	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1555281682	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	51	248	0	ENST00000380152.3:c.995T>A	p.Ile332Asn	p.I332N	ENST00000380152		332	aTt/aAt	10/27	0.267033698533631	4	FACETS	1	0.965	1	0.493	0.423	0.569	CLONAL	1	TRUE	1	0.368228868908838	4		248	256	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180609	56180609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	46	264	1	ENST00000399503.3:c.3938C>T	p.Thr1313Met	p.T1313M	ENST00000399503	NM_005921.1	1313	aCg/aTg	16/20	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.368228868908838	2		265	235	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323170	31323172	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	94	599	0	ENST00000412585.2:c.817_819del	p.Val273del	p.V273del	ENST00000412585	NM_005514.6	273	GTG/-	4/8	0.353823278473965	3	FACETS	0.701	0.622	0.784	0.35	0.311	0.392	SUBCLONAL	1	TRUE	1	0.368228868908838	3		599	863	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445514	49445514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356632640	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	106	495	0	ENST00000301067.7:c.1952C>T	p.Ser651Leu	p.S651L	ENST00000301067	NM_003482.3	651	tCg/tTg	10/54	1	2	FACETS	0.743	0.666	0.825	0.743	0.666	0.825	SUBCLONAL	1	TRUE	1	0.368228868908838	2		495	775	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78426120	78426120	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	72	351	0	ENST00000370768.2:c.1405del	p.His469MetfsTer196	p.H469Mfs*196	ENST00000370768	NM_003902.3	469	Cat/at	15/20	1	2	FACETS	0.792	0.693	0.897	0.792	0.693	0.897	SUBCLONAL	1	TRUE	1	0.368228868908838	2		351	494	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309886	65309886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	84	276	0	ENST00000342505.4:c.2264G>A	p.Arg755Gln	p.R755Q	ENST00000342505	NM_002227.2	755	cGa/cAa	17/25	1	2	FACETS	0.998	0.885	1	0.998	0.885	1	CLONAL	1	TRUE	1	0.368228868908838	2		276	457	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843709	156843709	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	150	641	0	ENST00000524377.1:c.1135A>G	p.Met379Val	p.M379V	ENST00000524377	NM_002529.3	379	Atg/Gtg	8/17	0.353823278473965	3	FACETS	0.862	0.786	0.942	0.431	0.393	0.471	CLONAL	1	TRUE	1	0.368228868908838	3		641	1119	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123260387	123260387	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	47	497	0	ENST00000358487.5:c.1514A>G	p.Lys505Arg	p.K505R	ENST00000358487	NM_000141.4	505	aAa/aGa	11/18	1	2	FACETS	0.345	0.29	0.406	0.345	0.29	0.406	SUBCLONAL	1	TRUE	1	0.368228868908838	2		497	740	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741864	17741864	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	26	148	0	ENST00000250003.3:c.535T>C	p.Tyr179His	p.Y179H	ENST00000250003	NM_002478.4	179	Tat/Cat	1/3	1	2	FACETS	0.732	0.584	0.899	0.732	0.584	0.899	SUBCLONAL	1	TRUE	1	0.368228868908838	2		148	193	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589812	69589812	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	54	69	0	ENST00000168712.1:c.41C>A	p.Ala14Glu	p.A14E	ENST00000168712	NM_002007.2	14	gCg/gAg	1/3	1	2	FACETS	0.772	0.67	0.88	1	0.971	1	SUBCLONAL	2	TRUE	1	0.368228868908838	2		69	190	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998390	100998390	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	43	142	0	ENST00000325455.5:c.1412A>G	p.Gln471Arg	p.Q471R	ENST00000325455	NM_001202474.3	471	cAg/cGg	1/8	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.368228868908838	2		142	210	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524621	103524621	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	91	297	0	ENST00000355739.4:c.2753del	p.Leu918TyrfsTer64	p.L918Yfs*64	ENST00000355739	NM_000123.3	918	Tta/ta	13/15	0.267033698533631	4	FACETS	1	0.974	1	0.445	0.396	0.496	CLONAL	1	TRUE	1	0.368228868908838	4		297	507	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748656	43748656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	101	508	0	ENST00000382044.4:c.2150G>A	p.Cys717Tyr	p.C717Y	ENST00000382044	NM_001141980.1	717	tGc/tAc	12/28	1	2	FACETS	0.829	0.741	0.921	0.829	0.741	0.921	CLONAL	1	TRUE	1	0.368228868908838	2		508	662	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533829	63533829	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	101	511	0	ENST00000307078.5:c.1325A>G	p.His442Arg	p.H442R	ENST00000307078	NM_004655.3	442	cAc/cGc	6/11	1	2	FACETS	0.838	0.749	0.931	0.838	0.749	0.931	CLONAL	1	TRUE	1	0.368228868908838	2		511	655	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584498	39584498	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	27	200	0	ENST00000262039.4:c.1163A>G	p.Asp388Gly	p.D388G	ENST00000262039	NM_002647.2	388	gAt/gGt	10/25	1	2	FACETS	0.401	0.319	0.494	0.401	0.319	0.494	SUBCLONAL	1	TRUE	1	0.368228868908838	2		200	366	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7168030	7168030	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1446729392	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	112	395	0	ENST00000302850.5:c.1559G>A	p.Trp520Ter	p.W520*	ENST00000302850	NM_000208.2	520	tGg/tAg	7/22	1	2	FACETS	0.836	0.752	0.924	0.836	0.752	0.924	CLONAL	1	TRUE	1	0.368228868908838	2		395	728	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141562	11141562	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	160	492	0	ENST00000358026.2:c.3539C>A	p.Pro1180His	p.P1180H	ENST00000358026	NM_001128849.1	1180	cCt/cAt	25/36	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.368228868908838	2		492	790	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46611776	46611776	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	127	527	0	ENST00000263734.3:c.2590A>G	p.Arg864Gly	p.R864G	ENST00000263734	NM_001430.4	864	Aga/Gga	16/16	1	2	FACETS	0.865	0.784	0.951	0.865	0.784	0.951	CLONAL	1	TRUE	1	0.368228868908838	2		527	797	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033667	48033667	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	47	292	0	ENST00000234420.5:c.3878C>A	p.Ala1293Asp	p.A1293D	ENST00000234420	NM_000179.2	1293	gCt/gAt	9/10	1	2	FACETS	0.813	0.689	0.948	0.813	0.689	0.948	CLONAL	1	TRUE	1	0.368228868908838	2		292	314	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662113	227662113	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	201	520	0	ENST00000305123.5:c.1342G>T	p.Asp448Tyr	p.D448Y	ENST00000305123	NM_005544.2	448	Gat/Tat	1/2	0.353823278473965	3	FACETS	0.896	0.834	0.961	0.896	0.834	0.961	CLONAL	2	TRUE	1	0.368228868908838	3		520	721	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264680	46264680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	48	240	0	ENST00000371998.3:c.1550G>A	p.Ser517Asn	p.S517N	ENST00000371998		517	aGc/aAc	12/23	0.353823278473965	3	FACETS	0.837	0.71	0.976	0.418	0.355	0.488	CLONAL	1	TRUE	1	0.368228868908838	3		240	369	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162933	47162933	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	50	300	0	ENST00000409792.3:c.3193C>A	p.Arg1065Ser	p.R1065S	ENST00000409792	NM_014159.6	1065	Cgt/Agt	3/21	1	2	FACETS	0.995	0.851	1	0.995	0.851	1	CLONAL	1	TRUE	1	0.368228868908838	2		300	273	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119585439	119585439	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs768507443	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	39	195	0	ENST00000316626.5:c.946C>T	p.Arg316Trp	p.R316W	ENST00000316626		316	Cgg/Tgg	9/12	1	2	FACETS	0.972	0.813	1	0.972	0.813	1	CLONAL	1	TRUE	1	0.368228868908838	2		195	218	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594080	55594080	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	63	277	0	ENST00000288135.5:c.1868del	p.Lys623ArgfsTer9	p.K623Rfs*9	ENST00000288135	NM_000222.2	622	gtA/gt	12/21	1	2	FACETS	0.86	0.747	0.981	0.86	0.747	0.981	CLONAL	1	TRUE	1	0.368228868908838	2		277	398	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197671	106197671	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587778701	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	33	186	0	ENST00000380013.4:c.6004A>G	p.Ile2002Val	p.I2002V	ENST00000380013	NM_001127208.2	2002	Ata/Gta	11/11	1	2	FACETS	0.826	0.678	0.99	0.826	0.678	0.99	CLONAL	1	TRUE	1	0.368228868908838	2		186	217	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250938	153250938	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	10	164	0	ENST00000281708.4:c.1123-1G>T		p.X375_splice	ENST00000281708	NM_033632.3	375			1	2	FACETS	0.428	0.291	0.598	0.428	0.291	0.598	SUBCLONAL	1	TRUE	1	0.368228868908838	2		164	127	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331966	81331966	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	46	222	0	ENST00000222390.5:c.2118del	p.Phe706LeufsTer4	p.F706Lfs*4	ENST00000222390	NM_000601.4	706	ttT/tt	18/18	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.368228868908838	2		222	239	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141557595	141557595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1444492303	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	178	647	0	ENST00000220592.5:c.1720G>A	p.Val574Met	p.V574M	ENST00000220592	NM_012154.3	574	Gtg/Atg	13/19	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.368228868908838	2		647	953	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250005	110250005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	46	611	1	ENST00000374672.4:c.670G>A	p.Gly224Arg	p.G224R	ENST00000374672	NM_004235.4	224	Ggg/Agg	3/5	1	2	FACETS	0.373	0.313	0.439	0.373	0.313	0.439	SUBCLONAL	1	TRUE	1	0.368228868908838	2		612	670	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	54	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.464952367946752	2		148	230	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578260	7578260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204041	NA	P-0049564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	153	533	0	ENST00000269305.4:c.589G>A	p.Val197Met	p.V197M	ENST00000269305	NM_001126112.2	197	Gtg/Atg	6/11	0.390382600827903	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.464952367946752	1		533	489	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589586	67589588	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	novel	NA	P-0049564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	66	182	0	ENST00000274335.5:c.1350_1352del	p.His450_Glu451delinsGln	p.H450_E451delinsQ	ENST00000274335		450	cATGaa/caa	10/15	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.464952367946752	2		182	251	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405615	70405619	+	frameshift_variant	Frame_Shift_Del	DEL	TGAAG	TGAAG	-	novel	NA	P-0049564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	119	376	0	ENST00000373644.4:c.3131_3135del	p.Glu1044GlyfsTer17	p.E1044Gfs*17	ENST00000373644	NM_030625.2	1043	aaTGAAGtg/aatg	4/12	0.464952367946752	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.464952367946752	1		376	350	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220674	1220674	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	155	808	0	ENST00000326873.7:c.692T>A	p.Phe231Tyr	p.F231Y	ENST00000326873	NM_000455.4	231	tTc/tAc	5/10	0.431899241352361	3	FACETS	0.848	0.776	0.924	0.424	0.388	0.462	CLONAL	1	TRUE	1	0.464952367946752	3		808	969	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972861	55972861	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	30	249	0	ENST00000263923.4:c.1529A>G	p.Lys510Arg	p.K510R	ENST00000263923	NM_002253.2	510	aAa/aGa	11/30	1	2	FACETS	0.304	0.244	0.371	0.304	0.244	0.371	SUBCLONAL	1	TRUE	1	0.464952367946752	2		249	425	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0049565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	227	423	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.534789128024132	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.534789128024132	3		423	524	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0049565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	140	559	2	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.534789128024132	2		561	504	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248444	212248444	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397514263	NA	P-0049565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	78	296	1	ENST00000342788.4:c.3823C>T	p.Arg1275Trp	p.R1275W	ENST00000342788	NM_005235.2	1275	Cgg/Tgg	28/28	0.14406391557047	0	FACETS	0.493	0.439	0.551			1	INDETERMINATE	1	TRUE	0	0.534789128024132	0		297	275	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099468	157099470	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	rs1429292576	NA	P-0049565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	88	378	2	ENST00000346085.5:c.413_415del	p.Asn138del	p.N138del	ENST00000346085	NM_020732.3	135	tcCAAc/tcc	1/20	1	2	FACETS	0.855	0.763	0.952	0.855	0.763	0.952	CLONAL	1	TRUE	1	0.534789128024132	2		380	385	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732958	30732958	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	88	321	0	ENST00000295754.5:c.1571A>G	p.Asp524Gly	p.D524G	ENST00000295754	NM_003242.5	524	gAc/gGc	7/7	1	2	FACETS	0.864	0.771	0.962	0.864	0.771	0.962	CLONAL	1	TRUE	1	0.534789128024132	2		321	381	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73334771	73334771	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	61	177	0	ENST00000377767.4:c.2689G>T	p.Glu897Ter	p.E897*	ENST00000377767	NM_014953.3	897	Gaa/Taa	20/21	1	2	FACETS	0.861	0.75	0.979	0.861	0.75	0.979	CLONAL	1	TRUE	1	0.534789128024132	2		177	265	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244249	153244250	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0049565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	65	273	0	ENST00000281708.4:c.1907_1908del	p.Phe636CysfsTer7	p.F636Cfs*7	ENST00000281708	NM_033632.3	636	tTT/t	12/12	1	2	FACETS	0.762	0.666	0.865	0.762	0.666	0.865	SUBCLONAL	1	TRUE	1	0.534789128024132	2		273	319	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268163	153268163	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	79	287	1	ENST00000281708.4:c.645del	p.Asn216MetfsTer23	p.N216Mfs*23	ENST00000281708	NM_033632.3	215	gcC/gc	4/12	1	2	FACETS	0.746	0.66	0.838	0.746	0.66	0.838	SUBCLONAL	1	TRUE	1	0.534789128024132	2		288	396	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324102	31324111	+	frameshift_variant	Frame_Shift_Del	DEL	AGGTCCTCGT	AGGTCCTCGT	-	novel	NA	P-0049565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	52	376	0	ENST00000412585.2:c.452_461del	p.Asn151SerfsTer60	p.N151Sfs*60	ENST00000412585	NM_005514.6	151	aACGAGGACCTg/ag	3/8	1	2	FACETS	0.831	0.715	0.955	0.831	0.715	0.955	CLONAL	1	TRUE	1	0.534789128024132	2		376	234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0049567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	506	662	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.629732065451309	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.629732065451309	1		662	973	SUCCESS
APC	324	MSKCC	GRCh37	5	112175360	112175360	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	152	184	0	ENST00000257430.4:c.4069G>T	p.Gly1357Ter	p.G1357*	ENST00000257430	NM_000038.5	1357	Gga/Tga	16/16	0.629732065451309	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.629732065451309	1		184	281	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951085	17951085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	338	463	0	ENST00000458235.1:c.1208G>A	p.Arg403His	p.R403H	ENST00000458235	NM_000215.3	403	cGc/cAc	9/24	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.629732065451309	2		463	1040	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912200	114912200	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0049567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	199	385	0	ENST00000543371.1:c.1269+1G>A		p.X423_splice	ENST00000543371	NM_001198531.1	423			0.364959200242998	1	FACETS	0.617	0.573	0.662	0.617	0.573	0.662	INDETERMINATE	1	TRUE	0	0.629732065451309	1		385	702	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861180	57861180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754075170	NA	P-0049567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	202	436	0	ENST00000228682.2:c.977C>T	p.Thr326Met	p.T326M	ENST00000228682	NM_005269.2	326	aCg/aTg	9/12	1	2	FACETS	0.747	0.693	0.802	0.747	0.693	0.802	SUBCLONAL	1	TRUE	1	0.629732065451309	2		436	859	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717727	89717727	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1554825226	NA	P-0049567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	143	327	0	ENST00000371953.3:c.752G>C	p.Gly251Ala	p.G251A	ENST00000371953	NM_000314.4	251	gGt/gCt	7/9	0.364959200242998	1	FACETS	0.624	0.572	0.677	0.624	0.572	0.677	INDETERMINATE	1	TRUE	0	0.629732065451309	1		327	499	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0049569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	50	237	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.819	0.697	0.952	0.819	0.697	0.952	CLONAL	1	TRUE	1	0.322213095254543	2		237	379	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101128	27101129	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	130	693	0	ENST00000324856.7:c.4412dup	p.Asn1471LysfsTer20	p.N1471Kfs*20	ENST00000324856	NM_006015.4	1470	-/A	18/20	0.322213095254543	1	FACETS	0.842	0.764	0.924	0.842	0.764	0.924	CLONAL	1	TRUE	0	0.322213095254543	1		693	804	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166601	118166601	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	74	300	0	ENST00000369448.3:c.1111T>A	p.Tyr371Asn	p.Y371N	ENST00000369448	NM_017709.3	371	Tac/Aac	2/2	1	2	FACETS	0.857	0.751	0.97	0.857	0.751	0.97	CLONAL	1	TRUE	1	0.322213095254543	2		300	536	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333828	70333828	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760983285	NA	P-0049569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	75	410	0	ENST00000373644.4:c.1733C>T	p.Thr578Ile	p.T578I	ENST00000373644	NM_030625.2	578	aCt/aTt	2/12	1	2	FACETS	0.883	0.776	0.999	0.883	0.776	0.999	CLONAL	1	TRUE	1	0.322213095254543	2		410	527	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440543	49440543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	137	690	1	ENST00000301067.7:c.4267C>T	p.Arg1423Cys	p.R1423C	ENST00000301067	NM_003482.3	1423	Cgt/Tgt	15/54	1	2	FACETS	0.713	0.647	0.783	0.713	0.647	0.783	SUBCLONAL	1	TRUE	1	0.322213095254543	2		691	1193	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066909	30066909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	78	420	0	ENST00000331968.5:c.2222G>T	p.Arg741Met	p.R741M	ENST00000331968	NM_002742.2	741	aGg/aTg	16/18	1	2	FACETS	0.798	0.701	0.901	0.798	0.701	0.901	CLONAL	1	TRUE	1	0.322213095254543	2		420	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573993	7573993	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	164	620	0	ENST00000269305.4:c.1034A>G	p.Asn345Ser	p.N345S	ENST00000269305	NM_001126112.2	345	aAt/aGt	10/11	1	2	FACETS	0.976	0.895	1	0.976	0.895	1	CLONAL	1	TRUE	1	0.322213095254543	2		620	1043	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550472	29550473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs786204255	NA	P-0049569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	10	167	0	ENST00000356175.3:c.1738dup	p.Tyr580LeufsTer8	p.Y580Lfs*8	ENST00000356175	NM_000267.3	578	ctt/cTtt	16/57	1	2	FACETS	0.336	0.227	0.471	0.336	0.227	0.471	SUBCLONAL	1	TRUE	1	0.322213095254543	2		167	185	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661996	29661997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	55	345	0	ENST00000356175.3:c.5895dup	p.Gln1966ThrfsTer22	p.Q1966Tfs*22	ENST00000356175	NM_000267.3	1964	gaa/gAaa	39/57	1	2	FACETS	0.873	0.749	1	0.873	0.749	1	CLONAL	1	TRUE	1	0.322213095254543	2		345	391	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649092	37649093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	57	357	0	ENST00000447079.4:c.2199dup	p.Gly734TrpfsTer10	p.G734Wfs*10	ENST00000447079	NM_015083.1	733	att/aTtt	4/14	1	2	FACETS	0.721	0.619	0.831	0.721	0.619	0.831	SUBCLONAL	1	TRUE	1	0.322213095254543	2		357	491	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864677	37864677	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs749711404	NA	P-0049569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	152	723	0	ENST00000269571.5:c.329A>G	p.Asp110Gly	p.D110G	ENST00000269571		110	gAc/gGc	3/27	1	2	FACETS	0.94	0.859	1	0.94	0.859	1	CLONAL	1	TRUE	1	0.322213095254543	2		723	1004	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207079	1207090	+	inframe_deletion	In_Frame_Del	DEL	GGGAAGGCTCTT	GGGAAGGCTCTT	-	novel	NA	P-0049569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	143	783	0	ENST00000326873.7:c.167_178del	p.Gly56_Tyr60delinsAsp	p.G56_Y60delinsD	ENST00000326873	NM_000455.4	56	gGGGAAGGCTCTTac/gac	1/10	0.322213095254543	1	FACETS	0.836	0.762	0.913	0.836	0.762	0.913	CLONAL	1	TRUE	0	0.322213095254543	1		783	891	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210484	2210484	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	174	908	0	ENST00000398665.3:c.1091T>C	p.Val364Ala	p.V364A	ENST00000398665	NM_032482.2	364	gTg/gCg	13/28	0.322213095254543	1	FACETS	0.92	0.846	0.996	0.92	0.846	0.996	CLONAL	1	TRUE	0	0.322213095254543	1		908	985	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470579	25470580	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1157280960	NA	P-0049569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	145	685	0	ENST00000264709.3:c.894dup	p.Lys299GlufsTer25	p.K299Efs*25	ENST00000264709	NM_175629.2	298	-/G	8/23	1	2	FACETS	0.806	0.734	0.882	0.806	0.734	0.882	CLONAL	1	TRUE	1	0.322213095254543	2		685	1117	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566523	41566523	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	86	300	0	ENST00000263253.7:c.4400A>G	p.Tyr1467Cys	p.Y1467C	ENST00000263253	NM_001429.3	1467	tAc/tGc	27/31	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.322213095254543	2		300	481	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008430	71008430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866381610	NA	P-0049569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	80	284	0	ENST00000318789.4:c.2002G>A	p.Glu668Lys	p.E668K	ENST00000318789	NM_032682.5	668	Gaa/Aaa	21/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.322213095254543	2		284	411	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0049569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	11	634	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.17	0.117	0.237	0.17	0.117	0.237	SUBCLONAL	1	TRUE	1	0.322213095254543	2		634	401	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508869	31508869	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	86	408	0	ENST00000344624.3:c.1446A>T	p.Glu482Asp	p.E482D	ENST00000344624		482	gaA/gaT	7/33	1	2	FACETS	0.925	0.82	1	0.925	0.82	1	CLONAL	1	TRUE	1	0.322213095254543	2		408	577	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042111	6042133	+	frameshift_variant	Frame_Shift_Del	DEL	ATGGCGCACAGGTAGTGTGGAAA	ATGGCGCACAGGTAGTGTGGAAA	-	novel	NA	P-0049569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	41	164	0	ENST00000265849.7:c.488_510del	p.Phe163Ter	p.F163*	ENST00000265849	NM_000535.5	163	tTTTCCACACTACCTGTGCGCCAT/t	5/15	0.322213095254543	1	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	0	0.322213095254543	1		164	204	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884394	151884394	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760014712	NA	P-0049569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	34	238	0	ENST00000262189.6:c.4961T>C	p.Val1654Ala	p.V1654A	ENST00000262189	NM_170606.2	1654	gTt/gCt	33/59	1	2	FACETS	0.715	0.587	0.859	0.715	0.587	0.859	SUBCLONAL	1	TRUE	1	0.322213095254543	2		238	295	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012391	152012392	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	24	240	0	ENST00000262189.6:c.421dup	p.Glu141GlyfsTer29	p.E141Gfs*29	ENST00000262189	NM_170606.2	141	gaa/gGaa	4/59	1	2	FACETS	0.53	0.416	0.661	0.53	0.416	0.661	SUBCLONAL	1	TRUE	1	0.322213095254543	2		240	281	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866539	117866539	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	43	353	0	ENST00000297338.2:c.1106T>C	p.Val369Ala	p.V369A	ENST00000297338	NM_006265.2	369	gTa/gCa	9/14	1	2	FACETS	0.872	0.733	1	0.872	0.733	1	CLONAL	1	TRUE	1	0.322213095254543	2		353	306	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0049569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	181	863	7	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	1	2	FACETS	0.833	0.766	0.903	0.833	0.766	0.903	CLONAL	1	TRUE	1	0.322213095254543	2		870	1349	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376722	8376722	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	78	324	0	ENST00000356435.5:c.4391A>C	p.Lys1464Thr	p.K1464T	ENST00000356435		1464	aAg/aCg	27/35	1	2	FACETS	0.913	0.804	1	0.913	0.804	1	CLONAL	1	TRUE	1	0.322213095254543	2		324	530	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480624	123480624	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	82	437	0	ENST00000371139.4:c.132T>G	p.Cys44Trp	p.C44W	ENST00000371139	NM_001114937.2	44	tgT/tgG	1/4	1	2	FACETS	0.752	0.663	0.847	0.752	0.663	0.847	SUBCLONAL	1	TRUE	1	0.322213095254543	2		437	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0049570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	141	498	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.26	2		498	785	SUCCESS
APC	324	MSKCC	GRCh37	5	112175760	112175761	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs398123122	NA	P-0049570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	25	311	0	ENST00000257430.4:c.4473dup	p.Ala1492CysfsTer22	p.A1492Cfs*22	ENST00000257430	NM_000038.5	1490	cat/caTt	16/16	1	2	FACETS	0.734	0.58	0.91	0.734	0.58	0.91	CLONAL	1	TRUE	1	0.26	2		311	262	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8501056	8501056	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs905180868	NA	P-0049570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	47	194	0	ENST00000356435.5:c.1826C>T	p.Pro609Leu	p.P609L	ENST00000356435		609	cCg/cTg	13/35	0.230027019696707	2	FACETS	0.818	0.698	0.948	0.818	0.698	0.948	CLONAL	2	TRUE	0	0.26	2		194	221	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647813	206647813	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs554685342	NA	P-0049570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	39	354	0	ENST00000367120.3:c.227C>T	p.Thr76Met	p.T76M	ENST00000367120	NM_014002.3	76	aCg/aTg	4/22	1	2	FACETS	0.537	0.444	0.64	0.537	0.444	0.64	SUBCLONAL	1	TRUE	1	0.26	2		354	559	SUCCESS
APC	324	MSKCC	GRCh37	5	112174022	112174022	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs398123119	NA	P-0049570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	29	272	0	ENST00000257430.4:c.2731G>T	p.Glu911Ter	p.E911*	ENST00000257430	NM_000038.5	911	Gaa/Taa	16/16	1	2	FACETS	0.761	0.613	0.93	0.761	0.613	0.93	CLONAL	1	TRUE	1	0.26	2		272	293	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0049571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	315	311	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.7083963224161	2	FACETS	0.999	0.962	1	0.999	0.962	1	CLONAL	2	TRUE	0	0.7083963224161	2		311	445	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0049571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	425	462	1	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.7083963224161	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.7083963224161	2		463	589	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011144	12011144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	153	342	0	ENST00000353533.5:c.551C>T	p.Ser184Leu	p.S184L	ENST00000353533	NM_003010.3	184	tCg/tTg	5/11	1	2	FACETS	0.876	0.807	0.947	0.876	0.807	0.947	CLONAL	1	TRUE	1	0.7083963224161	2		342	493	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338671	70338671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	206	603	0	ENST00000374080.3:c.67G>T	p.Asp23Tyr	p.D23Y	ENST00000374080		23	Gat/Tat	1/45	1	2	FACETS	0.914	0.853	0.977	0.914	0.853	0.977	CLONAL	1	TRUE	1	0.7083963224161	2		603	636	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106923	27106940	+	inframe_deletion	In_Frame_Del	DEL	CAGCCTGGCAGCTCGTGC	CAGCCTGGCAGCTCGTGC	-	novel	NA	P-0049571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	230	518	0	ENST00000324856.7:c.6536_6553del	p.Ser2179_Ala2184del	p.S2179_A2184del	ENST00000324856	NM_006015.4	2178	gaCAGCCTGGCAGCTCGTGCc/gac	20/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.7083963224161	2		518	599	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952065	178952065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	349	325	0	ENST00000263967.3:c.3120G>A	p.Met1040Ile	p.M1040I	ENST00000263967	NM_006218.2	1040	atG/atA	21/21	0.7083963224161	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.7083963224161	2		325	476	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107083	27107086	+	frameshift_variant	Frame_Shift_Del	DEL	CGGC	CGGC	-	novel	NA	P-0049571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	218	487	0	ENST00000324856.7:c.6694_6697del	p.Arg2232GlyfsTer34	p.R2232Gfs*34	ENST00000324856	NM_006015.4	2232	CGGCgg/gg	20/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.7083963224161	2		487	574	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0049572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	36	419	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.989	0.812	1	0.989	0.812	1	CLONAL	1	TRUE	1	0.14	2		419	520	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0049572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	29	380	1	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	1	2	FACETS	0.897	0.719	1	0.897	0.719	1	CLONAL	1	TRUE	1	0.14	2		381	462	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945355	71945355	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	47	825	0	ENST00000298229.2:c.2243T>C	p.Ile748Thr	p.I748T	ENST00000298229	NM_001567.3	748	aTt/aCt	20/28	1	2	FACETS	0.838	0.705	0.986	0.838	0.705	0.986	CLONAL	1	TRUE	1	0.14	2		825	801	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492895	56492895	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	40	297	0	ENST00000407977.2:c.44G>A	p.Trp15Ter	p.W15*	ENST00000407977		15	tGg/tAg	2/10	1	2	FACETS	0.754	0.628	0.894	1	0.955	1	SUBCLONAL	2	TRUE	1	0.14	2		297	379	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	113	148	0				ENST00000310581	NM_198253.2	-/1132			0.466853368636432	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.466582501720982	1		148	301	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	344	563	0	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	0.466582501720982	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.466582501720982	2		563	711	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	177	426	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.466853368636432	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.466582501720982	1		426	464	SUCCESS
APC	324	MSKCC	GRCh37	5	112177049	112177049	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	73	326	0	ENST00000257430.4:c.5758C>T	p.Arg1920Ter	p.R1920*	ENST00000257430	NM_000038.5	1920	Cga/Tga	16/16	1	2	FACETS	0.823	0.724	0.929	0.823	0.724	0.929	CLONAL	1	TRUE	1	0.466582501720982	2		326	380	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956220	55956220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190050670	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	118	434	0	ENST00000263923.4:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000263923	NM_002253.2	1032	cGa/cAa	23/30	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.466582501720982	2		434	476	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610162	43610162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	163	827	0	ENST00000355710.3:c.2114C>T	p.Ser705Phe	p.S705F	ENST00000355710	NM_020975.4	705	tCc/tTc	11/20	1	2	FACETS	0.88	0.809	0.954	0.88	0.809	0.954	CLONAL	1	TRUE	1	0.466582501720982	2		827	794	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543748	29543748	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	81	350	0	ENST00000389048.3:c.1415G>A	p.Arg472Gln	p.R472Q	ENST00000389048	NM_004304.4	472	cGg/cAg	7/29	0.452595107244801	3	FACETS	0.848	0.749	0.953	0.424	0.374	0.477	CLONAL	1	TRUE	1	0.466582501720982	3		350	505	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967209	93967209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	68	287	0	ENST00000369303.4:c.2143G>A	p.Glu715Lys	p.E715K	ENST00000369303	NM_004440.3	715	Gaa/Aaa	12/17	1	2	FACETS	0.794	0.695	0.9	0.794	0.695	0.9	SUBCLONAL	1	TRUE	1	0.466582501720982	2		287	367	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298174	123298174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	88	424	0	ENST00000358487.5:c.680G>A	p.Gly227Glu	p.G227E	ENST00000358487	NM_000141.4	227	gGa/gAa	6/18	1	2	FACETS	0.75	0.667	0.838	0.75	0.667	0.838	SUBCLONAL	1	TRUE	1	0.466582501720982	2		424	503	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992414	72992414	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs62620235	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	190	793	1	ENST00000268489.5:c.1631C>T	p.Ser544Leu	p.S544L	ENST00000268489	NM_006885.3	544	tCg/tTg	2/10	0.466582501720982	2	FACETS	0.957	0.886	1	0.479	0.443	0.516	CLONAL	1	TRUE	0	0.466582501720982	2		794	851	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381466	81381466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	63	249	0	ENST00000222390.5:c.595G>A	p.Glu199Lys	p.E199K	ENST00000222390	NM_000601.4	199	Gaa/Aaa	5/18	NA	2	FACETS	0.841	0.733	0.957			1	INDETERMINATE	1	TRUE	NA	0.466582501720982	2		249	321	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319913	8319913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	71	261	0	ENST00000356435.5:c.5588G>A	p.Arg1863Lys	p.R1863K	ENST00000356435		1863	aGa/aAa	34/35	0.466853368636432	1	FACETS	0.922	0.815	1	0.922	0.815	1	CLONAL	1	TRUE	0	0.466582501720982	1		261	253	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93629456	93629456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	82	294	0	ENST00000375746.1:c.890C>T	p.Ser297Phe	p.S297F	ENST00000375746	NM_001174167.1	297	tCc/tTc	7/14	1	2	FACETS	0.937	0.832	1	0.937	0.832	1	CLONAL	1	TRUE	1	0.466582501720982	2		294	375	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141128	55141128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	81	299	0	ENST00000257290.5:c.1774G>A	p.Gly592Arg	p.G592R	ENST00000257290	NM_006206.4	592	Gga/Aga	12/23	1	2	FACETS	0.914	0.81	1	0.914	0.81	1	CLONAL	1	TRUE	1	0.466582501720982	2		299	380	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650568	18650568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368805708	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	74	391	0	ENST00000266497.5:c.2779C>T	p.Arg927Cys	p.R927C	ENST00000266497		927	Cgt/Tgt	20/31	1	2	FACETS	0.719	0.632	0.813	0.719	0.632	0.813	SUBCLONAL	1	TRUE	1	0.466582501720982	2		391	441	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970906	21970906	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501275	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	219	777	0	ENST00000304494.5:c.452C>T	p.Pro151Leu	p.P151L	ENST00000304494	NM_000077.4	151	cCc/cTc	2/3	0.466853368636432	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.466582501720982	1		777	675	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662625	117662625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	116	406	0	ENST00000368508.3:c.4840C>T	p.Pro1614Ser	p.P1614S	ENST00000368508	NM_002944.2	1614	Cca/Tca	29/43	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.466582501720982	2		406	449	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225657	26225657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202067024	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	193	796	1	ENST00000360408.1:c.275C>T	p.Ala92Val	p.A92V	ENST00000360408	NM_003532.2	92	gCg/gTg	1/1	1	2	FACETS	0.971	0.899	1	0.971	0.899	1	CLONAL	1	TRUE	1	0.466582501720982	2		797	852	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866409	42866409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762928261	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	234	755	0	ENST00000398585.3:c.223G>A	p.Glu75Lys	p.E75K	ENST00000398585	NM_001135099.1	75	Gag/Aag	3/14	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.466582501720982	2		755	907	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628329	187628329	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	147	573	0	ENST00000441802.2:c.2653C>T	p.Arg885Ter	p.R885*	ENST00000441802	NM_005245.3	885	Cga/Tga	2/27	1	2	FACETS	0.948	0.868	1	0.948	0.868	1	CLONAL	1	TRUE	1	0.466582501720982	2		573	665	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858687	9858687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	109	448	0	ENST00000330684.3:c.2714C>T	p.Ser905Phe	p.S905F	ENST00000330684	NM_001134407.1	905	tCc/tTc	13/13	1	2	FACETS	0.923	0.833	1	0.923	0.833	1	CLONAL	1	TRUE	1	0.466582501720982	2		448	506	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40789994	40789994	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs746391800	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	80	426	0	ENST00000373198.4:c.2737G>A	p.Glu913Lys	p.E913K	ENST00000373198	NM_133170.3	913	Gag/Aag	18/32	1	2	FACETS	0.803	0.71	0.902	0.803	0.71	0.902	CLONAL	1	TRUE	1	0.466582501720982	2		426	427	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356361	66356361	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772108237	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	112	382	0	ENST00000273854.3:c.1136C>T	p.Pro379Leu	p.P379L	ENST00000273854	NM_004439.5	379	cCg/cTg	5/18	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.466582501720982	2		382	463	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747137	40747138	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	94	462	1	ENST00000373198.4:c.2944_2945delinsTT	p.Pro982Leu	p.P982L	ENST00000373198	NM_133170.3	982	CCg/TTg	22/32	1	2	FACETS	0.868	0.776	0.966	0.868	0.776	0.966	CLONAL	1	TRUE	1	0.466582501720982	2		463	464	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80057394	80057394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757559761	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	61	307	0	ENST00000265081.6:c.1793C>T	p.Ser598Leu	p.S598L	ENST00000265081	NM_002439.4	598	tCg/tTg	13/24	1	2	FACETS	0.692	0.599	0.791	0.692	0.599	0.791	SUBCLONAL	1	TRUE	1	0.466582501720982	2		307	378	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523482	106523482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762208681	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	63	236	0	ENST00000359195.3:c.2634G>A	p.Met878Ile	p.M878I	ENST00000359195	NM_002649.2	878	atG/atA	8/11	0.452595107244801	3	FACETS	1	0.873	1	0.502	0.436	0.571	CLONAL	1	TRUE	1	0.466582501720982	3		236	332	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031690	69031690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371787029	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	84	366	0	ENST00000288368.4:c.3445C>T	p.Arg1149Cys	p.R1149C	ENST00000288368	NM_024870.2	1149	Cgc/Tgc	28/40	1	2	FACETS	0.868	0.77	0.97	0.868	0.77	0.97	CLONAL	1	TRUE	1	0.466582501720982	2		366	415	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109309771	109309771	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	131	410	0	ENST00000436639.2:c.1544G>A	p.Trp515Ter	p.W515*	ENST00000436639	NM_014454.2	515	tGg/tAg	9/10	1	2	FACETS	0.91	0.828	0.995	0.91	0.828	0.995	CLONAL	1	TRUE	1	0.466582501720982	2		410	617	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551311	29551311	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	163	611	0	ENST00000389048.3:c.1319C>T	p.Ser440Phe	p.S440F	ENST00000389048	NM_004304.4	440	tCc/tTc	6/29	0.452595107244801	3	FACETS	1	0.921	1	0.502	0.46	0.545	CLONAL	1	TRUE	1	0.466582501720982	3		611	859	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678626	88678626	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	83	364	0	ENST00000360948.2:c.910C>T	p.Pro304Ser	p.P304S	ENST00000360948	NM_001012338.2	304	Ccc/Tcc	9/19	1	2	FACETS	0.927	0.823	1	0.927	0.823	1	CLONAL	1	TRUE	1	0.466582501720982	2		364	384	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770557	40770557	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	92	368	0	ENST00000373198.4:c.2825C>T	p.Ser942Phe	p.S942F	ENST00000373198	NM_133170.3	942	tCc/tTc	19/32	1	2	FACETS	0.884	0.79	0.984	0.884	0.79	0.984	CLONAL	1	TRUE	1	0.466582501720982	2		368	446	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442738	442738	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	107	462	0	ENST00000399788.2:c.1568C>T	p.Pro523Leu	p.P523L	ENST00000399788	NM_001042603.1	523	cCc/cTc	12/28	0.138632272421161	5	FACETS	1	0.952	1			1	INDETERMINATE	1	TRUE	NA	0.466582501720982	5		462	706	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619306	23619306	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	135	429	0	ENST00000261584.4:c.3229C>T	p.Pro1077Ser	p.P1077S	ENST00000261584	NM_024675.3	1077	Ccc/Tcc	12/13	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.466582501720982	2		429	553	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591862	48591862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	30	352	0	ENST00000342988.3:c.1025C>T	p.Pro342Leu	p.P342L	ENST00000342988	NM_005359.5	342	cCt/cTt	9/12	0.387746981605563	1	FACETS	0.245	0.197	0.3	0.245	0.197	0.3	SUBCLONAL	1	TRUE	0	0.466582501720982	1		352	402	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528774	8528774	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs758007107	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	73	308	0	ENST00000356435.5:c.358C>T	p.Gln120Ter	p.Q120*	ENST00000356435		120	Caa/Taa	4/35	0.466853368636432	1	FACETS	0.851	0.752	0.955	0.851	0.752	0.955	CLONAL	1	TRUE	0	0.466582501720982	1		308	282	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517880	8517880	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	54	310	0	ENST00000356435.5:c.1511C>T	p.Ser504Leu	p.S504L	ENST00000356435		504	tCa/tTa	10/35	0.466853368636432	1	FACETS	0.716	0.617	0.821	0.716	0.617	0.821	SUBCLONAL	1	TRUE	0	0.466582501720982	1		310	248	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007560	62007560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	148	758	1	ENST00000392795.3:c.307G>A	p.Glu103Lys	p.E103K	ENST00000392795	NM_001039933.1	103	Gaa/Aaa	3/6	0.452595107244801	3	FACETS	0.76	0.693	0.83	0.38	0.346	0.415	SUBCLONAL	1	TRUE	1	0.466582501720982	3		759	1030	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300446	11300446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	145	622	0	ENST00000361445.4:c.1700C>T	p.Ser567Phe	p.S567F	ENST00000361445	NM_004958.3	567	tCt/tTt	11/58	1	2	FACETS	0.983	0.9	1	0.983	0.9	1	CLONAL	1	TRUE	1	0.466582501720982	2		622	632	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276919	123276919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	78	364	0	ENST00000358487.5:c.998del	p.Thr333IlefsTer25	p.T333Ifs*25	ENST00000358487	NM_000141.4	333	aCt/at	8/18	1	2	FACETS	0.832	0.735	0.935	0.832	0.735	0.935	CLONAL	1	TRUE	1	0.466582501720982	2		364	402	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161481	2161481	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766960611	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	288	652	1	ENST00000434045.2:c.46G>A	p.Glu16Lys	p.E16K	ENST00000434045	NM_001127598.1	16	Gaa/Aaa	2/5	0.466582501720982	2	FACETS	0.954	0.904	1	0.954	0.904	1	CLONAL	2	TRUE	0	0.466582501720982	2		653	647	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425353	49425353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	176	859	1	ENST00000301067.7:c.13135C>T	p.Pro4379Ser	p.P4379S	ENST00000301067	NM_003482.3	4379	Ccc/Tcc	39/54	1	2	FACETS	0.873	0.805	0.944	0.873	0.805	0.944	CLONAL	1	TRUE	1	0.466582501720982	2		860	864	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433988	49433988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	198	901	0	ENST00000301067.7:c.7565C>T	p.Pro2522Leu	p.P2522L	ENST00000301067	NM_003482.3	2522	cCt/cTt	31/54	1	2	FACETS	0.901	0.835	0.97	0.901	0.835	0.97	CLONAL	1	TRUE	1	0.466582501720982	2		901	942	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435167	49435167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1232307242	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	139	600	0	ENST00000301067.7:c.6386C>T	p.Pro2129Leu	p.P2129L	ENST00000301067	NM_003482.3	2129	cCc/cTc	31/54	1	2	FACETS	0.963	0.879	1	0.963	0.879	1	CLONAL	1	TRUE	1	0.466582501720982	2		600	619	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811648	102811648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1188704136	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	135	585	1	ENST00000307046.8:c.536G>A	p.Arg179Lys	p.R179K	ENST00000307046	NM_001111285.1	179	aGg/aAg	4/4	1	2	FACETS	0.845	0.769	0.924	0.845	0.769	0.924	CLONAL	1	TRUE	1	0.466582501720982	2		586	685	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813373	102813373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868530917	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	160	600	0	ENST00000307046.8:c.316G>A	p.Glu106Lys	p.E106K	ENST00000307046	NM_001111285.1	106	Gag/Aag	3/4	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.466582501720982	2		600	638	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245480	133245480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	114	551	0	ENST00000320574.5:c.1840C>T	p.Pro614Ser	p.P614S	ENST00000320574	NM_006231.2	614	Ccc/Tcc	17/49	1	2	FACETS	0.917	0.829	1	0.917	0.829	1	CLONAL	1	TRUE	1	0.466582501720982	2		551	533	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004229	29004229	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	89	316	0	ENST00000282397.4:c.1064T>G	p.Leu355Arg	p.L355R	ENST00000282397	NM_002019.4	355	cTc/cGc	8/30	1	2	FACETS	0.865	0.771	0.965	0.865	0.771	0.965	CLONAL	1	TRUE	1	0.466582501720982	2		316	441	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95595863	95595863	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	75	328	0	ENST00000393063.1:c.680A>G	p.Glu227Gly	p.E227G	ENST00000393063	NM_030621.3	227	gAg/gGg	7/28	0.444374318774766	1	FACETS	0.74	0.654	0.832	0.74	0.654	0.832	SUBCLONAL	1	TRUE	0	0.466582501720982	1		328	333	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843432	3843432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772332532	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	95	366	0	ENST00000262367.5:c.1171G>A	p.Val391Ile	p.V391I	ENST00000262367	NM_004380.2	391	Gtt/Att	4/31	1	2	FACETS	0.834	0.746	0.928	0.834	0.746	0.928	CLONAL	1	TRUE	1	0.466582501720982	2		366	488	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858671	9858671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	123	480	0	ENST00000330684.3:c.2730G>A	p.Met910Ile	p.M910I	ENST00000330684	NM_001134407.1	910	atG/atA	13/13	1	2	FACETS	0.984	0.894	1	0.984	0.894	1	CLONAL	1	TRUE	1	0.466582501720982	2		480	536	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828473	72828473	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	159	658	0	ENST00000268489.5:c.8108C>T	p.Ala2703Val	p.A2703V	ENST00000268489	NM_006885.3	2703	gCt/gTt	9/10	0.466582501720982	2	FACETS	0.996	0.916	1	0.498	0.458	0.54	CLONAL	1	TRUE	0	0.466582501720982	2		658	684	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993824	72993824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	126	619	0	ENST00000268489.5:c.221C>T	p.Pro74Leu	p.P74L	ENST00000268489	NM_006885.3	74	cCc/cTc	2/10	0.466582501720982	2	FACETS	0.912	0.829	1	0.456	0.414	0.5	CLONAL	1	TRUE	0	0.466582501720982	2		619	592	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559104	29559104	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	67	164	0	ENST00000356175.3:c.3211G>A	p.Ala1071Thr	p.A1071T	ENST00000356175	NM_000267.3	1071	Gca/Aca	25/57	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.466582501720982	2		164	265	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677781	47677781	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	122	533	0	ENST00000347630.2:c.1084C>T	p.Pro362Ser	p.P362S	ENST00000347630	NM_001007230.1	362	Cct/Tct	11/11	1	2	FACETS	0.967	0.878	1	0.967	0.878	1	CLONAL	1	TRUE	1	0.466582501720982	2		533	541	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221035	5221035	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	113	563	0	ENST00000357368.4:c.3431A>T	p.Asp1144Val	p.D1144V	ENST00000357368	NM_002850.3	1144	gAc/gTc	20/38	1	2	FACETS	0.851	0.768	0.938	0.851	0.768	0.938	CLONAL	1	TRUE	1	0.466582501720982	2		563	569	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629023	14629023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367975514	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	203	647	0	ENST00000254322.2:c.139G>A	p.Glu47Lys	p.E47K	ENST00000254322	NM_006145.1	47	Gag/Aag	1/3	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.466582501720982	2		647	865	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792064	42792064	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	176	716	0	ENST00000575354.2:c.868G>A	p.Gly290Arg	p.G290R	ENST00000575354	NM_015125.3	290	Gga/Aga	6/20	1	2	FACETS	0.941	0.868	1	0.941	0.868	1	CLONAL	1	TRUE	1	0.466582501720982	2		716	802	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858937	45858937	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	158	617	0	ENST00000391945.4:c.1529C>T	p.Thr510Ile	p.T510I	ENST00000391945	NM_000400.3	510	aCc/aTc	16/23	1	2	FACETS	0.907	0.832	0.984	0.907	0.832	0.984	CLONAL	1	TRUE	1	0.466582501720982	2		617	747	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085717	16085717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	109	572	0	ENST00000281043.3:c.893C>T	p.Thr298Ile	p.T298I	ENST00000281043	NM_005378.4	298	aCc/aTc	3/3	0.452595107244801	3	FACETS	0.774	0.696	0.858	0.387	0.348	0.429	SUBCLONAL	1	TRUE	1	0.466582501720982	3		572	744	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416394	29416394	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	308	665	2	ENST00000389048.3:c.4559A>T	p.Asn1520Ile	p.N1520I	ENST00000389048	NM_004304.4	1520	aAt/aTt	29/29	0.452595107244801	3	FACETS	0.967	0.915	1	0.967	0.915	1	CLONAL	2	TRUE	1	0.466582501720982	3		667	842	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044279	128044279	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	113	432	0	ENST00000285398.2:c.1342G>A	p.Ala448Thr	p.A448T	ENST00000285398	NM_000122.1	448	Gcc/Acc	8/15	1	2	FACETS	0.952	0.86	1	0.952	0.86	1	CLONAL	1	TRUE	1	0.466582501720982	2		432	509	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872680	136872680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	117	392	0	ENST00000241393.3:c.818G>A	p.Gly273Glu	p.G273E	ENST00000241393	NM_003467.2	273	gGg/gAg	2/2	1	2	FACETS	0.917	0.83	1	0.917	0.83	1	CLONAL	1	TRUE	1	0.466582501720982	2		392	547	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543614	9543614	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	105	478	0	ENST00000353224.5:c.1540C>T	p.Leu514Phe	p.L514F	ENST00000353224	NM_177990.2	514	Ctt/Ttt	6/10	1	2	FACETS	0.826	0.742	0.914	0.826	0.742	0.914	CLONAL	1	TRUE	1	0.466582501720982	2		478	545	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019225	31019225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	123	466	0	ENST00000375687.4:c.820C>T	p.His274Tyr	p.H274Y	ENST00000375687	NM_015338.5	274	Cat/Tat	9/13	1	2	FACETS	0.947	0.859	1	0.947	0.859	1	CLONAL	1	TRUE	1	0.466582501720982	2		466	557	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743910	40743910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	113	475	1	ENST00000373198.4:c.3085G>A	p.Asp1029Asn	p.D1029N	ENST00000373198	NM_133170.3	1029	Gac/Aac	23/32	1	2	FACETS	0.825	0.745	0.91	0.825	0.745	0.91	CLONAL	1	TRUE	1	0.466582501720982	2		476	587	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306537	41306538	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	85	507	0	ENST00000373198.4:c.1121_1122delinsAA	p.Gly374Glu	p.G374E	ENST00000373198	NM_133170.3	374	gGG/gAA	7/32	1	2	FACETS	0.66	0.585	0.741	0.66	0.585	0.741	SUBCLONAL	1	TRUE	1	0.466582501720982	2		507	552	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12647706	12647706	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1472040007	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	63	256	0	ENST00000251849.4:c.674C>T	p.Pro225Leu	p.P225L	ENST00000251849	NM_002880.3	225	cCt/cTt	6/17	1	2	FACETS	0.964	0.842	1	0.964	0.842	1	CLONAL	1	TRUE	1	0.466582501720982	2		256	280	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447808	187447808	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	79	345	0	ENST00000232014.4:c.385G>A	p.Glu129Lys	p.E129K	ENST00000232014	NM_001130845.1	129	Gaa/Aaa	5/10	0.452595107244801	3	FACETS	0.934	0.825	1	0.467	0.412	0.526	CLONAL	1	TRUE	1	0.466582501720982	3		345	447	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499604	149499604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	111	484	0	ENST00000261799.4:c.2669G>A	p.Gly890Glu	p.G890E	ENST00000261799	NM_002609.3	890	gGg/gAg	19/23	1	2	FACETS	0.854	0.77	0.942	0.854	0.77	0.942	CLONAL	1	TRUE	1	0.466582501720982	2		484	557	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124453	94124453	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1339057136	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	71	328	0	ENST00000369303.4:c.130G>A	p.Glu44Lys	p.E44K	ENST00000369303	NM_004440.3	44	Gag/Aag	2/17	1	2	FACETS	0.841	0.738	0.95	0.841	0.738	0.95	CLONAL	1	TRUE	1	0.466582501720982	2		328	362	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536144	106536144	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	93	311	0	ENST00000369096.4:c.111G>A	p.Met37Ile	p.M37I	ENST00000369096	NM_001198.3	37	atG/atA	2/7	1	2	FACETS	0.949	0.849	1	0.949	0.849	1	CLONAL	1	TRUE	1	0.466582501720982	2		311	420	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678976	117678976	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138034064	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	62	241	0	ENST00000368508.3:c.3845C>T	p.Pro1282Leu	p.P1282L	ENST00000368508	NM_002944.2	1282	cCt/cTt	24/43	1	2	FACETS	0.773	0.671	0.881	0.773	0.671	0.881	SUBCLONAL	1	TRUE	1	0.466582501720982	2		241	344	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335070	81335070	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	64	215	0	ENST00000222390.5:c.1758-1G>A		p.X586_splice	ENST00000222390	NM_000601.4	586			NA	2	FACETS	0.809	0.705	0.921			1	INDETERMINATE	1	TRUE	NA	0.466582501720982	2		215	339	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398646	116398646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	66	312	0	ENST00000397752.3:c.2236G>A	p.Glu746Lys	p.E746K	ENST00000397752	NM_000245.2	746	Gaa/Aaa	9/21	0.452595107244801	3	FACETS	0.731	0.636	0.834	0.366	0.318	0.417	SUBCLONAL	1	TRUE	1	0.466582501720982	3		312	477	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968116	68968116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs977585815	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	73	383	0	ENST00000288368.4:c.1145G>A	p.Gly382Asp	p.G382D	ENST00000288368	NM_024870.2	382	gGt/gAt	10/40	1	2	FACETS	0.647	0.567	0.732	0.647	0.567	0.732	SUBCLONAL	1	TRUE	1	0.466582501720982	2		383	484	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981837	70981837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	153	828	0	ENST00000276594.2:c.259G>A	p.Glu87Lys	p.E87K	ENST00000276594	NM_024504.3	87	Gag/Aag	2/8	1	2	FACETS	0.828	0.758	0.901	0.828	0.758	0.901	CLONAL	1	TRUE	1	0.466582501720982	2		828	792	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90994956	90994957	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	47	233	0	ENST00000265433.3:c.164_165delinsTT	p.Thr55Ile	p.T55I	ENST00000265433	NM_002485.4	55	aCC/aTT	2/16	1	2	FACETS	0.582	0.493	0.68	0.582	0.493	0.68	SUBCLONAL	1	TRUE	1	0.466582501720982	2		233	346	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864256	117864257	+	missense_variant	Missense_Mutation	DNP	AG	AG	TA	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	114	364	2	ENST00000297338.2:c.1400_1401delinsTA	p.Ala467Val	p.A467V	ENST00000297338	NM_006265.2	467	gCT/gTA	11/14	1	2	FACETS	0.956	0.865	1	0.956	0.865	1	CLONAL	1	TRUE	1	0.466582501720982	2		366	511	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93640031	93640031	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	85	357	0	ENST00000375746.1:c.1360G>A	p.Gly454Ser	p.G454S	ENST00000375746	NM_001174167.1	454	Ggt/Agt	10/14	1	2	FACETS	0.937	0.833	1	0.937	0.833	1	CLONAL	1	TRUE	1	0.466582501720982	2		357	389	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760895	133760895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	175	734	0	ENST00000318560.5:c.3218C>T	p.Ser1073Phe	p.S1073F	ENST00000318560	NM_005157.4	1073	tCc/tTc	11/11	1	2	FACETS	0.888	0.818	0.96	0.888	0.818	0.96	CLONAL	1	TRUE	1	0.466582501720982	2		734	845	SUCCESS
AR	367	MSKCC	GRCh37	X	66765395	66765395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	197	393	0	ENST00000374690.3:c.407G>A	p.Gly136Glu	p.G136E	ENST00000374690	NM_000044.3	136	gGa/gAa	1/8	1	1	FACETS	0.813	0.764	0.862	1	0.993	1	CLONAL	2	TRUE	0	0.466582501720982	1		393	398	SUCCESS
BTK	695	MSKCC	GRCh37	X	100629547	100629547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	128	232	0	ENST00000308731.7:c.217C>T	p.Pro73Ser	p.P73S	ENST00000308731	NM_000061.2	73	Cct/Tct	3/19	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.466582501720982	1		232	316	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504150	123504150	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	100	189	0	ENST00000371139.4:c.326G>A	p.Arg109Lys	p.R109K	ENST00000371139	NM_001114937.2	109	aGa/aAa	3/4	1	1	FACETS	0.771	0.705	0.838	1	0.986	1	SUBCLONAL	2	TRUE	0	0.466582501720982	1		189	213	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061113	38061120	+	frameshift_variant	Frame_Shift_Del	DEL	CTCAGGGC	CTCAGGGC	-	novel	NA	P-0049584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	55	394	1	ENST00000250448.2:c.869_876del	p.Gly290GlufsTer10	p.G290Efs*10	ENST00000250448	NM_004496.3	290	gGCCCTGAG/g	2/2	0.167999282515021	1	FACETS	0.879	0.756	1	1	0.974	1	CLONAL	2	FALSE	0	0.167999282515021	1		395	341	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243268	123243268	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	26	701	0	ENST00000358487.5:c.2245A>C	p.Thr749Pro	p.T749P	ENST00000358487	NM_000141.4	749	Acg/Ccg	17/18	1	2	FACETS	0.986	0.789	1	1	0.952	1	CLONAL	2	FALSE	1	0.167999282515021	2		701	157	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753044	42753044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1390865410	NA	P-0049584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	111	854	0	ENST00000222329.4:c.1220G>A	p.Gly407Asp	p.G407D	ENST00000222329	NM_006494.2	407	gGc/gAc	4/4	0.167999282515021	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	FALSE	2	0.167999282515021	4		854	689	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753059	42753059	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326716475	NA	P-0049584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	113	839	0	ENST00000222329.4:c.1205G>A	p.Ser402Asn	p.S402N	ENST00000222329	NM_006494.2	402	aGc/aAc	4/4	0.167999282515021	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	FALSE	2	0.167999282515021	4		839	684	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753130	42753130	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	114	812	0	ENST00000222329.4:c.1134G>C	p.Lys378Asn	p.K378N	ENST00000222329	NM_006494.2	378	aaG/aaC	4/4	0.167999282515021	4	FACETS	0.952	0.86	1	1	0.983	1	CLONAL	3	FALSE	2	0.167999282515021	4		812	555	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754580	42754580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	115	785	0	ENST00000222329.4:c.160G>A	p.Glu54Lys	p.E54K	ENST00000222329	NM_006494.2	54	Gaa/Aaa	2/4	0.167999282515021	4	FACETS	0.842	0.76	0.928	1	0.976	1	CLONAL	3	FALSE	2	0.167999282515021	4		785	633	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	187	782	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.661	0.609	0.715	0.661	0.609	0.715	SUBCLONAL	1	TRUE	1	0.48	2		787	1179	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	100	352	1	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.72	0.644	0.799	0.72	0.644	0.799	SUBCLONAL	1	TRUE	1	0.48	2		353	579	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	323	695	3	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.48	2		698	1281	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	208	472	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.922	0.856	0.99	0.922	0.856	0.99	CLONAL	1	TRUE	1	0.48	2		475	940	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	186	828	2	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	1	2	FACETS	0.7	0.646	0.757	0.7	0.646	0.757	SUBCLONAL	1	TRUE	1	0.48	2		830	1107	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	51	680	3	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.259	0.22	0.303	0.259	0.22	0.303	SUBCLONAL	1	TRUE	1	0.48	2		683	819	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	167	409	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.973	0.897	1	0.973	0.897	1	CLONAL	1	TRUE	1	0.48	2		415	715	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	128	263	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.916	0.834	1	0.916	0.834	1	CLONAL	1	TRUE	1	0.48	2		263	582	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885144	111885145	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs892433462	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	205	720	2	ENST00000341259.2:c.1038dup	p.Leu347AlafsTer38	p.L347Afs*38	ENST00000341259	NM_005475.2	344	-/G	6/8	1	2	FACETS	0.912	0.846	0.979	0.912	0.846	0.979	CLONAL	1	TRUE	1	0.48	2		722	937	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298480	11298480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780622659	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	184	592	1	ENST00000361445.4:c.1981G>A	p.Val661Ile	p.V661I	ENST00000361445	NM_004958.3	661	Gta/Ata	12/58	1	2	FACETS	0.918	0.849	0.99	0.918	0.849	0.99	CLONAL	1	TRUE	1	0.48	2		593	835	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258394	16258394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	229	735	0	ENST00000375759.3:c.5659C>T	p.Leu1887Phe	p.L1887F	ENST00000375759	NM_015001.2	1887	Ctt/Ttt	11/15	1	2	FACETS	0.945	0.881	1	0.945	0.881	1	CLONAL	1	TRUE	1	0.48	2		735	1010	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057739	27057739	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	264	819	0	ENST00000324856.7:c.1447C>T	p.Pro483Ser	p.P483S	ENST00000324856	NM_006015.4	483	Cca/Tca	3/20	1	2	FACETS	0.97	0.909	1	0.97	0.909	1	CLONAL	1	TRUE	1	0.48	2		819	1134	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101612	27101612	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	292	1019	1	ENST00000324856.7:c.4899del	p.Met1634Ter	p.M1634*	ENST00000324856	NM_006015.4	1632	Ccc/cc	18/20	1	2	FACETS	0.919	0.863	0.976	0.919	0.863	0.976	CLONAL	1	TRUE	1	0.48	2		1020	1324	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804952	43804953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	124	489	0	ENST00000372470.3:c.408dup	p.Ser137GlnfsTer27	p.S137Qfs*27	ENST00000372470	NM_005373.2	134	-/C	4/12	1	2	FACETS	0.815	0.739	0.895	0.815	0.739	0.895	CLONAL	1	TRUE	1	0.48	2		489	634	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521525	46521525	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	144	655	2	ENST00000262741.5:c.883del	p.Met295Ter	p.M295*	ENST00000262741	NM_003629.3	295	Atg/tg	7/10	1	2	FACETS	0.651	0.593	0.711	0.651	0.593	0.711	SUBCLONAL	1	TRUE	1	0.48	2		657	922	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78421012	78421012	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	94	330	0	ENST00000370768.2:c.1708G>A	p.Asp570Asn	p.D570N	ENST00000370768	NM_003902.3	570	Gat/Aat	18/20	1	2	FACETS	0.911	0.815	1	0.911	0.815	1	CLONAL	1	TRUE	1	0.48	2		330	430	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429978	78429978	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	71	408	0	ENST00000370768.2:c.901del	p.Ile301TyrfsTer22	p.I301Yfs*22	ENST00000370768	NM_003902.3	301	Ata/ta	11/20	1	2	FACETS	0.539	0.471	0.612	0.539	0.471	0.612	SUBCLONAL	1	TRUE	1	0.48	2		408	549	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699360	117699360	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	150	601	1	ENST00000369458.3:c.281A>G	p.Asp94Gly	p.D94G	ENST00000369458	NM_024626.3	94	gAt/gGt	3/6	1	2	FACETS	0.804	0.736	0.876	0.804	0.736	0.876	CLONAL	1	TRUE	1	0.48	2		602	777	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166628	118166628	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs746449090	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	28	301	0	ENST00000369448.3:c.1138T>C	p.Tyr380His	p.Y380H	ENST00000369448	NM_017709.3	380	Tac/Cac	2/2	1	2	FACETS	0.25	0.199	0.308	0.25	0.199	0.308	SUBCLONAL	1	TRUE	1	0.48	2		301	467	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458203	120458203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1291690396	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	263	883	1	ENST00000256646.2:c.7142G>A	p.Gly2381Asp	p.G2381D	ENST00000256646	NM_024408.3	2381	gGc/gAc	34/34	1	2	FACETS	0.996	0.934	1	0.996	0.934	1	CLONAL	1	TRUE	1	0.48	2		884	1100	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458785	120458785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	53	757	2	ENST00000256646.2:c.6560C>T	p.Ala2187Val	p.A2187V	ENST00000256646	NM_024408.3	2187	gCc/gTc	34/34	1	2	FACETS	0.233	0.198	0.272	0.233	0.198	0.272	SUBCLONAL	1	TRUE	1	0.48	2		759	948	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468195	120468195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758275919	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	245	921	2	ENST00000256646.2:c.4244C>T	p.Thr1415Met	p.T1415M	ENST00000256646	NM_024408.3	1415	aCg/aTg	25/34	1	2	FACETS	0.952	0.89	1	0.952	0.89	1	CLONAL	1	TRUE	1	0.48	2		923	1072	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743260	162743260	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	101	275	0	ENST00000367921.3:c.1730T>C	p.Val577Ala	p.V577A	ENST00000367921	NM_006182.2	577	gTt/gCt	14/18	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.48	2		275	414	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091361	193091361	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	118	451	0	ENST00000367435.3:c.31T>C	p.Tyr11His	p.Y11H	ENST00000367435	NM_024529.4	11	Tac/Cac	1/17	1	2	FACETS	0.935	0.847	1	0.935	0.847	1	CLONAL	1	TRUE	1	0.48	2		451	526	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649617	206649617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	55	789	0	ENST00000367120.3:c.452G>A	p.Ser151Asn	p.S151N	ENST00000367120	NM_014002.3	151	aGc/aAc	6/22	1	2	FACETS	0.238	0.203	0.277	0.238	0.203	0.277	SUBCLONAL	1	TRUE	1	0.48	2		789	962	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021811	246021811	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1235722186	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	199	651	0	ENST00000388985.4:c.1063A>G	p.Met355Val	p.M355V	ENST00000388985		355	Atg/Gtg	10/12	1	2	FACETS	0.9	0.834	0.968	0.9	0.834	0.968	CLONAL	1	TRUE	1	0.48	2		651	921	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100806	8100806	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	207	805	0	ENST00000346208.3:c.778+2T>C		p.X260_splice	ENST00000346208		260			1	2	FACETS	0.955	0.887	1	0.955	0.887	1	CLONAL	1	TRUE	1	0.48	2		805	903	SUCCESS
RET	5979	MSKCC	GRCh37	10	43572719	43572719	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	72	289	0	ENST00000355710.3:c.13A>G	p.Thr5Ala	p.T5A	ENST00000355710	NM_020975.4	5	Acg/Gcg	1/20	1	2	FACETS	0.761	0.669	0.86	0.761	0.669	0.86	SUBCLONAL	1	TRUE	1	0.48	2		289	394	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597928	43597928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	263	1050	0	ENST00000355710.3:c.476C>T	p.Ser159Phe	p.S159F	ENST00000355710	NM_020975.4	159	tCc/tTc	3/20	1	2	FACETS	0.853	0.799	0.91	0.853	0.799	0.91	CLONAL	1	TRUE	1	0.48	2		1050	1284	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610111	43610111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	240	931	0	ENST00000355710.3:c.2063C>T	p.Ser688Phe	p.S688F	ENST00000355710	NM_020975.4	688	tCc/tTc	11/20	1	2	FACETS	0.957	0.894	1	0.957	0.894	1	CLONAL	1	TRUE	1	0.48	2		931	1045	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925492	114925492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs534110993	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	208	789	0	ENST00000543371.1:c.1570G>A	p.Asp524Asn	p.D524N	ENST00000543371	NM_001198531.1	524	Gac/Aac	14/14	1	2	FACETS	0.916	0.851	0.984	0.916	0.851	0.984	CLONAL	1	TRUE	1	0.48	2		789	946	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274710	123274710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753437208	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	148	687	1	ENST00000358487.5:c.1208C>T	p.Thr403Met	p.T403M	ENST00000358487	NM_000141.4	403	aCg/aTg	9/18	1	2	FACETS	0.729	0.666	0.795	0.729	0.666	0.795	SUBCLONAL	1	TRUE	1	0.48	2		688	846	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274734	123274734	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	192	666	0	ENST00000358487.5:c.1184T>A	p.Val395Asp	p.V395D	ENST00000358487	NM_000141.4	395	gTc/gAc	9/18	1	2	FACETS	0.973	0.902	1	0.973	0.902	1	CLONAL	1	TRUE	1	0.48	2		666	822	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14303193	14303193	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	119	590	0	ENST00000256196.4:c.482G>T	p.Arg161Met	p.R161M	ENST00000256196		161	aGg/aTg	5/6	1	2	FACETS	0.582	0.525	0.642	0.582	0.525	0.642	SUBCLONAL	1	TRUE	1	0.48	2		590	852	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417875	32417875	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	182	659	0	ENST00000332351.3:c.1177T>C	p.Cys393Arg	p.C393R	ENST00000332351	NM_024426.4	393	Tgt/Cgt	7/10	1	2	FACETS	0.875	0.808	0.944	0.875	0.808	0.944	CLONAL	1	TRUE	1	0.48	2		659	867	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456560	32456560	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	26	148	0	ENST00000332351.3:c.332del	p.Pro111ArgfsTer47	p.P111Rfs*47	ENST00000332351	NM_024426.4	111	cCg/cg	1/10	1	2	FACETS	0.586	0.467	0.719	0.586	0.467	0.719	SUBCLONAL	1	TRUE	1	0.48	2		148	185	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200811	67200811	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	116	742	0	ENST00000312629.5:c.799C>T	p.Pro267Ser	p.P267S	ENST00000312629	NM_003952.2	267	Ccg/Tcg	10/15	1	2	FACETS	0.593	0.534	0.655	0.593	0.534	0.655	SUBCLONAL	1	TRUE	1	0.48	2		742	815	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909847	100909847	+	stop_lost	Nonstop_Mutation	SNP	T	T	C	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	53	189	0	ENST00000325455.5:c.2802A>G	p.Ter934TrpextTer25	p.*934Wext*25	ENST00000325455	NM_001202474.3	934	tgA/tgG	8/8	1	2	FACETS	0.928	0.8	1	0.928	0.8	1	CLONAL	1	TRUE	1	0.48	2		189	238	SUCCESS
ATM	472	MSKCC	GRCh37	11	108127033	108127033	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	41	456	0	ENST00000278616.4:c.2216A>G	p.Glu739Gly	p.E739G	ENST00000278616	NM_000051.3	739	gAa/gGa	14/63	0.3	3	FACETS	0.29	0.241	0.345			1	SUBCLONAL	1	TRUE	NA	0.48	3		456	730	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505404	125505404	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	100	326	0	ENST00000428830.2:c.700del	p.Ile234SerfsTer6	p.I234Sfs*6	ENST00000428830	NM_001114121.2	232	Aaa/aa	7/14	1	2	FACETS	0.786	0.705	0.872	0.786	0.705	0.872	SUBCLONAL	1	TRUE	1	0.48	2		326	530	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	186	389	7	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.48	2		396	712	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022364	12022364	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1179480567	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	309	843	0	ENST00000396373.4:c.470G>A	p.Cys157Tyr	p.C157Y	ENST00000396373	NM_001987.4	157	tGt/tAt	5/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.48	2		843	1199	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380283	25380283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913528	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	116	528	1	ENST00000311936.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000311936	NM_004985.3	59	Gca/Aca	3/5	1	2	FACETS	0.693	0.626	0.765	0.693	0.626	0.765	SUBCLONAL	1	TRUE	1	0.48	2		529	697	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123837	46123837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	120	249	0	ENST00000334344.6:c.109del	p.Ile37SerfsTer21	p.I37Sfs*21	ENST00000334344	NM_152641.2	35	Aaa/aa	2/21	1	2	FACETS	0.951	0.862	1	0.951	0.862	1	CLONAL	1	TRUE	1	0.48	2		249	526	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244076	46244076	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	152	489	0	ENST00000334344.6:c.2173del	p.Gln725ArgfsTer33	p.Q725Rfs*33	ENST00000334344	NM_152641.2	724	Ccc/cc	15/21	1	2	FACETS	0.965	0.886	1	0.965	0.886	1	CLONAL	1	TRUE	1	0.48	2		489	656	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435137	49435137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754730634	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	208	757	1	ENST00000301067.7:c.6416C>T	p.Ala2139Val	p.A2139V	ENST00000301067	NM_003482.3	2139	gCg/gTg	31/54	1	2	FACETS	0.891	0.827	0.957	0.891	0.827	0.957	CLONAL	1	TRUE	1	0.48	2		758	973	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435199	49435199	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	235	879	3	ENST00000301067.7:c.6354del	p.Ala2119LeufsTer25	p.A2119Lfs*25	ENST00000301067	NM_003482.3	2118	ccC/cc	31/54	1	2	FACETS	0.973	0.908	1	0.973	0.908	1	CLONAL	1	TRUE	1	0.48	2		882	1006	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869423	102869423	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	166	513	0	ENST00000307046.8:c.218T>A	p.Phe73Tyr	p.F73Y	ENST00000307046	NM_001111285.1	73	tTc/tAc	2/4	1	2	FACETS	0.988	0.91	1	0.988	0.91	1	CLONAL	1	TRUE	1	0.48	2		513	700	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109959	115109959	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1030153498	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	82	1013	0	ENST00000257566.3:c.1919A>G	p.Tyr640Cys	p.Y640C	ENST00000257566	NM_016569.3	640	tAc/tGc	8/8	1	2	FACETS	0.308	0.27	0.348	0.308	0.27	0.348	SUBCLONAL	1	TRUE	1	0.48	2		1013	1111	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245483	133245483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200471266	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	156	640	0	ENST00000320574.5:c.1837G>A	p.Val613Ile	p.V613I	ENST00000320574	NM_006231.2	613	Gtt/Att	17/49	1	2	FACETS	0.714	0.653	0.777	0.714	0.653	0.777	SUBCLONAL	1	TRUE	1	0.48	2		640	911	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26971322	26971322	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	69	276	0	ENST00000381527.3:c.897del	p.Lys299AsnfsTer23	p.K299Nfs*23	ENST00000381527	NM_001260.1	298	gAa/ga	9/13	1	2	FACETS	0.907	0.796	1	0.907	0.796	1	CLONAL	1	TRUE	1	0.48	2		276	317	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913692	32913692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786202543	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	138	406	1	ENST00000380152.3:c.5200G>A	p.Glu1734Lys	p.E1734K	ENST00000380152		1734	Gaa/Aaa	11/27	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.48	2		407	569	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913716	32913716	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	128	441	0	ENST00000380152.3:c.5224A>G	p.Asn1742Asp	p.N1742D	ENST00000380152		1742	Aac/Gac	11/27	1	2	FACETS	0.86	0.782	0.942	0.86	0.782	0.942	CLONAL	1	TRUE	1	0.48	2		441	620	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133685	41133685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1216360372	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	137	405	1	ENST00000379561.5:c.1943C>T	p.Thr648Met	p.T648M	ENST00000379561	NM_002015.3	648	aCg/aTg	2/3	1	2	FACETS	0.968	0.884	1	0.968	0.884	1	CLONAL	1	TRUE	1	0.48	2		406	590	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48921987	48921987	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	34	344	0	ENST00000267163.4:c.527A>G	p.Gln176Arg	p.Q176R	ENST00000267163	NM_000321.2	176	cAa/cGa	5/27	1	2	FACETS	0.311	0.253	0.375	0.311	0.253	0.375	SUBCLONAL	1	TRUE	1	0.48	2		344	456	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514692	103514692	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	140	485	1	ENST00000355739.4:c.1193A>G	p.Asp398Gly	p.D398G	ENST00000355739	NM_000123.3	398	gAc/gGc	8/15	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.48	2		486	577	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871620	35871620	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	126	395	0	ENST00000216797.5:c.886A>G	p.Thr296Ala	p.T296A	ENST00000216797	NM_020529.2	296	Acg/Gcg	5/6	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.48	2		395	514	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81563045	81563045	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	127	382	1	ENST00000298171.2:c.608A>T	p.Asp203Val	p.D203V	ENST00000298171	NM_000369.2	203	gAt/gTt	7/10	1	2	FACETS	0.991	0.902	1	0.991	0.902	1	CLONAL	1	TRUE	1	0.48	2		383	534	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95599650	95599650	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	103	322	0	ENST00000393063.1:c.144+2T>C		p.X48_splice	ENST00000393063	NM_030621.3	48			1	2	FACETS	0.838	0.753	0.928	0.838	0.753	0.928	CLONAL	1	TRUE	1	0.48	2		322	512	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105236707	105236707	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	193	984	0	ENST00000349310.3:c.1414T>C	p.Phe472Leu	p.F472L	ENST00000349310	NM_001014432.1	472	Ttc/Ctc	15/15	1	2	FACETS	0.686	0.633	0.74	0.686	0.633	0.74	SUBCLONAL	1	TRUE	1	0.48	2		984	1173	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712844	43712844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2230449	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	258	859	0	ENST00000382044.4:c.4340G>A	p.Arg1447Gln	p.R1447Q	ENST00000382044	NM_001141980.1	1447	cGa/cAa	21/28	1	2	FACETS	0.948	0.887	1	0.948	0.887	1	CLONAL	1	TRUE	1	0.48	2		859	1134	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	359972	359972	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	61	821	1	ENST00000262320.3:c.1116+1G>A		p.X372_splice	ENST00000262320	NM_003502.3	372			1	2	FACETS	0.24	0.206	0.277	0.24	0.206	0.277	SUBCLONAL	1	TRUE	1	0.48	2		822	1059	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632639	3632639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753159332	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	312	1129	0	ENST00000294008.3:c.5209G>A	p.Glu1737Lys	p.E1737K	ENST00000294008	NM_032444.2	1737	Gag/Aag	15/15	1	2	FACETS	0.976	0.919	1	0.976	0.919	1	CLONAL	1	TRUE	1	0.48	2		1129	1332	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779445	3779445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567263168	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	346	1212	0	ENST00000262367.5:c.5603G>A	p.Arg1868Gln	p.R1868Q	ENST00000262367	NM_004380.2	1868	cGg/cAg	31/31	1	2	FACETS	0.971	0.918	1	0.971	0.918	1	CLONAL	1	TRUE	1	0.48	2		1212	1484	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860615	3860615	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778212	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	177	707	0	ENST00000262367.5:c.964G>A	p.Val322Met	p.V322M	ENST00000262367	NM_004380.2	322	Gtg/Atg	3/31	1	2	FACETS	0.847	0.781	0.915	0.847	0.781	0.915	CLONAL	1	TRUE	1	0.48	2		707	871	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56866271	56866271	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	82	419	0	ENST00000308159.5:c.1316A>T	p.Gln439Leu	p.Q439L	ENST00000308159	NM_014669.4	439	cAg/cTg	12/22	1	2	FACETS	0.66	0.583	0.741	0.66	0.583	0.741	SUBCLONAL	1	TRUE	1	0.48	2		419	518	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56873494	56873494	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	42	555	0	ENST00000308159.5:c.2198C>T	p.Ala733Val	p.A733V	ENST00000308159	NM_014669.4	733	gCc/gTc	20/22	1	2	FACETS	0.223	0.185	0.265	0.223	0.185	0.265	SUBCLONAL	1	TRUE	1	0.48	2		555	786	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992892	72992892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764687875	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	314	907	1	ENST00000268489.5:c.1153G>A	p.Ala385Thr	p.A385T	ENST00000268489	NM_006885.3	385	Gct/Act	2/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.48	2		908	1117	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347138	89347138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1225667881	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	176	979	0	ENST00000301030.4:c.5812C>T	p.Pro1938Ser	p.P1938S	ENST00000301030	NM_001256183.1	1938	Ccc/Tcc	9/13	1	2	FACETS	0.736	0.677	0.797	0.736	0.677	0.797	SUBCLONAL	1	TRUE	1	0.48	2		979	997	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347143	89347143	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	171	963	0	ENST00000301030.4:c.5807A>G	p.Glu1936Gly	p.E1936G	ENST00000301030	NM_001256183.1	1936	gAg/gGg	9/13	1	2	FACETS	0.717	0.659	0.777	0.717	0.659	0.777	SUBCLONAL	1	TRUE	1	0.48	2		963	994	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347852	89347852	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	57	861	1	ENST00000301030.4:c.5098C>T	p.Pro1700Ser	p.P1700S	ENST00000301030	NM_001256183.1	1700	Ccc/Tcc	9/13	1	2	FACETS	0.253	0.216	0.293	0.253	0.216	0.293	SUBCLONAL	1	TRUE	1	0.48	2		862	940	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805106	89805106	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs139532591	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	240	843	0	ENST00000389301.3:c.4271A>G	p.Asp1424Gly	p.D1424G	ENST00000389301	NM_000135.2	1424	gAt/gGt	43/43	1	2	FACETS	0.997	0.931	1	0.997	0.931	1	CLONAL	1	TRUE	1	0.48	2		843	1003	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89883016	89883016	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	101	438	0	ENST00000389301.3:c.8A>G	p.Asp3Gly	p.D3G	ENST00000389301	NM_000135.2	3	gAc/gGc	1/43	1	2	FACETS	0.868	0.779	0.961	0.868	0.779	0.961	CLONAL	1	TRUE	1	0.48	2		438	485	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974782	15974782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196308486	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	148	468	0	ENST00000268712.3:c.4093C>T	p.Arg1365Trp	p.R1365W	ENST00000268712	NM_006311.3	1365	Cgg/Tgg	30/46	1	2	FACETS	0.974	0.893	1	0.974	0.893	1	CLONAL	1	TRUE	1	0.48	2		468	633	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550473	29550473	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199474774	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	19	237	0	ENST00000356175.3:c.1733T>C	p.Leu578Pro	p.L578P	ENST00000356175	NM_000267.3	578	cTt/cCt	16/57	1	2	FACETS	0.22	0.166	0.283	0.22	0.166	0.283	SUBCLONAL	1	TRUE	1	0.48	2		237	360	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587387	29587388	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	rs1555618803	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	110	344	0	ENST00000356175.3:c.4373dup	p.Leu1459ProfsTer2	p.L1459Pfs*2	ENST00000356175	NM_000267.3	1456	-/T	33/57	1	2	FACETS	0.847	0.764	0.935	0.847	0.764	0.935	CLONAL	1	TRUE	1	0.48	2		344	541	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	278	1061	11	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	0.88	0.825	0.936	0.88	0.825	0.936	CLONAL	1	TRUE	1	0.48	2		1072	1317	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59870977	59870977	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	93	414	0	ENST00000259008.2:c.1454C>T	p.Ala485Val	p.A485V	ENST00000259008	NM_032043.2	485	gCt/gTt	10/20	1	2	FACETS	0.773	0.69	0.862	0.773	0.69	0.862	SUBCLONAL	1	TRUE	1	0.48	2		414	501	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117819	70117819	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs148407362	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	58	877	0	ENST00000245479.2:c.287A>G	p.Asn96Ser	p.N96S	ENST00000245479	NM_000346.3	96	aAc/aGc	1/3	1	2	FACETS	0.236	0.202	0.274	0.236	0.202	0.274	SUBCLONAL	1	TRUE	1	0.48	2		877	1023	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604785	48604785	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	118	443	0	ENST00000342988.3:c.1607T>C	p.Leu536Pro	p.L536P	ENST00000342988	NM_005359.5	536	cTa/cCa	12/12	1	2	FACETS	0.892	0.808	0.981	0.892	0.808	0.981	CLONAL	1	TRUE	1	0.48	2		443	551	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207084	1207084	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	213	1010	0	ENST00000326873.7:c.172G>T	p.Gly58Cys	p.G58C	ENST00000326873	NM_000455.4	58	Ggc/Tgc	1/10	1	2	FACETS	0.676	0.627	0.727	0.676	0.627	0.727	SUBCLONAL	1	TRUE	1	0.48	2		1010	1313	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220470	1220470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	73	1123	4	ENST00000326873.7:c.563G>A	p.Gly188Asp	p.G188D	ENST00000326873	NM_000455.4	188	gGc/gAc	4/10	1	2	FACETS	0.245	0.213	0.279	0.245	0.213	0.279	SUBCLONAL	1	TRUE	1	0.48	2		1127	1243	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221295	1221295	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761164605	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	254	920	0	ENST00000326873.7:c.818C>T	p.Ala273Val	p.A273V	ENST00000326873	NM_000455.4	273	gCc/gTc	6/10	1	2	FACETS	0.916	0.856	0.977	0.916	0.856	0.977	CLONAL	1	TRUE	1	0.48	2		920	1156	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2185901	2185901	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	55	626	0	ENST00000398665.3:c.173A>G	p.Tyr58Cys	p.Y58C	ENST00000398665	NM_032482.2	58	tAc/tGc	3/28	1	2	FACETS	0.272	0.232	0.316	0.272	0.232	0.316	SUBCLONAL	1	TRUE	1	0.48	2		626	843	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222723	5222723	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs745694014	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	237	1051	0	ENST00000357368.4:c.3080A>G	p.Tyr1027Cys	p.Y1027C	ENST00000357368	NM_002850.3	1027	tAc/tGc	18/38	1	2	FACETS	0.903	0.842	0.965	0.903	0.842	0.965	CLONAL	1	TRUE	1	0.48	2		1051	1094	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249282	10249282	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	41	589	0	ENST00000340748.4:c.3901-1G>A		p.X1301_splice	ENST00000340748		1301			1	2	FACETS	0.215	0.178	0.256	0.215	0.178	0.256	SUBCLONAL	1	TRUE	1	0.48	2		589	794	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260611	10260611	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	198	619	0	ENST00000340748.4:c.2251T>C	p.Cys751Arg	p.C751R	ENST00000340748		751	Tgc/Cgc	24/40	1	2	FACETS	0.915	0.848	0.984	0.915	0.848	0.984	CLONAL	1	TRUE	1	0.48	2		619	902	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602335	10602335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	367	1167	2	ENST00000171111.5:c.1243C>T	p.Arg415Cys	p.R415C	ENST00000171111	NM_203500.1	415	Cgc/Tgc	3/6	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.48	2		1169	1401	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11027407	11027407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778642042	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	332	1056	0	ENST00000327064.4:c.974C>T	p.Ala325Val	p.A325V	ENST00000327064	NM_199141.1	325	gCc/gTc	8/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.48	2		1056	1350	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296357	15296358	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1236	199	1171	1	ENST00000263388.2:c.2084dup	p.Ser696GlufsTer7	p.S696Efs*7	ENST00000263388	NM_000435.2	695	ccg/ccCg	13/33	1	2	FACETS	0.578	0.534	0.624	0.578	0.534	0.624	SUBCLONAL	1	TRUE	1	0.48	2		1172	1435	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298066	15298066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374767079	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	373	1207	3	ENST00000263388.2:c.1690G>A	p.Ala564Thr	p.A564T	ENST00000263388	NM_000435.2	564	Gcc/Acc	11/33	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.48	2		1210	1419	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349592	15349592	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	302	1279	1	ENST00000263377.2:c.3982G>A	p.Ala1328Thr	p.A1328T	ENST00000263377	NM_058243.2	1328	Gcc/Acc	19/20	1	2	FACETS	0.881	0.828	0.935	0.881	0.828	0.935	CLONAL	1	TRUE	1	0.48	2		1280	1428	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350524	15350524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	264	987	0	ENST00000263377.2:c.3391C>T	p.Pro1131Ser	p.P1131S	ENST00000263377	NM_058243.2	1131	Ccg/Tcg	16/20	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.48	2		987	1100	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945804	17945804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750102955	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	92	906	0	ENST00000458235.1:c.2056G>A	p.Asp686Asn	p.D686N	ENST00000458235	NM_000215.3	686	Gac/Aac	16/24	1	2	FACETS	0.333	0.295	0.374	0.333	0.295	0.374	SUBCLONAL	1	TRUE	1	0.48	2		906	1150	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256769	19256769	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	264	987	2	ENST00000162023.5:c.944del	p.Pro315GlnfsTer?	p.P315Qfs*?	ENST00000162023		315	cCa/ca	13/13	1	2	FACETS	0.973	0.911	1	0.973	0.911	1	CLONAL	1	TRUE	1	0.48	2		989	1131	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303648	30303648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	208	679	1	ENST00000262643.3:c.76G>A	p.Ala26Thr	p.A26T	ENST00000262643	NM_001238.2	26	Gct/Act	3/12	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.48	2		680	826	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224180	36224180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	227	993	0	ENST00000222270.7:c.6730C>T	p.Pro2244Ser	p.P2244S	ENST00000222270	NM_014727.1	2244	Ccc/Tcc	28/37	1	2	FACETS	0.781	0.727	0.838	0.781	0.727	0.838	SUBCLONAL	1	TRUE	1	0.48	2		993	1211	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744385	41744385	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	234	930	1	ENST00000301178.4:c.1010del	p.Pro337LeufsTer29	p.P337Lfs*29	ENST00000301178	NM_021913.4	335	ggC/gg	8/20	1	2	FACETS	0.929	0.867	0.994	0.929	0.867	0.994	CLONAL	1	TRUE	1	0.48	2		931	1049	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860919	45860919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs577723968	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	271	1018	0	ENST00000391945.4:c.1276C>T	p.Pro426Ser	p.P426S	ENST00000391945	NM_000400.3	426	Ccg/Tcg	13/23	1	2	FACETS	0.906	0.849	0.964	0.906	0.849	0.964	CLONAL	1	TRUE	1	0.48	2		1018	1247	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912858	50912858	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1306540639	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	343	918	1	ENST00000440232.2:c.2089G>A	p.Ala697Thr	p.A697T	ENST00000440232	NM_002691.3	697	Gcc/Acc	17/27	1	2	FACETS	0.971	0.917	1	0.971	0.917	1	CLONAL	1	TRUE	1	0.48	2		919	1472	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918992	50918992	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568638496	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	237	896	0	ENST00000440232.2:c.2729G>A	p.Arg910Gln	p.R910Q	ENST00000440232	NM_002691.3	910	cGg/cAg	22/27	1	2	FACETS	0.999	0.933	1	0.999	0.933	1	CLONAL	1	TRUE	1	0.48	2		896	988	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919699	50919699	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1343793547	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	383	1276	0	ENST00000440232.2:c.2867A>G	p.Tyr956Cys	p.Y956C	ENST00000440232	NM_002691.3	956	tAc/tGc	23/27	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.48	2		1276	1457	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724295	52724295	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	159	727	0	ENST00000322088.6:c.1427A>G	p.Glu476Gly	p.E476G	ENST00000322088	NM_014225.5	476	gAg/gGg	12/15	1	2	FACETS	0.679	0.622	0.739	0.679	0.622	0.739	SUBCLONAL	1	TRUE	1	0.48	2		727	975	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754901	29754901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1558370551	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	209	706	0	ENST00000389048.3:c.1034G>A	p.Cys345Tyr	p.C345Y	ENST00000389048	NM_004304.4	345	tGc/tAc	4/29	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.48	2		706	813	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635618	47635618	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	143	536	0	ENST00000233146.2:c.290del	p.Gln97ArgfsTer77	p.Q97Rfs*77	ENST00000233146	NM_000251.2	97	cAg/cg	2/16	0.0768049016068355	3	FACETS	0.909	0.829	0.992	0.454	0.414	0.496	INDETERMINATE	1	TRUE	1	0.48	3		536	813	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030692	48030693	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	rs267608092	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	135	410	0	ENST00000234420.5:c.3311_3312del	p.Phe1104TrpfsTer3	p.F1104Wfs*3	ENST00000234420	NM_000179.2	1102	acTTtt/actt	5/10	0.0768049016068355	3	FACETS	1	0.978	1	0.609	0.555	0.664	INDETERMINATE	1	TRUE	1	0.48	3		410	573	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033784	48033784	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	101	299	0	ENST00000234420.5:c.3995T>C	p.Leu1332Ser	p.L1332S	ENST00000234420	NM_000179.2	1332	tTa/tCa	9/10	0.0768049016068355	3	FACETS	1	0.959	1	0.567	0.509	0.628	INDETERMINATE	1	TRUE	1	0.48	3		299	460	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147770	61147771	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	67	261	0	ENST00000295025.8:c.1086dup	p.Glu363ArgfsTer8	p.E363Rfs*8	ENST00000295025	NM_002908.2	360	-/A	10/11	0.0768049016068355	3	FACETS	0.783	0.683	0.891	0.392	0.341	0.446	INDETERMINATE	1	TRUE	1	0.48	3		261	442	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61709534	61709534	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	130	357	0	ENST00000401558.2:c.2953G>A	p.Ala985Thr	p.A985T	ENST00000401558	NM_003400.3	985	Gcc/Acc	23/25	0.0768049016068355	3	FACETS	1	0.985	1	0.709	0.647	0.772	INDETERMINATE	1	TRUE	1	0.48	3		357	474	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881695	111881695	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	219	695	0	ENST00000393256.3:c.373A>G	p.Asn125Asp	p.N125D	ENST00000393256	NM_006538.4	125	Aac/Gac	2/4	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.48	2		695	851	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873410	136873410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	128	432	0	ENST00000241393.3:c.88C>T	p.Arg30Cys	p.R30C	ENST00000241393	NM_003467.2	30	Cgt/Tgt	2/2	1	2	FACETS	0.905	0.824	0.991	0.905	0.824	0.991	CLONAL	1	TRUE	1	0.48	2		432	589	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190656606	190656606	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1265410375	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	52	258	0	ENST00000441310.2:c.71T>C	p.Val24Ala	p.V24A	ENST00000441310	NM_000534.4	24	gTt/gCt	2/13	1	2	FACETS	0.59	0.504	0.684	0.59	0.504	0.684	SUBCLONAL	1	TRUE	1	0.48	2		258	367	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281529	198281529	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	160	556	0	ENST00000335508.6:c.602A>G	p.Asp201Gly	p.D201G	ENST00000335508	NM_012433.2	201	gAt/gGt	6/25	1	2	FACETS	0.732	0.671	0.795	0.732	0.671	0.795	SUBCLONAL	1	TRUE	1	0.48	2		556	911	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202123043	202123043	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	149	476	0	ENST00000358485.4:c.89A>G	p.His30Arg	p.H30R	ENST00000358485	NM_001080125.1	30	cAc/cGc	1/9	1	2	FACETS	0.929	0.852	1	0.929	0.852	1	CLONAL	1	TRUE	1	0.48	2		476	668	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151289	202151290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	104	427	0	ENST00000358485.4:c.1596dup	p.Leu533ThrfsTer6	p.L533Tfs*6	ENST00000358485	NM_001080125.1	530	aga/agAa	9/9	1	2	FACETS	0.748	0.672	0.829	0.748	0.672	0.829	SUBCLONAL	1	TRUE	1	0.48	2		427	579	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295776	212295776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758104381	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	127	591	2	ENST00000342788.4:c.2537C>T	p.Ala846Val	p.A846V	ENST00000342788	NM_005235.2	846	gCc/gTc	21/28	1	2	FACETS	0.71	0.644	0.78	0.71	0.644	0.78	SUBCLONAL	1	TRUE	1	0.48	2		593	745	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593530	215593530	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	27	386	0	ENST00000260947.4:c.2204A>C	p.Gln735Pro	p.Q735P	ENST00000260947	NM_000465.2	735	cAg/cCg	11/11	1	2	FACETS	0.209	0.166	0.26	0.209	0.166	0.26	SUBCLONAL	1	TRUE	1	0.48	2		386	537	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437172	220437172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199544141	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	347	1286	4	ENST00000243786.2:c.76C>T	p.Arg26Trp	p.R26W	ENST00000243786	NM_002191.3	26	Cgg/Tgg	1/2	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.48	2		1290	1417	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017141	31017141	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1190521844	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	93	256	0	ENST00000375687.4:c.472G>A	p.Ala158Thr	p.A158T	ENST00000375687	NM_015338.5	158	Gcg/Acg	7/13	1	2	FACETS	0.979	0.876	1	0.979	0.876	1	CLONAL	1	TRUE	1	0.48	2		256	396	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911144	40911144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776134993	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	106	347	1	ENST00000373198.4:c.2161C>T	p.Arg721Cys	p.R721C	ENST00000373198	NM_133170.3	721	Cgt/Tgt	13/32	1	2	FACETS	0.882	0.794	0.974	0.882	0.794	0.974	CLONAL	1	TRUE	1	0.48	2		348	501	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466864	57466864	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	117	359	0	ENST00000371085.3:c.83A>G	p.Lys28Arg	p.K28R	ENST00000371085	NM_000516.4	28	aAg/aGg	1/13	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.48	2		359	473	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57470690	57470690	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs797044895	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	102	342	0	ENST00000371085.3:c.163A>G	p.Thr55Ala	p.T55A	ENST00000371085	NM_000516.4	55	Acc/Gcc	2/13	1	2	FACETS	0.882	0.792	0.976	0.882	0.792	0.976	CLONAL	1	TRUE	1	0.48	2		342	482	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164721	36164721	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	218	1123	0	ENST00000300305.3:c.1154A>G	p.Tyr385Cys	p.Y385C	ENST00000300305		385	tAc/tGc	8/8	1	2	FACETS	0.711	0.66	0.764	0.711	0.66	0.764	SUBCLONAL	1	TRUE	1	0.48	2		1123	1277	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656890	45656890	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	243	834	0	ENST00000407780.3:c.266C>T	p.Ala89Val	p.A89V	ENST00000407780	NM_001283052.1	89	gCc/gTc	3/7	1	2	FACETS	0.988	0.923	1	0.988	0.923	1	CLONAL	1	TRUE	1	0.48	2		834	1025	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069405	30069405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763826793	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	57	893	0	ENST00000338641.4:c.1270C>T	p.Arg424Cys	p.R424C	ENST00000338641	NM_000268.3	424	Cgc/Tgc	12/16	1	2	FACETS	0.22	0.187	0.255	0.22	0.187	0.255	SUBCLONAL	1	TRUE	1	0.48	2		893	1081	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513754	41513754	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	267	758	0	ENST00000263253.7:c.658A>G	p.Thr220Ala	p.T220A	ENST00000263253	NM_001429.3	220	Act/Gct	2/31	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.48	2		758	997	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12647698	12647698	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	57	283	0	ENST00000251849.4:c.680+2T>C		p.X227_splice	ENST00000251849	NM_002880.3	227			1	2	FACETS	0.637	0.548	0.732	0.637	0.548	0.732	SUBCLONAL	1	TRUE	1	0.48	2		283	373	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713250	30713250	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	122	517	0	ENST00000295754.5:c.575A>G	p.Asn192Ser	p.N192S	ENST00000295754	NM_003242.5	192	aAc/aGc	4/7	1	2	FACETS	0.753	0.682	0.828	0.753	0.682	0.828	SUBCLONAL	1	TRUE	1	0.48	2		517	675	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182019	38182019	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	231	679	0	ENST00000396334.3:c.643A>G	p.Thr215Ala	p.T215A	ENST00000396334	NM_002468.4	215	Acc/Gcc	3/5	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.48	2		679	899	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098538	47098538	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	50	673	0	ENST00000409792.3:c.6736G>T	p.Gly2246Cys	p.G2246C	ENST00000409792	NM_014159.6	2246	Ggt/Tgt	15/21	1	2	FACETS	0.241	0.203	0.282	0.241	0.203	0.282	SUBCLONAL	1	TRUE	1	0.48	2		673	866	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098567	47098567	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	51	661	0	ENST00000409792.3:c.6707C>T	p.Ser2236Phe	p.S2236F	ENST00000409792	NM_014159.6	2236	tCc/tTc	15/21	1	2	FACETS	0.243	0.205	0.284	0.243	0.205	0.284	SUBCLONAL	1	TRUE	1	0.48	2		661	876	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940300	49940300	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	317	1044	0	ENST00000296474.3:c.743A>G	p.Glu248Gly	p.E248G	ENST00000296474	NM_002447.2	248	gAa/gGa	1/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.48	2		1044	1290	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	144	520	0	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	1	2	FACETS	0.853	0.78	0.93	0.853	0.78	0.93	CLONAL	1	TRUE	1	0.48	2		520	703	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281561	142281561	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	213	573	0	ENST00000350721.4:c.683T>C	p.Leu228Ser	p.L228S	ENST00000350721	NM_001184.3	228	tTa/tCa	4/47	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.48	2		573	854	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446247	187446247	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	268	880	2	ENST00000232014.4:c.1441C>T	p.Gln481Ter	p.Q481*	ENST00000232014	NM_001130845.1	481	Cag/Tag	6/10	1	2	FACETS	0.996	0.934	1	0.996	0.934	1	CLONAL	1	TRUE	1	0.48	2		882	1121	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748201	41748201	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	166	800	0	ENST00000226382.2:c.568A>G	p.Thr190Ala	p.T190A	ENST00000226382	NM_003924.3	190	Act/Gct	3/3	1	2	FACETS	0.699	0.642	0.759	0.699	0.642	0.759	SUBCLONAL	1	TRUE	1	0.48	2		800	989	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602961	55602961	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1201021287	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	86	357	0	ENST00000288135.5:c.2671A>G	p.Ser891Gly	p.S891G	ENST00000288135	NM_000222.2	891	Agc/Ggc	19/21	1	2	FACETS	0.64	0.567	0.717	0.64	0.567	0.717	SUBCLONAL	1	TRUE	1	0.48	2		357	560	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286237	66286238	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	24	378	0	ENST00000273854.3:c.1448dup	p.Asn483LysfsTer21	p.N483Kfs*21	ENST00000273854	NM_004439.5	483	aac/aaAc	6/18	1	2	FACETS	0.225	0.176	0.282	0.225	0.176	0.282	SUBCLONAL	1	TRUE	1	0.48	2		378	444	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356170	66356170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	44	585	0	ENST00000273854.3:c.1327G>A	p.Ala443Thr	p.A443T	ENST00000273854	NM_004439.5	443	Gca/Aca	5/18	1	2	FACETS	0.228	0.19	0.27	0.228	0.19	0.27	SUBCLONAL	1	TRUE	1	0.48	2		585	804	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196727	106196727	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	151	538	0	ENST00000380013.4:c.5060A>G	p.Gln1687Arg	p.Q1687R	ENST00000380013	NM_001127208.2	1687	cAg/cGg	11/11	1	2	FACETS	0.894	0.819	0.972	0.894	0.819	0.972	CLONAL	1	TRUE	1	0.48	2		538	704	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541628	187541628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	131	329	0	ENST00000441802.2:c.6112C>T	p.Pro2038Ser	p.P2038S	ENST00000441802	NM_005245.3	2038	Ccc/Tcc	10/27	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.48	2		329	516	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554939	187554939	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	146	393	0	ENST00000441802.2:c.4222A>G	p.Thr1408Ala	p.T1408A	ENST00000441802	NM_005245.3	1408	Act/Gct	7/27	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.48	2		393	582	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557782	187557782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200252550	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	98	398	0	ENST00000441802.2:c.3929C>T	p.Ser1310Leu	p.S1310L	ENST00000441802	NM_005245.3	1310	tCg/tTg	5/27	1	2	FACETS	0.763	0.683	0.848	0.763	0.683	0.848	SUBCLONAL	1	TRUE	1	0.48	2		398	535	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515235	31515235	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	65	849	0	ENST00000344624.3:c.1150T>C	p.Tyr384His	p.Y384H	ENST00000344624		384	Tat/Cat	5/33	1	2	FACETS	0.253	0.218	0.291	0.253	0.218	0.291	SUBCLONAL	1	TRUE	1	0.48	2		849	1071	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168732	56168732	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	42	475	0	ENST00000399503.3:c.1586C>T	p.Ala529Val	p.A529V	ENST00000399503	NM_005921.1	529	gCt/gTt	9/20	1	2	FACETS	0.237	0.197	0.282	0.237	0.197	0.282	SUBCLONAL	1	TRUE	1	0.48	2		475	737	SUCCESS
APC	324	MSKCC	GRCh37	5	112176674	112176674	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	101	248	0	ENST00000257430.4:c.5383T>A	p.Ser1795Thr	p.S1795T	ENST00000257430	NM_000038.5	1795	Tca/Aca	16/16	1	2	FACETS	0.981	0.882	1	0.981	0.882	1	CLONAL	1	TRUE	1	0.48	2		248	429	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721481	176721481	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	51	640	0	ENST00000439151.2:c.7112G>A	p.Arg2371Lys	p.R2371K	ENST00000439151	NM_022455.4	2371	aGg/aAg	23/23	1	2	FACETS	0.229	0.193	0.268	0.229	0.193	0.268	SUBCLONAL	1	TRUE	1	0.48	2		640	929	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046674	180046674	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	363	1149	0	ENST00000261937.6:c.2638A>G	p.Met880Val	p.M880V	ENST00000261937	NM_182925.4	880	Atg/Gtg	18/30	1	2	FACETS	0.992	0.939	1	0.992	0.939	1	CLONAL	1	TRUE	1	0.48	2		1149	1524	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052980	180052980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	341	1262	1	ENST00000261937.6:c.1310G>A	p.Arg437His	p.R437H	ENST00000261937	NM_182925.4	437	cGt/cAt	10/30	1	2	FACETS	0.992	0.937	1	0.992	0.937	1	CLONAL	1	TRUE	1	0.48	2		1263	1432	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481454	20481455	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	106	329	0	ENST00000346618.3:c.529dup	p.Thr177AsnfsTer4	p.T177Nfs*4	ENST00000346618	NM_001949.4	175	gaa/gAaa	3/7	1	2	FACETS	0.948	0.854	1	0.948	0.854	1	CLONAL	1	TRUE	1	0.48	2		329	466	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032258	26032258	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	124	442	0	ENST00000244661.2:c.31T>C	p.Ser11Pro	p.S11P	ENST00000244661	NM_003537.3	11	Tcc/Ccc	1/1	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.48	2		442	484	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858420	27858420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	220	764	0	ENST00000359303.2:c.151G>A	p.Glu51Lys	p.E51K	ENST00000359303	NM_003535.2	51	Gag/Aag	1/1	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.48	2		764	869	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670358	30670358	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	121	634	0	ENST00000376406.3:c.6074A>G	p.Tyr2025Cys	p.Y2025C	ENST00000376406	NM_014641.2	2025	tAc/tGc	14/15	1	2	FACETS	0.615	0.555	0.678	0.615	0.555	0.678	SUBCLONAL	1	TRUE	1	0.48	2		634	820	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815756	32815757	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	256	1044	0	ENST00000354258.4:c.1859dup	p.Gln621ThrfsTer13	p.Q621Tfs*13	ENST00000354258	NM_000593.5	620	gga/ggGa	8/11	1	2	FACETS	0.812	0.759	0.867	0.812	0.759	0.867	CLONAL	1	TRUE	1	0.48	2		1044	1314	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32819886	32819886	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	140	624	1	ENST00000354258.4:c.1024G>A	p.Gly342Ser	p.G342S	ENST00000354258	NM_000593.5	342	Ggt/Agt	3/11	1	2	FACETS	0.694	0.632	0.759	0.694	0.632	0.759	SUBCLONAL	1	TRUE	1	0.48	2		625	841	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790819	89790819	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	265	1088	5	ENST00000336032.3:c.211del	p.Gln71SerfsTer112	p.Q71Sfs*112	ENST00000336032	NM_006813.2	69	aCc/ac	1/2	1	2	FACETS	0.893	0.836	0.952	0.893	0.836	0.952	CLONAL	1	TRUE	1	0.48	2		1093	1236	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106543611	106543611	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	74	233	0	ENST00000369096.4:c.411+2T>C		p.X137_splice	ENST00000369096	NM_001198.3	137			1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.48	2		233	279	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552993	106552993	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	252	766	0	ENST00000369096.4:c.958A>G	p.Arg320Gly	p.R320G	ENST00000369096	NM_001198.3	320	Aga/Gga	5/7	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.48	2		766	998	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554787	106554787	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1442486319	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	121	354	0	ENST00000369096.4:c.1904T>C	p.Val635Ala	p.V635A	ENST00000369096	NM_001198.3	635	gTc/gCc	7/7	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.48	2		354	420	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112029124	112029124	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	90	321	0	ENST00000368678.4:c.443+1G>T		p.X148_splice	ENST00000368678		148			1	2	FACETS	0.889	0.793	0.989	0.889	0.793	0.989	CLONAL	1	TRUE	1	0.48	2		321	422	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196158	138196158	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	73	368	0	ENST00000237289.4:c.472T>C	p.Cys158Arg	p.C158R	ENST00000237289	NM_001270507.1	158	Tgc/Cgc	3/9	1	2	FACETS	0.613	0.537	0.694	0.613	0.537	0.694	SUBCLONAL	1	TRUE	1	0.48	2		368	496	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200122	138200122	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	143	635	0	ENST00000237289.4:c.1540A>T	p.Arg514Trp	p.R514W	ENST00000237289	NM_001270507.1	514	Agg/Tgg	7/9	1	2	FACETS	0.769	0.702	0.839	0.769	0.702	0.839	SUBCLONAL	1	TRUE	1	0.48	2		635	775	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2949762	2949762	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	249	872	0	ENST00000396946.4:c.3182C>T	p.Thr1061Ile	p.T1061I	ENST00000396946	NM_032415.4	1061	aCa/aTa	24/25	1	2	FACETS	0.903	0.844	0.964	0.903	0.844	0.964	CLONAL	1	TRUE	1	0.48	2		872	1149	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962853	2962854	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	200	1074	0	ENST00000396946.4:c.2054dup	p.Asn686GlnfsTer23	p.N686Qfs*23	ENST00000396946	NM_032415.4	685	ggc/ggGc	16/25	1	2	FACETS	0.616	0.569	0.665	0.616	0.569	0.665	SUBCLONAL	1	TRUE	1	0.48	2		1074	1353	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211049	55211049	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	176	554	0	ENST00000275493.2:c.292C>T	p.Arg98Ter	p.R98*	ENST00000275493	NM_005228.3	98	Cga/Tga	3/28	1	2	FACETS	0.925	0.853	0.999	0.925	0.853	0.999	CLONAL	1	TRUE	1	0.48	2		554	793	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55269042	55269042	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	180	701	1	ENST00000275493.2:c.3108C>A	p.Ser1036Arg	p.S1036R	ENST00000275493	NM_005228.3	1036	agC/agA	25/28	1	2	FACETS	0.78	0.719	0.843	0.78	0.719	0.843	SUBCLONAL	1	TRUE	1	0.48	2		702	962	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392132	81392132	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	100	387	0	ENST00000222390.5:c.145A>G	p.Thr49Ala	p.T49A	ENST00000222390	NM_000601.4	49	Acc/Gcc	2/18	1	2	FACETS	0.847	0.76	0.939	0.847	0.76	0.939	CLONAL	1	TRUE	1	0.48	2		387	492	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508560	106508560	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	33	547	0	ENST00000359195.3:c.554T>C	p.Met185Thr	p.M185T	ENST00000359195	NM_002649.2	185	aTg/aCg	2/11	1	2	FACETS	0.211	0.171	0.256	0.211	0.171	0.256	SUBCLONAL	1	TRUE	1	0.48	2		547	653	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148507423	148507423	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	89	443	0	ENST00000320356.2:c.2029+2T>C		p.X677_splice	ENST00000320356	NM_004456.4	677			1	2	FACETS	0.6	0.533	0.672	0.6	0.533	0.672	SUBCLONAL	1	TRUE	1	0.48	2		443	618	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835931	151835932	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	168	440	0	ENST00000262189.6:c.14592_14593del	p.Gly4865ThrfsTer20	p.G4865Tfs*20	ENST00000262189	NM_170606.2	4864	agAGga/agga	58/59	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.48	2		440	674	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874632	151874632	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	106	517	0	ENST00000262189.6:c.7906G>T	p.Gly2636Cys	p.G2636C	ENST00000262189	NM_170606.2	2636	Ggt/Tgt	38/59	1	2	FACETS	0.704	0.633	0.78	0.704	0.633	0.78	SUBCLONAL	1	TRUE	1	0.48	2		517	627	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146259	38146259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	166	624	0	ENST00000317025.8:c.3247G>A	p.Gly1083Arg	p.G1083R	ENST00000317025	NM_023034.1	1083	Gga/Aga	19/24	1	2	FACETS	0.856	0.787	0.928	0.856	0.787	0.928	CLONAL	1	TRUE	1	0.48	2		624	808	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273494	38273494	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1338	85	1176	0	ENST00000425967.3:c.1841A>G	p.Tyr614Cys	p.Y614C	ENST00000425967	NM_001174067.1	614	tAc/tGc	14/19	1	2	FACETS	0.249	0.219	0.281	0.249	0.219	0.281	SUBCLONAL	1	TRUE	1	0.48	2		1176	1423	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287386	38287386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1162148796	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	282	909	1	ENST00000425967.3:c.271C>T	p.Arg91Trp	p.R91W	ENST00000425967	NM_001174067.1	91	Cgg/Tgg	4/19	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.48	2		910	1103	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372025	55372025	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	134	759	0	ENST00000297316.4:c.715G>A	p.Ala239Thr	p.A239T	ENST00000297316	NM_022454.3	239	Gcc/Acc	2/2	1	2	FACETS	0.653	0.593	0.716	0.653	0.593	0.716	SUBCLONAL	1	TRUE	1	0.48	2		759	855	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738976	145738976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773424301	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	244	901	1	ENST00000428558.2:c.2179G>A	p.Ala727Thr	p.A727T	ENST00000428558	NM_004260.3	727	Gcc/Acc	13/22	1	2	FACETS	0.965	0.902	1	0.965	0.902	1	CLONAL	1	TRUE	1	0.48	2		902	1053	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741569	145741569	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	320	1111	1	ENST00000428558.2:c.934A>G	p.Ser312Gly	p.S312G	ENST00000428558	NM_004260.3	312	Agc/Ggc	5/22	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.48	2		1112	1322	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5070018	5070018	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	105	372	0	ENST00000381652.3:c.1607T>C	p.Val536Ala	p.V536A	ENST00000381652	NM_004972.3	536	gTg/gCg	12/25	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.48	2		372	419	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457091	5457091	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143235887	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	86	294	0	ENST00000381577.3:c.65C>T	p.Thr22Met	p.T22M	ENST00000381577	NM_014143.3	22	aCg/aTg	3/7	1	2	FACETS	0.916	0.816	1	0.916	0.816	1	CLONAL	1	TRUE	1	0.48	2		294	391	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471080	8471080	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	80	274	0	ENST00000356435.5:c.3419A>G	p.Tyr1140Cys	p.Y1140C	ENST00000356435		1140	tAc/tGc	20/35	1	2	FACETS	0.866	0.767	0.971	0.866	0.767	0.971	CLONAL	1	TRUE	1	0.48	2		274	385	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970981	21970981	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs104894098	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	316	1142	0	ENST00000304494.5:c.377T>A	p.Val126Asp	p.V126D	ENST00000304494	NM_000077.4	126	gTc/gAc	2/3	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.48	2		1142	1168	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971054	21971054	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs774904310	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	130	908	0	ENST00000304494.5:c.304del	p.Ala102ArgfsTer44	p.A102Rfs*44	ENST00000304494	NM_000077.4	102	Gcg/cg	2/3	1	2	FACETS	0.581	0.527	0.639	0.581	0.527	0.639	SUBCLONAL	1	TRUE	1	0.48	2		908	932	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971193	21971193	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	207	658	1	ENST00000579755.1:c.208C>T	p.Gln70Ter	p.Q70*	ENST00000579755		70	Cag/Tag	2/3	1	2	FACETS	0.986	0.916	1	0.986	0.916	1	CLONAL	1	TRUE	1	0.48	2		659	875	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430682	80430682	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs761095319	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	89	528	0	ENST00000286548.4:c.326A>G	p.His109Arg	p.H109R	ENST00000286548	NM_002072.3	109	cAt/cGt	3/7	1	2	FACETS	0.579	0.513	0.648	0.579	0.513	0.648	SUBCLONAL	1	TRUE	1	0.48	2		528	641	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97873921	97873921	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1343170313	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	134	642	0	ENST00000289081.3:c.1155-2A>G		p.X385_splice	ENST00000289081	NM_000136.2	385			1	2	FACETS	0.67	0.609	0.735	0.67	0.609	0.735	SUBCLONAL	1	TRUE	1	0.48	2		642	833	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232165	98232165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	125	397	0	ENST00000331920.6:c.1777C>T	p.Pro593Ser	p.P593S	ENST00000331920	NM_000264.3	593	Cct/Tct	13/24	1	2	FACETS	0.837	0.76	0.918	0.837	0.76	0.918	CLONAL	1	TRUE	1	0.48	2		397	622	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900288	101900288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111854391	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	146	442	1	ENST00000374994.4:c.722C>T	p.Ser241Leu	p.S241L	ENST00000374994	NM_004612.2	241	tCg/tTg	4/9	1	2	FACETS	0.958	0.877	1	0.958	0.877	1	CLONAL	1	TRUE	1	0.48	2		443	635	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730389	133730389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	223	616	0	ENST00000318560.5:c.455G>A	p.Arg152His	p.R152H	ENST00000318560	NM_005157.4	152	cGt/cAt	3/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.48	2		616	807	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781193	135781193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768985094	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	208	800	1	ENST00000298552.3:c.1772C>T	p.Pro591Leu	p.P591L	ENST00000298552	NM_001162426.1	591	cCg/cTg	15/23	1	2	FACETS	0.899	0.835	0.966	0.899	0.835	0.966	CLONAL	1	TRUE	1	0.48	2		801	964	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942755	44942755	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	181	350	0	ENST00000377967.4:c.3335T>C	p.Val1112Ala	p.V1112A	ENST00000377967	NM_021140.2	1112	gTc/gCc	23/29	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.48	1		350	440	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411596	63411596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1386291582	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	248	486	0	ENST00000330258.3:c.1571G>A	p.Cys524Tyr	p.C524Y	ENST00000330258	NM_152424.3	524	tGc/tAc	2/2	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.48	1		486	558	SUCCESS
BTK	695	MSKCC	GRCh37	X	100629549	100629549	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	139	313	0	ENST00000308731.7:c.215del	p.Asn72IlefsTer49	p.N72Ifs*49	ENST00000308731	NM_000061.2	72	aAt/at	3/19	1	1	FACETS	0.957	0.878	1	0.957	0.878	1	CLONAL	1	TRUE	0	0.48	1		313	460	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181339	123181339	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	71	149	0	ENST00000218089.9:c.803T>C	p.Leu268Pro	p.L268P	ENST00000218089	NM_001042749.1	268	cTa/cCa	9/35	1	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.48	1		149	177	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220437	123220437	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	65	291	0	ENST00000218089.9:c.3094C>A	p.Leu1032Ile	p.L1032I	ENST00000218089	NM_001042749.1	1032	Ctc/Atc	30/35	1	1	FACETS	0.503	0.438	0.574	0.503	0.438	0.574	SUBCLONAL	1	TRUE	0	0.48	1		291	409	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324892	31324892	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs765875917	NA	P-0049585-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	40	139	0	ENST00000412585.2:c.44del	p.Ala15GlyfsTer5	p.A15Gfs*5	ENST00000412585	NM_005514.6	15	gCg/gg	1/8	1	2	FACETS	0.246	0.204	0.294	0.246	0.204	0.294	SUBCLONAL	1	TRUE	1	0.48	2		139	677	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0049586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	177	263	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.271364195131443	4	FACETS	1	0.931	1	1	0.931	1	CLONAL	3	TRUE	1	0.289533495392402	4		263	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0049586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	305	559	0	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.289533495392402	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.289533495392402	2		559	948	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856655	111856655	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1014425313	NA	P-0049586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	178	573	0	ENST00000341259.2:c.706G>A	p.Val236Met	p.V236M	ENST00000341259	NM_005475.2	236	Gtg/Atg	2/8	0.279746258578307	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	2	0.289533495392402	4		573	757	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259504	16259528	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCCTTCTGAGGAAGGAATGGAGA	CAGCCTTCTGAGGAAGGAATGGAGA	-	novel	NA	P-0049586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	143	584	0	ENST00000375759.3:c.6772_6796del	p.Pro2258MetfsTer87	p.P2258Mfs*87	ENST00000375759	NM_015001.2	2257	CAGCCTTCTGAGGAAGGAATGGAGAca/ca	11/15	0.251723676789409	3	FACETS	0.836	0.764	0.912	0.836	0.764	0.912	CLONAL	2	TRUE	1	0.289533495392402	3		584	676	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004563	16004563	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0049586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	110	397	0	ENST00000268712.3:c.2690+1G>A		p.X897_splice	ENST00000268712	NM_006311.3	897			0.289533495392402	2	FACETS	0.995	0.902	1	0.995	0.902	1	CLONAL	2	TRUE	0	0.289533495392402	2		397	382	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245451	153245451	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	153	565	0	ENST00000281708.4:c.1740C>G	p.His580Gln	p.H580Q	ENST00000281708	NM_033632.3	580	caC/caG	11/12	0.289533495392402	2	FACETS	0.897	0.825	0.972	0.897	0.825	0.972	CLONAL	2	TRUE	0	0.289533495392402	2		565	589	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662561	117662561	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0049586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	58	378	0	ENST00000368508.3:c.4902+2T>C		p.X1634_splice	ENST00000368508	NM_002944.2	1634			1	2	FACETS	0.992	0.855	1	0.992	0.855	1	CLONAL	1	TRUE	1	0.289533495392402	2		378	404	SUCCESS
REL	5966	MSKCC	GRCh37	2	61144108	61144108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781499490	NA	P-0049590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	127	518	2	ENST00000295025.8:c.491C>T	p.Thr164Met	p.T164M	ENST00000295025	NM_002908.2	164	aCg/aTg	5/11	1	2	FACETS	0.931	0.852	1	0.931	0.852	1	CLONAL	1	TRUE	1	0.68532500759102	2		520	398	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140487360	140487360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507472	NA	P-0049590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	214	561	0	ENST00000288602.6:c.1165C>T	p.Arg389Cys	p.R389C	ENST00000288602	NM_004333.4	389	Cgt/Tgt	9/18	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.68532500759102	2		561	574	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37671997	37671997	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267604832	NA	P-0049590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	184	525	0	ENST00000447079.4:c.2782G>A	p.Glu928Lys	p.E928K	ENST00000447079	NM_015083.1	928	Gaa/Aaa	9/14	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.68532500759102	2		525	496	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720928	119720928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	203	512	1	ENST00000316626.5:c.247G>A	p.Ala83Thr	p.A83T	ENST00000316626		83	Gcc/Acc	2/12	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.68532500759102	2		513	576	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839678	42839678	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1268	307	791	0	ENST00000398585.3:c.1561A>T	p.Ile521Phe	p.I521F	ENST00000398585	NM_001135099.1	521	Att/Ttt	13/14	0.68532500759102	4	FACETS	0.959	0.901	1	0.32	0.3	0.34	CLONAL	1	TRUE	1	0.68532500759102	4		791	1575	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	167	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.842	0.781	0.905	0.842	0.781	0.905	CLONAL	1	TRUE	1	0.858411990504358	2		148	462	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874529	155874529	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	250	481	0	ENST00000368323.3:c.230C>G	p.Ala77Gly	p.A77G	ENST00000368323	NM_006912.5	77	gCt/gGt	4/6	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.858411990504358	2		481	550	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27190556	27190556	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373235916	NA	P-0049591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	316	612	0	ENST00000380036.4:c.1357G>A	p.Val453Met	p.V453M	ENST00000380036	NM_000459.3	453	Gtg/Atg	10/23	1	2	FACETS	0.932	0.884	0.981	0.932	0.884	0.981	CLONAL	1	TRUE	1	0.858411990504358	2		612	790	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923410	9923410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	304	622	1	ENST00000330684.3:c.1877C>T	p.Thr626Ile	p.T626I	ENST00000330684	NM_001134407.1	626	aCc/aTc	9/13	1	2	FACETS	0.933	0.884	0.983	0.933	0.884	0.983	CLONAL	1	TRUE	1	0.858411990504358	2		623	759	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188999	142188999	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	123	384	0	ENST00000350721.4:c.6248T>G	p.Ile2083Arg	p.I2083R	ENST00000350721	NM_001184.3	2083	aTa/aGa	37/47	1	2	FACETS	0.988	0.909	1	0.988	0.909	1	CLONAL	1	TRUE	1	0.858411990504358	2		384	290	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240729	55240729	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8584	6273	909	0	ENST00000275493.2:c.1973T>A	p.Leu658Gln	p.L658Q	ENST00000275493	NM_005228.3	658	cTg/cAg	17/28	0.858411990504358	19	FACETS	1	0.996	1	0.453	0.448	0.459	CLONAL	8	TRUE	1	0.858411990504358	19		909	14857	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0049592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	10	549	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	0.646875300209139	1	FACETS	0.06	0.04	0.085	0.06	0.04	0.085	SUBCLONAL	1	TRUE	0	0.77025721662576	1		549	266	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665042	29665042	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1060500356	NA	P-0049593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	259	431	0	ENST00000356175.3:c.6642-1G>A		p.X2214_splice	ENST00000356175	NM_000267.3	2214			0.931865191411554	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.931865191411554	1		431	286	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732469	74732469	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	442	428	0	ENST00000359995.5:c.440C>G	p.Ser147Trp	p.S147W	ENST00000359995	NM_001195427.1	147	tCg/tGg	2/3	0.605410085851995	3	FACETS	1	0.97	1			1	CLONAL	2	TRUE	NA	0.931865191411554	3		428	692	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534285	534285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894226	NA	P-0049593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	367	896	0	ENST00000451590.1:c.38G>A	p.Gly13Asp	p.G13D	ENST00000451590	NM_001130442.1	13	gGt/gAt	2/5	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.931865191411554	2		896	763	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468517	89468517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372257039	NA	P-0049593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	189	341	0	ENST00000336596.2:c.2051G>A	p.Arg684Gln	p.R684Q	ENST00000336596	NM_005233.5	684	cGa/cAa	11/17	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.931865191411554	2		341	405	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652009	36652010	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0049593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	80	1196	0	ENST00000244741.5:c.133dup	p.Ala45GlyfsTer3	p.A45Gfs*3	ENST00000244741	NM_000389.4	44	gag/gaGg	2/3	1	2	FACETS	0.158	0.138	0.179	0.158	0.138	0.179	SUBCLONAL	1	TRUE	1	0.931865191411554	2		1196	1090	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62323143	62323143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	417	797	0	ENST00000360203.5:c.2605G>A	p.Glu869Lys	p.E869K	ENST00000360203	NM_001283009.1	869	Gaa/Aaa	28/35	1	2	FACETS	0.952	0.911	0.994	0.952	0.911	0.994	CLONAL	1	TRUE	1	0.931865191411554	2		797	940	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522385	176522385	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	179	1072	1	ENST00000292408.4:c.1574A>G	p.Lys525Arg	p.K525R	ENST00000292408	NM_213647.1	525	aAg/aGg	12/18	1	2	FACETS	0.358	0.329	0.388	0.358	0.329	0.388	SUBCLONAL	1	TRUE	1	0.931865191411554	2		1073	1074	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0049595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	1002	1024	1	ENST00000269305.4:c.394A>T	p.Lys132Ter	p.K132*	ENST00000269305	NM_001126112.2	132	Aag/Tag	5/11	0.602709402791366	3	FACETS	0.958	0.938	0.977	0.958	0.938	0.977	CLONAL	3	TRUE	0	0.673252287480213	3		1025	1385	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590844	95590844	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	112	411	0	ENST00000393063.1:c.1065A>G	p.Ile355Met	p.I355M	ENST00000393063	NM_030621.3	355	atA/atG	9/28	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.673252287480213	2		411	293	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565526	41565526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	84	344	0	ENST00000263253.7:c.4192C>T	p.Leu1398Phe	p.L1398F	ENST00000263253	NM_001429.3	1398	Ctc/Ttc	26/31	1	2	FACETS	0.858	0.766	0.953	0.858	0.766	0.953	CLONAL	1	TRUE	1	0.673252287480213	2		344	291	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518427	69518427	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2276	605	218	0	ENST00000294312.3:c.218G>T	p.Gly73Val	p.G73V	ENST00000294312	NM_005117.2	73	gGc/gTc	1/3	0.673252287480213	23	FACETS	1	0.963	1			1	CLONAL	5	TRUE	NA	0.673252287480213	23		218	2881	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577457	64577457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1565652689	NA	P-0049595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	79	809	0	ENST00000312049.6:c.125G>T	p.Gly42Val	p.G42V	ENST00000312049	NM_130799.2	42	gGc/gTc	2/10	0.54007185277013	4	FACETS	0.418	0.367	0.474	0.139	0.122	0.158	SUBCLONAL	1	TRUE	1	0.673252287480213	4		809	939	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431357	49431357	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	221	748	0	ENST00000301067.7:c.9782A>C	p.Gln3261Pro	p.Q3261P	ENST00000301067	NM_003482.3	3261	cAg/cCg	34/54	0.602709402791366	3	FACETS	1	0.992	1	0.47	0.44	0.501	CLONAL	1	TRUE	0	0.673252287480213	3		748	622	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811771	102811771	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	74	615	0	ENST00000307046.8:c.413C>A	p.Pro138Gln	p.P138Q	ENST00000307046	NM_001111285.1	138	cCa/cAa	4/4	0.668191787767333	3	FACETS	0.353	0.308	0.401	0.118	0.102	0.134	SUBCLONAL	1	TRUE	0	0.673252287480213	3		615	833	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341275	89341275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	89	358	0	ENST00000301030.4:c.7660G>A	p.Ala2554Thr	p.A2554T	ENST00000301030	NM_001256183.1	2554	Gcc/Acc	11/13	0.658216711703187	2	FACETS	0.722	0.645	0.803	0.361	0.322	0.402	SUBCLONAL	1	TRUE	0	0.673252287480213	2		358	366	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584499	187584524	+	frameshift_variant	Frame_Shift_Del	DEL	AATTTTGTACATGAGCTTGTCATTAG	AATTTTGTACATGAGCTTGTCATTAG	-	novel	NA	P-0049595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	233	452	0	ENST00000441802.2:c.3509_3534del	p.Ser1170TyrfsTer14	p.S1170Yfs*14	ENST00000441802	NM_005245.3	1170	tCTAATGACAAGCTCATGTACAAAATT/t	3/27	0.665183204002407	2	FACETS	0.946	0.901	0.989	0.946	0.901	0.989	CLONAL	2	TRUE	0	0.673252287480213	2		452	366	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146219	38146219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1218	291	726	0	ENST00000317025.8:c.3287C>T	p.Pro1096Leu	p.P1096L	ENST00000317025	NM_023034.1	1096	cCc/cTc	19/24	0.543344534281146	4	FACETS	0.959	0.9	1	0.32	0.3	0.34	CLONAL	1	TRUE	1	0.673252287480213	4		726	1509	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207509	29207513	+	missense_variant	Missense_Mutation	ONP	CGGGC	CGGGC	TGGGG	novel	NA	P-0049595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	242	810	0	ENST00000240100.2:c.283_287delinsCCCCA	p.Ala95_Arg96delinsProHis	p.A95_R96delinsPH	ENST00000240100	NM_001394.6	95	GCCCGc/CCCCAc	1/4	0.673252287480213	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.673252287480213	1		810	463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579359	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGTTTT	novel	NA	P-0049596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	319	1005	3	ENST00000269305.4:c.328_329insAAAACC	p.Phe109_Arg110insGlnAsn	p.F109_R110insQN	ENST00000269305	NM_001126112.2	110	cgt/cAAAACCgt	4/11	0.455818858896608	2	FACETS	0.86	0.815	0.904	0.86	0.815	0.904	CLONAL	2	TRUE	0	0.461617831263137	2		1008	804	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632386	1632386	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	142	1065	0	ENST00000344749.5:c.164G>T	p.Ser55Ile	p.S55I	ENST00000344749	NM_001136139.2	55	aGc/aTc	4/19	NA	2	FACETS	0.763	0.696	0.834			1	INDETERMINATE	1	TRUE	NA	0.461617831263137	2		1065	806	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390879	139390880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTCTC	novel	NA	P-0049596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	492	1411	8	ENST00000277541.6:c.7307_7311dup	p.Pro2438GlufsTer41	p.P2438Efs*41	ENST00000277541	NM_017617.3	2437	-/GAGAG	34/34	0.411516839953322	3	FACETS	1	0.994	1	0.796	0.765	0.828	CLONAL	2	TRUE	0	0.461617831263137	3		1419	1098	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	62	148	0				ENST00000310581	NM_198253.2	-/1132			0.099817923256754	4	FACETS	0.844	0.732	0.964	0.844	0.732	0.964	INDETERMINATE	2	TRUE	2	0.23208896259368	4		148	390	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733217	40733217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	52	570	0	ENST00000373198.4:c.3589G>A	p.Glu1197Lys	p.E1197K	ENST00000373198	NM_133170.3	1197	Gaa/Aaa	26/32	1	2	FACETS	0.668	0.568	0.778	0.668	0.568	0.778	SUBCLONAL	1	TRUE	1	0.23208896259368	2		570	671	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030637	47030637	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	144	1032	0	ENST00000377604.3:c.412C>T	p.Gln138Ter	p.Q138*	ENST00000377604	NM_001204468.1	138	Cag/Tag	4/24	0.183219335876082	2	FACETS	1	0.987	1	0.738	0.673	0.806	CLONAL	1	TRUE	0	0.23208896259368	2		1032	841	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252856	36252856	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	88	352	0	ENST00000300305.3:c.506G>C	p.Arg169Thr	p.R169T	ENST00000300305		169	aGa/aCa	4/8	0.183281042712391	2	FACETS	0.98	0.874	1	0.98	0.874	1	CLONAL	2	TRUE	0	0.23208896259368	2		352	387	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983150	201983150	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	145	725	1	ENST00000359651.3:c.999G>A	p.Met333Ile	p.M333I	ENST00000359651		333	atG/atA	7/8	0.226812931100164	3	FACETS	1	0.919	1	1	0.919	1	CLONAL	2	TRUE	1	0.23208896259368	3		726	694	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349257	15349553	+	splice_donor_variant,splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTGGAGGAGAAAGGAAGGAGGGAGTCAGGAGGATGACCTAGCCACCCTGCAGCTACAAGCCCTCATACCCGCTACCAGCAGTCAGCCCCGTAGCCCTCCCCGTGGCTGACCCCTCATAGCGCTCACCCCGTCCACACAGCACTCAGGGCCCTACAGCTGAGTCCAGAGGACCACATGCCGACCAGCAGGGACGGGGCTCCCCCGCTGCCCCTCCCTGTCCAGGCTCCAGTCCCCCTTTCCCAGCTCCCTCAGGAGCTAATCCTTAGACCAGGGTCCCCACCAGGCCTCCAGACTCAC	CTGGAGGAGAAAGGAAGGAGGGAGTCAGGAGGATGACCTAGCCACCCTGCAGCTACAAGCCCTCATACCCGCTACCAGCAGTCAGCCCCGTAGCCCTCCCCGTGGCTGACCCCTCATAGCGCTCACCCCGTCCACACAGCACTCAGGGCCCTACAGCTGAGTCCAGAGGACCACATGCCGACCAGCAGGGACGGGGCTCCCCCGCTGCCCCTCCCTGTCCAGGCTCCAGTCCCCCTTTCCCAGCTCCCTCAGGAGCTAATCCTTAGACCAGGGTCCCCACCAGGCCTCCAGACTCAC	-	novel	NA	P-0049597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	34	503	1	ENST00000263377.2:c.4020+1_4021-1del		p.X1340_splice	ENST00000263377	NM_058243.2	1340			0.226812931100164	3	FACETS	0.637	0.52	0.77	0.319	0.26	0.385	SUBCLONAL	1	TRUE	1	0.23208896259368	3		504	513	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796325	42796325	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	126	1084	0	ENST00000575354.2:c.2974C>G	p.Gln992Glu	p.Q992E	ENST00000575354	NM_015125.3	992	Cag/Gag	12/20	0.226812931100164	3	FACETS	1	0.978	1	0.644	0.582	0.709	CLONAL	1	TRUE	1	0.23208896259368	3		1084	941	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213589	27213589	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	230	476	0	ENST00000380036.4:c.2985G>C	p.Lys995Asn	p.K995N	ENST00000380036	NM_000459.3	995	aaG/aaC	18/23	0.23208896259368	4	FACETS	0.948	0.889	1	0.948	0.889	1	CLONAL	4	TRUE	0	0.23208896259368	4		476	644	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0049598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	433	605	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.534599952248087	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.534599952248087	1		606	1155	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771344	68771344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555509646	NA	P-0049598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	81	615	0	ENST00000261769.5:c.26C>T	p.Ser9Leu	p.S9L	ENST00000261769	NM_004360.3	9	tCg/tTg	1/16	0.224698470045137	5	FACETS	0.507	0.445	0.573	0.169	0.148	0.191	INDETERMINATE	1	TRUE	2	0.534599952248087	5		615	1078	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428225	33428225	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs750621215	NA	P-0049598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	101	723	0	ENST00000345365.6:c.898C>T	p.Arg300Ter	p.R300*	ENST00000345365	NM_002878.3	300	Cga/Tga	9/10	0.534599952248087	1	FACETS	0.373	0.333	0.415	0.373	0.333	0.415	SUBCLONAL	1	TRUE	0	0.534599952248087	1		723	743	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275290	115275290	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	29	733	0	ENST00000438362.2:c.1123G>C	p.Glu375Gln	p.E375Q	ENST00000438362	NM_001242891.1	375	Gag/Cag	10/20	0.534599952248087	1	FACETS	0.256	0.206	0.314	0.256	0.206	0.314	SUBCLONAL	1	TRUE	0	0.534599952248087	1		733	310	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426889	49426890	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	AA	novel	NA	P-0049598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	288	805	0	ENST00000301067.7:c.11598_11599delinsTT	p.Gln3866_Gln3867delinsHisTer	p.Q3866_Q3867delinsH*	ENST00000301067	NM_003482.3	3866	caGCaa/caTTaa	39/54	0.481708017142887	2	FACETS	0.84	0.797	0.884	0.84	0.797	0.884	CLONAL	2	TRUE	0	0.534599952248087	2		805	641	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89865574	89865574	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	514	706	0	ENST00000389301.3:c.893G>C	p.Trp298Ser	p.W298S	ENST00000389301	NM_000135.2	298	tGg/tCg	10/43	0.224698470045137	5	FACETS	0.842	0.808	0.878	0.842	0.808	0.878	INDETERMINATE	3	TRUE	2	0.534599952248087	5		706	1371	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16062082	16062082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	92	475	0	ENST00000268712.3:c.724G>A	p.Glu242Lys	p.E242K	ENST00000268712	NM_006311.3	242	Gag/Aag	6/46	0.534599952248087	1	FACETS	0.793	0.712	0.877	0.793	0.712	0.877	SUBCLONAL	1	TRUE	0	0.534599952248087	1		475	318	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16062148	16062148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	241	710	1	ENST00000268712.3:c.658G>A	p.Glu220Lys	p.E220K	ENST00000268712	NM_006311.3	220	Gag/Aag	6/46	0.534599952248087	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.534599952248087	1		711	624	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159101	24159101	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	68	652	0	ENST00000263121.7:c.773C>A	p.Ser258Ter	p.S258*	ENST00000263121	NM_003073.3	258	tCa/tAa	6/9	0.219131279398766	2	FACETS	0.228	0.197	0.261	0.114	0.098	0.131	INDETERMINATE	1	TRUE	0	0.534599952248087	2		652	1118	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138383966	138383966	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	76	601	1	ENST00000289153.2:c.2584G>C	p.Asp862His	p.D862H	ENST00000289153	NM_006219.2	862	Gac/Cac	18/22	0.337226428723931	2	FACETS	0.516	0.453	0.583	0.258	0.226	0.292	SUBCLONAL	1	TRUE	0	0.534599952248087	2		602	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863224683	NA	P-0049599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	635	1092	0	ENST00000269305.4:c.388C>G	p.Leu130Val	p.L130V	ENST00000269305	NM_001126112.2	130	Ctc/Gtc	5/11	0.909216576294589	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.917098619139049	1		1092	726	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	193	467	6	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.38	2		473	705	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	144	590	2	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	2	FACETS	0.818	0.745	0.894	0.818	0.745	0.894	CLONAL	1	TRUE	1	0.38	2		592	927	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	60	263	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.892	0.773	1	0.892	0.773	1	CLONAL	1	TRUE	1	0.38	2		263	354	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	60	397	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.921	0.798	1	0.921	0.798	1	CLONAL	1	TRUE	1	0.38	2		397	343	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434367	121434367	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	172	628	0	ENST00000257555.6:c.1136del	p.Pro379LeufsTer5	p.P379Lfs*5	ENST00000257555		377	ctC/ct	6/10	1	2	FACETS	0.979	0.901	1	0.979	0.901	1	CLONAL	1	TRUE	1	0.38	2		628	925	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	59	208	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.802	0.693	0.92	0.802	0.693	0.92	CLONAL	1	TRUE	1	0.38	2		208	387	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	77	272	0	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	1	2	FACETS	0.97	0.855	1	0.97	0.855	1	CLONAL	1	TRUE	1	0.38	2		272	418	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	58	183	0	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.906	0.783	1	0.906	0.783	1	CLONAL	1	TRUE	1	0.38	2		183	337	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042483	42042483	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	97	368	0	ENST00000219905.7:c.6682del	p.Ser2228ValfsTer10	p.S2228Vfs*10	ENST00000219905	NM_001164273.1	2226	ggA/gg	17/24	1	2	FACETS	0.91	0.813	1	0.91	0.813	1	CLONAL	1	TRUE	1	0.38	2		368	561	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860604	45860604	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	226	705	0	ENST00000391945.4:c.1403C>A	p.Pro468His	p.P468H	ENST00000391945	NM_000400.3	468	cCc/cAc	15/23	1	2	FACETS	0.986	0.917	1	0.986	0.917	1	CLONAL	1	TRUE	1	0.38	2		705	1206	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561424	9561424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1234148699	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	102	355	0	ENST00000353224.5:c.358G>A	p.Ala120Thr	p.A120T	ENST00000353224	NM_177990.2	120	Gcg/Acg	4/10	1	2	FACETS	0.785	0.702	0.872	0.785	0.702	0.872	SUBCLONAL	1	TRUE	1	0.38	2		355	684	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054541	42054541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1458609443	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	105	288	0	ENST00000219905.7:c.7731del	p.Asp2578ThrfsTer10	p.D2578Tfs*10	ENST00000219905	NM_001164273.1	2575	agA/ag	22/24	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.38	2		288	487	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438211	49438211	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	146	416	2	ENST00000301067.7:c.5058del	p.Lys1686AsnfsTer36	p.K1686Nfs*36	ENST00000301067	NM_003482.3	1686	aaA/aa	20/54	1	2	FACETS	0.913	0.833	0.996	0.913	0.833	0.996	CLONAL	1	TRUE	1	0.38	2		418	842	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323362	31323363	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748204482	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	82	318	0	ENST00000412585.2:c.626dup	p.Thr211AspfsTer10	p.T211Dfs*10	ENST00000412585	NM_005514.6	209	cca/ccCa	4/8	1	2	FACETS	0.841	0.744	0.945	0.841	0.744	0.945	CLONAL	1	TRUE	1	0.38	2		318	513	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	155	667	2	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	1	2	FACETS	0.729	0.666	0.795	0.729	0.666	0.795	SUBCLONAL	1	TRUE	1	0.38	2		669	1119	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858047	45858047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142568756	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	178	595	0	ENST00000391945.4:c.1606G>A	p.Val536Met	p.V536M	ENST00000391945	NM_000400.3	536	Gtg/Atg	17/23	1	2	FACETS	0.998	0.92	1	0.998	0.92	1	CLONAL	1	TRUE	1	0.38	2		595	939	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998164	169998165	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	119	352	0	ENST00000295797.4:c.861dup	p.Glu288ArgfsTer4	p.E288Rfs*4	ENST00000295797	NM_002740.5	285	-/A	9/18	1	2	FACETS	0.904	0.817	0.995	0.904	0.817	0.995	CLONAL	1	TRUE	1	0.38	2		352	693	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250430	26250431	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs778901635	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	112	405	0	ENST00000446824.2:c.403_404del	p.Arg135GlyfsTer?	p.R135Gfs*?	ENST00000446824	NM_021018.2	135	AGg/g	1/1	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.38	2		405	586	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323253	31323253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45445194	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	98	279	0	ENST00000412585.2:c.736G>A	p.Glu246Lys	p.E246K	ENST00000412585	NM_005514.6	246	Gag/Aag	4/8	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.38	2		279	442	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976953	18976953	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764484697	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	119	441	0	ENST00000262803.5:c.3338C>T	p.Thr1113Met	p.T1113M	ENST00000262803	NM_002911.3	1113	aCg/aTg	23/24	1	2	FACETS	0.908	0.82	1	0.908	0.82	1	CLONAL	1	TRUE	1	0.38	2		441	690	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796340	42796340	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	250	638	1	ENST00000575354.2:c.2989C>A	p.Leu997Met	p.L997M	ENST00000575354	NM_015125.3	997	Ctg/Atg	12/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.38	2		639	1141	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999153	100999153	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	142	656	2	ENST00000325455.5:c.649G>A	p.Ala217Thr	p.A217T	ENST00000325455	NM_001202474.3	217	Gct/Act	1/8	1	2	FACETS	0.781	0.711	0.854	0.781	0.711	0.854	SUBCLONAL	1	TRUE	1	0.38	2		658	957	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156139	119156140	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	159	455	0	ENST00000264033.4:c.1808dup	p.Ser604LysfsTer4	p.S604Kfs*4	ENST00000264033	NM_005188.3	602	gcc/gCcc	11/16	1	2	FACETS	0.932	0.854	1	0.932	0.854	1	CLONAL	1	TRUE	1	0.38	2		455	898	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446370	49446371	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	168	497	0	ENST00000301067.7:c.1234_1235insA	p.Leu412HisfsTer4	p.L412Hfs*4	ENST00000301067	NM_003482.3	412	ctg/cAtg	9/54	1	2	FACETS	0.985	0.905	1	0.985	0.905	1	CLONAL	1	TRUE	1	0.38	2		497	898	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934321	81934321	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	202	534	1	ENST00000359376.3:c.1298C>A	p.Pro433His	p.P433H	ENST00000359376	NM_002661.3	433	cCc/cAc	14/33	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.38	2		535	933	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609350	39609350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	87	253	0	ENST00000262039.4:c.1652G>A	p.Arg551Gln	p.R551Q	ENST00000262039	NM_002647.2	551	cGg/cAg	15/25	1	2	FACETS	0.889	0.789	0.995	0.889	0.789	0.995	CLONAL	1	TRUE	1	0.38	2		253	515	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626032	12626032	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	120	355	0	ENST00000251849.4:c.1928del	p.Pro643ArgfsTer8	p.P643Rfs*8	ENST00000251849	NM_002880.3	643	cCg/cg	17/17	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.38	2		355	617	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437234	52437234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369065146	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	201	552	0	ENST00000460680.1:c.1810G>A	p.Val604Met	p.V604M	ENST00000460680	NM_004656.3	604	Gtg/Atg	14/17	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.38	2		552	1015	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72873689	72873690	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	112	236	0	ENST00000325599.8:c.612dup	p.Glu205Ter	p.E205*	ENST00000325599	NM_018130.2	204	-/T	6/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.38	2		236	499	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911050	29911051	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	257	842	0	ENST00000376809.5:c.352_353del	p.Thr118HisfsTer58	p.T118Hfs*58	ENST00000376809	NM_002116.7	117	CAc/c	3/8	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.38	2		842	1071	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528718	157528718	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	111	404	1	ENST00000346085.5:c.6443C>T	p.Ala2148Val	p.A2148V	ENST00000346085	NM_020732.3	2148	gCc/gTc	20/20	1	2	FACETS	0.969	0.873	1	0.969	0.873	1	CLONAL	1	TRUE	1	0.38	2		405	603	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860428	151860428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567984906	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	141	394	0	ENST00000262189.6:c.10234C>T	p.Arg3412Trp	p.R3412W	ENST00000262189	NM_170606.2	3412	Cgg/Tgg	43/59	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.38	2		394	724	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884485	151884485	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	82	264	0	ENST00000262189.6:c.4870G>T	p.Gly1624Ter	p.G1624*	ENST00000262189	NM_170606.2	1624	Gga/Tga	33/59	1	2	FACETS	0.926	0.82	1	0.926	0.82	1	CLONAL	1	TRUE	1	0.38	2		264	466	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181236	123181236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	29	193	0	ENST00000218089.9:c.700G>A	p.Ala234Thr	p.A234T	ENST00000218089	NM_001042749.1	234	Gca/Aca	9/35	1	2	FACETS	0.519	0.418	0.634	0.519	0.418	0.634	SUBCLONAL	1	TRUE	1	0.38	2		193	294	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575451	67575451	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	106	270	0	ENST00000274335.5:c.526del	p.Met176Ter	p.M176*	ENST00000274335		175	gAa/ga	4/15	NA	2	FACETS	0.863	0.779	0.951			1	INDETERMINATE	1	TRUE	NA	0.571069194999795	2		270	430	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711902	89711902	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782316	NA	P-0049601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	152	451	0	ENST00000371953.3:c.520T>A	p.Tyr174Asn	p.Y174N	ENST00000371953	NM_000314.4	174	Tat/Aat	6/9	0.559459704637014	1	FACETS	0.978	0.905	1	0.978	0.905	1	CLONAL	1	TRUE	0	0.571069194999795	1		451	389	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395587	31395587	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	118	677	1	ENST00000328111.2:c.2440C>T	p.His814Tyr	p.H814Y	ENST00000328111	NM_006892.3	814	Cac/Tac	23/23	1	2	FACETS	0.465	0.419	0.514	0.465	0.419	0.514	SUBCLONAL	1	TRUE	1	0.571069194999795	2		678	889	SUCCESS
APC	324	MSKCC	GRCh37	5	112177121	112177121	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	106	346	0	ENST00000257430.4:c.5833del	p.Ala1945GlnfsTer25	p.A1945Qfs*25	ENST00000257430	NM_000038.5	1944	Ggg/gg	16/16	1	2	FACETS	0.869	0.785	0.958	0.869	0.785	0.958	CLONAL	1	TRUE	1	0.571069194999795	2		346	427	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	125	431	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.386936647640732	2		431	615	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156069	106156069	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	73	338	0	ENST00000380013.4:c.970C>T	p.Gln324Ter	p.Q324*	ENST00000380013	NM_001127208.2	324	Caa/Taa	3/11	1	2	FACETS	0.786	0.689	0.89	0.786	0.689	0.89	SUBCLONAL	1	TRUE	1	0.386936647640732	2		338	480	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735585	204735585	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	121	418	1	ENST00000302823.3:c.386G>T	p.Cys129Phe	p.C129F	ENST00000302823	NM_005214.4	129	tGc/tTc	2/4	1	2	FACETS	0.921	0.834	1	0.921	0.834	1	CLONAL	1	TRUE	1	0.386936647640732	2		419	679	SUCCESS
APC	324	MSKCC	GRCh37	5	112173302	112173303	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0049602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	51	241	0	ENST00000257430.4:c.2013_2014del	p.His672Ter	p.H672*	ENST00000257430	NM_000038.5	671	TCt/t	16/16	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.386936647640732	2		241	237	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524343	148524343	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs973062748	NA	P-0049602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	29	323	1	ENST00000320356.2:c.641C>T	p.Pro214Leu	p.P214L	ENST00000320356	NM_004456.4	214	cCa/cTa	7/20	1	2	FACETS	0.366	0.294	0.449	0.366	0.294	0.449	SUBCLONAL	1	TRUE	1	0.386936647640732	2		324	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0049603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	93	679	2	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.152182321572464	2		681	1031	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	59	472	0	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.152182321572464	2		472	752	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971138	21971138	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs760640852	NA	P-0049603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	72	442	1	ENST00000304494.5:c.220G>T	p.Asp74Tyr	p.D74Y	ENST00000304494	NM_000077.4	74	Gac/Tac	2/3	1	2	FACETS	0.806	0.705	0.915	1	0.977	1	CLONAL	2	TRUE	1	0.152182321572464	2		443	587	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439922	51439922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	31	186	0	ENST00000262662.1:c.487G>A	p.Gly163Arg	p.G163R	ENST00000262662		163	Gga/Aga	4/4	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.152182321572464	2		186	316	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106424	27106424	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	73	444	0	ENST00000324856.7:c.6035G>A	p.Gly2012Asp	p.G2012D	ENST00000324856	NM_006015.4	2012	gGc/gAc	20/20	1	2	FACETS	0.799	0.7	0.907	1	0.977	1	CLONAL	2	TRUE	1	0.152182321572464	2		444	600	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222986	1222986	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	62	519	0	ENST00000326873.7:c.923G>C	p.Trp308Ser	p.W308S	ENST00000326873	NM_000455.4	308	tGg/tCg	8/10	0.152182321572464	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.152182321572464	1		519	549	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906310	50906310	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	62	627	0	ENST00000440232.2:c.971G>T	p.Gly324Val	p.G324V	ENST00000440232	NM_002691.3	324	gGc/gTc	9/27	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.152182321572464	2		627	624	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416373	29416373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	93	609	0	ENST00000389048.3:c.4580C>T	p.Pro1527Leu	p.P1527L	ENST00000389048	NM_004304.4	1527	cCa/cTa	29/29	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.152182321572464	2		609	828	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594996	158594996	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	64	273	0	ENST00000263640.3:c.1351G>C	p.Asp451His	p.D451H	ENST00000263640	NM_001105.4	451	Gat/Cat	10/11	0.0529895651612322	4	FACETS	0.78	0.675	0.894	0.78	0.675	0.894	INDETERMINATE	2	TRUE	2	0.152182321572464	4		273	621	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927456	178927456	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	48	269	0	ENST00000263967.3:c.1219T>C	p.Cys407Arg	p.C407R	ENST00000263967	NM_006218.2	407	Tgc/Cgc	7/21	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.152182321572464	2		269	591	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912172	29912172	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	75	286	0	ENST00000376809.5:c.893G>A	p.Trp298Ter	p.W298*	ENST00000376809	NM_002116.7	298	tGg/tAg	4/8	0.152182321572464	3	FACETS	0.985	0.869	1	0.985	0.869	1	CLONAL	3	TRUE	0	0.152182321572464	3		286	359	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932020	39932020	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	46	573	0	ENST00000378444.4:c.2579G>T	p.Gly860Val	p.G860V	ENST00000378444	NM_001123385.1	860	gGg/gTg	4/15	0.105096767934592	3	FACETS	0.915	0.769	1			1	CLONAL	1	TRUE	NA	0.152182321572464	3		573	711	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034487	47034487	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	79	521	0	ENST00000377604.3:c.572A>G	p.Asn191Ser	p.N191S	ENST00000377604	NM_001204468.1	191	aAt/aGt	6/24	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.152182321572464	2		521	732	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410589	63410589	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	44	619	1	ENST00000330258.3:c.2578C>A	p.Gln860Lys	p.Q860K	ENST00000330258	NM_152424.3	860	Caa/Aaa	2/2	1	2	FACETS	0.862	0.721	1	0.862	0.721	1	CLONAL	1	TRUE	1	0.152182321572464	2		620	671	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411918	63411918	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	47	668	0	ENST00000330258.3:c.1249C>G	p.Pro417Ala	p.P417A	ENST00000330258	NM_152424.3	417	Cca/Gca	2/2	1	2	FACETS	0.732	0.616	0.861	0.732	0.616	0.861	SUBCLONAL	1	TRUE	1	0.152182321572464	2		668	844	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518361	8518363	+	missense_variant	Missense_Mutation	TNP	CCC	CCC	ACA	novel	NA	P-0049603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	19	193	0	ENST00000356435.5:c.1028_1030delinsTGT	p.Trp343_Asp344delinsLeuTyr	p.W343_D344delinsLY	ENST00000356435		343	tGGGac/tTGTac	10/35	1	2	FACETS	0.775	0.588	0.996	0.775	0.588	0.996	CLONAL	1	TRUE	1	0.152182321572464	2		193	322	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415537	152415537	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519714	NA	P-0049605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	94	426	0	ENST00000206249.3:c.1387T>C	p.Ser463Pro	p.S463P	ENST00000206249	NM_000125.3	463	Tcc/Ccc	7/8	1	2	FACETS	0.768	0.686	0.856	1	0.981	1	SUBCLONAL	2	TRUE	1	0.22655865245135	2		426	540	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	119	516	0	ENST00000206249.3:c.1610A>G	p.Tyr537Cys	p.Y537C	ENST00000206249	NM_000125.3	537	tAt/tGt	8/8	1	2	FACETS	0.784	0.709	0.863	1	0.986	1	SUBCLONAL	2	TRUE	1	0.22655865245135	2		516	670	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	44	296	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.22655865245135	2		296	330	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0049605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	109	579	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.22655865245135	2		579	682	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953011	2953011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1172378918	NA	P-0049605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	125	701	3	ENST00000396946.4:c.2929G>A	p.Val977Met	p.V977M	ENST00000396946	NM_032415.4	977	Gtg/Atg	22/25	0.22655865245135	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.22655865245135	1		704	906	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118820	115118821	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0049605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	102	314	0	ENST00000257566.3:c.520_521del	p.Gly174Ter	p.G174*	ENST00000257566	NM_016569.3	174	GGt/t	2/8	0.22655865245135	1	FACETS	0.783	0.703	0.867	1	0.983	1	SUBCLONAL	2	TRUE	0	0.22655865245135	1		314	510	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120818	115120818	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	101	510	0	ENST00000257566.3:c.188del	p.Pro63ArgfsTer25	p.P63Rfs*25	ENST00000257566	NM_016569.3	63	cCg/cg	1/8	0.22655865245135	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.22655865245135	1		510	596	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188291	142188291	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	36	333	0	ENST00000350721.4:c.6440C>A	p.Ser2147Tyr	p.S2147Y	ENST00000350721	NM_001184.3	2147	tCt/tAt	38/47	1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	TRUE	1	0.22655865245135	2		333	310	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149450084	149450084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1419926665	NA	P-0049605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	126	629	0	ENST00000286301.3:c.1133G>A	p.Arg378His	p.R378H	ENST00000286301	NM_005211.3	378	cGc/cAc	8/22	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.22655865245135	2		629	803	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939895	76939895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	39	412	0	ENST00000373344.5:c.853G>A	p.Glu285Lys	p.E285K	ENST00000373344	NM_000489.3	285	Gag/Aag	9/35	0.22655865245135	1	FACETS	0.658	0.545	0.784	0.658	0.545	0.784	SUBCLONAL	1	TRUE	0	0.22655865245135	1		412	464	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842404	68842404	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	AG	novel	NA	P-0049605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	180	461	0	ENST00000261769.5:c.465delinsAG	p.Asp155GlufsTer13	p.D155Efs*13	ENST00000261769	NM_004360.3	155	gaC/gaAG	4/16	0.22655865245135	2	FACETS	0.873	0.809	0.938	1	0.987	1	CLONAL	3	TRUE	0	0.22655865245135	2		461	607	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	212	148	0				ENST00000310581	NM_198253.2	-/1132			0.804003473113992	3	FACETS	0.994	0.94	1	0.994	0.94	1	CLONAL	2	TRUE	1	0.804003473113992	3		148	372	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0049606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	195	402	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.89	0.83	0.951	0.89	0.83	0.951	CLONAL	1	TRUE	1	0.804003473113992	2		402	545	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451474	187451474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145456310	NA	P-0049606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	158	313	0	ENST00000232014.4:c.8C>T	p.Ser3Leu	p.S3L	ENST00000232014	NM_001130845.1	3	tCg/tTg	3/10	1	2	FACETS	0.834	0.771	0.899	0.834	0.771	0.899	CLONAL	1	TRUE	1	0.804003473113992	2		313	471	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	107	295	0	ENST00000371953.3:c.511C>G	p.Gln171Glu	p.Q171E	ENST00000371953	NM_000314.4	171	Cag/Gag	6/9	0.804003473113992	1	FACETS	0.925	0.859	0.99	0.925	0.859	0.99	CLONAL	1	TRUE	0	0.804003473113992	1		295	172	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338650	70338650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	263	539	3	ENST00000374080.3:c.46C>T	p.Arg16Trp	p.R16W	ENST00000374080		16	Cgg/Tgg	1/45	0.483501887037296	1	FACETS	0.603	0.569	0.637	0.603	0.569	0.637	SUBCLONAL	1	TRUE	0	0.804003473113992	1		542	649	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165914	118165914	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	141	292	0	ENST00000369448.3:c.424C>G	p.Leu142Val	p.L142V	ENST00000369448	NM_017709.3	142	Cta/Gta	2/2	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.804003473113992	2		292	345	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980316	201980317	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0049606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	338	638	0	ENST00000359651.3:c.54_55dup	p.Tyr19CysfsTer25	p.Y19Cfs*25	ENST00000359651		18	atg/aTGtg	1/8	0.804003473113992	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.804003473113992	1		638	479	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770075	56770075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	216	492	0	ENST00000337432.4:c.73del	p.Val25Ter	p.V25*	ENST00000337432	NM_058216.2	24	cGg/cg	1/9	1	2	FACETS	0.946	0.886	1	0.946	0.886	1	CLONAL	1	TRUE	1	0.804003473113992	2		492	568	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756691	756691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763332220	NA	P-0049606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	184	395	0	ENST00000314574.4:c.137C>T	p.Ser46Leu	p.S46L	ENST00000314574	NM_005433.3	46	tCa/tTa	2/12	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.804003473113992	2		395	431	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722934	49722934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	46	324	0	ENST00000449682.2:c.1393G>A	p.Asp465Asn	p.D465N	ENST00000449682	NM_020998.3	465	Gac/Aac	12/18	1	2	FACETS	0.313	0.264	0.367	0.313	0.264	0.367	SUBCLONAL	1	TRUE	1	0.804003473113992	2		324	365	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430215	181430215	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1205978762	NA	P-0049606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	185	328	0	ENST00000325404.1:c.67G>A	p.Gly23Ser	p.G23S	ENST00000325404	NM_003106.3	23	Ggc/Agc	1/1	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.804003473113992	2		328	391	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44910900	44910970	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTTCCTTAAAGATTATGTTAATTTTTCTCCAAATCTCTTTTTCTGTTCTTTAGAGGAAATATCATTCTGC	AGTTCCTTAAAGATTATGTTAATTTTTCTCCAAATCTCTTTTTCTGTTCTTTAGAGGAAATATCATTCTGC	-	novel	NA	P-0049606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	81	140	0	ENST00000377967.4:c.655-53_672del		p.X219_splice	ENST00000377967	NM_021140.2	219		9/29	0.483501887037296	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.804003473113992	1		140	93	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434005	49434005	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	34	859	1	ENST00000301067.7:c.7548del	p.Asn2517IlefsTer26	p.N2517Ifs*26	ENST00000301067	NM_003482.3	2516	ccC/cc	31/54	0.226135941547992	4	FACETS	0.776	0.633	0.939	0.388	0.316	0.47	CLONAL	1	TRUE	2	0.16	4		860	635	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0049607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	31	523	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.738	0.596	0.9	0.738	0.596	0.9	SUBCLONAL	1	TRUE	1	0.16	2		523	525	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354226	70354226	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1423751717	NA	P-0049607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	60	341	2	ENST00000374080.3:c.4637C>T	p.Thr1546Met	p.T1546M	ENST00000374080		1546	aCg/aTg	34/45	0.3	2	FACETS	0.906	0.783	1	0.906	0.783	1	CLONAL	2	TRUE	0	0.16	2		343	414	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245587	41245587	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357522	NA	P-0049607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	23	468	1	ENST00000357654.3:c.1961del	p.Lys654SerfsTer47	p.K654Sfs*47	ENST00000357654	NM_007294.3	654	aAg/ag	10/23	1	2	FACETS	0.975	0.761	1	0.975	0.761	1	CLONAL	1	TRUE	1	0.16	2		469	295	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696450	47696450	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	23	405	0	ENST00000347630.2:c.373T>G	p.Phe125Val	p.F125V	ENST00000347630	NM_001007230.1	125	Ttt/Gtt	6/11	1	2	FACETS	0.812	0.633	1	0.812	0.633	1	CLONAL	1	TRUE	1	0.16	2		405	354	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642785	3642785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373178144	NA	P-0049607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	61	774	0	ENST00000294008.3:c.2242G>A	p.Ala748Thr	p.A748T	ENST00000294008	NM_032444.2	748	Gcc/Acc	11/15	1	2	FACETS	0.897	0.772	1	0.897	0.772	1	CLONAL	1	TRUE	1	0.16	2		774	850	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0049607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	48	994	2	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.726	0.612	0.853	0.726	0.612	0.853	SUBCLONAL	1	TRUE	1	0.16	2		996	826	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458306	120458306	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370648780	NA	P-0049607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	30	675	0	ENST00000256646.2:c.7039C>T	p.Arg2347Cys	p.R2347C	ENST00000256646	NM_024408.3	2347	Cgt/Tgt	34/34	1	2	FACETS	0.747	0.601	0.913	0.747	0.601	0.913	CLONAL	1	TRUE	1	0.16	2		675	502	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272146	15272146	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866716310	NA	P-0049607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	53	861	3	ENST00000263388.2:c.6293C>T	p.Thr2098Met	p.T2098M	ENST00000263388	NM_000435.2	2098	aCg/aTg	33/33	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.16	2		864	632	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798133	45798133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774237159	NA	P-0049607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	58	801	0	ENST00000450313.1:c.718G>A	p.Ala240Thr	p.A240T	ENST00000450313	NM_012222.2	240	Gca/Aca	9/16	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.16	2		801	695	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406295	70406295	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762257556	NA	P-0049607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	24	470	0	ENST00000373644.4:c.3809C>T	p.Thr1270Met	p.T1270M	ENST00000373644	NM_030625.2	1270	aCg/aTg	4/12	1	2	FACETS	0.802	0.629	1	0.802	0.629	1	CLONAL	1	TRUE	1	0.16	2		470	374	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431648	49431648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587783730	NA	P-0049607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	46	838	0	ENST00000301067.7:c.9491G>A	p.Arg3164Gln	p.R3164Q	ENST00000301067	NM_003482.3	3164	cGg/cAg	34/54	0.226135941547992	4	FACETS	1	0.899	1	0.547	0.46	0.643	CLONAL	1	TRUE	2	0.16	4		838	610	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713238	43713238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1273385388	NA	P-0049607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	71	756	0	ENST00000382044.4:c.4235G>A	p.Arg1412Gln	p.R1412Q	ENST00000382044	NM_001141980.1	1412	cGg/cAg	20/28	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.16	2		756	839	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347758	347758	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	41	904	1	ENST00000262320.3:c.1748G>T	p.Gly583Val	p.G583V	ENST00000262320	NM_003502.3	583	gGc/gTc	6/11	1	2	FACETS	0.765	0.636	0.909	0.765	0.636	0.909	CLONAL	1	TRUE	1	0.16	2		905	670	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831718	72831718	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	32	572	0	ENST00000268489.5:c.4863A>C	p.Gln1621His	p.Q1621H	ENST00000268489	NM_006885.3	1621	caA/caC	9/10	1	2	FACETS	0.862	0.699	1	0.862	0.699	1	CLONAL	1	TRUE	1	0.16	2		572	464	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845816	72845838	+	frameshift_variant	Frame_Shift_Del	DEL	GATCTCCTCAGCTGTTTTTGGTC	GATCTCCTCAGCTGTTTTTGGTC	-	novel	NA	P-0049607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	33	536	1	ENST00000268489.5:c.3629_3651del	p.Arg1210GlnfsTer15	p.R1210Qfs*15	ENST00000268489	NM_006885.3	1210	cGACCAAAAACAGCTGAGGAGATC/c	6/10	1	2	FACETS	0.699	0.568	0.848	0.699	0.568	0.848	SUBCLONAL	1	TRUE	1	0.16	2		537	590	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78933980	78933980	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	28	704	0	ENST00000306801.3:c.3580G>A	p.Asp1194Asn	p.D1194N	ENST00000306801	NM_020761.2	1194	Gac/Aac	30/34	1	2	FACETS	0.639	0.509	0.787	0.639	0.509	0.787	SUBCLONAL	1	TRUE	1	0.16	2		704	548	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313353	30313353	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	23	489	0	ENST00000262643.3:c.953G>A	p.Gly318Glu	p.G318E	ENST00000262643	NM_001238.2	318	gGg/gAg	11/12	1	2	FACETS	0.796	0.621	1	0.796	0.621	1	CLONAL	1	TRUE	1	0.16	2		489	361	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264164	46264164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772825285	NA	P-0049607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	16	278	0	ENST00000371998.3:c.1211C>T	p.Ser404Leu	p.S404L	ENST00000371998		404	tCg/tTg	11/23	0.143917345909958	0	FACETS	0.672	0.497	0.881			1	SUBCLONAL	1	TRUE	0	0.16	0		278	250	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190938	185190938	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	56	710	0	ENST00000265026.3:c.1823del	p.Asn608ThrfsTer56	p.N608Tfs*56	ENST00000265026	NM_004721.4	607	Aaa/aa	11/14	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.16	2		710	680	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873395	151873397	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs1563251678	NA	P-0049607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	11	286	0	ENST00000262189.6:c.9141_9143del	p.Leu3048del	p.L3048del	ENST00000262189	NM_170606.2	3047	ctTCTa/cta	38/59	1	2	FACETS	0.712	0.492	0.985	0.712	0.492	0.985	CLONAL	1	TRUE	1	0.16	2		286	193	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0049609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	74	336	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.854	0.751	0.963	0.854	0.751	0.963	CLONAL	1	TRUE	1	0.43442370675511	2		336	399	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692886	89692886	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	79	288	0	ENST00000371953.3:c.370T>A	p.Cys124Ser	p.C124S	ENST00000371953	NM_000314.4	124	Tgt/Agt	5/9	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.43442370675511	2		288	301	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371799	55371820	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCCGCGCTGGGCCCCGAG	GGCGGCCGCGCTGGGCCCCGAG	-	novel	NA	P-0049609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	139	152	0	ENST00000297316.4:c.499_520del	p.Leu167TrpfsTer213	p.L167Wfs*213	ENST00000297316	NM_022454.3	163	caGGCGGCCGCGCTGGGCCCCGAG/ca	2/2	1	2	FACETS	0.922	0.851	0.994	1	0.991	1	CLONAL	2	TRUE	1	0.43442370675511	2		152	347	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696597	47696597	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	107	384	0	ENST00000347630.2:c.351G>A	p.Met117Ile	p.M117I	ENST00000347630	NM_001007230.1	117	atG/atA	5/11	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.43442370675511	2		384	474	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685304	89685320	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATATACAATCTGTAAGT	ATATACAATCTGTAAGT	-	novel	NA	P-0049609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	38	234	0	ENST00000371953.3:c.201_209+8del		p.X67_splice	ENST00000371953	NM_000314.4	67		3/9	1	2	FACETS	0.683	0.568	0.81	0.683	0.568	0.81	SUBCLONAL	1	TRUE	1	0.43442370675511	2		234	256	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396567	396568	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	363	631	0	ENST00000262320.3:c.458dup	p.Asn153LysfsTer31	p.N153Kfs*31	ENST00000262320	NM_003502.3	153	aat/aaAt	2/11	0.43442370675511	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.43442370675511	2		631	787	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559167	29559167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1457169236	NA	P-0049609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	97	349	0	ENST00000356175.3:c.3274G>A	p.Gly1092Ser	p.G1092S	ENST00000356175	NM_000267.3	1092	Ggt/Agt	25/57	1	2	FACETS	0.904	0.809	1	0.904	0.809	1	CLONAL	1	TRUE	1	0.43442370675511	2		349	494	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807188	1807188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1560437651	NA	P-0049609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	229	842	6	ENST00000260795.2:c.1519G>A	p.Val507Met	p.V507M	ENST00000260795		507	Gtg/Atg	10/17	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.43442370675511	2		848	860	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046368	69046368	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	142	478	0	ENST00000288368.4:c.3841C>T	p.Gln1281Ter	p.Q1281*	ENST00000288368	NM_024870.2	1281	Cag/Tag	32/40	1	2	FACETS	0.982	0.897	1	0.982	0.897	1	CLONAL	1	TRUE	1	0.43442370675511	2		478	666	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591133	67591136	+	protein_altering_variant	In_Frame_Del	DEL	ACGA	ACGA	G	novel	NA	P-0049609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	75	272	0	ENST00000274335.5:c.1726_1729delinsG	p.Thr576_Arg577delinsGly	p.T576_R577delinsG	ENST00000274335		576	ACGAga/Gga	12/15	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.43442370675511	2		272	299	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0049610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	203	263	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.618158566495978	3	FACETS	0.973	0.913	1	0.973	0.913	1	CLONAL	2	TRUE	1	0.618158566495978	3		263	442	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	166	646	1	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	0.618158566495978	3	FACETS	1	0.926	1	0.503	0.463	0.544	CLONAL	1	TRUE	1	0.618158566495978	3		647	699	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114690	108114691	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0049610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	17	208	0	ENST00000278616.4:c.510_511del	p.Tyr171LeufsTer13	p.Y171Lfs*13	ENST00000278616	NM_000051.3	169	tcTGtg/tctg	6/63	1	2	FACETS	0.199	0.148	0.259	0.199	0.148	0.259	SUBCLONAL	1	TRUE	1	0.618158566495978	2		208	277	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132954	30132954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763885568	NA	P-0049610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	138	567	0	ENST00000331968.5:c.647G>A	p.Arg216His	p.R216H	ENST00000331968	NM_002742.2	216	cGc/cAc	4/18	0.603917568396666	4	FACETS	1	0.922	1	0.337	0.307	0.369	CLONAL	1	TRUE	1	0.618158566495978	4		567	714	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026245	36026245	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766744528	NA	P-0049610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	94	1014	1	ENST00000358208.4:c.847G>A	p.Glu283Lys	p.E283K	ENST00000358208		283	Gag/Aag	7/12	0.618158566495978	5	FACETS	0.443	0.392	0.497	0.148	0.13	0.166	SUBCLONAL	1	TRUE	2	0.618158566495978	5		1015	1324	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231828	36231829	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	699	680	0	ENST00000300305.3:c.555dup	p.Val186SerfsTer27	p.V186Sfs*27	ENST00000300305		185	-/A	5/8	0.618158566495978	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.618158566495978	3		680	906	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97888824	97888824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	79	502	1	ENST00000289081.3:c.883G>A	p.Asp295Asn	p.D295N	ENST00000289081	NM_000136.2	295	Gat/Aat	9/15	1	2	FACETS	0.59	0.521	0.664	0.59	0.521	0.664	SUBCLONAL	1	TRUE	1	0.618158566495978	2		503	433	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411641	63411641	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs368417121	NA	P-0049610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	100	837	0	ENST00000330258.3:c.1526A>G	p.Tyr509Cys	p.Y509C	ENST00000330258	NM_152424.3	509	tAt/tGt	2/2	0.324648845268892	5	FACETS	0.643	0.574	0.718	0.214	0.191	0.24	INDETERMINATE	1	TRUE	2	0.618158566495978	5		837	969	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412884	49412884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	368	540	2	ENST00000418115.1:c.139G>A	p.Glu47Lys	p.E47K	ENST00000418115	NM_001664.2	47	Gag/Aag	2/5	0.902444865155455	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.902444865155455	1		542	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540652	NA	P-0049611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	474	679	0	ENST00000269305.4:c.743G>C	p.Arg248Pro	p.R248P	ENST00000269305	NM_001126112.2	248	cGg/cCg	7/11	0.902444865155455	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.902444865155455	1		679	566	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692953	89692953	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs786204933	NA	P-0049611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	215	482	0	ENST00000371953.3:c.437T>A	p.Leu146Ter	p.L146*	ENST00000371953	NM_000314.4	146	tTa/tAa	5/9	0.902444865155455	1	FACETS	0.983	0.947	1	0.983	0.947	1	CLONAL	1	TRUE	0	0.902444865155455	1		482	266	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169116	32169116	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1263727065	NA	P-0049611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	619	751	3	ENST00000375023.3:c.3917del	p.Pro1306GlnfsTer3	p.P1306Qfs*3	ENST00000375023	NM_004557.3	1306	cCa/ca	22/30	1	2	FACETS	0.998	0.962	1	0.998	0.962	1	CLONAL	1	TRUE	1	0.902444865155455	2		754	1375	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546787	9546787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	384	428	0	ENST00000353224.5:c.1235C>T	p.Pro412Leu	p.P412L	ENST00000353224	NM_177990.2	412	cCg/cTg	5/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.902444865155455	2		428	769	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651584	206651584	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	604	760	0	ENST00000367120.3:c.894C>G	p.Phe298Leu	p.F298L	ENST00000367120	NM_014002.3	298	ttC/ttG	9/22	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.902444865155455	2		760	1325	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562950	21562950	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	691	808	0	ENST00000382592.4:c.969del	p.Ala324ArgfsTer109	p.A324Rfs*109	ENST00000382592	NM_014572.2	323	ccC/cc	4/8	0.902444865155455	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.902444865155455	1		808	806	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121873	2121873	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	775	969	0	ENST00000219476.3:c.2035G>C	p.Val679Leu	p.V679L	ENST00000219476	NM_000548.3	679	Gtg/Ctg	19/42	0.902444865155455	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.902444865155455	1		969	913	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505582	25505582	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0049611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	540	655	0	ENST00000264709.3:c.178-2A>T		p.X60_splice	ENST00000264709	NM_175629.2	60			1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.902444865155455	2		655	1121	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711073	61711074	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CG	CG	GC	novel	NA	P-0049611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	124	325	1	ENST00000401558.2:c.2675_2676delinsGC	p.Thr892Ser	p.T892S	ENST00000401558	NM_003400.3	892	aCG/aGC	21/25	1	2	FACETS	0.82	0.752	0.89	0.82	0.752	0.89	CLONAL	1	TRUE	1	0.902444865155455	2		326	335	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561205	9561205	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	305	441	0	ENST00000353224.5:c.577G>T	p.Ala193Ser	p.A193S	ENST00000353224	NM_177990.2	193	Gcc/Tcc	4/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.902444865155455	2		441	675	SUCCESS
APC	324	MSKCC	GRCh37	5	112177805	112177805	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	151	259	0	ENST00000257430.4:c.6514G>T	p.Glu2172Ter	p.E2172*	ENST00000257430	NM_000038.5	2172	Gag/Tag	16/16	1	2	FACETS	0.984	0.914	1	0.984	0.914	1	CLONAL	1	TRUE	1	0.902444865155455	2		259	340	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433755	149433755	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	590	759	0	ENST00000286301.3:c.2796C>A	p.Ser932Arg	p.S932R	ENST00000286301	NM_005211.3	932	agC/agA	22/22	1	2	FACETS	0.992	0.956	1	0.992	0.956	1	CLONAL	1	TRUE	1	0.902444865155455	2		759	1318	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045788	180045788	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	550	737	0	ENST00000261937.6:c.2983del	p.Ala995LeufsTer12	p.A995Lfs*12	ENST00000261937	NM_182925.4	995	Gct/ct	21/30	1	2	FACETS	0.979	0.942	1	0.979	0.942	1	CLONAL	1	TRUE	1	0.902444865155455	2		737	1245	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411719	116411719	+	intron_variant	Intron	SNP	G	G	C	novel	NA	P-0049611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	333	694	0	ENST00000397752.3:c.2887+11G>C		p.*963*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.906	0.86	0.951	0.906	0.86	0.951	CLONAL	1	TRUE	1	0.902444865155455	2		694	815	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395183	139395183	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	790	939	0	ENST00000277541.6:c.5755A>G	p.Ser1919Gly	p.S1919G	ENST00000277541	NM_017617.3	1919	Agc/Ggc	31/34	0.902444865155455	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.902444865155455	1		939	906	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921494	39921494	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1305	431	727	0	ENST00000378444.4:c.4326G>T	p.Glu1442Asp	p.E1442D	ENST00000378444	NM_001123385.1	1442	gaG/gaT	10/15	0.902444865155455	3	FACETS	0.798	0.759	0.839	0.399	0.379	0.42	SUBCLONAL	1	TRUE	1	0.902444865155455	3		727	1736	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217322	123217323	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0049611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	160	468	0	ENST00000218089.9:c.2976_2977delinsAT	p.His992_Pro993delinsGlnSer	p.H992_P993delinsQS	ENST00000218089	NM_001042749.1	992	caTCca/caATca	29/35	0.336505319863951	1	FACETS	0.46	0.426	0.495	0.46	0.426	0.495	INDETERMINATE	1	TRUE	0	0.902444865155455	1		468	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0049612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	304	768	7	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.556981420904707	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.556981420904707	1		775	745	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0049612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	119	341	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.556981420904707	2		341	394	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970899	21970899	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0049612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	329	677	0	ENST00000304494.5:c.457+2T>A		p.X153_splice	ENST00000304494	NM_000077.4	153			0.556981420904707	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.556981420904707	1		677	678	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604791	48604798	+	frameshift_variant	Frame_Shift_Del	DEL	AAGTACTT	AAGTACTT	G	novel	NA	P-0049612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	107	306	0	ENST00000342988.3:c.1613_1620delinsG	p.Glu538GlyfsTer12	p.E538Gfs*12	ENST00000342988	NM_005359.5	538	gAAGTACTT/gG	12/12	0.556981420904707	1	FACETS	0.785	0.712	0.862	0.785	0.712	0.862	SUBCLONAL	1	TRUE	0	0.556981420904707	1		306	353	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0049617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	28	400	2	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.588	0.469	0.723	0.588	0.469	0.723	SUBCLONAL	1	TRUE	1	0.22	2		402	433	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881392	37881392	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	134	698	0	ENST00000269571.5:c.2584A>G	p.Thr862Ala	p.T862A	ENST00000269571		862	Aca/Gca	21/27	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.22	2		698	867	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603119	48603119	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	50	396	0	ENST00000342988.3:c.1420T>A	p.Ser474Thr	p.S474T	ENST00000342988	NM_005359.5	474	Tca/Aca	11/12	1	2	FACETS	0.951	0.808	1	0.951	0.808	1	CLONAL	1	TRUE	1	0.22	2		396	478	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589149	67589151	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	novel	NA	P-0049618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	96	211	0	ENST00000274335.5:c.1138_1140del	p.Leu380del	p.L380del	ENST00000274335		379	aaATTa/aaa	9/15	0.710122125557417	1	FACETS	0.974	0.894	1	0.974	0.894	1	CLONAL	1	TRUE	0	0.710122125557417	1		211	179	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494169	140494169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730880415	NA	P-0049618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	320	567	0	ENST00000288602.6:c.1079G>A	p.Arg360Gln	p.R360Q	ENST00000288602	NM_004333.4	360	cGa/cAa	8/18	0.705157645689336	2	FACETS	0.8	0.765	0.835	0.8	0.765	0.835	SUBCLONAL	2	TRUE	0	0.710122125557417	2		567	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519996	NA	P-0049618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	471	843	0	ENST00000269305.4:c.395A>C	p.Lys132Thr	p.K132T	ENST00000269305	NM_001126112.2	132	aAg/aCg	5/11	0.710122125557417	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.710122125557417	1		843	667	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0049619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	51	217	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.747	0.637	0.867	0.747	0.637	0.867	SUBCLONAL	1	TRUE	1	0.37	2		217	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0049620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	436	768	7	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.374680542706506	3	FACETS	0.884	0.847	0.92	0.884	0.847	0.92	CLONAL	3	TRUE	0	0.438880924720451	3		775	914	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0049620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	197	437	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.318786662259915	4	FACETS	1	0.981	1	0.762	0.711	0.815	CLONAL	2	TRUE	1	0.438880924720451	4		437	565	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0049620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	137	305	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.322640612125865	3	FACETS	0.994	0.914	1	0.663	0.609	0.717	CLONAL	2	TRUE	0	0.438880924720451	3		305	383	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182252	38182252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1559484916	NA	P-0049620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	97	526	1	ENST00000396334.3:c.688C>T	p.Arg230Cys	p.R230C	ENST00000396334	NM_002468.4	230	Cgc/Tgc	4/5	0.369531721010656	3	FACETS	0.86	0.768	0.957	0.43	0.384	0.479	CLONAL	1	TRUE	1	0.438880924720451	3		527	627	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860770	3860770	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	135	373	0	ENST00000262367.5:c.809C>A	p.Thr270Asn	p.T270N	ENST00000262367	NM_004380.2	270	aCt/aAt	3/31	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.438880924720451	2		373	421	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0049622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	55	333	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	1	2	FACETS	0.926	0.795	1	0.926	0.795	1	CLONAL	1	TRUE	1	0.317606734840216	2		333	374	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351578	89351578	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	103	678	0	ENST00000301030.4:c.1372C>T	p.Arg458Ter	p.R458*	ENST00000301030	NM_001256183.1	458	Cga/Tga	9/13	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.317606734840216	2		678	580	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442539	52442539	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	57	408	0	ENST00000460680.1:c.206del	p.Thr69SerfsTer3	p.T69Sfs*3	ENST00000460680	NM_004656.3	69	aCg/ag	4/17	0.313547104638679	1	FACETS	0.82	0.707	0.943	0.82	0.707	0.943	CLONAL	1	TRUE	0	0.317606734840216	1		408	368	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	52	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.996	0.852	1	0.996	0.852	1	CLONAL	1	TRUE	1	0.29	2		148	360	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637723	176637723	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1310684026	NA	P-0049623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	80	596	0	ENST00000439151.2:c.2323C>G	p.Gln775Glu	p.Q775E	ENST00000439151	NM_022455.4	775	Caa/Gaa	5/23	1	2	FACETS	0.759	0.668	0.857	0.759	0.668	0.857	SUBCLONAL	1	TRUE	1	0.29	2		596	727	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578197	7578197	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	130	623	0	ENST00000269305.4:c.652G>T	p.Val218Leu	p.V218L	ENST00000269305	NM_001126112.2	218	Gtg/Ttg	6/11	1	2	FACETS	0.993	0.9	1	0.993	0.9	1	CLONAL	1	TRUE	1	0.29	2		623	903	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971207	21971207	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	158	581	0	ENST00000304494.5:c.151del	p.Val51SerfsTer2	p.V51Sfs*2	ENST00000304494	NM_000077.4	51	Gtc/tc	2/3	0.235141818877552	2	FACETS	0.936	0.862	1	0.936	0.862	1	CLONAL	2	TRUE	0	0.29	2		581	582	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316389	14316389	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	144	452	0	ENST00000256196.4:c.216A>T	p.Gln72His	p.Q72H	ENST00000256196		72	caA/caT	3/6	0.303985092883196	1	FACETS	0.815	0.748	0.885	1	0.989	1	CLONAL	2	TRUE	0	0.29	1		452	521	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981869	101981869	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	186	741	0	ENST00000282441.5:c.290A>G	p.Lys97Arg	p.K97R	ENST00000282441	NM_001130145.2	97	aAg/aGg	1/9	0.11136112833351	3	FACETS	0.801	0.74	0.864	0.801	0.74	0.864	INDETERMINATE	2	TRUE	1	0.29	3		741	917	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116161	67116161	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1210173381	NA	P-0049623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	85	370	0	ENST00000412916.2:c.445A>G	p.Arg149Gly	p.R149G	ENST00000412916		149	Agg/Ggg	5/6	1	2	FACETS	0.862	0.762	0.969	0.862	0.762	0.969	CLONAL	1	TRUE	1	0.29	2		370	680	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980507	7980513	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	CTGAGCT	CTGAGCT	-	novel	NA	P-0049623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	63	517	0	ENST00000319144.4:c.1072-2_1076del		p.X358_splice	ENST00000319144	NM_001139.2	358		9/15	1	2	FACETS	0.772	0.668	0.884	0.772	0.668	0.884	SUBCLONAL	1	TRUE	1	0.29	2		517	563	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395773	45395773	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0049623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	46	366	0	ENST00000262160.6:c.361A>T	p.Lys121Ter	p.K121*	ENST00000262160	NM_005901.5	121	Aaa/Taa	4/11	1	2	FACETS	0.715	0.602	0.838	0.715	0.602	0.838	SUBCLONAL	1	TRUE	1	0.29	2		366	444	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438575	52438575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290266682	NA	P-0049623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	92	545	0	ENST00000460680.1:c.1144G>A	p.Gly382Ser	p.G382S	ENST00000460680	NM_004656.3	382	Ggc/Agc	12/17	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.29	2		545	613	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275319	142275319	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	44	504	0	ENST00000350721.4:c.1984A>T	p.Ser662Cys	p.S662C	ENST00000350721	NM_001184.3	662	Agc/Tgc	9/47	0.211158626875377	2	FACETS	0.465	0.389	0.549	0.232	0.194	0.275	SUBCLONAL	1	TRUE	0	0.29	2		504	653	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527316	187527317	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	201	523	0	ENST00000441802.2:c.10257_10258insT	p.Arg3420Ter	p.R3420*	ENST00000441802	NM_005245.3	3419	-/T	17/27	0.211158626875377	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.29	2		523	671	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068086	94068086	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	41	258	0	ENST00000369303.4:c.876G>C	p.Gln292His	p.Q292H	ENST00000369303	NM_004440.3	292	caG/caC	4/17	0.276912365280382	3	FACETS	0.996	0.833	1	0.498	0.416	0.588	CLONAL	1	TRUE	1	0.29	3		258	325	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111502	8111503	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0049624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	218	587	0	ENST00000346208.3:c.990dup	p.Asn331GlufsTer21	p.N331Efs*21	ENST00000346208		330	agg/aGgg	5/6	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.788144541646991	2		587	495	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754493	42754493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766762597	NA	P-0049624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	338	739	0	ENST00000222329.4:c.247C>T	p.Arg83Trp	p.R83W	ENST00000222329	NM_006494.2	83	Cgg/Tgg	2/4	0.337166746349246	3	FACETS	1	0.994	1	0.446	0.423	0.47	INDETERMINATE	1	TRUE	0	0.788144541646991	3		739	893	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519954	66519954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	29	323	0	ENST00000358598.2:c.437G>A	p.Arg146Lys	p.R146K	ENST00000358598	NM_212471.2	146	aGa/aAa	4/11	0.788144541646991	4	FACETS	0.587	0.474	0.715	0.294	0.237	0.358	SUBCLONAL	1	TRUE	2	0.788144541646991	4		323	224	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434154	49434155	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0049624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	218	845	1	ENST00000301067.7:c.7398_7399delinsTT	p.Leu2466_His2467delinsPheTyr	p.L2466_H2467delinsFY	ENST00000301067	NM_003482.3	2466	ttGCat/ttTTat	31/54	1	2	FACETS	0.856	0.801	0.913	0.856	0.801	0.913	CLONAL	1	TRUE	1	0.788144541646991	2		846	646	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917806	29917806	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	309	807	0	ENST00000389048.3:c.862T>A	p.Trp288Arg	p.W288R	ENST00000389048	NM_004304.4	288	Tgg/Agg	3/29	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.788144541646991	2		807	784	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80063873	80063873	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	41	389	0	ENST00000265081.6:c.2018T>C	p.Leu673Ser	p.L673S	ENST00000265081	NM_002439.4	673	tTa/tCa	14/24	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.788144541646991	2		389	94	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0049625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	52	237	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.309071120599925	1	FACETS	0.677	0.578	0.784	0.677	0.578	0.784	SUBCLONAL	1	TRUE	0	0.34	1		237	375	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0049625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	60	423	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.216383203342445	1	FACETS	0.612	0.528	0.703	0.612	0.528	0.703	SUBCLONAL	1	TRUE	0	0.34	1		423	479	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0049625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	48	591	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.309071120599925	3	FACETS	0.761	0.644	0.889			1	SUBCLONAL	1	TRUE	NA	0.34	3		592	434	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	29	199	0	ENST00000263967.3:c.1034A>G	p.Asn345Ser	p.N345S	ENST00000263967	NM_006218.2	345	aAt/aGt	5/21	0.309071120599925	2	FACETS	0.705	0.568	0.858			1	SUBCLONAL	1	TRUE	NA	0.34	2		199	242	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522449	187522449	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1342860045	NA	P-0049625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	71	227	1	ENST00000441802.2:c.11614C>T	p.Arg3872Ter	p.R3872*	ENST00000441802	NM_005245.3	3872	Cga/Tga	21/27	0.309071120599925	4	FACETS	1	0.965	1			1	CLONAL	1	TRUE	NA	0.34	4		228	432	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040962	47040963	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0049625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	117	200	0	ENST00000377604.3:c.1495_1496del	p.Ala499ProfsTer18	p.A499Pfs*18	ENST00000377604	NM_001204468.1	498	CGc/c	14/24	0.309071120599925	2	FACETS	0.961	0.876	1	0.961	0.876	1	CLONAL	2	TRUE	0	0.34	2		200	358	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274274	5274274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	84	301	0	ENST00000357368.4:c.173G>A	p.Gly58Asp	p.G58D	ENST00000357368	NM_002850.3	58	gGt/gAt	3/38	1	2	FACETS	0.792	0.7	0.89	0.792	0.7	0.89	SUBCLONAL	1	TRUE	1	0.34	2		301	624	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0049628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	111	336	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.74913491493035	2		336	273	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0049628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	21	601	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.195867759037188	3	FACETS	0.115	0.087	0.146	0.057	0.043	0.073	INDETERMINATE	1	TRUE	1	0.74913491493035	3		601	673	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057810	27057811	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAAC	novel	NA	P-0049628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	327	686	0	ENST00000324856.7:c.1521_1524dup	p.Pro509ThrfsTer115	p.P509Tfs*115	ENST00000324856	NM_006015.4	506	-/CAAC	3/20	1	2	FACETS	0.969	0.918	1	0.969	0.918	1	CLONAL	1	TRUE	1	0.74913491493035	2		686	901	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222000	1222001	+	missense_variant	Missense_Mutation	DNP	GC	GC	CT	novel	NA	P-0049628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	191	719	1	ENST00000326873.7:c.915_916delinsCT	p.Gln305_His306delinsHisTyr	p.Q305_H306delinsHY	ENST00000326873	NM_000455.4	305	caGCac/caCTac	7/10	0.74913491493035	1	FACETS	0.814	0.764	0.864	0.814	0.764	0.864	CLONAL	1	TRUE	0	0.74913491493035	1		720	392	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18975018	18975018	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	149	470	0	ENST00000262803.5:c.2815G>C	p.Glu939Gln	p.E939Q	ENST00000262803	NM_002911.3	939	Gag/Cag	20/24	0.74913491493035	1	FACETS	0.861	0.803	0.919	0.861	0.803	0.919	CLONAL	1	TRUE	0	0.74913491493035	1		470	289	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69011980	69011980	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs890042034	NA	P-0049628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	164	451	0	ENST00000288368.4:c.2617C>G	p.Leu873Val	p.L873V	ENST00000288368	NM_024870.2	873	Cta/Gta	23/40	1	2	FACETS	0.96	0.89	1	0.96	0.89	1	CLONAL	1	TRUE	1	0.74913491493035	2		451	456	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045696	47045697	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	256	893	0	ENST00000377604.3:c.2577_2578insT	p.Asn860Ter	p.N860*	ENST00000377604	NM_001204468.1	859	-/T	23/24	NA	2	FACETS	0.943	0.887	0.999			1	INDETERMINATE	1	TRUE	NA	0.74913491493035	2		893	725	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938814	76938814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	139	428	0	ENST00000373344.5:c.1934C>T	p.Ser645Leu	p.S645L	ENST00000373344	NM_000489.3	645	tCa/tTa	9/35	NA	2	FACETS	1	0.957	1			1	INDETERMINATE	1	TRUE	NA	0.74913491493035	2		428	352	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0049629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	275	616	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.121774317122404	4	FACETS	1	0.964	1	1	0.994	1	INDETERMINATE	3	FALSE	2	0.400814773491163	4		618	626	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913499	NA	P-0049629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	76	180	0	ENST00000345146.2:c.394C>A	p.Arg132Ser	p.R132S	ENST00000345146	NM_005896.2	132	Cgt/Agt	4/10	0.197017120610174	2	FACETS	0.878	0.796	0.959	1	0.978	1	INDETERMINATE	3	FALSE	0	0.400814773491163	2		180	144	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918952	76918955	+	frameshift_variant	Frame_Shift_Del	DEL	CAGT	CAGT	-	novel	NA	P-0049629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	130	397	0	ENST00000373344.5:c.4036_4039del	p.Thr1346Ter	p.T1346*	ENST00000373344	NM_000489.3	1346	ACTGtg/tg	12/35	0.400814773491163	1	FACETS	1	0.973	1	1	0.992	1	CLONAL	2	FALSE	0	0.400814773491163	1		397	236	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107136	27107137	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0049629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	19	460	0	ENST00000324856.7:c.6749_6750del	p.Glu2250ValfsTer27	p.E2250Vfs*27	ENST00000324856	NM_006015.4	2249	tcAGag/tcag	20/20	0.119864791265003	3	FACETS	0.316	0.239	0.407	0.158	0.119	0.204	INDETERMINATE	1	FALSE	1	0.400814773491163	3		460	360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578503	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	368	826	0	ENST00000269305.4:c.427del	p.Val143CysfsTer27	p.V143Cfs*27	ENST00000269305	NM_001126112.2	143	Gtg/tg	5/11	0.121774317122404	4	FACETS	1	0.968	1	1	0.996	1	INDETERMINATE	3	FALSE	2	0.400814773491163	4		826	842	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790908	89790910	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs746966684	NA	P-0049629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	20	596	0	ENST00000336032.3:c.301_303del	p.Lys101del	p.K101del	ENST00000336032	NM_006813.2	99	AAG/-	1/2	1	2	FACETS	0.251	0.191	0.321	0.251	0.191	0.321	SUBCLONAL	1	FALSE	1	0.400814773491163	2		596	398	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101133	27101133	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	110	611	0	ENST00000324856.7:c.4417del	p.Gln1473SerfsTer8	p.Q1473Sfs*8	ENST00000324856	NM_006015.4	1472	gCc/gc	18/20	0.119864791265003	3	FACETS	1	0.967	1	0.586	0.528	0.647	INDETERMINATE	1	FALSE	1	0.400814773491163	3		611	562	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102098	27102098	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	117	482	0	ENST00000324856.7:c.5024C>G	p.Ser1675Cys	p.S1675C	ENST00000324856	NM_006015.4	1675	tCc/tGc	19/20	0.119864791265003	3	FACETS	0.755	0.685	0.828	0.755	0.685	0.828	INDETERMINATE	2	FALSE	1	0.400814773491163	3		482	464	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135721	64135721	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	28	711	0	ENST00000334205.4:c.1189G>T	p.Ala397Ser	p.A397S	ENST00000334205	NM_003942.2	397	Gct/Tct	10/17	0.135104907307624	0	FACETS	0.359	0.287	0.442			1	INDETERMINATE	1	TRUE	0	0.278316700216972	0		711	404	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156273	106156273	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	43	265	0	ENST00000380013.4:c.1174T>G	p.Phe392Val	p.F392V	ENST00000380013	NM_001127208.2	392	Ttt/Gtt	3/11	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.278316700216972	2		265	266	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411883	116411907	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCTTTCTCTCTGTTTTAAGATCTG	TTCTTTCTCTCTGTTTTAAGATCTG	-	novel	NA	P-0049630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	234	729	0	ENST00000397752.3:c.2888-20_2892del		p.X963_splice	ENST00000397752	NM_000245.2	963		14/21	0.278316700216972	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.278316700216972	3		729	853	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346062	152346062	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	98	508	0	ENST00000359321.1:c.508G>T	p.Glu170Ter	p.E170*	ENST00000359321	NM_005431.1	170	Gag/Tag	3/3	0.278316700216972	3	FACETS	0.864	0.775	0.959	0.864	0.775	0.959	CLONAL	2	TRUE	1	0.278316700216972	3		508	464	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	83	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.849	0.764	0.936	0.849	0.764	0.936	CLONAL	1	TRUE	1	0.90966018536316	2		148	215	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0049631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	214	385	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.90966018536316	2		385	462	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0049632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	204	406	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.607650375621415	2		406	604	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0049632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	92	359	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.578	0.515	0.645	0.578	0.515	0.645	SUBCLONAL	1	TRUE	1	0.607650375621415	2		359	524	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144498	11144498	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746219091	NA	P-0049632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	122	662	0	ENST00000358026.2:c.3830C>T	p.Pro1277Leu	p.P1277L	ENST00000358026	NM_001128849.1	1277	cCg/cTg	27/36	1	2	FACETS	0.492	0.445	0.542	0.492	0.445	0.542	SUBCLONAL	1	TRUE	1	0.607650375621415	2		662	816	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0049632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	70	346	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.504	0.441	0.572	0.504	0.441	0.572	SUBCLONAL	1	TRUE	1	0.607650375621415	2		346	457	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070641	67070642	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	22	146	0	ENST00000412916.2:c.268dup	p.Arg90LysfsTer26	p.R90Kfs*26	ENST00000412916		89	gaa/gAaa	3/6	0.607650375621415	1	FACETS	0.35	0.274	0.436	0.35	0.274	0.436	SUBCLONAL	1	TRUE	0	0.607650375621415	1		146	144	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991899	72991899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750134476	NA	P-0049632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	101	611	0	ENST00000268489.5:c.2146G>A	p.Gly716Ser	p.G716S	ENST00000268489	NM_006885.3	716	Ggc/Agc	2/10	0.607650375621415	1	FACETS	0.451	0.405	0.5	0.451	0.405	0.5	SUBCLONAL	1	TRUE	0	0.607650375621415	1		611	513	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2214507	2214507	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	129	698	0	ENST00000398665.3:c.1835C>G	p.Ala612Gly	p.A612G	ENST00000398665	NM_032482.2	612	gCc/gGc	19/28	1	2	FACETS	0.508	0.46	0.558	0.508	0.46	0.558	SUBCLONAL	1	TRUE	1	0.607650375621415	2		698	836	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051162	13051162	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	81	502	0	ENST00000316448.5:c.598T>C	p.Trp200Arg	p.W200R	ENST00000316448	NM_004343.3	200	Tgg/Cgg	5/9	1	2	FACETS	0.463	0.408	0.521	0.463	0.408	0.521	SUBCLONAL	1	TRUE	1	0.607650375621415	2		502	576	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177665	56177665	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	56	347	0	ENST00000399503.3:c.2638C>T	p.Gln880Ter	p.Q880*	ENST00000399503	NM_005921.1	880	Caa/Taa	14/20	1	2	FACETS	0.387	0.332	0.447	0.387	0.332	0.447	SUBCLONAL	1	TRUE	1	0.607650375621415	2		347	476	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181815	56181831	+	frameshift_variant	Frame_Shift_Del	DEL	ATTAACTACACTGAACA	ATTAACTACACTGAACA	-	novel	NA	P-0049632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	33	275	0	ENST00000399503.3:c.4039_4055del	p.Ile1347ValfsTer10	p.I1347Vfs*10	ENST00000399503	NM_005921.1	1347	ATTAACTACACTGAACAg/g	17/20	1	2	FACETS	0.249	0.202	0.302	0.249	0.202	0.302	SUBCLONAL	1	TRUE	1	0.607650375621415	2		275	436	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874449	151874449	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0049632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	53	311	0	ENST00000262189.6:c.8089A>T	p.Lys2697Ter	p.K2697*	ENST00000262189	NM_170606.2	2697	Aag/Tag	38/59	1	2	FACETS	0.477	0.408	0.551	0.477	0.408	0.551	SUBCLONAL	1	TRUE	1	0.607650375621415	2		311	366	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349240	70349241	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0049632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	84	575	1	ENST00000374080.3:c.3652_3653delinsTT	p.Gly1218Leu	p.G1218L	ENST00000374080		1218	GGa/TTa	26/45	1	2	FACETS	0.338	0.297	0.381	0.338	0.297	0.381	SUBCLONAL	1	TRUE	1	0.607650375621415	2		576	819	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	90	350	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.513997292458694	2		350	322	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	383	419	0	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.981	1	1	0.997	1	CLONAL	2	TRUE	1	0.513997292458694	2		419	717	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	218	467	6	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.513997292458694	2		473	815	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	128	472	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.963	0.878	1	0.963	0.878	1	CLONAL	1	TRUE	1	0.513997292458694	2		475	517	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984022	2984022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753614569	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	220	471	0	ENST00000396946.4:c.508C>T	p.Arg170Cys	p.R170C	ENST00000396946	NM_032415.4	170	Cgc/Tgc	5/25	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.513997292458694	2		471	759	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324892	31324892	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs765875917	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	99	139	0	ENST00000412585.2:c.44del	p.Ala15GlyfsTer5	p.A15Gfs*5	ENST00000412585	NM_005514.6	15	gCg/gg	1/8	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.513997292458694	2		139	368	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438206	56438207	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	260	664	0	ENST00000407977.2:c.786_787del	p.Gly263GlufsTer18	p.G263Efs*18	ENST00000407977		262	tcAGgg/tcgg	7/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.513997292458694	2		664	943	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	50	584	2	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.231	0.195	0.271	0.231	0.195	0.271	SUBCLONAL	1	TRUE	1	0.513997292458694	2		586	841	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	245	651	7	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	1	2	FACETS	0.986	0.922	1	0.986	0.922	1	CLONAL	1	TRUE	1	0.513997292458694	2		658	967	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862749	9862749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150316865	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	221	515	0	ENST00000330684.3:c.2554G>A	p.Val852Met	p.V852M	ENST00000330684	NM_001134407.1	852	Gtg/Atg	12/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.513997292458694	2		515	747	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120115	70120115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	53	127	0	ENST00000245479.2:c.1121del	p.Pro374ArgfsTer9	p.P374Rfs*9	ENST00000245479	NM_000346.3	373	Ccc/cc	3/3	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.513997292458694	2		127	201	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	188	438	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.513997292458694	2		438	646	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345769	152345769	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs759063323	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	63	197	0	ENST00000359321.1:c.801del	p.Lys267AsnfsTer30	p.K267Nfs*30	ENST00000359321	NM_005431.1	267	aaA/aa	3/3	1	2	FACETS	0.798	0.696	0.908	0.798	0.696	0.908	CLONAL	1	TRUE	1	0.513997292458694	2		197	307	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100210	157100210	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	30	69	0	ENST00000346085.5:c.1151del	p.Gly384AlafsTer46	p.G384Afs*46	ENST00000346085	NM_020732.3	383	Ggg/gg	1/20	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.513997292458694	2		69	99	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987215	2987215	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	138	374	0	ENST00000396946.4:c.214C>T	p.Arg72Ter	p.R72*	ENST00000396946	NM_032415.4	72	Cga/Tga	3/25	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.513997292458694	2		374	530	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912075	50912077	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs398122386	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	324	695	1	ENST00000440232.2:c.1812_1814del	p.Ser605del	p.S605del	ENST00000440232	NM_002691.3	603	ttCTCc/ttc	15/27	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.513997292458694	2		696	1105	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800564	32800564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148663600	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	278	687	4	ENST00000374899.4:c.983C>T	p.Ala328Val	p.A328V	ENST00000374899	NM_018833.2	328	gCg/gTg	6/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.513997292458694	2		691	1000	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647657	3647657	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs774532876	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	287	666	4	ENST00000294008.3:c.1406del	p.Pro469HisfsTer4	p.P469Hfs*4	ENST00000294008	NM_032444.2	469	cCa/ca	7/15	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.513997292458694	2		670	1091	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910533	29910533	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	54	221	0	ENST00000376809.5:c.74-1G>T		p.X25_splice	ENST00000376809	NM_002116.7	25			1	2	FACETS	0.715	0.615	0.822	0.715	0.615	0.822	SUBCLONAL	1	TRUE	1	0.513997292458694	2		221	294	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599021	28599021	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	81	414	0	ENST00000241453.7:c.2267A>G	p.His756Arg	p.H756R	ENST00000241453	NM_004119.2	756	cAt/cGt	18/24	0.513997292458694	3	FACETS	0.735	0.649	0.827	0.368	0.324	0.414	SUBCLONAL	1	TRUE	1	0.513997292458694	3		414	539	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210893	36210893	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	321	789	5	ENST00000222270.7:c.649del	p.Arg217GlyfsTer22	p.R217Gfs*22	ENST00000222270	NM_014727.1	215	aCc/ac	3/37	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.513997292458694	2		794	1156	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527742	157527742	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	151	378	1	ENST00000346085.5:c.5471del	p.Gly1824ValfsTer27	p.G1824Vfs*27	ENST00000346085	NM_020732.3	1823	Ggg/gg	20/20	1	2	FACETS	0.955	0.877	1	0.955	0.877	1	CLONAL	1	TRUE	1	0.513997292458694	2		379	615	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923606	39923606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777165878	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	257	699	0	ENST00000378444.4:c.3485G>A	p.Arg1162His	p.R1162H	ENST00000378444	NM_001123385.1	1162	cGc/cAc	7/15	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.513997292458694	2		699	994	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779755	3779755	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	272	661	0	ENST00000262367.5:c.5293del	p.Gln1765ArgfsTer6	p.Q1765Rfs*6	ENST00000262367	NM_004380.2	1765	Cag/ag	31/31	1	2	FACETS	0.998	0.936	1	0.998	0.936	1	CLONAL	1	TRUE	1	0.513997292458694	2		661	1061	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162237	47162237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1000273506	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	137	356	1	ENST00000409792.3:c.3889C>T	p.Arg1297Cys	p.R1297C	ENST00000409792	NM_014159.6	1297	Cgt/Tgt	3/21	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.513997292458694	2		357	515	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981632	70981632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	279	685	0	ENST00000276594.2:c.464C>T	p.Ala155Val	p.A155V	ENST00000276594	NM_024504.3	155	gCg/gTg	2/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.513997292458694	2		685	1067	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391798	139391799	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	271	805	0	ENST00000277541.6:c.6392dup	p.Thr2132HisfsTer136	p.T2132Hfs*136	ENST00000277541	NM_017617.3	2131	ggc/ggGc	34/34	1	2	FACETS	0.971	0.911	1	0.971	0.911	1	CLONAL	1	TRUE	1	0.513997292458694	2		805	1086	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360585	118360587	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	133	317	0	ENST00000534358.1:c.4566_4568del	p.Lys1523del	p.K1523del	ENST00000534358	NM_005933.3	1520	AAG/-	12/36	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.513997292458694	2		317	491	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354455	40354455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752593400	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	269	740	0	ENST00000293328.3:c.2140G>A	p.Ala714Thr	p.A714T	ENST00000293328	NM_012448.3	714	Gca/Aca	18/19	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.513997292458694	2		740	1017	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599211	28599211	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	270	773	0	ENST00000253063.3:c.661del	p.Asp221MetfsTer26	p.D221Mfs*26	ENST00000253063	NM_031459.4	219	gaG/ga	5/10	1	2	FACETS	0.982	0.921	1	0.982	0.921	1	CLONAL	1	TRUE	1	0.513997292458694	2		773	1070	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805785	43805785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	234	595	0	ENST00000372470.3:c.841C>T	p.Pro281Ser	p.P281S	ENST00000372470	NM_005373.2	281	Cct/Tct	5/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.513997292458694	2		595	845	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651090	206651090	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	243	661	1	ENST00000367120.3:c.702-2A>G		p.X234_splice	ENST00000367120	NM_014002.3	234			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.513997292458694	2		662	884	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456560	32456560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886048229	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	61	130	0	ENST00000332351.3:c.332C>T	p.Pro111Leu	p.P111L	ENST00000332351	NM_024426.4	111	cCg/cTg	1/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.513997292458694	2		130	178	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456620	32456620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	116	298	0	ENST00000332351.3:c.272G>A	p.Gly91Asp	p.G91D	ENST00000332351	NM_024426.4	91	gGc/gAc	1/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.513997292458694	2		298	391	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646522	23646522	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	149	364	0	ENST00000261584.4:c.1345A>G	p.Lys449Glu	p.K449E	ENST00000261584	NM_024675.3	449	Aaa/Gaa	4/13	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.513997292458694	2		364	547	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229665	5229665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1364091998	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	21	42	0	ENST00000357368.4:c.2186C>T	p.Ala729Val	p.A729V	ENST00000357368	NM_002850.3	729	gCg/gTg	15/38	1	2	FACETS	0.973	0.767	1	0.973	0.767	1	CLONAL	1	TRUE	1	0.513997292458694	2		42	84	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945933	17945933	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	318	780	0	ENST00000458235.1:c.2006T>C	p.Leu669Pro	p.L669P	ENST00000458235	NM_000215.3	669	cTg/cCg	15/24	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.513997292458694	2		780	1198	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218093	36218095	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	149	328	0	ENST00000222270.7:c.4042_4044del	p.Asn1348del	p.N1348del	ENST00000222270	NM_014727.1	1347	gACAac/gac	15/37	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.513997292458694	2		328	558	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463305	25463305	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	164	464	0	ENST00000264709.3:c.2188C>T	p.Leu730Phe	p.L730F	ENST00000264709	NM_175629.2	730	Ctc/Ttc	19/23	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.513997292458694	2		464	618	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39212993	39212993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	194	517	0	ENST00000402219.2:c.3974C>T	p.Pro1325Leu	p.P1325L	ENST00000402219	NM_005633.3	1325	cCa/cTa	23/23	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.513997292458694	2		517	752	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672722	47672722	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	90	361	0	ENST00000233146.2:c.1312A>T	p.Thr438Ser	p.T438S	ENST00000233146	NM_000251.2	438	Act/Tct	8/16	1	2	FACETS	0.9	0.804	1	0.9	0.804	1	CLONAL	1	TRUE	1	0.513997292458694	2		361	389	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023692	31023692	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	214	538	0	ENST00000375687.4:c.3177G>T	p.Met1059Ile	p.M1059I	ENST00000375687	NM_015338.5	1059	atG/atT	13/13	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.513997292458694	2		538	803	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546005	41546005	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	246	575	0	ENST00000263253.7:c.2620C>A	p.Gln874Lys	p.Q874K	ENST00000263253	NM_001429.3	874	Cag/Aag	14/31	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.513997292458694	2		575	846	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610568	52610568	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	96	278	0	ENST00000394830.3:c.3605C>T	p.Thr1202Ile	p.T1202I	ENST00000394830	NM_018313.4	1202	aCa/aTa	23/30	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.513997292458694	2		278	345	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439392	149439392	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	190	495	0	ENST00000286301.3:c.2003A>G	p.Tyr668Cys	p.Y668C	ENST00000286301	NM_005211.3	668	tAt/tGt	15/22	1	2	FACETS	0.916	0.848	0.986	0.916	0.848	0.986	CLONAL	1	TRUE	1	0.513997292458694	2		495	807	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024144	112024144	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs761344763	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	118	320	0	ENST00000368678.4:c.641A>G	p.Tyr214Cys	p.Y214C	ENST00000368678		214	tAc/tGc	7/13	1	2	FACETS	0.971	0.881	1	0.971	0.881	1	CLONAL	1	TRUE	1	0.513997292458694	2		320	473	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851990	128851990	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	253	665	1	ENST00000249373.3:c.2066del	p.Pro689LeufsTer87	p.P689Lfs*87	ENST00000249373	NM_005631.4	688	Ccc/cc	12/12	1	2	FACETS	0.998	0.935	1	0.998	0.935	1	CLONAL	1	TRUE	1	0.513997292458694	2		666	986	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031713	69031713	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	130	381	0	ENST00000288368.4:c.3468C>A	p.Asp1156Glu	p.D1156E	ENST00000288368	NM_024870.2	1156	gaC/gaA	28/40	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.513997292458694	2		381	492	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5064943	5064943	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs368268750	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	55	260	0	ENST00000381652.3:c.1117T>C	p.Tyr373His	p.Y373H	ENST00000381652	NM_004972.3	373	Tat/Cat	9/25	1	2	FACETS	0.814	0.702	0.933	0.814	0.702	0.933	CLONAL	1	TRUE	1	0.513997292458694	2		260	263	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336307	80336307	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	94	267	0	ENST00000286548.4:c.1012C>A	p.Arg338Ser	p.R338S	ENST00000286548	NM_002072.3	338	Cgc/Agc	7/7	1	2	FACETS	0.903	0.809	1	0.903	0.809	1	CLONAL	1	TRUE	1	0.513997292458694	2		267	405	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851318	63851318	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	47	647	0	ENST00000279873.7:c.2096T>A	p.Val699Glu	p.V699E	ENST00000279873	NM_032199.2	699	gTg/gAg	10/10	1	2	FACETS	0.695	0.586	0.816	0.695	0.586	0.816	SUBCLONAL	1	FALSE	1	0.216001991919518	2		647	626	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578450	7578460	+	frameshift_variant	Frame_Shift_Del	DEL	CATGGCGCGGA	CATGGCGCGGA	-	novel	NA	P-0049635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	134	987	0	ENST00000269305.4:c.470_480del	p.Val157GlyfsTer20	p.V157Gfs*20	ENST00000269305	NM_001126112.2	157	gTCCGCGCCATG/g	5/11	0.155756637998209	2	FACETS	1	0.984	1	0.699	0.634	0.766	CLONAL	1	FALSE	0	0.216001991919518	2		987	888	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022628	31022628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	44	696	0	ENST00000375687.4:c.2113G>A	p.Glu705Lys	p.E705K	ENST00000375687	NM_015338.5	705	Gag/Aag	13/13	0.216001991919518	5	FACETS	0.638	0.533	0.755	0.16	0.133	0.189	SUBCLONAL	1	FALSE	1	0.216001991919518	5		696	845	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168476	56168476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	24	148	0	ENST00000399503.3:c.1432G>A	p.Glu478Lys	p.E478K	ENST00000399503	NM_005921.1	478	Gag/Aag	8/20	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	1	0.216001991919518	2		148	150	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681120	117681120	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0049635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	46	364	0	ENST00000368508.3:c.3500T>A	p.Leu1167Ter	p.L1167*	ENST00000368508	NM_002944.2	1167	tTa/tAa	23/43	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	1	0.216001991919518	2		364	331	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0049636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	14	424	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.208	0.149	0.28	0.208	0.149	0.28	SUBCLONAL	1	TRUE	1	0.27	2		424	498	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0049636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	76	383	1	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.27	2		384	524	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692961	89692961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060500122	NA	P-0049636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	61	468	0	ENST00000371953.3:c.445C>T	p.Gln149Ter	p.Q149*	ENST00000371953	NM_000314.4	149	Caa/Taa	5/9	1	2	FACETS	0.951	0.822	1	0.951	0.822	1	CLONAL	1	TRUE	1	0.27	2		468	475	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097665	27097665	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0049636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	39	461	0	ENST00000324856.7:c.3254C>G	p.Ser1085Ter	p.S1085*	ENST00000324856	NM_006015.4	1085	tCa/tGa	12/20	1	2	FACETS	0.507	0.419	0.605	0.507	0.419	0.605	SUBCLONAL	1	TRUE	1	0.27	2		461	570	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589630	67589645	+	protein_altering_variant	In_Frame_Del	DEL	AGATTATATGAAGAAT	AGATTATATGAAGAAT	G	novel	NA	P-0049636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	12	180	0	ENST00000274335.5:c.1393_1408delinsG	p.Arg465_Tyr470delinsAsp	p.R465_Y470delinsD	ENST00000274335		465	AGATTATATGAAGAATat/Gat	10/15	1	2	FACETS	0.465	0.327	0.635	0.465	0.327	0.635	SUBCLONAL	1	TRUE	1	0.27	2		180	191	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27093058	27093058	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0049637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	48	267	0	ENST00000324856.7:c.2988+1G>T		p.X996_splice	ENST00000324856	NM_006015.4	996			0.293871577038269	1	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	0	0.293871577038269	1		267	270	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849872	156849872	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370593942	NA	P-0049637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	99	631	1	ENST00000524377.1:c.2128G>A	p.Val710Met	p.V710M	ENST00000524377	NM_002529.3	710	Gtg/Atg	16/17	0.293871577038269	3	FACETS	0.867	0.773	0.968	0.434	0.386	0.484	CLONAL	1	TRUE	1	0.293871577038269	3		632	891	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604776	48604776	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs377767382	NA	P-0049637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	28	312	0	ENST00000342988.3:c.1598T>G	p.Leu533Arg	p.L533R	ENST00000342988	NM_005359.5	533	cTc/cGc	12/12	0.293871577038269	1	FACETS	0.454	0.363	0.558	0.454	0.363	0.558	SUBCLONAL	1	TRUE	0	0.293871577038269	1		312	358	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569680	41569680	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	37	181	0	ENST00000263253.7:c.4671C>A	p.Ser1557Arg	p.S1557R	ENST00000263253	NM_001429.3	1557	agC/agA	29/31	1	2	FACETS	0.995	0.826	1	0.995	0.826	1	CLONAL	1	TRUE	1	0.293871577038269	2		181	253	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713544	30713544	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	93	480	0	ENST00000295754.5:c.869A>G	p.Glu290Gly	p.E290G	ENST00000295754	NM_003242.5	290	gAg/gGg	4/7	0.293871577038269	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.293871577038269	1		480	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0049638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	225	485	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.361018910663856	2	FACETS	0.871	0.816	0.926	0.871	0.816	0.926	CLONAL	2	TRUE	0	0.418219873684917	2		486	618	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0049638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	54	400	2	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.376335615495716	3	FACETS	1	0.909	1	0.538	0.463	0.619	CLONAL	1	TRUE	1	0.418219873684917	3		402	290	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053589	37053589	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs63751615	NA	P-0049638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	45	332	0	ENST00000231790.2:c.676C>T	p.Arg226Ter	p.R226*	ENST00000231790	NM_000249.3	226	Cga/Tga	8/19	0.376335615495716	3	FACETS	0.662	0.557	0.777	0.331	0.278	0.389	SUBCLONAL	1	TRUE	1	0.418219873684917	3		332	393	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277225	41277225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760837728	NA	P-0049638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	44	223	0	ENST00000349496.5:c.1694G>A	p.Arg565His	p.R565H	ENST00000349496	NM_001904.3	565	cGc/cAc	11/15	0.376335615495716	3	FACETS	0.746	0.628	0.876	0.373	0.314	0.438	SUBCLONAL	1	TRUE	1	0.418219873684917	3		223	341	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991316	41991316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	100	397	1	ENST00000219905.7:c.2147C>T	p.Thr716Ile	p.T716I	ENST00000219905	NM_001164273.1	716	aCt/aTt	5/24	0.361018910663856	2	FACETS	1	0.982	1	0.72	0.65	0.793	CLONAL	1	TRUE	0	0.418219873684917	2		398	332	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210824	2210824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766521628	NA	P-0049638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	96	514	3	ENST00000398665.3:c.1321G>A	p.Val441Met	p.V441M	ENST00000398665	NM_032482.2	441	Gtg/Atg	14/28	0.376335615495716	3	FACETS	0.95	0.849	1	0.475	0.424	0.529	CLONAL	1	TRUE	1	0.418219873684917	3		517	584	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662029	227662029	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	98	649	0	ENST00000305123.5:c.1426C>G	p.Leu476Val	p.L476V	ENST00000305123	NM_005544.2	476	Ctg/Gtg	1/2	0.282654439485506	3	FACETS	0.841	0.751	0.936	0.42	0.375	0.468	CLONAL	1	TRUE	1	0.418219873684917	3		649	674	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0049640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	74	677	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.16	2		677	892	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248409	59248409	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1184098204	NA	P-0049640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	37	472	0	ENST00000371222.2:c.334G>C	p.Glu112Gln	p.E112Q	ENST00000371222	NM_002228.3	112	Gag/Cag	1/1	1	2	FACETS	0.635	0.522	0.763	0.635	0.522	0.763	SUBCLONAL	1	TRUE	1	0.16	2		472	728	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564698	86564698	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	58	620	0	ENST00000274376.6:c.434del	p.Pro145LeufsTer29	p.P145Lfs*29	ENST00000274376	NM_002890.2	144	Ccc/cc	1/25	0.207585881641377	3	FACETS	0.741	0.634	0.858	0.37	0.317	0.429	SUBCLONAL	1	TRUE	1	0.16	3		620	1057	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405180	139405180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs557590721	NA	P-0049640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	66	870	1	ENST00000277541.6:c.2665G>A	p.Gly889Ser	p.G889S	ENST00000277541	NM_017617.3	889	Ggc/Agc	17/34	1	2	FACETS	0.724	0.626	0.831	0.724	0.626	0.831	SUBCLONAL	1	TRUE	1	0.16	2		871	1139	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169359	11169359	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	26	386	0	ENST00000361445.4:c.7516G>C	p.Asp2506His	p.D2506H	ENST00000361445	NM_004958.3	2506	Gat/Cat	56/58	1	2	FACETS	0.658	0.52	0.817	0.658	0.52	0.817	SUBCLONAL	1	TRUE	1	0.16	2		386	494	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257746	16257746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	36	391	0	ENST00000375759.3:c.5011G>A	p.Glu1671Lys	p.E1671K	ENST00000375759	NM_015001.2	1671	Gag/Aag	11/15	1	2	FACETS	0.776	0.637	0.933	0.776	0.637	0.933	CLONAL	1	TRUE	1	0.16	2		391	580	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136259	202136259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	40	420	0	ENST00000358485.4:c.503C>T	p.Ser168Leu	p.S168L	ENST00000358485	NM_001080125.1	168	tCa/tTa	3/9	0.3	4	FACETS	0.902	0.748	1			1	CLONAL	1	TRUE	NA	0.16	4		420	643	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	37	431	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.692	0.572	0.826	0.692	0.572	0.826	SUBCLONAL	1	TRUE	1	0.31	2		431	345	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	71	419	0	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.839	0.733	0.953	0.839	0.733	0.953	CLONAL	1	TRUE	1	0.31	2		419	546	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	100	824	5	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.867	0.775	0.966	0.867	0.775	0.966	CLONAL	1	TRUE	1	0.31	2		829	744	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	80	795	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.823	0.725	0.928	0.823	0.725	0.928	CLONAL	1	TRUE	1	0.31	2		795	627	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	63	409	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.999	0.867	1	0.999	0.867	1	CLONAL	1	TRUE	1	0.31	2		415	407	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	121	994	2	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.789	0.711	0.87	0.789	0.711	0.87	SUBCLONAL	1	TRUE	1	0.31	2		996	990	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324892	31324892	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs765875917	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	22	139	0	ENST00000412585.2:c.44del	p.Ala15GlyfsTer5	p.A15Gfs*5	ENST00000412585	NM_005514.6	15	gCg/gg	1/8	1	2	FACETS	0.789	0.625	0.969	1	0.933	1	CLONAL	2	TRUE	1	0.31	2		139	90	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894904	101894904	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56014374	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	40	332	0	ENST00000374994.4:c.457G>A	p.Val153Ile	p.V153I	ENST00000374994	NM_004612.2	153	Gtc/Atc	3/9	1	2	FACETS	0.66	0.549	0.783	0.66	0.549	0.783	SUBCLONAL	1	TRUE	1	0.31	2		332	391	SUCCESS
APC	324	MSKCC	GRCh37	5	112175970	112175970	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1114167552	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	21	213	0	ENST00000257430.4:c.4682del	p.Lys1561ArgfsTer4	p.K1561Rfs*4	ENST00000257430	NM_000038.5	1560	gAa/ga	16/16	1	2	FACETS	0.779	0.604	0.98	0.779	0.604	0.98	CLONAL	1	TRUE	1	0.31	2		213	174	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	42	350	2	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.883	0.74	1	0.883	0.74	1	CLONAL	1	TRUE	1	0.31	2		352	307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577138	7577138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780075	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	97	574	0	ENST00000269305.4:c.800G>A	p.Arg267Gln	p.R267Q	ENST00000269305	NM_001126112.2	267	cGg/cAg	8/11	1	2	FACETS	0.928	0.828	1	0.928	0.828	1	CLONAL	1	TRUE	1	0.31	2		574	674	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755554	39755554	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	51	480	2	ENST00000288319.7:c.1211del	p.Pro404ArgfsTer25	p.P404Rfs*25	ENST00000288319	NM_182918.3	404	cCg/cg	10/10	1	2	FACETS	0.734	0.625	0.854	0.734	0.625	0.854	SUBCLONAL	1	TRUE	1	0.31	2		482	448	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465606	99465606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	65	503	0	ENST00000268035.6:c.2431G>A	p.Glu811Lys	p.E811K	ENST00000268035	NM_000875.3	811	Gag/Aag	11/21	1	2	FACETS	0.844	0.733	0.964	0.844	0.733	0.964	CLONAL	1	TRUE	1	0.31	2		503	497	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721049	176721049	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748597598	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	69	491	0	ENST00000439151.2:c.6680C>T	p.Pro2227Leu	p.P2227L	ENST00000439151	NM_022455.4	2227	cCg/cTg	23/23	1	2	FACETS	0.875	0.763	0.995	0.875	0.763	0.995	CLONAL	1	TRUE	1	0.31	2		491	509	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937914	36937914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs606231473	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	104	1035	0	ENST00000361632.4:c.922C>T	p.Arg308Cys	p.R308C	ENST00000361632		308	Cgc/Tgc	7/16	1	2	FACETS	0.815	0.73	0.906	0.815	0.73	0.906	CLONAL	1	TRUE	1	0.31	2		1035	823	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807363	3807364	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	38	337	0	ENST00000262367.5:c.3623dup	p.Gln1209ThrfsTer25	p.Q1209Tfs*25	ENST00000262367	NM_004380.2	1208	cca/ccCa	19/31	1	2	FACETS	0.757	0.627	0.9	0.757	0.627	0.9	SUBCLONAL	1	TRUE	1	0.31	2		337	324	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278073	18278073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	108	805	0	ENST00000222254.8:c.1693C>T	p.Pro565Ser	p.P565S	ENST00000222254	NM_005027.3	565	Ccg/Tcg	13/16	1	2	FACETS	0.85	0.762	0.943	0.85	0.762	0.943	CLONAL	1	TRUE	1	0.31	2		805	820	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021442	42021442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1193719928	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	53	376	1	ENST00000219905.7:c.3744del	p.Glu1249ArgfsTer42	p.E1249Rfs*42	ENST00000219905	NM_001164273.1	1246	cgA/cg	11/24	1	2	FACETS	0.706	0.603	0.82	0.706	0.603	0.82	SUBCLONAL	1	TRUE	1	0.31	2		377	484	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216725	2216725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200144638	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	132	953	5	ENST00000398665.3:c.2369C>T	p.Thr790Met	p.T790M	ENST00000398665	NM_032482.2	790	aCg/aTg	20/28	1	2	FACETS	0.899	0.816	0.988	0.899	0.816	0.988	CLONAL	1	TRUE	1	0.31	2		958	947	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120031	70120031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	10	132	0	ENST00000245479.2:c.1037del	p.Pro346ArgfsTer37	p.P346Rfs*37	ENST00000245479	NM_000346.3	345	Ccc/cc	3/3	1	2	FACETS	0.529	0.36	0.738	0.529	0.36	0.738	SUBCLONAL	1	TRUE	1	0.31	2		132	122	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165720	185165720	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	64	327	0	ENST00000265026.3:c.999del	p.Val334LeufsTer14	p.V334Lfs*14	ENST00000265026	NM_004721.4	332	gAa/ga	5/14	1	2	FACETS	0.916	0.795	1	0.916	0.795	1	CLONAL	1	TRUE	1	0.31	2		327	451	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839785	42839785	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773001010	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	56	478	0	ENST00000398585.3:c.1454C>T	p.Ser485Leu	p.S485L	ENST00000398585	NM_001135099.1	485	tCg/tTg	13/14	1	2	FACETS	0.751	0.644	0.867	0.751	0.644	0.867	SUBCLONAL	1	TRUE	1	0.31	2		478	481	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617680	39617680	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	37	280	0	ENST00000262039.4:c.1869del	p.Phe623LeufsTer43	p.F623Lfs*43	ENST00000262039	NM_002647.2	622	Ttt/tt	17/25	1	2	FACETS	0.826	0.684	0.983	0.826	0.684	0.983	CLONAL	1	TRUE	1	0.31	2		280	289	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082313	16082314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs780080562	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	109	923	3	ENST00000281043.3:c.134dup	p.Glu47GlyfsTer8	p.E47Gfs*8	ENST00000281043	NM_005378.4	43	acc/aCcc	2/3	1	2	FACETS	0.792	0.71	0.879	0.792	0.71	0.879	SUBCLONAL	1	TRUE	1	0.31	2		926	888	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137271	64137271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	105	852	0	ENST00000334205.4:c.1703C>T	p.Thr568Met	p.T568M	ENST00000334205	NM_003942.2	568	aCg/aTg	14/17	1	2	FACETS	0.815	0.73	0.906	0.815	0.73	0.906	CLONAL	1	TRUE	1	0.31	2		852	831	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119780	70119781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	72	561	0	ENST00000245479.2:c.788dup	p.Arg264GlnfsTer32	p.R264Qfs*32	ENST00000245479	NM_000346.3	261	gag/gaGg	3/3	1	2	FACETS	0.922	0.807	1	0.922	0.807	1	CLONAL	1	TRUE	1	0.31	2		561	504	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	113	842	2	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.893	0.804	0.988	0.893	0.804	0.988	CLONAL	1	TRUE	1	0.31	2		844	816	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041262	29041262	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	42	390	0	ENST00000282397.4:c.166del	p.Glu56LysfsTer12	p.E56Kfs*12	ENST00000282397	NM_002019.4	56	Gaa/aa	3/30	1	2	FACETS	0.795	0.666	0.937	0.795	0.666	0.937	CLONAL	1	TRUE	1	0.31	2		390	341	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945757	38945757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1032272899	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	16	230	0	ENST00000357387.3:c.4469C>T	p.Thr1490Met	p.T1490M	ENST00000357387	NM_152756.3	1490	aCg/aTg	34/38	1	2	FACETS	0.416	0.308	0.546	0.416	0.308	0.546	SUBCLONAL	1	TRUE	1	0.31	2		230	248	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435967	49435967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	121	715	1	ENST00000301067.7:c.6014G>A	p.Arg2005His	p.R2005H	ENST00000301067	NM_003482.3	2005	cGc/cAc	28/54	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.31	2		716	731	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216189	36216189	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	120	813	1	ENST00000222270.7:c.3602del	p.Pro1201ArgfsTer154	p.P1201Rfs*154	ENST00000222270	NM_014727.1	1199	ggC/gg	11/37	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.31	2		814	755	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651591	48651591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557020430	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	78	296	0	ENST00000376670.3:c.757C>T	p.Arg253Trp	p.R253W	ENST00000376670	NM_002049.3	253	Cgg/Tgg	5/6	1	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.31	1		296	313	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864218	57864218	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	83	661	4	ENST00000228682.2:c.1700del	p.Pro567LeufsTer46	p.P567Lfs*46	ENST00000228682	NM_005269.2	565	ttC/tt	12/12	1	2	FACETS	0.905	0.799	1	0.905	0.799	1	CLONAL	1	TRUE	1	0.31	2		665	592	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484058	50484058	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1442501952	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	90	559	1	ENST00000394963.4:c.908G>A	p.Arg303Gln	p.R303Q	ENST00000394963	NM_003076.4	303	cGa/cAa	8/13	1	2	FACETS	0.848	0.752	0.949	0.848	0.752	0.949	CLONAL	1	TRUE	1	0.31	2		560	685	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416692	29416692	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	53	434	0	ENST00000389048.3:c.4261del	p.Val1421PhefsTer56	p.V1421Ffs*56	ENST00000389048	NM_004304.4	1421	Gtt/tt	29/29	1	2	FACETS	0.855	0.731	0.99	0.855	0.731	0.99	CLONAL	1	TRUE	1	0.31	2		434	400	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288870	15288870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	53	358	0	ENST00000263388.2:c.3869C>T	p.Ala1290Val	p.A1290V	ENST00000263388	NM_000435.2	1290	gCg/gTg	24/33	1	2	FACETS	0.834	0.713	0.966	0.834	0.713	0.966	CLONAL	1	TRUE	1	0.31	2		358	410	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412248	63412248	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	91	439	0	ENST00000330258.3:c.919del	p.Asp307ThrfsTer3	p.D307Tfs*3	ENST00000330258	NM_152424.3	307	Gac/ac	2/2	1	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.31	1		439	361	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752347	55752347	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1485302383	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	145	911	0	ENST00000284073.2:c.805C>T	p.Arg269Trp	p.R269W	ENST00000284073	NM_138962.2	269	Cgg/Tgg	12/14	1	2	FACETS	0.966	0.881	1	0.966	0.881	1	CLONAL	1	TRUE	1	0.31	2		911	968	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609768	117609768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	54	456	0	ENST00000368508.3:c.6931G>A	p.Ala2311Thr	p.A2311T	ENST00000368508	NM_002944.2	2311	Gca/Aca	43/43	1	2	FACETS	0.67	0.572	0.777	0.67	0.572	0.777	SUBCLONAL	1	TRUE	1	0.31	2		456	520	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155691	119155691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	66	440	1	ENST00000264033.4:c.1444C>T	p.Pro482Ser	p.P482S	ENST00000264033	NM_005188.3	482	Cct/Tct	10/16	1	2	FACETS	0.97	0.845	1	0.97	0.845	1	CLONAL	1	TRUE	1	0.31	2		441	439	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233274	46233274	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	46	243	0	ENST00000334344.6:c.1496del	p.Pro499GlnfsTer7	p.P499Qfs*7	ENST00000334344	NM_152641.2	498	gCc/gc	11/21	1	2	FACETS	0.886	0.749	1	0.886	0.749	1	CLONAL	1	TRUE	1	0.31	2		243	335	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32890601	32890601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266625701	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	39	280	0	ENST00000380152.3:c.4C>T	p.Pro2Ser	p.P2S	ENST00000380152		2	Cct/Tct	2/27	1	2	FACETS	0.809	0.673	0.959	0.809	0.673	0.959	CLONAL	1	TRUE	1	0.31	2		280	311	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437838	110437838	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	81	438	1	ENST00000375856.3:c.563C>T	p.Ala188Val	p.A188V	ENST00000375856	NM_003749.2	188	gCt/gTt	1/2	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.31	2		439	468	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225347	2225347	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201904294	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	102	817	0	ENST00000326181.6:c.1432C>T	p.His478Tyr	p.H478Y	ENST00000326181	NM_032271.2	478	Cat/Tat	16/21	1	2	FACETS	0.966	0.865	1	0.966	0.865	1	CLONAL	1	TRUE	1	0.31	2		817	681	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991448	72991448	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	122	769	0	ENST00000268489.5:c.2597T>C	p.Leu866Pro	p.L866P	ENST00000268489	NM_006885.3	866	cTg/cCg	2/10	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.31	2		769	733	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108208	8108208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	93	663	0	ENST00000585124.1:c.1016C>T	p.Ala339Val	p.A339V	ENST00000585124	NM_004217.3	339	gCc/gTc	9/9	1	2	FACETS	0.719	0.639	0.805	0.719	0.639	0.805	SUBCLONAL	1	TRUE	1	0.31	2		663	834	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12044509	12044509	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771926980	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	41	353	0	ENST00000353533.5:c.1132G>A	p.Ala378Thr	p.A378T	ENST00000353533	NM_003010.3	378	Gca/Aca	11/11	1	2	FACETS	0.797	0.666	0.941	0.797	0.666	0.941	CLONAL	1	TRUE	1	0.31	2		353	332	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274112	18274112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770051333	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	81	642	0	ENST00000222254.8:c.1330G>A	p.Ala444Thr	p.A444T	ENST00000222254	NM_005027.3	444	Gcc/Acc	11/16	1	2	FACETS	0.722	0.636	0.814	0.722	0.636	0.814	SUBCLONAL	1	TRUE	1	0.31	2		642	724	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222923	36222923	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	130	936	1	ENST00000222270.7:c.5552G>T	p.Ser1851Ile	p.S1851I	ENST00000222270	NM_014727.1	1851	aGc/aTc	27/37	1	2	FACETS	0.909	0.824	0.998	0.909	0.824	0.998	CLONAL	1	TRUE	1	0.31	2		937	923	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753281	42753281	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	101	945	0	ENST00000222329.4:c.983C>A	p.Pro328His	p.P328H	ENST00000222329	NM_006494.2	328	cCc/cAc	4/4	1	2	FACETS	0.658	0.587	0.734	0.658	0.587	0.734	SUBCLONAL	1	TRUE	1	0.31	2		945	990	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47643489	47643489	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs63750468	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	78	490	0	ENST00000233146.2:c.997T>C	p.Cys333Arg	p.C333R	ENST00000233146	NM_000251.2	333	Tgt/Cgt	6/16	1	2	FACETS	0.937	0.825	1	0.937	0.825	1	CLONAL	1	TRUE	1	0.31	2		490	537	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939965	49939965	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751907940	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	135	823	1	ENST00000296474.3:c.1078G>A	p.Val360Met	p.V360M	ENST00000296474	NM_002447.2	360	Gtg/Atg	1/20	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.31	2		824	856	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594251	55594251	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	40	347	0	ENST00000288135.5:c.1954A>G	p.Asn652Asp	p.N652D	ENST00000288135	NM_000222.2	652	Aat/Gat	13/21	1	2	FACETS	0.757	0.631	0.896	0.757	0.631	0.896	SUBCLONAL	1	TRUE	1	0.31	2		347	341	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38971980	38971980	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1271519942	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	27	259	0	ENST00000357387.3:c.971G>A	p.Arg324Lys	p.R324K	ENST00000357387	NM_152756.3	324	aGg/aAg	11/38	1	2	FACETS	0.72	0.575	0.884	0.72	0.575	0.884	SUBCLONAL	1	TRUE	1	0.31	2		259	242	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738290	145738290	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	121	995	1	ENST00000428558.2:c.2695G>T	p.Gly899Cys	p.G899C	ENST00000428558	NM_004260.3	899	Ggc/Tgc	16/22	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.31	2		996	738	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760132	133760132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373527910	NA	P-0049661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	69	703	0	ENST00000318560.5:c.2455C>T	p.Arg819Trp	p.R819W	ENST00000318560	NM_005157.4	819	Cgg/Tgg	11/11	1	2	FACETS	0.698	0.608	0.795	0.698	0.608	0.795	SUBCLONAL	1	TRUE	1	0.31	2		703	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0049662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	281	768	7	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.60512195527655	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.60512195527655	1		775	634	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100175	27100176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	159	596	0	ENST00000324856.7:c.3977dup	p.Gln1327AlafsTer11	p.Q1327Afs*11	ENST00000324856	NM_006015.4	1324	tac/taCc	16/20	0.360199781182863	1	FACETS	0.713	0.658	0.77	0.713	0.658	0.77	INDETERMINATE	1	TRUE	0	0.60512195527655	1		596	514	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851286	156851286	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745776726	NA	P-0049662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	140	812	0	ENST00000524377.1:c.2243G>A	p.Arg748Gln	p.R748Q	ENST00000524377	NM_002529.3	748	cGg/cAg	17/17	0.360199781182863	1	FACETS	0.363	0.33	0.397	0.363	0.33	0.397	INDETERMINATE	1	TRUE	0	0.60512195527655	1		812	889	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710517	114710517	+	start_lost	Translation_Start_Site	SNP	T	T	A	novel	NA	P-0049662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	70	356	0	ENST00000543371.1:c.2T>A	p.Met1?	p.M1?	ENST00000543371	NM_001198531.1	1	aTg/aAg	1/14	1	2	FACETS	0.619	0.542	0.7	0.619	0.542	0.7	SUBCLONAL	1	TRUE	1	0.60512195527655	2		356	374	SUCCESS
APC	324	MSKCC	GRCh37	5	112174745	112174745	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064795228	NA	P-0049662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	13	197	0	ENST00000257430.4:c.3454C>T	p.Gln1152Ter	p.Q1152*	ENST00000257430	NM_000038.5	1152	Cag/Tag	16/16	0.559962239071875	2	FACETS	0.955	0.707	1	0.477	0.353	0.616	CLONAL	1	TRUE	0	0.60512195527655	2		197	45	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748093	72748093	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	83	545	0	ENST00000357731.5:c.85C>T	p.Pro29Ser	p.P29S	ENST00000357731	NM_173808.2	29	Ccc/Tcc	1/7	0.360199781182863	1	FACETS	0.347	0.306	0.39	0.347	0.306	0.39	INDETERMINATE	1	TRUE	0	0.60512195527655	1		545	552	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0049663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	181	479	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	0.122910361076078	4	FACETS	0.88	0.82	0.942	0.88	0.82	0.942	INDETERMINATE	2	TRUE	2	0.769250270936813	4		479	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	56	690	0	ENST00000269305.4:c.517G>C	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ctg	5/11	1	2	FACETS	0.494	0.422	0.574	0.494	0.422	0.574	SUBCLONAL	1	TRUE	1	0.23	2		690	985	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317529	1317529	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	56	552	0	ENST00000400841.2:c.536A>C	p.Lys179Thr	p.K179T	ENST00000400841		179	aAg/aCg	5/6	1	2	FACETS	0.58	0.496	0.673	0.58	0.496	0.673	SUBCLONAL	1	TRUE	1	0.23	2		552	839	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043438	180043438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373876329	NA	P-0049664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	100	790	0	ENST00000261937.6:c.3148G>A	p.Val1050Met	p.V1050M	ENST00000261937	NM_182925.4	1050	Gtg/Atg	23/30	1	2	FACETS	0.77	0.686	0.86	0.77	0.686	0.86	SUBCLONAL	1	TRUE	1	0.23	2		790	1129	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979529	7979529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768784091	NA	P-0049664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	53	472	0	ENST00000319144.4:c.1496G>A	p.Arg499His	p.R499H	ENST00000319144	NM_001139.2	499	cGc/cAc	11/15	1	2	FACETS	0.529	0.45	0.617	0.529	0.45	0.617	SUBCLONAL	1	TRUE	1	0.23	2		472	871	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0049665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	129	406	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.172999499571254	33	FACETS	1	0.939	1	0.288	0.261	0.316	CLONAL	8	FALSE	4	0.172999499571254	33		406	658	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950304	38950304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs895560221	NA	P-0049665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	27	384	1	ENST00000357387.3:c.3646C>T	p.Arg1216Cys	p.R1216C	ENST00000357387	NM_152756.3	1216	Cgt/Tgt	31/38	0.172999499571254	1	FACETS	0.932	0.75	1	1	0.952	1	CLONAL	2	FALSE	0	0.172999499571254	1		385	153	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245948	46245948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	21	269	0	ENST00000334344.6:c.4042G>A	p.Asp1348Asn	p.D1348N	ENST00000334344	NM_152641.2	1348	Gat/Aat	15/21	0.140837342072072	4	FACETS	1	0.872	1	1	0.938	1	CLONAL	3	FALSE	2	0.172999499571254	4		269	82	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198176	185198176	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs149975635	NA	P-0049665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1393	102	517	0	ENST00000265026.3:c.2658C>A	p.Asp886Glu	p.D886E	ENST00000265026	NM_004721.4	886	gaC/gaA	13/14	0.172999499571254	33	FACETS	0.968	0.862	1	0.1	0.089	0.112	CLONAL	3	FALSE	4	0.172999499571254	33		517	1495	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27192559	27192559	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	86	455	0	ENST00000380036.4:c.1562G>C	p.Arg521Pro	p.R521P	ENST00000380036	NM_000459.3	521	cGt/cCt	11/23	1	2	FACETS	1	0.963	1	1	0.987	1	CLONAL	2	FALSE	1	0.172999499571254	2		455	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0049666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	398	768	7	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.855436150281051	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.855436150281051	1		775	510	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612876	228612876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	391	847	0	ENST00000366696.1:c.151G>A	p.Glu51Lys	p.E51K	ENST00000366696	NM_003493.2	51	Gag/Aag	1/1	0.855436150281051	3	FACETS	0.945	0.897	0.994	0.473	0.448	0.497	CLONAL	1	TRUE	1	0.855436150281051	3		847	1381	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188370	142188370	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	84	361	0	ENST00000350721.4:c.6361A>G	p.Lys2121Glu	p.K2121E	ENST00000350721	NM_001184.3	2121	Aaa/Gaa	38/47	0.436840774921841	3	FACETS	0.464	0.41	0.522	0.232	0.205	0.261	INDETERMINATE	1	TRUE	1	0.855436150281051	3		361	604	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519896	NA	P-0049666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	192	281	0	ENST00000281708.4:c.1514G>T	p.Arg505Leu	p.R505L	ENST00000281708	NM_033632.3	505	cGc/cTc	10/12	0.855436150281051	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.855436150281051	1		281	237	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913492	NA	P-0049667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	23	370	0	ENST00000286548.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000286548	NM_002072.3	209	cAa/cTa	5/7	1	2	FACETS	0.998	0.78	1	0.998	0.78	1	CLONAL	1	TRUE	1	0.18	2		370	256	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451788	29451788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1490348940	NA	P-0049667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	44	595	1	ENST00000389048.3:c.2777G>A	p.Gly926Glu	p.G926E	ENST00000389048	NM_004304.4	926	gGg/gAg	16/29	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.18	2		596	455	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752411	57752412	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0049668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	60	192	0	ENST00000274289.3:c.1161_1162del	p.Arg387SerfsTer3	p.R387Sfs*3	ENST00000274289	NM_006622.3	387	agAGtg/agtg	9/14	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.453455278768541	2		192	258	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117335	115117335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	83	292	0	ENST00000257566.3:c.839C>T	p.Ala280Val	p.A280V	ENST00000257566	NM_016569.3	280	gCt/gTt	4/8	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.453455278768541	2		292	332	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844109	68844110	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACGCTGTG	novel	NA	P-0049668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	130	466	0	ENST00000261769.5:c.698_705dup	p.Ser236ThrfsTer17	p.S236Tfs*17	ENST00000261769	NM_004360.3	233	cac/cACGCTGTGac	6/16	0.453455278768541	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.453455278768541	1		466	418	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444345	50444345	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	94	363	0	ENST00000331340.3:c.275T>C	p.Met92Thr	p.M92T	ENST00000331340	NM_006060.4	92	aTg/aCg	4/8	0.296364310543677	1	FACETS	0.744	0.666	0.826	0.744	0.666	0.826	SUBCLONAL	1	TRUE	0	0.453455278768541	1		363	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0049669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	629	485	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.538666493838162	3	FACETS	0.951	0.921	0.981			1	CLONAL	2	TRUE	NA	0.845114279039228	3		486	1113	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0049669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	15214	913	0	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.845114279039228	24	FACETS	1	0.999	1			1	CLONAL	23	TRUE	NA	0.845114279039228	24		913	16061	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103675	47103675	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	193	390	0	ENST00000409792.3:c.6271G>T	p.Gly2091Ter	p.G2091*	ENST00000409792	NM_014159.6	2091	Gga/Tga	14/21	1	2	FACETS	0.889	0.829	0.949	0.889	0.829	0.949	CLONAL	1	TRUE	1	0.845114279039228	2		390	514	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0049669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	148	248	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.97	0.898	1	0.97	0.898	1	CLONAL	1	TRUE	1	0.845114279039228	2		249	361	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720669	89720669	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	105	298	0	ENST00000371953.3:c.820T>C	p.Trp274Arg	p.W274R	ENST00000371953	NM_000314.4	274	Tgg/Cgg	8/9	0.845114279039228	1	FACETS	0.854	0.793	0.914	0.854	0.793	0.914	CLONAL	1	TRUE	0	0.845114279039228	1		298	168	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0049670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	368	592	1	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.442828622801851	2	FACETS	0.897	0.856	0.938	0.897	0.856	0.938	CLONAL	2	TRUE	0	0.502811979124879	2		593	816	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858298	9858298	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540445580	NA	P-0049670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	112	361	0	ENST00000330684.3:c.3103G>A	p.Asp1035Asn	p.D1035N	ENST00000330684	NM_001134407.1	1035	Gat/Aat	13/13	1	2	FACETS	0.889	0.804	0.979	0.889	0.804	0.979	CLONAL	1	TRUE	1	0.502811979124879	2		361	501	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610076	43610076	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	189	673	2	ENST00000355710.3:c.2028C>A	p.Phe676Leu	p.F676L	ENST00000355710	NM_020975.4	676	ttC/ttA	11/20	1	2	FACETS	0.869	0.804	0.937	0.869	0.804	0.937	CLONAL	1	TRUE	1	0.502811979124879	2		675	865	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811652	102811652	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	189	620	1	ENST00000307046.8:c.532C>A	p.Gln178Lys	p.Q178K	ENST00000307046	NM_001111285.1	178	Cag/Aag	4/4	0.502811979124879	1	FACETS	0.836	0.776	0.898	0.836	0.776	0.898	CLONAL	1	TRUE	0	0.502811979124879	1		621	673	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656701	3656701	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0049670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	204	577	0	ENST00000294008.3:c.536-2A>T		p.X179_splice	ENST00000294008	NM_032444.2	179			1	2	FACETS	0.921	0.855	0.989	0.921	0.855	0.989	CLONAL	1	TRUE	1	0.502811979124879	2		577	881	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829870	72829870	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	221	575	0	ENST00000268489.5:c.6711G>C	p.Glu2237Asp	p.E2237D	ENST00000268489	NM_006885.3	2237	gaG/gaC	9/10	1	2	FACETS	0.915	0.852	0.98	0.915	0.852	0.98	CLONAL	1	TRUE	1	0.502811979124879	2		575	961	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872587	37872587	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	248	686	1	ENST00000269571.5:c.1547C>T	p.Ala516Val	p.A516V	ENST00000269571		516	gCc/gTc	13/27	0.502811979124879	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.502811979124879	1		687	674	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561855	55561855	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	81	311	0	ENST00000288135.5:c.245G>A	p.Trp82Ter	p.W82*	ENST00000288135	NM_000222.2	82	tGg/tAg	2/21	1	2	FACETS	0.724	0.641	0.813	0.724	0.641	0.813	SUBCLONAL	1	TRUE	1	0.502811979124879	2		311	445	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280008	66280008	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	43	187	0	ENST00000273854.3:c.1681C>G	p.Pro561Ala	p.P561A	ENST00000273854	NM_004439.5	561	Cca/Gca	7/18	1	2	FACETS	0.574	0.483	0.674	0.574	0.483	0.674	SUBCLONAL	1	TRUE	1	0.502811979124879	2		187	298	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981584	70981584	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	264	885	0	ENST00000276594.2:c.512C>G	p.Pro171Arg	p.P171R	ENST00000276594	NM_024504.3	171	cCt/cGt	2/8	1	2	FACETS	0.885	0.829	0.943	0.885	0.829	0.943	CLONAL	1	TRUE	1	0.502811979124879	2		885	1186	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	43	431	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.971	0.812	1	0.971	0.812	1	CLONAL	1	TRUE	1	0.17	2		431	521	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0049672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	30	161	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.754	0.611	0.915	1	0.942	1	CLONAL	2	TRUE	1	0.17	2		161	234	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0049672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	117	437	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.845	0.765	0.929	1	0.991	1	CLONAL	3	TRUE	1	0.17	2		437	543	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0049672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	86	499	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.17	2		499	795	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124717	108124717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751515818	NA	P-0049672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	22	347	0	ENST00000278616.4:c.2075G>A	p.Arg692His	p.R692H	ENST00000278616	NM_000051.3	692	cGc/cAc	13/63	1	2	FACETS	0.622	0.481	0.786	0.622	0.481	0.786	SUBCLONAL	1	TRUE	1	0.17	2		347	416	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941004	71941004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	89	880	0	ENST00000298229.2:c.884del	p.Pro295GlnfsTer20	p.P295Qfs*20	ENST00000298229	NM_001567.3	294	Ccc/cc	8/28	1	2	FACETS	0.772	0.682	0.869	0.772	0.682	0.869	SUBCLONAL	1	TRUE	1	0.17	2		880	1356	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	85	906	0	ENST00000227507.2:c.859C>A	p.Pro287Thr	p.P287T	ENST00000227507	NM_053056.2	287	Ccc/Acc	5/5	1	2	FACETS	0.844	0.743	0.952	0.844	0.743	0.952	CLONAL	1	TRUE	1	0.17	2		906	1185	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098803	178098803	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	62	571	0	ENST00000397062.3:c.242G>T	p.Gly81Val	p.G81V	ENST00000397062	NM_006164.4	81	gGt/gTt	2/5	1	2	FACETS	0.775	0.668	0.893	0.775	0.668	0.893	SUBCLONAL	1	TRUE	1	0.17	2		571	941	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868268	37868268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768206712	NA	P-0049672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	98	676	2	ENST00000269571.5:c.989G>A	p.Arg330Gln	p.R330Q	ENST00000269571		330	cGg/cAg	8/27	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.17	2		678	986	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100846	27100847	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0049672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	61	585	0	ENST00000324856.7:c.4130_4131del	p.Tyr1377TrpfsTer67	p.Y1377Wfs*67	ENST00000324856	NM_006015.4	1376	acATat/acat	18/20	1	2	FACETS	0.957	0.824	1	0.957	0.824	1	CLONAL	1	TRUE	1	0.17	2		585	750	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939298	71939298	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1055057066	NA	P-0049672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	73	907	0	ENST00000298229.2:c.246+1G>A		p.X82_splice	ENST00000298229	NM_001567.3	82			1	2	FACETS	0.741	0.646	0.844	0.741	0.646	0.844	SUBCLONAL	1	TRUE	1	0.17	2		907	1159	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577586	7577586	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587781589	NA	P-0049676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	75	594	0	ENST00000269305.4:c.695T>C	p.Ile232Thr	p.I232T	ENST00000269305	NM_001126112.2	232	aTc/aCc	7/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.15	2		594	845	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484233	8484233	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	220	501	0	ENST00000356435.5:c.3299C>A	p.Thr1100Lys	p.T1100K	ENST00000356435		1100	aCg/aAg	19/35	0.340630744487983	3	FACETS	1	0.987	1	0.799	0.749	0.849	CLONAL	2	TRUE	0	0.393010192787637	3		501	559	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55704641	55704641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	72	741	0	ENST00000284073.2:c.704C>T	p.Pro235Leu	p.P235L	ENST00000284073	NM_138962.2	235	cCa/cTa	10/14	0.393010192787637	6	FACETS	0.574	0.499	0.654	0.143	0.124	0.164	SUBCLONAL	1	TRUE	2	0.393010192787637	6		741	1141	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684286	29684286	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0049677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	220	343	0	ENST00000356175.3:c.7807-1G>T		p.X2603_splice	ENST00000356175	NM_000267.3	2603			0.393010192787637	6	FACETS	0.897	0.842	0.954	0.897	0.842	0.954	CLONAL	4	TRUE	2	0.393010192787637	6		343	557	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665042	29665042	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1060500356	NA	P-0049677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	154	431	0	ENST00000356175.3:c.6642-1G>A		p.X2214_splice	ENST00000356175	NM_000267.3	2214			0.393010192787637	6	FACETS	1	0.964	1	0.543	0.499	0.59	CLONAL	2	TRUE	2	0.393010192787637	6		431	644	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933447	100933447	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	61	287	0	ENST00000325455.5:c.1943T>A	p.Val648Glu	p.V648E	ENST00000325455	NM_001202474.3	648	gTg/gAg	4/8	0.393010192787637	8	FACETS	1	0.902	1	0.176	0.151	0.203	CLONAL	1	TRUE	2	0.393010192787637	8		287	640	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163474	108163474	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	112	412	0	ENST00000278616.4:c.4565G>T	p.Gly1522Val	p.G1522V	ENST00000278616	NM_000051.3	1522	gGt/gTt	30/63	0.21451774019068	3	FACETS	0.883	0.802	0.968	0.589	0.534	0.646	INDETERMINATE	2	TRUE	0	0.393010192787637	3		412	386	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433887	49433887	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	121	1025	0	ENST00000301067.7:c.7666C>G	p.Leu2556Val	p.L2556V	ENST00000301067	NM_003482.3	2556	Ctc/Gtc	31/54	0.372805278774201	4	FACETS	0.781	0.704	0.863	0.391	0.352	0.432	SUBCLONAL	1	TRUE	2	0.393010192787637	4		1025	1098	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433976	49433976	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	113	915	1	ENST00000301067.7:c.7577C>T	p.Ala2526Val	p.A2526V	ENST00000301067	NM_003482.3	2526	gCa/gTa	31/54	0.372805278774201	4	FACETS	0.703	0.631	0.78	0.352	0.315	0.39	SUBCLONAL	1	TRUE	2	0.393010192787637	4		916	1139	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637633	52637633	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	232	459	0	ENST00000394830.3:c.2683A>G	p.Thr895Ala	p.T895A	ENST00000394830	NM_018313.4	895	Aca/Gca	18/30	0.393010192787637	4	FACETS	0.963	0.906	1	0.963	0.906	1	CLONAL	3	TRUE	1	0.393010192787637	4		459	569	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029317	143029317	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	32	204	0	ENST00000262992.4:c.2303G>C	p.Ser768Thr	p.S768T	ENST00000262992	NM_001101669.1	768	aGt/aCt	21/24	0.365315010880489	3	FACETS	0.719	0.586	0.868	0.359	0.293	0.434	SUBCLONAL	1	TRUE	1	0.393010192787637	3		204	271	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628932	187628932	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1207942250	NA	P-0049677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	194	595	0	ENST00000441802.2:c.2050G>T	p.Ala684Ser	p.A684S	ENST00000441802	NM_005245.3	684	Gca/Tca	2/27	0.365315010880489	3	FACETS	0.973	0.906	1	0.973	0.906	1	CLONAL	2	TRUE	1	0.393010192787637	3		595	607	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523681	176523681	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	307	908	1	ENST00000292408.4:c.2092C>A	p.Leu698Met	p.L698M	ENST00000292408	NM_213647.1	698	Ctg/Atg	16/18	0.393010192787637	5	FACETS	0.862	0.814	0.911	0.862	0.814	0.911	CLONAL	3	TRUE	2	0.393010192787637	5		909	960	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468255	50468255	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	200	660	0	ENST00000331340.3:c.1490A>T	p.Tyr497Phe	p.Y497F	ENST00000331340	NM_006060.4	497	tAc/tTc	8/8	0.393010192787637	4	FACETS	1	0.985	1	0.796	0.742	0.851	CLONAL	2	TRUE	1	0.393010192787637	4		660	594	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376651	8376651	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	236	454	0	ENST00000356435.5:c.4462G>T	p.Val1488Leu	p.V1488L	ENST00000356435		1488	Gtg/Ttg	27/35	0.340630744487983	3	FACETS	1	0.99	1	0.833	0.784	0.883	CLONAL	2	TRUE	0	0.393010192787637	3		454	575	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504332	8504332	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs139581216	NA	P-0049677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	218	520	1	ENST00000356435.5:c.1751G>T	p.Arg584Leu	p.R584L	ENST00000356435		584	cGt/cTt	12/35	0.340630744487983	3	FACETS	1	0.985	1	0.776	0.728	0.826	CLONAL	2	TRUE	0	0.393010192787637	3		521	570	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937131	39937131	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	95	814	0	ENST00000378444.4:c.52G>T	p.Glu18Ter	p.E18*	ENST00000378444	NM_001123385.1	18	Gag/Tag	2/15	0.362374206580475	3	FACETS	0.66	0.586	0.738	0.33	0.293	0.369	SUBCLONAL	1	TRUE	1	0.393010192787637	3		814	877	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504139	123504139	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	44	375	0	ENST00000371139.4:c.315G>T	p.Lys105Asn	p.K105N	ENST00000371139	NM_001114937.2	105	aaG/aaT	3/4	0.362374206580475	3	FACETS	0.653	0.549	0.769	0.327	0.274	0.385	SUBCLONAL	1	TRUE	1	0.393010192787637	3		375	410	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0049678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	89	423	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.207114711431072	3	FACETS	1	0.97	1	0.638	0.566	0.715	CLONAL	1	TRUE	1	0.254398178750223	3		423	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0049678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	181	591	2	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.193451663017647	2	FACETS	0.8	0.739	0.865	0.8	0.739	0.865	SUBCLONAL	2	TRUE	0	0.254398178750223	2		593	889	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938263	36938263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138558210	NA	P-0049678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	250	893	0	ENST00000361632.4:c.698G>A	p.Arg233Gln	p.R233Q	ENST00000361632		233	cGg/cAg	6/16	1	2	FACETS	0.846	0.79	0.903	1	0.994	1	CLONAL	2	TRUE	1	0.254398178750223	2		893	1162	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581279	48581280	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0049678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	134	469	0	ENST00000342988.3:c.584dup	p.Tyr195Ter	p.Y195*	ENST00000342988	NM_005359.5	195	tac/tAac	5/12	0.193451663017647	2	FACETS	0.794	0.723	0.869	0.794	0.723	0.869	SUBCLONAL	2	TRUE	0	0.254398178750223	2		469	663	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106242	27106250	+	frameshift_variant	Frame_Shift_Del	DEL	CATCAAGAT	CATCAAGAT	A	novel	NA	P-0049678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	109	553	0	ENST00000324856.7:c.5853_5861delinsA	p.Asn1951LysfsTer9	p.N1951Kfs*9	ENST00000324856	NM_006015.4	1951	aaCATCAAGATc/aaAc	20/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.254398178750223	2		553	696	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0049679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	183	423	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.491978464500545	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.491978464500545	1		423	498	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473779	67473779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906850	NA	P-0049679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	304	641	1	ENST00000327367.4:c.859C>T	p.Arg287Trp	p.R287W	ENST00000327367	NM_005902.3	287	Cgg/Tgg	6/9	0.491978464500545	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.491978464500545	1		642	782	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604706	48604706	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	248	420	0	ENST00000342988.3:c.1528G>A	p.Gly510Arg	p.G510R	ENST00000342988	NM_005359.5	510	Gga/Aga	12/12	0.395318258350829	2	FACETS	0.837	0.789	0.886	0.837	0.789	0.886	CLONAL	2	TRUE	0	0.491978464500545	2		420	602	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783217	9783217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140820694	NA	P-0049679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	335	681	2	ENST00000377346.4:c.2461C>T	p.Arg821Cys	p.R821C	ENST00000377346	NM_005026.3	821	Cgc/Tgc	20/24	0.491978464500545	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.491978464500545	1		683	861	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0049679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	291	543	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.491978464500545	1	FACETS	0.922	0.869	0.977	0.922	0.869	0.977	CLONAL	1	TRUE	0	0.491978464500545	1		543	967	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0049681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	110	506	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.220803799599737	3	FACETS	0.976	0.885	1	0.976	0.885	1	CLONAL	3	TRUE	0	0.220803799599737	3		506	378	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0049683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	87	272	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.213381965159169	2	FACETS	0.779	0.697	0.865	0.779	0.697	0.865	INDETERMINATE	2	TRUE	0	0.357907246001017	2		272	312	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519927	NA	P-0049683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	76	329	0	ENST00000263967.3:c.1625A>G	p.Glu542Gly	p.E542G	ENST00000263967	NM_006218.2	542	gAa/gGa	10/21	0.213381965159169	2	FACETS	1	0.973	1	0.683	0.604	0.765	INDETERMINATE	1	TRUE	0	0.357907246001017	2		329	311	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115916	8115995	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	CGATGCACCCGCCATCCAGCCTGTCCTTTGGACCACACCACCCCTCCAGCATGGTCACCGCCATGGGTTAGAGCCCTGCT	CGATGCACCCGCCATCCAGCCTGTCCTTTGGACCACACCACCCCTCCAGCATGGTCACCGCCATGGGTTAGAGCCCTGCT	-	novel	NA	P-0049683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	53	418	0	ENST00000346208.3:c.1268_*15del		p.*423*	ENST00000346208		421		6/6	1	2	FACETS	0.731	0.625	0.847	0.731	0.625	0.847	SUBCLONAL	1	TRUE	1	0.357907246001017	2		418	405	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250826	26250826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049684-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	19	245	1	ENST00000446824.2:c.8G>A	p.Arg3His	p.R3H	ENST00000446824	NM_021018.2	3	cGc/cAc	1/1	1	2	FACETS	0.335	0.254	0.43	0.335	0.254	0.43	SUBCLONAL	1	TRUE	1	0.388646172091406	2		246	292	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0049685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	36	263	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.842	1	1	0.842	1	CLONAL	1	TRUE	1	0.22	2		263	320	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023696	27023696	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	53	474	0	ENST00000324856.7:c.802C>T	p.Gln268Ter	p.Q268*	ENST00000324856	NM_006015.4	268	Cag/Tag	1/20	1	2	FACETS	0.747	0.636	0.869	0.747	0.636	0.869	SUBCLONAL	1	TRUE	1	0.22	2		474	645	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028675	12028675	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	35	302	0	ENST00000353533.5:c.878T>C	p.Leu293Ser	p.L293S	ENST00000353533	NM_003010.3	293	tTg/tCg	8/11	1	2	FACETS	0.842	0.691	1	0.842	0.691	1	CLONAL	1	TRUE	1	0.22	2		302	378	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965503	18965503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	45	461	0	ENST00000262803.5:c.1250C>T	p.Ser417Leu	p.S417L	ENST00000262803	NM_002911.3	417	tCg/tTg	9/24	1	2	FACETS	0.6	0.503	0.707	0.6	0.503	0.707	SUBCLONAL	1	TRUE	1	0.22	2		461	682	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170156	32170156	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	54	648	0	ENST00000375023.3:c.3452G>C	p.Gly1151Ala	p.G1151A	ENST00000375023	NM_004557.3	1151	gGc/gCc	21/30	0.159744066024311	3	FACETS	0.607	0.517	0.706	0.303	0.258	0.353	SUBCLONAL	1	TRUE	1	0.22	3		648	898	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1977024	1977024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201530243	NA	P-0049686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	50	500	0	ENST00000382891.5:c.3518C>T	p.Thr1173Met	p.T1173M	ENST00000382891	NM_133335.3	1173	aCg/aTg	20/22	1	2	FACETS	0.233	0.197	0.273	0.233	0.197	0.273	SUBCLONAL	1	TRUE	1	0.606226590359311	2		500	708	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577582	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0049686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	339	482	0	ENST00000269305.4:c.699dup	p.Tyr234LeufsTer6	p.Y234Lfs*6	ENST00000269305	NM_001126112.2	233	-/C	7/11	0.602368570375979	2	FACETS	0.951	0.911	0.991	0.951	0.911	0.991	CLONAL	2	TRUE	0	0.606226590359311	2		482	588	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051482	30051655	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTTTACTGTTTTGTAAAAATGATGCATAATTATAAAAGTGGCAAACAATACCAAATTTACTTCATGTGTAGGTTTTTTATTTTGCTCTATTTTTTGGTAGGTAATAAATCTGTATCAGATGACTCCGGAAATGTGGGAGGAGAGAATTACTGCTTGGTACGCAGAGCACCGAG	GCTTTACTGTTTTGTAAAAATGATGCATAATTATAAAAGTGGCAAACAATACCAAATTTACTTCATGTGTAGGTTTTTTATTTTGCTCTATTTTTTGGTAGGTAATAAATCTGTATCAGATGACTCCGGAAATGTGGGAGGAGAGAATTACTGCTTGGTACGCAGAGCACCGAG	-	novel	NA	P-0049686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	21	60	0	ENST00000338641.4:c.517-99_591del		p.X173_splice	ENST00000338641	NM_000268.3	173		6/16	0.606226590359311	1	FACETS	0.928	0.749	1	0.928	0.749	1	CLONAL	1	TRUE	0	0.606226590359311	1		60	52	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247363	153247363	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	72	220	0	ENST00000281708.4:c.1439A>G	p.Asp480Gly	p.D480G	ENST00000281708	NM_033632.3	480	gAt/gGt	10/12	0.606226590359311	1	FACETS	0.915	0.817	1	0.915	0.817	1	CLONAL	1	TRUE	0	0.606226590359311	1		220	181	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578266	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	272	440	0	ENST00000269305.4:c.583dup	p.Ile195AsnfsTer14	p.I195Nfs*14	ENST00000269305	NM_001126112.2	195	atc/aAtc	6/11	0.812374507134006	2	FACETS	0.979	0.947	1	0.979	0.947	1	CLONAL	2	FALSE	0	0.824574400778826	2		440	337	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261571	16261571	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	298	367	0	ENST00000375759.3:c.8836C>G	p.Gln2946Glu	p.Q2946E	ENST00000375759	NM_015001.2	2946	Cag/Gag	11/15	0.591933661107487	4	FACETS	0.964	0.924	1	0.964	0.924	1	CLONAL	3	FALSE	1	0.824574400778826	4		367	456	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362034	118362034	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0049687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	12	181	0	ENST00000534358.1:c.4819+1G>A		p.X1607_splice	ENST00000534358	NM_005933.3	1607			0.554848326542826	4	FACETS	0.289	0.203	0.394	0.096	0.067	0.132	SUBCLONAL	1	FALSE	1	0.824574400778826	4		181	184	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514009	125514009	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1235097713	NA	P-0049688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	52	248	0	ENST00000428830.2:c.947G>A	p.Ser316Asn	p.S316N	ENST00000428830	NM_001114121.2	316	aGt/aAt	10/14	0.518008931531274	1	FACETS	0.658	0.567	0.756	0.658	0.567	0.756	SUBCLONAL	1	TRUE	0	0.518008931531274	1		248	226	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0049698-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	14	250	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	0.802300476962064	1	FACETS	0.081	0.058	0.108	0.081	0.058	0.108	SUBCLONAL	1	TRUE	0	0.802300476962064	1		250	259	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653818	89653818	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049698-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	64	443	0	ENST00000371953.3:c.116C>A	p.Ala39Glu	p.A39E	ENST00000371953	NM_000314.4	39	gCa/gAa	2/9	0.802300476962064	1	FACETS	0.234	0.203	0.267	0.234	0.203	0.267	SUBCLONAL	1	TRUE	0	0.802300476962064	1		443	408	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653852	89653854	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0049698-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	130	436	0	ENST00000371953.3:c.155_157del	p.Asp52del	p.D52del	ENST00000371953	NM_000314.4	50	atTGAt/att	2/9	0.802300476962064	1	FACETS	0.499	0.457	0.542	0.499	0.457	0.542	SUBCLONAL	1	TRUE	0	0.802300476962064	1		436	389	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39595453	39595453	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049698-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	190	387	0	ENST00000262039.4:c.1339A>T	p.Thr447Ser	p.T447S	ENST00000262039	NM_002647.2	447	Acc/Tcc	12/25	1	2	FACETS	0.808	0.752	0.866	0.808	0.752	0.866	CLONAL	1	TRUE	1	0.802300476962064	2		387	586	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133743	55133743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049698-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	4984	605	0	ENST00000257290.5:c.956C>T	p.Pro319Leu	p.P319L	ENST00000257290	NM_006206.4	319	cCc/cTc	7/23	0.802300476962064	15	FACETS	0.989	0.983	0.994			1	CLONAL	14	TRUE	NA	0.802300476962064	15		605	5579	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACAACCCCC	rs397517115	NA	P-0049728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	316	631	0	ENST00000275493.2:c.2311_2319dup	p.Asn771_His773dup	p.N771_H773dup	ENST00000275493	NM_005228.3	771	gac/gACAACCCCCac	20/28	0.423527555351808	3	FACETS	0.932	0.881	0.984	0.932	0.881	0.984	CLONAL	2	TRUE	1	0.423527555351808	3		631	970	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0049728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	151	405	1	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.423527555351808	1	FACETS	0.941	0.864	1	0.941	0.864	1	CLONAL	1	TRUE	0	0.423527555351808	1		406	597	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397807	116397807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	74	351	0	ENST00000397752.3:c.2081G>A	p.Gly694Glu	p.G694E	ENST00000397752	NM_000245.2	694	gGa/gAa	8/21	0.423527555351808	3	FACETS	0.829	0.727	0.938	0.414	0.363	0.469	CLONAL	1	TRUE	1	0.423527555351808	3		351	511	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	27	148	0				ENST00000310581	NM_198253.2	-/1132			0.216421788804248	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.840653671745383	0		148	81	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693003	89693003	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs786204900	NA	P-0049729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	93	297	0	ENST00000371953.3:c.491del	p.Lys164ArgfsTer3	p.K164Rfs*3	ENST00000371953	NM_000314.4	163	Aaa/aa	5/9	0.840653671745383	2	FACETS	1	0.984	1	0.687	0.632	0.742	CLONAL	1	FALSE	0	0.840653671745383	2		297	161	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0049730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	130	202	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.225597860304452	3	FACETS	0.922	0.846	1	1	0.985	1	CLONAL	3	TRUE	1	0.29	3		202	371	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657622	37657623	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGGAATAC	novel	NA	P-0049730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	33	165	0	ENST00000447079.4:c.2542_2549dup	p.Cys850TrpfsTer21	p.C850Wfs*21	ENST00000447079	NM_015083.1	847	ttg/tTGGAATACtg	6/14	1	2	FACETS	0.639	0.521	0.772	0.639	0.521	0.772	SUBCLONAL	1	TRUE	1	0.29	2		165	356	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	89	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.802	0.72	0.887	0.802	0.72	0.887	CLONAL	1	TRUE	1	0.778595958406364	2		148	285	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624263	89624263	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1554890348	NA	P-0049731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	89	214	1	ENST00000371953.3:c.37A>T	p.Lys13Ter	p.K13*	ENST00000371953	NM_000314.4	13	Aaa/Taa	1/9	0.778595958406364	1	FACETS	0.943	0.868	1	0.943	0.868	1	CLONAL	1	TRUE	0	0.778595958406364	1		215	148	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380003	116380003	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0049731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	132	219	0	ENST00000397752.3:c.1393-1G>C		p.X465_splice	ENST00000397752	NM_000245.2	465			0.778595958406364	3	FACETS	0.996	0.91	1	0.498	0.455	0.543	CLONAL	1	TRUE	1	0.778595958406364	3		219	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578453	7578453	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	85	824	0	ENST00000269305.4:c.477del	p.Met160TrpfsTer10	p.M160Wfs*10	ENST00000269305	NM_001126112.2	159	gcC/gc	5/11	0.363913641425797	1	FACETS	0.939	0.835	1	0.939	0.835	1	CLONAL	1	TRUE	0	0.363913641425797	1		824	407	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115836	8115837	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCCTCTCCAGACACATGTCCTCCCTGA	novel	NA	P-0049732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	76	604	0	ENST00000346208.3:c.1186_1213dup	p.His405ProfsTer111	p.H405Pfs*111	ENST00000346208		394	-/GCCCTCTCCAGACACATGTCCTCCCTGA	6/6	0.103314894001445	4	FACETS	1	0.893	1	0.509	0.447	0.575	INDETERMINATE	1	TRUE	2	0.363913641425797	4		604	560	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720803	89720804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs786204892	NA	P-0049733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	11	34	0	ENST00000371953.3:c.955dup	p.Thr319AsnfsTer6	p.T319Nfs*6	ENST00000371953	NM_000314.4	318	-/A	8/9	1	2	FACETS	0.767	0.536	1	0.767	0.536	1	CLONAL	1	TRUE	1	0.314994657310498	2		34	91	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110108	115110108	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0049733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	122	541	0	ENST00000257566.3:c.1771-1G>A		p.X591_splice	ENST00000257566	NM_016569.3	591			1	2	FACETS	0.992	0.897	1	0.992	0.897	1	CLONAL	1	TRUE	1	0.314994657310498	2		541	781	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849499	68849499	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	131	487	0	ENST00000261769.5:c.1402del	p.Thr468ProfsTer13	p.T468Pfs*13	ENST00000261769	NM_004360.3	468	Acc/cc	10/16	0.314994657310498	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.314994657310498	1		487	677	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319730	62319730	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs141229183	NA	P-0049733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	109	572	0	ENST00000360203.5:c.1713G>T	p.Glu571Asp	p.E571D	ENST00000360203	NM_001283009.1	571	gaG/gaT	20/35	1	2	FACETS	0.907	0.815	1	0.907	0.815	1	CLONAL	1	TRUE	1	0.314994657310498	2		572	763	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	221	148	0				ENST00000310581	NM_198253.2	-/1132			0.260143722418794	3	FACETS	0.944	0.883	1	1	0.991	1	CLONAL	3	TRUE	1	0.260143722418794	3		148	678	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100988	27100988	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	141	516	0	ENST00000324856.7:c.4270C>T	p.Gln1424Ter	p.Q1424*	ENST00000324856	NM_006015.4	1424	Cag/Tag	18/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.260143722418794	2		516	921	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933736	36933737	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	154	683	1	ENST00000361632.4:c.1662_1663delinsAA	p.Gly555Arg	p.G555R	ENST00000361632		554	ctGGgg/ctAAgg	12/16	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.260143722418794	2		684	1149	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367114	40367114	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	154	441	0	ENST00000397332.2:c.83G>A	p.Gly28Glu	p.G28E	ENST00000397332	NM_001033082.2	28	gGa/gAa	2/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.260143722418794	2		441	877	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301147	65301147	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	58	204	0	ENST00000342505.4:c.3301G>C	p.Val1101Leu	p.V1101L	ENST00000342505	NM_002227.2	1101	Gtc/Ctc	24/25	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.260143722418794	2		204	441	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551955	150551955	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	235	451	0	ENST00000369026.2:c.52G>A	p.Gly18Arg	p.G18R	ENST00000369026	NM_021960.4	18	Ggg/Agg	1/3	1	2	FACETS	0.827	0.771	0.885	1	0.993	1	CLONAL	2	TRUE	1	0.260143722418794	2		451	1092	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981831	201981831	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767015572	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	167	716	0	ENST00000359651.3:c.542C>T	p.Pro181Leu	p.P181L	ENST00000359651		181	cCc/cTc	4/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.260143722418794	2		716	1112	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578253	226578253	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	123	509	2	ENST00000366794.5:c.475C>T	p.His159Tyr	p.H159Y	ENST00000366794	NM_001618.3	159	Cat/Tat	4/23	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.260143722418794	2		511	885	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852482	63852482	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	114	441	0	ENST00000279873.7:c.3260G>T	p.Cys1087Phe	p.C1087F	ENST00000279873	NM_032199.2	1087	tGt/tTt	10/10	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.260143722418794	2		441	861	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922294	100922294	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1315135533	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	34	180	0	ENST00000325455.5:c.2218C>T	p.Arg740Ter	p.R740*	ENST00000325455	NM_001202474.3	740	Cga/Tga	5/8	1	2	FACETS	0.968	0.795	1	0.968	0.795	1	CLONAL	1	TRUE	1	0.260143722418794	2		180	270	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999566	100999566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745363836	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	155	738	1	ENST00000325455.5:c.236C>T	p.Ser79Leu	p.S79L	ENST00000325455	NM_001202474.3	79	tCg/tTg	1/8	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.260143722418794	2		739	1175	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343804	118343804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868981857	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	107	367	0	ENST00000534358.1:c.1930C>T	p.Arg644Cys	p.R644C	ENST00000534358	NM_005933.3	644	Cgc/Tgc	3/36	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.260143722418794	2		367	709	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360602	118360602	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	93	294	0	ENST00000534358.1:c.4575G>A	p.Trp1525Ter	p.W1525*	ENST00000534358	NM_005933.3	1525	tgG/tgA	12/36	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.260143722418794	2		294	645	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118368766	118368766	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	104	326	2	ENST00000534358.1:c.5780C>T	p.Ala1927Val	p.A1927V	ENST00000534358	NM_005933.3	1927	gCt/gTt	21/36	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.260143722418794	2		328	649	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149251	119149251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267606708	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	112	373	1	ENST00000264033.4:c.1259G>A	p.Arg420Gln	p.R420Q	ENST00000264033	NM_005188.3	420	cGa/cAa	9/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.260143722418794	2		374	735	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169125	119169125	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	98	449	0	ENST00000264033.4:c.2309A>G	p.Glu770Gly	p.E770G	ENST00000264033	NM_005188.3	770	gAg/gGg	15/16	1	2	FACETS	0.97	0.865	1	0.97	0.865	1	CLONAL	1	TRUE	1	0.260143722418794	2		449	777	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644490	18644490	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs181773550	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	16	182	0	ENST00000266497.5:c.2668G>A	p.Asp890Asn	p.D890N	ENST00000266497		890	Gat/Aat	18/31	1	2	FACETS	0.449	0.332	0.589	0.449	0.332	0.589	SUBCLONAL	1	TRUE	1	0.260143722418794	2		182	274	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800819	18800819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868545833	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	34	234	0	ENST00000266497.5:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000266497		1399	Gat/Aat	31/31	1	2	FACETS	0.934	0.766	1	0.934	0.766	1	CLONAL	1	TRUE	1	0.260143722418794	2		234	280	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444367	49444367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1323906289	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	203	542	0	ENST00000301067.7:c.3004C>T	p.Pro1002Ser	p.P1002S	ENST00000301067	NM_003482.3	1002	Ccc/Tcc	11/54	1	2	FACETS	0.769	0.713	0.827	1	0.991	1	SUBCLONAL	2	TRUE	1	0.260143722418794	2		542	1015	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865537	57865537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	163	608	0	ENST00000228682.2:c.3014G>A	p.Gly1005Glu	p.G1005E	ENST00000228682	NM_005269.2	1005	gGa/gAa	12/12	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.260143722418794	2		608	1083	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233343	69233343	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	59	249	1	ENST00000462284.1:c.1208C>T	p.Pro403Leu	p.P403L	ENST00000462284	NM_002392.5	403	cCa/cTa	11/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.260143722418794	2		250	336	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784089	120784089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265704785	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	205	691	1	ENST00000257552.2:c.896C>T	p.Ser299Leu	p.S299L	ENST00000257552	NM_002442.3	299	tCg/tTg	13/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.260143722418794	2		692	1203	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209315	133209315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	165	619	1	ENST00000320574.5:c.6071C>T	p.Pro2024Leu	p.P2024L	ENST00000320574	NM_006231.2	2024	cCc/cTc	44/49	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.260143722418794	2		620	1088	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880899	28880899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1315888360	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	118	325	0	ENST00000282397.4:c.3731G>A	p.Gly1244Asp	p.G1244D	ENST00000282397	NM_002019.4	1244	gGc/gAc	29/30	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.260143722418794	2		325	660	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919595	28919595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs553261958	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	96	375	0	ENST00000282397.4:c.2342G>A	p.Arg781Gln	p.R781Q	ENST00000282397	NM_002019.4	781	cGa/cAa	16/30	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.260143722418794	2		375	651	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931718	28931718	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	108	383	1	ENST00000282397.4:c.2221G>A	p.Glu741Lys	p.E741K	ENST00000282397	NM_002019.4	741	Gaa/Aaa	15/30	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.260143722418794	2		384	688	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093371	30093371	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	44	304	0	ENST00000331968.5:c.1892T>C	p.Val631Ala	p.V631A	ENST00000331968	NM_002742.2	631	gTt/gCt	13/18	1	2	FACETS	0.883	0.742	1	0.883	0.742	1	CLONAL	1	TRUE	1	0.260143722418794	2		304	383	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100221	30100221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	54	207	0	ENST00000331968.5:c.1399C>T	p.Pro467Ser	p.P467S	ENST00000331968	NM_002742.2	467	Cct/Tct	10/18	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.260143722418794	2		207	365	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331729	68331729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	51	135	0	ENST00000487270.1:c.325C>T	p.Pro109Ser	p.P109S	ENST00000487270	NM_133509.3	109	Cca/Tca	5/11	1	2	FACETS	0.827	0.71	0.953	1	0.971	1	CLONAL	2	TRUE	1	0.260143722418794	2		135	237	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729090	66729090	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	43	380	0	ENST00000307102.5:c.298C>T	p.His100Tyr	p.H100Y	ENST00000307102	NM_002755.3	100	Cat/Tat	3/11	0.22316057708961	1	FACETS	0.406	0.339	0.481	0.406	0.339	0.481	SUBCLONAL	1	TRUE	0	0.260143722418794	1		380	708	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678334	88678334	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	142	450	0	ENST00000360948.2:c.1202C>T	p.Pro401Leu	p.P401L	ENST00000360948	NM_001012338.2	401	cCa/cTa	9/19	0.22316057708961	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.260143722418794	1		450	792	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500617	99500617	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	133	503	0	ENST00000268035.6:c.4050C>G	p.Asn1350Lys	p.N1350K	ENST00000268035	NM_000875.3	1350	aaC/aaG	21/21	0.22316057708961	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.260143722418794	1		503	822	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347953	347953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	181	824	0	ENST00000262320.3:c.1553C>T	p.Pro518Leu	p.P518L	ENST00000262320	NM_003502.3	518	cCc/cTc	6/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.260143722418794	2		824	1241	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127693	2127693	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768241596	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	136	500	1	ENST00000219476.3:c.2932C>T	p.Arg978Cys	p.R978C	ENST00000219476	NM_000548.3	978	Cgc/Tgc	26/42	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.260143722418794	2		501	840	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640325	3640325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	176	633	0	ENST00000294008.3:c.3314C>T	p.Ser1105Phe	p.S1105F	ENST00000294008	NM_032444.2	1105	tCc/tTc	12/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.260143722418794	2		633	1116	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779208	3779208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	118	392	0	ENST00000262367.5:c.5840C>T	p.Pro1947Leu	p.P1947L	ENST00000262367	NM_004380.2	1947	cCc/cTc	31/31	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.260143722418794	2		392	647	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858184	9858184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	114	385	1	ENST00000330684.3:c.3217G>A	p.Glu1073Lys	p.E1073K	ENST00000330684	NM_001134407.1	1073	Gaa/Aaa	13/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.260143722418794	2		386	746	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858712	9858712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	82	333	1	ENST00000330684.3:c.2689C>T	p.Leu897Phe	p.L897F	ENST00000330684	NM_001134407.1	897	Ctc/Ttc	13/13	1	2	FACETS	0.993	0.876	1	0.993	0.876	1	CLONAL	1	TRUE	1	0.260143722418794	2		334	635	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032067	10032067	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	111	460	0	ENST00000330684.3:c.756T>A	p.Asp252Glu	p.D252E	ENST00000330684	NM_001134407.1	252	gaT/gaA	3/13	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.260143722418794	2		460	748	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634336	23634337	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	79	455	2	ENST00000261584.4:c.2949_2950delinsTT	p.Leu984Phe	p.L984F	ENST00000261584	NM_024675.3	983	acCCtt/acTTtt	9/13	1	2	FACETS	0.765	0.672	0.865	0.765	0.672	0.865	SUBCLONAL	1	TRUE	1	0.260143722418794	2		457	794	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647068	23647068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	109	451	0	ENST00000261584.4:c.799C>T	p.Pro267Ser	p.P267S	ENST00000261584	NM_024675.3	267	Cct/Tct	4/13	1	2	FACETS	0.921	0.826	1	0.921	0.826	1	CLONAL	1	TRUE	1	0.260143722418794	2		451	910	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783766	50783766	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1196482079	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	69	411	0	ENST00000398568.2:c.157C>T	p.Arg53Cys	p.R53C	ENST00000398568	NM_001042412.1	53	Cgt/Tgt	3/18	1	2	FACETS	0.901	0.785	1	0.901	0.785	1	CLONAL	1	TRUE	1	0.260143722418794	2		411	589	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862130	68862130	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773795943	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	151	438	1	ENST00000261769.5:c.2218C>T	p.Pro740Ser	p.P740S	ENST00000261769	NM_004360.3	740	Ccc/Tcc	14/16	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.260143722418794	2		439	829	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	160	516	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.260143722418794	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.260143722418794	1		516	864	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679365	29679366	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	103	350	1	ENST00000356175.3:c.7485_7486delinsTT	p.Arg2496Ter	p.R2496*	ENST00000356175	NM_000267.3	2495	ccCCga/ccTTga	50/57	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.260143722418794	2		351	708	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40476855	40476855	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	106	393	0	ENST00000264657.5:c.1474T>G	p.Phe492Val	p.F492V	ENST00000264657	NM_139276.2	492	Ttt/Gtt	17/24	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.260143722418794	2		393	692	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41209101	41209101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	119	414	0	ENST00000357654.3:c.5245C>T	p.Pro1749Ser	p.P1749S	ENST00000357654	NM_007294.3	1749	Cca/Tca	19/23	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.260143722418794	2		414	878	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761219	59761219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs575998972	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	97	491	0	ENST00000259008.2:c.3188C>T	p.Ser1063Leu	p.S1063L	ENST00000259008	NM_032043.2	1063	tCg/tTg	20/20	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.260143722418794	2		491	692	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006627	62006627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1063625	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	144	614	0	ENST00000392795.3:c.652G>A	p.Glu218Lys	p.E218K	ENST00000392795	NM_001039933.1	218	Gaa/Aaa	6/6	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.260143722418794	2		614	1009	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281203	15281203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	226	770	0	ENST00000263388.2:c.5053G>A	p.Asp1685Asn	p.D1685N	ENST00000263388	NM_000435.2	1685	Gac/Aac	27/33	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.260143722418794	2		770	1327	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943450	17943450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	178	668	0	ENST00000458235.1:c.2558C>T	p.Ala853Val	p.A853V	ENST00000458235	NM_000215.3	853	gCc/gTc	19/24	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.260143722418794	2		668	1130	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952229	17952229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	187	613	0	ENST00000458235.1:c.1111G>A	p.Glu371Lys	p.E371K	ENST00000458235	NM_000215.3	371	Gaa/Aaa	8/24	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.260143722418794	2		613	1171	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42384797	42384797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	79	287	0	ENST00000221972.3:c.559C>T	p.Leu187Phe	p.L187F	ENST00000221972	NM_021601.3	187	Ctt/Ttt	4/5	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.260143722418794	2		287	477	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797201	42797201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	204	748	0	ENST00000575354.2:c.3563C>T	p.Pro1188Leu	p.P1188L	ENST00000575354	NM_015125.3	1188	cCc/cTc	15/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.260143722418794	2		748	1271	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714577	52714577	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	182	600	0	ENST00000322088.6:c.335T>C	p.Leu112Ser	p.L112S	ENST00000322088	NM_014225.5	112	tTa/tCa	4/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.260143722418794	2		600	1058	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470997	25470997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	136	612	0	ENST00000264709.3:c.764C>T	p.Ser255Phe	p.S255F	ENST00000264709	NM_175629.2	255	tCc/tTc	7/23	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.260143722418794	2		612	1010	SUCCESS
ALK	238	MSKCC	GRCh37	2	29430044	29430044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	145	417	0	ENST00000389048.3:c.3931G>A	p.Asp1311Asn	p.D1311N	ENST00000389048	NM_004304.4	1311	Gac/Aac	26/29	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.260143722418794	2		417	836	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483982	212483982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	55	257	0	ENST00000342788.4:c.2221G>A	p.Gly741Arg	p.G741R	ENST00000342788	NM_005235.2	741	Gga/Aga	19/28	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.260143722418794	2		257	416	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645606	215645606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	110	423	0	ENST00000260947.4:c.992C>T	p.Pro331Leu	p.P331L	ENST00000260947	NM_000465.2	331	cCc/cTc	4/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.260143722418794	2		423	690	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794835	242794835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	163	617	0	ENST00000334409.5:c.374C>T	p.Ala125Val	p.A125V	ENST00000334409	NM_005018.2	125	gCc/gTc	2/5	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.260143722418794	2		617	1022	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790092	40790092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	136	497	0	ENST00000373198.4:c.2639C>T	p.Pro880Leu	p.P880L	ENST00000373198	NM_133170.3	880	cCc/cTc	18/32	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.260143722418794	2		497	911	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944530	40944530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	111	378	0	ENST00000373198.4:c.1972C>T	p.Leu658Phe	p.L658F	ENST00000373198	NM_133170.3	658	Ctc/Ttc	12/32	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.260143722418794	2		378	644	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100912	41100912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866253502	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	121	428	0	ENST00000373198.4:c.1444G>A	p.Glu482Lys	p.E482K	ENST00000373198	NM_133170.3	482	Gaa/Aaa	8/32	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.260143722418794	2		428	812	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264311	46264312	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	99	327	0	ENST00000371998.3:c.1358_1359delinsTT	p.Ser453Phe	p.S453F	ENST00000371998		453	tCC/tTT	11/23	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.260143722418794	2		327	648	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057251	30057251	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	142	512	0	ENST00000338641.4:c.733G>C	p.Asp245His	p.D245H	ENST00000338641	NM_000268.3	245	Gac/Cac	8/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.260143722418794	2		512	898	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545112	41545112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	136	407	1	ENST00000263253.7:c.2312C>T	p.Pro771Leu	p.P771L	ENST00000263253	NM_001429.3	771	cCa/cTa	13/31	0.207770525506278	4	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.260143722418794	4		408	919	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574739	41574739	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1486126836	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	309	595	0	ENST00000263253.7:c.7024C>T	p.Pro2342Ser	p.P2342S	ENST00000263253	NM_001429.3	2342	Cca/Tca	31/31	0.207770525506278	4	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.260143722418794	4		595	1254	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641709	12641709	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	126	406	0	ENST00000251849.4:c.932C>T	p.Pro311Leu	p.P311L	ENST00000251849	NM_002880.3	311	cCc/cTc	9/17	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.260143722418794	2		406	838	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186843	142186843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	48	249	0	ENST00000350721.4:c.6620C>T	p.Ser2207Phe	p.S2207F	ENST00000350721	NM_001184.3	2207	tCc/tTc	39/47	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.260143722418794	2		249	319	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189585728	189585728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	73	265	0	ENST00000264731.3:c.989G>A	p.Arg330Lys	p.R330K	ENST00000264731	NM_003722.4	330	aGa/aAa	7/14	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.260143722418794	2		265	525	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608578	189608578	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	86	353	0	ENST00000264731.3:c.1653T>A	p.Ser551Arg	p.S551R	ENST00000264731	NM_003722.4	551	agT/agA	13/14	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.260143722418794	2		353	614	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141026	55141026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765680542	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	70	288	1	ENST00000257290.5:c.1672C>T	p.Arg558Cys	p.R558C	ENST00000257290	NM_006206.4	558	Cgc/Tgc	12/23	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.260143722418794	2		289	508	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155881	106155881	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	76	308	0	ENST00000380013.4:c.782C>A	p.Ser261Tyr	p.S261Y	ENST00000380013	NM_001127208.2	261	tCc/tAc	3/11	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.260143722418794	2		308	552	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876323	35876323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201146815	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	229	429	0	ENST00000303115.3:c.1115G>A	p.Gly372Glu	p.G372E	ENST00000303115	NM_002185.3	372	gGg/gAg	8/8	0.260143722418794	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.260143722418794	3		429	836	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945821	38945821	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	41	178	0	ENST00000357387.3:c.4405C>G	p.Pro1469Ala	p.P1469A	ENST00000357387	NM_152756.3	1469	Cca/Gca	34/38	0.260143722418794	3	FACETS	1	0.954	1	0.724	0.608	0.851	CLONAL	1	TRUE	1	0.260143722418794	3		178	246	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38966783	38966783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	19	130	0	ENST00000357387.3:c.1259C>T	p.Ser420Leu	p.S420L	ENST00000357387	NM_152756.3	420	tCa/tTa	15/38	1	2	FACETS	0.825	0.63	1	0.825	0.63	1	CLONAL	1	TRUE	1	0.260143722418794	2		130	177	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638823	176638823	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	143	453	0	ENST00000439151.2:c.3423G>C	p.Met1141Ile	p.M1141I	ENST00000439151	NM_022455.4	1141	atG/atC	5/23	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.260143722418794	2		453	817	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721009	176721009	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587784213	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	105	498	0	ENST00000439151.2:c.6640G>A	p.Glu2214Lys	p.E2214K	ENST00000439151	NM_022455.4	2214	Gaa/Aaa	23/23	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.260143722418794	2		498	757	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185017	32185017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	158	573	0	ENST00000375023.3:c.1651G>A	p.Asp551Asn	p.D551N	ENST00000375023	NM_004557.3	551	Gat/Aat	10/30	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.260143722418794	2		573	1000	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967210	93967210	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	32	258	0	ENST00000369303.4:c.2142G>T	p.Met714Ile	p.M714I	ENST00000369303	NM_004440.3	714	atG/atT	12/17	1	2	FACETS	0.713	0.58	0.863	0.713	0.58	0.863	SUBCLONAL	1	TRUE	1	0.260143722418794	2		258	345	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967895	93967895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1256527658	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	75	401	0	ENST00000369303.4:c.2032G>A	p.Asp678Asn	p.D678N	ENST00000369303	NM_004440.3	678	Gac/Aac	11/17	1	2	FACETS	0.776	0.679	0.88	0.776	0.679	0.88	SUBCLONAL	1	TRUE	1	0.260143722418794	2		401	743	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962342	2962342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	155	665	0	ENST00000396946.4:c.2195C>T	p.Thr732Ile	p.T732I	ENST00000396946	NM_032415.4	732	aCc/aTc	17/25	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.260143722418794	2		665	1124	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984154	2984154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	84	397	0	ENST00000396946.4:c.376G>A	p.Gly126Ser	p.G126S	ENST00000396946	NM_032415.4	126	Ggc/Agc	5/25	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.260143722418794	2		397	617	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340252	116340252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773200558	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	78	285	1	ENST00000397752.3:c.1114G>A	p.Asp372Asn	p.D372N	ENST00000397752	NM_000245.2	372	Gac/Aac	2/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.260143722418794	2		286	468	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	70	292	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.260143722418794	2		292	486	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543608	148543608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	106	305	0	ENST00000320356.2:c.200C>T	p.Pro67Leu	p.P67L	ENST00000320356	NM_004456.4	67	cCt/cTt	3/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.260143722418794	2		305	736	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859270	151859270	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	73	233	0	ENST00000262189.6:c.11392A>G	p.Ile3798Val	p.I3798V	ENST00000262189	NM_170606.2	3798	Att/Gtt	43/59	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.260143722418794	2		233	405	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956771	68956771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774302685	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	144	497	0	ENST00000288368.4:c.889C>T	p.Arg297Cys	p.R297C	ENST00000288368	NM_024870.2	297	Cgt/Tgt	8/40	0.260143722418794	3	FACETS	1	0.979	1	0.626	0.57	0.685	CLONAL	1	TRUE	1	0.260143722418794	3		497	999	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028118	69028118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1375998072	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	73	349	0	ENST00000288368.4:c.3277G>A	p.Glu1093Lys	p.E1093K	ENST00000288368	NM_024870.2	1093	Gaa/Aaa	26/40	0.260143722418794	3	FACETS	0.857	0.749	0.974	0.429	0.374	0.487	CLONAL	1	TRUE	1	0.260143722418794	3		349	740	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141582931	141582932	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	281	472	1	ENST00000220592.5:c.315_316delinsTT	p.Leu106Phe	p.L106F	ENST00000220592	NM_012154.3	105	ccCCtt/ccTTtt	3/19	0.260143722418794	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.260143722418794	3		473	1061	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518385	8518385	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	64	223	0	ENST00000356435.5:c.1006G>A	p.Ala336Thr	p.A336T	ENST00000356435		336	Gct/Act	10/35	0.260143722418794	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.260143722418794	1		223	311	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636799	8636799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	109	333	1	ENST00000356435.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000356435		37	tCt/tTt	2/35	0.260143722418794	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.260143722418794	1		334	572	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27217687	27217687	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	376	345	0	ENST00000380036.4:c.2993G>A	p.Gly998Glu	p.G998E	ENST00000380036	NM_000459.3	998	gGa/gAa	19/23	0.260143722418794	3	FACETS	1	0.987	1	1	0.996	1	CLONAL	3	TRUE	1	0.260143722418794	3		345	989	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482242	87482242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	162	475	0	ENST00000277120.3:c.1529C>T	p.Ser510Leu	p.S510L	ENST00000277120		510	tCg/tTg	14/19	0.260143722418794	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.260143722418794	1		475	747	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127911957	127911957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	73	264	0	ENST00000373547.4:c.913C>T	p.Leu305Phe	p.L305F	ENST00000373547	NM_002721.4	305	Ctt/Ttt	7/7	0.22316057708961	1	FACETS	0.925	0.81	1	0.925	0.81	1	CLONAL	1	TRUE	0	0.260143722418794	1		264	528	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781304	135781304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	135	548	0	ENST00000298552.3:c.1661C>T	p.Pro554Leu	p.P554L	ENST00000298552	NM_001162426.1	554	cCc/cTc	15/23	0.22316057708961	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.260143722418794	1		548	854	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391526	139391526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779125725	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	198	744	1	ENST00000277541.6:c.6665C>T	p.Pro2222Leu	p.P2222L	ENST00000277541	NM_017617.3	2222	cCg/cTg	34/34	0.22316057708961	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.260143722418794	1		745	1175	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409119	139409119	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	175	651	0	ENST00000277541.6:c.2050G>A	p.Gly684Ser	p.G684S	ENST00000277541	NM_017617.3	684	Ggc/Agc	13/34	0.22316057708961	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.260143722418794	1		651	1082	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930238	39930238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202065982	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	138	426	1	ENST00000378444.4:c.3226G>A	p.Glu1076Lys	p.E1076K	ENST00000378444	NM_001123385.1	1076	Gaa/Aaa	6/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.260143722418794	2		427	845	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430406	47430406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	145	516	0	ENST00000377045.4:c.1681C>T	p.Pro561Ser	p.P561S	ENST00000377045	NM_001654.4	561	Ccc/Tcc	15/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.260143722418794	2		516	937	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649719	48649719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	147	610	0	ENST00000376670.3:c.203C>T	p.Ala68Val	p.A68V	ENST00000376670	NM_002049.3	68	gCc/gTc	2/6	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.260143722418794	2		610	1046	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413032	63413033	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	164	648	1	ENST00000330258.3:c.134_135delinsTT	p.Ser45Phe	p.S45F	ENST00000330258	NM_152424.3	45	tCC/tTT	2/2	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.260143722418794	2		649	1071	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351923	70351923	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	107	411	0	ENST00000374080.3:c.4120G>A	p.Glu1374Lys	p.E1374K	ENST00000374080		1374	Gag/Aag	30/45	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.260143722418794	2		411	752	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356736	70356736	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	122	504	0	ENST00000374080.3:c.5408G>A	p.Gly1803Glu	p.G1803E	ENST00000374080		1803	gGa/gAa	38/45	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.260143722418794	2		504	817	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855266	76855266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	32	222	0	ENST00000373344.5:c.5721G>A	p.Met1907Ile	p.M1907I	ENST00000373344	NM_000489.3	1907	atG/atA	24/35	1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	1	0.260143722418794	2		222	236	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76954067	76954067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	33	266	0	ENST00000373344.5:c.184G>A	p.Glu62Lys	p.E62K	ENST00000373344	NM_000489.3	62	Gaa/Aaa	3/35	1	2	FACETS	0.829	0.677	0.999	0.829	0.677	0.999	CLONAL	1	TRUE	1	0.260143722418794	2		266	306	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626668	100626668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	79	304	0	ENST00000308731.7:c.262G>A	p.Glu88Lys	p.E88K	ENST00000308731	NM_000061.2	88	Gaa/Aaa	4/19	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.260143722418794	2		304	494	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019877	123019877	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	126	472	0	ENST00000355640.3:c.365G>A	p.Gly122Glu	p.G122E	ENST00000355640		122	gGa/gAa	2/7	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.260143722418794	2		472	790	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185192	123185192	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	27	182	0	ENST00000218089.9:c.1144A>C	p.Lys382Gln	p.K382Q	ENST00000218089	NM_001042749.1	382	Aaa/Caa	13/35	1	2	FACETS	0.979	0.784	1	0.979	0.784	1	CLONAL	1	TRUE	1	0.260143722418794	2		182	212	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227968	123227968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	38	235	0	ENST00000218089.9:c.3679G>A	p.Asp1227Asn	p.D1227N	ENST00000218089	NM_001042749.1	1227	Gat/Aat	33/35	1	2	FACETS	0.732	0.606	0.873	0.732	0.606	0.873	SUBCLONAL	1	TRUE	1	0.260143722418794	2		235	399	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	82	248	1				ENST00000310581	NM_198253.2	-/1132			0.389732485115185	1	FACETS	0.903	0.802	1	0.903	0.802	1	CLONAL	1	TRUE	0	0.389732485115185	1		249	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	165	442	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.389732485115185	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.389732485115185	1		442	591	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733217	40733217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	100	570	0	ENST00000373198.4:c.3589G>A	p.Glu1197Lys	p.E1197K	ENST00000373198	NM_133170.3	1197	Gaa/Aaa	26/32	1	2	FACETS	0.93	0.833	1	0.93	0.833	1	CLONAL	1	TRUE	1	0.389732485115185	2		570	552	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	166	508	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.389732485115185	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.389732485115185	1		508	600	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947067	178947067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	62	230	0	ENST00000263967.3:c.2503C>T	p.Pro835Ser	p.P835S	ENST00000263967	NM_006218.2	835	Cct/Tct	18/21	1	2	FACETS	0.889	0.772	1	0.889	0.772	1	CLONAL	1	TRUE	1	0.389732485115185	2		230	358	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716344	18716344	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778895247	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	44	372	0	ENST00000266497.5:c.3691G>A	p.Glu1231Lys	p.E1231K	ENST00000266497		1231	Gaa/Aaa	26/31	1	2	FACETS	0.54	0.453	0.636	0.54	0.453	0.636	SUBCLONAL	1	TRUE	1	0.389732485115185	2		372	418	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729949	41729949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1165688714	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	113	575	0	ENST00000242208.4:c.580G>A	p.Glu194Lys	p.E194K	ENST00000242208	NM_002192.2	194	Gaa/Aaa	3/3	1	2	FACETS	0.871	0.785	0.961	0.871	0.785	0.961	CLONAL	1	TRUE	1	0.389732485115185	2		575	666	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622539	28622539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	61	301	0	ENST00000241453.7:c.1078G>A	p.Glu360Lys	p.E360K	ENST00000241453	NM_004119.2	360	Gaa/Aaa	9/24	1	2	FACETS	0.972	0.844	1	0.972	0.844	1	CLONAL	1	TRUE	1	0.389732485115185	2		301	322	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42002918	42002918	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	59	291	0	ENST00000219905.7:c.2455C>T	p.Arg819Cys	p.R819C	ENST00000219905	NM_001164273.1	819	Cgt/Tgt	8/24	1	2	FACETS	0.901	0.78	1	0.901	0.78	1	CLONAL	1	TRUE	1	0.389732485115185	2		291	336	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514131	69514131	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199891170	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	136	623	0	ENST00000294312.3:c.550G>A	p.Glu184Lys	p.E184K	ENST00000294312	NM_005117.2	184	Gaa/Aaa	3/3	0.256663803198874	1	FACETS	0.778	0.709	0.851	0.778	0.709	0.851	SUBCLONAL	1	TRUE	0	0.389732485115185	1		623	722	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743942	40743942	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868489194	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	81	365	0	ENST00000373198.4:c.3053G>A	p.Arg1018Gln	p.R1018Q	ENST00000373198	NM_133170.3	1018	cGa/cAa	23/32	1	2	FACETS	0.802	0.709	0.902	0.802	0.709	0.902	CLONAL	1	TRUE	1	0.389732485115185	2		365	518	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713775	30713775	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1226482581	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	116	559	1	ENST00000295754.5:c.1100C>T	p.Pro367Leu	p.P367L	ENST00000295754	NM_003242.5	367	cCa/cTa	4/7	0.256663803198874	1	FACETS	0.862	0.78	0.948	0.862	0.78	0.948	CLONAL	1	TRUE	0	0.389732485115185	1		560	556	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560043	29560043	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs868450405	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	87	258	0	ENST00000356175.3:c.3520C>T	p.Gln1174Ter	p.Q1174*	ENST00000356175	NM_000267.3	1174	Cag/Tag	27/57	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.389732485115185	2		258	371	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344107	118344107	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs727503777	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	80	366	1	ENST00000534358.1:c.2233C>T	p.Arg745Ter	p.R745*	ENST00000534358	NM_005933.3	745	Cga/Tga	3/36	0.389732485115185	1	FACETS	0.889	0.787	0.996	0.889	0.787	0.996	CLONAL	1	TRUE	0	0.389732485115185	1		367	372	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005901	69005901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	119	482	0	ENST00000288368.4:c.2312C>T	p.Ser771Phe	p.S771F	ENST00000288368	NM_024870.2	771	tCt/tTt	21/40	1	2	FACETS	0.99	0.896	1	0.99	0.896	1	CLONAL	1	TRUE	1	0.389732485115185	2		482	617	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716070	243716070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	91	407	0	ENST00000263826.5:c.1124C>T	p.Ser375Leu	p.S375L	ENST00000263826	NM_005465.4	375	tCa/tTa	10/13	1	2	FACETS	0.965	0.86	1	0.965	0.86	1	CLONAL	1	TRUE	1	0.389732485115185	2		407	484	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919517	78919517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	133	517	0	ENST00000306801.3:c.3076C>T	p.Pro1026Ser	p.P1026S	ENST00000306801	NM_020761.2	1026	Ccc/Tcc	26/34	1	2	FACETS	0.983	0.895	1	0.983	0.895	1	CLONAL	1	TRUE	1	0.389732485115185	2		517	694	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795473	39795473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	57	446	0	ENST00000288319.7:c.247G>A	p.Asp83Asn	p.D83N	ENST00000288319	NM_182918.3	83	Gat/Aat	3/10	0.256663803198874	1	FACETS	0.414	0.355	0.478	0.414	0.355	0.478	SUBCLONAL	1	TRUE	0	0.389732485115185	1		446	569	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885655	23885655	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748225151	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	147	576	0	ENST00000374561.5:c.263C>T	p.Ala88Val	p.A88V	ENST00000374561	NM_002167.4	88	gCc/gTc	1/3	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.389732485115185	2		576	725	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888106	81888106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746298243	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	121	406	0	ENST00000359376.3:c.251G>A	p.Arg84Gln	p.R84Q	ENST00000359376	NM_002661.3	84	cGa/cAa	3/33	0.389732485115185	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	0	0.389732485115185	1		406	499	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087929	27087929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	159	569	0	ENST00000324856.7:c.2216C>T	p.Pro739Leu	p.P739L	ENST00000324856	NM_006015.4	739	cCt/cTt	6/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.389732485115185	2		569	778	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157044	106157044	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	90	377	0	ENST00000380013.4:c.1945C>T	p.Gln649Ter	p.Q649*	ENST00000380013	NM_001127208.2	649	Caa/Taa	3/11	0.256663803198874	1	FACETS	0.676	0.601	0.756	0.676	0.601	0.756	SUBCLONAL	1	TRUE	0	0.389732485115185	1		377	550	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275057	41275057	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	87	341	0	ENST00000349496.5:c.1223T>C	p.Leu408Pro	p.L408P	ENST00000349496	NM_001904.3	408	cTt/cCt	9/15	0.256663803198874	1	FACETS	0.83	0.739	0.927	0.83	0.739	0.927	CLONAL	1	TRUE	0	0.389732485115185	1		341	433	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679756	88679756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780838684	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	167	496	0	ENST00000360948.2:c.707C>T	p.Ser236Leu	p.S236L	ENST00000360948	NM_001012338.2	236	tCa/tTa	7/19	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.389732485115185	2		496	613	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10286250	10286250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781646588	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	175	510	0	ENST00000340748.4:c.566C>T	p.Ser189Leu	p.S189L	ENST00000340748		189	tCg/tTg	6/40	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.389732485115185	2		510	893	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805741	43805741	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	157	622	1	ENST00000372470.3:c.797G>A	p.Gly266Asp	p.G266D	ENST00000372470	NM_005373.2	266	gGt/gAt	5/12	1	2	FACETS	0.975	0.894	1	0.975	0.894	1	CLONAL	1	TRUE	1	0.389732485115185	2		623	826	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551387	150551387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257167897	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	239	794	0	ENST00000369026.2:c.620G>A	p.Arg207Lys	p.R207K	ENST00000369026	NM_021960.4	207	aGg/aAg	1/3	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.389732485115185	2		794	862	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998183	100998183	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	84	477	0	ENST00000325455.5:c.1619C>T	p.Pro540Leu	p.P540L	ENST00000325455	NM_001202474.3	540	cCc/cTc	1/8	0.389732485115185	1	FACETS	0.811	0.72	0.907	0.811	0.72	0.907	CLONAL	1	TRUE	0	0.389732485115185	1		477	428	SUCCESS
ATM	472	MSKCC	GRCh37	11	108225543	108225543	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1060501563	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	27	320	0	ENST00000278616.4:c.8792G>C	p.Cys2931Ser	p.C2931S	ENST00000278616	NM_000051.3	2931	tGt/tCt	61/63	0.389732485115185	1	FACETS	0.323	0.257	0.399	0.323	0.257	0.399	SUBCLONAL	1	TRUE	0	0.389732485115185	1		320	345	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148916	119148916	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	76	310	0	ENST00000264033.4:c.1136A>C	p.Gln379Pro	p.Q379P	ENST00000264033	NM_005188.3	379	cAa/cCa	8/16	0.389732485115185	1	FACETS	0.978	0.866	1	0.978	0.866	1	CLONAL	1	TRUE	0	0.389732485115185	1		310	321	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611376	28611376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	90	453	0	ENST00000241453.7:c.1255C>T	p.His419Tyr	p.H419Y	ENST00000241453	NM_004119.2	419	Cat/Tat	10/24	1	2	FACETS	0.922	0.821	1	0.922	0.821	1	CLONAL	1	TRUE	1	0.389732485115185	2		453	501	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224391	36224391	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867077938	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	163	827	1	ENST00000222270.7:c.6941C>T	p.Pro2314Leu	p.P2314L	ENST00000222270	NM_014727.1	2314	cCa/cTa	28/37	1	2	FACETS	0.907	0.833	0.985	0.907	0.833	0.985	CLONAL	1	TRUE	1	0.389732485115185	2		828	922	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432654	29432654	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	98	539	0	ENST00000389048.3:c.3834C>A	p.Tyr1278Ter	p.Y1278*	ENST00000389048	NM_004304.4	1278	taC/taA	25/29	0.256663803198874	1	FACETS	0.673	0.601	0.748	0.673	0.601	0.748	SUBCLONAL	1	TRUE	0	0.389732485115185	1		539	602	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881536	111881536	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774211082	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	90	556	0	ENST00000393256.3:c.214C>T	p.Pro72Ser	p.P72S	ENST00000393256	NM_006538.4	72	Cct/Tct	2/4	0.256663803198874	1	FACETS	0.595	0.528	0.666	0.595	0.528	0.666	SUBCLONAL	1	TRUE	0	0.389732485115185	1		556	625	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485127	57485128	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	72	347	1	ENST00000371085.3:c.961_962delinsTT	p.Pro321Phe	p.P321F	ENST00000371085	NM_000516.4	321	CCt/TTt	11/13	1	2	FACETS	0.842	0.738	0.953	0.842	0.738	0.953	CLONAL	1	TRUE	1	0.389732485115185	2		348	439	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645708	12645708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	59	306	0	ENST00000251849.4:c.761G>A	p.Arg254Lys	p.R254K	ENST00000251849	NM_002880.3	254	aGg/aAg	7/17	0.256663803198874	1	FACETS	0.65	0.562	0.745	0.65	0.562	0.745	SUBCLONAL	1	TRUE	0	0.389732485115185	1		306	375	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620569	52620569	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	160	443	1	ENST00000394830.3:c.3184C>T	p.Pro1062Ser	p.P1062S	ENST00000394830	NM_018313.4	1062	Cct/Tct	21/30	0.256663803198874	1	FACETS	0.981	0.902	1	0.981	0.902	1	CLONAL	1	TRUE	0	0.389732485115185	1		444	674	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272181	142272181	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	104	434	0	ENST00000350721.4:c.2693C>T	p.Ser898Phe	p.S898F	ENST00000350721	NM_001184.3	898	tCc/tTc	13/47	0.389732485115185	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	0	0.389732485115185	1		434	425	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515274	31515274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201711846	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	150	567	1	ENST00000344624.3:c.1111C>T	p.Arg371Cys	p.R371C	ENST00000344624		371	Cgt/Tgt	5/33	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.389732485115185	2		568	720	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168510	56168510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	30	152	0	ENST00000399503.3:c.1466C>T	p.Pro489Leu	p.P489L	ENST00000399503	NM_005921.1	489	cCc/cTc	8/20	1	2	FACETS	1	0.837	1	1	0.837	1	CLONAL	1	TRUE	1	0.389732485115185	2		152	150	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040108	180040108	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	97	545	0	ENST00000261937.6:c.3334G>A	p.Ala1112Thr	p.A1112T	ENST00000261937	NM_182925.4	1112	Gcc/Acc	25/30	0.389732485115185	1	FACETS	0.837	0.749	0.929	0.837	0.749	0.929	CLONAL	1	TRUE	0	0.389732485115185	1		545	479	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26046042	26046042	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1296022073	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	43	314	0	ENST00000540144.1:c.404G>A	p.Arg135Lys	p.R135K	ENST00000540144	NM_003531.2	135	aGg/aAg	1/1	1	2	FACETS	0.553	0.463	0.652	0.553	0.463	0.652	SUBCLONAL	1	TRUE	1	0.389732485115185	2		314	399	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803010	32803010	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145822869	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	129	572	0	ENST00000374899.4:c.866C>T	p.Ser289Leu	p.S289L	ENST00000374899	NM_018833.2	289	tCg/tTg	5/12	1	2	FACETS	0.818	0.742	0.899	0.818	0.742	0.899	CLONAL	1	TRUE	1	0.389732485115185	2		572	809	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748570	43748570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	121	329	0	ENST00000523873.1:c.524C>T	p.Pro175Leu	p.P175L	ENST00000523873		175	cCc/cTc	6/8	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.389732485115185	2		329	549	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371927	55371927	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	133	475	1	ENST00000297316.4:c.617G>A	p.Cys206Tyr	p.C206Y	ENST00000297316	NM_022454.3	206	tGc/tAc	2/2	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.389732485115185	2		476	578	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939520	68939520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	57	318	0	ENST00000288368.4:c.505C>T	p.Pro169Ser	p.P169S	ENST00000288368	NM_024870.2	169	Cca/Tca	5/40	1	2	FACETS	0.799	0.689	0.919	0.799	0.689	0.919	CLONAL	1	TRUE	1	0.389732485115185	2		318	366	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93636986	93636986	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	84	377	0	ENST00000375746.1:c.1036G>A	p.Glu346Lys	p.E346K	ENST00000375746	NM_001174167.1	346	Gag/Aag	9/14	0.389732485115185	1	FACETS	0.865	0.769	0.968	0.865	0.769	0.968	CLONAL	1	TRUE	0	0.389732485115185	1		377	401	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0049736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	240	406	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.467375143552926	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.467375143552926	3		406	567	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0049736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	175	359	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.467375143552926	2		359	695	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0049736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	36	449	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	1	2	FACETS	0.219	0.179	0.263	0.219	0.179	0.263	SUBCLONAL	1	TRUE	1	0.467375143552926	2		449	705	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543781	212543781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866138670	NA	P-0049736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	131	353	1	ENST00000342788.4:c.1618G>A	p.Asp540Asn	p.D540N	ENST00000342788	NM_005235.2	540	Gat/Aat	13/28	1	2	FACETS	0.987	0.899	1	0.987	0.899	1	CLONAL	1	TRUE	1	0.467375143552926	2		354	568	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644679	134644679	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	47	445	0	ENST00000398015.3:c.80C>A	p.Thr27Lys	p.T27K	ENST00000398015	NM_004441.4	27	aCg/aAg	2/16	1	2	FACETS	0.294	0.248	0.346	0.294	0.248	0.346	SUBCLONAL	1	TRUE	1	0.467375143552926	2		445	683	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115971	8115972	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	249	414	1	ENST00000346208.3:c.1318dup	p.Thr440AsnfsTer67	p.T440Nfs*67	ENST00000346208		439	-/A	6/6	0.467375143552926	3	FACETS	0.897	0.842	0.952			1	CLONAL	2	TRUE	NA	0.467375143552926	3		415	733	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416438	49416438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	60	561	0	ENST00000301067.7:c.16273G>A	p.Glu5425Lys	p.E5425K	ENST00000301067	NM_003482.3	5425	Gag/Aag	51/54	1	2	FACETS	0.32	0.275	0.369	0.32	0.275	0.369	SUBCLONAL	1	TRUE	1	0.467375143552926	2		561	803	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070623	67070624	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0049736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	58	235	0	ENST00000412916.2:c.251_252dup	p.Tyr85SerfsTer5	p.Y85Sfs*5	ENST00000412916		83	cga/cGAga	3/6	0.467375143552926	1	FACETS	0.72	0.625	0.822	0.72	0.625	0.822	SUBCLONAL	1	TRUE	0	0.467375143552926	1		235	264	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656906	47656906	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	32	254	0	ENST00000233146.2:c.1102G>C	p.Glu368Gln	p.E368Q	ENST00000233146	NM_000251.2	368	Gaa/Caa	7/16	1	2	FACETS	0.353	0.286	0.428	0.353	0.286	0.428	SUBCLONAL	1	TRUE	1	0.467375143552926	2		254	388	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028885	47028885	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	46	371	0	ENST00000377604.3:c.189G>T	p.Glu63Asp	p.E63D	ENST00000377604	NM_001204468.1	63	gaG/gaT	3/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		371	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	96	678	0	ENST00000269305.4:c.880del	p.Glu294SerfsTer51	p.E294Sfs*51	ENST00000269305	NM_001126112.2	294	Gag/ag	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		678	892	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575200	48575200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500743	NA	P-0049741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	37	277	0	ENST00000342988.3:c.394C>T	p.His132Tyr	p.H132Y	ENST00000342988	NM_005359.5	132	Cac/Tac	3/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		277	344	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0049742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	46	263	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.853	0.721	0.997	0.853	0.721	0.997	CLONAL	1	FALSE	1	0.323824271750583	2		263	333	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0049742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	89	487	1	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	1	2	FACETS	0.741	0.657	0.831	0.741	0.657	0.831	SUBCLONAL	1	FALSE	1	0.323824271750583	2		488	742	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411576	63411576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	54	639	3	ENST00000330258.3:c.1591C>T	p.Arg531Ter	p.R531*	ENST00000330258	NM_152424.3	531	Cga/Tga	2/2	1	2	FACETS	0.359	0.305	0.418	0.359	0.305	0.418	SUBCLONAL	1	FALSE	1	0.323824271750583	2		642	929	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	47	316	0	ENST00000371953.3:c.388del	p.Arg130GlufsTer4	p.R130Efs*4	ENST00000371953	NM_000314.4	130	Cga/ga	5/9	0.323824271750583	1	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	FALSE	0	0.323824271750583	1		316	241	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11019809	11019809	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	114	519	0	ENST00000327064.4:c.484A>G	p.Met162Val	p.M162V	ENST00000327064	NM_199141.1	162	Atg/Gtg	4/16	1	2	FACETS	0.827	0.744	0.915	0.827	0.744	0.915	CLONAL	1	FALSE	1	0.323824271750583	2		519	851	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225338991	225338991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	44	339	0	ENST00000264414.4:c.2278G>A	p.Asp760Asn	p.D760N	ENST00000264414	NM_003590.4	760	Gat/Aat	16/16	1	2	FACETS	0.921	0.777	1	0.921	0.777	1	CLONAL	1	FALSE	1	0.323824271750583	2		339	295	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554955	187554956	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	61	293	0	ENST00000441802.2:c.4205dup	p.Asp1403ArgfsTer16	p.D1403Rfs*16	ENST00000441802	NM_005245.3	1402	ttc/ttTc	7/27	1	2	FACETS	0.986	0.855	1	0.986	0.855	1	CLONAL	1	FALSE	1	0.323824271750583	2		293	382	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181836	56181837	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCCGTGGCCTT	novel	NA	P-0049742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	44	313	0	ENST00000399503.3:c.4063_4073dup	p.Tyr1359ValfsTer22	p.Y1359Vfs*22	ENST00000399503	NM_005921.1	1354	ctc/cTCCGTGGCCTTtc	17/20	1	2	FACETS	0.871	0.734	1	0.871	0.734	1	CLONAL	1	FALSE	1	0.323824271750583	2		313	312	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200453	138200453	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	104	512	0	ENST00000237289.4:c.1871G>C	p.Cys624Ser	p.C624S	ENST00000237289	NM_001270507.1	624	tGc/tCc	7/9	1	2	FACETS	0.923	0.827	1	0.923	0.827	1	CLONAL	1	FALSE	1	0.323824271750583	2		512	696	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0049744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	378	536	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		536	1014	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0049744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	120	698	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		698	428	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045016	47045016	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0049744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	330	692	0	ENST00000377604.3:c.2342C>G	p.Ser781Ter	p.S781*	ENST00000377604	NM_001204468.1	781	tCa/tGa	20/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		692	1246	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572538	64572538	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	134	613	0	ENST00000312049.6:c.1318C>T	p.Leu440Phe	p.L440F	ENST00000312049	NM_130799.2	440	Ctt/Ttt	9/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		613	1082	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341347	89341354	+	frameshift_variant	Frame_Shift_Del	DEL	AGGATACG	AGGATACG	-	novel	NA	P-0049744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	239	473	0	ENST00000301030.4:c.7581_7588del	p.Ile2527MetfsTer2	p.I2527Mfs*2	ENST00000301030	NM_001256183.1	2527	atCGTATCCTgt/atgt	11/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		473	707	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233709	233709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1560994866	NA	P-0049744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	122	498	1	ENST00000264932.6:c.1013C>T	p.Ala338Val	p.A338V	ENST00000264932	NM_004168.2	338	gCg/gTg	8/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		499	798	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0049745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	22	490	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		490	818	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0049747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	19	476	3	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.491	0.372	0.631	0.491	0.372	0.631	SUBCLONAL	1	TRUE	1	0.238141875372011	2		479	325	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0049747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	10	272	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.326	0.22	0.459	0.326	0.22	0.459	SUBCLONAL	1	TRUE	1	0.238141875372011	2		272	258	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624274	89624274	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs587782187	NA	P-0049747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	87	299	0	ENST00000371953.3:c.48T>A	p.Tyr16Ter	p.Y16*	ENST00000371953	NM_000314.4	16	taT/taA	1/9	0.238141875372011	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	0	0.238141875372011	2		299	349	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844190	68844190	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	54	479	0	ENST00000261769.5:c.778C>A	p.Pro260Thr	p.P260T	ENST00000261769	NM_004360.3	260	Ccc/Acc	6/16	1	2	FACETS	0.69	0.589	0.802	0.69	0.589	0.802	SUBCLONAL	1	TRUE	1	0.238141875372011	2		479	657	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159754	20159754	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	71	441	0	ENST00000379607.5:c.5C>G	p.Pro2Arg	p.P2R	ENST00000379607	NM_001412.3	2	cCc/cGc	1/7	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.238141875372011	2		441	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	33	584	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	1	2	FACETS	0.307	0.249	0.373	0.307	0.249	0.373	SUBCLONAL	1	TRUE	1	0.388408914135795	2		584	553	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625251	69625251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782147248	NA	P-0049752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	70	808	1	ENST00000334134.2:c.542G>A	p.Arg181His	p.R181H	ENST00000334134	NM_005247.2	181	cGc/cAc	3/3	1	2	FACETS	0.314	0.273	0.359	0.314	0.273	0.359	SUBCLONAL	1	TRUE	1	0.388408914135795	2		809	1147	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878132	48878132	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	17	88	0	ENST00000267163.4:c.84del	p.Pro29LeufsTer36	p.P29Lfs*36	ENST00000267163	NM_000321.2	28	ccT/cc	1/27	1	2	FACETS	0.427	0.319	0.554	0.427	0.319	0.554	SUBCLONAL	1	TRUE	1	0.388408914135795	2		88	205	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340061	116340061	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	48	275	0	ENST00000397752.3:c.923C>G	p.Ser308Cys	p.S308C	ENST00000397752	NM_000245.2	308	tCc/tGc	2/21	0.388408914135795	3	FACETS	0.965	0.82	1	0.482	0.41	0.561	CLONAL	1	TRUE	1	0.388408914135795	3		275	306	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411895	116411898	+	splice_region_variant,intron_variant	Splice_Region	ONP	GTTT	GTTT	AAAA	novel	NA	P-0049752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	125	626	1	ENST00000397752.3:c.2888-8_2888-5delinsAAAA		p.X963_splice	ENST00000397752	NM_000245.2	963			0.388408914135795	3	FACETS	0.951	0.861	1	0.476	0.43	0.523	CLONAL	1	TRUE	1	0.388408914135795	3		627	808	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571900	64571900	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	104	732	1	ENST00000312049.6:c.1739C>A	p.Thr580Lys	p.T580K	ENST00000312049	NM_130799.2	580	aCg/aAg	10/10	0.202258418871389	1	FACETS	0.934	0.835	1	0.934	0.835	1	CLONAL	1	TRUE	0	0.202258418871389	1		733	990	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424702	49424702	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238014538	NA	P-0049753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	63	584	0	ENST00000301067.7:c.13645G>A	p.Glu4549Lys	p.E4549K	ENST00000301067	NM_003482.3	4549	Gag/Aag	40/54	0.181585670256416	3	FACETS	0.779	0.672	0.895			1	SUBCLONAL	1	TRUE	NA	0.202258418871389	3		584	881	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0049754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	130	536	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.217850979254094	4	FACETS	0.817	0.741	0.898	0.817	0.741	0.898	CLONAL	2	TRUE	2	0.217850979254094	4		536	889	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587781525	NA	P-0049754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	158	612	0	ENST00000269305.4:c.842A>T	p.Asp281Val	p.D281V	ENST00000269305	NM_001126112.2	281	gAc/gTc	8/11	0.196817359482748	2	FACETS	0.863	0.792	0.938	0.863	0.792	0.938	CLONAL	2	TRUE	0	0.217850979254094	2		612	840	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932321	39932321	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	88	714	0	ENST00000378444.4:c.2278C>A	p.Leu760Ile	p.L760I	ENST00000378444	NM_001123385.1	760	Ctc/Atc	4/15	NA	2	FACETS	0.946	0.837	1			1	INDETERMINATE	1	TRUE	NA	0.217850979254094	2		714	854	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632609	3632609	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201214017	NA	P-0049754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	69	648	0	ENST00000294008.3:c.5239G>A	p.Val1747Met	p.V1747M	ENST00000294008	NM_032444.2	1747	Gtg/Atg	15/15	1	2	FACETS	0.661	0.574	0.755	0.661	0.574	0.755	SUBCLONAL	1	TRUE	1	0.217850979254094	2		648	959	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50818246	50818246	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	22	214	0	ENST00000398568.2:c.1824T>A	p.Phe608Leu	p.F608L	ENST00000398568	NM_001042412.1	608	ttT/ttA	11/18	1	2	FACETS	0.68	0.527	0.857	0.68	0.527	0.857	SUBCLONAL	1	TRUE	1	0.217850979254094	2		214	297	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384802	17384802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	169	597	2	ENST00000359435.4:c.434C>T	p.Ala145Val	p.A145V	ENST00000359435	NM_001033549.1	145	gCa/gTa	4/9	0.205437171167807	3	FACETS	0.894	0.822	0.97	0.894	0.822	0.97	CLONAL	2	TRUE	1	0.217850979254094	3		599	962	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224771	36224771	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	94	717	0	ENST00000222270.7:c.7157C>T	p.Ser2386Leu	p.S2386L	ENST00000222270	NM_014727.1	2386	tCa/tTa	30/37	0.205437171167807	3	FACETS	0.902	0.801	1	0.451	0.4	0.506	CLONAL	1	TRUE	1	0.217850979254094	3		717	1061	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073616	8073617	+	frameshift_variant	Frame_Shift_Ins	INS	GG	GG	AAA	novel	NA	P-0049754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	54	338	2	ENST00000377482.5:c.1042_1043delinsTTT	p.Pro348PhefsTer8	p.P348Ffs*8	ENST00000377482	NM_018948.3	348	CCg/TTTg	4/4	1	2	FACETS	0.839	0.716	0.973	0.839	0.716	0.973	CLONAL	1	TRUE	1	0.217850979254094	2		340	591	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0049758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	62	200	0	ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	4/10	0.15573747447409	3	FACETS	1	0.901	1	1	0.901	1	CLONAL	2	TRUE	1	0.153965164442182	3		200	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0049759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	179	583	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.242374613365023	1	FACETS	1	0.981	1	1	0.981	1	INDETERMINATE	1	TRUE	0	0.548027642388864	1		583	418	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534365	63534365	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1173549577	NA	P-0049759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	201	858	0	ENST00000307078.5:c.1156G>C	p.Glu386Gln	p.E386Q	ENST00000307078	NM_004655.3	386	Gag/Cag	5/11	0.548027642388864	2	FACETS	1	0.97	1	0.539	0.501	0.577	CLONAL	1	TRUE	0	0.548027642388864	2		858	681	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	30	373	1	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	0.4	0.321	0.489	0.4	0.321	0.489	SUBCLONAL	1	TRUE	1	0.28	2		374	536	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	27	377	1	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.804	0.642	0.986	0.804	0.642	0.986	CLONAL	1	TRUE	1	0.28	2		378	240	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270085	198270085	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	56	448	0	ENST00000335508.6:c.1351C>T	p.Arg451Ter	p.R451*	ENST00000335508	NM_012433.2	451	Cga/Tga	10/25	1	2	FACETS	0.717	0.614	0.829	0.717	0.614	0.829	SUBCLONAL	1	TRUE	1	0.28	2		448	558	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37058999	37058999	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs63751194	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	29	309	0	ENST00000231790.2:c.793C>T	p.Arg265Cys	p.R265C	ENST00000231790	NM_000249.3	265	Cgt/Tgt	10/19	1	2	FACETS	0.485	0.389	0.595	0.485	0.389	0.595	SUBCLONAL	1	TRUE	1	0.28	2		309	427	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	28	353	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	0.541	0.432	0.664	0.541	0.432	0.664	SUBCLONAL	1	TRUE	1	0.28	2		353	370	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17371320	17371320	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs74315370	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	45	541	1	ENST00000375499.3:c.136C>T	p.Arg46Ter	p.R46*	ENST00000375499	NM_003000.2	46	Cga/Tga	2/8	1	2	FACETS	0.48	0.403	0.567	0.48	0.403	0.567	SUBCLONAL	1	TRUE	1	0.28	2		542	669	SUCCESS
APC	324	MSKCC	GRCh37	5	112175166	112175166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371113837	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	28	236	0	ENST00000257430.4:c.3875C>T	p.Thr1292Met	p.T1292M	ENST00000257430	NM_000038.5	1292	aCg/aTg	16/16	1	2	FACETS	0.93	0.748	1	0.93	0.748	1	CLONAL	1	TRUE	1	0.28	2		236	215	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508083	106508083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339698935	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	36	362	0	ENST00000359195.3:c.77G>A	p.Arg26His	p.R26H	ENST00000359195	NM_002649.2	26	cGc/cAc	2/11	1	2	FACETS	0.63	0.518	0.755	0.63	0.518	0.755	SUBCLONAL	1	TRUE	1	0.28	2		362	408	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518099	8518099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764400127	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	62	448	0	ENST00000356435.5:c.1292C>T	p.Ser431Leu	p.S431L	ENST00000356435		431	tCg/tTg	10/35	1	2	FACETS	0.714	0.617	0.82	0.714	0.617	0.82	SUBCLONAL	1	TRUE	1	0.28	2		448	620	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547022	9547022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs58486349	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	31	283	0	ENST00000353224.5:c.1000G>A	p.Asp334Asn	p.D334N	ENST00000353224	NM_177990.2	334	Gat/Aat	5/10	1	2	FACETS	0.701	0.568	0.85	0.701	0.568	0.85	SUBCLONAL	1	TRUE	1	0.28	2		283	316	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528778	157528778	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1381434956	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	67	545	1	ENST00000346085.5:c.6503C>T	p.Thr2168Met	p.T2168M	ENST00000346085	NM_020732.3	2168	aCg/aTg	20/20	1	2	FACETS	0.693	0.601	0.792	0.693	0.601	0.792	SUBCLONAL	1	TRUE	1	0.28	2		546	691	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857785	9857785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555482324	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	62	527	2	ENST00000330684.3:c.3616C>T	p.Arg1206Ter	p.R1206*	ENST00000330684	NM_001134407.1	1206	Cga/Tga	13/13	1	2	FACETS	0.63	0.543	0.724	0.63	0.543	0.724	SUBCLONAL	1	TRUE	1	0.28	2		529	703	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982356	25982356	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	53	244	0	ENST00000435504.4:c.934C>T	p.Arg312Ter	p.R312*	ENST00000435504		312	Cga/Tga	9/13	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.28	2		244	369	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242774	66242774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151302542	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	48	258	0	ENST00000273854.3:c.1798G>A	p.Glu600Lys	p.E600K	ENST00000273854	NM_004439.5	600	Gaa/Aaa	9/18	1	2	FACETS	0.851	0.721	0.993	0.851	0.721	0.993	CLONAL	1	TRUE	1	0.28	2		258	403	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97897778	97897778	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	23	343	0	ENST00000289081.3:c.693G>T	p.Lys231Asn	p.K231N	ENST00000289081	NM_000136.2	231	aaG/aaT	8/15	1	2	FACETS	0.413	0.321	0.519	0.413	0.321	0.519	SUBCLONAL	1	TRUE	1	0.28	2		343	398	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866552	78866552	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	86	601	0	ENST00000306801.3:c.2125C>T	p.Arg709Ter	p.R709*	ENST00000306801	NM_020761.2	709	Cga/Tga	19/34	1	2	FACETS	0.714	0.631	0.804	0.714	0.631	0.804	SUBCLONAL	1	TRUE	1	0.28	2		601	860	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499763	8499763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745717615	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	75	589	0	ENST00000356435.5:c.2206G>A	p.Val736Met	p.V736M	ENST00000356435		736	Gtg/Atg	14/35	1	2	FACETS	0.75	0.657	0.851	0.75	0.657	0.851	SUBCLONAL	1	TRUE	1	0.28	2		589	714	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790038	40790038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757402269	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	77	588	0	ENST00000373198.4:c.2693C>T	p.Thr898Met	p.T898M	ENST00000373198	NM_133170.3	898	aCg/aTg	18/32	1	2	FACETS	0.567	0.496	0.643	0.567	0.496	0.643	SUBCLONAL	1	TRUE	1	0.28	2		588	970	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857197	9857197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866121846	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	108	490	0	ENST00000330684.3:c.4204C>T	p.Arg1402Trp	p.R1402W	ENST00000330684	NM_001134407.1	1402	Cgg/Tgg	13/13	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.28	2		490	696	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005375	150005375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775410465	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	57	513	0	ENST00000253339.5:c.850G>A	p.Val284Ile	p.V284I	ENST00000253339		284	Gta/Ata	3/7	1	2	FACETS	0.594	0.508	0.687	0.594	0.508	0.687	SUBCLONAL	1	TRUE	1	0.28	2		513	686	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100172	27100172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775802127	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	61	584	0	ENST00000324856.7:c.3968G>A	p.Arg1323His	p.R1323H	ENST00000324856	NM_006015.4	1323	cGc/cAc	16/20	1	2	FACETS	0.633	0.546	0.729	0.633	0.546	0.729	SUBCLONAL	1	TRUE	1	0.28	2		584	688	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25498386	25498386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1274769751	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	58	524	1	ENST00000264709.3:c.475G>A	p.Glu159Lys	p.E159K	ENST00000264709	NM_175629.2	159	Gaa/Aaa	5/23	1	2	FACETS	0.641	0.55	0.741	0.641	0.55	0.741	SUBCLONAL	1	TRUE	1	0.28	2		525	646	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20483060	20483060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750169257	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	64	396	0	ENST00000346618.3:c.793G>A	p.Glu265Lys	p.E265K	ENST00000346618	NM_001949.4	265	Gag/Aag	4/7	1	2	FACETS	0.724	0.627	0.83	0.724	0.627	0.83	SUBCLONAL	1	TRUE	1	0.28	2		396	631	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021785	71021785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs112795301	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	34	318	1	ENST00000318789.4:c.1573C>T	p.Arg525Ter	p.R525*	ENST00000318789	NM_032682.5	525	Cga/Tga	18/21	1	2	FACETS	0.754	0.618	0.907	0.754	0.618	0.907	CLONAL	1	TRUE	1	0.28	2		319	322	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293551	1293551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	96	965	1	ENST00000310581.5:c.1450G>A	p.Glu484Lys	p.E484K	ENST00000310581	NM_198253.2	484	Gaa/Aaa	2/16	1	2	FACETS	0.638	0.567	0.714	0.638	0.567	0.714	SUBCLONAL	1	TRUE	1	0.28	2		966	1075	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539105	23539105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	57	482	0	ENST00000380871.4:c.334G>A	p.Ala112Thr	p.A112T	ENST00000380871	NM_006167.3	112	Gcc/Acc	2/2	1	2	FACETS	0.573	0.491	0.664	0.573	0.491	0.664	SUBCLONAL	1	TRUE	1	0.28	2		482	710	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252865	36252865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060499616	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	32	372	0	ENST00000300305.3:c.497G>A	p.Arg166Gln	p.R166Q	ENST00000300305		166	cGa/cAa	4/8	1	2	FACETS	0.46	0.373	0.559	0.46	0.373	0.559	SUBCLONAL	1	TRUE	1	0.28	2		372	497	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647754	2647754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs901482387	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	82	564	0	ENST00000342085.4:c.1657G>A	p.Ala553Thr	p.A553T	ENST00000342085	NM_002613.4	553	Gcc/Acc	14/14	1	2	FACETS	0.718	0.632	0.81	0.718	0.632	0.81	SUBCLONAL	1	TRUE	1	0.28	2		564	816	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105645	11105645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	91	564	1	ENST00000358026.2:c.1561C>T	p.Arg521Trp	p.R521W	ENST00000358026	NM_001128849.1	521	Cgg/Tgg	9/36	1	2	FACETS	0.698	0.619	0.783	0.698	0.619	0.783	SUBCLONAL	1	TRUE	1	0.28	2		565	931	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991736	25991736	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs530632623	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	38	394	0	ENST00000435504.4:c.506C>T	p.Ala169Val	p.A169V	ENST00000435504		169	gCg/gTg	7/13	1	2	FACETS	0.515	0.425	0.616	0.515	0.425	0.616	SUBCLONAL	1	TRUE	1	0.28	2		394	527	SUCCESS
APC	324	MSKCC	GRCh37	5	112164611	112164611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587783034	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	49	291	0	ENST00000257430.4:c.1685C>T	p.Thr562Met	p.T562M	ENST00000257430	NM_000038.5	562	aCg/aTg	14/16	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.28	2		291	340	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021428	42021428	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	50	434	0	ENST00000219905.7:c.3724C>T	p.Arg1242Ter	p.R1242*	ENST00000219905	NM_001164273.1	1242	Cga/Tga	11/24	1	2	FACETS	0.695	0.59	0.81	0.695	0.59	0.81	SUBCLONAL	1	TRUE	1	0.28	2		434	514	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937602	76937603	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	28	321	0	ENST00000373344.5:c.3145dup	p.Ile1049AsnfsTer4	p.I1049Nfs*4	ENST00000373344	NM_000489.3	1049	ata/aAta	9/35	1	2	FACETS	0.725	0.581	0.887	0.725	0.581	0.887	SUBCLONAL	1	TRUE	1	0.28	2		321	276	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166421	118166421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775789017	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	72	405	0	ENST00000369448.3:c.931C>T	p.Arg311Cys	p.R311C	ENST00000369448	NM_017709.3	311	Cgc/Tgc	2/2	1	2	FACETS	0.864	0.756	0.981	0.864	0.756	0.981	CLONAL	1	TRUE	1	0.28	2		405	595	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894916	101894916	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060502040	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	26	355	0	ENST00000374994.4:c.469C>T	p.Arg157Ter	p.R157*	ENST00000374994	NM_004612.2	157	Cga/Tga	3/9	1	2	FACETS	0.409	0.323	0.508	0.409	0.323	0.508	SUBCLONAL	1	TRUE	1	0.28	2		355	454	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435061	18435061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603400	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	21	304	0	ENST00000266497.5:c.46G>A	p.Glu16Lys	p.E16K	ENST00000266497		16	Gaa/Aaa	1/31	0.220287756186264	1	FACETS	0.433	0.333	0.549	0.433	0.333	0.549	SUBCLONAL	1	TRUE	0	0.28	1		304	298	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650710	67650710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243010179	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	96	465	1	ENST00000264010.4:c.1015C>T	p.Arg339Trp	p.R339W	ENST00000264010	NM_006565.3	339	Cgg/Tgg	5/12	1	2	FACETS	0.751	0.668	0.84	0.751	0.668	0.84	SUBCLONAL	1	TRUE	1	0.28	2		466	913	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969848	81969848	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568724894	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	70	563	0	ENST00000359376.3:c.2917G>A	p.Asp973Asn	p.D973N	ENST00000359376	NM_002661.3	973	Gac/Aac	27/33	1	2	FACETS	0.599	0.521	0.683	0.599	0.521	0.683	SUBCLONAL	1	TRUE	1	0.28	2		563	835	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971393	15971393	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759642635	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	36	492	0	ENST00000268712.3:c.4556C>T	p.Ser1519Leu	p.S1519L	ENST00000268712	NM_006311.3	1519	tCg/tTg	32/46	1	2	FACETS	0.393	0.322	0.473	0.393	0.322	0.473	SUBCLONAL	1	TRUE	1	0.28	2		492	654	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935595	13935595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776609162	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	55	437	3	ENST00000405192.2:c.1261G>A	p.Glu421Lys	p.E421K	ENST00000405192	NM_001163147.1	421	Gag/Aag	12/12	1	2	FACETS	0.601	0.513	0.697	0.601	0.513	0.697	SUBCLONAL	1	TRUE	1	0.28	2		440	654	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913023	32913023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376338226	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	51	461	0	ENST00000380152.3:c.4531G>A	p.Glu1511Lys	p.E1511K	ENST00000380152		1511	Gaa/Aaa	11/27	1	2	FACETS	0.795	0.677	0.925	0.795	0.677	0.925	CLONAL	1	TRUE	1	0.28	2		461	458	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176662842	176662842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779028625	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	16	367	0	ENST00000439151.2:c.3817C>T	p.Arg1273Cys	p.R1273C	ENST00000439151	NM_022455.4	1273	Cgc/Tgc	6/23	1	2	FACETS	0.366	0.27	0.481	0.366	0.27	0.481	SUBCLONAL	1	TRUE	1	0.28	2		367	312	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592099	67592099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	32	335	0	ENST00000274335.5:c.1915C>T	p.Arg639Ter	p.R639*	ENST00000274335		639	Cga/Tga	14/15	1	2	FACETS	0.505	0.409	0.613	0.505	0.409	0.613	SUBCLONAL	1	TRUE	1	0.28	2		335	453	SUCCESS
APC	324	MSKCC	GRCh37	5	112177901	112177901	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs752654519	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	30	216	0	ENST00000257430.4:c.6610C>T	p.Arg2204Ter	p.R2204*	ENST00000257430	NM_000038.5	2204	Cga/Tga	16/16	1	2	FACETS	0.642	0.518	0.782	0.642	0.518	0.782	SUBCLONAL	1	TRUE	1	0.28	2		216	334	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961330	41961330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	34	454	1	ENST00000219905.7:c.238G>A	p.Asp80Asn	p.D80N	ENST00000219905	NM_001164273.1	80	Gat/Aat	2/24	1	2	FACETS	0.629	0.514	0.758	0.629	0.514	0.758	SUBCLONAL	1	TRUE	1	0.28	2		455	386	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12653551	12653551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140884322	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	71	421	0	ENST00000251849.4:c.218G>A	p.Arg73Gln	p.R73Q	ENST00000251849	NM_002880.3	73	cGa/cAa	3/17	1	2	FACETS	0.831	0.726	0.945	0.831	0.726	0.945	CLONAL	1	TRUE	1	0.28	2		421	610	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94170371	94170371	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745614941	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	22	304	1	ENST00000323929.3:c.1898G>A	p.Arg633Gln	p.R633Q	ENST00000323929	NM_005591.3	633	cGa/cAa	17/20	1	2	FACETS	0.499	0.387	0.629	0.499	0.387	0.629	SUBCLONAL	1	TRUE	1	0.28	2		305	315	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169179	119169179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150811339	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	79	552	0	ENST00000264033.4:c.2363G>A	p.Arg788Gln	p.R788Q	ENST00000264033	NM_005188.3	788	cGa/cAa	15/16	1	2	FACETS	0.704	0.618	0.796	0.704	0.618	0.796	SUBCLONAL	1	TRUE	1	0.28	2		552	802	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056400	180056400	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	90	700	0	ENST00000261937.6:c.844C>T	p.Arg282Ter	p.R282*	ENST00000261937	NM_182925.4	282	Cga/Tga	7/30	1	2	FACETS	0.818	0.725	0.917	0.818	0.725	0.917	CLONAL	1	TRUE	1	0.28	2		700	786	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715410	117715410	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769599473	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	15	354	0	ENST00000368508.3:c.1079G>T	p.Arg360Ile	p.R360I	ENST00000368508	NM_002944.2	360	aGa/aTa	10/43	0.3	1	FACETS	0.363	0.265	0.48	0.363	0.265	0.48	SUBCLONAL	1	TRUE	0	0.28	1		354	254	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474351	40474351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780466766	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	55	531	0	ENST00000264657.5:c.2050G>A	p.Gly684Arg	p.G684R	ENST00000264657	NM_139276.2	684	Gga/Aga	21/24	1	2	FACETS	0.532	0.454	0.617	0.532	0.454	0.617	SUBCLONAL	1	TRUE	1	0.28	2		531	739	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164893	123164893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	38	351	1	ENST00000218089.9:c.206G>A	p.Arg69Gln	p.R69Q	ENST00000218089	NM_001042749.1	69	cGa/cAa	5/35	1	2	FACETS	0.734	0.607	0.874	0.734	0.607	0.874	SUBCLONAL	1	TRUE	1	0.28	2		352	370	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148504761	148504761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397515548	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	35	494	0	ENST00000320356.2:c.2233G>A	p.Glu745Lys	p.E745K	ENST00000320356	NM_004456.4	745	Gaa/Aaa	20/20	1	2	FACETS	0.387	0.316	0.467	0.387	0.316	0.467	SUBCLONAL	1	TRUE	1	0.28	2		494	646	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352765	70352765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759105512	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	130	615	1	ENST00000374080.3:c.4486C>T	p.Arg1496Cys	p.R1496C	ENST00000374080		1496	Cgc/Tgc	32/45	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.28	2		616	872	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211416	98211416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369966295	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	109	721	2	ENST00000331920.6:c.3739G>A	p.Ala1247Thr	p.A1247T	ENST00000331920	NM_000264.3	1247	Gcg/Acg	22/24	1	2	FACETS	0.783	0.702	0.87	0.783	0.702	0.87	SUBCLONAL	1	TRUE	1	0.28	2		723	994	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523486	106523486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750632554	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	28	247	0	ENST00000359195.3:c.2638G>A	p.Glu880Lys	p.E880K	ENST00000359195	NM_002649.2	880	Gag/Aag	8/11	1	2	FACETS	0.509	0.406	0.626	0.509	0.406	0.626	SUBCLONAL	1	TRUE	1	0.28	2		247	393	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73333960	73333960	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	38	427	0	ENST00000377767.4:c.2850G>T	p.Lys950Asn	p.K950N	ENST00000377767	NM_014953.3	950	aaG/aaT	21/21	1	2	FACETS	0.679	0.561	0.809	0.679	0.561	0.809	SUBCLONAL	1	TRUE	1	0.28	2		427	400	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609382	39609382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463795009	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	63	307	0	ENST00000262039.4:c.1684G>A	p.Glu562Lys	p.E562K	ENST00000262039	NM_002647.2	562	Gaa/Aaa	15/25	1	2	FACETS	0.814	0.704	0.932	0.814	0.704	0.932	CLONAL	1	TRUE	1	0.28	2		307	553	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238951	5238951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237159914	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	74	618	3	ENST00000357368.4:c.1828C>T	p.Arg610Trp	p.R610W	ENST00000357368	NM_002850.3	610	Cgg/Tgg	13/38	1	2	FACETS	0.65	0.568	0.739	0.65	0.568	0.739	SUBCLONAL	1	TRUE	1	0.28	2		621	813	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564512	41564512	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555911075	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	40	446	0	ENST00000263253.7:c.3934C>T	p.Arg1312Ter	p.R1312*	ENST00000263253	NM_001429.3	1312	Cga/Tga	24/31	1	2	FACETS	0.511	0.424	0.608	0.511	0.424	0.608	SUBCLONAL	1	TRUE	1	0.28	2		446	559	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857238	78857238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866939416	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	76	655	0	ENST00000306801.3:c.1604C>T	p.Thr535Met	p.T535M	ENST00000306801	NM_020761.2	535	aCg/aTg	15/34	1	2	FACETS	0.64	0.56	0.726	0.64	0.56	0.726	SUBCLONAL	1	TRUE	1	0.28	2		655	848	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467829	50467829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	64	690	0	ENST00000331340.3:c.1064C>T	p.Ala355Val	p.A355V	ENST00000331340	NM_006060.4	355	gCg/gTg	8/8	1	2	FACETS	0.619	0.536	0.711	0.619	0.536	0.711	SUBCLONAL	1	TRUE	1	0.28	2		690	738	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715624	30715624	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	33	280	0	ENST00000295754.5:c.1282G>T	p.Glu428Ter	p.E428*	ENST00000295754	NM_003242.5	428	Gaa/Taa	5/7	1	2	FACETS	0.649	0.529	0.784	0.649	0.529	0.784	SUBCLONAL	1	TRUE	1	0.28	2		280	363	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168682	32168682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs935064991	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	120	721	1	ENST00000375023.3:c.4241C>T	p.Ala1414Val	p.A1414V	ENST00000375023	NM_004557.3	1414	gCg/gTg	23/30	1	2	FACETS	0.853	0.769	0.942	0.853	0.769	0.942	CLONAL	1	TRUE	1	0.28	2		722	1005	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612735	228612735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	102	739	0	ENST00000366696.1:c.292G>A	p.Glu98Lys	p.E98K	ENST00000366696	NM_003493.2	98	Gag/Aag	1/1	1	2	FACETS	0.687	0.613	0.767	0.687	0.613	0.767	SUBCLONAL	1	TRUE	1	0.28	2		739	1060	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376627	8376627	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	40	426	0	ENST00000356435.5:c.4486C>T	p.Arg1496Ter	p.R1496*	ENST00000356435		1496	Cga/Tga	27/35	1	2	FACETS	0.521	0.433	0.62	0.521	0.433	0.62	SUBCLONAL	1	TRUE	1	0.28	2		426	548	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	66	497	0	ENST00000320574.5:c.1231G>C	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ctg	13/49	1	2	FACETS	0.84	0.73	0.96	0.84	0.73	0.96	CLONAL	1	TRUE	1	0.28	2		497	561	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012219	16012219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	39	366	0	ENST00000268712.3:c.2063G>A	p.Arg688Gln	p.R688Q	ENST00000268712	NM_006311.3	688	cGa/cAa	19/46	1	2	FACETS	0.747	0.62	0.888	0.747	0.62	0.888	SUBCLONAL	1	TRUE	1	0.28	2		366	373	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612869	228612869	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201904037	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	107	773	0	ENST00000366696.1:c.158G>A	p.Arg53His	p.R53H	ENST00000366696	NM_003493.2	53	cGc/cAc	1/1	1	2	FACETS	0.728	0.651	0.809	0.728	0.651	0.809	SUBCLONAL	1	TRUE	1	0.28	2		773	1050	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024169	112024169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465963577	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	19	373	0	ENST00000368678.4:c.616C>T	p.Arg206Cys	p.R206C	ENST00000368678		206	Cgc/Tgc	7/13	0.3	1	FACETS	0.315	0.239	0.406	0.315	0.239	0.406	SUBCLONAL	1	TRUE	0	0.28	1		373	370	SUCCESS
ALK	238	MSKCC	GRCh37	2	29448419	29448419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140733978	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	69	862	0	ENST00000389048.3:c.3080C>T	p.Pro1027Leu	p.P1027L	ENST00000389048	NM_004304.4	1027	cCg/cTg	19/29	1	2	FACETS	0.435	0.377	0.498	0.435	0.377	0.498	SUBCLONAL	1	TRUE	1	0.28	2		862	1133	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211461	46211461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	10	200	0	ENST00000334344.6:c.427C>T	p.Arg143Cys	p.R143C	ENST00000334344	NM_152641.2	143	Cgt/Tgt	5/21	0.220287756186264	1	FACETS	0.349	0.236	0.49	0.349	0.236	0.49	SUBCLONAL	1	TRUE	0	0.28	1		200	176	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472565	88472565	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371959662	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	75	498	1	ENST00000360948.2:c.1990G>A	p.Ala664Thr	p.A664T	ENST00000360948	NM_001012338.2	664	Gcc/Acc	16/19	1	2	FACETS	0.727	0.636	0.825	0.727	0.636	0.825	SUBCLONAL	1	TRUE	1	0.28	2		499	737	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273266	198273266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	40	492	0	ENST00000335508.6:c.944G>A	p.Arg315Gln	p.R315Q	ENST00000335508	NM_012433.2	315	cGa/cAa	8/25	1	2	FACETS	0.462	0.383	0.55	0.462	0.383	0.55	SUBCLONAL	1	TRUE	1	0.28	2		492	619	SUCCESS
ATR	545	MSKCC	GRCh37	3	142168390	142168390	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs749753899	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	33	409	1	ENST00000350721.4:c.7816C>T	p.Arg2606Ter	p.R2606*	ENST00000350721	NM_001184.3	2606	Cga/Tga	47/47	1	2	FACETS	0.648	0.528	0.782	0.648	0.528	0.782	SUBCLONAL	1	TRUE	1	0.28	2		410	364	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471050	8471050	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	33	387	0	ENST00000356435.5:c.3449C>A	p.Ser1150Tyr	p.S1150Y	ENST00000356435		1150	tCt/tAt	20/35	1	2	FACETS	0.597	0.486	0.721	0.597	0.486	0.721	SUBCLONAL	1	TRUE	1	0.28	2		387	395	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793432	18793432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187869576	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	19	385	0	ENST00000266497.5:c.4129C>T	p.Arg1377Cys	p.R1377C	ENST00000266497		1377	Cgt/Tgt	30/31	0.220287756186264	1	FACETS	0.35	0.266	0.451	0.35	0.266	0.451	SUBCLONAL	1	TRUE	0	0.28	1		385	333	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42050032	42050032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	20	283	0	ENST00000219905.7:c.7186C>T	p.Arg2396Ter	p.R2396*	ENST00000219905	NM_001164273.1	2396	Cga/Tga	19/24	1	2	FACETS	0.516	0.395	0.657	0.516	0.395	0.657	SUBCLONAL	1	TRUE	1	0.28	2		283	277	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200073	128200073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374457534	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	60	679	1	ENST00000341105.2:c.1232C>T	p.Ala411Val	p.A411V	ENST00000341105	NM_032638.4	411	gCg/gTg	6/6	1	2	FACETS	0.399	0.343	0.462	0.399	0.343	0.462	SUBCLONAL	1	TRUE	1	0.28	2		680	1073	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190872	185190872	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	89	674	0	ENST00000265026.3:c.1753C>T	p.Arg585Ter	p.R585*	ENST00000265026	NM_004721.4	585	Cga/Tga	11/14	1	2	FACETS	0.678	0.6	0.762	0.678	0.6	0.762	SUBCLONAL	1	TRUE	1	0.28	2		674	938	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294283	1294283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	104	839	4	ENST00000310581.5:c.718C>T	p.Arg240Cys	p.R240C	ENST00000310581	NM_198253.2	240	Cgt/Tgt	2/16	1	2	FACETS	0.677	0.605	0.754	0.677	0.605	0.754	SUBCLONAL	1	TRUE	1	0.28	2		843	1097	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950304	15950304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763924640	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	35	589	0	ENST00000268712.3:c.6640C>T	p.Arg2214Cys	p.R2214C	ENST00000268712	NM_006311.3	2214	Cgt/Tgt	42/46	1	2	FACETS	0.386	0.315	0.466	0.386	0.315	0.466	SUBCLONAL	1	TRUE	1	0.28	2		589	648	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426835	70426835	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	41	384	0	ENST00000373644.4:c.4495C>A	p.Leu1499Ile	p.L1499I	ENST00000373644	NM_030625.2	1499	Ctt/Att	7/12	1	2	FACETS	0.617	0.513	0.731	0.617	0.513	0.731	SUBCLONAL	1	TRUE	1	0.28	2		384	475	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067929	30067929	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	105	505	0	ENST00000338641.4:c.1114G>A	p.Glu372Lys	p.E372K	ENST00000338641	NM_000268.3	372	Gaa/Aaa	11/16	1	2	FACETS	0.915	0.819	1	0.915	0.819	1	CLONAL	1	TRUE	1	0.28	2		505	820	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527808	157527808	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766931727	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	58	478	0	ENST00000346085.5:c.5533C>T	p.Arg1845Cys	p.R1845C	ENST00000346085	NM_020732.3	1845	Cgc/Tgc	20/20	1	2	FACETS	0.717	0.616	0.827	0.717	0.616	0.827	SUBCLONAL	1	TRUE	1	0.28	2		478	578	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564766	41564766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303184977	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	53	533	0	ENST00000263253.7:c.4067G>A	p.Arg1356Gln	p.R1356Q	ENST00000263253	NM_001429.3	1356	cGa/cAa	25/31	1	2	FACETS	0.529	0.45	0.616	0.529	0.45	0.616	SUBCLONAL	1	TRUE	1	0.28	2		533	715	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222530	2222530	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760394488	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	92	717	1	ENST00000398665.3:c.3362C>T	p.Ser1121Leu	p.S1121L	ENST00000398665	NM_032482.2	1121	tCg/tTg	24/28	1	2	FACETS	0.621	0.55	0.697	0.621	0.55	0.697	SUBCLONAL	1	TRUE	1	0.28	2		718	1058	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417883	138417883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	34	430	0	ENST00000289153.2:c.1636C>T	p.Pro546Ser	p.P546S	ENST00000289153	NM_006219.2	546	Ccc/Tcc	11/22	1	2	FACETS	0.558	0.456	0.673	0.558	0.456	0.673	SUBCLONAL	1	TRUE	1	0.28	2		430	435	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939260	71939260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	51	751	1	ENST00000298229.2:c.209G>A	p.Arg70His	p.R70H	ENST00000298229	NM_001567.3	70	cGc/cAc	2/28	1	2	FACETS	0.368	0.311	0.43	0.368	0.311	0.43	SUBCLONAL	1	TRUE	1	0.28	2		752	991	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215595163	215595163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377227840	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	35	344	0	ENST00000260947.4:c.1973G>A	p.Arg658His	p.R658H	ENST00000260947	NM_000465.2	658	cGc/cAc	10/11	1	2	FACETS	0.786	0.646	0.942	0.786	0.646	0.942	CLONAL	1	TRUE	1	0.28	2		344	318	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044541	47044541	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	62	746	0	ENST00000377604.3:c.2038C>T	p.Arg680Ter	p.R680*	ENST00000377604	NM_001204468.1	680	Cga/Tga	18/24	1	2	FACETS	0.503	0.433	0.579	0.503	0.433	0.579	SUBCLONAL	1	TRUE	1	0.28	2		746	881	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799632	3799632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267606752	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	20	332	0	ENST00000262367.5:c.3832G>A	p.Glu1278Lys	p.E1278K	ENST00000262367	NM_004380.2	1278	Gaa/Aaa	21/31	1	2	FACETS	0.386	0.295	0.493	0.386	0.295	0.493	SUBCLONAL	1	TRUE	1	0.28	2		332	370	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923650	72923650	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	53	713	0	ENST00000268489.5:c.3428G>T	p.Arg1143Met	p.R1143M	ENST00000268489	NM_006885.3	1143	aGg/aTg	4/10	1	2	FACETS	0.417	0.354	0.486	0.417	0.354	0.486	SUBCLONAL	1	TRUE	1	0.28	2		713	908	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724542	162724542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1041487062	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	42	576	2	ENST00000367921.3:c.314G>A	p.Arg105His	p.R105H	ENST00000367921	NM_006182.2	105	cGc/cAc	5/18	1	2	FACETS	0.417	0.347	0.495	0.417	0.347	0.495	SUBCLONAL	1	TRUE	1	0.28	2		578	719	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609744	81609744	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201889708	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	47	420	0	ENST00000298171.2:c.1342G>A	p.Val448Ile	p.V448I	ENST00000298171	NM_000369.2	448	Gtc/Atc	10/10	1	2	FACETS	0.568	0.479	0.667	0.568	0.479	0.667	SUBCLONAL	1	TRUE	1	0.28	2		420	591	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706974	117706974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776027945	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	60	491	0	ENST00000368508.3:c.2176G>A	p.Val726Ile	p.V726I	ENST00000368508	NM_002944.2	726	Gtt/Att	15/43	0.3	1	FACETS	0.615	0.53	0.708	0.615	0.53	0.708	SUBCLONAL	1	TRUE	0	0.28	1		491	599	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80040392	80040392	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776668872	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	51	430	0	ENST00000265081.6:c.1721G>A	p.Arg574Gln	p.R574Q	ENST00000265081	NM_002439.4	574	cGg/cAg	12/24	1	2	FACETS	0.783	0.667	0.911	0.783	0.667	0.911	CLONAL	1	TRUE	1	0.28	2		430	465	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430352	47430352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	80	730	0	ENST00000377045.4:c.1627C>T	p.Arg543Trp	p.R543W	ENST00000377045	NM_001654.4	543	Cgg/Tgg	15/16	1	2	FACETS	0.529	0.464	0.599	0.529	0.464	0.599	SUBCLONAL	1	TRUE	1	0.28	2		730	1080	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804304	43804304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763568293	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	46	603	1	ENST00000372470.3:c.304C>T	p.Arg102Cys	p.R102C	ENST00000372470	NM_005373.2	102	Cgt/Tgt	3/12	1	2	FACETS	0.408	0.342	0.481	0.408	0.342	0.481	SUBCLONAL	1	TRUE	1	0.28	2		604	806	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40857132	40857132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316478374	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	58	463	2	ENST00000428826.2:c.1909G>A	p.Glu637Lys	p.E637K	ENST00000428826		637	Gaa/Aaa	17/21	1	2	FACETS	0.632	0.542	0.729	0.632	0.542	0.729	SUBCLONAL	1	TRUE	1	0.28	2		465	656	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343805	118343805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	55	474	0	ENST00000534358.1:c.1931G>A	p.Arg644His	p.R644H	ENST00000534358	NM_005933.3	644	cGc/cAc	3/36	1	2	FACETS	0.595	0.508	0.69	0.595	0.508	0.69	SUBCLONAL	1	TRUE	1	0.28	2		474	660	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50358661	50358661	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	31	286	0	ENST00000331340.3:c.4G>A	p.Asp2Asn	p.D2N	ENST00000331340	NM_006060.4	2	Gat/Aat	2/8	1	2	FACETS	0.769	0.624	0.932	0.769	0.624	0.932	CLONAL	1	TRUE	1	0.28	2		286	288	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509927	187509927	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555931755	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	32	483	0	ENST00000441802.2:c.13586C>T	p.Ala4529Val	p.A4529V	ENST00000441802	NM_005245.3	4529	gCg/gTg	27/27	1	2	FACETS	0.377	0.305	0.459	0.377	0.305	0.459	SUBCLONAL	1	TRUE	1	0.28	2		483	606	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955524	90955524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753270166	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	37	404	0	ENST00000265433.3:c.2141G>A	p.Arg714Gln	p.R714Q	ENST00000265433	NM_002485.4	714	cGa/cAa	14/16	1	2	FACETS	0.694	0.573	0.829	0.694	0.573	0.829	SUBCLONAL	1	TRUE	1	0.28	2		404	381	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350155	81350155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758567520	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	32	295	0	ENST00000222390.5:c.1177C>T	p.Arg393Cys	p.R393C	ENST00000222390	NM_000601.4	393	Cgt/Tgt	10/18	1	2	FACETS	0.757	0.616	0.915	0.757	0.616	0.915	CLONAL	1	TRUE	1	0.28	2		295	302	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780563	56780563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782332	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	34	430	0	ENST00000337432.4:c.578G>A	p.Arg193Gln	p.R193Q	ENST00000337432	NM_058216.2	193	cGa/cAa	4/9	1	2	FACETS	0.549	0.449	0.663	0.549	0.449	0.663	SUBCLONAL	1	TRUE	1	0.28	2		430	442	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851601	134851601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs961044599	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	70	606	0	ENST00000398015.3:c.1007C>T	p.Thr336Met	p.T336M	ENST00000398015	NM_004441.4	336	aCg/aTg	5/16	1	2	FACETS	0.661	0.575	0.753	0.661	0.575	0.753	SUBCLONAL	1	TRUE	1	0.28	2		606	757	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984022	2984022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753614569	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	82	471	0	ENST00000396946.4:c.508C>T	p.Arg170Cys	p.R170C	ENST00000396946	NM_032415.4	170	Cgc/Tgc	5/25	1	2	FACETS	0.684	0.602	0.772	0.684	0.602	0.772	SUBCLONAL	1	TRUE	1	0.28	2		471	856	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275364	115275364	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542388231	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	51	541	2	ENST00000438362.2:c.1049C>T	p.Thr350Met	p.T350M	ENST00000438362	NM_001242891.1	350	aCg/aTg	10/20	1	2	FACETS	0.589	0.5	0.686	0.589	0.5	0.686	SUBCLONAL	1	TRUE	1	0.28	2		543	619	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468065	50468065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749084924	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	57	607	0	ENST00000331340.3:c.1300G>A	p.Ala434Thr	p.A434T	ENST00000331340	NM_006060.4	434	Gcc/Acc	8/8	1	2	FACETS	0.544	0.466	0.63	0.544	0.466	0.63	SUBCLONAL	1	TRUE	1	0.28	2		607	748	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562142	21562142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1421513550	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	105	788	0	ENST00000382592.4:c.1777C>T	p.Arg593Cys	p.R593C	ENST00000382592	NM_014572.2	593	Cgc/Tgc	4/8	1	2	FACETS	0.628	0.561	0.7	0.628	0.561	0.7	SUBCLONAL	1	TRUE	1	0.28	2		788	1194	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390280	56390280	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs768976640	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	22	187	1	ENST00000348428.3:c.1019C>T	p.Ala340Val	p.A340V	ENST00000348428	NM_006785.3	340	gCg/gTg	10/17	1	2	FACETS	0.767	0.597	0.961	0.767	0.597	0.961	CLONAL	1	TRUE	1	0.28	2		188	205	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257113	16257113	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	33	491	0	ENST00000375759.3:c.4378G>T	p.Glu1460Ter	p.E1460*	ENST00000375759	NM_015001.2	1460	Gaa/Taa	11/15	1	2	FACETS	0.42	0.341	0.509	0.42	0.341	0.509	SUBCLONAL	1	TRUE	1	0.28	2		491	561	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373313	118373313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1335499500	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	44	405	0	ENST00000534358.1:c.6706G>A	p.Ala2236Thr	p.A2236T	ENST00000534358	NM_005933.3	2236	Gct/Act	27/36	1	2	FACETS	0.607	0.508	0.716	0.607	0.508	0.716	SUBCLONAL	1	TRUE	1	0.28	2		405	518	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132501	11132501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	107	823	2	ENST00000358026.2:c.2717G>A	p.Arg906His	p.R906H	ENST00000358026	NM_001128849.1	906	cGc/cAc	19/36	1	2	FACETS	0.734	0.657	0.816	0.734	0.657	0.816	SUBCLONAL	1	TRUE	1	0.28	2		825	1041	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524346	148524346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377467108	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	26	299	0	ENST00000320356.2:c.638G>A	p.Arg213His	p.R213H	ENST00000320356	NM_004456.4	213	cGc/cAc	7/20	1	2	FACETS	0.752	0.598	0.927	0.752	0.598	0.927	CLONAL	1	TRUE	1	0.28	2		299	247	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879429	151879429	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140631041	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	100	509	0	ENST00000262189.6:c.5516C>T	p.Thr1839Met	p.T1839M	ENST00000262189	NM_170606.2	1839	aCg/aTg	36/59	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.28	2		509	701	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326255	62326255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559104198	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	95	926	1	ENST00000360203.5:c.3271G>A	p.Asp1091Asn	p.D1091N	ENST00000360203	NM_001283009.1	1091	Gac/Aac	32/35	1	2	FACETS	0.628	0.557	0.703	0.628	0.557	0.703	SUBCLONAL	1	TRUE	1	0.28	2		927	1081	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420285	88420285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199690201	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	76	497	0	ENST00000360948.2:c.2401G>A	p.Asp801Asn	p.D801N	ENST00000360948	NM_001012338.2	801	Gat/Aat	19/19	1	2	FACETS	0.768	0.673	0.87	0.768	0.673	0.87	SUBCLONAL	1	TRUE	1	0.28	2		497	707	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652834	212652834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375361752	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	22	367	0	ENST00000342788.4:c.472G>A	p.Ala158Thr	p.A158T	ENST00000342788	NM_005235.2	158	Gca/Aca	4/28	1	2	FACETS	0.494	0.383	0.623	0.494	0.383	0.623	SUBCLONAL	1	TRUE	1	0.28	2		367	318	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527931	103527931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs4150388	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	39	385	0	ENST00000355739.4:c.3239G>A	p.Gly1080Glu	p.G1080E	ENST00000355739	NM_000123.3	1080	gGa/gAa	15/15	1	2	FACETS	0.69	0.572	0.82	0.69	0.572	0.82	SUBCLONAL	1	TRUE	1	0.28	2		385	404	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221667	36221667	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779863547	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	110	875	0	ENST00000222270.7:c.5336G>A	p.Arg1779Gln	p.R1779Q	ENST00000222270	NM_014727.1	1779	cGa/cAa	26/37	1	2	FACETS	0.683	0.612	0.758	0.683	0.612	0.758	SUBCLONAL	1	TRUE	1	0.28	2		875	1151	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024666	14024666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	33	406	0	ENST00000311895.7:c.892C>T	p.Leu298Phe	p.L298F	ENST00000311895	NM_005236.2	298	Ctc/Ttc	5/11	1	2	FACETS	0.563	0.458	0.68	0.563	0.458	0.68	SUBCLONAL	1	TRUE	1	0.28	2		406	419	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16055259	16055259	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	27	337	1	ENST00000268712.3:c.842+1G>A		p.X281_splice	ENST00000268712	NM_006311.3	281			1	2	FACETS	0.567	0.452	0.699	0.567	0.452	0.699	SUBCLONAL	1	TRUE	1	0.28	2		338	340	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741410	145741410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1220847881	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1221	85	920	2	ENST00000428558.2:c.1093C>T	p.Arg365Trp	p.R365W	ENST00000428558	NM_004260.3	365	Cgg/Tgg	5/22	1	2	FACETS	0.465	0.409	0.525	0.465	0.409	0.525	SUBCLONAL	1	TRUE	1	0.28	2		922	1306	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760790	133760790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367600262	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	85	763	0	ENST00000318560.5:c.3113C>T	p.Ala1038Val	p.A1038V	ENST00000318560	NM_005157.4	1038	gCg/gTg	11/11	1	2	FACETS	0.655	0.578	0.738	0.655	0.578	0.738	SUBCLONAL	1	TRUE	1	0.28	2		763	927	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350054	70350054	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs966195679	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	66	485	0	ENST00000374080.3:c.4037G>A	p.Arg1346His	p.R1346H	ENST00000374080		1346	cGc/cAc	28/45	1	2	FACETS	0.651	0.564	0.745	0.651	0.564	0.745	SUBCLONAL	1	TRUE	1	0.28	2		485	724	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606314	93606314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs16906862	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	92	910	0	ENST00000375746.1:c.134G>A	p.Arg45His	p.R45H	ENST00000375746	NM_001174167.1	45	cGc/cAc	2/14	1	2	FACETS	0.671	0.594	0.752	0.671	0.594	0.752	SUBCLONAL	1	TRUE	1	0.28	2		910	980	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199400	16199400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	41	425	0	ENST00000375759.3:c.173G>A	p.Ser58Asn	p.S58N	ENST00000375759	NM_015001.2	58	aGt/aAt	2/15	1	2	FACETS	0.477	0.396	0.567	0.477	0.396	0.567	SUBCLONAL	1	TRUE	1	0.28	2		425	614	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991293	41991293	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	23	437	0	ENST00000219905.7:c.2124G>T	p.Lys708Asn	p.K708N	ENST00000219905	NM_001164273.1	708	aaG/aaT	5/24	1	2	FACETS	0.357	0.278	0.45	0.357	0.278	0.45	SUBCLONAL	1	TRUE	1	0.28	2		437	460	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072541	5072541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368927897	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	29	359	0	ENST00000381652.3:c.1691G>A	p.Arg564Gln	p.R564Q	ENST00000381652	NM_004972.3	564	cGa/cAa	13/25	1	2	FACETS	0.632	0.507	0.772	0.632	0.507	0.772	SUBCLONAL	1	TRUE	1	0.28	2		359	328	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268984	142268984	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558627427	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	38	341	0	ENST00000350721.4:c.2966G>A	p.Arg989His	p.R989H	ENST00000350721	NM_001184.3	989	cGt/cAt	14/47	1	2	FACETS	0.667	0.552	0.795	0.667	0.552	0.795	SUBCLONAL	1	TRUE	1	0.28	2		341	407	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867355	68867355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622630	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	66	481	1	ENST00000261769.5:c.2602C>T	p.Arg868Cys	p.R868C	ENST00000261769	NM_004360.3	868	Cgc/Tgc	16/16	1	2	FACETS	0.706	0.612	0.807	0.706	0.612	0.807	SUBCLONAL	1	TRUE	1	0.28	2		482	668	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409089	139409089	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs79782048	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	67	843	1	ENST00000277541.6:c.2080G>A	p.Glu694Lys	p.E694K	ENST00000277541	NM_017617.3	694	Gag/Aag	13/34	1	2	FACETS	0.441	0.382	0.506	0.441	0.382	0.506	SUBCLONAL	1	TRUE	1	0.28	2		844	1085	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271204	153271204	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	24	246	0	ENST00000281708.4:c.574G>T	p.Glu192Ter	p.E192*	ENST00000281708	NM_033632.3	192	Gaa/Taa	3/12	1	2	FACETS	0.809	0.637	1	0.809	0.637	1	CLONAL	1	TRUE	1	0.28	2		246	212	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226387	41226387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28897691	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	59	577	2	ENST00000357654.3:c.4636G>A	p.Asp1546Asn	p.D1546N	ENST00000357654	NM_007294.3	1546	Gat/Aat	14/23	1	2	FACETS	0.516	0.443	0.596	0.516	0.443	0.596	SUBCLONAL	1	TRUE	1	0.28	2		579	817	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739731	41739731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	91	616	1	ENST00000242208.4:c.242C>T	p.Ala81Val	p.A81V	ENST00000242208	NM_002192.2	81	gCg/gTg	2/3	1	2	FACETS	0.738	0.654	0.827	0.738	0.654	0.827	SUBCLONAL	1	TRUE	1	0.28	2		617	881	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132676	67132676	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536749790	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	34	431	0	ENST00000412916.2:c.559C>T	p.Arg187Cys	p.R187C	ENST00000412916		187	Cgt/Tgt	6/6	1	2	FACETS	0.571	0.467	0.689	0.571	0.467	0.689	SUBCLONAL	1	TRUE	1	0.28	2		431	425	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129983	55129983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763718380	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	83	559	0	ENST00000257290.5:c.517G>A	p.Asp173Asn	p.D173N	ENST00000257290	NM_006206.4	173	Gac/Aac	4/23	1	2	FACETS	0.799	0.705	0.9	0.799	0.705	0.9	SUBCLONAL	1	TRUE	1	0.28	2		559	742	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946778	71946778	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs781674896	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	102	703	1	ENST00000298229.2:c.2719C>T	p.Arg907Ter	p.R907*	ENST00000298229	NM_001567.3	907	Cga/Tga	24/28	1	2	FACETS	0.902	0.806	1	0.902	0.806	1	CLONAL	1	TRUE	1	0.28	2		704	808	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461564	138461564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202220571	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	46	434	0	ENST00000289153.2:c.457C>T	p.Arg153Cys	p.R153C	ENST00000289153	NM_006219.2	153	Cgc/Tgc	3/22	1	2	FACETS	0.695	0.585	0.815	0.695	0.585	0.815	SUBCLONAL	1	TRUE	1	0.28	2		434	473	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665109	182665109	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	34	290	0	ENST00000292782.4:c.617G>A	p.Arg206Gln	p.R206Q	ENST00000292782	NM_020640.2	206	cGa/cAa	6/7	1	2	FACETS	0.706	0.578	0.849	0.706	0.578	0.849	SUBCLONAL	1	TRUE	1	0.28	2		290	344	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911410	32911410	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507296	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	16	409	0	ENST00000380152.3:c.2918C>T	p.Ser973Leu	p.S973L	ENST00000380152		973	tCg/tTg	11/27	1	2	FACETS	0.378	0.279	0.497	0.378	0.279	0.497	SUBCLONAL	1	TRUE	1	0.28	2		409	302	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947466	38947466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	28	270	1	ENST00000357387.3:c.4214G>A	p.Arg1405Gln	p.R1405Q	ENST00000357387	NM_152756.3	1405	cGa/cAa	32/38	1	2	FACETS	0.571	0.457	0.702	0.571	0.457	0.702	SUBCLONAL	1	TRUE	1	0.28	2		271	350	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054631	5054631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760174050	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	24	294	0	ENST00000381652.3:c.683G>A	p.Arg228Gln	p.R228Q	ENST00000381652	NM_004972.3	228	cGa/cAa	7/25	1	2	FACETS	0.602	0.472	0.75	0.602	0.472	0.75	SUBCLONAL	1	TRUE	1	0.28	2		294	285	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59871074	59871074	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780227	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	20	264	0	ENST00000259008.2:c.1357G>A	p.Ala453Thr	p.A453T	ENST00000259008	NM_032043.2	453	Gct/Act	10/20	1	2	FACETS	0.641	0.491	0.814	0.641	0.491	0.814	SUBCLONAL	1	TRUE	1	0.28	2		264	223	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988382	41988382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774833703	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	71	459	0	ENST00000219905.7:c.1174G>A	p.Glu392Lys	p.E392K	ENST00000219905	NM_001164273.1	392	Gaa/Aaa	3/24	1	2	FACETS	0.896	0.783	1	0.896	0.783	1	CLONAL	1	TRUE	1	0.28	2		459	566	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041927	14041927	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765253522	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	44	386	0	ENST00000311895.7:c.2474C>T	p.Ala825Val	p.A825V	ENST00000311895	NM_005236.2	825	gCg/gTg	11/11	1	2	FACETS	0.594	0.498	0.701	0.594	0.498	0.701	SUBCLONAL	1	TRUE	1	0.28	2		386	529	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651274	45651274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201791685	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	93	629	1	ENST00000407780.3:c.751G>A	p.Glu251Lys	p.E251K	ENST00000407780	NM_001283052.1	251	Gag/Aag	5/7	1	2	FACETS	0.722	0.641	0.809	0.722	0.641	0.809	SUBCLONAL	1	TRUE	1	0.28	2		630	920	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243026	105243026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773971502	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	100	842	2	ENST00000349310.3:c.257G>A	p.Arg86His	p.R86H	ENST00000349310	NM_001014432.1	86	cGc/cAc	5/15	1	2	FACETS	0.698	0.622	0.779	0.698	0.622	0.779	SUBCLONAL	1	TRUE	1	0.28	2		844	1024	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030469	47030469	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556772646	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	60	759	0	ENST00000377604.3:c.244C>T	p.Arg82Trp	p.R82W	ENST00000377604	NM_001204468.1	82	Cgg/Tgg	4/24	1	2	FACETS	0.396	0.34	0.458	0.396	0.34	0.458	SUBCLONAL	1	TRUE	1	0.28	2		759	1082	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916624	178916624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749956691	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	17	383	1	ENST00000263967.3:c.11G>A	p.Arg4Gln	p.R4Q	ENST00000263967	NM_006218.2	4	cGa/cAa	2/21	1	2	FACETS	0.413	0.308	0.538	0.413	0.308	0.538	SUBCLONAL	1	TRUE	1	0.28	2		384	294	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288743	33288743	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs533137350	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	57	569	0	ENST00000374542.5:c.809G>A	p.Arg270His	p.R270H	ENST00000374542	NM_001141970.1	270	cGc/cAc	3/8	1	2	FACETS	0.599	0.513	0.693	0.599	0.513	0.693	SUBCLONAL	1	TRUE	1	0.28	2		569	680	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346631	81346631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	34	364	0	ENST00000222390.5:c.1322G>A	p.Arg441Gln	p.R441Q	ENST00000222390	NM_000601.4	441	cGa/cAa	11/18	1	2	FACETS	0.557	0.455	0.672	0.557	0.455	0.672	SUBCLONAL	1	TRUE	1	0.28	2		364	436	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298063	11298063	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778348776	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	80	649	0	ENST00000361445.4:c.2045G>A	p.Arg682His	p.R682H	ENST00000361445	NM_004958.3	682	cGc/cAc	13/58	1	2	FACETS	0.665	0.584	0.752	0.665	0.584	0.752	SUBCLONAL	1	TRUE	1	0.28	2		649	859	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244952	41244952	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41286300	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	63	590	0	ENST00000357654.3:c.2596C>T	p.Arg866Cys	p.R866C	ENST00000357654	NM_007294.3	866	Cgc/Tgc	10/23	1	2	FACETS	0.733	0.634	0.841	0.733	0.634	0.841	SUBCLONAL	1	TRUE	1	0.28	2		590	614	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220604	1220604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555738372	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	70	775	1	ENST00000326873.7:c.622G>A	p.Asp208Asn	p.D208N	ENST00000326873	NM_000455.4	208	Gac/Aac	5/10	1	2	FACETS	0.482	0.418	0.55	0.482	0.418	0.55	SUBCLONAL	1	TRUE	1	0.28	2		776	1038	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281714	142281714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532495501	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	40	482	2	ENST00000350721.4:c.530G>A	p.Arg177Gln	p.R177Q	ENST00000350721	NM_001184.3	177	cGa/cAa	4/47	1	2	FACETS	0.639	0.531	0.759	0.639	0.531	0.759	SUBCLONAL	1	TRUE	1	0.28	2		484	447	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440121	49440121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	78	730	0	ENST00000301067.7:c.4505C>T	p.Ala1502Val	p.A1502V	ENST00000301067	NM_003482.3	1502	gCc/gTc	16/54	0.0499187687669078	3	FACETS	0.709	0.622	0.803			1	INDETERMINATE	1	TRUE	NA	0.28	3		730	896	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288572	33288572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1246408404	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	50	552	0	ENST00000374542.5:c.980G>A	p.Arg327Gln	p.R327Q	ENST00000374542	NM_001141970.1	327	cGa/cAa	3/8	1	2	FACETS	0.494	0.418	0.578	0.494	0.418	0.578	SUBCLONAL	1	TRUE	1	0.28	2		552	723	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630190	100630190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs128620185	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	42	489	0	ENST00000308731.7:c.83G>A	p.Arg28His	p.R28H	ENST00000308731	NM_000061.2	28	cGc/cAc	2/19	1	2	FACETS	0.466	0.388	0.553	0.466	0.388	0.553	SUBCLONAL	1	TRUE	1	0.28	2		489	644	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31464432	31464432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771607570	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	71	596	3	ENST00000344624.3:c.2485C>T	p.Arg829Trp	p.R829W	ENST00000344624		829	Cgg/Tgg	17/33	1	2	FACETS	0.708	0.618	0.806	0.708	0.618	0.806	SUBCLONAL	1	TRUE	1	0.28	2		599	716	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229294	36229294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	53	809	0	ENST00000222270.7:c.7984C>T	p.Arg2662Trp	p.R2662W	ENST00000222270	NM_014727.1	2662	Cgg/Tgg	37/37	1	2	FACETS	0.377	0.32	0.44	0.377	0.32	0.44	SUBCLONAL	1	TRUE	1	0.28	2		809	1003	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456254	32456254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756414084	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	83	739	2	ENST00000332351.3:c.638G>A	p.Arg213His	p.R213H	ENST00000332351	NM_024426.4	213	cGc/cAc	1/10	1	2	FACETS	0.688	0.606	0.776	0.688	0.606	0.776	SUBCLONAL	1	TRUE	1	0.28	2		741	862	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737485	204737485	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	29	364	0	ENST00000302823.3:c.622G>A	p.Glu208Lys	p.E208K	ENST00000302823	NM_005214.4	208	Gag/Aag	4/4	1	2	FACETS	0.656	0.527	0.801	0.656	0.527	0.801	SUBCLONAL	1	TRUE	1	0.28	2		364	316	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809754	36809754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs188394458	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	53	614	1	ENST00000373129.3:c.851G>A	p.Arg284His	p.R284H	ENST00000373129	NM_032017.1	284	cGc/cAc	9/12	1	2	FACETS	0.496	0.421	0.577	0.496	0.421	0.577	SUBCLONAL	1	TRUE	1	0.28	2		615	764	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008511	71008511	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs541340602	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	44	368	1	ENST00000318789.4:c.1921G>A	p.Asp641Asn	p.D641N	ENST00000318789	NM_032682.5	641	Gat/Aat	21/21	1	2	FACETS	0.637	0.535	0.751	0.637	0.535	0.751	SUBCLONAL	1	TRUE	1	0.28	2		369	493	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778371	3778371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754601626	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	97	774	0	ENST00000262367.5:c.6677C>T	p.Ala2226Val	p.A2226V	ENST00000262367	NM_004380.2	2226	gCg/gTg	31/31	1	2	FACETS	0.851	0.758	0.95	0.851	0.758	0.95	CLONAL	1	TRUE	1	0.28	2		774	814	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136198	64136198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	110	764	0	ENST00000334205.4:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000334205	NM_003942.2	453	Gaa/Aaa	12/17	1	2	FACETS	0.755	0.677	0.838	0.755	0.677	0.838	SUBCLONAL	1	TRUE	1	0.28	2		764	1041	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61722723	61722723	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1198868283	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	41	329	0	ENST00000401558.2:c.914G>A	p.Arg305Gln	p.R305Q	ENST00000401558	NM_003400.3	305	cGa/cAa	11/25	1	2	FACETS	0.696	0.58	0.824	0.696	0.58	0.824	SUBCLONAL	1	TRUE	1	0.28	2		329	421	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515145	31515145	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1202201920	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	43	626	0	ENST00000344624.3:c.1240C>T	p.Arg414Ter	p.R414*	ENST00000344624		414	Cga/Tga	5/33	1	2	FACETS	0.368	0.307	0.437	0.368	0.307	0.437	SUBCLONAL	1	TRUE	1	0.28	2		626	834	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803863	43803863	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs6087	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	82	625	1	ENST00000372470.3:c.173C>T	p.Ala58Val	p.A58V	ENST00000372470	NM_005373.2	58	gCg/gTg	2/12	1	2	FACETS	0.673	0.593	0.76	0.673	0.593	0.76	SUBCLONAL	1	TRUE	1	0.28	2		626	870	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267523	7267523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	82	539	1	ENST00000302850.5:c.485G>A	p.Arg162His	p.R162H	ENST00000302850	NM_000208.2	162	cGt/cAt	2/22	1	2	FACETS	0.718	0.632	0.81	0.718	0.632	0.81	SUBCLONAL	1	TRUE	1	0.28	2		540	816	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090968	77090968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	53	419	1	ENST00000356341.3:c.262G>A	p.Gly88Ser	p.G88S	ENST00000356341	NM_002576.4	88	Ggt/Agt	3/15	1	2	FACETS	0.688	0.587	0.799	0.688	0.587	0.799	SUBCLONAL	1	TRUE	1	0.28	2		420	550	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948206	71948206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753171921	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	112	835	2	ENST00000298229.2:c.2918C>T	p.Ala973Val	p.A973V	ENST00000298229	NM_001567.3	973	gCg/gTg	26/28	1	2	FACETS	0.787	0.707	0.873	0.787	0.707	0.873	SUBCLONAL	1	TRUE	1	0.28	2		837	1016	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944545	40944545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200852571	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	57	482	0	ENST00000373198.4:c.1957C>T	p.Arg653Trp	p.R653W	ENST00000373198	NM_133170.3	653	Cgg/Tgg	12/32	1	2	FACETS	0.656	0.562	0.758	0.656	0.562	0.758	SUBCLONAL	1	TRUE	1	0.28	2		482	621	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272779	142272779	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	38	403	0	ENST00000350721.4:c.2420G>A	p.Gly807Glu	p.G807E	ENST00000350721	NM_001184.3	807	gGa/gAa	11/47	1	2	FACETS	0.68	0.563	0.811	0.68	0.563	0.811	SUBCLONAL	1	TRUE	1	0.28	2		403	399	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457273	25457273	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	63	620	1	ENST00000264709.3:c.2614G>T	p.Val872Phe	p.V872F	ENST00000264709	NM_175629.2	872	Gtc/Ttc	23/23	1	2	FACETS	0.61	0.526	0.7	0.61	0.526	0.7	SUBCLONAL	1	TRUE	1	0.28	2		621	738	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593455	215593455	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881425	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	26	311	0	ENST00000260947.4:c.2279C>T	p.Ser760Leu	p.S760L	ENST00000260947	NM_000465.2	760	tCg/tTg	11/11	1	2	FACETS	0.454	0.359	0.563	0.454	0.359	0.563	SUBCLONAL	1	TRUE	1	0.28	2		311	409	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988119	85988119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	23	360	0	ENST00000263360.6:c.1064G>A	p.Arg355Gln	p.R355Q	ENST00000263360	NM_003797.3	355	cGa/cAa	10/12	1	2	FACETS	0.565	0.441	0.708	0.565	0.441	0.708	SUBCLONAL	1	TRUE	1	0.28	2		360	291	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118361991	118361991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1472952558	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	22	311	1	ENST00000534358.1:c.4777C>T	p.Arg1593Cys	p.R1593C	ENST00000534358	NM_005933.3	1593	Cgc/Tgc	14/36	1	2	FACETS	0.363	0.28	0.459	0.363	0.28	0.459	SUBCLONAL	1	TRUE	1	0.28	2		312	433	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100009	11100009	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769660597	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	87	647	3	ENST00000358026.2:c.1135G>A	p.Ala379Thr	p.A379T	ENST00000358026	NM_001128849.1	379	Gca/Aca	7/36	1	2	FACETS	0.673	0.595	0.758	0.673	0.595	0.758	SUBCLONAL	1	TRUE	1	0.28	2		650	923	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527822	103527822	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs768440346	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	32	360	0	ENST00000355739.4:c.3130G>T	p.Glu1044Ter	p.E1044*	ENST00000355739	NM_000123.3	1044	Gaa/Taa	15/15	1	2	FACETS	0.653	0.531	0.791	0.653	0.531	0.791	SUBCLONAL	1	TRUE	1	0.28	2		360	350	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467988	66467988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	21	288	0	ENST00000273854.3:c.281C>T	p.Ala94Val	p.A94V	ENST00000273854	NM_004439.5	94	gCc/gTc	3/18	1	2	FACETS	0.56	0.431	0.709	0.56	0.431	0.709	SUBCLONAL	1	TRUE	1	0.28	2		288	268	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724599	162724599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	41	541	0	ENST00000367921.3:c.371G>A	p.Arg124Gln	p.R124Q	ENST00000367921	NM_006182.2	124	cGg/cAg	5/18	1	2	FACETS	0.398	0.331	0.474	0.398	0.331	0.474	SUBCLONAL	1	TRUE	1	0.28	2		541	735	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912163	32912163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	60	550	0	ENST00000380152.3:c.3671G>A	p.Gly1224Asp	p.G1224D	ENST00000380152		1224	gGc/gAc	11/27	1	2	FACETS	0.757	0.652	0.871	0.757	0.652	0.871	SUBCLONAL	1	TRUE	1	0.28	2		550	566	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678002	117678002	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1008170196	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	42	392	1	ENST00000368508.3:c.3931C>T	p.Arg1311Ter	p.R1311*	ENST00000368508	NM_002944.2	1311	Cga/Tga	25/43	0.3	1	FACETS	0.672	0.562	0.793	0.672	0.562	0.793	SUBCLONAL	1	TRUE	0	0.28	1		393	384	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483129	29483129	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	30	354	0	ENST00000356175.3:c.189G>T	p.Lys63Asn	p.K63N	ENST00000356175	NM_000267.3	63	aaG/aaT	2/57	1	2	FACETS	0.676	0.546	0.823	0.676	0.546	0.823	SUBCLONAL	1	TRUE	1	0.28	2		354	317	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224548	224548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751645963	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	52	436	0	ENST00000264932.6:c.224G>A	p.Arg75Gln	p.R75Q	ENST00000264932	NM_004168.2	75	cGa/cAa	3/15	1	2	FACETS	0.548	0.465	0.638	0.548	0.465	0.638	SUBCLONAL	1	TRUE	1	0.28	2		436	678	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229343	36229343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	79	644	0	ENST00000222270.7:c.8033G>A	p.Arg2678His	p.R2678H	ENST00000222270	NM_014727.1	2678	cGc/cAc	37/37	1	2	FACETS	0.672	0.59	0.76	0.672	0.59	0.76	SUBCLONAL	1	TRUE	1	0.28	2		644	840	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684049	29684049	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	39	502	0	ENST00000356175.3:c.7747C>A	p.Leu2583Ile	p.L2583I	ENST00000356175	NM_000267.3	2583	Ctc/Atc	52/57	1	2	FACETS	0.57	0.472	0.679	0.57	0.472	0.679	SUBCLONAL	1	TRUE	1	0.28	2		502	489	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060638	38060638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764112817	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	113	838	1	ENST00000250448.2:c.1351G>A	p.Glu451Lys	p.E451K	ENST00000250448	NM_004496.3	451	Gag/Aag	2/2	1	2	FACETS	0.697	0.625	0.773	0.697	0.625	0.773	SUBCLONAL	1	TRUE	1	0.28	2		839	1158	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566300	141566300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	87	482	0	ENST00000220592.5:c.1112C>T	p.Ser371Leu	p.S371L	ENST00000220592	NM_012154.3	371	tCg/tTg	9/19	1	2	FACETS	0.751	0.664	0.844	0.751	0.664	0.844	SUBCLONAL	1	TRUE	1	0.28	2		482	828	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741343	17741343	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	66	741	0	ENST00000250003.3:c.14C>T	p.Ser5Leu	p.S5L	ENST00000250003	NM_002478.4	5	tCg/tTg	1/3	1	2	FACETS	0.572	0.495	0.656	0.572	0.495	0.656	SUBCLONAL	1	TRUE	1	0.28	2		741	824	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989689	68989689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1428676809	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	59	478	0	ENST00000288368.4:c.1627G>A	p.Gly543Arg	p.G543R	ENST00000288368	NM_024870.2	543	Gga/Aga	15/40	1	2	FACETS	0.663	0.57	0.764	0.663	0.57	0.764	SUBCLONAL	1	TRUE	1	0.28	2		478	636	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041882	14041882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	57	413	0	ENST00000311895.7:c.2429C>T	p.Ala810Val	p.A810V	ENST00000311895	NM_005236.2	810	gCg/gTg	11/11	1	2	FACETS	0.732	0.628	0.846	0.732	0.628	0.846	SUBCLONAL	1	TRUE	1	0.28	2		413	556	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911502	131911502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	39	396	0	ENST00000265335.6:c.247C>T	p.Arg83Cys	p.R83C	ENST00000265335		83	Cgt/Tgt	3/25	1	2	FACETS	0.819	0.681	0.973	0.819	0.681	0.973	CLONAL	1	TRUE	1	0.28	2		396	340	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56415021	56415021	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	51	444	0	ENST00000348428.3:c.2422A>C	p.Thr808Pro	p.T808P	ENST00000348428	NM_006785.3	808	Act/Cct	17/17	1	2	FACETS	0.734	0.625	0.855	0.734	0.625	0.855	SUBCLONAL	1	TRUE	1	0.28	2		444	496	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733527	85733527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200837308	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	73	474	0	ENST00000370580.1:c.485C>T	p.Thr162Met	p.T162M	ENST00000370580	NM_003921.4	162	aCg/aTg	3/3	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.28	2		474	507	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73340168	73340168	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs770832001	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	19	278	0	ENST00000377767.4:c.1912C>T	p.Arg638Ter	p.R638*	ENST00000377767	NM_014953.3	638	Cga/Tga	15/21	1	2	FACETS	0.47	0.356	0.603	0.47	0.356	0.603	SUBCLONAL	1	TRUE	1	0.28	2		278	289	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438192	49438192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	62	520	0	ENST00000301067.7:c.5077C>T	p.Arg1693Trp	p.R1693W	ENST00000301067	NM_003482.3	1693	Cgg/Tgg	20/54	0.0499187687669078	3	FACETS	0.72	0.621	0.828			1	INDETERMINATE	1	TRUE	NA	0.28	3		520	701	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467810	66467810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370146960	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	19	331	0	ENST00000273854.3:c.459G>A	p.Met153Ile	p.M153I	ENST00000273854	NM_004439.5	153	atG/atA	3/18	1	2	FACETS	0.404	0.306	0.519	0.404	0.306	0.519	SUBCLONAL	1	TRUE	1	0.28	2		331	336	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245390	41245390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80356875	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	52	578	0	ENST00000357654.3:c.2158G>A	p.Glu720Lys	p.E720K	ENST00000357654	NM_007294.3	720	Gaa/Aaa	10/23	1	2	FACETS	0.684	0.582	0.796	0.684	0.582	0.796	SUBCLONAL	1	TRUE	1	0.28	2		578	543	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40460232	40460232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746268770	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	86	614	0	ENST00000345506.4:c.1943C>T	p.Thr648Met	p.T648M	ENST00000345506	NM_003152.3	648	aCg/aTg	17/20	1	2	FACETS	0.73	0.644	0.821	0.73	0.644	0.821	SUBCLONAL	1	TRUE	1	0.28	2		614	842	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409427	31409427	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1195955783	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	50	371	0	ENST00000344624.3:c.3680C>T	p.Ala1227Val	p.A1227V	ENST00000344624		1227	gCg/gTg	29/33	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.28	2		371	329	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604293	189604293	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781366519	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	40	466	0	ENST00000264731.3:c.1460G>A	p.Arg487His	p.R487H	ENST00000264731	NM_003722.4	487	cGc/cAc	11/14	1	2	FACETS	0.387	0.321	0.462	0.387	0.321	0.462	SUBCLONAL	1	TRUE	1	0.28	2		466	738	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349009	70349009	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1405190651	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	81	624	1	ENST00000374080.3:c.3521G>A	p.Arg1174His	p.R1174H	ENST00000374080		1174	cGc/cAc	25/45	1	2	FACETS	0.603	0.53	0.682	0.603	0.53	0.682	SUBCLONAL	1	TRUE	1	0.28	2		625	959	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241973	39241973	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	36	271	1	ENST00000402219.2:c.1873C>T	p.Arg625Trp	p.R625W	ENST00000402219	NM_005633.3	625	Cgg/Tgg	11/23	1	2	FACETS	0.938	0.775	1	0.938	0.775	1	CLONAL	1	TRUE	1	0.28	2		272	274	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924292	112924292	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	80	643	0	ENST00000351677.2:c.1238G>T	p.Arg413Ile	p.R413I	ENST00000351677	NM_002834.3	413	aGa/aTa	11/16	1	2	FACETS	0.677	0.595	0.766	0.677	0.595	0.766	SUBCLONAL	1	TRUE	1	0.28	2		643	844	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656980	45656980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1399685576	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	90	646	1	ENST00000407780.3:c.176C>T	p.Ser59Leu	p.S59L	ENST00000407780	NM_001283052.1	59	tCg/tTg	3/7	1	2	FACETS	0.693	0.613	0.778	0.693	0.613	0.778	SUBCLONAL	1	TRUE	1	0.28	2		647	928	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482826	140482826	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1249895723	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	66	538	0	ENST00000288602.6:c.1309C>T	p.Arg437Ter	p.R437*	ENST00000288602	NM_004333.4	437	Cga/Tga	10/18	1	2	FACETS	0.76	0.66	0.869	0.76	0.66	0.869	SUBCLONAL	1	TRUE	1	0.28	2		538	620	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552729	226552729	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746139482	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	53	465	0	ENST00000366794.5:c.2632C>T	p.Arg878Trp	p.R878W	ENST00000366794	NM_001618.3	878	Cgg/Tgg	19/23	1	2	FACETS	0.55	0.468	0.64	0.55	0.468	0.64	SUBCLONAL	1	TRUE	1	0.28	2		465	688	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80071522	80071522	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	28	289	0	ENST00000265081.6:c.2263G>T	p.Glu755Ter	p.E755*	ENST00000265081	NM_002439.4	755	Gaa/Taa	16/24	1	2	FACETS	0.671	0.537	0.823	0.671	0.537	0.823	SUBCLONAL	1	TRUE	1	0.28	2		289	298	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262663	16262663	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747459170	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	61	539	1	ENST00000375759.3:c.9928G>A	p.Asp3310Asn	p.D3310N	ENST00000375759	NM_015001.2	3310	Gac/Aac	11/15	1	2	FACETS	0.555	0.478	0.639	0.555	0.478	0.639	SUBCLONAL	1	TRUE	1	0.28	2		540	785	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47061267	47061267	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	50	387	0	ENST00000409792.3:c.7414G>T	p.Glu2472Ter	p.E2472*	ENST00000409792	NM_014159.6	2472	Gaa/Taa	19/21	1	2	FACETS	0.602	0.51	0.703	0.602	0.51	0.703	SUBCLONAL	1	TRUE	1	0.28	2		387	593	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442757	187442757	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	76	569	3	ENST00000232014.4:c.1949G>A	p.Arg650Gln	p.R650Q	ENST00000232014	NM_001130845.1	650	cGa/cAa	9/10	1	2	FACETS	0.743	0.651	0.842	0.743	0.651	0.842	SUBCLONAL	1	TRUE	1	0.28	2		572	731	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554341	63554341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767445163	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	45	643	0	ENST00000307078.5:c.398C>T	p.Ala133Val	p.A133V	ENST00000307078	NM_004655.3	133	gCg/gTg	2/11	1	2	FACETS	0.389	0.326	0.46	0.389	0.326	0.46	SUBCLONAL	1	TRUE	1	0.28	2		643	826	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300192	15300192	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771875329	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	59	665	1	ENST00000263388.2:c.1084G>A	p.Glu362Lys	p.E362K	ENST00000263388	NM_000435.2	362	Gag/Aag	7/33	1	2	FACETS	0.404	0.346	0.467	0.404	0.346	0.467	SUBCLONAL	1	TRUE	1	0.28	2		666	1044	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40476762	40476762	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759053963	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	61	631	1	ENST00000264657.5:c.1567G>A	p.Glu523Lys	p.E523K	ENST00000264657	NM_139276.2	523	Gag/Aag	17/24	1	2	FACETS	0.536	0.461	0.618	0.536	0.461	0.618	SUBCLONAL	1	TRUE	1	0.28	2		632	813	SUCCESS
REL	5966	MSKCC	GRCh37	2	61144108	61144108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781499490	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	31	518	2	ENST00000295025.8:c.491C>T	p.Thr164Met	p.T164M	ENST00000295025	NM_002908.2	164	aCg/aTg	5/11	1	2	FACETS	0.561	0.453	0.682	0.561	0.453	0.682	SUBCLONAL	1	TRUE	1	0.28	2		520	395	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189004	11189004	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	50	385	0	ENST00000361445.4:c.5719C>T	p.Leu1907Phe	p.L1907F	ENST00000361445	NM_004958.3	1907	Ctc/Ttc	41/58	1	2	FACETS	0.833	0.708	0.969	0.833	0.708	0.969	CLONAL	1	TRUE	1	0.28	2		385	429	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257403	16257403	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	33	489	0	ENST00000375759.3:c.4668T>G	p.Ile1556Met	p.I1556M	ENST00000375759	NM_015001.2	1556	atT/atG	11/15	1	2	FACETS	0.439	0.357	0.532	0.439	0.357	0.532	SUBCLONAL	1	TRUE	1	0.28	2		489	537	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094462	27094462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	65	492	0	ENST00000324856.7:c.3170C>T	p.Ser1057Phe	p.S1057F	ENST00000324856	NM_006015.4	1057	tCt/tTt	11/20	1	2	FACETS	0.646	0.559	0.74	0.646	0.559	0.74	SUBCLONAL	1	TRUE	1	0.28	2		492	719	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105874	27105874	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	68	528	1	ENST00000324856.7:c.5485G>T	p.Asp1829Tyr	p.D1829Y	ENST00000324856	NM_006015.4	1829	Gat/Tat	20/20	1	2	FACETS	0.678	0.589	0.775	0.678	0.589	0.775	SUBCLONAL	1	TRUE	1	0.28	2		529	716	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107084	27107084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142878055	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	59	589	0	ENST00000324856.7:c.6695G>A	p.Arg2232Gln	p.R2232Q	ENST00000324856	NM_006015.4	2232	cGg/cAg	20/20	1	2	FACETS	0.583	0.501	0.673	0.583	0.501	0.673	SUBCLONAL	1	TRUE	1	0.28	2		589	723	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935262	36935262	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	48	731	0	ENST00000361632.4:c.1465C>A	p.Leu489Met	p.L489M	ENST00000361632		489	Ctg/Atg	10/16	1	2	FACETS	0.406	0.342	0.477	0.406	0.342	0.477	SUBCLONAL	1	TRUE	1	0.28	2		731	844	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39321507	39321507	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	46	457	0	ENST00000373001.3:c.514A>C	p.Asn172His	p.N172H	ENST00000373001	NM_022157.3	172	Aat/Cat	3/7	1	2	FACETS	0.704	0.593	0.826	0.704	0.593	0.826	SUBCLONAL	1	TRUE	1	0.28	2		457	467	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65323396	65323396	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	80	624	1	ENST00000342505.4:c.1401G>A	p.Trp467Ter	p.W467*	ENST00000342505	NM_002227.2	467	tgG/tgA	10/25	1	2	FACETS	0.708	0.622	0.8	0.708	0.622	0.8	SUBCLONAL	1	TRUE	1	0.28	2		625	807	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748169	72748169	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	29	390	0	ENST00000357731.5:c.9G>T	p.Met3Ile	p.M3I	ENST00000357731	NM_173808.2	3	atG/atT	1/7	1	2	FACETS	0.376	0.301	0.462	0.376	0.301	0.462	SUBCLONAL	1	TRUE	1	0.28	2		390	551	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733449	85733449	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	39	451	0	ENST00000370580.1:c.563C>A	p.Ser188Tyr	p.S188Y	ENST00000370580	NM_003921.4	188	tCt/tAt	3/3	1	2	FACETS	0.539	0.446	0.642	0.539	0.446	0.642	SUBCLONAL	1	TRUE	1	0.28	2		451	517	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256557	115256557	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	48	446	0	ENST00000369535.4:c.154T>G	p.Leu52Val	p.L52V	ENST00000369535	NM_002524.4	52	Ttg/Gtg	3/7	1	2	FACETS	0.729	0.617	0.853	0.729	0.617	0.853	SUBCLONAL	1	TRUE	1	0.28	2		446	470	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166560	118166560	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	43	409	0	ENST00000369448.3:c.1070A>G	p.Tyr357Cys	p.Y357C	ENST00000369448	NM_017709.3	357	tAc/tGc	2/2	1	2	FACETS	0.453	0.378	0.536	0.453	0.378	0.536	SUBCLONAL	1	TRUE	1	0.28	2		409	678	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459182	120459182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	58	593	0	ENST00000256646.2:c.6163C>T	p.His2055Tyr	p.H2055Y	ENST00000256646	NM_024408.3	2055	Cac/Tac	34/34	1	2	FACETS	0.544	0.466	0.629	0.544	0.466	0.629	SUBCLONAL	1	TRUE	1	0.28	2		593	762	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459289	120459289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201446896	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	33	470	0	ENST00000256646.2:c.6056G>A	p.Arg2019Gln	p.R2019Q	ENST00000256646	NM_024408.3	2019	cGg/cAg	34/34	1	2	FACETS	0.504	0.41	0.61	0.504	0.41	0.61	SUBCLONAL	1	TRUE	1	0.28	2		470	468	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874173	155874173	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	49	531	0	ENST00000368323.3:c.358C>T	p.Arg120Ter	p.R120*	ENST00000368323	NM_006912.5	120	Cga/Tga	5/6	1	2	FACETS	0.476	0.402	0.557	0.476	0.402	0.557	SUBCLONAL	1	TRUE	1	0.28	2		531	736	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163315568	163315568	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	26	360	0	ENST00000271452.3:c.908T>G	p.Leu303Arg	p.L303R	ENST00000271452	NM_145697.2	303	cTt/cGt	11/14	1	2	FACETS	0.586	0.464	0.725	0.586	0.464	0.725	SUBCLONAL	1	TRUE	1	0.28	2		360	317	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094334	193094334	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	39	295	0	ENST00000367435.3:c.224T>C	p.Val75Ala	p.V75A	ENST00000367435	NM_024529.4	75	gTc/gCc	2/17	1	2	FACETS	0.78	0.648	0.927	0.78	0.648	0.927	CLONAL	1	TRUE	1	0.28	2		295	357	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119495	193119495	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	39	279	0	ENST00000367435.3:c.890G>T	p.Arg297Ile	p.R297I	ENST00000367435	NM_024529.4	297	aGa/aTa	9/17	1	2	FACETS	0.857	0.713	1	0.857	0.713	1	CLONAL	1	TRUE	1	0.28	2		279	325	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852307	63852307	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	70	666	1	ENST00000279873.7:c.3085C>T	p.Arg1029Trp	p.R1029W	ENST00000279873	NM_032199.2	1029	Cgg/Tgg	10/10	1	2	FACETS	0.589	0.512	0.672	0.589	0.512	0.672	SUBCLONAL	1	TRUE	1	0.28	2		667	849	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70360781	70360781	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	21	239	0	ENST00000373644.4:c.1958A>G	p.Lys653Arg	p.K653R	ENST00000373644	NM_030625.2	653	aAa/aGa	3/12	1	2	FACETS	0.581	0.448	0.736	0.581	0.448	0.736	SUBCLONAL	1	TRUE	1	0.28	2		239	258	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711944	89711944	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	36	458	0	ENST00000371953.3:c.562T>G	p.Tyr188Asp	p.Y188D	ENST00000371953	NM_000314.4	188	Tat/Gat	6/9	1	2	FACETS	0.682	0.561	0.817	0.682	0.561	0.817	SUBCLONAL	1	TRUE	1	0.28	2		458	377	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14300926	14300926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781970568	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	23	215	2	ENST00000256196.4:c.572G>A	p.Arg191Gln	p.R191Q	ENST00000256196		191	cGg/cAg	6/6	1	2	FACETS	0.613	0.479	0.768	0.613	0.479	0.768	SUBCLONAL	1	TRUE	1	0.28	2		217	268	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741450	17741450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771216938	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	92	683	1	ENST00000250003.3:c.121C>T	p.Arg41Cys	p.R41C	ENST00000250003	NM_002478.4	41	Cgc/Tgc	1/3	1	2	FACETS	0.69	0.611	0.773	0.69	0.611	0.773	SUBCLONAL	1	TRUE	1	0.28	2		684	953	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518087	69518087	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	54	757	0	ENST00000294312.3:c.278A>C	p.Lys93Thr	p.K93T	ENST00000294312	NM_005117.2	93	aAg/aCg	2/3	1	2	FACETS	0.385	0.327	0.448	0.385	0.327	0.448	SUBCLONAL	1	TRUE	1	0.28	2		757	1002	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942063	71942063	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	92	741	0	ENST00000298229.2:c.1327A>G	p.Thr443Ala	p.T443A	ENST00000298229	NM_001567.3	443	Aca/Gca	12/28	1	2	FACETS	0.738	0.655	0.828	0.738	0.655	0.828	SUBCLONAL	1	TRUE	1	0.28	2		741	890	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948218	71948218	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1308271103	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	130	867	0	ENST00000298229.2:c.2930C>A	p.Pro977His	p.P977H	ENST00000298229	NM_001567.3	977	cCc/cAc	26/28	1	2	FACETS	0.884	0.8	0.972	0.884	0.8	0.972	CLONAL	1	TRUE	1	0.28	2		867	1051	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948500	71948500	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs141033838	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	69	909	1	ENST00000298229.2:c.3212C>A	p.Pro1071His	p.P1071H	ENST00000298229	NM_001567.3	1071	cCt/cAt	26/28	1	2	FACETS	0.438	0.38	0.501	0.438	0.38	0.501	SUBCLONAL	1	TRUE	1	0.28	2		910	1125	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192626	94192626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781378	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	57	548	0	ENST00000323929.3:c.1448G>A	p.Arg483Gln	p.R483Q	ENST00000323929	NM_005591.3	483	cGa/cAa	13/20	1	2	FACETS	0.708	0.607	0.818	0.708	0.607	0.818	SUBCLONAL	1	TRUE	1	0.28	2		548	575	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207715	102207715	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	21	347	0	ENST00000263464.3:c.1697C>T	p.Ser566Phe	p.S566F	ENST00000263464	NM_001165.4	566	tCc/tTc	9/9	1	2	FACETS	0.463	0.356	0.587	0.463	0.356	0.587	SUBCLONAL	1	TRUE	1	0.28	2		347	324	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362633	118362633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	30	426	1	ENST00000534358.1:c.4994G>A	p.Arg1665His	p.R1665H	ENST00000534358	NM_005933.3	1665	cGc/cAc	15/36	1	2	FACETS	0.409	0.329	0.5	0.409	0.329	0.5	SUBCLONAL	1	TRUE	1	0.28	2		427	524	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373862	118373862	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782181274	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	21	327	0	ENST00000534358.1:c.7255G>A	p.Glu2419Lys	p.E2419K	ENST00000534358	NM_005933.3	2419	Gaa/Aaa	27/36	1	2	FACETS	0.487	0.375	0.618	0.487	0.375	0.618	SUBCLONAL	1	TRUE	1	0.28	2		327	308	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374586	118374586	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	30	413	0	ENST00000534358.1:c.7979G>T	p.Gly2660Val	p.G2660V	ENST00000534358	NM_005933.3	2660	gGc/gTc	27/36	1	2	FACETS	0.443	0.356	0.541	0.443	0.356	0.541	SUBCLONAL	1	TRUE	1	0.28	2		413	484	SUCCESS
CBL	867	MSKCC	GRCh37	11	119158628	119158628	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	43	512	0	ENST00000264033.4:c.2008G>T	p.Ala670Ser	p.A670S	ENST00000264033	NM_005188.3	670	Gcc/Tcc	12/16	1	2	FACETS	0.569	0.475	0.672	0.569	0.475	0.672	SUBCLONAL	1	TRUE	1	0.28	2		512	540	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719968	18719968	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	18	375	0	ENST00000266497.5:c.3865A>C	p.Asn1289His	p.N1289H	ENST00000266497		1289	Aat/Cat	27/31	0.220287756186264	1	FACETS	0.312	0.235	0.405	0.312	0.235	0.405	SUBCLONAL	1	TRUE	0	0.28	1		375	354	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21627778	21627778	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	42	496	0	ENST00000421138.2:c.1352G>A	p.Ser451Asn	p.S451N	ENST00000421138		451	aGc/aAc	12/16	0.220287756186264	1	FACETS	0.662	0.553	0.781	0.662	0.553	0.781	SUBCLONAL	1	TRUE	0	0.28	1		496	390	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243541	46243541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	33	311	0	ENST00000334344.6:c.1894C>T	p.Pro632Ser	p.P632S	ENST00000334344	NM_152641.2	632	Cct/Tct	14/21	0.220287756186264	1	FACETS	0.745	0.61	0.897	0.745	0.61	0.897	SUBCLONAL	1	TRUE	0	0.28	1		311	272	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435191	49435191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765985953	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	41	611	1	ENST00000301067.7:c.6362C>T	p.Ala2121Val	p.A2121V	ENST00000301067	NM_003482.3	2121	gCc/gTc	31/54	0.0499187687669078	3	FACETS	0.48	0.399	0.571			1	INDETERMINATE	1	TRUE	NA	0.28	3		612	695	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416841	121416841	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	95	822	0	ENST00000257555.6:c.270G>T	p.Glu90Asp	p.E90D	ENST00000257555		90	gaG/gaT	1/10	1	2	FACETS	0.698	0.62	0.781	0.698	0.62	0.781	SUBCLONAL	1	TRUE	1	0.28	2		822	972	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562126	21562126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	59	801	0	ENST00000382592.4:c.1793C>T	p.Ser598Leu	p.S598L	ENST00000382592	NM_014572.2	598	tCg/tTg	4/8	1	2	FACETS	0.373	0.32	0.432	0.373	0.32	0.432	SUBCLONAL	1	TRUE	1	0.28	2		801	1129	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620119	21620119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285144450	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	86	577	0	ENST00000382592.4:c.47G>A	p.Arg16Gln	p.R16Q	ENST00000382592	NM_014572.2	16	cGg/cAg	2/8	1	2	FACETS	0.854	0.756	0.96	0.854	0.756	0.96	CLONAL	1	TRUE	1	0.28	2		577	719	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907387	32907387	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	25	364	0	ENST00000380152.3:c.1772T>G	p.Ile591Ser	p.I591S	ENST00000380152		591	aTt/aGt	10/27	1	2	FACETS	0.585	0.462	0.727	0.585	0.462	0.727	SUBCLONAL	1	TRUE	1	0.28	2		364	305	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913326	32913326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479815532	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	24	470	0	ENST00000380152.3:c.4834C>T	p.Pro1612Ser	p.P1612S	ENST00000380152		1612	Cca/Tca	11/27	1	2	FACETS	0.443	0.347	0.554	0.443	0.347	0.554	SUBCLONAL	1	TRUE	1	0.28	2		470	387	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281425	49281425	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	64	630	0	ENST00000282018.3:c.472C>A	p.Leu158Ile	p.L158I	ENST00000282018	NM_020377.2	158	Ctc/Atc	1/1	1	2	FACETS	0.644	0.557	0.739	0.644	0.557	0.739	SUBCLONAL	1	TRUE	1	0.28	2		630	710	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061507	38061507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	38	547	1	ENST00000250448.2:c.482C>T	p.Thr161Met	p.T161M	ENST00000250448	NM_004496.3	161	aCg/aTg	2/2	1	2	FACETS	0.375	0.309	0.449	0.375	0.309	0.449	SUBCLONAL	1	TRUE	1	0.28	2		548	724	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562869	95562869	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	24	330	0	ENST00000393063.1:c.4388T>G	p.Phe1463Cys	p.F1463C	ENST00000393063	NM_030621.3	1463	tTt/tGt	24/28	1	2	FACETS	0.493	0.386	0.616	0.493	0.386	0.616	SUBCLONAL	1	TRUE	1	0.28	2		330	348	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40678668	40678668	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	53	424	0	ENST00000249776.8:c.410A>C	p.Lys137Thr	p.K137T	ENST00000249776	NM_033286.3	137	aAa/aCa	3/9	1	2	FACETS	0.68	0.579	0.79	0.68	0.579	0.79	SUBCLONAL	1	TRUE	1	0.28	2		424	557	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046685	42046685	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	41	416	0	ENST00000219905.7:c.7059G>T	p.Glu2353Asp	p.E2353D	ENST00000219905	NM_001164273.1	2353	gaG/gaT	18/24	1	2	FACETS	0.51	0.424	0.606	0.51	0.424	0.606	SUBCLONAL	1	TRUE	1	0.28	2		416	574	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058521	42058521	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	38	393	0	ENST00000219905.7:c.8241T>G	p.Ile2747Met	p.I2747M	ENST00000219905	NM_001164273.1	2747	atT/atG	24/24	1	2	FACETS	0.711	0.588	0.847	0.711	0.588	0.847	SUBCLONAL	1	TRUE	1	0.28	2		393	382	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714197	43714197	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376460570	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	58	745	0	ENST00000382044.4:c.3956G>A	p.Arg1319His	p.R1319H	ENST00000382044	NM_001141980.1	1319	cGc/cAc	19/28	1	2	FACETS	0.412	0.353	0.478	0.412	0.353	0.478	SUBCLONAL	1	TRUE	1	0.28	2		745	1005	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66735658	66735658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	27	404	0	ENST00000307102.5:c.479G>A	p.Arg160Lys	p.R160K	ENST00000307102	NM_002755.3	160	aGa/aAa	4/11	1	2	FACETS	0.416	0.33	0.514	0.416	0.33	0.514	SUBCLONAL	1	TRUE	1	0.28	2		404	464	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483946	88483946	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764653626	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	70	585	1	ENST00000360948.2:c.1624C>T	p.Arg542Ter	p.R542*	ENST00000360948	NM_001012338.2	542	Cga/Tga	14/19	1	2	FACETS	0.682	0.594	0.778	0.682	0.594	0.778	SUBCLONAL	1	TRUE	1	0.28	2		586	733	SUCCESS
BLM	641	MSKCC	GRCh37	15	91306235	91306235	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	27	350	0	ENST00000355112.3:c.1922A>G	p.His641Arg	p.H641R	ENST00000355112	NM_000057.2	641	cAt/cGt	8/22	1	2	FACETS	0.482	0.383	0.595	0.482	0.383	0.595	SUBCLONAL	1	TRUE	1	0.28	2		350	400	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500490	99500490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753745798	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	92	784	0	ENST00000268035.6:c.3923C>T	p.Ser1308Leu	p.S1308L	ENST00000268035	NM_000875.3	1308	tCg/tTg	21/21	1	2	FACETS	0.664	0.589	0.745	0.664	0.589	0.745	SUBCLONAL	1	TRUE	1	0.28	2		784	989	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860755	3860755	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	53	409	0	ENST00000262367.5:c.824C>A	p.Pro275Gln	p.P275Q	ENST00000262367	NM_004380.2	275	cCa/cAa	3/31	1	2	FACETS	0.716	0.61	0.831	0.716	0.61	0.831	SUBCLONAL	1	TRUE	1	0.28	2		409	529	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632692	23632692	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555459362	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	29	359	0	ENST00000261584.4:c.3104T>C	p.Ile1035Thr	p.I1035T	ENST00000261584	NM_024675.3	1035	aTt/aCt	10/13	1	2	FACETS	0.535	0.429	0.656	0.535	0.429	0.656	SUBCLONAL	1	TRUE	1	0.28	2		359	387	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830716	72830716	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	67	587	0	ENST00000268489.5:c.5865G>T	p.Glu1955Asp	p.E1955D	ENST00000268489	NM_006885.3	1955	gaG/gaT	9/10	1	2	FACETS	0.59	0.512	0.675	0.59	0.512	0.675	SUBCLONAL	1	TRUE	1	0.28	2		587	811	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993866	72993866	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761842147	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	68	609	0	ENST00000268489.5:c.179G>A	p.Arg60His	p.R60H	ENST00000268489	NM_006885.3	60	cGc/cAc	2/10	1	2	FACETS	0.642	0.558	0.734	0.642	0.558	0.734	SUBCLONAL	1	TRUE	1	0.28	2		609	756	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346097	89346097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1212718041	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	21	290	0	ENST00000301030.4:c.6853G>A	p.Ala2285Thr	p.A2285T	ENST00000301030	NM_001256183.1	2285	Gca/Aca	9/13	1	2	FACETS	0.549	0.424	0.696	0.549	0.424	0.696	SUBCLONAL	1	TRUE	1	0.28	2		290	273	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346706	89346706	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1239700248	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	85	640	0	ENST00000301030.4:c.6244G>A	p.Glu2082Lys	p.E2082K	ENST00000301030	NM_001256183.1	2082	Gag/Aag	9/13	1	2	FACETS	0.77	0.679	0.866	0.77	0.679	0.866	SUBCLONAL	1	TRUE	1	0.28	2		640	789	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348652	89348652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1487348306	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	60	610	0	ENST00000301030.4:c.4298C>T	p.Ser1433Phe	p.S1433F	ENST00000301030	NM_001256183.1	1433	tCc/tTc	9/13	1	2	FACETS	0.523	0.449	0.603	0.523	0.449	0.603	SUBCLONAL	1	TRUE	1	0.28	2		610	820	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348938	89348938	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753576509	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	106	746	2	ENST00000301030.4:c.4012G>A	p.Ala1338Thr	p.A1338T	ENST00000301030	NM_001256183.1	1338	Gcc/Acc	9/13	1	2	FACETS	0.83	0.743	0.923	0.83	0.743	0.923	CLONAL	1	TRUE	1	0.28	2		748	912	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351129	89351129	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	94	639	0	ENST00000301030.4:c.1821G>T	p.Lys607Asn	p.K607N	ENST00000301030	NM_001256183.1	607	aaG/aaT	9/13	1	2	FACETS	0.753	0.669	0.843	0.753	0.669	0.843	SUBCLONAL	1	TRUE	1	0.28	2		639	892	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510665	38510665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763372641	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	104	687	3	ENST00000254066.5:c.919G>A	p.Asp307Asn	p.D307N	ENST00000254066	NM_000964.3	307	Gac/Aac	7/9	1	2	FACETS	0.801	0.716	0.892	0.801	0.716	0.892	CLONAL	1	TRUE	1	0.28	2		690	927	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474488	40474488	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	31	415	0	ENST00000264657.5:c.1913A>G	p.Glu638Gly	p.E638G	ENST00000264657	NM_139276.2	638	gAa/gGa	21/24	1	2	FACETS	0.372	0.299	0.454	0.372	0.299	0.454	SUBCLONAL	1	TRUE	1	0.28	2		415	596	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804288	46804288	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	80	707	0	ENST00000290295.7:c.719T>G	p.Phe240Cys	p.F240C	ENST00000290295	NM_006361.5	240	tTc/tGc	2/2	1	2	FACETS	0.653	0.574	0.739	0.653	0.574	0.739	SUBCLONAL	1	TRUE	1	0.28	2		707	875	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736933	736933	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	38	401	0	ENST00000314574.4:c.1166G>T	p.Arg389Ile	p.R389I	ENST00000314574	NM_005433.3	389	aGa/aTa	10/12	1	2	FACETS	0.656	0.542	0.782	0.656	0.542	0.782	SUBCLONAL	1	TRUE	1	0.28	2		401	414	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372044	45372044	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	34	388	0	ENST00000262160.6:c.1125A>C	p.Lys375Asn	p.K375N	ENST00000262160	NM_005901.5	375	aaA/aaC	9/11	1	2	FACETS	0.489	0.399	0.59	0.489	0.399	0.59	SUBCLONAL	1	TRUE	1	0.28	2		388	497	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7168013	7168013	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	42	545	1	ENST00000302850.5:c.1576G>T	p.Asp526Tyr	p.D526Y	ENST00000302850	NM_000208.2	526	Gac/Tac	7/22	1	2	FACETS	0.394	0.328	0.468	0.394	0.328	0.468	SUBCLONAL	1	TRUE	1	0.28	2		546	762	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248650	10248650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748486662	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	82	644	0	ENST00000340748.4:c.4103G>A	p.Arg1368Gln	p.R1368Q	ENST00000340748		1368	cGa/cAa	35/40	1	2	FACETS	0.756	0.666	0.853	0.756	0.666	0.853	SUBCLONAL	1	TRUE	1	0.28	2		644	775	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097009	11097009	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748340475	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	96	841	0	ENST00000358026.2:c.500G>A	p.Arg167Gln	p.R167Q	ENST00000358026	NM_001128849.1	167	cGg/cAg	4/36	1	2	FACETS	0.685	0.609	0.766	0.685	0.609	0.766	SUBCLONAL	1	TRUE	1	0.28	2		841	1001	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170435	11170435	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	70	664	0	ENST00000358026.2:c.4738G>T	p.Glu1580Ter	p.E1580*	ENST00000358026	NM_001128849.1	1580	Gaa/Taa	34/36	1	2	FACETS	0.628	0.547	0.716	0.628	0.547	0.716	SUBCLONAL	1	TRUE	1	0.28	2		664	796	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355552	15355552	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1568378738	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	53	653	3	ENST00000263377.2:c.2180del	p.Lys727ArgfsTer67	p.K727Rfs*67	ENST00000263377	NM_058243.2	727	aAg/ag	12/20	1	2	FACETS	0.402	0.342	0.469	0.402	0.342	0.469	SUBCLONAL	1	TRUE	1	0.28	2		656	941	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36217173	36217173	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	67	774	0	ENST00000222270.7:c.3922G>A	p.Ala1308Thr	p.A1308T	ENST00000222270	NM_014727.1	1308	Gca/Aca	14/37	1	2	FACETS	0.466	0.404	0.535	0.466	0.404	0.535	SUBCLONAL	1	TRUE	1	0.28	2		774	1026	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754660	41754660	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	99	676	1	ENST00000301178.4:c.1646C>A	p.Ala549Asp	p.A549D	ENST00000301178	NM_021913.4	549	gCt/gAt	14/20	1	2	FACETS	0.743	0.662	0.829	0.743	0.662	0.829	SUBCLONAL	1	TRUE	1	0.28	2		677	952	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383648	42383648	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	48	654	4	ENST00000221972.3:c.423G>T	p.Lys141Asn	p.K141N	ENST00000221972	NM_021601.3	141	aaG/aaT	3/5	1	2	FACETS	0.419	0.353	0.492	0.419	0.353	0.492	SUBCLONAL	1	TRUE	1	0.28	2		658	819	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910390	50910390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775734510	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	100	795	1	ENST00000440232.2:c.1645C>T	p.Arg549Cys	p.R549C	ENST00000440232	NM_002691.3	549	Cgt/Tgt	13/27	1	2	FACETS	0.691	0.616	0.772	0.691	0.616	0.772	SUBCLONAL	1	TRUE	1	0.28	2		796	1033	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607501	46607501	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	121	820	0	ENST00000263734.3:c.1690T>G	p.Phe564Val	p.F564V	ENST00000263734	NM_001430.4	564	Ttc/Gtc	12/16	1	2	FACETS	0.759	0.684	0.839	0.759	0.684	0.839	SUBCLONAL	1	TRUE	1	0.28	2		820	1138	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47601145	47601145	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	69	520	0	ENST00000263735.4:c.383A>G	p.Asp128Gly	p.D128G	ENST00000263735	NM_002354.2	128	gAc/gGc	3/9	1	2	FACETS	0.75	0.653	0.855	0.75	0.653	0.855	SUBCLONAL	1	TRUE	1	0.28	2		520	657	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026315	48026315	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	49	401	0	ENST00000234420.5:c.1193T>C	p.Val398Ala	p.V398A	ENST00000234420	NM_000179.2	398	gTg/gCg	4/10	1	2	FACETS	0.843	0.716	0.983	0.843	0.716	0.983	CLONAL	1	TRUE	1	0.28	2		401	415	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028136	48028136	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587782324	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	34	342	0	ENST00000234420.5:c.3014G>T	p.Arg1005Leu	p.R1005L	ENST00000234420	NM_000179.2	1005	cGa/cTa	4/10	1	2	FACETS	0.609	0.497	0.734	0.609	0.497	0.734	SUBCLONAL	1	TRUE	1	0.28	2		342	399	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61706101	61706101	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	34	410	0	ENST00000401558.2:c.3070G>A	p.Glu1024Lys	p.E1024K	ENST00000401558	NM_003400.3	1024	Gaa/Aaa	25/25	1	2	FACETS	0.552	0.451	0.666	0.552	0.451	0.666	SUBCLONAL	1	TRUE	1	0.28	2		410	440	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198269888	198269888	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	26	318	0	ENST00000335508.6:c.1451A>C	p.Glu484Ala	p.E484A	ENST00000335508	NM_012433.2	484	gAa/gCa	11/25	1	2	FACETS	0.597	0.473	0.738	0.597	0.473	0.738	SUBCLONAL	1	TRUE	1	0.28	2		318	311	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108158	209108158	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs755237893	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	32	328	0	ENST00000345146.2:c.691T>C	p.Tyr231His	p.Y231H	ENST00000345146	NM_005896.2	231	Tat/Cat	6/10	1	2	FACETS	0.788	0.642	0.952	0.788	0.642	0.952	CLONAL	1	TRUE	1	0.28	2		328	290	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251826	212251826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	32	298	0	ENST00000342788.4:c.3233C>T	p.Ser1078Phe	p.S1078F	ENST00000342788	NM_005235.2	1078	tCt/tTt	27/28	1	2	FACETS	0.592	0.481	0.718	0.592	0.481	0.718	SUBCLONAL	1	TRUE	1	0.28	2		298	386	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319662	62319662	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408202470	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	71	727	1	ENST00000360203.5:c.1645G>A	p.Ala549Thr	p.A549T	ENST00000360203	NM_001283009.1	549	Gcc/Acc	20/35	1	2	FACETS	0.592	0.516	0.675	0.592	0.516	0.675	SUBCLONAL	1	TRUE	1	0.28	2		728	856	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513247	44513247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	75	475	0	ENST00000291552.4:c.688C>T	p.Arg230Trp	p.R230W	ENST00000291552	NM_006758.2	230	Cgg/Tgg	8/8	1	2	FACETS	0.723	0.633	0.82	0.723	0.633	0.82	SUBCLONAL	1	TRUE	1	0.28	2		475	741	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573252	41573252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	81	787	0	ENST00000263253.7:c.5537G>A	p.Gly1846Asp	p.G1846D	ENST00000263253	NM_001429.3	1846	gGc/gAc	31/31	1	2	FACETS	0.631	0.555	0.713	0.631	0.555	0.713	SUBCLONAL	1	TRUE	1	0.28	2		787	917	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660099	12660099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145611571	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	54	450	1	ENST00000251849.4:c.122G>A	p.Arg41Gln	p.R41Q	ENST00000251849	NM_002880.3	41	cGg/cAg	2/17	1	2	FACETS	0.592	0.505	0.688	0.592	0.505	0.688	SUBCLONAL	1	TRUE	1	0.28	2		451	651	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067204	37067204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	57	422	0	ENST00000231790.2:c.1115C>T	p.Ser372Phe	p.S372F	ENST00000231790	NM_000249.3	372	tCt/tTt	12/19	1	2	FACETS	0.651	0.558	0.753	0.651	0.558	0.753	SUBCLONAL	1	TRUE	1	0.28	2		422	625	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165390	47165390	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	29	426	0	ENST00000409792.3:c.736G>A	p.Val246Ile	p.V246I	ENST00000409792	NM_014159.6	246	Gta/Ata	3/21	1	2	FACETS	0.456	0.366	0.56	0.456	0.366	0.56	SUBCLONAL	1	TRUE	1	0.28	2		426	454	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725025	49725025	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769228908	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	97	733	0	ENST00000449682.2:c.319C>T	p.Arg107Trp	p.R107W	ENST00000449682	NM_020998.3	107	Cgg/Tgg	3/18	1	2	FACETS	0.683	0.608	0.764	0.683	0.608	0.764	SUBCLONAL	1	TRUE	1	0.28	2		733	1014	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917481	178917481	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	17	249	0	ENST00000263967.3:c.356T>C	p.Phe119Ser	p.F119S	ENST00000263967	NM_006218.2	119	tTt/tCt	3/21	1	2	FACETS	0.636	0.476	0.824	0.636	0.476	0.824	SUBCLONAL	1	TRUE	1	0.28	2		249	191	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430831	181430831	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773650673	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	58	846	0	ENST00000325404.1:c.683C>T	p.Ser228Leu	p.S228L	ENST00000325404	NM_003106.3	228	tCg/tTg	1/1	1	2	FACETS	0.374	0.319	0.433	0.374	0.319	0.433	SUBCLONAL	1	TRUE	1	0.28	2		846	1109	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156631	55156631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553906650	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	73	652	0	ENST00000257290.5:c.3032G>A	p.Arg1011Lys	p.R1011K	ENST00000257290	NM_006206.4	1011	aGa/aAa	22/23	1	2	FACETS	0.639	0.558	0.727	0.639	0.558	0.727	SUBCLONAL	1	TRUE	1	0.28	2		652	816	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599269	55599269	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	27	421	0	ENST00000288135.5:c.2395C>A	p.Leu799Ile	p.L799I	ENST00000288135	NM_000222.2	799	Ctc/Atc	17/21	1	2	FACETS	0.542	0.431	0.668	0.542	0.431	0.668	SUBCLONAL	1	TRUE	1	0.28	2		421	356	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948775	55948775	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs759104314	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	23	389	0	ENST00000263923.4:c.3690G>T	p.Lys1230Asn	p.K1230N	ENST00000263923	NM_002253.2	1230	aaG/aaT	28/30	1	2	FACETS	0.39	0.303	0.491	0.39	0.303	0.491	SUBCLONAL	1	TRUE	1	0.28	2		389	421	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201703	66201703	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	46	453	0	ENST00000273854.3:c.2799C>G	p.Asp933Glu	p.D933E	ENST00000273854	NM_004439.5	933	gaC/gaG	16/18	1	2	FACETS	0.592	0.498	0.696	0.592	0.498	0.696	SUBCLONAL	1	TRUE	1	0.28	2		453	555	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213825	66213825	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	41	415	0	ENST00000273854.3:c.2605T>C	p.Trp869Arg	p.W869R	ENST00000273854	NM_004439.5	869	Tgg/Cgg	15/18	1	2	FACETS	0.727	0.606	0.86	0.727	0.606	0.86	SUBCLONAL	1	TRUE	1	0.28	2		415	403	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286185	66286185	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	16	338	0	ENST00000273854.3:c.1501G>T	p.Glu501Ter	p.E501*	ENST00000273854	NM_004439.5	501	Gag/Tag	6/18	1	2	FACETS	0.41	0.302	0.538	0.41	0.302	0.538	SUBCLONAL	1	TRUE	1	0.28	2		338	279	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159134	143159134	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	20	313	0	ENST00000262992.4:c.719G>T	p.Arg240Ile	p.R240I	ENST00000262992	NM_001101669.1	240	aGa/aTa	10/24	1	2	FACETS	0.616	0.472	0.783	0.616	0.472	0.783	SUBCLONAL	1	TRUE	1	0.28	2		313	232	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539295	187539295	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	35	436	0	ENST00000441802.2:c.8445G>T	p.Glu2815Asp	p.E2815D	ENST00000441802	NM_005245.3	2815	gaG/gaT	10/27	1	2	FACETS	0.543	0.445	0.654	0.543	0.445	0.654	SUBCLONAL	1	TRUE	1	0.28	2		436	460	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541619	187541619	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372908534	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	51	366	0	ENST00000441802.2:c.6121C>T	p.Arg2041Cys	p.R2041C	ENST00000441802	NM_005245.3	2041	Cgt/Tgt	10/27	1	2	FACETS	0.754	0.642	0.878	0.754	0.642	0.878	SUBCLONAL	1	TRUE	1	0.28	2		366	483	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628301	187628301	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	41	564	0	ENST00000441802.2:c.2681A>C	p.Lys894Thr	p.K894T	ENST00000441802	NM_005245.3	894	aAg/aCg	2/27	1	2	FACETS	0.383	0.318	0.456	0.383	0.318	0.456	SUBCLONAL	1	TRUE	1	0.28	2		564	764	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228428	228428	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	46	330	0	ENST00000264932.6:c.750G>T	p.Lys250Asn	p.K250N	ENST00000264932	NM_004168.2	250	aaG/aaT	6/15	1	2	FACETS	0.775	0.654	0.909	0.775	0.654	0.909	CLONAL	1	TRUE	1	0.28	2		330	424	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254528	1254528	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs750951309	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	105	865	0	ENST00000310581.5:c.3250C>T	p.Arg1084Ter	p.R1084*	ENST00000310581	NM_198253.2	1084	Cga/Tga	15/16	1	2	FACETS	0.681	0.608	0.758	0.681	0.608	0.758	SUBCLONAL	1	TRUE	1	0.28	2		865	1102	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31431749	31431749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	58	424	0	ENST00000344624.3:c.3079G>A	p.Gly1027Arg	p.G1027R	ENST00000344624		1027	Ggg/Agg	23/33	1	2	FACETS	0.716	0.615	0.825	0.716	0.615	0.825	SUBCLONAL	1	TRUE	1	0.28	2		424	579	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508822	31508822	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1373401772	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	84	465	0	ENST00000344624.3:c.1493A>G	p.Asp498Gly	p.D498G	ENST00000344624		498	gAc/gGc	7/33	1	2	FACETS	0.837	0.739	0.942	0.837	0.739	0.942	CLONAL	1	TRUE	1	0.28	2		465	717	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947452	38947452	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1406752443	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	24	290	0	ENST00000357387.3:c.4228C>T	p.Arg1410Trp	p.R1410W	ENST00000357387	NM_152756.3	1410	Cgg/Tgg	32/38	1	2	FACETS	0.474	0.371	0.592	0.474	0.371	0.592	SUBCLONAL	1	TRUE	1	0.28	2		290	362	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38996934	38996934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762282621	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	30	424	2	ENST00000357387.3:c.443G>A	p.Arg148Gln	p.R148Q	ENST00000357387	NM_152756.3	148	cGa/cAa	6/38	1	2	FACETS	0.557	0.448	0.679	0.557	0.448	0.679	SUBCLONAL	1	TRUE	1	0.28	2		426	385	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80168989	80168989	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	50	539	0	ENST00000265081.6:c.3185G>A	p.Gly1062Glu	p.G1062E	ENST00000265081	NM_002439.4	1062	gGa/gAa	23/24	1	2	FACETS	0.71	0.603	0.828	0.71	0.603	0.828	SUBCLONAL	1	TRUE	1	0.28	2		539	503	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628407	86628407	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs750237587	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	20	303	0	ENST00000274376.6:c.776T>C	p.Val259Ala	p.V259A	ENST00000274376	NM_002890.2	259	gTt/gCt	3/25	1	2	FACETS	0.552	0.422	0.702	0.552	0.422	0.702	SUBCLONAL	1	TRUE	1	0.28	2		303	259	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633801	86633801	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	21	209	1	ENST00000274376.6:c.910G>T	p.Gly304Ter	p.G304*	ENST00000274376	NM_002890.2	304	Gga/Tga	5/25	1	2	FACETS	0.938	0.728	1	0.938	0.728	1	CLONAL	1	TRUE	1	0.28	2		210	160	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665647	86665647	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	16	264	0	ENST00000274376.6:c.1628T>C	p.Ile543Thr	p.I543T	ENST00000274376	NM_002890.2	543	aTa/aCa	12/25	1	2	FACETS	0.435	0.321	0.57	0.435	0.321	0.57	SUBCLONAL	1	TRUE	1	0.28	2		264	263	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923737	131923737	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	20	334	0	ENST00000265335.6:c.1007C>A	p.Ser336Tyr	p.S336Y	ENST00000265335		336	tCt/tAt	7/25	1	2	FACETS	0.47	0.359	0.599	0.47	0.359	0.599	SUBCLONAL	1	TRUE	1	0.28	2		334	304	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953915	131953915	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	37	309	0	ENST00000265335.6:c.3318A>C	p.Glu1106Asp	p.E1106D	ENST00000265335		1106	gaA/gaC	21/25	1	2	FACETS	0.74	0.611	0.884	0.74	0.611	0.884	SUBCLONAL	1	TRUE	1	0.28	2		309	357	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638456	176638456	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	80	644	0	ENST00000439151.2:c.3056G>T	p.Arg1019Leu	p.R1019L	ENST00000439151	NM_022455.4	1019	cGc/cTc	5/23	1	2	FACETS	0.646	0.567	0.73	0.646	0.567	0.73	SUBCLONAL	1	TRUE	1	0.28	2		644	885	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672576	30672576	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	80	566	1	ENST00000376406.3:c.4384G>T	p.Asp1462Tyr	p.D1462Y	ENST00000376406	NM_014641.2	1462	Gac/Tac	10/15	1	2	FACETS	0.797	0.701	0.9	0.797	0.701	0.9	SUBCLONAL	1	TRUE	1	0.28	2		567	717	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680772	30680772	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1344404968	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	38	519	0	ENST00000376406.3:c.947T>C	p.Val316Ala	p.V316A	ENST00000376406	NM_014641.2	316	gTc/gCc	5/15	1	2	FACETS	0.421	0.347	0.505	0.421	0.347	0.505	SUBCLONAL	1	TRUE	1	0.28	2		519	644	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31946728	31946728	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750898436	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	48	551	1	ENST00000375333.2:c.616G>A	p.Asp206Asn	p.D206N	ENST00000375333	NM_032454.1	206	Gac/Aac	4/8	1	2	FACETS	0.414	0.348	0.486	0.414	0.348	0.486	SUBCLONAL	1	TRUE	1	0.28	2		552	829	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163332	32163332	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	84	781	1	ENST00000375023.3:c.5894T>G	p.Ile1965Ser	p.I1965S	ENST00000375023	NM_004557.3	1965	aTt/aGt	30/30	1	2	FACETS	0.599	0.528	0.676	0.599	0.528	0.676	SUBCLONAL	1	TRUE	1	0.28	2		782	1001	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169074	32169074	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	101	747	1	ENST00000375023.3:c.3959C>A	p.Ser1320Tyr	p.S1320Y	ENST00000375023	NM_004557.3	1320	tCc/tAc	22/30	1	2	FACETS	0.733	0.654	0.818	0.733	0.654	0.818	SUBCLONAL	1	TRUE	1	0.28	2		748	984	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187512	32187512	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	58	702	0	ENST00000375023.3:c.1367C>A	p.Pro456His	p.P456H	ENST00000375023	NM_004557.3	456	cCt/cAt	8/30	1	2	FACETS	0.417	0.357	0.483	0.417	0.357	0.483	SUBCLONAL	1	TRUE	1	0.28	2		702	993	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553380	106553380	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	69	461	0	ENST00000369096.4:c.1345A>C	p.Asn449His	p.N449H	ENST00000369096	NM_001198.3	449	Aat/Cat	5/7	1	2	FACETS	0.932	0.813	1	0.932	0.813	1	CLONAL	1	TRUE	1	0.28	2		461	529	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109415114	109415114	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	35	701	0	ENST00000436639.2:c.163A>C	p.Asn55His	p.N55H	ENST00000436639	NM_014454.2	55	Aat/Cat	1/10	0.3	1	FACETS	0.311	0.254	0.376	0.311	0.254	0.376	SUBCLONAL	1	TRUE	0	0.28	1		701	691	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024234	112024234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	18	276	0	ENST00000368678.4:c.551C>T	p.Ala184Val	p.A184V	ENST00000368678		184	gCc/gTc	7/13	0.3	1	FACETS	0.496	0.374	0.639	0.496	0.374	0.639	SUBCLONAL	1	TRUE	0	0.28	1		276	223	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631428	117631428	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	25	362	0	ENST00000368508.3:c.6250A>C	p.Asn2084His	p.N2084H	ENST00000368508	NM_002944.2	2084	Aat/Cat	40/43	0.3	1	FACETS	0.439	0.346	0.546	0.439	0.346	0.546	SUBCLONAL	1	TRUE	0	0.28	1		362	350	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642540	117642540	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1243356301	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	33	548	0	ENST00000368508.3:c.5659A>C	p.Lys1887Gln	p.K1887Q	ENST00000368508	NM_002944.2	1887	Aag/Cag	35/43	0.3	1	FACETS	0.358	0.29	0.434	0.358	0.29	0.434	SUBCLONAL	1	TRUE	0	0.28	1		548	567	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005386	150005386	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs190144122	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	36	536	0	ENST00000253339.5:c.839A>G	p.Asn280Ser	p.N280S	ENST00000253339		280	aAc/aGc	3/7	1	2	FACETS	0.374	0.306	0.45	0.374	0.306	0.45	SUBCLONAL	1	TRUE	1	0.28	2		536	688	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099767	157099767	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	32	318	0	ENST00000346085.5:c.704G>T	p.Gly235Val	p.G235V	ENST00000346085	NM_020732.3	235	gGc/gTc	1/20	1	2	FACETS	0.602	0.488	0.729	0.602	0.488	0.729	SUBCLONAL	1	TRUE	1	0.28	2		318	380	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521980	157521980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	38	655	0	ENST00000346085.5:c.4252C>T	p.Pro1418Ser	p.P1418S	ENST00000346085	NM_020732.3	1418	Ccc/Tcc	18/20	1	2	FACETS	0.375	0.309	0.45	0.375	0.309	0.45	SUBCLONAL	1	TRUE	1	0.28	2		655	723	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525017	157525017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	39	319	0	ENST00000346085.5:c.4912C>T	p.Arg1638Cys	p.R1638C	ENST00000346085	NM_020732.3	1638	Cgt/Tgt	19/20	1	2	FACETS	0.625	0.518	0.744	0.625	0.518	0.744	SUBCLONAL	1	TRUE	1	0.28	2		319	446	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528615	157528615	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	41	606	0	ENST00000346085.5:c.6340A>G	p.Thr2114Ala	p.T2114A	ENST00000346085	NM_020732.3	2114	Aca/Gca	20/20	1	2	FACETS	0.379	0.314	0.451	0.379	0.314	0.451	SUBCLONAL	1	TRUE	1	0.28	2		606	773	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394368	162394368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373822092	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	44	409	1	ENST00000366898.1:c.700C>T	p.Arg234Trp	p.R234W	ENST00000366898	NM_004562.2	234	Cgg/Tgg	6/12	1	2	FACETS	0.589	0.493	0.694	0.589	0.493	0.694	SUBCLONAL	1	TRUE	1	0.28	2		410	534	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977616	2977616	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	106	655	0	ENST00000396946.4:c.1068G>T	p.Lys356Asn	p.K356N	ENST00000396946	NM_032415.4	356	aaG/aaT	8/25	1	2	FACETS	0.784	0.701	0.872	0.784	0.701	0.872	SUBCLONAL	1	TRUE	1	0.28	2		655	966	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6439761	6439761	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	32	400	0	ENST00000356142.4:c.287T>C	p.Val96Ala	p.V96A	ENST00000356142	NM_018890.3	96	gTg/gCg	5/7	1	2	FACETS	0.474	0.384	0.576	0.474	0.384	0.576	SUBCLONAL	1	TRUE	1	0.28	2		400	482	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14027729	14027729	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	22	322	0	ENST00000405192.2:c.115C>A	p.Leu39Met	p.L39M	ENST00000405192	NM_001163147.1	39	Ctg/Atg	3/12	1	2	FACETS	0.425	0.329	0.537	0.425	0.329	0.537	SUBCLONAL	1	TRUE	1	0.28	2		322	370	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739633	41739633	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	35	446	0	ENST00000242208.4:c.340A>C	p.Asn114His	p.N114H	ENST00000242208	NM_002192.2	114	Aat/Cat	2/3	1	2	FACETS	0.402	0.328	0.485	0.402	0.328	0.485	SUBCLONAL	1	TRUE	1	0.28	2		446	622	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259431	55259431	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	64	446	0	ENST00000275493.2:c.2489A>G	p.Asp830Gly	p.D830G	ENST00000275493	NM_005228.3	830	gAc/gGc	21/28	1	2	FACETS	0.693	0.599	0.794	0.693	0.599	0.794	SUBCLONAL	1	TRUE	1	0.28	2		446	660	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508205	106508205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	61	445	0	ENST00000359195.3:c.199G>A	p.Val67Met	p.V67M	ENST00000359195	NM_002649.2	67	Gtg/Atg	2/11	1	2	FACETS	0.811	0.7	0.932	0.811	0.7	0.932	CLONAL	1	TRUE	1	0.28	2		445	537	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520054	106520054	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	15	302	0	ENST00000359195.3:c.2482A>C	p.Ile828Leu	p.I828L	ENST00000359195	NM_002649.2	828	Att/Ctt	6/11	1	2	FACETS	0.472	0.345	0.624	0.472	0.345	0.624	SUBCLONAL	1	TRUE	1	0.28	2		302	227	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524625	106524625	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	13	287	0	ENST00000359195.3:c.2786T>C	p.Val929Ala	p.V929A	ENST00000359195	NM_002649.2	929	gTt/gCt	9/11	1	2	FACETS	0.426	0.304	0.575	0.426	0.304	0.575	SUBCLONAL	1	TRUE	1	0.28	2		287	218	SUCCESS
MET	4233	MSKCC	GRCh37	7	116422060	116422061	+	missense_variant	Missense_Mutation	DNP	CT	CT	TG	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	30	374	0	ENST00000397752.3:c.3541_3542delinsTG	p.Leu1181Cys	p.L1181C	ENST00000397752	NM_000245.2	1181	CTt/TGt	18/21	1	2	FACETS	0.502	0.404	0.613	0.502	0.404	0.613	SUBCLONAL	1	TRUE	1	0.28	2		374	427	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494258	140494258	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	45	653	0	ENST00000288602.6:c.990T>G	p.Ile330Met	p.I330M	ENST00000288602	NM_004333.4	330	atT/atG	8/18	1	2	FACETS	0.402	0.337	0.475	0.402	0.337	0.475	SUBCLONAL	1	TRUE	1	0.28	2		653	799	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836278	151836278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	80	534	0	ENST00000262189.6:c.14527C>T	p.Pro4843Ser	p.P4843S	ENST00000262189	NM_170606.2	4843	Ccc/Tcc	57/59	1	2	FACETS	0.685	0.602	0.775	0.685	0.602	0.775	SUBCLONAL	1	TRUE	1	0.28	2		534	834	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272325	38272325	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	77	637	0	ENST00000425967.3:c.2042A>G	p.His681Arg	p.H681R	ENST00000425967	NM_001174067.1	681	cAc/cGc	15/19	1	2	FACETS	0.642	0.562	0.728	0.642	0.562	0.728	SUBCLONAL	1	TRUE	1	0.28	2		637	857	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56860185	56860185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	56	490	0	ENST00000519728.1:c.187G>A	p.Glu63Lys	p.E63K	ENST00000519728	NM_002350.3	63	Gaa/Aaa	4/13	1	2	FACETS	0.672	0.576	0.778	0.672	0.576	0.778	SUBCLONAL	1	TRUE	1	0.28	2		490	595	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5064942	5064942	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	34	385	0	ENST00000381652.3:c.1116T>G	p.Tyr372Ter	p.Y372*	ENST00000381652	NM_004972.3	372	taT/taG	9/25	1	2	FACETS	0.794	0.65	0.954	0.794	0.65	0.954	CLONAL	1	TRUE	1	0.28	2		385	306	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5077513	5077513	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	44	363	0	ENST00000381652.3:c.1925A>C	p.Lys642Thr	p.K642T	ENST00000381652	NM_004972.3	642	aAa/aCa	15/25	1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.28	2		363	314	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8497268	8497268	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	30	279	0	ENST00000356435.5:c.2323T>C	p.Trp775Arg	p.W775R	ENST00000356435		775	Tgg/Cgg	15/35	1	2	FACETS	0.84	0.68	1	0.84	0.68	1	CLONAL	1	TRUE	1	0.28	2		279	255	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636173	87636173	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	42	381	0	ENST00000277120.3:c.2338G>A	p.Glu780Lys	p.E780K	ENST00000277120		780	Gag/Aag	19/19	1	2	FACETS	0.612	0.511	0.725	0.612	0.511	0.725	SUBCLONAL	1	TRUE	1	0.28	2		381	490	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249860	110249860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770068428	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	79	829	0	ENST00000374672.4:c.815G>A	p.Arg272His	p.R272H	ENST00000374672	NM_004235.4	272	cGc/cAc	3/5	1	2	FACETS	0.578	0.507	0.654	0.578	0.507	0.654	SUBCLONAL	1	TRUE	1	0.28	2		829	977	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820238	139820238	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	102	690	0	ENST00000247668.2:c.1391A>G	p.Asn464Ser	p.N464S	ENST00000247668	NM_021138.3	464	aAc/aGc	11/11	1	2	FACETS	0.812	0.725	0.905	0.812	0.725	0.905	CLONAL	1	TRUE	1	0.28	2		690	897	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820638	44820638	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	34	328	0	ENST00000377967.4:c.334+1G>A		p.X112_splice	ENST00000377967	NM_021140.2	112			1	2	FACETS	0.906	0.744	1	0.906	0.744	1	CLONAL	1	TRUE	1	0.28	2		328	268	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430347	47430347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	82	756	0	ENST00000377045.4:c.1622C>T	p.Ala541Val	p.A541V	ENST00000377045	NM_001654.4	541	gCc/gTc	15/16	1	2	FACETS	0.549	0.482	0.621	0.549	0.482	0.621	SUBCLONAL	1	TRUE	1	0.28	2		756	1067	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652249	48652249	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	74	698	0	ENST00000376670.3:c.920G>A	p.Arg307His	p.R307H	ENST00000376670	NM_002049.3	307	cGc/cAc	6/6	1	2	FACETS	0.57	0.497	0.648	0.57	0.497	0.648	SUBCLONAL	1	TRUE	1	0.28	2		698	928	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222205	53222205	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	115	682	0	ENST00000375401.3:c.4627C>A	p.Leu1543Met	p.L1543M	ENST00000375401	NM_004187.3	1543	Ctg/Atg	26/26	1	2	FACETS	0.845	0.76	0.935	0.845	0.76	0.935	CLONAL	1	TRUE	1	0.28	2		682	972	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348270	70348270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	121	566	1	ENST00000374080.3:c.3334G>A	p.Asp1112Asn	p.D1112N	ENST00000374080		1112	Gat/Aat	23/45	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.28	2		567	856	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356169	70356169	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	87	716	0	ENST00000374080.3:c.5064G>A	p.Trp1688Ter	p.W1688*	ENST00000374080		1688	tgG/tgA	37/45	1	2	FACETS	0.632	0.558	0.711	0.632	0.558	0.711	SUBCLONAL	1	TRUE	1	0.28	2		716	984	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937199	76937199	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	28	495	1	ENST00000373344.5:c.3549G>T	p.Glu1183Asp	p.E1183D	ENST00000373344	NM_000489.3	1183	gaG/gaT	9/35	1	2	FACETS	0.462	0.369	0.568	0.462	0.369	0.568	SUBCLONAL	1	TRUE	1	0.28	2		496	433	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938607	76938607	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	25	465	0	ENST00000373344.5:c.2141A>C	p.Asn714Thr	p.N714T	ENST00000373344	NM_000489.3	714	aAt/aCt	9/35	1	2	FACETS	0.4	0.315	0.499	0.4	0.315	0.499	SUBCLONAL	1	TRUE	1	0.28	2		465	446	SUCCESS
BTK	695	MSKCC	GRCh37	X	100609643	100609643	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	68	452	0	ENST00000308731.7:c.1606A>G	p.Lys536Glu	p.K536E	ENST00000308731	NM_000061.2	536	Aaa/Gaa	16/19	1	2	FACETS	0.694	0.603	0.792	0.694	0.603	0.792	SUBCLONAL	1	TRUE	1	0.28	2		452	700	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617159	100617159	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	60	503	0	ENST00000308731.7:c.588+2T>C		p.X196_splice	ENST00000308731	NM_000061.2	196			1	2	FACETS	0.568	0.489	0.655	0.568	0.489	0.655	SUBCLONAL	1	TRUE	1	0.28	2		503	754	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185223	123185223	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	29	431	0	ENST00000218089.9:c.1175A>C	p.Lys392Thr	p.K392T	ENST00000218089	NM_001042749.1	392	aAa/aCa	13/35	1	2	FACETS	0.533	0.427	0.652	0.533	0.427	0.652	SUBCLONAL	1	TRUE	1	0.28	2		431	389	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190010	123190010	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	39	509	0	ENST00000218089.9:c.1229G>T	p.Cys410Phe	p.C410F	ENST00000218089	NM_001042749.1	410	tGt/tTt	14/35	1	2	FACETS	0.563	0.466	0.671	0.563	0.466	0.671	SUBCLONAL	1	TRUE	1	0.28	2		509	495	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504095	123504095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	35	422	0	ENST00000371139.4:c.271G>A	p.Asp91Asn	p.D91N	ENST00000371139	NM_001114937.2	91	Gat/Aat	3/4	1	2	FACETS	0.689	0.565	0.827	0.689	0.565	0.827	SUBCLONAL	1	TRUE	1	0.28	2		422	363	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152857987	152857987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146203325	NA	P-0049760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	41	317	0	ENST00000406277.2:c.628G>A	p.Glu210Lys	p.E210K	ENST00000406277	NM_152274.4	210	Gag/Aag	6/7	1	2	FACETS	0.789	0.659	0.934	0.789	0.659	0.934	CLONAL	1	TRUE	1	0.28	2		317	371	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	110	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.822	0.747	0.9	0.822	0.747	0.9	CLONAL	1	TRUE	1	0.778086285709482	2		148	344	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944450	40944450	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	252	536	0	ENST00000373198.4:c.2052T>A	p.Asn684Lys	p.N684K	ENST00000373198	NM_133170.3	684	aaT/aaA	12/32	0.766391515277692	3	FACETS	1	0.984	1	0.568	0.533	0.604	CLONAL	1	TRUE	1	0.778086285709482	3		536	792	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233052	55233052	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1906	4005	442	0	ENST00000275493.2:c.1802G>C	p.Gly601Ala	p.G601A	ENST00000275493	NM_005228.3	601	gGa/gCa	15/28	0.778086285709482	19	FACETS	1	0.997	1			1	CLONAL	13	TRUE	NA	0.778086285709482	19		442	5911	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	121	352	1	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.835	0.759	0.913	0.835	0.759	0.913	CLONAL	1	FALSE	1	0.645648262059303	2		353	449	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	68	363	3	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.565	0.494	0.641	0.565	0.494	0.641	SUBCLONAL	1	FALSE	1	0.645648262059303	2		366	373	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	367	472	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.962	0.925	0.998	1	0.997	1	CLONAL	2	FALSE	1	0.645648262059303	2		475	591	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	149	437	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.95	0.874	1	0.95	0.874	1	CLONAL	1	FALSE	1	0.645648262059303	2		437	486	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	342	409	6	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.972	0.933	1	1	0.997	1	CLONAL	2	FALSE	1	0.645648262059303	2		415	545	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	208	523	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.846	0.787	0.906	0.846	0.787	0.906	CLONAL	1	FALSE	1	0.645648262059303	2		523	762	SUCCESS
APC	324	MSKCC	GRCh37	5	112175166	112175166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371113837	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	77	236	0	ENST00000257430.4:c.3875C>T	p.Thr1292Met	p.T1292M	ENST00000257430	NM_000038.5	1292	aCg/aTg	16/16	1	2	FACETS	0.978	0.871	1	0.978	0.871	1	CLONAL	1	FALSE	1	0.645648262059303	2		236	244	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256363	16256363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	216	517	1	ENST00000375759.3:c.3628G>A	p.Glu1210Lys	p.E1210K	ENST00000375759	NM_015001.2	1210	Gag/Aag	11/15	1	2	FACETS	0.941	0.878	1	0.941	0.878	1	CLONAL	1	FALSE	1	0.645648262059303	2		518	711	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088659	27088659	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	219	666	2	ENST00000324856.7:c.2272del	p.Gln758ArgfsTer75	p.Q758Rfs*75	ENST00000324856	NM_006015.4	756	aaC/aa	7/20	1	2	FACETS	0.803	0.748	0.859	0.803	0.748	0.859	CLONAL	1	FALSE	1	0.645648262059303	2		668	845	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	143	369	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.94	0.864	1	0.94	0.864	1	CLONAL	1	FALSE	1	0.645648262059303	2		370	471	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276357	115276357	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	114	418	0	ENST00000438362.2:c.971del	p.Asn324ThrfsTer15	p.N324Tfs*15	ENST00000438362	NM_001242891.1	324	aAc/ac	9/20	1	2	FACETS	0.786	0.713	0.863	0.786	0.713	0.863	SUBCLONAL	1	FALSE	1	0.645648262059303	2		418	449	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163313582	163313582	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	61	239	0	ENST00000271452.3:c.729A>C	p.Lys243Asn	p.K243N	ENST00000271452	NM_145697.2	243	aaA/aaC	10/14	1	2	FACETS	0.825	0.721	0.935	0.825	0.721	0.935	CLONAL	1	FALSE	1	0.645648262059303	2		239	229	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	102	304	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.87	0.786	0.959	0.87	0.786	0.959	CLONAL	1	FALSE	1	0.645648262059303	2		305	363	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720721	89720721	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs786204905	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	21	155	0	ENST00000371953.3:c.875del	p.Asn292MetfsTer15	p.N292Mfs*15	ENST00000371953	NM_000314.4	291	gAa/ga	8/9	1	2	FACETS	0.547	0.427	0.682	0.547	0.427	0.682	SUBCLONAL	1	FALSE	1	0.645648262059303	2		155	119	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375134	104375134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1256959985	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	228	610	1	ENST00000369902.3:c.1132G>A	p.Gly378Arg	p.G378R	ENST00000369902	NM_016169.3	378	Gga/Aga	9/12	1	2	FACETS	0.927	0.867	0.989	0.927	0.867	0.989	CLONAL	1	FALSE	1	0.645648262059303	2		611	762	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138851	64138851	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780033520	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	335	867	1	ENST00000334205.4:c.2218G>A	p.Ala740Thr	p.A740T	ENST00000334205	NM_003942.2	740	Gcc/Acc	17/17	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.645648262059303	2		868	1006	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047227	77047227	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	259	577	0	ENST00000356341.3:c.1317G>T	p.Lys439Asn	p.K439N	ENST00000356341	NM_002576.4	439	aaG/aaT	13/15	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	1	0.645648262059303	2		577	790	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139307	108139307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	153	495	0	ENST00000278616.4:c.2809G>A	p.Glu937Lys	p.E937K	ENST00000278616	NM_000051.3	937	Gaa/Aaa	18/63	1	2	FACETS	0.931	0.858	1	0.931	0.858	1	CLONAL	1	FALSE	1	0.645648262059303	2		495	509	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170530	108170530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	142	450	0	ENST00000278616.4:c.5095G>A	p.Ala1699Thr	p.A1699T	ENST00000278616	NM_000051.3	1699	Gcc/Acc	34/63	1	2	FACETS	0.971	0.892	1	0.971	0.892	1	CLONAL	1	FALSE	1	0.645648262059303	2		450	453	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111957651	111957651	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	229	577	0	ENST00000375549.3:c.20T>C	p.Leu7Pro	p.L7P	ENST00000375549	NM_003002.3	7	cTg/cCg	1/4	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	1	0.645648262059303	2		577	699	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118353184	118353184	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	133	327	0	ENST00000534358.1:c.4060C>A	p.Pro1354Thr	p.P1354T	ENST00000534358	NM_005933.3	1354	Cct/Act	8/36	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	FALSE	1	0.645648262059303	2		327	394	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	109	575	0	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	1	2	FACETS	0.523	0.471	0.579	0.523	0.471	0.579	SUBCLONAL	1	FALSE	1	0.645648262059303	2		575	645	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863319	57863319	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	256	804	0	ENST00000228682.2:c.1418del	p.Gly473AlafsTer40	p.G473Afs*40	ENST00000228682	NM_005269.2	472	Ggg/gg	11/12	1	2	FACETS	0.877	0.823	0.933	0.877	0.823	0.933	CLONAL	1	FALSE	1	0.645648262059303	2		804	904	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557771	21557771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs575902148	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	240	662	1	ENST00000382592.4:c.2074G>A	p.Ala692Thr	p.A692T	ENST00000382592	NM_014572.2	692	Gcc/Acc	5/8	1	2	FACETS	0.986	0.924	1	0.986	0.924	1	CLONAL	1	FALSE	1	0.645648262059303	2		663	754	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953633	32953633	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359732	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	120	351	2	ENST00000380152.3:c.8940del	p.Glu2981LysfsTer7	p.E2981Kfs*7	ENST00000380152		2978	tcA/tc	22/27	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	FALSE	1	0.645648262059303	2		353	369	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610014	81610014	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151264748	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	176	445	0	ENST00000298171.2:c.1612G>A	p.Ala538Thr	p.A538T	ENST00000298171	NM_000369.2	538	Gca/Aca	10/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.645648262059303	2		445	457	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	149	312	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	0.86	0.79	0.932	0.86	0.79	0.932	CLONAL	1	FALSE	1	0.645648262059303	2		312	537	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007834	45007834	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	176	400	0	ENST00000558401.1:c.285del	p.Asp96MetfsTer7	p.D96Mfs*7	ENST00000558401	NM_004048.2	94	gAa/ga	2/4	1	2	FACETS	0.967	0.896	1	0.967	0.896	1	CLONAL	1	FALSE	1	0.645648262059303	2		400	564	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66679726	66679726	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1566991692	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	245	491	0	ENST00000307102.5:c.45del	p.Asp16ThrfsTer25	p.D16Tfs*25	ENST00000307102	NM_002755.3	14	gCc/gc	1/11	1	2	FACETS	0.995	0.933	1	0.995	0.933	1	CLONAL	1	FALSE	1	0.645648262059303	2		491	763	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2111956	2111956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771561593	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	245	697	0	ENST00000219476.3:c.1204G>A	p.Gly402Arg	p.G402R	ENST00000219476	NM_000548.3	402	Ggg/Agg	12/42	1	2	FACETS	0.846	0.792	0.902	0.846	0.792	0.902	CLONAL	1	FALSE	1	0.645648262059303	2		697	897	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063359	67063359	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	187	394	1	ENST00000412916.2:c.54del	p.Phe18LeufsTer4	p.F18Lfs*4	ENST00000412916		17	Ttt/tt	1/6	1	2	FACETS	0.972	0.903	1	0.972	0.903	1	CLONAL	1	FALSE	1	0.645648262059303	2		395	596	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835781	68835781	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060501215	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	234	506	2	ENST00000261769.5:c.377del	p.Pro126ArgfsTer89	p.P126Rfs*89	ENST00000261769	NM_004360.3	124	cgC/cg	3/16	1	2	FACETS	0.963	0.901	1	0.963	0.901	1	CLONAL	1	FALSE	1	0.645648262059303	2		508	753	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032504	12032504	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	28	343	0	ENST00000353533.5:c.940T>C	p.Phe314Leu	p.F314L	ENST00000353533	NM_003010.3	314	Ttt/Ctt	9/11	1	2	FACETS	0.188	0.15	0.232	0.188	0.15	0.232	SUBCLONAL	1	FALSE	1	0.645648262059303	2		343	461	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	208	480	0	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	0.928	0.865	0.993	0.928	0.865	0.993	CLONAL	1	FALSE	1	0.645648262059303	2		480	694	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66521914	66521914	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	51	302	0	ENST00000358598.2:c.569G>A	p.Trp190Ter	p.W190*	ENST00000358598	NM_212471.2	190	tGg/tAg	7/11	1	2	FACETS	0.427	0.364	0.496	0.427	0.364	0.496	SUBCLONAL	1	FALSE	1	0.645648262059303	2		302	370	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119910	70119910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1297203260	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	243	584	1	ENST00000245479.2:c.916del	p.Val306CysfsTer77	p.V306Cfs*77	ENST00000245479	NM_000346.3	304	ccG/cc	3/3	1	2	FACETS	0.949	0.89	1	0.949	0.89	1	CLONAL	1	FALSE	1	0.645648262059303	2		585	793	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252720	10252720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377078524	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	265	708	3	ENST00000340748.4:c.3245G>A	p.Arg1082His	p.R1082H	ENST00000340748		1082	cGc/cAc	29/40	1	2	FACETS	0.989	0.93	1	0.989	0.93	1	CLONAL	1	FALSE	1	0.645648262059303	2		711	830	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284997	15284997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	297	889	2	ENST00000263388.2:c.4618C>T	p.Arg1540Cys	p.R1540C	ENST00000263388	NM_000435.2	1540	Cgc/Tgc	25/33	1	2	FACETS	0.985	0.93	1	0.985	0.93	1	CLONAL	1	FALSE	1	0.645648262059303	2		891	934	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302441	15302441	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	343	877	0	ENST00000263388.2:c.830A>C	p.Glu277Ala	p.E277A	ENST00000263388	NM_000435.2	277	gAg/gCg	6/33	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.645648262059303	2		877	1016	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302909	15302909	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	343	1003	0	ENST00000263388.2:c.541T>G	p.Phe181Val	p.F181V	ENST00000263388	NM_000435.2	181	Ttc/Gtc	4/33	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.645648262059303	2		1003	1058	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223175	36223175	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	358	922	3	ENST00000222270.7:c.5730del	p.Arg1911AspfsTer23	p.R1911Dfs*23	ENST00000222270	NM_014727.1	1909	Ccc/cc	28/37	1	2	FACETS	0.981	0.931	1	0.981	0.931	1	CLONAL	1	FALSE	1	0.645648262059303	2		925	1130	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224340	36224340	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1568382485	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	127	778	1	ENST00000222270.7:c.6895del	p.Arg2299GlyfsTer26	p.R2299Gfs*26	ENST00000222270	NM_014727.1	2297	gCc/gc	28/37	1	2	FACETS	0.4	0.362	0.441	0.4	0.362	0.441	SUBCLONAL	1	FALSE	1	0.645648262059303	2		779	983	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765621	41765621	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	274	654	0	ENST00000301178.4:c.2501del	p.Pro834LeufsTer122	p.P834Lfs*122	ENST00000301178	NM_021913.4	833	Ccc/cc	20/20	1	2	FACETS	0.971	0.914	1	0.971	0.914	1	CLONAL	1	FALSE	1	0.645648262059303	2		654	874	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657020	47657020	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63751108	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	321	350	1	ENST00000233146.2:c.1216C>T	p.Arg406Ter	p.R406*	ENST00000233146	NM_000251.2	406	Cga/Tga	7/16	0.645648262059303	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	FALSE	0	0.645648262059303	2		351	479	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096268	178096268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	213	533	2	ENST00000397062.3:c.1063G>A	p.Ala355Thr	p.A355T	ENST00000397062	NM_006164.4	355	Gca/Aca	5/5	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	1	0.645648262059303	2		535	651	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266476	198266477	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1394586762	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	102	288	0	ENST00000335508.6:c.2359dup	p.Ile787AsnfsTer21	p.I787Nfs*21	ENST00000335508	NM_012433.2	787	att/aAtt	16/25	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	1	0.645648262059303	2		288	301	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151290	202151290	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	143	392	0	ENST00000358485.4:c.1596del	p.Lys532AsnfsTer73	p.K532Nfs*73	ENST00000358485	NM_001080125.1	530	agA/ag	9/9	1	2	FACETS	0.913	0.839	0.991	0.913	0.839	0.991	CLONAL	1	FALSE	1	0.645648262059303	2		392	485	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	276	854	1	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	NA	2	FACETS	0.9	0.846	0.955			1	INDETERMINATE	1	FALSE	NA	0.645648262059303	2		855	950	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021182	31021182	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201899433	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	265	591	0	ENST00000375687.4:c.1181G>A	p.Arg394His	p.R394H	ENST00000375687	NM_015338.5	394	cGt/cAt	12/13	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.645648262059303	2		591	781	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750720	39750720	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	20	277	1	ENST00000361337.2:c.2120A>T	p.Asp707Val	p.D707V	ENST00000361337	NM_003286.2	707	gAc/gTc	20/21	NA	2	FACETS	0.179	0.136	0.228			1	INDETERMINATE	1	FALSE	NA	0.645648262059303	2		278	347	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292821	62292822	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs769909059	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	86	452	0	ENST00000360203.5:c.287_289dup	p.Ala96dup	p.A96dup	ENST00000360203	NM_001283009.1	96	-/GCT	3/35	1	2	FACETS	0.524	0.465	0.587	0.524	0.465	0.587	SUBCLONAL	1	FALSE	1	0.645648262059303	2		452	508	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574522	41574522	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	253	695	0	ENST00000263253.7:c.6810del	p.Ser2271ProfsTer8	p.S2271Pfs*8	ENST00000263253	NM_001429.3	2269	atG/at	31/31	1	2	FACETS	0.956	0.897	1	0.956	0.897	1	CLONAL	1	FALSE	1	0.645648262059303	2		695	820	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928347	69928347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	186	504	2	ENST00000352241.4:c.167G>A	p.Arg56His	p.R56H	ENST00000352241	NM_198159.2	56	cGc/cAc	2/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.645648262059303	2		506	526	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430202	181430202	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	142	416	0	ENST00000325404.1:c.59del	p.Gly20AlafsTer26	p.G20Afs*26	ENST00000325404	NM_003106.3	18	tcG/tc	1/1	1	2	FACETS	0.956	0.878	1	0.956	0.878	1	CLONAL	1	FALSE	1	0.645648262059303	2		416	460	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526227	189526227	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	269	731	0	ENST00000264731.3:c.491C>A	p.Ala164Asp	p.A164D	ENST00000264731	NM_003722.4	164	gCc/gAc	4/14	1	2	FACETS	0.975	0.917	1	0.975	0.917	1	CLONAL	1	FALSE	1	0.645648262059303	2		731	855	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156139	106156139	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755979073	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	124	393	0	ENST00000380013.4:c.1040C>T	p.Ala347Val	p.A347V	ENST00000380013	NM_001127208.2	347	gCg/gTg	3/11	1	2	FACETS	0.859	0.783	0.938	0.859	0.783	0.938	CLONAL	1	FALSE	1	0.645648262059303	2		393	447	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867540	35867541	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs869312857	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	93	304	2	ENST00000303115.3:c.361dup	p.Ile121AsnfsTer8	p.I121Nfs*8	ENST00000303115	NM_002185.3	118	-/A	3/8	1	2	FACETS	0.915	0.822	1	0.915	0.822	1	CLONAL	1	FALSE	1	0.645648262059303	2		306	315	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	120	368	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	1	2	FACETS	0.832	0.756	0.91	0.832	0.756	0.91	CLONAL	1	FALSE	1	0.645648262059303	2		368	447	SUCCESS
APC	324	MSKCC	GRCh37	5	112175621	112175622	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	111	331	0	ENST00000257430.4:c.4333dup	p.Thr1445AsnfsTer10	p.T1445Nfs*10	ENST00000257430	NM_000038.5	1444	caa/cAaa	16/16	1	2	FACETS	0.825	0.747	0.906	0.825	0.747	0.906	CLONAL	1	FALSE	1	0.645648262059303	2		331	417	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056237	26056245	+	inframe_deletion	In_Frame_Del	DEL	CTTCTTGGG	CTTCTTGGG	-	rs749190253	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	147	523	0	ENST00000343677.2:c.412_420del	p.Pro138_Lys140del	p.P138_K140del	ENST00000343677	NM_005319.3	138	CCCAAGAAG/-	1/1	1	2	FACETS	0.717	0.657	0.78	0.717	0.657	0.78	SUBCLONAL	1	FALSE	1	0.645648262059303	2		523	635	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183057	32183057	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	288	753	0	ENST00000375023.3:c.1967del	p.Pro656LeufsTer37	p.P656Lfs*37	ENST00000375023	NM_004557.3	656	cCt/ct	12/30	1	2	FACETS	0.917	0.864	0.971	0.917	0.864	0.971	CLONAL	1	FALSE	1	0.645648262059303	2		753	973	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015704	112015704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1230972545	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	240	547	1	ENST00000368678.4:c.1138C>T	p.Arg380Cys	p.R380C	ENST00000368678		380	Cgc/Tgc	11/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.645648262059303	2		548	711	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099333	157099356	+	inframe_deletion	In_Frame_Del	DEL	CCACCACCACCACCACCATGCCCA	CCACCACCACCACCACCATGCCCA	-	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	74	453	0	ENST00000346085.5:c.275_298del	p.His92_His99del	p.H92_H99del	ENST00000346085	NM_020732.3	90	gcCCACCACCACCACCACCATGCCCAc/gcc	1/20	1	2	FACETS	0.495	0.435	0.56	0.495	0.435	0.56	SUBCLONAL	1	FALSE	1	0.645648262059303	2		453	463	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781225	161781225	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1801334	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	171	579	0	ENST00000366898.1:c.1180G>A	p.Asp394Asn	p.D394N	ENST00000366898	NM_004562.2	394	Gat/Aat	11/12	1	2	FACETS	0.814	0.751	0.878	0.814	0.751	0.878	CLONAL	1	FALSE	1	0.645648262059303	2		579	651	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760307	133760307	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	210	703	0	ENST00000318560.5:c.2630G>T	p.Arg877Met	p.R877M	ENST00000318560	NM_005157.4	877	aGg/aTg	11/11	1	2	FACETS	0.965	0.9	1	0.965	0.9	1	CLONAL	1	FALSE	1	0.645648262059303	2		703	674	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430386	47430386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs979276829	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	303	426	0	ENST00000377045.4:c.1661G>A	p.Arg554Gln	p.R554Q	ENST00000377045	NM_001654.4	554	cGg/cAg	15/16	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	FALSE	0	0.645648262059303	1		426	466	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	199	355	0	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	0	0.645648262059303	1		355	340	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982123	93982123	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	27	432	1	ENST00000369303.4:c.1342G>T	p.Gly448Ter	p.G448*	ENST00000369303	NM_004440.3	448	Gga/Tga	6/17	1	2	FACETS	0.181	0.143	0.224	0.181	0.143	0.224	SUBCLONAL	1	FALSE	1	0.645648262059303	2		433	463	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	110	431	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.94	0.848	1	0.94	0.848	1	CLONAL	1	TRUE	1	0.437532562758054	2		431	535	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911311	29911311	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs199474579	NA	P-0049763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	98	441	1	ENST00000376809.5:c.610C>T	p.Gln204Ter	p.Q204*	ENST00000376809	NM_002116.7	204	Cag/Tag	3/8	0.417754103252335	1	FACETS	0.522	0.466	0.582	0.522	0.466	0.582	SUBCLONAL	1	TRUE	0	0.437532562758054	1		442	670	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438169	56438169	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	303	727	0	ENST00000407977.2:c.824G>T	p.Cys275Phe	p.C275F	ENST00000407977		275	tGt/tTt	7/10	0.437532562758054	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.437532562758054	1		727	962	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911752	32911752	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs80359379	NA	P-0049763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	117	468	0	ENST00000380152.3:c.3263del	p.Pro1088LeufsTer16	p.P1088Lfs*16	ENST00000380152		1087	aCc/ac	11/27	1	2	FACETS	0.948	0.858	1	0.948	0.858	1	CLONAL	1	TRUE	1	0.437532562758054	2		468	564	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575103	48575103	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	108	327	0	ENST00000342988.3:c.297G>C	p.Trp99Cys	p.W99C	ENST00000342988	NM_005359.5	99	tgG/tgC	3/12	0.417754103252335	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.437532562758054	1		327	383	SUCCESS
APC	324	MSKCC	GRCh37	5	112178625	112178646	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAAGCTCCAAGCCCAACCTT	AAGAAGCTCCAAGCCCAACCTT	-	novel	NA	P-0049763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	104	335	0	ENST00000257430.4:c.7340_7361del	p.Ala2447GlufsTer31	p.A2447Efs*31	ENST00000257430	NM_000038.5	2445	aAAGAAGCTCCAAGCCCAACCTTa/aa	16/16	0.437532562758054	1	FACETS	0.913	0.823	1	0.913	0.823	1	CLONAL	1	TRUE	0	0.437532562758054	1		335	407	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106789	27106789	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1553153770	NA	P-0049764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	220	729	0	ENST00000324856.7:c.6400C>G	p.Leu2134Val	p.L2134V	ENST00000324856	NM_006015.4	2134	Ctg/Gtg	20/20	0.477014508586136	1	FACETS	0.942	0.879	1	0.942	0.879	1	CLONAL	1	TRUE	0	0.477014508586136	1		729	746	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205254	61205281	+	frameshift_variant	Frame_Shift_Del	DEL	CCAAAAGAGCCCGCCTGCTCTATGAGAG	CCAAAAGAGCCCGCCTGCTCTATGAGAG	-	novel	NA	P-0049764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	49	509	0	ENST00000301761.2:c.195_222del	p.Lys66GlufsTer23	p.K66Efs*23	ENST00000301761	NM_017841.2	65	aCCAAAAGAGCCCGCCTGCTCTATGAGAGc/ac	2/4	1	2	FACETS	0.271	0.229	0.318	0.271	0.229	0.318	SUBCLONAL	1	TRUE	1	0.477014508586136	2		509	757	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233378	69233378	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	98	231	0	ENST00000462284.1:c.1243G>C	p.Glu415Gln	p.E415Q	ENST00000462284	NM_002392.5	415	Gaa/Caa	11/11	0.477014508586136	1	FACETS	0.834	0.751	0.922	0.834	0.751	0.922	CLONAL	1	TRUE	0	0.477014508586136	1		231	375	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569813	95569813	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	109	396	0	ENST00000393063.1:c.3920G>T	p.Ser1307Ile	p.S1307I	ENST00000393063	NM_030621.3	1307	aGt/aTt	22/28	0.477014508586136	1	FACETS	0.994	0.902	1	0.994	0.902	1	CLONAL	1	TRUE	0	0.477014508586136	1		396	350	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41209095	41209095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs80357123	NA	P-0049764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	163	505	0	ENST00000357654.3:c.5251C>T	p.Arg1751Ter	p.R1751*	ENST00000357654	NM_007294.3	1751	Cga/Tga	19/23	0.477014508586136	1	FACETS	0.875	0.807	0.945	0.875	0.807	0.945	CLONAL	1	TRUE	0	0.477014508586136	1		505	595	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266965	18266965	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	140	542	2	ENST00000222254.8:c.280del	p.Arg94AlafsTer36	p.R94Afs*36	ENST00000222254	NM_005027.3	92	ggC/gg	2/16	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.477014508586136	2		544	584	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383617	42383617	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1409146033	NA	P-0049764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	158	567	0	ENST00000221972.3:c.392G>C	p.Arg131Thr	p.R131T	ENST00000221972	NM_021601.3	131	aGg/aCg	3/5	0.298097119734692	1	FACETS	0.754	0.693	0.817	0.754	0.693	0.817	SUBCLONAL	1	TRUE	0	0.477014508586136	1		567	669	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191378	185191378	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	209	702	0	ENST00000265026.3:c.2259G>C	p.Arg753Ser	p.R753S	ENST00000265026	NM_004721.4	753	agG/agC	11/14	1	2	FACETS	0.931	0.865	1	0.931	0.865	1	CLONAL	1	TRUE	1	0.477014508586136	2		702	941	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427730	49427732	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0049766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	67	673	0	ENST00000301067.7:c.10756_10758del	p.Lys3586del	p.K3586del	ENST00000301067	NM_003482.3	3586	AAG/-	39/54	1	2	FACETS	0.847	0.734	0.969	0.847	0.734	0.969	CLONAL	1	TRUE	1	0.17	2		673	931	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	435	148	0				ENST00000310581	NM_198253.2	-/1132			0.702375560952075	5	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	2	0.702375560952075	5		148	820	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0049767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	207	292	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.560036229576472	2	FACETS	0.864	0.819	0.909	0.864	0.819	0.909	CLONAL	2	TRUE	0	0.702375560952075	2		292	341	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0049767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	134	361	2	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	0.443896739358843	5	FACETS	1	0.947	1	0.353	0.321	0.387	CLONAL	1	TRUE	2	0.702375560952075	5		363	740	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880257	37880257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	519	421	0	ENST00000269571.5:c.2301C>G	p.Ile767Met	p.I767M	ENST00000269571		767	atC/atG	19/27	0.626676725344566	3	FACETS	0.988	0.962	1	0.988	0.962	1	CLONAL	3	TRUE	0	0.702375560952075	3		421	674	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	558	755	0	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	0.258562933145607	5	FACETS	1	0.995	1	0.496	0.477	0.515	INDETERMINATE	2	TRUE	0	0.702375560952075	5		755	1316	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104322	2104322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	365	599	0	ENST00000219476.3:c.362C>T	p.Ala121Val	p.A121V	ENST00000219476	NM_000548.3	121	gCc/gTc	5/42	0.187638007151168	2	FACETS	1	0.995	1	0.674	0.643	0.705	INDETERMINATE	1	TRUE	0	0.702375560952075	2		599	771	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0049767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	1252	705	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.58866597667876	4	FACETS	0.992	0.978	1			1	CLONAL	4	TRUE	NA	0.702375560952075	4		705	1529	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679547	86679547	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	127	347	0	ENST00000274376.6:c.2708G>T	p.Arg903Leu	p.R903L	ENST00000274376	NM_002890.2	903	cGa/cTa	21/25	1	2	FACETS	0.82	0.749	0.894	0.82	0.749	0.894	CLONAL	1	TRUE	1	0.702375560952075	2		347	441	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193202153	193202153	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	167	297	0	ENST00000367435.3:c.1185A>C	p.Gln395His	p.Q395H	ENST00000367435	NM_024529.4	395	caA/caC	14/17	0.443896739358843	5	FACETS	0.784	0.723	0.846	0.522	0.482	0.564	SUBCLONAL	2	TRUE	2	0.702375560952075	5		297	623	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659858	88659858	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	151	338	0	ENST00000372037.3:c.505A>C	p.Ile169Leu	p.I169L	ENST00000372037	NM_004329.2	169	Atc/Ctc	7/13	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.702375560952075	2		338	403	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219201	94219201	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0049767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	60	372	0	ENST00000323929.3:c.203C>G	p.Ser68Ter	p.S68*	ENST00000323929	NM_005591.3	68	tCa/tGa	4/20	0.702375560952075	3	FACETS	0.41	0.353	0.472	0.205	0.176	0.236	SUBCLONAL	1	TRUE	1	0.702375560952075	3		372	563	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94906451	94906451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751654999	NA	P-0049767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	190	447	0	ENST00000536441.1:c.1447G>A	p.Ala483Thr	p.A483T	ENST00000536441	NM_144665.3	483	Gct/Act	10/10	0.702375560952075	3	FACETS	1	0.971	1	0.543	0.504	0.583	CLONAL	1	TRUE	1	0.702375560952075	3		447	673	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355750	73355750	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	100	665	0	ENST00000377767.4:c.221T>C	p.Leu74Pro	p.L74P	ENST00000377767	NM_014953.3	74	cTg/cCg	1/21	0.258562933145607	5	FACETS	0.559	0.498	0.624	0.112	0.099	0.125	INDETERMINATE	1	TRUE	0	0.702375560952075	5		665	1046	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645585	215645585	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	41	520	0	ENST00000260947.4:c.1013C>T	p.Thr338Ile	p.T338I	ENST00000260947	NM_000465.2	338	aCc/aTc	4/11	0.702375560952075	2	FACETS	0.171	0.142	0.204	0.086	0.071	0.102	SUBCLONAL	1	TRUE	0	0.702375560952075	2		520	682	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566438	41566438	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	214	348	0	ENST00000263253.7:c.4315C>G	p.Pro1439Ala	p.P1439A	ENST00000263253	NM_001429.3	1439	Cca/Gca	27/31	0.260265459289145	4	FACETS	0.91	0.852	0.969	0.91	0.852	0.969	INDETERMINATE	2	TRUE	2	0.702375560952075	4		348	570	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72842089	72842089	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	207	247	0	ENST00000325599.8:c.1159T>A	p.Cys387Ser	p.C387S	ENST00000325599	NM_018130.2	387	Tgt/Agt	10/11	0.20520204880503	5	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.702375560952075	5		247	496	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024096	112024096	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1461865526	NA	P-0049767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	154	393	0	ENST00000368678.4:c.689A>G	p.His230Arg	p.H230R	ENST00000368678		230	cAt/cGt	7/13	0.197911004206937	3	FACETS	1	0.975	1	0.572	0.527	0.619	INDETERMINATE	1	TRUE	1	0.702375560952075	3		393	518	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041405	47041405	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	617	337	0	ENST00000377604.3:c.1753del	p.Gln585ArgfsTer119	p.Q585Rfs*119	ENST00000377604	NM_001204468.1	583	gaC/ga	16/24	0.58866597667876	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.702375560952075	2		337	774	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	98	431	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.328448461066409	2		431	583	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0049768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	162	498	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.328448461066409	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.328448461066409	1		498	757	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0049768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	57	367	7	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.732	0.629	0.844	0.732	0.629	0.844	SUBCLONAL	1	TRUE	1	0.328448461066409	2		374	474	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368208	45368208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	147	362	10	ENST00000262160.6:c.1394G>A	p.Ser465Asn	p.S465N	ENST00000262160	NM_005901.5	465	aGc/aAc	11/11	1	2	FACETS	0.997	0.918	1	1	0.992	1	CLONAL	2	TRUE	1	0.328448461066409	2		372	449	SUCCESS
APC	324	MSKCC	GRCh37	5	112175530	112175530	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	86	229	0	ENST00000257430.4:c.4240del	p.Val1414Ter	p.V1414*	ENST00000257430	NM_000038.5	1413	atG/at	16/16	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.328448461066409	2		229	482	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101750	71101751	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	47	232	3	ENST00000318789.4:c.447dup	p.Gln150ThrfsTer20	p.Q150Tfs*20	ENST00000318789	NM_032682.5	149	-/A	9/21	1	2	FACETS	0.793	0.671	0.926	0.793	0.671	0.926	CLONAL	1	TRUE	1	0.328448461066409	2		235	361	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119966	70120018	+	frameshift_variant	Frame_Shift_Del	DEL	GCACCGCGGCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAG	GCACCGCGGCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAG	-	novel	NA	P-0049768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	55	539	0	ENST00000245479.2:c.970_1022del	p.Thr324AlafsTer236	p.T324Afs*236	ENST00000245479	NM_000346.3	323	aGCACCGCGGCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAG/a	3/3	1	2	FACETS	0.521	0.445	0.604	0.521	0.445	0.604	SUBCLONAL	1	TRUE	1	0.328448461066409	2		539	643	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027160	49027161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAAGG	novel	NA	P-0049768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	145	391	9	ENST00000267163.4:c.1729_1733dup	p.Asp578GlufsTer35	p.D578Efs*35	ENST00000267163	NM_000321.2	576	tca/tcAAAGGa	18/27	0.326899642892762	2	FACETS	0.931	0.856	1	0.931	0.856	1	CLONAL	2	TRUE	0	0.328448461066409	2		400	474	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519231	137519231	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	23	441	0	ENST00000367739.4:c.1407T>A	p.Asp469Glu	p.D469E	ENST00000367739	NM_000416.2	469	gaT/gaA	7/7	1	2	FACETS	0.38	0.296	0.477	0.38	0.296	0.477	SUBCLONAL	1	TRUE	1	0.32568482875735	2		441	372	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	46	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.794	0.669	0.931	0.794	0.669	0.931	CLONAL	1	TRUE	1	0.259264653389396	2		148	447	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0049773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	142	445	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.249843820857648	3	FACETS	0.903	0.825	0.985	0.903	0.825	0.985	CLONAL	2	TRUE	1	0.259264653389396	3		445	685	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0049773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	66	589	1	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	1	2	FACETS	0.719	0.623	0.823	0.719	0.623	0.823	SUBCLONAL	1	TRUE	1	0.259264653389396	2		590	708	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790165	40790165	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	88	522	0	ENST00000373198.4:c.2566G>A	p.Glu856Lys	p.E856K	ENST00000373198	NM_133170.3	856	Gag/Aag	18/32	1	2	FACETS	0.915	0.81	1	0.915	0.81	1	CLONAL	1	TRUE	1	0.259264653389396	2		522	742	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925351	114925351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	89	584	0	ENST00000543371.1:c.1429G>A	p.Gly477Ser	p.G477S	ENST00000543371	NM_001198531.1	477	Ggc/Agc	14/14	1	2	FACETS	0.84	0.744	0.943	0.84	0.744	0.943	CLONAL	1	TRUE	1	0.259264653389396	2		584	817	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715665	18715665	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	37	237	0	ENST00000266497.5:c.3496C>T	p.Pro1166Ser	p.P1166S	ENST00000266497		1166	Cct/Tct	25/31	0.249843820857648	3	FACETS	0.858	0.708	1	0.429	0.354	0.512	CLONAL	1	TRUE	1	0.259264653389396	3		237	376	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895650	28895650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	64	446	0	ENST00000282397.4:c.3124G>A	p.Gly1042Ser	p.G1042S	ENST00000282397	NM_002019.4	1042	Ggc/Agc	23/30	1	2	FACETS	0.805	0.697	0.923	0.805	0.697	0.923	CLONAL	1	TRUE	1	0.259264653389396	2		446	613	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798334	42798334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1250296812	NA	P-0049773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	113	702	0	ENST00000575354.2:c.4205C>T	p.Ser1402Leu	p.S1402L	ENST00000575354	NM_015125.3	1402	tCa/tTa	18/20	1	2	FACETS	0.919	0.825	1	0.919	0.825	1	CLONAL	1	TRUE	1	0.259264653389396	2		702	949	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426668	212426668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	70	479	0	ENST00000342788.4:c.2447G>A	p.Gly816Glu	p.G816E	ENST00000342788	NM_005235.2	816	gGa/gAa	20/28	1	2	FACETS	0.794	0.692	0.905	0.794	0.692	0.905	CLONAL	1	TRUE	1	0.259264653389396	2		479	680	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530049	212530049	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	35	219	0	ENST00000342788.4:c.1870G>A	p.Gly624Arg	p.G624R	ENST00000342788	NM_005235.2	624	Ggg/Agg	15/28	1	2	FACETS	0.833	0.685	0.999	0.833	0.685	0.999	CLONAL	1	TRUE	1	0.259264653389396	2		219	324	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612094	189612094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	64	562	0	ENST00000264731.3:c.1846C>T	p.Leu616Phe	p.L616F	ENST00000264731	NM_003722.4	616	Ctc/Ttc	14/14	1	2	FACETS	0.703	0.608	0.807	0.703	0.608	0.807	SUBCLONAL	1	TRUE	1	0.259264653389396	2		562	702	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984906	55984906	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	76	417	0	ENST00000263923.4:c.223G>A	p.Glu75Lys	p.E75K	ENST00000263923	NM_002253.2	75	Gag/Aag	3/30	1	2	FACETS	0.845	0.741	0.957	0.845	0.741	0.957	CLONAL	1	TRUE	1	0.259264653389396	2		417	694	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128305426	128305427	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0049773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	78	442	2	ENST00000265960.3:c.869_870delinsTT	p.Ser290Phe	p.S290F	ENST00000265960	NM_001006617.1	290	tCC/tTT	7/12	1	2	FACETS	0.964	0.848	1	0.964	0.848	1	CLONAL	1	TRUE	1	0.259264653389396	2		444	624	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs104886003	NA	P-0049774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	21	452	0	ENST00000263967.3:c.1633G>C	p.Glu545Gln	p.E545Q	ENST00000263967	NM_006218.2	545	Gag/Cag	10/21	1	2	FACETS	0.465	0.357	0.591	0.465	0.357	0.591	SUBCLONAL	1	TRUE	1	0.21	2		452	430	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0049774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	13	431	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.375	0.267	0.508	0.375	0.267	0.508	SUBCLONAL	1	TRUE	1	0.21	2		431	330	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121909229	NA	P-0049774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	57	410	0	ENST00000371953.3:c.389G>C	p.Arg130Pro	p.R130P	ENST00000371953	NM_000314.4	130	cGa/cCa	5/9	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.21	2		410	445	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121913370	NA	P-0049774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	8	285	0	ENST00000288602.6:c.1742A>G	p.Asn581Ser	p.N581S	ENST00000288602	NM_004333.4	581	aAt/aGt	15/18	1	2	FACETS	0.323	0.207	0.473	0.323	0.207	0.473	SUBCLONAL	1	TRUE	1	0.21	2		285	236	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545687	63545687	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1567763495	NA	P-0049774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	55	546	0	ENST00000307078.5:c.907T>C	p.Ser303Pro	p.S303P	ENST00000307078	NM_004655.3	303	Tcc/Ccc	3/11	1	2	FACETS	0.798	0.682	0.926	0.798	0.682	0.926	CLONAL	1	TRUE	1	0.21	2		546	656	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589560	67589598	+	inframe_deletion	In_Frame_Del	DEL	TATTGAAGCTGTAGGGAAAAAATTACATGAATATAACAC	TATTGAAGCTGTAGGGAAAAAATTACATGAATATAACAC	-	novel	NA	P-0049774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	17	212	0	ENST00000274335.5:c.1324_1362del	p.Ile442_Thr454del	p.I442_T454del	ENST00000274335		441	aaTATTGAAGCTGTAGGGAAAAAATTACATGAATATAACACt/aat	10/15	1	2	FACETS	0.87	0.652	1	0.87	0.652	1	CLONAL	1	TRUE	1	0.21	2		212	186	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220295	55220295	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	99	812	0	ENST00000275493.2:c.685A>C	p.Ser229Arg	p.S229R	ENST00000275493	NM_005228.3	229	Agt/Cgt	6/28	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.21	2		812	869	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	87	431	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.909	0.812	1	0.909	0.812	1	CLONAL	1	TRUE	1	0.561381383432843	2		431	341	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	199	419	0	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.561381383432843	2		419	690	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913396	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	126	300	0	ENST00000349496.5:c.95A>T	p.Asp32Val	p.D32V	ENST00000349496	NM_001904.3	32	gAc/gTc	3/15	1	2	FACETS	0.972	0.886	1	0.972	0.886	1	CLONAL	1	TRUE	1	0.561381383432843	2		300	462	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	249	608	1	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.561381383432843	2		609	836	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	237	699	3	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.561381383432843	2		702	825	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	212	642	0	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.561381383432843	2		642	751	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210755	5210755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1157608522	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	256	840	0	ENST00000357368.4:c.5296C>T	p.Arg1766Cys	p.R1766C	ENST00000357368	NM_002850.3	1766	Cgc/Tgc	34/38	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.561381383432843	2		840	876	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	225	533	0	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.561381383432843	2		533	763	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	106	286	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.561381383432843	2		286	338	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165213	47165213	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	73	337	0	ENST00000409792.3:c.913del	p.Thr305GlnfsTer35	p.T305Qfs*35	ENST00000409792	NM_014159.6	305	Aca/ca	3/21	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.561381383432843	2		337	241	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561423	9561423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201131316	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	152	504	0	ENST00000353224.5:c.359C>T	p.Ala120Val	p.A120V	ENST00000353224	NM_177990.2	120	gCg/gTg	4/10	1	2	FACETS	0.94	0.864	1	0.94	0.864	1	CLONAL	1	TRUE	1	0.561381383432843	2		504	576	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	84	446	3	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.88	0.784	0.981	0.88	0.784	0.981	CLONAL	1	TRUE	1	0.561381383432843	2		449	340	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209631	98209631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56102979	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	111	741	1	ENST00000331920.6:c.3907C>T	p.Arg1303Cys	p.R1303C	ENST00000331920	NM_000264.3	1303	Cgc/Tgc	23/24	1	2	FACETS	0.567	0.51	0.628	0.567	0.51	0.628	SUBCLONAL	1	TRUE	1	0.561381383432843	2		742	697	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622138	1622138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370087169	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	268	947	0	ENST00000344749.5:c.737C>T	p.Pro246Leu	p.P246L	ENST00000344749	NM_001136139.2	246	cCg/cTg	10/19	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.561381383432843	2		947	897	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099579	157099579	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1562376341	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	24	134	0	ENST00000346085.5:c.521del	p.Pro174ArgfsTer6	p.P174Rfs*6	ENST00000346085	NM_020732.3	172	gaC/ga	1/20	1	2	FACETS	0.382	0.3	0.475	0.382	0.3	0.475	SUBCLONAL	1	TRUE	1	0.561381383432843	2		134	224	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439700	220439701	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	192	929	2	ENST00000243786.2:c.562_563dup	p.Leu189CysfsTer2	p.L189Cfs*2	ENST00000243786	NM_002191.3	185	gct/gCTct	2/2	1	2	FACETS	0.761	0.704	0.82	0.761	0.704	0.82	SUBCLONAL	1	TRUE	1	0.561381383432843	2		931	899	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526513	66526513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	159	451	1	ENST00000358598.2:c.1069C>T	p.Arg357Cys	p.R357C	ENST00000358598	NM_212471.2	357	Cgt/Tgt	11/11	1	2	FACETS	0.952	0.877	1	0.952	0.877	1	CLONAL	1	TRUE	1	0.561381383432843	2		452	595	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955064	17955064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749334592	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	258	870	1	ENST00000458235.1:c.163G>A	p.Val55Met	p.V55M	ENST00000458235	NM_000215.3	55	Gtg/Atg	2/24	1	2	FACETS	0.99	0.929	1	0.99	0.929	1	CLONAL	1	TRUE	1	0.561381383432843	2		871	928	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859899	151859899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148585727	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	106	426	0	ENST00000262189.6:c.10763C>T	p.Ser3588Leu	p.S3588L	ENST00000262189	NM_170606.2	3588	tCg/tTg	43/59	1	2	FACETS	0.942	0.851	1	0.942	0.851	1	CLONAL	1	TRUE	1	0.561381383432843	2		426	401	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	235	933	3	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	0.983	0.919	1	0.983	0.919	1	CLONAL	1	TRUE	1	0.561381383432843	2		936	852	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788633	3788633	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1271038944	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	114	382	0	ENST00000262367.5:c.4321C>T	p.Arg1441Trp	p.R1441W	ENST00000262367	NM_004380.2	1441	Cgg/Tgg	26/31	1	2	FACETS	0.911	0.825	1	0.911	0.825	1	CLONAL	1	TRUE	1	0.561381383432843	2		382	446	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976689	55976689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747477930	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	124	486	2	ENST00000263923.4:c.1136C>T	p.Ala379Val	p.A379V	ENST00000263923	NM_002253.2	379	gCg/gTg	9/30	1	2	FACETS	0.98	0.893	1	0.98	0.893	1	CLONAL	1	TRUE	1	0.561381383432843	2		488	451	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984856	9984856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	191	455	0	ENST00000330684.3:c.1109G>A	p.Arg370Gln	p.R370Q	ENST00000330684	NM_001134407.1	370	cGg/cAg	4/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.561381383432843	2		455	620	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643281	38643281	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1172820756	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	82	468	0	ENST00000299084.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000299084	NM_152594.2	251	Cga/Tga	7/7	1	2	FACETS	0.88	0.783	0.982	0.88	0.783	0.982	CLONAL	1	TRUE	1	0.561381383432843	2		468	332	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845625	72845625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200095250	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	229	708	1	ENST00000268489.5:c.3715C>T	p.Arg1239Trp	p.R1239W	ENST00000268489	NM_006885.3	1239	Cgg/Tgg	7/10	1	2	FACETS	0.985	0.921	1	0.985	0.921	1	CLONAL	1	TRUE	1	0.561381383432843	2		709	828	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943374	71943374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141305290	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	161	530	0	ENST00000298229.2:c.1706C>T	p.Thr569Met	p.T569M	ENST00000298229	NM_001567.3	569	aCg/aTg	14/28	1	2	FACETS	0.872	0.802	0.944	0.872	0.802	0.944	CLONAL	1	TRUE	1	0.561381383432843	2		530	658	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447553	187447553	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs189037992	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	213	648	1	ENST00000232014.4:c.640C>T	p.Arg214Trp	p.R214W	ENST00000232014	NM_001130845.1	214	Cgg/Tgg	5/10	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.561381383432843	2		649	755	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669526	88669526	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	130	429	0	ENST00000360948.2:c.1372C>T	p.Arg458Ter	p.R458*	ENST00000360948	NM_001012338.2	458	Cga/Tga	12/19	1	2	FACETS	0.949	0.866	1	0.949	0.866	1	CLONAL	1	TRUE	1	0.561381383432843	2		429	488	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36014578	36014578	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	153	561	0	ENST00000358208.4:c.350+1G>A		p.X117_splice	ENST00000358208		117			1	2	FACETS	0.986	0.907	1	0.986	0.907	1	CLONAL	1	TRUE	1	0.561381383432843	2		561	553	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606839	43606839	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs752322996	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	262	878	0	ENST00000355710.3:c.1448A>G	p.Tyr483Cys	p.Y483C	ENST00000355710	NM_020975.4	483	tAc/tGc	7/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.561381383432843	2		878	931	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357114	89357114	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	259	903	0	ENST00000301030.4:c.520C>T	p.Arg174Ter	p.R174*	ENST00000301030	NM_001256183.1	174	Cga/Tga	6/13	1	2	FACETS	0.987	0.926	1	0.987	0.926	1	CLONAL	1	TRUE	1	0.561381383432843	2		903	935	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40872414	40872414	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs541410310	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	184	548	1	ENST00000428826.2:c.541G>A	p.Asp181Asn	p.D181N	ENST00000428826		181	Gat/Aat	7/21	1	2	FACETS	0.961	0.891	1	0.961	0.891	1	CLONAL	1	TRUE	1	0.561381383432843	2		549	682	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223421	2223421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	206	690	0	ENST00000398665.3:c.3532G>A	p.Ala1178Thr	p.A1178T	ENST00000398665	NM_032482.2	1178	Gca/Aca	25/28	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.561381383432843	2		690	697	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7141749	7141749	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	210	652	0	ENST00000302850.5:c.2621C>A	p.Pro874Gln	p.P874Q	ENST00000302850	NM_000208.2	874	cCg/cAg	13/22	1	2	FACETS	0.929	0.865	0.996	0.929	0.865	0.996	CLONAL	1	TRUE	1	0.561381383432843	2		652	805	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934713	49934713	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs780150009	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	245	673	1	ENST00000296474.3:c.2183G>A	p.Arg728Gln	p.R728Q	ENST00000296474	NM_002447.2	728	cGg/cAg	7/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.561381383432843	2		674	805	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437821	52437821	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	216	726	1	ENST00000460680.1:c.1340T>A	p.Val447Asp	p.V447D	ENST00000460680	NM_004656.3	447	gTc/gAc	13/17	1	2	FACETS	0.897	0.835	0.96	0.897	0.835	0.96	CLONAL	1	TRUE	1	0.561381383432843	2		727	858	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722154	176722154	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	204	670	0	ENST00000439151.2:c.7785G>T	p.Lys2595Asn	p.K2595N	ENST00000439151	NM_022455.4	2595	aaG/aaT	23/23	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.561381383432843	2		670	702	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510912	157510912	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	98	446	0	ENST00000346085.5:c.3688del	p.Arg1230GlufsTer14	p.R1230Efs*14	ENST00000346085	NM_020732.3	1229	ggA/gg	14/20	1	2	FACETS	0.751	0.673	0.833	0.751	0.673	0.833	SUBCLONAL	1	TRUE	1	0.561381383432843	2		446	465	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209260	98209260	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	223	798	0	ENST00000331920.6:c.4278G>T	p.Lys1426Asn	p.K1426N	ENST00000331920	NM_000264.3	1426	aaG/aaT	23/24	1	2	FACETS	0.982	0.917	1	0.982	0.917	1	CLONAL	1	TRUE	1	0.561381383432843	2		798	809	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900261	101900261	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	97	374	0	ENST00000374994.4:c.695A>C	p.Lys232Thr	p.K232T	ENST00000374994	NM_004612.2	232	aAg/aCg	4/9	1	2	FACETS	0.912	0.819	1	0.912	0.819	1	CLONAL	1	TRUE	1	0.561381383432843	2		374	379	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731458	47731460	+	missense_variant	Missense_Mutation	TNP	CCA	CCA	GCG	novel	NA	P-0049775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	34	142	0	ENST00000449228.1:c.332_334delinsCGC	p.Leu111_Ala112delinsProPro	p.L111_A112delinsPP	ENST00000449228	NM_001127240.2	111	cTGGcc/cCGCcc	2/4	1	2	FACETS	0.713	0.589	0.847	0.713	0.589	0.847	SUBCLONAL	1	TRUE	1	0.561381383432843	2		142	170	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577095	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519984	NA	P-0049776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	629	710	0	ENST00000269305.4:c.843C>G	p.Asp281Glu	p.D281E	ENST00000269305	NM_001126112.2	281	gaC/gaG	8/11	0.476098085155071	3	FACETS	0.867	0.839	0.895	0.867	0.839	0.895	CLONAL	3	TRUE	0	0.541481562449075	3		710	1135	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947603	48947603	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	26	354	0	ENST00000267163.4:c.1190C>A	p.Ser397Ter	p.S397*	ENST00000267163	NM_000321.2	397	tCa/tAa	12/27	0.462005437348784	1	FACETS	0.693	0.561	0.837	0.693	0.561	0.837	SUBCLONAL	1	TRUE	0	0.541481562449075	1		354	101	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589623	67589634	+	inframe_deletion	In_Frame_Del	DEL	ATATGATAGATT	ATATGATAGATT	-	novel	NA	P-0049776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	41	222	0	ENST00000274335.5:c.1392_1403del	p.Asp464_Tyr467del	p.D464_Y467del	ENST00000274335		462	gaATATGATAGATTa/gaa	10/15	0.496462273519286	2	FACETS	0.773	0.666	0.883	0.773	0.666	0.883	SUBCLONAL	2	TRUE	0	0.541481562449075	2		222	98	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551215	29551215	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs777414641	NA	P-0049776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	346	631	0	ENST00000389048.3:c.1414+1G>A		p.X472_splice	ENST00000389048	NM_004304.4	472			0.18836780750029	5	FACETS	1	0.987	1	0.744	0.706	0.784	INDETERMINATE	2	TRUE	2	0.541481562449075	5		631	1037	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104356906	104356906	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	170	555	0	ENST00000369902.3:c.766G>C	p.Asp256His	p.D256H	ENST00000369902	NM_016169.3	256	Gac/Cac	7/12	0.541481562449075	3	FACETS	0.801	0.736	0.869	0.401	0.368	0.435	CLONAL	1	TRUE	1	0.541481562449075	3		555	996	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884782	111884782	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	156	628	0	ENST00000341259.2:c.871G>C	p.Asp291His	p.D291H	ENST00000341259	NM_005475.2	291	Gac/Cac	4/8	0.188279190223337	6	FACETS	1	0.956	1	0.358	0.327	0.39	INDETERMINATE	1	TRUE	3	0.541481562449075	6		628	1119	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288864	15288864	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	89	263	0	ENST00000263388.2:c.3875C>G	p.Ser1292Cys	p.S1292C	ENST00000263388	NM_000435.2	1292	tCc/tGc	24/33	0.524254769291151	3	FACETS	0.768	0.682	0.859	0.384	0.341	0.43	SUBCLONAL	1	TRUE	1	0.541481562449075	3		263	544	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965334	25965334	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	125	679	0	ENST00000435504.4:c.3872C>G	p.Ser1291Cys	p.S1291C	ENST00000435504		1291	tCt/tGt	13/13	0.18836780750029	5	FACETS	0.755	0.682	0.833	0.252	0.227	0.278	INDETERMINATE	1	TRUE	2	0.541481562449075	5		679	1108	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198272754	198272754	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	46	505	0	ENST00000335508.6:c.1207G>C	p.Glu403Gln	p.E403Q	ENST00000335508	NM_012433.2	403	Gaa/Caa	9/25	0.328559847405439	6	FACETS	0.589	0.495	0.693			1	SUBCLONAL	1	TRUE	NA	0.541481562449075	6		505	601	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175822	24175822	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	177	654	0	ENST00000263121.7:c.1050C>G	p.Cys350Trp	p.C350W	ENST00000263121	NM_003073.3	350	tgC/tgG	8/9	0.201432919637361	5	FACETS	1	0.942	1	0.343	0.315	0.372	INDETERMINATE	1	TRUE	2	0.541481562449075	5		654	1152	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182274	38182274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1432	91	593	0	ENST00000396334.3:c.710C>T	p.Ser237Phe	p.S237F	ENST00000396334	NM_002468.4	237	tCt/tTt	4/5	0.541481562449075	6	FACETS	0.46	0.406	0.517			1	SUBCLONAL	1	TRUE	NA	0.541481562449075	6		593	1523	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504304	186504304	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	25	198	0	ENST00000323963.5:c.641C>G	p.Ser214Cys	p.S214C	ENST00000323963		214	tCt/tGt	7/11	0.370111847104506	5	FACETS	0.867	0.688	1	0.289	0.229	0.357	CLONAL	1	TRUE	2	0.541481562449075	5		198	193	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681073	117681073	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	76	472	0	ENST00000368508.3:c.3547G>C	p.Val1183Leu	p.V1183L	ENST00000368508	NM_002944.2	1183	Gtt/Ctt	23/43	0.464159338901316	3	FACETS	0.721	0.634	0.814	0.36	0.317	0.407	SUBCLONAL	1	TRUE	1	0.541481562449075	3		472	495	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411736	139411736	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs749085650	NA	P-0049776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	474	776	0	ENST00000277541.6:c.1543G>C	p.Glu515Gln	p.E515Q	ENST00000277541	NM_017617.3	515	Gag/Cag	9/34	0.535002826022385	2	FACETS	0.939	0.903	0.975	0.939	0.903	0.975	CLONAL	2	TRUE	0	0.541481562449075	2		776	932	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0049778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	72	490	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.676	0.59	0.77	0.676	0.59	0.77	SUBCLONAL	1	TRUE	1	0.264194725631204	2		490	806	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879885	37879885	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	48	1082	0	ENST00000269571.5:c.2180G>C	p.Gly727Ala	p.G727A	ENST00000269571		727	gGa/gCa	18/27	1	2	FACETS	0.418	0.352	0.491	0.418	0.352	0.491	SUBCLONAL	1	TRUE	1	0.264194725631204	2		1082	870	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0049778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	64	579	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	0.559	0.483	0.643	0.559	0.483	0.643	SUBCLONAL	1	TRUE	1	0.264194725631204	2		579	866	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842594	68842594	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0049778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	69	582	0	ENST00000261769.5:c.532-2A>G		p.X178_splice	ENST00000261769	NM_004360.3	178			1	2	FACETS	0.997	0.87	1	0.997	0.87	1	CLONAL	1	TRUE	1	0.264194725631204	2		582	524	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112496	2112496	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0049778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	47	873	0	ENST00000219476.3:c.1258-2A>G		p.X420_splice	ENST00000219476	NM_000548.3	420			1	2	FACETS	0.398	0.334	0.469	0.398	0.334	0.469	SUBCLONAL	1	TRUE	1	0.264194725631204	2		873	894	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171643	36171644	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0049778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	81	521	0	ENST00000300305.3:c.921dup	p.Ser308GlnfsTer292	p.S308Qfs*292	ENST00000300305		307	-/C	7/8	1	2	FACETS	0.972	0.857	1	0.972	0.857	1	CLONAL	1	TRUE	1	0.264194725631204	2		521	631	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0049779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	304	263	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.677777002227846	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.712391935551777	3		263	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0049779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	495	626	2	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	1	2	FACETS	0.984	0.942	1	0.984	0.942	1	CLONAL	1	TRUE	1	0.712391935551777	2		628	1412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057520000	NA	P-0049779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	517	1042	1	ENST00000269305.4:c.452C>G	p.Pro151Arg	p.P151R	ENST00000269305	NM_001126112.2	151	cCc/cGc	5/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.712391935551777	2		1043	1411	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467823	50467823	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	358	761	1	ENST00000331340.3:c.1058C>A	p.Pro353Gln	p.P353Q	ENST00000331340	NM_006060.4	353	cCg/cAg	8/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.712391935551777	2		762	963	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916825	48916825	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	98	393	0	ENST00000267163.4:c.355G>T	p.Glu119Ter	p.E119*	ENST00000267163	NM_000321.2	119	Gag/Tag	3/27	0.712391935551777	1	FACETS	0.832	0.759	0.905	0.832	0.759	0.905	CLONAL	1	TRUE	0	0.712391935551777	1		393	213	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974759	21974759	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	188	436	0	ENST00000304494.5:c.68del	p.Gly23ValfsTer3	p.G23Vfs*3	ENST00000304494	NM_000077.4	23	gGt/gt	1/3	0.712391935551777	1	FACETS	0.894	0.839	0.949	0.894	0.839	0.949	CLONAL	1	TRUE	0	0.712391935551777	1		436	380	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858568	9858568	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	204	604	0	ENST00000330684.3:c.2833G>T	p.Asp945Tyr	p.D945Y	ENST00000330684	NM_001134407.1	945	Gac/Tac	13/13	1	2	FACETS	0.994	0.929	1	0.994	0.929	1	CLONAL	1	TRUE	1	0.712391935551777	2		604	576	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509843	106509843	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	272	634	0	ENST00000359195.3:c.1837A>G	p.Arg613Gly	p.R613G	ENST00000359195	NM_002649.2	613	Aga/Gga	2/11	1	2	FACETS	0.974	0.918	1	0.974	0.918	1	CLONAL	1	TRUE	1	0.712391935551777	2		634	784	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395032	139395032	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049779-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	429	940	3	ENST00000277541.6:c.5906T>C	p.Val1969Ala	p.V1969A	ENST00000277541	NM_017617.3	1969	gTg/gCg	31/34	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.712391935551777	2		943	1152	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0049780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	71	341	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.215501097582353	2		341	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0049780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	98	706	0	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.215501097582353	2		706	802	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628737	21628737	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	59	342	0	ENST00000421138.2:c.971A>G	p.Gln324Arg	p.Q324R	ENST00000421138		324	cAg/cGg	10/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.215501097582353	2		342	447	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900290	101900290	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs863223814	NA	P-0049780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	55	402	0	ENST00000374994.4:c.724T>C	p.Trp242Arg	p.W242R	ENST00000374994	NM_004612.2	242	Tgg/Cgg	4/9	0.215501097582353	1	FACETS	0.891	0.763	1	0.891	0.763	1	CLONAL	1	TRUE	0	0.215501097582353	1		402	511	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0049782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	191	594	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.428383889580627	1	FACETS	0.443	0.41	0.477	0.443	0.41	0.477	SUBCLONAL	1	TRUE	0	0.696544209225946	1		594	807	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913283	NA	P-0049782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	176	365	0	ENST00000263967.3:c.3129G>T	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atT	21/21	0.373873836141879	3	FACETS	1	0.98	1	0.582	0.539	0.627	INDETERMINATE	1	TRUE	1	0.696544209225946	3		365	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0049782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	560	938	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	0.696544209225946	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.696544209225946	1		938	911	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0049784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	338	514	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.492504520425932	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.492504520425932	1		514	978	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	183	448	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	0.492504520425932	1	FACETS	0.909	0.843	0.977	0.909	0.843	0.977	CLONAL	1	TRUE	0	0.492504520425932	1		448	616	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874286	155874286	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs868208063	NA	P-0049784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	431	531	0	ENST00000368323.3:c.245T>G	p.Phe82Cys	p.F82C	ENST00000368323	NM_006912.5	82	tTt/tGt	5/6	0.193549083522262	1	FACETS	1	0.994	1	1	0.994	1	INDETERMINATE	1	TRUE	0	0.492504520425932	1		531	1066	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756556	756556	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0049784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	212	372	0	ENST00000314574.4:c.271+1del		p.X91_splice	ENST00000314574	NM_005433.3	91			0.492504520425932	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.492504520425932	1		372	575	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584612	187584612	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	196	540	1	ENST00000441802.2:c.3421G>T	p.Glu1141Ter	p.E1141*	ENST00000441802	NM_005245.3	1141	Gag/Tag	3/27	0.492504520425932	1	FACETS	0.916	0.852	0.982	0.916	0.852	0.982	CLONAL	1	TRUE	0	0.492504520425932	1		541	655	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0049785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	57	782	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.933	0.798	1	0.933	0.798	1	CLONAL	1	TRUE	1	0.13	2		787	940	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0049785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	15	302	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.39	0.283	0.519	0.39	0.283	0.519	SUBCLONAL	1	TRUE	1	0.13	2		302	592	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0049785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	39	523	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.803	0.664	0.96	0.803	0.664	0.96	CLONAL	1	TRUE	1	0.13	2		523	747	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371799	55371820	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCCGCGCTGGGCCCCGAG	GGCGGCCGCGCTGGGCCCCGAG	-	novel	NA	P-0049785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	12	152	0	ENST00000297316.4:c.499_520del	p.Leu167TrpfsTer213	p.L167Wfs*213	ENST00000297316	NM_022454.3	163	caGGCGGCCGCGCTGGGCCCCGAG/ca	2/2	1	2	FACETS	0.875	0.615	1	0.875	0.615	1	CLONAL	1	TRUE	1	0.13	2		152	211	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0049785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	49	347	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.13	2		347	676	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0049785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	22	523	1	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	1	2	FACETS	0.467	0.36	0.592	0.467	0.36	0.592	SUBCLONAL	1	TRUE	1	0.13	2		524	725	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0049785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	43	596	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.88	0.734	1	0.88	0.734	1	CLONAL	1	TRUE	1	0.13	2		596	752	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0049785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	69	848	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.957	0.831	1	0.957	0.831	1	CLONAL	1	TRUE	1	0.13	2		848	1109	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31369176	31369176	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760640013	NA	P-0049785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	53	611	0	ENST00000328111.2:c.160C>T	p.Arg54Ter	p.R54*	ENST00000328111	NM_006892.3	54	Cga/Tga	3/23	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.13	2		611	750	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119781	70119781	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1274036689	NA	P-0049785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	51	729	0	ENST00000245479.2:c.788del	p.Gly263AlafsTer16	p.G263Afs*16	ENST00000245479	NM_000346.3	261	gaG/ga	3/3	1	2	FACETS	0.911	0.772	1	0.911	0.772	1	CLONAL	1	TRUE	1	0.13	2		729	861	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347983	347983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760961378	NA	P-0049785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	66	860	6	ENST00000262320.3:c.1523del	p.Gly508ValfsTer197	p.G508Vfs*197	ENST00000262320	NM_003502.3	508	gGt/gt	6/11	1	2	FACETS	0.962	0.832	1	0.962	0.832	1	CLONAL	1	TRUE	1	0.13	2		866	1056	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993849	72993849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758323451	NA	P-0049785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	45	615	1	ENST00000268489.5:c.196G>A	p.Ala66Thr	p.A66T	ENST00000268489	NM_006885.3	66	Gcg/Acg	2/10	1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.13	2		616	689	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627257	86627257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458179717	NA	P-0049785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	24	385	0	ENST00000274376.6:c.632G>A	p.Arg211Gln	p.R211Q	ENST00000274376	NM_002890.2	211	cGg/cAg	2/25	1	2	FACETS	0.792	0.62	0.992	0.792	0.62	0.992	CLONAL	1	TRUE	1	0.13	2		385	466	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340356	8340356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs553232071	NA	P-0049785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	46	556	0	ENST00000356435.5:c.5240G>A	p.Arg1747His	p.R1747H	ENST00000356435		1747	cGt/cAt	31/35	1	2	FACETS	0.87	0.731	1	0.87	0.731	1	CLONAL	1	TRUE	1	0.13	2		556	813	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	63	915	5	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.862	0.743	0.993	0.862	0.743	0.993	CLONAL	1	TRUE	1	0.13	2		920	1124	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902297	50902297	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	57	925	0	ENST00000440232.2:c.193del	p.Val65LeufsTer11	p.V65Lfs*11	ENST00000440232	NM_002691.3	63	gaG/ga	2/27	1	2	FACETS	0.833	0.712	0.966	0.833	0.712	0.966	CLONAL	1	TRUE	1	0.13	2		925	1053	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484048	50484048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1319486448	NA	P-0049785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	45	669	2	ENST00000394963.4:c.898C>T	p.Arg300Cys	p.R300C	ENST00000394963	NM_003076.4	300	Cgc/Tgc	8/13	1	2	FACETS	0.807	0.676	0.953	0.807	0.676	0.953	CLONAL	1	TRUE	1	0.13	2		671	858	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693886	47693886	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	59	429	0	ENST00000233146.2:c.1600del	p.Arg534ValfsTer9	p.R534Vfs*9	ENST00000233146	NM_000251.2	534	Cgt/gt	10/16	1	2	FACETS	0.858	0.739	0.988	1	0.974	1	CLONAL	2	TRUE	1	0.13	2		429	529	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885299	111885299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200936167	NA	P-0049785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	45	645	0	ENST00000341259.2:c.1187C>T	p.Thr396Met	p.T396M	ENST00000341259	NM_005475.2	396	aCg/aTg	6/8	1	2	FACETS	0.892	0.748	1	0.892	0.748	1	CLONAL	1	TRUE	1	0.13	2		645	776	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16056679	16056680	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	29	446	0	ENST00000268712.3:c.762dup	p.Glu255Ter	p.E255*	ENST00000268712	NM_006311.3	254	-/T	7/46	1	2	FACETS	0.882	0.706	1	0.882	0.706	1	CLONAL	1	TRUE	1	0.13	2		446	506	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836396	89836396	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	42	665	0	ENST00000389301.3:c.2353G>T	p.Ala785Ser	p.A785S	ENST00000389301	NM_000135.2	785	Gct/Tct	26/43	1	2	FACETS	0.804	0.669	0.954	0.804	0.669	0.954	CLONAL	1	TRUE	1	0.13	2		665	804	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168941	11168941	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1458830964	NA	P-0049785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	38	544	2	ENST00000358026.2:c.4531C>T	p.Arg1511Cys	p.R1511C	ENST00000358026	NM_001128849.1	1511	Cgt/Tgt	32/36	1	2	FACETS	0.774	0.638	0.927	0.774	0.638	0.927	CLONAL	1	TRUE	1	0.13	2		546	755	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0049787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	111	632	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.177800351126936	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.177800351126936	2		632	542	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073506	8073506	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	39	523	0	ENST00000377482.5:c.1153A>C	p.Asn385His	p.N385H	ENST00000377482	NM_018948.3	385	Aat/Cat	4/4	1	2	FACETS	0.93	0.77	1	0.93	0.77	1	CLONAL	1	TRUE	1	0.14	2		523	599	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105688	27105688	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	28	438	0	ENST00000324856.7:c.5299G>T	p.Glu1767Ter	p.E1767*	ENST00000324856	NM_006015.4	1767	Gaa/Taa	20/20	1	2	FACETS	0.725	0.578	0.893	0.725	0.578	0.893	SUBCLONAL	1	TRUE	1	0.14	2		438	552	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115284219	115284219	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	54	645	0	ENST00000438362.2:c.67T>G	p.Leu23Val	p.L23V	ENST00000438362	NM_001242891.1	23	Tta/Gta	2/20	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.14	2		645	672	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624245	89624245	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554890335	NA	P-0049788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	28	217	2	ENST00000371953.3:c.19G>T	p.Glu7Ter	p.E7*	ENST00000371953	NM_000314.4	7	Gag/Tag	1/9	1	2	FACETS	0.781	0.627	0.956	1	0.94	1	CLONAL	2	TRUE	1	0.14	2		219	256	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212851	94212851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368403414	NA	P-0049788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	28	505	0	ENST00000323929.3:c.391G>A	p.Asp131Asn	p.D131N	ENST00000323929	NM_005591.3	131	Gat/Aat	5/20	1	2	FACETS	0.857	0.684	1	0.857	0.684	1	CLONAL	1	TRUE	1	0.14	2		505	467	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0049788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	42	564	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	0.721	0.6	0.856	0.721	0.6	0.856	SUBCLONAL	1	TRUE	1	0.14	2		564	832	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906944	32906944	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs73169186	NA	P-0049788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	24	478	0	ENST00000380152.3:c.1329G>T	p.Glu443Asp	p.E443D	ENST00000380152		443	gaG/gaT	10/27	1	2	FACETS	0.786	0.616	0.984	0.786	0.616	0.984	CLONAL	1	TRUE	1	0.14	2		478	436	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681031	37681031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143648695	NA	P-0049788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	55	584	0	ENST00000447079.4:c.3200G>A	p.Arg1067Gln	p.R1067Q	ENST00000447079	NM_015083.1	1067	cGa/cAa	12/14	1	2	FACETS	0.952	0.813	1	0.952	0.813	1	CLONAL	1	TRUE	1	0.14	2		584	825	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763364	59763364	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	41	796	1	ENST00000259008.2:c.2738C>A	p.Ser913Tyr	p.S913Y	ENST00000259008	NM_032043.2	913	tCt/tAt	19/20	1	2	FACETS	0.839	0.697	0.998	0.839	0.697	0.998	CLONAL	1	TRUE	1	0.14	2		797	698	SUCCESS
YES1	7525	MSKCC	GRCh37	18	724431	724431	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	43	690	0	ENST00000314574.4:c.1625A>T	p.Asn542Ile	p.N542I	ENST00000314574	NM_005433.3	542	aAt/aTt	12/12	1	2	FACETS	0.794	0.662	0.94	0.794	0.662	0.94	CLONAL	1	TRUE	1	0.14	2		690	774	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145543	61145543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767519747	NA	P-0049788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	24	416	1	ENST00000295025.8:c.655C>T	p.Arg219Cys	p.R219C	ENST00000295025	NM_002908.2	219	Cgt/Tgt	7/11	1	2	FACETS	0.824	0.645	1	0.824	0.645	1	CLONAL	1	TRUE	1	0.14	2		417	416	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646164	215646164	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	38	526	0	ENST00000260947.4:c.434T>C	p.Met145Thr	p.M145T	ENST00000260947	NM_000465.2	145	aTg/aCg	4/11	1	2	FACETS	0.87	0.718	1	0.87	0.718	1	CLONAL	1	TRUE	1	0.14	2		526	624	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39762950	39762950	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	32	427	0	ENST00000288319.7:c.886C>A	p.Leu296Ile	p.L296I	ENST00000288319	NM_182918.3	296	Ctt/Att	9/10	1	2	FACETS	0.766	0.62	0.931	0.766	0.62	0.931	CLONAL	1	TRUE	1	0.14	2		427	597	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149245635	149245635	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	55	675	0	ENST00000360632.3:c.893C>A	p.Pro298His	p.P298H	ENST00000360632	NM_015472.4	298	cCt/cAt	5/7	1	2	FACETS	0.852	0.727	0.99	0.852	0.727	0.99	CLONAL	1	TRUE	1	0.14	2		675	922	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0049788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	36	424	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.665	0.545	0.801	0.665	0.545	0.801	SUBCLONAL	1	TRUE	1	0.14	2		424	773	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	21	440	0	ENST00000263967.3:c.333G>T	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaT	2/21	1	2	FACETS	0.637	0.489	0.81	0.637	0.489	0.81	SUBCLONAL	1	TRUE	1	0.14	2		440	471	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0049788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	23	292	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.711	0.553	0.895	0.711	0.553	0.895	SUBCLONAL	1	TRUE	1	0.14	2		292	462	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672260	86672260	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	32	511	1	ENST00000274376.6:c.2062G>T	p.Glu688Ter	p.E688*	ENST00000274376	NM_002890.2	688	Gaa/Taa	16/25	1	2	FACETS	0.818	0.662	0.994	0.818	0.662	0.994	CLONAL	1	TRUE	1	0.14	2		512	559	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971369	13971369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779937870	NA	P-0049788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	20	439	0	ENST00000405192.2:c.560G>A	p.Arg187His	p.R187H	ENST00000405192	NM_001163147.1	187	cGc/cAc	8/12	1	2	FACETS	0.475	0.361	0.608	0.475	0.361	0.608	SUBCLONAL	1	TRUE	1	0.14	2		439	602	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880126	151880126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146495785	NA	P-0049788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	39	594	0	ENST00000262189.6:c.5198C>T	p.Ser1733Leu	p.S1733L	ENST00000262189	NM_170606.2	1733	tCg/tTg	35/59	1	2	FACETS	0.802	0.663	0.957	0.802	0.663	0.957	CLONAL	1	TRUE	1	0.14	2		594	695	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072522	5072522	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	24	371	0	ENST00000381652.3:c.1672A>C	p.Lys558Gln	p.K558Q	ENST00000381652	NM_004972.3	558	Aag/Cag	13/25	1	2	FACETS	0.781	0.611	0.977	0.781	0.611	0.977	CLONAL	1	TRUE	1	0.14	2		371	439	SUCCESS
AR	367	MSKCC	GRCh37	X	66942700	66942700	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs200801099	NA	P-0049788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	41	620	0	ENST00000374690.3:c.2481C>A	p.Phe827Leu	p.F827L	ENST00000374690	NM_000044.3	827	ttC/ttA	7/8	1	2	FACETS	0.753	0.625	0.896	0.753	0.625	0.896	SUBCLONAL	1	TRUE	1	0.14	2		620	778	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0049789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	211	583	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		583	690	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045009	47045009	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	182	949	0	ENST00000377604.3:c.2335C>T	p.Gln779Ter	p.Q779*	ENST00000377604	NM_001204468.1	779	Cag/Tag	20/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		949	1014	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281768	49281768	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	345	860	0	ENST00000282018.3:c.815C>G	p.Thr272Arg	p.T272R	ENST00000282018	NM_020377.2	272	aCg/aGg	1/1	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		860	1109	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662103	227662103	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs564378481	NA	P-0049789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	397	752	1	ENST00000305123.5:c.1352G>T	p.Gly451Val	p.G451V	ENST00000305123	NM_005544.2	451	gGc/gTc	1/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		753	1118	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0049790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	52	437	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.437195388294818	3	FACETS	1	0.889	1	1	0.889	1	CLONAL	2	TRUE	1	0.437195388294818	3		437	142	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220409	1220409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	98	854	1	ENST00000326873.7:c.502C>T	p.His168Tyr	p.H168Y	ENST00000326873	NM_000455.4	168	Cat/Tat	4/10	0.437195388294818	3	FACETS	0.99	0.909	1	0.99	0.909	1	CLONAL	3	TRUE	0	0.437195388294818	3		855	184	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912277	32912277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80358620	NA	P-0049790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	42	587	0	ENST00000380152.3:c.3785C>T	p.Ser1262Leu	p.S1262L	ENST00000380152		1262	tCa/tTa	11/27	0.437195388294818	4	FACETS	1	0.892	1	0.36	0.302	0.422	CLONAL	1	TRUE	1	0.437195388294818	4		587	256	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36814313	36814313	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	24	591	0	ENST00000373129.3:c.727G>T	p.Asp243Tyr	p.D243Y	ENST00000373129	NM_032017.1	243	Gac/Tac	8/12	1	2	FACETS	0.858	0.682	1	0.858	0.682	1	CLONAL	1	TRUE	1	0.437195388294818	2		591	128	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366828	40366828	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	27	644	0	ENST00000397332.2:c.369C>A	p.Asp123Glu	p.D123E	ENST00000397332	NM_001033082.2	123	gaC/gaA	2/3	1	2	FACETS	0.722	0.58	0.881	0.722	0.58	0.881	SUBCLONAL	1	TRUE	1	0.437195388294818	2		644	171	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28882982	28882982	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	66	499	0	ENST00000282397.4:c.3718G>T	p.Asp1240Tyr	p.D1240Y	ENST00000282397	NM_002019.4	1240	Gat/Tat	28/30	0.437195388294818	4	FACETS	0.841	0.746	0.938	0.841	0.746	0.938	CLONAL	3	TRUE	1	0.437195388294818	4		499	172	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808018	3808018	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	35	450	1	ENST00000262367.5:c.3401A>G	p.Asp1134Gly	p.D1134G	ENST00000262367	NM_004380.2	1134	gAc/gGc	18/31	0.293688036567708	3	FACETS	1	0.952	1			1	CLONAL	1	TRUE	NA	0.437195388294818	3		451	133	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508206	38508206	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	20	604	0	ENST00000254066.5:c.516del	p.Glu173SerfsTer8	p.E173Sfs*8	ENST00000254066	NM_000964.3	172	Ccc/cc	5/9	0.437195388294818	5	FACETS	0.773	0.594	0.98	0.258	0.198	0.327	CLONAL	1	TRUE	2	0.437195388294818	5		604	196	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550397	39550397	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	40	313	0	ENST00000262039.4:c.508G>T	p.Asp170Tyr	p.D170Y	ENST00000262039	NM_002647.2	170	Gat/Tat	4/25	0.437195388294818	5	FACETS	0.971	0.82	1	0.647	0.547	0.755	CLONAL	2	TRUE	2	0.437195388294818	5		313	156	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38942936	38942936	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	31	313	0	ENST00000357387.3:c.5051A>T	p.Gln1684Leu	p.Q1684L	ENST00000357387	NM_152756.3	1684	cAa/cTa	37/38	0.437195388294818	5	FACETS	0.962	0.794	1			1	CLONAL	2	TRUE	NA	0.437195388294818	5		313	122	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467847	50467847	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	35	633	0	ENST00000331340.3:c.1082C>G	p.Ser361Cys	p.S361C	ENST00000331340	NM_006060.4	361	tCc/tGc	8/8	0.437195388294818	4	FACETS	1	0.949	1	0.479	0.398	0.568	CLONAL	1	TRUE	1	0.437195388294818	4		633	160	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508546	106508546	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	30	510	0	ENST00000359195.3:c.540G>T	p.Leu180Phe	p.L180F	ENST00000359195	NM_002649.2	180	ttG/ttT	2/11	0.341377329141691	4	FACETS	1	0.945	1	0.498	0.408	0.597	CLONAL	1	TRUE	1	0.437195388294818	4		510	132	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045688	47045689	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	T	novel	NA	P-0049790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	48	861	0	ENST00000377604.3:c.2569_2570delinsT	p.Gly857SerfsTer29	p.G857Sfs*29	ENST00000377604	NM_001204468.1	857	GGc/Tc	23/24	0.437195388294818	3	FACETS	1	0.96	1	0.693	0.594	0.799	CLONAL	1	TRUE	1	0.437195388294818	3		861	193	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0049794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	34	698	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.542946294310125	1	FACETS	0.853	0.715	0.999	0.853	0.715	0.999	CLONAL	1	TRUE	0	0.542946294310125	1		698	107	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051618	30051618	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	55	559	1	ENST00000338641.4:c.552G>A	p.Trp184Ter	p.W184*	ENST00000338641	NM_000268.3	184	tgG/tgA	6/16	0.481012579261035	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.542946294310125	1		560	135	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310909	123310929	+	inframe_deletion	In_Frame_Del	DEL	GTTGGCCGCAGGCACAGCATG	GTTGGCCGCAGGCACAGCATG	-	novel	NA	P-0049794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	73	663	1	ENST00000358487.5:c.499_519del	p.His167_Asn173del	p.H167_N173del	ENST00000358487	NM_000141.4	167	CATGCTGTGCCTGCGGCCAAC/-	5/18	0.481012579261035	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.542946294310125	1		664	159	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022399	12022399	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	12	926	0	ENST00000396373.4:c.505G>T	p.Val169Leu	p.V169L	ENST00000396373	NM_001987.4	169	Gtg/Ttg	5/8	0.542946294310125	1	FACETS	0.167	0.117	0.228	0.167	0.117	0.228	SUBCLONAL	1	TRUE	0	0.542946294310125	1		926	193	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325177	39325177	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	45	634	0	ENST00000373001.3:c.142del	p.Ala48GlnfsTer63	p.A48Qfs*63	ENST00000373001	NM_022157.3	48	Gca/ca	1/7	0.521683423487536	1	FACETS	0.839	0.72	0.964	0.839	0.72	0.964	CLONAL	1	TRUE	0	0.542946294310125	1		634	144	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641778	23641778	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144617793	NA	P-0049794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	31	341	0	ENST00000261584.4:c.1697G>A	p.Arg566His	p.R566H	ENST00000261584	NM_024675.3	566	cGt/cAt	5/13	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.542946294310125	2		341	93	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50827520	50827520	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	32	643	0	ENST00000398568.2:c.2405A>T	p.Asp802Val	p.D802V	ENST00000398568	NM_001042412.1	802	gAt/gTt	16/18	1	2	FACETS	0.63	0.517	0.756	0.63	0.517	0.756	SUBCLONAL	1	TRUE	1	0.542946294310125	2		643	187	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533153	63533153	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759825875	NA	P-0049794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	38	772	5	ENST00000307078.5:c.1741C>T	p.Arg581Cys	p.R581C	ENST00000307078	NM_004655.3	581	Cgc/Tgc	7/11	1	2	FACETS	0.696	0.582	0.822	0.696	0.582	0.822	SUBCLONAL	1	TRUE	1	0.542946294310125	2		777	201	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299916	15299916	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	67	976	2	ENST00000263388.2:c.1262G>A	p.Arg421His	p.R421H	ENST00000263388	NM_000435.2	421	cGt/cAt	8/33	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.542946294310125	2		978	230	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260094	16260118	+	frameshift_variant	Frame_Shift_Del	DEL	CATTGAAAGTGACCCGGTGACCCCA	CATTGAAAGTGACCCGGTGACCCCA	-	novel	NA	P-0049795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	365	614	0	ENST00000375759.3:c.7360_7384del	p.Ile2454ProfsTer14	p.I2454Pfs*14	ENST00000375759	NM_015001.2	2453	atCATTGAAAGTGACCCGGTGACCCCA/at	11/15	0.686594852641226	6	FACETS	0.87	0.828	0.911	0.87	0.828	0.911	CLONAL	3	TRUE	3	0.862621380590963	6		614	884	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0049796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	108	341	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.337090296622167	2	FACETS	1	0.977	1	0.625	0.568	0.684	CLONAL	1	TRUE	0	0.528353236156058	2		341	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579855	7579855	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1131691018	NA	P-0049796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	120	638	0	ENST00000269305.4:c.58del	p.Ser20GlnfsTer24	p.S20Qfs*24	ENST00000269305	NM_001126112.2	20	Tca/ca	2/11	0.522703832212371	1	FACETS	0.974	0.891	1	0.974	0.891	1	CLONAL	1	TRUE	0	0.528353236156058	1		638	343	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969405	44969405	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	92	263	0	ENST00000377967.4:c.4087C>T	p.Arg1363Ter	p.R1363*	ENST00000377967	NM_021140.2	1363	Cga/Tga	28/29	1	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.528353236156058	1		263	211	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63553932	63553951	+	frameshift_variant	Frame_Shift_Del	DEL	ACTGTCAACAGTTTCCGTGG	ACTGTCAACAGTTTCCGTGG	-	novel	NA	P-0049796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	54	463	0	ENST00000307078.5:c.788_807del	p.Ser263TrpfsTer12	p.S263Wfs*12	ENST00000307078	NM_004655.3	263	tCCACGGAAACTGTTGACAGT/t	2/11	1	2	FACETS	0.596	0.511	0.688	0.596	0.511	0.688	SUBCLONAL	1	TRUE	1	0.528353236156058	2		463	343	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0049799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	290	402	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.271966327618777	1	FACETS	0.564	0.535	0.594	0.564	0.535	0.594	INDETERMINATE	1	TRUE	0	0.869607073004554	1		402	668	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600525	43600525	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	157	619	0	ENST00000355710.3:c.751G>C	p.Glu251Gln	p.E251Q	ENST00000355710	NM_020975.4	251	Gag/Cag	4/20	1	2	FACETS	0.416	0.381	0.453	0.416	0.381	0.453	SUBCLONAL	1	TRUE	1	0.869607073004554	2		619	867	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944554	40944554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775796300	NA	P-0049799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	190	535	0	ENST00000373198.4:c.1948G>A	p.Val650Met	p.V650M	ENST00000373198	NM_133170.3	650	Gtg/Atg	12/32	1	2	FACETS	0.497	0.459	0.535	0.497	0.459	0.535	SUBCLONAL	1	TRUE	1	0.869607073004554	2		535	880	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124762	108124762	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	80	343	0	ENST00000278616.4:c.2120C>G	p.Ser707Cys	p.S707C	ENST00000278616	NM_000051.3	707	tCt/tGt	13/63	1	2	FACETS	0.473	0.419	0.531	0.473	0.419	0.531	SUBCLONAL	1	TRUE	1	0.869607073004554	2		343	389	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120402	94120402	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	116	380	0	ENST00000369303.4:c.649G>A	p.Asp217Asn	p.D217N	ENST00000369303	NM_004440.3	217	Gat/Aat	3/17	1	2	FACETS	0.517	0.468	0.568	0.517	0.468	0.568	SUBCLONAL	1	TRUE	1	0.869607073004554	2		380	516	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657053	47657053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	41	322	0	ENST00000233146.2:c.1249G>A	p.Val417Ile	p.V417I	ENST00000233146	NM_000251.2	417	Gtt/Att	7/16	0.220103770271577	1	FACETS	0.102	0.085	0.122	0.102	0.085	0.122	INDETERMINATE	1	TRUE	0	0.869607073004554	1		322	522	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928070	178928070	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	157	602	0	ENST00000263967.3:c.1348C>G	p.His450Asp	p.H450D	ENST00000263967	NM_006218.2	450	Cat/Gat	8/21	0.220103770271577	1	FACETS	0.296	0.271	0.321	0.296	0.271	0.321	INDETERMINATE	1	TRUE	0	0.869607073004554	1		602	690	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940443	31940443	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	251	784	1	ENST00000375333.2:c.476G>A	p.Arg159Gln	p.R159Q	ENST00000375333	NM_032454.1	159	cGa/cAa	3/8	1	2	FACETS	0.562	0.525	0.599	0.562	0.525	0.599	SUBCLONAL	1	TRUE	1	0.869607073004554	2		785	1028	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942816	44942817	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAACTATACATG	novel	NA	P-0049799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	338	332	0	ENST00000377967.4:c.3397_3408dup	p.Gln1133_Met1136dup	p.Q1133_M1136dup	ENST00000377967	NM_021140.2	1133	-/CAACTATACATG	23/29	1	1	FACETS	0.802	0.769	0.834	0.802	0.769	0.834	CLONAL	1	TRUE	0	0.869607073004554	1		332	548	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	106	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.819	0.738	0.904	0.819	0.738	0.904	CLONAL	1	TRUE	1	0.540300969437572	2		148	479	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945355	71945355	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	358	825	0	ENST00000298229.2:c.2243T>C	p.Ile748Thr	p.I748T	ENST00000298229	NM_001567.3	748	aTt/aCt	20/28	1	2	FACETS	0.998	0.945	1	0.998	0.945	1	CLONAL	1	TRUE	1	0.540300969437572	2		825	1328	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024029	27024029	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	52	150	0	ENST00000324856.7:c.1135C>T	p.Gln379Ter	p.Q379*	ENST00000324856	NM_006015.4	379	Cag/Tag	1/20	0.532353084932854	2	FACETS	1	0.916	1	0.541	0.468	0.617	CLONAL	1	TRUE	0	0.540300969437572	2		150	178	SUCCESS
FH	2271	MSKCC	GRCh37	1	241683007	241683007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	153	606	0	ENST00000366560.3:c.16C>T	p.Arg6Trp	p.R6W	ENST00000366560	NM_000143.3	6	Cgg/Tgg	1/10	0.274165893097348	2	FACETS	0.573	0.523	0.624	0.286	0.261	0.312	INDETERMINATE	1	TRUE	0	0.540300969437572	2		606	989	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118919	115118919	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	74	348	0	ENST00000257566.3:c.422C>T	p.Ser141Phe	p.S141F	ENST00000257566	NM_016569.3	141	tCt/tTt	2/8	0.305647860126562	1	FACETS	0.385	0.338	0.436	0.385	0.338	0.436	INDETERMINATE	1	TRUE	0	0.540300969437572	1		348	519	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518755	204518755	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	194	426	0	ENST00000367182.3:c.1418C>T	p.Ser473Leu	p.S473L	ENST00000367182	NM_001278516.1	473	tCa/tTa	11/11	0.274165893097348	2	FACETS	0.997	0.926	1	0.499	0.463	0.536	INDETERMINATE	1	TRUE	0	0.540300969437572	2		426	720	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101118	41101118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751886972	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	336	825	1	ENST00000373198.4:c.1238C>T	p.Ala413Val	p.A413V	ENST00000373198	NM_133170.3	413	gCg/gTg	8/32	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.540300969437572	2		826	1154	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402040	402040	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	256	567	0	ENST00000399788.2:c.4751G>A	p.Arg1584Lys	p.R1584K	ENST00000399788	NM_001042603.1	1584	aGa/aAa	27/28	0.305647860126562	1	FACETS	0.897	0.843	0.952	0.897	0.843	0.952	INDETERMINATE	1	TRUE	0	0.540300969437572	1		567	771	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942216	71942216	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	367	655	0	ENST00000298229.2:c.1480G>T	p.Asp494Tyr	p.D494Y	ENST00000298229	NM_001567.3	494	Gat/Tat	12/28	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.540300969437572	2		655	1181	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211277	36211277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200396386	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	401	1066	0	ENST00000222270.7:c.1028G>A	p.Arg343Lys	p.R343K	ENST00000222270	NM_014727.1	343	aGa/aAa	3/37	1	2	FACETS	0.99	0.94	1	0.99	0.94	1	CLONAL	1	TRUE	1	0.540300969437572	2		1066	1499	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31483733	31483733	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs769977886	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	24	251	0	ENST00000344624.3:c.1999C>T	p.Pro667Ser	p.P667S	ENST00000344624		667	Cct/Tct	13/33	1	2	FACETS	0.225	0.176	0.282	0.225	0.176	0.282	SUBCLONAL	1	TRUE	1	0.540300969437572	2		251	394	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073487	8073487	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	488	535	0	ENST00000377482.5:c.1172C>G	p.Ser391Ter	p.S391*	ENST00000377482	NM_018948.3	391	tCa/tGa	4/4	0.532353084932854	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.540300969437572	2		535	809	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489535	56489535	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	329	686	1	ENST00000267101.3:c.2000G>T	p.Arg667Leu	p.R667L	ENST00000267101	NM_001982.3	667	cGt/cTt	17/28	0.249736291097974	1	FACETS	1	0.968	1	1	0.968	1	INDETERMINATE	1	TRUE	0	0.540300969437572	1		687	865	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945102	151945102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	43	350	0	ENST00000262189.6:c.2417C>T	p.Ser806Phe	p.S806F	ENST00000262189	NM_170606.2	806	tCc/tTc	14/59	1	2	FACETS	0.235	0.196	0.279	0.235	0.196	0.279	SUBCLONAL	1	TRUE	1	0.540300969437572	2		350	676	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849663	68849663	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587780113	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	215	561	0	ENST00000261769.5:c.1565+1G>T		p.X522_splice	ENST00000261769	NM_004360.3	522			0.540300969437572	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.540300969437572	1		561	564	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515182	106515182	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	108	509	0	ENST00000359195.3:c.2325G>T	p.Gln775His	p.Q775H	ENST00000359195	NM_002649.2	775	caG/caT	5/11	1	2	FACETS	0.437	0.391	0.485	0.437	0.391	0.485	SUBCLONAL	1	TRUE	1	0.540300969437572	2		509	915	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37035134	37035134	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1553637356	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	194	502	0	ENST00000231790.2:c.96C>G	p.Ile32Met	p.I32M	ENST00000231790	NM_000249.3	32	atC/atG	1/19	1	2	FACETS	0.96	0.891	1	0.96	0.891	1	CLONAL	1	TRUE	1	0.540300969437572	2		502	748	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998441	100998441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	180	485	0	ENST00000325455.5:c.1361C>T	p.Ser454Leu	p.S454L	ENST00000325455	NM_001202474.3	454	tCg/tTg	1/8	1	2	FACETS	0.899	0.831	0.97	0.899	0.831	0.97	CLONAL	1	TRUE	1	0.540300969437572	2		485	741	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562427	95562427	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	228	568	0	ENST00000393063.1:c.4830C>A	p.Phe1610Leu	p.F1610L	ENST00000393063	NM_030621.3	1610	ttC/ttA	24/28	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.540300969437572	2		568	831	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094419	27094419	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	731	725	0	ENST00000324856.7:c.3127G>A	p.Ala1043Thr	p.A1043T	ENST00000324856	NM_006015.4	1043	Gct/Act	11/20	0.532353084932854	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.540300969437572	2		725	1193	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105946	27105946	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	375	697	0	ENST00000324856.7:c.5557G>T	p.Glu1853Ter	p.E1853*	ENST00000324856	NM_006015.4	1853	Gag/Tag	20/20	0.532353084932854	2	FACETS	1	0.993	1	0.634	0.602	0.666	CLONAL	1	TRUE	0	0.540300969437572	2		697	1095	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226561948	226561948	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	180	564	0	ENST00000366794.5:c.2049G>C	p.Lys683Asn	p.K683N	ENST00000366794	NM_001618.3	683	aaG/aaC	14/23	0.274165893097348	2	FACETS	0.74	0.683	0.8	0.37	0.341	0.4	INDETERMINATE	1	TRUE	0	0.540300969437572	2		564	900	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421573	32421573	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	93	684	0	ENST00000332351.3:c.1019A>G	p.Glu340Gly	p.E340G	ENST00000332351	NM_024426.4	340	gAg/gGg	6/10	1	2	FACETS	0.373	0.33	0.418	0.373	0.33	0.418	SUBCLONAL	1	TRUE	1	0.540300969437572	2		684	924	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989556	85989556	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	204	489	0	ENST00000263360.6:c.1315C>G	p.Arg439Gly	p.R439G	ENST00000263360	NM_003797.3	439	Cga/Gga	12/12	1	2	FACETS	0.927	0.861	0.994	0.927	0.861	0.994	CLONAL	1	TRUE	1	0.540300969437572	2		489	815	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106544	108106544	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	196	480	0	ENST00000278616.4:c.479C>G	p.Ser160Cys	p.S160C	ENST00000278616	NM_000051.3	160	tCt/tGt	5/63	1	2	FACETS	0.973	0.903	1	0.973	0.903	1	CLONAL	1	TRUE	1	0.540300969437572	2		480	746	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380800	118380800	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	181	430	1	ENST00000534358.1:c.11038G>A	p.Asp3680Asn	p.D3680N	ENST00000534358	NM_005933.3	3680	Gat/Aat	30/36	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.540300969437572	2		431	637	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390757	118390757	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	175	460	0	ENST00000534358.1:c.11407G>A	p.Glu3803Lys	p.E3803K	ENST00000534358	NM_005933.3	3803	Gag/Aag	33/36	1	2	FACETS	0.841	0.776	0.909	0.841	0.776	0.909	CLONAL	1	TRUE	1	0.540300969437572	2		460	770	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416894	416894	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	214	596	0	ENST00000399788.2:c.3656G>T	p.Arg1219Leu	p.R1219L	ENST00000399788	NM_001042603.1	1219	cGa/cTa	23/28	0.305647860126562	1	FACETS	0.793	0.74	0.848	0.793	0.74	0.848	INDETERMINATE	1	TRUE	0	0.540300969437572	1		596	729	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398100	4398100	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	119	718	0	ENST00000261254.3:c.664T>C	p.Ser222Pro	p.S222P	ENST00000261254	NM_001759.3	222	Tcg/Ccg	4/5	0.305647860126562	1	FACETS	0.355	0.32	0.392	0.355	0.32	0.392	INDETERMINATE	1	TRUE	0	0.540300969437572	1		718	905	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30102135	30102135	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	238	494	0	ENST00000331968.5:c.1332G>C	p.Trp444Cys	p.W444C	ENST00000331968	NM_002742.2	444	tgG/tgC	9/18	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.540300969437572	2		494	809	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060953	38060953	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	248	508	0	ENST00000250448.2:c.1036G>T	p.Ala346Ser	p.A346S	ENST00000250448	NM_004496.3	346	Gcc/Tcc	2/2	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.540300969437572	2		508	752	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707903	43707903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	392	774	0	ENST00000382044.4:c.4978G>A	p.Glu1660Lys	p.E1660K	ENST00000382044	NM_001141980.1	1660	Gaa/Aaa	23/28	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.540300969437572	2		774	1293	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396796	396796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	283	783	1	ENST00000262320.3:c.230C>T	p.Ser77Phe	p.S77F	ENST00000262320	NM_003502.3	77	tCc/tTc	2/11	1	2	FACETS	0.945	0.889	1	0.945	0.889	1	CLONAL	1	TRUE	1	0.540300969437572	2		784	1108	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662275	67662275	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	202	519	0	ENST00000264010.4:c.1521G>C	p.Glu507Asp	p.E507D	ENST00000264010	NM_006565.3	507	gaG/gaC	9/12	0.540300969437572	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.540300969437572	1		519	507	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618799	37618799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	156	613	0	ENST00000447079.4:c.475G>A	p.Asp159Asn	p.D159N	ENST00000447079	NM_015083.1	159	Gat/Aat	1/14	0.270896986233696	3	FACETS	0.698	0.638	0.761	0.233	0.212	0.254	INDETERMINATE	1	TRUE	0	0.540300969437572	3		613	1051	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41219655	41219655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80356958	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	386	486	0	ENST00000357654.3:c.5044G>A	p.Glu1682Lys	p.E1682K	ENST00000357654	NM_007294.3	1682	Gaa/Aaa	16/23	0.270896986233696	3	FACETS	1	0.958	1	0.669	0.638	0.7	INDETERMINATE	2	TRUE	0	0.540300969437572	3		486	904	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031401	11031402	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	262	855	1	ENST00000327064.4:c.1401_1402delinsAA	p.Asp468Asn	p.D468N	ENST00000327064	NM_199141.1	467	ctGGat/ctAAat	12/16	1	2	FACETS	0.806	0.754	0.859	0.806	0.754	0.859	CLONAL	1	TRUE	1	0.540300969437572	2		856	1204	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051396	13051396	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	203	517	0	ENST00000316448.5:c.744G>C	p.Lys248Asn	p.K248N	ENST00000316448	NM_004343.3	248	aaG/aaC	6/9	1	2	FACETS	0.967	0.899	1	0.967	0.899	1	CLONAL	1	TRUE	1	0.540300969437572	2		517	777	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349872	15349872	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	313	775	0	ENST00000263377.2:c.3780G>C	p.Met1260Ile	p.M1260I	ENST00000263377	NM_058243.2	1260	atG/atC	18/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.540300969437572	2		775	1034	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051259	128051259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	310	758	0	ENST00000285398.2:c.64G>A	p.Glu22Lys	p.E22K	ENST00000285398	NM_000122.1	22	Gaa/Aaa	2/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.540300969437572	2		758	1117	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288886	212288886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	162	260	0	ENST00000342788.4:c.2860G>A	p.Val954Ile	p.V954I	ENST00000342788	NM_005235.2	954	Gtc/Atc	23/28	0.106415144325237	5	FACETS	0.848	0.786	0.91	0.636	0.589	0.683	INDETERMINATE	3	TRUE	1	0.540300969437572	5		260	427	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589899	212589899	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	253	566	0	ENST00000342788.4:c.643G>C	p.Glu215Gln	p.E215Q	ENST00000342788	NM_005235.2	215	Gaa/Caa	6/28	0.106415144325237	5	FACETS	1	0.992	1	0.371	0.347	0.397	INDETERMINATE	1	TRUE	1	0.540300969437572	5		566	1141	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280067	66280067	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1342407694	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	53	364	0	ENST00000273854.3:c.1622G>A	p.Arg541Gln	p.R541Q	ENST00000273854	NM_004439.5	541	cGa/cAa	7/18	0.249736291097974	1	FACETS	0.259	0.221	0.302	0.259	0.221	0.302	INDETERMINATE	1	TRUE	0	0.540300969437572	1		364	552	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157123	106157123	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	268	545	0	ENST00000380013.4:c.2024C>T	p.Ser675Leu	p.S675L	ENST00000380013	NM_001127208.2	675	tCa/tTa	3/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.540300969437572	2		545	953	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589631	67589631	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	33	340	0	ENST00000274335.5:c.1394G>C	p.Arg465Thr	p.R465T	ENST00000274335		465	aGa/aCa	10/15	1	2	FACETS	0.228	0.185	0.276	0.228	0.185	0.276	SUBCLONAL	1	TRUE	1	0.540300969437572	2		340	536	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271563	26271563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	157	407	0	ENST00000305910.3:c.50C>T	p.Pro17Leu	p.P17L	ENST00000305910	NM_003534.2	17	cCg/cTg	1/1	1	2	FACETS	0.959	0.882	1	0.959	0.882	1	CLONAL	1	TRUE	1	0.540300969437572	2		407	606	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099872	157099872	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs762100979	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	238	514	0	ENST00000346085.5:c.809C>G	p.Ser270Cys	p.S270C	ENST00000346085	NM_020732.3	270	tCc/tGc	1/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.540300969437572	2		514	859	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505389	157505389	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554231811	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	218	527	0	ENST00000346085.5:c.3370G>T	p.Glu1124Ter	p.E1124*	ENST00000346085	NM_020732.3	1124	Gag/Tag	13/20	1	2	FACETS	0.935	0.871	1	0.935	0.871	1	CLONAL	1	TRUE	1	0.540300969437572	2		527	863	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979507	2979507	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	259	682	0	ENST00000396946.4:c.740G>C	p.Arg247Thr	p.R247T	ENST00000396946	NM_032415.4	247	aGa/aCa	6/25	1	2	FACETS	0.957	0.897	1	0.957	0.897	1	CLONAL	1	TRUE	1	0.540300969437572	2		682	1002	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015184	37015184	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	187	547	0	ENST00000358127.4:c.220G>C	p.Glu74Gln	p.E74Q	ENST00000358127	NM_001280556.1	74	Gag/Cag	3/10	1	2	FACETS	0.969	0.898	1	0.969	0.898	1	CLONAL	1	TRUE	1	0.540300969437572	2		547	714	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1327784	1327784	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1562	241	708	0	ENST00000400841.2:c.97C>G	p.Gln33Glu	p.Q33E	ENST00000400841		33	Cag/Gag	2/6	0.540300969437572	2	FACETS	0.495	0.46	0.531			1	SUBCLONAL	1	TRUE	NA	0.540300969437572	2		708	1803	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412017	63412017	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	300	382	0	ENST00000330258.3:c.1150G>C	p.Glu384Gln	p.E384Q	ENST00000330258	NM_152424.3	384	Gag/Cag	2/2	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.540300969437572	1		382	567	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0049802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	8	346	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.938	0.605	1	0.938	0.605	1	CLONAL	1	TRUE	1	0.11	2		346	155	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	rs786202799	NA	P-0049802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	50	616	0	ENST00000269305.4:c.376-2A>T		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.131536086756313	3	FACETS	1	0.9	1	1	0.9	1	CLONAL	2	TRUE	1	0.11	3		616	445	SUCCESS
RET	5979	MSKCC	GRCh37	10	43613871	43613871	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	40	754	0	ENST00000355710.3:c.2335C>A	p.Leu779Met	p.L779M	ENST00000355710	NM_020975.4	779	Ctg/Atg	13/20	0.131536086756313	3	FACETS	1	0.928	1	0.62	0.514	0.738	CLONAL	1	TRUE	1	0.11	3		754	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28934577	NA	P-0049803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	352	707	3	ENST00000269305.4:c.770T>C	p.Leu257Pro	p.L257P	ENST00000269305	NM_001126112.2	257	cTg/cCg	7/11	0.300493989631218	2	FACETS	0.918	0.871	0.966	0.918	0.871	0.966	CLONAL	2	TRUE	0	0.36150709166245	2		710	1061	SUCCESS
APC	324	MSKCC	GRCh37	5	112155042	112155042	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs863225310	NA	P-0049803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	160	490	2	ENST00000257430.4:c.1312+1G>A		p.X438_splice	ENST00000257430	NM_000038.5	438			0.162949494333097	4	FACETS	1	0.988	1	0.733	0.673	0.796	INDETERMINATE	1	TRUE	2	0.36150709166245	4		492	822	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432040	121432040	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771108132	NA	P-0049803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1301	166	872	0	ENST00000257555.6:c.787C>T	p.Arg263Cys	p.R263C	ENST00000257555		263	Cgt/Tgt	4/10	0.222711816318049	4	FACETS	0.852	0.78	0.928	0.426	0.39	0.464	CLONAL	1	TRUE	2	0.36150709166245	4		872	1467	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916860	178916862	+	missense_variant	Missense_Mutation	TNP	TTT	TTT	AAG	novel	NA	P-0049803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	64	701	1	ENST00000263967.3:c.247_249delinsAAG	p.Phe83Lys	p.F83K	ENST00000263967	NM_006218.2	83	TTT/AAG	2/21	0.222711816318049	4	FACETS	0.393	0.338	0.452	0.196	0.169	0.226	SUBCLONAL	1	TRUE	2	0.36150709166245	4		702	1228	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735548	40735548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	464	676	3	ENST00000373198.4:c.3325C>T	p.Arg1109Trp	p.R1109W	ENST00000373198	NM_133170.3	1109	Cgg/Tgg	25/32	0.36150709166245	5	FACETS	0.933	0.891	0.975			1	CLONAL	3	TRUE	NA	0.36150709166245	5		679	1415	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197599	106197599	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555385319	NA	P-0049803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	198	516	1	ENST00000380013.4:c.5932G>A	p.Val1978Met	p.V1978M	ENST00000380013	NM_001127208.2	1978	Gtg/Atg	11/11	0.254187318246919	3	FACETS	0.898	0.835	0.964	0.898	0.835	0.964	CLONAL	2	TRUE	1	0.36150709166245	3		517	720	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491276	2491276	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372896541	NA	P-0049803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	358	818	3	ENST00000355716.4:c.319G>A	p.Ala107Thr	p.A107T	ENST00000355716	NM_003820.2	107	Gcg/Acg	4/8	0.300493989631218	2	FACETS	0.916	0.869	0.964	0.916	0.869	0.964	CLONAL	2	TRUE	0	0.36150709166245	2		821	1081	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660154	227660154	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	73	913	1	ENST00000305123.5:c.3301T>A	p.Ser1101Thr	p.S1101T	ENST00000305123	NM_005544.2	1101	Tcc/Acc	1/2	0.36150709166245	3	FACETS	0.381	0.332	0.435	0.127	0.11	0.145	SUBCLONAL	1	TRUE	0	0.36150709166245	3		914	1250	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0049804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	274	583	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.549276897655944	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.549276897655944	1		583	549	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0049804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	40	344	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.507	0.424	0.6	0.507	0.424	0.6	SUBCLONAL	1	TRUE	1	0.549276897655944	2		344	287	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119924	70119924	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	59	511	0	ENST00000245479.2:c.926C>T	p.Thr309Met	p.T309M	ENST00000245479	NM_000346.3	309	aCg/aTg	3/3	0.302110909422177	1	FACETS	0.242	0.208	0.28	0.242	0.208	0.28	INDETERMINATE	1	TRUE	0	0.549276897655944	1		511	643	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433541	49433542	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGGA	novel	NA	P-0049804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	272	871	0	ENST00000301067.7:c.8008_8011dup	p.Gly2671ValfsTer4	p.G2671Vfs*4	ENST00000301067	NM_003482.3	2671	ggc/gTCCGgc	31/54	0.384343974806407	4	FACETS	0.794	0.746	0.843			1	SUBCLONAL	2	TRUE	NA	0.549276897655944	4		871	966	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438221	49438221	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	224	693	1	ENST00000301067.7:c.5048A>T	p.Glu1683Val	p.E1683V	ENST00000301067	NM_003482.3	1683	gAa/gTa	20/54	0.384343974806407	4	FACETS	1	0.992	1			1	CLONAL	1	TRUE	NA	0.549276897655944	4		694	843	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	197	782	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.727	0.672	0.784	0.727	0.672	0.784	SUBCLONAL	1	TRUE	1	0.497174369071187	2		787	1090	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	235	828	2	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	1	2	FACETS	0.802	0.748	0.859	0.802	0.748	0.859	CLONAL	1	TRUE	1	0.497174369071187	2		830	1178	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	144	263	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.497174369071187	2		263	546	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	190	994	2	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.628	0.579	0.679	0.628	0.579	0.679	SUBCLONAL	1	TRUE	1	0.497174369071187	2		996	1217	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	150	470	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.689	0.629	0.751	0.689	0.629	0.751	SUBCLONAL	1	TRUE	1	0.497174369071187	2		472	876	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156713	20156713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	195	536	0	ENST00000379607.5:c.44G>A	p.Gly15Asp	p.G15D	ENST00000379607	NM_001412.3	15	gGt/gAt	2/7	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.497174369071187	2		536	771	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306996	65306997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	161	469	4	ENST00000342505.4:c.2580dup	p.Pro861ThrfsTer4	p.P861Tfs*4	ENST00000342505	NM_002227.2	860	-/A	19/25	1	2	FACETS	0.915	0.841	0.991	0.915	0.841	0.991	CLONAL	1	TRUE	1	0.497174369071187	2		473	708	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567647	226567647	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1192	171	635	3	ENST00000366794.5:c.1519del	p.Ser507AlafsTer17	p.S507Afs*17	ENST00000366794	NM_001618.3	507	Agc/gc	10/23	0.497174369071187	4	FACETS	0.756	0.693	0.821	0.252	0.231	0.274	SUBCLONAL	1	TRUE	1	0.497174369071187	4		638	1363	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509045	106509045	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752896730	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	228	756	2	ENST00000359195.3:c.1039G>A	p.Glu347Lys	p.E347K	ENST00000359195	NM_002649.2	347	Gag/Aag	2/11	1	2	FACETS	0.914	0.852	0.979	0.914	0.852	0.979	CLONAL	1	TRUE	1	0.497174369071187	2		758	1003	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775719	9775719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557659540	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	222	768	1	ENST00000377346.4:c.262C>T	p.Arg88Cys	p.R88C	ENST00000377346	NM_005026.3	88	Cgt/Tgt	4/24	1	2	FACETS	0.723	0.671	0.776	0.723	0.671	0.776	SUBCLONAL	1	TRUE	1	0.497174369071187	2		769	1236	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199945	138199945	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	148	573	1	ENST00000237289.4:c.1368del	p.Pro457LeufsTer20	p.P457Lfs*20	ENST00000237289	NM_001270507.1	455	Ggg/gg	7/9	1	2	FACETS	0.724	0.662	0.79	0.724	0.662	0.79	SUBCLONAL	1	TRUE	1	0.497174369071187	2		574	822	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309887	65309887	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1304838920	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	63	489	1	ENST00000342505.4:c.2263C>T	p.Arg755Ter	p.R755*	ENST00000342505	NM_002227.2	755	Cga/Tga	17/25	1	2	FACETS	0.325	0.28	0.374	0.325	0.28	0.374	SUBCLONAL	1	TRUE	1	0.497174369071187	2		490	780	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260456	16260456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201347979	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	150	625	1	ENST00000375759.3:c.7721C>T	p.Pro2574Leu	p.P2574L	ENST00000375759	NM_015001.2	2574	cCg/cTg	11/15	1	2	FACETS	0.728	0.665	0.793	0.728	0.665	0.793	SUBCLONAL	1	TRUE	1	0.497174369071187	2		626	829	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56878487	56878487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752264053	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	186	537	1	ENST00000308159.5:c.2426C>T	p.Ala809Val	p.A809V	ENST00000308159	NM_014669.4	809	gCg/gTg	22/22	1	2	FACETS	0.806	0.745	0.87	0.806	0.745	0.87	CLONAL	1	TRUE	1	0.497174369071187	2		538	928	SUCCESS
EED	8726	MSKCC	GRCh37	11	85966300	85966300	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745786094	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	95	418	0	ENST00000263360.6:c.397C>T	p.Arg133Trp	p.R133W	ENST00000263360	NM_003797.3	133	Cgg/Tgg	4/12	1	2	FACETS	0.738	0.659	0.821	0.738	0.659	0.821	SUBCLONAL	1	TRUE	1	0.497174369071187	2		418	518	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021277	31021277	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	181	676	0	ENST00000375687.4:c.1281del	p.Lys427AsnfsTer35	p.K427Nfs*35	ENST00000375687	NM_015338.5	426	Aaa/aa	12/13	1	2	FACETS	0.826	0.763	0.893	0.826	0.763	0.893	CLONAL	1	TRUE	1	0.497174369071187	2		676	881	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444378	49444378	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	247	758	1	ENST00000301067.7:c.2993del	p.Pro998LeufsTer2	p.P998Lfs*2	ENST00000301067	NM_003482.3	998	cCt/ct	11/54	1	2	FACETS	0.936	0.875	0.999	0.936	0.875	0.999	CLONAL	1	TRUE	1	0.497174369071187	2		759	1061	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434235	49434235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375114492	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	311	953	0	ENST00000301067.7:c.7318G>A	p.Val2440Ile	p.V2440I	ENST00000301067	NM_003482.3	2440	Gtt/Att	31/54	1	2	FACETS	0.972	0.916	1	0.972	0.916	1	CLONAL	1	TRUE	1	0.497174369071187	2		953	1287	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027747	152027747	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	279	757	5	ENST00000262189.6:c.328C>T	p.Arg110Ter	p.R110*	ENST00000262189	NM_170606.2	110	Cga/Tga	3/59	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.497174369071187	2		762	1090	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692792	89692792	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	115	423	0	ENST00000371953.3:c.276C>G	p.Asp92Glu	p.D92E	ENST00000371953	NM_000314.4	92	gaC/gaG	5/9	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.497174369071187	2		423	451	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754535	42754535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745819984	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	191	796	0	ENST00000222329.4:c.205G>A	p.Val69Ile	p.V69I	ENST00000222329	NM_006494.2	69	Gtt/Att	2/4	1	2	FACETS	0.636	0.587	0.687	0.636	0.587	0.687	SUBCLONAL	1	TRUE	1	0.497174369071187	2		796	1208	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720741	89720742	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	11	197	0	ENST00000371953.3:c.894dup	p.Glu299ArgfsTer4	p.E299Rfs*4	ENST00000371953	NM_000314.4	298	caa/cAaa	8/9	1	2	FACETS	0.246	0.17	0.34	0.246	0.17	0.34	SUBCLONAL	1	TRUE	1	0.497174369071187	2		197	180	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678473	88678474	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	178	669	0	ENST00000360948.2:c.1062dup	p.Glu355ArgfsTer52	p.E355Rfs*52	ENST00000360948	NM_001012338.2	354	-/A	9/19	1	2	FACETS	0.789	0.727	0.853	0.789	0.727	0.853	SUBCLONAL	1	TRUE	1	0.497174369071187	2		669	908	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923290	9923290	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	166	578	0	ENST00000330684.3:c.1997G>T	p.Ser666Ile	p.S666I	ENST00000330684	NM_001134407.1	666	aGt/aTt	9/13	1	2	FACETS	0.739	0.679	0.801	0.739	0.679	0.801	SUBCLONAL	1	TRUE	1	0.497174369071187	2		578	904	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984451	72984451	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	305	666	0	ENST00000268489.5:c.3133T>C	p.Cys1045Arg	p.C1045R	ENST00000268489	NM_006885.3	1045	Tgt/Cgt	3/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.497174369071187	2		666	1158	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40477051	40477051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	204	553	0	ENST00000264657.5:c.1394C>T	p.Ser465Phe	p.S465F	ENST00000264657	NM_139276.2	465	tCc/tTc	16/24	1	2	FACETS	0.93	0.864	0.999	0.93	0.864	0.999	CLONAL	1	TRUE	1	0.497174369071187	2		553	882	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56411713	56411713	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	126	472	0	ENST00000348428.3:c.1897A>G	p.Thr633Ala	p.T633A	ENST00000348428	NM_006785.3	633	Act/Gct	15/17	1	2	FACETS	0.964	0.877	1	0.964	0.877	1	CLONAL	1	TRUE	1	0.497174369071187	2		472	526	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191624	10191624	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	258	707	0	ENST00000256474.2:c.617T>A	p.Ile206Asn	p.I206N	ENST00000256474	NM_000551.3	206	aTt/aAt	3/3	1	2	FACETS	0.954	0.893	1	0.954	0.893	1	CLONAL	1	TRUE	1	0.497174369071187	2		707	1088	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637516	176637516	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	180	671	1	ENST00000439151.2:c.2116A>T	p.Asn706Tyr	p.N706Y	ENST00000439151	NM_022455.4	706	Aac/Tac	5/23	1	2	FACETS	0.832	0.768	0.899	0.832	0.768	0.899	CLONAL	1	TRUE	1	0.497174369071187	2		672	870	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030231	180030232	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	134	724	0	ENST00000261937.6:c.4052dup	p.Ser1352ValfsTer92	p.S1352Vfs*92	ENST00000261937	NM_182925.4	1351	ccg/ccCg	30/30	1	2	FACETS	0.49	0.445	0.539	0.49	0.445	0.539	SUBCLONAL	1	TRUE	1	0.497174369071187	2		724	1099	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035175	6035175	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876658970	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	111	425	0	ENST00000265849.7:c.893A>G	p.Asp298Gly	p.D298G	ENST00000265849	NM_000535.5	298	gAc/gGc	8/15	1	2	FACETS	0.67	0.603	0.741	0.67	0.603	0.741	SUBCLONAL	1	TRUE	1	0.497174369071187	2		425	666	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371617	55371618	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	224	613	0	ENST00000297316.4:c.308_309dup	p.Lys104AlafsTer7	p.K104Afs*7	ENST00000297316	NM_022454.3	103	ggc/gGCgc		1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.497174369071187	2		613	875	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606395	93606395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200175081	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	219	715	0	ENST00000375746.1:c.215G>A	p.Gly72Asp	p.G72D	ENST00000375746	NM_001174167.1	72	gGc/gAc	2/14	1	2	FACETS	0.911	0.848	0.976	0.911	0.848	0.976	CLONAL	1	TRUE	1	0.497174369071187	2		715	967	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933205	39933205	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	327	828	1	ENST00000378444.4:c.1394T>C	p.Val465Ala	p.V465A	ENST00000378444	NM_001123385.1	465	gTc/gCc	4/15	1	2	FACETS	0.977	0.922	1	0.977	0.922	1	CLONAL	1	TRUE	1	0.497174369071187	2		829	1346	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061218	38061235	+	inframe_deletion	In_Frame_Del	DEL	GCCGTTCTCGAACATGTT	GCCGTTCTCGAACATGTT	-	novel	NA	P-0049806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	117	618	0	ENST00000250448.2:c.754_771del	p.Asn252_Gly257del	p.N252_G257del	ENST00000250448	NM_004496.3	252	AACATGTTCGAGAACGGC/-	2/2	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		618	717	SUCCESS
APC	324	MSKCC	GRCh37	5	112175696	112175696	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060503288	NA	P-0049807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	115	405	0	ENST00000257430.4:c.4405C>T	p.Gln1469Ter	p.Q1469*	ENST00000257430	NM_000038.5	1469	Caa/Taa	16/16	0.171728822940346	1	FACETS	0.899	0.815	0.986	1	0.991	1	CLONAL	3	TRUE	0	0.171728822940346	1		405	454	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061220	38061243	+	inframe_deletion	In_Frame_Del	DEL	CGTTCTCGAACATGTTGCCGGAGT	CGTTCTCGAACATGTTGCCGGAGT	-	novel	NA	P-0049807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	103	508	0	ENST00000250448.2:c.746_769del	p.Asp249_Asn256del	p.D249_N256del	ENST00000250448	NM_004496.3	249	gACTCCGGCAACATGTTCGAGAACGgc/ggc	2/2	1	2	FACETS	0.972	0.872	1	1	0.987	1	CLONAL	2	TRUE	1	0.171728822940346	2		508	617	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656483	3656483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201117707	NA	P-0049807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	159	787	1	ENST00000294008.3:c.752C>T	p.Ala251Val	p.A251V	ENST00000294008	NM_032444.2	251	gCg/gTg	3/15	1	2	FACETS	0.999	0.915	1	1	0.992	1	CLONAL	2	TRUE	1	0.171728822940346	2		788	927	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882331	89882331	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	106	655	0	ENST00000389301.3:c.143T>A	p.Val48Glu	p.V48E	ENST00000389301	NM_000135.2	48	gTg/gAg	2/43	1	2	FACETS	0.951	0.854	1	1	0.987	1	CLONAL	2	TRUE	1	0.171728822940346	2		655	649	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	166	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.999	0.933	1	1	0.995	1	CLONAL	7	FALSE	1	0.139195283201236	2		148	341	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0049808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	295	406	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.979	1	1	0.997	1	CLONAL	7	FALSE	1	0.139195283201236	2		406	576	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050864	49050864	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886042935	NA	P-0049808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	161	497	0	ENST00000267163.4:c.2548C>T	p.Gln850Ter	p.Q850*	ENST00000267163	NM_000321.2	850	Cag/Tag	25/27	1	2	FACETS	1	0.94	1	1	0.995	1	CLONAL	6	FALSE	1	0.139195283201236	2		497	381	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954188	48954188	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0049808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	108	296	0	ENST00000267163.4:c.1390-1G>A		p.X464_splice	ENST00000267163	NM_000321.2	464			1	2	FACETS	1	0.945	1	1	0.992	1	CLONAL	5	FALSE	1	0.139195283201236	2		296	295	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572986	7572986	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555524156	NA	P-0049808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	283	527	1	ENST00000269305.4:c.1123C>T	p.Gln375Ter	p.Q375*	ENST00000269305	NM_001126112.2	375	Cag/Tag	11/11	0.139195283201236	0	FACETS	0.958	0.931	0.984			1	CLONAL	11	FALSE	0	0.139195283201236	0		528	332	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860557	45860557	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	364	783	0	ENST00000391945.4:c.1450A>G	p.Thr484Ala	p.T484A	ENST00000391945	NM_000400.3	484	Acg/Gcg	15/23	1	2	FACETS	1	0.978	1	1	0.997	1	CLONAL	6	FALSE	1	0.139195283201236	2		783	836	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592079	55592079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200518498	NA	P-0049808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	268	626	0	ENST00000288135.5:c.1403C>T	p.Pro468Leu	p.P468L	ENST00000288135	NM_000222.2	468	cCg/cTg	9/21	1	2	FACETS	0.955	0.904	1	1	0.997	1	CLONAL	7	FALSE	1	0.139195283201236	2		626	576	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054837	5054837	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	186	533	1	ENST00000381652.3:c.889C>T	p.Gln297Ter	p.Q297*	ENST00000381652	NM_004972.3	297	Cag/Tag	7/25	0.139195283201236	1	FACETS	0.973	0.91	1	1	0.995	1	CLONAL	6	FALSE	0	0.139195283201236	1		534	426	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509431	149509431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	308	820	0	ENST00000261799.4:c.1468G>A	p.Glu490Lys	p.E490K	ENST00000261799	NM_002609.3	490	Gag/Aag	10/23	1	2	FACETS	0.941	0.894	0.988	1	0.997	1	CLONAL	7	FALSE	1	0.139195283201236	2		820	672	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158513	26158513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750700667	NA	P-0049808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	292	532	1	ENST00000289316.2:c.116C>T	p.Ser39Leu	p.S39L	ENST00000289316	NM_138720.2	39	tCa/tTa	1/2	1	2	FACETS	0.931	0.883	0.979	1	0.997	1	CLONAL	7	FALSE	1	0.139195283201236	2		533	644	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021673	31021673	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs899345535	NA	P-0049808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	309	643	1	ENST00000375687.4:c.1672G>A	p.Glu558Lys	p.E558K	ENST00000375687	NM_015338.5	558	Gaa/Aaa	12/13	1	2	FACETS	1	0.974	1	1	0.997	1	CLONAL	6	FALSE	1	0.139195283201236	2		644	711	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88651963	88651963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	167	434	0	ENST00000372037.3:c.310G>A	p.Glu104Lys	p.E104K	ENST00000372037	NM_004329.2	104	Gaa/Aaa	5/13	0.0758934478177988	4	FACETS	0.957	0.893	1	1	0.995	1	INDETERMINATE	8	FALSE	2	0.139195283201236	4		434	357	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510793	120510793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	266	572	0	ENST00000256646.2:c.1171G>A	p.Asp391Asn	p.D391N	ENST00000256646	NM_024408.3	391	Gac/Aac	7/34	1	2	FACETS	0.958	0.907	1	1	0.997	1	CLONAL	7	FALSE	1	0.139195283201236	2		572	570	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114799831	114799832	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0049808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	327	648	1	ENST00000543371.1:c.498_499delinsTT	p.Gln167Ter	p.Q167*	ENST00000543371	NM_001198531.1	166	ctCCag/ctTTag	5/14	0.0758934478177988	4	FACETS	1	0.962	1	1	0.997	1	INDETERMINATE	7	FALSE	2	0.139195283201236	4		649	754	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628726	21628726	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	196	560	0	ENST00000421138.2:c.982G>T	p.Glu328Ter	p.E328*	ENST00000421138		328	Gaa/Taa	10/16	0.139195283201236	0	FACETS	0.912	0.855	0.97			1	CLONAL	6	FALSE	0	0.139195283201236	0		560	443	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231151	46231151	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0049808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	163	509	0	ENST00000334344.6:c.1071del	p.His357GlnfsTer7	p.H357Qfs*7	ENST00000334344	NM_152641.2	357	caT/ca	9/21	0.139195283201236	5	FACETS	0.975	0.905	1	1	0.994	1	CLONAL	7	FALSE	3	0.139195283201236	5		509	415	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858433	9858433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	208	589	0	ENST00000330684.3:c.2968G>A	p.Glu990Lys	p.E990K	ENST00000330684	NM_001134407.1	990	Gag/Aag	13/13	1	2	FACETS	0.969	0.908	1	1	0.996	1	CLONAL	6	FALSE	1	0.139195283201236	2		589	514	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772201	68772201	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	260	734	0	ENST00000261769.5:c.50T>A	p.Val17Asp	p.V17D	ENST00000261769	NM_004360.3	17	gTc/gAc	2/16	1	2	FACETS	0.988	0.936	1	1	0.997	1	CLONAL	7	FALSE	1	0.139195283201236	2		734	540	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822501	72822501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1011459036	NA	P-0049808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	355	768	0	ENST00000268489.5:c.9674C>T	p.Pro3225Leu	p.P3225L	ENST00000268489	NM_006885.3	3225	cCa/cTa	10/10	1	2	FACETS	1	0.981	1	1	0.997	1	CLONAL	7	FALSE	1	0.139195283201236	2		768	695	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511670	66511670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	264	627	0	ENST00000358598.2:c.130G>A	p.Glu44Lys	p.E44K	ENST00000358598	NM_212471.2	44	Gag/Aag	2/11	0.139195283201236	7	FACETS	0.924	0.868	0.982	0.792	0.744	0.842	CLONAL	6	FALSE	0	0.139195283201236	7		627	922	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054408	13054408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	342	703	1	ENST00000316448.5:c.1018G>A	p.Glu340Lys	p.E340K	ENST00000316448	NM_004343.3	340	Gag/Aag	8/9	1	2	FACETS	1	0.982	1	1	0.997	1	CLONAL	6	FALSE	1	0.139195283201236	2		704	770	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966194	25966206	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGGTGCTATTT	TCTGGTGCTATTT	-	novel	NA	P-0049808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	286	724	0	ENST00000435504.4:c.3000_3012del	p.Asn1001ArgfsTer40	p.N1001Rfs*40	ENST00000435504		1000	gaAAATAGCACCAGA/ga	13/13	1	2	FACETS	1	0.948	1	1	0.997	1	CLONAL	6	FALSE	1	0.139195283201236	2		724	684	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46280009	46280036	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AACCAAATTATGGTAAATCTGACAATGA	AACCAAATTATGGTAAATCTGACAATGA	-	novel	NA	P-0049808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	282	567	1	ENST00000371998.3:c.3937_3946+18del		p.X1313_splice	ENST00000371998		1313		20/23	1	2	FACETS	0.931	0.882	0.979	1	0.997	1	CLONAL	7	FALSE	1	0.139195283201236	2		568	622	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247326	153247344	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGCCTGTCTCAATATCC	CTGGCCTGTCTCAATATCC	-	novel	NA	P-0049808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	155	406	0	ENST00000281708.4:c.1458_1476del	p.Trp486CysfsTer6	p.W486Cfs*6	ENST00000281708	NM_033632.3	486	tgGGATATTGAGACAGGCCAG/tg	10/12	1	2	FACETS	1	0.962	1	1	0.994	1	CLONAL	5	FALSE	1	0.139195283201236	2		406	419	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247373	153247373	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	158	290	0	ENST00000281708.4:c.1429G>C	p.Gly477Arg	p.G477R	ENST00000281708	NM_033632.3	477	Ggt/Cgt	10/12	1	2	FACETS	1	0.956	1	1	0.995	1	CLONAL	8	FALSE	1	0.139195283201236	2		290	277	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532512	187532541	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTTTCCTCTCAGATACATGGTAGGTTACCT	GTTTCCTCTCAGATACATGGTAGGTTACCT	-	novel	NA	P-0049808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	48	330	0	ENST00000441802.2:c.9852_9853+28del		p.X3284_splice	ENST00000441802	NM_005245.3	3284		14/27	1	2	FACETS	1	0.922	1	1	0.981	1	CLONAL	3	FALSE	1	0.139195283201236	2		330	205	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535405	187535405	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	216	581	0	ENST00000441802.2:c.9169G>T	p.Glu3057Ter	p.E3057*	ENST00000441802	NM_005245.3	3057	Gaa/Taa	12/27	1	2	FACETS	1	0.975	1	1	0.996	1	CLONAL	6	FALSE	1	0.139195283201236	2		581	483	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674212	86674212	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0049808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	112	395	0	ENST00000274376.6:c.2345-1G>A		p.X782_splice	ENST00000274376	NM_002890.2	782			1	2	FACETS	0.979	0.895	1	1	0.993	1	CLONAL	6	FALSE	1	0.139195283201236	2		395	274	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672575	30672575	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	257	669	0	ENST00000376406.3:c.4385A>G	p.Asp1462Gly	p.D1462G	ENST00000376406	NM_014641.2	1462	gAc/gGc	10/15	1	2	FACETS	1	0.977	1	1	0.997	1	CLONAL	6	FALSE	1	0.139195283201236	2		669	579	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129183	152129183	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	244	795	0	ENST00000206249.3:c.136A>C	p.Ser46Arg	p.S46R	ENST00000206249	NM_000125.3	46	Agc/Cgc	1/8	1	2	FACETS	1	0.977	1	1	0.996	1	CLONAL	6	FALSE	1	0.139195283201236	2		795	548	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136806	69136806	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	220	509	0	ENST00000288368.4:c.4720C>G	p.Gln1574Glu	p.Q1574E	ENST00000288368	NM_024870.2	1574	Cag/Gag	39/40	1	2	FACETS	1	0.974	1	1	0.996	1	CLONAL	6	FALSE	1	0.139195283201236	2		509	496	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922783	44922789	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAGTG	CAGAGTG	-	novel	NA	P-0049808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	256	555	0	ENST00000377967.4:c.1645_1651del	p.Arg549LeufsTer42	p.R549Lfs*42	ENST00000377967	NM_021140.2	548	acCAGAGTG/ac	16/29	0.139195283201236	1	FACETS	0.959	0.908	1	1	0.997	1	CLONAL	7	FALSE	0	0.139195283201236	1		555	510	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788634	3788645	+	protein_altering_variant	In_Frame_Del	DEL	GAAGAAATGAAT	GAAGAAATGAAT	AAG	novel	NA	P-0049808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	542	528	0	ENST00000262367.5:c.4309_4320delinsCTT	p.Ile1437_Phe1440delinsLeu	p.I1437_F1440delinsL	ENST00000262367	NM_004380.2	1437	ATTCATTTCTTC/CTT	26/31	0.139195283201236	3	FACETS	0.995	0.978	1			1	CLONAL	14	FALSE	1	0.139195283201236	3		528	598	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0049809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	184	616	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.472161855936923	1	FACETS	0.939	0.871	1	0.939	0.871	1	CLONAL	1	TRUE	0	0.472161855936923	1		618	634	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257325	16257371	+	frameshift_variant	Frame_Shift_Del	DEL	TTTACACAGCTCAATCTTTGAACAAGATTCCAAGCGATTGCAGCATC	TTTACACAGCTCAATCTTTGAACAAGATTCCAAGCGATTGCAGCATC	-	novel	NA	P-0049809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	155	743	0	ENST00000375759.3:c.4591_4637del	p.Leu1531ArgfsTer8	p.L1531Rfs*8	ENST00000375759	NM_015001.2	1530	ttTTTACACAGCTCAATCTTTGAACAAGATTCCAAGCGATTGCAGCATCta/ttta	11/15	1	2	FACETS	0.867	0.795	0.942	0.867	0.795	0.942	CLONAL	1	TRUE	1	0.472161855936923	2		743	757	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465437	99465437	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	139	541	0	ENST00000268035.6:c.2262C>A	p.Ser754Arg	p.S754R	ENST00000268035	NM_000875.3	754	agC/agA	11/21	1	2	FACETS	0.919	0.839	1	0.919	0.839	1	CLONAL	1	TRUE	1	0.472161855936923	2		541	641	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0049811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	235	377	1	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.522567895958641	5	FACETS	0.947	0.891	1	0.947	0.891	1	CLONAL	3	TRUE	2	0.522567895958641	5		378	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579448	7579448	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	1236	818	4	ENST00000269305.4:c.239del	p.Pro80LeufsTer43	p.P80Lfs*43	ENST00000269305	NM_001126112.2	80	cCt/ct	4/11	0.522567895958641	6	FACETS	0.969	0.952	0.986	0.969	0.952	0.986	CLONAL	6	TRUE	0	0.522567895958641	6		822	1664	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075280	16075280	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs761688012	NA	P-0049811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1277	180	588	0	ENST00000268712.3:c.272C>G	p.Pro91Arg	p.P91R	ENST00000268712	NM_006311.3	91	cCg/cGg	4/46	0.522567895958641	6	FACETS	0.967	0.889	1	0.161	0.148	0.175	CLONAL	1	TRUE	0	0.522567895958641	6		588	1457	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053005	180053005	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1244	232	808	0	ENST00000261937.6:c.1285G>T	p.Ala429Ser	p.A429S	ENST00000261937	NM_182925.4	429	Gcc/Tcc	10/30	0.524393840687596	4	FACETS	0.916	0.852	0.983	0.229	0.213	0.246	CLONAL	1	TRUE	0	0.522567895958641	4		808	1476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0049812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	35	797	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	1	2	FACETS	0.52	0.424	0.628	0.52	0.424	0.628	SUBCLONAL	1	TRUE	1	0.13	2		797	1036	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553397	41553397	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0049812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	47	572	0	ENST00000263253.7:c.3486C>G	p.Tyr1162Ter	p.Y1162*	ENST00000263253	NM_001429.3	1162	taC/taG	18/31	1	2	FACETS	0.882	0.742	1	0.882	0.742	1	CLONAL	1	TRUE	1	0.13	2		572	820	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001065	150001065	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	53	676	0	ENST00000253339.5:c.2539T>G	p.Phe847Val	p.F847V	ENST00000253339		847	Ttt/Gtt	4/7	1	2	FACETS	0.883	0.751	1	0.883	0.751	1	CLONAL	1	TRUE	1	0.13	2		676	923	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	148	148	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.977	0.895	1	0.977	0.895	1	CLONAL	1	TRUE	1	0.466922360958949	2		148	649	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	206	431	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.466922360958949	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.466922360958949	1		431	475	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058033	27058033	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	256	580	0	ENST00000324856.7:c.1741C>T	p.Gln581Ter	p.Q581*	ENST00000324856	NM_006015.4	581	Cag/Tag	3/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.466922360958949	2		580	1012	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646021	215646021	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	110	634	0	ENST00000260947.4:c.577G>C	p.Glu193Gln	p.E193Q	ENST00000260947	NM_000465.2	193	Gag/Cag	4/11	0.466922360958949	1	FACETS	0.828	0.749	0.911	0.828	0.749	0.911	CLONAL	1	TRUE	0	0.466922360958949	1		634	436	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295195	1295195	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0049813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	137	297	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.466922360958949	2		298	567	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431358	49431358	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	219	667	1	ENST00000301067.7:c.9781C>T	p.Gln3261Ter	p.Q3261*	ENST00000301067	NM_003482.3	3261	Cag/Tag	34/54	NA	3	FACETS	1	0.987	1	0.627	0.584	0.672	INDETERMINATE	1	TRUE	1	0.466922360958949	3		668	922	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087885	27087904	+	frameshift_variant	Frame_Shift_Del	DEL	GCCACCTCGGCCACCCAGTG	GCCACCTCGGCCACCCAGTG	-	novel	NA	P-0049813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	244	698	0	ENST00000324856.7:c.2176_2195del	p.Pro726ValfsTer84	p.P726Vfs*84	ENST00000324856	NM_006015.4	724	atGCCACCTCGGCCACCCAGTGgc/atgc	6/20	1	2	FACETS	0.872	0.814	0.933	0.872	0.814	0.933	CLONAL	1	TRUE	1	0.466922360958949	2		698	1198	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900498	3900498	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783509	NA	P-0049813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	267	858	0	ENST00000262367.5:c.598C>T	p.Gln200Ter	p.Q200*	ENST00000262367	NM_004380.2	200	Cag/Tag	2/31	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.466922360958949	2		858	1109	SUCCESS
AR	367	MSKCC	GRCh37	X	66765238	66765238	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	29	388	0	ENST00000374690.3:c.250C>G	p.Pro84Ala	p.P84A	ENST00000374690	NM_000044.3	84	Ccc/Gcc	1/8	0.466922360958949	1	FACETS	0.19	0.152	0.234	0.19	0.152	0.234	SUBCLONAL	1	TRUE	0	0.466922360958949	1		388	501	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	12	148	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	NA	NA		148	115	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0049814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	19	577	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		577	311	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100754	8100754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749708566	NA	P-0049814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	16	751	0	ENST00000346208.3:c.728C>T	p.Ser243Phe	p.S243F	ENST00000346208		243	tCc/tTc	3/6	0.139559400910528	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		751	283	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118350886	118350910	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAGGATGAGAAAATGTCAGAATCTA	TAGGATGAGAAAATGTCAGAATCTA	-	novel	NA	P-0049814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	19	451	0	ENST00000534358.1:c.3570-3_3591del		p.X1190_splice	ENST00000534358	NM_005933.3	1190		6/36	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		451	327	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993748	90993748	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	37	315	0	ENST00000265433.3:c.175C>G	p.Gln59Glu	p.Q59E	ENST00000265433	NM_002485.4	59	Caa/Gaa	3/16	0.21312369886603	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		315	538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0049941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	99	768	7	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.778	0.693	0.869	0.778	0.693	0.869	SUBCLONAL	1	TRUE	1	0.251372138869985	2		775	1012	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0049941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	38	380	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	1	2	FACETS	0.362	0.298	0.434	0.362	0.298	0.434	SUBCLONAL	1	TRUE	1	0.251372138869985	2		380	835	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630440	90630440	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	54	442	0	ENST00000330062.3:c.871G>T	p.Asp291Tyr	p.D291Y	ENST00000330062	NM_002168.2	291	Gat/Tat	7/11	1	2	FACETS	0.451	0.384	0.525	0.451	0.384	0.525	SUBCLONAL	1	TRUE	1	0.251372138869985	2		442	953	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0049943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	329	605	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.594694700081498	1	FACETS	0.894	0.848	0.94	0.894	0.848	0.94	CLONAL	1	TRUE	0	0.594694700081498	1		606	870	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879229	151879229	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763438739	NA	P-0049943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	168	413	0	ENST00000262189.6:c.5716C>T	p.Arg1906Ter	p.R1906*	ENST00000262189	NM_170606.2	1906	Cga/Tga	36/59	0.594694700081498	1	FACETS	0.896	0.832	0.961	0.896	0.832	0.961	CLONAL	1	TRUE	0	0.594694700081498	1		413	443	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240156	41240156	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	65	78	0	ENST00000379561.5:c.194C>G	p.Ala65Gly	p.A65G	ENST00000379561	NM_002015.3	65	gCt/gGt	1/3	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.594694700081498	2		78	210	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183763	10183763	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs869025621	NA	P-0049944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	106	749	0	ENST00000256474.2:c.232A>C	p.Asn78His	p.N78H	ENST00000256474	NM_000551.3	78	Aat/Cat	1/3	0.288454193423294	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.288454193423294	1		749	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579386	7579386	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0049946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	392	693	0	ENST00000269305.4:c.301A>T	p.Lys101Ter	p.K101*	ENST00000269305	NM_001126112.2	101	Aaa/Taa	4/11	0.820496660718699	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.820496660718699	1		693	518	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376911	118376911	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	151	342	0	ENST00000534358.1:c.10304C>A	p.Thr3435Asn	p.T3435N	ENST00000534358	NM_005933.3	3435	aCt/aAt	27/36	1	2	FACETS	0.883	0.815	0.951	0.883	0.815	0.951	CLONAL	1	TRUE	1	0.820496660718699	2		342	417	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748261	41748261	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	327	648	0	ENST00000226382.2:c.508G>A	p.Gly170Ser	p.G170S	ENST00000226382	NM_003924.3	170	Ggc/Agc	3/3	NA	2	FACETS	0.643	0.607	0.68			1	INDETERMINATE	1	TRUE	NA	0.820496660718699	2		648	1239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0049948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	58	485	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.865	0.742	0.998	0.865	0.742	0.998	CLONAL	1	TRUE	1	0.206063099878449	2		486	651	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0049948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	79	341	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.206063099878449	3	FACETS	1	0.975	1	0.723	0.636	0.815	CLONAL	1	TRUE	1	0.206063099878449	3		341	585	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030797	69030797	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	71	252	0	ENST00000288368.4:c.3339C>G	p.Ser1113Arg	p.S1113R	ENST00000288368	NM_024870.2	1113	agC/agG	27/40	0.156339825250903	2	FACETS	0.816	0.716	0.924	0.816	0.716	0.924	CLONAL	2	TRUE	0	0.206063099878449	2		252	422	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	160	148	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		148	343	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88635786	88635786	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	15	268	0	ENST00000372037.3:c.11T>G	p.Leu4Arg	p.L4R	ENST00000372037	NM_004329.2	4	cTa/cGa	3/13	0.223883175825313	1	FACETS	0.553	0.405	0.731	0.553	0.405	0.731	SUBCLONAL	1	TRUE	0	0.223883175825313	1		268	215	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95592960	95592960	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1060503600	NA	P-0049952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	32	391	0	ENST00000393063.1:c.860C>G	p.Ser287Cys	p.S287C	ENST00000393063	NM_030621.3	287	tCt/tGt	8/28	1	2	FACETS	0.821	0.668	0.995	0.821	0.668	0.995	CLONAL	1	TRUE	1	0.223883175825313	2		391	348	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061215	38061235	+	inframe_deletion	In_Frame_Del	DEL	GCAGCCGTTCTCGAACATGTT	GCAGCCGTTCTCGAACATGTT	-	novel	NA	P-0049954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	33	725	0	ENST00000250448.2:c.754_774del	p.Asn252_Cys258del	p.N252_C258del	ENST00000250448	NM_004496.3	252	AACATGTTCGAGAACGGCTGC/-	2/2	1	2	FACETS	0.435	0.353	0.527	0.435	0.353	0.527	SUBCLONAL	1	TRUE	1	0.311110462787465	2		725	488	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949985	44949985	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	20	180	0	ENST00000377967.4:c.3754G>C	p.Ala1252Pro	p.A1252P	ENST00000377967	NM_021140.2	1252	Gca/Cca	26/29	1	1	FACETS	0.658	0.507	0.832	0.658	0.507	0.832	SUBCLONAL	1	TRUE	0	0.311110462787465	1		180	165	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804149	46804163	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	CTCTTAAGGGGTAGC	CTCTTAAGGGGTAGC	-	novel	NA	P-0049954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	26	686	0	ENST00000290295.7:c.844_*3del		p.*282*	ENST00000290295	NM_006361.5	282		2/2	1	2	FACETS	0.398	0.315	0.494	0.398	0.315	0.494	SUBCLONAL	1	TRUE	1	0.311110462787465	2		686	420	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456528	189456528	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121908848	NA	P-0049954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	39	560	0	ENST00000264731.3:c.289C>A	p.Arg97Ser	p.R97S	ENST00000264731	NM_003722.4	97	Cgc/Agc	3/14	1	2	FACETS	0.497	0.412	0.593	0.497	0.412	0.593	SUBCLONAL	1	TRUE	1	0.311110462787465	2		560	504	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0049955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	76	261	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.537905861276761	2		261	278	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349937	70349937	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	158	842	0	ENST00000374080.3:c.3920T>C	p.Leu1307Pro	p.L1307P	ENST00000374080		1307	cTg/cCg	28/45	1	2	FACETS	0.7	0.642	0.761	0.7	0.642	0.761	SUBCLONAL	1	TRUE	1	0.537905861276761	2		842	839	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647711	206647903	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTACCAGCTACCTGCGGCCCCGCGAGGTGCAAGTGAGGGAGTTTGAGGTCCTGCGGAAGCTGAACCACCAGAACATTGTCAAGCTCTTTGCGGTGGAGGAGACGGTAGGTCCGGTGCTTGGTCAGAGAATGGTCTTGTCCTTGACCCTTATGGTCTGGGGAGAATCAGGCCACATGATAACAGAGATTTGGTC	CTACCAGCTACCTGCGGCCCCGCGAGGTGCAAGTGAGGGAGTTTGAGGTCCTGCGGAAGCTGAACCACCAGAACATTGTCAAGCTCTTTGCGGTGGAGGAGACGGTAGGTCCGGTGCTTGGTCAGAGAATGGTCTTGTCCTTGACCCTTATGGTCTGGGGAGAATCAGGCCACATGATAACAGAGATTTGGTC	-	novel	NA	P-0049955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	35	574	0	ENST00000367120.3:c.126_228+90del		p.X42_splice	ENST00000367120	NM_014002.3	42		4/22	0.421604448736975	3	FACETS	0.292	0.238	0.352	0.146	0.119	0.176	SUBCLONAL	1	TRUE	1	0.537905861276761	3		574	566	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562938	95562938	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	90	298	0	ENST00000393063.1:c.4319A>T	p.Asp1440Val	p.D1440V	ENST00000393063	NM_030621.3	1440	gAt/gTt	24/28	1	2	FACETS	0.94	0.841	1	0.94	0.841	1	CLONAL	1	TRUE	1	0.537905861276761	2		298	356	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470545	25470545	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587777508	NA	P-0049955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	196	910	1	ENST00000264709.3:c.929T>A	p.Ile310Asn	p.I310N	ENST00000264709	NM_175629.2	310	aTt/aAt	8/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.537905861276761	2		911	668	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	159	431	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.221779955236615	6	FACETS	1	0.964	1	1	0.989	1	CLONAL	4	TRUE	3	0.221779955236615	6		431	483	SUCCESS
APC	324	MSKCC	GRCh37	5	112157650	112157650	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1060503333	NA	P-0049957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	214	411	0	ENST00000257430.4:c.1370C>A	p.Ser457Ter	p.S457*	ENST00000257430	NM_000038.5	457	tCa/tAa	11/16	0.221779955236615	4	FACETS	0.945	0.887	1	1	0.993	1	CLONAL	5	TRUE	1	0.221779955236615	4		411	499	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106733	27106734	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0049957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	217	649	0	ENST00000324856.7:c.6347_6348del	p.Arg2116ThrfsTer33	p.R2116Tfs*33	ENST00000324856	NM_006015.4	2115	cAG/c	20/20	0.221779955236615	2	FACETS	0.981	0.917	1	1	0.992	1	CLONAL	3	TRUE	0	0.221779955236615	2		649	665	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431563	6431563	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1554263624	NA	P-0049957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	53	188	0	ENST00000356142.4:c.116A>G	p.Asn39Ser	p.N39S	ENST00000356142	NM_018890.3	39	aAt/aGt	3/7	0.221779955236615	6	FACETS	1	0.881	1	1	0.963	1	CLONAL	4	TRUE	3	0.221779955236615	6		188	170	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196798	108196798	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	107	289	0	ENST00000278616.4:c.6821C>A	p.Ala2274Glu	p.A2274E	ENST00000278616	NM_000051.3	2274	gCa/gAa	47/63	0.221779955236615	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	3	TRUE	1	0.221779955236615	4		289	344	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119901	70119917	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCCACCCGGGGGTGC	CGGCCACCCGGGGGTGC	-	novel	NA	P-0049957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	281	761	0	ENST00000245479.2:c.910_926del	p.Pro304AlafsTer268	p.P304Afs*268	ENST00000245479	NM_000346.3	301	aaCGGCCACCCGGGGGTGCcg/aacg	3/3	0.221779955236615	4	FACETS	0.97	0.915	1	1	0.992	1	CLONAL	4	TRUE	1	0.221779955236615	4		761	798	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357742	70357742	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1324299187	NA	P-0049957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	193	460	0	ENST00000374080.3:c.5993A>G	p.Tyr1998Cys	p.Y1998C	ENST00000374080		1998	tAt/tGt	41/45	0.221779955236615	4	FACETS	0.896	0.834	0.96			1	CLONAL	4	TRUE	NA	0.221779955236615	4		460	593	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711924	89711924	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	195	525	0	ENST00000371953.3:c.542T>C	p.Leu181Pro	p.L181P	ENST00000371953	NM_000314.4	181	cTg/cCg	6/9	0.781742184319782	2	FACETS	0.925	0.884	0.965	0.925	0.884	0.965	CLONAL	2	TRUE	0	0.792174803146909	2		525	266	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371638	55371638	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2472	192	866	1	ENST00000297316.4:c.328A>G	p.Thr110Ala	p.T110A	ENST00000297316	NM_022454.3	110	Acg/Gcg	2/2	0.792174803146909	9	FACETS	0.686	0.631	0.745			1	SUBCLONAL	1	TRUE	NA	0.792174803146909	9		867	2664	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555714	21555714	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs61745905	NA	P-0121443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	90	879	0	ENST00000382592.4:c.2556C>A	p.Asp852Glu	p.D852E	ENST00000382592	NM_014572.2	852	gaC/gaA	6/8	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	NA	1	0.179476740501344	2		879	959	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591118	67591126	+	inframe_deletion	In_Frame_Del	DEL	ATCCAGCTG	ATCCAGCTG	-	novel	NA	P-0121443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	24	292	0	ENST00000274335.5:c.1712_1720del	p.Ile571_Leu573del	p.I571_L573del	ENST00000274335		571	ATCCAGCTG/-	12/15	1	2	FACETS	0.689	0.54	0.862	0.689	0.54	0.862	SUBCLONAL	1	NA	1	0.179476740501344	2		292	388	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63829525	63829525	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs756529242	NA	P-0121443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	49	380	0	ENST00000279873.7:c.1168G>C	p.Ala390Pro	p.A390P	ENST00000279873	NM_032199.2	390	Gct/Cct	8/10	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	NA	1	0.179476740501344	2		380	508	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589558	67589559	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0121443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	20	247	0	ENST00000274335.5:c.1324_1325dup	p.Glu443LeufsTer4	p.E443Lfs*4	ENST00000274335		441	aat/aATat	10/15	1	2	FACETS	0.867	0.664	1	0.867	0.664	1	CLONAL	1	NA	1	0.179476740501344	2		247	257	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322999	31322999	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	113	1115	1	ENST00000412585.2:c.897G>T	p.Glu299Asp	p.E299D	ENST00000412585	NM_005514.6	299	gaG/gaT	5/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	NA	1	0.179476740501344	2		1116	1011	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536188	106536188	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs553795179	NA	P-0121443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	66	467	0	ENST00000369096.4:c.155C>A	p.Ala52Asp	p.A52D	ENST00000369096	NM_001198.3	52	gCt/gAt	2/7	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	NA	1	0.179476740501344	2		467	570	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913233	NA	P-0049965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	530	669	0	ENST00000451590.1:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000451590	NM_001130442.1	61	cAg/cTg	3/5	0.473695019184737	4	FACETS	0.953	0.918	0.989	0.953	0.918	0.989	CLONAL	3	TRUE	1	0.511606512527412	4		669	1095	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913351	NA	P-0049965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	169	298	0	ENST00000288602.6:c.1397G>A	p.Gly466Glu	p.G466E	ENST00000288602	NM_004333.4	466	gGa/gAa	11/18	0.428842764483349	5	FACETS	0.956	0.89	1	0.956	0.89	1	CLONAL	3	TRUE	2	0.511606512527412	5		298	407	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743858	40743858	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374930365	NA	P-0049965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	88	373	1	ENST00000373198.4:c.3137G>A	p.Arg1046His	p.R1046H	ENST00000373198	NM_133170.3	1046	cGc/cAc	23/32	0.466612470934383	3	FACETS	0.929	0.827	1	0.465	0.413	0.519	CLONAL	1	TRUE	1	0.511606512527412	3		374	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577047	7577047	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	510	597	0	ENST00000269305.4:c.891del	p.His297GlnfsTer48	p.H297Qfs*48	ENST00000269305	NM_001126112.2	297	caC/ca	8/11	0.48304210652341	3	FACETS	0.949	0.917	0.982	0.949	0.917	0.982	CLONAL	3	TRUE	0	0.511606512527412	3		597	879	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325911	65325911	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	71	407	0	ENST00000342505.4:c.1211C>T	p.Ser404Phe	p.S404F	ENST00000342505	NM_002227.2	404	tCc/tTc	9/25	0.459409513694469	3	FACETS	0.706	0.617	0.801	0.353	0.308	0.401	SUBCLONAL	1	TRUE	1	0.511606512527412	3		407	494	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809331	243809331	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	60	265	0	ENST00000263826.5:c.293G>T	p.Trp98Leu	p.W98L	ENST00000263826	NM_005465.4	98	tGg/tTg	4/13	0.473695019184737	4	FACETS	1	0.924	1	0.366	0.317	0.418	CLONAL	1	TRUE	1	0.511606512527412	4		265	323	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741900	17741900	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	45	174	0	ENST00000250003.3:c.571G>C	p.Glu191Gln	p.E191Q	ENST00000250003	NM_002478.4	191	Gag/Cag	1/3	0.473695019184737	4	FACETS	0.978	0.827	1	0.326	0.275	0.381	CLONAL	1	TRUE	1	0.511606512527412	4		174	272	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135348	30135348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	99	333	0	ENST00000331968.5:c.470C>T	p.Pro157Leu	p.P157L	ENST00000331968	NM_002742.2	157	cCa/cTa	3/18	0.466612470934383	3	FACETS	0.955	0.856	1	0.477	0.428	0.53	CLONAL	1	TRUE	1	0.511606512527412	3		333	509	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600506	10600506	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	256	526	0	ENST00000171111.5:c.1349G>T	p.Trp450Leu	p.W450L	ENST00000171111	NM_203500.1	450	tGg/tTg	4/6	0.473560689217465	2	FACETS	0.894	0.845	0.943	0.894	0.845	0.943	CLONAL	2	TRUE	0	0.511606512527412	2		526	560	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097206	11097206	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	361	817	0	ENST00000358026.2:c.697G>C	p.Gly233Arg	p.G233R	ENST00000358026	NM_001128849.1	233	Ggc/Cgc	4/36	0.473560689217465	2	FACETS	0.988	0.945	1	0.988	0.945	1	CLONAL	2	TRUE	0	0.511606512527412	2		817	714	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713874	30713874	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	136	532	0	ENST00000295754.5:c.1199T>C	p.Leu400Pro	p.L400P	ENST00000295754	NM_003242.5	400	cTt/cCt	4/7	0.398879903196312	3	FACETS	1	0.97	1	0.379	0.346	0.414	CLONAL	1	TRUE	0	0.511606512527412	3		532	587	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143017	47143017	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	200	384	0	ENST00000409792.3:c.4946G>T	p.Gly1649Val	p.G1649V	ENST00000409792	NM_014159.6	1649	gGg/gTg	8/21	0.398879903196312	3	FACETS	1	0.989	1	0.816	0.768	0.865	CLONAL	2	TRUE	0	0.511606512527412	3		384	401	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531137	187531137	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	69	291	0	ENST00000441802.2:c.9886G>T	p.Glu3296Ter	p.E3296*	ENST00000441802	NM_005245.3	3296	Gag/Tag	15/27	0.511606512527412	3	FACETS	0.916	0.802	1	0.458	0.401	0.519	CLONAL	1	TRUE	1	0.511606512527412	3		291	370	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346633	81346633	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	188	245	0	ENST00000222390.5:c.1320C>A	p.Cys440Ter	p.C440*	ENST00000222390	NM_000601.4	440	tgC/tgA	11/18	0.428842764483349	5	FACETS	0.834	0.777	0.892	0.834	0.777	0.892	CLONAL	3	TRUE	2	0.511606512527412	5		245	519	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930367	39930367	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	91	379	0	ENST00000378444.4:c.3097G>T	p.Gly1033Cys	p.G1033C	ENST00000378444	NM_001123385.1	1033	Ggt/Tgt	6/15	0.108606499828744	5	FACETS	1	0.963	1			1	INDETERMINATE	1	TRUE	NA	0.511606512527412	5		379	529	SUCCESS
AR	367	MSKCC	GRCh37	X	66765842	66765842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	185	764	0	ENST00000374690.3:c.854C>A	p.Ala285Asp	p.A285D	ENST00000374690	NM_000044.3	285	gCc/gAc	1/8	0.323243743076404	6	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.511606512527412	6		764	1118	SUCCESS
AR	367	MSKCC	GRCh37	X	66766280	66766280	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	85	425	0	ENST00000374690.3:c.1292C>A	p.Ala431Asp	p.A431D	ENST00000374690	NM_000044.3	431	gCt/gAt	1/8	0.323243743076404	6	FACETS	1	0.941	1			1	CLONAL	1	TRUE	NA	0.511606512527412	6		425	610	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185184	123185184	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	116	287	0	ENST00000218089.9:c.1136C>A	p.Thr379Asn	p.T379N	ENST00000218089	NM_001042749.1	379	aCc/aAc	13/35	0.299557359531153	6	FACETS	0.972	0.881	1	0.486	0.44	0.534	INDETERMINATE	2	TRUE	2	0.511606512527412	6		287	472	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45854918	45854918	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	302	690	0	ENST00000391945.4:c.2252A>C	p.Lys751Thr	p.K751T	ENST00000391945	NM_000400.3	751	aAg/aCg	23/23	0.511606512527412	3	FACETS	0.888	0.84	0.937	0.888	0.84	0.937	CLONAL	2	TRUE	1	0.511606512527412	3		690	835	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405103	70405103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199844508	NA	P-0049966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	23	552	1	ENST00000373644.4:c.2617G>A	p.Val873Ile	p.V873I	ENST00000373644	NM_030625.2	873	Gtt/Att	4/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		553	120	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510911	157510911	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	14	462	0	ENST00000346085.5:c.3686G>T	p.Gly1229Val	p.G1229V	ENST00000346085	NM_020732.3	1229	gGa/gTa	14/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		462	162	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0049967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	9	628	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.864533567208089	3	FACETS	0.069	0.045	0.1	0.023	0.015	0.034	SUBCLONAL	1	TRUE	0	0.864533567208089	3		628	432	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412493	80412493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514698	NA	P-0049967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	8	424	0	ENST00000286548.4:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000286548	NM_002072.3	183	cGa/cAa	4/7	0.844452874142224	4	FACETS	0.146	0.094	0.215	0.037	0.023	0.054	SUBCLONAL	1	TRUE	0	0.864533567208089	4		424	236	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587781845	NA	P-0049967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	501	908	1	ENST00000269305.4:c.511G>T	p.Glu171Ter	p.E171*	ENST00000269305	NM_001126112.2	171	Gag/Tag	5/11	0.864533567208089	3	FACETS	0.999	0.981	1	0.999	0.981	1	CLONAL	3	TRUE	0	0.864533567208089	3		909	554	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0049968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	82	583	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.251810734865579	2		583	465	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145770	11145770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	42	788	0	ENST00000358026.2:c.4132G>A	p.Asp1378Asn	p.D1378N	ENST00000358026	NM_001128849.1	1378	Gac/Aac	29/36	1	2	FACETS	0.48	0.4	0.57	0.48	0.4	0.57	SUBCLONAL	1	TRUE	1	0.251810734865579	2		788	695	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349405	89349405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	53	857	0	ENST00000301030.4:c.3545G>A	p.Arg1182Lys	p.R1182K	ENST00000301030	NM_001256183.1	1182	aGa/aAa	9/13	0.251810734865579	1	FACETS	0.507	0.431	0.59	0.507	0.431	0.59	SUBCLONAL	1	TRUE	0	0.251810734865579	1		857	726	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349497	89349497	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	33	626	0	ENST00000301030.4:c.3453G>C	p.Glu1151Asp	p.E1151D	ENST00000301030	NM_001256183.1	1151	gaG/gaC	9/13	0.251810734865579	1	FACETS	0.368	0.299	0.447	0.368	0.299	0.447	SUBCLONAL	1	TRUE	0	0.251810734865579	1		626	622	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161673	56161673	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	26	312	0	ENST00000399503.3:c.1170G>C	p.Gln390His	p.Q390H	ENST00000399503	NM_005921.1	390	caG/caC	6/20	0.165513580519668	2	FACETS	0.531	0.42	0.658	0.265	0.21	0.329	SUBCLONAL	1	TRUE	0	0.251810734865579	2		312	389	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	101	350	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.491885399957281	3	FACETS	0.839	0.759	0.921	0.839	0.759	0.921	CLONAL	2	TRUE	1	0.491885399957281	3		350	305	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	73	419	0	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.528	0.462	0.599	0.528	0.462	0.599	SUBCLONAL	1	TRUE	1	0.491885399957281	2		419	562	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	149	782	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.851	0.779	0.926	0.851	0.779	0.926	CLONAL	1	TRUE	1	0.491885399957281	2		787	712	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	119	616	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.706	0.638	0.778	0.706	0.638	0.778	SUBCLONAL	1	TRUE	1	0.491885399957281	2		618	685	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743932	41743933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs778012871	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	54	930	3	ENST00000301178.4:c.874dup	p.His292ProfsTer47	p.H292Pfs*47	ENST00000301178	NM_021913.4	289	-/C	7/20	1	2	FACETS	0.27	0.229	0.314	0.27	0.229	0.314	SUBCLONAL	1	TRUE	1	0.491885399957281	2		933	814	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	30	352	1	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.496	0.401	0.602	0.496	0.401	0.602	SUBCLONAL	1	TRUE	1	0.491885399957281	2		353	246	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	44	363	3	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.824	0.699	0.961	0.824	0.699	0.961	CLONAL	1	TRUE	1	0.491885399957281	2		366	217	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	41	302	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.689	0.578	0.81	0.689	0.578	0.81	SUBCLONAL	1	TRUE	1	0.491885399957281	2		302	242	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	115	363	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.491885399957281	2		363	411	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100728	8100728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs771019738	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	130	711	7	ENST00000346208.3:c.708del	p.Ser237AlafsTer28	p.S237Afs*28	ENST00000346208		234	ttC/tt	3/6	1	2	FACETS	0.936	0.852	1	0.936	0.852	1	CLONAL	1	TRUE	1	0.491885399957281	2		718	565	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	324	824	5	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.857	0.814	0.9	1	0.996	1	CLONAL	2	TRUE	1	0.491885399957281	2		829	769	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	61	695	3	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.318	0.274	0.367	0.318	0.274	0.367	SUBCLONAL	1	TRUE	1	0.491885399957281	2		698	779	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843429	128843429	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs115491500	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	92	485	0	ENST00000249373.3:c.536C>T	p.Thr179Met	p.T179M	ENST00000249373	NM_005631.4	179	aCg/aTg	2/12	0.491885399957281	3	FACETS	0.841	0.749	0.939	0.421	0.374	0.47	CLONAL	1	TRUE	1	0.491885399957281	3		485	554	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563296	21563296	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	174	1017	0	ENST00000382592.4:c.623C>T	p.Pro208Leu	p.P208L	ENST00000382592	NM_014572.2	208	cCg/cTg	4/8	1	2	FACETS	0.763	0.703	0.826	0.763	0.703	0.826	SUBCLONAL	1	TRUE	1	0.491885399957281	2		1017	927	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136949	64136949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749917386	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	131	688	0	ENST00000334205.4:c.1460G>A	p.Arg487Gln	p.R487Q	ENST00000334205	NM_003942.2	487	cGg/cAg	13/17	1	2	FACETS	0.779	0.708	0.853	0.779	0.708	0.853	SUBCLONAL	1	TRUE	1	0.491885399957281	2		688	684	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444659	78444659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs908264837	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	108	475	1	ENST00000370768.2:c.30del	p.Ser11LeufsTer43	p.S11Lfs*43	ENST00000370768	NM_003902.3	10	ccC/cc	1/20	1	2	FACETS	0.801	0.722	0.885	0.801	0.722	0.885	CLONAL	1	TRUE	1	0.491885399957281	2		476	548	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	83	467	6	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.614	0.542	0.69	0.614	0.542	0.69	SUBCLONAL	1	TRUE	1	0.491885399957281	2		473	550	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248860	133248860	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs116260568	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	50	664	3	ENST00000320574.5:c.1735C>T	p.Arg579Cys	p.R579C	ENST00000320574	NM_006231.2	579	Cgc/Tgc	16/49	1	2	FACETS	0.325	0.275	0.38	0.325	0.275	0.38	SUBCLONAL	1	TRUE	1	0.491885399957281	2		667	625	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612341	1612341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376471101	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	237	939	1	ENST00000344749.5:c.1678C>T	p.Arg560Trp	p.R560W	ENST00000344749	NM_001136139.2	560	Cgg/Tgg	18/19	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.491885399957281	2		940	904	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272336	15272337	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs771517374	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	171	973	5	ENST00000263388.2:c.6102dup	p.Gly2035ArgfsTer60	p.G2035Rfs*60	ENST00000263388	NM_000435.2	2034	-/C	33/33	1	2	FACETS	0.845	0.778	0.914	0.845	0.778	0.914	CLONAL	1	TRUE	1	0.491885399957281	2		978	823	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686901	37686901	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	118	420	1	ENST00000447079.4:c.3810del	p.Gly1271AspfsTer23	p.G1271Dfs*23	ENST00000447079	NM_015083.1	1269	Ccc/cc	14/14	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.491885399957281	2		421	458	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209652	98209652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372828014	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	53	703	1	ENST00000331920.6:c.3886G>A	p.Gly1296Arg	p.G1296R	ENST00000331920	NM_000264.3	1296	Gga/Aga	23/24	0.433767798020286	3	FACETS	0.393	0.334	0.458	0.197	0.167	0.229	SUBCLONAL	1	TRUE	1	0.491885399957281	3		704	683	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020769	37020769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	31	545	0	ENST00000358127.4:c.76del	p.Val26PhefsTer3	p.V26Ffs*3	ENST00000358127	NM_001280556.1	26	Gtt/tt	2/10	0.433767798020286	3	FACETS	0.273	0.22	0.333	0.137	0.11	0.167	SUBCLONAL	1	TRUE	1	0.491885399957281	3		545	575	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456355	99456355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	31	501	0	ENST00000268035.6:c.1672C>T	p.Pro558Ser	p.P558S	ENST00000268035	NM_000875.3	558	Ccc/Tcc	8/21	1	2	FACETS	0.285	0.23	0.347	0.285	0.23	0.347	SUBCLONAL	1	TRUE	1	0.491885399957281	2		501	442	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955112	17955112	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755706305	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	59	892	5	ENST00000458235.1:c.115del	p.Gln39SerfsTer108	p.Q39Sfs*108	ENST00000458235	NM_000215.3	39	Cag/ag	2/24	1	2	FACETS	0.29	0.248	0.335	0.29	0.248	0.335	SUBCLONAL	1	TRUE	1	0.491885399957281	2		897	828	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958190	2958190	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753952757	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	119	718	2	ENST00000396946.4:c.2542C>T	p.Arg848Cys	p.R848C	ENST00000396946	NM_032415.4	848	Cgc/Tgc	19/25	0.491885399957281	3	FACETS	0.773	0.698	0.852	0.386	0.349	0.426	SUBCLONAL	1	TRUE	1	0.491885399957281	3		720	780	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416952	416953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs771545848	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	74	451	2	ENST00000399788.2:c.3597dup	p.Gly1200ArgfsTer7	p.G1200Rfs*7	ENST00000399788	NM_001042603.1	1199	-/A	23/28	NA	2	FACETS	0.8	0.705	0.902			1	INDETERMINATE	1	TRUE	NA	0.491885399957281	2		453	376	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709529	176709529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777258117	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	12	322	0	ENST00000439151.2:c.5956C>T	p.Arg1986Cys	p.R1986C	ENST00000439151	NM_022455.4	1986	Cgc/Tgc	19/23	1	2	FACETS	0.214	0.15	0.293	0.214	0.15	0.293	SUBCLONAL	1	TRUE	1	0.491885399957281	2		322	228	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413710	138413710	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	131	423	2	ENST00000289153.2:c.1810del	p.Arg604GlyfsTer4	p.R604Gfs*4	ENST00000289153	NM_006219.2	604	Cgg/gg	12/22	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.491885399957281	2		425	492	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732911	30732911	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	65	265	0	ENST00000295754.5:c.1525-1G>T		p.X509_splice	ENST00000295754	NM_003242.5	509			1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.491885399957281	2		265	250	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	158	755	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.846	0.777	0.919	0.846	0.777	0.919	CLONAL	1	TRUE	1	0.491885399957281	2		758	759	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	103	472	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.491885399957281	2		475	357	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347117	89347117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184729090	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	35	725	0	ENST00000301030.4:c.5833G>A	p.Glu1945Lys	p.E1945K	ENST00000301030	NM_001256183.1	1945	Gag/Aag	9/13	1	2	FACETS	0.211	0.172	0.255	0.211	0.172	0.255	SUBCLONAL	1	TRUE	1	0.491885399957281	2		725	675	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907420	32907421	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359306	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	27	266	0	ENST00000380152.3:c.1813dup	p.Ile605AsnfsTer11	p.I605Nfs*11	ENST00000380152		602	gga/ggAa	10/27	1	2	FACETS	0.665	0.535	0.811	0.665	0.535	0.811	SUBCLONAL	1	TRUE	1	0.491885399957281	2		266	165	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	70	368	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	0.543	0.474	0.617	0.543	0.474	0.617	SUBCLONAL	1	TRUE	1	0.491885399957281	2		368	524	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845528	63845528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs993996582	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	23	247	0	ENST00000279873.7:c.1267C>T	p.Arg423Trp	p.R423W	ENST00000279873	NM_032199.2	423	Cgg/Tgg	9/10	1	2	FACETS	0.407	0.318	0.508	0.407	0.318	0.508	SUBCLONAL	1	TRUE	1	0.491885399957281	2		247	230	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614463	38614463	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	20	361	0	ENST00000299084.4:c.234del	p.Asp79ThrfsTer42	p.D79Tfs*42	ENST00000299084	NM_152594.2	77	Aaa/aa	3/7	1	2	FACETS	0.355	0.272	0.452	0.355	0.272	0.452	SUBCLONAL	1	TRUE	1	0.491885399957281	2		361	229	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133806	55133806	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs77524207	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	69	440	1	ENST00000257290.5:c.1019G>A	p.Arg340Gln	p.R340Q	ENST00000257290	NM_006206.4	340	cGg/cAg	7/23	1	2	FACETS	0.76	0.666	0.861	0.76	0.666	0.861	SUBCLONAL	1	TRUE	1	0.491885399957281	2		441	369	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228310	228310	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1235961098	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	12	253	0	ENST00000264932.6:c.632A>G	p.Tyr211Cys	p.Y211C	ENST00000264932	NM_004168.2	211	tAt/tGt	6/15	1	2	FACETS	0.274	0.193	0.374	0.274	0.193	0.374	SUBCLONAL	1	TRUE	1	0.491885399957281	2		253	178	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572693	141572693	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1438656302	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	114	583	1	ENST00000220592.5:c.377G>A	p.Arg126His	p.R126H	ENST00000220592	NM_012154.3	126	cGc/cAc	4/19	1	2	FACETS	0.849	0.767	0.935	0.849	0.767	0.935	CLONAL	1	TRUE	1	0.491885399957281	2		584	546	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500436	99500436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760362276	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	32	774	0	ENST00000268035.6:c.3869C>T	p.Pro1290Leu	p.P1290L	ENST00000268035	NM_000875.3	1290	cCg/cTg	21/21	1	2	FACETS	0.21	0.169	0.255	0.21	0.169	0.255	SUBCLONAL	1	TRUE	1	0.491885399957281	2		774	621	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218450	36218451	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	123	776	0	ENST00000222270.7:c.4235dup	p.Leu1413ProfsTer265	p.L1413Pfs*265	ENST00000222270	NM_014727.1	1410	cag/caGg	16/37	1	2	FACETS	0.784	0.71	0.861	0.784	0.71	0.861	SUBCLONAL	1	TRUE	1	0.491885399957281	2		776	638	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716199	243716199	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	84	490	0	ENST00000263826.5:c.995T>C	p.Leu332Pro	p.L332P	ENST00000263826	NM_005465.4	332	cTa/cCa	10/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.491885399957281	2		490	284	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145678	61145678	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773764180	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	33	421	0	ENST00000295025.8:c.790C>T	p.Arg264Trp	p.R264W	ENST00000295025	NM_002908.2	264	Cgg/Tgg	7/11	1	2	FACETS	0.393	0.321	0.475	0.393	0.321	0.475	SUBCLONAL	1	TRUE	1	0.491885399957281	2		421	341	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526140	63526140	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1285654850	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	127	542	0	ENST00000307078.5:c.2486C>T	p.Pro829Leu	p.P829L	ENST00000307078	NM_004655.3	829	cCg/cTg	11/11	1	2	FACETS	0.836	0.759	0.916	0.836	0.759	0.916	CLONAL	1	TRUE	1	0.491885399957281	2		542	618	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345918	70345918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751774081	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	61	528	1	ENST00000374080.3:c.2455C>T	p.Arg819Trp	p.R819W	ENST00000374080		819	Cgg/Tgg	18/45	1	2	FACETS	0.466	0.402	0.536	0.466	0.402	0.536	SUBCLONAL	1	TRUE	1	0.491885399957281	2		529	532	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874749	151874749	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	98	373	0	ENST00000262189.6:c.7789C>G	p.Pro2597Ala	p.P2597A	ENST00000262189	NM_170606.2	2597	Cca/Gca	38/59	0.491885399957281	3	FACETS	1	0.95	1	0.549	0.492	0.609	CLONAL	1	TRUE	1	0.491885399957281	3		373	452	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212236	36212236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301144035	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	167	705	1	ENST00000222270.7:c.1987G>A	p.Glu663Lys	p.E663K	ENST00000222270	NM_014727.1	663	Gaa/Aaa	3/37	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.491885399957281	2		706	643	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504591	103504591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778293	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	46	299	0	ENST00000355739.4:c.212G>A	p.Arg71His	p.R71H	ENST00000355739	NM_000123.3	71	cGt/cAt	2/15	1	2	FACETS	0.904	0.77	1	0.904	0.77	1	CLONAL	1	TRUE	1	0.491885399957281	2		299	207	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31504699	31504699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1032572786	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	71	390	1	ENST00000344624.3:c.1631G>A	p.Arg544His	p.R544H	ENST00000344624		544	cGc/cAc	8/33	1	2	FACETS	0.547	0.478	0.621	0.547	0.478	0.621	SUBCLONAL	1	TRUE	1	0.491885399957281	2		391	528	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204623	128204623	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	70	733	0	ENST00000341105.2:c.818del	p.Gly273AspfsTer53	p.G273Dfs*53	ENST00000341105	NM_032638.4	273	gGa/ga	3/6	1	2	FACETS	0.377	0.328	0.431	0.377	0.328	0.431	SUBCLONAL	1	TRUE	1	0.491885399957281	2		733	754	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165569	47165569	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	109	519	0	ENST00000409792.3:c.557C>A	p.Pro186Gln	p.P186Q	ENST00000409792	NM_014159.6	186	cCg/cAg	3/21	1	2	FACETS	0.876	0.79	0.966	0.876	0.79	0.966	CLONAL	1	TRUE	1	0.491885399957281	2		519	506	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735643	204735643	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	50	335	0	ENST00000302823.3:c.444G>T	p.Gln148His	p.Q148H	ENST00000302823	NM_005214.4	148	caG/caT	2/4	1	2	FACETS	0.779	0.666	0.9	0.779	0.666	0.9	SUBCLONAL	1	TRUE	1	0.491885399957281	2		335	261	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640404	3640404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373231418	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	67	838	1	ENST00000294008.3:c.3235C>T	p.Pro1079Ser	p.P1079S	ENST00000294008	NM_032444.2	1079	Cca/Tca	12/15	1	2	FACETS	0.318	0.276	0.365	0.318	0.276	0.365	SUBCLONAL	1	TRUE	1	0.491885399957281	2		839	856	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278818	1278818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs939537185	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	185	697	1	ENST00000310581.5:c.2224C>T	p.Arg742Cys	p.R742C	ENST00000310581	NM_198253.2	742	Cgt/Tgt	6/16	1	2	FACETS	0.99	0.916	1	0.99	0.916	1	CLONAL	1	TRUE	1	0.491885399957281	2		698	760	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394398	162394398	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	51	384	0	ENST00000366898.1:c.670G>T	p.Val224Leu	p.V224L	ENST00000366898	NM_004562.2	224	Gta/Tta	6/12	1	2	FACETS	0.738	0.632	0.853	0.738	0.632	0.853	SUBCLONAL	1	TRUE	1	0.491885399957281	2		384	281	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245023	133245024	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs752846614	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	47	895	6	ENST00000320574.5:c.2091dup	p.Phe699ValfsTer11	p.F699Vfs*11	ENST00000320574	NM_006231.2	697	-/C	19/49	1	2	FACETS	0.257	0.216	0.303	0.257	0.216	0.303	SUBCLONAL	1	TRUE	1	0.491885399957281	2		901	743	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797890	45797890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146044717	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	196	889	0	ENST00000450313.1:c.881G>A	p.Arg294His	p.R294H	ENST00000450313	NM_012222.2	294	cGc/cAc	10/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.491885399957281	2		889	762	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160330	108160330	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	12	195	0	ENST00000278616.4:c.4238A>C	p.Asp1413Ala	p.D1413A	ENST00000278616	NM_000051.3	1413	gAt/gCt	29/63	1	2	FACETS	0.452	0.32	0.61	0.452	0.32	0.61	SUBCLONAL	1	TRUE	1	0.491885399957281	2		195	108	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	495069	495069	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	61	374	0	ENST00000399788.2:c.237A>T	p.Glu79Asp	p.E79D	ENST00000399788	NM_001042603.1	79	gaA/gaT	2/28	NA	2	FACETS	0.919	0.8	1			1	INDETERMINATE	1	TRUE	NA	0.491885399957281	2		374	270	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435212	18435212	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	28	306	0	ENST00000266497.5:c.197C>A	p.Pro66His	p.P66H	ENST00000266497		66	cCc/cAc	1/31	1	2	FACETS	0.602	0.485	0.733	0.602	0.485	0.733	SUBCLONAL	1	TRUE	1	0.491885399957281	2		306	189	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112332	115112332	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	109	335	0	ENST00000257566.3:c.1408G>A	p.Ala470Thr	p.A470T	ENST00000257566	NM_016569.3	470	Gcg/Acg	7/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.491885399957281	2		335	364	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263889	133263889	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	108	483	0	ENST00000320574.5:c.13A>G	p.Ser5Gly	p.S5G	ENST00000320574	NM_006231.2	5	Agc/Ggc	1/49	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.491885399957281	2		483	430	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066734	30066734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	39	363	0	ENST00000331968.5:c.2397G>A	p.Met799Ile	p.M799I	ENST00000331968	NM_002742.2	799	atG/atA	16/18	1	2	FACETS	0.695	0.581	0.821	0.695	0.581	0.821	SUBCLONAL	1	TRUE	1	0.491885399957281	2		363	228	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778480	3778480	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	132	802	0	ENST00000262367.5:c.6568C>T	p.Arg2190Ter	p.R2190*	ENST00000262367	NM_004380.2	2190	Cga/Tga	31/31	1	2	FACETS	0.709	0.644	0.777	0.709	0.644	0.777	SUBCLONAL	1	TRUE	1	0.491885399957281	2		802	757	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991631	72991631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751779532	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	114	634	0	ENST00000268489.5:c.2414G>A	p.Arg805Gln	p.R805Q	ENST00000268489	NM_006885.3	805	cGg/cAg	2/10	1	2	FACETS	0.712	0.642	0.786	0.712	0.642	0.786	SUBCLONAL	1	TRUE	1	0.491885399957281	2		634	651	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942139	81942139	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	83	637	2	ENST00000359376.3:c.1676G>A	p.Gly559Asp	p.G559D	ENST00000359376	NM_002661.3	559	gGc/gAc	17/33	1	2	FACETS	0.579	0.511	0.651	0.579	0.511	0.651	SUBCLONAL	1	TRUE	1	0.491885399957281	2		639	583	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585450	29585450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753997885	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	31	477	0	ENST00000356175.3:c.4199C>T	p.Pro1400Leu	p.P1400L	ENST00000356175	NM_000267.3	1400	cCg/cTg	31/57	1	2	FACETS	0.383	0.31	0.465	0.383	0.31	0.465	SUBCLONAL	1	TRUE	1	0.491885399957281	2		477	329	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436091	56436092	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	151	592	0	ENST00000407977.2:c.1045dup	p.Ala349GlyfsTer94	p.A349Gfs*94	ENST00000407977		349	gcc/gGcc	9/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.491885399957281	2		592	576	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125355	7125355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372010924	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	41	771	0	ENST00000302850.5:c.3197G>A	p.Arg1066Gln	p.R1066Q	ENST00000302850	NM_000208.2	1066	cGa/cAa	17/22	1	2	FACETS	0.229	0.19	0.273	0.229	0.19	0.273	SUBCLONAL	1	TRUE	1	0.491885399957281	2		771	728	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252790	10252790	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	113	703	2	ENST00000340748.4:c.3175C>A	p.Arg1059Ser	p.R1059S	ENST00000340748		1059	Cgc/Agc	29/40	1	2	FACETS	0.623	0.56	0.688	0.623	0.56	0.688	SUBCLONAL	1	TRUE	1	0.491885399957281	2		705	738	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288831	15288831	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	109	281	0	ENST00000263388.2:c.3908C>T	p.Pro1303Leu	p.P1303L	ENST00000263388	NM_000435.2	1303	cCa/cTa	24/33	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.491885399957281	2		281	373	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298748	15298748	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	145	811	0	ENST00000263388.2:c.1550G>T	p.Arg517Met	p.R517M	ENST00000263388	NM_000435.2	517	aGg/aTg	10/33	1	2	FACETS	0.77	0.703	0.839	0.77	0.703	0.839	SUBCLONAL	1	TRUE	1	0.491885399957281	2		811	766	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763407	41763407	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	40	510	0	ENST00000301178.4:c.2209del	p.Val737Ter	p.V737*	ENST00000301178	NM_021913.4	736	Ggg/gg	19/20	1	2	FACETS	0.357	0.297	0.425	0.357	0.297	0.425	SUBCLONAL	1	TRUE	1	0.491885399957281	2		510	455	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143420	30143421	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	142	594	0	ENST00000389048.3:c.105dup	p.Pro36AlafsTer22	p.P36Afs*22	ENST00000389048	NM_004304.4	35	-/G	1/29	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.491885399957281	2		594	534	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150010	202150011	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	79	538	0	ENST00000358485.4:c.1452_1453del	p.Cys485ProfsTer12	p.C485Pfs*12	ENST00000358485	NM_001080125.1	484	cTT/c	8/9	1	2	FACETS	0.605	0.533	0.682	0.605	0.533	0.682	SUBCLONAL	1	TRUE	1	0.491885399957281	2		538	531	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151253	202151254	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	25	334	0	ENST00000358485.4:c.1557dup	p.Lys520GlufsTer19	p.K520Efs*19	ENST00000358485	NM_001080125.1	518	atg/atGg	9/9	1	2	FACETS	0.343	0.271	0.427	0.343	0.271	0.427	SUBCLONAL	1	TRUE	1	0.491885399957281	2		334	296	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547997	41547997	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	144	528	1	ENST00000263253.7:c.2978A>G	p.Gln993Arg	p.Q993R	ENST00000263253	NM_001429.3	993	cAg/cGg	15/31	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.491885399957281	2		529	502	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098311	47098311	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	33	284	0	ENST00000409792.3:c.6963G>T	p.Gln2321His	p.Q2321H	ENST00000409792	NM_014159.6	2321	caG/caT	15/21	1	2	FACETS	0.453	0.37	0.546	0.453	0.37	0.546	SUBCLONAL	1	TRUE	1	0.491885399957281	2		284	296	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149245706	149245707	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	132	574	0	ENST00000360632.3:c.821dup	p.Val275SerfsTer19	p.V275Sfs*19	ENST00000360632	NM_015472.4	274	cca/ccCa	5/7	1	2	FACETS	0.921	0.839	1	0.921	0.839	1	CLONAL	1	TRUE	1	0.491885399957281	2		574	583	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196873	106196873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1171920925	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	51	324	0	ENST00000380013.4:c.5206G>A	p.Ala1736Thr	p.A1736T	ENST00000380013	NM_001127208.2	1736	Gcc/Acc	11/11	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.491885399957281	2		324	188	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177644	56177644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149242419	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	99	389	1	ENST00000399503.3:c.2617G>A	p.Val873Ile	p.V873I	ENST00000399503	NM_005921.1	873	Gta/Ata	14/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.491885399957281	2		390	347	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397168	397168	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	112	441	0	ENST00000380956.4:c.553C>A	p.Gln185Lys	p.Q185K	ENST00000380956	NM_001195286.1	185	Cag/Aag	5/9	1	2	FACETS	0.979	0.886	1	0.979	0.886	1	CLONAL	1	TRUE	1	0.491885399957281	2		441	465	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324179	31324179	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	77	651	0	ENST00000412585.2:c.384del	p.Pro129ArgfsTer22	p.P129Rfs*22	ENST00000412585	NM_005514.6	128	ggG/gg	3/8	1	2	FACETS	0.578	0.508	0.652	0.578	0.508	0.652	SUBCLONAL	1	TRUE	1	0.491885399957281	2		651	542	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894827	101894827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	70	234	0	ENST00000374994.4:c.380C>T	p.Ala127Val	p.A127V	ENST00000374994	NM_004612.2	127	gCa/gTa	3/9	0.433767798020286	3	FACETS	1	0.941	1	0.559	0.491	0.631	CLONAL	1	TRUE	1	0.491885399957281	3		234	317	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223790	53223790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	63	954	0	ENST00000375401.3:c.3569G>A	p.Cys1190Tyr	p.C1190Y	ENST00000375401	NM_004187.3	1190	tGt/tAt	23/26	1	2	FACETS	0.3	0.259	0.346	0.3	0.259	0.346	SUBCLONAL	1	TRUE	1	0.491885399957281	2		954	853	SUCCESS
AR	367	MSKCC	GRCh37	X	66863145	66863145	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1233954307	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	82	577	0	ENST00000374690.3:c.1664C>A	p.Pro555Gln	p.P555Q	ENST00000374690	NM_000044.3	555	cCa/cAa	2/8	1	2	FACETS	0.825	0.732	0.924	0.825	0.732	0.924	CLONAL	1	TRUE	1	0.491885399957281	2		577	404	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352357	70352357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	66	571	1	ENST00000374080.3:c.4384C>T	p.Arg1462Cys	p.R1462C	ENST00000374080		1462	Cgc/Tgc	31/45	1	2	FACETS	0.542	0.471	0.619	0.542	0.471	0.619	SUBCLONAL	1	TRUE	1	0.491885399957281	2		572	495	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356781	70356781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761189421	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	175	691	2	ENST00000374080.3:c.5453C>T	p.Pro1818Leu	p.P1818L	ENST00000374080		1818	cCg/cTg	38/45	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.491885399957281	2		693	657	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360643	70360643	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	49	365	0	ENST00000374080.3:c.6203A>G	p.Gln2068Arg	p.Q2068R	ENST00000374080		2068	cAg/cGg	42/45	1	2	FACETS	0.561	0.477	0.653	0.561	0.477	0.653	SUBCLONAL	1	TRUE	1	0.491885399957281	2		365	355	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210228	123210228	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	31	484	0	ENST00000218089.9:c.2580G>T	p.Lys860Asn	p.K860N	ENST00000218089	NM_001042749.1	860	aaG/aaT	26/35	1	2	FACETS	0.387	0.313	0.47	0.387	0.313	0.47	SUBCLONAL	1	TRUE	1	0.491885399957281	2		484	326	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215368	123215368	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	19	348	0	ENST00000218089.9:c.2914A>G	p.Met972Val	p.M972V	ENST00000218089	NM_001042749.1	972	Atg/Gtg	28/35	1	2	FACETS	0.301	0.228	0.385	0.301	0.228	0.385	SUBCLONAL	1	TRUE	1	0.491885399957281	2		348	257	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0005905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	638	456	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.62991488687079	4	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	FALSE	2	0.62991488687079	4		456	1371	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	234	301	0				ENST00000310581	NM_198253.2	-/1132			0.62991488687079	7	FACETS	1	0.987	1	0.484	0.452	0.516	CLONAL	2	FALSE	2	0.62991488687079	7		301	791	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806555	1806555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1189213092	NA	P-0005905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	448	884	0	ENST00000260795.2:c.1271C>T	p.Ser424Phe	p.S424F	ENST00000260795		424	tCc/tTc	9/17	0.62991488687079	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	FALSE	2	0.62991488687079	4		884	1015	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638375	176638375	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	19	418	0	ENST00000439151.2:c.2975C>T	p.Ser992Phe	p.S992F	ENST00000439151	NM_022455.4	992	tCt/tTt	5/23	0.62991488687079	3	FACETS	0.891	0.69	1	0.446	0.345	0.559	CLONAL	1	FALSE	1	0.62991488687079	3		418	89	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652112	36652113	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0005905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	759	733	0	ENST00000244741.5:c.237dup	p.Thr80HisfsTer9	p.T80Hfs*9	ENST00000244741	NM_000389.4	78	-/C	2/3	0.62991488687079	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	FALSE	1	0.62991488687079	3		733	1454	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762246	43762246	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	12	297	1	ENST00000382044.4:c.1199C>T	p.Ser400Leu	p.S400L	ENST00000382044	NM_001141980.1	400	tCa/tTa	11/28	0.481056597436734	4	FACETS	0.828	0.592	1	0.414	0.296	0.554	CLONAL	1	FALSE	2	0.62991488687079	4		298	75	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847225	68847225	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	20	294	0	ENST00000261769.5:c.1147C>G	p.Gln383Glu	p.Q383E	ENST00000261769	NM_004360.3	383	Cag/Gag	9/16	0.469291723954057	5	FACETS	1	0.894	1	0.429	0.334	0.535	CLONAL	1	FALSE	2	0.62991488687079	5		294	96	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828561	72828561	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs772944287	NA	P-0005905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	34	475	0	ENST00000268489.5:c.8020A>G	p.Ile2674Val	p.I2674V	ENST00000268489	NM_006885.3	2674	Att/Gtt	9/10	0.469291723954057	5	FACETS	1	0.901	1	0.38	0.314	0.453	CLONAL	1	FALSE	2	0.62991488687079	5		475	184	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527422	41527422	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	25	353	0	ENST00000263253.7:c.1313G>C	p.Gly438Ala	p.G438A	ENST00000263253	NM_001429.3	438	gGa/gCa	6/31	0.62991488687079	5	FACETS	0.78	0.628	0.946	0.52	0.419	0.631	CLONAL	2	FALSE	2	0.62991488687079	5		353	99	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527636	41527636	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	12	205	0	ENST00000263253.7:c.1527G>A	p.Met509Ile	p.M509I	ENST00000263253	NM_001429.3	509	atG/atA	6/31	0.62991488687079	5	FACETS	0.95	0.678	1	0.317	0.226	0.424	CLONAL	1	FALSE	2	0.62991488687079	5		205	78	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564384	86564384	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs760851896	NA	P-0005905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	158	658	0	ENST00000274376.6:c.116C>A	p.Pro39His	p.P39H	ENST00000274376	NM_002890.2	39	cCc/cAc	1/25	0.62991488687079	3	FACETS	0.993	0.913	1	0.497	0.456	0.539	CLONAL	1	FALSE	1	0.62991488687079	3		658	664	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984385	201984389	+	protein_altering_variant	In_Frame_Del	DEL	CGTCT	CGTCT	AG	novel	NA	P-0005905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	89	597	1	ENST00000359651.3:c.1050_1054delinsAG	p.Val351_Tyr352delinsAsp	p.V351_Y352delinsD	ENST00000359651		350	ctCGTCTac/ctAGac	8/8	NA	2	FACETS	1	0.963	1			1	INDETERMINATE	1	FALSE	NA	0.62991488687079	2		598	246	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0006164-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	166	495	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.968	0.894	1	0.968	0.894	1	CLONAL	1	TRUE	1	0.607090628454265	2		495	565	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006164-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	207	301	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.607090628454265	2		301	614	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139157	108139157	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006164-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	184	472	0	ENST00000278616.4:c.2659G>A	p.Glu887Lys	p.E887K	ENST00000278616	NM_000051.3	887	Gaa/Aaa	18/63	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.607090628454265	2		472	596	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5463007	5463007	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006164-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	168	341	0	ENST00000381577.3:c.568C>G	p.Leu190Val	p.L190V	ENST00000381577	NM_014143.3	190	Ctt/Gtt	4/7	0.607090628454265	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.607090628454265	1		341	348	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41562649	41562649	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1417280123	NA	P-0006164-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	170	290	0	ENST00000263253.7:c.3853G>C	p.Glu1285Gln	p.E1285Q	ENST00000263253	NM_001429.3	1285	Gaa/Caa	23/31	0.607090628454265	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.607090628454265	1		290	380	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028880	47028880	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006164-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	269	310	0	ENST00000377604.3:c.184G>T	p.Glu62Ter	p.E62*	ENST00000377604	NM_001204468.1	62	Gag/Tag	3/24	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.607090628454265	1		310	437	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317156	11317156	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	192	531	1	ENST00000361445.4:c.338A>T	p.Asn113Ile	p.N113I	ENST00000361445	NM_004958.3	113	aAc/aTc	4/58	0.294541246169963	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	0	0.333704972617795	1		532	819	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781231	161781231	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	68	348	0	ENST00000366898.1:c.1174A>G	p.Arg392Gly	p.R392G	ENST00000366898	NM_004562.2	392	Aga/Gga	11/12	1	2	FACETS	0.568	0.494	0.649	0.568	0.494	0.649	SUBCLONAL	1	FALSE	1	0.333704972617795	2		348	717	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434122	121434122	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	118	510	0	ENST00000257555.6:c.1013G>C	p.Gly338Ala	p.G338A	ENST00000257555		338	gGc/gCc	5/10	0.333704972617795	1	FACETS	0.592	0.533	0.655	0.592	0.533	0.655	SUBCLONAL	1	FALSE	0	0.333704972617795	1		510	995	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20153859	20153859	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	62	145	0	ENST00000379607.5:c.201A>C	p.Lys67Asn	p.K67N	ENST00000379607	NM_001412.3	67	aaA/aaC	3/7	1	1	FACETS	0.853	0.763	0.942	1	0.985	1	CLONAL	3	FALSE	0	0.333704972617795	1		145	121	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860671	151860671	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006655-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	336	544	0	ENST00000262189.6:c.9991del	p.Ser3331ValfsTer30	p.S3331Vfs*30	ENST00000262189	NM_170606.2	3331	Agt/gt	43/59	1	2	FACETS	0.832	0.787	0.879	1	0.995	1	CLONAL	2	FALSE	1	0.333704972617795	2		544	1210	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0009122-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	180	576	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.358376724651524	3	FACETS	0.936	0.867	1	0.624	0.578	0.671	CLONAL	2	TRUE	0	0.358376724651524	3		576	633	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555525585	NA	P-0009122-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	200	468	1	ENST00000269305.4:c.673-2A>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.358376724651524	2	FACETS	0.922	0.86	0.986	0.922	0.86	0.986	CLONAL	2	TRUE	0	0.358376724651524	2		469	605	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431634	6431634	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009122-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	89	361	0	ENST00000356142.4:c.187G>C	p.Asp63His	p.D63H	ENST00000356142	NM_018890.3	63	Gat/Cat	3/7	0.281713442381464	4	FACETS	1	0.911	1	0.516	0.457	0.578	CLONAL	1	TRUE	2	0.358376724651524	4		361	654	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11999013	11999013	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0009122-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	100	237	0	ENST00000353533.5:c.513+2T>C		p.X171_splice	ENST00000353533	NM_003010.3	171			0.358376724651524	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	0	0.358376724651524	2		237	267	SUCCESS
ATR	545	MSKCC	GRCh37	3	142172040	142172040	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009122-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	299	445	0	ENST00000350721.4:c.7691A>G	p.Glu2564Gly	p.E2564G	ENST00000350721	NM_001184.3	2564	gAa/gGa	46/47	0.358376724651524	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	0	0.358376724651524	3		445	620	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968111	55968111	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009122-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	106	432	0	ENST00000263923.4:c.2219G>T	p.Cys740Phe	p.C740F	ENST00000263923	NM_002253.2	740	tGc/tTc	15/30	0.281713442381464	4	FACETS	1	0.955	1	0.56	0.502	0.621	CLONAL	1	TRUE	2	0.358376724651524	4		432	718	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576802	67576802	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009122-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	71	333	0	ENST00000274335.5:c.884C>A	p.Ser295Ter	p.S295*	ENST00000274335		295	tCa/tAa	6/15	0.358376724651524	2	FACETS	1	0.923	1	0.535	0.47	0.605	CLONAL	1	TRUE	0	0.358376724651524	2		333	370	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0012045-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	196	456	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.891	0.829	0.955	0.891	0.829	0.955	CLONAL	1	TRUE	1	0.681130882642033	2		456	646	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981851	201981852	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0012045-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	297	767	1	ENST00000359651.3:c.567dup	p.Ser190LeufsTer6	p.S190Lfs*6	ENST00000359651		188	gcc/gCcc	4/8	1	2	FACETS	0.957	0.904	1	0.957	0.904	1	CLONAL	1	TRUE	1	0.681130882642033	2		768	911	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982433	25982433	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012045-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	329	345	0	ENST00000435504.4:c.857T>C	p.Leu286Pro	p.L286P	ENST00000435504		286	cTg/cCg	9/13	0.663740130491377	2	FACETS	0.947	0.91	0.984	0.947	0.91	0.984	CLONAL	2	TRUE	0	0.681130882642033	2		345	510	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0012273-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	107	557	5	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.230999791594364	1	FACETS	0.993	0.89	1	0.993	0.89	1	CLONAL	1	FALSE	0	0.230999791594364	1		562	825	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256501	16256501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012273-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	114	474	0	ENST00000375759.3:c.3766G>A	p.Glu1256Lys	p.E1256K	ENST00000375759	NM_015001.2	1256	Gaa/Aaa	11/15	0.230999791594364	3	FACETS	1	0.973	1	0.62	0.557	0.686	CLONAL	1	FALSE	1	0.230999791594364	3		474	888	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849835	156849835	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012273-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	180	567	0	ENST00000524377.1:c.2091G>C	p.Glu697Asp	p.E697D	ENST00000524377	NM_002529.3	697	gaG/gaC	16/17	0.159628674568593	2	FACETS	0.806	0.743	0.871	0.806	0.743	0.871	CLONAL	2	FALSE	0	0.230999791594364	2		567	967	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464454	25464454	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012273-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	99	495	0	ENST00000264709.3:c.2059G>T	p.Val687Phe	p.V687F	ENST00000264709	NM_175629.2	687	Gtc/Ttc	17/23	0.230999791594364	4	FACETS	1	0.97	1			1	CLONAL	1	FALSE	NA	0.230999791594364	4		495	842	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120647	94120647	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012273-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	53	388	0	ENST00000369303.4:c.404G>C	p.Gly135Ala	p.G135A	ENST00000369303	NM_004440.3	135	gGc/gCc	3/17	0.230999791594364	1	FACETS	0.844	0.72	0.979	0.844	0.72	0.979	CLONAL	1	FALSE	0	0.230999791594364	1		388	481	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341917	8341917	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012273-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	23	362	1	ENST00000356435.5:c.4723C>A	p.His1575Asn	p.H1575N	ENST00000356435		1575	Cat/Aat	29/35	0.172618528282039	0	FACETS	0.372	0.289	0.468			1	SUBCLONAL	1	FALSE	0	0.230999791594364	0		363	412	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389245	8389245	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012273-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	26	417	0	ENST00000356435.5:c.4373A>G	p.Glu1458Gly	p.E1458G	ENST00000356435		1458	gAa/gGa	26/35	0.172618528282039	0	FACETS	0.354	0.28	0.44			1	SUBCLONAL	1	FALSE	0	0.230999791594364	0		417	489	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755519	133755519	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs62580066	NA	P-0012273-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	78	435	0	ENST00000318560.5:c.1488G>T	p.Met496Ile	p.M496I	ENST00000318560	NM_005157.4	496	atG/atT	9/11	0.230999791594364	1	FACETS	0.846	0.743	0.957	0.846	0.743	0.957	CLONAL	1	FALSE	0	0.230999791594364	1		435	706	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609007	43609007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398378776	NA	P-0012273-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	80	529	0	ENST00000355710.3:c.1763G>A	p.Gly588Asp	p.G588D	ENST00000355710	NM_020975.4	588	gGc/gAc	10/20	0.147023639718481	1	FACETS	0.697	0.612	0.788	0.697	0.612	0.788	SUBCLONAL	1	FALSE	0	0.230999791594364	1		529	879	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456485	32456485	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012273-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	47	294	1	ENST00000332351.3:c.407C>T	p.Pro136Leu	p.P136L	ENST00000332351	NM_024426.4	136	cCt/cTt	1/10	0.12312812381565	0	FACETS	0.811	0.686	0.948			1	INDETERMINATE	1	FALSE	0	0.230999791594364	0		295	386	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559764	29559764	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1567851029	NA	P-0012273-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	33	245	0	ENST00000356175.3:c.3361G>T	p.Glu1121Ter	p.E1121*	ENST00000356175	NM_000267.3	1121	Gaa/Taa	26/57	0.230999791594364	3	FACETS	0.702	0.571	0.849	0.351	0.285	0.425	SUBCLONAL	1	FALSE	1	0.230999791594364	3		245	454	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617679	39617679	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012273-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	33	310	0	ENST00000262039.4:c.1863G>T	p.Leu621Phe	p.L621F	ENST00000262039	NM_002647.2	621	ttG/ttT	17/25	0.230999791594364	5	FACETS	0.675	0.548	0.818			1	SUBCLONAL	1	FALSE	NA	0.230999791594364	5		310	570	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966723	44966723	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012273-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	34	234	0	ENST00000377967.4:c.3947A>T	p.Glu1316Val	p.E1316V	ENST00000377967	NM_021140.2	1316	gAg/gTg	27/29	0.143200801638824	0	FACETS	0.823	0.676	0.988			1	CLONAL	1	FALSE	NA	0.230999791594364	0		234	275	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240997	53240997	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012273-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	61	262	0	ENST00000375401.3:c.1214A>C	p.Lys405Thr	p.K405T	ENST00000375401	NM_004187.3	405	aAa/aCa	9/26	0.143200801638824	0	FACETS	1	0.898	1			1	CLONAL	1	FALSE	NA	0.230999791594364	0		262	389	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573508	48573539	+	frameshift_variant	Frame_Shift_Del	DEL	AGAGTGAAACATTTGCAAAAAGAGCAATTGAA	AGAGTGAAACATTTGCAAAAAGAGCAATTGAA	-	novel	NA	P-0012273-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	21	270	0	ENST00000342988.3:c.94_125del	p.Ser32PhefsTer11	p.S32Ffs*11	ENST00000342988	NM_005359.5	31	gAGAGTGAAACATTTGCAAAAAGAGCAATTGAA/g	2/12	0.230999791594364	1	FACETS	0.534	0.411	0.677	0.534	0.411	0.677	SUBCLONAL	1	FALSE	0	0.230999791594364	1		270	301	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515215	31515215	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012273-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1345	107	647	0	ENST00000344624.3:c.1170A>T	p.Lys390Asn	p.K390N	ENST00000344624		390	aaA/aaT	5/33	0.230999791594364	6	FACETS	0.933	0.834	1	0.233	0.208	0.26	CLONAL	1	FALSE	2	0.230999791594364	6		647	1452	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0012449-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	61	347	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.358638381331314	3	FACETS	0.799	0.697	0.907	0.799	0.697	0.907	CLONAL	2	TRUE	1	0.358638381331314	3		347	251	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189892	66189892	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012449-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	52	304	0	ENST00000273854.3:c.3054G>T	p.Lys1018Asn	p.K1018N	ENST00000273854	NM_004439.5	1018	aaG/aaT	18/18	0.358638381331314	3	FACETS	1	0.954	1	0.648	0.556	0.746	CLONAL	1	TRUE	1	0.358638381331314	3		304	264	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456842	32456842	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012449-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	44	775	0	ENST00000332351.3:c.50C>T	p.Thr17Met	p.T17M	ENST00000332351	NM_024426.4	17	aCg/aTg	1/10	0.358638381331314	3	FACETS	0.802	0.674	0.942	0.401	0.337	0.471	CLONAL	1	TRUE	1	0.358638381331314	3		775	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576857	7576857	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012449-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	109	541	0	ENST00000269305.4:c.989T>G	p.Leu330Arg	p.L330R	ENST00000269305	NM_001126112.2	330	cTt/cGt	9/11	0.358638381331314	2	FACETS	0.826	0.749	0.906	0.826	0.749	0.906	CLONAL	2	TRUE	0	0.358638381331314	2		541	368	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041657	47041657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012449-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	40	306	0	ENST00000377604.3:c.1882G>T	p.Glu628Ter	p.E628*	ENST00000377604	NM_001204468.1	628	Gag/Tag	17/24	1	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.358638381331314	1		306	126	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318766	163318766	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012449-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	84	246	0	ENST00000271452.3:c.1156G>T	p.Ala386Ser	p.A386S	ENST00000271452	NM_145697.2	386	Gct/Tct	13/14	0.358638381331314	3	FACETS	0.866	0.772	0.964	0.866	0.772	0.964	CLONAL	2	TRUE	1	0.358638381331314	3		246	319	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785767	50785767	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012449-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	23	386	0	ENST00000398568.2:c.757G>T	p.Asp253Tyr	p.D253Y	ENST00000398568	NM_001042412.1	253	Gat/Tat	4/18	1	2	FACETS	0.484	0.378	0.606	0.484	0.378	0.606	SUBCLONAL	1	TRUE	1	0.358638381331314	2		386	265	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	159	327	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.467917807689176	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.475655645852186	2		327	316	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0012673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	247	461	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.467917807689176	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.475655645852186	2		461	481	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190670397	190670397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576285843	NA	P-0012673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	78	283	0	ENST00000441310.2:c.335C>T	p.Thr112Met	p.T112M	ENST00000441310	NM_000534.4	112	aCg/aTg	4/13	0.261549596181898	3	FACETS	1	0.934	1	0.541	0.478	0.608	INDETERMINATE	1	TRUE	1	0.475655645852186	3		283	375	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444143	49444143	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	263	608	1	ENST00000301067.7:c.3228del	p.Val1078PhefsTer41	p.V1078Ffs*41	ENST00000301067	NM_003482.3	1076	gaG/ga	11/54	0.467917807689176	2	FACETS	0.926	0.876	0.977	0.926	0.876	0.977	CLONAL	2	TRUE	0	0.475655645852186	2		609	597	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891654	28891654	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61731345	NA	P-0012673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	247	427	0	ENST00000282397.4:c.3367G>A	p.Glu1123Lys	p.E1123K	ENST00000282397	NM_002019.4	1123	Gag/Aag	25/30	0.263441422738074	4	FACETS	0.89	0.839	0.941	0.667	0.629	0.706	INDETERMINATE	3	TRUE	0	0.475655645852186	4		427	574	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970960	21970977	+	inframe_deletion	In_Frame_Del	DEL	GCCGCGCGCAGGTACCGT	GCCGCGCGCAGGTACCGT	-	novel	NA	P-0012673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	347	670	0	ENST00000304494.5:c.381_398del	p.Arg128_Ala133del	p.R128_A133del	ENST00000304494	NM_000077.4	127	gcACGGTACCTGCGCGCGGCt/gct	2/3	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.475655645852186	2		670	683	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411826	139411826	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1440584630	NA	P-0012673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	291	773	0	ENST00000277541.6:c.1453G>T	p.Val485Leu	p.V485L	ENST00000277541	NM_017617.3	485	Gtg/Ttg	9/34	0.475655645852186	2	FACETS	0.893	0.846	0.941	0.893	0.846	0.941	CLONAL	2	TRUE	0	0.475655645852186	2		773	685	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0013674-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	346	527	1	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.60789315998184	2	FACETS	0.905	0.868	0.942	0.905	0.868	0.942	CLONAL	2	TRUE	0	0.658105688640104	2		528	581	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169988207	169988207	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0013674-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	105	234	0	ENST00000295797.4:c.451-2A>C		p.X151_splice	ENST00000295797	NM_002740.5	151			0.63145615866572	3	FACETS	0.996	0.898	1	0.498	0.449	0.549	CLONAL	1	TRUE	1	0.658105688640104	3		234	426	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610147	28610147	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0121470-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	36	448	0	ENST00000241453.7:c.1343G>T	p.Ser448Ile	p.S448I	ENST00000241453	NM_004119.2	448	aGt/aTt	11/24	1	2	FACETS	0.116	0.095	0.14	0.116	0.095	0.14	SUBCLONAL	1	NA	1	0.897893884316692	2		448	691	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688740	47688740	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0121470-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	145	422	0	ENST00000347630.2:c.560C>A	p.Ala187Glu	p.A187E	ENST00000347630	NM_001007230.1	187	gCa/gAa	7/11	0.548000040345808	4	FACETS	0.701	0.639	0.765	0.234	0.213	0.255	SUBCLONAL	1	NA	1	0.897893884316692	4		422	875	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400042	139400042	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0121470-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	243	967	0	ENST00000277541.6:c.4306G>C	p.Ala1436Pro	p.A1436P	ENST00000277541	NM_017617.3	1436	Gcc/Ccc	25/34	0.437767943757593	1	FACETS	0.309	0.289	0.33	0.309	0.289	0.33	INDETERMINATE	1	NA	0	0.897893884316692	1		967	965	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0017944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1229	261	823	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.247960964061972	3	FACETS	1	0.991	1	0.671	0.627	0.717	CLONAL	1	FALSE	1	0.3	3		823	1490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577599	7577600	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0017944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	70	529	0	ENST00000269305.4:c.681_682insTT	p.Asp228LeufsTer20	p.D228Lfs*20	ENST00000269305	NM_001126112.2	227	-/TT	7/11	0.247960964061972	3	FACETS	0.564	0.491	0.644	0.282	0.245	0.322	SUBCLONAL	1	FALSE	1	0.3	3		529	951	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246068	41246427	+	inframe_deletion	In_Frame_Del	DEL	GTATTATCTGTGGCTCAGTAACAAATGCTCCTATAATTAGATTTTCAGTTACATGGCTTAAGTTGGGGAGGCTTGCCTTCTTCCGATAGGTTTTCCCAAATATTTTGTCTTCAATATTACTCTCTACTGATTTGGAGTGAACTCTTTCACTTTTACATATTAAAGCCTCATGAGGATCACTGGCCAGTAAGTCTATTTTCTCTGAAGAACCAGAATATTCATCTACCTCATTTAGAACGTCCAATACATCAGCTACTTTGGCATTTGATTCAGACTCCCCATCATGTGAGTCATCAGAACCTAACAGTTCATCACTTCTGGAAAACCACTCATTAACTTTCTGAATGCTGCTATTTAGTG	GTATTATCTGTGGCTCAGTAACAAATGCTCCTATAATTAGATTTTCAGTTACATGGCTTAAGTTGGGGAGGCTTGCCTTCTTCCGATAGGTTTTCCCAAATATTTTGTCTTCAATATTACTCTCTACTGATTTGGAGTGAACTCTTTCACTTTTACATATTAAAGCCTCATGAGGATCACTGGCCAGTAAGTCTATTTTCTCTGAAGAACCAGAATATTCATCTACCTCATTTAGAACGTCCAATACATCAGCTACTTTGGCATTTGATTCAGACTCCCCATCATGTGAGTCATCAGAACCTAACAGTTCATCACTTCTGGAAAACCACTCATTAACTTTCTGAATGCTGCTATTTAGTG	-	novel	NA	P-0017944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	196	606	0	ENST00000357654.3:c.1121_1480del	p.Thr374_Gln494delinsLys	p.T374_Q494delinsK	ENST00000357654	NM_007294.3	374	aCACTAAATAGCAGCATTCAGAAAGTTAATGAGTGGTTTTCCAGAAGTGATGAACTGTTAGGTTCTGATGACTCACATGATGGGGAGTCTGAATCAAATGCCAAAGTAGCTGATGTATTGGACGTTCTAAATGAGGTAGATGAATATTCTGGTTCTTCAGAGAAAATAGACTTACTGGCCAGTGATCCTCATGAGGCTTTAATATGTAAAAGTGAAAGAGTTCACTCCAAATCAGTAGAGAGTAATATTGAAGACAAAATATTTGGGAAAACCTATCGGAAGAAGGCAAGCCTCCCCAACTTAAGCCATGTAACTGAAAATCTAATTATAGGAGCATTTGTTACTGAGCCACAGATAATACaa/aaa	10/23	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	FALSE	NA	0.3	2		606	1078	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0019552-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	27	576	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.199	0.157	0.246	0.199	0.157	0.246	SUBCLONAL	1	TRUE	1	0.458721691970427	2		576	593	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0019552-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	12	372	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	1	2	FACETS	0.115	0.08	0.159	0.115	0.08	0.159	SUBCLONAL	1	TRUE	1	0.458721691970427	2		372	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0019781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	146	1229	4	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.222180433384882	1	FACETS	0.777	0.71	0.847	1	0.988	1	SUBCLONAL	2	TRUE	0	0.222180433384882	1		1233	752	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416431	29416431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764315254	NA	P-0019781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	99	1082	0	ENST00000389048.3:c.4522G>A	p.Gly1508Ser	p.G1508S	ENST00000389048	NM_004304.4	1508	Ggc/Agc	29/29	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.222180433384882	2		1082	861	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431667	49431667	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	63	1081	2	ENST00000301067.7:c.9472C>T	p.Gln3158Ter	p.Q3158*	ENST00000301067	NM_003482.3	3158	Cag/Tag	34/54	1	2	FACETS	0.886	0.766	1	0.886	0.766	1	CLONAL	1	TRUE	1	0.222180433384882	2		1083	640	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876226	35876226	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	86	876	0	ENST00000303115.3:c.1018C>G	p.Leu340Val	p.L340V	ENST00000303115	NM_002185.3	340	Ctt/Gtt	8/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.222180433384882	2		876	599	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0019948-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	172	240	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.861506185520759	4	FACETS	0.804	0.747	0.863			1	CLONAL	2	TRUE	NA	0.861506185520759	4		240	462	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0019948-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	162	375	0	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	0.861506185520759	4	FACETS	1	0.97	1			1	CLONAL	1	TRUE	NA	0.861506185520759	4		375	631	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052601	42052601	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0019948-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	317	356	0	ENST00000219905.7:c.7272T>G	p.Tyr2424Ter	p.Y2424*	ENST00000219905	NM_001164273.1	2424	taT/taG	20/24	0.861506185520759	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.861506185520759	2		356	360	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204788	128204788	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019948-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	222	842	1	ENST00000341105.2:c.653C>T	p.Thr218Met	p.T218M	ENST00000341105	NM_032638.4	218	aCg/aTg	3/6	0.861506185520759	4	FACETS	0.69	0.64	0.741	0.172	0.16	0.186	SUBCLONAL	1	TRUE	0	0.861506185520759	4		843	1391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0020338-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	237	668	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.946	0.892	1	0.946	0.892	1	CLONAL	1	TRUE	1	0.937917269077452	2		669	534	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0020338-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	172	371	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.937917269077452	2	FACETS	0.991	0.965	1	0.991	0.965	1	CLONAL	2	TRUE	0	0.937917269077452	2		371	185	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882049	36882050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs780753361	NA	P-0020338-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	310	976	2	ENST00000358127.4:c.963dup	p.Ala322ArgfsTer19	p.A322Rfs*19	ENST00000358127	NM_001280556.1	321	-/C	8/10	0.937917269077452	3	FACETS	0.92	0.869	0.973	0.46	0.434	0.487	CLONAL	1	TRUE	1	0.937917269077452	3		978	1055	SUCCESS
APC	324	MSKCC	GRCh37	5	112175530	112175530	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020338-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	90	284	0	ENST00000257430.4:c.4240del	p.Val1414Ter	p.V1414*	ENST00000257430	NM_000038.5	1413	atG/at	16/16	0.937917269077452	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.937917269077452	1		284	100	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0020338-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	168	591	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			1	2	FACETS	0.94	0.876	1	0.94	0.876	1	CLONAL	1	TRUE	1	0.937917269077452	2		591	381	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874217	155874217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748272466	NA	P-0020338-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	341	505	0	ENST00000368323.3:c.314G>A	p.Arg105His	p.R105H	ENST00000368323	NM_006912.5	105	cGt/cAt	5/6	0.511195669895984	4	FACETS	0.839	0.805	0.872	0.839	0.805	0.872	INDETERMINATE	3	TRUE	1	0.937917269077452	4		505	560	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051119	13051119	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020338-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	210	542	0	ENST00000316448.5:c.555G>C	p.Lys185Asn	p.K185N	ENST00000316448	NM_004343.3	185	aaG/aaC	5/9	0.937917269077452	4	FACETS	1	0.961	1	0.349	0.324	0.374	CLONAL	1	TRUE	1	0.937917269077452	4		542	829	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0020770-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	138	523	2	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		525	617	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897002	28897002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554058758	NA	P-0020770-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	106	426	1	ENST00000282397.4:c.2878G>A	p.Val960Ile	p.V960I	ENST00000282397	NM_002019.4	960	Gtc/Atc	21/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		427	616	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658535	206658535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1281179215	NA	P-0020770-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	70	384	1	ENST00000367120.3:c.1508C>T	p.Ala503Val	p.A503V	ENST00000367120	NM_014002.3	503	gCg/gTg	15/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		385	597	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060568	38060571	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	AGCT	AGCT	-	novel	NA	P-0020770-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	215	706	0	ENST00000250448.2:c.1418_*2del		p.*473*	ENST00000250448	NM_004496.3	473		2/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		706	1016	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467921	50467921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020770-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	66	493	0	ENST00000331340.3:c.1156C>T	p.Arg386Cys	p.R386C	ENST00000331340	NM_006060.4	386	Cgc/Tgc	8/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		493	647	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56882298	56882298	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020770-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	119	380	1	ENST00000519728.1:c.996G>T	p.Lys332Asn	p.K332N	ENST00000519728	NM_002350.3	332	aaG/aaT	10/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		381	739	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38954964	38954964	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0020770-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	21	112	0	ENST00000357387.3:c.2610-1G>C		p.X870_splice	ENST00000357387	NM_152756.3	870			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		112	255	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0020792-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	46	158	0	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	0.125525311632939	0	FACETS	1	0.906	1			1	INDETERMINATE	1	TRUE	NA	0.411545445515705	0		158	124	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0020792-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	28	285	0	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	1	2	FACETS	0.497	0.398	0.608	0.497	0.398	0.608	SUBCLONAL	1	TRUE	1	0.411545445515705	2		285	274	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9928076	9928076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020792-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	48	281	0	ENST00000330684.3:c.1663G>A	p.Ala555Thr	p.A555T	ENST00000330684	NM_001134407.1	555	Gcc/Acc	8/13	1	2	FACETS	0.964	0.822	1	0.964	0.822	1	CLONAL	1	TRUE	1	0.411545445515705	2		281	242	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989481	85989481	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020792-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	69	345	0	ENST00000263360.6:c.1240C>G	p.Arg414Gly	p.R414G	ENST00000263360	NM_003797.3	414	Cga/Gga	12/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.411545445515705	2		345	281	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029190	26029190	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020792-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	64	339	0	ENST00000435504.4:c.160G>A	p.Ala54Thr	p.A54T	ENST00000435504		54	Gca/Aca	4/13	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.411545445515705	2		339	258	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0020951-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	209	619	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.326244293669042	3	FACETS	1	0.981	1	0.74	0.695	0.785	CLONAL	2	TRUE	0	0.502554444742404	3		619	469	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115952	8115953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0020951-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	167	397	0	ENST00000346208.3:c.1300dup	p.His434ProfsTer73	p.H434Pfs*73	ENST00000346208		433	cac/caCc	6/6	0.475908803512854	4	FACETS	0.888	0.821	0.958	0.888	0.821	0.958	CLONAL	2	TRUE	2	0.502554444742404	4		397	562	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685315	89685315	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0020951-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	95	96	0	ENST00000371953.3:c.209+1G>C		p.X70_splice	ENST00000371953	NM_000314.4	70			0.453922926474958	4	FACETS	1	0.916	1			1	CLONAL	3	TRUE	NA	0.502554444742404	4		96	189	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992720	68992721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs764112302	NA	P-0020951-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	72	369	6	ENST00000288368.4:c.1693dup	p.Ser565PhefsTer3	p.S565Ffs*3	ENST00000288368	NM_024870.2	562	cgt/cgTt	16/40	0.475908803512854	4	FACETS	1	0.972	1	0.69	0.608	0.777	CLONAL	1	TRUE	2	0.502554444742404	4		375	312	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863342	56863342	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020951-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	84	231	0	ENST00000519728.1:c.486A>C	p.Lys162Asn	p.K162N	ENST00000519728	NM_002350.3	162	aaA/aaC	6/13	0.475908803512854	4	FACETS	0.851	0.76	0.946	0.851	0.76	0.946	CLONAL	2	TRUE	2	0.502554444742404	4		231	295	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0020994-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	381	708	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	0.727599984048236	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.727599984048236	1		708	664	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935319	36935319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748675453	NA	P-0020994-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	418	692	0	ENST00000361632.4:c.1408G>A	p.Ala470Thr	p.A470T	ENST00000361632		470	Gcg/Acg	10/16	1	2	FACETS	0.992	0.946	1	0.992	0.946	1	CLONAL	1	TRUE	1	0.727599984048236	2		692	1158	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379426	225379427	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020994-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	148	357	0	ENST00000264414.4:c.441dup	p.Arg148SerfsTer11	p.R148Sfs*11	ENST00000264414	NM_003590.4	147	-/T	4/16	1	2	FACETS	0.787	0.723	0.853	0.787	0.723	0.853	SUBCLONAL	1	TRUE	1	0.727599984048236	2		357	517	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265614	152265614	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020994-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	174	328	0	ENST00000206249.3:c.1067A>C	p.His356Pro	p.H356P	ENST00000206249	NM_000125.3	356	cAc/cCc	4/8	1	2	FACETS	0.881	0.816	0.947	0.881	0.816	0.947	CLONAL	1	TRUE	1	0.727599984048236	2		328	543	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415537	152415537	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519714	NA	P-0020994-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	231	416	1	ENST00000206249.3:c.1387T>C	p.Ser463Pro	p.S463P	ENST00000206249	NM_000125.3	463	Tcc/Ccc	7/8	1	2	FACETS	0.971	0.911	1	0.971	0.911	1	CLONAL	1	TRUE	1	0.727599984048236	2		417	654	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5077570	5077570	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020994-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	115	231	0	ENST00000381652.3:c.1982T>C	p.Met661Thr	p.M661T	ENST00000381652	NM_004972.3	661	aTg/aCg	15/25	0.727599984048236	1	FACETS	0.976	0.904	1	0.976	0.904	1	CLONAL	1	TRUE	0	0.727599984048236	1		231	206	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	41	301	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.785	0.653	0.931	0.785	0.653	0.931	CLONAL	1	TRUE	1	0.207293736277932	2		301	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574004	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	79	611	1	ENST00000269305.4:c.1023_1024delinsTT	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	341	ttCCga/ttTTga	10/11	0.075301490199184	3	FACETS	0.979	0.86	1			1	INDETERMINATE	1	TRUE	NA	0.207293736277932	3		612	859	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973911	55973911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs941528100	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	50	372	0	ENST00000263923.4:c.1405G>A	p.Glu469Lys	p.E469K	ENST00000263923	NM_002253.2	469	Gag/Aag	10/30	1	2	FACETS	0.892	0.756	1	0.892	0.756	1	CLONAL	1	TRUE	1	0.207293736277932	2		372	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	69	487	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.075301490199184	3	FACETS	0.907	0.789	1			1	INDETERMINATE	1	TRUE	NA	0.207293736277932	3		487	810	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259388	89259388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	53	426	0	ENST00000336596.2:c.532G>A	p.Gly178Arg	p.G178R	ENST00000336596	NM_005233.5	178	Gga/Aga	3/17	1	2	FACETS	0.926	0.79	1	0.926	0.79	1	CLONAL	1	TRUE	1	0.207293736277932	2		426	552	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266482	55266482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	58	485	2	ENST00000275493.2:c.2774C>T	p.Ser925Phe	p.S925F	ENST00000275493	NM_005228.3	925	tCc/tTc	23/28	0.207293736277932	1	FACETS	0.83	0.713	0.958	0.83	0.713	0.958	CLONAL	1	TRUE	0	0.207293736277932	1		487	604	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944436	40944436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	47	434	0	ENST00000373198.4:c.2066G>A	p.Gly689Asp	p.G689D	ENST00000373198	NM_133170.3	689	gGc/gAc	12/32	1	2	FACETS	0.756	0.637	0.887	0.756	0.637	0.887	SUBCLONAL	1	TRUE	1	0.207293736277932	2		434	600	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661897	227661897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs544750977	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	71	627	3	ENST00000305123.5:c.1558C>T	p.Arg520Trp	p.R520W	ENST00000305123	NM_005544.2	520	Cgg/Tgg	1/2	1	2	FACETS	0.824	0.718	0.939	0.824	0.718	0.939	CLONAL	1	TRUE	1	0.207293736277932	2		630	831	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466432	120466432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194257253	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	67	502	0	ENST00000256646.2:c.4687C>T	p.Arg1563Cys	p.R1563C	ENST00000256646	NM_024408.3	1563	Cgc/Tgc	26/34	1	2	FACETS	0.917	0.796	1	0.917	0.796	1	CLONAL	1	TRUE	1	0.207293736277932	2		502	705	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971187	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	175	541	1	ENST00000304494.5:c.171_172delinsTT	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	57	gcCCga/gcTTga	2/3	0.166693445535954	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.207293736277932	2		542	712	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857436	9857436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	49	411	0	ENST00000330684.3:c.3965G>A	p.Gly1322Glu	p.G1322E	ENST00000330684	NM_001134407.1	1322	gGa/gAa	13/13	0.207293736277932	1	FACETS	0.824	0.698	0.963	0.824	0.698	0.963	CLONAL	1	TRUE	0	0.207293736277932	1		411	514	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404956	404956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773583219	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	36	279	1	ENST00000399788.2:c.4238C>T	p.Ser1413Phe	p.S1413F	ENST00000399788	NM_001042603.1	1413	tCt/tTt	26/28	1	2	FACETS	0.788	0.647	0.945	0.788	0.647	0.945	CLONAL	1	TRUE	1	0.207293736277932	2		280	441	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984061	2984061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	69	484	1	ENST00000396946.4:c.469C>T	p.Arg157Trp	p.R157W	ENST00000396946	NM_032415.4	157	Cgg/Tgg	5/25	0.16179702442165	3	FACETS	1	0.904	1	0.523	0.455	0.597	CLONAL	1	TRUE	1	0.207293736277932	3		485	702	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468036	120468036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs919872084	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	61	631	0	ENST00000256646.2:c.4403C>T	p.Ser1468Phe	p.S1468F	ENST00000256646	NM_024408.3	1468	tCc/tTc	25/34	1	2	FACETS	0.71	0.611	0.818	0.71	0.611	0.818	SUBCLONAL	1	TRUE	1	0.207293736277932	2		631	829	SUCCESS
APC	324	MSKCC	GRCh37	5	112174754	112174754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774847322	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	23	229	0	ENST00000257430.4:c.3463G>A	p.Glu1155Lys	p.E1155K	ENST00000257430	NM_000038.5	1155	Gaa/Aaa	16/16	1	2	FACETS	0.768	0.599	0.962	0.768	0.599	0.962	CLONAL	1	TRUE	1	0.207293736277932	2		229	289	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508811	106508811	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	54	461	0	ENST00000359195.3:c.805G>A	p.Asp269Asn	p.D269N	ENST00000359195	NM_002649.2	269	Gat/Aat	2/11	1	2	FACETS	0.847	0.723	0.983	0.847	0.723	0.983	CLONAL	1	TRUE	1	0.207293736277932	2		461	615	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675049	40675049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764271025	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	83	566	0	ENST00000249776.8:c.13G>A	p.Glu5Lys	p.E5K	ENST00000249776	NM_033286.3	5	Gaa/Aaa	1/9	0.207293736277932	1	FACETS	0.893	0.787	1	0.893	0.787	1	CLONAL	1	TRUE	0	0.207293736277932	1		566	804	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628266	187628266	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	60	492	0	ENST00000441802.2:c.2716C>T	p.Gln906Ter	p.Q906*	ENST00000441802	NM_005245.3	906	Cag/Tag	2/27	1	2	FACETS	0.761	0.654	0.877	0.761	0.654	0.877	SUBCLONAL	1	TRUE	1	0.207293736277932	2		492	761	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259352	16259352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	26	312	0	ENST00000375759.3:c.6617C>T	p.Pro2206Leu	p.P2206L	ENST00000375759	NM_015001.2	2206	cCt/cTt	11/15	0.075301490199184	3	FACETS	0.723	0.572	0.896			1	INDETERMINATE	1	TRUE	NA	0.207293736277932	3		312	383	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259955	16259955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1482002539	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	51	504	0	ENST00000375759.3:c.7220C>T	p.Ser2407Phe	p.S2407F	ENST00000375759	NM_015001.2	2407	tCc/tTc	11/15	0.075301490199184	3	FACETS	0.761	0.645	0.888			1	INDETERMINATE	1	TRUE	NA	0.207293736277932	3		504	714	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939164	36939164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757964586	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	95	804	0	ENST00000361632.4:c.545G>A	p.Gly182Glu	p.G182E	ENST00000361632		182	gGg/gAg	5/16	1	2	FACETS	0.855	0.759	0.958	0.855	0.759	0.958	CLONAL	1	TRUE	1	0.207293736277932	2		804	1072	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511759	46511759	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	44	344	0	ENST00000262741.5:c.1018A>G	p.Asn340Asp	p.N340D	ENST00000262741	NM_003629.3	340	Aac/Gac	9/10	1	2	FACETS	0.863	0.724	1	0.863	0.724	1	CLONAL	1	TRUE	1	0.207293736277932	2		344	492	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165957	118165957	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	57	335	0	ENST00000369448.3:c.467C>T	p.Ser156Phe	p.S156F	ENST00000369448	NM_017709.3	156	tCc/tTc	2/2	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.207293736277932	2		335	469	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458131	120458131	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1399142103	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	51	526	1	ENST00000256646.2:c.7214G>A	p.Ser2405Asn	p.S2405N	ENST00000256646	NM_024408.3	2405	aGt/aAt	34/34	1	2	FACETS	0.687	0.583	0.802	0.687	0.583	0.802	SUBCLONAL	1	TRUE	1	0.207293736277932	2		527	716	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446333	70446333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	64	486	0	ENST00000373644.4:c.5273G>A	p.Arg1758Lys	p.R1758K	ENST00000373644	NM_030625.2	1758	aGg/aAg	11/12	1	2	FACETS	0.849	0.735	0.974	0.849	0.735	0.974	CLONAL	1	TRUE	1	0.207293736277932	2		486	727	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066824	77066824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779095416	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	43	300	0	ENST00000356341.3:c.661C>T	p.Pro221Ser	p.P221S	ENST00000356341	NM_002576.4	221	Ccc/Tcc	7/15	1	2	FACETS	0.872	0.729	1	0.872	0.729	1	CLONAL	1	TRUE	1	0.207293736277932	2		300	476	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416224	416224	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	43	316	0	ENST00000399788.2:c.3962T>C	p.Phe1321Ser	p.F1321S	ENST00000399788	NM_001042603.1	1321	tTt/tCt	24/28	1	2	FACETS	0.76	0.635	0.898	0.76	0.635	0.898	SUBCLONAL	1	TRUE	1	0.207293736277932	2		316	546	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244112	46244112	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	38	341	1	ENST00000334344.6:c.2206G>A	p.Gly736Arg	p.G736R	ENST00000334344	NM_152641.2	736	Gga/Aga	15/21	1	2	FACETS	0.765	0.632	0.914	0.765	0.632	0.914	CLONAL	1	TRUE	1	0.207293736277932	2		342	479	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420493	49420494	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	83	624	0	ENST00000301067.7:c.15255_15256delinsTT	p.Arg5086Ter	p.R5086*	ENST00000301067	NM_003482.3	5085	caCCga/caTTga	48/54	1	2	FACETS	0.944	0.832	1	0.944	0.832	1	CLONAL	1	TRUE	1	0.207293736277932	2		624	848	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421706	49421706	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	46	583	1	ENST00000301067.7:c.14523G>T	p.Lys4841Asn	p.K4841N	ENST00000301067	NM_003482.3	4841	aaG/aaT	47/54	1	2	FACETS	0.571	0.48	0.673	0.571	0.48	0.673	SUBCLONAL	1	TRUE	1	0.207293736277932	2		584	777	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434445	49434445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1028524252	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	77	745	1	ENST00000301067.7:c.7108C>T	p.Arg2370Cys	p.R2370C	ENST00000301067	NM_003482.3	2370	Cgc/Tgc	31/54	1	2	FACETS	0.799	0.7	0.906	0.799	0.7	0.906	CLONAL	1	TRUE	1	0.207293736277932	2		746	930	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437451	49437452	+	missense_variant	Missense_Mutation	DNP	AG	AG	TA	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	40	603	1	ENST00000301067.7:c.5433_5434delinsTA	p.Ser1812Thr	p.S1812T	ENST00000301067	NM_003482.3	1811	ggCTca/ggTAca	23/54	1	2	FACETS	0.5	0.414	0.596	0.5	0.414	0.596	SUBCLONAL	1	TRUE	1	0.207293736277932	2		604	772	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861988	57861988	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	50	491	0	ENST00000228682.2:c.1289C>T	p.Thr430Ile	p.T430I	ENST00000228682	NM_005269.2	430	aCt/aTt	10/12	1	2	FACETS	0.842	0.714	0.983	0.842	0.714	0.983	CLONAL	1	TRUE	1	0.207293736277932	2		491	573	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874009	123874009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	23	56	0	ENST00000330479.4:c.40G>A	p.Glu14Lys	p.E14K	ENST00000330479	NM_020382.3	14	Gag/Aag	2/9	1	2	FACETS	0.816	0.644	1	1	0.935	1	CLONAL	2	TRUE	1	0.207293736277932	2		56	136	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100221	30100221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	42	298	0	ENST00000331968.5:c.1399C>T	p.Pro467Ser	p.P467S	ENST00000331968	NM_002742.2	467	Cct/Tct	10/18	1	2	FACETS	0.919	0.768	1	0.919	0.768	1	CLONAL	1	TRUE	1	0.207293736277932	2		298	441	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132959	30132960	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	60	443	0	ENST00000331968.5:c.641_642delinsTT	p.Thr214Ile	p.T214I	ENST00000331968	NM_002742.2	214	aCC/aTT	4/18	1	2	FACETS	0.88	0.757	1	0.88	0.757	1	CLONAL	1	TRUE	1	0.207293736277932	2		443	658	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353847	68353847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	56	354	0	ENST00000487270.1:c.682C>T	p.Leu228Phe	p.L228F	ENST00000487270	NM_133509.3	228	Ctc/Ttc	7/11	1	2	FACETS	0.916	0.784	1	0.916	0.784	1	CLONAL	1	TRUE	1	0.207293736277932	2		354	590	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831501	72831501	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	66	512	0	ENST00000268489.5:c.5080G>A	p.Gly1694Arg	p.G1694R	ENST00000268489	NM_006885.3	1694	Ggg/Agg	9/10	1	2	FACETS	0.889	0.771	1	0.889	0.771	1	CLONAL	1	TRUE	1	0.207293736277932	2		512	716	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958298	11958298	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	53	316	0	ENST00000353533.5:c.208A>T	p.Asn70Tyr	p.N70Y	ENST00000353533	NM_003010.3	70	Aac/Tac	2/11	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.207293736277932	2		316	481	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496952	29496952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	28	221	0	ENST00000356175.3:c.523C>T	p.His175Tyr	p.H175Y	ENST00000356175	NM_000267.3	175	Cat/Tat	5/57	1	2	FACETS	0.669	0.534	0.822	0.669	0.534	0.822	SUBCLONAL	1	TRUE	1	0.207293736277932	2		221	404	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883636	37883636	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	97	836	0	ENST00000269571.5:c.3248C>T	p.Ser1083Phe	p.S1083F	ENST00000269571		1083	tCc/tTc	26/27	1	2	FACETS	0.985	0.877	1	0.985	0.877	1	CLONAL	1	TRUE	1	0.207293736277932	2		836	950	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752420	55752421	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	98	896	1	ENST00000284073.2:c.878_879delinsTT	p.Ser293Phe	p.S293F	ENST00000284073	NM_138962.2	293	tCC/tTT	12/14	1	2	FACETS	0.834	0.742	0.932	0.834	0.742	0.932	CLONAL	1	TRUE	1	0.207293736277932	2		897	1134	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66518954	66518954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	79	327	0	ENST00000358598.2:c.235G>A	p.Glu79Lys	p.E79K	ENST00000358598	NM_212471.2	79	Gag/Aag	3/11	0.166693445535954	2	FACETS	1	0.976	1	0.734	0.647	0.827	CLONAL	1	TRUE	0	0.207293736277932	2		327	519	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39576673	39576673	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	51	251	0	ENST00000262039.4:c.963T>G	p.Tyr321Ter	p.Y321*	ENST00000262039	NM_002647.2	321	taT/taG	9/25	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.207293736277932	2		251	425	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271657	15271657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269967598	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	211	898	0	ENST00000263388.2:c.6782C>T	p.Pro2261Leu	p.P2261L	ENST00000263388	NM_000435.2	2261	cCc/cTc	33/33	0.16179702442165	3	FACETS	0.954	0.885	1	0.954	0.885	1	CLONAL	2	TRUE	1	0.207293736277932	3		898	1177	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212141	36212141	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	28	303	0	ENST00000222270.7:c.1892C>T	p.Pro631Leu	p.P631L	ENST00000222270	NM_014727.1	631	cCc/cTc	3/37	0.207293736277932	1	FACETS	0.853	0.683	1	0.853	0.683	1	CLONAL	1	TRUE	0	0.207293736277932	1		303	284	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762420	41762421	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	57	504	0	ENST00000301178.4:c.2100_2101delinsAA	p.Asp701Asn	p.D701N	ENST00000301178	NM_021913.4	700	ggGGac/ggAAac	18/20	0.207293736277932	1	FACETS	0.665	0.57	0.77	0.665	0.57	0.77	SUBCLONAL	1	TRUE	0	0.207293736277932	1		504	741	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797166	42797167	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	77	988	0	ENST00000575354.2:c.3528_3529delinsTT	p.Pro1177Ser	p.P1177S	ENST00000575354	NM_015125.3	1176	gcCCcc/gcTTcc	15/20	1	2	FACETS	0.732	0.641	0.831	0.732	0.641	0.831	SUBCLONAL	1	TRUE	1	0.207293736277932	2		988	1015	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446340	29446340	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	92	626	0	ENST00000389048.3:c.3227C>T	p.Pro1076Leu	p.P1076L	ENST00000389048	NM_004304.4	1076	cCt/cTt	20/29	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.207293736277932	2		626	856	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095926	178095926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	37	327	0	ENST00000397062.3:c.1405C>T	p.Pro469Ser	p.P469S	ENST00000397062	NM_006164.4	469	Cct/Tct	5/5	1	2	FACETS	0.8	0.66	0.958	0.8	0.66	0.958	CLONAL	1	TRUE	1	0.207293736277932	2		327	446	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719778	190719778	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	43	225	0	ENST00000441310.2:c.1780C>T	p.Pro594Ser	p.P594S	ENST00000441310	NM_000534.4	594	Cct/Tct	9/13	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.207293736277932	2		225	321	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281575	198281575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	62	421	0	ENST00000335508.6:c.556G>A	p.Gly186Arg	p.G186R	ENST00000335508	NM_012433.2	186	Gga/Aga	6/25	1	2	FACETS	0.864	0.746	0.994	0.864	0.746	0.994	CLONAL	1	TRUE	1	0.207293736277932	2		421	692	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537919	212537919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	33	399	0	ENST00000342788.4:c.1686G>A	p.Met562Ile	p.M562I	ENST00000342788	NM_005235.2	562	atG/atA	14/28	1	2	FACETS	0.497	0.404	0.604	0.497	0.404	0.604	SUBCLONAL	1	TRUE	1	0.207293736277932	2		399	640	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793364	242793364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	100	807	1	ENST00000334409.5:c.713C>T	p.Pro238Leu	p.P238L	ENST00000334409	NM_005018.2	238	cCc/cTc	5/5	1	2	FACETS	0.9	0.802	1	0.9	0.802	1	CLONAL	1	TRUE	1	0.207293736277932	2		808	1072	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164808	36164808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	108	841	1	ENST00000300305.3:c.1067C>T	p.Ser356Phe	p.S356F	ENST00000300305		356	tCc/tTc	8/8	1	2	FACETS	0.925	0.828	1	0.925	0.828	1	CLONAL	1	TRUE	1	0.207293736277932	2		842	1127	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764327	39764327	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	72	512	0	ENST00000288319.7:c.785G>A	p.Gly262Asp	p.G262D	ENST00000288319	NM_182918.3	262	gGt/gAt	7/10	1	2	FACETS	0.81	0.706	0.922	0.81	0.706	0.922	CLONAL	1	TRUE	1	0.207293736277932	2		512	858	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574184	41574185	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	36	513	1	ENST00000263253.7:c.6469_6470delinsTT	p.Pro2157Phe	p.P2157F	ENST00000263253	NM_001429.3	2157	CCc/TTc	31/31	1	2	FACETS	0.615	0.504	0.739	0.615	0.504	0.739	SUBCLONAL	1	TRUE	1	0.207293736277932	2		514	565	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266970	41266970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	49	379	0	ENST00000349496.5:c.641C>T	p.Thr214Ile	p.T214I	ENST00000349496	NM_001904.3	214	aCc/aTc	5/15	1	2	FACETS	0.765	0.647	0.895	0.765	0.647	0.895	SUBCLONAL	1	TRUE	1	0.207293736277932	2		379	618	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098669	47098669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	54	537	2	ENST00000409792.3:c.6605C>T	p.Pro2202Leu	p.P2202L	ENST00000409792	NM_014159.6	2202	cCt/cTt	15/21	1	2	FACETS	0.75	0.639	0.871	0.75	0.639	0.871	SUBCLONAL	1	TRUE	1	0.207293736277932	2		539	695	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098720	47098721	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	46	564	0	ENST00000409792.3:c.6553_6554delinsAA	p.Gly2185Lys	p.G2185K	ENST00000409792	NM_014159.6	2185	GGa/AAa	15/21	1	2	FACETS	0.651	0.547	0.766	0.651	0.547	0.766	SUBCLONAL	1	TRUE	1	0.207293736277932	2		564	682	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935504	49935505	+	missense_variant	Missense_Mutation	DNP	GG	GG	TA	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	76	668	1	ENST00000296474.3:c.1859_1860delinsTA	p.Pro620Leu	p.P620L	ENST00000296474	NM_002447.2	620	cCC/cTA	5/20	1	2	FACETS	0.875	0.766	0.993	0.875	0.766	0.993	CLONAL	1	TRUE	1	0.207293736277932	2		669	838	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119562156	119562156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772550262	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	40	359	0	ENST00000316626.5:c.1180C>T	p.His394Tyr	p.H394Y	ENST00000316626		394	Cat/Tat	11/12	1	2	FACETS	0.64	0.531	0.762	0.64	0.531	0.762	SUBCLONAL	1	TRUE	1	0.207293736277932	2		359	603	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212098	142212098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	103	401	0	ENST00000350721.4:c.5954C>T	p.Pro1985Leu	p.P1985L	ENST00000350721	NM_001184.3	1985	cCt/cTt	35/47	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.207293736277932	2		401	687	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215867	142215867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	56	268	0	ENST00000350721.4:c.5726G>A	p.Ser1909Asn	p.S1909N	ENST00000350721	NM_001184.3	1909	aGc/aAc	33/47	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.207293736277932	2		268	404	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502378	186502378	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	42	340	0	ENST00000323963.5:c.101A>G	p.Asn34Ser	p.N34S	ENST00000323963		34	aAc/aGc	3/11	1	2	FACETS	0.798	0.666	0.944	0.798	0.666	0.944	CLONAL	1	TRUE	1	0.207293736277932	2		340	508	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247247	153247247	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	52	298	0	ENST00000281708.4:c.1555T>C	p.Tyr519His	p.Y519H	ENST00000281708	NM_033632.3	519	Tat/Cat	10/12	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.207293736277932	2		298	467	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557870	187557870	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	44	387	0	ENST00000441802.2:c.3841G>T	p.Glu1281Ter	p.E1281*	ENST00000441802	NM_005245.3	1281	Gag/Tag	5/27	1	2	FACETS	0.813	0.682	0.959	0.813	0.682	0.959	CLONAL	1	TRUE	1	0.207293736277932	2		387	522	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226087	226088	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	39	353	1	ENST00000264932.6:c.546_547delinsAA	p.Gly183Ser	p.G183S	ENST00000264932	NM_004168.2	182	aaGGgc/aaAAgc	5/15	1	2	FACETS	0.801	0.663	0.954	0.801	0.663	0.954	CLONAL	1	TRUE	1	0.207293736277932	2		354	470	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184753	32184754	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	118	520	1	ENST00000375023.3:c.1829_1830delinsTT	p.Ala610Val	p.A610V	ENST00000375023	NM_004557.3	610	gCC/gTT	11/30	0.160746769104576	2	FACETS	0.814	0.736	0.897	0.814	0.736	0.897	CLONAL	2	TRUE	0	0.207293736277932	2		521	699	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956522	93956522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	29	256	0	ENST00000369303.4:c.2714G>A	p.Gly905Glu	p.G905E	ENST00000369303	NM_004440.3	905	gGa/gAa	15/17	0.160746769104576	2	FACETS	0.694	0.557	0.851	0.347	0.278	0.426	SUBCLONAL	1	TRUE	0	0.207293736277932	2		256	403	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708087	117708087	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1350752092	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	58	422	0	ENST00000368508.3:c.2090G>C	p.Gly697Ala	p.G697A	ENST00000368508	NM_002944.2	697	gGa/gCa	14/43	0.207293736277932	1	FACETS	0.974	0.838	1	0.974	0.838	1	CLONAL	1	TRUE	0	0.207293736277932	1		422	515	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150410	157150410	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs141260832	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	124	474	0	ENST00000346085.5:c.1592T>C	p.Met531Thr	p.M531T	ENST00000346085	NM_020732.3	531	aTg/aCg	2/20	0.16179702442165	3	FACETS	0.866	0.784	0.953	0.866	0.784	0.953	CLONAL	2	TRUE	1	0.207293736277932	3		474	762	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528667	157528667	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	86	545	0	ENST00000346085.5:c.6392C>T	p.Ser2131Phe	p.S2131F	ENST00000346085	NM_020732.3	2131	tCc/tTc	20/20	0.16179702442165	3	FACETS	1	0.964	1	0.614	0.543	0.69	CLONAL	1	TRUE	1	0.207293736277932	3		545	746	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026402	6026402	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	97	296	0	ENST00000265849.7:c.1994G>A	p.Arg665Lys	p.R665K	ENST00000265849	NM_000535.5	665	aGa/aAa	11/15	0.16179702442165	3	FACETS	0.949	0.849	1	0.949	0.849	1	CLONAL	2	TRUE	1	0.207293736277932	3		296	544	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386505	81386505	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1305340910	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	38	297	0	ENST00000222390.5:c.482G>T	p.Ser161Ile	p.S161I	ENST00000222390	NM_000601.4	161	aGc/aTc	4/18	1	2	FACETS	0.928	0.768	1	0.928	0.768	1	CLONAL	1	TRUE	1	0.207293736277932	2		297	395	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117874180	117874180	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	42	235	0	ENST00000297338.2:c.275-1G>A		p.X92_splice	ENST00000297338	NM_006265.2	92			0.16179702442165	3	FACETS	1	0.891	1	0.544	0.455	0.643	CLONAL	1	TRUE	1	0.207293736277932	3		235	411	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27172623	27172624	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	109	411	0	ENST00000380036.4:c.638_639delinsTT	p.Ala213Val	p.A213V	ENST00000380036	NM_000459.3	213	gCC/gTT	5/23	0.207293736277932	1	FACETS	0.773	0.695	0.854	1	0.984	1	SUBCLONAL	2	TRUE	0	0.207293736277932	1		411	610	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779196	135779196	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746909024	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	47	335	0	ENST00000298552.3:c.2050C>T	p.Pro684Ser	p.P684S	ENST00000298552	NM_001162426.1	684	Cct/Tct	17/23	0.166693445535954	2	FACETS	0.963	0.813	1	0.481	0.406	0.564	CLONAL	1	TRUE	0	0.207293736277932	2		335	471	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391585	139391586	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	146	876	2	ENST00000277541.6:c.6605_6606delinsTT	p.Ser2202Phe	p.S2202F	ENST00000277541	NM_017617.3	2202	tCC/tTT	34/34	0.166693445535954	2	FACETS	1	0.984	1	0.678	0.618	0.741	CLONAL	1	TRUE	0	0.207293736277932	2		878	1039	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401760	139401760	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	180	809	0	ENST00000277541.6:c.3640C>T	p.Gln1214Ter	p.Q1214*	ENST00000277541	NM_017617.3	1214	Cag/Tag	22/34	0.166693445535954	2	FACETS	0.898	0.828	0.971	0.898	0.828	0.971	CLONAL	2	TRUE	0	0.207293736277932	2		809	967	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933165	39933166	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	83	292	0	ENST00000378444.4:c.1433_1434delinsTT	p.Ser478Phe	p.S478F	ENST00000378444	NM_001123385.1	478	tCC/tTT	4/15	1	1	FACETS	0.772	0.684	0.865	1	0.979	1	SUBCLONAL	2	TRUE	0	0.207293736277932	1		292	465	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44733181	44733182	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	69	285	2	ENST00000377967.4:c.173_174delinsAA	p.Gly58Glu	p.G58E	ENST00000377967	NM_021140.2	58	gGG/gAA	2/29	1	1	FACETS	0.817	0.716	0.926	1	0.977	1	CLONAL	2	TRUE	0	0.207293736277932	1		287	365	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356210	70356210	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	88	315	0	ENST00000374080.3:c.5105G>T	p.Trp1702Leu	p.W1702L	ENST00000374080		1702	tGg/tTg	37/45	1	1	FACETS	0.798	0.71	0.891	1	0.981	1	SUBCLONAL	2	TRUE	0	0.207293736277932	1		315	477	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572104	95572104	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	42	343	0	ENST00000393063.1:c.3004C>A	p.Pro1002Thr	p.P1002T	ENST00000393063	NM_030621.3	1002	Cct/Act	20/28	1	2	FACETS	0.86	0.718	1	0.86	0.718	1	CLONAL	1	TRUE	1	0.207293736277932	2		343	471	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007643	45007643	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	38	232	0	ENST00000558401.1:c.90C>G	p.Tyr30Ter	p.Y30*	ENST00000558401	NM_004048.2	30	taC/taG	2/4	0.207293736277932	1	FACETS	0.849	0.703	1	0.849	0.703	1	CLONAL	1	TRUE	0	0.207293736277932	1		232	387	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29686034	29686034	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	58	245	0	ENST00000356175.3:c.8097+1G>T		p.X2699_splice	ENST00000356175	NM_000267.3	2699			1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.207293736277932	2		245	458	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657023	215657023	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0021769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	33	252	0	ENST00000260947.4:c.362C>G	p.Ser121Ter	p.S121*	ENST00000260947	NM_000465.2	121	tCa/tGa	3/11	1	2	FACETS	0.636	0.517	0.77	0.636	0.517	0.77	SUBCLONAL	1	TRUE	1	0.207293736277932	2		252	501	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880984	37880985	+	inframe_insertion	In_Frame_Ins	INS	-	-	TACGTGATGGCT	rs397516977	NA	P-0022097-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	629	136	0	ENST00000269571.5:c.2314_2325dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/TACGTGATGGCT	20/27	0.492895615383516	6	FACETS	1	0.964	1	0.752	0.723	0.78	CLONAL	3	TRUE	2	0.492895615383516	6		136	1686	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30103718	30103718	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022097-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	1663	89	0	ENST00000331968.5:c.1220T>C	p.Met407Thr	p.M407T	ENST00000331968	NM_002742.2	407	aTg/aCg	8/18	0.492895615383516	19	FACETS	1	0.997	1			1	CLONAL	18	TRUE	NA	0.492895615383516	19		89	1901	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577045	7577045	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022097-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	306	175	0	ENST00000269305.4:c.893del	p.Glu298GlyfsTer47	p.E298Gfs*47	ENST00000269305	NM_001126112.2	298	gAg/gg	8/11	0.329542335934419	2	FACETS	1	0.994	1	0.728	0.688	0.768	CLONAL	1	TRUE	0	0.492895615383516	2		175	853	SUCCESS
APC	324	MSKCC	GRCh37	5	112173885	112173885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022097-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	112	77	0	ENST00000257430.4:c.2594C>T	p.Pro865Leu	p.P865L	ENST00000257430	NM_000038.5	865	cCa/cTa	16/16	0.316305659556045	4	FACETS	0.872	0.791	0.956	0.872	0.791	0.956	CLONAL	2	TRUE	2	0.492895615383516	4		77	389	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660462	227660462	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143760685	NA	P-0022097-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	238	143	0	ENST00000305123.5:c.2993G>A	p.Arg998His	p.R998H	ENST00000305123	NM_005544.2	998	cGt/cAt	1/2	0.211353392517609	5	FACETS	0.897	0.839	0.958	0.598	0.559	0.639	INDETERMINATE	2	TRUE	2	0.492895615383516	5		143	936	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588887	69588887	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022097-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	126	142	0	ENST00000168712.1:c.349G>C	p.Glu117Gln	p.E117Q	ENST00000168712	NM_002007.2	117	Gag/Cag	2/3	0.383880649907912	4	FACETS	0.941	0.852	1	0.471	0.426	0.518	CLONAL	1	TRUE	2	0.492895615383516	4		142	811	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022642-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	181	301	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		301	416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0022762-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	545	696	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.441991645246803	3	FACETS	0.94	0.907	0.973	0.94	0.907	0.973	CLONAL	3	FALSE	0	0.468782321288204	3		697	1018	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022762-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	172	302	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.468782321288204	6	FACETS	0.882	0.822	0.943	0.882	0.822	0.943	CLONAL	4	FALSE	2	0.468782321288204	6		302	403	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061327	38061327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022762-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	404	719	2	ENST00000250448.2:c.662C>T	p.Ser221Leu	p.S221L	ENST00000250448	NM_004496.3	221	tCg/tTg	2/2	0.423082233736314	5	FACETS	1	0.964	1	0.678	0.644	0.713	CLONAL	2	FALSE	2	0.468782321288204	5		721	1443	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660154	12660154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022762-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	145	428	0	ENST00000251849.4:c.67G>A	p.Asp23Asn	p.D23N	ENST00000251849	NM_002880.3	23	Gat/Aat	2/17	0.316007239890764	4	FACETS	0.817	0.749	0.888	0.817	0.749	0.888	CLONAL	2	FALSE	2	0.468782321288204	4		428	556	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928074	178928074	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022762-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	300	375	0	ENST00000263967.3:c.1352G>T	p.Gly451Val	p.G451V	ENST00000263967	NM_006218.2	451	gGa/gTa	8/21	0.468782321288204	6	FACETS	0.92	0.873	0.967	0.92	0.873	0.967	CLONAL	4	FALSE	2	0.468782321288204	6		375	674	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961812	15961812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022762-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	33	364	0	ENST00000268712.3:c.5983G>A	p.Glu1995Lys	p.E1995K	ENST00000268712	NM_006311.3	1995	Gag/Aag	38/46	0.354533838472297	5	FACETS	0.456	0.37	0.552			1	SUBCLONAL	1	FALSE	NA	0.468782321288204	5		364	526	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172392	7172392	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022762-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	62	362	0	ENST00000302850.5:c.1177G>T	p.Gly393Trp	p.G393W	ENST00000302850	NM_000208.2	393	Ggg/Tgg	5/22	0.468782321288204	5	FACETS	0.692	0.597	0.795	0.231	0.199	0.265	SUBCLONAL	1	FALSE	2	0.468782321288204	5		362	651	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270168	66270168	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022762-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	43	242	0	ENST00000273854.3:c.1714A>T	p.Ile572Phe	p.I572F	ENST00000273854	NM_004439.5	572	Att/Ttt	8/18	0.296443385106025	6	FACETS	1	0.915	1	0.286	0.24	0.336	CLONAL	1	FALSE	2	0.468782321288204	6		242	311	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670982	30670982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022762-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1377	163	805	0	ENST00000376406.3:c.5764G>A	p.Glu1922Lys	p.E1922K	ENST00000376406	NM_014641.2	1922	Gag/Aag	12/15	0.468782321288204	6	FACETS	0.875	0.8	0.954			1	CLONAL	1	FALSE	NA	0.468782321288204	6		805	1540	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031697	69031697	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022762-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	32	348	1	ENST00000288368.4:c.3452C>A	p.Ser1151Tyr	p.S1151Y	ENST00000288368	NM_024870.2	1151	tCt/tAt	28/40	0.468782321288204	6	FACETS	0.445	0.36	0.542	0.111	0.09	0.136	SUBCLONAL	1	FALSE	2	0.468782321288204	6		349	594	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0024305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	190	351	0				ENST00000310581	NM_198253.2	-/1132			0.482550979014668	5	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	2	0.542587855327098	5		351	378	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8105964	8105964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	82	557	0	ENST00000346208.3:c.784G>A	p.Glu262Lys	p.E262K	ENST00000346208		262	Gag/Aag	4/6	0.376732677192799	3	FACETS	0.968	0.859	1	0.484	0.429	0.542	CLONAL	1	TRUE	1	0.542587855327098	3		557	397	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720805	89720806	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	123	423	0	ENST00000371953.3:c.959dup	p.Leu320PhefsTer5	p.L320Ffs*5	ENST00000371953	NM_000314.4	319	act/acTt	8/9	0.533896970959982	2	FACETS	1	0.985	1	0.693	0.635	0.752	CLONAL	1	TRUE	0	0.542587855327098	2		423	327	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37671991	37671991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	141	431	0	ENST00000447079.4:c.2776C>T	p.Leu926Phe	p.L926F	ENST00000447079	NM_015083.1	926	Ctt/Ttt	9/14	0.536242188153027	5	FACETS	0.806	0.737	0.877	0.537	0.491	0.585	CLONAL	2	TRUE	2	0.542587855327098	5		431	585	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223423	2223424	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	novel	NA	P-0024305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	157	723	1	ENST00000398665.3:c.3534_3535delinsTT	p.His1179Tyr	p.H1179Y	ENST00000398665	NM_032482.2	1178	gcACac/gcTTac	25/28	0.542587855327098	3	FACETS	0.874	0.809	0.94	0.874	0.809	0.94	CLONAL	2	TRUE	1	0.542587855327098	3		724	421	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292564	15292564	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	155	998	0	ENST00000263388.2:c.2615C>T	p.Ser872Phe	p.S872F	ENST00000263388	NM_000435.2	872	tCc/tTc	17/33	0.542587855327098	3	FACETS	1	0.963	1	0.543	0.498	0.589	CLONAL	1	TRUE	1	0.542587855327098	3		998	669	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211667	36211667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1199792737	NA	P-0024305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	105	745	0	ENST00000222270.7:c.1418C>T	p.Pro473Leu	p.P473L	ENST00000222270	NM_014727.1	473	cCc/cTc	3/37	0.542587855327098	3	FACETS	1	0.955	1	0.553	0.498	0.61	CLONAL	1	TRUE	1	0.542587855327098	3		745	445	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799250	42799251	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	99	910	0	ENST00000575354.2:c.4734_4735delinsTT	p.Pro1579Ser	p.P1579S	ENST00000575354	NM_015125.3	1578	ccCCca/ccTTca	20/20	0.542587855327098	3	FACETS	0.807	0.722	0.897	0.403	0.361	0.449	CLONAL	1	TRUE	1	0.542587855327098	3		910	575	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547004	9547004	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	109	364	0	ENST00000353224.5:c.1018C>T	p.Leu340Phe	p.L340F	ENST00000353224	NM_177990.2	340	Ctc/Ttc	5/10	0.303871672470458	5	FACETS	1	0.96	1	0.736	0.669	0.806	INDETERMINATE	2	TRUE	2	0.542587855327098	5		364	330	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866442	42866442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	155	1046	0	ENST00000398585.3:c.190C>T	p.Pro64Ser	p.P64S	ENST00000398585	NM_001135099.1	64	Ccc/Tcc	3/14	0.382985905487772	3	FACETS	0.915	0.838	0.995	0.457	0.419	0.498	CLONAL	1	TRUE	1	0.542587855327098	3		1046	794	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176561	142176561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	271	410	0	ENST00000350721.4:c.7540C>T	p.Arg2514Cys	p.R2514C	ENST00000350721	NM_001184.3	2514	Cgc/Tgc	45/47	0.542587855327098	5	FACETS	0.84	0.792	0.888	1	0.991	1	CLONAL	3	TRUE	3	0.542587855327098	5		410	719	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641144	117641144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866970127	NA	P-0024305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	222	718	0	ENST00000368508.3:c.5827G>A	p.Glu1943Lys	p.E1943K	ENST00000368508	NM_002944.2	1943	Gaa/Aaa	36/43	0.303871672470458	5	FACETS	1	0.949	1	0.679	0.634	0.724	INDETERMINATE	2	TRUE	2	0.542587855327098	5		718	729	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674200	117674200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	212	569	0	ENST00000368508.3:c.4274G>A	p.Arg1425Lys	p.R1425K	ENST00000368508	NM_002944.2	1425	aGg/aAg	26/43	0.303871672470458	5	FACETS	1	0.953	1	0.685	0.639	0.732	INDETERMINATE	2	TRUE	2	0.542587855327098	5		569	690	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0024305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	365	349	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.542587855327098	7	FACETS	0.942	0.902	0.982	0.942	0.902	0.982	CLONAL	5	TRUE	2	0.542587855327098	7		349	673	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500886	8500886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	193	515	0	ENST00000356435.5:c.1996C>T	p.Pro666Ser	p.P666S	ENST00000356435		666	Cct/Tct	13/35	0.533896970959982	2	FACETS	0.926	0.87	0.982	0.926	0.87	0.982	CLONAL	2	TRUE	0	0.542587855327098	2		515	384	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399191	139399191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243453790	NA	P-0024305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	255	835	2	ENST00000277541.6:c.4952C>T	p.Ser1651Leu	p.S1651L	ENST00000277541	NM_017617.3	1651	tCg/tTg	26/34	0.348228002200469	5	FACETS	1	0.988	1	0.793	0.746	0.84	CLONAL	2	TRUE	2	0.542587855327098	5		837	717	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228066	53228066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024305-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	135	421	0	ENST00000375401.3:c.2248C>T	p.Arg750Trp	p.R750W	ENST00000375401	NM_004187.3	750	Cgg/Tgg	16/26	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.542587855327098	1		421	253	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0025941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	17	247	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.151907095850319	5	FACETS	0.879	0.659	1			1	INDETERMINATE	1	TRUE	NA	0.355189633080932	5		247	167	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662554	227662554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866672328	NA	P-0025941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	23	525	0	ENST00000305123.5:c.901C>T	p.Arg301Cys	p.R301C	ENST00000305123	NM_005544.2	301	Cgc/Tgc	1/2	0.355189633080932	5	FACETS	0.827	0.647	1			1	CLONAL	1	TRUE	NA	0.355189633080932	5		525	240	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981469	55981469	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	17	234	0	ENST00000263923.4:c.468T>G	p.Asn156Lys	p.N156K	ENST00000263923	NM_002253.2	156	aaT/aaG	4/30	1	2	FACETS	0.58	0.435	0.75	0.58	0.435	0.75	SUBCLONAL	1	TRUE	1	0.355189633080932	2		234	165	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205183	38205183	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	29	460	0	ENST00000317025.8:c.507G>T	p.Glu169Asp	p.E169D	ENST00000317025	NM_023034.1	169	gaG/gaT	2/24	1	2	FACETS	0.638	0.514	0.777	0.638	0.514	0.777	SUBCLONAL	1	TRUE	1	0.355189633080932	2		460	256	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249019	55249019	+	protein_altering_variant	In_Frame_Ins	INS	C	C	TACAACCCCT	novel	NA	P-0025941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	21	496	0	ENST00000275493.2:c.2317delinsTACAACCCCT	p.His773delinsTyrAsnProTyr	p.H773delinsYNPY	ENST00000275493	NM_005228.3	773	Cac/TACAACCCCTac	20/28	1	2	FACETS	0.684	0.53	0.86	0.684	0.53	0.86	SUBCLONAL	1	TRUE	1	0.355189633080932	2		496	173	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0027242-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	197	336	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.894485172550763	2		336	407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577157	7577157	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1060501207	NA	P-0027242-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	348	457	0	ENST00000269305.4:c.783-2A>G		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.799506001615272	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	FALSE	0	0.894485172550763	1		457	391	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949002	44949003	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0027242-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	110	197	0	ENST00000377967.4:c.3565dup	p.Leu1189ProfsTer10	p.L1189Pfs*10	ENST00000377967	NM_021140.2	1188	ttc/ttCc	25/29	1	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	0	0.894485172550763	1		197	134	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889184	76889184	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs122445093	NA	P-0027242-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	151	197	0	ENST00000373344.5:c.4826A>G	p.His1609Arg	p.H1609R	ENST00000373344	NM_000489.3	1609	cAt/cGt	18/35	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	0	0.894485172550763	1		197	165	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135345	30135345	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027242-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	109	437	0	ENST00000331968.5:c.473C>G	p.Ala158Gly	p.A158G	ENST00000331968	NM_002742.2	158	gCt/gGt	3/18	1	2	FACETS	0.446	0.401	0.492	0.446	0.401	0.492	SUBCLONAL	1	FALSE	1	0.894485172550763	2		437	547	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627319	37627319	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027242-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	120	539	0	ENST00000447079.4:c.1234G>C	p.Ala412Pro	p.A412P	ENST00000447079	NM_015083.1	412	Gca/Cca	2/14	0.455801662775667	1	FACETS	0.328	0.298	0.359	0.328	0.298	0.359	INDETERMINATE	1	FALSE	0	0.894485172550763	1		539	452	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56859019	56859019	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027242-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	90	473	0	ENST00000519728.1:c.145C>T	p.Gln49Ter	p.Q49*	ENST00000519728	NM_002350.3	49	Cag/Tag	3/13	1	2	FACETS	0.391	0.348	0.437	0.391	0.348	0.437	SUBCLONAL	1	FALSE	1	0.894485172550763	2		473	515	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0028057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	302	763	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.41396389368221	2	FACETS	0.97	0.919	1	0.97	0.919	1	CLONAL	2	TRUE	0	0.41396389368221	2		763	752	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251542	251542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200397144	NA	P-0028057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	108	580	2	ENST00000264932.6:c.1753C>T	p.Arg585Trp	p.R585W	ENST00000264932	NM_004168.2	585	Cgg/Tgg	13/15	0.120494382082156	6	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.41396389368221	6		582	733	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875920	76875920	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	254	295	2	ENST00000373344.5:c.5215C>T	p.Arg1739Ter	p.R1739*	ENST00000373344	NM_000489.3	1739	Cga/Tga	20/35	0.330605223554691	2	FACETS	0.915	0.87	0.96			1	CLONAL	3	TRUE	NA	0.41396389368221	2		297	447	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036917	180036917	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	173	716	1	ENST00000261937.6:c.3795C>A	p.Tyr1265Ter	p.Y1265*	ENST00000261937	NM_182925.4	1265	taC/taA	28/30	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.41396389368221	2		717	769	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157752	106157752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028057-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	81	398	0	ENST00000380013.4:c.2653G>A	p.Glu885Lys	p.E885K	ENST00000380013	NM_001127208.2	885	Gaa/Aaa	3/11	0.341056361583007	3	FACETS	1	0.907	1			1	CLONAL	1	TRUE	NA	0.41396389368221	3		398	459	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0028162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	176	520	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.249967654449737	4	FACETS	0.963	0.892	1	0.963	0.892	1	CLONAL	3	TRUE	1	0.249967654449737	4		520	609	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0028162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	95	446	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.212371112947537	3	FACETS	0.883	0.79	0.982	0.883	0.79	0.982	CLONAL	2	TRUE	1	0.249967654449737	3		446	484	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928906	49928906	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	26	0	0	ENST00000296474.3:c.3460G>C	p.Glu1154Gln	p.E1154Q	ENST00000296474	NM_002447.2	1154	Gag/Cag	16/20	1	2	FACETS	0.383	0.302	0.476	0.383	0.302	0.476	SUBCLONAL	1	TRUE	1	0.249967654449737	2		0	543	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402665	20402665	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	28	416	0	ENST00000346618.3:c.202del	p.Thr68ProfsTer12	p.T68Pfs*12	ENST00000346618	NM_001949.4	68	Acc/cc	1/7	0.173551370446165	3	FACETS	0.497	0.396	0.612	0.166	0.132	0.204	SUBCLONAL	1	TRUE	0	0.249967654449737	3		416	507	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740766	145740766	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	89	589	0	ENST00000428558.2:c.1334G>C	p.Ser445Thr	p.S445T	ENST00000428558	NM_004260.3	445	aGc/aCc	7/22	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.249967654449737	2		589	600	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218780	36218780	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0028732-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	325	821	0	ENST00000222270.7:c.4393-2A>G		p.X1465_splice	ENST00000222270	NM_014727.1	1465			1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.892411001045345	2		821	671	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141022	55141045	+	inframe_deletion	In_Frame_Del	DEL	AATTCGCTGGAGGGTCATTGAATC	AATTCGCTGGAGGGTCATTGAATC	-	novel	NA	P-0028732-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	98	280	0	ENST00000257290.5:c.1671_1694del	p.Arg558_Ile565del	p.R558_I565del	ENST00000257290	NM_006206.4	556	gaAATTCGCTGGAGGGTCATTGAATCa/gaa	12/23	1	2	FACETS	0.79	0.715	0.867	0.79	0.715	0.867	SUBCLONAL	1	TRUE	1	0.892411001045345	2		280	278	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0029180-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	43	351	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.653	0.544	0.774	0.653	0.544	0.774	SUBCLONAL	1	TRUE	1	0.15	2		351	878	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223230	36223230	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs372039999	NA	P-0029180-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1311	89	626	0	ENST00000222270.7:c.5780G>T	p.Arg1927Leu	p.R1927L	ENST00000222270	NM_014727.1	1927	cGg/cTg	28/37	1	2	FACETS	0.848	0.749	0.954	0.848	0.749	0.954	CLONAL	1	TRUE	1	0.15	2		626	1400	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470611	25470611	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029180-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	65	474	0	ENST00000264709.3:c.863G>T	p.Arg288Leu	p.R288L	ENST00000264709	NM_175629.2	288	cGg/cTg	8/23	1	2	FACETS	0.84	0.726	0.964	0.84	0.726	0.964	CLONAL	1	TRUE	1	0.15	2		474	1032	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123711	11123711	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029180-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	56	485	0	ENST00000358026.2:c.2361C>G	p.Ile787Met	p.I787M	ENST00000358026	NM_001128849.1	787	atC/atG	16/36	1	2	FACETS	0.688	0.587	0.799	0.688	0.587	0.799	SUBCLONAL	1	TRUE	1	0.15	2		485	1086	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114854	73114854	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029180-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	15	64	0	ENST00000356692.5:c.1235A>G	p.Glu412Gly	p.E412G	ENST00000356692		412	gAa/gGa	9/9	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.15	2		64	139	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030237-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	23	301	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		301	186	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961005	55961005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	77	550	0	ENST00000263923.4:c.2935G>A	p.Glu979Lys	p.E979K	ENST00000263923	NM_002253.2	979	Gag/Aag	21/30	1	2	FACETS	0.886	0.778	1	0.886	0.778	1	CLONAL	1	TRUE	1	0.256644408403446	2		550	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578513	7578513	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567554121	NA	P-0030266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	160	873	1	ENST00000269305.4:c.417G>T	p.Lys139Asn	p.K139N	ENST00000269305	NM_001126112.2	139	aaG/aaT	5/11	0.254372133302928	1	FACETS	0.994	0.91	1	0.994	0.91	1	CLONAL	1	TRUE	0	0.256644408403446	1		874	1093	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089641	27089659	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCTTATGGCCCTAACAT	GGCCTTATGGCCCTAACAT	-	novel	NA	P-0030266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	126	718	0	ENST00000324856.7:c.2601_2619del	p.Tyr868IlefsTer17	p.Y868Ifs*17	ENST00000324856	NM_006015.4	866	cGGCCTTATGGCCCTAACATg/cg	8/20	0.254372133302928	1	FACETS	0.991	0.897	1	0.991	0.897	1	CLONAL	1	TRUE	0	0.256644408403446	1		718	864	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660457	67660457	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0030266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	62	356	0	ENST00000264010.4:c.1358-1G>C		p.X453_splice	ENST00000264010	NM_006565.3	453			1	2	FACETS	0.924	0.799	1	0.924	0.799	1	CLONAL	1	TRUE	1	0.256644408403446	2		356	523	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279181	142279198	+	inframe_deletion	In_Frame_Del	DEL	TCTCAATAACAGGATTCT	TCTCAATAACAGGATTCT	-	novel	NA	P-0030266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	58	405	0	ENST00000350721.4:c.1448_1465del	p.Lys483_Glu488del	p.K483_E488del	ENST00000350721	NM_001184.3	483	aAGAATCCTGTTATTGAGAtg/atg	6/47	1	2	FACETS	0.729	0.626	0.842	0.729	0.626	0.842	SUBCLONAL	1	TRUE	1	0.256644408403446	2		405	620	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456860	149456860	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	76	607	0	ENST00000286301.3:c.868T>C	p.Ser290Pro	p.S290P	ENST00000286301	NM_005211.3	290	Tcc/Ccc	6/22	1	2	FACETS	0.667	0.584	0.757	0.667	0.584	0.757	SUBCLONAL	1	TRUE	1	0.256644408403446	2		607	888	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	67	329	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.818	0.713	0.93	0.818	0.713	0.93	CLONAL	1	TRUE	1	0.37	2		329	443	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	165	475	0	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.37	2		475	834	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137487	202137487	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	161	615	0	ENST00000358485.4:c.715G>T	p.Glu239Ter	p.E239*	ENST00000358485	NM_001080125.1	239	Gaa/Taa	4/9	1	2	FACETS	0.889	0.815	0.967	0.889	0.815	0.967	CLONAL	1	TRUE	1	0.37	2		615	979	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546725	9546725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210292896	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	99	401	0	ENST00000353224.5:c.1297C>T	p.Arg433Trp	p.R433W	ENST00000353224	NM_177990.2	433	Cgg/Tgg	5/10	1	2	FACETS	0.954	0.854	1	0.954	0.854	1	CLONAL	1	TRUE	1	0.37	2		401	561	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	220	622	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.37	2		622	1082	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094280	27094280	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	70	398	0	ENST00000324856.7:c.2989-1G>A		p.X997_splice	ENST00000324856	NM_006015.4	997			1	2	FACETS	0.613	0.535	0.698	0.613	0.535	0.698	SUBCLONAL	1	TRUE	1	0.37	2		398	617	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266570	115266570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	111	587	0	ENST00000438362.2:c.1945C>T	p.Arg649Cys	p.R649C	ENST00000438362	NM_001242891.1	649	Cgc/Tgc	16/20	1	2	FACETS	0.69	0.62	0.765	0.69	0.62	0.765	SUBCLONAL	1	TRUE	1	0.37	2		587	869	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830895	156830895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	176	490	1	ENST00000524377.1:c.169G>A	p.Asp57Asn	p.D57N	ENST00000524377	NM_002529.3	57	Gat/Aat	1/17	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.37	2		491	827	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104704	193104704	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	32	286	0	ENST00000367435.3:c.408G>T	p.Lys136Asn	p.K136N	ENST00000367435	NM_024529.4	136	aaG/aaT	5/17	1	2	FACETS	0.496	0.403	0.6	0.496	0.403	0.6	SUBCLONAL	1	TRUE	1	0.37	2		286	349	SUCCESS
FH	2271	MSKCC	GRCh37	1	241661229	241661229	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	162	534	0	ENST00000366560.3:c.1432A>C	p.Asn478His	p.N478H	ENST00000366560	NM_000143.3	478	Aat/Cat	10/10	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.37	2		534	866	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716100	243716100	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	108	465	0	ENST00000263826.5:c.1094T>G	p.Phe365Cys	p.F365C	ENST00000263826	NM_005465.4	365	tTt/tGt	10/13	1	2	FACETS	0.978	0.88	1	0.978	0.88	1	CLONAL	1	TRUE	1	0.37	2		465	597	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597975	43597975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057521088	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	236	710	0	ENST00000355710.3:c.523C>T	p.Arg175Cys	p.R175C	ENST00000355710	NM_020975.4	175	Cgc/Tgc	3/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.37	2		710	1130	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845621	63845621	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	75	359	0	ENST00000279873.7:c.1360G>T	p.Glu454Ter	p.E454*	ENST00000279873	NM_032199.2	454	Gaa/Taa	9/10	1	2	FACETS	0.693	0.608	0.785	0.693	0.608	0.785	SUBCLONAL	1	TRUE	1	0.37	2		359	585	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724171	112724171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	59	555	0	ENST00000369452.4:c.55C>T	p.Pro19Ser	p.P19S	ENST00000369452	NM_007373.3	19	Cca/Tca	2/9	1	2	FACETS	0.406	0.349	0.469	0.406	0.349	0.469	SUBCLONAL	1	TRUE	1	0.37	2		555	785	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248592	8248592	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	64	657	0	ENST00000335790.3:c.295G>A	p.Glu99Lys	p.E99K	ENST00000335790	NM_002315.2	99	Gag/Aag	3/4	1	2	FACETS	0.334	0.288	0.384	0.334	0.288	0.384	SUBCLONAL	1	TRUE	1	0.37	2		657	1037	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204742	94204742	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs750098871	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	48	288	0	ENST00000323929.3:c.843G>T	p.Lys281Asn	p.K281N	ENST00000323929	NM_005591.3	281	aaG/aaT	8/20	1	2	FACETS	0.733	0.622	0.854	0.733	0.622	0.854	SUBCLONAL	1	TRUE	1	0.37	2		288	354	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204836	94204836	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	35	345	0	ENST00000323929.3:c.749A>C	p.Lys250Thr	p.K250T	ENST00000323929	NM_005591.3	250	aAa/aCa	8/20	1	2	FACETS	0.445	0.365	0.535	0.445	0.365	0.535	SUBCLONAL	1	TRUE	1	0.37	2		345	425	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911892	94911892	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	78	574	0	ENST00000536441.1:c.1038G>T	p.Leu346Phe	p.L346F	ENST00000536441	NM_144665.3	346	ttG/ttT	7/10	1	2	FACETS	0.586	0.515	0.663	0.586	0.515	0.663	SUBCLONAL	1	TRUE	1	0.37	2		574	719	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115600	108115600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772821016	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	69	448	0	ENST00000278616.4:c.748C>T	p.Arg250Ter	p.R250*	ENST00000278616	NM_000051.3	250	Cga/Tga	7/63	1	2	FACETS	0.794	0.693	0.902	0.794	0.693	0.902	CLONAL	1	TRUE	1	0.37	2		448	470	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203507	108203507	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	23	239	0	ENST00000278616.4:c.7807A>C	p.Asn2603His	p.N2603H	ENST00000278616	NM_000051.3	2603	Aat/Cat	53/63	1	2	FACETS	0.57	0.446	0.712	0.57	0.446	0.712	SUBCLONAL	1	TRUE	1	0.37	2		239	218	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214018	108214018	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	89	401	0	ENST00000278616.4:c.8338C>A	p.Leu2780Ile	p.L2780I	ENST00000278616	NM_000051.3	2780	Ctt/Att	57/63	1	2	FACETS	0.837	0.743	0.936	0.837	0.743	0.936	CLONAL	1	TRUE	1	0.37	2		401	575	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373443	118373443	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	105	471	0	ENST00000534358.1:c.6836A>C	p.Lys2279Thr	p.K2279T	ENST00000534358	NM_005933.3	2279	aAa/aCa	27/36	1	2	FACETS	0.821	0.736	0.911	0.821	0.736	0.911	CLONAL	1	TRUE	1	0.37	2		471	691	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376958	118376958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139366882	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	40	413	0	ENST00000534358.1:c.10351G>A	p.Glu3451Lys	p.E3451K	ENST00000534358	NM_005933.3	3451	Gaa/Aaa	27/36	1	2	FACETS	0.329	0.272	0.392	0.329	0.272	0.392	SUBCLONAL	1	TRUE	1	0.37	2		413	658	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025838	1025838	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	147	497	0	ENST00000358495.3:c.692C>T	p.Ala231Val	p.A231V	ENST00000358495	NM_134424.2	231	gCt/gTt	8/12	1	2	FACETS	0.888	0.81	0.969	0.888	0.81	0.969	CLONAL	1	TRUE	1	0.37	2		497	895	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415866	49415866	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	128	474	0	ENST00000301067.7:c.16481T>G	p.Ile5494Ser	p.I5494S	ENST00000301067	NM_003482.3	5494	aTc/aGc	53/54	0.0343068295047875	3	FACETS	1	0.914	1	0.504	0.457	0.554	INDETERMINATE	1	TRUE	1	0.37	3		474	813	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50490675	50490675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1473235153	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	200	606	0	ENST00000394963.4:c.1312C>T	p.Arg438Trp	p.R438W	ENST00000394963	NM_003076.4	438	Cgg/Tgg	11/13	0.0343068295047875	3	FACETS	1	0.982	1	0.593	0.549	0.639	INDETERMINATE	1	TRUE	1	0.37	3		606	1080	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	249	647	1	ENST00000267101.3:c.273G>T	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atT	3/28	0.0343068295047875	3	FACETS	1	0.989	1	0.636	0.594	0.68	INDETERMINATE	1	TRUE	1	0.37	3		648	1253	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215787	133215787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762000608	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	158	570	1	ENST00000320574.5:c.5476C>T	p.Arg1826Trp	p.R1826W	ENST00000320574	NM_006231.2	1826	Cgg/Tgg	40/49	1	2	FACETS	0.79	0.723	0.861	0.79	0.723	0.861	SUBCLONAL	1	TRUE	1	0.37	2		571	1081	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	205	571	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.37	2		571	1016	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549115	21549115	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776466850	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	123	549	0	ENST00000382592.4:c.3161G>A	p.Arg1054Gln	p.R1054Q	ENST00000382592	NM_014572.2	1054	cGa/cAa	8/8	1	2	FACETS	0.729	0.659	0.803	0.729	0.659	0.803	SUBCLONAL	1	TRUE	1	0.37	2		549	912	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620154	21620154	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	156	459	0	ENST00000382592.4:c.12G>T	p.Lys4Asn	p.K4N	ENST00000382592	NM_014572.2	4	aaG/aaT	2/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.37	2		459	800	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589369	28589369	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1048919218	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	114	479	0	ENST00000241453.7:c.2678C>T	p.Pro893Leu	p.P893L	ENST00000241453	NM_004119.2	893	cCg/cTg	22/24	1	2	FACETS	0.863	0.778	0.953	0.863	0.778	0.953	CLONAL	1	TRUE	1	0.37	2		479	714	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28883012	28883012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	150	597	1	ENST00000282397.4:c.3688G>T	p.Glu1230Ter	p.E1230*	ENST00000282397	NM_002019.4	1230	Gaa/Taa	28/30	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.37	2		598	793	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914877	32914877	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs886040653	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	56	308	0	ENST00000380152.3:c.6385G>T	p.Glu2129Ter	p.E2129*	ENST00000380152		2129	Gaa/Taa	11/27	1	2	FACETS	0.846	0.728	0.973	0.846	0.728	0.973	CLONAL	1	TRUE	1	0.37	2		308	358	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355072	73355072	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	55	487	0	ENST00000377767.4:c.298A>C	p.Asn100His	p.N100H	ENST00000377767	NM_014953.3	100	Aat/Cat	2/21	0.3	1	FACETS	0.414	0.354	0.48	0.414	0.354	0.48	SUBCLONAL	1	TRUE	0	0.37	1		487	585	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519195	103519195	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	73	296	0	ENST00000355739.4:c.2533G>A	p.Gly845Arg	p.G845R	ENST00000355739	NM_000123.3	845	Gga/Aga	11/15	0.3	1	FACETS	0.975	0.859	1	0.975	0.859	1	CLONAL	1	TRUE	0	0.37	1		296	330	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100143	30100143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs191202207	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	101	586	0	ENST00000331968.5:c.1477G>A	p.Glu493Lys	p.E493K	ENST00000331968	NM_002742.2	493	Gaa/Aaa	10/18	1	2	FACETS	0.745	0.666	0.829	0.745	0.666	0.829	SUBCLONAL	1	TRUE	1	0.37	2		586	733	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554305	81554305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777252114	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	125	473	0	ENST00000298171.2:c.325C>T	p.Arg109Trp	p.R109W	ENST00000298171	NM_000369.2	109	Cgg/Tgg	4/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.37	2		473	581	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003132	42003132	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1363709175	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	74	725	0	ENST00000219905.7:c.2669C>A	p.Ser890Tyr	p.S890Y	ENST00000219905	NM_001164273.1	890	tCt/tAt	8/24	0.3	1	FACETS	0.39	0.34	0.443	0.39	0.34	0.443	SUBCLONAL	1	TRUE	0	0.37	1		725	836	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707863	43707863	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	256	717	0	ENST00000382044.4:c.5018G>T	p.Arg1673Ile	p.R1673I	ENST00000382044	NM_001141980.1	1673	aGa/aTa	23/28	0.3	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.37	1		717	1026	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007672	45007672	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	74	387	0	ENST00000558401.1:c.119C>A	p.Ser40Ter	p.S40*	ENST00000558401	NM_004048.2	40	tCa/tAa	2/4	0.3	1	FACETS	0.692	0.608	0.783	0.692	0.608	0.783	SUBCLONAL	1	TRUE	0	0.37	1		387	471	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639099	3639099	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	215	632	2	ENST00000294008.3:c.4540T>C	p.Trp1514Arg	p.W1514R	ENST00000294008	NM_032444.2	1514	Tgg/Cgg	12/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.37	2		634	1042	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934560	9934560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	49	522	0	ENST00000330684.3:c.1595G>A	p.Gly532Glu	p.G532E	ENST00000330684	NM_001134407.1	532	gGa/gAa	7/13	1	2	FACETS	0.276	0.232	0.324	0.276	0.232	0.324	SUBCLONAL	1	TRUE	1	0.37	2		522	961	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032002	10032002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs539907710	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	181	654	2	ENST00000330684.3:c.821C>T	p.Ser274Leu	p.S274L	ENST00000330684	NM_001134407.1	274	tCg/tTg	3/13	1	2	FACETS	0.903	0.832	0.978	0.903	0.832	0.978	CLONAL	1	TRUE	1	0.37	2		656	1083	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646516	23646516	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs772691867	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	159	481	0	ENST00000261584.4:c.1351T>G	p.Leu451Val	p.L451V	ENST00000261584	NM_024675.3	451	Tta/Gta	4/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.37	2		481	780	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50811760	50811760	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	36	168	0	ENST00000398568.2:c.1037G>T	p.Arg346Ile	p.R346I	ENST00000398568	NM_001042412.1	346	aGa/aTa	7/18	1	2	FACETS	0.869	0.72	1	0.869	0.72	1	CLONAL	1	TRUE	1	0.37	2		168	224	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56862974	56862974	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	181	500	0	ENST00000308159.5:c.880C>T	p.Arg294Ter	p.R294*	ENST00000308159	NM_014669.4	294	Cga/Tga	9/22	1	2	FACETS	0.991	0.914	1	0.991	0.914	1	CLONAL	1	TRUE	1	0.37	2		500	987	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662453	67662453	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs879255516	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	197	558	0	ENST00000264010.4:c.1699C>T	p.Arg567Trp	p.R567W	ENST00000264010	NM_006565.3	567	Cgg/Tgg	9/12	1	2	FACETS	0.911	0.842	0.983	0.911	0.842	0.983	CLONAL	1	TRUE	1	0.37	2		558	1169	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348773	89348773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757166671	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1315	241	876	4	ENST00000301030.4:c.4177G>A	p.Glu1393Lys	p.E1393K	ENST00000301030	NM_001256183.1	1393	Gaa/Aaa	9/13	1	2	FACETS	0.837	0.779	0.897	0.837	0.779	0.897	CLONAL	1	TRUE	1	0.37	2		880	1556	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351227	89351227	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	211	642	0	ENST00000301030.4:c.1723A>C	p.Ser575Arg	p.S575R	ENST00000301030	NM_001256183.1	575	Agc/Cgc	9/13	1	2	FACETS	0.994	0.922	1	0.994	0.922	1	CLONAL	1	TRUE	1	0.37	2		642	1147	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958224	11958224	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	19	257	0	ENST00000353533.5:c.134A>C	p.Lys45Thr	p.K45T	ENST00000353533	NM_003010.3	45	aAg/aCg	2/11	1	2	FACETS	0.305	0.231	0.392	0.305	0.231	0.392	SUBCLONAL	1	TRUE	1	0.37	2		257	337	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15978955	15978955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779823128	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	169	525	0	ENST00000268712.3:c.3563C>T	p.Ser1188Leu	p.S1188L	ENST00000268712	NM_006311.3	1188	tCg/tTg	27/46	1	2	FACETS	0.971	0.892	1	0.971	0.892	1	CLONAL	1	TRUE	1	0.37	2		525	941	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	72	386	1	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.846	0.742	0.958	0.846	0.742	0.958	CLONAL	1	TRUE	1	0.37	2		387	460	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40486056	40486056	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	106	453	0	ENST00000264657.5:c.809T>C	p.Leu270Ser	p.L270S	ENST00000264657	NM_139276.2	270	tTa/tCa	9/24	1	2	FACETS	0.694	0.621	0.77	0.694	0.621	0.77	SUBCLONAL	1	TRUE	1	0.37	2		453	826	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256949	41256949	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	93	419	0	ENST00000357654.3:c.237T>G	p.Phe79Leu	p.F79L	ENST00000357654	NM_007294.3	79	ttT/ttG	5/23	1	2	FACETS	0.851	0.758	0.949	0.851	0.758	0.949	CLONAL	1	TRUE	1	0.37	2		419	591	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740836	58740836	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs747668756	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	227	619	1	ENST00000305921.3:c.1741C>T	p.Arg581Ter	p.R581*	ENST00000305921	NM_003620.3	581	Cga/Tga	6/6	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.37	2		620	1149	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119900	70119900	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1175902013	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	178	544	0	ENST00000245479.2:c.902A>G	p.Asn301Ser	p.N301S	ENST00000245479	NM_000346.3	301	aAc/aGc	3/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.37	2		544	863	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39600660	39600660	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	34	186	0	ENST00000262039.4:c.1475A>C	p.Tyr492Ser	p.Y492S	ENST00000262039	NM_002647.2	492	tAt/tCt	13/25	1	2	FACETS	0.738	0.606	0.884	0.738	0.606	0.884	SUBCLONAL	1	TRUE	1	0.37	2		186	249	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395775	45395775	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374809046	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	94	405	0	ENST00000262160.6:c.359G>A	p.Arg120Gln	p.R120Q	ENST00000262160	NM_005901.5	120	cGa/cAa	4/11	1	2	FACETS	0.801	0.714	0.894	0.801	0.714	0.894	CLONAL	1	TRUE	1	0.37	2		405	634	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45396873	45396873	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1234431657	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	34	404	0	ENST00000262160.6:c.299G>A	p.Gly100Asp	p.G100D	ENST00000262160	NM_005901.5	100	gGc/gAc	3/11	1	2	FACETS	0.338	0.275	0.408	0.338	0.275	0.408	SUBCLONAL	1	TRUE	1	0.37	2		404	544	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2180724	2180724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	59	622	0	ENST00000398665.3:c.94G>A	p.Asp32Asn	p.D32N	ENST00000398665	NM_032482.2	32	Gat/Aat	2/28	1	2	FACETS	0.287	0.245	0.332	0.287	0.245	0.332	SUBCLONAL	1	TRUE	1	0.37	2		622	1113	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792756	33792756	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	50	57	0	ENST00000498907.2:c.565C>T	p.Pro189Ser	p.P189S	ENST00000498907	NM_004364.3	189	Ccc/Tcc	1/1	1	2	FACETS	0.883	0.765	1	1	0.974	1	CLONAL	2	TRUE	1	0.37	2		57	153	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52693380	52693380	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	149	658	0	ENST00000322088.6:c.31T>C	p.Tyr11His	p.Y11H	ENST00000322088	NM_014225.5	11	Tac/Cac	1/15	1	2	FACETS	0.758	0.691	0.828	0.758	0.691	0.828	SUBCLONAL	1	TRUE	1	0.37	2		658	1063	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99137182	99137182	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	47	205	0	ENST00000074304.5:c.139G>T	p.Glu47Ter	p.E47*	ENST00000074304	NM_001134224.1	47	Gaa/Taa	4/26	1	2	FACETS	0.77	0.652	0.898	0.77	0.652	0.898	SUBCLONAL	1	TRUE	1	0.37	2		205	330	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095644	178095644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763240080	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	91	435	1	ENST00000397062.3:c.1687G>A	p.Glu563Lys	p.E563K	ENST00000397062	NM_006164.4	563	Gaa/Aaa	5/5	1	2	FACETS	0.845	0.752	0.944	0.845	0.752	0.944	CLONAL	1	TRUE	1	0.37	2		436	582	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266128	198266128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	67	319	0	ENST00000335508.6:c.2492G>A	p.Arg831Gln	p.R831Q	ENST00000335508	NM_012433.2	831	cGa/cAa	17/25	1	2	FACETS	0.854	0.745	0.971	0.854	0.745	0.971	CLONAL	1	TRUE	1	0.37	2		319	424	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248362	212248362	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	85	351	0	ENST00000342788.4:c.3905G>T	p.Arg1302Ile	p.R1302I	ENST00000342788	NM_005235.2	1302	aGa/aTa	28/28	1	2	FACETS	0.798	0.706	0.895	0.798	0.706	0.895	SUBCLONAL	1	TRUE	1	0.37	2		351	576	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225367746	225367746	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	38	456	0	ENST00000264414.4:c.1421T>G	p.Phe474Cys	p.F474C	ENST00000264414	NM_003590.4	474	tTt/tGt	10/16	1	2	FACETS	0.38	0.314	0.455	0.38	0.314	0.455	SUBCLONAL	1	TRUE	1	0.37	2		456	540	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422513	225422513	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	56	281	1	ENST00000264414.4:c.127G>T	p.Glu43Ter	p.E43*	ENST00000264414	NM_003590.4	43	Gaa/Taa	2/16	1	2	FACETS	0.788	0.678	0.908	0.788	0.678	0.908	CLONAL	1	TRUE	1	0.37	2		282	384	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021439	31021439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs545224250	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	203	510	1	ENST00000375687.4:c.1438G>A	p.Glu480Lys	p.E480K	ENST00000375687	NM_015338.5	480	Gaa/Aaa	12/13	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.37	2		511	936	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39725963	39725963	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	69	337	2	ENST00000361337.2:c.834C>A	p.Phe278Leu	p.F278L	ENST00000361337	NM_003286.2	278	ttC/ttA	10/21	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.37	2		339	361	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40709519	40709519	+	stop_lost	Nonstop_Mutation	SNP	C	C	A	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	151	482	0	ENST00000373198.4:c.4383G>T	p.Ter1461TyrextTer31	p.*1461Yext*31	ENST00000373198	NM_133170.3	1461	taG/taT	32/32	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.37	2		482	809	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278106	41278106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	46	469	0	ENST00000349496.5:c.1982G>A	p.Arg661Gln	p.R661Q	ENST00000349496	NM_001904.3	661	cGa/cAa	13/15	1	2	FACETS	0.321	0.269	0.378	0.321	0.269	0.378	SUBCLONAL	1	TRUE	1	0.37	2		469	775	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933725	49933725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	87	770	0	ENST00000296474.3:c.2552G>A	p.Gly851Asp	p.G851D	ENST00000296474	NM_002447.2	851	gGc/gAc	10/20	1	2	FACETS	0.391	0.345	0.441	0.391	0.345	0.441	SUBCLONAL	1	TRUE	1	0.37	2		770	1203	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439131	52439131	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	148	551	0	ENST00000460680.1:c.1111A>G	p.Met371Val	p.M371V	ENST00000460680	NM_004656.3	371	Atg/Gtg	11/17	1	2	FACETS	0.832	0.76	0.909	0.832	0.76	0.909	CLONAL	1	TRUE	1	0.37	2		551	961	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442611	52442611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	93	373	0	ENST00000460680.1:c.134G>A	p.Gly45Glu	p.G45E	ENST00000460680	NM_004656.3	45	gGa/gAa	4/17	1	2	FACETS	0.7	0.622	0.783	0.7	0.622	0.783	SUBCLONAL	1	TRUE	1	0.37	2		373	718	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026106	71026106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759521321	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	172	474	0	ENST00000318789.4:c.1516G>A	p.Ala506Thr	p.A506T	ENST00000318789	NM_032682.5	506	Gcg/Acg	17/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.37	2		474	822	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259536	89259536	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	143	453	0	ENST00000336596.2:c.680G>T	p.Arg227Ile	p.R227I	ENST00000336596	NM_005233.5	227	aGa/aTa	3/17	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.37	2		453	703	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468407	89468407	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs201062946	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	101	371	0	ENST00000336596.2:c.1941G>T	p.Glu647Asp	p.E647D	ENST00000336596	NM_005233.5	647	gaG/gaT	11/17	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.37	2		371	515	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498428	89498428	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	70	432	0	ENST00000336596.2:c.2400G>T	p.Lys800Asn	p.K800N	ENST00000336596	NM_005233.5	800	aaG/aaT	14/17	1	2	FACETS	0.581	0.506	0.662	0.581	0.506	0.662	SUBCLONAL	1	TRUE	1	0.37	2		432	651	SUCCESS
ATR	545	MSKCC	GRCh37	3	142172046	142172046	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	106	416	0	ENST00000350721.4:c.7685T>G	p.Leu2562Arg	p.L2562R	ENST00000350721	NM_001184.3	2562	cTt/cGt	46/47	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.37	2		416	573	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178129	142178129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	85	359	0	ENST00000350721.4:c.7289C>T	p.Pro2430Leu	p.P2430L	ENST00000350721	NM_001184.3	2430	cCc/cTc	43/47	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.37	2		359	448	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281637	142281637	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	24	460	0	ENST00000350721.4:c.607G>T	p.Glu203Ter	p.E203*	ENST00000350721	NM_001184.3	203	Gaa/Taa	4/47	1	2	FACETS	0.276	0.216	0.346	0.276	0.216	0.346	SUBCLONAL	1	TRUE	1	0.37	2		460	470	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149243898	149243898	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767747431	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	188	525	0	ENST00000360632.3:c.920C>T	p.Ser307Leu	p.S307L	ENST00000360632	NM_015472.4	307	tCg/tTg	6/7	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.37	2		525	991	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013719	170013719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388201066	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	72	319	1	ENST00000295797.4:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000295797	NM_002740.5	480	Cgc/Tgc	15/18	1	2	FACETS	0.717	0.627	0.813	0.717	0.627	0.813	SUBCLONAL	1	TRUE	1	0.37	2		320	543	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198064	185198064	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1368183396	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	54	452	1	ENST00000265026.3:c.2546G>T	p.Ser849Ile	p.S849I	ENST00000265026	NM_004721.4	849	aGc/aTc	13/14	1	2	FACETS	0.386	0.328	0.448	0.386	0.328	0.448	SUBCLONAL	1	TRUE	1	0.37	2		453	757	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584496	189584496	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	124	430	0	ENST00000264731.3:c.792G>T	p.Leu264Phe	p.L264F	ENST00000264731	NM_003722.4	264	ttG/ttT	6/14	1	2	FACETS	0.989	0.896	1	0.989	0.896	1	CLONAL	1	TRUE	1	0.37	2		430	678	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561767	55561767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780349712	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	44	402	1	ENST00000288135.5:c.157G>A	p.Glu53Lys	p.E53K	ENST00000288135	NM_000222.2	53	Gag/Aag	2/21	1	2	FACETS	0.338	0.282	0.4	0.338	0.282	0.4	SUBCLONAL	1	TRUE	1	0.37	2		403	704	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561851	55561851	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	84	505	0	ENST00000288135.5:c.241G>T	p.Glu81Ter	p.E81*	ENST00000288135	NM_000222.2	81	Gaa/Taa	2/21	1	2	FACETS	0.688	0.608	0.774	0.688	0.608	0.774	SUBCLONAL	1	TRUE	1	0.37	2		505	660	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968610	55968610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374980446	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	107	623	0	ENST00000263923.4:c.2053G>A	p.Glu685Lys	p.E685K	ENST00000263923	NM_002253.2	685	Gaa/Aaa	14/30	1	2	FACETS	0.625	0.559	0.694	0.625	0.559	0.694	SUBCLONAL	1	TRUE	1	0.37	2		623	926	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197721	66197721	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	71	531	1	ENST00000273854.3:c.2978C>A	p.Ser993Ter	p.S993*	ENST00000273854	NM_004439.5	993	tCa/tAa	17/18	1	2	FACETS	0.616	0.538	0.701	0.616	0.538	0.701	SUBCLONAL	1	TRUE	1	0.37	2		532	623	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197845	66197845	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	24	285	0	ENST00000273854.3:c.2854G>A	p.Val952Ile	p.V952I	ENST00000273854	NM_004439.5	952	Gta/Ata	17/18	1	2	FACETS	0.45	0.354	0.562	0.45	0.354	0.562	SUBCLONAL	1	TRUE	1	0.37	2		285	288	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280068	66280068	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	62	418	1	ENST00000273854.3:c.1621C>T	p.Arg541Ter	p.R541*	ENST00000273854	NM_004439.5	541	Cga/Tga	7/18	1	2	FACETS	0.552	0.477	0.634	0.552	0.477	0.634	SUBCLONAL	1	TRUE	1	0.37	2		419	607	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391547	84391547	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	53	374	0	ENST00000321945.7:c.285T>G	p.Asn95Lys	p.N95K	ENST00000321945	NM_139076.2	95	aaT/aaG	5/9	1	2	FACETS	0.768	0.657	0.888	0.768	0.657	0.888	SUBCLONAL	1	TRUE	1	0.37	2		374	373	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244181	153244181	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	55	498	0	ENST00000281708.4:c.1976A>G	p.Asn659Ser	p.N659S	ENST00000281708	NM_033632.3	659	aAc/aGc	12/12	1	2	FACETS	0.316	0.269	0.367	0.316	0.269	0.367	SUBCLONAL	1	TRUE	1	0.37	2		498	941	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628406	187628406	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	168	703	0	ENST00000441802.2:c.2576A>G	p.Tyr859Cys	p.Y859C	ENST00000441802	NM_005245.3	859	tAc/tGc	2/27	1	2	FACETS	0.839	0.77	0.911	0.839	0.77	0.911	CLONAL	1	TRUE	1	0.37	2		703	1083	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569301	67569301	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	139	386	0	ENST00000274335.5:c.418G>T	p.Glu140Ter	p.E140*	ENST00000274335		140	Gaa/Taa	2/15	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.37	2		386	706	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589627	67589627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	21	161	0	ENST00000274335.5:c.1390G>A	p.Asp464Asn	p.D464N	ENST00000274335		464	Gat/Aat	10/15	1	2	FACETS	0.641	0.497	0.807	0.641	0.497	0.807	SUBCLONAL	1	TRUE	1	0.37	2		161	177	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950549	79950549	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	102	289	0	ENST00000265081.6:c.3G>A	p.Met1?	p.M1?	ENST00000265081	NM_002439.4	1	atG/atA	1/24	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.37	2		289	494	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629097	86629097	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	35	221	0	ENST00000274376.6:c.842G>T	p.Arg281Ile	p.R281I	ENST00000274376	NM_002890.2	281	aGa/aTa	4/25	1	2	FACETS	0.616	0.507	0.738	0.616	0.507	0.738	SUBCLONAL	1	TRUE	1	0.37	2		221	307	SUCCESS
APC	324	MSKCC	GRCh37	5	112176863	112176863	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1270783041	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	57	367	0	ENST00000257430.4:c.5572C>T	p.Arg1858Ter	p.R1858*	ENST00000257430	NM_000038.5	1858	Cga/Tga	16/16	1	2	FACETS	0.647	0.556	0.746	0.647	0.556	0.746	SUBCLONAL	1	TRUE	1	0.37	2		367	476	SUCCESS
APC	324	MSKCC	GRCh37	5	112176906	112176906	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	34	373	1	ENST00000257430.4:c.5615T>C	p.Val1872Ala	p.V1872A	ENST00000257430	NM_000038.5	1872	gTt/gCt	16/16	1	2	FACETS	0.365	0.297	0.441	0.365	0.297	0.441	SUBCLONAL	1	TRUE	1	0.37	2		374	504	SUCCESS
APC	324	MSKCC	GRCh37	5	112177901	112177901	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs752654519	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	65	408	0	ENST00000257430.4:c.6610C>T	p.Arg2204Ter	p.R2204*	ENST00000257430	NM_000038.5	2204	Cga/Tga	16/16	1	2	FACETS	0.657	0.57	0.751	0.657	0.57	0.751	SUBCLONAL	1	TRUE	1	0.37	2		408	535	SUCCESS
APC	324	MSKCC	GRCh37	5	112178001	112178001	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1299714632	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	130	526	0	ENST00000257430.4:c.6710G>A	p.Arg2237Gln	p.R2237Q	ENST00000257430	NM_000038.5	2237	cGa/cAa	16/16	1	2	FACETS	0.959	0.871	1	0.959	0.871	1	CLONAL	1	TRUE	1	0.37	2		526	733	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637676	176637676	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587784084	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	61	694	0	ENST00000439151.2:c.2276C>A	p.Ser759Ter	p.S759*	ENST00000439151	NM_022455.4	759	tCa/tAa	5/23	1	2	FACETS	0.321	0.276	0.371	0.321	0.276	0.371	SUBCLONAL	1	TRUE	1	0.37	2		694	1027	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637739	176637739	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201327209	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	205	712	0	ENST00000439151.2:c.2339C>T	p.Ser780Leu	p.S780L	ENST00000439151	NM_022455.4	780	tCg/tTg	5/23	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.37	2		712	1070	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397138	397138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1461930692	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	139	470	0	ENST00000380956.4:c.523G>A	p.Asp175Asn	p.D175N	ENST00000380956	NM_001195286.1	175	Gac/Aac	5/9	1	2	FACETS	0.968	0.882	1	0.968	0.882	1	CLONAL	1	TRUE	1	0.37	2		470	776	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397209	397209	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	148	516	0	ENST00000380956.4:c.594T>G	p.Phe198Leu	p.F198L	ENST00000380956	NM_001195286.1	198	ttT/ttG	5/9	1	2	FACETS	0.932	0.852	1	0.932	0.852	1	CLONAL	1	TRUE	1	0.37	2		516	858	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288236	33288236	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	92	513	2	ENST00000374542.5:c.1172G>T	p.Arg391Ile	p.R391I	ENST00000374542	NM_001141970.1	391	aGa/aTa	4/8	1	2	FACETS	0.488	0.432	0.548	0.488	0.432	0.548	SUBCLONAL	1	TRUE	1	0.37	2		515	1019	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015596	112015596	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	57	491	0	ENST00000368678.4:c.1246G>T	p.Glu416Ter	p.E416*	ENST00000368678		416	Gag/Tag	11/13	1	2	FACETS	0.417	0.357	0.483	0.417	0.357	0.483	SUBCLONAL	1	TRUE	1	0.37	2		491	739	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642462	117642462	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1225424758	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	200	564	0	ENST00000368508.3:c.5737G>A	p.Ala1913Thr	p.A1913T	ENST00000368508	NM_002944.2	1913	Gca/Aca	35/43	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.37	2		564	986	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198260	138198260	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	61	335	0	ENST00000237289.4:c.853G>T	p.Asp285Tyr	p.D285Y	ENST00000237289	NM_001270507.1	285	Gac/Tac	6/9	1	2	FACETS	0.684	0.591	0.785	0.684	0.591	0.785	SUBCLONAL	1	TRUE	1	0.37	2		335	482	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983001	149983001	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	49	440	0	ENST00000253339.5:c.3257A>G	p.Asp1086Gly	p.D1086G	ENST00000253339		1086	gAc/gGc	7/7	1	2	FACETS	0.524	0.444	0.613	0.524	0.444	0.613	SUBCLONAL	1	TRUE	1	0.37	2		440	505	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001373	150001373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200119992	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	106	578	0	ENST00000253339.5:c.2231G>A	p.Arg744Gln	p.R744Q	ENST00000253339		744	cGa/cAa	4/7	1	2	FACETS	0.936	0.841	1	0.936	0.841	1	CLONAL	1	TRUE	1	0.37	2		578	612	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381529	81381529	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	99	350	0	ENST00000222390.5:c.532C>T	p.Arg178Ter	p.R178*	ENST00000222390	NM_000601.4	178	Cga/Tga	5/18	1	2	FACETS	0.879	0.786	0.977	0.879	0.786	0.977	CLONAL	1	TRUE	1	0.37	2		350	609	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526611	106526611	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	42	462	0	ENST00000359195.3:c.2904T>G	p.Ile968Met	p.I968M	ENST00000359195	NM_002649.2	968	atT/atG	10/11	1	2	FACETS	0.378	0.315	0.448	0.378	0.315	0.448	SUBCLONAL	1	TRUE	1	0.37	2		462	601	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418997	116418997	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200754673	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	87	291	0	ENST00000397752.3:c.3508C>T	p.Arg1170Ter	p.R1170*	ENST00000397752	NM_000245.2	1170	Cga/Tga	17/21	1	2	FACETS	0.933	0.829	1	0.933	0.829	1	CLONAL	1	TRUE	1	0.37	2		291	504	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992692	68992692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529924687	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	85	387	0	ENST00000288368.4:c.1657G>A	p.Glu553Lys	p.E553K	ENST00000288368	NM_024870.2	553	Gaa/Aaa	16/40	1	2	FACETS	0.953	0.846	1	0.953	0.846	1	CLONAL	1	TRUE	1	0.37	2		387	482	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69032446	69032446	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	47	511	0	ENST00000288368.4:c.3520A>G	p.Asn1174Asp	p.N1174D	ENST00000288368	NM_024870.2	1174	Aat/Gat	29/40	1	2	FACETS	0.286	0.24	0.337	0.286	0.24	0.337	SUBCLONAL	1	TRUE	1	0.37	2		511	889	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742042	145742042	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	253	663	0	ENST00000428558.2:c.461A>C	p.Lys154Thr	p.K154T	ENST00000428558	NM_004260.3	154	aAa/aCa	5/22	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.37	2		663	1201	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499811	8499811	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs372425454	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	176	540	1	ENST00000356435.5:c.2158G>T	p.Val720Leu	p.V720L	ENST00000356435		720	Gta/Tta	14/35	1	2	FACETS	0.986	0.908	1	0.986	0.908	1	CLONAL	1	TRUE	1	0.37	2		541	965	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412470	80412470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28764015	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	138	412	0	ENST00000286548.4:c.571G>A	p.Glu191Lys	p.E191K	ENST00000286548	NM_002072.3	191	Gaa/Aaa	4/7	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.37	2		412	734	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750334	133750334	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	213	607	0	ENST00000318560.5:c.1165A>G	p.Thr389Ala	p.T389A	ENST00000318560	NM_005157.4	389	Aca/Gca	7/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.37	2		607	1010	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916462	39916462	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1187192426	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	115	686	1	ENST00000378444.4:c.4541G>A	p.Arg1514Gln	p.R1514Q	ENST00000378444	NM_001123385.1	1514	cGa/cAa	11/15	1	2	FACETS	0.523	0.47	0.58	0.523	0.47	0.58	SUBCLONAL	1	TRUE	1	0.37	2		687	1188	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922873	39922873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	109	515	0	ENST00000378444.4:c.3835G>T	p.Asp1279Tyr	p.D1279Y	ENST00000378444	NM_001123385.1	1279	Gac/Tac	8/15	1	2	FACETS	0.623	0.559	0.692	0.623	0.559	0.692	SUBCLONAL	1	TRUE	1	0.37	2		515	945	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225871	53225871	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	126	553	0	ENST00000375401.3:c.2978C>T	p.Ala993Val	p.A993V	ENST00000375401	NM_004187.3	993	gCc/gTc	19/26	1	2	FACETS	0.702	0.635	0.773	0.702	0.635	0.773	SUBCLONAL	1	TRUE	1	0.37	2		553	970	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344018	70344018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747113641	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	222	603	0	ENST00000374080.3:c.1754G>A	p.Arg585Gln	p.R585Q	ENST00000374080		585	cGa/cAa	13/45	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.37	2		603	1069	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176490	123176490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	75	257	1	ENST00000218089.9:c.457G>A	p.Asp153Asn	p.D153N	ENST00000218089	NM_001042749.1	153	Gat/Aat	7/35	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.37	2		258	336	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123189991	123189991	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	82	414	0	ENST00000218089.9:c.1210G>T	p.Val404Phe	p.V404F	ENST00000218089	NM_001042749.1	404	Gtt/Ttt	14/35	1	2	FACETS	0.851	0.752	0.956	0.851	0.752	0.956	CLONAL	1	TRUE	1	0.37	2		414	521	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200039	123200039	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	14	205	0	ENST00000218089.9:c.2111C>A	p.Ser704Ter	p.S704*	ENST00000218089	NM_001042749.1	704	tCa/tAa	22/35	1	2	FACETS	0.279	0.201	0.374	0.279	0.201	0.374	SUBCLONAL	1	TRUE	1	0.37	2		205	271	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030954-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	137	301	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.946	0.872	1	0.946	0.872	1	CLONAL	1	TRUE	1	0.849824186796416	2		301	341	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599271	28599271	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs770146088	NA	P-0030954-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	44	586	0	ENST00000253063.3:c.722del	p.Pro241GlnfsTer6	p.P241Qfs*6	ENST00000253063	NM_031459.4	239	agC/ag	5/10	1	2	FACETS	0.123	0.102	0.145	0.123	0.102	0.145	SUBCLONAL	1	TRUE	1	0.849824186796416	2		586	845	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691039	NA	P-0030954-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	373	469	0	ENST00000269305.4:c.919+1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.849824186796416	2		469	819	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0030954-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1306	45	535	0	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.834559650158885	3	FACETS	0.112	0.093	0.133	0.056	0.046	0.067	SUBCLONAL	1	TRUE	1	0.849824186796416	3		535	1351	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039844	47039844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030954-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	46	268	0	ENST00000377604.3:c.1187G>A	p.Arg396His	p.R396H	ENST00000377604	NM_001204468.1	396	cGc/cAc	12/24	1	1	FACETS	0.132	0.111	0.155	0.132	0.111	0.155	SUBCLONAL	1	TRUE	0	0.849824186796416	1		268	472	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556079	29556079	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886041347	NA	P-0030954-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	103	155	0	ENST00000356175.3:c.2446C>T	p.Arg816Ter	p.R816*	ENST00000356175	NM_000267.3	816	Cga/Tga	21/57	1	2	FACETS	0.894	0.813	0.978	0.894	0.813	0.978	CLONAL	1	TRUE	1	0.849824186796416	2		155	271	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155421	99155421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769671156	NA	P-0030954-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	177	344	0	ENST00000074304.5:c.647G>A	p.Arg216Gln	p.R216Q	ENST00000074304	NM_001134224.1	216	cGa/cAa	9/26	1	2	FACETS	0.855	0.795	0.917	0.855	0.795	0.917	CLONAL	1	TRUE	1	0.849824186796416	2		344	487	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416952	416953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs771545848	NA	P-0030954-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	163	331	1	ENST00000399788.2:c.3597dup	p.Gly1200ArgfsTer7	p.G1200Rfs*7	ENST00000399788	NM_001042603.1	1199	-/A	23/28	0.849824186796416	1	FACETS	0.745	0.699	0.792	0.745	0.699	0.792	SUBCLONAL	1	TRUE	0	0.849824186796416	1		332	296	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067308	37067308	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057517541	NA	P-0030954-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	192	311	1	ENST00000231790.2:c.1219C>T	p.Gln407Ter	p.Q407*	ENST00000231790	NM_000249.3	407	Cag/Tag	12/19	1	2	FACETS	0.945	0.883	1	0.945	0.883	1	CLONAL	1	TRUE	1	0.849824186796416	2		312	478	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0030954-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	260	496	2	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	1	2	FACETS	0.75	0.705	0.796	0.75	0.705	0.796	SUBCLONAL	1	TRUE	1	0.849824186796416	2		498	816	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888166	112888166	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121918461	NA	P-0030954-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	35	407	0	ENST00000351677.2:c.182A>T	p.Asp61Val	p.D61V	ENST00000351677	NM_002834.3	61	gAt/gTt	3/16	1	2	FACETS	0.119	0.097	0.144	0.119	0.097	0.144	SUBCLONAL	1	TRUE	1	0.849824186796416	2		407	693	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527531	29527532	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs1555610893	NA	P-0030954-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	160	308	0	ENST00000356175.3:c.983_984del	p.Cys328Ter	p.C328*	ENST00000356175	NM_000267.3	327	cTG/c	9/57	1	2	FACETS	0.783	0.724	0.844	0.783	0.724	0.844	SUBCLONAL	1	TRUE	1	0.849824186796416	2		308	481	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756722	756722	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030954-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	259	326	0	ENST00000314574.4:c.106C>T	p.Pro36Ser	p.P36S	ENST00000314574	NM_005433.3	36	Ccc/Tcc	2/12	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.849824186796416	2		326	592	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510223	149510223	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030954-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	316	390	0	ENST00000261799.4:c.1246C>T	p.Pro416Ser	p.P416S	ENST00000261799	NM_002609.3	416	Cct/Tct	9/23	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.849824186796416	2		390	683	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685296	89685296	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030954-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	75	153	0	ENST00000371953.3:c.191A>C	p.His64Pro	p.H64P	ENST00000371953	NM_000314.4	64	cAt/cCt	3/9	0.849824186796416	1	FACETS	0.868	0.795	0.937	0.868	0.795	0.937	CLONAL	1	TRUE	0	0.849824186796416	1		153	117	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859574	57859574	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030954-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	245	427	1	ENST00000228682.2:c.628C>T	p.Pro210Ser	p.P210S	ENST00000228682	NM_005269.2	210	Ccc/Tcc	7/12	1	2	FACETS	0.942	0.887	0.998	0.942	0.887	0.998	CLONAL	1	TRUE	1	0.849824186796416	2		428	612	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15976820	15976820	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030954-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	194	332	0	ENST00000268712.3:c.3734G>A	p.Arg1245Lys	p.R1245K	ENST00000268712	NM_006311.3	1245	aGa/aAa	28/46	NA	2	FACETS	0.951	0.889	1			1	INDETERMINATE	1	TRUE	NA	0.849824186796416	2		332	480	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36814387	36814387	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030954-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	299	470	0	ENST00000373129.3:c.653G>A	p.Cys218Tyr	p.C218Y	ENST00000373129	NM_032017.1	218	tGc/tAc	8/12	1	2	FACETS	0.939	0.89	0.99	0.939	0.89	0.99	CLONAL	1	TRUE	1	0.849824186796416	2		470	749	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464406	464406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030954-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	189	292	0	ENST00000399788.2:c.788C>T	p.Thr263Ile	p.T263I	ENST00000399788	NM_001042603.1	263	aCc/aTc	7/28	0.849824186796416	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.849824186796416	1		292	249	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347096	347096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030954-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	409	637	1	ENST00000262320.3:c.1915G>A	p.Gly639Arg	p.G639R	ENST00000262320	NM_003502.3	639	Ggg/Agg	7/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.849824186796416	2		638	948	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681764	78681764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030954-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	341	499	1	ENST00000306801.3:c.472C>T	p.Pro158Ser	p.P158S	ENST00000306801	NM_020761.2	158	Ccc/Tcc	4/34	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.849824186796416	2		500	783	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57569909	57569909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030954-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	144	207	0	ENST00000316660.6:c.89G>A	p.Arg30Lys	p.R30K	ENST00000316660	NM_021127.2	30	aGg/aAg	2/2	1	2	FACETS	0.968	0.896	1	0.968	0.896	1	CLONAL	1	TRUE	1	0.849824186796416	2		207	350	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713195	30713195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030954-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	66	253	0	ENST00000295754.5:c.520C>T	p.Pro174Ser	p.P174S	ENST00000295754	NM_003242.5	174	Cca/Tca	4/7	1	2	FACETS	0.346	0.301	0.394	0.346	0.301	0.394	SUBCLONAL	1	TRUE	1	0.849824186796416	2		253	449	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37081742	37081742	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750192	NA	P-0030954-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	264	334	0	ENST00000231790.2:c.1624C>T	p.Gln542Ter	p.Q542*	ENST00000231790	NM_000249.3	542	Cag/Tag	14/19	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.849824186796416	2		334	570	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390914	89390914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030954-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	123	225	0	ENST00000336596.2:c.980C>T	p.Ser327Phe	p.S327F	ENST00000336596	NM_005233.5	327	tCt/tTt	5/17	1	2	FACETS	0.899	0.824	0.975	0.899	0.824	0.975	CLONAL	1	TRUE	1	0.849824186796416	2		225	322	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119634890	119634890	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0030954-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	107	158	0	ENST00000316626.5:c.608+1G>A		p.X203_splice	ENST00000316626		203			1	2	FACETS	0.954	0.871	1	0.954	0.871	1	CLONAL	1	TRUE	1	0.849824186796416	2		158	264	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280242	142280242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030954-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	158	227	1	ENST00000350721.4:c.1192G>A	p.Ala398Thr	p.A398T	ENST00000350721	NM_001184.3	398	Gca/Aca	5/47	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.849824186796416	2		228	363	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340036	116340036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030954-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	124	179	0	ENST00000397752.3:c.898C>T	p.Leu300Phe	p.L300F	ENST00000397752	NM_000245.2	300	Ctc/Ttc	2/21	0.849824186796416	3	FACETS	1	0.928	1	0.51	0.465	0.556	CLONAL	1	TRUE	1	0.849824186796416	3		179	408	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0031299-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	126	691	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.380980082975708	4	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.380980082975708	4		691	647	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0031299-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	49	911	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.259108206114454	2	FACETS	0.478	0.405	0.559	0.239	0.202	0.28	SUBCLONAL	1	TRUE	0	0.380980082975708	2		911	538	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241678	55241678	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517085	NA	P-0031299-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	151	823	0	ENST00000275493.2:c.2126A>C	p.Glu709Ala	p.E709A	ENST00000275493	NM_005228.3	709	gAa/gCa	18/28	0.380980082975708	4	FACETS	0.758	0.694	0.825			1	SUBCLONAL	2	TRUE	NA	0.380980082975708	4		823	722	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519975	NA	P-0031299-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	201	992	2	ENST00000269305.4:c.403T>A	p.Cys135Ser	p.C135S	ENST00000269305	NM_001126112.2	135	Tgc/Agc	5/11	0.256844376473451	2	FACETS	1	0.99	1	0.691	0.642	0.741	CLONAL	1	TRUE	0	0.380980082975708	2		994	764	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782329	NA	P-0033628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	49	643	0	ENST00000269305.4:c.746G>A	p.Arg249Lys	p.R249K	ENST00000269305	NM_001126112.2	249	aGg/aAg	7/11	1	2	FACETS	0.309	0.261	0.363	0.309	0.261	0.363	SUBCLONAL	1	TRUE	1	0.37	2		643	857	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849462	68849463	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0033628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	41	576	0	ENST00000261769.5:c.1367_1368dup	p.Thr457Ter	p.T457*	ENST00000261769	NM_004360.3	455	-/GT	10/16	1	2	FACETS	0.283	0.235	0.338	0.283	0.235	0.338	SUBCLONAL	1	TRUE	1	0.37	2		576	782	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112615	115112617	+	frameshift_variant	Frame_Shift_Del	DEL	GCT	GCT	A	novel	NA	P-0033628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1254	405	765	2	ENST00000257566.3:c.1123_1125delinsT	p.Ser375Ter	p.S375*	ENST00000257566	NM_016569.3	375	AGC/T	7/8	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.37	2		767	1659	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118943	115118944	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	C	novel	NA	P-0033628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	53	260	0	ENST00000257566.3:c.397_398delinsG	p.Phe133ValfsTer6	p.F133Vfs*6	ENST00000257566	NM_016569.3	133	TTt/Gt	2/8	1	2	FACETS	0.879	0.753	1	0.879	0.753	1	CLONAL	1	TRUE	1	0.37	2		260	326	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120787	115120787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033709-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	213	433	0	ENST00000257566.3:c.219G>T	p.Glu73Asp	p.E73D	ENST00000257566	NM_016569.3	73	gaG/gaT	1/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.4635566770214	2		433	853	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442667	442667	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033709-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	205	436	0	ENST00000399788.2:c.1639G>C	p.Glu547Gln	p.E547Q	ENST00000399788	NM_001042603.1	547	Gag/Cag	12/28	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.4635566770214	2		436	841	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609887	117609887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749542060	NA	P-0033709-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	166	389	1	ENST00000368508.3:c.6812G>A	p.Gly2271Glu	p.G2271E	ENST00000368508	NM_002944.2	2271	gGg/gAg	43/43	0.4635566770214	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.4635566770214	1		390	536	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0033764-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	50	361	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.235966311024358	5	FACETS	0.891	0.755	1	0.297	0.251	0.347	CLONAL	1	FALSE	2	0.268801227599743	5		361	586	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0033764-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	250	520	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.268801227599743	6	FACETS	0.968	0.909	1	0.968	0.909	1	CLONAL	4	FALSE	2	0.268801227599743	6		520	739	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0033764-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	151	829	1	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.268801227599743	3	FACETS	0.933	0.855	1	0.933	0.855	1	CLONAL	2	FALSE	1	0.268801227599743	3		830	683	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396464	396464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033764-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	64	474	0	ENST00000262320.3:c.562G>A	p.Glu188Lys	p.E188K	ENST00000262320	NM_003502.3	188	Gaa/Aaa	2/11	0.268801227599743	3	FACETS	0.782	0.676	0.896			1	SUBCLONAL	1	FALSE	NA	0.268801227599743	3		474	691	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056244	26056244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781319824	NA	P-0033764-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	62	314	0	ENST00000343677.2:c.413C>T	p.Pro138Leu	p.P138L	ENST00000343677	NM_005319.3	138	cCc/cTc	1/1	0.268801227599743	12	FACETS	1	0.936	1	0.144	0.124	0.166	CLONAL	1	FALSE	4	0.268801227599743	12		314	939	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391232	89391232	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033764-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	22	225	0	ENST00000336596.2:c.1298A>G	p.Asn433Ser	p.N433S	ENST00000336596	NM_005233.5	433	aAt/aGt	5/17	0.268801227599743	3	FACETS	0.54	0.418	0.681	0.27	0.209	0.341	SUBCLONAL	1	FALSE	1	0.268801227599743	3		225	344	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035247-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	65	301	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.599346487517495	2		301	217	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0035247-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	218	829	1	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.599346487517495	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.599346487517495	1		830	468	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438673	49438673	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0035247-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	223	824	1	ENST00000301067.7:c.4817C>G	p.Ser1606Ter	p.S1606*	ENST00000301067	NM_003482.3	1606	tCa/tGa	19/54	0.470382890408963	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.599346487517495	1		825	411	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937873	36937873	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035247-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	63	859	0	ENST00000361632.4:c.963G>C	p.Trp321Cys	p.W321C	ENST00000361632		321	tgG/tgC	7/16	0.599346487517495	3	FACETS	0.454	0.392	0.521	0.227	0.196	0.261	SUBCLONAL	1	TRUE	1	0.599346487517495	3		859	602	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738259	133738259	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs56271006	NA	P-0035247-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	164	691	0	ENST00000318560.5:c.659G>T	p.Arg220Leu	p.R220L	ENST00000318560	NM_005157.4	220	cGc/cTc	4/11	0.599346487517495	3	FACETS	1	0.963	1	0.359	0.331	0.389	CLONAL	1	TRUE	0	0.599346487517495	3		691	660	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575700	55575700	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1219033476	NA	P-0035267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	26	342	0	ENST00000288135.5:c.1226T>C	p.Val409Ala	p.V409A	ENST00000288135	NM_000222.2	409	gTg/gCg	7/21	1	2	FACETS	0.453	0.358	0.561	0.453	0.358	0.561	SUBCLONAL	1	TRUE	1	0.309466740499222	2		342	371	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512270	38512270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866777491	NA	P-0035267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	104	712	0	ENST00000254066.5:c.1181G>A	p.Arg394Gln	p.R394Q	ENST00000254066	NM_000964.3	394	cGg/cAg	9/9	0.19752003422787	4	FACETS	1	0.968	1	0.602	0.539	0.669	CLONAL	1	TRUE	2	0.309466740499222	4		712	731	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0035349-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	55	347	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.22	2		347	454	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087503	27087503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035349-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	51	592	1	ENST00000324856.7:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000324856	NM_006015.4	693	Cga/Tga	5/20	1	2	FACETS	0.624	0.529	0.729	0.624	0.529	0.729	SUBCLONAL	1	TRUE	1	0.22	2		593	743	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857125	9857125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138415164	NA	P-0035349-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	44	246	0	ENST00000330684.3:c.4276G>A	p.Glu1426Lys	p.E1426K	ENST00000330684	NM_001134407.1	1426	Gag/Aag	13/13	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.22	2		246	351	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201099	108201099	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035349-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	33	275	0	ENST00000278616.4:c.7466C>A	p.Ser2489Tyr	p.S2489Y	ENST00000278616	NM_000051.3	2489	tCc/tAc	50/63	0.195713706688045	1	FACETS	0.799	0.652	0.964	0.799	0.652	0.964	CLONAL	1	TRUE	0	0.22	1		275	334	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870187	155870187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773340979	NA	P-0035349-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	58	348	0	ENST00000368323.3:c.652G>A	p.Val218Ile	p.V218I	ENST00000368323	NM_006912.5	218	Gta/Ata	6/6	0.224354986009075	3	FACETS	1	0.939	1	0.586	0.504	0.676	CLONAL	1	TRUE	1	0.22	3		348	499	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041905	42041905	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035349-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	66	379	0	ENST00000219905.7:c.6100G>T	p.Glu2034Ter	p.E2034*	ENST00000219905	NM_001164273.1	2034	Gaa/Taa	17/24	0.195713706688045	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.22	1		379	460	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576234	88576234	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035349-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	71	452	0	ENST00000360948.2:c.1439C>A	p.Pro480Gln	p.P480Q	ENST00000360948	NM_001012338.2	480	cCa/cAa	13/19	0.3	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.22	1		452	516	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459927	99459927	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035349-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	56	295	0	ENST00000268035.6:c.2023G>T	p.Asp675Tyr	p.D675Y	ENST00000268035	NM_000875.3	675	Gac/Tac	10/21	0.3	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.22	1		295	396	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745967	745967	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035349-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	44	330	0	ENST00000314574.4:c.555A>T	p.Arg185Ser	p.R185S	ENST00000314574	NM_005433.3	185	agA/agT	5/12	1	2	FACETS	0.92	0.772	1	0.92	0.772	1	CLONAL	1	TRUE	1	0.22	2		330	435	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716037	52716037	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035349-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	100	586	0	ENST00000322088.6:c.602T>C	p.Val201Ala	p.V201A	ENST00000322088	NM_014225.5	201	gTc/gCc	5/15	NA	2	FACETS	1	0.954	1			1	INDETERMINATE	1	TRUE	NA	0.22	2		586	808	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156983	89156983	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035349-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	44	356	0	ENST00000336596.2:c.85G>T	p.Glu29Ter	p.E29*	ENST00000336596	NM_005233.5	29	Gaa/Taa	1/17	1	2	FACETS	0.86	0.722	1	0.86	0.722	1	CLONAL	1	TRUE	1	0.22	2		356	465	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664849	138664849	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035349-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	35	137	0	ENST00000330315.3:c.716C>A	p.Pro239His	p.P239H	ENST00000330315	NM_023067.3	239	cCt/cAt	1/1	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.22	2		137	266	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509999	106509999	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035349-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	47	362	0	ENST00000359195.3:c.1993C>A	p.Gln665Lys	p.Q665K	ENST00000359195	NM_002649.2	665	Cag/Aag	2/11	1	2	FACETS	0.954	0.806	1	0.954	0.806	1	CLONAL	1	TRUE	1	0.22	2		362	448	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223881	53223881	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035349-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	86	662	0	ENST00000375401.3:c.3478G>T	p.Gly1160Cys	p.G1160C	ENST00000375401	NM_004187.3	1160	Ggt/Tgt	23/26	0.195713706688045	1	FACETS	0.794	0.701	0.894	0.794	0.701	0.894	SUBCLONAL	1	TRUE	0	0.22	1		662	876	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480500	123480500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035349-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	26	407	0	ENST00000371139.4:c.8C>T	p.Ala3Val	p.A3V	ENST00000371139	NM_001114937.2	3	gCa/gTa	1/4	0.3	1	FACETS	0.417	0.33	0.518	0.417	0.33	0.518	SUBCLONAL	1	TRUE	0	0.22	1		407	504	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939029	48939029	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0035445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	139	191	0	ENST00000267163.4:c.862-1G>A		p.X288_splice	ENST00000267163	NM_000321.2	288			0.850814817692819	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.851493457139689	1		191	182	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724415	43724415	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	292	591	0	ENST00000382044.4:c.3652G>A	p.Asp1218Asn	p.D1218N	ENST00000382044	NM_001141980.1	1218	Gat/Aat	17/28	1	2	FACETS	0.908	0.859	0.958	0.908	0.859	0.958	CLONAL	1	TRUE	1	0.851493457139689	2		591	755	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164995	47164995	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0035445-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	167	243	0	ENST00000409792.3:c.1131T>G	p.Tyr377Ter	p.Y377*	ENST00000409792	NM_014159.6	377	taT/taG	3/21	1	2	FACETS	0.957	0.89	1	0.957	0.89	1	CLONAL	1	TRUE	1	0.851493457139689	2		243	410	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036383-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	319	607	0	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	0.91	0.862	0.959	0.91	0.862	0.959	CLONAL	1	TRUE	1	0.776247519061895	2		607	903	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247836	10247836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036383-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	195	864	1	ENST00000340748.4:c.4366C>T	p.Arg1456Trp	p.R1456W	ENST00000340748		1456	Cgg/Tgg	36/40	1	2	FACETS	0.4	0.369	0.432	0.4	0.369	0.432	SUBCLONAL	1	TRUE	1	0.776247519061895	2		865	1257	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227982	53227982	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1556840029	NA	P-0036383-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	941	365	1	ENST00000375401.3:c.2332C>T	p.Arg778Ter	p.R778*	ENST00000375401	NM_004187.3	778	Cga/Tga	16/26	0.651302577475531	2	FACETS	1	0.998	1			1	CLONAL	2	TRUE	NA	0.776247519061895	2		366	1052	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857925	9857925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs534440095	NA	P-0036383-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	858	707	0	ENST00000330684.3:c.3476G>A	p.Arg1159His	p.R1159H	ENST00000330684	NM_001134407.1	1159	cGc/cAc	13/13	0.776247519061895	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.776247519061895	3		707	1450	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094981	11094981	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502103	NA	P-0036383-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	467	854	0	ENST00000358026.2:c.154G>A	p.Ala52Thr	p.A52T	ENST00000358026	NM_001128849.1	52	Gca/Aca	2/36	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.776247519061895	2		854	1180	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443761	52443761	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0036383-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	478	724	1	ENST00000460680.1:c.38-2A>T		p.X13_splice	ENST00000460680	NM_004656.3	13			0.776247519061895	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.776247519061895	1		725	753	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447423	187447423	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036383-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	480	722	1	ENST00000232014.4:c.770A>G	p.Asn257Ser	p.N257S	ENST00000232014	NM_001130845.1	257	aAt/aGt	5/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.776247519061895	2		723	1138	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196491	106196491	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0036383-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	283	490	0	ENST00000380013.4:c.4824T>A	p.Tyr1608Ter	p.Y1608*	ENST00000380013	NM_001127208.2	1608	taT/taA	11/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.776247519061895	2		490	726	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0038412-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	313	668	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.883263974821658	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.883263974821658	1		669	376	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913558	32913559	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359479	NA	P-0038412-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	105	342	0	ENST00000380152.3:c.5073dup	p.Trp1692MetfsTer3	p.W1692Mfs*3	ENST00000380152		1689	gca/gcAa	11/27	0.883263974821658	1	FACETS	0.868	0.81	0.922	0.868	0.81	0.922	CLONAL	1	TRUE	0	0.883263974821658	1		342	153	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643216	38643216	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038412-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	104	227	0	ENST00000299084.4:c.686T>C	p.Val229Ala	p.V229A	ENST00000299084	NM_152594.2	229	gTc/gCc	7/7	1	2	FACETS	0.92	0.838	1	0.92	0.838	1	CLONAL	1	TRUE	1	0.883263974821658	2		227	256	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855593	45855593	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038412-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	334	648	0	ENST00000391945.4:c.2064C>G	p.Asp688Glu	p.D688E	ENST00000391945	NM_000400.3	688	gaC/gaG	22/23	1	2	FACETS	0.978	0.931	1	0.978	0.931	1	CLONAL	1	TRUE	1	0.883263974821658	2		648	773	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467690	66467690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038412-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	53	298	0	ENST00000273854.3:c.579G>A	p.Met193Ile	p.M193I	ENST00000273854	NM_004439.5	193	atG/atA	3/18	1	2	FACETS	0.393	0.337	0.454	0.393	0.337	0.454	SUBCLONAL	1	TRUE	1	0.883263974821658	2		298	305	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637558	23637558	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039221-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	45	356	0	ENST00000261584.4:c.2747A>T	p.Glu916Val	p.E916V	ENST00000261584	NM_024675.3	916	gAg/gTg	7/13	1	2	FACETS	0.115	0.096	0.136	0.115	0.096	0.136	SUBCLONAL	1	FALSE	1	0.937225763775252	2		356	836	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15280918	15280918	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039221-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	444	634	0	ENST00000263388.2:c.5178C>A	p.Cys1726Ter	p.C1726*	ENST00000263388	NM_000435.2	1726	tgC/tgA	28/33	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.937225763775252	2		634	896	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962662	38962662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039221-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	58	225	0	ENST00000357387.3:c.1593C>A	p.Asn531Lys	p.N531K	ENST00000357387	NM_152756.3	531	aaC/aaA	18/38	1	2	FACETS	0.192	0.164	0.222	0.192	0.164	0.222	SUBCLONAL	1	FALSE	1	0.937225763775252	2		225	646	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97887444	97887444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039221-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	131	423	0	ENST00000289081.3:c.920G>A	p.Gly307Glu	p.G307E	ENST00000289081	NM_000136.2	307	gGg/gAg	10/15	1	2	FACETS	0.258	0.233	0.284	0.258	0.233	0.284	SUBCLONAL	1	FALSE	1	0.937225763775252	2		423	1083	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0040210-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	66	339	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.210151313684718	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.305694691441242	1		340	277	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0040210-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	427	696	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.305694691441242	2	FACETS	1	0.971	1	1	0.997	1	CLONAL	4	TRUE	0	0.305694691441242	2		697	693	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040210-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	21	545	0	ENST00000269305.4:c.772G>C	p.Glu258Gln	p.E258Q	ENST00000269305	NM_001126112.2	258	Gaa/Caa	7/11	0.305694691441242	2	FACETS	0.226	0.173	0.288	0.113	0.086	0.144	SUBCLONAL	1	TRUE	0	0.305694691441242	2		545	608	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912075	76912075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782228142	NA	P-0040210-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	45	298	0	ENST00000373344.5:c.4189G>A	p.Glu1397Lys	p.E1397K	ENST00000373344	NM_000489.3	1397	Gaa/Aaa	13/35	1	2	FACETS	0.577	0.485	0.679	0.577	0.485	0.679	SUBCLONAL	1	TRUE	1	0.305694691441242	2		298	510	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163392	32163392	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0040210-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	94	693	1	ENST00000375023.3:c.5834C>G	p.Ser1945Ter	p.S1945*	ENST00000375023	NM_004557.3	1945	tCa/tGa	30/30	0.210151313684718	1	FACETS	0.697	0.619	0.779	0.697	0.619	0.779	SUBCLONAL	1	TRUE	0	0.305694691441242	1		694	748	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849221	76849221	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040210-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	77	306	0	ENST00000373344.5:c.6055A>G	p.Lys2019Glu	p.K2019E	ENST00000373344	NM_000489.3	2019	Aaa/Gaa	26/35	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.305694691441242	2		306	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0040504-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	119	619	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.388741600243231	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.388741600243231	1		619	461	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647301	23647301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040504-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	51	680	0	ENST00000261584.4:c.566G>A	p.Arg189Lys	p.R189K	ENST00000261584	NM_024675.3	189	aGa/aAa	4/13	0.33404195050635	2	FACETS	0.565	0.481	0.658	0.283	0.24	0.329	SUBCLONAL	1	TRUE	0	0.388741600243231	2		680	464	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213578	36213578	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040504-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	49	805	0	ENST00000222270.7:c.2680A>T	p.Ser894Cys	p.S894C	ENST00000222270	NM_014727.1	894	Agt/Tgt	5/37	1	2	FACETS	0.4	0.338	0.468	0.4	0.338	0.468	SUBCLONAL	1	TRUE	1	0.388741600243231	2		805	630	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0040505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	295	704	4	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.328108016186725	2	FACETS	0.841	0.793	0.891	0.841	0.793	0.891	CLONAL	2	TRUE	0	0.350388003755789	2		708	1001	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950288	15950288	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	175	569	0	ENST00000268712.3:c.6656C>G	p.Ser2219Cys	p.S2219C	ENST00000268712	NM_006311.3	2219	tCt/tGt	42/46	0.328108016186725	2	FACETS	0.951	0.883	1	0.951	0.883	1	CLONAL	2	TRUE	0	0.350388003755789	2		569	525	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438264	110438264	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	53	244	0	ENST00000375856.3:c.137G>C	p.Arg46Pro	p.R46P	ENST00000375856	NM_003749.2	46	cGc/cCc	1/2	0.24833015717359	4	FACETS	1	0.878	1	0.343	0.293	0.397	CLONAL	1	TRUE	1	0.350388003755789	4		244	397	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37863344	37863344	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	315	761	0	ENST00000269571.5:c.175A>C	p.Asn59His	p.N59H	ENST00000269571		59	Aac/Cac	2/27	0.328108016186725	2	FACETS	0.858	0.81	0.906	0.858	0.81	0.906	CLONAL	2	TRUE	0	0.350388003755789	2		761	1048	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400090	41400090	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	182	445	2	ENST00000373198.4:c.669C>A	p.Asp223Glu	p.D223E	ENST00000373198	NM_133170.3	223	gaC/gaA	5/32	0.24833015717359	4	FACETS	1	0.983	1	0.416	0.383	0.45	CLONAL	1	TRUE	1	0.350388003755789	4		447	1124	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197357	26197357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	106	577	1	ENST00000356476.2:c.122G>A	p.Arg41His	p.R41H	ENST00000356476		41	cGt/cAt	1/1	0.328108016186725	2	FACETS	0.823	0.738	0.913	0.412	0.369	0.457	CLONAL	1	TRUE	0	0.350388003755789	2		578	735	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0040686-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	360	347	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.0817697900325789	3	FACETS	1	0.989	1	1	0.997	1	INDETERMINATE	4	TRUE	1	0.23	3		347	784	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884940	111884940	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040686-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	69	506	1	ENST00000341259.2:c.938C>T	p.Thr313Ile	p.T313I	ENST00000341259	NM_005475.2	313	aCa/aTa	5/8	0.0817697900325789	3	FACETS	1	0.95	1	0.592	0.516	0.674	INDETERMINATE	1	TRUE	1	0.23	3		507	565	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240676	133240676	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040686-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	79	610	1	ENST00000320574.5:c.2620G>T	p.Glu874Ter	p.E874*	ENST00000320574	NM_006231.2	874	Gaa/Taa	23/49	NA	2	FACETS	1	0.934	1			1	INDETERMINATE	1	TRUE	NA	0.23	2		611	629	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962952	2962953	+	stop_gained	Nonsense_Mutation	DNP	CG	CG	TC	novel	NA	P-0040686-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	42	740	2	ENST00000396946.4:c.1955_1956delinsGA	p.Ser652Ter	p.S652*	ENST00000396946	NM_032415.4	652	tCG/tGA	16/25	1	2	FACETS	0.489	0.407	0.58	0.489	0.407	0.58	SUBCLONAL	1	TRUE	1	0.23	2		742	747	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	10	301	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.833	0.593	1	1	0.878	1	CLONAL	2	TRUE	1	0.387231687538768	2		301	31	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0041221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	651	711	0	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.387231687538768	148	FACETS	1	0.972	1			1	CLONAL	73	TRUE	NA	0.387231687538768	148		711	1340	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315513	30315513	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs774753677	NA	P-0041221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	10	323	0	ENST00000322652.5:c.1198A>G	p.Ile400Val	p.I400V	ENST00000322652	NM_015355.2	400	Att/Gtt	10/16	1	2	FACETS	1	0.717	1	1	0.717	1	CLONAL	1	TRUE	1	0.387231687538768	2		323	50	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210237	123210237	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	8	276	0	ENST00000218089.9:c.2591del	p.Leu864TyrfsTer8	p.L864Yfs*8	ENST00000218089	NM_001042749.1	863	aaT/aa	26/35	0.23148646060189	0	FACETS	0.575	0.396	0.773			1	INDETERMINATE	2	TRUE	NA	0.387231687538768	0		276	22	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0041883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	85	524	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	1	2	FACETS	0.987	0.874	1	0.987	0.874	1	CLONAL	1	TRUE	1	0.29	2		524	594	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599945	10599945	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	98	565	0	ENST00000171111.5:c.1631G>T	p.Trp544Leu	p.W544L	ENST00000171111	NM_203500.1	544	tGg/tTg	5/6	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.29	2		565	660	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166850	32166850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	70	586	0	ENST00000375023.3:c.4388G>A	p.Gly1463Glu	p.G1463E	ENST00000375023	NM_004557.3	1463	gGg/gAg	24/30	1	2	FACETS	0.686	0.597	0.781	0.686	0.597	0.781	SUBCLONAL	1	TRUE	1	0.29	2		586	704	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988474	41988474	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1295223907	NA	P-0041883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	16	325	0	ENST00000219905.7:c.1266A>G	p.Ile422Met	p.I422M	ENST00000219905	NM_001164273.1	422	atA/atG	3/24	1	2	FACETS	0.372	0.274	0.488	0.372	0.274	0.488	SUBCLONAL	1	TRUE	1	0.29	2		325	297	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043891-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	81	301	0				ENST00000310581	NM_198253.2	-/1132			0.123200979058412	4	FACETS	0.811	0.718	0.909	0.811	0.718	0.909	INDETERMINATE	2	TRUE	2	0.326235823254972	4		301	406	SUCCESS
APC	324	MSKCC	GRCh37	5	112154771	112154771	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1314843920	NA	P-0043891-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	35	331	0	ENST00000257430.4:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000257430	NM_000038.5	348	Cga/Tga	10/16	0.123200979058412	4	FACETS	0.556	0.455	0.669	0.278	0.227	0.335	INDETERMINATE	1	TRUE	2	0.326235823254972	4		331	512	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341555	89341555	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043891-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	159	534	0	ENST00000301030.4:c.7515C>G	p.Phe2505Leu	p.F2505L	ENST00000301030	NM_001256183.1	2505	ttC/ttG	10/13	0.185295827083761	4	FACETS	0.844	0.775	0.916	0.844	0.775	0.916	INDETERMINATE	2	TRUE	2	0.326235823254972	4		534	766	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4387995	4387995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043891-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	191	401	2	ENST00000261254.3:c.481G>A	p.Glu161Lys	p.E161K	ENST00000261254	NM_001759.3	161	Gag/Aag	3/5	0.244126399862362	3	FACETS	1	0.979	1	0.753	0.7	0.807	CLONAL	2	TRUE	0	0.326235823254972	3		403	603	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647921	3647921	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146021821	NA	P-0043891-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	202	697	0	ENST00000294008.3:c.1243G>A	p.Glu415Lys	p.E415K	ENST00000294008	NM_032444.2	415	Gag/Aag	6/15	0.239872491653275	2	FACETS	1	0.99	1	0.71	0.659	0.763	CLONAL	1	TRUE	0	0.326235823254972	2		697	872	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983111	201983111	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043891-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	149	475	0	ENST00000359651.3:c.960G>C	p.Lys320Asn	p.K320N	ENST00000359651		320	aaG/aaC	7/8	0.245788114432905	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.326235823254972	1		475	620	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057318	180057318	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043891-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	226	617	0	ENST00000261937.6:c.420C>G	p.Ile140Met	p.I140M	ENST00000261937	NM_182925.4	140	atC/atG	4/30	0.123200979058412	4	FACETS	1	0.94	1	1	0.94	1	INDETERMINATE	2	TRUE	2	0.326235823254972	4		617	911	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983030	201983030	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043891-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	218	597	0	ENST00000359651.3:c.879G>C	p.Met293Ile	p.M293I	ENST00000359651		293	atG/atC	7/8	0.245788114432905	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.326235823254972	1		597	831	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394715	394715	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043891-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	176	364	0	ENST00000399788.2:c.4980G>T	p.Lys1660Asn	p.K1660N	ENST00000399788	NM_001042603.1	1660	aaG/aaT	28/28	0.244126399862362	3	FACETS	1	0.98	1	0.772	0.716	0.829	CLONAL	2	TRUE	0	0.326235823254972	3		364	542	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028627	12028627	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043891-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	87	220	0	ENST00000353533.5:c.830C>G	p.Pro277Arg	p.P277R	ENST00000353533	NM_003010.3	277	cCa/cGa	8/11	0.185295827083761	4	FACETS	0.791	0.704	0.884	0.791	0.704	0.884	INDETERMINATE	2	TRUE	2	0.326235823254972	4		220	447	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41267767	41267767	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs80356880	NA	P-0043891-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	94	300	0	ENST00000357654.3:c.110C>G	p.Thr37Arg	p.T37R	ENST00000357654	NM_007294.3	37	aCa/aGa	3/23	0.185295827083761	4	FACETS	0.824	0.736	0.916	0.824	0.736	0.916	INDETERMINATE	2	TRUE	2	0.326235823254972	4		300	464	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170732	7170732	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043891-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	150	465	0	ENST00000302850.5:c.1299G>C	p.Gln433His	p.Q433H	ENST00000302850	NM_000208.2	433	caG/caC	6/22	0.239872491653275	2	FACETS	0.766	0.703	0.832	0.766	0.703	0.832	SUBCLONAL	2	TRUE	0	0.326235823254972	2		465	600	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256708	19256708	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1335518697	NA	P-0043891-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	172	626	0	ENST00000162023.5:c.1005G>T	p.Lys335Asn	p.K335N	ENST00000162023		335	aaG/aaT	13/13	0.185295827083761	4	FACETS	1	0.988	1	0.706	0.649	0.766	INDETERMINATE	1	TRUE	2	0.326235823254972	4		626	990	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949731	151949731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043891-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	105	251	0	ENST00000262189.6:c.1369G>A	p.Asp457Asn	p.D457N	ENST00000262189	NM_170606.2	457	Gac/Aac	10/59	0.185295827083761	4	FACETS	0.914	0.823	1	0.914	0.823	1	INDETERMINATE	2	TRUE	2	0.326235823254972	4		251	467	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660555	190660555	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043891-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	20	169	0	ENST00000441310.2:c.193G>C	p.Asp65His	p.D65H	ENST00000441310	NM_000534.4	65	Gat/Cat	3/13	0.185295827083761	4	FACETS	0.487	0.372	0.622	0.243	0.186	0.311	INDETERMINATE	1	TRUE	2	0.326235823254972	4		169	334	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627817	187627818	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATCATTG	novel	NA	P-0043891-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	56	394	0	ENST00000441802.2:c.3164_3165insCAATGAT	p.Val1056AsnfsTer7	p.V1056Nfs*7	ENST00000441802	NM_005245.3	1055	acg/acCAATGATg	2/27	0.239872491653275	2	FACETS	0.65	0.557	0.752	0.325	0.278	0.376	SUBCLONAL	1	TRUE	0	0.326235823254972	2		394	528	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627911	187627919	+	inframe_deletion	In_Frame_Del	DEL	TCAACCACC	TCAACCACC	-	novel	NA	P-0043891-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	59	436	0	ENST00000441802.2:c.3063_3071del	p.Glu1021_Val1023del	p.E1021_V1023del	ENST00000441802	NM_005245.3	1021	gaGGTGGTTGAt/gat	2/27	0.239872491653275	2	FACETS	0.594	0.511	0.685	0.297	0.255	0.343	SUBCLONAL	1	TRUE	0	0.326235823254972	2		436	609	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043891-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	61	301	0				ENST00000310581	NM_198253.2	-/1132			0.120496928793665	4	FACETS	0.842	0.731	0.961	0.842	0.731	0.961	INDETERMINATE	2	TRUE	2	0.285797068244852	4		301	326	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341555	89341555	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043891-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	114	534	0	ENST00000301030.4:c.7515C>G	p.Phe2505Leu	p.F2505L	ENST00000301030	NM_001256183.1	2505	ttC/ttG	10/13	0.120496928793665	4	FACETS	0.909	0.822	1	0.909	0.822	1	INDETERMINATE	2	TRUE	2	0.285797068244852	4		534	564	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4387995	4387995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043891-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	108	401	2	ENST00000261254.3:c.481G>A	p.Glu161Lys	p.E161K	ENST00000261254	NM_001759.3	161	Gag/Aag	3/5	0.282476197485125	2	FACETS	0.851	0.769	0.937	0.851	0.769	0.937	CLONAL	2	TRUE	0	0.285797068244852	2		403	444	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647921	3647921	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146021821	NA	P-0043891-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	217	697	0	ENST00000294008.3:c.1243G>A	p.Glu415Lys	p.E415K	ENST00000294008	NM_032444.2	415	Gag/Aag	6/15	0.285797068244852	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.285797068244852	2		697	663	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983111	201983111	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043891-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	109	475	0	ENST00000359651.3:c.960G>C	p.Lys320Asn	p.K320N	ENST00000359651		320	aaG/aaC	7/8	0.120496928793665	4	FACETS	0.847	0.767	0.93	1	0.977	1	INDETERMINATE	3	TRUE	2	0.285797068244852	4		475	386	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057318	180057318	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043891-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	121	617	0	ENST00000261937.6:c.420C>G	p.Ile140Met	p.I140M	ENST00000261937	NM_182925.4	140	atC/atG	4/30	0.120496928793665	4	FACETS	0.863	0.781	0.948	0.863	0.781	0.948	INDETERMINATE	2	TRUE	2	0.285797068244852	4		617	631	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983030	201983030	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043891-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	139	597	0	ENST00000359651.3:c.879G>C	p.Met293Ile	p.M293I	ENST00000359651		293	atG/atC	7/8	0.120496928793665	4	FACETS	1	0.973	1	1	0.973	1	INDETERMINATE	2	TRUE	2	0.285797068244852	4		597	543	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394715	394715	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043891-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	131	364	0	ENST00000399788.2:c.4980G>T	p.Lys1660Asn	p.K1660N	ENST00000399788	NM_001042603.1	1660	aaG/aaT	28/28	0.282476197485125	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.285797068244852	2		364	374	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028627	12028627	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043891-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	60	220	0	ENST00000353533.5:c.830C>G	p.Pro277Arg	p.P277R	ENST00000353533	NM_003010.3	277	cCa/cGa	8/11	0.120496928793665	4	FACETS	0.985	0.857	1	0.985	0.857	1	INDETERMINATE	2	TRUE	2	0.285797068244852	4		220	274	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41267767	41267767	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs80356880	NA	P-0043891-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	75	300	0	ENST00000357654.3:c.110C>G	p.Thr37Arg	p.T37R	ENST00000357654	NM_007294.3	37	aCa/aGa	3/23	0.120496928793665	4	FACETS	1	0.957	1	1	0.957	1	INDETERMINATE	2	TRUE	2	0.285797068244852	4		300	288	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170732	7170732	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043891-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	130	465	0	ENST00000302850.5:c.1299G>C	p.Gln433His	p.Q433H	ENST00000302850	NM_000208.2	433	caG/caC	6/22	0.285797068244852	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	2	TRUE	0	0.285797068244852	2		465	454	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256708	19256708	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1335518697	NA	P-0043891-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	145	626	0	ENST00000162023.5:c.1005G>T	p.Lys335Asn	p.K335N	ENST00000162023		335	aaG/aaT	13/13	0.120496928793665	4	FACETS	0.864	0.789	0.942	0.864	0.789	0.942	INDETERMINATE	2	TRUE	2	0.285797068244852	4		626	755	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949731	151949731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043891-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	65	251	0	ENST00000262189.6:c.1369G>A	p.Asp457Asn	p.D457N	ENST00000262189	NM_170606.2	457	Gac/Aac	10/59	0.120496928793665	4	FACETS	1	0.952	1	1	0.952	1	INDETERMINATE	2	TRUE	2	0.285797068244852	4		251	248	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274071	18274088	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGGACCAGATTGTCAAGG	AGGACCAGATTGTCAAGG	-	novel	NA	P-0044193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	155	558	0	ENST00000222254.8:c.1294_1311del		p.X432_splice	ENST00000222254	NM_005027.3	432		11/16	0.197807624702932	3	FACETS	0.909	0.833	0.989	0.909	0.833	0.989	CLONAL	2	TRUE	1	0.219753733892757	3		558	861	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753714	42753714	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	102	914	0	ENST00000222329.4:c.550G>C	p.Gly184Arg	p.G184R	ENST00000222329	NM_006494.2	184	Ggc/Cgc	4/4	0.197807624702932	3	FACETS	0.82	0.731	0.915	0.41	0.365	0.458	CLONAL	1	TRUE	1	0.219753733892757	3		914	1257	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739070	40739071	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0044193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	66	685	1	ENST00000373198.4:c.3213_3214delinsAA	p.Asp1071_His1072delinsGluAsn	p.D1071_H1072delinsEN	ENST00000373198	NM_133170.3	1071	gaCCac/gaAAac	24/32	0.197807624702932	3	FACETS	0.689	0.596	0.79	0.344	0.298	0.395	SUBCLONAL	1	TRUE	1	0.219753733892757	3		686	968	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485860	57485860	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	61	409	0	ENST00000371085.3:c.1161C>A	p.His387Gln	p.H387Q	ENST00000371085	NM_000516.4	387	caC/caA	13/13	0.197807624702932	3	FACETS	0.973	0.839	1	0.487	0.419	0.56	CLONAL	1	TRUE	1	0.219753733892757	3		409	633	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194704	29194704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044193-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	112	957	0	ENST00000240100.2:c.1024G>A	p.Glu342Lys	p.E342K	ENST00000240100	NM_001394.6	342	Gag/Aag	4/4	1	2	FACETS	0.838	0.752	0.93	0.838	0.752	0.93	CLONAL	1	TRUE	1	0.219753733892757	2		957	1216	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0044409-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	30	281	1	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	0.882	0.711	1	0.882	0.711	1	CLONAL	1	TRUE	1	0.16	2		282	425	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0044409-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	9	349	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.252	0.166	0.363	0.252	0.166	0.363	SUBCLONAL	1	TRUE	1	0.16	2		349	446	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653794	89653798	+	frameshift_variant	Frame_Shift_Del	DEL	ACATT	ACATT	C	novel	NA	P-0044409-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	27	240	0	ENST00000371953.3:c.92_96delinsC	p.Asn31ThrfsTer22	p.N31Tfs*22	ENST00000371953	NM_000314.4	31	aACATT/aC	2/9	1	2	FACETS	1	0.818	1	1	0.818	1	CLONAL	1	TRUE	1	0.16	2		240	328	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0044537-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	92	302	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.308446676555353	5	FACETS	1	0.971	1	0.825	0.739	0.914	CLONAL	2	TRUE	2	0.306706635210945	5		302	354	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044537-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	38	301	0				ENST00000310581	NM_198253.2	-/1132			0.308446676555353	3	FACETS	1	0.886	1	0.543	0.452	0.644	CLONAL	1	TRUE	1	0.306706635210945	3		301	263	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0044537-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	165	460	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	0.308446676555353	3	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	1	0.306706635210945	3		460	606	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434142	49434142	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057518571	NA	P-0044537-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	188	600	1	ENST00000301067.7:c.7411C>T	p.Arg2471Ter	p.R2471*	ENST00000301067	NM_003482.3	2471	Cga/Tga	31/54	0.27165733085665	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.306706635210945	4		601	707	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061774	38061774	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044537-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	195	583	1	ENST00000250448.2:c.215G>A	p.Gly72Asp	p.G72D	ENST00000250448	NM_004496.3	72	gGc/gAc	2/2	0.308446676555353	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.306706635210945	3		584	633	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475599	12475599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044537-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	132	421	0	ENST00000287820.6:c.1473G>A	p.Met491Ile	p.M491I	ENST00000287820	NM_015869.4	491	atG/atA	7/7	0.308446676555353	5	FACETS	1	0.963	1	0.736	0.671	0.804	CLONAL	2	TRUE	2	0.306706635210945	5		421	569	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972611	32972611	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1566261240	NA	P-0044537-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	82	346	0	ENST00000380152.3:c.9961C>T	p.Gln3321Ter	p.Q3321*	ENST00000380152		3321	Cag/Tag	27/27	0.220815242125611	4	FACETS	0.893	0.793	1	0.893	0.793	1	CLONAL	2	TRUE	2	0.306706635210945	4		346	391	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607794	46607794	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044537-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	121	641	1	ENST00000263734.3:c.1983C>A	p.Phe661Leu	p.F661L	ENST00000263734	NM_001430.4	661	ttC/ttA	12/16	0.308446676555353	3	FACETS	1	0.983	1	0.701	0.635	0.771	CLONAL	1	TRUE	1	0.306706635210945	3		642	649	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32969035	32969035	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs276174925	NA	P-0044537-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	76	295	0	ENST00000380152.3:c.9466C>T	p.Gln3156Ter	p.Q3156*	ENST00000380152		3156	Caa/Taa	25/27	0.220815242125611	4	FACETS	1	0.897	1	1	0.897	1	CLONAL	2	TRUE	2	0.306706635210945	4		295	319	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	443506	443506	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044537-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	105	315	0	ENST00000399788.2:c.1391C>G	p.Ser464Cys	p.S464C	ENST00000399788	NM_001042603.1	464	tCt/tGt	11/28	0.27165733085665	4	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	2	0.306706635210945	4		315	420	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109773	115109773	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs199572544	NA	P-0044537-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	153	650	0	ENST00000257566.3:c.2105G>T	p.Ser702Ile	p.S702I	ENST00000257566	NM_016569.3	702	aGc/aTc	8/8	0.27165733085665	4	FACETS	0.963	0.883	1	0.963	0.883	1	CLONAL	2	TRUE	2	0.306706635210945	4		650	677	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739688	145739688	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1259051495	NA	P-0044537-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	203	656	0	ENST00000428558.2:c.1763G>A	p.Gly588Glu	p.G588E	ENST00000428558	NM_004260.3	588	gGa/gAa	11/22	0.306706635210945	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.306706635210945	4		656	715	SUCCESS
ATR	545	MSKCC	GRCh37	3	142234358	142234358	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs774606125	NA	P-0044537-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	83	232	0	ENST00000350721.4:c.4383-1G>C		p.X1461_splice	ENST00000350721	NM_001184.3	1461			0.308446676555353	5	FACETS	1	0.956	1	0.766	0.681	0.855	CLONAL	2	TRUE	2	0.306706635210945	5		232	344	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0044740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	136	687	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.590904480061207	3	FACETS	1	0.977	1	0.75	0.697	0.802	CLONAL	2	TRUE	0	0.603049524239165	3		687	261	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609735	46609735	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	18	662	0	ENST00000263734.3:c.2459C>T	p.Ser820Leu	p.S820L	ENST00000263734	NM_001430.4	820	tCa/tTa	15/16	0.253326987853055	4	FACETS	0.563	0.426	0.722	0.188	0.142	0.241	INDETERMINATE	1	TRUE	1	0.603049524239165	4		662	170	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189444	94189445	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	46	346	0	ENST00000323929.3:c.1560dup	p.Glu521Ter	p.E521*	ENST00000323929	NM_005591.3	520	-/T	14/20	0.452940862075461	4	FACETS	1	0.953	1	0.661	0.564	0.764	CLONAL	1	TRUE	2	0.603049524239165	4		346	185	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720659	89720662	+	frameshift_variant	Frame_Shift_Del	DEL	GTTT	GTTT	CC	novel	NA	P-0044740-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	115	398	5	ENST00000371953.3:c.810_813delinsCC	p.Met270IlefsTer27	p.M270Ifs*27	ENST00000371953	NM_000314.4	270	atGTTT/atCC	8/9	0.583797893863383	2	FACETS	0.973	0.903	1	0.973	0.903	1	CLONAL	2	TRUE	0	0.603049524239165	2		403	196	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0045488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	94	274	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.919	0.83	1	1	0.987	1	CLONAL	2	TRUE	1	0.383086634879262	2		274	267	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0045695-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	40	351	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.2	2		351	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577543	7577543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1019340046	NA	P-0045695-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	51	602	0	ENST00000269305.4:c.738G>A	p.Met246Ile	p.M246I	ENST00000269305	NM_001126112.2	246	atG/atA	7/11	1	2	FACETS	0.681	0.577	0.795	0.681	0.577	0.795	SUBCLONAL	1	TRUE	1	0.2	2		602	749	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746037	162746037	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045695-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	28	359	0	ENST00000367921.3:c.2160G>C	p.Lys720Asn	p.K720N	ENST00000367921	NM_006182.2	720	aaG/aaC	16/18	1	2	FACETS	0.688	0.549	0.846	0.688	0.549	0.846	SUBCLONAL	1	TRUE	1	0.2	2		359	407	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961366	15961366	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045695-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	36	430	0	ENST00000268712.3:c.6023G>C	p.Arg2008Thr	p.R2008T	ENST00000268712	NM_006311.3	2008	aGa/aCa	39/46	1	2	FACETS	0.633	0.519	0.76	0.633	0.519	0.76	SUBCLONAL	1	TRUE	1	0.2	2		430	569	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753040	57753040	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045695-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	29	323	0	ENST00000274289.3:c.976G>C	p.Asp326His	p.D326H	ENST00000274289	NM_006622.3	326	Gat/Cat	7/14	0.217442781950941	3	FACETS	0.613	0.491	0.753	0.307	0.245	0.377	SUBCLONAL	1	TRUE	1	0.2	3		323	520	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971199	21971199	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894095	NA	P-0045695-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	49	551	0	ENST00000304494.5:c.159G>C	p.Met53Ile	p.M53I	ENST00000304494	NM_000077.4	53	atG/atC	2/3	0.137380683231843	0	FACETS	0.62	0.524	0.726			1	SUBCLONAL	1	TRUE	0	0.2	0		551	632	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391799	139391799	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1455334351	NA	P-0045906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	73	663	0	ENST00000277541.6:c.6392del	p.Gly2131AlafsTer117	p.G2131Afs*117	ENST00000277541	NM_017617.3	2131	gGc/gc	34/34	0.182445230505744	1	FACETS	0.94	0.821	1	0.94	0.821	1	CLONAL	1	TRUE	0	0.182445230505744	1		663	774	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937984	76937984	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373581602	NA	P-0045906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	62	293	1	ENST00000373344.5:c.2764G>A	p.Asp922Asn	p.D922N	ENST00000373344	NM_000489.3	922	Gat/Aat	9/35	1	1	FACETS	0.78	0.676	0.891	1	0.972	1	SUBCLONAL	2	TRUE	0	0.182445230505744	1		294	396	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100935	27100945	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCAGCCCAG	CCCCAGCCCAG	-	novel	NA	P-0045906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	61	548	0	ENST00000324856.7:c.4225_4235del	p.Gln1409CysfsTer32	p.Q1409Cfs*32	ENST00000324856	NM_006015.4	1406	cCCCCAGCCCAG/c	18/20	0.182445230505744	1	FACETS	0.898	0.774	1	0.898	0.774	1	CLONAL	1	TRUE	0	0.182445230505744	1		548	677	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307250	118307250	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	33	193	0	ENST00000534358.1:c.23G>C	p.Arg8Pro	p.R8P	ENST00000534358	NM_005933.3	8	cGc/cCc	1/36	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.182445230505744	2		193	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0046128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	255	489	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.861155461773966	2		489	563	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0046128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	76	428	0	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.318	0.279	0.36	0.318	0.279	0.36	SUBCLONAL	1	TRUE	1	0.861155461773966	2		428	555	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263973	104263974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776579	NA	P-0046128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	97	264	0	ENST00000369902.3:c.71dup	p.Ala25GlyfsTer23	p.A25Gfs*23	ENST00000369902	NM_016169.3	22	gcc/gCcc	1/12	0.861155461773966	1	FACETS	0.91	0.847	0.969	0.91	0.847	0.969	CLONAL	1	TRUE	0	0.861155461773966	1		264	141	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685301	89685301	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	133	247	0	ENST00000371953.3:c.196A>G	p.Lys66Glu	p.K66E	ENST00000371953	NM_000314.4	66	Aag/Gag	3/9	0.861155461773966	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.861155461773966	1		247	157	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412905	49412905	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519951	NA	P-0046128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	251	688	0	ENST00000418115.1:c.118G>A	p.Glu40Lys	p.E40K	ENST00000418115	NM_001664.2	40	Gag/Aag	2/5	1	2	FACETS	0.96	0.906	1	0.96	0.906	1	CLONAL	1	TRUE	1	0.861155461773966	2		688	607	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874012	151874013	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	24	504	0	ENST00000262189.6:c.8525dup	p.Asn2842LysfsTer2	p.N2842Kfs*2	ENST00000262189	NM_170606.2	2842	aat/aaAt	38/59	0.861155461773966	1	FACETS	0.153	0.12	0.191	0.153	0.12	0.191	SUBCLONAL	1	TRUE	0	0.861155461773966	1		504	207	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911039	94911039	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	211	511	1	ENST00000536441.1:c.1091T>A	p.Val364Glu	p.V364E	ENST00000536441	NM_144665.3	364	gTg/gAg	8/10	0.120659150425746	4	FACETS	0.914	0.857	0.971	0.914	0.857	0.971	INDETERMINATE	2	TRUE	2	0.861155461773966	4		512	499	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880861	28880861	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199599880	NA	P-0046128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	229	573	0	ENST00000282397.4:c.3769C>T	p.Arg1257Cys	p.R1257C	ENST00000282397	NM_002019.4	1257	Cgc/Tgc	29/30	0.671870728854529	1	FACETS	0.415	0.388	0.443	0.415	0.388	0.443	SUBCLONAL	1	TRUE	0	0.861155461773966	1		573	729	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303375	91303375	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs367543015	NA	P-0046128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	84	274	0	ENST00000355112.3:c.1088-2A>G		p.X363_splice	ENST00000355112	NM_000057.2	363			1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.861155461773966	2		274	189	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434766	99434766	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	273	782	0	ENST00000268035.6:c.853A>G	p.Ile285Val	p.I285V	ENST00000268035	NM_000875.3	285	Atc/Gtc	3/21	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.861155461773966	2		782	562	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353812	40353812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	630	737	0	ENST00000293328.3:c.2308G>A	p.Glu770Lys	p.E770K	ENST00000293328	NM_012448.3	770	Gag/Aag	19/19	0.861155461773966	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.861155461773966	3		737	1042	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359605	40359605	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	310	580	0	ENST00000293328.3:c.2048A>T	p.Tyr683Phe	p.Y683F	ENST00000293328	NM_012448.3	683	tAc/tTc	16/19	0.861155461773966	3	FACETS	1	0.986	1	0.559	0.528	0.59	CLONAL	1	TRUE	1	0.861155461773966	3		580	921	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989440	85989440	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0046128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	116	370	0	ENST00000263360.6:c.1200-1G>A		p.X400_splice	ENST00000263360	NM_003797.3	400			0.120659150425746	4	FACETS	0.889	0.815	0.965	0.889	0.815	0.965	INDETERMINATE	2	TRUE	2	0.861155461773966	4		370	282	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190780	108190780	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0046128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	57	296	0	ENST00000278616.4:c.6447T>A	p.Tyr2149Ter	p.Y2149*	ENST00000278616	NM_000051.3	2149	taT/taA	44/63	0.120659150425746	4	FACETS	1	0.972	1	0.742	0.65	0.838	INDETERMINATE	1	TRUE	2	0.861155461773966	4		296	166	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800853	120800853	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	225	680	0	ENST00000257552.2:c.395T>C	p.Phe132Ser	p.F132S	ENST00000257552	NM_002442.3	132	tTt/tCt	6/15	1	2	FACETS	0.789	0.739	0.841	0.789	0.739	0.841	SUBCLONAL	1	TRUE	1	0.861155461773966	2		680	662	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781799	3781799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	172	576	0	ENST00000262367.5:c.4868C>T	p.Ala1623Val	p.A1623V	ENST00000262367	NM_004380.2	1623	gCc/gTc	29/31	1	2	FACETS	0.825	0.766	0.886	0.825	0.766	0.886	CLONAL	1	TRUE	1	0.861155461773966	2		576	484	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7119544	7119545	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	178	584	0	ENST00000302850.5:c.3709dup	p.Tyr1237LeufsTer6	p.Y1237Lfs*6	ENST00000302850	NM_000208.2	1237	tac/tTac	21/22	1	2	FACETS	0.784	0.728	0.842	0.784	0.728	0.842	SUBCLONAL	1	TRUE	1	0.861155461773966	2		584	527	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298785	15298785	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	223	843	0	ENST00000263388.2:c.1513C>A	p.Gln505Lys	p.Q505K	ENST00000263388	NM_000435.2	505	Cag/Aag	10/33	1	2	FACETS	0.896	0.841	0.952	0.896	0.841	0.952	CLONAL	1	TRUE	1	0.861155461773966	2		843	578	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021256	31021256	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0046128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	172	579	0	ENST00000375687.4:c.1255A>T	p.Arg419Ter	p.R419*	ENST00000375687	NM_015338.5	419	Aga/Tga	12/13	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.861155461773966	2		579	299	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945548	54945548	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	175	820	1	ENST00000312783.6:c.1022T>A	p.Ile341Lys	p.I341K	ENST00000312783	NM_198436.1	341	aTa/aAa	9/10	1	2	FACETS	0.747	0.693	0.803	0.747	0.693	0.803	SUBCLONAL	1	TRUE	1	0.861155461773966	2		821	544	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058709	47058709	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	186	482	1	ENST00000409792.3:c.7569C>A	p.Tyr2523Ter	p.Y2523*	ENST00000409792	NM_014159.6	2523	taC/taA	21/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.861155461773966	2		483	397	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620491	52620491	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	197	532	0	ENST00000394830.3:c.3262A>G	p.Thr1088Ala	p.T1088A	ENST00000394830	NM_018313.4	1088	Aca/Gca	21/30	1	2	FACETS	0.769	0.716	0.823	0.769	0.716	0.823	SUBCLONAL	1	TRUE	1	0.861155461773966	2		532	595	SUCCESS
ATR	545	MSKCC	GRCh37	3	142285023	142285024	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	121	557	0	ENST00000350721.4:c.231dup	p.Ser78IlefsTer14	p.S78Ifs*14	ENST00000350721	NM_001184.3	77	-/A	3/47	1	2	FACETS	0.783	0.715	0.852	0.783	0.715	0.852	SUBCLONAL	1	TRUE	1	0.861155461773966	2		557	359	SUCCESS
APC	324	MSKCC	GRCh37	5	112154997	112154997	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	164	542	1	ENST00000257430.4:c.1268G>A	p.Trp423Ter	p.W423*	ENST00000257430	NM_000038.5	423	tGg/tAg	10/16	0.221238381114369	4	FACETS	1	0.989	1	0.735	0.681	0.791	INDETERMINATE	1	TRUE	2	0.861155461773966	4		543	482	SUCCESS
APC	324	MSKCC	GRCh37	5	112178913	112178913	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1554088540	NA	P-0046128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	99	373	0	ENST00000257430.4:c.7622T>C	p.Ile2541Thr	p.I2541T	ENST00000257430	NM_000038.5	2541	aTc/aCc	16/16	0.221238381114369	4	FACETS	0.81	0.735	0.888	0.81	0.735	0.888	INDETERMINATE	2	TRUE	2	0.861155461773966	4		373	264	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045823	180045823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1446557372	NA	P-0046128-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	143	729	1	ENST00000261937.6:c.2948C>T	p.Ala983Val	p.A983V	ENST00000261937	NM_182925.4	983	gCg/gTg	21/30	0.279546318395095	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.861155461773966	0		730	569	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211138	36211138	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	412	1092	0	ENST00000222270.7:c.889C>T	p.Arg297Ter	p.R297*	ENST00000222270	NM_014727.1	297	Cga/Tga	3/37	1	2	FACETS	0.97	0.923	1	0.97	0.923	1	CLONAL	1	TRUE	1	0.589705810646155	2		1092	1440	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	101	365	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	1	2	FACETS	0.78	0.702	0.863	0.78	0.702	0.863	SUBCLONAL	1	TRUE	1	0.589705810646155	2		365	439	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955382	48955382	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1485450031	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	72	203	0	ENST00000267163.4:c.1499-1G>A		p.X500_splice	ENST00000267163	NM_000321.2	500			1	2	FACETS	0.801	0.706	0.901	0.801	0.706	0.901	CLONAL	1	TRUE	1	0.589705810646155	2		203	305	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	301	844	0	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	1	2	FACETS	0.904	0.852	0.958	0.904	0.852	0.958	CLONAL	1	TRUE	1	0.589705810646155	2		844	1129	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	240	656	2	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.589705810646155	2		658	762	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878061	48878062	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1131690852	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	65	212	0	ENST00000267163.4:c.19dup	p.Arg7ProfsTer24	p.R7Pfs*24	ENST00000267163	NM_000321.2	5	acc/aCcc	1/27	1	2	FACETS	0.865	0.758	0.977	0.865	0.758	0.977	CLONAL	1	TRUE	1	0.589705810646155	2		212	255	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794515	42794515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	336	983	0	ENST00000575354.2:c.1595C>T	p.Pro532Leu	p.P532L	ENST00000575354	NM_015125.3	532	cCa/cTa	10/20	1	2	FACETS	0.947	0.896	1	0.947	0.896	1	CLONAL	1	TRUE	1	0.589705810646155	2		983	1203	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557738	21557738	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	256	703	0	ENST00000382592.4:c.2107G>A	p.Asp703Asn	p.D703N	ENST00000382592	NM_014572.2	703	Gat/Aat	5/8	1	2	FACETS	0.85	0.796	0.905	0.85	0.796	0.905	CLONAL	1	TRUE	1	0.589705810646155	2		703	1022	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972909	55972909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	174	495	2	ENST00000263923.4:c.1481G>A	p.Gly494Glu	p.G494E	ENST00000263923	NM_002253.2	494	gGa/gAa	11/30	1	2	FACETS	0.787	0.726	0.85	0.787	0.726	0.85	SUBCLONAL	1	TRUE	1	0.589705810646155	2		497	750	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760691	59760691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs929857537	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	438	588	0	ENST00000259008.2:c.3716C>T	p.Ser1239Phe	p.S1239F	ENST00000259008	NM_032043.2	1239	tCc/tTc	20/20	0.589705810646155	3	FACETS	0.876	0.837	0.915	0.876	0.837	0.915	CLONAL	2	TRUE	1	0.589705810646155	3		588	1098	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546725	9546725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210292896	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	125	401	0	ENST00000353224.5:c.1297C>T	p.Arg433Trp	p.R433W	ENST00000353224	NM_177990.2	433	Cgg/Tgg	5/10	1	2	FACETS	0.979	0.893	1	0.979	0.893	1	CLONAL	1	TRUE	1	0.589705810646155	2		401	433	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711875	89711875	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587782603	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	157	358	0	ENST00000371953.3:c.493G>A	p.Gly165Arg	p.G165R	ENST00000371953	NM_000314.4	165	Gga/Aga	6/9	1	2	FACETS	0.928	0.854	1	0.928	0.854	1	CLONAL	1	TRUE	1	0.589705810646155	2		358	574	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012462	29012462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	206	437	0	ENST00000282397.4:c.409G>A	p.Glu137Lys	p.E137K	ENST00000282397	NM_002019.4	137	Gag/Aag	4/30	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.589705810646155	2		437	699	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137731	64137731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	352	966	0	ENST00000334205.4:c.1832G>A	p.Gly611Glu	p.G611E	ENST00000334205	NM_003942.2	611	gGg/gAg	15/17	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.589705810646155	2		966	1151	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710542	117710542	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	87	222	0	ENST00000368508.3:c.1730G>A	p.Trp577Ter	p.W577*	ENST00000368508	NM_002944.2	577	tGg/tAg	12/43	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.589705810646155	2		222	264	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248401	212248401	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1365124530	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	106	301	0	ENST00000342788.4:c.3866C>T	p.Ser1289Phe	p.S1289F	ENST00000342788	NM_005235.2	1289	tCc/tTc	28/28	1	2	FACETS	0.879	0.794	0.968	0.879	0.794	0.968	CLONAL	1	TRUE	1	0.589705810646155	2		301	409	SUCCESS
APC	324	MSKCC	GRCh37	5	112173632	112173632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060503302	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	102	276	0	ENST00000257430.4:c.2341C>T	p.Pro781Ser	p.P781S	ENST00000257430	NM_000038.5	781	Ccc/Tcc	16/16	1	2	FACETS	0.738	0.663	0.816	0.738	0.663	0.816	SUBCLONAL	1	TRUE	1	0.589705810646155	2		276	469	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508472	106508472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	92	282	0	ENST00000359195.3:c.466G>A	p.Ala156Thr	p.A156T	ENST00000359195	NM_002649.2	156	Gcg/Acg	2/11	1	2	FACETS	0.975	0.876	1	0.975	0.876	1	CLONAL	1	TRUE	1	0.589705810646155	2		282	320	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458017	120458017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	217	576	1	ENST00000256646.2:c.7328C>T	p.Pro2443Leu	p.P2443L	ENST00000256646	NM_024408.3	2443	cCt/cTt	34/34	1	2	FACETS	0.941	0.878	1	0.941	0.878	1	CLONAL	1	TRUE	1	0.589705810646155	2		577	782	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197307	94197308	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	165	413	0	ENST00000323929.3:c.1196dup	p.Arg400GlnfsTer3	p.R400Qfs*3	ENST00000323929	NM_005591.3	399	ttc/ttTc	11/20	1	2	FACETS	0.825	0.76	0.893	0.825	0.76	0.893	CLONAL	1	TRUE	1	0.589705810646155	2		413	678	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690810	89690813	+	frameshift_variant	Frame_Shift_Del	DEL	GAAA	GAAA	-	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	117	286	0	ENST00000371953.3:c.219_222del	p.Glu73AspfsTer25	p.E73Dfs*25	ENST00000371953	NM_000314.4	73	GAAAga/ga	4/9	1	2	FACETS	0.868	0.788	0.952	0.868	0.788	0.952	CLONAL	1	TRUE	1	0.589705810646155	2		286	457	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259321	89259321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	128	361	0	ENST00000336596.2:c.465G>A	p.Met155Ile	p.M155I	ENST00000336596	NM_005233.5	155	atG/atA	3/17	0.565814117179253	1	FACETS	0.747	0.683	0.813	0.747	0.683	0.813	SUBCLONAL	1	TRUE	0	0.589705810646155	1		361	410	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468020	120468020	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	327	658	0	ENST00000256646.2:c.4419G>A	p.Trp1473Ter	p.W1473*	ENST00000256646	NM_024408.3	1473	tgG/tgA	25/34	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.589705810646155	2		658	1009	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781158	135781158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	265	650	0	ENST00000298552.3:c.1807C>T	p.Pro603Ser	p.P603S	ENST00000298552	NM_001162426.1	603	Ccg/Tcg	15/23	1	2	FACETS	0.976	0.917	1	0.976	0.917	1	CLONAL	1	TRUE	1	0.589705810646155	2		650	921	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807494	1807494	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1474187970	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	256	905	0	ENST00000260795.2:c.1663G>A	p.Val555Met	p.V555M	ENST00000260795		555	Gtg/Atg	12/17	1	2	FACETS	0.965	0.905	1	0.965	0.905	1	CLONAL	1	TRUE	1	0.589705810646155	2		905	900	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020808	26020808	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377197123	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	135	340	0	ENST00000357647.3:c.91C>T	p.Pro31Ser	p.P31S	ENST00000357647	NM_003529.2	31	Ccg/Tcg	1/1	1	2	FACETS	0.972	0.89	1	0.972	0.89	1	CLONAL	1	TRUE	1	0.589705810646155	2		340	471	SUCCESS
BLM	641	MSKCC	GRCh37	15	91298043	91298043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs755724766	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	122	279	0	ENST00000355112.3:c.962C>T	p.Thr321Met	p.T321M	ENST00000355112	NM_000057.2	321	aCg/aTg	5/22	0.589705810646155	1	FACETS	0.901	0.825	0.978	0.901	0.825	0.978	CLONAL	1	TRUE	0	0.589705810646155	1		279	324	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268875	115268875	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	215	468	0	ENST00000438362.2:c.1735A>T	p.Ile579Phe	p.I579F	ENST00000438362	NM_001242891.1	579	Att/Ttt	14/20	1	2	FACETS	0.867	0.807	0.928	0.867	0.807	0.928	CLONAL	1	TRUE	1	0.589705810646155	2		468	841	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619159	43619159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	269	628	0	ENST00000355710.3:c.2842G>A	p.Gly948Arg	p.G948R	ENST00000355710	NM_020975.4	948	Ggg/Agg	17/20	1	2	FACETS	0.977	0.918	1	0.977	0.918	1	CLONAL	1	TRUE	1	0.589705810646155	2		628	934	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852667	63852667	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	252	591	2	ENST00000279873.7:c.3445C>T	p.Pro1149Ser	p.P1149S	ENST00000279873	NM_032199.2	1149	Cct/Tct	10/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.589705810646155	2		593	830	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625282	69625282	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	297	857	0	ENST00000334134.2:c.511C>G	p.Arg171Gly	p.R171G	ENST00000334134	NM_005247.2	171	Cgc/Ggc	3/3	1	2	FACETS	0.985	0.928	1	0.985	0.928	1	CLONAL	1	TRUE	1	0.589705810646155	2		857	1023	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022540	12022540	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	252	648	0	ENST00000396373.4:c.646G>A	p.Glu216Lys	p.E216K	ENST00000396373	NM_001987.4	216	Gag/Aag	5/8	1	2	FACETS	0.918	0.86	0.977	0.918	0.86	0.977	CLONAL	1	TRUE	1	0.589705810646155	2		648	931	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243514	46243514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140086050	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	128	371	0	ENST00000334344.6:c.1867C>T	p.Arg623Cys	p.R623C	ENST00000334344	NM_152641.2	623	Cgt/Tgt	14/21	1	2	FACETS	0.848	0.773	0.926	0.848	0.773	0.926	CLONAL	1	TRUE	1	0.589705810646155	2		371	512	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28971139	28971140	+	stop_gained	Nonsense_Mutation	DNP	TA	TA	AT	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	157	372	3	ENST00000282397.4:c.1617_1618delinsAT	p.Asn539_Lys540delinsLysTer	p.N539_K540delinsK*	ENST00000282397	NM_002019.4	539	aaTAaa/aaATaa	12/30	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.589705810646155	2		375	531	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103513881	103513881	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	140	264	0	ENST00000355739.4:c.697C>T	p.Gln233Ter	p.Q233*	ENST00000355739	NM_000123.3	233	Caa/Taa	7/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.589705810646155	2		264	442	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435366	110435366	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781171890	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	245	510	0	ENST00000375856.3:c.3035C>T	p.Ser1012Phe	p.S1012F	ENST00000375856	NM_003749.2	1012	tCc/tTc	1/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.589705810646155	2		510	744	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843428	3843428	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	180	458	0	ENST00000262367.5:c.1175del	p.Leu392Ter	p.L392*	ENST00000262367	NM_004380.2	392	tTg/tg	4/31	1	2	FACETS	0.872	0.807	0.94	0.872	0.807	0.94	CLONAL	1	TRUE	1	0.589705810646155	2		458	700	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857582	9857582	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	184	481	0	ENST00000330684.3:c.3819G>T	p.Gln1273His	p.Q1273H	ENST00000330684	NM_001134407.1	1273	caG/caT	13/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.589705810646155	2		481	599	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133185	30133185	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	240	468	0	ENST00000263025.4:c.313G>A	p.Asp105Asn	p.D105N	ENST00000263025	NM_002746.2	105	Gac/Aac	2/9	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.589705810646155	2		468	740	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990336	81990336	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs994776637	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	226	481	0	ENST00000359376.3:c.3607C>G	p.Leu1203Val	p.L1203V	ENST00000359376	NM_002661.3	1203	Ctg/Gtg	32/33	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.589705810646155	2		481	754	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578493	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	371	938	0	ENST00000269305.4:c.437_438delinsAA	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tGG/tAA	5/11	1	2	FACETS	0.924	0.876	0.973	0.924	0.876	0.973	CLONAL	1	TRUE	1	0.589705810646155	2		938	1362	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979002	7979002	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	175	580	0	ENST00000319144.4:c.1565C>A	p.Pro522Gln	p.P522Q	ENST00000319144	NM_001139.2	522	cCg/cAg	12/15	1	2	FACETS	0.764	0.705	0.825	0.764	0.705	0.825	SUBCLONAL	1	TRUE	1	0.589705810646155	2		580	777	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191141	2191142	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	341	848	1	ENST00000398665.3:c.395_396delinsTT	p.Ser132Phe	p.S132F	ENST00000398665	NM_032482.2	132	tCC/tTT	5/28	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.589705810646155	2		849	1144	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353726	15353727	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	319	916	4	ENST00000263377.2:c.3153_3154delinsAA	p.Asp1052Asn	p.D1052N	ENST00000263377	NM_058243.2	1051	tcGGac/tcAAac	14/20	1	2	FACETS	0.849	0.801	0.899	0.849	0.801	0.899	CLONAL	1	TRUE	1	0.589705810646155	2		920	1274	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856058	45856059	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	267	783	0	ENST00000391945.4:c.1847_1848delinsAA	p.Arg616Gln	p.R616Q	ENST00000391945	NM_000400.3	616	cGG/cAA	20/23	1	2	FACETS	0.888	0.833	0.944	0.888	0.833	0.944	CLONAL	1	TRUE	1	0.589705810646155	2		783	1020	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909685	50909685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	311	861	0	ENST00000440232.2:c.1405C>T	p.Leu469Phe	p.L469F	ENST00000440232	NM_002691.3	469	Ctc/Ttc	12/27	1	2	FACETS	0.962	0.908	1	0.962	0.908	1	CLONAL	1	TRUE	1	0.589705810646155	2		861	1096	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085958	16085959	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	189	552	1	ENST00000281043.3:c.1134_1135delinsAA	p.Asp379Asn	p.D379N	ENST00000281043	NM_005378.4	378	gaGGac/gaAAac	3/3	1	2	FACETS	0.914	0.848	0.983	0.914	0.848	0.983	CLONAL	1	TRUE	1	0.589705810646155	2		553	701	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546766	9546766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	106	440	0	ENST00000353224.5:c.1256C>T	p.Ser419Phe	p.S419F	ENST00000353224	NM_177990.2	419	tCc/tTc	5/10	1	2	FACETS	0.813	0.734	0.897	0.813	0.734	0.897	CLONAL	1	TRUE	1	0.589705810646155	2		440	442	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022484	31022484	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	112	322	0	ENST00000375687.4:c.1969G>T	p.Glu657Ter	p.E657*	ENST00000375687	NM_015338.5	657	Gag/Tag	13/13	1	2	FACETS	0.904	0.82	0.993	0.904	0.82	0.993	CLONAL	1	TRUE	1	0.589705810646155	2		322	420	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023406	31023406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749746806	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	207	508	0	ENST00000375687.4:c.2891C>T	p.Ser964Phe	p.S964F	ENST00000375687	NM_015338.5	964	tCt/tTt	13/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.589705810646155	2		508	679	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145488	24145488	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	185	512	0	ENST00000263121.7:c.507T>G	p.Asp169Glu	p.D169E	ENST00000263121	NM_003073.3	169	gaT/gaG	5/9	1	2	FACETS	0.865	0.801	0.932	0.865	0.801	0.932	CLONAL	1	TRUE	1	0.589705810646155	2		512	725	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447567	187447567	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	214	594	2	ENST00000232014.4:c.626C>T	p.Ser209Phe	p.S209F	ENST00000232014	NM_001130845.1	209	tCc/tTc	5/10	1	2	FACETS	0.993	0.926	1	0.993	0.926	1	CLONAL	1	TRUE	1	0.589705810646155	2		596	731	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808913	1808913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369586843	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	354	904	1	ENST00000260795.2:c.2345C>T	p.Ser782Phe	p.S782F	ENST00000260795		782	tCc/tTc	17/17	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.589705810646155	2		905	1015	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527343	187527343	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	212	444	0	ENST00000441802.2:c.10231C>T	p.Gln3411Ter	p.Q3411*	ENST00000441802	NM_005245.3	3411	Caa/Taa	17/27	1	2	FACETS	0.884	0.823	0.947	0.884	0.823	0.947	CLONAL	1	TRUE	1	0.589705810646155	2		444	813	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549434	187549434	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	244	566	0	ENST00000441802.2:c.4684T>C	p.Phe1562Leu	p.F1562L	ENST00000441802	NM_005245.3	1562	Ttc/Ctc	9/27	1	2	FACETS	0.966	0.904	1	0.966	0.904	1	CLONAL	1	TRUE	1	0.589705810646155	2		566	857	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961088	79961088	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	231	486	0	ENST00000265081.6:c.485T>C	p.Val162Ala	p.V162A	ENST00000265081	NM_002439.4	162	gTt/gCt	3/24	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.589705810646155	2		486	765	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490403	20490404	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	187	381	1	ENST00000346618.3:c.1140_1141delinsAA	p.Ala381Thr	p.A381T	ENST00000346618	NM_001949.4	380	ttGGct/ttAAct	7/7	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.589705810646155	2		382	588	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026792	6026792	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	66	182	0	ENST00000265849.7:c.1604C>T	p.Ser535Phe	p.S535F	ENST00000265849	NM_000535.5	535	tCt/tTt	11/15	1	2	FACETS	0.903	0.793	1	0.903	0.793	1	CLONAL	1	TRUE	1	0.589705810646155	2		182	248	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340119	116340120	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	73	228	0	ENST00000397752.3:c.981_982delinsTT	p.Gln328Ter	p.Q328*	ENST00000397752	NM_000245.2	327	gcCCag/gcTTag	2/21	1	2	FACETS	0.904	0.799	1	0.904	0.799	1	CLONAL	1	TRUE	1	0.589705810646155	2		228	274	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931826	68931826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	210	574	0	ENST00000288368.4:c.256G>A	p.Glu86Lys	p.E86K	ENST00000288368	NM_024870.2	86	Gaa/Aaa	3/40	1	2	FACETS	0.897	0.835	0.961	0.897	0.835	0.961	CLONAL	1	TRUE	1	0.589705810646155	2		574	794	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742881	145742881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	139	391	0	ENST00000428558.2:c.130G>A	p.Glu44Lys	p.E44K	ENST00000428558	NM_004260.3	44	Gaa/Aaa	3/22	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.589705810646155	2		391	442	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0046580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	69	351	0				ENST00000310581	NM_198253.2	-/1132			0.164900175158632	0	FACETS	1	0.943	1			1	CLONAL	1	FALSE	0	0.218514195684004	0		351	432	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5206850	5206850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	68	668	0	ENST00000357368.4:c.5782G>A	p.Glu1928Lys	p.E1928K	ENST00000357368	NM_002850.3	1928	Gag/Aag	38/38	0.164900175158632	0	FACETS	0.495	0.429	0.567			1	SUBCLONAL	1	FALSE	0	0.218514195684004	0		668	982	SUCCESS
ATM	472	MSKCC	GRCh37	11	108183151	108183151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	22	261	0	ENST00000278616.4:c.5932G>A	p.Glu1978Lys	p.E1978K	ENST00000278616	NM_000051.3	1978	Gaa/Aaa	40/63	0.16608190143651	4	FACETS	0.753	0.583	0.949			1	CLONAL	1	FALSE	NA	0.218514195684004	4		261	326	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369231	118369231	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	59	310	0	ENST00000534358.1:c.5949G>C	p.Leu1983Phe	p.L1983F	ENST00000534358	NM_005933.3	1983	ttG/ttC	22/36	0.16608190143651	4	FACETS	1	0.942	1			1	CLONAL	1	FALSE	NA	0.218514195684004	4		310	556	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145488	58145488	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	58	366	0	ENST00000257904.6:c.13C>G	p.Arg5Gly	p.R5G	ENST00000257904	NM_000075.3	5	Cga/Gga	2/8	0.0960795989387806	3	FACETS	0.76	0.651	0.878	0.38	0.325	0.439	INDETERMINATE	1	FALSE	1	0.218514195684004	3		366	775	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089755	5089755	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	20	212	0	ENST00000381652.3:c.2653C>T	p.Gln885Ter	p.Q885*	ENST00000381652	NM_004972.3	885	Cag/Tag	20/25	0.218514195684004	1	FACETS	0.584	0.447	0.745	0.584	0.447	0.745	SUBCLONAL	1	FALSE	0	0.218514195684004	1		212	279	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322607	39322607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	53	499	0	ENST00000373001.3:c.385G>A	p.Asp129Asn	p.D129N	ENST00000373001	NM_022157.3	129	Gac/Aac	2/7	0.218514195684004	8	FACETS	0.818	0.695	0.953			1	CLONAL	1	FALSE	NA	0.218514195684004	8		499	982	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644418	18644418	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs376468347	NA	P-0046580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	17	315	0	ENST00000266497.5:c.2596G>C	p.Glu866Gln	p.E866Q	ENST00000266497		866	Gag/Cag	18/31	0.218514195684004	1	FACETS	0.515	0.384	0.67	0.515	0.384	0.67	SUBCLONAL	1	FALSE	0	0.218514195684004	1		315	269	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73334716	73334716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754234020	NA	P-0046580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	14	291	0	ENST00000377767.4:c.2744C>T	p.Ser915Leu	p.S915L	ENST00000377767	NM_014953.3	915	tCa/tTa	20/21	1	2	FACETS	0.48	0.346	0.642	0.48	0.346	0.642	SUBCLONAL	1	FALSE	1	0.218514195684004	2		291	267	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823847	3823847	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	69	631	0	ENST00000262367.5:c.2368C>T	p.Gln790Ter	p.Q790*	ENST00000262367	NM_004380.2	790	Cag/Tag	13/31	0.164900175158632	0	FACETS	0.483	0.419	0.552			1	SUBCLONAL	1	FALSE	0	0.218514195684004	0		631	1022	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524501	44524501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	22	260	0	ENST00000291552.4:c.56C>T	p.Ser19Leu	p.S19L	ENST00000291552	NM_006758.2	19	tCa/tTa	2/8	1	2	FACETS	0.491	0.38	0.621	0.491	0.38	0.621	SUBCLONAL	1	FALSE	1	0.218514195684004	2		260	410	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142949964	142949964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	20	430	0	ENST00000262992.4:c.2746G>A	p.Glu916Lys	p.E916K	ENST00000262992	NM_001101669.1	916	Gag/Aag	24/24	1	2	FACETS	0.52	0.397	0.664	0.52	0.397	0.664	SUBCLONAL	1	FALSE	1	0.218514195684004	2		430	352	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74868196	74868196	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	12	93	0	ENST00000284811.8:c.98G>C	p.Arg33Thr	p.R33T	ENST00000284811		33	aGa/aCa	3/4	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.218514195684004	NA		93	137	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	16	301	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	FALSE	1	0.495256630449971	2		301	50	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	138	569	0	ENST00000269571.5:c.829G>C	p.Asp277His	p.D277H	ENST00000269571		277	Gac/Cac	7/27	0.495256630449971	8	FACETS	0.999	0.916	1			1	CLONAL	3	FALSE	NA	0.495256630449971	8		569	462	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265579	198265579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	43	298	0	ENST00000335508.6:c.2578G>A	p.Glu860Lys	p.E860K	ENST00000335508	NM_012433.2	860	Gaa/Aaa	18/25	0.370136836878443	3	FACETS	1	0.961	1	0.488	0.416	0.564	CLONAL	1	FALSE	0	0.495256630449971	3		298	148	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923060	44923060	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	15	160	0	ENST00000377967.4:c.1921C>T	p.Gln641Ter	p.Q641*	ENST00000377967	NM_021140.2	641	Cag/Tag	16/29	0.495256630449971	2	FACETS	0.651	0.483	0.846			1	SUBCLONAL	1	FALSE	NA	0.495256630449971	2		160	93	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976481	25976481	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs774776226	NA	P-0046593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	16	245	0	ENST00000435504.4:c.1064G>C	p.Arg355Thr	p.R355T	ENST00000435504		355	aGa/aCa	11/13	0.495256630449971	3	FACETS	0.814	0.611	1	0.407	0.305	0.525	CLONAL	1	FALSE	1	0.495256630449971	3		245	99	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966722	44966722	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	30	179	0	ENST00000377967.4:c.3946G>T	p.Glu1316Ter	p.E1316*	ENST00000377967	NM_021140.2	1316	Gag/Tag	27/29	0.495256630449971	2	FACETS	1	0.926	1			1	CLONAL	2	FALSE	NA	0.495256630449971	2		179	53	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928730	49928730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771218531	NA	P-0046593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	10	696	1	ENST00000296474.3:c.3544G>A	p.Val1182Met	p.V1182M	ENST00000296474	NM_002447.2	1182	Gtg/Atg	17/20	0.495256630449971	3	FACETS	0.327	0.222	0.459	0.164	0.111	0.23	SUBCLONAL	1	FALSE	1	0.495256630449971	3		697	154	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436825	110436825	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	10	823	0	ENST00000375856.3:c.1576G>C	p.Glu526Gln	p.E526Q	ENST00000375856	NM_003749.2	526	Gag/Cag	1/2	0.31577937803776	5	FACETS	0.352	0.238	0.495	0.07	0.047	0.099	SUBCLONAL	1	FALSE	0	0.495256630449971	5		823	200	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073301	8073301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781338553	NA	P-0046593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	25	279	1	ENST00000377482.5:c.1358G>A	p.Arg453His	p.R453H	ENST00000377482	NM_018948.3	453	cGt/cAt	4/4	0.205153721256324	3	FACETS	0.586	0.464	0.724	0.195	0.154	0.242	INDETERMINATE	1	FALSE	0	0.495256630449971	3		280	215	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261989	16261989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	17	355	0	ENST00000375759.3:c.9254C>T	p.Thr3085Ile	p.T3085I	ENST00000375759	NM_015001.2	3085	aCc/aTc	11/15	0.437902625367249	6	FACETS	0.833	0.625	1	0.208	0.156	0.27	CLONAL	1	FALSE	2	0.495256630449971	6		355	164	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105748	27105749	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	16	268	0	ENST00000324856.7:c.5360dup	p.Ile1788AspfsTer14	p.I1788Dfs*14	ENST00000324856	NM_006015.4	1787	gag/gAag	20/20	0.437902625367249	6	FACETS	1	0.865	1	0.869	0.681	1	CLONAL	3	FALSE	2	0.495256630449971	6		268	37	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104386995	104386995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	27	243	0	ENST00000369902.3:c.1360G>A	p.Glu454Lys	p.E454K	ENST00000369902	NM_016169.3	454	Gag/Aag	11/12	0.437902625367249	6	FACETS	1	0.926	1	0.341	0.274	0.416	CLONAL	1	FALSE	2	0.495256630449971	6		243	159	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21643251	21643251	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	33	444	0	ENST00000421138.2:c.276C>G	p.Phe92Leu	p.F92L	ENST00000421138		92	ttC/ttG	5/16	0.495256630449971	5	FACETS	1	0.949	1	0.499	0.412	0.595	CLONAL	1	FALSE	2	0.495256630449971	5		444	155	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427306	49427306	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1426418887	NA	P-0046593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	32	468	0	ENST00000301067.7:c.11182A>G	p.Met3728Val	p.M3728V	ENST00000301067	NM_003482.3	3728	Atg/Gtg	39/54	0.495256630449971	5	FACETS	0.887	0.733	1	0.591	0.489	0.702	CLONAL	2	FALSE	2	0.495256630449971	5		468	127	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936788	32936788	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	31	275	0	ENST00000380152.3:c.7934G>C	p.Arg2645Thr	p.R2645T	ENST00000380152		2645	aGa/aCa	17/27	0.31577937803776	5	FACETS	0.925	0.763	1	0.37	0.305	0.44	CLONAL	2	FALSE	0	0.495256630449971	5		275	118	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714322	43714322	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	23	325	0	ENST00000382044.4:c.3831G>C	p.Glu1277Asp	p.E1277D	ENST00000382044	NM_001141980.1	1277	gaG/gaC	19/28	0.495256630449971	3	FACETS	1	0.899	1	0.616	0.491	0.754	CLONAL	1	FALSE	1	0.495256630449971	3		325	94	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042133	14042133	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	21	244	1	ENST00000311895.7:c.2680G>T	p.Ala894Ser	p.A894S	ENST00000311895	NM_005236.2	894	Gcc/Tcc	11/11	0.495256630449971	3	FACETS	1	0.917	1	0.696	0.551	0.855	CLONAL	1	FALSE	1	0.495256630449971	3		245	76	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1206976	1206976	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1174992777	NA	P-0046593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	133	478	0	ENST00000326873.7:c.64A>G	p.Met22Val	p.M22V	ENST00000326873	NM_000455.4	22	Atg/Gtg	1/10	0.494660228554009	4	FACETS	1	0.976	1	0.771	0.71	0.834	CLONAL	2	FALSE	1	0.495256630449971	4		478	347	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091175	29091175	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs778989252	NA	P-0046593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	58	276	0	ENST00000328354.6:c.1315C>T	p.Gln439Ter	p.Q439*	ENST00000328354	NM_007194.3	439	Cag/Tag	12/15	0.495256630449971	4	FACETS	1	0.953	1	0.842	0.754	0.928	CLONAL	3	FALSE	0	0.495256630449971	4		276	104	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402554	20402554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	41	453	0	ENST00000346618.3:c.91G>A	p.Ala31Thr	p.A31T	ENST00000346618	NM_001949.4	31	Gcc/Acc	1/7	NA	2	FACETS	0.466	0.389	0.552			1	INDETERMINATE	1	FALSE	NA	0.495256630449971	2		453	355	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918680	44918680	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	17	147	0	ENST00000377967.4:c.1163C>G	p.Ser388Cys	p.S388C	ENST00000377967	NM_021140.2	388	tCt/tGt	12/29	0.495256630449971	2	FACETS	0.995	0.762	1			1	CLONAL	1	FALSE	NA	0.495256630449971	2		147	69	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44920612	44920612	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	18	165	0	ENST00000377967.4:c.1373C>G	p.Pro458Arg	p.P458R	ENST00000377967	NM_021140.2	458	cCt/cGt	14/29	0.495256630449971	2	FACETS	0.799	0.613	1			1	CLONAL	1	FALSE	NA	0.495256630449971	2		165	91	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240816	53240816	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046593-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	16	206	1	ENST00000375401.3:c.1264G>T	p.Glu422Ter	p.E422*	ENST00000375401	NM_004187.3	422	Gag/Tag	10/26	0.495256630449971	2	FACETS	1	0.801	1			1	CLONAL	1	FALSE	NA	0.495256630449971	2		207	61	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1315	217	301	0				ENST00000310581	NM_198253.2	-/1132			0.353683305108754	4	FACETS	1	0.934	1	0.504	0.467	0.543	CLONAL	1	TRUE	2	0.39058606584258	4		301	1532	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023006	27023006	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	96	61	0	ENST00000324856.7:c.112G>T	p.Glu38Ter	p.E38*	ENST00000324856	NM_006015.4	38	Gag/Tag	1/20	0.274192509620212	3	FACETS	0.842	0.757	0.93	0.842	0.757	0.93	CLONAL	2	TRUE	1	0.39058606584258	3		61	349	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106255	27106255	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	42	440	0	ENST00000324856.7:c.5866G>C	p.Glu1956Gln	p.E1956Q	ENST00000324856	NM_006015.4	1956	Gag/Cag	20/20	0.274192509620212	3	FACETS	0.935	0.785	1	0.467	0.392	0.55	CLONAL	1	TRUE	1	0.39058606584258	3		440	275	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106279	27106279	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	51	487	2	ENST00000324856.7:c.5890G>T	p.Glu1964Ter	p.E1964*	ENST00000324856	NM_006015.4	1964	Gag/Tag	20/20	0.274192509620212	3	FACETS	1	0.896	1	0.529	0.452	0.612	CLONAL	1	TRUE	1	0.39058606584258	3		489	295	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120720	115120720	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	359	621	0	ENST00000257566.3:c.286G>A	p.Glu96Lys	p.E96K	ENST00000257566	NM_016569.3	96	Gaa/Aaa	1/8	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.39058606584258	2		621	1439	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120991	115120991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	321	529	0	ENST00000257566.3:c.15G>A	p.Met5Ile	p.M5I	ENST00000257566	NM_016569.3	5	atG/atA	1/8	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.39058606584258	2		529	1336	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954222	32954222	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs80359180	NA	P-0046677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	22	410	0	ENST00000380152.3:c.9196C>T	p.Gln3066Ter	p.Q3066*	ENST00000380152		3066	Cag/Tag	24/27	0.39058606584258	3	FACETS	0.756	0.6	0.929	0.756	0.6	0.929	CLONAL	2	TRUE	1	0.39058606584258	3		410	89	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43739612	43739612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	11	332	0	ENST00000382044.4:c.2788C>T	p.Leu930Phe	p.L930F	ENST00000382044	NM_001141980.1	930	Ctt/Ttt	13/28	1	2	FACETS	0.64	0.447	0.873	0.64	0.447	0.873	SUBCLONAL	1	TRUE	1	0.39058606584258	2		332	88	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655374	67655374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	30	300	0	ENST00000264010.4:c.1237C>A	p.His413Asn	p.H413N	ENST00000264010	NM_006565.3	413	Cat/Aat	7/12	0.277318611692564	3	FACETS	0.858	0.707	1	0.572	0.471	0.68	CLONAL	2	TRUE	0	0.39058606584258	3		300	107	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351980	89351980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	398	618	0	ENST00000301030.4:c.970G>A	p.Glu324Lys	p.E324K	ENST00000301030	NM_001256183.1	324	Gaa/Aaa	9/13	0.277318611692564	3	FACETS	0.943	0.897	0.991	0.629	0.598	0.661	CLONAL	2	TRUE	0	0.39058606584258	3		618	1291	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577077	7577079	+	frameshift_variant	Frame_Shift_Del	DEL	CTC	CTC	TT	novel	NA	P-0046677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	140	595	0	ENST00000269305.4:c.859_861delinsAA	p.Glu287LysfsTer58	p.E287Kfs*58	ENST00000269305	NM_001126112.2	287	GAG/AA	8/11	0.39058606584258	1	FACETS	0.819	0.748	0.895	0.819	0.748	0.895	CLONAL	1	TRUE	0	0.39058606584258	1		595	704	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0046677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	144	710	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.39058606584258	1	FACETS	0.859	0.785	0.936	0.859	0.785	0.936	CLONAL	1	TRUE	0	0.39058606584258	1		711	691	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0046677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	137	534	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.39058606584258	1	FACETS	0.875	0.798	0.956	0.875	0.798	0.956	CLONAL	1	TRUE	0	0.39058606584258	1		534	645	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802598	135802598	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	11	219	0	ENST00000298552.3:c.200C>T	p.Pro67Leu	p.P67L	ENST00000298552	NM_001162426.1	67	cCa/cTa	4/23	0.292665103328996	2	FACETS	0.679	0.475	0.924	0.339	0.237	0.462	SUBCLONAL	1	TRUE	0	0.39058606584258	2		219	83	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357577	89357577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	22	0	0	ENST00000301030.4:c.241G>A	p.Glu81Lys	p.E81K	ENST00000301030	NM_001256183.1	81	Gag/Aag	5/13	0.277318611692564	3	FACETS	0.118	0.09	0.15	0.039	0.03	0.05	SUBCLONAL	1	TRUE	0	0.39058606584258	3		0	1143	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89851368	89851368	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1429369721	NA	P-0046677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	16	0	0	ENST00000389301.3:c.1364C>A	p.Ser455Tyr	p.S455Y	ENST00000389301	NM_000135.2	455	tCc/tAc	15/43	0.277318611692564	3	FACETS	0.104	0.076	0.138	0.035	0.025	0.046	SUBCLONAL	1	TRUE	0	0.39058606584258	3		0	939	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440698	56440698	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	11	0	0	ENST00000407977.2:c.520G>C	p.Glu174Gln	p.E174Q	ENST00000407977		174	Gag/Cag	5/10	0.39058606584258	3	FACETS	0.126	0.086	0.176	0.063	0.043	0.088	SUBCLONAL	1	TRUE	1	0.39058606584258	3		0	535	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250151	39250151	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0046677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	8	0	0	ENST00000402219.2:c.1418C>G	p.Ser473Ter	p.S473*	ENST00000402219	NM_005633.3	473	tCa/tGa	10/23	1	2	FACETS	1	0.8	1	1	0.8	1	CLONAL	1	TRUE	1	0.39058606584258	2		0	31	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434827	128434827	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046677-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	8	0	0	ENST00000265960.3:c.27C>G	p.Ile9Met	p.I9M	ENST00000265960	NM_001006617.1	9	atC/atG	2/12	0.292665103328996	2	FACETS	0.561	0.366	0.807	0.281	0.183	0.404	SUBCLONAL	1	TRUE	0	0.39058606584258	2		0	73	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	189	701	0	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	0.281232755924411	2	FACETS	0.935	0.867	1	0.935	0.867	1	CLONAL	2	FALSE	0	0.281232755924411	2		701	719	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307316	118307316	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs9332745	NA	P-0047003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	14	8	1	ENST00000534358.1:c.89C>G	p.Ala30Gly	p.A30G	ENST00000534358	NM_005933.3	30	gCc/gGc	1/36	0.0755462350549093	6	FACETS	0.966	0.771	1			1	INDETERMINATE	7	FALSE	NA	0.281232755924411	6		9	23	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740776	145740776	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	145	852	0	ENST00000428558.2:c.1324G>T	p.Glu442Ter	p.E442*	ENST00000428558	NM_004260.3	442	Gag/Tag	7/22	0.281232755924411	8	FACETS	0.783	0.713	0.857	0.313	0.285	0.343	SUBCLONAL	2	FALSE	3	0.281232755924411	8		852	1214	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933342	39933342	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	165	869	1	ENST00000378444.4:c.1257A>C	p.Lys419Asn	p.K419N	ENST00000378444	NM_001123385.1	419	aaA/aaC	4/15	0.281232755924411	5	FACETS	1	0.985	1	0.451	0.413	0.491	CLONAL	1	FALSE	2	0.281232755924411	5		870	1232	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0047035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	45	745	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.772	0.647	0.91	0.772	0.647	0.91	CLONAL	1	TRUE	1	0.16	2		750	729	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572201	64572201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301120298	NA	P-0047035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	57	718	0	ENST00000312049.6:c.1438C>T	p.Arg480Trp	p.R480W	ENST00000312049	NM_130799.2	480	Cgg/Tgg	10/10	1	2	FACETS	0.979	0.838	1	0.979	0.838	1	CLONAL	1	TRUE	1	0.16	2		718	728	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047328	77048350	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTAGAAAAGAAAAATAAGAGAAAGAACATACATTTAGGATATACACTCACTTCAGTAAGTGTTGACTGTGTACCTACACATAGGTGACAAGATCCGCCTGGCTTCCAGCTCTGCTATCCTTTGTCTCTCCAAAGTCACTTGACTACCACCTTCATGTCTAGCTCCTAGCCTATTTCCTATTGAACCCTGAAGAGAAATAGAAGGAATATAAGAAACACCATCTCTGGCCTCCTACTTCTCCTCAAACCAGGGGACTTAGTGTTAAAGTCCAAGCTGCCCATTTTGGTCTTGATTGCTCATCCCAATTCTGCTTTGTTCTTGAAAAACCATTCCCATAATCCCAAATCTGGCGACTAGGTCCTTGTCTTATTCCTTGGGCACGAGTCCTTGATTTAAACCCCAATCACCTATGACTAGGCATGGCCCTGTTTTTATGCCCCAGACCCAGGGCTGCTAGCAGTCCTTCCATAAACTGCCCATCCACCCATGACACAGCCTGTTTGTCTGGTCTACTGGTCTTTACACCTTTGAACAAAATGCTCTACCTGCCATGGTTTTTACATTATATTGCAATTATAAATTTATTTAAATTAGGAAGCCTTTGAGAGTATGGATTATGTCCTCTTACTTGTCCTCATATCCCTAGAAGGACCAGCATGTACTGGACATTCAATAAAAGTTTGCTGAATAACTGAATGAAAGAAATTATACAAAACTCTTTTTTCTAATTATCTATTACACGTTTTCCATACTAGATTGAGAAGGTAGGGAAAATTTACTCTCAGTGCCCATCACAGGACCTAGCACAGAGTAACCATTCAGCAAAGTTTTTTGTGGTTGTTGTTAAATGTATAAATGAATGAAAAAATAATGAAATGATATCCTATGATTAATACAGAAAATATAAAACAGCCCTCATATCCCATGAAATCATAAAGACCCTTTGGTGAGTGTCGTAGTTACTATTATATGATGACCATCTCACAGGAGACAGGGCCCCACAGGCAGAGAAGTATTATCATT	CTAGAAAAGAAAAATAAGAGAAAGAACATACATTTAGGATATACACTCACTTCAGTAAGTGTTGACTGTGTACCTACACATAGGTGACAAGATCCGCCTGGCTTCCAGCTCTGCTATCCTTTGTCTCTCCAAAGTCACTTGACTACCACCTTCATGTCTAGCTCCTAGCCTATTTCCTATTGAACCCTGAAGAGAAATAGAAGGAATATAAGAAACACCATCTCTGGCCTCCTACTTCTCCTCAAACCAGGGGACTTAGTGTTAAAGTCCAAGCTGCCCATTTTGGTCTTGATTGCTCATCCCAATTCTGCTTTGTTCTTGAAAAACCATTCCCATAATCCCAAATCTGGCGACTAGGTCCTTGTCTTATTCCTTGGGCACGAGTCCTTGATTTAAACCCCAATCACCTATGACTAGGCATGGCCCTGTTTTTATGCCCCAGACCCAGGGCTGCTAGCAGTCCTTCCATAAACTGCCCATCCACCCATGACACAGCCTGTTTGTCTGGTCTACTGGTCTTTACACCTTTGAACAAAATGCTCTACCTGCCATGGTTTTTACATTATATTGCAATTATAAATTTATTTAAATTAGGAAGCCTTTGAGAGTATGGATTATGTCCTCTTACTTGTCCTCATATCCCTAGAAGGACCAGCATGTACTGGACATTCAATAAAAGTTTGCTGAATAACTGAATGAAAGAAATTATACAAAACTCTTTTTTCTAATTATCTATTACACGTTTTCCATACTAGATTGAGAAGGTAGGGAAAATTTACTCTCAGTGCCCATCACAGGACCTAGCACAGAGTAACCATTCAGCAAAGTTTTTTGTGGTTGTTGTTAAATGTATAAATGAATGAAAAAATAATGAAATGATATCCTATGATTAATACAGAAAATATAAAACAGCCCTCATATCCCATGAAATCATAAAGACCCTTTGGTGAGTGTCGTAGTTACTATTATATGATGACCATCTCACAGGAGACAGGGCCCCACAGGCAGAGAAGTATTATCATT	-	novel	NA	P-0047035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	46	319	0	ENST00000356341.3:c.1216+19_1217-1del		p.X406_splice	ENST00000356341	NM_002576.4	406			1	2	FACETS	0.803	0.678	0.94	1	0.964	1	CLONAL	2	TRUE	1	0.16	2		319	358	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090345	77090345	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	36	457	0	ENST00000356341.3:c.380T>A	p.Val127Glu	p.V127E	ENST00000356341	NM_002576.4	127	gTg/gAg	4/15	1	2	FACETS	0.898	0.738	1	0.898	0.738	1	CLONAL	1	TRUE	1	0.16	2		457	501	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090433	77090937	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTGTAAGAGAGACATGCAAGACTAACAGGAAGGCACAGTCACAGGGGAGCCTGAAAGAACATCAGAGCTAACTTTGACACTTGCTAGCAGCAAAAGATGCATTTATTAGTCATTCCTTTCTCTCTATACTCTCAGAGTTTACACAAGCCTCTTTTATAATATCTTTCTCATTGAATTAGTCATTTCTTAAGATGTCTGCTCCTTCACCAGGCTATACCTCCAGGATGGTAGGATAGGATGTTGTTCCTGCATGATCAGTGCCCCACACAGAGCCTGCTACCAAGCCTACCATTTAACAGAGGTTTATTATTTAAGGAACGGAGATGGAAAGGCTTCTCTGGATACAATTTTGGCGATGAAAGTGTCCCACTCATGAACGTGAGAAAATTGTAATCAGGGTCTCAGGCAAAGATAGAAGCATCAGGAAGATGAGAAAGGGTTGAATCTAACAGTGCACAGCCAGAACTCTAAAAGACTAAAGACCTTTCTGTGACCCAGGACTTA	CCTGTAAGAGAGACATGCAAGACTAACAGGAAGGCACAGTCACAGGGGAGCCTGAAAGAACATCAGAGCTAACTTTGACACTTGCTAGCAGCAAAAGATGCATTTATTAGTCATTCCTTTCTCTCTATACTCTCAGAGTTTACACAAGCCTCTTTTATAATATCTTTCTCATTGAATTAGTCATTTCTTAAGATGTCTGCTCCTTCACCAGGCTATACCTCCAGGATGGTAGGATAGGATGTTGTTCCTGCATGATCAGTGCCCCACACAGAGCCTGCTACCAAGCCTACCATTTAACAGAGGTTTATTATTTAAGGAACGGAGATGGAAAGGCTTCTCTGGATACAATTTTGGCGATGAAAGTGTCCCACTCATGAACGTGAGAAAATTGTAATCAGGGTCTCAGGCAAAGATAGAAGCATCAGGAAGATGAGAAAGGGTTGAATCTAACAGTGCACAGCCAGAACTCTAAAAGACTAAAGACCTTTCTGTGACCCAGGACTTA	-	novel	NA	P-0047035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	22	275	0	ENST00000356341.3:c.291+2_292del		p.X97_splice	ENST00000356341	NM_002576.4	97		4/15	1	2	FACETS	0.857	0.664	1	0.857	0.664	1	CLONAL	1	TRUE	1	0.16	2		275	321	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871052	12871053	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1555085575	NA	P-0047035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	31	365	1	ENST00000228872.4:c.285dup	p.Lys96GlnfsTer29	p.K96Qfs*29	ENST00000228872	NM_004064.3	93	-/C	1/3	0.147110169122378	3	FACETS	0.949	0.767	1	0.474	0.383	0.578	CLONAL	1	TRUE	1	0.16	3		366	441	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466903	18466903	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	17	274	0	ENST00000266497.5:c.1042T>C	p.Cys348Arg	p.C348R	ENST00000266497		348	Tgt/Cgt	5/31	0.147110169122378	3	FACETS	0.687	0.512	0.896	0.344	0.256	0.448	SUBCLONAL	1	TRUE	1	0.16	3		274	334	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489544	56489544	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761002408	NA	P-0047035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	67	465	0	ENST00000267101.3:c.2009G>A	p.Arg670Gln	p.R670Q	ENST00000267101	NM_001982.3	670	cGg/cAg	17/28	0.147110169122378	3	FACETS	0.822	0.715	0.938	0.822	0.715	0.938	CLONAL	2	TRUE	1	0.16	3		465	550	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032086	10032086	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	50	504	0	ENST00000330684.3:c.737T>C	p.Leu246Pro	p.L246P	ENST00000330684	NM_001134407.1	246	cTt/cCt	3/13	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.16	2		504	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578247	7578247	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	40	618	0	ENST00000269305.4:c.602del	p.Leu201CysfsTer46	p.L201Cfs*46	ENST00000269305	NM_001126112.2	201	tTg/tg	6/11	1	2	FACETS	0.686	0.568	0.818	0.686	0.568	0.818	SUBCLONAL	1	TRUE	1	0.16	2		618	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0047035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	42	784	0	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	1	2	FACETS	0.687	0.572	0.816	0.687	0.572	0.816	SUBCLONAL	1	TRUE	1	0.16	2		784	764	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244117	41244117	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs773638815	NA	P-0047035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	32	454	0	ENST00000357654.3:c.3431A>G	p.Gln1144Arg	p.Q1144R	ENST00000357654	NM_007294.3	1144	cAg/cGg	10/23	1	2	FACETS	0.883	0.716	1	0.883	0.716	1	CLONAL	1	TRUE	1	0.16	2		454	453	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30946606	30946606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	19	211	0	ENST00000375687.4:c.28G>A	p.Glu10Lys	p.E10K	ENST00000375687	NM_015338.5	10	Gag/Aag	1/13	1	2	FACETS	0.752	0.57	0.965	0.752	0.57	0.965	CLONAL	1	TRUE	1	0.16	2		211	316	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053589	37053589	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs63751615	NA	P-0047035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	39	357	0	ENST00000231790.2:c.676C>T	p.Arg226Ter	p.R226*	ENST00000231790	NM_000249.3	226	Cga/Tga	8/19	1	2	FACETS	0.764	0.636	0.906	1	0.955	1	CLONAL	2	TRUE	1	0.16	2		357	319	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162077	47162078	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	28	321	0	ENST00000409792.3:c.4048dup	p.Ser1350PhefsTer6	p.S1350Ffs*6	ENST00000409792	NM_014159.6	1350	tca/tTca	3/21	1	2	FACETS	1	0.838	1	1	0.838	1	CLONAL	1	TRUE	1	0.16	2		321	332	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436437	52436437	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	69	582	1	ENST00000460680.1:c.2057G>A	p.Gly686Asp	p.G686D	ENST00000460680	NM_004656.3	686	gGc/gAc	17/17	1	2	FACETS	0.765	0.666	0.871	1	0.974	1	SUBCLONAL	2	TRUE	1	0.16	2		583	564	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294417	1294417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1265726828	NA	P-0047035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	56	780	0	ENST00000310581.5:c.584G>A	p.Arg195Lys	p.R195K	ENST00000310581	NM_198253.2	195	aGg/aAg	2/16	1	2	FACETS	0.867	0.741	1	0.867	0.741	1	CLONAL	1	TRUE	1	0.16	2		780	807	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662468	117662468	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	23	408	0	ENST00000368508.3:c.4909G>T	p.Ala1637Ser	p.A1637S	ENST00000368508	NM_002944.2	1637	Gcc/Tcc	30/43	1	2	FACETS	0.678	0.528	0.853	0.678	0.528	0.853	SUBCLONAL	1	TRUE	1	0.16	2		408	424	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508608	106508608	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	50	498	0	ENST00000359195.3:c.602G>A	p.Trp201Ter	p.W201*	ENST00000359195	NM_002649.2	201	tGg/tAg	2/11	0.158161907948638	3	FACETS	1	0.926	1	0.58	0.492	0.677	CLONAL	1	TRUE	1	0.16	3		498	582	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965368	68965368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	37	351	0	ENST00000288368.4:c.980G>A	p.Gly327Glu	p.G327E	ENST00000288368	NM_024870.2	327	gGa/gAa	9/40	0.147110169122378	3	FACETS	1	0.881	1	0.545	0.449	0.653	CLONAL	1	TRUE	1	0.16	3		351	458	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020769	37020769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	31	444	1	ENST00000358127.4:c.76del	p.Val26PhefsTer3	p.V26Ffs*3	ENST00000358127	NM_001280556.1	26	Gtt/tt	2/10	1	2	FACETS	0.715	0.577	0.872	0.715	0.577	0.872	SUBCLONAL	1	TRUE	1	0.16	2		445	542	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759406	133759406	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1371645607	NA	P-0047035-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	41	630	0	ENST00000318560.5:c.1729C>T	p.Arg577Ter	p.R577*	ENST00000318560	NM_005157.4	577	Cga/Tga	11/11	1	2	FACETS	0.77	0.64	0.915	0.77	0.64	0.915	CLONAL	1	TRUE	1	0.16	2		630	666	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0047037-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	76	582	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.645455063689824	2		582	235	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222005	1222005	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047037-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	94	516	0	ENST00000326873.7:c.920+1del		p.S307fs	ENST00000326873	NM_000455.4	307	aGc/ac	7/10	0.645455063689824	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.645455063689824	1		516	192	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134488	2134504	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTGGACGGGGAAAGT	CCCTGGACGGGGAAAGT	A	novel	NA	P-0047037-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	101	856	0	ENST00000219476.3:c.4265_4281delinsA	p.Thr1422LysfsTer49	p.T1422Kfs*49	ENST00000219476	NM_000548.3	1422	aCCCTGGACGGGGAAAGT/aA	34/42	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.645455063689824	2		856	291	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743577	46743577	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047037-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	91	505	0	ENST00000371975.4:c.1958A>G	p.Glu653Gly	p.E653G	ENST00000371975	NM_003579.3	653	gAg/gGg	17/18	1	2	FACETS	0.887	0.796	0.982	0.887	0.796	0.982	CLONAL	1	TRUE	1	0.645455063689824	2		505	318	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112101	115112101	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047037-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	60	732	0	ENST00000257566.3:c.1639T>A	p.Ser547Thr	p.S547T	ENST00000257566	NM_016569.3	547	Tct/Act	7/8	1	2	FACETS	0.62	0.538	0.707	0.62	0.538	0.707	SUBCLONAL	1	TRUE	1	0.645455063689824	2		732	300	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235893	108235893	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs992563687	NA	P-0047037-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	52	254	0	ENST00000278616.4:c.8935G>C	p.Glu2979Gln	p.E2979Q	ENST00000278616	NM_000051.3	2979	Gag/Cag	62/63	1	2	FACETS	0.915	0.793	1	0.915	0.793	1	CLONAL	1	TRUE	1	0.645455063689824	2		254	176	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891346	101891346	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047037-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	45	344	0	ENST00000374994.4:c.307C>G	p.Gln103Glu	p.Q103E	ENST00000374994	NM_004612.2	103	Cag/Gag	2/9	0.611741883206687	1	FACETS	0.78	0.674	0.891	0.78	0.674	0.891	SUBCLONAL	1	TRUE	0	0.645455063689824	1		344	121	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480335	56480335	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047044-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	230	412	0	ENST00000267101.3:c.442T>C	p.Tyr148His	p.Y148H	ENST00000267101	NM_001982.3	148	Tat/Cat	4/28	1	2	FACETS	0.787	0.736	0.84	0.787	0.736	0.84	SUBCLONAL	1	TRUE	1	0.709919677661027	2		412	823	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288885	212288885	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047044-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	23	228	0	ENST00000342788.4:c.2861T>A	p.Val954Asp	p.V954D	ENST00000342788	NM_005235.2	954	gTc/gAc	23/28	1	2	FACETS	0.164	0.128	0.207	0.164	0.128	0.207	SUBCLONAL	1	TRUE	1	0.709919677661027	2		228	394	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395850	395850	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758443557	NA	P-0047044-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	62	481	0	ENST00000380956.4:c.407C>T	p.Ala136Val	p.A136V	ENST00000380956	NM_001195286.1	136	gCc/gTc	4/9	NA	2	FACETS	0.157	0.134	0.181			1	INDETERMINATE	1	TRUE	NA	0.709919677661027	2		481	1116	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878803	151878803	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047044-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	285	418	1	ENST00000262189.6:c.6142C>T	p.Gln2048Ter	p.Q2048*	ENST00000262189	NM_170606.2	2048	Caa/Taa	36/59	1	2	FACETS	0.952	0.898	1	0.952	0.898	1	CLONAL	1	TRUE	1	0.709919677661027	2		419	843	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0047182-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	29	327	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.2974423238102	1	FACETS	0.795	0.65	0.953	0.795	0.65	0.953	CLONAL	1	TRUE	0	0.463428827607598	1		327	121	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986567	36986568	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047182-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	116	577	1	ENST00000354822.5:c.1121dup	p.Ser375IlefsTer64	p.S375Ifs*64	ENST00000354822	NM_001079668.2	374	gta/gtTa	3/3	0.463428827607598	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.463428827607598	1		578	285	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205070	128205070	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569301892	NA	P-0047309-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	170	936	2	ENST00000341105.2:c.371C>T	p.Thr124Met	p.T124M	ENST00000341105	NM_032638.4	124	aCg/aTg	3/6	0.397160457090952	1	FACETS	0.876	0.807	0.948	0.876	0.807	0.948	CLONAL	1	TRUE	0	0.397160457090952	1		938	783	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680682	88680682	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047309-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	111	548	1	ENST00000360948.2:c.575C>A	p.Ala192Asp	p.A192D	ENST00000360948	NM_001012338.2	192	gCt/gAt	6/19	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.397160457090952	2		549	554	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443757	52443757	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs1208026193	NA	P-0047309-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	150	671	0	ENST00000460680.1:c.40C>G	p.Leu14Val	p.L14V	ENST00000460680	NM_004656.3	14	Ctc/Gtc	2/17	0.397160457090952	1	FACETS	0.927	0.85	1	0.927	0.85	1	CLONAL	1	TRUE	0	0.397160457090952	1		671	653	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729606	41729606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047470-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	382	566	0	ENST00000242208.4:c.923G>A	p.Arg308His	p.R308H	ENST00000242208	NM_002192.2	308	cGt/cAt	3/3	0.689504095091479	4	FACETS	0.992	0.946	1	0.992	0.946	1	CLONAL	2	FALSE	2	0.687513483828004	4		566	945	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578505	7578512	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCAGGT	GGGCAGGT	-	novel	NA	P-0047470-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	919	1009	0	ENST00000269305.4:c.418_425del	p.Thr140CysfsTer6	p.T140Cfs*6	ENST00000269305	NM_001126112.2	140	ACCTGCCCt/t	5/11	0.689504095091479	3	FACETS	0.999	0.979	1			1	CLONAL	3	FALSE	NA	0.687513483828004	3		1009	1199	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254002	133254002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047470-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	466	463	0	ENST00000320574.5:c.748G>A	p.Gly250Arg	p.G250R	ENST00000320574	NM_006231.2	250	Gga/Aga	8/49	0.687513483828004	6	FACETS	1	0.968	1	1	0.968	1	CLONAL	3	FALSE	3	0.687513483828004	6		463	1062	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647459	117647459	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047470-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	94	357	0	ENST00000368508.3:c.5485A>G	p.Arg1829Gly	p.R1829G	ENST00000368508	NM_002944.2	1829	Aga/Gga	33/43	0.689504095091479	3	FACETS	0.935	0.838	1	0.467	0.419	0.519	CLONAL	1	FALSE	1	0.687513483828004	3		357	393	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0047486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	108	474	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.207930381400117	2	FACETS	0.882	0.801	0.965	0.882	0.801	0.965	INDETERMINATE	2	TRUE	0	0.379222878069932	2		474	323	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098950	178098950	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	40	304	0	ENST00000397062.3:c.95T>G	p.Val32Gly	p.V32G	ENST00000397062	NM_006164.4	32	gTa/gGa	2/5	0.379222878069932	3	FACETS	1	0.944	1	0.654	0.549	0.767	CLONAL	1	TRUE	1	0.379222878069932	3		304	192	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576851	7576851	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0047486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	108	604	0	ENST00000269305.4:c.993+2T>C		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.207930381400117	2	FACETS	0.999	0.911	1	0.999	0.911	1	INDETERMINATE	2	TRUE	0	0.379222878069932	2		604	285	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023183	150023183	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	58	451	1	ENST00000253339.5:c.80G>T	p.Ser27Ile	p.S27I	ENST00000253339		27	aGc/aTc	1/7	0.297704330984966	3	FACETS	0.924	0.806	1	0.616	0.537	0.698	CLONAL	2	TRUE	0	0.379222878069932	3		452	197	SUCCESS
AR	367	MSKCC	GRCh37	X	66766462	66766462	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	49	455	0	ENST00000374690.3:c.1474G>T	p.Gly492Cys	p.G492C	ENST00000374690	NM_000044.3	492	Ggc/Tgc	1/8	0.207930381400117	2	FACETS	0.904	0.77	1	0.452	0.385	0.524	INDETERMINATE	1	TRUE	0	0.379222878069932	2		455	286	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937996	76937996	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	25	537	1	ENST00000373344.5:c.2752A>T	p.Thr918Ser	p.T918S	ENST00000373344	NM_000489.3	918	Act/Tct	9/35	0.207930381400117	2	FACETS	0.487	0.384	0.603	0.243	0.192	0.302	INDETERMINATE	1	TRUE	0	0.379222878069932	2		538	271	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261484	16261485	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0047486-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	19	571	0	ENST00000375759.3:c.8752_8753del	p.Ser2918GlyfsTer44	p.S2918Gfs*44	ENST00000375759	NM_015001.2	2917	CTc/c	11/15	0.228194812225205	2	FACETS	0.298	0.226	0.383	0.149	0.113	0.192	SUBCLONAL	1	TRUE	0	0.379222878069932	2		571	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579874	7579875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1555527002	NA	P-0047505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	102	543	0	ENST00000269305.4:c.38dup	p.Leu14SerfsTer15	p.L14Sfs*15	ENST00000269305	NM_001126112.2	13	cct/ccCt	2/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		543	731	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568668	41568668	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0047505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	108	227	0	ENST00000263253.7:c.4617+1G>C		p.X1539_splice	ENST00000263253	NM_001429.3	1539			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		227	351	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098423	11098423	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs549254467	NA	P-0047505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	94	521	0	ENST00000358026.2:c.941C>T	p.Ala314Val	p.A314V	ENST00000358026	NM_001128849.1	314	gCg/gTg	6/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		521	797	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106237	27106237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1003835206	NA	P-0047505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	112	496	0	ENST00000324856.7:c.5848C>T	p.Arg1950Trp	p.R1950W	ENST00000324856	NM_006015.4	1950	Cgg/Tgg	20/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		496	705	SUCCESS
MET	4233	MSKCC	GRCh37	7	116422151	116422151	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	78	313	0	ENST00000397752.3:c.3632T>C	p.Met1211Thr	p.M1211T	ENST00000397752	NM_000245.2	1211	aTg/aCg	18/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		313	470	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413894	139413894	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0047505-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	124	599	0	ENST00000277541.6:c.865+1G>A		p.X289_splice	ENST00000277541	NM_017617.3	289			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		599	834	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249002	55249003	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGTGGA	rs397517109	NA	P-0047580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	537	554	0	ENST00000275493.2:c.2303_2311dup	p.Ser768_Asp770dup	p.S768_D770dup	ENST00000275493	NM_005228.3	768	gcc/gcCAGCGTGGAc	20/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		554	1221	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930709	32930709	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	124	538	0	ENST00000380152.3:c.7580T>G	p.Val2527Gly	p.V2527G	ENST00000380152		2527	gTa/gGa	15/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		538	675	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104353802	104353802	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	37	512	0	ENST00000369902.3:c.736G>C	p.Glu246Gln	p.E246Q	ENST00000369902	NM_016169.3	246	Gag/Cag	6/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		512	625	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321162	62321162	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1422	171	579	0	ENST00000360203.5:c.2085C>G	p.Ile695Met	p.I695M	ENST00000360203	NM_001283009.1	695	atC/atG	24/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		579	1593	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517423	176517423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528745108	NA	P-0047580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	106	533	0	ENST00000292408.4:c.124G>A	p.Glu42Lys	p.E42K	ENST00000292408	NM_213647.1	42	Gag/Aag	3/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		533	1040	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0047802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	358	532	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.940374721784496	1	FACETS	0.994	0.971	1	0.994	0.971	1	CLONAL	1	TRUE	0	0.940374721784496	1		532	406	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133048	30133048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	381	355	0	ENST00000331968.5:c.553C>T	p.His185Tyr	p.H185Y	ENST00000331968	NM_002742.2	185	Cat/Tat	4/18	NA	2	FACETS	0.998	0.954	1			1	INDETERMINATE	1	TRUE	NA	0.940374721784496	2		355	812	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68982094	68982094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	645	457	0	ENST00000288368.4:c.1468C>T	p.His490Tyr	p.H490Y	ENST00000288368	NM_024870.2	490	Cat/Tat	13/40	0.940374721784496	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.940374721784496	1		457	688	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661913	29661913	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	423	323	0	ENST00000356175.3:c.5808del	p.Arg1937ValfsTer21	p.R1937Vfs*21	ENST00000356175	NM_000267.3	1936	gTt/gt	39/57	0.940374721784496	1	FACETS	0.977	0.955	0.997	0.977	0.955	0.997	CLONAL	1	TRUE	0	0.940374721784496	1		323	488	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64286802	64286802	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047802-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	280	278	2	ENST00000370651.3:c.17G>T	p.Arg6Leu	p.R6L	ENST00000370651	NM_003463.4	6	cGc/cTc	2/6	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.940374721784496	2		280	595	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169188	119169188	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0047827-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	56	409	0	ENST00000264033.4:c.2372C>G	p.Ser791Ter	p.S791*	ENST00000264033	NM_005188.3	791	tCa/tGa	15/16	0.0492513092517961	9	FACETS	1	0.88	1	0.688	0.589	0.796	CLONAL	4	FALSE	3	0.0492513092517961	9		409	646	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30047510	30047510	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047827-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	23	312	0	ENST00000331968.5:c.2491G>T	p.Asp831Tyr	p.D831Y	ENST00000331968	NM_002742.2	831	Gat/Tat	17/18	0.0492513092517961	10	FACETS	0.996	0.782	1	0.747	0.586	0.931	CLONAL	6	FALSE	2	0.0492513092517961	10		312	187	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0047827-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	191	498	0	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	0.0492513092517961	11	FACETS	1	0.953	1	1	0.986	1	CLONAL	11	FALSE	2	0.0492513092517961	11		498	830	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586263	48586263	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047827-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	14	322	0	ENST00000342988.3:c.932A>T	p.Gln311Leu	p.Q311L	ENST00000342988	NM_005359.5	311	cAg/cTg	8/12	0.0492513092517961	8	FACETS	1	0.783	1	0.824	0.597	1	CLONAL	3	FALSE	4	0.0492513092517961	8		322	198	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144147	11144147	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047827-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	157	500	0	ENST00000358026.2:c.3728G>T	p.Arg1243Leu	p.R1243L	ENST00000358026	NM_001128849.1	1243	cGg/cTg	26/36	0.0492513092517961	3	FACETS	0.946	0.868	1	1	0.994	1	CLONAL	9	FALSE	1	0.0492513092517961	3		500	767	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867348	45867348	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047827-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	69	662	0	ENST00000391945.4:c.845G>T	p.Arg282Leu	p.R282L	ENST00000391945	NM_000400.3	282	cGg/cTg	10/23	0.0492513092517961	12	FACETS	1	0.93	1	0.492	0.428	0.562	CLONAL	4	FALSE	3	0.0492513092517961	12		662	788	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530068	212530068	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047827-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	36	245	0	ENST00000342788.4:c.1851C>A	p.Cys617Ter	p.C617*	ENST00000342788	NM_005235.2	617	tgC/tgA	15/28	0.0492513092517961	9	FACETS	0.909	0.748	1	1	0.898	1	CLONAL	5	FALSE	5	0.0492513092517961	9		245	377	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349942	70349942	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047827-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	49	573	0	ENST00000374080.3:c.3925G>A	p.Asp1309Asn	p.D1309N	ENST00000374080		1309	Gac/Aac	28/45	1	2	FACETS	0.939	0.794	1	1	0.978	1	CLONAL	3	FALSE	1	0.0492513092517961	2		573	706	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	52	470	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.806	0.687	0.936	0.806	0.687	0.936	CLONAL	1	TRUE	1	0.272870337438513	2		470	473	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007635	45007635	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	82	214	0	ENST00000558401.1:c.82C>T	p.Gln28Ter	p.Q28*	ENST00000558401	NM_004048.2	28	Cag/Tag	2/4	0.272870337438513	2	FACETS	0.905	0.805	1	0.905	0.805	1	CLONAL	2	TRUE	0	0.272870337438513	2		214	332	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	112	460	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	1	2	FACETS	0.855	0.768	0.948	0.855	0.768	0.948	CLONAL	1	TRUE	1	0.272870337438513	2		460	960	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566418	139566418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374930413	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	191	998	0	ENST00000308874.7:c.677C>T	p.Ser226Leu	p.S226L	ENST00000308874		226	tCg/tTg	9/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.272870337438513	2		998	1269	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625438	69625438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	188	945	0	ENST00000334134.2:c.355G>A	p.Glu119Lys	p.E119K	ENST00000334134	NM_005247.2	119	Gag/Aag	3/3	0.272870337438513	1	FACETS	0.949	0.875	1	0.949	0.875	1	CLONAL	1	TRUE	0	0.272870337438513	1		945	1254	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017519	112017519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	108	400	0	ENST00000368678.4:c.994G>A	p.Glu332Lys	p.E332K	ENST00000368678		332	Gag/Aag	9/13	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.272870337438513	2		400	602	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207816	102207816	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	46	183	0	ENST00000263464.3:c.1798C>T	p.Arg600Cys	p.R600C	ENST00000263464	NM_001165.4	600	Cgt/Tgt	9/9	0.272870337438513	1	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	0	0.272870337438513	1		183	287	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2199905	2199905	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1432	220	1019	0	ENST00000398665.3:c.674C>T	p.Ser225Leu	p.S225L	ENST00000398665	NM_032482.2	225	tCa/tTa	8/28	0.272870337438513	3	FACETS	1	0.975	1	0.555	0.514	0.597	CLONAL	1	TRUE	1	0.272870337438513	3		1019	1652	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050866	49050866	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	49	271	0	ENST00000267163.4:c.2550G>C	p.Gln850His	p.Q850H	ENST00000267163	NM_000321.2	850	caG/caC	25/27	0.272870337438513	3	FACETS	1	0.914	1	0.556	0.472	0.647	CLONAL	1	TRUE	1	0.272870337438513	3		271	367	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678170	58678170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	220	913	2	ENST00000305921.3:c.395C>T	p.Ser132Leu	p.S132L	ENST00000305921	NM_003620.3	132	tCg/tTg	1/6	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.272870337438513	2		915	1393	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151932982	151932982	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs772146328	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	23	61	0	ENST00000262189.6:c.2689C>T	p.Arg897Ter	p.R897*	ENST00000262189	NM_170606.2	897	Cga/Tga	16/59	1	2	FACETS	0.803	0.638	0.986	1	0.936	1	CLONAL	2	TRUE	1	0.272870337438513	2		61	105	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437616	110437616	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	357	876	0	ENST00000375856.3:c.785C>G	p.Ser262Trp	p.S262W	ENST00000375856	NM_003749.2	262	tCg/tGg	1/2	0.272870337438513	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.272870337438513	3		876	1469	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994234	21994234	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1287464120	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	210	846	1	ENST00000579755.1:c.97G>T	p.Glu33Ter	p.E33*	ENST00000579755		33	Gag/Tag	1/3	1		FACETS		0.982	1				CLONAL	1	TRUE	1	0.272870337438513	2		847	1303	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912895	32912895	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555283769	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	61	277	0	ENST00000380152.3:c.4403C>G	p.Ser1468Cys	p.S1468C	ENST00000380152		1468	tCt/tGt	11/27	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.272870337438513	2		277	339	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136124	11136124	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1255	176	880	0	ENST00000358026.2:c.3108G>A	p.Met1036Ile	p.M1036I	ENST00000358026	NM_001128849.1	1036	atG/atA	22/36	0.272870337438513	3	FACETS	1	0.938	1	0.512	0.47	0.556	CLONAL	1	TRUE	1	0.272870337438513	3		880	1431	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690810	89690810	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	26	190	0	ENST00000371953.3:c.217G>C	p.Glu73Gln	p.E73Q	ENST00000371953	NM_000314.4	73	Gaa/Caa	4/9	1	2	FACETS	0.655	0.52	0.809	0.655	0.52	0.809	SUBCLONAL	1	TRUE	1	0.272870337438513	2		190	291	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878754	151878754	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	72	428	0	ENST00000262189.6:c.6191C>G	p.Ser2064Ter	p.S2064*	ENST00000262189	NM_170606.2	2064	tCa/tGa	36/59	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.272870337438513	2		428	482	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074246	8074246	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755160538	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	86	448	0	ENST00000377482.5:c.413C>T	p.Ser138Phe	p.S138F	ENST00000377482	NM_018948.3	138	tCc/tTc	4/4	1	2	FACETS	0.915	0.809	1	0.915	0.809	1	CLONAL	1	TRUE	1	0.272870337438513	2		448	689	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264093	16264093	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1265	216	956	0	ENST00000375759.3:c.10462C>G	p.Pro3488Ala	p.P3488A	ENST00000375759	NM_015001.2	3488	Cca/Gca	12/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.272870337438513	2		956	1481	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247748	59247748	+	stop_lost	Nonstop_Mutation	SNP	C	C	A	rs746392667	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	116	648	1	ENST00000371222.2:c.995G>T	p.Ter332LeuextTer7	p.*332Lext*7	ENST00000371222	NM_002228.3	332	tGa/tTa	1/1	0.272870337438513	3	FACETS	0.906	0.814	1	0.453	0.407	0.501	CLONAL	1	TRUE	1	0.272870337438513	3		649	1067	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226590068	226590068	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs946978561	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	103	587	0	ENST00000366794.5:c.133G>C	p.Asp45His	p.D45H	ENST00000366794	NM_001618.3	45	Gat/Cat	2/23	1	2	FACETS	0.902	0.807	1	0.902	0.807	1	CLONAL	1	TRUE	1	0.272870337438513	2		587	837	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456699	32456699	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	155	694	0	ENST00000332351.3:c.193G>C	p.Glu65Gln	p.E65Q	ENST00000332351	NM_024426.4	65	Gag/Cag	1/10	0.272870337438513	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.272870337438513	1		694	964	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246510	46246510	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	29	233	0	ENST00000334344.6:c.4604G>A	p.Gly1535Glu	p.G1535E	ENST00000334344	NM_152641.2	1535	gGa/gAa	15/21	1	2	FACETS	0.743	0.598	0.907	0.743	0.598	0.907	CLONAL	1	TRUE	1	0.272870337438513	2		233	286	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246617	46246617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	35	165	0	ENST00000334344.6:c.4711G>A	p.Glu1571Lys	p.E1571K	ENST00000334344	NM_152641.2	1571	Gaa/Aaa	15/21	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.272870337438513	2		165	224	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936817	32936817	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	40	268	0	ENST00000380152.3:c.7963C>G	p.Gln2655Glu	p.Q2655E	ENST00000380152		2655	Caa/Gaa	17/27	1	2	FACETS	0.821	0.684	0.973	0.821	0.684	0.973	CLONAL	1	TRUE	1	0.272870337438513	2		268	357	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609546	81609546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	95	444	0	ENST00000298171.2:c.1144G>A	p.Asp382Asn	p.D382N	ENST00000298171	NM_000369.2	382	Gac/Aac	10/10	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.272870337438513	2		444	626	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727545	66727545	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	202	464	0	ENST00000307102.5:c.261C>G	p.His87Gln	p.H87Q	ENST00000307102	NM_002755.3	87	caC/caG	2/11	0.272870337438513	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.272870337438513	2		464	681	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992738	72992738	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	167	775	0	ENST00000268489.5:c.1307C>T	p.Ser436Phe	p.S436F	ENST00000268489	NM_006885.3	436	tCt/tTt	2/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.272870337438513	2		775	1141	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118309	17118309	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	157	763	0	ENST00000285071.4:c.1528G>C	p.Glu510Gln	p.E510Q	ENST00000285071	NM_144997.5	510	Gag/Cag	13/14	1	2	FACETS	0.983	0.898	1	0.983	0.898	1	CLONAL	1	TRUE	1	0.272870337438513	2		763	1171	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118372	17118372	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1152	212	971	0	ENST00000285071.4:c.1465G>C	p.Ala489Pro	p.A489P	ENST00000285071	NM_144997.5	489	Gct/Cct	13/14	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.272870337438513	2		971	1364	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244517	41244517	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	81	473	0	ENST00000357654.3:c.3031G>T	p.Glu1011Ter	p.E1011*	ENST00000357654	NM_007294.3	1011	Gaa/Taa	10/23	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.272870337438513	2		473	556	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602915	10602915	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1486	229	1003	0	ENST00000171111.5:c.663C>G	p.Phe221Leu	p.F221L	ENST00000171111	NM_203500.1	221	ttC/ttG	3/6	0.272870337438513	3	FACETS	1	0.976	1	0.556	0.516	0.598	CLONAL	1	TRUE	1	0.272870337438513	3		1003	1715	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095967	11095967	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1307	173	901	0	ENST00000358026.2:c.241G>C	p.Glu81Gln	p.E81Q	ENST00000358026	NM_001128849.1	81	Gag/Cag	3/36	0.272870337438513	3	FACETS	0.974	0.893	1	0.487	0.446	0.529	CLONAL	1	TRUE	1	0.272870337438513	3		901	1480	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350812	15350812	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1224	213	838	0	ENST00000263377.2:c.3191C>T	p.Ser1064Phe	p.S1064F	ENST00000263377	NM_058243.2	1064	tCc/tTc	15/20	0.272870337438513	3	FACETS	1	0.985	1	0.617	0.572	0.665	CLONAL	1	TRUE	1	0.272870337438513	3		838	1437	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950334	17950334	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1489	230	1044	0	ENST00000458235.1:c.1393G>C	p.Asp465His	p.D465H	ENST00000458235	NM_000215.3	465	Gat/Cat	10/24	0.272870337438513	3	FACETS	1	0.976	1	0.557	0.517	0.599	CLONAL	1	TRUE	1	0.272870337438513	3		1044	1719	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910623	50910623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1474	209	923	0	ENST00000440232.2:c.1726G>A	p.Glu576Lys	p.E576K	ENST00000440232	NM_002691.3	576	Gag/Aag	14/27	0.272870337438513	3	FACETS	1	0.95	1	0.517	0.478	0.558	CLONAL	1	TRUE	1	0.272870337438513	3		923	1683	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52693425	52693425	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1527	224	971	0	ENST00000322088.6:c.76C>G	p.Gln26Glu	p.Q26E	ENST00000322088	NM_014225.5	26	Cag/Gag	1/15	0.272870337438513	3	FACETS	1	0.965	1	0.533	0.494	0.573	CLONAL	1	TRUE	1	0.272870337438513	3		971	1751	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370762	225370762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	61	321	0	ENST00000264414.4:c.1117G>A	p.Asp373Asn	p.D373N	ENST00000264414	NM_003590.4	373	Gac/Aac	8/16	1	2	FACETS	0.877	0.757	1	0.877	0.757	1	CLONAL	1	TRUE	1	0.272870337438513	2		321	510	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742637	39742637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	67	295	0	ENST00000361337.2:c.1480G>A	p.Glu494Lys	p.E494K	ENST00000361337	NM_003286.2	494	Gag/Aag	15/21	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.272870337438513	2		295	490	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44515827	44515827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	94	490	1	ENST00000291552.4:c.226G>A	p.Glu76Lys	p.E76K	ENST00000291552	NM_006758.2	76	Gaa/Aaa	4/8	1	2	FACETS	0.956	0.85	1	0.956	0.85	1	CLONAL	1	TRUE	1	0.272870337438513	2		491	721	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531880	41531880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	85	419	0	ENST00000263253.7:c.1592C>T	p.Ser531Leu	p.S531L	ENST00000263253	NM_001429.3	531	tCa/tTa	7/31	1	2	FACETS	0.927	0.82	1	0.927	0.82	1	CLONAL	1	TRUE	1	0.272870337438513	2		419	672	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610710	52610710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1360491739	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	47	236	0	ENST00000394830.3:c.3463G>A	p.Glu1155Lys	p.E1155K	ENST00000394830	NM_018313.4	1155	Gaa/Aaa	23/30	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.272870337438513	2		236	333	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526111	189526111	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs779179533	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	143	600	0	ENST00000264731.3:c.375G>C	p.Gln125His	p.Q125H	ENST00000264731	NM_003722.4	125	caG/caC	4/14	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.272870337438513	2		600	1021	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190783	106190783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	85	392	0	ENST00000380013.4:c.4061G>A	p.Arg1354Lys	p.R1354K	ENST00000380013	NM_001127208.2	1354	aGa/aAa	9/11	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.272870337438513	2		392	617	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250578	26250578	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs190976340	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	128	673	1	ENST00000446824.2:c.256C>T	p.Gln86Ter	p.Q86*	ENST00000446824	NM_021018.2	86	Cag/Tag	1/1	1	2	FACETS	0.994	0.9	1	0.994	0.9	1	CLONAL	1	TRUE	1	0.272870337438513	2		674	944	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164147	32164147	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	189	795	0	ENST00000375023.3:c.5252G>T	p.Arg1751Leu	p.R1751L	ENST00000375023	NM_004557.3	1751	cGc/cTc	29/30	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.272870337438513	2		795	1237	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534506	140534506	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	77	351	0	ENST00000288602.6:c.407C>G	p.Ser136Ter	p.S136*	ENST00000288602	NM_004333.4	136	tCa/tGa	3/18	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.272870337438513	2		351	551	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38148067	38148067	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	65	611	0	ENST00000317025.8:c.3044G>C	p.Arg1015Thr	p.R1015T	ENST00000317025	NM_023034.1	1015	aGa/aCa	17/24	0.272870337438513	3	FACETS	0.511	0.441	0.587	0.255	0.22	0.294	SUBCLONAL	1	TRUE	1	0.272870337438513	3		611	1060	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956754	68956754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	98	626	0	ENST00000288368.4:c.872G>A	p.Gly291Glu	p.G291E	ENST00000288368	NM_024870.2	291	gGa/gAa	8/40	0.272870337438513	3	FACETS	0.832	0.741	0.93	0.416	0.37	0.465	CLONAL	1	TRUE	1	0.272870337438513	3		626	981	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737407	145737407	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1517	246	1142	0	ENST00000428558.2:c.3280G>T	p.Glu1094Ter	p.E1094*	ENST00000428558	NM_004260.3	1094	Gag/Tag	20/22	0.272870337438513	3	FACETS	1	0.983	1	0.581	0.541	0.623	CLONAL	1	TRUE	1	0.272870337438513	3		1142	1763	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797253	135797253	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	44	211	0	ENST00000298552.3:c.616C>G	p.His206Asp	p.H206D	ENST00000298552	NM_001162426.1	206	Cat/Gat	7/23	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.272870337438513	2		211	297	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405630	139405630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1380	272	1176	0	ENST00000277541.6:c.2561C>T	p.Ser854Phe	p.S854F	ENST00000277541	NM_017617.3	854	tCc/tTc	16/34	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.272870337438513	2		1176	1652	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608305	100608305	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	119	296	0	ENST00000308731.7:c.1785G>T	p.Lys595Asn	p.K595N	ENST00000308731	NM_000061.2	595	aaG/aaT	18/19	1	1	FACETS	0.88	0.8	0.963	1	0.988	1	CLONAL	2	TRUE	0	0.272870337438513	1		296	428	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600417	10600417	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	92	787	0	ENST00000171111.5:c.1438G>T	p.Gly480Trp	p.G480W	ENST00000171111	NM_203500.1	480	Ggg/Tgg	4/6	0.602051633314697	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.602051633314697	1		787	208	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534385	187534385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778337700	NA	P-0048098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	33	557	2	ENST00000441802.2:c.9341C>T	p.Thr3114Met	p.T3114M	ENST00000441802	NM_005245.3	3114	aCg/aTg	13/27	0.203684869316257	1	FACETS	0.399	0.328	0.478	0.399	0.328	0.478	INDETERMINATE	1	TRUE	0	0.602051633314697	1		559	192	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168992	11168992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	114	664	0	ENST00000358026.2:c.4582G>A	p.Glu1528Lys	p.E1528K	ENST00000358026	NM_001128849.1	1528	Gag/Aag	32/36	0.602051633314697	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.602051633314697	1		664	231	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054591	5054591	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1443023071	NA	P-0048098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	45	308	0	ENST00000381652.3:c.643C>T	p.Arg215Ter	p.R215*	ENST00000381652	NM_004972.3	215	Cga/Tga	7/25	0.560931433486738	1	FACETS	0.925	0.801	1	0.925	0.801	1	CLONAL	1	TRUE	0	0.602051633314697	1		308	113	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207064	1207065	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0048098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	94	823	0	ENST00000326873.7:c.156_157dup	p.Asp53GlyfsTer12	p.D53Gfs*12	ENST00000326873	NM_000455.4	51	atg/atGGg	1/10	0.602051633314697	1	FACETS	0.87	0.787	0.955	0.87	0.787	0.955	CLONAL	1	TRUE	0	0.602051633314697	1		823	251	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213929	2213929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	104	687	1	ENST00000326181.6:c.8C>T	p.Ser3Leu	p.S3L	ENST00000326181	NM_032271.2	3	tCa/tTa	2/21	0.203684869316257	1	FACETS	0.762	0.69	0.835	0.762	0.69	0.835	INDETERMINATE	1	TRUE	0	0.602051633314697	1		688	317	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170442	11170442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555795874	NA	P-0048098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	111	670	0	ENST00000358026.2:c.4745C>T	p.Ser1582Phe	p.S1582F	ENST00000358026	NM_001128849.1	1582	tCc/tTc	34/36	0.602051633314697	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.602051633314697	1		670	201	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47602419	47602419	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	50	368	0	ENST00000263735.4:c.472G>T	p.Asp158Tyr	p.D158Y	ENST00000263735	NM_002354.2	158	Gat/Tat	4/9	1	2	FACETS	0.913	0.787	1	0.913	0.787	1	CLONAL	1	TRUE	1	0.602051633314697	2		368	182	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747075	40747075	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	31	637	0	ENST00000373198.4:c.3007G>C	p.Val1003Leu	p.V1003L	ENST00000373198	NM_133170.3	1003	Gtc/Ctc	22/32	0.300404752712198	1	FACETS	0.348	0.283	0.42	0.348	0.283	0.42	INDETERMINATE	1	TRUE	0	0.602051633314697	1		637	207	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516936	187516936	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	34	497	0	ENST00000441802.2:c.13045G>C	p.Glu4349Gln	p.E4349Q	ENST00000441802	NM_005245.3	4349	Gag/Cag	26/27	0.203684869316257	1	FACETS	0.389	0.32	0.464	0.389	0.32	0.464	INDETERMINATE	1	TRUE	0	0.602051633314697	1		497	203	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233756	233756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746611221	NA	P-0048098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	70	614	0	ENST00000264932.6:c.1060G>A	p.Gly354Arg	p.G354R	ENST00000264932	NM_004168.2	354	Gga/Aga	8/15	NA	2	FACETS	0.878	0.774	0.987			1	INDETERMINATE	1	TRUE	NA	0.602051633314697	2		614	265	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911159	29911159	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	117	626	0	ENST00000376809.5:c.458A>T	p.Asp153Val	p.D153V	ENST00000376809	NM_002116.7	153	gAc/gTc	3/8	0.338034275495529	4	FACETS	1	0.966	1	1	0.966	1	INDETERMINATE	2	TRUE	2	0.602051633314697	4		626	282	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911477	39911477	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	35	577	0	ENST00000378444.4:c.5153C>A	p.Pro1718His	p.P1718H	ENST00000378444	NM_001123385.1	1718	cCt/cAt	15/15	0.602051633314697	1	FACETS	0.432	0.358	0.514	0.432	0.358	0.514	SUBCLONAL	1	TRUE	0	0.602051633314697	1		577	188	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0048102-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	101	1140	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.210355414977659	2	FACETS	0.855	0.771	0.942	1	0.976	1	CLONAL	3	TRUE	0	0.217613727566237	2		1140	362	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918787	32918787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048102-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	14	231	0	ENST00000380152.3:c.6934G>A	p.Asp2312Asn	p.D2312N	ENST00000380152		2312	Gat/Aat	12/27	0.217613727566237	3	FACETS	0.721	0.522	0.96	0.36	0.261	0.48	CLONAL	1	TRUE	1	0.217613727566237	3		231	198	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341344	89341344	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048102-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	44	530	0	ENST00000301030.4:c.7591G>C	p.Glu2531Gln	p.E2531Q	ENST00000301030	NM_001256183.1	2531	Gag/Cag	11/13	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.217613727566237	2		530	314	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106676	27106676	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0048102-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	50	659	0	ENST00000324856.7:c.6287C>G	p.Ser2096Ter	p.S2096*	ENST00000324856	NM_006015.4	2096	tCa/tGa	20/20	0.164591071044567	3	FACETS	1	0.869	1	0.513	0.435	0.598	CLONAL	1	TRUE	1	0.217613727566237	3		659	497	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831181	72831181	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048102-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	36	552	0	ENST00000268489.5:c.5400C>G	p.Phe1800Leu	p.F1800L	ENST00000268489	NM_006885.3	1800	ttC/ttG	9/10	1	2	FACETS	0.917	0.755	1	0.917	0.755	1	CLONAL	1	TRUE	1	0.217613727566237	2		552	361	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582062	189582062	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048102-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	85	438	0	ENST00000264731.3:c.621G>C	p.Lys207Asn	p.K207N	ENST00000264731	NM_003722.4	207	aaG/aaC	5/14	0.217613727566237	6	FACETS	1	0.965	1	0.816	0.724	0.913	CLONAL	2	TRUE	3	0.217613727566237	6		438	458	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225365093	225365093	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs772779469	NA	P-0048102-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	42	405	0	ENST00000264414.4:c.1597G>C	p.Glu533Gln	p.E533Q	ENST00000264414	NM_003590.4	533	Gag/Cag	11/16	0.217613727566237	3	FACETS	1	0.849	1	0.508	0.425	0.601	CLONAL	1	TRUE	1	0.217613727566237	3		405	421	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098536	108098536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048102-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	44	346	0	ENST00000278616.4:c.106G>A	p.Asp36Asn	p.D36N	ENST00000278616	NM_000051.3	36	Gat/Aat	3/63	0.217613727566237	5	FACETS	0.903	0.761	1	0.602	0.507	0.706	CLONAL	2	TRUE	2	0.217613727566237	5		346	297	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098572	108098572	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048102-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	43	286	0	ENST00000278616.4:c.142G>C	p.Asp48His	p.D48H	ENST00000278616	NM_000051.3	48	Gat/Cat	3/63	0.217613727566237	5	FACETS	0.939	0.791	1	0.626	0.527	0.735	CLONAL	2	TRUE	2	0.217613727566237	5		286	279	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122649	108122649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048102-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	71	452	0	ENST00000278616.4:c.1693G>T	p.Glu565Ter	p.E565*	ENST00000278616	NM_000051.3	565	Gaa/Taa	11/63	0.217613727566237	5	FACETS	0.834	0.733	0.941	0.834	0.733	0.941	CLONAL	3	TRUE	2	0.217613727566237	5		452	346	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186749	108186749	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786204141	NA	P-0048102-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	86	395	0	ENST00000278616.4:c.6107A>G	p.Tyr2036Cys	p.Y2036C	ENST00000278616	NM_000051.3	2036	tAt/tGt	42/63	0.217613727566237	5	FACETS	1	0.967	1	0.824	0.733	0.921	CLONAL	2	TRUE	2	0.217613727566237	5		395	424	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031965	10031965	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048102-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	53	694	0	ENST00000330684.3:c.858C>A	p.Tyr286Ter	p.Y286*	ENST00000330684	NM_001134407.1	286	taC/taA	3/13	0.217613727566237	4	FACETS	1	0.896	1	0.355	0.302	0.413	CLONAL	1	TRUE	1	0.217613727566237	4		694	557	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37865672	37865672	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048102-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	65	636	0	ENST00000269571.5:c.541C>G	p.Leu181Val	p.L181V	ENST00000269571		181	Ctc/Gtc	4/27	0.217613727566237	5	FACETS	0.785	0.681	0.896	0.523	0.454	0.598	SUBCLONAL	2	TRUE	2	0.217613727566237	5		636	505	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215381	41215381	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048102-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	42	439	0	ENST00000357654.3:c.5162A>C	p.Gln1721Pro	p.Q1721P	ENST00000357654	NM_007294.3	1721	cAg/cCg	18/23	0.217613727566237	5	FACETS	1	0.923	1	0.396	0.331	0.468	CLONAL	1	TRUE	2	0.217613727566237	5		439	431	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917042	50917042	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1555792660	NA	P-0048102-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	66	756	0	ENST00000440232.2:c.2294T>G	p.Val765Gly	p.V765G	ENST00000440232	NM_002691.3	765	gTg/gGg	19/27	0.217613727566237	3	FACETS	1	0.957	1	0.625	0.543	0.714	CLONAL	1	TRUE	1	0.217613727566237	3		756	538	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793347	242793347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048102-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	58	805	1	ENST00000334409.5:c.730G>A	p.Glu244Lys	p.E244K	ENST00000334409	NM_005018.2	244	Gag/Aag	5/5	NA	2	FACETS	0.916	0.787	1			1	INDETERMINATE	1	TRUE	NA	0.217613727566237	2		806	582	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775433	39775433	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048102-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	37	424	0	ENST00000288319.7:c.587G>C	p.Arg196Thr	p.R196T	ENST00000288319	NM_182918.3	196	aGa/aCa	4/10	0.211263242104157	4	FACETS	0.836	0.689	1	0.418	0.344	0.501	CLONAL	1	TRUE	2	0.217613727566237	4		424	495	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074190	30074190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048102-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	45	421	0	ENST00000338641.4:c.1452G>A	p.Met484Ile	p.M484I	ENST00000338641	NM_000268.3	484	atG/atA	14/16	0.210355414977659	2	FACETS	1	0.938	1	0.619	0.522	0.725	CLONAL	1	TRUE	0	0.217613727566237	2		421	334	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361199	66361200	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0048102-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	63	358	0	ENST00000273854.3:c.972_973del	p.His325GlnfsTer5	p.H325Qfs*5	ENST00000273854	NM_004439.5	324	ccTCac/ccac	4/18	0.217613727566237	5	FACETS	1	0.909	1	0.705	0.613	0.804	CLONAL	2	TRUE	2	0.217613727566237	5		358	363	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38975652	38975652	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048102-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	40	539	0	ENST00000357387.3:c.876C>G	p.Phe292Leu	p.F292L	ENST00000357387	NM_152756.3	292	ttC/ttG	10/38	0.217613727566237	6	FACETS	0.929	0.771	1	0.232	0.192	0.277	CLONAL	1	TRUE	2	0.217613727566237	6		539	568	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741693	145741693	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1333353971	NA	P-0048102-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	52	813	0	ENST00000428558.2:c.810G>C	p.Glu270Asp	p.E270D	ENST00000428558	NM_004260.3	270	gaG/gaC	5/22	0.217613727566237	5	FACETS	0.975	0.829	1	0.488	0.414	0.568	CLONAL	1	TRUE	3	0.217613727566237	5		813	650	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954210	48954210	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1354030520	NA	P-0048114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	100	145	0	ENST00000267163.4:c.1411C>T	p.Gln471Ter	p.Q471*	ENST00000267163	NM_000321.2	471	Caa/Taa	15/27	0.951739379647579	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.951739379647579	1		145	110	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0048114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	252	605	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.951739379647579	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.951739379647579	1		605	270	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676271	29676271	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0048114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	143	197	0	ENST00000356175.3:c.7258+2T>A		p.X2420_splice	ENST00000356175	NM_000267.3	2420			1	2	FACETS	0.979	0.908	1	0.979	0.908	1	CLONAL	1	TRUE	1	0.951739379647579	2		197	307	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893659	28893659	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	225	335	0	ENST00000282397.4:c.3187C>G	p.Leu1063Val	p.L1063V	ENST00000282397	NM_002019.4	1063	Ctg/Gtg	24/30	0.951739379647579	1	FACETS	0.98	0.952	1	0.98	0.952	1	CLONAL	1	TRUE	0	0.951739379647579	1		335	253	SUCCESS
APC	324	MSKCC	GRCh37	5	112173992	112173992	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1114167559	NA	P-0048114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	207	256	0	ENST00000257430.4:c.2701C>T	p.Gln901Ter	p.Q901*	ENST00000257430	NM_000038.5	901	Cag/Tag	16/16	0.951739379647579	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.951739379647579	1		256	218	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692856	89692856	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	159	147	0	ENST00000371953.3:c.340G>T	p.Glu114Ter	p.E114*	ENST00000371953	NM_000314.4	114	Gaa/Taa	5/9	0.951739379647579	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.951739379647579	1		147	171	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617503	158617503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1034717563	NA	P-0048114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	283	406	0	ENST00000263640.3:c.1153G>A	p.Glu385Lys	p.E385K	ENST00000263640	NM_001105.4	385	Gaa/Aaa	9/11	1	2	FACETS	0.958	0.908	1	0.958	0.908	1	CLONAL	1	TRUE	1	0.951739379647579	2		406	621	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380282	25380282	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	247	415	0	ENST00000311936.3:c.176C>A	p.Ala59Glu	p.A59E	ENST00000311936	NM_004985.3	59	gCa/gAa	3/5	1	2	FACETS	0.959	0.906	1	0.959	0.906	1	CLONAL	1	TRUE	1	0.951739379647579	2		415	541	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309777	104309777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745958724	NA	P-0048114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	467	506	0	ENST00000369902.3:c.368G>A	p.Arg123His	p.R123H	ENST00000369902	NM_016169.3	123	cGt/cAt	3/12	0.951739379647579	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.951739379647579	1		506	492	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752859	42752859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780261925	NA	P-0048114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	389	915	1	ENST00000222329.4:c.1405G>A	p.Gly469Ser	p.G469S	ENST00000222329	NM_006494.2	469	Ggc/Agc	4/4	0.913134214300912	3	FACETS	0.951	0.903	0.999	0.475	0.451	0.5	CLONAL	1	TRUE	1	0.951739379647579	3		916	1269	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633294	3633294	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	670	872	1	ENST00000294008.3:c.4957del	p.Ala1653ProfsTer62	p.A1653Pfs*62	ENST00000294008	NM_032444.2	1653	Gcc/cc	14/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.951739379647579	2		873	1386	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681047	30681047	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	294	416	0	ENST00000376406.3:c.672A>C	p.Glu224Asp	p.E224D	ENST00000376406	NM_014641.2	224	gaA/gaC	5/15	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.951739379647579	2		416	594	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528727	8528727	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	329	346	0	ENST00000356435.5:c.405G>T	p.Lys135Asn	p.K135N	ENST00000356435		135	aaG/aaT	4/35	0.951739379647579	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.951739379647579	1		346	356	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738219	133738219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	818	463	1	ENST00000318560.5:c.619G>A	p.Asp207Asn	p.D207N	ENST00000318560	NM_005157.4	207	Gac/Aac	4/11	0.951739379647579	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.951739379647579	2		464	836	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376409	118376409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555047948	NA	P-0048114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	288	391	0	ENST00000534358.1:c.9802C>T	p.His3268Tyr	p.H3268Y	ENST00000534358	NM_005933.3	3268	Cat/Tat	27/36	1	2	FACETS	0.949	0.9	0.998	0.949	0.9	0.998	CLONAL	1	TRUE	1	0.951739379647579	2		391	638	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528932	157528932	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	47	455	0	ENST00000346085.5:c.6657G>C	p.Glu2219Asp	p.E2219D	ENST00000346085	NM_020732.3	2219	gaG/gaC	20/20	1	2	FACETS	0.113	0.095	0.134	0.113	0.095	0.134	SUBCLONAL	1	TRUE	1	0.951739379647579	2		455	872	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0048162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	158	898	1	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.205691448478585	2	FACETS	1	0.987	1	0.694	0.638	0.752	INDETERMINATE	1	TRUE	0	0.349643854831321	2		899	651	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0048162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	42	582	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.931	0.783	1	0.931	0.783	1	CLONAL	1	TRUE	1	0.349643854831321	2		582	258	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799817	72799817	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	70	485	0	ENST00000325599.8:c.1352G>T	p.Ser451Ile	p.S451I	ENST00000325599	NM_018130.2	451	aGc/aTc	11/11	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.349643854831321	2		485	379	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481418	140481418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913349	NA	P-0048162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	36	352	0	ENST00000288602.6:c.1390G>A	p.Gly464Arg	p.G464R	ENST00000288602	NM_004333.4	464	Gga/Aga	11/18	1	2	FACETS	0.804	0.665	0.959	0.804	0.665	0.959	CLONAL	1	TRUE	1	0.349643854831321	2		352	256	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390153	89390153	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	38	275	0	ENST00000336596.2:c.902C>A	p.Ser301Ter	p.S301*	ENST00000336596	NM_005233.5	301	tCa/tAa	4/17	0.319932889494246	1	FACETS	0.827	0.689	0.977	0.827	0.689	0.977	CLONAL	1	TRUE	0	0.349643854831321	1		275	217	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219432	5219432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1351608223	NA	P-0048162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	31	797	1	ENST00000357368.4:c.3812C>T	p.Pro1271Leu	p.P1271L	ENST00000357368	NM_002850.3	1271	cCg/cTg	23/38	0.239402007107162	1	FACETS	0.245	0.197	0.299	0.245	0.197	0.299	SUBCLONAL	1	TRUE	0	0.349643854831321	1		798	597	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607568	43607569	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0048162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	43	935	0	ENST00000355710.3:c.1549dup	p.Leu517ProfsTer13	p.L517Pfs*13	ENST00000355710	NM_020975.4	515	tgc/tgCc	8/20	0.239402007107162	1	FACETS	0.307	0.256	0.364	0.307	0.256	0.364	SUBCLONAL	1	TRUE	0	0.349643854831321	1		935	661	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503240	125503240	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	14	256	0	ENST00000428830.2:c.607G>C	p.Ala203Pro	p.A203P	ENST00000428830	NM_001114121.2	203	Gct/Cct	6/14	1	2	FACETS	0.527	0.383	0.699	0.527	0.383	0.699	SUBCLONAL	1	TRUE	1	0.349643854831321	2		256	152	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1040408	1040408	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	33	581	0	ENST00000358495.3:c.164G>T	p.Arg55Leu	p.R55L	ENST00000358495	NM_134424.2	55	cGc/cTc	3/12	1	2	FACETS	0.396	0.322	0.479	0.396	0.322	0.479	SUBCLONAL	1	TRUE	1	0.349643854831321	2		581	477	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487127	56487127	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0048162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	15	348	0	ENST00000267101.3:c.1275-2A>G		p.X425_splice	ENST00000267101	NM_001982.3	425			1	2	FACETS	0.302	0.22	0.4	0.302	0.22	0.4	SUBCLONAL	1	TRUE	1	0.349643854831321	2		348	284	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042028	42042028	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0048162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	50	487	0	ENST00000219905.7:c.6223A>T	p.Lys2075Ter	p.K2075*	ENST00000219905	NM_001164273.1	2075	Aag/Tag	17/24	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.349643854831321	2		487	286	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943800	9943800	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs757464009	NA	P-0048162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	19	451	0	ENST00000330684.3:c.1141C>A	p.His381Asn	p.H381N	ENST00000330684	NM_001134407.1	381	Cat/Aat	5/13	0.349643854831321	1	FACETS	0.285	0.216	0.366	0.285	0.216	0.366	SUBCLONAL	1	TRUE	0	0.349643854831321	1		451	315	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55704589	55704589	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0048162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	42	657	0	ENST00000284073.2:c.653-1G>T		p.X218_splice	ENST00000284073	NM_138962.2	218			0.16717480063319	5	FACETS	0.556	0.463	0.659	0.185	0.154	0.22	INDETERMINATE	1	TRUE	2	0.349643854831321	5		657	659	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149740	202149740	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	67	579	0	ENST00000358485.4:c.1181A>T	p.Glu394Val	p.E394V	ENST00000358485	NM_001080125.1	394	gAg/gTg	8/9	1	2	FACETS	0.898	0.783	1	0.898	0.783	1	CLONAL	1	TRUE	1	0.349643854831321	2		579	427	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713340	40713340	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	65	670	0	ENST00000373198.4:c.4175G>T	p.Arg1392Leu	p.R1392L	ENST00000373198	NM_133170.3	1392	cGt/cTt	30/32	0.349643854831321	1	FACETS	0.699	0.608	0.797	0.699	0.608	0.797	SUBCLONAL	1	TRUE	0	0.349643854831321	1		670	439	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143039	47143039	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	32	399	0	ENST00000409792.3:c.4924G>T	p.Val1642Leu	p.V1642L	ENST00000409792	NM_014159.6	1642	Gtg/Ttg	8/21	1	2	FACETS	0.532	0.432	0.644	0.532	0.432	0.644	SUBCLONAL	1	TRUE	1	0.349643854831321	2		399	344	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934970	49934971	+	stop_gained	Nonsense_Mutation	DNP	TC	TC	AA	novel	NA	P-0048162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	79	759	0	ENST00000296474.3:c.2028_2029delinsTT	p.Arg677Ter	p.R677*	ENST00000296474	NM_002447.2	676	ctGAga/ctTTga	6/20	1	2	FACETS	0.886	0.781	0.998	0.886	0.781	0.998	CLONAL	1	TRUE	1	0.349643854831321	2		759	510	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067056	143067056	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	30	370	0	ENST00000262992.4:c.1657G>T	p.Gly553Cys	p.G553C	ENST00000262992	NM_001101669.1	553	Ggc/Tgc	16/24	0.239402007107162	1	FACETS	0.502	0.406	0.611	0.502	0.406	0.611	SUBCLONAL	1	TRUE	0	0.349643854831321	1		370	282	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798216	32798216	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	61	628	0	ENST00000374899.4:c.1463G>T	p.Gly488Val	p.G488V	ENST00000374899	NM_018833.2	488	gGg/gTg	9/12	1	2	FACETS	0.658	0.568	0.756	0.658	0.568	0.756	SUBCLONAL	1	TRUE	1	0.349643854831321	2		628	530	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288722	33288722	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	65	440	0	ENST00000374542.5:c.830A>T	p.Lys277Met	p.K277M	ENST00000374542	NM_001141970.1	277	aAg/aTg	3/8	0.144664813197104	4	FACETS	1	0.898	1	0.519	0.451	0.593	INDETERMINATE	1	TRUE	2	0.349643854831321	4		440	483	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829279	128829279	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	46	672	2	ENST00000249373.3:c.287C>A	p.Ser96Ter	p.S96*	ENST00000249373	NM_005631.4	96	tCg/tAg	1/12	1	2	FACETS	0.496	0.417	0.582	0.496	0.417	0.582	SUBCLONAL	1	TRUE	1	0.349643854831321	2		674	531	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978665	70978665	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048162-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	38	583	0	ENST00000276594.2:c.988T>A	p.Cys330Ser	p.C330S	ENST00000276594	NM_024504.3	330	Tgt/Agt	5/8	0.239402007107162	1	FACETS	0.357	0.294	0.426	0.357	0.294	0.426	SUBCLONAL	1	TRUE	0	0.349643854831321	1		583	503	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048207-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	59	301	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.823	0.711	0.944	0.823	0.711	0.944	CLONAL	1	TRUE	1	0.367693619452236	2		301	390	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588751	29588751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760703505	NA	P-0048207-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	31	254	0	ENST00000356175.3:c.4537C>T	p.Arg1513Ter	p.R1513*	ENST00000356175	NM_000267.3	1513	Cga/Tga	34/57	1	2	FACETS	0.445	0.36	0.541	0.445	0.36	0.541	SUBCLONAL	1	TRUE	1	0.367693619452236	2		254	379	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664534	29664535	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0048207-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	100	434	0	ENST00000356175.3:c.6522_6523dup	p.Thr2175ArgfsTer5	p.T2175Rfs*5	ENST00000356175	NM_000267.3	2171	-/GA	42/57	1	2	FACETS	0.748	0.668	0.833	0.748	0.668	0.833	SUBCLONAL	1	TRUE	1	0.367693619452236	2		434	727	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522568	106522568	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs754441790	NA	P-0048207-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	70	271	1	ENST00000359195.3:c.2545C>T	p.Arg849Ter	p.R849*	ENST00000359195	NM_002649.2	849	Cga/Tga	7/11	0.360125852193992	3	FACETS	0.933	0.816	1	0.467	0.408	0.53	CLONAL	1	TRUE	1	0.367693619452236	3		272	483	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008987	152008992	+	inframe_deletion	In_Frame_Del	DEL	CTTACA	CTTACA	-	novel	NA	P-0048207-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	92	328	0	ENST00000262189.6:c.630_635del	p.Val211_Ser212del	p.V211_S212del	ENST00000262189	NM_170606.2	210	agTGTAAGc/agc	5/59	0.360125852193992	3	FACETS	0.971	0.864	1	0.486	0.432	0.543	CLONAL	1	TRUE	1	0.367693619452236	3		328	610	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	36	327	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.924	0.76	1	0.924	0.76	1	CLONAL	1	TRUE	1	0.18	2		327	433	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	42	407	1	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	1	2	FACETS	0.753	0.627	0.892	0.753	0.627	0.892	SUBCLONAL	1	TRUE	1	0.18	2		408	620	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	119	745	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.767	0.692	0.846	1	0.985	1	SUBCLONAL	2	TRUE	1	0.18	2		750	862	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	40	429	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.74	0.613	0.88	0.74	0.613	0.88	SUBCLONAL	1	TRUE	1	0.18	2		429	601	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	21	196	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.822	0.633	1	0.822	0.633	1	CLONAL	1	TRUE	1	0.18	2		196	284	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29579996	29579996	+	intron_variant	Intron	DEL	A	A	-	rs1567859802	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	31	261	1	ENST00000356175.3:c.4110+3865del		p.*1370*	ENST00000356175	NM_000267.3	1384/2839			1	2	FACETS	0.765	0.619	0.932	0.765	0.619	0.932	CLONAL	1	TRUE	1	0.18	2		262	450	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088788	27088788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	60	528	2	ENST00000324856.7:c.2402del	p.Gly801ValfsTer32	p.G801Vfs*32	ENST00000324856	NM_006015.4	799	caG/ca	7/20	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.18	2		530	616	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163695	32163695	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	50	550	0	ENST00000375023.3:c.5531G>C	p.Arg1844Pro	p.R1844P	ENST00000375023	NM_004557.3	1844	cGg/cCg	30/30	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.18	2		550	533	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720650	89720650	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	84	337	0	ENST00000371953.3:c.802-1G>C		p.X268_splice	ENST00000371953	NM_000314.4	268			1	2	FACETS	0.787	0.696	0.884	1	0.979	1	SUBCLONAL	2	TRUE	1	0.18	2		337	593	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517955	176517955	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs774203148	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	53	614	0	ENST00000292408.4:c.457del	p.Gln153SerfsTer58	p.Q153Sfs*58	ENST00000292408	NM_213647.1	151	caC/ca	5/18	1	2	FACETS	0.792	0.674	0.921	0.792	0.674	0.921	CLONAL	1	TRUE	1	0.18	2		614	744	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330610	65330611	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	34	353	0	ENST00000342505.4:c.1035dup	p.Leu346ThrfsTer4	p.L346Tfs*4	ENST00000342505	NM_002227.2	345	-/A	8/25	1	2	FACETS	0.659	0.538	0.797	0.659	0.538	0.797	SUBCLONAL	1	TRUE	1	0.18	2		353	573	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246061	41246061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28897677	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	44	530	0	ENST00000357654.3:c.1487G>A	p.Arg496His	p.R496H	ENST00000357654	NM_007294.3	496	cGt/cAt	10/23	1	2	FACETS	0.674	0.564	0.797	0.674	0.564	0.797	SUBCLONAL	1	TRUE	1	0.18	2		530	725	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	57	834	3	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	1	2	FACETS	0.568	0.485	0.658	0.568	0.485	0.658	SUBCLONAL	1	TRUE	1	0.18	2		837	1116	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522693	67522693	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	20	211	0	ENST00000274335.5:c.193del	p.Glu65LysfsTer10	p.E65Kfs*10	ENST00000274335		64	Ggg/gg	1/15	1	2	FACETS	0.782	0.599	0.997	0.782	0.599	0.997	CLONAL	1	TRUE	1	0.18	2		211	284	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341251	89341251	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	45	487	0	ENST00000301030.4:c.7684G>A	p.Glu2562Lys	p.E2562K	ENST00000301030	NM_001256183.1	2562	Gag/Aag	11/13	1	2	FACETS	0.805	0.676	0.949	0.805	0.676	0.949	CLONAL	1	TRUE	1	0.18	2		487	621	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376248	15376248	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	46	534	0	ENST00000263377.2:c.766del	p.Gln256SerfsTer27	p.Q256Sfs*27	ENST00000263377	NM_058243.2	256	Cag/ag	5/20	1	2	FACETS	0.807	0.679	0.95	0.807	0.679	0.95	CLONAL	1	TRUE	1	0.18	2		534	633	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754628	42754628	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568472872	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	64	803	0	ENST00000222329.4:c.112C>T	p.Arg38Trp	p.R38W	ENST00000222329	NM_006494.2	38	Cgg/Tgg	2/4	1	2	FACETS	0.752	0.65	0.865	0.752	0.65	0.865	SUBCLONAL	1	TRUE	1	0.18	2		803	945	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343021	70343021	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs875989806	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	72	538	0	ENST00000374080.3:c.1562G>A	p.Arg521His	p.R521H	ENST00000374080		521	cGt/cAt	11/45	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.18	2		538	755	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212519	133212519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371862779	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	39	401	0	ENST00000320574.5:c.5770G>A	p.Gly1924Arg	p.G1924R	ENST00000320574	NM_006231.2	1924	Gga/Aga	42/49	1	2	FACETS	0.759	0.628	0.905	0.759	0.628	0.905	CLONAL	1	TRUE	1	0.18	2		401	571	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949753	151949753	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	38	306	0	ENST00000262189.6:c.1347G>A	p.Trp449Ter	p.W449*	ENST00000262189	NM_170606.2	449	tgG/tgA	10/59	1	2	FACETS	0.916	0.757	1	0.916	0.757	1	CLONAL	1	TRUE	1	0.18	2		306	461	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73995362	73995362	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763918983	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	35	451	0	ENST00000318443.5:c.668G>A	p.Arg223His	p.R223H	ENST00000318443	NM_001024736.1	223	cGc/cAc	4/10	1	2	FACETS	0.606	0.495	0.731	0.606	0.495	0.731	SUBCLONAL	1	TRUE	1	0.18	2		451	642	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074275	8074276	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	43	432	0	ENST00000377482.5:c.383_384insA	p.Pro129SerfsTer19	p.P129Sfs*19	ENST00000377482	NM_018948.3	128	cct/ccAt	4/4	1	2	FACETS	0.878	0.734	1	0.878	0.734	1	CLONAL	1	TRUE	1	0.18	2		432	544	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780803	9780803	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1043871084	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	76	715	0	ENST00000377346.4:c.1525C>G	p.Leu509Val	p.L509V	ENST00000377346	NM_005026.3	509	Ctg/Gtg	13/24	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.18	2		715	837	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552737	226552737	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	58	436	0	ENST00000366794.5:c.2624A>G	p.Gln875Arg	p.Q875R	ENST00000366794	NM_001618.3	875	cAg/cGg	19/23	1	2	FACETS	0.952	0.817	1	0.952	0.817	1	CLONAL	1	TRUE	1	0.18	2		436	677	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106040	8106040	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	59	452	0	ENST00000346208.3:c.860G>A	p.Cys287Tyr	p.C287Y	ENST00000346208		287	tGc/tAc	4/6	1	2	FACETS	0.986	0.847	1	0.986	0.847	1	CLONAL	1	TRUE	1	0.18	2		452	665	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628407	21628407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770588203	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	34	376	0	ENST00000421138.2:c.1211G>A	p.Arg404His	p.R404H	ENST00000421138		404	cGt/cAt	11/16	1	2	FACETS	0.777	0.634	0.938	0.777	0.634	0.938	CLONAL	1	TRUE	1	0.18	2		376	486	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923141	48923141	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1421476380	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	34	217	0	ENST00000267163.4:c.589A>G	p.Thr197Ala	p.T197A	ENST00000267163	NM_000321.2	197	Aca/Gca	6/27	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.18	2		217	319	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828090	72828090	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	75	686	0	ENST00000268489.5:c.8491G>T	p.Asp2831Tyr	p.D2831Y	ENST00000268489	NM_006885.3	2831	Gac/Tac	9/10	1	2	FACETS	0.857	0.749	0.974	0.857	0.749	0.974	CLONAL	1	TRUE	1	0.18	2		686	972	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905054	50905055	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1291315726	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	58	675	0	ENST00000440232.2:c.342dup	p.Pro115AlafsTer19	p.P115Afs*19	ENST00000440232	NM_002691.3	112	-/G	4/27	1	2	FACETS	0.785	0.673	0.908	0.785	0.673	0.908	CLONAL	1	TRUE	1	0.18	2		675	821	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128030505	128030505	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	54	468	0	ENST00000285398.2:c.1763A>G	p.Glu588Gly	p.E588G	ENST00000285398	NM_000122.1	588	gAa/gGa	11/15	1	2	FACETS	0.847	0.723	0.985	0.847	0.723	0.985	CLONAL	1	TRUE	1	0.18	2		468	708	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30061035	30061035	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	41	329	0	ENST00000338641.4:c.867G>T	p.Lys289Asn	p.K289N	ENST00000338641	NM_000268.3	289	aaG/aaT	9/16	1	2	FACETS	0.878	0.731	1	0.878	0.731	1	CLONAL	1	TRUE	1	0.18	2		329	519	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139507	47139507	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	43	370	0	ENST00000409792.3:c.5080A>G	p.Arg1694Gly	p.R1694G	ENST00000409792	NM_014159.6	1694	Aga/Gga	9/21	1	2	FACETS	0.901	0.754	1	0.901	0.754	1	CLONAL	1	TRUE	1	0.18	2		370	530	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247303	153247303	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	39	256	0	ENST00000281708.4:c.1499A>G	p.His500Arg	p.H500R	ENST00000281708	NM_033632.3	500	cAt/cGt	10/12	1	2	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	TRUE	1	0.18	2		256	428	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35860985	35860990	+	inframe_deletion	In_Frame_Del	DEL	CTCATT	CTCATT	-	novel	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	34	314	0	ENST00000303115.3:c.119_124del	p.Phe40_Ser41del	p.F40_S41del	ENST00000303115	NM_002185.3	38	taCTCATTc/tac	2/8	1	2	FACETS	0.994	0.813	1	0.994	0.813	1	CLONAL	1	TRUE	1	0.18	2		314	380	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020872	26020872	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs202025373	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	31	439	0	ENST00000357647.3:c.155T>A	p.Ile52Asn	p.I52N	ENST00000357647	NM_003529.2	52	aTc/aAc	1/1	1	2	FACETS	0.629	0.507	0.767	0.629	0.507	0.767	SUBCLONAL	1	TRUE	1	0.18	2		439	548	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739435	145739440	+	inframe_deletion	In_Frame_Del	DEL	TGTGGC	TGTGGC	-	rs781471399	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	65	801	1	ENST00000428558.2:c.1930_1935del	p.Ala644_Thr645del	p.A644_T645del	ENST00000428558	NM_004260.3	644	GCCACA/-	12/22	1	2	FACETS	0.744	0.643	0.854	0.744	0.643	0.854	SUBCLONAL	1	TRUE	1	0.18	2		802	971	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137323807	137323807	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	92	914	1	ENST00000481739.1:c.1100T>C	p.Leu367Pro	p.L367P	ENST00000481739	NM_002957.4	367	cTg/cCg	8/10	1	2	FACETS	0.908	0.804	1	0.908	0.804	1	CLONAL	1	TRUE	1	0.18	2		915	1126	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0048239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	735	745	0	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.692801450429376	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.692801450429376	1		745	1109	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777893	NA	P-0048239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	169	365	0	ENST00000361445.4:c.5930C>T	p.Thr1977Ile	p.T1977I	ENST00000361445	NM_004958.3	1977	aCa/aTa	43/58	NA	2	FACETS	0.6	0.552	0.65			1	INDETERMINATE	1	TRUE	NA	0.692801450429376	2		365	813	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801184	1801184	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1558	433	833	1	ENST00000260795.2:c.313G>C	p.Gly105Arg	p.G105R	ENST00000260795		105	Ggg/Cgg	2/17	0.272099077367802	3	FACETS	0.845	0.803	0.889	0.282	0.267	0.297	INDETERMINATE	1	TRUE	0	0.692801450429376	3		834	1991	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662128	227662128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775603579	NA	P-0048239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	599	632	1	ENST00000305123.5:c.1327C>T	p.Arg443Cys	p.R443C	ENST00000305123	NM_005544.2	443	Cgc/Tgc	1/2	0.456673796798879	1	FACETS	0.964	0.931	0.997	0.964	0.931	0.997	CLONAL	1	TRUE	0	0.692801450429376	1		633	1172	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809525	36809525	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1638	333	684	0	ENST00000373129.3:c.940G>C	p.Asp314His	p.D314H	ENST00000373129	NM_032017.1	314	Gac/Cac	10/12	0.692801450429376	3	FACETS	0.657	0.618	0.696	0.328	0.309	0.348	SUBCLONAL	1	TRUE	1	0.692801450429376	3		684	1971	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716220	243716220	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	55	367	0	ENST00000263826.5:c.974G>C	p.Arg325Pro	p.R325P	ENST00000263826	NM_005465.4	325	cGa/cCa	10/13	NA	2	FACETS	0.548	0.472	0.629			1	INDETERMINATE	1	TRUE	NA	0.692801450429376	2		367	290	SUCCESS
ATM	472	MSKCC	GRCh37	11	108128245	108128245	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	12	235	0	ENST00000278616.4:c.2288T>G	p.Phe763Cys	p.F763C	ENST00000278616	NM_000051.3	763	tTt/tGt	15/63	NA	2	FACETS	0.172	0.121	0.236			1	INDETERMINATE	1	TRUE	NA	0.692801450429376	2		235	201	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348900	118348900	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	72	173	0	ENST00000534358.1:c.3553A>G	p.Lys1185Glu	p.K1185E	ENST00000534358	NM_005933.3	1185	Aag/Gag	5/36	0.557865468656995	3	FACETS	0.845	0.744	0.953			1	CLONAL	1	TRUE	NA	0.692801450429376	3		173	331	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144449	119144589	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTGAATTACGAGAATTGAAATTGGTATTGAGAGCTTAATGTGGCTCTCCTTCCTTTCCTTGATTATGGCGATGCCTGGAATTATCTCTGTTATTTCACTTTATGCCTCCTCTCCACCCCCTCCCCAGGACAATAGTCCC	TTTTGAATTACGAGAATTGAAATTGGTATTGAGAGCTTAATGTGGCTCTCCTTCCTTTCCTTGATTATGGCGATGCCTGGAATTATCTCTGTTATTTCACTTTATGCCTCCTCTCCACCCCCTCCCCAGGACAATAGTCCC	-	novel	NA	P-0048239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	57	54	0	ENST00000264033.4:c.591-127_604del		p.X197_splice	ENST00000264033	NM_005188.3	197		4/16	0.557865468656995	3	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.692801450429376	3		54	148	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871683	35871683	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	240	435	0	ENST00000216797.5:c.823G>C	p.Glu275Gln	p.E275Q	ENST00000216797	NM_020529.2	275	Gaa/Caa	5/6	0.692801450429376	2	FACETS	0.968	0.908	1	0.484	0.454	0.515	CLONAL	1	TRUE	0	0.692801450429376	2		435	716	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90633788	90633788	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1241	123	601	0	ENST00000330062.3:c.296A>G	p.Asp99Gly	p.D99G	ENST00000330062	NM_002168.2	99	gAc/gGc	3/11	NA	2	FACETS	0.26	0.234	0.288			1	INDETERMINATE	1	TRUE	NA	0.692801450429376	2		601	1364	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366888	15366890	+	inframe_deletion	In_Frame_Del	DEL	TGC	TGC	-	rs766142522	NA	P-0048239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	115	456	0	ENST00000263377.2:c.1736_1738del	p.Ser579del	p.S579del	ENST00000263377	NM_058243.2	579	aGCAac/aac	9/20	0.692801450429376	3	FACETS	0.428	0.385	0.474	0.214	0.192	0.237	SUBCLONAL	1	TRUE	1	0.692801450429376	3		456	1044	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791003	42791003	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	297	602	0	ENST00000575354.2:c.148G>C	p.Asp50His	p.D50H	ENST00000575354	NM_015125.3	50	Gac/Cac	2/20	0.241808741404869	2	FACETS	0.629	0.591	0.668	0.314	0.295	0.334	INDETERMINATE	1	TRUE	0	0.692801450429376	2		602	1364	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562321	176562321	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1174328264	NA	P-0048239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	117	469	0	ENST00000439151.2:c.217C>G	p.Arg73Gly	p.R73G	ENST00000439151	NM_022455.4	73	Cgg/Ggg	2/23	0.692801450429376	3	FACETS	0.49	0.441	0.542			1	SUBCLONAL	1	TRUE	NA	0.692801450429376	3		469	928	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0048249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	428	327	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.590597523223959	7	FACETS	1	0.98	1			1	CLONAL	6	TRUE	NA	0.590597523223959	7		327	590	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045854	180045854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1400281005	NA	P-0048249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	219	643	1	ENST00000261937.6:c.2917C>T	p.Arg973Trp	p.R973W	ENST00000261937	NM_182925.4	973	Cgg/Tgg	21/30	0.590597523223959	5	FACETS	1	0.965	1	0.355	0.329	0.381	CLONAL	1	TRUE	2	0.590597523223959	5		644	1315	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964491	70964491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1447674775	NA	P-0048249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	161	543	0	ENST00000276594.2:c.1537G>A	p.Gly513Arg	p.G513R	ENST00000276594	NM_024504.3	513	Ggg/Agg	8/8	0.149774524587751	5	FACETS	1	0.987	1	0.348	0.32	0.378	INDETERMINATE	1	TRUE	1	0.590597523223959	5		543	738	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023055	27023055	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	63	68	0	ENST00000324856.7:c.162del	p.Gln56ArgfsTer45	p.Q56Rfs*45	ENST00000324856	NM_006015.4	54	gCc/gc	1/20	0.582494897117607	2	FACETS	0.936	0.842	1	0.936	0.842	1	CLONAL	2	TRUE	0	0.590597523223959	2		68	114	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511198	157511198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	240	428	0	ENST00000346085.5:c.3716C>T	p.Pro1239Leu	p.P1239L	ENST00000346085	NM_020732.3	1239	cCa/cTa	15/20	0.590597523223959	2	FACETS	0.989	0.939	1	0.989	0.939	1	CLONAL	2	TRUE	0	0.590597523223959	2		428	411	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	40	302	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	FALSE	1	0.192773665898881	2		302	402	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	129	301	0				ENST00000310581	NM_198253.2	-/1132			0.191191762907807	4	FACETS	1	0.956	1	1	0.956	1	CLONAL	3	FALSE	1	0.192773665898881	4		301	494	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641750	23641750	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	28	241	0	ENST00000261584.4:c.1725G>C	p.Trp575Cys	p.W575C	ENST00000261584	NM_024675.3	575	tgG/tgC	5/13	0.157071379914445	2	FACETS	0.796	0.636	0.978	0.398	0.318	0.489	CLONAL	1	FALSE	0	0.192773665898881	2		241	365	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023633	27023634	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCGGCTC	novel	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	43	379	0	ENST00000324856.7:c.741_747dup	p.Lys250ArgfsTer152	p.K250Rfs*152	ENST00000324856	NM_006015.4	247	gcc/gCCGGCTCcc	1/20	0.191191762907807	4	FACETS	1	0.859	1	0.343	0.287	0.406	CLONAL	1	FALSE	1	0.192773665898881	4		379	517	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611804	1611804	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1343124101	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	55	573	0	ENST00000344749.5:c.1858G>C	p.Glu620Gln	p.E620Q	ENST00000344749	NM_001136139.2	620	Gag/Cag	19/19	1	2	FACETS	0.627	0.535	0.729	0.627	0.535	0.729	SUBCLONAL	1	FALSE	1	0.192773665898881	2		573	910	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051057	180051057	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756924526	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	40	495	0	ENST00000261937.6:c.1426C>T	p.Arg476Trp	p.R476W	ENST00000261937	NM_182925.4	476	Cgg/Tgg	11/30	0.192773665898881	1	FACETS	0.523	0.433	0.624	0.523	0.433	0.624	SUBCLONAL	1	FALSE	0	0.192773665898881	1		495	717	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888285	112888285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	34	301	0	ENST00000351677.2:c.301C>T	p.Pro101Ser	p.P101S	ENST00000351677	NM_002834.3	101	Cct/Tct	3/16	0.191191762907807	4	FACETS	0.819	0.668	0.988	0.273	0.222	0.33	CLONAL	1	FALSE	1	0.192773665898881	4		301	514	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439656	140439656	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	52	223	0	ENST00000288602.6:c.2083G>C	p.Glu695Gln	p.E695Q	ENST00000288602	NM_004333.4	695	Gag/Cag	17/18	0.166101947290139	3	FACETS	1	0.963	1	0.734	0.626	0.851	CLONAL	1	FALSE	1	0.192773665898881	3		223	403	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206728	36206728	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	278	609	1	ENST00000300305.3:c.784C>T	p.Gln262Ter	p.Q262*	ENST00000300305		262	Cag/Tag	6/8	0.192773665898881	2	FACETS	1	0.948	1	1	0.994	1	CLONAL	3	FALSE	0	0.192773665898881	2		610	953	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600398	10600398	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	134	635	0	ENST00000171111.5:c.1457C>T	p.Ser486Leu	p.S486L	ENST00000171111	NM_203500.1	486	tCa/tTa	4/6	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.192773665898881	2		635	1076	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246527	41246527	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	198	444	0	ENST00000357654.3:c.1021G>C	p.Asp341His	p.D341H	ENST00000357654	NM_007294.3	341	Gat/Cat	10/23	0.138600564942254	4	FACETS	1	0.948	1	1	0.948	1	CLONAL	3	FALSE	1	0.192773665898881	4		444	796	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866626	37866626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	110	504	0	ENST00000269571.5:c.793G>A	p.Glu265Lys	p.E265K	ENST00000269571		265	Gag/Aag	7/27	0.138600564942254	4	FACETS	0.755	0.677	0.837	0.503	0.451	0.558	SUBCLONAL	2	FALSE	1	0.192773665898881	4		504	902	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265364	152265364	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775405192	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	33	316	0	ENST00000206249.3:c.817G>A	p.Asp273Asn	p.D273N	ENST00000206249	NM_000125.3	273	Gat/Aat	4/8	0.157071379914445	2	FACETS	0.771	0.628	0.933	0.386	0.314	0.467	CLONAL	1	FALSE	0	0.192773665898881	2		316	444	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982963	201982963	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs549132954	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	41	560	0	ENST00000359651.3:c.812G>C	p.Arg271Thr	p.R271T	ENST00000359651		271	aGa/aCa	7/8	1	2	FACETS	0.548	0.455	0.652	0.548	0.455	0.652	SUBCLONAL	1	FALSE	1	0.192773665898881	2		560	776	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812513	43812513	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	48	416	0	ENST00000372470.3:c.1216C>G	p.Leu406Val	p.L406V	ENST00000372470	NM_005373.2	406	Ctg/Gtg	8/12	1	2	FACETS	0.806	0.68	0.944	0.806	0.68	0.944	CLONAL	1	FALSE	1	0.192773665898881	2		416	618	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344696	118344696	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	38	239	0	ENST00000534358.1:c.2822C>T	p.Ser941Phe	p.S941F	ENST00000534358	NM_005933.3	941	tCt/tTt	3/36	1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	FALSE	1	0.192773665898881	2		239	384	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820966	3820966	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	78	453	0	ENST00000262367.5:c.2485C>G	p.Leu829Val	p.L829V	ENST00000262367	NM_004380.2	829	Ctt/Gtt	14/31	0.157071379914445	2	FACETS	1	0.965	1	0.637	0.56	0.72	CLONAL	1	FALSE	0	0.192773665898881	2		453	635	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554598	29554598	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761023505	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	71	164	0	ENST00000356175.3:c.2383C>T	p.Pro795Ser	p.P795S	ENST00000356175	NM_000267.3	795	Cca/Tca	20/57	0.138600564942254	4	FACETS	1	0.955	1	0.794	0.697	0.897	CLONAL	2	FALSE	1	0.192773665898881	4		164	369	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37876034	37876063	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGCAGCTGTGTGGACCTGGATGACAAGGG	CTGCAGCTGTGTGGACCTGGATGACAAGGG	-	novel	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	138	515	0	ENST00000269571.5:c.1899-2_1926del		p.X633_splice	ENST00000269571		633		16/27	0.138600564942254	4	FACETS	0.935	0.851	1	0.623	0.567	0.683	CLONAL	2	FALSE	1	0.192773665898881	4		515	913	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32438087	32438087	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	87	392	0	ENST00000332351.3:c.951-1G>T		p.X317_splice	ENST00000332351	NM_024426.4	317			1	2	FACETS	0.79	0.701	0.886	1	0.98	1	SUBCLONAL	2	FALSE	1	0.192773665898881	2		392	571	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348714	118348714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	22	158	0	ENST00000534358.1:c.3367G>A	p.Glu1123Lys	p.E1123K	ENST00000534358	NM_005933.3	1123	Gaa/Aaa	5/36	1	2	FACETS	0.716	0.555	0.902	0.716	0.555	0.902	CLONAL	1	FALSE	1	0.192773665898881	2		158	319	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240084	41240084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	11	37	0	ENST00000379561.5:c.266C>T	p.Ser89Phe	p.S89F	ENST00000379561	NM_002015.3	89	tCc/tTc	1/3	0.157071379914445	2	FACETS	1	0.855	1	0.732	0.513	0.994	CLONAL	1	FALSE	0	0.192773665898881	2		37	78	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828258	50828258	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	69	369	0	ENST00000398568.2:c.2596A>G	p.Thr866Ala	p.T866A	ENST00000398568	NM_001042412.1	866	Aca/Gca	17/18	0.165881499029927	4	FACETS	1	0.959	1	0.316	0.275	0.361	CLONAL	1	FALSE	0	0.192773665898881	4		369	675	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56873511	56873511	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	112	233	0	ENST00000308159.5:c.2215G>A	p.Asp739Asn	p.D739N	ENST00000308159	NM_014669.4	739	Gat/Aat	20/22	0.165881499029927	4	FACETS	0.983	0.889	1	0.737	0.667	0.811	CLONAL	3	FALSE	0	0.192773665898881	4		233	470	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81962188	81962188	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	74	329	0	ENST00000359376.3:c.2540C>G	p.Ser847Cys	p.S847C	ENST00000359376	NM_002661.3	847	tCt/tGt	24/33	0.165881499029927	4	FACETS	1	0.945	1	0.287	0.25	0.326	CLONAL	1	FALSE	0	0.192773665898881	4		329	798	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627613	37627613	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	76	387	0	ENST00000447079.4:c.1528G>A	p.Glu510Lys	p.E510K	ENST00000447079	NM_015083.1	510	Gag/Aag	2/14	0.138600564942254	4	FACETS	1	0.96	1	0.412	0.361	0.468	CLONAL	1	FALSE	1	0.192773665898881	4		387	760	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140144	50140144	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	62	623	1	ENST00000246792.3:c.281G>T	p.Arg94Ile	p.R94I	ENST00000246792	NM_006270.3	94	aGa/aTa	3/6	1	2	FACETS	0.679	0.584	0.782	0.679	0.584	0.782	SUBCLONAL	1	FALSE	1	0.192773665898881	2		624	948	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416154	29416154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	44	427	0	ENST00000389048.3:c.4799G>A	p.Gly1600Glu	p.G1600E	ENST00000389048	NM_004304.4	1600	gGa/gAa	29/29	1	2	FACETS	0.712	0.596	0.841	0.712	0.596	0.841	SUBCLONAL	1	FALSE	1	0.192773665898881	2		427	641	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948521	54948521	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	38	259	0	ENST00000312783.6:c.797C>G	p.Ser266Ter	p.S266*	ENST00000312783	NM_198436.1	266	tCa/tGa	8/10	0.166101947290139	3	FACETS	0.811	0.67	0.969	0.405	0.335	0.485	CLONAL	1	FALSE	1	0.192773665898881	3		259	533	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326798	62326798	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1353	82	788	0	ENST00000360203.5:c.3617C>G	p.Ser1206Ter	p.S1206*	ENST00000360203	NM_001283009.1	1206	tCa/tGa	34/35	0.166101947290139	3	FACETS	0.65	0.571	0.736	0.325	0.285	0.368	SUBCLONAL	1	FALSE	1	0.192773665898881	3		788	1435	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527589	41527589	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	84	324	0	ENST00000263253.7:c.1480C>T	p.Gln494Ter	p.Q494*	ENST00000263253	NM_001429.3	494	Cag/Tag	6/31	0.191191762907807	4	FACETS	0.942	0.833	1	0.628	0.555	0.705	CLONAL	2	FALSE	1	0.192773665898881	4		324	552	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430267	181430267	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	39	426	0	ENST00000325404.1:c.119G>C	p.Arg40Pro	p.R40P	ENST00000325404	NM_003106.3	40	cGc/cCc	1/1	1	2	FACETS	0.649	0.537	0.775	0.649	0.537	0.775	SUBCLONAL	1	FALSE	1	0.192773665898881	2		426	623	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535319	66535319	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	101	601	0	ENST00000273854.3:c.142G>T	p.Ala48Ser	p.A48S	ENST00000273854	NM_004439.5	48	Gcc/Tcc	1/18	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.192773665898881	2		601	910	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540391	187540391	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	30	336	0	ENST00000441802.2:c.7349C>T	p.Ser2450Leu	p.S2450L	ENST00000441802	NM_005245.3	2450	tCa/tTa	10/27	1	2	FACETS	0.687	0.553	0.84	0.687	0.553	0.84	SUBCLONAL	1	FALSE	1	0.192773665898881	2		336	453	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564633	86564633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1187087405	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	66	698	0	ENST00000274376.6:c.365C>T	p.Ser122Leu	p.S122L	ENST00000274376	NM_002890.2	122	tCg/tTg	1/25	1	2	FACETS	0.683	0.591	0.783	0.683	0.591	0.783	SUBCLONAL	1	FALSE	1	0.192773665898881	2		698	1003	SUCCESS
APC	324	MSKCC	GRCh37	5	112090652	112090653	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	18	165	0	ENST00000257430.4:c.65_66del	p.Asn22ThrfsTer8	p.N22Tfs*8	ENST00000257430	NM_000038.5	22	aAT/a	2/16	1	2	FACETS	0.682	0.513	0.88	0.682	0.513	0.88	SUBCLONAL	1	FALSE	1	0.192773665898881	2		165	274	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169985	32169985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	63	745	1	ENST00000375023.3:c.3623C>T	p.Pro1208Leu	p.P1208L	ENST00000375023	NM_004557.3	1208	cCa/cTa	21/30	0.192773665898881	2	FACETS	0.649	0.559	0.747	0.325	0.279	0.374	SUBCLONAL	1	FALSE	0	0.192773665898881	2		746	1007	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133748385	133748385	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048291-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	32	356	0	ENST00000318560.5:c.1046C>T	p.Ser349Leu	p.S349L	ENST00000318560	NM_005157.4	349	tCa/tTa	6/11	0.192773665898881	1	FACETS	0.593	0.48	0.72	0.593	0.48	0.72	SUBCLONAL	1	FALSE	0	0.192773665898881	1		356	506	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	97	301	0				ENST00000310581	NM_198253.2	-/1132			0.208844155443654	3	FACETS	0.843	0.757	0.934	0.843	0.757	0.934	CLONAL	2	TRUE	1	0.327245372575619	3		301	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0048322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	182	497	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.327245372575619	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.327245372575619	1		498	694	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123260409	123260409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	100	635	0	ENST00000358487.5:c.1492G>A	p.Ala498Thr	p.A498T	ENST00000358487	NM_000141.4	498	Gcg/Acg	11/18	1	2	FACETS	0.97	0.868	1	0.97	0.868	1	CLONAL	1	TRUE	1	0.327245372575619	2		635	630	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425329	49425329	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	73	768	0	ENST00000301067.7:c.13159del	p.Gln4387ArgfsTer16	p.Q4387Rfs*16	ENST00000301067	NM_003482.3	4387	Cag/ag	39/54	0.208844155443654	3	FACETS	0.753	0.659	0.856	0.377	0.329	0.428	SUBCLONAL	1	TRUE	1	0.327245372575619	3		768	689	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096243	178096243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	71	537	0	ENST00000397062.3:c.1088C>T	p.Ser363Phe	p.S363F	ENST00000397062	NM_006164.4	363	tCt/tTt	5/5	0.208844155443654	3	FACETS	0.918	0.802	1	0.459	0.401	0.522	CLONAL	1	TRUE	1	0.327245372575619	3		537	550	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971179	21971180	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCACT	novel	NA	P-0048322-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	75	487	0	ENST00000304494.5:c.174_178dup	p.Ala60GlufsTer88	p.A60Efs*88	ENST00000304494	NM_000077.4	60	gcg/gAGTGGcg	2/3	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.327245372575619	2		487	405	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0048325-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	33	495	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.299552583146753	4	FACETS	0.807	0.668	0.958	0.807	0.668	0.958	CLONAL	2	FALSE	2	0.412621912197994	4		495	140	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048325-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	32	301	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.879	1	1	0.967	1	CLONAL	2	FALSE	1	0.412621912197994	2		301	74	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577069	7577069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55819519	NA	P-0048325-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	8	968	1	ENST00000269305.4:c.869G>A	p.Arg290His	p.R290H	ENST00000269305	NM_001126112.2	290	cGc/cAc	8/11	1	2	FACETS	0.129	0.082	0.189	0.129	0.082	0.189	SUBCLONAL	1	FALSE	1	0.412621912197994	2		969	301	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419049	419049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048325-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	10	720	0	ENST00000399788.2:c.3298G>A	p.Glu1100Lys	p.E1100K	ENST00000399788	NM_001042603.1	1100	Gaa/Aaa	22/28	NA	2	FACETS	0.332	0.225	0.465			1	INDETERMINATE	1	FALSE	NA	0.412621912197994	2		720	146	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777942	27777942	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200796448	NA	P-0048325-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	93	667	0	ENST00000369163.2:c.91C>T	p.Pro31Ser	p.P31S	ENST00000369163	NM_003536.2	31	Ccg/Tcg	1/1	0.412621912197994	4	FACETS	0.845	0.757	0.937	0.845	0.757	0.937	CLONAL	2	FALSE	2	0.412621912197994	4		667	377	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941029	71941029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200057735	NA	P-0048325-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	10	975	4	ENST00000298229.2:c.905G>A	p.Arg302His	p.R302H	ENST00000298229	NM_001567.3	302	cGt/cAt	8/28	1	2	FACETS	0.28	0.19	0.393	0.28	0.19	0.393	SUBCLONAL	1	FALSE	1	0.412621912197994	2		979	173	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729904	39729904	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048325-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	26	795	0	ENST00000361337.2:c.1219G>C	p.Asp407His	p.D407H	ENST00000361337	NM_003286.2	407	Gat/Cat	13/21	0.124685104039161	0	FACETS	0.529	0.424	0.645			1	INDETERMINATE	1	FALSE	0	0.412621912197994	0		795	140	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468270	50468270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048325-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	12	466	1	ENST00000331340.3:c.1505G>A	p.Arg502Gln	p.R502Q	ENST00000331340	NM_006060.4	502	cGg/cAg	8/8	1	2	FACETS	0.373	0.263	0.507	0.373	0.263	0.507	SUBCLONAL	1	FALSE	1	0.412621912197994	2		467	156	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937282	76937286	+	frameshift_variant	Frame_Shift_Del	DEL	ATGAT	ATGAT	-	novel	NA	P-0048339-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	20	157	0	ENST00000373344.5:c.3462_3466del	p.Ser1155Ter	p.S1155*	ENST00000373344	NM_000489.3	1154	tcATCATct/tcct	9/35	1	1	FACETS	0.781	0.66	0.888	1	0.948	1	SUBCLONAL	2	TRUE	0	0.612772547603722	1		157	29	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0048417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	660	763	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.819846906095054	2	FACETS	0.963	0.943	0.982	0.963	0.943	0.982	CLONAL	2	TRUE	0	0.844438063966284	2		763	812	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100204	30100204	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	123	401	0	ENST00000331968.5:c.1416G>T	p.Leu472Phe	p.L472F	ENST00000331968	NM_002742.2	472	ttG/ttT	10/18	0.466450186253575	2	FACETS	0.521	0.473	0.572	0.261	0.236	0.286	INDETERMINATE	1	TRUE	0	0.844438063966284	2		401	559	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72834022	72834022	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	254	374	0	ENST00000268489.5:c.3871A>G	p.Thr1291Ala	p.T1291A	ENST00000268489	NM_006885.3	1291	Acc/Gcc	8/10	1	2	FACETS	0.918	0.865	0.972	0.918	0.865	0.972	CLONAL	1	TRUE	1	0.844438063966284	2		374	655	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411704	63411704	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048417-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	413	328	0	ENST00000330258.3:c.1463G>T	p.Gly488Val	p.G488V	ENST00000330258	NM_152424.3	488	gGg/gTg	2/2	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.844438063966284	1		328	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0048426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	272	696	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.433479538874951	1	FACETS	0.687	0.646	0.728	0.687	0.646	0.728	SUBCLONAL	1	TRUE	0	0.629985951394108	1		697	861	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0048426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	52	314	1	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.293	0.249	0.341	0.293	0.249	0.341	SUBCLONAL	1	TRUE	1	0.629985951394108	2		315	563	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141507	11141507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	91	610	1	ENST00000358026.2:c.3484G>A	p.Gly1162Ser	p.G1162S	ENST00000358026	NM_001128849.1	1162	Ggc/Agc	25/36	1	2	FACETS	0.319	0.283	0.358	0.319	0.283	0.358	SUBCLONAL	1	TRUE	1	0.629985951394108	2		611	905	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541484	29541484	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	79	195	0	ENST00000356175.3:c.1408G>T	p.Glu470Ter	p.E470*	ENST00000356175	NM_000267.3	470	Gaa/Taa	13/57	0.226864866282587	3	FACETS	0.797	0.714	0.881	0.797	0.714	0.881	INDETERMINATE	2	TRUE	1	0.629985951394108	3		195	207	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512049	148512049	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	91	349	0	ENST00000320356.2:c.1629A>G	p.Ile543Met	p.I543M	ENST00000320356	NM_004456.4	543	atA/atG	14/20	1	2	FACETS	0.475	0.422	0.531	0.475	0.422	0.531	SUBCLONAL	1	TRUE	1	0.629985951394108	2		349	608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0048437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	216	668	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.288485970561133	2	FACETS	1	0.992	1	0.745	0.698	0.794	INDETERMINATE	1	TRUE	0	0.495416558710227	2		669	585	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0048437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	69	598	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.436939385395877	3	FACETS	1	0.939	1	0.557	0.489	0.629	CLONAL	1	TRUE	1	0.495416558710227	3		598	312	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681124	37681124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	63	428	0	ENST00000447079.4:c.3293C>T	p.Ala1098Val	p.A1098V	ENST00000447079	NM_015083.1	1098	gCt/gTt	12/14	0.149026396320935	3	FACETS	0.603	0.522	0.691	0.201	0.174	0.231	INDETERMINATE	1	TRUE	0	0.495416558710227	3		428	526	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0048451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	24	582	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.628	0.493	0.783	0.628	0.493	0.783	SUBCLONAL	1	TRUE	1	0.27	2		582	283	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215617244	215617244	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	45	273	0	ENST00000260947.4:c.1604A>T	p.Asp535Val	p.D535V	ENST00000260947	NM_000465.2	535	gAt/gTt	7/11	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.27	2		273	297	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981108	55981108	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	36	383	0	ENST00000263923.4:c.591G>T	p.Met197Ile	p.M197I	ENST00000263923	NM_002253.2	197	atG/atT	5/30	1	2	FACETS	0.729	0.6	0.872	0.729	0.6	0.872	SUBCLONAL	1	TRUE	1	0.27	2		383	366	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837945	156837945	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	52	744	0	ENST00000524377.1:c.478C>T	p.Gln160Ter	p.Q160*	ENST00000524377	NM_002529.3	160	Cag/Tag	5/17	0.209229667807372	3	FACETS	0.635	0.539	0.739	0.317	0.269	0.37	SUBCLONAL	1	TRUE	1	0.27	3		744	689	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444756	49444756	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	44	790	1	ENST00000301067.7:c.2710G>T	p.Gly904Trp	p.G904W	ENST00000301067	NM_003482.3	904	Ggg/Tgg	10/54	1	2	FACETS	0.485	0.406	0.573	0.485	0.406	0.573	SUBCLONAL	1	TRUE	1	0.27	2		791	672	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681003	37681003	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	56	411	0	ENST00000447079.4:c.3172G>C	p.Glu1058Gln	p.E1058Q	ENST00000447079	NM_015083.1	1058	Gaa/Caa	12/14	1	2	FACETS	0.934	0.802	1	0.934	0.802	1	CLONAL	1	TRUE	1	0.27	2		411	444	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207060	1207078	+	frameshift_variant	Frame_Shift_Del	DEL	CTGATGGGGGACCTGCTGG	CTGATGGGGGACCTGCTGG	-	novel	NA	P-0048451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	61	695	0	ENST00000326873.7:c.148_166del	p.Leu50GlyfsTer8	p.L50Gfs*8	ENST00000326873	NM_000455.4	50	CTGATGGGGGACCTGCTGGgg/gg	1/10	0.270679905994298	1	FACETS	0.768	0.663	0.881	0.768	0.663	0.881	SUBCLONAL	1	TRUE	0	0.27	1		695	509	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520266	9520266	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0048451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	28	304	0	ENST00000353224.5:c.2005-2A>G		p.X669_splice	ENST00000353224	NM_177990.2	669			1	2	FACETS	0.656	0.525	0.805	0.656	0.525	0.805	SUBCLONAL	1	TRUE	1	0.27	2		304	316	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021497	31021497	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	52	495	0	ENST00000375687.4:c.1496G>T	p.Arg499Leu	p.R499L	ENST00000375687	NM_015338.5	499	cGt/cTt	12/13	1	2	FACETS	0.816	0.696	0.948	0.816	0.696	0.948	CLONAL	1	TRUE	1	0.27	2		495	472	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1918753	1918753	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	26	251	0	ENST00000382891.5:c.916G>T	p.Glu306Ter	p.E306*	ENST00000382891	NM_133335.3	306	Gag/Tag	4/22	1	2	FACETS	0.631	0.501	0.781	0.631	0.501	0.781	SUBCLONAL	1	TRUE	1	0.27	2		251	305	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127351	55127351	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	55	405	0	ENST00000257290.5:c.139C>A	p.Leu47Met	p.L47M	ENST00000257290	NM_006206.4	47	Ctg/Atg	3/23	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.27	2		405	396	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35860997	35860997	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	25	265	0	ENST00000303115.3:c.126C>A	p.Cys42Ter	p.C42*	ENST00000303115	NM_002185.3	42	tgC/tgA	2/8	1	2	FACETS	0.611	0.482	0.759	0.611	0.482	0.759	SUBCLONAL	1	TRUE	1	0.27	2		265	303	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509483	106509483	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200755385	NA	P-0048451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	60	494	0	ENST00000359195.3:c.1477G>T	p.Asp493Tyr	p.D493Y	ENST00000359195	NM_002649.2	493	Gac/Tac	2/11	1	2	FACETS	0.997	0.861	1	0.997	0.861	1	CLONAL	1	TRUE	1	0.27	2		494	446	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967645	90967645	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	32	225	0	ENST00000265433.3:c.1263G>T	p.Leu421Phe	p.L421F	ENST00000265433	NM_002485.4	421	ttG/ttT	10/16	1	2	FACETS	0.809	0.659	0.977	0.809	0.659	0.977	CLONAL	1	TRUE	1	0.27	2		225	293	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517968	8517968	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	55	333	0	ENST00000356435.5:c.1423C>A	p.Gln475Lys	p.Q475K	ENST00000356435		475	Caa/Aaa	10/35	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.27	2		333	299	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652398	48652398	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	79	809	0	ENST00000376670.3:c.1069C>A	p.Pro357Thr	p.P357T	ENST00000376670	NM_002049.3	357	Ccc/Acc	6/6	1	2	FACETS	0.888	0.781	1	0.888	0.781	1	CLONAL	1	TRUE	1	0.27	2		809	659	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0048452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	143	528	2	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	NA	2	FACETS	0.823	0.763	0.883			1	INDETERMINATE	2	TRUE	NA	0.553638590886398	2		530	314	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592108	67592108	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1419325070	NA	P-0048452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	52	249	2	ENST00000274335.5:c.1924C>T	p.Arg642Ter	p.R642*	ENST00000274335		642	Cga/Tga	14/15	0.528193538984391	2	FACETS	0.978	0.846	1	0.489	0.423	0.56	CLONAL	1	TRUE	0	0.553638590886398	2		251	192	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138729528	NA	P-0048452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	264	774	0	ENST00000269305.4:c.523C>G	p.Arg175Gly	p.R175G	ENST00000269305	NM_001126112.2	175	Cgc/Ggc	5/11	0.493887641156595	2	FACETS	0.875	0.829	0.921	0.875	0.829	0.921	CLONAL	2	TRUE	0	0.553638590886398	2		774	545	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41222995	41222995	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs80357653	NA	P-0048452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	299	680	0	ENST00000357654.3:c.4936del	p.Val1646SerfsTer12	p.V1646Sfs*12	ENST00000357654	NM_007294.3	1646	Gtc/tc	15/23	0.474641343249204	3	FACETS	0.874	0.834	0.913	0.874	0.834	0.913	CLONAL	3	TRUE	0	0.553638590886398	3		680	526	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339115	65339115	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	148	458	0	ENST00000342505.4:c.421A>G	p.Lys141Glu	p.K141E	ENST00000342505	NM_002227.2	141	Aaa/Gaa	5/25	0.433676373787217	4	FACETS	0.968	0.893	1	0.968	0.893	1	CLONAL	2	TRUE	2	0.553638590886398	4		458	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0048453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	59	497	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.9	0.775	1	0.9	0.775	1	CLONAL	1	TRUE	1	0.248351079948748	2		498	528	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692803	89692803	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554898074	NA	P-0048453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	79	236	0	ENST00000371953.3:c.287C>T	p.Pro96Leu	p.P96L	ENST00000371953	NM_000314.4	96	cCa/cTa	5/9	0.245195347362692	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.248351079948748	3		236	306	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720849	89720853	+	frameshift_variant	Frame_Shift_Del	DEL	AACCG	AACCG	-	novel	NA	P-0048453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	44	272	0	ENST00000371953.3:c.1001_1005del	p.Asn334IlefsTer7	p.N334Ifs*7	ENST00000371953	NM_000314.4	334	AACCGa/a	8/9	0.245195347362692	3	FACETS	1	0.896	1	0.544	0.457	0.64	CLONAL	1	TRUE	1	0.248351079948748	3		272	366	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984382	72984382	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	25	401	0	ENST00000268489.5:c.3202del	p.Leu1068Ter	p.L1068*	ENST00000268489	NM_006885.3	1068	Ctg/tg	3/10	1	2	FACETS	0.426	0.335	0.531	0.426	0.335	0.531	SUBCLONAL	1	TRUE	1	0.248351079948748	2		401	473	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991876	72991876	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	68	547	0	ENST00000268489.5:c.2169C>A	p.Tyr723Ter	p.Y723*	ENST00000268489	NM_006885.3	723	taC/taA	2/10	1	2	FACETS	0.954	0.831	1	0.954	0.831	1	CLONAL	1	TRUE	1	0.248351079948748	2		547	574	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106912	27106912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	97	553	0	ENST00000324856.7:c.6523G>A	p.Ala2175Thr	p.A2175T	ENST00000324856	NM_006015.4	2175	Gct/Act	20/20	0.586688475179281	4	FACETS	1	0.949	1	0.548	0.491	0.608	CLONAL	1	TRUE	2	0.627633371197045	4		553	459	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531747	46531748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCATA	novel	NA	P-0048454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	74	204	0	ENST00000262741.5:c.595_599dup	p.Glu200AspfsTer14	p.E200Dfs*14	ENST00000262741	NM_003629.3	200	gaa/gaTATGAa	5/10	0.586688475179281	4	FACETS	0.897	0.799	0.998	0.897	0.799	0.998	CLONAL	2	TRUE	2	0.627633371197045	4		204	214	SUCCESS
ATM	472	MSKCC	GRCh37	11	108213959	108213959	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	31	227	0	ENST00000278616.4:c.8279T>G	p.Leu2760Arg	p.L2760R	ENST00000278616	NM_000051.3	2760	cTc/cGc	57/63	0.586688475179281	4	FACETS	0.566	0.459	0.686	0.283	0.229	0.343	SUBCLONAL	1	TRUE	2	0.627633371197045	4		227	284	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467904	99467904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	71	289	0	ENST00000268035.6:c.2773C>T	p.Gln925Ter	p.Q925*	ENST00000268035	NM_000875.3	925	Cag/Tag	13/21	0.585557490586055	2	FACETS	0.808	0.728	0.888	0.808	0.728	0.888	CLONAL	2	TRUE	0	0.627633371197045	2		289	140	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508168	38508168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	12	370	0	ENST00000254066.5:c.476G>A	p.Arg159Lys	p.R159K	ENST00000254066	NM_000964.3	159	aGa/aAa	5/9	NA	2	FACETS	0.175	0.123	0.24			1	INDETERMINATE	1	TRUE	NA	0.627633371197045	2		370	218	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18963797	18963797	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	109	307	0	ENST00000262803.5:c.974C>T	p.Thr325Ile	p.T325I	ENST00000262803	NM_002911.3	325	aCt/aTt	7/24	0.576244746366476	3	FACETS	0.992	0.911	1	0.992	0.911	1	CLONAL	2	TRUE	1	0.627633371197045	3		307	230	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872377	45872377	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	224	685	0	ENST00000391945.4:c.134G>C	p.Gly45Ala	p.G45A	ENST00000391945	NM_000400.3	45	gGc/gCc	3/23	0.627633371197045	4	FACETS	0.766	0.716	0.818	0.766	0.716	0.818	SUBCLONAL	2	TRUE	2	0.627633371197045	4		685	758	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141637	202141637	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0048454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	35	316	0	ENST00000358485.4:c.925A>T	p.Lys309Ter	p.K309*	ENST00000358485	NM_001080125.1	309	Aaa/Taa	7/9	0.627633371197045	6	FACETS	0.546	0.447	0.657	0.136	0.111	0.165	SUBCLONAL	1	TRUE	2	0.627633371197045	6		316	461	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468385	89468385	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0048454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	21	203	0	ENST00000336596.2:c.1919T>G	p.Leu640Ter	p.L640*	ENST00000336596	NM_005233.5	640	tTa/tGa	11/17	0.627633371197045	3	FACETS	0.633	0.492	0.792	0.316	0.246	0.396	SUBCLONAL	1	TRUE	1	0.627633371197045	3		203	139	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961331	1961331	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	63	511	1	ENST00000382891.5:c.3119A>G	p.Glu1040Gly	p.E1040G	ENST00000382891	NM_133335.3	1040	gAg/gGg	17/22	0.599819107733821	4	FACETS	0.633	0.548	0.725			1	SUBCLONAL	1	TRUE	NA	0.627633371197045	4		512	516	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983511	90983511	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	23	136	0	ENST00000265433.3:c.592C>G	p.Pro198Ala	p.P198A	ENST00000265433	NM_002485.4	198	Cca/Gca	6/16	0.627633371197045	6	FACETS	0.624	0.487	0.781	0.156	0.121	0.196	SUBCLONAL	1	TRUE	2	0.627633371197045	6		136	265	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002728	37002728	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	139	574	0	ENST00000358127.4:c.521del	p.Ser174TrpfsTer104	p.S174Wfs*104	ENST00000358127	NM_001280556.1	174	tCg/tg	5/10	0.476474102326927	4	FACETS	0.779	0.714	0.845	0.779	0.714	0.845	SUBCLONAL	2	TRUE	2	0.627633371197045	4		574	463	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904878	101904890	+	frameshift_variant	Frame_Shift_Del	DEL	TTGATTACTTAAA	TTGATTACTTAAA	-	novel	NA	P-0048454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	117	320	0	ENST00000374994.4:c.866_878del	p.Phe289SerfsTer10	p.F289Sfs*10	ENST00000374994	NM_004612.2	289	tTTGATTACTTAAAc/tc	5/9	0.627633371197045	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	0	0.627633371197045	2		320	185	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197000	123197000	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	47	346	0	ENST00000218089.9:c.1766T>C	p.Leu589Ser	p.L589S	ENST00000218089	NM_001042749.1	589	tTg/tCg	19/35	0.627633371197045	3	FACETS	0.845	0.72	0.979	0.422	0.36	0.49	CLONAL	1	TRUE	1	0.627633371197045	3		346	233	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0048455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	254	461	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.56120989988318	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.56120989988318	2		461	443	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205723	128205723	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	146	636	0	ENST00000341105.2:c.152A>G	p.His51Arg	p.H51R	ENST00000341105	NM_032638.4	51	cAc/cGc	2/6	NA	2	FACETS	0.709	0.648	0.773			1	INDETERMINATE	1	TRUE	NA	0.56120989988318	2		636	734	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628032	187628032	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	138	459	1	ENST00000441802.2:c.2950A>G	p.Arg984Gly	p.R984G	ENST00000441802	NM_005245.3	984	Agg/Ggg	2/27	0.561279612944021	3	FACETS	1	0.939	1	0.518	0.473	0.565	CLONAL	1	TRUE	1	0.56120989988318	3		460	608	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	109	576	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.436003816895705	2		576	433	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0048456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	46	329	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.436003816895705	2		329	206	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632788	23632788	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1567213009	NA	P-0048456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	65	377	0	ENST00000261584.4:c.3008del	p.Asn1003ThrfsTer4	p.N1003Tfs*4	ENST00000261584	NM_024675.3	1003	aAc/ac	10/13	1	2	FACETS	0.991	0.866	1	0.991	0.866	1	CLONAL	1	TRUE	1	0.436003816895705	2		377	301	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117861213	117861213	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	36	362	0	ENST00000297338.2:c.1676G>T	p.Arg559Met	p.R559M	ENST00000297338	NM_006265.2	559	aGg/aTg	13/14	1	2	FACETS	0.42	0.346	0.504	0.42	0.346	0.504	SUBCLONAL	1	TRUE	1	0.436003816895705	2		362	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577508	7577508	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060501201	NA	P-0048457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	214	591	0	ENST00000269305.4:c.773A>G	p.Glu258Gly	p.E258G	ENST00000269305	NM_001126112.2	258	gAa/gGa	7/11	0.580322740183236	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	4	TRUE	0	0.597588599469479	4		591	282	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0048457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	83	309	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.598464121009095	4	FACETS	1	0.964	1	0.766	0.692	0.842	CLONAL	2	TRUE	1	0.597588599469479	4		309	193	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913399	NA	P-0048457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	95	281	0	ENST00000349496.5:c.100G>C	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Cga	3/15	0.582220238065614	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.597588599469479	2		281	152	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023169	33023186	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGCAAAACCCAGCCGC	GGTGCAAAACCCAGCCGC	T	novel	NA	P-0048457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	109	535	0	ENST00000300177.4:c.278_295delinsT	p.Trp93PhefsTer2	p.W93Ffs*2	ENST00000300177	NM_001191322.1	93	tGGTGCAAAACCCAGCCGCtt/tTtt	2/2	0.32610644329017	5	FACETS	1	0.966	1	0.751	0.684	0.821	INDETERMINATE	2	TRUE	2	0.597588599469479	5		535	307	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151896	108151896	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs876660621	NA	P-0048458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	15	181	0	ENST00000278616.4:c.3576+1G>A		p.X1192_splice	ENST00000278616	NM_000051.3	1192			1	2	FACETS	0.844	0.618	1	0.844	0.618	1	CLONAL	1	TRUE	1	0.15	2		181	237	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29195978	29195978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1198556632	NA	P-0048458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	46	529	0	ENST00000240100.2:c.620G>A	p.Ser207Asn	p.S207N	ENST00000240100	NM_001394.6	207	aGt/aAt	3/4	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.15	2		529	607	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0048459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	20	202	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	0.193435162009173	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		202	242	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0048461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	366	456	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	2	TRUE	NA	0.727747402537294	2		456	484	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	91	301	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.727747402537294	2		301	246	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174420	11174420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587777900	NA	P-0048461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	196	390	0	ENST00000361445.4:c.7255G>A	p.Glu2419Lys	p.E2419K	ENST00000361445	NM_004958.3	2419	Gaa/Aaa	53/58	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.727747402537294	2		390	536	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440385	52440386	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0048461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	165	306	0	ENST00000460680.1:c.666dup	p.Tyr223LeufsTer20	p.Y223Lfs*20	ENST00000460680	NM_004656.3	222	-/C	9/17	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.727747402537294	2		306	446	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781827	9781827	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	207	543	0	ENST00000377346.4:c.1964T>A	p.Met655Lys	p.M655K	ENST00000377346	NM_005026.3	655	aTg/aAg	16/24	1	2	FACETS	0.991	0.926	1	0.991	0.926	1	CLONAL	1	TRUE	1	0.727747402537294	2		543	574	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142554	119142554	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	109	203	0	ENST00000264033.4:c.553G>C	p.Asp185His	p.D185H	ENST00000264033	NM_005188.3	185	Gat/Cat	3/16	1	2	FACETS	0.863	0.784	0.946	0.863	0.784	0.946	CLONAL	1	TRUE	1	0.727747402537294	2		203	347	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431254	49431255	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	187	393	0	ENST00000301067.7:c.9884dup	p.Met3295IlefsTer6	p.M3295Ifs*6	ENST00000301067	NM_003482.3	3295	atg/atTg	34/54	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.727747402537294	2		393	508	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434909	49434909	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	224	496	0	ENST00000301067.7:c.6644C>A	p.Ser2215Ter	p.S2215*	ENST00000301067	NM_003482.3	2215	tCa/tAa	31/54	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.727747402537294	2		496	588	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216560	7216561	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	206	327	0	ENST00000380728.2:c.774dup	p.Ala259CysfsTer2	p.A259Cfs*2	ENST00000380728		258	-/T	9/11	0.613421973246641	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.727747402537294	1		327	325	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513677	41513684	+	frameshift_variant	Frame_Shift_Del	DEL	GTTCAATT	GTTCAATT	-	novel	NA	P-0048461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	178	347	0	ENST00000263253.7:c.582_589del	p.Ile196ArgfsTer23	p.I196Rfs*23	ENST00000263253	NM_001429.3	194	gGTTCAATT/g	2/31	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.727747402537294	2		347	473	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439898	52439898	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	211	334	0	ENST00000460680.1:c.814C>T	p.Gln272Ter	p.Q272*	ENST00000460680	NM_004656.3	272	Cag/Tag	10/17	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.727747402537294	2		334	492	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081644	143081644	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	103	220	0	ENST00000262992.4:c.1430G>A	p.Arg477Lys	p.R477K	ENST00000262992	NM_001101669.1	477	aGg/aAg	15/24	1	2	FACETS	0.804	0.727	0.885	0.804	0.727	0.885	CLONAL	1	TRUE	1	0.727747402537294	2		220	352	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997406	149997406	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	177	318	0	ENST00000253339.5:c.2873C>A	p.Thr958Lys	p.T958K	ENST00000253339		958	aCa/aAa	6/7	1	2	FACETS	0.965	0.897	1	0.965	0.897	1	CLONAL	1	TRUE	1	0.727747402537294	2		318	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781504	NA	P-0048462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	317	675	0	ENST00000269305.4:c.314G>T	p.Gly105Val	p.G105V	ENST00000269305	NM_001126112.2	105	gGc/gTc	4/11	0.521295095728017	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.521295095728017	2		675	562	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570043	212570059	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CTGTTATCTCTCTGACT	CTGTTATCTCTCTGACT	-	novel	NA	P-0048462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	27	282	0	ENST00000342788.4:c.1182_1198del	p.Val395PhefsTer13	p.V395Ffs*13	ENST00000342788	NM_005235.2	394	acAGTCAGAGAGATAACAGgt/acgt	10/28	0.505668497984876	2	FACETS	0.456	0.365	0.56	0.228	0.182	0.28	SUBCLONAL	1	TRUE	0	0.521295095728017	2		282	227	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439311	52439311	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs9848343	NA	P-0048462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	208	511	0	ENST00000460680.1:c.932-1G>A		p.X311_splice	ENST00000460680	NM_004656.3	311			0.514970252746761	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.521295095728017	2		511	390	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980568	1980568	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs950025435	NA	P-0048462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	162	660	0	ENST00000382891.5:c.4030G>A	p.Glu1344Lys	p.E1344K	ENST00000382891	NM_133335.3	1344	Gag/Aag	22/22	0.505611238550864	2	FACETS	0.861	0.802	0.921	0.861	0.802	0.921	CLONAL	2	TRUE	0	0.521295095728017	2		660	361	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519694	137519694	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	48	271	0	ENST00000367739.4:c.944C>G	p.Ser315Cys	p.S315C	ENST00000367739	NM_000416.2	315	tCc/tGc	7/7	0.521295095728017	3	FACETS	0.951	0.812	1	0.476	0.406	0.551	CLONAL	1	TRUE	1	0.521295095728017	3		271	244	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578410	7578410	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	340	809	0	ENST00000269305.4:c.520A>T	p.Arg174Trp	p.R174W	ENST00000269305	NM_001126112.2	174	Agg/Tgg	5/11	0.864448779286698	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.864448779286698	1		809	400	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476310	88476310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760692815	NA	P-0048463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	100	593	0	ENST00000360948.2:c.1822G>A	p.Gly608Ser	p.G608S	ENST00000360948	NM_001012338.2	608	Ggc/Agc	15/19	1	2	FACETS	0.371	0.331	0.412	0.371	0.331	0.412	SUBCLONAL	1	TRUE	1	0.864448779286698	2		593	624	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150039	202150039	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1368296717	NA	P-0048463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	224	464	0	ENST00000358485.4:c.1480C>T	p.Arg494Ter	p.R494*	ENST00000358485	NM_001080125.1	494	Cga/Tga	8/9	1	2	FACETS	0.96	0.902	1	0.96	0.902	1	CLONAL	1	TRUE	1	0.864448779286698	2		464	540	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62008712	62008712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371573435	NA	P-0048463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	43	823	0	ENST00000392795.3:c.104G>A	p.Arg35Gln	p.R35Q	ENST00000392795	NM_001039933.1	35	cGg/cAg	2/6	0.864448779286698	2	FACETS	0.139	0.116	0.165	0.07	0.058	0.083	SUBCLONAL	1	TRUE	0	0.864448779286698	2		823	715	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627723	187627723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	32	287	0	ENST00000441802.2:c.3259G>A	p.Glu1087Lys	p.E1087K	ENST00000441802	NM_005245.3	1087	Gag/Aag	2/27	1	2	FACETS	0.277	0.226	0.335	0.277	0.226	0.335	SUBCLONAL	1	TRUE	1	0.864448779286698	2		287	267	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609994	81609994	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750198847	NA	P-0048475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	34	559	1	ENST00000298171.2:c.1592G>A	p.Arg531Gln	p.R531Q	ENST00000298171	NM_000369.2	531	cGg/cAg	10/10	0.239920860004364	4	FACETS	0.95	0.802	1	0.95	0.802	1	INDETERMINATE	2	TRUE	2	0.647821835164852	4		560	91	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566521	41566521	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	39	459	0	ENST00000263253.7:c.4398G>T	p.Trp1466Cys	p.W1466C	ENST00000263253	NM_001429.3	1466	tgG/tgT	27/31	0.232018229634999	3	FACETS	1	0.953	1	0.681	0.579	0.789	INDETERMINATE	1	TRUE	1	0.647821835164852	3		459	117	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692770	89692777	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TTGCACAA	TTGCACAA	-	novel	NA	P-0048475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	35	415	0	ENST00000371953.3:c.255_262del	p.Ala86SerfsTer3	p.A86Sfs*3	ENST00000371953	NM_000314.4	85	gTTGCACAA/g	5/9	0.647821835164852	1	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	0	0.647821835164852	1		415	73	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548294	41548294	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	23	360	0	ENST00000263253.7:c.3082G>C	p.Asp1028His	p.D1028H	ENST00000263253	NM_001429.3	1028	Gac/Cac	16/31	0.232018229634999	3	FACETS	1	0.884	1	0.58	0.465	0.706	INDETERMINATE	1	TRUE	1	0.647821835164852	3		360	81	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37628031	37628031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs578052035	NA	P-0048475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	32	1102	0	ENST00000249071.6:c.229G>A	p.Val77Ile	p.V77I	ENST00000249071	NM_002872.4	77	Gtc/Atc	4/7	0.232018229634999	3	FACETS	0.86	0.708	1	0.43	0.354	0.514	INDETERMINATE	1	TRUE	1	0.647821835164852	3		1102	152	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514191	69514191	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	36	1088	1	ENST00000294312.3:c.490C>A	p.His164Asn	p.H164N	ENST00000294312	NM_005117.2	164	Cat/Aat	3/3	0.361924715021288	3	FACETS	1	0.948	1	0.675	0.569	0.786	INDETERMINATE	1	TRUE	1	0.647821835164852	3		1089	109	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431880	49431880	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	48	1273	0	ENST00000301067.7:c.9259del	p.Arg3087GlyfsTer32	p.R3087Gfs*32	ENST00000301067	NM_003482.3	3087	Cgg/gg	34/54	0.309305655261157	4	FACETS	1	0.957	1	0.671	0.576	0.772	INDETERMINATE	1	TRUE	2	0.647821835164852	4		1273	182	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724442	43724442	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	109	1199	0	ENST00000382044.4:c.3625G>C	p.Glu1209Gln	p.E1209Q	ENST00000382044	NM_001141980.1	1209	Gag/Cag	17/28	0.147801571271098	4	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	2	TRUE	2	0.647821835164852	4		1199	229	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019457	31019457	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	54	866	0	ENST00000375687.4:c.954G>C	p.Gln318His	p.Q318H	ENST00000375687	NM_015338.5	318	caG/caC	10/13	0.329815223976738	3	FACETS	1	0.967	1	0.694	0.605	0.787	INDETERMINATE	1	TRUE	1	0.647821835164852	3		866	159	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547942	41547942	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	42	663	0	ENST00000263253.7:c.2923G>T	p.Glu975Ter	p.E975*	ENST00000263253	NM_001429.3	975	Gaa/Taa	15/31	0.232018229634999	3	FACETS	0.923	0.8	1	0.923	0.8	1	INDETERMINATE	2	TRUE	1	0.647821835164852	3		663	93	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442050	52442050	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	73	878	0	ENST00000460680.1:c.299T>C	p.Leu100Pro	p.L100P	ENST00000460680	NM_004656.3	100	cTc/cCc	5/17	0.625364491799595	2	FACETS	0.751	0.677	0.826	0.751	0.677	0.826	SUBCLONAL	2	TRUE	0	0.647821835164852	2		878	150	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522571	187522571	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	38	361	0	ENST00000441802.2:c.11492C>G	p.Ser3831Cys	p.S3831C	ENST00000441802	NM_005245.3	3831	tCt/tGt	21/27	0.147801571271098	4	FACETS	1	0.86	1	1	0.86	1	INDETERMINATE	2	TRUE	2	0.647821835164852	4		361	96	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609994	81609994	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750198847	NA	P-0048475-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	49	559	1	ENST00000298171.2:c.1592G>A	p.Arg531Gln	p.R531Q	ENST00000298171	NM_000369.2	531	cGg/cAg	10/10	1	2	FACETS	0.815	0.697	0.941	1	0.969	1	CLONAL	2	FALSE	1	0.257015289178036	2		560	234	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556727	41556727	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0048475-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	22	529	0	ENST00000263253.7:c.3671+1G>A		p.X1224_splice	ENST00000263253	NM_001429.3	1224			1	2	FACETS	0.688	0.534	0.865	0.688	0.534	0.865	SUBCLONAL	1	FALSE	1	0.257015289178036	2		529	249	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566521	41566521	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048475-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	58	459	0	ENST00000263253.7:c.4398G>T	p.Trp1466Cys	p.W1466C	ENST00000263253	NM_001429.3	1466	tgG/tgT	27/31	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	FALSE	1	0.257015289178036	2		459	373	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285702	46285702	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0048475-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	20	459	0	ENST00000334344.6:c.5061+1G>A		p.X1687_splice	ENST00000334344	NM_152641.2	1687			0.257015289178036	3	FACETS	0.658	0.504	0.838			1	SUBCLONAL	1	FALSE	NA	0.257015289178036	3		459	267	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692770	89692777	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TTGCACAA	TTGCACAA	-	novel	NA	P-0048475-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	49	415	0	ENST00000371953.3:c.255_262del	p.Ala86SerfsTer3	p.A86Sfs*3	ENST00000371953	NM_000314.4	85	gTTGCACAA/g	5/9	0.149498180942358	0	FACETS	0.653	0.559	0.753			1	INDETERMINATE	2	FALSE	0	0.257015289178036	0		415	217	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0048477-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	57	715	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.836	0.717	0.967	0.836	0.717	0.967	CLONAL	1	TRUE	1	0.21	2		715	649	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808315	99808315	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	62	253	0	ENST00000280892.6:c.374A>C	p.Glu125Ala	p.E125A	ENST00000280892	NM_001130678.1	125	gAg/gCg	5/7	1	2	FACETS	0.901	0.785	1	0.901	0.785	1	CLONAL	1	TRUE	1	0.44812121294591	2		253	307	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64289191	64289191	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	103	348	0	ENST00000370651.3:c.359T>G	p.Ile120Ser	p.I120S	ENST00000370651	NM_003463.4	120	aTt/aGt	5/6	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.44812121294591	2		348	425	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696430	47696430	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	85	451	0	ENST00000347630.2:c.393G>C	p.Trp131Cys	p.W131C	ENST00000347630	NM_001007230.1	131	tgG/tgC	6/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.382250518580887	2		451	325	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1255456	1255456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374968697	NA	P-0048479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	16	582	1	ENST00000310581.5:c.3103G>A	p.Val1035Ile	p.V1035I	ENST00000310581	NM_198253.2	1035	Gtc/Atc	14/16	1	2	FACETS	0.28	0.206	0.368	0.28	0.206	0.368	SUBCLONAL	1	TRUE	1	0.382250518580887	2		583	299	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026813	71026813	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs769448730	NA	P-0048479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	40	202	0	ENST00000318789.4:c.1409A>G	p.Tyr470Cys	p.Y470C	ENST00000318789	NM_032682.5	470	tAt/tGt	16/21	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.382250518580887	2		202	170	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670253	134670253	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	31	463	0	ENST00000398015.3:c.164T>A	p.Ile55Asn	p.I55N	ENST00000398015	NM_004441.4	55	aTc/aAc	3/16	1	2	FACETS	0.708	0.576	0.856	0.708	0.576	0.856	SUBCLONAL	1	TRUE	1	0.382250518580887	2		463	229	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851873	134851873	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1434117279	NA	P-0048479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	88	510	0	ENST00000398015.3:c.1279A>G	p.Ile427Val	p.I427V	ENST00000398015	NM_004441.4	427	Atc/Gtc	5/16	1	2	FACETS	0.853	0.766	0.942	1	0.984	1	CLONAL	2	TRUE	1	0.382250518580887	2		510	270	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781041	135781041	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	52	550	0	ENST00000298552.3:c.1924T>G	p.Ser642Ala	p.S642A	ENST00000298552	NM_001162426.1	642	Tct/Gct	15/23	1	2	FACETS	0.701	0.599	0.813	0.701	0.599	0.813	SUBCLONAL	1	TRUE	1	0.382250518580887	2		550	388	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0048481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	138	347	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.175431026043597	3	FACETS	0.954	0.884	1	1	0.992	1	CLONAL	6	TRUE	0	0.175431026043597	3		347	299	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450301	50450301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770551610	NA	P-0048481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	83	551	0	ENST00000331340.3:c.485G>A	p.Arg162Gln	p.R162Q	ENST00000331340	NM_006060.4	162	cGg/cAg	5/8	0.157756617486161	3	FACETS	1	0.934	1	1	0.934	1	CLONAL	3	TRUE	0	0.175431026043597	3		551	321	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852392	63852392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1300866874	NA	P-0048481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	37	566	0	ENST00000279873.7:c.3170C>T	p.Ala1057Val	p.A1057V	ENST00000279873	NM_032199.2	1057	gCg/gTg	10/10	0.175431026043597	7	FACETS	1	0.937	1	0.266	0.219	0.319	CLONAL	1	TRUE	2	0.175431026043597	7		566	456	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114901077	114901077	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0048481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	132	300	0	ENST00000543371.1:c.685+2T>G		p.X229_splice	ENST00000543371	NM_001198531.1	229			0.175431026043597	7	FACETS	1	0.951	1	1	0.99	1	CLONAL	8	TRUE	2	0.175431026043597	7		300	262	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093410	30093410	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771285195	NA	P-0048481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	76	395	0	ENST00000331968.5:c.1853G>A	p.Arg618Gln	p.R618Q	ENST00000331968	NM_002742.2	618	cGa/cAa	13/18	0.175431026043597	5	FACETS	1	0.931	1	0.807	0.713	0.906	CLONAL	3	TRUE	1	0.175431026043597	5		395	339	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572509	41572509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1254380600	NA	P-0048481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	136	736	0	ENST00000263253.7:c.5038C>T	p.Arg1680Cys	p.R1680C	ENST00000263253	NM_001429.3	1680	Cgc/Tgc	30/31	0.175431026043597	5	FACETS	0.938	0.858	1	0.938	0.858	1	CLONAL	4	TRUE	1	0.175431026043597	5		736	522	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156720	20156720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	38	166	1	ENST00000379607.5:c.37C>T	p.Arg13Cys	p.R13C	ENST00000379607	NM_001412.3	13	Cgc/Tgc	2/7	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		167	224	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0048484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	429	660	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.297152073319873	3	FACETS	1	0.99	1	0.759	0.724	0.795	CLONAL	2	TRUE	0	0.34	3		660	1296	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325763	30325763	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777479817	NA	P-0048484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	38	200	0	ENST00000322652.5:c.1961G>A	p.Arg654Gln	p.R654Q	ENST00000322652	NM_015355.2	654	cGa/cAa	16/16	1	2	FACETS	0.968	0.806	1	0.968	0.806	1	CLONAL	1	TRUE	1	0.34	2		200	231	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798543	32798543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	125	473	0	ENST00000374899.4:c.1313G>A	p.Gly438Glu	p.G438E	ENST00000374899	NM_018833.2	438	gGa/gAa	8/12	0.297152073319873	3	FACETS	1	0.916	1			1	CLONAL	1	TRUE	NA	0.34	3		473	849	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085746	16085746	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	135	441	0	ENST00000281043.3:c.922C>A	p.Leu308Met	p.L308M	ENST00000281043	NM_005378.4	308	Ctg/Atg	3/3	0.245942387054452	2	FACETS	1	0.984	1	0.683	0.624	0.746	CLONAL	1	TRUE	0	0.34	2		441	581	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873653	151873653	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	39	341	0	ENST00000262189.6:c.8885G>C	p.Gly2962Ala	p.G2962A	ENST00000262189	NM_170606.2	2962	gGc/gCc	38/59	0.264447732972566	3	FACETS	0.464	0.383	0.553	0.155	0.127	0.185	SUBCLONAL	1	TRUE	0	0.34	3		341	579	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	143	301	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.966	0.889	1	0.966	0.889	1	CLONAL	1	TRUE	1	0.717014800805271	2		301	413	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579349	7579349	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1567555667	NA	P-0048485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	274	692	0	ENST00000269305.4:c.338T>G	p.Phe113Cys	p.F113C	ENST00000269305	NM_001126112.2	113	tTc/tGc	4/11	0.646998822127894	1	FACETS	0.971	0.924	1	0.971	0.924	1	CLONAL	1	TRUE	0	0.717014800805271	1		692	505	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456347	99456347	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	194	436	0	ENST00000268035.6:c.1664A>G	p.Asp555Gly	p.D555G	ENST00000268035	NM_000875.3	555	gAc/gGc	8/21	NA	2	FACETS	0.938	0.874	1			1	INDETERMINATE	1	TRUE	NA	0.717014800805271	2		436	577	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118365476	118365476	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0048485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	99	242	0	ENST00000534358.1:c.5357C>G	p.Ser1786Ter	p.S1786*	ENST00000534358	NM_005933.3	1786	tCa/tGa	18/36	1	2	FACETS	0.911	0.824	1	0.911	0.824	1	CLONAL	1	TRUE	1	0.717014800805271	2		242	303	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272952	11272952	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	144	300	0	ENST00000361445.4:c.3299T>C	p.Ile1100Thr	p.I1100T	ENST00000361445	NM_004958.3	1100	aTc/aCc	22/58	1	2	FACETS	0.847	0.779	0.918	0.847	0.779	0.918	CLONAL	1	TRUE	1	0.717014800805271	2		300	474	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692927	89692928	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0048485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	346	497	0	ENST00000371953.3:c.413_414del	p.Tyr138PhefsTer41	p.Y138Ffs*41	ENST00000371953	NM_000314.4	137	gcATat/gcat	5/9	0.717014800805271	2	FACETS	0.917	0.883	0.951	0.917	0.883	0.951	CLONAL	2	TRUE	0	0.717014800805271	2		497	526	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344113	118344113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	132	433	0	ENST00000534358.1:c.2239G>A	p.Glu747Lys	p.E747K	ENST00000534358	NM_005933.3	747	Gaa/Aaa	3/36	1	2	FACETS	0.704	0.642	0.768	0.704	0.642	0.768	SUBCLONAL	1	TRUE	1	0.717014800805271	2		433	523	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21643239	21643239	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	196	552	0	ENST00000421138.2:c.288G>T	p.Gln96His	p.Q96H	ENST00000421138		96	caG/caT	5/16	1	2	FACETS	0.883	0.822	0.946	0.883	0.822	0.946	CLONAL	1	TRUE	1	0.717014800805271	2		552	619	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723043	52723043	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	241	595	0	ENST00000322088.6:c.1228G>C	p.Glu410Gln	p.E410Q	ENST00000322088	NM_014225.5	410	Gag/Cag	10/15	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.717014800805271	2		595	663	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271234	153271234	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	58	203	0	ENST00000281708.4:c.544T>C	p.Ser182Pro	p.S182P	ENST00000281708	NM_033632.3	182	Tct/Cct	3/12	0.615861168935363	3	FACETS	0.771	0.668	0.882	0.386	0.334	0.441	SUBCLONAL	1	TRUE	1	0.717014800805271	3		203	285	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176450	123176451	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	TT	novel	NA	P-0048485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	88	250	1	ENST00000218089.9:c.417_418delinsTT	p.Met139_Gln140delinsIleTer	p.M139_Q140delinsI*	ENST00000218089	NM_001042749.1	139	atGCag/atTTag	7/35	0.717014800805271	1	FACETS	0.966	0.883	1	0.966	0.883	1	CLONAL	1	TRUE	0	0.717014800805271	1		251	163	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806095	1806099	+	missense_variant	Missense_Mutation	ONP	GTGTA	GTGTA	CAGTG	novel	NA	P-0048485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	297	822	1	ENST00000260795.2:c.1114_1118delinsCAGTG	p.Val372_Tyr373delinsGlnCys	p.V372_Y373delinsQC	ENST00000260795		372	GTGTAt/CAGTGt	8/17	1	2	FACETS	0.99	0.935	1	0.99	0.935	1	CLONAL	1	TRUE	1	0.717014800805271	2		823	837	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0048489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	112	302	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.234397474644271	1	FACETS	0.775	0.704	0.848	0.775	0.704	0.848	INDETERMINATE	1	TRUE	0	0.565116243611347	1		302	367	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352697	NA	P-0048489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	21	543	0	ENST00000269305.4:c.587G>A	p.Arg196Gln	p.R196Q	ENST00000269305	NM_001126112.2	196	cGa/cAa	6/11	0.565116243611347	1	FACETS	0.064	0.049	0.082	0.064	0.049	0.082	SUBCLONAL	1	TRUE	0	0.565116243611347	1		543	834	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665358	176665358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	166	272	0	ENST00000439151.2:c.4042G>A	p.Glu1348Lys	p.E1348K	ENST00000439151	NM_022455.4	1348	Gag/Aag	7/23	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.565116243611347	2		272	585	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0048490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	28	158	0	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	0.68721292102974	2	FACETS	0.134	0.107	0.166			1	SUBCLONAL	1	TRUE	NA	0.909990889877209	2		158	458	SUCCESS
AR	367	MSKCC	GRCh37	X	66943552	66943552	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137852578	NA	P-0048490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	140	173	0	ENST00000374690.3:c.2632A>G	p.Thr878Ala	p.T878A	ENST00000374690	NM_000044.3	878	Act/Gct	8/8	0.68721292102974	2	FACETS	0.631	0.578	0.685			1	SUBCLONAL	1	TRUE	NA	0.909990889877209	2		173	488	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795103	242795104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768249210	NA	P-0048490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	428	1006	0	ENST00000334409.5:c.105dup	p.Thr36HisfsTer70	p.T36Hfs*70	ENST00000334409	NM_005018.2	35	-/C	2/5	1	2	FACETS	0.628	0.597	0.659	0.628	0.597	0.659	SUBCLONAL	1	TRUE	1	0.909990889877209	2		1006	1499	SUCCESS
AR	367	MSKCC	GRCh37	X	66931504	66931504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1340026226	NA	P-0048490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	85	303	0	ENST00000374690.3:c.2146G>A	p.Val716Met	p.V716M	ENST00000374690	NM_000044.3	716	Gtg/Atg	4/8	0.68721292102974	2	FACETS	0.268	0.237	0.302			1	SUBCLONAL	1	TRUE	NA	0.909990889877209	2		303	697	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0048492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	22	327	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	4	FACETS	0.794	0.615	1	0.397	0.307	0.501	INDETERMINATE	1	FALSE	2	0.203273675918244	4		327	328	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575209	48575209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767326	NA	P-0048492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	16	213	0	ENST00000342988.3:c.403C>T	p.Arg135Ter	p.R135*	ENST00000342988	NM_005359.5	135	Cga/Tga	3/12	1	2	FACETS	0.725	0.537	0.949	0.725	0.537	0.949	CLONAL	1	FALSE	1	0.203273675918244	2		213	217	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39251221	39251221	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	25	413	0	ENST00000402219.2:c.1132A>T	p.Thr378Ser	p.T378S	ENST00000402219	NM_005633.3	378	Aca/Tca	9/23	1	2	FACETS	0.612	0.482	0.762	0.612	0.482	0.762	SUBCLONAL	1	FALSE	1	0.203273675918244	2		413	402	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919601	96919601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144326855	NA	P-0048492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	39	679	1	ENST00000258439.3:c.662C>T	p.Pro221Leu	p.P221L	ENST00000258439	NM_001193304.2	221	cCg/cTg	4/4	1	2	FACETS	0.601	0.497	0.718	0.601	0.497	0.718	SUBCLONAL	1	FALSE	1	0.203273675918244	2		680	638	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482863	67482874	+	frameshift_variant,stop_lost	Frame_Shift_Del	DEL	AGTGTGTCTTAG	AGTGTGTCTTAG	TA	novel	NA	P-0048492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	42	486	1	ENST00000327367.4:c.1267_1278delinsTA	p.Ser423Ter	p.S423*	ENST00000327367	NM_005902.3	423	AGTGTGTCTTAG/TA	9/9	1	2	FACETS	0.688	0.573	0.815	0.688	0.573	0.815	SUBCLONAL	1	FALSE	1	0.203273675918244	2		487	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519985	NA	P-0048493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	250	864	0	ENST00000269305.4:c.857A>G	p.Glu286Gly	p.E286G	ENST00000269305	NM_001126112.2	286	gAa/gGa	8/11	0.160705091876656	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.205065596590913	2		864	1060	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0048493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	151	398	1	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	0.205065596590913	5	FACETS	1	0.937	1	1	0.937	1	CLONAL	3	TRUE	2	0.205065596590913	5		399	626	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163298091	163298091	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	71	358	0	ENST00000271452.3:c.272A>T	p.His91Leu	p.H91L	ENST00000271452	NM_145697.2	91	cAt/cTt	4/14	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.205065596590913	2		358	511	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374861	45374861	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	80	375	0	ENST00000262160.6:c.982A>C	p.Thr328Pro	p.T328P	ENST00000262160	NM_005901.5	328	Aca/Cca	8/11	0.0801845679253184	3	FACETS	0.771	0.68	0.868	0.771	0.68	0.868	INDETERMINATE	2	TRUE	1	0.205065596590913	3		375	558	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961559	54961559	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	38	332	0	ENST00000312783.6:c.73G>T	p.Val25Phe	p.V25F	ENST00000312783	NM_198436.1	25	Gtt/Ttt	4/10	1	2	FACETS	0.795	0.657	0.949	0.795	0.657	0.949	CLONAL	1	TRUE	1	0.205065596590913	2		332	466	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637728	52637730	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	TCA	TCA	-	novel	NA	P-0048493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	58	289	0	ENST00000394830.3:c.2586_2588del	p.Tyr862_Glu863delinsTer	p.Y862_E863delins*	ENST00000394830	NM_018313.4	862	taTGAa/taa	18/30	0.205065596590913	2	FACETS	1	0.967	1	0.735	0.634	0.844	CLONAL	1	TRUE	0	0.205065596590913	2		289	385	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168962	32168963	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0048493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	107	1038	1	ENST00000375023.3:c.4070_4071delinsAA	p.Pro1357Gln	p.P1357Q	ENST00000375023	NM_004557.3	1357	cCC/cAA	22/30	1	2	FACETS	0.948	0.848	1	0.948	0.848	1	CLONAL	1	TRUE	1	0.205065596590913	2		1039	1101	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962343	2962343	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	116	828	0	ENST00000396946.4:c.2194A>T	p.Thr732Ser	p.T732S	ENST00000396946	NM_032415.4	732	Acc/Tcc	17/25	0.0801845679253184	3	FACETS	1	0.976	1	0.644	0.58	0.713	INDETERMINATE	1	TRUE	1	0.205065596590913	3		828	968	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179149	123179149	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	38	201	0	ENST00000218089.9:c.598G>T	p.Val200Phe	p.V200F	ENST00000218089	NM_001042749.1	200	Gtc/Ttc	8/35	1	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.205065596590913	1		201	224	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058654	47058654	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	64	546	0	ENST00000409792.3:c.7624G>T	p.Glu2542Ter	p.E2542*	ENST00000409792	NM_014159.6	2542	Gag/Tag	21/21	0.338193151505375	1	FACETS	0.656	0.571	0.748	0.656	0.571	0.748	SUBCLONAL	1	FALSE	0	0.404265684043589	1		546	385	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134425	41134425	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	87	485	0	ENST00000379561.5:c.1203G>T	p.Gln401His	p.Q401H	ENST00000379561	NM_002015.3	401	caG/caT	2/3	1	2	FACETS	0.651	0.577	0.731	0.651	0.577	0.731	SUBCLONAL	1	FALSE	1	0.404265684043589	2		485	661	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183803	10183804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	169	976	0	ENST00000256474.2:c.272_273insA	p.Phe91LeufsTer41	p.F91Lfs*41	ENST00000256474	NM_000551.3	91	ttc/ttAc	1/3	0.338193151505375	1	FACETS	0.777	0.714	0.841	0.777	0.714	0.841	SUBCLONAL	1	FALSE	0	0.404265684043589	1		976	859	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0048497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	260	302	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.584371539328319	4	FACETS	0.926	0.89	0.96	0.926	0.89	0.96	CLONAL	4	TRUE	0	0.66383781897674	4		302	352	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0048497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	570	523	2	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.631135610669156	2	FACETS	0.924	0.895	0.953	0.924	0.895	0.953	CLONAL	2	TRUE	0	0.66383781897674	2		525	929	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280332	1280332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194223999	NA	P-0048497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1501	428	995	33	ENST00000310581.5:c.1891C>T	p.Arg631Trp	p.R631W	ENST00000310581	NM_198253.2	631	Cgg/Tgg	4/16	0.64273947858946	3	FACETS	0.89	0.846	0.936	0.445	0.423	0.468	CLONAL	1	TRUE	1	0.66383781897674	3		1028	1929	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068927	30068927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	113	477	9	ENST00000331968.5:c.2002G>A	p.Glu668Lys	p.E668K	ENST00000331968	NM_002742.2	668	Gaa/Aaa	14/18	NA	2	FACETS	1	0.919	1			1	INDETERMINATE	1	TRUE	NA	0.66383781897674	2		486	337	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610153	10610153	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	56	785	0	ENST00000171111.5:c.557G>C	p.Gly186Ala	p.G186A	ENST00000171111	NM_203500.1	186	gGc/gCc	2/6	0.648456723935423	1	FACETS	0.136	0.116	0.159	0.136	0.116	0.159	SUBCLONAL	1	TRUE	0	0.66383781897674	1		785	826	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928491	69928491	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1410219254	NA	P-0048497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	358	706	6	ENST00000352241.4:c.311C>G	p.Thr104Ser	p.T104S	ENST00000352241	NM_198159.2	104	aCc/aGc	2/10	0.60156012732811	2	FACETS	0.934	0.886	0.983	0.467	0.443	0.492	CLONAL	1	TRUE	0	0.66383781897674	2		712	1155	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539947	187539947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	102	306	3	ENST00000441802.2:c.7793C>T	p.Ala2598Val	p.A2598V	ENST00000441802	NM_005245.3	2598	gCa/gTa	10/27	0.619650275678074	2	FACETS	0.819	0.739	0.903	0.41	0.369	0.452	CLONAL	1	TRUE	0	0.66383781897674	2		309	375	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266512	198266512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	81	206	0	ENST00000335508.6:c.2324G>A	p.Arg775Gln	p.R775Q	ENST00000335508	NM_012433.2	775	cGa/cAa	16/25	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		206	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0048500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	160	619	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	NA	2	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.365111507184518	2		619	741	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644406	18644406	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	24	177	0	ENST00000266497.5:c.2584G>T	p.Gly862Cys	p.G862C	ENST00000266497		862	Ggc/Tgc	18/31	0.231650470496196	1	FACETS	0.425	0.334	0.529	0.425	0.334	0.529	SUBCLONAL	1	TRUE	0	0.365111507184518	1		177	253	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46597559	46597560	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0048500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	71	285	0	ENST00000262741.5:c.65dup	p.Tyr22Ter	p.Y22*	ENST00000262741	NM_003629.3	22	tat/taAt	1/10	1	2	FACETS	0.638	0.557	0.725	0.638	0.557	0.725	SUBCLONAL	1	TRUE	1	0.365111507184518	2		285	610	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845413	42845455	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACCCCGCAGGCTGAGGATGACAAACAGGAGGCCAGTGGGGTG	GACCCCGCAGGCTGAGGATGACAAACAGGAGGCCAGTGGGGTG	-	novel	NA	P-0048500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	106	527	0	ENST00000398585.3:c.839-32_849del		p.X280_splice	ENST00000398585	NM_001135099.1	280		9/14	1	2	FACETS	0.813	0.729	0.902	0.813	0.729	0.902	CLONAL	1	TRUE	1	0.365111507184518	2		527	714	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0048501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	63	336	0	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	1	2	FACETS	0.791	0.688	0.903	0.791	0.688	0.903	CLONAL	1	TRUE	1	0.426815000201929	2		336	373	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652290	48652290	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs782391440	NA	P-0048501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	157	381	0	ENST00000376670.3:c.961C>G	p.Leu321Val	p.L321V	ENST00000376670	NM_002049.3	321	Ctg/Gtg	6/6	0.311979458435705	2	FACETS	0.754	0.696	0.813			1	SUBCLONAL	2	TRUE	NA	0.426815000201929	2		381	488	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830863	156830863	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866270701	NA	P-0048501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	97	618	0	ENST00000524377.1:c.137C>T	p.Ser46Leu	p.S46L	ENST00000524377	NM_002529.3	46	tCg/tTg	1/17	0.292444055301308	4	FACETS	0.836	0.745	0.933	0.418	0.372	0.467	CLONAL	1	TRUE	2	0.426815000201929	4		618	776	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748192	41748192	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	191	571	0	ENST00000226382.2:c.577G>T	p.Asp193Tyr	p.D193Y	ENST00000226382	NM_003924.3	193	Gac/Tac	3/3	0.267945870650331	4	FACETS	0.837	0.776	0.9	0.837	0.776	0.9	CLONAL	2	TRUE	2	0.426815000201929	4		571	763	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938769	76938769	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048501-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	67	226	0	ENST00000373344.5:c.1979A>G	p.Lys660Arg	p.K660R	ENST00000373344	NM_000489.3	660	aAg/aGg	9/35	0.426815000201929	2	FACETS	0.701	0.611	0.798			1	SUBCLONAL	1	TRUE	NA	0.426815000201929	2		226	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0048502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	560	487	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.744657407139874	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.744657407139874	2		487	715	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415537	152415537	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519714	NA	P-0048502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	206	416	1	ENST00000206249.3:c.1387T>C	p.Ser463Pro	p.S463P	ENST00000206249	NM_000125.3	463	Tcc/Ccc	7/8	0.744657407139874	1	FACETS	0.647	0.605	0.689	0.647	0.605	0.689	SUBCLONAL	1	TRUE	0	0.744657407139874	1		417	537	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627721	187627721	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	115	257	0	ENST00000441802.2:c.3261G>C	p.Glu1087Asp	p.E1087D	ENST00000441802	NM_005245.3	1087	gaG/gaC	2/27	0.55785732884241	3	FACETS	1	0.954	1	0.541	0.491	0.592	CLONAL	1	TRUE	1	0.744657407139874	3		257	392	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115952	8115953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0048502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	185	397	0	ENST00000346208.3:c.1300dup	p.His434ProfsTer73	p.H434Pfs*73	ENST00000346208		433	cac/caCc	6/6	0.744657407139874	3	FACETS	0.932	0.862	1	0.466	0.431	0.502	CLONAL	1	TRUE	1	0.744657407139874	3		397	732	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163313655	163313655	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	40	100	0	ENST00000271452.3:c.802G>T	p.Ala268Ser	p.A268S	ENST00000271452	NM_145697.2	268	Gcc/Tcc	10/14	0.63152678185627	4	FACETS	0.756	0.632	0.891			1	SUBCLONAL	1	TRUE	NA	0.744657407139874	4		100	248	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024574	14024574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143479220	NA	P-0048502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	112	218	0	ENST00000311895.7:c.800G>A	p.Arg267His	p.R267H	ENST00000311895	NM_005236.2	267	cGc/cAc	5/11	0.55785732884241	3	FACETS	1	0.965	1	0.565	0.514	0.619	CLONAL	1	TRUE	1	0.744657407139874	3		218	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0048504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	23	489	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.506444286017381	1	FACETS	0.189	0.147	0.238	0.189	0.147	0.238	SUBCLONAL	1	TRUE	0	0.506444286017381	1		489	359	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0048504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	51	192	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	0.506444286017381	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.506444286017381	1		192	124	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578537	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs879254214	NA	P-0048504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	279	743	0	ENST00000269305.4:c.393_395del	p.Asn131del	p.N131del	ENST00000269305	NM_001126112.2	131	aaCAAg/aag	5/11	0.506444286017381	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.506444286017381	1		743	619	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519390	176519390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs550870047	NA	P-0048504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	168	706	1	ENST00000292408.4:c.796G>A	p.Asp266Asn	p.D266N	ENST00000292408	NM_213647.1	266	Gac/Aac	7/18	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.506444286017381	2		707	559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0048505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	67	426	0	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.1499416831392	2		426	650	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62305429	62305429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373849709	NA	P-0048505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	107	560	1	ENST00000360203.5:c.902C>T	p.Ala301Val	p.A301V	ENST00000360203	NM_001283009.1	301	gCg/gTg	10/35	0.1499416831392	2	FACETS	0.806	0.722	0.896	0.806	0.722	0.896	CLONAL	2	TRUE	0	0.1499416831392	2		561	885	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953592	38953592	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	36	205	0	ENST00000357387.3:c.2761A>C	p.Lys921Gln	p.K921Q	ENST00000357387	NM_152756.3	921	Aaa/Caa	28/38	0.1499416831392	2	FACETS	1	0.884	1	0.551	0.453	0.661	CLONAL	1	TRUE	0	0.1499416831392	2		205	436	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0048506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	100	327	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.22807944305014	5	FACETS	1	0.95	1	1	0.95	1	CLONAL	3	TRUE	2	0.22807944305014	5		327	361	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0048506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	72	369	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.986	0.869	1	1	0.982	1	CLONAL	2	TRUE	1	0.22807944305014	2		370	320	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042713	42042726	+	frameshift_variant	Frame_Shift_Del	DEL	AAGATGATGAAGAT	AAGATGATGAAGAT	-	novel	NA	P-0048507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	72	336	0	ENST00000219905.7:c.6908_6921del	p.Glu2303GlyfsTer2	p.E2303Gfs*2	ENST00000219905	NM_001164273.1	2303	gAAGATGATGAAGAT/g	17/24	0.49697294118443	1	FACETS	0.723	0.638	0.814	0.723	0.638	0.814	SUBCLONAL	1	TRUE	0	0.49697294118443	1		336	301	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251763	212251763	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1355545264	NA	P-0048507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	24	257	1	ENST00000342788.4:c.3296C>A	p.Ala1099Asp	p.A1099D	ENST00000342788	NM_005235.2	1099	gCt/gAt	27/28	1	2	FACETS	0.3	0.235	0.375	0.3	0.235	0.375	SUBCLONAL	1	TRUE	1	0.49697294118443	2		258	322	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207077	1207077	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs121913319	NA	P-0048509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	146	647	0	ENST00000326873.7:c.169del	p.Glu57LysfsTer7	p.E57Kfs*7	ENST00000326873	NM_000455.4	55	ctG/ct	1/10	0.308927730260538	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.28	1		647	784	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0048512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	55	347	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.0966665196830176	4	FACETS	1	0.948	1	0.619	0.531	0.715	INDETERMINATE	1	TRUE	2	0.27	4		347	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0048512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	94	487	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.3	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.27	1		487	582	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729984	41729984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	111	499	1	ENST00000242208.4:c.545C>T	p.Pro182Leu	p.P182L	ENST00000242208	NM_002192.2	182	cCg/cTg	3/3	1	2	FACETS	0.984	0.884	1	0.984	0.884	1	CLONAL	1	TRUE	1	0.27	2		500	836	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965472	68965472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200682883	NA	P-0048512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	70	707	1	ENST00000288368.4:c.1084C>T	p.Arg362Trp	p.R362W	ENST00000288368	NM_024870.2	362	Cgg/Tgg	9/40	1	2	FACETS	0.858	0.749	0.977	0.858	0.749	0.977	CLONAL	1	TRUE	1	0.27	2		708	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0048513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	454	696	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.447449431660738	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.447449431660738	1		697	1422	SUCCESS
APC	324	MSKCC	GRCh37	5	112175687	112175687	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	187	215	0	ENST00000257430.4:c.4396G>T	p.Gly1466Ter	p.G1466*	ENST00000257430	NM_000038.5	1466	Gga/Tga	16/16	0.447449431660738	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.447449431660738	2		215	398	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989345	7989345	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745541957	NA	P-0048513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	427	750	0	ENST00000319144.4:c.341G>A	p.Arg114Gln	p.R114Q	ENST00000319144	NM_001139.2	114	cGg/cAg	2/15	0.447449431660738	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.447449431660738	1		750	1382	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665777	29665777	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	10	153	0	ENST00000356175.3:c.6812A>G	p.Glu2271Gly	p.E2271G	ENST00000356175	NM_000267.3	2271	gAa/gGa	45/57	0.268029156949114	1	FACETS	0.265	0.18	0.371	0.265	0.18	0.371	INDETERMINATE	1	TRUE	0	0.447449431660738	1		153	131	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860449	151860449	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1485613651	NA	P-0048513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	375	432	1	ENST00000262189.6:c.10213C>T	p.Arg3405Ter	p.R3405*	ENST00000262189	NM_170606.2	3405	Cga/Tga	43/59	0.447449431660738	2	FACETS	0.951	0.907	0.996	0.951	0.907	0.996	CLONAL	2	TRUE	0	0.447449431660738	2		433	881	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21969825	21970847	+	intron_variant	Intron	DEL	GGGCCGAGTAAAGAAGAACTTCGCGTCTTTAACTTCGAAGGTGATTTTGCGTTCTGTATTTACAGCATCTCCAAGCAGAGGGCTTAGAGCTAACTCTTCACCCTGTCCTCCCCAGCTCCCCTATGGCCCAAGGAGCCCAATGCCCCCGTTCTGGGCCAAAATAAGATGGATTTCATAATCTTCAAGGTCATGTTTTACCTTAAATATTCGTGTTAATTCCCGTGTACTGTTTCATATATCTATTTTGTTTCAAAAAAAAATGTTCCTCCCCCCAGAAACAATTGAGTAATGTTGGCAGTTTCAGCAGACAGCTGTGGGAGTAGGGAACTGGGGCCATGGAATGGGGGCGGAGGGAGGATGCTTTGAGATCACAAAAAGGAAAGGCAAGGGCAAGGAGGACCATAATTCTACCTTCATCGCTCAGCGATCTCTTGCACAAGTTTAAGAGGGAAAGGAGCCAACTCCGGTGCACAGACTGCCAGGGTCAGCGAAGTCTTGGTCCTGATGTCCCCAGAACCCCCTGGGGCAGCTCTGGAAAACTCTACCGCATAAAGCGGAGGGTCAGATTAGCTGAGGAGGGTCAGATTAGTTGAGTTGTGCAGAAGAGCCGAGATCGAGAGATCTCCAGATGATGCCACGCACAATTGGGTTTGGAAATCCTGAGGTTGGTCCAGCCAGCTTGGTATGCAAATGAGGAAACAGACCTGGTAAGTGGATGCAACTGGCCCTAGTTTGGAGGAAGAGGGGGCACTAGACCTCTAGCCTCTTGAGTCTTCATTGCTCCGCAGTCTAGGCCTTGAACTAGCAGAGGGTAGGTGTTTGGGTGGTGGTATGCTTTGGGAAGTATAATGTACAAAATGGGCTTTCACGTGCGCAAGTCCATTTCGGGATTATTTCCCATTTGCCGCCCTGGCGGGGCAGGGCGATAGGGAGACTCAGGCCGTCCCACCGATTGGCGCGTGAGCTGAGGCAAGACCGGAGACTGGTCTCCCGGGCTGAACTTTCTGTGCTGGAAAATGAATG	GGGCCGAGTAAAGAAGAACTTCGCGTCTTTAACTTCGAAGGTGATTTTGCGTTCTGTATTTACAGCATCTCCAAGCAGAGGGCTTAGAGCTAACTCTTCACCCTGTCCTCCCCAGCTCCCCTATGGCCCAAGGAGCCCAATGCCCCCGTTCTGGGCCAAAATAAGATGGATTTCATAATCTTCAAGGTCATGTTTTACCTTAAATATTCGTGTTAATTCCCGTGTACTGTTTCATATATCTATTTTGTTTCAAAAAAAAATGTTCCTCCCCCCAGAAACAATTGAGTAATGTTGGCAGTTTCAGCAGACAGCTGTGGGAGTAGGGAACTGGGGCCATGGAATGGGGGCGGAGGGAGGATGCTTTGAGATCACAAAAAGGAAAGGCAAGGGCAAGGAGGACCATAATTCTACCTTCATCGCTCAGCGATCTCTTGCACAAGTTTAAGAGGGAAAGGAGCCAACTCCGGTGCACAGACTGCCAGGGTCAGCGAAGTCTTGGTCCTGATGTCCCCAGAACCCCCTGGGGCAGCTCTGGAAAACTCTACCGCATAAAGCGGAGGGTCAGATTAGCTGAGGAGGGTCAGATTAGTTGAGTTGTGCAGAAGAGCCGAGATCGAGAGATCTCCAGATGATGCCACGCACAATTGGGTTTGGAAATCCTGAGGTTGGTCCAGCCAGCTTGGTATGCAAATGAGGAAACAGACCTGGTAAGTGGATGCAACTGGCCCTAGTTTGGAGGAAGAGGGGGCACTAGACCTCTAGCCTCTTGAGTCTTCATTGCTCCGCAGTCTAGGCCTTGAACTAGCAGAGGGTAGGTGTTTGGGTGGTGGTATGCTTTGGGAAGTATAATGTACAAAATGGGCTTTCACGTGCGCAAGTCCATTTCGGGATTATTTCCCATTTGCCGCCCTGGCGGGGCAGGGCGATAGGGAGACTCAGGCCGTCCCACCGATTGGCGCGTGAGCTGAGGCAAGACCGGAGACTGGTCTCCCGGGCTGAACTTTCTGTGCTGGAAAATGAATG	-	novel	NA	P-0048513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	240	0	0	ENST00000304494.5:c.457+55_457+1077del		p.*153*	ENST00000304494	NM_000077.4	-/156			0.447449431660738	1	FACETS	0.668	0.622	0.715	0.668	0.622	0.715	SUBCLONAL	1	TRUE	0	0.447449431660738	1		0	1247	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0048514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	54	327	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.447702427499498	2		327	216	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107084	27107095	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGGCTGCCC	GGCGGGCTGCCC	A	novel	NA	P-0048514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	66	462	0	ENST00000324856.7:c.6695_6706delinsA	p.Arg2232GlnfsTer42	p.R2232Qfs*42	ENST00000324856	NM_006015.4	2232	cGGCGGGCTGCCCgc/cAgc	20/20	1	2	FACETS	0.942	0.824	1	0.942	0.824	1	CLONAL	1	TRUE	1	0.447702427499498	2		462	313	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0048516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	88	290	1	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.275063815876166	3	FACETS	0.892	0.801	0.986	0.892	0.801	0.986	CLONAL	3	TRUE	0	0.275063815876166	3		291	272	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0048516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	52	495	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.275063815876166	2		495	262	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	88	576	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.0575352974075312	4	FACETS	0.829	0.737	0.927	0.829	0.737	0.927	INDETERMINATE	2	TRUE	2	0.275063815876166	4		576	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0048516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	156	527	1	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	2	TRUE	NA	0.275063815876166	2		528	498	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777893	NA	P-0048516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	87	365	0	ENST00000361445.4:c.5930C>T	p.Thr1977Ile	p.T1977I	ENST00000361445	NM_004958.3	1977	aCa/aTa	43/58	0.275063815876166	1	FACETS	0.8	0.714	0.89	1	0.982	1	SUBCLONAL	2	TRUE	0	0.275063815876166	1		365	341	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042709	42042710	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0048516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	63	257	0	ENST00000219905.7:c.6904_6905del	p.Glu2302ArgfsTer3	p.E2302Rfs*3	ENST00000219905	NM_001164273.1	2302	GAa/a	17/24	0.0575352974075312	4	FACETS	0.904	0.787	1	0.904	0.787	1	INDETERMINATE	2	TRUE	2	0.275063815876166	4		257	323	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151621	55151621	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	123	400	1	ENST00000257290.5:c.2407G>T	p.Ala803Ser	p.A803S	ENST00000257290	NM_006206.4	803	Gcc/Tcc	17/23	0.268906924511208	2	FACETS	0.97	0.883	1	0.97	0.883	1	CLONAL	2	TRUE	0	0.275063815876166	2		401	461	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	113	620	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.954	0.862	1	0.954	0.862	1	CLONAL	1	TRUE	1	0.414722392391968	2		620	571	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	170	774	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.923	0.849	1	0.923	0.849	1	CLONAL	1	TRUE	1	0.414722392391968	2		778	888	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	63	351	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.414722392391968	2		351	300	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	110	434	0	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.414722392391968	2		434	513	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599271	28599271	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs770146088	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	203	586	0	ENST00000253063.3:c.722del	p.Pro241GlnfsTer6	p.P241Qfs*6	ENST00000253063	NM_031459.4	239	agC/ag	5/10	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.414722392391968	2		586	976	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	87	450	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.414722392391968	2		450	340	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739820	46739820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555234707	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	80	359	0	ENST00000371975.4:c.1621G>A	p.Val541Ile	p.V541I	ENST00000371975	NM_003579.3	541	Gtc/Atc	15/18	1	2	FACETS	0.96	0.85	1	0.96	0.85	1	CLONAL	1	TRUE	1	0.414722392391968	2		359	402	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	153	894	1	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	2	FACETS	0.905	0.829	0.985	0.905	0.829	0.985	CLONAL	1	TRUE	1	0.414722392391968	2		895	815	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060499964	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	318	926	0	ENST00000326873.7:c.667G>A	p.Glu223Lys	p.E223K	ENST00000326873	NM_000455.4	223	Gag/Aag	5/10	1	2	FACETS	0.766	0.724	0.809	1	0.995	1	SUBCLONAL	2	TRUE	1	0.414722392391968	2		926	1001	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482927	140482927	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	83	539	2	ENST00000288602.6:c.1208del	p.Pro403LeufsTer8	p.P403Lfs*8	ENST00000288602	NM_004333.4	403	cCt/ct	10/18	1	2	FACETS	0.762	0.674	0.856	0.762	0.674	0.856	SUBCLONAL	1	TRUE	1	0.414722392391968	2		541	525	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023769	27023769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	69	420	0	ENST00000324856.7:c.879del	p.Thr294ProfsTer69	p.T294Pfs*69	ENST00000324856	NM_006015.4	292	aCc/ac	1/20	1	2	FACETS	0.693	0.605	0.788	0.693	0.605	0.788	SUBCLONAL	1	TRUE	1	0.414722392391968	2		420	480	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793211	139793212	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748531430	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	163	822	5	ENST00000247668.2:c.26dup	p.Gly10TrpfsTer70	p.G10Wfs*70	ENST00000247668	NM_021138.3	7	acc/aCcc	2/11	1	2	FACETS	0.868	0.796	0.942	0.868	0.796	0.942	CLONAL	1	TRUE	1	0.414722392391968	2		827	906	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	85	294	0	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.965	0.857	1	0.965	0.857	1	CLONAL	1	TRUE	1	0.414722392391968	2		294	425	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740623	58740624	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs763475304	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	75	497	0	ENST00000305921.3:c.1535dup	p.Asn512LysfsTer16	p.N512Kfs*16	ENST00000305921	NM_003620.3	510	caa/cAaa	6/6	1	2	FACETS	0.859	0.756	0.969	0.859	0.756	0.969	CLONAL	1	TRUE	1	0.414722392391968	2		497	421	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913471	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	156	904	0	ENST00000269571.5:c.2329G>A	p.Val777Met	p.V777M	ENST00000269571		777	Gtg/Atg	20/27	1	2	FACETS	0.795	0.728	0.866	0.795	0.728	0.866	SUBCLONAL	1	TRUE	1	0.414722392391968	2		904	946	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272336	15272337	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs771517374	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	179	947	1	ENST00000263388.2:c.6102dup	p.Gly2035ArgfsTer60	p.G2035Rfs*60	ENST00000263388	NM_000435.2	2034	-/C	33/33	1	2	FACETS	0.93	0.858	1	0.93	0.858	1	CLONAL	1	TRUE	1	0.414722392391968	2		948	928	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129199	64129199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545430280	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	175	975	1	ENST00000334205.4:c.737C>T	p.Thr246Met	p.T246M	ENST00000334205	NM_003942.2	246	aCg/aTg	7/17	1	2	FACETS	0.878	0.808	0.951	0.878	0.808	0.951	CLONAL	1	TRUE	1	0.414722392391968	2		976	961	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346157	89346158	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs878855327	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	44	447	1	ENST00000301030.4:c.6792dup	p.Ala2265ArgfsTer8	p.A2265Rfs*8	ENST00000301030	NM_001256183.1	2264	-/C	9/13	1	2	FACETS	0.619	0.52	0.726	0.619	0.52	0.726	SUBCLONAL	1	TRUE	1	0.414722392391968	2		448	343	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087372	27087373	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	119	521	0	ENST00000324856.7:c.1950dup	p.Met651HisfsTer25	p.M651Hfs*25	ENST00000324856	NM_006015.4	649	ctc/ctCc	5/20	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.414722392391968	2		521	556	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248079	98248079	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs758656848	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	117	540	0	ENST00000331920.6:c.472A>G	p.Met158Val	p.M158V	ENST00000331920	NM_000264.3	158	Atg/Gtg	3/24	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.414722392391968	2		540	555	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448408	49448408	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs797045661	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	144	816	0	ENST00000301067.7:c.303del	p.Ser102AlafsTer28	p.S102Afs*28	ENST00000301067	NM_003482.3	101	ggG/gg	3/54	1	2	FACETS	0.88	0.803	0.961	0.88	0.803	0.961	CLONAL	1	TRUE	1	0.414722392391968	2		816	789	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237569	133237569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147692158	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	130	523	0	ENST00000320574.5:c.3046G>A	p.Val1016Met	p.V1016M	ENST00000320574	NM_006231.2	1016	Gtg/Atg	25/49	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.414722392391968	2		523	565	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30047521	30047521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	67	364	0	ENST00000331968.5:c.2480G>A	p.Arg827His	p.R827H	ENST00000331968	NM_002742.2	827	cGc/cAc	17/18	1	2	FACETS	0.948	0.829	1	0.948	0.829	1	CLONAL	1	TRUE	1	0.414722392391968	2		364	341	SUCCESS
APC	324	MSKCC	GRCh37	5	112102982	112102982	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201764637	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	72	379	0	ENST00000257430.4:c.317G>A	p.Arg106His	p.R106H	ENST00000257430	NM_000038.5	106	cGt/cAt	4/16	1	2	FACETS	0.9	0.79	1	0.9	0.79	1	CLONAL	1	TRUE	1	0.414722392391968	2		379	386	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204506585	204506585	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	109	418	0	ENST00000367182.3:c.371A>C	p.Gln124Pro	p.Q124P	ENST00000367182	NM_001278516.1	124	cAg/cCg	6/11	0.414722392391968	3	FACETS	0.963	0.866	1	0.482	0.433	0.533	CLONAL	1	TRUE	1	0.414722392391968	3		418	659	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711940	89711940	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	84	391	0	ENST00000371953.3:c.559del	p.Asp187IlefsTer12	p.D187Ifs*12	ENST00000371953	NM_000314.4	186	ctG/ct	6/9	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.414722392391968	2		391	343	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905424	11905424	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	60	386	0	ENST00000396373.4:c.74C>A	p.Pro25Gln	p.P25Q	ENST00000396373	NM_001987.4	25	cCg/cAg	2/8	NA	2	FACETS	0.526	0.453	0.605			1	INDETERMINATE	1	TRUE	NA	0.414722392391968	2		386	550	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650626	18650626	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	62	355	0	ENST00000266497.5:c.2837A>G	p.Glu946Gly	p.E946G	ENST00000266497		946	gAa/gGa	20/31	1	2	FACETS	0.926	0.805	1	0.926	0.805	1	CLONAL	1	TRUE	1	0.414722392391968	2		355	323	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845574	72845574	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	187	859	0	ENST00000268489.5:c.3766C>A	p.Leu1256Met	p.L1256M	ENST00000268489	NM_006885.3	1256	Ctg/Atg	7/10	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.414722392391968	2		859	889	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117878	70117878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	109	636	0	ENST00000245479.2:c.346G>A	p.Ala116Thr	p.A116T	ENST00000245479	NM_000346.3	116	Gcg/Acg	1/3	1	2	FACETS	0.914	0.823	1	0.914	0.823	1	CLONAL	1	TRUE	1	0.414722392391968	2		636	575	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573850	41573851	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	198	877	0	ENST00000263253.7:c.6138_6139del	p.Gln2048ThrfsTer24	p.Q2048Tfs*24	ENST00000263253	NM_001429.3	2045	acTGtg/actg	31/31	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.414722392391968	2		877	885	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902466	1902466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754895784	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	157	578	0	ENST00000382891.5:c.85G>A	p.Gly29Ser	p.G29S	ENST00000382891	NM_133335.3	29	Ggc/Agc	2/22	1	2	FACETS	0.986	0.904	1	0.986	0.904	1	CLONAL	1	TRUE	1	0.414722392391968	2		578	768	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410939	31410939	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	186	736	0	ENST00000344624.3:c.3581T>C	p.Leu1194Pro	p.L1194P	ENST00000344624		1194	cTg/cCg	28/33	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.414722392391968	2		736	837	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589154	67589154	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	27	247	0	ENST00000274335.5:c.1142T>A	p.Ile381Asn	p.I381N	ENST00000274335		381	aTc/aAc	9/15	1	2	FACETS	0.629	0.504	0.77	0.629	0.504	0.77	SUBCLONAL	1	TRUE	1	0.414722392391968	2		247	207	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589226	67589226	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	43	253	1	ENST00000274335.5:c.1214T>A	p.Ile405Lys	p.I405K	ENST00000274335		405	aTa/aAa	9/15	1	2	FACETS	0.78	0.657	0.914	0.78	0.657	0.914	CLONAL	1	TRUE	1	0.414722392391968	2		254	266	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141567306	141567306	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1045459491	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	145	622	0	ENST00000220592.5:c.908C>T	p.Thr303Met	p.T303M	ENST00000220592	NM_012154.3	303	aCg/aTg	8/19	0.414722392391968	3	FACETS	1	0.97	1	0.567	0.518	0.619	CLONAL	1	TRUE	1	0.414722392391968	3		622	744	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772861	135772861	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	115	620	0	ENST00000298552.3:c.2762A>G	p.His921Arg	p.H921R	ENST00000298552	NM_001162426.1	921	cAc/cGc	21/23	1	2	FACETS	0.824	0.743	0.909	0.824	0.743	0.909	CLONAL	1	TRUE	1	0.414722392391968	2		620	673	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417434	139417434	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1256895718	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	184	968	0	ENST00000277541.6:c.610T>C	p.Cys204Arg	p.C204R	ENST00000277541	NM_017617.3	204	Tgc/Cgc	4/34	1	2	FACETS	0.848	0.782	0.917	0.848	0.782	0.917	CLONAL	1	TRUE	1	0.414722392391968	2		968	1046	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933735	39933735	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	128	718	0	ENST00000378444.4:c.864del	p.Trp289GlyfsTer89	p.W289Gfs*89	ENST00000378444	NM_001123385.1	288	ccG/cc	4/15	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.414722392391968	2		718	612	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0048522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	80	327	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.193383133527738	3	FACETS	1	0.972	1	0.447	0.396	0.501	INDETERMINATE	1	TRUE	0	0.362394176046587	3		327	389	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0048522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	61	290	1	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.362394176046587	2		291	316	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0048522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	41	286	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.686	0.573	0.81	0.686	0.573	0.81	SUBCLONAL	1	TRUE	1	0.362394176046587	2		286	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0048522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	233	715	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.269456315498613	2	FACETS	1	0.992	1	0.748	0.699	0.798	CLONAL	1	TRUE	0	0.362394176046587	2		715	860	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0048522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	27	302	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.569	0.454	0.699	0.569	0.454	0.699	SUBCLONAL	1	TRUE	1	0.362394176046587	2		302	262	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101084	26101117	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	TCCCTCATGTCGGGTCTTGAACTGACTGGGAGGC	TCCCTCATGTCGGGTCTTGAACTGACTGGGAGGC	-	novel	NA	P-0048522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	52	756	0	ENST00000435504.4:c.-26_8del		p.*9*	ENST00000435504		?-3/1435		1/13	1	2	FACETS	0.357	0.303	0.417	0.357	0.303	0.417	SUBCLONAL	1	TRUE	1	0.362394176046587	2		756	804	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549181	87549181	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	110	462	1	ENST00000277120.3:c.1738C>A	p.Gln580Lys	p.Q580K	ENST00000277120		580	Cag/Aag	15/19	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.362394176046587	2		463	515	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0048523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	717	470	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.510562079719803	5	FACETS	0.983	0.951	1			1	CLONAL	3	TRUE	NA	0.558911219684378	5		470	1599	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061191	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs879499034	NA	P-0048523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	223	478	0	ENST00000250448.2:c.798C>A	p.Phe266Leu	p.F266L	ENST00000250448	NM_004496.3	266	ttC/ttA	2/2	1	2	FACETS	0.961	0.897	1	0.961	0.897	1	CLONAL	1	TRUE	1	0.558911219684378	2		478	830	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845760	68845760	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	145	303	0	ENST00000261769.5:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000261769	NM_004360.3	336	Gag/Tag	7/16	0.55866329687274	1	FACETS	0.964	0.889	1	0.964	0.889	1	CLONAL	1	TRUE	0	0.558911219684378	1		303	388	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31422972	31422972	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs776736153	NA	P-0048523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	261	551	0	ENST00000344624.3:c.3341T>C	p.Ile1114Thr	p.I1114T	ENST00000344624		1114	aTt/aCt	26/33	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.558911219684378	2		551	913	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609660	117609660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048523-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	109	284	0	ENST00000368508.3:c.7039G>A	p.Asp2347Asn	p.D2347N	ENST00000368508	NM_002944.2	2347	Gat/Aat	43/43	1	2	FACETS	0.949	0.859	1	0.949	0.859	1	CLONAL	1	TRUE	1	0.558911219684378	2		284	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0048524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	423	681	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.413529876227608	2	FACETS	0.836	0.799	0.872	0.836	0.799	0.872	CLONAL	2	TRUE	0	0.521220136865637	2		681	971	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643682	52643682	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0048524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	173	359	0	ENST00000394830.3:c.2214C>G	p.Tyr738Ter	p.Y738*	ENST00000394830	NM_018313.4	738	taC/taG	17/30	0.401993798117902	3	FACETS	0.781	0.723	0.839	0.781	0.723	0.839	SUBCLONAL	2	TRUE	1	0.521220136865637	3		359	536	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510124	120510124	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0048524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	91	373	0	ENST00000256646.2:c.1385C>G	p.Ser462Ter	p.S462*	ENST00000256646	NM_024408.3	462	tCa/tGa	8/34	0.312719168534969	4	FACETS	0.793	0.704	0.887	0.396	0.352	0.444	INDETERMINATE	1	TRUE	2	0.521220136865637	4		373	670	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998286	100998288	+	inframe_deletion	In_Frame_Del	DEL	CGG	CGG	-	rs766303231	NA	P-0048524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	10	299	3	ENST00000325455.5:c.1514_1516del	p.Ala505del	p.A505del	ENST00000325455	NM_001202474.3	505	gCCGgg/ggg	1/8	0.521220136865637	3	FACETS	0.243	0.164	0.342	0.122	0.082	0.171	SUBCLONAL	1	TRUE	1	0.521220136865637	3		302	199	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266693	41266693	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	36	300	0	ENST00000349496.5:c.490G>C	p.Asp164His	p.D164H	ENST00000349496	NM_001904.3	164	Gac/Cac	4/15	0.401993798117902	3	FACETS	0.341	0.28	0.41	0.171	0.14	0.205	SUBCLONAL	1	TRUE	1	0.521220136865637	3		300	510	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	723	714	0	ENST00000269305.4:c.569del	p.Pro190LeufsTer57	p.P190Lfs*57	ENST00000269305	NM_001126112.2	190	cCt/ct	6/11	0.748840971148298	4	FACETS	0.945	0.926	0.964	0.945	0.926	0.964	CLONAL	4	TRUE	0	0.748840971148298	4		714	893	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314608	30314608	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2739	191	712	0	ENST00000262643.3:c.1157C>T	p.Ala386Val	p.A386V	ENST00000262643	NM_001238.2	386	gCt/gTt	12/12	0.748840971148298	11	FACETS	0.761	0.699	0.826			1	SUBCLONAL	1	TRUE	NA	0.748840971148298	11		712	2930	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203621	108203621	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	47	179	0	ENST00000278616.4:c.7921C>G	p.Gln2641Glu	p.Q2641E	ENST00000278616	NM_000051.3	2641	Cag/Gag	53/63	0.735825050601575	2	FACETS	0.765	0.657	0.88	0.383	0.328	0.44	SUBCLONAL	1	TRUE	0	0.748840971148298	2		179	164	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0048527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	63	302	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.998	0.872	1	0.998	0.872	1	CLONAL	1	TRUE	1	0.48	2		302	263	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0048527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	20	388	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.182	0.138	0.233	0.182	0.138	0.233	SUBCLONAL	1	TRUE	1	0.48	2		388	458	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0048527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	76	247	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.996	0.881	1	0.996	0.881	1	CLONAL	1	TRUE	1	0.48	2		247	318	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088787	27088788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0048527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	145	589	0	ENST00000324856.7:c.2402dup	p.Gln802SerfsTer15	p.Q802Sfs*15	ENST00000324856	NM_006015.4	799	cag/caGg	7/20	1	2	FACETS	0.974	0.892	1	0.974	0.892	1	CLONAL	1	TRUE	1	0.48	2		589	620	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717609	89717609	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs876661024	NA	P-0048527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	72	319	0	ENST00000371953.3:c.635-1G>C		p.X212_splice	ENST00000371953	NM_000314.4	212			1	2	FACETS	0.85	0.747	0.959	0.85	0.747	0.959	CLONAL	1	TRUE	1	0.48	2		319	353	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653785	89653785	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1355570425	NA	P-0048527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	49	225	0	ENST00000371953.3:c.83T>C	p.Ile28Thr	p.I28T	ENST00000371953	NM_000314.4	28	aTt/aCt	2/9	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.48	2		225	200	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624270	89624270	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs398123324	NA	P-0048527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	101	362	0	ENST00000371953.3:c.44G>C	p.Arg15Thr	p.R15T	ENST00000371953	NM_000314.4	15	aGa/aCa	1/9	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.48	2		362	398	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	164	576	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.926	0.854	1	0.926	0.854	1	CLONAL	1	TRUE	1	0.561151228805618	2		576	631	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0048530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	115	281	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.53035050350117	1	FACETS	0.98	0.896	1	0.98	0.896	1	CLONAL	1	TRUE	0	0.561151228805618	1		281	301	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782177	NA	P-0048530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	227	623	0	ENST00000269305.4:c.644G>T	p.Ser215Ile	p.S215I	ENST00000269305	NM_001126112.2	215	aGt/aTt	6/11	0.561151228805618	1	FACETS	0.968	0.909	1	0.968	0.909	1	CLONAL	1	TRUE	0	0.561151228805618	1		623	601	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189835	66189835	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs55784741	NA	P-0048530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	108	339	0	ENST00000273854.3:c.3111G>T	p.Leu1037Phe	p.L1037F	ENST00000273854	NM_004439.5	1037	ttG/ttT	18/18	1	2	FACETS	0.912	0.824	1	0.912	0.824	1	CLONAL	1	TRUE	1	0.561151228805618	2		339	422	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685303	89685303	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	41	183	0	ENST00000371953.3:c.198G>C	p.Lys66Asn	p.K66N	ENST00000371953	NM_000314.4	66	aaG/aaC	3/9	0.561151228805618	1	FACETS	0.601	0.507	0.701	0.601	0.507	0.701	SUBCLONAL	1	TRUE	0	0.561151228805618	1		183	175	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839699	27839699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	138	492	0	ENST00000328488.2:c.395G>A	p.Arg132Gln	p.R132Q	ENST00000328488	NM_003533.2	132	cGa/cAa	1/1	1	2	FACETS	0.926	0.847	1	0.926	0.847	1	CLONAL	1	TRUE	1	0.561151228805618	2		492	531	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954353	48954353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060503084	NA	P-0048530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	79	274	0	ENST00000267163.4:c.1474G>A	p.Glu492Lys	p.E492K	ENST00000267163	NM_000321.2	492	Gag/Aag	16/27	0.561151228805618	1	FACETS	0.739	0.658	0.824	0.739	0.658	0.824	SUBCLONAL	1	TRUE	0	0.561151228805618	1		274	274	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405101	70405101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	123	434	0	ENST00000373644.4:c.2615C>T	p.Pro872Leu	p.P872L	ENST00000373644	NM_030625.2	872	cCc/cTc	4/12	0.561151228805618	1	FACETS	0.944	0.865	1	0.944	0.865	1	CLONAL	1	TRUE	0	0.561151228805618	1		434	334	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796886	45796886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	185	560	0	ENST00000450313.1:c.1444C>T	p.His482Tyr	p.H482Y	ENST00000450313	NM_012222.2	482	Cac/Tac	14/16	1	2	FACETS	0.933	0.864	1	0.933	0.864	1	CLONAL	1	TRUE	1	0.561151228805618	2		560	707	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800901	18800901	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	44	314	0	ENST00000266497.5:c.4277G>T	p.Arg1426Leu	p.R1426L	ENST00000266497		1426	cGa/cTa	31/31	0.381623137029084	1	FACETS	0.307	0.258	0.362	0.307	0.258	0.362	SUBCLONAL	1	TRUE	0	0.561151228805618	1		314	367	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054048	42054048	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	36	213	0	ENST00000219905.7:c.7510G>T	p.Gly2504Cys	p.G2504C	ENST00000219905	NM_001164273.1	2504	Ggt/Tgt	21/24	0.414526321469562	0	FACETS	0.329	0.274	0.39			1	SUBCLONAL	1	TRUE	0	0.561151228805618	0		213	171	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420318	88420318	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	150	413	1	ENST00000360948.2:c.2368G>T	p.Glu790Ter	p.E790*	ENST00000360948	NM_001012338.2	790	Gag/Tag	19/19	0.381623137029084	1	FACETS	0.842	0.776	0.909	0.842	0.776	0.909	CLONAL	1	TRUE	0	0.561151228805618	1		414	457	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81941300	81941300	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	172	560	0	ENST00000359376.3:c.1478G>T	p.Arg493Leu	p.R493L	ENST00000359376	NM_002661.3	493	cGg/cTg	16/33	0.561151228805618	1	FACETS	0.913	0.848	0.98	0.913	0.848	0.98	CLONAL	1	TRUE	0	0.561151228805618	1		560	483	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006606	62006606	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	145	649	0	ENST00000392795.3:c.673G>C	p.Glu225Gln	p.E225Q	ENST00000392795	NM_001039933.1	225	Gag/Cag	6/6	0.282208715913747	3	FACETS	0.955	0.873	1	0.477	0.436	0.52	INDETERMINATE	1	TRUE	1	0.561151228805618	3		649	693	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006808	62006808	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	246	754	0	ENST00000392795.3:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000392795	NM_001039933.1	194	Gat/Tat	5/6	0.282208715913747	3	FACETS	1	0.987	1	0.606	0.567	0.646	INDETERMINATE	1	TRUE	1	0.561151228805618	3		754	926	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617724	39617724	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	88	284	0	ENST00000262039.4:c.1908G>T	p.Lys636Asn	p.K636N	ENST00000262039	NM_002647.2	636	aaG/aaT	17/25	1	2	FACETS	0.855	0.763	0.951	0.855	0.763	0.951	CLONAL	1	TRUE	1	0.561151228805618	2		284	367	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29120973	29120973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	120	354	0	ENST00000328354.6:c.584G>C	p.Arg195Thr	p.R195T	ENST00000328354	NM_007194.3	195	aGa/aCa	4/15	0.322982805916703	1	FACETS	0.736	0.67	0.805	0.736	0.67	0.805	INDETERMINATE	1	TRUE	0	0.561151228805618	1		354	418	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670621	134670621	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	211	732	0	ENST00000398015.3:c.532C>G	p.Gln178Glu	p.Q178E	ENST00000398015	NM_004441.4	178	Cag/Gag	3/16	1	2	FACETS	0.932	0.867	0.998	0.932	0.867	0.998	CLONAL	1	TRUE	1	0.561151228805618	2		732	807	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920140	1920140	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	221	649	0	ENST00000382891.5:c.1200G>T	p.Arg400Ser	p.R400S	ENST00000382891	NM_133335.3	400	agG/agT	5/22	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.561151228805618	2		649	773	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866565	117866565	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	76	362	0	ENST00000297338.2:c.1080G>C	p.Leu360Phe	p.L360F	ENST00000297338	NM_006265.2	360	ttG/ttC	9/14	NA	2	FACETS	0.451	0.396	0.511			1	INDETERMINATE	1	TRUE	NA	0.561151228805618	2		362	600	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740421	145740421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778655	NA	P-0048530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	352	958	0	ENST00000428558.2:c.1519G>A	p.Gly507Ser	p.G507S	ENST00000428558	NM_004260.3	507	Ggc/Agc	9/22	0.561151228805618	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.561151228805618	1		958	804	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814804	139814804	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0048530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	263	867	0	ENST00000247668.2:c.797C>G	p.Ser266Ter	p.S266*	ENST00000247668	NM_021138.3	266	tCa/tGa	8/11	1	2	FACETS	0.947	0.888	1	0.947	0.888	1	CLONAL	1	TRUE	1	0.561151228805618	2		867	990	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226979	53226979	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	232	367	0	ENST00000375401.3:c.2596G>T	p.Ala866Ser	p.A866S	ENST00000375401	NM_004187.3	866	Gcc/Tcc	18/26	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.561151228805618	1		367	411	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70355010	70355010	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	286	363	0	ENST00000374080.3:c.4932G>T	p.Gln1644His	p.Q1644H	ENST00000374080		1644	caG/caT	36/45	1	1	FACETS	0.831	0.796	0.866	1	0.996	1	CLONAL	2	TRUE	0	0.561151228805618	1		363	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0048531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	130	828	1	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.179550422377698	2	FACETS	0.842	0.765	0.923	0.842	0.765	0.923	CLONAL	2	FALSE	0	0.219924663935296	2		829	702	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223019	41223019	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	152	766	1	ENST00000357654.3:c.4912G>T	p.Glu1638Ter	p.E1638*	ENST00000357654	NM_007294.3	1638	Gaa/Taa	15/23	0.179550422377698	2	FACETS	0.985	0.903	1	0.985	0.903	1	CLONAL	2	FALSE	0	0.219924663935296	2		767	702	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170737	99170737	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	38	484	0	ENST00000074304.5:c.1366C>G	p.Arg456Gly	p.R456G	ENST00000074304	NM_001134224.1	456	Cgg/Ggg	16/26	1	2	FACETS	0.858	0.71	1	0.858	0.71	1	CLONAL	1	FALSE	1	0.219924663935296	2		484	403	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138064	64138064	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	71	1104	0	ENST00000334205.4:c.1987C>G	p.Leu663Val	p.L663V	ENST00000334205	NM_003942.2	663	Ctg/Gtg	16/17	0.219924663935296	1	FACETS	0.742	0.647	0.846	0.742	0.647	0.846	SUBCLONAL	1	FALSE	0	0.219924663935296	1		1104	774	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250442	26250442	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	96	628	0	ENST00000446824.2:c.392T>A	p.Ile131Asn	p.I131N	ENST00000446824	NM_021018.2	131	aTt/aAt	1/1	0.154109719616718	4	FACETS	0.848	0.757	0.945	0.848	0.757	0.945	CLONAL	2	FALSE	2	0.219924663935296	4		628	628	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	178	301	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.98	0.914	1	0.98	0.914	1	CLONAL	1	TRUE	1	0.867112307463764	2		301	419	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191385	185191385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	387	800	0	ENST00000265026.3:c.2266G>A	p.Asp756Asn	p.D756N	ENST00000265026	NM_004721.4	756	Gac/Aac	11/14	1	2	FACETS	0.9	0.858	0.943	0.9	0.858	0.943	CLONAL	1	TRUE	1	0.867112307463764	2		800	992	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0048532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	426	726	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.867112307463764	2		727	913	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106732	27106732	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	745	701	0	ENST00000324856.7:c.6343C>T	p.Gln2115Ter	p.Q2115*	ENST00000324856	NM_006015.4	2115	Cag/Tag	20/20	0.864830038044619	2	FACETS	0.989	0.972	1	0.989	0.972	1	CLONAL	2	TRUE	0	0.867112307463764	2		701	869	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626883	14626883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	462	728	0	ENST00000254322.2:c.892C>T	p.Pro298Ser	p.P298S	ENST00000254322	NM_006145.1	298	Cct/Tct	3/3	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.867112307463764	2		728	1040	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981140	201981141	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0048532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	572	843	0	ENST00000359651.3:c.219_220del	p.Asp74LeufsTer17	p.D74Lfs*17	ENST00000359651		73	ctGGac/ctac	2/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.867112307463764	2		843	1244	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204852	94204852	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	167	385	0	ENST00000323929.3:c.733C>T	p.His245Tyr	p.H245Y	ENST00000323929	NM_005591.3	245	Cat/Tat	8/20	1	2	FACETS	0.98	0.912	1	0.98	0.912	1	CLONAL	1	TRUE	1	0.867112307463764	2		385	393	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118370579	118370579	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	129	316	0	ENST00000534358.1:c.6109C>G	p.Leu2037Val	p.L2037V	ENST00000534358	NM_005933.3	2037	Cta/Gta	24/36	1	2	FACETS	0.731	0.669	0.795	0.731	0.669	0.795	SUBCLONAL	1	TRUE	1	0.867112307463764	2		316	407	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443596	49443596	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	402	826	1	ENST00000301067.7:c.3775C>A	p.Leu1259Ile	p.L1259I	ENST00000301067	NM_003482.3	1259	Ctc/Atc	11/54	1	2	FACETS	0.926	0.884	0.969	0.926	0.884	0.969	CLONAL	1	TRUE	1	0.867112307463764	2		827	1001	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611750	1611750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	512	936	0	ENST00000344749.5:c.1912C>T	p.His638Tyr	p.H638Y	ENST00000344749	NM_001136139.2	638	Cac/Tac	19/19	1	2	FACETS	0.939	0.902	0.978	0.939	0.902	0.978	CLONAL	1	TRUE	1	0.867112307463764	2		936	1257	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2202733	2202733	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	421	725	0	ENST00000398665.3:c.742G>C	p.Glu248Gln	p.E248Q	ENST00000398665	NM_032482.2	248	Gag/Cag	9/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.867112307463764	2		725	955	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096213	71096213	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	201	291	0	ENST00000318789.4:c.544C>T	p.Gln182Ter	p.Q182*	ENST00000318789	NM_032682.5	182	Cag/Tag	10/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.867112307463764	2		291	436	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191103	185191103	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	355	679	0	ENST00000265026.3:c.1984G>C	p.Asp662His	p.D662H	ENST00000265026	NM_004721.4	662	Gac/Cac	11/14	1	2	FACETS	0.951	0.905	0.997	0.951	0.905	0.997	CLONAL	1	TRUE	1	0.867112307463764	2		679	861	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191349	185191349	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	360	758	0	ENST00000265026.3:c.2230G>A	p.Asp744Asn	p.D744N	ENST00000265026	NM_004721.4	744	Gac/Aac	11/14	1	2	FACETS	0.901	0.857	0.945	0.901	0.857	0.945	CLONAL	1	TRUE	1	0.867112307463764	2		758	922	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405706	139405706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	645	1083	0	ENST00000277541.6:c.2485G>A	p.Val829Met	p.V829M	ENST00000277541	NM_017617.3	829	Gtg/Atg	16/34	0.867112307463764	1	FACETS	0.968	0.944	0.991	0.968	0.944	0.991	CLONAL	1	TRUE	0	0.867112307463764	1		1083	871	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038832	47038851	+	frameshift_variant	Frame_Shift_Del	DEL	GAGTCCTGGCCTCCCAAGCC	GAGTCCTGGCCTCCCAAGCC	A	novel	NA	P-0048532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	551	500	0	ENST00000377604.3:c.839_858delinsA	p.Gly280AspfsTer22	p.G280Dfs*22	ENST00000377604	NM_001204468.1	280	gGAGTCCTGGCCTCCCAAGCC/gA	9/24	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.867112307463764	1		500	682	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579483	7579484	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0048538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	74	741	0	ENST00000269305.4:c.203_204del	p.Glu68GlyfsTer80	p.E68Gfs*80	ENST00000269305	NM_001126112.2	68	gAG/g	4/11	0.218618059237114	3	FACETS	0.932	0.846	1	0.932	0.846	1	INDETERMINATE	3	TRUE	0	0.496699092856148	3		741	133	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211339	36211339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757604369	NA	P-0048538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	23	659	2	ENST00000222270.7:c.1090G>A	p.Glu364Lys	p.E364K	ENST00000222270	NM_014727.1	364	Gag/Aag	3/37	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.496699092856148	2		661	78	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098966	178098966	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	22	209	0	ENST00000397062.3:c.79G>C	p.Asp27His	p.D27H	ENST00000397062	NM_006164.4	27	Gat/Cat	2/5	0.496699092856148	6	FACETS	0.81	0.638	1			1	CLONAL	2	TRUE	NA	0.496699092856148	6		209	109	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099403	157099429	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAGCAACAG	CAGCAGCAGCAGCAGCAGCAGCAACAG	-	rs910569810	NA	P-0048539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	88	275	0	ENST00000346085.5:c.360_386del	p.Gln123_Gln131del	p.Q123_Q131del	ENST00000346085	NM_020732.3	114	CAGCAGCAGCAGCAGCAGCAGCAACAG/-	1/20	1	2	FACETS	0.813	0.729	0.901	0.813	0.729	0.901	CLONAL	1	TRUE	1	0.723662151487782	2		275	299	SUCCESS
MET	4233	MSKCC	GRCh37	7	116409810	116409810	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753911898	NA	P-0048539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	101	209	0	ENST00000397752.3:c.2695G>A	p.Asp899Asn	p.D899N	ENST00000397752	NM_000245.2	899	Gac/Aac	12/21	0.723662151487782	3	FACETS	1	0.96	1	0.561	0.506	0.617	CLONAL	1	TRUE	1	0.723662151487782	3		209	339	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535424	66535424	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	147	288	1	ENST00000273854.3:c.37C>T	p.Arg13Trp	p.R13W	ENST00000273854	NM_004439.5	13	Cgg/Tgg	1/18	0.581782851320186	3	FACETS	1	0.988	1	0.722	0.667	0.778	CLONAL	1	TRUE	1	0.723662151487782	3		289	383	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32814895	32814895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	344	693	0	ENST00000354258.4:c.2170C>T	p.Leu724Phe	p.L724F	ENST00000354258	NM_000593.5	724	Ctt/Ttt	10/11	0.472400117861078	1	FACETS	0.829	0.79	0.868	0.829	0.79	0.868	CLONAL	1	TRUE	0	0.723662151487782	1		693	732	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93953166	93953166	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	66	227	0	ENST00000369303.4:c.2975A>G	p.His992Arg	p.H992R	ENST00000369303	NM_004440.3	992	cAt/cGt	17/17	1	2	FACETS	0.704	0.618	0.795	0.704	0.618	0.795	SUBCLONAL	1	TRUE	1	0.723662151487782	2		227	259	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0048540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	83	302	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.399287091406724	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	0	0.399287091406724	2		302	201	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0048540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	97	450	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.393083793737217	3	FACETS	0.814	0.732	0.899	0.814	0.732	0.899	CLONAL	2	TRUE	1	0.399287091406724	3		450	358	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112064	115112064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757023811	NA	P-0048540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	398	668	0	ENST00000257566.3:c.1676C>T	p.Thr559Met	p.T559M	ENST00000257566	NM_016569.3	559	aCg/aTg	7/8	0.399287091406724	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.399287091406724	3		668	1091	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250272	39250272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397517147	NA	P-0048540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	174	693	0	ENST00000402219.2:c.1297G>A	p.Glu433Lys	p.E433K	ENST00000402219	NM_005633.3	433	Gag/Aag	10/23	0.393083793737217	3	FACETS	0.891	0.824	0.959	0.891	0.824	0.959	CLONAL	2	TRUE	1	0.399287091406724	3		693	587	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105723	27105727	+	frameshift_variant	Frame_Shift_Del	DEL	AGAGG	AGAGG	-	novel	NA	P-0048540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	53	413	0	ENST00000324856.7:c.5335_5339del	p.Glu1779SerfsTer3	p.E1779Sfs*3	ENST00000324856	NM_006015.4	1778	gaAGAGGaa/gaaa	20/20	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.399287091406724	2		413	231	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521978	157521988	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCCATCCAG	GGCCCATCCAG	-	novel	NA	P-0048540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	220	550	0	ENST00000346085.5:c.4254_4264del	p.Ile1419ValfsTer36	p.I1419Vfs*36	ENST00000346085	NM_020732.3	1417	aGGCCCATCCAG/a	18/20	0.168026532094448	3	FACETS	1	0.976	1	0.725	0.679	0.772	INDETERMINATE	2	TRUE	0	0.399287091406724	3		550	608	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942749	44942749	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	93	575	0	ENST00000377967.4:c.3329T>C	p.Val1110Ala	p.V1110A	ENST00000377967	NM_021140.2	1110	gTg/gCg	23/29	1	2	FACETS	0.997	0.891	1	0.997	0.891	1	CLONAL	1	TRUE	1	0.399287091406724	2		575	467	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0048540-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	505	302	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.668079953503359	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.668079953503359	3		302	650	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0048540-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	465	450	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.668079953503359	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.668079953503359	3		450	838	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112064	115112064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757023811	NA	P-0048540-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	506	668	0	ENST00000257566.3:c.1676C>T	p.Thr559Met	p.T559M	ENST00000257566	NM_016569.3	559	aCg/aTg	7/8	0.668079953503359	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.668079953503359	3		668	946	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250272	39250272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397517147	NA	P-0048540-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	701	693	0	ENST00000402219.2:c.1297G>A	p.Glu433Lys	p.E433K	ENST00000402219	NM_005633.3	433	Gag/Aag	10/23	0.668079953503359	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.668079953503359	3		693	1375	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105723	27105727	+	frameshift_variant	Frame_Shift_Del	DEL	AGAGG	AGAGG	-	novel	NA	P-0048540-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	170	413	0	ENST00000324856.7:c.5335_5339del	p.Glu1779SerfsTer3	p.E1779Sfs*3	ENST00000324856	NM_006015.4	1778	gaAGAGGaa/gaaa	20/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.668079953503359	2		413	440	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521978	157521988	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCCATCCAG	GGCCCATCCAG	-	novel	NA	P-0048540-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	408	550	0	ENST00000346085.5:c.4254_4264del	p.Ile1419ValfsTer36	p.I1419Vfs*36	ENST00000346085	NM_020732.3	1417	aGGCCCATCCAG/a	18/20	0.668079953503359	3	FACETS	0.975	0.933	1	0.975	0.933	1	CLONAL	2	TRUE	1	0.668079953503359	3		550	836	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942749	44942749	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048540-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	281	575	0	ENST00000377967.4:c.3329T>C	p.Val1110Ala	p.V1110A	ENST00000377967	NM_021140.2	1110	gTg/gCg	23/29	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.668079953503359	2		575	831	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0048541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	97	450	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.283245736147091	2	FACETS	0.766	0.687	0.85	0.766	0.687	0.85	SUBCLONAL	2	TRUE	0	0.283245736147091	2		450	447	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0048541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	211	657	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.283245736147091	4	FACETS	0.996	0.925	1	0.996	0.925	1	CLONAL	2	TRUE	2	0.283245736147091	4		657	960	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894230	NA	P-0048541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	167	577	0	ENST00000451590.1:c.35G>A	p.Gly12Asp	p.G12D	ENST00000451590	NM_001130442.1	12	gGc/gAc	2/5	0.270804604818843	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	0	0.283245736147091	2		577	582	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0048541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	234	762	0	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	0.283245736147091	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.283245736147091	4		762	1007	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342967	225342967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	88	374	0	ENST00000264414.4:c.2125C>T	p.Arg709Trp	p.R709W	ENST00000264414	NM_003590.4	709	Cgg/Tgg	15/16	0.270891840445322	2	FACETS	0.765	0.682	0.853	0.765	0.682	0.853	SUBCLONAL	2	TRUE	0	0.283245736147091	2		374	406	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679794	30679794	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	210	612	0	ENST00000376406.3:c.1925G>C	p.Arg642Thr	p.R642T	ENST00000376406	NM_014641.2	642	aGa/aCa	5/15	0.283245736147091	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	2	0.283245736147091	4		612	886	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0048542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	39	302	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.992	0.825	1	0.992	0.825	1	CLONAL	1	TRUE	1	0.2383573738835	2		302	330	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0048542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	60	370	1	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	1	2	FACETS	0.79	0.68	0.91	0.79	0.68	0.91	CLONAL	1	TRUE	1	0.2383573738835	2		371	637	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061191	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	56	472	0	ENST00000250448.2:c.798C>G	p.Phe266Leu	p.F266L	ENST00000250448	NM_004496.3	266	ttC/ttG	2/2	0.2383573738835	1	FACETS	0.666	0.57	0.772	0.666	0.57	0.772	SUBCLONAL	1	TRUE	0	0.2383573738835	1		472	621	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321351	1321351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763354527	NA	P-0048542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	80	528	0	ENST00000400841.2:c.404C>T	p.Thr135Met	p.T135M	ENST00000400841		135	aCg/aTg	4/6	0.2383573738835	1	FACETS	0.91	0.801	1	0.91	0.801	1	CLONAL	1	TRUE	0	0.2383573738835	1		528	650	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636203	87636203	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	65	392	0	ENST00000277120.3:c.2368C>T	p.Arg790Ter	p.R790*	ENST00000277120		790	Cga/Tga	19/19	0.2383573738835	1	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	0	0.2383573738835	1		392	477	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800571	32800571	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	104	670	1	ENST00000374899.4:c.976G>A	p.Ala326Thr	p.A326T	ENST00000374899	NM_018833.2	326	Gcc/Acc	6/12	1	2	FACETS	0.833	0.745	0.928	0.833	0.745	0.928	CLONAL	1	TRUE	1	0.2383573738835	2		671	1047	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553065	106553078	+	frameshift_variant	Frame_Shift_Del	DEL	GACCAAAGCCTCAA	GACCAAAGCCTCAA	-	novel	NA	P-0048542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	94	627	0	ENST00000369096.4:c.1032_1045del	p.Asp344GlufsTer75	p.D344Efs*75	ENST00000369096	NM_001198.3	344	GACCAAAGCCTCAAg/g	5/7	1	2	FACETS	0.911	0.809	1	0.911	0.809	1	CLONAL	1	TRUE	1	0.2383573738835	2		627	866	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0048543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	8	162	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.181	0.116	0.266	0.181	0.116	0.266	SUBCLONAL	1	TRUE	1	0.428196775530585	2		162	206	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0048543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	137	682	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	1	2	FACETS	0.899	0.819	0.982	0.899	0.819	0.982	CLONAL	1	TRUE	1	0.428196775530585	2		682	712	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212252714	212252714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	43	99	0	ENST00000342788.4:c.3139G>A	p.Glu1047Lys	p.E1047K	ENST00000342788	NM_005235.2	1047	Gaa/Aaa	26/28	0.398082378254385	3	FACETS	0.945	0.81	1	0.945	0.81	1	CLONAL	2	TRUE	1	0.428196775530585	3		99	129	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16174631	16174631	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1238783602	NA	P-0048543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	27	251	0	ENST00000375759.3:c.69C>G	p.Ile23Met	p.I23M	ENST00000375759	NM_015001.2	23	atC/atG	1/15	1	2	FACETS	0.324	0.258	0.4	0.324	0.258	0.4	SUBCLONAL	1	TRUE	1	0.428196775530585	2		251	389	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456451	99456451	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	34	416	0	ENST00000268035.6:c.1768G>T	p.Glu590Ter	p.E590*	ENST00000268035	NM_000875.3	590	Gag/Tag	8/21	1	2	FACETS	0.288	0.235	0.349	0.288	0.235	0.349	SUBCLONAL	1	TRUE	1	0.428196775530585	2		416	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579694	7579698	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CCTTA	CCTTA	-	novel	NA	P-0048543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	93	517	0	ENST00000269305.4:c.96+2_96+6del		p.X32_splice	ENST00000269305	NM_001126112.2	32			1	2	FACETS	0.821	0.732	0.915	0.821	0.732	0.915	CLONAL	1	TRUE	1	0.428196775530585	2		517	529	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0048545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	87	351	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.889	1	1	0.985	1	CLONAL	2	TRUE	1	0.19	2		351	458	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170136	32170136	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771019003	NA	P-0048545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	127	783	1	ENST00000375023.3:c.3472C>T	p.Arg1158Ter	p.R1158*	ENST00000375023	NM_004557.3	1158	Cga/Tga	21/30	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.19	2		784	1120	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448571	89448571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	102	399	0	ENST00000336596.2:c.1535G>A	p.Arg512Gln	p.R512Q	ENST00000336596	NM_005233.5	512	cGa/cAa	7/17	NA	2	FACETS	0.81	0.725	0.9			1	INDETERMINATE	2	TRUE	NA	0.19	2		399	663	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123353268	123353268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377570596	NA	P-0048545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	118	508	1	ENST00000358487.5:c.64C>T	p.Arg22Trp	p.R22W	ENST00000358487	NM_000141.4	22	Cgg/Tgg	2/18	1	2	FACETS	0.848	0.766	0.935	1	0.987	1	CLONAL	2	TRUE	1	0.19	2		509	732	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954587	17954587	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs761583890	NA	P-0048545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	96	711	0	ENST00000458235.1:c.307C>T	p.Arg103Cys	p.R103C	ENST00000458235	NM_000215.3	103	Cgc/Tgc	3/24	1	2	FACETS	0.974	0.866	1	0.974	0.866	1	CLONAL	1	TRUE	1	0.19	2		711	1037	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578197	7578198	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0048545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	105	613	2	ENST00000269305.4:c.651_652delinsAA	p.Val218Met	p.V218M	ENST00000269305	NM_001126112.2	217	gtGGtg/gtAAtg	6/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.19	2		615	931	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577095	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0048545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	118	676	2	ENST00000269305.4:c.843_844delinsAT	p.Asp281_Arg282delinsGluTrp	p.D281_R282delinsEW	ENST00000269305	NM_001126112.2	281	gaCCgg/gaATgg	8/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.19	2		678	1025	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645138	67645138	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	100	482	0	ENST00000264010.4:c.403C>T	p.Gln135Ter	p.Q135*	ENST00000264010	NM_006565.3	135	Cag/Tag	3/12	NA	2	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.19	2		482	808	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221991	98221991	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	146	401	0	ENST00000331920.6:c.2778G>A	p.Trp926Ter	p.W926*	ENST00000331920	NM_000264.3	926	tgG/tgA	17/24	0.197732513210014	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.19	2		401	624	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647607	3647607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483311055	NA	P-0048545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	114	786	0	ENST00000294008.3:c.1456C>T	p.Arg486Cys	p.R486C	ENST00000294008	NM_032444.2	486	Cgt/Tgt	7/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.19	2		786	1038	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417916	138417916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	67	295	0	ENST00000289153.2:c.1603C>T	p.Leu535Phe	p.L535F	ENST00000289153	NM_006219.2	535	Ctt/Ttt	11/22	0.176318537734018	3	FACETS	0.949	0.828	1	0.949	0.828	1	CLONAL	2	TRUE	1	0.19	3		295	407	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857635	9857635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866748846	NA	P-0048545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	72	389	1	ENST00000330684.3:c.3766G>A	p.Glu1256Lys	p.E1256K	ENST00000330684	NM_001134407.1	1256	Gag/Aag	13/13	0.3	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.19	1		390	460	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575077	48575077	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	46	228	0	ENST00000342988.3:c.271C>T	p.Pro91Ser	p.P91S	ENST00000342988	NM_005359.5	91	Cct/Tct	3/12	0.235529162453743	3	FACETS	1	0.95	1	0.669	0.565	0.784	CLONAL	1	TRUE	1	0.19	3		228	396	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295283	1295283	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs544702659	NA	P-0048545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	79	487	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.19	2		487	761	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100856	27100856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	83	467	1	ENST00000324856.7:c.4138C>T	p.Pro1380Ser	p.P1380S	ENST00000324856	NM_006015.4	1380	Cct/Tct	18/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.19	2		468	748	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601866	43601866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	109	726	0	ENST00000355710.3:c.910G>A	p.Val304Ile	p.V304I	ENST00000355710	NM_020975.4	304	Gta/Ata	5/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.19	2		726	968	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88678962	88678963	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0048545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	26	199	0	ENST00000372037.3:c.902_903delinsTT	p.Ser301Phe	p.S301F	ENST00000372037	NM_004329.2	301	tCC/tTT	10/13	1	2	FACETS	1	0.838	1	1	0.838	1	CLONAL	1	TRUE	1	0.19	2		199	257	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421861	49421861	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	110	770	1	ENST00000301067.7:c.14446G>T	p.Glu4816Ter	p.E4816*	ENST00000301067	NM_003482.3	4816	Gag/Tag	46/54	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.19	2		771	1059	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696378	47696380	+	frameshift_variant	Frame_Shift_Del	DEL	GCC	GCC	TT	novel	NA	P-0048545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	59	431	2	ENST00000347630.2:c.443_445delinsAA	p.Gly148GlufsTer14	p.G148Efs*14	ENST00000347630	NM_001007230.1	148	gGGCtt/gAAtt	6/11	1	2	FACETS	0.917	0.788	1	0.917	0.788	1	CLONAL	1	TRUE	1	0.19	2		433	677	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435585	56435585	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	109	714	0	ENST00000407977.2:c.1552C>T	p.Gln518Ter	p.Q518*	ENST00000407977		518	Cag/Tag	9/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.19	2		714	1008	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940476	29940476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	57	305	0	ENST00000389048.3:c.755C>T	p.Ser252Phe	p.S252F	ENST00000389048	NM_004304.4	252	tCc/tTc	2/29	1	2	FACETS	0.811	0.699	0.932	1	0.972	1	CLONAL	2	TRUE	1	0.19	2		305	370	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142964	30142964	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1306212162	NA	P-0048545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	179	929	0	ENST00000389048.3:c.562C>T	p.Arg188Cys	p.R188C	ENST00000389048	NM_004304.4	188	Cgc/Tgc	1/29	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.19	2		929	1266	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265106	198265106	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	59	301	0	ENST00000335508.6:c.2771G>T	p.Arg924Leu	p.R924L	ENST00000335508	NM_012433.2	924	cGa/cTa	19/25	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.19	2		301	482	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177438	56177438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	40	289	0	ENST00000399503.3:c.2411C>T	p.Ser804Phe	p.S804F	ENST00000399503	NM_005921.1	804	tCc/tTc	14/20	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.19	2		289	370	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490546	20490546	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	85	471	0	ENST00000346618.3:c.1283C>T	p.Pro428Leu	p.P428L	ENST00000346618	NM_001949.4	428	cCc/cTc	7/7	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.19	2		471	678	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739747	41739748	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0048545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	98	583	1	ENST00000242208.4:c.225_226delinsTT	p.Gln76Ter	p.Q76*	ENST00000242208	NM_002192.2	75	acCCag/acTTag	2/3	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.19	2		584	857	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38148108	38148108	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	99	513	0	ENST00000317025.8:c.3003C>G	p.Phe1001Leu	p.F1001L	ENST00000317025	NM_023034.1	1001	ttC/ttG	17/24	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.19	2		513	814	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965371	68965371	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1270240284	NA	P-0048545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	49	442	0	ENST00000288368.4:c.983G>A	p.Trp328Ter	p.W328*	ENST00000288368	NM_024870.2	328	tGg/tAg	9/40	0.149603301784557	0	FACETS	0.827	0.701	0.966			1	CLONAL	1	TRUE	0	0.19	0		442	505	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137033	64137033	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759826654	NA	P-0048546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	111	597	1	ENST00000334205.4:c.1544C>T	p.Ser515Leu	p.S515L	ENST00000334205	NM_003942.2	515	tCg/tTg	13/17	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.225366458290937	2		598	964	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0048547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	163	340	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.982	0.907	1	0.982	0.907	1	CLONAL	1	TRUE	1	0.63235809491381	2		340	525	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593640	55593660	+	inframe_deletion	In_Frame_Del	DEL	TTTACATAGACCCAACACAAC	TTTACATAGACCCAACACAAC	-	novel	NA	P-0048547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	145	362	0	ENST00000288135.5:c.1708_1728del	p.Tyr570_Leu576del	p.Y570_L576del	ENST00000288135	NM_000222.2	569	gTTTACATAGACCCAACACAACtt/gtt	11/21	1	2	FACETS	0.906	0.832	0.983	0.906	0.832	0.983	CLONAL	1	TRUE	1	0.63235809491381	2		362	506	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042453	42042454	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	TT	novel	NA	P-0048547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	158	365	2	ENST00000219905.7:c.6648_6649delinsTT	p.Gln2216_Gln2217delinsHisTer	p.Q2216_Q2217delinsH*	ENST00000219905	NM_001164273.1	2216	caGCaa/caTTaa	17/24	0.63235809491381	1	FACETS	0.926	0.86	0.992	0.926	0.86	0.992	CLONAL	1	TRUE	0	0.63235809491381	1		367	369	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0048549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	35	351	0				ENST00000310581	NM_198253.2	-/1132			0.490832408626254	1	FACETS	0.215	0.176	0.259	0.215	0.176	0.259	SUBCLONAL	1	TRUE	0	0.648354911258037	1		351	339	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631302	117631302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138376257	NA	P-0048549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	223	403	0	ENST00000368508.3:c.6376C>T	p.Arg2126Trp	p.R2126W	ENST00000368508	NM_002944.2	2126	Cgg/Tgg	40/43	0.331034296983289	1	FACETS	0.926	0.871	0.981	0.926	0.871	0.981	INDETERMINATE	1	TRUE	0	0.648354911258037	1		403	502	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0048549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	699	557	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.581841001430474	4	FACETS	1	0.98	1			1	CLONAL	3	TRUE	NA	0.648354911258037	4		557	1171	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857524	9857524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778230379	NA	P-0048549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	132	465	0	ENST00000330684.3:c.3877G>A	p.Asp1293Asn	p.D1293N	ENST00000330684	NM_001134407.1	1293	Gat/Aat	13/13	NA	2	FACETS	0.698	0.636	0.763			1	INDETERMINATE	1	TRUE	NA	0.648354911258037	2		465	583	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523319	9523319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1416163895	NA	P-0048549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	212	507	1	ENST00000353224.5:c.1918G>A	p.Glu640Lys	p.E640K	ENST00000353224	NM_177990.2	640	Gag/Aag	9/10	0.206548530644425	3	FACETS	1	0.984	1	0.589	0.549	0.63	INDETERMINATE	1	TRUE	1	0.648354911258037	3		508	735	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458690	120458690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1386606005	NA	P-0048549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	222	562	0	ENST00000256646.2:c.6655C>T	p.Pro2219Ser	p.P2219S	ENST00000256646	NM_024408.3	2219	Ccc/Tcc	34/34	1	2	FACETS	0.971	0.908	1	0.971	0.908	1	CLONAL	1	TRUE	1	0.648354911258037	2		562	705	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375086	104375086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs36049457	NA	P-0048549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	268	639	0	ENST00000369902.3:c.1084C>T	p.Arg362Cys	p.R362C	ENST00000369902	NM_016169.3	362	Cgc/Tgc	9/12	0.648354911258037	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.648354911258037	1		639	502	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68999979	68999979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	209	601	0	ENST00000288368.4:c.2048C>T	p.Ser683Leu	p.S683L	ENST00000288368	NM_024870.2	683	tCa/tTa	19/40	0.331034296983289	1	FACETS	0.804	0.753	0.856	0.804	0.753	0.856	INDETERMINATE	1	TRUE	0	0.648354911258037	1		601	542	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484270	8484270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867884876	NA	P-0048549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	307	442	0	ENST00000356435.5:c.3262C>T	p.Arg1088Cys	p.R1088C	ENST00000356435		1088	Cgt/Tgt	19/35	0.648354911258037	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.648354911258037	1		442	537	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285570	46285570	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs78222561	NA	P-0048549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	114	286	0	ENST00000334344.6:c.4930C>T	p.Gln1644Ter	p.Q1644*	ENST00000334344	NM_152641.2	1644	Cag/Tag	17/21	0.331034296983289	1	FACETS	0.9	0.825	0.976	0.9	0.825	0.976	INDETERMINATE	1	TRUE	0	0.648354911258037	1		286	264	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675097	40675097	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	153	916	1	ENST00000249776.8:c.61G>A	p.Glu21Lys	p.E21K	ENST00000249776	NM_033286.3	21	Gag/Aag	1/9	0.325671921235944	0	FACETS	0.256	0.234	0.278			1	INDETERMINATE	1	TRUE	0	0.648354911258037	0		917	649	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258956	153258956	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	77	223	0	ENST00000281708.4:c.859G>A	p.Glu287Lys	p.E287K	ENST00000281708	NM_033632.3	287	Gag/Aag	5/12	0.242410833304661	1	FACETS	1	0.968	1	1	0.968	1	INDETERMINATE	1	TRUE	0	0.648354911258037	1		223	139	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026897	6026897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	156	300	0	ENST00000265849.7:c.1499C>T	p.Ser500Phe	p.S500F	ENST00000265849	NM_000535.5	500	tCc/tTc	11/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.648354911258037	2		300	452	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263761	16263762	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0048549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	203	614	1	ENST00000375759.3:c.10130_10131delinsTT	p.Pro3377Leu	p.P3377L	ENST00000375759	NM_015001.2	3377	cCC/cTT	12/15	0.331034296983289	1	FACETS	0.733	0.685	0.783	0.733	0.685	0.783	INDETERMINATE	1	TRUE	0	0.648354911258037	1		615	577	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266537	115266537	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	638	561	0	ENST00000438362.2:c.1978G>A	p.Glu660Lys	p.E660K	ENST00000438362	NM_001242891.1	660	Gag/Aag	16/20	0.581841001430474	4	FACETS	0.979	0.948	1			1	CLONAL	3	TRUE	NA	0.648354911258037	4		561	1105	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449559	32449559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138073760	NA	P-0048549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	380	1018	0	ENST00000332351.3:c.815C>T	p.Thr272Ile	p.T272I	ENST00000332351	NM_024426.4	272	aCc/aTc	3/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.648354911258037	2		1018	1170	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719918	18719918	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	111	425	0	ENST00000266497.5:c.3815C>T	p.Ser1272Leu	p.S1272L	ENST00000266497		1272	tCa/tTa	27/31	1	2	FACETS	0.778	0.704	0.855	0.778	0.704	0.855	SUBCLONAL	1	TRUE	1	0.648354911258037	2		425	440	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446115	49446115	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	410	876	0	ENST00000301067.7:c.1351C>T	p.Pro451Ser	p.P451S	ENST00000301067	NM_003482.3	451	Cca/Tca	10/54	0.331034296983289	1	FACETS	0.913	0.873	0.954	0.913	0.873	0.954	INDETERMINATE	1	TRUE	0	0.648354911258037	1		876	936	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562696	21562696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	222	657	0	ENST00000382592.4:c.1223C>T	p.Ser408Phe	p.S408F	ENST00000382592	NM_014572.2	408	tCc/tTc	4/8	1	2	FACETS	0.834	0.778	0.892	0.834	0.778	0.892	CLONAL	1	TRUE	1	0.648354911258037	2		657	821	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857238	9857238	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	297	586	1	ENST00000330684.3:c.4163A>T	p.Lys1388Ile	p.K1388I	ENST00000330684	NM_001134407.1	1388	aAa/aTa	13/13	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.648354911258037	2		587	721	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943638	9943638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	225	622	2	ENST00000330684.3:c.1303C>T	p.Pro435Ser	p.P435S	ENST00000330684	NM_001134407.1	435	Cca/Tca	5/13	NA	2	FACETS	0.748	0.697	0.8			1	INDETERMINATE	1	TRUE	NA	0.648354911258037	2		624	928	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974904	15974904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	81	451	0	ENST00000268712.3:c.3971C>T	p.Pro1324Leu	p.P1324L	ENST00000268712	NM_006311.3	1324	cCc/cTc	30/46	0.300476500904177	1	FACETS	0.345	0.304	0.388	0.345	0.304	0.388	INDETERMINATE	1	TRUE	0	0.648354911258037	1		451	490	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761433	59761433	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1276811545	NA	P-0048549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	145	434	0	ENST00000259008.2:c.2974A>G	p.Thr992Ala	p.T992A	ENST00000259008	NM_032043.2	992	Act/Gct	20/20	0.331034296983289	1	FACETS	0.69	0.635	0.747	0.69	0.635	0.747	INDETERMINATE	1	TRUE	0	0.648354911258037	1		434	438	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141491	11141492	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0048549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	269	775	2	ENST00000358026.2:c.3468_3469delinsTT	p.Arg1157Trp	p.R1157W	ENST00000358026	NM_001128849.1	1156	acCCgg/acTTgg	25/36	1	2	FACETS	0.905	0.85	0.961	0.905	0.85	0.961	CLONAL	1	TRUE	1	0.648354911258037	2		777	917	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967140	25967140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	107	541	0	ENST00000435504.4:c.2066C>T	p.Thr689Ile	p.T689I	ENST00000435504		689	aCc/aTc	13/13	0.331034296983289	1	FACETS	0.389	0.349	0.43	0.389	0.349	0.43	INDETERMINATE	1	TRUE	0	0.648354911258037	1		541	574	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61720189	61720189	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0048549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	64	264	0	ENST00000401558.2:c.1246-1G>T		p.X416_splice	ENST00000401558	NM_003400.3	416			0.331034296983289	1	FACETS	0.399	0.348	0.455	0.399	0.348	0.455	INDETERMINATE	1	TRUE	0	0.648354911258037	1		264	334	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096236	178096236	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	211	453	0	ENST00000397062.3:c.1095C>A	p.Ser365Arg	p.S365R	ENST00000397062	NM_006164.4	365	agC/agA	5/5	0.331034296983289	1	FACETS	0.818	0.766	0.87	0.818	0.766	0.87	INDETERMINATE	1	TRUE	0	0.648354911258037	1		453	538	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332921	153332921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	188	340	0	ENST00000281708.4:c.35G>A	p.Arg12Lys	p.R12K	ENST00000281708	NM_033632.3	12	aGa/aAa	2/12	0.242410833304661	1	FACETS	1	0.987	1	1	0.987	1	INDETERMINATE	1	TRUE	0	0.648354911258037	1		340	336	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911479	131911479	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	109	275	0	ENST00000265335.6:c.224A>G	p.Glu75Gly	p.E75G	ENST00000265335		75	gAa/gGa	3/25	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.648354911258037	2		275	333	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858479	27858479	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	217	516	0	ENST00000359303.2:c.92C>T	p.Pro31Leu	p.P31L	ENST00000359303	NM_003535.2	31	cCa/cTa	1/1	1	2	FACETS	0.984	0.92	1	0.984	0.92	1	CLONAL	1	TRUE	1	0.648354911258037	2		516	680	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709044	117709053	+	frameshift_variant	Frame_Shift_Del	DEL	TCAGGTACAT	TCAGGTACAT	-	novel	NA	P-0048549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	115	528	0	ENST00000368508.3:c.1904_1913del	p.Asn635SerfsTer6	p.N635Sfs*6	ENST00000368508	NM_002944.2	635	aATGTACCTGAg/ag	13/43	0.331034296983289	1	FACETS	0.421	0.38	0.463	0.421	0.38	0.463	INDETERMINATE	1	TRUE	0	0.648354911258037	1		528	570	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997819	149997819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	120	540	0	ENST00000253339.5:c.2648C>T	p.Ser883Leu	p.S883L	ENST00000253339		883	tCa/tTa	5/7	0.331034296983289	1	FACETS	0.409	0.37	0.45	0.409	0.37	0.45	INDETERMINATE	1	TRUE	0	0.648354911258037	1		540	612	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340153	116340153	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463245808	NA	P-0048549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	125	249	0	ENST00000397752.3:c.1015G>A	p.Asp339Asn	p.D339N	ENST00000397752	NM_000245.2	339	Gat/Aat	2/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.648354911258037	2		249	352	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	147	576	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.514700154641632	2		576	513	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180542	56180543	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	50	278	0	ENST00000399503.3:c.3872dup	p.Arg1292LysfsTer17	p.R1292Kfs*17	ENST00000399503	NM_005921.1	1291	cta/cTta	16/20	1	2	FACETS	0.765	0.655	0.884	0.765	0.655	0.884	SUBCLONAL	1	TRUE	1	0.514700154641632	2		278	254	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435482	56435482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778996473	NA	P-0048550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	125	702	0	ENST00000407977.2:c.1655G>A	p.Arg552His	p.R552H	ENST00000407977		552	cGc/cAc	9/10	1	2	FACETS	0.64	0.579	0.704	0.64	0.579	0.704	SUBCLONAL	1	TRUE	1	0.514700154641632	2		702	759	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0048551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	533	833	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.430460199319462	3	FACETS	0.877	0.845	0.909	0.877	0.845	0.909	CLONAL	3	TRUE	0	0.474958850110285	3		833	1056	SUCCESS
APC	324	MSKCC	GRCh37	5	112175271	112175271	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	17	205	0	ENST00000257430.4:c.3980C>A	p.Ser1327Ter	p.S1327*	ENST00000257430	NM_000038.5	1327	tCa/tAa	16/16	0.452990463985155	2	FACETS	0.31	0.231	0.403	0.155	0.115	0.202	SUBCLONAL	1	TRUE	0	0.474958850110285	2		205	231	SUCCESS
APC	324	MSKCC	GRCh37	5	112175322	112175322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	18	176	0	ENST00000257430.4:c.4031C>T	p.Ser1344Leu	p.S1344L	ENST00000257430	NM_000038.5	1344	tCa/tTa	16/16	0.452990463985155	2	FACETS	0.337	0.254	0.434	0.168	0.127	0.217	SUBCLONAL	1	TRUE	0	0.474958850110285	2		176	225	SUCCESS
APC	324	MSKCC	GRCh37	5	112175262	112175262	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	16	209	0	ENST00000257430.4:c.3971C>T	p.Pro1324Leu	p.P1324L	ENST00000257430	NM_000038.5	1324	cCa/cTa	16/16	0.452990463985155	2	FACETS	0.297	0.219	0.389	0.148	0.109	0.195	SUBCLONAL	1	TRUE	0	0.474958850110285	2		209	227	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668821	52668821	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0048551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	183	249	0	ENST00000394830.3:c.1098T>G	p.Tyr366Ter	p.Y366*	ENST00000394830	NM_018313.4	366	taT/taG	12/30	0.430460199319462	3	FACETS	1	0.945	1	1	0.945	1	CLONAL	3	TRUE	0	0.474958850110285	3		249	317	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973136	55973991	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGACAATGAAGGAAAAGGTTCTAGGTAGATTCATTCAGGATACAGGAGGGAAGCAGCTATTCTGGGAATAAACCTTCATTCATAAATTGGATCGACAAGACAATTCAAGTTAATTTAGTTCAAAGGAAGGCAAGGAAACTTAGAAGCCACTGGGCTCCTTAAAGTAATTTCTCTGGGACCATGGTCTCTGTGAAGGAAATGATCAGCAGCTGAGGAAGAAGCTCATAGTGGCCATTTCAAAAACAACAACAGGAAGTGGACTGCTTAGGGTGGTGGTGGGTTGGCTGCTGTTGTTGTGTTTTTCCCTAAGGATGTCTGGACTTGTGTCAGAGCATGATAAGCTGGGCCTGAGACCCTGAGGACTGGGGCTGGGTCTATCACTGCCTCTCATCTATCAGCATTTCCTCTGAGAGATGGATCTTCACACACACAAGAAGGAGGGATGTGGTATTCACCAGCCGATTGGTATCGGGAGAAAAACCAAAGACTGGCAATTAGCAAACTGAGCAAATAGCCTGTGTTTGGAGAAGTGTACCTCACGGCTAACCTAACAAGGCTGAGCTTAGCTAACCCCAAAGGAGGATACTCCAAGCAAAGACATCCCCTAAAATGTAAGACACAGAGAAAGATGGATGGAGATTCAGGCTACCTCTTGAGAGAAAACTTTTTTTGGTTTAGGCTTCTCCATTTAGGATGGAGTCATATCATAGCTCAGCTGTAAGAAATGCAAGATGGCAGGAAAGCAAAGAGCATGTGGCCTTACTCACCTGGGCTCGTTGGCGCACTCTTCCTCCAACTGCCAATACCAGTGGATGTGATGCGGGGGAGGAATGGCATAGACCGTACATGTCAGCG	TTGACAATGAAGGAAAAGGTTCTAGGTAGATTCATTCAGGATACAGGAGGGAAGCAGCTATTCTGGGAATAAACCTTCATTCATAAATTGGATCGACAAGACAATTCAAGTTAATTTAGTTCAAAGGAAGGCAAGGAAACTTAGAAGCCACTGGGCTCCTTAAAGTAATTTCTCTGGGACCATGGTCTCTGTGAAGGAAATGATCAGCAGCTGAGGAAGAAGCTCATAGTGGCCATTTCAAAAACAACAACAGGAAGTGGACTGCTTAGGGTGGTGGTGGGTTGGCTGCTGTTGTTGTGTTTTTCCCTAAGGATGTCTGGACTTGTGTCAGAGCATGATAAGCTGGGCCTGAGACCCTGAGGACTGGGGCTGGGTCTATCACTGCCTCTCATCTATCAGCATTTCCTCTGAGAGATGGATCTTCACACACACAAGAAGGAGGGATGTGGTATTCACCAGCCGATTGGTATCGGGAGAAAAACCAAAGACTGGCAATTAGCAAACTGAGCAAATAGCCTGTGTTTGGAGAAGTGTACCTCACGGCTAACCTAACAAGGCTGAGCTTAGCTAACCCCAAAGGAGGATACTCCAAGCAAAGACATCCCCTAAAATGTAAGACACAGAGAAAGATGGATGGAGATTCAGGCTACCTCTTGAGAGAAAACTTTTTTTGGTTTAGGCTTCTCCATTTAGGATGGAGTCATATCATAGCTCAGCTGTAAGAAATGCAAGATGGCAGGAAAGCAAAGAGCATGTGGCCTTACTCACCTGGGCTCGTTGGCGCACTCTTCCTCCAACTGCCAATACCAGTGGATGTGATGCGGGGGAGGAATGGCATAGACCGTACATGTCAGCG	-	novel	NA	P-0048551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	21	57	0	ENST00000263923.4:c.1325_1413-159del		p.X442_splice	ENST00000263923	NM_002253.2	442		10/30	1	2	FACETS	1	0.8	1	1	0.8	1	CLONAL	1	TRUE	1	0.474958850110285	2		57	87	SUCCESS
APC	324	MSKCC	GRCh37	5	112175235	112175235	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	14	205	0	ENST00000257430.4:c.3944C>T	p.Ser1315Leu	p.S1315L	ENST00000257430	NM_000038.5	1315	tCa/tTa	16/16	0.452990463985155	2	FACETS	0.29	0.21	0.387	0.145	0.105	0.194	SUBCLONAL	1	TRUE	0	0.474958850110285	2		205	203	SUCCESS
APC	324	MSKCC	GRCh37	5	112175621	112175621	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1287444666	NA	P-0048551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	17	251	0	ENST00000257430.4:c.4330C>G	p.Gln1444Glu	p.Q1444E	ENST00000257430	NM_000038.5	1444	Caa/Gaa	16/16	0.452990463985155	2	FACETS	0.259	0.193	0.338	0.13	0.096	0.169	SUBCLONAL	1	TRUE	0	0.474958850110285	2		251	276	SUCCESS
APC	324	MSKCC	GRCh37	5	112176054	112176054	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0048551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	24	238	0	ENST00000257430.4:c.4763C>G	p.Ser1588Ter	p.S1588*	ENST00000257430	NM_000038.5	1588	tCa/tGa	16/16	0.452990463985155	2	FACETS	0.335	0.262	0.418	0.167	0.131	0.209	SUBCLONAL	1	TRUE	0	0.474958850110285	2		238	302	SUCCESS
APC	324	MSKCC	GRCh37	5	112176564	112176564	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	21	186	0	ENST00000257430.4:c.5273C>A	p.Ser1758Tyr	p.S1758Y	ENST00000257430	NM_000038.5	1758	tCt/tAt	16/16	0.452990463985155	2	FACETS	0.32	0.247	0.406	0.16	0.123	0.203	SUBCLONAL	1	TRUE	0	0.474958850110285	2		186	276	SUCCESS
APC	324	MSKCC	GRCh37	5	112177370	112177370	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	18	223	0	ENST00000257430.4:c.6079C>G	p.Leu2027Val	p.L2027V	ENST00000257430	NM_000038.5	2027	Ctc/Gtc	16/16	0.452990463985155	2	FACETS	0.3	0.226	0.387	0.15	0.113	0.194	SUBCLONAL	1	TRUE	0	0.474958850110285	2		223	253	SUCCESS
APC	324	MSKCC	GRCh37	5	112177751	112177751	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1003613894	NA	P-0048551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	12	221	0	ENST00000257430.4:c.6460C>G	p.Gln2154Glu	p.Q2154E	ENST00000257430	NM_000038.5	2154	Caa/Gaa	16/16	0.452990463985155	2	FACETS	0.232	0.163	0.317	0.116	0.081	0.159	SUBCLONAL	1	TRUE	0	0.474958850110285	2		221	218	SUCCESS
APC	324	MSKCC	GRCh37	5	112178084	112178084	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	24	278	0	ENST00000257430.4:c.6793C>G	p.Gln2265Glu	p.Q2265E	ENST00000257430	NM_000038.5	2265	Caa/Gaa	16/16	0.452990463985155	2	FACETS	0.317	0.248	0.396	0.158	0.124	0.198	SUBCLONAL	1	TRUE	0	0.474958850110285	2		278	319	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609948	43609948	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs75076352	NA	P-0048553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	307	766	0	ENST00000355710.3:c.1900T>C	p.Cys634Arg	p.C634R	ENST00000355710	NM_020975.4	634	Tgc/Cgc	11/20	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		766	848	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359363	118359363	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1131691433	NA	P-0048553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	22	301	0	ENST00000534358.1:c.4367A>G	p.His1456Arg	p.H1456R	ENST00000534358	NM_005933.3	1456	cAc/cGc	11/36	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		301	424	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0048554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	458	789	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.663121411574263	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.663121411574263	1		789	667	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70355027	70355027	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	81	687	0	ENST00000374080.3:c.4949C>A	p.Thr1650Lys	p.T1650K	ENST00000374080		1650	aCg/aAg	36/45	1	2	FACETS	0.328	0.289	0.371	0.328	0.289	0.371	SUBCLONAL	1	TRUE	1	0.663121411574263	2		687	744	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0048555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	151	495	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.851	0.785	0.918	0.851	0.785	0.918	CLONAL	1	TRUE	1	0.805026637543788	2		495	441	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0048555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	212	351	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.805026637543788	2		351	524	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813307	102813307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764732420	NA	P-0048555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	337	548	1	ENST00000307046.8:c.382G>A	p.Asp128Asn	p.D128N	ENST00000307046	NM_001111285.1	128	Gac/Aac	3/4	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.805026637543788	2		549	785	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589631	67589632	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATTATATGAAGA	novel	NA	P-0048555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	43	294	0	ENST00000274335.5:c.1397_1408dup	p.Leu466_Glu469dup	p.L466_E469dup	ENST00000274335		466	aga/agATTATATGAAGAa	10/15	1	2	FACETS	0.571	0.484	0.665	0.571	0.484	0.665	SUBCLONAL	1	TRUE	1	0.805026637543788	2		294	187	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467856	50467856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771544454	NA	P-0048555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	257	616	0	ENST00000331340.3:c.1091C>T	p.Ser364Leu	p.S364L	ENST00000331340	NM_006060.4	364	tCg/tTg	8/8	1	2	FACETS	0.993	0.936	1	0.993	0.936	1	CLONAL	1	TRUE	1	0.805026637543788	2		616	643	SUCCESS
MET	4233	MSKCC	GRCh37	7	116399528	116399528	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	200	342	0	ENST00000397752.3:c.2348G>A	p.Gly783Glu	p.G783E	ENST00000397752	NM_000245.2	783	gGa/gAa	10/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.805026637543788	2		342	470	SUCCESS
CBL	867	MSKCC	GRCh37	11	119146732	119146732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1053471259	NA	P-0048555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	257	481	0	ENST00000264033.4:c.895C>T	p.Arg299Cys	p.R299C	ENST00000264033	NM_005188.3	299	Cgt/Tgt	6/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.805026637543788	2		481	616	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22413029	22413029	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	109	184	0	ENST00000344548.3:c.276C>A	p.Asn92Lys	p.N92K	ENST00000344548	NM_001039802.1	92	aaC/aaA	5/7	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.805026637543788	2		184	253	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037867	49037869	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	ATT	ATT	-	novel	NA	P-0048555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	179	207	0	ENST00000267163.4:c.2109_2111del	p.Ile703del	p.I703del	ENST00000267163	NM_000321.2	703	ATT/-	21/27	0.805026637543788	3	FACETS	0.984	0.926	1	0.984	0.926	1	CLONAL	2	TRUE	1	0.805026637543788	3		207	317	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92300823	92300824	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0048555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	180	376	0	ENST00000265734.4:c.563_564delinsTT	p.Pro188Leu	p.P188L	ENST00000265734	NM_001259.6	188	cCC/cTT	5/8	1	2	FACETS	0.824	0.765	0.884	0.824	0.765	0.884	CLONAL	1	TRUE	1	0.805026637543788	2		376	543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0048557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	71	829	1	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	1	2	FACETS	0.713	0.62	0.813	0.713	0.62	0.813	SUBCLONAL	1	TRUE	1	0.21	2		830	949	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844211	68844212	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	42	524	0	ENST00000261769.5:c.799_800insA	p.Phe267TyrfsTer2	p.F267Yfs*2	ENST00000261769	NM_004360.3	267	ttt/tAtt	6/16	1	2	FACETS	0.644	0.537	0.764	0.644	0.537	0.764	SUBCLONAL	1	TRUE	1	0.21	2		524	621	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936004	49936004	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0048557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	82	728	0	ENST00000296474.3:c.1666A>T	p.Lys556Ter	p.K556*	ENST00000296474	NM_002447.2	556	Aag/Tag	4/20	1	2	FACETS	0.888	0.782	1	0.888	0.782	1	CLONAL	1	TRUE	1	0.21	2		728	879	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964972	55964972	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0048557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	24	174	0	ENST00000263923.4:c.2267-2A>T		p.X756_splice	ENST00000263923	NM_002253.2	756			1	2	FACETS	1	0.813	1	1	0.813	1	CLONAL	1	TRUE	1	0.21	2		174	221	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0048558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	83	347	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.782	0.691	0.879	0.782	0.691	0.879	SUBCLONAL	1	TRUE	1	0.379138091656246	2		347	560	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482864	67482864	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	265	489	0	ENST00000327367.4:c.1268G>T	p.Ser423Ile	p.S423I	ENST00000327367	NM_005902.3	423	aGt/aTt	9/9	NA	2	FACETS	0.915	0.861	0.969			1	INDETERMINATE	2	TRUE	NA	0.379138091656246	2		489	764	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974782	21974782	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs138677674	NA	P-0048558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	102	230	0	ENST00000304494.5:c.45G>A	p.Trp15Ter	p.W15*	ENST00000304494	NM_000077.4	15	tgG/tgA	1/3	0.379138091656246	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.379138091656246	1		230	303	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444216	49444216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	195	939	0	ENST00000301067.7:c.3155C>T	p.Pro1052Leu	p.P1052L	ENST00000301067	NM_003482.3	1052	cCc/cTc	11/54	1	2	FACETS	0.727	0.671	0.786	0.727	0.671	0.786	SUBCLONAL	1	TRUE	1	0.379138091656246	2		939	1415	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383273	42383274	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0048558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	88	665	0	ENST00000221972.3:c.295_296del	p.Ser99ProfsTer82	p.S99Pfs*82	ENST00000221972	NM_021601.3	98	aAG/a	2/5	1	2	FACETS	0.406	0.358	0.457	0.406	0.358	0.457	SUBCLONAL	1	TRUE	1	0.379138091656246	2		665	1143	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577595	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0048559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	248	497	0	ENST00000269305.4:c.686_687del	p.Cys229TyrfsTer10	p.C229Yfs*10	ENST00000269305	NM_001126112.2	229	tGT/t	7/11	0.484286020564769	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.502508393682457	2		497	490	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163298638	163298638	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	92	491	0	ENST00000271452.3:c.278A>G	p.Asp93Gly	p.D93G	ENST00000271452	NM_145697.2	93	gAc/gGc	5/14	0.198528832912215	3	FACETS	0.983	0.878	1	0.328	0.292	0.365	INDETERMINATE	1	TRUE	0	0.502508393682457	3		491	466	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36421157	36421157	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	40	265	0	ENST00000300305.3:c.40C>T	p.Pro14Ser	p.P14S	ENST00000300305		14	Cca/Tca	1/8	0.166678813933585	6	FACETS	0.812	0.676	0.963	0.271	0.225	0.321	INDETERMINATE	1	TRUE	3	0.502508393682457	6		265	393	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	197	301	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.952	0.887	1	0.952	0.887	1	CLONAL	1	TRUE	1	0.700431883745827	2		301	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934578	NA	P-0048560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	609	649	0	ENST00000269305.4:c.524G>T	p.Arg175Leu	p.R175L	ENST00000269305	NM_001126112.2	175	cGc/cTc	5/11	0.682131703848064	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.700431883745827	1		649	1121	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0048560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	225	262	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	0.700431883745827	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.700431883745827	1		262	404	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023471	27023471	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	308	512	1	ENST00000324856.7:c.577G>T	p.Glu193Ter	p.E193*	ENST00000324856	NM_006015.4	193	Gag/Tag	1/20	0.230895266452111	1	FACETS	0.553	0.521	0.585	0.553	0.521	0.585	INDETERMINATE	1	TRUE	0	0.700431883745827	1		513	1034	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527428	137527428	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	63	199	0	ENST00000367739.4:c.218G>A	p.Trp73Ter	p.W73*	ENST00000367739	NM_000416.2	73	tGg/tAg	3/7	0.36730876589068	1	FACETS	0.425	0.371	0.483	0.425	0.371	0.483	INDETERMINATE	1	TRUE	0	0.700431883745827	1		199	275	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879854	37879854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1260	547	659	0	ENST00000269571.5:c.2149G>A	p.Glu717Lys	p.E717K	ENST00000269571		717	Gag/Aag	18/27	0.341494112318033	3	FACETS	1	0.993	1	0.584	0.559	0.609	INDETERMINATE	1	TRUE	1	0.700431883745827	3		659	1807	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922884	44922884	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0048560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	334	394	0	ENST00000377967.4:c.1745C>G	p.Ser582Ter	p.S582*	ENST00000377967	NM_021140.2	582	tCa/tGa	16/29	1	2	FACETS	0.992	0.941	1	0.992	0.941	1	CLONAL	1	TRUE	1	0.700431883745827	2		394	961	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519244	187519245	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0048560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	274	369	0	ENST00000441802.2:c.12138dup	p.Thr4047AspfsTer4	p.T4047Dfs*4	ENST00000441802	NM_005245.3	4046	-/G	23/27	0.348980039677369	1	FACETS	0.727	0.687	0.768	0.727	0.687	0.768	INDETERMINATE	1	TRUE	0	0.700431883745827	1		369	699	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863449	57863449	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781683841	NA	P-0048560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	451	509	1	ENST00000228682.2:c.1544G>A	p.Arg515Gln	p.R515Q	ENST00000228682	NM_005269.2	515	cGg/cAg	11/12	1	2	FACETS	0.999	0.954	1	0.999	0.954	1	CLONAL	1	TRUE	1	0.700431883745827	2		510	1289	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955381	48955381	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0048560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	51	146	0	ENST00000267163.4:c.1499-2A>G		p.X500_splice	ENST00000267163	NM_000321.2	500			0.700431883745827	1	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	0	0.700431883745827	1		146	94	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289085	33289085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	555	584	1	ENST00000374542.5:c.467C>T	p.Ser156Phe	p.S156F	ENST00000374542	NM_001141970.1	156	tCt/tTt	3/8	0.230895266452111	1	FACETS	0.751	0.722	0.781	0.751	0.722	0.781	INDETERMINATE	1	TRUE	0	0.700431883745827	1		585	1371	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859595	151859595	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	304	382	0	ENST00000262189.6:c.11067C>G	p.Phe3689Leu	p.F3689L	ENST00000262189	NM_170606.2	3689	ttC/ttG	43/59	1	2	FACETS	0.962	0.909	1	0.962	0.909	1	CLONAL	1	TRUE	1	0.700431883745827	2		382	902	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941061	36941061	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	550	658	0	ENST00000361632.4:c.278A>G	p.Asn93Ser	p.N93S	ENST00000361632		93	aAc/aGc	3/16	0.230895266452111	1	FACETS	0.767	0.737	0.797	0.767	0.737	0.797	INDETERMINATE	1	TRUE	0	0.700431883745827	1		658	1330	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194802	30194802	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	175	447	1	ENST00000331968.5:c.343C>T	p.Gln115Ter	p.Q115*	ENST00000331968	NM_002742.2	115	Cag/Tag	2/18	0.299409179668893	1	FACETS	0.474	0.438	0.512	0.474	0.438	0.512	INDETERMINATE	1	TRUE	0	0.700431883745827	1		448	685	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59934566	59934566	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	136	201	0	ENST00000259008.2:c.232G>C	p.Glu78Gln	p.E78Q	ENST00000259008	NM_032043.2	78	Gaa/Caa	4/20	0.364207915059779	1	FACETS	0.804	0.742	0.865	0.804	0.742	0.865	INDETERMINATE	1	TRUE	0	0.700431883745827	1		201	314	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153252004	153252005	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	70	297	0	ENST00000281708.4:c.1001dup	p.Leu334PhefsTer29	p.L334Ffs*29	ENST00000281708	NM_033632.3	334	ttg/ttTg	7/12	0.348980039677369	1	FACETS	0.476	0.419	0.535	0.476	0.419	0.535	INDETERMINATE	1	TRUE	0	0.700431883745827	1		297	273	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220252	55220252	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	567	606	0	ENST00000275493.2:c.642C>G	p.Ile214Met	p.I214M	ENST00000275493	NM_005228.3	214	atC/atG	6/28	1	2	FACETS	0.999	0.959	1	0.999	0.959	1	CLONAL	1	TRUE	1	0.700431883745827	2		606	1621	SUCCESS
AR	367	MSKCC	GRCh37	X	66937463	66937463	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	353	411	0	ENST00000374690.3:c.2317G>A	p.Glu773Lys	p.E773K	ENST00000374690	NM_000044.3	773	Gag/Aag	5/8	1	2	FACETS	0.966	0.917	1	0.966	0.917	1	CLONAL	1	TRUE	1	0.700431883745827	2		411	1043	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845349	76845349	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1473492502	NA	P-0048560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	95	286	0	ENST00000373344.5:c.6172A>G	p.Ser2058Gly	p.S2058G	ENST00000373344	NM_000489.3	2058	Agt/Ggt	27/35	NA	2	FACETS	1	0.905	1			1	INDETERMINATE	1	TRUE	NA	0.700431883745827	2		286	271	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577067	7577067	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0048579-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	553	683	0	ENST00000269305.4:c.871A>T	p.Lys291Ter	p.K291*	ENST00000269305	NM_001126112.2	291	Aag/Tag	8/11	0.782369507483885	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.777803190700131	1		683	670	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	24	301	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		301	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0048583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	135	687	0	ENST00000269305.4:c.376-1G>T		p.X126_splice	ENST00000269305	NM_001126112.2	126			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		687	851	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739035	46739035	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	33	429	0	ENST00000371975.4:c.1384C>G	p.Leu462Val	p.L462V	ENST00000371975	NM_003579.3	462	Cta/Gta	13/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		429	482	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737148	162737148	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	40	376	0	ENST00000367921.3:c.1292A>T	p.Lys431Met	p.K431M	ENST00000367921	NM_006182.2	431	aAg/aTg	11/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		376	506	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69458637	69458637	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	44	459	0	ENST00000227507.2:c.452A>G	p.Asn151Ser	p.N151S	ENST00000227507	NM_053056.2	151	aAc/aGc	3/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		459	579	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965170	25965170	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	75	556	0	ENST00000435504.4:c.4036C>G	p.Pro1346Ala	p.P1346A	ENST00000435504		1346	Cca/Gca	13/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		556	755	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913517	NA	P-0048586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	168	233	0	ENST00000288135.5:c.1676T>A	p.Val559Asp	p.V559D	ENST00000288135	NM_000222.2	559	gTt/gAt	11/21	1	2	FACETS	0.866	0.8	0.934	0.866	0.8	0.934	CLONAL	1	TRUE	1	0.667696432164169	2		233	581	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277547	142277547	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	141	212	1	ENST00000350721.4:c.1804C>A	p.His602Asn	p.H602N	ENST00000350721	NM_001184.3	602	Cat/Aat	8/47	1	2	FACETS	0.978	0.899	1	0.978	0.899	1	CLONAL	1	TRUE	1	0.667696432164169	2		213	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0048587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	83	898	1	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	1	2	FACETS	0.682	0.601	0.77	0.682	0.601	0.77	SUBCLONAL	1	FALSE	1	0.276131722031806	2		899	881	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692977	89692977	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	49	575	0	ENST00000371953.3:c.461T>G	p.Phe154Cys	p.F154C	ENST00000371953	NM_000314.4	154	tTc/tGc	5/9	1	2	FACETS	0.495	0.418	0.58	0.495	0.418	0.58	SUBCLONAL	1	FALSE	1	0.276131722031806	2		575	717	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658225	18658225	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0048587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	42	576	0	ENST00000266497.5:c.3031-1G>T		p.X1011_splice	ENST00000266497		1011			1	2	FACETS	0.496	0.413	0.588	0.496	0.413	0.588	SUBCLONAL	1	FALSE	1	0.276131722031806	2		576	613	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885247	111885247	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1332773263	NA	P-0048587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	59	796	0	ENST00000341259.2:c.1135C>G	p.Gln379Glu	p.Q379E	ENST00000341259	NM_005475.2	379	Cag/Gag	6/8	1	2	FACETS	0.476	0.408	0.55	0.476	0.408	0.55	SUBCLONAL	1	FALSE	1	0.276131722031806	2		796	898	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849512	89849512	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0048587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	96	581	0	ENST00000389301.3:c.1471-2A>G		p.X491_splice	ENST00000389301	NM_000135.2	491			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	1	0.276131722031806	2		581	635	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30323856	30323856	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	60	435	1	ENST00000322652.5:c.1834G>T	p.Glu612Ter	p.E612*	ENST00000322652	NM_015355.2	612	Gaa/Taa	15/16	1	2	FACETS	0.76	0.655	0.874	0.76	0.655	0.874	SUBCLONAL	1	FALSE	1	0.276131722031806	2		436	572	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677876	47677876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	125	606	0	ENST00000347630.2:c.989C>T	p.Ser330Leu	p.S330L	ENST00000347630	NM_001007230.1	330	tCg/tTg	11/11	0.156653973782513	2	FACETS	1	0.974	1	0.608	0.551	0.669	INDETERMINATE	1	FALSE	0	0.276131722031806	2		606	744	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169543	11169543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	73	711	0	ENST00000358026.2:c.4709C>T	p.Thr1570Ile	p.T1570I	ENST00000358026	NM_001128849.1	1570	aCc/aTc	33/36	0.276131722031806	1	FACETS	0.563	0.491	0.64	0.563	0.491	0.64	SUBCLONAL	1	FALSE	0	0.276131722031806	1		711	810	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873410	136873410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	36	568	0	ENST00000241393.3:c.88C>T	p.Arg30Cys	p.R30C	ENST00000241393	NM_003467.2	30	Cgt/Tgt	2/2	1	2	FACETS	0.368	0.302	0.443	0.368	0.302	0.443	SUBCLONAL	1	FALSE	1	0.276131722031806	2		568	708	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267912	46267912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	66	678	1	ENST00000371998.3:c.2673G>A	p.Met891Ile	p.M891I	ENST00000371998		891	atG/atA	14/23	1	2	FACETS	0.517	0.447	0.593	0.517	0.447	0.593	SUBCLONAL	1	FALSE	1	0.276131722031806	2		679	925	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409419	31409419	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs771619776	NA	P-0048587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	95	553	0	ENST00000344624.3:c.3688A>G	p.Ile1230Val	p.I1230V	ENST00000344624		1230	Att/Gtt	29/33	0.185121765200482	3	FACETS	1	0.914	1	0.516	0.459	0.577	CLONAL	1	FALSE	1	0.276131722031806	3		553	759	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956612	93956612	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	48	540	0	ENST00000369303.4:c.2624del	p.Lys875ArgfsTer12	p.K875Rfs*12	ENST00000369303	NM_004440.3	875	aAg/ag	15/17	1	2	FACETS	0.559	0.472	0.655	0.559	0.472	0.655	SUBCLONAL	1	FALSE	1	0.276131722031806	2		540	622	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371968	55371968	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	50	382	0	ENST00000297316.4:c.658C>A	p.Pro220Thr	p.P220T	ENST00000297316	NM_022454.3	220	Ccc/Acc	2/2	0.185121765200482	3	FACETS	0.694	0.588	0.81	0.347	0.294	0.405	SUBCLONAL	1	FALSE	1	0.276131722031806	3		382	594	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339311	70339311	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	46	615	0	ENST00000374080.3:c.188G>T	p.Ser63Ile	p.S63I	ENST00000374080		63	aGc/aTc	2/45	1	2	FACETS	0.436	0.366	0.513	0.436	0.366	0.513	SUBCLONAL	1	FALSE	1	0.276131722031806	2		615	765	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0048588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	417	882	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.619914099891213	2		882	621	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965472	68965472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200682883	NA	P-0048588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	109	707	1	ENST00000288368.4:c.1084C>T	p.Arg362Trp	p.R362W	ENST00000288368	NM_024870.2	362	Cgg/Tgg	9/40	0.619914099891213	6	FACETS	0.768	0.688	0.853	0.154	0.137	0.171	SUBCLONAL	1	TRUE	1	0.619914099891213	6		708	1026	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298720	46298720	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1444599005	NA	P-0048588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	84	353	0	ENST00000334344.6:c.5367G>T	p.Leu1789Phe	p.L1789F	ENST00000334344	NM_152641.2	1789	ttG/ttT	21/21	0.553354134584308	3	FACETS	0.981	0.873	1			1	CLONAL	1	TRUE	NA	0.619914099891213	3		353	362	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820942	3820942	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	210	836	0	ENST00000262367.5:c.2509G>A	p.Gly837Arg	p.G837R	ENST00000262367	NM_004380.2	837	Ggg/Agg	14/31	0.354228372440564	4	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.619914099891213	4		836	1018	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538180	187538180	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	122	562	0	ENST00000441802.2:c.9054C>G	p.Asp3018Glu	p.D3018E	ENST00000441802	NM_005245.3	3018	gaC/gaG	11/27	0.619914099891213	3	FACETS	0.908	0.824	0.996	0.454	0.412	0.498	CLONAL	1	TRUE	1	0.619914099891213	3		562	568	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0048589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	313	774	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.873	0.829	0.918	0.873	0.829	0.918	CLONAL	1	TRUE	1	0.960927693899895	2		778	746	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	35	434	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.133	0.109	0.161	0.133	0.109	0.161	SUBCLONAL	1	TRUE	1	0.960927693899895	2		435	547	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0048589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	92	350	3	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.529	0.474	0.587	0.529	0.474	0.587	SUBCLONAL	1	TRUE	1	0.960927693899895	2		353	362	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	191	589	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.493	0.457	0.531	0.493	0.457	0.531	SUBCLONAL	1	TRUE	1	0.960927693899895	2		589	806	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	169	622	6	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.532	0.491	0.575	0.532	0.491	0.575	SUBCLONAL	1	TRUE	1	0.960927693899895	2		628	661	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272493	11272493	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	175	575	0	ENST00000361445.4:c.3437T>G	p.Leu1146Arg	p.L1146R	ENST00000361445	NM_004958.3	1146	cTg/cGg	23/58	1	2	FACETS	0.537	0.496	0.58	0.537	0.496	0.58	SUBCLONAL	1	TRUE	1	0.960927693899895	2		575	678	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248289	59248289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	27	140	0	ENST00000371222.2:c.454G>A	p.Gly152Arg	p.G152R	ENST00000371222	NM_002228.3	152	Ggg/Agg	1/1	1	2	FACETS	0.375	0.301	0.456	0.375	0.301	0.456	SUBCLONAL	1	TRUE	1	0.960927693899895	2		140	150	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692911	89692911	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121909241	NA	P-0048589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	175	497	0	ENST00000371953.3:c.395G>T	p.Gly132Val	p.G132V	ENST00000371953	NM_000314.4	132	gGt/gTt	5/9	0.555180367747044	2	FACETS	1	0.985	1	0.582	0.547	0.617	INDETERMINATE	1	TRUE	0	0.960927693899895	2		497	313	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924738	94924738	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	151	633	0	ENST00000536441.1:c.172C>G	p.Arg58Gly	p.R58G	ENST00000536441	NM_144665.3	58	Cgt/Ggt	3/10	1	2	FACETS	0.59	0.542	0.639	0.59	0.542	0.639	SUBCLONAL	1	TRUE	1	0.960927693899895	2		633	533	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438211	49438211	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	194	630	2	ENST00000301067.7:c.5058del	p.Lys1686AsnfsTer36	p.K1686Nfs*36	ENST00000301067	NM_003482.3	1686	aaA/aa	20/54	1	2	FACETS	0.451	0.418	0.486	0.451	0.418	0.486	SUBCLONAL	1	TRUE	1	0.960927693899895	2		632	895	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0048589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	167	699	16	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.454	0.417	0.492	0.454	0.417	0.492	SUBCLONAL	1	TRUE	1	0.960927693899895	2		715	766	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252351	133252351	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	162	455	0	ENST00000320574.5:c.1076T>C	p.Met359Thr	p.M359T	ENST00000320574	NM_006231.2	359	aTg/aCg	11/49	1	2	FACETS	0.502	0.462	0.544	0.502	0.462	0.544	SUBCLONAL	1	TRUE	1	0.960927693899895	2		455	671	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987172	36987172	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	168	602	1	ENST00000354822.5:c.517C>A	p.Leu173Met	p.L173M	ENST00000354822	NM_001079668.2	173	Ctg/Atg	3/3	1	2	FACETS	0.509	0.469	0.55	0.509	0.469	0.55	SUBCLONAL	1	TRUE	1	0.960927693899895	2		603	687	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560487	65560487	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	185	574	0	ENST00000358664.4:c.110A>C	p.Asp37Ala	p.D37A	ENST00000358664	NM_002382.4	37	gAc/gCc	3/5	1	2	FACETS	0.575	0.533	0.618	0.575	0.533	0.618	SUBCLONAL	1	TRUE	1	0.960927693899895	2		574	670	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43771610	43771610	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	155	537	0	ENST00000382044.4:c.773del	p.Asn258IlefsTer165	p.N258Ifs*165	ENST00000382044	NM_001141980.1	258	aAt/at	7/28	1	2	FACETS	0.515	0.473	0.559	0.515	0.473	0.559	SUBCLONAL	1	TRUE	1	0.960927693899895	2		537	626	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136754	2136754	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs137854221	NA	P-0048589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	175	734	0	ENST00000219476.3:c.4871T>C	p.Leu1624Pro	p.L1624P	ENST00000219476	NM_000548.3	1624	cTg/cCg	38/42	1	2	FACETS	0.375	0.345	0.406	0.375	0.345	0.406	SUBCLONAL	1	TRUE	1	0.960927693899895	2		734	972	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782242	56782242	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	195	557	0	ENST00000308159.5:c.83A>G	p.His28Arg	p.H28R	ENST00000308159	NM_014669.4	28	cAt/cGt	2/22	1	2	FACETS	0.516	0.478	0.555	0.516	0.478	0.555	SUBCLONAL	1	TRUE	1	0.960927693899895	2		557	787	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830426	72830426	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	83	331	0	ENST00000268489.5:c.6155del	p.Pro2052ArgfsTer49	p.P2052Rfs*49	ENST00000268489	NM_006885.3	2052	cCg/cg	9/10	1	2	FACETS	0.443	0.393	0.496	0.443	0.393	0.496	SUBCLONAL	1	TRUE	1	0.960927693899895	2		331	390	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341589	89341589	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	29	443	0	ENST00000301030.4:c.7481del	p.Pro2494LeufsTer8	p.P2494Lfs*8	ENST00000301030	NM_001256183.1	2494	cCt/ct	10/13	1	2	FACETS	0.126	0.101	0.155	0.126	0.101	0.155	SUBCLONAL	1	TRUE	1	0.960927693899895	2		443	478	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0048589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	197	755	2	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.433	0.401	0.467	0.433	0.401	0.467	SUBCLONAL	1	TRUE	1	0.960927693899895	2		757	946	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390434	56390434	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	69	342	0	ENST00000348428.3:c.1173G>C	p.Met391Ile	p.M391I	ENST00000348428	NM_006785.3	391	atG/atC	10/17	1	2	FACETS	0.469	0.412	0.53	0.469	0.412	0.53	SUBCLONAL	1	TRUE	1	0.960927693899895	2		342	306	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211137	36211138	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0048589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	237	811	1	ENST00000222270.7:c.888_889delinsTT	p.Arg297Ter	p.R297*	ENST00000222270	NM_014727.1	296	ggCCga/ggTTga	3/37	1	2	FACETS	0.501	0.467	0.535	0.501	0.467	0.535	SUBCLONAL	1	TRUE	1	0.960927693899895	2		812	985	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791286	42791286	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs61741480	NA	P-0048589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	179	693	0	ENST00000575354.2:c.346G>T	p.Val116Leu	p.V116L	ENST00000575354	NM_015125.3	116	Gtg/Ttg	3/20	1	2	FACETS	0.499	0.461	0.538	0.499	0.461	0.538	SUBCLONAL	1	TRUE	1	0.960927693899895	2		693	747	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436911	29436911	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	170	639	0	ENST00000389048.3:c.3682C>T	p.His1228Tyr	p.H1228Y	ENST00000389048	NM_004304.4	1228	Cac/Tac	24/29	1	2	FACETS	0.46	0.423	0.497	0.46	0.423	0.497	SUBCLONAL	1	TRUE	1	0.960927693899895	2		639	770	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035092	30035092	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	97	406	0	ENST00000338641.4:c.254A>G	p.Asp85Gly	p.D85G	ENST00000338641	NM_000268.3	85	gAt/gGt	3/16	1	2	FACETS	0.474	0.425	0.525	0.474	0.425	0.525	SUBCLONAL	1	TRUE	1	0.960927693899895	2		406	426	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952073	178952073	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519937	NA	P-0048589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	65	430	0	ENST00000263967.3:c.3128T>C	p.Met1043Thr	p.M1043T	ENST00000263967	NM_006218.2	1043	aTg/aCg	21/21	1	2	FACETS	0.448	0.391	0.508	0.448	0.391	0.508	SUBCLONAL	1	TRUE	1	0.960927693899895	2		430	302	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591270	67591270	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1289880098	NA	P-0048589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	75	408	0	ENST00000274335.5:c.1768C>T	p.Arg590Trp	p.R590W	ENST00000274335		590	Cgg/Tgg	13/15	1	2	FACETS	0.5	0.442	0.562	0.5	0.442	0.562	SUBCLONAL	1	TRUE	1	0.960927693899895	2		408	312	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401544	401544	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	130	561	0	ENST00000380956.4:c.866A>G	p.Gln289Arg	p.Q289R	ENST00000380956	NM_001195286.1	289	cAg/cGg	7/9	1	2	FACETS	0.454	0.413	0.497	0.454	0.413	0.497	SUBCLONAL	1	TRUE	1	0.960927693899895	2		561	596	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467774	50467774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148169768	NA	P-0048589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	203	683	0	ENST00000331340.3:c.1009G>A	p.Gly337Ser	p.G337S	ENST00000331340	NM_006060.4	337	Ggt/Agt	8/8	1	2	FACETS	0.547	0.509	0.587	0.547	0.509	0.587	SUBCLONAL	1	TRUE	1	0.960927693899895	2		683	772	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434510	140434510	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	106	347	0	ENST00000288602.6:c.2188G>T	p.Glu730Ter	p.E730*	ENST00000288602	NM_004333.4	730	Gaa/Taa	18/18	1	2	FACETS	0.472	0.426	0.522	0.472	0.426	0.522	SUBCLONAL	1	TRUE	1	0.960927693899895	2		347	467	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971098	21971099	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0048589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	94	411	0	ENST00000304494.5:c.259dup	p.Arg87ProfsTer33	p.R87Pfs*33	ENST00000304494	NM_000077.4	87	cgg/cCgg	2/3	1	2	FACETS	0.36	0.321	0.402	0.36	0.321	0.402	SUBCLONAL	1	TRUE	1	0.960927693899895	2		411	543	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	140	457	0	ENST00000304494.5:c.172del	p.Arg58GlufsTer88	p.R58Efs*88	ENST00000304494	NM_000077.4	58	Cga/ga	2/3	1	2	FACETS	0.478	0.437	0.522	0.478	0.437	0.522	SUBCLONAL	1	TRUE	1	0.960927693899895	2		457	609	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	19	301	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.524	0.397	0.673	0.524	0.397	0.673	SUBCLONAL	1	FALSE	1	0.228217356142568	2		301	318	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143341	30143341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	47	512	0	ENST00000389048.3:c.185C>T	p.Ser62Leu	p.S62L	ENST00000389048	NM_004304.4	62	tCg/tTg	1/29	1	2	FACETS	0.741	0.625	0.869	0.741	0.625	0.869	SUBCLONAL	1	FALSE	1	0.228217356142568	2		512	556	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696719	47696719	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	18	375	0	ENST00000347630.2:c.229G>C	p.Asp77His	p.D77H	ENST00000347630	NM_001007230.1	77	Gat/Cat	5/11	1	2	FACETS	0.674	0.508	0.869	0.674	0.508	0.869	SUBCLONAL	1	FALSE	1	0.228217356142568	2		375	234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577572	7577572	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882004	NA	P-0048590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	34	540	0	ENST00000269305.4:c.709A>G	p.Met237Val	p.M237V	ENST00000269305	NM_001126112.2	237	Atg/Gtg	7/11	1	2	FACETS	0.494	0.403	0.598	0.494	0.403	0.598	SUBCLONAL	1	FALSE	1	0.228217356142568	2		540	603	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564485	41564485	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	17	388	0	ENST00000263253.7:c.3907G>C	p.Glu1303Gln	p.E1303Q	ENST00000263253	NM_001429.3	1303	Gag/Cag	24/31	1	2	FACETS	0.463	0.345	0.603	0.463	0.345	0.603	SUBCLONAL	1	FALSE	1	0.228217356142568	2		388	322	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303244	11303244	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1392170596	NA	P-0048590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	38	645	0	ENST00000361445.4:c.1339G>A	p.Glu447Lys	p.E447K	ENST00000361445	NM_004958.3	447	Gag/Aag	9/58	1	2	FACETS	0.498	0.41	0.596	0.498	0.41	0.596	SUBCLONAL	1	FALSE	1	0.228217356142568	2		645	669	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105238746	105238746	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749544983	NA	P-0048590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	55	650	1	ENST00000349310.3:c.1216C>T	p.Arg406Cys	p.R406C	ENST00000349310	NM_001014432.1	406	Cgc/Tgc	13/15	0.228217356142568	1	FACETS	0.562	0.479	0.652	0.562	0.479	0.652	SUBCLONAL	1	FALSE	0	0.228217356142568	1		651	760	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519518	137519518	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs963564493	NA	P-0048590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	15	395	0	ENST00000367739.4:c.1120A>G	p.Ile374Val	p.I374V	ENST00000367739	NM_000416.2	374	Ata/Gta	7/7	1	2	FACETS	0.48	0.35	0.635	0.48	0.35	0.635	SUBCLONAL	1	FALSE	1	0.228217356142568	2		395	274	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	334	301	0				ENST00000310581	NM_198253.2	-/1132			0.388722458215444	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.388722458215444	3		301	641	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936995	48936995	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778842	NA	P-0048591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	141	479	0	ENST00000267163.4:c.763C>T	p.Arg255Ter	p.R255*	ENST00000267163	NM_000321.2	255	Cga/Tga	8/27	0.388722458215444	1	FACETS	0.841	0.768	0.917	0.841	0.768	0.917	CLONAL	1	TRUE	0	0.388722458215444	1		479	695	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288486	15288486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	264	300	0	ENST00000263388.2:c.4253C>T	p.Ser1418Leu	p.S1418L	ENST00000263388	NM_000435.2	1418	tCg/tTg	24/33	0.388188097620076	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.388722458215444	3		300	658	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912185	114912185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs976821949	NA	P-0048591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	96	670	1	ENST00000543371.1:c.1255G>A	p.Ala419Thr	p.A419T	ENST00000543371	NM_001198531.1	419	Gcg/Acg	11/14	0.347517081668084	1	FACETS	0.439	0.39	0.491	0.439	0.39	0.491	SUBCLONAL	1	TRUE	0	0.388722458215444	1		671	906	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223262	36223262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1407	266	937	0	ENST00000222270.7:c.5812C>T	p.Gln1938Ter	p.Q1938*	ENST00000222270	NM_014727.1	1938	Cag/Tag	28/37	0.316801595462069	3	FACETS	0.977	0.913	1			1	CLONAL	1	TRUE	NA	0.388722458215444	3		937	1673	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683453	88683453	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	10	21	0	ENST00000372037.3:c.1576G>C	p.Glu526Gln	p.E526Q	ENST00000372037	NM_004329.2	526	Gaa/Caa	13/13	NA	2	FACETS	1	0.83	1			1	INDETERMINATE	1	TRUE	NA	0.388722458215444	2		21	39	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436971	49436971	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0048591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	164	711	2	ENST00000301067.7:c.5534-2A>T		p.X1845_splice	ENST00000301067	NM_003482.3	1845			1	2	FACETS	0.809	0.742	0.879	0.809	0.742	0.879	CLONAL	1	TRUE	1	0.388722458215444	2		713	1043	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423546	88423546	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	140	707	0	ENST00000360948.2:c.2289C>G	p.Ile763Met	p.I763M	ENST00000360948	NM_001012338.2	763	atC/atG	18/19	0.388722458215444	1	FACETS	0.675	0.614	0.738	0.675	0.614	0.738	SUBCLONAL	1	TRUE	0	0.388722458215444	1		707	860	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81916914	81916914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	99	704	0	ENST00000359376.3:c.733G>A	p.Asp245Asn	p.D245N	ENST00000359376	NM_002661.3	245	Gac/Aac	9/33	0.285156185492271	1	FACETS	0.446	0.397	0.497	0.446	0.397	0.497	SUBCLONAL	1	TRUE	0	0.388722458215444	1		704	921	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366198	15366198	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	206	801	0	ENST00000263377.2:c.1957G>T	p.Glu653Ter	p.E653*	ENST00000263377	NM_058243.2	653	Gaa/Taa	10/20	0.388188097620076	3	FACETS	1	0.94	1	0.508	0.471	0.548	CLONAL	1	TRUE	1	0.388722458215444	3		801	1245	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159155	143159155	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	50	365	0	ENST00000262992.4:c.698A>T	p.Asn233Ile	p.N233I	ENST00000262992	NM_001101669.1	233	aAc/aTc	10/24	1	2	FACETS	0.558	0.474	0.65	0.558	0.474	0.65	SUBCLONAL	1	TRUE	1	0.388722458215444	2		365	461	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652084	36652111	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGCCTTGGCCTGCCCAAGCTCTACCT	GGGGCCTTGGCCTGCCCAAGCTCTACCT	-	novel	NA	P-0048591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	462	861	0	ENST00000244741.5:c.206_233del	p.Arg69LeufsTer70	p.R69Lfs*70	ENST00000244741	NM_000389.4	69	cGGGGCCTTGGCCTGCCCAAGCTCTACCTt/ct	2/3	0.388722458215444	3	FACETS	0.976	0.931	1	0.976	0.931	1	CLONAL	2	TRUE	1	0.388722458215444	3		861	1455	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335637	81335637	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	143	571	0	ENST00000222390.5:c.1723G>T	p.Glu575Ter	p.E575*	ENST00000222390	NM_000601.4	575	Gaa/Taa	15/18	1	2	FACETS	0.913	0.833	0.997	0.913	0.833	0.997	CLONAL	1	TRUE	1	0.388722458215444	2		571	806	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372398	55372398	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	201	765	0	ENST00000297316.4:c.1088T>A	p.Phe363Tyr	p.F363Y	ENST00000297316	NM_022454.3	363	tTt/tAt	2/2	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.388722458215444	2		765	1021	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0048592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	445	495	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.799460002239768	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.837884457797137	3		495	748	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0048592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	34	528	2	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.837884457797137	1	FACETS	0.124	0.101	0.15	0.124	0.101	0.15	SUBCLONAL	1	TRUE	0	0.837884457797137	1		530	380	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178942545	178942545	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	175	473	0	ENST00000263967.3:c.2352G>C	p.Glu784Asp	p.E784D	ENST00000263967	NM_006218.2	784	gaG/gaC	16/21	1	2	FACETS	0.906	0.843	0.971	0.906	0.843	0.971	CLONAL	1	TRUE	1	0.837884457797137	2		473	461	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405201	139405201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767886377	NA	P-0048592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	368	868	1	ENST00000277541.6:c.2644G>A	p.Ala882Thr	p.A882T	ENST00000277541	NM_017617.3	882	Gca/Aca	17/34	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.837884457797137	2		869	861	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125235	47125235	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	207	515	0	ENST00000409792.3:c.6035T>C	p.Leu2012Pro	p.L2012P	ENST00000409792	NM_014159.6	2012	cTc/cCc	12/21	1	2	FACETS	0.956	0.895	1	0.956	0.895	1	CLONAL	1	TRUE	1	0.837884457797137	2		515	517	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240233	5240233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202189767	NA	P-0048592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	343	838	2	ENST00000357368.4:c.1681C>T	p.Arg561Trp	p.R561W	ENST00000357368	NM_002850.3	561	Cgg/Tgg	12/38	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.837884457797137	2		840	812	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628173	187628173	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs547340067	NA	P-0048592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	375	782	0	ENST00000441802.2:c.2809C>T	p.Arg937Ter	p.R937*	ENST00000441802	NM_005245.3	937	Cga/Tga	2/27	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.837884457797137	2		782	886	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447389	49447389	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	389	827	0	ENST00000301067.7:c.709G>T	p.Glu237Ter	p.E237*	ENST00000301067	NM_003482.3	237	Gag/Tag	6/54	0.383416037902998	1	FACETS	0.717	0.686	0.747	0.717	0.686	0.747	INDETERMINATE	1	TRUE	0	0.837884457797137	1		827	753	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434423	49434423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	352	857	0	ENST00000301067.7:c.7130C>T	p.Pro2377Leu	p.P2377L	ENST00000301067	NM_003482.3	2377	cCa/cTa	31/54	0.383416037902998	1	FACETS	0.713	0.681	0.744	0.713	0.681	0.744	INDETERMINATE	1	TRUE	0	0.837884457797137	1		857	685	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849509	89849509	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	248	579	0	ENST00000389301.3:c.1472T>C	p.Val491Ala	p.V491A	ENST00000389301	NM_000135.2	491	gTg/gCg	16/43	1	2	FACETS	0.943	0.888	0.998	0.943	0.888	0.998	CLONAL	1	TRUE	1	0.837884457797137	2		579	628	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982803	7982803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	359	806	0	ENST00000319144.4:c.982G>A	p.Glu328Lys	p.E328K	ENST00000319144	NM_001139.2	328	Gag/Aag	8/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.837884457797137	2		806	824	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231391	5231392	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTGATGCGGTACTGGGTCCACTTCT	novel	NA	P-0048592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	256	776	0	ENST00000357368.4:c.2060_2084dup	p.Thr696GlufsTer101	p.T696Efs*101	ENST00000357368	NM_002850.3	695	acg/acAGAAGTGGACCCAGTACCGCATCACg	14/38	1	2	FACETS	0.594	0.557	0.633	0.594	0.557	0.633	SUBCLONAL	1	TRUE	1	0.837884457797137	2		776	1028	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0048593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	1015	668	2	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.581469974909774	8	FACETS	1	0.997	1	1	0.997	1	CLONAL	8	FALSE	0	0.581469974909774	8		670	1146	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524297	176524297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371591154	NA	P-0048593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	143	768	0	ENST00000292408.4:c.2158G>A	p.Gly720Arg	p.G720R	ENST00000292408	NM_213647.1	720	Ggg/Agg	17/18	0.581469974909774	11	FACETS	0.954	0.87	1	0.191	0.174	0.209	CLONAL	2	FALSE	1	0.581469974909774	11		768	932	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262415	16262415	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	330	457	0	ENST00000375759.3:c.9680A>T	p.Gln3227Leu	p.Q3227L	ENST00000375759	NM_015001.2	3227	cAg/cTg	11/15	0.581469974909774	15	FACETS	1	0.982	1			1	CLONAL	8	FALSE	NA	0.581469974909774	15		457	641	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615527	43615527	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0048593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	32	560	0	ENST00000355710.3:c.2608-2A>C		p.X870_splice	ENST00000355710	NM_020975.4	870			0.581363900357872	4	FACETS	0.411	0.333	0.498	0.137	0.111	0.166	SUBCLONAL	1	FALSE	1	0.581469974909774	4		560	424	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910426	32910426	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	42	385	0	ENST00000380152.3:c.1934G>T	p.Arg645Ile	p.R645I	ENST00000380152		645	aGa/aTa	11/27	0.581469974909774	7	FACETS	1	0.93	1	0.242	0.203	0.285	CLONAL	1	FALSE	2	0.581469974909774	7		385	293	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259221	89259221	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	34	497	0	ENST00000336596.2:c.365T>A	p.Leu122Gln	p.L122Q	ENST00000336596	NM_005233.5	122	cTg/cAg	3/17	0.217445563599704	5	FACETS	1	0.922	1	0.245	0.202	0.292	INDETERMINATE	1	FALSE	0	0.581469974909774	5		497	179	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911548	131911548	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	69	494	0	ENST00000265335.6:c.293G>C	p.Arg98Thr	p.R98T	ENST00000265335		98	aGa/aCa	3/25	0.581363900357872	4	FACETS	0.847	0.74	0.962	0.282	0.246	0.321	CLONAL	1	FALSE	1	0.581469974909774	4		494	443	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937003	178937003	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	67	577	0	ENST00000263967.3:c.1684C>G	p.Pro562Ala	p.P562A	ENST00000263967	NM_006218.2	562	Ccc/Gcc	11/21	0.581469974909774	6	FACETS	0.663	0.575	0.758	0.166	0.143	0.19	SUBCLONAL	1	FALSE	2	0.581469974909774	6		577	752	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937002	178937002	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	66	572	0	ENST00000263967.3:c.1686del	p.Glu563LysfsTer18	p.E563Kfs*18	ENST00000263967	NM_006218.2	561	atC/at	11/21	0.581469974909774	6	FACETS	0.653	0.566	0.748	0.163	0.141	0.187	SUBCLONAL	1	FALSE	2	0.581469974909774	6		572	752	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0048594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	433	582	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.204597975876939	5	FACETS	1	0.983	1	1	0.983	1	CLONAL	5	TRUE	0	0.204597975876939	5		582	1049	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0048594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	219	1059	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	NA	2	FACETS	0.838	0.778	0.9			1	INDETERMINATE	2	TRUE	NA	0.204597975876939	2		1059	1278	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130353	11130353	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	64	972	0	ENST00000358026.2:c.2592C>G	p.Ile864Met	p.I864M	ENST00000358026	NM_001128849.1	864	atC/atG	18/36	0.164870710252989	2	FACETS	0.578	0.499	0.665	0.289	0.249	0.333	SUBCLONAL	1	TRUE	0	0.204597975876939	2		972	1082	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924456	131924456	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs773142865	NA	P-0048594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	83	540	0	ENST00000265335.6:c.1129C>G	p.Gln377Glu	p.Q377E	ENST00000265335		377	Cag/Gag	8/25	1	2	FACETS	0.988	0.871	1	0.988	0.871	1	CLONAL	1	TRUE	1	0.204597975876939	2		540	821	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559308	141559308	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	121	1000	3	ENST00000220592.5:c.1493C>T	p.Ala498Val	p.A498V	ENST00000220592	NM_012154.3	498	gCg/gTg	12/19	1	2	FACETS	0.968	0.872	1	0.968	0.872	1	CLONAL	1	TRUE	1	0.204597975876939	2		1003	1222	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106681	27106681	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	63	908	0	ENST00000324856.7:c.6292G>T	p.Glu2098Ter	p.E2098*	ENST00000324856	NM_006015.4	2098	Gaa/Taa	20/20	1	2	FACETS	0.564	0.486	0.65	0.564	0.486	0.65	SUBCLONAL	1	TRUE	1	0.204597975876939	2		908	1091	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245912928	245912928	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	90	607	0	ENST00000388985.4:c.1224C>A	p.His408Gln	p.H408Q	ENST00000388985		408	caC/caA	12/12	0.204597975876939	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.204597975876939	1		607	704	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109783	115109783	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	274	940	0	ENST00000257566.3:c.2095C>A	p.Leu699Ile	p.L699I	ENST00000257566	NM_016569.3	699	Ctc/Atc	8/8	0.204597975876939	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.204597975876939	2		940	1176	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90633864	90633864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1163791289	NA	P-0048594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	96	824	1	ENST00000330062.3:c.220C>T	p.His74Tyr	p.H74Y	ENST00000330062	NM_002168.2	74	Cac/Tac	3/11	1	2	FACETS	0.836	0.743	0.936	0.836	0.743	0.936	CLONAL	1	TRUE	1	0.204597975876939	2		825	1122	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533766	63533766	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	148	886	1	ENST00000307078.5:c.1388G>T	p.Arg463Leu	p.R463L	ENST00000307078	NM_004655.3	463	cGc/cTc	6/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.204597975876939	2		887	1014	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439460	220439460	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	99	852	0	ENST00000243786.2:c.313G>A	p.Glu105Lys	p.E105K	ENST00000243786	NM_002191.3	105	Gag/Aag	2/2	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.204597975876939	2		852	914	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62323169	62323169	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	138	728	0	ENST00000360203.5:c.2631G>T	p.Lys877Asn	p.K877N	ENST00000360203	NM_001283009.1	877	aaG/aaT	28/35	0.204597975876939	3	FACETS	0.764	0.695	0.837	0.509	0.463	0.558	SUBCLONAL	2	TRUE	0	0.204597975876939	3		728	973	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637649	176637655	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTCTC	CTCTCTC	-	novel	NA	P-0048594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	102	777	0	ENST00000439151.2:c.2249_2255del	p.Ala750ValfsTer16	p.A750Vfs*16	ENST00000439151	NM_022455.4	750	gCTCTCTCt/gt	5/23	1	2	FACETS	0.942	0.84	1	0.942	0.84	1	CLONAL	1	TRUE	1	0.204597975876939	2		777	1059	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194592	29194592	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	129	1115	1	ENST00000240100.2:c.1136G>A	p.Ser379Asn	p.S379N	ENST00000240100	NM_001394.6	379	aGc/aAc	4/4	1	2	FACETS	0.986	0.891	1	0.986	0.891	1	CLONAL	1	TRUE	1	0.204597975876939	2		1116	1279	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426749	47426749	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048594-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	117	937	0	ENST00000377045.4:c.994G>T	p.Asp332Tyr	p.D332Y	ENST00000377045	NM_001654.4	332	Gat/Tat	10/16	0.204597975876939	1	FACETS	0.958	0.862	1	0.958	0.862	1	CLONAL	1	TRUE	0	0.204597975876939	1		937	1072	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0048595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	190	339	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.828418132042084	2		340	457	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	193	301	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.828418132042084	2		301	460	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0048595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	175	337	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.828418132042084	2		337	392	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413070	139413072	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0048595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	41	783	0	ENST00000277541.6:c.1070_1072del	p.Phe357del	p.F357del	ENST00000277541	NM_017617.3	357	tTCTac/tac	6/34	1	2	FACETS	0.124	0.102	0.148	0.124	0.102	0.148	SUBCLONAL	1	TRUE	1	0.828418132042084	2		783	799	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0048596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	330	696	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.334382383606907	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.334382383606907	2		697	915	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0048596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	48	495	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.319528663789219	3	FACETS	1	0.873	1	0.516	0.438	0.6	CLONAL	1	TRUE	1	0.334382383606907	3		495	325	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436026	56436026	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771831816	NA	P-0048596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	197	652	1	ENST00000407977.2:c.1111C>T	p.Arg371Ter	p.R371*	ENST00000407977		371	Cga/Tga	9/10	0.334382383606907	2	FACETS	0.964	0.898	1	0.964	0.898	1	CLONAL	2	TRUE	0	0.334382383606907	2		653	611	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913495	NA	P-0048596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	211	649	0	ENST00000371085.3:c.602G>T	p.Arg201Leu	p.R201L	ENST00000371085	NM_000516.4	201	cGt/cTt	8/13	0.135094678005619	6	FACETS	1	0.986	1	0.816	0.759	0.875	INDETERMINATE	2	TRUE	3	0.334382383606907	6		649	860	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56801431	56801431	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779834376	NA	P-0048596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	82	639	1	ENST00000337432.4:c.935G>A	p.Arg312Gln	p.R312Q	ENST00000337432	NM_058216.2	312	cGg/cAg	7/9	0.334382383606907	2	FACETS	0.774	0.689	0.863	0.774	0.689	0.863	SUBCLONAL	2	TRUE	0	0.334382383606907	2		640	317	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978470	70978470	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	62	476	0	ENST00000276594.2:c.1183G>T	p.Glu395Ter	p.E395*	ENST00000276594	NM_024504.3	395	Gag/Tag	5/8	0.334382383606907	5	FACETS	0.845	0.729	0.971	0.211	0.182	0.243	CLONAL	1	TRUE	1	0.334382383606907	5		476	659	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144711	119144711	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	67	571	0	ENST00000264033.4:c.724G>C	p.Asp242His	p.D242H	ENST00000264033	NM_005188.3	242	Gac/Cac	4/16	0.235078686899909	4	FACETS	0.955	0.831	1	0.318	0.277	0.363	CLONAL	1	TRUE	1	0.334382383606907	4		571	560	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918980	50918980	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0048596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	218	655	0	ENST00000440232.2:c.2718-1G>C		p.X906_splice	ENST00000440232	NM_002691.3	906			0.334382383606907	5	FACETS	1	0.968	1	0.711	0.662	0.762	CLONAL	2	TRUE	2	0.334382383606907	5		655	918	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713847	30714869	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAACCTGCTGCCTGTGTGACTTTGGGCTTTCCCTGCGTCTGGACCCTACTCTGTCTGTGGATGACCTGGCTAACAGTGGGCAGGTAAGTTAGAGCTAGTGCTAGATCCCCTTTACCTTGAGCCTGGCCTCACCCTACCTCTTGATCCATATCTCCTGGCTCTTATCTCAAACAGCCCTGTACTCTGGACACTGGTCTAGGGAATCTAGCCAAAGTATGGAGTCTGCCTTGAGCATACTCTGCTCTGTCCTGCCTGAGCATTTTTGCTAATGGACAGCATTTCTCCTCCTATCTTCAAATCCTTCCCAGTTCAGCACATTTTTTCCTCCTGGATCAATCCTCATTTCTCTTCCAGCAAATGTTTTTTCTTTGTTTCAAGCACTGTTAGTACTTTACCTCTATTTTTTCCCTCTCTTATGGTTGTACTCAGTCCTTTCTGCTCTATACTAGCTGTAGTTGTGTTGGTTTCTTTGTATTAAAAGCATCGTGGAAGGCAATCTCCCTGAAGTCCAAATCTACATCCACATGGTCACCCAAGATATGTAGCACAATGCCTTGAACATTGAAAGTAAAATAAGTACTTGTCGACTGAGTGAGCACTTCCACTCTTGAAGCACTCTCACAGATTAAAATGGAAATGTTTTTGGCTAAGAAACTATTGGAAGGTGATTGGAAATCACCACAACATCCCTTATAAATGATGAGCCCAGTGTTTTCACACAGTGGAGTCCATGGAGAGCAGCACTGTCTTCTTTAGCCAGGTGGCAGGACACACTTTGAAGCACTCGGTTACTGCTCAGTCAGCCCTGTGTCCATGGCAGCGCACGCAGTGTTGAGGTAAACATCGAAATATGGACAGACTAATGTGCCAGAGTAATGAGCCATGCAATGACCTCTTGAGAAGAAAAAAACTCTCTAATACATGCCAATAAGAAACATTCCTTGGAATGATAATATCAACTCACTTGGCTTCCCTAGATCCTTGGGAAGGTAGGACTTTATTGTTATTTAGTCAGTTTATACA	TAACCTGCTGCCTGTGTGACTTTGGGCTTTCCCTGCGTCTGGACCCTACTCTGTCTGTGGATGACCTGGCTAACAGTGGGCAGGTAAGTTAGAGCTAGTGCTAGATCCCCTTTACCTTGAGCCTGGCCTCACCCTACCTCTTGATCCATATCTCCTGGCTCTTATCTCAAACAGCCCTGTACTCTGGACACTGGTCTAGGGAATCTAGCCAAAGTATGGAGTCTGCCTTGAGCATACTCTGCTCTGTCCTGCCTGAGCATTTTTGCTAATGGACAGCATTTCTCCTCCTATCTTCAAATCCTTCCCAGTTCAGCACATTTTTTCCTCCTGGATCAATCCTCATTTCTCTTCCAGCAAATGTTTTTTCTTTGTTTCAAGCACTGTTAGTACTTTACCTCTATTTTTTCCCTCTCTTATGGTTGTACTCAGTCCTTTCTGCTCTATACTAGCTGTAGTTGTGTTGGTTTCTTTGTATTAAAAGCATCGTGGAAGGCAATCTCCCTGAAGTCCAAATCTACATCCACATGGTCACCCAAGATATGTAGCACAATGCCTTGAACATTGAAAGTAAAATAAGTACTTGTCGACTGAGTGAGCACTTCCACTCTTGAAGCACTCTCACAGATTAAAATGGAAATGTTTTTGGCTAAGAAACTATTGGAAGGTGATTGGAAATCACCACAACATCCCTTATAAATGATGAGCCCAGTGTTTTCACACAGTGGAGTCCATGGAGAGCAGCACTGTCTTCTTTAGCCAGGTGGCAGGACACACTTTGAAGCACTCGGTTACTGCTCAGTCAGCCCTGTGTCCATGGCAGCGCACGCAGTGTTGAGGTAAACATCGAAATATGGACAGACTAATGTGCCAGAGTAATGAGCCATGCAATGACCTCTTGAGAAGAAAAAAACTCTCTAATACATGCCAATAAGAAACATTCCTTGGAATGATAATATCAACTCACTTGGCTTCCCTAGATCCTTGGGAAGGTAGGACTTTATTGTTATTTAGTCAGTTTATACA	-	novel	NA	P-0048596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	129	890	0	ENST00000295754.5:c.1174_1255-726del		p.X392_splice	ENST00000295754	NM_003242.5	392		4/7	0.243605695849204	3	FACETS	1	0.982	1	0.445	0.404	0.488	CLONAL	1	TRUE	0	0.334382383606907	3		890	674	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287989	33287989	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs371370699	NA	P-0048596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	205	743	0	ENST00000374542.5:c.1264A>G	p.Met422Val	p.M422V	ENST00000374542	NM_001141970.1	422	Atg/Gtg	5/8	0.334382383606907	5	FACETS	1	0.964	1	0.706	0.656	0.758	CLONAL	2	TRUE	2	0.334382383606907	5		743	869	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123085	5123122	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TTTCACATACATTGAGAAGAGTAAAAGTCCACCAGCGG	TTTCACATACATTGAGAAGAGTAAAAGTCCACCAGCGG	-	novel	NA	P-0048596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	39	612	0	ENST00000381652.3:c.3142_3177+2del		p.X1048_splice	ENST00000381652	NM_004972.3	1048		23/25	0.334382383606907	1	FACETS	0.594	0.494	0.705	0.594	0.494	0.705	SUBCLONAL	1	TRUE	0	0.334382383606907	1		612	327	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891144	101891144	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	40	479	0	ENST00000374994.4:c.105G>C	p.Gln35His	p.Q35H	ENST00000374994	NM_004612.2	35	caG/caC	2/9	0.319528663789219	3	FACETS	0.846	0.705	1	0.423	0.352	0.501	CLONAL	1	TRUE	1	0.334382383606907	3		479	330	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	185	576	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.672792484003182	2		576	451	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820792	3820792	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	50	838	0	ENST00000262367.5:c.2659C>G	p.Gln887Glu	p.Q887E	ENST00000262367	NM_004380.2	887	Cag/Gag	14/31	1	2	FACETS	0.153	0.129	0.18	0.153	0.129	0.18	SUBCLONAL	1	TRUE	1	0.672792484003182	2		838	969	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155426	99155426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	212	502	0	ENST00000074304.5:c.652G>A	p.Asp218Asn	p.D218N	ENST00000074304	NM_001134224.1	218	Gac/Aac	9/26	1	2	FACETS	0.967	0.903	1	0.967	0.903	1	CLONAL	1	TRUE	1	0.672792484003182	2		502	652	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755640	39755640	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	245	685	0	ENST00000288319.7:c.1125G>C	p.Lys375Asn	p.K375N	ENST00000288319	NM_182918.3	375	aaG/aaC	10/10	1	2	FACETS	0.998	0.937	1	0.998	0.937	1	CLONAL	1	TRUE	1	0.672792484003182	2		685	730	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303332	11303332	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	214	712	1	ENST00000361445.4:c.1251G>A	p.Met417Ile	p.M417I	ENST00000361445	NM_004958.3	417	atG/atA	9/58	1	2	FACETS	0.888	0.829	0.95	0.888	0.829	0.95	CLONAL	1	TRUE	1	0.672792484003182	2		713	716	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46714199	46714199	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	220	580	0	ENST00000371975.4:c.19C>G	p.Pro7Ala	p.P7A	ENST00000371975	NM_003579.3	7	Ccc/Gcc	2/18	1	2	FACETS	0.921	0.861	0.983	0.921	0.861	0.983	CLONAL	1	TRUE	1	0.672792484003182	2		580	710	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175877	176175877	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	73	162	0	ENST00000367669.3:c.238G>A	p.Gly80Arg	p.G80R	ENST00000367669	NM_022457.5	80	Ggg/Agg	1/20	0.672792484003182	3	FACETS	1	0.966	1	0.622	0.552	0.695	CLONAL	1	TRUE	1	0.672792484003182	3		162	233	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373799	118373799	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	39	422	0	ENST00000534358.1:c.7192G>T	p.Glu2398Ter	p.E2398*	ENST00000534358	NM_005933.3	2398	Gaa/Taa	27/36	1	2	FACETS	0.212	0.175	0.254	0.212	0.175	0.254	SUBCLONAL	1	TRUE	1	0.672792484003182	2		422	546	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374909	118374909	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	54	494	0	ENST00000534358.1:c.8302G>C	p.Glu2768Gln	p.E2768Q	ENST00000534358	NM_005933.3	2768	Gaa/Caa	27/36	1	2	FACETS	0.273	0.233	0.317	0.273	0.233	0.317	SUBCLONAL	1	TRUE	1	0.672792484003182	2		494	588	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375181	118375181	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	47	498	0	ENST00000534358.1:c.8574G>C	p.Lys2858Asn	p.K2858N	ENST00000534358	NM_005933.3	2858	aaG/aaC	27/36	1	2	FACETS	0.236	0.198	0.277	0.236	0.198	0.277	SUBCLONAL	1	TRUE	1	0.672792484003182	2		498	593	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375266	118375266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782113711	NA	P-0048598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	50	458	0	ENST00000534358.1:c.8659G>A	p.Asp2887Asn	p.D2887N	ENST00000534358	NM_005933.3	2887	Gac/Aac	27/36	1	2	FACETS	0.249	0.211	0.291	0.249	0.211	0.291	SUBCLONAL	1	TRUE	1	0.672792484003182	2		458	597	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375278	118375278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	49	448	0	ENST00000534358.1:c.8671G>A	p.Glu2891Lys	p.E2891K	ENST00000534358	NM_005933.3	2891	Gaa/Aaa	27/36	1	2	FACETS	0.248	0.21	0.291	0.248	0.21	0.291	SUBCLONAL	1	TRUE	1	0.672792484003182	2		448	587	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375380	118375380	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	44	475	0	ENST00000534358.1:c.8773G>C	p.Glu2925Gln	p.E2925Q	ENST00000534358	NM_005933.3	2925	Gag/Cag	27/36	1	2	FACETS	0.26	0.218	0.307	0.26	0.218	0.307	SUBCLONAL	1	TRUE	1	0.672792484003182	2		475	503	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375547	118375548	+	missense_variant	Missense_Mutation	DNP	GA	GA	TG	novel	NA	P-0048598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	32	438	0	ENST00000534358.1:c.8940_8941delinsTG	p.Ser2981Gly	p.S2981G	ENST00000534358	NM_005933.3	2980	ctGAgc/ctTGgc	27/36	1	2	FACETS	0.19	0.154	0.231	0.19	0.154	0.231	SUBCLONAL	1	TRUE	1	0.672792484003182	2		438	500	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376193	118376193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	53	513	1	ENST00000534358.1:c.9586G>A	p.Asp3196Asn	p.D3196N	ENST00000534358	NM_005933.3	3196	Gat/Aat	27/36	1	2	FACETS	0.249	0.212	0.29	0.249	0.212	0.29	SUBCLONAL	1	TRUE	1	0.672792484003182	2		514	632	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376632	118376632	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	56	490	0	ENST00000534358.1:c.10025C>G	p.Ser3342Cys	p.S3342C	ENST00000534358	NM_005933.3	3342	tCt/tGt	27/36	1	2	FACETS	0.277	0.237	0.321	0.277	0.237	0.321	SUBCLONAL	1	TRUE	1	0.672792484003182	2		490	600	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377202	118377202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	40	527	0	ENST00000534358.1:c.10595C>T	p.Ser3532Leu	p.S3532L	ENST00000534358	NM_005933.3	3532	tCa/tTa	27/36	1	2	FACETS	0.191	0.158	0.228	0.191	0.158	0.228	SUBCLONAL	1	TRUE	1	0.672792484003182	2		527	622	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562669	95562669	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	175	557	0	ENST00000393063.1:c.4588C>G	p.Pro1530Ala	p.P1530A	ENST00000393063	NM_030621.3	1530	Cca/Gca	24/28	1	2	FACETS	0.882	0.816	0.949	0.882	0.816	0.949	CLONAL	1	TRUE	1	0.672792484003182	2		557	590	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358376	91358376	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	62	614	0	ENST00000355112.3:c.4121C>G	p.Ser1374Cys	p.S1374C	ENST00000355112	NM_000057.2	1374	tCc/tGc	22/22	1	2	FACETS	0.256	0.22	0.294	0.256	0.22	0.294	SUBCLONAL	1	TRUE	1	0.672792484003182	2		614	721	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358503	91358503	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1567069125	NA	P-0048598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	37	479	0	ENST00000355112.3:c.4248C>G	p.Phe1416Leu	p.F1416L	ENST00000355112	NM_000057.2	1416	ttC/ttG	22/22	1	2	FACETS	0.205	0.169	0.246	0.205	0.169	0.246	SUBCLONAL	1	TRUE	1	0.672792484003182	2		479	536	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844229	68844229	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	259	576	0	ENST00000261769.5:c.817G>C	p.Glu273Gln	p.E273Q	ENST00000261769	NM_004360.3	273	Gaa/Caa	6/16	0.594789407642341	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.672792484003182	1		576	476	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349640	89349640	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	295	804	0	ENST00000301030.4:c.3310G>C	p.Asp1104His	p.D1104H	ENST00000301030	NM_001256183.1	1104	Gat/Cat	9/13	0.672792484003182	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.672792484003182	1		804	564	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526510	66526510	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	195	572	0	ENST00000358598.2:c.1066G>T	p.Glu356Ter	p.E356*	ENST00000358598	NM_212471.2	356	Gaa/Taa	11/11	0.672792484003182	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.672792484003182	1		572	369	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223403	2223403	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	40	646	0	ENST00000398665.3:c.3514C>G	p.Leu1172Val	p.L1172V	ENST00000398665	NM_032482.2	1172	Ctg/Gtg	25/28	1	2	FACETS	0.165	0.136	0.197	0.165	0.136	0.197	SUBCLONAL	1	TRUE	1	0.672792484003182	2		646	722	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538314	9538314	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	47	653	0	ENST00000353224.5:c.1684C>T	p.Gln562Ter	p.Q562*	ENST00000353224	NM_177990.2	562	Caa/Taa	7/10	1	2	FACETS	0.198	0.166	0.233	0.198	0.166	0.233	SUBCLONAL	1	TRUE	1	0.672792484003182	2		653	706	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799586	72799586	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	243	589	0	ENST00000325599.8:c.1583C>G	p.Ser528Cys	p.S528C	ENST00000325599	NM_018130.2	528	tCt/tGt	11/11	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.672792484003182	2		589	713	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952119	178952119	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	27	440	0	ENST00000263967.3:c.3174C>G	p.Ile1058Met	p.I1058M	ENST00000263967	NM_006218.2	1058	atC/atG	21/21	1	2	FACETS	0.177	0.14	0.219	0.177	0.14	0.219	SUBCLONAL	1	TRUE	1	0.672792484003182	2		440	454	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189436	56189436	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	75	616	0	ENST00000399503.3:c.4468G>C	p.Glu1490Gln	p.E1490Q	ENST00000399503	NM_005921.1	1490	Gaa/Caa	20/20	1	2	FACETS	0.354	0.31	0.401	0.354	0.31	0.401	SUBCLONAL	1	TRUE	1	0.672792484003182	2		616	630	SUCCESS
APC	324	MSKCC	GRCh37	5	112173602	112173602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	167	460	0	ENST00000257430.4:c.2311G>A	p.Glu771Lys	p.E771K	ENST00000257430	NM_000038.5	771	Gaa/Aaa	16/16	0.672792484003182	3	FACETS	0.998	0.92	1			1	CLONAL	1	TRUE	NA	0.672792484003182	3		460	665	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040788	47040788	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	109	812	0	ENST00000377604.3:c.1423C>T	p.Pro475Ser	p.P475S	ENST00000377604	NM_001204468.1	475	Ccc/Tcc	13/24	0.638683419653199	1	FACETS	0.37	0.333	0.409	0.37	0.333	0.409	SUBCLONAL	1	TRUE	0	0.672792484003182	1		812	581	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874392	76874392	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	111	619	0	ENST00000373344.5:c.5330G>T	p.Arg1777Met	p.R1777M	ENST00000373344	NM_000489.3	1777	aGg/aTg	21/35	0.207830542806844	1	FACETS	0.467	0.422	0.514	0.467	0.422	0.514	INDETERMINATE	1	TRUE	0	0.672792484003182	1		619	469	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951053	48951053	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs587778831	NA	P-0048599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	57	305	1	ENST00000267163.4:c.1216-1G>A		p.X406_splice	ENST00000267163	NM_000321.2	406			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		306	160	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789629	3789629	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	117	627	2	ENST00000262367.5:c.4230del	p.Phe1410LeufsTer49	p.F1410Lfs*49	ENST00000262367	NM_004380.2	1410	ttT/tt	25/31	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.520559955761974	2		629	393	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052611	42052611	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	214	643	0	ENST00000219905.7:c.7282C>G	p.His2428Asp	p.H2428D	ENST00000219905	NM_001164273.1	2428	Cac/Gac	20/24	0.208324912394929	1	FACETS	0.897	0.852	0.941	1	0.995	1	INDETERMINATE	2	TRUE	0	0.520559955761974	1		643	339	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753053	42753056	+	frameshift_variant	Frame_Shift_Del	DEL	CCAC	CCAC	-	novel	NA	P-0048600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	132	846	0	ENST00000222329.4:c.1208_1211del	p.Gly403AlafsTer13	p.G403Afs*13	ENST00000222329	NM_006494.2	403	gGTGGc/gc	4/4	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.520559955761974	2		846	423	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70005654	70005654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1362047425	NA	P-0048600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	134	613	0	ENST00000394351.3:c.683G>A	p.Gly228Asp	p.G228D	ENST00000394351	NM_000248.3	228	gGt/gAt	7/9	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.520559955761974	2		613	378	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0048601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	15	470	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.136	0.098	0.181	0.136	0.098	0.181	SUBCLONAL	1	TRUE	1	0.437421885256892	2		470	506	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	64	301	0				ENST00000310581	NM_198253.2	-/1132			0.244199106918153	1	FACETS	0.699	0.61	0.795	0.699	0.61	0.795	INDETERMINATE	1	TRUE	0	0.437421885256892	1		301	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201059	NA	P-0048601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	255	746	1	ENST00000269305.4:c.856G>T	p.Glu286Ter	p.E286*	ENST00000269305	NM_001126112.2	286	Gaa/Taa	8/11	0.437421885256892	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.437421885256892	1		747	786	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519710	176519710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150737523	NA	P-0048601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	218	767	0	ENST00000292408.4:c.982G>A	p.Ala328Thr	p.A328T	ENST00000292408	NM_213647.1	328	Gca/Aca	8/18	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.437421885256892	2		767	767	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0048601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	166	622	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.437421885256892	2		622	711	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568636	41568636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	64	474	0	ENST00000263253.7:c.4586G>A	p.Arg1529Gln	p.R1529Q	ENST00000263253	NM_001429.3	1529	cGa/cAa	28/31	1	2	FACETS	0.542	0.47	0.62	0.542	0.47	0.62	SUBCLONAL	1	TRUE	1	0.437421885256892	2		474	540	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519958	NA	P-0048601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	289	849	0	ENST00000481739.1:c.1280C>A	p.Ser427Tyr	p.S427Y	ENST00000481739	NM_002957.4	427	tCc/tAc	10/10	0.437421885256892	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.437421885256892	1		849	756	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938390	44938390	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0048601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	148	260	0	ENST00000377967.4:c.2939-1G>C		p.X980_splice	ENST00000377967	NM_021140.2	980			0.393892869294694	2	FACETS	0.978	0.906	1			1	CLONAL	2	TRUE	NA	0.437421885256892	2		260	346	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115962	8115963	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0048601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	181	500	0	ENST00000346208.3:c.1309_1310dup	p.Ser437ArgfsTer39	p.S437Rfs*39	ENST00000346208		436	-/AG	6/6	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.437421885256892	2		500	623	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105238761	105238761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	146	761	0	ENST00000349310.3:c.1201G>A	p.Glu401Lys	p.E401K	ENST00000349310	NM_001014432.1	401	Gag/Aag	13/15	1	2	FACETS	0.844	0.771	0.92	0.844	0.771	0.92	CLONAL	1	TRUE	1	0.437421885256892	2		761	791	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347409	91347409	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	108	383	0	ENST00000355112.3:c.3571G>A	p.Glu1191Lys	p.E1191K	ENST00000355112	NM_000057.2	1191	Gaa/Aaa	19/22	0.301783058279927	2	FACETS	1	0.926	1	0.515	0.465	0.569	CLONAL	1	TRUE	0	0.437421885256892	2		383	479	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143033780	143033780	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	80	556	0	ENST00000262992.4:c.2191C>G	p.Leu731Val	p.L731V	ENST00000262992	NM_001101669.1	731	Cta/Gta	20/24	1	2	FACETS	0.563	0.495	0.635	0.563	0.495	0.635	SUBCLONAL	1	TRUE	1	0.437421885256892	2		556	650	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524534	176524534	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs192201146	NA	P-0048601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	165	850	0	ENST00000292408.4:c.2266G>A	p.Asp756Asn	p.D756N	ENST00000292408	NM_213647.1	756	Gac/Aac	18/18	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.437421885256892	2		850	735	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250592	26250599	+	frameshift_variant	Frame_Shift_Del	DEL	GTCTTGAA	GTCTTGAA	-	novel	NA	P-0048601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	167	801	0	ENST00000446824.2:c.235_242del	p.Phe79ArgfsTer25	p.F79Rfs*25	ENST00000446824	NM_021018.2	79	TTCAAGACc/c	1/1	1	2	FACETS	0.967	0.889	1	0.967	0.889	1	CLONAL	1	TRUE	1	0.437421885256892	2		801	790	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56882326	56882326	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	491	642	0	ENST00000519728.1:c.1024C>A	p.Pro342Thr	p.P342T	ENST00000519728	NM_002350.3	342	Cca/Aca	10/13	0.20891243568054	5	FACETS	1	0.991	1	0.663	0.636	0.69	INDETERMINATE	3	TRUE	0	0.437421885256892	5		642	1122	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0048602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	55	932	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.223965445811592	1	FACETS	0.996	0.863	1	1	0.978	1	CLONAL	2	FALSE	0	0.223965445811592	1		934	219	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061215	38061235	+	inframe_deletion	In_Frame_Del	DEL	GCAGCCGTTCTCGAACATGTT	GCAGCCGTTCTCGAACATGTT	-	novel	NA	P-0048602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	143	712	0	ENST00000250448.2:c.754_774del	p.Asn252_Cys258del	p.N252_C258del	ENST00000250448	NM_004496.3	252	AACATGTTCGAGAACGGCTGC/-	2/2	0.223965445811592	5	FACETS	1	0.969	1	0.838	0.769	0.91	CLONAL	3	FALSE	1	0.223965445811592	5		712	509	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0048602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	87	827	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	0.119125000462283	4	FACETS	0.845	0.754	0.942	1	0.971	1	INDETERMINATE	3	FALSE	2	0.223965445811592	4		827	375	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040933	42040934	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0048602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	50	1006	1	ENST00000219905.7:c.5313_5314del	p.Pro1772TyrfsTer3	p.P1772Yfs*3	ENST00000219905	NM_001164273.1	1771	TCt/t	16/24	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.223965445811592	2		1007	334	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645688	12645688	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121434594	NA	P-0048602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	56	497	0	ENST00000251849.4:c.781C>A	p.Pro261Thr	p.P261T	ENST00000251849	NM_002880.3	261	Cct/Act	7/17	1	2	FACETS	0.965	0.835	1	1	0.977	1	CLONAL	2	FALSE	1	0.223965445811592	2		497	259	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713339	30713339	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	62	804	0	ENST00000295754.5:c.664G>T	p.Asp222Tyr	p.D222Y	ENST00000295754	NM_003242.5	222	Gat/Tat	4/7	1	2	FACETS	1	0.898	1	1	0.981	1	CLONAL	2	FALSE	1	0.223965445811592	2		804	268	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372460	55372460	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	95	1164	1	ENST00000297316.4:c.1150T>C	p.Ser384Pro	p.S384P	ENST00000297316	NM_022454.3	384	Tcc/Ccc	2/2	0.223965445811592	4	FACETS	0.919	0.835	1	1	0.985	1	CLONAL	5	FALSE	1	0.223965445811592	4		1165	226	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0048603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	450	702	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.850660391282011	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.874248293054559	1		702	562	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993296	72993296	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757253455	NA	P-0048603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	738	767	0	ENST00000268489.5:c.749C>T	p.Ser250Phe	p.S250F	ENST00000268489	NM_006885.3	250	tCt/tTt	2/10	0.874248293054559	2	FACETS	0.973	0.955	0.989	0.973	0.955	0.989	CLONAL	2	TRUE	0	0.874248293054559	2		767	868	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509541	29509541	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1567826623	NA	P-0048603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	71	498	0	ENST00000356175.3:c.746T>C	p.Leu249Pro	p.L249P	ENST00000356175	NM_000267.3	249	cTa/cCa	8/57	0.874248293054559	1	FACETS	0.28	0.246	0.316	0.28	0.246	0.316	SUBCLONAL	1	TRUE	0	0.874248293054559	1		498	327	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562891	21562891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	192	642	1	ENST00000382592.4:c.1028C>A	p.Pro343His	p.P343H	ENST00000382592	NM_014572.2	343	cCc/cAc	4/8	1	2	FACETS	0.477	0.441	0.514	0.477	0.441	0.514	SUBCLONAL	1	TRUE	1	0.874248293054559	2		643	921	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998959	11998959	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	216	458	0	ENST00000353533.5:c.461G>C	p.Arg154Pro	p.R154P	ENST00000353533	NM_003010.3	154	cGg/cCg	4/11	0.850660391282011	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.874248293054559	1		458	266	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169992	32169992	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	431	838	0	ENST00000375023.3:c.3616G>T	p.Gly1206Ter	p.G1206*	ENST00000375023	NM_004557.3	1206	Gga/Tga	21/30	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.874248293054559	2		838	946	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846194	151846194	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	89	616	0	ENST00000262189.6:c.12818C>G	p.Pro4273Arg	p.P4273R	ENST00000262189	NM_170606.2	4273	cCt/cGt	52/59	0.490121509712879	3	FACETS	0.306	0.27	0.344	0.153	0.135	0.172	INDETERMINATE	1	TRUE	1	0.874248293054559	3		616	956	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592352	29592367	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACGGAGGTAAGAAATA	ACGGAGGTAAGAAATA	CTGG	novel	NA	P-0048603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	16	506	1	ENST00000356175.3:c.4767_4772+10delinsCTGG		p.X1589_splice	ENST00000356175	NM_000267.3	1589		35/57	0.874248293054559	1	FACETS	0.073	0.054	0.096	0.073	0.054	0.096	SUBCLONAL	1	TRUE	0	0.874248293054559	1		507	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0048608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	136	823	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.913	0.83	1	0.913	0.83	1	CLONAL	1	TRUE	1	0.332419242017061	2		823	896	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0048608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	66	558	1	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.622	0.54	0.712	0.622	0.54	0.712	SUBCLONAL	1	TRUE	1	0.332419242017061	2		559	638	SUCCESS
APC	324	MSKCC	GRCh37	5	112175199	112175199	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	62	276	0	ENST00000257430.4:c.3910del	p.Ile1304Ter	p.I1304*	ENST00000257430	NM_000038.5	1303	cAa/ca	16/16	1	2	FACETS	0.872	0.755	0.997	0.872	0.755	0.997	CLONAL	1	TRUE	1	0.332419242017061	2		276	428	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776562	9776562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1216060233	NA	P-0048608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	84	767	0	ENST00000377346.4:c.665G>A	p.Arg222Gln	p.R222Q	ENST00000377346	NM_005026.3	222	cGg/cAg	6/24	1	2	FACETS	0.612	0.54	0.69	0.612	0.54	0.69	SUBCLONAL	1	TRUE	1	0.332419242017061	2		767	826	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0048609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	82	577	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.203246638760576	0	FACETS	0.537	0.481	0.595			1	INDETERMINATE	1	TRUE	0	0.553883165372282	0		577	246	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541484	29541484	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	52	195	0	ENST00000356175.3:c.1408G>T	p.Glu470Ter	p.E470*	ENST00000356175	NM_000267.3	470	Gaa/Taa	13/57	NA	2	FACETS	1	0.907	1			1	INDETERMINATE	2	TRUE	NA	0.553883165372282	2		195	92	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913384	NA	P-0048609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	111	582	0	ENST00000304494.5:c.262G>T	p.Glu88Ter	p.E88*	ENST00000304494	NM_000077.4	88	Gag/Tag	2/3	0.553883165372282	1	FACETS	0.938	0.855	1	0.938	0.855	1	CLONAL	1	TRUE	0	0.553883165372282	1		582	309	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578507	7578507	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	193	966	1	ENST00000269305.4:c.423C>A	p.Cys141Ter	p.C141*	ENST00000269305	NM_001126112.2	141	tgC/tgA	5/11	0.524786088236588	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.553883165372282	1		967	462	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783647	50783647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	63	623	0	ENST00000398568.2:c.38C>T	p.Ser13Leu	p.S13L	ENST00000398568	NM_001042412.1	13	tCa/tTa	3/18	1	2	FACETS	0.821	0.717	0.932	0.821	0.717	0.932	CLONAL	1	TRUE	1	0.553883165372282	2		623	277	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0048611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	144	351	0				ENST00000310581	NM_198253.2	-/1132			0.395184789100584	3	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	1	0.395425494676321	3		351	423	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045136	47045136	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	123	607	1	ENST00000377604.3:c.2377C>T	p.Arg793Ter	p.R793*	ENST00000377604	NM_001204468.1	793	Cga/Tga	21/24	1	2	FACETS	0.977	0.885	1	0.977	0.885	1	CLONAL	1	TRUE	1	0.395425494676321	2		608	637	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363380	40363380	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	106	772	0	ENST00000397332.2:c.849G>C	p.Glu283Asp	p.E283D	ENST00000397332	NM_001033082.2	283	gaG/gaC	3/3	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.363419230706127	2		772	535	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827483	72827495	+	frameshift_variant	Frame_Shift_Del	DEL	TACTTGATGCCAC	TACTTGATGCCAC	-	novel	NA	P-0048612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	76	859	1	ENST00000268489.5:c.9086_9098del	p.Cys3029SerfsTer43	p.C3029Sfs*43	ENST00000268489	NM_006885.3	3029	tGTGGCATCAAGTAc/tc	9/10	0.341819731928349	3	FACETS	0.858	0.753	0.97	0.429	0.376	0.485	CLONAL	1	TRUE	1	0.363419230706127	3		860	576	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188207	10188208	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0048612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	64	636	1	ENST00000256474.2:c.350_351delinsCT	p.Trp117Ser	p.W117S	ENST00000256474	NM_000551.3	117	tGG/tCT	2/3	0.363419230706127	1	FACETS	0.86	0.75	0.978	0.86	0.75	0.978	CLONAL	1	TRUE	0	0.363419230706127	1		637	335	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584442	52584443	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTGTGTGT	novel	NA	P-0048612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	34	576	0	ENST00000394830.3:c.4570_4571insACACACAC	p.Leu1524HisfsTer26	p.L1524Hfs*26	ENST00000394830	NM_018313.4	1524	ctg/cACACACACtg	29/30	0.363419230706127	1	FACETS	0.649	0.533	0.777	0.649	0.533	0.777	SUBCLONAL	1	TRUE	0	0.363419230706127	1		576	236	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0048613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	74	495	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.986	0.866	1	0.986	0.866	1	CLONAL	1	TRUE	1	0.31	2		495	484	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867546	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs11466445	NA	P-0048613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	10	26	0	ENST00000374994.4:c.70_78del	p.Ala24_Ala26del	p.A24_A26del	ENST00000374994	NM_004612.2	17	ctGGCGGCGGCg/ctg	1/9	1	2	FACETS	1	0.804	1	1	0.804	1	CLONAL	1	TRUE	1	0.31	2		26	52	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577507	7577507	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	177	655	0	ENST00000269305.4:c.774A>C	p.Glu258Asp	p.E258D	ENST00000269305	NM_001126112.2	258	gaA/gaC	7/11	0.303329781774782	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.31	1		655	845	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224165	36224165	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs749912335	NA	P-0048613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	58	587	0	ENST00000222270.7:c.6715C>G	p.Leu2239Val	p.L2239V	ENST00000222270	NM_014727.1	2239	Ctc/Gtc	28/37	0.303329781774782	5	FACETS	0.473	0.405	0.549			1	SUBCLONAL	1	TRUE	NA	0.31	5		587	1158	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89444996	89444996	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	30	393	0	ENST00000336596.2:c.1316C>G	p.Pro439Arg	p.P439R	ENST00000336596	NM_005233.5	439	cCt/cGt	6/17	1	2	FACETS	0.362	0.291	0.444	0.362	0.291	0.444	SUBCLONAL	1	TRUE	1	0.31	2		393	534	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189850	66189850	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs777006749	NA	P-0048613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	76	481	0	ENST00000273854.3:c.3096C>A	p.Asn1032Lys	p.N1032K	ENST00000273854	NM_004439.5	1032	aaC/aaA	18/18	0.303329781774782	1	FACETS	0.769	0.675	0.869	0.769	0.675	0.869	SUBCLONAL	1	TRUE	0	0.31	1		481	539	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129198	152129198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	171	630	0	ENST00000206249.3:c.151G>A	p.Val51Met	p.V51M	ENST00000206249	NM_000125.3	51	Gtg/Atg	1/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.31	2		630	847	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420046	152420046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781018265	NA	P-0048613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	48	558	0	ENST00000206249.3:c.1733C>T	p.Ser578Phe	p.S578F	ENST00000206249	NM_000125.3	578	tCc/tTc	8/8	1	2	FACETS	0.457	0.386	0.537	0.457	0.386	0.537	SUBCLONAL	1	TRUE	1	0.31	2		558	677	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0048614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	358	347	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.362430530319089	9	FACETS	1	0.965	1			1	CLONAL	7	TRUE	NA	0.362430530319089	9		347	635	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260550	10260550	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0048614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	58	655	0	ENST00000340748.4:c.2312C>G	p.Ser771Ter	p.S771*	ENST00000340748		771	tCa/tGa	24/40	0.362430530319089	1	FACETS	0.514	0.442	0.592	0.514	0.442	0.592	SUBCLONAL	1	TRUE	0	0.362430530319089	1		655	510	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233178	69233178	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	101	386	0	ENST00000462284.1:c.1043C>A	p.Ser348Tyr	p.S348Y	ENST00000462284	NM_002392.5	348	tCt/tAt	11/11	0.199585340223861	3	FACETS	0.835	0.752	0.922	0.835	0.752	0.922	INDETERMINATE	2	TRUE	1	0.362430530319089	3		386	394	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029509	14029509	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	45	477	0	ENST00000311895.7:c.1720G>T	p.Glu574Ter	p.E574*	ENST00000311895	NM_005236.2	574	Gag/Tag	8/11	0.226962121211383	1	FACETS	0.438	0.368	0.515	0.438	0.368	0.515	SUBCLONAL	1	TRUE	0	0.362430530319089	1		477	464	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795511	42795511	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	58	756	0	ENST00000575354.2:c.2591T>C	p.Phe864Ser	p.F864S	ENST00000575354	NM_015125.3	864	tTc/tCc	10/20	0.165881206483901	2	FACETS	0.395	0.338	0.457	0.197	0.169	0.229	INDETERMINATE	1	TRUE	0	0.362430530319089	2		756	811	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114055	73114055	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	17	148	0	ENST00000356692.5:c.693del	p.Lys231AsnfsTer15	p.K231Nfs*15	ENST00000356692		231	Aaa/aa	8/9	NA	2	FACETS	0.823	0.622	1			1	INDETERMINATE	1	TRUE	NA	0.362430530319089	2		148	114	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0048617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	129	286	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.993	0.909	1	0.993	0.909	1	CLONAL	1	TRUE	1	0.659404064724888	2		286	394	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	131	576	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.659404064724888	2		576	379	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0048617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	152	582	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.659404064724888	2		582	417	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0048617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	187	369	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.997	0.927	1	0.997	0.927	1	CLONAL	1	TRUE	1	0.659404064724888	2		370	569	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631837	90631837	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	283	539	0	ENST00000330062.3:c.516G>T	p.Arg172Ser	p.R172S	ENST00000330062	NM_002168.2	172	agG/agT	4/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.659404064724888	2		539	774	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117872	70117872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	471	474	0	ENST00000245479.2:c.340G>A	p.Val114Met	p.V114M	ENST00000245479	NM_000346.3	114	Gtg/Atg	1/3	0.659174588436199	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.659404064724888	2		474	707	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035238	6035238	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1805322	NA	P-0048617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	158	292	0	ENST00000265849.7:c.830C>T	p.Thr277Met	p.T277M	ENST00000265849	NM_000535.5	277	aCg/aTg	8/15	1	2	FACETS	0.966	0.892	1	0.966	0.892	1	CLONAL	1	TRUE	1	0.659404064724888	2		292	496	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656949	47656949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267607947	NA	P-0048617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	120	248	0	ENST00000233146.2:c.1145G>A	p.Arg382His	p.R382H	ENST00000233146	NM_000251.2	382	cGt/cAt	7/16	1	2	FACETS	0.94	0.857	1	0.94	0.857	1	CLONAL	1	TRUE	1	0.659404064724888	2		248	387	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259007	153259007	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	86	264	0	ENST00000281708.4:c.808C>T	p.Gln270Ter	p.Q270*	ENST00000281708	NM_033632.3	270	Caa/Taa	5/12	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.659404064724888	2		264	258	SUCCESS
APC	324	MSKCC	GRCh37	5	112175753	112175754	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0048617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	132	287	0	ENST00000257430.4:c.4462_4463insG	p.Leu1488CysfsTer26	p.L1488Cfs*26	ENST00000257430	NM_000038.5	1488	tta/tGta	16/16	1	2	FACETS	0.96	0.88	1	0.96	0.88	1	CLONAL	1	TRUE	1	0.659404064724888	2		287	417	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922173	39922174	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	32	225	0	ENST00000378444.4:c.3998dup	p.Cys1334ValfsTer75	p.C1334Vfs*75	ENST00000378444	NM_001123385.1	1333	ctg/ctTg	9/15	1	1	FACETS	0.183	0.148	0.222	0.183	0.148	0.222	SUBCLONAL	1	TRUE	0	0.659404064724888	1		225	356	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931723	39931723	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	51	252	0	ENST00000378444.4:c.2876del	p.Pro959HisfsTer62	p.P959Hfs*62	ENST00000378444	NM_001123385.1	959	cCa/ca	4/15	1	1	FACETS	0.244	0.207	0.284	0.244	0.207	0.284	SUBCLONAL	1	TRUE	0	0.659404064724888	1		252	425	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932610	39932611	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0048617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	39	317	0	ENST00000378444.4:c.1988_1989del	p.Pro663ArgfsTer76	p.P663Rfs*76	ENST00000378444	NM_001123385.1	663	cCT/c	4/15	1	1	FACETS	0.156	0.129	0.186	0.156	0.129	0.186	SUBCLONAL	1	TRUE	0	0.659404064724888	1		317	508	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0048618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	112	582	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.106928645688615	4	FACETS	0.959	0.869	1	1	0.983	1	INDETERMINATE	3	TRUE	2	0.22228070286514	4		582	428	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17743046	17743046	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	69	601	0	ENST00000250003.3:c.954G>T	p.Gln318His	p.Q318H	ENST00000250003	NM_002478.4	318	caG/caT	3/3	0.106928645688615	4	FACETS	1	0.958	1	0.625	0.544	0.712	INDETERMINATE	1	TRUE	2	0.22228070286514	4		601	607	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949339	71949339	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	53	524	0	ENST00000298229.2:c.3719G>C	p.Gly1240Ala	p.G1240A	ENST00000298229	NM_001567.3	1240	gGg/gCg	28/28	0.106928645688615	4	FACETS	1	0.89	1	0.526	0.448	0.611	INDETERMINATE	1	TRUE	2	0.22228070286514	4		524	554	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998952	100998952	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	76	665	0	ENST00000325455.5:c.850G>T	p.Glu284Ter	p.E284*	ENST00000325455	NM_001202474.3	284	Gag/Tag	1/8	0.22228070286514	2	FACETS	1	0.973	1	0.704	0.619	0.794	CLONAL	1	TRUE	0	0.22228070286514	2		665	486	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199896	108199896	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	65	189	0	ENST00000278616.4:c.7238A>G	p.Lys2413Arg	p.K2413R	ENST00000278616	NM_000051.3	2413	aAg/aGg	49/63	0.22228070286514	2	FACETS	0.89	0.783	1	1	0.968	1	CLONAL	3	TRUE	0	0.22228070286514	2		189	219	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169067	119169067	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0048618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	31	324	0	ENST00000264033.4:c.2252-1G>T		p.X751_splice	ENST00000264033	NM_005188.3	751			0.22228070286514	2	FACETS	0.949	0.77	1	0.474	0.385	0.575	CLONAL	1	TRUE	0	0.22228070286514	2		324	294	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21643202	21643202	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	58	460	0	ENST00000421138.2:c.325G>T	p.Val109Leu	p.V109L	ENST00000421138		109	Gta/Tta	5/16	0.106928645688615	4	FACETS	1	0.936	1	0.58	0.498	0.669	INDETERMINATE	1	TRUE	2	0.22228070286514	4		460	550	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945085	31945085	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747057753	NA	P-0048618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	128	499	0	ENST00000340398.3:c.16C>G	p.Gln6Glu	p.Q6E	ENST00000340398	NM_001013699.2	6	Cag/Gag	1/1	0.106928645688615	4	FACETS	1	0.975	1	1	0.975	1	INDETERMINATE	2	TRUE	2	0.22228070286514	4		499	583	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105605	30105605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	147	489	1	ENST00000331968.5:c.1081G>A	p.Glu361Lys	p.E361K	ENST00000331968	NM_002742.2	361	Gaa/Aaa	7/18	0.22228070286514	5	FACETS	0.891	0.816	0.969	0.891	0.816	0.969	CLONAL	3	TRUE	2	0.22228070286514	5		490	660	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610162	81610162	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	117	360	0	ENST00000298171.2:c.1760T>A	p.Leu587Gln	p.L587Q	ENST00000298171	NM_000369.2	587	cTg/cAg	10/10	0.22228070286514	5	FACETS	0.989	0.897	1	0.989	0.897	1	CLONAL	3	TRUE	2	0.22228070286514	5		360	473	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273902	10273902	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	53	614	2	ENST00000330684.3:c.367C>A	p.Pro123Thr	p.P123T	ENST00000330684	NM_001134407.1	123	Ccc/Acc	2/13	0.22228070286514	6	FACETS	0.921	0.784	1	0.23	0.196	0.268	CLONAL	1	TRUE	2	0.22228070286514	6		616	748	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619007	37619007	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	37	462	0	ENST00000447079.4:c.683C>T	p.Ser228Phe	p.S228F	ENST00000447079	NM_015083.1	228	tCt/tTt	1/14	0.17586607953369	3	FACETS	0.705	0.58	0.844	0.352	0.29	0.422	SUBCLONAL	1	TRUE	1	0.22228070286514	3		462	525	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774158	56774158	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	48	388	0	ENST00000337432.4:c.509T>G	p.Val170Gly	p.V170G	ENST00000337432	NM_058216.2	170	gTa/gGa	3/9	0.22228070286514	6	FACETS	0.976	0.824	1	0.244	0.206	0.286	CLONAL	1	TRUE	2	0.22228070286514	6		388	639	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732442	74732442	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	69	286	0	ENST00000359995.5:c.467G>T	p.Arg156Leu	p.R156L	ENST00000359995	NM_001195427.1	156	cGa/cTa	2/3	0.22228070286514	6	FACETS	1	0.928	1	0.544	0.476	0.617	CLONAL	2	TRUE	2	0.22228070286514	6		286	412	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590664	189590664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	32	311	0	ENST00000264731.3:c.1229C>T	p.Thr410Ile	p.T410I	ENST00000264731	NM_003722.4	410	aCt/aTt	10/14	0.207852036221704	3	FACETS	0.831	0.675	1	0.415	0.337	0.504	CLONAL	1	TRUE	1	0.22228070286514	3		311	385	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067061	143067062	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0048618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	36	323	1	ENST00000262992.4:c.1651_1652delinsTT	p.Gly551Phe	p.G551F	ENST00000262992	NM_001101669.1	551	GGc/TTc	16/24	0.22228070286514	3	FACETS	0.911	0.75	1	0.456	0.375	0.546	CLONAL	1	TRUE	1	0.22228070286514	3		324	395	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672536	30672536	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	51	480	0	ENST00000376406.3:c.4424G>T	p.Arg1475Met	p.R1475M	ENST00000376406	NM_014641.2	1475	aGg/aTg	10/15	0.17586607953369	3	FACETS	1	0.892	1	0.53	0.451	0.617	CLONAL	1	TRUE	1	0.22228070286514	3		480	481	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741562	145741562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	185	639	0	ENST00000428558.2:c.941C>T	p.Pro314Leu	p.P314L	ENST00000428558	NM_004260.3	314	cCa/cTa	5/22	0.156882107239365	5	FACETS	0.929	0.86	1	0.929	0.86	1	CLONAL	3	TRUE	2	0.22228070286514	5		639	796	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0048619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	93	691	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	1	2	FACETS	0.964	0.858	1	0.964	0.858	1	CLONAL	1	FALSE	1	0.28155018771544	2		691	685	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922020	39922020	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	72	497	0	ENST00000378444.4:c.4152C>A	p.Tyr1384Ter	p.Y1384*	ENST00000378444	NM_001123385.1	1384	taC/taA	9/15	1	2	FACETS	0.833	0.728	0.946	0.833	0.728	0.946	CLONAL	1	FALSE	1	0.28155018771544	2		497	614	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405168	70405168	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	92	443	0	ENST00000373644.4:c.2682A>G	p.Ile894Met	p.I894M	ENST00000373644	NM_030625.2	894	atA/atG	4/12	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.28155018771544	2		443	539	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068862	30068862	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	74	339	0	ENST00000331968.5:c.2067G>T	p.Gln689His	p.Q689H	ENST00000331968	NM_002742.2	689	caG/caT	14/18	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	1	0.28155018771544	2		339	486	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538256	9538256	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	73	370	0	ENST00000353224.5:c.1742G>T	p.Arg581Leu	p.R581L	ENST00000353224	NM_177990.2	581	cGg/cTg	7/10	1	2	FACETS	0.918	0.804	1	0.918	0.804	1	CLONAL	1	FALSE	1	0.28155018771544	2		370	565	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032569	47032570	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	92	604	0	ENST00000377604.3:c.477dup	p.Arg160SerfsTer20	p.R160Sfs*20	ENST00000377604	NM_001204468.1	159	gtt/gTtt	5/24	1	2	FACETS	0.957	0.851	1	0.957	0.851	1	CLONAL	1	FALSE	1	0.28155018771544	2		604	683	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	123	388	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.888	0.808	0.972	0.888	0.808	0.972	CLONAL	1	TRUE	1	0.556162523956438	2		388	498	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	40	603	0	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.283	0.234	0.336	0.283	0.234	0.336	SUBCLONAL	1	TRUE	1	0.556162523956438	2		603	509	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	387	774	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.845	0.808	0.883	1	0.996	1	CLONAL	2	TRUE	1	0.556162523956438	2		778	823	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	43	745	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.202	0.168	0.239	0.202	0.168	0.239	SUBCLONAL	1	TRUE	1	0.556162523956438	2		750	767	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	203	888	9	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.556162523956438	2		897	706	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647657	3647657	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs774532876	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	192	732	4	ENST00000294008.3:c.1406del	p.Pro469HisfsTer4	p.P469Hfs*4	ENST00000294008	NM_032444.2	469	cCa/ca	7/15	1	2	FACETS	0.922	0.855	0.991	0.922	0.855	0.991	CLONAL	1	TRUE	1	0.556162523956438	2		736	749	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	165	913	0	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	0.759	0.698	0.822	0.759	0.698	0.822	SUBCLONAL	1	TRUE	1	0.556162523956438	2		913	782	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	124	435	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.921	0.839	1	0.921	0.839	1	CLONAL	1	TRUE	1	0.556162523956438	2		436	484	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	106	453	7	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	0.556162523956438	3	FACETS	0.686	0.615	0.761	0.343	0.307	0.381	SUBCLONAL	1	TRUE	1	0.556162523956438	3		460	710	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	204	703	3	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.985	0.916	1	0.985	0.916	1	CLONAL	1	TRUE	1	0.556162523956438	2		706	745	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	54	622	6	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.31	0.264	0.36	0.31	0.264	0.36	SUBCLONAL	1	TRUE	1	0.556162523956438	2		628	627	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796883	42796883	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	256	973	3	ENST00000575354.2:c.3347del	p.Pro1116GlnfsTer45	p.P1116Qfs*45	ENST00000575354	NM_015125.3	1114	gCc/gc	14/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.556162523956438	2		976	896	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	45	221	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.686	0.581	0.799	0.686	0.581	0.799	SUBCLONAL	1	TRUE	1	0.556162523956438	2		221	236	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662338	227662338	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147944503	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	54	858	1	ENST00000305123.5:c.1117C>T	p.Arg373Cys	p.R373C	ENST00000305123	NM_005544.2	373	Cgc/Tgc	1/2	0.556162523956438	3	FACETS	0.3	0.255	0.349	0.15	0.127	0.175	SUBCLONAL	1	TRUE	1	0.556162523956438	3		859	827	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039339	49039339	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	102	458	0	ENST00000267163.4:c.2326-2A>G		p.X776_splice	ENST00000267163	NM_000321.2	776			1	2	FACETS	0.822	0.74	0.909	0.822	0.74	0.909	CLONAL	1	TRUE	1	0.556162523956438	2		458	446	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692916	89692918	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	rs1554898152	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	69	404	0	ENST00000371953.3:c.402_404del	p.Met134del	p.M134del	ENST00000371953	NM_000314.4	134	ATG/-	5/9	1	2	FACETS	0.73	0.64	0.825	0.73	0.64	0.825	SUBCLONAL	1	TRUE	1	0.556162523956438	2		404	340	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725055	89725055	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	48	178	0	ENST00000371953.3:c.1038C>G	p.Tyr346Ter	p.Y346*	ENST00000371953	NM_000314.4	346	taC/taG	9/9	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.556162523956438	2		178	158	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306996	65306997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	105	367	6	ENST00000342505.4:c.2580dup	p.Pro861ThrfsTer4	p.P861Tfs*4	ENST00000342505	NM_002227.2	860	-/A	19/25	1	2	FACETS	0.793	0.714	0.876	0.793	0.714	0.876	SUBCLONAL	1	TRUE	1	0.556162523956438	2		373	476	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285059	15285059	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs367543285	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	228	942	0	ENST00000263388.2:c.4556T>C	p.Leu1519Pro	p.L1519P	ENST00000263388	NM_000435.2	1519	cTg/cCg	25/33	1	2	FACETS	0.997	0.932	1	0.997	0.932	1	CLONAL	1	TRUE	1	0.556162523956438	2		942	822	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821214	72821214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1044596115	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	40	604	1	ENST00000268489.5:c.10961C>T	p.Ser3654Leu	p.S3654L	ENST00000268489	NM_006885.3	3654	tCg/tTg	10/10	1	2	FACETS	0.189	0.156	0.226	0.189	0.156	0.226	SUBCLONAL	1	TRUE	1	0.556162523956438	2		605	760	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112571	115112571	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	51	810	1	ENST00000257566.3:c.1169G>A	p.Cys390Tyr	p.C390Y	ENST00000257566	NM_016569.3	390	tGc/tAc	7/8	0.542391857243758	3	FACETS	0.233	0.197	0.272	0.116	0.098	0.136	SUBCLONAL	1	TRUE	1	0.556162523956438	3		811	1008	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	220	600	1	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	0.542391857243758	3	FACETS	1	0.992	1	0.736	0.688	0.785	CLONAL	1	TRUE	1	0.556162523956438	3		601	687	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524581	187524581	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	159	563	0	ENST00000441802.2:c.11099A>G	p.Lys3700Arg	p.K3700R	ENST00000441802	NM_005245.3	3700	aAa/aGa	19/27	1	2	FACETS	0.853	0.785	0.925	0.853	0.785	0.925	CLONAL	1	TRUE	1	0.556162523956438	2		563	670	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933458	36933458	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs764132853	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	205	823	0	ENST00000361632.4:c.1829A>G	p.Asn610Ser	p.N610S	ENST00000361632		610	aAc/aGc	13/16	1	2	FACETS	0.924	0.859	0.991	0.924	0.859	0.991	CLONAL	1	TRUE	1	0.556162523956438	2		823	798	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24134057	24134057	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	38	415	0	ENST00000263121.7:c.214del	p.Thr72GlnfsTer13	p.T72Qfs*13	ENST00000263121	NM_003073.3	70	Aaa/aa	2/9	1	2	FACETS	0.272	0.225	0.326	0.272	0.225	0.326	SUBCLONAL	1	TRUE	1	0.556162523956438	2		415	502	SUCCESS
CBL	867	MSKCC	GRCh37	11	119146766	119146766	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764199611	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	49	417	0	ENST00000264033.4:c.929C>T	p.Ala310Val	p.A310V	ENST00000264033	NM_005188.3	310	gCt/gTt	6/16	1	2	FACETS	0.316	0.267	0.37	0.316	0.267	0.37	SUBCLONAL	1	TRUE	1	0.556162523956438	2		417	557	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436791	110436793	+	inframe_deletion	In_Frame_Del	DEL	CCG	CCG	-	rs769193882	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	167	864	1	ENST00000375856.3:c.1608_1610del	p.Gly537del	p.G537del	ENST00000375856	NM_003749.2	536	ggCGGt/ggt	1/2	1	2	FACETS	0.759	0.699	0.822	0.759	0.699	0.822	SUBCLONAL	1	TRUE	1	0.556162523956438	2		865	791	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098975	178098975	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	136	245	0	ENST00000397062.3:c.70T>G	p.Trp24Gly	p.W24G	ENST00000397062	NM_006164.4	24	Tgg/Ggg	2/5	0.556162523956438	3	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	1	0.556162523956438	3		245	306	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798864	135798864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372215435	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	21	289	0	ENST00000298552.3:c.379G>A	p.Val127Ile	p.V127I	ENST00000298552	NM_001162426.1	127	Gtt/Att	6/23	1	2	FACETS	0.196	0.15	0.249	0.196	0.15	0.249	SUBCLONAL	1	TRUE	1	0.556162523956438	2		289	386	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793028	33793028	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1490895935	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	42	211	0	ENST00000498907.2:c.293C>T	p.Thr98Met	p.T98M	ENST00000498907	NM_004364.3	98	aCg/aTg	1/1	1	2	FACETS	0.787	0.665	0.918	0.787	0.665	0.918	CLONAL	1	TRUE	1	0.556162523956438	2		211	192	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219152	133219152	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775590365	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	425	819	0	ENST00000320574.5:c.4892G>A	p.Arg1631His	p.R1631H	ENST00000320574	NM_006231.2	1631	cGc/cAc	37/49	0.542391857243758	3	FACETS	0.914	0.874	0.956	0.914	0.874	0.956	CLONAL	2	TRUE	1	0.556162523956438	3		819	1068	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105571	27105571	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	152	497	0	ENST00000324856.7:c.5184del	p.Phe1728LeufsTer4	p.F1728Lfs*4	ENST00000324856	NM_006015.4	1728	Ttt/tt	20/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.556162523956438	2		497	515	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733555	85733555	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	145	475	0	ENST00000370580.1:c.457A>G	p.Met153Val	p.M153V	ENST00000370580	NM_003921.4	153	Atg/Gtg	3/3	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.556162523956438	2		475	506	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731137	162731137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	155	573	0	ENST00000367921.3:c.992C>T	p.Ala331Val	p.A331V	ENST00000367921	NM_006182.2	331	gCt/gTt	9/18	0.542391857243758	3	FACETS	0.923	0.846	1	0.461	0.423	0.502	CLONAL	1	TRUE	1	0.556162523956438	3		573	772	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132098	176132098	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	76	400	0	ENST00000367669.3:c.669A>C	p.Gln223His	p.Q223H	ENST00000367669	NM_022457.5	223	caA/caC	5/20	0.542391857243758	3	FACETS	1	0.887	1	0.502	0.443	0.564	CLONAL	1	TRUE	1	0.556162523956438	3		400	348	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200284	67200284	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs187592167	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	47	787	1	ENST00000312629.5:c.592G>A	p.Glu198Lys	p.E198K	ENST00000312629	NM_003952.2	198	Gag/Aag	7/15	1	2	FACETS	0.226	0.19	0.266	0.226	0.19	0.266	SUBCLONAL	1	TRUE	1	0.556162523956438	2		788	749	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911063	94911063	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	28	363	0	ENST00000536441.1:c.1067G>T	p.Trp356Leu	p.W356L	ENST00000536441	NM_144665.3	356	tGg/tTg	8/10	1	2	FACETS	0.274	0.219	0.337	0.274	0.219	0.337	SUBCLONAL	1	TRUE	1	0.556162523956438	2		363	367	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245023	133245024	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs752846614	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	65	811	1	ENST00000320574.5:c.2091dup	p.Phe699ValfsTer11	p.F699Vfs*11	ENST00000320574	NM_006231.2	697	-/C	19/49	0.542391857243758	3	FACETS	0.289	0.249	0.332	0.144	0.124	0.166	SUBCLONAL	1	TRUE	1	0.556162523956438	3		812	1035	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032282	42032282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	177	586	0	ENST00000219905.7:c.4466G>A	p.Arg1489Lys	p.R1489K	ENST00000219905	NM_001164273.1	1489	aGg/aAg	14/24	1	2	FACETS	0.978	0.905	1	0.978	0.905	1	CLONAL	1	TRUE	1	0.556162523956438	2		586	651	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669529	88669529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	85	430	0	ENST00000360948.2:c.1369G>A	p.Gly457Ser	p.G457S	ENST00000360948	NM_001012338.2	457	Ggt/Agt	12/19	1	2	FACETS	0.614	0.544	0.688	0.614	0.544	0.688	SUBCLONAL	1	TRUE	1	0.556162523956438	2		430	498	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805322	89805322	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	126	687	0	ENST00000389301.3:c.4228T>C	p.Cys1410Arg	p.C1410R	ENST00000389301	NM_000135.2	1410	Tgc/Cgc	42/43	1	2	FACETS	0.607	0.55	0.667	0.607	0.55	0.667	SUBCLONAL	1	TRUE	1	0.556162523956438	2		687	747	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881616	37881616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758222990	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	167	635	1	ENST00000269571.5:c.2686C>T	p.Arg896Cys	p.R896C	ENST00000269571		896	Cgc/Tgc	22/27	1	2	FACETS	0.812	0.747	0.878	0.812	0.747	0.878	CLONAL	1	TRUE	1	0.556162523956438	2		636	740	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62322274	62322274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368297230	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	230	971	4	ENST00000360203.5:c.2530C>T	p.Arg844Trp	p.R844W	ENST00000360203	NM_001283009.1	844	Cgg/Tgg	27/35	1	2	FACETS	0.954	0.891	1	0.954	0.891	1	CLONAL	1	TRUE	1	0.556162523956438	2		975	867	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231180	142231180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	32	565	1	ENST00000350721.4:c.4774G>A	p.Ala1592Thr	p.A1592T	ENST00000350721	NM_001184.3	1592	Gca/Aca	27/47	1	2	FACETS	0.182	0.147	0.222	0.182	0.147	0.222	SUBCLONAL	1	TRUE	1	0.556162523956438	2		566	632	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964941	55964941	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs141493431	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	28	360	1	ENST00000263923.4:c.2296A>G	p.Ile766Val	p.I766V	ENST00000263923	NM_002253.2	766	Att/Gtt	16/30	1	2	FACETS	0.227	0.181	0.279	0.227	0.181	0.279	SUBCLONAL	1	TRUE	1	0.556162523956438	2		361	444	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233081	66233081	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	90	339	0	ENST00000273854.3:c.1918G>A	p.Gly640Arg	p.G640R	ENST00000273854	NM_004439.5	640	Ggg/Agg	10/18	1	2	FACETS	0.93	0.833	1	0.93	0.833	1	CLONAL	1	TRUE	1	0.556162523956438	2		339	348	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155639	56155639	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	164	377	0	ENST00000399503.3:c.731C>A	p.Ala244Asp	p.A244D	ENST00000399503	NM_005921.1	244	gCt/gAt	3/20	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.556162523956438	2		377	579	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064788	80064790	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	65	263	0	ENST00000265081.6:c.2221_2223del	p.Ser741del	p.S741del	ENST00000265081	NM_002439.4	740	cCTTct/cct	15/24	1	2	FACETS	0.835	0.731	0.945	0.835	0.731	0.945	CLONAL	1	TRUE	1	0.556162523956438	2		263	280	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797289	32797289	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	166	682	0	ENST00000374899.4:c.1820T>C	p.Leu607Pro	p.L607P	ENST00000374899	NM_018833.2	607	cTg/cCg	11/12	1	2	FACETS	0.79	0.727	0.855	0.79	0.727	0.855	SUBCLONAL	1	TRUE	1	0.556162523956438	2		682	756	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5078333	5078333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	18	274	0	ENST00000381652.3:c.2020G>A	p.Val674Ile	p.V674I	ENST00000381652	NM_004972.3	674	Gta/Ata	16/25	0.556162523956438	2	FACETS	0.231	0.174	0.299	0.116	0.087	0.15	SUBCLONAL	1	TRUE	0	0.556162523956438	2		274	280	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019779	123019779	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	155	532	0	ENST00000355640.3:c.267T>A	p.Asn89Lys	p.N89K	ENST00000355640		89	aaT/aaA	2/7	1	2	FACETS	0.99	0.911	1	0.99	0.911	1	CLONAL	1	TRUE	1	0.556162523956438	2		532	563	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0048621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	59	636	0	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	1	2	FACETS	0.92	0.789	1	0.92	0.789	1	CLONAL	1	TRUE	1	0.14	2		636	916	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578464	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	62	744	0	ENST00000269305.4:c.466del	p.Arg156AlafsTer14	p.R156Afs*14	ENST00000269305	NM_001126112.2	156	Cgc/gc	5/11	1	2	FACETS	0.76	0.654	0.876	0.76	0.654	0.876	SUBCLONAL	1	TRUE	1	0.14	2		744	1166	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0048621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	22	331	0	ENST00000288602.6:c.1397G>T	p.Gly466Val	p.G466V	ENST00000288602	NM_004333.4	466	gGa/gTa	11/18	1	2	FACETS	0.614	0.474	0.777	0.614	0.474	0.777	SUBCLONAL	1	TRUE	1	0.14	2		331	512	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041419	42041419	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	48	416	0	ENST00000219905.7:c.5614G>T	p.Gly1872Trp	p.G1872W	ENST00000219905	NM_001164273.1	1872	Ggg/Tgg	17/24	1	2	FACETS	0.987	0.833	1	0.987	0.833	1	CLONAL	1	TRUE	1	0.14	2		416	695	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38949913	38949913	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	49	314	0	ENST00000357387.3:c.4037C>G	p.Ser1346Cys	p.S1346C	ENST00000357387	NM_152756.3	1346	tCt/tGt	31/38	0.19627252157993	3	FACETS	1	0.945	1	0.637	0.539	0.745	CLONAL	1	TRUE	1	0.14	3		314	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0048622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	126	549	0	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	0.272321076975201	3	FACETS	0.912	0.826	1	0.456	0.413	0.502	CLONAL	1	TRUE	1	0.393497073702659	3		549	840	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0048622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	146	287	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	0.273401678449217	2	FACETS	0.778	0.715	0.842	0.778	0.715	0.842	SUBCLONAL	2	TRUE	0	0.393497073702659	2		287	477	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201854	67201854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	128	597	0	ENST00000312629.5:c.1054G>C	p.Glu352Gln	p.E352Q	ENST00000312629	NM_003952.2	352	Gag/Cag	13/15	0.201922636368699	4	FACETS	0.893	0.808	0.983	0.447	0.404	0.492	INDETERMINATE	1	TRUE	2	0.393497073702659	4		597	1015	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692886	89692886	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	210	296	0	ENST00000371953.3:c.370T>A	p.Cys124Ser	p.C124S	ENST00000371953	NM_000314.4	124	Tgt/Agt	5/9	0.393497073702659	3	FACETS	0.843	0.791	0.896	0.843	0.791	0.896	CLONAL	3	TRUE	0	0.393497073702659	3		296	505	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593477	48593477	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	133	329	0	ENST00000342988.3:c.1228C>T	p.Gln410Ter	p.Q410*	ENST00000342988	NM_005359.5	410	Cag/Tag	10/12	0.273401678449217	2	FACETS	0.837	0.767	0.908	0.837	0.767	0.908	CLONAL	2	TRUE	0	0.393497073702659	2		329	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	286	755	0	ENST00000269305.4:c.524del	p.Arg175ProfsTer72	p.R175Pfs*72	ENST00000269305	NM_001126112.2	175	cGc/cc	5/11	0.272321076975201	3	FACETS	1	0.993	1	0.743	0.698	0.789	CLONAL	1	TRUE	1	0.393497073702659	3		755	1171	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087349	27087349	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	134	399	0	ENST00000324856.7:c.1923del	p.Leu642TyrfsTer5	p.L642Yfs*5	ENST00000324856	NM_006015.4	641	gaT/ga	5/20	0.273401678449217	2	FACETS	1	0.987	1	0.748	0.685	0.814	CLONAL	1	TRUE	0	0.393497073702659	2		399	455	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984447	201984447	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	191	464	1	ENST00000359651.3:c.1112A>T	p.Asn371Ile	p.N371I	ENST00000359651		371	aAc/aTc	8/8	0.272321076975201	3	FACETS	0.779	0.722	0.837	0.779	0.722	0.837	SUBCLONAL	2	TRUE	1	0.393497073702659	3		465	746	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755461	39755461	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	90	504	0	ENST00000288319.7:c.1304C>T	p.Pro435Leu	p.P435L	ENST00000288319	NM_182918.3	435	cCt/cTt	10/10	1	2	FACETS	0.685	0.608	0.767	0.685	0.608	0.767	SUBCLONAL	1	TRUE	1	0.393497073702659	2		504	668	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356281	66356281	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	98	578	0	ENST00000273854.3:c.1216G>C	p.Glu406Gln	p.E406Q	ENST00000273854	NM_004439.5	406	Gag/Cag	5/18	0.272321076975201	3	FACETS	0.76	0.678	0.848	0.38	0.339	0.424	SUBCLONAL	1	TRUE	1	0.393497073702659	3		578	784	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020922	26020922	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs181930473	NA	P-0048623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	30	452	1	ENST00000357647.3:c.205C>T	p.Gln69Ter	p.Q69*	ENST00000357647	NM_003529.2	69	Cag/Tag	1/1	1	2	FACETS	0.93	0.749	1	0.93	0.749	1	CLONAL	1	TRUE	1	0.15	2		453	430	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924672	94924672	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	45	544	1	ENST00000536441.1:c.238A>T	p.Ser80Cys	p.S80C	ENST00000536441	NM_144665.3	80	Agt/Tgt	3/10	1	2	FACETS	0.96	0.806	1	0.96	0.806	1	CLONAL	1	TRUE	1	0.15	2		545	625	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936996	48936996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	29	303	0	ENST00000267163.4:c.764G>A	p.Arg255Gln	p.R255Q	ENST00000267163	NM_000321.2	255	cGa/cAa	8/27	1	2	FACETS	0.976	0.784	1	0.976	0.784	1	CLONAL	1	TRUE	1	0.15	2		303	396	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	85	301	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		301	280	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578196	7578197	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0048625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	86	513	0	ENST00000269305.4:c.652dup	p.Val218GlyfsTer4	p.V218Gfs*4	ENST00000269305	NM_001126112.2	218	gtg/gGtg	6/11	0.217531081309973	2	FACETS	1	0.98	1	0.749	0.67	0.831	INDETERMINATE	1	TRUE	0	0.384066033509244	2		513	299	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	140	482	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.493943783398059	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.493943783398059	1		482	411	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849545	68849545	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	166	488	0	ENST00000261769.5:c.1452del	p.Ile485SerfsTer37	p.I485Sfs*37	ENST00000261769	NM_004360.3	483	gCc/gc	10/16	1	2	FACETS	0.889	0.818	0.963	0.889	0.818	0.963	CLONAL	1	TRUE	1	0.493943783398059	2		488	756	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842746	68842756	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TACACTGTAAG	TACACTGTAAG	-	novel	NA	P-0048627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	104	337	0	ENST00000261769.5:c.684_687+7del		p.X228_splice	ENST00000261769	NM_004360.3	228		5/16	1	2	FACETS	0.888	0.8	0.982	0.888	0.8	0.982	CLONAL	1	TRUE	1	0.493943783398059	2		337	474	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171612	36171613	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0048627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	102	261	0	ENST00000300305.3:c.952_953del	p.Ser318GlnfsTer281	p.S318Qfs*281	ENST00000300305		318	TCc/c	7/8	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.493943783398059	2		261	410	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170002367	170002367	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	67	205	0	ENST00000295797.4:c.1186G>C	p.Asp396His	p.D396H	ENST00000295797	NM_002740.5	396	Gac/Cac	12/18	1	2	FACETS	0.949	0.832	1	0.949	0.832	1	CLONAL	1	TRUE	1	0.493943783398059	2		205	286	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094314	27094316	+	frameshift_variant	Frame_Shift_Del	DEL	ATC	ATC	G	novel	NA	P-0048627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	156	328	0	ENST00000324856.7:c.3022_3024delinsG	p.Ile1008AspfsTer5	p.I1008Dfs*5	ENST00000324856	NM_006015.4	1008	ATC/G	11/20	0.444277003085227	2	FACETS	0.761	0.704	0.819	0.761	0.704	0.819	SUBCLONAL	2	TRUE	0	0.493943783398059	2		328	415	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	232	301	0				ENST00000310581	NM_198253.2	-/1132			0.676714332753364	3	FACETS	0.997	0.943	1	0.997	0.943	1	CLONAL	2	TRUE	1	0.676714332753364	3		301	460	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528489	29528489	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764079291	NA	P-0048628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	91	427	0	ENST00000356175.3:c.1246C>T	p.Arg416Ter	p.R416*	ENST00000356175	NM_000267.3	416	Cga/Tga	11/57	0.281421033780208	1	FACETS	0.385	0.343	0.429	0.385	0.343	0.429	INDETERMINATE	1	TRUE	0	0.676714332753364	1		427	462	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588859	29588859	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	79	259	0	ENST00000356175.3:c.4645G>T	p.Glu1549Ter	p.E1549*	ENST00000356175	NM_000267.3	1549	Gag/Tag	34/57	0.281421033780208	1	FACETS	0.445	0.394	0.499	0.445	0.394	0.499	INDETERMINATE	1	TRUE	0	0.676714332753364	1		259	347	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56402553	56402553	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	77	131	0	ENST00000348428.3:c.1595T>C	p.Val532Ala	p.V532A	ENST00000348428	NM_006785.3	532	gTt/gCt	13/17	0.180711399589011	6	FACETS	0.93	0.825	1			1	INDETERMINATE	2	TRUE	NA	0.676714332753364	6		131	288	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245204	46245204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	242	457	0	ENST00000334344.6:c.3298C>T	p.Gln1100Ter	p.Q1100*	ENST00000334344	NM_152641.2	1100	Cag/Tag	15/21	1	2	FACETS	0.984	0.923	1	0.984	0.923	1	CLONAL	1	TRUE	1	0.676714332753364	2		457	727	SUCCESS
BLM	641	MSKCC	GRCh37	15	91290720	91290720	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs139282091	NA	P-0048628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	62	223	0	ENST00000355112.3:c.98C>T	p.Ser33Leu	p.S33L	ENST00000355112	NM_000057.2	33	tCa/tTa	2/22	0.320828461788773	1	FACETS	0.394	0.342	0.448	0.394	0.342	0.448	INDETERMINATE	1	TRUE	0	0.676714332753364	1		223	308	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546098	29546098	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1567843917	NA	P-0048628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	223	381	0	ENST00000356175.3:c.1603C>T	p.Gln535Ter	p.Q535*	ENST00000356175	NM_000267.3	535	Cag/Tag	14/57	0.281421033780208	1	FACETS	0.78	0.732	0.829	0.78	0.732	0.829	INDETERMINATE	1	TRUE	0	0.676714332753364	1		381	559	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468319	50468319	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	586	482	0	ENST00000331340.3:c.1554G>A	p.Met518Ile	p.M518I	ENST00000331340	NM_006060.4	518	atG/atA	8/8	0.589844012889288	4	FACETS	0.944	0.914	0.975	0.944	0.914	0.975	CLONAL	3	TRUE	1	0.676714332753364	4		482	1025	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100496	8100496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	175	714	0	ENST00000346208.3:c.470C>T	p.Pro157Leu	p.P157L	ENST00000346208		157	cCg/cTg	3/6	0.320828461788773	1	FACETS	0.405	0.373	0.439	0.405	0.373	0.439	INDETERMINATE	1	TRUE	0	0.676714332753364	1		714	844	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160464	108160464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	188	429	0	ENST00000278616.4:c.4372G>A	p.Gly1458Arg	p.G1458R	ENST00000278616	NM_000051.3	1458	Gga/Aga	29/63	0.338527765227442	3	FACETS	1	0.977	1	0.564	0.523	0.606	INDETERMINATE	1	TRUE	1	0.676714332753364	3		429	659	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288350	33288350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141322869	NA	P-0048628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	427	481	0	ENST00000374542.5:c.1058C>T	p.Ser353Leu	p.S353L	ENST00000374542	NM_001141970.1	353	tCa/tTa	4/8	0.610620381536026	3	FACETS	0.933	0.894	0.972	0.933	0.894	0.972	CLONAL	2	TRUE	1	0.676714332753364	3		481	905	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435082	18435082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	169	334	0	ENST00000266497.5:c.67G>A	p.Glu23Lys	p.E23K	ENST00000266497		23	Gaa/Aaa	1/31	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.676714332753364	2		334	463	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805722	43805722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	416	593	1	ENST00000372470.3:c.778C>T	p.Pro260Ser	p.P260S	ENST00000372470	NM_005373.2	260	Cct/Tct	5/12	0.259407939000228	3	FACETS	0.83	0.793	0.867	0.83	0.793	0.867	INDETERMINATE	2	TRUE	1	0.676714332753364	3		594	991	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221268	2221268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	183	713	1	ENST00000326181.6:c.352C>T	p.Pro118Ser	p.P118S	ENST00000326181	NM_032271.2	118	Cca/Tca	6/21	0.320828461788773	1	FACETS	0.424	0.392	0.458	0.424	0.392	0.458	INDETERMINATE	1	TRUE	0	0.676714332753364	1		714	843	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089901	16089901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	104	340	0	ENST00000268712.3:c.209C>T	p.Ser70Phe	p.S70F	ENST00000268712	NM_006311.3	70	tCc/tTc	3/46	0.281421033780208	1	FACETS	0.398	0.358	0.441	0.398	0.358	0.441	INDETERMINATE	1	TRUE	0	0.676714332753364	1		340	511	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858871	78858871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	346	719	0	ENST00000306801.3:c.1906C>T	p.His636Tyr	p.H636Y	ENST00000306801	NM_020761.2	636	Cac/Tac	17/34	1	2	FACETS	0.953	0.903	1	0.953	0.903	1	CLONAL	1	TRUE	1	0.676714332753364	2		719	1073	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956146	55956146	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867547352	NA	P-0048628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	196	447	0	ENST00000263923.4:c.3169C>T	p.Pro1057Ser	p.P1057S	ENST00000263923	NM_002253.2	1057	Cca/Tca	23/30	1	2	FACETS	0.871	0.81	0.934	0.871	0.81	0.934	CLONAL	1	TRUE	1	0.676714332753364	2		447	665	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510063	187510063	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	217	368	0	ENST00000441802.2:c.13450T>C	p.Phe4484Leu	p.F4484L	ENST00000441802	NM_005245.3	4484	Ttc/Ctc	27/27	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.676714332753364	2		368	600	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805718	32805718	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	314	681	0	ENST00000374899.4:c.293C>T	p.Pro98Leu	p.P98L	ENST00000374899	NM_018833.2	98	cCt/cTt	2/12	0.610620381536026	3	FACETS	1	0.993	1	0.667	0.631	0.704	CLONAL	1	TRUE	1	0.676714332753364	3		681	931	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0048629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	449	577	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.752455301732985	5	FACETS	0.931	0.893	0.968	0.931	0.893	0.968	CLONAL	3	TRUE	2	0.752455301732985	5		577	910	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573563	48573564	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs786203560	NA	P-0048629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	216	280	1	ENST00000342988.3:c.153dup	p.Asp52ArgfsTer2	p.D52Rfs*2	ENST00000342988	NM_005359.5	49	-/A	2/12	0.752455301732985	2	FACETS	0.897	0.855	0.938	0.897	0.855	0.938	CLONAL	2	TRUE	0	0.752455301732985	2		281	320	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579484	7579484	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	486	601	0	ENST00000269305.4:c.203del	p.Glu68GlyfsTer55	p.E68Gfs*55	ENST00000269305	NM_001126112.2	68	gAg/gg	4/11	0.752455301732985	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.752455301732985	2		601	636	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938466	44938468	+	frameshift_variant	Frame_Shift_Ins	INS	TGC	TGC	ATCA	novel	NA	P-0048629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	245	257	0	ENST00000377967.4:c.3014_3016delinsATCA	p.Leu1005TyrfsTer6	p.L1005Yfs*6	ENST00000377967	NM_021140.2	1005	tTGCag/tATCAag	20/29	0.726097616545838	2	FACETS	0.975	0.936	1			1	CLONAL	2	TRUE	NA	0.752455301732985	2		257	334	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041656	42041656	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	137	432	0	ENST00000219905.7:c.5851G>T	p.Gly1951Ter	p.G1951*	ENST00000219905	NM_001164273.1	1951	Gga/Tga	17/24	1	2	FACETS	0.456	0.415	0.498	0.456	0.415	0.498	SUBCLONAL	1	TRUE	1	0.87	2		432	691	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249269	10249269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1197552228	NA	P-0048630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	323	504	12	ENST00000340748.4:c.3913G>A	p.Gly1305Ser	p.G1305S	ENST00000340748		1305	Ggc/Agc	34/40	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.87	2		516	722	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0048649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	143	327	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.524321857712191	2		327	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579361	7579361	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1064796722	NA	P-0048649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	299	663	0	ENST00000269305.4:c.326T>C	p.Phe109Ser	p.F109S	ENST00000269305	NM_001126112.2	109	tTc/tCc	4/11	0.524321857712191	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.524321857712191	1		663	764	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436247	110436247	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	125	276	0	ENST00000375856.3:c.2154G>T	p.Arg718Ser	p.R718S	ENST00000375856	NM_003749.2	718	agG/agT	1/2	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.524321857712191	2		276	473	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156554	55156554	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	242	513	0	ENST00000257290.5:c.2955C>G	p.Asp985Glu	p.D985E	ENST00000257290	NM_006206.4	985	gaC/gaG	22/23	1	2	FACETS	0.987	0.923	1	0.987	0.923	1	CLONAL	1	TRUE	1	0.524321857712191	2		513	935	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117650557	117650557	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	220	508	0	ENST00000368508.3:c.5301T>G	p.Asn1767Lys	p.N1767K	ENST00000368508	NM_002944.2	1767	aaT/aaG	32/43	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.524321857712191	2		508	769	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992733	68992733	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1247482872	NA	P-0048649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	133	411	1	ENST00000288368.4:c.1698T>A	p.Asp566Glu	p.D566E	ENST00000288368	NM_024870.2	566	gaT/gaA	16/40	1	2	FACETS	0.861	0.785	0.941	0.861	0.785	0.941	CLONAL	1	TRUE	1	0.524321857712191	2		412	589	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141549421	141549421	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1156411831	NA	P-0048649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	151	308	1	ENST00000220592.5:c.2167C>T	p.Arg723Trp	p.R723W	ENST00000220592	NM_012154.3	723	Cgg/Tgg	16/19	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.524321857712191	2		309	530	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	37	301	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.975	0.808	1	0.975	0.808	1	CLONAL	1	TRUE	1	0.27	2		301	281	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0048650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	102	604	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.935	0.836	1	0.935	0.836	1	CLONAL	1	TRUE	1	0.27	2		604	808	SUCCESS
AR	367	MSKCC	GRCh37	X	66766193	66766193	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866450936	NA	P-0048650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	68	485	0	ENST00000374690.3:c.1205C>T	p.Ala402Val	p.A402V	ENST00000374690	NM_000044.3	402	gCg/gTg	1/8	0.160881218284286	0	FACETS	0.685	0.596	0.78			1	INDETERMINATE	1	TRUE	0	0.27	0		485	537	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397742	49397742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552757	NA	P-0048650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	80	453	0	ENST00000418115.1:c.482C>T	p.Ala161Val	p.A161V	ENST00000418115	NM_001664.2	161	gCa/gTa	5/5	1	2	FACETS	0.702	0.617	0.794	0.702	0.617	0.794	SUBCLONAL	1	TRUE	1	0.27	2		453	844	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779172	135779172	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203631	NA	P-0048650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	34	409	0	ENST00000298552.3:c.2074C>T	p.Arg692Ter	p.R692*	ENST00000298552	NM_001162426.1	692	Cga/Tga	17/23	0.296726206381925	1	FACETS	0.471	0.384	0.568	0.471	0.384	0.568	SUBCLONAL	1	TRUE	0	0.27	1		409	463	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	186	576	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.264259889713879	3	FACETS	1	0.965	1	0.531	0.493	0.57	INDETERMINATE	1	TRUE	1	0.869466347668641	3		576	578	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0048652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	838	932	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.869466347668641	2	FACETS	0.989	0.973	1	0.989	0.973	1	CLONAL	2	TRUE	0	0.869466347668641	2		934	975	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0048652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	101	69	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	0.869466347668641	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.869466347668641	3		69	150	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0048652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	132	405	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.264259889713879	3	FACETS	0.604	0.549	0.662	0.302	0.274	0.331	INDETERMINATE	1	TRUE	1	0.869466347668641	3		405	721	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907651	76907651	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	324	584	2	ENST00000373344.5:c.4510C>T	p.Arg1504Ter	p.R1504*	ENST00000373344	NM_000489.3	1504	Cga/Tga	15/35	1	2	FACETS	0.96	0.912	1	0.96	0.912	1	CLONAL	1	TRUE	1	0.869466347668641	2		586	776	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0048653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	65	220	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.789182731373082	1	FACETS	0.75	0.671	0.829	0.75	0.671	0.829	SUBCLONAL	1	TRUE	0	0.789182731373082	1		220	133	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374865	45374865	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	206	396	0	ENST00000262160.6:c.978A>C	p.Glu326Asp	p.E326D	ENST00000262160	NM_005901.5	326	gaA/gaC	8/11	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.789182731373082	2		396	519	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0048655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	282	660	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.200630313374942	5	FACETS	1	0.954	1			1	INDETERMINATE	4	TRUE	NA	0.47770381763139	5		660	506	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519896	NA	P-0048655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	42	341	1	ENST00000281708.4:c.1514G>A	p.Arg505His	p.R505H	ENST00000281708	NM_033632.3	505	cGc/cAc	10/12	0.258005278134639	3	FACETS	0.772	0.649	0.908	0.386	0.324	0.454	INDETERMINATE	1	TRUE	1	0.47770381763139	3		342	282	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431212	49431233	+	frameshift_variant	Frame_Shift_Del	DEL	GGACCCAGCCAAACTGGGAGAA	GGACCCAGCCAAACTGGGAGAA	-	novel	NA	P-0048655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	28	755	0	ENST00000301067.7:c.9906_9927del	p.Ser3303AsnfsTer20	p.S3303Nfs*20	ENST00000301067	NM_003482.3	3302	tcTTCTCCCAGTTTGGCTGGGTCC/tc	34/54	0.303824915097512	5	FACETS	0.45	0.359	0.554	0.15	0.119	0.185	SUBCLONAL	1	TRUE	2	0.47770381763139	5		755	447	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891642	28891642	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	123	545	0	ENST00000282397.4:c.3379C>G	p.Pro1127Ala	p.P1127A	ENST00000282397	NM_002019.4	1127	Cct/Gct	25/30	0.41133105612664	4	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	2	0.47770381763139	4		545	365	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540450	187540451	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTCA	novel	NA	P-0048655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	87	472	0	ENST00000441802.2:c.7289_7290insTGAA	p.Ser2431GlufsTer5	p.S2431Efs*5	ENST00000441802	NM_005245.3	2430	ctg/ctTGAAg	10/27	0.258005278134639	3	FACETS	0.902	0.812	0.996	0.902	0.812	0.996	INDETERMINATE	2	TRUE	1	0.47770381763139	3		472	250	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518012	8518012	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	23	493	0	ENST00000356435.5:c.1379C>G	p.Thr460Ser	p.T460S	ENST00000356435		460	aCt/aGt	10/35	0.259431495731238	1	FACETS	0.261	0.203	0.327	0.261	0.203	0.327	INDETERMINATE	1	TRUE	0	0.47770381763139	1		493	281	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114581	73114581	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	159	276	0	ENST00000356692.5:c.962A>G	p.Glu321Gly	p.E321G	ENST00000356692		321	gAa/gGa	9/9	0.125125178286081	3	FACETS	1	0.988	1	0.673	0.625	0.721	INDETERMINATE	1	TRUE	1	0.91	3		276	378	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31939973	31939973	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	505	677	0	ENST00000375333.2:c.200G>A	p.Arg67Gln	p.R67Q	ENST00000375333	NM_032454.1	67	cGg/cAg	1/8	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.91	2		677	1020	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110251216	110251216	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	181	732	0	ENST00000374672.4:c.121A>T	p.Asn41Tyr	p.N41Y	ENST00000374672	NM_004235.4	41	Aat/Tat	2/5	1	2	FACETS	0.555	0.513	0.598	0.555	0.513	0.598	SUBCLONAL	1	TRUE	1	0.91	2		732	717	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0048657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	167	362	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.395754689833588	2	FACETS	0.848	0.785	0.912	0.848	0.785	0.912	CLONAL	2	TRUE	0	0.39634723021228	2		362	497	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0048657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	92	302	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.873	0.778	0.973	0.873	0.778	0.973	CLONAL	1	TRUE	1	0.39634723021228	2		302	532	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0048657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	74	305	0	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	1	2	FACETS	0.796	0.699	0.9	0.796	0.699	0.9	SUBCLONAL	1	TRUE	1	0.39634723021228	2		305	469	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0048657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	71	162	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.39634723021228	1	FACETS	0.871	0.766	0.982	0.871	0.766	0.982	CLONAL	1	TRUE	0	0.39634723021228	1		162	330	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0048657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	106	429	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.833	0.748	0.923	0.833	0.748	0.923	CLONAL	1	TRUE	1	0.39634723021228	2		429	642	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593558	48593558	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587781618	NA	P-0048657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	28	184	0	ENST00000342988.3:c.1308+1G>A		p.X436_splice	ENST00000342988	NM_005359.5	436			0.39634723021228	1	FACETS	0.431	0.345	0.527	0.431	0.345	0.527	SUBCLONAL	1	TRUE	0	0.39634723021228	1		184	263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579709	7579710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	125	534	0	ENST00000269305.4:c.86dup	p.Asn29LysfsTer14	p.N29Kfs*14	ENST00000269305	NM_001126112.2	29	aac/aaAc	3/11	0.39634723021228	1	FACETS	0.889	0.808	0.974	0.889	0.808	0.974	CLONAL	1	TRUE	0	0.39634723021228	1		534	569	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107206	27107206	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	148	488	0	ENST00000324856.7:c.6817C>T	p.Gln2273Ter	p.Q2273*	ENST00000324856	NM_006015.4	2273	Caa/Taa	20/20	1	2	FACETS	0.941	0.86	1	0.941	0.86	1	CLONAL	1	TRUE	1	0.39634723021228	2		488	794	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811766	102811766	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1373199598	NA	P-0048657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	136	508	0	ENST00000307046.8:c.418A>G	p.Thr140Ala	p.T140A	ENST00000307046	NM_001111285.1	140	Acc/Gcc	4/4	0.395754689833588	2	FACETS	0.941	0.857	1	0.471	0.428	0.515	CLONAL	1	TRUE	0	0.39634723021228	2		508	729	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570102	95570103	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0048657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	109	433	0	ENST00000393063.1:c.3630dup	p.Val1211ArgfsTer24	p.V1211Rfs*24	ENST00000393063	NM_030621.3	1210	-/C	22/28	1	2	FACETS	0.889	0.8	0.982	0.889	0.8	0.982	CLONAL	1	TRUE	1	0.39634723021228	2		433	619	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533949	63533950	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0048657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	103	505	0	ENST00000307078.5:c.1204dup	p.Glu402GlyfsTer60	p.E402Gfs*60	ENST00000307078	NM_004655.3	402	gaa/gGaa	6/11	1	2	FACETS	0.92	0.826	1	0.92	0.826	1	CLONAL	1	TRUE	1	0.39634723021228	2		505	565	SUCCESS
APC	324	MSKCC	GRCh37	5	112176575	112176575	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	75	292	2	ENST00000257430.4:c.5288del	p.Asn1763IlefsTer3	p.N1763Ifs*3	ENST00000257430	NM_000038.5	1762	Aaa/aa	16/16	1	2	FACETS	0.79	0.694	0.893	0.79	0.694	0.893	SUBCLONAL	1	TRUE	1	0.39634723021228	2		294	479	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111495	8111496	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGGA	novel	NA	P-0048659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	252	534	1	ENST00000346208.3:c.982_985dup	p.Arg329MetfsTer24	p.R329Mfs*24	ENST00000346208		327	-/TGGA	5/6	0.650201792492086	12	FACETS	0.984	0.926	1			1	CLONAL	5	TRUE	NA	0.650201792492086	12		535	670	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633634	69633634	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	13	26	0	ENST00000334134.2:c.68C>T	p.Ala23Val	p.A23V	ENST00000334134	NM_005247.2	23	gCg/gTg	1/3	0.650201792492086	8	FACETS	0.837	0.619	1	0.418	0.309	0.541	CLONAL	3	TRUE	2	0.650201792492086	8		26	47	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132955	30132955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145651161	NA	P-0048659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	37	525	1	ENST00000331968.5:c.646C>T	p.Arg216Cys	p.R216C	ENST00000331968	NM_002742.2	216	Cgc/Tgc	4/18	NA	2	FACETS	0.515	0.428	0.611			1	INDETERMINATE	1	TRUE	NA	0.650201792492086	2		526	221	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	179	589	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.650201792492086	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.650201792492086	3		589	219	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	123	495	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.964	0.873	1	0.964	0.873	1	CLONAL	1	TRUE	1	0.385575748794412	2		495	662	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	369	745	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.992	0.944	1	1	0.996	1	CLONAL	2	TRUE	1	0.385575748794412	2		750	965	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	155	434	0	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.385575748794412	2		434	780	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646085	215646085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	326	522	1	ENST00000260947.4:c.513del	p.Asp172MetfsTer40	p.D172Mfs*40	ENST00000260947	NM_000465.2	171	aaA/aa	4/11	0.368839441472431	3	FACETS	0.967	0.915	1	0.967	0.915	1	CLONAL	2	TRUE	1	0.385575748794412	3		523	1043	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	128	430	2	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	0.962	0.874	1	0.962	0.874	1	CLONAL	1	TRUE	1	0.385575748794412	2		432	690	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	206	571	2	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.385575748794412	2		573	1042	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023544	31023544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs116112525	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	155	516	0	ENST00000375687.4:c.3029C>T	p.Thr1010Met	p.T1010M	ENST00000375687	NM_015338.5	1010	aCg/aTg	13/13	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.385575748794412	2		516	766	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	216	515	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.372054655726536	2	FACETS	1	0.991	1	0.707	0.659	0.757	CLONAL	1	TRUE	0	0.385575748794412	2		515	792	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	99	277	0	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.385575748794412	2		277	469	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	229	679	1	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.385575748794412	2		680	1152	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680656	88680656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761690006	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	167	574	0	ENST00000360948.2:c.601C>T	p.Arg201Cys	p.R201C	ENST00000360948	NM_001012338.2	201	Cgc/Tgc	6/19	0.236918283334391	3	FACETS	1	0.964	1	0.544	0.499	0.59	CLONAL	1	TRUE	1	0.385575748794412	3		574	950	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	215	739	3	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.385575748794412	2		742	1061	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	150	464	1	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	1	2	FACETS	0.884	0.808	0.964	0.884	0.808	0.964	CLONAL	1	TRUE	1	0.385575748794412	2		465	880	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214646	133214646	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199979862	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	168	545	0	ENST00000320574.5:c.5632C>T	p.Arg1878Cys	p.R1878C	ENST00000320574	NM_006231.2	1878	Cgc/Tgc	41/49	1	2	FACETS	0.976	0.897	1	0.976	0.897	1	CLONAL	1	TRUE	1	0.385575748794412	2		545	893	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	208	480	7	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	0.236918283334391	3	FACETS	0.779	0.724	0.835	0.779	0.724	0.835	SUBCLONAL	2	TRUE	1	0.385575748794412	3		487	826	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907421	32907421	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359306	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	193	281	0	ENST00000380152.3:c.1813del	p.Ile605TyrfsTer9	p.I605Yfs*9	ENST00000380152		602	ggA/gg	10/27	0.354455158314079	2	FACETS	0.985	0.92	1	0.985	0.92	1	CLONAL	2	TRUE	0	0.385575748794412	2		281	508	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	104	384	1	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	0.895	0.803	0.992	0.895	0.803	0.992	CLONAL	1	TRUE	1	0.385575748794412	2		385	603	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884834	111884834	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs181079548	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	140	465	0	ENST00000341259.2:c.923G>A	p.Arg308Gln	p.R308Q	ENST00000341259	NM_005475.2	308	cGa/cAa	4/8	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.385575748794412	2		465	711	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720964	176720964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	170	487	0	ENST00000439151.2:c.6595C>T	p.Arg2199Cys	p.R2199C	ENST00000439151	NM_022455.4	2199	Cgt/Tgt	23/23	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.385575748794412	2		487	807	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30946592	30946594	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs752094508	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	46	185	2	ENST00000375687.4:c.25_27del	p.Lys9del	p.K9del	ENST00000375687	NM_015338.5	5	cAGAag/cag	1/13	1	2	FACETS	0.753	0.637	0.879	0.753	0.637	0.879	SUBCLONAL	1	TRUE	1	0.385575748794412	2		187	317	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716329	52716329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863225094	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	38	651	1	ENST00000322088.6:c.773G>A	p.Arg258His	p.R258H	ENST00000322088	NM_014225.5	258	cGc/cAc	6/15	1	2	FACETS	0.217	0.178	0.261	0.217	0.178	0.261	SUBCLONAL	1	TRUE	1	0.385575748794412	2		652	908	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149355	119149356	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATG	rs397507494	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	86	374	0	ENST00000264033.4:c.1380_1382dup	p.Asp460dup	p.D460dup	ENST00000264033	NM_005188.3	460	tat/tATGat	9/16	1	2	FACETS	0.75	0.664	0.841	0.75	0.664	0.841	SUBCLONAL	1	TRUE	1	0.385575748794412	2		374	595	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573123	64573123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761102084	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	130	360	0	ENST00000312049.6:c.1169C>T	p.Pro390Leu	p.P390L	ENST00000312049	NM_130799.2	390	cCg/cTg	8/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.385575748794412	2		360	631	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663454	29663454	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	146	429	0	ENST00000356175.3:c.6047C>T	p.Ala2016Val	p.A2016V	ENST00000356175	NM_000267.3	2016	gCt/gTt	40/57	1	2	FACETS	0.985	0.9	1	0.985	0.9	1	CLONAL	1	TRUE	1	0.385575748794412	2		429	769	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442811	442811	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	105	317	1	ENST00000399788.2:c.1495del	p.Glu499SerfsTer19	p.E499Sfs*19	ENST00000399788	NM_001042603.1	499	Gag/ag	12/28	1	2	FACETS	0.952	0.856	1	0.952	0.856	1	CLONAL	1	TRUE	1	0.385575748794412	2		318	572	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	160	585	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	0.859	0.787	0.934	0.859	0.787	0.934	CLONAL	1	TRUE	1	0.385575748794412	2		585	966	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	rs267608078	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	80	444	0	ENST00000234420.5:c.3260_3261dup	p.Phe1088ProfsTer3	p.F1088Pfs*3	ENST00000234420	NM_000179.2	1085	acc/aCCcc	5/10	1	2	FACETS	0.54	0.475	0.611	0.54	0.475	0.611	SUBCLONAL	1	TRUE	1	0.385575748794412	2		444	768	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878749	151878749	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1211949081	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	111	386	0	ENST00000262189.6:c.6196C>T	p.Arg2066Ter	p.R2066*	ENST00000262189	NM_170606.2	2066	Cga/Tga	36/59	1	2	FACETS	0.834	0.751	0.923	0.834	0.751	0.923	CLONAL	1	TRUE	1	0.385575748794412	2		386	690	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375486	40375486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138255473	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	191	731	1	ENST00000293328.3:c.464C>T	p.Thr155Met	p.T155M	ENST00000293328	NM_012448.3	155	aCg/aTg	5/19	1	2	FACETS	0.911	0.842	0.984	0.911	0.842	0.984	CLONAL	1	TRUE	1	0.385575748794412	2		732	1087	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307639	118307639	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	126	596	0	ENST00000534358.1:c.416del	p.Gly139GlufsTer11	p.G139Efs*11	ENST00000534358	NM_005933.3	138	Ggg/gg	1/36	1	2	FACETS	0.811	0.734	0.892	0.811	0.734	0.892	CLONAL	1	TRUE	1	0.385575748794412	2		596	806	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527742	157527742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1315767745	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	156	470	0	ENST00000346085.5:c.5467G>A	p.Gly1823Arg	p.G1823R	ENST00000346085	NM_020732.3	1823	Ggg/Agg	20/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.385575748794412	2		470	776	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31493321	31493322	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1330233722	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	92	343	0	ENST00000344624.3:c.1834dup	p.Leu612ProfsTer8	p.L612Pfs*8	ENST00000344624		612	ctg/cCtg	10/33	1	2	FACETS	0.816	0.726	0.911	0.816	0.726	0.911	CLONAL	1	TRUE	1	0.385575748794412	2		343	585	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243778402	243778402	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	114	331	0	ENST00000263826.5:c.623del	p.Leu208Ter	p.L208*	ENST00000263826	NM_005465.4	208	tTa/ta	6/13	1	2	FACETS	0.979	0.884	1	0.979	0.884	1	CLONAL	1	TRUE	1	0.385575748794412	2		331	604	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983134	201983134	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	181	575	0	ENST00000359651.3:c.983A>C	p.Lys328Thr	p.K328T	ENST00000359651		328	aAg/aCg	7/8	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.385575748794412	2		575	917	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204513799	204513799	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	78	235	0	ENST00000367182.3:c.809T>C	p.Val270Ala	p.V270A	ENST00000367182	NM_001278516.1	270	gTa/gCa	9/11	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.385575748794412	2		235	395	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022718	12022719	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	145	565	0	ENST00000396373.4:c.827dup	p.Leu277SerfsTer23	p.L277Sfs*23	ENST00000396373	NM_001987.4	275	cac/caCc	5/8	1	2	FACETS	0.856	0.781	0.934	0.856	0.781	0.934	CLONAL	1	TRUE	1	0.385575748794412	2		565	879	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435325	121435325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	75	792	2	ENST00000257555.6:c.1358G>A	p.Gly453Asp	p.G453D	ENST00000257555		453	gGc/gAc	7/10	1	2	FACETS	0.346	0.302	0.394	0.346	0.302	0.394	SUBCLONAL	1	TRUE	1	0.385575748794412	2		794	1123	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994790	73994790	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	254	560	0	ENST00000318443.5:c.274C>A	p.Arg92Ser	p.R92S	ENST00000318443	NM_001024736.1	92	Cgc/Agc	3/10	0.236918283334391	3	FACETS	0.874	0.82	0.93	0.874	0.82	0.93	CLONAL	2	TRUE	1	0.385575748794412	3		560	899	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351409	89351409	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	159	611	0	ENST00000301030.4:c.1541T>C	p.Leu514Pro	p.L514P	ENST00000301030	NM_001256183.1	514	cTg/cCg	9/13	1	2	FACETS	0.928	0.85	1	0.928	0.85	1	CLONAL	1	TRUE	1	0.385575748794412	2		611	889	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40491345	40491345	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567723290	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	178	508	1	ENST00000264657.5:c.455G>A	p.Arg152Gln	p.R152Q	ENST00000264657	NM_139276.2	152	cGg/cAg	5/24	1	2	FACETS	0.978	0.901	1	0.978	0.901	1	CLONAL	1	TRUE	1	0.385575748794412	2		509	944	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223130	1223130	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	180	663	0	ENST00000326873.7:c.1067T>A	p.Ile356Asn	p.I356N	ENST00000326873	NM_000455.4	356	aTc/aAc	8/10	1	2	FACETS	0.922	0.849	0.997	0.922	0.849	0.997	CLONAL	1	TRUE	1	0.385575748794412	2		663	1013	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611788	1611788	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	174	666	0	ENST00000344749.5:c.1874G>A	p.Gly625Asp	p.G625D	ENST00000344749	NM_001136139.2	625	gGt/gAt	19/19	1	2	FACETS	0.949	0.874	1	0.949	0.874	1	CLONAL	1	TRUE	1	0.385575748794412	2		666	951	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602631	10602631	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	222	818	0	ENST00000171111.5:c.947T>C	p.Val316Ala	p.V316A	ENST00000171111	NM_203500.1	316	gTg/gCg	3/6	1	2	FACETS	0.943	0.876	1	0.943	0.876	1	CLONAL	1	TRUE	1	0.385575748794412	2		818	1221	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220973	36220973	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	158	557	0	ENST00000222270.7:c.5023C>A	p.Gln1675Lys	p.Q1675K	ENST00000222270	NM_014727.1	1675	Cag/Aag	23/37	1	2	FACETS	0.959	0.879	1	0.959	0.879	1	CLONAL	1	TRUE	1	0.385575748794412	2		557	855	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095914	178095914	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	133	412	0	ENST00000397062.3:c.1417del	p.Ile473SerfsTer12	p.I473Sfs*12	ENST00000397062	NM_006164.4	473	Atc/tc	5/5	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.385575748794412	2		412	666	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729380	41729380	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	151	544	0	ENST00000242208.4:c.1149del	p.Phe384LeufsTer13	p.F384Lfs*13	ENST00000242208	NM_002192.2	383	ccC/cc	3/3	1	2	FACETS	0.967	0.885	1	0.967	0.885	1	CLONAL	1	TRUE	1	0.385575748794412	2		544	810	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845996	151845996	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	144	488	0	ENST00000262189.6:c.13016A>G	p.His4339Arg	p.H4339R	ENST00000262189	NM_170606.2	4339	cAt/cGt	52/59	1	2	FACETS	0.888	0.81	0.97	0.888	0.81	0.97	CLONAL	1	TRUE	1	0.385575748794412	2		488	841	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900240	101900240	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	123	372	0	ENST00000374994.4:c.677del	p.Gly226GlufsTer27	p.G226Efs*27	ENST00000374994	NM_004612.2	225	cGg/cg	4/9	1	2	FACETS	0.961	0.871	1	0.961	0.871	1	CLONAL	1	TRUE	1	0.385575748794412	2		372	664	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045909	47045909	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782208940	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	181	327	0	ENST00000377604.3:c.2704C>T	p.Arg902Trp	p.R902W	ENST00000377604	NM_001204468.1	902	Cgg/Tgg	24/24	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.385575748794412	1		327	529	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020156	123020156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs947711542	NA	P-0048660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	193	343	0	ENST00000355640.3:c.644G>A	p.Arg215His	p.R215H	ENST00000355640		215	cGt/cAt	2/7	1	1	FACETS	0.77	0.718	0.822	1	0.992	1	SUBCLONAL	2	TRUE	0	0.385575748794412	1		343	525	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264244	46264244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	51	358	0	ENST00000371998.3:c.1291G>A	p.Ala431Thr	p.A431T	ENST00000371998		431	Gct/Act	11/23	1	2	FACETS	1	0.871	1	1	0.976	1	CLONAL	2	FALSE	1	0.202446638016941	2		358	248	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	74	301	0				ENST00000310581	NM_198253.2	-/1132			0.819248828178994	3	FACETS	0.965	0.855	1	0.482	0.427	0.54	CLONAL	1	TRUE	1	0.819248828178994	3		301	264	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	247	545	0	ENST00000269305.4:c.772G>C	p.Glu258Gln	p.E258Q	ENST00000269305	NM_001126112.2	258	Gaa/Caa	7/11	0.819248828178994	2	FACETS	0.954	0.919	0.987	0.954	0.919	0.987	CLONAL	2	TRUE	0	0.819248828178994	2		545	316	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067836	30067836	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315499	NA	P-0048662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	123	379	0	ENST00000338641.4:c.1021C>T	p.Arg341Ter	p.R341*	ENST00000338641	NM_000268.3	341	Cga/Tga	11/16	0.819248828178994	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.819248828178994	1		379	160	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43772156	43772156	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	123	574	0	ENST00000382044.4:c.559G>C	p.Glu187Gln	p.E187Q	ENST00000382044	NM_001141980.1	187	Gag/Cag	6/28	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.819248828178994	2		574	297	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426969	70426980	+	inframe_deletion	In_Frame_Del	DEL	ATACAATGGGCA	ATACAATGGGCA	-	novel	NA	P-0048662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	105	351	0	ENST00000373644.4:c.4629_4640del	p.Tyr1544_His1547del	p.Y1544_H1547del	ENST00000373644	NM_030625.2	1543	tcATACAATGGGCAc/tcc	7/12	0.819248828178994	1	FACETS	0.97	0.905	1	0.97	0.905	1	CLONAL	1	TRUE	0	0.819248828178994	1		351	156	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912785	100912785	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0048662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	125	399	0	ENST00000325455.5:c.2537C>G	p.Ser846Ter	p.S846*	ENST00000325455	NM_001202474.3	846	tCa/tGa	7/8	1	2	FACETS	0.975	0.896	1	0.975	0.896	1	CLONAL	1	TRUE	1	0.819248828178994	2		399	313	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727949	78727949	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	207	440	0	ENST00000306801.3:c.794C>G	p.Ser265Cys	p.S265C	ENST00000306801	NM_020761.2	265	tCc/tGc	6/34	0.819248828178994	3	FACETS	0.937	0.885	0.989	0.937	0.885	0.989	CLONAL	2	TRUE	1	0.819248828178994	3		440	380	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639697	47639697	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	13	327	0	ENST00000233146.2:c.790C>G	p.Gln264Glu	p.Q264E	ENST00000233146	NM_000251.2	264	Cag/Gag	4/16	1	2	FACETS	0.15	0.107	0.203	0.15	0.107	0.203	SUBCLONAL	1	TRUE	1	0.819248828178994	2		327	211	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670473	134670473	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	134	514	0	ENST00000398015.3:c.384C>G	p.Phe128Leu	p.F128L	ENST00000398015	NM_004441.4	128	ttC/ttG	3/16	1	2	FACETS	0.997	0.92	1	0.997	0.92	1	CLONAL	1	TRUE	1	0.819248828178994	2		514	328	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534506	140534506	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	106	357	1	ENST00000288602.6:c.407C>A	p.Ser136Ter	p.S136*	ENST00000288602	NM_004333.4	136	tCa/tAa	3/18	1	2	FACETS	0.999	0.912	1	0.999	0.912	1	CLONAL	1	TRUE	1	0.819248828178994	2		358	259	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93629445	93629445	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	100	325	0	ENST00000375746.1:c.879C>G	p.Ile293Met	p.I293M	ENST00000375746	NM_001174167.1	293	atC/atG	7/14	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.819248828178994	2		325	223	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938477	44938477	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	115	430	0	ENST00000377967.4:c.3025G>C	p.Asp1009His	p.D1009H	ENST00000377967	NM_021140.2	1009	Gat/Cat	20/29	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.819248828178994	2		430	273	SUCCESS
AR	367	MSKCC	GRCh37	X	66765079	66765079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	127	563	1	ENST00000374690.3:c.91C>T	p.Arg31Cys	p.R31C	ENST00000374690	NM_000044.3	31	Cgc/Tgc	1/8	1	2	FACETS	0.838	0.768	0.91	0.838	0.768	0.91	CLONAL	1	TRUE	1	0.819248828178994	2		564	370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0048664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	110	932	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.177117086053128	2	FACETS	1	0.981	1	0.707	0.636	0.781	CLONAL	1	TRUE	0	0.253989138920107	2		934	613	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0048664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	110	566	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.196460592068854	4	FACETS	1	0.979	1	0.687	0.617	0.762	CLONAL	1	TRUE	2	0.253989138920107	4		566	790	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0048664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	47	247	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.239421034775319	3	FACETS	1	0.895	1	0.537	0.454	0.629	CLONAL	1	TRUE	1	0.253989138920107	3		247	388	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412494	80412494	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	105	394	1	ENST00000286548.4:c.547C>T	p.Arg183Ter	p.R183*	ENST00000286548	NM_002072.3	183	Cga/Tga	4/7	0.253989138920107	2	FACETS	1	0.982	1	0.734	0.66	0.813	CLONAL	1	TRUE	0	0.253989138920107	2		395	563	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984233	7984233	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	92	639	0	ENST00000319144.4:c.496G>C	p.Val166Leu	p.V166L	ENST00000319144	NM_001139.2	166	Gtg/Ctg	4/15	0.177117086053128	2	FACETS	1	0.89	1	0.501	0.445	0.561	CLONAL	1	TRUE	0	0.253989138920107	2		639	723	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0048665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	54	495	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.919	0.791	1	1	0.975	1	CLONAL	2	TRUE	1	0.209065192537704	2		495	281	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	56	301	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.964	0.832	1	1	0.977	1	CLONAL	2	TRUE	1	0.209065192537704	2		301	278	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0048666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	213	347	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.501639929432894	2	FACETS	0.997	0.939	1	0.997	0.939	1	CLONAL	2	TRUE	0	0.501639929432894	2		347	426	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0048666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	118	371	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.501639929432894	1	FACETS	0.99	0.903	1	0.99	0.903	1	CLONAL	1	TRUE	0	0.501639929432894	1		371	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0048666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	361	657	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.501639929432894	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.501639929432894	2		657	683	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	84	271	3	ENST00000257430.4:c.3919dup	p.Ile1307AsnfsTer8	p.I1307Nfs*8	ENST00000257430	NM_000038.5	1306	gaa/gAaa	16/16	0.156106815609366	6	FACETS	0.839	0.745	0.937	0.559	0.497	0.625	INDETERMINATE	2	TRUE	3	0.501639929432894	6		274	400	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439832	51439832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	208	386	0	ENST00000262662.1:c.397C>T	p.Arg133Trp	p.R133W	ENST00000262662		133	Cgg/Tgg	4/4	0.350221825166568	4	FACETS	0.941	0.877	1	0.941	0.877	1	CLONAL	2	TRUE	2	0.501639929432894	4		386	662	SUCCESS
APC	324	MSKCC	GRCh37	5	112174471	112174475	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAC	AAAAC	-	rs587779352	NA	P-0048666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	137	304	0	ENST00000257430.4:c.3183_3187del	p.Gln1062Ter	p.Q1062*	ENST00000257430	NM_000038.5	1060	atAAAACaa/ataa	16/16	0.156106815609366	6	FACETS	0.842	0.773	0.914	0.842	0.773	0.914	INDETERMINATE	3	TRUE	3	0.501639929432894	6		304	433	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678052	117678052	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	58	330	0	ENST00000368508.3:c.3881A>T	p.Asn1294Ile	p.N1294I	ENST00000368508	NM_002944.2	1294	aAt/aTt	25/43	0.239873732530643	3	FACETS	0.694	0.598	0.798	0.231	0.199	0.266	INDETERMINATE	1	TRUE	0	0.501639929432894	3		330	417	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540380	23540380	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	248	416	2	ENST00000380871.4:c.23G>T	p.Arg8Leu	p.R8L	ENST00000380871	NM_006167.3	8	cGg/cTg	1/2	0.501639929432894	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.501639929432894	3		418	592	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18963074	18963074	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1485824312	NA	P-0048667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	256	687	0	ENST00000262803.5:c.941C>T	p.Ala314Val	p.A314V	ENST00000262803	NM_002911.3	314	gCc/gTc	6/24	0.182264510121034	4	FACETS	0.943	0.887	1	0.943	0.887	1	INDETERMINATE	2	TRUE	2	0.562397407183256	4		687	754	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100294	8100305	+	inframe_deletion	In_Frame_Del	DEL	CTTCATGGATCC	CTTCATGGATCC	-	novel	NA	P-0048667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	113	787	0	ENST00000346208.3:c.270_281del	p.His91_Leu94del	p.H91_L94del	ENST00000346208		90	CTTCATGGATCC/-	3/6	1	2	FACETS	0.411	0.369	0.455	0.411	0.369	0.455	SUBCLONAL	1	TRUE	1	0.562397407183256	2		787	978	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115880	8115881	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0048667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	269	612	0	ENST00000346208.3:c.1227dup	p.Ser410GlnfsTer97	p.S410Qfs*97	ENST00000346208		409	ttc/ttCc	6/6	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.562397407183256	2		612	886	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976197	18976197	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	267	826	0	ENST00000262803.5:c.2957A>G	p.Asn986Ser	p.N986S	ENST00000262803	NM_002911.3	986	aAc/aGc	21/24	0.182264510121034	4	FACETS	0.872	0.82	0.925	0.872	0.82	0.925	INDETERMINATE	2	TRUE	2	0.562397407183256	4		826	851	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55603427	55603427	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	32	383	1	ENST00000288135.5:c.2783T>A	p.Ile928Asn	p.I928N	ENST00000288135	NM_000222.2	928	aTt/aAt	20/21	0.308627068639902	1	FACETS	0.39	0.318	0.468	0.39	0.318	0.468	INDETERMINATE	1	TRUE	0	0.562397407183256	1		384	210	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs786203436	NA	P-0048668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	542	648	0	ENST00000269305.4:c.487T>A	p.Tyr163Asn	p.Y163N	ENST00000269305	NM_001126112.2	163	Tac/Aac	5/11	0.80245542937228	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.80245542937228	1		648	768	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675472	30675472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775063662	NA	P-0048668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	501	597	1	ENST00000376406.3:c.2884G>A	p.Ala962Thr	p.A962T	ENST00000376406	NM_014641.2	962	Gcc/Acc	8/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.80245542937228	2		598	1181	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392798	118392801	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	novel	NA	P-0048668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	356	464	0	ENST00000534358.1:c.11832_11835del	p.Tyr3945ThrfsTer26	p.Y3945Tfs*26	ENST00000534358	NM_005933.3	3944	ACTTac/ac	36/36	0.80245542937228	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.80245542937228	1		464	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0048669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	708	898	1	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.771336028972396	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	FALSE	0	0.771336028972396	3		899	809	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0048669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	2192	399	0	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	0.771336028972396	24	FACETS	0.986	0.973	0.998			1	CLONAL	19	FALSE	NA	0.771336028972396	24		399	2878	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11552822	NA	P-0048669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	204	741	0	ENST00000304494.5:c.250G>T	p.Asp84Tyr	p.D84Y	ENST00000304494	NM_000077.4	84	Gac/Tac	2/3	0.771336028972396	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	0	0.771336028972396	1		741	296	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434148	12434148	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	334	413	0	ENST00000287820.6:c.516C>G	p.Ile172Met	p.I172M	ENST00000287820	NM_015869.4	172	atC/atG	4/7	0.771336028972396	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	FALSE	0	0.771336028972396	3		413	385	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112430	115112430	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs375076522	NA	P-0048669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	325	692	0	ENST00000257566.3:c.1310A>G	p.His437Arg	p.H437R	ENST00000257566	NM_016569.3	437	cAt/cGt	7/8	0.342482380327874	4	FACETS	0.991	0.942	1	0.991	0.942	1	INDETERMINATE	2	FALSE	2	0.771336028972396	4		692	753	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602854	10602854	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	501	885	0	ENST00000171111.5:c.724G>A	p.Glu242Lys	p.E242K	ENST00000171111	NM_203500.1	242	Gag/Aag	3/6	0.771336028972396	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	FALSE	0	0.771336028972396	2		885	617	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100646	8100646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	478	800	0	ENST00000346208.3:c.620C>T	p.Ala207Val	p.A207V	ENST00000346208		207	gCc/gTc	3/6	0.377554239339616	3	FACETS	1	0.996	1	0.795	0.77	0.82	INDETERMINATE	2	FALSE	0	0.771336028972396	3		800	720	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374487	118374487	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	33	481	1	ENST00000534358.1:c.7880G>A	p.Arg2627His	p.R2627H	ENST00000534358	NM_005933.3	2627	cGt/cAt	27/36	0.612033171756683	4	FACETS	0.237	0.192	0.288	0.079	0.064	0.096	SUBCLONAL	1	FALSE	1	0.771336028972396	4		482	640	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432590	49432590	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	326	802	1	ENST00000301067.7:c.8549del	p.Leu2850GlnfsTer60	p.L2850Qfs*60	ENST00000301067	NM_003482.3	2850	cTa/ca	34/54	0.452794173443929	4	FACETS	0.944	0.897	0.992	0.944	0.897	0.992	INDETERMINATE	2	FALSE	2	0.771336028972396	4		803	793	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435236	49435243	+	frameshift_variant	Frame_Shift_Del	DEL	ATGCGGAG	ATGCGGAG	-	novel	NA	P-0048669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	278	707	0	ENST00000301067.7:c.6310_6317del	p.Leu2104SerfsTer48	p.L2104Sfs*48	ENST00000301067	NM_003482.3	2104	CTCCGCATt/t	31/54	0.452794173443929	4	FACETS	0.96	0.908	1	0.96	0.908	1	INDETERMINATE	2	FALSE	2	0.771336028972396	4		707	665	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120912	115120912	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1410475056	NA	P-0048669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	306	696	0	ENST00000257566.3:c.94G>T	p.Ala32Ser	p.A32S	ENST00000257566	NM_016569.3	32	Gcg/Tcg	1/8	0.342482380327874	4	FACETS	0.919	0.87	0.967	0.919	0.87	0.967	INDETERMINATE	2	FALSE	2	0.771336028972396	4		696	765	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135409	30135409	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	222	386	0	ENST00000331968.5:c.409G>C	p.Ala137Pro	p.A137P	ENST00000331968	NM_002742.2	137	Gcc/Ccc	3/18	0.501437570987124	5	FACETS	0.936	0.884	0.989	0.936	0.884	0.989	CLONAL	3	FALSE	2	0.771336028972396	5		386	442	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303498	91303498	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555419741	NA	P-0048669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	337	408	0	ENST00000355112.3:c.1209G>C	p.Gln403His	p.Q403H	ENST00000355112	NM_000057.2	403	caG/caC	6/22	0.771336028972396	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	FALSE	0	0.771336028972396	3		408	400	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873104	136873104	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	321	515	1	ENST00000241393.3:c.394C>A	p.Leu132Met	p.L132M	ENST00000241393	NM_003467.2	132	Ctg/Atg	2/2	0.732083239200886	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	FALSE	1	0.771336028972396	3		516	518	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523642	41523642	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	334	728	0	ENST00000263253.7:c.1058G>T	p.Arg353Leu	p.R353L	ENST00000263253	NM_001429.3	353	cGc/cTc	4/31	0.426996774641228	4	FACETS	0.86	0.816	0.904	0.86	0.816	0.904	INDETERMINATE	2	FALSE	2	0.771336028972396	4		728	892	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390966	89390967	+	missense_variant	Missense_Mutation	DNP	CT	CT	AA	novel	NA	P-0048669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	111	510	1	ENST00000336596.2:c.1032_1033delinsAA	p.Asp344_Trp345delinsGluArg	p.D344_W345delinsER	ENST00000336596	NM_005233.5	344	gaCTgg/gaAAgg	5/17	0.771336028972396	2	FACETS	0.959	0.875	1	0.48	0.437	0.523	CLONAL	1	FALSE	0	0.771336028972396	2		511	300	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955134	55955134	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	2075	383	1	ENST00000263923.4:c.3411G>T	p.Gln1137His	p.Q1137H	ENST00000263923	NM_002253.2	1137	caG/caT	26/30	0.771336028972396	19	FACETS	0.992	0.982	1			1	CLONAL	17	FALSE	NA	0.771336028972396	19		384	2411	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230789	66230789	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs750508480	NA	P-0048669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	172	400	1	ENST00000273854.3:c.2182A>G	p.Met728Val	p.M728V	ENST00000273854	NM_004439.5	728	Atg/Gtg	12/18	0.771336028972396	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	FALSE	0	0.771336028972396	2		401	201	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948457	31948457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355123936	NA	P-0048669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	190	374	0	ENST00000375333.2:c.940C>T	p.Arg314Trp	p.R314W	ENST00000375333	NM_032454.1	314	Cgg/Tgg	7/8	0.771336028972396	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	FALSE	0	0.771336028972396	2		374	234	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124453	94124453	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	189	492	0	ENST00000369303.4:c.130G>T	p.Glu44Ter	p.E44*	ENST00000369303	NM_004440.3	44	Gag/Tag	2/17	0.771336028972396	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	FALSE	0	0.771336028972396	3		492	211	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923363	36923363	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	390	607	1	ENST00000358127.4:c.899C>A	p.Pro300His	p.P300H	ENST00000358127	NM_001280556.1	300	cCc/cAc	7/10	0.638290640388885	3	FACETS	1	0.978	1			1	CLONAL	2	FALSE	NA	0.771336028972396	3		608	682	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039696	47039696	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	307	725	0	ENST00000377604.3:c.1148A>G	p.Lys383Arg	p.K383R	ENST00000377604	NM_001204468.1	383	aAg/aGg	11/24	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	FALSE	NA	0.771336028972396	2		725	628	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0048670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	223	775	1	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	0.535894488027251	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.535894488027251	1		776	538	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923353	9923353	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	153	565	0	ENST00000330684.3:c.1934A>G	p.Tyr645Cys	p.Y645C	ENST00000330684	NM_001134407.1	645	tAc/tGc	9/13	0.533215656883458	3	FACETS	1	0.97	1	0.56	0.514	0.608	CLONAL	1	TRUE	1	0.535894488027251	3		565	646	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858208	59858208	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	126	484	0	ENST00000259008.2:c.1787C>G	p.Pro596Arg	p.P596R	ENST00000259008	NM_032043.2	596	cCa/cGa	12/20	0.535894488027251	3	FACETS	0.962	0.873	1	0.321	0.291	0.352	CLONAL	1	TRUE	0	0.535894488027251	3		484	620	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0048671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	92	282	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.426332264114486	1	FACETS	0.487	0.436	0.539	0.487	0.436	0.539	INDETERMINATE	1	TRUE	0	0.728541269616687	1		282	330	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404587	8404587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	67	320	0	ENST00000356435.5:c.4160C>T	p.Ala1387Val	p.A1387V	ENST00000356435		1387	gCg/gTg	25/35	1	2	FACETS	0.411	0.358	0.469	0.411	0.358	0.469	SUBCLONAL	1	TRUE	1	0.728541269616687	2		320	447	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620051	21620051	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750829854	NA	P-0048671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	166	509	0	ENST00000382592.4:c.115G>A	p.Ala39Thr	p.A39T	ENST00000382592	NM_014572.2	39	Gca/Aca	2/8	0.426332264114486	1	FACETS	0.416	0.383	0.451	0.416	0.383	0.451	INDETERMINATE	1	TRUE	0	0.728541269616687	1		509	696	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554338	81554338	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759773701	NA	P-0048671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	84	358	0	ENST00000298171.2:c.358G>A	p.Asp120Asn	p.D120N	ENST00000298171	NM_000369.2	120	Gat/Aat	4/10	0.382428390479417	3	FACETS	0.48	0.424	0.54	0.16	0.141	0.18	INDETERMINATE	1	TRUE	0	0.728541269616687	3		358	655	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0048671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	20	282	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.214881644933434	1	FACETS	0.216	0.164	0.276	0.216	0.164	0.276	INDETERMINATE	1	TRUE	0	0.432662405626699	1		282	336	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404587	8404587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	36	320	0	ENST00000356435.5:c.4160C>T	p.Ala1387Val	p.A1387V	ENST00000356435		1387	gCg/gTg	25/35	0.288497877717715	1	FACETS	0.473	0.39	0.564	0.473	0.39	0.564	SUBCLONAL	1	TRUE	0	0.432662405626699	1		320	276	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620051	21620051	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750829854	NA	P-0048671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	64	509	0	ENST00000382592.4:c.115G>A	p.Ala39Thr	p.A39T	ENST00000382592	NM_014572.2	39	Gca/Aca	2/8	0.33754226854366	1	FACETS	0.404	0.35	0.463	0.404	0.35	0.463	SUBCLONAL	1	TRUE	0	0.432662405626699	1		509	574	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554338	81554338	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759773701	NA	P-0048671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	30	358	0	ENST00000298171.2:c.358G>A	p.Asp120Asn	p.D120N	ENST00000298171	NM_000369.2	120	Gat/Aat	4/10	0.226027144145905	3	FACETS	0.405	0.326	0.495	0.135	0.108	0.165	INDETERMINATE	1	TRUE	0	0.432662405626699	3		358	416	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0048672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	136	309	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.206232082068162	6	FACETS	1	0.944	1	1	0.983	1	CLONAL	6	TRUE	1	0.206232082068162	6		309	303	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604707	48604707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	80	437	0	ENST00000342988.3:c.1529G>A	p.Gly510Glu	p.G510E	ENST00000342988	NM_005359.5	510	gGa/gAa	12/12	0.185335643789077	0	FACETS	0.782	0.703	0.862			1	SUBCLONAL	4	TRUE	0	0.206232082068162	0		437	197	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138409909	138409909	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	113	428	0	ENST00000289153.2:c.1969T>C	p.Ser657Pro	p.S657P	ENST00000289153	NM_006219.2	657	Tct/Cct	13/22	0.206473013306805	4	FACETS	0.961	0.874	1			1	CLONAL	4	TRUE	NA	0.206232082068162	4		428	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577525	7577527	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0048673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	273	585	0	ENST00000269305.4:c.754_756del	p.Leu252del	p.L252del	ENST00000269305	NM_001126112.2	252	CTC/-	7/11	0.761637861818712	1	FACETS	0.927	0.883	0.97	0.927	0.883	0.97	CLONAL	1	TRUE	0	0.761637861818712	1		585	479	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781276	3781276	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1261	368	869	0	ENST00000262367.5:c.5089A>G	p.Thr1697Ala	p.T1697A	ENST00000262367	NM_004380.2	1697	Acc/Gcc	30/31	0.729867695323127	4	FACETS	1	0.973	1	0.348	0.329	0.368	CLONAL	1	TRUE	1	0.761637861818712	4		869	1629	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416148	29416148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	216	500	1	ENST00000389048.3:c.4805G>A	p.Gly1602Asp	p.G1602D	ENST00000389048	NM_004304.4	1602	gGt/gAt	29/29	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.761637861818712	2		501	558	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37034006	37034006	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1401484095	NA	P-0048673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	196	383	1	ENST00000358127.4:c.23C>T	p.Pro8Leu	p.P8L	ENST00000358127	NM_001280556.1	8	cCg/cTg	1/10	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.761637861818712	NA		384	331	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913499	NA	P-0048674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	106	266	0	ENST00000345146.2:c.394C>A	p.Arg132Ser	p.R132S	ENST00000345146	NM_005896.2	132	Cgt/Agt	4/10	1	2	FACETS	1	0.959	1	1	0.989	1	CLONAL	2	FALSE	1	0.311053341112233	2		266	310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0048674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	653	745	0	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.311053341112233	2	FACETS	1	0.993	1	1	0.998	1	CLONAL	4	FALSE	0	0.311053341112233	2		745	983	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474357	40474357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	257	548	0	ENST00000264657.5:c.2044G>A	p.Ala682Thr	p.A682T	ENST00000264657	NM_139276.2	682	Gca/Aca	21/24	1	2	FACETS	1	0.966	1	1	0.995	1	CLONAL	2	FALSE	1	0.311053341112233	2		548	794	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972874	25972874	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	104	438	0	ENST00000435504.4:c.1551C>G	p.Ser517Arg	p.S517R	ENST00000435504		517	agC/agG	12/13	0.311053341112233	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	0	0.311053341112233	1		438	547	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778759	76778759	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	146	257	0	ENST00000373344.5:c.6820G>C	p.Ala2274Pro	p.A2274P	ENST00000373344	NM_000489.3	2274	Gct/Cct	31/35	1	1	FACETS	1	0.954	1	1	0.994	1	CLONAL	4	FALSE	0	0.311053341112233	1		257	197	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0048675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	771	696	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.834141553926203	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.834328966462139	2		697	884	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968265	15968265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	400	346	0	ENST00000268712.3:c.5020C>T	p.Pro1674Ser	p.P1674S	ENST00000268712	NM_006311.3	1674	Ccc/Tcc	34/46	0.834141553926203	2	FACETS	0.991	0.965	1	0.991	0.965	1	CLONAL	2	TRUE	0	0.834328966462139	2		346	484	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462404	89462404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	192	435	0	ENST00000336596.2:c.1876G>A	p.Val626Ile	p.V626I	ENST00000336596	NM_005233.5	626	Gtt/Att	10/17	0.502896958639728	1	FACETS	0.568	0.531	0.606	0.568	0.531	0.606	SUBCLONAL	1	TRUE	0	0.834328966462139	1		435	472	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802595	135802595	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	208	288	0	ENST00000298552.3:c.203A>C	p.His68Pro	p.H68P	ENST00000298552	NM_001162426.1	68	cAt/cCt	4/23	0.834328966462139	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.834328966462139	1		288	274	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0048686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	36	470	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.263744985109665	5	FACETS	1	0.935	1	0.822	0.694	0.959	INDETERMINATE	2	FALSE	2	0.44058874325145	5		470	110	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0048686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	33	365	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	0.263744985109665	5	FACETS	1	0.893	1	0.734	0.611	0.865	INDETERMINATE	2	FALSE	2	0.44058874325145	5		365	113	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058033	27058033	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	24	488	0	ENST00000324856.7:c.1741C>T	p.Gln581Ter	p.Q581*	ENST00000324856	NM_006015.4	581	Cag/Tag	3/20	0.20336675513745	5	FACETS	0.649	0.509	0.808	0.216	0.169	0.27	INDETERMINATE	1	FALSE	2	0.44058874325145	5		488	279	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	102	528	0	ENST00000346208.3:c.878T>A	p.Met293Lys	p.M293K	ENST00000346208		293	aTg/aAg	4/6	0.251980376835944	2	FACETS	0.965	0.88	1	0.965	0.88	1	INDETERMINATE	2	FALSE	0	0.44058874325145	2		528	240	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189389	56189389	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	73	450	0	ENST00000399503.3:c.4421C>T	p.Pro1474Leu	p.P1474L	ENST00000399503	NM_005921.1	1474	cCt/cTt	20/20	0.352545583634178	5	FACETS	0.971	0.867	1	0.971	0.867	1	CLONAL	3	FALSE	2	0.44058874325145	5		450	189	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505389	157505389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	77	457	0	ENST00000346085.5:c.3370G>A	p.Glu1124Lys	p.E1124K	ENST00000346085	NM_020732.3	1124	Gag/Aag	13/20	0.366418496914481	3	FACETS	0.927	0.827	1	0.927	0.827	1	CLONAL	2	FALSE	1	0.44058874325145	3		457	230	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242764	16242764	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	28	418	0	ENST00000375759.3:c.1385G>A	p.Gly462Glu	p.G462E	ENST00000375759	NM_015001.2	462	gGa/gAa	6/15	0.20336675513745	5	FACETS	1	0.872	1	0.37	0.298	0.451	INDETERMINATE	1	FALSE	2	0.44058874325145	5		418	190	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265369	16265369	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	59	636	0	ENST00000375759.3:c.10861C>T	p.Gln3621Ter	p.Q3621*	ENST00000375759	NM_015001.2	3621	Cag/Tag	14/15	0.20336675513745	5	FACETS	0.869	0.755	0.99	0.579	0.503	0.66	INDETERMINATE	2	FALSE	2	0.44058874325145	5		636	256	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243053	105243053	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	136	825	0	ENST00000349310.3:c.230G>T	p.Cys77Phe	p.C77F	ENST00000349310	NM_001014432.1	77	tGc/tTc	5/15	0.260935135311917	4	FACETS	1	0.928	1	1	0.928	1	INDETERMINATE	2	FALSE	2	0.44058874325145	4		825	439	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175811	24175811	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	45	656	1	ENST00000263121.7:c.1039G>A	p.Asp347Asn	p.D347N	ENST00000263121	NM_003073.3	347	Gac/Aac	8/9	0.299236193915028	3	FACETS	0.857	0.724	1	0.428	0.362	0.501	CLONAL	1	FALSE	1	0.44058874325145	3		657	291	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183345	56183345	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	39	347	0	ENST00000399503.3:c.4255G>C	p.Glu1419Gln	p.E1419Q	ENST00000399503	NM_005921.1	1419	Gag/Cag	18/20	0.352545583634178	5	FACETS	1	0.914	1	0.748	0.633	0.87	CLONAL	2	FALSE	2	0.44058874325145	5		347	131	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0048687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	45	932	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.756	0.634	0.892	0.756	0.634	0.892	SUBCLONAL	1	FALSE	1	0.17119043153148	2		934	695	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0048687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	28	162	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.965	0.772	1	0.965	0.772	1	CLONAL	1	FALSE	1	0.17119043153148	2		162	339	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481659	56481659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140656187	NA	P-0048687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	44	676	1	ENST00000267101.3:c.694G>A	p.Ala232Thr	p.A232T	ENST00000267101	NM_001982.3	232	Gcc/Acc	6/28	1	2	FACETS	0.677	0.566	0.801	0.677	0.566	0.801	SUBCLONAL	1	FALSE	1	0.17119043153148	2		677	759	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866484	56866484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779606369	NA	P-0048687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	38	588	0	ENST00000519728.1:c.731G>A	p.Arg244Gln	p.R244Q	ENST00000519728	NM_002350.3	244	cGg/cAg	8/13	1	2	FACETS	0.586	0.483	0.703	0.586	0.483	0.703	SUBCLONAL	1	FALSE	1	0.17119043153148	2		588	757	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0048688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	107	329	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		329	325	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	284	620	0	ENST00000269305.4:c.528C>A	p.Cys176Ter	p.C176*	ENST00000269305	NM_001126112.2	176	tgC/tgA	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		620	800	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937600	76937603	+	frameshift_variant	Frame_Shift_Del	DEL	TTAT	TTAT	-	novel	NA	P-0048688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	187	284	0	ENST00000373344.5:c.3145_3148del	p.Ile1049GlufsTer68	p.I1049Efs*68	ENST00000373344	NM_000489.3	1049	ATAAga/ga	9/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		284	522	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684305	29684305	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1567627155	NA	P-0048688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	43	325	0	ENST00000356175.3:c.7825A>G	p.Thr2609Ala	p.T2609A	ENST00000356175	NM_000267.3	2609	Acc/Gcc	53/57	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		325	593	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0048690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	292	660	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.573869280709478	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.573869280709478	1		660	725	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042172	14042172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	40	239	0	ENST00000311895.7:c.2719G>A	p.Glu907Lys	p.E907K	ENST00000311895	NM_005236.2	907	Gaa/Aaa	11/11	1	2	FACETS	0.36	0.3	0.428	0.36	0.3	0.428	SUBCLONAL	1	TRUE	1	0.573869280709478	2		239	387	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474072	29474072	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	108	618	2	ENST00000389048.3:c.2103C>A	p.Cys701Ter	p.C701*	ENST00000389048	NM_004304.4	701	tgC/tgA	12/29	1	2	FACETS	0.436	0.39	0.484	0.436	0.39	0.484	SUBCLONAL	1	TRUE	1	0.573869280709478	2		620	864	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729735	41729741	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTCTT	TCTTCTT	-	novel	NA	P-0048690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	42	364	0	ENST00000242208.4:c.788_794del	p.Lys263ArgfsTer94	p.K263Rfs*94	ENST00000242208	NM_002192.2	263	aAAGAAGAg/ag	3/3	1	2	FACETS	0.237	0.197	0.282	0.237	0.197	0.282	SUBCLONAL	1	TRUE	1	0.573869280709478	2		364	617	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200252	123200252	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	42	396	0	ENST00000218089.9:c.2231A>T	p.Gln744Leu	p.Q744L	ENST00000218089	NM_001042749.1	744	cAa/cTa	23/35	0.333871644039457	1	FACETS	0.308	0.258	0.363	0.308	0.258	0.363	INDETERMINATE	1	TRUE	0	0.573869280709478	1		396	339	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964925	55964925	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	251	277	0	ENST00000263923.4:c.2312C>G	p.Thr771Arg	p.T771R	ENST00000263923	NM_002253.2	771	aCg/aGg	16/30	0.219755932144712	5	FACETS	0.981	0.928	1	1	0.989	1	CLONAL	6	FALSE	0	0.219755932144712	5		277	516	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037427	12037427	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	135	395	0	ENST00000396373.4:c.1058G>C	p.Arg353Pro	p.R353P	ENST00000396373	NM_001987.4	353	cGg/cCg	6/8	0.219755932144712	6	FACETS	0.908	0.828	0.993			1	CLONAL	3	FALSE	NA	0.219755932144712	6		395	649	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103510719	103510719	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	61	313	0	ENST00000355739.4:c.623T>A	p.Met208Lys	p.M208K	ENST00000355739	NM_000123.3	208	aTg/aAg	6/15	0.105668331700711	0	FACETS	0.69	0.599	0.787			1	INDETERMINATE	2	FALSE	0	0.219755932144712	0		313	314	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0048692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	51	470	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.316	0.269	0.368	0.316	0.269	0.368	SUBCLONAL	1	TRUE	1	0.667935596639018	2		470	483	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398278	25398279	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGC	novel	NA	P-0048692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	186	377	0	ENST00000311936.3:c.38_40dup	p.Gly13dup	p.G13dup	ENST00000311936	NM_004985.3	13	gta/gGCGta	2/5	0.557174002819747	3	FACETS	1	0.947	1	0.514	0.476	0.553	CLONAL	1	TRUE	1	0.667935596639018	3		377	723	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140915	37140915	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	68	474	0	ENST00000373509.5:c.751G>C	p.Gly251Arg	p.G251R	ENST00000373509	NM_002648.3	251	Ggc/Cgc	5/6	1	2	FACETS	0.324	0.281	0.37	0.324	0.281	0.37	SUBCLONAL	1	TRUE	1	0.667935596639018	2		474	629	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	72	301	0				ENST00000310581	NM_198253.2	-/1132			0.179791829073669	1	FACETS	0.948	0.834	1	0.948	0.834	1	INDETERMINATE	1	TRUE	0	0.36	1		301	346	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0048694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	103	561	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.179791829073669	1	FACETS	0.895	0.804	0.991	0.895	0.804	0.991	INDETERMINATE	1	TRUE	0	0.36	1		561	524	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0048694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	58	281	1	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	0.918	0.793	1	0.918	0.793	1	CLONAL	1	TRUE	1	0.36	2		282	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	rs879253905	NA	P-0048694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	166	522	0	ENST00000269305.4:c.785del	p.Gly262ValfsTer83	p.G262Vfs*83	ENST00000269305	NM_001126112.2	262	gGt/gt	8/11	0.205222652717455	3	FACETS	1	0.977	1			1	INDETERMINATE	2	TRUE	NA	0.36	3		522	479	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625159	69625159	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554980306	NA	P-0048694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	51	684	1	ENST00000334134.2:c.634C>T	p.Arg212Trp	p.R212W	ENST00000334134	NM_005247.2	212	Cgg/Tgg	3/3	0.29519930749817	2	FACETS	0.557	0.473	0.648	0.278	0.236	0.324	SUBCLONAL	1	TRUE	0	0.36	2		685	509	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471012	8471012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	17	380	0	ENST00000356435.5:c.3487G>T	p.Glu1163Ter	p.E1163*	ENST00000356435		1163	Gaa/Taa	20/35	0.29519930749817	1	FACETS	0.279	0.208	0.363	0.279	0.208	0.363	SUBCLONAL	1	TRUE	0	0.36	1		380	278	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245788	46245797	+	frameshift_variant	Frame_Shift_Del	DEL	AAATGGGAGA	AAATGGGAGA	-	novel	NA	P-0048694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	89	388	0	ENST00000334344.6:c.3884_3893del	p.Asn1295SerfsTer24	p.N1295Sfs*24	ENST00000334344	NM_152641.2	1294	ttAAATGGGAGA/tt	15/21	0.29519930749817	2	FACETS	1	0.976	1	0.674	0.602	0.749	CLONAL	1	TRUE	0	0.36	2		388	367	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632396	3632396	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	59	733	1	ENST00000294008.3:c.5452C>T	p.Leu1818Phe	p.L1818F	ENST00000294008	NM_032444.2	1818	Ctc/Ttc	15/15	0.29519930749817	1	FACETS	0.434	0.373	0.5	0.434	0.373	0.5	SUBCLONAL	1	TRUE	0	0.36	1		734	620	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280021	66280021	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	19	187	0	ENST00000273854.3:c.1668G>T	p.Glu556Asp	p.E556D	ENST00000273854	NM_004439.5	556	gaG/gaT	7/18	0.235453355307435	1	FACETS	0.476	0.363	0.607	0.476	0.363	0.607	SUBCLONAL	1	TRUE	0	0.36	1		187	182	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271362	26271362	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	71	520	0	ENST00000305910.3:c.251G>T	p.Arg84Leu	p.R84L	ENST00000305910	NM_003534.2	84	cGc/cTc	1/1	1	2	FACETS	0.817	0.715	0.926	0.817	0.715	0.926	CLONAL	1	TRUE	1	0.36	2		520	483	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622199	117622199	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	30	332	1	ENST00000368508.3:c.6671A>G	p.Asn2224Ser	p.N2224S	ENST00000368508	NM_002944.2	2224	aAt/aGt	42/43	0.29519930749817	1	FACETS	0.618	0.501	0.749	0.618	0.501	0.749	SUBCLONAL	1	TRUE	0	0.36	1		333	221	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0048695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	246	742	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.443160651650064	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.460243174043818	1		742	760	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137857	64137857	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0048695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	107	975	0	ENST00000334205.4:c.1957+1G>A		p.X653_splice	ENST00000334205	NM_003942.2	653			NA	2	FACETS	0.388	0.347	0.432			1	INDETERMINATE	1	TRUE	NA	0.460243174043818	2		975	1199	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281735	46281735	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	96	674	0	ENST00000371998.3:c.4182C>A	p.His1394Gln	p.H1394Q	ENST00000371998		1394	caC/caA	22/23	0.273942193402975	3	FACETS	0.449	0.398	0.502	0.224	0.199	0.251	INDETERMINATE	1	TRUE	1	0.460243174043818	3		674	1144	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955069	55955069	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	70	478	0	ENST00000263923.4:c.3476A>C	p.His1159Pro	p.H1159P	ENST00000263923	NM_002253.2	1159	cAt/cCt	26/30	0.31379424538141	1	FACETS	0.327	0.284	0.373	0.327	0.284	0.373	SUBCLONAL	1	TRUE	0	0.460243174043818	1		478	717	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557873	187557873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	42	532	0	ENST00000441802.2:c.3838G>A	p.Asp1280Asn	p.D1280N	ENST00000441802	NM_005245.3	1280	Gat/Aat	5/27	NA	2	FACETS	0.236	0.196	0.281			1	INDETERMINATE	1	TRUE	NA	0.460243174043818	2		532	773	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0048696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	46	309	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	0.704	0.593	0.828	0.704	0.593	0.828	SUBCLONAL	1	TRUE	1	0.237509479111667	2		309	550	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0048697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	41	620	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.581	0.482	0.691	0.581	0.482	0.691	SUBCLONAL	1	TRUE	1	0.2	2		620	706	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0048697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	14	275	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.332	0.239	0.445	0.332	0.239	0.445	SUBCLONAL	1	TRUE	1	0.2	2		275	422	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107135	27107136	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	70	483	0	ENST00000324856.7:c.6747dup	p.Glu2250ArgfsTer28	p.E2250Rfs*28	ENST00000324856	NM_006015.4	2249	tca/tcAa	20/20	1	2	FACETS	0.951	0.828	1	0.951	0.828	1	CLONAL	1	TRUE	1	0.2	2		483	736	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712018	89712018	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs727504114	NA	P-0048697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	41	225	0	ENST00000371953.3:c.634+2T>C		p.X212_splice	ENST00000371953	NM_000314.4	212			1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.2	2		225	346	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591251	67591256	+	frameshift_variant	Frame_Shift_Del	DEL	GTTGAC	GTTGAC	T	novel	NA	P-0048697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	29	319	0	ENST00000274335.5:c.1749_1754delinsT	p.Trp583CysfsTer17	p.W583Cfs*17	ENST00000274335		583	tgGTTGACt/tgTt	13/15	1	2	FACETS	0.625	0.501	0.767	0.625	0.501	0.767	SUBCLONAL	1	TRUE	1	0.2	2		319	464	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0048698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	169	582	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.35620253127212	4	FACETS	1	0.988	1	0.719	0.663	0.778	CLONAL	1	TRUE	2	0.469860370346733	4		582	735	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202738	108202738	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	132	282	0	ENST00000278616.4:c.7762C>G	p.Pro2588Ala	p.P2588A	ENST00000278616	NM_000051.3	2588	Cct/Gct	52/63	0.390297984335738	3	FACETS	1	0.987	1	0.744	0.681	0.811	CLONAL	1	TRUE	1	0.469860370346733	3		282	466	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435189	49435189	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	187	450	0	ENST00000301067.7:c.6364C>G	p.Pro2122Ala	p.P2122A	ENST00000301067	NM_003482.3	2122	Ccc/Gcc	31/54	0.35620253127212	4	FACETS	1	0.99	1	0.733	0.678	0.79	CLONAL	1	TRUE	2	0.469860370346733	4		450	798	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003701	45003749	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	TCGCGCTGGCGGGCATTCCTGAAGCTGACAGCATTCGGGCCGAGATGTC	TCGCGCTGGCGGGCATTCCTGAAGCTGACAGCATTCGGGCCGAGATGTC	-	novel	NA	P-0048698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	149	274	0	ENST00000558401.1:c.-40_9del		p.*14*	ENST00000558401	NM_004048.2	?-2/119		1/4	0.399046325778956	2	FACETS	1	0.987	1	0.692	0.638	0.748	CLONAL	1	TRUE	0	0.469860370346733	2		274	458	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923397	9923397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	96	505	0	ENST00000330684.3:c.1890G>A	p.Met630Ile	p.M630I	ENST00000330684	NM_001134407.1	630	atG/atA	9/13	0.469860370346733	1	FACETS	0.592	0.529	0.659	0.592	0.529	0.659	SUBCLONAL	1	TRUE	0	0.469860370346733	1		505	528	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347628	89347628	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	319	507	0	ENST00000301030.4:c.5322C>A	p.Asn1774Lys	p.N1774K	ENST00000301030	NM_001256183.1	1774	aaC/aaA	9/13	0.390297984335738	3	FACETS	0.948	0.898	0.999	0.948	0.898	0.999	CLONAL	2	TRUE	1	0.469860370346733	3		507	884	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0048698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	283	468	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.390297984335738	3	FACETS	0.847	0.798	0.897	0.847	0.798	0.897	CLONAL	2	TRUE	1	0.469860370346733	3		468	878	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011106	12011106	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0048698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	93	284	0	ENST00000353533.5:c.514-1G>A		p.X172_splice	ENST00000353533	NM_003010.3	172			0.390297984335738	3	FACETS	1	0.906	1	0.508	0.454	0.566	CLONAL	1	TRUE	1	0.469860370346733	3		284	481	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220505	1220505	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs886039554	NA	P-0048698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	311	593	1	ENST00000326873.7:c.597+1G>T		p.X199_splice	ENST00000326873	NM_000455.4	199			NA	2	FACETS	0.791	0.749	0.833			1	INDETERMINATE	2	TRUE	NA	0.469860370346733	2		594	837	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610293	10610293	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	387	653	1	ENST00000171111.5:c.417del	p.Phe139LeufsTer18	p.F139Lfs*18	ENST00000171111	NM_203500.1	139	ttC/tt	2/6	0.397387033822914	2	FACETS	0.798	0.76	0.837	0.798	0.76	0.837	SUBCLONAL	2	TRUE	0	0.469860370346733	2		654	1032	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017724	31017724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1005458245	NA	P-0048698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	116	438	0	ENST00000375687.4:c.586G>A	p.Asp196Asn	p.D196N	ENST00000375687	NM_015338.5	196	Gat/Aat	8/13	0.197043291845568	5	FACETS	0.989	0.891	1	0.33	0.297	0.365	INDETERMINATE	1	TRUE	2	0.469860370346733	5		438	851	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713506	30713506	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs886038794	NA	P-0048698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	219	392	0	ENST00000295754.5:c.831G>T	p.Lys277Asn	p.K277N	ENST00000295754	NM_003242.5	277	aaG/aaT	4/7	0.399046325778956	2	FACETS	0.778	0.729	0.828	0.778	0.729	0.828	SUBCLONAL	2	TRUE	0	0.469860370346733	2		392	599	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179378	56179378	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	85	171	2	ENST00000399503.3:c.3691A>T	p.Thr1231Ser	p.T1231S	ENST00000399503	NM_005921.1	1231	Acc/Tcc	15/20	0.382368155869221	3	FACETS	0.894	0.802	0.988	0.894	0.802	0.988	CLONAL	2	TRUE	1	0.469860370346733	3		173	250	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441306	149441306	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	123	503	0	ENST00000286301.3:c.1733C>G	p.Pro578Arg	p.P578R	ENST00000286301	NM_005211.3	578	cCc/cGc	12/22	1	2	FACETS	0.719	0.651	0.791	0.719	0.651	0.791	SUBCLONAL	1	TRUE	1	0.469860370346733	2		503	728	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397738	116397738	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	109	431	0	ENST00000397752.3:c.2012G>T	p.Gly671Val	p.G671V	ENST00000397752	NM_000245.2	671	gGt/gTt	8/21	0.382368155869221	3	FACETS	0.754	0.677	0.835	0.377	0.338	0.418	SUBCLONAL	1	TRUE	1	0.469860370346733	3		431	760	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942745	68942745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781270008	NA	P-0048699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	61	368	0	ENST00000288368.4:c.557G>A	p.Arg186Gln	p.R186Q	ENST00000288368	NM_024870.2	186	cGg/cAg	6/40	1	2	FACETS	0.667	0.579	0.762	0.667	0.579	0.762	SUBCLONAL	1	TRUE	1	0.539621629568316	2		368	339	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458702	120458702	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1242882244	NA	P-0048699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	108	448	0	ENST00000256646.2:c.6643A>G	p.Ser2215Gly	p.S2215G	ENST00000256646	NM_024408.3	2215	Agc/Ggc	34/34	1	2	FACETS	0.878	0.792	0.967	0.878	0.792	0.967	CLONAL	1	TRUE	1	0.539621629568316	2		448	456	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226568871	226568871	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	138	473	0	ENST00000366794.5:c.1198A>G	p.Lys400Glu	p.K400E	ENST00000366794	NM_001618.3	400	Aag/Gag	9/23	1	2	FACETS	0.958	0.876	1	0.958	0.876	1	CLONAL	1	TRUE	1	0.539621629568316	2		473	534	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924228	11924228	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	19	15	0	ENST00000353533.5:c.25G>T	p.Gly9Cys	p.G9C	ENST00000353533	NM_003010.3	9	Ggc/Tgc	1/11	0.539621629568316	1	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	0	0.539621629568316	1		15	44	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659212	86659212	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	14	163	0	ENST00000274376.6:c.1501G>C	p.Asp501His	p.D501H	ENST00000274376	NM_002890.2	501	Gat/Cat	11/25	1	2	FACETS	0.504	0.368	0.663	0.504	0.368	0.663	SUBCLONAL	1	TRUE	1	0.539621629568316	2		163	103	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738361	133738361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	134	453	0	ENST00000318560.5:c.761G>A	p.Gly254Glu	p.G254E	ENST00000318560	NM_005157.4	254	gGg/gAg	4/11	1	2	FACETS	0.855	0.78	0.933	0.855	0.78	0.933	CLONAL	1	TRUE	1	0.539621629568316	2		453	581	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0048701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	69	582	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.389724133972578	1	FACETS	0.773	0.678	0.873	0.773	0.678	0.873	SUBCLONAL	1	TRUE	0	0.43104172156834	1		582	325	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602289	10602289	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	184	685	0	ENST00000171111.5:c.1289G>T	p.Gly430Val	p.G430V	ENST00000171111	NM_203500.1	430	gGc/gTc	3/6	0.43104172156834	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.43104172156834	1		685	623	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688662	47688663	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0048701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	58	320	0	ENST00000347630.2:c.637_638delinsTT	p.Ala213Phe	p.A213F	ENST00000347630	NM_001007230.1	213	GCt/TTt	7/11	1	2	FACETS	0.681	0.587	0.783	0.681	0.587	0.783	SUBCLONAL	1	TRUE	1	0.43104172156834	2		320	395	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266868	18266868	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	112	537	0	ENST00000222254.8:c.179T>A	p.Leu60His	p.L60H	ENST00000222254	NM_005027.3	60	cTc/cAc	2/16	0.43104172156834	1	FACETS	0.842	0.762	0.927	0.842	0.762	0.927	CLONAL	1	TRUE	0	0.43104172156834	1		537	484	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646134	215646134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	82	489	0	ENST00000260947.4:c.464G>A	p.Arg155Lys	p.R155K	ENST00000260947	NM_000465.2	155	aGa/aAa	4/11	1	2	FACETS	0.84	0.744	0.942	0.84	0.744	0.942	CLONAL	1	TRUE	1	0.43104172156834	2		489	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0048702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	399	564	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.358852568655581	3	FACETS	0.98	0.937	1	0.98	0.937	1	CLONAL	3	TRUE	0	0.358852568655581	3		564	892	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244586	46244586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	207	479	0	ENST00000334344.6:c.2680C>T	p.Gln894Ter	p.Q894*	ENST00000334344	NM_152641.2	894	Cag/Tag	15/21	0.353417543789964	2	FACETS	0.866	0.808	0.926	0.866	0.808	0.926	CLONAL	2	TRUE	0	0.358852568655581	2		479	666	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70360756	70360756	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	33	229	0	ENST00000373644.4:c.1933A>G	p.Arg645Gly	p.R645G	ENST00000373644	NM_030625.2	645	Agg/Ggg	3/12	0.358852568655581	3	FACETS	0.545	0.444	0.659	0.273	0.222	0.33	SUBCLONAL	1	TRUE	1	0.358852568655581	3		229	398	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231780	36231780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	151	532	1	ENST00000300305.3:c.604G>A	p.Glu202Lys	p.E202K	ENST00000300305		202	Gaa/Aaa	5/8	0.329001480203299	3	FACETS	1	0.971	1	0.38	0.347	0.414	CLONAL	1	TRUE	0	0.358852568655581	3		533	871	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0048703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	266	619	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.495513892676411	1	FACETS	0.895	0.843	0.948	0.895	0.843	0.948	CLONAL	1	TRUE	0	0.564837571922138	1		619	755	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979502	7979502	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	207	420	0	ENST00000319144.4:c.1523C>A	p.Ala508Glu	p.A508E	ENST00000319144	NM_001139.2	508	gCa/gAa	11/15	0.495513892676411	1	FACETS	0.868	0.81	0.927	0.868	0.81	0.927	CLONAL	1	TRUE	0	0.564837571922138	1		420	606	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	67	301	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.401804882436765	2		301	306	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0048705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	60	340	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	1	2	FACETS	0.851	0.737	0.973	0.851	0.737	0.973	CLONAL	1	TRUE	1	0.401804882436765	2		340	351	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349700	15349701	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0048705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	107	651	0	ENST00000263377.2:c.3873_3874delinsAA	p.Glu1292Lys	p.E1292K	ENST00000263377	NM_058243.2	1291	caGGag/caAAag	19/20	1	2	FACETS	0.897	0.806	0.992	0.897	0.806	0.992	CLONAL	1	TRUE	1	0.401804882436765	2		651	594	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981097	201981097	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	51	493	0	ENST00000359651.3:c.176G>A	p.Trp59Ter	p.W59*	ENST00000359651		59	tGg/tAg	2/8	1	2	FACETS	0.475	0.404	0.554	0.475	0.404	0.554	SUBCLONAL	1	TRUE	1	0.401804882436765	2		493	534	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982980	201982980	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	97	646	0	ENST00000359651.3:c.829G>A	p.Glu277Lys	p.E277K	ENST00000359651		277	Gag/Aag	7/8	1	2	FACETS	0.702	0.626	0.782	0.702	0.626	0.782	SUBCLONAL	1	TRUE	1	0.401804882436765	2		646	688	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982387	201982387	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	99	767	0	ENST00000359651.3:c.766G>C	p.Glu256Gln	p.E256Q	ENST00000359651		256	Gag/Cag	6/8	1	2	FACETS	0.545	0.485	0.608	0.545	0.485	0.608	SUBCLONAL	1	TRUE	1	0.401804882436765	2		767	905	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982309	201982309	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0048705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	70	695	0	ENST00000359651.3:c.689-1G>C		p.X230_splice	ENST00000359651		230			1	2	FACETS	0.497	0.433	0.567	0.497	0.433	0.567	SUBCLONAL	1	TRUE	1	0.401804882436765	2		695	701	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982405	201982405	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	101	699	0	ENST00000359651.3:c.784G>C	p.Glu262Gln	p.E262Q	ENST00000359651		262	Gag/Cag	6/8	1	2	FACETS	0.617	0.551	0.687	0.617	0.551	0.687	SUBCLONAL	1	TRUE	1	0.401804882436765	2		699	815	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983076	201983076	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	95	643	0	ENST00000359651.3:c.925G>C	p.Glu309Gln	p.E309Q	ENST00000359651		309	Gag/Cag	7/8	1	2	FACETS	0.739	0.659	0.824	0.739	0.659	0.824	SUBCLONAL	1	TRUE	1	0.401804882436765	2		643	640	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690617	88690617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201527669	NA	P-0048705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	68	381	1	ENST00000360948.2:c.413G>A	p.Arg138Gln	p.R138Q	ENST00000360948	NM_001012338.2	138	cGg/cAg	5/19	1	2	FACETS	0.691	0.602	0.786	0.691	0.602	0.786	SUBCLONAL	1	TRUE	1	0.401804882436765	2		382	490	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925128	81925128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	117	510	0	ENST00000359376.3:c.919G>A	p.Asp307Asn	p.D307N	ENST00000359376	NM_002661.3	307	Gac/Aac	11/33	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.401804882436765	2		510	581	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089956	16089956	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	94	383	0	ENST00000268712.3:c.154C>T	p.Gln52Ter	p.Q52*	ENST00000268712	NM_006311.3	52	Cag/Tag	3/46	0.401804882436765	1	FACETS	0.835	0.746	0.927	0.835	0.746	0.927	CLONAL	1	TRUE	0	0.401804882436765	1		383	448	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867706	45867706	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	125	681	0	ENST00000391945.4:c.694G>T	p.Val232Phe	p.V232F	ENST00000391945	NM_000400.3	232	Gtc/Ttc	8/23	1	2	FACETS	0.881	0.799	0.968	0.881	0.799	0.968	CLONAL	1	TRUE	1	0.401804882436765	2		681	706	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147175	61147175	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0048705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	64	295	1	ENST00000295025.8:c.854-1G>A		p.X285_splice	ENST00000295025	NM_002908.2	285			1	2	FACETS	0.951	0.829	1	0.951	0.829	1	CLONAL	1	TRUE	1	0.401804882436765	2		296	335	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562225	176562225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	82	641	0	ENST00000439151.2:c.121G>A	p.Glu41Lys	p.E41K	ENST00000439151	NM_022455.4	41	Gag/Aag	2/23	0.405043818021762	1	FACETS	0.54	0.476	0.608	0.54	0.476	0.608	SUBCLONAL	1	TRUE	0	0.401804882436765	1		641	604	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781167	135781167	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	125	627	0	ENST00000298552.3:c.1798C>T	p.Gln600Ter	p.Q600*	ENST00000298552	NM_001162426.1	600	Cag/Tag	15/23	0.405043818021762	0	FACETS	0.822	0.749	0.897			1	CLONAL	1	TRUE	0	0.401804882436765	0		627	453	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815605	139815605	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0048705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	86	600	0	ENST00000247668.2:c.1076C>G	p.Ser359Ter	p.S359*	ENST00000247668	NM_021138.3	359	tCa/tGa	9/11	0.405043818021762	0	FACETS	0.478	0.423	0.536			1	SUBCLONAL	1	TRUE	0	0.401804882436765	0		600	536	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937712	44937712	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048705-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	123	469	0	ENST00000377967.4:c.2901del	p.Thr968GlnfsTer2	p.T968Qfs*2	ENST00000377967	NM_021140.2	967	gTt/gt	19/29	0.405043818021762	1	FACETS	0.828	0.751	0.908	0.828	0.751	0.908	CLONAL	1	TRUE	0	0.401804882436765	1		469	591	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991625	25991626	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0048708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	61	176	0	ENST00000435504.4:c.616_617del	p.Val206ThrfsTer13	p.V206Tfs*13	ENST00000435504		206	GTa/a	7/13	1	2	FACETS	0.84	0.725	0.964	0.84	0.725	0.964	CLONAL	1	TRUE	1	0.27	2		176	538	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589662	69589662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	26	154	0	ENST00000168712.1:c.191C>T	p.Pro64Leu	p.P64L	ENST00000168712	NM_002007.2	64	cCc/cTc	1/3	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.419855429130628	2		154	90	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499073	149499073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs550187329	NA	P-0048710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	10	694	0	ENST00000261799.4:c.2755C>T	p.Arg919Trp	p.R919W	ENST00000261799	NM_002609.3	919	Cgg/Tgg	20/23	0.196480331276503	4	FACETS	0.476	0.323	0.667	0.238	0.161	0.334	INDETERMINATE	1	FALSE	2	0.392632363857644	4		694	149	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231782	36231782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs74315450	NA	P-0048710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	8	596	1	ENST00000300305.3:c.602G>A	p.Arg201Gln	p.R201Q	ENST00000300305		201	cGa/cAa	5/8	0.2905612343402	3	FACETS	0.24	0.154	0.352	0.12	0.077	0.176	SUBCLONAL	1	FALSE	1	0.392632363857644	3		597	203	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347873	347873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199666954	NA	P-0048710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	10	827	0	ENST00000262320.3:c.1633C>T	p.Arg545Trp	p.R545W	ENST00000262320	NM_003502.3	545	Cgg/Tgg	6/11	0.125350317837625	0	FACETS	0.219	0.149	0.307			1	INDETERMINATE	1	FALSE	0	0.392632363857644	0		827	141	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639690	3639690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	11	832	0	ENST00000294008.3:c.3949C>T	p.Pro1317Ser	p.P1317S	ENST00000294008	NM_032444.2	1317	Ccg/Tcg	12/15	0.125350317837625	0	FACETS	0.362	0.253	0.495			1	INDETERMINATE	1	FALSE	0	0.392632363857644	0		832	94	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179448	56179454	+	frameshift_variant	Frame_Shift_Del	DEL	TTTCTTC	TTTCTTC	-	novel	NA	P-0048710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	16	275	0	ENST00000399503.3:c.3763_3769del	p.Ser1255ValfsTer12	p.S1255Vfs*12	ENST00000399503	NM_005921.1	1254	tTTTCTTCt/tt	15/20	0.196480331276503	4	FACETS	0.822	0.623	1	0.822	0.623	1	INDETERMINATE	2	FALSE	2	0.392632363857644	4		275	69	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109323542	109323542	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	40	532	0	ENST00000436639.2:c.284T>G	p.Leu95Arg	p.L95R	ENST00000436639	NM_014454.2	95	cTt/cGt	2/10	0.392632363857644	4	FACETS	0.972	0.822	1	0.972	0.822	1	CLONAL	2	FALSE	2	0.392632363857644	4		532	146	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177631	56177632	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	T	novel	NA	P-0048710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	23	424	0	ENST00000399503.3:c.2604_2605delinsT	p.Ile869SerfsTer5	p.I869Sfs*5	ENST00000399503	NM_005921.1	868	gcCAtc/gcTtc	14/20	0.196480331276503	4	FACETS	0.896	0.715	1	0.896	0.715	1	INDETERMINATE	2	FALSE	2	0.392632363857644	4		424	91	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432664	29432664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113994087	NA	P-0048711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	11	478	0	ENST00000389048.3:c.3824G>A	p.Arg1275Gln	p.R1275Q	ENST00000389048	NM_004304.4	1275	cGa/cAa	25/29	1	2	FACETS	0.13	0.089	0.181	0.13	0.089	0.181	SUBCLONAL	1	TRUE	1	0.346039475250715	2		478	489	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255881	16255881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	36	411	0	ENST00000375759.3:c.3146C>T	p.Ser1049Phe	p.S1049F	ENST00000375759	NM_015001.2	1049	tCt/tTt	11/15	0.211897976173468	1	FACETS	0.52	0.428	0.622	0.52	0.428	0.622	SUBCLONAL	1	TRUE	0	0.346039475250715	1		411	331	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509377	46509377	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	118	571	0	ENST00000262741.5:c.1354del	p.Val452PhefsTer39	p.V452Ffs*39	ENST00000262741	NM_003629.3	452	Gtt/tt	10/10	0.211897976173468	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.346039475250715	1		571	473	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2089944	2089944	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	71	546	0	ENST00000219066.1:c.920C>A	p.Pro307Gln	p.P307Q	ENST00000219066	NM_002528.5	307	cCg/cAg	6/6	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.346039475250715	2		546	321	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713714	52713714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1289736713	NA	P-0048711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	37	365	0	ENST00000394830.3:c.14G>A	p.Arg5Lys	p.R5K	ENST00000394830	NM_018313.4	5	aGa/aAa	2/30	0.149215972389627	3	FACETS	0.762	0.63	0.909	0.381	0.315	0.455	INDETERMINATE	1	TRUE	1	0.346039475250715	3		365	329	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176590	56176591	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0048711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	90	429	1	ENST00000399503.3:c.2141dup	p.Gly715ArgfsTer21	p.G715Rfs*21	ENST00000399503	NM_005921.1	714	gca/gCca	12/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.346039475250715	2		430	407	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	139	301	0				ENST00000310581	NM_198253.2	-/1132			0.350539659893046	4	FACETS	1	0.976	1	0.774	0.711	0.838	CLONAL	2	TRUE	1	0.414175177473627	4		301	409	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257090	16257090	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	32	495	0	ENST00000375759.3:c.4355A>T	p.Lys1452Ile	p.K1452I	ENST00000375759	NM_015001.2	1452	aAa/aTa	11/15	1	2	FACETS	0.401	0.326	0.487	0.401	0.326	0.487	SUBCLONAL	1	TRUE	1	0.414175177473627	2		495	385	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023867	27023885	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGGCAAGGGCCCGGCGG	GCCGGCAAGGGCCCGGCGG	-	novel	NA	P-0048712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	25	184	0	ENST00000324856.7:c.973_991del	p.Ala325ThrfsTer32	p.A325Tfs*32	ENST00000324856	NM_006015.4	325	GCCGGCAAGGGCCCGGCGGac/ac	1/20	1	2	FACETS	0.759	0.604	0.933	0.759	0.604	0.933	CLONAL	1	TRUE	1	0.414175177473627	2		184	159	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774196	56774196	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	62	345	0	ENST00000337432.4:c.547A>T	p.Ile183Leu	p.I183L	ENST00000337432	NM_058216.2	183	Ata/Tta	3/9	0.414175177473627	3	FACETS	0.936	0.812	1	0.468	0.406	0.535	CLONAL	1	TRUE	1	0.414175177473627	3		345	386	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814905	139814905	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1353852370	NA	P-0048712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	34	644	0	ENST00000247668.2:c.898G>T	p.Ala300Ser	p.A300S	ENST00000247668	NM_021138.3	300	Gcc/Tcc	8/11	0.414175177473627	3	FACETS	0.337	0.275	0.408	0.169	0.137	0.204	SUBCLONAL	1	TRUE	1	0.414175177473627	3		644	588	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0048714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	245	501	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.509549271445091	2		501	737	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0048714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	177	286	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.509549271445091	2	FACETS	0.895	0.837	0.954	0.895	0.837	0.954	CLONAL	2	TRUE	0	0.509549271445091	2		286	388	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729613	41729613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564878978	NA	P-0048714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	133	432	0	ENST00000242208.4:c.916C>T	p.Arg306Cys	p.R306C	ENST00000242208	NM_002192.2	306	Cgc/Tgc	3/3	0.182218334158106	3	FACETS	1	0.965	1	0.558	0.508	0.61	INDETERMINATE	1	TRUE	1	0.509549271445091	3		432	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578207	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0048714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	468	714	0	ENST00000269305.4:c.642_643del	p.His214GlnfsTer7	p.H214Qfs*7	ENST00000269305	NM_001126112.2	214	caTAgt/cagt	6/11	0.509549271445091	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.509549271445091	2		714	868	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477139	67477139	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	296	593	0	ENST00000327367.4:c.946C>T	p.Gln316Ter	p.Q316*	ENST00000327367	NM_005902.3	316	Cag/Tag	7/9	0.484347828043619	2	FACETS	0.924	0.877	0.97	0.924	0.877	0.97	CLONAL	2	TRUE	0	0.509549271445091	2		593	629	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434055	49434055	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746638965	NA	P-0048714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	45	755	0	ENST00000301067.7:c.7498G>A	p.Ala2500Thr	p.A2500T	ENST00000301067	NM_003482.3	2500	Gcg/Acg	31/54	0.229070366360356	3	FACETS	0.279	0.234	0.33	0.14	0.117	0.165	INDETERMINATE	1	TRUE	1	0.509549271445091	3		755	794	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024372	16024372	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	124	286	0	ENST00000268712.3:c.1846G>T	p.Glu616Ter	p.E616*	ENST00000268712	NM_006311.3	616	Gaa/Taa	16/46	0.509549271445091	2	FACETS	1	0.983	1	0.656	0.6	0.714	CLONAL	1	TRUE	0	0.509549271445091	2		286	371	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873041	134873041	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	71	617	0	ENST00000398015.3:c.1345A>G	p.Ser449Gly	p.S449G	ENST00000398015	NM_004441.4	449	Agc/Ggc	6/16	0.509549271445091	2	FACETS	0.382	0.333	0.435	0.191	0.166	0.218	SUBCLONAL	1	TRUE	0	0.509549271445091	2		617	730	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683327	182683327	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	113	406	0	ENST00000292782.4:c.218A>C	p.Lys73Thr	p.K73T	ENST00000292782	NM_020640.2	73	aAa/aCa	2/7	0.509549271445091	2	FACETS	0.763	0.689	0.842	0.382	0.344	0.421	SUBCLONAL	1	TRUE	0	0.509549271445091	2		406	581	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36208923	36208925	+	start_lost,inframe_deletion	Translation_Start_Site	DEL	GGC	GGC	-	rs898578503	NA	P-0048715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	10	26	0	ENST00000222270.7:c.14_16del	p.Ala5?	p.A5?	ENST00000222270	NM_014727.1	1	atGGCg/atg	1/37	0.893229975070514	4	FACETS	0.314	0.213	0.439			1	SUBCLONAL	1	TRUE	NA	0.893229975070514	4		26	135	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92300822	92300822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1311537790	NA	P-0048715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	37	429	0	ENST00000265734.4:c.565G>A	p.Glu189Lys	p.E189K	ENST00000265734	NM_001259.6	189	Gaa/Aaa	5/8	0.391248399612635	3	FACETS	0.212	0.174	0.255	0.106	0.087	0.128	INDETERMINATE	1	TRUE	1	0.893229975070514	3		429	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578374	7578374	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	570	584	2	ENST00000269305.4:c.556del	p.Asp186MetfsTer61	p.D186Mfs*61	ENST00000269305	NM_001126112.2	186	Gat/at	5/11	0.893229975070514	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.893229975070514	2		586	635	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718665	190718665	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	204	263	0	ENST00000441310.2:c.823T>G	p.Leu275Val	p.L275V	ENST00000441310	NM_000534.4	275	Tta/Gta	8/13	0.345571937107631	3	FACETS	0.812	0.764	0.859	0.812	0.764	0.859	INDETERMINATE	2	TRUE	1	0.893229975070514	3		263	407	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	70	301	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.843	0.736	0.958	0.843	0.736	0.958	CLONAL	1	TRUE	1	0.318751114437859	2		301	521	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0048716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	158	689	1	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.220877323052066	3	FACETS	1	0.944	1	0.521	0.476	0.568	CLONAL	1	TRUE	1	0.318751114437859	3		690	1103	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151863	108151863	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs377349886	NA	P-0048716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	94	421	0	ENST00000278616.4:c.3544G>C	p.Glu1182Gln	p.E1182Q	ENST00000278616	NM_000051.3	1182	Gag/Cag	24/63	1	2	FACETS	0.878	0.781	0.98	0.878	0.781	0.98	CLONAL	1	TRUE	1	0.318751114437859	2		421	672	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830754	3830754	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	77	455	0	ENST00000262367.5:c.1802G>C	p.Arg601Pro	p.R601P	ENST00000262367	NM_004380.2	601	cGg/cCg	8/31	0.318751114437859	1	FACETS	0.744	0.654	0.84	0.744	0.654	0.84	SUBCLONAL	1	TRUE	0	0.318751114437859	1		455	546	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807891	1807891	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28928868	NA	P-0048716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	897	859	0	ENST00000260795.2:c.1950G>C	p.Lys650Asn	p.K650N	ENST00000260795		650	aaG/aaC	13/17	0.318751114437859	7	FACETS	1	0.986	1			1	CLONAL	6	TRUE	NA	0.318751114437859	7		859	1652	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971091	21971100	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCTCCCGG	GCCCTCCCGG	-	novel	NA	P-0048716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	70	521	0	ENST00000304494.5:c.258_267del	p.Arg87SerfsTer56	p.R87Sfs*56	ENST00000304494	NM_000077.4	86	gcCCGGGAGGGC/gc	2/3	0.318751114437859	1	FACETS	0.688	0.6	0.782	0.688	0.6	0.782	SUBCLONAL	1	TRUE	0	0.318751114437859	1		521	537	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891190	101891190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	70	378	0	ENST00000374994.4:c.151G>A	p.Asp51Asn	p.D51N	ENST00000374994	NM_004612.2	51	Gat/Aat	2/9	0.318751114437859	1	FACETS	0.815	0.713	0.925	0.815	0.713	0.925	CLONAL	1	TRUE	0	0.318751114437859	1		378	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs28934577	NA	P-0048722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	375	609	0	ENST00000269305.4:c.770T>A	p.Leu257Gln	p.L257Q	ENST00000269305	NM_001126112.2	257	cTg/cAg	7/11	NA	2	FACETS	0.846	0.809	0.883			1	INDETERMINATE	3	TRUE	NA	0.391362685119669	2		609	755	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360516	118360516	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	180	369	0	ENST00000534358.1:c.4489G>T	p.Glu1497Ter	p.E1497*	ENST00000534358	NM_005933.3	1497	Gag/Tag	12/36	0.391362685119669	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.391362685119669	2		369	394	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027790	152027791	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCAGCATCCTCTTC	novel	NA	P-0048722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	72	587	0	ENST00000262189.6:c.271_284dup	p.Ala96LysfsTer14	p.A96Kfs*14	ENST00000262189	NM_170606.2	95	gaa/gaGAAGAGGATGCTGAa	3/59	0.348319366634679	1	FACETS	0.494	0.432	0.561	0.494	0.432	0.561	SUBCLONAL	1	TRUE	0	0.391362685119669	1		587	599	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0048724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	17	329	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.458	0.342	0.597	0.458	0.342	0.597	SUBCLONAL	1	TRUE	1	0.263088005592328	2		329	282	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528466	29528466	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876660344	NA	P-0048724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	26	396	0	ENST00000356175.3:c.1223A>G	p.Tyr408Cys	p.Y408C	ENST00000356175	NM_000267.3	408	tAt/tGt	11/57	1	2	FACETS	0.445	0.352	0.552	0.445	0.352	0.552	SUBCLONAL	1	TRUE	1	0.263088005592328	2		396	444	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057324	30057330	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	AGGAGGT	AGGAGGT	-	novel	NA	P-0048725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	117	335	0	ENST00000338641.4:c.810_810+6del		p.X270_splice	ENST00000338641	NM_000268.3	270		8/16	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		335	266	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0048726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	131	495	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.602929518096781	2		495	414	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0048727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	173	302	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.427502409871233	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.427502409871233	2		302	360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0048727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	272	606	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.420458082616149	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.427502409871233	2		606	621	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0048727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	200	475	0	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	NA	2	FACETS	0.975	0.913	1			1	INDETERMINATE	2	TRUE	NA	0.427502409871233	2		475	480	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149589	202149589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1045485	NA	P-0048743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	124	347	0	ENST00000358485.4:c.1030G>A	p.Asp344Asn	p.D344N	ENST00000358485	NM_001080125.1	344	Gat/Aat	8/9	0.152201923503873	6	FACETS	1	0.95	1	0.707	0.645	0.772	INDETERMINATE	2	TRUE	3	0.584012568974197	6		347	434	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708102	117708102	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	226	315	0	ENST00000368508.3:c.2075A>G	p.Asn692Ser	p.N692S	ENST00000368508	NM_002944.2	692	aAt/aGt	14/43	0.577666014206054	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.584012568974197	2		315	383	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	84	301	0				ENST00000310581	NM_198253.2	-/1132			0.223567853743937	2	FACETS	0.594	0.529	0.663	0.297	0.264	0.332	INDETERMINATE	1	FALSE	0	0.83608324874872	2		301	338	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913343	NA	P-0048744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	476	463	1	ENST00000269305.4:c.817C>A	p.Arg273Ser	p.R273S	ENST00000269305	NM_001126112.2	273	Cgt/Agt	8/11	NA	2	FACETS	0.988	0.965	1			1	INDETERMINATE	2	FALSE	NA	0.83608324874872	2		464	576	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667555	29667556	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0048744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	463	415	0	ENST00000356175.3:c.6891_6892del	p.Ala2298CysfsTer7	p.A2298Cfs*7	ENST00000356175	NM_000267.3	2297	gtAGct/gtct	46/57	0.355206157883893	3	FACETS	0.979	0.958	0.998	0.979	0.958	0.998	INDETERMINATE	3	FALSE	0	0.83608324874872	3		415	535	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928975	49928975	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048744-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	375	616	0	ENST00000296474.3:c.3391G>T	p.Glu1131Ter	p.E1131*	ENST00000296474	NM_002447.2	1131	Gag/Tag	16/20	0.170834357155884	3	FACETS	0.942	0.903	0.981	0.628	0.602	0.654	INDETERMINATE	2	FALSE	0	0.83608324874872	3		616	675	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	81	454	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.706	0.624	0.794	0.706	0.624	0.794	SUBCLONAL	1	TRUE	1	0.471935450529801	2		454	486	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0048745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	113	354	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.471935450529801	2		354	471	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951964	178951964	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	102	369	0	ENST00000263967.3:c.3019G>C	p.Gly1007Arg	p.G1007R	ENST00000263967	NM_006218.2	1007	Ggc/Cgc	21/21	1	2	FACETS	0.971	0.874	1	0.971	0.874	1	CLONAL	1	TRUE	1	0.471935450529801	2		369	445	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692816	89692817	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554898084	NA	P-0048745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	93	201	1	ENST00000371953.3:c.301dup	p.Ile101AsnfsTer6	p.I101Nfs*6	ENST00000371953	NM_000314.4	100	-/A	5/9	0.471935450529801	2	FACETS	0.825	0.746	0.904	0.825	0.746	0.904	CLONAL	2	TRUE	0	0.471935450529801	2		202	239	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813797	50813797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200451975	NA	P-0048745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	234	631	1	ENST00000398568.2:c.1351G>A	p.Val451Ile	p.V451I	ENST00000398568	NM_001042412.1	451	Gtc/Atc	8/18	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.471935450529801	2		632	915	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107017	27107017	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	45	517	0	ENST00000324856.7:c.6628C>T	p.Gln2210Ter	p.Q2210*	ENST00000324856	NM_006015.4	2210	Cag/Tag	20/20	1	2	FACETS	0.229	0.191	0.271	0.229	0.191	0.271	SUBCLONAL	1	TRUE	1	0.471935450529801	2		517	833	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056313	27056314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0048745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	90	474	0	ENST00000324856.7:c.1312dup	p.Ala438GlyfsTer185	p.A438Gfs*185	ENST00000324856	NM_006015.4	437	cgg/cGgg	2/20	1	2	FACETS	0.524	0.465	0.587	0.524	0.465	0.587	SUBCLONAL	1	TRUE	1	0.471935450529801	2		474	728	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654610	67654610	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0048745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	155	376	0	ENST00000264010.4:c.1097T>G	p.Leu366Ter	p.L366*	ENST00000264010	NM_006565.3	366	tTa/tGa	6/12	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.471935450529801	2		376	572	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537093	41537093	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	85	227	0	ENST00000263253.7:c.1921del	p.Gln641ArgfsTer4	p.Q641Rfs*4	ENST00000263253	NM_001429.3	640	atC/at	10/31	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.471935450529801	2		227	340	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097628	27097635	+	frameshift_variant	Frame_Shift_Ins	INS	TGGCGGGA	TGGCGGGA	AAGGCCGGG	novel	NA	P-0048745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	122	413	0	ENST00000324856.7:c.3217_3224delinsAAGGCCGGG	p.Trp1073LysfsTer32	p.W1073Kfs*32	ENST00000324856	NM_006015.4	1073	TGGCGGGAa/AAGGCCGGGa	12/20	1	2	FACETS	0.757	0.685	0.832	0.757	0.685	0.832	SUBCLONAL	1	TRUE	1	0.471935450529801	2		413	683	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	37	576	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.17	2		576	397	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0048746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	82	604	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.107356595155924	4	FACETS	1	0.949	1	0.574	0.505	0.649	CLONAL	1	TRUE	2	0.17	4		604	983	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0048746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	58	358	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.292137674465493	0	FACETS	1	0.954	1			1	CLONAL	1	TRUE	0	0.17	0		358	445	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696716	47696716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	35	312	0	ENST00000347630.2:c.232G>A	p.Glu78Lys	p.E78K	ENST00000347630	NM_001007230.1	78	Gaa/Aaa	5/11	1	2	FACETS	0.795	0.651	0.957	0.795	0.651	0.957	CLONAL	1	TRUE	1	0.17	2		312	518	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651382	52651382	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	45	398	0	ENST00000394830.3:c.1714G>T	p.Glu572Ter	p.E572*	ENST00000394830	NM_018313.4	572	Gag/Tag	15/30	0.0894018585800103	3	FACETS	0.931	0.781	1			1	INDETERMINATE	1	TRUE	NA	0.17	3		398	617	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419043	419043	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	42	351	0	ENST00000399788.2:c.3304G>A	p.Glu1102Lys	p.E1102K	ENST00000399788	NM_001042603.1	1102	Gaa/Aaa	22/28	0.271477646374373	3	FACETS	0.804	0.67	0.953			1	CLONAL	1	TRUE	NA	0.17	3		351	667	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023376	27023385	+	frameshift_variant	Frame_Shift_Del	DEL	TCGCCGCCGC	TCGCCGCCGC	-	novel	NA	P-0048746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	73	385	0	ENST00000324856.7:c.482_491del	p.Val161AlafsTer68	p.V161Afs*68	ENST00000324856	NM_006015.4	161	gTCGCCGCCGCc/gc	1/20	0.221182613632528	4	FACETS	0.784	0.683	0.894			1	SUBCLONAL	1	TRUE	NA	0.17	4		385	1282	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094437	27094437	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	52	433	0	ENST00000324856.7:c.3145C>G	p.Leu1049Val	p.L1049V	ENST00000324856	NM_006015.4	1049	Ctg/Gtg	11/20	0.221182613632528	4	FACETS	0.84	0.713	0.98			1	CLONAL	1	TRUE	NA	0.17	4		433	852	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43773221	43773221	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0048746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	36	251	0	ENST00000382044.4:c.372-1G>T		p.X124_splice	ENST00000382044	NM_001141980.1	124			1	2	FACETS	1	0.84	1	1	0.84	1	CLONAL	1	TRUE	1	0.17	2		251	414	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225137	2225137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1195	71	754	0	ENST00000326181.6:c.1372G>A	p.Asp458Asn	p.D458N	ENST00000326181	NM_032271.2	458	Gac/Aac	15/21	1	2	FACETS	0.66	0.574	0.754	0.66	0.574	0.754	SUBCLONAL	1	TRUE	1	0.17	2		754	1266	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642839	3642839	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	67	539	0	ENST00000294008.3:c.2188G>C	p.Glu730Gln	p.E730Q	ENST00000294008	NM_032444.2	730	Gag/Cag	11/15	1	2	FACETS	0.678	0.587	0.777	0.678	0.587	0.777	SUBCLONAL	1	TRUE	1	0.17	2		539	1163	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9927991	9927991	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	24	290	0	ENST00000330684.3:c.1748G>C	p.Gly583Ala	p.G583A	ENST00000330684	NM_001134407.1	583	gGa/gCa	8/13	0.258854215553454	0	FACETS	0.766	0.601	0.955			1	CLONAL	1	TRUE	0	0.17	0		290	306	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50830342	50830342	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	56	325	0	ENST00000398568.2:c.2785C>G	p.Gln929Glu	p.Q929E	ENST00000398568	NM_001042412.1	929	Caa/Gaa	18/18	0.107356595155924	4	FACETS	1	0.942	1	0.601	0.514	0.696	CLONAL	1	TRUE	2	0.17	4		325	641	SUCCESS
AR	367	MSKCC	GRCh37	X	66765625	66765625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1480539040	NA	P-0048746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1306	113	825	0	ENST00000374690.3:c.637G>A	p.Glu213Lys	p.E213K	ENST00000374690	NM_000044.3	213	Gag/Aag	1/8	0.3	3	FACETS	1	0.91	1			1	CLONAL	1	TRUE	NA	0.17	3		825	1419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578518	7578518	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934875	NA	P-0048747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	29	742	0	ENST00000269305.4:c.412G>C	p.Ala138Pro	p.A138P	ENST00000269305	NM_001126112.2	138	Gcc/Ccc	5/11	0.182687124818506	1	FACETS	0.225	0.179	0.277	0.225	0.179	0.277	SUBCLONAL	1	TRUE	0	0.246585001827033	1		742	918	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518086	187518086	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	75	428	0	ENST00000441802.2:c.12608G>T	p.Arg4203Leu	p.R4203L	ENST00000441802	NM_005245.3	4203	cGt/cTt	25/27	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.246585001827033	2		428	589	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77091035	77091035	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	34	247	0	ENST00000356341.3:c.195T>G	p.Asn65Lys	p.N65K	ENST00000356341	NM_002576.4	65	aaT/aaG	3/15	1	2	FACETS	0.884	0.724	1	0.884	0.724	1	CLONAL	1	TRUE	1	0.246585001827033	2		247	312	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544697	65544697	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0048747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	97	595	0	ENST00000358664.4:c.229A>T	p.Lys77Ter	p.K77*	ENST00000358664	NM_002382.4	77	Aaa/Taa	4/5	0.246585001827033	1	FACETS	0.962	0.858	1	0.962	0.858	1	CLONAL	1	TRUE	0	0.246585001827033	1		595	717	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667529	29667529	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	145	342	0	ENST00000356175.3:c.6866del	p.Pro2289LeufsTer9	p.P2289Lfs*9	ENST00000356175	NM_000267.3	2289	Cct/ct	46/57	0.201116256535387	3	FACETS	1	0.973	1	0.765	0.701	0.831	CLONAL	2	TRUE	0	0.246585001827033	3		342	576	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0048748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	92	577	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.391593728952947	3	FACETS	1	0.975	1	0.647	0.58	0.716	CLONAL	1	TRUE	1	0.562653578438599	3		577	324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0048748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	146	523	2	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.41893144914242	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.562653578438599	1		525	357	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335485	73335505	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATGAGAAATACCGTACCTCAT	ATGAGAAATACCGTACCTCAT	-	novel	NA	P-0048748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	19	166	0	ENST00000377767.4:c.2666_2670+16del		p.X889_splice	ENST00000377767	NM_014953.3	889		19/21	1	2	FACETS	0.814	0.632	1	0.814	0.632	1	CLONAL	1	TRUE	1	0.562653578438599	2		166	83	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0048750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	122	619	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.204735472220663	2	FACETS	1	0.983	1	0.709	0.642	0.779	CLONAL	1	TRUE	0	0.259698423843559	2		619	663	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397800	49397800	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	46	363	0	ENST00000418115.1:c.424G>A	p.Glu142Lys	p.E142K	ENST00000418115	NM_001664.2	142	Gaa/Aaa	5/5	NA	3	FACETS	0.824	0.694	0.967	0.412	0.347	0.484	INDETERMINATE	1	TRUE	1	0.259698423843559	3		363	486	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999713	100999713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	50	810	1	ENST00000325455.5:c.89G>A	p.Arg30His	p.R30H	ENST00000325455	NM_001202474.3	30	cGc/cAc	1/8	0.192591670323255	3	FACETS	0.657	0.557	0.768	0.329	0.278	0.384	SUBCLONAL	1	TRUE	1	0.259698423843559	3		811	662	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846036	68846036	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0048750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	140	439	0	ENST00000261769.5:c.1009-2A>C		p.X337_splice	ENST00000261769	NM_004360.3	337			0.246003638857406	2	FACETS	0.92	0.841	1	0.92	0.841	1	CLONAL	2	TRUE	0	0.259698423843559	2		439	586	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90645558	90645558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770871840	NA	P-0048750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	21	190	0	ENST00000330062.3:c.65C>T	p.Ala22Val	p.A22V	ENST00000330062	NM_002168.2	22	gCg/gTg	1/11	1	2	FACETS	0.534	0.411	0.677	0.534	0.411	0.677	SUBCLONAL	1	TRUE	1	0.259698423843559	2		190	303	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100144	27100145	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGACTCGGG	novel	NA	P-0048750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	68	639	0	ENST00000324856.7:c.3941_3950dup	p.Met1318ArgfsTer8	p.M1318Rfs*8	ENST00000324856	NM_006015.4	1314	cca/cCAGACTCGGGca	16/20	0.192591670323255	3	FACETS	0.907	0.789	1	0.454	0.394	0.518	CLONAL	1	TRUE	1	0.259698423843559	3		639	652	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243215	123243216	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTGGTTGTGAGAGTGAGAATTCGATCCAAGTCTTCTACCAACTGCTTGAACG	novel	NA	P-0048750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13202	4201	569	1	ENST00000358487.5:c.2246_2297dup	p.Glu767ValfsTer18	p.E767Vfs*18	ENST00000358487	NM_000141.4	766	aat/aaCGTTCAAGCAGTTGGTAGAAGACTTGGATCGAATTCTCACTCTCACAACCAAt	17/18	0.259698423843559	111	FACETS	1	0.989	1			1	CLONAL	28	TRUE	NA	0.259698423843559	111		570	17403	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917032	50917032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs769650989	NA	P-0048750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	103	684	1	ENST00000440232.2:c.2284C>T	p.Arg762Ter	p.R762*	ENST00000440232	NM_002691.3	762	Cga/Tga	19/27	NA	3	FACETS	1	0.973	1	0.637	0.571	0.708	INDETERMINATE	1	TRUE	1	0.259698423843559	3		685	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0048751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	248	696	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.454769841954908	1	FACETS	0.868	0.813	0.924	0.868	0.813	0.924	CLONAL	1	TRUE	0	0.483965906936377	1		697	895	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0048751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	56	470	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.126655129271261	0	FACETS	0.476	0.412	0.544			1	INDETERMINATE	1	TRUE	0	0.483965906936377	0		470	251	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0048751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	53	515	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.483965906936377	1	FACETS	0.191	0.162	0.223	0.191	0.162	0.223	SUBCLONAL	1	TRUE	0	0.483965906936377	1		515	867	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0048751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	20	204	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	0.457768263240922	1	FACETS	0.493	0.382	0.621	0.493	0.382	0.621	SUBCLONAL	1	TRUE	0	0.483965906936377	1		204	127	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659287	86659290	+	frameshift_variant	Frame_Shift_Del	DEL	TCTG	TCTG	-	novel	NA	P-0048751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	20	193	0	ENST00000274376.6:c.1579_1582del	p.Val527MetfsTer16	p.V527Mfs*16	ENST00000274376	NM_002890.2	526	TCTGtc/tc	11/25	0.457768263240922	1	FACETS	0.87	0.685	1	0.87	0.685	1	CLONAL	1	TRUE	0	0.483965906936377	1		193	72	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344053	118344055	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1555036383	NA	P-0048751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	40	275	0	ENST00000534358.1:c.2184_2186del	p.Ser729del	p.S729del	ENST00000534358	NM_005933.3	727	TCT/-	3/36	0.126655129271261	0	FACETS	0.377	0.316	0.444			1	INDETERMINATE	1	TRUE	0	0.483965906936377	0		275	226	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344789	118344789	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs782663858	NA	P-0048751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	64	270	0	ENST00000534358.1:c.2915C>A	p.Thr972Asn	p.T972N	ENST00000534358	NM_005933.3	972	aCc/aAc	3/36	0.126655129271261	0	FACETS	0.424	0.369	0.482			1	INDETERMINATE	1	TRUE	0	0.483965906936377	0		270	322	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0048752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	24	504	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.439	0.342	0.551	0.439	0.342	0.551	SUBCLONAL	1	TRUE	1	0.15	2		504	729	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063317	67063317	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	40	287	0	ENST00000412916.2:c.7C>T	p.Arg3Cys	p.R3C	ENST00000412916		3	Cgc/Tgc	1/6	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.15	2		287	467	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847393	68847407	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCAAAGGTTTGTATG	GCAAAGGTTTGTATG	-	novel	NA	P-0048752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	42	429	0	ENST00000261769.5:c.1316_1320+10del		p.X439_splice	ENST00000261769	NM_004360.3	439		9/16	1	2	FACETS	0.979	0.816	1	0.979	0.816	1	CLONAL	1	TRUE	1	0.15	2		429	572	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426345	49426345	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs527255553	NA	P-0048753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	94	792	0	ENST00000301067.7:c.12143C>T	p.Pro4048Leu	p.P4048L	ENST00000301067	NM_003482.3	4048	cCg/cTg	39/54	0.300517362927119	4	FACETS	1	0.979	1	0.695	0.623	0.77	INDETERMINATE	1	TRUE	2	0.59131506900302	4		792	364	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247007	53247007	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	44	355	0	ENST00000375401.3:c.493G>T	p.Glu165Ter	p.E165*	ENST00000375401	NM_004187.3	165	Gaa/Taa	4/26	0.59131506900302	2	FACETS	1	0.91	1	0.543	0.465	0.625	CLONAL	1	TRUE	0	0.59131506900302	2		355	137	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864437	57864437	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	65	685	1	ENST00000228682.2:c.1914G>T	p.Arg638Ser	p.R638S	ENST00000228682	NM_005269.2	638	agG/agT	12/12	0.300517362927119	4	FACETS	1	0.971	1	0.703	0.616	0.793	INDETERMINATE	1	TRUE	2	0.59131506900302	4		686	249	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117204	115117384	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGACTCTCGTCTCCACTCTCTTGTAACTTTCTCATCCTGACTTAAAGCAGCTTTTAAGGGGAAGGCAAAATATCACCATTAAAAAGGAAAGCCCCTTGAGTTTACCTTATCATTCTGGTATGCAGTCACAGCGATGAATTCAGTTTCGGGGAACAAGTATGTCCGAAATGTACTATAAGG	AAGACTCTCGTCTCCACTCTCTTGTAACTTTCTCATCCTGACTTAAAGCAGCTTTTAAGGGGAAGGCAAAATATCACCATTAAAAAGGAAAGCCCCTTGAGTTTACCTTATCATTCTGGTATGCAGTCACAGCGATGAATTCAGTTTCGGGGAACAAGTATGTCCGAAATGTACTATAAGG	-	novel	NA	P-0048753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	42	50	0	ENST00000257566.3:c.790_864+106del		p.X264_splice	ENST00000257566	NM_016569.3	264		4/8	0.300517362927119	4	FACETS	1	0.948	1	1	0.98	1	INDETERMINATE	4	TRUE	2	0.59131506900302	4		50	53	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634374	23634374	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	48	450	0	ENST00000261584.4:c.2912G>A	p.Gly971Asp	p.G971D	ENST00000261584	NM_024675.3	971	gGc/gAc	9/13	0.313852929990361	3	FACETS	1	0.941	1	0.598	0.513	0.687	INDETERMINATE	1	TRUE	1	0.59131506900302	3		450	176	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661882	29661889	+	frameshift_variant	Frame_Shift_Del	DEL	GAATACAT	GAATACAT	-	novel	NA	P-0048753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	32	281	0	ENST00000356175.3:c.5778_5785del	p.Glu1926AspfsTer14	p.E1926Dfs*14	ENST00000356175	NM_000267.3	1926	GAATACATg/g	39/57	0.275422695280591	3	FACETS	1	0.877	1	0.539	0.446	0.641	INDETERMINATE	1	TRUE	1	0.59131506900302	3		281	130	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733215	74733215	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	208	709	1	ENST00000359995.5:c.28G>T	p.Val10Leu	p.V10L	ENST00000359995	NM_001195427.1	10	Gtg/Ttg	1/3	0.59131506900302	4	FACETS	0.814	0.758	0.87	0.542	0.505	0.58	CLONAL	2	TRUE	1	0.59131506900302	4		710	688	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180050991	180050991	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	67	781	0	ENST00000261937.6:c.1492G>T	p.Val498Leu	p.V498L	ENST00000261937	NM_182925.4	498	Gtg/Ttg	11/30	0.449298283827657	1	FACETS	0.576	0.506	0.651	0.576	0.506	0.651	SUBCLONAL	1	TRUE	0	0.59131506900302	1		781	277	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032174	26032174	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	107	469	1	ENST00000244661.2:c.115C>A	p.Pro39Thr	p.P39T	ENST00000244661	NM_003537.3	39	Cct/Act	1/1	0.59131506900302	7	FACETS	0.859	0.774	0.949			1	CLONAL	2	TRUE	NA	0.59131506900302	7		470	522	SUCCESS
MET	4233	MSKCC	GRCh37	7	116422084	116422084	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	34	338	0	ENST00000397752.3:c.3565G>C	p.Ala1189Pro	p.A1189P	ENST00000397752	NM_000245.2	1189	Gcc/Ccc	18/21	1	2	FACETS	0.827	0.688	0.978	0.827	0.688	0.978	CLONAL	1	TRUE	1	0.59131506900302	2		338	139	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874838	151874853	+	frameshift_variant	Frame_Shift_Del	DEL	TCAGGAGCCCTATGTC	TCAGGAGCCCTATGTC	-	novel	NA	P-0048753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	12	283	0	ENST00000262189.6:c.7685_7700del	p.Arg2562ThrfsTer16	p.R2562Tfs*16	ENST00000262189	NM_170606.2	2562	aGACATAGGGCTCCTGAc/ac	38/59	1	2	FACETS	0.31	0.219	0.42	0.31	0.219	0.42	SUBCLONAL	1	TRUE	1	0.59131506900302	2		283	131	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0048755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	717	565	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	0.707726821377034	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.707726821377034	2		565	948	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913286	NA	P-0048755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	147	412	0	ENST00000263967.3:c.1636C>G	p.Gln546Glu	p.Q546E	ENST00000263967	NM_006218.2	546	Cag/Gag	10/21	1	2	FACETS	0.858	0.789	0.929	0.858	0.789	0.929	CLONAL	1	TRUE	1	0.707726821377034	2		412	484	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467428	25467428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763336898	NA	P-0048755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1387	256	499	1	ENST00000264709.3:c.1648G>A	p.Gly550Arg	p.G550R	ENST00000264709	NM_175629.2	550	Gga/Aga	14/23	0.651870439005075	4	FACETS	0.752	0.702	0.804	0.376	0.351	0.402	SUBCLONAL	1	TRUE	2	0.707726821377034	4		500	1643	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725590	117725590	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	158	293	1	ENST00000368508.3:c.291A>T	p.Glu97Asp	p.E97D	ENST00000368508	NM_002944.2	97	gaA/gaT	5/43	0.707726821377034	2	FACETS	0.898	0.829	0.969	0.449	0.414	0.485	CLONAL	1	TRUE	0	0.707726821377034	2		294	497	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349955	15349955	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	241	562	0	ENST00000263377.2:c.3697G>A	p.Glu1233Lys	p.E1233K	ENST00000263377	NM_058243.2	1233	Gag/Aag	18/20	1	2	FACETS	0.863	0.809	0.919	1	0.995	1	CLONAL	3	TRUE	1	0.240396205580658	2		562	774	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	78	689	1	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.16	2		690	947	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	50	438	2	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.947	0.802	1	0.947	0.802	1	CLONAL	1	TRUE	1	0.16	2		440	660	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	71	745	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.92	0.801	1	0.92	0.801	1	CLONAL	1	TRUE	1	0.16	2		750	965	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703631	47703631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750636	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	41	427	0	ENST00000233146.2:c.2131C>T	p.Arg711Ter	p.R711*	ENST00000233146	NM_000251.2	711	Cga/Tga	13/16	1	2	FACETS	0.805	0.669	0.956	0.805	0.669	0.956	CLONAL	1	TRUE	1	0.16	2		427	637	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796980	78796980	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	69	506	0	ENST00000306801.3:c.1093G>A	p.Val365Ile	p.V365I	ENST00000306801	NM_020761.2	365	Gtc/Atc	9/34	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.16	2		506	750	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	40	396	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.975	0.809	1	0.975	0.809	1	CLONAL	1	TRUE	1	0.16	2		396	513	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	8	202	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	1	2	FACETS	0.427	0.274	0.626	0.427	0.274	0.626	SUBCLONAL	1	TRUE	1	0.16	2		202	234	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652158	36652158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1236971182	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	90	767	0	ENST00000244741.5:c.280C>T	p.Arg94Trp	p.R94W	ENST00000244741	NM_000389.4	94	Cgg/Tgg	2/3	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.16	2		767	1123	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721157	176721157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373571733	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	60	410	0	ENST00000439151.2:c.6788C>T	p.Ser2263Leu	p.S2263L	ENST00000439151	NM_022455.4	2263	tCg/tTg	23/23	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.16	2		410	583	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497950	25497950	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	65	627	0	ENST00000264709.3:c.499C>T	p.Arg167Trp	p.R167W	ENST00000264709	NM_175629.2	167	Cgg/Tgg	6/23	1	2	FACETS	0.981	0.849	1	0.981	0.849	1	CLONAL	1	TRUE	1	0.16	2		627	828	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	65	634	3	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.915	0.791	1	0.915	0.791	1	CLONAL	1	TRUE	1	0.16	2		637	888	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	27	435	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.509	0.403	0.631	0.509	0.403	0.631	SUBCLONAL	1	TRUE	1	0.16	2		436	663	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205807	108205807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782719	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	22	322	0	ENST00000278616.4:c.8122G>A	p.Asp2708Asn	p.D2708N	ENST00000278616	NM_000051.3	2708	Gat/Aat	55/63	1	2	FACETS	0.653	0.505	0.826	0.653	0.505	0.826	SUBCLONAL	1	TRUE	1	0.16	2		322	421	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264357	30264357	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	28	282	1	ENST00000322652.5:c.92T>C	p.Val31Ala	p.V31A	ENST00000322652	NM_015355.2	31	gTg/gCg	1/16	1	2	FACETS	0.803	0.641	0.988	0.803	0.641	0.988	CLONAL	1	TRUE	1	0.16	2		283	436	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006224	22006224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	80	798	1	ENST00000276925.6:c.179G>A	p.Arg60His	p.R60H	ENST00000276925	NM_004936.3	60	cGc/cAc	2/2	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.16	2		799	975	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046263	128046263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1308398082	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	42	391	1	ENST00000285398.2:c.1000C>T	p.Arg334Cys	p.R334C	ENST00000285398	NM_000122.1	334	Cgt/Tgt	7/15	1	2	FACETS	0.778	0.648	0.923	0.778	0.648	0.923	CLONAL	1	TRUE	1	0.16	2		392	675	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371649	89371649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750217123	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	85	713	0	ENST00000301030.4:c.191C>T	p.Ala64Val	p.A64V	ENST00000301030	NM_001256183.1	64	gCg/gTg	4/13	1	2	FACETS	0.988	0.871	1	0.988	0.871	1	CLONAL	1	TRUE	1	0.16	2		713	1075	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248450	212248450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1480034665	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	39	328	0	ENST00000342788.4:c.3817C>T	p.Arg1273Trp	p.R1273W	ENST00000342788	NM_005235.2	1273	Cgg/Tgg	28/28	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.16	2		328	458	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434142	49434142	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057518571	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	85	600	1	ENST00000301067.7:c.7411C>T	p.Arg2471Ter	p.R2471*	ENST00000301067	NM_003482.3	2471	Cga/Tga	31/54	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.16	2		601	1017	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736388	85736388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs949558985	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	24	314	0	ENST00000370580.1:c.259C>T	p.Arg87Trp	p.R87W	ENST00000370580	NM_003921.4	87	Cgg/Tgg	2/3	1	2	FACETS	0.644	0.504	0.806	0.644	0.504	0.806	SUBCLONAL	1	TRUE	1	0.16	2		314	466	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435153	56435153	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768648593	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	62	734	2	ENST00000407977.2:c.1984G>A	p.Glu662Lys	p.E662K	ENST00000407977		662	Gag/Aag	9/10	1	2	FACETS	0.802	0.691	0.924	0.802	0.691	0.924	CLONAL	1	TRUE	1	0.16	2		736	966	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786013	135786013	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs118203504	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	71	657	0	ENST00000298552.3:c.1208C>T	p.Ser403Leu	p.S403L	ENST00000298552	NM_001162426.1	403	tCg/tTg	12/23	1	2	FACETS	0.905	0.787	1	0.905	0.787	1	CLONAL	1	TRUE	1	0.16	2		657	981	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681713	78681713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1299432885	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	61	539	0	ENST00000306801.3:c.421G>A	p.Ala141Thr	p.A141T	ENST00000306801	NM_020761.2	141	Gcc/Acc	4/34	1	2	FACETS	0.941	0.81	1	0.941	0.81	1	CLONAL	1	TRUE	1	0.16	2		539	810	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528505	157528505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	48	538	0	ENST00000346085.5:c.6230C>T	p.Ser2077Leu	p.S2077L	ENST00000346085	NM_020732.3	2077	tCg/tTg	20/20	1	2	FACETS	0.792	0.667	0.929	0.792	0.667	0.929	CLONAL	1	TRUE	1	0.16	2		538	758	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856048	151856048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs577099359	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	39	389	0	ENST00000262189.6:c.11570C>T	p.Thr3857Met	p.T3857M	ENST00000262189	NM_170606.2	3857	aCg/aTg	44/59	1	2	FACETS	0.759	0.628	0.907	0.759	0.628	0.907	CLONAL	1	TRUE	1	0.16	2		389	642	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533547	63533547	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750084404	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	87	839	0	ENST00000307078.5:c.1607C>T	p.Thr536Met	p.T536M	ENST00000307078	NM_004655.3	536	aCg/aTg	6/11	1	2	FACETS	0.957	0.845	1	0.957	0.845	1	CLONAL	1	TRUE	1	0.16	2		839	1136	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612836	228612836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	74	813	0	ENST00000366696.1:c.191G>A	p.Arg64His	p.R64H	ENST00000366696	NM_003493.2	64	cGc/cAc	1/1	1	2	FACETS	0.832	0.726	0.947	0.832	0.726	0.947	CLONAL	1	TRUE	1	0.16	2		813	1112	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935762	15935762	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	37	376	2	ENST00000268712.3:c.7171C>T	p.Arg2391Trp	p.R2391W	ENST00000268712	NM_006311.3	2391	Cgg/Tgg	46/46	1	2	FACETS	0.802	0.66	0.961	0.802	0.66	0.961	CLONAL	1	TRUE	1	0.16	2		378	577	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950316	17950316	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	63	774	1	ENST00000458235.1:c.1411C>T	p.Leu471Phe	p.L471F	ENST00000458235	NM_000215.3	471	Ctc/Ttc	10/24	1	2	FACETS	0.702	0.605	0.809	0.702	0.605	0.809	SUBCLONAL	1	TRUE	1	0.16	2		775	1121	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976216	18976216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	60	957	1	ENST00000262803.5:c.2976G>A	p.Met992Ile	p.M992I	ENST00000262803	NM_002911.3	992	atG/atA	21/24	1	2	FACETS	0.642	0.55	0.742	0.642	0.55	0.742	SUBCLONAL	1	TRUE	1	0.16	2		958	1169	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032074	48032074	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	38	274	0	ENST00000234420.5:c.3464A>C	p.Gln1155Pro	p.Q1155P	ENST00000234420	NM_000179.2	1155	cAg/cCg	6/10	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.16	2		274	439	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902875	1902875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373161300	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	42	454	0	ENST00000382891.5:c.494C>T	p.Ala165Val	p.A165V	ENST00000382891	NM_133335.3	165	gCg/gTg	2/22	1	2	FACETS	0.746	0.621	0.885	0.746	0.621	0.885	SUBCLONAL	1	TRUE	1	0.16	2		454	704	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540190	187540190	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199785192	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	39	394	0	ENST00000441802.2:c.7550C>T	p.Thr2517Met	p.T2517M	ENST00000441802	NM_005245.3	2517	aCg/aTg	10/27	1	2	FACETS	0.811	0.671	0.968	0.811	0.671	0.968	CLONAL	1	TRUE	1	0.16	2		394	601	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31485055	31485055	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	14	254	0	ENST00000344624.3:c.1929A>C	p.Lys643Asn	p.K643N	ENST00000344624		643	aaA/aaC	12/33	1	2	FACETS	0.658	0.475	0.879	0.658	0.475	0.879	SUBCLONAL	1	TRUE	1	0.16	2		254	266	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176678803	176678803	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	57	393	0	ENST00000439151.2:c.4714G>T	p.Gly1572Ter	p.G1572*	ENST00000439151	NM_022455.4	1572	Gga/Tga	12/23	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.16	2		393	672	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0048758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	45	369	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.76	0.639	0.894	0.76	0.639	0.894	SUBCLONAL	1	TRUE	1	0.240193094833315	2		370	493	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519893	NA	P-0048758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	88	673	0	ENST00000267101.3:c.310G>T	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ttg	3/28	0.232648542803831	1	FACETS	0.888	0.787	0.997	0.888	0.787	0.997	CLONAL	1	TRUE	0	0.240193094833315	1		673	726	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575209	48575209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767326	NA	P-0048758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	35	213	0	ENST00000342988.3:c.403C>T	p.Arg135Ter	p.R135*	ENST00000342988	NM_005359.5	135	Cga/Tga	3/12	0.230359246897181	1	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	0	0.240193094833315	1		213	237	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0048758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	52	452	0	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	1	2	FACETS	0.805	0.685	0.936	0.805	0.685	0.936	CLONAL	1	TRUE	1	0.240193094833315	2		452	538	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352670	118352670	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	58	479	0	ENST00000534358.1:c.3876del	p.Lys1293SerfsTer63	p.K1293Sfs*63	ENST00000534358	NM_005933.3	1292	aGg/ag	7/36	1	2	FACETS	0.898	0.772	1	0.898	0.772	1	CLONAL	1	TRUE	1	0.240193094833315	2		479	538	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100569	157100569	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1295091154	NA	P-0048758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	43	434	1	ENST00000346085.5:c.1509del	p.Gly504AlafsTer19	p.G504Afs*19	ENST00000346085	NM_020732.3	502	agC/ag	1/20	1	2	FACETS	0.647	0.541	0.765	0.647	0.541	0.765	SUBCLONAL	1	TRUE	1	0.240193094833315	2		435	553	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	38	302	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.739	0.61	0.884	0.739	0.61	0.884	SUBCLONAL	1	TRUE	1	0.18	2		302	571	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	59	227	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.794	0.685	0.911	1	0.972	1	CLONAL	2	TRUE	1	0.18	2		228	413	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	40	445	0	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	1	2	FACETS	0.645	0.535	0.769	0.645	0.535	0.769	SUBCLONAL	1	TRUE	1	0.18	2		445	689	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	53	619	3	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.692	0.588	0.806	0.692	0.588	0.806	SUBCLONAL	1	TRUE	1	0.18	2		622	851	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150520	157150520	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765362265	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	40	330	0	ENST00000346085.5:c.1702G>A	p.Gly568Arg	p.G568R	ENST00000346085	NM_020732.3	568	Ggg/Agg	2/20	1	2	FACETS	0.788	0.654	0.938	0.788	0.654	0.938	CLONAL	1	TRUE	1	0.18	2		330	564	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971138	21971138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760640852	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	38	473	2	ENST00000304494.5:c.220G>A	p.Asp74Asn	p.D74N	ENST00000304494	NM_000077.4	74	Gac/Aac	2/3	1	2	FACETS	0.617	0.509	0.739	0.617	0.509	0.739	SUBCLONAL	1	TRUE	1	0.18	2		475	684	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268383	198268383	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1172363633	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	44	258	0	ENST00000335508.6:c.1645C>T	p.Arg549Cys	p.R549C	ENST00000335508	NM_012433.2	549	Cgt/Tgt	12/25	1	2	FACETS	0.951	0.797	1	0.951	0.797	1	CLONAL	1	TRUE	1	0.18	2		258	514	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165644	118165644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs538766512	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	26	290	0	ENST00000369448.3:c.154G>A	p.Val52Ile	p.V52I	ENST00000369448	NM_017709.3	52	Gtc/Atc	2/2	1	2	FACETS	0.649	0.513	0.805	0.649	0.513	0.805	SUBCLONAL	1	TRUE	1	0.18	2		290	445	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003746	45003746	+	start_lost	Translation_Start_Site	SNP	T	T	A	novel	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	63	347	0	ENST00000558401.1:c.2T>A	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	aTg/aAg	1/4	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.18	2		347	537	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100727	8100728	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs771019738	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	49	593	0	ENST00000346208.3:c.708dup	p.Ser237GlnfsTer66	p.S237Qfs*66	ENST00000346208		234	ttc/ttCc	3/6	1	2	FACETS	0.724	0.612	0.848	0.724	0.612	0.848	SUBCLONAL	1	TRUE	1	0.18	2		593	752	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278055	18278055	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781265051	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	46	515	0	ENST00000222254.8:c.1675C>T	p.Arg559Cys	p.R559C	ENST00000222254	NM_005027.3	559	Cgc/Tgc	13/16	1	2	FACETS	0.58	0.487	0.684	0.58	0.487	0.684	SUBCLONAL	1	TRUE	1	0.18	2		515	881	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271606	26271606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763475502	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	21	264	0	ENST00000305910.3:c.7C>T	p.Arg3Cys	p.R3C	ENST00000305910	NM_003534.2	3	Cgc/Tgc	1/1	1	2	FACETS	0.621	0.477	0.788	0.621	0.477	0.788	SUBCLONAL	1	TRUE	1	0.18	2		264	376	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829075	128829075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1247591045	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	16	48	0	ENST00000249373.3:c.88del	p.Ala30ArgfsTer25	p.A30Rfs*25	ENST00000249373	NM_005631.4	28	cGg/cg	1/12	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.18	2		48	126	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670340	134670340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415689583	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	26	279	0	ENST00000398015.3:c.251G>A	p.Arg84His	p.R84H	ENST00000398015	NM_004441.4	84	cGc/cAc	3/16	1	2	FACETS	0.664	0.525	0.824	0.664	0.525	0.824	SUBCLONAL	1	TRUE	1	0.18	2		279	435	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534428	63534428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761901627	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	61	538	0	ENST00000307078.5:c.1093G>A	p.Val365Met	p.V365M	ENST00000307078	NM_004655.3	365	Gtg/Atg	5/11	1	2	FACETS	0.884	0.761	1	0.884	0.761	1	CLONAL	1	TRUE	1	0.18	2		538	767	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155650	56155650	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	23	238	0	ENST00000399503.3:c.742C>T	p.Arg248Ter	p.R248*	ENST00000399503	NM_005921.1	248	Cga/Tga	3/20	1	2	FACETS	0.59	0.459	0.742	0.59	0.459	0.742	SUBCLONAL	1	TRUE	1	0.18	2		238	433	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332454	153332454	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	27	189	0	ENST00000281708.4:c.501+1G>A		p.X167_splice	ENST00000281708	NM_033632.3	167			1	2	FACETS	0.882	0.703	1	0.882	0.703	1	CLONAL	1	TRUE	1	0.18	2		189	340	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867626	78867626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781190662	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	69	527	1	ENST00000306801.3:c.2362C>T	p.Arg788Cys	p.R788C	ENST00000306801	NM_020761.2	788	Cgc/Tgc	20/34	1	2	FACETS	0.85	0.738	0.971	0.85	0.738	0.971	CLONAL	1	TRUE	1	0.18	2		528	902	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934810	49934810	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573668188	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	54	540	0	ENST00000296474.3:c.2086C>T	p.Arg696Trp	p.R696W	ENST00000296474	NM_002447.2	696	Cgg/Tgg	7/20	1	2	FACETS	0.733	0.624	0.852	0.733	0.624	0.852	SUBCLONAL	1	TRUE	1	0.18	2		540	819	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370254	40370254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750053820	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	47	526	2	ENST00000293328.3:c.1084G>A	p.Val362Met	p.V362M	ENST00000293328	NM_012448.3	362	Gtg/Atg	9/19	1	2	FACETS	0.659	0.554	0.774	0.659	0.554	0.774	SUBCLONAL	1	TRUE	1	0.18	2		528	793	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149570	202149570	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	35	264	0	ENST00000358485.4:c.1014del	p.Phe338LeufsTer11	p.F338Lfs*11	ENST00000358485	NM_001080125.1	337	caT/ca	8/9	1	2	FACETS	0.755	0.618	0.909	0.755	0.618	0.909	CLONAL	1	TRUE	1	0.18	2		264	515	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444932	49444932	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201392255	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	56	449	0	ENST00000301067.7:c.2534G>A	p.Arg845Gln	p.R845Q	ENST00000301067	NM_003482.3	845	cGg/cAg	10/54	1	2	FACETS	0.983	0.841	1	0.983	0.841	1	CLONAL	1	TRUE	1	0.18	2		449	633	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684371	29684372	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	43	303	0	ENST00000356175.3:c.7892_7893del	p.Lys2631SerfsTer7	p.K2631Sfs*7	ENST00000356175	NM_000267.3	2631	AAa/a	53/57	1	2	FACETS	0.893	0.747	1	0.893	0.747	1	CLONAL	1	TRUE	1	0.18	2		303	535	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981163	201981165	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	156	597	0	ENST00000359651.3:c.246_248del	p.Lys82del	p.K82del	ENST00000359651		81	gAGAag/gag	2/8	1	2	FACETS	0.851	0.779	0.927	1	0.99	1	CLONAL	2	TRUE	1	0.18	2		597	1018	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830777	72830777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752574946	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	31	375	0	ENST00000268489.5:c.5804G>A	p.Arg1935His	p.R1935H	ENST00000268489	NM_006885.3	1935	cGc/cAc	9/10	1	2	FACETS	0.639	0.516	0.779	0.639	0.516	0.779	SUBCLONAL	1	TRUE	1	0.18	2		375	539	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180820	106180820	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	26	198	1	ENST00000380013.4:c.3848C>T	p.Ala1283Val	p.A1283V	ENST00000380013	NM_001127208.2	1283	gCc/gTc	7/11	1	2	FACETS	0.731	0.579	0.906	0.731	0.579	0.906	CLONAL	1	TRUE	1	0.18	2		199	395	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336379	80336379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	23	245	0	ENST00000286548.4:c.940G>A	p.Val314Met	p.V314M	ENST00000286548	NM_002072.3	314	Gtg/Atg	7/7	1	2	FACETS	0.587	0.457	0.739	0.587	0.457	0.739	SUBCLONAL	1	TRUE	1	0.18	2		245	435	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961183	41961183	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774786155	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	46	232	0	ENST00000219905.7:c.91C>T	p.Pro31Ser	p.P31S	ENST00000219905	NM_001164273.1	31	Cca/Tca	2/24	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.18	2		232	427	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585497	29585497	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	15	165	0	ENST00000356175.3:c.4246A>G	p.Arg1416Gly	p.R1416G	ENST00000356175	NM_000267.3	1416	Agg/Ggg	31/57	1	2	FACETS	0.6	0.438	0.794	0.6	0.438	0.794	SUBCLONAL	1	TRUE	1	0.18	2		165	278	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684335	29684336	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	33	332	0	ENST00000356175.3:c.7856_7857del	p.Tyr2619Ter	p.Y2619*	ENST00000356175	NM_000267.3	2619	TAt/t	53/57	1	2	FACETS	0.593	0.482	0.72	0.593	0.482	0.72	SUBCLONAL	1	TRUE	1	0.18	2		332	618	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50143319	50143320	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	10	99	0	ENST00000246792.3:c.36dup	p.Arg13AlafsTer45	p.R13Afs*45	ENST00000246792	NM_006270.3	12	-/G	1/6	1	2	FACETS	0.694	0.471	0.974	0.694	0.471	0.974	SUBCLONAL	1	TRUE	1	0.18	2		99	160	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027003	71027006	+	frameshift_variant	Frame_Shift_Del	DEL	TGTC	TGTC	-	novel	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	47	332	0	ENST00000318789.4:c.1321_1324del	p.Asp441AsnfsTer32	p.D441Nfs*32	ENST00000318789	NM_032682.5	441	GACAaa/aa	15/21	1	2	FACETS	0.828	0.697	0.972	0.828	0.697	0.972	CLONAL	1	TRUE	1	0.18	2		332	631	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873087	134873087	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	43	431	0	ENST00000398015.3:c.1391T>C	p.Ile464Thr	p.I464T	ENST00000398015	NM_004441.4	464	aTc/aCc	6/16	1	2	FACETS	0.665	0.555	0.787	0.665	0.555	0.787	SUBCLONAL	1	TRUE	1	0.18	2		431	719	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729350	41729350	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	45	376	0	ENST00000242208.4:c.1179del	p.Thr394ProfsTer3	p.T394Pfs*3	ENST00000242208	NM_002192.2	393	ccC/cc	3/3	1	2	FACETS	0.747	0.627	0.881	0.747	0.627	0.881	SUBCLONAL	1	TRUE	1	0.18	2		376	669	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041215	47041216	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	66	607	0	ENST00000377604.3:c.1646_1647del	p.Leu549ProfsTer27	p.L549Pfs*27	ENST00000377604	NM_001204468.1	548	gCT/g	15/24	1	2	FACETS	0.954	0.827	1	0.954	0.827	1	CLONAL	1	TRUE	1	0.18	2		607	769	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227709	53227709	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	52	468	0	ENST00000375401.3:c.2479T>A	p.Ser827Thr	p.S827T	ENST00000375401	NM_004187.3	827	Tcc/Acc	17/26	1	2	FACETS	0.737	0.626	0.859	0.737	0.626	0.859	SUBCLONAL	1	TRUE	1	0.18	2		468	784	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578491	7578491	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1567553924	NA	P-0048762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	478	759	1	ENST00000269305.4:c.439del	p.Val147LeufsTer23	p.V147Lfs*23	ENST00000269305	NM_001126112.2	147	Gtt/tt	5/11	0.487855949157785	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.487855949157785	2		760	915	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098800	178098800	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	291	490	0	ENST00000397062.3:c.245A>C	p.Glu82Ala	p.E82A	ENST00000397062	NM_006164.4	82	gAa/gCa	2/5	0.16811809143202	6	FACETS	0.886	0.836	0.937	0.886	0.836	0.937	INDETERMINATE	3	TRUE	3	0.487855949157785	6		490	887	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464890	120464890	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	214	428	0	ENST00000256646.2:c.5182G>T	p.Glu1728Ter	p.E1728*	ENST00000256646	NM_024408.3	1728	Gag/Tag	28/34	0.487855949157785	3	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	1	0.487855949157785	3		428	545	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060887	38060887	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	298	562	0	ENST00000250448.2:c.1102G>T	p.Ala368Ser	p.A368S	ENST00000250448	NM_004496.3	368	Gcc/Tcc	2/2	0.487855949157785	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.487855949157785	2		562	551	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145665	11145666	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0048762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	410	669	0	ENST00000358026.2:c.4028_4029del	p.Leu1343ProfsTer17	p.L1343Pfs*17	ENST00000358026	NM_001128849.1	1343	CTc/c	29/36	0.487855949157785	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.487855949157785	2		669	770	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867247	45867247	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757790912	NA	P-0048762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	388	835	0	ENST00000391945.4:c.946C>T	p.Gln316Ter	p.Q316*	ENST00000391945	NM_000400.3	316	Cag/Tag	10/23	0.487855949157785	3	FACETS	0.999	0.953	1	0.999	0.953	1	CLONAL	2	TRUE	1	0.487855949157785	3		835	990	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443595	29443595	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	174	635	2	ENST00000389048.3:c.3622C>A	p.Leu1208Ile	p.L1208I	ENST00000389048	NM_004304.4	1208	Ctc/Atc	23/29	0.487855949157785	3	FACETS	1	0.975	1	0.568	0.524	0.614	CLONAL	1	TRUE	1	0.487855949157785	3		637	781	SUCCESS
APC	324	MSKCC	GRCh37	5	112175261	112175261	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	111	202	0	ENST00000257430.4:c.3971del	p.Pro1324GlnfsTer91	p.P1324Qfs*91	ENST00000257430	NM_000038.5	1324	Cca/ca	16/16	0.487855949157785	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.487855949157785	2		202	217	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396204	139396204	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	364	692	0	ENST00000277541.6:c.5634del	p.Pro1879LeufsTer8	p.P1879Lfs*8	ENST00000277541	NM_017617.3	1878	ggG/gg	30/34	0.487855949157785	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.487855949157785	2		692	729	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931942	39931943	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0048762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	147	669	0	ENST00000378444.4:c.2656_2657delinsTT	p.Gly886Phe	p.G886F	ENST00000378444	NM_001123385.1	886	GGt/TTt	4/15	0.487855949157785	3	FACETS	0.886	0.809	0.967	0.443	0.404	0.484	CLONAL	1	TRUE	1	0.487855949157785	3		669	846	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361139	70361139	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	127	588	2	ENST00000374080.3:c.6327G>T	p.Gln2109His	p.Q2109H	ENST00000374080		2109	caG/caT	43/45	0.487855949157785	3	FACETS	0.757	0.686	0.833	0.379	0.343	0.417	SUBCLONAL	1	TRUE	1	0.487855949157785	3		590	855	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	161	301	0				ENST00000310581	NM_198253.2	-/1132			0.561789756435352	3	FACETS	0.831	0.769	0.893	0.831	0.769	0.893	CLONAL	2	FALSE	1	0.561716031739702	3		301	442	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0048763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	37	604	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.214487202796785	4	FACETS	0.237	0.194	0.285	0.119	0.097	0.143	INDETERMINATE	1	FALSE	2	0.561716031739702	4		604	868	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793881	NA	P-0048763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	308	577	0	ENST00000269305.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGg/gAg	8/11	0.46171933777623	2	FACETS	0.879	0.836	0.921	0.879	0.836	0.921	CLONAL	2	FALSE	0	0.561716031739702	2		577	624	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204495530	204495530	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	107	270	0	ENST00000367182.3:c.121G>T	p.Gly41Cys	p.G41C	ENST00000367182	NM_001278516.1	41	Ggt/Tgt	3/11	1	2	FACETS	0.704	0.634	0.778	0.704	0.634	0.778	SUBCLONAL	1	FALSE	1	0.561716031739702	2		270	541	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240816	53240816	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	26	236	0	ENST00000375401.3:c.1264G>C	p.Glu422Gln	p.E422Q	ENST00000375401	NM_004187.3	422	Gag/Cag	10/26	1	1	FACETS	0.202	0.16	0.251	0.202	0.16	0.251	SUBCLONAL	1	FALSE	0	0.561716031739702	1		236	329	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0048764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	90	339	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.798	0.717	0.882	0.798	0.717	0.882	SUBCLONAL	1	FALSE	1	0.786248582802493	2		340	287	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0048764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	354	668	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.923	0.876	0.97	0.923	0.876	0.97	CLONAL	1	FALSE	1	0.786248582802493	2		669	976	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0048764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1210	28	974	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	0.058	0.045	0.072	0.058	0.045	0.072	SUBCLONAL	1	FALSE	1	0.786248582802493	2		974	1238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577536	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCCGG	novel	NA	P-0048764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	269	535	0	ENST00000269305.4:c.741_745dup	p.Arg249ThrfsTer98	p.R249Tfs*98	ENST00000269305	NM_001126112.2	249	agg/aCCGGAgg	7/11	1	2	FACETS	0.772	0.726	0.82	0.772	0.726	0.82	SUBCLONAL	1	FALSE	1	0.786248582802493	2		535	886	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93953157	93953157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755519422	NA	P-0048764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	118	219	0	ENST00000369303.4:c.2984G>A	p.Gly995Asp	p.G995D	ENST00000369303	NM_004440.3	995	gGc/gAc	17/17	1	2	FACETS	0.875	0.799	0.953	0.875	0.799	0.953	CLONAL	1	FALSE	1	0.786248582802493	2		219	343	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937525	76937526	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CA	CA	-	novel	NA	P-0048764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	174	144	0	ENST00000373344.5:c.3222_3223del	p.Cys1074Ter	p.C1074*	ENST00000373344	NM_000489.3	1074	tgTGac/tgac	9/35	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	0	0.786248582802493	1		144	240	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	60	351	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.893	1			1	INDETERMINATE	1	TRUE	NA	0.27	2		351	428	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049724	16049724	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	33	326	0	ENST00000268712.3:c.1048C>T	p.Arg350Ter	p.R350*	ENST00000268712	NM_006311.3	350	Cga/Tga	10/46	1	2	FACETS	0.416	0.338	0.505	0.416	0.338	0.505	SUBCLONAL	1	TRUE	1	0.27	2		326	587	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468270	50468270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	77	466	1	ENST00000331340.3:c.1505G>A	p.Arg502Gln	p.R502Q	ENST00000331340	NM_006060.4	502	cGg/cAg	8/8	1	2	FACETS	0.632	0.554	0.717	0.632	0.554	0.717	SUBCLONAL	1	TRUE	1	0.27	2		467	902	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729613	41729613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564878978	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	88	432	0	ENST00000242208.4:c.916C>T	p.Arg306Cys	p.R306C	ENST00000242208	NM_002192.2	306	Cgc/Tgc	3/3	1	2	FACETS	0.852	0.754	0.957	0.852	0.754	0.957	CLONAL	1	TRUE	1	0.27	2		432	765	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	78	435	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.857	0.753	0.969	0.857	0.753	0.969	CLONAL	1	TRUE	1	0.27	2		436	674	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670340	134670340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415689583	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	81	279	0	ENST00000398015.3:c.251G>A	p.Arg84His	p.R84H	ENST00000398015	NM_004441.4	84	cGc/cAc	3/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.27	2		279	504	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781201	161781201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55830907	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	61	398	1	ENST00000366898.1:c.1204C>T	p.Arg402Cys	p.R402C	ENST00000366898	NM_004562.2	402	Cgt/Tgt	11/12	1	2	FACETS	0.639	0.551	0.736	0.639	0.551	0.736	SUBCLONAL	1	TRUE	1	0.27	2		399	707	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265348	16265348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746234410	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	134	470	0	ENST00000375759.3:c.10840G>A	p.Val3614Ile	p.V3614I	ENST00000375759	NM_015001.2	3614	Gtt/Att	14/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.27	2		470	913	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	66	436	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.792	0.688	0.906	0.792	0.688	0.906	CLONAL	1	TRUE	1	0.27	2		436	617	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246137	46246137	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	65	259	0	ENST00000334344.6:c.4231C>T	p.Gln1411Ter	p.Q1411*	ENST00000334344	NM_152641.2	1411	Caa/Taa	15/21	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.27	2		259	476	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178681	108178681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	35	161	0	ENST00000278616.4:c.5732C>T	p.Ala1911Val	p.A1911V	ENST00000278616	NM_000051.3	1911	gCt/gTt	38/63	1	2	FACETS	0.767	0.63	0.92	0.767	0.63	0.92	CLONAL	1	TRUE	1	0.27	2		161	338	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547022	9547022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs58486349	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	40	189	0	ENST00000353224.5:c.1000G>A	p.Asp334Asn	p.D334N	ENST00000353224	NM_177990.2	334	Gat/Aat	5/10	1	2	FACETS	0.947	0.79	1	0.947	0.79	1	CLONAL	1	TRUE	1	0.27	2		189	313	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866552	78866552	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	105	482	1	ENST00000306801.3:c.2125C>T	p.Arg709Ter	p.R709*	ENST00000306801	NM_020761.2	709	Cga/Tga	19/34	1	2	FACETS	0.888	0.795	0.987	0.888	0.795	0.987	CLONAL	1	TRUE	1	0.27	2		483	876	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683659	162683659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769099303	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	96	427	1	ENST00000366898.1:c.310C>T	p.Arg104Trp	p.R104W	ENST00000366898	NM_004562.2	104	Cgg/Tgg	3/12	1	2	FACETS	0.955	0.85	1	0.955	0.85	1	CLONAL	1	TRUE	1	0.27	2		428	745	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153709	55153709	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	102	386	0	ENST00000257290.5:c.2674+1G>A		p.X892_splice	ENST00000257290	NM_006206.4	892			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.27	2		386	660	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781371	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	103	595	1	ENST00000269305.4:c.328C>T	p.Arg110Cys	p.R110C	ENST00000269305	NM_001126112.2	110	Cgt/Tgt	4/11	1	2	FACETS	0.828	0.739	0.921	0.828	0.739	0.921	CLONAL	1	TRUE	1	0.27	2		596	922	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455090	50455090	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	44	257	0	ENST00000331340.3:c.637C>T	p.Arg213Ter	p.R213*	ENST00000331340	NM_006060.4	213	Cga/Tga	6/8	1	2	FACETS	0.689	0.578	0.812	0.689	0.578	0.812	SUBCLONAL	1	TRUE	1	0.27	2		257	473	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143985	11143985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	133	444	0	ENST00000358026.2:c.3566G>A	p.Arg1189Gln	p.R1189Q	ENST00000358026	NM_001128849.1	1189	cGa/cAa	26/36	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.27	2		444	851	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176338	24176338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	122	570	0	ENST00000263121.7:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000263121	NM_003073.3	377	Cgt/Tgt	9/9	1	2	FACETS	0.911	0.822	1	0.911	0.822	1	CLONAL	1	TRUE	1	0.27	2		570	992	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027998	48027998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757653982	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	56	226	0	ENST00000234420.5:c.2876G>A	p.Arg959His	p.R959H	ENST00000234420	NM_000179.2	959	cGc/cAc	4/10	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.27	2		226	392	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041527	14041527	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs756155469	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	44	290	0	ENST00000311895.7:c.2074C>T	p.Arg692Ter	p.R692*	ENST00000311895	NM_005236.2	692	Cga/Tga	11/11	1	2	FACETS	0.6	0.503	0.708	0.6	0.503	0.708	SUBCLONAL	1	TRUE	1	0.27	2		290	543	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950622	38950622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748585755	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	60	236	1	ENST00000357387.3:c.3328C>T	p.Arg1110Cys	p.R1110C	ENST00000357387	NM_152756.3	1110	Cgt/Tgt	31/38	1	2	FACETS	0.905	0.781	1	0.905	0.781	1	CLONAL	1	TRUE	1	0.27	2		237	491	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508793	106508793	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370152741	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	74	368	1	ENST00000359195.3:c.787G>A	p.Glu263Lys	p.E263K	ENST00000359195	NM_002649.2	263	Gaa/Aaa	2/11	1	2	FACETS	0.762	0.667	0.865	0.762	0.667	0.865	SUBCLONAL	1	TRUE	1	0.27	2		369	719	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428511	78428511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408536007	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	92	304	0	ENST00000370768.2:c.1288C>T	p.Arg430Cys	p.R430C	ENST00000370768	NM_003902.3	430	Cgt/Tgt	14/20	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.27	2		304	661	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858492	27858492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	82	382	0	ENST00000359303.2:c.79C>T	p.Arg27Cys	p.R27C	ENST00000359303	NM_003535.2	27	Cgc/Tgc	1/1	1	2	FACETS	0.874	0.771	0.985	0.874	0.771	0.985	CLONAL	1	TRUE	1	0.27	2		382	695	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98011564	98011564	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	66	255	0	ENST00000289081.3:c.10G>T	p.Asp4Tyr	p.D4Y	ENST00000289081	NM_000136.2	4	Gat/Tat	2/15	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.27	2		255	484	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622039	43622039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1371891301	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	56	269	0	ENST00000355710.3:c.3056C>T	p.Ala1019Val	p.A1019V	ENST00000355710	NM_020975.4	1019	gCg/gTg	19/20	1	2	FACETS	0.833	0.714	0.962	0.833	0.714	0.962	CLONAL	1	TRUE	1	0.27	2		269	498	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205756	108205756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531980488	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	46	200	1	ENST00000278616.4:c.8071C>T	p.Arg2691Cys	p.R2691C	ENST00000278616	NM_000051.3	2691	Cgc/Tgc	55/63	1	2	FACETS	0.825	0.696	0.967	0.825	0.696	0.967	CLONAL	1	TRUE	1	0.27	2		201	413	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	21	341	0	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	0.255	0.195	0.325	0.255	0.195	0.325	SUBCLONAL	1	TRUE	1	0.27	2		341	611	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523708	148523708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520183	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	42	192	0	ENST00000320356.2:c.745G>A	p.Glu249Lys	p.E249K	ENST00000320356	NM_004456.4	249	Gaa/Aaa	8/20	1	2	FACETS	0.804	0.672	0.949	0.804	0.672	0.949	CLONAL	1	TRUE	1	0.27	2		192	387	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249847	133249847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	61	322	0	ENST00000320574.5:c.1376C>T	p.Ser459Phe	p.S459F	ENST00000320574	NM_006231.2	459	tCt/tTt	14/49	1	2	FACETS	0.817	0.705	0.939	0.817	0.705	0.939	CLONAL	1	TRUE	1	0.27	2		322	553	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623625	28623625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1279372452	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	34	323	0	ENST00000241453.7:c.932G>A	p.Arg311Gln	p.R311Q	ENST00000241453	NM_004119.2	311	cGg/cAg	8/24	1	2	FACETS	0.41	0.334	0.496	0.41	0.334	0.496	SUBCLONAL	1	TRUE	1	0.27	2		323	614	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598084	55598084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746503007	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	68	297	0	ENST00000288135.5:c.2281G>A	p.Glu761Lys	p.E761K	ENST00000288135	NM_000222.2	761	Gag/Aag	16/21	1	2	FACETS	0.861	0.749	0.982	0.861	0.749	0.982	CLONAL	1	TRUE	1	0.27	2		297	585	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148513849	148513849	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	76	305	0	ENST00000320356.2:c.1432G>T	p.Glu478Ter	p.E478*	ENST00000320356	NM_004456.4	478	Gaa/Taa	12/20	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.27	2		305	550	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467500	66467500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757521167	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	55	226	0	ENST00000273854.3:c.769G>A	p.Glu257Lys	p.E257K	ENST00000273854	NM_004439.5	257	Gaa/Aaa	3/18	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.27	2		226	406	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301111	65301111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370434553	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	39	194	0	ENST00000342505.4:c.3337C>T	p.Arg1113Cys	p.R1113C	ENST00000342505	NM_002227.2	1113	Cgc/Tgc	24/25	1	2	FACETS	0.852	0.708	1	0.852	0.708	1	CLONAL	1	TRUE	1	0.27	2		194	339	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542861	187542861	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1340793072	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	52	240	0	ENST00000441802.2:c.4879C>T	p.Arg1627Ter	p.R1627*	ENST00000441802	NM_005245.3	1627	Cga/Tga	10/27	1	2	FACETS	0.839	0.715	0.974	0.839	0.715	0.974	CLONAL	1	TRUE	1	0.27	2		240	459	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72866457	72866457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375075276	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	51	243	0	ENST00000325599.8:c.806G>A	p.Arg269His	p.R269H	ENST00000325599	NM_018130.2	269	cGt/cAt	7/11	1	2	FACETS	0.745	0.634	0.868	0.745	0.634	0.868	SUBCLONAL	1	TRUE	1	0.27	2		243	507	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436128	56436128	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	99	441	1	ENST00000407977.2:c.1009C>T	p.Arg337Ter	p.R337*	ENST00000407977		337	Cga/Tga	9/10	1	2	FACETS	0.918	0.819	1	0.918	0.819	1	CLONAL	1	TRUE	1	0.27	2		442	799	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560970	9560970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781706438	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	62	263	0	ENST00000353224.5:c.812C>T	p.Ser271Leu	p.S271L	ENST00000353224	NM_177990.2	271	tCg/tTg	4/10	1	2	FACETS	0.827	0.715	0.949	0.827	0.715	0.949	CLONAL	1	TRUE	1	0.27	2		263	555	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356152	66356152	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370633345	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	77	301	0	ENST00000273854.3:c.1345G>A	p.Asp449Asn	p.D449N	ENST00000273854	NM_004439.5	449	Gac/Aac	5/18	1	2	FACETS	0.929	0.816	1	0.929	0.816	1	CLONAL	1	TRUE	1	0.27	2		301	614	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170811	11170811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	139	598	0	ENST00000358026.2:c.4955C>T	p.Ser1652Phe	p.S1652F	ENST00000358026	NM_001128849.1	1652	tCc/tTc	35/36	1	2	FACETS	0.969	0.88	1	0.969	0.88	1	CLONAL	1	TRUE	1	0.27	2		598	1063	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521544	8521544	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	56	259	1	ENST00000356435.5:c.694C>T	p.Arg232Cys	p.R232C	ENST00000356435		232	Cgc/Tgc	9/35	1	2	FACETS	0.815	0.699	0.942	0.815	0.699	0.942	CLONAL	1	TRUE	1	0.27	2		260	509	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082313	16082314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs780080562	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	110	775	2	ENST00000281043.3:c.134dup	p.Glu47GlyfsTer8	p.E47Gfs*8	ENST00000281043	NM_005378.4	43	acc/aCcc	2/3	1	2	FACETS	0.663	0.594	0.737	0.663	0.594	0.737	SUBCLONAL	1	TRUE	1	0.27	2		777	1229	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539690	187539690	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs748166431	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	72	258	0	ENST00000441802.2:c.8050G>T	p.Glu2684Ter	p.E2684*	ENST00000441802	NM_005245.3	2684	Gaa/Taa	10/27	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.27	2		258	505	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953874	131953874	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121912628	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	40	236	0	ENST00000265335.6:c.3277C>T	p.Arg1093Ter	p.R1093*	ENST00000265335		1093	Cga/Tga	21/25	1	2	FACETS	0.7	0.582	0.832	0.7	0.582	0.832	SUBCLONAL	1	TRUE	1	0.27	2		236	423	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984024	7984024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	51	264	0	ENST00000319144.4:c.602G>A	p.Arg201His	p.R201H	ENST00000319144	NM_001139.2	201	cGc/cAc	5/15	1	2	FACETS	0.928	0.791	1	0.928	0.791	1	CLONAL	1	TRUE	1	0.27	2		264	407	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379426	225379426	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	91	317	0	ENST00000264414.4:c.442C>T	p.Arg148Ter	p.R148*	ENST00000264414	NM_003590.4	148	Cga/Tga	4/16	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.27	2		317	646	SUCCESS
APC	324	MSKCC	GRCh37	5	112128185	112128185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779805	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	81	233	0	ENST00000257430.4:c.688C>T	p.Arg230Cys	p.R230C	ENST00000257430	NM_000038.5	230	Cgt/Tgt	7/16	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.27	2		233	532	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687431	117687431	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	63	203	0	ENST00000368508.3:c.2620G>T	p.Glu874Ter	p.E874*	ENST00000368508	NM_002944.2	874	Gaa/Taa	18/43	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.27	2		203	430	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650096	93650096	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	79	392	0	ENST00000375746.1:c.1647C>A	p.Phe549Leu	p.F549L	ENST00000375746	NM_001174167.1	549	ttC/ttA	12/14	1	2	FACETS	0.881	0.775	0.995	0.881	0.775	0.995	CLONAL	1	TRUE	1	0.27	2		392	664	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650568	18650568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368805708	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	69	312	0	ENST00000266497.5:c.2779C>T	p.Arg927Cys	p.R927C	ENST00000266497		927	Cgt/Tgt	20/31	1	2	FACETS	0.849	0.74	0.967	0.849	0.74	0.967	CLONAL	1	TRUE	1	0.27	2		312	602	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864193	57864193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746398371	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	121	496	3	ENST00000228682.2:c.1670G>A	p.Arg557His	p.R557H	ENST00000228682	NM_005269.2	557	cGc/cAc	12/12	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.27	2		499	854	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137487	202137487	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	27	615	0	ENST00000358485.4:c.715G>T	p.Glu239Ter	p.E239*	ENST00000358485	NM_001080125.1	239	Gaa/Taa	4/9	1	2	FACETS	0.38	0.302	0.471	0.38	0.302	0.471	SUBCLONAL	1	TRUE	1	0.27	2		615	526	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027958	48027958	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1558666905	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	42	203	0	ENST00000234420.5:c.2836G>T	p.Glu946Ter	p.E946*	ENST00000234420	NM_000179.2	946	Gaa/Taa	4/10	1	2	FACETS	0.855	0.715	1	0.855	0.715	1	CLONAL	1	TRUE	1	0.27	2		203	364	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149880	202149880	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	105	342	0	ENST00000358485.4:c.1321G>T	p.Glu441Ter	p.E441*	ENST00000358485	NM_001080125.1	441	Gaa/Taa	8/9	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.27	2		342	742	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916669	178916669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	60	210	0	ENST00000263967.3:c.56G>T	p.Arg19Ile	p.R19I	ENST00000263967	NM_006218.2	19	aGa/aTa	2/21	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.27	2		210	438	SUCCESS
APC	324	MSKCC	GRCh37	5	112176686	112176686	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	42	149	0	ENST00000257430.4:c.5395T>G	p.Leu1799Val	p.L1799V	ENST00000257430	NM_000038.5	1799	Tta/Gta	16/16	1	2	FACETS	1	0.842	1	1	0.842	1	CLONAL	1	TRUE	1	0.27	2		149	310	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956135	175956135	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	67	250	0	ENST00000367669.3:c.2077G>T	p.Glu693Ter	p.E693*	ENST00000367669	NM_022457.5	693	Gaa/Taa	18/20	1	2	FACETS	0.962	0.837	1	0.962	0.837	1	CLONAL	1	TRUE	1	0.27	2		250	516	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524603	176524603	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758782236	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	151	688	1	ENST00000292408.4:c.2335G>A	p.Asp779Asn	p.D779N	ENST00000292408	NM_213647.1	779	Gat/Aat	18/18	1	2	FACETS	0.961	0.877	1	0.961	0.877	1	CLONAL	1	TRUE	1	0.27	2		689	1164	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260648	1260648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	118	520	1	ENST00000310581.5:c.2911C>T	p.Arg971Cys	p.R971C	ENST00000310581	NM_198253.2	971	Cgt/Tgt	12/16	NA	2	FACETS	1	0.935	1			1	INDETERMINATE	1	TRUE	NA	0.27	2		521	835	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940241	71940241	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113909227	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	127	548	3	ENST00000298229.2:c.626G>A	p.Arg209His	p.R209H	ENST00000298229	NM_001567.3	209	cGt/cAt	5/28	1	2	FACETS	0.952	0.861	1	0.952	0.861	1	CLONAL	1	TRUE	1	0.27	2		551	988	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103520549	103520549	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121434576	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	37	214	0	ENST00000355739.4:c.2620G>A	p.Ala874Thr	p.A874T	ENST00000355739	NM_000123.3	874	Gcc/Acc	12/15	1	2	FACETS	0.727	0.6	0.868	0.727	0.6	0.868	SUBCLONAL	1	TRUE	1	0.27	2		214	377	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069387	30069387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765540111	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	126	552	0	ENST00000338641.4:c.1252C>T	p.Arg418Cys	p.R418C	ENST00000338641	NM_000268.3	418	Cgc/Tgc	12/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.27	2		552	875	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200960	108200960	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434220	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	66	251	0	ENST00000278616.4:c.7327C>T	p.Arg2443Ter	p.R2443*	ENST00000278616	NM_000051.3	2443	Cga/Tga	50/63	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.27	2		251	432	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390185	89390185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746351940	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	41	201	0	ENST00000336596.2:c.934C>T	p.Arg312Trp	p.R312W	ENST00000336596	NM_005233.5	312	Cgg/Tgg	4/17	1	2	FACETS	0.801	0.669	0.948	0.801	0.669	0.948	CLONAL	1	TRUE	1	0.27	2		201	379	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332884	65332884	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	30	132	0	ENST00000342505.4:c.655C>T	p.Arg219Ter	p.R219*	ENST00000342505	NM_002227.2	219	Cga/Tga	7/25	1	2	FACETS	0.785	0.635	0.955	0.785	0.635	0.955	CLONAL	1	TRUE	1	0.27	2		132	283	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425038	49425038	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783690	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	156	676	1	ENST00000301067.7:c.13450C>T	p.Arg4484Ter	p.R4484*	ENST00000301067	NM_003482.3	4484	Cga/Tga	39/54	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.27	2		677	1109	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263839	16263839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs549789481	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	127	560	0	ENST00000375759.3:c.10208G>A	p.Arg3403His	p.R3403H	ENST00000375759	NM_015001.2	3403	cGc/cAc	12/15	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.27	2		560	853	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924403	131924403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1184353235	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	48	175	0	ENST00000265335.6:c.1076G>A	p.Arg359His	p.R359H	ENST00000265335		359	cGc/cAc	8/25	1	2	FACETS	0.953	0.808	1	0.953	0.808	1	CLONAL	1	TRUE	1	0.27	2		175	373	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930273	39930273	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769721734	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	24	214	0	ENST00000378444.4:c.3191C>T	p.Ser1064Leu	p.S1064L	ENST00000378444	NM_001123385.1	1064	tCg/tTg	6/15	1	1	FACETS	0.324	0.253	0.406	0.324	0.253	0.406	SUBCLONAL	1	TRUE	0	0.27	1		214	475	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804367	43804367	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1443655691	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	85	376	0	ENST00000372470.3:c.367C>T	p.Arg123Ter	p.R123*	ENST00000372470	NM_005373.2	123	Cga/Tga	3/12	1	2	FACETS	0.982	0.869	1	0.982	0.869	1	CLONAL	1	TRUE	1	0.27	2		376	641	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31486610	31486610	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	47	223	0	ENST00000344624.3:c.1902G>T	p.Glu634Asp	p.E634D	ENST00000344624		634	gaG/gaT	11/33	1	2	FACETS	0.819	0.692	0.959	0.819	0.692	0.959	CLONAL	1	TRUE	1	0.27	2		223	425	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468517	89468517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372257039	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	39	206	0	ENST00000336596.2:c.2051G>A	p.Arg684Gln	p.R684Q	ENST00000336596	NM_005233.5	684	cGa/cAa	11/17	1	2	FACETS	0.828	0.688	0.983	0.828	0.688	0.983	CLONAL	1	TRUE	1	0.27	2		206	349	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539936	187539936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751129087	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	51	261	0	ENST00000441802.2:c.7804G>A	p.Glu2602Lys	p.E2602K	ENST00000441802	NM_005245.3	2602	Gaa/Aaa	10/27	1	2	FACETS	0.784	0.667	0.912	0.784	0.667	0.912	CLONAL	1	TRUE	1	0.27	2		261	482	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413578	32413578	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121907909	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	29	281	0	ENST00000332351.3:c.1372C>T	p.Arg458Ter	p.R458*	ENST00000332351	NM_024426.4	458	Cga/Tga	9/10	1	2	FACETS	0.444	0.355	0.545	0.444	0.355	0.545	SUBCLONAL	1	TRUE	1	0.27	2		281	484	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525071	9525071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	89	356	2	ENST00000353224.5:c.1814G>A	p.Gly605Asp	p.G605D	ENST00000353224	NM_177990.2	605	gGc/gAc	8/10	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.27	2		358	589	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89871774	89871774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144420697	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	114	411	0	ENST00000389301.3:c.623C>T	p.Ser208Leu	p.S208L	ENST00000389301	NM_000135.2	208	tCg/tTg	7/43	0.3	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.27	1		411	672	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748129	41748129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776131193	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	40	232	1	ENST00000226382.2:c.640G>A	p.Gly214Ser	p.G214S	ENST00000226382	NM_003924.3	214	Ggc/Agc	3/3	1	2	FACETS	0.859	0.716	1	0.859	0.716	1	CLONAL	1	TRUE	1	0.27	2		233	345	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845485	128845485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779548739	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	50	563	1	ENST00000249373.3:c.782G>A	p.Arg261His	p.R261H	ENST00000249373	NM_005631.4	261	cGc/cAc	4/12	1	2	FACETS	0.379	0.32	0.444	0.379	0.32	0.444	SUBCLONAL	1	TRUE	1	0.27	2		564	978	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643705	38643705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1345810751	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	102	468	0	ENST00000299084.4:c.1175C>T	p.Ser392Leu	p.S392L	ENST00000299084	NM_152594.2	392	tCg/tTg	7/7	1	2	FACETS	0.863	0.77	0.961	0.863	0.77	0.961	CLONAL	1	TRUE	1	0.27	2		468	876	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934254	48934254	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1131690904	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	93	223	0	ENST00000267163.4:c.709G>T	p.Glu237Ter	p.E237*	ENST00000267163	NM_000321.2	237	Gaa/Taa	7/27	1	2	FACETS	0.868	0.777	0.963	1	0.985	1	CLONAL	2	TRUE	1	0.27	2		223	397	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726567	41726567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781049505	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	88	463	0	ENST00000301178.4:c.112G>A	p.Val38Met	p.V38M	ENST00000301178	NM_021913.4	38	Gtg/Atg	2/20	0.245618879799679	3	FACETS	0.861	0.762	0.968	0.431	0.381	0.484	CLONAL	1	TRUE	1	0.27	3		463	859	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396856	396856	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs574168909	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	130	520	1	ENST00000262320.3:c.170C>T	p.Ser57Leu	p.S57L	ENST00000262320	NM_003502.3	57	tCg/tTg	2/11	1	2	FACETS	0.958	0.868	1	0.958	0.868	1	CLONAL	1	TRUE	1	0.27	2		521	1005	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015123	71015123	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	63	244	0	ENST00000318789.4:c.1807C>T	p.Arg603Trp	p.R603W	ENST00000318789	NM_032682.5	603	Cgg/Tgg	20/21	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.27	2		244	455	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52729039	52729039	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	45	365	0	ENST00000322088.6:c.1731C>A	p.Tyr577Ter	p.Y577*	ENST00000322088	NM_014225.5	577	taC/taA	14/15	0.245618879799679	3	FACETS	0.5	0.419	0.591	0.25	0.209	0.296	SUBCLONAL	1	TRUE	1	0.27	3		365	756	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677804	47677804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1438495852	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	69	355	0	ENST00000347630.2:c.1061G>A	p.Arg354His	p.R354H	ENST00000347630	NM_001007230.1	354	cGc/cAc	11/11	1	2	FACETS	0.776	0.675	0.884	0.776	0.675	0.884	SUBCLONAL	1	TRUE	1	0.27	2		355	659	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512334	38512334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	114	458	0	ENST00000254066.5:c.1245G>T	p.Glu415Asp	p.E415D	ENST00000254066	NM_000964.3	415	gaG/gaT	9/9	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.27	2		458	829	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729363	41729363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	89	444	0	ENST00000242208.4:c.1166C>T	p.Ser389Leu	p.S389L	ENST00000242208	NM_002192.2	389	tCg/tTg	3/3	1	2	FACETS	0.852	0.755	0.956	0.852	0.755	0.956	CLONAL	1	TRUE	1	0.27	2		444	774	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800519	32800519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376467259	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	151	645	1	ENST00000374899.4:c.1028G>A	p.Arg343His	p.R343H	ENST00000374899	NM_018833.2	343	cGc/cAc	6/12	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.27	2		646	1092	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040892	42040892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463241547	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	90	357	0	ENST00000219905.7:c.5270G>A	p.Arg1757His	p.R1757H	ENST00000219905	NM_001164273.1	1757	cGt/cAt	16/24	1	2	FACETS	0.994	0.882	1	0.994	0.882	1	CLONAL	1	TRUE	1	0.27	2		357	671	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096296	2096296	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	138	629	0	ENST00000219066.1:c.211T>C	p.Ser71Pro	p.S71P	ENST00000219066	NM_002528.5	71	Tcg/Ccg	2/6	1	2	FACETS	0.894	0.811	0.98	0.894	0.811	0.98	CLONAL	1	TRUE	1	0.27	2		629	1144	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510219	187510219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276553545	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	39	316	0	ENST00000441802.2:c.13294G>A	p.Glu4432Lys	p.E4432K	ENST00000441802	NM_005245.3	4432	Gaa/Aaa	27/27	1	2	FACETS	0.472	0.39	0.564	0.472	0.39	0.564	SUBCLONAL	1	TRUE	1	0.27	2		316	612	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705429	43705429	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs752678808	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	126	556	0	ENST00000382044.4:c.5193G>T	p.Lys1731Asn	p.K1731N	ENST00000382044	NM_001141980.1	1731	aaG/aaT	24/28	1	2	FACETS	0.991	0.896	1	0.991	0.896	1	CLONAL	1	TRUE	1	0.27	2		556	942	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158129	106158129	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs770136804	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	49	228	0	ENST00000380013.4:c.3030G>T	p.Glu1010Asp	p.E1010D	ENST00000380013	NM_001127208.2	1010	gaG/gaT	3/11	1	2	FACETS	0.838	0.711	0.978	0.838	0.711	0.978	CLONAL	1	TRUE	1	0.27	2		228	433	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419064	419064	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	68	284	2	ENST00000399788.2:c.3283G>T	p.Glu1095Ter	p.E1095*	ENST00000399788	NM_001042603.1	1095	Gaa/Taa	22/28	1	2	FACETS	0.99	0.863	1	0.99	0.863	1	CLONAL	1	TRUE	1	0.27	2		286	509	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313289	65313289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	42	370	0	ENST00000342505.4:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000342505	NM_002227.2	609	Gaa/Aaa	13/25	1	2	FACETS	0.453	0.377	0.537	0.453	0.377	0.537	SUBCLONAL	1	TRUE	1	0.27	2		370	687	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134383	30134383	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	73	503	0	ENST00000263025.4:c.148G>A	p.Glu50Lys	p.E50K	ENST00000263025	NM_002746.2	50	Gag/Aag	1/9	1	2	FACETS	0.612	0.534	0.696	0.612	0.534	0.696	SUBCLONAL	1	TRUE	1	0.27	2		503	884	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828867	26828867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	56	329	1	ENST00000381527.3:c.89G>A	p.Gly30Asp	p.G30D	ENST00000381527	NM_001260.1	30	gGc/gAc	1/13	1	2	FACETS	0.805	0.691	0.931	0.805	0.691	0.931	CLONAL	1	TRUE	1	0.27	2		330	515	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244077	153244077	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	62	296	0	ENST00000281708.4:c.2080G>T	p.Glu694Ter	p.E694*	ENST00000281708	NM_033632.3	694	Gaa/Taa	12/12	1	2	FACETS	0.786	0.679	0.903	0.786	0.679	0.903	CLONAL	1	TRUE	1	0.27	2		296	584	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523708	176523708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	148	593	0	ENST00000292408.4:c.2119C>T	p.Arg707Trp	p.R707W	ENST00000292408	NM_213647.1	707	Cgg/Tgg	16/18	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.27	2		593	962	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497842	25497842	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	127	607	3	ENST00000264709.3:c.607C>T	p.Arg203Trp	p.R203W	ENST00000264709	NM_175629.2	203	Cgg/Tgg	6/23	1	2	FACETS	0.916	0.828	1	0.916	0.828	1	CLONAL	1	TRUE	1	0.27	2		610	1027	SUCCESS
AR	367	MSKCC	GRCh37	X	66942713	66942713	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	81	147	0	ENST00000374690.3:c.2494C>T	p.Arg832Ter	p.R832*	ENST00000374690	NM_000044.3	832	Cga/Tga	7/8	1	1	FACETS	0.917	0.817	1	1	0.984	1	CLONAL	2	TRUE	0	0.27	1		147	283	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958217	11958217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	49	201	0	ENST00000353533.5:c.127G>A	p.Ala43Thr	p.A43T	ENST00000353533	NM_003010.3	43	Gca/Aca	2/11	1	2	FACETS	0.933	0.792	1	0.933	0.792	1	CLONAL	1	TRUE	1	0.27	2		201	389	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40684192	40684192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199907924	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	59	280	0	ENST00000249776.8:c.790G>A	p.Glu264Lys	p.E264K	ENST00000249776	NM_033286.3	264	Gaa/Aaa	8/9	1	2	FACETS	0.707	0.608	0.815	0.707	0.608	0.815	SUBCLONAL	1	TRUE	1	0.27	2		280	618	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50481152	50481152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	65	241	0	ENST00000394963.4:c.538C>T	p.Arg180Trp	p.R180W	ENST00000394963	NM_003076.4	180	Cgg/Tgg	5/13	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.27	2		241	470	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630711	187630711	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1420866272	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	93	381	1	ENST00000441802.2:c.271G>A	p.Gly91Arg	p.G91R	ENST00000441802	NM_005245.3	91	Gga/Aga	2/27	1	2	FACETS	0.916	0.814	1	0.916	0.814	1	CLONAL	1	TRUE	1	0.27	2		382	752	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79952236	79952236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1445966245	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	19	160	0	ENST00000265081.6:c.244G>A	p.Glu82Lys	p.E82K	ENST00000265081	NM_002439.4	82	Gaa/Aaa	2/24	1	2	FACETS	0.414	0.314	0.532	0.414	0.314	0.532	SUBCLONAL	1	TRUE	1	0.27	2		160	340	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202813	16202813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1557739895	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	76	331	0	ENST00000375759.3:c.521G>A	p.Arg174Gln	p.R174Q	ENST00000375759	NM_015001.2	174	cGa/cAa	3/15	1	2	FACETS	0.891	0.782	1	0.891	0.782	1	CLONAL	1	TRUE	1	0.27	2		331	632	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255868	16255868	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	48	248	0	ENST00000375759.3:c.3133C>T	p.Leu1045Phe	p.L1045F	ENST00000375759	NM_015001.2	1045	Ctt/Ttt	11/15	1	2	FACETS	0.688	0.581	0.805	0.688	0.581	0.805	SUBCLONAL	1	TRUE	1	0.27	2		248	517	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099457	27099457	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	67	308	0	ENST00000324856.7:c.3694C>A	p.Pro1232Thr	p.P1232T	ENST00000324856	NM_006015.4	1232	Cct/Act	14/20	1	2	FACETS	0.922	0.803	1	0.922	0.803	1	CLONAL	1	TRUE	1	0.27	2		308	538	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933704	36933704	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	112	557	0	ENST00000361632.4:c.1695C>A	p.Phe565Leu	p.F565L	ENST00000361632		565	ttC/ttA	12/16	1	2	FACETS	0.822	0.738	0.912	0.822	0.738	0.912	CLONAL	1	TRUE	1	0.27	2		557	1009	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363449	40363449	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	84	416	2	ENST00000397332.2:c.780G>T	p.Glu260Asp	p.E260D	ENST00000397332	NM_001033082.2	260	gaG/gaT	3/3	1	2	FACETS	0.777	0.685	0.875	0.777	0.685	0.875	SUBCLONAL	1	TRUE	1	0.27	2		418	801	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818196	43818196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781129953	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	72	370	0	ENST00000372470.3:c.1661C>T	p.Ala554Val	p.A554V	ENST00000372470	NM_005373.2	554	gCc/gTc	12/12	1	2	FACETS	0.918	0.803	1	0.918	0.803	1	CLONAL	1	TRUE	1	0.27	2		370	581	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313286	65313286	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	91	370	0	ENST00000342505.4:c.1828G>T	p.Gly610Ter	p.G610*	ENST00000342505	NM_002227.2	610	Gga/Tga	13/25	1	2	FACETS	0.976	0.866	1	0.976	0.866	1	CLONAL	1	TRUE	1	0.27	2		370	691	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161298247	161298247	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	71	282	0	ENST00000367975.2:c.139G>T	p.Gly47Cys	p.G47C	ENST00000367975	NM_003001.3	47	Ggt/Tgt	3/6	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.27	2		282	521	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163315505	163315505	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	65	298	0	ENST00000271452.3:c.845C>A	p.Ser282Ter	p.S282*	ENST00000271452	NM_145697.2	282	tCa/tAa	11/14	1	2	FACETS	0.963	0.836	1	0.963	0.836	1	CLONAL	1	TRUE	1	0.27	2		298	500	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226558188	226558188	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	77	367	0	ENST00000366794.5:c.2101C>A	p.Leu701Met	p.L701M	ENST00000366794	NM_001618.3	701	Ctg/Atg	15/23	1	2	FACETS	0.895	0.786	1	0.895	0.786	1	CLONAL	1	TRUE	1	0.27	2		367	637	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667345	241667345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	77	254	0	ENST00000366560.3:c.1105C>T	p.Pro369Ser	p.P369S	ENST00000366560	NM_000143.3	369	Cca/Tca	7/10	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.27	2		254	532	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106055	8106055	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	97	320	0	ENST00000346208.3:c.875A>G	p.Lys292Arg	p.K292R	ENST00000346208		292	aAa/aGa	4/6	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.27	2		320	660	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70360782	70360782	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	35	159	0	ENST00000373644.4:c.1959A>C	p.Lys653Asn	p.K653N	ENST00000373644	NM_030625.2	653	aaA/aaC	3/12	1	2	FACETS	0.986	0.812	1	0.986	0.812	1	CLONAL	1	TRUE	1	0.27	2		159	263	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653803	89653803	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	42	232	0	ENST00000371953.3:c.101C>A	p.Ala34Asp	p.A34D	ENST00000371953	NM_000314.4	34	gCt/gAt	2/9	1	2	FACETS	0.845	0.708	0.998	0.845	0.708	0.998	CLONAL	1	TRUE	1	0.27	2		232	368	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724144	112724144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1392683472	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	66	234	0	ENST00000369452.4:c.28G>A	p.Asp10Asn	p.D10N	ENST00000369452	NM_007373.3	10	Gac/Aac	2/9	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.27	2		234	444	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114905808	114905808	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	92	338	0	ENST00000543371.1:c.827T>G	p.Phe276Cys	p.F276C	ENST00000543371	NM_001198531.1	276	tTc/tGc	8/14	1	2	FACETS	0.971	0.863	1	0.971	0.863	1	CLONAL	1	TRUE	1	0.27	2		338	702	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156732	2156732	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	119	490	0	ENST00000434045.2:c.190T>C	p.Ser64Pro	p.S64P	ENST00000434045	NM_001127598.1	64	Tcg/Ccg	3/5	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.27	2		490	867	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316118	14316118	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	51	194	1	ENST00000256196.4:c.307G>T	p.Glu103Ter	p.E103*	ENST00000256196		103	Gaa/Taa	4/6	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.27	2		195	348	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456833	32456833	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	102	551	1	ENST00000332351.3:c.59C>T	p.Ser20Phe	p.S20F	ENST00000332351	NM_024426.4	20	tCc/tTc	1/10	1	2	FACETS	0.834	0.745	0.929	0.834	0.745	0.929	CLONAL	1	TRUE	1	0.27	2		552	906	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514115	69514115	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	98	419	1	ENST00000294312.3:c.566C>A	p.Ser189Tyr	p.S189Y	ENST00000294312	NM_005117.2	189	tCt/tAt	3/3	1	2	FACETS	0.903	0.805	1	0.903	0.805	1	CLONAL	1	TRUE	1	0.27	2		420	804	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588793	69588793	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	84	546	0	ENST00000168712.1:c.443C>T	p.Ser148Leu	p.S148L	ENST00000168712	NM_002007.2	148	tCg/tTg	2/3	1	2	FACETS	0.709	0.625	0.8	0.709	0.625	0.8	SUBCLONAL	1	TRUE	1	0.27	2		546	877	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589836	69589836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1390579117	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	27	63	0	ENST00000168712.1:c.17C>T	p.Thr6Met	p.T6M	ENST00000168712	NM_002007.2	6	aCg/aTg	1/3	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.27	2		63	147	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150247	108150247	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141999815	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	49	249	0	ENST00000278616.4:c.3314C>T	p.Ser1105Phe	p.S1105F	ENST00000278616	NM_000051.3	1105	tCc/tTc	23/63	1	2	FACETS	0.736	0.624	0.86	0.736	0.624	0.86	SUBCLONAL	1	TRUE	1	0.27	2		249	493	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374529	118374529	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	60	219	0	ENST00000534358.1:c.7922G>T	p.Arg2641Ile	p.R2641I	ENST00000534358	NM_005933.3	2641	aGa/aTa	27/36	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.27	2		219	443	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377081	118377081	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559663507	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	77	320	0	ENST00000534358.1:c.10474G>A	p.Ala3492Thr	p.A3492T	ENST00000534358	NM_005933.3	3492	Gct/Act	27/36	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.27	2		320	537	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1039268	1039268	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	82	368	0	ENST00000358495.3:c.229G>T	p.Glu77Ter	p.E77*	ENST00000358495	NM_134424.2	77	Gag/Tag	4/12	1	2	FACETS	0.819	0.721	0.923	0.819	0.721	0.923	CLONAL	1	TRUE	1	0.27	2		368	742	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715653	18715653	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	33	190	0	ENST00000266497.5:c.3484C>A	p.Leu1162Met	p.L1162M	ENST00000266497		1162	Ctg/Atg	25/31	1	2	FACETS	0.702	0.573	0.848	0.702	0.573	0.848	SUBCLONAL	1	TRUE	1	0.27	2		190	348	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378658	25378658	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	30	221	0	ENST00000311936.3:c.340G>T	p.Val114Leu	p.V114L	ENST00000311936	NM_004985.3	114	Gta/Tta	4/5	1	2	FACETS	0.556	0.447	0.678	0.556	0.447	0.678	SUBCLONAL	1	TRUE	1	0.27	2		221	400	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242755	46242755	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	34	200	0	ENST00000334344.6:c.1715+2T>C		p.X572_splice	ENST00000334344	NM_152641.2	572			1	2	FACETS	0.903	0.741	1	0.903	0.741	1	CLONAL	1	TRUE	1	0.27	2		200	279	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49423248	49423261	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	CCTCTGAAGTATCT	CCTCTGAAGTATCT	-	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	85	451	0	ENST00000301067.7:c.14000-2_14011del		p.X4667_splice	ENST00000301067	NM_003482.3	4667		43/54	1	2	FACETS	0.826	0.73	0.93	0.826	0.73	0.93	CLONAL	1	TRUE	1	0.27	2		451	762	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428394	49428394	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	120	563	0	ENST00000301067.7:c.10411del	p.Gln3471ArgfsTer31	p.Q3471Rfs*31	ENST00000301067	NM_003482.3	3471	Cag/ag	36/54	1	2	FACETS	0.881	0.794	0.973	0.881	0.794	0.973	CLONAL	1	TRUE	1	0.27	2		563	1009	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860033	57860033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	140	537	0	ENST00000228682.2:c.773G>A	p.Ser258Asn	p.S258N	ENST00000228682	NM_005269.2	258	aGc/aAc	8/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.27	2		537	959	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864279	57864279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	119	512	1	ENST00000228682.2:c.1756C>T	p.His586Tyr	p.H586Y	ENST00000228682	NM_005269.2	586	Cac/Tac	12/12	1	2	FACETS	0.959	0.865	1	0.959	0.865	1	CLONAL	1	TRUE	1	0.27	2		513	919	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117729	115117729	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	62	225	0	ENST00000257566.3:c.706T>G	p.Phe236Val	p.F236V	ENST00000257566	NM_016569.3	236	Ttt/Gtt	3/8	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.27	2		225	436	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29002009	29002009	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	53	222	0	ENST00000282397.4:c.1156C>A	p.Arg386Ser	p.R386S	ENST00000282397	NM_002019.4	386	Cgt/Agt	9/30	1	2	FACETS	0.767	0.654	0.89	0.767	0.654	0.89	SUBCLONAL	1	TRUE	1	0.27	2		222	512	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29007982	29007982	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	51	215	0	ENST00000282397.4:c.787C>A	p.Gln263Lys	p.Q263K	ENST00000282397	NM_002019.4	263	Caa/Aaa	6/30	1	2	FACETS	0.992	0.846	1	0.992	0.846	1	CLONAL	1	TRUE	1	0.27	2		215	381	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913195	32913195	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	90	320	0	ENST00000380152.3:c.4703A>C	p.Lys1568Thr	p.K1568T	ENST00000380152		1568	aAg/aCg	11/27	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.27	2		320	648	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913218	32913218	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	83	303	0	ENST00000380152.3:c.4726C>A	p.Leu1576Ile	p.L1576I	ENST00000380152		1576	Ctt/Att	11/27	1	2	FACETS	0.926	0.817	1	0.926	0.817	1	CLONAL	1	TRUE	1	0.27	2		303	664	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915264	32915264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881549	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	66	350	0	ENST00000380152.3:c.6772G>A	p.Glu2258Lys	p.E2258K	ENST00000380152		2258	Gaa/Aaa	11/27	1	2	FACETS	0.732	0.635	0.837	0.732	0.635	0.837	SUBCLONAL	1	TRUE	1	0.27	2		350	668	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134381	41134381	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	103	338	0	ENST00000379561.5:c.1247C>A	p.Ser416Ter	p.S416*	ENST00000379561	NM_002015.3	416	tCa/tAa	2/3	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.27	2		338	716	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058229	42058229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	53	168	0	ENST00000219905.7:c.7949G>A	p.Arg2650Gln	p.R2650Q	ENST00000219905	NM_001164273.1	2650	cGa/cAa	24/24	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.27	2		168	311	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292885	91292885	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	109	351	0	ENST00000355112.3:c.387G>T	p.Lys129Asn	p.K129N	ENST00000355112	NM_000057.2	129	aaG/aaT	3/22	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.27	2		351	740	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251130	99251130	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	50	401	0	ENST00000268035.6:c.434A>G	p.Lys145Arg	p.K145R	ENST00000268035	NM_000875.3	145	aAa/aGa	2/21	1	2	FACETS	0.507	0.429	0.593	0.507	0.429	0.593	SUBCLONAL	1	TRUE	1	0.27	2		401	731	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642817	3642817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146901714	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	133	578	0	ENST00000294008.3:c.2210G>A	p.Arg737His	p.R737H	ENST00000294008	NM_032444.2	737	cGt/cAt	11/15	1	2	FACETS	0.983	0.892	1	0.983	0.892	1	CLONAL	1	TRUE	1	0.27	2		578	1002	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020532	14020532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2020961	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	61	258	0	ENST00000311895.7:c.503C>T	p.Ala168Val	p.A168V	ENST00000311895	NM_005236.2	168	gCt/gTt	3/11	1	2	FACETS	0.877	0.758	1	0.877	0.758	1	CLONAL	1	TRUE	1	0.27	2		258	515	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853188	68853188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761180883	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	72	316	0	ENST00000261769.5:c.1571G>A	p.Arg524Gln	p.R524Q	ENST00000261769	NM_004360.3	524	cGg/cAg	11/16	0.3	1	FACETS	0.899	0.787	1	0.899	0.787	1	CLONAL	1	TRUE	0	0.27	1		316	513	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664415	29664415	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	70	304	0	ENST00000356175.3:c.6394C>A	p.Leu2132Met	p.L2132M	ENST00000356175	NM_000267.3	2132	Ctg/Atg	42/57	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.27	2		304	517	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40457694	40457694	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	107	447	0	ENST00000345506.4:c.1447C>A	p.Leu483Met	p.L483M	ENST00000345506	NM_003152.3	483	Ctg/Atg	13/20	1	2	FACETS	0.981	0.88	1	0.981	0.88	1	CLONAL	1	TRUE	1	0.27	2		447	808	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59821874	59821874	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	46	257	1	ENST00000259008.2:c.2176G>T	p.Glu726Ter	p.E726*	ENST00000259008	NM_032043.2	726	Gaa/Taa	15/20	1	2	FACETS	0.597	0.502	0.702	0.597	0.502	0.702	SUBCLONAL	1	TRUE	1	0.27	2		258	571	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554477	63554477	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	46	449	0	ENST00000307078.5:c.262G>A	p.Asp88Asn	p.D88N	ENST00000307078	NM_004655.3	88	Gat/Aat	2/11	1	2	FACETS	0.453	0.38	0.534	0.453	0.38	0.534	SUBCLONAL	1	TRUE	1	0.27	2		449	752	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617729	39617729	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	44	223	0	ENST00000262039.4:c.1913G>A	p.Gly638Glu	p.G638E	ENST00000262039	NM_002647.2	638	gGa/gAa	17/25	1	2	FACETS	0.696	0.584	0.821	0.696	0.584	0.821	SUBCLONAL	1	TRUE	1	0.27	2		223	468	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745162	41745162	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	133	502	0	ENST00000301178.4:c.1228A>G	p.Thr410Ala	p.T410A	ENST00000301178	NM_021913.4	410	Act/Gct	9/20	0.245618879799679	3	FACETS	1	0.951	1	0.537	0.487	0.59	CLONAL	1	TRUE	1	0.27	3		502	1041	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902125	50902125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778275831	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	195	483	0	ENST00000440232.2:c.17G>A	p.Arg6Gln	p.R6Q	ENST00000440232	NM_002691.3	6	cGg/cAg	2/27	0.245618879799679	3	FACETS	0.95	0.88	1	0.95	0.88	1	CLONAL	2	TRUE	1	0.27	3		483	863	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918180	50918180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1206	81	694	1	ENST00000440232.2:c.2497C>T	p.Arg833Cys	p.R833C	ENST00000440232	NM_002691.3	833	Cgc/Tgc	20/27	0.245618879799679	3	FACETS	0.529	0.464	0.599	0.265	0.232	0.3	SUBCLONAL	1	TRUE	1	0.27	3		695	1287	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224097	39224097	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	63	351	0	ENST00000402219.2:c.3047T>C	p.Ile1016Thr	p.I1016T	ENST00000402219	NM_005633.3	1016	aTa/aCa	19/23	1	2	FACETS	0.694	0.6	0.797	0.694	0.6	0.797	SUBCLONAL	1	TRUE	1	0.27	2		351	672	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39294834	39294834	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	53	239	0	ENST00000402219.2:c.148G>T	p.Glu50Ter	p.E50*	ENST00000402219	NM_005633.3	50	Gaa/Taa	2/23	1	2	FACETS	0.828	0.707	0.961	0.828	0.707	0.961	CLONAL	1	TRUE	1	0.27	2		239	474	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027239	48027239	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587779231	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	70	219	0	ENST00000234420.5:c.2117T>C	p.Phe706Ser	p.F706S	ENST00000234420	NM_000179.2	706	tTt/tCt	4/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.27	2		219	432	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715875	61715875	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	73	327	0	ENST00000401558.2:c.2054T>G	p.Val685Gly	p.V685G	ENST00000401558	NM_003400.3	685	gTc/gGc	18/25	1	2	FACETS	0.99	0.867	1	0.99	0.867	1	CLONAL	1	TRUE	1	0.27	2		327	546	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715907	61715907	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	33	232	0	ENST00000401558.2:c.2023-1G>T		p.X675_splice	ENST00000401558	NM_003400.3	675			1	2	FACETS	0.605	0.493	0.731	0.605	0.493	0.731	SUBCLONAL	1	TRUE	1	0.27	2		232	404	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726044	61726044	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	44	200	0	ENST00000401558.2:c.595T>C	p.Cys199Arg	p.C199R	ENST00000401558	NM_003400.3	199	Tgc/Cgc	8/25	1	2	FACETS	0.731	0.613	0.861	0.731	0.613	0.861	SUBCLONAL	1	TRUE	1	0.27	2		200	446	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265062	198265062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	65	275	0	ENST00000335508.6:c.2815C>T	p.Arg939Cys	p.R939C	ENST00000335508	NM_012433.2	939	Cgt/Tgt	19/25	1	2	FACETS	0.863	0.749	0.986	0.863	0.749	0.986	CLONAL	1	TRUE	1	0.27	2		275	558	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543795	212543795	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	60	245	0	ENST00000342788.4:c.1604C>A	p.Ser535Tyr	p.S535Y	ENST00000342788	NM_005235.2	535	tCt/tAt	13/28	1	2	FACETS	0.799	0.689	0.919	0.799	0.689	0.919	CLONAL	1	TRUE	1	0.27	2		245	556	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645352	215645352	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	67	315	0	ENST00000260947.4:c.1246C>A	p.Leu416Met	p.L416M	ENST00000260947	NM_000465.2	416	Ctg/Atg	4/11	1	2	FACETS	0.749	0.65	0.855	0.749	0.65	0.855	SUBCLONAL	1	TRUE	1	0.27	2		315	663	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437278	220437278	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	138	698	1	ENST00000243786.2:c.182G>T	p.Arg61Ile	p.R61I	ENST00000243786	NM_002191.3	61	aGa/aTa	1/2	1	2	FACETS	0.811	0.736	0.891	0.811	0.736	0.891	CLONAL	1	TRUE	1	0.27	2		699	1260	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514446	41514446	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	59	320	0	ENST00000373198.4:c.214+1G>A		p.X72_splice	ENST00000373198	NM_133170.3	72			1	2	FACETS	0.836	0.72	0.962	0.836	0.72	0.962	CLONAL	1	TRUE	1	0.27	2		320	523	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130460	29130460	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	132	430	0	ENST00000328354.6:c.250G>T	p.Glu84Ter	p.E84*	ENST00000328354	NM_007194.3	84	Gaa/Taa	2/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.27	2		430	784	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573270	41573270	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	145	642	0	ENST00000263253.7:c.5555C>A	p.Pro1852His	p.P1852H	ENST00000263253	NM_001429.3	1852	cCt/cAt	31/31	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.27	2		642	1056	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458452	12458452	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	128	406	0	ENST00000287820.6:c.1069A>C	p.Met357Leu	p.M357L	ENST00000287820	NM_015869.4	357	Atg/Ctg	6/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.27	2		406	757	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52685778	52685778	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	51	290	0	ENST00000394830.3:c.694A>G	p.Thr232Ala	p.T232A	ENST00000394830	NM_018313.4	232	Acc/Gcc	7/30	1	2	FACETS	0.757	0.644	0.881	0.757	0.644	0.881	SUBCLONAL	1	TRUE	1	0.27	2		290	499	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73113255	73113255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	32	84	0	ENST00000356692.5:c.596G>A	p.Ser199Asn	p.S199N	ENST00000356692		199	aGc/aAc	7/9	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.27	2		84	178	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521754	89521754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	40	253	0	ENST00000336596.2:c.2831C>T	p.Ala944Val	p.A944V	ENST00000336596	NM_005233.5	944	gCc/gTc	16/17	1	2	FACETS	0.615	0.511	0.731	0.615	0.511	0.731	SUBCLONAL	1	TRUE	1	0.27	2		253	482	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898774	134898774	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	62	252	1	ENST00000398015.3:c.1832C>T	p.Ala611Val	p.A611V	ENST00000398015	NM_004441.4	611	gCc/gTc	10/16	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.27	2		253	458	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433404	138433404	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	64	329	0	ENST00000289153.2:c.1208C>A	p.Ala403Asp	p.A403D	ENST00000289153	NM_006219.2	403	gCt/gAt	7/22	1	2	FACETS	0.809	0.701	0.926	0.809	0.701	0.926	CLONAL	1	TRUE	1	0.27	2		329	586	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474700	138474700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	35	286	0	ENST00000289153.2:c.293G>A	p.Arg98Lys	p.R98K	ENST00000289153	NM_006219.2	98	aGa/aAa	2/22	1	2	FACETS	0.386	0.315	0.466	0.386	0.315	0.466	SUBCLONAL	1	TRUE	1	0.27	2		286	672	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169977805	169977805	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	79	290	0	ENST00000295797.4:c.272G>T	p.Arg91Ile	p.R91I	ENST00000295797	NM_002740.5	91	aGa/aTa	3/18	1	2	FACETS	0.927	0.816	1	0.927	0.816	1	CLONAL	1	TRUE	1	0.27	2		290	631	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948147	178948147	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	42	140	0	ENST00000263967.3:c.2919G>T	p.Lys973Asn	p.K973N	ENST00000263967	NM_006218.2	973	aaG/aaT	20/21	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.27	2		140	275	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184691	185184691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	59	235	0	ENST00000265026.3:c.1583C>T	p.Ala528Val	p.A528V	ENST00000265026	NM_004721.4	528	gCc/gTc	10/14	1	2	FACETS	0.837	0.721	0.964	0.837	0.721	0.964	CLONAL	1	TRUE	1	0.27	2		235	522	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955137	1955137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	107	458	0	ENST00000382891.5:c.2224G>A	p.Ala742Thr	p.A742T	ENST00000382891	NM_133335.3	742	Gct/Act	12/22	1	2	FACETS	0.963	0.863	1	0.963	0.863	1	CLONAL	1	TRUE	1	0.27	2		458	823	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141108	55141108	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1060501505	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	45	239	0	ENST00000257290.5:c.1754G>T	p.Arg585Ile	p.R585I	ENST00000257290	NM_006206.4	585	aGa/aTa	12/23	1	2	FACETS	0.782	0.658	0.919	0.782	0.658	0.919	CLONAL	1	TRUE	1	0.27	2		239	426	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961766	55961766	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	41	301	0	ENST00000263923.4:c.2795G>A	p.Arg932Lys	p.R932K	ENST00000263923	NM_002253.2	932	aGa/aAa	20/30	1	2	FACETS	0.547	0.455	0.65	0.547	0.455	0.65	SUBCLONAL	1	TRUE	1	0.27	2		301	555	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213774	66213774	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	61	259	0	ENST00000273854.3:c.2656G>T	p.Asp886Tyr	p.D886Y	ENST00000273854	NM_004439.5	886	Gat/Tat	15/18	1	2	FACETS	0.97	0.838	1	0.97	0.838	1	CLONAL	1	TRUE	1	0.27	2		259	466	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218774	66218774	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	29	149	0	ENST00000273854.3:c.2284G>T	p.Asp762Tyr	p.D762Y	ENST00000273854	NM_004439.5	762	Gat/Tat	13/18	1	2	FACETS	0.873	0.704	1	0.873	0.704	1	CLONAL	1	TRUE	1	0.27	2		149	246	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231655	66231655	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	62	251	0	ENST00000273854.3:c.2045G>A	p.Gly682Glu	p.G682E	ENST00000273854	NM_004439.5	682	gGa/gAa	11/18	1	2	FACETS	0.973	0.842	1	0.973	0.842	1	CLONAL	1	TRUE	1	0.27	2		251	472	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467713	66467713	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs777341649	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	50	222	0	ENST00000273854.3:c.556C>A	p.Leu186Ile	p.L186I	ENST00000273854	NM_004439.5	186	Ctt/Att	3/18	1	2	FACETS	0.884	0.752	1	0.884	0.752	1	CLONAL	1	TRUE	1	0.27	2		222	419	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509087	66509087	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	41	176	0	ENST00000273854.3:c.240A>T	p.Lys80Asn	p.K80N	ENST00000273854	NM_004439.5	80	aaA/aaT	2/18	1	2	FACETS	0.793	0.662	0.938	0.793	0.662	0.938	CLONAL	1	TRUE	1	0.27	2		176	383	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155544	106155544	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs746373398	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	66	235	0	ENST00000380013.4:c.445G>T	p.Glu149Ter	p.E149*	ENST00000380013	NM_001127208.2	149	Gaa/Taa	3/11	1	2	FACETS	0.9	0.782	1	0.9	0.782	1	CLONAL	1	TRUE	1	0.27	2		235	543	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155568	106155568	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	51	222	0	ENST00000380013.4:c.469G>T	p.Glu157Ter	p.E157*	ENST00000380013	NM_001127208.2	157	Gaa/Taa	3/11	1	2	FACETS	0.742	0.631	0.864	0.742	0.631	0.864	SUBCLONAL	1	TRUE	1	0.27	2		222	509	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249365	153249365	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	53	224	0	ENST00000281708.4:c.1413A>C	p.Glu471Asp	p.E471D	ENST00000281708	NM_033632.3	471	gaA/gaC	9/12	1	2	FACETS	0.748	0.638	0.868	0.748	0.638	0.868	SUBCLONAL	1	TRUE	1	0.27	2		224	525	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259009	153259009	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	44	207	0	ENST00000281708.4:c.806T>C	p.Met269Thr	p.M269T	ENST00000281708	NM_033632.3	269	aTg/aCg	5/12	1	2	FACETS	0.838	0.704	0.985	0.838	0.704	0.985	CLONAL	1	TRUE	1	0.27	2		207	389	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540175	187540175	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	74	306	0	ENST00000441802.2:c.7565G>A	p.Gly2522Asp	p.G2522D	ENST00000441802	NM_005245.3	2522	gGt/gAt	10/27	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.27	2		306	540	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628293	187628293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1459213050	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	88	437	0	ENST00000441802.2:c.2689G>A	p.Ala897Thr	p.A897T	ENST00000441802	NM_005245.3	897	Gcc/Acc	2/27	1	2	FACETS	0.841	0.745	0.944	0.841	0.745	0.944	CLONAL	1	TRUE	1	0.27	2		437	775	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630776	187630776	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	97	375	0	ENST00000441802.2:c.206A>G	p.Glu69Gly	p.E69G	ENST00000441802	NM_005245.3	69	gAa/gGa	2/27	1	2	FACETS	0.916	0.817	1	0.916	0.817	1	CLONAL	1	TRUE	1	0.27	2		375	784	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576789	67576789	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	43	190	0	ENST00000274335.5:c.871G>T	p.Glu291Ter	p.E291*	ENST00000274335		291	Gaa/Taa	6/15	1	2	FACETS	0.804	0.674	0.948	0.804	0.674	0.948	CLONAL	1	TRUE	1	0.27	2		190	396	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633862	86633862	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	39	232	0	ENST00000274376.6:c.971G>T	p.Arg324Ile	p.R324I	ENST00000274376	NM_002890.2	324	aGa/aTa	5/25	1	2	FACETS	0.84	0.698	0.997	0.84	0.698	0.997	CLONAL	1	TRUE	1	0.27	2		232	344	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645081	86645081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	43	201	0	ENST00000274376.6:c.1153G>A	p.Asp385Asn	p.D385N	ENST00000274376	NM_002890.2	385	Gat/Aat	8/25	1	2	FACETS	0.726	0.608	0.856	0.726	0.608	0.856	SUBCLONAL	1	TRUE	1	0.27	2		201	439	SUCCESS
APC	324	MSKCC	GRCh37	5	112176882	112176882	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	63	208	0	ENST00000257430.4:c.5591C>A	p.Ser1864Tyr	p.S1864Y	ENST00000257430	NM_000038.5	1864	tCt/tAt	16/16	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.27	2		208	441	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500850	149500850	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765478860	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	47	464	0	ENST00000261799.4:c.2380G>A	p.Glu794Lys	p.E794K	ENST00000261799	NM_002609.3	794	Gag/Aag	17/23	1	2	FACETS	0.401	0.337	0.472	0.401	0.337	0.472	SUBCLONAL	1	TRUE	1	0.27	2		464	868	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562951	176562951	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	45	251	0	ENST00000439151.2:c.847G>T	p.Asp283Tyr	p.D283Y	ENST00000439151	NM_022455.4	283	Gat/Tat	2/23	1	2	FACETS	0.636	0.534	0.749	0.636	0.534	0.749	SUBCLONAL	1	TRUE	1	0.27	2		251	524	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055967	180055967	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	115	563	0	ENST00000261937.6:c.1018G>T	p.Gly340Ter	p.G340*	ENST00000261937	NM_182925.4	340	Gga/Tga	8/30	NA	2	FACETS	0.897	0.807	0.992			1	INDETERMINATE	1	TRUE	NA	0.27	2		563	950	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020797	26020797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372738098	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	47	269	0	ENST00000357647.3:c.80G>A	p.Arg27His	p.R27H	ENST00000357647	NM_003529.2	27	cGc/cAc	1/1	1	2	FACETS	0.668	0.564	0.784	0.668	0.564	0.784	SUBCLONAL	1	TRUE	1	0.27	2		269	521	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250552	26250552	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	88	506	0	ENST00000446824.2:c.282G>T	p.Gln94His	p.Q94H	ENST00000446824	NM_021018.2	94	caG/caT	1/1	1	2	FACETS	0.732	0.648	0.823	0.732	0.648	0.823	SUBCLONAL	1	TRUE	1	0.27	2		506	890	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805902	32805902	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	107	616	0	ENST00000374899.4:c.109G>T	p.Gly37Ter	p.G37*	ENST00000374899	NM_018833.2	37	Gga/Tga	2/12	1	2	FACETS	0.718	0.642	0.799	0.718	0.642	0.799	SUBCLONAL	1	TRUE	1	0.27	2		616	1104	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32819886	32819886	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	58	362	0	ENST00000354258.4:c.1024G>T	p.Gly342Cys	p.G342C	ENST00000354258	NM_000593.5	342	Ggt/Tgt	3/11	1	2	FACETS	0.55	0.471	0.636	0.55	0.471	0.636	SUBCLONAL	1	TRUE	1	0.27	2		362	781	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33290679	33290684	+	5_prime_UTR_variant	5'UTR	DEL	CAGAAC	CAGAAC	-	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	82	428	0	ENST00000374542.5:c.-98_-93del		p.*33*	ENST00000374542	NM_001141970.1	-/740		1/8	1	2	FACETS	0.81	0.714	0.913	0.81	0.714	0.913	CLONAL	1	TRUE	1	0.27	2		428	750	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609761	117609761	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	69	293	0	ENST00000368508.3:c.6938A>C	p.Lys2313Thr	p.K2313T	ENST00000368508	NM_002944.2	2313	aAa/aCa	43/43	1	2	FACETS	0.754	0.656	0.86	0.754	0.656	0.86	SUBCLONAL	1	TRUE	1	0.27	2		293	678	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687392	117687392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	63	200	0	ENST00000368508.3:c.2659G>A	p.Ala887Thr	p.A887T	ENST00000368508	NM_002944.2	887	Gca/Aca	18/43	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.27	2		200	421	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527319	157527319	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	52	224	0	ENST00000346085.5:c.5044C>A	p.Leu1682Ile	p.L1682I	ENST00000346085	NM_020732.3	1682	Ctt/Att	20/20	1	2	FACETS	0.911	0.777	1	0.911	0.777	1	CLONAL	1	TRUE	1	0.27	2		224	423	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527367	157527367	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	64	286	0	ENST00000346085.5:c.5092C>A	p.Leu1698Ile	p.L1698I	ENST00000346085	NM_020732.3	1698	Ctt/Att	20/20	1	2	FACETS	0.944	0.819	1	0.944	0.819	1	CLONAL	1	TRUE	1	0.27	2		286	502	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527434	157527434	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs757383409	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	48	294	0	ENST00000346085.5:c.5159A>G	p.Asp1720Gly	p.D1720G	ENST00000346085	NM_020732.3	1720	gAc/gGc	20/20	1	2	FACETS	0.665	0.562	0.778	0.665	0.562	0.778	SUBCLONAL	1	TRUE	1	0.27	2		294	535	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431644	6431644	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	71	307	0	ENST00000356142.4:c.197G>T	p.Arg66Ile	p.R66I	ENST00000356142	NM_018890.3	66	aGa/aTa	3/7	1	2	FACETS	0.924	0.808	1	0.924	0.808	1	CLONAL	1	TRUE	1	0.27	2		307	569	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978813	13978813	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	84	327	0	ENST00000405192.2:c.294A>C	p.Glu98Asp	p.E98D	ENST00000405192	NM_001163147.1	98	gaA/gaC	6/12	1	2	FACETS	0.842	0.743	0.948	0.842	0.743	0.948	CLONAL	1	TRUE	1	0.27	2		327	739	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55225392	55225392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	72	314	0	ENST00000275493.2:c.1244C>T	p.Thr415Met	p.T415M	ENST00000275493	NM_005228.3	415	aCg/aTg	11/28	1	2	FACETS	0.837	0.732	0.951	0.837	0.732	0.951	CLONAL	1	TRUE	1	0.27	2		314	637	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509270	106509270	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	119	421	0	ENST00000359195.3:c.1264G>T	p.Asp422Tyr	p.D422Y	ENST00000359195	NM_002649.2	422	Gac/Tac	2/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.27	2		421	826	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873937	151873937	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1475341096	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	83	255	0	ENST00000262189.6:c.8601G>T	p.Lys2867Asn	p.K2867N	ENST00000262189	NM_170606.2	2867	aaG/aaT	38/59	1	2	FACETS	0.971	0.858	1	0.971	0.858	1	CLONAL	1	TRUE	1	0.27	2		255	633	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874428	151874428	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	46	245	0	ENST00000262189.6:c.8110C>A	p.Leu2704Ile	p.L2704I	ENST00000262189	NM_170606.2	2704	Ctt/Att	38/59	1	2	FACETS	0.659	0.555	0.774	0.659	0.555	0.774	SUBCLONAL	1	TRUE	1	0.27	2		245	517	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880211	151880211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1405586437	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	62	251	0	ENST00000262189.6:c.5113C>T	p.Arg1705Cys	p.R1705C	ENST00000262189	NM_170606.2	1705	Cgc/Tgc	35/59	1	2	FACETS	0.871	0.754	0.999	0.871	0.754	0.999	CLONAL	1	TRUE	1	0.27	2		251	527	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346422	152346422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	50	276	0	ENST00000359321.1:c.148G>A	p.Glu50Lys	p.E50K	ENST00000359321	NM_005431.1	50	Gaa/Aaa	3/3	1	2	FACETS	0.772	0.655	0.899	0.772	0.655	0.899	SUBCLONAL	1	TRUE	1	0.27	2		276	480	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38135906	38135906	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	60	315	0	ENST00000317025.8:c.3785A>C	p.Asn1262Thr	p.N1262T	ENST00000317025	NM_023034.1	1262	aAc/aCc	22/24	1	2	FACETS	0.751	0.647	0.864	0.751	0.647	0.864	SUBCLONAL	1	TRUE	1	0.27	2		315	592	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8338987	8338987	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	53	281	1	ENST00000356435.5:c.5314G>T	p.Asp1772Tyr	p.D1772Y	ENST00000356435		1772	Gat/Tat	32/35	1	2	FACETS	0.806	0.688	0.935	0.806	0.688	0.935	CLONAL	1	TRUE	1	0.27	2		282	487	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500913	8500913	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1563873199	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	73	303	0	ENST00000356435.5:c.1969G>T	p.Asp657Tyr	p.D657Y	ENST00000356435		657	Gac/Tac	13/35	1	2	FACETS	0.894	0.782	1	0.894	0.782	1	CLONAL	1	TRUE	1	0.27	2		303	605	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994316	21994316	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	80	463	0	ENST00000579755.1:c.15C>A	p.Phe5Leu	p.F5L	ENST00000579755		5	ttC/ttA	1/3	1		FACETS		0.61	0.786				SUBCLONAL	1	TRUE	1	0.27	2		463	853	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342796	87342796	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	62	269	0	ENST00000277120.3:c.1081C>A	p.Leu361Ile	p.L361I	ENST00000277120		361	Cta/Ata	9/19	1	2	FACETS	0.892	0.771	1	0.892	0.771	1	CLONAL	1	TRUE	1	0.27	2		269	515	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215899	98215899	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	90	435	0	ENST00000331920.6:c.3310T>G	p.Phe1104Val	p.F1104V	ENST00000331920	NM_000264.3	1104	Ttt/Gtt	20/24	1	2	FACETS	0.91	0.807	1	0.91	0.807	1	CLONAL	1	TRUE	1	0.27	2		435	733	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564380	139564380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	138	658	1	ENST00000308874.7:c.328C>T	p.Pro110Ser	p.P110S	ENST00000308874		110	Cca/Tca	6/10	1	2	FACETS	0.876	0.795	0.961	0.876	0.795	0.961	CLONAL	1	TRUE	1	0.27	2		659	1167	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1327767	1327767	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	93	394	0	ENST00000400841.2:c.114T>A	p.Asn38Lys	p.N38K	ENST00000400841		38	aaT/aaA	2/6	1	1	FACETS	0.86	0.765	0.961	0.86	0.765	0.961	CLONAL	1	TRUE	0	0.27	1		394	693	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966702	44966702	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	57	167	0	ENST00000377967.4:c.3926C>T	p.Ala1309Val	p.A1309V	ENST00000377967	NM_021140.2	1309	gCt/gTt	27/29	1	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.27	1		167	294	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171417	123171417	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	74	157	0	ENST00000218089.9:c.329G>A	p.Arg110Gln	p.R110Q	ENST00000218089	NM_001042749.1	110	cGa/cAa	6/35	1	1	FACETS	0.806	0.713	0.905	1	0.979	1	CLONAL	2	TRUE	0	0.27	1		157	294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0048766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	86	932	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.229317884131578	2		934	717	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0048766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	60	558	1	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.229317884131578	2		559	520	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0048766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	26	305	0	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	1	2	FACETS	0.671	0.532	0.83	0.671	0.532	0.83	SUBCLONAL	1	TRUE	1	0.229317884131578	2		305	338	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346648	89346648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778906199	NA	P-0048766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	79	617	0	ENST00000301030.4:c.6302G>A	p.Ser2101Asn	p.S2101N	ENST00000301030	NM_001256183.1	2101	aGc/aAc	9/13	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.229317884131578	2		617	663	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0048767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	176	577	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.169699078390336	5	FACETS	1	0.976	1	0.744	0.691	0.799	INDETERMINATE	2	TRUE	2	0.593381266375661	5		577	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0048767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	312	823	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.593381266375661	2	FACETS	0.878	0.837	0.919	0.878	0.837	0.919	CLONAL	2	TRUE	0	0.593381266375661	2		823	599	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971039	21971058	+	frameshift_variant	Frame_Shift_Del	DEL	GCACGTCCAGCCGCGCCCCG	GCACGTCCAGCCGCGCCCCG	-	novel	NA	P-0048767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	445	526	0	ENST00000304494.5:c.300_319del	p.Gly101ArgfsTer12	p.G101Rfs*12	ENST00000304494	NM_000077.4	100	gcCGGGGCGCGGCTGGACGTGCgc/gcgc	2/3	0.593381266375661	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.593381266375661	2		526	750	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100181	27100182	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCA	rs374564889	NA	P-0048769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	269	540	0	ENST00000324856.7:c.3999_4001dup	p.Gln1334dup	p.Q1334dup	ENST00000324856	NM_006015.4	1334	ccg/ccGCAg	16/20	0.692983474469458	2	FACETS	1	0.993	1	0.688	0.652	0.725	CLONAL	1	TRUE	0	0.692983474469458	2		540	564	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003374	42003374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372252914	NA	P-0048769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	468	462	0	ENST00000219905.7:c.2911C>T	p.Arg971Trp	p.R971W	ENST00000219905	NM_001164273.1	971	Cgg/Tgg	8/24	0.692983474469458	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.692983474469458	2		462	667	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164911	106164911	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs367866583	NA	P-0048769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	470	346	0	ENST00000380013.4:c.3779A>G	p.Asn1260Ser	p.N1260S	ENST00000380013	NM_001127208.2	1260	aAt/aGt	6/11	0.692983474469458	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.692983474469458	2		346	662	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151882673	151882673	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs762509937	NA	P-0048769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	68	387	0	ENST00000262189.6:c.5052del	p.Ala1685GlnfsTer32	p.A1685Qfs*32	ENST00000262189	NM_170606.2	1684	aaA/aa	34/59	0.692983474469458	2	FACETS	0.388	0.338	0.442	0.194	0.169	0.221	SUBCLONAL	1	TRUE	0	0.692983474469458	2		387	506	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2218138	2218138	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs369733800	NA	P-0048769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	633	847	0	ENST00000326181.6:c.200C>G	p.Ala67Gly	p.A67G	ENST00000326181	NM_032271.2	67	gCc/gGc	4/21	0.692983474469458	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.692983474469458	2		847	820	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149243895	149243895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048769-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	229	413	0	ENST00000360632.3:c.923G>A	p.Arg308Lys	p.R308K	ENST00000360632	NM_015472.4	308	aGg/aAg	6/7	0.692983474469458	3	FACETS	0.846	0.788	0.906	0.282	0.262	0.302	CLONAL	1	TRUE	0	0.692983474469458	3		413	1052	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936995	48936995	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778842	NA	P-0048770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	202	479	0	ENST00000267163.4:c.763C>T	p.Arg255Ter	p.R255*	ENST00000267163	NM_000321.2	255	Cga/Tga	8/27	1	2	FACETS	0.885	0.827	0.943	0.885	0.827	0.943	CLONAL	1	TRUE	1	0.890299227248724	2		479	513	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037891	49037892	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0048770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	206	379	0	ENST00000267163.4:c.2133_2134del	p.Ile711MetfsTer9	p.I711Mfs*9	ENST00000267163	NM_000321.2	711	ATa/a	21/27	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.890299227248724	2		379	461	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935502	49935502	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	292	741	0	ENST00000296474.3:c.1862A>C	p.Lys621Thr	p.K621T	ENST00000296474	NM_002447.2	621	aAg/aCg	5/20	1	2	FACETS	0.626	0.589	0.663	0.626	0.589	0.663	SUBCLONAL	1	TRUE	1	0.890299227248724	2		741	1048	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980434	55980434	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0048770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	54	219	0	ENST00000263923.4:c.659-2A>T		p.X220_splice	ENST00000263923	NM_002253.2	220			1	2	FACETS	0.408	0.351	0.47	0.408	0.351	0.47	SUBCLONAL	1	TRUE	1	0.890299227248724	2		219	297	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	252	576	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.966	0.908	1	1	0.995	1	CLONAL	2	FALSE	1	0.374420505292646	2		576	697	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391956	139391956	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	384	781	0	ENST00000277541.6:c.6235G>A	p.Val2079Met	p.V2079M	ENST00000277541	NM_017617.3	2079	Gtg/Atg	34/34	0.374420505292646	1	FACETS	0.98	0.936	1	1	0.997	1	CLONAL	2	FALSE	0	0.374420505292646	1		781	851	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101061	27101062	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0048772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	483	683	0	ENST00000324856.7:c.4344_4345dup	p.Gly1449GlufsTer33	p.G1449Efs*33	ENST00000324856	NM_006015.4	1448	gca/gcAGa	18/20	0.316835274718586	2	FACETS	0.914	0.879	0.949	1	0.996	1	CLONAL	3	FALSE	0	0.374420505292646	2		683	941	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572954	41572954	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	324	662	0	ENST00000263253.7:c.5239C>T	p.Gln1747Ter	p.Q1747*	ENST00000263253	NM_001429.3	1747	Cag/Tag	31/31	1	2	FACETS	0.888	0.84	0.936	1	0.996	1	CLONAL	2	FALSE	1	0.374420505292646	2		662	975	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356163	66356163	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	50	397	0	ENST00000273854.3:c.1334A>G	p.Asn445Ser	p.N445S	ENST00000273854	NM_004439.5	445	aAt/aGt	5/18	1	2	FACETS	0.481	0.408	0.562	0.481	0.408	0.562	SUBCLONAL	1	FALSE	1	0.374420505292646	2		397	555	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023927	27023949	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCGGCGGCCGCCTCGGGAGG	GCGGCGGCGGCCGCCTCGGGAGG	AGGC	novel	NA	P-0048772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	109	175	3	ENST00000324856.7:c.1033_1055delinsAGGC	p.Ala345ArgfsTer12	p.A345Rfs*12	ENST00000324856	NM_006015.4	345	GCGGCGGCGGCCGCCTCGGGAGGg/AGGCg	1/20	0.316835274718586	2	FACETS	0.774	0.702	0.85	0.774	0.702	0.85	SUBCLONAL	2	FALSE	0	0.374420505292646	2		178	376	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	629	301	0				ENST00000310581	NM_198253.2	-/1132			0.726620635314512	6	FACETS	0.951	0.921	0.981	0.951	0.921	0.981	CLONAL	4	TRUE	2	0.726620635314512	6		301	1116	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0048773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	1108	697	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.613794737651786	4	FACETS	0.998	0.983	1			1	CLONAL	4	TRUE	NA	0.726620635314512	4		697	1319	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481806	56481806	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	464	472	0	ENST00000267101.3:c.734C>T	p.Ala245Val	p.A245V	ENST00000267101	NM_001982.3	245	gCc/gTc	7/28	0.726620635314512	3	FACETS	0.993	0.955	1	0.993	0.955	1	CLONAL	2	TRUE	1	0.726620635314512	3		472	877	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923093	48923094	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0048773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	121	262	0	ENST00000267163.4:c.543_544del	p.Ser182TyrfsTer2	p.S182Yfs*2	ENST00000267163	NM_000321.2	181	ATa/a	6/27	0.726620635314512	3	FACETS	0.908	0.838	0.978	0.908	0.838	0.978	CLONAL	2	TRUE	1	0.726620635314512	3		262	250	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037866	49037866	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0048773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	83	251	1	ENST00000267163.4:c.2107-1G>T		p.X703_splice	ENST00000267163	NM_000321.2	703			0.726620635314512	3	FACETS	1	0.92	1	0.519	0.463	0.578	CLONAL	1	TRUE	1	0.726620635314512	3		252	300	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464961	120464961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764895571	NA	P-0048773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	164	440	0	ENST00000256646.2:c.5111G>A	p.Arg1704His	p.R1704H	ENST00000256646	NM_024408.3	1704	cGt/cAt	28/34	1	2	FACETS	0.873	0.807	0.941	0.873	0.807	0.941	CLONAL	1	TRUE	1	0.726620635314512	2		440	517	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350517	15350517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	365	730	1	ENST00000263377.2:c.3398C>T	p.Pro1133Leu	p.P1133L	ENST00000263377	NM_058243.2	1133	cCc/cTc	16/20	0.625921702209465	4	FACETS	1	0.989	1	0.576	0.545	0.607	CLONAL	1	TRUE	2	0.726620635314512	4		731	1507	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50816350	50816350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868852255	NA	P-0048773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	223	290	0	ENST00000398568.2:c.1790C>T	p.Ser597Phe	p.S597F	ENST00000398568	NM_001042412.1	597	tCt/tTt	10/18	0.726620635314512	2	FACETS	0.927	0.884	0.969	0.927	0.884	0.969	CLONAL	2	TRUE	0	0.726620635314512	2		290	331	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748081	72748081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	247	516	0	ENST00000357731.5:c.97C>T	p.Pro33Ser	p.P33S	ENST00000357731	NM_173808.2	33	Ccg/Tcg	1/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.726620635314512	2		516	634	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717685	89717708	+	inframe_deletion	In_Frame_Del	DEL	AGTTCATGTACTTTGAGTTCCCTC	AGTTCATGTACTTTGAGTTCCCTC	-	novel	NA	P-0048773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	240	372	0	ENST00000371953.3:c.712_735del	p.Phe238_Gln245del	p.F238_Q245del	ENST00000371953	NM_000314.4	237	aAGTTCATGTACTTTGAGTTCCCTCag/aag	7/9	0.726620635314512	2	FACETS	0.912	0.871	0.953	0.912	0.871	0.953	CLONAL	2	TRUE	0	0.726620635314512	2		372	362	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574748	95574748	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	135	377	0	ENST00000393063.1:c.2349T>G	p.Asp783Glu	p.D783E	ENST00000393063	NM_030621.3	783	gaT/gaG	16/28	0.726620635314512	3	FACETS	0.984	0.899	1	0.492	0.449	0.536	CLONAL	1	TRUE	1	0.726620635314512	3		377	515	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924231	11924231	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	25	31	0	ENST00000353533.5:c.28G>T	p.Gly10Cys	p.G10C	ENST00000353533	NM_003010.3	10	Ggc/Tgc	1/11	0.726620635314512	4	FACETS	1	0.938	1			1	CLONAL	1	TRUE	NA	0.726620635314512	4		31	80	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349738	15349738	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	641	789	0	ENST00000263377.2:c.3836C>G	p.Ala1279Gly	p.A1279G	ENST00000263377	NM_058243.2	1279	gCa/gGa	19/20	0.625921702209465	4	FACETS	0.968	0.933	1	0.968	0.933	1	CLONAL	2	TRUE	2	0.726620635314512	4		789	1574	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147720	61147735	+	frameshift_variant	Frame_Shift_Del	DEL	GAGAGACCAAGACCTG	GAGAGACCAAGACCTG	-	novel	NA	P-0048773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	105	269	0	ENST00000295025.8:c.1031_1046del	p.Glu344ValfsTer25	p.E344Vfs*25	ENST00000295025	NM_002908.2	344	GAGAGACCAAGACCTGgt/gt	10/11	0.726620635314512	2	FACETS	0.84	0.779	0.9	0.84	0.779	0.9	CLONAL	2	TRUE	0	0.726620635314512	2		269	172	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513586	41513586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148575477	NA	P-0048773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	199	557	0	ENST00000263253.7:c.490G>A	p.Gly164Arg	p.G164R	ENST00000263253	NM_001429.3	164	Gga/Aga	2/31	1	2	FACETS	0.973	0.908	1	0.973	0.908	1	CLONAL	1	TRUE	1	0.726620635314512	2		557	563	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935631	13935631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	322	402	2	ENST00000405192.2:c.1225C>A	p.Pro409Thr	p.P409T	ENST00000405192	NM_001163147.1	409	Cca/Aca	12/12	0.726620635314512	3	FACETS	0.989	0.944	1	0.989	0.944	1	CLONAL	2	TRUE	1	0.726620635314512	3		404	611	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798773	135798773	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	166	217	0	ENST00000298552.3:c.470T>G	p.Ile157Ser	p.I157S	ENST00000298552	NM_001162426.1	157	aTt/aGt	6/23	0.726620635314512	3	FACETS	0.903	0.843	0.963	0.903	0.843	0.963	CLONAL	2	TRUE	1	0.726620635314512	3		217	345	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0048774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	119	327	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.743	0.672	0.816	0.743	0.672	0.816	SUBCLONAL	1	TRUE	1	0.548768774289862	2		327	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0048774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	239	487	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.531311695359199	1	FACETS	0.929	0.873	0.987	0.929	0.873	0.987	CLONAL	1	TRUE	0	0.548768774289862	1		487	680	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921567	178921567	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553821144	NA	P-0048774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	20	277	0	ENST00000263967.3:c.1049A>G	p.Asp350Gly	p.D350G	ENST00000263967	NM_006218.2	350	gAc/gGc	5/21	1	2	FACETS	0.228	0.174	0.292	0.228	0.174	0.292	SUBCLONAL	1	TRUE	1	0.548768774289862	2		277	319	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152018	55152018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs79948560	NA	P-0048774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	33	434	0	ENST00000257290.5:c.2450G>A	p.Arg817His	p.R817H	ENST00000257290	NM_006206.4	817	cGt/cAt	18/23	1	2	FACETS	0.201	0.163	0.245	0.201	0.163	0.245	SUBCLONAL	1	TRUE	1	0.548768774289862	2		434	597	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217556	142217557	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1268253442	NA	P-0048774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	62	390	0	ENST00000350721.4:c.5440dup	p.Arg1814LysfsTer8	p.R1814Kfs*8	ENST00000350721	NM_001184.3	1814	aga/aAga	32/47	1	2	FACETS	0.409	0.353	0.469	0.409	0.353	0.469	SUBCLONAL	1	TRUE	1	0.548768774289862	2		390	553	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985558	60985558	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	206	558	0	ENST00000333681.4:c.342G>T	p.Glu114Asp	p.E114D	ENST00000333681		114	gaG/gaT	2/3	0.531311695359199	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.548768774289862	1		558	520	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276868	15276868	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	78	825	0	ENST00000263388.2:c.5397T>G	p.Cys1799Trp	p.C1799W	ENST00000263388	NM_000435.2	1799	tgT/tgG	30/33	0.525987110166931	2	FACETS	0.277	0.242	0.314	0.139	0.121	0.157	SUBCLONAL	1	TRUE	0	0.548768774289862	2		825	1026	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39283859	39283859	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	46	388	1	ENST00000402219.2:c.494C>A	p.Ala165Glu	p.A165E	ENST00000402219	NM_005633.3	165	gCa/gAa	4/23	1	2	FACETS	0.409	0.345	0.479	0.409	0.345	0.479	SUBCLONAL	1	TRUE	1	0.548768774289862	2		389	410	SUCCESS
APC	324	MSKCC	GRCh37	5	112173880	112173880	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	97	321	0	ENST00000257430.4:c.2590del	p.His864IlefsTer52	p.H864Ifs*52	ENST00000257430	NM_000038.5	863	taC/ta	16/16	1	2	FACETS	0.918	0.825	1	0.918	0.825	1	CLONAL	1	TRUE	1	0.548768774289862	2		321	385	SUCCESS
APC	324	MSKCC	GRCh37	5	112175494	112175495	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCAGCTCCGTTCAGAGTGAACCATGCAGTGGAATGGTAAGTG	novel	NA	P-0048774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	52	326	0	ENST00000257430.4:c.4206_4248dup	p.Ile1417GlnfsTer6	p.I1417Qfs*6	ENST00000257430	NM_000038.5	1401	-/GCCAGCTCCGTTCAGAGTGAACCATGCAGTGGAATGGTAAGTG	16/16	1	2	FACETS	0.401	0.341	0.466	0.401	0.341	0.466	SUBCLONAL	1	TRUE	1	0.548768774289862	2		326	473	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779803	135779803	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	84	424	0	ENST00000298552.3:c.2036T>G	p.Phe679Cys	p.F679C	ENST00000298552	NM_001162426.1	679	tTt/tGt	16/23	1	2	FACETS	0.534	0.472	0.6	0.534	0.472	0.6	SUBCLONAL	1	TRUE	1	0.548768774289862	2		424	573	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102136	27102137	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0048775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	112	453	0	ENST00000324856.7:c.5063_5064dup	p.Asp1689Ter	p.D1689*	ENST00000324856	NM_006015.4	1688	tta/tTAta	19/20	0.442123543821027	2	FACETS	0.936	0.846	1	0.468	0.423	0.516	CLONAL	1	TRUE	0	0.442123543821027	2		453	541	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197120	26197120	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	137	630	0	ENST00000356476.2:c.359T>G	p.Ile120Ser	p.I120S	ENST00000356476		120	aTc/aGc	1/1	0.34351983589499	4	FACETS	0.992	0.902	1	0.496	0.451	0.544	CLONAL	1	TRUE	2	0.442123543821027	4		630	901	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	30	576	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.463	0.375	0.56	0.463	0.375	0.56	SUBCLONAL	1	FALSE	1	0.614570281494586	2		576	211	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0048776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	125	974	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	0.535	0.485	0.589	0.535	0.485	0.589	SUBCLONAL	1	FALSE	1	0.614570281494586	2		974	760	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0048776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	33	436	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.36	0.294	0.434	0.36	0.294	0.434	SUBCLONAL	1	FALSE	1	0.614570281494586	2		436	298	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0048776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	47	416	2	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	0.433	0.367	0.506	0.433	0.367	0.506	SUBCLONAL	1	FALSE	1	0.614570281494586	2		418	353	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0048776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	38	291	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	0.465	0.386	0.552	0.465	0.386	0.552	SUBCLONAL	1	FALSE	1	0.614570281494586	2		291	266	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	46	234	1	ENST00000324856.7:c.1010G>A	p.Trp337Ter	p.W337*	ENST00000324856	NM_006015.4	337	tGg/tAg	1/20	1	2	FACETS	0.509	0.431	0.594	0.509	0.431	0.594	SUBCLONAL	1	FALSE	1	0.614570281494586	2		235	294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578177	7578177	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	344	392	0	ENST00000269305.4:c.672G>C	p.Glu224Asp	p.E224D	ENST00000269305	NM_001126112.2	224	gaG/gaC	6/11	0.423085628345438	3	FACETS	0.922	0.881	0.964	0.922	0.881	0.964	CLONAL	3	TRUE	0	0.459013126502106	3		392	666	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782087	9782087	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	254	560	1	ENST00000377346.4:c.2110C>T	p.Gln704Ter	p.Q704*	ENST00000377346	NM_005026.3	704	Cag/Tag	17/24	0.352552970669402	4	FACETS	0.805	0.754	0.858	0.805	0.754	0.858	CLONAL	2	TRUE	2	0.459013126502106	4		561	1003	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	186	301	0				ENST00000310581	NM_198253.2	-/1132			0.572118277799694	6	FACETS	0.788	0.729	0.848	0.525	0.486	0.566	SUBCLONAL	2	TRUE	3	0.834703774857132	6		301	755	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	22	576	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.526649069326108	1	FACETS	0.427	0.341	0.519	0.427	0.341	0.519	SUBCLONAL	1	TRUE	0	0.834703774857132	1		576	72	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652171	36652171	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	522	573	0	ENST00000244741.5:c.293C>A	p.Ser98Ter	p.S98*	ENST00000244741	NM_000389.4	98	tCa/tAa	2/3	0.38848849779535	4	FACETS	0.886	0.85	0.922	0.886	0.85	0.922	INDETERMINATE	2	TRUE	2	0.834703774857132	4		573	1295	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131205	17131205	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs757060348	NA	P-0048778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	438	552	1	ENST00000285071.4:c.247G>A	p.Glu83Lys	p.E83K	ENST00000285071	NM_144997.5	83	Gag/Aag	4/14	0.399128037622061	6	FACETS	0.979	0.938	1	0.734	0.703	0.765	INDETERMINATE	3	TRUE	2	0.834703774857132	6		553	954	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270593	98270595	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs756897237	NA	P-0048778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	13	91	0	ENST00000331920.6:c.49_51del	p.Gly17del	p.G17del	ENST00000331920	NM_000264.3	17	GGC/-	1/24	0.579645744111608	5	FACETS	0.349	0.249	0.471	0.07	0.049	0.095	SUBCLONAL	1	TRUE	0	0.834703774857132	5		91	201	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175942	176175942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs964768927	NA	P-0048778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	110	84	1	ENST00000367669.3:c.173C>T	p.Ser58Leu	p.S58L	ENST00000367669	NM_022457.5	58	tCg/tTg	1/20	0.448395238374239	6	FACETS	1	0.924	1	0.51	0.463	0.558	INDETERMINATE	2	TRUE	2	0.834703774857132	6		85	345	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0048778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	553	554	1	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.564745480703192	4	FACETS	1	0.996	1	0.842	0.821	0.862	CLONAL	3	TRUE	0	0.834703774857132	4		555	722	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004817	16004817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	127	401	0	ENST00000268712.3:c.2437C>T	p.Pro813Ser	p.P813S	ENST00000268712	NM_006311.3	813	Ccc/Tcc	20/46	0.399128037622061	6	FACETS	0.887	0.824	0.949	0.887	0.824	0.949	INDETERMINATE	4	TRUE	2	0.834703774857132	6		401	229	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004664	16004664	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	105	378	0	ENST00000268712.3:c.2590C>T	p.Gln864Ter	p.Q864*	ENST00000268712	NM_006311.3	864	Cag/Tag	20/46	0.399128037622061	6	FACETS	1	0.969	1	0.835	0.768	0.902	INDETERMINATE	3	TRUE	2	0.834703774857132	6		378	201	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426859	49426859	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	245	414	0	ENST00000301067.7:c.11629C>T	p.Gln3877Ter	p.Q3877*	ENST00000301067	NM_003482.3	3877	Cag/Tag	39/54	0.845583269189893	4	FACETS	0.826	0.777	0.876	0.826	0.777	0.876	CLONAL	2	TRUE	2	0.834703774857132	4		414	652	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871770	12871770	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	36	101	0	ENST00000228872.4:c.487C>G	p.Gln163Glu	p.Q163E	ENST00000228872	NM_004064.3	163	Caa/Gaa	2/3	0.38848849779535	4	FACETS	0.833	0.707	0.964	0.833	0.707	0.964	INDETERMINATE	2	TRUE	2	0.834703774857132	4		101	95	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741564	17741564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757423869	NA	P-0048778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1309	277	431	0	ENST00000250003.3:c.235G>A	p.Glu79Lys	p.E79K	ENST00000250003	NM_002478.4	79	Gag/Aag	1/3	0.845583269189893	4	FACETS	0.768	0.719	0.818			1	SUBCLONAL	1	TRUE	NA	0.834703774857132	4		431	1586	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909973	100909973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	69	230	0	ENST00000325455.5:c.2676G>C	p.Leu892Phe	p.L892F	ENST00000325455	NM_001202474.3	892	ttG/ttC	8/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.834703774857132	2		230	121	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131214	17131214	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	485	592	0	ENST00000285071.4:c.238G>C	p.Asp80His	p.D80H	ENST00000285071	NM_144997.5	80	Gac/Cac	4/14	0.399128037622061	6	FACETS	1	0.963	1	0.752	0.722	0.782	INDETERMINATE	3	TRUE	2	0.834703774857132	6		592	1031	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42759149	42759149	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0048778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	349	299	0	ENST00000222329.4:c.3G>A	p.Met1?	p.M1?	ENST00000222329	NM_006494.2	1	atG/atA	1/4	0.845583269189893	4	FACETS	0.925	0.881	0.97	0.925	0.881	0.97	CLONAL	2	TRUE	2	0.834703774857132	4		299	829	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159072	24159072	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	43	369	0	ENST00000263121.7:c.747del	p.Thr250ArgfsTer17	p.T250Rfs*17	ENST00000263121	NM_003073.3	248	taC/ta	6/9	0.399128037622061	6	FACETS	1	0.947	1	0.326	0.275	0.381	INDETERMINATE	1	TRUE	2	0.834703774857132	6		369	211	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205751	128205751	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	597	584	0	ENST00000341105.2:c.124C>G	p.Pro42Ala	p.P42A	ENST00000341105	NM_032638.4	42	Cca/Gca	2/6	0.675503893519804	4	FACETS	0.848	0.815	0.88	0.848	0.815	0.88	CLONAL	2	TRUE	2	0.834703774857132	4		584	1548	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2966410	2966410	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	82	485	0	ENST00000396946.4:c.1770C>G	p.Asp590Glu	p.D590E	ENST00000396946	NM_032415.4	590	gaC/gaG	14/25	0.498728575915897	6	FACETS	0.907	0.801	1	0.302	0.267	0.341	INDETERMINATE	1	TRUE	3	0.834703774857132	6		485	578	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918338	44918338	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	22	136	1	ENST00000377967.4:c.963G>A	p.Trp321Ter	p.W321*	ENST00000377967	NM_021140.2	321	tgG/tgA	11/29	0.845583269189893	2	FACETS	0.976	0.858	1			1	CLONAL	2	TRUE	NA	0.834703774857132	2		137	27	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0048780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	49	461	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.948	0.802	1	0.948	0.802	1	CLONAL	1	TRUE	1	0.15	2		462	689	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260456	16260456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201347979	NA	P-0048780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	26	311	0	ENST00000375759.3:c.7721C>T	p.Pro2574Leu	p.P2574L	ENST00000375759	NM_015001.2	2574	cCg/cTg	11/15	1	2	FACETS	0.784	0.62	0.973	0.784	0.62	0.973	CLONAL	1	TRUE	1	0.15	2		311	442	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988788	41988788	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	27	278	0	ENST00000219905.7:c.1583del	p.Asn528MetfsTer19	p.N528Mfs*19	ENST00000219905	NM_001164273.1	527	gAa/ga	3/24	1	2	FACETS	0.804	0.639	0.993	0.804	0.639	0.993	CLONAL	1	TRUE	1	0.15	2		278	448	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12043155	12043155	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0048780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	14	88	0	ENST00000353533.5:c.1041-1G>A		p.X347_splice	ENST00000353533	NM_003010.3	347			1	2	FACETS	1	0.727	1	1	0.727	1	CLONAL	1	TRUE	1	0.15	2		88	186	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0048781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	124	327	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.995	0.906	1	0.995	0.906	1	CLONAL	1	TRUE	1	0.529130268853707	2		327	471	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606696	29606696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769910087	NA	P-0048781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	155	376	0	ENST00000389048.3:c.1184G>A	p.Arg395His	p.R395H	ENST00000389048	NM_004304.4	395	cGt/cAt	5/29	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.529130268853707	2		376	572	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732996	30732996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893809	NA	P-0048781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	298	346	1	ENST00000295754.5:c.1609C>T	p.Arg537Cys	p.R537C	ENST00000295754	NM_003242.5	537	Cgc/Tgc	7/7	0.526331602530744	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.529130268853707	2		347	555	SUCCESS
APC	324	MSKCC	GRCh37	5	112175621	112175622	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	72	248	0	ENST00000257430.4:c.4333dup	p.Thr1445AsnfsTer10	p.T1445Nfs*10	ENST00000257430	NM_000038.5	1444	caa/cAaa	16/16	0.529130268853707	1	FACETS	0.886	0.786	0.989	0.886	0.786	0.989	CLONAL	1	TRUE	0	0.529130268853707	1		248	226	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0048782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	299	572	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	0.399616301087192	3	FACETS	0.935	0.883	0.988	0.935	0.883	0.988	CLONAL	2	TRUE	1	0.434608933798347	3		572	896	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578291	226578291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757712451	NA	P-0048782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	99	435	0	ENST00000366794.5:c.437C>T	p.Pro146Leu	p.P146L	ENST00000366794	NM_001618.3	146	cCg/cTg	4/23	0.399616301087192	3	FACETS	0.835	0.746	0.93	0.418	0.373	0.465	CLONAL	1	TRUE	1	0.434608933798347	3		435	664	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0048782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	326	402	0	ENST00000269305.4:c.673-1G>C		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.434608933798347	3	FACETS	0.98	0.936	1	0.98	0.936	1	CLONAL	3	TRUE	0	0.434608933798347	3		402	621	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871940	45871940	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142462393	NA	P-0048782-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	163	529	0	ENST00000391945.4:c.308C>T	p.Pro103Leu	p.P103L	ENST00000391945	NM_000400.3	103	cCg/cTg	5/23	0.399616301087192	3	FACETS	0.985	0.904	1	0.493	0.452	0.535	CLONAL	1	TRUE	1	0.434608933798347	3		529	927	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0048783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	144	347	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		347	516	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219357	1219357	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730881970	NA	P-0048783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	252	638	0	ENST00000326873.7:c.409C>T	p.Gln137Ter	p.Q137*	ENST00000326873	NM_000455.4	137	Cag/Tag	3/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		638	698	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628857	187628858	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	162	411	0	ENST00000441802.2:c.2124dup	p.Val709CysfsTer9	p.V709Cfs*9	ENST00000441802	NM_005245.3	708	-/T	2/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		411	656	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171377	123171377	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	115	224	0	ENST00000218089.9:c.289T>A	p.Ser97Thr	p.S97T	ENST00000218089	NM_001042749.1	97	Tcg/Acg	6/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		224	395	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098586	108098591	+	frameshift_variant	Frame_Shift_Del	DEL	AAAATA	AAAATA	T	novel	NA	P-0048783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	63	184	0	ENST00000278616.4:c.156_161delinsT	p.Lys53PhefsTer8	p.K53Ffs*8	ENST00000278616	NM_000051.3	52	ggAAAATAt/ggTt	3/63	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		184	302	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0048784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	40	302	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.243741484716806	2		302	321	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0048784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	25	582	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.6	0.473	0.746	0.6	0.473	0.746	SUBCLONAL	1	TRUE	1	0.243741484716806	2		582	342	SUCCESS
APC	324	MSKCC	GRCh37	5	112175358	112175358	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	54	153	0	ENST00000257430.4:c.4067C>A	p.Ser1356Ter	p.S1356*	ENST00000257430	NM_000038.5	1356	tCa/tAa	16/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.243741484716806	2		153	312	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577138	7577138	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587780075	NA	P-0048784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	77	393	0	ENST00000269305.4:c.800G>C	p.Arg267Pro	p.R267P	ENST00000269305	NM_001126112.2	267	cGg/cCg	8/11	0.243741484716806	1	FACETS	0.892	0.784	1	0.892	0.784	1	CLONAL	1	TRUE	0	0.243741484716806	1		393	622	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	24	150	0	ENST00000257430.4:c.4057del	p.Glu1353AsnfsTer62	p.E1353Nfs*62	ENST00000257430	NM_000038.5	1353	Gaa/aa	16/16	1	2	FACETS	0.679	0.533	0.847	0.679	0.533	0.847	SUBCLONAL	1	TRUE	1	0.243741484716806	2		150	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578551	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	223	597	0	ENST00000269305.4:c.379T>A	p.Ser127Thr	p.S127T	ENST00000269305	NM_001126112.2	127	Tcc/Acc	5/11	0.493011743853282	2	FACETS	1	0.993	1	0.72	0.678	0.762	CLONAL	1	TRUE	0	0.637573010919159	2		597	486	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533774	533774	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	194	531	1	ENST00000451590.1:c.282C>A	p.His94Gln	p.H94Q	ENST00000451590	NM_001130442.1	94	caC/caA	3/5	0.329136919158189	4	FACETS	0.825	0.768	0.884	0.825	0.768	0.884	INDETERMINATE	2	TRUE	2	0.637573010919159	4		532	604	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643568	52643568	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	127	308	1	ENST00000394830.3:c.2328del	p.Leu776PhefsTer2	p.L776Ffs*2	ENST00000394830	NM_018313.4	776	ttG/tt	17/30	0.486840386631348	2	FACETS	1	0.988	1	0.749	0.692	0.806	CLONAL	1	TRUE	0	0.637573010919159	2		309	266	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0048786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	120	351	0				ENST00000310581	NM_198253.2	-/1132			0.637375414816299	3	FACETS	0.97	0.894	1	0.97	0.894	1	CLONAL	2	TRUE	1	0.637375414816299	3		351	256	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294163	1294163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199701877	NA	P-0048786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	138	779	0	ENST00000310581.5:c.838G>A	p.Glu280Lys	p.E280K	ENST00000310581	NM_198253.2	280	Gaa/Aaa	2/16	0.637375414816299	3	FACETS	1	0.93	1	0.51	0.466	0.556	CLONAL	1	TRUE	1	0.637375414816299	3		779	560	SUCCESS
APC	324	MSKCC	GRCh37	5	112175876	112175876	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085992	NA	P-0048786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	88	176	0	ENST00000257430.4:c.4585C>T	p.Gln1529Ter	p.Q1529*	ENST00000257430	NM_000038.5	1529	Cag/Tag	16/16	0.637375414816299	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.637375414816299	3		176	151	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955063	55955063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	90	361	0	ENST00000263923.4:c.3482G>A	p.Gly1161Glu	p.G1161E	ENST00000263923	NM_002253.2	1161	gGa/gAa	26/30	0.637375414816299	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.637375414816299	1		361	183	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273258	198273258	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	155	372	0	ENST00000335508.6:c.952C>T	p.Arg318Ter	p.R318*	ENST00000335508	NM_012433.2	318	Cga/Tga	8/25	0.637375414816299	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.637375414816299	4		372	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	rs786202799	NA	P-0048786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	238	552	0	ENST00000269305.4:c.376-2A>T		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.60508198700648	2	FACETS	0.99	0.944	1	0.99	0.944	1	CLONAL	2	TRUE	0	0.637375414816299	2		552	377	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857530	68857530	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0048786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	59	308	0	ENST00000261769.5:c.2164+1G>A		p.X722_splice	ENST00000261769	NM_004360.3	722			1	2	FACETS	0.873	0.762	0.99	0.873	0.762	0.99	CLONAL	1	TRUE	1	0.637375414816299	2		308	212	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721024	176721024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	170	399	0	ENST00000439151.2:c.6655C>T	p.Arg2219Cys	p.R2219C	ENST00000439151	NM_022455.4	2219	Cgt/Tgt	23/23	0.637375414816299	3	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	1	0.637375414816299	3		399	350	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120386	94120386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	52	198	0	ENST00000369303.4:c.665C>T	p.Ser222Leu	p.S222L	ENST00000369303	NM_004440.3	222	tCa/tTa	3/17	0.130888802719739	4	FACETS	1	0.966	1	0.714	0.618	0.817	INDETERMINATE	1	TRUE	2	0.637375414816299	4		198	187	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031999	26031999	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1411351920	NA	P-0048786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	228	335	0	ENST00000244661.2:c.290G>C	p.Cys97Ser	p.C97S	ENST00000244661	NM_003537.3	97	tGt/tCt	1/1	0.637375414816299	4	FACETS	0.848	0.794	0.903	0.565	0.529	0.602	CLONAL	2	TRUE	1	0.637375414816299	4		335	691	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432719	49432719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1410236197	NA	P-0048786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	131	473	0	ENST00000301067.7:c.8420C>T	p.Ser2807Phe	p.S2807F	ENST00000301067	NM_003482.3	2807	tCc/tTc	34/54	0.637375414816299	3	FACETS	1	0.967	1	0.56	0.511	0.611	CLONAL	1	TRUE	1	0.637375414816299	3		473	484	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587415	29587415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1265291141	NA	P-0048786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	113	297	0	ENST00000356175.3:c.4396C>T	p.Pro1466Ser	p.P1466S	ENST00000356175	NM_000267.3	1466	Cct/Tct	33/57	0.637375414816299	3	FACETS	0.906	0.831	0.982	0.906	0.831	0.982	CLONAL	2	TRUE	1	0.637375414816299	3		297	258	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367293	50367293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	171	306	1	ENST00000331340.3:c.100C>T	p.Pro34Ser	p.P34S	ENST00000331340	NM_006060.4	34	Ccc/Tcc	3/8	0.457100960686644	2	FACETS	0.941	0.887	0.995	0.941	0.887	0.995	CLONAL	2	TRUE	0	0.637375414816299	2		307	285	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256381	16256381	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	191	400	0	ENST00000375759.3:c.3646C>T	p.Gln1216Ter	p.Q1216*	ENST00000375759	NM_015001.2	1216	Caa/Taa	11/15	0.637375414816299	3	FACETS	0.983	0.922	1	0.983	0.922	1	CLONAL	2	TRUE	1	0.637375414816299	3		400	402	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251200	115251200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	811	358	0	ENST00000369535.4:c.526G>A	p.Asp176Asn	p.D176N	ENST00000369535	NM_002524.4	176	Gat/Aat	5/7	0.637375414816299	9	FACETS	1	0.993	1	1	0.993	1	CLONAL	8	TRUE	1	0.637375414816299	9		358	1000	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258746	+	missense_variant	Missense_Mutation	DNP	CA	CA	GT	novel	NA	P-0048786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	712	248	0	ENST00000369535.4:c.36_37delinsAC	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	12	ggTGgt/ggACgt	2/7	0.637375414816299	9	FACETS	1	0.989	1	1	0.989	1	CLONAL	8	TRUE	1	0.637375414816299	9		248	889	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342793	118342793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	75	179	0	ENST00000534358.1:c.919C>T	p.Pro307Ser	p.P307S	ENST00000534358	NM_005933.3	307	Cca/Tca	3/36	0.631511352682135	2	FACETS	0.989	0.905	1	0.989	0.905	1	CLONAL	2	TRUE	0	0.637375414816299	2		179	119	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	461378	461378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	50	200	0	ENST00000399788.2:c.1142C>T	p.Pro381Leu	p.P381L	ENST00000399788	NM_001042603.1	381	cCa/cTa	9/28	0.637375414816299	3	FACETS	0.99	0.851	1	0.495	0.425	0.57	CLONAL	1	TRUE	1	0.637375414816299	3		200	209	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800872	18800872	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	137	314	0	ENST00000266497.5:c.4248A>C	p.Lys1416Asn	p.K1416N	ENST00000266497		1416	aaA/aaC	31/31	0.637375414816299	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.637375414816299	3		314	234	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589353	28589353	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	115	279	0	ENST00000241453.7:c.2694C>A	p.Phe898Leu	p.F898L	ENST00000241453	NM_004119.2	898	ttC/ttA	22/24	0.637375414816299	3	FACETS	0.875	0.802	0.949	0.875	0.802	0.949	CLONAL	2	TRUE	1	0.637375414816299	3		279	272	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339458	339458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1168217580	NA	P-0048786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	116	628	0	ENST00000262320.3:c.2444C>T	p.Thr815Ile	p.T815I	ENST00000262320	NM_003502.3	815	aCc/aTc	10/11	1	2	FACETS	0.892	0.811	0.977	0.892	0.811	0.977	CLONAL	1	TRUE	1	0.637375414816299	2		628	408	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435194	56435194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	117	571	0	ENST00000407977.2:c.1943C>T	p.Ser648Phe	p.S648F	ENST00000407977		648	tCt/tTt	9/10	0.637375414816299	3	FACETS	1	0.964	1	0.56	0.509	0.614	CLONAL	1	TRUE	1	0.637375414816299	3		571	432	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443616	29443617	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0048786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	189	529	0	ENST00000389048.3:c.3600_3601delinsAA	p.Gly1201Arg	p.G1201R	ENST00000389048	NM_004304.4	1200	gcGGgg/gcAAgg	23/29	0.593399617317553	5	FACETS	0.892	0.828	0.958	0.595	0.552	0.639	CLONAL	2	TRUE	2	0.637375414816299	5		529	650	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944397	40944397	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	155	402	0	ENST00000373198.4:c.2105G>T	p.Ser702Ile	p.S702I	ENST00000373198	NM_133170.3	702	aGc/aTc	12/32	0.586009312414012	4	FACETS	0.988	0.915	1	0.988	0.915	1	CLONAL	2	TRUE	2	0.637375414816299	4		402	403	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755555	39755556	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0048786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	239	371	0	ENST00000288319.7:c.1209_1210delinsTT	p.Pro404Ser	p.P404S	ENST00000288319	NM_182918.3	403	ccCCcg/ccTTcg	10/10	0.637375414816299	3	FACETS	0.975	0.934	1	0.975	0.934	1	CLONAL	3	TRUE	0	0.637375414816299	3		371	338	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755768	39755768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	251	354	0	ENST00000288319.7:c.997G>A	p.Glu333Lys	p.E333K	ENST00000288319	NM_182918.3	333	Gaa/Aaa	10/10	0.637375414816299	3	FACETS	0.962	0.921	1	0.962	0.921	1	CLONAL	3	TRUE	0	0.637375414816299	3		354	360	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448582	89448582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	95	413	0	ENST00000336596.2:c.1546G>A	p.Gly516Arg	p.G516R	ENST00000336596	NM_005233.5	516	Gga/Aga	7/17	0.637375414816299	4	FACETS	0.996	0.891	1	0.332	0.297	0.37	CLONAL	1	TRUE	1	0.637375414816299	4		413	490	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191539	185191539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771860470	NA	P-0048786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	250	395	0	ENST00000265026.3:c.2420C>T	p.Pro807Leu	p.P807L	ENST00000265026	NM_004721.4	807	cCt/cTt	11/14	0.628010724764038	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	3	TRUE	1	0.637375414816299	4		395	425	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178552	32178552	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	345	504	0	ENST00000375023.3:c.2842C>T	p.Gln948Ter	p.Q948*	ENST00000375023	NM_004557.3	948	Cag/Tag	18/30	0.628010724764038	4	FACETS	0.995	0.953	1	0.995	0.953	1	CLONAL	3	TRUE	1	0.637375414816299	4		504	594	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202388	138202388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	91	499	0	ENST00000237289.4:c.2305C>T	p.His769Tyr	p.H769Y	ENST00000237289	NM_001270507.1	769	Cat/Tat	9/9	0.637375414816299	1	FACETS	0.861	0.779	0.944	0.861	0.779	0.944	CLONAL	1	TRUE	0	0.637375414816299	1		499	226	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0048787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	147	715	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.24	2		715	936	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0048789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	319	347	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.93116553359023	4	FACETS	0.953	0.917	0.987	0.953	0.917	0.987	CLONAL	3	TRUE	1	0.962795609983598	4		347	455	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271301	1271301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	364	481	0	ENST00000310581.5:c.2401G>A	p.Ala801Thr	p.A801T	ENST00000310581	NM_198253.2	801	Gcc/Acc	8/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.962795609983598	2		481	729	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	52	211	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.345696714043255	1	FACETS	0.773	0.663	0.892	0.773	0.663	0.892	SUBCLONAL	1	TRUE	0	0.382987022849058	1		211	284	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	91	434	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.874	0.778	0.975	0.874	0.778	0.975	CLONAL	1	TRUE	1	0.382987022849058	2		435	544	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391024	89391024	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	65	492	0	ENST00000336596.2:c.1095del	p.Lys365AsnfsTer6	p.K365Nfs*6	ENST00000336596	NM_005233.5	364	Aaa/aa	5/17	1	2	FACETS	0.444	0.384	0.509	0.444	0.384	0.509	SUBCLONAL	1	TRUE	1	0.382987022849058	2		492	764	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	132	428	0	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	0.382987022849058	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.382987022849058	1		428	516	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211674	5211674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1351895585	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	95	673	1	ENST00000357368.4:c.5161C>T	p.Arg1721Trp	p.R1721W	ENST00000357368	NM_002850.3	1721	Cgg/Tgg	33/38	1	2	FACETS	0.48	0.426	0.538	0.48	0.426	0.538	SUBCLONAL	1	TRUE	1	0.382987022849058	2		674	1033	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1232964733	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	86	265	0	ENST00000324856.7:c.1015del	p.Ala339LeufsTer24	p.A339Lfs*24	ENST00000324856	NM_006015.4	337	tGg/tg	1/20	1	2	FACETS	0.954	0.847	1	0.954	0.847	1	CLONAL	1	TRUE	1	0.382987022849058	2		265	471	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	199	478	2	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.382987022849058	2		480	852	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	81	350	3	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.761	0.671	0.856	0.761	0.671	0.856	SUBCLONAL	1	TRUE	1	0.382987022849058	2		353	556	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574678	41574679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs754418509	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	231	843	1	ENST00000263253.7:c.6970dup	p.His2324ProfsTer55	p.H2324Pfs*55	ENST00000263253	NM_001429.3	2321	-/C	31/31	1	2	FACETS	0.902	0.839	0.967	0.902	0.839	0.967	CLONAL	1	TRUE	1	0.382987022849058	2		844	1337	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209616	98209617	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761353734	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	105	713	2	ENST00000331920.6:c.3921dup	p.Arg1308GlnfsTer17	p.R1308Qfs*17	ENST00000331920	NM_000264.3	1307	-/C	23/24	1	2	FACETS	0.533	0.476	0.593	0.533	0.476	0.593	SUBCLONAL	1	TRUE	1	0.382987022849058	2		715	1029	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953730	48953730	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs3092891	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	51	166	0	ENST00000267163.4:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000267163	NM_000321.2	445	Cga/Tga	14/27	0.350553453007553	1	FACETS	0.988	0.85	1	0.988	0.85	1	CLONAL	1	TRUE	0	0.382987022849058	1		166	218	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	132	430	2	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.382987022849058	2		432	683	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089705	27089706	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1286891446	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	202	723	0	ENST00000324856.7:c.2666dup	p.Met890HisfsTer46	p.M890Hfs*46	ENST00000324856	NM_006015.4	887	-/G	8/20	1	2	FACETS	0.867	0.803	0.935	0.867	0.803	0.935	CLONAL	1	TRUE	1	0.382987022849058	2		723	1216	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056329	26056329	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	125	478	0	ENST00000343677.2:c.328A>G	p.Lys110Glu	p.K110E	ENST00000343677	NM_005319.3	110	Aag/Gag	1/1	1	2	FACETS	0.95	0.861	1	0.95	0.861	1	CLONAL	1	TRUE	1	0.382987022849058	2		478	687	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549353	21549353	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753092502	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	234	690	0	ENST00000382592.4:c.2923G>A	p.Ala975Thr	p.A975T	ENST00000382592	NM_014572.2	975	Gcc/Acc	8/8	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.382987022849058	2		690	996	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996200	73996200	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757435411	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	196	646	1	ENST00000318443.5:c.934G>A	p.Ala312Thr	p.A312T	ENST00000318443	NM_001024736.1	312	Gcc/Acc	5/10	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.382987022849058	2		647	1015	SUCCESS
BTK	695	MSKCC	GRCh37	X	100612524	100612524	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	121	268	0	ENST00000308731.7:c.1150G>A	p.Ala384Thr	p.A384T	ENST00000308731	NM_000061.2	384	Gca/Aca	13/19	1	1	FACETS	0.776	0.711	0.844	1	0.987	1	SUBCLONAL	2	TRUE	0	0.382987022849058	1		268	329	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973231	25973231	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	122	351	0	ENST00000435504.4:c.1194T>A	p.Asp398Glu	p.D398E	ENST00000435504		398	gaT/gaA	12/13	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.382987022849058	2		351	620	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108787	2108788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs137854024	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	232	763	0	ENST00000219476.3:c.894dup	p.Val299CysfsTer39	p.V299Cfs*39	ENST00000219476	NM_000548.3	296	-/T	10/42	0.382987022849058	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.382987022849058	1		763	945	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782074	66782075	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	84	317	0	ENST00000307102.5:c.1047_1048del	p.Arg349SerfsTer16	p.R349Sfs*16	ENST00000307102	NM_002755.3	347	gcAGag/gcag	10/11	1	2	FACETS	0.933	0.828	1	0.933	0.828	1	CLONAL	1	TRUE	1	0.382987022849058	2		317	470	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869656	117869656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	97	434	0	ENST00000297338.2:c.538G>A	p.Asp180Asn	p.D180N	ENST00000297338	NM_006265.2	180	Gac/Aac	6/14	1	2	FACETS	0.767	0.685	0.855	0.767	0.685	0.855	SUBCLONAL	1	TRUE	1	0.382987022849058	2		434	660	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554345	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs748399150	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1218	151	861	4	ENST00000220592.5:c.1806del	p.Ala603ProfsTer92	p.A603Pfs*92	ENST00000220592	NM_012154.3	602	ccC/cc	14/19	1	2	FACETS	0.576	0.525	0.63	0.576	0.525	0.63	SUBCLONAL	1	TRUE	1	0.382987022849058	2		865	1369	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820866	36820866	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	204	565	0	ENST00000373129.3:c.511G>A	p.Glu171Lys	p.E171K	ENST00000373129	NM_032017.1	171	Gag/Aag	6/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.382987022849058	2		565	932	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427983	49427983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866777837	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	253	693	0	ENST00000301067.7:c.10607G>A	p.Arg3536His	p.R3536H	ENST00000301067	NM_003482.3	3536	cGc/cAc	38/54	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.382987022849058	2		693	1073	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440431	49440431	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1240601136	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	219	705	2	ENST00000301067.7:c.4379del	p.Pro1460HisfsTer46	p.P1460Hfs*46	ENST00000301067	NM_003482.3	1460	cCa/ca	15/54	1	2	FACETS	0.949	0.882	1	0.949	0.882	1	CLONAL	1	TRUE	1	0.382987022849058	2		707	1205	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880956	134880956	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	166	611	0	ENST00000398015.3:c.1519C>T	p.Arg507Cys	p.R507C	ENST00000398015	NM_004441.4	507	Cgt/Tgt	7/16	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.382987022849058	2		611	851	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843243	128843243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173715127	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	275	829	0	ENST00000249373.3:c.350G>A	p.Arg117His	p.R117H	ENST00000249373	NM_005631.4	117	cGc/cAc	2/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.382987022849058	2		829	1278	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522651	176522651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138800021	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	366	942	1	ENST00000292408.4:c.1748C>T	p.Pro583Leu	p.P583L	ENST00000292408	NM_213647.1	583	cCg/cTg	13/18	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.382987022849058	2		943	1482	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885938	111885939	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs751076276	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	96	676	0	ENST00000341259.2:c.1566dup	p.Glu523ArgfsTer23	p.E523Rfs*23	ENST00000341259	NM_005475.2	520	-/C	8/8	1	2	FACETS	0.482	0.428	0.539	0.482	0.428	0.539	SUBCLONAL	1	TRUE	1	0.382987022849058	2		676	1041	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097761	8097761	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	266	775	0	ENST00000346208.3:c.143A>T	p.Asp48Val	p.D48V	ENST00000346208		48	gAt/gTt	2/6	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.382987022849058	2		775	1305	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90634852	90634852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201173543	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	147	560	2	ENST00000330062.3:c.140C>T	p.Ala47Val	p.A47V	ENST00000330062	NM_002168.2	47	gCg/gTg	2/11	1	2	FACETS	0.914	0.835	0.997	0.914	0.835	0.997	CLONAL	1	TRUE	1	0.382987022849058	2		562	840	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909673	50909673	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771858429	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	297	788	0	ENST00000440232.2:c.1393C>T	p.Arg465Trp	p.R465W	ENST00000440232	NM_002691.3	465	Cgg/Tgg	12/27	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.382987022849058	2		788	1264	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859569	151859569	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138747124	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	123	496	3	ENST00000262189.6:c.11093C>T	p.Thr3698Met	p.T3698M	ENST00000262189	NM_170606.2	3698	aCg/aTg	43/59	1	2	FACETS	0.976	0.885	1	0.976	0.885	1	CLONAL	1	TRUE	1	0.382987022849058	2		499	658	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349259	89349259	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	248	757	0	ENST00000301030.4:c.3691G>C	p.Asp1231His	p.D1231H	ENST00000301030	NM_001256183.1	1231	Gat/Cat	9/13	0.382987022849058	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.382987022849058	1		757	922	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495415	56495415	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	84	720	1	ENST00000267101.3:c.3605G>T	p.Arg1202Leu	p.R1202L	ENST00000267101	NM_001982.3	1202	cGg/cTg	28/28	1	2	FACETS	0.412	0.363	0.466	0.412	0.363	0.466	SUBCLONAL	1	TRUE	1	0.382987022849058	2		721	1064	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240987	133240987	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	70	609	0	ENST00000320574.5:c.2530A>G	p.Thr844Ala	p.T844A	ENST00000320574	NM_006231.2	844	Acc/Gcc	22/49	1	2	FACETS	0.35	0.304	0.4	0.35	0.304	0.4	SUBCLONAL	1	TRUE	1	0.382987022849058	2		609	1045	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103510654	103510654	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	91	335	0	ENST00000355739.4:c.558A>G	p.Ile186Met	p.I186M	ENST00000355739	NM_000123.3	186	atA/atG	6/15	1	2	FACETS	0.984	0.877	1	0.984	0.877	1	CLONAL	1	TRUE	1	0.382987022849058	2		335	483	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991782	72991782	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	165	689	0	ENST00000268489.5:c.2263C>T	p.Gln755Ter	p.Q755*	ENST00000268489	NM_006885.3	755	Cag/Tag	2/10	0.382987022849058	1	FACETS	0.914	0.841	0.99	0.914	0.841	0.99	CLONAL	1	TRUE	0	0.382987022849058	1		689	762	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993350	72993350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765589758	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	286	772	1	ENST00000268489.5:c.695G>A	p.Arg232His	p.R232H	ENST00000268489	NM_006885.3	232	cGc/cAc	2/10	0.382987022849058	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.382987022849058	1		773	1016	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559901	29559901	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	89	239	0	ENST00000356175.3:c.3496+2T>C		p.X1166_splice	ENST00000356175	NM_000267.3	1166			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.382987022849058	2		239	377	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676250	37676250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	197	608	0	ENST00000447079.4:c.3005C>T	p.Thr1002Ile	p.T1002I	ENST00000447079	NM_015083.1	1002	aCa/aTa	11/14	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.382987022849058	2		608	909	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120191	70120191	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057524043	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	200	583	0	ENST00000245479.2:c.1193A>G	p.Lys398Arg	p.K398R	ENST00000245479	NM_000346.3	398	aAg/aGg	3/3	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.382987022849058	2		583	885	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632373	1632373	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	311	888	1	ENST00000344749.5:c.177G>A	p.Trp59Ter	p.W59*	ENST00000344749	NM_001136139.2	59	tgG/tgA	4/19	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.382987022849058	2		889	1467	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121187	11121187	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	183	637	0	ENST00000358026.2:c.2254G>A	p.Gly752Ser	p.G752S	ENST00000358026	NM_001128849.1	752	Ggt/Agt	15/36	1	2	FACETS	0.931	0.858	1	0.931	0.858	1	CLONAL	1	TRUE	1	0.382987022849058	2		637	1027	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292523	15292523	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1325474998	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	325	950	0	ENST00000263388.2:c.2656C>T	p.Arg886Cys	p.R886C	ENST00000263388	NM_000435.2	886	Cgc/Tgc	17/33	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.382987022849058	2		950	1449	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61710178	61710178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	92	386	1	ENST00000401558.2:c.2726C>T	p.Ala909Val	p.A909V	ENST00000401558	NM_003400.3	909	gCt/gTt	22/25	1	2	FACETS	0.795	0.708	0.889	0.795	0.708	0.889	SUBCLONAL	1	TRUE	1	0.382987022849058	2		387	604	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940327	49940327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	248	816	0	ENST00000296474.3:c.716C>T	p.Pro239Leu	p.P239L	ENST00000296474	NM_002447.2	239	cCc/cTc	1/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.382987022849058	2		816	1243	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806150	1806150	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	292	940	0	ENST00000260795.2:c.1169T>C	p.Val390Ala	p.V390A	ENST00000260795		390	gTg/gCg	8/17	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.382987022849058	2		940	1418	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253807	153253807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760675122	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	93	352	0	ENST00000281708.4:c.926G>A	p.Arg309His	p.R309H	ENST00000281708	NM_033632.3	309	cGc/cAc	6/12	1	2	FACETS	0.969	0.865	1	0.969	0.865	1	CLONAL	1	TRUE	1	0.382987022849058	2		352	501	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31448696	31448696	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs757854835	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	109	413	0	ENST00000344624.3:c.2840A>C	p.Asn947Thr	p.N947T	ENST00000344624		947	aAt/aCt	20/33	1	2	FACETS	0.968	0.872	1	0.968	0.872	1	CLONAL	1	TRUE	1	0.382987022849058	2		413	588	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149436870	149436870	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774348652	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	234	663	0	ENST00000286301.3:c.2299G>A	p.Ala767Thr	p.A767T	ENST00000286301	NM_005211.3	767	Gcc/Acc	17/22	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.382987022849058	2		663	997	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271513	26271513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	203	624	0	ENST00000305910.3:c.100G>A	p.Gly34Ser	p.G34S	ENST00000305910	NM_003534.2	34	Ggc/Agc	1/1	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.382987022849058	2		624	999	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066752	94066752	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	78	340	0	ENST00000369303.4:c.1007A>G	p.Gln336Arg	p.Q336R	ENST00000369303	NM_004440.3	336	cAg/cGg	5/17	0.382987022849058	1	FACETS	0.874	0.772	0.981	0.874	0.772	0.981	CLONAL	1	TRUE	0	0.382987022849058	1		340	377	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372236	55372236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	301	872	1	ENST00000297316.4:c.926G>A	p.Arg309His	p.R309H	ENST00000297316	NM_022454.3	309	cGc/cAc	2/2	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.382987022849058	2		873	1245	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518378	8518378	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	62	252	0	ENST00000356435.5:c.1013G>A	p.Ser338Asn	p.S338N	ENST00000356435		338	aGc/aAc	10/35	1	2	FACETS	0.854	0.741	0.976	0.854	0.741	0.976	CLONAL	1	TRUE	1	0.382987022849058	2		252	379	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937386	76937386	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	33	202	0	ENST00000373344.5:c.3362G>A	p.Gly1121Asp	p.G1121D	ENST00000373344	NM_000489.3	1121	gGt/gAt	9/35	1	1	FACETS	0.479	0.391	0.577	0.479	0.391	0.577	SUBCLONAL	1	TRUE	0	0.382987022849058	1		202	291	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061202	38061213	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCGCAAGT	GGCGGCGCAAGT	AG	novel	NA	P-0048790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	610	679	2	ENST00000250448.2:c.776_787delinsCT	p.Tyr259SerfsTer59	p.Y259Sfs*59	ENST00000250448	NM_004496.3	259	tACTTGCGCCGCCag/tCTag	2/2	0.382987022849058	3	FACETS	0.845	0.814	0.877			1	CLONAL	3	TRUE	NA	0.382987022849058	3		681	1497	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0048792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	58	582	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.943	0.811	1	0.943	0.811	1	CLONAL	1	TRUE	1	0.237863753075868	2		582	517	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544683	65544684	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0048792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	104	654	0	ENST00000358664.4:c.242_243del	p.His81ProfsTer5	p.H81Pfs*5	ENST00000358664	NM_002382.4	81	cAC/c	4/5	0.237863753075868	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.237863753075868	1		654	732	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	145	456	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.823	0.751	0.898	0.823	0.751	0.898	CLONAL	1	TRUE	1	0.423716477473937	2		456	832	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	119	351	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.423716477473937	2		351	543	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665213	138665213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	177	688	0	ENST00000330315.3:c.352G>A	p.Glu118Lys	p.E118K	ENST00000330315	NM_023067.3	118	Gag/Aag	1/1	1	2	FACETS	0.858	0.79	0.928	0.858	0.79	0.928	CLONAL	1	TRUE	1	0.423716477473937	2		688	974	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652129	36652129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34916193	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	194	701	0	ENST00000244741.5:c.251G>A	p.Arg84Gln	p.R84Q	ENST00000244741	NM_000389.4	84	cGa/cAa	2/3	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.423716477473937	2		701	900	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247244	153247244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	82	339	0	ENST00000281708.4:c.1558G>A	p.Asp520Asn	p.D520N	ENST00000281708	NM_033632.3	520	Gat/Aat	10/12	1	2	FACETS	0.87	0.77	0.975	0.87	0.77	0.975	CLONAL	1	TRUE	1	0.423716477473937	2		339	445	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134252	11134252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	138	537	0	ENST00000358026.2:c.2918G>A	p.Arg973Gln	p.R973Q	ENST00000358026	NM_001128849.1	973	cGg/cAg	20/36	1	2	FACETS	0.859	0.783	0.94	0.859	0.783	0.94	CLONAL	1	TRUE	1	0.423716477473937	2		537	758	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440379	52440379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	184	529	0	ENST00000460680.1:c.673G>A	p.Asp225Asn	p.D225N	ENST00000460680	NM_004656.3	225	Gac/Aac	9/17	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.423716477473937	2		529	738	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143521	30143521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1459946897	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	96	375	0	ENST00000389048.3:c.5G>A	p.Gly2Glu	p.G2E	ENST00000389048	NM_004304.4	2	gGa/gAa	1/29	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.423716477473937	2		375	412	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55087046	55087046	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	100	323	1	ENST00000275493.2:c.76G>A	p.Glu26Lys	p.E26K	ENST00000275493	NM_005228.3	26	Gag/Aag	1/28	1	2	FACETS	0.909	0.815	1	0.909	0.815	1	CLONAL	1	TRUE	1	0.423716477473937	2		324	519	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393183	393183	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	122	569	0	ENST00000380956.4:c.31G>A	p.Glu11Lys	p.E11K	ENST00000380956	NM_001195286.1	11	Gag/Aag	2/9	1	2	FACETS	0.843	0.763	0.927	0.843	0.763	0.927	CLONAL	1	TRUE	1	0.423716477473937	2		569	683	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023126	33023126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	114	497	0	ENST00000300177.4:c.235G>A	p.Glu79Lys	p.E79K	ENST00000300177	NM_001191322.1	79	Gag/Aag	2/2	1	2	FACETS	0.944	0.853	1	0.944	0.853	1	CLONAL	1	TRUE	1	0.423716477473937	2		497	570	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860556	45860556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	199	705	0	ENST00000391945.4:c.1451C>T	p.Thr484Met	p.T484M	ENST00000391945	NM_000400.3	484	aCg/aTg	15/23	1	2	FACETS	0.932	0.863	1	0.932	0.863	1	CLONAL	1	TRUE	1	0.423716477473937	2		705	1008	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051153	128051153	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	161	616	0	ENST00000285398.2:c.170G>A	p.Gly57Glu	p.G57E	ENST00000285398	NM_000122.1	57	gGa/gAa	2/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.423716477473937	2		616	718	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640169	3640169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769688259	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	553	668	0	ENST00000294008.3:c.3470C>T	p.Ser1157Leu	p.S1157L	ENST00000294008	NM_032444.2	1157	tCg/tTg	12/15	0.416426395887499	4	FACETS	0.943	0.906	0.979	0.943	0.906	0.979	CLONAL	3	TRUE	1	0.423716477473937	4		668	1314	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112000	115112000	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	188	735	1	ENST00000257566.3:c.1740C>A	p.Phe580Leu	p.F580L	ENST00000257566	NM_016569.3	580	ttC/ttA	7/8	1	2	FACETS	0.928	0.858	1	0.928	0.858	1	CLONAL	1	TRUE	1	0.423716477473937	2		736	956	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873483	151873483	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	119	417	0	ENST00000262189.6:c.9055C>T	p.Gln3019Ter	p.Q3019*	ENST00000262189	NM_170606.2	3019	Cag/Tag	38/59	1	2	FACETS	0.97	0.879	1	0.97	0.879	1	CLONAL	1	TRUE	1	0.423716477473937	2		417	579	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139045	37139045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	170	618	0	ENST00000373509.5:c.385C>T	p.Leu129Phe	p.L129F	ENST00000373509	NM_002648.3	129	Ctc/Ttc	4/6	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.423716477473937	2		618	723	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202456	123202456	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	83	205	0	ENST00000218089.9:c.2308C>T	p.Gln770Ter	p.Q770*	ENST00000218089	NM_001042749.1	770	Cag/Tag	24/35	1	1	FACETS	0.919	0.834	1	1	0.986	1	CLONAL	2	TRUE	0	0.423716477473937	1		205	168	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111459	56111459	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	99	311	0	ENST00000399503.3:c.59C>T	p.Thr20Met	p.T20M	ENST00000399503	NM_005921.1	20	aCg/aTg	1/20	1	2	FACETS	0.98	0.879	1	0.98	0.879	1	CLONAL	1	TRUE	1	0.423716477473937	2		311	477	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510849	120510849	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	56	300	0	ENST00000256646.2:c.1115T>G	p.Leu372Arg	p.L372R	ENST00000256646	NM_024408.3	372	cTg/cGg	7/34	1	2	FACETS	0.839	0.723	0.964	0.839	0.723	0.964	CLONAL	1	TRUE	1	0.423716477473937	2		300	315	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925489	131925489	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501946	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	51	266	0	ENST00000265335.6:c.1412C>T	p.Ser471Leu	p.S471L	ENST00000265335		471	tCa/tTa	9/25	1	2	FACETS	0.908	0.778	1	0.908	0.778	1	CLONAL	1	TRUE	1	0.423716477473937	2		266	265	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023207	33023207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	145	571	0	ENST00000300177.4:c.316G>A	p.Glu106Lys	p.E106K	ENST00000300177	NM_001191322.1	106	Gaa/Aaa	2/2	1	2	FACETS	0.979	0.895	1	0.979	0.895	1	CLONAL	1	TRUE	1	0.423716477473937	2		571	699	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41542802	41542802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	202	346	0	ENST00000263253.7:c.2113C>T	p.Arg705Ter	p.R705*	ENST00000263253	NM_001429.3	705	Cga/Tga	11/31	0.197507862499199	3	FACETS	1	0.949	1	0.679	0.634	0.725	INDETERMINATE	2	TRUE	0	0.423716477473937	3		346	567	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295295	1295295	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	179	622	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.977	0.901	1	0.977	0.901	1	CLONAL	1	TRUE	1	0.423716477473937	2		622	865	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805384	46805384	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	213	686	1	ENST00000290295.7:c.572C>T	p.Pro191Leu	p.P191L	ENST00000290295	NM_006361.5	191	cCa/cTa	1/2	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.423716477473937	2		687	944	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935343	36935343	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	185	673	0	ENST00000361632.4:c.1384G>A	p.Glu462Lys	p.E462K	ENST00000361632		462	Gag/Aag	10/16	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.423716477473937	2		673	848	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120478185	120478185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs185917176	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	106	326	0	ENST00000256646.2:c.3565G>A	p.Asp1189Asn	p.D1189N	ENST00000256646	NM_024408.3	1189	Gat/Aat	22/34	1	2	FACETS	0.991	0.892	1	0.991	0.892	1	CLONAL	1	TRUE	1	0.423716477473937	2		326	505	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253412	226253412	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	73	86	0	ENST00000366813.1:c.184C>G	p.Leu62Val	p.L62V	ENST00000366813		62	Ctg/Gtg	2/3	0.423716477473937	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.423716477473937	3		86	174	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850642	63850642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	53	238	0	ENST00000279873.7:c.1420G>A	p.Glu474Lys	p.E474K	ENST00000279873	NM_032199.2	474	Gaa/Aaa	10/10	1	2	FACETS	0.916	0.788	1	0.916	0.788	1	CLONAL	1	TRUE	1	0.423716477473937	2		238	273	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	532722	532722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564787942	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	172	800	0	ENST00000451590.1:c.484G>A	p.Glu162Lys	p.E162K	ENST00000451590	NM_001130442.1	162	Gag/Aag	5/5	1	2	FACETS	0.946	0.871	1	0.946	0.871	1	CLONAL	1	TRUE	1	0.423716477473937	2		800	858	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955392	48955392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	24	186	0	ENST00000267163.4:c.1508C>T	p.Ser503Phe	p.S503F	ENST00000267163	NM_000321.2	503	tCt/tTt	17/27	1	2	FACETS	0.75	0.594	0.926	0.75	0.594	0.926	CLONAL	1	TRUE	1	0.423716477473937	2		186	151	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023102	33023102	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1479073274	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	96	463	0	ENST00000300177.4:c.211G>A	p.Glu71Lys	p.E71K	ENST00000300177	NM_001191322.1	71	Gag/Aag	2/2	1	2	FACETS	0.844	0.754	0.939	0.844	0.754	0.939	CLONAL	1	TRUE	1	0.423716477473937	2		463	537	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714105	43714105	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	184	667	0	ENST00000382044.4:c.4048G>C	p.Glu1350Gln	p.E1350Q	ENST00000382044	NM_001141980.1	1350	Gaa/Caa	19/28	1	2	FACETS	0.979	0.904	1	0.979	0.904	1	CLONAL	1	TRUE	1	0.423716477473937	2		667	887	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738627	43738627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	110	455	0	ENST00000382044.4:c.2998G>A	p.Glu1000Lys	p.E1000K	ENST00000382044	NM_001141980.1	1000	Gag/Aag	14/28	1	2	FACETS	0.947	0.854	1	0.947	0.854	1	CLONAL	1	TRUE	1	0.423716477473937	2		455	548	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748225	43748225	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	157	519	0	ENST00000382044.4:c.2581C>T	p.Gln861Ter	p.Q861*	ENST00000382044	NM_001141980.1	861	Cag/Tag	12/28	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.423716477473937	2		519	731	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293231	91293231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772711706	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	56	335	0	ENST00000355112.3:c.733G>A	p.Glu245Lys	p.E245K	ENST00000355112	NM_000057.2	245	Gaa/Aaa	3/22	1	2	FACETS	0.734	0.632	0.845	0.734	0.632	0.845	SUBCLONAL	1	TRUE	1	0.423716477473937	2		335	360	SUCCESS
BLM	641	MSKCC	GRCh37	15	91334044	91334044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	88	354	0	ENST00000355112.3:c.2989G>A	p.Asp997Asn	p.D997N	ENST00000355112	NM_000057.2	997	Gat/Aat	15/22	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.423716477473937	2		354	403	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632800	23632800	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs754465466	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	262	343	0	ENST00000261584.4:c.2997-1G>C		p.X999_splice	ENST00000261584	NM_024675.3	999			0.416426395887499	4	FACETS	1	0.952	1	1	0.952	1	CLONAL	3	TRUE	1	0.423716477473937	4		343	583	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832535	72832535	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	114	400	1	ENST00000268489.5:c.4046C>T	p.Ala1349Val	p.A1349V	ENST00000268489	NM_006885.3	1349	gCt/gTt	9/10	1	2	FACETS	0.98	0.886	1	0.98	0.886	1	CLONAL	1	TRUE	1	0.423716477473937	2		401	549	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657368	29657368	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	86	431	0	ENST00000356175.3:c.5601C>G	p.Ile1867Met	p.I1867M	ENST00000356175	NM_000267.3	1867	atC/atG	38/57	1	2	FACETS	0.784	0.695	0.878	0.784	0.695	0.878	SUBCLONAL	1	TRUE	1	0.423716477473937	2		431	518	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428366	33428366	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137886232	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	156	505	2	ENST00000345365.6:c.757C>T	p.Arg253Ter	p.R253*	ENST00000345365	NM_002878.3	253	Cga/Tga	9/10	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.423716477473937	2		507	719	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456629	40456629	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	168	633	0	ENST00000345506.4:c.1339C>T	p.Gln447Ter	p.Q447*	ENST00000345506	NM_003152.3	447	Cag/Tag	12/20	1	2	FACETS	0.901	0.829	0.977	0.901	0.829	0.977	CLONAL	1	TRUE	1	0.423716477473937	2		633	880	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223246	41223246	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	86	383	0	ENST00000357654.3:c.4685C>G	p.Pro1562Arg	p.P1562R	ENST00000357654	NM_007294.3	1562	cCt/cGt	15/23	1	2	FACETS	0.92	0.818	1	0.92	0.818	1	CLONAL	1	TRUE	1	0.423716477473937	2		383	441	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39620703	39620703	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	63	247	0	ENST00000262039.4:c.2101C>T	p.Gln701Ter	p.Q701*	ENST00000262039	NM_002647.2	701	Cag/Tag	19/25	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.423716477473937	2		247	252	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56363645	56363645	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	101	371	0	ENST00000348428.3:c.424C>T	p.Gln142Ter	p.Q142*	ENST00000348428	NM_006785.3	142	Cag/Tag	3/17	1	2	FACETS	0.859	0.77	0.953	0.859	0.77	0.953	CLONAL	1	TRUE	1	0.423716477473937	2		371	555	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223451	2223451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	112	409	0	ENST00000398665.3:c.3562G>A	p.Glu1188Lys	p.E1188K	ENST00000398665	NM_032482.2	1188	Gag/Aag	25/28	1	2	FACETS	0.941	0.849	1	0.941	0.849	1	CLONAL	1	TRUE	1	0.423716477473937	2		409	562	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168964	11168964	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	156	575	0	ENST00000358026.2:c.4554C>G	p.Ile1518Met	p.I1518M	ENST00000358026	NM_001128849.1	1518	atC/atG	32/36	1	2	FACETS	0.987	0.906	1	0.987	0.906	1	CLONAL	1	TRUE	1	0.423716477473937	2		575	746	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17949140	17949140	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	171	706	0	ENST00000458235.1:c.1501C>T	p.Gln501Ter	p.Q501*	ENST00000458235	NM_000215.3	501	Cag/Tag	11/24	1	2	FACETS	0.957	0.882	1	0.957	0.882	1	CLONAL	1	TRUE	1	0.423716477473937	2		706	843	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968319	18968319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479019968	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	203	656	1	ENST00000262803.5:c.2159C>T	p.Ser720Phe	p.S720F	ENST00000262803	NM_002911.3	720	tCc/tTc	15/24	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.423716477473937	2		657	923	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905157	50905157	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1326137249	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	238	767	0	ENST00000440232.2:c.439T>G	p.Tyr147Asp	p.Y147D	ENST00000440232	NM_002691.3	147	Tac/Gac	4/27	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.423716477473937	2		767	1082	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605856	46605856	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	144	532	2	ENST00000263734.3:c.1504G>A	p.Glu502Lys	p.E502K	ENST00000263734	NM_001430.4	502	Gag/Aag	11/16	1	2	FACETS	0.988	0.903	1	0.988	0.903	1	CLONAL	1	TRUE	1	0.423716477473937	2		534	688	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172190	99172190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	166	573	0	ENST00000074304.5:c.1756G>A	p.Glu586Lys	p.E586K	ENST00000074304	NM_001134224.1	586	Gaa/Aaa	17/26	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.423716477473937	2		573	735	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190717411	190717411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	54	287	0	ENST00000441310.2:c.730G>A	p.Asp244Asn	p.D244N	ENST00000441310	NM_000534.4	244	Gat/Aat	7/13	1	2	FACETS	0.772	0.663	0.89	0.772	0.663	0.89	SUBCLONAL	1	TRUE	1	0.423716477473937	2		287	330	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388678	31388678	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	138	580	1	ENST00000328111.2:c.1943G>A	p.Gly648Glu	p.G648E	ENST00000328111	NM_006892.3	648	gGa/gAa	18/23	1	2	FACETS	0.915	0.834	1	0.915	0.834	1	CLONAL	1	TRUE	1	0.423716477473937	2		581	712	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268726	46268726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139276261	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	140	533	1	ENST00000371998.3:c.3011C>T	p.Ser1004Phe	p.S1004F	ENST00000371998		1004	tCt/tTt	16/23	1	2	FACETS	0.869	0.793	0.95	0.869	0.793	0.95	CLONAL	1	TRUE	1	0.423716477473937	2		534	760	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41522021	41522021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	209	385	0	ENST00000263253.7:c.883C>T	p.Pro295Ser	p.P295S	ENST00000263253	NM_001429.3	295	Cct/Tct	3/31	0.197507862499199	3	FACETS	1	0.987	1	0.799	0.749	0.849	INDETERMINATE	2	TRUE	0	0.423716477473937	3		385	499	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523570	41523570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	266	510	0	ENST00000263253.7:c.986C>T	p.Thr329Ile	p.T329I	ENST00000263253	NM_001429.3	329	aCa/aTa	4/31	0.197507862499199	3	FACETS	1	0.969	1	0.695	0.655	0.736	INDETERMINATE	2	TRUE	0	0.423716477473937	3		510	730	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564741	41564741	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	48	504	0	ENST00000263253.7:c.4042G>A	p.Glu1348Lys	p.E1348K	ENST00000263253	NM_001429.3	1348	Gag/Aag	25/31	0.197507862499199	3	FACETS	0.381	0.321	0.447	0.127	0.107	0.149	INDETERMINATE	1	TRUE	0	0.423716477473937	3		504	721	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960129	134960129	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	118	507	0	ENST00000398015.3:c.2486C>G	p.Ser829Cys	p.S829C	ENST00000398015	NM_004441.4	829	tCc/tGc	13/16	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.423716477473937	2		507	541	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981458	55981458	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	63	291	0	ENST00000263923.4:c.479C>T	p.Ser160Leu	p.S160L	ENST00000263923	NM_002253.2	160	tCa/tTa	4/30	1	2	FACETS	0.808	0.702	0.922	0.808	0.702	0.922	CLONAL	1	TRUE	1	0.423716477473937	2		291	368	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268224	153268224	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	50	146	0	ENST00000281708.4:c.585-1G>C		p.X195_splice	ENST00000281708	NM_033632.3	195			1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.423716477473937	2		146	202	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111467	56111467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	90	289	0	ENST00000399503.3:c.67G>A	p.Glu23Lys	p.E23K	ENST00000399503	NM_005921.1	23	Gag/Aag	1/20	1	2	FACETS	0.965	0.861	1	0.965	0.861	1	CLONAL	1	TRUE	1	0.423716477473937	2		289	440	SUCCESS
APC	324	MSKCC	GRCh37	5	112173723	112173723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	61	292	0	ENST00000257430.4:c.2432C>T	p.Ser811Leu	p.S811L	ENST00000257430	NM_000038.5	811	tCa/tTa	16/16	1	2	FACETS	0.989	0.861	1	0.989	0.861	1	CLONAL	1	TRUE	1	0.423716477473937	2		292	291	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696631	176696631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs794727176	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	64	218	1	ENST00000439151.2:c.5332C>T	p.Arg1778Ter	p.R1778*	ENST00000439151	NM_022455.4	1778	Cga/Tga	16/23	1	2	FACETS	0.962	0.839	1	0.962	0.839	1	CLONAL	1	TRUE	1	0.423716477473937	2		219	314	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745253	43745253	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	140	565	0	ENST00000523873.1:c.166G>A	p.Glu56Lys	p.E56K	ENST00000523873		56	Gag/Aag	3/8	1	2	FACETS	0.9	0.821	0.983	0.9	0.821	0.983	CLONAL	1	TRUE	1	0.423716477473937	2		565	734	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151164264	151164264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	112	335	0	ENST00000262187.5:c.496G>A	p.Glu166Lys	p.E166K	ENST00000262187	NM_005614.3	166	Gag/Aag	8/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.423716477473937	2		335	484	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864636	68864636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371341697	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	64	252	0	ENST00000288368.4:c.7G>A	p.Glu3Lys	p.E3K	ENST00000288368	NM_024870.2	3	Gag/Aag	1/40	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.423716477473937	2		252	268	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97887436	97887436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1354527553	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	130	445	0	ENST00000289081.3:c.928G>A	p.Glu310Lys	p.E310K	ENST00000289081	NM_000136.2	310	Gaa/Aaa	10/15	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.423716477473937	2		445	602	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797340	135797340	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	72	228	0	ENST00000298552.3:c.529C>T	p.Leu177Phe	p.L177F	ENST00000298552	NM_001162426.1	177	Ctc/Ttc	7/23	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.423716477473937	2		228	338	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411748	139411748	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	222	823	1	ENST00000277541.6:c.1531G>A	p.Glu511Lys	p.E511K	ENST00000277541	NM_017617.3	511	Gag/Aag	9/34	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.423716477473937	2		824	1042	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942735	44942761	+	inframe_deletion	In_Frame_Del	DEL	ACTTCCTGCTTTTGTGCGTGTCGTATC	ACTTCCTGCTTTTGTGCGTGTCGTATC	-	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	82	204	0	ENST00000377967.4:c.3316_3342del	p.Leu1106_Ser1114del	p.L1106_S1114del	ENST00000377967	NM_021140.2	1105	aaACTTCCTGCTTTTGTGCGTGTCGTATCa/aaa	23/29	1	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.423716477473937	1		204	241	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339290	70339290	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	111	246	0	ENST00000374080.3:c.167A>C	p.His56Pro	p.H56P	ENST00000374080		56	cAt/cCt	2/45	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.423716477473937	1		246	285	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341219	70341219	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	127	218	0	ENST00000374080.3:c.778G>C	p.Glu260Gln	p.E260Q	ENST00000374080		260	Gag/Cag	6/45	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.423716477473937	1		218	320	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060601	38060626	+	frameshift_variant	Frame_Shift_Del	DEL	ACACCTTGGTAGTACGCCGGCTCCAG	ACACCTTGGTAGTACGCCGGCTCCAG	-	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	202	788	0	ENST00000250448.2:c.1363_1388del	p.Leu455ValfsTer94	p.L455Vfs*94	ENST00000250448	NM_004496.3	455	CTGGAGCCGGCGTACTACCAAGGTGTg/g	2/2	1	2	FACETS	0.915	0.848	0.985	0.915	0.848	0.985	CLONAL	1	TRUE	1	0.423716477473937	2		788	1042	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953150	17953159	+	protein_altering_variant	In_Frame_Del	DEL	ATGCCGCCGT	ATGCCGCCGT	G	novel	NA	P-0048793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	150	751	0	ENST00000458235.1:c.827_836delinsC	p.Asp276_Ile279delinsAla	p.D276_I279delinsA	ENST00000458235	NM_000215.3	276	gACGGCGGCATc/gCc	6/24	1	2	FACETS	0.775	0.708	0.846	0.775	0.708	0.846	SUBCLONAL	1	TRUE	1	0.423716477473937	2		751	913	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	140	576	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.175677476169281	3	FACETS	1	0.929	1	1	0.929	1	CLONAL	3	TRUE	0	0.175677476169281	3		576	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	221	761	0	ENST00000269305.4:c.383del	p.Pro128LeufsTer42	p.P128Lfs*42	ENST00000269305	NM_001126112.2	128	cCt/ct	5/11	0.292387733851208	2	FACETS	0.88	0.821	0.941	0.88	0.821	0.941	CLONAL	2	TRUE	0	0.305861422760712	2		761	821	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244099	133244099	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	142	416	0	ENST00000320574.5:c.2309G>C	p.Gly770Ala	p.G770A	ENST00000320574	NM_006231.2	770	gGg/gCg	20/49	0.292387733851208	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	0	0.305861422760712	2		416	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0048802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	209	394	1	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.41585546865426	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.41585546865426	2		395	420	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089532	27089532	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	179	468	0	ENST00000324856.7:c.2488G>T	p.Gly830Ter	p.G830*	ENST00000324856	NM_006015.4	830	Gga/Tga	8/20	0.41585546865426	4	FACETS	0.999	0.926	1	0.999	0.926	1	CLONAL	2	TRUE	2	0.41585546865426	4		468	610	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89815068	89815074	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	ATCTCAG	ATCTCAG	-	novel	NA	P-0048802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	169	406	0	ENST00000389301.3:c.3341_3347del	p.Ser1114Ter	p.S1114*	ENST00000389301	NM_000135.2	1114	tCTGAGATg/tg	33/43	0.41585546865426	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.41585546865426	2		406	383	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460502	8460502	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	23	313	0	ENST00000356435.5:c.3784G>C	p.Asp1262His	p.D1262H	ENST00000356435		1262	Gat/Cat	22/35	0.41585546865426	2	FACETS	0.425	0.332	0.533	0.213	0.166	0.267	SUBCLONAL	1	TRUE	0	0.41585546865426	2		313	260	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509006	106509006	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201525740	NA	P-0048803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	114	398	1	ENST00000359195.3:c.1000G>A	p.Gly334Ser	p.G334S	ENST00000359195	NM_002649.2	334	Ggc/Agc	2/11	0.232333229989864	3	FACETS	0.765	0.692	0.843	0.765	0.692	0.843	SUBCLONAL	2	TRUE	1	0.314598665210543	3		399	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579590	7579591	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0048803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	75	454	0	ENST00000269305.4:c.97-2_97-1dup	p.Leu35ProfsTer10	p.L35Pfs*10	ENST00000269305	NM_001126112.2	32	-/AG		0.284323007179575	1	FACETS	0.83	0.729	0.938	0.83	0.729	0.938	CLONAL	1	TRUE	0	0.314598665210543	1		454	484	SUCCESS
APC	324	MSKCC	GRCh37	5	112175235	112175235	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0048803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	93	183	0	ENST00000257430.4:c.3944C>G	p.Ser1315Ter	p.S1315*	ENST00000257430	NM_000038.5	1315	tCa/tGa	16/16	0.304629712211888	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.314598665210543	2		183	262	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719992	18719992	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs376472161	NA	P-0048803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	11	185	0	ENST00000266497.5:c.3888+1G>A		p.X1296_splice	ENST00000266497		1296			0.314598665210543	1	FACETS	0.273	0.188	0.378	0.273	0.188	0.378	SUBCLONAL	1	TRUE	0	0.314598665210543	1		185	216	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791997	42791997	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	105	577	0	ENST00000575354.2:c.801G>A	p.Trp267Ter	p.W267*	ENST00000575354	NM_015125.3	267	tgG/tgA	6/20	1	2	FACETS	0.945	0.848	1	0.945	0.848	1	CLONAL	1	TRUE	1	0.314598665210543	2		577	706	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0048804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	166	620	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.685240455933862	2		620	470	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0048804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	17	504	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.101	0.075	0.132	0.101	0.075	0.132	SUBCLONAL	1	TRUE	1	0.685240455933862	2		504	492	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374244	138374244	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	114	302	0	ENST00000289153.2:c.3200A>T	p.Asp1067Val	p.D1067V	ENST00000289153	NM_006219.2	1067	gAc/gTc	22/22	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.685240455933862	2		302	328	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519886	NA	P-0048804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	105	238	0	ENST00000349496.5:c.97T>C	p.Ser33Pro	p.S33P	ENST00000349496	NM_001904.3	33	Tct/Cct	3/15	1	2	FACETS	0.946	0.858	1	0.946	0.858	1	CLONAL	1	TRUE	1	0.685240455933862	2		238	324	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106159	27106159	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	147	360	0	ENST00000324856.7:c.5770G>T	p.Glu1924Ter	p.E1924*	ENST00000324856	NM_006015.4	1924	Gag/Tag	20/20	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.685240455933862	2		360	425	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685296	89685297	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	151	172	0	ENST00000371953.3:c.193dup	p.Tyr65LeufsTer9	p.Y65Lfs*9	ENST00000371953	NM_000314.4	64	cat/caTt	3/9	0.685240455933862	2	FACETS	0.958	0.903	1	0.958	0.903	1	CLONAL	2	TRUE	0	0.685240455933862	2		172	230	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921739	111921746	+	frameshift_variant	Frame_Shift_Del	DEL	AGACCACC	AGACCACC	-	novel	NA	P-0048804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	90	239	0	ENST00000393256.3:c.528_535del	p.Glu176AspfsTer86	p.E176Dfs*86	ENST00000393256	NM_006538.4	176	gaAGACCACCca/gaca	4/4	1	2	FACETS	0.858	0.77	0.95	0.858	0.77	0.95	CLONAL	1	TRUE	1	0.685240455933862	2		239	306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0048806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	323	524	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.56820814276664	2	FACETS	0.957	0.914	1	0.957	0.914	1	CLONAL	2	TRUE	0	0.56820814276664	2		524	594	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591125	67591126	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0048806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	41	151	0	ENST00000274335.5:c.1718_1719del	p.Leu573GlnfsTer28	p.L573Qfs*28	ENST00000274335		573	cTG/c	12/15	0.383941618392707	1	FACETS	0.422	0.354	0.496	0.422	0.354	0.496	SUBCLONAL	1	TRUE	0	0.56820814276664	1		151	245	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041812	42041812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567080761	NA	P-0048806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	71	301	0	ENST00000219905.7:c.6007C>T	p.Pro2003Ser	p.P2003S	ENST00000219905	NM_001164273.1	2003	Cct/Tct	17/24	0.448782629383005	1	FACETS	0.471	0.413	0.533	0.471	0.413	0.533	SUBCLONAL	1	TRUE	0	0.56820814276664	1		301	380	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868220	37868220	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	1338	477	0	ENST00000269571.5:c.941T>G	p.Val314Gly	p.V314G	ENST00000269571		314	gTc/gGc	8/27	0.56820814276664	7	FACETS	1	0.997	1			1	CLONAL	7	TRUE	NA	0.56820814276664	7		477	1580	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410406	63410406	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	63	549	0	ENST00000330258.3:c.2761C>A	p.Leu921Met	p.L921M	ENST00000330258	NM_152424.3	921	Ctg/Atg	2/2	0.383941618392707	1	FACETS	0.284	0.245	0.326	0.284	0.245	0.326	SUBCLONAL	1	TRUE	0	0.56820814276664	1		549	559	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0048807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	11	582	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.17	0.116	0.237	0.17	0.116	0.237	SUBCLONAL	1	TRUE	1	0.27	2		582	480	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024458	31024458	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048807-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	102	404	7	ENST00000375687.4:c.3943C>T	p.Gln1315Ter	p.Q1315*	ENST00000375687	NM_015338.5	1315	Cag/Tag	13/13	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.27	2		411	693	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0048808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	474	696	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.376983140357523	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.376983140357523	3		697	910	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145362	58145362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	111	404	0	ENST00000257904.6:c.139G>A	p.Gly47Arg	p.G47R	ENST00000257904	NM_000075.3	47	Gga/Aga	2/8	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.376983140357523	2		404	577	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193786	106193786	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	55	209	0	ENST00000380013.4:c.4248C>G	p.His1416Gln	p.H1416Q	ENST00000380013	NM_001127208.2	1416	caC/caG	10/11	0.376983140357523	1	FACETS	0.9	0.777	1	0.9	0.777	1	CLONAL	1	TRUE	0	0.376983140357523	1		209	263	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476872	140476872	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	57	286	0	ENST00000288602.6:c.1534A>G	p.Asn512Asp	p.N512D	ENST00000288602	NM_004333.4	512	Aat/Gat	13/18	0.376983140357523	3	FACETS	0.819	0.704	0.943	0.409	0.352	0.472	CLONAL	1	TRUE	1	0.376983140357523	3		286	439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0048809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	300	882	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.646849883224957	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.644391685453773	1		882	497	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039379	49039379	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	253	451	0	ENST00000267163.4:c.2366del	p.Pro789LeufsTer21	p.P789Lfs*21	ENST00000267163	NM_000321.2	788	agC/ag	23/27	0.637489893744206	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.644391685453773	1		451	409	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827502	72827502	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	280	532	0	ENST00000268489.5:c.9079A>G	p.Thr3027Ala	p.T3027A	ENST00000268489	NM_006885.3	3027	Act/Gct	9/10	0.646849883224957	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.644391685453773	1		532	469	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868472	117868472	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	236	409	0	ENST00000297338.2:c.870G>C	p.Met290Ile	p.M290I	ENST00000297338	NM_006265.2	290	atG/atC	8/14	0.127618205046347	1	FACETS	0.847	0.797	0.898	0.847	0.797	0.898	INDETERMINATE	1	TRUE	0	0.644391685453773	1		409	586	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352332	70352333	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0048809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	397	235	0	ENST00000374080.3:c.4360_4361del	p.Gly1454SerfsTer12	p.G1454Sfs*12	ENST00000374080		1453	aaGGgt/aagt	31/45	0.54341067183016	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.644391685453773	2		235	512	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814234	76814235	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0048809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	258	128	1	ENST00000373344.5:c.6409_6410delinsAA	p.Ala2137Asn	p.A2137N	ENST00000373344	NM_000489.3	2137	GCt/AAt	29/35	0.54341067183016	2	FACETS	0.881	0.854	0.905			1	CLONAL	3	TRUE	NA	0.644391685453773	2		129	303	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654545	29654545	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	41	198	0	ENST00000356175.3:c.5234C>A	p.Ser1745Ter	p.S1745*	ENST00000356175	NM_000267.3	1745	tCa/tAa	37/57	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.25	2		198	223	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223189	5223189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151114416	NA	P-0048810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	57	781	0	ENST00000357368.4:c.2614C>T	p.Arg872Cys	p.R872C	ENST00000357368	NM_002850.3	872	Cgt/Tgt	18/38	1	2	FACETS	0.981	0.843	1	0.981	0.843	1	CLONAL	1	TRUE	1	0.25	2		781	465	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0048811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	291	327	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.848285416643143	2		327	617	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0048811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	526	497	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.848285416643143	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.848285416643143	1		498	688	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0048811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	604	474	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.848285416643143	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.848285416643143	1		474	757	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518458	69518458	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	365	250	0	ENST00000294312.3:c.187C>T	p.Arg63Cys	p.R63C	ENST00000294312	NM_005117.2	63	Cgt/Tgt	1/3	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.848285416643143	2		250	835	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942515	17942515	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149452625	NA	P-0048811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	714	670	0	ENST00000458235.1:c.2773C>T	p.Arg925Cys	p.R925C	ENST00000458235	NM_000215.3	925	Cgc/Tgc	20/24	0.479285712858932	1	FACETS	0.763	0.74	0.786	0.763	0.74	0.786	INDETERMINATE	1	TRUE	0	0.848285416643143	1		670	1270	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487288	56487288	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	189	317	0	ENST00000267101.3:c.1435del	p.Glu479LysfsTer4	p.E479Kfs*4	ENST00000267101	NM_001982.3	478	acG/ac	12/28	1	2	FACETS	0.536	0.496	0.578	0.536	0.496	0.578	SUBCLONAL	1	TRUE	1	0.848285416643143	2		317	831	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857460	68857460	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121964874	NA	P-0048812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	165	440	0	ENST00000261769.5:c.2095C>T	p.Gln699Ter	p.Q699*	ENST00000261769	NM_004360.3	699	Cag/Tag	13/16	0.502413979706781	1	FACETS	0.99	0.916	1	0.99	0.916	1	CLONAL	1	TRUE	0	0.502413979706781	1		440	497	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112602	115112602	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs865915137	NA	P-0048812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	262	647	1	ENST00000257566.3:c.1138G>T	p.Glu380Ter	p.E380*	ENST00000257566	NM_016569.3	380	Gag/Tag	7/8	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.502413979706781	2		648	964	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0048813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	664	347	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.47801466077924	7	FACETS	1	0.992	1	0.897	0.873	0.92	CLONAL	6	TRUE	0	0.47801466077924	7		347	971	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577115	7577115	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519983	NA	P-0048813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	392	722	0	ENST00000269305.4:c.823T>C	p.Cys275Arg	p.C275R	ENST00000269305	NM_001126112.2	275	Tgt/Cgt	8/11	0.460064868764308	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.47801466077924	2		722	805	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336402	80336402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769315863	NA	P-0048813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	112	417	0	ENST00000286548.4:c.917G>A	p.Arg306Gln	p.R306Q	ENST00000286548	NM_002072.3	306	cGa/cAa	7/7	NA	2	FACETS	0.972	0.879	1			1	INDETERMINATE	1	TRUE	NA	0.47801466077924	2		417	482	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138375052	138375052	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	216	443	0	ENST00000289153.2:c.3007C>G	p.Leu1003Val	p.L1003V	ENST00000289153	NM_006219.2	1003	Ctc/Gtc	21/22	0.429645573872287	3	FACETS	0.873	0.817	0.931	0.582	0.544	0.621	CLONAL	2	TRUE	0	0.47801466077924	3		443	641	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662700	117662700	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	92	405	1	ENST00000368508.3:c.4765G>T	p.Glu1589Ter	p.E1589*	ENST00000368508	NM_002944.2	1589	Gaa/Taa	29/43	0.316017933027668	2	FACETS	0.755	0.673	0.842	0.377	0.336	0.421	SUBCLONAL	1	TRUE	0	0.47801466077924	2		406	510	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966664	36966664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142210825	NA	P-0048813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	132	533	0	ENST00000358127.4:c.662G>A	p.Arg221Gln	p.R221Q	ENST00000358127	NM_001280556.1	221	cGg/cAg	6/10	0.230698230957544	4	FACETS	1	0.968	1	0.381	0.346	0.417	INDETERMINATE	1	TRUE	1	0.47801466077924	4		533	715	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774218	56774218	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	20	297	1	ENST00000337432.4:c.569A>G	p.Glu190Gly	p.E190G	ENST00000337432	NM_058216.2	190	gAg/gGg	3/9	0.460064868764308	2	FACETS	0.246	0.188	0.315	0.123	0.094	0.158	SUBCLONAL	1	TRUE	0	0.47801466077924	2		298	340	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310911	123310911	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	268	498	0	ENST00000358487.5:c.517A>G	p.Asn173Asp	p.N173D	ENST00000358487	NM_000141.4	173	Aac/Gac	5/18	0.47801466077924	2	FACETS	0.945	0.895	0.996	0.945	0.895	0.996	CLONAL	2	TRUE	0	0.47801466077924	2		498	593	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169561	11169561	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	274	606	0	ENST00000358026.2:c.4729del	p.Leu1577Ter	p.L1577*	ENST00000358026	NM_001128849.1	1576	tCc/tc	33/36	0.460064868764308	2	FACETS	0.834	0.788	0.881	0.834	0.788	0.881	CLONAL	2	TRUE	0	0.47801466077924	2		606	687	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257071	198257071	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	173	376	0	ENST00000335508.6:c.3871G>T	p.Asp1291Tyr	p.D1291Y	ENST00000335508	NM_012433.2	1291	Gat/Tat	25/25	0.42938464424948	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	0	0.47801466077924	2		376	361	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89444995	89444996	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0048813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	390	348	1	ENST00000336596.2:c.1315_1316delinsTA	p.Pro439Tyr	p.P439Y	ENST00000336596	NM_005233.5	439	CCt/TAt	6/17	0.47801466077924	4	FACETS	0.956	0.92	0.991	0.956	0.92	0.991	CLONAL	4	TRUE	0	0.47801466077924	4		349	631	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541658	187541658	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	50	356	0	ENST00000441802.2:c.6082A>T	p.Thr2028Ser	p.T2028S	ENST00000441802	NM_005245.3	2028	Act/Tct	10/27	1	2	FACETS	0.583	0.496	0.677	0.583	0.496	0.677	SUBCLONAL	1	TRUE	1	0.47801466077924	2		356	359	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188200	10188200	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	93	426	0	ENST00000256474.2:c.343C>A	p.His115Asn	p.H115N	ENST00000256474	NM_000551.3	115	Cac/Aac	2/3	0.383967203932398	1	FACETS	0.783	0.699	0.872	0.783	0.699	0.872	SUBCLONAL	1	TRUE	0	0.403423347789437	1		426	470	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644563	21644563	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	132	470	0	ENST00000421138.2:c.104T>A	p.Leu35His	p.L35H	ENST00000421138		35	cTt/cAt	4/16	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.403423347789437	2		470	606	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0048815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	155	347	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.233306941933662	4	FACETS	0.885	0.826	0.944			1	INDETERMINATE	3	TRUE	NA	0.620130780988875	4		347	305	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024662	31024662	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143770363	NA	P-0048815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	141	583	2	ENST00000375687.4:c.4147G>A	p.Glu1383Lys	p.E1383K	ENST00000375687	NM_015338.5	1383	Gag/Aag	13/13	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.620130780988875	2		585	422	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420213	49420213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267607237	NA	P-0048816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	266	667	3	ENST00000301067.7:c.15536G>A	p.Arg5179His	p.R5179H	ENST00000301067	NM_003482.3	5179	cGt/cAt	48/54	0.849538197972689	4	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.849538197972689	4		670	902	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0048816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	302	680	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.849538197972689	4	FACETS	1	0.991	1	0.631	0.595	0.668	CLONAL	1	TRUE	2	0.849538197972689	4		680	1042	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208356	5208356	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1257575436	NA	P-0048816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	78	675	0	ENST00000357368.4:c.5534C>T	p.Pro1845Leu	p.P1845L	ENST00000357368	NM_002850.3	1845	cCg/cTg	36/38	0.332817146275492	1	FACETS	0.274	0.242	0.308	0.274	0.242	0.308	INDETERMINATE	1	TRUE	0	0.849538197972689	1		675	386	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907037	101907037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	21	302	0	ENST00000374994.4:c.997G>A	p.Asp333Asn	p.D333N	ENST00000374994	NM_004612.2	333	Gat/Aat	6/9	0.233810124806692	3	FACETS	0.719	0.564	0.892	0.359	0.282	0.446	INDETERMINATE	1	TRUE	1	0.849538197972689	3		302	98	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221229	1221229	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	155	650	2	ENST00000326873.7:c.752G>T	p.Gly251Val	p.G251V	ENST00000326873	NM_000455.4	251	gGt/gTt	6/10	0.427209299750119	1	FACETS	0.935	0.86	1	0.935	0.86	1	CLONAL	1	TRUE	0	0.427209299750119	1		652	610	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602763	10602763	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs774469695	NA	P-0048818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	218	833	1	ENST00000171111.5:c.815G>T	p.Arg272Leu	p.R272L	ENST00000171111	NM_203500.1	272	cGc/cTc	3/6	0.427209299750119	1	FACETS	0.974	0.908	1	0.974	0.908	1	CLONAL	1	TRUE	0	0.427209299750119	1		834	824	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169464	11169464	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	155	564	0	ENST00000358026.2:c.4630G>T	p.Glu1544Ter	p.E1544*	ENST00000358026	NM_001128849.1	1544	Gag/Tag	33/36	0.427209299750119	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.427209299750119	1		564	531	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163307846	163307846	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs61747498	NA	P-0048818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	77	293	0	ENST00000271452.3:c.472G>T	p.Ala158Ser	p.A158S	ENST00000271452	NM_145697.2	158	Gca/Tca	7/14	0.268053469530152	3	FACETS	0.935	0.823	1	0.467	0.411	0.527	CLONAL	1	TRUE	1	0.427209299750119	3		293	468	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555661	21555661	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	186	668	2	ENST00000382592.4:c.2609C>T	p.Ala870Val	p.A870V	ENST00000382592	NM_014572.2	870	gCa/gTa	6/8	0.425360770604845	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.427209299750119	1		670	635	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0048819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	171	362	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	1	0.938	1	1	0.993	1	CLONAL	2	TRUE	1	0.31	2		362	544	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0048819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	243	774	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.781	0.73	0.833	1	0.993	1	SUBCLONAL	2	TRUE	1	0.31	2		778	1004	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0048819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	58	745	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.394	0.337	0.457	0.394	0.337	0.457	SUBCLONAL	1	TRUE	1	0.31	2		750	949	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs121913292	NA	P-0048819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	71	390	0	ENST00000371953.3:c.389del	p.Arg130GlnfsTer4	p.R130Qfs*4	ENST00000371953	NM_000314.4	130	cGa/ca	5/9	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.31	2		390	399	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	101	434	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.31	2		435	503	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	76	396	0	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	0.735	0.645	0.833	0.735	0.645	0.833	SUBCLONAL	1	TRUE	1	0.31	2		396	667	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0048819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	57	337	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	1	2	FACETS	0.821	0.713	0.935	1	0.974	1	CLONAL	2	TRUE	1	0.31	2		337	224	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	197	778	0	ENST00000227507.2:c.859C>T	p.Pro287Ser	p.P287S	ENST00000227507	NM_053056.2	287	Ccc/Tcc	5/5	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.31	2		778	1122	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026959	6026959	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs63750685	NA	P-0048819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	14	77	1	ENST00000265849.7:c.1437C>G	p.His479Gln	p.H479Q	ENST00000265849	NM_000535.5	479	caC/caG	11/15	1	2	FACETS	0.706	0.514	0.934	0.706	0.514	0.934	CLONAL	1	TRUE	1	0.31	2		78	128	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690848	89690848	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1224040268	NA	P-0048819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	68	259	0	ENST00000371953.3:c.253+2T>C		p.X85_splice	ENST00000371953	NM_000314.4	85			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.31	2		259	358	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097625	11097625	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	162	893	3	ENST00000358026.2:c.810del	p.Met272CysfsTer31	p.M272Cfs*31	ENST00000358026	NM_001128849.1	269	Ccc/cc	5/36	1	2	FACETS	0.883	0.808	0.961	0.883	0.808	0.961	CLONAL	1	TRUE	1	0.31	2		896	1184	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779703	3779703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	67	747	0	ENST00000262367.5:c.5345C>T	p.Ala1782Val	p.A1782V	ENST00000262367	NM_004380.2	1782	gCg/gTg	31/31	1	2	FACETS	0.472	0.409	0.541	0.472	0.409	0.541	SUBCLONAL	1	TRUE	1	0.31	2		747	915	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67646013	67646014	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs1470210640	NA	P-0048819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	74	398	3	ENST00000264010.4:c.950_951del	p.Thr317ArgfsTer91	p.T317Rfs*91	ENST00000264010	NM_006565.3	314	aAC/a	4/12	1	2	FACETS	0.787	0.689	0.892	0.787	0.689	0.892	SUBCLONAL	1	TRUE	1	0.31	2		401	607	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589576	67589576	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1289537429	NA	P-0048819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	34	195	0	ENST00000274335.5:c.1344del	p.Lys448AsnfsTer32	p.K448Nfs*32	ENST00000274335		447	Aaa/aa	10/15	1	2	FACETS	0.795	0.652	0.954	0.795	0.652	0.954	CLONAL	1	TRUE	1	0.31	2		195	276	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986865	36986865	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748087644	NA	P-0048819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	33	326	0	ENST00000354822.5:c.824C>T	p.Pro275Leu	p.P275L	ENST00000354822	NM_001079668.2	275	cCg/cTg	3/3	1	2	FACETS	0.459	0.373	0.556	0.459	0.373	0.556	SUBCLONAL	1	TRUE	1	0.31	2		326	464	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214871	36214871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	80	742	8	ENST00000222270.7:c.3302del	p.Pro1101LeufsTer81	p.P1101Lfs*81	ENST00000222270	NM_014727.1	1099	ggC/gg	8/37	1	2	FACETS	0.464	0.407	0.526	0.464	0.407	0.526	SUBCLONAL	1	TRUE	1	0.31	2		750	1112	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76949319	76949320	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	19	305	0	ENST00000373344.5:c.477dup	p.Arg160ThrfsTer29	p.R160Tfs*29	ENST00000373344	NM_000489.3	159	-/A	6/35	1	2	FACETS	0.326	0.247	0.42	0.326	0.247	0.42	SUBCLONAL	1	TRUE	1	0.31	2		305	376	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300039	137300040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755912201	NA	P-0048819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	112	813	7	ENST00000481739.1:c.331dup	p.Leu111ProfsTer70	p.L111Pfs*70	ENST00000481739	NM_002957.4	108	-/C	3/10	1	2	FACETS	0.72	0.647	0.799	0.72	0.647	0.799	SUBCLONAL	1	TRUE	1	0.31	2		820	1003	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711913	89711913	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs878853012	NA	P-0048819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	45	436	0	ENST00000371953.3:c.531T>G	p.Tyr177Ter	p.Y177*	ENST00000371953	NM_000314.4	177	taT/taG	6/9	1	2	FACETS	0.606	0.509	0.713	0.606	0.509	0.713	SUBCLONAL	1	TRUE	1	0.31	2		436	479	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582342	119582342	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	30	344	0	ENST00000316626.5:c.1059del	p.Phe353LeufsTer?	p.F353Lfs*?	ENST00000316626		353	ttT/tt	10/12	1	2	FACETS	0.359	0.288	0.44	0.359	0.288	0.44	SUBCLONAL	1	TRUE	1	0.31	2		344	539	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097702	27097702	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	132	550	0	ENST00000324856.7:c.3292del	p.Gln1098SerfsTer63	p.Q1098Sfs*63	ENST00000324856	NM_006015.4	1097	atC/at	12/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.31	2		550	731	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711930	89711930	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	40	413	0	ENST00000371953.3:c.548A>C	p.Lys183Thr	p.K183T	ENST00000371953	NM_000314.4	183	aAg/aCg	6/9	1	2	FACETS	0.555	0.461	0.66	0.555	0.461	0.66	SUBCLONAL	1	TRUE	1	0.31	2		413	465	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896611	78896611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	66	630	1	ENST00000306801.3:c.2608C>T	p.His870Tyr	p.H870Y	ENST00000306801	NM_020761.2	870	Cac/Tac	22/34	1	2	FACETS	0.479	0.415	0.549	0.479	0.415	0.549	SUBCLONAL	1	TRUE	1	0.31	2		631	889	SUCCESS
APC	324	MSKCC	GRCh37	5	112174077	112174077	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs730881242	NA	P-0048819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	60	257	0	ENST00000257430.4:c.2786A>G	p.His929Arg	p.H929R	ENST00000257430	NM_000038.5	929	cAt/cGt	16/16	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.31	2		257	386	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109319889	109319889	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	35	523	0	ENST00000436639.2:c.799C>T	p.His267Tyr	p.H267Y	ENST00000436639	NM_014454.2	267	Cac/Tac	5/10	1	2	FACETS	0.331	0.27	0.399	0.331	0.27	0.399	SUBCLONAL	1	TRUE	1	0.31	2		523	683	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878293	151878293	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	37	468	0	ENST00000262189.6:c.6652del	p.Tyr2218ThrfsTer21	p.Y2218Tfs*21	ENST00000262189	NM_170606.2	2218	Tac/ac	36/59	1	2	FACETS	0.375	0.308	0.45	0.375	0.308	0.45	SUBCLONAL	1	TRUE	1	0.31	2		468	637	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371798	55371819	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCGGCCGCGCTGGGCCCCGA	AGGCGGCCGCGCTGGGCCCCGA	-	novel	NA	P-0048819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	120	210	0	ENST00000297316.4:c.488_509del	p.Gln163ArgfsTer217	p.Q163Rfs*217	ENST00000297316	NM_022454.3	163	cAGGCGGCCGCGCTGGGCCCCGAg/cg	2/2	1	2	FACETS	1	0.955	1	1	0.99	1	CLONAL	2	TRUE	1	0.31	2		210	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0048820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	525	489	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.728107784709258	2	FACETS	0.972	0.944	0.999	0.972	0.944	0.999	CLONAL	2	TRUE	0	0.728107784709258	2		489	742	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030367	49030368	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	239	330	0	ENST00000267163.4:c.1848dup	p.Gly617ArgfsTer36	p.G617Rfs*36	ENST00000267163	NM_000321.2	614	-/A	19/27	0.393246940045361	5	FACETS	1	0.989	1	0.813	0.766	0.861	INDETERMINATE	2	TRUE	2	0.728107784709258	5		330	563	SUCCESS
APC	324	MSKCC	GRCh37	5	112170777	112170780	+	frameshift_variant	Frame_Shift_Del	DEL	CAGA	CAGA	-	rs878853420	NA	P-0048820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	130	567	0	ENST00000257430.4:c.1875_1878del	p.Asn627LeufsTer2	p.N627Lfs*2	ENST00000257430	NM_000038.5	625	CAGAca/ca	15/16	0.700059356337957	2	FACETS	0.616	0.56	0.673	0.308	0.28	0.337	SUBCLONAL	1	TRUE	0	0.728107784709258	2		567	580	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857307	68857307	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs971882211	NA	P-0048820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	158	350	1	ENST00000261769.5:c.1942G>T	p.Glu648Ter	p.E648*	ENST00000261769	NM_004360.3	648	Gaa/Taa	13/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.728107784709258	2		351	383	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412898	49412898	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519954	NA	P-0048820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	280	687	0	ENST00000418115.1:c.125A>G	p.Tyr42Cys	p.Y42C	ENST00000418115	NM_001664.2	42	tAt/tGt	2/5	1	2	FACETS	0.98	0.924	1	0.98	0.924	1	CLONAL	1	TRUE	1	0.728107784709258	2		687	785	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845371	156845371	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	578	960	0	ENST00000524377.1:c.1414G>T	p.Gly472Cys	p.G472C	ENST00000524377	NM_002529.3	472	Ggt/Tgt	12/17	0.24017062613466	5	FACETS	0.834	0.803	0.866	0.834	0.803	0.866	INDETERMINATE	3	TRUE	2	0.728107784709258	5		960	1327	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420661	49420661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555185875	NA	P-0048820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	315	792	0	ENST00000301067.7:c.15088C>T	p.Arg5030Cys	p.R5030C	ENST00000301067	NM_003482.3	5030	Cgt/Tgt	48/54	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.728107784709258	2		792	829	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967048	18967048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762952797	NA	P-0048820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	329	937	4	ENST00000262803.5:c.1763C>T	p.Ser588Leu	p.S588L	ENST00000262803	NM_002911.3	588	tCg/tTg	13/24	0.567753293941635	4	FACETS	1	0.991	1	0.407	0.384	0.431	CLONAL	1	TRUE	1	0.728107784709258	4		941	1279	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612623	228612623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1277450211	NA	P-0048820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	102	794	0	ENST00000366696.1:c.404G>A	p.Arg135Gln	p.R135Q	ENST00000366696	NM_003493.2	135	cGg/cAg	1/1	0.24017062613466	5	FACETS	0.565	0.504	0.63	0.188	0.168	0.21	INDETERMINATE	1	TRUE	2	0.728107784709258	5		794	1038	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575113	64575113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1225847249	NA	P-0048820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	159	775	0	ENST00000312049.6:c.694C>T	p.Arg232Cys	p.R232C	ENST00000312049	NM_130799.2	232	Cgc/Tgc	4/10	0.334027719517096	2	FACETS	0.509	0.467	0.553	0.255	0.233	0.277	INDETERMINATE	1	TRUE	0	0.728107784709258	2		775	858	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922288	100922288	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	47	302	0	ENST00000325455.5:c.2224T>G	p.Leu742Val	p.L742V	ENST00000325455	NM_001202474.3	742	Tta/Gta	5/8	0.334027719517096	2	FACETS	0.402	0.341	0.469	0.201	0.17	0.235	INDETERMINATE	1	TRUE	0	0.728107784709258	2		302	321	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947575	48947576	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	246	379	0	ENST00000267163.4:c.1166dup	p.Leu389PhefsTer6	p.L389Ffs*6	ENST00000267163	NM_000321.2	388	att/aTtt	12/27	0.393246940045361	5	FACETS	1	0.95	1	0.675	0.634	0.717	INDETERMINATE	2	TRUE	2	0.728107784709258	5		379	698	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847398	68847398	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1555515925	NA	P-0048820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	152	544	0	ENST00000261769.5:c.1320G>T	p.Lys440Asn	p.K440N	ENST00000261769	NM_004360.3	440	aaG/aaT	9/16	1	2	FACETS	0.82	0.755	0.887	0.82	0.755	0.887	CLONAL	1	TRUE	1	0.728107784709258	2		544	509	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968103	55968103	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	183	497	0	ENST00000263923.4:c.2227C>A	p.Leu743Ile	p.L743I	ENST00000263923	NM_002253.2	743	Ctt/Att	15/30	0.401227453317614	1	FACETS	0.692	0.645	0.74	0.692	0.645	0.74	INDETERMINATE	1	TRUE	0	0.728107784709258	1		497	462	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	640	576	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.380859430599328	9	FACETS	0.978	0.95	1			1	CLONAL	8	TRUE	NA	0.380859430599328	9		576	1002	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0048821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	138	557	5	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.25573925407944	1	FACETS	0.811	0.739	0.887	0.811	0.739	0.887	CLONAL	1	TRUE	0	0.380859430599328	1		562	723	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060886	38060886	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773225075	NA	P-0048821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	118	678	0	ENST00000250448.2:c.1103C>T	p.Ala368Val	p.A368V	ENST00000250448	NM_004496.3	368	gCc/gTc	2/2	1	2	FACETS	0.821	0.741	0.905	0.821	0.741	0.905	CLONAL	1	TRUE	1	0.380859430599328	2		678	755	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170876	56170877	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	47	298	0	ENST00000399503.3:c.1704_1705insA	p.Val569SerfsTer7	p.V569Sfs*7	ENST00000399503	NM_005921.1	568	-/A	10/20	NA	2	FACETS	0.673	0.569	0.786			1	INDETERMINATE	1	TRUE	NA	0.380859430599328	2		298	367	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0048824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	50	394	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			1	2	FACETS	0.843	0.718	0.978	0.843	0.718	0.978	CLONAL	1	TRUE	1	0.350023638885339	2		394	339	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560239	95560239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	34	251	0	ENST00000393063.1:c.5350G>A	p.Gly1784Arg	p.G1784R	ENST00000393063	NM_030621.3	1784	Gga/Aga	25/28	1	2	FACETS	0.722	0.593	0.866	0.722	0.593	0.866	SUBCLONAL	1	TRUE	1	0.350023638885339	2		251	269	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974763	21974764	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCCGC	novel	NA	P-0048824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	60	321	0	ENST00000304494.5:c.58_63dup	p.Ala20_Ala21dup	p.A20_A21dup	ENST00000304494	NM_000077.4	20	-/GCGGCC	1/3	0.350023638885339	3	FACETS	1	0.948	1	0.598	0.518	0.683	CLONAL	1	TRUE	1	0.350023638885339	3		321	337	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506946	186506946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	32	84	0	ENST00000323963.5:c.1112G>A	p.Gly371Asp	p.G371D	ENST00000323963		371	gGt/gAt	11/11	1	2	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	1	0.255618449858901	2		84	238	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922704	44922704	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	27	321	1	ENST00000377967.4:c.1565G>A	p.Gly522Glu	p.G522E	ENST00000377967	NM_021140.2	522	gGa/gAa	16/29	0.255618449858901	1	FACETS	0.501	0.398	0.618	0.501	0.398	0.618	SUBCLONAL	1	TRUE	0	0.255618449858901	1		322	368	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663906	29663906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	27	171	0	ENST00000356175.3:c.6338G>A	p.Cys2113Tyr	p.C2113Y	ENST00000356175	NM_000267.3	2113	tGt/tAt	41/57	0.181107242725958	2	FACETS	0.585	0.466	0.722	0.293	0.233	0.361	SUBCLONAL	1	TRUE	0	0.255618449858901	2		171	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934874	NA	P-0048829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	30	669	0	ENST00000269305.4:c.451C>A	p.Pro151Thr	p.P151T	ENST00000269305	NM_001126112.2	151	Ccc/Acc	5/11	1	2	FACETS	0.253	0.203	0.311	0.253	0.203	0.311	SUBCLONAL	1	TRUE	1	0.252077507559092	2		669	940	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039600	180039600	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	40	633	0	ENST00000261937.6:c.3443T>C	p.Met1148Thr	p.M1148T	ENST00000261937	NM_182925.4	1148	aTg/aCg	26/30	0.111810989972883	3	FACETS	0.469	0.388	0.559	0.234	0.194	0.28	INDETERMINATE	1	TRUE	1	0.252077507559092	3		633	762	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0048831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	16	369	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.376	0.276	0.496	0.376	0.276	0.496	SUBCLONAL	1	TRUE	1	0.12	2		370	710	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0048831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	11	289	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	1	2	FACETS	0.362	0.249	0.505	0.362	0.249	0.505	SUBCLONAL	1	TRUE	1	0.12	2		289	506	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117848	70117848	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0048831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	72	409	0	ENST00000245479.2:c.316A>T	p.Lys106Ter	p.K106*	ENST00000245479	NM_000346.3	106	Aag/Tag	1/3	1	2	FACETS	0.8	0.698	0.91	1	0.976	1	CLONAL	2	TRUE	1	0.12	2		409	750	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016330	150016330	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0121602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	47	377	0	ENST00000253339.5:c.376A>G	p.Thr126Ala	p.T126A	ENST00000253339		126	Act/Gct	2/7	1	2	FACETS	0.213	0.18	0.251	0.213	0.18	0.251	SUBCLONAL	1	NA	1	0.818629140747143	2		377	538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1064795203	NA	P-0048835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	223	354	0	ENST00000269305.4:c.532C>G	p.His178Asp	p.H178D	ENST00000269305	NM_001126112.2	178	Cac/Gac	5/11	0.781258300531946	1	FACETS	0.82	0.775	0.865	0.82	0.775	0.865	CLONAL	1	TRUE	0	0.781258300531946	1		354	424	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440019	220440019	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	396	398	0	ENST00000243786.2:c.872G>C	p.Cys291Ser	p.C291S	ENST00000243786	NM_002191.3	291	tGt/tCt	2/2	1	2	FACETS	0.961	0.916	1	0.961	0.916	1	CLONAL	1	TRUE	1	0.781258300531946	2		398	1055	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456683	138456683	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	47	187	0	ENST00000289153.2:c.667G>C	p.Val223Leu	p.V223L	ENST00000289153	NM_006219.2	223	Gta/Cta	4/22	0.127201363391298	3	FACETS	0.329	0.278	0.386	0.165	0.139	0.193	INDETERMINATE	1	TRUE	1	0.781258300531946	3		187	508	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775611	9775611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1375117381	NA	P-0048836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	285	608	1	ENST00000377346.4:c.154C>T	p.Arg52Cys	p.R52C	ENST00000377346	NM_005026.3	52	Cgc/Tgc	4/24	0.767046232288267	1	FACETS	0.998	0.954	1	0.998	0.954	1	CLONAL	1	TRUE	0	0.767046232288267	1		609	459	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557885	21557886	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	248	330	0	ENST00000382592.4:c.1959dup	p.Asn654Ter	p.N654*	ENST00000382592	NM_014572.2	653	-/T	5/8	0.767046232288267	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.767046232288267	1		330	363	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222753	5222753	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	205	484	0	ENST00000357368.4:c.3050G>A	p.Gly1017Asp	p.G1017D	ENST00000357368	NM_002850.3	1017	gGc/gAc	18/38	0.410640037139637	1	FACETS	0.486	0.453	0.52	0.486	0.453	0.52	INDETERMINATE	1	TRUE	0	0.767046232288267	1		484	678	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150022994	150023012	+	frameshift_variant	Frame_Shift_Del	DEL	TTTGCAAATGGAAGCAGAG	TTTGCAAATGGAAGCAGAG	-	novel	NA	P-0048836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	353	399	0	ENST00000253339.5:c.251_269del	p.Ser84LeufsTer42	p.S84Lfs*42	ENST00000253339		84	tCTCTGCTTCCATTTGCAAAt/tt	1/7	0.767046232288267	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.767046232288267	1		399	468	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023020	150023020	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	380	446	0	ENST00000253339.5:c.243T>G	p.Ile81Met	p.I81M	ENST00000253339		81	atT/atG	1/7	0.767046232288267	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.767046232288267	1		446	507	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411479	63411479	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	209	697	0	ENST00000330258.3:c.1688C>T	p.Thr563Ile	p.T563I	ENST00000330258	NM_152424.3	563	aCc/aTc	2/2	0.444682380689082	1	FACETS	0.414	0.385	0.444	0.414	0.385	0.444	INDETERMINATE	1	TRUE	0	0.767046232288267	1		697	811	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0048837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	1063	370	1	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	0.613561848041313	9	FACETS	0.989	0.971	1			1	CLONAL	8	TRUE	NA	0.613561848041313	9		371	1379	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856020	68856020	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	158	412	1	ENST00000261769.5:c.1828C>T	p.Gln610Ter	p.Q610*	ENST00000261769	NM_004360.3	610	Cag/Tag	12/16	0.613561848041313	1	FACETS	0.897	0.832	0.963	0.897	0.832	0.963	CLONAL	1	TRUE	0	0.613561848041313	1		413	398	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754827	29754827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373120394	NA	P-0048837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	155	420	0	ENST00000389048.3:c.1108G>A	p.Glu370Lys	p.E370K	ENST00000389048	NM_004304.4	370	Gag/Aag	4/29	1	2	FACETS	0.912	0.84	0.987	0.912	0.84	0.987	CLONAL	1	TRUE	1	0.613561848041313	2		420	554	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120764	115120765	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0048837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	235	503	0	ENST00000257566.3:c.241dup	p.Leu81ProfsTer30	p.L81Pfs*30	ENST00000257566	NM_016569.3	81	ctg/cCtg	1/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.613561848041313	2		503	741	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0048842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	84	351	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	NA	2	FACETS	0.914	0.808	1			1	INDETERMINATE	1	TRUE	NA	0.312683508269569	2		351	588	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946174	13946174	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1176085263	NA	P-0048842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	81	366	0	ENST00000405192.2:c.922C>T	p.Arg308Trp	p.R308W	ENST00000405192	NM_001163147.1	308	Cgg/Tgg	10/12	1	2	FACETS	0.826	0.728	0.931	0.826	0.728	0.931	CLONAL	1	TRUE	1	0.312683508269569	2		366	627	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484218	8484218	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	83	425	0	ENST00000356435.5:c.3314C>A	p.Pro1105Gln	p.P1105Q	ENST00000356435		1105	cCa/cAa	19/35	1	2	FACETS	0.843	0.744	0.948	0.843	0.744	0.948	CLONAL	1	TRUE	1	0.312683508269569	2		425	630	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643297	38643298	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0048842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	61	315	0	ENST00000299084.4:c.768_769dup	p.Arg257LeufsTer47	p.R257Lfs*47	ENST00000299084	NM_152594.2	256	cgt/cgTCt	7/7	1	2	FACETS	0.841	0.727	0.964	0.841	0.727	0.964	CLONAL	1	TRUE	1	0.312683508269569	2		315	464	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937641	76937641	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	38	178	0	ENST00000373344.5:c.3107A>G	p.Lys1036Arg	p.K1036R	ENST00000373344	NM_000489.3	1036	aAg/aGg	9/35	1	2	FACETS	0.827	0.686	0.982	0.827	0.686	0.982	CLONAL	1	TRUE	1	0.312683508269569	2		178	294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0048843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	371	823	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.882498705794983	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.882498705794983	1		823	464	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	272	327	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.718122877721794	2		327	512	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	576	774	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.962	0.935	0.988	1	0.998	1	CLONAL	2	TRUE	1	0.718122877721794	2		778	834	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	168	403	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.818	0.756	0.882	0.818	0.756	0.882	CLONAL	1	TRUE	1	0.718122877721794	2		404	572	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	218	745	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.824	0.769	0.88	0.824	0.769	0.88	CLONAL	1	TRUE	1	0.718122877721794	2		750	737	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	226	434	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.894	0.851	0.936	1	0.995	1	CLONAL	2	TRUE	1	0.718122877721794	2		435	352	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979987	7979987	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746723399	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	240	517	2	ENST00000319144.4:c.1350del	p.Leu451SerfsTer16	p.L451Sfs*16	ENST00000319144	NM_001139.2	450	ggG/gg	10/15	1	2	FACETS	0.943	0.885	1	0.943	0.885	1	CLONAL	1	TRUE	1	0.718122877721794	2		519	709	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522598	157522598	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554236040	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	191	415	0	ENST00000346085.5:c.4870C>T	p.Arg1624Ter	p.R1624*	ENST00000346085	NM_020732.3	1624	Cga/Tga	18/20	1	2	FACETS	0.866	0.805	0.929	0.866	0.805	0.929	CLONAL	1	TRUE	1	0.718122877721794	2		415	614	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308383	15308383	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	242	562	0	ENST00000263388.2:c.125del	p.Pro42LeufsTer194	p.P42Lfs*194	ENST00000263388	NM_000435.2	42	cCt/ct	2/33	1	2	FACETS	0.847	0.793	0.901	0.847	0.793	0.901	CLONAL	1	TRUE	1	0.718122877721794	2		562	796	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	117	274	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.99	0.905	1	0.99	0.905	1	CLONAL	1	TRUE	1	0.718122877721794	2		274	329	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438316	110438317	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	rs532810290	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	62	218	0	ENST00000375856.3:c.82_84dup	p.Asn28dup	p.N28dup	ENST00000375856	NM_003749.2	28	-/AAC	1/2	1	2	FACETS	0.526	0.458	0.6	0.526	0.458	0.6	SUBCLONAL	1	TRUE	1	0.718122877721794	2		218	328	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983058	149983058	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	116	335	0	ENST00000253339.5:c.3200del	p.Asn1067MetfsTer61	p.N1067Mfs*61	ENST00000253339		1067	aAt/at	7/7	1	2	FACETS	0.818	0.744	0.895	0.818	0.744	0.895	CLONAL	1	TRUE	1	0.718122877721794	2		335	395	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422384	47422384	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	160	402	0	ENST00000377045.4:c.23del	p.Pro8LeufsTer26	p.P8Lfs*26	ENST00000377045	NM_001654.4	6	ggC/gg	2/16	1	2	FACETS	0.85	0.785	0.918	0.85	0.785	0.918	CLONAL	1	TRUE	1	0.718122877721794	2		402	524	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465952	69465952	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	247	621	1	ENST00000227507.2:c.790C>T	p.Gln264Ter	p.Q264*	ENST00000227507	NM_053056.2	264	Cag/Tag	5/5	1	2	FACETS	0.936	0.879	0.994	0.936	0.879	0.994	CLONAL	1	TRUE	1	0.718122877721794	2		622	735	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439853	51439853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1557609882	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	126	280	0	ENST00000262662.1:c.418G>A	p.Ala140Thr	p.A140T	ENST00000262662		140	Gcc/Acc	4/4	1	2	FACETS	0.875	0.8	0.953	0.875	0.8	0.953	CLONAL	1	TRUE	1	0.718122877721794	2		280	401	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	145	280	0	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.971	0.895	1	0.971	0.895	1	CLONAL	1	TRUE	1	0.718122877721794	2		280	416	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720741	89720741	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs371387815	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	48	144	0	ENST00000371953.3:c.892C>T	p.Gln298Ter	p.Q298*	ENST00000371953	NM_000314.4	298	Caa/Taa	8/9	0.718122877721794	2	FACETS	1	0.969	1	0.704	0.619	0.788	CLONAL	1	TRUE	0	0.718122877721794	2		144	95	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435468	121435468	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs371807951	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	305	742	1	ENST00000257555.6:c.1501G>A	p.Ala501Thr	p.A501T	ENST00000257555		501	Gcc/Acc	7/10	1	2	FACETS	0.869	0.82	0.918	0.869	0.82	0.918	CLONAL	1	TRUE	1	0.718122877721794	2		743	978	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106951	27106951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	197	425	0	ENST00000324856.7:c.6562C>T	p.Gln2188Ter	p.Q2188*	ENST00000324856	NM_006015.4	2188	Cag/Tag	20/20	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.718122877721794	2		425	546	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843236	128843237	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1248200595	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	248	559	0	ENST00000249373.3:c.349dup	p.Arg117ProfsTer19	p.R117Pfs*19	ENST00000249373	NM_005631.4	115	gcc/gCcc	2/12	1	2	FACETS	0.815	0.764	0.868	0.815	0.764	0.868	CLONAL	1	TRUE	1	0.718122877721794	2		559	847	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498235	498235	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	61	237	1	ENST00000399788.2:c.23del	p.Gly8AlafsTer58	p.G8Afs*58	ENST00000399788	NM_001042603.1	8	gGc/gc	1/28	1	2	FACETS	0.394	0.341	0.452	0.394	0.341	0.452	SUBCLONAL	1	TRUE	1	0.718122877721794	2		238	431	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447429	12447429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573789959	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	213	414	0	ENST00000287820.6:c.668C>T	p.Ala223Val	p.A223V	ENST00000287820	NM_015869.4	223	gCg/gTg	5/7	1	2	FACETS	0.984	0.92	1	0.984	0.92	1	CLONAL	1	TRUE	1	0.718122877721794	2		414	603	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936093	178936093	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913275	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	146	427	0	ENST00000263967.3:c.1635G>C	p.Glu545Asp	p.E545D	ENST00000263967	NM_006218.2	545	gaG/gaC	10/21	1	2	FACETS	0.916	0.843	0.99	0.916	0.843	0.99	CLONAL	1	TRUE	1	0.718122877721794	2		427	444	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284970	15284970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	345	789	0	ENST00000263388.2:c.4645G>A	p.Ala1549Thr	p.A1549T	ENST00000263388	NM_000435.2	1549	Gcg/Acg	25/33	1	2	FACETS	0.923	0.875	0.972	0.923	0.875	0.972	CLONAL	1	TRUE	1	0.718122877721794	2		789	1041	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141570600	141570600	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	185	382	0	ENST00000220592.5:c.528del	p.Val177TrpfsTer37	p.V177Wfs*37	ENST00000220592	NM_012154.3	176	ccC/cc	5/19	1	2	FACETS	0.906	0.841	0.971	0.906	0.841	0.971	CLONAL	1	TRUE	1	0.718122877721794	2		382	569	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58700941	58700941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	219	457	0	ENST00000305921.3:c.532G>A	p.Val178Ile	p.V178I	ENST00000305921	NM_003620.3	178	Gtc/Atc	2/6	1	2	FACETS	0.935	0.875	0.997	0.935	0.875	0.997	CLONAL	1	TRUE	1	0.718122877721794	2		457	652	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439649	220439649	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	354	784	0	ENST00000243786.2:c.502T>C	p.Ser168Pro	p.S168P	ENST00000243786	NM_002191.3	168	Tct/Cct	2/2	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.718122877721794	2		784	965	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615005	43615005	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760012685	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	220	592	0	ENST00000355710.3:c.2419G>A	p.Ala807Thr	p.A807T	ENST00000355710	NM_020975.4	807	Gcc/Acc	14/20	1	2	FACETS	0.894	0.836	0.954	0.894	0.836	0.954	CLONAL	1	TRUE	1	0.718122877721794	2		592	685	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457796	149457796	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	157	397	0	ENST00000286301.3:c.608del	p.Pro203GlnfsTer3	p.P203Qfs*3	ENST00000286301	NM_005211.3	203	cCa/ca	5/22	1	2	FACETS	0.762	0.701	0.824	0.762	0.701	0.824	SUBCLONAL	1	TRUE	1	0.718122877721794	2		397	574	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373586	118373586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	133	259	0	ENST00000534358.1:c.6979G>A	p.Ala2327Thr	p.A2327T	ENST00000534358	NM_005933.3	2327	Gct/Act	27/36	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.718122877721794	2		259	364	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398041	4398041	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	65	458	0	ENST00000261254.3:c.605T>A	p.Ile202Asn	p.I202N	ENST00000261254	NM_001759.3	202	aTc/aAc	4/5	1	2	FACETS	0.329	0.285	0.376	0.329	0.285	0.376	SUBCLONAL	1	TRUE	1	0.718122877721794	2		458	551	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254683	46254683	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	168	282	0	ENST00000334344.6:c.4873A>T	p.Met1625Leu	p.M1625L	ENST00000334344	NM_152641.2	1625	Atg/Ttg	16/21	1	2	FACETS	0.919	0.851	0.989	0.919	0.851	0.989	CLONAL	1	TRUE	1	0.718122877721794	2		282	509	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965188	81965188	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	212	459	0	ENST00000359376.3:c.2668A>G	p.Thr890Ala	p.T890A	ENST00000359376	NM_002661.3	890	Aca/Gca	25/33	1	2	FACETS	0.906	0.846	0.967	0.906	0.846	0.967	CLONAL	1	TRUE	1	0.718122877721794	2		459	652	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838157	89838157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201589909	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	222	467	0	ENST00000389301.3:c.2080G>A	p.Asp694Asn	p.D694N	ENST00000389301	NM_000135.2	694	Gac/Aac	23/43	1	2	FACETS	0.916	0.857	0.976	0.916	0.857	0.976	CLONAL	1	TRUE	1	0.718122877721794	2		467	675	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646952	37646952	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	237	400	0	ENST00000447079.4:c.2074A>G	p.Thr692Ala	p.T692A	ENST00000447079	NM_015083.1	692	Aca/Gca	3/14	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.718122877721794	2		400	654	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138513	11138513	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	234	450	0	ENST00000358026.2:c.3269C>A	p.Pro1090His	p.P1090H	ENST00000358026	NM_001128849.1	1090	cCc/cAc	24/36	1	2	FACETS	0.949	0.889	1	0.949	0.889	1	CLONAL	1	TRUE	1	0.718122877721794	2		450	687	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272188	15272188	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1431728665	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	191	571	0	ENST00000263388.2:c.6251T>C	p.Leu2084Pro	p.L2084P	ENST00000263388	NM_000435.2	2084	cTg/cCg	33/33	1	2	FACETS	0.852	0.792	0.914	0.852	0.792	0.914	CLONAL	1	TRUE	1	0.718122877721794	2		571	624	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214068	36214068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	366	698	0	ENST00000222270.7:c.2894G>A	p.Arg965Gln	p.R965Q	ENST00000222270	NM_014727.1	965	cGa/cAa	6/37	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.718122877721794	2		698	967	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50138869	50138869	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	391	694	0	ENST00000246792.3:c.621G>T	p.Arg207Ser	p.R207S	ENST00000246792	NM_006270.3	207	agG/agT	6/6	1	2	FACETS	0.985	0.938	1	0.985	0.938	1	CLONAL	1	TRUE	1	0.718122877721794	2		694	1105	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617509	158617509	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	221	366	0	ENST00000263640.3:c.1147G>C	p.Ala383Pro	p.A383P	ENST00000263640	NM_001105.4	383	Gcc/Ccc	9/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.718122877721794	2		366	603	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248510	212248510	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	166	303	0	ENST00000342788.4:c.3757C>A	p.Leu1253Ile	p.L1253I	ENST00000342788	NM_005235.2	1253	Ctt/Att	28/28	1	2	FACETS	0.886	0.819	0.954	0.886	0.819	0.954	CLONAL	1	TRUE	1	0.718122877721794	2		303	522	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31495455	31495455	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	170	385	0	ENST00000344624.3:c.1693A>G	p.Thr565Ala	p.T565A	ENST00000344624		565	Acc/Gcc	9/33	1	2	FACETS	0.785	0.726	0.847	0.785	0.726	0.847	SUBCLONAL	1	TRUE	1	0.718122877721794	2		385	603	SUCCESS
APC	324	MSKCC	GRCh37	5	112174803	112174803	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372481703	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	62	128	0	ENST00000257430.4:c.3512G>A	p.Arg1171His	p.R1171H	ENST00000257430	NM_000038.5	1171	cGt/cAt	16/16	1	2	FACETS	0.818	0.718	0.924	0.818	0.718	0.924	CLONAL	1	TRUE	1	0.718122877721794	2		128	211	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287565	33287565	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760674231	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	228	486	0	ENST00000374542.5:c.1532G>A	p.Gly511Asp	p.G511D	ENST00000374542	NM_001141970.1	511	gGc/gAc	6/8	1	2	FACETS	0.883	0.826	0.941	0.883	0.826	0.941	CLONAL	1	TRUE	1	0.718122877721794	2		486	719	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700250	117700250	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs752798332	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	128	314	1	ENST00000368508.3:c.2569C>A	p.Leu857Met	p.L857M	ENST00000368508	NM_002944.2	857	Ctg/Atg	17/43	1	2	FACETS	0.969	0.888	1	0.969	0.888	1	CLONAL	1	TRUE	1	0.718122877721794	2		315	368	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469756	157469756	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	217	461	0	ENST00000346085.5:c.2552-2A>G		p.X851_splice	ENST00000346085	NM_020732.3	851			1	2	FACETS	0.972	0.909	1	0.972	0.909	1	CLONAL	1	TRUE	1	0.718122877721794	2		461	622	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469794	157469794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	242	530	1	ENST00000346085.5:c.2588C>T	p.Pro863Leu	p.P863L	ENST00000346085	NM_020732.3	863	cCc/cTc	9/20	1	2	FACETS	0.88	0.825	0.936	0.88	0.825	0.936	CLONAL	1	TRUE	1	0.718122877721794	2		531	766	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15818017	15818017	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs748769419	NA	P-0048844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	56	164	0	ENST00000307771.7:c.144G>T	p.Glu48Asp	p.E48D	ENST00000307771	NM_005089.3	48	gaG/gaT	3/11	1	2	FACETS	0.808	0.703	0.918	0.808	0.703	0.918	CLONAL	1	TRUE	1	0.718122877721794	2		164	193	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577520	7577521	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGG	novel	NA	P-0048845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	305	547	0	ENST00000269305.4:c.758_760dup	p.Thr253dup	p.T253dup	ENST00000269305	NM_001126112.2	253	atc/aCCAtc	7/11	0.115182003271348	5	FACETS	1	0.97	1	1	0.995	1	INDETERMINATE	4	TRUE	2	0.807008442477023	5		547	415	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560476	95560476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	220	463	0	ENST00000393063.1:c.5113G>A	p.Glu1705Lys	p.E1705K	ENST00000393063	NM_030621.3	1705	Gaa/Aaa	25/28	0.807008442477023	2	FACETS	0.963	0.926	0.999	0.963	0.926	0.999	CLONAL	2	TRUE	0	0.807008442477023	2		463	283	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352720	70352720	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	59	444	0	ENST00000374080.3:c.4441T>C	p.Phe1481Leu	p.F1481L	ENST00000374080		1481	Ttc/Ctc	32/45	0.40301442922399	3	FACETS	0.769	0.668	0.876	0.256	0.222	0.292	INDETERMINATE	1	TRUE	0	0.807008442477023	3		444	267	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0048846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	654	829	1	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.770226510739003	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.770226510739003	2		830	813	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274911	41274911	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs868651538	NA	P-0048846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	134	304	0	ENST00000349496.5:c.1161T>A	p.Asn387Lys	p.N387K	ENST00000349496	NM_001904.3	387	aaT/aaA	8/15	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.770226510739003	2		304	337	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609313	39609313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760479037	NA	P-0048846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	71	228	0	ENST00000262039.4:c.1615C>T	p.Arg539Cys	p.R539C	ENST00000262039	NM_002647.2	539	Cgt/Tgt	15/25	0.770226510739003	3	FACETS	0.721	0.634	0.815	0.361	0.317	0.408	SUBCLONAL	1	TRUE	1	0.770226510739003	3		228	354	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023039	33023039	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	154	444	1	ENST00000300177.4:c.148C>T	p.Pro50Ser	p.P50S	ENST00000300177	NM_001191322.1	50	Ccc/Tcc	2/2	0.762548623405191	4	FACETS	1	0.978	1	0.395	0.363	0.429	CLONAL	1	TRUE	1	0.770226510739003	4		445	597	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349086	11349086	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	206	429	1	ENST00000332029.2:c.250C>A	p.Leu84Met	p.L84M	ENST00000332029	NM_003745.1	84	Ctg/Atg	2/2	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.770226510739003	2		430	489	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0048847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	188	932	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.457394568884964	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.457394568884964	1		934	581	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0048847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	58	194	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.845	0.732	0.967	0.845	0.732	0.967	CLONAL	1	TRUE	1	0.457394568884964	2		194	300	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100196	27100196	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	58	403	0	ENST00000324856.7:c.3992del	p.Gln1331ArgfsTer150	p.Q1331Rfs*150	ENST00000324856	NM_006015.4	1331	cAg/cg	16/20	0.221384824113119	1	FACETS	0.37	0.318	0.427	0.37	0.318	0.427	INDETERMINATE	1	TRUE	0	0.457394568884964	1		403	529	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048632	180048632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	236	756	2	ENST00000261937.6:c.1930G>A	p.Ala644Thr	p.A644T	ENST00000261937	NM_182925.4	644	Gcg/Acg	13/30	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.457394568884964	2		758	1019	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630491	47630491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768661914	NA	P-0048847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	283	694	0	ENST00000233146.2:c.161C>T	p.Ala54Val	p.A54V	ENST00000233146	NM_000251.2	54	gCc/gTc	1/16	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.457394568884964	2		694	1088	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0048848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	762	887	1	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.651259931969898	3	FACETS	0.898	0.875	0.921			1	CLONAL	3	FALSE	NA	0.651259931969898	3		888	1151	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374404	81374404	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1486090533	NA	P-0048848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	283	366	0	ENST00000222390.5:c.658C>T	p.Arg220Ter	p.R220*	ENST00000222390	NM_000601.4	220	Cga/Tga	6/18	0.651259931969898	3	FACETS	0.962	0.925	0.999			1	CLONAL	3	FALSE	NA	0.651259931969898	3		366	399	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026721	6026721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751153838	NA	P-0048848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	291	669	0	ENST00000265849.7:c.1675G>A	p.Gly559Arg	p.G559R	ENST00000265849	NM_000535.5	559	Gga/Aga	11/15	0.651259931969898	8	FACETS	0.859	0.806	0.914	0.43	0.403	0.457	CLONAL	2	FALSE	4	0.651259931969898	8		669	1536	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915940	127915940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	121	378	0	ENST00000373547.4:c.541C>T	p.Arg181Trp	p.R181W	ENST00000373547	NM_002721.4	181	Cgg/Tgg	6/7	0.651259931969898	9	FACETS	0.927	0.835	1			1	CLONAL	1	FALSE	NA	0.651259931969898	9		378	1315	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97873873	97873873	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881722	NA	P-0048848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	1195	674	6	ENST00000289081.3:c.1201G>A	p.Gly401Arg	p.G401R	ENST00000289081	NM_000136.2	401	Gga/Aga	13/15	0.651259931969898	8	FACETS	0.95	0.933	0.967			1	CLONAL	7	FALSE	NA	0.651259931969898	8		680	1630	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0048849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	105	165	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	0.356639958025764	3	FACETS	1	0.972	1	0.618	0.556	0.685	CLONAL	1	TRUE	1	0.356639958025764	3		165	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577508	7577508	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060501201	NA	P-0048849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	374	591	0	ENST00000269305.4:c.773A>G	p.Glu258Gly	p.E258G	ENST00000269305	NM_001126112.2	258	gAa/gGa	7/11	0.355053977929207	2	FACETS	0.986	0.937	1	0.986	0.937	1	CLONAL	2	TRUE	0	0.356639958025764	2		591	1064	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736334	243736334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771134997	NA	P-0048849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	178	189	0	ENST00000263826.5:c.713C>T	p.Ser238Leu	p.S238L	ENST00000263826	NM_005465.4	238	tCg/tTg	8/13	0.355053977929207	2	FACETS	0.894	0.83	0.961	0.894	0.83	0.961	CLONAL	2	TRUE	0	0.356639958025764	2		189	558	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741406	17741406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs993043194	NA	P-0048849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	276	566	2	ENST00000250003.3:c.77C>T	p.Thr26Met	p.T26M	ENST00000250003	NM_002478.4	26	aCg/aTg	1/3	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.356639958025764	2		568	1359	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223211	2223211	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1567252202	NA	P-0048849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1271	256	491	0	ENST00000326181.6:c.823T>C	p.Tyr275His	p.Y275H	ENST00000326181	NM_032271.2	275	Tac/Cac	10/21	0.356639958025764	3	FACETS	1	0.978	1	0.554	0.517	0.592	CLONAL	1	TRUE	1	0.356639958025764	3		491	1527	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845640	68845641	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0048849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	403	373	0	ENST00000261769.5:c.887dup	p.Tyr296Ter	p.Y296*	ENST00000261769	NM_004360.3	296	tac/tAac	7/16	0.356639958025764	3	FACETS	0.99	0.941	1	0.99	0.941	1	CLONAL	2	TRUE	1	0.356639958025764	3		373	1345	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661669	227661669	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769250896	NA	P-0048849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	183	401	0	ENST00000305123.5:c.1786G>T	p.Gly596Trp	p.G596W	ENST00000305123	NM_005544.2	596	Ggg/Tgg	1/2	1	2	FACETS	0.999	0.922	1	0.999	0.922	1	CLONAL	1	TRUE	1	0.356639958025764	2		401	1027	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266071	41266097	+	inframe_deletion	In_Frame_Del	DEL	GTCACTGGCAGCAACAGTCTTACCTGG	GTCACTGGCAGCAACAGTCTTACCTGG	-	novel	NA	P-0048849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	144	128	0	ENST00000349496.5:c.68_94del	p.Ser23_Asp32delinsAsn	p.S23_D32delinsN	ENST00000349496	NM_001904.3	23	aGTCACTGGCAGCAACAGTCTTACCTGGac/aac	3/15	0.355053977929207	2	FACETS	0.916	0.842	0.991	0.916	0.842	0.991	CLONAL	2	TRUE	0	0.356639958025764	2		128	441	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602691	55602691	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	52	163	0	ENST00000288135.5:c.2512C>A	p.Pro838Thr	p.P838T	ENST00000288135	NM_000222.2	838	Cct/Act	18/21	0.267639804370257	1	FACETS	0.433	0.369	0.504	0.433	0.369	0.504	SUBCLONAL	1	TRUE	0	0.356639958025764	1		163	553	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397175	397175	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1322810804	NA	P-0048849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	100	263	0	ENST00000380956.4:c.560A>G	p.His187Arg	p.H187R	ENST00000380956	NM_001195286.1	187	cAc/cGc	5/9	1	2	FACETS	0.861	0.77	0.958	0.861	0.77	0.958	CLONAL	1	TRUE	1	0.356639958025764	2		263	651	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735466	40735466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182388300	NA	P-0048850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	129	524	0	ENST00000373198.4:c.3407G>A	p.Arg1136His	p.R1136H	ENST00000373198	NM_133170.3	1136	cGt/cAt	25/32	0.331504464637432	3	FACETS	0.635	0.574	0.699			1	SUBCLONAL	1	TRUE	NA	0.402879499253384	3		524	1212	SUCCESS
APC	324	MSKCC	GRCh37	5	112175171	112175171	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085373	NA	P-0048850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	48	137	0	ENST00000257430.4:c.3880C>T	p.Gln1294Ter	p.Q1294*	ENST00000257430	NM_000038.5	1294	Cag/Tag	16/16	1	2	FACETS	0.946	0.806	1	0.946	0.806	1	CLONAL	1	TRUE	1	0.402879499253384	2		137	252	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0048850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	185	438	0	ENST00000269305.4:c.672+1G>C		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.402879499253384	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.402879499253384	1		438	621	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872935	136872935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1289033947	NA	P-0048850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	116	311	0	ENST00000241393.3:c.563G>A	p.Arg188His	p.R188H	ENST00000241393	NM_003467.2	188	cGc/cAc	2/2	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.402879499253384	2		311	501	SUCCESS
APC	324	MSKCC	GRCh37	5	112170676	112170676	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	96	257	0	ENST00000257430.4:c.1773del	p.Leu592TyrfsTer18	p.L592Yfs*18	ENST00000257430	NM_000038.5	591	gCc/gc	15/16	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.402879499253384	2		257	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555525585	NA	P-0048851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	159	468	1	ENST00000269305.4:c.673-2A>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.586265517129625	2	FACETS	0.884	0.83	0.938	0.884	0.83	0.938	CLONAL	2	TRUE	0	0.653818226574912	2		469	275	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142578	119142578	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	44	223	0	ENST00000264033.4:c.577G>T	p.Ala193Ser	p.A193S	ENST00000264033	NM_005188.3	193	Gct/Tct	3/16	0.550831400581808	4	FACETS	0.863	0.729	1	0.431	0.364	0.505	CLONAL	1	TRUE	2	0.653818226574912	4		223	258	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100799	8100799	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	51	452	0	ENST00000346208.3:c.773G>C	p.Ser258Thr	p.S258T	ENST00000346208		258	aGc/aCc	3/6	0.653818226574912	6	FACETS	0.47	0.398	0.549	0.117	0.099	0.138	SUBCLONAL	1	TRUE	2	0.653818226574912	6		452	766	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380348	14380349	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0048851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	297	211	2	ENST00000256196.4:c.68_69delinsTT	p.Gly23Val	p.G23V	ENST00000256196		23	gGC/gTT	1/6	0.464247525540365	5	FACETS	0.891	0.845	0.937	0.891	0.845	0.937	CLONAL	3	TRUE	2	0.653818226574912	5		213	673	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984513	72984513	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	157	596	0	ENST00000268489.5:c.3071C>G	p.Ala1024Gly	p.A1024G	ENST00000268489	NM_006885.3	1024	gCc/gGc	3/10	0.569824353279145	4	FACETS	1	0.939	1	0.343	0.314	0.373	CLONAL	1	TRUE	1	0.653818226574912	4		596	772	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615817	1615827	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGCCCTGCAAC	AGCCCTGCAAC	-	novel	NA	P-0048851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	71	362	0	ENST00000344749.5:c.1451-7_1454del		p.X484_splice	ENST00000344749	NM_001136139.2	484		17/19	0.640537508474088	2	FACETS	0.793	0.699	0.891	0.396	0.349	0.446	SUBCLONAL	1	TRUE	0	0.653818226574912	2		362	274	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223494	53223494	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	242	582	0	ENST00000375401.3:c.3865C>T	p.Gln1289Ter	p.Q1289*	ENST00000375401	NM_004187.3	1289	Caa/Taa	23/26	0.640739500643886	2	FACETS	0.928	0.883	0.972	0.928	0.883	0.972	CLONAL	2	TRUE	0	0.653818226574912	2		582	399	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0048852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	86	290	1	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.460348404679927	1	FACETS	0.872	0.778	0.969	0.872	0.778	0.969	CLONAL	1	TRUE	0	0.460348404679927	1		291	330	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0048852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	145	501	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.956	0.875	1	0.956	0.875	1	CLONAL	1	TRUE	1	0.460348404679927	2		501	659	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0048852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	114	302	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.842	0.761	0.928	0.842	0.761	0.928	CLONAL	1	TRUE	1	0.460348404679927	2		302	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0048852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	195	497	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.460348404679927	1	FACETS	0.941	0.874	1	0.941	0.874	1	CLONAL	1	TRUE	0	0.460348404679927	1		498	693	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864658	68864658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1418006656	NA	P-0048852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	102	290	1	ENST00000288368.4:c.29G>A	p.Arg10His	p.R10H	ENST00000288368	NM_024870.2	10	cGc/cAc	1/40	0.460348404679927	3	FACETS	1	0.955	1	0.556	0.5	0.616	CLONAL	1	TRUE	1	0.460348404679927	3		291	490	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720728	89720741	+	frameshift_variant	Frame_Shift_Del	DEL	AAGTCTATGTGATC	AAGTCTATGTGATC	-	novel	NA	P-0048852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	89	128	0	ENST00000371953.3:c.882_895del	p.Ser294ArgfsTer4	p.S294Rfs*4	ENST00000371953	NM_000314.4	293	ggAAGTCTATGTGATCaa/ggaa	8/9	0.450184455856673	2	FACETS	0.786	0.708	0.866	0.786	0.708	0.866	SUBCLONAL	2	TRUE	0	0.460348404679927	2		128	246	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843727	151843727	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	238	306	0	ENST00000262189.6:c.13988T>G	p.Leu4663Arg	p.L4663R	ENST00000262189	NM_170606.2	4663	cTg/cGg	53/59	0.450184455856673	2	FACETS	0.89	0.838	0.943	0.89	0.838	0.943	CLONAL	2	TRUE	0	0.460348404679927	2		306	581	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912354	32912354	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	62	244	0	ENST00000380152.3:c.3862A>T	p.Asn1288Tyr	p.N1288Y	ENST00000380152		1288	Aat/Tat	11/27	1	2	FACETS	0.985	0.861	1	0.985	0.861	1	CLONAL	1	TRUE	1	0.514065852905807	2		244	245	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593637	55593660	+	protein_altering_variant	In_Frame_Del	DEL	ATGTTTACATAGACCCAACACAAC	ATGTTTACATAGACCCAACACAAC	GTG	novel	NA	P-0048853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	74	310	1	ENST00000288135.5:c.1703_1726delinsGTG	p.Tyr568_Leu576delinsCysVal	p.Y568_L576delinsCV	ENST00000288135	NM_000222.2	568	tATGTTTACATAGACCCAACACAACtt/tGTGtt	11/21	1	2	FACETS	0.76	0.669	0.856	0.76	0.669	0.856	SUBCLONAL	1	TRUE	1	0.514065852905807	2		311	379	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0048862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	609	1140	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.380511126835867	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.394728493130192	3		1140	1166	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913233	NA	P-0048862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	605	524	0	ENST00000451590.1:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000451590	NM_001130442.1	61	cAg/cTg	3/5	0.394728493130192	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	1	0.394728493130192	3		524	1581	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574004	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0048862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	249	611	1	ENST00000269305.4:c.1023_1024delinsTT	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	341	ttCCga/ttTTga	10/11	0.388683961739925	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.394728493130192	1		612	1007	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55225397	55225397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	140	321	0	ENST00000275493.2:c.1249C>T	p.Leu417Phe	p.L417F	ENST00000275493	NM_005228.3	417	Ctc/Ttc	11/28	1	2	FACETS	0.871	0.794	0.953	0.871	0.794	0.953	CLONAL	1	TRUE	1	0.394728493130192	2		321	814	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335737	81335737	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	76	199	0	ENST00000222390.5:c.1623G>T	p.Leu541Phe	p.L541F	ENST00000222390	NM_000601.4	541	ttG/ttT	15/18	1	2	FACETS	0.935	0.824	1	0.935	0.824	1	CLONAL	1	TRUE	1	0.394728493130192	2		199	412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577595	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0048887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	410	497	0	ENST00000269305.4:c.686_687del	p.Cys229TyrfsTer10	p.C229Yfs*10	ENST00000269305	NM_001126112.2	229	tGT/t	7/11	0.506811411025865	2	FACETS	0.988	0.948	1	0.988	0.948	1	CLONAL	2	TRUE	0	0.514701373349586	2		497	806	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922321	178922321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	242	420	0	ENST00000263967.3:c.1090G>A	p.Gly364Arg	p.G364R	ENST00000263967	NM_006218.2	364	Gga/Aga	6/21	0.224545217788795	5	FACETS	1	0.964	1	0.693	0.65	0.738	INDETERMINATE	2	TRUE	2	0.514701373349586	5		420	801	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948044	178948044	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	166	289	0	ENST00000263967.3:c.2816A>G	p.Asp939Gly	p.D939G	ENST00000263967	NM_006218.2	939	gAt/gGt	20/21	0.224545217788795	5	FACETS	0.999	0.923	1	0.666	0.615	0.719	INDETERMINATE	2	TRUE	2	0.514701373349586	5		289	572	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916248	9916248	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	50	412	0	ENST00000330684.3:c.2041del	p.Arg681AspfsTer25	p.R681Dfs*25	ENST00000330684	NM_001134407.1	681	Cga/ga	10/13	0.224545217788795	5	FACETS	0.404	0.341	0.473	0.135	0.113	0.158	INDETERMINATE	1	TRUE	2	0.514701373349586	5		412	853	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210698	5210698	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	348	572	0	ENST00000357368.4:c.5353A>G	p.Met1785Val	p.M1785V	ENST00000357368	NM_002850.3	1785	Atg/Gtg	34/38	0.474428230623353	2	FACETS	0.909	0.867	0.951	0.909	0.867	0.951	CLONAL	2	TRUE	0	0.514701373349586	2		572	744	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948814	17948814	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1558	225	588	0	ENST00000458235.1:c.1628T>C	p.Val543Ala	p.V543A	ENST00000458235	NM_000215.3	543	gTg/gCg	12/24	0.514701373349586	5	FACETS	0.869	0.806	0.935			1	CLONAL	1	TRUE	NA	0.514701373349586	5		588	1783	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980342	55980342	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	117	422	0	ENST00000263923.4:c.749C>A	p.Thr250Asn	p.T250N	ENST00000263923	NM_002253.2	250	aCt/aAt	6/30	0.467351948404247	2	FACETS	0.803	0.727	0.883	0.402	0.363	0.442	CLONAL	1	TRUE	0	0.514701373349586	2		422	566	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958466	90958466	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	103	450	0	ENST00000265433.3:c.1972G>T	p.Glu658Ter	p.E658*	ENST00000265433	NM_002485.4	658	Gaa/Taa	13/16	0.474428230623353	2	FACETS	0.843	0.758	0.932	0.421	0.379	0.466	CLONAL	1	TRUE	0	0.514701373349586	2		450	475	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449782	8449782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1214286773	NA	P-0048887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	289	500	0	ENST00000356435.5:c.3931C>T	p.Pro1311Ser	p.P1311S	ENST00000356435		1311	Cct/Tct	23/35	0.514701373349586	3	FACETS	1	0.992	1	0.445	0.418	0.472	CLONAL	1	TRUE	0	0.514701373349586	3		500	1058	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0048888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	28	520	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.454122242521599	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	FALSE	0	0.454122242521599	1		520	73	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0048888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	59	511	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.454122242521599	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	0	0.454122242521599	1		511	168	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161298222	161298222	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868556406	NA	P-0048888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	15	364	0	ENST00000367975.2:c.114G>A	p.Met38Ile	p.M38I	ENST00000367975	NM_003001.3	38	atG/atA	3/6	0.396114746047349	1	FACETS	0.594	0.442	0.77	0.594	0.442	0.77	SUBCLONAL	1	FALSE	0	0.454122242521599	1		364	86	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804343	46804343	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	46	544	0	ENST00000290295.7:c.664C>A	p.Pro222Thr	p.P222T	ENST00000290295	NM_006361.5	222	Ccg/Acg	2/2	0.436922451388985	2	FACETS	0.837	0.711	0.973	0.419	0.355	0.487	CLONAL	1	FALSE	0	0.454122242521599	2		544	242	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880138	151880138	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	16	420	0	ENST00000262189.6:c.5186C>G	p.Ser1729Cys	p.S1729C	ENST00000262189	NM_170606.2	1729	tCt/tGt	35/59	0.422960792829195	5	FACETS	1	0.827	1	0.38	0.284	0.49	CLONAL	1	FALSE	2	0.454122242521599	5		420	104	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0048889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	116	405	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.254439673079788	2		405	612	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252988	36252988	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	63	337	0	ENST00000300305.3:c.374del	p.Pro125GlnfsTer8	p.P125Qfs*8	ENST00000300305		125	cCa/ca	4/8	1	2	FACETS	0.736	0.636	0.845	0.736	0.636	0.845	SUBCLONAL	1	TRUE	1	0.254439673079788	2		337	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577579	7577579	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0048889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	123	504	0	ENST00000269305.4:c.702C>G	p.Tyr234Ter	p.Y234*	ENST00000269305	NM_001126112.2	234	taC/taG	7/11	0.254439673079788	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.254439673079788	1		504	769	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226561941	226561941	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	43	412	0	ENST00000366794.5:c.2056A>T	p.Met686Leu	p.M686L	ENST00000366794	NM_001618.3	686	Atg/Ttg	14/23	0.175282347750868	2	FACETS	0.449	0.374	0.532	0.224	0.187	0.266	SUBCLONAL	1	TRUE	0	0.254439673079788	2		412	753	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627538	14627538	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	103	454	0	ENST00000254322.2:c.532G>T	p.Gly178Cys	p.G178C	ENST00000254322	NM_006145.1	178	Ggc/Tgc	2/3	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.254439673079788	2		454	792	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436929	29436929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	59	443	0	ENST00000389048.3:c.3664G>A	p.Ala1222Thr	p.A1222T	ENST00000389048	NM_004304.4	1222	Gcc/Acc	24/29	1	2	FACETS	0.566	0.486	0.654	0.566	0.486	0.654	SUBCLONAL	1	TRUE	1	0.254439673079788	2		443	819	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645700	215645700	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793050	NA	P-0048889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	65	422	0	ENST00000260947.4:c.898C>T	p.Pro300Ser	p.P300S	ENST00000260947	NM_000465.2	300	Cct/Tct	4/11	0.178823672573804	1	FACETS	0.604	0.523	0.693	0.604	0.523	0.693	SUBCLONAL	1	TRUE	0	0.254439673079788	1		422	738	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577571	7577571	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs765848205	NA	P-0048890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	522	508	0	ENST00000269305.4:c.710T>A	p.Met237Lys	p.M237K	ENST00000269305	NM_001126112.2	237	aTg/aAg	7/11	0.642869438965539	3	FACETS	0.949	0.923	0.974	0.949	0.923	0.974	CLONAL	3	TRUE	0	0.702952917761634	3		508	705	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121094	3121094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776555145	NA	P-0048890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	111	549	0	ENST00000078429.4:c.997G>A	p.Asp333Asn	p.D333N	ENST00000078429	NM_002067.2	333	Gac/Aac	7/7	0.176887970653573	3	FACETS	0.672	0.605	0.743	0.224	0.201	0.248	INDETERMINATE	1	TRUE	0	0.702952917761634	3		549	635	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0048891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	76	456	0	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	0.158664395500468	1	FACETS	0.799	0.7	0.905	0.799	0.7	0.905	CLONAL	1	TRUE	0	0.239962636746302	1		456	698	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127399	55127399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	179	568	0	ENST00000257290.5:c.187G>A	p.Glu63Lys	p.E63K	ENST00000257290	NM_006206.4	63	Gaa/Aaa	3/23	1	2	FACETS	0.804	0.741	0.869	1	0.991	1	CLONAL	2	TRUE	1	0.239962636746302	2		568	928	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873118	134873118	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	59	482	1	ENST00000398015.3:c.1422G>T	p.Lys474Asn	p.K474N	ENST00000398015	NM_004441.4	474	aaG/aaT	6/16	1	2	FACETS	0.676	0.581	0.781	0.676	0.581	0.781	SUBCLONAL	1	TRUE	1	0.239962636746302	2		483	727	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112884199	112884199	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	67	524	0	ENST00000351677.2:c.134T>G	p.Val45Gly	p.V45G	ENST00000351677	NM_002834.3	45	gTt/gGt	2/16	1	2	FACETS	0.733	0.636	0.838	0.733	0.636	0.838	SUBCLONAL	1	TRUE	1	0.239962636746302	2		524	762	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634702	158634702	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	68	341	0	ENST00000263640.3:c.484G>T	p.Val162Leu	p.V162L	ENST00000263640	NM_001105.4	162	Gtg/Ttg	5/11	1	2	FACETS	0.902	0.785	1	0.902	0.785	1	CLONAL	1	TRUE	1	0.239962636746302	2		341	628	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57474001	57474001	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	41	359	0	ENST00000371085.3:c.218G>T	p.Gly73Val	p.G73V	ENST00000371085	NM_000516.4	73	gGc/gTc	3/13	1	2	FACETS	0.564	0.469	0.67	0.564	0.469	0.67	SUBCLONAL	1	TRUE	1	0.239962636746302	2		359	606	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092905	29092905	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	57	513	0	ENST00000328354.6:c.1079A>T	p.Glu360Val	p.E360V	ENST00000328354	NM_007194.3	360	gAg/gTg	10/15	1	2	FACETS	0.835	0.716	0.964	0.835	0.716	0.964	CLONAL	1	TRUE	1	0.239962636746302	2		513	569	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201698	66201698	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	71	506	0	ENST00000273854.3:c.2804T>A	p.Leu935Gln	p.L935Q	ENST00000273854	NM_004439.5	935	cTg/cAg	16/18	1	2	FACETS	0.773	0.673	0.88	0.773	0.673	0.88	SUBCLONAL	1	TRUE	1	0.239962636746302	2		506	766	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026972	6026972	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	74	254	0	ENST00000265849.7:c.1424T>G	p.Val475Gly	p.V475G	ENST00000265849	NM_000535.5	475	gTg/gGg	11/15	0.228914383891077	3	FACETS	0.842	0.741	0.951	0.842	0.741	0.951	CLONAL	2	TRUE	1	0.239962636746302	3		254	410	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468125	50468125	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	62	501	0	ENST00000331340.3:c.1360A>T	p.Thr454Ser	p.T454S	ENST00000331340	NM_006060.4	454	Acc/Tcc	8/8	0.228914383891077	3	FACETS	0.842	0.727	0.968	0.421	0.363	0.484	CLONAL	1	TRUE	1	0.239962636746302	3		501	687	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851964	128851964	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	61	634	0	ENST00000249373.3:c.2036A>G	p.Lys679Arg	p.K679R	ENST00000249373	NM_005631.4	679	aAg/aGg	12/12	1	2	FACETS	0.657	0.566	0.757	0.657	0.566	0.757	SUBCLONAL	1	TRUE	1	0.239962636746302	2		634	774	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934382	39934382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	85	346	0	ENST00000378444.4:c.217G>A	p.Asp73Asn	p.D73N	ENST00000378444	NM_001123385.1	73	Gac/Aac	4/15	0.239962636746302	4	FACETS	1	0.966	1	0.314	0.277	0.354	CLONAL	1	TRUE	0	0.239962636746302	4		346	699	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630136	100630136	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	56	301	0	ENST00000308731.7:c.137G>T	p.Arg46Leu	p.R46L	ENST00000308731	NM_000061.2	46	cGt/cTt	2/19	0.239962636746302	4	FACETS	1	0.924	1	0.281	0.241	0.325	CLONAL	1	TRUE	0	0.239962636746302	4		301	515	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184046	123184046	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	26	239	0	ENST00000218089.9:c.904G>C	p.Ala302Pro	p.A302P	ENST00000218089	NM_001042749.1	302	Gct/Cct	11/35	0.239962636746302	4	FACETS	0.685	0.543	0.849	0.171	0.135	0.213	SUBCLONAL	1	TRUE	0	0.239962636746302	4		239	392	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0048892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	147	1140	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.956	1	1	0.992	1	CLONAL	2	TRUE	1	0.273858149078744	2		1140	506	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220116	5220116	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781371580	NA	P-0048892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	206	592	1	ENST00000357368.4:c.3599G>A	p.Arg1200His	p.R1200H	ENST00000357368	NM_002850.3	1200	cGt/cAt	22/38	0.0702534128610313	4	FACETS	1	0.984	1	1	0.984	1	INDETERMINATE	2	TRUE	2	0.273858149078744	4		593	801	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0048892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	249	585	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.273858149078744	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.273858149078744	2		585	818	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	188	434	0	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.789	0.73	0.851	1	0.991	1	SUBCLONAL	2	TRUE	1	0.27892065829324	2		434	854	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	87	434	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.998	0.885	1	0.998	0.885	1	CLONAL	1	TRUE	1	0.27892065829324	2		435	625	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193214	11193214	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	122	606	0	ENST00000361445.4:c.5287G>T	p.Gly1763Cys	p.G1763C	ENST00000361445	NM_004958.3	1763	Ggc/Tgc	38/58	1	2	FACETS	0.866	0.782	0.956	0.866	0.782	0.956	CLONAL	1	TRUE	1	0.27892065829324	2		606	1010	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106803	27106804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	104	611	0	ENST00000324856.7:c.6420dup	p.Phe2141LeufsTer9	p.F2141Lfs*9	ENST00000324856	NM_006015.4	2138	-/C	20/20	1	2	FACETS	0.77	0.689	0.858	0.77	0.689	0.858	SUBCLONAL	1	TRUE	1	0.27892065829324	2		611	968	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599271	28599271	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs770146088	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	114	586	0	ENST00000253063.3:c.722del	p.Pro241GlnfsTer6	p.P241Qfs*6	ENST00000253063	NM_031459.4	239	agC/ag	5/10	1	2	FACETS	0.827	0.743	0.915	0.827	0.743	0.915	CLONAL	1	TRUE	1	0.27892065829324	2		586	989	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310468	65310468	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	41	457	0	ENST00000342505.4:c.2220del	p.Gly741AlafsTer30	p.G741Afs*30	ENST00000342505	NM_002227.2	740	ccC/cc	16/25	1	2	FACETS	0.378	0.314	0.45	0.378	0.314	0.45	SUBCLONAL	1	TRUE	1	0.27892065829324	2		457	777	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404571	70404578	+	frameshift_variant	Frame_Shift_Del	DEL	AACTAAAA	AACTAAAA	-	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	105	462	1	ENST00000373644.4:c.2086_2093del	p.Thr696Ter	p.T696*	ENST00000373644	NM_030625.2	695	gtAACTAAAAat/gtat	4/12	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.27892065829324	2		463	698	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	63	331	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	0.837	0.724	0.958	0.837	0.724	0.958	CLONAL	1	TRUE	1	0.27892065829324	2		331	540	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911953	94911953	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764991422	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	123	556	1	ENST00000536441.1:c.977G>A	p.Arg326Gln	p.R326Q	ENST00000536441	NM_144665.3	326	cGa/cAa	7/10	1	2	FACETS	0.924	0.834	1	0.924	0.834	1	CLONAL	1	TRUE	1	0.27892065829324	2		557	955	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981861	101981863	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	89	553	1	ENST00000282441.5:c.286_288del	p.Phe96del	p.F96del	ENST00000282441	NM_001130145.2	94	tcCTTc/tcc	1/9	1	2	FACETS	0.801	0.709	0.899	0.801	0.709	0.899	CLONAL	1	TRUE	1	0.27892065829324	2		554	797	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352594	118352594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376303494	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	98	468	0	ENST00000534358.1:c.3799G>A	p.Val1267Ile	p.V1267I	ENST00000534358	NM_005933.3	1267	Gtc/Atc	7/36	1	2	FACETS	0.84	0.748	0.937	0.84	0.748	0.937	CLONAL	1	TRUE	1	0.27892065829324	2		468	837	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445375	49445375	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	151	729	2	ENST00000301067.7:c.2091del	p.Thr698HisfsTer232	p.T698Hfs*232	ENST00000301067	NM_003482.3	697	ccC/cc	10/54	1	2	FACETS	0.89	0.811	0.972	0.89	0.811	0.972	CLONAL	1	TRUE	1	0.27892065829324	2		731	1217	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860074	57860075	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs759448855	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	125	659	0	ENST00000228682.2:c.821dup	p.Cys275LeufsTer32	p.C275Lfs*32	ENST00000228682	NM_005269.2	272	tgg/tGgg	8/12	1	2	FACETS	0.831	0.75	0.916	0.831	0.75	0.916	CLONAL	1	TRUE	1	0.27892065829324	2		659	1079	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115398	115115398	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs779733514	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	99	529	0	ENST00000257566.3:c.928C>T	p.Arg310Ter	p.R310*	ENST00000257566	NM_016569.3	310	Cga/Tga	5/8	1	2	FACETS	0.841	0.75	0.938	0.841	0.75	0.938	CLONAL	1	TRUE	1	0.27892065829324	2		529	844	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117410	115117410	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	43	389	0	ENST00000257566.3:c.764T>A	p.Val255Glu	p.V255E	ENST00000257566	NM_016569.3	255	gTa/gAa	4/8	1	2	FACETS	0.457	0.381	0.541	0.457	0.381	0.541	SUBCLONAL	1	TRUE	1	0.27892065829324	2		389	675	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506135	103506135	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375404851	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	67	299	1	ENST00000355739.4:c.293C>T	p.Ala98Val	p.A98V	ENST00000355739	NM_000123.3	98	gCg/gTg	3/15	1	2	FACETS	0.886	0.771	1	0.886	0.771	1	CLONAL	1	TRUE	1	0.27892065829324	2		300	542	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246532	105246532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	146	567	0	ENST00000349310.3:c.68G>A	p.Arg23Gln	p.R23Q	ENST00000349310	NM_001014432.1	23	cGg/cAg	4/15	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.27892065829324	2		567	966	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479831	67479831	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	109	511	1	ENST00000327367.4:c.1138T>C	p.Trp380Arg	p.W380R	ENST00000327367	NM_005902.3	380	Tgg/Cgg	8/9	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.27892065829324	2		512	780	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647657	3647657	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs774532876	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	135	732	4	ENST00000294008.3:c.1406del	p.Pro469HisfsTer4	p.P469Hfs*4	ENST00000294008	NM_032444.2	469	cCa/ca	7/15	1	2	FACETS	0.908	0.824	0.997	0.908	0.824	0.997	CLONAL	1	TRUE	1	0.27892065829324	2		736	1066	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993846	72993846	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs891634906	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	99	470	0	ENST00000268489.5:c.199T>C	p.Ser67Pro	p.S67P	ENST00000268489	NM_006885.3	67	Tcg/Ccg	2/10	0.271894211057653	2	FACETS	1	0.906	1	0.508	0.453	0.566	CLONAL	1	TRUE	0	0.27892065829324	2		470	699	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346534	89346534	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753112904	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	125	561	0	ENST00000301030.4:c.6416C>T	p.Pro2139Leu	p.P2139L	ENST00000301030	NM_001256183.1	2139	cCg/cTg	9/13	0.271894211057653	2	FACETS	1	0.929	1	0.516	0.466	0.568	CLONAL	1	TRUE	0	0.27892065829324	2		561	869	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348152	89348152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1300503919	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	137	719	3	ENST00000301030.4:c.4798C>T	p.Arg1600Trp	p.R1600W	ENST00000301030	NM_001256183.1	1600	Cgg/Tgg	9/13	0.271894211057653	2	FACETS	0.884	0.803	0.97	0.442	0.401	0.485	CLONAL	1	TRUE	0	0.27892065829324	2		722	1111	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572991	7572991	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	98	397	0	ENST00000269305.4:c.1118del	p.Lys373ArgfsTer49	p.K373Rfs*49	ENST00000269305	NM_001126112.2	373	aAg/ag	11/11	1	2	FACETS	0.957	0.854	1	0.957	0.854	1	CLONAL	1	TRUE	1	0.27892065829324	2		397	734	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	140	681	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	1	2	FACETS	0.883	0.802	0.968	0.883	0.802	0.968	CLONAL	1	TRUE	1	0.27892065829324	2		681	1137	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979987	7979987	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746723399	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	131	517	2	ENST00000319144.4:c.1350del	p.Leu451SerfsTer16	p.L451Sfs*16	ENST00000319144	NM_001139.2	450	ggG/gg	10/15	1	2	FACETS	0.96	0.871	1	0.96	0.871	1	CLONAL	1	TRUE	1	0.27892065829324	2		519	978	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510560	38510560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	92	368	2	ENST00000254066.5:c.814C>T	p.Arg272Trp	p.R272W	ENST00000254066	NM_000964.3	272	Cgg/Tgg	7/9	1	2	FACETS	0.963	0.856	1	0.963	0.856	1	CLONAL	1	TRUE	1	0.27892065829324	2		370	685	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	144	564	1	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.27892065829324	2		565	966	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866607	78866607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	134	551	0	ENST00000306801.3:c.2180G>A	p.Arg727His	p.R727H	ENST00000306801	NM_020761.2	727	cGt/cAt	19/34	1	2	FACETS	0.923	0.837	1	0.923	0.837	1	CLONAL	1	TRUE	1	0.27892065829324	2		551	1041	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226558	1226558	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	99	475	2	ENST00000326873.7:c.1214G>T	p.Arg405Met	p.R405M	ENST00000326873	NM_000455.4	405	aGg/aTg	9/10	1	2	FACETS	0.903	0.806	1	0.903	0.806	1	CLONAL	1	TRUE	1	0.27892065829324	2		477	786	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245898	5245898	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376695892	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	115	713	2	ENST00000357368.4:c.877G>A	p.Val293Met	p.V293M	ENST00000357368	NM_002850.3	293	Gtg/Atg	10/38	1	2	FACETS	0.741	0.666	0.821	0.741	0.666	0.821	SUBCLONAL	1	TRUE	1	0.27892065829324	2		715	1113	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291084	10291084	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	122	635	1	ENST00000340748.4:c.387del	p.Lys130AsnfsTer129	p.K130Nfs*129	ENST00000340748		129	ccC/cc	4/40	1	2	FACETS	0.848	0.766	0.936	0.848	0.766	0.936	CLONAL	1	TRUE	1	0.27892065829324	2		636	1031	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223481	36223481	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	147	691	1	ENST00000222270.7:c.6034del	p.Ala2012ProfsTer28	p.A2012Pfs*28	ENST00000222270	NM_014727.1	2011	Ggg/gg	28/37	0.248614545202902	3	FACETS	0.986	0.898	1	0.493	0.449	0.54	CLONAL	1	TRUE	1	0.27892065829324	3		692	1218	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136304	202136304	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	112	483	0	ENST00000358485.4:c.548T>C	p.Leu183Ser	p.L183S	ENST00000358485	NM_001080125.1	183	tTg/tCg	3/9	1	2	FACETS	0.95	0.854	1	0.95	0.854	1	CLONAL	1	TRUE	1	0.27892065829324	2		483	845	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646085	215646085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	126	522	1	ENST00000260947.4:c.513del	p.Asp172MetfsTer40	p.D172Mfs*40	ENST00000260947	NM_000465.2	171	aaA/aa	4/11	1	2	FACETS	0.924	0.835	1	0.924	0.835	1	CLONAL	1	TRUE	1	0.27892065829324	2		523	978	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944562	40944562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868189942	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	89	418	0	ENST00000373198.4:c.1940C>T	p.Ser647Leu	p.S647L	ENST00000373198	NM_133170.3	647	tCg/tTg	12/32	1	2	FACETS	0.872	0.773	0.978	0.872	0.773	0.978	CLONAL	1	TRUE	1	0.27892065829324	2		418	732	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484840	57484840	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	116	562	0	ENST00000371085.3:c.820A>G	p.Lys274Glu	p.K274E	ENST00000371085	NM_000516.4	274	Aag/Gag	10/13	1	2	FACETS	0.988	0.89	1	0.988	0.89	1	CLONAL	1	TRUE	1	0.27892065829324	2		562	842	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324609	62324609	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139221232	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	124	524	2	ENST00000360203.5:c.2965C>T	p.Arg989Trp	p.R989W	ENST00000360203	NM_001283009.1	989	Cgg/Tgg	30/35	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.27892065829324	2		526	860	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288246	21288246	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200712124	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	146	627	0	ENST00000354336.3:c.491G>A	p.Arg164Gln	p.R164Q	ENST00000354336	NM_005207.3	164	cGg/cAg	2/3	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.27892065829324	2		627	993	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69998221	69998221	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	75	408	0	ENST00000394351.3:c.461T>C	p.Leu154Ser	p.L154S	ENST00000394351	NM_000248.3	154	tTg/tCg	5/9	1	2	FACETS	0.799	0.7	0.906	0.799	0.7	0.906	CLONAL	1	TRUE	1	0.27892065829324	2		408	673	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190831	185190831	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	112	627	0	ENST00000265026.3:c.1712G>A	p.Gly571Glu	p.G571E	ENST00000265026	NM_004721.4	571	gGa/gAa	11/14	1	2	FACETS	0.855	0.768	0.948	0.855	0.768	0.948	CLONAL	1	TRUE	1	0.27892065829324	2		627	939	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604658	55604658	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778433	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	116	444	0	ENST00000288135.5:c.2866C>T	p.Arg956Trp	p.R956W	ENST00000288135	NM_000222.2	956	Cgg/Tgg	21/21	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.27892065829324	2		444	826	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973916	55973916	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1414415639	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	79	447	0	ENST00000263923.4:c.1400C>A	p.Ala467Asp	p.A467D	ENST00000263923	NM_002253.2	467	gCc/gAc	10/30	1	2	FACETS	0.885	0.779	0.999	0.885	0.779	0.999	CLONAL	1	TRUE	1	0.27892065829324	2		447	640	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258980	153258980	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	55	314	0	ENST00000281708.4:c.835G>T	p.Asp279Tyr	p.D279Y	ENST00000281708	NM_033632.3	279	Gac/Tac	5/12	1	2	FACETS	0.81	0.694	0.937	0.81	0.694	0.937	CLONAL	1	TRUE	1	0.27892065829324	2		314	487	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564667	86564667	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	119	572	0	ENST00000274376.6:c.402del	p.Pro136LeufsTer38	p.P136Lfs*38	ENST00000274376	NM_002890.2	133	ggT/gg	1/25	1	2	FACETS	0.847	0.763	0.936	0.847	0.763	0.936	CLONAL	1	TRUE	1	0.27892065829324	2		572	1007	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562993	176562993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	88	382	0	ENST00000439151.2:c.889G>A	p.Gly297Arg	p.G297R	ENST00000439151	NM_022455.4	297	Gga/Aga	2/23	1	2	FACETS	0.927	0.821	1	0.927	0.821	1	CLONAL	1	TRUE	1	0.27892065829324	2		382	681	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638531	176638531	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	121	596	1	ENST00000439151.2:c.3131A>G	p.Asn1044Ser	p.N1044S	ENST00000439151	NM_022455.4	1044	aAc/aGc	5/23	1	2	FACETS	0.862	0.777	0.951	0.862	0.777	0.951	CLONAL	1	TRUE	1	0.27892065829324	2		597	1007	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038480	180038480	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	77	502	0	ENST00000261937.6:c.3538-1G>A		p.X1180_splice	ENST00000261937	NM_182925.4	1180			1	2	FACETS	0.746	0.654	0.845	0.746	0.654	0.845	SUBCLONAL	1	TRUE	1	0.27892065829324	2		502	740	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402614	20402614	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	27	238	0	ENST00000346618.3:c.151G>A	p.Ala51Thr	p.A51T	ENST00000346618	NM_001949.4	51	Gcc/Acc	1/7	1	2	FACETS	0.457	0.363	0.564	0.457	0.363	0.564	SUBCLONAL	1	TRUE	1	0.27892065829324	2		238	424	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170313	32170313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201260854	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	131	667	0	ENST00000375023.3:c.3295G>A	p.Gly1099Arg	p.G1099R	ENST00000375023	NM_004557.3	1099	Gga/Aga	21/30	1	2	FACETS	0.849	0.769	0.934	0.849	0.769	0.934	CLONAL	1	TRUE	1	0.27892065829324	2		667	1106	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	121	913	0	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	0.904	0.815	0.997	0.904	0.815	0.997	CLONAL	1	TRUE	1	0.27892065829324	2		913	960	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951871	2951871	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	138	594	0	ENST00000396946.4:c.3079C>T	p.Arg1027Ter	p.R1027*	ENST00000396946	NM_032415.4	1027	Cga/Tga	23/25	1	2	FACETS	0.994	0.903	1	0.994	0.903	1	CLONAL	1	TRUE	1	0.27892065829324	2		594	996	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729730	41729730	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	85	501	1	ENST00000242208.4:c.799G>T	p.Gly267Trp	p.G267W	ENST00000242208	NM_002192.2	267	Ggg/Tgg	3/3	1	2	FACETS	0.797	0.704	0.897	0.797	0.704	0.897	SUBCLONAL	1	TRUE	1	0.27892065829324	2		502	765	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509606	106509606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	88	519	0	ENST00000359195.3:c.1600C>T	p.Pro534Ser	p.P534S	ENST00000359195	NM_002649.2	534	Ccc/Tcc	2/11	1	2	FACETS	0.793	0.702	0.89	0.793	0.702	0.89	SUBCLONAL	1	TRUE	1	0.27892065829324	2		519	796	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187222	38187222	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1297	111	682	0	ENST00000317025.8:c.1255del	p.Thr419ProfsTer8	p.T419Pfs*8	ENST00000317025	NM_023034.1	419	Acc/cc	6/24	0.248614545202902	3	FACETS	0.644	0.577	0.716	0.322	0.288	0.358	SUBCLONAL	1	TRUE	1	0.27892065829324	3		682	1408	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56859006	56859006	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	94	448	0	ENST00000519728.1:c.133-1G>T		p.X45_splice	ENST00000519728	NM_002350.3	45			0.248614545202902	3	FACETS	0.901	0.801	1	0.451	0.4	0.505	CLONAL	1	TRUE	1	0.27892065829324	3		448	852	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56910950	56910950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	119	536	1	ENST00000519728.1:c.1096C>T	p.Arg366Trp	p.R366W	ENST00000519728	NM_002350.3	366	Cgg/Tgg	11/13	0.248614545202902	3	FACETS	0.929	0.837	1	0.464	0.418	0.513	CLONAL	1	TRUE	1	0.27892065829324	3		537	1047	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750639	128750639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775522201	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	109	519	0	ENST00000377970.2:c.176C>T	p.Ala59Val	p.A59V	ENST00000377970	NM_002467.4	59	gCg/gTg	2/3	0.248614545202902	3	FACETS	0.889	0.797	0.987	0.444	0.398	0.494	CLONAL	1	TRUE	1	0.27892065829324	3		519	1002	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970951	21970951	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	107	469	1	ENST00000304494.5:c.407del	p.Gly136AlafsTer10	p.G136Afs*10	ENST00000304494	NM_000077.4	136	gGc/gc	2/3	1	2	FACETS	0.99	0.888	1	0.99	0.888	1	CLONAL	1	TRUE	1	0.27892065829324	2		470	775	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606278	93606278	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	139	594	0	ENST00000375746.1:c.98G>T	p.Gly33Val	p.G33V	ENST00000375746	NM_001174167.1	33	gGc/gTc	2/14	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.27892065829324	2		594	995	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759623	133759623	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	125	566	0	ENST00000318560.5:c.1950del	p.Leu651TrpfsTer43	p.L651Wfs*43	ENST00000318560	NM_005157.4	649	aCc/ac	11/11	1	2	FACETS	0.899	0.812	0.991	0.899	0.812	0.991	CLONAL	1	TRUE	1	0.27892065829324	2		566	997	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759697	133759697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776289598	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	114	534	0	ENST00000318560.5:c.2020C>T	p.Arg674Trp	p.R674W	ENST00000318560	NM_005157.4	674	Cgg/Tgg	11/11	1	2	FACETS	0.949	0.854	1	0.949	0.854	1	CLONAL	1	TRUE	1	0.27892065829324	2		534	861	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923086	39923087	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	53	645	0	ENST00000378444.4:c.3621dup	p.Gln1208ThrfsTer8	p.Q1208Tfs*8	ENST00000378444	NM_001123385.1	1207	-/A	8/15	0.239547905564972	1	FACETS	0.323	0.274	0.377	0.323	0.274	0.377	SUBCLONAL	1	TRUE	0	0.27892065829324	1		645	1012	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430809	47430809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	55	551	2	ENST00000377045.4:c.1774G>A	p.Asp592Asn	p.D592N	ENST00000377045	NM_001654.4	592	Gat/Aat	16/16	0.239547905564972	1	FACETS	0.37	0.315	0.43	0.37	0.315	0.43	SUBCLONAL	1	TRUE	0	0.27892065829324	1		553	918	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608266	100608266	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	72	640	0	ENST00000308731.7:c.1824A>T	p.Glu608Asp	p.E608D	ENST00000308731	NM_000061.2	608	gaA/gaT	18/19	0.239547905564972	1	FACETS	0.454	0.396	0.518	0.454	0.396	0.518	SUBCLONAL	1	TRUE	0	0.27892065829324	1		640	978	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910372	29910372	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs41548119	NA	P-0048893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	137	635	0	ENST00000376809.5:c.46del	p.Ala16ProfsTer4	p.A16Pfs*4	ENST00000376809	NM_002116.7	14	tcG/tc	1/8	1	2	FACETS	0.906	0.823	0.994	0.906	0.823	0.994	CLONAL	1	TRUE	1	0.27892065829324	2		635	1084	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	197	576	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.316285207855931	2	FACETS	0.855	0.797	0.916	0.855	0.797	0.916	CLONAL	2	TRUE	0	0.38	2		576	606	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0048894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	97	351	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.954	0.853	1	0.954	0.853	1	CLONAL	1	TRUE	1	0.38	2		351	535	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0048894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	77	450	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.819	0.721	0.924	0.819	0.721	0.924	CLONAL	1	TRUE	1	0.38	2		450	495	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188188	32188188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370312303	NA	P-0048894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	68	595	2	ENST00000375023.3:c.1153C>T	p.Arg385Cys	p.R385C	ENST00000375023	NM_004557.3	385	Cgc/Tgc	6/30	1	2	FACETS	0.597	0.52	0.681	0.597	0.52	0.681	SUBCLONAL	1	TRUE	1	0.38	2		597	599	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602836	10602836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	146	724	1	ENST00000171111.5:c.742G>A	p.Ala248Thr	p.A248T	ENST00000171111	NM_203500.1	248	Gcc/Acc	3/6	1	2	FACETS	0.769	0.701	0.841	0.769	0.701	0.841	SUBCLONAL	1	TRUE	1	0.38	2		725	999	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099063	27099064	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	217	598	0	ENST00000324856.7:c.3482dup	p.Pro1162AlafsTer31	p.P1162Afs*31	ENST00000324856	NM_006015.4	1160	tta/ttAa	13/20	0.316285207855931	2	FACETS	0.753	0.703	0.805	0.753	0.703	0.805	SUBCLONAL	2	TRUE	0	0.38	2		598	758	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670733	67670733	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	99	486	0	ENST00000264010.4:c.1979del	p.Asn660ThrfsTer26	p.N660Tfs*26	ENST00000264010	NM_006565.3	660	Aac/ac	11/12	1	2	FACETS	0.698	0.623	0.778	0.698	0.623	0.778	SUBCLONAL	1	TRUE	1	0.38	2		486	746	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628800	187628800	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	118	635	0	ENST00000441802.2:c.2182G>T	p.Glu728Ter	p.E728*	ENST00000441802	NM_005245.3	728	Gaa/Taa	2/27	1	2	FACETS	0.746	0.673	0.824	0.746	0.673	0.824	SUBCLONAL	1	TRUE	1	0.38	2		635	832	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0048895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	152	657	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.261025299807127	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.261025299807127	1		657	866	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976267	7976267	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1366953758	NA	P-0048895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	104	383	0	ENST00000319144.4:c.1928G>A	p.Arg643Gln	p.R643Q	ENST00000319144	NM_001139.2	643	cGg/cAg	15/15	0.261025299807127	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.261025299807127	1		383	541	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715721	30715721	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs104893816	NA	P-0048895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	101	337	0	ENST00000295754.5:c.1379G>T	p.Arg460Leu	p.R460L	ENST00000295754	NM_003242.5	460	cGc/cTc	5/7	0.261025299807127	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.261025299807127	1		337	550	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354384	354404	+	inframe_deletion	In_Frame_Del	DEL	GCTCCTCCGCGAACTTCTGAG	GCTCCTCCGCGAACTTCTGAG	-	novel	NA	P-0048895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	152	542	0	ENST00000262320.3:c.1154_1174del	p.Pro385_Glu391del	p.P385_E391del	ENST00000262320	NM_003502.3	385	cCTCAGAAGTTCGCGGAGGAGCtc/ctc	5/11	0.261025299807127	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.261025299807127	1		542	847	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647821	3647821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	155	639	1	ENST00000294008.3:c.1343C>T	p.Ser448Phe	p.S448F	ENST00000294008	NM_032444.2	448	tCt/tTt	6/15	0.261025299807127	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.261025299807127	1		640	837	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796819	135796819	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	60	279	0	ENST00000298552.3:c.668T>A	p.Met223Lys	p.M223K	ENST00000298552	NM_001162426.1	223	aTg/aAg	8/23	0.256354337714429	1	FACETS	0.894	0.772	1	0.894	0.772	1	CLONAL	1	TRUE	0	0.261025299807127	1		279	447	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	112	301	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.955	1			1	INDETERMINATE	1	TRUE	NA	0.744509458798714	2		301	281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0048896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	353	932	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.744509458798714	2		934	689	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976857	55976857	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151317075	NA	P-0048896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	124	477	0	ENST00000263923.4:c.1055C>T	p.Ala352Val	p.A352V	ENST00000263923	NM_002253.2	352	gCg/gTg	8/30	1	2	FACETS	0.47	0.426	0.517	0.47	0.426	0.517	SUBCLONAL	1	TRUE	1	0.744509458798714	2		477	708	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508152	106508152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1446853033	NA	P-0048896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	92	291	0	ENST00000359195.3:c.146G>A	p.Arg49His	p.R49H	ENST00000359195	NM_002649.2	49	cGc/cAc	2/11	0.744509458798714	3	FACETS	0.76	0.679	0.846	0.38	0.339	0.423	SUBCLONAL	1	TRUE	1	0.744509458798714	3		291	446	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509636	106509636	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867282260	NA	P-0048896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	172	488	0	ENST00000359195.3:c.1630C>T	p.Arg544Ter	p.R544*	ENST00000359195	NM_002649.2	544	Cga/Tga	2/11	0.744509458798714	3	FACETS	0.883	0.815	0.954	0.442	0.407	0.477	CLONAL	1	TRUE	1	0.744509458798714	3		488	718	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104352455	104352455	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs869263892	NA	P-0048896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	219	543	2	ENST00000369902.3:c.573del	p.Phe192LeufsTer3	p.F192Lfs*3	ENST00000369902	NM_016169.3	191	Ccc/cc	4/12	0.744509458798714	1	FACETS	0.945	0.894	0.995	0.945	0.894	0.995	CLONAL	1	TRUE	0	0.744509458798714	1		545	391	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519945	66519945	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1296031514	NA	P-0048896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	143	373	0	ENST00000358598.2:c.428A>G	p.Asp143Gly	p.D143G	ENST00000358598	NM_212471.2	143	gAt/gGt	4/11	1	2	FACETS	0.635	0.581	0.691	0.635	0.581	0.691	SUBCLONAL	1	TRUE	1	0.744509458798714	2		373	605	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055904	180055904	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	159	445	0	ENST00000261937.6:c.1081T>C	p.Tyr361His	p.Y361H	ENST00000261937	NM_182925.4	361	Tac/Cac	8/30	1	2	FACETS	0.821	0.758	0.887	0.821	0.758	0.887	CLONAL	1	TRUE	1	0.744509458798714	2		445	520	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888178	81888178	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs535715020	NA	P-0048898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	422	471	0	ENST00000359376.3:c.323C>T	p.Thr108Met	p.T108M	ENST00000359376	NM_002661.3	108	aCg/aTg	3/33	0.820756273623803	3	FACETS	0.959	0.922	0.996	0.959	0.922	0.996	CLONAL	2	TRUE	1	0.820756273623803	3		471	756	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0048898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	1039	828	1	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.779788304683054	4	FACETS	1	0.993	1			1	CLONAL	4	TRUE	NA	0.820756273623803	4		829	1143	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629928	187629928	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	450	611	0	ENST00000441802.2:c.1054G>C	p.Val352Leu	p.V352L	ENST00000441802	NM_005245.3	352	Gtc/Ctc	2/27	0.694296587728861	3	FACETS	0.995	0.959	1			1	CLONAL	2	TRUE	NA	0.820756273623803	3		611	777	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939711	76939711	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	453	557	0	ENST00000373344.5:c.1037del	p.Leu346GlnfsTer7	p.L346Qfs*7	ENST00000373344	NM_000489.3	346	cTa/ca	9/35	0.820756273623803	2	FACETS	0.994	0.97	1	0.994	0.97	1	CLONAL	2	TRUE	0	0.820756273623803	2		557	555	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499073	149499073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs550187329	NA	P-0048899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1686	243	694	0	ENST00000261799.4:c.2755C>T	p.Arg919Trp	p.R919W	ENST00000261799	NM_002609.3	919	Cgg/Tgg	20/23	0.805666611593017	4	FACETS	0.548	0.509	0.588	0.183	0.169	0.196	SUBCLONAL	1	TRUE	1	0.851778502320549	4		694	1929	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115948	8115949	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	302	384	0	ENST00000346208.3:c.1294_1295insA	p.Pro432HisfsTer75	p.P432Hfs*75	ENST00000346208		432	cca/cAca	6/6	1	2	FACETS	0.907	0.858	0.956	0.907	0.858	0.956	CLONAL	1	TRUE	1	0.851778502320549	2		384	782	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503817	186503818	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	321	468	0	ENST00000323963.5:c.495dup	p.Met166TyrfsTer19	p.M166Yfs*19	ENST00000323963		165	gat/gaTt	5/11	1	2	FACETS	0.874	0.829	0.921	0.874	0.829	0.921	CLONAL	1	TRUE	1	0.851778502320549	2		468	862	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913237	NA	P-0048901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	1674	393	0	ENST00000369535.4:c.35G>C	p.Gly12Ala	p.G12A	ENST00000369535	NM_002524.4	12	gGt/gCt	2/7	0.707676460353674	12	FACETS	1	0.996	1			1	CLONAL	10	TRUE	NA	0.707676460353674	12		393	2095	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765164	+	missense_variant	Missense_Mutation	ONP	AGCA	AGCA	TGCT	novel	NA	P-0048901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	109	280	1	ENST00000374690.3:c.173_176inv	p.Gln58_Gln59delinsLeuLeu	p.Q58_Q59delinsLL	ENST00000374690	NM_000044.3	58	cAGCAg/cTGCTg	1/8	0.707676460353674	2	FACETS	0.842	0.78	0.902	0.842	0.78	0.902	CLONAL	2	TRUE	0	0.707676460353674	2		281	183	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729658	41729658	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	33	588	0	ENST00000242208.4:c.871C>A	p.Pro291Thr	p.P291T	ENST00000242208	NM_002192.2	291	Cct/Act	3/3	1	2	FACETS	0.561	0.46	0.674	0.561	0.46	0.674	SUBCLONAL	1	TRUE	1	0.506698821691464	2		588	232	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684041	29684041	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0048902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	51	598	0	ENST00000356175.3:c.7739C>G	p.Ser2580Ter	p.S2580*	ENST00000356175	NM_000267.3	2580	tCa/tGa	52/57	0.499812231682289	1	FACETS	0.9	0.779	1	0.9	0.779	1	CLONAL	1	TRUE	0	0.506698821691464	1		598	167	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612129	189612129	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	33	632	0	ENST00000264731.3:c.1881T>A	p.Ser627Arg	p.S627R	ENST00000264731	NM_003722.4	627	agT/agA	14/14	1	2	FACETS	0.525	0.43	0.631	0.525	0.43	0.631	SUBCLONAL	1	TRUE	1	0.506698821691464	2		632	248	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612144	189612825	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	GACCCGGGGTGAGCGTGTTATTGATGCTGTGCGATTCACCCTCCGCCAGACCATCTCTTTCCCACCCCGAGATGAGTGGAATGACTTCAACTTTGACATGGATGCTCGCCGCAATAAGCAACAGCGCATCAAAGAGGAGGGGGAGTGAGCCTCACCATGTGAGCTCTTCCTATCCCTCTCCTAACTGCCAGCCCCCTAAAAGCACTCCTGCTTAATCTTCAAAGCCTTCTCCCTAGCTCCTCCCCTTCCTCTTGTCTGATTTCTTAGGGGAAGGAGAAGTAAGAGGCTACCTCTTACCTAACATCTGACCTGGCATCTAATTCTGATTCTGGCTTTAAGCCTTCAAAACTATAGCTTGCAGAACTGTAGCTGCCATGGCTAGGTAGAAGTGAGCAAAAAAGAGTTGGGTGTCTCCTTAAGCTGCAGAGATTTCTCATTGACTTTTATAAAGCATGTTCACCCTTATAGTCTAAGACTATATATATAAATGTATAAATATACAGTATAGATTTTTGGGTGGGGGGCATTGAGTATTGTTTAAAATGTAATTTAAATGAAAGAAAATTGAGTTGCACTTATTGACCATTTTTTAATTTACTTGTTTTGGATGGCTTGTCTATACTCCTTCCCTTAAGGGGTATCATGTATGGTGATAGGTATCTAGAGCTTAATGCTACATGTG	GACCCGGGGTGAGCGTGTTATTGATGCTGTGCGATTCACCCTCCGCCAGACCATCTCTTTCCCACCCCGAGATGAGTGGAATGACTTCAACTTTGACATGGATGCTCGCCGCAATAAGCAACAGCGCATCAAAGAGGAGGGGGAGTGAGCCTCACCATGTGAGCTCTTCCTATCCCTCTCCTAACTGCCAGCCCCCTAAAAGCACTCCTGCTTAATCTTCAAAGCCTTCTCCCTAGCTCCTCCCCTTCCTCTTGTCTGATTTCTTAGGGGAAGGAGAAGTAAGAGGCTACCTCTTACCTAACATCTGACCTGGCATCTAATTCTGATTCTGGCTTTAAGCCTTCAAAACTATAGCTTGCAGAACTGTAGCTGCCATGGCTAGGTAGAAGTGAGCAAAAAAGAGTTGGGTGTCTCCTTAAGCTGCAGAGATTTCTCATTGACTTTTATAAAGCATGTTCACCCTTATAGTCTAAGACTATATATATAAATGTATAAATATACAGTATAGATTTTTGGGTGGGGGGCATTGAGTATTGTTTAAAATGTAATTTAAATGAAAGAAAATTGAGTTGCACTTATTGACCATTTTTTAATTTACTTGTTTTGGATGGCTTGTCTATACTCCTTCCCTTAAGGGGTATCATGTATGGTGATAGGTATCTAGAGCTTAATGCTACATGTG	-	novel	NA	P-0048902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	26	623	0	ENST00000264731.3:c.1896_*534del		p.*632*	ENST00000264731	NM_003722.4	632		14/14	1	2	FACETS	0.409	0.325	0.504	0.409	0.325	0.504	SUBCLONAL	1	TRUE	1	0.506698821691464	2		623	251	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729801	41729801	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	11	438	0	ENST00000242208.4:c.728C>T	p.Ala243Val	p.A243V	ENST00000242208	NM_002192.2	243	gCc/gTc	3/3	1	2	FACETS	0.224	0.154	0.31	0.224	0.154	0.31	SUBCLONAL	1	TRUE	1	0.506698821691464	2		438	194	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578387	7578399	+	protein_altering_variant	In_Frame_Del	DEL	GCGCTCATGGTGG	GCGCTCATGGTGG	CCGC	novel	NA	P-0048902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	106	641	1	ENST00000269305.4:c.531_543delinsGCGG	p.His178_Glu180del	p.H178_E180del	ENST00000269305	NM_001126112.2	177	ccCCACCATGAGCGC/ccGCGG	5/11	0.499812231682289	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.506698821691464	1		642	262	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	67	351	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.315670948061527	2		351	322	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612890	228612890	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757564822	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	50	600	1	ENST00000366696.1:c.137C>T	p.Thr46Met	p.T46M	ENST00000366696	NM_003493.2	46	aCg/aTg	1/1	0.162371343735341	1	FACETS	0.522	0.443	0.609	0.522	0.443	0.609	INDETERMINATE	1	TRUE	0	0.315670948061527	1		601	511	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644490	18644490	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs181773550	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	37	438	0	ENST00000266497.5:c.2668G>A	p.Asp890Asn	p.D890N	ENST00000266497		890	Gat/Aat	18/31	1	2	FACETS	0.358	0.294	0.43	0.358	0.294	0.43	SUBCLONAL	1	TRUE	1	0.315670948061527	2		438	655	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321372	1321372	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1319865856	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	30	495	0	ENST00000400841.2:c.383C>T	p.Ser128Leu	p.S128L	ENST00000400841		128	tCg/tTg	4/6	1	1	FACETS	0.269	0.216	0.33	0.269	0.216	0.33	SUBCLONAL	1	TRUE	0	0.315670948061527	1		495	595	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499732	8499732	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	71	616	0	ENST00000356435.5:c.2237G>A	p.Gly746Glu	p.G746E	ENST00000356435		746	gGa/gAa	14/35	0.171220931934522	3	FACETS	0.597	0.52	0.681			1	INDETERMINATE	1	TRUE	NA	0.315670948061527	3		616	872	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636727	8636727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159852	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	39	319	0	ENST00000356435.5:c.182G>A	p.Gly61Glu	p.G61E	ENST00000356435		61	gGa/gAa	2/35	0.171220931934522	3	FACETS	0.553	0.458	0.66			1	INDETERMINATE	1	TRUE	NA	0.315670948061527	3		319	517	SUCCESS
APC	324	MSKCC	GRCh37	5	112178162	112178162	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561610839	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	85	382	0	ENST00000257430.4:c.6871C>T	p.Gln2291Ter	p.Q2291*	ENST00000257430	NM_000038.5	2291	Caa/Taa	16/16	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.315670948061527	2		382	487	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199573	138199573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1406164317	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	32	293	0	ENST00000237289.4:c.991G>A	p.Asp331Asn	p.D331N	ENST00000237289	NM_001270507.1	331	Gat/Aat	7/9	0.315670948061527	1	FACETS	0.547	0.445	0.662	0.547	0.445	0.662	SUBCLONAL	1	TRUE	0	0.315670948061527	1		293	312	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047190	180047190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770500099	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	37	605	2	ENST00000261937.6:c.2525G>A	p.Arg842Gln	p.R842Q	ENST00000261937	NM_182925.4	842	cGa/cAa	17/30	0.315670948061527	1	FACETS	0.365	0.3	0.438	0.365	0.3	0.438	SUBCLONAL	1	TRUE	0	0.315670948061527	1		607	541	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271264	26271264	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	52	559	1	ENST00000305910.3:c.349C>T	p.Arg117Ter	p.R117*	ENST00000305910	NM_003534.2	117	Cga/Tga	1/1	0.173875424641175	4	FACETS	0.607	0.516	0.708	0.304	0.258	0.354	INDETERMINATE	1	TRUE	2	0.315670948061527	4		560	714	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864630	56864630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210415750	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	150	603	1	ENST00000519728.1:c.593G>A	p.Arg198Gln	p.R198Q	ENST00000519728	NM_002350.3	198	cGa/cAa	7/13	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.315670948061527	2		604	846	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444362	50444362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	98	388	0	ENST00000331340.3:c.292G>A	p.Asp98Asn	p.D98N	ENST00000331340	NM_006060.4	98	Gac/Aac	4/8	0.197021893749333	4	FACETS	1	0.981	1	0.744	0.666	0.827	CLONAL	1	TRUE	2	0.315670948061527	4		388	549	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591587	38591587	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057517941	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	109	421	1	ENST00000299084.4:c.46C>T	p.Arg16Ter	p.R16*	ENST00000299084	NM_152594.2	16	Cga/Tga	2/7	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.315670948061527	2		422	605	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148931	119148931	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	91	483	0	ENST00000264033.4:c.1151G>C	p.Cys384Ser	p.C384S	ENST00000264033	NM_005188.3	384	tGt/tCt	8/16	0.315670948061527	1	FACETS	0.904	0.805	1	0.904	0.805	1	CLONAL	1	TRUE	0	0.315670948061527	1		483	537	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470970	25470970	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	43	555	0	ENST00000264709.3:c.791C>T	p.Pro264Leu	p.P264L	ENST00000264709	NM_175629.2	264	cCc/cTc	7/23	1	2	FACETS	0.372	0.31	0.44	0.372	0.31	0.44	SUBCLONAL	1	TRUE	1	0.315670948061527	2		555	733	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967241	93967241	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	39	337	0	ENST00000369303.4:c.2111G>A	p.Gly704Glu	p.G704E	ENST00000369303	NM_004440.3	704	gGg/gAg	12/17	0.310860926781939	1	FACETS	0.682	0.568	0.809	0.682	0.568	0.809	SUBCLONAL	1	TRUE	0	0.315670948061527	1		337	305	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509460	46509460	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	108	535	0	ENST00000262741.5:c.1271C>T	p.Ser424Phe	p.S424F	ENST00000262741	NM_003629.3	424	tCt/tTt	10/10	0.162371343735341	1	FACETS	0.919	0.826	1	0.919	0.826	1	INDETERMINATE	1	TRUE	0	0.315670948061527	1		535	627	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46597576	46597576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	58	560	0	ENST00000262741.5:c.49G>A	p.Glu17Lys	p.E17K	ENST00000262741	NM_003629.3	17	Gag/Aag	1/10	0.162371343735341	1	FACETS	0.457	0.392	0.528	0.457	0.392	0.528	INDETERMINATE	1	TRUE	0	0.315670948061527	1		560	677	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458453	120458453	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1270274564	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	67	573	0	ENST00000256646.2:c.6892C>T	p.Arg2298Trp	p.R2298W	ENST00000256646	NM_024408.3	2298	Cgg/Tgg	34/34	0.162371343735341	1	FACETS	0.623	0.541	0.711	0.623	0.541	0.711	INDETERMINATE	1	TRUE	0	0.315670948061527	1		573	574	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023000	33023000	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	135	426	0	ENST00000300177.4:c.109G>C	p.Asp37His	p.D37H	ENST00000300177	NM_001191322.1	37	Gac/Cac	2/2	0.315670948061527	5	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.315670948061527	5		426	860	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989145	41989145	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754269369	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	118	567	0	ENST00000219905.7:c.1937C>T	p.Pro646Leu	p.P646L	ENST00000219905	NM_001164273.1	646	cCt/cTt	3/24	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.315670948061527	2		567	739	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844193	68844193	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	114	627	0	ENST00000261769.5:c.781G>C	p.Glu261Gln	p.E261Q	ENST00000261769	NM_004360.3	261	Gaa/Caa	6/16	0.162371343735341	1	FACETS	0.9	0.811	0.993	0.9	0.811	0.993	INDETERMINATE	1	TRUE	0	0.315670948061527	1		627	676	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960850	15960850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1403202191	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	42	250	0	ENST00000268712.3:c.6370C>T	p.Leu2124Phe	p.L2124F	ENST00000268712	NM_006311.3	2124	Ctt/Ttt	40/46	1	2	FACETS	0.693	0.58	0.818	0.693	0.58	0.818	SUBCLONAL	1	TRUE	1	0.315670948061527	2		250	384	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17120484	17120484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs184718358	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	85	637	0	ENST00000285071.4:c.1075C>T	p.Pro359Ser	p.P359S	ENST00000285071	NM_144997.5	359	Cct/Tct	10/14	1	2	FACETS	0.782	0.691	0.879	0.782	0.691	0.879	SUBCLONAL	1	TRUE	1	0.315670948061527	2		637	689	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325886	30325886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	79	360	0	ENST00000322652.5:c.2084C>T	p.Ser695Phe	p.S695F	ENST00000322652	NM_015355.2	695	tCc/tTc	16/16	1	2	FACETS	0.946	0.834	1	0.946	0.834	1	CLONAL	1	TRUE	1	0.315670948061527	2		360	529	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367872	15367872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	121	669	1	ENST00000263377.2:c.1454C>T	p.Ser485Phe	p.S485F	ENST00000263377	NM_058243.2	485	tCc/tTc	8/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.315670948061527	2		670	664	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742718	39742718	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	118	511	0	ENST00000361337.2:c.1561C>A	p.Gln521Lys	p.Q521K	ENST00000361337	NM_003286.2	521	Cag/Aag	15/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.315670948061527	2		511	620	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319897	62319897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	48	651	0	ENST00000360203.5:c.1739G>A	p.Arg580Lys	p.R580K	ENST00000360203	NM_001283009.1	580	aGg/aAg	21/35	1	2	FACETS	0.502	0.424	0.588	0.502	0.424	0.588	SUBCLONAL	1	TRUE	1	0.315670948061527	2		651	606	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715663	30715663	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	109	367	0	ENST00000295754.5:c.1321T>A	p.Ser441Thr	p.S441T	ENST00000295754	NM_003242.5	441	Tcc/Acc	5/7	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.315670948061527	2		367	580	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164935	47164935	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	78	303	0	ENST00000409792.3:c.1191A>T	p.Glu397Asp	p.E397D	ENST00000409792	NM_014159.6	397	gaA/gaT	3/21	1	2	FACETS	0.979	0.862	1	0.979	0.862	1	CLONAL	1	TRUE	1	0.315670948061527	2		303	505	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49929005	49929005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	117	534	0	ENST00000296474.3:c.3361G>A	p.Glu1121Lys	p.E1121K	ENST00000296474	NM_002447.2	1121	Gag/Aag	16/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.315670948061527	2		534	577	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72881556	72881556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	114	391	0	ENST00000325599.8:c.563C>T	p.Ala188Val	p.A188V	ENST00000325599	NM_018130.2	188	gCc/gTc	5/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.315670948061527	2		391	607	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554860	187554860	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	92	377	0	ENST00000441802.2:c.4301G>T	p.Gly1434Val	p.G1434V	ENST00000441802	NM_005245.3	1434	gGa/gTa	7/27	0.315670948061527	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.315670948061527	1		377	439	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630942	187630942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458285250	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	44	520	0	ENST00000441802.2:c.40C>T	p.Leu14Phe	p.L14F	ENST00000441802	NM_005245.3	14	Ctc/Ttc	2/27	0.315670948061527	1	FACETS	0.467	0.391	0.55	0.467	0.391	0.55	SUBCLONAL	1	TRUE	0	0.315670948061527	1		520	503	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	223658	223658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747557411	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	85	534	0	ENST00000264932.6:c.125G>A	p.Arg42Lys	p.R42K	ENST00000264932	NM_004168.2	42	aGg/aAg	2/15	0.104609645015002	4	FACETS	1	0.915	1	0.521	0.46	0.586	INDETERMINATE	1	TRUE	2	0.315670948061527	4		534	680	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526756	31526756	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs541915232	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	62	598	0	ENST00000344624.3:c.284C>G	p.Pro95Arg	p.P95R	ENST00000344624		95	cCc/cGc	2/33	0.104609645015002	4	FACETS	0.696	0.6	0.8	0.348	0.3	0.4	INDETERMINATE	1	TRUE	2	0.315670948061527	4		598	743	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564767	86564767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	83	603	0	ENST00000274376.6:c.499G>A	p.Glu167Lys	p.E167K	ENST00000274376	NM_002890.2	167	Gaa/Aaa	1/25	1	2	FACETS	0.713	0.628	0.803	0.713	0.628	0.803	SUBCLONAL	1	TRUE	1	0.315670948061527	2		603	738	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176516670	176516670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	33	588	0	ENST00000292408.4:c.67G>A	p.Glu23Lys	p.E23K	ENST00000292408	NM_213647.1	23	Gag/Aag	2/18	0.24404349554672	1	FACETS	0.335	0.272	0.407	0.335	0.272	0.407	SUBCLONAL	1	TRUE	0	0.315670948061527	1		588	525	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729717	41729717	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	113	505	0	ENST00000242208.4:c.812A>T	p.Lys271Met	p.K271M	ENST00000242208	NM_002192.2	271	aAg/aTg	3/3	0.197021893749333	4	FACETS	1	0.984	1	0.748	0.674	0.825	CLONAL	1	TRUE	2	0.315670948061527	4		505	630	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860262	151860262	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	97	477	0	ENST00000262189.6:c.10400G>A	p.Gly3467Glu	p.G3467E	ENST00000262189	NM_170606.2	3467	gGa/gAa	43/59	0.197021893749333	4	FACETS	1	0.91	1	0.512	0.456	0.571	CLONAL	1	TRUE	2	0.315670948061527	4		477	790	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205347	38205347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	74	652	1	ENST00000317025.8:c.343G>A	p.Glu115Lys	p.E115K	ENST00000317025	NM_023034.1	115	Gaa/Aaa	2/24	1	2	FACETS	0.489	0.427	0.557	0.489	0.427	0.557	SUBCLONAL	1	TRUE	1	0.315670948061527	2		653	958	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295253	1295255	+	upstream_gene_variant	5'Flank	DEL	GGG	GGG	AA	novel	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	21	349	2				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.401	0.308	0.509			1	INDETERMINATE	1	TRUE	NA	0.315670948061527	2		351	332	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63537575	63537577	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GGA	GGA	AT	novel	NA	P-0048904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	141	458	1	ENST00000307078.5:c.1055_1057delinsAT	p.Phe352TyrfsTer11	p.F352Yfs*11	ENST00000307078	NM_004655.3	352	tTCCcg/tATcg	4/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.315670948061527	2		459	626	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0048905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	100	351	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.891	0.796	0.991	0.891	0.796	0.991	CLONAL	1	TRUE	1	0.338682990070177	2		351	663	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs121913292	NA	P-0048905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	91	390	0	ENST00000371953.3:c.389del	p.Arg130GlnfsTer4	p.R130Qfs*4	ENST00000371953	NM_000314.4	130	cGa/ca	5/9	0.321303070982279	3	FACETS	0.909	0.808	1	0.455	0.404	0.509	CLONAL	1	TRUE	1	0.338682990070177	3		390	691	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951891	2951891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs116583746	NA	P-0048905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	116	575	0	ENST00000396946.4:c.3059C>T	p.Thr1020Met	p.T1020M	ENST00000396946	NM_032415.4	1020	aCg/aTg	23/25	0.321303070982279	3	FACETS	0.828	0.745	0.916	0.414	0.372	0.458	CLONAL	1	TRUE	1	0.338682990070177	3		575	967	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0048905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	199	528	2	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.321303070982279	3	FACETS	0.928	0.863	0.996	0.928	0.863	0.996	CLONAL	2	TRUE	1	0.338682990070177	3		530	740	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0048905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	56	479	0	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	1	2	FACETS	0.424	0.362	0.492	0.424	0.362	0.492	SUBCLONAL	1	TRUE	1	0.338682990070177	2		479	780	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417865	138417865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	100	499	1	ENST00000289153.2:c.1654G>A	p.Glu552Lys	p.E552K	ENST00000289153	NM_006219.2	552	Gaa/Aaa	11/22	1	2	FACETS	0.815	0.728	0.907	0.815	0.728	0.907	CLONAL	1	TRUE	1	0.338682990070177	2		500	725	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101273	27101273	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	48	599	0	ENST00000324856.7:c.4555C>T	p.Gln1519Ter	p.Q1519*	ENST00000324856	NM_006015.4	1519	Cag/Tag	18/20	1	2	FACETS	0.357	0.3	0.419	0.357	0.3	0.419	SUBCLONAL	1	TRUE	1	0.338682990070177	2		599	795	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831708	72831708	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	44	566	0	ENST00000268489.5:c.4873C>T	p.Arg1625Trp	p.R1625W	ENST00000268489	NM_006885.3	1625	Cgg/Tgg	9/10	1	2	FACETS	0.332	0.277	0.393	0.332	0.277	0.393	SUBCLONAL	1	TRUE	1	0.338682990070177	2		566	783	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592088	67592088	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	87	349	0	ENST00000274335.5:c.1907del	p.Asn636ThrfsTer26	p.N636Tfs*26	ENST00000274335		635	gAa/ga	14/15	1	2	FACETS	0.939	0.833	1	0.939	0.833	1	CLONAL	1	TRUE	1	0.338682990070177	2		349	547	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101252	27101252	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	157	602	0	ENST00000324856.7:c.4534C>T	p.Gln1512Ter	p.Q1512*	ENST00000324856	NM_006015.4	1512	Cag/Tag	18/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.338682990070177	2		602	834	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482408	56482408	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	118	602	0	ENST00000267101.3:c.956T>C	p.Met319Thr	p.M319T	ENST00000267101	NM_001982.3	319	aTg/aCg	8/28	1	2	FACETS	0.868	0.783	0.958	0.868	0.783	0.958	CLONAL	1	TRUE	1	0.338682990070177	2		602	803	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828719	72828719	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	104	566	2	ENST00000268489.5:c.7862del	p.Lys2621ArgfsTer24	p.K2621Rfs*24	ENST00000268489	NM_006885.3	2621	aAg/ag	9/10	1	2	FACETS	0.707	0.632	0.786	0.707	0.632	0.786	SUBCLONAL	1	TRUE	1	0.338682990070177	2		568	869	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010438	48010443	+	inframe_deletion	In_Frame_Del	DEL	GGCCTC	GGCCTC	-	novel	NA	P-0048905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	72	372	0	ENST00000234420.5:c.70_75del	p.Ser24_Ala25del	p.S24_A25del	ENST00000234420	NM_000179.2	22	aaGGCCTCg/aag	1/10	1	2	FACETS	0.716	0.626	0.813	0.716	0.626	0.813	SUBCLONAL	1	TRUE	1	0.338682990070177	2		372	594	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370838	55370839	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	C	novel	NA	P-0048905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	47	455	0	ENST00000297316.4:c.140_141delinsC	p.Glu47AlafsTer26	p.E47Afs*26	ENST00000297316	NM_022454.3	47	gAG/gC	1/2	1	2	FACETS	0.54	0.455	0.633	0.54	0.455	0.633	SUBCLONAL	1	TRUE	1	0.338682990070177	2		455	514	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524552	187524552	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	219	563	0	ENST00000441802.2:c.11128C>T	p.Gln3710Ter	p.Q3710*	ENST00000441802	NM_005245.3	3710	Caa/Taa	19/27	1	2	FACETS	0.852	0.793	0.912	0.852	0.793	0.912	CLONAL	1	TRUE	1	0.560842191689773	2		563	917	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578393	7578393	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876660821	NA	P-0048907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	147	493	0	ENST00000269305.4:c.537T>G	p.His179Gln	p.H179Q	ENST00000269305	NM_001126112.2	179	caT/caG	5/11	0.449443513478143	1	FACETS	0.857	0.785	0.931	0.857	0.785	0.931	CLONAL	1	TRUE	0	0.449443513478143	1		493	592	SUCCESS
ATR	545	MSKCC	GRCh37	3	142280234	142280234	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	137	348	0	ENST00000350721.4:c.1200G>C	p.Leu400Phe	p.L400F	ENST00000350721	NM_001184.3	400	ttG/ttC	5/47	1	2	FACETS	0.975	0.89	1	0.975	0.89	1	CLONAL	1	TRUE	1	0.449443513478143	2		348	625	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77064624	77064624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1392857529	NA	P-0048907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	90	447	0	ENST00000356341.3:c.793G>A	p.Asp265Asn	p.D265N	ENST00000356341	NM_002576.4	265	Gat/Aat	8/15	0.449443513478143	1	FACETS	0.556	0.495	0.622	0.556	0.495	0.622	SUBCLONAL	1	TRUE	0	0.449443513478143	1		447	558	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436929	110436929	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	78	274	0	ENST00000375856.3:c.1472C>T	p.Ser491Phe	p.S491F	ENST00000375856	NM_003749.2	491	tCc/tTc	1/2	0.449443513478143	1	FACETS	0.818	0.725	0.916	0.818	0.725	0.916	CLONAL	1	TRUE	0	0.449443513478143	1		274	329	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271219	26271219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	31	301	0	ENST00000305910.3:c.394C>T	p.Arg132Cys	p.R132C	ENST00000305910	NM_003534.2	132	Cgt/Tgt	1/1	1	2	FACETS	0.233	0.188	0.285	0.233	0.188	0.285	SUBCLONAL	1	TRUE	1	0.449443513478143	2		301	591	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489234	2489235	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0048907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	180	564	0	ENST00000355716.4:c.139_140insC	p.Tyr47SerfsTer30	p.Y47Sfs*30	ENST00000355716	NM_003820.2	47	tac/tCac	2/8	1	2	FACETS	0.994	0.918	1	0.994	0.918	1	CLONAL	1	TRUE	1	0.449443513478143	2		564	806	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117024	193117024	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	48	351	0	ENST00000367435.3:c.757C>G	p.Leu253Val	p.L253V	ENST00000367435	NM_024529.4	253	Ctt/Gtt	8/17	0.441264880995504	3	FACETS	0.319	0.268	0.374			1	SUBCLONAL	1	TRUE	NA	0.449443513478143	3		351	821	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97879635	97879635	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	65	426	0	ENST00000289081.3:c.1034C>G	p.Ser345Cys	p.S345C	ENST00000289081	NM_000136.2	345	tCt/tGt	11/15	0.449443513478143	1	FACETS	0.378	0.327	0.432	0.378	0.327	0.432	SUBCLONAL	1	TRUE	0	0.449443513478143	1		426	594	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419923	+	missense_variant	Missense_Mutation	ONP	TCTA	TCTA	CCTC	novel	NA	P-0048907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	45	457	0	ENST00000206249.3:c.1607_1610delinsCCTC	p.Leu536_Tyr537delinsProSer	p.L536_Y537delinsPS	ENST00000206249	NM_000125.3	536	cTCTAt/cCCTCt	8/8	1	2	FACETS	0.253	0.212	0.299	0.253	0.212	0.299	SUBCLONAL	1	TRUE	1	0.449443513478143	2		457	792	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0048908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	297	327	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.64445075730831	4	FACETS	0.95	0.907	0.992	0.95	0.907	0.992	CLONAL	3	TRUE	1	0.677742249257996	4		327	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577123	7577123	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876660333	NA	P-0048908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	325	617	1	ENST00000269305.4:c.815T>A	p.Val272Glu	p.V272E	ENST00000269305	NM_001126112.2	272	gTg/gAg	8/11	0.677742249257996	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.677742249257996	2		618	449	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	269	554	0	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	0.677742249257996	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.677742249257996	2		554	393	SUCCESS
APC	324	MSKCC	GRCh37	5	112175651	112175651	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	343	337	0	ENST00000257430.4:c.4364del	p.Asn1455IlefsTer18	p.N1455Ifs*18	ENST00000257430	NM_000038.5	1454	Aaa/aa	16/16	0.677742249257996	4	FACETS	0.923	0.892	0.952	0.923	0.892	0.952	CLONAL	4	TRUE	0	0.677742249257996	4		337	460	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943662	9943662	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560839364	NA	P-0048908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	285	527	2	ENST00000330684.3:c.1279G>A	p.Glu427Lys	p.E427K	ENST00000330684	NM_001134407.1	427	Gag/Aag	5/13	0.677742249257996	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.677742249257996	3		529	555	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685309	89685309	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	128	310	0	ENST00000371953.3:c.204C>A	p.Tyr68Ter	p.Y68*	ENST00000371953	NM_000314.4	68	taC/taA	3/9	NA	2	FACETS	1	0.974	1			1	INDETERMINATE	2	TRUE	NA	0.677742249257996	2		310	178	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996816	100996816	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	124	515	0	ENST00000325455.5:c.1711G>C	p.Gly571Arg	p.G571R	ENST00000325455	NM_001202474.3	571	Ggg/Cgg	2/8	0.677742249257996	3	FACETS	1	0.943	1	0.523	0.476	0.572	CLONAL	1	TRUE	1	0.677742249257996	3		515	468	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578374	212578374	+	splice_acceptor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0048908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	12	212	0	ENST00000342788.4:c.884-1del		p.X295_splice	ENST00000342788	NM_005235.2	295			0.677742249257996	3	FACETS	0.269	0.189	0.367	0.135	0.094	0.184	SUBCLONAL	1	TRUE	1	0.677742249257996	3		212	176	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564516	41564517	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0048908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	272	455	2	ENST00000263253.7:c.3939_3940del	p.Asn1314SerfsTer3	p.N1314Sfs*3	ENST00000263253	NM_001429.3	1313	cAG/c	24/31	0.677742249257996	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.677742249257996	2		457	401	SUCCESS
APC	324	MSKCC	GRCh37	5	112175659	112175659	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	369	328	1	ENST00000257430.4:c.4368A>C	p.Lys1456Asn	p.K1456N	ENST00000257430	NM_000038.5	1456	aaA/aaC	16/16	0.677742249257996	4	FACETS	0.991	0.962	1	0.991	0.962	1	CLONAL	4	TRUE	0	0.677742249257996	4		329	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0048909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	517	668	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.666416129648471	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.666416129648471	2		669	744	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916933	+	missense_variant	Missense_Mutation	ONP	GCAA	GCAA	TCAG	novel	NA	P-0048909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	239	407	0	ENST00000263967.3:c.317_320delinsTCAG	p.Gly106_Asn107delinsValSer	p.G106_N107delinsVS	ENST00000263967	NM_006218.2	106	gGCAAc/gTCAGc	2/21	0.55469456192617	3	FACETS	0.897	0.846	0.948	0.897	0.846	0.948	CLONAL	2	TRUE	1	0.666416129648471	3		407	533	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110251213	110251213	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	389	478	0	ENST00000374672.4:c.124A>G	p.Asn42Asp	p.N42D	ENST00000374672	NM_004235.4	42	Aac/Gac	2/5	0.662553993261702	2	FACETS	0.948	0.912	0.982	0.948	0.912	0.982	CLONAL	2	TRUE	0	0.666416129648471	2		478	616	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0048910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	178	696	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.294697570838849	1	FACETS	0.765	0.708	0.825	1	0.99	1	SUBCLONAL	2	TRUE	0	0.294697570838849	1		697	673	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0048910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	132	501	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.294697570838849	2		501	783	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482425	56482425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	173	425	0	ENST00000267101.3:c.973G>A	p.Gly325Arg	p.G325R	ENST00000267101	NM_001982.3	325	Gga/Aga	8/28	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.294697570838849	2		425	868	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257176	16257176	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	131	482	0	ENST00000375759.3:c.4441G>C	p.Glu1481Gln	p.E1481Q	ENST00000375759	NM_015001.2	1481	Gaa/Caa	11/15	1	2	FACETS	0.934	0.847	1	0.934	0.847	1	CLONAL	1	TRUE	1	0.294697570838849	2		482	952	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725469	162725469	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	73	432	0	ENST00000367921.3:c.581A>T	p.Tyr194Phe	p.Y194F	ENST00000367921	NM_006182.2	194	tAc/tTc	7/18	1	2	FACETS	0.59	0.515	0.671	0.59	0.515	0.671	SUBCLONAL	1	TRUE	1	0.294697570838849	2		432	840	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2214559	2214559	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	114	455	1	ENST00000398665.3:c.1887G>T	p.Gln629His	p.Q629H	ENST00000398665	NM_032482.2	629	caG/caT	19/28	0.294697570838849	1	FACETS	0.972	0.876	1	0.972	0.876	1	CLONAL	1	TRUE	0	0.294697570838849	1		456	679	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0048911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	102	290	1	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.187058394175301	3	FACETS	1	0.971	1	0.607	0.546	0.671	INDETERMINATE	1	TRUE	1	0.489990487999324	3		291	427	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0048911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	80	347	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.0607244909124813	4	FACETS	1	0.971	1	0.657	0.583	0.737	INDETERMINATE	1	TRUE	2	0.489990487999324	4		347	370	SUCCESS
APC	324	MSKCC	GRCh37	5	112174096	112174096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs137854575	NA	P-0048911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	69	326	0	ENST00000257430.4:c.2805C>A	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	taC/taA	16/16	0.187058394175301	3	FACETS	1	0.961	1	0.62	0.545	0.698	INDETERMINATE	1	TRUE	1	0.489990487999324	3		326	283	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0048911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	112	371	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.489990487999324	1	FACETS	0.913	0.829	1	0.913	0.829	1	CLONAL	1	TRUE	0	0.489990487999324	1		371	378	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259497	89259497	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	106	420	0	ENST00000336596.2:c.641A>G	p.Asp214Gly	p.D214G	ENST00000336596	NM_005233.5	214	gAc/gGc	3/17	1	2	FACETS	0.977	0.881	1	0.977	0.881	1	CLONAL	1	TRUE	1	0.489990487999324	2		420	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782082	NA	P-0048911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	298	511	0	ENST00000269305.4:c.745A>T	p.Arg249Trp	p.R249W	ENST00000269305	NM_001126112.2	249	Agg/Tgg	7/11	0.329621388534272	2	FACETS	1	0.993	1	0.675	0.637	0.714	CLONAL	1	TRUE	0	0.489990487999324	2		511	901	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087503	27087503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	145	592	1	ENST00000324856.7:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000324856	NM_006015.4	693	Cga/Tga	5/20	0.242160669546881	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.242160669546881	1		593	929	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591931	48591931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	98	455	0	ENST00000342988.3:c.1094G>A	p.Gly365Asp	p.G365D	ENST00000342988	NM_005359.5	365	gGt/gAt	9/12	0.242160669546881	1	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	0	0.242160669546881	1		455	698	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717615	89717615	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909227	NA	P-0048912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	46	401	0	ENST00000371953.3:c.640C>T	p.Gln214Ter	p.Q214*	ENST00000371953	NM_000314.4	214	Cag/Tag	7/9	1	2	FACETS	0.536	0.45	0.631	0.536	0.45	0.631	SUBCLONAL	1	TRUE	1	0.242160669546881	2		401	709	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717609	89717609	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs876661024	NA	P-0048912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	95	360	0	ENST00000371953.3:c.635-1G>A		p.X212_splice	ENST00000371953	NM_000314.4	212			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.242160669546881	2		360	669	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508173	106508173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1315748037	NA	P-0048912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	42	309	0	ENST00000359195.3:c.167C>T	p.Thr56Met	p.T56M	ENST00000359195	NM_002649.2	56	aCg/aTg	2/11	1	2	FACETS	0.683	0.57	0.808	0.683	0.57	0.808	SUBCLONAL	1	TRUE	1	0.242160669546881	2		309	508	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711973	89711973	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	36	376	0	ENST00000371953.3:c.591G>C	p.Lys197Asn	p.K197N	ENST00000371953	NM_000314.4	197	aaG/aaC	6/9	1	2	FACETS	0.465	0.381	0.559	0.465	0.381	0.559	SUBCLONAL	1	TRUE	1	0.242160669546881	2		376	640	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371774	45371774	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	91	454	1	ENST00000262160.6:c.1217A>G	p.Tyr406Cys	p.Y406C	ENST00000262160	NM_005901.5	406	tAt/tGt	10/11	0.242160669546881	1	FACETS	0.905	0.803	1	0.905	0.803	1	CLONAL	1	TRUE	0	0.242160669546881	1		455	730	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717734	89717734	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	39	435	0	ENST00000371953.3:c.759C>G	p.Ile253Met	p.I253M	ENST00000371953	NM_000314.4	253	atC/atG	7/9	1	2	FACETS	0.487	0.403	0.582	0.487	0.403	0.582	SUBCLONAL	1	TRUE	1	0.242160669546881	2		435	661	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245886	5245886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs948978539	NA	P-0048912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	75	669	0	ENST00000357368.4:c.889G>A	p.Val297Met	p.V297M	ENST00000357368	NM_002850.3	297	Gtg/Atg	10/38	1	2	FACETS	0.541	0.473	0.616	0.541	0.473	0.616	SUBCLONAL	1	TRUE	1	0.242160669546881	2		669	1144	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627788	14627789	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0048912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	201	618	0	ENST00000254322.2:c.281_282del	p.Phe94SerfsTer10	p.F94Sfs*10	ENST00000254322	NM_006145.1	94	tTC/t	2/3	1	2	FACETS	0.798	0.739	0.859	1	0.991	1	SUBCLONAL	2	TRUE	1	0.242160669546881	2		618	1040	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293888	1293888	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	70	642	0	ENST00000310581.5:c.1113G>C	p.Trp371Cys	p.W371C	ENST00000310581	NM_198253.2	371	tgG/tgC	2/16	0.172483859624501	2	FACETS	0.529	0.459	0.605	0.264	0.229	0.303	SUBCLONAL	1	TRUE	0	0.242160669546881	2		642	1093	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712008	89712008	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	24	255	0	ENST00000371953.3:c.626G>A	p.Gly209Glu	p.G209E	ENST00000371953	NM_000314.4	209	gGa/gAa	6/9	1	2	FACETS	0.469	0.367	0.587	0.469	0.367	0.587	SUBCLONAL	1	TRUE	1	0.242160669546881	2		255	423	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	231	301	0				ENST00000310581	NM_198253.2	-/1132			0.709275089792524	9	FACETS	1	0.965	1	0.301	0.28	0.323	CLONAL	2	FALSE	2	0.709275089792524	9		301	1076	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0048913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	780	710	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.696972543025147	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	FALSE	0	0.709275089792524	3		711	972	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599314	55599314	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	328	584	1	ENST00000288135.5:c.2440G>A	p.Ala814Thr	p.A814T	ENST00000288135	NM_000222.2	814	Gcc/Acc	17/21	0.709275089792524	4	FACETS	1	0.99	1	0.569	0.541	0.596	CLONAL	2	FALSE	0	0.709275089792524	4		585	695	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874011	123874013	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs780061449	NA	P-0048913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	11	50	0	ENST00000330479.4:c.62_64del	p.Ala21del	p.A21del	ENST00000330479	NM_020382.3	14	gaGGCg/gag	2/9	0.709275089792524	3	FACETS	0.447	0.312	0.611	0.149	0.104	0.204	SUBCLONAL	1	FALSE	0	0.709275089792524	3		50	94	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123685	11123685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	520	639	0	ENST00000358026.2:c.2335G>A	p.Asp779Asn	p.D779N	ENST00000358026	NM_001128849.1	779	Gac/Aac	16/36	0.709275089792524	3	FACETS	1	0.993	1	0.733	0.708	0.758	CLONAL	2	FALSE	0	0.709275089792524	3		639	903	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180280	38180280	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	171	669	0	ENST00000396334.3:c.128G>T	p.Arg43Leu	p.R43L	ENST00000396334	NM_002468.4	43	cGg/cTg	1/5	0.301134413810194	6	FACETS	1	0.978	1	0.196	0.18	0.213	INDETERMINATE	1	FALSE	0	0.709275089792524	6		669	991	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163793	72163793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	71	470	0	ENST00000357731.5:c.565G>A	p.Asp189Asn	p.D189N	ENST00000357731	NM_173808.2	189	Gac/Aac	4/7	0.709275089792524	4	FACETS	0.512	0.447	0.583	0.256	0.223	0.292	SUBCLONAL	1	FALSE	2	0.709275089792524	4		470	668	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725069	162725069	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	461	456	0	ENST00000367921.3:c.541G>A	p.Glu181Lys	p.E181K	ENST00000367921	NM_006182.2	181	Gag/Aag	6/18	0.709275089792524	6	FACETS	1	0.993	1	0.859	0.825	0.893	CLONAL	3	FALSE	2	0.709275089792524	6		456	915	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390476	118390476	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	169	520	0	ENST00000534358.1:c.11290C>A	p.His3764Asn	p.H3764N	ENST00000534358	NM_005933.3	3764	Cac/Aac	32/36	0.709275089792524	3	FACETS	0.826	0.76	0.893	0.413	0.38	0.447	CLONAL	1	FALSE	1	0.709275089792524	3		520	782	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644954	67644954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1933	172	590	0	ENST00000264010.4:c.219G>A	p.Met73Ile	p.M73I	ENST00000264010	NM_006565.3	73	atG/atA	3/12	0.709275089792524	10	FACETS	0.884	0.81	0.963			1	CLONAL	1	FALSE	NA	0.709275089792524	10		590	2105	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067374	37067374	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	148	514	0	ENST00000231790.2:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000231790	NM_000249.3	429	Gag/Tag	12/19	0.301134413810194	6	FACETS	1	0.976	1	0.198	0.181	0.217	INDETERMINATE	1	FALSE	0	0.709275089792524	6		514	848	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502374	186502374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	224	457	0	ENST00000323963.5:c.97G>A	p.Asp33Asn	p.D33N	ENST00000323963		33	Gat/Aat	3/11	0.709275089792524	4	FACETS	1	0.991	1	0.687	0.641	0.734	CLONAL	1	FALSE	2	0.709275089792524	4		457	786	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404405	139404405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	214	685	0	ENST00000277541.6:c.2749C>T	p.His917Tyr	p.H917Y	ENST00000277541	NM_017617.3	917	Cac/Tac	18/34	1	2	FACETS	0.794	0.74	0.849	0.794	0.74	0.849	SUBCLONAL	1	FALSE	1	0.709275089792524	2		685	760	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	48	301	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.213750395492893	2		301	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0048914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	155	736	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	1	2	FACETS	0.911	0.835	0.99	1	0.991	1	CLONAL	2	TRUE	1	0.213750395492893	2		736	796	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048602	180048602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778453271	NA	P-0048914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	58	759	0	ENST00000261937.6:c.1960G>A	p.Glu654Lys	p.E654K	ENST00000261937	NM_182925.4	654	Gaa/Aaa	13/30	1	2	FACETS	0.768	0.659	0.887	0.768	0.659	0.887	SUBCLONAL	1	TRUE	1	0.213750395492893	2		759	707	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275415	115275415	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	28	501	0	ENST00000438362.2:c.998T>A	p.Ile333Asn	p.I333N	ENST00000438362	NM_001242891.1	333	aTc/aAc	10/20	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.213750395492893	2		501	183	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032856	30032856	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	38	385	1	ENST00000338641.4:c.232del	p.Asp78ThrfsTer45	p.D78Tfs*45	ENST00000338641	NM_000268.3	77	atG/at	2/16	0.213750395492893	1	FACETS	0.918	0.761	1	0.918	0.761	1	CLONAL	1	TRUE	0	0.213750395492893	1		386	346	SUCCESS
APC	324	MSKCC	GRCh37	5	112174508	112174508	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	22	455	0	ENST00000257430.4:c.3217A>G	p.Thr1073Ala	p.T1073A	ENST00000257430	NM_000038.5	1073	Aca/Gca	16/16	1	2	FACETS	1	0.797	1	1	0.797	1	CLONAL	1	TRUE	1	0.213750395492893	2		455	201	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	262	327	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.949	0.894	1	0.949	0.894	1	CLONAL	1	TRUE	1	0.797180282613206	2		327	693	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589631	67589632	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATTATATGAAGA	novel	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	146	294	0	ENST00000274335.5:c.1397_1408dup	p.Leu466_Glu469dup	p.L466_E469dup	ENST00000274335		466	aga/agATTATATGAAGAa	10/15	1	2	FACETS	0.774	0.712	0.839	0.774	0.712	0.839	SUBCLONAL	1	TRUE	1	0.797180282613206	2		294	473	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	240	407	1	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	1	2	FACETS	0.829	0.778	0.882	0.829	0.778	0.882	CLONAL	1	TRUE	1	0.797180282613206	2		408	726	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	205	388	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.958	0.896	1	0.958	0.896	1	CLONAL	1	TRUE	1	0.797180282613206	2		388	537	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	288	603	0	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.797180282613206	2		603	682	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	319	438	2	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.993	0.942	1	0.993	0.942	1	CLONAL	1	TRUE	1	0.797180282613206	2		440	806	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	70	421	2	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.31	0.27	0.353	0.31	0.27	0.353	SUBCLONAL	1	TRUE	1	0.797180282613206	2		423	567	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	313	625	1	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.797180282613206	2		626	776	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934239	81934239	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	351	662	1	ENST00000359376.3:c.1216G>A	p.Glu406Lys	p.E406K	ENST00000359376	NM_002661.3	406	Gag/Aag	14/33	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.797180282613206	2		663	837	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909463	50909463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568626065	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	413	852	0	ENST00000440232.2:c.1267C>T	p.Arg423Cys	p.R423C	ENST00000440232	NM_002691.3	423	Cgt/Tgt	11/27	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.797180282613206	2		852	1004	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850704	63850705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	271	528	3	ENST00000279873.7:c.1489dup	p.Ile497AsnfsTer31	p.I497Nfs*31	ENST00000279873	NM_032199.2	494	-/A	10/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.797180282613206	2		531	652	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371799	55371820	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCCGCGCTGGGCCCCGAG	GGCGGCCGCGCTGGGCCCCGAG	-	novel	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	239	178	0	ENST00000297316.4:c.499_520del	p.Leu167TrpfsTer213	p.L167Wfs*213	ENST00000297316	NM_022454.3	163	caGGCGGCCGCGCTGGGCCCCGAG/ca	2/2	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.797180282613206	2		178	447	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467573	66467573	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	200	444	0	ENST00000273854.3:c.696del	p.Lys232AsnfsTer36	p.K232Nfs*36	ENST00000273854	NM_004439.5	232	aaA/aa	3/18	0.17759376142134	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.797180282613206	0		444	520	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119910	70119910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1297203260	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	309	534	1	ENST00000245479.2:c.916del	p.Val306CysfsTer77	p.V306Cfs*77	ENST00000245479	NM_000346.3	304	ccG/cc	3/3	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.797180282613206	2		535	773	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	436	774	4	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.797180282613206	2		778	1023	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110129	8110130	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs745673717	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	365	620	0	ENST00000585124.1:c.475dup	p.Arg159ProfsTer15	p.R159Pfs*15	ENST00000585124	NM_004217.3	159	cgc/cCgc	6/9	1	2	FACETS	0.948	0.902	0.995	0.948	0.902	0.995	CLONAL	1	TRUE	1	0.797180282613206	2		620	966	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351595	89351595	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	436	822	0	ENST00000301030.4:c.1355del	p.Asn452IlefsTer3	p.N452Ifs*3	ENST00000301030	NM_001256183.1	452	aAt/at	9/13	1	2	FACETS	0.919	0.878	0.961	0.919	0.878	0.961	CLONAL	1	TRUE	1	0.797180282613206	2		822	1190	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644874	67644874	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	183	727	0	ENST00000264010.4:c.143del	p.Gly48ValfsTer14	p.G48Vfs*14	ENST00000264010	NM_006565.3	47	Ggg/gg	3/12	1	2	FACETS	0.561	0.519	0.606	0.561	0.519	0.606	SUBCLONAL	1	TRUE	1	0.797180282613206	2		727	818	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	592	551	23	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	0.774741797164993	3	FACETS	0.881	0.85	0.911	0.881	0.85	0.911	CLONAL	2	TRUE	1	0.797180282613206	3		574	1179	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964923	55964923	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1062832	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	78	512	0	ENST00000263923.4:c.2314G>A	p.Ala772Thr	p.A772T	ENST00000263923	NM_002253.2	772	Gcg/Acg	16/30	0.17759376142134	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.797180282613206	0		512	689	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351959	89351959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1323276539	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	564	937	0	ENST00000301030.4:c.991G>A	p.Ala331Thr	p.A331T	ENST00000301030	NM_001256183.1	331	Gcc/Acc	9/13	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.797180282613206	2		937	1303	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089539	27089540	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	465	785	0	ENST00000324856.7:c.2497_2498dup	p.Asn833LysfsTer27	p.N833Kfs*27	ENST00000324856	NM_006015.4	832	ata/atAAa	8/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.797180282613206	2		785	1084	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306998	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	240	492	0	ENST00000342505.4:c.2579_2580del	p.Lys860ThrfsTer4	p.K860Tfs*4	ENST00000342505	NM_002227.2	860	aAA/a	19/25	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.797180282613206	2		492	595	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70412334	70412334	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	32	351	0	ENST00000373644.4:c.4444T>C	p.Cys1482Arg	p.C1482R	ENST00000373644	NM_030625.2	1482	Tgt/Cgt	6/12	1	2	FACETS	0.134	0.108	0.164	0.134	0.108	0.164	SUBCLONAL	1	TRUE	1	0.797180282613206	2		351	598	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720664	89720664	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1114167648	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	132	142	0	ENST00000371953.3:c.815A>C	p.His272Pro	p.H272P	ENST00000371953	NM_000314.4	272	cAc/cCc	8/9	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.797180282613206	2		142	255	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727490	66727490	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	323	593	0	ENST00000307102.5:c.206A>G	p.Glu69Gly	p.E69G	ENST00000307102	NM_002755.3	69	gAg/gGg	2/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.797180282613206	2		593	800	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785756	50785756	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	354	535	0	ENST00000398568.2:c.746T>C	p.Val249Ala	p.V249A	ENST00000398568	NM_001042412.1	249	gTt/gCt	4/18	1	2	FACETS	0.958	0.911	1	0.958	0.911	1	CLONAL	1	TRUE	1	0.797180282613206	2		535	927	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660581	67660581	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770889045	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	476	711	2	ENST00000264010.4:c.1481G>A	p.Arg494His	p.R494H	ENST00000264010	NM_006565.3	494	cGc/cAc	8/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.797180282613206	2		713	1179	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350981	89350981	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	549	1014	0	ENST00000301030.4:c.1969T>C	p.Phe657Leu	p.F657L	ENST00000301030	NM_001256183.1	657	Ttt/Ctt	9/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.797180282613206	2		1014	1318	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244202	41244204	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs80358336	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	90	656	0	ENST00000357654.3:c.3344_3346del	p.Glu1115del	p.E1115del	ENST00000357654	NM_007294.3	1115	gAAGta/gta	10/23	1	2	FACETS	0.268	0.237	0.3	0.268	0.237	0.3	SUBCLONAL	1	TRUE	1	0.797180282613206	2		656	844	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632390	1632390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	402	758	0	ENST00000344749.5:c.160C>T	p.Pro54Ser	p.P54S	ENST00000344749	NM_001136139.2	54	Ccc/Tcc	4/19	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.797180282613206	2		758	994	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470911	25470911	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	396	765	0	ENST00000264709.3:c.850T>C	p.Tyr284His	p.Y284H	ENST00000264709	NM_175629.2	284	Tac/Cac	7/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.797180282613206	2		765	979	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044393	128044393	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	427	752	1	ENST00000285398.2:c.1228T>C	p.Tyr410His	p.Y410H	ENST00000285398	NM_000122.1	410	Tac/Cac	8/15	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.797180282613206	2		753	952	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024833	31024833	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	388	719	0	ENST00000375687.4:c.4321del	p.Tyr1441MetfsTer9	p.Y1441Mfs*9	ENST00000375687	NM_015338.5	1440	Ttt/tt	13/13	1	2	FACETS	0.987	0.941	1	0.987	0.941	1	CLONAL	1	TRUE	1	0.797180282613206	2		719	986	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934319	49934319	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1447912459	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	295	624	0	ENST00000296474.3:c.2188A>G	p.Ser730Gly	p.S730G	ENST00000296474	NM_002447.2	730	Agt/Ggt	8/20	1	2	FACETS	0.979	0.926	1	0.979	0.926	1	CLONAL	1	TRUE	1	0.797180282613206	2		624	756	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936341	49936341	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	390	751	0	ENST00000296474.3:c.1507A>C	p.Ser503Arg	p.S503R	ENST00000296474	NM_002447.2	503	Agt/Cgt	3/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.797180282613206	2		751	963	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443285	187443285	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	126	312	0	ENST00000232014.4:c.1839+2T>C		p.X613_splice	ENST00000232014	NM_001130845.1	613			1	2	FACETS	0.758	0.692	0.826	0.758	0.692	0.826	SUBCLONAL	1	TRUE	1	0.797180282613206	2		312	417	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467834	50467834	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	309	632	0	ENST00000331340.3:c.1069G>T	p.Gly357Cys	p.G357C	ENST00000331340	NM_006060.4	357	Ggc/Tgc	8/8	0.774741797164993	3	FACETS	1	0.98	1	0.539	0.509	0.57	CLONAL	1	TRUE	1	0.797180282613206	3		632	1005	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29195954	29195954	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs769412960	NA	P-0048915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	507	809	0	ENST00000240100.2:c.644A>G	p.Asp215Gly	p.D215G	ENST00000240100	NM_001394.6	215	gAc/gGc	3/4	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.797180282613206	2		809	1170	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117733	108117734	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	59	252	1	ENST00000278616.4:c.945dup	p.Tyr316IlefsTer2	p.Y316Ifs*2	ENST00000278616	NM_000051.3	315	tta/ttAa	8/63	0.2769212921022	5	FACETS	1	0.953	1	0.8	0.699	0.905	CLONAL	2	TRUE	2	0.392883843023226	5		253	199	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204687	108204687	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	67	219	0	ENST00000278616.4:c.8002G>T	p.Glu2668Ter	p.E2668*	ENST00000278616	NM_000051.3	2668	Gaa/Taa	54/63	0.2769212921022	5	FACETS	1	0.954	1	1	0.954	1	CLONAL	3	TRUE	2	0.392883843023226	5		219	159	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	141	301	0				ENST00000310581	NM_198253.2	-/1132			0.62420426911615	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.62420426911615	2		301	206	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867546	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs11466445	NA	P-0048917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	16	26	0	ENST00000374994.4:c.70_78del	p.Ala24_Ala26del	p.A24_A26del	ENST00000374994	NM_004612.2	17	ctGGCGGCGGCg/ctg	1/9	0.62420426911615	2	FACETS	1	0.827	1	0.545	0.42	0.68	CLONAL	1	TRUE	0	0.62420426911615	2		26	47	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200024	123200024	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0048917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	100	126	0	ENST00000218089.9:c.2097-1G>A		p.X699_splice	ENST00000218089	NM_001042749.1	699			0.62420426911615	2	FACETS	0.89	0.844	0.93			1	CLONAL	3	TRUE	NA	0.62420426911615	2		126	120	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820528	44820528	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0048917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	110	227	0	ENST00000377967.4:c.226-1G>A		p.X76_splice	ENST00000377967	NM_021140.2	76			0.62420426911615	2	FACETS	1	0.981	1			1	CLONAL	2	TRUE	NA	0.62420426911615	2		227	155	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201933	102201933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	47	370	0	ENST00000263464.3:c.1285G>A	p.Glu429Lys	p.E429K	ENST00000263464	NM_001165.4	429	Gaa/Aaa	6/9	0.408579687843667	2	FACETS	0.761	0.65	0.879	0.38	0.325	0.44	SUBCLONAL	1	TRUE	0	0.62420426911615	2		370	198	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499765	8499765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	38	619	0	ENST00000356435.5:c.2204C>T	p.Pro735Leu	p.P735L	ENST00000356435		735	cCc/cTc	14/35	0.62420426911615	2	FACETS	0.402	0.333	0.478	0.201	0.166	0.239	SUBCLONAL	1	TRUE	0	0.62420426911615	2		619	303	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264619	1264619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	151	759	0	ENST00000310581.5:c.2743G>A	p.Gly915Ser	p.G915S	ENST00000310581	NM_198253.2	915	Ggt/Agt	11/16	0.62420426911615	2	FACETS	1	0.986	1	0.65	0.602	0.699	CLONAL	1	TRUE	0	0.62420426911615	2		759	372	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579484	7579491	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGGCAT	TCTGGCAT	-	novel	NA	P-0048917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	357	710	0	ENST00000269305.4:c.196_203del	p.Met66GlyfsTer80	p.M66Gfs*80	ENST00000269305	NM_001126112.2	66	ATGCCAGAg/g	4/11	0.564940211769534	4	FACETS	0.929	0.897	0.96	1	0.997	1	CLONAL	4	TRUE	2	0.62420426911615	4		710	500	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369246	40369246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	40	660	0	ENST00000293328.3:c.1312G>A	p.Glu438Lys	p.E438K	ENST00000293328	NM_012448.3	438	Gaa/Aaa	11/19	0.330969958935366	4	FACETS	0.335	0.278	0.399	0.168	0.139	0.2	INDETERMINATE	1	TRUE	2	0.62420426911615	4		660	621	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680734	88680734	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	31	667	1	ENST00000360948.2:c.523C>A	p.Gln175Lys	p.Q175K	ENST00000360948	NM_001012338.2	175	Cag/Aag	6/19	0.2364653048238	3	FACETS	0.358	0.29	0.435	0.179	0.145	0.218	INDETERMINATE	1	TRUE	1	0.62420426911615	3		668	364	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786784	3786784	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	213	467	0	ENST00000262367.5:c.4427del	p.Pro1476GlnfsTer74	p.P1476Qfs*74	ENST00000262367	NM_004380.2	1476	cCa/ca	27/31	0.444244190293883	3	FACETS	0.916	0.871	0.959	0.916	0.871	0.959	CLONAL	3	TRUE	0	0.62420426911615	3		467	326	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217123	66217123	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	22	411	0	ENST00000273854.3:c.2492C>G	p.Ala831Gly	p.A831G	ENST00000273854	NM_004439.5	831	gCa/gGa	14/18	0.573489065513326	3	FACETS	0.27	0.209	0.341	0.135	0.104	0.171	SUBCLONAL	1	TRUE	1	0.62420426911615	3		411	343	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874363	76874363	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	217	309	0	ENST00000373344.5:c.5359G>T	p.Gly1787Cys	p.G1787C	ENST00000373344	NM_000489.3	1787	Ggt/Tgt	21/35	0.62420426911615	2	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.62420426911615	2		309	296	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0048918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	28	582	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.75	0.598	0.923	0.75	0.598	0.923	CLONAL	1	TRUE	1	0.15	2		582	498	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0048918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	16	247	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.426	0.313	0.561	0.426	0.313	0.561	SUBCLONAL	1	TRUE	1	0.15	2		247	501	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207061	1207063	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0048918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	80	631	0	ENST00000326873.7:c.151_153del	p.Met51del	p.M51del	ENST00000326873	NM_000455.4	50	cTGAtg/ctg	1/10	0.3	2	FACETS	1	0.89	1			1	CLONAL	1	TRUE	NA	0.15	2		631	1051	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763976	76763976	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	51	626	1	ENST00000373344.5:c.7332G>T	p.Leu2444Phe	p.L2444F	ENST00000373344	NM_000489.3	2444	ttG/ttT	35/35	0.0750850369394516	0	FACETS	0.733	0.621	0.856			1	INDETERMINATE	1	TRUE	0	0.15	0		627	789	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600446	10600446	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	82	621	0	ENST00000171111.5:c.1409G>T	p.Arg470Leu	p.R470L	ENST00000171111	NM_203500.1	470	cGt/cTt	4/6	0.159781245440028	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.15	1		621	874	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680046	30680046	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	49	561	0	ENST00000376406.3:c.1673del	p.Gly558AspfsTer10	p.G558Dfs*10	ENST00000376406	NM_014641.2	558	gGa/ga	5/15	1	2	FACETS	0.772	0.652	0.905	0.772	0.652	0.905	CLONAL	1	TRUE	1	0.15	2		561	846	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794135	242794135	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	59	603	0	ENST00000334409.5:c.593G>A	p.Gly198Glu	p.G198E	ENST00000334409	NM_005018.2	198	gGg/gAg	4/5	1	2	FACETS	0.947	0.813	1	0.947	0.813	1	CLONAL	1	TRUE	1	0.15	2		603	831	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251208	115251208	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	29	498	0	ENST00000369535.4:c.518G>T	p.Ser173Ile	p.S173I	ENST00000369535	NM_002524.4	173	aGc/aTc	5/7	1	2	FACETS	0.677	0.542	0.832	0.677	0.542	0.832	SUBCLONAL	1	TRUE	1	0.15	2		498	571	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100469	8100469	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	58	665	0	ENST00000346208.3:c.443C>G	p.Pro148Arg	p.P148R	ENST00000346208		148	cCg/cGg	3/6	1	2	FACETS	0.926	0.794	1	0.926	0.794	1	CLONAL	1	TRUE	1	0.15	2		665	835	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482652	56482652	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	51	499	0	ENST00000267101.3:c.1109G>C	p.Gly370Ala	p.G370A	ENST00000267101	NM_001982.3	370	gGa/gCa	9/28	1	2	FACETS	0.875	0.742	1	0.875	0.742	1	CLONAL	1	TRUE	1	0.15	2		499	777	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038692	14038692	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	37	305	0	ENST00000311895.7:c.2017G>T	p.Gly673Cys	p.G673C	ENST00000311895	NM_005236.2	673	Ggt/Tgt	10/11	1	2	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	TRUE	1	0.15	2		305	484	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81891874	81891874	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs982584766	NA	P-0048918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	35	399	0	ENST00000359376.3:c.344C>G	p.Ser115Cys	p.S115C	ENST00000359376	NM_002661.3	115	tCt/tGt	4/33	0.0750850369394516	0	FACETS	0.719	0.588	0.866			1	INDETERMINATE	1	TRUE	0	0.15	0		399	552	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39567820	39567820	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	17	330	0	ENST00000262039.4:c.576G>C	p.Trp192Cys	p.W192C	ENST00000262039	NM_002647.2	192	tgG/tgC	5/25	1	2	FACETS	0.753	0.562	0.981	0.753	0.562	0.981	CLONAL	1	TRUE	1	0.15	2		330	301	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2220122	2220122	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	56	552	0	ENST00000398665.3:c.2709del	p.Val904CysfsTer164	p.V904Cfs*164	ENST00000398665	NM_032482.2	903	Ccc/cc	23/28	0.159781245440028	0	FACETS	0.842	0.72	0.976			1	CLONAL	1	TRUE	0	0.15	0		552	754	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129845	55129845	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	34	429	0	ENST00000257290.5:c.379G>T	p.Ala127Ser	p.A127S	ENST00000257290	NM_006206.4	127	Gcc/Tcc	4/23	1	2	FACETS	0.734	0.598	0.887	0.734	0.598	0.887	SUBCLONAL	1	TRUE	1	0.15	2		429	618	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217156	66217156	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	38	487	0	ENST00000273854.3:c.2459G>T	p.Gly820Val	p.G820V	ENST00000273854	NM_004439.5	820	gGa/gTa	14/18	1	2	FACETS	0.717	0.591	0.858	0.717	0.591	0.858	SUBCLONAL	1	TRUE	1	0.15	2		487	707	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026530	6026530	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	57	673	0	ENST00000265849.7:c.1866G>T	p.Met622Ile	p.M622I	ENST00000265849	NM_000535.5	622	atG/atT	11/15	1	2	FACETS	0.955	0.817	1	0.955	0.817	1	CLONAL	1	TRUE	1	0.15	2		673	796	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444399	50444399	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	32	427	0	ENST00000331340.3:c.329T>A	p.Ile110Asn	p.I110N	ENST00000331340	NM_006060.4	110	aTt/aAt	4/8	0.159781245440028	1	FACETS	0.702	0.569	0.854	0.702	0.569	0.854	SUBCLONAL	1	TRUE	0	0.15	1		427	562	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55086992	55086992	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754259847	NA	P-0048918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	37	356	0	ENST00000275493.2:c.22G>A	p.Gly8Arg	p.G8R	ENST00000275493	NM_005228.3	8	Ggg/Agg	1/28	0.159781245440028	1	FACETS	0.983	0.811	1	0.983	0.811	1	CLONAL	1	TRUE	0	0.15	1		356	464	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639953	93639953	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	32	355	0	ENST00000375746.1:c.1282G>T	p.Asp428Tyr	p.D428Y	ENST00000375746	NM_001174167.1	428	Gac/Tac	10/14	0.159781245440028	1	FACETS	0.829	0.672	1	0.829	0.672	1	CLONAL	1	TRUE	0	0.15	1		355	476	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349673	70349673	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	44	561	0	ENST00000374080.3:c.3835G>T	p.Ala1279Ser	p.A1279S	ENST00000374080		1279	Gcc/Tcc	27/45	0.0750850369394516	0	FACETS	0.599	0.501	0.709			1	INDETERMINATE	1	TRUE	0	0.15	0		561	832	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608315	100608315	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	39	574	0	ENST00000308731.7:c.1775C>A	p.Ser592Tyr	p.S592Y	ENST00000308731	NM_000061.2	592	tCc/tAc	18/19	0.0750850369394516	0	FACETS	0.666	0.55	0.795			1	INDETERMINATE	1	TRUE	0	0.15	0		574	664	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035983	47035985	+	missense_variant,splice_region_variant	Missense_Mutation	TNP	AAG	AAG	CAT	novel	NA	P-0048918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	62	641	0	ENST00000377604.3:c.661_663delinsCAT	p.Lys221His	p.K221H	ENST00000377604	NM_001204468.1	221	AAG/CAT	7/24	0.0750850369394516	0	FACETS	0.767	0.661	0.883			1	INDETERMINATE	1	TRUE	0	0.15	0		641	916	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794118	242794118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758277335	NA	P-0048919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	233	581	0	ENST00000334409.5:c.610C>T	p.Arg204Cys	p.R204C	ENST00000334409	NM_005018.2	204	Cgc/Tgc	4/5	0.533894115115312	3	FACETS	1	0.945	1	0.505	0.473	0.539	CLONAL	1	TRUE	1	0.832773205828796	3		581	784	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587781702	NA	P-0048919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	479	468	0	ENST00000269305.4:c.920-1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.784801020866036	2	FACETS	0.955	0.931	0.979	0.955	0.931	0.979	CLONAL	2	TRUE	0	0.832773205828796	2		468	602	SUCCESS
APC	324	MSKCC	GRCh37	5	112178904	112178904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	170	388	0	ENST00000257430.4:c.7613G>A	p.Arg2538Lys	p.R2538K	ENST00000257430	NM_000038.5	2538	aGa/aAa	16/16	0.832773205828796	3	FACETS	0.953	0.88	1			1	CLONAL	1	TRUE	NA	0.832773205828796	3		388	607	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226561941	226561941	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	96	491	0	ENST00000366794.5:c.2056A>G	p.Met686Val	p.M686V	ENST00000366794	NM_001618.3	686	Atg/Gtg	14/23	0.832773205828796	4	FACETS	0.388	0.345	0.435			1	SUBCLONAL	1	TRUE	NA	0.832773205828796	4		491	1089	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945564	151945591	+	frameshift_variant	Frame_Shift_Del	DEL	TTTTCTGTCACTTCCATTTTATCTTCAA	TTTTCTGTCACTTCCATTTTATCTTCAA	-	novel	NA	P-0048919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	142	200	0	ENST00000262189.6:c.1928_1955del	p.Ile643ThrfsTer19	p.I643Tfs*19	ENST00000262189	NM_170606.2	643	aTTGAAGATAAAATGGAAGTGACAGAAAAc/ac	14/59	0.258363586130171	6	FACETS	1	0.979	1	0.785	0.724	0.848	INDETERMINATE	2	TRUE	3	0.832773205828796	6		200	386	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249840	110249840	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	435	640	0	ENST00000374672.4:c.835C>A	p.Gln279Lys	p.Q279K	ENST00000374672	NM_004235.4	279	Cag/Aag	3/5	0.281854961112482	4	FACETS	1	0.993	1	1	0.993	1	INDETERMINATE	2	TRUE	2	0.832773205828796	4		640	836	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0048920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	41	347	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.994	0.83	1	0.994	0.83	1	CLONAL	1	TRUE	1	0.22	2		347	375	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0048920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	52	302	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.22	2		302	393	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0048920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	24	345	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	0.54	0.423	0.676	0.54	0.423	0.676	SUBCLONAL	1	TRUE	1	0.22	2		345	404	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821594	72821620	+	inframe_deletion	In_Frame_Del	DEL	GCCGCCGCCGCCGCCGCCGCCGCCACC	GCCGCCGCCGCCGCCGCCGCCGCCACC	-	rs1318451799	NA	P-0048920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	19	69	1	ENST00000268489.5:c.10555_10581del	p.Gly3519_Gly3527del	p.G3519_G3527del	ENST00000268489	NM_006885.3	3519	GGTGGCGGCGGCGGCGGCGGCGGCGGC/-	10/10	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.22	2		70	121	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849921	151849921	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	GAG	novel	NA	P-0048920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	38	445	0	ENST00000262189.6:c.12395delinsCTC	p.Ile4132ThrfsTer27	p.I4132Tfs*27	ENST00000262189	NM_170606.2	4132	aTc/aCTCc	49/59	1	2	FACETS	0.564	0.466	0.675	0.564	0.466	0.675	SUBCLONAL	1	TRUE	1	0.22	2		445	612	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0048921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	582	351	0				ENST00000310581	NM_198253.2	-/1132			0.805673191282177	6	FACETS	0.903	0.878	0.927	1	0.996	1	CLONAL	5	TRUE	2	0.805673191282177	6		351	836	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0048921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	612	882	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.587787308451856	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.805673191282177	2		882	759	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882319	89882319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	245	587	0	ENST00000389301.3:c.155G>A	p.Arg52Gln	p.R52Q	ENST00000389301	NM_000135.2	52	cGa/cAa	2/43	0.715586002802717	3	FACETS	1	0.955	1	0.512	0.479	0.545	CLONAL	1	TRUE	1	0.805673191282177	3		587	834	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913409	NA	P-0048921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	166	373	0	ENST00000349496.5:c.134C>G	p.Ser45Cys	p.S45C	ENST00000349496	NM_001904.3	45	tCt/tGt	3/15	0.798976118129849	3	FACETS	1	0.947	1	0.515	0.476	0.556	CLONAL	1	TRUE	1	0.805673191282177	3		373	561	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244139	46244139	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	376	468	0	ENST00000334344.6:c.2233C>T	p.Gln745Ter	p.Q745*	ENST00000334344	NM_152641.2	745	Cag/Tag	15/21	0.688105176273269	4	FACETS	0.973	0.928	1	0.973	0.928	1	CLONAL	2	TRUE	2	0.805673191282177	4		468	866	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246490544	246490544	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	146	547	0	ENST00000388985.4:c.490C>T	p.Gln164Ter	p.Q164*	ENST00000388985		164	Cag/Tag	5/12	0.755096236097135	3	FACETS	0.535	0.487	0.584	0.267	0.243	0.292	SUBCLONAL	1	TRUE	1	0.805673191282177	3		547	951	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023069	27023069	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	21	99	0	ENST00000324856.7:c.175G>T	p.Glu59Ter	p.E59*	ENST00000324856	NM_006015.4	59	Gag/Tag	1/20	0.79767450704669	4	FACETS	0.517	0.401	0.651	0.259	0.2	0.326	SUBCLONAL	1	TRUE	2	0.805673191282177	4		99	182	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983105	201983106	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	366	606	0	ENST00000359651.3:c.959dup	p.Asn321GlufsTer150	p.N321Efs*150	ENST00000359651		318	-/A	7/8	0.755096236097135	3	FACETS	1	0.989	1	0.572	0.542	0.601	CLONAL	1	TRUE	1	0.805673191282177	3		606	1115	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477109	67477109	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	124	522	0	ENST00000327367.4:c.916G>A	p.Glu306Lys	p.E306K	ENST00000327367	NM_005902.3	306	Gag/Aag	7/9	0.805673191282177	3	FACETS	0.44	0.397	0.485	0.22	0.198	0.243	SUBCLONAL	1	TRUE	1	0.805673191282177	3		522	982	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867123	45867123	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	206	582	1	ENST00000391945.4:c.996C>A	p.Phe332Leu	p.F332L	ENST00000391945	NM_000400.3	332	ttC/ttA	11/23	0.805673191282177	3	FACETS	0.808	0.75	0.867	0.404	0.375	0.434	CLONAL	1	TRUE	1	0.805673191282177	3		583	888	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39239479	39239479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	56	415	0	ENST00000402219.2:c.2178G>A	p.Met726Ile	p.M726I	ENST00000402219	NM_005633.3	726	atG/atA	14/23	0.622764914184422	4	FACETS	0.298	0.254	0.346	0.075	0.063	0.087	SUBCLONAL	1	TRUE	0	0.805673191282177	4		415	842	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021805	71021805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	208	236	0	ENST00000318789.4:c.1553G>A	p.Ser518Asn	p.S518N	ENST00000318789	NM_032682.5	518	aGt/aAt	18/21	0.798976118129849	3	FACETS	0.951	0.898	1	0.951	0.898	1	CLONAL	2	TRUE	1	0.805673191282177	3		236	381	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044956	47044956	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	428	360	0	ENST00000377604.3:c.2282G>T	p.Cys761Phe	p.C761F	ENST00000377604	NM_001204468.1	761	tGt/tTt	20/24	0.69511899299212	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.805673191282177	2		360	492	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68758609	68758609	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	115	315	0	ENST00000487270.1:c.765G>C	p.Leu255Phe	p.L255F	ENST00000487270	NM_133509.3	255	ttG/ttC	8/11	0.181369705348788	3	FACETS	1	0.916	1	0.674	0.611	0.741	CLONAL	2	TRUE	0	0.271916452641162	3		315	475	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981232	201981232	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs58166377	NA	P-0048922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	180	602	0	ENST00000359651.3:c.311A>G	p.Asn104Ser	p.N104S	ENST00000359651		104	aAt/aGt	2/8	0.177849825904617	5	FACETS	1	0.953	1	0.697	0.643	0.754	CLONAL	2	TRUE	2	0.271916452641162	5		602	891	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206665076	206665076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196740276	NA	P-0048922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	122	297	1	ENST00000367120.3:c.1829G>A	p.Arg610Lys	p.R610K	ENST00000367120	NM_014002.3	610	aGg/aAg	18/22	0.177849825904617	5	FACETS	1	0.953	1	0.72	0.653	0.79	CLONAL	2	TRUE	2	0.271916452641162	5		298	585	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752697	42752697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771156538	NA	P-0048922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	86	574	1	ENST00000222329.4:c.1567G>A	p.Gly523Arg	p.G523R	ENST00000222329	NM_006494.2	523	Ggg/Agg	4/4	0.271916452641162	3	FACETS	0.846	0.748	0.952	0.423	0.374	0.476	CLONAL	1	TRUE	1	0.271916452641162	3		575	849	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030056	36030056	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	51	511	0	ENST00000358208.4:c.1091C>G	p.Pro364Arg	p.P364R	ENST00000358208		364	cCt/cGt	9/12	0.271916452641162	4	FACETS	0.579	0.491	0.677	0.29	0.245	0.339	SUBCLONAL	1	TRUE	2	0.271916452641162	4		511	824	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916660	178916661	+	missense_variant	Missense_Mutation	DNP	TG	TG	AT	novel	NA	P-0048922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	256	377	0	ENST00000263967.3:c.47_48delinsAT	p.Met16Asn	p.M16N	ENST00000263967	NM_006218.2	16	aTG/aAT	2/21	0.271916452641162	9	FACETS	0.902	0.847	0.958			1	CLONAL	5	TRUE	NA	0.271916452641162	9		377	815	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932761	39932761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	58	651	0	ENST00000378444.4:c.1838G>T	p.Ser613Ile	p.S613I	ENST00000378444	NM_001123385.1	613	aGc/aTc	4/15	0.271916452641162	3	FACETS	0.578	0.495	0.668	0.289	0.247	0.334	SUBCLONAL	1	TRUE	1	0.271916452641162	3		651	839	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361188	70361188	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	90	432	0	ENST00000374080.3:c.6376C>A	p.Pro2126Thr	p.P2126T	ENST00000374080		2126	Cct/Act	43/45	0.271916452641162	4	FACETS	1	0.959	1			1	CLONAL	1	TRUE	NA	0.271916452641162	4		432	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578192	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CCTCAGGCGGCTCATAG	CCTCAGGCGGCTCATAG	-	novel	NA	P-0048922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	145	497	0	ENST00000269305.4:c.657_672+1del		p.X219_splice	ENST00000269305	NM_001126112.2	219		6/11	NA	2	FACETS	0.775	0.709	0.844			1	INDETERMINATE	2	TRUE	NA	0.271916452641162	2		497	688	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019818	123019824	+	frameshift_variant	Frame_Shift_Del	DEL	CACGCAG	CACGCAG	AC	novel	NA	P-0048922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	119	550	2	ENST00000355640.3:c.306_312delinsAC	p.Thr103LeufsTer14	p.T103Lfs*14	ENST00000355640		102	gcCACGCAG/gcAC	2/7	0.271916452641162	3	FACETS	1	0.984	1	0.736	0.666	0.811	CLONAL	1	TRUE	1	0.271916452641162	3		552	675	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438058	49438058	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0048923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	126	594	0	ENST00000301067.7:c.5113A>T	p.Lys1705Ter	p.K1705*	ENST00000301067	NM_003482.3	1705	Aaa/Taa	21/54	0.512437553268614	3	FACETS	0.935	0.848	1	0.467	0.424	0.513	CLONAL	1	TRUE	1	0.512437553268614	3		594	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577554	7577562	+	inframe_deletion	In_Frame_Del	DEL	TGCAGGAAC	TGCAGGAAC	-	novel	NA	P-0048923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	234	572	0	ENST00000269305.4:c.719_727del	p.Ser240_Cys242del	p.S240_C242del	ENST00000269305	NM_001126112.2	240	aGTTCCTGCAtg/atg	7/11	0.512437553268614	2	FACETS	0.943	0.891	0.996	0.943	0.891	0.996	CLONAL	2	TRUE	0	0.512437553268614	2		572	484	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064406	30064406	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315500	NA	P-0048923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	219	412	0	ENST00000338641.4:c.970C>T	p.Gln324Ter	p.Q324*	ENST00000338641	NM_000268.3	324	Cag/Tag	10/16	0.508918351398999	2	FACETS	0.939	0.885	0.994	0.939	0.885	0.994	CLONAL	2	TRUE	0	0.512437553268614	2		412	455	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0048924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	417	582	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.201832084715042	8	FACETS	1	0.972	1			1	CLONAL	7	TRUE	NA	0.201832084715042	8		582	929	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045016	47045016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556782040	NA	P-0048924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	102	669	0	ENST00000377604.3:c.2342C>T	p.Ser781Leu	p.S781L	ENST00000377604	NM_001204468.1	781	tCa/tTa	20/24	0.201832084715042	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.201832084715042	1		669	715	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024024	27024024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	33	125	0	ENST00000324856.7:c.1133del	p.Pro378LeufsTer13	p.P378Lfs*13	ENST00000324856	NM_006015.4	377	aCc/ac	1/20	0.201832084715042	2	FACETS	0.913	0.752	1	0.913	0.752	1	CLONAL	2	TRUE	0	0.201832084715042	2		125	179	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775716	9775716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768486795	NA	P-0048924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	131	646	1	ENST00000377346.4:c.259C>T	p.Arg87Trp	p.R87W	ENST00000377346	NM_005026.3	87	Cgg/Tgg	4/24	0.201832084715042	2	FACETS	0.771	0.699	0.846	0.771	0.699	0.846	SUBCLONAL	2	TRUE	0	0.201832084715042	2		647	842	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99802271	99802271	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	21	170	1	ENST00000280892.6:c.622G>T	p.Gly208Ter	p.G208*	ENST00000280892	NM_001130678.1	208	Gga/Tga	7/7	1	2	FACETS	0.955	0.738	1	0.955	0.738	1	CLONAL	1	TRUE	1	0.201832084715042	2		171	218	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876272	35876272	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	37	528	0	ENST00000303115.3:c.1064T>G	p.Val355Gly	p.V355G	ENST00000303115	NM_002185.3	355	gTc/gGc	8/8	1	2	FACETS	0.54	0.444	0.648	0.54	0.444	0.648	SUBCLONAL	1	TRUE	1	0.201832084715042	2		528	679	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38186901	38186901	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	36	504	0	ENST00000317025.8:c.1576A>G	p.Thr526Ala	p.T526A	ENST00000317025	NM_023034.1	526	Aca/Gca	6/24	0.201832084715042	1	FACETS	0.631	0.518	0.758	0.631	0.518	0.758	SUBCLONAL	1	TRUE	0	0.201832084715042	1		504	508	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908864	101908864	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	77	548	0	ENST00000374994.4:c.1228G>T	p.Glu410Ter	p.E410*	ENST00000374994	NM_004612.2	410	Gaa/Taa	7/9	0.201832084715042	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.201832084715042	1		548	589	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0048925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	366	351	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.240459846041994	3	FACETS	0.972	0.926	1	1	0.996	1	CLONAL	4	FALSE	1	0.240459846041994	3		351	877	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0048925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	161	351	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.165865328217134	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	FALSE	1	0.240459846041994	3		351	632	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723126	49723128	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs751306787	NA	P-0048925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	53	452	0	ENST00000449682.2:c.1288_1290del	p.Glu430del	p.E430del	ENST00000449682	NM_020998.3	430	GAG/-	11/18	1	2	FACETS	0.523	0.445	0.609	0.523	0.445	0.609	SUBCLONAL	1	FALSE	1	0.240459846041994	2		452	843	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729775	41729775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	220	346	0	ENST00000242208.4:c.754G>A	p.Ala252Thr	p.A252T	ENST00000242208	NM_002192.2	252	Gcc/Acc	3/3	0.165865328217134	3	FACETS	0.948	0.885	1	1	0.991	1	CLONAL	3	FALSE	1	0.240459846041994	3		346	721	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332577	153332577	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	152	335	0	ENST00000281708.4:c.379C>T	p.Gln127Ter	p.Q127*	ENST00000281708	NM_033632.3	127	Cag/Tag	2/12	1	2	FACETS	1	0.948	1	1	0.992	1	CLONAL	2	FALSE	1	0.240459846041994	2		335	606	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604797	48604797	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	219	335	0	ENST00000342988.3:c.1619T>C	p.Leu540Pro	p.L540P	ENST00000342988	NM_005359.5	540	cTt/cCt	12/12	0.215991926298484	0	FACETS	1	0.948	1			1	CLONAL	3	FALSE	0	0.240459846041994	0		335	458	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893604	28893604	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	212	423	1	ENST00000282397.4:c.3242A>T	p.Asp1081Val	p.D1081V	ENST00000282397	NM_002019.4	1081	gAc/gTc	24/30	0.240459846041994	4	FACETS	1	0.963	1	0.704	0.653	0.756	CLONAL	2	FALSE	1	0.240459846041994	4		424	1036	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701870	43701870	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	164	317	0	ENST00000382044.4:c.5375T>G	p.Ile1792Ser	p.I1792S	ENST00000382044	NM_001141980.1	1792	aTc/aGc	25/28	0.240459846041994	5	FACETS	1	0.981	1			1	CLONAL	2	FALSE	NA	0.240459846041994	5		317	766	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78931510	78931510	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	547	502	0	ENST00000306801.3:c.3457G>A	p.Asp1153Asn	p.D1153N	ENST00000306801	NM_020761.2	1153	Gac/Aac	29/34	0.240459846041994	2	FACETS	0.989	0.957	1	1	0.998	1	CLONAL	5	FALSE	0	0.240459846041994	2		502	920	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455546	189455546	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	52	394	0	ENST00000264731.3:c.80C>A	p.Ala27Asp	p.A27D	ENST00000264731	NM_003722.4	27	gCt/gAt	2/14	1	2	FACETS	0.69	0.587	0.803	0.69	0.587	0.803	SUBCLONAL	1	FALSE	1	0.240459846041994	2		394	627	SUCCESS
APC	324	MSKCC	GRCh37	5	112175751	112175752	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTTATTACAT	novel	NA	P-0048925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	160	344	0	ENST00000257430.4:c.4464_4473dup	p.Ala1492IlefsTer25	p.A1492Ifs*25	ENST00000257430	NM_000038.5	1487	act/acTTTATTACATt	16/16	0.165865328217134	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	FALSE	1	0.240459846041994	3		344	640	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663629	117663629	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	163	493	0	ENST00000368508.3:c.4603del	p.Tyr1535IlefsTer68	p.Y1535Ifs*68	ENST00000368508	NM_002944.2	1535	Tat/at	28/43	0.215991926298484	0	FACETS	0.973	0.899	1			1	CLONAL	2	FALSE	0	0.240459846041994	0		493	529	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0048926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	111	351	0				ENST00000310581	NM_198253.2	-/1132			0.290041093567023	1	FACETS	0.741	0.671	0.815	0.741	0.671	0.815	INDETERMINATE	1	FALSE	0	0.49929799920692	1		351	450	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729104	66729109	+	inframe_deletion	In_Frame_Del	DEL	ACCCGC	ACCCGC	-	novel	NA	P-0048926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	267	615	0	ENST00000307102.5:c.313_318del	p.Pro105_Ala106del	p.P105_A106del	ENST00000307102	NM_002755.3	104	aaACCCGCa/aaa	3/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.49929799920692	2		615	957	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314896	1314896	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs756815530	NA	P-0048926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	133	421	0	ENST00000400841.2:c.765G>A	p.Trp255Ter	p.W255*	ENST00000400841		255	tgG/tgA	6/6	0.49929799920692	1	FACETS	0.921	0.844	1	0.921	0.844	1	CLONAL	1	FALSE	0	0.49929799920692	1		421	434	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8497265	8497265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1270795879	NA	P-0048926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	102	359	0	ENST00000356435.5:c.2326G>A	p.Glu776Lys	p.E776K	ENST00000356435		776	Gaa/Aaa	15/35	0.49929799920692	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	0	0.49929799920692	1		359	297	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972418	81972418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758678624	NA	P-0048926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	74	553	0	ENST00000359376.3:c.3211C>T	p.Arg1071Cys	p.R1071C	ENST00000359376	NM_002661.3	1071	Cgc/Tgc	29/33	1	2	FACETS	0.335	0.292	0.381	0.335	0.292	0.381	SUBCLONAL	1	FALSE	1	0.49929799920692	2		553	886	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575392	64575392	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1565647767	NA	P-0048926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	255	698	0	ENST00000312049.6:c.625C>T	p.Gln209Ter	p.Q209*	ENST00000312049	NM_130799.2	209	Cag/Tag	3/10	0.49929799920692	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	0	0.49929799920692	1		698	719	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0048934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	111	327	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.306546935672378	2		327	721	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0048934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	105	403	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.838	0.751	0.932	0.838	0.751	0.932	CLONAL	1	TRUE	1	0.306546935672378	2		404	817	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0048934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	120	359	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.306546935672378	2		359	685	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196879	108196880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs773570504	NA	P-0048934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	97	368	0	ENST00000278616.4:c.6908dup	p.Glu2304GlyfsTer69	p.E2304Gfs*69	ENST00000278616	NM_000051.3	2301	gca/gcAa	47/63	0.239878640074164	1	FACETS	0.95	0.849	1	0.95	0.849	1	CLONAL	1	TRUE	0	0.306546935672378	1		368	564	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591140	67591145	+	inframe_deletion	In_Frame_Del	DEL	ACCAAT	ACCAAT	-	rs751582616	NA	P-0048934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	69	280	0	ENST00000274335.5:c.1735_1740del	p.Gln579_Tyr580del	p.Q579_Y580del	ENST00000274335		578	gACCAATac/gac	12/15	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.306546935672378	2		280	430	SUCCESS
APC	324	MSKCC	GRCh37	5	112174349	112174349	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	57	254	0	ENST00000257430.4:c.3058G>T	p.Glu1020Ter	p.E1020*	ENST00000257430	NM_000038.5	1020	Gaa/Taa	16/16	1	2	FACETS	0.911	0.785	1	0.911	0.785	1	CLONAL	1	TRUE	1	0.306546935672378	2		254	408	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589609	67589610	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	79	274	0	ENST00000274335.5:c.1378dup	p.Ser460LysfsTer5	p.S460Kfs*5	ENST00000274335		458	gaa/gAaa	10/15	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.306546935672378	2		274	463	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696449	47696449	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	49	387	0	ENST00000347630.2:c.374T>G	p.Phe125Cys	p.F125C	ENST00000347630	NM_001007230.1	125	tTt/tGt	6/11	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.420116217205657	2		387	203	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026101	71026116	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCGCGTTGCGTCGG	GGCCGCGTTGCGTCGG	-	novel	NA	P-0048935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	13	345	0	ENST00000318789.4:c.1506_1521del	p.Phe502LeufsTer20	p.F502Lfs*20	ENST00000318789	NM_032682.5	502	ttCCGACGCAACGCGGCC/tt	17/21	0.250905424277537	1	FACETS	0.211	0.15	0.285	0.211	0.15	0.285	INDETERMINATE	1	TRUE	0	0.420116217205657	1		345	232	SUCCESS
APC	324	MSKCC	GRCh37	5	112177235	112177238	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	novel	NA	P-0048935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	27	316	0	ENST00000257430.4:c.5947_5950del	p.Glu1983MetfsTer60	p.E1983Mfs*60	ENST00000257430	NM_000038.5	1982	AAAGaa/aa	16/16	0.420116217205657	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	0	0.420116217205657	1		316	86	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619122	1619122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374172636	NA	P-0048936-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	46	490	0	ENST00000344749.5:c.1438G>A	p.Asp480Asn	p.D480N	ENST00000344749	NM_001136139.2	480	Gac/Aac	16/19	0.448395639695987	1	FACETS	0.176	0.148	0.207	0.176	0.148	0.207	SUBCLONAL	1	TRUE	0	0.714533290721821	1		490	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	981	701	0	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	0.860506600976689	3	FACETS	1	0.998	1	1	0.998	1	CLONAL	3	TRUE	0	0.860506600976689	3		701	1046	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425694	49425694	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	474	821	0	ENST00000301067.7:c.12794del	p.Gly4265AlafsTer13	p.G4265Afs*13	ENST00000301067	NM_003482.3	4265	gGc/gc	39/54	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.860506600976689	2		821	1037	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881543	48881543	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0048937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	177	249	0	ENST00000267163.4:c.264+1G>T		p.X88_splice	ENST00000267163	NM_000321.2	88			0.860506600976689	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.860506600976689	2		249	205	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472666	88472666	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0048937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	209	429	0	ENST00000360948.2:c.1890-1G>A		p.X630_splice	ENST00000360948	NM_001012338.2	630			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.860506600976689	2		429	445	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628322	86628322	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0048937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	192	229	0	ENST00000274376.6:c.693-2A>G		p.X231_splice	ENST00000274376	NM_002890.2	231			0.860506600976689	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.860506600976689	2		229	208	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89791121	89791121	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	172	215	0	ENST00000336032.3:c.508G>T	p.Ala170Ser	p.A170S	ENST00000336032	NM_006813.2	170	Gcg/Tcg	1/2	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.860506600976689	2		215	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578463	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371524413	NA	P-0048938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	438	756	0	ENST00000269305.4:c.467G>C	p.Arg156Pro	p.R156P	ENST00000269305	NM_001126112.2	156	cGc/cCc	5/11	0.770164377189925	1	FACETS	0.989	0.954	1	0.989	0.954	1	CLONAL	1	TRUE	0	0.770164377189925	1		756	707	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047254	77047254	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	253	456	0	ENST00000356341.3:c.1290G>T	p.Trp430Cys	p.W430C	ENST00000356341	NM_002576.4	430	tgG/tgT	13/15	1	2	FACETS	0.842	0.791	0.895	0.842	0.791	0.895	CLONAL	1	TRUE	1	0.770164377189925	2		456	780	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916798	48916799	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0048938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	277	353	0	ENST00000267163.4:c.328_329del	p.Leu110ArgfsTer2	p.L110Rfs*2	ENST00000267163	NM_000321.2	110	CTa/a	3/27	0.770164377189925	1	FACETS	0.99	0.946	1	0.99	0.946	1	CLONAL	1	TRUE	0	0.770164377189925	1		353	447	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	182	576	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.519810834426456	2		576	684	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256831	16256831	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	43	466	0	ENST00000375759.3:c.4096C>T	p.Arg1366Ter	p.R1366*	ENST00000375759	NM_015001.2	1366	Cga/Tga	11/15	1	2	FACETS	0.212	0.177	0.252	0.212	0.177	0.252	SUBCLONAL	1	TRUE	1	0.519810834426456	2		466	780	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0048941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	159	281	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	0.943	0.87	1	0.943	0.87	1	CLONAL	1	TRUE	1	0.660254010698762	2		281	511	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692995	89692995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554898225	NA	P-0048941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	332	395	0	ENST00000371953.3:c.479C>T	p.Thr160Ile	p.T160I	ENST00000371953	NM_000314.4	160	aCc/aTc	5/9	0.660254010698762	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.660254010698762	2		395	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0048941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	436	697	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.604599185126849	2	FACETS	0.878	0.845	0.911	0.878	0.845	0.911	CLONAL	2	TRUE	0	0.660254010698762	2		697	752	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88651951	88651951	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	84	366	0	ENST00000372037.3:c.298T>C	p.Cys100Arg	p.C100R	ENST00000372037	NM_004329.2	100	Tgt/Cgt	5/13	0.660254010698762	2	FACETS	0.478	0.423	0.537	0.239	0.211	0.269	SUBCLONAL	1	TRUE	0	0.660254010698762	2		366	532	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649108	37649108	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	100	357	0	ENST00000447079.4:c.2213A>G	p.Tyr738Cys	p.Y738C	ENST00000447079	NM_015083.1	738	tAt/tGt	4/14	0.399786586052314	1	FACETS	0.363	0.325	0.403	0.363	0.325	0.403	SUBCLONAL	1	TRUE	0	0.660254010698762	1		357	559	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631549	119631549	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0048941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	133	279	0	ENST00000316626.5:c.715+2T>C		p.X239_splice	ENST00000316626		239			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.660254010698762	2		279	388	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0048943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	144	470	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.355889123533167	3	FACETS	0.884	0.81	0.959	0.884	0.81	0.959	CLONAL	2	TRUE	1	0.359393345959737	3		470	535	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186599	108186599	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876658415	NA	P-0048943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	94	286	0	ENST00000278616.4:c.6056A>G	p.Tyr2019Cys	p.Y2019C	ENST00000278616	NM_000051.3	2019	tAt/tGt	41/63	1	2	FACETS	0.981	0.876	1	0.981	0.876	1	CLONAL	1	TRUE	1	0.359393345959737	2		286	533	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117792	108117792	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	75	328	0	ENST00000278616.4:c.1004del	p.Gly335AspfsTer11	p.G335Dfs*11	ENST00000278616	NM_000051.3	335	Gga/ga	8/63	1	2	FACETS	0.749	0.657	0.848	0.749	0.657	0.848	SUBCLONAL	1	TRUE	1	0.359393345959737	2		328	557	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007740	45007741	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0048943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	103	353	0	ENST00000558401.1:c.194_195dup	p.Ile66GlufsTer38	p.I66Efs*38	ENST00000558401	NM_004048.2	63	gga/gGAga	2/4	0.359393345959737	1	FACETS	0.812	0.729	0.9	0.812	0.729	0.9	CLONAL	1	TRUE	0	0.359393345959737	1		353	579	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183724	10183740	+	frameshift_variant	Frame_Shift_Del	DEL	TCGGTGAACTCGCGCGA	TCGGTGAACTCGCGCGA	-	novel	NA	P-0048943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	174	715	0	ENST00000256474.2:c.193_209del	p.Ser65AlafsTer61	p.S65Afs*61	ENST00000256474	NM_000551.3	65	TCGGTGAACTCGCGCGAg/g	1/3	0.359393345959737	1	FACETS	0.802	0.737	0.868	0.802	0.737	0.868	CLONAL	1	TRUE	0	0.359393345959737	1		715	991	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165522	47165523	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0048943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	126	481	0	ENST00000409792.3:c.603_604del	p.Ser203IlefsTer33	p.S203Ifs*33	ENST00000409792	NM_014159.6	201	acACtc/actc	3/21	0.359393345959737	1	FACETS	0.793	0.719	0.871	0.793	0.719	0.871	SUBCLONAL	1	TRUE	0	0.359393345959737	1		481	725	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623150	52623150	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	122	512	0	ENST00000394830.3:c.2901del	p.Glu967AspfsTer41	p.E967Dfs*41	ENST00000394830	NM_018313.4	967	gaA/ga	19/30	0.359393345959737	1	FACETS	0.769	0.696	0.846	0.769	0.696	0.846	SUBCLONAL	1	TRUE	0	0.359393345959737	1		512	724	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0048945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	171	470	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.829409417806404	3	FACETS	1	0.94	1	0.509	0.471	0.548	CLONAL	1	TRUE	1	0.829409417806404	3		470	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519986	NA	P-0048945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	275	512	0	ENST00000269305.4:c.809T>C	p.Phe270Ser	p.F270S	ENST00000269305	NM_001126112.2	270	tTt/tCt	8/11	1	2	FACETS	0.95	0.897	1	0.95	0.897	1	CLONAL	1	TRUE	1	0.829409417806404	2		512	698	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953760	48953760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913302	NA	P-0048945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	109	166	0	ENST00000267163.4:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000267163	NM_000321.2	455	Cga/Tga	14/27	0.829409417806404	1	FACETS	0.98	0.917	1	0.98	0.917	1	CLONAL	1	TRUE	0	0.829409417806404	1		166	157	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118607	17118607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	236	447	0	ENST00000285071.4:c.1324C>T	p.His442Tyr	p.H442Y	ENST00000285071	NM_144997.5	442	Cac/Tac	12/14	1	2	FACETS	0.952	0.895	1	0.952	0.895	1	CLONAL	1	TRUE	1	0.829409417806404	2		447	598	SUCCESS
ALK	238	MSKCC	GRCh37	2	29473997	29473997	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	326	590	2	ENST00000389048.3:c.2178G>A	p.Trp726Ter	p.W726*	ENST00000389048	NM_004304.4	726	tgG/tgA	12/29	1	2	FACETS	0.954	0.905	1	0.954	0.905	1	CLONAL	1	TRUE	1	0.829409417806404	2		592	824	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164865	36164865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	370	721	1	ENST00000300305.3:c.1010C>T	p.Pro337Leu	p.P337L	ENST00000300305		337	cCc/cTc	8/8	1	2	FACETS	0.964	0.918	1	0.964	0.918	1	CLONAL	1	TRUE	1	0.829409417806404	2		722	926	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464553	25464553	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1371093470	NA	P-0048945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	365	563	0	ENST00000264709.3:c.1960G>A	p.Gly654Ser	p.G654S	ENST00000264709	NM_175629.2	654	Ggc/Agc	17/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.829409417806404	2		563	837	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752662	128752662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	145	211	0	ENST00000377970.2:c.823G>A	p.Glu275Lys	p.E275K	ENST00000377970	NM_002467.4	275	Gaa/Aaa	3/3	0.818832881969738	5	FACETS	1	0.966	1	0.278	0.254	0.303	CLONAL	1	TRUE	1	0.829409417806404	5		211	706	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612045	43612045	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	256	700	0	ENST00000355710.3:c.2150G>A	p.Trp717Ter	p.W717*	ENST00000355710	NM_020975.4	717	tGg/tAg	12/20	1	2	FACETS	0.883	0.831	0.936	0.883	0.831	0.936	CLONAL	1	TRUE	1	0.829409417806404	2		700	699	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92247433	92247433	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	148	269	0	ENST00000265734.4:c.787G>C	p.Glu263Gln	p.E263Q	ENST00000265734	NM_001259.6	263	Gag/Cag	7/8	1	2	FACETS	0.989	0.915	1	0.989	0.915	1	CLONAL	1	TRUE	1	0.829409417806404	2		269	361	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726255	46726255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	249	511	0	ENST00000371975.4:c.449G>A	p.Ser150Asn	p.S150N	ENST00000371975	NM_003579.3	150	aGt/aAt	6/18	1	2	FACETS	0.972	0.915	1	0.972	0.915	1	CLONAL	1	TRUE	1	0.829409417806404	2		511	618	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1040385	1040385	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0048945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	222	420	0	ENST00000358495.3:c.186+1G>A		p.X62_splice	ENST00000358495	NM_134424.2	62			NA	2	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.829409417806404	2		420	513	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287468	46287468	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0048945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	164	303	0	ENST00000334344.6:c.5327T>A	p.Leu1776Ter	p.L1776*	ENST00000334344	NM_152641.2	1776	tTa/tAa	20/21	1	2	FACETS	0.93	0.864	0.999	0.93	0.864	0.999	CLONAL	1	TRUE	1	0.829409417806404	2		303	425	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416845	121416845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	367	718	0	ENST00000257555.6:c.274C>T	p.Leu92Phe	p.L92F	ENST00000257555		92	Ctc/Ttc	1/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.829409417806404	2		718	778	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437950	110437950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	54	67	1	ENST00000375856.3:c.451G>A	p.Gly151Arg	p.G151R	ENST00000375856	NM_003749.2	151	Gga/Aga	1/2	0.829409417806404	3	FACETS	1	0.954	1	0.61	0.533	0.69	CLONAL	1	TRUE	1	0.829409417806404	3		68	151	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41011061	41011061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	292	511	0	ENST00000267868.3:c.494C>T	p.Thr165Ile	p.T165I	ENST00000267868	NM_002875.4	165	aCc/aTc	6/10	1	2	FACETS	0.982	0.93	1	0.982	0.93	1	CLONAL	1	TRUE	1	0.829409417806404	2		511	717	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035178	42035178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	305	530	0	ENST00000219905.7:c.5020G>A	p.Ala1674Thr	p.A1674T	ENST00000219905	NM_001164273.1	1674	Gct/Act	15/24	1	2	FACETS	0.96	0.91	1	0.96	0.91	1	CLONAL	1	TRUE	1	0.829409417806404	2		530	766	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808857	3808857	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	407	355	0	ENST00000262367.5:c.3367C>T	p.Pro1123Ser	p.P1123S	ENST00000262367	NM_004380.2	1123	Cca/Tca	17/31	0.829409417806404	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.829409417806404	2		355	479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579312	7579322	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CGTGCAAGTCA	CGTGCAAGTCA	-	novel	NA	P-0048945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	280	536	0	ENST00000269305.4:c.365_375del	p.Thr123LeufsTer22	p.T123Lfs*22	ENST00000269305	NM_001126112.2	122	gTGACTTGCACG/g	4/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.829409417806404	2		536	658	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912398	50912398	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	309	695	0	ENST00000440232.2:c.1912A>T	p.Ile638Phe	p.I638F	ENST00000440232	NM_002691.3	638	Atc/Ttc	16/27	0.819084606365545	3	FACETS	0.965	0.911	1	0.483	0.455	0.511	CLONAL	1	TRUE	1	0.829409417806404	3		695	1092	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326314	62326315	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0048945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	306	751	0	ENST00000360203.5:c.3330_3331delinsTT	p.Pro1111Ser	p.P1111S	ENST00000360203	NM_001283009.1	1110	ttCCcc/ttTTcc	32/35	1	2	FACETS	0.936	0.887	0.986	0.936	0.887	0.986	CLONAL	1	TRUE	1	0.829409417806404	2		751	788	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279572	1279572	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	347	733	0	ENST00000310581.5:c.1964C>T	p.Thr655Ile	p.T655I	ENST00000310581	NM_198253.2	655	aCc/aTc	5/16	1	2	FACETS	0.989	0.941	1	0.989	0.941	1	CLONAL	1	TRUE	1	0.829409417806404	2		733	846	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294426	1294427	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0048945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	275	534	0	ENST00000310581.5:c.574_575delinsAA	p.Gly192Lys	p.G192K	ENST00000310581	NM_198253.2	192	GGa/AAa	2/16	1	2	FACETS	0.916	0.865	0.968	0.916	0.865	0.968	CLONAL	1	TRUE	1	0.829409417806404	2		534	724	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671212	30671212	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	278	609	0	ENST00000376406.3:c.5665G>C	p.Glu1889Gln	p.E1889Q	ENST00000376406	NM_014641.2	1889	Gaa/Caa	11/15	1	2	FACETS	0.917	0.866	0.969	0.917	0.866	0.969	CLONAL	1	TRUE	1	0.829409417806404	2		609	731	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633439	8633440	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0048945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	137	304	0	ENST00000356435.5:c.229_230delinsAA	p.Gly77Lys	p.G77K	ENST00000356435		77	GGg/AAg	3/35	0.819084606365545	3	FACETS	0.848	0.775	0.924	0.424	0.387	0.462	CLONAL	1	TRUE	1	0.829409417806404	3		304	551	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27109620	27109620	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	487	438	0	ENST00000380036.4:c.32G>T	p.Gly11Val	p.G11V	ENST00000380036	NM_000459.3	11	gGa/gTa	1/23	0.819084606365545	3	FACETS	0.949	0.915	0.983	0.949	0.915	0.983	CLONAL	2	TRUE	1	0.829409417806404	3		438	875	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94201011	94201011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs939694506	NA	P-0048948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	22	389	0	ENST00000323929.3:c.1066C>T	p.His356Tyr	p.H356Y	ENST00000323929	NM_005591.3	356	Cac/Tac	10/20	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.235482129981392	2		389	162	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687531	37687531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	59	365	0	ENST00000447079.4:c.4435C>T	p.Pro1479Ser	p.P1479S	ENST00000447079	NM_015083.1	1479	Cca/Tca	14/14	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.235482129981392	2		365	481	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31504699	31504699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1032572786	NA	P-0048948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	70	530	0	ENST00000344624.3:c.1631G>A	p.Arg544His	p.R544H	ENST00000344624		544	cGc/cAc	8/33	0.232060180807059	3	FACETS	0.878	0.764	1	0.439	0.382	0.501	CLONAL	1	TRUE	1	0.235482129981392	3		530	757	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0048949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	200	461	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.378120553178453	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.378120553178453	1		462	816	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662023	227662023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776903727	NA	P-0048949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	149	568	0	ENST00000305123.5:c.1432G>A	p.Ala478Thr	p.A478T	ENST00000305123	NM_005544.2	478	Gcc/Acc	1/2	1	2	FACETS	0.855	0.781	0.933	0.855	0.781	0.933	CLONAL	1	TRUE	1	0.378120553178453	2		568	922	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137060	64137060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370422690	NA	P-0048949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	161	598	2	ENST00000334205.4:c.1571C>T	p.Ala524Val	p.A524V	ENST00000334205	NM_003942.2	524	gCg/gTg	13/17	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.378120553178453	2		600	831	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488683	212488683	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1422888414	NA	P-0048949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	126	400	0	ENST00000342788.4:c.2166A>C	p.Lys722Asn	p.K722N	ENST00000342788	NM_005235.2	722	aaA/aaC	18/28	1	2	FACETS	0.921	0.834	1	0.921	0.834	1	CLONAL	1	TRUE	1	0.378120553178453	2		400	724	SUCCESS
APC	324	MSKCC	GRCh37	5	112174372	112174372	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0048949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	157	281	0	ENST00000257430.4:c.3081T>G	p.Tyr1027Ter	p.Y1027*	ENST00000257430	NM_000038.5	1027	taT/taG	16/16	0.378120553178453	2	FACETS	0.986	0.913	1	0.986	0.913	1	CLONAL	2	TRUE	0	0.378120553178453	2		281	421	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842603	68842603	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	188	515	0	ENST00000261769.5:c.539C>A	p.Ser180Tyr	p.S180Y	ENST00000261769	NM_004360.3	180	tCc/tAc	5/16	0.515000373482709	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	0	0.515000373482709	1		515	532	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228046	36228046	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	263	727	1	ENST00000222270.7:c.7432C>T	p.Gln2478Ter	p.Q2478*	ENST00000222270	NM_014727.1	2478	Cag/Tag	33/37	0.273163433987615	1	FACETS	0.818	0.768	0.869	0.818	0.768	0.869	INDETERMINATE	1	FALSE	0	0.515000373482709	1		728	927	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0048952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	216	333	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	0.261692919549267	3	FACETS	0.999	0.935	1	0.999	0.935	1	CLONAL	3	TRUE	0	0.280584693811946	3		333	586	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0048952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	17	311	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.669	0.502	0.867	0.669	0.502	0.867	SUBCLONAL	1	TRUE	1	0.280584693811946	2		311	181	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0048952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	18	220	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.275514266542054	3	FACETS	1	0.766	1	0.504	0.383	0.646	CLONAL	1	TRUE	1	0.280584693811946	3		220	145	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578491	7578491	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1567553924	NA	P-0048952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	431	759	1	ENST00000269305.4:c.439del	p.Val147LeufsTer23	p.V147Lfs*23	ENST00000269305	NM_001126112.2	147	Gtt/tt	5/11	0.280584693811946	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.280584693811946	2		760	1433	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713331	30713331	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	43	490	0	ENST00000295754.5:c.656T>C	p.Ile219Thr	p.I219T	ENST00000295754	NM_003242.5	219	aTc/aCc	4/7	1	2	FACETS	0.384	0.32	0.455	0.384	0.32	0.455	SUBCLONAL	1	TRUE	1	0.280584693811946	2		490	799	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0048953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	114	449	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	0.857	0.78	0.936	0.857	0.78	0.936	CLONAL	1	TRUE	1	0.759963487738875	2		449	350	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212015	36212015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1475021403	NA	P-0048953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	289	754	1	ENST00000222270.7:c.1766C>T	p.Pro589Leu	p.P589L	ENST00000222270	NM_014727.1	589	cCt/cTt	3/37	1	2	FACETS	0.994	0.94	1	0.994	0.94	1	CLONAL	1	TRUE	1	0.759963487738875	2		755	765	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617734	39617734	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	75	345	0	ENST00000262039.4:c.1918G>T	p.Asp640Tyr	p.D640Y	ENST00000262039	NM_002647.2	640	Gat/Tat	17/25	0.531263360520925	1	FACETS	0.658	0.589	0.728	0.658	0.589	0.728	SUBCLONAL	1	TRUE	0	0.759963487738875	1		345	186	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617764	39617764	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	63	327	0	ENST00000262039.4:c.1948A>C	p.Ile650Leu	p.I650L	ENST00000262039	NM_002647.2	650	Atc/Ctc	17/25	0.531263360520925	1	FACETS	0.623	0.551	0.697	0.623	0.551	0.697	SUBCLONAL	1	TRUE	0	0.759963487738875	1		327	165	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163779	47163779	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	69	446	0	ENST00000409792.3:c.2347del	p.Val783PhefsTer15	p.V783Ffs*15	ENST00000409792	NM_014159.6	783	Gtt/tt	3/21	0.759963487738875	1	FACETS	0.962	0.874	1	0.962	0.874	1	CLONAL	1	TRUE	0	0.759963487738875	1		446	117	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0048954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	201	932	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.235689144170115	2	FACETS	0.982	0.911	1	0.982	0.911	1	CLONAL	2	TRUE	0	0.24	2		934	853	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796979	42796979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145102151	NA	P-0048954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	292	986	1	ENST00000575354.2:c.3437C>T	p.Pro1146Leu	p.P1146L	ENST00000575354	NM_015125.3	1146	cCa/cTa	14/20	0.235689144170115	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.24	2		987	1096	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100980	41100980	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs868706902	NA	P-0048954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	87	656	1	ENST00000373198.4:c.1376G>T	p.Arg459Leu	p.R459L	ENST00000373198	NM_133170.3	459	cGg/cTg	8/32	0.150915615743614	3	FACETS	0.885	0.782	0.995	0.442	0.391	0.498	CLONAL	1	TRUE	1	0.24	3		657	918	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564500	41564500	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	62	462	0	ENST00000263253.7:c.3922G>T	p.Asp1308Tyr	p.D1308Y	ENST00000263253	NM_001429.3	1308	Gac/Tac	24/31	0.3	3	FACETS	0.821	0.708	0.944	0.41	0.354	0.472	CLONAL	1	TRUE	1	0.24	3		462	705	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827928	72827928	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	94	678	0	ENST00000268489.5:c.8653G>T	p.Glu2885Ter	p.E2885*	ENST00000268489	NM_006885.3	2885	Gag/Tag	9/10	0.3	3	FACETS	0.888	0.788	0.995	0.444	0.394	0.498	CLONAL	1	TRUE	1	0.24	3		678	988	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733348	40733348	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	127	494	0	ENST00000373198.4:c.3458T>G	p.Val1153Gly	p.V1153G	ENST00000373198	NM_133170.3	1153	gTg/gGg	26/32	0.150915615743614	3	FACETS	0.815	0.739	0.895	0.815	0.739	0.895	CLONAL	2	TRUE	1	0.24	3		494	727	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431045	181431045	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1324858330	NA	P-0048954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	114	707	1	ENST00000325404.1:c.897G>T	p.Gln299His	p.Q299H	ENST00000325404	NM_003106.3	299	caG/caT	1/1	1	2	FACETS	0.983	0.884	1	0.983	0.884	1	CLONAL	1	TRUE	1	0.24	2		708	966	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0048955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	48	243	1	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.397626631081583	1	FACETS	0.449	0.381	0.524	0.449	0.381	0.524	SUBCLONAL	1	TRUE	0	0.434462166900483	1		244	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0048955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	247	887	1	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.397626631081583	1	FACETS	0.9	0.842	0.96	0.9	0.842	0.96	CLONAL	1	TRUE	0	0.434462166900483	1		888	989	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873066	134873066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762457030	NA	P-0048955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	129	569	0	ENST00000398015.3:c.1370C>T	p.Pro457Leu	p.P457L	ENST00000398015	NM_004441.4	457	cCg/cTg	6/16	1	2	FACETS	0.61	0.553	0.671	0.61	0.553	0.671	SUBCLONAL	1	TRUE	1	0.434462166900483	2		569	973	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089569	27089569	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1421023459	NA	P-0048955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	174	709	0	ENST00000324856.7:c.2525A>G	p.His842Arg	p.H842R	ENST00000324856	NM_006015.4	842	cAt/cGt	8/20	1	2	FACETS	0.736	0.677	0.798	0.736	0.677	0.798	SUBCLONAL	1	TRUE	1	0.434462166900483	2		709	1088	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0048956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	239	561	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.50987508142166	2		561	892	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973911	55973911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs941528100	NA	P-0048956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	208	372	0	ENST00000263923.4:c.1405G>A	p.Glu469Lys	p.E469K	ENST00000263923	NM_002253.2	469	Gag/Aag	10/30	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.50987508142166	2		372	757	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023141	27023143	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs1015322780	NA	P-0048956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	12	70	0	ENST00000324856.7:c.258_260del	p.Gly87del	p.G87del	ENST00000324856	NM_006015.4	83	GGC/-	1/20	1	2	FACETS	0.38	0.268	0.514	0.38	0.268	0.514	SUBCLONAL	1	TRUE	1	0.50987508142166	2		70	124	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016635	12016636	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0048956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	27	291	0	ENST00000353533.5:c.772_773del	p.Ile258CysfsTer9	p.I258Cfs*9	ENST00000353533	NM_003010.3	257	tcTAtt/tctt	7/11	0.50987508142166	1	FACETS	0.147	0.117	0.183	0.147	0.117	0.183	SUBCLONAL	1	TRUE	0	0.50987508142166	1		291	535	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420011	41420011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773011187	NA	P-0048956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	278	497	0	ENST00000373198.4:c.310G>A	p.Asp104Asn	p.D104N	ENST00000373198	NM_133170.3	104	Gac/Aac	3/32	1	2	FACETS	0.96	0.901	1	0.96	0.901	1	CLONAL	1	TRUE	1	0.50987508142166	2		497	1136	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383249	42383249	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137953079	NA	P-0048956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	272	530	1	ENST00000221972.3:c.269C>T	p.Thr90Met	p.T90M	ENST00000221972	NM_021601.3	90	aCg/aTg	2/5	1	2	FACETS	0.971	0.911	1	0.971	0.911	1	CLONAL	1	TRUE	1	0.50987508142166	2		531	1099	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578225	7578225	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	348	516	0	ENST00000269305.4:c.624del	p.Asp208GlufsTer39	p.D208Efs*39	ENST00000269305	NM_001126112.2	208	gaC/ga	6/11	0.50987508142166	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.50987508142166	1		516	904	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135307	30135307	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	183	353	0	ENST00000331968.5:c.511G>A	p.Val171Ile	p.V171I	ENST00000331968	NM_002742.2	171	Gta/Ata	3/18	1	2	FACETS	0.96	0.888	1	0.96	0.888	1	CLONAL	1	TRUE	1	0.50987508142166	2		353	748	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217871	7217892	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTCCTTCATCTTCTGTTCCA	TCTTCCTTCATCTTCTGTTCCA	-	novel	NA	P-0048956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	243	417	1	ENST00000380728.2:c.119_140del	p.Met40AsnfsTer16	p.M40Nfs*16	ENST00000380728		40	aTGGAACAGAAGATGAAGGAAGAa/aa	3/11	0.50987508142166	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.50987508142166	1		418	666	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511592	38511592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758706699	NA	P-0048956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	88	612	0	ENST00000254066.5:c.1090C>T	p.Arg364Trp	p.R364W	ENST00000254066	NM_000964.3	364	Cgg/Tgg	8/9	0.50987508142166	1	FACETS	0.275	0.243	0.31	0.275	0.243	0.31	SUBCLONAL	1	TRUE	0	0.50987508142166	1		612	935	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0121466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	145	301	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.989	0.918	1	0.989	0.918	1	CLONAL	1	NA	1	0.930833739169933	2		301	315	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436859	29436859	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs863225283	NA	P-0121466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	606	466	10	ENST00000389048.3:c.3734T>G	p.Phe1245Cys	p.F1245C	ENST00000389048	NM_004304.4	1245	tTc/tGc	24/29	0.87461612874279	3	FACETS	0.963	0.933	0.992	0.963	0.933	0.992	CLONAL	2	NA	1	0.930833739169933	3		476	991	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs397517201	NA	P-0048958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	125	394	0	ENST00000263967.3:c.1637A>T	p.Gln546Leu	p.Q546L	ENST00000263967	NM_006218.2	546	cAg/cTg	10/21	0.140677707469484	3	FACETS	1	0.969	1	0.752	0.688	0.817	INDETERMINATE	2	TRUE	0	0.358149327176035	3		394	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0048958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	313	697	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.331073801996224	3	FACETS	0.973	0.919	1	0.973	0.919	1	CLONAL	2	TRUE	1	0.358149327176035	3		697	1059	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813315	102813315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761462868	NA	P-0048958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	247	588	1	ENST00000307046.8:c.374G>A	p.Arg125His	p.R125H	ENST00000307046	NM_001111285.1	125	cGc/cAc	3/4	0.168870864627241	5	FACETS	0.978	0.914	1	0.652	0.609	0.696	INDETERMINATE	2	TRUE	2	0.358149327176035	5		589	1084	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579462	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGGCCACG	AGGGGCCACG	-	novel	NA	P-0048958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	205	722	0	ENST00000269305.4:c.216_225del	p.Val73HisfsTer47	p.V73Hfs*47	ENST00000269305	NM_001126112.2	72	ccCGTGGCCCCT/cc	4/11	0.331073801996224	3	FACETS	1	0.973	1	0.552	0.511	0.595	CLONAL	1	TRUE	1	0.358149327176035	3		722	1222	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118871	70118871	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	147	547	0	ENST00000245479.2:c.443A>G	p.Glu148Gly	p.E148G	ENST00000245479	NM_000346.3	148	gAg/gGg	2/3	0.331073801996224	3	FACETS	1	0.973	1	0.578	0.528	0.631	CLONAL	1	TRUE	1	0.358149327176035	3		547	837	SUCCESS
APC	324	MSKCC	GRCh37	5	112163701	112163701	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	56	280	0	ENST00000257430.4:c.1624C>T	p.Gln542Ter	p.Q542*	ENST00000257430	NM_000038.5	542	Cag/Tag	13/16	0.144314317369484	5	FACETS	0.773	0.666	0.887	0.515	0.444	0.592	INDETERMINATE	2	TRUE	2	0.358149327176035	5		280	311	SUCCESS
APC	324	MSKCC	GRCh37	5	112175136	112175136	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0048958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	46	229	0	ENST00000257430.4:c.3845C>G	p.Ser1282Ter	p.S1282*	ENST00000257430	NM_000038.5	1282	tCa/tGa	16/16	0.144314317369484	5	FACETS	1	0.886	1	0.696	0.595	0.806	INDETERMINATE	2	TRUE	2	0.358149327176035	5		229	189	SUCCESS
APC	324	MSKCC	GRCh37	5	112175770	112175771	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0048958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	66	300	0	ENST00000257430.4:c.4479_4480del	p.Glu1494LysfsTer19	p.E1494Kfs*19	ENST00000257430	NM_000038.5	1493	acGGaa/acaa	16/16	0.144314317369484	5	FACETS	0.941	0.824	1	0.627	0.549	0.711	INDETERMINATE	2	TRUE	2	0.358149327176035	5		300	301	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459776	149459776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765232439	NA	P-0048958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	326	768	0	ENST00000286301.3:c.431G>A	p.Arg144His	p.R144H	ENST00000286301	NM_005211.3	144	cGt/cAt	4/22	0.144314317369484	5	FACETS	1	0.97	1	0.695	0.655	0.735	INDETERMINATE	2	TRUE	2	0.358149327176035	5		768	1343	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	25	576	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.258547846412512	4	FACETS	1	0.925	1	0.474	0.377	0.584	CLONAL	1	FALSE	1	0.258547846412512	4		576	171	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263783	16263783	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	154	409	0	ENST00000375759.3:c.10152G>C	p.Lys3384Asn	p.K3384N	ENST00000375759	NM_015001.2	3384	aaG/aaC	12/15	0.258547846412512	7	FACETS	0.911	0.833	0.994	0.456	0.416	0.497	CLONAL	2	FALSE	3	0.258547846412512	7		409	1076	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111116	193111116	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	24	229	0	ENST00000367435.3:c.649G>A	p.Glu217Lys	p.E217K	ENST00000367435	NM_024529.4	217	Gag/Aag	7/17	0.258547846412512	9	FACETS	1	0.875	1	0.385	0.305	0.476	CLONAL	2	FALSE	3	0.258547846412512	9		229	153	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193202134	193202134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	62	198	0	ENST00000367435.3:c.1166C>T	p.Ser389Leu	p.S389L	ENST00000367435	NM_024529.4	389	tCa/tTa	14/17	0.258547846412512	9	FACETS	0.955	0.83	1	0.477	0.415	0.544	CLONAL	3	FALSE	3	0.258547846412512	9		198	319	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615014	43615014	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	143	508	0	ENST00000355710.3:c.2428G>T	p.Gly810Cys	p.G810C	ENST00000355710	NM_020975.4	810	Ggc/Tgc	14/20	0.146288758893677	2	FACETS	1	0.98	1	0.634	0.577	0.692	INDETERMINATE	1	FALSE	0	0.258547846412512	2		508	873	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1040389	1040389	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	44	360	0	ENST00000358495.3:c.183G>C	p.Gln61His	p.Q61H	ENST00000358495	NM_134424.2	61	caG/caC	3/12	0.186111363159868	4	FACETS	0.621	0.519	0.734	0.31	0.259	0.367	SUBCLONAL	1	FALSE	2	0.258547846412512	4		360	690	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881435	48881435	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	25	142	0	ENST00000267163.4:c.157G>T	p.Glu53Ter	p.E53*	ENST00000267163	NM_000321.2	53	Gaa/Taa	2/27	0.258547846412512	5	FACETS	1	0.925	1	0.476	0.378	0.587	CLONAL	1	FALSE	2	0.258547846412512	5		142	188	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56871603	56871603	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	107	344	0	ENST00000308159.5:c.1983G>C	p.Glu661Asp	p.E661D	ENST00000308159	NM_014669.4	661	gaG/gaC	18/22	0.258547846412512	7	FACETS	0.815	0.731	0.905			1	CLONAL	2	FALSE	NA	0.258547846412512	7		344	836	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953195	81953195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs187454354	NA	P-0048968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	51	288	0	ENST00000359376.3:c.2161G>A	p.Glu721Lys	p.E721K	ENST00000359376	NM_002661.3	721	Gag/Aag	20/33	0.138645395471068	3	FACETS	0.946	0.805	1	0.473	0.402	0.55	INDETERMINATE	1	FALSE	1	0.258547846412512	3		288	471	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89806439	89806439	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs151241802	NA	P-0048968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	117	379	0	ENST00000389301.3:c.3897G>C	p.Lys1299Asn	p.K1299N	ENST00000389301	NM_000135.2	1299	aaG/aaC	39/43	0.258547846412512	6	FACETS	1	0.983	1			1	CLONAL	1	FALSE	NA	0.258547846412512	6		379	932	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0048968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	133	441	0	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.258547846412512	4	FACETS	0.795	0.722	0.872	0.53	0.481	0.581	SUBCLONAL	2	FALSE	1	0.258547846412512	4		441	814	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942524	17942524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763951351	NA	P-0048968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	200	585	3	ENST00000458235.1:c.2764G>A	p.Asp922Asn	p.D922N	ENST00000458235	NM_000215.3	922	Gat/Aat	20/24	0.186111363159868	4	FACETS	0.756	0.699	0.815	0.756	0.699	0.815	SUBCLONAL	2	FALSE	2	0.258547846412512	4		588	1288	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61760981	61760981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	21	283	0	ENST00000401558.2:c.52G>A	p.Asp18Asn	p.D18N	ENST00000401558	NM_003400.3	18	Gat/Aat	2/25	0.258547846412512	5	FACETS	0.689	0.531	0.875	0.172	0.132	0.219	SUBCLONAL	1	FALSE	1	0.258547846412512	5		283	327	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193530	99193530	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	227	546	0	ENST00000074304.5:c.2725G>C	p.Glu909Gln	p.E909Q	ENST00000074304	NM_001134224.1	909	Gag/Cag	25/26	0.120981859548673	3	FACETS	0.995	0.928	1			1	INDETERMINATE	2	FALSE	NA	0.258547846412512	3		546	996	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24129410	24129410	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	76	319	0	ENST00000263121.7:c.54G>C	p.Gln18His	p.Q18H	ENST00000263121	NM_003073.3	18	caG/caC	1/9	0.186111363159868	4	FACETS	0.729	0.638	0.828	0.364	0.319	0.414	SUBCLONAL	1	FALSE	2	0.258547846412512	4		319	1015	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430380	181430380	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	59	409	0	ENST00000325404.1:c.232G>C	p.Glu78Gln	p.E78Q	ENST00000325404	NM_003106.3	78	Gag/Cag	1/1	0.258547846412512	4	FACETS	0.695	0.597	0.803	0.232	0.199	0.268	SUBCLONAL	1	FALSE	1	0.258547846412512	4		409	826	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593431	55593431	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs72550822	NA	P-0048968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	18	275	0	ENST00000288135.5:c.1588G>A	p.Val530Ile	p.V530I	ENST00000288135	NM_000222.2	530	Gta/Ata	10/21	1	2	FACETS	0.529	0.399	0.683	0.529	0.399	0.683	SUBCLONAL	1	FALSE	1	0.258547846412512	2		275	263	SUCCESS
APC	324	MSKCC	GRCh37	5	112178031	112178031	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	27	247	0	ENST00000257430.4:c.6740C>G	p.Ser2247Cys	p.S2247C	ENST00000257430	NM_000038.5	2247	tCt/tGt	16/16	0.258547846412512	5	FACETS	0.712	0.566	0.879	0.237	0.188	0.293	SUBCLONAL	1	FALSE	2	0.258547846412512	5		247	407	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514390	148514390	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	20	329	0	ENST00000320356.2:c.1334T>A	p.Phe445Tyr	p.F445Y	ENST00000320356	NM_004456.4	445	tTt/tAt	11/20	0.245925532399762	5	FACETS	0.902	0.692	1	0.301	0.23	0.383	CLONAL	1	FALSE	2	0.258547846412512	5		329	238	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277050	38277050	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0048968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	101	370	1	ENST00000425967.3:c.1377+1G>A		p.X459_splice	ENST00000425967	NM_001174067.1	459			0.186111363159868	4	FACETS	1	0.981	1	0.735	0.657	0.817	CLONAL	1	FALSE	2	0.258547846412512	4		371	669	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44970630	44970630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	31	284	0	ENST00000377967.4:c.4180C>T	p.Pro1394Ser	p.P1394S	ENST00000377967	NM_021140.2	1394	Cct/Tct	29/29	0.258547846412512	5	FACETS	0.832	0.673	1			1	CLONAL	1	FALSE	NA	0.258547846412512	5		284	400	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346195	70346195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	132	457	0	ENST00000374080.3:c.2546C>T	p.Ser849Phe	p.S849F	ENST00000374080		849	tCc/tTc	19/45	0.258547846412512	4	FACETS	1	0.985	1			1	CLONAL	1	FALSE	NA	0.258547846412512	4		457	866	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224464	123224464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	47	351	0	ENST00000218089.9:c.3317G>A	p.Arg1106Lys	p.R1106K	ENST00000218089	NM_001042749.1	1106	aGa/aAa	31/35	0.187370671388763	1	FACETS	0.907	0.768	1	0.907	0.768	1	CLONAL	1	FALSE	0	0.258547846412512	1		351	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0048969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	85	429	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.224949800498277	1	FACETS	0.968	0.856	1	0.968	0.856	1	CLONAL	1	TRUE	0	0.224949800498277	1		429	693	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593413	55593413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	35	273	0	ENST00000288135.5:c.1570C>T	p.Pro524Ser	p.P524S	ENST00000288135	NM_000222.2	524	Cct/Tct	10/21	1	2	FACETS	0.776	0.636	0.932	0.776	0.636	0.932	CLONAL	1	TRUE	1	0.224949800498277	2		273	401	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399444	139399444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1333725995	NA	P-0048969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	90	566	0	ENST00000277541.6:c.4699G>A	p.Glu1567Lys	p.E1567K	ENST00000277541	NM_017617.3	1567	Gag/Aag	26/34	0.224949800498277	1	FACETS	0.793	0.702	0.89	0.793	0.702	0.89	SUBCLONAL	1	TRUE	0	0.224949800498277	1		566	896	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503914	149503914	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56339845	NA	P-0048969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	81	490	4	ENST00000261799.4:c.1922G>A	p.Arg641His	p.R641H	ENST00000261799	NM_002609.3	641	cGc/cAc	14/23	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.224949800498277	2		494	672	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602918	10602918	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	112	467	0	ENST00000171111.5:c.660C>G	p.Phe220Leu	p.F220L	ENST00000171111	NM_203500.1	220	ttC/ttG	3/6	0.224949800498277	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.224949800498277	1		467	808	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207197	1207198	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0048969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	93	461	0	ENST00000326873.7:c.286_287dup	p.Lys97ArgfsTer7	p.K97Rfs*7	ENST00000326873	NM_000455.4	95	-/AA	1/10	0.224949800498277	1	FACETS	0.944	0.839	1	0.944	0.839	1	CLONAL	1	TRUE	0	0.224949800498277	1		461	777	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026998	48026998	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1553413253	NA	P-0048969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	57	329	1	ENST00000234420.5:c.1876C>T	p.Gln626Ter	p.Q626*	ENST00000234420	NM_000179.2	626	Cag/Tag	4/10	1	2	FACETS	0.872	0.748	1	0.872	0.748	1	CLONAL	1	TRUE	1	0.224949800498277	2		330	581	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306733	41306733	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	91	449	0	ENST00000373198.4:c.926C>G	p.Pro309Arg	p.P309R	ENST00000373198	NM_133170.3	309	cCa/cGa	7/32	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.224949800498277	2		449	753	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067863	30067863	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	45	351	0	ENST00000338641.4:c.1048G>T	p.Glu350Ter	p.E350*	ENST00000338641	NM_000268.3	350	Gaa/Taa	11/16	0.224949800498277	1	FACETS	0.549	0.46	0.647	0.549	0.46	0.647	SUBCLONAL	1	TRUE	0	0.224949800498277	1		351	647	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505011	149505011	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	56	279	0	ENST00000261799.4:c.1804C>A	p.Leu602Met	p.L602M	ENST00000261799	NM_002609.3	602	Ctg/Atg	12/23	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.224949800498277	2		279	490	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729266	41729266	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	38	262	0	ENST00000242208.4:c.1263G>T	p.Glu421Asp	p.E421D	ENST00000242208	NM_002192.2	421	gaG/gaT	3/3	1	2	FACETS	0.589	0.486	0.704	0.589	0.486	0.704	SUBCLONAL	1	TRUE	1	0.224949800498277	2		262	574	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90990552	90990552	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0048969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	44	214	0	ENST00000265433.3:c.481-1G>A		p.X161_splice	ENST00000265433	NM_002485.4	161			1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.224949800498277	2		214	363	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894941	101894941	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	46	273	0	ENST00000374994.4:c.494C>A	p.Ser165Ter	p.S165*	ENST00000374994	NM_004612.2	165	tCa/tAa	3/9	0.224949800498277	1	FACETS	0.825	0.696	0.967	0.825	0.696	0.967	CLONAL	1	TRUE	0	0.224949800498277	1		273	440	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0048970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	238	696	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.541596194896241	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.541596194896241	1		697	578	SUCCESS
APC	324	MSKCC	GRCh37	5	112175456	112175457	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0048970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	133	237	0	ENST00000257430.4:c.4166_4167del	p.Ser1389CysfsTer5	p.S1389Cfs*5	ENST00000257430	NM_000038.5	1389	TCt/t	16/16	0.541596194896241	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.541596194896241	2		237	236	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89176365	89176365	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	38	201	0	ENST00000336596.2:c.95T>C	p.Leu32Pro	p.L32P	ENST00000336596	NM_005233.5	32	cTa/cCa	2/17	1	2	FACETS	0.974	0.82	1	0.974	0.82	1	CLONAL	1	TRUE	1	0.541596194896241	2		201	144	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037152	71037152	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	57	284	0	ENST00000318789.4:c.1139del	p.Pro380LeufsTer4	p.P380Lfs*4	ENST00000318789	NM_032682.5	380	cCt/ct	14/21	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.2290706474604	2		284	453	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321727	62321729	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs771771098	NA	P-0048973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	44	514	0	ENST00000360203.5:c.2351_2353del	p.Phe784del	p.F784del	ENST00000360203	NM_001283009.1	782	ccCTTc/ccc	26/35	0.339664129877757	1	FACETS	0.409	0.342	0.482	0.409	0.342	0.482	SUBCLONAL	1	TRUE	0	0.339664129877757	1		514	526	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0048974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	99	620	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.966	0.864	1	0.966	0.864	1	CLONAL	1	TRUE	1	0.333387443726403	2		620	615	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	165	440	0	ENST00000397062.3:c.246A>T	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaT	2/5	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.333387443726403	2		440	781	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	42	476	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	0.359	0.299	0.426	0.359	0.299	0.426	SUBCLONAL	1	TRUE	1	0.333387443726403	2		476	702	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0048974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	81	418	0	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	1	2	FACETS	0.94	0.83	1	0.94	0.83	1	CLONAL	1	TRUE	1	0.333387443726403	2		418	517	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720670	89720670	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786204875	NA	P-0048974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	85	207	0	ENST00000371953.3:c.821G>A	p.Trp274Ter	p.W274*	ENST00000371953	NM_000314.4	274	tGg/tAg	8/9	0.295671185979407	3	FACETS	0.813	0.724	0.906	0.813	0.724	0.906	CLONAL	2	TRUE	1	0.333387443726403	3		207	366	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660469	67660469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	82	310	0	ENST00000264010.4:c.1369C>T	p.Arg457Ter	p.R457*	ENST00000264010	NM_006565.3	457	Cga/Tga	8/12	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.333387443726403	2		310	476	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562378	21562378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772963885	NA	P-0048974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	99	560	0	ENST00000382592.4:c.1541C>T	p.Pro514Leu	p.P514L	ENST00000382592	NM_014572.2	514	cCg/cTg	4/8	1	2	FACETS	0.727	0.648	0.811	0.727	0.648	0.811	SUBCLONAL	1	TRUE	1	0.333387443726403	2		560	817	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197129	26197129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	85	477	0	ENST00000356476.2:c.350G>A	p.Arg117Gln	p.R117Q	ENST00000356476		117	cGa/cAa	1/1	1	2	FACETS	0.904	0.801	1	0.904	0.801	1	CLONAL	1	TRUE	1	0.333387443726403	2		477	564	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474492	40474492	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113994139	NA	P-0048974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	112	361	0	ENST00000264657.5:c.1909G>A	p.Val637Met	p.V637M	ENST00000264657	NM_139276.2	637	Gtg/Atg	21/24	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.333387443726403	2		361	591	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711918	89711924	+	frameshift_variant	Frame_Shift_Del	DEL	GCTACCT	GCTACCT	-	novel	NA	P-0048974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	41	377	0	ENST00000371953.3:c.537_543del	p.Tyr180Ter	p.Y180*	ENST00000371953	NM_000314.4	179	aGCTACCTg/ag	6/9	0.295671185979407	3	FACETS	0.646	0.539	0.766	0.323	0.269	0.383	SUBCLONAL	1	TRUE	1	0.333387443726403	3		377	444	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032806	48032806	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	92	330	0	ENST00000234420.5:c.3606G>A	p.Met1202Ile	p.M1202I	ENST00000234420	NM_000179.2	1202	atG/atA	7/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.333387443726403	2		330	428	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39746860	39746860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	46	239	0	ENST00000361337.2:c.1874C>T	p.Ala625Val	p.A625V	ENST00000361337	NM_003286.2	625	gCt/gTt	18/21	1	2	FACETS	0.911	0.771	1	0.911	0.771	1	CLONAL	1	TRUE	1	0.333387443726403	2		239	303	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916958	178916959	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAAATT	novel	NA	P-0048974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	62	279	0	ENST00000263967.3:c.347_352dup	p.Glu116_Ile117dup	p.E116_I117dup	ENST00000263967	NM_006218.2	116	-/GAAATT	2/21	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.333387443726403	2		279	310	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681792	30681792	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	112	457	0	ENST00000376406.3:c.305G>T	p.Arg102Ile	p.R102I	ENST00000376406	NM_014641.2	102	aGa/aTa	3/15	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.333387443726403	2		457	639	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139004	37139005	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	135	569	0	ENST00000373509.5:c.347dup	p.Val117ArgfsTer92	p.V117Rfs*92	ENST00000373509	NM_002648.3	115	agt/agTt	4/6	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.333387443726403	2		569	807	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526197	189526197	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	18	619	0	ENST00000264731.3:c.461C>G	p.Ser154Cys	p.S154C	ENST00000264731	NM_003722.4	154	tCc/tGc	4/14	0.254263357079483	4	FACETS	0.871	0.661	1	0.436	0.33	0.558	CLONAL	1	TRUE	2	0.37	4		619	153	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696688	47696688	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519971	NA	P-0048979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	59	492	0	ENST00000347630.2:c.260A>G	p.Tyr87Cys	p.Y87C	ENST00000347630	NM_001007230.1	87	tAc/tGc	5/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	1	0.380931359575093	2		492	265	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049724	16049724	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	34	326	0	ENST00000268712.3:c.1048C>T	p.Arg350Ter	p.R350*	ENST00000268712	NM_006311.3	350	Cga/Tga	10/46	1	2	FACETS	0.569	0.466	0.683	0.569	0.466	0.683	SUBCLONAL	1	FALSE	1	0.380931359575093	2		326	314	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406444	70406444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149434944	NA	P-0048980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	86	625	1	ENST00000373644.4:c.3958C>T	p.Arg1320Trp	p.R1320W	ENST00000373644	NM_030625.2	1320	Cgg/Tgg	4/12	0.461951532651299	3	FACETS	0.9	0.798	1	0.45	0.399	0.504	CLONAL	1	TRUE	1	0.471655989234002	3		626	501	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464412	120464412	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	68	489	0	ENST00000256646.2:c.5234C>T	p.Ser1745Leu	p.S1745L	ENST00000256646	NM_024408.3	1745	tCa/tTa	29/34	0.461951532651299	3	FACETS	0.966	0.845	1	0.483	0.422	0.548	CLONAL	1	TRUE	1	0.471655989234002	3		489	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573991	7573992	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	211	684	0	ENST00000269305.4:c.1035dup	p.Glu346Ter	p.E346*	ENST00000269305	NM_001126112.2	345	-/T	10/11	0.435767360166882	2	FACETS	0.95	0.892	1	0.95	0.892	1	CLONAL	2	TRUE	0	0.471655989234002	2		684	471	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271765	18271765	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	100	706	0	ENST00000222254.8:c.452C>A	p.Pro151His	p.P151H	ENST00000222254	NM_005027.3	151	cCc/cAc	4/16	0.454104975899913	4	FACETS	0.975	0.872	1	0.325	0.29	0.362	CLONAL	1	TRUE	1	0.471655989234002	4		706	640	SUCCESS
APC	324	MSKCC	GRCh37	5	112175869	112175870	+	missense_variant	Missense_Mutation	DNP	TC	TC	CT	novel	NA	P-0048980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	37	273	0	ENST00000257430.4:c.4578_4579delinsCT	p.Pro1527Ser	p.P1527S	ENST00000257430	NM_000038.5	1526	ccTCca/ccCTca	16/16	0.461951532651299	3	FACETS	0.723	0.6	0.86	0.362	0.3	0.43	SUBCLONAL	1	TRUE	1	0.471655989234002	3		273	268	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94128966	94128966	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	66	408	0	ENST00000369303.4:c.94G>C	p.Glu32Gln	p.E32Q	ENST00000369303	NM_004440.3	32	Gaa/Caa	1/17	0.461951532651299	3	FACETS	0.991	0.866	1	0.496	0.433	0.563	CLONAL	1	TRUE	1	0.471655989234002	3		408	349	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141583032	141583032	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0048980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	143	473	0	ENST00000220592.5:c.216-1G>T		p.X72_splice	ENST00000220592	NM_012154.3	72			0.418602700534419	4	FACETS	0.96	0.882	1	0.96	0.882	1	CLONAL	2	TRUE	2	0.471655989234002	4		473	465	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913283	NA	P-0048982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	70	450	0	ENST00000263967.3:c.3129G>T	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atT	21/21	0.395771084563549	3	FACETS	0.879	0.768	0.998	0.44	0.384	0.499	CLONAL	1	TRUE	1	0.395771084563549	3		450	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0048982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	265	708	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	0.367014633133873	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.395771084563549	1		708	1054	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891308	101891308	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	114	587	0	ENST00000374994.4:c.269C>A	p.Ser90Ter	p.S90*	ENST00000374994	NM_004612.2	90	tCa/tAa	2/9	0.395771084563549	1	FACETS	0.869	0.785	0.956	0.869	0.785	0.956	CLONAL	1	TRUE	0	0.395771084563549	1		587	532	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112448	115112448	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398394014	NA	P-0048982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	162	728	1	ENST00000257566.3:c.1292C>T	p.Ala431Val	p.A431V	ENST00000257566	NM_016569.3	431	gCg/gTg	7/8	1	2	FACETS	0.75	0.687	0.816	0.75	0.687	0.816	SUBCLONAL	1	TRUE	1	0.395771084563549	2		729	1091	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429400	78429400	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	122	476	0	ENST00000370768.2:c.1042G>A	p.Ala348Thr	p.A348T	ENST00000370768	NM_003902.3	348	Gct/Act	13/20	1	2	FACETS	0.937	0.849	1	0.937	0.849	1	CLONAL	1	TRUE	1	0.395771084563549	2		476	658	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0048983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	652	432	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	0.890620129870748	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.890620129870748	2		432	728	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188183	11188183	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057524049	NA	P-0048983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	268	464	0	ENST00000361445.4:c.5911G>A	p.Ala1971Thr	p.A1971T	ENST00000361445	NM_004958.3	1971	Gcc/Acc	43/58	0.890620129870748	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.890620129870748	1		464	330	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0048984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	139	327	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.469192982582519	2		327	585	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0048984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	200	302	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.465499216814872	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.469192982582519	2		302	417	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0048984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	104	421	2	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.899	0.809	0.994	0.899	0.809	0.994	CLONAL	1	TRUE	1	0.469192982582519	2		423	493	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137387	202137387	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	89	368	0	ENST00000358485.4:c.615G>A	p.Met205Ile	p.M205I	ENST00000358485	NM_001080125.1	205	atG/atA	4/9	1	2	FACETS	0.821	0.731	0.916	0.821	0.731	0.916	CLONAL	1	TRUE	1	0.469192982582519	2		368	462	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514420	125514420	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	80	352	0	ENST00000428830.2:c.1115G>T	p.Arg372Leu	p.R372L	ENST00000428830	NM_001114121.2	372	cGg/cTg	11/14	1	2	FACETS	0.674	0.595	0.758	0.674	0.595	0.758	SUBCLONAL	1	TRUE	1	0.469192982582519	2		352	506	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0048984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	46	333	2	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	2	FACETS	0.708	0.6	0.825	0.708	0.6	0.825	SUBCLONAL	1	TRUE	1	0.469192982582519	2		335	277	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0048984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	380	745	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.937	0.895	0.98	1	0.997	1	CLONAL	2	TRUE	1	0.469192982582519	2		750	864	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0048984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	112	410	1	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	0.465499216814872	2	FACETS	0.906	0.818	0.998	0.453	0.409	0.499	CLONAL	1	TRUE	0	0.469192982582519	2		411	527	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	168	440	0	ENST00000397062.3:c.246A>T	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaT	2/5	1	2	FACETS	0.886	0.816	0.96	0.886	0.816	0.96	CLONAL	1	TRUE	1	0.469192982582519	2		440	808	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0048984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	53	888	9	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	0.28	0.237	0.326	0.28	0.237	0.326	SUBCLONAL	1	TRUE	1	0.469192982582519	2		897	808	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952142	178952142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253171657	NA	P-0048984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	56	239	0	ENST00000263967.3:c.3197C>T	p.Ala1066Val	p.A1066V	ENST00000263967	NM_006218.2	1066	gCa/gTa	21/21	0.465499216814872	2	FACETS	0.775	0.668	0.89	0.388	0.334	0.445	SUBCLONAL	1	TRUE	0	0.469192982582519	2		239	308	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247373	153247373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	106	259	0	ENST00000281708.4:c.1429G>A	p.Gly477Ser	p.G477S	ENST00000281708	NM_033632.3	477	Ggt/Agt	10/12	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.469192982582519	2		259	419	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0048984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	200	707	1	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	0.967	0.897	1	0.967	0.897	1	CLONAL	1	TRUE	1	0.469192982582519	2		708	882	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962930	2962930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349831751	NA	P-0048984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	212	814	1	ENST00000396946.4:c.1978C>T	p.Arg660Trp	p.R660W	ENST00000396946	NM_032415.4	660	Cgg/Tgg	16/25	1	2	FACETS	0.997	0.928	1	0.997	0.928	1	CLONAL	1	TRUE	1	0.469192982582519	2		815	906	SUCCESS
AR	367	MSKCC	GRCh37	X	66765164	66765164	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs867801558	NA	P-0048984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	23	346	1	ENST00000374690.3:c.176A>T	p.Gln59Leu	p.Q59L	ENST00000374690	NM_000044.3	59	cAg/cTg	1/8	1	2	FACETS	0.371	0.29	0.465	0.371	0.29	0.465	SUBCLONAL	1	TRUE	1	0.469192982582519	2		347	264	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674222	117674222	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777817381	NA	P-0048984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	116	559	0	ENST00000368508.3:c.4252G>A	p.Val1418Ile	p.V1418I	ENST00000368508	NM_002944.2	1418	Gtt/Att	26/43	1	2	FACETS	0.813	0.735	0.896	0.813	0.735	0.896	CLONAL	1	TRUE	1	0.469192982582519	2		559	608	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910712	29910712	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	266	1036	2	ENST00000376809.5:c.252G>T	p.Trp84Cys	p.W84C	ENST00000376809	NM_002116.7	84	tgG/tgT	2/8	1	2	FACETS	0.967	0.906	1	0.967	0.906	1	CLONAL	1	TRUE	1	0.469192982582519	2		1038	1172	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0048984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	160	434	0	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.815	0.748	0.885	0.815	0.748	0.885	CLONAL	1	TRUE	1	0.469192982582519	2		434	837	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717712	89717712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782350	NA	P-0048984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	27	379	0	ENST00000371953.3:c.737C>T	p.Pro246Leu	p.P246L	ENST00000371953	NM_000314.4	246	cCg/cTg	7/9	1	2	FACETS	0.204	0.162	0.253	0.204	0.162	0.253	SUBCLONAL	1	TRUE	1	0.469192982582519	2		379	563	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211138	36211138	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	274	1092	0	ENST00000222270.7:c.889C>T	p.Arg297Ter	p.R297*	ENST00000222270	NM_014727.1	297	Cga/Tga	3/37	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.469192982582519	2		1092	1128	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790170	40790170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373191879	NA	P-0048984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	98	518	0	ENST00000373198.4:c.2561G>A	p.Arg854His	p.R854H	ENST00000373198	NM_133170.3	854	cGc/cAc	18/32	1	2	FACETS	0.785	0.703	0.872	0.785	0.703	0.872	SUBCLONAL	1	TRUE	1	0.469192982582519	2		518	532	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023744	27023744	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	114	469	0	ENST00000324856.7:c.854del	p.Gly285GlufsTer78	p.G285Efs*78	ENST00000324856	NM_006015.4	284	Ggg/gg	1/20	1	2	FACETS	0.831	0.75	0.915	0.831	0.75	0.915	CLONAL	1	TRUE	1	0.469192982582519	2		469	585	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229638	5229638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1254439512	NA	P-0048984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	33	108	1	ENST00000357368.4:c.2213G>A	p.Arg738His	p.R738H	ENST00000357368	NM_002850.3	738	cGc/cAc	15/38	1	2	FACETS	0.832	0.686	0.993	0.832	0.686	0.993	CLONAL	1	TRUE	1	0.469192982582519	2		109	169	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11027422	11027422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	90	787	0	ENST00000327064.4:c.989C>T	p.Ala330Val	p.A330V	ENST00000327064	NM_199141.1	330	gCg/gTg	8/16	1	2	FACETS	0.385	0.341	0.433	0.385	0.341	0.433	SUBCLONAL	1	TRUE	1	0.469192982582519	2		787	996	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665047	138665047	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	20	230	0	ENST00000330315.3:c.518C>G	p.Ala173Gly	p.A173G	ENST00000330315	NM_023067.3	173	gCa/gGa	1/1	1	2	FACETS	0.323	0.247	0.411	0.323	0.247	0.411	SUBCLONAL	1	TRUE	1	0.469192982582519	2		230	264	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399195	139399195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	181	760	0	ENST00000277541.6:c.4948G>A	p.Ala1650Thr	p.A1650T	ENST00000277541	NM_017617.3	1650	Gcc/Acc	26/34	1	2	FACETS	0.944	0.872	1	0.944	0.872	1	CLONAL	1	TRUE	1	0.469192982582519	2		760	817	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	70	301	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.682	0.601	0.767	0.682	0.601	0.767	SUBCLONAL	1	TRUE	1	0.741419316583886	2		301	277	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922896	39922896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs892857458	NA	P-0048985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	194	608	0	ENST00000378444.4:c.3812C>T	p.Ser1271Leu	p.S1271L	ENST00000378444	NM_001123385.1	1271	tCg/tTg	8/15	1	2	FACETS	0.864	0.804	0.925	0.864	0.804	0.925	CLONAL	1	TRUE	1	0.741419316583886	2		608	606	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0048986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	223	504	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.474872998363835	2	FACETS	0.921	0.866	0.976	0.921	0.866	0.976	CLONAL	2	TRUE	0	0.474872998363835	2		504	510	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966468	25966468	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	167	651	0	ENST00000435504.4:c.2738C>A	p.Ser913Ter	p.S913*	ENST00000435504		913	tCa/tAa	13/13	0.474872998363835	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.474872998363835	1		651	528	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0048987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	184	577	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.944	0.874	1	1	0.995	1	CLONAL	5	TRUE	1	0.11	2		577	709	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0048987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	167	302	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.996	0.919	1	1	0.995	1	CLONAL	5	TRUE	1	0.11	2		302	610	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249348	110249348	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	236	771	0	ENST00000374672.4:c.1225A>C	p.Lys409Gln	p.K409Q	ENST00000374672	NM_004235.4	409	Aag/Cag	4/5	1	2	FACETS	1	0.965	1	1	0.996	1	CLONAL	4	TRUE	1	0.11	2		771	1021	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438249	56438250	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0048987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	254	691	1	ENST00000407977.2:c.743dup	p.Tyr248Ter	p.Y248*	ENST00000407977		248	tac/taAc	7/10	0.293483639664418	1	FACETS	0.923	0.867	0.98	1	0.996	1	CLONAL	6	TRUE	0	0.11	1		692	788	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0048988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	160	470	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.56235717086546	2		470	492	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0048988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	122	282	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.917	0.834	1	0.917	0.834	1	CLONAL	1	TRUE	1	0.56235717086546	2		282	473	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102110	27102111	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0048988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	238	492	0	ENST00000324856.7:c.5036_5037del	p.Gly1679AlafsTer18	p.G1679Afs*18	ENST00000324856	NM_006015.4	1679	gGT/g	19/20	0.555438283330894	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.56235717086546	1		492	608	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066778	30066778	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	214	424	0	ENST00000331968.5:c.2353G>A	p.Glu785Lys	p.E785K	ENST00000331968	NM_002742.2	785	Gaa/Aaa	16/18	1	2	FACETS	0.992	0.925	1	0.992	0.925	1	CLONAL	1	TRUE	1	0.56235717086546	2		424	767	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281161	46281161	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	171	437	0	ENST00000371998.3:c.3958C>A	p.Gln1320Lys	p.Q1320K	ENST00000371998		1320	Caa/Aaa	21/23	1	2	FACETS	0.845	0.779	0.913	0.845	0.779	0.913	CLONAL	1	TRUE	1	0.56235717086546	2		437	720	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545781	41545781	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	192	424	0	ENST00000263253.7:c.2396C>T	p.Ser799Phe	p.S799F	ENST00000263253	NM_001429.3	799	tCt/tTt	14/31	1	2	FACETS	0.904	0.839	0.972	0.904	0.839	0.972	CLONAL	1	TRUE	1	0.56235717086546	2		424	755	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042458	37042458	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	174	380	0	ENST00000231790.2:c.220G>T	p.Asp74Tyr	p.D74Y	ENST00000231790	NM_000249.3	74	Gat/Tat	3/19	0.543157820796596	1	FACETS	0.872	0.809	0.937	0.872	0.809	0.937	CLONAL	1	TRUE	0	0.56235717086546	1		380	510	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125716	47125716	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	195	406	0	ENST00000409792.3:c.5554C>G	p.His1852Asp	p.H1852D	ENST00000409792	NM_014159.6	1852	Cat/Gat	12/21	0.543157820796596	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.56235717086546	1		406	496	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390146	89390146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	156	305	0	ENST00000336596.2:c.895G>A	p.Asp299Asn	p.D299N	ENST00000336596	NM_005233.5	299	Gat/Aat	4/17	NA	2	FACETS	0.955	0.879	1			1	INDETERMINATE	1	TRUE	NA	0.56235717086546	2		305	581	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31401646	31401646	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	188	390	0	ENST00000344624.3:c.4018C>T	p.Gln1340Ter	p.Q1340*	ENST00000344624		1340	Cag/Tag	33/33	0.562075926940163	3	FACETS	0.923	0.853	0.996	0.462	0.426	0.498	CLONAL	1	TRUE	1	0.56235717086546	3		390	928	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522513	67522513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762586316	NA	P-0048988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	18	182	0	ENST00000274335.5:c.10G>A	p.Glu4Lys	p.E4K	ENST00000274335		4	Gag/Aag	1/15	0.543157820796596	1	FACETS	0.204	0.153	0.263	0.204	0.153	0.263	SUBCLONAL	1	TRUE	0	0.56235717086546	1		182	226	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633812	86633812	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	125	215	0	ENST00000274376.6:c.921C>G	p.Phe307Leu	p.F307L	ENST00000274376	NM_002890.2	307	ttC/ttG	5/25	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.56235717086546	2		215	437	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042344	42042344	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375801764	NA	P-0048991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	51	495	0	ENST00000219905.7:c.6539G>A	p.Gly2180Asp	p.G2180D	ENST00000219905	NM_001164273.1	2180	gGc/gAc	17/24	0.10047299524937	0	FACETS	0.478	0.407	0.556			1	INDETERMINATE	1	TRUE	0	0.34	0		495	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0048992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	493	882	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.709092405204415	2	FACETS	0.96	0.931	0.988	0.96	0.931	0.988	CLONAL	2	TRUE	0	0.73049153714574	2		882	703	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612890	228612890	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757564822	NA	P-0048992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1731	335	600	1	ENST00000366696.1:c.137C>T	p.Thr46Met	p.T46M	ENST00000366696	NM_003493.2	46	aCg/aTg	1/1	0.73049153714574	7	FACETS	1	0.991	1	0.314	0.295	0.333	CLONAL	1	TRUE	3	0.73049153714574	7		601	2066	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120479964	120479964	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	407	613	0	ENST00000256646.2:c.3463T>A	p.Ser1155Thr	p.S1155T	ENST00000256646	NM_024408.3	1155	Tcc/Acc	21/34	0.49155406173441	4	FACETS	0.885	0.844	0.927	0.885	0.844	0.927	CLONAL	2	TRUE	2	0.73049153714574	4		613	1089	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504321	186504321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	116	195	0	ENST00000323963.5:c.658G>A	p.Asp220Asn	p.D220N	ENST00000323963		220	Gat/Aat	7/11	0.216111989286444	6	FACETS	1	0.976	1	0.802	0.732	0.873	INDETERMINATE	2	TRUE	3	0.73049153714574	6		195	325	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0048993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	133	416	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.393224708569361	2	FACETS	0.912	0.84	0.985	0.912	0.84	0.985	CLONAL	2	FALSE	0	0.438147474816978	2		416	333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0048993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	85	715	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.438147474816978	1	FACETS	0.73	0.649	0.816	0.73	0.649	0.816	SUBCLONAL	1	FALSE	0	0.438147474816978	1		715	415	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796805	135796805	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203427	NA	P-0048993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	32	333	0	ENST00000298552.3:c.682C>T	p.Arg228Ter	p.R228*	ENST00000298552	NM_001162426.1	228	Cga/Tga	8/23	0.438147474816978	1	FACETS	0.559	0.457	0.672	0.559	0.457	0.672	SUBCLONAL	1	FALSE	0	0.438147474816978	1		333	204	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819663	81819663	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	48	580	0	ENST00000359376.3:c.69G>C	p.Glu23Asp	p.E23D	ENST00000359376	NM_002661.3	23	gaG/gaC	2/33	0.207056366075017	1	FACETS	0.324	0.274	0.38	0.324	0.274	0.38	INDETERMINATE	1	FALSE	0	0.438147474816978	1		580	528	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770021	56770021	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	63	613	0	ENST00000337432.4:c.17T>C	p.Phe6Ser	p.F6S	ENST00000337432	NM_058216.2	6	tTc/tCc	1/9	0.438147474816978	1	FACETS	0.619	0.538	0.705	0.619	0.538	0.705	SUBCLONAL	1	FALSE	0	0.438147474816978	1		613	363	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589226	67589237	+	inframe_deletion	In_Frame_Del	DEL	TAAACCACTACC	TAAACCACTACC	-	novel	NA	P-0048993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	47	367	0	ENST00000274335.5:c.1214_1225del	p.Ile405_Tyr408del	p.I405_Y408del	ENST00000274335		405	aTAAACCACTACCgg/agg	9/15	0.438147474816978	1	FACETS	0.698	0.594	0.81	0.698	0.594	0.81	SUBCLONAL	1	FALSE	0	0.438147474816978	1		367	240	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652383	48652383	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	58	971	0	ENST00000376670.3:c.1054G>C	p.Gly352Arg	p.G352R	ENST00000376670	NM_002049.3	352	Ggc/Cgc	6/6	0.207056366075017	1	FACETS	0.401	0.344	0.462	0.401	0.344	0.462	INDETERMINATE	1	FALSE	0	0.438147474816978	1		971	516	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154350	2154350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1268163024	NA	P-0048994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	78	739	2	ENST00000434045.2:c.578G>A	p.Arg193His	p.R193H	ENST00000434045	NM_001127598.1	193	cGc/cAc	5/5	1	2	FACETS	0.656	0.575	0.744	0.656	0.575	0.744	SUBCLONAL	1	TRUE	1	0.246014215245892	2		741	966	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437158	220437158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs75409408	NA	P-0048994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	101	776	0	ENST00000243786.2:c.62G>A	p.Gly21Glu	p.G21E	ENST00000243786	NM_002191.3	21	gGg/gAg	1/2	1	2	FACETS	0.908	0.811	1	0.908	0.811	1	CLONAL	1	TRUE	1	0.246014215245892	2		776	904	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	262	452	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.372034661096192	2	FACETS	0.973	0.917	1	0.973	0.917	1	CLONAL	2	TRUE	0	0.379812969083074	2		452	709	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894230	NA	P-0048995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	33	566	1	ENST00000451590.1:c.35G>T	p.Gly12Val	p.G12V	ENST00000451590	NM_001130442.1	12	gGc/gTc	2/5	0.310839912825854	4	FACETS	0.225	0.182	0.274	0.113	0.091	0.137	SUBCLONAL	1	TRUE	2	0.379812969083074	4		567	1064	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs121913292	NA	P-0048995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	82	390	0	ENST00000371953.3:c.389del	p.Arg130GlnfsTer4	p.R130Qfs*4	ENST00000371953	NM_000314.4	130	cGa/ca	5/9	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.379812969083074	2		390	338	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505330	25505330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745432645	NA	P-0048995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	159	696	2	ENST00000264709.3:c.428G>A	p.Arg143Gln	p.R143Q	ENST00000264709	NM_175629.2	143	cGa/cAa	4/23	0.37625885923275	4	FACETS	0.918	0.839	1	0.306	0.279	0.334	CLONAL	1	TRUE	1	0.379812969083074	4		698	1259	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916747	48916747	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690915	NA	P-0048995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	200	365	0	ENST00000267163.4:c.277C>T	p.Gln93Ter	p.Q93*	ENST00000267163	NM_000321.2	93	Caa/Taa	3/27	0.374870712752842	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	3	TRUE	0	0.379812969083074	3		365	411	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195702	102195712	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTGCCTTGA	TTCTGCCTTGA	-	novel	NA	P-0048995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	87	438	0	ENST00000263464.3:c.463_473del	p.Ser155GlufsTer10	p.S155Efs*10	ENST00000263464	NM_001165.4	154	ttTTCTGCCTTGAtg/tttg	2/9	0.379812969083074	3	FACETS	0.85	0.753	0.954	0.425	0.376	0.477	CLONAL	1	TRUE	1	0.379812969083074	3		438	641	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023212	1023212	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs56164975	NA	P-0048995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2653	506	577	0	ENST00000358495.3:c.1043G>C	p.Arg348Thr	p.R348T	ENST00000358495	NM_134424.2	348	aGa/aCa	11/12	0.379812969083074	18	FACETS	1	0.99	1			1	CLONAL	3	TRUE	NA	0.379812969083074	18		577	3159	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239624	105239624	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	170	692	0	ENST00000349310.3:c.921G>C	p.Lys307Asn	p.K307N	ENST00000349310	NM_001014432.1	307	aaG/aaC	11/15	0.372034661096192	2	FACETS	1	0.966	1	0.545	0.502	0.59	CLONAL	1	TRUE	0	0.379812969083074	2		692	821	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976161	18976161	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	201	802	2	ENST00000262803.5:c.2921G>T	p.Ser974Ile	p.S974I	ENST00000262803	NM_002911.3	974	aGc/aTc	21/24	0.379812969083074	3	FACETS	1	0.942	1	0.51	0.472	0.55	CLONAL	1	TRUE	1	0.379812969083074	3		804	1234	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039378	47039379	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	145	347	0	ENST00000377604.3:c.1004dup	p.Asp336GlyfsTer45	p.D336Gfs*45	ENST00000377604	NM_001204468.1	334	ata/atAa	10/24	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.379812969083074	1		347	488	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0048997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	123	327	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		327	327	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432447	49432447	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	58	629	0	ENST00000301067.7:c.8692C>T	p.Gln2898Ter	p.Q2898*	ENST00000301067	NM_003482.3	2898	Cag/Tag	34/54	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.15	2		629	751	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942871	15942895	+	frameshift_variant	Frame_Shift_Del	DEL	GTCATCAAAGCTTCCCATGAGAGCC	GTCATCAAAGCTTCCCATGAGAGCC	-	novel	NA	P-0048998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	40	444	0	ENST00000268712.3:c.6807_6831del	p.Ala2270LysfsTer15	p.A2270Kfs*15	ENST00000268712	NM_006311.3	2269	aaGGCTCTCATGGGAAGCTTTGATGAC/aa	44/46	1	2	FACETS	1	0.837	1	1	0.837	1	CLONAL	1	TRUE	1	0.15	2		444	529	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229623	5229623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	10	118	0	ENST00000357368.4:c.2228C>T	p.Ser743Leu	p.S743L	ENST00000357368	NM_002850.3	743	tCg/tTg	15/38	1	2	FACETS	0.709	0.481	0.996	0.709	0.481	0.996	CLONAL	1	TRUE	1	0.15	2		118	188	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949629	151949629	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0048998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	15	307	0	ENST00000262189.6:c.1469+2T>G		p.X490_splice	ENST00000262189	NM_170606.2	490			1	2	FACETS	0.752	0.55	0.995	0.752	0.55	0.995	CLONAL	1	TRUE	1	0.15	2		307	266	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0049000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	93	286	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.217918698485873	2	FACETS	1	0.98	1	0.732	0.654	0.814	CLONAL	1	TRUE	0	0.28	2		286	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0049000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	174	860	5	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	0.3	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.28	1		865	998	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480459	89480459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	47	392	0	ENST00000336596.2:c.2296G>A	p.Gly766Arg	p.G766R	ENST00000336596	NM_005233.5	766	Gga/Aga	13/17	1	2	FACETS	0.572	0.482	0.671	0.572	0.482	0.671	SUBCLONAL	1	TRUE	1	0.28	2		392	587	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247369	153247369	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	54	297	0	ENST00000281708.4:c.1433C>T	p.Ser478Phe	p.S478F	ENST00000281708	NM_033632.3	478	tCt/tTt	10/12	1	2	FACETS	0.934	0.8	1	0.934	0.8	1	CLONAL	1	TRUE	1	0.28	2		297	413	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245521	153245521	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	28	414	0	ENST00000281708.4:c.1670G>T	p.Gly557Val	p.G557V	ENST00000281708	NM_033632.3	557	gGa/gTa	11/12	1	2	FACETS	0.518	0.414	0.637	0.518	0.414	0.637	SUBCLONAL	1	TRUE	1	0.28	2		414	386	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482342	56482342	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519892	NA	P-0049000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	85	613	0	ENST00000267101.3:c.890A>T	p.Asp297Val	p.D297V	ENST00000267101	NM_001982.3	297	gAt/gTt	8/28	1	2	FACETS	0.855	0.756	0.962	0.855	0.756	0.962	CLONAL	1	TRUE	1	0.28	2		613	710	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608032	28608033	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0049000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	76	488	0	ENST00000241453.7:c.1933dup	p.Met645AsnfsTer10	p.M645Nfs*10	ENST00000241453	NM_004119.2	645	atg/aAtg	15/24	0.287173865765364	3	FACETS	0.822	0.72	0.932	0.411	0.36	0.466	CLONAL	1	TRUE	1	0.28	3		488	753	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189088	38189088	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	56	488	0	ENST00000317025.8:c.926A>G	p.His309Arg	p.H309R	ENST00000317025	NM_023034.1	309	cAt/cGt	5/24	0.3	1	FACETS	0.791	0.679	0.912	0.791	0.679	0.912	CLONAL	1	TRUE	0	0.28	1		488	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0049001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	390	668	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.639382229641758	1	FACETS	0.911	0.87	0.953	0.911	0.87	0.953	CLONAL	1	TRUE	0	0.639382229641758	1		669	911	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0049001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	111	286	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.866	0.785	0.95	0.866	0.785	0.95	CLONAL	1	TRUE	1	0.639382229641758	2		286	401	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129249	152129249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771540162	NA	P-0049001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	373	581	1	ENST00000206249.3:c.202G>A	p.Ala68Thr	p.A68T	ENST00000206249	NM_000125.3	68	Gcc/Acc	1/8	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.639382229641758	2		582	1037	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831993	72831993	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	318	570	0	ENST00000268489.5:c.4588G>C	p.Gly1530Arg	p.G1530R	ENST00000268489	NM_006885.3	1530	Ggt/Cgt	9/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.639382229641758	2		570	966	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265158	5265158	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	436	737	0	ENST00000357368.4:c.429G>C	p.Leu143Phe	p.L143F	ENST00000357368	NM_002850.3	143	ttG/ttC	5/38	1	2	FACETS	0.979	0.933	1	0.979	0.933	1	CLONAL	1	TRUE	1	0.639382229641758	2		737	1393	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250157	39250157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397517151	NA	P-0049001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	291	621	0	ENST00000402219.2:c.1412G>A	p.Cys471Tyr	p.C471Y	ENST00000402219	NM_005633.3	471	tGt/tAt	10/23	0.639382229641758	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.639382229641758	1		621	580	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484357	8484357	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	50	412	0	ENST00000356435.5:c.3175A>G	p.Met1059Val	p.M1059V	ENST00000356435		1059	Atg/Gtg	19/35	1	2	FACETS	0.458	0.389	0.532	0.458	0.389	0.532	SUBCLONAL	1	TRUE	1	0.56477932304988	2		412	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578410	7578410	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	320	809	0	ENST00000269305.4:c.520A>T	p.Arg174Trp	p.R174W	ENST00000269305	NM_001126112.2	174	Agg/Tgg	5/11	NA	2	FACETS	0.852	0.808	0.897			1	INDETERMINATE	2	TRUE	NA	0.446343378022147	2		809	841	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027253	48027253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878853714	NA	P-0049004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	40	352	0	ENST00000234420.5:c.2131C>T	p.Pro711Ser	p.P711S	ENST00000234420	NM_000179.2	711	Ccc/Tcc	4/10	0.336085957117413	3	FACETS	0.437	0.362	0.519	0.146	0.12	0.173	SUBCLONAL	1	TRUE	0	0.446343378022147	3		352	502	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717719	89717720	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs780264945	NA	P-0049004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	248	443	0	ENST00000371953.3:c.750_751del	p.Cys250TrpfsTer2	p.C250Wfs*2	ENST00000371953	NM_000314.4	248	ccTGtg/cctg	7/9	0.336085957117413	3	FACETS	1	0.98	1	0.725	0.683	0.768	CLONAL	2	TRUE	0	0.446343378022147	3		443	625	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518120	8518120	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	68	471	1	ENST00000356435.5:c.1271T>A	p.Val424Asp	p.V424D	ENST00000356435		424	gTc/gAc	10/35	0.393574649430204	2	FACETS	0.543	0.473	0.619	0.272	0.236	0.31	SUBCLONAL	1	TRUE	0	0.446343378022147	2		472	561	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864613	57864613	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	91	833	0	ENST00000228682.2:c.2090C>A	p.Ala697Asp	p.A697D	ENST00000228682	NM_005269.2	697	gCc/gAc	12/12	0.355817340638007	3	FACETS	0.475	0.42	0.533	0.158	0.14	0.178	SUBCLONAL	1	TRUE	0	0.446343378022147	3		833	1051	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912941	32912942	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0049004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	79	506	0	ENST00000380152.3:c.4450_4451del	p.Asp1484HisfsTer3	p.D1484Hfs*3	ENST00000380152		1483	acAGac/acac	11/27	0.446343378022147	1	FACETS	0.472	0.416	0.533	0.472	0.416	0.533	SUBCLONAL	1	TRUE	0	0.446343378022147	1		506	582	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061019	38061030	+	inframe_deletion	In_Frame_Del	DEL	GCGCGCCCTCTA	GCGCGCCCTCTA	-	novel	NA	P-0049004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	736	344	0	ENST00000250448.2:c.959_970del	p.Leu320_Ala323del	p.L320_A323del	ENST00000250448	NM_004496.3	320	cTAGAGGGCGCGCcg/ccg	2/2	0.446343378022147	9	FACETS	0.963	0.941	0.984			1	CLONAL	9	TRUE	NA	0.446343378022147	9		344	975	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849437	89849553	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGGCCAATGAGATGTAGTCTGTGAGGAGGGAGCGGTACTTGCCGGGAACCAGGGGTGGGTGGAGAATGTGCACCTGAGGATAGATAGCAGAGCGCAGCACCGTTAGTCTGGGAACT	TTGGCCAATGAGATGTAGTCTGTGAGGAGGGAGCGGTACTTGCCGGGAACCAGGGGTGGGTGGAGAATGTGCACCTGAGGATAGATAGCAGAGCGCAGCACCGTTAGTCTGGGAACT	-	novel	NA	P-0049004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	66	711	0	ENST00000389301.3:c.1471-43_1544del		p.X491_splice	ENST00000389301	NM_000135.2	491		16/43	0.446343378022147	1	FACETS	0.361	0.313	0.413	0.361	0.313	0.413	SUBCLONAL	1	TRUE	0	0.446343378022147	1		711	636	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556448	29556448	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	43	488	0	ENST00000356175.3:c.2815A>C	p.Asn939His	p.N939H	ENST00000356175	NM_000267.3	939	Aat/Cat	21/57	0.385797566245805	2	FACETS	0.273	0.227	0.323	0.136	0.113	0.162	SUBCLONAL	1	TRUE	0	0.446343378022147	2		488	706	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117391	7117391	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	82	690	0	ENST00000302850.5:c.3825C>G	p.Phe1275Leu	p.F1275L	ENST00000302850	NM_000208.2	1275	ttC/ttG	22/22	0.446343378022147	3	FACETS	0.526	0.463	0.594	0.175	0.154	0.198	SUBCLONAL	1	TRUE	0	0.446343378022147	3		690	855	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506840	186506922	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AACAAGTGGATCGTCATGTTCAGTAGTTTATACATTATGTGAGAAGTAACGTTCTGATTCTTTTTCTTACACAGAATTGGCAG	AACAAGTGGATCGTCATGTTCAGTAGTTTATACATTATGTGAGAAGTAACGTTCTGATTCTTTTTCTTACACAGAATTGGCAG	-	novel	NA	P-0049004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	86	81	0	ENST00000323963.5:c.1080-73_1089del		p.X360_splice	ENST00000323963		360		11/11	0.446343378022147	3	FACETS	1	0.963	1	0.759	0.686	0.834	CLONAL	2	TRUE	0	0.446343378022147	3		81	207	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519273	187519273	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	67	416	0	ENST00000441802.2:c.12110A>G	p.Tyr4037Cys	p.Y4037C	ENST00000441802	NM_005245.3	4037	tAc/tGc	23/27	0.446343378022147	1	FACETS	0.517	0.451	0.589	0.517	0.451	0.589	SUBCLONAL	1	TRUE	0	0.446343378022147	1		416	451	SUCCESS
APC	324	MSKCC	GRCh37	5	112103018	112103018	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	72	442	0	ENST00000257430.4:c.353T>C	p.Phe118Ser	p.F118S	ENST00000257430	NM_000038.5	118	tTt/tCt	4/16	0.411786926800826	1	FACETS	0.448	0.391	0.508	0.448	0.391	0.508	SUBCLONAL	1	TRUE	0	0.446343378022147	1		442	560	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324506	31324507	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0049004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	190	953	0	ENST00000412585.2:c.301_302del	p.Ser101ProfsTer37	p.S101Pfs*37	ENST00000412585	NM_005514.6	101	AGc/c	2/8	1	2	FACETS	0.802	0.741	0.866	0.802	0.741	0.866	CLONAL	1	TRUE	1	0.446343378022147	2		953	1061	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0049005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	201	898	1	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.246509270710091	2	FACETS	0.828	0.768	0.889	0.828	0.768	0.889	CLONAL	2	TRUE	0	0.292980153058448	2		899	829	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920307	50920307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501858	NA	P-0049005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	212	701	9	ENST00000440232.2:c.3073G>A	p.Val1025Met	p.V1025M	ENST00000440232	NM_002691.3	1025	Gtg/Atg	25/27	0.179176151169985	4	FACETS	0.934	0.867	1	0.934	0.867	1	CLONAL	2	TRUE	2	0.292980153058448	4		710	1002	SUCCESS
ATM	472	MSKCC	GRCh37	11	108159822	108159822	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	42	114	0	ENST00000278616.4:c.4228A>G	p.Lys1410Glu	p.K1410E	ENST00000278616	NM_000051.3	1410	Aaa/Gaa	28/63	0.292980153058448	5	FACETS	0.997	0.841	1	0.665	0.561	0.777	CLONAL	2	TRUE	2	0.292980153058448	5		114	207	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643455	38643455	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	127	522	0	ENST00000299084.4:c.925G>A	p.Val309Met	p.V309M	ENST00000299084	NM_152594.2	309	Gtg/Atg	7/7	0.234166055764337	3	FACETS	1	0.981	1	0.67	0.607	0.736	CLONAL	1	TRUE	1	0.292980153058448	3		522	742	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020796	37020796	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	132	374	0	ENST00000358127.4:c.49C>T	p.His17Tyr	p.H17Y	ENST00000358127	NM_001280556.1	17	Cat/Tat	2/10	0.234166055764337	3	FACETS	0.921	0.839	1	0.921	0.839	1	CLONAL	2	TRUE	1	0.292980153058448	3		374	561	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938563	44938563	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	138	455	0	ENST00000377967.4:c.3111G>C	p.Gln1037His	p.Q1037H	ENST00000377967	NM_021140.2	1037	caG/caC	20/29	0.179176151169985	4	FACETS	0.863	0.786	0.942	0.863	0.786	0.942	CLONAL	2	TRUE	2	0.292980153058448	4		455	706	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579485	7579485	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs869312782	NA	P-0049006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	172	753	0	ENST00000269305.4:c.202G>T	p.Glu68Ter	p.E68*	ENST00000269305	NM_001126112.2	68	Gag/Tag	4/11	NA	2	FACETS	1	0.938	1			1	INDETERMINATE	2	TRUE	NA	0.24	2		753	704	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602252	10602252	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0049006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	97	583	0	ENST00000171111.5:c.1325+1G>A		p.X442_splice	ENST00000171111	NM_203500.1	442			0.3	1	FACETS	0.767	0.687	0.851	1	0.982	1	SUBCLONAL	2	TRUE	0	0.24	1		583	464	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955060	1955060	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	68	557	0	ENST00000382891.5:c.2147C>A	p.Ser716Ter	p.S716*	ENST00000382891	NM_133335.3	716	tCa/tAa	12/22	0.3	1	FACETS	0.902	0.785	1	0.902	0.785	1	CLONAL	1	TRUE	0	0.24	1		557	553	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741823	145741823	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	78	783	0	ENST00000428558.2:c.680T>C	p.Val227Ala	p.V227A	ENST00000428558	NM_004260.3	227	gTc/gCc	5/22	0.213771205307112	3	FACETS	0.971	0.852	1	0.485	0.426	0.549	CLONAL	1	TRUE	1	0.24	3		783	750	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615121	100615121	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	61	256	0	ENST00000308731.7:c.794C>G	p.Pro265Arg	p.P265R	ENST00000308731	NM_000061.2	265	cCt/cGt	9/19	0.188761285385877	2	FACETS	0.856	0.744	0.975			1	CLONAL	2	TRUE	NA	0.24	2		256	297	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0049007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	173	495	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.255015162655128	5	FACETS	1	0.977	1	0.758	0.702	0.815	INDETERMINATE	2	TRUE	2	0.486930536681355	5		495	541	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	229	301	0				ENST00000310581	NM_198253.2	-/1132			0.493765600315217	3	FACETS	0.876	0.828	0.924	1	0.992	1	CLONAL	3	TRUE	1	0.486930536681355	3		301	445	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729162	66729162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519732	NA	P-0049007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	187	713	0	ENST00000307102.5:c.370C>T	p.Pro124Ser	p.P124S	ENST00000307102	NM_002755.3	124	Ccg/Tcg	3/11	1	2	FACETS	0.937	0.867	1	0.937	0.867	1	CLONAL	1	TRUE	1	0.486930536681355	2		713	820	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164535	36164535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1399289174	NA	P-0049007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	145	533	1	ENST00000300305.3:c.1340C>T	p.Pro447Leu	p.P447L	ENST00000300305		447	cCg/cTg	8/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.486930536681355	2		534	561	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18956828	18956828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759056334	NA	P-0049007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	176	656	0	ENST00000262803.5:c.271G>A	p.Asp91Asn	p.D91N	ENST00000262803	NM_002911.3	91	Gac/Aac	2/24	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.486930536681355	2		656	696	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100933	41100933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	180	580	1	ENST00000373198.4:c.1423G>A	p.Glu475Lys	p.E475K	ENST00000373198	NM_133170.3	475	Gag/Aag	8/32	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.486930536681355	2		581	690	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141582948	141582948	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	91	680	0	ENST00000220592.5:c.299T>C	p.Leu100Pro	p.L100P	ENST00000220592	NM_012154.3	100	cTa/cCa	3/19	0.22989897372753	2	FACETS	0.429	0.38	0.481	0.214	0.19	0.241	INDETERMINATE	1	TRUE	0	0.486930536681355	2		680	872	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938350	76938350	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	177	627	0	ENST00000373344.5:c.2398A>T	p.Ser800Cys	p.S800C	ENST00000373344	NM_000489.3	800	Agc/Tgc	9/35	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.486930536681355	2		627	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0049008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	220	696	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.335274168532479	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.335274168532479	1		697	1083	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287809	33287809	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150463674	NA	P-0049008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	188	892	0	ENST00000374542.5:c.1444G>A	p.Glu482Lys	p.E482K	ENST00000374542	NM_001141970.1	482	Gaa/Aaa	5/8	0.335274168532479	1	FACETS	0.642	0.591	0.695	0.642	0.591	0.695	SUBCLONAL	1	TRUE	0	0.335274168532479	1		892	1455	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981813	201981813	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	65	778	0	ENST00000359651.3:c.524A>T	p.Gln175Leu	p.Q175L	ENST00000359651		175	cAa/cTa	4/8	0.335274168532479	1	FACETS	0.286	0.247	0.329	0.286	0.247	0.329	SUBCLONAL	1	TRUE	0	0.335274168532479	1		778	1128	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66520216	66520216	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	55	348	0	ENST00000358598.2:c.500A>C	p.Gln167Pro	p.Q167P	ENST00000358598	NM_212471.2	167	cAa/cCa	5/11	0.335274168532479	1	FACETS	0.454	0.388	0.527	0.454	0.388	0.527	SUBCLONAL	1	TRUE	0	0.335274168532479	1		348	601	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189292	99189292	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	44	408	0	ENST00000074304.5:c.2548C>G	p.Arg850Gly	p.R850G	ENST00000074304	NM_001134224.1	850	Cgc/Ggc	24/26	0.335274168532479	1	FACETS	0.289	0.241	0.342	0.289	0.241	0.342	SUBCLONAL	1	TRUE	0	0.335274168532479	1		408	756	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149447818	149447818	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	115	597	0	ENST00000286301.3:c.1586T>C	p.Leu529Pro	p.L529P	ENST00000286301	NM_005211.3	529	cTg/cCg	11/22	0.335274168532479	1	FACETS	0.649	0.584	0.718	0.649	0.584	0.718	SUBCLONAL	1	TRUE	0	0.335274168532479	1		597	880	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212809	27212809	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	77	719	0	ENST00000380036.4:c.2791A>G	p.Ser931Gly	p.S931G	ENST00000380036	NM_000459.3	931	Agc/Ggc	17/23	0.335274168532479	1	FACETS	0.305	0.266	0.347	0.305	0.266	0.347	SUBCLONAL	1	TRUE	0	0.335274168532479	1		719	1254	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0049009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	16	309	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	0.538	0.396	0.709	0.538	0.396	0.709	SUBCLONAL	1	TRUE	1	0.12	2		309	496	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692981	89692982	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0049009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	32	503	0	ENST00000371953.3:c.469dup	p.Glu157GlyfsTer23	p.E157Gfs*23	ENST00000371953	NM_000314.4	155	-/G	5/9	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.12	2		503	465	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589577	67589606	+	inframe_deletion	In_Frame_Del	DEL	AAAAATTACATGAATATAACACTCAGTTTC	AAAAATTACATGAATATAACACTCAGTTTC	-	novel	NA	P-0049009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	14	250	0	ENST00000274335.5:c.1342_1371del	p.Lys448_Gln457del	p.K448_Q457del	ENST00000274335		447	aAAAAATTACATGAATATAACACTCAGTTTCaa/aaa	10/15	1	2	FACETS	0.887	0.641	1	0.887	0.641	1	CLONAL	1	TRUE	1	0.12	2		250	263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0049010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	171	668	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.297308927503855	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.29	1		669	809	SUCCESS
APC	324	MSKCC	GRCh37	5	112111408	112111411	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	-	rs387906231	NA	P-0049010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	43	242	0	ENST00000257430.4:c.509_512del	p.Asp170ValfsTer4	p.D170Vfs*4	ENST00000257430	NM_000038.5	169	ATAGat/at	5/16	0.297308927503855	1	FACETS	0.874	0.736	1	0.874	0.736	1	CLONAL	1	TRUE	0	0.29	1		242	290	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508614	106508614	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377001952	NA	P-0049010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	96	422	0	ENST00000359195.3:c.608C>T	p.Thr203Met	p.T203M	ENST00000359195	NM_002649.2	203	aCg/aTg	2/11	0.297308927503855	3	FACETS	1	0.934	1	0.534	0.476	0.596	CLONAL	1	TRUE	1	0.29	3		422	710	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724585	162724585	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	111	488	0	ENST00000367921.3:c.357G>T	p.Lys119Asn	p.K119N	ENST00000367921	NM_006182.2	119	aaG/aaT	5/18	1	2	FACETS	0.986	0.887	1	0.986	0.887	1	CLONAL	1	TRUE	1	0.29	2		488	776	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563123	21563123	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	434	636	2	ENST00000382592.4:c.796G>C	p.Gly266Arg	p.G266R	ENST00000382592	NM_014572.2	266	Ggc/Cgc	4/8	0.297308927503855	5	FACETS	0.993	0.95	1	0.993	0.95	1	CLONAL	4	TRUE	1	0.29	5		638	1081	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99460090	99460090	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	27	333	0	ENST00000268035.6:c.2186C>A	p.Ser729Tyr	p.S729Y	ENST00000268035	NM_000875.3	729	tCc/tAc	10/21	0.297308927503855	1	FACETS	0.322	0.256	0.399	0.322	0.256	0.399	SUBCLONAL	1	TRUE	0	0.29	1		333	494	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916247	9916247	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753203288	NA	P-0049010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	148	363	0	ENST00000330684.3:c.2042G>A	p.Arg681Gln	p.R681Q	ENST00000330684	NM_001134407.1	681	cGa/cAa	10/13	0.297308927503855	3	FACETS	0.913	0.837	0.993	0.913	0.837	0.993	CLONAL	2	TRUE	1	0.29	3		363	640	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117641	70117641	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	118	541	0	ENST00000245479.2:c.109T>C	p.Ser37Pro	p.S37P	ENST00000245479	NM_000346.3	37	Tcg/Ccg	1/3	0.297308927503855	3	FACETS	1	0.958	1	0.557	0.502	0.615	CLONAL	1	TRUE	1	0.29	3		541	837	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597495	10597495	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0049010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	200	408	23	ENST00000171111.5:c.1709-1G>A		p.X570_splice	ENST00000171111	NM_203500.1	570			1	2	FACETS	0.942	0.876	1	1	0.993	1	CLONAL	2	TRUE	1	0.29	2		431	732	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	28	301	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.874	0.697	1	0.874	0.697	1	CLONAL	1	TRUE	1	0.13	2		301	493	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713606	52713607	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0049011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	33	544	0	ENST00000394830.3:c.121_122del	p.Leu41SerfsTer11	p.L41Sfs*11	ENST00000394830	NM_018313.4	41	CTt/t	2/30	1	2	FACETS	0.831	0.675	1	0.831	0.675	1	CLONAL	1	TRUE	1	0.13	2		544	611	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191547	10191547	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	45	602	0	ENST00000256474.2:c.540del	p.Ile180MetfsTer22	p.I180Mfs*22	ENST00000256474	NM_000551.3	180	atC/at	3/3	1	2	FACETS	1	0.84	1	1	0.84	1	CLONAL	1	TRUE	1	0.13	2		602	691	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604679	43604679	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0049011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	45	599	0	ENST00000355710.3:c.1263+1G>A		p.X421_splice	ENST00000355710	NM_020975.4	421			1	2	FACETS	0.963	0.807	1	0.963	0.807	1	CLONAL	1	TRUE	1	0.13	2		599	719	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0049072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	277	576	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.36867977058201	3	FACETS	0.868	0.826	0.91	0.868	0.826	0.91	INDETERMINATE	2	TRUE	1	0.902564034352984	3		576	513	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0049072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	63	69	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	0.374705554634589	3	FACETS	1	0.951	1	0.576	0.508	0.646	INDETERMINATE	1	TRUE	1	0.902564034352984	3		69	176	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740521	58740521	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1296018768	NA	P-0049072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	321	504	0	ENST00000305921.3:c.1426G>T	p.Glu476Ter	p.E476*	ENST00000305921	NM_003620.3	476	Gaa/Taa	6/6	0.527799080366719	1	FACETS	0.71	0.679	0.74	0.71	0.679	0.74	INDETERMINATE	1	TRUE	0	0.902564034352984	1		504	550	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739007	40739007	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs761497190	NA	P-0049072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	324	511	0	ENST00000373198.4:c.3277C>G	p.Pro1093Ala	p.P1093A	ENST00000373198	NM_133170.3	1093	Ccc/Gcc	24/32	0.445549877620976	3	FACETS	1	0.988	1	0.568	0.538	0.599	INDETERMINATE	1	TRUE	1	0.902564034352984	3		511	917	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248998	55248999	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCAGCGTGGACAACCCCC	novel	NA	P-0049072-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1590	105	586	0	ENST00000275493.2:c.2297_2317dup	p.Pro772_His773insLeuAlaSerValAspAsnPro	p.P772_H773insLASVDNP	ENST00000275493	NM_005228.3	766	atg/aTGGCCAGCGTGGACAACCCCCtg	20/28	0.475004290298258	6	FACETS	0.385	0.343	0.43	0.128	0.114	0.144	INDETERMINATE	1	TRUE	3	0.902564034352984	6		586	1695	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	155	301	0				ENST00000310581	NM_198253.2	-/1132			0.248198752121105	4	FACETS	1	0.957	1	1	0.993	1	CLONAL	4	TRUE	2	0.307652668217272	4		301	318	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850341	128850341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121918347	NA	P-0049112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	155	444	0	ENST00000249373.3:c.1604G>T	p.Trp535Leu	p.W535L	ENST00000249373	NM_005631.4	535	tGg/tTg	9/12	0.248198752121105	4	FACETS	0.834	0.764	0.907	0.834	0.764	0.907	CLONAL	2	TRUE	2	0.307652668217272	4		444	790	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0049112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	312	549	0	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	0.248198752121105	4	FACETS	1	0.976	1	1	0.996	1	CLONAL	4	TRUE	2	0.307652668217272	4		549	637	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449600	187449600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781532443	NA	P-0049112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	33	269	0	ENST00000232014.4:c.280C>T	p.Arg94Trp	p.R94W	ENST00000232014	NM_001130845.1	94	Cgg/Tgg	4/10	0.248198752121105	4	FACETS	0.495	0.402	0.6	0.247	0.201	0.3	SUBCLONAL	1	TRUE	2	0.307652668217272	4		269	567	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380277	+	inframe_insertion	In_Frame_Ins	INS	-	-	GACCTGCTGTGTCGAGAATATCCAAGA	novel	NA	P-0049113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	46	420	0	ENST00000311936.3:c.155_181dup	p.Leu52_Gly60dup	p.L52_G60dup	ENST00000311936	NM_004985.3	52	caa/cTCTTGGATATTCTCGACACAGCAGGTCaa	3/5	1	2	FACETS	0.495	0.417	0.581	0.495	0.417	0.581	SUBCLONAL	1	TRUE	1	0.409496653398762	2		420	454	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30047522	30047522	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	68	344	0	ENST00000331968.5:c.2479C>G	p.Arg827Gly	p.R827G	ENST00000331968	NM_002742.2	827	Cgc/Ggc	17/18	1	2	FACETS	0.954	0.836	1	0.954	0.836	1	CLONAL	1	TRUE	1	0.409496653398762	2		344	348	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443695	29443695	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs863225281	NA	P-0121453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	89	505	0	ENST00000389048.3:c.3522C>A	p.Phe1174Leu	p.F1174L	ENST00000389048	NM_004304.4	1174	ttC/ttA	23/29	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	NA	1	0.454206639854975	2		505	277	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879855	44879855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	83	137	0	ENST00000377967.4:c.444G>A	p.Trp148Ter	p.W148*	ENST00000377967	NM_021140.2	148	tgG/tgA	6/29	1	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.686351055924206	1		137	148	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023122	31023128	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCTCA	TGGCTCA	GG	novel	NA	P-0049117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	145	534	1	ENST00000375687.4:c.2607_2613delinsGG	p.Gly870ValfsTer8	p.G870Vfs*8	ENST00000375687	NM_015338.5	869	ggTGGCTCA/ggGG	13/13	1	2	FACETS	0.702	0.643	0.763	0.702	0.643	0.763	SUBCLONAL	1	TRUE	1	0.686351055924206	2		535	602	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0049118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	194	351	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.674711412860354	2		351	476	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0049118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	283	503	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.674711412860354	2		503	718	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098800	178098800	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	744	578	0	ENST00000397062.3:c.245A>G	p.Glu82Gly	p.E82G	ENST00000397062	NM_006164.4	82	gAa/gGa	2/5	1	2	FACETS	0.873	0.848	0.898	1	0.998	1	CLONAL	2	TRUE	1	0.674711412860354	2		578	1263	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419951	41419951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	225	544	0	ENST00000373198.4:c.370G>A	p.Val124Met	p.V124M	ENST00000373198	NM_133170.3	124	Gtg/Atg	3/32	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.674711412860354	2		544	643	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971194	21971194	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	240	479	0	ENST00000304494.5:c.164del	p.Gly55AlafsTer91	p.G55Afs*91	ENST00000304494	NM_000077.4	55	gGc/gc	2/3	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.674711412860354	2		479	679	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253850	30253850	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751979681	NA	P-0049118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	247	503	0	ENST00000307677.4:c.604G>A	p.Glu202Lys	p.E202K	ENST00000307677	NM_138578.1	202	Gag/Aag	3/3	1	2	FACETS	0.892	0.836	0.949	0.892	0.836	0.949	CLONAL	1	TRUE	1	0.674711412860354	2		503	821	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123674	46123674	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	111	262	0	ENST00000334344.6:c.55T>G	p.Phe19Val	p.F19V	ENST00000334344	NM_152641.2	19	Ttc/Gtc	1/21	1	2	FACETS	0.924	0.84	1	0.924	0.84	1	CLONAL	1	TRUE	1	0.674711412860354	2		262	356	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031937	10031937	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	178	693	0	ENST00000330684.3:c.886A>T	p.Ile296Phe	p.I296F	ENST00000330684	NM_001134407.1	296	Att/Ttt	3/13	1	2	FACETS	0.903	0.837	0.971	0.903	0.837	0.971	CLONAL	1	TRUE	1	0.674711412860354	2		693	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577101	7577109	+	inframe_deletion	In_Frame_Del	DEL	CCCAGGACA	CCCAGGACA	-	novel	NA	P-0049118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	354	710	0	ENST00000269305.4:c.829_837del	p.Cys277_Gly279del	p.C277_G279del	ENST00000269305	NM_001126112.2	277	TGTCCTGGG/-	8/11	0.674711412860354	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.674711412860354	1		710	663	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912242	32912258	+	frameshift_variant	Frame_Shift_Del	DEL	AACTTCTGCAGAGGTAC	AACTTCTGCAGAGGTAC	-	novel	NA	P-0049119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	151	370	0	ENST00000380152.3:c.3751_3767del	p.Thr1251SerfsTer8	p.T1251Sfs*8	ENST00000380152		1250	gaAACTTCTGCAGAGGTACat/gaat	11/27	1	2	FACETS	0.969	0.892	1	0.969	0.892	1	CLONAL	1	TRUE	1	0.622048122278915	2		370	501	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000359	42000359	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	122	281	0	ENST00000219905.7:c.2378A>T	p.Lys793Met	p.K793M	ENST00000219905	NM_001164273.1	793	aAg/aTg	7/24	1	2	FACETS	0.95	0.866	1	0.95	0.866	1	CLONAL	1	TRUE	1	0.622048122278915	2		281	413	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134688	2134688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778740	NA	P-0049119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	263	652	2	ENST00000219476.3:c.4465G>A	p.Ala1489Thr	p.A1489T	ENST00000219476	NM_000548.3	1489	Gca/Aca	34/42	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.622048122278915	2		654	801	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134505	30134505	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	89	208	0	ENST00000263025.4:c.26G>T	p.Gly9Val	p.G9V	ENST00000263025	NM_002746.2	9	gGc/gTc	1/9	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.622048122278915	2		208	282	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	87	301	0				ENST00000310581	NM_198253.2	-/1132			0.338514863947956	1	FACETS	0.578	0.524	0.632	0.578	0.524	0.632	INDETERMINATE	1	TRUE	0	0.889141380461614	1		301	188	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577560	7577560	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520002	NA	P-0049120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	260	464	0	ENST00000269305.4:c.721T>C	p.Ser241Pro	p.S241P	ENST00000269305	NM_001126112.2	241	Tcc/Ccc	7/11	0.889141380461614	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.889141380461614	1		464	299	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692980	89692980	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060500126	NA	P-0049120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	278	366	0	ENST00000371953.3:c.464A>G	p.Tyr155Cys	p.Y155C	ENST00000371953	NM_000314.4	155	tAt/tGt	5/9	0.889141380461614	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.889141380461614	1		366	318	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172103	99172103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1193458054	NA	P-0049120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	191	440	1	ENST00000074304.5:c.1669G>A	p.Glu557Lys	p.E557K	ENST00000074304	NM_001134224.1	557	Gag/Aag	17/26	1	2	FACETS	0.985	0.922	1	0.985	0.922	1	CLONAL	1	TRUE	1	0.889141380461614	2		441	436	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238509	142238509	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0049120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	97	166	0	ENST00000350721.4:c.4382+2T>C		p.X1461_splice	ENST00000350721	NM_001184.3	1461			1	2	FACETS	0.866	0.785	0.948	0.866	0.785	0.948	CLONAL	1	TRUE	1	0.889141380461614	2		166	252	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502259	186502259	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	169	241	0	ENST00000323963.5:c.68T>A	p.Val23Asp	p.V23D	ENST00000323963		23	gTc/gAc	2/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.889141380461614	2		241	342	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0049122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	156	351	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.295294893448352	2	FACETS	0.968	0.891	1	0.968	0.891	1	CLONAL	2	TRUE	0	0.29	2		351	556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577035	7577036	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0049122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	108	533	0	ENST00000269305.4:c.902dup	p.Gly302ArgfsTer4	p.G302Rfs*4	ENST00000269305	NM_001126112.2	301	cca/ccCa	8/11	0.295294893448352	1	FACETS	0.931	0.836	1	0.931	0.836	1	CLONAL	1	TRUE	0	0.29	1		533	684	SUCCESS
APC	324	MSKCC	GRCh37	5	112175162	112175162	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561588104	NA	P-0049122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	84	181	0	ENST00000257430.4:c.3871C>T	p.Gln1291Ter	p.Q1291*	ENST00000257430	NM_000038.5	1291	Cag/Tag	16/16	0.285332881895197	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	2	TRUE	0	0.29	2		181	284	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912188	114912188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	125	437	0	ENST00000543371.1:c.1258C>T	p.Arg420Trp	p.R420W	ENST00000543371	NM_001198531.1	420	Cgg/Tgg	11/14	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.29	2		437	770	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950736	79950736	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs2405877	NA	P-0049122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	21	96	2	ENST00000265081.6:c.190C>G	p.Pro64Ala	p.P64A	ENST00000265081	NM_002439.4	64	Cca/Gca	1/24	0.285332881895197	2	FACETS	1	0.854	1	0.566	0.441	0.707	CLONAL	1	TRUE	0	0.29	2		98	128	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484151	50484151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs575681571	NA	P-0049122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	83	458	0	ENST00000394963.4:c.1001G>A	p.Arg334Gln	p.R334Q	ENST00000394963	NM_003076.4	334	cGg/cAg	8/13	0.0852765973659819	3	FACETS	0.862	0.76	0.972	0.431	0.38	0.486	INDETERMINATE	1	TRUE	1	0.29	3		458	760	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	18	301	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.923	0.696	1	0.923	0.696	1	CLONAL	1	TRUE	1	0.15	2		301	260	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	90	678	0	ENST00000269305.4:c.379T>C	p.Ser127Pro	p.S127P	ENST00000269305	NM_001126112.2	127	Tcc/Ccc	5/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.15	2		678	986	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942835	44942835	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	37	229	0	ENST00000377967.4:c.3416del	p.Pro1139GlnfsTer19	p.P1139Qfs*19	ENST00000377967	NM_021140.2	1139	Cca/ca	23/29	1	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.15	1		229	349	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983019	201983019	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	53	751	1	ENST00000359651.3:c.868G>T	p.Glu290Ter	p.E290*	ENST00000359651		290	Gag/Tag	7/8	1	2	FACETS	0.895	0.761	1	0.895	0.761	1	CLONAL	1	TRUE	1	0.15	2		752	790	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0049125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	183	347	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.252606226685114	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.252606226685114	3		347	662	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0049125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	69	302	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.153273844553027	5	FACETS	0.919	0.804	1	0.612	0.536	0.695	CLONAL	2	TRUE	2	0.252606226685114	5		302	410	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913273	NA	P-0049125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	93	340	0	ENST00000263967.3:c.1624G>C	p.Glu542Gln	p.E542Q	ENST00000263967	NM_006218.2	542	Gaa/Caa	10/21	0.153273844553027	5	FACETS	0.884	0.792	0.98	0.884	0.792	0.98	CLONAL	3	TRUE	2	0.252606226685114	5		340	383	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0049125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	246	761	0	ENST00000269305.4:c.383del	p.Pro128LeufsTer42	p.P128Lfs*42	ENST00000269305	NM_001126112.2	128	cCt/ct	5/11	0.252606226685114	4	FACETS	1	0.969	1	0.708	0.662	0.757	CLONAL	2	TRUE	1	0.252606226685114	4		761	1148	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560838	9560838	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	49	323	0	ENST00000353224.5:c.944C>T	p.Ser315Phe	p.S315F	ENST00000353224	NM_177990.2	315	tCc/tTc	4/10	0.153273844553027	5	FACETS	0.772	0.653	0.904	0.257	0.217	0.302	CLONAL	1	TRUE	2	0.252606226685114	5		323	693	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532627	187532627	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	42	284	0	ENST00000441802.2:c.9766A>C	p.Ser3256Arg	p.S3256R	ENST00000441802	NM_005245.3	3256	Agt/Cgt	14/27	0.129602576274164	5	FACETS	0.957	0.799	1	0.319	0.266	0.378	INDETERMINATE	1	TRUE	2	0.252606226685114	5		284	479	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554844	106554844	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	37	294	0	ENST00000369096.4:c.1961C>G	p.Ser654Cys	p.S654C	ENST00000369096	NM_001198.3	654	tCt/tGt	7/7	0.250901333412481	3	FACETS	0.579	0.476	0.694	0.289	0.238	0.347	SUBCLONAL	1	TRUE	1	0.252606226685114	3		294	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0049127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	263	523	2	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.827406173670101	1	FACETS	0.986	0.947	1	0.986	0.947	1	CLONAL	1	TRUE	0	0.844465189331935	1		525	365	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117347	115117347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049127-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	135	328	0	ENST00000257566.3:c.827C>T	p.Thr276Ile	p.T276I	ENST00000257566	NM_016569.3	276	aCt/aTt	4/8	0.844465189331935	3	FACETS	0.961	0.88	1	0.481	0.44	0.523	CLONAL	1	TRUE	1	0.844465189331935	3		328	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0049128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	80	529	1	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	1	2	FACETS	0.835	0.734	0.942	0.835	0.734	0.942	CLONAL	1	TRUE	1	0.27	2		530	710	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0049128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	27	364	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	0.374	0.296	0.463	0.374	0.296	0.463	SUBCLONAL	1	TRUE	1	0.27	2		364	535	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023151	27023179	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	-	novel	NA	P-0049128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	16	43	0	ENST00000324856.7:c.267_295del	p.Ser90ProfsTer11	p.S90Pfs*11	ENST00000324856	NM_006015.4	86	gGCGGAGCCGGCAGCGGCGGCGGGCCCGGC/g	1/20	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.27	2		43	81	SUCCESS
AR	367	MSKCC	GRCh37	X	66943552	66943552	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137852578	NA	P-0049144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	190	173	0	ENST00000374690.3:c.2632A>G	p.Thr878Ala	p.T878A	ENST00000374690	NM_000044.3	878	Act/Gct	8/8	0.841283655306276	4	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.841283655306276	4		173	722	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242511	55242511	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913418	NA	P-0049144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	128	284	0	ENST00000275493.2:c.2281G>T	p.Asp761Tyr	p.D761Y	ENST00000275493	NM_005228.3	761	Gat/Tat	19/28	0.841283655306276	5	FACETS	0.918	0.832	1	0.306	0.277	0.336	CLONAL	1	TRUE	2	0.841283655306276	5		284	750	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477854	140477854	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	508	444	0	ENST00000288602.6:c.1454T>G	p.Leu485Trp	p.L485W	ENST00000288602	NM_004333.4	485	tTg/tGg	12/18	0.841283655306276	5	FACETS	0.982	0.947	1	0.982	0.947	1	CLONAL	3	TRUE	2	0.841283655306276	5		444	927	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061242	38061247	+	inframe_deletion	In_Frame_Del	DEL	GTCCGG	GTCCGG	-	novel	NA	P-0049144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	280	553	0	ENST00000250448.2:c.742_747del	p.Pro248_Asp249del	p.P248_D249del	ENST00000250448	NM_004496.3	248	CCGGAC/-	2/2	0.841283655306276	3	FACETS	1	0.984	1	0.558	0.525	0.59	CLONAL	1	TRUE	1	0.841283655306276	3		553	848	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821412	72821431	+	frameshift_variant	Frame_Shift_Del	DEL	TGCGAGGTAGATGCGGTGCT	TGCGAGGTAGATGCGGTGCT	-	novel	NA	P-0049144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	309	478	0	ENST00000268489.5:c.10744_10763del	p.Ser3582ValfsTer77	p.S3582Vfs*77	ENST00000268489	NM_006885.3	3582	AGCACCGCATCTACCTCGCAg/g	10/10	0.841283655306276	3	FACETS	0.942	0.899	0.984	0.942	0.899	0.984	CLONAL	2	TRUE	1	0.841283655306276	3		478	554	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602760	55602760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553893452	NA	P-0049144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	277	325	0	ENST00000288135.5:c.2581G>A	p.Glu861Lys	p.E861K	ENST00000288135	NM_000222.2	861	Gag/Aag	18/21	0.841283655306276	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.841283655306276	3		325	462	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678757	52678757	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	208	369	1	ENST00000394830.3:c.862G>T	p.Glu288Ter	p.E288*	ENST00000394830	NM_018313.4	288	Gaa/Taa	9/30	0.671644183493701	2	FACETS	0.938	0.891	0.985	0.938	0.891	0.985	CLONAL	2	TRUE	0	0.671644183493701	2		370	330	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041074	180041076	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs587776833	NA	P-0049145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	212	736	0	ENST00000261937.6:c.3323_3325del	p.Phe1108del	p.F1108del	ENST00000261937	NM_182925.4	1108	tTCTct/tct	24/30	0.608032619589247	4	FACETS	0.911	0.845	0.98	0.456	0.422	0.49	CLONAL	1	TRUE	2	0.671644183493701	4		736	1158	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333965	70333965	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	216	273	0	ENST00000373644.4:c.1870T>G	p.Cys624Gly	p.C624G	ENST00000373644	NM_030625.2	624	Tgt/Ggt	2/12	0.671644183493701	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.671644183493701	2		273	309	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581361	48581361	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	122	385	0	ENST00000342988.3:c.665C>T	p.Thr222Ile	p.T222I	ENST00000342988	NM_005359.5	222	aCa/aTa	5/12	0.671644183493701	3	FACETS	1	0.939	1	0.521	0.473	0.57	CLONAL	1	TRUE	1	0.671644183493701	3		385	466	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096873	11096873	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	311	821	3	ENST00000358026.2:c.364T>A	p.Ser122Thr	p.S122T	ENST00000358026	NM_001128849.1	122	Tcg/Acg	4/36	0.671644183493701	2	FACETS	1	0.965	1	0.513	0.485	0.541	CLONAL	1	TRUE	0	0.671644183493701	2		824	903	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138620	11138620	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	321	445	0	ENST00000358026.2:c.3376C>A	p.Leu1126Ile	p.L1126I	ENST00000358026	NM_001128849.1	1126	Ctt/Att	24/36	0.671644183493701	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.671644183493701	2		445	474	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437179	52437179	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	339	556	0	ENST00000460680.1:c.1865del	p.Leu622Ter	p.L622*	ENST00000460680	NM_004656.3	622	tTg/tg	14/17	0.671644183493701	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.671644183493701	2		556	501	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427637	72427637	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	140	382	1	ENST00000477973.2:c.853C>T	p.Gln285Ter	p.Q285*	ENST00000477973	NM_012234.5	285	Cag/Tag	4/4	0.671644183493701	2	FACETS	1	0.941	1	0.513	0.472	0.556	CLONAL	1	TRUE	0	0.671644183493701	2		383	406	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191560	10191570	+	protein_altering_variant	In_Frame_Del	DEL	TACGAAGATCT	TACGAAGATCT	AA	novel	NA	P-0049145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	307	484	2	ENST00000256474.2:c.553_563delinsAA	p.Tyr185_Leu188delinsLys	p.Y185_L188delinsK	ENST00000256474	NM_000551.3	185	TACGAAGATCTg/AAg	3/3	0.671644183493701	2	FACETS	0.981	0.941	1	0.981	0.941	1	CLONAL	2	TRUE	0	0.671644183493701	2		486	466	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0049146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	85	302	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.34	2		302	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0049146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	87	523	2	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.296068223252158	1	FACETS	0.883	0.785	0.987	0.883	0.785	0.987	CLONAL	1	TRUE	0	0.34	1		525	481	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0049146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	45	282	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.549	0.461	0.646	0.549	0.461	0.646	SUBCLONAL	1	TRUE	1	0.34	2		282	482	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013741	12013741	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	45	271	0	ENST00000353533.5:c.683G>A	p.Arg228Lys	p.R228K	ENST00000353533	NM_003010.3	228	aGa/aAa	6/11	0.296068223252158	1	FACETS	0.662	0.558	0.775	0.662	0.558	0.775	SUBCLONAL	1	TRUE	0	0.34	1		271	332	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828134	243828134	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	80	369	0	ENST00000263826.5:c.224G>C	p.Arg75Thr	p.R75T	ENST00000263826	NM_005465.4	75	aGa/aCa	3/13	0.227002097691717	5	FACETS	0.898	0.79	1	0.225	0.197	0.254	CLONAL	1	TRUE	1	0.34	5		369	791	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156182	119156182	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs376094293	NA	P-0049146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	95	445	0	ENST00000264033.4:c.1847A>C	p.Asn616Thr	p.N616T	ENST00000264033	NM_005188.3	616	aAc/aCc	11/16	NA	2	FACETS	0.984	0.878	1			1	INDETERMINATE	1	TRUE	NA	0.34	2		445	568	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445197	49445197	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	102	802	0	ENST00000301067.7:c.2269G>A	p.Glu757Lys	p.E757K	ENST00000301067	NM_003482.3	757	Gag/Aag	10/54	0.110222772186677	3	FACETS	0.985	0.881	1	0.492	0.44	0.547	INDETERMINATE	1	TRUE	1	0.34	3		802	713	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473627	67473627	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	107	554	0	ENST00000327367.4:c.707C>G	p.Ser236Cys	p.S236C	ENST00000327367	NM_005902.3	236	tCc/tGc	6/9	0.296068223252158	1	FACETS	0.966	0.869	1	0.966	0.869	1	CLONAL	1	TRUE	0	0.34	1		554	541	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862889	117862889	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	93	395	0	ENST00000297338.2:c.1588G>C	p.Glu530Gln	p.E530Q	ENST00000297338	NM_006265.2	530	Gag/Cag	12/14	0.296068223252158	6	FACETS	1	0.954	1	0.19	0.168	0.213	CLONAL	1	TRUE	0	0.34	6		395	806	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0049148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	57	470	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.136759778837321	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.16	1		470	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0049148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	27	932	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.395	0.313	0.49	0.395	0.313	0.49	SUBCLONAL	1	TRUE	1	0.16	2		934	854	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820309	139820309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142412558	NA	P-0049148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	53	579	0	ENST00000247668.2:c.1462G>A	p.Asp488Asn	p.D488N	ENST00000247668	NM_021138.3	488	Gat/Aat	11/11	0.136759778837321	1	FACETS	0.732	0.622	0.852	0.732	0.622	0.852	SUBCLONAL	1	TRUE	0	0.16	1		579	833	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796754	135796754	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203434	NA	P-0049148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	22	222	0	ENST00000298552.3:c.733C>T	p.Arg245Ter	p.R245*	ENST00000298552	NM_001162426.1	245	Cga/Tga	8/23	1	2	FACETS	0.743	0.575	0.939	0.743	0.575	0.939	CLONAL	1	TRUE	1	0.16	2		222	370	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0049148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	43	400	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	1	2	FACETS	0.908	0.759	1	0.908	0.759	1	CLONAL	1	TRUE	1	0.16	2		400	592	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467924	50467924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	39	516	0	ENST00000331340.3:c.1159G>A	p.Glu387Lys	p.E387K	ENST00000331340	NM_006060.4	387	Gag/Aag	8/8	1	2	FACETS	0.771	0.638	0.921	0.771	0.638	0.921	CLONAL	1	TRUE	1	0.16	2		516	632	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259301	89259301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	33	371	0	ENST00000336596.2:c.445G>A	p.Asp149Asn	p.D149N	ENST00000336596	NM_005233.5	149	Gat/Aat	3/17	0.136759778837321	1	FACETS	0.789	0.642	0.955	0.789	0.642	0.955	CLONAL	1	TRUE	0	0.16	1		371	481	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098450	11098450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886054151	NA	P-0049148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	46	382	0	ENST00000358026.2:c.968C>T	p.Ser323Leu	p.S323L	ENST00000358026	NM_001128849.1	323	tCg/tTg	6/36	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.16	2		382	491	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186751	108186751	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1448711296	NA	P-0049148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	49	380	0	ENST00000278616.4:c.6109G>A	p.Glu2037Lys	p.E2037K	ENST00000278616	NM_000051.3	2037	Gaa/Aaa	42/63	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.16	2		380	607	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862851	9862851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555483699	NA	P-0049148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	60	589	0	ENST00000330684.3:c.2452G>A	p.Ala818Thr	p.A818T	ENST00000330684	NM_001134407.1	818	Gcg/Acg	12/13	1	2	FACETS	0.899	0.773	1	0.899	0.773	1	CLONAL	1	TRUE	1	0.16	2		589	834	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827349	72827349	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	59	630	0	ENST00000268489.5:c.9232C>G	p.Gln3078Glu	p.Q3078E	ENST00000268489	NM_006885.3	3078	Caa/Gaa	9/10	1	2	FACETS	0.785	0.674	0.908	0.785	0.674	0.908	CLONAL	1	TRUE	1	0.16	2		630	939	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249711	110249711	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1190671294	NA	P-0049148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	89	791	0	ENST00000374672.4:c.964G>C	p.Glu322Gln	p.E322Q	ENST00000374672	NM_004235.4	322	Gag/Cag	3/5	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.16	2		791	1039	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827295	72827295	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	48	568	0	ENST00000268489.5:c.9286C>T	p.Gln3096Ter	p.Q3096*	ENST00000268489	NM_006885.3	3096	Cag/Tag	9/10	1	2	FACETS	0.692	0.583	0.813	0.692	0.583	0.813	SUBCLONAL	1	TRUE	1	0.16	2		568	867	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102033286	102033286	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201865017	NA	P-0049148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	60	482	0	ENST00000282441.5:c.672G>A	p.Met224Ile	p.M224I	ENST00000282441	NM_001130145.2	224	atG/atA	3/9	1	2	FACETS	0.842	0.723	0.971	0.842	0.723	0.971	CLONAL	1	TRUE	1	0.16	2		482	891	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102098267	102098267	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	68	444	0	ENST00000282441.5:c.1231C>T	p.Arg411Ter	p.R411*	ENST00000282441	NM_001130145.2	411	Cga/Tga	8/9	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.16	2		444	702	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022483	12022483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	68	675	0	ENST00000396373.4:c.589G>A	p.Glu197Lys	p.E197K	ENST00000396373	NM_001987.4	197	Gag/Aag	5/8	1	2	FACETS	0.933	0.81	1	0.933	0.81	1	CLONAL	1	TRUE	1	0.16	2		675	911	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845856	72845856	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	50	527	0	ENST00000268489.5:c.3611C>G	p.Ser1204Cys	p.S1204C	ENST00000268489	NM_006885.3	1204	tCt/tGt	6/10	1	2	FACETS	0.868	0.735	1	0.868	0.735	1	CLONAL	1	TRUE	1	0.16	2		527	720	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227852	36227852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751187730	NA	P-0049148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	83	823	0	ENST00000222270.7:c.7337G>A	p.Arg2446Gln	p.R2446Q	ENST00000222270	NM_014727.1	2446	cGa/cAa	32/37	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.16	2		823	1037	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645961	215645961	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	48	363	0	ENST00000260947.4:c.637G>T	p.Glu213Ter	p.E213*	ENST00000260947	NM_000465.2	213	Gaa/Taa	4/11	1	2	FACETS	0.984	0.831	1	0.984	0.831	1	CLONAL	1	TRUE	1	0.16	2		363	610	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400336	225400336	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0049148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	29	197	0	ENST00000264414.4:c.287C>G	p.Ser96Ter	p.S96*	ENST00000264414	NM_003590.4	96	tCa/tGa	3/16	1	2	FACETS	1	0.806	1	1	0.806	1	CLONAL	1	TRUE	1	0.16	2		197	361	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920134	1920134	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	51	579	0	ENST00000382891.5:c.1194G>C	p.Lys398Asn	p.K398N	ENST00000382891	NM_133335.3	398	aaG/aaC	5/22	1	2	FACETS	0.729	0.617	0.851	0.729	0.617	0.851	SUBCLONAL	1	TRUE	1	0.16	2		579	875	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553602	106553602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1562174876	NA	P-0049148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	47	350	0	ENST00000369096.4:c.1567G>A	p.Ala523Thr	p.A523T	ENST00000369096	NM_001198.3	523	Gcc/Acc	5/7	0.3	2	FACETS	1	0.908	1			1	CLONAL	1	TRUE	NA	0.16	2		350	528	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859839	151859842	+	frameshift_variant	Frame_Shift_Del	DEL	CTTG	CTTG	-	novel	NA	P-0049148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	36	292	0	ENST00000262189.6:c.10820_10823del	p.Thr3607LysfsTer22	p.T3607Kfs*22	ENST00000262189	NM_170606.2	3607	aCAAGa/aa	43/59	1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	1	0.16	2		292	436	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859888	117859888	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	23	264	0	ENST00000297338.2:c.1747G>C	p.Glu583Gln	p.E583Q	ENST00000297338	NM_006265.2	583	Gag/Cag	14/14	1	2	FACETS	0.79	0.615	0.992	0.79	0.615	0.992	CLONAL	1	TRUE	1	0.16	2		264	364	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864267	117864267	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	30	322	0	ENST00000297338.2:c.1390G>C	p.Asp464His	p.D464H	ENST00000297338	NM_006265.2	464	Gat/Cat	11/14	1	2	FACETS	0.667	0.536	0.817	0.667	0.536	0.817	SUBCLONAL	1	TRUE	1	0.16	2		322	562	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742031	145742031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1387642543	NA	P-0049148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	75	660	0	ENST00000428558.2:c.472G>A	p.Glu158Lys	p.E158K	ENST00000428558	NM_004260.3	158	Gag/Aag	5/22	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.16	2		660	933	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0049149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	230	313	0	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	0.393540510978749	2	FACETS	0.95	0.901	0.999			1	CLONAL	3	TRUE	NA	0.393540510978749	2		313	410	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873811	35873811	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	119	356	0	ENST00000216797.5:c.40del	p.Glu14ArgfsTer7	p.E14Rfs*7	ENST00000216797	NM_020529.2	14	Gag/ag	1/6	0.213869493134534	3	FACETS	0.912	0.83	0.996	0.912	0.83	0.996	INDETERMINATE	2	TRUE	1	0.393540510978749	3		356	397	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933926	39933926	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	277	640	1	ENST00000378444.4:c.673C>T	p.Gln225Ter	p.Q225*	ENST00000378444	NM_001123385.1	225	Cag/Tag	4/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.812627229076368	2		641	628	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809029	36809029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	235	551	0	ENST00000373129.3:c.1025G>A	p.Ser342Asn	p.S342N	ENST00000373129	NM_032017.1	342	aGt/aAt	11/12	1	2	FACETS	0.927	0.871	0.984	0.927	0.871	0.984	CLONAL	1	TRUE	1	0.812627229076368	2		551	624	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450384	50450384	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	31	474	0	ENST00000331340.3:c.568G>A	p.Gly190Ser	p.G190S	ENST00000331340	NM_006060.4	190	Ggc/Agc	5/8	1	2	FACETS	0.133	0.107	0.163	0.133	0.107	0.163	SUBCLONAL	1	TRUE	1	0.812627229076368	2		474	574	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0049286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	154	327	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.988	0.908	1	0.988	0.908	1	CLONAL	1	TRUE	1	0.507573963369462	2		327	614	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0049286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	113	290	1	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.998	0.904	1	0.998	0.904	1	CLONAL	1	TRUE	1	0.507573963369462	2		291	446	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0049286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	106	286	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.974	0.879	1	0.974	0.879	1	CLONAL	1	TRUE	1	0.507573963369462	2		286	429	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs749415085	NA	P-0049286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	126	430	0	ENST00000263967.3:c.112C>A	p.Arg38Ser	p.R38S	ENST00000263967	NM_006218.2	38	Cgt/Agt	2/21	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.507573963369462	2		430	478	SUCCESS
REL	5966	MSKCC	GRCh37	2	61148906	61148924	+	frameshift_variant	Frame_Shift_Del	DEL	TTGTTTTCTCATGATGCAG	TTGTTTTCTCATGATGCAG	-	novel	NA	P-0049286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	78	261	0	ENST00000295025.8:c.1100_1118del	p.Phe367Ter	p.F367*	ENST00000295025	NM_002908.2	366	TTGTTTTCTCATGATGCAGtt/tt	11/11	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.507573963369462	2		261	291	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0049287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	44	339	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.248133875602619	2		340	340	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625386	69625386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782272422	NA	P-0049287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	43	675	1	ENST00000334134.2:c.407C>T	p.Thr136Met	p.T136M	ENST00000334134	NM_005247.2	136	aCg/aTg	3/3	1	2	FACETS	0.458	0.382	0.543	0.458	0.382	0.543	SUBCLONAL	1	TRUE	1	0.248133875602619	2		676	756	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032833	30032833	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	56	359	0	ENST00000338641.4:c.208G>A	p.Asp70Asn	p.D70N	ENST00000338641	NM_000268.3	70	Gac/Aac	2/16	1	2	FACETS	0.873	0.749	1	0.873	0.749	1	CLONAL	1	TRUE	1	0.248133875602619	2		359	517	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140507833	140507833	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	41	485	0	ENST00000288602.6:c.638A>C	p.Asp213Ala	p.D213A	ENST00000288602	NM_004333.4	213	gAt/gCt	5/18	1	2	FACETS	0.587	0.488	0.697	0.587	0.488	0.697	SUBCLONAL	1	TRUE	1	0.248133875602619	2		485	563	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270487	98270487	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	63	479	0	ENST00000331920.6:c.157C>G	p.Pro53Ala	p.P53A	ENST00000331920	NM_000264.3	53	Ccc/Gcc	1/24	1	2	FACETS	0.998	0.864	1	0.998	0.864	1	CLONAL	1	TRUE	1	0.248133875602619	2		479	509	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039391	47039399	+	inframe_deletion	In_Frame_Del	DEL	GACCCAACT	GACCCAACT	-	novel	NA	P-0049287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	85	350	0	ENST00000377604.3:c.1016_1024del	p.Thr339_Leu341del	p.T339_L341del	ENST00000377604	NM_001204468.1	338	caGACCCAACTg/cag	10/24	1	1	FACETS	0.836	0.745	0.932	1	0.982	1	CLONAL	2	TRUE	0	0.248133875602619	1		350	359	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0049288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	173	347	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.25285023916579	1	FACETS	0.889	0.822	0.96	1	0.992	1	CLONAL	2	TRUE	0	0.25285023916579	1		347	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0049288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	99	696	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.25285023916579	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	0	0.25285023916579	1		697	675	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937709	44937709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	81	256	1	ENST00000377967.4:c.2897C>T	p.Pro966Leu	p.P966L	ENST00000377967	NM_021140.2	966	cCt/cTt	19/29	1	1	FACETS	0.965	0.86	1	1	0.985	1	CLONAL	2	TRUE	0	0.25285023916579	1		257	290	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056314	26056314	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0049288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	77	426	0	ENST00000343677.2:c.343G>T	p.Glu115Ter	p.E115*	ENST00000343677	NM_005319.3	115	Gaa/Taa	1/1	0.237016296061721	1	FACETS	0.942	0.828	1	0.942	0.828	1	CLONAL	1	TRUE	0	0.25285023916579	1		426	565	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805921	32805921	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	91	753	0	ENST00000374899.4:c.90G>C	p.Leu30Phe	p.L30F	ENST00000374899	NM_018833.2	30	ttG/ttC	2/12	0.25285023916579	3	FACETS	0.769	0.681	0.863	0.384	0.34	0.432	SUBCLONAL	1	TRUE	1	0.25285023916579	3		753	1055	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139440198	139440198	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	18	131	0	ENST00000277541.6:c.41T>A	p.Leu14Gln	p.L14Q	ENST00000277541	NM_017617.3	14	cTg/cAg	1/34	0.25285023916579	1	FACETS	0.763	0.578	0.978	0.763	0.578	0.978	CLONAL	1	TRUE	0	0.25285023916579	1		131	163	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0049289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	114	799	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	0.956	0.861	1	0.956	0.861	1	CLONAL	1	FALSE	1	0.288994970917612	2		799	825	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0049290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	465	461	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.898405712248046	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.898405712248046	1		462	541	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0049290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	286	470	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.664396134604826	5	FACETS	1	0.99	1	0.31	0.291	0.329	CLONAL	1	TRUE	1	0.898405712248046	5		470	1206	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295274	1295274	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0049290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	255	698	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.975	0.921	1	0.975	0.921	1	CLONAL	1	TRUE	1	0.898405712248046	2		698	582	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623229	52623229	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0049290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	224	458	0	ENST00000394830.3:c.2822C>G	p.Ser941Ter	p.S941*	ENST00000394830	NM_018313.4	941	tCa/tGa	19/30	0.898405712248046	1	FACETS	0.981	0.945	1	0.981	0.945	1	CLONAL	1	TRUE	0	0.898405712248046	1		458	280	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038872	12038872	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	205	428	0	ENST00000396373.4:c.1165A>C	p.Met389Leu	p.M389L	ENST00000396373	NM_001987.4	389	Atg/Ctg	7/8	0.898405712248046	3	FACETS	0.916	0.853	0.981	0.458	0.426	0.491	CLONAL	1	TRUE	1	0.898405712248046	3		428	722	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440118	49440118	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	428	879	0	ENST00000301067.7:c.4508G>A	p.Ser1503Asn	p.S1503N	ENST00000301067	NM_003482.3	1503	aGc/aAc	16/54	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.898405712248046	2		879	948	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026025	14026025	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	180	342	0	ENST00000311895.7:c.985C>G	p.Leu329Val	p.L329V	ENST00000311895	NM_005236.2	329	Ctt/Gtt	6/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.898405712248046	2		342	383	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671459	30671459	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0049290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	439	939	0	ENST00000376406.3:c.5501A>C	p.Gln1834Pro	p.Q1834P	ENST00000376406	NM_014641.2	1834	cAg/cCg	10/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.898405712248046	2		939	975	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981687	70981687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	515	1155	3	ENST00000276594.2:c.409G>A	p.Asp137Asn	p.D137N	ENST00000276594	NM_024504.3	137	Gac/Aac	2/8	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.898405712248046	2		1158	1057	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344614	70344614	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	308	745	0	ENST00000374080.3:c.1975G>A	p.Asp659Asn	p.D659N	ENST00000374080		659	Gat/Aat	14/45	0.230669288803925	1	FACETS	0.521	0.494	0.548	0.521	0.494	0.548	INDETERMINATE	1	TRUE	0	0.898405712248046	1		745	725	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0049293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	115	456	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.789	0.711	0.872	0.789	0.711	0.872	SUBCLONAL	1	TRUE	1	0.36237240062064	2		456	804	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589619	67589630	+	inframe_deletion	In_Frame_Del	DEL	GAGAATATGATA	GAGAATATGATA	-	novel	NA	P-0049293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	46	388	0	ENST00000274335.5:c.1384_1395del	p.Glu462_Arg465del	p.E462_R465del	ENST00000274335		461	cGAGAATATGATAga/cga	10/15	1	2	FACETS	0.784	0.663	0.916	0.784	0.663	0.916	CLONAL	1	TRUE	1	0.36237240062064	2		388	324	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717722	89717724	+	inframe_deletion	In_Frame_Del	DEL	GTG	GTG	-	novel	NA	P-0049293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	100	562	0	ENST00000371953.3:c.747_749del	p.Cys250del	p.C250del	ENST00000371953	NM_000314.4	249	gtGTGt/gtt	7/9	0.36237240062064	1	FACETS	0.941	0.845	1	0.941	0.845	1	CLONAL	1	TRUE	0	0.36237240062064	1		562	480	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027817	48027817	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748574765	NA	P-0049293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	85	555	0	ENST00000234420.5:c.2695G>A	p.Glu899Lys	p.E899K	ENST00000234420	NM_000179.2	899	Gaa/Aaa	4/10	1	2	FACETS	0.836	0.741	0.938	0.836	0.741	0.938	CLONAL	1	TRUE	1	0.36237240062064	2		555	561	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189098	38189099	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0049293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	97	617	0	ENST00000317025.8:c.915_916del	p.Glu307IlefsTer7	p.E307Ifs*7	ENST00000317025	NM_023034.1	305	gcCCga/gcga	5/24	1	2	FACETS	0.814	0.726	0.907	0.814	0.726	0.907	CLONAL	1	TRUE	1	0.36237240062064	2		617	658	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0049327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	14	495	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.0907890838987551	3	FACETS	0.507	0.365	0.679	0.253	0.182	0.34	INDETERMINATE	1	TRUE	1	0.16	3		495	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0049327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	67	715	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.999	0.867	1	0.999	0.867	1	CLONAL	1	TRUE	1	0.16	2		715	838	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0049327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	18	211	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.859	0.647	1	0.859	0.647	1	CLONAL	1	TRUE	1	0.16	2		211	262	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624305	89624305	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	rs746128825	NA	P-0049327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	64	528	0	ENST00000371953.3:c.79T>A	p.Tyr27Asn	p.Y27N	ENST00000371953	NM_000314.4	27	Tat/Aat	1/9	0.0907890838987551	3	FACETS	1	0.969	1	0.728	0.631	0.834	INDETERMINATE	1	TRUE	1	0.16	3		528	593	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409892	63409892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	35	680	1	ENST00000330258.3:c.3275C>T	p.Pro1092Leu	p.P1092L	ENST00000330258	NM_152424.3	1092	cCt/cTt	2/2	1	2	FACETS	0.785	0.643	0.946	0.785	0.643	0.946	CLONAL	1	TRUE	1	0.16	2		681	557	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889148	76889148	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs122445106	NA	P-0049327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	20	434	0	ENST00000373344.5:c.4862C>T	p.Thr1621Met	p.T1621M	ENST00000373344	NM_000489.3	1621	aCg/aTg	18/35	1	2	FACETS	0.742	0.567	0.947	0.742	0.567	0.947	CLONAL	1	TRUE	1	0.16	2		434	337	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480601	123480601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1484550706	NA	P-0049327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	39	730	0	ENST00000371139.4:c.109G>A	p.Val37Met	p.V37M	ENST00000371139	NM_001114937.2	37	Gtg/Atg	1/4	1	2	FACETS	0.697	0.576	0.833	0.697	0.576	0.833	SUBCLONAL	1	TRUE	1	0.16	2		730	699	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0049329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	230	362	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		362	403	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	132	263	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		263	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0049329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	169	668	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		669	630	SUCCESS
APC	324	MSKCC	GRCh37	5	112175921	112175921	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0049329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	49	233	0	ENST00000257430.4:c.4630G>T	p.Glu1544Ter	p.E1544*	ENST00000257430	NM_000038.5	1544	Gaa/Taa	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		233	165	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782177	NA	P-0049329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	149	514	1	ENST00000269305.4:c.644G>A	p.Ser215Asn	p.S215N	ENST00000269305	NM_001126112.2	215	aGt/aAt	6/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		515	611	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0049330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	154	302	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.235379176198661	3	FACETS	1	0.947	1	1	0.99	1	CLONAL	3	TRUE	1	0.235379176198661	3		302	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578445	7578445	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	142	971	0	ENST00000269305.4:c.485T>A	p.Ile162Asn	p.I162N	ENST00000269305	NM_001126112.2	162	aTc/aAc	5/11	0.234013015047405	2	FACETS	0.801	0.731	0.875	0.801	0.731	0.875	CLONAL	2	TRUE	0	0.235379176198661	2		971	753	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435771	110435771	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775002025	NA	P-0049330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	66	312	1	ENST00000375856.3:c.2630C>T	p.Pro877Leu	p.P877L	ENST00000375856	NM_003749.2	877	cCg/cTg	1/2	0.0638271365523595	3	FACETS	1	0.887	1	1	0.887	1	INDETERMINATE	2	TRUE	1	0.235379176198661	3		313	309	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248240	59248240	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	40	91	0	ENST00000371222.2:c.503C>G	p.Pro168Arg	p.P168R	ENST00000371222	NM_002228.3	168	cCg/cGg	1/1	0.636076563241355	3	FACETS	1	0.931	1			1	CLONAL	1	FALSE	NA	0.668646500222952	3		91	135	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120478123	120478123	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	115	515	0	ENST00000256646.2:c.3627C>G	p.Phe1209Leu	p.F1209L	ENST00000256646	NM_024408.3	1209	ttC/ttG	22/34	0.662287739799622	4	FACETS	0.871	0.786	0.961	0.29	0.262	0.321	CLONAL	1	FALSE	1	0.668646500222952	4		515	659	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614820	23614820	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	116	448	0	ENST00000261584.4:c.3521G>C	p.Gly1174Ala	p.G1174A	ENST00000261584	NM_024675.3	1174	gGa/gCa	13/13	0.676580238643378	3	FACETS	0.663	0.598	0.732			1	SUBCLONAL	1	FALSE	NA	0.668646500222952	3		448	698	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	202	737	0	ENST00000269571.5:c.829G>A	p.Asp277Asn	p.D277N	ENST00000269571		277	Gac/Aac	7/27	0.643025822648076	5	FACETS	1	0.978	1			1	CLONAL	1	FALSE	NA	0.668646500222952	5		737	1062	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866671	37866671	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	222	752	0	ENST00000269571.5:c.838G>C	p.Glu280Gln	p.E280Q	ENST00000269571		280	Gag/Cag	7/27	0.643025822648076	5	FACETS	1	0.983	1			1	CLONAL	1	FALSE	NA	0.668646500222952	5		752	1126	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866719	37866719	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	222	705	0	ENST00000269571.5:c.886G>C	p.Val296Leu	p.V296L	ENST00000269571		296	Gtg/Ctg	7/27	0.643025822648076	5	FACETS	1	0.986	1			1	CLONAL	1	FALSE	NA	0.668646500222952	5		705	1082	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	285	399	0	ENST00000335508.6:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000335508	NM_012433.2	902	Gaa/Aaa	18/25	0.576228142762125	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	FALSE	1	0.668646500222952	4		399	457	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29083957	29083957	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	20	145	1	ENST00000328354.6:c.1560G>T	p.Lys520Asn	p.K520N	ENST00000328354	NM_007194.3	520	aaG/aaT	15/15	0.454677303243745	4	FACETS	0.916	0.711	1	0.458	0.355	0.574	CLONAL	1	FALSE	2	0.668646500222952	4		146	109	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	47	301	0				ENST00000310581	NM_198253.2	-/1132			0.587904060703503	1	FACETS	0.487	0.417	0.563	0.487	0.417	0.563	SUBCLONAL	1	FALSE	0	0.668646500222952	1		301	192	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918582	44918582	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	325	253	0	ENST00000377967.4:c.1065G>A	p.Trp355Ter	p.W355*	ENST00000377967	NM_021140.2	355	tgG/tgA	12/29	0.676580238643378	2	FACETS	1	0.995	1			1	CLONAL	2	FALSE	NA	0.668646500222952	2		253	405	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0049332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	54	412	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	1	2	FACETS	0.586	0.503	0.675	0.586	0.503	0.675	SUBCLONAL	1	TRUE	1	0.574181055604804	2		412	321	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591125	67591125	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	46	319	1	ENST00000274335.5:c.1718T>C	p.Leu573Pro	p.L573P	ENST00000274335		573	cTg/cCg	12/15	1	2	FACETS	0.694	0.59	0.806	0.694	0.59	0.806	SUBCLONAL	1	TRUE	1	0.574181055604804	2		320	231	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900329	101900329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	24	364	0	ENST00000374994.4:c.763C>T	p.Arg255Cys	p.R255C	ENST00000374994	NM_004612.2	255	Cgt/Tgt	4/9	1	2	FACETS	0.228	0.178	0.285	0.228	0.178	0.285	SUBCLONAL	1	TRUE	1	0.574181055604804	2		364	367	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259397	11259397	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	83	694	0	ENST00000361445.4:c.4171C>G	p.Arg1391Gly	p.R1391G	ENST00000361445	NM_004958.3	1391	Cga/Gga	28/58	1	2	FACETS	0.343	0.302	0.388	0.343	0.302	0.388	SUBCLONAL	1	TRUE	1	0.574181055604804	2		694	842	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147184	61147184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752907267	NA	P-0049332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	75	392	0	ENST00000295025.8:c.862G>A	p.Gly288Ser	p.G288S	ENST00000295025	NM_002908.2	288	Ggc/Agc	8/11	1	2	FACETS	0.764	0.674	0.859	0.764	0.674	0.859	SUBCLONAL	1	TRUE	1	0.574181055604804	2		392	342	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964100	28964100	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	85	492	0	ENST00000282397.4:c.1802A>G	p.His601Arg	p.H601R	ENST00000282397	NM_002019.4	601	cAc/cGc	13/30	1	2	FACETS	0.783	0.697	0.874	0.783	0.697	0.874	SUBCLONAL	1	TRUE	1	0.574181055604804	2		492	378	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590756	95590756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746886465	NA	P-0049332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	56	355	1	ENST00000393063.1:c.1153C>T	p.Arg385Cys	p.R385C	ENST00000393063	NM_030621.3	385	Cgc/Tgc	9/28	1	2	FACETS	0.707	0.611	0.81	0.707	0.611	0.81	SUBCLONAL	1	TRUE	1	0.574181055604804	2		356	276	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023972	27023979	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCCCAT	GCGCCCAT	-	novel	NA	P-0049332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	51	188	0	ENST00000324856.7:c.1079_1086del	p.Ala360GlufsTer37	p.A360Efs*37	ENST00000324856	NM_006015.4	360	GCGCCCATg/g	1/20	1	2	FACETS	0.783	0.673	0.9	0.783	0.673	0.9	SUBCLONAL	1	TRUE	1	0.574181055604804	2		188	227	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106951	27107003	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAAGGGCAGTATCGGCAACCTCCTGGGCTTCCTAGAGGACAGCCTTGCCGC	CAGAAGGGCAGTATCGGCAACCTCCTGGGCTTCCTAGAGGACAGCCTTGCCGC	-	novel	NA	P-0049332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	172	626	0	ENST00000324856.7:c.6564_6616del	p.Gln2188HisfsTer19	p.Q2188Hfs*19	ENST00000324856	NM_006015.4	2188	CAGAAGGGCAGTATCGGCAACCTCCTGGGCTTCCTAGAGGACAGCCTTGCCGCc/c	20/20	1	2	FACETS	0.846	0.781	0.914	0.846	0.781	0.914	CLONAL	1	TRUE	1	0.574181055604804	2		626	708	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008317	29008317	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	60	331	0	ENST00000282397.4:c.554T>C	p.Ile185Thr	p.I185T	ENST00000282397	NM_002019.4	185	aTc/aCc	5/30	1	2	FACETS	0.738	0.642	0.842	0.738	0.642	0.842	SUBCLONAL	1	TRUE	1	0.574181055604804	2		331	283	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404372	139404372	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	163	902	0	ENST00000277541.6:c.2782A>G	p.Thr928Ala	p.T928A	ENST00000277541	NM_017617.3	928	Acg/Gcg	18/34	1	2	FACETS	0.479	0.438	0.521	0.479	0.438	0.521	SUBCLONAL	1	TRUE	1	0.574181055604804	2		902	1186	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242470	+	missense_variant	Missense_Mutation	ONP	GAATT	GAATT	ATTCC	novel	NA	P-0049332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	126	547	1	ENST00000275493.2:c.2236_2240delinsATTCC	p.Glu746_Leu747delinsIlePro	p.E746_L747delinsIP	ENST00000275493	NM_005228.3	746	GAATTa/ATTCCa	19/28	1	2	FACETS	0.784	0.712	0.858	0.784	0.712	0.858	SUBCLONAL	1	TRUE	1	0.574181055604804	2		548	560	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0049334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	28	347	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.531	0.423	0.655	0.531	0.423	0.655	SUBCLONAL	1	TRUE	1	0.18	2		347	586	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771923	135771923	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753388676	NA	P-0049334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	46	520	0	ENST00000298552.3:c.3194C>T	p.Thr1065Met	p.T1065M	ENST00000298552	NM_001162426.1	1065	aCg/aTg	23/23	1	2	FACETS	0.838	0.705	0.985	0.838	0.705	0.985	CLONAL	1	TRUE	1	0.18	2		520	610	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971115	21971116	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0049334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	37	540	0	ENST00000304494.5:c.242_243del	p.Pro81ArgfsTer38	p.P81Rfs*38	ENST00000304494	NM_000077.4	81	cCC/c	2/3	0.169630085241344	0	FACETS	0.661	0.544	0.792			1	SUBCLONAL	1	TRUE	0	0.18	0		540	510	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221720	55221720	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372202099	NA	P-0049334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	34	413	0	ENST00000275493.2:c.764G>A	p.Arg255Gln	p.R255Q	ENST00000275493	NM_005228.3	255	cGa/cAa	7/28	1	2	FACETS	0.757	0.618	0.914	0.757	0.618	0.914	CLONAL	1	TRUE	1	0.18	2		413	499	SUCCESS
ATM	472	MSKCC	GRCh37	11	108128246	108128247	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	36	369	0	ENST00000278616.4:c.2294dup	p.Asn765LysfsTer2	p.N765Kfs*2	ENST00000278616	NM_000051.3	763	-/A	15/63	1	2	FACETS	0.672	0.551	0.808	0.672	0.551	0.808	SUBCLONAL	1	TRUE	1	0.18	2		369	595	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0049335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	234	347	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.426813197668048	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.426813197668048	3		347	588	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578133	7578473	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CACCCTTAACCCCTCCTCCCAGAGACCCCAGTTGCAAACCAGACCTCAGGCGGCTCATAGGGCACCACCACACTATGTCGAAAAGTGTTTCTGTCATCCAAATACTCCACACGCAAATTTCCTTCCACTCGGATAAGATGCTGAGGAGGGGCCAGACCTAAGAGCAATCAGTGAGGAATCAGAGGCCTGGGGACCCTGGGCAACCAGCCCTGTCGTCTCTCCAGCCCCAGCTGCTCACCATCGCTATCTGAGCAGCGCTCATGGTGGGGGCAGCGCCTCACAACCTCCGTCATGTGCTGTGACTGCTTGTAGATGGCCATGGCGCGGACGCGGGTGCCGGG	CACCCTTAACCCCTCCTCCCAGAGACCCCAGTTGCAAACCAGACCTCAGGCGGCTCATAGGGCACCACCACACTATGTCGAAAAGTGTTTCTGTCATCCAAATACTCCACACGCAAATTTCCTTCCACTCGGATAAGATGCTGAGGAGGGGCCAGACCTAAGAGCAATCAGTGAGGAATCAGAGGCCTGGGGACCCTGGGCAACCAGCCCTGTCGTCTCTCCAGCCCCAGCTGCTCACCATCGCTATCTGAGCAGCGCTCATGGTGGGGGCAGCGCCTCACAACCTCCGTCATGTGCTGTGACTGCTTGTAGATGGCCATGGCGCGGACGCGGGTGCCGGG	-	novel	NA	P-0049335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	156	574	0	ENST00000269305.4:c.457_672+44del		p.X153_splice	ENST00000269305	NM_001126112.2	153		5-6/11	0.426813197668048	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.426813197668048	1		574	426	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974732	21974732	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs878853650	NA	P-0049336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	28	361	0	ENST00000304494.5:c.95T>C	p.Leu32Pro	p.L32P	ENST00000304494	NM_000077.4	32	cTg/cCg	1/3	0.276772747519682	1	FACETS	0.46	0.367	0.565	0.46	0.367	0.565	SUBCLONAL	1	FALSE	0	0.276772747519682	1		361	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519991	NA	P-0049336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	54	617	0	ENST00000269305.4:c.536A>C	p.His179Pro	p.H179P	ENST00000269305	NM_001126112.2	179	cAt/cCt	5/11	0.276772747519682	1	FACETS	0.529	0.451	0.614	0.529	0.451	0.614	SUBCLONAL	1	FALSE	0	0.276772747519682	1		617	636	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398282	+	missense_variant	Missense_Mutation	DNP	CC	CC	GG	novel	NA	P-0049336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	42	416	1	ENST00000311936.3:c.37_38inv	p.Gly13Pro	p.G13P	ENST00000311936	NM_004985.3	13	GGc/CCc	2/5	1	2	FACETS	0.542	0.452	0.642	0.542	0.452	0.642	SUBCLONAL	1	FALSE	1	0.276772747519682	2		417	560	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230604	46230604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	33	455	0	ENST00000334344.6:c.853C>T	p.Arg285Trp	p.R285W	ENST00000334344	NM_152641.2	285	Cgg/Tgg	8/21	1	2	FACETS	0.411	0.335	0.497	0.411	0.335	0.497	SUBCLONAL	1	TRUE	1	0.421305118075325	2		455	381	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658481	3658481	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140876043	NA	P-0049337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	34	597	0	ENST00000294008.3:c.485C>T	p.Thr162Met	p.T162M	ENST00000294008	NM_032444.2	162	aCg/aTg	2/15	1	2	FACETS	0.27	0.22	0.327	0.27	0.22	0.327	SUBCLONAL	1	TRUE	1	0.421305118075325	2		597	598	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0049343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	60	591	1	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.375710925732521	2	FACETS	0.918	0.837	0.993	1	0.984	1	CLONAL	4	TRUE	0	0.375710925732521	2		592	87	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028660	12028660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	35	359	0	ENST00000353533.5:c.863C>T	p.Ser288Phe	p.S288F	ENST00000353533	NM_003010.3	288	tCt/tTt	8/11	0.375710925732521	2	FACETS	0.991	0.885	1	1	0.975	1	CLONAL	4	TRUE	0	0.375710925732521	2		359	47	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115903	8115904	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	61	576	2	ENST00000346208.3:c.1251dup	p.Thr418HisfsTer89	p.T418Hfs*89	ENST00000346208		417	acc/aCcc	6/6	0.375710925732521	5	FACETS	0.881	0.774	0.994	0.881	0.774	0.994	CLONAL	3	TRUE	2	0.375710925732521	5		578	192	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991697	72991699	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs757316139	NA	P-0049343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	11	311	2	ENST00000268489.5:c.2346_2348del	p.Ala784del	p.A784del	ENST00000268489	NM_006885.3	782	gcGGCa/gca	2/10	0.375710925732521	2	FACETS	0.76	0.533	1	0.38	0.266	0.517	CLONAL	1	TRUE	0	0.375710925732521	2		313	77	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69230527	69230527	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	10	209	0	ENST00000462284.1:c.916G>A	p.Ala306Thr	p.A306T	ENST00000462284	NM_002392.5	306	Gct/Act	10/11	0.356917385025079	4	FACETS	1	0.768	1	0.381	0.263	0.524	CLONAL	1	TRUE	1	0.375710925732521	4		209	64	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022025	5022025	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	27	412	25	ENST00000381652.3:c.38G>C	p.Gly13Ala	p.G13A	ENST00000381652	NM_004972.3	13	gGa/gCa	3/25	1	2	FACETS	0.921	0.776	1	1	0.968	1	CLONAL	3	TRUE	1	0.375710925732521	2		437	52	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578445	7578450	+	inframe_deletion	In_Frame_Del	DEL	ATGGCC	ATGGCC	-	novel	NA	P-0049344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	492	748	0	ENST00000269305.4:c.480_485del	p.Met160_Ala161del	p.M160_A161del	ENST00000269305	NM_001126112.2	160	atGGCCATc/atc	5/11	0.610590862268274	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.610590862268274	1		748	971	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43773093	43773093	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	35	435	0	ENST00000382044.4:c.499G>A	p.Asp167Asn	p.D167N	ENST00000382044	NM_001141980.1	167	Gat/Aat	5/28	0.610590862268274	1	FACETS	0.335	0.276	0.4	0.335	0.276	0.4	SUBCLONAL	1	TRUE	0	0.610590862268274	1		435	238	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212209	36212209	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	251	511	0	ENST00000222270.7:c.1960C>G	p.Pro654Ala	p.P654A	ENST00000222270	NM_014727.1	654	Cca/Gca	3/37	0.151207068572091	3	FACETS	1	0.992	1	0.706	0.663	0.75	INDETERMINATE	1	TRUE	1	0.610590862268274	3		511	760	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0049345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	18	302	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.733	0.552	0.946	0.733	0.552	0.946	CLONAL	1	FALSE	1	0.188262555232018	2		302	261	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853186	68853186	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs876659716	NA	P-0049345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	21	363	0	ENST00000261769.5:c.1569T>A	p.Tyr523Ter	p.Y523*	ENST00000261769	NM_004360.3	523	taT/taA	11/16	1	2	FACETS	0.882	0.68	1	0.882	0.68	1	CLONAL	1	FALSE	1	0.188262555232018	2		363	253	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129145	2129145	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	39	556	0	ENST00000219476.3:c.3079C>A	p.Leu1027Met	p.L1027M	ENST00000219476	NM_000548.3	1027	Ctg/Atg	27/42	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	FALSE	1	0.188262555232018	2		556	380	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165816	118165816	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	170	502	0	ENST00000369448.3:c.326G>C	p.Arg109Thr	p.R109T	ENST00000369448	NM_017709.3	109	aGa/aCa	2/2	0.867905204476974	2	FACETS	0.989	0.921	1	0.494	0.46	0.529	CLONAL	1	TRUE	0	0.859734668008275	2		502	400	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163313616	163313616	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	120	220	0	ENST00000271452.3:c.763A>C	p.Lys255Gln	p.K255Q	ENST00000271452	NM_145697.2	255	Aaa/Caa	10/14	0.611676076903499	4	FACETS	1	0.952	1	0.537	0.488	0.589	CLONAL	1	TRUE	2	0.859734668008275	4		220	483	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720848	89720849	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0049346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	.	315	292	0	ENST00000371953.3:c.1001dup	p.Asn334LysfsTer9	p.N334Kfs*9	ENST00000371953	NM_000314.4	333	-/A	8/9	0.867905204476974	2	FACETS		NA	1			1	NA	NA	TRUE	0	0.859734668008275	2		292	315	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090987	77090987	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	209	446	0	ENST00000356341.3:c.243T>G	p.Phe81Leu	p.F81L	ENST00000356341	NM_002576.4	81	ttT/ttG	3/15	0.540114135802807	4	FACETS	1	0.99	1			1	CLONAL	1	TRUE	NA	0.859734668008275	4		446	676	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352342	73352342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	195	374	0	ENST00000377767.4:c.563G>A	p.Gly188Glu	p.G188E	ENST00000377767	NM_014953.3	188	gGa/gAa	3/21	0.867905204476974	2	FACETS	1	0.94	1	0.502	0.47	0.534	CLONAL	1	TRUE	0	0.859734668008275	2		374	452	SUCCESS
NF2	4771	MSKCC	GRCh37	22	29999995	29999995	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1333560181	NA	P-0049346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	184	387	1	ENST00000338641.4:c.8G>A	p.Gly3Glu	p.G3E	ENST00000338641	NM_000268.3	3	gGg/gAg	1/16	0.867905204476974	2	FACETS	1	0.983	1	0.571	0.535	0.607	CLONAL	1	TRUE	0	0.859734668008275	2		388	375	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540146	187540146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	177	416	0	ENST00000441802.2:c.7594G>A	p.Val2532Ile	p.V2532I	ENST00000441802	NM_005245.3	2532	Gta/Ata	10/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.859734668008275	2		416	369	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713326	43713326	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	302	520	0	ENST00000382044.4:c.4147G>T	p.Asp1383Tyr	p.D1383Y	ENST00000382044	NM_001141980.1	1383	Gat/Tat	20/28	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.461065133296198	2		520	1149	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856424	111856424	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	22	100	0	ENST00000341259.2:c.475A>C	p.Thr159Pro	p.T159P	ENST00000341259	NM_005475.2	159	Acc/Ccc	2/8	1	2	FACETS	0.282	0.218	0.357	0.282	0.218	0.357	SUBCLONAL	1	TRUE	1	0.461065133296198	2		100	338	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106236	27106264	+	frameshift_variant	Frame_Shift_Del	DEL	CCGGAACATCAAGATCCTAGAGGACGAAC	CCGGAACATCAAGATCCTAGAGGACGAAC	-	novel	NA	P-0049348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	196	359	1	ENST00000324856.7:c.5849_5877del	p.Arg1950ProfsTer3	p.R1950Pfs*3	ENST00000324856	NM_006015.4	1949	caCCGGAACATCAAGATCCTAGAGGACGAACcc/cacc	20/20	0.461065133296198	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.461065133296198	1		360	625	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037947	49037948	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GATCTTCCTCATGCTGTTCAGGAGGT	novel	NA	P-0049349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	105	321	0	ENST00000267163.4:c.2188_2211+2dup		p.-729fs	ENST00000267163	NM_000321.2	729	-/GATCTTCCTCATGCTGTTCAGGAGGT	21/27	0.839505373696347	1	FACETS	0.51	0.465	0.557	0.51	0.465	0.557	SUBCLONAL	1	TRUE	0	0.874105220731918	1		321	265	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546647	9546647	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0049349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	34	392	0	ENST00000353224.5:c.1375T>A	p.Ser459Thr	p.S459T	ENST00000353224	NM_177990.2	459	Tca/Aca	5/10	1	2	FACETS	0.193	0.157	0.232	0.193	0.157	0.232	SUBCLONAL	1	TRUE	1	0.874105220731918	2		392	404	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574674	41574674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	291	605	0	ENST00000263253.7:c.6959C>T	p.Ser2320Phe	p.S2320F	ENST00000263253	NM_001429.3	2320	tCc/tTc	31/31	1	2	FACETS	0.948	0.898	0.999	0.948	0.898	0.999	CLONAL	1	TRUE	1	0.874105220731918	2		605	702	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447174	187447174	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049349-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	240	486	0	ENST00000232014.4:c.1019A>T	p.Gln340Leu	p.Q340L	ENST00000232014	NM_001130845.1	340	cAg/cTg	5/10	1	2	FACETS	0.935	0.881	0.991	0.935	0.881	0.991	CLONAL	1	TRUE	1	0.874105220731918	2		486	587	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	156	301	0				ENST00000310581	NM_198253.2	-/1132			0.482133021609365	6	FACETS	0.942	0.883	0.999	1	0.985	1	CLONAL	5	TRUE	2	0.482133021609365	6		301	270	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	154	576	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.44588004822269	4	FACETS	0.867	0.798	0.938	0.867	0.798	0.938	CLONAL	2	TRUE	2	0.482133021609365	4		576	546	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443345	187443345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	130	258	0	ENST00000232014.4:c.1781G>A	p.Arg594Gln	p.R594Q	ENST00000232014	NM_001130845.1	594	cGa/cAa	8/10	0.44588004822269	4	FACETS	0.961	0.879	1	0.961	0.879	1	CLONAL	2	TRUE	2	0.482133021609365	4		258	416	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712008	89712008	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	37	119	0	ENST00000371953.3:c.626G>T	p.Gly209Val	p.G209V	ENST00000371953	NM_000314.4	209	gGa/gTa	6/9	0.482133021609365	5	FACETS	1	0.953	1	0.493	0.411	0.581	CLONAL	1	TRUE	2	0.482133021609365	5		119	179	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245513	153245513	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	79	212	0	ENST00000281708.4:c.1678G>C	p.Asp560His	p.D560H	ENST00000281708	NM_033632.3	560	Gat/Cat	11/12	0.395479521900058	3	FACETS	1	0.966	1	0.62	0.55	0.694	CLONAL	1	TRUE	1	0.482133021609365	3		212	328	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863656	68863656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	220	296	0	ENST00000261769.5:c.2395C>T	p.Pro799Ser	p.P799S	ENST00000261769	NM_004360.3	799	Ccc/Tcc	15/16	0.482133021609365	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.482133021609365	2		296	399	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106662	27106662	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	127	394	0	ENST00000324856.7:c.6273G>A	p.Trp2091Ter	p.W2091*	ENST00000324856	NM_006015.4	2091	tgG/tgA	20/20	0.194269606493567	5	FACETS	0.791	0.719	0.866	0.527	0.479	0.577	INDETERMINATE	2	TRUE	2	0.482133021609365	5		394	574	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372190	55372190	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	69	230	2	ENST00000297316.4:c.880C>T	p.His294Tyr	p.H294Y	ENST00000297316	NM_022454.3	294	Cac/Tac	2/2	0.482133021609365	3	FACETS	0.866	0.758	0.983	0.433	0.379	0.492	CLONAL	1	TRUE	1	0.482133021609365	3		232	410	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859492	151859492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	185	291	0	ENST00000262189.6:c.11170G>A	p.Glu3724Lys	p.E3724K	ENST00000262189	NM_170606.2	3724	Gag/Aag	43/59	0.482133021609365	6	FACETS	1	0.985	1	0.62	0.575	0.666	CLONAL	2	TRUE	2	0.482133021609365	6		291	608	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863596	68863596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660183	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	290	354	0	ENST00000261769.5:c.2335C>T	p.Arg779Trp	p.R779W	ENST00000261769	NM_004360.3	779	Cgg/Tgg	15/16	0.482133021609365	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.482133021609365	2		354	495	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188989	11188989	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	61	241	0	ENST00000361445.4:c.5734G>C	p.Asp1912His	p.D1912H	ENST00000361445	NM_004958.3	1912	Gat/Cat	41/58	0.482133021609365	2	FACETS	0.764	0.664	0.873	0.382	0.332	0.437	SUBCLONAL	1	TRUE	0	0.482133021609365	2		241	331	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105695	27105705	+	frameshift_variant	Frame_Shift_Del	DEL	TAGGTCCTAAA	TAGGTCCTAAA	-	novel	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	149	191	0	ENST00000324856.7:c.5306_5316del	p.Leu1769ProfsTer11	p.L1769Pfs*11	ENST00000324856	NM_006015.4	1769	cTAGGTCCTAAA/c	20/20	0.194269606493567	5	FACETS	0.897	0.835	0.958	1	0.984	1	INDETERMINATE	4	TRUE	2	0.482133021609365	5		191	297	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161293444	161293444	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1553261768	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	118	203	0	ENST00000367975.2:c.61C>G	p.Gln21Glu	p.Q21E	ENST00000367975	NM_003001.3	21	Cag/Gag	2/6	0.482133021609365	5	FACETS	1	0.981	1	0.45	0.407	0.495	CLONAL	1	TRUE	2	0.482133021609365	5		203	625	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14303150	14303150	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	99	182	0	ENST00000256196.4:c.525C>G	p.Ile175Met	p.I175M	ENST00000256196		175	atC/atG	5/6	0.166404093045995	4	FACETS	0.963	0.87	1	0.642	0.58	0.707	INDETERMINATE	2	TRUE	1	0.482133021609365	4		182	316	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198903	67198903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	146	383	0	ENST00000312629.5:c.374C>T	p.Ser125Leu	p.S125L	ENST00000312629	NM_003952.2	125	tCa/tTa	5/15	0.166404093045995	4	FACETS	1	0.987	1	0.492	0.451	0.535	INDETERMINATE	1	TRUE	1	0.482133021609365	4		383	608	SUCCESS
EED	8726	MSKCC	GRCh37	11	85979536	85979536	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	147	160	0	ENST00000263360.6:c.899C>G	p.Ser300Cys	p.S300C	ENST00000263360	NM_003797.3	300	tCt/tGt	9/12	0.166404093045995	4	FACETS	1	0.98	1	0.789	0.729	0.85	INDETERMINATE	2	TRUE	1	0.482133021609365	4		160	382	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343567	118343567	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	116	246	0	ENST00000534358.1:c.1693C>G	p.Leu565Val	p.L565V	ENST00000534358	NM_005933.3	565	Ctg/Gtg	3/36	0.166404093045995	4	FACETS	1	0.962	1	0.731	0.668	0.797	INDETERMINATE	2	TRUE	1	0.482133021609365	4		246	325	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343898	118343898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	123	269	0	ENST00000534358.1:c.2024C>T	p.Ser675Leu	p.S675L	ENST00000534358	NM_005933.3	675	tCa/tTa	3/36	0.166404093045995	4	FACETS	1	0.916	1	0.669	0.611	0.728	INDETERMINATE	2	TRUE	1	0.482133021609365	4		269	377	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344111	118344111	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	127	222	0	ENST00000534358.1:c.2237C>G	p.Ser746Cys	p.S746C	ENST00000534358	NM_005933.3	746	tCt/tGt	3/36	0.166404093045995	4	FACETS	1	0.98	1	0.808	0.743	0.875	INDETERMINATE	2	TRUE	1	0.482133021609365	4		222	322	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344314	118344314	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	122	191	0	ENST00000534358.1:c.2440C>G	p.Gln814Glu	p.Q814E	ENST00000534358	NM_005933.3	814	Cag/Gag	3/36	0.166404093045995	4	FACETS	1	0.965	1	0.735	0.673	0.799	INDETERMINATE	2	TRUE	1	0.482133021609365	4		191	340	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344404	118344404	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	82	130	0	ENST00000534358.1:c.2530C>G	p.Gln844Glu	p.Q844E	ENST00000534358	NM_005933.3	844	Cag/Gag	3/36	0.166404093045995	4	FACETS	1	0.939	1	0.712	0.638	0.788	INDETERMINATE	2	TRUE	1	0.482133021609365	4		130	236	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426147	49426147	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1342813038	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	269	403	0	ENST00000301067.7:c.12341G>A	p.Gly4114Glu	p.G4114E	ENST00000301067	NM_003482.3	4114	gGa/gAa	39/54	0.482133021609365	5	FACETS	0.916	0.864	0.968	1	0.993	1	CLONAL	3	TRUE	3	0.482133021609365	5		403	700	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865543	57865543	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	199	409	0	ENST00000228682.2:c.3020C>G	p.Thr1007Arg	p.T1007R	ENST00000228682	NM_005269.2	1007	aCa/aGa	12/12	0.346214243524352	4	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	2	0.482133021609365	4		409	596	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233401	69233401	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	132	199	0	ENST00000462284.1:c.1266G>C	p.Arg422Ser	p.R422S	ENST00000462284	NM_002392.5	422	agG/agC	11/11	0.346214243524352	4	FACETS	1	0.925	1	1	0.925	1	CLONAL	2	TRUE	2	0.482133021609365	4		199	402	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134434	41134434	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	92	282	0	ENST00000379561.5:c.1194G>T	p.Met398Ile	p.M398I	ENST00000379561	NM_002015.3	398	atG/atT	2/3	0.395479521900058	3	FACETS	1	0.909	1	0.51	0.455	0.568	CLONAL	1	TRUE	1	0.482133021609365	3		282	464	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916775	48916895	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTATCTTTATTGCAGCAGTTGACCTAGATGAGATGTCGTTCACTTTTACTGAGCTACAGAAAAACATAGAAATCAGGTAAAGTTTCTTGTATAAATATAAGCCTCTGCCATAAAAGGAAAC	GTATCTTTATTGCAGCAGTTGACCTAGATGAGATGTCGTTCACTTTTACTGAGCTACAGAAAAACATAGAAATCAGGTAAAGTTTCTTGTATAAATATAAGCCTCTGCCATAAAAGGAAAC	-	novel	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	37	132	0	ENST00000267163.4:c.306_380+46del		p.X102_splice	ENST00000267163	NM_000321.2	102		3/27	0.430512128314164	1	FACETS	0.597	0.498	0.706	0.597	0.498	0.706	SUBCLONAL	1	TRUE	0	0.482133021609365	1		132	195	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867208	68867208	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	228	283	0	ENST00000261769.5:c.2455G>C	p.Asp819His	p.D819H	ENST00000261769	NM_004360.3	819	Gat/Cat	16/16	0.482133021609365	2	FACETS	0.852	0.81	0.893	1	0.992	1	CLONAL	3	TRUE	0	0.482133021609365	2		283	370	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347087	89347087	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762574237	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	223	426	0	ENST00000301030.4:c.5863G>A	p.Glu1955Lys	p.E1955K	ENST00000301030	NM_001256183.1	1955	Gag/Aag	9/13	0.482133021609365	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.482133021609365	2		426	390	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866119	37866119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	125	304	0	ENST00000269571.5:c.628G>A	p.Glu210Lys	p.E210K	ENST00000269571		210	Gag/Aag	5/27	0.482133021609365	5	FACETS	0.878	0.799	0.96	0.585	0.532	0.64	CLONAL	2	TRUE	2	0.482133021609365	5		304	509	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10305520	10305520	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747559452	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	99	329	0	ENST00000340748.4:c.56C>T	p.Ser19Leu	p.S19L	ENST00000340748		19	tCg/tTg	1/40	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.482133021609365	2		329	387	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714623	52714623	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	119	434	0	ENST00000322088.6:c.381C>G	p.His127Gln	p.H127Q	ENST00000322088	NM_014225.5	127	caC/caG	4/15	0.482133021609365	6	FACETS	1	0.959	1	0.224	0.201	0.247	CLONAL	1	TRUE	1	0.482133021609365	6		434	867	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919763	96919763	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	72	348	0	ENST00000258439.3:c.500C>G	p.Ser167Cys	p.S167C	ENST00000258439	NM_001193304.2	167	tCc/tGc	4/4	0.166404093045995	4	FACETS	1	0.92	1	0.355	0.311	0.401	INDETERMINATE	1	TRUE	1	0.482133021609365	4		348	416	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447438	12447438	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	276	372	0	ENST00000287820.6:c.677C>G	p.Ser226Cys	p.S226C	ENST00000287820	NM_015869.4	226	tCc/tGc	5/7	0.482133021609365	5	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	2	0.482133021609365	5		372	628	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070399	37070399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	105	186	1	ENST00000231790.2:c.1534G>A	p.Glu512Lys	p.E512K	ENST00000231790	NM_000249.3	512	Gaa/Aaa	13/19	0.482133021609365	5	FACETS	0.977	0.883	1	0.652	0.589	0.717	CLONAL	2	TRUE	2	0.482133021609365	5		187	384	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963026	38963026	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	104	174	0	ENST00000357387.3:c.1518G>C	p.Gln506His	p.Q506H	ENST00000357387	NM_152756.3	506	caG/caC	17/38	0.482133021609365	6	FACETS	0.791	0.71	0.875	0.395	0.355	0.438	SUBCLONAL	2	TRUE	2	0.482133021609365	6		174	536	SUCCESS
APC	324	MSKCC	GRCh37	5	112177851	112177851	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	74	136	0	ENST00000257430.4:c.6560G>C	p.Gly2187Ala	p.G2187A	ENST00000257430	NM_000038.5	2187	gGa/gCa	16/16	0.234392704345474	5	FACETS	1	0.962	1	0.794	0.707	0.885	INDETERMINATE	2	TRUE	2	0.482133021609365	5		136	222	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816896	32816896	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	182	227	0	ENST00000354258.4:c.1429-1G>C		p.X477_splice	ENST00000354258	NM_000593.5	477			0.482133021609365	6	FACETS	1	0.983	1	0.604	0.56	0.649	CLONAL	2	TRUE	2	0.482133021609365	6		227	614	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012253	152012253	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1563831738	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	222	177	0	ENST00000262189.6:c.560C>G	p.Ser187Ter	p.S187*	ENST00000262189	NM_170606.2	187	tCa/tGa	4/59	0.437852601834064	5	FACETS	0.94	0.882	0.998	0.94	0.882	0.998	CLONAL	3	TRUE	2	0.482133021609365	5		177	563	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820595	44820595	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	230	89	0	ENST00000377967.4:c.292C>T	p.Gln98Ter	p.Q98*	ENST00000377967	NM_021140.2	98	Caa/Taa	3/29	0.482133021609365	3	FACETS	0.894	0.855	0.932			1	CLONAL	4	TRUE	NA	0.482133021609365	3		89	331	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420213	49420213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267607237	NA	P-0049436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	86	667	3	ENST00000301067.7:c.15536G>A	p.Arg5179His	p.R5179H	ENST00000301067	NM_003482.3	5179	cGt/cAt	48/54	0.188457861753482	3	FACETS	0.589	0.52	0.665	0.295	0.26	0.333	SUBCLONAL	1	TRUE	1	0.29	3		670	1152	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427057	49427058	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0049436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	56	689	0	ENST00000301067.7:c.11430dup	p.Gln3811AlafsTer201	p.Q3811Afs*201	ENST00000301067	NM_003482.3	3810	-/G	39/54	0.188457861753482	3	FACETS	0.45	0.384	0.522	0.225	0.192	0.261	SUBCLONAL	1	TRUE	1	0.29	3		689	983	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0049436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	75	932	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.469	0.409	0.533	0.469	0.409	0.533	SUBCLONAL	1	TRUE	1	0.29	2		934	1104	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954327	48954327	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	79	338	0	ENST00000267163.4:c.1448A>G	p.His483Arg	p.H483R	ENST00000267163	NM_000321.2	483	cAt/cGt	16/27	0.415244436550395	1	FACETS	0.914	0.81	1	0.914	0.81	1	CLONAL	1	TRUE	0	0.415244436550395	1		338	330	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845806	72845806	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	74	631	1	ENST00000268489.5:c.3661C>T	p.Gln1221Ter	p.Q1221*	ENST00000268489	NM_006885.3	1221	Cag/Tag	6/10	0.383368770064141	1	FACETS	0.41	0.358	0.465	0.41	0.358	0.465	SUBCLONAL	1	TRUE	0	0.415244436550395	1		632	689	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763490	59763490	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0049439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	108	594	0	ENST00000259008.2:c.2612A>T	p.His871Leu	p.H871L	ENST00000259008	NM_032043.2	871	cAt/cTt	19/20	1	2	FACETS	0.917	0.826	1	0.917	0.826	1	CLONAL	1	TRUE	1	0.415244436550395	2		594	567	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221249	36221249	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	222	821	2	ENST00000222270.7:c.5083G>A	p.Val1695Met	p.V1695M	ENST00000222270	NM_014727.1	1695	Gtg/Atg	24/37	0.415244436550395	1	FACETS	0.898	0.837	0.962	0.898	0.837	0.962	CLONAL	1	TRUE	0	0.415244436550395	1		823	943	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44733213	44733213	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	166	291	0	ENST00000377967.4:c.205A>G	p.Thr69Ala	p.T69A	ENST00000377967	NM_021140.2	69	Acg/Gcg	2/29	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.415244436550395	1		291	428	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27205056	27205056	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0049441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	391	569	0	ENST00000380036.4:c.2360del	p.Asn787ThrfsTer2	p.N787Tfs*2	ENST00000380036	NM_000459.3	786	cAa/ca	14/23	0.621185580022488	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.621185580022488	1		569	744	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427060	49427061	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0049441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	461	747	0	ENST00000301067.7:c.11427_11428del	p.Leu3810AlafsTer201	p.L3810Afs*201	ENST00000301067	NM_003482.3	3809	gtGTtg/gttg	39/54	0.558828642412577	2	FACETS	0.842	0.81	0.875	0.842	0.81	0.875	CLONAL	2	TRUE	0	0.621185580022488	2		747	881	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108798	2108798	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	602	911	0	ENST00000219476.3:c.899G>T	p.Gly300Val	p.G300V	ENST00000219476	NM_000548.3	300	gGc/gTc	10/42	0.621185580022488	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.621185580022488	1		911	1142	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578194	7578195	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0049441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	461	711	0	ENST00000269305.4:c.654_655del	p.Pro219LeufsTer2	p.P219Lfs*2	ENST00000269305	NM_001126112.2	218	gtGCcc/gtcc	6/11	0.558828642412577	2	FACETS	0.817	0.785	0.849	0.817	0.785	0.849	CLONAL	2	TRUE	0	0.621185580022488	2		711	908	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46602958	46602958	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	463	814	2	ENST00000263734.3:c.1016G>T	p.Cys339Phe	p.C339F	ENST00000263734	NM_001430.4	339	tGt/tTt	8/16	0.313334565149225	1	FACETS	0.875	0.837	0.913	0.875	0.837	0.913	INDETERMINATE	1	TRUE	0	0.621185580022488	1		816	1175	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530162	212530162	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	116	418	0	ENST00000342788.4:c.1757G>C	p.Gly586Ala	p.G586A	ENST00000342788	NM_005235.2	586	gGc/gCc	15/28	0.616660861917866	2	FACETS	0.671	0.606	0.738	0.335	0.303	0.369	SUBCLONAL	1	TRUE	0	0.621185580022488	2		418	557	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117629959	117629970	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	ATCATCAGGACA	ATCATCAGGACA	-	novel	NA	P-0049441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	118	366	0	ENST00000368508.3:c.6556_6567del	p.Cys2186_Asp2189del	p.C2186_D2189del	ENST00000368508	NM_002944.2	2186	TGTCCTGATGAT/-	41/43	0.621185580022488	1	FACETS	0.862	0.789	0.936	0.862	0.789	0.936	CLONAL	1	TRUE	0	0.621185580022488	1		366	304	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508771	106508798	+	frameshift_variant	Frame_Shift_Del	DEL	GAAATCTCTGATGGATATTCCCGAAAGC	GAAATCTCTGATGGATATTCCCGAAAGC	-	novel	NA	P-0049441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	297	656	0	ENST00000359195.3:c.765_792del	p.Lys255AsnfsTer30	p.K255Nfs*30	ENST00000359195	NM_002649.2	255	aaGAAATCTCTGATGGATATTCCCGAAAGC/aa	2/11	0.185572808242024	3	FACETS	1	0.988	1	0.392	0.369	0.415	INDETERMINATE	1	TRUE	0	0.621185580022488	3		656	1066	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509340	106509340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776863655	NA	P-0049441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	318	658	1	ENST00000359195.3:c.1334C>T	p.Ala445Val	p.A445V	ENST00000359195	NM_002649.2	445	gCc/gTc	2/11	0.185572808242024	3	FACETS	1	0.992	1	0.421	0.397	0.445	INDETERMINATE	1	TRUE	0	0.621185580022488	3		659	1063	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0049444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	326	576	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.509638815367822	4	FACETS	0.915	0.878	0.952	0.915	0.878	0.952	CLONAL	4	FALSE	0	0.530136874666638	4		576	514	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101300	27101300	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	211	777	0	ENST00000324856.7:c.4582C>T	p.Arg1528Ter	p.R1528*	ENST00000324856	NM_006015.4	1528	Cga/Tga	18/20	0.530136874666638	6	FACETS	1	0.987	1	0.82	0.765	0.876	CLONAL	2	FALSE	3	0.530136874666638	6		777	667	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106438	27106439	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0049444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	177	505	0	ENST00000324856.7:c.6050_6051dup	p.His2018CysfsTer13	p.H2018Cfs*13	ENST00000324856	NM_006015.4	2017	ctg/cTGtg	20/20	0.530136874666638	6	FACETS	1	0.983	1	0.8	0.742	0.86	CLONAL	2	FALSE	3	0.530136874666638	6		505	573	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631837	90631837	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519736	NA	P-0049445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	324	614	0	ENST00000330062.3:c.516G>C	p.Arg172Ser	p.R172S	ENST00000330062	NM_002168.2	172	agG/agC	4/11	0.300064883143975	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.28	3		614	1287	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66468007	66468007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868264524	NA	P-0049445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	65	246	0	ENST00000273854.3:c.262G>A	p.Glu88Lys	p.E88K	ENST00000273854	NM_004439.5	88	Gaa/Aaa	3/18	0.168764049970436	0	FACETS	1	0.904	1			1	CLONAL	1	TRUE	0	0.28	0		246	321	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870776	12870776	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs756190836	NA	P-0049445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	60	186	0	ENST00000228872.4:c.3G>A	p.Met1?	p.M1?	ENST00000228872	NM_004064.3	1	atG/atA	1/3	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.28	2		186	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0049452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	369	461	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.0968029172696414	6	FACETS	1	0.994	1			1	INDETERMINATE	5	TRUE	NA	0.712140078383803	6		462	460	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087458	27087458	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0049453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	59	590	0	ENST00000324856.7:c.2032C>T	p.Gln678Ter	p.Q678*	ENST00000324856	NM_006015.4	678	Cag/Tag	5/20	0.259342461727226	1	FACETS	0.333	0.287	0.383	0.333	0.287	0.383	INDETERMINATE	1	TRUE	0	0.555207979805662	1		590	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577137	7577137	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0049453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	111	564	0	ENST00000269305.4:c.801del	p.Asn268ThrfsTer77	p.N268Tfs*77	ENST00000269305	NM_001126112.2	267	cgG/cg	8/11	0.436528754395381	1	FACETS	0.735	0.666	0.806	0.735	0.666	0.806	SUBCLONAL	1	TRUE	0	0.555207979805662	1		564	393	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279965	18279965	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1483549709	NA	P-0049453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	105	517	0	ENST00000222254.8:c.2048A>G	p.Tyr683Cys	p.Y683C	ENST00000222254	NM_005027.3	683	tAc/tGc	16/16	0.377086669717798	1	FACETS	0.641	0.578	0.707	0.641	0.578	0.707	SUBCLONAL	1	TRUE	0	0.555207979805662	1		517	426	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087426	27087426	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	45	598	0	ENST00000324856.7:c.2000C>G	p.Ser667Cys	p.S667C	ENST00000324856	NM_006015.4	667	tCc/tGc	5/20	0.259342461727226	1	FACETS	0.276	0.232	0.324	0.276	0.232	0.324	INDETERMINATE	1	TRUE	0	0.555207979805662	1		598	425	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087552	27087552	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	65	641	0	ENST00000324856.7:c.2126C>G	p.Ser709Cys	p.S709C	ENST00000324856	NM_006015.4	709	tCt/tGt	5/20	0.259342461727226	1	FACETS	0.324	0.281	0.371	0.324	0.281	0.371	INDETERMINATE	1	TRUE	0	0.555207979805662	1		641	522	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087921	27087921	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0049453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	51	595	0	ENST00000324856.7:c.2208C>G	p.Ile736Met	p.I736M	ENST00000324856	NM_006015.4	736	atC/atG	6/20	0.259342461727226	1	FACETS	0.302	0.256	0.351	0.302	0.256	0.351	INDETERMINATE	1	TRUE	0	0.555207979805662	1		595	440	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416654	49416654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1350174178	NA	P-0049453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	101	443	0	ENST00000301067.7:c.16057C>T	p.His5353Tyr	p.H5353Y	ENST00000301067	NM_003482.3	5353	Cat/Tat	51/54	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.555207979805662	2		443	330	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948023	178948023	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0049453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	21	256	0	ENST00000263967.3:c.2795T>C	p.Ile932Thr	p.I932T	ENST00000263967	NM_006218.2	932	aTa/aCa	20/21	0.509349518301883	4	FACETS	0.422	0.325	0.534	0.211	0.162	0.267	SUBCLONAL	1	TRUE	2	0.555207979805662	4		256	279	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508561	106508561	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0049453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	60	365	0	ENST00000359195.3:c.555G>T	p.Met185Ile	p.M185I	ENST00000359195	NM_002649.2	185	atG/atT	2/11	0.259342461727226	1	FACETS	0.635	0.553	0.721	0.635	0.553	0.721	INDETERMINATE	1	TRUE	0	0.555207979805662	1		365	246	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440487	49440488	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0049453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	110	615	0	ENST00000301067.7:c.4322_4323del	p.Arg1441ProfsTer5	p.R1441Pfs*5	ENST00000301067	NM_003482.3	1441	cGC/c	15/54	1	2	FACETS	0.836	0.755	0.921	0.836	0.755	0.921	CLONAL	1	TRUE	1	0.555207979805662	2		615	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0049456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	61	668	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.3	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.22	1		669	354	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0049456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	23	577	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	1	0.22	2		577	189	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385239	41385239	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377294483	NA	P-0049456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	19	498	0	ENST00000373198.4:c.722G>A	p.Arg241His	p.R241H	ENST00000373198	NM_133170.3	241	cGt/cAt	6/32	1	2	FACETS	0.523	0.397	0.672	0.523	0.397	0.672	SUBCLONAL	1	TRUE	1	0.22	2		498	330	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932259	36932259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	572	729	0	ENST00000361632.4:c.2210C>T	p.Ser737Phe	p.S737F	ENST00000361632		737	tCc/tTc	16/16	0.442768900442145	3	FACETS	0.992	0.959	1	0.992	0.959	1	CLONAL	3	TRUE	0	0.484439309812082	3		729	986	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0049457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	427	361	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.442768900442145	3	FACETS	0.91	0.874	0.946	0.91	0.874	0.946	CLONAL	3	TRUE	0	0.484439309812082	3		361	802	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228613001	228613001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373549345	NA	P-0049457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	137	460	0	ENST00000366696.1:c.26G>A	p.Arg9His	p.R9H	ENST00000366696	NM_003493.2	9	cGc/cAc	1/1	0.442768900442145	3	FACETS	1	0.953	1	0.356	0.324	0.389	CLONAL	1	TRUE	0	0.484439309812082	3		460	658	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435088	18435088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	96	328	0	ENST00000266497.5:c.73C>T	p.Leu25Phe	p.L25F	ENST00000266497		25	Ctc/Ttc	1/31	0.457979267569336	1	FACETS	0.747	0.67	0.828	0.747	0.67	0.828	SUBCLONAL	1	TRUE	0	0.484439309812082	1		328	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579854	7579854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	301	630	0	ENST00000269305.4:c.59C>T	p.Ser20Leu	p.S20L	ENST00000269305	NM_001126112.2	20	tCa/tTa	2/11	0.402475592759711	0	FACETS	0.875	0.829	0.922			1	CLONAL	1	TRUE	0	0.484439309812082	0		630	732	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687567	37687567	+	stop_lost	Nonstop_Mutation	SNP	T	T	G	novel	NA	P-0049457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	179	283	0	ENST00000447079.4:c.4471T>G	p.Ter1491GluextTer32	p.*1491Eext*32	ENST00000447079	NM_015083.1	1491	Taa/Gaa	14/14	0.472369104646429	2	FACETS	0.965	0.903	1	0.965	0.903	1	CLONAL	2	TRUE	0	0.484439309812082	2		283	383	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793099	42793099	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	166	745	0	ENST00000575354.2:c.991C>T	p.Pro331Ser	p.P331S	ENST00000575354	NM_015125.3	331	Ccg/Tcg	7/20	1	2	FACETS	0.783	0.72	0.849	0.783	0.72	0.849	SUBCLONAL	1	TRUE	1	0.484439309812082	2		745	875	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960074	134960074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0049457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	137	568	0	ENST00000398015.3:c.2431G>A	p.Gly811Arg	p.G811R	ENST00000398015	NM_004441.4	811	Ggg/Agg	13/16	0.437966467286196	3	FACETS	0.793	0.721	0.869	0.397	0.36	0.435	SUBCLONAL	1	TRUE	1	0.484439309812082	3		568	886	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190776	185190776	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0049457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	144	482	0	ENST00000265026.3:c.1657A>G	p.Arg553Gly	p.R553G	ENST00000265026	NM_004721.4	553	Aga/Gga	11/14	0.437966467286196	3	FACETS	0.935	0.853	1	0.467	0.426	0.51	CLONAL	1	TRUE	1	0.484439309812082	3		482	790	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526275	189526275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	268	529	0	ENST00000264731.3:c.539C>T	p.Ser180Phe	p.S180F	ENST00000264731	NM_003722.4	180	tCc/tTc	4/14	0.437966467286196	3	FACETS	0.867	0.816	0.918	0.867	0.816	0.918	CLONAL	2	TRUE	1	0.484439309812082	3		529	793	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750441	41750441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	127	502	0	ENST00000226382.2:c.187G>A	p.Gly63Arg	p.G63R	ENST00000226382	NM_003924.3	63	Gga/Aga	1/3	1	2	FACETS	0.851	0.773	0.933	0.851	0.773	0.933	CLONAL	1	TRUE	1	0.484439309812082	2		502	616	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244148	153244148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	159	477	0	ENST00000281708.4:c.2009G>A	p.Gly670Glu	p.G670E	ENST00000281708	NM_033632.3	670	gGa/gAa	12/12	1	2	FACETS	0.963	0.885	1	0.963	0.885	1	CLONAL	1	TRUE	1	0.484439309812082	2		477	682	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0049457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	70	351	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.484439309812082	2		351	285	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80057405	80057405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0049457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	76	295	0	ENST00000265081.6:c.1804C>T	p.His602Tyr	p.H602Y	ENST00000265081	NM_002439.4	602	Cat/Tat	13/24	1	2	FACETS	0.725	0.638	0.817	0.725	0.638	0.817	SUBCLONAL	1	TRUE	1	0.484439309812082	2		295	433	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641169	93641169	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0049457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	68	483	0	ENST00000375746.1:c.1515A>C	p.Gln505His	p.Q505H	ENST00000375746	NM_001174167.1	505	caA/caC	11/14	0.47944833536258	1	FACETS	0.425	0.371	0.485	0.425	0.371	0.485	SUBCLONAL	1	TRUE	0	0.484439309812082	1		483	500	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0049458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	99	566	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.158776271772327	3	FACETS	0.996	0.89	1	0.498	0.445	0.554	INDETERMINATE	1	TRUE	1	0.342540410189407	3		566	680	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0049458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	107	579	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.126480194896755	5	FACETS	1	0.98	1	0.351	0.315	0.39	INDETERMINATE	1	TRUE	1	0.342540410189407	5		579	673	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs397517201	NA	P-0049458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	78	394	0	ENST00000263967.3:c.1637A>T	p.Gln546Leu	p.Q546L	ENST00000263967	NM_006218.2	546	cAg/cTg	10/21	0.242772378359307	3	FACETS	0.874	0.769	0.988	0.437	0.384	0.494	CLONAL	1	TRUE	1	0.342540410189407	3		394	610	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045845	143045845	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0049458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	53	419	0	ENST00000262992.4:c.1789C>T	p.Arg597Ter	p.R597*	ENST00000262992	NM_001101669.1	597	Cga/Tga	17/24	1	2	FACETS	0.523	0.445	0.608	0.523	0.445	0.608	SUBCLONAL	1	TRUE	1	0.342540410189407	2		419	592	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271353	26271353	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0049458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	46	558	0	ENST00000305910.3:c.260G>T	p.Ser87Ile	p.S87I	ENST00000305910	NM_003534.2	87	aGt/aTt	1/1	0.285811221887915	4	FACETS	0.461	0.387	0.543	0.23	0.193	0.272	SUBCLONAL	1	TRUE	2	0.342540410189407	4		558	783	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	36	314	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.600284172279605	2		314	103	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670234	134670234	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	134	321	0	ENST00000398015.3:c.145G>T	p.Asp49Tyr	p.D49Y	ENST00000398015	NM_004441.4	49	Gat/Tat	3/16	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.600284172279605	2		321	383	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2115535	2115535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	269	499	1	ENST00000219476.3:c.1615C>T	p.Leu539Phe	p.L539F	ENST00000219476	NM_000548.3	539	Ctc/Ttc	16/42	0.600284172279605	4	FACETS	1	0.971	1	0.531	0.497	0.566	CLONAL	1	TRUE	2	0.600284172279605	4		500	1350	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178518	56178518	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0000220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	21	157	0	ENST00000399503.3:c.3491del	p.Asp1164ValfsTer8	p.D1164Vfs*8	ENST00000399503	NM_005921.1	1164	gAt/gt	14/20	1	2	FACETS	0.875	0.691	1	0.875	0.691	1	CLONAL	1	TRUE	1	0.600284172279605	2		157	80	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849572	68849572	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	402	580	0	ENST00000261769.5:c.1475del	p.Arg492LysfsTer30	p.R492Kfs*30	ENST00000261769	NM_004360.3	492	aGa/aa	10/16	0.600284172279605	2	FACETS	0.989	0.951	1	0.989	0.951	1	CLONAL	2	TRUE	0	0.600284172279605	2		580	677	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0005063-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	218	432	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.861407773670062	2	FACETS	0.943	0.885	1	0.471	0.442	0.501	CLONAL	1	TRUE	0	0.861407773670062	2		432	537	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0005063-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1788	501	630	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.833826488342811	5	FACETS	1	0.992	1	0.388	0.37	0.407	CLONAL	1	TRUE	2	0.861407773670062	5		630	2289	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0005063-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	413	107	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	0.833826488342811	5	FACETS	1	0.986	1	0.718	0.685	0.75	CLONAL	2	TRUE	2	0.861407773670062	5		107	1021	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574022	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005063-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	412	296	0	ENST00000269305.4:c.1005dup	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	335	-/T	10/11	0.850719015460876	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.861407773670062	1		296	536	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776888	76776888	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005063-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	249	76	0	ENST00000373344.5:c.7064C>T	p.Ser2355Leu	p.S2355L	ENST00000373344	NM_000489.3	2355	tCa/tTa	33/35	0.861407773670062	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.861407773670062	1		76	310	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349235	11349235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1019392987	NA	P-0005063-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	120	186	0	ENST00000332029.2:c.101C>T	p.Ala34Val	p.A34V	ENST00000332029	NM_003745.1	34	gCg/gTg	2/2	0.861407773670062	2	FACETS	1	0.939	1	0.512	0.471	0.554	CLONAL	1	TRUE	0	0.861407773670062	2		186	272	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295786	15295786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005063-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2089	140	685	0	ENST00000263388.2:c.2341G>A	p.Glu781Lys	p.E781K	ENST00000263388	NM_000435.2	781	Gag/Aag	15/33	0.861407773670062	3	FACETS	0.209	0.189	0.23	0.07	0.063	0.077	SUBCLONAL	1	TRUE	0	0.861407773670062	3		685	2229	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242741	98242741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776187586	NA	P-0005063-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	61	105	0	ENST00000331920.6:c.876G>A	p.Met292Ile	p.M292I	ENST00000331920	NM_000264.3	292	atG/atA	6/24	0.861407773670062	2	FACETS	0.181	0.156	0.209	0.091	0.078	0.105	SUBCLONAL	1	TRUE	0	0.861407773670062	2		105	781	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0007266-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	223	347	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.235023789940416	5	FACETS	0.929	0.878	0.98			1	INDETERMINATE	4	FALSE	NA	0.500160727820339	5		347	420	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479774	67479774	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs387906856	NA	P-0007266-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	338	573	0	ENST00000327367.4:c.1081G>C	p.Glu361Gln	p.E361Q	ENST00000327367	NM_005902.3	361	Gag/Cag	8/9	0.500160727820339	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	FALSE	1	0.500160727820339	3		573	766	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073495	8073497	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0007266-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	228	336	0	ENST00000377482.5:c.1162_1164del	p.Lys388del	p.K388del	ENST00000377482	NM_018948.3	388	AAG/-	4/4	0.500160727820339	5	FACETS	1	0.987	1			1	CLONAL	2	FALSE	NA	0.500160727820339	5		336	660	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57569909	57569916	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGATTT	GGAGATTT	-	novel	NA	P-0007266-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	88	206	0	ENST00000316660.6:c.94_101del	p.Phe32GlnfsTer53	p.F32Qfs*53	ENST00000316660	NM_021127.2	30	aGGAGATTT/a	2/2	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	1	0.500160727820339	2		206	315	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249743	39249743	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007266-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	142	344	0	ENST00000402219.2:c.1826T>G	p.Leu609Arg	p.L609R	ENST00000402219	NM_005633.3	609	cTt/cGt	10/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.500160727820339	2		344	420	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055929	180055931	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0007266-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	109	894	0	ENST00000261937.6:c.1054_1056del	p.Val352del	p.V352del	ENST00000261937	NM_182925.4	352	GTG/-	8/30	NA	2	FACETS	0.645	0.58	0.714			1	INDETERMINATE	1	FALSE	NA	0.500160727820339	2		894	676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0008978-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	300	643	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.625800538898246	2	FACETS	0.905	0.866	0.944	0.905	0.866	0.944	CLONAL	2	TRUE	0	0.669439382508101	2		643	495	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0008978-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	202	483	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.5255033012519	5	FACETS	1	0.982	1	0.759	0.71	0.81	CLONAL	2	TRUE	2	0.669439382508101	5		483	531	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0008978-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	381	630	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.5255033012519	5	FACETS	1	0.969	1	0.683	0.65	0.717	CLONAL	2	TRUE	2	0.669439382508101	5		630	1113	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976922	18976922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008978-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	85	797	0	ENST00000262803.5:c.3307G>A	p.Gly1103Arg	p.G1103R	ENST00000262803	NM_002911.3	1103	Gga/Aga	23/24	1	2	FACETS	0.43	0.38	0.483	0.43	0.38	0.483	SUBCLONAL	1	TRUE	1	0.669439382508101	2		797	591	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249091	55249091	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008978-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	273	886	1	ENST00000275493.2:c.2389T>G	p.Cys797Gly	p.C797G	ENST00000275493	NM_005228.3	797	Tgc/Ggc	20/28	0.5255033012519	5	FACETS	1	0.993	1	0.486	0.455	0.517	CLONAL	1	TRUE	2	0.669439382508101	5		887	1122	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0009791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	88	228	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.263316102049858	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.263316102049858	3		228	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0009791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	202	722	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.217267599878431	3	FACETS	1	0.971	1	0.724	0.673	0.778	CLONAL	2	TRUE	0	0.263316102049858	3		722	799	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386565	81386565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868138405	NA	P-0009791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	28	355	0	ENST00000222390.5:c.422C>T	p.Ser141Phe	p.S141F	ENST00000222390	NM_000601.4	141	tCt/tTt	4/18	0.254547664931704	2	FACETS	0.433	0.345	0.534	0.217	0.172	0.267	SUBCLONAL	1	TRUE	0	0.263316102049858	2		355	491	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199553	16199553	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	30	473	0	ENST00000375759.3:c.326G>T	p.Gly109Val	p.G109V	ENST00000375759	NM_015001.2	109	gGa/gTa	2/15	1	2	FACETS	0.409	0.329	0.501	0.409	0.329	0.501	SUBCLONAL	1	TRUE	1	0.263316102049858	2		473	557	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671979	30671979	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	87	812	0	ENST00000376406.3:c.4981G>C	p.Glu1661Gln	p.E1661Q	ENST00000376406	NM_014641.2	1661	Gag/Cag	10/15	0.135599665926972	3	FACETS	0.87	0.769	0.978	0.435	0.384	0.489	INDETERMINATE	1	TRUE	1	0.263316102049858	3		812	860	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857771	9857771	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	123	583	1	ENST00000330684.3:c.3630C>A	p.Asn1210Lys	p.N1210K	ENST00000330684	NM_001134407.1	1210	aaC/aaA	13/13	0.23112629337577	3	FACETS	0.803	0.728	0.883	0.536	0.485	0.589	CLONAL	2	TRUE	0	0.263316102049858	3		584	658	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917851	29917851	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	55	925	0	ENST00000389048.3:c.817G>T	p.Glu273Ter	p.E273*	ENST00000389048	NM_004304.4	273	Gag/Tag	3/29	0.159216223780737	2	FACETS	0.461	0.393	0.536	0.231	0.196	0.268	SUBCLONAL	1	TRUE	0	0.263316102049858	2		925	906	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279579	18279579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1403656005	NA	P-0009791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	61	764	0	ENST00000222254.8:c.1852G>A	p.Glu618Lys	p.E618K	ENST00000222254	NM_005027.3	618	Gag/Aag	15/16	0.262271684210912	2	FACETS	0.552	0.475	0.636	0.276	0.237	0.318	SUBCLONAL	1	TRUE	0	0.263316102049858	2		764	840	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044965	47044965	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1233	74	1283	0	ENST00000377604.3:c.2291G>A	p.Cys764Tyr	p.C764Y	ENST00000377604	NM_001204468.1	764	tGc/tAc	20/24	NA	2	FACETS	0.43	0.375	0.49			1	INDETERMINATE	1	TRUE	NA	0.263316102049858	2		1283	1307	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52722992	52722992	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1362406458	NA	P-0009791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	60	884	0	ENST00000322088.6:c.1177G>A	p.Glu393Lys	p.E393K	ENST00000322088	NM_014225.5	393	Gag/Aag	10/15	0.159216223780737	2	FACETS	0.489	0.42	0.565	0.244	0.21	0.283	SUBCLONAL	1	TRUE	0	0.263316102049858	2		884	932	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748070	72748070	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	39	676	0	ENST00000357731.5:c.108G>C	p.Gln36His	p.Q36H	ENST00000357731	NM_173808.2	36	caG/caC	1/7	1	2	FACETS	0.443	0.366	0.529	0.443	0.366	0.529	SUBCLONAL	1	TRUE	1	0.263316102049858	2		676	669	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256206	123256206	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	23	433	0	ENST00000358487.5:c.1703C>G	p.Ser568Cys	p.S568C	ENST00000358487	NM_000141.4	568	tCt/tGt	13/18	0.172564913247408	2	FACETS	0.403	0.314	0.508	0.202	0.157	0.254	SUBCLONAL	1	TRUE	0	0.263316102049858	2		433	433	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344720	118344720	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	44	296	0	ENST00000534358.1:c.2846C>G	p.Thr949Ser	p.T949S	ENST00000534358	NM_005933.3	949	aCt/aGt	3/36	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.263316102049858	2		296	310	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114156	115114156	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	50	756	0	ENST00000257566.3:c.1061C>T	p.Ser354Phe	p.S354F	ENST00000257566	NM_016569.3	354	tCt/tTt	6/8	0.172564913247408	2	FACETS	0.5	0.423	0.585	0.25	0.211	0.293	SUBCLONAL	1	TRUE	0	0.263316102049858	2		756	759	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114170	115114170	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	57	772	0	ENST00000257566.3:c.1047C>A	p.Phe349Leu	p.F349L	ENST00000257566	NM_016569.3	349	ttC/ttA	6/8	0.172564913247408	2	FACETS	0.534	0.457	0.618	0.267	0.228	0.309	SUBCLONAL	1	TRUE	0	0.263316102049858	2		772	811	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893378	32893378	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	30	278	0	ENST00000380152.3:c.232C>G	p.Pro78Ala	p.P78A	ENST00000380152		78	Cca/Gca	3/27	0.237979526028033	4	FACETS	0.598	0.481	0.732	0.199	0.16	0.244	SUBCLONAL	1	TRUE	1	0.263316102049858	4		278	481	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105236746	105236746	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	55	925	0	ENST00000349310.3:c.1375G>C	p.Glu459Gln	p.E459Q	ENST00000349310	NM_001014432.1	459	Gag/Cag	15/15	0.168235546784372	2	FACETS	0.426	0.363	0.495	0.213	0.181	0.248	SUBCLONAL	1	TRUE	0	0.263316102049858	2		925	981	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630670	90630670	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0009791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	46	594	0	ENST00000330062.3:c.815+1G>C		p.X272_splice	ENST00000330062	NM_002168.2	272			1	2	FACETS	0.528	0.443	0.621	0.528	0.443	0.621	SUBCLONAL	1	TRUE	1	0.263316102049858	2		594	662	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387655	17387655	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	54	823	0	ENST00000359435.4:c.723C>G	p.Phe241Leu	p.F241L	ENST00000359435	NM_001033549.1	241	ttC/ttG	8/9	0.262271684210912	2	FACETS	0.404	0.344	0.471	0.202	0.172	0.236	SUBCLONAL	1	TRUE	0	0.263316102049858	2		823	1015	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511274	157511274	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	42	552	0	ENST00000346085.5:c.3792G>C	p.Met1264Ile	p.M1264I	ENST00000346085	NM_020732.3	1264	atG/atC	15/20	1	2	FACETS	0.526	0.438	0.623	0.526	0.438	0.623	SUBCLONAL	1	TRUE	1	0.263316102049858	2		552	607	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268844	98268844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1192030415	NA	P-0009791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	29	414	0	ENST00000331920.6:c.239G>A	p.Arg80Lys	p.R80K	ENST00000331920	NM_000264.3	80	aGa/aAa	2/24	0.263316102049858	3	FACETS	0.609	0.489	0.747	0.305	0.244	0.374	SUBCLONAL	1	TRUE	1	0.263316102049858	3		414	409	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192035	108192035	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	32	339	0	ENST00000278616.4:c.6460G>C	p.Glu2154Gln	p.E2154Q	ENST00000278616	NM_000051.3	2154	Gaa/Caa	45/63	0.263316102049858	3	FACETS	0.564	0.457	0.685			1	SUBCLONAL	1	TRUE	NA	0.263316102049858	3		339	488	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870813	12870813	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	20	259	0	ENST00000228872.4:c.40G>C	p.Glu14Gln	p.E14Q	ENST00000228872	NM_004064.3	14	Gag/Cag	1/3	0.263316102049858	4	FACETS	0.688	0.526	0.876			1	SUBCLONAL	1	TRUE	NA	0.263316102049858	4		259	279	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961577	41961577	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	31	406	0	ENST00000219905.7:c.485C>G	p.Ser162Cys	p.S162C	ENST00000219905	NM_001164273.1	162	tCt/tGt	2/24	1	2	FACETS	0.415	0.335	0.507	0.415	0.335	0.507	SUBCLONAL	1	TRUE	1	0.263316102049858	2		406	567	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526864	31526864	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009791-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	61	763	0	ENST00000344624.3:c.176C>A	p.Pro59His	p.P59H	ENST00000344624		59	cCt/cAt	2/33	0.263316102049858	3	FACETS	0.534	0.459	0.617	0.267	0.229	0.309	SUBCLONAL	1	TRUE	1	0.263316102049858	3		763	981	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0010276-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	378	622	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.879075304869483	2	FACETS	1	0.962	1			1	CLONAL	4	TRUE	NA	0.23	2		622	815	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0010538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	27	502	1	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.706570455353598	1	FACETS	0.159	0.127	0.197	0.159	0.127	0.197	SUBCLONAL	1	TRUE	0	0.706570455353598	1		503	310	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0010538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	98	279	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	0.706570455353598	1	FACETS	0.838	0.765	0.912	0.838	0.765	0.912	CLONAL	1	TRUE	0	0.706570455353598	1		279	214	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0010538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	153	509	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	NA	2	FACETS	0.868	0.8	0.938			1	INDETERMINATE	1	TRUE	NA	0.706570455353598	2		509	499	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878563	151878563	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	473	538	3	ENST00000262189.6:c.6382C>T	p.Gln2128Ter	p.Q2128*	ENST00000262189	NM_170606.2	2128	Cag/Tag	36/59	0.604803121837314	4	FACETS	0.896	0.863	0.929			1	CLONAL	3	TRUE	NA	0.706570455353598	4		541	850	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413597	32413597	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	129	357	0	ENST00000332351.3:c.1353C>A	p.Phe451Leu	p.F451L	ENST00000332351	NM_024426.4	451	ttC/ttA	9/10	1	2	FACETS	0.92	0.842	1	0.92	0.842	1	CLONAL	1	TRUE	1	0.706570455353598	2		357	397	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041349	42041350	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	203	1009	1	ENST00000219905.7:c.5544_5545insA	p.Ser1849IlefsTer2	p.S1849Ifs*2	ENST00000219905	NM_001164273.1	1848	-/A	17/24	0.706570455353598	1	FACETS	0.569	0.53	0.609	0.569	0.53	0.609	SUBCLONAL	1	TRUE	0	0.706570455353598	1		1010	653	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604770	48604770	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs377767378	NA	P-0010538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	17	350	0	ENST00000342988.3:c.1594del	p.Ala532ProfsTer5	p.A532Pfs*5	ENST00000342988	NM_005359.5	531	cGg/cg	12/12	0.706570455353598	1	FACETS	0.099	0.073	0.13	0.099	0.073	0.13	SUBCLONAL	1	TRUE	0	0.706570455353598	1		350	314	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415856	49415858	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	rs587783704	NA	P-0010538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	179	627	0	ENST00000301067.7:c.16489_16491del	p.Ile5497del	p.I5497del	ENST00000301067	NM_003482.3	5497	ATC/-	53/54	NA	2	FACETS	0.887	0.823	0.953			1	INDETERMINATE	1	TRUE	NA	0.706570455353598	2		627	571	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0016624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	74	383	0				ENST00000310581	NM_198253.2	-/1132			0.194578809889128	5	FACETS	1	0.953	1	0.772	0.682	0.868	CLONAL	2	TRUE	2	0.287645604814499	5		383	318	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0016624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	9	276	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	0.257875013091946	3	FACETS	0.2	0.131	0.288	0.1	0.065	0.144	SUBCLONAL	1	TRUE	1	0.287645604814499	3		276	358	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	202	649	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.287645604814499	4	FACETS	0.998	0.931	1	0.998	0.931	1	CLONAL	3	TRUE	1	0.287645604814499	4		649	604	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109672	115109672	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	57	802	0	ENST00000257566.3:c.2206G>C	p.Asp736His	p.D736H	ENST00000257566	NM_016569.3	736	Gac/Cac	8/8	0.276932486585066	4	FACETS	0.56	0.479	0.649	0.14	0.119	0.163	SUBCLONAL	1	TRUE	0	0.287645604814499	4		802	912	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0016624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	1116	684	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.287645604814499	15	FACETS	1	0.984	1			1	CLONAL	12	TRUE	NA	0.287645604814499	15		684	1841	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827844	170827844	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs544573727	NA	P-0016624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	16	139	0	ENST00000296930.5:c.584C>T	p.Ser195Phe	p.S195F	ENST00000296930	NM_002520.6	195	tCt/tTt	8/11	0.287645604814499	2	FACETS	0.783	0.583	1	0.392	0.291	0.509	CLONAL	1	TRUE	0	0.287645604814499	2		139	142	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075591	8075591	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	45	464	0	ENST00000377482.5:c.89G>A	p.Arg30Lys	p.R30K	ENST00000377482	NM_018948.3	30	aGg/aAg	2/4	0.194578809889128	5	FACETS	0.845	0.71	0.995	0.282	0.236	0.332	CLONAL	1	TRUE	2	0.287645604814499	5		464	530	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295181	1295181	+	upstream_gene_variant	5'Flank	SNP	G	G	C	novel	NA	P-0016624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	49	164	0				ENST00000310581	NM_198253.2	-/1132			0.194578809889128	5	FACETS	1	0.881	1	0.689	0.589	0.796	CLONAL	2	TRUE	2	0.287645604814499	5		164	236	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295411	1295411	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0016624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	27	83	0				ENST00000310581	NM_198253.2	-/1132			0.194578809889128	5	FACETS	1	0.904	1	0.8	0.649	0.965	CLONAL	2	TRUE	2	0.287645604814499	5		83	112	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459615	149459615	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	64	599	0	ENST00000286301.3:c.592G>A	p.Val198Ile	p.V198I	ENST00000286301	NM_005211.3	198	Gtc/Atc	4/22	0.287645604814499	2	FACETS	0.857	0.743	0.981	0.429	0.371	0.491	CLONAL	1	TRUE	0	0.287645604814499	2		599	519	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40872313	40872313	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	100	582	0	ENST00000428826.2:c.642G>C	p.Lys214Asn	p.K214N	ENST00000428826		214	aaG/aaC	7/21	0.287645604814499	6	FACETS	0.839	0.75	0.933			1	CLONAL	2	TRUE	NA	0.287645604814499	6		582	653	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70432683	70432683	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	48	465	0	ENST00000373644.4:c.4705G>C	p.Glu1569Gln	p.E1569Q	ENST00000373644	NM_030625.2	1569	Gag/Cag	8/12	1	2	FACETS	0.722	0.611	0.845	0.722	0.611	0.845	SUBCLONAL	1	TRUE	1	0.287645604814499	2		465	462	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343051	118343051	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	68	266	0	ENST00000534358.1:c.1177C>T	p.Gln393Ter	p.Q393*	ENST00000534358	NM_005933.3	393	Cag/Tag	3/36	0.286475000226609	3	FACETS	0.889	0.781	1			1	CLONAL	2	TRUE	NA	0.287645604814499	3		266	304	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16022782	16022782	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	59	330	0	ENST00000268712.3:c.1870G>T	p.Glu624Ter	p.E624*	ENST00000268712	NM_006311.3	624	Gag/Tag	17/46	0.287645604814499	4	FACETS	0.831	0.719	0.95	0.554	0.479	0.633	CLONAL	2	TRUE	1	0.287645604814499	4		330	318	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024405	16024405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	76	473	0	ENST00000268712.3:c.1813G>A	p.Glu605Lys	p.E605K	ENST00000268712	NM_006311.3	605	Gaa/Aaa	16/46	0.287645604814499	4	FACETS	0.753	0.663	0.849	0.502	0.442	0.566	SUBCLONAL	2	TRUE	1	0.287645604814499	4		473	452	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029454	16029454	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	64	378	0	ENST00000268712.3:c.1576G>C	p.Glu526Gln	p.E526Q	ENST00000268712	NM_006311.3	526	Gaa/Caa	15/46	0.287645604814499	4	FACETS	0.921	0.804	1	0.614	0.536	0.698	CLONAL	2	TRUE	1	0.287645604814499	4		378	311	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927486	178927486	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	13	348	1	ENST00000263967.3:c.1249G>A	p.Glu417Lys	p.E417K	ENST00000263967	NM_006218.2	417	Gag/Aag	7/21	0.287645604814499	3	FACETS	0.407	0.29	0.55	0.204	0.145	0.275	SUBCLONAL	1	TRUE	1	0.287645604814499	3		349	254	SUCCESS
APC	324	MSKCC	GRCh37	5	112154981	112154981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	179	603	0	ENST00000257430.4:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000257430	NM_000038.5	418	Gaa/Aaa	10/16	0.287645604814499	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.287645604814499	2		603	542	SUCCESS
APC	324	MSKCC	GRCh37	5	112177392	112177422	+	frameshift_variant	Frame_Shift_Del	DEL	CTGAAGATGACCTGTTGCAGGAATGTATAAG	CTGAAGATGACCTGTTGCAGGAATGTATAAG	-	novel	NA	P-0016624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	65	278	0	ENST00000257430.4:c.6103_6133del	p.Glu2035ProfsTer28	p.E2035Pfs*28	ENST00000257430	NM_000038.5	2034	tCTGAAGATGACCTGTTGCAGGAATGTATAAGc/tc	16/16	0.287645604814499	2	FACETS	0.978	0.86	1	0.978	0.86	1	CLONAL	2	TRUE	0	0.287645604814499	2		278	231	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513482	149513482	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	34	690	0	ENST00000261799.4:c.721G>C	p.Glu241Gln	p.E241Q	ENST00000261799	NM_002609.3	241	Gag/Cag	5/23	0.287645604814499	2	FACETS	0.382	0.311	0.462	0.191	0.155	0.231	SUBCLONAL	1	TRUE	0	0.287645604814499	2		690	619	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418886	116418886	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs745437003	NA	P-0016624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	57	333	0	ENST00000397752.3:c.3397G>C	p.Asp1133His	p.D1133H	ENST00000397752	NM_000245.2	1133	Gat/Cat	17/21	0.287645604814499	3	FACETS	1	0.947	1	0.608	0.523	0.699	CLONAL	1	TRUE	1	0.287645604814499	3		333	373	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966749	44966749	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	130	274	1	ENST00000377967.4:c.3973G>T	p.Glu1325Ter	p.E1325*	ENST00000377967	NM_021140.2	1325	Gaa/Taa	27/29	0.287645604814499	2	FACETS	1	0.964	1			1	CLONAL	3	TRUE	NA	0.287645604814499	2		275	281	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179121	123179121	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016624-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	78	238	0	ENST00000218089.9:c.570C>G	p.Ile190Met	p.I190M	ENST00000218089	NM_001042749.1	190	atC/atG	8/35	0.287645604814499	2	FACETS	1	0.955	1			1	CLONAL	2	TRUE	NA	0.287645604814499	2		238	238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782329	NA	P-0017325-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	278	618	0	ENST00000269305.4:c.746G>A	p.Arg249Lys	p.R249K	ENST00000269305	NM_001126112.2	249	aGg/aAg	7/11	0.294781149709173	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.294781149709173	3		618	1043	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100420	8100420	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs991194737	NA	P-0017325-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	129	861	1	ENST00000346208.3:c.394G>A	p.Val132Ile	p.V132I	ENST00000346208		132	Gtc/Atc	3/6	0.108085701530651	5	FACETS	1	0.919	1	0.254	0.23	0.281	INDETERMINATE	1	TRUE	1	0.294781149709173	5		862	1240	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141565	11141565	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017325-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	117	670	0	ENST00000358026.2:c.3542A>C	p.His1181Pro	p.H1181P	ENST00000358026	NM_001128849.1	1181	cAc/cCc	25/36	0.198048841613966	3	FACETS	0.911	0.82	1	0.304	0.273	0.336	CLONAL	1	TRUE	0	0.294781149709173	3		670	1000	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970831	55970831	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017325-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	59	423	0	ENST00000263923.4:c.1966G>T	p.Val656Phe	p.V656F	ENST00000263923	NM_002253.2	656	Gtc/Ttc	13/30	0.217297379786659	2	FACETS	0.768	0.662	0.884	0.384	0.331	0.442	SUBCLONAL	1	TRUE	0	0.294781149709173	2		423	521	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118339536	118339536	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782279632	NA	P-0017325-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	44	472	0	ENST00000534358.1:c.479G>A	p.Arg160Gln	p.R160Q	ENST00000534358	NM_005933.3	160	cGa/cAa	2/36	0.2617725733402	3	FACETS	0.502	0.419	0.593	0.251	0.209	0.297	SUBCLONAL	1	TRUE	1	0.294781149709173	3		472	683	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120163	70120163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017325-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	82	392	0	ENST00000245479.2:c.1165C>T	p.Pro389Ser	p.P389S	ENST00000245479	NM_000346.3	389	Ccg/Tcg	3/3	0.294781149709173	3	FACETS	1	0.962	1	0.608	0.537	0.683	CLONAL	1	TRUE	1	0.294781149709173	3		392	525	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417477	139417477	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017325-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	164	785	0	ENST00000277541.6:c.567C>G	p.Cys189Trp	p.C189W	ENST00000277541	NM_017617.3	189	tgC/tgG	4/34	0.217297379786659	2	FACETS	0.873	0.799	0.95	0.436	0.399	0.475	CLONAL	1	TRUE	0	0.294781149709173	2		785	1275	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842032	3842039	+	frameshift_variant	Frame_Shift_Del	DEL	CAGTCATG	CAGTCATG	A	novel	NA	P-0017325-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	28	314	0	ENST00000262367.5:c.1273_1280delinsT	p.His425PhefsTer7	p.H425Ffs*7	ENST00000262367	NM_004380.2	425	CATGACTGt/Tt	5/31	0.24287031662039	2	FACETS	0.386	0.308	0.476	0.193	0.154	0.238	SUBCLONAL	1	TRUE	0	0.294781149709173	2		314	492	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018529-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	103	566	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.164376534371759	5	FACETS	0.917	0.828	1	0.917	0.828	1	INDETERMINATE	3	TRUE	2	0.288523727793043	5		566	372	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0018529-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	36	453	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.244228407776054	3	FACETS	0.457	0.374	0.55	0.228	0.187	0.275	SUBCLONAL	1	TRUE	1	0.288523727793043	3		453	625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018529-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	267	1084	1	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.232660964243787	2	FACETS	0.814	0.763	0.866	0.814	0.763	0.866	CLONAL	2	TRUE	0	0.288523727793043	2		1085	1137	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs753143066	NA	P-0019023-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	45	438	3	ENST00000295797.4:c.826dup	p.Thr276AsnfsTer16	p.T276Nfs*16	ENST00000295797	NM_002740.5	273	tta/ttAa	9/18	1	2	FACETS	0.51	0.434	0.592	0.51	0.434	0.592	SUBCLONAL	1	TRUE	1	0.890717856971592	2		441	198	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609722	28609722	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019023-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	47	638	0	ENST00000241453.7:c.1507A>T	p.Met503Leu	p.M503L	ENST00000241453	NM_004119.2	503	Atg/Ttg	12/24	0.284086418474438	1	FACETS	0.325	0.278	0.375	0.325	0.278	0.375	INDETERMINATE	1	TRUE	0	0.890717856971592	1		638	180	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569849	95569849	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019023-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	72	320	0	ENST00000393063.1:c.3884G>T	p.Gly1295Val	p.G1295V	ENST00000393063	NM_030621.3	1295	gGa/gTa	22/28	0.216357001778437	3	FACETS	1	0.975	1	0.679	0.608	0.752	INDETERMINATE	1	TRUE	1	0.890717856971592	3		320	172	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46276064	46276064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370656650	NA	P-0019023-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	103	515	0	ENST00000371998.3:c.3500C>T	p.Pro1167Leu	p.P1167L	ENST00000371998		1167	cCc/cTc	18/23	1	2	FACETS	0.857	0.779	0.936	0.857	0.779	0.936	CLONAL	1	TRUE	1	0.890717856971592	2		515	270	SUCCESS
APC	324	MSKCC	GRCh37	5	112179225	112179225	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019023-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	58	317	0	ENST00000257430.4:c.7934A>T	p.Tyr2645Phe	p.Y2645F	ENST00000257430	NM_000038.5	2645	tAt/tTt	16/16	0.890717856971592	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.890717856971592	1		317	65	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152025	11152025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057518049	NA	P-0019023-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	21	538	0	ENST00000358026.2:c.4309C>T	p.Arg1437Trp	p.R1437W	ENST00000358026	NM_001128849.1	1437	Cgg/Tgg	31/36	NA	2	FACETS	0.352	0.274	0.441			1	INDETERMINATE	1	TRUE	NA	0.890717856971592	2		538	134	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36814313	36814313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1343428672	NA	P-0019023-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	41	643	1	ENST00000373129.3:c.727G>A	p.Asp243Asn	p.D243N	ENST00000373129	NM_032017.1	243	Gac/Aac	8/12	0.216357001778437	3	FACETS	0.622	0.523	0.729	0.311	0.261	0.365	INDETERMINATE	1	TRUE	1	0.890717856971592	3		644	214	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	82	376	1	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.965	0.852	1	0.965	0.852	1	CLONAL	1	TRUE	1	0.277309962818246	2		377	613	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	80	227	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.957	0.843	1	0.957	0.843	1	CLONAL	1	TRUE	1	0.277309962818246	2		227	603	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	98	453	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.277309962818246	2		453	640	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	162	550	1	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.885	0.81	0.964	0.885	0.81	0.964	CLONAL	1	TRUE	1	0.277309962818246	2		551	1320	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371737	118371737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	76	167	0	ENST00000534358.1:c.6194G>A	p.Arg2065His	p.R2065H	ENST00000534358	NM_005933.3	2065	cGc/cAc	25/36	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.277309962818246	2		167	396	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586470	189586470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147148566	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	67	191	0	ENST00000264731.3:c.1094C>T	p.Ser365Leu	p.S365L	ENST00000264731	NM_003722.4	365	tCg/tTg	8/14	1	2	FACETS	0.922	0.803	1	0.922	0.803	1	CLONAL	1	TRUE	1	0.277309962818246	2		191	524	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806119	1806119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931614	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	162	492	0	ENST00000260795.2:c.1138G>A	p.Gly380Arg	p.G380R	ENST00000260795		380	Ggg/Agg	8/17	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.277309962818246	2		492	1075	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	118	408	4	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.813	0.732	0.899	0.813	0.732	0.899	CLONAL	1	TRUE	1	0.277309962818246	2		412	1047	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216477	108216477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587782558	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	25	122	0	ENST00000278616.4:c.8432del	p.Lys2811SerfsTer46	p.K2811Sfs*46	ENST00000278616	NM_000051.3	2809	cAa/ca	58/63	1	2	FACETS	0.751	0.594	0.93	0.751	0.594	0.93	CLONAL	1	TRUE	1	0.277309962818246	2		122	240	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350625	15350625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35676845	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	163	527	1	ENST00000263377.2:c.3290G>A	p.Arg1097His	p.R1097H	ENST00000263377	NM_058243.2	1097	cGt/cAt	16/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.277309962818246	2		528	1130	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139269	108139269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782298	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	132	282	0	ENST00000278616.4:c.2771G>A	p.Arg924Gln	p.R924Q	ENST00000278616	NM_000051.3	924	cGg/cAg	18/63	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.277309962818246	2		282	786	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563296	21563296	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	170	538	0	ENST00000382592.4:c.623C>T	p.Pro208Leu	p.P208L	ENST00000382592	NM_014572.2	208	cCg/cTg	4/8	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.277309962818246	2		538	1222	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	115	344	2	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.277309962818246	2		346	794	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39629562	39629562	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	54	204	0	ENST00000262039.4:c.2260del	p.Thr754GlnfsTer7	p.T754Qfs*7	ENST00000262039	NM_002647.2	752	acA/ac	21/25	1	2	FACETS	0.879	0.752	1	0.879	0.752	1	CLONAL	1	TRUE	1	0.277309962818246	2		204	443	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404809	70404809	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	89	235	0	ENST00000373644.4:c.2328del	p.Lys776AsnfsTer19	p.K776Nfs*19	ENST00000373644	NM_030625.2	775	Aaa/aa	4/12	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.277309962818246	2		235	615	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671654	67671655	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	82	305	0	ENST00000264010.4:c.2070dup	p.Glu691ArgfsTer5	p.E691Rfs*5	ENST00000264010	NM_006565.3	688	gta/gtAa	12/12	1	2	FACETS	0.954	0.842	1	0.954	0.842	1	CLONAL	1	TRUE	1	0.277309962818246	2		305	620	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631917	90631918	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs747216375	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	138	375	0	ENST00000330062.3:c.435dup	p.Thr146AspfsTer126	p.T146Dfs*126	ENST00000330062	NM_002168.2	145	-/G	4/11	1	2	FACETS	0.961	0.873	1	0.961	0.873	1	CLONAL	1	TRUE	1	0.277309962818246	2		375	1036	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221971	98221971	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768558478	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	113	318	0	ENST00000331920.6:c.2798C>T	p.Ala933Val	p.A933V	ENST00000331920	NM_000264.3	933	gCg/gTg	17/24	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.277309962818246	2		318	724	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935322	36935323	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs747437399	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	117	398	1	ENST00000361632.4:c.1404dup	p.Ser469GlnfsTer5	p.S469Qfs*5	ENST00000361632		468	-/C	10/16	1	2	FACETS	0.831	0.748	0.919	0.831	0.748	0.919	CLONAL	1	TRUE	1	0.277309962818246	2		399	1016	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665280	176665280	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784107	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	60	195	0	ENST00000439151.2:c.3964C>T	p.Arg1322Ter	p.R1322*	ENST00000439151	NM_022455.4	1322	Cga/Tga	7/23	1	2	FACETS	0.871	0.751	1	0.871	0.751	1	CLONAL	1	TRUE	1	0.277309962818246	2		195	497	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255141	16255142	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	68	215	2	ENST00000375759.3:c.2417_2418dup	p.Arg807AspfsTer3	p.R807Dfs*3	ENST00000375759	NM_015001.2	802	-/GA	11/15	1	2	FACETS	0.922	0.803	1	0.922	0.803	1	CLONAL	1	TRUE	1	0.277309962818246	2		217	532	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	153	544	4	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.277309962818246	2		548	1099	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	166	334	1	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.751	0.691	0.814	1	0.989	1	SUBCLONAL	2	TRUE	1	0.277309962818246	2		335	797	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475550	12475550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479145908	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	98	621	1	ENST00000287820.6:c.1424C>T	p.Thr475Met	p.T475M	ENST00000287820	NM_015869.4	475	aCg/aTg	7/7	0.277309962818246	2	FACETS	1	0.892	1	0.5	0.446	0.557	CLONAL	1	TRUE	0	0.277309962818246	2		622	707	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	123	461	5	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.952	0.86	1	0.952	0.86	1	CLONAL	1	TRUE	1	0.277309962818246	2		466	932	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905543	50905543	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373001984	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	147	561	3	ENST00000440232.2:c.671G>A	p.Arg224His	p.R224H	ENST00000440232	NM_002691.3	224	cGc/cAc	6/27	1	2	FACETS	0.855	0.779	0.935	0.855	0.779	0.935	CLONAL	1	TRUE	1	0.277309962818246	2		564	1240	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599271	28599271	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs770146088	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	151	414	1	ENST00000253063.3:c.722del	p.Pro241GlnfsTer6	p.P241Qfs*6	ENST00000253063	NM_031459.4	239	agC/ag	5/10	1	2	FACETS	0.958	0.874	1	0.958	0.874	1	CLONAL	1	TRUE	1	0.277309962818246	2		415	1137	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924315	112924315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1355732645	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	126	380	0	ENST00000351677.2:c.1261C>T	p.Arg421Trp	p.R421W	ENST00000351677	NM_002834.3	421	Cgg/Tgg	11/16	1	2	FACETS	0.898	0.812	0.989	0.898	0.812	0.989	CLONAL	1	TRUE	1	0.277309962818246	2		380	1012	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466515	120466515	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	126	361	0	ENST00000256646.2:c.4604C>T	p.Ala1535Val	p.A1535V	ENST00000256646	NM_024408.3	1535	gCt/gTt	26/34	1	2	FACETS	0.978	0.885	1	0.978	0.885	1	CLONAL	1	TRUE	1	0.277309962818246	2		361	929	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137077	64137077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	152	431	1	ENST00000334205.4:c.1588G>A	p.Asp530Asn	p.D530N	ENST00000334205	NM_003942.2	530	Gac/Aac	13/17	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.277309962818246	2		432	1016	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625218	69625218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168737490	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	153	502	2	ENST00000334134.2:c.575G>A	p.Arg192Gln	p.R192Q	ENST00000334134	NM_005247.2	192	cGg/cAg	3/3	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.277309962818246	2		504	1096	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343712	118343712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782339326	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	92	202	0	ENST00000534358.1:c.1838G>A	p.Arg613Gln	p.R613Q	ENST00000534358	NM_005933.3	613	cGa/cAa	3/36	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.277309962818246	2		202	647	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426973	49426973	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1565778024	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	128	435	0	ENST00000301067.7:c.11515del	p.Gln3839SerfsTer42	p.Q3839Sfs*42	ENST00000301067	NM_003482.3	3839	Cag/ag	39/54	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.277309962818246	2		435	893	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220011	133220011	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	124	419	0	ENST00000320574.5:c.4426T>C	p.Phe1476Leu	p.F1476L	ENST00000320574	NM_006231.2	1476	Ttc/Ctc	34/49	1	2	FACETS	0.919	0.83	1	0.919	0.83	1	CLONAL	1	TRUE	1	0.277309962818246	2		419	973	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562178	21562178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775892552	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	178	493	0	ENST00000382592.4:c.1741C>T	p.Arg581Cys	p.R581C	ENST00000382592	NM_014572.2	581	Cgc/Tgc	4/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.277309962818246	2		493	1136	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103513869	103513869	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	55	157	0	ENST00000355739.4:c.685T>G	p.Phe229Val	p.F229V	ENST00000355739	NM_000123.3	229	Ttt/Gtt	7/15	1	2	FACETS	0.954	0.818	1	0.954	0.818	1	CLONAL	1	TRUE	1	0.277309962818246	2		157	416	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129568	2129568	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776855601	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	165	569	0	ENST00000219476.3:c.3295G>A	p.Gly1099Arg	p.G1099R	ENST00000219476	NM_000548.3	1099	Ggg/Agg	29/42	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.277309962818246	2		569	1076	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831211	3831212	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	75	206	0	ENST00000262367.5:c.1669dup	p.Ala557GlyfsTer14	p.A557Gfs*14	ENST00000262367	NM_004380.2	557	gcc/gGcc	7/31	1	2	FACETS	0.931	0.817	1	0.931	0.817	1	CLONAL	1	TRUE	1	0.277309962818246	2		206	581	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822609	72822609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771122441	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	113	295	0	ENST00000268489.5:c.9566C>T	p.Ala3189Val	p.A3189V	ENST00000268489	NM_006885.3	3189	gCg/gTg	10/10	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.277309962818246	2		295	810	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81941375	81941375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1031437038	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	84	239	0	ENST00000359376.3:c.1553C>T	p.Pro518Leu	p.P518L	ENST00000359376	NM_002661.3	518	cCc/cTc	16/33	1	2	FACETS	0.982	0.868	1	0.982	0.868	1	CLONAL	1	TRUE	1	0.277309962818246	2		239	617	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14628987	14628987	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757131921	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	133	410	0	ENST00000254322.2:c.175C>T	p.Arg59Cys	p.R59C	ENST00000254322	NM_006145.1	59	Cgc/Tgc	1/3	1	2	FACETS	0.924	0.838	1	0.924	0.838	1	CLONAL	1	TRUE	1	0.277309962818246	2		410	1038	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211082	36211082	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	138	526	2	ENST00000222270.7:c.837del	p.Arg280GlyfsTer25	p.R280Gfs*25	ENST00000222270	NM_014727.1	278	aCc/ac	3/37	1	2	FACETS	0.842	0.764	0.924	0.842	0.764	0.924	CLONAL	1	TRUE	1	0.277309962818246	2		528	1182	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867349	45867349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375415853	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	182	479	0	ENST00000391945.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000391945	NM_000400.3	282	Cgg/Tgg	10/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.277309962818246	2		479	1094	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905960	50905960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777944185	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	171	459	0	ENST00000440232.2:c.932G>A	p.Arg311His	p.R311H	ENST00000440232	NM_002691.3	311	cGc/cAc	8/27	1	2	FACETS	0.967	0.887	1	0.967	0.887	1	CLONAL	1	TRUE	1	0.277309962818246	2		459	1276	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660217	227660217	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1340940219	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	149	485	0	ENST00000305123.5:c.3238A>G	p.Asn1080Asp	p.N1080D	ENST00000305123	NM_005544.2	1080	Aac/Gac	1/2	1	2	FACETS	0.998	0.91	1	0.998	0.91	1	CLONAL	1	TRUE	1	0.277309962818246	2		485	1077	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902419	1902420	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1324457447	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	91	314	0	ENST00000382891.5:c.40_41del	p.Ser14CysfsTer42	p.S14Cfs*42	ENST00000382891	NM_133335.3	13	cAG/c	2/22	1	2	FACETS	0.793	0.703	0.889	0.793	0.703	0.889	SUBCLONAL	1	TRUE	1	0.277309962818246	2		314	828	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976876	55976876	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	126	305	0	ENST00000263923.4:c.1036del	p.Glu346SerfsTer17	p.E346Sfs*17	ENST00000263923	NM_002253.2	346	Gag/ag	8/30	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.277309962818246	2		305	799	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694712	176694712	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	80	208	0	ENST00000439151.2:c.5296C>T	p.Arg1766Ter	p.R1766*	ENST00000439151	NM_022455.4	1766	Cga/Tga	15/23	1	2	FACETS	0.952	0.839	1	0.952	0.839	1	CLONAL	1	TRUE	1	0.277309962818246	2		208	606	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178641	32178641	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769456012	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	160	387	2	ENST00000375023.3:c.2753G>A	p.Cys918Tyr	p.C918Y	ENST00000375023	NM_004557.3	918	tGc/tAc	18/30	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.277309962818246	2		389	1118	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651912	36651912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	151	378	0	ENST00000244741.5:c.34C>T	p.Pro12Ser	p.P12S	ENST00000244741	NM_000389.4	12	Cca/Tca	2/3	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.277309962818246	2		378	967	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652302	36652302	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774390644	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	91	354	0	ENST00000244741.5:c.424C>T	p.Arg142Trp	p.R142W	ENST00000244741	NM_000389.4	142	Cgg/Tgg	2/3	1	2	FACETS	0.8	0.71	0.897	0.8	0.71	0.897	SUBCLONAL	1	TRUE	1	0.277309962818246	2		354	820	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157470017	157470018	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	95	269	0	ENST00000346085.5:c.2813_2814del	p.Val938GlufsTer3	p.V938Efs*3	ENST00000346085	NM_020732.3	937	acTGtg/actg	9/20	1	2	FACETS	0.858	0.763	0.958	0.858	0.763	0.958	CLONAL	1	TRUE	1	0.277309962818246	2		269	799	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47735818	47735818	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	158	411	0	ENST00000449228.1:c.42G>T	p.Gln14His	p.Q14H	ENST00000449228	NM_001127240.2	14	caG/caT	1/4	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.277309962818246	2		411	1101	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453453	40453453	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	140	388	0	ENST00000345506.4:c.1154del	p.Asn385MetfsTer13	p.N385Mfs*13	ENST00000345506	NM_003152.3	384	Aaa/aa	10/20	1	2	FACETS	0.934	0.849	1	0.934	0.849	1	CLONAL	1	TRUE	1	0.277309962818246	2		388	1081	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484314	120484314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201100122	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	93	197	0	ENST00000256646.2:c.2816C>T	p.Pro939Leu	p.P939L	ENST00000256646	NM_024408.3	939	cCg/cTg	18/34	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.277309962818246	2		197	579	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11027439	11027439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	140	432	0	ENST00000327064.4:c.1006C>T	p.Arg336Trp	p.R336W	ENST00000327064	NM_199141.1	336	Cgg/Tgg	8/16	1	2	FACETS	0.931	0.847	1	0.931	0.847	1	CLONAL	1	TRUE	1	0.277309962818246	2		432	1084	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224510	39224510	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	88	253	0	ENST00000402219.2:c.2848del	p.Arg950AspfsTer7	p.R950Dfs*7	ENST00000402219	NM_005633.3	950	Aga/ga	18/23	1	2	FACETS	0.912	0.808	1	0.912	0.808	1	CLONAL	1	TRUE	1	0.277309962818246	2		253	696	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23625383	23625383	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1555458822	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	92	249	0	ENST00000261584.4:c.3143del	p.Lys1048ArgfsTer27	p.K1048Rfs*27	ENST00000261584	NM_024675.3	1048	aAg/ag	11/13	1	2	FACETS	0.992	0.882	1	0.992	0.882	1	CLONAL	1	TRUE	1	0.277309962818246	2		249	669	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827723	72827723	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	103	333	0	ENST00000268489.5:c.8858T>C	p.Met2953Thr	p.M2953T	ENST00000268489	NM_006885.3	2953	aTg/aCg	9/10	1	2	FACETS	0.942	0.842	1	0.942	0.842	1	CLONAL	1	TRUE	1	0.277309962818246	2		333	789	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831570	72831570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	149	333	0	ENST00000268489.5:c.5011G>A	p.Ala1671Thr	p.A1671T	ENST00000268489	NM_006885.3	1671	Gct/Act	9/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.277309962818246	2		333	890	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108628	8108628	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	113	358	0	ENST00000585124.1:c.767T>G	p.Leu256Arg	p.L256R	ENST00000585124	NM_004217.3	256	cTg/cGg	8/9	1	2	FACETS	0.859	0.772	0.951	0.859	0.772	0.951	CLONAL	1	TRUE	1	0.277309962818246	2		358	949	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11027082	11027082	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	134	336	0	ENST00000327064.4:c.848-1G>T		p.X283_splice	ENST00000327064	NM_199141.1	283			1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.277309962818246	2		336	921	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262563	39262566	+	frameshift_variant	Frame_Shift_Del	DEL	ACTG	ACTG	-	novel	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	83	226	0	ENST00000402219.2:c.940_943del	p.Gln314TyrfsTer13	p.Q314Yfs*13	ENST00000402219	NM_005633.3	314	CAGTta/ta	7/23	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.277309962818246	2		226	590	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935595	49935595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1332084619	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	167	451	2	ENST00000296474.3:c.1769G>A	p.Cys590Tyr	p.C590Y	ENST00000296474	NM_002447.2	590	tGt/tAt	5/20	0.277309962818246	2	FACETS	1	0.966	1	0.549	0.504	0.597	CLONAL	1	TRUE	0	0.277309962818246	2		453	1096	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52663052	52663052	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	41	104	0	ENST00000394830.3:c.1302-1G>T		p.X434_splice	ENST00000394830	NM_018313.4	434			1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.277309962818246	2		104	255	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	231053	231053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057523490	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	108	364	0	ENST00000264932.6:c.833C>T	p.Ala278Val	p.A278V	ENST00000264932	NM_004168.2	278	gCc/gTc	7/15	1	2	FACETS	0.858	0.769	0.952	0.858	0.769	0.952	CLONAL	1	TRUE	1	0.277309962818246	2		364	908	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222652	157222652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558155146	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	102	273	0	ENST00000346085.5:c.1919C>T	p.Pro640Leu	p.P640L	ENST00000346085	NM_020732.3	640	cCg/cTg	4/20	1	2	FACETS	0.965	0.863	1	0.965	0.863	1	CLONAL	1	TRUE	1	0.277309962818246	2		273	762	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527693	157527693	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	114	272	0	ENST00000346085.5:c.5421del	p.Arg1808ValfsTer43	p.R1808Vfs*43	ENST00000346085	NM_020732.3	1806	ttG/tt	20/20	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.277309962818246	2		272	770	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418304	139418304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022520-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	183	576	1	ENST00000277541.6:c.268G>A	p.Ala90Thr	p.A90T	ENST00000277541	NM_017617.3	90	Gcc/Acc	3/34	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.277309962818246	2		577	1281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0023366-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	299	621	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.224880452755007	3	FACETS	1	0.981	1	0.733	0.689	0.778	CLONAL	2	TRUE	0	0.224880452755007	3		621	1346	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0023366-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	21	122	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.224880452755007	3	FACETS	0.274	0.21	0.35	0.091	0.07	0.117	SUBCLONAL	1	TRUE	0	0.224880452755007	3		122	757	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048638	6048638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023366-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1271	217	245	0	ENST00000265849.7:c.13G>A	p.Glu5Lys	p.E5K	ENST00000265849	NM_000535.5	5	Gag/Aag	1/15	0.224880452755007	6	FACETS	0.94	0.872	1	0.627	0.581	0.675	CLONAL	2	TRUE	3	0.224880452755007	6		245	1488	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610136	10610136	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023366-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	173	255	0	ENST00000171111.5:c.574G>T	p.Glu192Ter	p.E192*	ENST00000171111	NM_203500.1	192	Gag/Tag	2/6	0.191005317441508	2	FACETS	0.772	0.71	0.837	0.772	0.71	0.837	SUBCLONAL	2	TRUE	0	0.224880452755007	2		255	996	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174420	11174420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587777900	NA	P-0023366-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	72	226	0	ENST00000361445.4:c.7255G>A	p.Glu2419Lys	p.E2419K	ENST00000361445	NM_004958.3	2419	Gaa/Aaa	53/58	0.144611269604474	3	FACETS	0.878	0.766	1	0.439	0.383	0.5	CLONAL	1	TRUE	1	0.224880452755007	3		226	811	SUCCESS
ATR	545	MSKCC	GRCh37	3	142222289	142222289	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023366-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	51	71	0	ENST00000350721.4:c.5203C>G	p.His1735Asp	p.H1735D	ENST00000350721	NM_001184.3	1735	Cat/Gat	30/47	0.225783023484312	3	FACETS	1	0.88	1	0.52	0.442	0.606	CLONAL	1	TRUE	1	0.224880452755007	3		71	485	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736239	243736239	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1439435818	NA	P-0023366-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	27	100	0	ENST00000263826.5:c.808C>A	p.Arg270Ser	p.R270S	ENST00000263826	NM_005465.4	270	Cgt/Agt	8/13	0.225783023484312	3	FACETS	0.655	0.521	0.808	0.327	0.26	0.404	SUBCLONAL	1	TRUE	1	0.224880452755007	3		100	408	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58701022	58701022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023366-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	201	150	0	ENST00000305921.3:c.613G>A	p.Asp205Asn	p.D205N	ENST00000305921	NM_003620.3	205	Gat/Aat	2/6	0.221844707737012	4	FACETS	0.838	0.777	0.901	1	0.986	1	CLONAL	3	TRUE	2	0.224880452755007	4		150	871	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366198	15366198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023366-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	90	218	0	ENST00000263377.2:c.1957G>A	p.Glu653Lys	p.E653K	ENST00000263377	NM_058243.2	653	Gaa/Aaa	10/20	0.191005317441508	2	FACETS	0.922	0.817	1	0.461	0.408	0.518	CLONAL	1	TRUE	0	0.224880452755007	2		218	868	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753824	42753824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023366-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1358	87	329	0	ENST00000222329.4:c.440C>T	p.Ser147Leu	p.S147L	ENST00000222329	NM_006494.2	147	tCa/tTa	4/4	0.224880452755007	3	FACETS	0.596	0.525	0.672	0.199	0.175	0.224	SUBCLONAL	1	TRUE	0	0.224880452755007	3		329	1445	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523302	9523302	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023366-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	60	173	0	ENST00000353224.5:c.1935T>A	p.Asn645Lys	p.N645K	ENST00000353224	NM_177990.2	645	aaT/aaA	9/10	0.224880452755007	3	FACETS	0.857	0.737	0.987	0.286	0.245	0.329	CLONAL	1	TRUE	0	0.224880452755007	3		173	693	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714369	40714369	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023366-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	135	131	0	ENST00000373198.4:c.4028G>T	p.Arg1343Leu	p.R1343L	ENST00000373198	NM_133170.3	1343	cGg/cTg	29/32	0.224880452755007	3	FACETS	1	0.962	1	0.732	0.668	0.8	CLONAL	2	TRUE	0	0.224880452755007	3		131	608	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52685805	52685805	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023366-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	27	90	0	ENST00000394830.3:c.667A>G	p.Ile223Val	p.I223V	ENST00000394830	NM_018313.4	223	Ata/Gta	7/30	0.225783023484312	3	FACETS	0.503	0.399	0.622	0.252	0.199	0.311	SUBCLONAL	1	TRUE	1	0.224880452755007	3		90	531	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146457	185146457	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023366-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	43	131	0	ENST00000265026.3:c.88G>C	p.Glu30Gln	p.E30Q	ENST00000265026	NM_004721.4	30	Gag/Cag	2/14	0.225783023484312	3	FACETS	0.818	0.684	0.967	0.409	0.342	0.484	CLONAL	1	TRUE	1	0.224880452755007	3		131	520	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80168964	80168964	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023366-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	59	222	0	ENST00000265081.6:c.3160A>T	p.Thr1054Ser	p.T1054S	ENST00000265081	NM_002439.4	1054	Acc/Tcc	23/24	0.225783023484312	3	FACETS	0.582	0.499	0.673	0.291	0.249	0.337	SUBCLONAL	1	TRUE	1	0.224880452755007	3		222	1003	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517606	176517606	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023366-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	281	330	0	ENST00000292408.4:c.307G>T	p.Ala103Ser	p.A103S	ENST00000292408	NM_213647.1	103	Gca/Tca	3/18	0.225783023484312	3	FACETS	0.946	0.886	1	0.946	0.886	1	CLONAL	2	TRUE	1	0.224880452755007	3		330	1470	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912352	29912352	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs746131702	NA	P-0023366-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1152	79	257	0	ENST00000376809.5:c.971G>C	p.Gly324Ala	p.G324A	ENST00000376809	NM_002116.7	324	gGa/gCa	5/8	0.225783023484312	3	FACETS	0.635	0.556	0.72	0.317	0.278	0.36	SUBCLONAL	1	TRUE	1	0.224880452755007	3		257	1231	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739621	41739621	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023366-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	98	138	0	ENST00000242208.4:c.352G>C	p.Glu118Gln	p.E118Q	ENST00000242208	NM_002192.2	118	Gag/Cag	2/3	0.207445070039294	4	FACETS	0.763	0.681	0.85	0.763	0.681	0.85	SUBCLONAL	2	TRUE	2	0.224880452755007	4		138	700	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846380	128846380	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023366-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	165	236	0	ENST00000249373.3:c.1216G>T	p.Ala406Ser	p.A406S	ENST00000249373	NM_005631.4	406	Gcc/Tcc	6/12	0.225783023484312	3	FACETS	0.791	0.725	0.859	0.791	0.725	0.859	SUBCLONAL	2	TRUE	1	0.224880452755007	3		236	1032	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525841	148525841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023366-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	31	66	0	ENST00000320356.2:c.616C>T	p.His206Tyr	p.H206Y	ENST00000320356	NM_004456.4	206	Cac/Tac	6/20	0.225783023484312	3	FACETS	0.708	0.573	0.862	0.354	0.286	0.431	SUBCLONAL	1	TRUE	1	0.224880452755007	3		66	433	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412488	63412488	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0023366-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	127	139	0	ENST00000330258.3:c.679G>T	p.Glu227Ter	p.E227*	ENST00000330258	NM_152424.3	227	Gaa/Taa	2/2	0.225783023484312	2	FACETS	1	0.96	1			1	CLONAL	2	TRUE	NA	0.224880452755007	2		139	515	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0025930-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	91	483	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.437203443711524	6	FACETS	0.762	0.679	0.85			1	SUBCLONAL	2	TRUE	NA	0.437203443711524	6		483	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0025930-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	177	463	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.326528864301065	3	FACETS	1	0.978	1	0.746	0.695	0.798	CLONAL	2	TRUE	0	0.437203443711524	3		463	441	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11270903	11270903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200402195	NA	P-0025930-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	55	250	0	ENST00000361445.4:c.3622C>T	p.Arg1208Cys	p.R1208C	ENST00000361445	NM_004958.3	1208	Cgc/Tgc	24/58	0.437203443711524	3	FACETS	0.842	0.724	0.971	0.421	0.362	0.486	CLONAL	1	TRUE	1	0.437203443711524	3		250	364	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31437377	31437377	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1160335586	NA	P-0025930-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	60	324	0	ENST00000344624.3:c.2911C>A	p.Leu971Met	p.L971M	ENST00000344624		971	Ctg/Atg	21/33	0.383175216040726	4	FACETS	0.89	0.769	1	0.445	0.384	0.511	CLONAL	1	TRUE	2	0.437203443711524	4		324	443	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976681	90976681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025930-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	60	285	0	ENST00000265433.3:c.951G>A	p.Met317Ile	p.M317I	ENST00000265433	NM_002485.4	317	atG/atA	8/16	0.437203443711524	15	FACETS	1	0.898	1	0.106	0.09	0.122	CLONAL	1	TRUE	5	0.437203443711524	15		285	998	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195115	123195115	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025930-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	74	308	0	ENST00000218089.9:c.1458C>A	p.Asp486Glu	p.D486E	ENST00000218089	NM_001042749.1	486	gaC/gaA	16/35	0.437203443711524	2	FACETS	0.97	0.855	1	0.485	0.427	0.546	CLONAL	1	TRUE	0	0.437203443711524	2		308	349	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026375-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	72	349	1				ENST00000310581	NM_198253.2	-/1132			0.36290031766478	3	FACETS	0.957	0.847	1	0.957	0.847	1	CLONAL	2	TRUE	1	0.36290031766478	3		350	245	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0026375-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	407	684	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.36290031766478	5	FACETS	0.945	0.908	0.982			1	CLONAL	5	TRUE	NA	0.36290031766478	5		686	733	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0026375-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	178	384	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	0.36290031766478	5	FACETS	0.996	0.926	1	0.996	0.926	1	CLONAL	3	TRUE	2	0.36290031766478	5		384	507	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814798	139814798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201857326	NA	P-0026375-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	96	528	1	ENST00000247668.2:c.791C>T	p.Ala264Val	p.A264V	ENST00000247668	NM_021138.3	264	gCg/gTg	8/11	0.327300150835237	3	FACETS	0.918	0.818	1	0.459	0.409	0.512	CLONAL	1	TRUE	1	0.36290031766478	3		529	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0026648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	50	507	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	1	2	FACETS	0.503	0.426	0.587	0.503	0.426	0.587	SUBCLONAL	1	TRUE	1	0.33	2		507	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578179	7578179	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031560-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	497	446	0	ENST00000269305.4:c.670G>T	p.Glu224Ter	p.E224*	ENST00000269305	NM_001126112.2	224	Gag/Tag	6/11	0.298944255671589	4	FACETS	0.949	0.916	0.982			1	CLONAL	4	TRUE	NA	0.442016616684444	4		446	854	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115967	8115968	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031560-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	86	324	0	ENST00000346208.3:c.1315dup	p.Val439GlyfsTer68	p.V439Gfs*68	ENST00000346208		438	atg/atGg	6/6	0.3588176836807	3	FACETS	1	0.95	1	0.562	0.499	0.628	CLONAL	1	TRUE	1	0.442016616684444	3		324	423	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519308	137519308	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031560-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	135	252	0	ENST00000367739.4:c.1330G>T	p.Glu444Ter	p.E444*	ENST00000367739	NM_000416.2	444	Gag/Tag	7/7	0.442016616684444	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.442016616684444	2		252	257	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321067	137321067	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031560-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	147	552	0	ENST00000481739.1:c.1024G>A	p.Val342Met	p.V342M	ENST00000481739	NM_002957.4	342	Gtg/Atg	7/10	0.442016616684444	4	FACETS	1	0.944	1	0.349	0.318	0.381	CLONAL	1	TRUE	1	0.442016616684444	4		552	917	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123873987	123873987	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031560-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	16	54	0	ENST00000330479.4:c.18G>T	p.Lys6Asn	p.K6N	ENST00000330479	NM_020382.3	6	aaG/aaT	2/9	1	2	FACETS	0.787	0.591	1	0.787	0.591	1	CLONAL	1	TRUE	1	0.442016616684444	2		54	92	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866349	42866349	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031560-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	82	631	0	ENST00000398585.3:c.283A>T	p.Thr95Ser	p.T95S	ENST00000398585	NM_001135099.1	95	Acg/Tcg	3/14	0.442016616684444	3	FACETS	0.527	0.464	0.596	0.264	0.232	0.298	SUBCLONAL	1	TRUE	1	0.442016616684444	3		631	859	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0031619-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	615	436	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.359429712115657	4	FACETS	0.951	0.919	0.983	0.951	0.919	0.983	CLONAL	4	TRUE	0	0.367588122330947	4		439	1203	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478161	138478161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031619-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	130	249	0	ENST00000289153.2:c.25C>T	p.Pro9Ser	p.P9S	ENST00000289153	NM_006219.2	9	Cct/Tct	1/22	0.307627415039578	4	FACETS	0.914	0.833	0.998	0.914	0.833	0.998	CLONAL	2	TRUE	2	0.367588122330947	4		249	529	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591140	67591145	+	inframe_deletion	In_Frame_Del	DEL	ACCAAT	ACCAAT	-	rs751582616	NA	P-0031619-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	20	173	0	ENST00000274335.5:c.1735_1740del	p.Gln579_Tyr580del	p.Q579_Y580del	ENST00000274335		578	gACCAATac/gac	12/15	0.367588122330947	2	FACETS	0.486	0.372	0.618	0.243	0.186	0.309	SUBCLONAL	1	TRUE	0	0.367588122330947	2		173	224	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136840	69136840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746734356	NA	P-0031619-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	88	266	1	ENST00000288368.4:c.4754G>A	p.Arg1585Gln	p.R1585Q	ENST00000288368	NM_024870.2	1585	cGg/cAg	39/40	0.262831977159895	4	FACETS	0.776	0.691	0.865	0.776	0.691	0.865	SUBCLONAL	2	TRUE	2	0.367588122330947	4		267	422	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428201	49428201	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0031619-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1359	274	640	0	ENST00000301067.7:c.10499del	p.Gly3500GlufsTer2	p.G3500Efs*2	ENST00000301067	NM_003482.3	3500	gGa/ga	37/54	0.367588122330947	7	FACETS	0.876	0.82	0.934			1	CLONAL	2	TRUE	NA	0.367588122330947	7		640	1633	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434310	49434328	+	frameshift_variant	Frame_Shift_Del	DEL	GACTGGCAGGCACTCGGGA	GACTGGCAGGCACTCGGGA	-	novel	NA	P-0031619-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	725	717	0	ENST00000301067.7:c.7225_7243del	p.Ser2409LeufsTer11	p.S2409Lfs*11	ENST00000301067	NM_003482.3	2409	TCCCGAGTGCCTGCCAGTCct/ct	31/54	0.367588122330947	7	FACETS	1	0.991	1			1	CLONAL	4	TRUE	NA	0.367588122330947	7		717	1768	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031619-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	52	386	0	ENST00000401558.2:c.2246G>C	p.Arg749Pro	p.R749P	ENST00000401558	NM_003400.3	749	cGa/cCa	19/25	0.367588122330947	3	FACETS	0.796	0.679	0.923	0.398	0.339	0.462	CLONAL	1	TRUE	1	0.367588122330947	3		386	421	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40828006	40828006	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031619-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	63	342	0	ENST00000373198.4:c.2422G>C	p.Glu808Gln	p.E808Q	ENST00000373198	NM_133170.3	808	Gag/Cag	17/32	0.367588122330947	2	FACETS	0.788	0.684	0.901	0.394	0.342	0.451	CLONAL	1	TRUE	0	0.367588122330947	2		342	435	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515243	149515243	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031619-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	420	615	0	ENST00000261799.4:c.239C>A	p.Thr80Asn	p.T80N	ENST00000261799	NM_002609.3	80	aCc/aAc	3/23	0.364291423686578	3	FACETS	0.939	0.898	0.98	0.939	0.898	0.98	CLONAL	3	TRUE	0	0.367588122330947	3		615	960	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750920	128750920	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031619-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1897	1465	478	0	ENST00000377970.2:c.457T>A	p.Phe153Ile	p.F153I	ENST00000377970	NM_002467.4	153	Ttc/Atc	2/3	0.367588122330947	23	FACETS	0.96	0.937	0.983			1	CLONAL	12	TRUE	NA	0.367588122330947	23		478	3362	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0032183-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	504	609	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.80990032623021	2		609	614	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386450	31386450	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0032183-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	195	578	0	ENST00000328111.2:c.1674+1G>C		p.X558_splice	ENST00000328111	NM_006892.3	558			0.80990032623021	4	FACETS	0.694	0.641	0.75	0.231	0.213	0.25	SUBCLONAL	1	TRUE	1	0.80990032623021	4		578	1255	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100403	8100403	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032183-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	251	839	0	ENST00000346208.3:c.377C>A	p.Ser126Tyr	p.S126Y	ENST00000346208		126	tCc/tAc	3/6	0.115101214559891	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.80990032623021	0		839	660	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670880	134670880	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032183-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	91	287	0	ENST00000398015.3:c.791G>T	p.Ser264Ile	p.S264I	ENST00000398015	NM_004441.4	264	aGc/aTc	3/16	0.80990032623021	3	FACETS	0.915	0.82	1	0.458	0.41	0.508	CLONAL	1	TRUE	1	0.80990032623021	3		287	345	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507321	8507321	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750349056	NA	P-0032183-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	206	246	0	ENST00000356435.5:c.1657G>A	p.Asp553Asn	p.D553N	ENST00000356435		553	Gat/Aat	11/35	0.80990032623021	2	FACETS	0.997	0.96	1	0.997	0.96	1	CLONAL	2	TRUE	0	0.80990032623021	2		246	255	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187817	11187817	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032183-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	143	408	1	ENST00000361445.4:c.6080G>T	p.Trp2027Leu	p.W2027L	ENST00000361445	NM_004958.3	2027	tGg/tTg	44/58	1	2	FACETS	0.915	0.844	0.988	0.915	0.844	0.988	CLONAL	1	TRUE	1	0.80990032623021	2		409	386	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316145	11316145	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032183-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	217	525	0	ENST00000361445.4:c.609G>C	p.Gln203His	p.Q203H	ENST00000361445	NM_004958.3	203	caG/caC	5/58	1	2	FACETS	0.919	0.861	0.978	0.919	0.861	0.978	CLONAL	1	TRUE	1	0.80990032623021	2		525	583	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175996765	175996765	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032183-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	165	371	0	ENST00000367669.3:c.1672G>T	p.Val558Leu	p.V558L	ENST00000367669	NM_022457.5	558	Gtg/Ttg	15/20	0.80990032623021	3	FACETS	0.965	0.891	1	0.483	0.445	0.521	CLONAL	1	TRUE	1	0.80990032623021	3		371	593	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192687	94192710	+	inframe_deletion	In_Frame_Del	DEL	CCACAAATTCTTGTACTGCTTCAC	CCACAAATTCTTGTACTGCTTCAC	-	novel	NA	P-0032183-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	306	387	0	ENST00000323929.3:c.1364_1387del	p.Gly455_Val462del	p.G455_V462del	ENST00000323929	NM_005591.3	455	gGTGAAGCAGTACAAGAATTTGTGGac/gac	13/20	0.80990032623021	3	FACETS	0.869	0.827	0.911	0.869	0.827	0.911	CLONAL	2	TRUE	1	0.80990032623021	3		387	611	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204761	94204761	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032183-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	134	264	0	ENST00000323929.3:c.824C>A	p.Ser275Tyr	p.S275Y	ENST00000323929	NM_005591.3	275	tCc/tAc	8/20	0.80990032623021	3	FACETS	0.971	0.888	1	0.485	0.444	0.528	CLONAL	1	TRUE	1	0.80990032623021	3		264	479	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497576	125497576	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032183-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	94	198	0	ENST00000428830.2:c.140A>G	p.Asp47Gly	p.D47G	ENST00000428830	NM_001114121.2	47	gAc/gGc	3/14	0.80990032623021	3	FACETS	0.937	0.842	1	0.469	0.421	0.519	CLONAL	1	TRUE	1	0.80990032623021	3		198	348	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337660	73337660	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1175752033	NA	P-0032183-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	138	139	0	ENST00000377767.4:c.2056G>C	p.Ala686Pro	p.A686P	ENST00000377767	NM_014953.3	686	Gct/Cct	16/21	0.80990032623021	3	FACETS	0.993	0.927	1	0.993	0.927	1	CLONAL	2	TRUE	1	0.80990032623021	3		139	241	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544683	65544684	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0032183-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	382	525	0	ENST00000358664.4:c.242_243del	p.His81ProfsTer5	p.H81Pfs*5	ENST00000358664	NM_002382.4	81	cAC/c	4/5	0.80990032623021	2	FACETS	0.905	0.876	0.933	0.905	0.876	0.933	CLONAL	2	TRUE	0	0.80990032623021	2		525	521	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43772156	43772156	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032183-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	238	540	0	ENST00000382044.4:c.559G>C	p.Glu187Gln	p.E187Q	ENST00000382044	NM_001141980.1	187	Gag/Cag	6/28	0.80990032623021	2	FACETS	0.943	0.887	1	0.472	0.443	0.501	CLONAL	1	TRUE	0	0.80990032623021	2		540	623	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614983	23614983	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs876658773	NA	P-0032183-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	226	256	0	ENST00000261584.4:c.3358G>T	p.Glu1120Ter	p.E1120*	ENST00000261584	NM_024675.3	1120	Gaa/Taa	13/13	0.80990032623021	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.80990032623021	2		256	267	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56867141	56867141	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032183-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	406	481	0	ENST00000308159.5:c.1360A>T	p.Thr454Ser	p.T454S	ENST00000308159	NM_014669.4	454	Acg/Tcg	13/22	0.80990032623021	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.80990032623021	2		481	486	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435602	56435602	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032183-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	238	624	0	ENST00000407977.2:c.1535G>T	p.Ser512Ile	p.S512I	ENST00000407977		512	aGc/aTc	9/10	0.80990032623021	3	FACETS	0.997	0.933	1	0.499	0.466	0.532	CLONAL	1	TRUE	1	0.80990032623021	3		624	828	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226361	2226361	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032183-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	619	901	0	ENST00000398665.3:c.3841G>T	p.Glu1281Ter	p.E1281*	ENST00000398665	NM_032482.2	1281	Gag/Tag	27/28	0.80990032623021	2	FACETS	0.999	0.977	1	0.999	0.977	1	CLONAL	2	TRUE	0	0.80990032623021	2		901	765	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18964065	18964065	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032183-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	262	441	0	ENST00000262803.5:c.1062G>T	p.Met354Ile	p.M354I	ENST00000262803	NM_002911.3	354	atG/atT	8/24	0.80990032623021	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.80990032623021	2		441	322	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794361	242794361	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200312345	NA	P-0032183-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	211	750	0	ENST00000334409.5:c.581G>A	p.Arg194Gln	p.R194Q	ENST00000334409	NM_005018.2	194	cGg/cAg	3/5	NA	2	FACETS	0.659	0.613	0.706			1	INDETERMINATE	1	TRUE	NA	0.80990032623021	2		750	791	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52649469	52649469	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032183-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	129	345	0	ENST00000394830.3:c.1822T>G	p.Tyr608Asp	p.Y608D	ENST00000394830	NM_018313.4	608	Tat/Gat	16/30	1	2	FACETS	0.934	0.858	1	0.934	0.858	1	CLONAL	1	TRUE	1	0.80990032623021	2		345	341	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137522018	137522018	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032183-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	104	115	0	ENST00000367739.4:c.861G>C	p.Leu287Phe	p.L287F	ENST00000367739	NM_000416.2	287	ttG/ttC	6/7	0.80990032623021	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.80990032623021	2		115	127	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69103970	69103970	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032183-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	163	336	0	ENST00000288368.4:c.4360G>T	p.Asp1454Tyr	p.D1454Y	ENST00000288368	NM_024870.2	1454	Gac/Tac	36/40	1	2	FACETS	0.934	0.866	1	0.934	0.866	1	CLONAL	1	TRUE	1	0.80990032623021	2		336	431	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133748425	133748425	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0032183-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	194	310	0	ENST00000318560.5:c.1085+1G>T		p.X362_splice	ENST00000318560	NM_005157.4	362			0.80990032623021	2	FACETS	0.962	0.922	0.999	0.962	0.922	0.999	CLONAL	2	TRUE	0	0.80990032623021	2		310	249	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617573	100617574	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0032183-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	193	261	1	ENST00000308731.7:c.495_496delinsAA	p.Cys165_Gln166delinsTer	p.C165_Q166delins*	ENST00000308731	NM_000061.2	165	tgCCaa/tgAAaa	6/19	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.80990032623021	1		262	245	SUCCESS
FH	2271	MSKCC	GRCh37	1	241676920	241676920	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032183-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	111	312	0	ENST00000366560.3:c.361A>G	p.Met121Val	p.M121V	ENST00000366560	NM_000143.3	121	Atg/Gtg	3/10	0.80990032623021	3	FACETS	0.896	0.811	0.984	0.448	0.405	0.492	CLONAL	1	TRUE	1	0.80990032623021	3		312	430	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55693391	55693391	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032183-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	232	602	0	ENST00000284073.2:c.598G>T	p.Ala200Ser	p.A200S	ENST00000284073	NM_138962.2	200	Gcc/Tcc	9/14	0.80990032623021	3	FACETS	0.955	0.892	1	0.477	0.446	0.51	CLONAL	1	TRUE	1	0.80990032623021	3		602	843	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827927	40827927	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs536150112	NA	P-0032183-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	149	477	0	ENST00000373198.4:c.2501G>T	p.Arg834Leu	p.R834L	ENST00000373198	NM_133170.3	834	cGc/cTc	17/32	0.265861090345153	6	FACETS	1	0.98	1	0.208	0.189	0.226	INDETERMINATE	1	TRUE	0	0.80990032623021	6		477	774	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37628870	37628870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748613308	NA	P-0032183-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	227	681	0	ENST00000249071.6:c.196C>T	p.Arg66Cys	p.R66C	ENST00000249071	NM_002872.4	66	Cgt/Tgt	3/7	0.804530970516531	2	FACETS	0.911	0.855	0.969	0.456	0.427	0.485	CLONAL	1	TRUE	0	0.80990032623021	2		681	615	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438568	52438568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032183-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	173	480	0	ENST00000460680.1:c.1151G>A	p.Ser384Asn	p.S384N	ENST00000460680	NM_004656.3	384	aGc/aAc	12/17	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.80990032623021	2		480	402	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143326387	143326387	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032183-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	142	325	0	ENST00000262992.4:c.227C>T	p.Thr76Ile	p.T76I	ENST00000262992	NM_001101669.1	76	aCa/aTa	4/24	0.80990032623021	2	FACETS	0.911	0.84	0.984	0.455	0.42	0.492	CLONAL	1	TRUE	0	0.80990032623021	2		325	385	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974719	21974721	+	frameshift_variant	Frame_Shift_Del	DEL	CGC	CGC	GG	novel	NA	P-0032183-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	259	367	2	ENST00000304494.5:c.106_108delinsCC	p.Ala36ProfsTer17	p.A36Pfs*17	ENST00000304494	NM_000077.4	36	GCG/CC	1/3	0.80990032623021	2	FACETS	0.914	0.878	0.947	0.914	0.878	0.947	CLONAL	2	TRUE	0	0.80990032623021	2		369	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0032293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	363	875	1	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.245314085671169	2	FACETS	0.837	0.792	0.883	0.837	0.792	0.883	CLONAL	2	TRUE	0	0.29177559708074	2		876	1487	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050864	49050864	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886042935	NA	P-0032293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	31	239	0	ENST00000267163.4:c.2548C>T	p.Gln850Ter	p.Q850*	ENST00000267163	NM_000321.2	850	Cag/Tag	25/27	0.29177559708074	1	FACETS	0.639	0.518	0.774	0.639	0.518	0.774	SUBCLONAL	1	TRUE	0	0.29177559708074	1		239	284	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509421	106509421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751167601	NA	P-0032293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	121	454	0	ENST00000359195.3:c.1415G>A	p.Arg472His	p.R472H	ENST00000359195	NM_002649.2	472	cGt/cAt	2/11	1	2	FACETS	0.836	0.754	0.923	0.836	0.754	0.923	CLONAL	1	TRUE	1	0.29177559708074	2		454	992	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484028	50484028	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	60	534	0	ENST00000394963.4:c.878C>T	p.Pro293Leu	p.P293L	ENST00000394963	NM_003076.4	293	cCc/cTc	8/13	0.16216684735907	2	FACETS	0.514	0.442	0.593	0.257	0.221	0.297	INDETERMINATE	1	TRUE	0	0.29177559708074	2		534	800	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646686	23646686	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	104	395	0	ENST00000261584.4:c.1181A>G	p.His394Arg	p.H394R	ENST00000261584	NM_024675.3	394	cAt/cGt	4/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.29177559708074	2		395	602	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289985	15289985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1501	362	936	0	ENST00000263388.2:c.3569G>C	p.Arg1190Pro	p.R1190P	ENST00000263388	NM_000435.2	1190	cGc/cCc	22/33	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.29177559708074	2		936	1863	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989641	68989641	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199776134	NA	P-0032293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	40	390	0	ENST00000288368.4:c.1579C>T	p.Arg527Cys	p.R527C	ENST00000288368	NM_024870.2	527	Cgc/Tgc	15/40	0.29177559708074	3	FACETS	0.502	0.416	0.598	0.251	0.208	0.299	SUBCLONAL	1	TRUE	1	0.29177559708074	3		390	626	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389273	8389273	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	31	416	0	ENST00000356435.5:c.4345G>A	p.Ala1449Thr	p.A1449T	ENST00000356435		1449	Gcc/Acc	26/35	0.16216684735907	2	FACETS	0.372	0.3	0.454	0.186	0.15	0.227	INDETERMINATE	1	TRUE	0	0.29177559708074	2		416	571	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412345	139412345	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1325	124	784	0	ENST00000277541.6:c.1300G>T	p.Gly434Cys	p.G434C	ENST00000277541	NM_017617.3	434	Ggc/Tgc	8/34	0.162227885456346	2	FACETS	0.587	0.529	0.648	0.293	0.264	0.324	INDETERMINATE	1	TRUE	0	0.29177559708074	2		784	1449	SUCCESS
AR	367	MSKCC	GRCh37	X	66863212	66863212	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0032293-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	112	445	0	ENST00000374690.3:c.1731T>A	p.Cys577Ter	p.C577*	ENST00000374690	NM_000044.3	577	tgT/tgA	2/8	0.29177559708074	3	FACETS	0.936	0.841	1	0.468	0.42	0.519	CLONAL	1	TRUE	1	0.29177559708074	3		445	940	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0032986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	118	347	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.553852009968842	3	FACETS	0.889	0.804	0.978	0.445	0.402	0.489	CLONAL	1	TRUE	1	0.568111865398997	3		347	600	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374244	138374244	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	179	422	0	ENST00000289153.2:c.3200A>T	p.Asp1067Val	p.D1067V	ENST00000289153	NM_006219.2	1067	gAc/gTc	22/22	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.568111865398997	2		422	628	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663004	227663004	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	269	724	0	ENST00000305123.5:c.451T>G	p.Tyr151Asp	p.Y151D	ENST00000305123	NM_005544.2	151	Tac/Gac	1/2	1	2	FACETS	0.961	0.903	1	0.961	0.903	1	CLONAL	1	TRUE	1	0.568111865398997	2		724	985	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417781	138417781	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1215972519	NA	P-0032986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	141	302	0	ENST00000289153.2:c.1738A>G	p.Ile580Val	p.I580V	ENST00000289153	NM_006219.2	580	Atc/Gtc	11/22	1	2	FACETS	0.805	0.735	0.876	0.805	0.735	0.876	CLONAL	1	TRUE	1	0.568111865398997	2		302	617	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058570	42058574	+	frameshift_variant	Frame_Shift_Del	DEL	AGAGG	AGAGG	-	novel	NA	P-0032986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	75	181	0	ENST00000219905.7:c.8290_8294del	p.Arg2764GlyfsTer12	p.R2764Gfs*12	ENST00000219905	NM_001164273.1	2764	AGAGGg/g	24/24	1	2	FACETS	0.807	0.713	0.907	0.807	0.713	0.907	CLONAL	1	TRUE	1	0.568111865398997	2		181	327	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641626	23641626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	200	412	0	ENST00000261584.4:c.1849G>A	p.Glu617Lys	p.E617K	ENST00000261584	NM_024675.3	617	Gaa/Aaa	5/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.568111865398997	2		412	648	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699401	47699401	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	100	209	0	ENST00000347630.2:c.107G>C	p.Trp36Ser	p.W36S	ENST00000347630	NM_001007230.1	36	tGg/tCg	4/11	1	2	FACETS	0.912	0.821	1	0.912	0.821	1	CLONAL	1	TRUE	1	0.568111865398997	2		209	386	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225360594	225360594	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	89	172	0	ENST00000264414.4:c.1797G>T	p.Met599Ile	p.M599I	ENST00000264414	NM_003590.4	599	atG/atT	13/16	1	2	FACETS	0.801	0.715	0.892	0.801	0.715	0.892	CLONAL	1	TRUE	1	0.568111865398997	2		172	391	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971155	21971168	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCCGTGGAGCAG	GCGCCGTGGAGCAG	-	novel	NA	P-0032986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	240	606	0	ENST00000304494.5:c.190_203del	p.Leu64GlyfsTer51	p.L64Gfs*51	ENST00000304494	NM_000077.4	64	CTGCTCCACGGCGCg/g	2/3	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.568111865398997	2		606	674	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971155	21971169	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCCGTGGAGCAGC	GCGCCGTGGAGCAGC	T	novel	NA	P-0032986-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	240	606	0	ENST00000304494.5:c.189_203delinsA	p.Leu64GlyfsTer51	p.L64Gfs*51	ENST00000304494	NM_000077.4	63	ctGCTGCTCCACGGCGCg/ctAg	2/3	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.568111865398997	2		606	674	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444879	49444879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370622706	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	244	1697	1	ENST00000301067.7:c.2587C>T	p.Arg863Trp	p.R863W	ENST00000301067	NM_003482.3	863	Cgg/Tgg	10/54	NA	2	FACETS	0.86	0.806	0.915			1	INDETERMINATE	1	TRUE	NA	0.72185111969597	2		1698	786	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803788	43803788	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1228227826	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	212	937	0	ENST00000372470.3:c.98C>G	p.Ser33Ter	p.S33*	ENST00000372470	NM_005373.2	33	tCa/tGa	2/12	0.145788645215797	4	FACETS	0.776	0.724	0.828	0.776	0.724	0.828	INDETERMINATE	2	TRUE	2	0.72185111969597	4		937	652	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852095	63852095	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	46	896	1	ENST00000279873.7:c.2873C>T	p.Ser958Leu	p.S958L	ENST00000279873	NM_032199.2	958	tCa/tTa	10/10	1	2	FACETS	0.207	0.174	0.244	0.207	0.174	0.244	SUBCLONAL	1	TRUE	1	0.72185111969597	2		897	615	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742925	17742925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	219	1640	2	ENST00000250003.3:c.833C>T	p.Ser278Leu	p.S278L	ENST00000250003	NM_002478.4	278	tCg/tTg	3/3	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.72185111969597	2		1642	583	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464334	464334	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs769099791	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	41	780	0	ENST00000399788.2:c.860C>G	p.Ser287Cys	p.S287C	ENST00000399788	NM_001042603.1	287	tCt/tGt	7/28	1	2	FACETS	0.204	0.169	0.242	0.204	0.169	0.242	SUBCLONAL	1	TRUE	1	0.72185111969597	2		780	558	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025625	1025625	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1221779344	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	215	1445	0	ENST00000358495.3:c.750G>C	p.Glu250Asp	p.E250D	ENST00000358495	NM_134424.2	250	gaG/gaC	9/12	1	2	FACETS	0.955	0.893	1	0.955	0.893	1	CLONAL	1	TRUE	1	0.72185111969597	2		1445	624	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445068	49445068	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	217	1360	3	ENST00000301067.7:c.2398C>T	p.Gln800Ter	p.Q800*	ENST00000301067	NM_003482.3	800	Cag/Tag	10/54	NA	2	FACETS	0.893	0.835	0.953			1	INDETERMINATE	1	TRUE	NA	0.72185111969597	2		1363	673	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589808	28589808	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568745490	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	67	965	0	ENST00000241453.7:c.2572G>A	p.Glu858Lys	p.E858K	ENST00000241453	NM_004119.2	858	Gaa/Aaa	21/24	0.676757955570068	2	FACETS	0.321	0.279	0.367	0.161	0.139	0.184	SUBCLONAL	1	TRUE	0	0.72185111969597	2		965	578	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32932053	32932053	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1135401919	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	28	326	0	ENST00000380152.3:c.7792G>T	p.Glu2598Ter	p.E2598*	ENST00000380152		2598	Gaa/Taa	16/27	0.676757955570068	2	FACETS	0.326	0.261	0.399	0.163	0.13	0.2	SUBCLONAL	1	TRUE	0	0.72185111969597	2		326	238	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336214	73336214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1447466472	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	83	310	0	ENST00000377767.4:c.2189C>T	p.Ser730Phe	p.S730F	ENST00000377767	NM_014953.3	730	tCt/tTt	17/21	0.676757955570068	2	FACETS	0.878	0.785	0.974	0.439	0.392	0.487	CLONAL	1	TRUE	0	0.72185111969597	2		310	262	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060789	38060789	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	82	2027	0	ENST00000250448.2:c.1200C>G	p.Phe400Leu	p.F400L	ENST00000250448	NM_004496.3	400	ttC/ttG	2/2	1	2	FACETS	0.254	0.223	0.287	0.254	0.223	0.287	SUBCLONAL	1	TRUE	1	0.72185111969597	2		2027	894	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724519	43724519	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	304	1179	0	ENST00000382044.4:c.3548G>C	p.Cys1183Ser	p.C1183S	ENST00000382044	NM_001141980.1	1183	tGt/tCt	17/28	1	2	FACETS	0.949	0.897	1	0.949	0.897	1	CLONAL	1	TRUE	1	0.72185111969597	2		1179	888	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43769953	43769953	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	96	343	0	ENST00000382044.4:c.793G>C	p.Glu265Gln	p.E265Q	ENST00000382044	NM_001141980.1	265	Gag/Cag	8/28	1	2	FACETS	0.908	0.819	0.999	0.908	0.819	0.999	CLONAL	1	TRUE	1	0.72185111969597	2		343	293	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346908	89347081	+	inframe_deletion	In_Frame_Del	DEL	CGGCGCCTCCGAGGCGCTGAAGGGCCCTGGGGCGGCAGAGTGGAGGGGGTCCGCGGGGCAGAAACGCTTTGGGGACTCGGGGAATCTCTGTGGAGACTTCAGCAGGAGGTCCGAGCCCACAGGCCAGCTCACAGGGTTTTCAGAGGTGCCCCCGATCAGGCTAGAGGCAAGCGC	CGGCGCCTCCGAGGCGCTGAAGGGCCCTGGGGCGGCAGAGTGGAGGGGGTCCGCGGGGCAGAAACGCTTTGGGGACTCGGGGAATCTCTGTGGAGACTTCAGCAGGAGGTCCGAGCCCACAGGCCAGCTCACAGGGTTTTCAGAGGTGCCCCCGATCAGGCTAGAGGCAAGCGC	-	novel	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	38	950	0	ENST00000301030.4:c.5869_6042del	p.Ala1957_Pro2014del	p.A1957_P2014del	ENST00000301030	NM_001256183.1	1957	GCGCTTGCCTCTAGCCTGATCGGGGGCACCTCTGAAAACCCTGTGAGCTGGCCTGTGGGCTCGGACCTCCTGCTGAAGTCTCCACAGAGATTCCCCGAGTCCCCAAAGCGTTTCTGCCCCGCGGACCCCCTCCACTCTGCCGCCCCAGGGCCCTTCAGCGCCTCGGAGGCGCCG/-	9/13	1	2	FACETS	0.282	0.233	0.337	0.282	0.233	0.337	SUBCLONAL	1	TRUE	1	0.72185111969597	2		950	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577595	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	379	875	0	ENST00000269305.4:c.686_687del	p.Cys229TyrfsTer10	p.C229Yfs*10	ENST00000269305	NM_001126112.2	229	tGT/t	7/11	0.636541800741792	2	FACETS	0.875	0.842	0.907	0.875	0.842	0.907	CLONAL	2	TRUE	0	0.72185111969597	2		875	600	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740438	58740439	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs758630849	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	35	800	0	ENST00000305921.3:c.1349dup	p.Leu450PhefsTer6	p.L450Ffs*6	ENST00000305921	NM_003620.3	448	aat/aaTt	6/6	0.647201293759404	2	FACETS	0.165	0.135	0.2	0.083	0.067	0.1	SUBCLONAL	1	TRUE	0	0.72185111969597	2		800	587	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575080	48575080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	179	536	1	ENST00000342988.3:c.274C>T	p.His92Tyr	p.H92Y	ENST00000342988	NM_005359.5	92	Cat/Tat	3/12	0.667845417680177	2	FACETS	0.852	0.805	0.899	0.852	0.805	0.899	CLONAL	2	TRUE	0	0.72185111969597	2		537	291	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855871	45855871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370377312	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	84	1530	3	ENST00000391945.4:c.1939C>T	p.Arg647Cys	p.R647C	ENST00000391945	NM_000400.3	647	Cgt/Tgt	21/23	1	2	FACETS	0.263	0.232	0.297	0.263	0.232	0.297	SUBCLONAL	1	TRUE	1	0.72185111969597	2		1533	885	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919074	50919074	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	228	1602	1	ENST00000440232.2:c.2811G>T	p.Met937Ile	p.M937I	ENST00000440232	NM_002691.3	937	atG/atT	22/27	1	2	FACETS	0.892	0.835	0.951	0.892	0.835	0.951	CLONAL	1	TRUE	1	0.72185111969597	2		1603	708	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130394	29130394	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	166	587	0	ENST00000328354.6:c.316C>A	p.Leu106Ile	p.L106I	ENST00000328354	NM_007194.3	106	Ctt/Att	2/15	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.72185111969597	2		587	449	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130540	29130540	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881695	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	171	1071	0	ENST00000328354.6:c.170C>T	p.Ser57Phe	p.S57F	ENST00000328354	NM_007194.3	57	tCt/tTt	2/15	1	2	FACETS	0.827	0.765	0.891	0.827	0.765	0.891	CLONAL	1	TRUE	1	0.72185111969597	2		1071	573	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130552	29130552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	169	1167	2	ENST00000328354.6:c.158C>T	p.Ser53Phe	p.S53F	ENST00000328354	NM_007194.3	53	tCt/tTt	2/15	1	2	FACETS	0.774	0.715	0.835	0.774	0.715	0.835	SUBCLONAL	1	TRUE	1	0.72185111969597	2		1169	605	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523735	41523735	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1186117620	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	215	1069	1	ENST00000263253.7:c.1151C>T	p.Ser384Leu	p.S384L	ENST00000263253	NM_001429.3	384	tCa/tTa	4/31	1	2	FACETS	0.747	0.696	0.8	0.747	0.696	0.8	SUBCLONAL	1	TRUE	1	0.72185111969597	2		1070	797	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670281	134670281	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	52	725	0	ENST00000398015.3:c.192C>G	p.Phe64Leu	p.F64L	ENST00000398015	NM_004441.4	64	ttC/ttG	3/16	0.72185111969597	3	FACETS	0.324	0.275	0.378	0.162	0.137	0.189	SUBCLONAL	1	TRUE	1	0.72185111969597	3		725	605	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176461	142176461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	75	336	0	ENST00000350721.4:c.7640G>A	p.Arg2547Gln	p.R2547Q	ENST00000350721	NM_001184.3	2547	cGa/cAa	45/47	0.72185111969597	3	FACETS	0.797	0.703	0.896	0.398	0.351	0.448	SUBCLONAL	1	TRUE	1	0.72185111969597	3		336	355	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186838	142186838	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1339292607	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	116	341	0	ENST00000350721.4:c.6625G>C	p.Glu2209Gln	p.E2209Q	ENST00000350721	NM_001184.3	2209	Gag/Cag	39/47	0.72185111969597	3	FACETS	0.931	0.844	1	0.465	0.422	0.511	CLONAL	1	TRUE	1	0.72185111969597	3		341	470	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902959	1902959	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	31	649	0	ENST00000382891.5:c.578C>G	p.Ser193Ter	p.S193*	ENST00000382891	NM_133335.3	193	tCa/tGa	2/22	1	2	FACETS	0.151	0.122	0.185	0.151	0.122	0.185	SUBCLONAL	1	TRUE	1	0.72185111969597	2		649	568	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549745	187549745	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	14	538	0	ENST00000441802.2:c.4496del	p.Pro1499HisfsTer2	p.P1499Hfs*2	ENST00000441802	NM_005245.3	1499	cCa/ca	8/27	0.700159000983321	1	FACETS	0.091	0.065	0.122	0.091	0.065	0.122	SUBCLONAL	1	TRUE	0	0.72185111969597	1		538	273	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235281	235281	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	34	781	1	ENST00000264932.6:c.1087C>A	p.His363Asn	p.H363N	ENST00000264932	NM_004168.2	363	Cac/Aac	9/15	0.109742236029153	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.72185111969597	0		782	437	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176969	56176969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766783359	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	101	446	1	ENST00000399503.3:c.2239G>A	p.Glu747Lys	p.E747K	ENST00000399503	NM_005921.1	747	Gaa/Aaa	13/20	0.158233363622356	2	FACETS	0.886	0.801	0.973	0.443	0.4	0.487	INDETERMINATE	1	TRUE	0	0.72185111969597	2		447	316	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519721	137519721	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	68	337	0	ENST00000367739.4:c.917C>G	p.Ser306Ter	p.S306*	ENST00000367739	NM_000416.2	306	tCa/tGa	7/7	0.688123779692912	1	FACETS	0.634	0.562	0.708	0.634	0.562	0.708	SUBCLONAL	1	TRUE	0	0.72185111969597	1		337	190	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729569	41729569	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	219	1105	0	ENST00000242208.4:c.960C>G	p.Ile320Met	p.I320M	ENST00000242208	NM_002192.2	320	atC/atG	3/3	1	2	FACETS	0.996	0.933	1	0.996	0.933	1	CLONAL	1	TRUE	1	0.72185111969597	2		1105	609	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444296	50444296	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	112	617	1	ENST00000331340.3:c.226G>A	p.Glu76Lys	p.E76K	ENST00000331340	NM_006060.4	76	Gaa/Aaa	4/8	1	2	FACETS	0.8	0.726	0.877	0.8	0.726	0.877	SUBCLONAL	1	TRUE	1	0.72185111969597	2		618	388	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220298	55220298	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	119	1494	0	ENST00000275493.2:c.688G>C	p.Asp230His	p.D230H	ENST00000275493	NM_005228.3	230	Gac/Cac	6/28	1	2	FACETS	0.387	0.349	0.427	0.387	0.349	0.427	SUBCLONAL	1	TRUE	1	0.72185111969597	2		1494	852	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220345	55220345	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	99	1369	0	ENST00000275493.2:c.735G>C	p.Glu245Asp	p.E245D	ENST00000275493	NM_005228.3	245	gaG/gaC	6/28	1	2	FACETS	0.373	0.332	0.415	0.373	0.332	0.415	SUBCLONAL	1	TRUE	1	0.72185111969597	2		1369	736	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412167	63412167	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033162-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	209	662	0	ENST00000330258.3:c.1000G>C	p.Glu334Gln	p.E334Q	ENST00000330258	NM_152424.3	334	Gaa/Caa	2/2	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.72185111969597	1		662	309	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363243	40363243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033799-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	40	441	0	ENST00000397332.2:c.986C>T	p.Ser329Leu	p.S329L	ENST00000397332	NM_001033082.2	329	tCg/tTg	3/3	1	2	FACETS	0.564	0.468	0.671	0.564	0.468	0.671	SUBCLONAL	1	TRUE	1	0.27	2		441	525	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397742	49397742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552757	NA	P-0033799-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	67	384	1	ENST00000418115.1:c.482C>T	p.Ala161Val	p.A161V	ENST00000418115	NM_001664.2	161	gCa/gTa	5/5	1	2	FACETS	0.831	0.723	0.949	0.831	0.723	0.949	CLONAL	1	TRUE	1	0.27	2		385	597	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521253	187521253	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033799-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	36	467	0	ENST00000441802.2:c.11902C>T	p.Gln3968Ter	p.Q3968*	ENST00000441802	NM_005245.3	3968	Caa/Taa	22/27	1	2	FACETS	0.575	0.472	0.69	0.575	0.472	0.69	SUBCLONAL	1	TRUE	1	0.27	2		467	464	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216899	7216899	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033799-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	45	323	0	ENST00000380728.2:c.622C>T	p.Gln208Ter	p.Q208*	ENST00000380728		208	Cag/Tag	7/11	1	2	FACETS	0.734	0.617	0.863	0.734	0.617	0.863	SUBCLONAL	1	TRUE	1	0.27	2		323	454	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056181	27056181	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033799-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	91	372	1	ENST00000324856.7:c.1177C>T	p.Gln393Ter	p.Q393*	ENST00000324856	NM_006015.4	393	Cag/Tag	2/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.27	2		373	532	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797891	45797891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199840380	NA	P-0033799-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	38	565	0	ENST00000450313.1:c.880C>T	p.Arg294Cys	p.R294C	ENST00000450313	NM_012222.2	294	Cgc/Tgc	10/16	1	2	FACETS	0.389	0.32	0.466	0.389	0.32	0.466	SUBCLONAL	1	TRUE	1	0.27	2		565	724	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118354897	118354897	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0033799-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	41	242	0	ENST00000534358.1:c.4087-1G>A		p.X1363_splice	ENST00000534358	NM_005933.3	1363			1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.27	2		242	291	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807967	3807967	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033799-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	44	378	0	ENST00000262367.5:c.3452G>A	p.Trp1151Ter	p.W1151*	ENST00000262367	NM_004380.2	1151	tGg/tAg	18/31	1	2	FACETS	0.6	0.503	0.708	0.6	0.503	0.708	SUBCLONAL	1	TRUE	1	0.27	2		378	543	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56401603	56401603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033799-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	19	261	0	ENST00000348428.3:c.1465G>A	p.Gly489Arg	p.G489R	ENST00000348428	NM_006785.3	489	Gga/Aga	12/17	1	2	FACETS	0.444	0.337	0.57	0.444	0.337	0.57	SUBCLONAL	1	TRUE	1	0.27	2		261	317	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513814	41513814	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033799-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	57	394	0	ENST00000263253.7:c.718C>T	p.Gln240Ter	p.Q240*	ENST00000263253	NM_001429.3	240	Cag/Tag	2/31	1	2	FACETS	0.768	0.659	0.886	0.768	0.659	0.886	SUBCLONAL	1	TRUE	1	0.27	2		394	550	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138913	37138913	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033799-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	78	499	0	ENST00000373509.5:c.253C>T	p.Arg85Ter	p.R85*	ENST00000373509	NM_002648.3	85	Cga/Tga	4/6	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.27	2		499	574	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918645	44918646	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AATGC	novel	NA	P-0033799-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	41	188	0	ENST00000377967.4:c.1131_1135dup	p.Thr379MetfsTer62	p.T379Mfs*62	ENST00000377967	NM_021140.2	376	-/AATGC	12/29	0.3	2	FACETS	1	0.957	1	0.737	0.62	0.864	CLONAL	1	TRUE	0	0.27	2		188	206	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0034502-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	22	432	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.33	0.255	0.419	0.33	0.255	0.419	SUBCLONAL	1	TRUE	1	0.218109353296945	2		432	611	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0034502-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	119	418	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.224685382351532	3	FACETS	0.797	0.72	0.879	0.797	0.72	0.879	SUBCLONAL	2	TRUE	1	0.218109353296945	3		418	759	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519988	NA	P-0034502-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	121	646	0	ENST00000269305.4:c.808T>G	p.Phe270Val	p.F270V	ENST00000269305	NM_001126112.2	270	Ttt/Gtt	8/11	1	2	FACETS	0.887	0.799	0.98	0.887	0.799	0.98	CLONAL	1	TRUE	1	0.218109353296945	2		646	1251	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692792	89692792	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034502-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	66	357	0	ENST00000371953.3:c.277del	p.His93IlefsTer6	p.H93Ifs*6	ENST00000371953	NM_000314.4	92	gaC/ga	5/9	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.218109353296945	2		357	513	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578503	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034605-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	105	922	0	ENST00000269305.4:c.427del	p.Val143CysfsTer27	p.V143Cfs*27	ENST00000269305	NM_001126112.2	143	Gtg/tg	5/11	1	2	FACETS	0.719	0.642	0.801	0.719	0.642	0.801	SUBCLONAL	1	TRUE	1	0.24	2		922	1217	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845798	151845798	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034605-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	70	541	0	ENST00000262189.6:c.13214G>C	p.Cys4405Ser	p.C4405S	ENST00000262189	NM_170606.2	4405	tGt/tCt	52/59	0.186085716738465	3	FACETS	0.802	0.698	0.914	0.401	0.349	0.457	CLONAL	1	TRUE	1	0.24	3		541	815	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0034729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	618	910	0	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.306328005369206	3	FACETS	0.972	0.936	1	0.972	0.936	1	CLONAL	3	FALSE	0	0.306328005369206	3		910	1595	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971138	21971138	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs760640852	NA	P-0034729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	314	642	0	ENST00000304494.5:c.220G>T	p.Asp74Tyr	p.D74Y	ENST00000304494	NM_000077.4	74	Gac/Tac	2/3	0.209241753118179	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	FALSE	0	0.306328005369206	2		642	955	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390917	89390917	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	60	205	0	ENST00000336596.2:c.983C>A	p.Ser328Ter	p.S328*	ENST00000336596	NM_005233.5	328	tCa/tAa	5/17	0.224029722446211	2	FACETS	1	0.887	1	0.514	0.445	0.589	CLONAL	1	FALSE	0	0.306328005369206	2		205	381	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46597522	46597522	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	87	236	0	ENST00000262741.5:c.103C>A	p.Pro35Thr	p.P35T	ENST00000262741	NM_003629.3	35	Cca/Aca	1/10	0.224029722446211	2	FACETS	1	0.977	1	0.708	0.631	0.79	CLONAL	1	FALSE	0	0.306328005369206	2		236	401	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29002018	29002018	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	TG	novel	NA	P-0034729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	79	313	0	ENST00000282397.4:c.1147delinsCA	p.Tyr383GlnfsTer15	p.Y383Qfs*15	ENST00000282397	NM_002019.4	383	Tat/CAat	9/30	0.20630021327543	2	FACETS	1	0.963	1	0.615	0.544	0.692	CLONAL	1	FALSE	0	0.306328005369206	2		313	419	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	43	648	0	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.702	0.585	0.832	0.702	0.585	0.832	SUBCLONAL	1	TRUE	1	0.15	2		648	817	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	22	566	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.508	0.392	0.644	0.508	0.392	0.644	SUBCLONAL	1	TRUE	1	0.15	2		566	577	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720677	89720677	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	21	217	0	ENST00000371953.3:c.828T>G	p.Asn276Lys	p.N276K	ENST00000371953	NM_000314.4	276	aaT/aaG	8/9	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.15	2		217	222	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036163-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	494	539	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.978130623322327	1	FACETS	0.553	0.532	0.573	0.553	0.532	0.573	SUBCLONAL	1	TRUE	0	0.978130623322327	1		539	934	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0036163-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	1067	762	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	0.973928387812811	1	FACETS	1	0.999	1	1	0.999	1	CLONAL	1	TRUE	0	0.978130623322327	1		762	1080	SUCCESS
APC	324	MSKCC	GRCh37	5	112179080	112179080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036163-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	143	159	0	ENST00000257430.4:c.7789G>A	p.Gly2597Arg	p.G2597R	ENST00000257430	NM_000038.5	2597	Gga/Aga	16/16	0.528360635322977	1	FACETS	0.348	0.32	0.377	0.348	0.32	0.377	INDETERMINATE	1	TRUE	0	0.978130623322327	1		159	429	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550502	29550502	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036163-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	122	172	0	ENST00000356175.3:c.1762C>A	p.His588Asn	p.H588N	ENST00000356175	NM_000267.3	588	Cat/Aat	16/57	NA	2	FACETS	0.465	0.422	0.51			1	INDETERMINATE	1	TRUE	NA	0.978130623322327	2		172	536	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036373-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	225	463	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.380602046074114	4	FACETS	1	0.977	1	0.732	0.684	0.781	CLONAL	2	TRUE	1	0.380602046074114	4		463	743	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036373-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	221	372	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	0.380602046074114	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.380602046074114	3		372	612	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608062	28608062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036373-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	77	336	0	ENST00000241453.7:c.1904C>T	p.Thr635Ile	p.T635I	ENST00000241453	NM_004119.2	635	aCa/aTa	15/24	1	2	FACETS	0.934	0.824	1	0.934	0.824	1	CLONAL	1	TRUE	1	0.380602046074114	2		336	433	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0036725-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	182	703	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	FALSE	1	0.849499514548097	2		703	428	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058072	27058072	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036725-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	114	390	1	ENST00000324856.7:c.1780C>T	p.Gln594Ter	p.Q594*	ENST00000324856	NM_006015.4	594	Cag/Tag	3/20	1	2	FACETS	0.969	0.887	1	0.969	0.887	1	CLONAL	1	FALSE	1	0.849499514548097	2		391	277	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100739	8100739	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1156455762	NA	P-0036725-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	278	763	0	ENST00000346208.3:c.713G>C	p.Ser238Thr	p.S238T	ENST00000346208		238	aGc/aCc	3/6	0.201652009896996	3	FACETS	0.802	0.761	0.844	0.802	0.761	0.844	INDETERMINATE	2	FALSE	1	0.849499514548097	3		763	581	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143994	11143994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036725-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	33	629	1	ENST00000358026.2:c.3575G>A	p.Arg1192His	p.R1192H	ENST00000358026	NM_001128849.1	1192	cGc/cAc	26/36	1	2	FACETS	0.137	0.111	0.167	0.137	0.111	0.167	SUBCLONAL	1	FALSE	1	0.849499514548097	2		630	566	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44935940	44935940	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0036725-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	103	107	0	ENST00000377967.4:c.2703-2A>T		p.X901_splice	ENST00000377967	NM_021140.2	901			1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	0	0.849499514548097	1		107	115	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0037381-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	105	432	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.344581532083219	2		432	590	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037381-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	68	566	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.301706824618302	3	FACETS	1	0.972	1	0.723	0.634	0.818	CLONAL	1	TRUE	1	0.344581532083219	3		566	320	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0037381-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	51	502	1	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.344581532083219	2		503	268	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578214	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs864309495	NA	P-0037381-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	123	679	0	ENST00000269305.4:c.635_636del	p.Phe212SerfsTer3	p.F212Sfs*3	ENST00000269305	NM_001126112.2	212	tTT/t	6/11	0.248194647174754	2	FACETS	1	0.982	1	0.668	0.607	0.733	CLONAL	1	TRUE	0	0.344581532083219	2		679	534	SUCCESS
APC	324	MSKCC	GRCh37	5	112173582	112173582	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0037381-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	26	229	0	ENST00000257430.4:c.2291T>A	p.Leu764Ter	p.L764*	ENST00000257430	NM_000038.5	764	tTa/tAa	16/16	1	2	FACETS	0.68	0.541	0.837	0.68	0.541	0.837	SUBCLONAL	1	TRUE	1	0.344581532083219	2		229	222	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929426	81929426	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1364308657	NA	P-0037381-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	40	522	0	ENST00000359376.3:c.1087G>A	p.Gly363Arg	p.G363R	ENST00000359376	NM_002661.3	363	Ggg/Agg	13/33	0.301706824618302	3	FACETS	0.609	0.506	0.723	0.304	0.253	0.362	SUBCLONAL	1	TRUE	1	0.344581532083219	3		522	447	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813903	50813903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1363261645	NA	P-0037381-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	118	525	0	ENST00000398568.2:c.1457G>A	p.Arg486His	p.R486H	ENST00000398568	NM_001042412.1	486	cGt/cAt	8/18	0.301706824618302	3	FACETS	1	0.983	1	0.711	0.643	0.781	CLONAL	1	TRUE	1	0.344581532083219	3		525	565	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62322275	62322275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758245234	NA	P-0037381-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	190	966	0	ENST00000360203.5:c.2531G>A	p.Arg844Gln	p.R844Q	ENST00000360203	NM_001283009.1	844	cGg/cAg	27/35	0.20915347357506	5	FACETS	0.8	0.739	0.863	0.533	0.492	0.576	SUBCLONAL	2	TRUE	2	0.344581532083219	5		966	1046	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047882	180047882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037381-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	96	994	5	ENST00000261937.6:c.2293G>A	p.Val765Met	p.V765M	ENST00000261937	NM_182925.4	765	Gtg/Atg	15/30	1	2	FACETS	0.649	0.577	0.725	0.649	0.577	0.725	SUBCLONAL	1	TRUE	1	0.344581532083219	2		999	859	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039030-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	170	566	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.725644139722567	3	FACETS	0.899	0.84	0.959	0.899	0.84	0.959	CLONAL	2	TRUE	1	0.725644139722567	3		566	355	SUCCESS
APC	324	MSKCC	GRCh37	5	112175746	112175746	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039030-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	148	410	6	ENST00000257430.4:c.4455del	p.Asp1486IlefsTer21	p.D1486Ifs*21	ENST00000257430	NM_000038.5	1485	gcT/gc	16/16	0.722066438078902	3	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	1	0.725644139722567	3		416	276	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946355	2946355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372251654	NA	P-0039030-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	538	905	25	ENST00000396946.4:c.3382G>A	p.Val1128Ile	p.V1128I	ENST00000396946	NM_032415.4	1128	Gta/Ata	25/25	0.66101645679458	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.725644139722567	4		930	1230	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111132	193111132	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039030-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	140	426	6	ENST00000367435.3:c.665G>A	p.Arg222Gln	p.R222Q	ENST00000367435	NM_024529.4	222	cGa/cAa	7/17	0.725644139722567	3	FACETS	0.891	0.827	0.956	0.891	0.827	0.956	CLONAL	2	TRUE	1	0.725644139722567	3		432	295	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876540	35876540	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039030-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	111	568	8	ENST00000303115.3:c.1332T>G	p.Asn444Lys	p.N444K	ENST00000303115	NM_002185.3	444	aaT/aaG	8/8	1	2	FACETS	0.908	0.826	0.993	0.908	0.826	0.993	CLONAL	1	TRUE	1	0.725644139722567	2		576	337	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64286880	64286880	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039030-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	94	399	1	ENST00000370651.3:c.95A>G	p.Lys32Arg	p.K32R	ENST00000370651	NM_003463.4	32	aAa/aGa	2/6	0.334429645403627	3	FACETS	1	0.982	1	0.721	0.652	0.79	INDETERMINATE	1	TRUE	1	0.725644139722567	3		400	245	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540131	23540131	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs768675345	NA	P-0039030-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	85	146	0	ENST00000380871.4:c.272C>G	p.Ala91Gly	p.A91G	ENST00000380871	NM_006167.3	91	gCa/gGa	1/2	0.725644139722567	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.725644139722567	1		146	149	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	77	349	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.28	2		350	511	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857524	9857524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778230379	NA	P-0039415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	130	421	1	ENST00000330684.3:c.3877G>A	p.Asp1293Asn	p.D1293N	ENST00000330684	NM_001134407.1	1293	Gat/Aat	13/13	0.3	4	FACETS	1	0.977	1	0.807	0.736	0.88	CLONAL	2	TRUE	1	0.28	4		422	491	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0039415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	148	510	1	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.3	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.28	1		511	620	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859016	57859016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765428970	NA	P-0039415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	74	652	0	ENST00000228682.2:c.512G>A	p.Arg171Gln	p.R171Q	ENST00000228682	NM_005269.2	171	cGg/cAg	5/12	1	2	FACETS	0.578	0.505	0.658	0.578	0.505	0.658	SUBCLONAL	1	TRUE	1	0.28	2		652	914	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972913	55972913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	64	353	0	ENST00000263923.4:c.1477G>A	p.Gly493Arg	p.G493R	ENST00000263923	NM_002253.2	493	Gga/Aga	11/30	0.0753991574077044	3	FACETS	1	0.907	1	0.529	0.458	0.604	INDETERMINATE	1	TRUE	1	0.28	3		353	493	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9787030	9787030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397518423	NA	P-0039415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	75	498	1	ENST00000377346.4:c.3061G>A	p.Glu1021Lys	p.E1021K	ENST00000377346	NM_005026.3	1021	Gaa/Aaa	24/24	0.3	1	FACETS	0.704	0.617	0.798	0.704	0.617	0.798	SUBCLONAL	1	TRUE	0	0.28	1		499	654	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266485	198266485	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	21	194	0	ENST00000335508.6:c.2351T>C	p.Met784Thr	p.M784T	ENST00000335508	NM_012433.2	784	aTg/aCg	16/25	1	2	FACETS	0.521	0.401	0.66	0.521	0.401	0.66	SUBCLONAL	1	TRUE	1	0.28	2		194	288	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0039415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	281	801	1	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	0.194318237235752	3	FACETS	0.93	0.873	0.989	0.93	0.873	0.989	CLONAL	2	TRUE	1	0.28	3		802	1230	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745609	162745609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	55	386	0	ENST00000367921.3:c.2024C>T	p.Ser675Phe	p.S675F	ENST00000367921	NM_006182.2	675	tCc/tTc	15/18	0.0753991574077044	3	FACETS	0.746	0.638	0.865	0.373	0.319	0.433	INDETERMINATE	1	TRUE	1	0.28	3		386	600	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476403	88476403	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	102	384	0	ENST00000360948.2:c.1729C>T	p.Pro577Ser	p.P577S	ENST00000360948	NM_001012338.2	577	Ccc/Tcc	15/19	0.194318237235752	3	FACETS	1	0.978	1	0.688	0.616	0.763	CLONAL	1	TRUE	1	0.28	3		384	604	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672800	86672800	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764802465	NA	P-0039415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	25	255	0	ENST00000274376.6:c.2287G>A	p.Glu763Lys	p.E763K	ENST00000274376	NM_002890.2	763	Gaa/Aaa	17/25	1	2	FACETS	0.562	0.443	0.698	0.562	0.443	0.698	SUBCLONAL	1	TRUE	1	0.28	2		255	318	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521067	187521067	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	33	350	0	ENST00000441802.2:c.12088C>T	p.Pro4030Ser	p.P4030S	ENST00000441802	NM_005245.3	4030	Ccg/Tcg	22/27	0.0753991574077044	3	FACETS	0.6	0.488	0.726	0.3	0.244	0.363	INDETERMINATE	1	TRUE	1	0.28	3		350	448	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858913	243858913	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs866698621	NA	P-0039415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	23	299	0	ENST00000263826.5:c.152T>G	p.Leu51Arg	p.L51R	ENST00000263826	NM_005465.4	51	cTc/cGc	2/13	0.0753991574077044	3	FACETS	0.446	0.347	0.561	0.223	0.173	0.281	INDETERMINATE	1	TRUE	1	0.28	3		299	420	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38173545	38173545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	66	350	0	ENST00000317025.8:c.1871C>T	p.Ser624Leu	p.S624L	ENST00000317025	NM_023034.1	624	tCa/tTa	10/24	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.28	2		350	433	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165783	118165783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	88	337	0	ENST00000369448.3:c.293C>T	p.Ala98Val	p.A98V	ENST00000369448	NM_017709.3	98	gCt/gTt	2/2	0.3	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.28	1		337	426	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510217	120510217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	44	351	0	ENST00000256646.2:c.1292G>A	p.Gly431Glu	p.G431E	ENST00000256646	NM_024408.3	431	gGa/gAa	8/34	0.0753991574077044	3	FACETS	0.634	0.531	0.748	0.317	0.265	0.374	INDETERMINATE	1	TRUE	1	0.28	3		351	565	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589385	28589385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	51	254	0	ENST00000241453.7:c.2662C>T	p.Pro888Ser	p.P888S	ENST00000241453	NM_004119.2	888	Cct/Tct	22/24	0.0753991574077044	3	FACETS	1	0.906	1	0.542	0.462	0.629	INDETERMINATE	1	TRUE	1	0.28	3		254	383	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576180	88576180	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	90	620	0	ENST00000360948.2:c.1493C>T	p.Pro498Leu	p.P498L	ENST00000360948	NM_001012338.2	498	cCc/cTc	13/19	0.194318237235752	3	FACETS	0.651	0.576	0.732	0.326	0.288	0.366	SUBCLONAL	1	TRUE	1	0.28	3		620	1125	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349103	11349103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	77	584	1	ENST00000332029.2:c.233G>A	p.Gly78Glu	p.G78E	ENST00000332029	NM_003745.1	78	gGa/gAa	2/2	0.3	4	FACETS	0.842	0.738	0.954	0.281	0.246	0.318	CLONAL	1	TRUE	1	0.28	4		585	836	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50818352	50818352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	41	226	0	ENST00000398568.2:c.1930C>T	p.Pro644Ser	p.P644S	ENST00000398568	NM_001042412.1	644	Cct/Tct	11/18	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.28	2		226	280	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448342	56448342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	87	784	0	ENST00000407977.2:c.305G>A	p.Gly102Glu	p.G102E	ENST00000407977		102	gGa/gAa	3/10	1	2	FACETS	0.598	0.528	0.674	0.598	0.528	0.674	SUBCLONAL	1	TRUE	1	0.28	2		784	1039	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790090	40790090	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	157	639	0	ENST00000373198.4:c.2641C>G	p.Arg881Gly	p.R881G	ENST00000373198	NM_133170.3	881	Cgg/Ggg	18/32	0.194318237235752	3	FACETS	1	0.984	1	0.658	0.602	0.717	CLONAL	1	TRUE	1	0.28	3		639	971	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196646	106196646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	72	442	0	ENST00000380013.4:c.4979G>A	p.Arg1660Lys	p.R1660K	ENST00000380013	NM_001127208.2	1660	aGg/aAg	11/11	0.0753991574077044	3	FACETS	1	0.946	1	0.576	0.504	0.653	INDETERMINATE	1	TRUE	1	0.28	3		442	509	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293790	1293790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	144	1067	0	ENST00000310581.5:c.1211C>T	p.Pro404Leu	p.P404L	ENST00000310581	NM_198253.2	404	cCc/cTc	2/16	1	2	FACETS	0.859	0.781	0.94	0.859	0.781	0.94	CLONAL	1	TRUE	1	0.28	2		1067	1198	SUCCESS
APC	324	MSKCC	GRCh37	5	112173792	112173792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	25	248	0	ENST00000257430.4:c.2501C>T	p.Ser834Phe	p.S834F	ENST00000257430	NM_000038.5	834	tCc/tTc	16/16	1	2	FACETS	0.612	0.483	0.759	0.612	0.483	0.759	SUBCLONAL	1	TRUE	1	0.28	2		248	292	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721607	176721607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	64	456	0	ENST00000439151.2:c.7238C>T	p.Ser2413Phe	p.S2413F	ENST00000439151	NM_022455.4	2413	tCt/tTt	23/23	1	2	FACETS	0.737	0.638	0.845	0.737	0.638	0.845	SUBCLONAL	1	TRUE	1	0.28	2		456	620	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056973	180056973	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	83	858	0	ENST00000261937.6:c.646C>A	p.Leu216Ile	p.L216I	ENST00000261937	NM_182925.4	216	Ctt/Att	5/30	1	2	FACETS	0.578	0.508	0.653	0.578	0.508	0.653	SUBCLONAL	1	TRUE	1	0.28	2		858	1026	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518308	8518308	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	41	207	0	ENST00000356435.5:c.1083A>T	p.Lys361Asn	p.K361N	ENST00000356435		361	aaA/aaT	10/35	0.3	1	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	0	0.28	1		207	235	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938305	76938305	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	45	206	0	ENST00000373344.5:c.2443T>G	p.Ser815Ala	p.S815A	ENST00000373344	NM_000489.3	815	Tct/Gct	9/35	0.114475034025003	2	FACETS	1	0.886	1			1	INDETERMINATE	1	TRUE	NA	0.28	2		206	303	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615576	100615576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	135	186	0	ENST00000308731.7:c.756G>A	p.Trp252Ter	p.W252*	ENST00000308731	NM_000061.2	252	tgG/tgA	8/19	0.114475034025003	2	FACETS	1	0.971	1			1	INDETERMINATE	3	TRUE	NA	0.28	2		186	292	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453131	140453136	+	protein_altering_variant	In_Frame_Del	DEL	ATTTCA	ATTTCA	TAT	novel	NA	P-0039415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	66	295	1	ENST00000288602.6:c.1799_1804delinsATA	p.Val600_Ser602delinsAspThr	p.V600_S602delinsDT	ENST00000288602	NM_004333.4	600	gTGAAATct/gATAct	15/18	0.194318237235752	3	FACETS	1	0.972	1	0.738	0.644	0.839	CLONAL	1	TRUE	1	0.28	3		296	364	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0039465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	375	738	1	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.423826037446315	2	FACETS	0.885	0.842	0.928	0.885	0.842	0.928	CLONAL	2	TRUE	0	0.423826037446315	2		739	1000	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456714	32456714	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	187	649	0	ENST00000332351.3:c.178G>T	p.Gly60Trp	p.G60W	ENST00000332351	NM_024426.4	60	Ggg/Tgg	1/10	0.423826037446315	2	FACETS	0.963	0.89	1	0.482	0.445	0.52	CLONAL	1	TRUE	0	0.423826037446315	2		649	916	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414251	32414251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121907910	NA	P-0039465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	128	380	3	ENST00000332351.3:c.1300C>T	p.Arg434Cys	p.R434C	ENST00000332351	NM_024426.4	434	Cgt/Tgt	8/10	0.423826037446315	2	FACETS	1	0.917	1	0.504	0.458	0.552	CLONAL	1	TRUE	0	0.423826037446315	2		383	599	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491366	2491366	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	135	935	0	ENST00000355716.4:c.409G>T	p.Ala137Ser	p.A137S	ENST00000355716	NM_003820.2	137	Gcg/Tcg	4/8	1	2	FACETS	0.505	0.457	0.555	0.505	0.457	0.555	SUBCLONAL	1	TRUE	1	0.423826037446315	2		935	1262	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841455	156841455	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	254	527	0	ENST00000524377.1:c.758A>T	p.Asn253Ile	p.N253I	ENST00000524377	NM_002529.3	253	aAt/aTt	7/17	0.423826037446315	6	FACETS	0.787	0.735	0.841	0.393	0.367	0.421	SUBCLONAL	2	TRUE	2	0.423826037446315	6		527	1407	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112079	115112079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764962945	NA	P-0039465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	125	770	0	ENST00000257566.3:c.1661C>T	p.Ser554Leu	p.S554L	ENST00000257566	NM_016569.3	554	tCg/tTg	7/8	0.334631562289214	3	FACETS	0.549	0.496	0.607	0.183	0.165	0.203	SUBCLONAL	1	TRUE	0	0.423826037446315	3		770	1301	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609667	28609667	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	71	479	0	ENST00000241453.7:c.1562G>T	p.Gly521Val	p.G521V	ENST00000241453	NM_004119.2	521	gGc/gTc	12/24	1	2	FACETS	0.557	0.486	0.633	0.557	0.486	0.633	SUBCLONAL	1	TRUE	1	0.423826037446315	2		479	602	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670439	88670439	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	99	325	0	ENST00000360948.2:c.1247C>A	p.Thr416Lys	p.T416K	ENST00000360948	NM_001012338.2	416	aCa/aAa	11/19	0.380803841810441	2	FACETS	0.971	0.871	1	0.486	0.435	0.539	CLONAL	1	TRUE	0	0.423826037446315	2		325	481	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862937	9862937	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	120	440	0	ENST00000330684.3:c.2366A>T	p.Glu789Val	p.E789V	ENST00000330684	NM_001134407.1	789	gAg/gTg	12/13	0.164971280497839	3	FACETS	1	0.917	1	0.338	0.306	0.373	INDETERMINATE	1	TRUE	0	0.423826037446315	3		440	676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577552	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0039465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	236	536	1	ENST00000269305.4:c.729_730delinsTT	p.Met243_Gly244delinsIleCys	p.M243_G244delinsIC	ENST00000269305	NM_001126112.2	243	atGGgc/atTTgc	7/11	NA	2	FACETS	0.821	0.77	0.873			1	INDETERMINATE	2	TRUE	NA	0.423826037446315	2		537	678	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321691	30321691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749409035	NA	P-0039465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	136	450	0	ENST00000322652.5:c.1546C>T	p.Arg516Cys	p.R516C	ENST00000322652	NM_015355.2	516	Cgc/Tgc	13/16	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.423826037446315	2		450	633	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17389765	17389765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	229	797	0	ENST00000359435.4:c.898G>A	p.Ala300Thr	p.A300T	ENST00000359435	NM_001033549.1	300	Gcc/Acc	9/9	0.423826037446315	2	FACETS	0.94	0.876	1	0.47	0.438	0.504	CLONAL	1	TRUE	0	0.423826037446315	2		797	1149	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530072	212530072	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	55	248	0	ENST00000342788.4:c.1847del	p.Pro616HisfsTer37	p.P616Hfs*37	ENST00000342788	NM_005235.2	616	cCa/ca	15/28	0.164971280497839	3	FACETS	0.909	0.782	1	0.303	0.26	0.349	INDETERMINATE	1	TRUE	0	0.423826037446315	3		248	346	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523306	9523306	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	150	490	0	ENST00000353224.5:c.1931T>G	p.Phe644Cys	p.F644C	ENST00000353224	NM_177990.2	644	tTc/tGc	9/10	0.314435601134997	4	FACETS	1	0.977	1	0.598	0.547	0.652	CLONAL	1	TRUE	2	0.423826037446315	4		490	842	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561168	9561168	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	105	392	0	ENST00000353224.5:c.614C>A	p.Ser205Ter	p.S205*	ENST00000353224	NM_177990.2	205	tCa/tAa	4/10	0.314435601134997	4	FACETS	1	0.935	1	0.529	0.474	0.587	CLONAL	1	TRUE	2	0.423826037446315	4		392	667	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920300	1920300	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	84	574	0	ENST00000382891.5:c.1360G>T	p.Gly454Ter	p.G454*	ENST00000382891	NM_133335.3	454	Gga/Tga	5/22	0.423826037446315	3	FACETS	0.496	0.437	0.559	0.248	0.218	0.28	SUBCLONAL	1	TRUE	1	0.423826037446315	3		574	969	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602920	55602931	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	CTAAGTTCTACA	CTAAGTTCTACA	-	novel	NA	P-0039465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	40	283	0	ENST00000288135.5:c.2630_2641del	p.Ser877_Lys881delinsTer	p.S877_K881delins*	ENST00000288135	NM_000222.2	877	tCTAAGTTCTACAag/tag	19/21	0.423826037446315	3	FACETS	0.417	0.346	0.497	0.209	0.173	0.249	SUBCLONAL	1	TRUE	1	0.423826037446315	3		283	548	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963042	38963042	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	34	289	0	ENST00000357387.3:c.1502del	p.Ala501GlufsTer29	p.A501Efs*29	ENST00000357387	NM_152756.3	501	gCa/ga	17/38	0.41503339260975	5	FACETS	0.531	0.433	0.642	0.133	0.108	0.161	SUBCLONAL	1	TRUE	1	0.423826037446315	5		289	494	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032201	26032201	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	46	402	0	ENST00000244661.2:c.88G>T	p.Ala30Ser	p.A30S	ENST00000244661	NM_003537.3	30	Gcg/Tcg	1/1	0.334631562289214	3	FACETS	0.426	0.358	0.502	0.142	0.119	0.168	SUBCLONAL	1	TRUE	0	0.423826037446315	3		402	617	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820877	32820877	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	257	793	0	ENST00000354258.4:c.717C>G	p.Cys239Trp	p.C239W	ENST00000354258	NM_000593.5	239	tgC/tgG	1/11	0.236886368438778	2	FACETS	0.993	0.929	1	0.497	0.464	0.53	INDETERMINATE	1	TRUE	0	0.423826037446315	2		793	1221	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340348	8340348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1372695674	NA	P-0039465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	108	397	0	ENST00000356435.5:c.5248G>A	p.Gly1750Ser	p.G1750S	ENST00000356435		1750	Ggc/Agc	31/35	0.423826037446315	1	FACETS	0.862	0.778	0.95	0.862	0.778	0.95	CLONAL	1	TRUE	0	0.423826037446315	1		397	466	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396455	139396455	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs775793303	NA	P-0039465-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	166	689	1	ENST00000277541.6:c.5470C>T	p.Arg1824Trp	p.R1824W	ENST00000277541	NM_017617.3	1824	Cgg/Tgg	29/34	1	2	FACETS	0.884	0.812	0.959	0.884	0.812	0.959	CLONAL	1	TRUE	1	0.423826037446315	2		690	886	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0040159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	104	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.993	0.895	1	0.993	0.895	1	CLONAL	1	TRUE	1	0.512382944163689	2		327	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0040159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	238	712	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.50852351981584	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.512382944163689	1		712	633	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971029	21971029	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519852	NA	P-0040159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	242	523	0	ENST00000304494.5:c.329G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tGg/tAg	2/3	0.512382944163689	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.512382944163689	1		523	551	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575152	48575152	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	79	268	0	ENST00000342988.3:c.346C>T	p.Gln116Ter	p.Q116*	ENST00000342988	NM_005359.5	116	Cag/Tag	3/12	0.50852351981584	1	FACETS	0.952	0.85	1	0.952	0.85	1	CLONAL	1	TRUE	0	0.512382944163689	1		268	241	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409053	139409053	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1358	220	751	1	ENST00000277541.6:c.2116G>T	p.Glu706Ter	p.E706*	ENST00000277541	NM_017617.3	706	Gag/Tag	13/34	0.352922076378963	3	FACETS	0.929	0.862	1	0.465	0.431	0.5	CLONAL	1	TRUE	1	0.352922076378963	3		752	1578	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246113	41246113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064794100	NA	P-0040817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	117	415	1	ENST00000357654.3:c.1435G>A	p.Glu479Lys	p.E479K	ENST00000357654	NM_007294.3	479	Gaa/Aaa	10/23	1	2	FACETS	0.927	0.837	1	0.927	0.837	1	CLONAL	1	TRUE	1	0.352922076378963	2		416	715	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929578	44929578	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0040817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	62	264	0	ENST00000377967.4:c.2678C>G	p.Ser893Ter	p.S893*	ENST00000377967	NM_021140.2	893	tCa/tGa	17/29	0.176988125004907	1	FACETS	0.668	0.579	0.765	0.668	0.579	0.765	INDETERMINATE	1	TRUE	0	0.352922076378963	1		264	433	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821086	32821086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs2228108	NA	P-0040817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	462	760	0	ENST00000354258.4:c.508C>T	p.Leu170Phe	p.L170F	ENST00000354258	NM_000593.5	170	Ctt/Ttt	1/11	0.305932339435569	2	FACETS	0.853	0.814	0.893	0.853	0.814	0.893	CLONAL	2	TRUE	0	0.352922076378963	2		760	1534	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868444	117868444	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	180	424	0	ENST00000297338.2:c.898G>C	p.Glu300Gln	p.E300Q	ENST00000297338	NM_006265.2	300	Gag/Cag	8/14	0.352922076378963	3	FACETS	1	0.983	1	0.617	0.568	0.667	CLONAL	1	TRUE	1	0.352922076378963	3		424	973	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321065	137321065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	140	583	1	ENST00000481739.1:c.1022G>A	p.Gly341Glu	p.G341E	ENST00000481739	NM_002957.4	341	gGg/gAg	7/10	0.352922076378963	3	FACETS	0.897	0.816	0.983	0.449	0.408	0.492	CLONAL	1	TRUE	1	0.352922076378963	3		584	1040	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411748	139411748	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1268	169	782	1	ENST00000277541.6:c.1531G>C	p.Glu511Gln	p.E511Q	ENST00000277541	NM_017617.3	511	Gag/Cag	9/34	0.352922076378963	3	FACETS	0.784	0.719	0.853	0.392	0.359	0.427	SUBCLONAL	1	TRUE	1	0.352922076378963	3		783	1437	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652290	48652290	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs782391440	NA	P-0040817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	164	761	0	ENST00000376670.3:c.961C>G	p.Leu321Val	p.L321V	ENST00000376670	NM_002049.3	321	Ctg/Gtg	6/6	0.352922076378963	1	FACETS	0.768	0.704	0.834	0.768	0.704	0.834	SUBCLONAL	1	TRUE	0	0.352922076378963	1		761	997	SUCCESS
AR	367	MSKCC	GRCh37	X	66766446	66766447	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0040817-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	114	475	0	ENST00000374690.3:c.1458_1459delinsTA	p.Pro487Thr	p.P487T	ENST00000374690	NM_000044.3	486	ccCCct/ccTAct	1/8	1	2	FACETS	0.97	0.875	1	0.97	0.875	1	CLONAL	1	TRUE	1	0.352922076378963	2		475	666	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508746	29508746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041409-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	112	346	0	ENST00000356175.3:c.673G>A	p.Glu225Lys	p.E225K	ENST00000356175	NM_000267.3	225	Gaa/Aaa	7/57	0.883000205547996	3	FACETS	0.923	0.838	1	0.462	0.419	0.506	CLONAL	1	TRUE	1	0.886352152233254	3		346	395	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575553	64575553	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041409-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	140	521	0	ENST00000312049.6:c.464C>G	p.Ser155Cys	p.S155C	ENST00000312049	NM_130799.2	155	tCc/tGc	3/10	0.501460062557123	2	FACETS	1	0.934	1	0.505	0.467	0.543	INDETERMINATE	1	TRUE	0	0.886352152233254	2		521	313	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968928	32968928	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041409-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	269	269	0	ENST00000380152.3:c.9359T>G	p.Ile3120Ser	p.I3120S	ENST00000380152		3120	aTt/aGt	25/27	0.886352152233254	7	FACETS	0.897	0.851	0.943			1	CLONAL	4	TRUE	NA	0.886352152233254	7		269	544	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004792	16004792	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041409-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	149	500	0	ENST00000268712.3:c.2462C>A	p.Ser821Tyr	p.S821Y	ENST00000268712	NM_006311.3	821	tCt/tAt	20/46	0.883000205547996	3	FACETS	0.97	0.893	1	0.485	0.446	0.526	CLONAL	1	TRUE	1	0.886352152233254	3		500	500	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120789199	120789199	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041409-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	19	333	0	ENST00000257552.2:c.738C>G	p.Phe246Leu	p.F246L	ENST00000257552	NM_002442.3	246	ttC/ttG	11/15	0.876053509171268	2	FACETS	0.123	0.093	0.158	0.061	0.046	0.079	SUBCLONAL	1	TRUE	0	0.886352152233254	2		333	349	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029198	26029198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041409-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	14	290	1	ENST00000435504.4:c.152C>T	p.Ser51Phe	p.S51F	ENST00000435504		51	tCt/tTt	4/13	0.886352152233254	3	FACETS	0.179	0.129	0.239	0.089	0.064	0.12	SUBCLONAL	1	TRUE	1	0.886352152233254	3		291	255	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716212	52716212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555791268	NA	P-0042572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	194	748	0	ENST00000322088.6:c.656C>T	p.Ser219Leu	p.S219L	ENST00000322088	NM_014225.5	219	tCg/tTg	6/15	1	2	FACETS	0.879	0.815	0.946	0.879	0.815	0.946	CLONAL	1	TRUE	1	0.530974296777277	2		748	831	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513268	44513268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761081553	NA	P-0042572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	268	827	0	ENST00000291552.4:c.667G>A	p.Gly223Arg	p.G223R	ENST00000291552	NM_006758.2	223	Gga/Aga	8/8	0.200467693774083	1	FACETS	0.701	0.657	0.745	0.701	0.657	0.745	INDETERMINATE	1	TRUE	0	0.530974296777277	1		827	1058	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912075	56912075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	84	521	2	ENST00000519728.1:c.1303G>A	p.Glu435Lys	p.E435K	ENST00000519728	NM_002350.3	435	Gaa/Aaa	12/13	0.378739756687526	1	FACETS	0.804	0.714	0.901	0.804	0.714	0.901	CLONAL	1	TRUE	0	0.378739756687526	1		523	447	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405911	157405911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779271100	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	85	473	0	ENST00000346085.5:c.2153C>T	p.Ser718Leu	p.S718L	ENST00000346085	NM_020732.3	718	tCg/tTg	6/20	0.30001555881907	2	FACETS	0.701	0.62	0.788	0.351	0.31	0.394	SUBCLONAL	1	TRUE	0	0.378739756687526	2		473	640	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289863	15289863	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201680145	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	139	879	0	ENST00000263388.2:c.3691C>T	p.Arg1231Cys	p.R1231C	ENST00000263388	NM_000435.2	1231	Cgt/Tgt	22/33	0.234480736200534	3	FACETS	0.814	0.74	0.893	0.407	0.37	0.447	CLONAL	1	TRUE	1	0.378739756687526	3		879	1072	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037966	49037966	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	59	266	0	ENST00000267163.4:c.2206C>T	p.Gln736Ter	p.Q736*	ENST00000267163	NM_000321.2	736	Cag/Tag	21/27	0.344348775098057	2	FACETS	1	0.967	1	0.692	0.603	0.786	CLONAL	1	TRUE	0	0.378739756687526	2		266	225	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984860	9984860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs77772378	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	79	435	0	ENST00000330684.3:c.1105G>A	p.Asp369Asn	p.D369N	ENST00000330684	NM_001134407.1	369	Gac/Aac	4/13	0.0537353495343527	3	FACETS	0.805	0.709	0.909	0.403	0.354	0.455	INDETERMINATE	1	TRUE	1	0.378739756687526	3		435	616	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188836	32188836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1046104152	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	135	739	0	ENST00000375023.3:c.718C>T	p.Pro240Ser	p.P240S	ENST00000375023	NM_004557.3	240	Cct/Tct	4/30	0.229913456282344	3	FACETS	0.859	0.78	0.943	0.43	0.39	0.472	CLONAL	1	TRUE	1	0.378739756687526	3		739	987	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041554	14041554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772728961	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	50	447	0	ENST00000311895.7:c.2101C>T	p.Arg701Cys	p.R701C	ENST00000311895	NM_005236.2	701	Cgt/Tgt	11/11	0.0537353495343527	3	FACETS	0.528	0.447	0.616	0.264	0.223	0.308	INDETERMINATE	1	TRUE	1	0.378739756687526	3		447	595	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28963960	28963960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773035381	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	25	308	0	ENST00000282397.4:c.1942C>T	p.Leu648Phe	p.L648F	ENST00000282397	NM_002019.4	648	Ctc/Ttc	13/30	0.344348775098057	2	FACETS	0.514	0.406	0.637	0.257	0.203	0.319	SUBCLONAL	1	TRUE	0	0.378739756687526	2		308	257	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673803	30673803	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1387652060	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	61	382	0	ENST00000376406.3:c.3157C>T	p.Leu1053Phe	p.L1053F	ENST00000376406	NM_014641.2	1053	Ctt/Ttt	10/15	0.229913456282344	3	FACETS	0.706	0.609	0.81	0.353	0.304	0.405	SUBCLONAL	1	TRUE	1	0.378739756687526	3		382	543	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500886	8500886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	52	452	1	ENST00000356435.5:c.1996C>T	p.Pro666Ser	p.P666S	ENST00000356435		666	Cct/Tct	13/35	1	2	FACETS	0.473	0.402	0.55	0.473	0.402	0.55	SUBCLONAL	1	TRUE	1	0.378739756687526	2		453	581	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111000	193111000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	27	180	0	ENST00000367435.3:c.533C>T	p.Ser178Leu	p.S178L	ENST00000367435	NM_024529.4	178	tCa/tTa	7/17	0.370824018255723	3	FACETS	0.883	0.72	1	0.589	0.48	0.706	CLONAL	2	TRUE	0	0.378739756687526	3		180	96	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015115	37015115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	86	510	0	ENST00000358127.4:c.289G>A	p.Glu97Lys	p.E97K	ENST00000358127	NM_001280556.1	97	Gaa/Aaa	3/10	1	2	FACETS	0.571	0.505	0.643	0.571	0.505	0.643	SUBCLONAL	1	TRUE	1	0.378739756687526	2		510	795	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	94	332	1				ENST00000310581	NM_198253.2	-/1132			0.229913456282344	3	FACETS	0.789	0.708	0.875	0.789	0.708	0.875	SUBCLONAL	2	TRUE	1	0.378739756687526	3		333	374	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467924	50467924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	77	571	0	ENST00000331340.3:c.1159G>A	p.Glu387Lys	p.E387K	ENST00000331340	NM_006060.4	387	Gag/Aag	8/8	0.229913456282344	3	FACETS	0.589	0.516	0.668	0.295	0.258	0.334	SUBCLONAL	1	TRUE	1	0.378739756687526	3		571	821	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681434	88681434	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782496	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	68	557	0	ENST00000372037.3:c.1324C>T	p.Arg442Cys	p.R442C	ENST00000372037	NM_004329.2	442	Cgt/Tgt	11/13	1	2	FACETS	0.629	0.547	0.717	0.629	0.547	0.717	SUBCLONAL	1	TRUE	1	0.378739756687526	2		557	571	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154321	2154321	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150866176	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	141	892	0	ENST00000434045.2:c.607G>A	p.Glu203Lys	p.E203K	ENST00000434045	NM_001127598.1	203	Gag/Aag	5/5	1	2	FACETS	0.973	0.888	1	0.973	0.888	1	CLONAL	1	TRUE	1	0.378739756687526	2		892	765	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191243	185191243	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	85	491	0	ENST00000265026.3:c.2124G>A	p.Trp708Ter	p.W708*	ENST00000265026	NM_004721.4	708	tgG/tgA	11/14	0.230286570226595	5	FACETS	0.968	0.856	1	0.323	0.285	0.363	CLONAL	1	TRUE	2	0.378739756687526	5		491	727	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331729	68331729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	31	184	1	ENST00000487270.1:c.325C>T	p.Pro109Ser	p.P109S	ENST00000487270	NM_133509.3	109	Cca/Tca	5/11	1	2	FACETS	0.963	0.788	1	0.963	0.788	1	CLONAL	1	TRUE	1	0.378739756687526	2		185	170	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149901	202149901	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs747862347	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	70	524	2	ENST00000358485.4:c.1342C>T	p.Gln448Ter	p.Q448*	ENST00000358485	NM_001080125.1	448	Caa/Taa	8/9	1	2	FACETS	0.77	0.673	0.874	0.77	0.673	0.874	SUBCLONAL	1	TRUE	1	0.378739756687526	2		526	480	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743942	40743942	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868489194	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	55	387	0	ENST00000373198.4:c.3053G>A	p.Arg1018Gln	p.R1018Q	ENST00000373198	NM_133170.3	1018	cGa/cAa	23/32	0.234480736200534	3	FACETS	0.616	0.527	0.713	0.308	0.263	0.357	SUBCLONAL	1	TRUE	1	0.378739756687526	3		387	561	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086133	16086133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	40	494	0	ENST00000281043.3:c.1309G>A	p.Glu437Lys	p.E437K	ENST00000281043	NM_005378.4	437	Gag/Aag	3/3	1	2	FACETS	0.381	0.316	0.454	0.381	0.316	0.454	SUBCLONAL	1	TRUE	1	0.378739756687526	2		494	554	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589797	55589797	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1306680919	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	64	396	0	ENST00000288135.5:c.1279C>T	p.Gln427Ter	p.Q427*	ENST00000288135	NM_000222.2	427	Caa/Taa	8/21	1	2	FACETS	0.786	0.683	0.897	0.786	0.683	0.897	SUBCLONAL	1	TRUE	1	0.378739756687526	2		396	430	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729162	66729162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519732	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	97	537	0	ENST00000307102.5:c.370C>T	p.Pro124Ser	p.P124S	ENST00000307102	NM_002755.3	124	Ccg/Tcg	3/11	1	2	FACETS	0.677	0.603	0.755	0.677	0.603	0.755	SUBCLONAL	1	TRUE	1	0.378739756687526	2		537	757	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876265	35876265	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770274946	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	110	450	0	ENST00000303115.3:c.1057G>A	p.Asp353Asn	p.D353N	ENST00000303115	NM_002185.3	353	Gat/Aat	8/8	0.229913456282344	3	FACETS	1	0.967	1	0.584	0.526	0.646	CLONAL	1	TRUE	1	0.378739756687526	3		450	591	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440081	220440081	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	124	750	0	ENST00000243786.2:c.934C>T	p.Pro312Ser	p.P312S	ENST00000243786	NM_002191.3	312	Cct/Tct	2/2	0.378739756687526	1	FACETS	0.727	0.658	0.799	0.727	0.658	0.799	SUBCLONAL	1	TRUE	0	0.378739756687526	1		750	730	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744378	41744378	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	75	580	0	ENST00000301178.4:c.998C>T	p.Pro333Leu	p.P333L	ENST00000301178	NM_021913.4	333	cCc/cTc	8/20	0.234480736200534	3	FACETS	0.79	0.693	0.895	0.395	0.346	0.448	SUBCLONAL	1	TRUE	1	0.378739756687526	3		580	596	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940120	31940120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	109	751	2	ENST00000375333.2:c.262G>A	p.Glu88Lys	p.E88K	ENST00000375333	NM_032454.1	88	Gaa/Aaa	2/8	0.229913456282344	3	FACETS	0.624	0.559	0.693	0.312	0.279	0.347	SUBCLONAL	1	TRUE	1	0.378739756687526	3		753	1097	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197187	26197187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	76	475	0	ENST00000356476.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000356476		98	Gag/Aag	1/1	0.229913456282344	3	FACETS	0.813	0.714	0.92	0.407	0.357	0.46	CLONAL	1	TRUE	1	0.378739756687526	3		475	587	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432368	432368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1362895739	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	18	168	0	ENST00000399788.2:c.2155C>T	p.Arg719Cys	p.R719C	ENST00000399788	NM_001042603.1	719	Cgc/Tgc	16/28	NA	2	FACETS	0.694	0.527	0.887			1	INDETERMINATE	1	TRUE	NA	0.378739756687526	2		168	137	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790129	40790129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	121	579	0	ENST00000373198.4:c.2602C>T	p.Pro868Ser	p.P868S	ENST00000373198	NM_133170.3	868	Ccc/Tcc	18/32	0.234480736200534	3	FACETS	0.894	0.807	0.986	0.447	0.403	0.493	CLONAL	1	TRUE	1	0.378739756687526	3		579	850	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520138	9520138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	116	368	0	ENST00000353224.5:c.2131C>T	p.Pro711Ser	p.P711S	ENST00000353224	NM_177990.2	711	Ccc/Tcc	10/10	0.234480736200534	3	FACETS	1	0.984	1	0.723	0.655	0.794	CLONAL	1	TRUE	1	0.378739756687526	3		368	504	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984094	2984094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	269	496	0	ENST00000396946.4:c.436G>A	p.Asp146Asn	p.D146N	ENST00000396946	NM_032415.4	146	Gac/Aac	5/25	0.229913456282344	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.378739756687526	3		496	829	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509537	106509537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774366285	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	64	494	0	ENST00000359195.3:c.1531G>A	p.Glu511Lys	p.E511K	ENST00000359195	NM_002649.2	511	Gag/Aag	2/11	0.229913456282344	3	FACETS	0.661	0.572	0.757	0.331	0.286	0.379	SUBCLONAL	1	TRUE	1	0.378739756687526	3		494	608	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519330	176519330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	195	621	0	ENST00000292408.4:c.736C>T	p.Pro246Ser	p.P246S	ENST00000292408	NM_213647.1	246	Ccg/Tcg	7/18	0.230286570226595	5	FACETS	0.875	0.81	0.942	0.583	0.54	0.628	CLONAL	2	TRUE	2	0.378739756687526	5		621	923	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572607	141572607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	210	605	0	ENST00000220592.5:c.463C>T	p.Pro155Ser	p.P155S	ENST00000220592	NM_012154.3	155	Cct/Tct	4/19	NA	2	FACETS	0.992	0.928	1			1	INDETERMINATE	2	TRUE	NA	0.378739756687526	2		605	559	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937185	76937185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	31	261	0	ENST00000373344.5:c.3563C>T	p.Ser1188Phe	p.S1188F	ENST00000373344	NM_000489.3	1188	tCc/tTc	9/35	1	1	FACETS	0.84	0.688	1	0.84	0.688	1	CLONAL	1	TRUE	0	0.378739756687526	1		261	158	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391980	139391980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	381	725	0	ENST00000277541.6:c.6211G>A	p.Glu2071Lys	p.E2071K	ENST00000277541	NM_017617.3	2071	Gag/Aag	34/34	0.321031737953562	3	FACETS	0.979	0.935	1	0.979	0.935	1	CLONAL	3	TRUE	0	0.378739756687526	3		725	815	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445629	49445629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	126	761	0	ENST00000301067.7:c.1837G>A	p.Glu613Lys	p.E613K	ENST00000301067	NM_003482.3	613	Gag/Aag	10/54	0.229913456282344	3	FACETS	0.821	0.742	0.904	0.41	0.371	0.452	CLONAL	1	TRUE	1	0.378739756687526	3		761	964	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226890	2226890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760426764	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	71	262	0	ENST00000398665.3:c.4370C>T	p.Ser1457Phe	p.S1457F	ENST00000398665	NM_032482.2	1457	tCc/tTc	27/28	0.234480736200534	3	FACETS	1	0.904	1	0.519	0.454	0.587	CLONAL	1	TRUE	1	0.378739756687526	3		262	430	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424092	49424092	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs748791941	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	129	703	0	ENST00000301067.7:c.13970C>G	p.Ser4657Cys	p.S4657C	ENST00000301067	NM_003482.3	4657	tCt/tGt	42/54	0.229913456282344	3	FACETS	0.769	0.696	0.846	0.384	0.348	0.423	SUBCLONAL	1	TRUE	1	0.378739756687526	3		703	1054	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533069	63533069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1389567952	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	110	587	0	ENST00000307078.5:c.1825C>T	p.Pro609Ser	p.P609S	ENST00000307078	NM_004655.3	609	Ccc/Tcc	7/11	0.378739756687526	1	FACETS	0.842	0.759	0.93	0.842	0.759	0.93	CLONAL	1	TRUE	0	0.378739756687526	1		587	559	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196370	106196370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	49	382	0	ENST00000380013.4:c.4703C>T	p.Pro1568Leu	p.P1568L	ENST00000380013	NM_001127208.2	1568	cCa/cTa	11/11	1	2	FACETS	0.711	0.604	0.827	0.711	0.604	0.827	SUBCLONAL	1	TRUE	1	0.378739756687526	2		382	364	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295201	1295201	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	57	223	1				ENST00000310581	NM_198253.2	-/1132			0.229913456282344	3	FACETS	0.997	0.86	1	0.499	0.43	0.573	CLONAL	1	TRUE	1	0.378739756687526	3		224	359	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56878417	56878417	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs190188561	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	45	350	1	ENST00000308159.5:c.2356C>T	p.Arg786Ter	p.R786*	ENST00000308159	NM_014669.4	786	Cga/Tga	22/22	1	2	FACETS	0.551	0.464	0.648	0.551	0.464	0.648	SUBCLONAL	1	TRUE	1	0.378739756687526	2		351	431	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416782	121416782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1447883891	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	143	746	1	ENST00000257555.6:c.211G>A	p.Glu71Lys	p.E71K	ENST00000257555		71	Gag/Aag	1/10	1	2	FACETS	0.932	0.85	1	0.932	0.85	1	CLONAL	1	TRUE	1	0.378739756687526	2		747	810	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212886	94212886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	22	308	0	ENST00000323929.3:c.356C>T	p.Ser119Leu	p.S119L	ENST00000323929	NM_005591.3	119	tCa/tTa	5/20	0.234480736200534	3	FACETS	0.51	0.396	0.642	0.255	0.198	0.321	SUBCLONAL	1	TRUE	1	0.378739756687526	3		308	271	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577101	7577102	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	249	610	0	ENST00000269305.4:c.836_837delinsAA	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGG/gAA	8/11	0.25214679882605	2	FACETS	0.858	0.806	0.912	0.858	0.806	0.912	CLONAL	2	TRUE	0	0.378739756687526	2		610	766	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287215	33287215	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs550192421	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	73	489	0	ENST00000374542.5:c.1882C>T	p.Pro628Ser	p.P628S	ENST00000374542	NM_001141970.1	628	Ccc/Tcc	6/8	0.378739756687526	5	FACETS	0.808	0.706	0.919			1	CLONAL	1	TRUE	NA	0.378739756687526	5		489	748	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865899	56865899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779103749	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	47	291	0	ENST00000308159.5:c.1231G>A	p.Glu411Lys	p.E411K	ENST00000308159	NM_014669.4	411	Gag/Aag	11/22	1	2	FACETS	0.64	0.541	0.748	0.64	0.541	0.748	SUBCLONAL	1	TRUE	1	0.378739756687526	2		291	388	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189853	11189853	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	70	541	0	ENST00000361445.4:c.5656C>T	p.Gln1886Ter	p.Q1886*	ENST00000361445	NM_004958.3	1886	Cag/Tag	40/58	1	2	FACETS	0.517	0.45	0.589	0.517	0.45	0.589	SUBCLONAL	1	TRUE	1	0.378739756687526	2		541	715	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11313919	11313920	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	59	499	0	ENST00000361445.4:c.816_817delinsTT	p.Arg273Ter	p.R273*	ENST00000361445	NM_004958.3	272	gtCCga/gtTTga	6/58	1	2	FACETS	0.54	0.464	0.622	0.54	0.464	0.622	SUBCLONAL	1	TRUE	1	0.378739756687526	2		499	577	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260270	16260270	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs753578272	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	71	464	0	ENST00000375759.3:c.7535C>G	p.Ser2512Cys	p.S2512C	ENST00000375759	NM_015001.2	2512	tCt/tGt	11/15	1	2	FACETS	0.756	0.661	0.858	0.756	0.661	0.858	SUBCLONAL	1	TRUE	1	0.378739756687526	2		464	496	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798316	45798316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749896967	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	145	716	0	ENST00000450313.1:c.620C>T	p.Thr207Ile	p.T207I	ENST00000450313	NM_012222.2	207	aCc/aTc	8/16	0.378739756687526	3	FACETS	0.874	0.796	0.956	0.437	0.398	0.478	CLONAL	1	TRUE	1	0.378739756687526	3		716	1042	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733407	85733408	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	38	374	0	ENST00000370580.1:c.604_605delinsTT	p.Pro202Phe	p.P202F	ENST00000370580	NM_003921.4	202	CCt/TTt	3/3	0.378739756687526	3	FACETS	0.567	0.469	0.676	0.283	0.234	0.338	SUBCLONAL	1	TRUE	1	0.378739756687526	3		374	421	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458886	120458887	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	82	605	1	ENST00000256646.2:c.6458_6459delinsTT	p.Ser2153Phe	p.S2153F	ENST00000256646	NM_024408.3	2153	tCC/tTT	34/34	0.378739756687526	3	FACETS	0.666	0.587	0.752	0.333	0.293	0.376	SUBCLONAL	1	TRUE	1	0.378739756687526	3		606	773	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176055001	176055001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781466000	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	44	421	0	ENST00000367669.3:c.1052G>A	p.Ser351Asn	p.S351N	ENST00000367669	NM_022457.5	351	aGc/aAc	10/20	0.370824018255723	3	FACETS	0.544	0.456	0.641	0.181	0.152	0.214	SUBCLONAL	1	TRUE	0	0.378739756687526	3		421	508	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204515994	204515994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	76	258	0	ENST00000367182.3:c.892G>A	p.Val298Ile	p.V298I	ENST00000367182	NM_001278516.1	298	Gtt/Att	10/11	0.370824018255723	3	FACETS	0.986	0.878	1	0.657	0.585	0.733	CLONAL	2	TRUE	0	0.378739756687526	3		258	242	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606835	43606835	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	96	870	0	ENST00000355710.3:c.1444C>T	p.His482Tyr	p.H482Y	ENST00000355710	NM_020975.4	482	Cac/Tac	7/20	1	2	FACETS	0.577	0.514	0.646	0.577	0.514	0.646	SUBCLONAL	1	TRUE	1	0.378739756687526	2		870	878	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615185	43615185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758950128	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	103	740	0	ENST00000355710.3:c.2599G>A	p.Glu867Lys	p.E867K	ENST00000355710	NM_020975.4	867	Gag/Aag	14/20	1	2	FACETS	0.748	0.67	0.831	0.748	0.67	0.831	SUBCLONAL	1	TRUE	1	0.378739756687526	2		740	727	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119706	108119706	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	30	163	0	ENST00000278616.4:c.1112C>G	p.Thr371Ser	p.T371S	ENST00000278616	NM_000051.3	371	aCt/aGt	9/63	0.234480736200534	3	FACETS	0.933	0.758	1	0.466	0.379	0.564	CLONAL	1	TRUE	1	0.378739756687526	3		163	202	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375551	118375551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	68	276	0	ENST00000534358.1:c.8944C>T	p.Pro2982Ser	p.P2982S	ENST00000534358	NM_005933.3	2982	Cca/Tca	27/36	0.234480736200534	3	FACETS	0.777	0.683	0.876	0.777	0.683	0.876	SUBCLONAL	2	TRUE	1	0.378739756687526	3		276	275	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149224	119149224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	59	464	0	ENST00000264033.4:c.1232C>T	p.Ser411Leu	p.S411L	ENST00000264033	NM_005188.3	411	tCa/tTa	9/16	0.234480736200534	3	FACETS	0.822	0.709	0.944	0.411	0.354	0.472	CLONAL	1	TRUE	1	0.378739756687526	3		464	451	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246119	46246119	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	26	262	0	ENST00000334344.6:c.4213G>C	p.Asp1405His	p.D1405H	ENST00000334344	NM_152641.2	1405	Gat/Cat	15/21	0.229913456282344	3	FACETS	0.583	0.463	0.72	0.292	0.231	0.36	SUBCLONAL	1	TRUE	1	0.378739756687526	3		262	280	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427513	49427514	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	93	628	0	ENST00000301067.7:c.10974_10975delinsTT	p.Pro3659Ser	p.P3659S	ENST00000301067	NM_003482.3	3658	acCCct/acTTct	39/54	0.229913456282344	3	FACETS	0.832	0.74	0.93	0.416	0.37	0.465	CLONAL	1	TRUE	1	0.378739756687526	3		628	702	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427976	49427977	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	118	675	0	ENST00000301067.7:c.10613_10614delinsTT	p.Ser3538Phe	p.S3538F	ENST00000301067	NM_003482.3	3538	tCC/tTT	38/54	0.229913456282344	3	FACETS	0.904	0.815	0.997	0.452	0.407	0.499	CLONAL	1	TRUE	1	0.378739756687526	3		675	820	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442485	49442485	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	58	473	0	ENST00000301067.7:c.4088C>T	p.Thr1363Ile	p.T1363I	ENST00000301067	NM_003482.3	1363	aCc/aTc	13/54	0.229913456282344	3	FACETS	0.672	0.578	0.775	0.336	0.289	0.388	SUBCLONAL	1	TRUE	1	0.378739756687526	3		473	542	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563180	21563180	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758975100	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	175	865	0	ENST00000382592.4:c.739C>T	p.Pro247Ser	p.P247S	ENST00000382592	NM_014572.2	247	Ccg/Tcg	4/8	0.344348775098057	2	FACETS	0.938	0.864	1	0.469	0.432	0.508	CLONAL	1	TRUE	0	0.378739756687526	2		865	985	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620029	21620029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763662441	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	105	572	0	ENST00000382592.4:c.137C>T	p.Ser46Phe	p.S46F	ENST00000382592	NM_014572.2	46	tCc/tTc	2/8	0.344348775098057	2	FACETS	0.74	0.663	0.822	0.37	0.331	0.411	SUBCLONAL	1	TRUE	0	0.378739756687526	2		572	749	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281897	49281897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61735167	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	61	478	0	ENST00000282018.3:c.944G>A	p.Arg315Lys	p.R315K	ENST00000282018	NM_020377.2	315	aGa/aAa	1/1	0.344348775098057	2	FACETS	0.739	0.639	0.847	0.369	0.319	0.424	SUBCLONAL	1	TRUE	0	0.378739756687526	2		478	436	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066952	30066952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	44	277	0	ENST00000331968.5:c.2179G>A	p.Asp727Asn	p.D727N	ENST00000331968	NM_002742.2	727	Gat/Aat	16/18	1	2	FACETS	0.557	0.468	0.656	0.557	0.468	0.656	SUBCLONAL	1	TRUE	1	0.378739756687526	2		277	417	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242062	105242062	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457484217	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	153	804	0	ENST00000349310.3:c.362G>A	p.Arg121Gln	p.R121Q	ENST00000349310	NM_001014432.1	121	cGg/cAg	6/15	1	2	FACETS	0.816	0.746	0.89	0.816	0.746	0.89	CLONAL	1	TRUE	1	0.378739756687526	2		804	990	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989112	41989112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	44	398	0	ENST00000219905.7:c.1904C>T	p.Ser635Phe	p.S635F	ENST00000219905	NM_001164273.1	635	tCt/tTt	3/24	1	2	FACETS	0.577	0.484	0.678	0.577	0.484	0.678	SUBCLONAL	1	TRUE	1	0.378739756687526	2		398	403	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000314	42000314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	23	322	0	ENST00000219905.7:c.2333C>T	p.Pro778Leu	p.P778L	ENST00000219905	NM_001164273.1	778	cCc/cTc	7/24	1	2	FACETS	0.443	0.346	0.555	0.443	0.346	0.555	SUBCLONAL	1	TRUE	1	0.378739756687526	2		322	274	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019600	42019600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	29	341	0	ENST00000219905.7:c.3653C>T	p.Pro1218Leu	p.P1218L	ENST00000219905	NM_001164273.1	1218	cCt/cTt	10/24	1	2	FACETS	0.559	0.45	0.682	0.559	0.45	0.682	SUBCLONAL	1	TRUE	1	0.378739756687526	2		341	274	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058462	42058462	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776084698	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	36	361	0	ENST00000219905.7:c.8182C>T	p.Pro2728Ser	p.P2728S	ENST00000219905	NM_001164273.1	2728	Cca/Tca	24/24	1	2	FACETS	0.54	0.445	0.646	0.54	0.445	0.646	SUBCLONAL	1	TRUE	1	0.378739756687526	2		361	352	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762100	43762101	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	56	576	2	ENST00000382044.4:c.1344_1345delinsTT	p.Pro449Ser	p.P449S	ENST00000382044	NM_001141980.1	448	ttCCct/ttTTct	11/28	1	2	FACETS	0.44	0.376	0.51	0.44	0.376	0.51	SUBCLONAL	1	TRUE	1	0.378739756687526	2		578	672	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632685	3632686	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	179	669	2	ENST00000294008.3:c.5162_5163delinsAT	p.Ser1721Tyr	p.S1721Y	ENST00000294008	NM_032444.2	1721	tCC/tAT	15/15	0.0537353495343527	3	FACETS	1	0.988	1	0.697	0.644	0.753	INDETERMINATE	1	TRUE	1	0.378739756687526	3		671	806	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832852	3832852	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	57	454	0	ENST00000262367.5:c.1406C>T	p.Ser469Phe	p.S469F	ENST00000262367	NM_004380.2	469	tCt/tTt	6/31	0.0537353495343527	3	FACETS	0.587	0.503	0.678	0.293	0.251	0.339	INDETERMINATE	1	TRUE	1	0.378739756687526	3		454	610	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56839444	56839445	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	163	475	1	ENST00000308159.5:c.389_390delinsAA	p.Arg130Gln	p.R130Q	ENST00000308159	NM_014669.4	130	cGG/cAA	5/22	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.378739756687526	2		476	658	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992090	72992090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	112	666	0	ENST00000268489.5:c.1955C>T	p.Ser652Phe	p.S652F	ENST00000268489	NM_006885.3	652	tCc/tTc	2/10	1	2	FACETS	0.817	0.735	0.903	0.817	0.735	0.903	CLONAL	1	TRUE	1	0.378739756687526	2		666	724	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89824992	89824992	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs967438026	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	89	472	0	ENST00000389301.3:c.2974C>T	p.His992Tyr	p.H992Y	ENST00000389301	NM_000135.2	992	Cac/Tac	30/43	1	2	FACETS	0.756	0.671	0.846	0.756	0.671	0.846	SUBCLONAL	1	TRUE	1	0.378739756687526	2		472	622	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89825043	89825043	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369565161	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	133	520	0	ENST00000389301.3:c.2923G>A	p.Gly975Arg	p.G975R	ENST00000389301	NM_000135.2	975	Gga/Aga	30/43	1	2	FACETS	0.879	0.799	0.963	0.879	0.799	0.963	CLONAL	1	TRUE	1	0.378739756687526	2		520	799	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40500473	40500473	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	94	473	0	ENST00000264657.5:c.62T>C	p.Leu21Pro	p.L21P	ENST00000264657	NM_139276.2	21	cTc/cCc	2/24	0.321031737953562	3	FACETS	0.911	0.811	1	0.304	0.27	0.339	CLONAL	1	TRUE	0	0.378739756687526	3		473	648	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59878814	59878814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	18	192	0	ENST00000259008.2:c.940C>T	p.His314Tyr	p.H314Y	ENST00000259008	NM_032043.2	314	Cat/Tat	8/20	0.378739756687526	1	FACETS	0.497	0.377	0.637	0.497	0.377	0.637	SUBCLONAL	1	TRUE	0	0.378739756687526	1		192	155	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622127	1622128	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	124	787	0	ENST00000344749.5:c.747_748delinsTT	p.Pro250Ser	p.P250S	ENST00000344749	NM_001136139.2	249	ctCCcg/ctTTcg	10/19	0.234480736200534	3	FACETS	0.887	0.802	0.977	0.444	0.401	0.489	CLONAL	1	TRUE	1	0.378739756687526	3		787	878	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5225794	5225794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	129	732	0	ENST00000357368.4:c.2438C>T	p.Thr813Ile	p.T813I	ENST00000357368	NM_002850.3	813	aCc/aTc	17/38	0.234480736200534	3	FACETS	0.882	0.799	0.969	0.441	0.399	0.485	CLONAL	1	TRUE	1	0.378739756687526	3		732	919	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249236	10249236	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	90	649	0	ENST00000340748.4:c.3946C>G	p.Leu1316Val	p.L1316V	ENST00000340748		1316	Ctg/Gtg	34/40	0.234480736200534	3	FACETS	0.705	0.625	0.791	0.352	0.312	0.396	SUBCLONAL	1	TRUE	1	0.378739756687526	3		649	802	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355315	15355315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	66	398	0	ENST00000263377.2:c.2308C>T	p.Pro770Ser	p.P770S	ENST00000263377	NM_058243.2	770	Ccg/Tcg	13/20	0.234480736200534	3	FACETS	1	0.91	1	0.527	0.46	0.6	CLONAL	1	TRUE	1	0.378739756687526	3		398	393	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212277	36212278	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	141	699	1	ENST00000222270.7:c.2028_2029delinsTT	p.Pro677Ser	p.P677S	ENST00000222270	NM_014727.1	676	gcCCct/gcTTct	3/37	0.234480736200534	3	FACETS	1	0.979	1	0.621	0.567	0.678	CLONAL	1	TRUE	1	0.378739756687526	3		700	713	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753464	42753464	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1212114312	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	182	899	0	ENST00000222329.4:c.800C>T	p.Ala267Val	p.A267V	ENST00000222329	NM_006494.2	267	gCt/gTt	4/4	0.234480736200534	3	FACETS	1	0.968	1	0.546	0.503	0.591	CLONAL	1	TRUE	1	0.378739756687526	3		899	1046	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498338	29498339	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	53	475	0	ENST00000389048.3:c.1841_1842delinsAA	p.Trp614Ter	p.W614*	ENST00000389048	NM_004304.4	614	tGG/tAA	10/29	1	2	FACETS	0.505	0.431	0.587	0.505	0.431	0.587	SUBCLONAL	1	TRUE	1	0.378739756687526	2		475	554	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46588066	46588066	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	119	571	0	ENST00000263734.3:c.616C>T	p.Pro206Ser	p.P206S	ENST00000263734	NM_001430.4	206	Cct/Tct	6/16	1	2	FACETS	0.847	0.765	0.933	0.847	0.765	0.933	CLONAL	1	TRUE	1	0.378739756687526	2		571	742	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209110046	209110046	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	28	365	0	ENST00000345146.2:c.517G>C	p.Glu173Gln	p.E173Q	ENST00000345146	NM_005896.2	173	Gaa/Caa	5/10	1	2	FACETS	0.538	0.431	0.659	0.538	0.431	0.659	SUBCLONAL	1	TRUE	1	0.378739756687526	2		365	275	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560890	9560890	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	148	435	1	ENST00000353224.5:c.892C>T	p.Pro298Ser	p.P298S	ENST00000353224	NM_177990.2	298	Cca/Tca	4/10	0.234480736200534	3	FACETS	1	0.985	1	0.675	0.617	0.734	CLONAL	1	TRUE	1	0.378739756687526	3		436	689	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023883	31023883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11549643	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	150	583	0	ENST00000375687.4:c.3368C>T	p.Pro1123Leu	p.P1123L	ENST00000375687	NM_015338.5	1123	cCa/cTa	13/13	0.234480736200534	3	FACETS	1	0.98	1	0.614	0.562	0.669	CLONAL	1	TRUE	1	0.378739756687526	3		583	767	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980816	40980816	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs761093954	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	176	576	0	ENST00000373198.4:c.1670A>T	p.Tyr557Phe	p.Y557F	ENST00000373198	NM_133170.3	557	tAc/tTc	10/32	0.234480736200534	3	FACETS	1	0.988	1	0.701	0.647	0.758	CLONAL	1	TRUE	1	0.378739756687526	3		576	788	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543945	41543945	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	96	533	0	ENST00000263253.7:c.2236A>C	p.Asn746His	p.N746H	ENST00000263253	NM_001429.3	746	Aac/Cac	12/31	1	2	FACETS	0.673	0.6	0.752	0.673	0.6	0.752	SUBCLONAL	1	TRUE	1	0.378739756687526	2		533	753	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458492	12458492	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1215517121	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	81	527	0	ENST00000287820.6:c.1109C>T	p.Ser370Phe	p.S370F	ENST00000287820	NM_015869.4	370	tCc/tTc	6/7	0.242854992845353	3	FACETS	0.747	0.658	0.843	0.249	0.219	0.281	SUBCLONAL	1	TRUE	0	0.378739756687526	3		527	681	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164123	47164124	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	18	271	1	ENST00000409792.3:c.2002_2003delinsTT	p.Pro668Phe	p.P668F	ENST00000409792	NM_014159.6	668	CCc/TTc	3/21	0.242854992845353	3	FACETS	0.628	0.475	0.807	0.209	0.158	0.269	SUBCLONAL	1	TRUE	0	0.378739756687526	3		272	180	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013725	170013725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	49	300	0	ENST00000295797.4:c.1444C>T	p.Pro482Ser	p.P482S	ENST00000295797	NM_002740.5	482	Cca/Tca	15/18	0.230286570226595	5	FACETS	0.869	0.737	1	0.29	0.245	0.338	CLONAL	1	TRUE	2	0.378739756687526	5		300	467	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1940224	1940225	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	45	328	0	ENST00000382891.5:c.1721_1722delinsTT	p.Ala574Val	p.A574V	ENST00000382891	NM_133335.3	574	gCC/gTT	8/22	1	2	FACETS	0.539	0.453	0.633	0.539	0.453	0.633	SUBCLONAL	1	TRUE	1	0.378739756687526	2		328	441	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604689	55604689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	88	487	0	ENST00000288135.5:c.2897C>T	p.Ser966Phe	p.S966F	ENST00000288135	NM_000222.2	966	tCc/tTc	21/21	1	2	FACETS	0.757	0.671	0.848	0.757	0.671	0.848	SUBCLONAL	1	TRUE	1	0.378739756687526	2		487	614	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189461	56189461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	97	437	0	ENST00000399503.3:c.4493C>T	p.Pro1498Leu	p.P1498L	ENST00000399503	NM_005921.1	1498	cCa/cTa	20/20	0.25214679882605	2	FACETS	1	0.963	1	0.582	0.522	0.646	CLONAL	1	TRUE	0	0.378739756687526	2		437	440	SUCCESS
APC	324	MSKCC	GRCh37	5	112173755	112173755	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	28	281	0	ENST00000257430.4:c.2464C>T	p.Leu822Phe	p.L822F	ENST00000257430	NM_000038.5	822	Ctt/Ttt	16/16	0.25214679882605	2	FACETS	0.675	0.543	0.824	0.338	0.271	0.412	SUBCLONAL	1	TRUE	0	0.378739756687526	2		281	219	SUCCESS
APC	324	MSKCC	GRCh37	5	112175372	112175373	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	26	237	2	ENST00000257430.4:c.4081_4082delinsTT	p.Pro1361Phe	p.P1361F	ENST00000257430	NM_000038.5	1361	CCc/TTc	16/16	0.25214679882605	2	FACETS	0.645	0.513	0.793	0.322	0.256	0.397	SUBCLONAL	1	TRUE	0	0.378739756687526	2		239	213	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149447878	149447878	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1459171593	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	103	676	0	ENST00000286301.3:c.1526C>T	p.Pro509Leu	p.P509L	ENST00000286301	NM_005211.3	509	cCc/cTc	11/22	0.25214679882605	2	FACETS	0.761	0.681	0.845	0.38	0.34	0.423	SUBCLONAL	1	TRUE	0	0.378739756687526	2		676	715	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497332	149497332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	86	609	0	ENST00000261799.4:c.2986C>T	p.His996Tyr	p.H996Y	ENST00000261799	NM_002609.3	996	Cat/Tat	22/23	0.25214679882605	2	FACETS	0.782	0.693	0.877	0.391	0.346	0.439	SUBCLONAL	1	TRUE	0	0.378739756687526	2		609	581	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523699	176523699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	139	831	0	ENST00000292408.4:c.2110G>A	p.Glu704Lys	p.E704K	ENST00000292408	NM_213647.1	704	Gag/Aag	16/18	0.230286570226595	5	FACETS	0.94	0.854	1	0.313	0.284	0.344	CLONAL	1	TRUE	2	0.378739756687526	5		831	1224	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665475	176665475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	57	386	0	ENST00000439151.2:c.4159C>T	p.Leu1387Phe	p.L1387F	ENST00000439151	NM_022455.4	1387	Ctt/Ttt	7/23	0.230286570226595	5	FACETS	0.645	0.552	0.746	0.215	0.184	0.249	SUBCLONAL	1	TRUE	2	0.378739756687526	5		386	732	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490507	20490507	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1322442077	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	106	501	0	ENST00000346618.3:c.1244C>T	p.Pro415Leu	p.P415L	ENST00000346618	NM_001949.4	415	cCt/cTt	7/7	0.229913456282344	3	FACETS	0.988	0.887	1	0.494	0.443	0.548	CLONAL	1	TRUE	1	0.378739756687526	3		501	674	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163315	32163315	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	132	783	0	ENST00000375023.3:c.5911T>G	p.Cys1971Gly	p.C1971G	ENST00000375023	NM_004557.3	1971	Tgc/Ggc	30/30	0.229913456282344	3	FACETS	0.602	0.545	0.663	0.301	0.272	0.332	SUBCLONAL	1	TRUE	1	0.378739756687526	3		783	1377	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020788	112020788	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	87	366	0	ENST00000368678.4:c.783G>A	p.Trp261Ter	p.W261*	ENST00000368678		261	tgG/tgA	8/13	0.30001555881907	2	FACETS	0.99	0.88	1	0.495	0.44	0.554	CLONAL	1	TRUE	0	0.378739756687526	2		366	464	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665230	117665230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	10	212	0	ENST00000368508.3:c.4517G>A	p.Arg1506Lys	p.R1506K	ENST00000368508	NM_002944.2	1506	aGa/aAa	27/43	0.30001555881907	2	FACETS	0.345	0.234	0.484	0.173	0.117	0.242	SUBCLONAL	1	TRUE	0	0.378739756687526	2		212	153	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444360	50444360	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	166	313	0	ENST00000331340.3:c.290G>A	p.Arg97Lys	p.R97K	ENST00000331340	NM_006060.4	97	aGg/aAg	4/8	0.229913456282344	3	FACETS	0.867	0.801	0.936	0.867	0.801	0.936	CLONAL	2	TRUE	1	0.378739756687526	3		313	601	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359065	81359065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760721822	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	47	397	0	ENST00000222390.5:c.896C>T	p.Pro299Leu	p.P299L	ENST00000222390	NM_000601.4	299	cCt/cTt	8/18	0.229913456282344	3	FACETS	0.734	0.621	0.859	0.367	0.31	0.43	SUBCLONAL	1	TRUE	1	0.378739756687526	3		397	402	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339466	116339466	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs762059386	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	70	308	0	ENST00000397752.3:c.328G>T	p.Gly110Cys	p.G110C	ENST00000397752	NM_000245.2	110	Ggt/Tgt	2/21	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.378739756687526	2		308	342	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380952	116380952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	92	593	0	ENST00000397752.3:c.1574C>T	p.Ser525Phe	p.S525F	ENST00000397752	NM_000245.2	525	tCc/tTc	5/21	1	2	FACETS	0.595	0.528	0.667	0.595	0.528	0.667	SUBCLONAL	1	TRUE	1	0.378739756687526	2		593	816	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852143	128852143	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	151	890	0	ENST00000249373.3:c.2215C>T	p.Pro739Ser	p.P739S	ENST00000249373	NM_005631.4	739	Cca/Tca	12/12	1	2	FACETS	0.768	0.701	0.838	0.768	0.701	0.838	SUBCLONAL	1	TRUE	1	0.378739756687526	2		890	1038	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140549967	140549967	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	26	312	0	ENST00000288602.6:c.184G>C	p.Glu62Gln	p.E62Q	ENST00000288602	NM_004333.4	62	Gag/Cag	2/18	1	2	FACETS	0.496	0.393	0.612	0.496	0.393	0.612	SUBCLONAL	1	TRUE	1	0.378739756687526	2		312	277	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272347	38272347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	169	582	0	ENST00000425967.3:c.2020G>A	p.Gly674Ser	p.G674S	ENST00000425967	NM_001174067.1	674	Ggc/Agc	15/19	0.378739756687526	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.378739756687526	1		582	571	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624594	93624595	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	71	456	2	ENST00000375746.1:c.685_686delinsTT	p.Pro229Phe	p.P229F	ENST00000375746	NM_001174167.1	229	CCc/TTc	4/14	1	2	FACETS	0.696	0.608	0.79	0.696	0.608	0.79	SUBCLONAL	1	TRUE	1	0.378739756687526	2		458	539	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760673	133760673	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042796-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	316	857	0	ENST00000318560.5:c.2996C>G	p.Ser999Cys	p.S999C	ENST00000318560	NM_005157.4	999	tCc/tGc	11/11	0.321031737953562	3	FACETS	0.974	0.92	1	0.649	0.613	0.686	CLONAL	2	TRUE	0	0.378739756687526	3		857	1019	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0043278-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	941	436	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	0.997	0.979	1			1	INDETERMINATE	2	TRUE	NA	0.802559177169276	2		439	1176	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0043278-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	126	227	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.872	0.799	0.947	0.872	0.799	0.947	CLONAL	1	TRUE	1	0.802559177169276	2		227	360	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0043504-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	97	314	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	1	2	FACETS	0.76	0.681	0.844	0.76	0.681	0.844	SUBCLONAL	1	TRUE	1	0.543929038255413	2		314	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0043504-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	247	724	0	ENST00000269305.4:c.672+1G>C		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.536901654965159	1	FACETS	0.996	0.937	1	0.996	0.937	1	CLONAL	1	TRUE	0	0.543929038255413	1		724	664	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412506	63412506	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043504-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	262	837	0	ENST00000330258.3:c.661T>A	p.Phe221Ile	p.F221I	ENST00000330258	NM_152424.3	221	Ttc/Atc	2/2	0.543929038255413	1	FACETS	0.981	0.924	1	0.981	0.924	1	CLONAL	1	TRUE	0	0.543929038255413	1		837	715	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354065	15354065	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043504-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	254	758	1	ENST00000263377.2:c.2815C>T	p.Gln939Ter	p.Q939*	ENST00000263377	NM_058243.2	939	Cag/Tag	14/20	1	2	FACETS	0.912	0.854	0.972	0.912	0.854	0.972	CLONAL	1	TRUE	1	0.543929038255413	2		759	1024	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0044129-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	112	303	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.633473366361048	2		303	343	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0044129-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	118	269	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.866	0.787	0.948	0.866	0.787	0.948	CLONAL	1	TRUE	1	0.633473366361048	2		269	430	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602737	10602737	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044129-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	438	800	0	ENST00000171111.5:c.841C>A	p.Leu281Met	p.L281M	ENST00000171111	NM_203500.1	281	Ctg/Atg	3/6	0.633473366361048	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.633473366361048	1		800	845	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156066	106156066	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1244473694	NA	P-0044129-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	136	284	0	ENST00000380013.4:c.967C>T	p.Gln323Ter	p.Q323*	ENST00000380013	NM_001127208.2	323	Caa/Taa	3/11	1	2	FACETS	0.871	0.797	0.948	0.871	0.797	0.948	CLONAL	1	TRUE	1	0.633473366361048	2		284	493	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207015	1207015	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044129-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	285	679	0	ENST00000326873.7:c.103del	p.Ile35SerfsTer16	p.I35Sfs*16	ENST00000326873	NM_000455.4	35	Atc/tc	1/10	0.633473366361048	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.633473366361048	1		679	610	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590439	67590439	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044129-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	76	135	0	ENST00000274335.5:c.1501C>T	p.Gln501Ter	p.Q501*	ENST00000274335		501	Caa/Taa	11/15	1	2	FACETS	0.899	0.798	1	0.899	0.798	1	CLONAL	1	TRUE	1	0.633473366361048	2		135	267	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs786201057	NA	P-0044206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	240	564	0	ENST00000269305.4:c.374C>G	p.Thr125Arg	p.T125R	ENST00000269305	NM_001126112.2	125	aCg/aGg	4/11	0.535255534474903	2	FACETS	0.769	0.724	0.815	0.769	0.724	0.815	SUBCLONAL	2	TRUE	0	0.535255534474903	2		564	583	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325035	123325035	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1041970177	NA	P-0044206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	74	523	0	ENST00000358487.5:c.293C>G	p.Thr98Arg	p.T98R	ENST00000358487	NM_000141.4	98	aCg/aGg	3/18	0.1726683443998	2	FACETS	0.377	0.329	0.428	0.188	0.164	0.214	INDETERMINATE	1	TRUE	0	0.535255534474903	2		523	734	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944282	81944282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	142	653	0	ENST00000359376.3:c.1891C>T	p.Leu631Phe	p.L631F	ENST00000359376	NM_002661.3	631	Ctc/Ttc	18/33	0.535255534474903	1	FACETS	0.558	0.51	0.609	0.558	0.51	0.609	SUBCLONAL	1	TRUE	0	0.535255534474903	1		653	696	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940914	49940914	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	74	700	0	ENST00000296474.3:c.129G>C	p.Lys43Asn	p.K43N	ENST00000296474	NM_002447.2	43	aaG/aaC	1/20	1	2	FACETS	0.272	0.237	0.31	0.272	0.237	0.31	SUBCLONAL	1	TRUE	1	0.535255534474903	2		700	1017	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061131	38061185	+	stop_gained	Nonsense_Mutation	DEL	GCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCG	GCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCG	T	novel	NA	P-0044206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	221	145	0	ENST00000250448.2:c.804_858delinsA	p.Cys268_Gly286delinsTer	p.C268_G286delins*	ENST00000250448	NM_004496.3	268	tgCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGGC/tgA	2/2	0.137703414389037	4	FACETS	1	0.968	1	1	0.968	1	INDETERMINATE	4	TRUE	0	0.535255534474903	4		145	312	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044527-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	102	349	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.42857705300107	2		350	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578513	7578513	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567554121	NA	P-0044527-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	392	1220	2	ENST00000269305.4:c.417G>T	p.Lys139Asn	p.K139N	ENST00000269305	NM_001126112.2	139	aaG/aaT	5/11	0.35167632070712	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.42857705300107	1		1222	1268	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099146	157099146	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044527-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	177	548	0	ENST00000346085.5:c.83G>T	p.Gly28Val	p.G28V	ENST00000346085	NM_020732.3	28	gGt/gTt	1/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.42857705300107	2		548	672	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044527-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	141	349	1				ENST00000310581	NM_198253.2	-/1132			0.2164039331825	3	FACETS	0.997	0.914	1	0.997	0.914	1	CLONAL	2	TRUE	1	0.314085293887396	3		350	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578513	7578513	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567554121	NA	P-0044527-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	291	1220	2	ENST00000269305.4:c.417G>T	p.Lys139Asn	p.K139N	ENST00000269305	NM_001126112.2	139	aaG/aaT	5/11	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.314085293887396	2		1222	1246	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099146	157099146	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044527-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	111	548	0	ENST00000346085.5:c.83G>T	p.Gly28Val	p.G28V	ENST00000346085	NM_020732.3	28	gGt/gTt	1/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.314085293887396	2		548	572	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	375	566	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.555949420522807	5	FACETS	1	0.983	1			1	CLONAL	3	TRUE	NA	0.555949420522807	5		566	782	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0044889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	421	712	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.505963907519738	2	FACETS	0.9	0.863	0.937	0.9	0.863	0.937	CLONAL	2	TRUE	0	0.555949420522807	2		712	841	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974744	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAGCAGCGCCCGCA	CCTCCAGCAGCGCCCGCA	-	novel	NA	P-0044889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	204	364	0	ENST00000304494.5:c.83_100del	p.Val28_Glu33del	p.V28_E33del	ENST00000304494	NM_000077.4	28	gTGCGGGCGCTGCTGGAGGcg/gcg	1/3	0.498333682607242	2	FACETS	0.805	0.755	0.855	0.805	0.755	0.855	CLONAL	2	TRUE	0	0.555949420522807	2		364	456	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225652	133225652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751555395	NA	P-0044889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	313	676	0	ENST00000320574.5:c.4012G>A	p.Glu1338Lys	p.E1338K	ENST00000320574	NM_006231.2	1338	Gag/Aag	32/49	0.15351998056849	5	FACETS	0.834	0.79	0.879			1	INDETERMINATE	3	TRUE	NA	0.555949420522807	5		676	825	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393322	393322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044889-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	137	504	1	ENST00000380956.4:c.170C>T	p.Ala57Val	p.A57V	ENST00000380956	NM_001195286.1	57	gCg/gTg	2/9	0.227535321374486	6	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.555949420522807	6		505	829	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045036-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	33	349	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.685	0.56	0.825	0.685	0.56	0.825	SUBCLONAL	1	TRUE	1	0.351546515188429	2		350	274	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911535	101911535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113605875	NA	P-0045036-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	59	318	0	ENST00000374994.4:c.1460G>A	p.Arg487Gln	p.R487Q	ENST00000374994	NM_004612.2	487	cGg/cAg	9/9	0.351546515188429	1	FACETS	0.89	0.771	1	0.89	0.771	1	CLONAL	1	TRUE	0	0.351546515188429	1		318	311	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261011	16261011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780025497	NA	P-0045036-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	83	544	0	ENST00000375759.3:c.8276C>T	p.Thr2759Met	p.T2759M	ENST00000375759	NM_015001.2	2759	aCg/aTg	11/15	1	2	FACETS	0.888	0.785	0.997	0.888	0.785	0.997	CLONAL	1	TRUE	1	0.351546515188429	2		544	532	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984398	201984399	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0045036-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	160	618	0	ENST00000359651.3:c.1064_1065dup	p.Lys356AlafsTer92	p.K356Afs*92	ENST00000359651		355	ggc/gGCgc	8/8	0.159483637339158	2	FACETS	1	0.982	1	0.618	0.568	0.671	INDETERMINATE	1	TRUE	0	0.351546515188429	2		618	736	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786674	3786674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045036-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	87	579	1	ENST00000262367.5:c.4537G>A	p.Glu1513Lys	p.E1513K	ENST00000262367	NM_004380.2	1513	Gag/Aag	27/31	1	2	FACETS	0.876	0.777	0.981	0.876	0.777	0.981	CLONAL	1	TRUE	1	0.351546515188429	2		580	565	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786790	3786790	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045036-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	36	385	0	ENST00000262367.5:c.4421G>C	p.Cys1474Ser	p.C1474S	ENST00000262367	NM_004380.2	1474	tGt/tCt	27/31	1	2	FACETS	0.756	0.624	0.901	0.756	0.624	0.901	CLONAL	1	TRUE	1	0.351546515188429	2		385	271	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0045414-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	223	534	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.227471865636788	3	FACETS	1	0.988	1	0.824	0.772	0.877	CLONAL	2	TRUE	0	0.344458420188107	3		534	614	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027133	49027133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853292	NA	P-0045414-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	49	222	0	ENST00000267163.4:c.1700C>T	p.Ser567Leu	p.S567L	ENST00000267163	NM_000321.2	567	tCa/tTa	18/27	0.344458420188107	5	FACETS	0.817	0.692	0.955	0.204	0.173	0.239	CLONAL	1	TRUE	1	0.344458420188107	5		222	528	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528611	8528611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201846121	NA	P-0045414-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	133	349	0	ENST00000356435.5:c.521G>A	p.Arg174His	p.R174H	ENST00000356435		174	cGt/cAt	4/35	0.344458420188107	3	FACETS	0.77	0.702	0.841	0.77	0.702	0.841	SUBCLONAL	2	TRUE	1	0.344458420188107	3		349	588	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448391	49448391	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045414-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	101	656	0	ENST00000301067.7:c.320A>G	p.Glu107Gly	p.E107G	ENST00000301067	NM_003482.3	107	gAg/gGg	3/54	0.254955262912167	4	FACETS	0.979	0.875	1	0.49	0.437	0.546	CLONAL	1	TRUE	2	0.344458420188107	4		656	805	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136277	202136277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045414-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	268	433	0	ENST00000358485.4:c.521C>T	p.Ser174Leu	p.S174L	ENST00000358485	NM_001080125.1	174	tCa/tTa	3/9	0.297413857857745	4	FACETS	1	0.987	1	0.859	0.812	0.906	CLONAL	3	TRUE	0	0.344458420188107	4		433	609	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259152	36259156	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCA	GGGCA	-	novel	NA	P-0045414-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	84	581	0	ENST00000300305.3:c.335_339del	p.Leu112HisfsTer24	p.L112Hfs*24	ENST00000300305		112	cTGCCC/c	3/8	0.344458420188107	5	FACETS	0.817	0.721	0.922	0.272	0.24	0.308	CLONAL	1	TRUE	2	0.344458420188107	5		581	905	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565544	41565544	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045414-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	212	299	0	ENST00000263253.7:c.4211del	p.Phe1404SerfsTer6	p.F1404Sfs*6	ENST00000263253	NM_001429.3	1404	Ttc/tc	26/31	0.344458420188107	3	FACETS	0.986	0.925	1	0.986	0.925	1	CLONAL	3	TRUE	0	0.344458420188107	3		299	488	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665299	138665299	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1226344391	NA	P-0045414-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	351	687	0	ENST00000330315.3:c.266C>G	p.Pro89Arg	p.P89R	ENST00000330315	NM_023067.3	89	cCg/cGg	1/1	0.344458420188107	5	FACETS	0.982	0.932	1	0.982	0.932	1	CLONAL	3	TRUE	2	0.344458420188107	5		687	1049	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918557	44918557	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0045414-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	178	187	0	ENST00000377967.4:c.1040T>A	p.Leu347Ter	p.L347*	ENST00000377967	NM_021140.2	347	tTg/tAg	12/29	0.344458420188107	2	FACETS	0.888	0.83	0.946			1	CLONAL	3	TRUE	NA	0.344458420188107	2		187	388	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740273	162740273	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045414-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	44	297	0	ENST00000367921.3:c.1475C>A	p.Pro492Gln	p.P492Q	ENST00000367921	NM_006182.2	492	cCa/cAa	12/18	0.344458420188107	5	FACETS	0.652	0.546	0.77	0.217	0.182	0.257	SUBCLONAL	1	TRUE	2	0.344458420188107	5		297	594	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499611	149499611	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	110	589	0	ENST00000261799.4:c.2662T>C	p.Ser888Pro	p.S888P	ENST00000261799	NM_002609.3	888	Tcc/Ccc	19/23	1	2	FACETS	0.377	0.339	0.418	0.377	0.339	0.418	SUBCLONAL	1	TRUE	1	0.804043552490453	2		589	725	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263973	104263974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776579	NA	P-0046128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	112	342	1	ENST00000369902.3:c.71dup	p.Ala25GlyfsTer23	p.A25Gfs*23	ENST00000369902	NM_016169.3	22	gcc/gCcc	1/12	0.804043552490453	1	FACETS	0.817	0.755	0.878	0.817	0.755	0.878	CLONAL	1	TRUE	0	0.804043552490453	1		343	204	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0046128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	306	629	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	1	2	FACETS	0.962	0.911	1	0.962	0.911	1	CLONAL	1	TRUE	1	0.804043552490453	2		629	791	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685301	89685301	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	82	120	0	ENST00000371953.3:c.196A>G	p.Lys66Glu	p.K66E	ENST00000371953	NM_000314.4	66	Aag/Gag	3/9	0.804043552490453	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.804043552490453	1		120	115	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412905	49412905	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519951	NA	P-0046128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	408	664	0	ENST00000418115.1:c.118G>A	p.Glu40Lys	p.E40K	ENST00000418115	NM_001664.2	40	Gag/Aag	2/5	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.804043552490453	2		664	948	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784112	9784112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	337	796	0	ENST00000377346.4:c.2680C>T	p.Arg894Trp	p.R894W	ENST00000377346	NM_005026.3	894	Cgg/Tgg	21/24	1	2	FACETS	0.983	0.934	1	0.983	0.934	1	CLONAL	1	TRUE	1	0.804043552490453	2		796	853	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197713	66197713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238493512	NA	P-0046128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	186	346	0	ENST00000273854.3:c.2986G>A	p.Ala996Thr	p.A996T	ENST00000273854	NM_004439.5	996	Gct/Act	17/18	1	2	FACETS	0.97	0.905	1	0.97	0.905	1	CLONAL	1	TRUE	1	0.804043552490453	2		346	477	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911039	94911039	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	278	443	1	ENST00000536441.1:c.1091T>A	p.Val364Glu	p.V364E	ENST00000536441	NM_144665.3	364	gTg/gAg	8/10	1	2	FACETS	0.986	0.932	1	0.986	0.932	1	CLONAL	1	TRUE	1	0.804043552490453	2		444	701	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118781	115118781	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	148	572	0	ENST00000257566.3:c.560A>G	p.His187Arg	p.H187R	ENST00000257566	NM_016569.3	187	cAc/cGc	2/8	1	2	FACETS	0.495	0.453	0.54	0.495	0.453	0.54	SUBCLONAL	1	TRUE	1	0.804043552490453	2		572	743	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880861	28880861	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199599880	NA	P-0046128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	326	595	0	ENST00000282397.4:c.3769C>T	p.Arg1257Cys	p.R1257C	ENST00000282397	NM_002019.4	1257	Cgc/Tgc	29/30	0.796868195897119	3	FACETS	0.986	0.932	1	0.493	0.466	0.521	CLONAL	1	TRUE	1	0.804043552490453	3		595	1153	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303375	91303375	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs367543015	NA	P-0046128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	108	151	0	ENST00000355112.3:c.1088-2A>G		p.X363_splice	ENST00000355112	NM_000057.2	363			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.804043552490453	2		151	238	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434766	99434766	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	342	767	0	ENST00000268035.6:c.853A>G	p.Ile285Val	p.I285V	ENST00000268035	NM_000875.3	285	Atc/Gtc	3/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.804043552490453	2		767	830	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353812	40353812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	677	741	1	ENST00000293328.3:c.2308G>A	p.Glu770Lys	p.E770K	ENST00000293328	NM_012448.3	770	Gag/Aag	19/19	0.804043552490453	3	FACETS	0.977	0.947	1	0.977	0.947	1	CLONAL	2	TRUE	1	0.804043552490453	3		742	1208	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359605	40359605	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	317	577	0	ENST00000293328.3:c.2048A>T	p.Tyr683Phe	p.Y683F	ENST00000293328	NM_012448.3	683	tAc/tTc	16/19	0.804043552490453	3	FACETS	0.925	0.873	0.979	0.463	0.436	0.49	CLONAL	1	TRUE	1	0.804043552490453	3		577	1195	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054596	13054596	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	235	484	0	ENST00000316448.5:c.1123A>G	p.Lys375Glu	p.K375E	ENST00000316448	NM_004343.3	375	Aaa/Gaa	9/9	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.804043552490453	2		484	543	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198269843	198269843	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	204	295	0	ENST00000335508.6:c.1496A>G	p.Lys499Arg	p.K499R	ENST00000335508	NM_012433.2	499	aAg/aGg	11/25	1	2	FACETS	0.995	0.931	1	0.995	0.931	1	CLONAL	1	TRUE	1	0.804043552490453	2		295	510	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162021	47162022	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	171	376	0	ENST00000409792.3:c.4104dup	p.Ala1369SerfsTer3	p.A1369Sfs*3	ENST00000409792	NM_014159.6	1368	-/A	3/21	1	2	FACETS	0.96	0.893	1	0.96	0.893	1	CLONAL	1	TRUE	1	0.804043552490453	2		376	443	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940497	49940498	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	474	1121	0	ENST00000296474.3:c.545dup	p.Leu182PhefsTer9	p.L182Ffs*9	ENST00000296474	NM_002447.2	182	ttg/ttTg	1/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.804043552490453	2		1121	1158	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435773	116435773	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	350	566	0	ENST00000397752.3:c.3863A>G	p.Asn1288Ser	p.N1288S	ENST00000397752	NM_000245.2	1288	aAc/aGc	20/21	0.804043552490453	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.804043552490453	1		566	484	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437418	110437419	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGT	novel	NA	P-0046179-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	85	504	0	ENST00000375856.3:c.980_982dup	p.His327dup	p.H327dup	ENST00000375856	NM_003749.2	327	ctg/cACCtg	1/2	1	2	FACETS	0.986	0.872	1	0.986	0.872	1	CLONAL	1	TRUE	1	0.236095497508523	2		504	730	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986591	36986601	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGGCGGCGT	GCTGGCGGCGT	-	novel	NA	P-0046179-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	70	496	0	ENST00000354822.5:c.1088_1098del	p.His363ProfsTer72	p.H363Pfs*72	ENST00000354822	NM_001079668.2	363	cACGCCGCCAGC/c	3/3	0.236095497508523	1	FACETS	0.737	0.642	0.839	0.737	0.642	0.839	SUBCLONAL	1	TRUE	0	0.236095497508523	1		496	710	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	185	349	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.885	0.825	0.946	0.885	0.825	0.946	CLONAL	1	TRUE	1	0.867577310558795	2		350	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0046347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	316	683	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	0.864	0.819	0.91	0.864	0.819	0.91	CLONAL	1	TRUE	1	0.867577310558795	2		683	843	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0046347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	296	543	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.867577310558795	2		543	658	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80040380	80040380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	217	439	0	ENST00000265081.6:c.1709C>T	p.Ser570Leu	p.S570L	ENST00000265081	NM_002439.4	570	tCa/tTa	12/24	1	2	FACETS	0.854	0.8	0.909	0.854	0.8	0.909	CLONAL	1	TRUE	1	0.867577310558795	2		439	586	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197373	27197373	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	189	550	0	ENST00000380036.4:c.1685C>G	p.Thr562Ser	p.T562S	ENST00000380036	NM_000459.3	562	aCc/aGc	12/23	1	2	FACETS	0.707	0.657	0.759	0.707	0.657	0.759	SUBCLONAL	1	TRUE	1	0.867577310558795	2		550	616	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039452	49039453	+	frameshift_variant	Frame_Shift_Ins	INS	TA	TA	ATG	novel	NA	P-0046347-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	206	435	0	ENST00000267163.4:c.2437_2438delinsATG	p.Tyr813MetfsTer2	p.Y813Mfs*2	ENST00000267163	NM_000321.2	813	TAt/ATGt	23/27	0.867577310558795	1	FACETS	0.974	0.932	1	0.974	0.932	1	CLONAL	1	TRUE	0	0.867577310558795	1		435	276	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0046467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	41	328	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.166116581853054	2		328	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579547	7579547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567557016	NA	P-0046467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	81	771	1	ENST00000269305.4:c.140del	p.Pro47ArgfsTer76	p.P47Rfs*76	ENST00000269305	NM_001126112.2	47	cCg/cg	4/11	1	2	FACETS	0.883	0.775	0.998	0.883	0.775	0.998	CLONAL	1	TRUE	1	0.166116581853054	2		772	1105	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575151	48575151	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	34	284	0	ENST00000342988.3:c.345T>G	p.Cys115Trp	p.C115W	ENST00000342988	NM_005359.5	115	tgT/tgG	3/12	0.166116581853054	1	FACETS	0.996	0.814	1	0.996	0.814	1	CLONAL	1	TRUE	0	0.166116581853054	1		284	377	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794464	242794464	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1227	97	1016	0	ENST00000334409.5:c.478C>G	p.Pro160Ala	p.P160A	ENST00000334409	NM_005018.2	160	Ccc/Gcc	3/5	1	2	FACETS	0.882	0.784	0.988	0.882	0.784	0.988	CLONAL	1	TRUE	1	0.166116581853054	2		1016	1324	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020351	69020351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201443824	NA	P-0046467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	77	319	0	ENST00000288368.4:c.2723G>A	p.Arg908His	p.R908H	ENST00000288368	NM_024870.2	908	cGt/cAt	24/40	0.166116581853054	3	FACETS	1	0.88	1	1	0.88	1	CLONAL	2	TRUE	1	0.166116581853054	3		319	502	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0046494-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	95	347	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.348515808354542	1	FACETS	0.764	0.688	0.843	0.764	0.688	0.843	SUBCLONAL	1	TRUE	0	0.563596185814871	1		347	317	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711880	89711881	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACT	novel	NA	P-0046494-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	97	373	0	ENST00000371953.3:c.500_502dup	p.Thr167dup	p.T167dup	ENST00000371953	NM_000314.4	167	-/ACT	6/9	0.563596185814871	1	FACETS	0.883	0.798	0.97	0.883	0.798	0.97	CLONAL	1	TRUE	0	0.563596185814871	1		373	280	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274753	123274753	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781714766	NA	P-0046494-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	70	605	0	ENST00000358487.5:c.1165G>A	p.Ala389Thr	p.A389T	ENST00000358487	NM_000141.4	389	Gcc/Acc	9/18	0.563596185814871	1	FACETS	0.43	0.376	0.487	0.43	0.376	0.487	SUBCLONAL	1	TRUE	0	0.563596185814871	1		605	415	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721757	176721757	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046494-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	122	510	0	ENST00000439151.2:c.7388C>T	p.Pro2463Leu	p.P2463L	ENST00000439151	NM_022455.4	2463	cCt/cTt	23/23	1	2	FACETS	0.864	0.785	0.946	0.864	0.785	0.946	CLONAL	1	TRUE	1	0.563596185814871	2		510	501	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166839	32166839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs535575989	NA	P-0046494-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	567	1120	0	ENST00000375023.3:c.4399G>A	p.Val1467Ile	p.V1467I	ENST00000375023	NM_004557.3	1467	Gtc/Atc	24/30	0.507533260802476	3	FACETS	0.938	0.902	0.974	0.938	0.902	0.974	CLONAL	2	TRUE	1	0.563596185814871	3		1120	1375	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188177	11188177	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	40	298	0	ENST00000361445.4:c.5917A>T	p.Ile1973Phe	p.I1973F	ENST00000361445	NM_004958.3	1973	Atc/Ttc	43/58	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.430848024925496	2		298	124	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923059	39923059	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	158	222	0	ENST00000378444.4:c.3649C>T	p.Arg1217Ter	p.R1217*	ENST00000378444	NM_001123385.1	1217	Cga/Tga	8/15	0.230045652943927	2	FACETS	1	0.99	1			1	INDETERMINATE	4	TRUE	NA	0.430848024925496	2		222	172	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123784	11123784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046587-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	64	324	0	ENST00000358026.2:c.2434C>T	p.Leu812Phe	p.L812F	ENST00000358026	NM_001128849.1	812	Ctc/Ttc	16/36	1	2	FACETS	0.997	0.887	1	1	0.983	1	CLONAL	2	TRUE	1	0.430848024925496	2		324	149	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0046631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	105	436	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.28	2		439	726	SUCCESS
APC	324	MSKCC	GRCh37	5	112173600	112173600	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1060503310	NA	P-0046631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	54	304	0	ENST00000257430.4:c.2309C>G	p.Ser770Ter	p.S770*	ENST00000257430	NM_000038.5	770	tCa/tGa	16/16	1	2	FACETS	0.989	0.848	1	0.989	0.848	1	CLONAL	1	TRUE	1	0.28	2		304	390	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162742000	162742000	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	32	480	0	ENST00000367921.3:c.1691C>G	p.Thr564Ser	p.T564S	ENST00000367921	NM_006182.2	564	aCt/aGt	13/18	1	2	FACETS	0.402	0.326	0.489	0.402	0.326	0.489	SUBCLONAL	1	TRUE	1	0.28	2		480	568	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912140	114912141	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	T	novel	NA	P-0046631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	54	565	0	ENST00000543371.1:c.1210_1211delinsT	p.Arg404Ter	p.R404*	ENST00000543371	NM_001198531.1	404	CGg/Tg	11/14	0.3	1	FACETS	0.529	0.451	0.614	0.529	0.451	0.614	SUBCLONAL	1	TRUE	0	0.28	1		565	627	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994295	21994311	+	frameshift_variant	Frame_Shift_Del	DEL	CCGAATCCGGAGGGTCA	CCGAATCCGGAGGGTCA	-	novel	NA	P-0046813-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	71	900	0	ENST00000579755.1:c.20_36del	p.Val7AlafsTer50	p.V7Afs*50	ENST00000579755		7	gTGACCCTCCGGATTCGG/g	1/3	1		FACETS		0.6	0.786				SUBCLONAL	1	TRUE	1	0.22	2		900	937	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0046893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	62	510	1	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.18	2		511	650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0046893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	51	660	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	1	2	FACETS	0.689	0.584	0.804	0.689	0.584	0.804	SUBCLONAL	1	TRUE	1	0.18	2		660	823	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652129	36652129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34916193	NA	P-0046893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	59	723	1	ENST00000244741.5:c.251G>A	p.Arg84Gln	p.R84Q	ENST00000244741	NM_000389.4	84	cGa/cAa	2/3	1	2	FACETS	0.679	0.583	0.785	0.679	0.583	0.785	SUBCLONAL	1	TRUE	1	0.18	2		724	965	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189412	56189412	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	62	396	0	ENST00000399503.3:c.4444C>T	p.Arg1482Ter	p.R1482*	ENST00000399503	NM_005921.1	1482	Cga/Tga	20/20	1	2	FACETS	0.909	0.784	1	0.909	0.784	1	CLONAL	1	TRUE	1	0.18	2		396	758	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057781	27057781	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	69	562	0	ENST00000324856.7:c.1489C>T	p.Gln497Ter	p.Q497*	ENST00000324856	NM_006015.4	497	Caa/Taa	3/20	1	2	FACETS	0.877	0.762	1	0.877	0.762	1	CLONAL	1	TRUE	1	0.18	2		562	874	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217783	2217783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	52	986	1	ENST00000398665.3:c.2557C>T	p.Arg853Cys	p.R853C	ENST00000398665	NM_032482.2	853	Cgc/Tgc	22/28	0.205753104886347	1	FACETS	0.508	0.431	0.593	0.508	0.431	0.593	SUBCLONAL	1	TRUE	0	0.18	1		987	1035	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435168	56435168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766439784	NA	P-0046893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	86	720	1	ENST00000407977.2:c.1969C>T	p.Arg657Trp	p.R657W	ENST00000407977		657	Cgg/Tgg	9/10	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.18	2		721	909	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37045935	37045935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750781	NA	P-0046893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	56	326	0	ENST00000231790.2:c.350C>T	p.Thr117Met	p.T117M	ENST00000231790	NM_000249.3	117	aCg/aTg	4/19	1	2	FACETS	0.916	0.784	1	0.916	0.784	1	CLONAL	1	TRUE	1	0.18	2		326	679	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427369	49427369	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1565779294	NA	P-0046893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	76	928	0	ENST00000301067.7:c.11119C>T	p.Arg3707Ter	p.R3707*	ENST00000301067	NM_003482.3	3707	Cga/Tga	39/54	1	2	FACETS	0.882	0.772	1	0.882	0.772	1	CLONAL	1	TRUE	1	0.18	2		928	957	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856056	111856056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs574829930	NA	P-0046893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	80	995	0	ENST00000341259.2:c.107C>T	p.Ala36Val	p.A36V	ENST00000341259	NM_005475.2	36	gCg/gTg	2/8	1	2	FACETS	0.778	0.682	0.881	0.778	0.682	0.881	SUBCLONAL	1	TRUE	1	0.18	2		995	1143	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745533	162745533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	37	355	0	ENST00000367921.3:c.1948C>T	p.Leu650Phe	p.L650F	ENST00000367921	NM_006182.2	650	Ctc/Ttc	15/18	1	2	FACETS	0.832	0.686	0.996	0.832	0.686	0.996	CLONAL	1	TRUE	1	0.18	2		355	494	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176470	123176470	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	39	243	1	ENST00000218089.9:c.437G>T	p.Arg146Leu	p.R146L	ENST00000218089	NM_001042749.1	146	cGa/cTa	7/35	1	2	FACETS	0.721	0.596	0.86	0.721	0.596	0.86	SUBCLONAL	1	TRUE	1	0.18	2		244	601	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528015	103528015	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	27	268	0	ENST00000355739.4:c.3323C>T	p.Ser1108Leu	p.S1108L	ENST00000355739	NM_000123.3	1108	tCa/tTa	15/15	1	2	FACETS	0.733	0.583	0.906	0.733	0.583	0.906	CLONAL	1	TRUE	1	0.18	2		268	409	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961358	15961358	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	51	406	0	ENST00000268712.3:c.6031G>A	p.Glu2011Lys	p.E2011K	ENST00000268712	NM_006311.3	2011	Gaa/Aaa	39/46	1	2	FACETS	0.86	0.73	1	0.86	0.73	1	CLONAL	1	TRUE	1	0.18	2		406	659	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748563	40748563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761598534	NA	P-0046893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	81	895	0	ENST00000392038.2:c.319G>A	p.Ala107Thr	p.A107T	ENST00000392038	NM_001626.4	107	Gcc/Acc	5/14	0.205753104886347	1	FACETS	0.758	0.665	0.857	0.758	0.665	0.857	SUBCLONAL	1	TRUE	0	0.18	1		895	1081	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605150	46605150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	51	569	0	ENST00000263734.3:c.1367C>T	p.Ala456Val	p.A456V	ENST00000263734	NM_001430.4	456	gCc/gTc	10/16	1	2	FACETS	0.883	0.749	1	0.883	0.749	1	CLONAL	1	TRUE	1	0.18	2		569	642	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016213	31016213	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	37	249	0	ENST00000375687.4:c.459A>T	p.Arg153Ser	p.R153S	ENST00000375687	NM_015338.5	153	agA/agT	6/13	1	2	FACETS	0.898	0.74	1	0.898	0.74	1	CLONAL	1	TRUE	1	0.18	2		249	458	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030845	36030845	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0046893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	39	380	0	ENST00000358208.4:c.1124C>G	p.Ser375Ter	p.S375*	ENST00000358208		375	tCa/tGa	10/12	1	2	FACETS	0.867	0.718	1	0.867	0.718	1	CLONAL	1	TRUE	1	0.18	2		380	500	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442576	52442576	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	46	329	0	ENST00000460680.1:c.169C>T	p.Arg57Trp	p.R57W	ENST00000460680	NM_004656.3	57	Cgg/Tgg	4/17	1	2	FACETS	0.919	0.774	1	0.919	0.774	1	CLONAL	1	TRUE	1	0.18	2		329	556	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955545	55955545	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	34	324	0	ENST00000263923.4:c.3400G>C	p.Glu1134Gln	p.E1134Q	ENST00000263923	NM_002253.2	1134	Gaa/Caa	25/30	0.205753104886347	1	FACETS	0.614	0.501	0.742	0.614	0.501	0.742	SUBCLONAL	1	TRUE	0	0.18	1		324	560	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170974	56170975	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGCACTG	novel	NA	P-0046893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	33	318	0	ENST00000399503.3:c.1805_1812dup	p.Asn605AlafsTer54	p.N605Afs*54	ENST00000399503	NM_005921.1	601	gag/gaGAGCACTGg	10/20	1	2	FACETS	0.82	0.668	0.992	0.82	0.668	0.992	CLONAL	1	TRUE	1	0.18	2		318	447	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150022979	150022979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	64	381	0	ENST00000253339.5:c.284C>T	p.Ser95Phe	p.S95F	ENST00000253339		95	tCt/tTt	1/7	0.205753104886347	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.18	1		381	599	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977593	2977593	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867822144	NA	P-0046893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	90	618	0	ENST00000396946.4:c.1091G>A	p.Arg364His	p.R364H	ENST00000396946	NM_032415.4	364	cGc/cAc	8/25	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.18	2		618	873	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485828	8485828	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	24	296	0	ENST00000356435.5:c.2989C>G	p.His997Asp	p.H997D	ENST00000356435		997	Cat/Gat	17/35	1	2	FACETS	0.595	0.466	0.745	0.595	0.466	0.745	SUBCLONAL	1	TRUE	1	0.18	2		296	448	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508823	106508823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	99	559	0	ENST00000359195.3:c.817C>T	p.Arg273Cys	p.R273C	ENST00000359195	NM_002649.2	273	Cgc/Tgc	2/11	1	2	FACETS	0.652	0.585	0.723	0.652	0.585	0.723	SUBCLONAL	1	TRUE	1	0.64581245984183	2		559	470	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0046911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	121	504	5	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	0.578996429017167	3	FACETS	0.741	0.671	0.815	0.37	0.335	0.408	SUBCLONAL	1	TRUE	1	0.64581245984183	3		509	669	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0046911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	234	580	2	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.481169759203351	4	FACETS	0.842	0.789	0.896	0.842	0.789	0.896	CLONAL	2	TRUE	2	0.64581245984183	4		582	708	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0046911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	70	357	2	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	0.573786162221277	3	FACETS	0.794	0.697	0.898	0.397	0.348	0.449	SUBCLONAL	1	TRUE	1	0.64581245984183	3		359	361	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383118	42383118	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	98	672	0	ENST00000221972.3:c.142del	p.Glu48LysfsTer44	p.E48Kfs*44	ENST00000221972	NM_021601.3	46	ctG/ct	2/5	0.578996429017167	3	FACETS	0.637	0.569	0.709	0.319	0.284	0.355	SUBCLONAL	1	TRUE	1	0.64581245984183	3		672	630	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953040	2953040	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141751925	NA	P-0046911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	491	977	1	ENST00000396946.4:c.2900G>A	p.Arg967His	p.R967H	ENST00000396946	NM_032415.4	967	cGc/cAc	22/25	0.404941875655951	5	FACETS	0.881	0.846	0.917	0.881	0.846	0.917	CLONAL	3	TRUE	2	0.64581245984183	5		978	1132	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420108	49420108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123729	NA	P-0046911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	240	648	0	ENST00000301067.7:c.15641G>A	p.Arg5214His	p.R5214H	ENST00000301067	NM_003482.3	5214	cGc/cAc	48/54	0.515740334745415	3	FACETS	0.769	0.723	0.816	0.769	0.723	0.816	SUBCLONAL	2	TRUE	1	0.64581245984183	3		648	639	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987289	2987289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765680532	NA	P-0046911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	124	654	1	ENST00000396946.4:c.140G>A	p.Arg47His	p.R47H	ENST00000396946	NM_032415.4	47	cGt/cAt	3/25	0.404941875655951	5	FACETS	0.895	0.809	0.985	0.298	0.269	0.329	CLONAL	1	TRUE	2	0.64581245984183	5		655	845	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868196	37868196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1308928763	NA	P-0046911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	146	765	1	ENST00000269571.5:c.917C>T	p.Thr306Met	p.T306M	ENST00000269571		306	aCg/aTg	8/27	0.578996429017167	3	FACETS	0.774	0.707	0.844	0.387	0.353	0.422	SUBCLONAL	1	TRUE	1	0.64581245984183	3		766	773	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087904	27087904	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	128	662	2	ENST00000324856.7:c.2191G>T	p.Gly731Cys	p.G731C	ENST00000324856	NM_006015.4	731	Ggc/Tgc	6/20	0.481169759203351	4	FACETS	0.746	0.676	0.821	0.373	0.338	0.411	SUBCLONAL	1	TRUE	2	0.64581245984183	4		664	874	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949149	71949149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs991937669	NA	P-0046911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	186	960	0	ENST00000298229.2:c.3616C>T	p.Arg1206Trp	p.R1206W	ENST00000298229	NM_001567.3	1206	Cgg/Tgg	27/28	0.578996429017167	3	FACETS	0.871	0.805	0.939	0.435	0.402	0.47	CLONAL	1	TRUE	1	0.64581245984183	3		960	875	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067437	37067441	+	frameshift_variant	Frame_Shift_Del	DEL	GATAC	GATAC	-	novel	NA	P-0046911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	214	564	0	ENST00000231790.2:c.1348_1352del	p.Asp450AsnfsTer27	p.D450Nfs*27	ENST00000231790	NM_000249.3	450	GATACa/a	12/19	0.565869405797338	2	FACETS	0.791	0.746	0.836	0.791	0.746	0.836	SUBCLONAL	2	TRUE	0	0.64581245984183	2		564	419	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937788	76937788	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	204	552	0	ENST00000373344.5:c.2960del	p.Lys987ArgfsTer16	p.K987Rfs*16	ENST00000373344	NM_000489.3	987	aAg/ag	9/35	0.578996429017167	3	FACETS	0.826	0.773	0.879	0.826	0.773	0.879	CLONAL	2	TRUE	1	0.64581245984183	3		552	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0047008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	159	743	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.317802937894082	1	FACETS	0.808	0.741	0.878	0.808	0.741	0.878	CLONAL	1	TRUE	0	0.375396238963127	1		743	852	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972614	32972614	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	50	322	0	ENST00000380152.3:c.9964A>T	p.Met3322Leu	p.M3322L	ENST00000380152		3322	Atg/Ttg	27/27	0.375396238963127	1	FACETS	0.676	0.577	0.784	0.676	0.577	0.784	SUBCLONAL	1	TRUE	0	0.375396238963127	1		322	320	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029321	16029452	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCCTATATCTACAAAAATAAAAATAAAATAAAAATAAACATTTAACTTATTATATAACTAATTATTTAACTCACTTGGAGTCTTCTTTTTCATCTTTTTCCTCTTCATCTTTCTTTTCTTCTTCTTTTTTT	TCCCTATATCTACAAAAATAAAAATAAAATAAAAATAAACATTTAACTTATTATATAACTAATTATTTAACTCACTTGGAGTCTTCTTTTTCATCTTTTTCCTCTTCATCTTTCTTTTCTTCTTCTTTTTTT	-	novel	NA	P-0047008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	31	73	0	ENST00000268712.3:c.1578_1634+75del		p.X526_splice	ENST00000268712	NM_006311.3	526		15/46	1	2	FACETS	0.843	0.7	0.995	1	0.957	1	CLONAL	2	TRUE	1	0.375396238963127	2		73	98	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588966	67588966	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	38	194	0	ENST00000274335.5:c.1057G>C	p.Gly353Arg	p.G353R	ENST00000274335		353	Ggg/Cgg	8/15	0.317802937894082	1	FACETS	0.623	0.518	0.739	0.623	0.518	0.739	SUBCLONAL	1	TRUE	0	0.375396238963127	1		194	264	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636784	176636784	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	72	385	0	ENST00000439151.2:c.1384A>G	p.Asn462Asp	p.N462D	ENST00000439151	NM_022455.4	462	Aat/Gat	5/23	0.348581710741132	3	FACETS	0.812	0.71	0.922	0.406	0.355	0.461	CLONAL	1	TRUE	1	0.375396238963127	3		385	561	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468096	50468096	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047008-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	138	590	0	ENST00000331340.3:c.1331A>T	p.Asn444Ile	p.N444I	ENST00000331340	NM_006060.4	444	aAc/aTc	8/8	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.375396238963127	2		590	705	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0047029-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	123	643	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.357919058613734	2		643	623	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0047029-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	150	760	1	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.357919058613734	2		761	800	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980435	7980435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760428119	NA	P-0047029-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	110	653	0	ENST00000319144.4:c.1148C>T	p.Thr383Met	p.T383M	ENST00000319144	NM_001139.2	383	aCg/aTg	9/15	1	2	FACETS	0.937	0.843	1	0.937	0.843	1	CLONAL	1	TRUE	1	0.357919058613734	2		653	656	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249002	55249003	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGTGGA	rs397517109	NA	P-0047029-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	1051	515	0	ENST00000275493.2:c.2303_2311dup	p.Ser768_Asp770dup	p.S768_D770dup	ENST00000275493	NM_005228.3	768	gcc/gcCAGCGTGGAc	20/28	0.357919058613734	17	FACETS	1	0.99	1			1	CLONAL	12	TRUE	NA	0.357919058613734	17		515	1758	SUCCESS
AR	367	MSKCC	GRCh37	X	66765097	66765097	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047029-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	85	607	0	ENST00000374690.3:c.109C>A	p.Pro37Thr	p.P37T	ENST00000374690	NM_000044.3	37	Ccg/Acg	1/8	1	2	FACETS	0.845	0.748	0.948	0.845	0.748	0.948	CLONAL	1	TRUE	1	0.357919058613734	2		607	562	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344036	118344036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047031-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	26	267	0	ENST00000534358.1:c.2162G>A	p.Arg721Gln	p.R721Q	ENST00000534358	NM_005933.3	721	cGa/cAa	3/36	1	2	FACETS	0.623	0.493	0.772	0.623	0.493	0.772	SUBCLONAL	1	FALSE	1	0.200177207099433	2		267	417	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873715	37873715	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047031-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	120	647	0	ENST00000269571.5:c.1880C>T	p.Pro627Leu	p.P627L	ENST00000269571		627	cCc/cTc	15/27	1	2	FACETS	0.814	0.736	0.897	1	0.986	1	CLONAL	2	FALSE	1	0.200177207099433	2		647	736	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0047031-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	117	289	0	ENST00000288602.6:c.1397G>T	p.Gly466Val	p.G466V	ENST00000288602	NM_004333.4	466	gGa/gTa	11/18	1	2	FACETS	0.913	0.829	0.999	1	0.991	1	CLONAL	3	FALSE	1	0.200177207099433	2		289	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0047031-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	150	663	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.200177207099433	1	FACETS	0.969	0.888	1	1	0.991	1	CLONAL	2	FALSE	0	0.200177207099433	1		663	696	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913237	NA	P-0047031-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	82	293	1	ENST00000369535.4:c.35G>T	p.Gly12Val	p.G12V	ENST00000369535	NM_002524.4	12	gGt/gTt	2/7	0.166460422394872	1	FACETS	0.908	0.805	1	1	0.983	1	CLONAL	2	FALSE	0	0.200177207099433	1		294	406	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041007	47041007	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047031-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	255	417	2	ENST00000377604.3:c.1537G>T	p.Glu513Ter	p.E513*	ENST00000377604	NM_001204468.1	513	Gag/Tag	14/24	0.200177207099433	4	FACETS	1	0.982	1			1	CLONAL	5	FALSE	NA	0.200177207099433	4		419	562	SUCCESS
AR	367	MSKCC	GRCh37	X	66942786	66942786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs9332971	NA	P-0047031-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	65	168	0	ENST00000374690.3:c.2567G>A	p.Arg856His	p.R856H	ENST00000374690	NM_000044.3	856	cGc/cAc	7/8	1	1	FACETS	1	0.95	1	1	0.983	1	CLONAL	2	FALSE	0	0.200177207099433	1		168	250	SUCCESS
RET	5979	MSKCC	GRCh37	10	43613888	43613888	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047031-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	120	687	1	ENST00000355710.3:c.2354del	p.Pro785HisfsTer84	p.P785Hfs*84	ENST00000355710	NM_020975.4	784	caC/ca	13/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.200177207099433	2		688	827	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769051	112769051	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047031-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	76	361	0	ENST00000369452.4:c.1330C>T	p.Leu444Phe	p.L444F	ENST00000369452	NM_007373.3	444	Ctt/Ttt	7/9	1	2	FACETS	0.844	0.743	0.951	1	0.98	1	CLONAL	2	FALSE	1	0.200177207099433	2		361	450	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204925	94204925	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047031-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	60	277	0	ENST00000323929.3:c.660G>T	p.Arg220Ser	p.R220S	ENST00000323929	NM_005591.3	220	agG/agT	8/20	1	2	FACETS	0.771	0.666	0.883	1	0.971	1	SUBCLONAL	2	FALSE	1	0.200177207099433	2		277	389	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319080	62319080	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047031-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	172	935	3	ENST00000360203.5:c.1438G>T	p.Gly480Cys	p.G480C	ENST00000360203	NM_001283009.1	480	Ggc/Tgc	17/35	1	2	FACETS	0.858	0.789	0.931	1	0.991	1	CLONAL	2	FALSE	1	0.200177207099433	2		938	1001	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508695	106508695	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047031-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	70	512	0	ENST00000359195.3:c.689G>T	p.Ser230Ile	p.S230I	ENST00000359195	NM_002649.2	230	aGc/aTc	2/11	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	FALSE	1	0.200177207099433	2		512	676	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251059	99251059	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047031-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	68	497	0	ENST00000268035.6:c.363G>C	p.Glu121Asp	p.E121D	ENST00000268035	NM_000875.3	121	gaG/gaC	2/21	0.166460422394872	1	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	FALSE	0	0.200177207099433	1		497	605	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0047037-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	61	259	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.44041411845558	2		259	212	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0047037-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	25	491	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.44041411845558	1	FACETS	0.118	0.092	0.148	0.118	0.092	0.148	SUBCLONAL	1	TRUE	0	0.44041411845558	1		491	748	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222005	1222005	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047037-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	176	803	0	ENST00000326873.7:c.920+1del		p.S307fs	ENST00000326873	NM_000455.4	307	aGc/ac	7/10	0.44041411845558	1	FACETS	0.858	0.793	0.926	0.858	0.793	0.926	CLONAL	1	TRUE	0	0.44041411845558	1		803	726	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134488	2134504	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTGGACGGGGAAAGT	CCCTGGACGGGGAAAGT	A	novel	NA	P-0047037-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	260	1059	0	ENST00000219476.3:c.4265_4281delinsA	p.Thr1422LysfsTer49	p.T1422Kfs*49	ENST00000219476	NM_000548.3	1422	aCCCTGGACGGGGAAAGT/aA	34/42	1	2	FACETS	0.888	0.831	0.948	0.888	0.831	0.948	CLONAL	1	TRUE	1	0.44041411845558	2		1059	1329	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743577	46743577	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047037-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	171	643	0	ENST00000371975.4:c.1958A>G	p.Glu653Gly	p.E653G	ENST00000371975	NM_003579.3	653	gAg/gGg	17/18	0.317792655649321	3	FACETS	0.946	0.869	1			1	CLONAL	1	TRUE	NA	0.44041411845558	3		643	1002	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112101	115112101	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047037-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	251	958	0	ENST00000257566.3:c.1639T>A	p.Ser547Thr	p.S547T	ENST00000257566	NM_016569.3	547	Tct/Act	7/8	1	2	FACETS	0.947	0.885	1	0.947	0.885	1	CLONAL	1	TRUE	1	0.44041411845558	2		958	1204	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405830	157405830	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047037-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	105	426	0	ENST00000346085.5:c.2072G>T	p.Gly691Val	p.G691V	ENST00000346085	NM_020732.3	691	gGa/gTa	6/20	1	2	FACETS	0.844	0.758	0.934	0.844	0.758	0.934	CLONAL	1	TRUE	1	0.44041411845558	2		426	565	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0047120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	204	314	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.175536048793577	5	FACETS	0.919	0.862	0.977	0.919	0.862	0.977	INDETERMINATE	3	TRUE	2	0.582644991045835	5		314	476	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087898	27087907	+	frameshift_variant	Frame_Shift_Del	DEL	CCCAGTGGCC	CCCAGTGGCC	-	novel	NA	P-0047120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	614	566	0	ENST00000324856.7:c.2185_2194del	p.Pro729SerfsTer10	p.P729Sfs*10	ENST00000324856	NM_006015.4	729	CCCAGTGGCCag/ag	6/20	0.582644991045835	2	FACETS	0.927	0.907	0.946	1	0.998	1	CLONAL	3	TRUE	0	0.582644991045835	2		566	758	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682898	241682898	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	162	197	0	ENST00000366560.3:c.125C>A	p.Ala42Asp	p.A42D	ENST00000366560	NM_000143.3	42	gCt/gAt	1/10	0.307201351161804	4	FACETS	0.865	0.807	0.924	1	0.988	1	INDETERMINATE	3	TRUE	2	0.582644991045835	4		197	339	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884401	151884401	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	191	295	0	ENST00000262189.6:c.4954del	p.Ala1652ProfsTer13	p.A1652Pfs*13	ENST00000262189	NM_170606.2	1652	Gcc/cc	33/59	0.154120613160763	4	FACETS	1	0.973	1	1	0.973	1	INDETERMINATE	2	TRUE	2	0.582644991045835	4		295	481	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512309	38512309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	286	610	0	ENST00000254066.5:c.1220C>T	p.Pro407Leu	p.P407L	ENST00000254066	NM_000964.3	407	cCg/cTg	9/9	0.582644991045835	5	FACETS	0.753	0.707	0.8	0.376	0.353	0.4	SUBCLONAL	2	TRUE	1	0.582644991045835	5		610	1222	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372696	81372696	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	153	321	0	ENST00000222390.5:c.838T>A	p.Trp280Arg	p.W280R	ENST00000222390	NM_000601.4	280	Tgg/Agg	7/18	0.154120613160763	4	FACETS	0.945	0.872	1	0.945	0.872	1	INDETERMINATE	2	TRUE	2	0.582644991045835	4		321	440	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5258034	5258034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1435990354	NA	P-0047120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	219	511	1	ENST00000357368.4:c.700G>A	p.Val234Met	p.V234M	ENST00000357368	NM_002850.3	234	Gtg/Atg	8/38	0.0912064844408331	4	FACETS	1	0.982	1	1	0.982	1	INDETERMINATE	2	TRUE	2	0.582644991045835	4		512	532	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0047120-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	45	314	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.839	0.707	0.985	0.839	0.707	0.985	CLONAL	1	TRUE	1	0.28	2		314	383	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0047120-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	11	293	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.152	0.104	0.212	0.152	0.104	0.212	SUBCLONAL	1	TRUE	1	0.28	2		293	517	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911588	39911588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372913827	NA	P-0047120-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	98	586	0	ENST00000378444.4:c.5042G>A	p.Arg1681His	p.R1681H	ENST00000378444	NM_001123385.1	1681	cGc/cAc	15/15	1	2	FACETS	0.887	0.791	0.99	0.887	0.791	0.99	CLONAL	1	TRUE	1	0.28	2		586	789	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087898	27087907	+	frameshift_variant	Frame_Shift_Del	DEL	CCCAGTGGCC	CCCAGTGGCC	-	novel	NA	P-0047120-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	104	566	0	ENST00000324856.7:c.2185_2194del	p.Pro729SerfsTer10	p.P729Sfs*10	ENST00000324856	NM_006015.4	729	CCCAGTGGCCag/ag	6/20	1	2	FACETS	0.956	0.856	1	0.956	0.856	1	CLONAL	1	TRUE	1	0.28	2		566	777	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682898	241682898	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047120-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	45	197	0	ENST00000366560.3:c.125C>A	p.Ala42Asp	p.A42D	ENST00000366560	NM_000143.3	42	gCt/gAt	1/10	0.3	3	FACETS	1	0.903	1	0.549	0.463	0.643	CLONAL	1	TRUE	1	0.28	3		197	334	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884401	151884401	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047120-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	45	295	0	ENST00000262189.6:c.4954del	p.Ala1652ProfsTer13	p.A1652Pfs*13	ENST00000262189	NM_170606.2	1652	Gcc/cc	33/59	1	2	FACETS	0.79	0.665	0.927	0.79	0.665	0.927	CLONAL	1	TRUE	1	0.28	2		295	407	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106805	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	A	novel	NA	P-0047120-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	105	613	2	ENST00000324856.7:c.6415_6416delinsA	p.Pro2139ThrfsTer61	p.P2139Tfs*61	ENST00000324856	NM_006015.4	2139	CCc/Ac	20/20	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.28	2		615	729	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	118	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.109396672611123	5	FACETS	1	0.978	1	0.807	0.74	0.875	INDETERMINATE	2	TRUE	2	0.697565119730925	5		327	286	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0047188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	118	303	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.697565119730925	2		303	252	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992901	72992901	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	136	761	0	ENST00000268489.5:c.1144G>T	p.Gly382Cys	p.G382C	ENST00000268489	NM_006885.3	382	Ggc/Tgc	2/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.697565119730925	2		761	340	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209098	36209098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	20	104	0	ENST00000222270.7:c.178G>A	p.Glu60Lys	p.E60K	ENST00000222270	NM_014727.1	60	Gag/Aag	1/37	1	2	FACETS	0.765	0.601	0.945	0.765	0.601	0.945	CLONAL	1	TRUE	1	0.697565119730925	2		104	75	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468085	120468085	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	162	725	0	ENST00000256646.2:c.4354G>T	p.Gly1452Trp	p.G1452W	ENST00000256646	NM_024408.3	1452	Ggg/Tgg	25/34	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.697565119730925	2		725	368	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219263	133219263	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	153	839	1	ENST00000320574.5:c.4781A>T	p.Lys1594Met	p.K1594M	ENST00000320574	NM_006231.2	1594	aAg/aTg	37/49	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.697565119730925	2		840	339	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56852581	56852581	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	147	478	0	ENST00000308159.5:c.495C>A	p.Ser165Arg	p.S165R	ENST00000308159	NM_014669.4	165	agC/agA	6/22	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.697565119730925	2		478	359	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523285	9523285	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	189	600	1	ENST00000353224.5:c.1952C>A	p.Ala651Glu	p.A651E	ENST00000353224	NM_177990.2	651	gCg/gAg	9/10	0.595172323542152	2	FACETS	0.829	0.782	0.875	0.829	0.782	0.875	CLONAL	2	TRUE	0	0.697565119730925	2		601	327	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249590	110249590	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs139364854	NA	P-0047188-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	155	1170	0	ENST00000374672.4:c.1085C>G	p.Pro362Arg	p.P362R	ENST00000374672	NM_004235.4	362	cCg/cGg	3/5	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.697565119730925	2		1170	371	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0047234-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	106	378	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	1	2	FACETS	0.947	0.853	1	0.947	0.853	1	CLONAL	1	TRUE	1	0.458687089436596	2		378	488	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790494	3790494	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867855180	NA	P-0047234-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	52	547	1	ENST00000262367.5:c.4039C>T	p.Arg1347Trp	p.R1347W	ENST00000262367	NM_004380.2	1347	Cgg/Tgg	24/31	1	2	FACETS	0.33	0.28	0.384	0.33	0.28	0.384	SUBCLONAL	1	TRUE	1	0.458687089436596	2		548	688	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270108	66270108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756653935	NA	P-0047234-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	99	291	1	ENST00000273854.3:c.1774G>A	p.Val592Ile	p.V592I	ENST00000273854	NM_004439.5	592	Gtc/Atc	8/18	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.458687089436596	2		292	395	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922182	39922182	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047234-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	91	273	0	ENST00000378444.4:c.3990del	p.Asp1331MetfsTer38	p.D1331Mfs*38	ENST00000378444	NM_001123385.1	1330	acA/ac	9/15	1	1	FACETS	0.751	0.671	0.836	0.751	0.671	0.836	SUBCLONAL	1	TRUE	0	0.458687089436596	1		273	407	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44910970	44910971	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047234-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	14	93	0	ENST00000377967.4:c.675dup	p.Glu226ArgfsTer4	p.E226Rfs*4	ENST00000377967	NM_021140.2	224	gca/gcAa	9/29	1	1	FACETS	0.198	0.143	0.264	0.198	0.143	0.264	SUBCLONAL	1	TRUE	0	0.458687089436596	1		93	238	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650859	48650859	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047234-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	27	347	0	ENST00000376670.3:c.728G>A	p.Arg243Gln	p.R243Q	ENST00000376670	NM_002049.3	243	cGg/cAg	4/6	1	1	FACETS	0.251	0.2	0.31	0.251	0.2	0.31	SUBCLONAL	1	TRUE	0	0.458687089436596	1		347	361	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266107	41266107	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047273-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	249	277	0	ENST00000349496.5:c.104T>C	p.Ile35Thr	p.I35T	ENST00000349496	NM_001904.3	35	aTc/aCc	3/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		277	579	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060797	38060797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	481	1073	0	ENST00000250448.2:c.1192C>T	p.His398Tyr	p.H398Y	ENST00000250448	NM_004496.3	398	Cac/Tac	2/2	0.249135452573512	4	FACETS	1	0.991	1			1	CLONAL	3	TRUE	NA	0.292348507870089	4		1073	1255	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637540	176637540	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047364-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	74	420	1	ENST00000439151.2:c.2140G>A	p.Gly714Ser	p.G714S	ENST00000439151	NM_022455.4	714	Ggt/Agt	5/23	1	2	FACETS	0.972	0.852	1	0.972	0.852	1	CLONAL	1	TRUE	1	0.292348507870089	2		421	521	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503838	149503838	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs864309711	NA	P-0047366-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	153	597	0	ENST00000261799.4:c.1998C>A	p.Asn666Lys	p.N666K	ENST00000261799	NM_002609.3	666	aaC/aaA	14/23	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.485928730562947	2		597	580	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443345	187443345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047366-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	10	347	1	ENST00000232014.4:c.1781G>A	p.Arg594Gln	p.R594Q	ENST00000232014	NM_001130845.1	594	cGa/cAa	8/10	1	2	FACETS	0.106	0.071	0.15	0.106	0.071	0.15	SUBCLONAL	1	FALSE	1	0.485928730562947	2		348	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882005	NA	P-0047366-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	80	466	0	ENST00000269305.4:c.713G>C	p.Cys238Ser	p.C238S	ENST00000269305	NM_001126112.2	238	tGt/tCt	7/11	0.140292371658595	1	FACETS	0.744	0.66	0.832	0.744	0.66	0.832	INDETERMINATE	1	FALSE	0	0.485928730562947	1		466	335	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503838	149503838	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs864309711	NA	P-0047366-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	239	597	0	ENST00000261799.4:c.1998C>A	p.Asn666Lys	p.N666K	ENST00000261799	NM_002609.3	666	aaC/aaA	14/23	0.234836416780432	5	FACETS	1	0.98	1	0.743	0.694	0.793	CLONAL	2	TRUE	2	0.348587887310298	5		597	937	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882005	NA	P-0047366-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	243	466	0	ENST00000269305.4:c.713G>C	p.Cys238Ser	p.C238S	ENST00000269305	NM_001126112.2	238	tGt/tCt	7/11	NA	2	FACETS	0.996	0.935	1			1	INDETERMINATE	2	TRUE	NA	0.348587887310298	2		466	700	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260167	10260167	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047366-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	127	532	0	ENST00000340748.4:c.2500G>T	p.Val834Phe	p.V834F	ENST00000340748		834	Gtc/Ttc	25/40	0.348587887310298	3	FACETS	0.96	0.869	1	0.48	0.434	0.528	CLONAL	1	TRUE	1	0.348587887310298	3		532	891	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967213	93967213	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047366-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	40	263	0	ENST00000369303.4:c.2139C>A	p.Phe713Leu	p.F713L	ENST00000369303	NM_004440.3	713	ttC/ttA	12/17	0.348587887310298	5	FACETS	1	0.942	1	0.436	0.365	0.515	CLONAL	1	TRUE	2	0.348587887310298	5		263	267	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0047400-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	80	383	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.39	1		383	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0047400-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	146	783	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.39	2		783	592	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0047400-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	117	806	1	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.111196552810457	3	FACETS	1	0.98	1	0.664	0.601	0.73	INDETERMINATE	1	TRUE	1	0.39	3		807	540	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570097	212570097	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047400-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	39	315	0	ENST00000342788.4:c.1144G>T	p.Glu382Ter	p.E382*	ENST00000342788	NM_005235.2	382	Gaa/Taa	10/28	1	2	FACETS	0.639	0.531	0.758	0.639	0.531	0.758	SUBCLONAL	1	TRUE	1	0.39	2		315	313	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133517	55133517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047400-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	63	436	0	ENST00000257290.5:c.821C>T	p.Thr274Ile	p.T274I	ENST00000257290	NM_006206.4	274	aCt/aTt	6/23	1	2	FACETS	0.739	0.641	0.845	0.739	0.641	0.845	SUBCLONAL	1	TRUE	1	0.39	2		436	437	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868406	117868407	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047400-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	149	374	0	ENST00000297338.2:c.935_936insA	p.Val313CysfsTer2	p.V313Cfs*2	ENST00000297338	NM_006265.2	312	act/acAt	8/14	0.3	4	FACETS	1	0.948	1	0.694	0.638	0.752	CLONAL	2	TRUE	1	0.39	4		374	510	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0047421-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	38	317	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	1	2	FACETS	0.482	0.399	0.574	0.482	0.399	0.574	SUBCLONAL	1	TRUE	1	0.438428363788977	2		317	360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782177	NA	P-0047421-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	212	625	0	ENST00000269305.4:c.644G>T	p.Ser215Ile	p.S215I	ENST00000269305	NM_001126112.2	215	aGt/aTt	6/11	0.438428363788977	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.438428363788977	1		625	688	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608473	28608473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35958982	NA	P-0047421-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	132	505	0	ENST00000241453.7:c.1669G>A	p.Val557Ile	p.V557I	ENST00000241453	NM_004119.2	557	Gtt/Att	13/24	0.438428363788977	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.438428363788977	1		505	420	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981514	201981523	+	frameshift_variant	Frame_Shift_Del	DEL	TGGAGAAGGA	TGGAGAAGGA	-	novel	NA	P-0047421-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	329	795	0	ENST00000359651.3:c.431_440del	p.Glu144AlafsTer8	p.E144Afs*8	ENST00000359651		143	cTGGAGAAGGAt/ct	3/8	0.245217059666232	2	FACETS	0.832	0.789	0.876	0.832	0.789	0.876	INDETERMINATE	2	TRUE	0	0.438428363788977	2		795	902	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433247	49433247	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047421-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	102	895	0	ENST00000301067.7:c.8200C>T	p.Arg2734Ter	p.R2734*	ENST00000301067	NM_003482.3	2734	Cga/Tga	32/54	1	2	FACETS	0.549	0.491	0.612	0.549	0.491	0.612	SUBCLONAL	1	TRUE	1	0.438428363788977	2		895	847	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369291	40369291	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047421-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	146	530	0	ENST00000293328.3:c.1267C>T	p.Arg423Ter	p.R423*	ENST00000293328	NM_012448.3	423	Cga/Tga	11/19	0.175660073381159	3	FACETS	1	0.975	1	0.587	0.537	0.639	INDETERMINATE	1	TRUE	1	0.438428363788977	3		530	692	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092894	29092895	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047421-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	107	328	0	ENST00000328354.6:c.1089dup	p.Ile364TyrfsTer5	p.I364Yfs*5	ENST00000328354	NM_007194.3	363	-/T	10/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.438428363788977	2		328	432	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245548	153245548	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0047421-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	57	261	0	ENST00000281708.4:c.1645-2A>G		p.X549_splice	ENST00000281708	NM_033632.3	549			1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.438428363788977	2		261	247	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271227	153271227	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047421-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	33	210	0	ENST00000281708.4:c.551del	p.Gly184GlufsTer55	p.G184Efs*55	ENST00000281708	NM_033632.3	184	gGa/ga	3/12	1	2	FACETS	0.545	0.446	0.657	0.545	0.446	0.657	SUBCLONAL	1	TRUE	1	0.438428363788977	2		210	276	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374293	138374293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	14	502	0	ENST00000289153.2:c.3151G>A	p.Glu1051Lys	p.E1051K	ENST00000289153	NM_006219.2	1051	Gaa/Aaa	22/22	0.242432324070485	4	FACETS	1	0.856	1	0.631	0.468	0.816	INDETERMINATE	1	TRUE	2	0.571285078821274	4		502	61	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183802	10183802	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	16	798	0	ENST00000256474.2:c.272del	p.Phe91SerfsTer68	p.F91Sfs*68	ENST00000256474	NM_000551.3	91	Ttc/tc	1/3	0.571285078821274	1	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	0	0.571285078821274	1		798	35	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713654	52713655	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	32	424	0	ENST00000394830.3:c.73dup	p.Ser25PhefsTer28	p.S25Ffs*28	ENST00000394830	NM_018313.4	25	tct/tTct	2/30	0.571285078821274	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.571285078821274	1		424	63	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520017	NA	P-0047455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	238	761	0	ENST00000326873.7:c.647C>T	p.Ser216Phe	p.S216F	ENST00000326873	NM_000455.4	216	tCc/tTc	5/10	0.30837058486211	2	FACETS	0.908	0.851	0.966	0.908	0.851	0.966	CLONAL	2	TRUE	0	0.358753752811432	2		761	731	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912664	NA	P-0047455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	303	552	0	ENST00000269305.4:c.1010G>C	p.Arg337Pro	p.R337P	ENST00000269305	NM_001126112.2	337	cGc/cCc	10/11	0.335527524350988	3	FACETS	0.91	0.862	0.957	0.91	0.862	0.957	CLONAL	3	TRUE	0	0.358753752811432	3		552	730	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206843	162206843	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	59	384	0	ENST00000366898.1:c.832G>T	p.Val278Phe	p.V278F	ENST00000366898	NM_004562.2	278	Gtt/Ttt	7/12	0.358753752811432	10	FACETS	0.983	0.844	1			1	CLONAL	1	TRUE	NA	0.358753752811432	10		384	815	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355206	81355206	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	19	207	0	ENST00000222390.5:c.1168G>T	p.Asp390Tyr	p.D390Y	ENST00000222390	NM_000601.4	390	Gat/Tat	9/18	0.293472907183875	3	FACETS	0.622	0.474	0.794	0.311	0.237	0.397	SUBCLONAL	1	TRUE	1	0.358753752811432	3		207	201	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105657	11105657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	77	452	0	ENST00000358026.2:c.1573G>T	p.Glu525Ter	p.E525*	ENST00000358026	NM_001128849.1	525	Gag/Tag	9/36	0.30837058486211	2	FACETS	0.805	0.708	0.909	0.403	0.354	0.455	CLONAL	1	TRUE	0	0.358753752811432	2		452	533	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912069	32912069	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	44	471	1	ENST00000380152.3:c.3577G>T	p.Ala1193Ser	p.A1193S	ENST00000380152		1193	Gct/Tct	11/27	1	2	FACETS	0.912	0.77	1	0.912	0.77	1	CLONAL	1	TRUE	1	0.358753752811432	2		472	269	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786795	3786795	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	208	350	0	ENST00000262367.5:c.4416G>T	p.Trp1472Cys	p.W1472C	ENST00000262367	NM_004380.2	1472	tgG/tgT	27/31	0.358753752811432	3	FACETS	0.925	0.867	0.983	0.925	0.867	0.983	CLONAL	3	TRUE	0	0.358753752811432	3		350	493	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277036	18277036	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	59	462	0	ENST00000222254.8:c.1483G>T	p.Gly495Cys	p.G495C	ENST00000222254	NM_005027.3	495	Ggc/Tgc	12/16	0.30837058486211	2	FACETS	0.69	0.594	0.793	0.345	0.297	0.397	SUBCLONAL	1	TRUE	0	0.358753752811432	2		462	477	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268853	115268853	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	66	422	0	ENST00000438362.2:c.1757A>C	p.Lys586Thr	p.K586T	ENST00000438362	NM_001242891.1	586	aAg/aCg	14/20	0.257654774128815	3	FACETS	1	0.886	1	0.67	0.59	0.753	CLONAL	2	TRUE	0	0.358753752811432	3		422	216	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465000	120465000	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	138	351	0	ENST00000256646.2:c.5072T>G	p.Phe1691Cys	p.F1691C	ENST00000256646	NM_024408.3	1691	tTt/tGt	28/34	0.257654774128815	3	FACETS	1	0.973	1	0.758	0.697	0.821	CLONAL	2	TRUE	0	0.358753752811432	3		351	399	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600411	43600411	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	103	582	0	ENST00000355710.3:c.639del	p.Phe214SerfsTer10	p.F214Sfs*10	ENST00000355710	NM_020975.4	213	Ccc/cc	4/20	0.218888932075611	2	FACETS	0.913	0.818	1	0.456	0.409	0.507	CLONAL	1	TRUE	0	0.358753752811432	2		582	629	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691219	18691219	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1303514822	NA	P-0047455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	43	260	0	ENST00000266497.5:c.3330C>A	p.Ser1110Arg	p.S1110R	ENST00000266497		1110	agC/agA	23/31	0.293472907183875	3	FACETS	0.836	0.711	0.971	0.836	0.711	0.971	CLONAL	2	TRUE	1	0.358753752811432	3		260	169	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860111	57860111	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	154	717	1	ENST00000228682.2:c.851C>A	p.Ala284Asp	p.A284D	ENST00000228682	NM_005269.2	284	gCc/gAc	8/12	0.358753752811432	3	FACETS	1	0.971	1	0.569	0.521	0.62	CLONAL	1	TRUE	1	0.358753752811432	3		718	889	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562203	21562203	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	124	832	0	ENST00000382592.4:c.1716G>T	p.Gln572His	p.Q572H	ENST00000382592	NM_014572.2	572	caG/caT	4/8	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.358753752811432	2		832	666	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248566	212248566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1210422013	NA	P-0047455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	238	466	0	ENST00000342788.4:c.3701A>G	p.Lys1234Arg	p.K1234R	ENST00000342788	NM_005235.2	1234	aAg/aGg	28/28	0.328069018069945	3	FACETS	0.926	0.873	0.981	0.926	0.873	0.981	CLONAL	3	TRUE	0	0.358753752811432	3		466	563	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405983	49405983	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0047455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	62	380	0	ENST00000418115.1:c.157-2A>G		p.X53_splice	ENST00000418115	NM_001664.2	53			0.24899574843349	3	FACETS	0.968	0.839	1	0.323	0.279	0.369	CLONAL	1	TRUE	0	0.358753752811432	3		380	421	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880893	134880893	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	72	479	0	ENST00000398015.3:c.1456A>T	p.Ser486Cys	p.S486C	ENST00000398015	NM_004441.4	486	Agt/Tgt	7/16	0.293472907183875	3	FACETS	0.829	0.725	0.941	0.415	0.362	0.471	CLONAL	1	TRUE	1	0.358753752811432	3		479	571	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230896	66230896	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	19	300	0	ENST00000273854.3:c.2075G>T	p.Gly692Val	p.G692V	ENST00000273854	NM_004439.5	692	gGa/gTa	12/18	0.293472907183875	3	FACETS	0.961	0.753	1	0.961	0.753	1	CLONAL	2	TRUE	1	0.358753752811432	3		300	65	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983089	149983089	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	23	408	0	ENST00000253339.5:c.3169G>T	p.Val1057Leu	p.V1057L	ENST00000253339		1057	Gta/Tta	7/7	0.295758555984278	4	FACETS	0.917	0.719	1	0.229	0.179	0.286	CLONAL	1	TRUE	0	0.358753752811432	4		408	190	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517382	157517382	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs199674889	NA	P-0047455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	181	485	1	ENST00000346085.5:c.3946G>T	p.Gly1316Ter	p.G1316*	ENST00000346085	NM_020732.3	1316	Gga/Tga	16/20	0.295758555984278	4	FACETS	1	0.952	1	0.519	0.48	0.558	CLONAL	2	TRUE	0	0.358753752811432	4		486	661	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468101	50468101	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	98	518	0	ENST00000331340.3:c.1336C>A	p.Gln446Lys	p.Q446K	ENST00000331340	NM_006060.4	446	Cag/Aag	8/8	0.293472907183875	3	FACETS	1	0.932	1	0.528	0.472	0.588	CLONAL	1	TRUE	1	0.358753752811432	3		518	610	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55272981	55272981	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1268506326	NA	P-0047455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	140	517	0	ENST00000275493.2:c.3304G>T	p.Ala1102Ser	p.A1102S	ENST00000275493	NM_005228.3	1102	Gct/Tct	28/28	0.293472907183875	3	FACETS	1	0.986	1	0.717	0.655	0.782	CLONAL	1	TRUE	1	0.358753752811432	3		517	642	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624416	140624416	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	35	146	0	ENST00000288602.6:c.88G>C	p.Gly30Arg	p.G30R	ENST00000288602	NM_004333.4	30	Ggc/Cgc	1/18	0.293472907183875	3	FACETS	0.951	0.784	1	0.475	0.392	0.568	CLONAL	1	TRUE	1	0.358753752811432	3		146	242	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211418	98211418	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047455-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	122	583	0	ENST00000331920.6:c.3737G>T	p.Gly1246Val	p.G1246V	ENST00000331920	NM_000264.3	1246	gGc/gTc	22/24	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.358753752811432	2		583	656	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	1039	830	0	ENST00000269305.4:c.470T>G	p.Val157Gly	p.V157G	ENST00000269305	NM_001126112.2	157	gTc/gGc	5/11	0.866146985148331	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.868805428459121	2		830	1196	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430276	181430276	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	277	558	3	ENST00000325404.1:c.128G>A	p.Arg43Gln	p.R43Q	ENST00000325404	NM_003106.3	43	cGg/cAg	1/1	0.865678873997944	2	FACETS	0.959	0.907	1	0.479	0.453	0.506	CLONAL	1	TRUE	0	0.868805428459121	2		561	665	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670720	86670720	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	40	114	0	ENST00000274376.6:c.1998A>C	p.Lys666Asn	p.K666N	ENST00000274376	NM_002890.2	666	aaA/aaC	15/25	0.868805428459121	3	FACETS	0.93	0.814	1	0.93	0.814	1	CLONAL	2	TRUE	1	0.868805428459121	3		114	71	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166743	32166743	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs961810048	NA	P-0047466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1263	519	1084	9	ENST00000375023.3:c.4495C>T	p.Arg1499Ter	p.R1499*	ENST00000375023	NM_004557.3	1499	Cga/Tga	24/30	0.864769939762223	3	FACETS	0.962	0.92	1	0.481	0.46	0.502	CLONAL	1	TRUE	1	0.868805428459121	3		1093	1782	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683772	162683772	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	109	548	0	ENST00000366898.1:c.197T>C	p.Ile66Thr	p.I66T	ENST00000366898	NM_004562.2	66	aTt/aCt	3/12	0.864769939762223	3	FACETS	0.499	0.448	0.552	0.249	0.224	0.276	SUBCLONAL	1	TRUE	1	0.868805428459121	3		548	722	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683788	162683788	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	92	482	0	ENST00000366898.1:c.181C>A	p.Leu61Met	p.L61M	ENST00000366898	NM_004562.2	61	Ctg/Atg	3/12	0.864769939762223	3	FACETS	0.515	0.458	0.575	0.257	0.229	0.288	SUBCLONAL	1	TRUE	1	0.868805428459121	3		482	590	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874616	151874616	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	163	410	0	ENST00000262189.6:c.7922C>T	p.Ser2641Leu	p.S2641L	ENST00000262189	NM_170606.2	2641	tCa/tTa	38/59	0.868805428459121	2	FACETS	1	0.941	1	0.506	0.47	0.541	CLONAL	1	TRUE	0	0.868805428459121	2		410	371	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635279	87635279	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	200	565	2	ENST00000277120.3:c.2331G>T	p.Glu777Asp	p.E777D	ENST00000277120		777	gaG/gaT	18/19	0.868805428459121	3	FACETS	1	0.954	1	0.516	0.48	0.552	CLONAL	1	TRUE	1	0.868805428459121	3		567	640	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0047474-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	75	561	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.455933788304189	3	FACETS	0.842	0.74	0.951	0.421	0.37	0.476	CLONAL	1	TRUE	1	0.455933788304189	3		561	480	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0047474-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	45	250	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	0.375253581277525	2	FACETS	0.751	0.635	0.876	0.375	0.317	0.438	SUBCLONAL	1	TRUE	0	0.455933788304189	2		250	263	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047474-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	124	767	0	ENST00000269305.4:c.859G>T	p.Glu287Ter	p.E287*	ENST00000269305	NM_001126112.2	287	Gag/Tag	8/11	0.399717414816055	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.455933788304189	1		767	365	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073950	8073950	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047474-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	47	380	0	ENST00000377482.5:c.709C>A	p.Pro237Thr	p.P237T	ENST00000377482	NM_018948.3	237	Cct/Act	4/4	0.332796429639288	4	FACETS	0.912	0.773	1	0.304	0.257	0.355	CLONAL	1	TRUE	1	0.455933788304189	4		380	329	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902725	1902725	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047474-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	50	581	0	ENST00000382891.5:c.347del	p.Pro116LeufsTer11	p.P116Lfs*11	ENST00000382891	NM_133335.3	115	aCc/ac	2/22	0.267792019646254	1	FACETS	0.546	0.466	0.633	0.546	0.466	0.633	INDETERMINATE	1	TRUE	0	0.455933788304189	1		581	310	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506437	148506437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047480-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	101	258	0	ENST00000320356.2:c.2075C>T	p.Ala692Val	p.A692V	ENST00000320356	NM_004456.4	692	gCa/gTa	18/20	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		258	475	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0047488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	66	259	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.151702100520509	2	FACETS	1	0.971	1	0.733	0.638	0.834	CLONAL	1	TRUE	0	0.211961918233911	2		259	425	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612623	228612623	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	44	657	0	ENST00000366696.1:c.404G>T	p.Arg135Leu	p.R135L	ENST00000366696	NM_003493.2	135	cGg/cTg	1/1	0.211961918233911	3	FACETS	0.569	0.476	0.673	0.284	0.238	0.337	SUBCLONAL	1	TRUE	1	0.211961918233911	3		657	807	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236117	108236117	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	108	419	0	ENST00000278616.4:c.9053A>T	p.Lys3018Ile	p.K3018I	ENST00000278616	NM_000051.3	3018	aAa/aTa	63/63	0.151702100520509	2	FACETS	0.889	0.8	0.983	0.889	0.8	0.983	CLONAL	2	TRUE	0	0.211961918233911	2		419	573	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499063	149499063	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	152	694	0	ENST00000261799.4:c.2765G>T	p.Arg922Leu	p.R922L	ENST00000261799	NM_002609.3	922	cGc/cTc	20/23	0.101018397741589	3	FACETS	0.903	0.826	0.984	0.903	0.826	0.984	INDETERMINATE	2	TRUE	1	0.211961918233911	3		694	878	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043477	180043477	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	106	661	0	ENST00000261937.6:c.3109G>C	p.Asp1037His	p.D1037H	ENST00000261937	NM_182925.4	1037	Gac/Cac	23/30	0.101018397741589	3	FACETS	1	0.972	1	0.629	0.563	0.698	INDETERMINATE	1	TRUE	1	0.211961918233911	3		661	880	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553668	106553668	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047488-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	33	389	0	ENST00000369096.4:c.1633G>T	p.Glu545Ter	p.E545*	ENST00000369096	NM_001198.3	545	Gaa/Taa	5/7	1	2	FACETS	0.722	0.588	0.874	0.722	0.588	0.874	SUBCLONAL	1	TRUE	1	0.211961918233911	2		389	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0047576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	86	643	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.561347212366379	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.750140450952349	1		643	135	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739324	46739325	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0047576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	53	491	0	ENST00000371975.4:c.1517_1518dup	p.Val507ArgfsTer2	p.V507Rfs*2	ENST00000371975	NM_003579.3	505	-/GC	14/18	0.215505209918692	3	FACETS	1	0.938	1	0.571	0.496	0.65	INDETERMINATE	1	TRUE	1	0.750140450952349	3		491	170	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104385	2104480	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTCAAGGCCCTCACAGACAATGGGAGACACATCACCTACTTGGAGGAAGAGCTGGGTGGGTGCCACCTTGGGTTGGAGGTTTCTCTGGCCTTGA	TTTTCAAGGCCCTCACAGACAATGGGAGACACATCACCTACTTGGAGGAAGAGCTGGGTGGGTGCCACCTTGGGTTGGAGGTTTCTCTGGCCTTGA	-	novel	NA	P-0047576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	39	822	0	ENST00000219476.3:c.425_481+39del		p.X142_splice	ENST00000219476	NM_000548.3	142		5/42	0.750140450952349	1	FACETS	0.855	0.742	0.967	0.855	0.742	0.967	CLONAL	1	TRUE	0	0.750140450952349	1		822	76	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0047579-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	38	561	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.281668387402287	1	FACETS	0.902	0.748	1	0.902	0.748	1	CLONAL	1	TRUE	0	0.24	1		561	309	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0047579-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	39	604	1	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.281668387402287	1	FACETS	0.908	0.755	1	0.908	0.755	1	CLONAL	1	TRUE	0	0.24	1		605	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577533	7577570	+	frameshift_variant	Frame_Shift_Del	DEL	GCCTCCGGTTCATGCCGCCCATGCAGGAACTGTTACAC	GCCTCCGGTTCATGCCGCCCATGCAGGAACTGTTACAC	-	novel	NA	P-0047579-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	41	678	0	ENST00000269305.4:c.711_748del	p.Met237IlefsTer14	p.M237Ifs*14	ENST00000269305	NM_001126112.2	237	atGTGTAACAGTTCCTGCATGGGCGGCATGAACCGGAGGCcc/atcc	7/11	1	2	FACETS	0.848	0.707	1	0.848	0.707	1	CLONAL	1	TRUE	1	0.24	2		678	403	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0047583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	1359	561	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.18734492647825	22	FACETS	0.997	0.977	1	0.947	0.928	0.966	CLONAL	19	TRUE	2	0.18734492647825	22		561	2201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0047583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	198	584	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	1	2	FACETS	1	0.973	1	1	0.994	1	CLONAL	2	TRUE	1	0.18734492647825	2		584	958	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0047583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	1898	768	2	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.18734492647825	22	FACETS	1	0.993	1	0.92	0.904	0.936	CLONAL	18	TRUE	2	0.18734492647825	22		770	3165	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852523	63852523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1164426377	NA	P-0047583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	35	370	1	ENST00000279873.7:c.3301C>T	p.His1101Tyr	p.H1101Y	ENST00000279873	NM_032199.2	1101	Cat/Tat	10/10	1	2	FACETS	0.634	0.519	0.765	0.634	0.519	0.765	SUBCLONAL	1	TRUE	1	0.18734492647825	2		371	589	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437369	121437369	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	99	765	0	ENST00000257555.6:c.1707C>A	p.Ser569Arg	p.S569R	ENST00000257555		569	agC/agA	9/10	1	2	FACETS	0.983	0.876	1	0.983	0.876	1	CLONAL	1	TRUE	1	0.18734492647825	2		765	1075	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632778	23632778	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	38	345	0	ENST00000261584.4:c.3018G>C	p.Leu1006Phe	p.L1006F	ENST00000261584	NM_024675.3	1006	ttG/ttC	10/13	0.157632496422458	4	FACETS	0.937	0.774	1			1	CLONAL	1	TRUE	NA	0.18734492647825	4		345	514	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040983	47040984	+	frameshift_variant	Frame_Shift_Ins	INS	CC	CC	GCT	novel	NA	P-0047583-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	145	423	1	ENST00000377604.3:c.1513_1514delinsGCT	p.Pro505AlafsTer13	p.P505Afs*13	ENST00000377604	NM_001204468.1	505	CCt/GCTt	14/24	1	1	FACETS	1	0.952	1	1	0.991	1	CLONAL	2	TRUE	0	0.18734492647825	1		424	663	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755645	39755645	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047625-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	408	857	0	ENST00000288319.7:c.1120G>T	p.Asp374Tyr	p.D374Y	ENST00000288319	NM_182918.3	374	Gac/Tac	10/10	0.170486433052643	3	FACETS	1	0.989	1	1	0.996	1	INDETERMINATE	3	FALSE	1	0.3	3		857	948	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523527	41523528	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0047625-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	289	602	0	ENST00000263253.7:c.944_945dup	p.Val316TrpfsTer2	p.V316Wfs*2	ENST00000263253	NM_001429.3	315	ctg/cTGtg	4/31	0.3	1	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	FALSE	0	0.3	1		602	685	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs760043106	NA	P-0047640-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	122	702	1	ENST00000269305.4:c.584T>A	p.Ile195Asn	p.I195N	ENST00000269305	NM_001126112.2	195	aTc/aAc	6/11	0.323298525755748	0	FACETS	0.893	0.81	0.98			1	CLONAL	1	TRUE	0	0.323298525755748	0		703	572	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612035	189612035	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047640-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	87	531	0	ENST00000264731.3:c.1787del	p.Ala596GlyfsTer108	p.A596Gfs*108	ENST00000264731	NM_003722.4	596	gCg/gg	14/14	0.321819809781182	4	FACETS	0.773	0.683	0.87	0.387	0.341	0.435	SUBCLONAL	1	TRUE	2	0.323298525755748	4		531	921	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420005	152420005	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047640-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	202	703	0	ENST00000206249.3:c.1692C>G	p.Asp564Glu	p.D564E	ENST00000206249	NM_000125.3	564	gaC/gaG	8/8	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.323298525755748	2		703	899	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	136	376	1	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.548681845249727	2		377	489	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	101	251	1	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	0.925	0.833	1	0.925	0.833	1	CLONAL	1	TRUE	1	0.548681845249727	2		252	398	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	124	432	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.913	0.831	0.999	0.913	0.831	0.999	CLONAL	1	TRUE	1	0.548681845249727	2		432	495	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920469	134920469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	178	688	1	ENST00000398015.3:c.2284G>A	p.Asp762Asn	p.D762N	ENST00000398015	NM_004441.4	762	Gac/Aac	12/16	1	2	FACETS	0.861	0.795	0.929	0.861	0.795	0.929	CLONAL	1	TRUE	1	0.548681845249727	2		689	754	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	200	706	8	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.798	0.74	0.859	0.798	0.74	0.859	SUBCLONAL	1	TRUE	1	0.548681845249727	2		714	913	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088787	27088788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	169	464	1	ENST00000324856.7:c.2402dup	p.Gln802SerfsTer15	p.Q802Sfs*15	ENST00000324856	NM_006015.4	799	cag/caGg	7/20	1	2	FACETS	0.832	0.767	0.9	0.832	0.767	0.9	CLONAL	1	TRUE	1	0.548681845249727	2		465	740	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	38	190	0	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	1	2	FACETS	0.594	0.495	0.704	0.594	0.495	0.704	SUBCLONAL	1	TRUE	1	0.548681845249727	2		190	233	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	179	648	0	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.833	0.77	0.899	0.833	0.77	0.899	CLONAL	1	TRUE	1	0.548681845249727	2		648	783	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	213	688	4	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	0.929	0.865	0.995	0.929	0.865	0.995	CLONAL	1	TRUE	1	0.548681845249727	2		692	836	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450244	50450244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	140	410	1	ENST00000331340.3:c.428G>A	p.Arg143Gln	p.R143Q	ENST00000331340	NM_006060.4	143	cGg/cAg	5/8	0.548681845249727	3	FACETS	0.993	0.907	1	0.496	0.453	0.542	CLONAL	1	TRUE	1	0.548681845249727	3		411	655	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940012	76940012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs122445105	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	153	220	3	ENST00000373344.5:c.736C>T	p.Arg246Cys	p.R246C	ENST00000373344	NM_000489.3	246	Cgc/Tgc	9/35	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.548681845249727	1		223	287	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11210203	11210203	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	107	511	0	ENST00000361445.4:c.4550C>T	p.Ala1517Val	p.A1517V	ENST00000361445	NM_004958.3	1517	gCt/gTt	31/58	1	2	FACETS	0.543	0.487	0.602	0.543	0.487	0.602	SUBCLONAL	1	TRUE	1	0.548681845249727	2		511	718	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	218	331	1	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.831	0.782	0.881	1	0.994	1	CLONAL	2	TRUE	1	0.548681845249727	2		332	478	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646981	23646981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	122	492	3	ENST00000261584.4:c.886del	p.Met296Ter	p.M296*	ENST00000261584	NM_024675.3	296	Atg/tg	4/13	1	2	FACETS	0.581	0.525	0.639	0.581	0.525	0.639	SUBCLONAL	1	TRUE	1	0.548681845249727	2		495	766	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434592	110434592	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	200	605	3	ENST00000375856.3:c.3809C>A	p.Pro1270Gln	p.P1270Q	ENST00000375856	NM_003749.2	1270	cCg/cAg	1/2	1	2	FACETS	0.93	0.864	0.998	0.93	0.864	0.998	CLONAL	1	TRUE	1	0.548681845249727	2		608	784	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189085	32189085	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762851866	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	149	441	0	ENST00000375023.3:c.469C>T	p.Arg157Trp	p.R157W	ENST00000375023	NM_004557.3	157	Cgg/Tgg	4/30	1	2	FACETS	0.817	0.748	0.888	0.817	0.748	0.888	CLONAL	1	TRUE	1	0.548681845249727	2		441	665	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154241	2154242	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755455183	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	171	807	3	ENST00000434045.2:c.686dup	p.Glu230ArgfsTer50	p.E230Rfs*50	ENST00000434045	NM_001127598.1	229	cca/ccCa	5/5	1	2	FACETS	0.61	0.56	0.662	0.61	0.56	0.662	SUBCLONAL	1	TRUE	1	0.548681845249727	2		810	1022	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945008	31945008	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	227	731	0	ENST00000340398.3:c.93del	p.Ser32LeufsTer5	p.S32Lfs*5	ENST00000340398	NM_001013699.2	31	ccC/cc	1/1	1	2	FACETS	0.857	0.799	0.917	0.857	0.799	0.917	CLONAL	1	TRUE	1	0.548681845249727	2		731	965	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930730	32930730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs74047012	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	120	285	0	ENST00000380152.3:c.7601C>T	p.Ala2534Val	p.A2534V	ENST00000380152		2534	gCg/gTg	15/27	1	2	FACETS	0.904	0.821	0.99	0.904	0.821	0.99	CLONAL	1	TRUE	1	0.548681845249727	2		285	484	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725019	47725019	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs762488821	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	144	930	0	ENST00000449228.1:c.725del	p.Gly242AlafsTer48	p.G242Afs*48	ENST00000449228	NM_001127240.2	242	gGc/gc	4/4	1	2	FACETS	0.403	0.367	0.442	0.403	0.367	0.442	SUBCLONAL	1	TRUE	1	0.548681845249727	2		930	1301	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363274	40363274	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	216	543	0	ENST00000397332.2:c.955C>A	p.Leu319Met	p.L319M	ENST00000397332	NM_001033082.2	319	Ctg/Atg	3/3	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.548681845249727	2		543	720	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	197	689	3	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.811	0.752	0.873	0.811	0.752	0.873	CLONAL	1	TRUE	1	0.548681845249727	2		692	885	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280036	18280036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	155	377	2	ENST00000222254.8:c.2119G>A	p.Ala707Thr	p.A707T	ENST00000222254	NM_005027.3	707	Gcg/Acg	16/16	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.548681845249727	2		379	553	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343528	118343529	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	135	320	0	ENST00000534358.1:c.1660dup	p.Gln554ProfsTer27	p.Q554Pfs*27	ENST00000534358	NM_005933.3	552	gcc/gCcc	3/36	1	2	FACETS	0.996	0.911	1	0.996	0.911	1	CLONAL	1	TRUE	1	0.548681845249727	2		320	494	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968144	18968144	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	220	763	3	ENST00000262803.5:c.1984G>A	p.Asp662Asn	p.D662N	ENST00000262803	NM_002911.3	662	Gac/Aac	15/24	1	2	FACETS	0.904	0.842	0.968	0.904	0.842	0.968	CLONAL	1	TRUE	1	0.548681845249727	2		766	887	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512408	38512408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747666789	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	253	709	1	ENST00000254066.5:c.1319C>T	p.Pro440Leu	p.P440L	ENST00000254066	NM_000964.3	440	cCg/cTg	9/9	1	2	FACETS	0.927	0.868	0.987	0.927	0.868	0.987	CLONAL	1	TRUE	1	0.548681845249727	2		710	995	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042709	42042711	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs1159823543	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	119	347	0	ENST00000219905.7:c.6909_6911del	p.Glu2303del	p.E2303del	ENST00000219905	NM_001164273.1	2302	GAA/-	17/24	1	2	FACETS	0.913	0.829	1	0.913	0.829	1	CLONAL	1	TRUE	1	0.548681845249727	2		347	475	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733022	74733022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	211	575	0	ENST00000359995.5:c.221C>T	p.Ala74Val	p.A74V	ENST00000359995	NM_001195427.1	74	gCc/gTc	1/3	1	2	FACETS	0.957	0.891	1	0.957	0.891	1	CLONAL	1	TRUE	1	0.548681845249727	2		575	804	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120557	2120557	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	293	863	2	ENST00000219476.3:c.1817T>C	p.Ile606Thr	p.I606T	ENST00000219476	NM_000548.3	606	aTc/aCc	17/42	1	2	FACETS	0.977	0.92	1	0.977	0.92	1	CLONAL	1	TRUE	1	0.548681845249727	2		865	1093	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222816	5222816	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775778266	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	278	747	1	ENST00000357368.4:c.2987C>T	p.Thr996Met	p.T996M	ENST00000357368	NM_002850.3	996	aCg/aTg	18/38	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.548681845249727	2		748	948	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856274	111856274	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	18	40	0	ENST00000341259.2:c.325G>A	p.Gly109Ser	p.G109S	ENST00000341259	NM_005475.2	109	Ggc/Agc	2/8	1	2	FACETS	0.875	0.675	1	0.875	0.675	1	CLONAL	1	TRUE	1	0.548681845249727	2		40	75	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574584	41574584	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	220	714	1	ENST00000263253.7:c.6869A>G	p.Gln2290Arg	p.Q2290R	ENST00000263253	NM_001429.3	2290	cAg/cGg	31/31	1	2	FACETS	0.862	0.803	0.924	0.862	0.803	0.924	CLONAL	1	TRUE	1	0.548681845249727	2		715	930	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023765	27023765	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	95	356	0	ENST00000324856.7:c.871G>C	p.Ala291Pro	p.A291P	ENST00000324856	NM_006015.4	291	Gcc/Ccc	1/20	1	2	FACETS	0.698	0.624	0.777	0.698	0.624	0.777	SUBCLONAL	1	TRUE	1	0.548681845249727	2		356	496	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803902	43803902	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs368753117	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	173	473	2	ENST00000372470.3:c.212G>A	p.Arg71Gln	p.R71Q	ENST00000372470	NM_005373.2	71	cGg/cAg	2/12	1	2	FACETS	0.999	0.924	1	0.999	0.924	1	CLONAL	1	TRUE	1	0.548681845249727	2		475	631	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438235	49438236	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	185	597	0	ENST00000301067.7:c.5033_5034del	p.Lys1678ArgfsTer12	p.K1678Rfs*12	ENST00000301067	NM_003482.3	1678	aAA/a	20/54	1	2	FACETS	0.896	0.829	0.964	0.896	0.829	0.964	CLONAL	1	TRUE	1	0.548681845249727	2		597	753	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384783	17384783	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772589405	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	200	672	1	ENST00000359435.4:c.415G>A	p.Asp139Asn	p.D139N	ENST00000359435	NM_001033549.1	139	Gac/Aac	4/9	1	2	FACETS	0.806	0.748	0.867	0.806	0.748	0.867	CLONAL	1	TRUE	1	0.548681845249727	2		673	904	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439680	220439680	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	282	927	0	ENST00000243786.2:c.533T>C	p.Val178Ala	p.V178A	ENST00000243786	NM_002191.3	178	gTg/gCg	2/2	1	2	FACETS	0.918	0.862	0.975	0.918	0.862	0.975	CLONAL	1	TRUE	1	0.548681845249727	2		927	1120	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542762	187542762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	126	323	2	ENST00000441802.2:c.4978G>A	p.Ala1660Thr	p.A1660T	ENST00000441802	NM_005245.3	1660	Gct/Act	10/27	1	2	FACETS	0.909	0.828	0.994	0.909	0.828	0.994	CLONAL	1	TRUE	1	0.548681845249727	2		325	505	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402523	20402523	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770338281	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	186	520	0	ENST00000346618.3:c.64del	p.Ala22ArgfsTer18	p.A22Rfs*18	ENST00000346618	NM_001949.4	20	gaG/ga	1/7	NA	2	FACETS	0.966	0.895	1			1	INDETERMINATE	1	TRUE	NA	0.548681845249727	2		520	702	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729357	41729357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	163	489	0	ENST00000242208.4:c.1172G>A	p.Cys391Tyr	p.C391Y	ENST00000242208	NM_002192.2	391	tGt/tAt	3/3	0.548681845249727	3	FACETS	0.931	0.856	1	0.466	0.428	0.505	CLONAL	1	TRUE	1	0.548681845249727	3		489	813	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8525033	8525033	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	61	246	0	ENST00000356435.5:c.571G>A	p.Ala191Thr	p.A191T	ENST00000356435		191	Gcc/Acc	7/35	1	2	FACETS	0.872	0.76	0.99	0.872	0.76	0.99	CLONAL	1	TRUE	1	0.548681845249727	2		246	255	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144158	11144158	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	244	616	0	ENST00000358026.2:c.3739C>A	p.Leu1247Met	p.L1247M	ENST00000358026	NM_001128849.1	1247	Ctg/Atg	26/36	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.548681845249727	2		616	869	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082727	16082727	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	43	82	0	ENST00000281043.3:c.541C>A	p.His181Asn	p.H181N	ENST00000281043	NM_005378.4	181	Cac/Aac	2/3	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.548681845249727	2		82	112	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249423	110249423	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	290	889	1	ENST00000374672.4:c.1150G>A	p.Gly384Arg	p.G384R	ENST00000374672	NM_004235.4	384	Gga/Aga	4/5	1	2	FACETS	0.88	0.827	0.934	0.88	0.827	0.934	CLONAL	1	TRUE	1	0.548681845249727	2		890	1201	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16056679	16056680	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	71	191	0	ENST00000268712.3:c.762dup	p.Glu255Ter	p.E255*	ENST00000268712	NM_006311.3	254	-/T	7/46	1	2	FACETS	0.914	0.806	1	0.914	0.806	1	CLONAL	1	TRUE	1	0.548681845249727	2		191	283	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47700122	47700122	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	70	347	0	ENST00000347630.2:c.51del	p.Val18Ter	p.V18*	ENST00000347630	NM_001007230.1	17	ccC/cc	3/11	1	2	FACETS	0.475	0.415	0.54	0.475	0.415	0.54	SUBCLONAL	1	TRUE	1	0.548681845249727	2		347	537	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021788	69021788	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	137	483	0	ENST00000288368.4:c.3076T>A	p.Tyr1026Asn	p.Y1026N	ENST00000288368	NM_024870.2	1026	Tat/Aat	25/40	1	2	FACETS	0.864	0.789	0.942	0.864	0.789	0.942	CLONAL	1	TRUE	1	0.548681845249727	2		483	578	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630131	100630131	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0047668-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	39	140	0	ENST00000308731.7:c.141+1del		p.X47_splice	ENST00000308731	NM_000061.2	47			1	1	FACETS	0.452	0.378	0.534	0.452	0.378	0.534	SUBCLONAL	1	TRUE	0	0.548681845249727	1		140	228	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0047687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	575	765	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.333404996178926	7	FACETS	1	0.971	1	1	0.971	1	CLONAL	6	TRUE	1	0.333404996178926	7		766	1049	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612028	189612028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs900140738	NA	P-0047687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	49	545	0	ENST00000264731.3:c.1780C>T	p.Arg594Ter	p.R594*	ENST00000264731	NM_003722.4	594	Cga/Tga	14/14	1	2	FACETS	0.71	0.603	0.828	0.71	0.603	0.828	SUBCLONAL	1	TRUE	1	0.333404996178926	2		545	414	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259967	16259967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	50	748	1	ENST00000375759.3:c.7232C>T	p.Ser2411Leu	p.S2411L	ENST00000375759	NM_015001.2	2411	tCg/tTg	11/15	1	2	FACETS	0.523	0.443	0.61	0.523	0.443	0.61	SUBCLONAL	1	TRUE	1	0.333404996178926	2		749	574	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0047687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	47	240	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.976	0.828	1	0.976	0.828	1	CLONAL	1	TRUE	1	0.333404996178926	2		242	289	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441821	49441821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202217665	NA	P-0047687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	90	643	0	ENST00000301067.7:c.4163G>A	p.Arg1388Gln	p.R1388Q	ENST00000301067	NM_003482.3	1388	cGg/cAg	14/54	1	2	FACETS	0.892	0.793	0.998	0.892	0.793	0.998	CLONAL	1	TRUE	1	0.333404996178926	2		643	605	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266963	41266963	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770795614	NA	P-0047687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	65	447	0	ENST00000349496.5:c.634C>T	p.Arg212Cys	p.R212C	ENST00000349496	NM_001904.3	212	Cgt/Tgt	5/15	1	2	FACETS	0.853	0.742	0.973	0.853	0.742	0.973	CLONAL	1	TRUE	1	0.333404996178926	2		447	457	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916274	9916274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	48	348	0	ENST00000330684.3:c.2015G>A	p.Arg672Lys	p.R672K	ENST00000330684	NM_001134407.1	672	aGa/aAa	10/13	0.333404996178926	1	FACETS	0.676	0.573	0.788	0.676	0.573	0.788	SUBCLONAL	1	TRUE	0	0.333404996178926	1		348	355	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295283	1295283	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs544702659	NA	P-0047687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	57	581	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.791	0.681	0.912	0.791	0.681	0.912	CLONAL	1	TRUE	1	0.333404996178926	2		581	432	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673756	176673756	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047687-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	41	390	0	ENST00000439151.2:c.4456G>A	p.Val1486Met	p.V1486M	ENST00000439151	NM_022455.4	1486	Gtg/Atg	10/23	1	2	FACETS	0.668	0.558	0.79	0.668	0.558	0.79	SUBCLONAL	1	TRUE	1	0.333404996178926	2		390	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0047695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	272	757	1	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.388242706580611	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.388242706580611	2		758	629	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437104	110437104	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	12	141	0	ENST00000375856.3:c.1297A>T	p.Met433Leu	p.M433L	ENST00000375856	NM_003749.2	433	Atg/Ttg	1/2	0.318005946451989	5	FACETS	0.466	0.327	0.636	0.155	0.109	0.212	SUBCLONAL	1	TRUE	2	0.388242706580611	5		141	210	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206595	108206595	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1431188311	NA	P-0047696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	66	189	0	ENST00000278616.4:c.8175T>A	p.Asp2725Glu	p.D2725E	ENST00000278616	NM_000051.3	2725	gaT/gaA	56/63	0.343896160862962	1	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	0	0.343896160862962	1		189	308	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070876	30070876	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	149	510	0	ENST00000338641.4:c.1393del	p.Glu465SerfsTer20	p.E465Sfs*20	ENST00000338641	NM_000268.3	464	gcG/gc	13/16	0.343896160862962	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.343896160862962	1		510	566	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52692321	52692321	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	26	234	0	ENST00000394830.3:c.539C>A	p.Ala180Asp	p.A180D	ENST00000394830	NM_018313.4	180	gCt/gAt	6/30	1	2	FACETS	0.482	0.382	0.596	0.482	0.382	0.596	SUBCLONAL	1	TRUE	1	0.343896160862962	2		234	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0047697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	646	858	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.494651592948063	3	FACETS	0.969	0.939	0.998	0.969	0.939	0.998	CLONAL	3	TRUE	0	0.494651592948063	3		858	1121	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844174	68844174	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	206	629	0	ENST00000261769.5:c.762T>A	p.Asp254Glu	p.D254E	ENST00000261769	NM_004360.3	254	gaT/gaA	6/16	0.488036225487659	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.494651592948063	2		629	393	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970913	21970913	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	222	894	0	ENST00000304494.5:c.445G>T	p.Glu149Ter	p.E149*	ENST00000304494	NM_000077.4	149	Gaa/Taa	2/3	0.187345199701907	2	FACETS	1	0.991	1	0.677	0.633	0.721	INDETERMINATE	1	TRUE	0	0.494651592948063	2		894	663	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216494	108216494	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	18	200	0	ENST00000278616.4:c.8443G>C	p.Glu2815Gln	p.E2815Q	ENST00000278616	NM_000051.3	2815	Gag/Cag	58/63	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.494651592948063	2		200	52	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918799	50918799	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146344351	NA	P-0047697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	677	1075	0	ENST00000440232.2:c.2669C>T	p.Ala890Val	p.A890V	ENST00000440232	NM_002691.3	890	gCg/gTg	21/27	0.250036688373081	6	FACETS	1	0.992	1			1	INDETERMINATE	3	TRUE	NA	0.494651592948063	6		1075	1662	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100907	27100907	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	263	603	0	ENST00000324856.7:c.4189C>T	p.Gln1397Ter	p.Q1397*	ENST00000324856	NM_006015.4	1397	Cag/Tag	18/20	0.494651592948063	6	FACETS	1	0.99	1	0.624	0.586	0.662	CLONAL	2	TRUE	2	0.494651592948063	6		603	848	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483286	120483286	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	85	335	0	ENST00000256646.2:c.3075G>C	p.Glu1025Asp	p.E1025D	ENST00000256646	NM_024408.3	1025	gaG/gaC	19/34	0.315477610411518	5	FACETS	1	0.976	1	0.467	0.415	0.523	CLONAL	1	TRUE	2	0.494651592948063	5		335	427	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114905769	114905769	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0047697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	171	312	2	ENST00000543371.1:c.789-1G>T		p.X263_splice	ENST00000543371	NM_001198531.1	263			0.494651592948063	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	3	TRUE	0	0.494651592948063	3		314	284	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415902	49415912	+	frameshift_variant	Frame_Shift_Del	DEL	ACACAGTTAGG	ACACAGTTAGG	-	novel	NA	P-0047697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	209	485	0	ENST00000301067.7:c.16435_16445del	p.Pro5479GlyfsTer7	p.P5479Gfs*7	ENST00000301067	NM_003482.3	5479	CCTAACTGTGTg/g	53/54	0.494651592948063	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	3	TRUE	1	0.494651592948063	4		485	415	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391133	89391133	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	121	473	1	ENST00000336596.2:c.1199T>A	p.Leu400Gln	p.L400Q	ENST00000336596	NM_005233.5	400	cTg/cAg	5/17	0.193143381305548	2	FACETS	1	0.923	1	0.509	0.462	0.557	INDETERMINATE	1	TRUE	0	0.494651592948063	2		474	481	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287574	33287574	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	124	681	0	ENST00000374542.5:c.1523T>G	p.Leu508Arg	p.L508R	ENST00000374542	NM_001141970.1	508	cTg/cGg	6/8	0.494651592948063	4	FACETS	0.781	0.705	0.86	0.39	0.352	0.43	SUBCLONAL	1	TRUE	2	0.494651592948063	4		681	960	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933463	39933463	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	133	795	0	ENST00000378444.4:c.1136T>A	p.Val379Asp	p.V379D	ENST00000378444	NM_001123385.1	379	gTt/gAt	4/15	0.343061624236673	2	FACETS	0.714	0.649	0.782	0.357	0.324	0.391	SUBCLONAL	1	TRUE	0	0.494651592948063	2		795	753	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347790	70347790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	58	501	0	ENST00000374080.3:c.3029C>T	p.Pro1010Leu	p.P1010L	ENST00000374080		1010	cCa/cTa	22/45	0.343061624236673	2	FACETS	0.385	0.33	0.445	0.193	0.165	0.223	SUBCLONAL	1	TRUE	0	0.494651592948063	2		501	609	SUCCESS
AR	367	MSKCC	GRCh37	X	66766399	66766399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	12	122	0	ENST00000374690.3:c.1411G>A	p.Gly471Ser	p.G471S	ENST00000374690	NM_000044.3	471	Ggc/Agc	1/8	0.343061624236673	2	FACETS	0.578	0.412	0.775	0.289	0.206	0.388	SUBCLONAL	1	TRUE	0	0.494651592948063	2		122	84	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0047698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	280	383	0				ENST00000310581	NM_198253.2	-/1132			0.643523113559367	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.661262449049549	2		383	390	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0047698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8261	530	405	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.661262449049549	38	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.661262449049549	38		405	8791	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717696	89717696	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1554825207	NA	P-0047698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	154	332	0	ENST00000371953.3:c.721T>G	p.Phe241Val	p.F241V	ENST00000371953	NM_000314.4	241	Ttt/Gtt	7/9	0.661262449049549	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.661262449049549	1		332	308	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984022	2984022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753614569	NA	P-0047698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	191	553	0	ENST00000396946.4:c.508C>T	p.Arg170Cys	p.R170C	ENST00000396946	NM_032415.4	170	Cgc/Tgc	5/25	0.600427430153009	4	FACETS	0.993	0.919	1	0.331	0.306	0.357	CLONAL	1	TRUE	1	0.661262449049549	4		553	966	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788642	3788642	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	114	351	0	ENST00000262367.5:c.4312C>A	p.His1438Asn	p.H1438N	ENST00000262367	NM_004380.2	1438	Cat/Aat	26/31	1	2	FACETS	0.942	0.857	1	0.942	0.857	1	CLONAL	1	TRUE	1	0.661262449049549	2		351	366	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241182	55241617	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTGTCCATGATGGACTTCGCCACAGCCCAGTCCTGTGCTGGAAGCCATGTTCTCTGGAAAGAGCAACCCAGCGGCTCATAAGCATAAGCGCGTGTGATGTGCCCCAACCAAACGACCGCCATGCACAACTTCCCTACCGGAGTTTTCAATCCAGTTAATAGGCGTGGAAACAGACATAGAAATTGTGTTTGTTGAAAGGTAGCTGTTCAGTTAAAGAACACCTGTATCAGAGCCTGTGTTTCTACCAACTTCTGTCAAGCTCTGTAGAGAAGGCGTACATTTGTCCTTCCAAATGAGCTGGCAAGTGCCGTGTCCTGGCACCCAAGCCCATGCCGTGGCTGCTGGTCCCCCTGCTGGGCCATGTCTGGCACTGCTTTCCAGCATGGTGAGGGCTGAGGTGACCCTTGTCTCTGTGTTCTTGTCCCCCCCAGCTTG	TTTGTCCATGATGGACTTCGCCACAGCCCAGTCCTGTGCTGGAAGCCATGTTCTCTGGAAAGAGCAACCCAGCGGCTCATAAGCATAAGCGCGTGTGATGTGCCCCAACCAAACGACCGCCATGCACAACTTCCCTACCGGAGTTTTCAATCCAGTTAATAGGCGTGGAAACAGACATAGAAATTGTGTTTGTTGAAAGGTAGCTGTTCAGTTAAAGAACACCTGTATCAGAGCCTGTGTTTCTACCAACTTCTGTCAAGCTCTGTAGAGAAGGCGTACATTTGTCCTTCCAAATGAGCTGGCAAGTGCCGTGTCCTGGCACCCAAGCCCATGCCGTGGCTGCTGGTCCCCCTGCTGGGCCATGTCTGGCACTGCTTTCCAGCATGGTGAGGGCTGAGGTGACCCTTGTCTCTGTGTTCTTGTCCCCCCCAGCTTG	-	novel	NA	P-0047698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11357	1439	730	0	ENST00000275493.2:c.2061+366_2066del		p.X687_splice	ENST00000275493	NM_005228.3	687		18/28	0.661262449049549	38	FACETS	1	0.995	1			1	CLONAL	4	TRUE	NA	0.661262449049549	38		730	12796	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92404015	92404015	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	78	310	0	ENST00000265734.4:c.364A>G	p.Ile122Val	p.I122V	ENST00000265734	NM_001259.6	122	Ata/Gta	3/8	0.661262449049549	4	FACETS	0.553	0.485	0.625	0.184	0.161	0.209	SUBCLONAL	1	TRUE	1	0.661262449049549	4		310	709	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0047699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	52	684	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.907	0.77	1	0.907	0.77	1	CLONAL	1	TRUE	1	0.16	2		686	717	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481471	40481471	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	51	422	1	ENST00000264657.5:c.1238T>A	p.Leu413Gln	p.L413Q	ENST00000264657	NM_139276.2	413	cTg/cAg	14/24	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.16	2		423	540	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46597066	46597066	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	37	383	0	ENST00000263734.3:c.880C>T	p.Gln294Ter	p.Q294*	ENST00000263734	NM_001430.4	294	Cag/Tag	7/16	1	2	FACETS	0.978	0.806	1	0.978	0.806	1	CLONAL	1	TRUE	1	0.16	2		383	473	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197391	26197391	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	27	383	1	ENST00000356476.2:c.88G>A	p.Ala30Thr	p.A30T	ENST00000356476		30	Gct/Act	1/1	1	2	FACETS	0.753	0.599	0.931	0.753	0.599	0.931	CLONAL	1	TRUE	1	0.16	2		384	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0047701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	311	722	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	0.23573960143389	4	FACETS	1	0.979	1			1	CLONAL	3	TRUE	NA	0.330184348997602	4		722	787	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246613	46246613	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	16	142	0	ENST00000334344.6:c.4708del	p.Ile1570Ter	p.I1570*	ENST00000334344	NM_152641.2	1569	gcA/gc	15/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		142	147	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0047704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	106	712	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.308608947916117	1	FACETS	0.817	0.733	0.906	0.817	0.733	0.906	CLONAL	1	TRUE	0	0.308608947916117	1		712	711	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0047704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	79	248	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.282502783488765	2	FACETS	0.877	0.779	0.979	0.877	0.779	0.979	CLONAL	2	TRUE	0	0.308608947916117	2		248	292	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0047704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	13	480	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.163	0.115	0.222	0.163	0.115	0.222	SUBCLONAL	1	TRUE	1	0.308608947916117	2		480	517	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912670	32912670	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398122776	NA	P-0047704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	52	275	0	ENST00000380152.3:c.4178C>T	p.Ala1393Val	p.A1393V	ENST00000380152		1393	gCg/gTg	11/27	0.308608947916117	3	FACETS	0.985	0.841	1	0.492	0.42	0.571	CLONAL	1	TRUE	1	0.308608947916117	3		275	395	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572002	64572002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779413959	NA	P-0047704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	138	767	0	ENST00000312049.6:c.1637C>T	p.Pro546Leu	p.P546L	ENST00000312049	NM_130799.2	546	cCg/cTg	10/10	1	2	FACETS	0.865	0.786	0.948	0.865	0.786	0.948	CLONAL	1	TRUE	1	0.308608947916117	2		767	1034	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562378	21562378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772963885	NA	P-0047704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	248	806	1	ENST00000382592.4:c.1541C>T	p.Pro514Leu	p.P514L	ENST00000382592	NM_014572.2	514	cCg/cTg	4/8	0.308608947916117	3	FACETS	0.905	0.846	0.965	0.905	0.846	0.965	CLONAL	2	TRUE	1	0.308608947916117	3		807	1025	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397219	397219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143144957	NA	P-0047704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	66	320	0	ENST00000380956.4:c.604G>A	p.Gly202Ser	p.G202S	ENST00000380956	NM_001195286.1	202	Ggc/Agc	5/9	1	2	FACETS	0.997	0.869	1	0.997	0.869	1	CLONAL	1	TRUE	1	0.308608947916117	2		320	429	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910787	114910788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	92	410	0	ENST00000543371.1:c.907dup	p.Thr303AsnfsTer25	p.T303Nfs*25	ENST00000543371	NM_001198531.1	302	-/A	9/14	1	2	FACETS	0.91	0.809	1	0.91	0.809	1	CLONAL	1	TRUE	1	0.308608947916117	2		410	655	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0047707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	251	660	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	NA	2	FACETS	0.889	0.839	0.939			1	INDETERMINATE	2	TRUE	NA	0.495458798799478	2		660	570	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528244	157528244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762342896	NA	P-0047707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	63	599	0	ENST00000346085.5:c.5969G>A	p.Arg1990Gln	p.R1990Q	ENST00000346085	NM_020732.3	1990	cGa/cAa	20/20	0.346774468750659	1	FACETS	0.36	0.312	0.413	0.36	0.312	0.413	SUBCLONAL	1	TRUE	0	0.495458798799478	1		599	531	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853423	151853437	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTATTCTGCTGCAG	ATTATTCTGCTGCAG	-	novel	NA	P-0047707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	54	315	0	ENST00000262189.6:c.11671-6_11679del		p.X3891_splice	ENST00000262189	NM_170606.2	3891		45/59	0.497047807361999	3	FACETS	0.712	0.61	0.823	0.356	0.305	0.412	SUBCLONAL	1	TRUE	1	0.495458798799478	3		315	382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577078	7577081	+	missense_variant	Missense_Mutation	ONP	TCTT	TCTT	CCTG	novel	NA	P-0047707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	347	833	0	ENST00000269305.4:c.857_860delinsCAGG	p.Glu286_Glu287delinsAlaGly	p.E286_E287delinsAG	ENST00000269305	NM_001126112.2	286	gAAGAg/gCAGGg	8/11	0.477592388972644	2	FACETS	0.903	0.86	0.946	0.903	0.86	0.946	CLONAL	2	TRUE	0	0.495458798799478	2		833	776	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976476	25976476	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	70	329	1	ENST00000435504.4:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000435504		357	Cga/Tga	11/13	0.347662212997838	1	FACETS	0.976	0.857	1	0.976	0.857	1	CLONAL	1	TRUE	0	0.347662212997838	1		330	341	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0047708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	50	660	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.464	0.393	0.542	0.464	0.393	0.542	SUBCLONAL	1	TRUE	1	0.347662212997838	2		660	620	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020769	37020769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	67	459	1	ENST00000358127.4:c.76del	p.Val26PhefsTer3	p.V26Ffs*3	ENST00000358127	NM_001280556.1	26	Gtt/tt	2/10	1	2	FACETS	0.619	0.537	0.707	0.619	0.537	0.707	SUBCLONAL	1	TRUE	1	0.347662212997838	2		460	623	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521525	46521525	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	65	434	4	ENST00000262741.5:c.883del	p.Met295Ter	p.M295*	ENST00000262741	NM_003629.3	295	Atg/tg	7/10	1	2	FACETS	0.769	0.668	0.878	0.769	0.668	0.878	SUBCLONAL	1	TRUE	1	0.347662212997838	2		438	486	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100728	8100728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs771019738	NA	P-0047708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	143	879	12	ENST00000346208.3:c.708del	p.Ser237AlafsTer28	p.S237Afs*28	ENST00000346208		234	ttC/tt	3/6	1	2	FACETS	0.918	0.837	1	0.918	0.837	1	CLONAL	1	TRUE	1	0.347662212997838	2		891	896	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519927	NA	P-0047708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	33	443	0	ENST00000263967.3:c.1625A>G	p.Glu542Gly	p.E542G	ENST00000263967	NM_006218.2	542	gAa/gGa	10/21	1	2	FACETS	0.398	0.324	0.482	0.398	0.324	0.482	SUBCLONAL	1	TRUE	1	0.347662212997838	2		443	477	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061249	38061249	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	155	851	0	ENST00000250448.2:c.740A>G	p.His247Arg	p.H247R	ENST00000250448	NM_004496.3	247	cAc/cGc	2/2	1	2	FACETS	0.986	0.903	1	0.986	0.903	1	CLONAL	1	TRUE	1	0.347662212997838	2		851	904	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	43	504	0	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	1	2	FACETS	0.408	0.34	0.482	0.408	0.34	0.482	SUBCLONAL	1	TRUE	1	0.347662212997838	2		504	607	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026095	71026095	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	30	277	0	ENST00000318789.4:c.1527G>A	p.Trp509Ter	p.W509*	ENST00000318789	NM_032682.5	509	tgG/tgA	17/21	1	2	FACETS	0.444	0.357	0.542	0.444	0.357	0.542	SUBCLONAL	1	TRUE	1	0.347662212997838	2		277	389	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0047708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	38	572	0	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	1	2	FACETS	0.338	0.279	0.405	0.338	0.279	0.405	SUBCLONAL	1	TRUE	1	0.347662212997838	2		572	646	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575049	64575049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs386134259	NA	P-0047708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	106	542	1	ENST00000312049.6:c.758C>T	p.Ser253Leu	p.S253L	ENST00000312049	NM_130799.2	253	tCg/tTg	4/10	1	2	FACETS	0.898	0.806	0.996	0.898	0.806	0.996	CLONAL	1	TRUE	1	0.347662212997838	2		543	679	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575422	64575422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	152	850	3	ENST00000312049.6:c.595C>T	p.His199Tyr	p.H199Y	ENST00000312049	NM_130799.2	199	Cac/Tac	3/10	1	2	FACETS	0.94	0.86	1	0.94	0.86	1	CLONAL	1	TRUE	1	0.347662212997838	2		853	930	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696757	176696757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752685166	NA	P-0047708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	60	302	0	ENST00000439151.2:c.5458G>A	p.Val1820Met	p.V1820M	ENST00000439151	NM_022455.4	1820	Gtg/Atg	16/23	1	2	FACETS	0.908	0.786	1	0.908	0.786	1	CLONAL	1	TRUE	1	0.347662212997838	2		302	380	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259043	16259043	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	71	463	1	ENST00000375759.3:c.6313del	p.Ala2105LeufsTer33	p.A2105Lfs*33	ENST00000375759	NM_015001.2	2103	aGg/ag	11/15	1	2	FACETS	0.823	0.72	0.934	0.823	0.72	0.934	CLONAL	1	TRUE	1	0.347662212997838	2		464	496	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655410	67655410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	98	508	0	ENST00000264010.4:c.1273C>T	p.His425Tyr	p.H425Y	ENST00000264010	NM_006565.3	425	Cac/Tac	7/12	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.347662212997838	2		508	556	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265833	16265834	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	rs972442854	NA	P-0047708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	133	754	0	ENST00000375759.3:c.10909_10910del	p.His3638ProfsTer7	p.H3638Pfs*7	ENST00000375759	NM_015001.2	3636	GAg/g	15/15	1	2	FACETS	0.926	0.841	1	0.926	0.841	1	CLONAL	1	TRUE	1	0.347662212997838	2		754	826	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117313	115117315	+	inframe_deletion	In_Frame_Del	DEL	ATC	ATC	-	novel	NA	P-0047708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	30	241	0	ENST00000257566.3:c.859_861del	p.Asp287del	p.D287del	ENST00000257566	NM_016569.3	287	GAT/-	4/8	1	2	FACETS	0.685	0.554	0.831	0.685	0.554	0.831	SUBCLONAL	1	TRUE	1	0.347662212997838	2		241	252	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570799	226570799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1407958928	NA	P-0047708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	116	663	0	ENST00000366794.5:c.1097C>T	p.Ala366Val	p.A366V	ENST00000366794	NM_001618.3	366	gCg/gTg	8/23	1	2	FACETS	0.867	0.781	0.957	0.867	0.781	0.957	CLONAL	1	TRUE	1	0.347662212997838	2		663	770	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244269	5244269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568465790	NA	P-0047708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	93	1207	3	ENST00000357368.4:c.1213G>A	p.Val405Ile	p.V405I	ENST00000357368	NM_002850.3	405	Gtc/Atc	11/38	1	2	FACETS	0.531	0.471	0.596	0.531	0.471	0.596	SUBCLONAL	1	TRUE	1	0.347662212997838	2		1210	1007	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726574	46726574	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145410495	NA	P-0047708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	53	584	1	ENST00000371975.4:c.653C>T	p.Ser218Leu	p.S218L	ENST00000371975	NM_003579.3	218	tCg/tTg	7/18	1	2	FACETS	0.503	0.429	0.585	0.503	0.429	0.585	SUBCLONAL	1	TRUE	1	0.347662212997838	2		585	606	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28601412	28601412	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	147	709	0	ENST00000253063.3:c.1097A>C	p.Lys366Thr	p.K366T	ENST00000253063	NM_031459.4	366	aAg/aCg	8/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.347662212997838	2		709	774	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21627799	21627799	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	71	472	0	ENST00000421138.2:c.1331T>C	p.Val444Ala	p.V444A	ENST00000421138		444	gTa/gCa	12/16	1	2	FACETS	0.89	0.779	1	0.89	0.779	1	CLONAL	1	TRUE	1	0.347662212997838	2		472	459	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988963	41988963	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	66	360	0	ENST00000219905.7:c.1757del	p.Lys586ArgfsTer14	p.K586Rfs*14	ENST00000219905	NM_001164273.1	585	agA/ag	3/24	1	2	FACETS	0.869	0.757	0.99	0.869	0.757	0.99	CLONAL	1	TRUE	1	0.347662212997838	2		360	437	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005391	42005391	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	88	418	0	ENST00000219905.7:c.3127C>T	p.Arg1043Ter	p.R1043*	ENST00000219905	NM_001164273.1	1043	Cga/Tga	9/24	1	2	FACETS	0.952	0.845	1	0.952	0.845	1	CLONAL	1	TRUE	1	0.347662212997838	2		418	532	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252895	36252895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	23	360	0	ENST00000300305.3:c.467C>T	p.Ala156Val	p.A156V	ENST00000300305		156	gCa/gTa	4/8	1	2	FACETS	0.293	0.228	0.369	0.293	0.228	0.369	SUBCLONAL	1	TRUE	1	0.347662212997838	2		360	451	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519629	137519629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776745485	NA	P-0047708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	68	351	0	ENST00000367739.4:c.1009G>A	p.Glu337Lys	p.E337K	ENST00000367739	NM_000416.2	337	Gaa/Aaa	7/7	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.347662212997838	2		351	347	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968138	68968138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	23	477	0	ENST00000288368.4:c.1167G>A	p.Met389Ile	p.M389I	ENST00000288368	NM_024870.2	389	atG/atA	10/40	1	2	FACETS	0.352	0.274	0.442	0.352	0.274	0.442	SUBCLONAL	1	TRUE	1	0.347662212997838	2		477	376	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782130	135782130	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	65	392	0	ENST00000298552.3:c.1426G>A	p.Asp476Asn	p.D476N	ENST00000298552	NM_001162426.1	476	Gat/Aat	14/23	1	2	FACETS	0.956	0.833	1	0.956	0.833	1	CLONAL	1	TRUE	1	0.347662212997838	2		392	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579364	7579364	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	373	942	0	ENST00000269305.4:c.323del	p.Gly108ValfsTer15	p.G108Vfs*15	ENST00000269305	NM_001126112.2	108	gGt/gt	4/11	0.306695201931435	4	FACETS	0.938	0.891	0.985	0.938	0.891	0.985	CLONAL	3	TRUE	1	0.306695201931435	4		942	1130	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942188	17942188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760901179	NA	P-0047709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	67	793	0	ENST00000458235.1:c.2827C>T	p.Arg943Cys	p.R943C	ENST00000458235	NM_000215.3	943	Cgc/Tgc	21/24	0.291930257800913	4	FACETS	0.627	0.544	0.718	0.314	0.272	0.359	SUBCLONAL	1	TRUE	2	0.306695201931435	4		793	910	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436438	52436438	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0047709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	252	673	0	ENST00000460680.1:c.2057-1G>T		p.X686_splice	ENST00000460680	NM_004656.3	686			0.306695201931435	4	FACETS	0.938	0.881	0.996	0.938	0.881	0.996	CLONAL	3	TRUE	1	0.306695201931435	4		673	763	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683534	29683534	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	56	281	0	ENST00000356175.3:c.7609G>A	p.Glu2537Lys	p.E2537K	ENST00000356175	NM_000267.3	2537	Gaa/Aaa	51/57	0.306695201931435	4	FACETS	0.814	0.703	0.934	0.543	0.468	0.623	CLONAL	2	TRUE	1	0.306695201931435	4		281	293	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309869	65309869	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	178	513	0	ENST00000342505.4:c.2281C>G	p.Pro761Ala	p.P761A	ENST00000342505	NM_002227.2	761	Cct/Gct	17/25	0.306695201931435	5	FACETS	0.844	0.781	0.91	0.844	0.781	0.91	CLONAL	3	TRUE	2	0.306695201931435	5		513	669	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351573	89351573	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	74	805	0	ENST00000301030.4:c.1377G>C	p.Lys459Asn	p.K459N	ENST00000301030	NM_001256183.1	459	aaG/aaC	9/13	0.306695201931435	3	FACETS	0.593	0.518	0.675			1	SUBCLONAL	1	TRUE	NA	0.306695201931435	3		805	938	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098355	47098356	+	stop_gained	Nonsense_Mutation	DNP	CA	CA	AT	novel	NA	P-0047709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	143	491	1	ENST00000409792.3:c.6918_6919delinsAT	p.Tyr2306_Gly2307delinsTer	p.Y2306_G2307delins*	ENST00000409792	NM_014159.6	2306	taTGgt/taATgt	15/21	0.306695201931435	4	FACETS	1	0.975	1	0.775	0.711	0.842	CLONAL	2	TRUE	1	0.306695201931435	4		492	524	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349637	89349640	+	missense_variant	Missense_Mutation	ONP	CATC	CATC	AATA	novel	NA	P-0047709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	58	793	1	ENST00000301030.4:c.3310_3313delinsTATT	p.Asp1104_Asp1105delinsTyrTyr	p.D1104_D1105delinsYY	ENST00000301030	NM_001256183.1	1104	GATGac/TATTac	9/13	0.306695201931435	3	FACETS	0.468	0.401	0.542			1	SUBCLONAL	1	TRUE	NA	0.306695201931435	3		794	932	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0047710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	52	566	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.94	0.801	1	0.94	0.801	1	CLONAL	1	TRUE	1	0.224359847999301	2		566	493	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433847	78433848	+	splice_donor_variant	Splice_Site	DEL	AC	AC	-	rs1477051807	NA	P-0047710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	31	231	1	ENST00000370768.2:c.250+1_250+2del		p.X84_splice	ENST00000370768	NM_003902.3	84			1	2	FACETS	0.872	0.707	1	0.872	0.707	1	CLONAL	1	TRUE	1	0.224359847999301	2		232	317	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059242	27059242	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	87	406	0	ENST00000324856.7:c.1879del	p.Asp627IlefsTer2	p.D627Ifs*2	ENST00000324856	NM_006015.4	627	Gat/at	4/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.224359847999301	2		406	680	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608248	28608248	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	72	412	2	ENST00000241453.7:c.1808G>A	p.Trp603Ter	p.W603*	ENST00000241453	NM_004119.2	603	tGg/tAg	14/24	1	2	FACETS	0.989	0.864	1	0.989	0.864	1	CLONAL	1	TRUE	1	0.224359847999301	2		414	649	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579343	7579346	+	frameshift_variant	Frame_Shift_Del	DEL	TGCA	TGCA	GC	novel	NA	P-0047710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	135	657	0	ENST00000269305.4:c.341_344delinsGC	p.Leu114CysfsTer34	p.L114Cfs*34	ENST00000269305	NM_001126112.2	114	tTGCAt/tGCt	4/11	0.224359847999301	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.224359847999301	1		657	890	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0047711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	304	424	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	1	2	FACETS	0.922	0.873	0.972	0.922	0.873	0.972	CLONAL	1	TRUE	1	0.82133960061005	2		424	803	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0047711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	114	269	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.938	0.857	1	0.938	0.857	1	CLONAL	1	TRUE	1	0.82133960061005	2		269	296	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553402	41553402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	105	228	2	ENST00000263253.7:c.3491G>A	p.Cys1164Tyr	p.C1164Y	ENST00000263253	NM_001429.3	1164	tGt/tAt	18/31	1	2	FACETS	0.847	0.769	0.927	0.847	0.769	0.927	CLONAL	1	TRUE	1	0.82133960061005	2		230	302	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670324	134670324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775406650	NA	P-0047711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	292	332	0	ENST00000398015.3:c.235C>T	p.Arg79Trp	p.R79W	ENST00000398015	NM_004441.4	79	Cgg/Tgg	3/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.82133960061005	2		332	665	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441780	49441780	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555195442	NA	P-0047711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	395	490	0	ENST00000301067.7:c.4204C>T	p.Gln1402Ter	p.Q1402*	ENST00000301067	NM_003482.3	1402	Cag/Tag	14/54	1	2	FACETS	0.961	0.916	1	0.961	0.916	1	CLONAL	1	TRUE	1	0.82133960061005	2		490	1001	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220094	133220094	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs150545516	NA	P-0047711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	434	600	1	ENST00000320574.5:c.4343A>G	p.Asn1448Ser	p.N1448S	ENST00000320574	NM_006231.2	1448	aAt/aGt	34/49	1	2	FACETS	0.957	0.915	1	0.957	0.915	1	CLONAL	1	TRUE	1	0.82133960061005	2		601	1104	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026603	6026603	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	450	685	0	ENST00000265849.7:c.1793A>C	p.Gln598Pro	p.Q598P	ENST00000265849	NM_000535.5	598	cAg/cCg	11/15	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.82133960061005	2		685	1068	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578264	7578275	+	frameshift_variant	Frame_Shift_Del	DEL	GATAAGATGCTG	GATAAGATGCTG	CATA	novel	NA	P-0047711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	321	510	2	ENST00000269305.4:c.574_585delinsTATG	p.Gln192TyrfsTer14	p.Q192Yfs*14	ENST00000269305	NM_001126112.2	192	CAGCATCTTATC/TATG	6/11	1	2	FACETS	0.967	0.918	1	0.967	0.918	1	CLONAL	1	TRUE	1	0.82133960061005	2		512	808	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0047712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	198	259	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.472008338880999	3	FACETS	0.956	0.892	1	0.956	0.892	1	CLONAL	2	TRUE	1	0.4769195945353	3		259	538	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220703	1220703	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	202	689	0	ENST00000326873.7:c.721G>C	p.Ala241Pro	p.A241P	ENST00000326873	NM_000455.4	241	Gct/Cct	5/10	0.4769195945353	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.4769195945353	1		689	620	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073488	8073492	+	frameshift_variant	Frame_Shift_Del	DEL	AACTA	AACTA	-	novel	NA	P-0047712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	129	240	0	ENST00000377482.5:c.1167_1171del	p.Ser390AsnfsTer8	p.S390Nfs*8	ENST00000377482	NM_018948.3	389	gtTAGTTca/gtca	4/4	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.4769195945353	2		240	465	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367541	40367541	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	16	37	0	ENST00000397332.2:c.20G>T	p.Cys7Phe	p.C7F	ENST00000397332	NM_001033082.2	7	tGc/tTc	1/3	1	2	FACETS	0.799	0.62	0.988	1	0.919	1	CLONAL	2	TRUE	1	0.4769195945353	2		37	42	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121799	108121799	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	119	200	0	ENST00000278616.4:c.1607+1del		p.C536fs	ENST00000278616	NM_000051.3	536	tGt/tt	10/63	0.420557609049678	2	FACETS	0.761	0.696	0.828	0.761	0.696	0.828	SUBCLONAL	2	TRUE	0	0.4769195945353	2		200	328	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265153	46265154	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0047712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	62	216	0	ENST00000371998.3:c.2023_2024delinsCT	p.Gly675Leu	p.G675L	ENST00000371998		675	GGg/CTg	12/23	0.273428277566124	1	FACETS	0.667	0.58	0.759	0.667	0.58	0.759	INDETERMINATE	1	TRUE	0	0.4769195945353	1		216	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0047713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	126	646	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	NA	3	FACETS	1	0.957	1			1	INDETERMINATE	1	TRUE	NA	0.349678949062247	3		646	771	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0047713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	79	282	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	0.119350324530211	4	FACETS	0.95	0.843	1	0.475	0.421	0.531	INDETERMINATE	2	TRUE	0	0.349678949062247	4		282	321	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934022	49934022	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	106	610	0	ENST00000296474.3:c.2390G>T	p.Trp797Leu	p.W797L	ENST00000296474	NM_002447.2	797	tGg/tTg	9/20	1	2	FACETS	0.737	0.66	0.818	0.737	0.66	0.818	SUBCLONAL	1	TRUE	1	0.349678949062247	2		610	823	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928067	178928067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	108	340	0	ENST00000263967.3:c.1345C>T	p.Pro449Ser	p.P449S	ENST00000263967	NM_006218.2	449	Cct/Tct	8/21	0.119350324530211	4	FACETS	0.963	0.87	1	0.481	0.435	0.53	INDETERMINATE	2	TRUE	0	0.349678949062247	4		340	433	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803678	1803678	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	145	838	0	ENST00000260795.2:c.856C>A	p.Gln286Lys	p.Q286K	ENST00000260795		286	Cag/Aag	6/17	0.120211998846638	5	FACETS	1	0.941	1			1	INDETERMINATE	1	TRUE	NA	0.349678949062247	5		838	1212	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683673	162683673	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1443653639	NA	P-0047713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	117	510	0	ENST00000366898.1:c.296C>A	p.Pro99His	p.P99H	ENST00000366898	NM_004562.2	99	cCc/cAc	3/12	1	2	FACETS	0.99	0.894	1	0.99	0.894	1	CLONAL	1	TRUE	1	0.349678949062247	2		510	676	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117218	7117218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1432736648	NA	P-0047713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	111	597	0	ENST00000302850.5:c.3998C>T	p.Ser1333Leu	p.S1333L	ENST00000302850	NM_000208.2	1333	tCg/tTg	22/22	1	2	FACETS	0.843	0.758	0.933	0.843	0.758	0.933	CLONAL	1	TRUE	1	0.349678949062247	2		597	753	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518509	69518509	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	86	640	0	ENST00000294312.3:c.136C>A	p.His46Asn	p.H46N	ENST00000294312	NM_005117.2	46	Cac/Aac	1/3	0.32021814071715	3	FACETS	0.673	0.594	0.757	0.336	0.297	0.379	SUBCLONAL	1	TRUE	1	0.349678949062247	3		640	859	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684323	29684323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	40	343	1	ENST00000356175.3:c.7843C>A	p.Gln2615Lys	p.Q2615K	ENST00000356175	NM_000267.3	2615	Caa/Aaa	53/57	0.349678949062247	1	FACETS	0.658	0.549	0.777	0.658	0.549	0.777	SUBCLONAL	1	TRUE	0	0.349678949062247	1		344	287	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140166	50140166	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	108	558	0	ENST00000246792.3:c.259C>A	p.Gln87Lys	p.Q87K	ENST00000246792	NM_006270.3	87	Cag/Aag	3/6	1	2	FACETS	0.879	0.789	0.973	0.879	0.789	0.973	CLONAL	1	TRUE	1	0.349678949062247	2		558	703	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150022963	150022963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	49	361	0	ENST00000253339.5:c.300del	p.Val101LeufsTer31	p.V101Lfs*31	ENST00000253339		100	gaA/ga	1/7	1	2	FACETS	0.789	0.671	0.919	0.789	0.671	0.919	CLONAL	1	TRUE	1	0.349678949062247	2		361	355	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0047714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	531	566	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.68060689680346	4	FACETS	0.909	0.88	0.938	0.909	0.88	0.938	CLONAL	3	TRUE	1	0.8404040881088	4		566	853	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587782272	NA	P-0047714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	403	267	0	ENST00000269305.4:c.994-1G>C		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.828708240920324	1	FACETS	0.976	0.944	1	0.976	0.944	1	CLONAL	1	TRUE	0	0.8404040881088	1		267	570	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642499	117642499	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs757333668	NA	P-0047714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	185	341	0	ENST00000368508.3:c.5700A>G	p.Ile1900Met	p.I1900M	ENST00000368508	NM_002944.2	1900	atA/atG	35/43	0.8404040881088	1	FACETS	0.502	0.467	0.537	0.502	0.467	0.537	SUBCLONAL	1	TRUE	0	0.8404040881088	1		341	509	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	23	703	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.1	0.078	0.127	0.1	0.078	0.127	SUBCLONAL	1	TRUE	1	0.641442494615711	2		703	714	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	225	570	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.641442494615711	2		571	684	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	289	619	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.641442494615711	2		619	899	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513482	149513482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	197	490	0	ENST00000261799.4:c.721G>A	p.Glu241Lys	p.E241K	ENST00000261799	NM_002609.3	241	Gag/Aag	5/23	1	2	FACETS	0.917	0.853	0.983	0.917	0.853	0.983	CLONAL	1	TRUE	1	0.641442494615711	2		490	670	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250867	153250867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	85	269	0	ENST00000281708.4:c.1193C>T	p.Ser398Phe	p.S398F	ENST00000281708	NM_033632.3	398	tCt/tTt	8/12	NA	2	FACETS	1	0.933	1			1	INDETERMINATE	1	TRUE	NA	0.641442494615711	2		269	252	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935641	49935641	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs191131637	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	245	528	0	ENST00000296474.3:c.1723C>T	p.His575Tyr	p.H575Y	ENST00000296474	NM_002447.2	575	Cac/Tac	5/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.641442494615711	2		528	731	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913471	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	312	729	0	ENST00000269571.5:c.2329G>A	p.Val777Met	p.V777M	ENST00000269571		777	Gtg/Atg	20/27	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.641442494615711	2		729	856	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80646085	80646085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	89	162	0	ENST00000286548.4:c.67G>A	p.Asp23Asn	p.D23N	ENST00000286548	NM_002072.3	23	Gac/Aac	1/7	0.31008297586096	2	FACETS	1	0.982	1	0.712	0.646	0.778	INDETERMINATE	1	TRUE	0	0.641442494615711	2		162	195	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564773	86564773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	244	594	0	ENST00000274376.6:c.505G>A	p.Val169Met	p.V169M	ENST00000274376	NM_002890.2	169	Gtg/Atg	1/25	1	2	FACETS	0.993	0.932	1	0.993	0.932	1	CLONAL	1	TRUE	1	0.641442494615711	2		594	766	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	293	630	0	ENST00000269571.5:c.829G>A	p.Asp277Asn	p.D277N	ENST00000269571		277	Gac/Aac	7/27	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.641442494615711	2		630	768	SUCCESS
AR	367	MSKCC	GRCh37	X	66765229	66765229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	107	191	0	ENST00000374690.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000374690	NM_000044.3	81	Gag/Aag	1/8	1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.641442494615711	1		191	189	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878910	117878910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	150	296	0	ENST00000297338.2:c.59C>T	p.Ala20Val	p.A20V	ENST00000297338	NM_006265.2	20	gCg/gTg	2/14	1	2	FACETS	0.968	0.892	1	0.968	0.892	1	CLONAL	1	TRUE	1	0.641442494615711	2		296	483	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019961	123019961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	235	251	1	ENST00000355640.3:c.449C>T	p.Ser150Leu	p.S150L	ENST00000355640		150	tCa/tTa	2/7	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.641442494615711	1		252	354	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742483	17742483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs922852099	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	251	657	1	ENST00000250003.3:c.665G>A	p.Arg222Gln	p.R222Q	ENST00000250003	NM_002478.4	222	cGg/cAg	2/3	0.641442494615711	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.641442494615711	1		658	500	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249510	153249510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	77	347	0	ENST00000281708.4:c.1268G>A	p.Gly423Glu	p.G423E	ENST00000281708	NM_033632.3	423	gGa/gAa	9/12	NA	2	FACETS	0.619	0.546	0.696			1	INDETERMINATE	1	TRUE	NA	0.641442494615711	2		347	388	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885161	111885161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748009957	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	435	554	0	ENST00000341259.2:c.1049C>T	p.Pro350Leu	p.P350L	ENST00000341259	NM_005475.2	350	cCg/cTg	6/8	0.641442494615711	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.641442494615711	2		554	675	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754908	29754908	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	189	406	0	ENST00000389048.3:c.1027G>A	p.Glu343Lys	p.E343K	ENST00000389048	NM_004304.4	343	Gag/Aag	4/29	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.641442494615711	2		406	578	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777742	3777742	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	348	730	0	ENST00000262367.5:c.7306G>C	p.Glu2436Gln	p.E2436Q	ENST00000262367	NM_004380.2	2436	Gag/Cag	31/31	1	2	FACETS	0.964	0.913	1	0.964	0.913	1	CLONAL	1	TRUE	1	0.641442494615711	2		730	1126	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082749	16082749	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	49	113	0	ENST00000281043.3:c.563A>C	p.Asp188Ala	p.D188A	ENST00000281043	NM_005378.4	188	gAt/gCt	2/3	1	2	FACETS	0.698	0.598	0.805	0.698	0.598	0.805	SUBCLONAL	1	TRUE	1	0.641442494615711	2		113	219	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105782	27105782	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	147	312	0	ENST00000324856.7:c.5393C>A	p.Ser1798Ter	p.S1798*	ENST00000324856	NM_006015.4	1798	tCa/tAa	20/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.641442494615711	2		312	402	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742868	17742880	+	frameshift_variant	Frame_Shift_Del	DEL	TCTCCACCGAGAG	TCTCCACCGAGAG	-	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	246	784	0	ENST00000250003.3:c.776_788del	p.Ile259ThrfsTer73	p.I259Tfs*73	ENST00000250003	NM_002478.4	259	aTCTCCACCGAGAGc/ac	3/3	0.641442494615711	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.641442494615711	1		784	516	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378630	25378630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	105	274	0	ENST00000311936.3:c.368G>A	p.Arg123Lys	p.R123K	ENST00000311936	NM_004985.3	123	aGa/aAa	4/5	0.225312291556398	1	FACETS	0.658	0.596	0.722	0.658	0.596	0.722	INDETERMINATE	1	TRUE	0	0.641442494615711	1		274	338	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959381	26959382	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	128	259	0	ENST00000381527.3:c.551dup	p.Leu184PhefsTer20	p.L184Ffs*20	ENST00000381527	NM_001260.1	183	cct/ccTt	6/13	0.372308922998466	1	FACETS	0.795	0.73	0.862	0.795	0.73	0.862	INDETERMINATE	1	TRUE	0	0.641442494615711	1		259	341	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931780	28931780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	76	314	0	ENST00000282397.4:c.2159G>A	p.Arg720Lys	p.R720K	ENST00000282397	NM_002019.4	720	aGa/aAa	15/30	0.372308922998466	1	FACETS	0.421	0.372	0.474	0.421	0.372	0.474	INDETERMINATE	1	TRUE	0	0.641442494615711	1		314	382	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643466	38643466	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	102	356	0	ENST00000299084.4:c.936G>C	p.Lys312Asn	p.K312N	ENST00000299084	NM_152594.2	312	aaG/aaC	7/7	0.225312291556398	1	FACETS	0.523	0.471	0.578	0.523	0.471	0.578	INDETERMINATE	1	TRUE	0	0.641442494615711	1		356	413	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303920	91303920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	105	388	1	ENST00000355112.3:c.1317G>A	p.Met439Ile	p.M439I	ENST00000355112	NM_000057.2	439	atG/atA	7/22	0.225312291556398	1	FACETS	0.496	0.447	0.548	0.496	0.447	0.548	INDETERMINATE	1	TRUE	0	0.641442494615711	1		389	448	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3824629	3824629	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	193	467	0	ENST00000262367.5:c.2224C>G	p.Arg742Gly	p.R742G	ENST00000262367	NM_004380.2	742	Cgt/Ggt	12/31	1	2	FACETS	0.967	0.9	1	0.967	0.9	1	CLONAL	1	TRUE	1	0.641442494615711	2		467	622	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004925	16004925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	281	512	0	ENST00000268712.3:c.2329G>A	p.Asp777Asn	p.D777N	ENST00000268712	NM_006311.3	777	Gat/Aat	20/46	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.641442494615711	2		512	769	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135006	11135006	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs10401806	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	193	471	0	ENST00000358026.2:c.2974-1G>A		p.X992_splice	ENST00000358026	NM_001128849.1	992			0.372308922998466	1	FACETS	0.795	0.742	0.849	0.795	0.742	0.849	INDETERMINATE	1	TRUE	0	0.641442494615711	1		471	514	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629108	14629108	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	92	432	0	ENST00000254322.2:c.54G>T	p.Glu18Asp	p.E18D	ENST00000254322	NM_006145.1	18	gaG/gaT	1/3	0.372308922998466	1	FACETS	0.416	0.371	0.464	0.416	0.371	0.464	INDETERMINATE	1	TRUE	0	0.641442494615711	1		432	468	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872375	45872375	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	295	609	0	ENST00000391945.4:c.136A>T	p.Thr46Ser	p.T46S	ENST00000391945	NM_000400.3	46	Acc/Tcc	3/23	0.641442494615711	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.641442494615711	1		609	589	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61708412	61708412	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	84	183	0	ENST00000401558.2:c.2977C>A	p.Gln993Lys	p.Q993K	ENST00000401558	NM_003400.3	993	Caa/Aaa	24/25	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.641442494615711	2		183	247	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728693	190728693	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	67	222	0	ENST00000441310.2:c.2081T>G	p.Ile694Ser	p.I694S	ENST00000441310	NM_000534.4	694	aTt/aGt	10/13	1	2	FACETS	0.937	0.826	1	0.937	0.826	1	CLONAL	1	TRUE	1	0.641442494615711	2		222	223	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495226	212495226	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	103	317	0	ENST00000342788.4:c.2040C>G	p.Ile680Met	p.I680M	ENST00000342788	NM_005235.2	680	atC/atG	17/28	1	2	FACETS	0.89	0.804	0.979	0.89	0.804	0.979	CLONAL	1	TRUE	1	0.641442494615711	2		317	361	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794896	242794896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	299	719	0	ENST00000334409.5:c.313G>A	p.Asp105Asn	p.D105N	ENST00000334409	NM_005018.2	105	Gac/Aac	2/5	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.641442494615711	2		719	835	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180454	38180454	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	260	601	2	ENST00000396334.3:c.302G>A	p.Arg101Gln	p.R101Q	ENST00000396334	NM_002468.4	101	cGa/cAa	1/5	1	2	FACETS	0.987	0.928	1	0.987	0.928	1	CLONAL	1	TRUE	1	0.641442494615711	2		603	821	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428401	72428401	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	135	390	0	ENST00000477973.2:c.600+1G>A		p.X200_splice	ENST00000477973	NM_012234.5	200			1	2	FACETS	0.907	0.831	0.986	0.907	0.831	0.986	CLONAL	1	TRUE	1	0.641442494615711	2		390	464	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444642	187444642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	210	457	0	ENST00000232014.4:c.1585G>A	p.Glu529Lys	p.E529K	ENST00000232014	NM_001130845.1	529	Gag/Aag	7/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.641442494615711	2		457	625	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467626	66467626	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1044929860	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	102	211	0	ENST00000273854.3:c.643C>G	p.Gln215Glu	p.Q215E	ENST00000273854	NM_004439.5	215	Caa/Gaa	3/18	0.372308922998466	1	FACETS	0.871	0.793	0.95	0.871	0.793	0.95	INDETERMINATE	1	TRUE	0	0.641442494615711	1		211	248	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540036	187540037	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	124	307	0	ENST00000441802.2:c.7702_7703dup	p.Leu2568PhefsTer2	p.L2568Ffs*2	ENST00000441802	NM_005245.3	2568	tta/ttTTa	10/27	0.641442494615711	1	FACETS	0.893	0.822	0.966	0.893	0.822	0.966	CLONAL	1	TRUE	0	0.641442494615711	1		307	294	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950244	38950244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	124	337	0	ENST00000357387.3:c.3706C>T	p.Pro1236Ser	p.P1236S	ENST00000357387	NM_152756.3	1236	Cct/Tct	31/38	1	2	FACETS	0.943	0.861	1	0.943	0.861	1	CLONAL	1	TRUE	1	0.641442494615711	2		337	410	SUCCESS
APC	324	MSKCC	GRCh37	5	112162907	112162907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	94	283	0	ENST00000257430.4:c.1511C>T	p.Ala504Val	p.A504V	ENST00000257430	NM_000038.5	504	gCt/gTt	12/16	1	2	FACETS	0.98	0.883	1	0.98	0.883	1	CLONAL	1	TRUE	1	0.641442494615711	2		283	299	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433930	149433930	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	293	705	0	ENST00000286301.3:c.2718C>G	p.Ile906Met	p.I906M	ENST00000286301	NM_005211.3	906	atC/atG	21/22	1	2	FACETS	0.984	0.929	1	0.984	0.929	1	CLONAL	1	TRUE	1	0.641442494615711	2		705	928	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513518	149513518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	212	486	0	ENST00000261799.4:c.685G>A	p.Glu229Lys	p.E229K	ENST00000261799	NM_002609.3	229	Gag/Aag	5/23	1	2	FACETS	0.974	0.909	1	0.974	0.909	1	CLONAL	1	TRUE	1	0.641442494615711	2		486	679	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176563006	176563006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	117	239	0	ENST00000439151.2:c.902C>T	p.Ser301Leu	p.S301L	ENST00000439151	NM_022455.4	301	tCa/tTa	2/23	1	2	FACETS	0.914	0.832	1	0.914	0.832	1	CLONAL	1	TRUE	1	0.641442494615711	2		239	399	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198228	138198228	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	59	153	0	ENST00000237289.4:c.821C>G	p.Pro274Arg	p.P274R	ENST00000237289	NM_001270507.1	274	cCa/cGa	6/9	1	2	FACETS	0.92	0.804	1	0.92	0.804	1	CLONAL	1	TRUE	1	0.641442494615711	2		153	200	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335714	81335714	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1178057695	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	83	217	0	ENST00000222390.5:c.1646G>C	p.Gly549Ala	p.G549A	ENST00000222390	NM_000601.4	549	gGa/gCa	15/18	1	2	FACETS	0.883	0.788	0.982	0.883	0.788	0.982	CLONAL	1	TRUE	1	0.641442494615711	2		217	293	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859557	151859557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	135	352	0	ENST00000262189.6:c.11105C>T	p.Ser3702Leu	p.S3702L	ENST00000262189	NM_170606.2	3702	tCa/tTa	43/59	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.641442494615711	2		352	415	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295166	1295168	+	upstream_gene_variant	5'Flank	TNP	CTC	CTC	ATG	novel	NA	P-0047715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	103	299	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.923	0.834	1	0.923	0.834	1	CLONAL	1	TRUE	1	0.641442494615711	2		299	348	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0047716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	47	208	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	NA	2	FACETS	1	0.934	1			1	INDETERMINATE	1	FALSE	NA	0.398858225865927	2		208	201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0047716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	229	698	1	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	0.188412010207976	3	FACETS	0.954	0.893	1	0.636	0.595	0.678	INDETERMINATE	2	FALSE	0	0.398858225865927	3		699	722	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0047716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	25	189	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	NA	2	FACETS	0.64	0.507	0.789			1	INDETERMINATE	1	FALSE	NA	0.398858225865927	2		189	196	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209050	133209050	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs773908359	NA	P-0047716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	39	452	0	ENST00000320574.5:c.6181C>G	p.Gln2061Glu	p.Q2061E	ENST00000320574	NM_006231.2	2061	Cag/Gag	45/49	0.283461758487561	3	FACETS	0.564	0.468	0.671	0.282	0.234	0.336	SUBCLONAL	1	FALSE	1	0.398858225865927	3		452	416	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090428	37090428	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	117	363	0	ENST00000231790.2:c.2023A>G	p.Ser675Gly	p.S675G	ENST00000231790	NM_000249.3	675	Agc/Ggc	18/19	0.321482748736486	5	FACETS	0.927	0.84	1	0.618	0.56	0.678	CLONAL	2	FALSE	2	0.398858225865927	5		363	506	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213902	66213902	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	18	305	1	ENST00000273854.3:c.2528G>T	p.Arg843Ile	p.R843I	ENST00000273854	NM_004439.5	843	aGa/aTa	15/18	0.404651819075982	0	FACETS	0.577	0.442	0.73			1	SUBCLONAL	1	FALSE	0	0.398858225865927	0		306	94	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0047719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	487	432	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.855504585777704	6	FACETS	1	0.966	1	0.666	0.644	0.688	CLONAL	4	TRUE	0	0.855504585777704	6		432	772	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0047719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	147	249	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.855504585777704	3	FACETS	0.977	0.915	1	0.977	0.915	1	CLONAL	2	TRUE	1	0.855504585777704	3		249	251	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0047719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	1316	838	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.855504585777704	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	4	TRUE	0	0.855504585777704	4		838	1417	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039583	180039583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs75614493	NA	P-0047719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	276	784	1	ENST00000261937.6:c.3460G>A	p.Gly1154Arg	p.G1154R	ENST00000261937	NM_182925.4	1154	Gga/Aga	26/30	0.658305256944998	4	FACETS	1	0.956	1	0.511	0.479	0.544	CLONAL	1	TRUE	2	0.855504585777704	4		785	1171	SUCCESS
APC	324	MSKCC	GRCh37	5	112175366	112175366	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs863225352	NA	P-0047719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	63	173	0	ENST00000257430.4:c.4075A>T	p.Lys1359Ter	p.K1359*	ENST00000257430	NM_000038.5	1359	Aaa/Taa	16/16	0.717248777473938	3	FACETS	0.922	0.809	1	0.461	0.404	0.521	CLONAL	1	TRUE	1	0.855504585777704	3		173	228	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546574	9546574	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs991533102	NA	P-0047719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	202	320	0	ENST00000353224.5:c.1448G>A	p.Arg483Gln	p.R483Q	ENST00000353224	NM_177990.2	483	cGg/cAg	5/10	0.825031039502357	4	FACETS	0.885	0.829	0.942			1	CLONAL	2	TRUE	NA	0.855504585777704	4		320	495	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692965	89692965	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	103	374	1	ENST00000371953.3:c.449A>T	p.Glu150Val	p.E150V	ENST00000371953	NM_000314.4	150	gAg/gTg	5/9	0.658305256944998	4	FACETS	1	0.925	1	0.516	0.464	0.57	CLONAL	1	TRUE	2	0.855504585777704	4		375	433	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108105	30108105	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	93	321	0	ENST00000331968.5:c.702A>T	p.Lys234Asn	p.K234N	ENST00000331968	NM_002742.2	234	aaA/aaT	5/18	0.853510026893543	3	FACETS	0.97	0.872	1	0.323	0.29	0.358	CLONAL	1	TRUE	0	0.855504585777704	3		321	320	SUCCESS
APC	324	MSKCC	GRCh37	5	112174170	112174170	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	99	212	0	ENST00000257430.4:c.2879C>A	p.Ser960Ter	p.S960*	ENST00000257430	NM_000038.5	960	tCa/tAa	16/16	0.717248777473938	3	FACETS	0.989	0.913	1	0.989	0.913	1	CLONAL	2	TRUE	1	0.855504585777704	3		212	167	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	158	349	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.60702411608622	2		350	507	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0047720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	164	277	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.60702411608622	2		277	469	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0047720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	209	270	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.60702411608622	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.60702411608622	2		270	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577508	7577508	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060501201	NA	P-0047720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	300	534	0	ENST00000269305.4:c.773A>G	p.Glu258Gly	p.E258G	ENST00000269305	NM_001126112.2	258	gAa/gGa	7/11	0.60702411608622	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.60702411608622	1		534	554	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453132	140453132	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913365	NA	P-0047720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	129	228	0	ENST00000288602.6:c.1803A>C	p.Lys601Asn	p.K601N	ENST00000288602	NM_004333.4	601	aaA/aaC	15/18	0.392804482982091	3	FACETS	1	0.969	1	0.568	0.518	0.62	CLONAL	1	TRUE	1	0.60702411608622	3		228	488	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562670	21562670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	332	682	1	ENST00000382592.4:c.1249G>A	p.Gly417Ser	p.G417S	ENST00000382592	NM_014572.2	417	Ggt/Agt	4/8	0.60702411608622	2	FACETS	1	0.994	1	0.661	0.628	0.695	CLONAL	1	TRUE	0	0.60702411608622	2		683	827	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665024	138665024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	73	172	0	ENST00000330315.3:c.541G>A	p.Ala181Thr	p.A181T	ENST00000330315	NM_023067.3	181	Gcc/Acc	1/1	NA	2	FACETS	0.824	0.728	0.925			1	INDETERMINATE	1	TRUE	NA	0.60702411608622	2		172	292	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0047721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	222	371	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.40773586747234	2	FACETS	0.994	0.933	1	0.994	0.933	1	CLONAL	2	TRUE	0	0.41	2		371	545	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591085	67591085	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519839	NA	P-0047721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	55	201	0	ENST00000274335.5:c.1678G>T	p.Asp560Tyr	p.D560Y	ENST00000274335		560	Gac/Tac	12/15	1	2	FACETS	0.932	0.803	1	0.932	0.803	1	CLONAL	1	TRUE	1	0.41	2		201	288	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101005	27101005	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	174	636	1	ENST00000324856.7:c.4288del	p.Gln1430SerfsTer51	p.Q1430Sfs*51	ENST00000324856	NM_006015.4	1429	aaC/aa	18/20	1	2	FACETS	0.821	0.755	0.89	0.821	0.755	0.89	CLONAL	1	TRUE	1	0.41	2		637	1034	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256891	16256892	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0047721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	131	511	0	ENST00000375759.3:c.4158_4159dup	p.Glu1387ValfsTer23	p.E1387Vfs*23	ENST00000375759	NM_015001.2	1386	ggt/gGTgt	11/15	1	2	FACETS	0.805	0.731	0.883	0.805	0.731	0.883	CLONAL	1	TRUE	1	0.41	2		511	794	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101146	27101146	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	202	688	0	ENST00000324856.7:c.4428del	p.Met1476IlefsTer5	p.M1476Ifs*5	ENST00000324856	NM_006015.4	1476	atG/at	18/20	1	2	FACETS	0.906	0.839	0.975	0.906	0.839	0.975	CLONAL	1	TRUE	1	0.41	2		688	1088	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103520549	103520549	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	53	222	0	ENST00000355739.4:c.2620G>T	p.Ala874Ser	p.A874S	ENST00000355739	NM_000123.3	874	Gcc/Tcc	12/15	1	2	FACETS	0.728	0.624	0.842	0.728	0.624	0.842	SUBCLONAL	1	TRUE	1	0.41	2		222	355	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39573277	39573277	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	77	300	0	ENST00000262039.4:c.758T>C	p.Val253Ala	p.V253A	ENST00000262039	NM_002647.2	253	gTg/gCg	7/25	1	2	FACETS	0.986	0.871	1	0.986	0.871	1	CLONAL	1	TRUE	1	0.41	2		300	381	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589619	67589620	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGAATATGATAGATT	novel	NA	P-0047721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	29	164	0	ENST00000274335.5:c.1384_1398dup	p.Glu462_Leu466dup	p.E462_L466dup	ENST00000274335		462	cga/cgAGAATATGATAGATTa	10/15	1	2	FACETS	0.605	0.488	0.736	0.605	0.488	0.736	SUBCLONAL	1	TRUE	1	0.41	2		164	234	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966020	18966020	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	92	669	0	ENST00000262803.5:c.1513A>G	p.Ile505Val	p.I505V	ENST00000262803	NM_002911.3	505	Atc/Gtc	11/24	0.432460551570624	3	FACETS	0.972	0.868	1	0.324	0.289	0.361	CLONAL	1	TRUE	0	0.522218829047029	3		669	457	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812204	43812204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs751975712	NA	P-0047732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	72	552	0	ENST00000372470.3:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000372470	NM_005373.2	357	Cga/Tga	7/12	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.285646267839545	2		552	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0047732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	136	576	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.285646267839545	2	FACETS	0.856	0.782	0.933	0.856	0.782	0.933	CLONAL	2	TRUE	0	0.285646267839545	2		576	556	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216497	36216497	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568374133	NA	P-0047732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	59	1015	0	ENST00000222270.7:c.3760G>A	p.Val1254Ile	p.V1254I	ENST00000222270	NM_014727.1	1254	Gtc/Atc	12/37	0.285646267839545	3	FACETS	0.535	0.459	0.618	0.267	0.229	0.309	SUBCLONAL	1	TRUE	1	0.285646267839545	3		1015	883	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0047737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	38	643	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.366441799240218	1	FACETS	0.221	0.181	0.265	0.221	0.181	0.265	SUBCLONAL	1	TRUE	0	0.366441799240218	1		643	768	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937984	76937984	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373581602	NA	P-0047737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	17	248	0	ENST00000373344.5:c.2764G>A	p.Asp922Asn	p.D922N	ENST00000373344	NM_000489.3	922	Gat/Aat	9/35	1	1	FACETS	0.268	0.199	0.349	0.268	0.199	0.349	SUBCLONAL	1	TRUE	0	0.366441799240218	1		248	283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0047737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	208	743	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.366441799240218	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.366441799240218	1		743	857	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729688	41729688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	155	671	1	ENST00000242208.4:c.841G>A	p.Ala281Thr	p.A281T	ENST00000242208	NM_002192.2	281	Gca/Aca	3/3	1	2	FACETS	0.926	0.847	1	0.926	0.847	1	CLONAL	1	TRUE	1	0.366441799240218	2		672	914	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775242	73775242	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	76	598	0	ENST00000254810.4:c.14A>T	p.Lys5Met	p.K5M	ENST00000254810	NM_005324.3	5	aAg/aTg	2/4	1	2	FACETS	0.548	0.48	0.621	0.548	0.48	0.621	SUBCLONAL	1	TRUE	1	0.366441799240218	2		598	757	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250428	10250428	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	84	655	0	ENST00000340748.4:c.3824A>G	p.Lys1275Arg	p.K1275R	ENST00000340748		1275	aAg/aGg	33/40	0.155332985008198	3	FACETS	0.594	0.523	0.669	0.198	0.174	0.223	INDETERMINATE	1	TRUE	0	0.366441799240218	3		655	914	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102067	27102067	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0047737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	27	486	0	ENST00000324856.7:c.4994-1G>A		p.X1665_splice	ENST00000324856	NM_006015.4	1665			0.289292322725052	2	FACETS	0.273	0.217	0.339	0.137	0.108	0.17	SUBCLONAL	1	TRUE	0	0.366441799240218	2		486	539	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523027	25523027	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	91	947	0	ENST00000264709.3:c.158G>A	p.Arg53Lys	p.R53K	ENST00000264709	NM_175629.2	53	aGg/aAg	3/23	1	2	FACETS	0.4	0.354	0.45	0.4	0.354	0.45	SUBCLONAL	1	TRUE	1	0.366441799240218	2		947	1242	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201689	66201689	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	106	417	0	ENST00000273854.3:c.2813A>C	p.Asn938Thr	p.N938T	ENST00000273854	NM_004439.5	938	aAc/aCc	16/18	0.366441799240218	1	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	0	0.366441799240218	1		417	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0047739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	454	712	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.63956297937252	3	FACETS	0.983	0.955	1	0.983	0.955	1	CLONAL	3	TRUE	0	0.664520493442989	3		712	617	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0047739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	80	267	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.657640627055389	2	FACETS	0.872	0.797	0.946	0.872	0.797	0.946	CLONAL	2	TRUE	0	0.664520493442989	2		267	138	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535403	66535403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	69	469	0	ENST00000273854.3:c.58G>A	p.Asp20Asn	p.D20N	ENST00000273854	NM_004439.5	20	Gac/Aac	1/18	0.664520493442989	3	FACETS	0.974	0.857	1	0.487	0.428	0.549	CLONAL	1	TRUE	1	0.664520493442989	3		469	284	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178578	32178578	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	207	749	0	ENST00000375023.3:c.2816G>T	p.Cys939Phe	p.C939F	ENST00000375023	NM_004557.3	939	tGc/tTc	18/30	0.436930041209931	6	FACETS	1	0.937	1	0.503	0.468	0.539	CLONAL	2	TRUE	2	0.664520493442989	6		749	721	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	125	349	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.974	0.892	1	0.974	0.892	1	CLONAL	1	FALSE	1	0.708865201028139	2		350	362	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0047741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	244	703	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA	2	FACETS	0.914	0.858	0.972			1	INDETERMINATE	1	FALSE	NA	0.708865201028139	2		703	753	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057727	27057727	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	269	636	0	ENST00000324856.7:c.1435C>T	p.Gln479Ter	p.Q479*	ENST00000324856	NM_006015.4	479	Cag/Tag	3/20	1	2	FACETS	0.899	0.846	0.954	0.899	0.846	0.954	CLONAL	1	FALSE	1	0.708865201028139	2		636	844	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138158	64138158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747011048	NA	P-0047741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	410	863	0	ENST00000334205.4:c.2081C>T	p.Ser694Phe	p.S694F	ENST00000334205	NM_003942.2	694	tCt/tTt	16/17	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.708865201028139	2		863	1127	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852733	63852733	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	93	421	0	ENST00000279873.7:c.3511C>G	p.Gln1171Glu	p.Q1171E	ENST00000279873	NM_032199.2	1171	Caa/Gaa	10/10	1	2	FACETS	0.455	0.405	0.508	0.455	0.405	0.508	SUBCLONAL	1	FALSE	1	0.708865201028139	2		421	577	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204859	94204859	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	64	367	0	ENST00000323929.3:c.726C>G	p.Ile242Met	p.I242M	ENST00000323929	NM_005591.3	242	atC/atG	8/20	1	2	FACETS	0.612	0.534	0.695	0.612	0.534	0.695	SUBCLONAL	1	FALSE	1	0.708865201028139	2		367	295	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244550	46244550	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	185	401	1	ENST00000334344.6:c.2645del	p.Gly882ValfsTer10	p.G882Vfs*10	ENST00000334344	NM_152641.2	882	Ggt/gt	15/21	1	2	FACETS	0.937	0.871	1	0.937	0.871	1	CLONAL	1	FALSE	1	0.708865201028139	2		402	557	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108013	30108013	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	224	458	0	ENST00000331968.5:c.794C>G	p.Ser265Cys	p.S265C	ENST00000331968	NM_002742.2	265	tCt/tGt	5/18	1	2	FACETS	0.953	0.892	1	0.953	0.892	1	CLONAL	1	FALSE	1	0.708865201028139	2		458	663	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872524	35872524	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	240	467	0	ENST00000216797.5:c.379G>T	p.Ala127Ser	p.A127S	ENST00000216797	NM_020529.2	127	Gct/Tct	3/6	1	2	FACETS	0.967	0.908	1	0.967	0.908	1	CLONAL	1	FALSE	1	0.708865201028139	2		467	700	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961995	41961995	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	127	438	0	ENST00000219905.7:c.903G>T	p.Glu301Asp	p.E301D	ENST00000219905	NM_001164273.1	301	gaG/gaT	2/24	1	2	FACETS	0.759	0.692	0.829	0.759	0.692	0.829	SUBCLONAL	1	FALSE	1	0.708865201028139	2		438	472	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992838	72992838	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	144	643	0	ENST00000268489.5:c.1207C>A	p.Leu403Ile	p.L403I	ENST00000268489	NM_006885.3	403	Ctt/Att	2/10	1	2	FACETS	0.492	0.449	0.538	0.492	0.449	0.538	SUBCLONAL	1	FALSE	1	0.708865201028139	2		643	825	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81891908	81891908	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	198	429	0	ENST00000359376.3:c.378G>C	p.Leu126Phe	p.L126F	ENST00000359376	NM_002661.3	126	ttG/ttC	4/33	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.708865201028139	2		429	541	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461473	138461473	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	161	446	0	ENST00000289153.2:c.548C>T	p.Ser183Phe	p.S183F	ENST00000289153	NM_006219.2	183	tCc/tTc	3/22	1	2	FACETS	0.857	0.791	0.925	0.857	0.791	0.925	CLONAL	1	FALSE	1	0.708865201028139	2		446	530	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443403	187443403	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	160	331	0	ENST00000232014.4:c.1723C>G	p.Arg575Gly	p.R575G	ENST00000232014	NM_001130845.1	575	Cgt/Ggt	8/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.708865201028139	2		331	425	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074252	39074252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	242	568	0	ENST00000357387.3:c.58G>A	p.Asp20Asn	p.D20N	ENST00000357387	NM_152756.3	20	Gac/Aac	2/38	1	2	FACETS	0.937	0.879	0.996	0.937	0.879	0.996	CLONAL	1	FALSE	1	0.708865201028139	2		568	729	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929160	44929161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	227	579	0	ENST00000377967.4:c.2261dup	p.Met754IlefsTer10	p.M754Ifs*10	ENST00000377967	NM_021140.2	754	atg/aTtg	17/29	0.465579283620035	1	FACETS	0.771	0.725	0.818	0.771	0.725	0.818	SUBCLONAL	1	FALSE	0	0.708865201028139	1		579	536	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039414	47039415	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTTGT	novel	NA	P-0047741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	272	647	0	ENST00000377604.3:c.1037_1038insTTTGT	p.Phe347LeufsTer140	p.F347Lfs*140	ENST00000377604	NM_001204468.1	346	gcc/gcTTTGTc	10/24	NA	2	FACETS	0.923	0.869	0.979			1	INDETERMINATE	1	FALSE	NA	0.708865201028139	2		647	831	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0047758-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	340	944	1	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.578619830891485	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.680386467585701	2		945	483	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915788	112915788	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047758-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	73	342	0	ENST00000351677.2:c.1061T>C	p.Val354Ala	p.V354A	ENST00000351677	NM_002834.3	354	gTc/gCc	9/16	0.50795592291199	3	FACETS	1	0.925	1			1	CLONAL	1	TRUE	NA	0.680386467585701	3		342	271	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729909	30729909	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047758-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	67	383	0	ENST00000295754.5:c.1430A>G	p.Lys477Arg	p.K477R	ENST00000295754	NM_003242.5	477	aAg/aGg	6/7	1	2	FACETS	0.842	0.741	0.947	0.842	0.741	0.947	CLONAL	1	TRUE	1	0.680386467585701	2		383	234	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061233	38061233	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	224	979	0	ENST00000250448.2:c.756C>A	p.Asn252Lys	p.N252K	ENST00000250448	NM_004496.3	252	aaC/aaA	2/2	0.210354667090464	5	FACETS	1	0.934	1	0.667	0.622	0.714	INDETERMINATE	2	FALSE	2	0.413382125695081	5		979	877	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657663	37657666	+	frameshift_variant	Frame_Shift_Del	DEL	TAAG	TAAG	-	novel	NA	P-0047762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	49	384	0	ENST00000447079.4:c.2581_2584del	p.Lys861ValfsTer6	p.K861Vfs*6	ENST00000447079	NM_015083.1	860	atTAAG/at	6/14	0.325833906215927	3	FACETS	0.753	0.647	0.866	0.753	0.647	0.866	SUBCLONAL	2	FALSE	1	0.413382125695081	3		384	190	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981527	70981527	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs781532439	NA	P-0047762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1317	302	1141	1	ENST00000276594.2:c.569A>G	p.Lys190Arg	p.K190R	ENST00000276594	NM_024504.3	190	aAg/aGg	2/8	0.413382125695081	6	FACETS	0.824	0.774	0.876	0.55	0.516	0.584	CLONAL	2	FALSE	3	0.413382125695081	6		1142	1619	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032068	26032068	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	11	460	0	ENST00000244661.2:c.221A>G	p.Glu74Gly	p.E74G	ENST00000244661	NM_003537.3	74	gAa/gGa	1/1	0.238484619708931	5	FACETS	0.234	0.161	0.326	0.078	0.053	0.109	INDETERMINATE	1	FALSE	2	0.413382125695081	5		460	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577573	7577573	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0047763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	259	680	0	ENST00000269305.4:c.708C>G	p.Tyr236Ter	p.Y236*	ENST00000269305	NM_001126112.2	236	taC/taG	7/11	NA	2	FACETS	0.873	0.831	0.913			1	INDETERMINATE	2	FALSE	NA	0.679236990847697	2		680	437	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793382	18793382	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs77070108	NA	P-0047763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	91	340	3	ENST00000266497.5:c.4079C>T	p.Ala1360Val	p.A1360V	ENST00000266497		1360	gCg/gTg	30/31	0.392603577355083	4	FACETS	0.76	0.683	0.84	0.76	0.683	0.84	INDETERMINATE	2	FALSE	2	0.679236990847697	4		343	296	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878988	151878988	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138373177	NA	P-0047763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	81	509	0	ENST00000262189.6:c.5957G>A	p.Arg1986Gln	p.R1986Q	ENST00000262189	NM_170606.2	1986	cGg/cAg	36/59	0.679236990847697	6	FACETS	0.837	0.738	0.944	0.209	0.184	0.236	CLONAL	1	FALSE	2	0.679236990847697	6		509	672	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999191	100999191	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	427	1204	0	ENST00000325455.5:c.611A>C	p.His204Pro	p.H204P	ENST00000325455	NM_001202474.3	204	cAc/cCc	1/8	0.489647677578509	6	FACETS	0.962	0.919	1	0.962	0.919	1	CLONAL	3	FALSE	3	0.679236990847697	6		1204	1028	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749373	41749373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	67	401	0	ENST00000226382.2:c.422G>A	p.Arg141Gln	p.R141Q	ENST00000226382	NM_003924.3	141	cGa/cAa	2/3	0.679236990847697	4	FACETS	0.785	0.685	0.893			1	SUBCLONAL	1	FALSE	NA	0.679236990847697	4		401	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0047764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	216	494	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.412879470080754	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.412173661497183	1		494	751	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107258	193107258	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	53	253	0	ENST00000367435.3:c.467G>A	p.Arg156His	p.R156H	ENST00000367435	NM_024529.4	156	cGt/cAt	6/17	0.339445858356293	4	FACETS	0.877	0.75	1	0.439	0.375	0.508	CLONAL	1	TRUE	2	0.412173661497183	4		253	414	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031585	36031585	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1221989600	NA	P-0047764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	157	905	1	ENST00000358208.4:c.1414C>T	p.Arg472Cys	p.R472C	ENST00000358208		472	Cgc/Tgc	12/12	0.412879470080754	4	FACETS	0.776	0.708	0.847			1	SUBCLONAL	1	TRUE	NA	0.412173661497183	4		906	1387	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212248	5212248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776677741	NA	P-0047764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	329	831	2	ENST00000357368.4:c.4783C>T	p.Arg1595Cys	p.R1595C	ENST00000357368	NM_002850.3	1595	Cgc/Tgc	32/38	0.412879470080754	2	FACETS	0.962	0.913	1	0.962	0.913	1	CLONAL	2	TRUE	0	0.412173661497183	2		833	830	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820004	36820004	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	239	590	0	ENST00000373129.3:c.584A>G	p.His195Arg	p.H195R	ENST00000373129	NM_032017.1	195	cAc/cGc	7/12	0.412349467721963	3	FACETS	0.885	0.829	0.943	0.885	0.829	0.943	CLONAL	2	TRUE	1	0.412173661497183	3		590	790	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552197	29552197	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	89	389	0	ENST00000356175.3:c.1930T>C	p.Ser644Pro	p.S644P	ENST00000356175	NM_000267.3	644	Tcc/Ccc	17/57	1	2	FACETS	0.993	0.885	1	0.993	0.885	1	CLONAL	1	TRUE	1	0.412173661497183	2		389	435	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940042	76940042	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782319601	NA	P-0047764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	113	274	0	ENST00000373344.5:c.706C>T	p.His236Tyr	p.H236Y	ENST00000373344	NM_000489.3	236	Cat/Tat	9/35	0.186598854845596	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.412173661497183	2		274	416	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0047765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	212	320	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.444430965451376	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	3	TRUE	0	0.444430965451376	3		320	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0047765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	384	660	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.444430965451376	2	FACETS	0.985	0.94	1	0.985	0.94	1	CLONAL	2	TRUE	0	0.444430965451376	2		660	877	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341269	8341269	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0047765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	84	162	0	ENST00000356435.5:c.4948-1G>A		p.X1650_splice	ENST00000356435		1650			0.261290696297043	5	FACETS	0.991	0.884	1			1	INDETERMINATE	2	TRUE	NA	0.444430965451376	5		162	318	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111886089	111886089	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs766652046	NA	P-0047765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	245	465	1	ENST00000341259.2:c.1711C>T	p.Gln571Ter	p.Q571*	ENST00000341259	NM_005475.2	571	Cag/Tag	8/8	0.424573376210549	3	FACETS	0.934	0.877	0.993	0.934	0.877	0.993	CLONAL	2	TRUE	1	0.444430965451376	3		466	721	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226373	133226373	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	213	863	0	ENST00000320574.5:c.3685G>C	p.Val1229Leu	p.V1229L	ENST00000320574	NM_006231.2	1229	Gtg/Ctg	30/49	0.424573376210549	3	FACETS	0.992	0.92	1	0.496	0.46	0.533	CLONAL	1	TRUE	1	0.444430965451376	3		863	1181	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210635	2210635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1488643062	NA	P-0047765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	316	684	0	ENST00000398665.3:c.1132G>A	p.Glu378Lys	p.E378K	ENST00000398665	NM_032482.2	378	Gaa/Aaa	14/28	0.444430965451376	2	FACETS	0.981	0.932	1	0.981	0.932	1	CLONAL	2	TRUE	0	0.444430965451376	2		684	725	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142952	7142952	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415079005	NA	P-0047765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	215	742	0	ENST00000302850.5:c.2417C>T	p.Ser806Leu	p.S806L	ENST00000302850	NM_000208.2	806	tCg/tTg	12/22	0.444430965451376	2	FACETS	1	0.937	1	0.504	0.468	0.541	CLONAL	1	TRUE	0	0.444430965451376	2		742	960	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1953884	1953884	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	244	999	0	ENST00000382891.5:c.2063G>A	p.Gly688Glu	p.G688E	ENST00000382891	NM_133335.3	688	gGa/gAa	11/22	0.433378103912672	3	FACETS	0.957	0.892	1	0.478	0.446	0.512	CLONAL	1	TRUE	1	0.444430965451376	3		999	1403	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763887	76763887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781835425	NA	P-0047765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	168	546	0	ENST00000373344.5:c.7421G>A	p.Arg2474His	p.R2474H	ENST00000373344	NM_000489.3	2474	cGt/cAt	35/35	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.444430965451376	2		546	700	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	76	432	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.917	0.808	1	0.917	0.808	1	CLONAL	1	TRUE	1	0.39	2		432	425	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953022	2953022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141681466	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	118	790	1	ENST00000396946.4:c.2918G>A	p.Arg973His	p.R973H	ENST00000396946	NM_032415.4	973	cGc/cAc	22/25	1	2	FACETS	0.511	0.459	0.565	0.511	0.459	0.565	SUBCLONAL	1	TRUE	1	0.39	2		791	1185	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960059	134960059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	178	508	0	ENST00000398015.3:c.2416G>A	p.Asp806Asn	p.D806N	ENST00000398015	NM_004441.4	806	Gac/Aac	13/16	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.39	2		508	860	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850705	63850705	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs201178069	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	56	205	0	ENST00000279873.7:c.1489del	p.Ile497Ter	p.I497*	ENST00000279873	NM_032199.2	495	Aaa/aa	10/10	1	2	FACETS	0.926	0.799	1	0.926	0.799	1	CLONAL	1	TRUE	1	0.39	2		205	310	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739820	46739820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555234707	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	78	313	1	ENST00000371975.4:c.1621G>A	p.Val541Ile	p.V541I	ENST00000371975	NM_003579.3	541	Gtc/Atc	15/18	1	2	FACETS	0.805	0.709	0.907	0.805	0.709	0.907	CLONAL	1	TRUE	1	0.39	2		314	497	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685288	89685289	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	28	152	0	ENST00000371953.3:c.188dup	p.Asn63LysfsTer11	p.N63Kfs*11	ENST00000371953	NM_000314.4	61	-/A	3/9	1	2	FACETS	0.756	0.609	0.92	0.756	0.609	0.92	CLONAL	1	TRUE	1	0.39	2		152	190	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	19	268	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	0.238	0.18	0.306	0.238	0.18	0.306	SUBCLONAL	1	TRUE	1	0.39	2		268	410	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	85	282	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.39	2		282	434	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519886	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	12	267	0	ENST00000349496.5:c.97T>C	p.Ser33Pro	p.S33P	ENST00000349496	NM_001904.3	33	Tct/Cct	3/15	1	2	FACETS	0.144	0.1	0.198	0.144	0.1	0.198	SUBCLONAL	1	TRUE	1	0.39	2		267	428	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290214	15290214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373181668	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	220	859	1	ENST00000263388.2:c.3421G>A	p.Val1141Met	p.V1141M	ENST00000263388	NM_000435.2	1141	Gtg/Atg	21/33	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.39	2		860	1106	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267410	7267410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	148	398	0	ENST00000302850.5:c.598G>A	p.Val200Ile	p.V200I	ENST00000302850	NM_000208.2	200	Gtc/Atc	2/22	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.39	2		398	751	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841258	15841258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763087055	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	189	481	0	ENST00000307771.7:c.1342C>T	p.Arg448Cys	p.R448C	ENST00000307771	NM_005089.3	448	Cgc/Tgc	11/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.39	2		481	781	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801148	1801148	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199968400	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	232	1049	3	ENST00000260795.2:c.277C>T	p.Arg93Trp	p.R93W	ENST00000260795		93	Cgg/Tgg	2/17	1	2	FACETS	0.906	0.843	0.971	0.906	0.843	0.971	CLONAL	1	TRUE	1	0.39	2		1052	1313	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597373	10597373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	191	686	0	ENST00000171111.5:c.1830G>A	p.Met610Ile	p.M610I	ENST00000171111	NM_203500.1	610	atG/atA	6/6	1	2	FACETS	0.88	0.813	0.95	0.88	0.813	0.95	CLONAL	1	TRUE	1	0.39	2		686	1113	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072537	5072537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs895187915	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	49	260	0	ENST00000381652.3:c.1687G>A	p.Val563Ile	p.V563I	ENST00000381652	NM_004972.3	563	Gta/Ata	13/25	1	2	FACETS	0.778	0.662	0.904	0.778	0.662	0.904	CLONAL	1	TRUE	1	0.39	2		260	323	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026792	48026793	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	64	286	0	ENST00000234420.5:c.1675_1676del	p.Cys559LeufsTer3	p.C559Lfs*3	ENST00000234420	NM_000179.2	557	gGT/g	4/10	1	2	FACETS	0.864	0.751	0.984	0.864	0.751	0.984	CLONAL	1	TRUE	1	0.39	2		286	380	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	122	416	0	ENST00000256196.4:c.68G>A	p.Gly23Asp	p.G23D	ENST00000256196		23	gGc/gAc	1/6	1	2	FACETS	0.96	0.869	1	0.96	0.869	1	CLONAL	1	TRUE	1	0.39	2		416	652	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279530	1279530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	74	959	0	ENST00000310581.5:c.2006G>A	p.Arg669Gln	p.R669Q	ENST00000310581	NM_198253.2	669	cGg/cAg	5/16	1	2	FACETS	0.303	0.264	0.346	0.303	0.264	0.346	SUBCLONAL	1	TRUE	1	0.39	2		959	1252	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443634	49443634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs112921115	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	134	645	0	ENST00000301067.7:c.3737C>T	p.Thr1246Met	p.T1246M	ENST00000301067	NM_003482.3	1246	aCg/aTg	11/54	1	2	FACETS	0.84	0.763	0.921	0.84	0.763	0.921	CLONAL	1	TRUE	1	0.39	2		645	818	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858976	45858976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757432268	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	163	534	0	ENST00000391945.4:c.1490G>A	p.Arg497His	p.R497H	ENST00000391945	NM_000400.3	497	cGt/cAt	16/23	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.39	2		534	802	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281768	49281768	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148425155	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	177	631	0	ENST00000282018.3:c.815C>T	p.Thr272Met	p.T272M	ENST00000282018	NM_020377.2	272	aCg/aTg	1/1	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.39	2		631	849	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524949	8524949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771217760	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	74	236	1	ENST00000356435.5:c.655G>A	p.Ala219Thr	p.A219T	ENST00000356435		219	Gct/Act	7/35	1	2	FACETS	0.968	0.852	1	0.968	0.852	1	CLONAL	1	TRUE	1	0.39	2		237	392	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725085	49725085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1189053822	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	169	804	0	ENST00000449682.2:c.259G>A	p.Val87Met	p.V87M	ENST00000449682	NM_020998.3	87	Gtg/Atg	3/18	1	2	FACETS	0.815	0.749	0.885	0.815	0.749	0.885	CLONAL	1	TRUE	1	0.39	2		804	1063	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816544	32816544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376553490	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	230	725	0	ENST00000354258.4:c.1631G>A	p.Arg544His	p.R544H	ENST00000354258	NM_000593.5	544	cGc/cAc	7/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.39	2		725	1115	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958497	175958497	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	57	236	0	ENST00000367669.3:c.1847+1G>A		p.X616_splice	ENST00000367669	NM_022457.5	616			1	2	FACETS	0.931	0.804	1	0.931	0.804	1	CLONAL	1	TRUE	1	0.39	2		236	314	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405911	157405911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779271100	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	127	473	0	ENST00000346085.5:c.2153C>T	p.Ser718Leu	p.S718L	ENST00000346085	NM_020732.3	718	tCg/tTg	6/20	1	2	FACETS	0.905	0.82	0.993	0.905	0.82	0.993	CLONAL	1	TRUE	1	0.39	2		473	720	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562493	21562493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1417916199	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	18	114	0	ENST00000382592.4:c.1426G>A	p.Ala476Thr	p.A476T	ENST00000382592	NM_014572.2	476	Gcc/Acc	4/8	1	2	FACETS	0.769	0.586	0.98	0.769	0.586	0.98	CLONAL	1	TRUE	1	0.39	2		114	120	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130259	2130259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45448801	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	248	973	1	ENST00000219476.3:c.3491C>T	p.Ala1164Val	p.A1164V	ENST00000219476	NM_000548.3	1164	gCg/gTg	30/42	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.39	2		974	1190	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974726	21974726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554656344	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	94	367	1	ENST00000304494.5:c.101C>T	p.Ala34Val	p.A34V	ENST00000304494	NM_000077.4	34	gCg/gTg	1/3	1	2	FACETS	0.949	0.847	1	0.949	0.847	1	CLONAL	1	TRUE	1	0.39	2		368	508	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155594	106155594	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1560540913	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	59	255	0	ENST00000380013.4:c.499del	p.Ser167GlnfsTer16	p.S167Qfs*16	ENST00000380013	NM_001127208.2	165	agT/ag	3/11	1	2	FACETS	0.796	0.688	0.913	0.796	0.688	0.913	CLONAL	1	TRUE	1	0.39	2		255	380	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028656	12028656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	53	240	0	ENST00000353533.5:c.859C>T	p.Arg287Cys	p.R287C	ENST00000353533	NM_003010.3	287	Cgc/Tgc	8/11	1	2	FACETS	0.558	0.476	0.648	0.558	0.476	0.648	SUBCLONAL	1	TRUE	1	0.39	2		240	487	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39709872	39709872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	20	105	0	ENST00000361337.2:c.499G>A	p.Glu167Lys	p.E167K	ENST00000361337	NM_003286.2	167	Gaa/Aaa	7/21	1	2	FACETS	0.554	0.426	0.703	0.554	0.426	0.703	SUBCLONAL	1	TRUE	1	0.39	2		105	185	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112302	115112302	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	103	267	0	ENST00000257566.3:c.1438G>A	p.Ala480Thr	p.A480T	ENST00000257566	NM_016569.3	480	Gcg/Acg	7/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.39	2		267	403	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433352	78433352	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	52	226	0	ENST00000370768.2:c.251-2A>G		p.X84_splice	ENST00000370768	NM_003902.3	84			1	2	FACETS	0.839	0.718	0.969	0.839	0.718	0.969	CLONAL	1	TRUE	1	0.39	2		226	318	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982164	201982164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs144239428	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	159	721	0	ENST00000359651.3:c.688G>A	p.Asp230Asn	p.D230N	ENST00000359651		230	Gat/Aat	5/8	1	2	FACETS	0.926	0.849	1	0.926	0.849	1	CLONAL	1	TRUE	1	0.39	2		721	881	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17743013	17743013	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	209	849	0	ENST00000250003.3:c.921C>A	p.Cys307Ter	p.C307*	ENST00000250003	NM_002478.4	307	tgC/tgA	3/3	1	2	FACETS	0.978	0.907	1	0.978	0.907	1	CLONAL	1	TRUE	1	0.39	2		849	1096	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118355596	118355596	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	38	334	0	ENST00000534358.1:c.4238A>G	p.Asn1413Ser	p.N1413S	ENST00000534358	NM_005933.3	1413	aAt/aGt	10/36	1	2	FACETS	0.35	0.289	0.419	0.35	0.289	0.419	SUBCLONAL	1	TRUE	1	0.39	2		334	556	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435269	49435269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374216845	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	221	878	1	ENST00000301067.7:c.6284G>A	p.Arg2095His	p.R2095H	ENST00000301067	NM_003482.3	2095	cGt/cAt	31/54	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.39	2		879	1129	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480663	50480663	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	63	173	0	ENST00000394963.4:c.531+2T>C		p.X177_splice	ENST00000394963	NM_003076.4	177			1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.39	2		173	296	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226040	133226040	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771823596	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	209	762	0	ENST00000320574.5:c.3857G>A	p.Arg1286His	p.R1286H	ENST00000320574	NM_006231.2	1286	cGc/cAc	31/49	1	2	FACETS	0.994	0.922	1	0.994	0.922	1	CLONAL	1	TRUE	1	0.39	2		762	1078	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988982	41988982	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	77	297	0	ENST00000219905.7:c.1774A>T	p.Lys592Ter	p.K592*	ENST00000219905	NM_001164273.1	592	Aag/Tag	3/24	1	2	FACETS	0.965	0.852	1	0.965	0.852	1	CLONAL	1	TRUE	1	0.39	2		297	409	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993164	72993164	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	56	694	1	ENST00000268489.5:c.881T>C	p.Val294Ala	p.V294A	ENST00000268489	NM_006885.3	294	gTc/gCc	2/10	1	2	FACETS	0.257	0.219	0.299	0.257	0.219	0.299	SUBCLONAL	1	TRUE	1	0.39	2		695	1116	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976160	7976160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	163	639	0	ENST00000319144.4:c.2035C>T	p.Arg679Cys	p.R679C	ENST00000319144	NM_001139.2	679	Cgc/Tgc	15/15	1	2	FACETS	0.919	0.843	0.997	0.919	0.843	0.997	CLONAL	1	TRUE	1	0.39	2		639	910	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872067	37872067	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	221	862	0	ENST00000269571.5:c.1388G>A	p.Ser463Asn	p.S463N	ENST00000269571		463	aGt/aAt	12/27	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.39	2		862	1131	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610258	10610258	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	163	808	1	ENST00000171111.5:c.452G>T	p.Cys151Phe	p.C151F	ENST00000171111	NM_203500.1	151	tGt/tTt	2/6	1	2	FACETS	0.701	0.642	0.763	0.701	0.642	0.763	SUBCLONAL	1	TRUE	1	0.39	2		809	1193	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026919	48026919	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	58	247	0	ENST00000234420.5:c.1799del	p.Asn600IlefsTer10	p.N600Ifs*10	ENST00000234420	NM_000179.2	599	ggA/gg	4/10	1	2	FACETS	0.921	0.796	1	0.921	0.796	1	CLONAL	1	TRUE	1	0.39	2		247	323	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932635	49932635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367999599	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	149	676	1	ENST00000296474.3:c.3236G>A	p.Arg1079Gln	p.R1079Q	ENST00000296474	NM_002447.2	1079	cGg/cAg	14/20	1	2	FACETS	0.825	0.754	0.9	0.825	0.754	0.9	CLONAL	1	TRUE	1	0.39	2		677	926	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589160	67589160	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	36	190	0	ENST00000274335.5:c.1148T>A	p.Ile383Lys	p.I383K	ENST00000274335		383	aTa/aAa	9/15	1	2	FACETS	0.747	0.618	0.89	0.747	0.618	0.89	SUBCLONAL	1	TRUE	1	0.39	2		190	247	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590974	67590974	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	15	99	0	ENST00000274335.5:c.1569-2A>T		p.X523_splice	ENST00000274335		523			1	2	FACETS	0.754	0.559	0.982	0.754	0.559	0.982	CLONAL	1	TRUE	1	0.39	2		99	102	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158563	26158563	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	45	524	0	ENST00000289316.2:c.166T>C	p.Ser56Pro	p.S56P	ENST00000289316	NM_138720.2	56	Tct/Cct	1/2	1	2	FACETS	0.313	0.262	0.37	0.313	0.262	0.37	SUBCLONAL	1	TRUE	1	0.39	2		524	737	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391908	139391908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780873661	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	242	1122	2	ENST00000277541.6:c.6283C>T	p.Arg2095Cys	p.R2095C	ENST00000277541	NM_017617.3	2095	Cgc/Tgc	34/34	1	2	FACETS	0.947	0.883	1	0.947	0.883	1	CLONAL	1	TRUE	1	0.39	2		1124	1311	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922074	39922074	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	191	669	0	ENST00000378444.4:c.4098A>T	p.Lys1366Asn	p.K1366N	ENST00000378444	NM_001123385.1	1366	aaA/aaT	9/15	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.39	2		669	948	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220135	5220135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269111261	NA	P-0047766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	44	635	0	ENST00000357368.4:c.3580C>T	p.Arg1194Cys	p.R1194C	ENST00000357368	NM_002850.3	1194	Cgc/Tgc	22/38	1	2	FACETS	0.292	0.244	0.346	0.292	0.244	0.346	SUBCLONAL	1	TRUE	1	0.39	2		635	772	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0047767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	11	249	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.584	0.402	0.811	0.584	0.402	0.811	SUBCLONAL	1	TRUE	1	0.12	2		249	314	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0047767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	24	496	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.644	0.503	0.808	0.644	0.503	0.808	SUBCLONAL	1	TRUE	1	0.12	2		496	621	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094488	27094488	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	28	385	0	ENST00000324856.7:c.3196C>T	p.Gln1066Ter	p.Q1066*	ENST00000324856	NM_006015.4	1066	Cag/Tag	11/20	1	2	FACETS	0.999	0.798	1	0.999	0.798	1	CLONAL	1	TRUE	1	0.12	2		385	467	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41219703	41219703	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047767-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	21	267	0	ENST00000357654.3:c.4996T>G	p.Tyr1666Asp	p.Y1666D	ENST00000357654	NM_007294.3	1666	Tac/Gac	16/23	1	2	FACETS	0.972	0.748	1	0.972	0.748	1	CLONAL	1	TRUE	1	0.12	2		267	360	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	61	432	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.988	0.857	1	0.988	0.857	1	CLONAL	1	TRUE	1	0.34	2		432	363	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	161	706	8	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.983	0.902	1	0.983	0.902	1	CLONAL	1	TRUE	1	0.34	2		714	963	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	158	436	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.884	0.809	0.963	0.884	0.809	0.963	CLONAL	1	TRUE	1	0.34	2		439	1051	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004242	29004242	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766441216	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	97	268	0	ENST00000282397.4:c.1051C>T	p.Arg351Trp	p.R351W	ENST00000282397	NM_002019.4	351	Cgg/Tgg	8/30	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.34	2		268	517	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433417	138433417	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	64	350	0	ENST00000289153.2:c.1195C>T	p.Arg399Ter	p.R399*	ENST00000289153	NM_006219.2	399	Cga/Tga	7/22	1	2	FACETS	0.909	0.79	1	0.909	0.79	1	CLONAL	1	TRUE	1	0.34	2		350	414	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	79	390	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.833	0.734	0.939	0.833	0.734	0.939	CLONAL	1	TRUE	1	0.34	2		390	558	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	166	386	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.969	0.897	1	1	0.992	1	CLONAL	2	TRUE	1	0.34	2		386	504	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	159	632	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.831	0.76	0.905	0.831	0.76	0.905	CLONAL	1	TRUE	1	0.34	2		632	1126	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	127	671	0	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	1	2	FACETS	0.863	0.781	0.949	0.863	0.781	0.949	CLONAL	1	TRUE	1	0.34	2		671	866	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	154	634	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	1	2	FACETS	0.911	0.833	0.993	0.911	0.833	0.993	CLONAL	1	TRUE	1	0.34	2		634	994	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	42	231	0	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.34	2		231	227	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796883	42796883	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1185	215	1106	2	ENST00000575354.2:c.3347del	p.Pro1116GlnfsTer45	p.P1116Qfs*45	ENST00000575354	NM_015125.3	1114	gCc/gc	14/20	1	2	FACETS	0.903	0.837	0.972	0.903	0.837	0.972	CLONAL	1	TRUE	1	0.34	2		1108	1400	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114817	108114817	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs786204543	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	75	303	0	ENST00000278616.4:c.640del	p.Ser214ProfsTer16	p.S214Pfs*16	ENST00000278616	NM_000051.3	212	Ttt/tt	6/63	1	2	FACETS	0.945	0.831	1	0.945	0.831	1	CLONAL	1	TRUE	1	0.34	2		303	467	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039371	47039371	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	163	717	0	ENST00000377604.3:c.994C>T	p.Arg332Cys	p.R332C	ENST00000377604	NM_001204468.1	332	Cgc/Tgc	10/24	1	2	FACETS	0.934	0.856	1	0.934	0.856	1	CLONAL	1	TRUE	1	0.34	2		717	1027	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528154	29528154	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	92	468	0	ENST00000356175.3:c.1162C>A	p.Pro388Thr	p.P388T	ENST00000356175	NM_000267.3	388	Cct/Act	10/57	1	2	FACETS	0.892	0.793	0.996	0.892	0.793	0.996	CLONAL	1	TRUE	1	0.34	2		468	607	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354597	70354597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767396596	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	92	476	0	ENST00000374080.3:c.4762G>A	p.Val1588Met	p.V1588M	ENST00000374080		1588	Gtg/Atg	35/45	1	2	FACETS	0.772	0.686	0.864	0.772	0.686	0.864	SUBCLONAL	1	TRUE	1	0.34	2		476	701	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63760023	63760023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	72	270	0	ENST00000279873.7:c.676C>T	p.Arg226Trp	p.R226W	ENST00000279873	NM_032199.2	226	Cgg/Tgg	4/10	1	2	FACETS	0.947	0.831	1	0.947	0.831	1	CLONAL	1	TRUE	1	0.34	2		270	447	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205807	108205807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782719	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	54	286	0	ENST00000278616.4:c.8122G>A	p.Asp2708Asn	p.D2708N	ENST00000278616	NM_000051.3	2708	Gat/Aat	55/63	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.34	2		286	294	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654643	67654643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs968244943	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	146	374	0	ENST00000264010.4:c.1130G>A	p.Arg377His	p.R377H	ENST00000264010	NM_006565.3	377	cGt/cAt	6/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.34	2		374	704	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214591	5214591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770889503	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	172	823	0	ENST00000357368.4:c.4475G>A	p.Arg1492Gln	p.R1492Q	ENST00000357368	NM_002850.3	1492	cGg/cAg	29/38	1	2	FACETS	0.939	0.863	1	0.939	0.863	1	CLONAL	1	TRUE	1	0.34	2		823	1078	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006218	22006218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1204549439	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	152	777	1	ENST00000276925.6:c.185C>T	p.Ala62Val	p.A62V	ENST00000276925	NM_004936.3	62	gCg/gTg	2/2	1	2	FACETS	0.95	0.869	1	0.95	0.869	1	CLONAL	1	TRUE	1	0.34	2		778	941	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467589	66467589	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772693559	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	55	250	0	ENST00000273854.3:c.680G>A	p.Arg227His	p.R227H	ENST00000273854	NM_004439.5	227	cGt/cAt	3/18	1	2	FACETS	0.986	0.849	1	0.986	0.849	1	CLONAL	1	TRUE	1	0.34	2		250	328	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289908	15289908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257835251	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1301	257	1087	3	ENST00000263388.2:c.3646G>A	p.Ala1216Thr	p.A1216T	ENST00000263388	NM_000435.2	1216	Gcg/Acg	22/33	1	2	FACETS	0.97	0.906	1	0.97	0.906	1	CLONAL	1	TRUE	1	0.34	2		1090	1558	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148544338	148544338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	107	454	1	ENST00000320356.2:c.53G>A	p.Arg18His	p.R18H	ENST00000320356	NM_004456.4	18	cGt/cAt	2/20	1	2	FACETS	0.918	0.824	1	0.918	0.824	1	CLONAL	1	TRUE	1	0.34	2		455	686	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223601	53223601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	142	863	2	ENST00000375401.3:c.3758C>T	p.Pro1253Leu	p.P1253L	ENST00000375401	NM_004187.3	1253	cCg/cTg	23/26	1	2	FACETS	0.913	0.832	0.998	0.913	0.832	0.998	CLONAL	1	TRUE	1	0.34	2		865	915	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511221	148511221	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1268069858	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	86	397	0	ENST00000320356.2:c.1681C>T	p.Arg561Cys	p.R561C	ENST00000320356	NM_004456.4	561	Cgc/Tgc	15/20	1	2	FACETS	0.685	0.606	0.771	0.685	0.606	0.771	SUBCLONAL	1	TRUE	1	0.34	2		397	738	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527259	187527259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201982861	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	141	450	0	ENST00000441802.2:c.10315G>A	p.Val3439Ile	p.V3439I	ENST00000441802	NM_005245.3	3439	Gtc/Atc	17/27	1	2	FACETS	0.906	0.825	0.992	0.906	0.825	0.992	CLONAL	1	TRUE	1	0.34	2		450	915	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813075	89813075	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143671872	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	97	526	2	ENST00000389301.3:c.3430C>T	p.Arg1144Trp	p.R1144W	ENST00000389301	NM_000135.2	1144	Cgg/Tgg	35/43	1	2	FACETS	0.763	0.68	0.851	0.763	0.68	0.851	SUBCLONAL	1	TRUE	1	0.34	2		528	748	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915853	127915853	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	96	382	0	ENST00000373547.4:c.628C>T	p.Arg210Ter	p.R210*	ENST00000373547	NM_002721.4	210	Cga/Tga	6/7	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.34	2		382	563	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186820	108186820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778078	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	64	299	1	ENST00000278616.4:c.6178C>T	p.Arg2060Cys	p.R2060C	ENST00000278616	NM_000051.3	2060	Cgc/Tgc	42/63	1	2	FACETS	0.764	0.662	0.873	0.764	0.662	0.873	SUBCLONAL	1	TRUE	1	0.34	2		300	493	SUCCESS
BLM	641	MSKCC	GRCh37	15	91333930	91333930	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs762354041	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	69	369	0	ENST00000355112.3:c.2875C>T	p.Arg959Ter	p.R959*	ENST00000355112	NM_000057.2	959	Cga/Tga	15/22	1	2	FACETS	0.823	0.719	0.936	0.823	0.719	0.936	CLONAL	1	TRUE	1	0.34	2		369	493	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865869	56865869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761782738	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	89	288	0	ENST00000308159.5:c.1201G>A	p.Asp401Asn	p.D401N	ENST00000308159	NM_014669.4	401	Gac/Aac	11/22	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.34	2		288	439	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387698	17387698	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199960321	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	101	476	1	ENST00000359435.4:c.766G>A	p.Glu256Lys	p.E256K	ENST00000359435	NM_001033549.1	256	Gag/Aag	8/9	1	2	FACETS	0.861	0.77	0.957	0.861	0.77	0.957	CLONAL	1	TRUE	1	0.34	2		477	690	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857442	68857442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs386833398	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	104	417	0	ENST00000261769.5:c.2077G>A	p.Gly693Ser	p.G693S	ENST00000261769	NM_004360.3	693	Ggc/Agc	13/16	1	2	FACETS	0.717	0.642	0.798	0.717	0.642	0.798	SUBCLONAL	1	TRUE	1	0.34	2		417	853	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934144	39934144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375342424	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	51	575	0	ENST00000378444.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000378444	NM_001123385.1	152	cCg/cTg	4/15	1	2	FACETS	0.346	0.293	0.405	0.346	0.293	0.405	SUBCLONAL	1	TRUE	1	0.34	2		575	867	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669523	88669523	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750055690	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	59	387	0	ENST00000360948.2:c.1375C>T	p.Arg459Trp	p.R459W	ENST00000360948	NM_001012338.2	459	Cgg/Tgg	12/19	1	2	FACETS	0.686	0.591	0.789	0.686	0.591	0.789	SUBCLONAL	1	TRUE	1	0.34	2		387	506	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438262	49438262	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	147	591	0	ENST00000301067.7:c.5007del	p.Val1670SerfsTer52	p.V1670Sfs*52	ENST00000301067	NM_003482.3	1669	ccC/cc	20/54	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.34	2		591	857	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112301	115112301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1284348347	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	60	284	0	ENST00000257566.3:c.1439C>T	p.Ala480Val	p.A480V	ENST00000257566	NM_016569.3	480	gCg/gTg	7/8	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.34	2		284	343	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256232	16256232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749550885	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	49	374	0	ENST00000375759.3:c.3497C>T	p.Thr1166Met	p.T1166M	ENST00000375759	NM_015001.2	1166	aCg/aTg	11/15	1	2	FACETS	0.563	0.477	0.658	0.563	0.477	0.658	SUBCLONAL	1	TRUE	1	0.34	2		374	512	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089777	27089777	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	37	503	0	ENST00000324856.7:c.2732+1G>A		p.X911_splice	ENST00000324856	NM_006015.4	911			1	2	FACETS	0.324	0.266	0.389	0.324	0.266	0.389	SUBCLONAL	1	TRUE	1	0.34	2		503	672	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346505	89346505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024078594	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	286	710	0	ENST00000301030.4:c.6445G>A	p.Ala2149Thr	p.A2149T	ENST00000301030	NM_001256183.1	2149	Gca/Aca	9/13	1	2	FACETS	0.976	0.92	1	1	0.995	1	CLONAL	2	TRUE	1	0.34	2		710	862	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032092	10032092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201674066	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	105	544	0	ENST00000330684.3:c.731G>A	p.Arg244His	p.R244H	ENST00000330684	NM_001134407.1	244	cGc/cAc	3/13	1	2	FACETS	0.929	0.833	1	0.929	0.833	1	CLONAL	1	TRUE	1	0.34	2		544	665	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431622	6431622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	49	322	0	ENST00000356142.4:c.175G>A	p.Ala59Thr	p.A59T	ENST00000356142	NM_018890.3	59	Gct/Act	3/7	1	2	FACETS	0.643	0.546	0.751	0.643	0.546	0.751	SUBCLONAL	1	TRUE	1	0.34	2		322	448	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792660	33792660	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	16	175	0	ENST00000498907.2:c.661C>T	p.Gln221Ter	p.Q221*	ENST00000498907	NM_004364.3	221	Cag/Tag	1/1	1	2	FACETS	0.38	0.28	0.498	0.38	0.28	0.498	SUBCLONAL	1	TRUE	1	0.34	2		175	248	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133958	38133958	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	47	610	0	ENST00000317025.8:c.3928C>T	p.Arg1310Ter	p.R1310*	ENST00000317025	NM_023034.1	1310	Cga/Tga	23/24	1	2	FACETS	0.307	0.258	0.361	0.307	0.258	0.361	SUBCLONAL	1	TRUE	1	0.34	2		610	901	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47679356	47679356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	73	358	0	ENST00000347630.2:c.851G>A	p.Arg284His	p.R284H	ENST00000347630	NM_001007230.1	284	cGc/cAc	10/11	1	2	FACETS	0.761	0.667	0.863	0.761	0.667	0.863	SUBCLONAL	1	TRUE	1	0.34	2		358	564	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244110	5244110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141022401	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	235	1015	1	ENST00000357368.4:c.1372C>T	p.Arg458Cys	p.R458C	ENST00000357368	NM_002850.3	458	Cgc/Tgc	11/38	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.34	2		1016	1375	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249602	110249602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	226	1111	1	ENST00000374672.4:c.1073C>T	p.Pro358Leu	p.P358L	ENST00000374672	NM_004235.4	358	cCg/cTg	3/5	1	2	FACETS	0.983	0.914	1	0.983	0.914	1	CLONAL	1	TRUE	1	0.34	2		1112	1352	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014383	70014383	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780036017	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	120	474	1	ENST00000394351.3:c.1244C>T	p.Thr415Met	p.T415M	ENST00000394351	NM_000248.3	415	aCg/aTg	9/9	1	2	FACETS	0.959	0.867	1	0.959	0.867	1	CLONAL	1	TRUE	1	0.34	2		475	736	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443502	49443502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751561975	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	141	628	0	ENST00000301067.7:c.3869G>A	p.Arg1290Gln	p.R1290Q	ENST00000301067	NM_003482.3	1290	cGg/cAg	11/54	1	2	FACETS	0.903	0.823	0.988	0.903	0.823	0.988	CLONAL	1	TRUE	1	0.34	2		628	918	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517446	157517446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761133847	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	79	360	1	ENST00000346085.5:c.4010G>A	p.Arg1337Gln	p.R1337Q	ENST00000346085	NM_020732.3	1337	cGa/cAa	16/20	1	2	FACETS	0.833	0.734	0.939	0.833	0.734	0.939	CLONAL	1	TRUE	1	0.34	2		361	558	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775978	9775978	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778360032	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	174	862	0	ENST00000377346.4:c.442G>A	p.Glu148Lys	p.E148K	ENST00000377346	NM_005026.3	148	Gag/Aag	5/24	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.34	2		862	1003	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647732	206647732	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150428746	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	125	575	0	ENST00000367120.3:c.146G>A	p.Arg49His	p.R49H	ENST00000367120	NM_014002.3	49	cGc/cAc	4/22	1	2	FACETS	0.821	0.742	0.903	0.821	0.742	0.903	CLONAL	1	TRUE	1	0.34	2		575	896	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432319	432319	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	100	400	0	ENST00000399788.2:c.2204G>T	p.Arg735Met	p.R735M	ENST00000399788	NM_001042603.1	735	aGg/aTg	16/28	0.3	2	FACETS	0.961	0.86	1			1	CLONAL	1	TRUE	NA	0.34	2		400	612	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515168	103515168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144645075	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	36	194	0	ENST00000355739.4:c.1669G>A	p.Asp557Asn	p.D557N	ENST00000355739	NM_000123.3	557	Gat/Aat	8/15	1	2	FACETS	0.779	0.643	0.929	0.779	0.643	0.929	CLONAL	1	TRUE	1	0.34	2		194	272	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946275	81946275	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	190	805	0	ENST00000359376.3:c.2008C>A	p.Leu670Met	p.L670M	ENST00000359376	NM_002661.3	670	Ctg/Atg	19/33	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.34	2		805	1008	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351721	89351721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756611123	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	132	738	1	ENST00000301030.4:c.1229C>T	p.Thr410Met	p.T410M	ENST00000301030	NM_001256183.1	410	aCg/aTg	9/13	1	2	FACETS	0.667	0.604	0.734	0.667	0.604	0.734	SUBCLONAL	1	TRUE	1	0.34	2		739	1164	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805806	46805806	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	152	713	0	ENST00000290295.7:c.150del	p.Leu51TrpfsTer47	p.L51Wfs*47	ENST00000290295	NM_006361.5	50	ccC/cc	1/2	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.34	2		713	820	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10305544	10305544	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	201	911	0	ENST00000340748.4:c.32C>A	p.Pro11His	p.P11H	ENST00000340748		11	cCc/cAc	1/40	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.34	2		911	1111	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951056	17951056	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	144	539	0	ENST00000458235.1:c.1237C>A	p.Leu413Ile	p.L413I	ENST00000458235	NM_000215.3	413	Ctc/Atc	9/24	1	2	FACETS	0.864	0.787	0.945	0.864	0.787	0.945	CLONAL	1	TRUE	1	0.34	2		539	980	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918163	50918163	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	104	1061	0	ENST00000440232.2:c.2480A>G	p.Lys827Arg	p.K827R	ENST00000440232	NM_002691.3	827	aAg/aGg	20/27	1	2	FACETS	0.509	0.454	0.567	0.509	0.454	0.567	SUBCLONAL	1	TRUE	1	0.34	2		1061	1202	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46602865	46602865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	175	679	1	ENST00000263734.3:c.923G>A	p.Arg308Gln	p.R308Q	ENST00000263734	NM_001430.4	308	cGg/cAg	8/16	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.34	2		680	1023	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027113	48027114	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	52	308	0	ENST00000234420.5:c.1992dup	p.Glu665ArgfsTer3	p.E665Rfs*3	ENST00000234420	NM_000179.2	664	tca/tcAa	4/10	1	2	FACETS	0.79	0.675	0.916	0.79	0.675	0.916	CLONAL	1	TRUE	1	0.34	2		308	387	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182151	99182151	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	105	482	0	ENST00000074304.5:c.2216T>C	p.Leu739Ser	p.L739S	ENST00000074304	NM_001134224.1	739	tTg/tCg	21/26	1	2	FACETS	0.804	0.72	0.893	0.804	0.72	0.893	CLONAL	1	TRUE	1	0.34	2		482	768	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645681	215645681	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	80	359	0	ENST00000260947.4:c.917del	p.Asn306IlefsTer11	p.N306Ifs*11	ENST00000260947	NM_000465.2	306	aAt/at	4/11	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.34	2		359	442	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1956900	1956900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239708011	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	215	683	0	ENST00000382891.5:c.2351G>A	p.Arg784Gln	p.R784Q	ENST00000382891	NM_133335.3	784	cGg/cAg	13/22	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.34	2		683	1202	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178223	56178224	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	30	271	0	ENST00000399503.3:c.3200dup	p.Gly1068ArgfsTer2	p.G1068Rfs*2	ENST00000399503	NM_005921.1	1066	acc/aCcc	14/20	1	2	FACETS	0.507	0.409	0.618	0.507	0.409	0.618	SUBCLONAL	1	TRUE	1	0.34	2		271	348	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040014	180040014	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	179	986	0	ENST00000261937.6:c.3428C>T	p.Ala1143Val	p.A1143V	ENST00000261937	NM_182925.4	1143	gCc/gTc	25/30	1	2	FACETS	0.905	0.832	0.98	0.905	0.832	0.98	CLONAL	1	TRUE	1	0.34	2		986	1164	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199813	138199813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1373396587	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	100	454	1	ENST00000237289.4:c.1231C>T	p.Arg411Trp	p.R411W	ENST00000237289	NM_001270507.1	411	Cgg/Tgg	7/9	1	2	FACETS	0.926	0.829	1	0.926	0.829	1	CLONAL	1	TRUE	1	0.34	2		455	635	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100243	157100243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	30	132	0	ENST00000346085.5:c.1180G>A	p.Ala394Thr	p.A394T	ENST00000346085	NM_020732.3	394	Gcc/Acc	1/20	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.34	2		132	163	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974112	2974112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761547989	NA	P-0047768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	109	480	1	ENST00000396946.4:c.1493G>A	p.Arg498His	p.R498H	ENST00000396946	NM_032415.4	498	cGc/cAc	10/25	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.34	2		481	599	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0047770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	74	277	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.861	0.756	0.974	0.861	0.756	0.974	CLONAL	1	TRUE	1	0.360344035382905	2		277	477	SUCCESS
APC	324	MSKCC	GRCh37	5	112175761	112175761	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	32	275	0	ENST00000257430.4:c.4473del	p.Phe1491LeufsTer16	p.F1491Lfs*16	ENST00000257430	NM_000038.5	1490	caT/ca	16/16	1	2	FACETS	0.708	0.577	0.853	0.708	0.577	0.853	SUBCLONAL	1	TRUE	1	0.360344035382905	2		275	251	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0047770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	41	384	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.914	0.767	1	0.914	0.767	1	CLONAL	1	TRUE	1	0.360344035382905	2		384	249	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120199	70120199	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	154	653	0	ENST00000245479.2:c.1201C>T	p.Gln401Ter	p.Q401*	ENST00000245479	NM_000346.3	401	Cag/Tag	3/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.360344035382905	2		653	642	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653867	89653867	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1554893835	NA	P-0047770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	33	291	0	ENST00000371953.3:c.164+1G>T		p.X55_splice	ENST00000371953	NM_000314.4	55			0.360344035382905	1	FACETS	0.981	0.811	1	0.981	0.811	1	CLONAL	1	TRUE	0	0.360344035382905	1		291	153	SUCCESS
APC	324	MSKCC	GRCh37	5	112151191	112151191	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0047770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	41	299	0	ENST00000257430.4:c.835-1G>A		p.X279_splice	ENST00000257430	NM_000038.5	279			1	2	FACETS	0.756	0.633	0.892	0.756	0.633	0.892	SUBCLONAL	1	TRUE	1	0.360344035382905	2		299	301	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129101	152129104	+	missense_variant	Missense_Mutation	ONP	CCAA	CCAA	ATAT	novel	NA	P-0047770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	46	975	2	ENST00000206249.3:c.54_57delinsATAT	p.Gln19Tyr	p.Q19Y	ENST00000206249	NM_000125.3	18	atCCAA/atATAT	1/8	1	2	FACETS	0.367	0.308	0.433	0.367	0.308	0.433	SUBCLONAL	1	TRUE	1	0.360344035382905	2		977	695	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778812	76778812	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	55	383	0	ENST00000373344.5:c.6767C>A	p.Ser2256Tyr	p.S2256Y	ENST00000373344	NM_000489.3	2256	tCt/tAt	31/35	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.25	2		383	436	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	35	315	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.72	0.59	0.865	0.72	0.59	0.865	SUBCLONAL	1	TRUE	1	0.25	2		315	389	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	42	447	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.68	0.568	0.805	0.68	0.568	0.805	SUBCLONAL	1	TRUE	1	0.25	2		447	494	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	15	191	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	0.538	0.394	0.711	0.538	0.394	0.711	SUBCLONAL	1	TRUE	1	0.25	2		191	223	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654642	67654642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	58	432	0	ENST00000264010.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000264010	NM_006565.3	377	Cgt/Tgt	6/12	1	2	FACETS	0.959	0.825	1	0.959	0.825	1	CLONAL	1	TRUE	1	0.25	2		432	484	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333143	70333143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767493807	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	60	593	0	ENST00000373644.4:c.1048G>A	p.Glu350Lys	p.E350K	ENST00000373644	NM_030625.2	350	Gaa/Aaa	2/12	1	2	FACETS	0.826	0.712	0.951	0.826	0.712	0.951	CLONAL	1	TRUE	1	0.25	2		593	581	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171607	36171607	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1569008655	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	34	299	0	ENST00000300305.3:c.958C>T	p.Arg320Ter	p.R320*	ENST00000300305		320	Cga/Tga	7/8	1	2	FACETS	0.932	0.764	1	0.932	0.764	1	CLONAL	1	TRUE	1	0.25	2		299	292	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748596	40748596	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754546663	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	32	455	1	ENST00000373198.4:c.2920C>T	p.Arg974Trp	p.R974W	ENST00000373198	NM_133170.3	974	Cgg/Tgg	21/32	1	2	FACETS	0.711	0.578	0.861	0.711	0.578	0.861	SUBCLONAL	1	TRUE	1	0.25	2		456	360	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919244	48919244	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913296	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	18	94	0	ENST00000267163.4:c.409G>T	p.Glu137Ter	p.E137*	ENST00000267163	NM_000321.2	137	Gaa/Taa	4/27	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.25	2		94	121	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029297	143029297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757219824	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	23	172	0	ENST00000262992.4:c.2323G>A	p.Glu775Lys	p.E775K	ENST00000262992	NM_001101669.1	775	Gaa/Aaa	21/24	1	2	FACETS	0.754	0.59	0.943	0.754	0.59	0.943	CLONAL	1	TRUE	1	0.25	2		172	244	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001374	150001374	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	35	456	0	ENST00000253339.5:c.2230C>T	p.Arg744Ter	p.R744*	ENST00000253339		744	Cga/Tga	4/7	1	2	FACETS	0.698	0.573	0.839	0.698	0.573	0.839	SUBCLONAL	1	TRUE	1	0.25	2		456	401	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844193	68844193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121964873	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	67	541	0	ENST00000261769.5:c.781G>A	p.Glu261Lys	p.E261K	ENST00000261769	NM_004360.3	261	Gaa/Aaa	6/16	1	2	FACETS	0.872	0.757	0.995	0.872	0.757	0.995	CLONAL	1	TRUE	1	0.25	2		541	615	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095836	178095836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1328262363	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	36	357	0	ENST00000397062.3:c.1495C>T	p.Arg499Trp	p.R499W	ENST00000397062	NM_006164.4	499	Cgg/Tgg	5/5	1	2	FACETS	0.75	0.617	0.898	0.75	0.617	0.898	SUBCLONAL	1	TRUE	1	0.25	2		357	384	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381529	81381529	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	15	286	0	ENST00000222390.5:c.532C>T	p.Arg178Ter	p.R178*	ENST00000222390	NM_000601.4	178	Cga/Tga	5/18	1	2	FACETS	0.478	0.349	0.633	0.478	0.349	0.633	SUBCLONAL	1	TRUE	1	0.25	2		286	251	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961867	41961867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	30	284	0	ENST00000219905.7:c.775C>T	p.Arg259Trp	p.R259W	ENST00000219905	NM_001164273.1	259	Cgg/Tgg	2/24	1	2	FACETS	0.886	0.716	1	0.886	0.716	1	CLONAL	1	TRUE	1	0.25	2		284	271	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78914356	78914356	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1451626205	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	80	765	2	ENST00000306801.3:c.2980C>T	p.Arg994Ter	p.R994*	ENST00000306801	NM_020761.2	994	Cga/Tga	25/34	1	2	FACETS	0.893	0.785	1	0.893	0.785	1	CLONAL	1	TRUE	1	0.25	2		767	717	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140900	37140900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773910971	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	54	532	1	ENST00000373509.5:c.736G>A	p.Glu246Lys	p.E246K	ENST00000373509	NM_002648.3	246	Gaa/Aaa	5/6	1	2	FACETS	0.817	0.698	0.947	0.817	0.698	0.947	CLONAL	1	TRUE	1	0.25	2		533	529	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231757	66231757	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	26	300	1	ENST00000273854.3:c.1943G>T	p.Arg648Ile	p.R648I	ENST00000273854	NM_004439.5	648	aGa/aTa	11/18	1	2	FACETS	0.819	0.651	1	0.819	0.651	1	CLONAL	1	TRUE	1	0.25	2		301	254	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267797	7267797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	75	527	1	ENST00000302850.5:c.211G>A	p.Glu71Lys	p.E71K	ENST00000302850	NM_000208.2	71	Gaa/Aaa	2/22	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.25	2		528	579	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	20	500	0	ENST00000320574.5:c.1231G>C	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ctg	13/49	1	2	FACETS	0.385	0.293	0.492	0.385	0.293	0.492	SUBCLONAL	1	TRUE	1	0.25	2		500	416	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845627	63845627	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	18	175	0	ENST00000279873.7:c.1366G>T	p.Glu456Ter	p.E456*	ENST00000279873	NM_032199.2	456	Gaa/Taa	9/10	1	2	FACETS	0.809	0.612	1	0.809	0.612	1	CLONAL	1	TRUE	1	0.25	2		175	178	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438057	438057	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	56	338	0	ENST00000399788.2:c.1912G>T	p.Glu638Ter	p.E638*	ENST00000399788	NM_001042603.1	638	Gaa/Taa	14/28	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.25	2		338	371	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040934	42040934	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	70	628	0	ENST00000219905.7:c.5312C>A	p.Ser1771Tyr	p.S1771Y	ENST00000219905	NM_001164273.1	1771	tCt/tAt	16/24	1	2	FACETS	0.929	0.81	1	0.929	0.81	1	CLONAL	1	TRUE	1	0.25	2		628	603	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870376	155870376	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	51	467	0	ENST00000368323.3:c.463G>T	p.Glu155Ter	p.E155*	ENST00000368323	NM_006912.5	155	Gaa/Taa	6/6	1	2	FACETS	0.857	0.729	0.997	0.857	0.729	0.997	CLONAL	1	TRUE	1	0.25	2		467	476	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626736	12626736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149580968	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	42	412	0	ENST00000251849.4:c.1553G>A	p.Arg518Gln	p.R518Q	ENST00000251849	NM_002880.3	518	cGa/cAa	15/17	1	2	FACETS	0.96	0.804	1	0.96	0.804	1	CLONAL	1	TRUE	1	0.25	2		412	350	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624299	89624299	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs398123326	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	76	446	0	ENST00000371953.3:c.73T>G	p.Leu25Val	p.L25V	ENST00000371953	NM_000314.4	25	Ttg/Gtg	1/9	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.25	2		446	593	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489544	56489544	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761002408	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	74	400	0	ENST00000267101.3:c.2009G>A	p.Arg670Gln	p.R670Q	ENST00000267101	NM_001982.3	670	cGg/cAg	17/28	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.25	2		400	568	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355325	81355325	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750575553	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	12	199	0	ENST00000222390.5:c.1049G>A	p.Arg350Gln	p.R350Q	ENST00000222390	NM_000601.4	350	cGa/cAa	9/18	1	2	FACETS	0.555	0.391	0.756	0.555	0.391	0.756	SUBCLONAL	1	TRUE	1	0.25	2		199	173	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37680983	37680983	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	39	473	1	ENST00000447079.4:c.3152G>A	p.Arg1051Gln	p.R1051Q	ENST00000447079	NM_015083.1	1051	cGa/cAa	12/14	1	2	FACETS	0.703	0.583	0.837	0.703	0.583	0.837	SUBCLONAL	1	TRUE	1	0.25	2		474	444	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637232	176637232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1424984701	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	65	563	0	ENST00000439151.2:c.1832G>A	p.Arg611Gln	p.R611Q	ENST00000439151	NM_022455.4	611	cGa/cAa	5/23	1	2	FACETS	0.875	0.759	1	0.875	0.759	1	CLONAL	1	TRUE	1	0.25	2		563	594	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055755	152055755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1403418496	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	52	379	0	ENST00000262189.6:c.167G>A	p.Arg56Gln	p.R56Q	ENST00000262189	NM_170606.2	56	cGa/cAa	2/59	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.25	2		379	327	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210233	123210233	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	62	459	1	ENST00000218089.9:c.2585G>T	p.Arg862Ile	p.R862I	ENST00000218089	NM_001042749.1	862	aGa/aTa	26/35	1	2	FACETS	0.87	0.752	0.999	0.87	0.752	0.999	CLONAL	1	TRUE	1	0.25	2		460	570	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942036	81942036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	31	459	0	ENST00000359376.3:c.1573G>A	p.Glu525Lys	p.E525K	ENST00000359376	NM_002661.3	525	Gaa/Aaa	17/33	1	2	FACETS	0.687	0.556	0.835	0.687	0.556	0.835	SUBCLONAL	1	TRUE	1	0.25	2		459	361	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165730	108165730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765759912	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	42	293	0	ENST00000278616.4:c.4853G>A	p.Arg1618Gln	p.R1618Q	ENST00000278616	NM_000051.3	1618	cGa/cAa	32/63	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.25	2		293	325	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582062	189582062	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	48	361	0	ENST00000264731.3:c.621G>T	p.Lys207Asn	p.K207N	ENST00000264731	NM_003722.4	207	aaG/aaT	5/14	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.25	2		361	362	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076800	102076800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768834182	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	110	760	0	ENST00000282441.5:c.979C>T	p.Arg327Trp	p.R327W	ENST00000282441	NM_001130145.2	327	Cgg/Tgg	5/9	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.25	2		760	852	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542870	187542870	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	35	249	1	ENST00000441802.2:c.4870G>T	p.Glu1624Ter	p.E1624*	ENST00000441802	NM_005245.3	1624	Gaa/Taa	10/27	1	2	FACETS	0.976	0.803	1	0.976	0.803	1	CLONAL	1	TRUE	1	0.25	2		250	287	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67459152	67459152	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	59	656	0	ENST00000327367.4:c.568G>T	p.Glu190Ter	p.E190*	ENST00000327367	NM_005902.3	190	Gaa/Taa	4/9	1	2	FACETS	0.797	0.686	0.919	0.797	0.686	0.919	CLONAL	1	TRUE	1	0.25	2		656	592	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259436	55259436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745812480	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	63	480	0	ENST00000275493.2:c.2494C>T	p.Arg832Cys	p.R832C	ENST00000275493	NM_005228.3	832	Cgc/Tgc	21/28	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.25	2		480	472	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265106	198265106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1559265118	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	41	335	0	ENST00000335508.6:c.2771G>A	p.Arg924Gln	p.R924Q	ENST00000335508	NM_012433.2	924	cGa/cAa	19/25	1	2	FACETS	0.894	0.746	1	0.894	0.746	1	CLONAL	1	TRUE	1	0.25	2		335	367	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127991	64127991	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	94	1003	1	ENST00000334205.4:c.389G>A	p.Arg130His	p.R130H	ENST00000334205	NM_003942.2	130	cGc/cAc	4/17	1	2	FACETS	0.868	0.772	0.972	0.868	0.772	0.972	CLONAL	1	TRUE	1	0.25	2		1004	866	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105552	27105552	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	53	416	0	ENST00000324856.7:c.5163del	p.Arg1722AspfsTer3	p.R1722Dfs*3	ENST00000324856	NM_006015.4	1721	cgA/cg	20/20	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.25	2		416	419	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248037	59248037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	84	629	0	ENST00000371222.2:c.706C>T	p.Pro236Ser	p.P236S	ENST00000371222	NM_002228.3	236	Ccc/Tcc	1/1	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.25	2		629	642	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600450	43600450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1455266037	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	81	973	0	ENST00000355710.3:c.676C>T	p.Arg226Cys	p.R226C	ENST00000355710	NM_020975.4	226	Cgc/Tgc	4/20	1	2	FACETS	0.911	0.803	1	0.911	0.803	1	CLONAL	1	TRUE	1	0.25	2		973	711	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405523	70405523	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	37	419	0	ENST00000373644.4:c.3037T>C	p.Ser1013Pro	p.S1013P	ENST00000373644	NM_030625.2	1013	Tcc/Ccc	4/12	1	2	FACETS	0.785	0.648	0.938	0.785	0.648	0.938	CLONAL	1	TRUE	1	0.25	2		419	377	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406484	70406484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147498630	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	55	652	0	ENST00000373644.4:c.3998G>A	p.Arg1333Lys	p.R1333K	ENST00000373644	NM_030625.2	1333	aGa/aAa	4/12	1	2	FACETS	0.757	0.648	0.877	0.757	0.648	0.877	SUBCLONAL	1	TRUE	1	0.25	2		652	581	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88672028	88672028	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879254272	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	35	410	0	ENST00000372037.3:c.562C>T	p.Arg188Cys	p.R188C	ENST00000372037	NM_004329.2	188	Cgt/Tgt	8/13	1	2	FACETS	0.714	0.586	0.858	0.714	0.586	0.858	SUBCLONAL	1	TRUE	1	0.25	2		410	392	SUCCESS
ATM	472	MSKCC	GRCh37	11	108137931	108137931	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs876660430	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	29	297	0	ENST00000278616.4:c.2500G>T	p.Glu834Ter	p.E834*	ENST00000278616	NM_000051.3	834	Gaa/Taa	17/63	1	2	FACETS	0.811	0.653	0.99	0.811	0.653	0.99	CLONAL	1	TRUE	1	0.25	2		297	286	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402142	402142	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	48	426	0	ENST00000399788.2:c.4649A>G	p.Lys1550Arg	p.K1550R	ENST00000399788	NM_001042603.1	1550	aAa/aGa	27/28	1	2	FACETS	0.807	0.682	0.943	0.807	0.682	0.943	CLONAL	1	TRUE	1	0.25	2		426	476	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644482	21644482	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	35	343	0	ENST00000421138.2:c.185A>C	p.Asp62Ala	p.D62A	ENST00000421138		62	gAt/gCt	4/16	1	2	FACETS	0.718	0.589	0.863	0.718	0.589	0.863	SUBCLONAL	1	TRUE	1	0.25	2		343	390	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913368	32913368	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	37	304	0	ENST00000380152.3:c.4876A>T	p.Asn1626Tyr	p.N1626Y	ENST00000380152		1626	Aat/Tat	11/27	1	2	FACETS	0.848	0.701	1	0.848	0.701	1	CLONAL	1	TRUE	1	0.25	2		304	349	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562351	95562351	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	35	351	0	ENST00000393063.1:c.4906G>T	p.Asp1636Tyr	p.D1636Y	ENST00000393063	NM_030621.3	1636	Gac/Tac	24/28	1	2	FACETS	0.819	0.672	0.982	0.819	0.672	0.982	CLONAL	1	TRUE	1	0.25	2		351	342	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032285	42032285	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	48	572	0	ENST00000219905.7:c.4469A>C	p.Lys1490Thr	p.K1490T	ENST00000219905	NM_001164273.1	1490	aAa/aCa	14/24	1	2	FACETS	0.805	0.681	0.941	0.805	0.681	0.941	CLONAL	1	TRUE	1	0.25	2		572	477	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467202	99467202	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	38	344	0	ENST00000268035.6:c.2583G>T	p.Leu861Phe	p.L861F	ENST00000268035	NM_000875.3	861	ttG/ttT	12/21	1	2	FACETS	0.891	0.739	1	0.891	0.739	1	CLONAL	1	TRUE	1	0.25	2		344	341	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127654	2127654	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	79	749	1	ENST00000219476.3:c.2893G>T	p.Glu965Ter	p.E965*	ENST00000219476	NM_000548.3	965	Gaa/Taa	26/42	1	2	FACETS	0.94	0.827	1	0.94	0.827	1	CLONAL	1	TRUE	1	0.25	2		750	672	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658792	3658792	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	61	653	0	ENST00000294008.3:c.174T>G	p.Phe58Leu	p.F58L	ENST00000294008	NM_032444.2	58	ttT/ttG	2/15	1	2	FACETS	0.849	0.732	0.975	0.849	0.732	0.975	CLONAL	1	TRUE	1	0.25	2		653	575	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827733	72827733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1362078452	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	57	601	0	ENST00000268489.5:c.8848C>T	p.Arg2950Cys	p.R2950C	ENST00000268489	NM_006885.3	2950	Cgc/Tgc	9/10	1	2	FACETS	0.826	0.709	0.954	0.826	0.709	0.954	CLONAL	1	TRUE	1	0.25	2		601	552	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271350	18271350	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	80	755	0	ENST00000222254.8:c.392T>G	p.Leu131Arg	p.L131R	ENST00000222254	NM_005027.3	131	cTt/cGt	3/16	1	2	FACETS	0.905	0.797	1	0.905	0.797	1	CLONAL	1	TRUE	1	0.25	2		755	707	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249779	39249779	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	25	423	0	ENST00000402219.2:c.1790G>A	p.Gly597Glu	p.G597E	ENST00000402219	NM_005633.3	597	gGa/gAa	10/23	1	2	FACETS	0.562	0.443	0.699	0.562	0.443	0.699	SUBCLONAL	1	TRUE	1	0.25	2		423	356	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630500	47630500	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	83	997	0	ENST00000233146.2:c.170T>C	p.Val57Ala	p.V57A	ENST00000233146	NM_000251.2	57	gTg/gCg	1/16	1	2	FACETS	0.849	0.749	0.957	0.849	0.749	0.957	CLONAL	1	TRUE	1	0.25	2		997	782	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256470	46256470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568737050	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	43	289	0	ENST00000371998.3:c.698G>A	p.Arg233Gln	p.R233Q	ENST00000371998		233	cGa/cAa	7/23	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.25	2		289	310	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573738	41573738	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	79	872	1	ENST00000263253.7:c.6023C>A	p.Ser2008Tyr	p.S2008Y	ENST00000263253	NM_001429.3	2008	tCt/tAt	31/31	1	2	FACETS	0.919	0.808	1	0.919	0.808	1	CLONAL	1	TRUE	1	0.25	2		873	688	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165150	47165150	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	27	179	0	ENST00000409792.3:c.976G>T	p.Asp326Tyr	p.D326Y	ENST00000409792	NM_014159.6	326	Gat/Tat	3/21	1	2	FACETS	0.995	0.797	1	0.995	0.797	1	CLONAL	1	TRUE	1	0.25	2		179	217	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114289	73114289	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	17	138	0	ENST00000356692.5:c.925G>T	p.Glu309Ter	p.E309*	ENST00000356692		309	Gaa/Taa	8/9	1	2	FACETS	1	0.804	1	1	0.804	1	CLONAL	1	TRUE	1	0.25	2		138	126	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456478	89456478	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142865154	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	38	327	0	ENST00000336596.2:c.1654G>A	p.Ala552Thr	p.A552T	ENST00000336596	NM_005233.5	552	Gca/Aca	8/17	1	2	FACETS	0.869	0.72	1	0.869	0.72	1	CLONAL	1	TRUE	1	0.25	2		327	350	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825433	134825433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	38	550	0	ENST00000398015.3:c.949G>A	p.Val317Met	p.V317M	ENST00000398015	NM_004441.4	317	Gtg/Atg	4/16	1	2	FACETS	0.659	0.545	0.787	0.659	0.545	0.787	SUBCLONAL	1	TRUE	1	0.25	2		550	461	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880943	134880943	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	50	644	0	ENST00000398015.3:c.1506T>G	p.Tyr502Ter	p.Y502*	ENST00000398015	NM_004441.4	502	taT/taG	7/16	1	2	FACETS	0.726	0.616	0.847	0.726	0.616	0.847	SUBCLONAL	1	TRUE	1	0.25	2		644	551	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960107	134960107	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	55	640	0	ENST00000398015.3:c.2464G>T	p.Glu822Ter	p.E822*	ENST00000398015	NM_004441.4	822	Gag/Tag	13/16	1	2	FACETS	0.769	0.658	0.891	0.769	0.658	0.891	SUBCLONAL	1	TRUE	1	0.25	2		640	572	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215961	142215961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	31	348	0	ENST00000350721.4:c.5632G>A	p.Glu1878Lys	p.E1878K	ENST00000350721	NM_001184.3	1878	Gaa/Aaa	33/47	1	2	FACETS	0.642	0.52	0.781	0.642	0.52	0.781	SUBCLONAL	1	TRUE	1	0.25	2		348	386	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	27	334	0	ENST00000263967.3:c.317G>C	p.Gly106Ala	p.G106A	ENST00000263967	NM_006218.2	106	gGc/gCc	2/21	1	2	FACETS	0.607	0.483	0.748	0.607	0.483	0.748	SUBCLONAL	1	TRUE	1	0.25	2		334	356	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970930	55970930	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	52	505	0	ENST00000263923.4:c.1867G>T	p.Asp623Tyr	p.D623Y	ENST00000263923	NM_002253.2	623	Gac/Tac	13/30	1	2	FACETS	0.993	0.847	1	0.993	0.847	1	CLONAL	1	TRUE	1	0.25	2		505	419	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247381	153247381	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	17	174	0	ENST00000281708.4:c.1421T>G	p.Val474Gly	p.V474G	ENST00000281708	NM_033632.3	474	gTt/gGt	10/12	1	2	FACETS	0.768	0.576	0.994	0.768	0.576	0.994	CLONAL	1	TRUE	1	0.25	2		174	177	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259069	153259069	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	13	152	0	ENST00000281708.4:c.746A>C	p.Lys249Thr	p.K249T	ENST00000281708	NM_033632.3	249	aAa/aCa	5/12	1	2	FACETS	0.832	0.598	1	0.832	0.598	1	CLONAL	1	TRUE	1	0.25	2		152	125	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519233	187519233	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	48	547	0	ENST00000441802.2:c.12150G>T	p.Glu4050Asp	p.E4050D	ENST00000441802	NM_005245.3	4050	gaG/gaT	23/27	1	2	FACETS	0.715	0.604	0.837	0.715	0.604	0.837	SUBCLONAL	1	TRUE	1	0.25	2		547	537	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180522	56180524	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs1397309724	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	25	220	0	ENST00000399503.3:c.3857_3859del	p.Glu1286del	p.E1286del	ENST00000399503	NM_005921.1	1284	cAAGaa/caa	16/20	1	2	FACETS	0.943	0.748	1	0.943	0.748	1	CLONAL	1	TRUE	1	0.25	2		220	212	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181849	56181849	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	34	249	0	ENST00000399503.3:c.4073del	p.Ser1358CysfsTer19	p.S1358Cfs*19	ENST00000399503	NM_005921.1	1358	tCg/tg	17/20	1	2	FACETS	0.8	0.655	0.962	0.8	0.655	0.962	CLONAL	1	TRUE	1	0.25	2		249	340	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639155	176639155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	41	439	0	ENST00000439151.2:c.3755G>A	p.Gly1252Glu	p.G1252E	ENST00000439151	NM_022455.4	1252	gGa/gAa	5/23	1	2	FACETS	0.814	0.679	0.964	0.814	0.679	0.964	CLONAL	1	TRUE	1	0.25	2		439	403	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987367	2987367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	73	592	0	ENST00000396946.4:c.62C>T	p.Ala21Val	p.A21V	ENST00000396946	NM_032415.4	21	gCc/gTc	3/25	0.3	0	FACETS	0.746	0.653	0.846			1	SUBCLONAL	1	TRUE	0	0.25	0		592	587	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6031673	6031673	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	50	496	0	ENST00000265849.7:c.919A>G	p.Asn307Asp	p.N307D	ENST00000265849	NM_000535.5	307	Aat/Gat	9/15	1	2	FACETS	0.795	0.675	0.927	0.795	0.675	0.927	CLONAL	1	TRUE	1	0.25	2		496	503	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148516780	148516780	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	42	217	0	ENST00000320356.2:c.908-1G>A		p.X303_splice	ENST00000320356	NM_004456.4	303			1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.25	2		217	277	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133992	38133992	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	67	511	0	ENST00000317025.8:c.3894G>T	p.Glu1298Asp	p.E1298D	ENST00000317025	NM_023034.1	1298	gaG/gaT	23/24	1	2	FACETS	0.993	0.864	1	0.993	0.864	1	CLONAL	1	TRUE	1	0.25	2		511	540	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5563210	5563210	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	27	251	0	ENST00000397747.3:c.815C>A	p.Ala272Asp	p.A272D	ENST00000397747	NM_025239.3	272	gCt/gAt	6/7	1	2	FACETS	0.593	0.472	0.732	0.593	0.472	0.732	SUBCLONAL	1	TRUE	1	0.25	2		251	364	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524937	8524937	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	25	288	0	ENST00000356435.5:c.667T>G	p.Leu223Val	p.L223V	ENST00000356435		223	Tta/Gta	7/35	1	2	FACETS	0.545	0.429	0.678	0.545	0.429	0.678	SUBCLONAL	1	TRUE	1	0.25	2		288	367	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169591	27169591	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1564073304	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	77	731	0	ENST00000380036.4:c.592C>A	p.Leu198Ile	p.L198I	ENST00000380036	NM_000459.3	198	Ctc/Atc	4/23	1	2	FACETS	0.981	0.862	1	0.981	0.862	1	CLONAL	1	TRUE	1	0.25	2		731	628	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270538	98270538	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	45	414	0	ENST00000331920.6:c.106A>G	p.Thr36Ala	p.T36A	ENST00000331920	NM_000264.3	36	Acg/Gcg	1/24	1	2	FACETS	0.889	0.748	1	0.889	0.748	1	CLONAL	1	TRUE	1	0.25	2		414	405	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	54	416	0	ENST00000324856.7:c.5164C>G	p.Arg1722Gly	p.R1722G	ENST00000324856	NM_006015.4	1722	Cga/Gga	20/20	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.25	2		416	423	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175550	108175550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782236	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	43	333	0	ENST00000278616.4:c.5645G>A	p.Arg1882Gln	p.R1882Q	ENST00000278616	NM_000051.3	1882	cGa/cAa	37/63	1	2	FACETS	0.78	0.653	0.92	0.78	0.653	0.92	CLONAL	1	TRUE	1	0.25	2		333	441	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421012	49421012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1243355591	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	33	413	0	ENST00000301067.7:c.14737G>T	p.Glu4913Ter	p.E4913*	ENST00000301067	NM_003482.3	4913	Gaa/Taa	48/54	1	2	FACETS	0.812	0.663	0.98	0.812	0.663	0.98	CLONAL	1	TRUE	1	0.25	2		413	325	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281392	49281392	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	83	741	0	ENST00000282018.3:c.439C>A	p.Leu147Met	p.L147M	ENST00000282018	NM_020377.2	147	Ctg/Atg	1/1	1	2	FACETS	0.926	0.817	1	0.926	0.817	1	CLONAL	1	TRUE	1	0.25	2		741	717	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39704860	39704860	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	12	84	0	ENST00000361337.2:c.205C>A	p.His69Asn	p.H69N	ENST00000361337	NM_003286.2	69	Cac/Aac	4/21	1	2	FACETS	0.842	0.597	1	0.842	0.597	1	CLONAL	1	TRUE	1	0.25	2		84	114	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39713114	39713114	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	11	119	0	ENST00000361337.2:c.520A>C	p.Lys174Gln	p.K174Q	ENST00000361337	NM_003286.2	174	Aaa/Caa	8/21	1	2	FACETS	0.772	0.537	1	0.772	0.537	1	CLONAL	1	TRUE	1	0.25	2		119	114	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151948013	151948013	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	53	368	0	ENST00000262189.6:c.1660C>A	p.Gln554Lys	p.Q554K	ENST00000262189	NM_170606.2	554	Caa/Aaa	12/59	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.25	2		368	421	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229247	123229247	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	28	245	0	ENST00000218089.9:c.3731G>T	p.Arg1244Ile	p.R1244I	ENST00000218089	NM_001042749.1	1244	aGa/aTa	34/35	1	2	FACETS	0.73	0.584	0.895	0.73	0.584	0.895	SUBCLONAL	1	TRUE	1	0.25	2		245	307	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	95	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.989	0.885	1	0.989	0.885	1	CLONAL	1	TRUE	1	0.42511769174349	2		327	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0047772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	169	604	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.42511769174349	1	FACETS	0.999	0.922	1	0.999	0.922	1	CLONAL	1	TRUE	0	0.42511769174349	1		604	627	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0047783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	30	383	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.15	2		383	295	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0047783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	36	743	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.15	2		744	467	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950352	17950352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	25	862	0	ENST00000458235.1:c.1375G>A	p.Asp459Asn	p.D459N	ENST00000458235	NM_000215.3	459	Gat/Aat	10/24	1	2	FACETS	0.728	0.573	0.907	0.728	0.573	0.907	CLONAL	1	TRUE	1	0.15	2		862	458	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671265	30671265	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	18	579	0	ENST00000376406.3:c.5612A>G	p.Glu1871Gly	p.E1871G	ENST00000376406	NM_014641.2	1871	gAg/gGg	11/15	1	2	FACETS	0.71	0.534	0.919	0.71	0.534	0.919	CLONAL	1	TRUE	1	0.15	2		579	338	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340991	70340991	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	23	290	0	ENST00000374080.3:c.724T>C	p.Phe242Leu	p.F242L	ENST00000374080		242	Ttc/Ctc	5/45	1	1	FACETS	0.788	0.619	0.981	1	0.93	1	CLONAL	2	TRUE	0	0.15	1		290	180	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0047784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	242	277	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.618097622243869	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.680440578587687	4		277	567	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577101	7577101	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	428	842	0	ENST00000269305.4:c.837del	p.Arg280GlufsTer65	p.R280Efs*65	ENST00000269305	NM_001126112.2	279	ggG/gg	8/11	0.680440578587687	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.680440578587687	2		842	606	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254578	10254578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	44	618	0	ENST00000340748.4:c.2932G>A	p.Asp978Asn	p.D978N	ENST00000340748		978	Gac/Aac	28/40	0.680440578587687	2	FACETS	0.231	0.193	0.273	0.116	0.096	0.137	SUBCLONAL	1	TRUE	0	0.680440578587687	2		618	559	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50482369	50482369	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	94	519	0	ENST00000394963.4:c.720G>T	p.Leu240Phe	p.L240F	ENST00000394963	NM_003076.4	240	ttG/ttT	6/13	0.618097622243869	4	FACETS	0.662	0.589	0.74	0.331	0.294	0.37	SUBCLONAL	1	TRUE	2	0.680440578587687	4		519	701	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332540	153332541	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0047784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	173	364	0	ENST00000281708.4:c.415_416del	p.His139TyrfsTer2	p.H139Yfs*2	ENST00000281708	NM_033632.3	139	CAt/t	2/12	0.680440578587687	3	FACETS	0.901	0.842	0.962	0.901	0.842	0.962	CLONAL	2	TRUE	1	0.680440578587687	3		364	378	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045855	26045855	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	88	578	1	ENST00000540144.1:c.217C>T	p.Arg73Ter	p.R73*	ENST00000540144	NM_003531.2	73	Cga/Tga	1/1	0.542894657841424	4	FACETS	0.694	0.616	0.778	0.347	0.308	0.389	SUBCLONAL	1	TRUE	2	0.680440578587687	4		579	626	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0047785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	43	371	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.822	0.691	0.966	0.822	0.691	0.966	CLONAL	1	TRUE	1	0.33	2		371	317	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0047785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	83	496	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.8	0.706	0.9	0.8	0.706	0.9	SUBCLONAL	1	TRUE	1	0.33	2		496	629	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0047785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	48	262	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.846	0.718	0.985	0.846	0.718	0.985	CLONAL	1	TRUE	1	0.33	2		262	344	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560514	65560514	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	62	293	0	ENST00000358664.4:c.83A>G	p.His28Arg	p.H28R	ENST00000358664	NM_002382.4	28	cAt/cGt	3/5	1	2	FACETS	0.743	0.642	0.851	0.743	0.642	0.851	SUBCLONAL	1	TRUE	1	0.33	2		293	506	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948136	178948136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	32	165	0	ENST00000263967.3:c.2908G>A	p.Glu970Lys	p.E970K	ENST00000263967	NM_006218.2	970	Gaa/Aaa	20/21	1	2	FACETS	1	0.819	1	1	0.819	1	CLONAL	1	TRUE	1	0.33	2		165	194	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023756	27023756	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	93	457	2	ENST00000324856.7:c.862C>T	p.Gln288Ter	p.Q288*	ENST00000324856	NM_006015.4	288	Cag/Tag	1/20	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.33	2		459	531	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913277	NA	P-0047785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	27	227	0	ENST00000263967.3:c.3145G>A	p.Gly1049Ser	p.G1049S	ENST00000263967	NM_006218.2	1049	Ggt/Agt	21/21	1	2	FACETS	0.679	0.543	0.833	0.679	0.543	0.833	SUBCLONAL	1	TRUE	1	0.33	2		227	241	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711971	89711971	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1554900629	NA	P-0047785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	54	298	0	ENST00000371953.3:c.589A>T	p.Lys197Ter	p.K197*	ENST00000371953	NM_000314.4	197	Aag/Tag	6/9	1	2	FACETS	0.917	0.786	1	0.917	0.786	1	CLONAL	1	TRUE	1	0.33	2		298	357	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442550	52442570	+	inframe_deletion	In_Frame_Del	DEL	CAAGGTAGAGACCTTTCGCCG	CAAGGTAGAGACCTTTCGCCG	-	novel	NA	P-0047785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	42	361	0	ENST00000460680.1:c.175_195del	p.Arg59_Leu65del	p.R59_L65del	ENST00000460680	NM_004656.3	59	CGGCGAAAGGTCTCTACCTTG/-	4/17	1	2	FACETS	0.556	0.464	0.657	0.556	0.464	0.657	SUBCLONAL	1	TRUE	1	0.33	2		361	458	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0047786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	615	432	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.624850059897107	4	FACETS	0.977	0.949	1	0.977	0.949	1	CLONAL	3	TRUE	1	0.755126237264898	4		432	975	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947596	48947596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1566196458	NA	P-0047786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	94	277	0	ENST00000267163.4:c.1183C>T	p.Gln395Ter	p.Q395*	ENST00000267163	NM_000321.2	395	Caa/Taa	12/27	1	2	FACETS	0.833	0.75	0.918	0.833	0.75	0.918	CLONAL	1	TRUE	1	0.755126237264898	2		277	299	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681129	86681129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	17	219	0	ENST00000274376.6:c.2770C>T	p.Pro924Ser	p.P924S	ENST00000274376	NM_002890.2	924	Cct/Tct	22/25	1	2	FACETS	0.172	0.128	0.224	0.172	0.128	0.224	SUBCLONAL	1	TRUE	1	0.755126237264898	2		219	262	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836768	151836768	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	162	362	0	ENST00000262189.6:c.14452G>T	p.Glu4818Ter	p.E4818*	ENST00000262189	NM_170606.2	4818	Gag/Tag	56/59	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.755126237264898	2		362	424	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0047788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	1538	561	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.322066393611614	12	FACETS	0.972	0.956	0.988	1	0.997	1	CLONAL	12	TRUE	1	0.322066393611614	12		561	2138	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0047788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	1467	604	1	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.322066393611614	12	FACETS	0.981	0.965	0.997	1	0.997	1	CLONAL	12	TRUE	1	0.322066393611614	12		605	2020	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858414	9858414	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	87	430	0	ENST00000330684.3:c.2987T>C	p.Val996Ala	p.V996A	ENST00000330684	NM_001134407.1	996	gTg/gCg	13/13	0.322066393611614	2	FACETS	0.913	0.809	1	0.456	0.404	0.512	CLONAL	1	TRUE	0	0.322066393611614	2		430	592	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240998	53240998	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	149	283	0	ENST00000375401.3:c.1213A>G	p.Lys405Glu	p.K405E	ENST00000375401	NM_004187.3	405	Aaa/Gaa	9/26	1	1	FACETS	1	0.932	1	1	0.992	1	CLONAL	2	TRUE	0	0.322066393611614	1		283	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0047789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	470	436	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.519299968186235	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.551897055255396	2		439	771	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0047789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	120	566	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.401215690653	3	FACETS	0.823	0.753	0.896			1	CLONAL	2	TRUE	NA	0.551897055255396	3		566	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0047790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	510	643	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.661867338384424	2	FACETS	0.968	0.937	0.998	0.968	0.937	0.998	CLONAL	2	TRUE	0	0.66368769982682	2		643	794	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0047790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	138	147	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.66368769982682	3	FACETS	0.839	0.787	0.89	0.839	0.787	0.89	CLONAL	3	TRUE	0	0.66368769982682	3		147	220	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947827	178947827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	18	231	1	ENST00000263967.3:c.2702G>T	p.Cys901Phe	p.C901F	ENST00000263967	NM_006218.2	901	tGt/tTt	19/21	0.66368769982682	3	FACETS	0.189	0.141	0.245	0.094	0.07	0.123	SUBCLONAL	1	TRUE	1	0.66368769982682	3		232	383	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275420	38275420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369356672	NA	P-0047790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	584	642	1	ENST00000425967.3:c.1613G>A	p.Arg538His	p.R538H	ENST00000425967	NM_001174067.1	538	cGt/cAt	12/19	0.66368769982682	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.66368769982682	3		643	1079	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929465	81929465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766133588	NA	P-0047790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	166	454	0	ENST00000359376.3:c.1126C>T	p.Arg376Trp	p.R376W	ENST00000359376	NM_002661.3	376	Cgg/Tgg	13/33	1	2	FACETS	0.932	0.861	1	0.932	0.861	1	CLONAL	1	TRUE	1	0.66368769982682	2		454	537	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	62	349	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.966	0.841	1	0.966	0.841	1	CLONAL	1	TRUE	1	0.447473952358545	2		350	287	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667635	29667638	+	frameshift_variant	Frame_Shift_Del	DEL	TAGA	TAGA	-	novel	NA	P-0047791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	75	317	0	ENST00000356175.3:c.6974_6977del	p.Asp2325ValfsTer49	p.D2325Vfs*49	ENST00000356175	NM_000267.3	2324	tTAGAt/tt	46/57	0.447473952358545	1	FACETS	0.779	0.688	0.875	0.779	0.688	0.875	SUBCLONAL	1	TRUE	0	0.447473952358545	1		317	334	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653852	89653854	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0047791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	63	186	0	ENST00000371953.3:c.155_157del	p.Asp52del	p.D52del	ENST00000371953	NM_000314.4	50	atTGAt/att	2/9	0.447473952358545	1	FACETS	0.889	0.778	1	0.889	0.778	1	CLONAL	1	TRUE	0	0.447473952358545	1		186	246	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753789	42753789	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	149	752	0	ENST00000222329.4:c.475C>T	p.Pro159Ser	p.P159S	ENST00000222329	NM_006494.2	159	Ccc/Tcc	4/4	1	2	FACETS	0.796	0.727	0.867	0.796	0.727	0.867	SUBCLONAL	1	TRUE	1	0.447473952358545	2		752	837	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233138	69233138	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	23	219	0	ENST00000462284.1:c.1003T>A	p.Trp335Arg	p.W335R	ENST00000462284	NM_002392.5	335	Tgg/Agg	11/11	1	2	FACETS	0.346	0.27	0.434	0.346	0.27	0.434	SUBCLONAL	1	TRUE	1	0.447473952358545	2		219	297	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0047792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	62	566	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.132335393574939	0	FACETS	0.536	0.465	0.612			1	INDETERMINATE	1	TRUE	0	0.392532005608789	0		566	358	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922973	44922973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	134	259	0	ENST00000377967.4:c.1834C>T	p.Arg612Ter	p.R612*	ENST00000377967	NM_021140.2	612	Cga/Tga	16/29	1	1	FACETS	0.793	0.73	0.857	1	0.989	1	SUBCLONAL	2	TRUE	0	0.392532005608789	1		259	346	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748583	40748583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444440253	NA	P-0047792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	65	378	1	ENST00000373198.4:c.2933C>T	p.Ala978Val	p.A978V	ENST00000373198	NM_133170.3	978	gCg/gTg	21/32	0.392532005608789	1	FACETS	0.57	0.495	0.651	0.57	0.495	0.651	SUBCLONAL	1	TRUE	0	0.392532005608789	1		379	467	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0047792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	83	389	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.392532005608789	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.392532005608789	1		389	307	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88635839	88635843	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CAAGG	CAAGG	-	novel	NA	P-0047792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	58	427	0	ENST00000372037.3:c.64_67+1del		p.X22_splice	ENST00000372037	NM_004329.2	22		3/13	1	2	FACETS	0.912	0.789	1	0.912	0.789	1	CLONAL	1	TRUE	1	0.392532005608789	2		427	324	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166772	32166780	+	inframe_deletion	In_Frame_Del	DEL	CGAGTGAAA	CGAGTGAAA	-	novel	NA	P-0047792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	201	943	0	ENST00000375023.3:c.4458_4466del	p.Phe1487_Arg1489del	p.F1487_R1489del	ENST00000375023	NM_004557.3	1486	ggTTTCACTCGa/gga	24/30	0.155825011444362	3	FACETS	1	0.968	1	0.541	0.5	0.583	INDETERMINATE	1	TRUE	1	0.392532005608789	3		943	1133	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0047794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	137	279	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	0.273754042405161	3	FACETS	1	0.925	1	1	0.925	1	CLONAL	2	TRUE	1	0.29	3		279	534	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188173	108188173	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1060501712	NA	P-0047794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	118	186	0	ENST00000278616.4:c.6272G>A	p.Trp2091Ter	p.W2091*	ENST00000278616	NM_000051.3	2091	tGg/tAg	43/63	0.295386716921714	3	FACETS	0.95	0.868	1	0.95	0.868	1	CLONAL	3	TRUE	0	0.29	3		186	327	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424116	49424116	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	218	683	0	ENST00000301067.7:c.13946G>T	p.Gly4649Val	p.G4649V	ENST00000301067	NM_003482.3	4649	gGg/gTg	42/54	0.295386716921714	3	FACETS	0.841	0.782	0.902	0.841	0.782	0.902	CLONAL	2	TRUE	1	0.29	3		683	1024	SUCCESS
APC	324	MSKCC	GRCh37	5	112174601	112174601	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	89	258	0	ENST00000257430.4:c.3310T>G	p.Ser1104Ala	p.S1104A	ENST00000257430	NM_000038.5	1104	Tca/Gca	16/16	0.17407530913978	5	FACETS	1	0.927	1	0.701	0.625	0.781	CLONAL	2	TRUE	2	0.29	5		258	419	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604665	48604665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660045	NA	P-0047795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	82	260	0	ENST00000342988.3:c.1487G>A	p.Arg496His	p.R496H	ENST00000342988	NM_005359.5	496	cGt/cAt	12/12	0.679302397500661	1	FACETS	0.866	0.783	0.951	0.866	0.783	0.951	CLONAL	1	FALSE	0	0.679302397500661	1		260	184	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186757	108186757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs864622251	NA	P-0047795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	85	324	0	ENST00000278616.4:c.6115G>A	p.Glu2039Lys	p.E2039K	ENST00000278616	NM_000051.3	2039	Gaa/Aaa	42/63	1	2	FACETS	0.805	0.719	0.895	0.805	0.719	0.895	CLONAL	1	FALSE	1	0.679302397500661	2		324	311	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129714	108129715	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0047795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	100	276	0	ENST00000278616.4:c.2380_2381del	p.Pro795LysfsTer2	p.P795Kfs*2	ENST00000278616	NM_000051.3	793	aAG/a	16/63	1	2	FACETS	0.947	0.856	1	0.947	0.856	1	CLONAL	1	FALSE	1	0.679302397500661	2		276	311	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442564	52442575	+	inframe_deletion	In_Frame_Del	DEL	TTCGCCGGGACC	TTCGCCGGGACC	-	novel	NA	P-0047795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	96	311	0	ENST00000460680.1:c.170_181del	p.Arg57_Lys61delinsGln	p.R57_K61delinsQ	ENST00000460680	NM_004656.3	57	cGGTCCCGGCGAAag/cag	4/17	1	2	FACETS	0.532	0.476	0.592	0.532	0.476	0.592	SUBCLONAL	1	FALSE	1	0.679302397500661	2		311	531	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0047796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	53	246	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.134675453061756	3	FACETS	1	0.886	1	0.52	0.445	0.601	INDETERMINATE	1	TRUE	1	0.339986464995746	3		246	351	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367867	15367867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1454979767	NA	P-0047796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	79	890	1	ENST00000263377.2:c.1459G>A	p.Asp487Asn	p.D487N	ENST00000263377	NM_058243.2	487	Gac/Aac	8/20	0.305516268793695	3	FACETS	0.544	0.477	0.616	0.272	0.238	0.308	SUBCLONAL	1	TRUE	1	0.339986464995746	3		891	1000	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912670	32912670	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398122776	NA	P-0047796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	67	275	0	ENST00000380152.3:c.4178C>T	p.Ala1393Val	p.A1393V	ENST00000380152		1393	gCg/gTg	11/27	0.131093255394905	5	FACETS	0.785	0.686	0.892	0.523	0.457	0.595	INDETERMINATE	2	TRUE	2	0.339986464995746	5		275	379	SUCCESS
APC	324	MSKCC	GRCh37	5	112175349	112175350	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0047796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	70	168	0	ENST00000257430.4:c.4058_4059del	p.Glu1353ValfsTer21	p.E1353Vfs*21	ENST00000257430	NM_000038.5	1353	gAA/g	16/16	0.339986464995746	2	FACETS	0.967	0.857	1	0.967	0.857	1	CLONAL	2	TRUE	0	0.339986464995746	2		168	213	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575448	64575449	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0047796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	114	794	0	ENST00000312049.6:c.568_569delinsTT	p.Gly190Leu	p.G190L	ENST00000312049	NM_130799.2	190	GGg/TTg	3/10	0.305516268793695	3	FACETS	0.814	0.732	0.901	0.407	0.366	0.451	CLONAL	1	TRUE	1	0.339986464995746	3		794	964	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578243	7578243	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	331	631	0	ENST00000269305.4:c.606del	p.Val203TrpfsTer44	p.V203Wfs*44	ENST00000269305	NM_001126112.2	202	cgT/cg	6/11	0.306634197981742	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	0	0.339986464995746	3		631	738	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381475	81381475	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	44	298	0	ENST00000222390.5:c.586G>T	p.Val196Leu	p.V196L	ENST00000222390	NM_000601.4	196	Gta/Tta	5/18	0.16278405887423	4	FACETS	0.88	0.74	1	0.44	0.37	0.518	INDETERMINATE	1	TRUE	2	0.339986464995746	4		298	394	SUCCESS
AR	367	MSKCC	GRCh37	X	66931382	66931382	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	29	299	0	ENST00000374690.3:c.2024T>C	p.Leu675Pro	p.L675P	ENST00000374690	NM_000044.3	675	cTg/cCg	4/8	0.174580885295459	2	FACETS	0.365	0.293	0.448			1	INDETERMINATE	1	TRUE	NA	0.339986464995746	2		299	467	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	180	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.82	0.767	0.873	1	0.993	1	CLONAL	2	TRUE	1	0.571959876195606	2		327	384	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0047797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	108	405	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.919	0.831	1	0.919	0.831	1	CLONAL	1	TRUE	1	0.571959876195606	2		405	411	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099023	27099023	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	157	467	0	ENST00000324856.7:c.3442del	p.Gln1148SerfsTer13	p.Q1148Sfs*13	ENST00000324856	NM_006015.4	1147	Ccc/cc	13/20	1	2	FACETS	0.951	0.876	1	0.951	0.876	1	CLONAL	1	TRUE	1	0.571959876195606	2		467	577	SUCCESS
APC	324	MSKCC	GRCh37	5	112163671	112163671	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554081901	NA	P-0047797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	57	199	0	ENST00000257430.4:c.1594C>T	p.Gln532Ter	p.Q532*	ENST00000257430	NM_000038.5	532	Caa/Taa	13/16	1	2	FACETS	0.863	0.749	0.984	0.863	0.749	0.984	CLONAL	1	TRUE	1	0.571959876195606	2		199	231	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045641	26045641	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs778244215	NA	P-0047797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	61	224	0	ENST00000540144.1:c.3G>A	p.Met1?	p.M1?	ENST00000540144	NM_003531.2	1	atG/atA	1/1	1	2	FACETS	0.978	0.856	1	0.978	0.856	1	CLONAL	1	TRUE	1	0.571959876195606	2		224	218	SUCCESS
APC	324	MSKCC	GRCh37	5	112175957	112175958	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	G	novel	NA	P-0047797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	35	157	0	ENST00000257430.4:c.4666_4667delinsG	p.Thr1556ValfsTer9	p.T1556Vfs*9	ENST00000257430	NM_000038.5	1556	ACt/Gt	16/16	1	2	FACETS	0.76	0.632	0.9	0.76	0.632	0.9	SUBCLONAL	1	TRUE	1	0.571959876195606	2		157	161	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0047798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	92	357	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	0.848	0.764	0.935	0.848	0.764	0.935	CLONAL	1	TRUE	1	0.788773128933958	2		357	275	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0047798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	101	264	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	0.908	0.824	0.995	0.908	0.824	0.995	CLONAL	1	TRUE	1	0.788773128933958	2		264	282	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748068	72748068	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	353	498	0	ENST00000357731.5:c.110G>C	p.Ser37Thr	p.S37T	ENST00000357731	NM_173808.2	37	aGt/aCt	1/7	0.788773128933958	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.788773128933958	1		498	471	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443849	52443879	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTCCTCACCTGGGTCGCTCTCCAGCTCCAG	CCTCCTCACCTGGGTCGCTCTCCAGCTCCAG	-	novel	NA	P-0047798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	228	836	0	ENST00000460680.1:c.16_37+9del		p.X6_splice	ENST00000460680	NM_004656.3	6		1/17	0.788773128933958	1	FACETS	0.858	0.813	0.903	0.858	0.813	0.903	CLONAL	1	TRUE	0	0.788773128933958	1		836	408	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0047799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	145	885	1	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	1	0.3	2		886	923	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881002	37881003	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCTCCCCA	rs397516982	NA	P-0047800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	395	893	0	ENST00000269571.5:c.2332_2340dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	-/GGCTCCCCA	20/27	0.610348025676666	1	FACETS	0.988	0.943	1	0.988	0.943	1	CLONAL	1	TRUE	0	0.609641044384637	1		893	912	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030378	49030378	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0047800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	44	279	0	ENST00000267163.4:c.1853C>G	p.Ser618Ter	p.S618*	ENST00000267163	NM_000321.2	618	tCa/tGa	19/27	0.609641044384637	1	FACETS	0.327	0.275	0.383	0.327	0.275	0.383	SUBCLONAL	1	TRUE	0	0.609641044384637	1		279	307	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097775	8097776	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	313	817	0	ENST00000346208.3:c.158dup	p.Asp54ArgfsTer249	p.D54Rfs*249	ENST00000346208		53	atc/aTtc	2/6	NA	2	FACETS	0.918	0.867	0.971			1	INDETERMINATE	1	TRUE	NA	0.609641044384637	2		817	1118	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120756	115120756	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	321	770	0	ENST00000257566.3:c.250C>T	p.Gln84Ter	p.Q84*	ENST00000257566	NM_016569.3	84	Cag/Tag	1/8	1	2	FACETS	0.943	0.891	0.996	0.943	0.891	0.996	CLONAL	1	TRUE	1	0.609641044384637	2		770	1117	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060881	38060881	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	322	755	0	ENST00000250448.2:c.1108G>T	p.Val370Leu	p.V370L	ENST00000250448	NM_004496.3	370	Gtg/Ttg	2/2	1	2	FACETS	0.945	0.893	0.998	0.945	0.893	0.998	CLONAL	1	TRUE	1	0.609641044384637	2		755	1118	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060979	38061200	+	inframe_deletion	In_Frame_Del	DEL	TGGTCCAGAGTCTGGGGGCTGGCGGCGGGCCCGGGGGCCGGCGCGCCCTCTAGCTGGCCGGTCTTCCCGTGCACACCCCGATGGAGGGGCGAGTCGGCGCTGGGGTTAGAGGCGCCAGAGGGGTCCTTGCGGCTCTCAGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTC	TGGTCCAGAGTCTGGGGGCTGGCGGCGGGCCCGGGGGCCGGCGCGCCCTCTAGCTGGCCGGTCTTCCCGTGCACACCCCGATGGAGGGGCGAGTCGGCGCTGGGGTTAGAGGCGCCAGAGGGGTCCTTGCGGCTCTCAGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTC	-	novel	NA	P-0047800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	430	575	0	ENST00000250448.2:c.789_1010del	p.Gln263_Asp336del	p.Q263_D336del	ENST00000250448	NM_004496.3	263	caGAAGCGCTTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGGCGCCAAGGGCGGCCCTGAGAGCCGCAAGGACCCCTCTGGCGCCTCTAACCCCAGCGCCGACTCGCCCCTCCATCGGGGTGTGCACGGGAAGACCGGCCAGCTAGAGGGCGCGCCGGCCCCCGGGCCCGCCGCCAGCCCCCAGACTCTGGACCAc/cac	2/2	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.609641044384637	2		575	955	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38064133	38064133	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1157025978	NA	P-0047800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	226	428	0	ENST00000250448.2:c.45G>C	p.Trp15Cys	p.W15C	ENST00000250448	NM_004496.3	15	tgG/tgC	1/2	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.609641044384637	2		428	690	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849434	68849434	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	256	577	0	ENST00000261769.5:c.1338del	p.Lys447SerfsTer8	p.K447Sfs*8	ENST00000261769	NM_004360.3	446	gCc/gc	10/16	0.610348025676666	1	FACETS	0.991	0.936	1	0.991	0.936	1	CLONAL	1	TRUE	0	0.609641044384637	1		577	589	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46266470	46266470	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	136	378	2	ENST00000371998.3:c.2455T>C	p.Ser819Pro	p.S819P	ENST00000371998		819	Tca/Cca	13/23	1	2	FACETS	0.868	0.794	0.945	0.868	0.794	0.945	CLONAL	1	TRUE	1	0.609641044384637	2		380	514	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271395	26271395	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	239	566	0	ENST00000305910.3:c.218G>T	p.Arg73Leu	p.R73L	ENST00000305910	NM_003534.2	73	cGa/cTa	1/1	1	2	FACETS	0.956	0.895	1	0.956	0.895	1	CLONAL	1	TRUE	1	0.609641044384637	2		566	820	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412704	63412704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	235	567	0	ENST00000330258.3:c.463G>A	p.Val155Met	p.V155M	ENST00000330258	NM_152424.3	155	Gtg/Atg	2/2	NA	2	FACETS	0.954	0.893	1			1	INDETERMINATE	1	TRUE	NA	0.609641044384637	2		567	808	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576886	7576889	+	frameshift_variant	Frame_Shift_Del	DEL	CTTC	CTTC	TTA	novel	NA	P-0047800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	278	704	1	ENST00000269305.4:c.957_960delinsTAA	p.Lys319AsnfsTer26	p.K319Nfs*26	ENST00000269305	NM_001126112.2	319	aaGAAG/aaTAA	9/11	0.610348025676666	1	FACETS	0.942	0.891	0.994	0.942	0.891	0.994	CLONAL	1	TRUE	0	0.609641044384637	1		705	673	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968202	68968202	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047800-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	159	480	0	ENST00000288368.4:c.1231C>A	p.Leu411Ile	p.L411I	ENST00000288368	NM_024870.2	411	Ctt/Att	10/40	1	2	FACETS	0.764	0.702	0.828	0.764	0.702	0.828	SUBCLONAL	1	TRUE	1	0.609641044384637	2		480	683	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	154	706	8	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.24	2		714	1261	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	51	386	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.752	0.639	0.877	0.752	0.639	0.877	SUBCLONAL	1	TRUE	1	0.24	2		386	565	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	115	458	3	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.984	0.885	1	0.984	0.885	1	CLONAL	1	TRUE	1	0.24	2		461	974	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	88	496	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.81	0.717	0.911	0.81	0.717	0.911	CLONAL	1	TRUE	1	0.24	2		496	905	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913250	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	70	320	0	ENST00000369535.4:c.34G>T	p.Gly12Cys	p.G12C	ENST00000369535	NM_002524.4	12	Ggt/Tgt	2/7	1	2	FACETS	0.994	0.867	1	0.994	0.867	1	CLONAL	1	TRUE	1	0.24	2		320	587	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	75	659	1	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.554	0.484	0.63	0.554	0.484	0.63	SUBCLONAL	1	TRUE	1	0.24	2		660	1128	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1385	76	918	7	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.433	0.378	0.493	0.433	0.378	0.493	SUBCLONAL	1	TRUE	1	0.24	2		925	1461	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489544	56489544	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761002408	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	123	400	0	ENST00000267101.3:c.2009G>A	p.Arg670Gln	p.R670Q	ENST00000267101	NM_001982.3	670	cGg/cAg	17/28	0.103419894997621	3	FACETS	1	0.983	1	0.708	0.64	0.779	INDETERMINATE	1	TRUE	1	0.24	3		400	811	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725042	89725042	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1085308041	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	26	163	0	ENST00000371953.3:c.1027-2A>G		p.X343_splice	ENST00000371953	NM_000314.4	343			1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.24	2		163	183	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967512	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1349928568	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	29	196	1	ENST00000265433.3:c.1396del	p.Arg466GlyfsTer18	p.R466Gfs*18	ENST00000265433	NM_002485.4	466	Agg/gg	10/16	0.103419894997621	3	FACETS	0.974	0.784	1	0.487	0.392	0.594	INDETERMINATE	1	TRUE	1	0.24	3		197	278	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628149	187628149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377150532	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	104	548	3	ENST00000441802.2:c.2833G>A	p.Val945Ile	p.V945I	ENST00000441802	NM_005245.3	945	Gtc/Atc	2/27	1	2	FACETS	0.931	0.832	1	0.931	0.832	1	CLONAL	1	TRUE	1	0.24	2		551	931	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752960	128752960	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	157	307	0	ENST00000377970.2:c.1121A>G	p.His374Arg	p.H374R	ENST00000377970	NM_002467.4	374	cAc/cGc	3/3	0.103419894997621	3	FACETS	1	0.945	1	1	0.945	1	INDETERMINATE	2	TRUE	1	0.24	3		307	706	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	94	311	1	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.24	2		312	703	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	133	513	2	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.24	2		515	1009	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916726	178916726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772110575	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	24	256	0	ENST00000263967.3:c.113G>A	p.Arg38His	p.R38H	ENST00000263967	NM_006218.2	38	cGt/cAt	2/21	1	2	FACETS	0.741	0.582	0.923	0.741	0.582	0.923	CLONAL	1	TRUE	1	0.24	2		256	270	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021422	42021422	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	46	329	0	ENST00000219905.7:c.3718C>T	p.Arg1240Ter	p.R1240*	ENST00000219905	NM_001164273.1	1240	Cga/Tga	11/24	1	2	FACETS	0.805	0.678	0.945	0.805	0.678	0.945	CLONAL	1	TRUE	1	0.24	2		329	476	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991757	72991758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760959844	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	102	435	1	ENST00000268489.5:c.2287dup	p.Glu763GlyfsTer26	p.E763Gfs*26	ENST00000268489	NM_006885.3	763	gag/gGag	2/10	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.24	2		436	799	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528636	89528636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	19	131	0	ENST00000336596.2:c.2936G>A	p.Gly979Asp	p.G979D	ENST00000336596	NM_005233.5	979	gGc/gAc	17/17	1	2	FACETS	0.66	0.502	0.845	0.66	0.502	0.845	SUBCLONAL	1	TRUE	1	0.24	2		131	240	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194110	94194110	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773469981	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	15	305	0	ENST00000323929.3:c.1318G>A	p.Ala440Thr	p.A440T	ENST00000323929	NM_005591.3	440	Gca/Aca	12/20	1	2	FACETS	0.496	0.363	0.656	0.496	0.363	0.656	SUBCLONAL	1	TRUE	1	0.24	2		305	252	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512370	38512370	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567767560	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	90	525	1	ENST00000254066.5:c.1286del	p.Gly429ValfsTer214	p.G429Vfs*214	ENST00000254066	NM_000964.3	427	ccG/cc	9/9	1	2	FACETS	0.933	0.827	1	0.933	0.827	1	CLONAL	1	TRUE	1	0.24	2		526	804	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948208	71948209	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs749079348	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1345	180	814	5	ENST00000298229.2:c.2927dup	p.Pro977ThrfsTer7	p.P977Tfs*7	ENST00000298229	NM_001567.3	974	gcc/gCcc	26/28	1	2	FACETS	0.984	0.904	1	0.984	0.904	1	CLONAL	1	TRUE	1	0.24	2		819	1525	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832266	72832266	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	80	408	0	ENST00000268489.5:c.4315C>T	p.Arg1439Ter	p.R1439*	ENST00000268489	NM_006885.3	1439	Cga/Tga	9/10	1	2	FACETS	0.864	0.759	0.976	0.864	0.759	0.976	CLONAL	1	TRUE	1	0.24	2		408	772	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132498	11132498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	139	801	3	ENST00000358026.2:c.2714G>A	p.Arg905His	p.R905H	ENST00000358026	NM_001128849.1	905	cGc/cAc	19/36	1	2	FACETS	0.887	0.805	0.973	0.887	0.805	0.973	CLONAL	1	TRUE	1	0.24	2		804	1306	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784098	120784098	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1414	239	973	3	ENST00000257552.2:c.887del	p.Pro296LeufsTer57	p.P296Lfs*57	ENST00000257552	NM_002442.3	296	cCt/ct	13/15	0.103419894997621	3	FACETS	1	0.99	1	0.675	0.628	0.724	INDETERMINATE	1	TRUE	1	0.24	3		976	1653	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288377	21288377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	118	560	3	ENST00000354336.3:c.622G>A	p.Ala208Thr	p.A208T	ENST00000354336	NM_005207.3	208	Gct/Act	2/3	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.24	2		563	950	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134407	30134407	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1188	92	794	0	ENST00000263025.4:c.124T>C	p.Tyr42His	p.Y42H	ENST00000263025	NM_002746.2	42	Tac/Cac	1/9	1	2	FACETS	0.599	0.53	0.673	0.599	0.53	0.673	SUBCLONAL	1	TRUE	1	0.24	2		794	1280	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139935	50139935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773258112	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1381	192	835	2	ENST00000246792.3:c.394C>T	p.Arg132Cys	p.R132C	ENST00000246792	NM_006270.3	132	Cgc/Tgc	4/6	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.24	2		837	1573	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663427	227663427	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	94	375	0	ENST00000305123.5:c.28T>C	p.Phe10Leu	p.F10L	ENST00000305123	NM_005544.2	10	Ttc/Ctc	1/2	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.24	2		375	753	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794962	242794962	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1432	177	944	1	ENST00000334409.5:c.247C>A	p.Pro83Thr	p.P83T	ENST00000334409	NM_005018.2	83	Ccc/Acc	2/5	1	2	FACETS	0.917	0.842	0.996	0.917	0.842	0.996	CLONAL	1	TRUE	1	0.24	2		945	1609	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664534	138664534	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	77	299	0	ENST00000330315.3:c.1031A>G	p.Gln344Arg	p.Q344R	ENST00000330315	NM_023067.3	344	cAg/cGg	1/1	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.24	2		299	537	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504425	186504426	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	rs1228653804	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	47	383	0	ENST00000323963.5:c.770_771dup	p.Glu258ArgfsTer15	p.E258Rfs*15	ENST00000323963		254	-/GA	7/11	1	2	FACETS	0.896	0.757	1	0.896	0.757	1	CLONAL	1	TRUE	1	0.24	2		383	437	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592070	55592070	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	58	350	0	ENST00000288135.5:c.1394C>A	p.Ser465Tyr	p.S465Y	ENST00000288135	NM_000222.2	465	tCt/tAt	9/21	1	2	FACETS	0.914	0.786	1	0.914	0.786	1	CLONAL	1	TRUE	1	0.24	2		350	529	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797736	32797736	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	113	500	0	ENST00000374899.4:c.1766T>C	p.Ile589Thr	p.I589T	ENST00000374899	NM_018833.2	589	aTc/aCc	10/12	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.24	2		500	907	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993066	90993066	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	54	248	0	ENST00000265433.3:c.376del	p.Thr126LeufsTer3	p.T126Lfs*3	ENST00000265433	NM_002485.4	126	Act/ct	4/16	0.103419894997621	3	FACETS	0.764	0.656	0.88	0.764	0.656	0.88	INDETERMINATE	2	TRUE	1	0.24	3		248	330	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753821	133753821	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	120	486	0	ENST00000318560.5:c.1290G>A	p.Trp430Ter	p.W430*	ENST00000318560	NM_005157.4	430	tgG/tgA	8/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.24	2		486	836	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591253	67591253	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	25	287	0	ENST00000274335.5:c.1751T>C	p.Leu584Ser	p.L584S	ENST00000274335		584	tTg/tCg	13/15	1	2	FACETS	0.574	0.452	0.714	0.574	0.452	0.714	SUBCLONAL	1	TRUE	1	0.24	2		287	363	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409462	80409462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	23	316	0	ENST00000286548.4:c.652C>T	p.His218Tyr	p.H218Y	ENST00000286548	NM_002072.3	218	Cac/Tac	5/7	1	2	FACETS	0.541	0.422	0.68	0.541	0.422	0.68	SUBCLONAL	1	TRUE	1	0.24	2		316	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0047802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	148	619	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.398562509761527	1	FACETS	0.775	0.709	0.845	0.775	0.709	0.845	SUBCLONAL	1	FALSE	0	0.398562509761527	1		619	767	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133048	30133048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	82	354	0	ENST00000331968.5:c.553C>T	p.His185Tyr	p.H185Y	ENST00000331968	NM_002742.2	185	Cat/Tat	4/18	0.398562509761527	1	FACETS	0.756	0.669	0.847	0.756	0.669	0.847	SUBCLONAL	1	FALSE	0	0.398562509761527	1		354	436	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68982094	68982094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	86	453	0	ENST00000288368.4:c.1468C>T	p.His490Tyr	p.H490Y	ENST00000288368	NM_024870.2	490	Cat/Tat	13/40	0.398562509761527	1	FACETS	0.785	0.698	0.878	0.785	0.698	0.878	SUBCLONAL	1	FALSE	0	0.398562509761527	1		453	440	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661913	29661913	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	86	392	0	ENST00000356175.3:c.5808del	p.Arg1937ValfsTer21	p.R1937Vfs*21	ENST00000356175	NM_000267.3	1936	gTt/gt	39/57	0.398562509761527	1	FACETS	0.873	0.777	0.974	0.873	0.777	0.974	CLONAL	1	FALSE	0	0.398562509761527	1		392	396	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0047803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	133	432	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.969	0.882	1	0.969	0.882	1	CLONAL	1	TRUE	1	0.421713009874354	2		432	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0047803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	21	730	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.397132560368935	1	FACETS	0.093	0.071	0.119	0.093	0.071	0.119	SUBCLONAL	1	TRUE	0	0.421713009874354	1		730	847	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527570	29527571	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1555610905	NA	P-0047803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	75	390	0	ENST00000356175.3:c.1020dup	p.Val341CysfsTer12	p.V341Cfs*12	ENST00000356175	NM_000267.3	340	tct/tcTt	9/57	0.397132560368935	1	FACETS	0.605	0.532	0.683	0.605	0.532	0.683	SUBCLONAL	1	TRUE	0	0.421713009874354	1		390	464	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678058	58678058	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	113	429	0	ENST00000305921.3:c.283C>G	p.Arg95Gly	p.R95G	ENST00000305921	NM_003620.3	95	Cgt/Ggt	1/6	1	2	FACETS	0.812	0.732	0.897	0.812	0.732	0.897	CLONAL	1	TRUE	1	0.421713009874354	2		429	660	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860918	45860918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377739888	NA	P-0047804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	321	840	0	ENST00000391945.4:c.1277C>T	p.Pro426Leu	p.P426L	ENST00000391945	NM_000400.3	426	cCg/cTg	13/23	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.651243489076862	2		840	909	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916920	178916925	+	inframe_deletion	In_Frame_Del	DEL	GAACCA	GAACCA	-	novel	NA	P-0047804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	163	341	0	ENST00000263967.3:c.308_313del	p.Glu103_Pro104del	p.E103_P104del	ENST00000263967	NM_006218.2	103	GAACCA/-	2/21	0.121018246841345	3	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.651243489076862	3		341	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577554	7577554	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	274	589	0	ENST00000269305.4:c.727del	p.Met243TrpfsTer4	p.M243Wfs*4	ENST00000269305	NM_001126112.2	243	Atg/tg	7/11	0.626570805162059	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.651243489076862	1		589	519	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566576	41566576	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0047804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	84	232	0	ENST00000263253.7:c.4452+1G>A		p.X1484_splice	ENST00000263253	NM_001429.3	1484			1	2	FACETS	0.874	0.781	0.972	0.874	0.781	0.972	CLONAL	1	TRUE	1	0.651243489076862	2		232	295	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919315	48919332	+	inframe_deletion	In_Frame_Del	DEL	ACTCTTCAGCAAATTGGA	ACTCTTCAGCAAATTGGA	-	novel	NA	P-0047804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	34	131	0	ENST00000267163.4:c.481_498del	p.Leu161_Glu166del	p.L161_E166del	ENST00000267163	NM_000321.2	160	gcACTCTTCAGCAAATTGGAa/gca	4/27	0.651243489076862	1	FACETS	0.711	0.598	0.831	0.711	0.598	0.831	SUBCLONAL	1	TRUE	0	0.651243489076862	1		131	99	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133126	30133178	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGCCAAGGTGAAGGATACACATCTCTCATGGCTTCCAGGGTGGACGCCCGCA	TGGCCAAGGTGAAGGATACACATCTCTCATGGCTTCCAGGGTGGACGCCCGCA	-	novel	NA	P-0047804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	93	297	0	ENST00000263025.4:c.320_353+19del		p.X107_splice	ENST00000263025	NM_002746.2	107		2/9	1	2	FACETS	0.939	0.845	1	0.939	0.845	1	CLONAL	1	TRUE	1	0.651243489076862	2		297	304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0047805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	156	507	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.279535416396731	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	0	0.279535416396731	1		507	888	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844231	68844233	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0047805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	138	419	0	ENST00000261769.5:c.819_821del	p.Glu273_Gly274delinsAsp	p.E273_G274delinsD	ENST00000261769	NM_004360.3	273	gaAGGt/gat	6/16	0.279535416396731	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	0	0.279535416396731	1		419	660	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16247364	16247364	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0047806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	75	177	0	ENST00000375759.3:c.1636-1G>A		p.X546_splice	ENST00000375759	NM_015001.2	546			1	2	FACETS	0.849	0.757	0.945	0.849	0.757	0.945	CLONAL	1	TRUE	1	0.80301286122613	2		177	220	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749146	43749146	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	298	728	0	ENST00000382044.4:c.1660G>T	p.Glu554Ter	p.E554*	ENST00000382044	NM_001141980.1	554	Gaa/Taa	12/28	0.803067824331234	1	FACETS	0.976	0.936	1	0.976	0.936	1	CLONAL	1	TRUE	0	0.80301286122613	1		728	455	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538829	23538831	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	novel	NA	P-0047806-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	246	514	0	ENST00000380871.4:c.608_610del	p.Glu203del	p.E203del	ENST00000380871	NM_006167.3	203	gAGGcc/gcc	2/2	0.80301286122613	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.80301286122613	1		514	333	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941657	48941657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1060503077	NA	P-0047808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	15	118	0	ENST00000267163.4:c.967G>T	p.Glu323Ter	p.E323*	ENST00000267163	NM_000321.2	323	Gaa/Taa	10/27	0.383553175658344	1	FACETS	0.8	0.597	1	0.8	0.597	1	CLONAL	1	TRUE	0	0.383553175658344	1		118	79	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578450	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0047808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	290	832	11	ENST00000269305.4:c.480_481delinsTT	p.Met160_Ala161delinsIleSer	p.M160_A161delinsIS	ENST00000269305	NM_001126112.2	160	atGGcc/atTTcc	5/11	0.371990132080723	2	FACETS	0.979	0.926	1	0.979	0.926	1	CLONAL	2	TRUE	0	0.383553175658344	2		843	772	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715823	18715823	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	45	169	2	ENST00000266497.5:c.3654T>G	p.Ser1218Arg	p.S1218R	ENST00000266497		1218	agT/agG	25/31	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.383553175658344	2		171	217	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786796	3786796	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	79	324	2	ENST00000262367.5:c.4415G>T	p.Trp1472Leu	p.W1472L	ENST00000262367	NM_004380.2	1472	tGg/tTg	27/31	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.383553175658344	2		326	361	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805552	46805552	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	319	853	9	ENST00000290295.7:c.404G>T	p.Gly135Val	p.G135V	ENST00000290295	NM_006361.5	135	gGa/gTa	1/2	0.383553175658344	3	FACETS	0.998	0.944	1	0.998	0.944	1	CLONAL	2	TRUE	1	0.383553175658344	3		862	993	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885815	23885815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	68	484	0	ENST00000374561.5:c.103G>A	p.Glu35Lys	p.E35K	ENST00000374561	NM_002167.4	35	Gag/Aag	1/3	1	2	FACETS	0.855	0.742	0.979	0.855	0.742	0.979	CLONAL	1	TRUE	1	0.16	2		484	994	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	63	418	2	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.16	2		420	779	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0047809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	52	410	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	0.966	0.821	1	0.966	0.821	1	CLONAL	1	TRUE	1	0.16	2		410	673	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	115	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.316254603920809	3	FACETS	0.952	0.871	1	0.952	0.871	1	CLONAL	3	TRUE	0	0.316254603920809	3		327	295	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507429	8507429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757372220	NA	P-0047810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	62	213	0	ENST00000356435.5:c.1549G>A	p.Gly517Arg	p.G517R	ENST00000356435		517	Ggg/Agg	11/35	0.19968158019541	4	FACETS	0.992	0.866	1	0.992	0.866	1	CLONAL	2	TRUE	2	0.316254603920809	4		213	260	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023064	27023064	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	31	79	0	ENST00000324856.7:c.172del	p.Ser58AlafsTer43	p.S58Afs*43	ENST00000324856	NM_006015.4	57	gAa/ga	1/20	0.118170600319678	5	FACETS	1	0.869	1	0.535	0.44	0.639	INDETERMINATE	2	TRUE	1	0.316254603920809	5		79	135	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117785	70117785	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368623884	NA	P-0047810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	140	775	1	ENST00000245479.2:c.253G>A	p.Asp85Asn	p.D85N	ENST00000245479	NM_000346.3	85	Gac/Aac	1/3	0.283925306845382	3	FACETS	0.946	0.866	1	0.946	0.866	1	CLONAL	2	TRUE	1	0.316254603920809	3		776	542	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948788	17948788	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	90	678	0	ENST00000458235.1:c.1654G>A	p.Glu552Lys	p.E552K	ENST00000458235	NM_000215.3	552	Gag/Aag	12/24	0.182050290644109	2	FACETS	0.872	0.774	0.976	0.436	0.387	0.488	INDETERMINATE	1	TRUE	0	0.316254603920809	2		678	653	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42851118	42851118	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	26	235	0	ENST00000398585.3:c.775T>G	p.Tyr259Asp	p.Y259D	ENST00000398585	NM_001135099.1	259	Tat/Gat	7/14	0.182050290644109	2	FACETS	0.956	0.764	1	0.478	0.382	0.586	INDETERMINATE	1	TRUE	0	0.316254603920809	2		235	172	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707603	176707603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	107	418	0	ENST00000439151.2:c.5660C>T	p.Ala1887Val	p.A1887V	ENST00000439151	NM_022455.4	1887	gCa/gTa	18/23	0.242323512708004	3	FACETS	0.916	0.827	1	0.916	0.827	1	CLONAL	2	TRUE	1	0.316254603920809	3		418	428	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0047811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	417	722	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			NA	2	FACETS	1	0.98	1			1	INDETERMINATE	2	TRUE	NA	0.558166739302	2		722	726	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39214712	39214712	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs56248239	NA	P-0047811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	61	300	0	ENST00000402219.2:c.3412A>G	p.Ile1138Val	p.I1138V	ENST00000402219	NM_005633.3	1138	Ata/Gta	22/23	0.535392278506199	3	FACETS	0.708	0.613	0.81	0.354	0.306	0.405	SUBCLONAL	1	TRUE	1	0.558166739302	3		300	395	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288663	33288663	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	300	387	0	ENST00000374542.5:c.889del	p.Ala297LeufsTer73	p.A297Lfs*73	ENST00000374542	NM_001141970.1	297	Gct/ct	3/8	0.558166739302	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.558166739302	3		387	440	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486338	8486338	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs752452602	NA	P-0047811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	44	215	0	ENST00000356435.5:c.2479C>G	p.Pro827Ala	p.P827A	ENST00000356435		827	Cct/Gct	17/35	0.535392278506199	3	FACETS	0.873	0.739	1	0.436	0.369	0.509	CLONAL	1	TRUE	1	0.558166739302	3		215	231	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0047812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	241	496	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.657905798356641	2		496	617	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0047812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	143	222	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	0.657905798356641	3	FACETS	1	0.959	1	0.537	0.492	0.583	CLONAL	1	TRUE	1	0.657905798356641	3		222	538	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654633	67654633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	181	301	0	ENST00000264010.4:c.1120A>G	p.Thr374Ala	p.T374A	ENST00000264010	NM_006565.3	374	Act/Gct	6/12	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.657905798356641	2		301	537	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828912	72828913	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0047812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	207	510	0	ENST00000268489.5:c.7668_7669del	p.Gln2557GlufsTer21	p.Q2557Efs*21	ENST00000268489	NM_006885.3	2556	gcGCag/gcag	9/10	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.657905798356641	2		510	628	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	145	343	0	ENST00000324856.7:c.5164del	p.Arg1722AspfsTer3	p.R1722Dfs*3	ENST00000324856	NM_006015.4	1722	Cga/ga	20/20	1	2	FACETS	0.936	0.86	1	0.936	0.86	1	CLONAL	1	TRUE	1	0.657905798356641	2		343	471	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692924	89692924	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0047812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	352	387	0	ENST00000371953.3:c.408T>A	p.Cys136Ter	p.C136*	ENST00000371953	NM_000314.4	136	tgT/tgA	5/9	0.657905798356641	3	FACETS	0.965	0.932	0.998	0.965	0.932	0.998	CLONAL	3	TRUE	0	0.657905798356641	3		387	491	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591204	67591269	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCAGGATGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAAAAGGTGTT	TTCAGGATGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGGTTGACTCAAAAAGGTGTT	-	novel	NA	P-0047812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	70	198	0	ENST00000274335.5:c.1746-44_1767del		p.X582_splice	ENST00000274335		582		13/15	1	2	FACETS	0.765	0.674	0.862	0.765	0.674	0.862	SUBCLONAL	1	TRUE	1	0.657905798356641	2		198	278	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045828	26045828	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	167	413	0	ENST00000540144.1:c.190C>T	p.Arg64Trp	p.R64W	ENST00000540144	NM_003531.2	64	Cgg/Tgg	1/1	1	2	FACETS	0.897	0.829	0.967	0.897	0.829	0.967	CLONAL	1	TRUE	1	0.657905798356641	2		413	566	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	189	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.224131614791042	5	FACETS	0.955	0.888	1	0.955	0.888	1	CLONAL	4	TRUE	1	0.224131614791042	5		327	590	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663491	29663491	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	50	271	1	ENST00000356175.3:c.6084G>T	p.Lys2028Asn	p.K2028N	ENST00000356175	NM_000267.3	2028	aaG/aaT	40/57	0.224131614791042	3	FACETS	1	0.861	1	0.507	0.431	0.592	CLONAL	1	TRUE	1	0.224131614791042	3		272	489	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805034	43805037	+	frameshift_variant	Frame_Shift_Del	DEL	AGTG	AGTG	-	novel	NA	P-0047813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	94	673	0	ENST00000372470.3:c.485_488del	p.Ser162IlefsTer3	p.S162Ifs*3	ENST00000372470	NM_005373.2	162	AGTGat/at	4/12	0.224131614791042	3	FACETS	1	0.905	1	0.51	0.453	0.571	CLONAL	1	TRUE	1	0.224131614791042	3		673	914	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258708	115258709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0047813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	55	301	0	ENST00000369535.4:c.73dup	p.Gln25ProfsTer7	p.Q25Pfs*7	ENST00000369535	NM_002524.4	25	cag/cCag	2/7	0.224131614791042	3	FACETS	1	0.884	1	0.519	0.444	0.601	CLONAL	1	TRUE	1	0.224131614791042	3		301	526	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944635	38944635	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	43	223	0	ENST00000357387.3:c.4826G>C	p.Arg1609Pro	p.R1609P	ENST00000357387	NM_152756.3	1609	cGt/cCt	36/38	0.204280192086114	2	FACETS	1	0.84	1	0.501	0.42	0.59	CLONAL	1	TRUE	0	0.224131614791042	2		223	383	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984127	2984127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	146	509	0	ENST00000396946.4:c.403G>A	p.Val135Ile	p.V135I	ENST00000396946	NM_032415.4	135	Gtc/Atc	5/25	0.224131614791042	5	FACETS	0.961	0.877	1	0.64	0.584	0.699	CLONAL	2	TRUE	2	0.224131614791042	5		509	906	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59937204	59937204	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs751182362	NA	P-0047813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	44	352	0	ENST00000259008.2:c.158G>T	p.Ser53Ile	p.S53I	ENST00000259008	NM_032043.2	53	aGc/aTc	3/20	0.224131614791042	3	FACETS	0.777	0.651	0.917	0.388	0.325	0.459	CLONAL	1	TRUE	1	0.224131614791042	3		352	562	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	52	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.2	2		327	416	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0047814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	46	405	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.875	0.736	1	0.875	0.736	1	CLONAL	1	TRUE	1	0.2	2		405	526	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0047814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	71	371	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.824	0.722	0.933	1	0.978	1	CLONAL	2	TRUE	1	0.2	2		371	431	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097808	27097808	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	28	259	0	ENST00000324856.7:c.3399del	p.Ser1134LeufsTer27	p.S1134Lfs*27	ENST00000324856	NM_006015.4	1133	Ccc/cc	12/20	1	2	FACETS	0.733	0.586	0.901	0.733	0.586	0.901	CLONAL	1	TRUE	1	0.2	2		259	382	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435828	56435828	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	56	543	0	ENST00000407977.2:c.1309del	p.Arg437GlyfsTer65	p.R437Gfs*65	ENST00000407977		437	Cgg/gg	9/10	1	2	FACETS	0.979	0.839	1	0.979	0.839	1	CLONAL	1	TRUE	1	0.2	2		543	572	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211612	36211612	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	47	447	0	ENST00000222270.7:c.1363G>T	p.Glu455Ter	p.E455*	ENST00000222270	NM_014727.1	455	Gaa/Taa	3/37	1	2	FACETS	0.983	0.83	1	0.983	0.83	1	CLONAL	1	TRUE	1	0.2	2		447	478	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050292	128050292	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	49	441	0	ENST00000285398.2:c.365C>T	p.Ser122Phe	p.S122F	ENST00000285398	NM_000122.1	122	tCc/tTc	3/15	1	2	FACETS	0.72	0.608	0.842	0.72	0.608	0.842	SUBCLONAL	1	TRUE	1	0.2	2		441	681	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324228	62324228	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1211605868	NA	P-0047814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	91	875	0	ENST00000360203.5:c.2723G>A	p.Ser908Asn	p.S908N	ENST00000360203	NM_001283009.1	908	aGc/aAc	29/35	1	2	FACETS	0.81	0.717	0.909	0.81	0.717	0.909	CLONAL	1	TRUE	1	0.2	2		875	1124	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0047815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	321	607	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.837144358979445	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.837144358979445	1		608	434	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0047815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	73	168	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.851	0.758	0.947	0.851	0.758	0.947	CLONAL	1	TRUE	1	0.837144358979445	2		168	205	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0047815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	833	394	8	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	0.837144358979445	6	FACETS	0.964	0.944	0.984			1	CLONAL	5	TRUE	NA	0.837144358979445	6		402	1104	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881392	37881392	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	1888	712	34	ENST00000269571.5:c.2584A>G	p.Thr862Ala	p.T862A	ENST00000269571		862	Aca/Gca	21/27	0.837144358979445	6	FACETS	1	0.994	1			1	CLONAL	5	TRUE	NA	0.837144358979445	6		746	2386	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681119	117681120	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs748436511	NA	P-0047815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	44	376	0	ENST00000368508.3:c.3500dup	p.Leu1167PhefsTer26	p.L1167Ffs*26	ENST00000368508	NM_002944.2	1167	tta/ttTa	23/43	1	2	FACETS	0.242	0.203	0.285	0.242	0.203	0.285	SUBCLONAL	1	TRUE	1	0.837144358979445	2		376	434	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124609	108124610	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	163	280	0	ENST00000278616.4:c.1971dup	p.Asp658Ter	p.D658*	ENST00000278616	NM_000051.3	656	act/acTt	13/63	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.837144358979445	2		280	363	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231386	46231386	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0047815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	176	285	3	ENST00000334344.6:c.1226T>A	p.Leu409Ter	p.L409*	ENST00000334344	NM_152641.2	409	tTa/tAa	10/21	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.837144358979445	2		288	370	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244146	46244147	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0047815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	189	344	1	ENST00000334344.6:c.2241_2242del	p.His747GlnfsTer93	p.H747Qfs*93	ENST00000334344	NM_152641.2	747	cAT/c	15/21	NA	2	FACETS	1	0.938	1			1	INDETERMINATE	1	TRUE	NA	0.837144358979445	2		345	450	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68934958	68934958	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	139	297	2	ENST00000487270.1:c.1027G>T	p.Val343Phe	p.V343F	ENST00000487270	NM_133509.3	343	Gtt/Ttt	10/11	1	2	FACETS	0.876	0.807	0.947	0.876	0.807	0.947	CLONAL	1	TRUE	1	0.837144358979445	2		299	379	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858511	9858511	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs751186803	NA	P-0047815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	198	502	1	ENST00000330684.3:c.2890C>T	p.Gln964Ter	p.Q964*	ENST00000330684	NM_001134407.1	964	Caa/Taa	13/13	1	2	FACETS	0.893	0.833	0.953	0.893	0.833	0.953	CLONAL	1	TRUE	1	0.837144358979445	2		503	530	SUCCESS
APC	324	MSKCC	GRCh37	5	112173409	112173410	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0047815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	100	209	0	ENST00000257430.4:c.2120_2121dup	p.Lys708SerfsTer11	p.K708Sfs*11	ENST00000257430	NM_000038.5	706	-/CT	16/16	1	2	FACETS	0.885	0.803	0.969	0.885	0.803	0.969	CLONAL	1	TRUE	1	0.837144358979445	2		209	270	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973908	131973908	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	111	207	2	ENST00000265335.6:c.3611G>T	p.Gly1204Val	p.G1204V	ENST00000265335		1204	gGa/gTa	23/25	1	2	FACETS	0.911	0.832	0.993	0.911	0.832	0.993	CLONAL	1	TRUE	1	0.837144358979445	2		209	291	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878973	151878973	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0047815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	212	447	2	ENST00000262189.6:c.5972C>G	p.Ser1991Ter	p.S1991*	ENST00000262189	NM_170606.2	1991	tCa/tGa	36/59	1	2	FACETS	0.94	0.88	1	0.94	0.88	1	CLONAL	1	TRUE	1	0.837144358979445	2		449	539	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	160	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.45906859157942	2	FACETS	0.922	0.858	0.988	0.922	0.858	0.988	CLONAL	2	TRUE	0	0.471404475419645	2		327	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0047816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	219	519	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.466704586914259	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.471404475419645	1		519	691	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512270	38512270	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs866777491	NA	P-0047816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	111	730	0	ENST00000254066.5:c.1181G>T	p.Arg394Leu	p.R394L	ENST00000254066	NM_000964.3	394	cGg/cTg	9/9	0.280700306411209	1	FACETS	0.36	0.323	0.4	0.36	0.323	0.4	INDETERMINATE	1	TRUE	0	0.471404475419645	1		730	1000	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591888	48591888	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	45	296	0	ENST00000342988.3:c.1051G>T	p.Asp351Tyr	p.D351Y	ENST00000342988	NM_005359.5	351	Gat/Tat	9/12	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.16	2		296	491	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796754	135796754	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203434	NA	P-0047817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	37	141	0	ENST00000298552.3:c.733C>T	p.Arg245Ter	p.R245*	ENST00000298552	NM_001162426.1	245	Cga/Tga	8/23	0.204515246545537	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.16	1		141	300	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090446	37090446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750217	NA	P-0047817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	48	270	1	ENST00000231790.2:c.2041G>A	p.Ala681Thr	p.A681T	ENST00000231790	NM_000249.3	681	Gct/Act	18/19	0.167130565661438	1	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	0	0.16	1		271	525	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212174	36212174	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1177191130	NA	P-0047817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	42	422	0	ENST00000222270.7:c.1925G>A	p.Arg642Gln	p.R642Q	ENST00000222270	NM_014727.1	642	cGg/cAg	3/37	1	2	FACETS	0.839	0.699	0.994	0.839	0.699	0.994	CLONAL	1	TRUE	1	0.16	2		422	626	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702612	52702614	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0047817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	27	244	0	ENST00000394830.3:c.284_286del	p.Met95del	p.M95del	ENST00000394830	NM_018313.4	95	aTGAaa/aaa	4/30	0.167130565661438	1	FACETS	0.772	0.614	0.953	0.772	0.614	0.953	CLONAL	1	TRUE	0	0.16	1		244	402	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522578	176522578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	110	742	1	ENST00000292408.4:c.1675C>T	p.Arg559Trp	p.R559W	ENST00000292408	NM_213647.1	559	Cgg/Tgg	13/18	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.16	2		743	1178	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800875	120800875	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	64	570	2	ENST00000257552.2:c.373G>A	p.Val125Met	p.V125M	ENST00000257552	NM_002442.3	125	Gtg/Atg	6/15	1	2	FACETS	0.725	0.626	0.834	0.725	0.626	0.834	SUBCLONAL	1	TRUE	1	0.16	2		572	1103	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73340158	73340158	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	18	158	0	ENST00000377767.4:c.1922T>C	p.Met641Thr	p.M641T	ENST00000377767	NM_014953.3	641	aTg/aCg	15/21	1	2	FACETS	0.697	0.524	0.901	0.697	0.524	0.901	SUBCLONAL	1	TRUE	1	0.16	2		158	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0047818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	81	551	0	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.151765899696088	2	FACETS	0.698	0.614	0.787	0.349	0.307	0.394	INDETERMINATE	1	TRUE	0	0.327051470167408	2		551	710	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434931	49434931	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	104	605	1	ENST00000301067.7:c.6622C>T	p.Gln2208Ter	p.Q2208*	ENST00000301067	NM_003482.3	2208	Cag/Tag	31/54	0.248735255209719	3	FACETS	0.896	0.802	0.996	0.448	0.401	0.498	CLONAL	1	TRUE	1	0.327051470167408	3		606	826	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422609	49422609	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0047818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	50	436	0	ENST00000301067.7:c.14382+2T>C		p.X4794_splice	ENST00000301067	NM_003482.3	4794			0.248735255209719	3	FACETS	0.491	0.416	0.575	0.246	0.208	0.288	SUBCLONAL	1	TRUE	1	0.327051470167408	3		436	724	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18958561	18958561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	79	438	0	ENST00000262803.5:c.380G>A	p.Gly127Glu	p.G127E	ENST00000262803	NM_002911.3	127	gGa/gAa	3/24	0.144776807040761	3	FACETS	0.68	0.597	0.769			1	INDETERMINATE	1	TRUE	NA	0.327051470167408	3		438	827	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233082	55233082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	53	447	1	ENST00000275493.2:c.1832C>T	p.Ala611Val	p.A611V	ENST00000275493	NM_005228.3	611	gCa/gTa	15/28	0.247349319933633	3	FACETS	0.526	0.447	0.612	0.263	0.223	0.306	SUBCLONAL	1	TRUE	1	0.327051470167408	3		448	717	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845181	151845181	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	51	447	0	ENST00000262189.6:c.13831T>G	p.Phe4611Val	p.F4611V	ENST00000262189	NM_170606.2	4611	Ttt/Gtt	52/59	1	2	FACETS	0.475	0.403	0.555	0.475	0.403	0.555	SUBCLONAL	1	TRUE	1	0.327051470167408	2		447	656	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425558	49425587	+	inframe_deletion	In_Frame_Del	DEL	TGGAGGTGTGGGATGGACAGGGCCAAGGAC	TGGAGGTGTGGGATGGACAGGGCCAAGGAC	-	novel	NA	P-0047820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	54	902	0	ENST00000301067.7:c.12901_12930del	p.Val4301_Pro4310del	p.V4301_P4310del	ENST00000301067	NM_003482.3	4301	GTCCTTGGCCCTGTCCATCCCACACCTCCA/-	39/54	0.0712377300766636	3	FACETS	0.473	0.402	0.55	0.236	0.201	0.275	INDETERMINATE	1	FALSE	1	0.309724360085943	3		902	852	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439157	52439157	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	52	651	0	ENST00000460680.1:c.1085del	p.Asp362AlafsTer68	p.D362Afs*68	ENST00000460680	NM_004656.3	362	gAc/gc	11/17	1	2	FACETS	0.467	0.397	0.545	0.467	0.397	0.545	SUBCLONAL	1	FALSE	1	0.309724360085943	2		651	719	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813309	102813309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776234219	NA	P-0047821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	122	522	0	ENST00000307046.8:c.380C>T	p.Thr127Ile	p.T127I	ENST00000307046	NM_001111285.1	127	aCc/aTc	3/4	0.264770818286526	5	FACETS	1	0.983	1	0.468	0.424	0.515	CLONAL	1	FALSE	2	0.418076212352373	5		522	676	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339126	65339126	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	60	417	0	ENST00000342505.4:c.410G>T	p.Gly137Val	p.G137V	ENST00000342505	NM_002227.2	137	gGc/gTc	5/25	0.264770818286526	5	FACETS	1	0.952	1	0.411	0.355	0.471	CLONAL	1	FALSE	2	0.418076212352373	5		417	379	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961845	41961845	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	43	314	0	ENST00000219905.7:c.753C>A	p.Tyr251Ter	p.Y251*	ENST00000219905	NM_001164273.1	251	taC/taA	2/24	0.412340960270833	2	FACETS	0.816	0.7	0.938	0.816	0.7	0.938	CLONAL	2	FALSE	0	0.418076212352373	2		314	126	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385156	41385156	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	118	757	1	ENST00000373198.4:c.805A>T	p.Ile269Phe	p.I269F	ENST00000373198	NM_133170.3	269	Atc/Ttc	6/32	0.418076212352373	4	FACETS	0.947	0.854	1	0.316	0.284	0.349	CLONAL	1	FALSE	1	0.418076212352373	4		758	845	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38981962	38981969	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCCTACC	TTCCTACC	-	novel	NA	P-0047821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	23	193	0	ENST00000357387.3:c.753_753+7del		p.X251_splice	ENST00000357387	NM_152756.3	251		8/38	0.418076212352373	3	FACETS	1	0.875	1	0.578	0.458	0.713	CLONAL	1	FALSE	1	0.418076212352373	3		193	115	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275619	41275633	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGTTTTTCAGGCTA	CTGTTTTTCAGGCTA	-	novel	NA	P-0047821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	41	286	0	ENST00000349496.5:c.1525-6_1533del		p.X509_splice	ENST00000349496	NM_001904.3	509		10/15	0.418076212352373	4	FACETS	1	0.938	1	0.418	0.351	0.49	CLONAL	1	FALSE	1	0.418076212352373	4		286	222	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578473	7578515	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGGGGTGTGGAATCAACCCACAGCTGCACAGGGCAGGTCTT	GCGGGGGTGTGGAATCAACCCACAGCTGCACAGGGCAGGTCTT	ACGGG	novel	NA	P-0047821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	467	942	1	ENST00000269305.4:c.415_457delinsCCCGT	p.Lys139ProfsTer29	p.K139Pfs*29	ENST00000269305	NM_001126112.2	139	AAGACCTGCCCTGTGCAGCTGTGGGTTGATTCCACACCCCCGCcc/CCCGTcc	5/11	0.331434919168272	3	FACETS	0.856	0.821	0.891	0.856	0.821	0.891	CLONAL	3	FALSE	0	0.418076212352373	3		943	1052	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	106	706	8	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.938	0.838	1	0.938	0.838	1	CLONAL	1	TRUE	1	0.19	2		714	1190	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	10	347	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.721	0.49	1	0.721	0.49	1	CLONAL	1	TRUE	1	0.19	2		347	146	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1216	120	848	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.105394515878548	3	FACETS	1	0.926	1	0.518	0.466	0.573	INDETERMINATE	1	TRUE	1	0.19	3		848	1336	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434367	121434367	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	118	739	1	ENST00000257555.6:c.1136del	p.Pro379LeufsTer5	p.P379Lfs*5	ENST00000257555		377	ctC/ct	6/10	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.19	2		740	1203	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	33	453	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.534	0.434	0.648	0.534	0.434	0.648	SUBCLONAL	1	TRUE	1	0.19	2		453	650	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	21	249	1	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.704	0.542	0.893	0.704	0.542	0.893	SUBCLONAL	1	TRUE	1	0.19	2		250	314	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	60	430	3	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	0.3	3	FACETS	1	0.897	1			1	CLONAL	1	TRUE	NA	0.19	3		433	658	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1434	138	918	7	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.924	0.838	1	0.924	0.838	1	CLONAL	1	TRUE	1	0.19	2		925	1572	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	77	307	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.927	0.818	1	1	0.982	1	CLONAL	2	TRUE	1	0.19	2		308	437	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843688	156843688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754611476	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1253	116	866	1	ENST00000524377.1:c.1114G>A	p.Ala372Thr	p.A372T	ENST00000524377	NM_002529.3	372	Gcc/Acc	8/17	1	2	FACETS	0.892	0.801	0.989	0.892	0.801	0.989	CLONAL	1	TRUE	1	0.19	2		867	1369	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303605	30303605	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	77	441	0	ENST00000262643.3:c.33G>T	p.Lys11Asn	p.K11N	ENST00000262643	NM_001238.2	11	aaG/aaT	3/12	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.19	2		441	798	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053022	180053023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750808726	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1345	94	943	1	ENST00000261937.6:c.1267dup	p.Gln423ProfsTer4	p.Q423Pfs*4	ENST00000261937	NM_182925.4	423	cag/cCag	10/30	1	2	FACETS	0.688	0.609	0.772	0.688	0.609	0.772	SUBCLONAL	1	TRUE	1	0.19	2		944	1439	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755554	39755554	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	53	441	2	ENST00000288319.7:c.1211del	p.Pro404ArgfsTer25	p.P404Rfs*25	ENST00000288319	NM_182918.3	404	cCg/cg	10/10	1	2	FACETS	0.79	0.673	0.919	0.79	0.673	0.919	CLONAL	1	TRUE	1	0.19	2		443	706	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683192	88683192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199907158	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	33	294	1	ENST00000372037.3:c.1402G>A	p.Glu468Lys	p.E468K	ENST00000372037	NM_004329.2	468	Gaa/Aaa	12/13	1	2	FACETS	0.936	0.763	1	0.936	0.763	1	CLONAL	1	TRUE	1	0.19	2		295	371	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466021	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1308	135	899	0	ENST00000227507.2:c.859C>G	p.Pro287Ala	p.P287A	ENST00000227507	NM_053056.2	287	Ccc/Gcc	5/5	1	2	FACETS	0.985	0.892	1	0.985	0.892	1	CLONAL	1	TRUE	1	0.19	2		899	1443	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	118	791	3	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.19	2		794	1101	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882050	36882050	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs780753361	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	105	884	5	ENST00000358127.4:c.963del	p.Ala322LeufsTer11	p.A322Lfs*11	ENST00000358127	NM_001280556.1	321	ccC/cc	8/10	1	2	FACETS	0.897	0.801	0.999	0.897	0.801	0.999	CLONAL	1	TRUE	1	0.19	2		889	1232	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	63	639	4	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	1	2	FACETS	0.877	0.757	1	0.877	0.757	1	CLONAL	1	TRUE	1	0.19	2		643	756	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561250	9561250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	48	348	0	ENST00000353224.5:c.532G>A	p.Gly178Arg	p.G178R	ENST00000353224	NM_177990.2	178	Ggg/Agg	4/10	1	2	FACETS	0.959	0.81	1	0.959	0.81	1	CLONAL	1	TRUE	1	0.19	2		348	527	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934243	49934243	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1407832113	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	110	726	4	ENST00000296474.3:c.2264del	p.Gly755ValfsTer19	p.G755Vfs*19	ENST00000296474	NM_002447.2	755	gGt/gt	8/20	1	2	FACETS	0.996	0.893	1	0.996	0.893	1	CLONAL	1	TRUE	1	0.19	2		730	1162	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155778	106155779	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs759055581	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	27	318	0	ENST00000380013.4:c.685dup	p.Thr229AsnfsTer25	p.T229Nfs*25	ENST00000380013	NM_001127208.2	227	gaa/gAaa	3/11	1	2	FACETS	0.783	0.623	0.966	0.783	0.623	0.966	CLONAL	1	TRUE	1	0.19	2		318	363	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076932	41076932	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	40	442	0	ENST00000373198.4:c.1488del	p.Phe498LeufsTer103	p.F498Lfs*103	ENST00000373198	NM_133170.3	496	ggG/gg	9/32	1	2	FACETS	0.72	0.597	0.857	0.72	0.597	0.857	SUBCLONAL	1	TRUE	1	0.19	2		442	585	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800902	120800903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748469666	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	96	644	2	ENST00000257552.2:c.345dup	p.Leu116AlafsTer15	p.L116Afs*15	ENST00000257552	NM_002442.3	115	-/G	6/15	1	2	FACETS	0.976	0.868	1	0.976	0.868	1	CLONAL	1	TRUE	1	0.19	2		646	1035	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749571	41749571	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200850031	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	75	602	1	ENST00000301178.4:c.1496G>A	p.Arg499His	p.R499H	ENST00000301178	NM_021913.4	499	cGc/cAc	12/20	1	2	FACETS	0.797	0.697	0.906	0.797	0.697	0.906	CLONAL	1	TRUE	1	0.19	2		603	990	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244325	5244325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1270	151	912	0	ENST00000357368.4:c.1157G>A	p.Arg386His	p.R386H	ENST00000357368	NM_002850.3	386	cGt/cAt	11/38	0.105394515878548	0	FACETS	0.906	0.826	0.991			1	INDETERMINATE	1	TRUE	0	0.19	0		912	1421	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421002	49421002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529656123	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	38	374	0	ENST00000301067.7:c.14747C>T	p.Pro4916Leu	p.P4916L	ENST00000301067	NM_003482.3	4916	cCg/cTg	48/54	0.105394515878548	3	FACETS	0.69	0.569	0.825	0.345	0.284	0.413	INDETERMINATE	1	TRUE	1	0.19	3		374	635	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371771	116371771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	36	294	0	ENST00000397752.3:c.1250G>A	p.Arg417Gln	p.R417Q	ENST00000397752	NM_000245.2	417	cGa/cAa	3/21	1	2	FACETS	0.805	0.661	0.966	0.805	0.661	0.966	CLONAL	1	TRUE	1	0.19	2		294	471	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127460	55127460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779332376	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	60	445	0	ENST00000257290.5:c.248C>T	p.Thr83Met	p.T83M	ENST00000257290	NM_006206.4	83	aCg/aTg	3/23	1	2	FACETS	0.838	0.72	0.966	0.838	0.72	0.966	CLONAL	1	TRUE	1	0.19	2		445	754	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209298	98209298	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149667902	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	105	772	0	ENST00000331920.6:c.4240G>A	p.Val1414Met	p.V1414M	ENST00000331920	NM_000264.3	1414	Gtg/Atg	23/24	1	2	FACETS	0.935	0.835	1	0.935	0.835	1	CLONAL	1	TRUE	1	0.19	2		772	1182	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211135	36211135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201417711	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1464	151	972	0	ENST00000222270.7:c.886G>A	p.Gly296Ser	p.G296S	ENST00000222270	NM_014727.1	296	Ggc/Agc	3/37	1	2	FACETS	0.984	0.896	1	0.984	0.896	1	CLONAL	1	TRUE	1	0.19	2		972	1615	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805356	89805356	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	47	531	0	ENST00000389301.3:c.4194del	p.Ala1399LeufsTer8	p.A1399Lfs*8	ENST00000389301	NM_000135.2	1398	aaA/aa	42/43	1	2	FACETS	0.684	0.576	0.804	0.684	0.576	0.804	SUBCLONAL	1	TRUE	1	0.19	2		531	723	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435116	49435116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs563981206	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	110	597	0	ENST00000301067.7:c.6437C>T	p.Pro2146Leu	p.P2146L	ENST00000301067	NM_003482.3	2146	cCg/cTg	31/54	0.105394515878548	3	FACETS	1	0.964	1	0.583	0.523	0.648	INDETERMINATE	1	TRUE	1	0.19	3		597	1087	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412530	63412530	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	73	559	0	ENST00000330258.3:c.637C>T	p.Gln213Ter	p.Q213*	ENST00000330258	NM_152424.3	213	Cag/Tag	2/2	1	2	FACETS	0.918	0.801	1	0.918	0.801	1	CLONAL	1	TRUE	1	0.19	2		559	837	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968288	18968288	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776533487	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	112	905	0	ENST00000262803.5:c.2128G>A	p.Ala710Thr	p.A710T	ENST00000262803	NM_002911.3	710	Gcc/Acc	15/24	1	2	FACETS	0.908	0.814	1	0.908	0.814	1	CLONAL	1	TRUE	1	0.19	2		905	1298	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784110	9784110	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	80	615	0	ENST00000377346.4:c.2678A>C	p.Asp893Ala	p.D893A	ENST00000377346	NM_005026.3	893	gAt/gCt	21/24	1	2	FACETS	0.756	0.663	0.856	0.756	0.663	0.856	SUBCLONAL	1	TRUE	1	0.19	2		615	1114	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107219	27107219	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	42	305	0	ENST00000324856.7:c.6830A>C	p.Asp2277Ala	p.D2277A	ENST00000324856	NM_006015.4	2277	gAt/gCt	20/20	1	2	FACETS	0.761	0.634	0.902	0.761	0.634	0.902	CLONAL	1	TRUE	1	0.19	2		305	581	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28601483	28601483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1430082772	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	92	591	2	ENST00000253063.3:c.1168C>T	p.Arg390Cys	p.R390C	ENST00000253063	NM_031459.4	390	Cgc/Tgc	8/10	1	2	FACETS	0.915	0.811	1	0.915	0.811	1	CLONAL	1	TRUE	1	0.19	2		593	1058	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551940	150551940	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	125	545	0	ENST00000369026.2:c.67del	p.Ala23ProfsTer26	p.A23Pfs*26	ENST00000369026	NM_021960.4	23	Gcc/cc	1/3	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.19	2		545	1162	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851075	63851075	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	54	445	0	ENST00000279873.7:c.1853C>T	p.Ala618Val	p.A618V	ENST00000279873	NM_032199.2	618	gCc/gTc	10/10	1	2	FACETS	0.73	0.622	0.848	0.73	0.622	0.848	SUBCLONAL	1	TRUE	1	0.19	2		445	779	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114799844	114799844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	63	465	0	ENST00000543371.1:c.511G>A	p.Ala171Thr	p.A171T	ENST00000543371	NM_001198531.1	171	Gcc/Acc	5/14	1	2	FACETS	0.817	0.705	0.939	0.817	0.705	0.939	CLONAL	1	TRUE	1	0.19	2		465	812	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420742	49420742	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	99	649	0	ENST00000301067.7:c.15007C>T	p.Gln5003Ter	p.Q5003*	ENST00000301067	NM_003482.3	5003	Cag/Tag	48/54	0.105394515878548	3	FACETS	1	0.919	1	0.52	0.462	0.581	INDETERMINATE	1	TRUE	1	0.19	3		649	1098	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690569	88690569	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	43	329	0	ENST00000360948.2:c.461A>G	p.Glu154Gly	p.E154G	ENST00000360948	NM_001012338.2	154	gAa/gGa	5/19	1	2	FACETS	0.857	0.717	1	0.857	0.717	1	CLONAL	1	TRUE	1	0.19	2		329	528	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892132	9892132	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	45	354	0	ENST00000330684.3:c.2356+2T>C		p.X786_splice	ENST00000330684	NM_001134407.1	786			1	2	FACETS	0.849	0.713	1	0.849	0.713	1	CLONAL	1	TRUE	1	0.19	2		354	558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578498	7578498	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786201419	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1417	165	949	2	ENST00000269305.4:c.432G>T	p.Gln144His	p.Q144H	ENST00000269305	NM_001126112.2	144	caG/caT	5/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.19	2		951	1582	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796934	78796934	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	40	494	0	ENST00000306801.3:c.1052del	p.Leu351TyrfsTer7	p.L351Yfs*7	ENST00000306801	NM_020761.2	349	aaT/aa	9/34	1	2	FACETS	0.668	0.554	0.796	0.668	0.554	0.796	SUBCLONAL	1	TRUE	1	0.19	2		494	630	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272305	15272305	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1330	140	938	1	ENST00000263388.2:c.6134C>A	p.Pro2045His	p.P2045H	ENST00000263388	NM_000435.2	2045	cCt/cAt	33/33	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.19	2		939	1470	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223355	36223355	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1490	176	1010	4	ENST00000222270.7:c.5909del	p.Pro1970LeufsTer17	p.P1970Lfs*17	ENST00000222270	NM_014727.1	1969	Ccc/cc	28/37	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.19	2		1014	1666	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905962	50905962	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1476	164	1004	0	ENST00000440232.2:c.934del	p.Val312CysfsTer81	p.V312Cfs*81	ENST00000440232	NM_002691.3	312	Gtg/tg	8/27	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.19	2		1004	1640	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617527	158617527	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	80	390	1	ENST00000263640.3:c.1129G>A	p.Gly377Ser	p.G377S	ENST00000263640	NM_001105.4	377	Ggc/Agc	9/11	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.19	2		391	809	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636858	158636858	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1423804322	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	44	357	0	ENST00000263640.3:c.322C>T	p.Pro108Ser	p.P108S	ENST00000263640	NM_001105.4	108	Ccc/Tcc	4/11	1	2	FACETS	0.827	0.693	0.976	0.827	0.693	0.976	CLONAL	1	TRUE	1	0.19	2		357	560	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989542	212989542	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	35	297	0	ENST00000342788.4:c.169G>C	p.Glu57Gln	p.E57Q	ENST00000342788	NM_005235.2	57	Gag/Cag	2/28	1	2	FACETS	0.768	0.629	0.924	0.768	0.629	0.924	CLONAL	1	TRUE	1	0.19	2		297	480	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793427	242793427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	88	757	1	ENST00000334409.5:c.650C>T	p.Pro217Leu	p.P217L	ENST00000334409	NM_005018.2	217	cCt/cTt	5/5	1	2	FACETS	0.832	0.735	0.937	0.832	0.735	0.937	CLONAL	1	TRUE	1	0.19	2		758	1113	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514499	41514499	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	60	460	0	ENST00000373198.4:c.162G>A	p.Trp54Ter	p.W54*	ENST00000373198	NM_133170.3	54	tgG/tgA	2/32	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.19	2		460	617	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321534	62321534	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1347	77	857	3	ENST00000360203.5:c.2236G>A	p.Ala746Thr	p.A746T	ENST00000360203	NM_001283009.1	746	Gcc/Acc	25/35	1	2	FACETS	0.569	0.497	0.647	0.569	0.497	0.647	SUBCLONAL	1	TRUE	1	0.19	2		860	1424	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514808	44514808	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	71	512	0	ENST00000291552.4:c.439G>A	p.Val147Met	p.V147M	ENST00000291552	NM_006758.2	147	Gtg/Atg	6/8	1	2	FACETS	0.897	0.782	1	0.897	0.782	1	CLONAL	1	TRUE	1	0.19	2		512	833	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288207	21288207	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	69	477	0	ENST00000354336.3:c.452T>C	p.Val151Ala	p.V151A	ENST00000354336	NM_005207.3	151	gTg/gCg	2/3	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.19	2		477	655	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050656	30050656	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	45	286	0	ENST00000338641.4:c.458A>G	p.Tyr153Cys	p.Y153C	ENST00000338641	NM_000268.3	153	tAc/tGc	5/16	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.19	2		286	439	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458317	12458317	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	86	495	0	ENST00000287820.6:c.934G>T	p.Gly312Cys	p.G312C	ENST00000287820	NM_015869.4	312	Ggc/Tgc	6/7	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.19	2		495	832	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648419	30648419	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1253	135	684	0	ENST00000295754.5:c.44T>C	p.Val15Ala	p.V15A	ENST00000295754	NM_003242.5	15	gTc/gCc	1/7	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.19	2		684	1388	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933766	49933766	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	94	789	0	ENST00000296474.3:c.2511G>T	p.Trp837Cys	p.W837C	ENST00000296474	NM_002447.2	837	tgG/tgT	10/20	1	2	FACETS	0.849	0.753	0.952	0.849	0.753	0.952	CLONAL	1	TRUE	1	0.19	2		789	1165	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526558	31526558	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	44	427	0	ENST00000344624.3:c.482C>A	p.Pro161Gln	p.P161Q	ENST00000344624		161	cCg/cAg	2/33	1	2	FACETS	0.758	0.635	0.895	0.758	0.635	0.895	SUBCLONAL	1	TRUE	1	0.19	2		427	611	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631142	176631142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769733603	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	39	376	0	ENST00000439151.2:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000439151	NM_022455.4	362	cGg/cAg	4/23	1	2	FACETS	0.692	0.573	0.826	0.692	0.573	0.826	SUBCLONAL	1	TRUE	1	0.19	2		376	593	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867493	101867493	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	25	94	0	ENST00000374994.4:c.6G>T	p.Glu2Asp	p.E2D	ENST00000374994	NM_004612.2	2	gaG/gaT	1/9	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.19	2		94	178	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128322020	128322020	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	66	510	0	ENST00000265960.3:c.740del	p.Pro247ArgfsTer27	p.P247Rfs*27	ENST00000265960	NM_001006617.1	247	cCg/cg	6/12	1	2	FACETS	0.995	0.863	1	0.995	0.863	1	CLONAL	1	TRUE	1	0.19	2		510	698	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771900	135771900	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	66	564	0	ENST00000298552.3:c.3217A>G	p.Ser1073Gly	p.S1073G	ENST00000298552	NM_001162426.1	1073	Agc/Ggc	23/23	1	2	FACETS	0.83	0.719	0.951	0.83	0.719	0.951	CLONAL	1	TRUE	1	0.19	2		564	837	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820198	139820198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147459885	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	91	607	0	ENST00000247668.2:c.1351G>A	p.Val451Met	p.V451M	ENST00000247668	NM_021138.3	451	Gtg/Atg	11/11	1	2	FACETS	0.851	0.754	0.956	0.851	0.754	0.956	CLONAL	1	TRUE	1	0.19	2		607	1125	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933575	39933575	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	111	619	0	ENST00000378444.4:c.1024del	p.Arg342GlufsTer36	p.R342Efs*36	ENST00000378444	NM_001123385.1	342	Cga/ga	4/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.19	2		619	1015	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343072	70343072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	73	379	0	ENST00000374080.3:c.1613C>T	p.Ala538Val	p.A538V	ENST00000374080		538	gCt/gTt	11/45	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.19	2		379	660	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89791142	89791143	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	38	204	0	ENST00000336032.3:c.529_530insA	p.Leu177HisfsTer31	p.L177Hfs*31	ENST00000336032	NM_006813.2	177	ctc/cAtc	1/2	0.105394515878548	3	FACETS	0.924	0.764	1	0.462	0.382	0.552	INDETERMINATE	1	TRUE	1	0.19	3		204	474	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593430	215593430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881409	NA	P-0047822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	16	169	0	ENST00000260947.4:c.2304G>A	p.Met768Ile	p.M768I	ENST00000260947	NM_000465.2	768	atG/atA	11/11	1	2	FACETS	0.726	0.537	0.951	0.726	0.537	0.951	CLONAL	1	TRUE	1	0.19	2		169	232	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0047823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	103	328	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.529105195093014	2	FACETS	0.948	0.855	1			1	CLONAL	1	TRUE	NA	0.53	2		328	410	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952048	178952048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	90	302	0	ENST00000263967.3:c.3103G>A	p.Ala1035Thr	p.A1035T	ENST00000263967	NM_006218.2	1035	Gct/Act	21/21	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.53	2		302	333	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006424	12006424	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	151	499	0	ENST00000396373.4:c.392del	p.Ser131TyrfsTer78	p.S131Yfs*78	ENST00000396373	NM_001987.4	131	tCa/ta	4/8	0.505656233113342	1	FACETS	0.945	0.872	1	0.945	0.872	1	CLONAL	1	TRUE	0	0.53	1		499	443	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346831	91346831	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	98	350	0	ENST00000355112.3:c.3443del	p.Lys1148SerfsTer2	p.K1148Sfs*2	ENST00000355112	NM_000057.2	1147	Aaa/aa	18/22	1	2	FACETS	0.953	0.857	1	0.953	0.857	1	CLONAL	1	TRUE	1	0.53	2		350	388	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245404	153245404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	37	487	0	ENST00000281708.4:c.1787C>T	p.Ser596Phe	p.S596F	ENST00000281708	NM_033632.3	596	tCt/tTt	11/12	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.12	2		487	615	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0047824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	28	255	1	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	1	2	FACETS	1	0.837	1	1	0.837	1	CLONAL	1	TRUE	1	0.12	2		256	442	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153703	55153703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	33	457	0	ENST00000257290.5:c.2669C>T	p.Ser890Phe	p.S890F	ENST00000257290	NM_006206.4	890	tCc/tTc	19/23	1	2	FACETS	0.858	0.697	1	0.858	0.697	1	CLONAL	1	TRUE	1	0.12	2		457	641	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858273	9858273	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567277910	NA	P-0047824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	28	426	0	ENST00000330684.3:c.3128C>T	p.Thr1043Ile	p.T1043I	ENST00000330684	NM_001134407.1	1043	aCc/aTc	13/13	1	2	FACETS	0.931	0.743	1	0.931	0.743	1	CLONAL	1	TRUE	1	0.12	2		426	501	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586488	189586488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	23	291	0	ENST00000264731.3:c.1112G>A	p.Gly371Asp	p.G371D	ENST00000264731	NM_003722.4	371	gGt/gAt	8/14	1	2	FACETS	0.867	0.675	1	0.867	0.675	1	CLONAL	1	TRUE	1	0.12	2		291	442	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438218	49438218	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	47	691	2	ENST00000301067.7:c.5051G>A	p.Ser1684Asn	p.S1684N	ENST00000301067	NM_003482.3	1684	aGc/aAc	20/54	1	2	FACETS	0.852	0.717	1	0.852	0.717	1	CLONAL	1	TRUE	1	0.12	2		693	919	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245156	46245157	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	30	413	0	ENST00000334344.6:c.3252dup	p.Pro1085SerfsTer4	p.P1085Sfs*4	ENST00000334344	NM_152641.2	1084	att/aTtt	15/21	1	2	FACETS	0.879	0.706	1	0.879	0.706	1	CLONAL	1	TRUE	1	0.12	2		413	569	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608875	100608875	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	22	187	0	ENST00000308731.7:c.1733C>T	p.Ser578Phe	p.S578F	ENST00000308731	NM_000061.2	578	tCt/tTt	17/19	1	1	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	0	0.12	1		187	295	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0047827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	104	250	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.33	2		250	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0047827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	193	775	1	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	0.297072759746021	2	FACETS	0.855	0.794	0.918	0.855	0.794	0.918	CLONAL	2	TRUE	0	0.33	2		776	684	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144147	11144147	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	199	781	1	ENST00000358026.2:c.3728G>T	p.Arg1243Leu	p.R1243L	ENST00000358026	NM_001128849.1	1243	cGg/cTg	26/36	0.274445277616707	2	FACETS	0.799	0.742	0.857	0.799	0.742	0.857	SUBCLONAL	2	TRUE	0	0.33	2		782	755	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182871	123182871	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	26	262	0	ENST00000218089.9:c.836A>G	p.Asp279Gly	p.D279G	ENST00000218089	NM_001042749.1	279	gAt/gGt	10/35	0.274445277616707	2	FACETS	0.8	0.638	0.983	0.4	0.319	0.492	CLONAL	1	TRUE	0	0.33	2		262	197	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349942	70349942	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	80	828	0	ENST00000374080.3:c.3925G>A	p.Asp1309Asn	p.D1309N	ENST00000374080		1309	Gac/Aac	28/45	0.163212882831789	1	FACETS	0.585	0.515	0.661	0.585	0.515	0.661	INDETERMINATE	1	TRUE	0	0.33	1		828	692	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169188	119169188	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0047827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	91	506	0	ENST00000264033.4:c.2372C>G	p.Ser791Ter	p.S791*	ENST00000264033	NM_005188.3	791	tCa/tGa	15/16	0.233743574414258	3	FACETS	1	0.958	1	0.578	0.514	0.645	CLONAL	1	TRUE	1	0.33	3		506	556	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30047510	30047510	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	38	411	0	ENST00000331968.5:c.2491G>T	p.Asp831Tyr	p.D831Y	ENST00000331968	NM_002742.2	831	Gat/Tat	17/18	0.297072759746021	3	FACETS	0.733	0.607	0.873	0.367	0.303	0.437	SUBCLONAL	1	TRUE	1	0.33	3		411	366	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586263	48586263	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	40	458	0	ENST00000342988.3:c.932A>T	p.Gln311Leu	p.Q311L	ENST00000342988	NM_005359.5	311	cAg/cTg	8/12	1	2	FACETS	0.792	0.661	0.937	0.792	0.661	0.937	CLONAL	1	TRUE	1	0.33	2		458	306	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867348	45867348	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	137	953	0	ENST00000391945.4:c.845G>T	p.Arg282Leu	p.R282L	ENST00000391945	NM_000400.3	282	cGg/cTg	10/23	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.33	2		953	778	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711216	61711217	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0047827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	46	445	0	ENST00000401558.2:c.2532_2533del	p.His844GlnfsTer28	p.H844Qfs*28	ENST00000401558	NM_003400.3	844	caTAga/caga	21/25	0.274445277616707	2	FACETS	0.914	0.774	1	0.457	0.387	0.534	CLONAL	1	TRUE	0	0.33	2		445	305	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530068	212530068	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	46	324	0	ENST00000342788.4:c.1851C>A	p.Cys617Ter	p.C617*	ENST00000342788	NM_005235.2	617	tgC/tgA	15/28	0.233743574414258	3	FACETS	0.958	0.81	1	0.479	0.405	0.56	CLONAL	1	TRUE	1	0.33	3		324	339	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371740	55371740	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	85	637	0	ENST00000297316.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000297316	NM_022454.3	144	Cag/Tag	2/2	0.211665225879686	4	FACETS	0.948	0.837	1	0.474	0.418	0.533	CLONAL	1	TRUE	2	0.33	4		637	723	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0047836-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	65	561	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.981	0.854	1	1	0.98	1	CLONAL	2	TRUE	1	0.16	2		561	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578484	7578485	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1064793929	NA	P-0047836-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	83	1113	1	ENST00000269305.4:c.445dup	p.Ser149PhefsTer32	p.S149Ffs*32	ENST00000269305	NM_001126112.2	149	tcc/tTcc	5/11	0.181736895458204	3	FACETS	0.979	0.866	1	0.979	0.866	1	CLONAL	2	TRUE	1	0.16	3		1114	572	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692910	89692910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047836-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	36	599	0	ENST00000371953.3:c.394G>A	p.Gly132Ser	p.G132S	ENST00000371953	NM_000314.4	132	Ggt/Agt	5/9	1	2	FACETS	0.755	0.623	0.902	1	0.951	1	CLONAL	2	TRUE	1	0.16	2		599	298	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0047845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	32	249	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.12	2		249	463	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574678	41574679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs754418509	NA	P-0047845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	48	616	1	ENST00000263253.7:c.6970dup	p.His2324ProfsTer55	p.H2324Pfs*55	ENST00000263253	NM_001429.3	2321	-/C	31/31	1	2	FACETS	0.878	0.74	1	0.878	0.74	1	CLONAL	1	TRUE	1	0.12	2		617	911	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0047845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	51	660	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	1	2	FACETS	0.988	0.838	1	0.988	0.838	1	CLONAL	1	TRUE	1	0.12	2		660	860	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0047846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	42	566	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.816	0.683	0.963	0.816	0.683	0.963	CLONAL	1	TRUE	1	0.266016253882339	2		566	387	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604656	48604656	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	17	266	0	ENST00000342988.3:c.1478A>G	p.Asp493Gly	p.D493G	ENST00000342988	NM_005359.5	493	gAt/gGt	12/12	1	2	FACETS	0.382	0.284	0.498	0.382	0.284	0.498	SUBCLONAL	1	TRUE	1	0.266016253882339	2		266	335	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119808	70119808	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	51	519	0	ENST00000245479.2:c.811del	p.Arg271AlafsTer8	p.R271Afs*8	ENST00000245479	NM_000346.3	270	ttC/tt	3/3	1	2	FACETS	0.707	0.601	0.824	0.707	0.601	0.824	SUBCLONAL	1	TRUE	1	0.266016253882339	2		519	542	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218365	1218440	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CATCATCCTGACGTTGGGTCGGCTGATACACCCCTGTCCTCTCTGTCCCAGGGAAATTCAACTACTGAGGAGGTTA	CATCATCCTGACGTTGGGTCGGCTGATACACCCCTGTCCTCTCTGTCCCAGGGAAATTCAACTACTGAGGAGGTTA	-	novel	NA	P-0047846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	27	190	0	ENST00000326873.7:c.291-50_316del		p.X97_splice	ENST00000326873	NM_000455.4	97		2/10	0.142970583922098	0	FACETS	0.645	0.516	0.791			1	INDETERMINATE	1	TRUE	0	0.266016253882339	0		190	231	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	178	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.437554611109075	4	FACETS	1	0.969	1			1	CLONAL	3	TRUE	NA	0.437554611109075	4		327	368	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0047847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	92	314	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.437554611109075	4	FACETS	0.975	0.876	1	0.975	0.876	1	CLONAL	2	TRUE	2	0.437554611109075	4		314	310	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903753	114903753	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	90	382	0	ENST00000543371.1:c.757A>G	p.Ile253Val	p.I253V	ENST00000543371	NM_001198531.1	253	Atc/Gtc	7/14	0.437554611109075	3	FACETS	0.937	0.834	1	0.469	0.417	0.524	CLONAL	1	TRUE	1	0.437554611109075	3		382	535	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181846	56181846	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	115	225	2	ENST00000399503.3:c.4072del	p.Ser1358ArgfsTer19	p.S1358Rfs*19	ENST00000399503	NM_005921.1	1357	cTt/ct	17/20	0.436795745719424	3	FACETS	0.92	0.848	0.993	0.92	0.848	0.993	CLONAL	3	TRUE	0	0.437554611109075	3		227	232	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753095	57753096	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0047847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	140	326	0	ENST00000274289.3:c.920_921delinsTT	p.Ala307Val	p.A307V	ENST00000274289	NM_006622.3	307	gCC/gTT	7/14	0.436795745719424	3	FACETS	0.867	0.803	0.93	0.867	0.803	0.93	CLONAL	3	TRUE	0	0.437554611109075	3		326	300	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	48	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.144085324837214	3	FACETS	1	0.916	1	1	0.916	1	CLONAL	2	TRUE	1	0.13	3		327	351	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023782	27023783	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0047848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	24	332	0	ENST00000324856.7:c.888_889insG	p.Gln297AlafsTer103	p.Q297Afs*103	ENST00000324856	NM_006015.4	296	-/G	1/20	1	2	FACETS	0.824	0.645	1	0.824	0.645	1	CLONAL	1	TRUE	1	0.13	2		332	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578453	7578460	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGCGGA	GGCGCGGA	-	novel	NA	P-0047848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	46	727	0	ENST00000269305.4:c.470_477del	p.Val157AspfsTer21	p.V157Dfs*21	ENST00000269305	NM_001126112.2	157	gTCCGCGCC/g	5/11	1	2	FACETS	0.804	0.675	0.948	0.804	0.675	0.948	CLONAL	1	TRUE	1	0.13	2		727	880	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0047849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	191	571	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	1	2	FACETS	0.639	0.592	0.687	0.639	0.592	0.687	SUBCLONAL	1	TRUE	1	0.82161334167253	2		571	728	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061517	38061517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771653601	NA	P-0047849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	76	332	0	ENST00000250448.2:c.472G>A	p.Asp158Asn	p.D158N	ENST00000250448	NM_004496.3	158	Gac/Aac	2/2	1	2	FACETS	0.367	0.322	0.415	0.367	0.322	0.415	SUBCLONAL	1	TRUE	1	0.82161334167253	2		332	504	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774737	73774737	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	90	140	0	ENST00000254810.4:c.350G>C	p.Arg117Thr	p.R117T	ENST00000254810	NM_005324.3	117	aGa/aCa	4/4	1	2	FACETS	0.733	0.658	0.811	0.733	0.658	0.811	SUBCLONAL	1	TRUE	1	0.82161334167253	2		140	299	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325092	39325092	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	44	457	0	ENST00000373001.3:c.227C>A	p.Ser76Tyr	p.S76Y	ENST00000373001	NM_022157.3	76	tCc/tAc	1/7	1	2	FACETS	0.154	0.129	0.183	0.154	0.129	0.183	SUBCLONAL	1	TRUE	1	0.82161334167253	2		457	694	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853773	59853773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	34	250	0	ENST00000259008.2:c.2086C>T	p.Pro696Ser	p.P696S	ENST00000259008	NM_032043.2	696	Cca/Tca	14/20	1	2	FACETS	0.207	0.169	0.25	0.207	0.169	0.25	SUBCLONAL	1	TRUE	1	0.82161334167253	2		250	399	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774687	73774687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	23	53	0	ENST00000254810.4:c.400G>A	p.Glu134Lys	p.E134K	ENST00000254810	NM_005324.3	134	Gag/Aag	4/4	1	2	FACETS	0.622	0.496	0.76	0.622	0.496	0.76	SUBCLONAL	1	TRUE	1	0.82161334167253	2		53	90	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774995	73774995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	100	177	0	ENST00000254810.4:c.178G>A	p.Glu60Lys	p.E60K	ENST00000254810	NM_005324.3	60	Gag/Aag	3/4	1	2	FACETS	0.708	0.638	0.78	0.708	0.638	0.78	SUBCLONAL	1	TRUE	1	0.82161334167253	2		177	344	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	71	331	1	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.21	2		332	477	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	34	302	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.639	0.521	0.771	0.639	0.521	0.771	SUBCLONAL	1	TRUE	1	0.21	2		302	507	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	31	227	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.539	0.435	0.657	0.539	0.435	0.657	SUBCLONAL	1	TRUE	1	0.21	2		227	548	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	75	848	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.868	0.759	0.985	0.868	0.759	0.985	CLONAL	1	TRUE	1	0.21	2		848	823	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435160	56435161	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs755128667	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	71	604	1	ENST00000407977.2:c.1976dup	p.Pro660SerfsTer87	p.P660Sfs*87	ENST00000407977		659	ggt/ggGt	9/10	1	2	FACETS	0.876	0.763	0.998	0.876	0.763	0.998	CLONAL	1	TRUE	1	0.21	2		605	772	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	54	565	0	ENST00000324856.7:c.4555del	p.Gln1519ArgfsTer8	p.Q1519Rfs*8	ENST00000324856	NM_006015.4	1517	gCc/gc	18/20	1	2	FACETS	0.708	0.604	0.823	0.708	0.604	0.823	SUBCLONAL	1	TRUE	1	0.21	2		565	726	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606696	29606696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769910087	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	43	468	0	ENST00000389048.3:c.1184G>A	p.Arg395His	p.R395H	ENST00000389048	NM_004304.4	395	cGt/cAt	5/29	1	2	FACETS	0.702	0.587	0.831	0.702	0.587	0.831	SUBCLONAL	1	TRUE	1	0.21	2		468	583	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675268	176675269	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	32	236	0	ENST00000439151.2:c.4591dup	p.Met1531AsnfsTer4	p.M1531Nfs*4	ENST00000439151	NM_022455.4	1528	-/A	11/23	1	2	FACETS	0.76	0.617	0.921	0.76	0.617	0.921	CLONAL	1	TRUE	1	0.21	2		236	401	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993708	72993708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs62640010	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	48	535	0	ENST00000268489.5:c.337G>A	p.Ala113Thr	p.A113T	ENST00000268489	NM_006885.3	113	Gcc/Acc	2/10	1	2	FACETS	0.697	0.588	0.817	0.697	0.588	0.817	SUBCLONAL	1	TRUE	1	0.21	2		535	656	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007824	45007825	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	53	303	0	ENST00000558401.1:c.276dup	p.Thr93HisfsTer2	p.T93Hfs*2	ENST00000558401	NM_004048.2	91	acc/aCcc	2/4	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.21	2		303	496	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494996	56494996	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201958747	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	68	496	0	ENST00000267101.3:c.3353G>A	p.Arg1118Gln	p.R1118Q	ENST00000267101	NM_001982.3	1118	cGg/cAg	27/28	1	2	FACETS	0.962	0.837	1	0.962	0.837	1	CLONAL	1	TRUE	1	0.21	2		496	673	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120535068	120535068	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1012300179	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	47	376	2	ENST00000229340.5:c.587G>A	p.Arg196Gln	p.R196Q	ENST00000229340	NM_006861.6	196	cGa/cAa	6/6	1	2	FACETS	0.741	0.625	0.87	0.741	0.625	0.87	SUBCLONAL	1	TRUE	1	0.21	2		378	604	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007619	45007619	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs111482205	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	28	185	0	ENST00000558401.1:c.68-2A>G		p.X23_splice	ENST00000558401	NM_004048.2	23			1	2	FACETS	0.97	0.777	1	0.97	0.777	1	CLONAL	1	TRUE	1	0.21	2		185	275	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141492	11141492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	78	613	1	ENST00000358026.2:c.3469C>T	p.Arg1157Trp	p.R1157W	ENST00000358026	NM_001128849.1	1157	Cgg/Tgg	25/36	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.21	2		614	740	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796882	42796883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761345552	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	101	812	1	ENST00000575354.2:c.3347dup	p.Ser1117LysfsTer34	p.S1117Kfs*34	ENST00000575354	NM_015125.3	1114	gcc/gCcc	14/20	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.21	2		813	955	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	47	361	2	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.843	0.711	0.989	0.843	0.711	0.989	CLONAL	1	TRUE	1	0.21	2		363	531	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710595	114710597	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs754968616	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	54	321	0	ENST00000543371.1:c.85_87del	p.Glu29del	p.E29del	ENST00000543371	NM_001198531.1	27	cAGGag/cag	1/14	1	2	FACETS	0.89	0.76	1	0.89	0.76	1	CLONAL	1	TRUE	1	0.21	2		321	578	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158647	26158647	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	18	106	0	ENST00000289316.2:c.250T>C	p.Tyr84His	p.Y84H	ENST00000289316	NM_138720.2	84	Tac/Cac	1/2	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.21	2		106	135	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020769	37020769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	55	459	1	ENST00000358127.4:c.76del	p.Val26PhefsTer3	p.V26Ffs*3	ENST00000358127	NM_001280556.1	26	Gtt/tt	2/10	1	2	FACETS	0.795	0.679	0.922	0.795	0.679	0.922	CLONAL	1	TRUE	1	0.21	2		460	659	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233024	55233024	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144943614	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	51	386	0	ENST00000275493.2:c.1774G>A	p.Val592Ile	p.V592I	ENST00000275493	NM_005228.3	592	Gtc/Atc	15/28	1	2	FACETS	0.826	0.702	0.963	0.826	0.702	0.963	CLONAL	1	TRUE	1	0.21	2		386	588	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41021807	41021807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555429623	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	64	405	1	ENST00000267868.3:c.749G>A	p.Arg250Gln	p.R250Q	ENST00000267868	NM_002875.4	250	cGg/cAg	8/10	1	2	FACETS	0.935	0.809	1	0.935	0.809	1	CLONAL	1	TRUE	1	0.21	2		406	652	SUCCESS
APC	324	MSKCC	GRCh37	5	112164664	112164664	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1060503259	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	21	149	0	ENST00000257430.4:c.1742del	p.Lys581ArgfsTer9	p.K581Rfs*9	ENST00000257430	NM_000038.5	580	Aaa/aa	14/16	1	2	FACETS	0.725	0.559	0.918	0.725	0.559	0.918	CLONAL	1	TRUE	1	0.21	2		149	276	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521525	46521525	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	77	434	4	ENST00000262741.5:c.883del	p.Met295Ter	p.M295*	ENST00000262741	NM_003629.3	295	Atg/tg	7/10	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.21	2		438	687	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508470	106508470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1463222028	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	28	284	0	ENST00000359195.3:c.464C>T	p.Thr155Met	p.T155M	ENST00000359195	NM_002649.2	155	aCg/aTg	2/11	1	2	FACETS	0.745	0.596	0.915	0.745	0.596	0.915	CLONAL	1	TRUE	1	0.21	2		284	358	SUCCESS
ATM	472	MSKCC	GRCh37	11	108137897	108137897	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	22	210	0	ENST00000278616.4:c.2467-1G>T		p.X823_splice	ENST00000278616	NM_000051.3	823			1	2	FACETS	0.631	0.489	0.796	0.631	0.489	0.796	SUBCLONAL	1	TRUE	1	0.21	2		210	332	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513539	41513539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753658203	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	62	505	0	ENST00000263253.7:c.443C>T	p.Thr148Met	p.T148M	ENST00000263253	NM_001429.3	148	aCg/aTg	2/31	1	2	FACETS	0.966	0.835	1	0.966	0.835	1	CLONAL	1	TRUE	1	0.21	2		505	611	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110188	3110188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587777021	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	78	590	0	ENST00000078429.4:c.178C>T	p.Arg60Cys	p.R60C	ENST00000078429	NM_002067.2	60	Cgc/Tgc	2/7	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.21	2		590	682	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567685	226567685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	54	480	1	ENST00000366794.5:c.1481C>T	p.Ala494Val	p.A494V	ENST00000366794	NM_001618.3	494	gCc/gTc	10/23	1	2	FACETS	0.761	0.649	0.884	0.761	0.649	0.884	SUBCLONAL	1	TRUE	1	0.21	2		481	676	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025856	48025857	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs267608041	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	17	211	0	ENST00000234420.5:c.741dup	p.Arg248ThrfsTer8	p.R248Tfs*8	ENST00000234420	NM_000179.2	245	ata/atAa	4/10	1	2	FACETS	0.504	0.376	0.657	0.504	0.376	0.657	SUBCLONAL	1	TRUE	1	0.21	2		211	321	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960039	134960039	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533462328	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	62	469	1	ENST00000398015.3:c.2396G>A	p.Arg799His	p.R799H	ENST00000398015	NM_004441.4	799	cGc/cAc	13/16	1	2	FACETS	0.892	0.77	1	0.892	0.77	1	CLONAL	1	TRUE	1	0.21	2		470	662	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864125	57864125	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	64	603	1	ENST00000228682.2:c.1607del	p.Pro536GlnfsTer77	p.P536Qfs*77	ENST00000228682	NM_005269.2	534	ggC/gg	12/12	1	2	FACETS	0.918	0.794	1	0.918	0.794	1	CLONAL	1	TRUE	1	0.21	2		604	664	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983016	149983016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326200282	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	47	410	1	ENST00000253339.5:c.3242G>A	p.Arg1081Gln	p.R1081Q	ENST00000253339		1081	cGa/cAa	7/7	1	2	FACETS	0.853	0.719	1	0.853	0.719	1	CLONAL	1	TRUE	1	0.21	2		411	525	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905944	50905944	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755457889	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	115	849	2	ENST00000440232.2:c.916C>T	p.Arg306Cys	p.R306C	ENST00000440232	NM_002691.3	306	Cgc/Tgc	8/27	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.21	2		851	1058	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891205	151891205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776685589	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	45	345	0	ENST00000262189.6:c.4549G>A	p.Gly1517Arg	p.G1517R	ENST00000262189	NM_170606.2	1517	Gga/Aga	31/59	1	2	FACETS	0.783	0.658	0.922	0.783	0.658	0.922	CLONAL	1	TRUE	1	0.21	2		345	547	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89383342	89383342	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	66	509	3	ENST00000301030.4:c.86del	p.Lys29ArgfsTer8	p.K29Rfs*8	ENST00000301030	NM_001256183.1	29	aAg/ag	3/13	1	2	FACETS	0.887	0.769	1	0.887	0.769	1	CLONAL	1	TRUE	1	0.21	2		512	709	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55693419	55693419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759162213	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	64	581	0	ENST00000284073.2:c.626C>T	p.Ala209Val	p.A209V	ENST00000284073	NM_138962.2	209	gCg/gTg	9/14	1	2	FACETS	0.724	0.625	0.831	0.724	0.625	0.831	SUBCLONAL	1	TRUE	1	0.21	2		581	842	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224532	36224532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759167832	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	99	731	2	ENST00000222270.7:c.6994C>T	p.Arg2332Cys	p.R2332C	ENST00000222270	NM_014727.1	2332	Cgt/Tgt	29/37	1	2	FACETS	0.994	0.885	1	0.994	0.885	1	CLONAL	1	TRUE	1	0.21	2		733	949	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912134	50912134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781327088	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	98	652	2	ENST00000440232.2:c.1868G>A	p.Arg623Gln	p.R623Q	ENST00000440232	NM_002691.3	623	cGg/cAg	15/27	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.21	2		654	886	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303634	65303634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1180745512	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	53	414	0	ENST00000342505.4:c.3121C>T	p.Arg1041Trp	p.R1041W	ENST00000342505	NM_002227.2	1041	Cgg/Tgg	22/25	1	2	FACETS	0.73	0.622	0.85	0.73	0.622	0.85	SUBCLONAL	1	TRUE	1	0.21	2		414	691	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134473	2134473	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343536158	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	89	805	1	ENST00000219476.3:c.4250G>A	p.Arg1417Gln	p.R1417Q	ENST00000219476	NM_000548.3	1417	cGg/cAg	34/42	1	2	FACETS	0.853	0.754	0.958	0.853	0.754	0.958	CLONAL	1	TRUE	1	0.21	2		806	994	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229048	36229048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866415691	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	78	643	0	ENST00000222270.7:c.7828C>T	p.Arg2610Cys	p.R2610C	ENST00000222270	NM_014727.1	2610	Cgc/Tgc	36/37	1	2	FACETS	0.836	0.733	0.947	0.836	0.733	0.947	CLONAL	1	TRUE	1	0.21	2		643	889	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62305359	62305359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200429535	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	71	645	1	ENST00000360203.5:c.832G>A	p.Val278Ile	p.V278I	ENST00000360203	NM_001283009.1	278	Gtc/Atc	10/35	1	2	FACETS	0.873	0.76	0.994	0.873	0.76	0.994	CLONAL	1	TRUE	1	0.21	2		646	775	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285675	46285675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1201192337	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	44	314	0	ENST00000334344.6:c.5035C>T	p.Arg1679Trp	p.R1679W	ENST00000334344	NM_152641.2	1679	Cgg/Tgg	17/21	1	2	FACETS	0.773	0.648	0.912	0.773	0.648	0.912	CLONAL	1	TRUE	1	0.21	2		314	542	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56401613	56401613	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs769025149	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	44	300	0	ENST00000348428.3:c.1475C>T	p.Thr492Met	p.T492M	ENST00000348428	NM_006785.3	492	aCg/aTg	12/17	1	2	FACETS	0.84	0.704	0.99	0.84	0.704	0.99	CLONAL	1	TRUE	1	0.21	2		300	499	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156695	2156695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142012621	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	85	630	1	ENST00000434045.2:c.227C>T	p.Ser76Leu	p.S76L	ENST00000434045	NM_001127598.1	76	tCg/tTg	3/5	1	2	FACETS	0.969	0.856	1	0.969	0.856	1	CLONAL	1	TRUE	1	0.21	2		631	835	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484366	50484366	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	43	305	0	ENST00000394963.4:c.1126G>A	p.Val376Ile	p.V376I	ENST00000394963	NM_003076.4	376	Gtc/Atc	9/13	1	2	FACETS	0.857	0.717	1	0.857	0.717	1	CLONAL	1	TRUE	1	0.21	2		305	478	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492533	50492533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	79	561	1	ENST00000394963.4:c.1429C>T	p.Arg477Cys	p.R477C	ENST00000394963	NM_003076.4	477	Cgc/Tgc	12/13	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.21	2		562	749	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56474152	56474152	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	89	587	0	ENST00000267101.3:c.68G>A	p.Gly23Asp	p.G23D	ENST00000267101	NM_001982.3	23	gGc/gAc	1/28	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.21	2		587	837	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877396	28877396	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	62	431	0	ENST00000282397.4:c.3925T>C	p.Tyr1309His	p.Y1309H	ENST00000282397	NM_002019.4	1309	Tac/Cac	30/30	1	2	FACETS	0.891	0.769	1	0.891	0.769	1	CLONAL	1	TRUE	1	0.21	2		431	663	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680674	88680674	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	65	589	0	ENST00000360948.2:c.583T>G	p.Ser195Ala	p.S195A	ENST00000360948	NM_001012338.2	195	Tcc/Gcc	6/19	1	2	FACETS	0.876	0.758	1	0.876	0.758	1	CLONAL	1	TRUE	1	0.21	2		589	707	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2097715	2097715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1482983792	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	78	611	2	ENST00000219066.1:c.134C>T	p.Ala45Val	p.A45V	ENST00000219066	NM_002528.5	45	gCa/gTa	1/6	1	2	FACETS	0.927	0.814	1	0.927	0.814	1	CLONAL	1	TRUE	1	0.21	2		613	801	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348110	89348110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1170699512	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	81	671	2	ENST00000301030.4:c.4840C>T	p.Arg1614Trp	p.R1614W	ENST00000301030	NM_001256183.1	1614	Cgg/Tgg	9/13	1	2	FACETS	0.941	0.828	1	0.941	0.828	1	CLONAL	1	TRUE	1	0.21	2		673	820	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369469	40369469	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	63	442	0	ENST00000293328.3:c.1183G>A	p.Glu395Lys	p.E395K	ENST00000293328	NM_012448.3	395	Gag/Aag	10/19	1	2	FACETS	0.894	0.773	1	0.894	0.773	1	CLONAL	1	TRUE	1	0.21	2		442	671	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250371	10250371	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	66	417	0	ENST00000340748.4:c.3881G>A	p.Cys1294Tyr	p.C1294Y	ENST00000340748		1294	tGc/tAc	33/40	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.21	2		417	528	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169524	11169524	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778775484	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	85	578	0	ENST00000358026.2:c.4690C>A	p.Leu1564Met	p.L1564M	ENST00000358026	NM_001128849.1	1564	Ctg/Atg	33/36	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.21	2		578	757	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376433	15376433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	105	638	0	ENST00000263377.2:c.581C>T	p.Ser194Phe	p.S194F	ENST00000263377	NM_058243.2	194	tCc/tTc	5/20	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.21	2		638	937	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256732	19256732	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs745423920	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	79	570	4	ENST00000162023.5:c.981del	p.Gly329AlafsTer?	p.G329Afs*?	ENST00000162023		327	ccC/cc	13/13	1	2	FACETS	0.989	0.869	1	0.989	0.869	1	CLONAL	1	TRUE	1	0.21	2		574	761	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758299	41758299	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	51	569	0	ENST00000301178.4:c.1755A>C	p.Glu585Asp	p.E585D	ENST00000301178	NM_021913.4	585	gaA/gaC	15/20	1	2	FACETS	0.697	0.591	0.813	0.697	0.591	0.813	SUBCLONAL	1	TRUE	1	0.21	2		569	697	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795812	42795812	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141269383	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	66	651	1	ENST00000575354.2:c.2801G>A	p.Arg934Gln	p.R934Q	ENST00000575354	NM_015125.3	934	cGg/cAg	11/20	1	2	FACETS	0.767	0.664	0.878	0.767	0.664	0.878	SUBCLONAL	1	TRUE	1	0.21	2		652	820	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128030524	128030524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1172169844	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	33	319	0	ENST00000285398.2:c.1744G>A	p.Gly582Arg	p.G582R	ENST00000285398	NM_000122.1	582	Gga/Aga	11/15	1	2	FACETS	0.585	0.476	0.709	0.585	0.476	0.709	SUBCLONAL	1	TRUE	1	0.21	2		319	537	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375199	31375199	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	95	580	0	ENST00000328111.2:c.596G>C	p.Gly199Ala	p.G199A	ENST00000328111	NM_006892.3	199	gGc/gCc	6/23	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.21	2		580	876	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936678	49936678	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	56	559	0	ENST00000296474.3:c.1249A>G	p.Ser417Gly	p.S417G	ENST00000296474	NM_002447.2	417	Agc/Ggc	2/20	1	2	FACETS	0.871	0.746	1	0.871	0.746	1	CLONAL	1	TRUE	1	0.21	2		559	612	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332643	153332643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	29	339	0	ENST00000281708.4:c.313G>A	p.Ala105Thr	p.A105T	ENST00000281708	NM_033632.3	105	Gct/Act	2/12	1	2	FACETS	0.585	0.469	0.718	0.585	0.469	0.718	SUBCLONAL	1	TRUE	1	0.21	2		339	472	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509768	106509768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146487441	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	53	451	0	ENST00000359195.3:c.1762G>A	p.Ala588Thr	p.A588T	ENST00000359195	NM_002649.2	588	Gca/Aca	2/11	1	2	FACETS	0.893	0.762	1	0.893	0.762	1	CLONAL	1	TRUE	1	0.21	2		451	565	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341511	70341511	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	51	555	1	ENST00000374080.3:c.946T>A	p.Ser316Thr	p.S316T	ENST00000374080		316	Tca/Aca	7/45	1	2	FACETS	0.567	0.481	0.663	0.567	0.481	0.663	SUBCLONAL	1	TRUE	1	0.21	2		556	856	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0047851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	33	566	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.15	2		566	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577060	7577060	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	TCTTT	novel	NA	P-0047851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	47	597	0	ENST00000269305.4:c.878delinsAAAGA	p.Gly293GlufsTer14	p.G293Efs*14	ENST00000269305	NM_001126112.2	293	gGg/gAAAGAg	8/11	1	2	FACETS	0.86	0.724	1	0.86	0.724	1	CLONAL	1	TRUE	1	0.15	2		597	729	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0047852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	273	566	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.3145631714249	4	FACETS	0.882	0.833	0.933	0.882	0.833	0.933	INDETERMINATE	2	TRUE	2	0.74083727437526	4		566	727	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0047852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	530	875	1	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.733622449799332	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.74083727437526	1		876	838	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087895	27087898	+	frameshift_variant	Frame_Shift_Del	DEL	CCAC	CCAC	-	novel	NA	P-0047852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	831	445	2	ENST00000324856.7:c.2185_2188del	p.Pro729ValfsTer12	p.P729Vfs*12	ENST00000324856	NM_006015.4	728	CCACcc/cc	6/20	0.74083727437526	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.74083727437526	2		447	1085	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573556	48573557	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0047852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	116	197	0	ENST00000342988.3:c.140_141del	p.Leu47GlnfsTer6	p.L47Qfs*6	ENST00000342988	NM_005359.5	47	cTG/c	2/12	0.733622449799332	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.74083727437526	1		197	177	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974405	21974718	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCATCTAATACAAATATGTTCCCCCCTTCAGATCTTCTCAGCATTCGAGAGATCTGTACGCGCGTGGCTCCTCATTCCTCTTCCTTGGCTTCCCAAGCCCCCAGGGCGTCGCCAGGAGGAGGTCTGTGATTACAAACCCCTTCTGAAAACTCCCCAGGAAGCCTCCCCTTTTTCCGGAGAATCGAAGCGCTACCTGATTCCAATTCCCCTGCAAACTTCGTCCTCCAGAGTCGCCCGCCATCCCCTGCTCCCGCTGCAGACCCTCTACCCACCTGGATCGGCCTCCGACCGTAACTATTCGGTGCGTTGGGCAG	CCATCTAATACAAATATGTTCCCCCCTTCAGATCTTCTCAGCATTCGAGAGATCTGTACGCGCGTGGCTCCTCATTCCTCTTCCTTGGCTTCCCAAGCCCCCAGGGCGTCGCCAGGAGGAGGTCTGTGATTACAAACCCCTTCTGAAAACTCCCCAGGAAGCCTCCCCTTTTTCCGGAGAATCGAAGCGCTACCTGATTCCAATTCCCCTGCAAACTTCGTCCTCCAGAGTCGCCCGCCATCCCCTGCTCCCGCTGCAGACCCTCTACCCACCTGGATCGGCCTCCGACCGTAACTATTCGGTGCGTTGGGCAG	-	novel	NA	P-0047852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	95	139	1	ENST00000304494.5:c.109_150+272del		p.X37_splice	ENST00000304494	NM_000077.4	37		1/3	0.74083727437526	1	FACETS	0.979	0.901	1	0.979	0.901	1	CLONAL	1	TRUE	0	0.74083727437526	1		140	165	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0047853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	472	875	1	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.541480533285178	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.541480533285178	2		876	802	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0047853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	297	543	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.111347540889448	4	FACETS	0.857	0.813	0.901			1	INDETERMINATE	3	TRUE	NA	0.541480533285178	4		543	658	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69465988	69465996	+	inframe_deletion	In_Frame_Del	DEL	GAGGAGGAG	GAGGAGGAG	-	novel	NA	P-0047853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	295	677	0	ENST00000227507.2:c.833_841del	p.Glu278_Glu280del	p.E278_E280del	ENST00000227507	NM_053056.2	276	GAGGAGGAG/-	5/5	0.469930251328429	4	FACETS	0.965	0.912	1	0.965	0.912	1	CLONAL	2	TRUE	2	0.541480533285178	4		677	870	SUCCESS
BLM	641	MSKCC	GRCh37	15	91341420	91341420	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs794727180	NA	P-0047853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	43	204	0	ENST00000355112.3:c.3211G>A	p.Asp1071Asn	p.D1071N	ENST00000355112	NM_000057.2	1071	Gat/Aat	17/22	0.469930251328429	4	FACETS	1	0.875	1	0.521	0.439	0.609	CLONAL	1	TRUE	2	0.541480533285178	4		204	235	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs886039483	NA	P-0047854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	367	589	0	ENST00000269305.4:c.376T>G	p.Tyr126Asp	p.Y126D	ENST00000269305	NM_001126112.2	126	Tac/Gac	5/11	0.286466497104189	3	FACETS	1	0.992	1	0.796	0.757	0.835	CLONAL	2	TRUE	0	0.368234973368206	3		589	989	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394407	162394407	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	24	253	0	ENST00000366898.1:c.661G>T	p.Glu221Ter	p.E221*	ENST00000366898	NM_004562.2	221	Gaa/Taa	6/12	0.30261250692519	3	FACETS	0.422	0.33	0.527	0.141	0.11	0.176	SUBCLONAL	1	TRUE	0	0.368234973368206	3		253	366	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242481	+	inframe_deletion	In_Frame_Del	DEL	AATTAAGAGAAGCAA	AATTAAGAGAAGCAA	-	rs121913425	NA	P-0047854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	184	275	0	ENST00000275493.2:c.2237_2251del	p.Glu746_Thr751delinsAla	p.E746_T751delinsA	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAAca/gca	19/28	0.368234973368206	6	FACETS	0.991	0.92	1	0.743	0.69	0.797	CLONAL	3	TRUE	2	0.368234973368206	6		275	584	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0047854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	516	630	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.368234973368206	6	FACETS	0.936	0.898	0.974	0.936	0.898	0.974	CLONAL	4	TRUE	2	0.368234973368206	6		630	1300	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0047855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	62	249	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.767	0.667	0.874	0.767	0.667	0.874	SUBCLONAL	1	TRUE	1	0.491298682927129	2		249	329	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0047855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	194	640	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.491298682927129	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.491298682927129	1		642	550	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0047855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	111	306	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.491298682927129	2		306	427	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977949	134977949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56186270	NA	P-0047855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	177	445	0	ENST00000398015.3:c.2942C>T	p.Thr981Met	p.T981M	ENST00000398015	NM_004441.4	981	aCg/aTg	16/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.491298682927129	2		445	636	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056425	26056427	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	rs774779034	NA	P-0047855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	86	319	0	ENST00000343677.2:c.230_232del	p.Asn77del	p.N77del	ENST00000343677	NM_005319.3	77	aACAgc/agc	1/1	1	2	FACETS	0.814	0.724	0.91	0.814	0.724	0.91	CLONAL	1	TRUE	1	0.491298682927129	2		319	430	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591145	67591154	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TACTTGATGT	TACTTGATGT	-	novel	NA	P-0047855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	30	235	0	ENST00000274335.5:c.1738_1745+2del		p.X580_splice	ENST00000274335		580		12/15	1	2	FACETS	0.555	0.45	0.673	0.555	0.45	0.673	SUBCLONAL	1	TRUE	1	0.491298682927129	2		235	220	SUCCESS
APC	324	MSKCC	GRCh37	5	112170816	112170816	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	120	491	0	ENST00000257430.4:c.1912del	p.Ile638TyrfsTer8	p.I638Yfs*8	ENST00000257430	NM_000038.5	638	Ata/ta	15/16	1	2	FACETS	0.945	0.857	1	0.945	0.857	1	CLONAL	1	TRUE	1	0.491298682927129	2		491	517	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222282	2222282	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375818110	NA	P-0047855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	285	739	1	ENST00000326181.6:c.566G>A	p.Arg189Gln	p.R189Q	ENST00000326181	NM_032271.2	189	cGg/cAg	8/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.491298682927129	2		740	1071	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233193	69233193	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	19	235	1	ENST00000462284.1:c.1058T>A	p.Leu353Gln	p.L353Q	ENST00000462284	NM_002392.5	353	cTg/cAg	11/11	1	2	FACETS	0.336	0.256	0.431	0.336	0.256	0.431	SUBCLONAL	1	TRUE	1	0.491298682927129	2		236	230	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233201	69233201	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	24	227	0	ENST00000462284.1:c.1066T>A	p.Ser356Thr	p.S356T	ENST00000462284	NM_002392.5	356	Tca/Aca	11/11	1	2	FACETS	0.436	0.343	0.542	0.436	0.343	0.542	SUBCLONAL	1	TRUE	1	0.491298682927129	2		227	224	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056432	26056432	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	94	320	0	ENST00000343677.2:c.225A>T	p.Lys75Asn	p.K75N	ENST00000343677	NM_005319.3	75	aaA/aaT	1/1	1	2	FACETS	0.924	0.828	1	0.924	0.828	1	CLONAL	1	TRUE	1	0.491298682927129	2		320	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0047856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	535	466	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.767336347642403	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.767336347642403	2		466	653	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21643226	21643226	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	74	401	0	ENST00000421138.2:c.301A>C	p.Asn101His	p.N101H	ENST00000421138		101	Aac/Cac	5/16	0.472458679400685	5	FACETS	0.51	0.446	0.58	0.102	0.089	0.116	SUBCLONAL	1	TRUE	0	0.767336347642403	5		401	813	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217244	66217244	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	85	267	0	ENST00000273854.3:c.2371C>A	p.Leu791Ile	p.L791I	ENST00000273854	NM_004439.5	791	Ctt/Att	14/18	0.415057789347636	1	FACETS	0.591	0.532	0.652	0.591	0.532	0.652	INDETERMINATE	1	TRUE	0	0.767336347642403	1		267	231	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0047857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	13	259	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.751	0.538	1	0.751	0.538	1	CLONAL	1	TRUE	1	0.2	2		259	173	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169917	32169917	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	45	475	0	ENST00000375023.3:c.3691C>A	p.Pro1231Thr	p.P1231T	ENST00000375023	NM_004557.3	1231	Cca/Aca	21/30	0.318750536846547	3	FACETS	0.69	0.579	0.814	0.345	0.289	0.407	SUBCLONAL	1	TRUE	1	0.2	3		475	717	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133781	55133781	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	12	256	0	ENST00000257290.5:c.994G>T	p.Val332Phe	p.V332F	ENST00000257290	NM_006206.4	332	Gtc/Ttc	7/23	0.151970146669	1	FACETS	0.482	0.339	0.659	0.482	0.339	0.659	SUBCLONAL	1	TRUE	0	0.2	1		256	224	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410657	32410657	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	26	374	0	ENST00000332351.3:c.1501C>G	p.Arg501Gly	p.R501G	ENST00000332351	NM_024426.4	501	Cgc/Ggc	10/10	1	2	FACETS	0.634	0.502	0.786	0.634	0.502	0.786	SUBCLONAL	1	TRUE	1	0.2	2		374	410	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933282	100933282	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	22	344	0	ENST00000325455.5:c.2108A>T	p.His703Leu	p.H703L	ENST00000325455	NM_001202474.3	703	cAt/cTt	4/8	1	2	FACETS	0.905	0.704	1	0.905	0.704	1	CLONAL	1	TRUE	1	0.2	2		344	243	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375999	118375999	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	21	308	0	ENST00000534358.1:c.9392G>A	p.Gly3131Asp	p.G3131D	ENST00000534358	NM_005933.3	3131	gGt/gAt	27/36	1	2	FACETS	0.875	0.676	1	0.875	0.676	1	CLONAL	1	TRUE	1	0.2	2		308	240	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436596	110436596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1438903340	NA	P-0047857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	53	564	2	ENST00000375856.3:c.1805G>A	p.Arg602Gln	p.R602Q	ENST00000375856	NM_003749.2	602	cGg/cAg	1/2	1	2	FACETS	0.708	0.602	0.824	0.708	0.602	0.824	SUBCLONAL	1	TRUE	1	0.2	2		566	749	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094979	11094979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	45	542	0	ENST00000358026.2:c.152C>T	p.Ser51Leu	p.S51L	ENST00000358026	NM_001128849.1	51	tCa/tTa	2/36	1	2	FACETS	0.74	0.621	0.872	0.74	0.621	0.872	SUBCLONAL	1	TRUE	1	0.2	2		542	608	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946256	55946256	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	42	292	0	ENST00000263923.4:c.3923G>T	p.Gly1308Val	p.G1308V	ENST00000263923	NM_002253.2	1308	gGa/gTa	30/30	0.151970146669	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.2	1		292	303	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322947	31322947	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	113	436	0	ENST00000412585.2:c.949G>C	p.Val317Leu	p.V317L	ENST00000412585	NM_005514.6	317	Gtc/Ctc	5/8	0.318750536846547	3	FACETS	0.798	0.718	0.882	0.798	0.718	0.882	SUBCLONAL	2	TRUE	1	0.2	3		436	779	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720649	89720649	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs587782455	NA	P-0047858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	69	216	3	ENST00000371953.3:c.802-2A>T		p.X268_splice	ENST00000371953	NM_000314.4	268			0.345072560007198	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.345072560007198	1		219	294	SUCCESS
AR	367	MSKCC	GRCh37	X	66766441	66766441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	25	212	1	ENST00000374690.3:c.1453C>T	p.Arg485Trp	p.R485W	ENST00000374690	NM_000044.3	485	Cgg/Tgg	1/8	1	2	FACETS	0.41	0.323	0.511	0.41	0.323	0.511	SUBCLONAL	1	TRUE	1	0.345072560007198	2		213	353	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120510	94120510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	59	221	0	ENST00000369303.4:c.541G>A	p.Gly181Arg	p.G181R	ENST00000369303	NM_004440.3	181	Gga/Aga	3/17	1	2	FACETS	0.958	0.828	1	0.958	0.828	1	CLONAL	1	TRUE	1	0.345072560007198	2		221	357	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858114	152858114	+	synonymous_variant	Silent	SNP	G	G	A	rs376060545	NA	P-0047858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	119	568	1	ENST00000406277.2:c.501C>T	p.Thr167=	p.T167=	ENST00000406277	NM_152274.4	167	acC/acT	6/7	1	2	FACETS	0.746	0.672	0.823	0.746	0.672	0.823	SUBCLONAL	1	TRUE	1	0.345072560007198	2		569	925	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46714229	46714230	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0047858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	48	363	0	ENST00000371975.4:c.49_50delinsAT	p.Gly17Ile	p.G17I	ENST00000371975	NM_003579.3	17	GGc/ATc	2/18	0.345072560007198	1	FACETS	0.504	0.426	0.589	0.504	0.426	0.589	SUBCLONAL	1	TRUE	0	0.345072560007198	1		363	457	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156139	119156139	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1365230067	NA	P-0047858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	43	421	0	ENST00000264033.4:c.1804G>T	p.Ala602Ser	p.A602S	ENST00000264033	NM_005188.3	602	Gcc/Tcc	11/16	1	2	FACETS	0.401	0.334	0.474	0.401	0.334	0.474	SUBCLONAL	1	TRUE	1	0.345072560007198	2		421	622	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193742	106193742	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	22	158	0	ENST00000380013.4:c.4204G>T	p.Asp1402Tyr	p.D1402Y	ENST00000380013	NM_001127208.2	1402	Gac/Tac	10/11	0.166493370579152	1	FACETS	0.417	0.324	0.525	0.417	0.324	0.525	INDETERMINATE	1	TRUE	0	0.345072560007198	1		158	253	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0047859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	136	480	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	0.353273564344205	3	FACETS	0.923	0.846	1	0.923	0.846	1	CLONAL	2	TRUE	1	0.384362028121682	3		480	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578529	7578529	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	274	547	0	ENST00000269305.4:c.401T>C	p.Phe134Ser	p.F134S	ENST00000269305	NM_001126112.2	134	tTt/tCt	5/11	0.384362028121682	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.384362028121682	1		547	787	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012382	152012382	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	46	212	0	ENST00000262189.6:c.431C>A	p.Ser144Tyr	p.S144Y	ENST00000262189	NM_170606.2	144	tCc/tAc	4/59	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.384362028121682	2		212	238	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0047861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	74	287	2	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	0.3	7	FACETS	1	0.901	1	0.514	0.452	0.58	CLONAL	2	FALSE	3	0.3	7		289	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578192	7578192	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	197	447	0	ENST00000269305.4:c.657del	p.Tyr220MetfsTer27	p.Y220Mfs*27	ENST00000269305	NM_001126112.2	219	ccC/cc	6/11	0.3	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	FALSE	1	0.3	3		447	737	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372503	118372503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	64	366	0	ENST00000534358.1:c.6436C>T	p.Pro2146Ser	p.P2146S	ENST00000534358	NM_005933.3	2146	Ccc/Tcc	26/36	0.3	3	FACETS	0.847	0.734	0.97	0.424	0.367	0.485	CLONAL	1	FALSE	1	0.3	3		366	579	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204499918	204499918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1242872664	NA	P-0047861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	20	310	1	ENST00000367182.3:c.260G>A	p.Arg87His	p.R87H	ENST00000367182	NM_001278516.1	87	cGt/cAt	4/11	0.242977097057662	5	FACETS	0.528	0.403	0.675	0.176	0.134	0.225	SUBCLONAL	1	FALSE	2	0.3	5		311	366	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376694	31376694	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	55	324	0	ENST00000328111.2:c.689G>A	p.Trp230Ter	p.W230*	ENST00000328111	NM_006892.3	230	tGg/tAg	7/23	0.3	7	FACETS	0.773	0.66	0.898	0.193	0.165	0.225	SUBCLONAL	1	FALSE	3	0.3	7		324	830	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293590	1293590	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750721558	NA	P-0047861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1349	151	654	2	ENST00000310581.5:c.1411C>T	p.Arg471Trp	p.R471W	ENST00000310581	NM_198253.2	471	Cgg/Tgg	2/16	0.3	5	FACETS	0.973	0.887	1	0.324	0.295	0.355	CLONAL	1	FALSE	2	0.3	5		656	1500	SUCCESS
APC	324	MSKCC	GRCh37	5	112174516	112174516	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0047861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	36	248	0	ENST00000257430.4:c.3225T>G	p.Tyr1075Ter	p.Y1075*	ENST00000257430	NM_000038.5	1075	taT/taG	16/16	0.3	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	FALSE	0	0.3	2		248	103	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	308	706	8	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.965	1	1	0.996	1	CLONAL	2	TRUE	1	0.483887790298295	2		714	626	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	99	347	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.483887790298295	2		347	374	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	27	222	2	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	0.483887790298295	3	FACETS	0.272	0.215	0.336	0.136	0.107	0.168	SUBCLONAL	1	TRUE	1	0.483887790298295	3		224	510	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	221	578	5	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.483887790298295	2		583	828	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	150	659	1	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.483887790298295	2		660	592	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434070	121434070	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766770471	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	119	386	2	ENST00000257555.6:c.961C>T	p.Arg321Cys	p.R321C	ENST00000257555		321	Cgc/Tgc	5/10	1	2	FACETS	0.95	0.861	1	0.95	0.861	1	CLONAL	1	TRUE	1	0.483887790298295	2		388	518	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485241	8485241	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168709750	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	77	215	0	ENST00000356435.5:c.3139G>A	p.Ala1047Thr	p.A1047T	ENST00000356435		1047	Gcc/Acc	18/35	1	2	FACETS	0.858	0.758	0.964	0.858	0.758	0.964	CLONAL	1	TRUE	1	0.483887790298295	2		215	371	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741849	17741849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750173588	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	59	138	0	ENST00000250003.3:c.520G>A	p.Ala174Thr	p.A174T	ENST00000250003	NM_002478.4	174	Gcc/Acc	1/3	0.483887790298295	2	FACETS	1	0.966	1	0.666	0.584	0.753	CLONAL	1	TRUE	0	0.483887790298295	2		138	183	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514998	148515000	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs775039041	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	105	233	2	ENST00000320356.2:c.1209_1211del	p.Glu404del	p.E404del	ENST00000320356	NM_004456.4	403	gaAGAg/gag	10/20	1	2	FACETS	0.998	0.9	1	0.998	0.9	1	CLONAL	1	TRUE	1	0.483887790298295	2		235	435	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568865	212568866	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	71	275	0	ENST00000342788.4:c.1252dup	p.Ser418PhefsTer2	p.S418Ffs*2	ENST00000342788	NM_005235.2	418	tct/tTct	11/28	1	2	FACETS	0.735	0.645	0.832	0.735	0.645	0.832	SUBCLONAL	1	TRUE	1	0.483887790298295	2		275	399	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120031	70120031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	12	48	0	ENST00000245479.2:c.1037del	p.Pro346ArgfsTer37	p.P346Rfs*37	ENST00000245479	NM_000346.3	345	Ccc/cc	3/3	1	2	FACETS	0.729	0.523	0.972	0.729	0.523	0.972	CLONAL	1	TRUE	1	0.483887790298295	2		48	68	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151290	202151290	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	92	226	0	ENST00000358485.4:c.1596del	p.Lys532AsnfsTer73	p.K532Nfs*73	ENST00000358485	NM_001080125.1	530	agA/ag	9/9	1	2	FACETS	0.925	0.827	1	0.925	0.827	1	CLONAL	1	TRUE	1	0.483887790298295	2		226	411	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729394	41729394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	117	386	0	ENST00000242208.4:c.1135C>T	p.Arg379Trp	p.R379W	ENST00000242208	NM_002192.2	379	Cgg/Tgg	3/3	1	2	FACETS	0.887	0.803	0.975	0.887	0.803	0.975	CLONAL	1	TRUE	1	0.483887790298295	2		386	545	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096967	11096967	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs539710314	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	162	589	1	ENST00000358026.2:c.458C>T	p.Pro153Leu	p.P153L	ENST00000358026	NM_001128849.1	153	cCg/cTg	4/36	1	2	FACETS	0.904	0.831	0.979	0.904	0.831	0.979	CLONAL	1	TRUE	1	0.483887790298295	2		590	741	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389095	31389095	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756558325	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	73	291	0	ENST00000328111.2:c.2008C>T	p.Arg670Trp	p.R670W	ENST00000328111	NM_006892.3	670	Cgg/Tgg	19/23	1	2	FACETS	0.782	0.687	0.882	0.782	0.687	0.882	SUBCLONAL	1	TRUE	1	0.483887790298295	2		291	386	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719525	61719525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	85	250	0	ENST00000401558.2:c.1658G>A	p.Arg553His	p.R553H	ENST00000401558	NM_003400.3	553	cGt/cAt	15/25	1	2	FACETS	0.76	0.675	0.851	0.76	0.675	0.851	SUBCLONAL	1	TRUE	1	0.483887790298295	2		250	462	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467083	25467083	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs568207978	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	146	473	0	ENST00000264709.3:c.1792C>T	p.Arg598Ter	p.R598*	ENST00000264709	NM_175629.2	598	Cga/Tga	15/23	1	2	FACETS	0.92	0.842	1	0.92	0.842	1	CLONAL	1	TRUE	1	0.483887790298295	2		473	656	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	136	580	2	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.483887790298295	2		582	551	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27192562	27192562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138894008	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	138	308	0	ENST00000380036.4:c.1565G>A	p.Arg522His	p.R522H	ENST00000380036	NM_000459.3	522	cGt/cAt	11/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.483887790298295	2		308	504	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214866	36214866	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568372429	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	176	506	3	ENST00000222270.7:c.3296del	p.Gly1099AlafsTer83	p.G1099Afs*83	ENST00000222270	NM_014727.1	1098	Ggg/gg	8/37	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.483887790298295	2		509	702	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944267	81944267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	183	529	0	ENST00000359376.3:c.1876G>A	p.Glu626Lys	p.E626K	ENST00000359376	NM_002661.3	626	Gag/Aag	18/33	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.483887790298295	2		529	730	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216184	36216184	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	130	475	1	ENST00000222270.7:c.3596del	p.Gly1199AlafsTer156	p.G1199Afs*156	ENST00000222270	NM_014727.1	1198	Ggg/gg	11/37	1	2	FACETS	0.778	0.706	0.852	0.778	0.706	0.852	SUBCLONAL	1	TRUE	1	0.483887790298295	2		476	691	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632303	215632303	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	113	311	0	ENST00000260947.4:c.1471G>T	p.Gly491Trp	p.G491W	ENST00000260947	NM_000465.2	491	Ggg/Tgg	6/11	1	2	FACETS	0.905	0.818	0.996	0.905	0.818	0.996	CLONAL	1	TRUE	1	0.483887790298295	2		311	516	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211861	36211861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747570960	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	144	536	1	ENST00000222270.7:c.1612C>T	p.Arg538Cys	p.R538C	ENST00000222270	NM_014727.1	538	Cgt/Tgt	3/37	1	2	FACETS	0.806	0.737	0.88	0.806	0.737	0.88	CLONAL	1	TRUE	1	0.483887790298295	2		537	738	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986838	36986838	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	98	165	0	ENST00000354822.5:c.851C>T	p.Ser284Leu	p.S284L	ENST00000354822	NM_001079668.2	284	tCg/tTg	3/3	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.483887790298295	2		165	345	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186821	108186821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376521407	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	96	258	1	ENST00000278616.4:c.6179G>A	p.Arg2060His	p.R2060H	ENST00000278616	NM_000051.3	2060	cGc/cAc	42/63	1	2	FACETS	0.868	0.777	0.964	0.868	0.777	0.964	CLONAL	1	TRUE	1	0.483887790298295	2		259	457	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778371	3778371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754601626	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	51	529	1	ENST00000262367.5:c.6677C>T	p.Ala2226Val	p.A2226V	ENST00000262367	NM_004380.2	2226	gCg/gTg	31/31	1	2	FACETS	0.367	0.312	0.428	0.367	0.312	0.428	SUBCLONAL	1	TRUE	1	0.483887790298295	2		530	574	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528243	157528243	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs797045283	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	129	333	0	ENST00000346085.5:c.5968C>T	p.Arg1990Ter	p.R1990*	ENST00000346085	NM_020732.3	1990	Cga/Tga	20/20	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.483887790298295	2		333	505	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031954	10031954	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199528312	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	108	427	0	ENST00000330684.3:c.869C>T	p.Ala290Val	p.A290V	ENST00000330684	NM_001134407.1	290	gCg/gTg	3/13	1	2	FACETS	0.845	0.762	0.933	0.845	0.762	0.933	CLONAL	1	TRUE	1	0.483887790298295	2		427	528	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438210	49438211	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1555194303	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	44	372	1	ENST00000301067.7:c.5058dup	p.Arg1687ThrfsTer4	p.R1687Tfs*4	ENST00000301067	NM_003482.3	1686	-/A	20/54	1	2	FACETS	0.291	0.243	0.344	0.291	0.243	0.344	SUBCLONAL	1	TRUE	1	0.483887790298295	2		373	625	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274832	38274832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760702592	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	82	254	0	ENST00000425967.3:c.1748C>T	p.Thr583Met	p.T583M	ENST00000425967	NM_001174067.1	583	aCg/aTg	13/19	0.483887790298295	3	FACETS	0.937	0.83	1	0.469	0.415	0.526	CLONAL	1	TRUE	1	0.483887790298295	3		254	449	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865040	57865040	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	141	467	0	ENST00000228682.2:c.2520del	p.Pro842HisfsTer104	p.P842Hfs*104	ENST00000228682	NM_005269.2	839	gaG/ga	12/12	1	2	FACETS	0.872	0.797	0.951	0.872	0.797	0.951	CLONAL	1	TRUE	1	0.483887790298295	2		467	668	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462969	120462969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	120	280	0	ENST00000256646.2:c.5362C>T	p.Pro1788Ser	p.P1788S	ENST00000256646	NM_024408.3	1788	Cca/Tca	30/34	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.483887790298295	2		280	491	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649616	206649616	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	144	405	0	ENST00000367120.3:c.451A>G	p.Ser151Gly	p.S151G	ENST00000367120	NM_014002.3	151	Agc/Ggc	6/22	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.483887790298295	2		405	549	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691185	18691185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	26	280	0	ENST00000266497.5:c.3296G>A	p.Cys1099Tyr	p.C1099Y	ENST00000266497		1099	tGc/tAc	23/31	1	2	FACETS	0.275	0.217	0.341	0.275	0.217	0.341	SUBCLONAL	1	TRUE	1	0.483887790298295	2		280	391	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915661	112915661	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	36	264	0	ENST00000351677.2:c.934C>T	p.Pro312Ser	p.P312S	ENST00000351677	NM_002834.3	312	Cct/Tct	9/16	1	2	FACETS	0.356	0.292	0.427	0.356	0.292	0.427	SUBCLONAL	1	TRUE	1	0.483887790298295	2		264	418	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929217	32929217	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1555286052	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	98	268	0	ENST00000380152.3:c.7230del	p.Phe2410LeufsTer57	p.F2410Lfs*57	ENST00000380152		2409	ccT/cc	14/27	0.483887790298295	3	FACETS	0.86	0.769	0.956	0.43	0.384	0.478	CLONAL	1	TRUE	1	0.483887790298295	3		268	585	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003788	45003788	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	215	385	0	ENST00000558401.1:c.46del	p.Ser16LeufsTer28	p.S16Lfs*28	ENST00000558401	NM_004048.2	15	cTt/ct	1/4	0.483887790298295	2	FACETS	0.89	0.836	0.945	0.89	0.836	0.945	CLONAL	2	TRUE	0	0.483887790298295	2		385	499	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993780	72993780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1314855387	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	108	412	0	ENST00000268489.5:c.265G>A	p.Ala89Thr	p.A89T	ENST00000268489	NM_006885.3	89	Gcc/Acc	2/10	1	2	FACETS	0.905	0.817	0.999	0.905	0.817	0.999	CLONAL	1	TRUE	1	0.483887790298295	2		412	493	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752422	55752422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757898294	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	223	604	1	ENST00000284073.2:c.880G>A	p.Gly294Arg	p.G294R	ENST00000284073	NM_138962.2	294	Gga/Aga	12/14	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.483887790298295	2		605	832	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39620659	39620659	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	70	220	0	ENST00000262039.4:c.2057A>G	p.Gln686Arg	p.Q686R	ENST00000262039	NM_002647.2	686	cAg/cGg	19/25	1	2	FACETS	0.866	0.761	0.978	0.866	0.761	0.978	CLONAL	1	TRUE	1	0.483887790298295	2		220	334	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326503	62326503	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	205	569	0	ENST00000360203.5:c.3428T>C	p.Met1143Thr	p.M1143T	ENST00000360203	NM_001283009.1	1143	aTg/aCg	33/35	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.483887790298295	2		569	772	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221649	22221649	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	25	206	0	ENST00000215832.6:c.82C>A	p.Leu28Ile	p.L28I	ENST00000215832	NM_002745.4	28	Ctc/Atc	1/9	1	2	FACETS	0.308	0.242	0.383	0.308	0.242	0.383	SUBCLONAL	1	TRUE	1	0.483887790298295	2		206	336	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648382	30648383	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	107	342	0	ENST00000295754.5:c.12dup	p.Leu5AlafsTer29	p.L5Afs*29	ENST00000295754	NM_003242.5	3	cgg/cGgg	1/7	1	2	FACETS	0.933	0.841	1	0.933	0.841	1	CLONAL	1	TRUE	1	0.483887790298295	2		342	474	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205106	128205106	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	186	651	0	ENST00000341105.2:c.335A>G	p.His112Arg	p.H112R	ENST00000341105	NM_032638.4	112	cAc/cGc	3/6	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.483887790298295	2		651	719	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184690	185184690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	77	264	0	ENST00000265026.3:c.1582G>A	p.Ala528Thr	p.A528T	ENST00000265026	NM_004721.4	528	Gcc/Acc	10/14	1	2	FACETS	0.754	0.665	0.849	0.754	0.665	0.849	SUBCLONAL	1	TRUE	1	0.483887790298295	2		264	422	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806102	1806102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	177	507	0	ENST00000260795.2:c.1121C>T	p.Ala374Val	p.A374V	ENST00000260795		374	gCa/gTa	8/17	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.483887790298295	2		507	698	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902409	1902410	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	131	375	0	ENST00000382891.5:c.31dup	p.Ser11PhefsTer46	p.S11Ffs*46	ENST00000382891	NM_133335.3	10	ctt/cTtt	2/22	1	2	FACETS	0.979	0.892	1	0.979	0.892	1	CLONAL	1	TRUE	1	0.483887790298295	2		375	553	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158443	106158443	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	71	133	0	ENST00000380013.4:c.3344C>T	p.Pro1115Leu	p.P1115L	ENST00000380013	NM_001127208.2	1115	cCt/cTt	3/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.483887790298295	2		133	242	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724407	117724407	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1215188906	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	136	377	0	ENST00000368508.3:c.472C>A	p.Leu158Met	p.L158M	ENST00000368508	NM_002944.2	158	Ctg/Atg	6/43	1	2	FACETS	0.981	0.896	1	0.981	0.896	1	CLONAL	1	TRUE	1	0.483887790298295	2		377	573	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117862860	117862860	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	51	198	0	ENST00000297338.2:c.1617A>C	p.Glu539Asp	p.E539D	ENST00000297338	NM_006265.2	539	gaA/gaC	12/14	0.483887790298295	3	FACETS	0.721	0.615	0.837	0.361	0.307	0.419	SUBCLONAL	1	TRUE	1	0.483887790298295	3		198	363	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044860	47044860	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	165	583	0	ENST00000377604.3:c.2186T>C	p.Val729Ala	p.V729A	ENST00000377604	NM_001204468.1	729	gTg/gCg	20/24	1	2	FACETS	0.955	0.879	1	0.955	0.879	1	CLONAL	1	TRUE	1	0.483887790298295	2		583	714	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573984	7573984	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0047863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	98	456	0	ENST00000269305.4:c.1043T>A	p.Leu348Ter	p.L348*	ENST00000269305	NM_001126112.2	348	tTg/tAg	10/11	0.187953660715187	3	FACETS	1	0.909	1	0.512	0.455	0.573	CLONAL	1	TRUE	1	0.17	3		456	1221	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376718	31376718	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	69	321	0	ENST00000328111.2:c.714del	p.Trp238CysfsTer92	p.W238Cfs*92	ENST00000328111	NM_006892.3	238	tGg/tg	7/23	1	2	FACETS	0.982	0.853	1	0.982	0.853	1	CLONAL	1	TRUE	1	0.17	2		321	827	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829787	76829787	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057517948	NA	P-0047863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	10	169	0	ENST00000373344.5:c.6254G>T	p.Arg2085Leu	p.R2085L	ENST00000373344	NM_000489.3	2085	cGt/cTt	28/35	1	1	FACETS	1	0.829	1	1	0.829	1	CLONAL	1	TRUE	0	0.17	1		169	78	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047863-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	82	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.546552093292017	4	FACETS	0.829	0.732	0.932	0.414	0.366	0.466	CLONAL	1	FALSE	2	0.546552093292017	4		327	560	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0047863-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	82	600	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.199196583784345	6	FACETS	0.93	0.821	1	0.31	0.273	0.35	INDETERMINATE	1	FALSE	3	0.546552093292017	6		600	675	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0047863-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	43	400	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.199196583784345	6	FACETS	0.742	0.621	0.875	0.247	0.207	0.292	INDETERMINATE	1	FALSE	3	0.546552093292017	6		400	444	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0047863-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	69	208	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.546552093292017	3	FACETS	1	0.956	1	0.595	0.524	0.671	CLONAL	1	FALSE	1	0.546552093292017	3		208	270	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662817	227662817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1273995645	NA	P-0047863-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	60	798	0	ENST00000305123.5:c.638G>A	p.Arg213His	p.R213H	ENST00000305123	NM_005544.2	213	cGc/cAc	1/2	0.42888660550681	5	FACETS	0.865	0.747	0.993			1	CLONAL	1	FALSE	NA	0.546552093292017	5		798	462	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117757	70117758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0047863-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	117	868	0	ENST00000245479.2:c.227_228dup	p.Val77ArgfsTer34	p.V77Rfs*34	ENST00000245479	NM_000346.3	75	-/GC	1/3	0.199196583784345	6	FACETS	0.98	0.89	1	0.654	0.593	0.717	INDETERMINATE	2	FALSE	3	0.546552093292017	6		868	457	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131084	55131084	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0047863-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	18	366	0	ENST00000257290.5:c.629-2A>T		p.X210_splice	ENST00000257290	NM_006206.4	210			1	2	FACETS	0.235	0.177	0.304	0.235	0.177	0.304	SUBCLONAL	1	FALSE	1	0.546552093292017	2		366	280	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039888	47039900	+	frameshift_variant	Frame_Shift_Del	DEL	CAGTGGGCCATCT	CAGTGGGCCATCT	-	novel	NA	P-0047863-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	72	459	0	ENST00000377604.3:c.1233_1245del	p.Gln411HisfsTer70	p.Q411Hfs*70	ENST00000377604	NM_001204468.1	411	CAGTGGGCCATCTca/ca	12/24	0.48089102000397	2	FACETS	0.842	0.742	0.948			1	CLONAL	1	FALSE	NA	0.546552093292017	2		459	313	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047863-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	52	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.32	2		327	310	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0047863-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	51	600	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.702	0.597	0.817	0.702	0.597	0.817	SUBCLONAL	1	TRUE	1	0.32	2		600	454	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0047863-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	47	400	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.856	0.725	1	0.856	0.725	1	CLONAL	1	TRUE	1	0.32	2		400	343	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0047863-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	55	208	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.246338058468384	2	FACETS	0.881	0.766	1	0.881	0.766	1	CLONAL	2	TRUE	0	0.32	2		208	195	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662817	227662817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1273995645	NA	P-0047863-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	100	798	0	ENST00000305123.5:c.638G>A	p.Arg213His	p.R213H	ENST00000305123	NM_005544.2	213	cGc/cAc	1/2	1	2	FACETS	0.748	0.667	0.833	0.748	0.667	0.833	SUBCLONAL	1	TRUE	1	0.32	2		798	836	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117757	70117758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0047863-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	123	868	0	ENST00000245479.2:c.227_228dup	p.Val77ArgfsTer34	p.V77Rfs*34	ENST00000245479	NM_000346.3	75	-/GC	1/3	1	2	FACETS	0.813	0.735	0.897	0.813	0.735	0.897	CLONAL	1	TRUE	1	0.32	2		868	945	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131084	55131084	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0047863-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	55	366	0	ENST00000257290.5:c.629-2A>T		p.X210_splice	ENST00000257290	NM_006206.4	210			1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.32	2		366	299	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039888	47039900	+	frameshift_variant	Frame_Shift_Del	DEL	CAGTGGGCCATCT	CAGTGGGCCATCT	-	novel	NA	P-0047863-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	97	459	0	ENST00000377604.3:c.1233_1245del	p.Gln411HisfsTer70	p.Q411Hfs*70	ENST00000377604	NM_001204468.1	411	CAGTGGGCCATCTca/ca	12/24	0.059237382182161	2	FACETS	1	0.972	1			1	INDETERMINATE	1	TRUE	NA	0.32	2		459	480	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047863-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	102	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.181054859364517	8	FACETS	1	0.926	1	0.78	0.7	0.865	CLONAL	3	FALSE	4	0.181054859364517	8		327	557	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0047863-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	149	600	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.181054859364517	6	FACETS	1	0.968	1	0.835	0.765	0.908	CLONAL	3	FALSE	2	0.181054859364517	6		600	671	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0047863-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	93	400	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.181054859364517	6	FACETS	0.978	0.873	1	0.733	0.655	0.816	CLONAL	3	FALSE	2	0.181054859364517	6		400	477	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0047863-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	109	208	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.181054859364517	6	FACETS	1	0.958	1	1	0.958	1	CLONAL	5	FALSE	1	0.181054859364517	6		208	301	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662817	227662817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1273995645	NA	P-0047863-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	155	798	0	ENST00000305123.5:c.638G>A	p.Arg213His	p.R213H	ENST00000305123	NM_005544.2	213	cGc/cAc	1/2	0.181054859364517	6	FACETS	0.907	0.833	0.983	0.907	0.833	0.983	CLONAL	4	FALSE	2	0.181054859364517	6		798	643	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117757	70117758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0047863-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	259	868	0	ENST00000245479.2:c.227_228dup	p.Val77ArgfsTer34	p.V77Rfs*34	ENST00000245479	NM_000346.3	75	-/GC	1/3	0.181054859364517	11	FACETS	1	0.97	1			1	CLONAL	6	FALSE	NA	0.181054859364517	11		868	823	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131084	55131084	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0047863-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	79	366	0	ENST00000257290.5:c.629-2A>T		p.X210_splice	ENST00000257290	NM_006206.4	210			0.17329625313759	4	FACETS	1	0.949	1	1	0.982	1	CLONAL	3	FALSE	2	0.181054859364517	4		366	306	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039888	47039900	+	frameshift_variant	Frame_Shift_Del	DEL	CAGTGGGCCATCT	CAGTGGGCCATCT	-	novel	NA	P-0047863-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	91	459	0	ENST00000377604.3:c.1233_1245del	p.Gln411HisfsTer70	p.Q411Hfs*70	ENST00000377604	NM_001204468.1	411	CAGTGGGCCATCTca/ca	12/24	0.181054859364517	4	FACETS	0.983	0.883	1			1	CLONAL	4	FALSE	NA	0.181054859364517	4		459	302	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758765	41758765	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047863-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	63	920	0	ENST00000301178.4:c.1819G>T	p.Gly607Cys	p.G607C	ENST00000301178	NM_021913.4	607	Ggt/Tgt	16/20	0.181054859364517	5	FACETS	1	0.967	1	0.474	0.41	0.544	CLONAL	1	FALSE	2	0.181054859364517	5		920	622	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964511	70964511	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047863-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	111	651	0	ENST00000276594.2:c.1517C>G	p.Thr506Arg	p.T506R	ENST00000276594	NM_024504.3	506	aCa/aGa	8/8	0.181054859364517	6	FACETS	0.929	0.838	1	0.929	0.838	1	CLONAL	3	FALSE	3	0.181054859364517	6		651	599	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0047864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	191	405	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.457799118352925	5	FACETS	0.886	0.832	0.941	1	0.986	1	CLONAL	4	FALSE	2	0.457799118352925	5		405	397	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0047864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	180	434	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.457799118352925	2	FACETS	0.952	0.889	1	0.952	0.889	1	CLONAL	2	FALSE	0	0.457799118352925	2		434	413	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0047864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	14	356	1	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	0.457799118352925	5	FACETS	0.174	0.125	0.234	0.058	0.041	0.078	SUBCLONAL	1	FALSE	2	0.457799118352925	5		357	593	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066739	5066739	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1340580425	NA	P-0047864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	33	198	0	ENST00000381652.3:c.1276C>T	p.Arg426Ter	p.R426*	ENST00000381652	NM_004972.3	426	Cga/Tga	10/25	0.21774145729907	5	FACETS	0.918	0.751	1	0.306	0.25	0.368	INDETERMINATE	1	FALSE	2	0.457799118352925	5		198	265	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80160645	80160645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	76	308	0	ENST00000265081.6:c.3014C>T	p.Thr1005Ile	p.T1005I	ENST00000265081	NM_002439.4	1005	aCc/aTc	22/24	0.457799118352925	3	FACETS	1	0.961	1	0.605	0.535	0.68	CLONAL	1	FALSE	1	0.457799118352925	3		308	337	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465282	120465282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	45	290	0	ENST00000256646.2:c.4979C>T	p.Ser1660Leu	p.S1660L	ENST00000256646	NM_024408.3	1660	tCa/tTa	27/34	0.221783768702602	4	FACETS	0.701	0.59	0.823			1	INDETERMINATE	1	FALSE	NA	0.457799118352925	4		290	409	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465274	120465274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752668646	NA	P-0047864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	37	250	0	ENST00000256646.2:c.4987C>T	p.Leu1663Phe	p.L1663F	ENST00000256646	NM_024408.3	1663	Ctt/Ttt	27/34	0.221783768702602	4	FACETS	0.658	0.544	0.786			1	INDETERMINATE	1	FALSE	NA	0.457799118352925	4		250	358	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942714	48942715	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0047864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	21	157	0	ENST00000267163.4:c.1102_1103del	p.Val368AsnfsTer8	p.V368Nfs*8	ENST00000267163	NM_000321.2	367	aaTGta/aata	11/27	0.441399395712143	1	FACETS	0.532	0.414	0.666	0.532	0.414	0.666	SUBCLONAL	1	FALSE	0	0.457799118352925	1		157	133	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116174	67116398	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGAAGATAGAGACAGGTCTCATCGGGAGGAAATGGAGGTGAGAGTTTCACAGCTGCTGGCAGTAACTGGTTAGTACTTTCCCCCAAACTCTCAGGCTGTGTTTGTGATGTTTGTGCATAATGCTTTTTAATAGTTTAATTTTGTCTTTCATTTTTAAAAAGTTGTACTCTCTGGCTTTGTGTTTATTAAATGTAATTGCTATAAAGAAATTTATTTTAATTTTA	TTGAAGATAGAGACAGGTCTCATCGGGAGGAAATGGAGGTGAGAGTTTCACAGCTGCTGGCAGTAACTGGTTAGTACTTTCCCCCAAACTCTCAGGCTGTGTTTGTGATGTTTGTGCATAATGCTTTTTAATAGTTTAATTTTGTCTTTCATTTTTAAAAAGTTGTACTCTCTGGCTTTGTGTTTATTAAATGTAATTGCTATAAAGAAATTTATTTTAATTTTA	-	novel	NA	P-0047864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	61	327	0	ENST00000412916.2:c.458_495+187del		p.X153_splice	ENST00000412916		153		5/6	0.457799118352925	2	FACETS	1	0.936	1	0.56	0.489	0.635	CLONAL	1	FALSE	0	0.457799118352925	2		327	238	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156919	106156919	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	15	255	0	ENST00000380013.4:c.1820G>C	p.Gly607Ala	p.G607A	ENST00000380013	NM_001127208.2	607	gGa/gCa	3/11	0.405172470558408	3	FACETS	0.273	0.199	0.362	0.136	0.099	0.181	SUBCLONAL	1	FALSE	1	0.457799118352925	3		255	295	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588984	67588984	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	11	158	0	ENST00000274335.5:c.1075G>C	p.Asp359His	p.D359H	ENST00000274335		359	Gat/Cat	8/15	0.457799118352925	3	FACETS	0.3	0.207	0.415	0.15	0.103	0.208	SUBCLONAL	1	FALSE	1	0.457799118352925	3		158	197	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0047877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	28	555	0	ENST00000269305.4:c.920-2A>C		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.418885199096237	1	FACETS	0.935	0.763	1	0.935	0.763	1	CLONAL	1	TRUE	0	0.418885199096237	1		555	113	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004945	150004945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	15	319	0	ENST00000253339.5:c.1280C>G	p.Pro427Arg	p.P427R	ENST00000253339		427	cCt/cGt	3/7	NA	2	FACETS	0.873	0.651	1			1	INDETERMINATE	1	TRUE	NA	0.418885199096237	2		319	82	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872400	35872400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	19	668	0	ENST00000216797.5:c.503C>T	p.Thr168Ile	p.T168I	ENST00000216797	NM_020529.2	168	aCc/aTc	3/6	1	2	FACETS	0.388	0.295	0.496	0.388	0.295	0.496	SUBCLONAL	1	TRUE	1	0.418885199096237	2		668	234	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243920	41243920	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	35	492	1	ENST00000357654.3:c.3628G>T	p.Glu1210Ter	p.E1210*	ENST00000357654	NM_007294.3	1210	Gag/Tag	10/23	0.418885199096237	1	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	0	0.418885199096237	1		493	120	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142984	7142984	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	17	629	0	ENST00000302850.5:c.2385C>A	p.His795Gln	p.H795Q	ENST00000302850	NM_000208.2	795	caC/caA	12/22	0.263335948899675	0	FACETS	0.33	0.248	0.425			1	SUBCLONAL	1	TRUE	0	0.418885199096237	0		629	143	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054702	13054702	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866651711	NA	P-0047877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	35	368	0	ENST00000316448.5:c.1229C>T	p.Pro410Leu	p.P410L	ENST00000316448	NM_004343.3	410	cCc/cTc	9/9	NA	2	FACETS	1	0.892	1			1	INDETERMINATE	1	TRUE	NA	0.418885199096237	2		368	152	SUCCESS
AXL	558	MSKCC	GRCh37	19	41736880	41736901	+	frameshift_variant	Frame_Shift_Del	DEL	AAGACATCCTCTTTCTCCTGCG	AAGACATCCTCTTTCTCCTGCG	-	novel	NA	P-0047877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	32	619	0	ENST00000301178.4:c.598_619del	p.Thr200ProfsTer43	p.T200Pfs*43	ENST00000301178	NM_021913.4	199	AAGACATCCTCTTTCTCCTGCGaa/aa	5/20	0.183751791446001	4	FACETS	1	0.903	1	0.583	0.478	0.699	INDETERMINATE	1	TRUE	2	0.418885199096237	4		619	186	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62317164	62317165	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGTCACCGGAGGACGGCTCAGCGGTCTGATGCC	novel	NA	P-0047877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	39	814	0	ENST00000360203.5:c.1288_1320dup	p.Gly430_Ala440dup	p.G430_A440dup	ENST00000360203	NM_001283009.1	430	-/GGTCACCGGAGGACGGCTCAGCGGTCTGATGCC	16/35	1	2	FACETS	0.605	0.503	0.717	0.605	0.503	0.717	SUBCLONAL	1	TRUE	1	0.418885199096237	2		814	308	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004919	150004920	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0047877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	17	324	0	ENST00000253339.5:c.1305dup	p.Ser436ValfsTer15	p.S436Vfs*15	ENST00000253339		435	-/G	3/7	NA	2	FACETS	0.902	0.685	1			1	INDETERMINATE	1	TRUE	NA	0.418885199096237	2		324	90	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242433	55242433	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	23	340	0	ENST00000275493.2:c.2203G>C	p.Gly735Arg	p.G735R	ENST00000275493	NM_005228.3	735	Ggt/Cgt	19/28	0.166719307491973	2	FACETS	1	0.845	1	0.538	0.428	0.661	INDETERMINATE	1	TRUE	0	0.418885199096237	2		340	102	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974730	21974731	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AT	novel	NA	P-0047877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	34	412	1	ENST00000304494.5:c.96_97delinsAT	p.Glu33Ter	p.E33*	ENST00000304494	NM_000077.4	32	ctGGag/ctATag	1/3	0.219859723752734	1	FACETS	1	0.93	1	1	0.93	1	INDETERMINATE	1	TRUE	0	0.418885199096237	1		413	105	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426123	138426123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217537873	NA	P-0047878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	52	191	0	ENST00000289153.2:c.1408G>A	p.Glu470Lys	p.E470K	ENST00000289153	NM_006219.2	470	Gaa/Aaa	9/22	0.3	4	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	4		191	398	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100998	41100998	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772057709	NA	P-0047878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	24	538	0	ENST00000373198.4:c.1358G>A	p.Arg453His	p.R453H	ENST00000373198	NM_133170.3	453	cGc/cAc	8/32	0.3	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		538	430	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061028	38061028	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	143	300	0	ENST00000250448.2:c.961G>C	p.Glu321Gln	p.E321Q	ENST00000250448	NM_004496.3	321	Gag/Cag	2/2	0.150598896288319	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		300	450	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591147	67591148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	49	183	0	ENST00000274335.5:c.1742dup	p.Leu581PhefsTer21	p.L581Ffs*21	ENST00000274335		580	-/T	12/15	0.3	6	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	6		183	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0047879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	64	607	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.381164182756037	2		608	302	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339072	225339072	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	38	249	0	ENST00000264414.4:c.2197C>T	p.Arg733Ter	p.R733*	ENST00000264414	NM_003590.4	733	Cga/Tga	16/16	0.205090781308345	2	FACETS	1	0.942	1	0.647	0.544	0.759	INDETERMINATE	1	TRUE	0	0.381164182756037	2		249	154	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552821	226552821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182639036	NA	P-0047879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	18	483	0	ENST00000366794.5:c.2540G>A	p.Arg847His	p.R847H	ENST00000366794	NM_001618.3	847	cGt/cAt	19/23	1	2	FACETS	0.365	0.275	0.471	0.365	0.275	0.471	SUBCLONAL	1	TRUE	1	0.381164182756037	2		483	259	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310913	123310913	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	13	542	0	ENST00000358487.5:c.515C>A	p.Ala172Asp	p.A172D	ENST00000358487	NM_000141.4	172	gCc/gAc	5/18	0.380921392192988	1	FACETS	0.213	0.152	0.288	0.213	0.152	0.288	SUBCLONAL	1	TRUE	0	0.381164182756037	1		542	259	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545650	106545650	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	33	366	0	ENST00000359195.3:c.3127A>C	p.Thr1043Pro	p.T1043P	ENST00000359195	NM_002649.2	1043	Aca/Cca	11/11	0.36074491381407	3	FACETS	0.968	0.795	1	0.484	0.397	0.58	CLONAL	1	TRUE	1	0.381164182756037	3		366	213	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0047881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	18	432	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.554	0.416	0.719	0.554	0.416	0.719	SUBCLONAL	1	TRUE	1	0.15	2		432	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs587781433	NA	P-0047881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	36	572	0	ENST00000269305.4:c.766A>C	p.Thr256Pro	p.T256P	ENST00000269305	NM_001126112.2	256	Aca/Cca	7/11	1	2	FACETS	0.741	0.607	0.891	0.741	0.607	0.891	SUBCLONAL	1	TRUE	1	0.15	2		572	648	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714218	43714218	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	54	718	0	ENST00000382044.4:c.3935C>G	p.Ser1312Cys	p.S1312C	ENST00000382044	NM_001141980.1	1312	tCc/tGc	19/28	1	2	FACETS	0.781	0.665	0.909	0.781	0.665	0.909	CLONAL	1	TRUE	1	0.15	2		718	922	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845262	151845262	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747850540	NA	P-0047882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	132	408	0	ENST00000262189.6:c.13750C>T	p.Arg4584Trp	p.R4584W	ENST00000262189	NM_170606.2	4584	Cgg/Tgg	52/59	1	2	FACETS	0.848	0.771	0.929	0.848	0.771	0.929	CLONAL	1	TRUE	1	0.436547334143263	2		408	713	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0047883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	377	424	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.785600162450163	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.794205635282664	2		424	456	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004331	150004331	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	186	259	0	ENST00000253339.5:c.1894C>T	p.Gln632Ter	p.Q632*	ENST00000253339		632	Caa/Taa	3/7	0.716450185429713	4	FACETS	0.793	0.738	0.849	0.793	0.738	0.849	SUBCLONAL	2	TRUE	2	0.794205635282664	4		259	530	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620411	43620411	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs759798237	NA	P-0047883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	134	337	0	ENST00000355710.3:c.3020A>T	p.Lys1007Met	p.K1007M	ENST00000355710	NM_020975.4	1007	aAg/aTg	18/20	0.516403329955653	4	FACETS	1	0.977	1	0.399	0.364	0.435	CLONAL	1	TRUE	1	0.794205635282664	4		337	506	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794476	242794476	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs761603116	NA	P-0047883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	216	592	0	ENST00000334409.5:c.466C>A	p.Pro156Thr	p.P156T	ENST00000334409	NM_005018.2	156	Ccc/Acc	3/5	0.794205635282664	4	FACETS	1	0.974	1	0.364	0.339	0.391	CLONAL	1	TRUE	1	0.794205635282664	4		592	893	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138785	37138785	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3509	566	403	1	ENST00000373509.5:c.218G>T	p.Arg73Leu	p.R73L	ENST00000373509	NM_002648.3	73	cGg/cTg	3/6	0.794205635282664	26	FACETS	0.921	0.879	0.964			1	CLONAL	4	TRUE	NA	0.794205635282664	26		404	4075	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139042	37139042	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4388	692	498	0	ENST00000373509.5:c.382G>T	p.Asp128Tyr	p.D128Y	ENST00000373509	NM_002648.3	128	Gat/Tat	4/6	0.794205635282664	26	FACETS	0.903	0.865	0.942			1	CLONAL	4	TRUE	NA	0.794205635282664	26		498	5080	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0047884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	19	259	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.488	0.371	0.626	0.488	0.371	0.626	SUBCLONAL	1	FALSE	1	0.277025697801516	2		259	281	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211894	36211894	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	85	903	0	ENST00000222270.7:c.1645G>T	p.Glu549Ter	p.E549*	ENST00000222270	NM_014727.1	549	Gaa/Taa	3/37	1	2	FACETS	0.573	0.505	0.646	0.573	0.505	0.646	SUBCLONAL	1	FALSE	1	0.277025697801516	2		903	1071	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0047884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	15	320	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.39	0.284	0.516	0.39	0.284	0.516	SUBCLONAL	1	FALSE	1	0.277025697801516	2		320	278	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323193	31323193	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	63	724	0	ENST00000412585.2:c.796C>T	p.Gln266Ter	p.Q266*	ENST00000412585	NM_005514.6	266	Cag/Tag	4/8	1	2	FACETS	0.736	0.636	0.844	0.736	0.636	0.844	SUBCLONAL	1	FALSE	1	0.277025697801516	2		724	618	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858615	57858615	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	73	643	0	ENST00000228682.2:c.353G>T	p.Gly118Val	p.G118V	ENST00000228682	NM_005269.2	118	gGa/gTa	4/12	1	2	FACETS	0.692	0.604	0.786	0.692	0.604	0.786	SUBCLONAL	1	FALSE	1	0.277025697801516	2		643	762	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219902	133219902	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555222924	NA	P-0047884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	62	733	0	ENST00000320574.5:c.4459A>G	p.Ile1487Val	p.I1487V	ENST00000320574	NM_006231.2	1487	Atc/Gtc	35/49	1	2	FACETS	0.588	0.507	0.677	0.588	0.507	0.677	SUBCLONAL	1	FALSE	1	0.277025697801516	2		733	761	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347746	347746	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs746551099	NA	P-0047884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	71	949	1	ENST00000262320.3:c.1760A>T	p.Asn587Ile	p.N587I	ENST00000262320	NM_003502.3	587	aAc/aTc	6/11	1	2	FACETS	0.555	0.483	0.633	0.555	0.483	0.633	SUBCLONAL	1	FALSE	1	0.277025697801516	2		950	923	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819300	3819300	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	79	688	0	ENST00000262367.5:c.2935G>T	p.Ala979Ser	p.A979S	ENST00000262367	NM_004380.2	979	Gcc/Tcc	15/31	1	2	FACETS	0.69	0.606	0.781	0.69	0.606	0.781	SUBCLONAL	1	FALSE	1	0.277025697801516	2		688	826	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928652	49928652	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	76	829	0	ENST00000296474.3:c.3622G>C	p.Asp1208His	p.D1208H	ENST00000296474	NM_002447.2	1208	Gac/Cac	17/20	1	2	FACETS	0.587	0.514	0.667	0.587	0.514	0.667	SUBCLONAL	1	FALSE	1	0.277025697801516	2		829	934	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508080	106508080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	25	287	0	ENST00000359195.3:c.74C>T	p.Pro25Leu	p.P25L	ENST00000359195	NM_002649.2	25	cCg/cTg	2/11	1	2	FACETS	0.492	0.387	0.612	0.492	0.387	0.612	SUBCLONAL	1	FALSE	1	0.277025697801516	2		287	367	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68999959	68999959	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	18	480	3	ENST00000288368.4:c.2028G>T	p.Glu676Asp	p.E676D	ENST00000288368	NM_024870.2	676	gaG/gaT	19/40	1	2	FACETS	0.381	0.286	0.493	0.381	0.286	0.493	SUBCLONAL	1	FALSE	1	0.277025697801516	2		483	341	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300960	137300960	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	65	732	0	ENST00000481739.1:c.605G>T	p.Arg202Leu	p.R202L	ENST00000481739	NM_002957.4	202	cGg/cTg	4/10	1	2	FACETS	0.572	0.495	0.656	0.572	0.495	0.656	SUBCLONAL	1	FALSE	1	0.277025697801516	2		732	820	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	142	331	1	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.500695792991733	2		332	560	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	104	566	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.771	0.692	0.853	0.771	0.692	0.853	SUBCLONAL	1	TRUE	1	0.500695792991733	2		566	539	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	59	228	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.783	0.679	0.895	0.783	0.679	0.895	SUBCLONAL	1	TRUE	1	0.500695792991733	2		228	301	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	29	277	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.212	0.169	0.26	0.212	0.169	0.26	SUBCLONAL	1	TRUE	1	0.500695792991733	2		277	547	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	124	473	6	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.68	0.616	0.748	0.68	0.616	0.748	SUBCLONAL	1	TRUE	1	0.500695792991733	2		479	728	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	152	691	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.573	0.523	0.625	0.573	0.523	0.625	SUBCLONAL	1	TRUE	1	0.500695792991733	2		692	1060	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781324	3781326	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs587783502	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	295	730	0	ENST00000262367.5:c.5039_5041del	p.Ser1680del	p.S1680del	ENST00000262367	NM_004380.2	1680	tCCTtg/ttg	30/31	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.500695792991733	2		730	1164	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	25	660	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.167	0.131	0.208	0.167	0.131	0.208	SUBCLONAL	1	TRUE	1	0.500695792991733	2		660	599	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	150	461	5	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.701	0.641	0.764	0.701	0.641	0.764	SUBCLONAL	1	TRUE	1	0.500695792991733	2		466	855	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	169	650	2	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.727	0.668	0.788	0.727	0.668	0.788	SUBCLONAL	1	TRUE	1	0.500695792991733	2		652	929	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998127	169998128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs753143066	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	134	438	3	ENST00000295797.4:c.826dup	p.Thr276AsnfsTer16	p.T276Nfs*16	ENST00000295797	NM_002740.5	273	tta/ttAa	9/18	1	2	FACETS	0.744	0.677	0.815	0.744	0.677	0.815	SUBCLONAL	1	TRUE	1	0.500695792991733	2		441	719	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438316	110438317	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	rs532810290	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	42	161	2	ENST00000375856.3:c.82_84dup	p.Asn28dup	p.N28dup	ENST00000375856	NM_003749.2	28	-/AAC	1/2	1	2	FACETS	0.441	0.369	0.521	0.441	0.369	0.521	SUBCLONAL	1	TRUE	1	0.500695792991733	2		163	380	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991757	72991758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760959844	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	94	435	1	ENST00000268489.5:c.2287dup	p.Glu763GlyfsTer26	p.E763Gfs*26	ENST00000268489	NM_006885.3	763	gag/gGag	2/10	1	2	FACETS	0.576	0.513	0.643	0.576	0.513	0.643	SUBCLONAL	1	TRUE	1	0.500695792991733	2		436	652	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941125	36941125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375879178	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	216	560	0	ENST00000361632.4:c.214G>A	p.Gly72Arg	p.G72R	ENST00000361632		72	Ggg/Agg	3/16	1	2	FACETS	0.946	0.88	1	0.946	0.88	1	CLONAL	1	TRUE	1	0.500695792991733	2		560	912	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733513	85733513	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs387906350	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	148	304	7	ENST00000370580.1:c.499del	p.Ser167LeufsTer6	p.S167Lfs*6	ENST00000370580	NM_003921.4	167	Tct/ct	3/3	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.500695792991733	2		311	580	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843626	156843626	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	65	606	0	ENST00000524377.1:c.1052C>A	p.Pro351His	p.P351H	ENST00000524377	NM_002529.3	351	cCc/cAc	8/17	1	2	FACETS	0.276	0.238	0.317	0.276	0.238	0.317	SUBCLONAL	1	TRUE	1	0.500695792991733	2		606	942	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745569	162745569	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	100	402	0	ENST00000367921.3:c.1984C>A	p.Leu662Ile	p.L662I	ENST00000367921	NM_006182.2	662	Ctc/Atc	15/18	1	2	FACETS	0.697	0.624	0.774	0.697	0.624	0.774	SUBCLONAL	1	TRUE	1	0.500695792991733	2		402	573	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111171	193111171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	83	238	0	ENST00000367435.3:c.704C>T	p.Thr235Ile	p.T235I	ENST00000367435	NM_024529.4	235	aCa/aTa	7/17	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.500695792991733	2		238	324	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983031	201983031	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	194	518	0	ENST00000359651.3:c.881del	p.Lys294SerfsTer31	p.K294Sfs*31	ENST00000359651		294	Aag/ag	7/8	1	2	FACETS	0.795	0.735	0.857	0.795	0.735	0.857	SUBCLONAL	1	TRUE	1	0.500695792991733	2		518	975	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716118	243716118	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	42	414	0	ENST00000263826.5:c.1076T>C	p.Leu359Ser	p.L359S	ENST00000263826	NM_005465.4	359	tTa/tCa	10/13	1	2	FACETS	0.303	0.252	0.359	0.303	0.252	0.359	SUBCLONAL	1	TRUE	1	0.500695792991733	2		414	554	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533536	533536	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369106578	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	248	629	0	ENST00000451590.1:c.367C>T	p.Arg123Cys	p.R123C	ENST00000451590	NM_001130442.1	123	Cgc/Tgc	4/5	1	2	FACETS	0.989	0.925	1	0.989	0.925	1	CLONAL	1	TRUE	1	0.500695792991733	2		629	1002	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462801	69462801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1271260640	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	155	516	1	ENST00000227507.2:c.614C>T	p.Ala205Val	p.A205V	ENST00000227507	NM_053056.2	205	gCg/gTg	4/5	1	2	FACETS	0.75	0.687	0.816	0.75	0.687	0.816	SUBCLONAL	1	TRUE	1	0.500695792991733	2		517	825	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514265	69514265	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	161	573	0	ENST00000294312.3:c.416A>G	p.His139Arg	p.H139R	ENST00000294312	NM_005117.2	139	cAc/cGc	3/3	1	2	FACETS	0.738	0.677	0.801	0.738	0.677	0.801	SUBCLONAL	1	TRUE	1	0.500695792991733	2		573	872	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434005	49434005	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	256	704	0	ENST00000301067.7:c.7548del	p.Asn2517IlefsTer26	p.N2517Ifs*26	ENST00000301067	NM_003482.3	2516	ccC/cc	31/54	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.500695792991733	2		704	978	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856521	111856521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	149	279	0	ENST00000341259.2:c.572C>T	p.Pro191Leu	p.P191L	ENST00000341259	NM_005475.2	191	cCg/cTg	2/8	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.500695792991733	2		279	536	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562397	21562397	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	45	558	0	ENST00000382592.4:c.1522G>T	p.Gly508Cys	p.G508C	ENST00000382592	NM_014572.2	508	Ggc/Tgc	4/8	1	2	FACETS	0.233	0.195	0.275	0.233	0.195	0.275	SUBCLONAL	1	TRUE	1	0.500695792991733	2		558	772	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913837	32913837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359507	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	16	254	0	ENST00000380152.3:c.5351del	p.Asn1784ThrfsTer7	p.N1784Tfs*7	ENST00000380152		1782	cAa/ca	11/27	1	2	FACETS	0.218	0.161	0.287	0.218	0.161	0.287	SUBCLONAL	1	TRUE	1	0.500695792991733	2		254	293	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954272	32954273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359752	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	88	313	0	ENST00000380152.3:c.9253dup	p.Thr3085AsnfsTer26	p.T3085Nfs*26	ENST00000380152		3082	-/A	24/27	1	2	FACETS	0.839	0.747	0.936	0.839	0.747	0.936	CLONAL	1	TRUE	1	0.500695792991733	2		313	419	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514050	103514050	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	51	248	0	ENST00000355739.4:c.866A>G	p.Tyr289Cys	p.Y289C	ENST00000355739	NM_000123.3	289	tAc/tGc	7/15	1	2	FACETS	0.59	0.504	0.685	0.59	0.504	0.685	SUBCLONAL	1	TRUE	1	0.500695792991733	2		248	345	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435597	110435597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762535630	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	165	331	0	ENST00000375856.3:c.2804C>T	p.Ala935Val	p.A935V	ENST00000375856	NM_003749.2	935	gCg/gTg	1/2	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.500695792991733	2		331	631	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2224294	2224294	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	160	671	0	ENST00000326181.6:c.1306G>T	p.Glu436Ter	p.E436*	ENST00000326181	NM_032271.2	436	Gag/Tag	14/21	1	2	FACETS	0.658	0.602	0.715	0.658	0.602	0.715	SUBCLONAL	1	TRUE	1	0.500695792991733	2		671	972	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50788275	50788275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	133	440	0	ENST00000398568.2:c.853C>T	p.Leu285Phe	p.L285F	ENST00000398568	NM_001042412.1	285	Ctt/Ttt	5/18	1	2	FACETS	0.667	0.606	0.731	0.667	0.606	0.731	SUBCLONAL	1	TRUE	1	0.500695792991733	2		440	797	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89809209	89809209	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	175	384	0	ENST00000389301.3:c.3764A>T	p.Glu1255Val	p.E1255V	ENST00000389301	NM_000135.2	1255	gAg/gTg	37/43	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.500695792991733	2		384	692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	254	599	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	1	2	FACETS	0.993	0.93	1	0.993	0.93	1	CLONAL	1	TRUE	1	0.500695792991733	2		599	1022	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541593	29541593	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	17	203	0	ENST00000356175.3:c.1517T>G	p.Leu506Arg	p.L506R	ENST00000356175	NM_000267.3	506	cTc/cGc	13/57	1	2	FACETS	0.266	0.199	0.347	0.266	0.199	0.347	SUBCLONAL	1	TRUE	1	0.500695792991733	2		203	255	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	238	600	0	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.500695792991733	2		600	922	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63531841	63531841	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	133	388	0	ENST00000307078.5:c.2142-2A>G		p.X714_splice	ENST00000307078	NM_004655.3	714			1	2	FACETS	0.795	0.724	0.87	0.795	0.724	0.87	SUBCLONAL	1	TRUE	1	0.500695792991733	2		388	668	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899179	78899179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760865448	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	106	369	0	ENST00000306801.3:c.2818G>A	p.Asp940Asn	p.D940N	ENST00000306801	NM_020761.2	940	Gac/Aac	24/34	1	2	FACETS	0.731	0.657	0.809	0.731	0.657	0.809	SUBCLONAL	1	TRUE	1	0.500695792991733	2		369	579	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78934001	78934001	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	181	484	0	ENST00000306801.3:c.3601G>A	p.Glu1201Lys	p.E1201K	ENST00000306801	NM_020761.2	1201	Gaa/Aaa	30/34	1	2	FACETS	0.992	0.917	1	0.992	0.917	1	CLONAL	1	TRUE	1	0.500695792991733	2		484	729	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	171	531	2	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	0.767	0.706	0.831	0.767	0.706	0.831	SUBCLONAL	1	TRUE	1	0.500695792991733	2		533	890	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276289	15276289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755817475	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	224	614	0	ENST00000263388.2:c.5705G>A	p.Arg1902His	p.R1902H	ENST00000263388	NM_000435.2	1902	cGc/cAc	31/33	1	2	FACETS	0.963	0.898	1	0.963	0.898	1	CLONAL	1	TRUE	1	0.500695792991733	2		614	929	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273010	18273010	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	59	469	0	ENST00000222254.8:c.902-2A>G		p.X301_splice	ENST00000222254	NM_005027.3	301			1	2	FACETS	0.252	0.216	0.292	0.252	0.216	0.292	SUBCLONAL	1	TRUE	1	0.500695792991733	2		469	935	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221698	36221698	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	195	642	0	ENST00000222270.7:c.5367G>T	p.Arg1789Ser	p.R1789S	ENST00000222270	NM_014727.1	1789	agG/agT	26/37	1	2	FACETS	0.737	0.681	0.795	0.737	0.681	0.795	SUBCLONAL	1	TRUE	1	0.500695792991733	2		642	1057	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762509	41762509	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	40	300	0	ENST00000301178.4:c.2189G>A	p.Ser730Asn	p.S730N	ENST00000301178	NM_021913.4	730	aGc/aAc	18/20	1	2	FACETS	0.289	0.239	0.344	0.289	0.239	0.344	SUBCLONAL	1	TRUE	1	0.500695792991733	2		300	553	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793480	42793480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs565187692	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	50	547	0	ENST00000575354.2:c.1282C>T	p.Arg428Cys	p.R428C	ENST00000575354	NM_015125.3	428	Cgt/Tgt	8/20	1	2	FACETS	0.218	0.184	0.255	0.218	0.184	0.255	SUBCLONAL	1	TRUE	1	0.500695792991733	2		547	917	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795712	42795715	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CAGT	CAGT	-	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	273	637	0	ENST00000575354.2:c.2705_2708del	p.Ser902PhefsTer21	p.S902Ffs*21	ENST00000575354	NM_015125.3	901	CAGTca/ca	11/20	1	2	FACETS	0.967	0.907	1	0.967	0.907	1	CLONAL	1	TRUE	1	0.500695792991733	2		637	1128	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902258	50902263	+	inframe_deletion	In_Frame_Del	DEL	GCAGGA	GCAGGA	-	rs760207160	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	106	632	0	ENST00000440232.2:c.157_162del	p.Gln53_Glu54del	p.Q53_E54del	ENST00000440232	NM_002691.3	50	ctGCAGGAg/ctg	2/27	1	2	FACETS	0.416	0.372	0.463	0.416	0.372	0.463	SUBCLONAL	1	TRUE	1	0.500695792991733	2		632	1018	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910268	50910268	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	144	528	0	ENST00000440232.2:c.1523T>C	p.Leu508Pro	p.L508P	ENST00000440232	NM_002691.3	508	cTg/cCg	13/27	1	2	FACETS	0.67	0.611	0.732	0.67	0.611	0.732	SUBCLONAL	1	TRUE	1	0.500695792991733	2		528	858	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738224	190738224	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	36	109	0	ENST00000441310.2:c.2476G>A	p.Val826Ile	p.V826I	ENST00000441310	NM_000534.4	826	Gtt/Att	12/13	1	2	FACETS	0.904	0.754	1	0.904	0.754	1	CLONAL	1	TRUE	1	0.500695792991733	2		109	159	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713861	30713861	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	216	481	0	ENST00000295754.5:c.1186T>C	p.Cys396Arg	p.C396R	ENST00000295754	NM_003242.5	396	Tgt/Cgt	4/7	0.478798725309606	2	FACETS	0.972	0.904	1	0.486	0.452	0.521	CLONAL	1	TRUE	0	0.500695792991733	2		481	888	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182341	38182341	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	70	324	0	ENST00000396334.3:c.775+2T>C		p.X259_splice	ENST00000396334	NM_002468.4	259			0.478798725309606	2	FACETS	0.487	0.425	0.554	0.244	0.212	0.277	SUBCLONAL	1	TRUE	0	0.500695792991733	2		324	574	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987137	69987137	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	146	430	0	ENST00000394351.3:c.201del	p.Ser68AlafsTer38	p.S68Afs*38	ENST00000394351	NM_000248.3	66	ccG/cc	2/9	1	2	FACETS	0.933	0.855	1	0.933	0.855	1	CLONAL	1	TRUE	1	0.500695792991733	2		430	625	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509085	66509085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	54	226	0	ENST00000273854.3:c.242del	p.Asn81MetfsTer24	p.N81Mfs*24	ENST00000273854	NM_004439.5	81	aAt/at	2/18	1	2	FACETS	0.833	0.718	0.956	0.833	0.718	0.956	CLONAL	1	TRUE	1	0.500695792991733	2		226	259	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156652	106156652	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	26	266	1	ENST00000380013.4:c.1557del	p.Phe519LeufsTer14	p.F519Lfs*14	ENST00000380013	NM_001127208.2	518	aTt/at	3/11	1	2	FACETS	0.25	0.198	0.311	0.25	0.198	0.311	SUBCLONAL	1	TRUE	1	0.500695792991733	2		267	415	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247373	153247373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	77	200	0	ENST00000281708.4:c.1429G>A	p.Gly477Ser	p.G477S	ENST00000281708	NM_033632.3	477	Ggt/Agt	10/12	1	2	FACETS	0.935	0.828	1	0.935	0.828	1	CLONAL	1	TRUE	1	0.500695792991733	2		200	329	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541228	187541228	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753722602	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	68	302	0	ENST00000441802.2:c.6512C>T	p.Pro2171Leu	p.P2171L	ENST00000441802	NM_005245.3	2171	cCg/cTg	10/27	1	2	FACETS	0.551	0.48	0.627	0.551	0.48	0.627	SUBCLONAL	1	TRUE	1	0.500695792991733	2		302	493	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630629	187630629	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	171	432	1	ENST00000441802.2:c.353T>A	p.Leu118Ter	p.L118*	ENST00000441802	NM_005245.3	118	tTg/tAg	2/27	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.500695792991733	2		433	614	SUCCESS
APC	324	MSKCC	GRCh37	5	112116499	112116499	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1256814873	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	38	197	0	ENST00000257430.4:c.544A>G	p.Thr182Ala	p.T182A	ENST00000257430	NM_000038.5	182	Aca/Gca	6/16	1	2	FACETS	0.696	0.581	0.823	0.696	0.581	0.823	SUBCLONAL	1	TRUE	1	0.500695792991733	2		197	218	SUCCESS
APC	324	MSKCC	GRCh37	5	112170780	112170783	+	frameshift_variant	Frame_Shift_Del	DEL	ACAA	ACAA	-	rs1060503360	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	136	509	0	ENST00000257430.4:c.1879_1882del	p.Asn627LeufsTer2	p.N627Lfs*2	ENST00000257430	NM_000038.5	626	ACAAac/ac	15/16	1	2	FACETS	0.785	0.715	0.858	0.785	0.715	0.858	SUBCLONAL	1	TRUE	1	0.500695792991733	2		509	692	SUCCESS
APC	324	MSKCC	GRCh37	5	112173785	112173785	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	75	257	0	ENST00000257430.4:c.2496del	p.Ser833AlafsTer9	p.S833Afs*9	ENST00000257430	NM_000038.5	832	Ccc/cc	16/16	1	2	FACETS	0.784	0.691	0.883	0.784	0.691	0.883	SUBCLONAL	1	TRUE	1	0.500695792991733	2		257	382	SUCCESS
APC	324	MSKCC	GRCh37	5	112178262	112178262	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	70	289	0	ENST00000257430.4:c.6971C>T	p.Pro2324Leu	p.P2324L	ENST00000257430	NM_000038.5	2324	cCt/cTt	16/16	1	2	FACETS	0.612	0.535	0.694	0.612	0.535	0.694	SUBCLONAL	1	TRUE	1	0.500695792991733	2		289	457	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449859	149449859	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	196	616	0	ENST00000286301.3:c.1205del	p.Pro402GlnfsTer3	p.P402Qfs*3	ENST00000286301	NM_005211.3	402	cCa/ca	9/22	1	2	FACETS	0.918	0.851	0.987	0.918	0.851	0.987	CLONAL	1	TRUE	1	0.500695792991733	2		616	853	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679442	30679442	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	125	394	0	ENST00000376406.3:c.2128+2T>C		p.X710_splice	ENST00000376406	NM_014641.2	710			1	2	FACETS	0.693	0.628	0.762	0.693	0.628	0.762	SUBCLONAL	1	TRUE	1	0.500695792991733	2		394	720	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798511	32798511	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs765335850	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	58	549	0	ENST00000374899.4:c.1345C>T	p.Arg449Ter	p.R449*	ENST00000374899	NM_018833.2	449	Cga/Tga	8/12	1	2	FACETS	0.258	0.221	0.299	0.258	0.221	0.299	SUBCLONAL	1	TRUE	1	0.500695792991733	2		549	897	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805789	32805790	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	61	595	0	ENST00000374899.4:c.221_222insA	p.Leu75ProfsTer92	p.L75Pfs*92	ENST00000374899	NM_018833.2	74	ccc/ccAc	2/12	1	2	FACETS	0.241	0.207	0.278	0.241	0.207	0.278	SUBCLONAL	1	TRUE	1	0.500695792991733	2		595	1011	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609768	117609768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	107	439	0	ENST00000368508.3:c.6931G>A	p.Ala2311Thr	p.A2311T	ENST00000368508	NM_002944.2	2311	Gca/Aca	43/43	1	2	FACETS	0.723	0.65	0.8	0.723	0.65	0.8	SUBCLONAL	1	TRUE	1	0.500695792991733	2		439	591	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199687	138199687	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1035582992	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	116	425	2	ENST00000237289.4:c.1105G>A	p.Ala369Thr	p.A369T	ENST00000237289	NM_001270507.1	369	Gcc/Acc	7/9	1	2	FACETS	0.68	0.614	0.75	0.68	0.614	0.75	SUBCLONAL	1	TRUE	1	0.500695792991733	2		427	681	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450357	50450357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	175	475	0	ENST00000331340.3:c.541G>A	p.Ala181Thr	p.A181T	ENST00000331340	NM_006060.4	181	Gcc/Acc	5/8	1	2	FACETS	0.946	0.873	1	0.946	0.873	1	CLONAL	1	TRUE	1	0.500695792991733	2		475	739	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468270	50468270	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	124	573	1	ENST00000331340.3:c.1505G>T	p.Arg502Leu	p.R502L	ENST00000331340	NM_006060.4	502	cGg/cTg	8/8	1	2	FACETS	0.686	0.621	0.754	0.686	0.621	0.754	SUBCLONAL	1	TRUE	1	0.500695792991733	2		574	722	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233037	55233037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1477025000	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	195	409	0	ENST00000275493.2:c.1787C>T	p.Pro596Leu	p.P596L	ENST00000275493	NM_005228.3	596	cCg/cTg	15/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.500695792991733	2		409	704	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345759	152345760	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs730882049	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	48	180	0	ENST00000359321.1:c.810dup	p.Ile271TyrfsTer8	p.I271Yfs*8	ENST00000359321	NM_005431.1	270	-/T	3/3	1	2	FACETS	0.639	0.543	0.743	0.639	0.543	0.743	SUBCLONAL	1	TRUE	1	0.500695792991733	2		180	300	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152357857	152357857	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759291002	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	82	278	4	ENST00000359321.1:c.50G>A	p.Arg17Gln	p.R17Q	ENST00000359321	NM_005431.1	17	cGa/cAa	2/3	1	2	FACETS	0.736	0.652	0.826	0.736	0.652	0.826	SUBCLONAL	1	TRUE	1	0.500695792991733	2		282	445	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900210	101900210	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	124	265	0	ENST00000374994.4:c.644G>C	p.Arg215Pro	p.R215P	ENST00000374994	NM_004612.2	215	cGa/cCa	4/9	1	2	FACETS	0.907	0.824	0.994	0.907	0.824	0.994	CLONAL	1	TRUE	1	0.500695792991733	2		265	546	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354253	70354253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1436223575	NA	P-0047886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	164	292	1	ENST00000374080.3:c.4664C>T	p.Thr1555Met	p.T1555M	ENST00000374080		1555	aCg/aTg	34/45	1	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.500695792991733	1		293	459	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0047887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	20	432	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.786	1	1	0.786	1	CLONAL	1	TRUE	1	0.11	2		432	353	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161674	56161674	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	23	316	0	ENST00000399503.3:c.1173del	p.Lys391AsnfsTer45	p.K391Nfs*45	ENST00000399503	NM_005921.1	391	Aaa/aa	6/20	1	2	FACETS	0.909	0.707	1	0.909	0.707	1	CLONAL	1	TRUE	1	0.11	2		316	460	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189432	56189432	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0047887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	28	394	0	ENST00000399503.3:c.4464T>A	p.Cys1488Ter	p.C1488*	ENST00000399503	NM_005921.1	1488	tgT/tgA	20/20	1	2	FACETS	0.917	0.731	1	0.917	0.731	1	CLONAL	1	TRUE	1	0.11	2		394	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0047889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	110	621	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.15959061934265	2		621	944	SUCCESS
AR	367	MSKCC	GRCh37	X	66941796	66941796	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	37	215	0	ENST00000374690.3:c.2440T>G	p.Phe814Val	p.F814V	ENST00000374690	NM_000044.3	814	Ttc/Gtc	6/8	1	1	FACETS	0.77	0.638	0.916	1	0.954	1	CLONAL	2	TRUE	0	0.15959061934265	1		215	277	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032541	12032541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267604739	NA	P-0047889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	51	269	0	ENST00000353533.5:c.977C>T	p.Pro326Leu	p.P326L	ENST00000353533	NM_003010.3	326	cCg/cTg	9/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.15959061934265	2		269	479	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144027	11144027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770680174	NA	P-0047889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	62	456	0	ENST00000358026.2:c.3608G>A	p.Arg1203His	p.R1203H	ENST00000358026	NM_001128849.1	1203	cGc/cAc	26/36	0.15959061934265	1	FACETS	0.897	0.773	1	0.897	0.773	1	CLONAL	1	TRUE	0	0.15959061934265	1		456	797	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115069	3115069	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	60	428	0	ENST00000078429.4:c.604C>T	p.Arg202Trp	p.R202W	ENST00000078429	NM_002067.2	202	Cgg/Tgg	4/7	0.15959061934265	1	FACETS	0.926	0.797	1	0.926	0.797	1	CLONAL	1	TRUE	0	0.15959061934265	1		428	747	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930087	68930087	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	46	247	0	ENST00000288368.4:c.148T>G	p.Leu50Val	p.L50V	ENST00000288368	NM_024870.2	50	Tta/Gta	2/40	0.15959061934265	1	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	0	0.15959061934265	1		247	485	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883114	37883114	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749454186	NA	P-0047889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	87	552	0	ENST00000269571.5:c.3017G>A	p.Arg1006His	p.R1006H	ENST00000269571		1006	cGc/cAc	25/27	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.15959061934265	2		552	798	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396543	30396543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	77	293	0	ENST00000331968.5:c.176G>A	p.Arg59His	p.R59H	ENST00000331968	NM_002742.2	59	cGt/cAt	1/18	0.15959061934265	2	FACETS	0.844	0.741	0.953	0.844	0.741	0.953	CLONAL	2	TRUE	0	0.15959061934265	2		293	572	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566706	212566706	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	57	223	0	ENST00000342788.4:c.1475A>T	p.Lys492Ile	p.K492I	ENST00000342788	NM_005235.2	492	aAa/aTa	12/28	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.15959061934265	2		223	491	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058490	69058490	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047889-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	64	388	0	ENST00000288368.4:c.4134A>C	p.Lys1378Asn	p.K1378N	ENST00000288368	NM_024870.2	1378	aaA/aaC	34/40	0.15959061934265	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.15959061934265	1		388	544	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0047890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	690	703	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.89	0.868	0.913	1	0.998	1	CLONAL	2	TRUE	1	0.785176300035752	2		703	987	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0047890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	225	383	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.785176300035752	2		383	521	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741756	17741756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	302	319	1	ENST00000250003.3:c.427C>T	p.Arg143Trp	p.R143W	ENST00000250003	NM_002478.4	143	Cgg/Tgg	1/3	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.785176300035752	2		320	763	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161317	55161317	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	234	256	0	ENST00000257290.5:c.3148A>G	p.Ile1050Val	p.I1050V	ENST00000257290	NM_006206.4	1050	Att/Gtt	23/23	1	2	FACETS	0.945	0.887	1	0.945	0.887	1	CLONAL	1	TRUE	1	0.785176300035752	2		256	631	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115871	8115872	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0047891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	223	425	0	ENST00000346208.3:c.1219_1220del	p.Ser407AlafsTer99	p.S407Afs*99	ENST00000346208		406	aTC/a	6/6	0.533461694800931	3	FACETS	1	0.992	1	0.709	0.664	0.754	CLONAL	1	TRUE	1	0.671356321404453	3		425	626	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589696	69589696	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	97	136	1	ENST00000168712.1:c.157C>A	p.Leu53Ile	p.L53I	ENST00000168712	NM_002007.2	53	Ctc/Atc	1/3	0.253157939089324	5	FACETS	0.986	0.902	1	0.986	0.902	1	INDETERMINATE	3	TRUE	2	0.671356321404453	5		137	196	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774150	66774150	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	65	727	0	ENST00000307102.5:c.626T>G	p.Phe209Cys	p.F209C	ENST00000307102	NM_002755.3	209	tTt/tGt	6/11	0.447286330573576	4	FACETS	0.327	0.282	0.375			1	SUBCLONAL	1	TRUE	NA	0.671356321404453	4		727	991	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032550	12032551	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	159	310	0	ENST00000353533.5:c.987dup	p.Asn330Ter	p.N330*	ENST00000353533	NM_003010.3	329	agt/agTt	9/11	0.671356321404453	2	FACETS	0.995	0.94	1	0.995	0.94	1	CLONAL	2	TRUE	0	0.671356321404453	2		310	238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578541	7578541	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1131691013	NA	P-0047892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	200	639	0	ENST00000269305.4:c.389T>C	p.Leu130Pro	p.L130P	ENST00000269305	NM_001126112.2	130	cTc/cCc	5/11	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.501421336175942	2		639	789	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs587781702	NA	P-0047892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	161	442	1	ENST00000269305.4:c.920-1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			1	2	FACETS	0.966	0.889	1	0.966	0.889	1	CLONAL	1	TRUE	1	0.501421336175942	2		443	665	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970900	21970900	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0047892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	173	512	0	ENST00000304494.5:c.457+1G>A		p.X153_splice	ENST00000304494	NM_000077.4	153			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.501421336175942	2		512	671	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566854	212566854	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	61	204	0	ENST00000342788.4:c.1327A>G	p.Thr443Ala	p.T443A	ENST00000342788	NM_005235.2	443	Acc/Gcc	12/28	0.455998833316791	4	FACETS	0.937	0.811	1	0.468	0.405	0.536	CLONAL	1	TRUE	2	0.501421336175942	4		204	390	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205174	128205175	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	177	525	0	ENST00000341105.2:c.266dup	p.Leu89PhefsTer96	p.L89Ffs*96	ENST00000341105	NM_032638.4	89	ttg/ttTg	3/6	0.501421336175942	3	FACETS	0.991	0.914	1	0.496	0.457	0.536	CLONAL	1	TRUE	1	0.501421336175942	3		525	891	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0047893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	28	253	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	NA	2	FACETS	0.595	0.477	0.728			1	INDETERMINATE	1	TRUE	NA	0.369012036902308	2		253	255	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577520	7577520	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1330865474	NA	P-0047893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	285	541	0	ENST00000269305.4:c.761T>G	p.Ile254Ser	p.I254S	ENST00000269305	NM_001126112.2	254	aTc/aGc	7/11	0.221180566755354	4	FACETS	1	0.99	1	0.615	0.58	0.651	INDETERMINATE	2	TRUE	0	0.369012036902308	4		541	860	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247516	123247516	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519795	NA	P-0047893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	132	404	0	ENST00000358487.5:c.1975A>G	p.Lys659Glu	p.K659E	ENST00000358487	NM_000141.4	659	Aag/Gag	14/18	0.200811139873091	3	FACETS	0.768	0.7	0.838	0.512	0.466	0.559	INDETERMINATE	2	TRUE	0	0.369012036902308	3		404	552	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244097	153244097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	190	393	0	ENST00000281708.4:c.2060G>A	p.Gly687Glu	p.G687E	ENST00000281708	NM_033632.3	687	gGg/gAg	12/12	0.200811139873091	3	FACETS	1	0.931	1	0.668	0.62	0.716	INDETERMINATE	2	TRUE	0	0.369012036902308	3		393	609	SUCCESS
APC	324	MSKCC	GRCh37	5	112175617	112175617	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	35	246	0	ENST00000257430.4:c.4326del	p.Pro1443LeufsTer30	p.P1443Lfs*30	ENST00000257430	NM_000038.5	1442	ccT/cc	16/16	NA	2	FACETS	0.577	0.474	0.692			1	INDETERMINATE	1	TRUE	NA	0.369012036902308	2		246	329	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933540	36933540	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	102	595	0	ENST00000361632.4:c.1747C>G	p.Arg583Gly	p.R583G	ENST00000361632		583	Cgt/Ggt	13/16	0.219184639243243	5	FACETS	0.679	0.605	0.758	0.226	0.201	0.253	INDETERMINATE	1	TRUE	2	0.369012036902308	5		595	1265	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247569	123247569	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519047	NA	P-0047893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	133	435	0	ENST00000358487.5:c.1922A>G	p.Lys641Arg	p.K641R	ENST00000358487	NM_000141.4	641	aAa/aGa	14/18	0.200811139873091	3	FACETS	1	0.979	1	0.419	0.381	0.459	INDETERMINATE	1	TRUE	0	0.369012036902308	3		435	679	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549094	21549094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1336721510	NA	P-0047893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	53	347	1	ENST00000382592.4:c.3182C>T	p.Ala1061Val	p.A1061V	ENST00000382592	NM_014572.2	1061	gCa/gTa	8/8	0.369012036902308	5	FACETS	0.565	0.48	0.658	0.188	0.16	0.22	SUBCLONAL	1	TRUE	2	0.369012036902308	5		348	790	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250698	26250698	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	67	493	0	ENST00000446824.2:c.136A>G	p.Thr46Ala	p.T46A	ENST00000446824	NM_021018.2	46	Act/Gct	1/1	0.369012036902308	4	FACETS	0.523	0.453	0.599	0.262	0.226	0.3	SUBCLONAL	1	TRUE	2	0.369012036902308	4		493	950	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400089	139400089	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	109	697	0	ENST00000277541.6:c.4259T>C	p.Phe1420Ser	p.F1420S	ENST00000277541	NM_017617.3	1420	tTc/tCc	25/34	0.369012036902308	3	FACETS	0.567	0.507	0.63	0.283	0.253	0.315	SUBCLONAL	1	TRUE	1	0.369012036902308	3		697	1235	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0047894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	116	566	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.170693492365243	2	FACETS	1	0.984	1	0.718	0.652	0.788	INDETERMINATE	1	TRUE	0	0.358914927117957	2		566	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577518	7577518	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519995	NA	P-0047894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	125	397	1	ENST00000269305.4:c.763A>T	p.Ile255Phe	p.I255F	ENST00000269305	NM_001126112.2	255	Atc/Ttc	7/11	0.358914927117957	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.358914927117957	1		398	535	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578136	226578136	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	86	338	0	ENST00000366794.5:c.592C>T	p.Gln198Ter	p.Q198*	ENST00000366794	NM_001618.3	198	Cag/Tag	4/23	1	2	FACETS	0.922	0.818	1	0.922	0.818	1	CLONAL	1	TRUE	1	0.358914927117957	2		338	520	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207084	1207084	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	124	545	0	ENST00000326873.7:c.172G>C	p.Gly58Arg	p.G58R	ENST00000326873	NM_000455.4	58	Ggc/Cgc	1/10	0.210142776060305	1	FACETS	0.933	0.846	1	0.933	0.846	1	INDETERMINATE	1	TRUE	0	0.358914927117957	1		545	608	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214386	36214386	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	92	411	0	ENST00000222270.7:c.3040G>T	p.Glu1014Ter	p.E1014*	ENST00000222270	NM_014727.1	1014	Gaa/Taa	7/37	0.358914927117957	7	FACETS	0.786	0.696	0.882	0.131	0.116	0.147	SUBCLONAL	1	TRUE	1	0.358914927117957	7		411	1238	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039165	49039202	+	frameshift_variant	Frame_Shift_Del	DEL	AGTATGATTCTATTATAGTATTCTATAACTCGGTCTTC	AGTATGATTCTATTATAGTATTCTATAACTCGGTCTTC	CGTATG	novel	NA	P-0047894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	41	239	0	ENST00000267163.4:c.2243_2280delinsCGTATG	p.Glu748AlafsTer36	p.E748Afs*36	ENST00000267163	NM_000321.2	748	gAGTATGATTCTATTATAGTATTCTATAACTCGGTCTTC/gCGTATG	22/27	0.358914927117957	1	FACETS	0.815	0.685	0.957	0.815	0.685	0.957	CLONAL	1	TRUE	0	0.358914927117957	1		239	230	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111505	8111506	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATGCCAATGGGGACCCTGTCTGCAATGCCTGTGGGCTCTACTACAAGCTTCACAATGT	novel	NA	P-0047895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	86	550	0	ENST00000346208.3:c.993_1047+3dup		p.N331fs	ENST00000346208		331	aat/aATGCCAATGGGGACCCTGTCTGCAATGCCTGTGGGCTCTACTACAAGCTTCACAATGTat	5/6	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		550	916	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0047896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	10	328	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.45603719344332	4	FACETS	0.918	0.635	1	0.459	0.317	0.63	CLONAL	1	FALSE	2	0.555283797634097	4		328	61	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896543	78896543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762927626	NA	P-0047896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2108	263	591	0	ENST00000306801.3:c.2540C>T	p.Pro847Leu	p.P847L	ENST00000306801	NM_020761.2	847	cCg/cTg	22/34	0.45603719344332	4	FACETS	0.621	0.579	0.665	0.311	0.289	0.333	SUBCLONAL	1	FALSE	2	0.555283797634097	4		591	2371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577028	7577053	+	frameshift_variant	Frame_Shift_Del	DEL	TGCTCCCTGGGGGCAGCTCGTGGTGA	TGCTCCCTGGGGGCAGCTCGTGGTGA	-	novel	NA	P-0047896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	26	561	0	ENST00000269305.4:c.885_910del	p.His296Ter	p.H296*	ENST00000269305	NM_001126112.2	295	ccTCACCACGAGCTGCCCCCAGGGAGCAct/ccct	8/11	0.399639101693636	4	FACETS	1	0.866	1	0.552	0.443	0.672	CLONAL	1	FALSE	2	0.555283797634097	4		561	132	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	128	432	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.982	1	1	0.992	1	CLONAL	2	TRUE	1	0.35	2		432	293	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856520	45856520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751318902	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	295	670	0	ENST00000391945.4:c.1738G>A	p.Ala580Thr	p.A580T	ENST00000391945	NM_000400.3	580	Gcc/Acc	18/23	1	2	FACETS	1	0.985	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		670	761	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522598	157522598	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554236040	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	212	514	0	ENST00000346085.5:c.4870C>T	p.Arg1624Ter	p.R1624*	ENST00000346085	NM_020732.3	1624	Cga/Tga	18/20	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	1	0.35	2		514	498	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672759	86672759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	19	298	0	ENST00000274376.6:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000274376	NM_002890.2	749	cGa/cAa	17/25	1	2	FACETS	0.434	0.33	0.557	0.434	0.33	0.557	SUBCLONAL	1	TRUE	1	0.35	2		298	250	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040978	42040978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755286142	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	162	622	0	ENST00000219905.7:c.5356C>T	p.Arg1786Trp	p.R1786W	ENST00000219905	NM_001164273.1	1786	Cgg/Tgg	16/24	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.35	2		622	770	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803500	32803500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550712305	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	381	732	1	ENST00000374899.4:c.659G>A	p.Arg220Gln	p.R220Q	ENST00000374899	NM_018833.2	220	cGa/cAa	4/12	0.273655677041051	4	FACETS	0.952	0.906	0.998	1	0.995	1	CLONAL	3	TRUE	2	0.35	4		733	1029	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439518	220439518	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540215120	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	310	779	0	ENST00000243786.2:c.371G>A	p.Arg124His	p.R124H	ENST00000243786	NM_002191.3	124	cGc/cAc	2/2	1	2	FACETS	0.885	0.842	0.929	1	0.997	1	CLONAL	3	TRUE	1	0.35	2		779	667	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572534	95572534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555370340	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	73	286	0	ENST00000393063.1:c.2831G>A	p.Arg944Gln	p.R944Q	ENST00000393063	NM_030621.3	944	cGa/cAa	19/28	1	2	FACETS	0.869	0.781	0.958	1	0.987	1	CLONAL	3	TRUE	1	0.35	2		286	160	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923392	9923392	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057520116	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	150	558	0	ENST00000330684.3:c.1895C>T	p.Ser632Phe	p.S632F	ENST00000330684	NM_001134407.1	632	tCt/tTt	9/13	0.121266034753738	0	FACETS	0.69	0.637	0.743			1	INDETERMINATE	2	TRUE	0	0.35	0		558	404	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	98	321	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.918	0.829	1	1	0.987	1	CLONAL	2	TRUE	1	0.35	2		321	305	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225338988	225338988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759758641	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	98	335	0	ENST00000264414.4:c.2281C>T	p.Arg761Cys	p.R761C	ENST00000264414	NM_003590.4	761	Cgc/Tgc	16/16	1	2	FACETS	1	0.973	1	1	0.99	1	CLONAL	2	TRUE	1	0.35	2		335	234	SUCCESS
APC	324	MSKCC	GRCh37	5	112178000	112178000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768922431	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	104	374	0	ENST00000257430.4:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000257430	NM_000038.5	2237	Cga/Tga	16/16	1	2	FACETS	1	0.961	1	1	0.99	1	CLONAL	2	TRUE	1	0.35	2		374	269	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508955	106508955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759136884	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	183	485	0	ENST00000359195.3:c.949G>A	p.Glu317Lys	p.E317K	ENST00000359195	NM_002649.2	317	Gag/Aag	2/11	1	2	FACETS	1	0.966	1	1	0.994	1	CLONAL	2	TRUE	1	0.35	2		485	493	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	170	500	0	ENST00000320574.5:c.1231G>C	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ctg	13/49	1	2	FACETS	1	0.978	1	1	0.993	1	CLONAL	2	TRUE	1	0.35	2		500	432	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800902	120800903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748469666	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	324	644	2	ENST00000257552.2:c.345dup	p.Leu116AlafsTer15	p.L116Afs*15	ENST00000257552	NM_002442.3	115	-/G	6/15	1	2	FACETS	0.996	0.944	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		646	929	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723034	49723034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771296103	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	46	377	0	ENST00000449682.2:c.1382G>A	p.Arg461His	p.R461H	ENST00000449682	NM_020998.3	461	cGc/cAc	11/18	1	2	FACETS	0.672	0.567	0.788	0.672	0.567	0.788	SUBCLONAL	1	TRUE	1	0.35	2		377	391	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	110	350	10	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	0.121266034753738	0	FACETS	0.672	0.612	0.733			1	INDETERMINATE	2	TRUE	0	0.35	0		360	304	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522532	67522532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767837787	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	52	181	0	ENST00000274335.5:c.29C>T	p.Ala10Val	p.A10V	ENST00000274335		10	gCg/gTg	1/15	1	2	FACETS	0.959	0.834	1	1	0.977	1	CLONAL	2	TRUE	1	0.35	2		181	155	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074255	8074255	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	215	441	0	ENST00000377482.5:c.404del	p.Asn135ThrfsTer40	p.N135Tfs*40	ENST00000377482	NM_018948.3	135	aAc/ac	4/4	0.3	1	FACETS	0.986	0.925	1	1	0.994	1	CLONAL	2	TRUE	0	0.35	1		441	514	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298590	11298590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs913197212	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	57	710	1	ENST00000361445.4:c.1871G>A	p.Arg624His	p.R624H	ENST00000361445	NM_004958.3	624	cGc/cAc	12/58	0.3	1	FACETS	0.366	0.313	0.424	0.366	0.313	0.424	SUBCLONAL	1	TRUE	0	0.35	1		711	734	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319445	11319445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748801456	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	329	681	0	ENST00000361445.4:c.22G>A	p.Ala8Thr	p.A8T	ENST00000361445	NM_004958.3	8	Gcc/Acc	2/58	0.3	1	FACETS	0.923	0.876	0.971	1	0.996	1	CLONAL	2	TRUE	0	0.35	1		681	840	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199321	16199321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	143	321	0	ENST00000375759.3:c.94G>A	p.Val32Met	p.V32M	ENST00000375759	NM_015001.2	32	Gtg/Atg	2/15	0.3	1	FACETS	1	0.983	1	1	0.994	1	CLONAL	3	TRUE	0	0.35	1		321	202	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262067	16262067	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	172	420	0	ENST00000375759.3:c.9332G>A	p.Ser3111Asn	p.S3111N	ENST00000375759	NM_015001.2	3111	aGc/aAc	11/15	0.3	3	FACETS	0.897	0.835	0.961			1	CLONAL	3	TRUE	NA	0.35	3		420	429	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265794	16265794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	277	544	0	ENST00000375759.3:c.10867G>A	p.Ala3623Thr	p.A3623T	ENST00000375759	NM_015001.2	3623	Gcc/Acc	15/15	0.3	3	FACETS	0.888	0.839	0.938			1	CLONAL	3	TRUE	NA	0.35	3		544	698	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088655	27088655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	79	633	0	ENST00000324856.7:c.2264G>A	p.Arg755Lys	p.R755K	ENST00000324856	NM_006015.4	755	aGg/aAg	7/20	0.3	3	FACETS	0.703	0.618	0.795			1	SUBCLONAL	1	TRUE	NA	0.35	3		633	754	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101051	27101051	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471914196	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	325	690	0	ENST00000324856.7:c.4333C>T	p.Arg1445Cys	p.R1445C	ENST00000324856	NM_006015.4	1445	Cgc/Tgc	18/20	0.3	3	FACETS	0.917	0.871	0.964			1	CLONAL	3	TRUE	NA	0.35	3		690	793	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	283	550	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	0.3	3	FACETS	0.897	0.848	0.947			1	CLONAL	3	TRUE	NA	0.35	3		550	706	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807564	36807564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202225847	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	189	637	1	ENST00000373129.3:c.1100C>T	p.Thr367Met	p.T367M	ENST00000373129	NM_032017.1	367	aCg/aTg	12/12	1	2	FACETS	1	0.98	1	1	0.994	1	CLONAL	2	TRUE	1	0.35	2		638	478	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804972	43804972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	188	464	0	ENST00000372470.3:c.422C>T	p.Ala141Val	p.A141V	ENST00000372470	NM_005373.2	141	gCc/gTc	4/12	1	2	FACETS	1	0.985	1	1	0.994	1	CLONAL	2	TRUE	1	0.35	2		464	451	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797139	45797139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150792276	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	312	895	0	ENST00000450313.1:c.1276C>T	p.Arg426Cys	p.R426C	ENST00000450313	NM_012222.2	426	Cgt/Tgt	13/16	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		895	771	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798990	45798990	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	278	773	0	ENST00000450313.1:c.355G>T	p.Asp119Tyr	p.D119Y	ENST00000450313	NM_012222.2	119	Gat/Tat	4/16	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		773	661	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739824	46739824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764040025	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	27	384	0	ENST00000371975.4:c.1625G>A	p.Arg542His	p.R542H	ENST00000371975	NM_003579.3	542	cGc/cAc	15/18	1	2	FACETS	0.339	0.269	0.419	0.339	0.269	0.419	SUBCLONAL	1	TRUE	1	0.35	2		384	455	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436066	51436066	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	78	386	0	ENST00000262662.1:c.26T>C	p.Leu9Ser	p.L9S	ENST00000262662		9	tTg/tCg	3/4	1	2	FACETS	0.897	0.79	1	0.897	0.79	1	CLONAL	1	TRUE	1	0.35	2		386	497	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301168	65301168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	112	262	0	ENST00000342505.4:c.3280C>T	p.Pro1094Ser	p.P1094S	ENST00000342505	NM_002227.2	1094	Cca/Tca	24/25	1	2	FACETS	0.843	0.773	0.914	1	0.991	1	CLONAL	3	TRUE	1	0.35	2		262	253	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307173	65307173	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs181919006	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	20	407	0	ENST00000342505.4:c.2515C>T	p.Arg839Ter	p.R839*	ENST00000342505	NM_002227.2	839	Cga/Tga	18/25	1	2	FACETS	0.307	0.234	0.393	0.307	0.234	0.393	SUBCLONAL	1	TRUE	1	0.35	2		407	372	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325811	65325811	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	167	470	0	ENST00000342505.4:c.1311G>T	p.Gln437His	p.Q437H	ENST00000342505	NM_002227.2	437	caG/caT	9/25	1	2	FACETS	1	0.933	1	1	0.993	1	CLONAL	2	TRUE	1	0.35	2		470	474	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414925	78414925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	166	476	0	ENST00000370768.2:c.1841C>T	p.Ala614Val	p.A614V	ENST00000370768	NM_003902.3	614	gCc/gTc	19/20	1	2	FACETS	1	0.97	1	1	0.993	1	CLONAL	2	TRUE	1	0.35	2		476	438	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273208	115273208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	108	439	0	ENST00000438362.2:c.1250G>A	p.Arg417His	p.R417H	ENST00000438362	NM_001242891.1	417	cGt/cAt	11/20	1	2	FACETS	0.986	0.896	1	1	0.989	1	CLONAL	2	TRUE	1	0.35	2		439	313	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166403	118166403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1391512260	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	122	349	0	ENST00000369448.3:c.913G>A	p.Asp305Asn	p.D305N	ENST00000369448	NM_017709.3	305	Gac/Aac	2/2	1	2	FACETS	1	0.973	1	1	0.991	1	CLONAL	2	TRUE	1	0.35	2		349	305	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458579	120458579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147522485	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	222	601	1	ENST00000256646.2:c.6766C>T	p.Arg2256Cys	p.R2256C	ENST00000256646	NM_024408.3	2256	Cgc/Tgc	34/34	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.35	2		602	544	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497807	120497807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782026650	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	98	532	0	ENST00000256646.2:c.2075G>A	p.Arg692His	p.R692H	ENST00000256646	NM_024408.3	692	cGc/cAc	13/34	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.35	2		532	537	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512179	120512179	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781979575	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	220	463	0	ENST00000256646.2:c.1063G>A	p.Asp355Asn	p.D355N	ENST00000256646	NM_024408.3	355	Gac/Aac	6/34	1	2	FACETS	1	0.979	1	1	0.995	1	CLONAL	2	TRUE	1	0.35	2		463	573	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162722894	162722894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1340393535	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	180	489	0	ENST00000367921.3:c.92G>A	p.Arg31His	p.R31H	ENST00000367921	NM_006182.2	31	cGc/cAc	4/18	1	2	FACETS	1	0.965	1	1	0.994	1	CLONAL	2	TRUE	1	0.35	2		489	486	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725556	162725556	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	99	362	0	ENST00000367921.3:c.668A>G	p.Tyr223Cys	p.Y223C	ENST00000367921	NM_006182.2	223	tAc/tGc	7/18	1	2	FACETS	1	0.969	1	1	0.989	1	CLONAL	2	TRUE	1	0.35	2		362	245	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740231	162740231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773598662	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	236	445	1	ENST00000367921.3:c.1433G>A	p.Arg478His	p.R478H	ENST00000367921	NM_006182.2	478	cGc/cAc	12/18	1	2	FACETS	1	0.989	1	1	0.995	1	CLONAL	2	TRUE	1	0.35	2		446	553	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163309266	163309266	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs144627000	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	119	292	0	ENST00000271452.3:c.605C>T	p.Thr202Met	p.T202M	ENST00000271452	NM_145697.2	202	aCg/aTg	8/14	1	2	FACETS	0.899	0.829	0.971	1	0.992	1	CLONAL	3	TRUE	1	0.35	2		292	252	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218886	193218886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	63	216	0	ENST00000367435.3:c.1444G>A	p.Glu482Lys	p.E482K	ENST00000367435	NM_024529.4	482	Gaa/Aaa	16/17	1	2	FACETS	1	0.929	1	1	0.983	1	CLONAL	2	TRUE	1	0.35	2		216	168	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648325	206648325	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	274	672	2	ENST00000367120.3:c.346C>A	p.Leu116Met	p.L116M	ENST00000367120	NM_014002.3	116	Ctg/Atg	5/22	1	2	FACETS	1	0.985	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		674	699	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206941988	206941988	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376415487	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	95	254	0	ENST00000423557.1:c.530G>A	p.Arg177Gln	p.R177Q	ENST00000423557	NM_000572.2	177	cGa/cAa	5/5	1	2	FACETS	1	0.973	1	1	0.989	1	CLONAL	2	TRUE	1	0.35	2		254	227	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405927	70405928	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	113	480	0	ENST00000373644.4:c.3446dup	p.Thr1150AspfsTer23	p.T1150Dfs*23	ENST00000373644	NM_030625.2	1147	-/A	4/12	1	2	FACETS	1	0.936	1	1	0.99	1	CLONAL	2	TRUE	1	0.35	2		480	313	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70411660	70411660	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs916364742	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	125	375	0	ENST00000373644.4:c.4334G>A	p.Ser1445Asn	p.S1445N	ENST00000373644	NM_030625.2	1445	aGt/aAt	5/12	1	2	FACETS	1	0.981	1	1	0.992	1	CLONAL	2	TRUE	1	0.35	2		375	291	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88678943	88678943	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	70	293	0	ENST00000372037.3:c.883G>A	p.Asp295Asn	p.D295N	ENST00000372037	NM_004329.2	295	Gac/Aac	10/13	1	2	FACETS	0.943	0.837	1	1	0.982	1	CLONAL	2	TRUE	1	0.35	2		293	212	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903733	114903733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	199	569	0	ENST00000543371.1:c.737C>T	p.Ser246Leu	p.S246L	ENST00000543371	NM_001198531.1	246	tCg/tTg	7/14	1	2	FACETS	1	0.954	1	1	0.994	1	CLONAL	2	TRUE	1	0.35	2		569	553	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251941	8251941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	282	846	1	ENST00000335790.3:c.136G>A	p.Glu46Lys	p.E46K	ENST00000335790	NM_002315.2	46	Gaa/Aaa	2/4	1	2	FACETS	1	0.97	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		847	773	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741604	17741604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866359886	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	160	272	0	ENST00000250003.3:c.275G>A	p.Arg92His	p.R92H	ENST00000250003	NM_002478.4	92	cGc/cAc	1/3	1	2	FACETS	0.932	0.87	0.994	1	0.994	1	CLONAL	3	TRUE	1	0.35	2		272	327	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17743032	17743032	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	219	730	0	ENST00000250003.3:c.940A>G	p.Asn314Asp	p.N314D	ENST00000250003	NM_002478.4	314	Aac/Gac	3/3	1	2	FACETS	1	0.978	1	1	0.995	1	CLONAL	2	TRUE	1	0.35	2		730	572	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205158	61205158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777442412	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	63	558	0	ENST00000301761.2:c.98G>A	p.Arg33His	p.R33H	ENST00000301761	NM_017841.2	33	cGc/cAc	2/4	1	2	FACETS	0.726	0.629	0.831	0.726	0.629	0.831	SUBCLONAL	1	TRUE	1	0.35	2		558	496	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127764	64127764	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	342	723	1	ENST00000334205.4:c.257G>A	p.Arg86His	p.R86H	ENST00000334205	NM_003942.2	86	cGc/cAc	3/17	1	2	FACETS	1	0.991	1	1	0.997	1	CLONAL	2	TRUE	1	0.35	2		724	821	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128622	64128622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	297	614	0	ENST00000334205.4:c.479G>A	p.Arg160Gln	p.R160Q	ENST00000334205	NM_003942.2	160	cGa/cAa	5/17	1	2	FACETS	0.842	0.799	0.885	1	0.996	1	CLONAL	3	TRUE	1	0.35	2		614	672	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128690	64128690	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs751103067	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	302	712	0	ENST00000334205.4:c.547A>G	p.Ser183Gly	p.S183G	ENST00000334205	NM_003942.2	183	Agc/Ggc	5/17	1	2	FACETS	1	0.976	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		712	818	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138902	64138902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1192515568	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	111	435	0	ENST00000334205.4:c.2269G>A	p.Ala757Thr	p.A757T	ENST00000334205	NM_003942.2	757	Gcc/Acc	17/17	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.35	2		435	518	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201724	67201725	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	337	735	1	ENST00000312629.5:c.1031dup	p.Arg346GlnfsTer14	p.R346Qfs*14	ENST00000312629	NM_003952.2	342	gac/gaCc	12/15	1	2	FACETS	1	0.981	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		736	901	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942172	71942172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs896238433	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	345	695	0	ENST00000298229.2:c.1436G>A	p.Arg479His	p.R479H	ENST00000298229	NM_001567.3	479	cGc/cAc	12/28	1	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	2	TRUE	1	0.35	2		695	864	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066743	77066743	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	144	361	0	ENST00000356341.3:c.742A>C	p.Met248Leu	p.M248L	ENST00000356341	NM_002576.4	248	Atg/Ctg	7/15	1	2	FACETS	1	0.983	1	1	0.993	1	CLONAL	2	TRUE	1	0.35	2		361	337	SUCCESS
EED	8726	MSKCC	GRCh37	11	85963189	85963189	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	29	248	0	ENST00000263360.6:c.268-1G>A		p.X90_splice	ENST00000263360	NM_003797.3	90			1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.35	2		248	137	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189497	94189497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774057024	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	89	354	0	ENST00000323929.3:c.1508G>A	p.Arg503His	p.R503H	ENST00000323929	NM_005591.3	503	cGt/cAt	14/20	1	2	FACETS	1	0.962	1	1	0.988	1	CLONAL	2	TRUE	1	0.35	2		354	224	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141998	108141998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755896387	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	25	497	2	ENST00000278616.4:c.2942G>A	p.Arg981His	p.R981H	ENST00000278616	NM_000051.3	981	cGt/cAt	20/63	1	2	FACETS	0.442	0.349	0.55	0.442	0.349	0.55	SUBCLONAL	1	TRUE	1	0.35	2		499	323	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343976	118343976	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	106	353	2	ENST00000534358.1:c.2102G>T	p.Arg701Ile	p.R701I	ENST00000534358	NM_005933.3	701	aGa/aTa	3/36	1	2	FACETS	1	0.958	1	1	0.99	1	CLONAL	2	TRUE	1	0.35	2		355	278	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371742	118371742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	28	269	0	ENST00000534358.1:c.6199C>T	p.Arg2067Cys	p.R2067C	ENST00000534358	NM_005933.3	2067	Cgc/Tgc	25/36	1	2	FACETS	0.506	0.405	0.621	0.506	0.405	0.621	SUBCLONAL	1	TRUE	1	0.35	2		269	316	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375114	118375114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	132	353	0	ENST00000534358.1:c.8507C>T	p.Ser2836Leu	p.S2836L	ENST00000534358	NM_005933.3	2836	tCa/tTa	27/36	1	2	FACETS	0.882	0.816	0.949	1	0.993	1	CLONAL	3	TRUE	1	0.35	2		353	285	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375498	118375498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	71	313	0	ENST00000534358.1:c.8891C>T	p.Thr2964Ile	p.T2964I	ENST00000534358	NM_005933.3	2964	aCc/aTc	27/36	1	2	FACETS	0.944	0.837	1	1	0.983	1	CLONAL	2	TRUE	1	0.35	2		313	215	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402196	402196	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	199	636	0	ENST00000399788.2:c.4595A>T	p.Lys1532Ile	p.K1532I	ENST00000399788	NM_001042603.1	1532	aAa/aTa	27/28	0.3	1	FACETS	0.88	0.822	0.939	1	0.993	1	CLONAL	2	TRUE	0	0.35	1		636	533	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905492	11905492	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	192	382	0	ENST00000396373.4:c.142A>G	p.Ile48Val	p.I48V	ENST00000396373	NM_001987.4	48	Atc/Gtc	2/8	0.121266034753738	3	FACETS	0.955	0.893	1	1	0.991	1	INDETERMINATE	3	TRUE	1	0.35	3		382	450	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499688	18499688	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	170	420	0	ENST00000266497.5:c.1543T>C	p.Ser515Pro	p.S515P	ENST00000266497		515	Tcc/Ccc	10/31	0.121266034753738	3	FACETS	0.933	0.868	0.998	1	0.99	1	INDETERMINATE	3	TRUE	1	0.35	3		420	408	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25368455	25368455	+	intron_variant	Intron	SNP	G	G	A	rs200186819	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	91	305	1	ENST00000311936.3:c.451-5610C>T		p.*151*	ENST00000311936	NM_004985.3	164/189			0.121266034753738	3	FACETS	1	0.97	1	1	0.97	1	INDETERMINATE	2	TRUE	1	0.35	3		306	254	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46240657	46240657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757456378	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	113	329	0	ENST00000334344.6:c.1517C>T	p.Ala506Val	p.A506V	ENST00000334344	NM_152641.2	506	gCg/gTg	12/21	0.121266034753738	3	FACETS	1	0.928	1	1	0.987	1	INDETERMINATE	3	TRUE	1	0.35	3		329	250	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287500	46287500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457405698	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	25	358	0	ENST00000334344.6:c.5359C>T	p.Arg1787Cys	p.R1787C	ENST00000334344	NM_152641.2	1787	Cgc/Tgc	20/21	0.121266034753738	3	FACETS	0.56	0.441	0.695	0.28	0.22	0.348	INDETERMINATE	1	TRUE	1	0.35	3		358	300	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425037	49425037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1480605988	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	392	856	0	ENST00000301067.7:c.13451G>A	p.Arg4484Gln	p.R4484Q	ENST00000301067	NM_003482.3	4484	cGa/cAa	39/54	0.121266034753738	3	FACETS	0.912	0.87	0.954	1	0.995	1	INDETERMINATE	3	TRUE	1	0.35	3		856	962	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425376	49425376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	321	801	1	ENST00000301067.7:c.13112G>A	p.Ser4371Asn	p.S4371N	ENST00000301067	NM_003482.3	4371	aGc/aAc	39/54	0.121266034753738	3	FACETS	0.918	0.871	0.965	1	0.994	1	INDETERMINATE	3	TRUE	1	0.35	3		802	783	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426877	49426877	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1365753920	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	214	554	0	ENST00000301067.7:c.11611G>A	p.Ala3871Thr	p.A3871T	ENST00000301067	NM_003482.3	3871	Gca/Aca	39/54	0.121266034753738	3	FACETS	0.923	0.866	0.981	1	0.991	1	INDETERMINATE	3	TRUE	1	0.35	3		554	519	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434568	49434568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs938203622	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	283	723	0	ENST00000301067.7:c.6985G>A	p.Ala2329Thr	p.A2329T	ENST00000301067	NM_003482.3	2329	Gcc/Acc	31/54	0.121266034753738	3	FACETS	0.901	0.852	0.95	1	0.993	1	INDETERMINATE	3	TRUE	1	0.35	3		723	703	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490845	56490845	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	187	448	0	ENST00000267101.3:c.2291G>A	p.Gly764Asp	p.G764D	ENST00000267101	NM_001982.3	764	gGc/gAc	20/28	0.121266034753738	3	FACETS	0.865	0.806	0.924	1	0.988	1	INDETERMINATE	3	TRUE	1	0.35	3		448	484	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495049	56495049	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs79759315	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	323	632	0	ENST00000267101.3:c.3406C>T	p.Arg1136Cys	p.R1136C	ENST00000267101	NM_001982.3	1136	Cgc/Tgc	27/28	0.121266034753738	3	FACETS	0.921	0.874	0.968	1	0.994	1	INDETERMINATE	3	TRUE	1	0.35	3		632	785	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857826	57857826	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs537495636	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	327	766	1	ENST00000228682.2:c.145G>A	p.Gly49Ser	p.G49S	ENST00000228682	NM_005269.2	49	Ggc/Agc	3/12	0.121266034753738	3	FACETS	0.895	0.849	0.941	1	0.994	1	INDETERMINATE	3	TRUE	1	0.35	3		767	818	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885930	111885930	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs138410505	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	235	629	0	ENST00000341259.2:c.1552C>T	p.Arg518Ter	p.R518*	ENST00000341259	NM_005475.2	518	Cga/Tga	8/8	1	2	FACETS	1	0.981	1	1	0.995	1	CLONAL	2	TRUE	1	0.35	2		629	606	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431346	121431346	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1452663012	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	209	473	0	ENST00000257555.6:c.550G>T	p.Gly184Trp	p.G184W	ENST00000257555		184	Ggg/Tgg	3/10	1	2	FACETS	0.887	0.834	0.94	1	0.995	1	CLONAL	3	TRUE	1	0.35	2		473	449	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434136	121434136	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	61	799	0	ENST00000257555.6:c.1027A>G	p.Thr343Ala	p.T343A	ENST00000257555		343	Aca/Gca	5/10	1	2	FACETS	0.369	0.317	0.426	0.369	0.317	0.426	SUBCLONAL	1	TRUE	1	0.35	2		799	944	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201371	133201371	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs71452531	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	250	783	0	ENST00000320574.5:c.6773T>C	p.Phe2258Ser	p.F2258S	ENST00000320574	NM_006231.2	2258	tTc/tCc	49/49	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		783	578	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252691	133252691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	143	474	0	ENST00000320574.5:c.1009G>A	p.Glu337Lys	p.E337K	ENST00000320574	NM_006231.2	337	Gaa/Aaa	10/49	1	2	FACETS	1	0.969	1	1	0.992	1	CLONAL	2	TRUE	1	0.35	2		474	373	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563383	21563383	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	50	938	0	ENST00000382592.4:c.536C>T	p.Ser179Leu	p.S179L	ENST00000382592	NM_014572.2	179	tCg/tTg	4/8	1	2	FACETS	0.365	0.309	0.427	0.365	0.309	0.427	SUBCLONAL	1	TRUE	1	0.35	2		938	783	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26927938	26927938	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	12	324	0	ENST00000381527.3:c.377G>A	p.Gly126Glu	p.G126E	ENST00000381527	NM_001260.1	126	gGa/gAa	4/13	1	2	FACETS	0.309	0.217	0.422	0.309	0.217	0.422	SUBCLONAL	1	TRUE	1	0.35	2		324	222	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588620	28588620	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	34	405	0	ENST00000241453.7:c.2828del	p.Leu943Ter	p.L943*	ENST00000241453	NM_004119.2	943	tTa/ta	23/24	1	2	FACETS	0.672	0.551	0.807	0.672	0.551	0.807	SUBCLONAL	1	TRUE	1	0.35	2		405	289	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913183	32913183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	107	434	0	ENST00000380152.3:c.4691C>T	p.Ala1564Val	p.A1564V	ENST00000380152		1564	gCa/gTa	11/27	1	2	FACETS	1	0.93	1	1	0.989	1	CLONAL	2	TRUE	1	0.35	2		434	298	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913401	32913401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	99	388	0	ENST00000380152.3:c.4909G>A	p.Val1637Ile	p.V1637I	ENST00000380152		1637	Gtt/Att	11/27	1	2	FACETS	0.846	0.771	0.921	1	0.99	1	CLONAL	3	TRUE	1	0.35	2		388	223	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134030	41134030	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	71	611	0	ENST00000379561.5:c.1598C>T	p.Ala533Val	p.A533V	ENST00000379561	NM_002015.3	533	gCa/gTa	2/3	1	2	FACETS	0.731	0.639	0.83	0.731	0.639	0.83	SUBCLONAL	1	TRUE	1	0.35	2		611	555	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954199	48954199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	28	208	1	ENST00000267163.4:c.1400G>A	p.Arg467Gln	p.R467Q	ENST00000267163	NM_000321.2	467	cGa/cAa	15/27	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.35	2		209	110	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281840	49281840	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	158	607	1	ENST00000282018.3:c.887C>T	p.Ala296Val	p.A296V	ENST00000282018	NM_020377.2	296	gCc/gTc	1/1	1	2	FACETS	1	0.963	1	1	0.993	1	CLONAL	2	TRUE	1	0.35	2		608	424	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335930	73335930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs961788436	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	107	348	1	ENST00000377767.4:c.2365C>T	p.Arg789Trp	p.R789W	ENST00000377767	NM_014953.3	789	Cgg/Tgg	18/21	1	2	FACETS	1	0.972	1	1	0.99	1	CLONAL	2	TRUE	1	0.35	2		349	263	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336251	73336251	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	70	187	0	ENST00000377767.4:c.2152G>A	p.Ala718Thr	p.A718T	ENST00000377767	NM_014953.3	718	Gcc/Acc	17/21	1	2	FACETS	0.883	0.792	0.975	1	0.986	1	CLONAL	3	TRUE	1	0.35	2		187	151	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73351619	73351619	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	83	208	0	ENST00000377767.4:c.593T>C	p.Val198Ala	p.V198A	ENST00000377767	NM_014953.3	198	gTa/gCa	4/21	1	2	FACETS	1	0.953	1	1	0.987	1	CLONAL	2	TRUE	1	0.35	2		208	215	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434629	110434629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	261	580	1	ENST00000375856.3:c.3772G>A	p.Val1258Met	p.V1258M	ENST00000375856	NM_003749.2	1258	Gtg/Atg	1/2	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		581	620	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435054	110435054	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	354	743	2	ENST00000375856.3:c.3347G>T	p.Gly1116Val	p.G1116V	ENST00000375856	NM_003749.2	1116	gGa/gTa	1/2	1	2	FACETS	0.939	0.897	0.981	1	0.997	1	CLONAL	3	TRUE	1	0.35	2		745	718	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435464	110435464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	51	624	1	ENST00000375856.3:c.2937G>A	p.Met979Ile	p.M979I	ENST00000375856	NM_003749.2	979	atG/atA	1/2	1	2	FACETS	0.448	0.38	0.523	0.448	0.38	0.523	SUBCLONAL	1	TRUE	1	0.35	2		625	650	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873817	35873817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	157	367	0	ENST00000216797.5:c.34G>A	p.Ala12Thr	p.A12T	ENST00000216797	NM_020529.2	12	Gcc/Acc	1/6	1	2	FACETS	1	0.948	1	1	0.992	1	CLONAL	2	TRUE	1	0.35	2		367	435	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060937	38060937	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	171	538	0	ENST00000250448.2:c.1052C>T	p.Thr351Ile	p.T351I	ENST00000250448	NM_004496.3	351	aCt/aTt	2/2	1	2	FACETS	1	0.962	1	1	0.993	1	CLONAL	2	TRUE	1	0.35	2		538	463	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572100	95572100	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	128	402	2	ENST00000393063.1:c.3008G>A	p.Arg1003Gln	p.R1003Q	ENST00000393063	NM_030621.3	1003	cGa/cAa	20/28	1	2	FACETS	1	0.979	1	1	0.992	1	CLONAL	2	TRUE	1	0.35	2		404	306	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590560	95590560	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	69	229	0	ENST00000393063.1:c.1349G>T	p.Arg450Ile	p.R450I	ENST00000393063	NM_030621.3	450	aGa/aTa	9/28	1	2	FACETS	1	0.938	1	1	0.984	1	CLONAL	2	TRUE	1	0.35	2		229	182	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40998424	40998424	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	220	594	0	ENST00000267868.3:c.275T>G	p.Phe92Cys	p.F92C	ENST00000267868	NM_002875.4	92	tTc/tGc	4/10	1	2	FACETS	1	0.989	1	1	0.995	1	CLONAL	2	TRUE	1	0.35	2		594	508	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961353	41961353	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	121	424	0	ENST00000219905.7:c.261G>T	p.Glu87Asp	p.E87D	ENST00000219905	NM_001164273.1	87	gaG/gaT	2/24	1	2	FACETS	1	0.953	1	1	0.991	1	CLONAL	2	TRUE	1	0.35	2		424	326	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003747	45003747	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs1057519877	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	61	574	0	ENST00000558401.1:c.3G>A	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	atG/atA	1/4	1	2	FACETS	0.47	0.405	0.542	0.47	0.405	0.542	SUBCLONAL	1	TRUE	1	0.35	2		574	741	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727440	66727441	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	207	392	0	ENST00000307102.5:c.159dup	p.Leu54SerfsTer13	p.L54Sfs*13	ENST00000307102	NM_002755.3	52	-/T	2/11	1	2	FACETS	1	0.973	1	1	0.994	1	CLONAL	2	TRUE	1	0.35	2		392	550	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457295	67457295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886038803	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	58	849	2	ENST00000327367.4:c.269G>A	p.Arg90His	p.R90H	ENST00000327367	NM_005902.3	90	cGc/cAc	2/9	1	2	FACETS	0.437	0.374	0.505	0.437	0.374	0.505	SUBCLONAL	1	TRUE	1	0.35	2		851	759	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67462934	67462934	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	186	555	0	ENST00000327367.4:c.650A>C	p.Asn217Thr	p.N217T	ENST00000327367	NM_005902.3	217	aAt/aCt	5/9	1	2	FACETS	1	0.957	1	1	0.994	1	CLONAL	2	TRUE	1	0.35	2		555	512	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473635	67473635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906853	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	317	674	2	ENST00000327367.4:c.715G>A	p.Glu239Lys	p.E239K	ENST00000327367	NM_005902.3	239	Gag/Aag	6/9	1	2	FACETS	1	0.992	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		676	733	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477106	67477106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1348033858	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	231	640	1	ENST00000327367.4:c.913G>A	p.Ala305Thr	p.A305T	ENST00000327367	NM_005902.3	305	Gca/Aca	7/9	1	2	FACETS	1	0.966	1	1	0.995	1	CLONAL	2	TRUE	1	0.35	2		641	632	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996083	73996083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776686900	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	290	868	0	ENST00000318443.5:c.817G>A	p.Glu273Lys	p.E273K	ENST00000318443	NM_001024736.1	273	Gag/Aag	5/10	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		868	703	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996221	73996221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	149	451	2	ENST00000318443.5:c.955G>A	p.Ala319Thr	p.A319T	ENST00000318443	NM_001024736.1	319	Gca/Aca	5/10	1	2	FACETS	1	0.961	1	1	0.992	1	CLONAL	2	TRUE	1	0.35	2		453	400	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500382	99500382	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750032832	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	224	674	0	ENST00000268035.6:c.3815C>T	p.Pro1272Leu	p.P1272L	ENST00000268035	NM_000875.3	1272	cCt/cTt	21/21	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.35	2		674	560	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094723	2094723	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs374489979	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	578	946	3	ENST00000219066.1:c.457C>T	p.Arg153Ter	p.R153*	ENST00000219066	NM_002528.5	153	Cga/Tga	3/6	0.121266034753738	4	FACETS	1	0.994	1	1	0.997	1	INDETERMINATE	3	TRUE	2	0.35	4		949	1298	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106216	2106216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139929314	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	184	848	2	ENST00000219476.3:c.619G>A	p.Val207Ile	p.V207I	ENST00000219476	NM_000548.3	207	Gtc/Atc	7/42	0.121266034753738	4	FACETS	1	0.988	1	0.698	0.644	0.754	INDETERMINATE	1	TRUE	2	0.35	4		850	1017	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2114313	2114313	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	382	755	0	ENST00000219476.3:c.1484A>G	p.His495Arg	p.H495R	ENST00000219476	NM_000548.3	495	cAc/cGc	15/42	0.121266034753738	4	FACETS	1	0.976	1	1	0.996	1	INDETERMINATE	3	TRUE	2	0.35	4		755	948	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129396	2129396	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	414	793	0	ENST00000219476.3:c.3251A>G	p.Asp1084Gly	p.D1084G	ENST00000219476	NM_000548.3	1084	gAc/gGc	28/42	0.121266034753738	4	FACETS	1	0.985	1	1	0.996	1	INDETERMINATE	3	TRUE	2	0.35	4		793	995	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134439	2134439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147719291	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	404	1013	2	ENST00000219476.3:c.4216G>A	p.Asp1406Asn	p.D1406N	ENST00000219476	NM_000548.3	1406	Gac/Aac	34/42	0.121266034753738	4	FACETS	1	0.965	1	1	0.996	1	INDETERMINATE	3	TRUE	2	0.35	4		1015	1025	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138267	2138267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751990617	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	432	871	2	ENST00000219476.3:c.5200G>A	p.Asp1734Asn	p.D1734N	ENST00000219476	NM_000548.3	1734	Gat/Aat	41/42	0.121266034753738	4	FACETS	1	0.988	1	1	0.996	1	INDETERMINATE	3	TRUE	2	0.35	4		873	1020	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642833	3642833	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202189103	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	357	735	0	ENST00000294008.3:c.2194G>A	p.Gly732Arg	p.G732R	ENST00000294008	NM_032444.2	732	Ggg/Agg	11/15	0.121266034753738	4	FACETS	1	0.962	1	1	0.995	1	INDETERMINATE	3	TRUE	2	0.35	4		735	906	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778258	3778258	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	357	768	0	ENST00000262367.5:c.6790A>G	p.Met2264Val	p.M2264V	ENST00000262367	NM_004380.2	2264	Atg/Gtg	31/31	0.121266034753738	4	FACETS	1	0.99	1	1	0.996	1	INDETERMINATE	3	TRUE	2	0.35	4		768	801	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779091	3779091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759638164	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	250	754	1	ENST00000262367.5:c.5957C>T	p.Thr1986Met	p.T1986M	ENST00000262367	NM_004380.2	1986	aCg/aTg	31/31	0.121266034753738	4	FACETS	1	0.979	1	1	0.994	1	INDETERMINATE	3	TRUE	2	0.35	4		755	596	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828780	3828780	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	321	546	0	ENST00000262367.5:c.1862T>G	p.Leu621Arg	p.L621R	ENST00000262367	NM_004380.2	621	cTa/cGa	9/31	0.121266034753738	4	FACETS	1	0.98	1	1	0.995	1	INDETERMINATE	3	TRUE	2	0.35	4		546	777	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014092	14014092	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1225226851	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	241	749	1	ENST00000311895.7:c.70C>A	p.Leu24Met	p.L24M	ENST00000311895	NM_005236.2	24	Ctg/Atg	1/11	0.121266034753738	0	FACETS	0.728	0.685	0.772			1	INDETERMINATE	2	TRUE	0	0.35	0		750	615	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020538	14020538	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	105	406	0	ENST00000311895.7:c.509C>T	p.Ala170Val	p.A170V	ENST00000311895	NM_005236.2	170	gCc/gTc	3/11	0.121266034753738	0	FACETS	0.668	0.607	0.73			1	INDETERMINATE	2	TRUE	0	0.35	0		406	292	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619279	23619279	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587776527	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	185	556	1	ENST00000261584.4:c.3256C>T	p.Arg1086Ter	p.R1086*	ENST00000261584	NM_024675.3	1086	Cga/Tga	12/13	0.121266034753738	0	FACETS	0.75	0.7	0.801			1	INDETERMINATE	2	TRUE	0	0.35	0		557	458	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23635360	23635360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769009609	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	105	487	0	ENST00000261584.4:c.2804C>T	p.Ala935Val	p.A935V	ENST00000261584	NM_024675.3	935	gCt/gTt	8/13	0.121266034753738	0	FACETS	0.637	0.578	0.698			1	INDETERMINATE	2	TRUE	0	0.35	0		487	306	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641487	23641487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1462734899	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	33	598	0	ENST00000261584.4:c.1988G>A	p.Arg663His	p.R663H	ENST00000261584	NM_024675.3	663	cGc/cAc	5/13	0.121266034753738	0	FACETS	0.316	0.257	0.382			1	INDETERMINATE	1	TRUE	0	0.35	0		598	388	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853305	68853305	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	228	473	0	ENST00000261769.5:c.1688C>G	p.Ala563Gly	p.A563G	ENST00000261769	NM_004360.3	563	gCc/gGc	11/16	0.3	3	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.35	3		473	613	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828204	72828204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs953508094	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	97	549	1	ENST00000268489.5:c.8377G>A	p.Glu2793Lys	p.E2793K	ENST00000268489	NM_006885.3	2793	Gaa/Aaa	9/10	0.3	3	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.35	3		550	459	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993339	72993339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368995910	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	303	834	0	ENST00000268489.5:c.706G>A	p.Val236Met	p.V236M	ENST00000268489	NM_006885.3	236	Gtg/Atg	2/10	0.3	3	FACETS	0.939	0.891	0.988			1	CLONAL	3	TRUE	NA	0.35	3		834	722	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993822	72993822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374552910	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	171	649	1	ENST00000268489.5:c.223G>A	p.Ala75Thr	p.A75T	ENST00000268489	NM_006885.3	75	Gcc/Acc	2/10	0.3	3	FACETS	1	0.985	1			1	CLONAL	2	TRUE	NA	0.35	3		650	469	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888076	81888076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1353659689	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	112	351	0	ENST00000359376.3:c.221G>A	p.Arg74His	p.R74H	ENST00000359376	NM_002661.3	74	cGc/cAc	3/33	0.231957665260561	0	FACETS	0.7	0.639	0.763			1	SUBCLONAL	2	TRUE	0	0.35	0		351	297	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957130	81957130	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	218	610	0	ENST00000359376.3:c.2348A>G	p.Lys783Arg	p.K783R	ENST00000359376	NM_002661.3	783	aAg/aGg	22/33	0.231957665260561	0	FACETS	0.786	0.738	0.834			1	SUBCLONAL	2	TRUE	0	0.35	0		610	515	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990306	81990306	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs527970615	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	87	405	0	ENST00000359376.3:c.3577G>A	p.Glu1193Lys	p.E1193K	ENST00000359376	NM_002661.3	1193	Gaa/Aaa	32/33	0.231957665260561	0	FACETS	0.812	0.723	0.905			1	CLONAL	1	TRUE	0	0.35	0		405	398	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89345532	89345532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765378650	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	149	405	0	ENST00000301030.4:c.7418C>T	p.Thr2473Met	p.T2473M	ENST00000301030	NM_001256183.1	2473	aCg/aTg	9/13	0.3	3	FACETS	0.975	0.904	1			1	CLONAL	3	TRUE	NA	0.35	3		405	342	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352058	89352058	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	257	584	0	ENST00000301030.4:c.893-1G>T		p.X298_splice	ENST00000301030	NM_001256183.1	298			0.3	3	FACETS	0.896	0.845	0.948			1	CLONAL	3	TRUE	NA	0.35	3		584	642	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89825016	89825016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	286	552	0	ENST00000389301.3:c.2950C>T	p.Leu984Phe	p.L984F	ENST00000389301	NM_000135.2	984	Ctt/Ttt	30/43	0.3	3	FACETS	0.85	0.803	0.897			1	CLONAL	3	TRUE	NA	0.35	3		552	753	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577091	7577091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149633775	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	343	734	0	ENST00000269305.4:c.847C>T	p.Arg283Cys	p.R283C	ENST00000269305	NM_001126112.2	283	Cgc/Tgc	8/11	1	2	FACETS	1	0.979	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		734	927	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578412	7578412	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519747	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	377	729	0	ENST00000269305.4:c.518T>C	p.Val173Ala	p.V173A	ENST00000269305	NM_001126112.2	173	gTg/gCg	5/11	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	1	0.35	2		729	913	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	388	858	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	1	2	FACETS	1	0.986	1	1	0.997	1	CLONAL	2	TRUE	1	0.35	2		858	1017	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958212	11958212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760186886	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	70	295	0	ENST00000353533.5:c.122G>A	p.Arg41His	p.R41H	ENST00000353533	NM_003010.3	41	cGc/cAc	2/11	1	2	FACETS	1	0.913	1	1	0.984	1	CLONAL	2	TRUE	1	0.35	2		295	194	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17117129	17117129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777826268	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	88	598	2	ENST00000285071.4:c.1580G>A	p.Arg527Gln	p.R527Q	ENST00000285071	NM_144997.5	527	cGa/cAa	14/14	1	2	FACETS	0.888	0.789	0.995	0.888	0.789	0.995	CLONAL	1	TRUE	1	0.35	2		600	566	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17120384	17120384	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs570066243	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	173	440	0	ENST00000285071.4:c.1175G>A	p.Arg392Gln	p.R392Q	ENST00000285071	NM_144997.5	392	cGg/cAg	10/14	1	2	FACETS	1	0.982	1	1	0.994	1	CLONAL	2	TRUE	1	0.35	2		440	423	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554277	29554277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1383770460	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	267	519	2	ENST00000356175.3:c.2293C>T	p.Arg765Cys	p.R765C	ENST00000356175	NM_000267.3	765	Cgc/Tgc	19/57	1	2	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		521	612	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562747	29562747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137854556	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	125	371	0	ENST00000356175.3:c.3827G>A	p.Arg1276Gln	p.R1276Q	ENST00000356175	NM_000267.3	1276	cGa/cAa	28/57	1	2	FACETS	1	0.935	1	1	0.991	1	CLONAL	2	TRUE	1	0.35	2		371	349	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657420	29657420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	239	571	0	ENST00000356175.3:c.5653C>T	p.Leu1885Phe	p.L1885F	ENST00000356175	NM_000267.3	1885	Ctc/Ttc	38/57	1	2	FACETS	0.87	0.821	0.92	1	0.996	1	CLONAL	3	TRUE	1	0.35	2		571	523	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29662007	29662007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	101	403	0	ENST00000356175.3:c.5901G>A	p.Met1967Ile	p.M1967I	ENST00000356175	NM_000267.3	1967	atG/atA	39/57	1	2	FACETS	1	0.963	1	1	0.989	1	CLONAL	2	TRUE	1	0.35	2		403	258	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682340	37682340	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	284	582	0	ENST00000447079.4:c.3531G>C	p.Glu1177Asp	p.E1177D	ENST00000447079	NM_015083.1	1177	gaG/gaC	13/14	0.3	3	FACETS	0.9	0.851	0.95			1	CLONAL	3	TRUE	NA	0.35	3		582	706	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883240	37883240	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749539903	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	182	789	0	ENST00000269571.5:c.3143G>A	p.Arg1048His	p.R1048H	ENST00000269571		1048	cGc/cAc	25/27	0.3	3	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.35	3		789	963	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508266	38508266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	292	561	0	ENST00000254066.5:c.574C>T	p.Arg192Cys	p.R192C	ENST00000254066	NM_000964.3	192	Cgc/Tgc	5/9	0.3	3	FACETS	0.904	0.856	0.953			1	CLONAL	3	TRUE	NA	0.35	3		561	723	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438216	56438216	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	302	754	0	ENST00000407977.2:c.777G>A	p.Trp259Ter	p.W259*	ENST00000407977		259	tgG/tgA	7/10	1	2	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		754	720	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439918	56439918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367688879	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	323	594	0	ENST00000407977.2:c.674G>A	p.Arg225His	p.R225H	ENST00000407977		225	cGc/cAc	6/10	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		594	806	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007514	62007514	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	295	696	0	ENST00000392795.3:c.353A>G	p.Asn118Ser	p.N118S	ENST00000392795	NM_001039933.1	118	aAt/aGt	3/6	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		696	718	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554117	63554117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	237	655	1	ENST00000307078.5:c.622G>A	p.Ala208Thr	p.A208T	ENST00000307078	NM_004655.3	208	Gct/Act	2/11	1	2	FACETS	0.999	0.937	1	1	0.995	1	CLONAL	2	TRUE	1	0.35	2		656	678	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78831689	78831689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755927307	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	64	732	0	ENST00000306801.3:c.1498G>A	p.Ala500Thr	p.A500T	ENST00000306801	NM_020761.2	500	Gca/Aca	13/34	1	2	FACETS	0.385	0.332	0.443	0.385	0.332	0.443	SUBCLONAL	1	TRUE	1	0.35	2		732	950	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584336	39584336	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	56	233	0	ENST00000262039.4:c.1001T>C	p.Leu334Ser	p.L334S	ENST00000262039	NM_002647.2	334	tTg/tCg	10/25	1	2	FACETS	1	0.92	1	1	0.981	1	CLONAL	2	TRUE	1	0.35	2		233	150	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375025	45375025	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	81	332	0	ENST00000262160.6:c.818T>G	p.Phe273Cys	p.F273C	ENST00000262160	NM_005901.5	273	tTt/tGt	8/11	1	2	FACETS	1	0.95	1	1	0.987	1	CLONAL	2	TRUE	1	0.35	2		332	211	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581262	48581262	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759288477	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	197	482	0	ENST00000342988.3:c.566G>A	p.Arg189His	p.R189H	ENST00000342988	NM_005359.5	189	cGt/cAt	5/12	1	2	FACETS	1	0.98	1	1	0.994	1	CLONAL	2	TRUE	1	0.35	2		482	502	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56412994	56412994	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1439049639	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	130	388	0	ENST00000348428.3:c.2008A>G	p.Thr670Ala	p.T670A	ENST00000348428	NM_006785.3	670	Acc/Gcc	16/17	1	2	FACETS	0.891	0.823	0.958	1	0.993	1	CLONAL	3	TRUE	1	0.35	2		388	278	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226490	2226490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780810017	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	68	945	5	ENST00000398665.3:c.3970G>A	p.Ala1324Thr	p.A1324T	ENST00000398665	NM_032482.2	1324	Gcg/Acg	27/28	1	2	FACETS	0.356	0.308	0.408	0.356	0.308	0.408	SUBCLONAL	1	TRUE	1	0.35	2		950	1092	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110295	3110295	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	301	669	0	ENST00000078429.4:c.285G>T	p.Glu95Asp	p.E95D	ENST00000078429	NM_002067.2	95	gaG/gaT	2/7	1	2	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		669	713	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099304	4099304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757240576	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	326	850	0	ENST00000262948.5:c.814G>A	p.Ala272Thr	p.A272T	ENST00000262948	NM_030662.3	272	Gcc/Acc	7/11	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		850	815	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5206806	5206806	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	269	665	0	ENST00000357368.4:c.5826C>A	p.Ser1942Arg	p.S1942R	ENST00000357368	NM_002850.3	1942	agC/agA	38/38	1	2	FACETS	1	0.987	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		665	667	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215522	5215522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	359	778	0	ENST00000357368.4:c.4181C>T	p.Ser1394Phe	p.S1394F	ENST00000357368	NM_002850.3	1394	tCc/tTc	27/38	1	2	FACETS	1	0.991	1	1	0.997	1	CLONAL	2	TRUE	1	0.35	2		778	877	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222192	5222192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	108	650	1	ENST00000357368.4:c.3143C>T	p.Thr1048Ile	p.T1048I	ENST00000357368	NM_002850.3	1048	aCa/aTa	19/38	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.35	2		651	599	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5225815	5225815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	346	810	0	ENST00000357368.4:c.2417C>T	p.Ser806Phe	p.S806F	ENST00000357368	NM_002850.3	806	tCc/tTc	17/38	1	2	FACETS	1	0.99	1	1	0.997	1	CLONAL	2	TRUE	1	0.35	2		810	850	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231336	5231336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776822913	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	294	734	1	ENST00000357368.4:c.2140C>T	p.Arg714Cys	p.R714C	ENST00000357368	NM_002850.3	714	Cgc/Tgc	14/38	1	2	FACETS	1	0.978	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		735	788	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231557	5231557	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150939732	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	302	600	0	ENST00000357368.4:c.1919G>A	p.Arg640His	p.R640H	ENST00000357368	NM_002850.3	640	cGc/cAc	14/38	1	2	FACETS	1	0.992	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		600	701	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240271	5240271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145504993	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	326	831	0	ENST00000357368.4:c.1643C>T	p.Pro548Leu	p.P548L	ENST00000357368	NM_002850.3	548	cCg/cTg	12/38	1	2	FACETS	1	0.984	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		831	858	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245810	5245810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	338	843	0	ENST00000357368.4:c.965C>T	p.Ala322Val	p.A322V	ENST00000357368	NM_002850.3	322	gCg/gTg	10/38	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		843	850	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7128956	7128956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146472806	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	19	345	0	ENST00000302850.5:c.2852C>T	p.Pro951Leu	p.P951L	ENST00000302850	NM_000208.2	951	cCg/cTg	15/22	1	2	FACETS	0.355	0.269	0.456	0.355	0.269	0.456	SUBCLONAL	1	TRUE	1	0.35	2		345	306	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132306	7132306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753474375	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	294	630	0	ENST00000302850.5:c.2705G>A	p.Arg902His	p.R902H	ENST00000302850	NM_000208.2	902	cGc/cAc	14/22	1	2	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		630	697	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250768	10250768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746456488	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	127	837	1	ENST00000340748.4:c.3712C>T	p.Arg1238Cys	p.R1238C	ENST00000340748		1238	Cgc/Tgc	32/40	1	2	FACETS	0.851	0.77	0.935	0.851	0.77	0.935	CLONAL	1	TRUE	1	0.35	2		838	853	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252720	10252720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377078524	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	327	664	1	ENST00000340748.4:c.3245G>A	p.Arg1082His	p.R1082H	ENST00000340748		1082	cGc/cAc	29/40	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		665	808	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252829	10252829	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs548883904	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	301	755	0	ENST00000340748.4:c.3136G>A	p.Asp1046Asn	p.D1046N	ENST00000340748		1046	Gac/Aac	29/40	1	2	FACETS	1	0.984	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		755	782	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252856	10252856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370786558	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	289	734	2	ENST00000340748.4:c.3109G>A	p.Ala1037Thr	p.A1037T	ENST00000340748		1037	Gca/Aca	29/40	1	2	FACETS	1	0.978	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		736	773	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610306	10610306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	393	857	0	ENST00000171111.5:c.404G>A	p.Arg135His	p.R135H	ENST00000171111	NM_203500.1	135	cGc/cAc	2/6	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	1	0.35	2		857	961	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105642	11105642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	366	580	0	ENST00000358026.2:c.1558G>A	p.Glu520Lys	p.E520K	ENST00000358026	NM_001128849.1	520	Gag/Aag	9/36	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	1	0.35	2		580	882	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144467	11144467	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764152134	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	424	776	0	ENST00000358026.2:c.3799G>A	p.Gly1267Ser	p.G1267S	ENST00000358026	NM_001128849.1	1267	Ggc/Agc	27/36	1	2	FACETS	1	0.994	1	1	0.997	1	CLONAL	2	TRUE	1	0.35	2		776	971	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145591	11145591	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	333	691	0	ENST00000358026.2:c.3953G>A	p.Arg1318His	p.R1318H	ENST00000358026	NM_001128849.1	1318	cGc/cAc	29/36	1	2	FACETS	1	0.991	1	1	0.997	1	CLONAL	2	TRUE	1	0.35	2		691	809	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627501	14627501	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	259	499	0	ENST00000254322.2:c.569T>G	p.Leu190Arg	p.L190R	ENST00000254322	NM_006145.1	190	cTa/cGa	2/3	1	2	FACETS	1	0.985	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		499	653	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291828	15291828	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376187165	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	73	946	1	ENST00000263388.2:c.2938G>A	p.Ala980Thr	p.A980T	ENST00000263388	NM_000435.2	980	Gcc/Acc	18/33	1	2	FACETS	0.5	0.436	0.568	0.5	0.436	0.568	SUBCLONAL	1	TRUE	1	0.35	2		947	835	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376248	15376248	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	146	479	5	ENST00000263377.2:c.766del	p.Gln256SerfsTer27	p.Q256Sfs*27	ENST00000263377	NM_058243.2	256	Cag/ag	5/20	1	2	FACETS	1	0.937	1	1	0.992	1	CLONAL	2	TRUE	1	0.35	2		484	410	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17947956	17947956	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1040476469	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	396	737	0	ENST00000458235.1:c.1768G>A	p.Val590Met	p.V590M	ENST00000458235	NM_000215.3	590	Gtg/Atg	13/24	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	1	0.35	2		737	970	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266808	18266808	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750411325	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	339	477	2	ENST00000222254.8:c.119C>T	p.Ala40Val	p.A40V	ENST00000222254	NM_005027.3	40	gCg/gTg	2/16	1	2	FACETS	0.879	0.837	0.92	1	0.997	1	CLONAL	3	TRUE	1	0.35	2		479	735	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272853	18272853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148193042	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	302	690	0	ENST00000222254.8:c.893C>T	p.Ala298Val	p.A298V	ENST00000222254	NM_005027.3	298	gCg/gTg	7/16	1	2	FACETS	1	0.979	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		690	810	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258560	19258560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372543417	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	97	880	2	ENST00000162023.5:c.340C>T	p.Arg114Trp	p.R114W	ENST00000162023		114	Cgg/Tgg	8/13	1	2	FACETS	0.572	0.509	0.64	0.572	0.509	0.64	SUBCLONAL	1	TRUE	1	0.35	2		882	969	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793049	33793049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	101	337	0	ENST00000498907.2:c.272C>T	p.Ala91Val	p.A91V	ENST00000498907	NM_004364.3	91	gCc/gTc	1/1	1	2	FACETS	1	0.969	1	1	0.99	1	CLONAL	2	TRUE	1	0.35	2		337	250	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211688	36211688	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs909409167	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	119	632	1	ENST00000222270.7:c.1439C>T	p.Ala480Val	p.A480V	ENST00000222270	NM_014727.1	480	gCg/gTg	3/37	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.35	2		633	586	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223601	36223601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773621382	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	331	957	1	ENST00000222270.7:c.6151G>A	p.Ala2051Thr	p.A2051T	ENST00000222270	NM_014727.1	2051	Gct/Act	28/37	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		958	815	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224310	36224310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775685548	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	305	829	0	ENST00000222270.7:c.6860G>A	p.Arg2287Gln	p.R2287Q	ENST00000222270	NM_014727.1	2287	cGg/cAg	28/37	1	2	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		829	729	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228800	36228800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393734909	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	237	783	0	ENST00000222270.7:c.7699C>T	p.Arg2567Cys	p.R2567C	ENST00000222270	NM_014727.1	2567	Cgt/Tgt	35/37	1	2	FACETS	1	0.974	1	1	0.995	1	CLONAL	2	TRUE	1	0.35	2		783	635	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40761125	40761125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	43	718	0	ENST00000392038.2:c.227G>A	p.Arg76His	p.R76H	ENST00000392038	NM_001626.4	76	cGc/cAc	4/14	1	2	FACETS	0.296	0.246	0.351	0.296	0.246	0.351	SUBCLONAL	1	TRUE	1	0.35	2		718	831	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765717	41765717	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1466592724	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	225	633	0	ENST00000301178.4:c.2593C>T	p.Arg865Cys	p.R865C	ENST00000301178	NM_021913.4	865	Cgc/Tgc	20/20	1	2	FACETS	1	0.962	1	1	0.995	1	CLONAL	2	TRUE	1	0.35	2		633	620	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752964	42752964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749808726	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	394	852	2	ENST00000222329.4:c.1300G>A	p.Glu434Lys	p.E434K	ENST00000222329	NM_006494.2	434	Gag/Aag	4/4	1	2	FACETS	1	0.994	1	1	0.997	1	CLONAL	2	TRUE	1	0.35	2		854	901	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753774	42753774	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	68	958	0	ENST00000222329.4:c.490G>A	p.Ala164Thr	p.A164T	ENST00000222329	NM_006494.2	164	Gcc/Acc	4/4	1	2	FACETS	0.374	0.324	0.429	0.374	0.324	0.429	SUBCLONAL	1	TRUE	1	0.35	2		958	1038	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754607	42754607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs914128913	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	251	794	0	ENST00000222329.4:c.133G>A	p.Val45Ile	p.V45I	ENST00000222329	NM_006494.2	45	Gtc/Atc	2/4	1	2	FACETS	1	0.961	1	1	0.995	1	CLONAL	2	TRUE	1	0.35	2		794	697	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794096	42794096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568511345	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	200	407	0	ENST00000575354.2:c.1457G>A	p.Gly486Asp	p.G486D	ENST00000575354	NM_015125.3	486	gGc/gAc	9/20	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	1	0.35	2		407	458	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794533	42794533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs951245986	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	401	866	0	ENST00000575354.2:c.1613C>T	p.Ser538Leu	p.S538L	ENST00000575354	NM_015125.3	538	tCg/tTg	10/20	1	2	FACETS	1	0.993	1	1	0.997	1	CLONAL	2	TRUE	1	0.35	2		866	953	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45864851	45864851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369191500	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	415	867	1	ENST00000391945.4:c.1168G>A	p.Asp390Asn	p.D390N	ENST00000391945	NM_000400.3	390	Gac/Aac	12/23	1	2	FACETS	1	0.994	1	1	0.997	1	CLONAL	2	TRUE	1	0.35	2		868	972	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918105	50918105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	105	856	0	ENST00000440232.2:c.2422C>T	p.Arg808Cys	p.R808C	ENST00000440232	NM_002691.3	808	Cgc/Tgc	20/27	1	2	FACETS	0.88	0.789	0.976	0.88	0.789	0.976	CLONAL	1	TRUE	1	0.35	2		856	682	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470926	25470926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1203141216	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	277	784	0	ENST00000264709.3:c.835G>A	p.Asp279Asn	p.D279N	ENST00000264709	NM_175629.2	279	Gat/Aat	7/23	1	2	FACETS	1	0.98	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		784	733	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967341	25967341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1312749456	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	143	278	0	ENST00000435504.4:c.1865C>T	p.Pro622Leu	p.P622L	ENST00000435504		622	cCg/cTg	13/13	1	2	FACETS	0.838	0.776	0.901	1	0.993	1	CLONAL	3	TRUE	1	0.35	2		278	325	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754924	29754924	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	240	572	1	ENST00000389048.3:c.1011G>A	p.Trp337Ter	p.W337*	ENST00000389048	NM_004304.4	337	tgG/tgA	4/29	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	1	0.35	2		573	580	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46608817	46608817	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	251	764	2	ENST00000263734.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000263734	NM_001430.4	710	Cga/Tga	13/16	1	2	FACETS	1	0.982	1	1	0.995	1	CLONAL	2	TRUE	1	0.35	2		766	650	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47613717	47613717	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	65	323	0	ENST00000263735.4:c.910G>A	p.Glu304Lys	p.E304K	ENST00000263735	NM_002354.2	304	Gag/Aag	9/9	1	2	FACETS	1	0.901	1	1	0.983	1	CLONAL	2	TRUE	1	0.35	2		323	182	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026620	48026620	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786204127	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	85	353	0	ENST00000234420.5:c.1498G>A	p.Ala500Thr	p.A500T	ENST00000234420	NM_000179.2	500	Gca/Aca	4/10	1	2	FACETS	0.971	0.872	1	1	0.986	1	CLONAL	2	TRUE	1	0.35	2		353	250	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719233	61719233	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	13	342	0	ENST00000401558.2:c.1824G>A	p.Met608Ile	p.M608I	ENST00000401558	NM_003400.3	608	atG/atA	16/25	1	2	FACETS	0.31	0.22	0.418	0.31	0.22	0.418	SUBCLONAL	1	TRUE	1	0.35	2		342	240	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630600	158630600	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	75	216	0	ENST00000263640.3:c.643G>A	p.Gly215Arg	p.G215R	ENST00000263640	NM_001105.4	215	Ggg/Agg	6/11	1	2	FACETS	0.835	0.751	0.921	1	0.987	1	CLONAL	3	TRUE	1	0.35	2		216	171	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728713	190728713	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	65	276	0	ENST00000441310.2:c.2104del	p.Ser702LeufsTer2	p.S702Lfs*2	ENST00000441310	NM_000534.4	701	Ttt/tt	10/13	1	2	FACETS	1	0.965	1	1	0.985	1	CLONAL	2	TRUE	1	0.35	2		276	151	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274548	198274548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778869024	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	310	580	3	ENST00000335508.6:c.850G>A	p.Ala284Thr	p.A284T	ENST00000335508	NM_012433.2	284	Gca/Aca	7/25	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		583	757	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281496	198281496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	94	524	0	ENST00000335508.6:c.635C>T	p.Pro212Leu	p.P212L	ENST00000335508	NM_012433.2	212	cCc/cTc	6/25	1	2	FACETS	0.926	0.826	1	0.926	0.826	1	CLONAL	1	TRUE	1	0.35	2		524	580	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131315	202131315	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	127	423	0	ENST00000358485.4:c.283G>T	p.Glu95Ter	p.E95*	ENST00000358485	NM_001080125.1	95	Gaa/Taa	2/9	1	2	FACETS	1	0.965	1	1	0.991	1	CLONAL	2	TRUE	1	0.35	2		423	332	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136238	202136238	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	134	388	0	ENST00000358485.4:c.483-1G>T		p.X161_splice	ENST00000358485	NM_001080125.1	161			1	2	FACETS	1	0.982	1	1	0.992	1	CLONAL	2	TRUE	1	0.35	2		388	312	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141656	202141656	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	106	321	0	ENST00000358485.4:c.944G>T	p.Ser315Ile	p.S315I	ENST00000358485	NM_001080125.1	315	aGc/aTc	7/9	1	2	FACETS	1	0.949	1	1	0.989	1	CLONAL	2	TRUE	1	0.35	2		321	285	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587121	212587121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	87	339	0	ENST00000342788.4:c.880C>T	p.Pro294Ser	p.P294S	ENST00000342788	NM_005235.2	294	Cca/Tca	7/28	1	2	FACETS	1	0.961	1	1	0.988	1	CLONAL	2	TRUE	1	0.35	2		339	220	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812326	212812326	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	92	282	0	ENST00000342788.4:c.250A>G	p.Thr84Ala	p.T84A	ENST00000342788	NM_005235.2	84	Aca/Gca	3/28	1	2	FACETS	1	0.965	1	1	0.989	1	CLONAL	2	TRUE	1	0.35	2		282	230	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342921	225342921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766952042	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	21	398	0	ENST00000264414.4:c.2171C>T	p.Ala724Val	p.A724V	ENST00000264414	NM_003590.4	724	gCg/gTg	15/16	1	2	FACETS	0.355	0.273	0.451	0.355	0.273	0.451	SUBCLONAL	1	TRUE	1	0.35	2		398	338	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662128	227662128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775603579	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	229	706	0	ENST00000305123.5:c.1327C>T	p.Arg443Cys	p.R443C	ENST00000305123	NM_005544.2	443	Cgc/Tgc	1/2	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	1	0.35	2		706	542	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662223	227662223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	305	777	0	ENST00000305123.5:c.1232G>A	p.Arg411Gln	p.R411Q	ENST00000305123	NM_005544.2	411	cGa/cAa	1/2	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		777	734	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793269	242793269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1381223113	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	367	872	2	ENST00000334409.5:c.808G>A	p.Gly270Ser	p.G270S	ENST00000334409	NM_005018.2	270	Ggc/Agc	5/5	1	2	FACETS	1	0.993	1	1	0.997	1	CLONAL	2	TRUE	1	0.35	2		874	853	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538257	9538257	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs746240534	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	57	513	0	ENST00000353224.5:c.1741C>T	p.Arg581Trp	p.R581W	ENST00000353224	NM_177990.2	581	Cgg/Tgg	7/10	0.121266034753738	0	FACETS	0.505	0.435	0.582			1	INDETERMINATE	1	TRUE	0	0.35	0		513	419	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561147	9561147	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	105	409	0	ENST00000353224.5:c.635A>G	p.Tyr212Cys	p.Y212C	ENST00000353224	NM_177990.2	212	tAc/tGc	4/10	0.121266034753738	0	FACETS	0.694	0.631	0.758			1	INDETERMINATE	2	TRUE	0	0.35	0		409	281	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021250	31021250	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs375215583	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	185	502	0	ENST00000375687.4:c.1249C>T	p.Arg417Ter	p.R417*	ENST00000375687	NM_015338.5	417	Cga/Tga	12/13	0.121266034753738	0	FACETS	0.72	0.671	0.77			1	INDETERMINATE	2	TRUE	0	0.35	0		502	477	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022979	31022979	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	144	520	0	ENST00000375687.4:c.2464A>G	p.Thr822Ala	p.T822A	ENST00000375687	NM_015338.5	822	Aca/Gca	13/13	0.121266034753738	0	FACETS	0.76	0.702	0.818			1	INDETERMINATE	2	TRUE	0	0.35	0		520	352	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385071	31385071	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	275	789	0	ENST00000328111.2:c.1456G>T	p.Glu486Ter	p.E486*	ENST00000328111	NM_006892.3	486	Gag/Tag	14/23	0.121266034753738	0	FACETS	0.758	0.716	0.8			1	INDETERMINATE	2	TRUE	0	0.35	0		789	674	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031588	36031588	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	35	687	0	ENST00000358208.4:c.1417G>A	p.Glu473Lys	p.E473K	ENST00000358208		473	Gag/Aag	12/12	0.121266034753738	0	FACETS	0.196	0.16	0.237			1	INDETERMINATE	1	TRUE	0	0.35	0		687	664	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39725893	39725893	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	120	318	1	ENST00000361337.2:c.764A>T	p.Glu255Val	p.E255V	ENST00000361337	NM_003286.2	255	gAa/gTa	10/21	0.121266034753738	0	FACETS	0.841	0.774	0.909			1	INDETERMINATE	2	TRUE	0	0.35	0		319	265	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076880	41076880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	109	509	0	ENST00000373198.4:c.1540G>A	p.Gly514Arg	p.G514R	ENST00000373198	NM_133170.3	514	Ggg/Agg	9/32	0.121266034753738	0	FACETS	0.651	0.592	0.711			1	INDETERMINATE	2	TRUE	0	0.35	0		509	311	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419980	41419980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	225	584	1	ENST00000373198.4:c.341G>A	p.Arg114Lys	p.R114K	ENST00000373198	NM_133170.3	114	aGg/aAg	3/32	0.121266034753738	0	FACETS	0.778	0.731	0.825			1	INDETERMINATE	2	TRUE	0	0.35	0		585	537	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420011	41420011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773011187	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	197	567	0	ENST00000373198.4:c.310G>A	p.Asp104Asn	p.D104N	ENST00000373198	NM_133170.3	104	Gac/Aac	3/32	0.121266034753738	0	FACETS	0.742	0.694	0.791			1	INDETERMINATE	2	TRUE	0	0.35	0		567	493	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948572	54948572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373550419	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	92	386	0	ENST00000312783.6:c.746C>T	p.Ser249Leu	p.S249L	ENST00000312783	NM_198436.1	249	tCg/tTg	8/10	0.121266034753738	0	FACETS	0.756	0.685	0.829			1	INDETERMINATE	2	TRUE	0	0.35	0		386	226	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62297432	62297432	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	206	454	0	ENST00000360203.5:c.614G>T	p.Arg205Met	p.R205M	ENST00000360203	NM_001283009.1	205	aGg/aTg	7/35	0.121266034753738	0	FACETS	0.692	0.647	0.738			1	INDETERMINATE	2	TRUE	0	0.35	0		454	553	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817460	39817460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774083516	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	249	577	1	ENST00000288319.7:c.103G>A	p.Ala35Thr	p.A35T	ENST00000288319	NM_182918.3	35	Gcg/Acg	2/10	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		578	608	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537206	41537206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1246231485	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	212	512	0	ENST00000263253.7:c.2033C>T	p.Pro678Leu	p.P678L	ENST00000263253	NM_001429.3	678	cCg/cTg	10/31	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.35	2		512	527	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546002	41546002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	410	685	0	ENST00000263253.7:c.2617C>T	p.Pro873Ser	p.P873S	ENST00000263253	NM_001429.3	873	Cca/Tca	14/31	1	2	FACETS	1	0.993	1	1	0.997	1	CLONAL	2	TRUE	1	0.35	2		685	982	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556655	41556655	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	63	411	0	ENST00000263253.7:c.3600C>A	p.Phe1200Leu	p.F1200L	ENST00000263253	NM_001429.3	1200	ttC/ttA	20/31	1	2	FACETS	0.706	0.611	0.808	0.706	0.611	0.808	SUBCLONAL	1	TRUE	1	0.35	2		411	510	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191488	10191488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs5030818	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	58	430	0	ENST00000256474.2:c.481C>T	p.Arg161Ter	p.R161*	ENST00000256474	NM_000551.3	161	Cga/Tga	3/3	1	2	FACETS	0.738	0.636	0.849	0.738	0.636	0.849	SUBCLONAL	1	TRUE	1	0.35	2		430	449	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458536	12458536	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs780238349	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	32	598	1	ENST00000287820.6:c.1153C>T	p.Arg385Ter	p.R385*	ENST00000287820	NM_015869.4	385	Cga/Tga	6/7	1	2	FACETS	0.386	0.313	0.469	0.386	0.313	0.469	SUBCLONAL	1	TRUE	1	0.35	2		599	474	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12653551	12653551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140884322	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	71	453	0	ENST00000251849.4:c.218G>A	p.Arg73Gln	p.R73Q	ENST00000251849	NM_002880.3	73	cGa/cAa	3/17	1	2	FACETS	0.922	0.808	1	0.922	0.808	1	CLONAL	1	TRUE	1	0.35	2		453	440	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37058999	37058999	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs63751194	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	96	335	0	ENST00000231790.2:c.793C>T	p.Arg265Cys	p.R265C	ENST00000231790	NM_000249.3	265	Cgt/Tgt	10/19	1	2	FACETS	1	0.966	1	1	0.989	1	CLONAL	2	TRUE	1	0.35	2		335	240	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37083763	37083763	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63751081	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	76	357	1	ENST00000231790.2:c.1672G>T	p.Glu558Ter	p.E558*	ENST00000231790	NM_000249.3	558	Gaa/Taa	15/19	1	2	FACETS	1	0.957	1	1	0.986	1	CLONAL	2	TRUE	1	0.35	2		358	191	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280637	41280637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753246841	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	217	644	0	ENST00000349496.5:c.2150G>A	p.Arg717His	p.R717H	ENST00000349496	NM_001904.3	717	cGt/cAt	15/15	1	2	FACETS	1	0.975	1	1	0.995	1	CLONAL	2	TRUE	1	0.35	2		644	576	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165848	47165848	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	175	514	0	ENST00000409792.3:c.278G>T	p.Gly93Val	p.G93V	ENST00000409792	NM_014159.6	93	gGc/gTc	3/21	1	2	FACETS	1	0.984	1	1	0.994	1	CLONAL	2	TRUE	1	0.35	2		514	420	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932636	49932636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780949671	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	133	790	0	ENST00000296474.3:c.3235C>T	p.Arg1079Trp	p.R1079W	ENST00000296474	NM_002447.2	1079	Cgg/Tgg	14/20	1	2	FACETS	0.862	0.782	0.945	0.862	0.782	0.945	CLONAL	1	TRUE	1	0.35	2		790	882	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940888	49940888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774898447	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	360	875	0	ENST00000296474.3:c.155G>A	p.Gly52Glu	p.G52E	ENST00000296474	NM_002447.2	52	gGa/gAa	1/20	1	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	2	TRUE	1	0.35	2		875	914	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588797	52588797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	351	667	0	ENST00000394830.3:c.4231C>T	p.Pro1411Ser	p.P1411S	ENST00000394830	NM_018313.4	1411	Cct/Tct	27/30	1	2	FACETS	1	0.993	1	1	0.997	1	CLONAL	2	TRUE	1	0.35	2		667	811	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620556	52620556	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	51	545	0	ENST00000394830.3:c.3197C>A	p.Pro1066His	p.P1066H	ENST00000394830	NM_018313.4	1066	cCt/cAt	21/30	1	2	FACETS	0.397	0.336	0.463	0.397	0.336	0.463	SUBCLONAL	1	TRUE	1	0.35	2		545	735	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637709	52637709	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	91	382	0	ENST00000394830.3:c.2607G>T	p.Gln869His	p.Q869H	ENST00000394830	NM_018313.4	869	caG/caT	18/30	1	2	FACETS	1	0.926	1	1	0.987	1	CLONAL	2	TRUE	1	0.35	2		382	252	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259572	89259572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	30	438	0	ENST00000336596.2:c.716C>T	p.Pro239Leu	p.P239L	ENST00000336596	NM_005233.5	239	cCt/cTt	3/17	1	2	FACETS	0.591	0.478	0.719	0.591	0.478	0.719	SUBCLONAL	1	TRUE	1	0.35	2		438	290	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204752	128204752	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1265283318	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	361	890	0	ENST00000341105.2:c.689G>A	p.Arg230His	p.R230H	ENST00000341105	NM_032638.4	230	cGc/cAc	3/6	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	1	0.35	2		890	858	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851891	134851891	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs769821589	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	164	520	0	ENST00000398015.3:c.1297G>A	p.Ala433Thr	p.A433T	ENST00000398015	NM_004441.4	433	Gcc/Acc	5/16	1	2	FACETS	1	0.951	1	1	0.993	1	CLONAL	2	TRUE	1	0.35	2		520	453	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456659	138456659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777549389	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	105	427	0	ENST00000289153.2:c.691C>T	p.Arg231Cys	p.R231C	ENST00000289153	NM_006219.2	231	Cgt/Tgt	4/22	1	2	FACETS	1	0.944	1	1	0.989	1	CLONAL	2	TRUE	1	0.35	2		427	285	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231125	142231125	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	165	489	0	ENST00000350721.4:c.4829A>G	p.Asn1610Ser	p.N1610S	ENST00000350721	NM_001184.3	1610	aAc/aGc	27/47	1	2	FACETS	0.834	0.776	0.892	1	0.994	1	CLONAL	3	TRUE	1	0.35	2		489	377	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278281	142278281	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs746970647	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	44	409	0	ENST00000350721.4:c.1544G>A	p.Arg515His	p.R515H	ENST00000350721	NM_001184.3	515	cGt/cAt	7/47	1	2	FACETS	0.722	0.608	0.848	0.722	0.608	0.848	SUBCLONAL	1	TRUE	1	0.35	2		409	348	SUCCESS
ATR	545	MSKCC	GRCh37	3	142284961	142284961	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	113	403	0	ENST00000350721.4:c.292+2T>C		p.X98_splice	ENST00000350721	NM_001184.3	98			1	2	FACETS	1	0.977	1	1	0.991	1	CLONAL	2	TRUE	1	0.35	2		403	270	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149375015	149375015	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	480	841	2	ENST00000360632.3:c.79G>A	p.Asp27Asn	p.D27N	ENST00000360632	NM_015472.4	27	Gac/Aac	2/7	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	1	0.35	2		843	1204	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927427	178927427	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	100	354	0	ENST00000263967.3:c.1190C>A	p.Pro397His	p.P397H	ENST00000263967	NM_006218.2	397	cCt/cAt	7/21	1	2	FACETS	0.985	0.892	1	1	0.988	1	CLONAL	2	TRUE	1	0.35	2		354	290	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	83	373	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	0.996	0.894	1	1	0.986	1	CLONAL	2	TRUE	1	0.35	2		373	238	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183540	185183540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	19	310	1	ENST00000265026.3:c.1394C>T	p.Ala465Val	p.A465V	ENST00000265026	NM_004721.4	465	gCg/gTg	9/14	1	2	FACETS	0.374	0.284	0.481	0.374	0.284	0.481	SUBCLONAL	1	TRUE	1	0.35	2		311	290	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442768	187442768	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	235	521	0	ENST00000232014.4:c.1938G>T	p.Lys646Asn	p.K646N	ENST00000232014	NM_001130845.1	646	aaG/aaT	9/10	1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	1	0.35	2		521	572	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586383	189586383	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	177	379	1	ENST00000264731.3:c.1007G>A	p.Gly336Asp	p.G336D	ENST00000264731	NM_003722.4	336	gGc/gAc	8/14	1	2	FACETS	1	0.966	1	1	0.993	1	CLONAL	2	TRUE	1	0.35	2		380	476	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612175	189612175	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1560311554	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	127	604	1	ENST00000264731.3:c.1927C>T	p.Arg643Ter	p.R643*	ENST00000264731	NM_003722.4	643	Cga/Tga	14/14	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.35	2		605	654	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807288	1807288	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs121913112	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	132	654	0	ENST00000260795.2:c.1537G>A	p.Asp513Asn	p.D513N	ENST00000260795		513	Gat/Aat	11/17	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.35	2		654	663	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980527	1980527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760185069	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	353	755	1	ENST00000382891.5:c.3989C>T	p.Ala1330Val	p.A1330V	ENST00000382891	NM_133335.3	1330	gCg/gTg	22/22	1	2	FACETS	1	0.99	1	1	0.997	1	CLONAL	2	TRUE	1	0.35	2		756	870	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129896	55129896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	146	560	0	ENST00000257290.5:c.430G>A	p.Asp144Asn	p.D144N	ENST00000257290	NM_006206.4	144	Gat/Aat	4/23	1	2	FACETS	1	0.948	1	1	0.992	1	CLONAL	2	TRUE	1	0.35	2		560	403	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129972	55129972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	225	552	0	ENST00000257290.5:c.506C>T	p.Pro169Leu	p.P169L	ENST00000257290	NM_006206.4	169	cCt/cTt	4/23	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	1	0.35	2		552	533	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564576	55564576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367719489	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	209	555	0	ENST00000288135.5:c.464C>T	p.Pro155Leu	p.P155L	ENST00000288135	NM_000222.2	155	cCt/cTt	3/21	1	2	FACETS	1	0.951	1	1	0.994	1	CLONAL	2	TRUE	1	0.35	2		555	585	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589791	55589791	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	112	409	0	ENST00000288135.5:c.1273A>G	p.Met425Val	p.M425V	ENST00000288135	NM_000222.2	425	Atg/Gtg	8/21	1	2	FACETS	0.925	0.841	1	1	0.989	1	CLONAL	2	TRUE	1	0.35	2		409	346	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984846	55984846	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371800274	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	204	549	2	ENST00000263923.4:c.283G>A	p.Gly95Arg	p.G95R	ENST00000263923	NM_002253.2	95	Gga/Aga	3/30	1	2	FACETS	1	0.975	1	1	0.994	1	CLONAL	2	TRUE	1	0.35	2		551	536	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233128	66233128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	107	452	0	ENST00000273854.3:c.1871G>A	p.Ser624Asn	p.S624N	ENST00000273854	NM_004439.5	624	aGc/aAc	10/18	1	2	FACETS	1	0.95	1	1	0.99	1	CLONAL	2	TRUE	1	0.35	2		452	287	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467556	66467556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147719164	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	44	329	0	ENST00000273854.3:c.713G>A	p.Arg238Gln	p.R238Q	ENST00000273854	NM_004439.5	238	cGa/cAa	3/18	1	2	FACETS	0.99	0.837	1	0.99	0.837	1	CLONAL	1	TRUE	1	0.35	2		329	254	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535423	66535423	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	127	279	0	ENST00000273854.3:c.38G>A	p.Arg13Gln	p.R13Q	ENST00000273854	NM_004439.5	13	cGg/cAg	1/18	1	2	FACETS	0.945	0.874	1	1	0.993	1	CLONAL	3	TRUE	1	0.35	2		279	256	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84393410	84393410	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	41	279	0	ENST00000321945.7:c.247C>T	p.Gln83Ter	p.Q83*	ENST00000321945	NM_139076.2	83	Caa/Taa	4/9	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.35	2		279	168	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808246	99808246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776434815	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	60	485	0	ENST00000280892.6:c.443G>A	p.Arg148His	p.R148H	ENST00000280892	NM_001130678.1	148	cGc/cAc	5/7	1	2	FACETS	0.96	0.832	1	0.96	0.832	1	CLONAL	1	TRUE	1	0.35	2		485	357	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197260	106197260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	131	317	0	ENST00000380013.4:c.5593G>A	p.Ala1865Thr	p.A1865T	ENST00000380013	NM_001127208.2	1865	Gct/Act	11/11	1	2	FACETS	1	0.974	1	1	0.992	1	CLONAL	2	TRUE	1	0.35	2		317	329	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247384	153247384	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	89	216	0	ENST00000281708.4:c.1419-1G>T		p.X473_splice	ENST00000281708	NM_033632.3	473			1	2	FACETS	1	0.971	1	1	0.989	1	CLONAL	2	TRUE	1	0.35	2		216	212	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524835	187524835	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	218	615	1	ENST00000441802.2:c.10845C>A	p.Ser3615Arg	p.S3615R	ENST00000441802	NM_005245.3	3615	agC/agA	19/27	1	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	2	TRUE	1	0.35	2		616	537	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532921	187532921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	36	232	0	ENST00000441802.2:c.9472C>T	p.Arg3158Trp	p.R3158W	ENST00000441802	NM_005245.3	3158	Cgg/Tgg	14/27	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.35	2		232	167	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628655	187628655	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	167	631	0	ENST00000441802.2:c.2327T>G	p.Ile776Ser	p.I776S	ENST00000441802	NM_005245.3	776	aTt/aGt	2/27	1	2	FACETS	1	0.963	1	1	0.993	1	CLONAL	2	TRUE	1	0.35	2		631	451	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630017	187630017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1350772893	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	27	591	0	ENST00000441802.2:c.965G>A	p.Gly322Asp	p.G322D	ENST00000441802	NM_005245.3	322	gGc/gAc	2/27	1	2	FACETS	0.327	0.259	0.404	0.327	0.259	0.404	SUBCLONAL	1	TRUE	1	0.35	2		591	472	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228415	228415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745309710	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	93	407	1	ENST00000264932.6:c.737G>A	p.Arg246His	p.R246H	ENST00000264932	NM_004168.2	246	cGc/cAc	6/15	0.121266034753738	0	FACETS	1	0.939	1			1	INDETERMINATE	1	TRUE	0	0.35	0		408	325	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233612	233612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	131	298	0	ENST00000264932.6:c.916C>T	p.Leu306Phe	p.L306F	ENST00000264932	NM_004168.2	306	Ctc/Ttc	8/15	0.121266034753738	0	FACETS	0.947	0.878	1			1	INDETERMINATE	2	TRUE	0	0.35	0		298	257	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282710	1282710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	242	624	0	ENST00000310581.5:c.1603C>T	p.Arg535Cys	p.R535C	ENST00000310581	NM_198253.2	535	Cgt/Tgt	3/16	0.121266034753738	0	FACETS	0.788	0.743	0.834			1	INDETERMINATE	2	TRUE	0	0.35	0		624	570	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293547	1293547	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	128	953	2	ENST00000310581.5:c.1454G>A	p.Arg485His	p.R485H	ENST00000310581	NM_198253.2	485	cGc/cAc	2/16	0.121266034753738	0	FACETS	0.7	0.636	0.768			1	INDETERMINATE	1	TRUE	0	0.35	0		955	679	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294069	1294069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs974018889	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	136	946	0	ENST00000310581.5:c.932C>T	p.Ser311Leu	p.S311L	ENST00000310581	NM_198253.2	311	tCg/tTg	2/16	0.121266034753738	0	FACETS	0.731	0.666	0.799			1	INDETERMINATE	1	TRUE	0	0.35	0		946	691	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410988	31410988	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1295265844	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	213	572	1	ENST00000344624.3:c.3532C>T	p.Arg1178Ter	p.R1178*	ENST00000344624		1178	Cga/Tga	28/33	0.121266034753738	0	FACETS	0.771	0.723	0.819			1	INDETERMINATE	2	TRUE	0	0.35	0		573	513	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752780	57752780	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	55	262	0	ENST00000274289.3:c.1148A>G	p.Asp383Gly	p.D383G	ENST00000274289	NM_006622.3	383	gAc/gGc	8/14	1	2	FACETS	0.845	0.735	0.961	1	0.975	1	CLONAL	2	TRUE	1	0.35	2		262	186	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591249	67591249	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	132	414	0	ENST00000274335.5:c.1747T>C	p.Trp583Arg	p.W583R	ENST00000274335		583	Tgg/Cgg	13/15	1	2	FACETS	1	0.972	1	1	0.992	1	CLONAL	2	TRUE	1	0.35	2		414	335	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80074556	80074556	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199791286	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	128	393	0	ENST00000265081.6:c.2336G>A	p.Arg779His	p.R779H	ENST00000265081	NM_002439.4	779	cGc/cAc	17/24	1	2	FACETS	1	0.967	1	1	0.991	1	CLONAL	2	TRUE	1	0.35	2		393	332	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629147	86629147	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	53	293	1	ENST00000274376.6:c.892G>T	p.Glu298Ter	p.E298*	ENST00000274376	NM_002890.2	298	Gaa/Taa	4/25	1	2	FACETS	0.814	0.706	0.929	1	0.972	1	CLONAL	2	TRUE	1	0.35	2		294	186	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672842	86672842	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	56	267	0	ENST00000274376.6:c.2329G>T	p.Glu777Ter	p.E777*	ENST00000274376	NM_002890.2	777	Gaa/Taa	17/25	1	2	FACETS	0.889	0.775	1	1	0.977	1	CLONAL	2	TRUE	1	0.35	2		267	180	SUCCESS
APC	324	MSKCC	GRCh37	5	112137021	112137021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762117133	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	140	376	1	ENST00000257430.4:c.775C>T	p.Arg259Trp	p.R259W	ENST00000257430	NM_000038.5	259	Cgg/Tgg	8/16	1	2	FACETS	1	0.973	1	1	0.992	1	CLONAL	2	TRUE	1	0.35	2		377	357	SUCCESS
APC	324	MSKCC	GRCh37	5	112154771	112154771	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1314843920	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	166	474	1	ENST00000257430.4:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000257430	NM_000038.5	348	Cga/Tga	10/16	1	2	FACETS	1	0.983	1	1	0.994	1	CLONAL	2	TRUE	1	0.35	2		475	398	SUCCESS
APC	324	MSKCC	GRCh37	5	112175364	112175364	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881249	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	96	246	0	ENST00000257430.4:c.4073C>T	p.Ala1358Val	p.A1358V	ENST00000257430	NM_000038.5	1358	gCg/gTg	16/16	1	2	FACETS	0.847	0.771	0.923	1	0.99	1	CLONAL	3	TRUE	1	0.35	2		246	216	SUCCESS
APC	324	MSKCC	GRCh37	5	112177049	112177049	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	105	341	0	ENST00000257430.4:c.5758C>T	p.Arg1920Ter	p.R1920*	ENST00000257430	NM_000038.5	1920	Cga/Tga	16/16	1	2	FACETS	1	0.965	1	1	0.99	1	CLONAL	2	TRUE	1	0.35	2		341	267	SUCCESS
APC	324	MSKCC	GRCh37	5	112179692	112179692	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242407699	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	131	271	0	ENST00000257430.4:c.8401C>T	p.Arg2801Trp	p.R2801W	ENST00000257430	NM_000038.5	2801	Cgg/Tgg	16/16	1	2	FACETS	1	0.976	1	1	0.992	1	CLONAL	2	TRUE	1	0.35	2		271	324	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977965	131977965	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	126	394	0	ENST00000265335.6:c.3848T>C	p.Val1283Ala	p.V1283A	ENST00000265335		1283	gTg/gCg	25/25	0.121266034753738	0	FACETS	0.77	0.708	0.832			1	INDETERMINATE	2	TRUE	0	0.35	0		394	304	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512376	149512376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746410632	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	339	753	0	ENST00000261799.4:c.1064G>A	p.Arg355His	p.R355H	ENST00000261799	NM_002609.3	355	cGc/cAc	7/23	0.121266034753738	0	FACETS	0.764	0.726	0.802			1	INDETERMINATE	2	TRUE	0	0.35	0		753	824	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513226	149513226	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749560540	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	236	704	0	ENST00000261799.4:c.857C>T	p.Ser286Leu	p.S286L	ENST00000261799	NM_002609.3	286	tCg/tTg	6/23	0.121266034753738	0	FACETS	0.723	0.68	0.767			1	INDETERMINATE	2	TRUE	0	0.35	0		704	606	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514381	149514381	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	216	571	0	ENST00000261799.4:c.563A>G	p.Tyr188Cys	p.Y188C	ENST00000261799	NM_002609.3	188	tAc/tGc	4/23	0.121266034753738	0	FACETS	0.807	0.758	0.856			1	INDETERMINATE	2	TRUE	0	0.35	0		571	497	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722233	176722233	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	70	493	0	ENST00000439151.2:c.7864C>T	p.Gln2622Ter	p.Q2622*	ENST00000439151	NM_022455.4	2622	Caa/Taa	23/23	0.121266034753738	0	FACETS	0.559	0.489	0.635			1	INDETERMINATE	1	TRUE	0	0.35	0		493	465	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038389	180038389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774642243	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	207	854	2	ENST00000261937.6:c.3628G>A	p.Ala1210Thr	p.A1210T	ENST00000261937	NM_182925.4	1210	Gcc/Acc	27/30	0.121266034753738	0	FACETS	0.63	0.588	0.673			1	INDETERMINATE	2	TRUE	0	0.35	0		856	610	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053006	180053006	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	243	925	0	ENST00000261937.6:c.1284G>T	p.Glu428Asp	p.E428D	ENST00000261937	NM_182925.4	428	gaG/gaT	10/30	0.121266034753738	0	FACETS	0.723	0.68	0.767			1	INDETERMINATE	2	TRUE	0	0.35	0		925	624	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056073	26056073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746063918	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	270	435	0	ENST00000343677.2:c.584C>T	p.Pro195Leu	p.P195L	ENST00000343677	NM_005319.3	195	cCc/cTc	1/1	0.497130804546415	4	FACETS	0.934	0.881	0.989	1	0.993	1	CLONAL	3	TRUE	2	0.35	4		435	743	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911221	29911221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	59	239	0	ENST00000376809.5:c.520G>A	p.Ala174Thr	p.A174T	ENST00000376809	NM_002116.7	174	Gcc/Acc	3/8	1	2	FACETS	0.81	0.708	0.919	1	0.975	1	CLONAL	2	TRUE	1	0.35	2		239	208	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671961	30671961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	57	695	0	ENST00000376406.3:c.4999G>A	p.Asp1667Asn	p.D1667N	ENST00000376406	NM_014641.2	1667	Gac/Aac	10/15	0.273655677041051	4	FACETS	0.523	0.447	0.606	0.261	0.223	0.303	SUBCLONAL	1	TRUE	2	0.35	4		695	841	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680406	30680406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764942978	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	244	583	0	ENST00000376406.3:c.1313G>A	p.Arg438His	p.R438H	ENST00000376406	NM_014641.2	438	cGt/cAt	5/15	0.273655677041051	4	FACETS	0.994	0.936	1	1	0.993	1	CLONAL	3	TRUE	2	0.35	4		583	631	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31947213	31947213	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs570620120	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	290	563	0	ENST00000375333.2:c.698G>A	p.Arg233Gln	p.R233Q	ENST00000375333	NM_032454.1	233	cGa/cAa	5/8	0.273655677041051	4	FACETS	0.961	0.908	1	1	0.994	1	CLONAL	3	TRUE	2	0.35	4		563	776	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164776	32164776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	60	687	0	ENST00000375023.3:c.5126C>T	p.Ala1709Val	p.A1709V	ENST00000375023	NM_004557.3	1709	gCc/gTc	28/30	0.273655677041051	4	FACETS	0.46	0.395	0.532	0.23	0.197	0.266	SUBCLONAL	1	TRUE	2	0.35	4		687	1006	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800429	32800429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750440758	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	439	758	1	ENST00000374899.4:c.1118G>A	p.Arg373His	p.R373H	ENST00000374899	NM_018833.2	373	cGc/cAc	6/12	0.273655677041051	4	FACETS	1	0.964	1	1	0.996	1	CLONAL	3	TRUE	2	0.35	4		759	1118	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138560	37138560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	244	489	0	ENST00000373509.5:c.94G>A	p.Glu32Lys	p.E32K	ENST00000373509	NM_002648.3	32	Gag/Aag	2/6	1	2	FACETS	1	0.971	1	1	0.995	1	CLONAL	2	TRUE	1	0.35	2		489	662	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138197221	138197221	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	139	407	0	ENST00000237289.4:c.723G>T	p.Gln241His	p.Q241H	ENST00000237289	NM_001270507.1	241	caG/caT	5/9	1	2	FACETS	1	0.956	1	1	0.992	1	CLONAL	2	TRUE	1	0.35	2		407	376	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001092	150001092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755260603	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	26	420	2	ENST00000253339.5:c.2512C>T	p.Arg838Cys	p.R838C	ENST00000253339		838	Cgt/Tgt	4/7	1	2	FACETS	0.55	0.437	0.679	0.55	0.437	0.679	SUBCLONAL	1	TRUE	1	0.35	2		422	270	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265353	152265353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188957694	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	218	461	0	ENST00000206249.3:c.806G>A	p.Arg269His	p.R269H	ENST00000206249	NM_000125.3	269	cGc/cAc	4/8	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	1	0.35	2		461	516	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100021	157100021	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs201842850	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	18	39	0	ENST00000346085.5:c.958A>G	p.Ser320Gly	p.S320G	ENST00000346085	NM_020732.3	320	Agc/Ggc	1/20	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.35	2		39	75	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157192780	157192780	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	156	456	0	ENST00000346085.5:c.1770C>A	p.Phe590Leu	p.F590L	ENST00000346085	NM_020732.3	590	ttC/ttA	3/20	1	2	FACETS	1	0.974	1	1	0.993	1	CLONAL	2	TRUE	1	0.35	2		456	400	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222613	157222613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1296046545	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	304	636	0	ENST00000346085.5:c.1880C>T	p.Ala627Val	p.A627V	ENST00000346085	NM_020732.3	627	gCg/gTg	4/20	1	2	FACETS	1	0.984	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		636	792	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522169	157522169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1368764248	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	79	661	0	ENST00000346085.5:c.4441C>T	p.Pro1481Ser	p.P1481S	ENST00000346085	NM_020732.3	1481	Cct/Tct	18/20	1	2	FACETS	0.821	0.723	0.925	0.821	0.723	0.925	CLONAL	1	TRUE	1	0.35	2		661	550	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522455	157522455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1455506883	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	288	664	0	ENST00000346085.5:c.4727C>T	p.Pro1576Leu	p.P1576L	ENST00000346085	NM_020732.3	1576	cCg/cTg	18/20	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		664	689	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528132	157528132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1562353202	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	204	570	0	ENST00000346085.5:c.5857C>T	p.Arg1953Cys	p.R1953C	ENST00000346085	NM_020732.3	1953	Cgt/Tgt	20/20	1	2	FACETS	1	0.978	1	1	0.994	1	CLONAL	2	TRUE	1	0.35	2		570	530	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528682	157528682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	212	546	1	ENST00000346085.5:c.6407C>T	p.Ser2136Leu	p.S2136L	ENST00000346085	NM_020732.3	2136	tCg/tTg	20/20	1	2	FACETS	1	0.981	1	1	0.995	1	CLONAL	2	TRUE	1	0.35	2		547	541	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968242	2968242	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	265	833	0	ENST00000396946.4:c.1744C>T	p.Pro582Ser	p.P582S	ENST00000396946	NM_032415.4	582	Ccc/Tcc	13/25	0.121266034753738	0	FACETS	0.755	0.713	0.798			1	INDETERMINATE	2	TRUE	0	0.35	0		833	652	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2969629	2969629	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	193	641	0	ENST00000396946.4:c.1650G>T	p.Lys550Asn	p.K550N	ENST00000396946	NM_032415.4	550	aaG/aaT	12/25	0.121266034753738	0	FACETS	0.731	0.683	0.781			1	INDETERMINATE	2	TRUE	0	0.35	0		641	490	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971232	13971232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758005694	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	192	534	0	ENST00000405192.2:c.697G>A	p.Asp233Asn	p.D233N	ENST00000405192	NM_001163147.1	233	Gac/Aac	8/12	0.121266034753738	0	FACETS	0.729	0.681	0.778			1	INDETERMINATE	2	TRUE	0	0.35	0		534	489	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210105	55210105	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	122	466	1	ENST00000275493.2:c.215G>T	p.Arg72Met	p.R72M	ENST00000275493	NM_005228.3	72	aGg/aTg	2/28	0.121266034753738	0	FACETS	0.743	0.682	0.805			1	INDETERMINATE	2	TRUE	0	0.35	0		467	305	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374362	81374362	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1224184344	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	119	391	0	ENST00000222390.5:c.700C>T	p.Arg234Cys	p.R234C	ENST00000222390	NM_000601.4	234	Cgc/Tgc	6/18	1	2	FACETS	1	0.931	1	1	0.99	1	CLONAL	2	TRUE	1	0.35	2		391	333	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509723	106509723	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	161	469	0	ENST00000359195.3:c.1717G>T	p.Glu573Ter	p.E573*	ENST00000359195	NM_002649.2	573	Gaa/Taa	2/11	1	2	FACETS	1	0.976	1	1	0.993	1	CLONAL	2	TRUE	1	0.35	2		469	411	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476821	140476821	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	144	467	0	ENST00000288602.6:c.1585A>G	p.Thr529Ala	p.T529A	ENST00000288602	NM_004333.4	529	Acc/Gcc	13/18	1	2	FACETS	1	0.981	1	1	0.993	1	CLONAL	2	TRUE	1	0.35	2		467	347	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140507829	140507829	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	113	398	0	ENST00000288602.6:c.642T>G	p.Ile214Met	p.I214M	ENST00000288602	NM_004333.4	214	atT/atG	5/18	1	2	FACETS	1	0.962	1	1	0.99	1	CLONAL	2	TRUE	1	0.35	2		398	294	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523690	148523690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	96	281	0	ENST00000320356.2:c.763G>A	p.Ala255Thr	p.A255T	ENST00000320356	NM_004456.4	255	Gca/Aca	8/20	1	2	FACETS	1	0.968	1	1	0.989	1	CLONAL	2	TRUE	1	0.35	2		281	237	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859281	151859281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	125	326	0	ENST00000262189.6:c.11381C>T	p.Pro3794Leu	p.P3794L	ENST00000262189	NM_170606.2	3794	cCt/cTt	43/59	1	2	FACETS	1	0.98	1	1	0.992	1	CLONAL	2	TRUE	1	0.35	2		326	294	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859551	151859551	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1331420366	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	22	484	0	ENST00000262189.6:c.11111T>C	p.Val3704Ala	p.V3704A	ENST00000262189	NM_170606.2	3704	gTa/gCa	43/59	1	2	FACETS	0.297	0.23	0.376	0.297	0.23	0.376	SUBCLONAL	1	TRUE	1	0.35	2		484	423	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945601	151945601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770827883	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	86	336	1	ENST00000262189.6:c.1918G>A	p.Glu640Lys	p.E640K	ENST00000262189	NM_170606.2	640	Gaa/Aaa	14/59	0.3	1	FACETS	0.848	0.763	0.936	1	0.984	1	CLONAL	2	TRUE	0	0.35	1		337	239	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38184304	38184304	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	166	511	0	ENST00000317025.8:c.1652G>T	p.Arg551Ile	p.R551I	ENST00000317025	NM_023034.1	551	aGa/aTa	7/24	1	2	FACETS	1	0.985	1	1	0.994	1	CLONAL	2	TRUE	1	0.35	2		511	391	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189055	38189055	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1250796714	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	167	558	0	ENST00000317025.8:c.959C>T	p.Ala320Val	p.A320V	ENST00000317025	NM_023034.1	320	gCg/gTg	5/24	1	2	FACETS	1	0.973	1	1	0.993	1	CLONAL	2	TRUE	1	0.35	2		558	435	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279324	38279324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774768179	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	245	682	1	ENST00000425967.3:c.1165G>A	p.Val389Ile	p.V389I	ENST00000425967	NM_001174067.1	389	Gtt/Att	9/19	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	1	0.35	2		683	591	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372324	55372324	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	64	730	0	ENST00000297316.4:c.1014G>T	p.Glu338Asp	p.E338D	ENST00000297316	NM_022454.3	338	gaG/gaT	2/2	1	2	FACETS	0.334	0.288	0.385	0.334	0.288	0.385	SUBCLONAL	1	TRUE	1	0.35	2		730	1094	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56911011	56911011	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	205	600	0	ENST00000519728.1:c.1157T>C	p.Phe386Ser	p.F386S	ENST00000519728	NM_002350.3	386	tTt/tCt	11/13	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.35	2		600	506	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046462	69046462	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761455338	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	222	549	1	ENST00000288368.4:c.3935C>T	p.Ala1312Val	p.A1312V	ENST00000288368	NM_024870.2	1312	gCg/gTg	32/40	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.35	2		550	557	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982014	70982014	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1224885523	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	55	900	0	ENST00000276594.2:c.82G>A	p.Ala28Thr	p.A28T	ENST00000276594	NM_024504.3	28	Gcg/Acg	2/8	1	2	FACETS	0.406	0.346	0.472	0.406	0.346	0.472	SUBCLONAL	1	TRUE	1	0.35	2		900	774	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955499	90955499	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	37	421	0	ENST00000265433.3:c.2166G>A	p.Trp722Ter	p.W722*	ENST00000265433	NM_002485.4	722	tgG/tgA	14/16	1	2	FACETS	0.604	0.499	0.721	0.604	0.499	0.721	SUBCLONAL	1	TRUE	1	0.35	2		421	350	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866533	117866533	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	145	445	0	ENST00000297338.2:c.1112A>G	p.Lys371Arg	p.K371R	ENST00000297338	NM_006265.2	371	aAa/aGa	9/14	1	2	FACETS	1	0.982	1	1	0.993	1	CLONAL	2	TRUE	1	0.35	2		445	345	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542145	141542145	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	36	500	0	ENST00000220592.5:c.2578T>C	p.Ter860ArgextTer29	p.*860Rext*29	ENST00000220592	NM_012154.3	860	Tga/Cga	19/19	1	2	FACETS	0.346	0.283	0.416	0.346	0.283	0.416	SUBCLONAL	1	TRUE	1	0.35	2		500	595	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145736880	145736880	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	426	784	1	ENST00000428558.2:c.3561C>A	p.Tyr1187Ter	p.Y1187*	ENST00000428558	NM_004260.3	1187	taC/taA	22/22	1	2	FACETS	1	0.993	1	1	0.997	1	CLONAL	2	TRUE	1	0.35	2		785	1011	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486265	8486265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143196383	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	111	354	0	ENST00000356435.5:c.2552G>A	p.Gly851Glu	p.G851E	ENST00000356435		851	gGa/gAa	17/35	1	2	FACETS	1	0.967	1	1	0.99	1	CLONAL	2	TRUE	1	0.35	2		354	282	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492874	8492874	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	259	506	0	ENST00000356435.5:c.2455A>G	p.Thr819Ala	p.T819A	ENST00000356435		819	Acc/Gcc	16/35	1	2	FACETS	0.848	0.801	0.894	1	0.996	1	CLONAL	3	TRUE	1	0.35	2		506	582	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006063	22006063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	290	602	0	ENST00000276925.6:c.340C>T	p.Arg114Cys	p.R114C	ENST00000276925	NM_004936.3	114	Cgt/Tgt	2/2	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		602	709	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87366973	87366973	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	159	551	0	ENST00000277120.3:c.1369G>A	p.Ala457Thr	p.A457T	ENST00000277120		457	Gca/Aca	12/19	1	2	FACETS	1	0.976	1	1	0.993	1	CLONAL	2	TRUE	1	0.35	2		551	404	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606314	93606314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs16906862	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	253	764	1	ENST00000375746.1:c.134G>A	p.Arg45His	p.R45H	ENST00000375746	NM_001174167.1	45	cGc/cAc	2/14	1	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	2	TRUE	1	0.35	2		765	636	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209597	98209597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1400282737	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	229	690	0	ENST00000331920.6:c.3941C>T	p.Pro1314Leu	p.P1314L	ENST00000331920	NM_000264.3	1314	cCc/cTc	23/24	1	2	FACETS	0.918	0.866	0.97	1	0.996	1	CLONAL	3	TRUE	1	0.35	2		690	475	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101895004	101895004	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144313652	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	51	249	0	ENST00000374994.4:c.557C>T	p.Thr186Met	p.T186M	ENST00000374994	NM_004612.2	186	aCg/aTg	3/9	1	2	FACETS	1	0.945	1	1	0.98	1	CLONAL	2	TRUE	1	0.35	2		249	126	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128419998	128419998	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749947914	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	182	611	0	ENST00000265960.3:c.430G>A	p.Val144Ile	p.V144I	ENST00000265960	NM_001006617.1	144	Gta/Ata	4/12	1	2	FACETS	1	0.973	1	1	0.994	1	CLONAL	2	TRUE	1	0.35	2		611	479	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760019	133760019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753588128	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	287	759	0	ENST00000318560.5:c.2342C>T	p.Thr781Met	p.T781M	ENST00000318560	NM_005157.4	781	aCg/aTg	11/11	1	2	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	TRUE	1	0.35	2		759	680	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760486	133760486	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	41	755	1	ENST00000318560.5:c.2809C>A	p.Leu937Met	p.L937M	ENST00000318560	NM_005157.4	937	Ctg/Atg	11/11	1	2	FACETS	0.33	0.274	0.393	0.33	0.274	0.393	SUBCLONAL	1	TRUE	1	0.35	2		756	709	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133761054	133761054	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	234	734	0	ENST00000318560.5:c.3377A>G	p.Asp1126Gly	p.D1126G	ENST00000318560	NM_005157.4	1126	gAc/gGc	11/11	1	2	FACETS	1	0.979	1	1	0.995	1	CLONAL	2	TRUE	1	0.35	2		734	613	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779093	135779093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060503207	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	228	559	1	ENST00000298552.3:c.2153G>A	p.Arg718Gln	p.R718Q	ENST00000298552	NM_001162426.1	718	cGg/cAg	17/23	1	2	FACETS	1	0.98	1	1	0.995	1	CLONAL	2	TRUE	1	0.35	2		560	592	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300836	137300836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	45	848	2	ENST00000481739.1:c.481C>T	p.Arg161Trp	p.R161W	ENST00000481739	NM_002957.4	161	Cgg/Tgg	4/10	1	2	FACETS	0.34	0.284	0.401	0.34	0.284	0.401	SUBCLONAL	1	TRUE	1	0.35	2		850	757	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393674	139393674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1371022203	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	357	854	0	ENST00000277541.6:c.5972G>A	p.Arg1991His	p.R1991H	ENST00000277541	NM_017617.3	1991	cGc/cAc	32/34	1	2	FACETS	1	0.991	1	1	0.997	1	CLONAL	2	TRUE	1	0.35	2		854	877	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399240	139399240	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs911387577	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	423	769	0	ENST00000277541.6:c.4903G>A	p.Ala1635Thr	p.A1635T	ENST00000277541	NM_017617.3	1635	Gcc/Acc	26/34	1	2	FACETS	1	0.994	1	1	0.997	1	CLONAL	2	TRUE	1	0.35	2		769	985	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411802	139411802	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554729862	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	418	829	2	ENST00000277541.6:c.1477G>A	p.Glu493Lys	p.E493K	ENST00000277541	NM_017617.3	493	Gag/Aag	9/34	1	2	FACETS	1	0.993	1	1	0.997	1	CLONAL	2	TRUE	1	0.35	2		831	1003	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15827389	15827389	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	117	418	2	ENST00000307771.7:c.505C>T	p.Arg169Ter	p.R169*	ENST00000307771	NM_005089.3	169	Cga/Tga	7/11	0.231957665260561	0	FACETS	0.909	0.838	0.98			1	CLONAL	2	TRUE	0	0.35	0		420	239	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921622	39921622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761673955	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	234	472	1	ENST00000378444.4:c.4198C>T	p.Arg1400Trp	p.R1400W	ENST00000378444	NM_001123385.1	1400	Cgg/Tgg	10/15	0.231957665260561	0	FACETS	0.935	0.883	0.986			1	CLONAL	2	TRUE	0	0.35	0		473	465	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933013	39933013	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	164	836	0	ENST00000378444.4:c.1586del	p.Asn529ThrfsTer60	p.N529Tfs*60	ENST00000378444	NM_001123385.1	529	aAc/ac	4/15	0.231957665260561	0	FACETS	1	0.976	1			1	CLONAL	1	TRUE	0	0.35	0		836	536	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933427	39933427	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1480861473	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	171	821	0	ENST00000378444.4:c.1172G>A	p.Gly391Asp	p.G391D	ENST00000378444	NM_001123385.1	391	gGc/gAc	4/15	0.231957665260561	0	FACETS	1	0.98	1			1	CLONAL	1	TRUE	0	0.35	0		821	542	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426704	47426704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161562116	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	170	800	0	ENST00000377045.4:c.949G>A	p.Gly317Arg	p.G317R	ENST00000377045	NM_001654.4	317	Ggg/Agg	10/16	0.231957665260561	0	FACETS	1	0.931	1			1	CLONAL	1	TRUE	0	0.35	0		800	626	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650778	48650778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104894809	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	156	772	0	ENST00000376670.3:c.647G>A	p.Arg216Gln	p.R216Q	ENST00000376670	NM_002049.3	216	cGg/cAg	4/6	0.231957665260561	0	FACETS	0.979	0.9	1			1	CLONAL	1	TRUE	0	0.35	0		772	592	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245129	53245129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	217	647	0	ENST00000375401.3:c.811G>A	p.Val271Ile	p.V271I	ENST00000375401	NM_004187.3	271	Gta/Ata	7/26	0.231957665260561	0	FACETS	0.906	0.853	0.958			1	CLONAL	2	TRUE	0	0.35	0		647	445	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412095	63412095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852217	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	239	795	0	ENST00000330258.3:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000330258	NM_152424.3	358	Cga/Tga	2/2	0.231957665260561	0	FACETS	0.681	0.639	0.723			1	SUBCLONAL	2	TRUE	0	0.35	0		795	652	SUCCESS
AR	367	MSKCC	GRCh37	X	66766279	66766279	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1474848506	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	105	343	2	ENST00000374690.3:c.1291G>A	p.Ala431Thr	p.A431T	ENST00000374690	NM_000044.3	431	Gct/Act	1/8	0.231957665260561	0	FACETS	1	0.955	1			1	CLONAL	1	TRUE	0	0.35	0		345	356	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340952	70340952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	317	670	0	ENST00000374080.3:c.685G>A	p.Ala229Thr	p.A229T	ENST00000374080		229	Gca/Aca	5/45	0.231957665260561	0	FACETS	0.983	0.938	1			1	CLONAL	2	TRUE	0	0.35	0		670	599	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197886	123197886	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	11	327	0	ENST00000218089.9:c.2010A>C	p.Glu670Asp	p.E670D	ENST00000218089	NM_001042749.1	670	gaA/gaC	20/35	0.231957665260561	0	FACETS	0.223	0.154	0.309			1	SUBCLONAL	1	TRUE	0	0.35	0		327	183	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220572	123220572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	178	473	0	ENST00000218089.9:c.3229C>T	p.Pro1077Ser	p.P1077S	ENST00000218089	NM_001042749.1	1077	Cca/Tca	30/35	0.231957665260561	0	FACETS	0.913	0.855	0.971			1	CLONAL	2	TRUE	0	0.35	0		473	362	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0047902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	179	566	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.287322482181525	5	FACETS	1	0.962	1	0.706	0.654	0.76	CLONAL	2	TRUE	2	0.44905023058026	5		566	630	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0047902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	314	760	1	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.44905023058026	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.44905023058026	1		761	785	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591892	48591892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767345	NA	P-0047902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	186	385	0	ENST00000342988.3:c.1055G>A	p.Gly352Glu	p.G352E	ENST00000342988	NM_005359.5	352	gGa/gAa	9/12	0.44905023058026	2	FACETS	0.92	0.86	0.982	0.92	0.86	0.982	CLONAL	2	TRUE	0	0.44905023058026	2		385	450	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579439	7579439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201717599	NA	P-0047902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	44	616	0	ENST00000269305.4:c.248C>T	p.Ala83Val	p.A83V	ENST00000269305	NM_001126112.2	83	gCg/gTg	4/11	0.44905023058026	1	FACETS	0.248	0.207	0.293	0.248	0.207	0.293	SUBCLONAL	1	TRUE	0	0.44905023058026	1		616	613	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149250	119149250	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200341293	NA	P-0047902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	300	490	1	ENST00000264033.4:c.1258C>T	p.Arg420Ter	p.R420*	ENST00000264033	NM_005188.3	420	Cga/Tga	9/16	0.44905023058026	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.44905023058026	3		491	794	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446295	29446295	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1252535185	NA	P-0047902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	133	680	0	ENST00000389048.3:c.3272A>G	p.Asp1091Gly	p.D1091G	ENST00000389048	NM_004304.4	1091	gAc/gGc	20/29	0.44905023058026	1	FACETS	0.695	0.633	0.76	0.695	0.633	0.76	SUBCLONAL	1	TRUE	0	0.44905023058026	1		680	661	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488647	212488647	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	170	283	0	ENST00000342788.4:c.2202A>T	p.Lys734Asn	p.K734N	ENST00000342788	NM_005235.2	734	aaA/aaT	18/28	0.44905023058026	3	FACETS	0.96	0.89	1	0.96	0.89	1	CLONAL	2	TRUE	1	0.44905023058026	3		283	483	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197246	26197246	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	84	372	0	ENST00000356476.2:c.233A>T	p.Asp78Val	p.D78V	ENST00000356476		78	gAc/gTc	1/1	0.151717718148964	5	FACETS	1	0.969	1	0.427	0.378	0.479	INDETERMINATE	1	TRUE	2	0.44905023058026	5		372	489	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553252	106553252	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	82	577	0	ENST00000369096.4:c.1217A>T	p.Tyr406Phe	p.Y406F	ENST00000369096	NM_001198.3	406	tAc/tTc	5/7	0.151717718148964	5	FACETS	0.817	0.72	0.921	0.272	0.24	0.307	INDETERMINATE	1	TRUE	2	0.44905023058026	5		577	748	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729696	41729696	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	257	606	0	ENST00000242208.4:c.833G>C	p.Gly278Ala	p.G278A	ENST00000242208	NM_002192.2	278	gGg/gCg	3/3	0.389580476237486	3	FACETS	0.887	0.834	0.942	0.887	0.834	0.942	CLONAL	2	TRUE	1	0.44905023058026	3		606	790	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0047903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	235	347	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.404365534282507	5	FACETS	0.898	0.846	0.949	0.898	0.846	0.949	CLONAL	4	TRUE	1	0.404365534282507	5		347	520	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024639	11024641	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	novel	NA	P-0047903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	315	581	4	ENST00000327064.4:c.763_765del	p.Ile255del	p.I255del	ENST00000327064	NM_199141.1	252	gaCATc/gac	6/16	0.39033595361438	3	FACETS	0.912	0.862	0.963	0.912	0.862	0.963	CLONAL	2	TRUE	1	0.404365534282507	3		585	1027	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0047904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	19	384	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	0.262138408855877	4	FACETS	0.764	0.596	0.95	0.764	0.596	0.95	INDETERMINATE	2	TRUE	2	0.516488398298593	4		384	73	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475550	12475550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479145908	NA	P-0047904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	82	621	1	ENST00000287820.6:c.1424C>T	p.Thr475Met	p.T475M	ENST00000287820	NM_015869.4	475	aCg/aTg	7/7	0.511636139627666	2	FACETS	0.912	0.846	0.975	1	0.985	1	CLONAL	3	TRUE	0	0.516488398298593	2		622	116	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	53	677	0	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	0.459585568762035	2	FACETS	0.924	0.817	1	0.924	0.817	1	CLONAL	2	TRUE	0	0.516488398298593	2		677	111	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370320	40370320	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs760876362	NA	P-0047904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	31	923	0	ENST00000293328.3:c.1018C>G	p.Gln340Glu	p.Q340E	ENST00000293328	NM_012448.3	340	Cag/Gag	9/19	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.516488398298593	2		923	81	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652140	3652140	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759447034	NA	P-0047904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	11	886	1	ENST00000294008.3:c.929G>A	p.Arg310Gln	p.R310Q	ENST00000294008	NM_032444.2	310	cGa/cAa	4/15	1	2	FACETS	0.333	0.231	0.458	0.333	0.231	0.458	SUBCLONAL	1	TRUE	1	0.516488398298593	2		887	128	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099173	157099173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757718031	NA	P-0047904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	58	505	0	ENST00000346085.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000346085	NM_020732.3	37	tCc/tTc	1/20	0.203077392246376	3	FACETS	0.936	0.824	1	0.624	0.549	0.701	INDETERMINATE	2	TRUE	0	0.516488398298593	3		505	151	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099179	157099179	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs995863053	NA	P-0047904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	62	527	0	ENST00000346085.5:c.116C>T	p.Ser39Phe	p.S39F	ENST00000346085	NM_020732.3	39	tCc/tTc	1/20	0.203077392246376	3	FACETS	0.921	0.814	1	0.614	0.542	0.688	INDETERMINATE	2	TRUE	0	0.516488398298593	3		527	164	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170491	108170491	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs145453814	NA	P-0047904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	15	278	0	ENST00000278616.4:c.5056A>G	p.Ile1686Val	p.I1686V	ENST00000278616	NM_000051.3	1686	Ata/Gta	34/63	0.412263244350432	4	FACETS	1	0.842	1	0.397	0.296	0.512	CLONAL	1	TRUE	1	0.516488398298593	4		278	74	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099233	157099233	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1478614436	NA	P-0047904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	64	667	1	ENST00000346085.5:c.170C>T	p.Ser57Leu	p.S57L	ENST00000346085	NM_020732.3	57	tCg/tTg	1/20	0.203077392246376	3	FACETS	0.843	0.744	0.945	0.562	0.496	0.63	INDETERMINATE	2	TRUE	0	0.516488398298593	3		668	185	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107116	27107116	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0047904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	73	634	0	ENST00000324856.7:c.6727A>T	p.Lys2243Ter	p.K2243*	ENST00000324856	NM_006015.4	2243	Aag/Tag	20/20	0.459585568762035	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	0	0.516488398298593	2		634	138	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864199	57864199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	32	769	0	ENST00000228682.2:c.1676C>T	p.Ser559Phe	p.S559F	ENST00000228682	NM_005269.2	559	tCc/tTc	12/12	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.516488398298593	2		769	88	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145550	24145550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	32	850	0	ENST00000263121.7:c.569G>T	p.Arg190Leu	p.R190L	ENST00000263121	NM_003073.3	190	cGg/cTg	5/9	0.231061097466373	1	FACETS	1	0.951	1	1	0.951	1	INDETERMINATE	1	TRUE	0	0.516488398298593	1		850	67	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675424	30675424	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	13	742	1	ENST00000376406.3:c.2932G>A	p.Gly978Arg	p.G978R	ENST00000376406	NM_014641.2	978	Gga/Aga	8/15	0.455957196768813	3	FACETS	0.546	0.393	0.729	0.273	0.196	0.365	SUBCLONAL	1	TRUE	1	0.516488398298593	3		743	116	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206664	27206664	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	13	482	0	ENST00000380036.4:c.2449C>G	p.Pro817Ala	p.P817A	ENST00000380036	NM_000459.3	817	Cca/Gca	15/23	0.221510326578601	0	FACETS	0.529	0.391	0.683			1	INDETERMINATE	1	TRUE	0	0.516488398298593	0		482	46	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0047905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1204	69	824	1	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.252	0.218	0.289	0.252	0.218	0.289	SUBCLONAL	1	TRUE	1	0.43	2		825	1273	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397682	49397683	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0047905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	49	493	1	ENST00000418115.1:c.541_542delinsTT	p.Ala181Phe	p.A181F	ENST00000418115	NM_001664.2	181	GCt/TTt	5/5	1	2	FACETS	0.292	0.246	0.342	0.292	0.246	0.342	SUBCLONAL	1	TRUE	1	0.43	2		494	781	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880998	37880998	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs144434331	NA	P-0047906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	215	780	0	ENST00000269571.5:c.2327G>T	p.Gly776Val	p.G776V	ENST00000269571		776	gGt/gTt	20/27	0.246744147065513	3	FACETS	1	0.953	1	0.689	0.64	0.74	CLONAL	2	TRUE	0	0.2	3		780	1144	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750600586	NA	P-0047906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	161	769	1	ENST00000269305.4:c.413C>T	p.Ala138Val	p.A138V	ENST00000269305	NM_001126112.2	138	gCc/gTc	5/11	0.121739577106168	3	FACETS	0.794	0.727	0.864	0.794	0.727	0.864	SUBCLONAL	2	TRUE	1	0.2	3		770	1115	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0047906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	169	754	1	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.121739577106168	3	FACETS	0.813	0.746	0.882	0.813	0.746	0.882	CLONAL	2	TRUE	1	0.2	3		755	1144	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437527	56437527	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	156	579	0	ENST00000407977.2:c.935G>A	p.Cys312Tyr	p.C312Y	ENST00000407977		312	tGc/tAc	8/10	0.216782297584024	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.2	2		579	724	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604706	48604706	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	36	391	0	ENST00000342988.3:c.1528G>C	p.Gly510Arg	p.G510R	ENST00000342988	NM_005359.5	510	Gga/Cga	12/12	0.3	1	FACETS	0.728	0.598	0.873	0.728	0.598	0.873	SUBCLONAL	1	TRUE	0	0.2	1		391	445	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935114	49935114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	46	456	0	ENST00000296474.3:c.1885G>A	p.Val629Met	p.V629M	ENST00000296474	NM_002447.2	629	Gtg/Atg	6/20	1	2	FACETS	0.786	0.661	0.925	0.786	0.661	0.925	CLONAL	1	TRUE	1	0.2	2		456	585	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202435	138202435	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	56	525	0	ENST00000237289.4:c.2352G>T	p.Gln784His	p.Q784H	ENST00000237289	NM_001270507.1	784	caG/caT	9/9	0.3	1	FACETS	0.792	0.678	0.917	0.792	0.678	0.917	CLONAL	1	TRUE	0	0.2	1		525	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0047907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	34	643	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		643	805	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578266	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	269	519	0	ENST00000269305.4:c.583dup	p.Ile195AsnfsTer14	p.I195Nfs*14	ENST00000269305	NM_001126112.2	195	atc/aAtc	6/11	0.497139517828238	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.717270731499619	1		519	445	SUCCESS
APC	324	MSKCC	GRCh37	5	112175952	112175952	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587783031	NA	P-0047937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	67	135	0	ENST00000257430.4:c.4666del	p.Thr1556LeufsTer9	p.T1556Lfs*9	ENST00000257430	NM_000038.5	1554	gAa/ga	16/16	0.717270731499619	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.717270731499619	1		135	118	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665501	138665501	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	188	687	0	ENST00000330315.3:c.64C>G	p.Arg22Gly	p.R22G	ENST00000330315	NM_023067.3	22	Cgc/Ggc	1/1	0.106130708293495	4	FACETS	1	0.973	1	0.554	0.512	0.597	INDETERMINATE	1	TRUE	2	0.717270731499619	4		687	813	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163561	32163561	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	80	617	0	ENST00000375023.3:c.5665C>G	p.Arg1889Gly	p.R1889G	ENST00000375023	NM_004557.3	1889	Cgg/Ggg	30/30	0.312268633699371	2	FACETS	0.402	0.354	0.453	0.201	0.177	0.227	INDETERMINATE	1	TRUE	0	0.717270731499619	2		617	555	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0047938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	24	660	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.645	0.506	0.805	0.645	0.506	0.805	SUBCLONAL	1	TRUE	1	0.24	2		660	310	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0047938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	26	320	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.91	0.724	1	0.91	0.724	1	CLONAL	1	TRUE	1	0.24	2		320	238	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855984	68855984	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121964877	NA	P-0047938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	39	376	0	ENST00000261769.5:c.1792C>T	p.Arg598Ter	p.R598*	ENST00000261769	NM_004360.3	598	Cga/Tga	12/16	0.174050677718829	1	FACETS	0.888	0.739	1	0.888	0.739	1	CLONAL	1	TRUE	0	0.24	1		376	322	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581219	48581219	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	16	307	0	ENST00000342988.3:c.523G>T	p.Glu175Ter	p.E175*	ENST00000342988	NM_005359.5	175	Gaa/Taa	5/12	0.174050677718829	1	FACETS	0.412	0.304	0.541	0.412	0.304	0.541	SUBCLONAL	1	TRUE	0	0.24	1		307	285	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976711	55976711	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	29	337	0	ENST00000263923.4:c.1114G>C	p.Glu372Gln	p.E372Q	ENST00000263923	NM_002253.2	372	Gag/Cag	9/30	1	2	FACETS	0.677	0.544	0.828	0.677	0.544	0.828	SUBCLONAL	1	TRUE	1	0.24	2		337	357	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21643241	21643241	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	47	416	0	ENST00000421138.2:c.286C>T	p.Gln96Ter	p.Q96*	ENST00000421138		96	Cag/Tag	5/16	1	2	FACETS	0.646	0.545	0.759	0.646	0.545	0.759	SUBCLONAL	1	TRUE	1	0.24	2		416	606	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112641	115112641	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0047938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	116	562	0	ENST00000257566.3:c.1100-1G>C		p.X367_splice	ENST00000257566	NM_016569.3	367			0.174050677718829	1	FACETS	0.791	0.715	0.869	1	0.986	1	SUBCLONAL	2	TRUE	0	0.24	1		562	538	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918132	50918132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148176230	NA	P-0047938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	49	764	1	ENST00000440232.2:c.2449C>T	p.Arg817Trp	p.R817W	ENST00000440232	NM_002691.3	817	Cgg/Tgg	20/27	0.3	1	FACETS	0.793	0.673	0.926	0.793	0.673	0.926	CLONAL	1	TRUE	0	0.24	1		765	453	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997856	149997856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	28	403	0	ENST00000253339.5:c.2611G>A	p.Asp871Asn	p.D871N	ENST00000253339		871	Gat/Aat	5/7	1	2	FACETS	0.526	0.419	0.647	0.526	0.419	0.647	SUBCLONAL	1	TRUE	1	0.24	2		403	444	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	48	349	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.758	0.644	0.883	0.758	0.644	0.883	SUBCLONAL	1	TRUE	1	0.39074390992404	2		350	324	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0047939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	159	227	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.372522006221834	2	FACETS	0.916	0.858	0.975	1	0.99	1	CLONAL	3	TRUE	0	0.39074390992404	2		227	296	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578194	7578194	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879253894	NA	P-0047939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	88	451	0	ENST00000269305.4:c.655C>T	p.Pro219Ser	p.P219S	ENST00000269305	NM_001126112.2	219	Ccc/Tcc	6/11	1	2	FACETS	0.806	0.715	0.902	0.806	0.715	0.902	CLONAL	1	TRUE	1	0.39074390992404	2		451	559	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409131	4409131	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	101	308	0	ENST00000261254.3:c.826G>A	p.Asp276Asn	p.D276N	ENST00000261254	NM_001759.3	276	Gac/Aac	5/5	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.39074390992404	2		308	477	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149511581	149511581	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	114	464	0	ENST00000261799.4:c.1204G>T	p.Asp402Tyr	p.D402Y	ENST00000261799	NM_002609.3	402	Gat/Tat	8/23	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.39074390992404	2		464	565	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0047940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	93	253	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.338953786276514	2	FACETS	0.776	0.697	0.858	0.776	0.697	0.858	SUBCLONAL	2	TRUE	0	0.363379485286967	2		253	330	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591105	67591106	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	44	175	0	ENST00000274335.5:c.1701dup	p.Pro568ThrfsTer34	p.P568Tfs*34	ENST00000274335		566	-/A	12/15	1	2	FACETS	0.935	0.79	1	0.935	0.79	1	CLONAL	1	TRUE	1	0.363379485286967	2		175	259	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444932	49444933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767415197	NA	P-0047940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	27	478	0	ENST00000301067.7:c.2533dup	p.Arg845ProfsTer3	p.R845Pfs*3	ENST00000301067	NM_003482.3	845	cgg/cCgg	10/54	1	2	FACETS	0.306	0.243	0.379	0.306	0.243	0.379	SUBCLONAL	1	TRUE	1	0.363379485286967	2		478	485	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247515	123247515	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	93	339	0	ENST00000358487.5:c.1976A>T	p.Lys659Met	p.K659M	ENST00000358487	NM_000141.4	659	aAg/aTg	14/18	0.338953786276514	2	FACETS	1	0.911	1	0.512	0.457	0.57	CLONAL	1	TRUE	0	0.363379485286967	2		339	500	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228979	36228979	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555734923	NA	P-0047940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	110	633	0	ENST00000222270.7:c.7759C>T	p.Arg2587Ter	p.R2587*	ENST00000222270	NM_014727.1	2587	Cga/Tga	36/37	1	2	FACETS	0.975	0.878	1	0.975	0.878	1	CLONAL	1	TRUE	1	0.363379485286967	2		633	621	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344554	118344554	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	21	256	0	ENST00000534358.1:c.2684del	p.Lys895ArgfsTer54	p.K895Rfs*54	ENST00000534358	NM_005933.3	894	Aaa/aa	3/36	1	2	FACETS	0.369	0.284	0.468	0.369	0.284	0.468	SUBCLONAL	1	TRUE	1	0.363379485286967	2		256	313	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942647	71942647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	48	501	0	ENST00000298229.2:c.1603G>A	p.Ala535Thr	p.A535T	ENST00000298229	NM_001567.3	535	Gcc/Acc	13/28	1	2	FACETS	0.423	0.357	0.496	0.423	0.357	0.496	SUBCLONAL	1	TRUE	1	0.363379485286967	2		501	624	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591031	67591033	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs1370788402	NA	P-0047940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	14	120	0	ENST00000274335.5:c.1630_1632del	p.Arg544del	p.R544del	ENST00000274335		542	AGA/-	12/15	1	2	FACETS	0.461	0.335	0.614	0.461	0.335	0.614	SUBCLONAL	1	TRUE	1	0.363379485286967	2		120	167	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609849	81609849	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	27	371	0	ENST00000298171.2:c.1447A>G	p.Asn483Asp	p.N483D	ENST00000298171	NM_000369.2	483	Aac/Gac	10/10	1	2	FACETS	0.396	0.315	0.489	0.396	0.315	0.489	SUBCLONAL	1	TRUE	1	0.363379485286967	2		371	375	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145729	61145729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	17	212	0	ENST00000295025.8:c.841C>T	p.Pro281Ser	p.P281S	ENST00000295025	NM_002908.2	281	Cca/Tca	7/11	1	2	FACETS	0.328	0.245	0.428	0.328	0.245	0.428	SUBCLONAL	1	TRUE	1	0.363379485286967	2		212	285	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5466809	5466809	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	19	76	0	ENST00000381577.3:c.830C>A	p.Thr277Lys	p.T277K	ENST00000381577	NM_014143.3	277	aCa/aAa	6/7	1	2	FACETS	0.925	0.712	1	0.925	0.712	1	CLONAL	1	TRUE	1	0.363379485286967	2		76	113	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22008918	22008918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	48	627	0	ENST00000276925.6:c.35del	p.Gly12AlafsTer15	p.G12Afs*15	ENST00000276925	NM_004936.3	12	gGc/gc	1/2	1	2	FACETS	0.373	0.314	0.437	0.373	0.314	0.437	SUBCLONAL	1	TRUE	1	0.363379485286967	2		627	709	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0047941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	59	491	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.184623264063612	1	FACETS	0.542	0.467	0.624	0.542	0.467	0.624	INDETERMINATE	1	TRUE	0	0.353440001568695	1		491	507	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911589	32911589	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs780279081	NA	P-0047941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	12	188	0	ENST00000380152.3:c.3097G>C	p.Asp1033His	p.D1033H	ENST00000380152		1033	Gat/Cat	11/27	1	2	FACETS	0.419	0.295	0.571	0.419	0.295	0.571	SUBCLONAL	1	TRUE	1	0.353440001568695	2		188	162	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398537	116398537	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	16	286	0	ENST00000397752.3:c.2127T>G	p.Cys709Trp	p.C709W	ENST00000397752	NM_000245.2	709	tgT/tgG	9/21	0.311398277268022	5	FACETS	0.448	0.331	0.589			1	SUBCLONAL	1	TRUE	NA	0.353440001568695	5		286	309	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891309	151891492	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTACCTGGAATTTTATATAATTTTCCAAGAATTGCTCCTAGAATAAATTAAAAAAAAAAAAGAAACATTAACAGCTACTAATTCAATATACTGATATAAAATAGTATTTAACTGACAGAAATAATTAGAAGTTAAATTATAACCATGCAAAAATCTTTAAAAATCATATTTACTCAGGTCTTT	TTTACCTGGAATTTTATATAATTTTCCAAGAATTGCTCCTAGAATAAATTAAAAAAAAAAAAGAAACATTAACAGCTACTAATTCAATATACTGATATAAAATAGTATTTAACTGACAGAAATAATTAGAAGTTAAATTATAACCATGCAAAAATCTTTAAAAATCATATTTACTCAGGTCTTT	-	novel	NA	P-0047941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	34	221	0	ENST00000262189.6:c.4507+33_4540+5del		p.X1503_splice	ENST00000262189	NM_170606.2	1503		30/59	1	2	FACETS	0.829	0.682	0.992	0.829	0.682	0.992	CLONAL	1	TRUE	1	0.353440001568695	2		221	232	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0047943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	42	315	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.92	0.768	1	0.92	0.768	1	CLONAL	1	TRUE	1	0.18	2		315	507	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796080	78796080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	58	445	0	ENST00000306801.3:c.970G>A	p.Ala324Thr	p.A324T	ENST00000306801	NM_020761.2	324	Gcg/Acg	8/34	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.18	2		445	568	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519927	NA	P-0047944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	73	443	0	ENST00000263967.3:c.1625A>G	p.Glu542Gly	p.E542G	ENST00000263967	NM_006218.2	542	gAa/gGa	10/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.318147914940427	2		443	366	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357514	89357514	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	121	612	0	ENST00000301030.4:c.304C>A	p.Leu102Met	p.L102M	ENST00000301030	NM_001256183.1	102	Ctg/Atg	5/13	1	2	FACETS	0.978	0.884	1	0.978	0.884	1	CLONAL	1	TRUE	1	0.318147914940427	2		612	778	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541623	187541626	+	frameshift_variant	Frame_Shift_Del	DEL	GAAG	GAAG	-	novel	NA	P-0047944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	84	212	0	ENST00000441802.2:c.6114_6117del	p.Phe2039IlefsTer12	p.F2039Ifs*12	ENST00000441802	NM_005245.3	2038	ccCTTC/cc	10/27	0.178994670654683	2	FACETS	0.791	0.704	0.881	0.791	0.704	0.881	INDETERMINATE	2	TRUE	0	0.318147914940427	2		212	334	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489599	40489619	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GATGCTCTGGTTGGAAACCAA	GATGCTCTGGTTGGAAACCAA	-	novel	NA	P-0047944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	73	347	0	ENST00000264657.5:c.646-15_651del		p.X216_splice	ENST00000264657	NM_139276.2	216		8/24	1	2	FACETS	0.888	0.778	1	0.888	0.778	1	CLONAL	1	TRUE	1	0.318147914940427	2		347	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0047945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	140	436	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.967	1	1	0.991	1	CLONAL	2	TRUE	1	0.16	2		439	779	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	15	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.473	0.345	0.629	0.473	0.345	0.629	SUBCLONAL	1	TRUE	1	0.16	2		327	396	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0047945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	39	453	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.778	0.643	0.928	0.778	0.643	0.928	CLONAL	1	TRUE	1	0.16	2		453	627	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399309	139399309	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1166328821	NA	P-0047945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	79	1092	1	ENST00000277541.6:c.4834G>A	p.Gly1612Ser	p.G1612S	ENST00000277541	NM_017617.3	1612	Ggc/Agc	26/34	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.16	2		1093	956	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741606	17741606	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	27	458	0	ENST00000250003.3:c.277del	p.Cys93AlafsTer30	p.C93Afs*30	ENST00000250003	NM_002478.4	93	Tgc/gc	1/3	1	2	FACETS	0.874	0.696	1	0.874	0.696	1	CLONAL	1	TRUE	1	0.16	2		458	386	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39537648	39537648	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	35	297	0	ENST00000262039.4:c.182G>T	p.Cys61Phe	p.C61F	ENST00000262039	NM_002647.2	61	tGt/tTt	2/25	0.326896458700257	1	FACETS	0.656	0.54	0.785	0.656	0.54	0.785	SUBCLONAL	1	TRUE	0	0.326896458700257	1		297	273	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411556	63411556	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	160	877	0	ENST00000330258.3:c.1611C>A	p.Asp537Glu	p.D537E	ENST00000330258	NM_152424.3	537	gaC/gaA	2/2	1	2	FACETS	0.968	0.887	1	0.968	0.887	1	CLONAL	1	TRUE	1	0.326896458700257	2		877	1011	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042725	42042725	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	171	378	0	ENST00000219905.7:c.6920A>G	p.Asp2307Gly	p.D2307G	ENST00000219905	NM_001164273.1	2307	gAt/gGt	17/24	0.546282008556925	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.546282008556925	1		378	429	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440035	99440035	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	179	472	0	ENST00000268035.6:c.1003G>A	p.Glu335Lys	p.E335K	ENST00000268035	NM_000875.3	335	Gaa/Aaa	4/21	0.546282008556925	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.546282008556925	1		472	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578528	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	novel	NA	P-0047947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	420	1125	0	ENST00000269305.4:c.402_404del	p.Cys135del	p.C135del	ENST00000269305	NM_001126112.2	134	ttTTGc/ttc	5/11	0.546282008556925	1	FACETS	0.933	0.89	0.977	0.933	0.89	0.977	CLONAL	1	TRUE	0	0.546282008556925	1		1125	1198	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349213	15349213	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0047947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	57	418	0	ENST00000263377.2:c.4064C>G	p.Ser1355Ter	p.S1355*	ENST00000263377	NM_058243.2	1355	tCa/tGa	20/20	0.338650776289776	1	FACETS	0.286	0.245	0.331	0.286	0.245	0.331	SUBCLONAL	1	TRUE	0	0.546282008556925	1		418	530	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910647	29910647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1258	91	1249	0	ENST00000376809.5:c.187G>A	p.Asp63Asn	p.D63N	ENST00000376809	NM_002116.7	63	Gac/Aac	2/8	1	2	FACETS	0.262	0.231	0.295	0.262	0.231	0.295	SUBCLONAL	1	TRUE	1	0.515246718122531	2		1249	1349	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0047949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	92	228	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.97	0.869	1	0.97	0.869	1	CLONAL	1	TRUE	1	0.515246718122531	2		228	368	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844113	68844124	+	inframe_deletion	In_Frame_Del	DEL	CTGTGTCATCCA	CTGTGTCATCCA	-	novel	NA	P-0047949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	113	444	0	ENST00000261769.5:c.701_712del	p.Ala234_Asn238delinsAsp	p.A234_N238delinsD	ENST00000261769	NM_004360.3	234	gCTGTGTCATCCAac/gac	6/16	0.515246718122531	1	FACETS	0.822	0.746	0.901	0.822	0.746	0.901	CLONAL	1	TRUE	0	0.515246718122531	1		444	396	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0047951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	186	269	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.821	0.763	0.88	0.821	0.763	0.88	CLONAL	1	TRUE	1	0.81246687737271	2		269	558	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109968	115109968	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	454	925	1	ENST00000257566.3:c.1910G>T	p.Arg637Leu	p.R637L	ENST00000257566	NM_016569.3	637	cGg/cTg	8/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.81246687737271	2		926	1054	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945678	206945678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1216	227	600	0	ENST00000423557.1:c.103G>A	p.Gly35Ser	p.G35S	ENST00000423557	NM_000572.2	35	Ggc/Agc	1/5	0.720052841116457	4	FACETS	0.702	0.652	0.754	0.351	0.326	0.377	SUBCLONAL	1	TRUE	2	0.81246687737271	4		600	1443	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609936	43609936	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	361	1152	1	ENST00000355710.3:c.1888T>A	p.Cys630Ser	p.C630S	ENST00000355710	NM_020975.4	630	Tgc/Agc	11/20	1	2	FACETS	0.658	0.623	0.694	0.658	0.623	0.694	SUBCLONAL	1	TRUE	1	0.81246687737271	2		1153	1351	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88671996	88671996	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0047951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	226	481	0	ENST00000372037.3:c.531-1G>A		p.X177_splice	ENST00000372037	NM_004329.2	177			1	2	FACETS	0.86	0.806	0.915	0.86	0.806	0.915	CLONAL	1	TRUE	1	0.81246687737271	2		481	647	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160374	108160374	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	104	194	2	ENST00000278616.4:c.4282G>C	p.Glu1428Gln	p.E1428Q	ENST00000278616	NM_000051.3	1428	Gaa/Caa	29/63	1	2	FACETS	0.818	0.742	0.897	0.818	0.742	0.897	CLONAL	1	TRUE	1	0.81246687737271	2		196	313	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219402	1219402	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	301	728	0	ENST00000326873.7:c.454C>T	p.Gln152Ter	p.Q152*	ENST00000326873	NM_000455.4	152	Cag/Tag	3/10	0.81246687737271	1	FACETS	0.94	0.901	0.978	0.94	0.901	0.978	CLONAL	1	TRUE	0	0.81246687737271	1		728	468	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610350	10610366	+	frameshift_variant	Frame_Shift_Del	DEL	CATGCCCTGCTCCCGCA	CATGCCCTGCTCCCGCA	AAT	novel	NA	P-0047951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	574	1111	3	ENST00000171111.5:c.344_360delinsATT	p.Leu115HisfsTer2	p.L115Hfs*2	ENST00000171111	NM_203500.1	115	cTGCGGGAGCAGGGCATG/cATT	2/6	0.81246687737271	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.81246687737271	1		1114	832	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282666	1282666	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	400	777	0	ENST00000310581.5:c.1647G>T	p.Met549Ile	p.M549I	ENST00000310581	NM_198253.2	549	atG/atT	3/16	1	2	FACETS	0.942	0.898	0.987	0.942	0.898	0.987	CLONAL	1	TRUE	1	0.81246687737271	2		777	1045	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409205	31409205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	283	540	0	ENST00000344624.3:c.3812C>T	p.Thr1271Ile	p.T1271I	ENST00000344624		1271	aCa/aTa	30/33	1	2	FACETS	0.943	0.891	0.995	0.943	0.891	0.995	CLONAL	1	TRUE	1	0.81246687737271	2		540	739	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0047953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	96	303	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.492364960517566	3	FACETS	0.986	0.882	1	0.493	0.441	0.548	CLONAL	1	TRUE	1	0.492364960517566	3		303	493	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276409	115276409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771102271	NA	P-0047953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	113	468	0	ENST00000438362.2:c.919G>A	p.Glu307Lys	p.E307K	ENST00000438362	NM_001242891.1	307	Gaa/Aaa	9/20	1	2	FACETS	0.898	0.812	0.989	0.898	0.812	0.989	CLONAL	1	TRUE	1	0.492364960517566	2		468	511	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913535	NA	P-0047953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	324	411	0	ENST00000311936.3:c.37G>C	p.Gly13Arg	p.G13R	ENST00000311936	NM_004985.3	13	Ggc/Cgc	2/5	0.492364960517566	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.492364960517566	3		411	768	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865149	57865149	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1299	947	994	0	ENST00000228682.2:c.2626G>T	p.Glu876Ter	p.E876*	ENST00000228682	NM_005269.2	876	Gaa/Taa	12/12	0.492364960517566	5	FACETS	0.993	0.963	1			1	CLONAL	3	TRUE	NA	0.492364960517566	5		994	2246	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599048	28599048	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	131	497	0	ENST00000241453.7:c.2240C>A	p.Pro747Gln	p.P747Q	ENST00000241453	NM_004119.2	747	cCg/cAg	18/24	0.467783895852774	2	FACETS	1	0.987	1	0.723	0.664	0.784	CLONAL	1	TRUE	0	0.492364960517566	2		497	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576870	7576870	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs876659384	NA	P-0047953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	229	777	0	ENST00000269305.4:c.976G>T	p.Glu326Ter	p.E326*	ENST00000269305	NM_001126112.2	326	Gaa/Taa	9/11	0.492364960517566	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.492364960517566	1		777	700	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215872	142215872	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	78	316	0	ENST00000350721.4:c.5721A>T	p.Leu1907Phe	p.L1907F	ENST00000350721	NM_001184.3	1907	ttA/ttT	33/47	0.492364960517566	4	FACETS	0.863	0.76	0.973	0.288	0.253	0.325	CLONAL	1	TRUE	1	0.492364960517566	4		316	548	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564465	86564466	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	213	765	0	ENST00000274376.6:c.200dup	p.Leu67PhefsTer45	p.L67Ffs*45	ENST00000274376	NM_002890.2	66	gct/gcTt	1/25	1	2	FACETS	0.846	0.786	0.908	0.846	0.786	0.908	CLONAL	1	TRUE	1	0.492364960517566	2		765	1023	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340386	8340386	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	135	566	0	ENST00000356435.5:c.5210C>A	p.Ser1737Tyr	p.S1737Y	ENST00000356435		1737	tCc/tAc	31/35	0.287969009559052	0	FACETS	0.513	0.468	0.559			1	INDETERMINATE	1	TRUE	0	0.492364960517566	0		566	543	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931969	39931969	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	235	940	1	ENST00000378444.4:c.2630C>A	p.Thr877Asn	p.T877N	ENST00000378444	NM_001123385.1	877	aCc/aAc	4/15	0.492364960517566	3	FACETS	0.894	0.832	0.958	0.447	0.416	0.479	CLONAL	1	TRUE	1	0.492364960517566	3		941	1331	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332839	152332840	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	T	novel	NA	P-0047953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	275	494	0	ENST00000206249.3:c.1145_1146delinsT	p.Ala382ValfsTer3	p.A382Vfs*3	ENST00000206249	NM_000125.3	382	gCC/gT	5/8	0.478723787682824	2	FACETS	0.958	0.908	1	0.958	0.908	1	CLONAL	2	TRUE	0	0.492364960517566	2		494	583	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	86	349	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.287493722333198	2		350	445	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0047954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	80	432	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.622	0.546	0.703	0.622	0.546	0.703	SUBCLONAL	1	TRUE	1	0.287493722333198	2		432	895	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0047954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	137	1076	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.287493722333198	1	FACETS	0.695	0.631	0.763	0.695	0.631	0.763	SUBCLONAL	1	TRUE	0	0.287493722333198	1		1076	1174	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855984	68855984	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121964877	NA	P-0047954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	113	376	0	ENST00000261769.5:c.1792C>T	p.Arg598Ter	p.R598*	ENST00000261769	NM_004360.3	598	Cga/Tga	12/16	0.25165351955807	1	FACETS	0.974	0.878	1	0.974	0.878	1	CLONAL	1	TRUE	0	0.287493722333198	1		376	691	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139831	55139831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758137485	NA	P-0047954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	56	511	0	ENST00000257290.5:c.1492G>A	p.Ala498Thr	p.A498T	ENST00000257290	NM_006206.4	498	Gcc/Acc	10/23	1	2	FACETS	0.457	0.39	0.53	0.457	0.39	0.53	SUBCLONAL	1	TRUE	1	0.287493722333198	2		511	853	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0047954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	136	730	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	0.287493722333198	1	FACETS	0.821	0.745	0.9	0.821	0.745	0.9	CLONAL	1	TRUE	0	0.287493722333198	1		730	987	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057874	27057874	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	192	822	0	ENST00000324856.7:c.1582C>T	p.Gln528Ter	p.Q528*	ENST00000324856	NM_006015.4	528	Cag/Tag	3/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.287493722333198	2		822	1130	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122397	17122397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	79	825	1	ENST00000285071.4:c.998C>T	p.Ser333Leu	p.S333L	ENST00000285071	NM_144997.5	333	tCa/tTa	9/14	0.287493722333198	1	FACETS	0.558	0.489	0.631	0.558	0.489	0.631	SUBCLONAL	1	TRUE	0	0.287493722333198	1		826	844	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649908	88649908	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	60	405	0	ENST00000372037.3:c.157G>C	p.Glu53Gln	p.E53Q	ENST00000372037	NM_004329.2	53	Gag/Cag	4/13	1	2	FACETS	0.703	0.605	0.809	0.703	0.605	0.809	SUBCLONAL	1	TRUE	1	0.287493722333198	2		405	594	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197387	26197387	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1344624542	NA	P-0047954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	65	503	0	ENST00000356476.2:c.92C>T	p.Pro31Leu	p.P31L	ENST00000356476		31	cCa/cTa	1/1	1	2	FACETS	0.687	0.595	0.787	0.687	0.595	0.787	SUBCLONAL	1	TRUE	1	0.287493722333198	2		503	658	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142964	47142964	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	37	423	0	ENST00000409792.3:c.4999C>G	p.Gln1667Glu	p.Q1667E	ENST00000409792	NM_014159.6	1667	Cag/Gag	8/21	1	2	FACETS	0.354	0.291	0.425	0.354	0.291	0.425	SUBCLONAL	1	TRUE	1	0.287493722333198	2		423	727	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115252235	115252235	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	53	381	0	ENST00000369535.4:c.405G>C	p.Lys135Asn	p.K135N	ENST00000369535	NM_002524.4	135	aaG/aaC	4/7	1	2	FACETS	0.583	0.497	0.678	0.583	0.497	0.678	SUBCLONAL	1	TRUE	1	0.287493722333198	2		381	632	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275290	115275290	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	75	517	0	ENST00000438362.2:c.1123G>C	p.Glu375Gln	p.E375Q	ENST00000438362	NM_001242891.1	375	Gag/Cag	10/20	1	2	FACETS	0.539	0.471	0.613	0.539	0.471	0.613	SUBCLONAL	1	TRUE	1	0.287493722333198	2		517	968	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117041	193117043	+	inframe_deletion	In_Frame_Del	DEL	CAG	CAG	-	novel	NA	P-0047954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	58	363	0	ENST00000367435.3:c.774_776del	p.Arg259del	p.R259del	ENST00000367435	NM_024529.4	258	gcCAGa/gca	8/17	1	2	FACETS	0.724	0.622	0.835	0.724	0.622	0.835	SUBCLONAL	1	TRUE	1	0.287493722333198	2		363	557	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845617	63845621	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAG	GAAAG	CAAA	novel	NA	P-0047954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	28	181	1	ENST00000279873.7:c.1356_1360delinsCAAA	p.Lys452AsnfsTer27	p.K452Nfs*27	ENST00000279873	NM_032199.2	452	aaGAAAGaa/aaCAAAaa	9/10	1	2	FACETS	0.647	0.518	0.793	0.647	0.518	0.793	SUBCLONAL	1	TRUE	1	0.287493722333198	2		182	301	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156604	2156604	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	37	725	0	ENST00000434045.2:c.318C>G	p.Phe106Leu	p.F106L	ENST00000434045	NM_001127598.1	106	ttC/ttG	3/5	0.287493722333198	1	FACETS	0.308	0.253	0.37	0.308	0.253	0.37	SUBCLONAL	1	TRUE	0	0.287493722333198	1		725	716	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180895	108180895	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0047954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	37	185	0	ENST00000278616.4:c.5771C>G	p.Ser1924Ter	p.S1924*	ENST00000278616	NM_000051.3	1924	tCa/tGa	39/63	1	2	FACETS	0.755	0.624	0.901	0.755	0.624	0.901	CLONAL	1	TRUE	1	0.287493722333198	2		185	341	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118368738	118368738	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	46	388	0	ENST00000534358.1:c.5752G>A	p.Asp1918Asn	p.D1918N	ENST00000534358	NM_005933.3	1918	Gac/Aac	21/36	1	2	FACETS	0.495	0.416	0.582	0.495	0.416	0.582	SUBCLONAL	1	TRUE	1	0.287493722333198	2		388	647	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911258	32911258	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	75	463	0	ENST00000380152.3:c.2766C>G	p.Phe922Leu	p.F922L	ENST00000380152		922	ttC/ttG	11/27	1	2	FACETS	0.651	0.569	0.739	0.651	0.569	0.739	SUBCLONAL	1	TRUE	1	0.287493722333198	2		463	802	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911391	32911391	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs80358539	NA	P-0047954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	42	350	0	ENST00000380152.3:c.2899C>G	p.Leu967Val	p.L967V	ENST00000380152		967	Cta/Gta	11/27	1	2	FACETS	0.468	0.39	0.555	0.468	0.39	0.555	SUBCLONAL	1	TRUE	1	0.287493722333198	2		350	624	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911487	32911487	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	55	368	0	ENST00000380152.3:c.2995C>G	p.Pro999Ala	p.P999A	ENST00000380152		999	Cca/Gca	11/27	1	2	FACETS	0.675	0.577	0.782	0.675	0.577	0.782	SUBCLONAL	1	TRUE	1	0.287493722333198	2		368	567	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953748	48953748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	58	198	0	ENST00000267163.4:c.1351del	p.Arg451AlafsTer6	p.R451Afs*6	ENST00000267163	NM_000321.2	451	Cgc/gc	14/27	0.287493722333198	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.287493722333198	1		198	276	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000389	42000389	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	38	323	0	ENST00000219905.7:c.2408C>T	p.Ser803Phe	p.S803F	ENST00000219905	NM_001164273.1	803	tCt/tTt	7/24	1	2	FACETS	0.496	0.409	0.593	0.496	0.409	0.593	SUBCLONAL	1	TRUE	1	0.287493722333198	2		323	533	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007777	45007777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760823225	NA	P-0047954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	63	365	0	ENST00000558401.1:c.224C>T	p.Ser75Phe	p.S75F	ENST00000558401	NM_004048.2	75	tCt/tTt	2/4	1	2	FACETS	0.816	0.707	0.935	0.816	0.707	0.935	CLONAL	1	TRUE	1	0.287493722333198	2		365	537	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965127	81965127	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	54	548	0	ENST00000359376.3:c.2607G>C	p.Gln869His	p.Q869H	ENST00000359376	NM_002661.3	869	caG/caC	25/33	0.25165351955807	1	FACETS	0.475	0.405	0.552	0.475	0.405	0.552	SUBCLONAL	1	TRUE	0	0.287493722333198	1		548	677	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965149	81965149	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	69	620	0	ENST00000359376.3:c.2629G>C	p.Glu877Gln	p.E877Q	ENST00000359376	NM_002661.3	877	Gag/Cag	25/33	0.25165351955807	1	FACETS	0.514	0.446	0.587	0.514	0.446	0.587	SUBCLONAL	1	TRUE	0	0.287493722333198	1		620	800	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973143	25973143	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	30	354	1	ENST00000435504.4:c.1282C>T	p.Gln428Ter	p.Q428*	ENST00000435504		428	Cag/Tag	12/13	1	2	FACETS	0.351	0.282	0.43	0.351	0.282	0.43	SUBCLONAL	1	TRUE	1	0.287493722333198	2		355	594	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718969	190718969	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	21	185	0	ENST00000441310.2:c.971C>T	p.Ser324Phe	p.S324F	ENST00000441310	NM_000534.4	324	tCt/tTt	9/13	1	2	FACETS	0.462	0.356	0.586	0.462	0.356	0.586	SUBCLONAL	1	TRUE	1	0.287493722333198	2		185	316	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735501	204735501	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	76	549	0	ENST00000302823.3:c.302C>T	p.Ser101Phe	p.S101F	ENST00000302823	NM_005214.4	101	tCc/tTc	2/4	1	2	FACETS	0.81	0.71	0.917	0.81	0.71	0.917	CLONAL	1	TRUE	1	0.287493722333198	2		549	653	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530104	212530104	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	52	319	0	ENST00000342788.4:c.1815C>G	p.Phe605Leu	p.F605L	ENST00000342788	NM_005235.2	605	ttC/ttG	15/28	1	2	FACETS	0.749	0.638	0.87	0.749	0.638	0.87	SUBCLONAL	1	TRUE	1	0.287493722333198	2		319	483	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637554	52637554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1428187629	NA	P-0047954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	41	321	0	ENST00000394830.3:c.2762G>A	p.Arg921Gln	p.R921Q	ENST00000394830	NM_018313.4	921	cGa/cAa	18/30	1	2	FACETS	0.507	0.421	0.602	0.507	0.421	0.602	SUBCLONAL	1	TRUE	1	0.287493722333198	2		321	563	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79965940	79965940	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	94	382	0	ENST00000265081.6:c.604C>T	p.Gln202Ter	p.Q202*	ENST00000265081	NM_002439.4	202	Cag/Tag	4/24	0.287493722333198	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.287493722333198	1		382	494	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169908	32169908	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	108	878	0	ENST00000375023.3:c.3700G>A	p.Asp1234Asn	p.D1234N	ENST00000375023	NM_004557.3	1234	Gac/Aac	21/30	1	2	FACETS	0.667	0.597	0.741	0.667	0.597	0.741	SUBCLONAL	1	TRUE	1	0.287493722333198	2		878	1127	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0047955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	639	436	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.615245956253823	2	FACETS	0.956	0.928	0.984	0.956	0.928	0.984	CLONAL	2	TRUE	0	0.637028184652868	2		439	1049	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060499964	NA	P-0047955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	734	1216	1	ENST00000326873.7:c.667G>A	p.Glu223Lys	p.E223K	ENST00000326873	NM_000455.4	223	Gag/Aag	5/10	0.615245956253823	2	FACETS	0.979	0.952	1	0.979	0.952	1	CLONAL	2	TRUE	0	0.637028184652868	2		1217	1177	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602443	10602443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1321752702	NA	P-0047955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	768	1081	0	ENST00000171111.5:c.1135G>A	p.Gly379Ser	p.G379S	ENST00000171111	NM_203500.1	379	Ggc/Agc	3/6	0.615245956253823	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.637028184652868	2		1081	1193	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239498	123239498	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0047955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	324	704	0	ENST00000358487.5:c.2339C>G	p.Ser780Ter	p.S780*	ENST00000358487	NM_000141.4	780	tCa/tGa	18/18	0.604662968634683	3	FACETS	1	0.967	1	0.517	0.488	0.548	CLONAL	1	TRUE	1	0.637028184652868	3		704	1296	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199881	108199881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881315	NA	P-0047956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	73	160	0	ENST00000278616.4:c.7223C>T	p.Ser2408Leu	p.S2408L	ENST00000278616	NM_000051.3	2408	tCg/tTg	49/63	0.275683908042657	4	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	2	0.295223843362593	4		160	300	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0047957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	106	418	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.29	2		418	729	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857475	9857475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	49	390	0	ENST00000330684.3:c.3926G>A	p.Arg1309Gln	p.R1309Q	ENST00000330684	NM_001134407.1	1309	cGg/cAg	13/13	1	2	FACETS	0.503	0.425	0.589	0.503	0.425	0.589	SUBCLONAL	1	TRUE	1	0.29	2		390	672	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675064	40675064	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	91	682	3	ENST00000249776.8:c.28G>T	p.Asp10Tyr	p.D10Y	ENST00000249776	NM_033286.3	10	Gac/Tac	1/9	1	2	FACETS	0.511	0.452	0.574	0.511	0.452	0.574	SUBCLONAL	1	TRUE	1	0.29	2		685	1228	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600046	10600046	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0047957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	174	676	0	ENST00000171111.5:c.1532-2A>G		p.X511_splice	ENST00000171111	NM_203500.1	511			0.3	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.29	1		676	964	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190708759	190708759	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1559289491	NA	P-0047957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	74	312	0	ENST00000441310.2:c.652G>C	p.Val218Leu	p.V218L	ENST00000441310	NM_000534.4	218	Gtt/Ctt	6/13	1	2	FACETS	0.817	0.715	0.926	0.817	0.715	0.926	CLONAL	1	TRUE	1	0.29	2		312	625	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628099	187628099	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	119	491	0	ENST00000441802.2:c.2883G>T	p.Gln961His	p.Q961H	ENST00000441802	NM_005245.3	961	caG/caT	2/27	1	2	FACETS	0.937	0.845	1	0.937	0.845	1	CLONAL	1	TRUE	1	0.29	2		491	876	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480611	120480611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146014987	NA	P-0047958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	52	386	1	ENST00000256646.2:c.3206G>A	p.Arg1069Gln	p.R1069Q	ENST00000256646	NM_024408.3	1069	cGg/cAg	20/34	0.146577751013286	3	FACETS	0.808	0.689	0.939	0.808	0.689	0.939	CLONAL	2	TRUE	1	0.146577751013286	3		387	471	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462864	120462864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	28	312	0	ENST00000256646.2:c.5467G>A	p.Val1823Ile	p.V1823I	ENST00000256646	NM_024408.3	1823	Gtc/Atc	30/34	0.146577751013286	3	FACETS	1	0.929	1	0.705	0.564	0.863	CLONAL	1	TRUE	1	0.146577751013286	3		312	291	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577529	7577534	+	inframe_deletion	In_Frame_Del	DEL	ATGGGC	ATGGGC	-	novel	NA	P-0047958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	140	726	0	ENST00000269305.4:c.747_752del	p.Arg249_Ile251delinsSer	p.R249_I251delinsS	ENST00000269305	NM_001126112.2	249	agGCCCATc/agc	7/11	0.146577751013286	3	FACETS	0.975	0.89	1	1	0.986	1	CLONAL	3	TRUE	1	0.146577751013286	3		726	701	SUCCESS
ATR	545	MSKCC	GRCh37	3	142285085	142285085	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	28	281	0	ENST00000350721.4:c.170A>G	p.Lys57Arg	p.K57R	ENST00000350721	NM_001184.3	57	aAg/aGg	3/47	0.146577751013286	5	FACETS	1	0.869	1	0.28	0.223	0.345	CLONAL	1	TRUE	1	0.146577751013286	5		281	416	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250443	26250443	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	35	587	0	ENST00000446824.2:c.391A>T	p.Ile131Phe	p.I131F	ENST00000446824	NM_021018.2	131	Att/Ttt	1/1	0.146577751013286	5	FACETS	0.998	0.816	1	0.2	0.163	0.241	CLONAL	1	TRUE	0	0.146577751013286	5		587	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0047959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	82	607	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.896824889671964	2		608	176	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582873	95582873	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	36	251	0	ENST00000393063.1:c.1669A>T	p.Ile557Phe	p.I557F	ENST00000393063	NM_030621.3	557	Atc/Ttc	11/28	0.65641043662832	3	FACETS	0.994	0.836	1			1	CLONAL	1	TRUE	NA	0.896824889671964	3		251	117	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68982069	68982069	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0047959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	132	458	0	ENST00000288368.4:c.1444-1G>T		p.X482_splice	ENST00000288368	NM_024870.2	482			0.795084819770803	4	FACETS	0.987	0.912	1	0.987	0.912	1	CLONAL	2	TRUE	2	0.896824889671964	4		458	283	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0047960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	284	660	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.14195539269047	3	FACETS	1	0.993	1	0.69	0.651	0.729	INDETERMINATE	1	TRUE	1	0.717178124688718	3		660	780	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348536	70348536	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387907360	NA	P-0047960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	114	557	0	ENST00000374080.3:c.3443G>A	p.Arg1148His	p.R1148H	ENST00000374080		1148	cGc/cAc	24/45	1	2	FACETS	0.436	0.393	0.482	0.436	0.393	0.482	SUBCLONAL	1	TRUE	1	0.717178124688718	2		557	729	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831342	89831342	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	56	628	0	ENST00000389301.3:c.2734A>G	p.Thr912Ala	p.T912A	ENST00000389301	NM_000135.2	912	Aca/Gca	28/43	0.717178124688718	1	FACETS	0.166	0.142	0.192	0.166	0.142	0.192	SUBCLONAL	1	TRUE	0	0.717178124688718	1		628	604	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196162	138196162	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	95	273	0	ENST00000237289.4:c.476A>C	p.Tyr159Ser	p.Y159S	ENST00000237289	NM_001270507.1	159	tAt/tCt	3/9	1	2	FACETS	0.69	0.619	0.764	0.69	0.619	0.764	SUBCLONAL	1	TRUE	1	0.717178124688718	2		273	384	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233264	69233264	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	110	251	0	ENST00000462284.1:c.1129A>G	p.Arg377Gly	p.R377G	ENST00000462284	NM_002392.5	377	Aga/Gga	11/11	0.14195539269047	3	FACETS	1	0.98	1	0.649	0.59	0.71	INDETERMINATE	1	TRUE	1	0.717178124688718	3		251	321	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858774	9858774	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs199784503	NA	P-0047960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	220	241	0	ENST00000330684.3:c.2627T>A	p.Ile876Asn	p.I876N	ENST00000330684	NM_001134407.1	876	aTt/aAt	13/13	0.717178124688718	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.717178124688718	3		241	403	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662229	227662229	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	73	907	0	ENST00000305123.5:c.1226C>A	p.Pro409Gln	p.P409Q	ENST00000305123	NM_005544.2	409	cCa/cAa	1/2	0.243009205185355	3	FACETS	0.229	0.199	0.261	0.114	0.099	0.131	INDETERMINATE	1	TRUE	1	0.717178124688718	3		907	1210	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982963	201982963	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs549132954	NA	P-0047961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	228	819	0	ENST00000359651.3:c.812G>C	p.Arg271Thr	p.R271T	ENST00000359651		271	aGa/aCa	7/8	0.315754219291303	3	FACETS	0.871	0.812	0.932	0.871	0.812	0.932	CLONAL	2	TRUE	1	0.315754219291303	3		819	960	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456573	32456573	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	36	79	0	ENST00000332351.3:c.319G>T	p.Asp107Tyr	p.D107Y	ENST00000332351	NM_024426.4	107	Gac/Tac	1/10	0.315754219291303	1	FACETS	1	0.925	1	1	0.972	1	CLONAL	2	TRUE	0	0.315754219291303	1		79	84	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864552	57864552	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	201	970	0	ENST00000228682.2:c.2029G>C	p.Asp677His	p.D677H	ENST00000228682	NM_005269.2	677	Gat/Cat	12/12	0.278339914201083	3	FACETS	0.801	0.743	0.862	0.801	0.743	0.862	CLONAL	2	TRUE	1	0.315754219291303	3		970	920	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226071	133226071	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	98	917	0	ENST00000320574.5:c.3826A>C	p.Lys1276Gln	p.K1276Q	ENST00000320574	NM_006231.2	1276	Aag/Cag	31/49	0.278339914201083	3	FACETS	0.828	0.738	0.924	0.414	0.369	0.462	CLONAL	1	TRUE	1	0.315754219291303	3		917	868	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435486	110435487	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0047961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	139	684	4	ENST00000375856.3:c.2914_2915delinsTT	p.Arg972Leu	p.R972L	ENST00000375856	NM_003749.2	972	CGg/TTg	1/2	0.27420927222698	2	FACETS	1	0.983	1	0.662	0.604	0.723	CLONAL	1	TRUE	0	0.315754219291303	2		688	665	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872616	37872616	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	97	1086	0	ENST00000269571.5:c.1576A>G	p.Thr526Ala	p.T526A	ENST00000269571		526	Acc/Gcc	13/27	1	2	FACETS	0.634	0.564	0.709	0.634	0.564	0.709	SUBCLONAL	1	TRUE	1	0.315754219291303	2		1086	969	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732254	74732254	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	29	334	0	ENST00000359995.5:c.655G>T	p.Val219Leu	p.V219L	ENST00000359995	NM_001195427.1	219	Gtg/Ttg	2/3	1	2	FACETS	0.528	0.424	0.646	0.528	0.424	0.646	SUBCLONAL	1	TRUE	1	0.315754219291303	2		334	348	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221232	1221233	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0047961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	275	823	1	ENST00000326873.7:c.756_757del	p.Tyr253ProfsTer12	p.Y253Pfs*12	ENST00000326873	NM_000455.4	252	cTG/c	6/10	0.315754219291303	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.315754219291303	2		824	803	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135010	11135010	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	214	708	0	ENST00000358026.2:c.2977G>T	p.Glu993Ter	p.E993*	ENST00000358026	NM_001128849.1	993	Gag/Tag	21/36	0.315754219291303	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.315754219291303	2		708	640	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470614	25470614	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	281	805	0	ENST00000264709.3:c.860G>T	p.Gly287Val	p.G287V	ENST00000264709	NM_175629.2	287	gGc/gTc	8/23	0.272268080326242	3	FACETS	0.858	0.809	0.907	0.858	0.809	0.907	CLONAL	3	TRUE	0	0.315754219291303	3		805	801	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495203	212495203	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	57	365	0	ENST00000342788.4:c.2063G>C	p.Arg688Thr	p.R688T	ENST00000342788	NM_005235.2	688	aGa/aCa	17/28	1	2	FACETS	0.776	0.667	0.895	0.776	0.667	0.895	SUBCLONAL	1	TRUE	1	0.315754219291303	2		365	465	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447486	187447486	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	92	824	0	ENST00000232014.4:c.707G>T	p.Arg236Met	p.R236M	ENST00000232014	NM_001130845.1	236	aGg/aTg	5/10	0.0848297004394944	4	FACETS	0.825	0.732	0.925	0.413	0.366	0.463	INDETERMINATE	1	TRUE	2	0.315754219291303	4		824	929	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593616	55593616	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	49	339	0	ENST00000288135.5:c.1682A>G	p.Glu561Gly	p.E561G	ENST00000288135	NM_000222.2	561	gAg/gGg	11/21	1	2	FACETS	0.828	0.703	0.964	0.828	0.703	0.964	CLONAL	1	TRUE	1	0.315754219291303	2		339	375	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557964	187557964	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	158	388	0	ENST00000441802.2:c.3747C>G	p.Phe1249Leu	p.F1249L	ENST00000441802	NM_005245.3	1249	ttC/ttG	5/27	0.27420927222698	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	0	0.315754219291303	2		388	492	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004246	150004246	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	48	218	0	ENST00000253339.5:c.1979G>T	p.Arg660Leu	p.R660L	ENST00000253339		660	cGt/cTt	3/7	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.315754219291303	2		218	256	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873510	151873510	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	140	503	0	ENST00000262189.6:c.9028G>T	p.Ala3010Ser	p.A3010S	ENST00000262189	NM_170606.2	3010	Gca/Tca	38/59	0.231636536555492	5	FACETS	0.843	0.768	0.921	0.562	0.512	0.614	CLONAL	2	TRUE	2	0.315754219291303	5		503	775	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753838	133753838	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	137	677	0	ENST00000318560.5:c.1307G>A	p.Gly436Asp	p.G436D	ENST00000318560	NM_005157.4	436	gGc/gAc	8/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.315754219291303	2		677	671	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841247	15841247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1180602444	NA	P-0047961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	16	264	0	ENST00000307771.7:c.1331G>A	p.Arg444Gln	p.R444Q	ENST00000307771	NM_005089.3	444	cGg/cAg	11/11	0.315754219291303	2	FACETS	0.361	0.266	0.474			1	SUBCLONAL	1	TRUE	NA	0.315754219291303	2		264	281	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0047962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	83	518	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	0.869	0.77	0.975	0.869	0.77	0.975	CLONAL	1	TRUE	1	0.406397223956997	2		518	470	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93636522	93636522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	95	501	0	ENST00000375746.1:c.952G>A	p.Val318Met	p.V318M	ENST00000375746	NM_001174167.1	318	Gtg/Atg	8/14	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.406397223956997	2		501	415	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0047964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	189	485	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.72	2		485	496	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	36	349	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.562	0.462	0.674	0.562	0.462	0.674	SUBCLONAL	1	TRUE	1	0.320272845206355	2		350	400	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0047965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	100	347	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.287194431077708	3	FACETS	1	0.978	1	0.683	0.612	0.758	CLONAL	1	TRUE	1	0.320272845206355	3		347	530	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857197	9857197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866121846	NA	P-0047965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	73	481	0	ENST00000330684.3:c.4204C>T	p.Arg1402Trp	p.R1402W	ENST00000330684	NM_001134407.1	1402	Cgg/Tgg	13/13	1	2	FACETS	0.636	0.555	0.723	0.636	0.555	0.723	SUBCLONAL	1	TRUE	1	0.320272845206355	2		481	717	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863443	57863443	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	50	662	2	ENST00000228682.2:c.1538G>A	p.Gly513Glu	p.G513E	ENST00000228682	NM_005269.2	513	gGg/gAg	11/12	1	2	FACETS	0.335	0.283	0.393	0.335	0.283	0.393	SUBCLONAL	1	TRUE	1	0.320272845206355	2		664	932	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383682	42383682	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	60	696	0	ENST00000221972.3:c.457C>G	p.Leu153Val	p.L153V	ENST00000221972	NM_021601.3	153	Ctg/Gtg	3/5	1	2	FACETS	0.391	0.335	0.451	0.391	0.335	0.451	SUBCLONAL	1	TRUE	1	0.320272845206355	2		696	959	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281785	46281785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	82	589	0	ENST00000371998.3:c.4232C>T	p.Pro1411Leu	p.P1411L	ENST00000371998		1411	cCc/cTc	22/23	1	2	FACETS	0.637	0.561	0.719	0.637	0.561	0.719	SUBCLONAL	1	TRUE	1	0.320272845206355	2		589	804	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760411	133760411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	73	773	0	ENST00000318560.5:c.2734G>A	p.Gly912Arg	p.G912R	ENST00000318560	NM_005157.4	912	Gga/Aga	11/11	1	2	FACETS	0.559	0.488	0.636	0.559	0.488	0.636	SUBCLONAL	1	TRUE	1	0.320272845206355	2		773	816	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0047966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	109	485	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.620966112510338	2		485	290	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090296	77090296	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	25	479	0	ENST00000356341.3:c.429G>A	p.Met143Ile	p.M143I	ENST00000356341	NM_002576.4	143	atG/atA	4/15	1	2	FACETS	0.237	0.186	0.295	0.237	0.186	0.295	SUBCLONAL	1	TRUE	1	0.620966112510338	2		479	340	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067919	30067919	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	268	431	0	ENST00000338641.4:c.1105del	p.Met369TrpfsTer6	p.M369Wfs*6	ENST00000338641	NM_000268.3	368	acA/ac	11/16	0.707743861423679	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.707743861423679	1		431	484	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	127	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.654376214911964	2		327	310	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591925	48591925	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	95	480	0	ENST00000342988.3:c.1088G>T	p.Cys363Phe	p.C363F	ENST00000342988	NM_005359.5	363	tGt/tTt	9/12	0.654376214911964	1	FACETS	0.896	0.815	0.978	0.896	0.815	0.978	CLONAL	1	TRUE	0	0.654376214911964	1		480	218	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392802	118392802	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	67	449	0	ENST00000534358.1:c.11834A>G	p.Tyr3945Cys	p.Y3945C	ENST00000534358	NM_005933.3	3945	tAc/tGc	36/36	1	2	FACETS	0.383	0.333	0.438	0.383	0.333	0.438	SUBCLONAL	1	TRUE	1	0.654376214911964	2		449	534	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599915	10599916	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCGG	novel	NA	P-0047969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	278	1813	0	ENST00000171111.5:c.1656_1660dup	p.Arg554ProfsTer43	p.R554Pfs*43	ENST00000171111	NM_203500.1	554	cga/cCCGGCga	5/6	0.654376214911964	1	FACETS	0.882	0.835	0.93	0.882	0.835	0.93	CLONAL	1	TRUE	0	0.654376214911964	1		1813	648	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174915	56174915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	84	373	0	ENST00000399503.3:c.2074G>A	p.Ala692Thr	p.A692T	ENST00000399503	NM_005921.1	692	Gca/Aca	11/20	0.272733303538011	3	FACETS	1	0.893	1	0.501	0.446	0.559	INDETERMINATE	1	TRUE	1	0.654376214911964	3		373	340	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797176	45797177	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0047973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	179	798	0	ENST00000450313.1:c.1238_1239del	p.Glu413AlafsTer118	p.E413Afs*118	ENST00000450313	NM_012222.2	413	gAG/g	13/16	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.240219450001105	2		798	1057	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487552	56487552	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	49	453	0	ENST00000267101.3:c.1485del	p.Glu496ArgfsTer35	p.E496Rfs*35	ENST00000267101	NM_001982.3	495	gcA/gc	13/28	0.184727408976934	1	FACETS	0.754	0.639	0.88	0.754	0.639	0.88	SUBCLONAL	1	TRUE	0	0.240219450001105	1		453	476	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865363	57865363	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	79	712	0	ENST00000228682.2:c.2840C>T	p.Thr947Ile	p.T947I	ENST00000228682	NM_005269.2	947	aCa/aTa	12/12	0.184727408976934	1	FACETS	0.734	0.644	0.83	0.734	0.644	0.83	SUBCLONAL	1	TRUE	0	0.240219450001105	1		712	789	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024616	14024616	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	31	267	0	ENST00000311895.7:c.842C>A	p.Thr281Asn	p.T281N	ENST00000311895	NM_005236.2	281	aCt/aAt	5/11	1	2	FACETS	0.599	0.484	0.729	0.599	0.484	0.729	SUBCLONAL	1	TRUE	1	0.240219450001105	2		267	431	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650698	67650698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	45	520	0	ENST00000264010.4:c.1003G>A	p.Gly335Arg	p.G335R	ENST00000264010	NM_006565.3	335	Gga/Aga	5/12	1	2	FACETS	0.61	0.512	0.719	0.61	0.512	0.719	SUBCLONAL	1	TRUE	1	0.240219450001105	2		520	614	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853258	68853259	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTGGACAGGGAGGATTTTGAGCACGTGAAGAA	novel	NA	P-0047973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	44	483	0	ENST00000261769.5:c.1643_1674dup	p.Ser559TrpfsTer9	p.S559Wfs*9	ENST00000261769	NM_004360.3	547	-/CTGGACAGGGAGGATTTTGAGCACGTGAAGAA	11/16	0.165477131422244	0	FACETS	0.543	0.455	0.64			1	SUBCLONAL	1	TRUE	0	0.240219450001105	0		483	513	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519975	NA	P-0047973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	206	861	0	ENST00000269305.4:c.403T>G	p.Cys135Gly	p.C135G	ENST00000269305	NM_001126112.2	135	Tgc/Ggc	5/11	0.240219450001105	1	FACETS	0.778	0.722	0.836	1	0.991	1	SUBCLONAL	2	TRUE	0	0.240219450001105	1		861	970	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141473	11141490	+	inframe_deletion	In_Frame_Del	DEL	CATCTTCCTGCTCAGCAC	CATCTTCCTGCTCAGCAC	-	novel	NA	P-0047973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	56	655	0	ENST00000358026.2:c.3451_3468del	p.Ile1151_Thr1156del	p.I1151_T1156del	ENST00000358026	NM_001128849.1	1150	ttCATCTTCCTGCTCAGCACc/ttc	25/36	0.150250849786633	0	FACETS	0.508	0.434	0.588			1	SUBCLONAL	1	TRUE	0	0.240219450001105	0		655	698	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033618	48033618	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	39	328	0	ENST00000234420.5:c.3829G>T	p.Asp1277Tyr	p.D1277Y	ENST00000234420	NM_000179.2	1277	Gac/Tac	9/10	1	2	FACETS	0.964	0.801	1	0.964	0.801	1	CLONAL	1	TRUE	1	0.240219450001105	2		328	337	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309712	30309712	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	58	566	0	ENST00000307677.4:c.310G>T	p.Ala104Ser	p.A104S	ENST00000307677	NM_138578.1	104	Gca/Tca	2/3	0.240219450001105	1	FACETS	0.648	0.556	0.748	0.648	0.556	0.748	SUBCLONAL	1	TRUE	0	0.240219450001105	1		566	656	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517735	187517736	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0047973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	17	210	0	ENST00000441802.2:c.12958_12959del	p.Ser4320ArgfsTer7	p.S4320Rfs*7	ENST00000441802	NM_005245.3	4320	AGc/c	25/27	0.240219450001105	1	FACETS	0.639	0.478	0.828	0.639	0.478	0.828	SUBCLONAL	1	TRUE	0	0.240219450001105	1		210	195	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79966004	79966004	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	37	333	0	ENST00000265081.6:c.668A>G	p.Lys223Arg	p.K223R	ENST00000265081	NM_002439.4	223	aAa/aGa	4/24	0.184727408976934	1	FACETS	0.622	0.513	0.744	0.622	0.513	0.744	SUBCLONAL	1	TRUE	0	0.240219450001105	1		333	436	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152357831	152357831	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	42	324	0	ENST00000359321.1:c.76G>C	p.Glu26Gln	p.E26Q	ENST00000359321	NM_005431.1	26	Gaa/Caa	2/3	0.240219450001105	1	FACETS	0.54	0.45	0.64	0.54	0.45	0.64	SUBCLONAL	1	TRUE	0	0.240219450001105	1		324	570	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021785	71021785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs112795301	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	59	229	1	ENST00000318789.4:c.1573C>T	p.Arg525Ter	p.R525*	ENST00000318789	NM_032682.5	525	Cga/Tga	18/21	1	2	FACETS	0.836	0.723	0.958	0.836	0.723	0.958	CLONAL	1	TRUE	1	0.39	2		230	362	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827580	72827580	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	147	470	0	ENST00000268489.5:c.9001G>T	p.Glu3001Ter	p.E3001*	ENST00000268489	NM_006885.3	3001	Gaa/Taa	9/10	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.39	2		470	746	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	101	390	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.873	0.782	0.97	0.873	0.782	0.97	CLONAL	1	TRUE	1	0.39	2		390	593	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	28	529	1	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.172	0.137	0.213	0.172	0.137	0.213	SUBCLONAL	1	TRUE	1	0.39	2		530	833	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273905	10273905	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	156	662	3	ENST00000330684.3:c.364G>A	p.Val122Ile	p.V122I	ENST00000330684	NM_001134407.1	122	Gtc/Atc	2/13	1	2	FACETS	0.87	0.796	0.946	0.87	0.796	0.946	CLONAL	1	TRUE	1	0.39	2		665	920	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	170	463	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.39	2		463	788	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104712	193104712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	49	199	0	ENST00000367435.3:c.416G>A	p.Arg139Gln	p.R139Q	ENST00000367435	NM_024529.4	139	cGa/cAa	5/17	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.39	2		199	244	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	45	253	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.708	0.597	0.829	0.708	0.597	0.829	SUBCLONAL	1	TRUE	1	0.39	2		253	326	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518099	8518099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764400127	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	11	304	0	ENST00000356435.5:c.1292C>T	p.Ser431Leu	p.S431L	ENST00000356435		431	tCg/tTg	10/35	1	2	FACETS	0.111	0.076	0.156	0.111	0.076	0.156	SUBCLONAL	1	TRUE	1	0.39	2		304	506	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562981	29562981	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs376576925	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	60	323	0	ENST00000356175.3:c.3916C>T	p.Arg1306Ter	p.R1306*	ENST00000356175	NM_000267.3	1306	Cga/Tga	29/57	1	2	FACETS	0.843	0.73	0.965	0.843	0.73	0.965	CLONAL	1	TRUE	1	0.39	2		323	365	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106355	27106355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773909963	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	121	446	0	ENST00000324856.7:c.5966G>A	p.Arg1989Gln	p.R1989Q	ENST00000324856	NM_006015.4	1989	cGa/cAa	20/20	1	2	FACETS	0.936	0.847	1	0.936	0.847	1	CLONAL	1	TRUE	1	0.39	2		446	663	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845621	63845621	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	36	131	0	ENST00000279873.7:c.1360G>T	p.Glu454Ter	p.E454*	ENST00000279873	NM_032199.2	454	Gaa/Taa	9/10	1	2	FACETS	0.932	0.774	1	0.932	0.774	1	CLONAL	1	TRUE	1	0.39	2		131	198	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587777894	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	147	446	0	ENST00000361445.4:c.6644C>A	p.Ser2215Tyr	p.S2215Y	ENST00000361445	NM_004958.3	2215	tCt/tAt	47/58	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.39	2		446	742	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575594	55575594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs73137716	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	50	230	0	ENST00000288135.5:c.1120G>A	p.Val374Ile	p.V374I	ENST00000288135	NM_000222.2	374	Gta/Ata	7/21	1	2	FACETS	0.765	0.652	0.888	0.765	0.652	0.888	SUBCLONAL	1	TRUE	1	0.39	2		230	335	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	91	295	0	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	1	2	FACETS	0.966	0.861	1	0.966	0.861	1	CLONAL	1	TRUE	1	0.39	2		295	483	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624245	89624245	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554890335	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	36	131	0	ENST00000371953.3:c.19G>T	p.Glu7Ter	p.E7*	ENST00000371953	NM_000314.4	7	Gag/Tag	1/9	1	2	FACETS	0.796	0.659	0.947	0.796	0.659	0.947	CLONAL	1	TRUE	1	0.39	2		131	232	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539690	187539690	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs748166431	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	62	261	0	ENST00000441802.2:c.8050G>T	p.Glu2684Ter	p.E2684*	ENST00000441802	NM_005245.3	2684	Gaa/Taa	10/27	1	2	FACETS	0.946	0.823	1	0.946	0.823	1	CLONAL	1	TRUE	1	0.39	2		261	336	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178943780	178943780	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	44	178	0	ENST00000263967.3:c.2447T>G	p.Ile816Ser	p.I816S	ENST00000263967	NM_006218.2	816	aTt/aGt	17/21	1	2	FACETS	0.921	0.779	1	0.921	0.779	1	CLONAL	1	TRUE	1	0.39	2		178	245	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630476	90630476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	121	399	1	ENST00000330062.3:c.835G>A	p.Asp279Asn	p.D279N	ENST00000330062	NM_002168.2	279	Gac/Aac	7/11	1	2	FACETS	0.985	0.892	1	0.985	0.892	1	CLONAL	1	TRUE	1	0.39	2		400	630	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253151	133253151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	88	306	0	ENST00000320574.5:c.890C>T	p.Ser297Phe	p.S297F	ENST00000320574	NM_006231.2	297	tCc/tTc	9/49	1	2	FACETS	0.927	0.824	1	0.927	0.824	1	CLONAL	1	TRUE	1	0.39	2		306	487	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508177	38508177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749735817	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	92	364	0	ENST00000254066.5:c.485G>A	p.Arg162Gln	p.R162Q	ENST00000254066	NM_000964.3	162	cGa/cAa	5/9	1	2	FACETS	0.815	0.725	0.91	0.815	0.725	0.91	CLONAL	1	TRUE	1	0.39	2		364	579	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716081	52716081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	176	679	0	ENST00000322088.6:c.646G>A	p.Glu216Lys	p.E216K	ENST00000322088	NM_014225.5	216	Gag/Aag	5/15	1	2	FACETS	0.966	0.89	1	0.966	0.89	1	CLONAL	1	TRUE	1	0.39	2		679	934	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482181	87482181	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	101	463	0	ENST00000277120.3:c.1468G>T	p.Asp490Tyr	p.D490Y	ENST00000277120		490	Gat/Tat	14/19	1	2	FACETS	0.935	0.838	1	0.935	0.838	1	CLONAL	1	TRUE	1	0.39	2		463	554	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287809	33287809	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150463674	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	205	730	0	ENST00000374542.5:c.1444G>A	p.Glu482Lys	p.E482K	ENST00000374542	NM_001141970.1	482	Gaa/Aaa	5/8	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.39	2		730	1019	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942524	17942524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763951351	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	116	791	0	ENST00000458235.1:c.2764G>A	p.Asp922Asn	p.D922N	ENST00000458235	NM_000215.3	922	Gat/Aat	20/24	1	2	FACETS	0.567	0.509	0.627	0.567	0.509	0.627	SUBCLONAL	1	TRUE	1	0.39	2		791	1050	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094807	143094807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	46	208	0	ENST00000262992.4:c.1337C>A	p.Ser446Tyr	p.S446Y	ENST00000262992	NM_001101669.1	446	tCt/tAt	14/24	1	2	FACETS	0.802	0.68	0.936	0.802	0.68	0.936	CLONAL	1	TRUE	1	0.39	2		208	294	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627849	187627849	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	122	458	0	ENST00000441802.2:c.3133G>T	p.Glu1045Ter	p.E1045*	ENST00000441802	NM_005245.3	1045	Gaa/Taa	2/27	1	2	FACETS	0.821	0.742	0.904	0.821	0.742	0.904	CLONAL	1	TRUE	1	0.39	2		458	762	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599975	28599975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1450092599	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	182	637	1	ENST00000253063.3:c.857G>A	p.Arg286His	p.R286H	ENST00000253063	NM_031459.4	286	cGc/cAc	6/10	1	2	FACETS	0.988	0.911	1	0.988	0.911	1	CLONAL	1	TRUE	1	0.39	2		638	945	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272439	11272439	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	128	403	0	ENST00000361445.4:c.3491A>G	p.Asp1164Gly	p.D1164G	ENST00000361445	NM_004958.3	1164	gAc/gGc	23/58	1	2	FACETS	0.962	0.874	1	0.962	0.874	1	CLONAL	1	TRUE	1	0.39	2		403	682	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432877	432877	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	111	336	0	ENST00000399788.2:c.2039G>T	p.Arg680Ile	p.R680I	ENST00000399788	NM_001042603.1	680	aGa/aTa	15/28	0.3	2	FACETS	1	0.939	1			1	CLONAL	1	TRUE	NA	0.39	2		336	539	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636088	28636088	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	142	482	0	ENST00000241453.7:c.284T>C	p.Val95Ala	p.V95A	ENST00000241453	NM_004119.2	95	gTc/gCc	3/24	1	2	FACETS	0.992	0.906	1	0.992	0.906	1	CLONAL	1	TRUE	1	0.39	2		482	734	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590794	95590794	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	47	227	0	ENST00000393063.1:c.1115T>G	p.Phe372Cys	p.F372C	ENST00000393063	NM_030621.3	372	tTt/tGt	9/28	1	2	FACETS	0.846	0.718	0.984	0.846	0.718	0.984	CLONAL	1	TRUE	1	0.39	2		227	285	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640277	3640277	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1060501792	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	168	770	0	ENST00000294008.3:c.3362C>A	p.Ser1121Tyr	p.S1121Y	ENST00000294008	NM_032444.2	1121	tCt/tAt	12/15	1	2	FACETS	0.797	0.731	0.866	0.797	0.731	0.866	SUBCLONAL	1	TRUE	1	0.39	2		770	1081	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729898	39729898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	77	383	0	ENST00000361337.2:c.1213C>T	p.Arg405Trp	p.R405W	ENST00000361337	NM_003286.2	405	Cgg/Tgg	13/21	1	2	FACETS	0.768	0.676	0.867	0.768	0.676	0.867	SUBCLONAL	1	TRUE	1	0.39	2		383	514	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961315	54961315	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	110	369	0	ENST00000312783.6:c.317C>A	p.Pro106His	p.P106H	ENST00000312783	NM_198436.1	106	cCt/cAt	4/10	1	2	FACETS	0.873	0.786	0.965	0.873	0.786	0.965	CLONAL	1	TRUE	1	0.39	2		369	646	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70005647	70005647	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs147682682	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	51	269	0	ENST00000394351.3:c.676G>T	p.Glu226Ter	p.E226*	ENST00000394351	NM_000248.3	226	Gaa/Taa	7/9	1	2	FACETS	0.795	0.679	0.921	0.795	0.679	0.921	CLONAL	1	TRUE	1	0.39	2		269	329	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498478	89498478	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	75	243	0	ENST00000336596.2:c.2450T>C	p.Val817Ala	p.V817A	ENST00000336596	NM_005233.5	817	gTg/gCg	14/17	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.39	2		243	327	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1976662	1976662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	165	509	0	ENST00000382891.5:c.3445G>A	p.Glu1149Lys	p.E1149K	ENST00000382891	NM_133335.3	1149	Gag/Aag	19/22	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.39	2		509	809	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146638	55146638	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	29	404	0	ENST00000257290.5:c.2312A>C	p.Lys771Thr	p.K771T	ENST00000257290	NM_006206.4	771	aAa/aCa	16/23	1	2	FACETS	0.256	0.205	0.315	0.256	0.205	0.315	SUBCLONAL	1	TRUE	1	0.39	2		404	580	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84388642	84388642	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	60	304	0	ENST00000321945.7:c.646A>C	p.Asn216His	p.N216H	ENST00000321945	NM_139076.2	216	Aat/Cat	7/9	1	2	FACETS	0.787	0.681	0.902	0.787	0.681	0.902	CLONAL	1	TRUE	1	0.39	2		304	391	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106162570	106162570	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	37	178	0	ENST00000380013.4:c.3484G>T	p.Glu1162Ter	p.E1162*	ENST00000380013	NM_001127208.2	1162	Gaa/Taa	4/11	1	2	FACETS	0.843	0.701	1	0.843	0.701	1	CLONAL	1	TRUE	1	0.39	2		178	225	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622173	117622173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1385257970	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	39	227	0	ENST00000368508.3:c.6697G>A	p.Ala2233Thr	p.A2233T	ENST00000368508	NM_002944.2	2233	Gca/Aca	42/43	1	2	FACETS	0.658	0.547	0.78	0.658	0.547	0.78	SUBCLONAL	1	TRUE	1	0.39	2		227	304	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346626	81346626	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	52	184	0	ENST00000222390.5:c.1327C>A	p.Pro443Thr	p.P443T	ENST00000222390	NM_000601.4	443	Cca/Aca	11/18	1	2	FACETS	0.855	0.732	0.988	0.855	0.732	0.988	CLONAL	1	TRUE	1	0.39	2		184	312	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486198	8486198	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	29	319	0	ENST00000356435.5:c.2619C>A	p.Phe873Leu	p.F873L	ENST00000356435		873	ttC/ttA	17/35	1	2	FACETS	0.402	0.322	0.492	0.402	0.322	0.492	SUBCLONAL	1	TRUE	1	0.39	2		319	370	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772618	135772618	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	96	370	0	ENST00000298552.3:c.2928A>C	p.Lys976Asn	p.K976N	ENST00000298552	NM_001162426.1	976	aaA/aaC	22/23	1	2	FACETS	0.801	0.714	0.892	0.801	0.714	0.892	CLONAL	1	TRUE	1	0.39	2		370	615	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0047975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	214	432	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.596040285403157	2		432	635	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0047975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	146	566	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.596040285403157	2		566	476	SUCCESS
APC	324	MSKCC	GRCh37	5	112175548	112175548	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	89	245	0	ENST00000257430.4:c.4260del	p.Ser1421ValfsTer52	p.S1421Vfs*52	ENST00000257430	NM_000038.5	1419	agC/ag	16/16	0.596040285403157	1	FACETS	0.892	0.805	0.981	0.892	0.805	0.981	CLONAL	1	TRUE	0	0.596040285403157	1		245	235	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145732	61145732	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1278232982	NA	P-0047975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	120	200	0	ENST00000295025.8:c.844G>A	p.Asp282Asn	p.D282N	ENST00000295025	NM_002908.2	282	Gat/Aat	7/11	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.596040285403157	2		200	386	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481423	140481423	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs180177032	NA	P-0047975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	145	272	0	ENST00000288602.6:c.1385G>T	p.Arg462Ile	p.R462I	ENST00000288602	NM_004333.4	462	aGa/aTa	11/18	1	2	FACETS	0.958	0.879	1	0.958	0.879	1	CLONAL	1	TRUE	1	0.596040285403157	2		272	508	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0047977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	149	561	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.298908183653842	3	FACETS	0.835	0.765	0.907	0.835	0.765	0.907	CLONAL	2	TRUE	1	0.322214401467559	3		561	643	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0047977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	115	630	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.298908183653842	3	FACETS	1	0.952	1	0.546	0.492	0.603	CLONAL	1	TRUE	1	0.322214401467559	3		630	759	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637347	47637347	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	59	588	0	ENST00000233146.2:c.481G>T	p.Val161Phe	p.V161F	ENST00000233146	NM_000251.2	161	Gtt/Ttt	3/16	1	2	FACETS	0.497	0.427	0.574	0.497	0.427	0.574	SUBCLONAL	1	TRUE	1	0.322214401467559	2		588	737	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55270011	55270243	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TACAGCACCCAGCACAGCCCTGCTGCCCACCCTGCAGCCTGTGGCCCAGTAGCACCAGCACCCACCAGGGTGCAGACTCTCAGGCCTGCCCAACCTACTAATCAGAACCAGCATCTCAAGGAGATCTCGGGTGATTTTTGCAAACACTGAAGTTGGGGCAGCCCTGACCGGAGTAACCTTCCCTCATTTCCTCCTGCAGCTGCAAAGCTGTCCCATCAAGGAAGACAGCTTCT	TACAGCACCCAGCACAGCCCTGCTGCCCACCCTGCAGCCTGTGGCCCAGTAGCACCAGCACCCACCAGGGTGCAGACTCTCAGGCCTGCCCAACCTACTAATCAGAACCAGCATCTCAAGGAGATCTCGGGTGATTTTTGCAAACACTGAAGTTGGGGCAGCCCTGACCGGAGTAACCTTCCCTCATTTCCTCCTGCAGCTGCAAAGCTGTCCCATCAAGGAAGACAGCTTCT	-	novel	NA	P-0047977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	127	532	0	ENST00000275493.2:c.3163-198_3197del		p.X1055_splice	ENST00000275493	NM_005228.3	1055		27/28	0.298908183653842	3	FACETS	1	0.981	1	0.657	0.596	0.721	CLONAL	1	TRUE	1	0.322214401467559	3		532	697	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041316	47041351	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGAATAGTGTGACCCCGTTCCCCTCACCCCCTAGCT	GGAATAGTGTGACCCCGTTCCCCTCACCCCCTAGCT	CG	novel	NA	P-0047977-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	51	333	2	ENST00000377604.3:c.1694-34_1695delinsCG		p.X565_splice	ENST00000377604	NM_001204468.1	565		16/24	1	1	FACETS	0.922	0.789	1	0.922	0.789	1	CLONAL	1	TRUE	0	0.322214401467559	1		335	288	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0047978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	101	712	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.358805156462451	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.358805156462451	1		712	346	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0047978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	63	634	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.358805156462451	2		634	339	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733279	40733279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201275244	NA	P-0047978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	124	401	0	ENST00000373198.4:c.3527G>A	p.Arg1176His	p.R1176H	ENST00000373198	NM_133170.3	1176	cGt/cAt	26/32	0.354887446054447	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	3	TRUE	0	0.358805156462451	3		401	252	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591892	48591892	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	25	332	0	ENST00000342988.3:c.1055G>T	p.Gly352Val	p.G352V	ENST00000342988	NM_005359.5	352	gGa/gTa	9/12	0.293076818580511	2	FACETS	1	0.878	1	0.571	0.457	0.697	CLONAL	1	TRUE	0	0.358805156462451	2		332	122	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117900	70117900	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	98	569	0	ENST00000245479.2:c.368T>A	p.Leu123His	p.L123H	ENST00000245479	NM_000346.3	123	cTc/cAc	1/3	0.358805156462451	2	FACETS	0.851	0.776	0.926	1	0.979	1	CLONAL	3	TRUE	0	0.358805156462451	2		569	214	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976510	25976510	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0047978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	19	201	1	ENST00000435504.4:c.1037-2A>G		p.X346_splice	ENST00000435504		346			1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.358805156462451	2		202	92	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991627	25991628	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0047978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	40	249	0	ENST00000435504.4:c.614_615del	p.Ser205CysfsTer14	p.S205Cfs*14	ENST00000435504		205	tCT/t	7/13	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.358805156462451	2		249	191	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856071	151856071	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	31	327	0	ENST00000262189.6:c.11547G>T	p.Gln3849His	p.Q3849H	ENST00000262189	NM_170606.2	3849	caG/caT	44/59	1	2	FACETS	0.789	0.642	0.952	0.789	0.642	0.952	CLONAL	1	TRUE	1	0.358805156462451	2		327	219	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950099	38950099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757900166	NA	P-0047981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	105	502	1	ENST00000357387.3:c.3851C>T	p.Ser1284Leu	p.S1284L	ENST00000357387	NM_152756.3	1284	tCg/tTg	31/38	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.831546518136544	2		503	242	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0047981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	48	229	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.946	0.823	1	0.946	0.823	1	CLONAL	1	TRUE	1	0.831546518136544	2		229	122	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0047981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	80	332	1				ENST00000310581	NM_198253.2	-/1132			0.831546518136544	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.831546518136544	1		333	100	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0047981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	369	817	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.831546518136544	2		817	807	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477854	140477854	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	113	472	0	ENST00000288602.6:c.1454T>G	p.Leu485Trp	p.L485W	ENST00000288602	NM_004333.4	485	tTg/tGg	12/18	0.157316680265624	3	FACETS	1	0.976	1	0.603	0.55	0.658	INDETERMINATE	1	TRUE	1	0.831546518136544	3		472	319	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332271	70332271	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs114779544	NA	P-0047981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	83	310	0	ENST00000373644.4:c.176A>G	p.Lys59Arg	p.K59R	ENST00000373644	NM_030625.2	59	aAg/aGg	2/12	0.831546518136544	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.831546518136544	1		310	107	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980798	40980798	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	158	612	0	ENST00000373198.4:c.1688C>T	p.Ser563Phe	p.S563F	ENST00000373198	NM_133170.3	563	tCc/tTc	10/32	0.156097721943419	1	FACETS	0.545	0.505	0.586	0.545	0.505	0.586	INDETERMINATE	1	TRUE	0	0.831546518136544	1		612	407	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912825	100912825	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	60	312	0	ENST00000325455.5:c.2497G>A	p.Glu833Lys	p.E833K	ENST00000325455	NM_001202474.3	833	Gaa/Aaa	7/8	1	2	FACETS	0.943	0.833	1	0.943	0.833	1	CLONAL	1	TRUE	1	0.831546518136544	2		312	153	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18439794	18439795	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0047981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	74	291	1	ENST00000266497.5:c.692_693delinsTT	p.Ser231Phe	p.S231F	ENST00000266497		231	tCC/tTT	2/31	0.171246701758419	4	FACETS	1	0.92	1	1	0.92	1	INDETERMINATE	2	TRUE	2	0.831546518136544	4		292	159	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509229	106509229	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	171	636	0	ENST00000359195.3:c.1223T>G	p.Val408Gly	p.V408G	ENST00000359195	NM_002649.2	408	gTg/gGg	2/11	0.157316680265624	3	FACETS	1	0.989	1	0.69	0.642	0.739	INDETERMINATE	1	TRUE	1	0.831546518136544	3		636	422	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216494	36216497	+	frameshift_variant	Frame_Shift_Del	DEL	CACG	CACG	TTA	novel	NA	P-0047981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	281	960	2	ENST00000222270.7:c.3757_3760delinsTTA	p.His1253LeufsTer102	p.H1253Lfs*102	ENST00000222270	NM_014727.1	1253	CACGtc/TTAtc	12/37	1	2	FACETS	0.972	0.92	1	0.972	0.92	1	CLONAL	1	TRUE	1	0.831546518136544	2		962	695	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0047982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	524	491	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.844364507502299	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.844364507502299	1		491	661	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374293	138374293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	1238	502	0	ENST00000289153.2:c.3151G>A	p.Glu1051Lys	p.E1051K	ENST00000289153	NM_006219.2	1051	Gaa/Aaa	22/22	0.804318283509377	5	FACETS	0.953	0.935	0.971	0.953	0.935	0.971	CLONAL	4	TRUE	1	0.844364507502299	5		502	1743	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435234	110435234	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769819684	NA	P-0047982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	161	513	1	ENST00000375856.3:c.3167C>T	p.Pro1056Leu	p.P1056L	ENST00000375856	NM_003749.2	1056	cCg/cTg	1/2	1	2	FACETS	0.494	0.454	0.536	0.494	0.454	0.536	SUBCLONAL	1	TRUE	1	0.844364507502299	2		514	772	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0047983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	150	371	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.213863888974498	3	FACETS	0.771	0.708	0.837	0.771	0.708	0.837	INDETERMINATE	2	TRUE	1	0.38	3		371	609	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0047983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	73	660	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.55	0.481	0.625	0.55	0.481	0.625	SUBCLONAL	1	TRUE	1	0.38	2		660	698	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266112	41266112	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913228	NA	P-0047983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	91	323	0	ENST00000349496.5:c.109T>C	p.Ser37Pro	p.S37P	ENST00000349496	NM_001904.3	37	Tct/Cct	3/15	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.38	2		323	456	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs149680468	NA	P-0047983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	51	302	2	ENST00000281708.4:c.1513C>A	p.Arg505Ser	p.R505S	ENST00000281708	NM_033632.3	505	Cgc/Agc	10/12	1	2	FACETS	0.555	0.472	0.646	0.555	0.472	0.646	SUBCLONAL	1	TRUE	1	0.38	2		304	484	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226859	2226879	+	inframe_deletion	In_Frame_Del	DEL	GCGGCGTCCTCCGCAGGCGGC	GCGGCGTCCTCCGCAGGCGGC	-	rs748637415	NA	P-0047984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	152	331	0	ENST00000398665.3:c.4353_4373del	p.Gly1452_Ala1458del	p.G1452_A1458del	ENST00000398665	NM_032482.2	1447	GCGGCGTCCTCCGCAGGCGGC/-	27/28	0.179886073802965	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	TRUE	0	0.179886073802965	3		331	552	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109314091	109314093	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs201384588	NA	P-0047984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	74	340	0	ENST00000436639.2:c.1130_1132del	p.Glu377del	p.E377del	ENST00000436639	NM_014454.2	377	gAAGtt/gtt	7/10	0.179886073802965	3	FACETS	0.946	0.831	1	0.631	0.554	0.713	CLONAL	2	TRUE	0	0.179886073802965	3		340	474	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950697	79950705	+	inframe_deletion	In_Frame_Del	DEL	GCTGCAGCG	GCTGCAGCG	-	rs758595508	NA	P-0047984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	80	183	0	ENST00000265081.6:c.162_170del	p.Ala60_Ala62del	p.A60_A62del	ENST00000265081	NM_002439.4	51	GCTGCAGCG/-	1/24	0.179886073802965	3	FACETS	0.982	0.872	1	0.982	0.872	1	CLONAL	3	TRUE	0	0.179886073802965	3		183	329	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610206	81610206	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs577092617	NA	P-0047984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	111	423	0	ENST00000298171.2:c.1804G>A	p.Val602Met	p.V602M	ENST00000298171	NM_000369.2	602	Gtg/Atg	10/10	0.179886073802965	3	FACETS	1	0.946	1	0.717	0.646	0.792	CLONAL	2	TRUE	0	0.179886073802965	3		423	625	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	140	349	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.592060190724905	2		350	472	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	329	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.583852634173013	2	FACETS	0.918	0.878	0.959	0.918	0.878	0.959	CLONAL	2	TRUE	0	0.592060190724905	2		327	605	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982392	201982393	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1185	73	950	0	ENST00000359651.3:c.772dup	p.Trp258LeufsTer43	p.W258Lfs*43	ENST00000359651		257	-/T	6/8	1	2	FACETS	0.196	0.17	0.224	0.196	0.17	0.224	SUBCLONAL	1	TRUE	1	0.592060190724905	2		950	1258	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123650	11123650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140016398	NA	P-0047985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	237	676	2	ENST00000358026.2:c.2300C>T	p.Ser767Phe	p.S767F	ENST00000358026	NM_001128849.1	767	tCc/tTc	16/36	1	2	FACETS	0.805	0.751	0.86	0.805	0.751	0.86	CLONAL	1	TRUE	1	0.592060190724905	2		678	995	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983019	201983020	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	97	883	1	ENST00000359651.3:c.869dup	p.Leu292ProfsTer9	p.L292Pfs*9	ENST00000359651		290	gag/gAag	7/8	1	2	FACETS	0.257	0.228	0.288	0.257	0.228	0.288	SUBCLONAL	1	TRUE	1	0.592060190724905	2		884	1274	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984391	201984391	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0047985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	62	736	0	ENST00000359651.3:c.1056C>G	p.Tyr352Ter	p.Y352*	ENST00000359651		352	taC/taG	8/8	1	2	FACETS	0.202	0.173	0.233	0.202	0.173	0.233	SUBCLONAL	1	TRUE	1	0.592060190724905	2		736	1039	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984689	72984689	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	90	901	0	ENST00000268489.5:c.2895G>C	p.Met965Ile	p.M965I	ENST00000268489	NM_006885.3	965	atG/atC	3/10	1	2	FACETS	0.246	0.217	0.277	0.246	0.217	0.277	SUBCLONAL	1	TRUE	1	0.592060190724905	2		901	1238	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0047986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	217	571	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	0.607978523086361	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.607978523086361	1		571	484	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65316513	65316513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755406627	NA	P-0047986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	134	388	0	ENST00000342505.4:c.1729C>T	p.Arg577Trp	p.R577W	ENST00000342505	NM_002227.2	577	Cgg/Tgg	12/25	1	2	FACETS	0.858	0.784	0.934	0.858	0.784	0.934	CLONAL	1	TRUE	1	0.607978523086361	2		388	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578262	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs483352697	NA	P-0047986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	193	654	0	ENST00000269305.4:c.587G>C	p.Arg196Pro	p.R196P	ENST00000269305	NM_001126112.2	196	cGa/cCa	6/11	0.607978523086361	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.607978523086361	1		654	427	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988089	85988089	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1207890235	NA	P-0047986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	91	258	0	ENST00000263360.6:c.1034C>G	p.Pro345Arg	p.P345R	ENST00000263360	NM_003797.3	345	cCc/cGc	10/12	0.57381490765282	3	FACETS	1	0.897	1	0.502	0.448	0.558	CLONAL	1	TRUE	1	0.607978523086361	3		258	389	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472628	88472628	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	105	417	0	ENST00000360948.2:c.1927C>G	p.Gln643Glu	p.Q643E	ENST00000360948	NM_001012338.2	643	Cag/Gag	16/19	0.57381490765282	3	FACETS	0.91	0.819	1	0.455	0.409	0.503	CLONAL	1	TRUE	1	0.607978523086361	3		417	495	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593504	48593504	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	124	274	0	ENST00000342988.3:c.1257del	p.Arg420ValfsTer16	p.R420Vfs*16	ENST00000342988	NM_005359.5	419	Ggg/gg	10/12	0.607978523086361	1	FACETS	0.996	0.917	1	0.996	0.917	1	CLONAL	1	TRUE	0	0.607978523086361	1		274	285	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057897	27057899	+	frameshift_variant	Frame_Shift_Del	DEL	CTC	CTC	TT	novel	NA	P-0047986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	198	703	0	ENST00000324856.7:c.1605_1607delinsTT	p.Gln537SerfsTer82	p.Q537Sfs*82	ENST00000324856	NM_006015.4	535	ccCTCc/ccTTc	3/20	NA	2	FACETS	0.944	0.878	1			1	INDETERMINATE	1	TRUE	NA	0.607978523086361	2		703	690	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753468	42753468	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	416	1454	0	ENST00000222329.4:c.796C>G	p.Pro266Ala	p.P266A	ENST00000222329	NM_006494.2	266	Ccg/Gcg	4/4	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		1454	1262	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948006	17948006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	9	2738	2	ENST00000458235.1:c.1718C>T	p.Ala573Val	p.A573V	ENST00000458235	NM_000215.3	573	gCg/gTg	13/24	0.371271596056481	4	FACETS	0.092	0.06	0.133	0.046	0.03	0.067	INDETERMINATE	1	TRUE	2	0.842881643821474	4		2740	426	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28586449	28586449	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0047988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	51	1523	0	ENST00000253063.3:c.90+1G>T		p.X30_splice	ENST00000253063	NM_031459.4	30			0.842881643821474	2	FACETS	0.558	0.48	0.641	0.279	0.24	0.321	SUBCLONAL	1	TRUE	0	0.842881643821474	2		1523	217	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12043945	12043945	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047988-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	33	652	1	ENST00000396373.4:c.1324C>A	p.Leu442Met	p.L442M	ENST00000396373	NM_001987.4	442	Ctg/Atg	8/8	0.74030015702831	4	FACETS	0.839	0.69	1	0.28	0.23	0.334	CLONAL	1	TRUE	1	0.74030015702831	4		653	185	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	200	349	1				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		350	306	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743924	40743924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199514226	NA	P-0048004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	49	470	0	ENST00000373198.4:c.3071C>T	p.Thr1024Met	p.T1024M	ENST00000373198	NM_133170.3	1024	aCg/aTg	23/32	0.218800998625471	5	FACETS	0.745	0.63	0.874	0.149	0.126	0.175	SUBCLONAL	1	TRUE	0	0.218800998625471	5		470	798	SUCCESS
APC	324	MSKCC	GRCh37	5	112175756	112175756	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	104	306	0	ENST00000257430.4:c.4466del	p.Leu1489TyrfsTer18	p.L1489Yfs*18	ENST00000257430	NM_000038.5	1489	Tta/ta	16/16	0.206272374448603	3	FACETS	0.958	0.866	1	0.958	0.866	1	CLONAL	3	TRUE	0	0.218800998625471	3		306	367	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262745	16262745	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	41	439	0	ENST00000375759.3:c.10010C>G	p.Thr3337Ser	p.T3337S	ENST00000375759	NM_015001.2	3337	aCc/aGc	11/15	0.20735918787726	2	FACETS	0.976	0.815	1	0.488	0.407	0.578	CLONAL	1	TRUE	0	0.218800998625471	2		439	384	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482426	56482426	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	164	662	0	ENST00000267101.3:c.974G>C	p.Gly325Ala	p.G325A	ENST00000267101	NM_001982.3	325	gGa/gCa	8/28	0.218800998625471	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.218800998625471	3		662	736	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915709	112915709	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	59	452	0	ENST00000351677.2:c.982A>C	p.Ile328Leu	p.I328L	ENST00000351677	NM_002834.3	328	Att/Ctt	9/16	0.218800998625471	3	FACETS	0.901	0.775	1	0.451	0.387	0.52	CLONAL	1	TRUE	1	0.218800998625471	3		452	664	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562068	21562068	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0048004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1258	138	1319	0	ENST00000382592.4:c.1851C>G	p.Tyr617Ter	p.Y617*	ENST00000382592	NM_014572.2	617	taC/taG	4/8	0.206601549020786	3	FACETS	1	0.909	1	0.334	0.303	0.367	CLONAL	1	TRUE	0	0.218800998625471	3		1319	1396	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303600	30303600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	48	486	0	ENST00000262643.3:c.28G>A	p.Ala10Thr	p.A10T	ENST00000262643	NM_001238.2	10	Gcg/Acg	3/12	0.216639475679367	3	FACETS	1	0.871	1	0.517	0.437	0.604	CLONAL	1	TRUE	1	0.218800998625471	3		486	471	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201847	152201847	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	26	399	0	ENST00000206249.3:c.701G>T	p.Arg234Met	p.R234M	ENST00000206249	NM_000125.3	234	aGg/aTg	3/8	0.218800998625471	3	FACETS	0.535	0.423	0.664	0.267	0.211	0.332	SUBCLONAL	1	TRUE	1	0.218800998625471	3		399	493	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939074	76939074	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	65	231	0	ENST00000373344.5:c.1674T>G	p.Ser558Arg	p.S558R	ENST00000373344	NM_000489.3	558	agT/agG	9/35	0.218800998625471	2	FACETS	0.758	0.66	0.863			1	SUBCLONAL	2	TRUE	NA	0.218800998625471	2		231	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	564	736	6	ENST00000269305.4:c.383del	p.Pro128LeufsTer42	p.P128Lfs*42	ENST00000269305	NM_001126112.2	128	cCt/ct	5/11	0.786027604148156	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.786027604148156	1		742	859	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442510	49442510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	248	436	0	ENST00000301067.7:c.4063G>A	p.Glu1355Lys	p.E1355K	ENST00000301067	NM_003482.3	1355	Gaa/Aaa	13/54	0.786027604148156	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.786027604148156	1		436	355	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442516	49442516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	226	411	0	ENST00000301067.7:c.4057G>A	p.Glu1353Lys	p.E1353K	ENST00000301067	NM_003482.3	1353	Gag/Aag	13/54	0.786027604148156	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.786027604148156	1		411	323	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033932	49033932	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	217	273	0	ENST00000267163.4:c.2069A>G	p.Asn690Ser	p.N690S	ENST00000267163	NM_000321.2	690	aAt/aGt	20/27	0.786027604148156	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.786027604148156	1		273	322	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913517	NA	P-0048006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	509	408	0	ENST00000288135.5:c.1676T>G	p.Val559Gly	p.V559G	ENST00000288135	NM_000222.2	559	gTt/gGt	11/21	0.68535688719362	4	FACETS	1	0.996	1			1	CLONAL	4	TRUE	NA	0.739833701923124	4		408	565	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486027	29486027	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs1555605362	NA	P-0048007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	20	149	0	ENST00000356175.3:c.205-1G>C		p.X69_splice	ENST00000356175	NM_000267.3	69			NA	2	FACETS	1	0.835	1			1	INDETERMINATE	1	TRUE	NA	0.541050084557559	2		149	69	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502423	186502423	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1328591615	NA	P-0048007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	30	328	0	ENST00000323963.5:c.146A>G	p.Tyr49Cys	p.Y49C	ENST00000323963		49	tAt/tGt	3/11	0.201281007081729	4	FACETS	0.55	0.444	0.669	0.183	0.148	0.223	INDETERMINATE	1	TRUE	1	0.541050084557559	4		328	311	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864090	97864090	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	101	508	0	ENST00000289081.3:c.1576C>A	p.Leu526Ile	p.L526I	ENST00000289081	NM_000136.2	526	Ctt/Att	15/15	0.537930340258391	2	FACETS	0.876	0.788	0.969	0.438	0.394	0.485	CLONAL	1	TRUE	0	0.541050084557559	2		508	426	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354295	70354295	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	165	955	0	ENST00000374080.3:c.4706C>T	p.Thr1569Ile	p.T1569I	ENST00000374080		1569	aCt/aTt	34/45	0.541050084557559	5	FACETS	1	0.934	1			1	CLONAL	1	TRUE	NA	0.541050084557559	5		955	1082	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888694	76888694	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0048007-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	83	293	0	ENST00000373344.5:c.5134+1G>T		p.X1712_splice	ENST00000373344	NM_000489.3	1712			0.541050084557559	5	FACETS	0.776	0.69	0.867			1	SUBCLONAL	2	TRUE	NA	0.541050084557559	5		293	358	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	881	349	1				ENST00000310581	NM_198253.2	-/1132			0.6552077614473	5	FACETS	0.926	0.908	0.944	0.926	0.908	0.944	CLONAL	5	TRUE	0	0.671681578497894	5		350	1137	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936983	48936983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690863	NA	P-0048009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	168	308	0	ENST00000267163.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000267163	NM_000321.2	251	Cga/Tga	8/27	0.671681578497894	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.671681578497894	1		308	304	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478922	56478922	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	704	765	1	ENST00000267101.3:c.378C>A	p.Asn126Lys	p.N126K	ENST00000267101	NM_001982.3	126	aaC/aaA	3/28	0.671681578497894	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.671681578497894	2		766	1013	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561764	55561764	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913505	NA	P-0048009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	58	308	0	ENST00000288135.5:c.154G>A	p.Asp52Asn	p.D52N	ENST00000288135	NM_000222.2	52	Gac/Aac	2/21	0.556223019693346	1	FACETS	0.348	0.3	0.399	0.348	0.3	0.399	SUBCLONAL	1	TRUE	0	0.671681578497894	1		308	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28934873	NA	P-0048009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	831	882	0	ENST00000269305.4:c.398T>C	p.Met133Thr	p.M133T	ENST00000269305	NM_001126112.2	133	aTg/aCg	5/11	0.671681578497894	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.671681578497894	2		882	1163	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459340	99459340	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs45451896	NA	P-0048009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	82	449	0	ENST00000268035.6:c.1976G>C	p.Arg659Pro	p.R659P	ENST00000268035	NM_000875.3	659	cGg/cCg	9/21	0.385502871601054	2	FACETS	0.557	0.494	0.625	0.279	0.247	0.313	INDETERMINATE	1	TRUE	0	0.671681578497894	2		449	438	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383249	42383249	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137953079	NA	P-0048009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	107	753	0	ENST00000221972.3:c.269C>T	p.Thr90Met	p.T90M	ENST00000221972	NM_021601.3	90	aCg/aTg	2/5	0.120209286939325	4	FACETS	0.606	0.543	0.673	0.303	0.271	0.337	INDETERMINATE	1	TRUE	2	0.671681578497894	4		753	879	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872197	45872197	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	313	655	0	ENST00000391945.4:c.237G>C	p.Glu79Asp	p.E79D	ENST00000391945	NM_000400.3	79	gaG/gaC	4/23	0.120209286939325	4	FACETS	0.865	0.818	0.912	0.865	0.818	0.912	INDETERMINATE	2	TRUE	2	0.671681578497894	4		655	901	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371824	118371824	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	163	386	0	ENST00000534358.1:c.6284del	p.Asn2095ThrfsTer26	p.N2095Tfs*26	ENST00000534358	NM_005933.3	2094	gAa/ga	25/36	0.238710747521841	1	FACETS	0.672	0.621	0.723	0.672	0.621	0.723	INDETERMINATE	1	TRUE	0	0.671681578497894	1		386	480	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380680	118380699	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGAGGAAAGTAATTTCAG	GAAGAGGAAAGTAATTTCAG	-	novel	NA	P-0048009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	73	271	0	ENST00000534358.1:c.10918_10937del	p.Glu3640LeufsTer19	p.E3640Lfs*19	ENST00000534358	NM_005933.3	3640	GAAGAGGAAAGTAATTTCAGc/c	30/36	0.238710747521841	1	FACETS	0.463	0.408	0.521	0.463	0.408	0.521	INDETERMINATE	1	TRUE	0	0.671681578497894	1		271	312	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114195	115114195	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751859591	NA	P-0048009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	48	652	0	ENST00000257566.3:c.1022G>A	p.Ser341Asn	p.S341N	ENST00000257566	NM_016569.3	341	aGt/aAt	6/8	0.671681578497894	2	FACETS	0.19	0.159	0.223	0.095	0.079	0.112	SUBCLONAL	1	TRUE	0	0.671681578497894	2		652	754	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756664	756664	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	660	481	0	ENST00000314574.4:c.164G>T	p.Ser55Ile	p.S55I	ENST00000314574	NM_005433.3	55	aGc/aTc	2/12	0.22580179412053	6	FACETS	0.934	0.909	0.959			1	INDETERMINATE	5	TRUE	NA	0.671681578497894	6		481	986	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524138	187524138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543576319	NA	P-0048009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	106	498	0	ENST00000441802.2:c.11401G>A	p.Glu3801Lys	p.E3801K	ENST00000441802	NM_005245.3	3801	Gag/Aag	20/27	0.485849243687078	1	FACETS	0.448	0.403	0.495	0.448	0.403	0.495	SUBCLONAL	1	TRUE	0	0.671681578497894	1		498	468	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156732	20156732	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	235	388	0	ENST00000379607.5:c.25G>C	p.Gly9Arg	p.G9R	ENST00000379607	NM_001412.3	9	Ggt/Cgt	2/7	1	2	FACETS	0.937	0.88	0.994	0.937	0.88	0.994	CLONAL	1	TRUE	1	0.81178541412831	2		388	618	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	248	463	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.942	0.883	1	0.942	0.883	1	CLONAL	1	TRUE	1	0.665163087381299	2		463	792	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195628	123195631	+	frameshift_variant	Frame_Shift_Del	DEL	AGAT	AGAT	-	novel	NA	P-0048012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	16	166	0	ENST00000218089.9:c.1544_1547del	p.Asp515GlyfsTer6	p.D515Gfs*6	ENST00000218089	NM_001042749.1	514	acAGAT/ac	17/35	1	2	FACETS	0.276	0.204	0.36	0.276	0.204	0.36	SUBCLONAL	1	TRUE	1	0.663638813740886	2		166	175	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321484	62321484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777153220	NA	P-0048012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	142	775	2	ENST00000360203.5:c.2186G>A	p.Arg729His	p.R729H	ENST00000360203	NM_001283009.1	729	cGt/cAt	25/35	0.663638813740886	3	FACETS	0.453	0.411	0.496	0.226	0.205	0.248	SUBCLONAL	1	TRUE	1	0.663638813740886	3		777	1259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0048031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	35	512	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.201	0.164	0.242	0.201	0.164	0.242	SUBCLONAL	1	FALSE	1	0.843933251879086	2		512	413	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0048031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	25	712	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.118	0.092	0.147	0.118	0.092	0.147	SUBCLONAL	1	FALSE	1	0.843933251879086	2		712	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0048031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	21	499	0	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	1	2	FACETS	0.145	0.111	0.184	0.145	0.111	0.184	SUBCLONAL	1	FALSE	1	0.843933251879086	2		499	344	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958804	55958804	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	76	345	0	ENST00000263923.4:c.3049G>A	p.Glu1017Lys	p.E1017K	ENST00000263923	NM_002253.2	1017	Gag/Aag	22/30	1	2	FACETS	0.519	0.458	0.583	0.519	0.458	0.583	SUBCLONAL	1	FALSE	1	0.843933251879086	2		345	347	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65312347	65312347	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519753	NA	P-0048032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	40	484	0	ENST00000342505.4:c.1972G>T	p.Val658Phe	p.V658F	ENST00000342505	NM_002227.2	658	Gtc/Ttc	14/25	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		484	640	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0048033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	47	566	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.309713691432292	2	FACETS	0.776	0.664	0.895	0.776	0.664	0.895	SUBCLONAL	2	TRUE	0	0.327567636690883	2		566	185	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0048033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	106	621	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	1	2	FACETS	0.967	0.868	1	0.967	0.868	1	CLONAL	1	TRUE	1	0.327567636690883	2		621	669	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974679	21974679	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs864622636	NA	P-0048033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	64	454	0	ENST00000304494.5:c.148C>T	p.Gln50Ter	p.Q50*	ENST00000304494	NM_000077.4	50	Cag/Tag	1/3	0.327567636690883	1	FACETS	0.807	0.701	0.92	0.807	0.701	0.92	CLONAL	1	TRUE	0	0.327567636690883	1		454	405	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199897	138199897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751928111	NA	P-0048033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	20	455	0	ENST00000237289.4:c.1315C>T	p.Arg439Trp	p.R439W	ENST00000237289	NM_001270507.1	439	Cgg/Tgg	7/9	0.327567636690883	1	FACETS	0.274	0.209	0.35	0.274	0.209	0.35	SUBCLONAL	1	TRUE	0	0.327567636690883	1		455	373	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436137	116436137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	44	288	0	ENST00000397752.3:c.4132G>A	p.Glu1378Lys	p.E1378K	ENST00000397752	NM_000245.2	1378	Gag/Aag	21/21	0.267166042243441	4	FACETS	0.892	0.749	1	0.446	0.374	0.525	CLONAL	1	TRUE	2	0.327567636690883	4		288	400	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874827	151874827	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779874722	NA	P-0048033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	76	256	0	ENST00000262189.6:c.7711C>T	p.Arg2571Trp	p.R2571W	ENST00000262189	NM_170606.2	2571	Cgg/Tgg	38/59	0.267166042243441	4	FACETS	0.901	0.796	1	0.901	0.796	1	CLONAL	2	TRUE	2	0.327567636690883	4		256	342	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127933380	127933380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	38	373	0	ENST00000373547.4:c.155G>A	p.Gly52Glu	p.G52E	ENST00000373547	NM_002721.4	52	gGa/gAa	2/7	1	2	FACETS	0.853	0.709	1	0.853	0.709	1	CLONAL	1	TRUE	1	0.327567636690883	2		373	272	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0048034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	162	287	2	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	0.31466842912073	4	FACETS	1	0.981	1			1	CLONAL	2	TRUE	NA	0.314939410257126	4		289	563	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0048034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	43	253	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.314939410257126	1	FACETS	0.959	0.809	1	0.959	0.809	1	CLONAL	1	TRUE	0	0.314939410257126	1		253	240	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119781	70119781	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1274036689	NA	P-0048034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	111	575	0	ENST00000245479.2:c.788del	p.Gly263AlafsTer16	p.G263Afs*16	ENST00000245479	NM_000346.3	261	gaG/ga	3/3	1	2	FACETS	0.975	0.877	1	0.975	0.877	1	CLONAL	1	TRUE	1	0.314939410257126	2		575	723	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033252	69033252	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	62	331	0	ENST00000288368.4:c.3692C>A	p.Thr1231Asn	p.T1231N	ENST00000288368	NM_024870.2	1231	aCt/aAt	30/40	0.314939410257126	3	FACETS	0.772	0.667	0.887	0.257	0.222	0.296	SUBCLONAL	1	TRUE	0	0.314939410257126	3		331	590	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912181	114912181	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	82	387	0	ENST00000543371.1:c.1251G>C	p.Trp417Cys	p.W417C	ENST00000543371	NM_001198531.1	417	tgG/tgC	11/14	1	2	FACETS	0.833	0.735	0.938	0.833	0.735	0.938	CLONAL	1	TRUE	1	0.314939410257126	2		387	625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578207	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	117	518	1	ENST00000269305.4:c.642dup	p.Ser215Ter	p.S215*	ENST00000269305	NM_001126112.2	214	-/T	6/11	0.314939410257126	1	FACETS	0.995	0.899	1	0.995	0.899	1	CLONAL	1	TRUE	0	0.314939410257126	1		519	629	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370266	40370266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745315653	NA	P-0048034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	88	633	0	ENST00000293328.3:c.1072G>A	p.Gly358Arg	p.G358R	ENST00000293328	NM_012448.3	358	Ggg/Agg	9/19	1	2	FACETS	0.63	0.557	0.708	0.63	0.557	0.708	SUBCLONAL	1	TRUE	1	0.314939410257126	2		633	887	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509780	187509780	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755374400	NA	P-0048034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	21	209	0	ENST00000441802.2:c.13733C>T	p.Pro4578Leu	p.P4578L	ENST00000441802	NM_005245.3	4578	cCg/cTg	27/27	1	2	FACETS	0.387	0.297	0.491	0.387	0.297	0.491	SUBCLONAL	1	TRUE	1	0.314939410257126	2		209	345	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101910006	101910006	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	41	138	0	ENST00000374994.4:c.1329del	p.Val444LeufsTer7	p.V444Lfs*7	ENST00000374994	NM_004612.2	442	agA/ag	8/9	1	2	FACETS	0.975	0.817	1	0.975	0.817	1	CLONAL	1	TRUE	1	0.314939410257126	2		138	267	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs371769427	NA	P-0048035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	21	152	0	ENST00000291552.4:c.101C>A	p.Ser34Tyr	p.S34Y	ENST00000291552	NM_006758.2	34	tCt/tAt	2/8	0.256254034421743	1	FACETS	0.321	0.247	0.407	0.321	0.247	0.407	SUBCLONAL	1	TRUE	0	0.33872858837348	1		152	321	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716327	52716327	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	105	621	0	ENST00000322088.6:c.771G>C	p.Trp257Cys	p.W257C	ENST00000322088	NM_014225.5	257	tgG/tgC	6/15	0.175376357683517	1	FACETS	0.665	0.596	0.739	0.665	0.596	0.739	INDETERMINATE	1	TRUE	0	0.33872858837348	1		621	774	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578507	7578507	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519977	NA	P-0048035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	221	941	0	ENST00000269305.4:c.423C>G	p.Cys141Trp	p.C141W	ENST00000269305	NM_001126112.2	141	tgC/tgG	5/11	0.33872858837348	1	FACETS	0.958	0.891	1	0.958	0.891	1	CLONAL	1	TRUE	0	0.33872858837348	1		941	1131	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101453	27101453	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	112	559	0	ENST00000324856.7:c.4735C>T	p.Gln1579Ter	p.Q1579*	ENST00000324856	NM_006015.4	1579	Cag/Tag	18/20	1	2	FACETS	0.829	0.745	0.917	0.829	0.745	0.917	CLONAL	1	TRUE	1	0.33872858837348	2		559	798	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466000	69466000	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	174	799	2	ENST00000227507.2:c.838G>A	p.Glu280Lys	p.E280K	ENST00000227507	NM_053056.2	280	Gag/Aag	5/5	0.33872858837348	1	FACETS	0.874	0.805	0.947	0.874	0.805	0.947	CLONAL	1	TRUE	0	0.33872858837348	1		801	976	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029111	26029111	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	21	228	0	ENST00000435504.4:c.239T>C	p.Val80Ala	p.V80A	ENST00000435504		80	gTa/gCa	4/13	0.175376357683517	1	FACETS	0.356	0.274	0.452	0.356	0.274	0.452	INDETERMINATE	1	TRUE	0	0.33872858837348	1		228	289	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626032	12626032	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	73	340	0	ENST00000251849.4:c.1928C>G	p.Pro643Arg	p.P643R	ENST00000251849	NM_002880.3	643	cCg/cGg	17/17	0.175376357683517	1	FACETS	0.74	0.649	0.837	0.74	0.649	0.837	INDETERMINATE	1	TRUE	0	0.33872858837348	1		340	484	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0048036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	116	383	0				ENST00000310581	NM_198253.2	-/1132			0.570760980174405	3	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	1	0.570760980174405	3		383	259	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827982	40827982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	193	435	0	ENST00000373198.4:c.2446G>A	p.Glu816Lys	p.E816K	ENST00000373198	NM_133170.3	816	Gag/Aag	17/32	0.304532502543124	5	FACETS	1	0.987	1	0.827	0.772	0.883	INDETERMINATE	2	TRUE	2	0.570760980174405	5		435	506	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155180	55155180	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600187	NA	P-0048036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	118	343	0	ENST00000257290.5:c.2779G>A	p.Glu927Lys	p.E927K	ENST00000257290	NM_006206.4	927	Gag/Aag	21/23	0.489372512199068	3	FACETS	0.963	0.884	1	0.963	0.884	1	CLONAL	2	TRUE	1	0.570760980174405	3		343	276	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350909	89350909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	239	573	0	ENST00000301030.4:c.2041G>A	p.Glu681Lys	p.E681K	ENST00000301030	NM_001256183.1	681	Gaa/Aaa	9/13	0.570760980174405	3	FACETS	0.905	0.851	0.959	0.905	0.851	0.959	CLONAL	2	TRUE	1	0.570760980174405	3		573	595	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460560	149460560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1188913271	NA	P-0048036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	113	599	0	ENST00000286301.3:c.77G>A	p.Ser26Asn	p.S26N	ENST00000286301	NM_005211.3	26	aGt/aAt	3/22	0.570760980174405	3	FACETS	0.969	0.876	1	0.485	0.438	0.534	CLONAL	1	TRUE	1	0.570760980174405	3		599	525	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633290	3633290	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1330131811	NA	P-0048036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	312	867	0	ENST00000294008.3:c.4961A>G	p.His1654Arg	p.H1654R	ENST00000294008	NM_032444.2	1654	cAt/cGt	14/15	0.570760980174405	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.570760980174405	3		867	690	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556893	29556893	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	38	116	0	ENST00000356175.3:c.2891C>T	p.Thr964Ile	p.T964I	ENST00000356175	NM_000267.3	964	aCc/aTc	22/57	0.567955518954206	4	FACETS	1	0.944	1	0.658	0.552	0.772	CLONAL	1	TRUE	2	0.570760980174405	4		116	159	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78704413	78704417	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCC	CAGCC	-	novel	NA	P-0048036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	155	368	0	ENST00000306801.3:c.562_566del	p.Ser188ValfsTer72	p.S188Vfs*72	ENST00000306801	NM_020761.2	187	ggCAGCCcg/ggcg	5/34	0.567955518954206	4	FACETS	0.935	0.864	1	0.935	0.864	1	CLONAL	2	TRUE	2	0.570760980174405	4		368	456	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240239	5240239	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	147	735	0	ENST00000357368.4:c.1675C>T	p.Leu559Phe	p.L559F	ENST00000357368	NM_002850.3	559	Ctc/Ttc	12/38	0.570760980174405	3	FACETS	1	0.919	1	0.502	0.459	0.546	CLONAL	1	TRUE	1	0.570760980174405	3		735	660	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795001	42795001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	123	824	1	ENST00000575354.2:c.2081C>T	p.Ser694Phe	p.S694F	ENST00000575354	NM_015125.3	694	tCt/tTt	10/20	0.570760980174405	3	FACETS	0.901	0.817	0.989	0.45	0.408	0.495	CLONAL	1	TRUE	1	0.570760980174405	3		825	615	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906436	50906436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	280	871	0	ENST00000440232.2:c.1097C>T	p.Ala366Val	p.A366V	ENST00000440232	NM_002691.3	366	gCc/gTc	9/27	NA	2	FACETS	0.962	0.916	1			1	INDETERMINATE	2	TRUE	NA	0.570760980174405	2		871	510	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520485	176520485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778723081	NA	P-0048036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	219	832	1	ENST00000292408.4:c.1330G>A	p.Ala444Thr	p.A444T	ENST00000292408	NM_213647.1	444	Gcc/Acc	10/18	0.570760980174405	3	FACETS	1	0.976	1	0.553	0.515	0.592	CLONAL	1	TRUE	1	0.570760980174405	3		833	892	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0048037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1195	45	760	1	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	1	2	FACETS	0.186	0.156	0.221	0.186	0.156	0.221	SUBCLONAL	1	TRUE	1	0.389382640771902	2		761	1240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0048037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	54	622	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	1	2	FACETS	0.327	0.278	0.381	0.327	0.278	0.381	SUBCLONAL	1	TRUE	1	0.389382640771902	2		622	848	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038335	180038335	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369284915	NA	P-0048037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	43	681	1	ENST00000261937.6:c.3682G>A	p.Ala1228Thr	p.A1228T	ENST00000261937	NM_182925.4	1228	Gcc/Acc	27/30	0.16182627050531	0	FACETS	0.163	0.136	0.194			1	INDETERMINATE	1	TRUE	0	0.389382640771902	0		682	826	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0048038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	261	743	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.527146583422824	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.538248006161173	1		744	700	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632308	215632308	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	135	430	0	ENST00000260947.4:c.1466C>A	p.Thr489Asn	p.T489N	ENST00000260947	NM_000465.2	489	aCc/aAc	6/11	1	2	FACETS	0.866	0.791	0.945	0.866	0.791	0.945	CLONAL	1	TRUE	1	0.538248006161173	2		430	579	SUCCESS
APC	324	MSKCC	GRCh37	5	112174086	112174086	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	83	215	0	ENST00000257430.4:c.2795del	p.Ser932Ter	p.S932*	ENST00000257430	NM_000038.5	932	tCa/ta	16/16	0.527146583422824	1	FACETS	0.92	0.825	1	0.92	0.825	1	CLONAL	1	TRUE	0	0.538248006161173	1		215	245	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244392	5244392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377318412	NA	P-0048040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	160	837	6	ENST00000357368.4:c.1090G>A	p.Val364Ile	p.V364I	ENST00000357368	NM_002850.3	364	Gtc/Atc	11/38	0.194800130613525	3	FACETS	0.931	0.854	1	0.931	0.854	1	CLONAL	2	TRUE	1	0.2087914813386	3		843	909	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519988	NA	P-0048040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	64	646	0	ENST00000269305.4:c.808T>G	p.Phe270Val	p.F270V	ENST00000269305	NM_001126112.2	270	Ttt/Gtt	8/11	1	2	FACETS	0.927	0.803	1	0.927	0.803	1	CLONAL	1	TRUE	1	0.2087914813386	2		646	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0048040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	85	798	1	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	1	2	FACETS	0.998	0.881	1	0.998	0.881	1	CLONAL	1	TRUE	1	0.2087914813386	2		799	816	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	44	252	0	ENST00000257430.4:c.4199C>A	p.Ser1400Ter	p.S1400*	ENST00000257430	NM_000038.5	1400	tCg/tAg	16/16	0.2087914813386	2	FACETS	0.772	0.652	0.903	0.772	0.652	0.903	CLONAL	2	TRUE	0	0.2087914813386	2		252	273	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0048041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	33	483	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.151524280679913	3	FACETS	0.764	0.623	0.922	0.382	0.311	0.461	INDETERMINATE	1	TRUE	1	0.277935757642275	3		483	354	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0048041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	22	222	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.474	0.367	0.598	0.474	0.367	0.598	SUBCLONAL	1	TRUE	1	0.277935757642275	2		222	334	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188049	151188049	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519950	NA	P-0048041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	29	146	0	ENST00000262187.5:c.104A>G	p.Tyr35Cys	p.Y35C	ENST00000262187	NM_005614.3	35	tAc/tGc	2/8	0.151524280679913	3	FACETS	0.594	0.477	0.728	0.297	0.238	0.364	INDETERMINATE	1	TRUE	1	0.277935757642275	3		146	400	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510639	38510639	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	52	651	0	ENST00000254066.5:c.893A>G	p.His298Arg	p.H298R	ENST00000254066	NM_000964.3	298	cAc/cGc	7/9	1	2	FACETS	0.47	0.399	0.548	0.47	0.399	0.548	SUBCLONAL	1	TRUE	1	0.277935757642275	2		651	796	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604761	48604766	+	frameshift_variant	Frame_Shift_Del	DEL	ACTTAC	ACTTAC	TT	novel	NA	P-0048041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	28	236	1	ENST00000342988.3:c.1583_1588delinsTT	p.His528LeufsTer8	p.H528Lfs*8	ENST00000342988	NM_005359.5	528	cACTTACac/cTTac	12/12	1	2	FACETS	0.564	0.451	0.693	0.564	0.451	0.693	SUBCLONAL	1	TRUE	1	0.277935757642275	2		237	357	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0048045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	153	357	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	0.229747229576343	1	FACETS	1	0.952	1	1	0.994	1	CLONAL	3	TRUE	0	0.229747229576343	1		357	379	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159748	20159748	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	214	316	0	ENST00000379607.5:c.11A>G	p.Asn4Ser	p.N4S	ENST00000379607	NM_001412.3	4	aAt/aGt	1/7	0.114943641125711	2	FACETS	0.95	0.921	0.977			1	INDETERMINATE	8	TRUE	NA	0.229747229576343	2		316	245	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225990	53225998	+	inframe_deletion	In_Frame_Del	DEL	CAGTCCTCG	CAGTCCTCG	-	novel	NA	P-0048045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	248	622	0	ENST00000375401.3:c.2851_2859del	p.Arg951_Leu953del	p.R951_L953del	ENST00000375401	NM_004187.3	951	CGAGGACTG/-	19/26	0.114943641125711	2	FACETS	1	0.987	1			1	INDETERMINATE	5	TRUE	NA	0.229747229576343	2		622	394	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0048046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	25	357	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	0.25563959982402	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		357	86	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156740	20156740	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	31	177	0	ENST00000379607.5:c.17G>T	p.Gly6Val	p.G6V	ENST00000379607	NM_001412.3	6	gGt/gTt	2/7	1	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		177	68	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459100	120459100	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1360817753	NA	P-0048047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	153	645	0	ENST00000256646.2:c.6245C>G	p.Pro2082Arg	p.P2082R	ENST00000256646	NM_024408.3	2082	cCt/cGt	34/34	1	2	FACETS	0.926	0.849	1	0.926	0.849	1	CLONAL	1	TRUE	1	0.435847675316089	2		645	758	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265112	10265112	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	125	676	0	ENST00000340748.4:c.1828del	p.Glu610ArgfsTer87	p.E610Rfs*87	ENST00000340748		610	Gag/ag	21/40	1	2	FACETS	0.836	0.758	0.918	0.836	0.758	0.918	CLONAL	1	TRUE	1	0.435847675316089	2		676	686	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502725	149502725	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs756032678	NA	P-0048047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	144	806	0	ENST00000261799.4:c.2063A>G	p.Asp688Gly	p.D688G	ENST00000261799	NM_002609.3	688	gAc/gGc	15/23	1	2	FACETS	0.858	0.783	0.936	0.858	0.783	0.936	CLONAL	1	TRUE	1	0.435847675316089	2		806	770	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519990	NA	P-0048048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	399	705	0	ENST00000269305.4:c.796G>C	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Cga	8/11	0.505743255870021	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.539857566372195	2		705	722	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843242	128843242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs912880810	NA	P-0048048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	371	966	0	ENST00000249373.3:c.349C>T	p.Arg117Cys	p.R117C	ENST00000249373	NM_005631.4	117	Cgc/Tgc	2/12	0.272495224582221	4	FACETS	0.822	0.779	0.865	0.822	0.779	0.865	INDETERMINATE	2	TRUE	2	0.539857566372195	4		966	1288	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321555	62321555	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755033095	NA	P-0048048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	618	1036	1	ENST00000360203.5:c.2257G>A	p.Glu753Lys	p.E753K	ENST00000360203	NM_001283009.1	753	Gag/Aag	25/35	0.242698344712455	3	FACETS	1	0.995	1	0.764	0.737	0.79	INDETERMINATE	2	TRUE	0	0.539857566372195	3		1037	1269	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401031	139401031	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	166	1193	0	ENST00000277541.6:c.3962C>T	p.Thr1321Ile	p.T1321I	ENST00000277541	NM_017617.3	1321	aCc/aTc	24/34	0.258896393346318	2	FACETS	0.489	0.448	0.532	0.244	0.224	0.266	INDETERMINATE	1	TRUE	0	0.539857566372195	2		1193	1258	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929224	44929227	+	frameshift_variant	Frame_Shift_Del	DEL	CAGA	CAGA	-	rs886039398	NA	P-0048048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	221	350	0	ENST00000377967.4:c.2326_2329del	p.Asp776IlefsTer8	p.D776Ifs*8	ENST00000377967	NM_021140.2	775	tCAGAc/tc	17/29	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.539857566372195	1		350	406	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0048049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	54	480	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.99	0.844	1	0.99	0.844	1	CLONAL	1	TRUE	1	0.16	2		480	682	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0048049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	58	572	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.755	0.647	0.874	0.755	0.647	0.874	SUBCLONAL	1	TRUE	1	0.16	2		573	960	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121909229	NA	P-0048049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	53	478	1	ENST00000371953.3:c.389G>T	p.Arg130Leu	p.R130L	ENST00000371953	NM_000314.4	130	cGa/cTa	5/9	0.168527976512311	3	FACETS	0.868	0.742	1	0.868	0.742	1	CLONAL	2	TRUE	1	0.16	3		479	412	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650711	67650711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567610917	NA	P-0048049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	82	552	2	ENST00000264010.4:c.1016G>A	p.Arg339Gln	p.R339Q	ENST00000264010	NM_006565.3	339	cGg/cAg	5/12	1	2	FACETS	0.877	0.771	0.992	0.877	0.771	0.992	CLONAL	1	TRUE	1	0.16	2		554	1169	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926249	112926249	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs397509344	NA	P-0048049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	76	492	0	ENST00000351677.2:c.1382C>G	p.Ala461Gly	p.A461G	ENST00000351677	NM_002834.3	461	gCt/gGt	12/16	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.16	2		492	860	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579592	7579592	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0048050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	224	704	0	ENST00000269305.4:c.97-2A>T		p.X33_splice	ENST00000269305	NM_001126112.2	33			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		704	378	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939108	48939108	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0048050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	99	192	0	ENST00000267163.4:c.939+1G>T		p.X313_splice	ENST00000267163	NM_000321.2	313			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		192	181	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0048051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	312	411	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		411	363	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544748	65544748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	345	436	0	ENST00000358664.4:c.178C>T	p.Arg60Trp	p.R60W	ENST00000358664	NM_002382.4	60	Cgg/Tgg	4/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		436	392	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593662	55593664	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0048051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	318	432	0	ENST00000288135.5:c.1729_1731del	p.Pro577del	p.P577del	ENST00000288135	NM_000222.2	576	ctTCCt/ctt	11/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		432	731	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659551	88659551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	92	383	0	ENST00000372037.3:c.334G>A	p.Asp112Asn	p.D112N	ENST00000372037	NM_004329.2	112	Gat/Aat	6/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		383	396	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475158	475158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	393	550	0	ENST00000399788.2:c.479C>T	p.Ser160Leu	p.S160L	ENST00000399788	NM_001042603.1	160	tCa/tTa	4/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		550	850	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991092	41991092	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	275	397	0	ENST00000219905.7:c.2045C>G	p.Thr682Arg	p.T682R	ENST00000219905	NM_001164273.1	682	aCa/aGa	4/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		397	319	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022324	36022324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760138531	NA	P-0048051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	612	934	2	ENST00000358208.4:c.377C>T	p.Ser126Leu	p.S126L	ENST00000358208		126	tCg/tTg	4/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		936	1368	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440833	52440853	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGGGCCCTTACCCTGCAGTG	CAGGGCCCTTACCCTGCAGTG	-	novel	NA	P-0048051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	481	651	0	ENST00000460680.1:c.651_659+12del		p.X217_splice	ENST00000460680	NM_004656.3	217		8/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		651	575	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342452	118342452	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	GATCT	novel	NA	P-0048051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	83	197	0	ENST00000534358.1:c.578delinsGATCT	p.Pro193ArgfsTer10	p.P193Rfs*10	ENST00000534358	NM_005933.3	193	cCa/cGATCTa	3/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		197	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0048053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	154	494	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.284735016017612	1	FACETS	0.972	0.889	1	0.972	0.889	1	CLONAL	1	TRUE	0	0.284735016017612	1		494	954	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0048053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	76	424	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.284735016017612	1	FACETS	0.936	0.824	1	0.936	0.824	1	CLONAL	1	TRUE	0	0.284735016017612	1		424	489	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481671	56481671	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	187	809	0	ENST00000267101.3:c.706T>C	p.Ser236Pro	p.S236P	ENST00000267101	NM_001982.3	236	Tca/Cca	6/28	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.284735016017612	2		809	1261	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293605	1293605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1389	260	1302	1	ENST00000310581.5:c.1396C>T	p.Arg466Trp	p.R466W	ENST00000310581	NM_198253.2	466	Cgg/Tgg	2/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.284735016017612	2		1303	1649	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158148	106158148	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	69	317	0	ENST00000380013.4:c.3049G>A	p.Asp1017Asn	p.D1017N	ENST00000380013	NM_001127208.2	1017	Gat/Aat	3/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.284735016017612	2		317	437	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729668	162729668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	105	615	1	ENST00000367921.3:c.754C>T	p.Pro252Ser	p.P252S	ENST00000367921	NM_006182.2	252	Ccc/Tcc	8/18	1	2	FACETS	0.874	0.782	0.971	0.874	0.782	0.971	CLONAL	1	TRUE	1	0.284735016017612	2		616	844	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105522	11105522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	113	510	0	ENST00000358026.2:c.1438C>T	p.Leu480Phe	p.L480F	ENST00000358026	NM_001128849.1	480	Ctc/Ttc	9/36	0.284735016017612	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.284735016017612	1		510	616	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211048	36211048	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0048053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1398	226	1164	1	ENST00000222270.7:c.799A>T	p.Lys267Ter	p.K267*	ENST00000222270	NM_014727.1	267	Aaa/Taa	3/37	1	2	FACETS	0.977	0.907	1	0.977	0.907	1	CLONAL	1	TRUE	1	0.284735016017612	2		1165	1624	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599331	55599331	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	83	403	1	ENST00000288135.5:c.2457T>A	p.Asn819Lys	p.N819K	ENST00000288135	NM_000222.2	819	aaT/aaA	17/21	1	2	FACETS	0.951	0.84	1	0.951	0.84	1	CLONAL	1	TRUE	1	0.284735016017612	2		404	613	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913527	NA	P-0048054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	166	378	0	ENST00000311936.3:c.436G>C	p.Ala146Pro	p.A146P	ENST00000311936	NM_004985.3	146	Gca/Cca	4/5	0.208307510857839	3	FACETS	0.92	0.861	0.98	0.614	0.574	0.653	INDETERMINATE	2	TRUE	0	0.764816048710357	3		378	326	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481412	140481412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913353	NA	P-0048054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	139	373	0	ENST00000288602.6:c.1396G>A	p.Gly466Arg	p.G466R	ENST00000288602	NM_004333.4	466	Gga/Aga	11/18	0.762843014530268	3	FACETS	0.964	0.883	1	0.482	0.441	0.525	CLONAL	1	TRUE	1	0.764816048710357	3		373	521	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125296	7125296	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs777937157	NA	P-0048054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	298	670	0	ENST00000302850.5:c.3256G>A	p.Val1086Met	p.V1086M	ENST00000302850	NM_000208.2	1086	Gtg/Atg	17/22	1	2	FACETS	0.932	0.881	0.984	0.932	0.881	0.984	CLONAL	1	TRUE	1	0.764816048710357	2		670	836	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627818	187627818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149283579	NA	P-0048054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	323	600	0	ENST00000441802.2:c.3164C>T	p.Thr1055Met	p.T1055M	ENST00000441802	NM_005245.3	1055	aCg/aTg	2/27	1	2	FACETS	0.958	0.908	1	0.958	0.908	1	CLONAL	1	TRUE	1	0.764816048710357	2		600	882	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340177	116340177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200074800	NA	P-0048054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	265	294	0	ENST00000397752.3:c.1039G>A	p.Ala347Thr	p.A347T	ENST00000397752	NM_000245.2	347	Gca/Aca	2/21	0.762843014530268	3	FACETS	0.994	0.945	1	0.994	0.945	1	CLONAL	2	TRUE	1	0.764816048710357	3		294	482	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092947	29092947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881688	NA	P-0048054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	271	453	1	ENST00000328354.6:c.1037G>A	p.Arg346His	p.R346H	ENST00000328354	NM_007194.3	346	cGt/cAt	10/15	0.208307510857839	3	FACETS	0.938	0.891	0.985	0.626	0.594	0.657	INDETERMINATE	2	TRUE	0	0.764816048710357	3		454	522	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456773	32456773	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	434	929	0	ENST00000332351.3:c.119G>A	p.Trp40Ter	p.W40*	ENST00000332351	NM_024426.4	40	tGg/tAg	1/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.764816048710357	2		929	1131	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295773	212295773	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	183	581	0	ENST00000342788.4:c.2540G>T	p.Arg847Leu	p.R847L	ENST00000342788	NM_005235.2	847	cGt/cTt	21/28	1	2	FACETS	0.838	0.778	0.899	0.838	0.778	0.899	CLONAL	1	TRUE	1	0.764816048710357	2		581	571	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111058	193111058	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	87	190	0	ENST00000367435.3:c.591C>G	p.Ile197Met	p.I197M	ENST00000367435	NM_024529.4	197	atC/atG	7/17	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.764816048710357	2		190	191	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871250	12871250	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0048054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	148	224	0	ENST00000228872.4:c.475+2T>A		p.X159_splice	ENST00000228872	NM_004064.3	159			0.69010823196425	3	FACETS	0.966	0.901	1	0.966	0.901	1	CLONAL	2	TRUE	1	0.764816048710357	3		224	277	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289316	33289316	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	197	456	2	ENST00000374542.5:c.236C>T	p.Ala79Val	p.A79V	ENST00000374542	NM_001141970.1	79	gCa/gTa	3/8	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.764816048710357	2		458	515	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900164	101900164	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	230	262	0	ENST00000374994.4:c.598A>C	p.Thr200Pro	p.T200P	ENST00000374994	NM_004612.2	200	Aca/Cca	4/9	0.764816048710357	2	FACETS	0.996	0.957	1	0.996	0.957	1	CLONAL	2	TRUE	0	0.764816048710357	2		262	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0048055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	232	491	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.713553410471717	1	FACETS	0.927	0.877	0.978	0.927	0.877	0.978	CLONAL	1	TRUE	0	0.713553410471717	1		491	451	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0048055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	221	277	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.993	0.949	1	1	0.995	1	CLONAL	2	TRUE	1	0.713553410471717	2		277	312	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175481	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0048055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	89	262	0	ENST00000257430.4:c.4192_4193del	p.Arg1399PhefsTer9	p.R1399Ffs*9	ENST00000257430	NM_000038.5	1397	GAg/g	16/16	1	2	FACETS	0.823	0.738	0.912	0.823	0.738	0.912	CLONAL	1	TRUE	1	0.713553410471717	2		262	303	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943658	9943658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	222	579	0	ENST00000330684.3:c.1283C>T	p.Thr428Met	p.T428M	ENST00000330684	NM_001134407.1	428	aCg/aTg	5/13	1	2	FACETS	0.888	0.83	0.947	0.888	0.83	0.947	CLONAL	1	TRUE	1	0.713553410471717	2		579	701	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26970440	26970441	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	30	133	0	ENST00000381527.3:c.815dup	p.Met273AspfsTer3	p.M273Dfs*3	ENST00000381527	NM_001260.1	270	ata/atAa	8/13	0.687545767378551	3	FACETS	0.967	0.795	1	0.483	0.397	0.577	CLONAL	1	TRUE	1	0.713553410471717	3		133	118	SUCCESS
APC	324	MSKCC	GRCh37	5	112111380	112111381	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0048055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	49	190	0	ENST00000257430.4:c.478dup	p.Ala160GlyfsTer8	p.A160Gfs*8	ENST00000257430	NM_000038.5	159	-/G	5/16	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.713553410471717	2		190	115	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077427	30077427	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0048056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	13	141	0	ENST00000338641.4:c.1575-1G>C		p.X525_splice	ENST00000338641	NM_000268.3	525			1	2	FACETS	0.765	0.55	1	0.765	0.55	1	CLONAL	1	TRUE	1	0.278692412006816	2		141	122	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224163	98224163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138154222	NA	P-0048056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	25	280	0	ENST00000331920.6:c.2678G>A	p.Arg893His	p.R893H	ENST00000331920	NM_000264.3	893	cGc/cAc	16/24	0.278692412006816	1	FACETS	0.708	0.561	0.876	0.708	0.561	0.876	SUBCLONAL	1	TRUE	0	0.278692412006816	1		280	218	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908873	101908873	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200595614	NA	P-0048056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	43	352	0	ENST00000374994.4:c.1237C>T	p.Arg413Ter	p.R413*	ENST00000374994	NM_004612.2	413	Cga/Tga	7/9	0.278692412006816	1	FACETS	0.781	0.656	0.919	0.781	0.656	0.919	CLONAL	1	TRUE	0	0.278692412006816	1		352	340	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497215	149497215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748918501	NA	P-0048056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	49	580	0	ENST00000261799.4:c.3103G>A	p.Glu1035Lys	p.E1035K	ENST00000261799	NM_002609.3	1035	Gag/Aag	22/23	0.278692412006816	1	FACETS	0.648	0.549	0.756	0.648	0.549	0.756	SUBCLONAL	1	TRUE	0	0.278692412006816	1		580	467	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106532	27106532	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	72	614	0	ENST00000324856.7:c.6143G>A	p.Trp2048Ter	p.W2048*	ENST00000324856	NM_006015.4	2048	tGg/tAg	20/20	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.278692412006816	2		614	468	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781494	135781494	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	32	356	0	ENST00000298552.3:c.1471A>G	p.Thr491Ala	p.T491A	ENST00000298552	NM_001162426.1	491	Aca/Gca	15/23	0.278692412006816	1	FACETS	0.727	0.592	0.877	0.727	0.592	0.877	SUBCLONAL	1	TRUE	0	0.278692412006816	1		356	272	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422317	422317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763626820	NA	P-0048056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	34	320	0	ENST00000399788.2:c.2941G>A	p.Ala981Thr	p.A981T	ENST00000399788	NM_001042603.1	981	Gcc/Acc	20/28	1	2	FACETS	0.777	0.637	0.934	0.777	0.637	0.934	CLONAL	1	TRUE	1	0.278692412006816	2		320	314	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679265	88679265	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	26	427	0	ENST00000360948.2:c.772C>A	p.Leu258Met	p.L258M	ENST00000360948	NM_001012338.2	258	Ctg/Atg	8/19	1	2	FACETS	0.536	0.425	0.664	0.536	0.425	0.664	SUBCLONAL	1	TRUE	1	0.278692412006816	2		427	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579454	7579457	+	frameshift_variant	Frame_Shift_Del	DEL	GCTG	GCTG	-	novel	NA	P-0048056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	38	708	0	ENST00000269305.4:c.230_233del	p.Pro77GlnfsTer45	p.P77Qfs*45	ENST00000269305	NM_001126112.2	77	cCAGCa/ca	4/11	1	2	FACETS	0.741	0.614	0.883	0.741	0.614	0.883	SUBCLONAL	1	TRUE	1	0.278692412006816	2		708	368	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702555	52702555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	28	296	0	ENST00000394830.3:c.343G>A	p.Asp115Asn	p.D115N	ENST00000394830	NM_018313.4	115	Gac/Aac	4/30	1	2	FACETS	0.552	0.441	0.678	0.552	0.441	0.678	SUBCLONAL	1	TRUE	1	0.278692412006816	2		296	364	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778056	27778056	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	51	508	0	ENST00000369163.2:c.205C>T	p.Gln69Ter	p.Q69*	ENST00000369163	NM_003536.2	69	Cag/Tag	1/1	1	2	FACETS	0.922	0.786	1	0.922	0.786	1	CLONAL	1	TRUE	1	0.278692412006816	2		508	397	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527362	137527362	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0048056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	23	378	0	ENST00000367739.4:c.284C>G	p.Ser95Ter	p.S95*	ENST00000367739	NM_000416.2	95	tCa/tGa	3/7	1	2	FACETS	0.433	0.337	0.545	0.433	0.337	0.545	SUBCLONAL	1	TRUE	1	0.278692412006816	2		378	381	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993014	72993014	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1425268929	NA	P-0048056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	52	641	0	ENST00000268489.5:c.1031A>C	p.Asn344Thr	p.N344T	ENST00000268489	NM_006885.3	344	aAc/aCc	2/10	1	2	FACETS	0.716	0.61	0.833	0.716	0.61	0.833	SUBCLONAL	1	TRUE	1	0.278692412006816	2		641	521	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993008	72993008	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	49	636	0	ENST00000268489.5:c.1037del	p.Asn346ThrfsTer6	p.N346Tfs*6	ENST00000268489	NM_006885.3	346	aAc/ac	2/10	1	2	FACETS	0.687	0.582	0.802	0.687	0.582	0.802	SUBCLONAL	1	TRUE	1	0.278692412006816	2		636	512	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0048058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	85	314	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.783455340817981	3	FACETS	0.965	0.862	1	0.482	0.431	0.537	CLONAL	1	TRUE	1	0.783455340817981	3		314	313	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106915	27106915	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	181	592	0	ENST00000324856.7:c.6526C>T	p.Gln2176Ter	p.Q2176*	ENST00000324856	NM_006015.4	2176	Cag/Tag	20/20	1	2	FACETS	0.928	0.863	0.994	0.928	0.863	0.994	CLONAL	1	TRUE	1	0.783455340817981	2		592	498	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115726	8115726	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0048058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	160	282	0	ENST00000346208.3:c.1072A>T	p.Lys358Ter	p.K358*	ENST00000346208		358	Aag/Tag	6/6	0.639351695786651	4	FACETS	0.839	0.777	0.902	0.839	0.777	0.902	CLONAL	2	TRUE	2	0.783455340817981	4		282	434	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063390	67063390	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0048058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	250	323	0	ENST00000412916.2:c.78+2T>A		p.X26_splice	ENST00000412916		26			0.781338045772091	2	FACETS	0.982	0.945	1	0.982	0.945	1	CLONAL	2	TRUE	0	0.783455340817981	2		323	325	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859435	151859436	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	200	384	1	ENST00000262189.6:c.11226dup	p.Lys3743Ter	p.K3743*	ENST00000262189	NM_170606.2	3742	-/T	43/59	0.639351695786651	4	FACETS	0.842	0.786	0.898	0.842	0.786	0.898	CLONAL	2	TRUE	2	0.783455340817981	4		385	541	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517896	8517896	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	59	245	0	ENST00000356435.5:c.1495G>T	p.Gly499Ter	p.G499*	ENST00000356435		499	Gga/Tga	10/35	0.779005695932396	3	FACETS	0.62	0.537	0.71	0.31	0.268	0.355	SUBCLONAL	1	TRUE	1	0.783455340817981	3		245	338	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0048059-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	124	561	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.309620448112415	2		561	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555525585	NA	P-0048060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	95	297	0	ENST00000269305.4:c.673-2A>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.494672484528772	1	FACETS	0.318	0.285	0.352	0.318	0.285	0.352	INDETERMINATE	1	TRUE	0	0.897653068955314	1		297	367	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56871625	56871625	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	212	294	1	ENST00000308159.5:c.2005T>C	p.Ser669Pro	p.S669P	ENST00000308159	NM_014669.4	669	Tcc/Ccc	18/22	1	2	FACETS	0.945	0.887	1	0.945	0.887	1	CLONAL	1	TRUE	1	0.897653068955314	2		295	500	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576918	7576918	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	212	402	0	ENST00000269305.4:c.928A>T	p.Asn310Tyr	p.N310Y	ENST00000269305	NM_001126112.2	310	Aac/Tac	9/11	0.494672484528772	1	FACETS	0.604	0.569	0.639	0.604	0.569	0.639	INDETERMINATE	1	TRUE	0	0.897653068955314	1		402	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576926	7576937	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTAGGAAAGAG	GCTAGGAAAGAG	-	novel	NA	P-0048060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	199	386	0	ENST00000269305.4:c.920-11_920del		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	0.494672484528772	1	FACETS	0.59	0.554	0.626	0.59	0.554	0.626	INDETERMINATE	1	TRUE	0	0.897653068955314	1		386	414	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947484	38947484	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	38	151	0	ENST00000357387.3:c.4196A>C	p.Asn1399Thr	p.N1399T	ENST00000357387	NM_152756.3	1399	aAt/aCt	32/38	0.897653068955314	5	FACETS	0.45	0.372	0.538	0.113	0.093	0.135	SUBCLONAL	1	TRUE	1	0.897653068955314	5		151	441	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21968240	21968260	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTCTGCAGAGGGCAGAAAGAA	GTCTGCAGAGGGCAGAAAGAA	-	novel	NA	P-0048060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	96	210	0	ENST00000304494.5:c.458-19_459del		p.X153_splice	ENST00000304494	NM_000077.4	153		3/3	0.897653068955314	1	FACETS	0.907	0.849	0.961	0.907	0.849	0.961	CLONAL	1	TRUE	0	0.897653068955314	1		210	130	SUCCESS
BLM	641	MSKCC	GRCh37	15	91328225	91328225	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	31	441	0	ENST00000355112.3:c.2737C>A	p.Leu913Ile	p.L913I	ENST00000355112	NM_000057.2	913	Ctc/Atc	14/22	1	2	FACETS	0.878	0.709	1	0.878	0.709	1	CLONAL	1	TRUE	1	0.13	2		441	543	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56862941	56862941	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	25	445	0	ENST00000308159.5:c.847C>A	p.Leu283Met	p.L283M	ENST00000308159	NM_014669.4	283	Ctg/Atg	9/22	1	2	FACETS	0.851	0.67	1	0.851	0.67	1	CLONAL	1	TRUE	1	0.13	2		445	452	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879630	37879630	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	59	836	0	ENST00000269571.5:c.2005G>T	p.Val669Leu	p.V669L	ENST00000269571		669	Gtg/Ttg	17/27	1	2	FACETS	0.988	0.847	1	0.988	0.847	1	CLONAL	1	TRUE	1	0.13	2		836	919	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921745	111921745	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	21	370	0	ENST00000393256.3:c.534C>A	p.His178Gln	p.H178Q	ENST00000393256	NM_006538.4	178	caC/caA	4/4	0.0983790315244055	0	FACETS	0.812	0.625	1			1	CLONAL	1	TRUE	0	0.13	0		370	346	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0048062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	74	347	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.564944599709442	2		347	203	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020733	37020733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	206	509	1	ENST00000358127.4:c.112C>T	p.Arg38Cys	p.R38C	ENST00000358127	NM_001280556.1	38	Cgc/Tgc	2/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.564944599709442	2		510	679	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0048062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	225	516	0	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.564944599709442	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.564944599709442	1		516	508	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872436	35872436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	237	706	2	ENST00000216797.5:c.467G>A	p.Cys156Tyr	p.C156Y	ENST00000216797	NM_020529.2	156	tGc/tAc	3/6	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.564944599709442	2		708	811	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135025	2135025	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	211	774	0	ENST00000219476.3:c.4567G>T	p.Glu1523Ter	p.E1523*	ENST00000219476	NM_000548.3	1523	Gag/Tag	35/42	0.564944599709442	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.564944599709442	1		774	457	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492739	56492739	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	124	471	0	ENST00000407977.2:c.200G>T	p.Gly67Val	p.G67V	ENST00000407977		67	gGt/gTt	2/10	0.564944599709442	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.564944599709442	1		471	295	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395242	139395242	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	287	976	0	ENST00000277541.6:c.5696A>G	p.Asn1899Ser	p.N1899S	ENST00000277541	NM_017617.3	1899	aAc/aGc	31/34	1	2	FACETS	0.937	0.882	0.994	0.937	0.882	0.994	CLONAL	1	TRUE	1	0.564944599709442	2		976	1084	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0048064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	37	566	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.981	0.81	1	0.981	0.81	1	CLONAL	1	TRUE	1	0.19	2		566	397	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0048065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	11	383	0				ENST00000310581	NM_198253.2	-/1132			0.128129383620082	0	FACETS	0.298	0.207	0.41			1	INDETERMINATE	1	TRUE	0	0.371129659146883	0		383	125	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0048065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	22	510	1	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	0.433	0.336	0.545	0.433	0.336	0.545	SUBCLONAL	1	TRUE	1	0.371129659146883	2		511	274	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0048065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	27	640	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.498	0.397	0.613	0.498	0.397	0.613	SUBCLONAL	1	TRUE	1	0.371129659146883	2		642	292	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956220	55956220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190050670	NA	P-0048065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	16	402	0	ENST00000263923.4:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000263923	NM_002253.2	1032	cGa/cAa	23/30	NA	2	FACETS	0.315	0.232	0.413			1	INDETERMINATE	1	TRUE	NA	0.371129659146883	2		402	274	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156495	55156495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	21	426	0	ENST00000257290.5:c.2896C>T	p.His966Tyr	p.H966Y	ENST00000257290	NM_006206.4	966	Cac/Tac	22/23	0.371129659146883	3	FACETS	0.461	0.355	0.584			1	SUBCLONAL	1	TRUE	NA	0.371129659146883	3		426	291	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0048065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	64	892	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	0.371129659146883	4	FACETS	0.963	0.836	1	0.482	0.418	0.551	CLONAL	1	TRUE	2	0.371129659146883	4		892	491	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675108	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0048065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	24	797	0	ENST00000249776.8:c.71_72delinsTT	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCC/tTT	1/9	0.127701926079753	4	FACETS	0.388	0.303	0.486	0.194	0.151	0.243	INDETERMINATE	1	TRUE	2	0.371129659146883	4		797	457	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981315	68981315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866864487	NA	P-0048065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	22	267	0	ENST00000288368.4:c.1387C>T	p.Arg463Cys	p.R463C	ENST00000288368	NM_024870.2	463	Cgc/Tgc	12/40	1	2	FACETS	0.395	0.306	0.498	0.395	0.306	0.498	SUBCLONAL	1	TRUE	1	0.371129659146883	2		267	300	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510816	120510817	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0048065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	24	406	0	ENST00000256646.2:c.1147_1148delinsTT	p.Pro383Phe	p.P383F	ENST00000256646	NM_024408.3	383	CCt/TTt	7/34	0.184325584032599	4	FACETS	0.57	0.447	0.712	0.285	0.223	0.356	INDETERMINATE	1	TRUE	2	0.371129659146883	4		406	311	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884350	151884350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	13	186	0	ENST00000262189.6:c.5005C>T	p.Pro1669Ser	p.P1669S	ENST00000262189	NM_170606.2	1669	Cct/Tct	33/59	1	2	FACETS	0.464	0.332	0.623	0.464	0.332	0.623	SUBCLONAL	1	TRUE	1	0.371129659146883	2		186	151	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101135	27101135	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	29	738	0	ENST00000324856.7:c.4417C>T	p.Gln1473Ter	p.Q1473*	ENST00000324856	NM_006015.4	1473	Cag/Tag	18/20	1	2	FACETS	0.465	0.374	0.569	0.465	0.374	0.569	SUBCLONAL	1	TRUE	1	0.371129659146883	2		738	336	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113822	11113822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	15	694	0	ENST00000358026.2:c.1930G>A	p.Glu644Lys	p.E644K	ENST00000358026	NM_001128849.1	644	Gag/Aag	12/36	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.371129659146883	NA		694	256	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220408	98220409	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0048065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	20	580	0	ENST00000331920.6:c.3054_3055delinsAA	p.Trp1018_Glu1019delinsTer	p.W1018_E1019delins*	ENST00000331920	NM_000264.3	1018	tgGGag/tgAAag	18/24	1	2	FACETS	0.372	0.284	0.474	0.372	0.284	0.474	SUBCLONAL	1	TRUE	1	0.371129659146883	2		580	290	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373237	118373238	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0048065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	14	391	1	ENST00000534358.1:c.6630_6631delinsTT	p.Arg2211Trp	p.R2211W	ENST00000534358	NM_005933.3	2210	ctCCgg/ctTTgg	27/36	0.233780617906414	4	FACETS	0.414	0.299	0.553	0.207	0.149	0.277	SUBCLONAL	1	TRUE	2	0.371129659146883	4		392	250	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642832	3642832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	17	783	0	ENST00000294008.3:c.2195G>A	p.Gly732Glu	p.G732E	ENST00000294008	NM_032444.2	732	gGg/gAg	11/15	1	2	FACETS	0.318	0.237	0.414	0.318	0.237	0.414	SUBCLONAL	1	TRUE	1	0.371129659146883	2		783	288	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579372	7579373	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCCT	novel	NA	P-0048065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	27	807	0	ENST00000269305.4:c.311_314dup	p.Ser106GlyfsTer44	p.S106Gfs*44	ENST00000269305	NM_001126112.2	105	ggc/ggAGGGc	4/11	1	2	FACETS	0.396	0.315	0.489	0.396	0.315	0.489	SUBCLONAL	1	TRUE	1	0.371129659146883	2		807	367	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094879	11094880	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0048065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	19	1020	1	ENST00000358026.2:c.52_53delinsTT	p.Pro18Leu	p.P18L	ENST00000358026	NM_001128849.1	18	CCg/TTg	2/36	1	2	FACETS	0.307	0.232	0.394	0.307	0.232	0.394	SUBCLONAL	1	TRUE	1	0.371129659146883	2		1021	334	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302643	15302643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761407832	NA	P-0048065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	18	971	1	ENST00000263388.2:c.715G>A	p.Asp239Asn	p.D239N	ENST00000263388	NM_000435.2	239	Gac/Aac	5/33	1	2	FACETS	0.29	0.218	0.376	0.29	0.218	0.376	SUBCLONAL	1	TRUE	1	0.371129659146883	2		972	334	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023523	31023523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	13	415	0	ENST00000375687.4:c.3008C>T	p.Ser1003Phe	p.S1003F	ENST00000375687	NM_015338.5	1003	tCt/tTt	13/13	1	2	FACETS	0.28	0.199	0.379	0.28	0.199	0.379	SUBCLONAL	1	TRUE	1	0.371129659146883	2		415	250	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170011293	170011293	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	14	354	0	ENST00000295797.4:c.1414C>T	p.Gln472Ter	p.Q472*	ENST00000295797	NM_002740.5	472	Caa/Taa	14/18	0.184325584032599	4	FACETS	0.387	0.28	0.518	0.194	0.14	0.259	INDETERMINATE	1	TRUE	2	0.371129659146883	4		354	267	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750458	41750458	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553898212	NA	P-0048065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	31	559	1	ENST00000226382.2:c.170G>A	p.Cys57Tyr	p.C57Y	ENST00000226382	NM_003924.3	57	tGc/tAc	1/3	0.371129659146883	3	FACETS	0.621	0.503	0.754			1	SUBCLONAL	1	TRUE	NA	0.371129659146883	3		560	319	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187468	32187468	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753266937	NA	P-0048065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	19	770	2	ENST00000375023.3:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000375023	NM_004557.3	471	Cgt/Tgt	8/30	1	2	FACETS	0.334	0.253	0.428	0.334	0.253	0.428	SUBCLONAL	1	TRUE	1	0.371129659146883	2		772	307	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220546	98220547	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0048065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	12	430	2	ENST00000331920.6:c.2916_2917delinsTT	p.Gln973Ter	p.Q973*	ENST00000331920	NM_000264.3	972	gcCCag/gcTTag	18/24	1	2	FACETS	0.325	0.228	0.444	0.325	0.228	0.444	SUBCLONAL	1	TRUE	1	0.371129659146883	2		432	199	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992414	72992414	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs62620235	NA	P-0048066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	42	735	0	ENST00000268489.5:c.1631C>T	p.Ser544Leu	p.S544L	ENST00000268489	NM_006885.3	544	tCg/tTg	2/10	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.200356156860471	2		735	347	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481403	+	missense_variant	Missense_Mutation	DNP	CC	CC	GA	rs1057519720	NA	P-0048066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	16	244	0	ENST00000288602.6:c.1405_1406delinsTC	p.Gly469Ser	p.G469S	ENST00000288602	NM_004333.4	469	GGa/TCa	11/18	1	2	FACETS	0.859	0.637	1	0.859	0.637	1	CLONAL	1	TRUE	1	0.200356156860471	2		244	186	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467800	66467800	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	21	221	0	ENST00000273854.3:c.469G>C	p.Glu157Gln	p.E157Q	ENST00000273854	NM_004439.5	157	Gag/Cag	3/18	0.126135729243395	1	FACETS	1	0.829	1	1	0.829	1	CLONAL	1	TRUE	0	0.200356156860471	1		221	174	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242716	66242716	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	16	216	0	ENST00000273854.3:c.1856G>T	p.Trp619Leu	p.W619L	ENST00000273854	NM_004439.5	619	tGg/tTg	9/18	0.126135729243395	1	FACETS	0.866	0.643	1	0.866	0.643	1	CLONAL	1	TRUE	0	0.200356156860471	1		216	166	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259862	16259862	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	19	410	0	ENST00000375759.3:c.7127A>G	p.Gln2376Arg	p.Q2376R	ENST00000375759	NM_015001.2	2376	cAg/cGg	11/15	1	2	FACETS	0.753	0.572	0.964	0.753	0.572	0.964	CLONAL	1	TRUE	1	0.200356156860471	2		410	252	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574011	7574012	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CGAAGCGCTCACGCCCACGGATCTGCAGCAACAGAGGAGGGGGAGA	novel	NA	P-0048066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	15	706	0	ENST00000269305.4:c.994-24_1015dup	p.Glu339ValfsTer13	p.E339Vfs*13	ENST00000269305	NM_001126112.2	339	gag/gTCTCCCCCTCCTCTGTTGCTGCAGATCCGTGGGCGTGAGCGCTTCGag	10/11	0.191460474383811	1	FACETS	0.483	0.353	0.64	0.483	0.353	0.64	SUBCLONAL	1	TRUE	0	0.200356156860471	1		706	279	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546078	29546079	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0048066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	32	356	0	ENST00000356175.3:c.1583_1584delinsTT	p.Gly528Val	p.G528V	ENST00000356175	NM_000267.3	528	gGG/gTT	14/57	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.200356156860471	2		356	273	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10264980	10264980	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	34	326	0	ENST00000340748.4:c.1960G>T	p.Gly654Cys	p.G654C	ENST00000340748		654	Ggc/Tgc	21/40	0.200356156860471	1	FACETS	0.76	0.626	0.907	1	0.95	1	CLONAL	2	TRUE	0	0.200356156860471	1		326	201	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982461	25982461	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	20	226	0	ENST00000435504.4:c.829A>T	p.Ile277Phe	p.I277F	ENST00000435504		277	Att/Ttt	9/13	1	2	FACETS	1	0.81	1	1	0.81	1	CLONAL	1	TRUE	1	0.200356156860471	2		226	188	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169977798	169977798	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	39	256	1	ENST00000295797.4:c.265G>T	p.Ala89Ser	p.A89S	ENST00000295797	NM_002740.5	89	Gcc/Tcc	3/18	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.200356156860471	2		257	346	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729708	41729708	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	28	532	0	ENST00000242208.4:c.821G>T	p.Gly274Val	p.G274V	ENST00000242208	NM_002192.2	274	gGa/gTa	3/3	1	2	FACETS	0.998	0.8	1	0.998	0.8	1	CLONAL	1	TRUE	1	0.200356156860471	2		532	280	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513009	106513009	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	23	172	0	ENST00000359195.3:c.2023A>T	p.Ser675Cys	p.S675C	ENST00000359195	NM_002649.2	675	Agc/Tgc	3/11	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.200356156860471	2		172	155	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981635	70981635	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	27	890	0	ENST00000276594.2:c.461C>A	p.Pro154His	p.P154H	ENST00000276594	NM_024504.3	154	cCt/cAt	2/8	0.200356156860471	1	FACETS	0.722	0.575	0.889	0.722	0.575	0.889	SUBCLONAL	1	TRUE	0	0.200356156860471	1		890	336	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209735	98209735	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0048066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	41	656	0	ENST00000331920.6:c.3805-2A>C		p.X1269_splice	ENST00000331920	NM_000264.3	1269			0.118009931557516	1	FACETS	1	0.955	1	1	0.955	1	INDETERMINATE	1	TRUE	0	0.200356156860471	1		656	252	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0048067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	57	277	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.85	0.741	0.966	0.85	0.741	0.966	CLONAL	1	TRUE	1	0.667128302268292	2		277	201	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0048067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	32	147	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.905	0.753	1	0.905	0.753	1	CLONAL	1	TRUE	1	0.667128302268292	2		147	106	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0048067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	58	302	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.848	0.74	0.962	0.848	0.74	0.962	CLONAL	1	TRUE	1	0.667128302268292	2		302	205	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0048067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	136	588	3	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.667128302268292	1	FACETS	0.964	0.893	1	0.964	0.893	1	CLONAL	1	TRUE	0	0.667128302268292	1		591	282	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32819964	32819964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531615408	NA	P-0048067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	259	710	0	ENST00000354258.4:c.946G>A	p.Val316Met	p.V316M	ENST00000354258	NM_000593.5	316	Gtg/Atg	3/11	1	2	FACETS	0.973	0.915	1	0.973	0.915	1	CLONAL	1	TRUE	1	0.667128302268292	2		710	798	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64288905	64288905	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	99	454	0	ENST00000370651.3:c.301G>A	p.Ala101Thr	p.A101T	ENST00000370651	NM_003463.4	101	Gct/Act	4/6	0.667128302268292	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.667128302268292	1		454	192	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951087	48951088	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs1131690889	NA	P-0048071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	142	192	0	ENST00000267163.4:c.1251_1252del	p.Arg418SerfsTer9	p.R418Sfs*9	ENST00000267163	NM_000321.2	417	AAa/a	13/27	0.809838275830847	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.809838275830847	2		192	150	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932618	39932622	+	frameshift_variant	Frame_Shift_Del	DEL	GGTAA	GGTAA	-	novel	NA	P-0048071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	181	1067	0	ENST00000378444.4:c.1977_1981del	p.Tyr660SerfsTer3	p.Y660Sfs*3	ENST00000378444	NM_001123385.1	659	ccTTACCca/ccca	4/15	0.462868815407899	1	FACETS	0.235	0.216	0.255	0.235	0.216	0.255	INDETERMINATE	1	TRUE	0	0.809838275830847	1		1067	1132	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023472	31023472	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs145132837	NA	P-0048073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	143	521	0	ENST00000375687.4:c.2957A>G	p.Asn986Ser	p.N986S	ENST00000375687	NM_015338.5	986	aAc/aGc	13/13	0.508286545146004	4	FACETS	1	0.961	1	0.363	0.331	0.396	CLONAL	1	TRUE	1	0.653368979949591	4		521	665	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945098	31945098	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0048073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	51	739	0	ENST00000340398.3:c.3G>A	p.Met1?	p.M1?	ENST00000340398	NM_001013699.2	1	atG/atA	1/1	0.652546518851802	3	FACETS	0.233	0.197	0.273	0.117	0.098	0.137	SUBCLONAL	1	TRUE	1	0.653368979949591	3		739	888	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522408	176522408	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2190	7343	844	0	ENST00000292408.4:c.1597A>G	p.Ile533Val	p.I533V	ENST00000292408	NM_213647.1	533	Atc/Gtc	12/18	0.653368979949591	24	FACETS	1	0.998	1			1	CLONAL	19	TRUE	NA	0.653368979949591	24		844	9533	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	135	349	1				ENST00000310581	NM_198253.2	-/1132			0.673870082474182	6	FACETS	0.952	0.886	1	0.952	0.886	1	CLONAL	4	FALSE	2	0.673870082474182	6		350	247	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0048074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	257	703	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA	2	FACETS		NA	1			1	INDETERMINATE	3	FALSE	NA	0.673870082474182	2		703	305	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416552	49416552	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	190	648	0	ENST00000301067.7:c.16159C>T	p.Gln5387Ter	p.Q5387*	ENST00000301067	NM_003482.3	5387	Cag/Tag	51/54	0.225055918952802	6	FACETS	0.925	0.864	0.987	0.925	0.864	0.987	INDETERMINATE	3	FALSE	3	0.673870082474182	6		648	477	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017833	31017833	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	290	907	0	ENST00000375687.4:c.695G>A	p.Arg232Lys	p.R232K	ENST00000375687	NM_015338.5	232	aGa/aAa	8/13	0.316785860884583	4	FACETS	0.89	0.841	0.941	0.89	0.841	0.941	INDETERMINATE	2	FALSE	2	0.673870082474182	4		907	809	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41560083	41560106	+	inframe_deletion	In_Frame_Del	DEL	GAAAGATGCATCAGATCTGTGTCC	GAAAGATGCATCAGATCTGTGTCC	-	novel	NA	P-0048074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	94	300	0	ENST00000263253.7:c.3755_3778del	p.Arg1252_Leu1260delinsIle	p.R1252_L1260delinsI	ENST00000263253	NM_001429.3	1252	aGAAAGATGCATCAGATCTGTGTCCtt/att	22/31	0.203465908893837	5	FACETS	0.845	0.759	0.934	0.563	0.506	0.623	INDETERMINATE	2	FALSE	2	0.673870082474182	5		300	332	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569771	41569771	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	85	176	0	ENST00000263253.7:c.4762A>G	p.Met1588Val	p.M1588V	ENST00000263253	NM_001429.3	1588	Atg/Gtg	29/31	0.203465908893837	5	FACETS	0.858	0.776	0.942	0.858	0.776	0.942	INDETERMINATE	3	FALSE	2	0.673870082474182	5		176	197	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057078	180057078	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	43	984	1	ENST00000261937.6:c.541C>A	p.Gln181Lys	p.Q181K	ENST00000261937	NM_182925.4	181	Cag/Aag	5/30	0.673870082474182	1	FACETS	0.281	0.236	0.33	0.281	0.236	0.33	SUBCLONAL	1	FALSE	0	0.673870082474182	1		985	301	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878607	151878607	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	234	568	1	ENST00000262189.6:c.6338C>A	p.Ser2113Ter	p.S2113*	ENST00000262189	NM_170606.2	2113	tCa/tAa	36/59	0.673870082474182	4	FACETS	0.933	0.876	0.991	0.933	0.876	0.991	CLONAL	2	FALSE	2	0.673870082474182	4		569	623	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179116	123179579	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTATCATATATGATGAGTATATGATGGATACAGTCATTTCACTTCTTACAGGATTGTCTGACTCACAAGTCAGAGCATTTCGACATACAAGCACCCTGGCAGGTCGGTATTTAGAAATATTTTCTGCATATTGTCTTAGATTTGAGATGAAAAAGATTCTCATTTAAAGAGAAAGGAAATAACAGAGATACAAATTAATTTTATTTATAAAGTGACCACTAAGAGGACACTCCCCCATCCCTCCTGCGAATTCCTGGAAATGGGATGATAATTTCAGTTTTGATTTTGTGAAGGTATACTATAACTAGTATTTGGTAATTTTCTTGTATACTATGCATACTGTGCCACAGCAGGGGAGAATTGGACAATAGGTATGTGTTGGGTTCTTGAAAAATACTATGCCACAGCAAGGGAAAATTGGACTATAGGTATGCATTGGATTATTGAAAAATACCATGCCACA	AGTATCATATATGATGAGTATATGATGGATACAGTCATTTCACTTCTTACAGGATTGTCTGACTCACAAGTCAGAGCATTTCGACATACAAGCACCCTGGCAGGTCGGTATTTAGAAATATTTTCTGCATATTGTCTTAGATTTGAGATGAAAAAGATTCTCATTTAAAGAGAAAGGAAATAACAGAGATACAAATTAATTTTATTTATAAAGTGACCACTAAGAGGACACTCCCCCATCCCTCCTGCGAATTCCTGGAAATGGGATGATAATTTCAGTTTTGATTTTGTGAAGGTATACTATAACTAGTATTTGGTAATTTTCTTGTATACTATGCATACTGTGCCACAGCAGGGGAGAATTGGACAATAGGTATGTGTTGGGTTCTTGAAAAATACTATGCCACAGCAAGGGAAAATTGGACTATAGGTATGCATTGGATTATTGAAAAATACCATGCCACA	-	novel	NA	P-0048074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	195	285	0	ENST00000218089.9:c.567_667+363del		p.X189_splice	ENST00000218089	NM_001042749.1	189		8/35	0.673870082474182	2	FACETS	1	0.97	1			1	CLONAL	2	FALSE	NA	0.673870082474182	2		285	282	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0048076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	49	303	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.434649189278028	3	FACETS	0.845	0.72	0.98	0.422	0.36	0.49	CLONAL	1	FALSE	1	0.504513548564747	3		303	288	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0048076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	149	277	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.469257716649097	2	FACETS	0.914	0.849	0.98	0.914	0.849	0.98	CLONAL	2	FALSE	0	0.504513548564747	2		277	323	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0048076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	60	300	1	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	0.815	0.707	0.929	0.815	0.707	0.929	CLONAL	1	FALSE	1	0.504513548564747	2		301	292	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0048076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	207	916	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.454502188460805	1	FACETS	0.875	0.816	0.937	0.875	0.816	0.937	CLONAL	1	FALSE	0	0.504513548564747	1		916	701	SUCCESS
APC	324	MSKCC	GRCh37	5	112174112	112174112	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	48	276	0	ENST00000257430.4:c.2821G>T	p.Glu941Ter	p.E941*	ENST00000257430	NM_000038.5	941	Gaa/Taa	16/16	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	FALSE	1	0.504513548564747	2		276	179	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771828	135771828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779599439	NA	P-0048076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	176	820	0	ENST00000298552.3:c.3289C>T	p.Arg1097Cys	p.R1097C	ENST00000298552	NM_001162426.1	1097	Cgt/Tgt	23/23	0.110437187752326	0	FACETS	0.534	0.494	0.576			1	INDETERMINATE	1	FALSE	0	0.504513548564747	0		820	647	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325792	65325792	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	102	440	0	ENST00000342505.4:c.1330A>G	p.Ile444Val	p.I444V	ENST00000342505	NM_002227.2	444	Atc/Gtc	9/25	1	2	FACETS	0.832	0.748	0.921	0.832	0.748	0.921	CLONAL	1	FALSE	1	0.504513548564747	2		440	486	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212459	5212459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs182037655	NA	P-0048076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	206	1001	0	ENST00000357368.4:c.4658C>T	p.Thr1553Met	p.T1553M	ENST00000357368	NM_002850.3	1553	aCg/aTg	31/38	1	2	FACETS	0.854	0.793	0.918	0.854	0.793	0.918	CLONAL	1	FALSE	1	0.504513548564747	2		1001	956	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435756	110435756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	70	187	0	ENST00000375856.3:c.2645G>A	p.Gly882Asp	p.G882D	ENST00000375856	NM_003749.2	882	gGc/gAc	1/2	0.217593626757466	3	FACETS	1	0.974	1	0.715	0.632	0.802	INDETERMINATE	1	FALSE	1	0.504513548564747	3		187	243	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74000691	74000691	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	220	868	0	ENST00000318443.5:c.1381A>G	p.Thr461Ala	p.T461A	ENST00000318443	NM_001024736.1	461	Aca/Gca	7/10	0.504513548564747	1	FACETS	0.972	0.909	1	0.972	0.909	1	CLONAL	1	FALSE	0	0.504513548564747	1		868	671	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145537	61145537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	58	329	0	ENST00000295025.8:c.649G>A	p.Glu217Lys	p.E217K	ENST00000295025	NM_002908.2	217	Gaa/Aaa	7/11	1	2	FACETS	0.946	0.822	1	0.946	0.822	1	CLONAL	1	FALSE	1	0.504513548564747	2		329	243	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0048077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	52	371	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.956	0.816	1	0.956	0.816	1	CLONAL	1	TRUE	1	0.25	2		371	435	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0048077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	60	393	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	1	2	FACETS	0.97	0.837	1	0.97	0.837	1	CLONAL	1	TRUE	1	0.25	2		393	495	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249457	153249457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	40	441	1	ENST00000281708.4:c.1321C>T	p.Arg441Trp	p.R441W	ENST00000281708	NM_033632.3	441	Cgg/Tgg	9/12	1	2	FACETS	0.623	0.517	0.74	0.623	0.517	0.74	SUBCLONAL	1	TRUE	1	0.25	2		442	514	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022914	27022945	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCCGCCGCCAGCAGCCTGGGCAACCCGCCG	CCGCCGCCGCCAGCAGCCTGGGCAACCCGCCG	-	novel	NA	P-0048077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	17	27	0	ENST00000324856.7:c.31_62del	p.Ser11LeufsTer89	p.S11Lfs*89	ENST00000324856	NM_006015.4	7	cCCGCCGCCGCCAGCAGCCTGGGCAACCCGCCG/c	1/20	0.24812046925231	2	FACETS	0.872	0.676	1	1	0.893	1	CLONAL	3	TRUE	0	0.25	2		27	52	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753512	42753512	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	116	1024	1	ENST00000222329.4:c.752C>T	p.Ser251Leu	p.S251L	ENST00000222329	NM_006494.2	251	tCg/tTg	4/4	1	2	FACETS	0.95	0.855	1	0.95	0.855	1	CLONAL	1	TRUE	1	0.25	2		1025	977	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073678	8073679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0048077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	155	350	0	ENST00000377482.5:c.980dup	p.Ser328GlufsTer2	p.S328Efs*2	ENST00000377482	NM_018948.3	327	ccg/ccCg	4/4	0.24812046925231	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.25	2		350	530	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098814	178098822	+	inframe_deletion	In_Frame_Del	DEL	ATCTAGTTG	ATCTAGTTG	-	novel	NA	P-0048077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	78	533	0	ENST00000397062.3:c.223_231del	p.Gln75_Asp77del	p.Q75_D77del	ENST00000397062	NM_006164.4	75	CAACTAGAT/-	2/5	1	2	FACETS	0.862	0.757	0.975	0.862	0.757	0.975	CLONAL	1	TRUE	1	0.25	2		533	724	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591135	67591140	+	inframe_deletion	In_Frame_Del	DEL	GAGAGA	GAGAGA	-	novel	NA	P-0048077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	25	215	0	ENST00000274335.5:c.1728_1733del	p.Arg577_Asp578del	p.R577_D578del	ENST00000274335		576	acGAGAGAc/acc	12/15	1	2	FACETS	0.633	0.499	0.786	0.633	0.499	0.786	SUBCLONAL	1	TRUE	1	0.25	2		215	316	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994128	21994163	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTTTCCTACCTGGTCTTCTAGGAAGCGGCTGCTGC	CCTTTCCTACCTGGTCTTCTAGGAAGCGGCTGCTGC	-	novel	NA	P-0048077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	85	549	0	ENST00000579755.1:c.168_193+10del		p.X56_splice	ENST00000579755		56		1/3	0.253281829886805		FACETS		0.965	1				CLONAL	1	TRUE	0	0.25	2		549	549	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385170	41385171	+	missense_variant	Missense_Mutation	DNP	TT	TT	GG	novel	NA	P-0048078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	19	858	0	ENST00000373198.4:c.790_791delinsCC	p.Lys264Pro	p.K264P	ENST00000373198	NM_133170.3	264	AAg/CCg	6/32	1	2	FACETS	0.147	0.111	0.189	0.147	0.111	0.189	SUBCLONAL	1	TRUE	1	0.879398965670987	2		858	294	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991835	72991835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	105	631	1	ENST00000268489.5:c.2210C>T	p.Thr737Ile	p.T737I	ENST00000268489	NM_006885.3	737	aCc/aTc	2/10	1	2	FACETS	0.737	0.668	0.808	0.737	0.668	0.808	SUBCLONAL	1	TRUE	1	0.879398965670987	2		632	324	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651322	45651322	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	87	554	1	ENST00000407780.3:c.703G>T	p.Asp235Tyr	p.D235Y	ENST00000407780	NM_001283052.1	235	Gac/Tac	5/7	NA	2	FACETS	0.853	0.768	0.939			1	INDETERMINATE	1	TRUE	NA	0.879398965670987	2		555	232	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0048079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	19	383	0				ENST00000310581	NM_198253.2	-/1132			0.230431686503683	1	FACETS	0.857	0.657	1	0.857	0.657	1	CLONAL	1	TRUE	0	0.27	1		383	142	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0048079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	40	571	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	0.146494288503828	3	FACETS	1	0.862	1	0.519	0.433	0.614	INDETERMINATE	1	TRUE	1	0.27	3		571	324	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023212	27023228	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGGGCCCTAGGCCCG	CGCGGGCCCTAGGCCCG	-	novel	NA	P-0048079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	12	274	0	ENST00000324856.7:c.319_335del	p.Ala107ProfsTer4	p.A107Pfs*4	ENST00000324856	NM_006015.4	106	aaCGCGGGCCCTAGGCCCGcc/aacc	1/20	1	2	FACETS	0.444	0.312	0.607	0.444	0.312	0.607	SUBCLONAL	1	TRUE	1	0.27	2		274	200	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771330	68771330	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555509636	NA	P-0048079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	24	467	0	ENST00000261769.5:c.12G>A	p.Trp4Ter	p.W4*	ENST00000261769	NM_004360.3	4	tgG/tgA	1/16	0.3	1	FACETS	0.864	0.683	1	0.864	0.683	1	CLONAL	1	TRUE	0	0.27	1		467	178	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43766907	43766907	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	14	181	0	ENST00000382044.4:c.1144G>T	p.Val382Phe	p.V382F	ENST00000382044	NM_001141980.1	382	Gtt/Ttt	10/28	1	2	FACETS	0.513	0.372	0.684	0.513	0.372	0.684	SUBCLONAL	1	TRUE	1	0.27	2		181	202	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828666	72828666	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1267854671	NA	P-0048079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	29	574	0	ENST00000268489.5:c.7915C>G	p.Gln2639Glu	p.Q2639E	ENST00000268489	NM_006885.3	2639	Cag/Gag	9/10	0.3	1	FACETS	0.707	0.569	0.861	0.707	0.569	0.861	SUBCLONAL	1	TRUE	0	0.27	1		574	263	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652093	36652100	+	frameshift_variant	Frame_Shift_Del	DEL	GCCTGCCC	GCCTGCCC	-	novel	NA	P-0048079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	44	908	0	ENST00000244741.5:c.215_222del	p.Gly72GlufsTer14	p.G72Efs*14	ENST00000244741	NM_000389.4	72	gGCCTGCCC/g	2/3	1	2	FACETS	0.763	0.641	0.898	0.763	0.641	0.898	SUBCLONAL	1	TRUE	1	0.27	2		908	427	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	44	349	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.914	0.78	1	0.914	0.78	1	CLONAL	1	TRUE	1	0.60960675814585	2		350	158	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0048080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	264	475	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.543385768252294	4	FACETS	0.976	0.928	1	0.976	0.928	1	CLONAL	3	TRUE	1	0.60960675814585	4		475	476	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588626	28588626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548609046	NA	P-0048080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	63	323	0	ENST00000241453.7:c.2822C>T	p.Ser941Leu	p.S941L	ENST00000241453	NM_004119.2	941	tCg/tTg	23/24	1	2	FACETS	0.883	0.774	0.999	0.883	0.774	0.999	CLONAL	1	TRUE	1	0.60960675814585	2		323	234	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918761	32918761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1239798218	NA	P-0048080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	43	152	0	ENST00000380152.3:c.6908C>T	p.Ser2303Phe	p.S2303F	ENST00000380152		2303	tCc/tTc	12/27	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.60960675814585	2		152	129	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374369	31374369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767930436	NA	P-0048080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	97	713	1	ENST00000328111.2:c.368C>T	p.Ser123Phe	p.S123F	ENST00000328111	NM_006892.3	123	tCc/tTc	5/23	1	2	FACETS	0.917	0.826	1	0.917	0.826	1	CLONAL	1	TRUE	1	0.60960675814585	2		714	347	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210688	36210688	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	115	578	0	ENST00000222270.7:c.439C>T	p.Arg147Ter	p.R147*	ENST00000222270	NM_014727.1	147	Cga/Tga	3/37	0.143222043383501	0	FACETS	0.448	0.408	0.488			1	INDETERMINATE	1	TRUE	0	0.60960675814585	0		578	329	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024515	31024515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	103	544	0	ENST00000375687.4:c.4000C>T	p.Pro1334Ser	p.P1334S	ENST00000375687	NM_015338.5	1334	Ccc/Tcc	13/13	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.60960675814585	2		544	326	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518073	8518073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1480778931	NA	P-0048080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	133	407	0	ENST00000356435.5:c.1318G>A	p.Glu440Lys	p.E440K	ENST00000356435		440	Gaa/Aaa	10/35	NA	2	FACETS	0.82	0.761	0.88			1	INDETERMINATE	2	TRUE	NA	0.60960675814585	2		407	266	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213554	27213554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	54	429	0	ENST00000380036.4:c.2950G>A	p.Gly984Arg	p.G984R	ENST00000380036	NM_000459.3	984	Gga/Aga	18/23	0.611735385917427	1	FACETS	0.592	0.513	0.677	0.592	0.513	0.677	SUBCLONAL	1	TRUE	0	0.60960675814585	1		429	208	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468219	120468219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395144495	NA	P-0048080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	106	696	0	ENST00000256646.2:c.4220C>T	p.Ser1407Leu	p.S1407L	ENST00000256646	NM_024408.3	1407	tCg/tTg	25/34	0.543385768252294	4	FACETS	0.982	0.883	1	0.327	0.294	0.363	CLONAL	1	TRUE	1	0.60960675814585	4		696	570	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92244500	92244500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	88	313	0	ENST00000265734.4:c.935C>T	p.Ser312Phe	p.S312F	ENST00000265734	NM_001259.6	312	tCc/tTc	8/8	0.611735385917427	3	FACETS	1	0.933	1	0.531	0.474	0.59	CLONAL	1	TRUE	1	0.60960675814585	3		313	355	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400795	72400795	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	67	234	0	ENST00000357731.5:c.376C>T	p.Pro126Ser	p.P126S	ENST00000357731	NM_173808.2	126	Ccc/Tcc	2/7	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.60960675814585	NA		234	258	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112760193	112760193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	62	307	0	ENST00000369452.4:c.862C>T	p.Arg288Cys	p.R288C	ENST00000369452	NM_007373.3	288	Cgt/Tgt	4/9	1	2	FACETS	0.992	0.871	1	0.992	0.871	1	CLONAL	1	TRUE	1	0.60960675814585	2		307	205	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243478	46243478	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	82	324	0	ENST00000334344.6:c.1831T>A	p.Tyr611Asn	p.Y611N	ENST00000334344	NM_152641.2	611	Tac/Aac	14/21	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.60960675814585	2		324	262	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246479	46246479	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	52	180	0	ENST00000334344.6:c.4573G>T	p.Glu1525Ter	p.E1525*	ENST00000334344	NM_152641.2	1525	Gaa/Taa	15/21	1	2	FACETS	0.964	0.835	1	0.964	0.835	1	CLONAL	1	TRUE	1	0.60960675814585	2		180	177	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285642	46285642	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	101	313	0	ENST00000334344.6:c.5002del	p.Leu1668PhefsTer33	p.L1668Ffs*33	ENST00000334344	NM_152641.2	1668	Ctt/tt	17/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.60960675814585	2		313	297	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608258	28608258	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	60	417	0	ENST00000241453.7:c.1798G>A	p.Asp600Asn	p.D600N	ENST00000241453	NM_004119.2	600	Gat/Aat	14/24	1	2	FACETS	0.845	0.737	0.959	0.845	0.737	0.959	CLONAL	1	TRUE	1	0.60960675814585	2		417	233	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40384066	40384066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	179	385	0	ENST00000293328.3:c.80C>T	p.Pro27Leu	p.P27L	ENST00000293328	NM_012448.3	27	cCc/cTc	2/19	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.60960675814585	2		385	410	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753603	42753603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	132	955	0	ENST00000222329.4:c.661C>T	p.Pro221Ser	p.P221S	ENST00000222329	NM_006494.2	221	Ccg/Tcg	4/4	0.143222043383501	0	FACETS	0.397	0.363	0.432			1	INDETERMINATE	1	TRUE	0	0.60960675814585	0		955	426	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25990541	25990541	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	74	438	0	ENST00000435504.4:c.686A>T	p.Asn229Ile	p.N229I	ENST00000435504		229	aAc/aTc	8/13	1	2	FACETS	0.913	0.809	1	0.913	0.809	1	CLONAL	1	TRUE	1	0.60960675814585	2		438	266	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498009	29498009	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138534542	NA	P-0048080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	87	503	0	ENST00000389048.3:c.1997C>T	p.Pro666Leu	p.P666L	ENST00000389048	NM_004304.4	666	cCc/cTc	11/29	1	2	FACETS	0.918	0.821	1	0.918	0.821	1	CLONAL	1	TRUE	1	0.60960675814585	2		503	311	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519881	29519881	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs780939762	NA	P-0048080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	79	538	0	ENST00000389048.3:c.1690G>C	p.Val564Leu	p.V564L	ENST00000389048	NM_004304.4	564	Gtg/Ctg	9/29	1	2	FACETS	0.785	0.697	0.879	0.785	0.697	0.879	SUBCLONAL	1	TRUE	1	0.60960675814585	2		538	330	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57470672	57470672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	48	265	0	ENST00000371085.3:c.145G>A	p.Gly49Arg	p.G49R	ENST00000371085	NM_000516.4	49	Gga/Aga	2/13	1	2	FACETS	0.984	0.848	1	0.984	0.848	1	CLONAL	1	TRUE	1	0.60960675814585	2		265	160	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955557	55955557	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	65	371	0	ENST00000263923.4:c.3388T>A	p.Tyr1130Asn	p.Y1130N	ENST00000263923	NM_002253.2	1130	Tat/Aat	25/30	1	2	FACETS	0.889	0.78	1	0.889	0.78	1	CLONAL	1	TRUE	1	0.60960675814585	2		371	240	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106519963	106519963	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0048080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	46	119	0	ENST00000359195.3:c.2392-1G>A		p.X798_splice	ENST00000359195	NM_002649.2	798			0.611735385917427	3	FACETS	0.871	0.756	0.99	0.871	0.756	0.99	CLONAL	2	TRUE	1	0.60960675814585	3		119	113	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554345	141554346	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0048080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	90	964	0	ENST00000220592.5:c.1805_1806delinsTT	p.Pro602Leu	p.P602L	ENST00000220592	NM_012154.3	602	cCC/cTT	14/19	1	2	FACETS	0.718	0.641	0.8	0.718	0.641	0.8	SUBCLONAL	1	TRUE	1	0.60960675814585	2		964	411	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	138	432	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.510807193655753	2		432	489	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0048081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	101	482	0	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	1	2	FACETS	0.651	0.583	0.724	0.651	0.583	0.724	SUBCLONAL	1	TRUE	1	0.510807193655753	2		482	607	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0048081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	9	405	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.083	0.054	0.12	0.083	0.054	0.12	SUBCLONAL	1	TRUE	1	0.510807193655753	2		405	423	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0048081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	41	222	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	1	2	FACETS	0.803	0.676	0.94	0.803	0.676	0.94	CLONAL	1	TRUE	1	0.510807193655753	2		222	200	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0048081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	22	277	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.256	0.198	0.323	0.256	0.198	0.323	SUBCLONAL	1	TRUE	1	0.510807193655753	2		277	337	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204864	NA	P-0048081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	76	347	0	ENST00000371953.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000371953	NM_000314.4	171	Cag/Tag	6/9	0.510807193655753	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.510807193655753	1		347	218	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0048081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	89	249	1	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.510807193655753	2		250	286	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0048081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	24	292	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	0.367	0.288	0.457	0.367	0.288	0.457	SUBCLONAL	1	TRUE	1	0.510807193655753	2		292	256	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0048081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	116	394	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.933	0.845	1	0.933	0.845	1	CLONAL	1	TRUE	1	0.510807193655753	2		394	487	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411576	63411576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	45	741	0	ENST00000330258.3:c.1591C>T	p.Arg531Ter	p.R531*	ENST00000330258	NM_152424.3	531	Cga/Tga	2/2	1	2	FACETS	0.222	0.185	0.262	0.222	0.185	0.262	SUBCLONAL	1	TRUE	1	0.510807193655753	2		741	795	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411678	63411678	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	197	730	0	ENST00000330258.3:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000330258	NM_152424.3	497	Cga/Tga	2/2	1	2	FACETS	0.909	0.842	0.977	0.909	0.842	0.977	CLONAL	1	TRUE	1	0.510807193655753	2		730	849	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0048081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	34	576	0	ENST00000269305.4:c.994-1G>T		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.510807193655753	1	FACETS	0.159	0.129	0.192	0.159	0.129	0.192	SUBCLONAL	1	TRUE	0	0.510807193655753	1		576	624	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260247	149260247	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753225952	NA	P-0048081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	285	798	0	ENST00000360632.3:c.646G>A	p.Ala216Thr	p.A216T	ENST00000360632	NM_015472.4	216	Gca/Aca	4/7	1	2	FACETS	0.96	0.902	1	0.96	0.902	1	CLONAL	1	TRUE	1	0.510807193655753	2		798	1162	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653811	89653811	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	19	329	0	ENST00000371953.3:c.111del	p.Pro38LeufsTer16	p.P38Lfs*16	ENST00000371953	NM_000314.4	37	Ttt/tt	2/9	0.510807193655753	1	FACETS	0.26	0.198	0.333	0.26	0.198	0.333	SUBCLONAL	1	TRUE	0	0.510807193655753	1		329	213	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374205	118374205	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	18	325	0	ENST00000534358.1:c.7601del	p.Asn2534MetfsTer9	p.N2534Mfs*9	ENST00000534358	NM_005933.3	2533	gAa/ga	27/36	1	2	FACETS	0.225	0.169	0.291	0.225	0.169	0.291	SUBCLONAL	1	TRUE	1	0.510807193655753	2		325	313	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244982	46244982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	154	484	0	ENST00000334344.6:c.3076G>A	p.Val1026Ile	p.V1026I	ENST00000334344	NM_152641.2	1026	Gta/Ata	15/21	1	2	FACETS	0.856	0.786	0.93	0.856	0.786	0.93	CLONAL	1	TRUE	1	0.510807193655753	2		484	704	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351457	89351457	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	202	601	0	ENST00000301030.4:c.1493G>C	p.Ser498Thr	p.S498T	ENST00000301030	NM_001256183.1	498	aGc/aCc	9/13	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.510807193655753	2		601	751	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120283	70120284	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0048081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	89	855	0	ENST00000245479.2:c.1286_1287dup	p.Pro430AlafsTer41	p.P430Afs*41	ENST00000245479	NM_000346.3	429	agc/aGCgc	3/3	0.173935257852497	3	FACETS	0.323	0.285	0.363	0.161	0.142	0.182	INDETERMINATE	1	TRUE	1	0.510807193655753	3		855	1356	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368207	45368207	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	53	268	0	ENST00000262160.6:c.1395C>G	p.Ser465Arg	p.S465R	ENST00000262160	NM_005901.5	465	agC/agG	11/11	0.510807193655753	1	FACETS	0.863	0.749	0.984	0.863	0.749	0.984	CLONAL	1	TRUE	0	0.510807193655753	1		268	179	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272862	18272862	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0048081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	218	707	0	ENST00000222254.8:c.901+1G>A		p.X301_splice	ENST00000222254	NM_005027.3	301			1	2	FACETS	0.958	0.892	1	0.958	0.892	1	CLONAL	1	TRUE	1	0.510807193655753	2		707	891	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951986	178951986	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	15	326	0	ENST00000263967.3:c.3041A>G	p.Gln1014Arg	p.Q1014R	ENST00000263967	NM_006218.2	1014	cAa/cGa	21/21	1	2	FACETS	0.204	0.149	0.27	0.204	0.149	0.27	SUBCLONAL	1	TRUE	1	0.510807193655753	2		326	288	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896437	151896437	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	16	384	0	ENST00000262189.6:c.4200C>A	p.Asn1400Lys	p.N1400K	ENST00000262189	NM_170606.2	1400	aaC/aaA	27/59	1	2	FACETS	0.199	0.146	0.262	0.199	0.146	0.262	SUBCLONAL	1	TRUE	1	0.510807193655753	2		384	315	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	63	331	1	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.77	0.67	0.877	1	0.973	1	SUBCLONAL	2	TRUE	1	0.24	2		332	341	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	38	249	1	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.24	2		250	283	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	112	580	2	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.941	0.85	1	1	0.988	1	CLONAL	2	TRUE	1	0.24	2		582	496	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	32	461	5	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.454	0.368	0.553	0.454	0.368	0.553	SUBCLONAL	1	TRUE	1	0.24	2		466	587	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100728	8100728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs771019738	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	30	879	12	ENST00000346208.3:c.708del	p.Ser237AlafsTer28	p.S237Afs*28	ENST00000346208		234	ttC/tt	3/6	1	2	FACETS	0.438	0.352	0.536	0.438	0.352	0.536	SUBCLONAL	1	TRUE	1	0.24	2		891	571	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446284	70446284	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	51	457	0	ENST00000373644.4:c.5230del	p.Arg1744GlufsTer18	p.R1744Efs*18	ENST00000373644	NM_030625.2	1742	Aaa/aa	11/12	1	2	FACETS	0.938	0.799	1	0.938	0.799	1	CLONAL	1	TRUE	1	0.24	2		457	453	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	19	382	0	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	0.468	0.355	0.602	0.468	0.355	0.602	SUBCLONAL	1	TRUE	1	0.24	2		382	338	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467828	50467828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1040607869	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	45	543	0	ENST00000331340.3:c.1063G>A	p.Ala355Thr	p.A355T	ENST00000331340	NM_006060.4	355	Gcg/Acg	8/8	1	2	FACETS	0.868	0.73	1	0.868	0.73	1	CLONAL	1	TRUE	1	0.24	2		543	432	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	40	817	1	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.446	0.369	0.531	0.446	0.369	0.531	SUBCLONAL	1	TRUE	1	0.24	2		818	748	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168741	56168741	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775802110	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	22	273	0	ENST00000399503.3:c.1595G>A	p.Arg532Gln	p.R532Q	ENST00000399503	NM_005921.1	532	cGa/cAa	9/20	1	2	FACETS	0.471	0.365	0.596	0.471	0.365	0.596	SUBCLONAL	1	TRUE	1	0.24	2		273	389	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	43	318	3	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.24	2		321	253	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858185	27858185	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	44	486	0	ENST00000359303.2:c.386G>A	p.Arg129His	p.R129H	ENST00000359303	NM_003535.2	129	cGt/cAt	1/1	1	2	FACETS	0.851	0.714	1	0.851	0.714	1	CLONAL	1	TRUE	1	0.24	2		486	431	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835781	68835781	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060501215	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	35	506	0	ENST00000261769.5:c.377del	p.Pro126ArgfsTer89	p.P126Rfs*89	ENST00000261769	NM_004360.3	124	cgC/cg	3/16	1	2	FACETS	0.533	0.436	0.643	0.533	0.436	0.643	SUBCLONAL	1	TRUE	1	0.24	2		506	547	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245586	41245587	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs80357522	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	83	513	5	ENST00000357654.3:c.1961dup	p.Tyr655ValfsTer18	p.Y655Vfs*18	ENST00000357654	NM_007294.3	654	aag/aaAg	10/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.24	2		518	516	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274196	10274196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	64	493	0	ENST00000330684.3:c.73G>A	p.Ala25Thr	p.A25T	ENST00000330684	NM_001134407.1	25	Gcg/Acg	2/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.24	2		493	389	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271699	15271699	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	45	1035	1	ENST00000263388.2:c.6740del	p.Pro2247HisfsTer82	p.P2247Hfs*82	ENST00000263388	NM_000435.2	2247	cCa/ca	33/33	1	2	FACETS	0.464	0.388	0.547	0.464	0.388	0.547	SUBCLONAL	1	TRUE	1	0.24	2		1036	809	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070324	37070324	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63749795	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	50	321	0	ENST00000231790.2:c.1459C>T	p.Arg487Ter	p.R487*	ENST00000231790	NM_000249.3	487	Cga/Tga	13/19	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.24	2		321	319	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128420047	128420047	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	70	531	0	ENST00000265960.3:c.381del	p.Lys127AsnfsTer20	p.K127Nfs*20	ENST00000265960	NM_001006617.1	127	aaA/aa	4/12	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.24	2		531	475	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182001	38182001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853064	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	62	539	0	ENST00000396334.3:c.625C>T	p.Arg209Cys	p.R209C	ENST00000396334	NM_002468.4	209	Cgc/Tgc	3/5	1	2	FACETS	0.939	0.812	1	0.939	0.812	1	CLONAL	1	TRUE	1	0.24	2		539	550	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825539	50825539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762650238	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	44	317	0	ENST00000398568.2:c.2170G>A	p.Val724Ile	p.V724I	ENST00000398568	NM_001042412.1	724	Gtt/Att	14/18	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.24	2		317	292	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026915	6026915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782602	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	18	123	1	ENST00000265849.7:c.1481C>T	p.Ser494Leu	p.S494L	ENST00000265849	NM_000535.5	494	tCg/tTg	11/15	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.24	2		124	121	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874013	151874013	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1248944002	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	22	377	0	ENST00000262189.6:c.8525del	p.Asn2842MetfsTer21	p.N2842Mfs*21	ENST00000262189	NM_170606.2	2842	aAt/at	38/59	1	2	FACETS	0.577	0.447	0.727	0.577	0.447	0.727	SUBCLONAL	1	TRUE	1	0.24	2		377	318	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326695	62326695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140411308	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	116	901	0	ENST00000360203.5:c.3514G>A	p.Glu1172Lys	p.E1172K	ENST00000360203	NM_001283009.1	1172	Gag/Aag	34/35	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.24	2		901	738	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230692	46230692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs916056847	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	12	322	0	ENST00000334344.6:c.941G>A	p.Arg314His	p.R314H	ENST00000334344	NM_152641.2	314	cGt/cAt	8/21	1	2	FACETS	0.375	0.263	0.513	0.375	0.263	0.513	SUBCLONAL	1	TRUE	1	0.24	2		322	267	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813325	102813325	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1214292132	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	40	553	0	ENST00000307046.8:c.364C>T	p.Arg122Cys	p.R122C	ENST00000307046	NM_001111285.1	122	Cgt/Tgt	3/4	1	2	FACETS	0.661	0.549	0.786	0.661	0.549	0.786	SUBCLONAL	1	TRUE	1	0.24	2		553	504	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741892	145741892	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs757780731	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	53	804	1	ENST00000428558.2:c.611C>G	p.Ala204Gly	p.A204G	ENST00000428558	NM_004260.3	204	gCc/gGc	5/22	1	2	FACETS	0.656	0.559	0.763	0.656	0.559	0.763	SUBCLONAL	1	TRUE	1	0.24	2		805	673	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129646	2129646	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747420910	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	44	975	4	ENST00000219476.3:c.3373C>T	p.Arg1125Trp	p.R1125W	ENST00000219476	NM_000548.3	1125	Cgg/Tgg	29/42	1	2	FACETS	0.465	0.389	0.55	0.465	0.389	0.55	SUBCLONAL	1	TRUE	1	0.24	2		979	788	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37081682	37081682	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63751703	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	27	304	0	ENST00000231790.2:c.1564C>T	p.Arg522Trp	p.R522W	ENST00000231790	NM_000249.3	522	Cgg/Tgg	14/19	1	2	FACETS	0.583	0.464	0.719	0.583	0.464	0.719	SUBCLONAL	1	TRUE	1	0.24	2		304	386	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141587	202141587	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	20	323	0	ENST00000358485.4:c.878del	p.Gly293AspfsTer4	p.G293Dfs*4	ENST00000358485	NM_001080125.1	292	cGg/cg	7/9	1	2	FACETS	0.463	0.353	0.591	0.463	0.353	0.591	SUBCLONAL	1	TRUE	1	0.24	2		323	360	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196381	106196381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764470309	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	31	319	0	ENST00000380013.4:c.4714C>T	p.Arg1572Trp	p.R1572W	ENST00000380013	NM_001127208.2	1572	Cgg/Tgg	11/11	1	2	FACETS	0.831	0.673	1	0.831	0.673	1	CLONAL	1	TRUE	1	0.24	2		319	311	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651313	52651313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777012889	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	27	345	0	ENST00000394830.3:c.1783C>T	p.Arg595Trp	p.R595W	ENST00000394830	NM_018313.4	595	Cgg/Tgg	15/30	1	2	FACETS	0.676	0.538	0.833	0.676	0.538	0.833	SUBCLONAL	1	TRUE	1	0.24	2		345	333	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097672	11097672	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	66	831	2	ENST00000358026.2:c.852G>A	p.Trp284Ter	p.W284*	ENST00000358026	NM_001128849.1	284	tgG/tgA	5/36	1	2	FACETS	0.74	0.642	0.847	0.74	0.642	0.847	SUBCLONAL	1	TRUE	1	0.24	2		833	743	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255077	16255077	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778639822	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	27	338	0	ENST00000375759.3:c.2342G>A	p.Arg781His	p.R781H	ENST00000375759	NM_015001.2	781	cGt/cAt	11/15	1	2	FACETS	0.717	0.571	0.882	0.717	0.571	0.882	SUBCLONAL	1	TRUE	1	0.24	2		338	314	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120509040	120509040	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	48	444	0	ENST00000256646.2:c.1526G>T	p.Cys509Phe	p.C509F	ENST00000256646	NM_024408.3	509	tGt/tTt	9/34	1	2	FACETS	0.924	0.782	1	0.924	0.782	1	CLONAL	1	TRUE	1	0.24	2		444	433	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845875	156845875	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	46	855	0	ENST00000524377.1:c.1505T>C	p.Val502Ala	p.V502A	ENST00000524377	NM_002529.3	502	gTt/gCt	13/17	1	2	FACETS	0.515	0.433	0.607	0.515	0.433	0.607	SUBCLONAL	1	TRUE	1	0.24	2		855	744	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012327	176012327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	21	272	0	ENST00000367669.3:c.1607C>T	p.Ala536Val	p.A536V	ENST00000367669	NM_022457.5	536	gCa/gTa	14/20	1	2	FACETS	0.754	0.583	0.953	0.754	0.583	0.953	CLONAL	1	TRUE	1	0.24	2		272	232	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394705	394706	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	30	438	0	ENST00000399788.2:c.4989dup	p.Pro1664AlafsTer3	p.P1664Afs*3	ENST00000399788	NM_001042603.1	1663	-/G	28/28	1	2	FACETS	0.59	0.475	0.72	0.59	0.475	0.72	SUBCLONAL	1	TRUE	1	0.24	2		438	424	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427420	427421	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	80	559	0	ENST00000399788.2:c.2748dup	p.Val917SerfsTer28	p.V917Sfs*28	ENST00000399788	NM_001042603.1	916	-/A	19/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.24	2		559	571	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436550	49436550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200741577	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	40	655	1	ENST00000301067.7:c.5756C>T	p.Thr1919Met	p.T1919M	ENST00000301067	NM_003482.3	1919	aCg/aTg	26/54	1	2	FACETS	0.547	0.454	0.652	0.547	0.454	0.652	SUBCLONAL	1	TRUE	1	0.24	2		656	609	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860047	57860047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs574196970	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	84	738	1	ENST00000228682.2:c.787G>A	p.Gly263Arg	p.G263R	ENST00000228682	NM_005269.2	263	Ggg/Agg	8/12	1	2	FACETS	0.908	0.801	1	0.908	0.801	1	CLONAL	1	TRUE	1	0.24	2		739	771	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416720	121416722	+	inframe_deletion	In_Frame_Del	DEL	GCG	GCG	-	novel	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	97	916	0	ENST00000257555.6:c.156_158del	p.Gly53del	p.G53del	ENST00000257555		50	tGCGgc/tgc	1/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.24	2		916	690	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250288	133250288	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1031999052	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	28	514	0	ENST00000320574.5:c.1232T>C	p.Val411Ala	p.V411A	ENST00000320574	NM_006231.2	411	gTg/gCg	13/49	1	2	FACETS	0.575	0.459	0.707	0.575	0.459	0.707	SUBCLONAL	1	TRUE	1	0.24	2		514	406	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959365	26959365	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs181880846	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	35	276	1	ENST00000381527.3:c.532C>T	p.Arg178Ter	p.R178*	ENST00000381527	NM_001260.1	178	Cga/Tga	6/13	1	2	FACETS	0.935	0.769	1	0.935	0.769	1	CLONAL	1	TRUE	1	0.24	2		277	312	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346034	73346034	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs752549514	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	20	177	0	ENST00000377767.4:c.1504G>A	p.Val502Ile	p.V502I	ENST00000377767	NM_014953.3	502	Gtt/Att	11/21	1	2	FACETS	0.891	0.685	1	0.891	0.685	1	CLONAL	1	TRUE	1	0.24	2		177	187	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040859	42040859	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	37	422	0	ENST00000219905.7:c.5237C>G	p.Ala1746Gly	p.A1746G	ENST00000219905	NM_001164273.1	1746	gCt/gGt	16/24	1	2	FACETS	0.881	0.728	1	0.881	0.728	1	CLONAL	1	TRUE	1	0.24	2		422	350	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250814	99250814	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	40	432	0	ENST00000268035.6:c.118C>T	p.Arg40Cys	p.R40C	ENST00000268035	NM_000875.3	40	Cgc/Tgc	2/21	1	2	FACETS	0.88	0.732	1	0.88	0.732	1	CLONAL	1	TRUE	1	0.24	2		432	379	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070659	67070659	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	10	133	0	ENST00000412916.2:c.282+1G>A		p.X94_splice	ENST00000412916		94			1	2	FACETS	0.505	0.343	0.708	0.505	0.343	0.708	SUBCLONAL	1	TRUE	1	0.24	2		133	165	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351463	89351464	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	53	650	0	ENST00000301030.4:c.1486_1487del	p.Leu496GlyfsTer82	p.L496Gfs*82	ENST00000301030	NM_001256183.1	496	CTg/g	9/13	1	2	FACETS	0.876	0.748	1	0.876	0.748	1	CLONAL	1	TRUE	1	0.24	2		650	504	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351898	89351898	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	48	834	0	ENST00000301030.4:c.1052A>C	p.Glu351Ala	p.E351A	ENST00000301030	NM_001256183.1	351	gAg/gCg	9/13	1	2	FACETS	0.507	0.427	0.595	0.507	0.427	0.595	SUBCLONAL	1	TRUE	1	0.24	2		834	789	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985347	60985347	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	40	646	0	ENST00000333681.4:c.553C>A	p.Leu185Met	p.L185M	ENST00000333681		185	Ctg/Atg	2/3	1	2	FACETS	0.484	0.401	0.577	0.484	0.401	0.577	SUBCLONAL	1	TRUE	1	0.24	2		646	689	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4102386	4102386	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	53	781	0	ENST00000262948.5:c.516A>C	p.Lys172Asn	p.K172N	ENST00000262948	NM_030662.3	172	aaA/aaC	4/11	1	2	FACETS	0.666	0.567	0.775	0.666	0.567	0.775	SUBCLONAL	1	TRUE	1	0.24	2		781	663	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170813	11170813	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs955207258	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	61	714	0	ENST00000358026.2:c.4957C>T	p.Arg1653Ter	p.R1653*	ENST00000358026	NM_001128849.1	1653	Cga/Tga	35/36	1	2	FACETS	0.746	0.643	0.859	0.746	0.643	0.859	SUBCLONAL	1	TRUE	1	0.24	2		714	681	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130401	29130401	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	36	411	0	ENST00000328354.6:c.309del	p.Phe103LeufsTer7	p.F103Lfs*7	ENST00000328354	NM_007194.3	103	ttT/tt	2/15	1	2	FACETS	0.754	0.62	0.903	0.754	0.62	0.903	CLONAL	1	TRUE	1	0.24	2		411	398	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574678	41574679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	51	769	0	ENST00000263253.7:c.6969_6970dup	p.His2324ProfsTer30	p.H2324Pfs*30	ENST00000263253	NM_001429.3	2321	-/CC	31/31	1	2	FACETS	0.632	0.537	0.738	0.632	0.537	0.738	SUBCLONAL	1	TRUE	1	0.24	2		769	672	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37059000	37059000	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs63751448	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	35	259	0	ENST00000231790.2:c.794G>C	p.Arg265Pro	p.R265P	ENST00000231790	NM_000249.3	265	cGt/cCt	10/19	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.24	2		259	274	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935983	49935983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	37	781	1	ENST00000296474.3:c.1687C>T	p.Gln563Ter	p.Q563*	ENST00000296474	NM_002447.2	563	Caa/Taa	4/20	1	2	FACETS	0.484	0.398	0.581	0.484	0.398	0.581	SUBCLONAL	1	TRUE	1	0.24	2		782	637	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456496	89456497	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	31	311	0	ENST00000336596.2:c.1674dup	p.Val559CysfsTer13	p.V559Cfs*13	ENST00000336596	NM_005233.5	558	gtt/gTtt	8/17	1	2	FACETS	0.771	0.625	0.936	0.771	0.625	0.936	CLONAL	1	TRUE	1	0.24	2		311	335	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538268	187538269	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	35	438	0	ENST00000441802.2:c.8965dup	p.Arg2989LysfsTer12	p.R2989Kfs*12	ENST00000441802	NM_005245.3	2989	agg/aAgg	11/27	1	2	FACETS	0.633	0.518	0.761	0.633	0.518	0.761	SUBCLONAL	1	TRUE	1	0.24	2		438	461	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31521285	31521285	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	60	403	0	ENST00000344624.3:c.892C>T	p.Arg298Ter	p.R298*	ENST00000344624		298	Cga/Tga	3/33	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.24	2		403	448	SUCCESS
APC	324	MSKCC	GRCh37	5	112175181	112175182	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	18	182	0	ENST00000257430.4:c.3892dup	p.Ser1298PhefsTer3	p.S1298Ffs*3	ENST00000257430	NM_000038.5	1297	gat/gaTt	16/16	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.24	2		182	119	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249630	110249630	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	71	995	2	ENST00000374672.4:c.1045C>A	p.Pro349Thr	p.P349T	ENST00000374672	NM_004235.4	349	Cca/Aca	3/5	1	2	FACETS	0.692	0.603	0.789	0.692	0.603	0.789	SUBCLONAL	1	TRUE	1	0.24	2		997	855	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399458	139399458	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	110	987	2	ENST00000277541.6:c.4685C>A	p.Ala1562Glu	p.A1562E	ENST00000277541	NM_017617.3	1562	gCg/gAg	26/34	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.24	2		989	899	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041418	47041418	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	23	330	0	ENST00000377604.3:c.1762C>A	p.Leu588Ile	p.L588I	ENST00000377604	NM_001204468.1	588	Ctc/Atc	16/24	1	1	FACETS	0.598	0.467	0.749	0.598	0.467	0.749	SUBCLONAL	1	TRUE	0	0.24	1		330	282	SUCCESS
AR	367	MSKCC	GRCh37	X	66765913	66765913	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	34	465	0	ENST00000374690.3:c.925T>C	p.Tyr309His	p.Y309H	ENST00000374690	NM_000044.3	309	Tat/Cat	1/8	1	1	FACETS	0.681	0.557	0.82	0.681	0.557	0.82	SUBCLONAL	1	TRUE	0	0.24	1		465	366	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0048083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	175	640	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.576370672648076	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.577097739114552	1		642	422	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0048083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	85	208	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.944	0.843	1	0.944	0.843	1	CLONAL	1	TRUE	1	0.577097739114552	2		208	312	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	74	706	8	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.219285203912979	2		714	661	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	63	307	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.764	0.664	0.872	1	0.972	1	SUBCLONAL	2	TRUE	1	0.219285203912979	2		308	376	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	77	461	5	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.219285203912979	2		466	622	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743924	40743924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199514226	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	66	470	0	ENST00000373198.4:c.3071C>T	p.Thr1024Met	p.T1024M	ENST00000373198	NM_133170.3	1024	aCg/aTg	23/32	0.219285203912979	2	FACETS	1	0.944	1	0.581	0.505	0.663	CLONAL	1	TRUE	0	0.219285203912979	2		470	518	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489535	56489535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1403278713	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	59	441	0	ENST00000267101.3:c.2000G>A	p.Arg667His	p.R667H	ENST00000267101	NM_001982.3	667	cGt/cAt	17/28	1	2	FACETS	0.914	0.786	1	0.914	0.786	1	CLONAL	1	TRUE	1	0.219285203912979	2		441	589	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070349	37070349	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs63750855	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	29	301	1	ENST00000231790.2:c.1489del	p.Arg497GlyfsTer11	p.R497Gfs*11	ENST00000231790	NM_000249.3	495	aCc/ac	13/19	1	2	FACETS	0.67	0.537	0.82	0.67	0.537	0.82	SUBCLONAL	1	TRUE	1	0.219285203912979	2		302	395	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	73	862	1	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	0.219285203912979	1	FACETS	0.844	0.738	0.959	0.844	0.738	0.959	CLONAL	1	TRUE	0	0.219285203912979	1		863	702	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736307	243736307	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	48	348	2	ENST00000263826.5:c.740G>A	p.Arg247His	p.R247H	ENST00000263826	NM_005465.4	247	cGc/cAc	8/13	1	2	FACETS	0.941	0.797	1	0.941	0.797	1	CLONAL	1	TRUE	1	0.219285203912979	2		350	465	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426701	121426701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753998395	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	91	746	0	ENST00000257555.6:c.392G>A	p.Arg131Gln	p.R131Q	ENST00000257555		131	cGg/cAg	2/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.219285203912979	2		746	664	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31025035	31025035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375101983	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	33	479	0	ENST00000375687.4:c.4520C>T	p.Ala1507Val	p.A1507V	ENST00000375687	NM_015338.5	1507	gCg/gTg	13/13	0.219285203912979	2	FACETS	0.624	0.508	0.756	0.312	0.254	0.378	SUBCLONAL	1	TRUE	0	0.219285203912979	2		479	482	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	71	371	2	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.219285203912979	2		373	451	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271747	15271747	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs773656789	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	79	1074	0	ENST00000263388.2:c.6692del	p.Pro2231GlnfsTer15	p.P2231Qfs*15	ENST00000263388	NM_000435.2	2231	cCa/ca	33/33	0.219285203912979	1	FACETS	0.826	0.725	0.934	0.826	0.725	0.934	CLONAL	1	TRUE	0	0.219285203912979	1		1074	777	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215231	123215231	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	45	126	0	ENST00000218089.9:c.2781del	p.Phe927LeufsTer4	p.F927Lfs*4	ENST00000218089	NM_001042749.1	926	cTt/ct	28/35	1	1	FACETS	0.858	0.736	0.986	1	0.978	1	CLONAL	3	TRUE	0	0.219285203912979	1		126	142	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165283	47165283	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	42	299	1	ENST00000409792.3:c.843del	p.Glu282LysfsTer19	p.E282Kfs*19	ENST00000409792	NM_014159.6	281	aaA/aa	3/21	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.219285203912979	2		300	377	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812205	43812205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866559375	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	69	490	1	ENST00000372470.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000372470	NM_005373.2	357	cGa/cAa	7/12	1	2	FACETS	0.946	0.824	1	0.946	0.824	1	CLONAL	1	TRUE	1	0.219285203912979	2		491	665	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762511	41762511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200253980	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	48	394	0	ENST00000301178.4:c.2191G>A	p.Asp731Asn	p.D731N	ENST00000301178	NM_021913.4	731	Gat/Aat	18/20	0.219285203912979	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.219285203912979	1		394	325	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511593	38511593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1353021557	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	76	765	0	ENST00000254066.5:c.1091G>A	p.Arg364Gln	p.R364Q	ENST00000254066	NM_000964.3	364	cGg/cAg	8/9	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.219285203912979	2		765	658	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347194	89347194	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773848887	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	34	697	2	ENST00000301030.4:c.5756C>T	p.Ala1919Val	p.A1919V	ENST00000301030	NM_001256183.1	1919	gCg/gTg	9/13	1	2	FACETS	0.599	0.488	0.723	0.599	0.488	0.723	SUBCLONAL	1	TRUE	1	0.219285203912979	2		699	518	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214870	36214870	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs200663900	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	96	889	0	ENST00000222270.7:c.3296G>C	p.Gly1099Ala	p.G1099A	ENST00000222270	NM_014727.1	1099	gGc/gCc	8/37	0.219285203912979	1	FACETS	0.964	0.858	1	0.964	0.858	1	CLONAL	1	TRUE	0	0.219285203912979	1		889	809	SUCCESS
APC	324	MSKCC	GRCh37	5	112173918	112173918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373428732	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	28	285	0	ENST00000257430.4:c.2627G>A	p.Arg876Gln	p.R876Q	ENST00000257430	NM_000038.5	876	cGa/cAa	16/16	1	2	FACETS	0.786	0.629	0.964	0.786	0.629	0.964	CLONAL	1	TRUE	1	0.219285203912979	2		285	325	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846280	156846280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs554180226	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	40	882	1	ENST00000524377.1:c.1721G>A	p.Arg574His	p.R574H	ENST00000524377	NM_002529.3	574	cGc/cAc	14/17	1	2	FACETS	0.506	0.419	0.603	0.506	0.419	0.603	SUBCLONAL	1	TRUE	1	0.219285203912979	2		883	721	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100667	8100667	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	75	869	0	ENST00000346208.3:c.641C>T	p.Ser214Leu	p.S214L	ENST00000346208		214	tCg/tTg	3/6	NA	2	FACETS	0.95	0.832	1			1	INDETERMINATE	1	TRUE	NA	0.219285203912979	2		869	720	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163423	108163423	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064795883	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	40	471	0	ENST00000278616.4:c.4514C>T	p.Ala1505Val	p.A1505V	ENST00000278616	NM_000051.3	1505	gCc/gTc	30/63	1	2	FACETS	0.595	0.493	0.709	0.595	0.493	0.709	SUBCLONAL	1	TRUE	1	0.219285203912979	2		471	613	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428411	49428411	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	86	743	1	ENST00000301067.7:c.10394del	p.Gly3465AspfsTer37	p.G3465Dfs*37	ENST00000301067	NM_003482.3	3465	gGa/ga	36/54	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.219285203912979	2		744	758	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915103	32915103	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	48	366	0	ENST00000380152.3:c.6611C>A	p.Pro2204His	p.P2204H	ENST00000380152		2204	cCt/cAt	11/27	1	2	FACETS	0.931	0.788	1	0.931	0.788	1	CLONAL	1	TRUE	1	0.219285203912979	2		366	470	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472531	88472531	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	55	622	1	ENST00000360948.2:c.2024T>C	p.Phe675Ser	p.F675S	ENST00000360948	NM_001012338.2	675	tTt/tCt	16/19	1	2	FACETS	0.936	0.801	1	0.936	0.801	1	CLONAL	1	TRUE	1	0.219285203912979	2		623	536	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347849	347849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772146771	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	114	1274	0	ENST00000262320.3:c.1657G>A	p.Glu553Lys	p.E553K	ENST00000262320	NM_003502.3	553	Gag/Aag	6/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.219285203912979	2		1274	886	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554557	29554557	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	30	194	0	ENST00000356175.3:c.2342A>G	p.His781Arg	p.H781R	ENST00000356175	NM_000267.3	781	cAt/cGt	20/57	1	2	FACETS	0.995	0.805	1	0.995	0.805	1	CLONAL	1	TRUE	1	0.219285203912979	2		194	275	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40490808	40490808	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	57	330	0	ENST00000264657.5:c.491T>C	p.Val164Ala	p.V164A	ENST00000264657	NM_139276.2	164	gTg/gCg	6/24	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.219285203912979	2		330	520	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372087	45372087	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	65	446	0	ENST00000262160.6:c.1082A>T	p.Asn361Ile	p.N361I	ENST00000262160	NM_005901.5	361	aAt/aTt	9/11	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.219285203912979	2		446	521	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966817	18966817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	96	981	0	ENST00000262803.5:c.1628G>A	p.Arg543His	p.R543H	ENST00000262803	NM_002911.3	543	cGc/cAc	12/24	0.219285203912979	1	FACETS	0.894	0.796	0.999	0.894	0.796	0.999	CLONAL	1	TRUE	0	0.219285203912979	1		981	872	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149809	202149809	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	52	516	0	ENST00000358485.4:c.1250A>G	p.Gln417Arg	p.Q417R	ENST00000358485	NM_001080125.1	417	cAg/cGg	8/9	1	2	FACETS	0.964	0.821	1	0.964	0.821	1	CLONAL	1	TRUE	1	0.219285203912979	2		516	492	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37637627	37637627	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	92	847	0	ENST00000249071.6:c.107T>C	p.Val36Ala	p.V36A	ENST00000249071	NM_002872.4	36	gTg/gCg	2/7	0.219285203912979	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.219285203912979	1		847	616	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157890	106157890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	23	229	0	ENST00000380013.4:c.2791C>T	p.Pro931Ser	p.P931S	ENST00000380013	NM_001127208.2	931	Cct/Tct	3/11	1	2	FACETS	0.801	0.626	1	0.801	0.626	1	CLONAL	1	TRUE	1	0.219285203912979	2		229	262	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181849	56181849	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	36	267	1	ENST00000399503.3:c.4073C>T	p.Ser1358Leu	p.S1358L	ENST00000399503	NM_005921.1	1358	tCg/tTg	17/20	1	2	FACETS	0.876	0.721	1	0.876	0.721	1	CLONAL	1	TRUE	1	0.219285203912979	2		268	375	SUCCESS
APC	324	MSKCC	GRCh37	5	112179780	112179780	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1393740164	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	30	222	0	ENST00000257430.4:c.8489G>T	p.Ser2830Ile	p.S2830I	ENST00000257430	NM_000038.5	2830	aGt/aTt	16/16	1	2	FACETS	0.918	0.742	1	0.918	0.742	1	CLONAL	1	TRUE	1	0.219285203912979	2		222	298	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057655	180057655	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	49	957	0	ENST00000261937.6:c.300G>T	p.Glu100Asp	p.E100D	ENST00000261937	NM_182925.4	100	gaG/gaT	3/30	1	2	FACETS	0.593	0.501	0.694	0.593	0.501	0.694	SUBCLONAL	1	TRUE	1	0.219285203912979	2		957	754	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675725	30675726	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	113	688	0	ENST00000376406.3:c.2630dup	p.Asn877LysfsTer8	p.N877Kfs*8	ENST00000376406	NM_014641.2	877	aat/aaAt	8/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.219285203912979	2		688	825	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940238	31940238	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	101	898	0	ENST00000375333.2:c.380G>T	p.Arg127Met	p.R127M	ENST00000375333	NM_032454.1	127	aGg/aTg	2/8	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.219285203912979	2		898	823	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225129	53225129	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs967652938	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	58	376	0	ENST00000375401.3:c.3089G>T	p.Arg1030Leu	p.R1030L	ENST00000375401	NM_004187.3	1030	cGg/cTg	20/26	1	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.219285203912979	1		376	340	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225892	53225892	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	80	463	0	ENST00000375401.3:c.2957A>G	p.Lys986Arg	p.K986R	ENST00000375401	NM_004187.3	986	aAa/aGa	19/26	1	1	FACETS	0.837	0.741	0.939	1	0.981	1	CLONAL	2	TRUE	0	0.219285203912979	1		463	388	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061220	38061225	+	inframe_deletion	In_Frame_Del	DEL	CGTTCT	CGTTCT	-	novel	NA	P-0048085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	108	666	0	ENST00000250448.2:c.764_769del	p.Glu255_Asn256del	p.E255_N256del	ENST00000250448	NM_004496.3	255	gAGAACGgc/ggc	2/2	0.3	3	FACETS	1	0.98	1	0.684	0.616	0.757	CLONAL	1	TRUE	1	0.31	3		666	588	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132088	176132088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	120	288	0	ENST00000367669.3:c.679G>A	p.Gly227Arg	p.G227R	ENST00000367669	NM_022457.5	227	Gga/Aga	5/20	0.245596195618549	4	FACETS	0.969	0.885	1	0.969	0.885	1	CLONAL	3	TRUE	1	0.31	4		288	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579524	7579530	+	frameshift_variant	Frame_Shift_Del	DEL	TGAACCA	TGAACCA	-	novel	NA	P-0048085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	118	704	0	ENST00000269305.4:c.157_163del	p.Trp53LeufsTer68	p.W53Lfs*68	ENST00000269305	NM_001126112.2	53	TGGTTCAct/ct	4/11	0.3	2	FACETS	0.8	0.726	0.877	0.8	0.726	0.877	SUBCLONAL	2	TRUE	0	0.31	2		704	476	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0048086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	90	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.903	0.809	1	0.903	0.809	1	CLONAL	1	TRUE	1	0.625169285134082	2		327	319	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0048086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	59	279	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.625169285134082	2		279	182	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0048086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	50	168	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.625169285134082	2		168	156	SUCCESS
APC	324	MSKCC	GRCh37	5	112175536	112175536	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	72	228	0	ENST00000257430.4:c.4245del	p.Ser1415ArgfsTer4	p.S1415Rfs*4	ENST00000257430	NM_000038.5	1415	agT/ag	16/16	1	2	FACETS	0.968	0.858	1	0.968	0.858	1	CLONAL	1	TRUE	1	0.625169285134082	2		228	238	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347732	89347732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764052859	NA	P-0048086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	243	765	2	ENST00000301030.4:c.5218G>A	p.Ala1740Thr	p.A1740T	ENST00000301030	NM_001256183.1	1740	Gcc/Acc	9/13	1	2	FACETS	0.993	0.931	1	0.993	0.931	1	CLONAL	1	TRUE	1	0.625169285134082	2		767	783	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928368	69928368	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	106	398	0	ENST00000352241.4:c.188T>C	p.Leu63Pro	p.L63P	ENST00000352241	NM_198159.2	63	cTc/cCc	2/10	1	2	FACETS	0.907	0.82	0.997	0.907	0.82	0.997	CLONAL	1	TRUE	1	0.625169285134082	2		398	374	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468107	50468107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765655969	NA	P-0048086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	184	558	0	ENST00000331340.3:c.1342G>A	p.Ala448Thr	p.A448T	ENST00000331340	NM_006060.4	448	Gcg/Acg	8/8	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.625169285134082	2		558	554	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	41	524	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.321436332747595	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.321436332747595	1		524	180	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141570521	141570521	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	11	618	0	ENST00000220592.5:c.607C>T	p.His203Tyr	p.H203Y	ENST00000220592	NM_012154.3	203	Cat/Tat	5/19	0.20709467539717	3	FACETS	0.377	0.26	0.521			1	SUBCLONAL	1	TRUE	NA	0.321436332747595	3		618	211	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951169	48951169	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	77	209	0	ENST00000267163.4:c.1331del	p.Gln444ArgfsTer13	p.Q444Rfs*13	ENST00000267163	NM_000321.2	444	cAg/cg	13/27	0.321436332747595	3	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	1	0.321436332747595	3		209	263	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528910	157528910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146468586	NA	P-0048087-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	18	486	0	ENST00000346085.5:c.6635G>A	p.Arg2212His	p.R2212H	ENST00000346085	NM_020732.3	2212	cGc/cAc	20/20	0.231953548123339	5	FACETS	0.634	0.477	0.818	0.211	0.159	0.273	SUBCLONAL	1	TRUE	2	0.321436332747595	5		486	262	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578157	226578157	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	19	572	0	ENST00000366794.5:c.571G>C	p.Asp191His	p.D191H	ENST00000366794	NM_001618.3	191	Gat/Cat	4/23	0.446984854106086	5	FACETS	0.883	0.678	1	0.294	0.226	0.373	CLONAL	1	TRUE	2	0.67796997003258	5		572	128	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915033	32915033	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs371067421	NA	P-0048088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	62	361	0	ENST00000380152.3:c.6541G>T	p.Gly2181Ter	p.G2181*	ENST00000380152		2181	Gga/Tga	11/27	0.67796997003258	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.67796997003258	2		361	79	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049723	16049723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	18	338	0	ENST00000268712.3:c.1049G>A	p.Arg350Gln	p.R350Q	ENST00000268712	NM_006311.3	350	cGa/cAa	10/46	0.67796997003258	1	FACETS	0.575	0.448	0.715	0.575	0.448	0.715	SUBCLONAL	1	TRUE	0	0.67796997003258	1		338	61	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0048089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	174	314	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.765170498652899	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.765170498652899	3		314	302	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0048089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	393	610	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.765170498652899	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.765170498652899	2		610	477	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101300	27101300	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	177	640	0	ENST00000324856.7:c.4582C>T	p.Arg1528Ter	p.R1528*	ENST00000324856	NM_006015.4	1528	Cga/Tga	18/20	0.515516970953514	1	FACETS	0.866	0.813	0.918	0.866	0.813	0.918	CLONAL	1	TRUE	0	0.765170498652899	1		640	330	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880998	37880998	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs144434331	NA	P-0048089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1380	686	780	0	ENST00000269571.5:c.2327G>T	p.Gly776Val	p.G776V	ENST00000269571		776	gGt/gTt	20/27	0.765170498652899	8	FACETS	0.953	0.918	0.989			1	CLONAL	3	TRUE	NA	0.765170498652899	8		780	2066	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772299	68772321	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGCGTCCTGGGCAGAGGTGAGGG	CGCGTCCTGGGCAGAGGTGAGGG	-	novel	NA	P-0048089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	195	779	0	ENST00000261769.5:c.152_163+11del		p.X51_splice	ENST00000261769	NM_004360.3	51		2/16	0.765170498652899	1	FACETS	0.942	0.89	0.994	0.942	0.89	0.994	CLONAL	1	TRUE	0	0.765170498652899	1		779	334	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070608	67070608	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	105	167	1	ENST00000412916.2:c.232C>T	p.Arg78Ter	p.R78*	ENST00000412916		78	Cga/Tga	3/6	0.765170498652899	1	FACETS	0.887	0.818	0.956	0.887	0.818	0.956	CLONAL	1	TRUE	0	0.765170498652899	1		168	191	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272138	15272138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	227	775	0	ENST00000263388.2:c.6301C>T	p.Pro2101Ser	p.P2101S	ENST00000263388	NM_000435.2	2101	Ccc/Tcc	33/33	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.765170498652899	2		775	580	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176662828	176662828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368706736	NA	P-0048089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	76	198	0	ENST00000439151.2:c.3803G>A	p.Arg1268Gln	p.R1268Q	ENST00000439151	NM_022455.4	1268	cGg/cAg	6/23	1	2	FACETS	0.845	0.753	0.941	0.845	0.753	0.941	CLONAL	1	TRUE	1	0.765170498652899	2		198	235	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915096	32915096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	112	322	0	ENST00000380152.3:c.6604G>A	p.Asp2202Asn	p.D2202N	ENST00000380152		2202	Gat/Aat	11/27	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.765170498652899	2		322	274	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779876	3779876	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0048089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	183	580	0	ENST00000262367.5:c.5173-1G>A		p.X1725_splice	ENST00000262367	NM_004380.2	1725			0.765170498652899	3	FACETS	0.942	0.872	1	0.471	0.436	0.507	CLONAL	1	TRUE	1	0.765170498652899	3		580	702	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089038	37089038	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587778945	NA	P-0048089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	95	248	2	ENST00000231790.2:c.1760T>C	p.Met587Thr	p.M587T	ENST00000231790	NM_000249.3	587	aTg/aCg	16/19	0.765170498652899	3	FACETS	0.928	0.833	1	0.464	0.416	0.514	CLONAL	1	TRUE	1	0.765170498652899	3		250	370	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0048091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	9	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.506940131829337	4	FACETS	0.168	0.11	0.241	0.084	0.055	0.121	SUBCLONAL	1	TRUE	2	0.551815595613307	4		327	302	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0048091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	144	317	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.533313107501686	2	FACETS	0.885	0.822	0.947	0.885	0.822	0.947	CLONAL	2	TRUE	0	0.551815595613307	2		317	295	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0048091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	456	722	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.544686496972138	3	FACETS	0.997	0.964	1	0.997	0.964	1	CLONAL	3	TRUE	0	0.551815595613307	3		722	705	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0048091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	33	168	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.551815595613307	1	FACETS	0.984	0.828	1	0.984	0.828	1	CLONAL	1	TRUE	0	0.551815595613307	1		168	88	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132581	11132581	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	148	799	0	ENST00000358026.2:c.2797T>G	p.Phe933Val	p.F933V	ENST00000358026	NM_001128849.1	933	Ttc/Gtc	19/36	0.551815595613307	3	FACETS	0.985	0.902	1	0.492	0.451	0.536	CLONAL	1	TRUE	1	0.551815595613307	3		799	695	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	115	432	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.372199078046652	3	FACETS	1	0.938	1	0.526	0.475	0.58	CLONAL	1	TRUE	1	0.396900271289152	3		432	660	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575671	48575671	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0048092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	81	326	0	ENST00000342988.3:c.431C>G	p.Ser144Ter	p.S144*	ENST00000342988	NM_005359.5	144	tCa/tGa	4/12	0.396900271289152	1	FACETS	0.752	0.666	0.844	0.752	0.666	0.844	SUBCLONAL	1	TRUE	0	0.396900271289152	1		326	435	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936624	49936624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs531433657	NA	P-0048092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	171	674	0	ENST00000296474.3:c.1303C>T	p.Arg435Cys	p.R435C	ENST00000296474	NM_002447.2	435	Cgt/Tgt	2/20	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.396900271289152	2		674	862	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740597	145740597	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	207	822	0	ENST00000428558.2:c.1420G>C	p.Glu474Gln	p.E474Q	ENST00000428558	NM_004260.3	474	Gag/Cag	8/22	0.396900271289152	1	FACETS	0.923	0.857	0.991	0.923	0.857	0.991	CLONAL	1	TRUE	0	0.396900271289152	1		822	906	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0048095-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	120	259	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA	2	FACETS	0.946	0.859	1			1	INDETERMINATE	1	TRUE	NA	0.501410551747179	2		259	506	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048095-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	227	432	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.501410551747179	3	FACETS	0.97	0.91	1	0.97	0.91	1	CLONAL	2	TRUE	1	0.501410551747179	3		432	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579536	7579536	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567556930	NA	P-0048095-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	661	461	0	ENST00000269305.4:c.151G>T	p.Glu51Ter	p.E51*	ENST00000269305	NM_001126112.2	51	Gaa/Taa	4/11	0.472409827402548	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	0	0.501410551747179	3		461	1088	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857148	9857148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048095-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	129	274	2	ENST00000330684.3:c.4253G>A	p.Gly1418Asp	p.G1418D	ENST00000330684	NM_001134407.1	1418	gGc/gAc	13/13	1	2	FACETS	0.995	0.907	1	0.995	0.907	1	CLONAL	1	TRUE	1	0.501410551747179	2		276	517	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971375	13971375	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0048095-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	62	244	0	ENST00000405192.2:c.555-1G>C		p.X185_splice	ENST00000405192	NM_001163147.1	185			1	2	FACETS	0.625	0.541	0.714	0.625	0.541	0.714	SUBCLONAL	1	TRUE	1	0.501410551747179	2		244	396	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992288	72992288	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048095-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	241	586	0	ENST00000268489.5:c.1757G>A	p.Arg586Lys	p.R586K	ENST00000268489	NM_006885.3	586	aGg/aAg	2/10	0.501410551747179	1	FACETS	0.991	0.929	1	0.991	0.929	1	CLONAL	1	TRUE	0	0.501410551747179	1		586	727	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39600606	39600606	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048095-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	69	152	0	ENST00000262039.4:c.1421A>T	p.Asp474Val	p.D474V	ENST00000262039	NM_002647.2	474	gAt/gTt	13/25	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.501410551747179	2		152	227	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617187	100617187	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048095-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	179	195	0	ENST00000308731.7:c.562C>T	p.Leu188Phe	p.L188F	ENST00000308731	NM_000061.2	188	Ctt/Ttt	7/19	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.501410551747179	1		195	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs967461896	NA	P-0048107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	413	794	8	ENST00000269305.4:c.526T>C	p.Cys176Arg	p.C176R	ENST00000269305	NM_001126112.2	176	Tgc/Cgc	5/11	0.800369250022778	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.800369250022778	1		802	607	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243859016	243859016	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs397514606	NA	P-0048107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	140	80	0	ENST00000263826.5:c.49G>A	p.Glu17Lys	p.E17K	ENST00000263826	NM_005465.4	17	Gaa/Aaa	2/13	0.800369250022778	2	FACETS	0.953	0.879	1	0.477	0.439	0.515	CLONAL	1	TRUE	0	0.800369250022778	2		80	367	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954299	48954299	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs1395304450	NA	P-0048107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	149	126	0	ENST00000267163.4:c.1422-2A>T		p.X474_splice	ENST00000267163	NM_000321.2	474			0.705532002988362	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.800369250022778	1		126	208	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420137	420137	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	185	459	0	ENST00000399788.2:c.3130G>T	p.Glu1044Ter	p.E1044*	ENST00000399788	NM_001042603.1	1044	Gaa/Taa	21/28	NA	2	FACETS	0.551	0.509	0.594			1	INDETERMINATE	1	TRUE	NA	0.800369250022778	2		459	839	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778922	3778922	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1052723403	NA	P-0048107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	302	690	3	ENST00000262367.5:c.6126G>T	p.Met2042Ile	p.M2042I	ENST00000262367	NM_004380.2	2042	atG/atT	31/31	NA	2	FACETS	0.989	0.937	1			1	INDETERMINATE	1	TRUE	NA	0.800369250022778	2		693	763	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0048108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	315	436	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.367685923527502	2	FACETS	0.887	0.841	0.935	0.887	0.841	0.935	CLONAL	2	TRUE	0	0.418103475652651	2		439	849	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0048108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	138	208	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.367685923527502	2	FACETS	0.885	0.815	0.956	0.885	0.815	0.956	CLONAL	2	TRUE	0	0.418103475652651	2		208	373	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920469	134920469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	87	688	1	ENST00000398015.3:c.2284G>A	p.Asp762Asn	p.D762N	ENST00000398015	NM_004441.4	762	Gac/Aac	12/16	0.151925241328576	5	FACETS	1	0.958	1	0.392	0.347	0.44	INDETERMINATE	1	TRUE	2	0.35	5		689	645	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189914	66189914	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	64	336	0	ENST00000273854.3:c.3032C>A	p.Thr1011Asn	p.T1011N	ENST00000273854	NM_004439.5	1011	aCt/aAt	18/18	1	2	FACETS	0.96	0.835	1	0.96	0.835	1	CLONAL	1	TRUE	1	0.35	2		336	381	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377169	118377169	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	62	396	0	ENST00000534358.1:c.10562C>G	p.Ser3521Cys	p.S3521C	ENST00000534358	NM_005933.3	3521	tCt/tGt	27/36	0.267557698562045	4	FACETS	1	0.941	1	0.579	0.502	0.662	CLONAL	1	TRUE	2	0.35	4		396	413	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133884	41133884	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	15	394	0	ENST00000379561.5:c.1744A>T	p.Ser582Cys	p.S582C	ENST00000379561	NM_002015.3	582	Agc/Tgc	2/3	1	2	FACETS	0.341	0.249	0.452	0.341	0.249	0.452	SUBCLONAL	1	TRUE	1	0.35	2		394	251	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215674145	215674145	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	94	574	0	ENST00000260947.4:c.149G>C	p.Cys50Ser	p.C50S	ENST00000260947	NM_000465.2	50	tGc/tCc	1/11	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.35	2		574	517	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974740	21974771	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCACCTCCTCTACCCGACCCCGGGCCGCGG	CCGCACCTCCTCTACCCGACCCCGGGCCGCGG	-	novel	NA	P-0048109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	95	349	0	ENST00000304494.5:c.56_87del	p.Ala19GlyfsTer14	p.A19Gfs*14	ENST00000304494	NM_000077.4	19	gCCGCGGCCCGGGGTCGGGTAGAGGAGGTGCGG/g	1/3	0.303968792187137	2	FACETS	0.956	0.863	1	0.956	0.863	1	CLONAL	2	TRUE	0	0.35	2		349	284	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966872	25966873	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	124	663	2	ENST00000435504.4:c.2333dup	p.Val779SerfsTer25	p.V779Sfs*25	ENST00000435504		778	cca/ccCa	13/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		665	784	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	632	743	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		743	1178	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	354	660	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		660	873	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804278	43804278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	131	634	0	ENST00000372470.3:c.278G>A	p.Cys93Tyr	p.C93Y	ENST00000372470	NM_005373.2	93	tGc/tAc	3/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		634	856	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107284	193107284	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	100	307	0	ENST00000367435.3:c.493G>T	p.Val165Leu	p.V165L	ENST00000367435	NM_024529.4	165	Gta/Tta	6/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		307	345	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121568	193121569	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	36	285	0	ENST00000367435.3:c.967_968del	p.Val323AsnfsTer53	p.V323Nfs*53	ENST00000367435	NM_024529.4	322	tcTGta/tcta	10/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		285	204	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652330	206652330	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	59	871	0	ENST00000367120.3:c.1042del	p.Arg348AspfsTer32	p.R348Dfs*32	ENST00000367120	NM_014002.3	346	gCc/gc	10/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		871	1180	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851657	63851657	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	131	624	0	ENST00000279873.7:c.2435A>G	p.Lys812Arg	p.K812R	ENST00000279873	NM_032199.2	812	aAa/aGa	10/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		624	581	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310934	123310934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146244307	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	123	534	0	ENST00000358487.5:c.494G>A	p.Arg165Gln	p.R165Q	ENST00000358487	NM_000141.4	165	cGg/cAg	5/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		534	562	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456753	32456753	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1212035248	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	425	736	1	ENST00000332351.3:c.139G>A	p.Glu47Lys	p.E47K	ENST00000332351	NM_024426.4	47	Gag/Aag	1/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		737	1183	SUCCESS
EED	8726	MSKCC	GRCh37	11	85979605	85979605	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	58	315	0	ENST00000263360.6:c.966+2T>C		p.X322_splice	ENST00000263360	NM_003797.3	322			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		315	279	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347620	118347620	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	277	597	0	ENST00000534358.1:c.3257T>C	p.Phe1086Ser	p.F1086S	ENST00000534358	NM_005933.3	1086	tTt/tCt	4/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		597	869	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103164	119103164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730880429	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	172	438	2	ENST00000264033.4:c.202C>T	p.Arg68Trp	p.R68W	ENST00000264033	NM_005188.3	68	Cgg/Tgg	2/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		440	697	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641388	18641389	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1229278001	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	22	235	0	ENST00000266497.5:c.2393dup	p.Asn798LysfsTer5	p.N798Kfs*5	ENST00000266497		796	cta/ctAa	17/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		235	166	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420661	49420661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555185875	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	164	745	1	ENST00000301067.7:c.15088C>T	p.Arg5030Cys	p.R5030C	ENST00000301067	NM_003482.3	5030	Cgt/Tgt	48/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		746	1039	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881489	48881490	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs587778862	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	60	291	0	ENST00000267163.4:c.219_220del	p.Arg73SerfsTer36	p.R73Sfs*36	ENST00000267163	NM_000321.2	71	AGa/a	2/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		291	160	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349428	73349428	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	98	407	0	ENST00000377767.4:c.908T>C	p.Val303Ala	p.V303A	ENST00000377767	NM_014953.3	303	gTa/gCa	6/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		407	531	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961829	41961829	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	88	374	0	ENST00000219905.7:c.737A>G	p.Gln246Arg	p.Q246R	ENST00000219905	NM_001164273.1	246	cAg/cGg	2/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		374	269	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900302	3900302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	167	634	0	ENST00000262367.5:c.794C>T	p.Ala265Val	p.A265V	ENST00000262367	NM_004380.2	265	gCc/gTc	2/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		634	841	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041873	14041873	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	157	387	0	ENST00000311895.7:c.2420A>G	p.His807Arg	p.H807R	ENST00000311895	NM_005236.2	807	cAt/cGt	11/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		387	473	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993365	72993365	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	413	918	0	ENST00000268489.5:c.680T>C	p.Val227Ala	p.V227A	ENST00000268489	NM_006885.3	227	gTc/gCc	2/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		918	1169	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984226	7984226	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	179	734	0	ENST00000319144.4:c.503G>T	p.Arg168Met	p.R168M	ENST00000319144	NM_001139.2	168	aGg/aTg	4/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		734	982	SUCCESS
YES1	7525	MSKCC	GRCh37	18	748019	748019	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	181	469	1	ENST00000314574.4:c.372-1G>T		p.X124_splice	ENST00000314574	NM_005433.3	124			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		470	480	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56415030	56415030	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	48	432	0	ENST00000348428.3:c.2431A>C	p.Ile811Leu	p.I811L	ENST00000348428	NM_006785.3	811	Ata/Cta	17/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		432	371	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248651	10248651	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1568220903	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	128	649	1	ENST00000340748.4:c.4102C>T	p.Arg1368Ter	p.R1368*	ENST00000340748		1368	Cga/Tga	35/40	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		650	705	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366260	15366260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1463941396	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	165	749	1	ENST00000263377.2:c.1895G>A	p.Arg632His	p.R632H	ENST00000263377	NM_058243.2	632	cGc/cAc	10/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		750	972	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218383	36218383	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	389	1047	0	ENST00000222270.7:c.4162T>C	p.Tyr1388His	p.Y1388H	ENST00000222270	NM_014727.1	1388	Tac/Cac	16/37	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1047	1390	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218623	36218623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	447	904	0	ENST00000222270.7:c.4327C>T	p.His1443Tyr	p.H1443Y	ENST00000222270	NM_014727.1	1443	Cac/Tac	17/37	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		904	1389	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224774	36224774	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	212	1014	0	ENST00000222270.7:c.7159+1G>T		p.X2387_splice	ENST00000222270	NM_014727.1	2387			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1014	1365	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725130	47725130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1330	260	1056	0	ENST00000449228.1:c.614C>A	p.Pro205His	p.P205H	ENST00000449228	NM_001127240.2	205	cCt/cAt	4/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1056	1590	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966264	25966264	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	149	639	0	ENST00000435504.4:c.2942C>T	p.Pro981Leu	p.P981L	ENST00000435504		981	cCa/cTa	13/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		639	736	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543672	9543672	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	94	371	0	ENST00000353224.5:c.1483-1G>T		p.X495_splice	ENST00000353224	NM_177990.2	495			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		371	527	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281749	46281749	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	209	771	1	ENST00000371998.3:c.4196G>A	p.Ser1399Asn	p.S1399N	ENST00000371998		1399	aGt/aAt	22/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		772	1062	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478817	57478817	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	195	408	0	ENST00000371085.3:c.403A>C	p.Met135Leu	p.M135L	ENST00000371085	NM_000516.4	135	Atg/Ctg	5/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		408	585	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231810	36231811	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	309	698	0	ENST00000300305.3:c.573_574del	p.Arg191SerfsTer21	p.R191Sfs*21	ENST00000300305		191	agAGcc/agcc	5/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		698	944	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259206	36259206	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	116	731	0	ENST00000300305.3:c.285del	p.Asn96ThrfsTer26	p.N96Tfs*26	ENST00000300305		95	ccC/cc	3/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		731	855	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37092009	37092009	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs63750499	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	185	505	0	ENST00000231790.2:c.2136G>A	p.Trp712Ter	p.W712*	ENST00000231790	NM_000249.3	712	tgG/tgA	19/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		505	446	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127758	47127758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	235	518	0	ENST00000409792.3:c.5324G>A	p.Gly1775Glu	p.G1775E	ENST00000409792	NM_014159.6	1775	gGg/gAg	11/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		518	548	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933431	49933431	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	381	853	0	ENST00000296474.3:c.2759del	p.Pro920HisfsTer16	p.P920Hfs*16	ENST00000296474	NM_002447.2	920	cCa/ca	11/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		853	872	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670334	134670334	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	96	456	0	ENST00000398015.3:c.245C>G	p.Ala82Gly	p.A82G	ENST00000398015	NM_004441.4	82	gCc/gGc	3/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		456	676	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186847	142186847	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	69	345	0	ENST00000350721.4:c.6616A>G	p.Lys2206Glu	p.K2206E	ENST00000350721	NM_001184.3	2206	Aaa/Gaa	39/47	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		345	244	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801184	1801184	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	166	952	1	ENST00000260795.2:c.316del	p.Ala106ProfsTer20	p.A106Pfs*20	ENST00000260795		105	Ggg/gg	2/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		953	1292	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522532	67522532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767837787	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	12	181	0	ENST00000274335.5:c.29C>T	p.Ala10Val	p.A10V	ENST00000274335		10	gCg/gTg	1/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		181	188	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86642543	86642543	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	26	284	0	ENST00000274376.6:c.1102+2T>C		p.X368_splice	ENST00000274376	NM_002890.2	368			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		284	71	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056985	180056985	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	225	924	0	ENST00000261937.6:c.634G>T	p.Asp212Tyr	p.D212Y	ENST00000261937	NM_182925.4	212	Gac/Tac	5/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		924	1001	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163554	32163554	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	130	688	2	ENST00000375023.3:c.5672del	p.Gly1891AlafsTer13	p.G1891Afs*13	ENST00000375023	NM_004557.3	1891	gGc/gc	30/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		690	808	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536164	106536164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	90	413	1	ENST00000369096.4:c.131C>T	p.Ala44Val	p.A44V	ENST00000369096	NM_001198.3	44	gCg/gTg	2/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		414	592	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683807	117683808	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	64	510	0	ENST00000368508.3:c.3339dup	p.Gln1114SerfsTer3	p.Q1114Sfs*3	ENST00000368508	NM_002944.2	1113	-/T	21/43	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		510	419	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398590	116398590	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs767770443	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	52	485	0	ENST00000397752.3:c.2180A>C	p.Asp727Ala	p.D727A	ENST00000397752	NM_000245.2	727	gAc/gCc	9/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		485	312	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162915	38162915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199766344	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	148	639	0	ENST00000317025.8:c.2291G>A	p.Arg764His	p.R764H	ENST00000317025	NM_023034.1	764	cGt/cAt	13/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		639	778	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982764	90982764	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1434146100	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	60	302	0	ENST00000265433.3:c.724G>T	p.Val242Phe	p.V242F	ENST00000265433	NM_002485.4	242	Gtt/Ttt	7/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		302	328	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932717	39932717	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	420	486	0	ENST00000378444.4:c.1882G>T	p.Ala628Ser	p.A628S	ENST00000378444	NM_001123385.1	628	Gca/Tca	4/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		486	722	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349635	70349635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780391	NA	P-0048110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	159	367	1	ENST00000374080.3:c.3797G>A	p.Arg1266His	p.R1266H	ENST00000374080		1266	cGc/cAc	27/45	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		368	734	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0048111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	100	383	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.223736024516511	2		383	601	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0048111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	224	622	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.169130281024009	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.223736024516511	4		622	983	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916747	48916747	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690915	NA	P-0048111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	61	318	0	ENST00000267163.4:c.277C>T	p.Gln93Ter	p.Q93*	ENST00000267163	NM_000321.2	93	Caa/Taa	3/27	0.165332526463924	3	FACETS	1	0.918	1	1	0.918	1	CLONAL	2	TRUE	1	0.223736024516511	3		318	282	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033877	49033877	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1131690903	NA	P-0048111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	53	391	0	ENST00000267163.4:c.2014G>T	p.Glu672Ter	p.E672*	ENST00000267163	NM_000321.2	672	Gag/Tag	20/27	0.165332526463924	3	FACETS	1	0.877	1	0.515	0.44	0.598	CLONAL	1	TRUE	1	0.223736024516511	3		391	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577113	7577113	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555525279	NA	P-0048111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	164	791	0	ENST00000269305.4:c.825T>G	p.Cys275Trp	p.C275W	ENST00000269305	NM_001126112.2	275	tgT/tgG	8/11	1	2	FACETS	0.971	0.893	1	1	0.992	1	CLONAL	2	TRUE	1	0.223736024516511	2		791	755	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145543	61145543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767519747	NA	P-0048111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	67	331	0	ENST00000295025.8:c.655C>T	p.Arg219Cys	p.R219C	ENST00000295025	NM_002908.2	219	Cgt/Tgt	7/11	1	2	FACETS	0.868	0.759	0.984	1	0.978	1	CLONAL	2	TRUE	1	0.223736024516511	2		331	345	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272525	15272525	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	133	587	0	ENST00000263388.2:c.5914G>A	p.Glu1972Lys	p.E1972K	ENST00000263388	NM_000435.2	1972	Gag/Aag	33/33	0.124418837416631	5	FACETS	1	0.955	1			1	INDETERMINATE	2	TRUE	NA	0.223736024516511	5		587	734	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215386	5215386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	157	663	0	ENST00000357368.4:c.4232C>T	p.Ser1411Phe	p.S1411F	ENST00000357368	NM_002850.3	1411	tCc/tTc	28/38	0.223736024516511	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.223736024516511	2		663	667	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950309	17950309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	190	843	0	ENST00000458235.1:c.1418C>T	p.Ser473Phe	p.S473F	ENST00000458235	NM_000215.3	473	tCc/tTc	10/24	1	2	FACETS	0.875	0.809	0.944	1	0.992	1	CLONAL	2	TRUE	1	0.223736024516511	2		843	970	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903687	114903687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	57	554	1	ENST00000543371.1:c.691C>T	p.Pro231Ser	p.P231S	ENST00000543371	NM_001198531.1	231	Cca/Tca	7/14	1	2	FACETS	0.784	0.672	0.906	0.784	0.672	0.906	CLONAL	1	TRUE	1	0.223736024516511	2		555	650	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180310	32180310	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	174	755	1	ENST00000375023.3:c.2621G>A	p.Trp874Ter	p.W874*	ENST00000375023	NM_004557.3	874	tGg/tAg	17/30	0.223736024516511	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	0	0.223736024516511	2		756	770	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598254	28598254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768069936	NA	P-0048111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	283	928	0	ENST00000253063.3:c.226G>A	p.Val76Ile	p.V76I	ENST00000253063	NM_031459.4	76	Gta/Ata	3/10	0.169130281024009	4	FACETS	0.865	0.812	0.919	1	0.991	1	CLONAL	3	TRUE	2	0.223736024516511	4		928	1193	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417938	32417938	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1437575773	NA	P-0048111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	66	516	1	ENST00000332351.3:c.1114C>T	p.Pro372Ser	p.P372S	ENST00000332351	NM_024426.4	372	Cct/Tct	7/10	0.212018192505605	2	FACETS	0.932	0.809	1	0.466	0.404	0.533	CLONAL	1	TRUE	0	0.223736024516511	2		517	633	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68934916	68934916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057226577	NA	P-0048111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	97	438	0	ENST00000487270.1:c.985C>T	p.Pro329Ser	p.P329S	ENST00000487270	NM_133509.3	329	Ccc/Tcc	10/11	0.169130281024009	4	FACETS	0.99	0.885	1	0.99	0.885	1	CLONAL	2	TRUE	2	0.223736024516511	4		438	536	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855601	45855602	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0048111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	175	777	1	ENST00000391945.4:c.2055_2056delinsTT	p.Arg686Cys	p.R686C	ENST00000391945	NM_000400.3	685	gcCCgt/gcTTgt	22/23	1	2	FACETS	0.954	0.88	1	1	0.992	1	CLONAL	2	TRUE	1	0.223736024516511	2		778	820	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293209	212293209	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1489485973	NA	P-0048111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	22	247	0	ENST00000342788.4:c.2644-1G>A		p.X882_splice	ENST00000342788	NM_005235.2	882			1	2	FACETS	0.713	0.553	0.897	0.713	0.553	0.897	SUBCLONAL	1	TRUE	1	0.223736024516511	2		247	276	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458543	12458543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	82	655	0	ENST00000287820.6:c.1160C>T	p.Pro387Leu	p.P387L	ENST00000287820	NM_015869.4	387	cCt/cTt	6/7	1	2	FACETS	0.926	0.815	1	0.926	0.815	1	CLONAL	1	TRUE	1	0.223736024516511	2		655	792	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057708	180057708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	120	895	0	ENST00000261937.6:c.247G>A	p.Asp83Asn	p.D83N	ENST00000261937	NM_182925.4	83	Gac/Aac	3/30	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.223736024516511	2		895	968	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923203	39923203	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs761866885	NA	P-0048111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	50	460	0	ENST00000378444.4:c.3505G>A	p.Asp1169Asn	p.D1169N	ENST00000378444	NM_001123385.1	1169	Gac/Aac	8/15	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.223736024516511	2		460	390	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	144	349	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.747654184862648	2		350	357	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121913370	NA	P-0048113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	17	236	0	ENST00000288602.6:c.1742A>G	p.Asn581Ser	p.N581S	ENST00000288602	NM_004333.4	581	aAt/aGt	15/18	1	2	FACETS	0.174	0.13	0.227	0.174	0.13	0.227	SUBCLONAL	1	TRUE	1	0.747654184862648	2		236	261	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0048113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	379	824	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.747654184862648	2		824	896	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157059	106157059	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	220	421	0	ENST00000380013.4:c.1960C>T	p.Gln654Ter	p.Q654*	ENST00000380013	NM_001127208.2	654	Caa/Taa	3/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.747654184862648	2		421	524	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608277	100608277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	304	669	0	ENST00000308731.7:c.1813G>A	p.Glu605Lys	p.E605K	ENST00000308731	NM_000061.2	605	Gag/Aag	18/19	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.747654184862648	2		669	753	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151932982	151932982	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs772146328	NA	P-0048113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	41	60	0	ENST00000262189.6:c.2689C>T	p.Arg897Ter	p.R897*	ENST00000262189	NM_170606.2	897	Cga/Tga	16/59	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.747654184862648	2		60	85	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349165	70349165	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0048113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	29	595	0	ENST00000374080.3:c.3578-1G>A		p.X1193_splice	ENST00000374080		1193			1	2	FACETS	0.137	0.109	0.168	0.137	0.109	0.168	SUBCLONAL	1	TRUE	1	0.747654184862648	2		595	567	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433896	49433896	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	363	912	2	ENST00000301067.7:c.7657C>T	p.Gln2553Ter	p.Q2553*	ENST00000301067	NM_003482.3	2553	Cag/Tag	31/54	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.747654184862648	2		914	873	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425524	49425524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	358	791	0	ENST00000301067.7:c.12964C>T	p.Gln4322Ter	p.Q4322*	ENST00000301067	NM_003482.3	4322	Caa/Taa	39/54	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.747654184862648	2		791	823	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434352	49434352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748969699	NA	P-0048113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	316	757	1	ENST00000301067.7:c.7201C>T	p.Arg2401Cys	p.R2401C	ENST00000301067	NM_003482.3	2401	Cgc/Tgc	31/54	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.747654184862648	2		758	742	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40854906	40854906	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	245	503	0	ENST00000428826.2:c.2172C>G	p.Phe724Leu	p.F724L	ENST00000428826		724	ttC/ttG	20/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.747654184862648	2		503	592	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575606	55575606	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	171	349	0	ENST00000288135.5:c.1132C>G	p.His378Asp	p.H378D	ENST00000288135	NM_000222.2	378	Cat/Gat	7/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.747654184862648	2		349	390	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942775	44942775	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	313	542	0	ENST00000377967.4:c.3355C>G	p.Leu1119Val	p.L1119V	ENST00000377967	NM_021140.2	1119	Cta/Gta	23/29	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.747654184862648	2		542	690	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0048114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	325	570	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	NA	2	FACETS	0.957	0.911	1			1	INDETERMINATE	2	TRUE	NA	0.491273561755972	2		571	691	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954210	48954210	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1354030520	NA	P-0048114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	49	198	0	ENST00000267163.4:c.1411C>T	p.Gln471Ter	p.Q471*	ENST00000267163	NM_000321.2	471	Caa/Taa	15/27	0.462742182812323	2	FACETS	1	0.964	1	0.697	0.604	0.795	CLONAL	1	TRUE	0	0.491273561755972	2		198	143	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676271	29676271	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0048114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	45	290	0	ENST00000356175.3:c.7258+2T>A		p.X2420_splice	ENST00000356175	NM_000267.3	2420			0.463542301889298	3	FACETS	0.792	0.67	0.926	0.396	0.335	0.463	CLONAL	1	TRUE	1	0.491273561755972	3		290	288	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893659	28893659	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	185	453	0	ENST00000282397.4:c.3187C>G	p.Leu1063Val	p.L1063V	ENST00000282397	NM_002019.4	1063	Ctg/Gtg	24/30	0.462742182812323	2	FACETS	0.901	0.842	0.96	0.901	0.842	0.96	CLONAL	2	TRUE	0	0.491273561755972	2		453	418	SUCCESS
APC	324	MSKCC	GRCh37	5	112173992	112173992	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1114167559	NA	P-0048114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	143	335	0	ENST00000257430.4:c.2701C>T	p.Gln901Ter	p.Q901*	ENST00000257430	NM_000038.5	901	Cag/Tag	16/16	0.457866381621208	2	FACETS	0.849	0.785	0.913	0.849	0.785	0.913	CLONAL	2	TRUE	0	0.491273561755972	2		335	343	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692856	89692856	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	90	154	0	ENST00000371953.3:c.340G>T	p.Glu114Ter	p.E114*	ENST00000371953	NM_000314.4	114	Gaa/Taa	5/9	0.457866381621208	2	FACETS	0.916	0.832	1	0.916	0.832	1	CLONAL	2	TRUE	0	0.491273561755972	2		154	200	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617503	158617503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1034717563	NA	P-0048114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	265	470	0	ENST00000263640.3:c.1153G>A	p.Glu385Lys	p.E385K	ENST00000263640	NM_001105.4	385	Gaa/Aaa	9/11	0.434751329714982	4	FACETS	0.955	0.898	1	0.955	0.898	1	CLONAL	2	TRUE	2	0.491273561755972	4		470	842	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380282	25380282	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	231	543	0	ENST00000311936.3:c.176C>A	p.Ala59Glu	p.A59E	ENST00000311936	NM_004985.3	59	gCa/gAa	3/5	0.463542301889298	3	FACETS	0.854	0.8	0.909	0.854	0.8	0.909	CLONAL	2	TRUE	1	0.491273561755972	3		543	686	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309777	104309777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745958724	NA	P-0048114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	347	694	1	ENST00000369902.3:c.368G>A	p.Arg123His	p.R123H	ENST00000369902	NM_016169.3	123	cGt/cAt	3/12	0.457866381621208	2	FACETS	0.894	0.851	0.937	0.894	0.851	0.937	CLONAL	2	TRUE	0	0.491273561755972	2		695	790	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752859	42752859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780261925	NA	P-0048114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	460	918	1	ENST00000222329.4:c.1405G>A	p.Gly469Ser	p.G469S	ENST00000222329	NM_006494.2	469	Ggc/Agc	4/4	0.306835711265115	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.491273561755972	4		919	1345	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633294	3633294	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	242	1064	2	ENST00000294008.3:c.4957del	p.Ala1653ProfsTer62	p.A1653Pfs*62	ENST00000294008	NM_032444.2	1653	Gcc/cc	14/15	0.463542301889298	3	FACETS	0.895	0.834	0.958	0.448	0.417	0.479	CLONAL	1	TRUE	1	0.491273561755972	3		1066	1371	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681047	30681047	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	355	505	0	ENST00000376406.3:c.672A>C	p.Glu224Asp	p.E224D	ENST00000376406	NM_014641.2	224	gaA/gaC	5/15	0.491273561755972	5	FACETS	0.993	0.945	1	0.993	0.945	1	CLONAL	3	TRUE	2	0.491273561755972	5		505	843	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528727	8528727	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	272	413	0	ENST00000356435.5:c.405G>T	p.Lys135Asn	p.K135N	ENST00000356435		135	aaG/aaT	4/35	0.457866381621208	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.491273561755972	2		413	524	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738219	133738219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	599	611	2	ENST00000318560.5:c.619G>A	p.Asp207Asn	p.D207N	ENST00000318560	NM_005157.4	207	Gac/Aac	4/11	0.46078664990486	4	FACETS	0.965	0.936	0.993	0.965	0.936	0.993	CLONAL	4	TRUE	0	0.491273561755972	4		613	942	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289742	15289751	+	protein_altering_variant,splice_region_variant	In_Frame_Del	DEL	ACAGCGAGGA	ACAGCGAGGA	T	novel	NA	P-0048114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	288	892	0	ENST00000263388.2:c.3720_3729delinsA	p.Pro1241_Cys1243del	p.P1241_C1243del	ENST00000263388	NM_000435.2	1240	ggTCCTCGCTGT/ggA	23/33	0.423969920696076	3	FACETS	1	0.981	1	0.554	0.52	0.589	CLONAL	1	TRUE	1	0.491273561755972	3		892	1318	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0048115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	125	147	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.570267235890787	2	FACETS	0.821	0.758	0.885	0.821	0.758	0.885	CLONAL	2	TRUE	0	0.570267235890787	2		147	267	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0048115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	439	646	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.570267235890787	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.570267235890787	1		646	894	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73351584	73351584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	150	179	0	ENST00000377767.4:c.628C>T	p.Arg210Cys	p.R210C	ENST00000377767	NM_014953.3	210	Cgt/Tgt	4/21	0.570267235890787	4	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.570267235890787	4		179	569	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81971495	81971495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767605816	NA	P-0048115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	115	394	0	ENST00000359376.3:c.3185C>T	p.Thr1062Met	p.T1062M	ENST00000359376	NM_002661.3	1062	aCg/aTg	28/33	0.266039822726576	2	FACETS	0.547	0.492	0.604	0.273	0.246	0.302	INDETERMINATE	1	TRUE	0	0.570267235890787	2		394	738	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374383	81374383	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	184	309	0	ENST00000222390.5:c.679G>T	p.Glu227Ter	p.E227*	ENST00000222390	NM_000601.4	227	Gaa/Taa	6/18	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.570267235890787	2		309	508	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970966	21970966	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1563888782	NA	P-0048115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	124	587	1	ENST00000304494.5:c.392G>A	p.Arg131His	p.R131H	ENST00000304494	NM_000077.4	131	cGc/cAc	2/3	1	2	FACETS	0.439	0.396	0.484	0.439	0.396	0.484	SUBCLONAL	1	TRUE	1	0.570267235890787	2		588	991	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007581	62007581	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1277301487	NA	P-0048115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	570	714	1	ENST00000392795.3:c.286C>T	p.Arg96Cys	p.R96C	ENST00000392795	NM_001039933.1	96	Cgc/Tgc	3/6	0.285554438946696	3	FACETS	1	0.985	1	0.695	0.669	0.72	INDETERMINATE	2	TRUE	0	0.570267235890787	3		715	1233	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119634940	119634940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	71	253	0	ENST00000316626.5:c.559C>T	p.Leu187Phe	p.L187F	ENST00000316626		187	Ctc/Ttc	5/12	0.185242414712195	2	FACETS	0.579	0.507	0.656	0.29	0.253	0.328	INDETERMINATE	1	TRUE	0	0.570267235890787	2		253	430	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0048117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	24	765	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.639092389796247	3	FACETS	0.206	0.161	0.258	0.103	0.08	0.129	SUBCLONAL	1	TRUE	1	0.639092389796247	3		766	481	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	406	349	1				ENST00000310581	NM_198253.2	-/1132			0.637321814884266	5	FACETS	0.889	0.85	0.929	0.889	0.85	0.929	CLONAL	3	TRUE	2	0.639092389796247	5		350	933	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593247	67593247	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	49	391	0	ENST00000274335.5:c.1994del	p.Gly665AlafsTer3	p.G665Afs*3	ENST00000274335		665	Ggc/gc	15/15	0.639092389796247	3	FACETS	1	0.868	1	0.337	0.289	0.389	CLONAL	1	TRUE	0	0.639092389796247	3		391	200	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593252	67593253	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0048117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	11	424	0	ENST00000274335.5:c.1999_2000dup	p.Lys668Ter	p.K668*	ENST00000274335		666	-/GT	15/15	0.639092389796247	3	FACETS	0.214	0.148	0.297	0.071	0.049	0.099	SUBCLONAL	1	TRUE	0	0.639092389796247	3		424	212	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	124	349	1				ENST00000310581	NM_198253.2	-/1132			0.234665787100357	4	FACETS	0.822	0.746	0.902			1	CLONAL	2	TRUE	NA	0.346462923298143	4		350	586	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0048135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	225	703	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.296098960826076	2	FACETS	0.835	0.78	0.891	0.835	0.78	0.891	CLONAL	2	TRUE	0	0.346462923298143	2		703	778	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220428	123220428	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	126	289	0	ENST00000218089.9:c.3085C>T	p.Gln1029Ter	p.Q1029*	ENST00000218089	NM_001042749.1	1029	Cag/Tag	30/35	0.270862681462134	2	FACETS	0.878	0.81	0.947			1	CLONAL	3	TRUE	NA	0.346462923298143	2		289	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0048135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	203	498	0	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	0.297892706896776	2	FACETS	0.988	0.922	1	0.988	0.922	1	CLONAL	2	TRUE	0	0.346462923298143	2		498	593	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588981	67588981	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	50	277	0	ENST00000274335.5:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000274335		358	Cga/Tga	8/15	0.23354510253507	4	FACETS	0.957	0.823	1	0.957	0.823	1	CLONAL	2	TRUE	2	0.346462923298143	4		277	203	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720741	89720741	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs371387815	NA	P-0048135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	27	162	0	ENST00000371953.3:c.892C>T	p.Gln298Ter	p.Q298*	ENST00000371953	NM_000314.4	298	Caa/Taa	8/9	0.346462923298143	3	FACETS	0.854	0.694	1	0.57	0.463	0.686	CLONAL	2	TRUE	0	0.346462923298143	3		162	107	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129103	2129103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45517279	NA	P-0048135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	216	619	0	ENST00000219476.3:c.3037G>A	p.Asp1013Asn	p.D1013N	ENST00000219476	NM_000548.3	1013	Gat/Aat	27/42	0.279916539342929	4	FACETS	0.85	0.791	0.912	0.85	0.791	0.912	CLONAL	2	TRUE	2	0.346462923298143	4		619	987	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554045	63554045	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	216	549	0	ENST00000307078.5:c.694G>C	p.Glu232Gln	p.E232Q	ENST00000307078	NM_004655.3	232	Gag/Cag	2/11	0.23354510253507	4	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	2	0.346462923298143	4		549	835	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817843	3817843	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0048135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	142	454	0	ENST00000262367.5:c.3128C>G	p.Ser1043Ter	p.S1043*	ENST00000262367	NM_004380.2	1043	tCa/tGa	16/31	0.279916539342929	4	FACETS	0.951	0.871	1	0.951	0.871	1	CLONAL	2	TRUE	2	0.346462923298143	4		454	580	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262834	46262834	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	236	400	0	ENST00000371998.3:c.1007C>T	p.Ser336Leu	p.S336L	ENST00000371998		336	tCg/tTg	10/23	0.346462923298143	5	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	TRUE	2	0.346462923298143	5		400	635	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949085	44949085	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	130	214	1	ENST00000377967.4:c.3646G>T	p.Asp1216Tyr	p.D1216Y	ENST00000377967	NM_021140.2	1216	Gat/Tat	25/29	0.270862681462134	2	FACETS	0.854	0.788	0.92			1	CLONAL	3	TRUE	NA	0.346462923298143	2		215	293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0048136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	37	494	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.618	0.508	0.743	0.618	0.508	0.743	SUBCLONAL	1	TRUE	1	0.16	2		494	748	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0048136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	49	346	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.16	2		346	463	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726712	88726712	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs765578547	NA	P-0048136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	25	430	0	ENST00000360948.2:c.332A>G	p.Lys111Arg	p.K111R	ENST00000360948	NM_001012338.2	111	aAg/aGg	4/19	1	2	FACETS	0.657	0.516	0.818	0.657	0.516	0.818	SUBCLONAL	1	TRUE	1	0.16	2		430	476	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	103	349	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.978	1	1	0.99	1	CLONAL	2	FALSE	1	0.364934032116889	2		350	229	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0048137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	160	620	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.364934032116889	0	FACETS	0.824	0.768	0.88			1	CLONAL	2	FALSE	0	0.364934032116889	0		620	338	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0048137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	45	188	0	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	0.364934032116889	0	FACETS	0.779	0.698	0.855			1	SUBCLONAL	3	FALSE	0	0.364934032116889	0		188	67	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0048137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	121	645	1	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.364934032116889	0	FACETS	1	0.944	1			1	CLONAL	1	FALSE	0	0.364934032116889	0		646	402	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523505	106523505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	88	233	0	ENST00000359195.3:c.2657C>T	p.Thr886Met	p.T886M	ENST00000359195	NM_002649.2	886	aCg/aTg	8/11	1	2	FACETS	0.992	0.894	1	1	0.987	1	CLONAL	2	FALSE	1	0.364934032116889	2		233	243	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652198	36652199	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0048137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	209	689	0	ENST00000244741.5:c.322dup	p.Glu108GlyfsTer21	p.E108Gfs*21	ENST00000244741	NM_000389.4	107	gag/gaGg	2/3	0.137245409946998	3	FACETS	0.868	0.813	0.924	1	0.99	1	INDETERMINATE	3	FALSE	1	0.364934032116889	3		689	520	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918141	50918141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753609023	NA	P-0048137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	40	755	0	ENST00000440232.2:c.2458G>A	p.Ala820Thr	p.A820T	ENST00000440232	NM_002691.3	820	Gcc/Acc	20/27	0.364934032116889	3	FACETS	0.412	0.342	0.491	0.206	0.171	0.246	SUBCLONAL	1	FALSE	1	0.364934032116889	3		755	629	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486587	56486587	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	181	507	0	ENST00000267101.3:c.1166C>T	p.Thr389Ile	p.T389I	ENST00000267101	NM_001982.3	389	aCa/aTa	10/28	0.149278335992808	4	FACETS	0.868	0.807	0.93			1	INDETERMINATE	3	FALSE	NA	0.364934032116889	4		507	520	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102083	27102083	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	169	479	1	ENST00000324856.7:c.5009G>A	p.Trp1670Ter	p.W1670*	ENST00000324856	NM_006015.4	1670	tGg/tAg	19/20	1	2	FACETS	1	0.94	1	1	0.993	1	CLONAL	2	FALSE	1	0.364934032116889	2		480	457	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244202	46244202	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	100	345	0	ENST00000334344.6:c.2296C>G	p.Pro766Ala	p.P766A	ENST00000334344	NM_152641.2	766	Cca/Gca	15/21	1	2	FACETS	1	0.976	1	1	0.99	1	CLONAL	2	FALSE	1	0.364934032116889	2		345	226	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562739	21562739	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	210	589	1	ENST00000382592.4:c.1180G>A	p.Val394Met	p.V394M	ENST00000382592	NM_014572.2	394	Gtg/Atg	4/8	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	FALSE	1	0.364934032116889	2		590	471	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749094	43749094	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	107	530	0	ENST00000382044.4:c.1712G>T	p.Ser571Ile	p.S571I	ENST00000382044	NM_001141980.1	571	aGt/aTt	12/28	1	2	FACETS	0.888	0.806	0.973	1	0.988	1	CLONAL	2	FALSE	1	0.364934032116889	2		530	330	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78704489	78704489	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	235	355	0	ENST00000306801.3:c.637C>T	p.Arg213Trp	p.R213W	ENST00000306801	NM_020761.2	213	Cgg/Tgg	5/34	0.364934032116889	3	FACETS	0.887	0.841	0.934	1	0.995	1	CLONAL	4	FALSE	1	0.364934032116889	3		355	429	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293875	1293875	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	48	858	0	ENST00000310581.5:c.1126C>G	p.Pro376Ala	p.P376A	ENST00000310581	NM_198253.2	376	Ccc/Gcc	2/16	1	2	FACETS	0.525	0.444	0.614	0.525	0.444	0.614	SUBCLONAL	1	FALSE	1	0.364934032116889	2		858	501	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818267	32818267	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	214	520	0	ENST00000354258.4:c.1258C>G	p.Leu420Val	p.L420V	ENST00000354258	NM_000593.5	420	Ctg/Gtg	5/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.364934032116889	NA		520	566	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913514	NA	P-0048138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	204	371	0	ENST00000288135.5:c.2466T>A	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaA	17/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.792009219957523	2		371	481	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028385	42028466	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGGAAGTCTTCCTGCAATGAAGGAGAATCCTCTTCTACTTCTTATATGCATCAGAGGTCACCTGGTGGTCCCACCAAACT	GCTGGAAGTCTTCCTGCAATGAAGGAGAATCCTCTTCTACTTCTTATATGCATCAGAGGTCACCTGGTGGTCCCACCAAACT	-	novel	NA	P-0048138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	120	223	0	ENST00000219905.7:c.3924_4005del	p.Ser1308ArgfsTer18	p.S1308Rfs*18	ENST00000219905	NM_001164273.1	1308	aGCTGGAAGTCTTCCTGCAATGAAGGAGAATCCTCTTCTACTTCTTATATGCATCAGAGGTCACCTGGTGGTCCCACCAAACTg/ag	13/24	0.792009219957523	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.792009219957523	1		223	167	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86637138	86637138	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	99	240	0	ENST00000274376.6:c.1049T>C	p.Ile350Thr	p.I350T	ENST00000274376	NM_002890.2	350	aTa/aCa	6/25	1	2	FACETS	0.916	0.83	1	0.916	0.83	1	CLONAL	1	TRUE	1	0.792009219957523	2		240	273	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593602	55593612	+	protein_altering_variant	In_Frame_Del	DEL	GTGGAAGGTTG	GTGGAAGGTTG	CT	novel	NA	P-0048138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	173	380	0	ENST00000288135.5:c.1668_1678delinsCT	p.Gln556_Val560delinsHisPhe	p.Q556_V560delinsHF	ENST00000288135	NM_000222.2	556	caGTGGAAGGTTGtt/caCTtt	11/21	1	2	FACETS	0.89	0.826	0.955	0.89	0.826	0.955	CLONAL	1	TRUE	1	0.792009219957523	2		380	491	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275399	142275399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202162034	NA	P-0048139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	21	251	0	ENST00000350721.4:c.1904G>A	p.Arg635Gln	p.R635Q	ENST00000350721	NM_001184.3	635	cGa/cAa	9/47	0.160966000875943	2	FACETS	0.23	0.177	0.292	0.115	0.088	0.146	INDETERMINATE	1	TRUE	0	0.693927239097578	2		251	263	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967831	93967831	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	69	339	0	ENST00000369303.4:c.2096G>C	p.Gly699Ala	p.G699A	ENST00000369303	NM_004440.3	699	gGg/gCg	11/17	0.22459486515321	2	FACETS	0.581	0.51	0.658	0.291	0.255	0.329	INDETERMINATE	1	TRUE	0	0.693927239097578	2		339	342	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511591	46511591	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs778594341	NA	P-0048139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	67	318	0	ENST00000262741.5:c.1186G>A	p.Val396Met	p.V396M	ENST00000262741	NM_003629.3	396	Gtg/Atg	9/10	0.693927239097578	5	FACETS	0.444	0.385	0.509			1	SUBCLONAL	1	TRUE	NA	0.693927239097578	5		318	887	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929053	32929053	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	39	386	0	ENST00000380152.3:c.7063G>C	p.Glu2355Gln	p.E2355Q	ENST00000380152		2355	Gaa/Caa	14/27	0.596529323288006	4	FACETS	0.329	0.272	0.393			1	SUBCLONAL	1	TRUE	NA	0.693927239097578	4		386	579	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098928	178098928	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	25	272	0	ENST00000397062.3:c.117C>G	p.Phe39Leu	p.F39L	ENST00000397062	NM_006164.4	39	ttC/ttG	2/5	0.160966000875943	2	FACETS	0.193	0.152	0.241	0.097	0.076	0.121	INDETERMINATE	1	TRUE	0	0.693927239097578	2		272	373	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022910	31022910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	121	431	1	ENST00000375687.4:c.2395G>A	p.Asp799Asn	p.D799N	ENST00000375687	NM_015338.5	799	Gat/Aat	13/13	0.307675508830752	3	FACETS	0.83	0.753	0.911	0.415	0.376	0.456	INDETERMINATE	1	TRUE	1	0.693927239097578	3		432	566	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72842140	72842140	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	76	240	0	ENST00000325599.8:c.1108C>A	p.Gln370Lys	p.Q370K	ENST00000325599	NM_018130.2	370	Cag/Aag	10/11	0.693927239097578	1	FACETS	0.492	0.435	0.55	0.492	0.435	0.55	SUBCLONAL	1	TRUE	0	0.693927239097578	1		240	291	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524927	187524927	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	108	506	0	ENST00000441802.2:c.10753C>T	p.Gln3585Ter	p.Q3585*	ENST00000441802	NM_005245.3	3585	Cag/Tag	19/27	0.427270004958769	3	FACETS	0.667	0.599	0.738	0.222	0.199	0.246	SUBCLONAL	1	TRUE	0	0.693927239097578	3		506	629	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86667964	86667964	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	73	258	0	ENST00000274376.6:c.1728C>A	p.Cys576Ter	p.C576*	ENST00000274376	NM_002890.2	576	tgC/tgA	13/25	0.119878206733978	5	FACETS	1	0.97	1	0.449	0.395	0.505	INDETERMINATE	1	TRUE	2	0.693927239097578	5		258	319	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402854	20402854	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	10	18	0	ENST00000346618.3:c.391C>T	p.Pro131Ser	p.P131S	ENST00000346618	NM_001949.4	131	Ccg/Tcg	1/7	0.200321105989149	3	FACETS	1	0.823	1	0.417	0.297	0.551	INDETERMINATE	1	TRUE	0	0.693927239097578	3		18	31	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555351	106555351	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	55	305	1	ENST00000369096.4:c.2468T>A	p.Met823Lys	p.M823K	ENST00000369096	NM_001198.3	823	aTg/aAg	7/7	0.22459486515321	2	FACETS	0.6	0.518	0.689	0.3	0.259	0.345	INDETERMINATE	1	TRUE	0	0.693927239097578	2		306	264	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341734	8341734	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	21	451	0	ENST00000356435.5:c.4906G>T	p.Glu1636Ter	p.E1636*	ENST00000356435		1636	Gaa/Taa	29/35	0.693927239097578	1	FACETS	0.112	0.086	0.143	0.112	0.086	0.143	SUBCLONAL	1	TRUE	0	0.693927239097578	1		451	353	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0048141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	61	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.83	0.72	0.948	0.83	0.72	0.948	CLONAL	1	TRUE	1	0.407252691483654	2		327	361	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0048141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	48	222	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	1	2	FACETS	0.883	0.752	1	0.883	0.752	1	CLONAL	1	TRUE	1	0.407252691483654	2		222	267	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0048141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	64	300	1	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	0.856	0.745	0.975	0.856	0.745	0.975	CLONAL	1	TRUE	1	0.407252691483654	2		301	367	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119772	17119772	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	162	706	0	ENST00000285071.4:c.1222C>T	p.Gln408Ter	p.Q408*	ENST00000285071	NM_144997.5	408	Cag/Tag	11/14	0.407252691483654	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.407252691483654	1		706	551	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281611	15281611	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	87	642	6	ENST00000263388.2:c.4762A>C	p.Asn1588His	p.N1588H	ENST00000263388	NM_000435.2	1588	Aac/Cac	26/33	1	2	FACETS	0.592	0.524	0.665	0.592	0.524	0.665	SUBCLONAL	1	TRUE	1	0.407252691483654	2		648	722	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538374	9538374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868564987	NA	P-0048144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	51	317	0	ENST00000353224.5:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000353224	NM_177990.2	542	Gaa/Aaa	7/10	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.863977524829792	2		317	117	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0048145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	661	383	0				ENST00000310581	NM_198253.2	-/1132			0.436527035009338	6	FACETS	0.991	0.97	1	1	0.997	1	CLONAL	7	TRUE	0	0.436527035009338	6		383	818	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41209088	41209088	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs397509246	NA	P-0048145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	98	546	0	ENST00000357654.3:c.5258G>C	p.Arg1753Thr	p.R1753T	ENST00000357654	NM_007294.3	1753	aGa/aCa	19/23	1	2	FACETS	0.839	0.751	0.932	0.839	0.751	0.932	CLONAL	1	TRUE	1	0.436527035009338	2		546	535	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736544	85736544	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	111	296	0	ENST00000370580.1:c.103G>C	p.Glu35Gln	p.E35Q	ENST00000370580	NM_003921.4	35	Gag/Cag	2/3	0.21139228254109	2	FACETS	0.871	0.795	0.949	0.871	0.795	0.949	INDETERMINATE	2	TRUE	0	0.436527035009338	2		296	292	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40678683	40678683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	72	392	0	ENST00000249776.8:c.425G>A	p.Arg142Lys	p.R142K	ENST00000249776	NM_033286.3	142	aGa/aAa	3/9	1	2	FACETS	0.809	0.71	0.914	0.809	0.71	0.914	CLONAL	1	TRUE	1	0.436527035009338	2		392	408	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550365	39550365	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	47	257	0	ENST00000262039.4:c.476C>G	p.Thr159Ser	p.T159S	ENST00000262039	NM_002647.2	159	aCt/aGt	4/25	1	2	FACETS	0.758	0.644	0.883	0.758	0.644	0.883	SUBCLONAL	1	TRUE	1	0.436527035009338	2		257	284	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478794	57478794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	73	419	0	ENST00000371085.3:c.380G>A	p.Arg127Lys	p.R127K	ENST00000371085	NM_000516.4	127	aGa/aAa	5/13	1	2	FACETS	0.909	0.8	1	0.909	0.8	1	CLONAL	1	TRUE	1	0.436527035009338	2		419	368	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042503	37042503	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	37	451	0	ENST00000231790.2:c.265G>A	p.Glu89Lys	p.E89K	ENST00000231790	NM_000249.3	89	Gag/Aag	3/19	1	2	FACETS	0.326	0.268	0.391	0.326	0.268	0.391	SUBCLONAL	1	TRUE	1	0.436527035009338	2		451	520	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151833976	151833976	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	81	456	0	ENST00000262189.6:c.14677G>C	p.Asp4893His	p.D4893H	ENST00000262189	NM_170606.2	4893	Gac/Cac	59/59	1	2	FACETS	0.871	0.771	0.977	0.871	0.771	0.977	CLONAL	1	TRUE	1	0.436527035009338	2		456	426	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034476	47034476	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048145-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	128	587	0	ENST00000377604.3:c.561G>C	p.Trp187Cys	p.W187C	ENST00000377604	NM_001204468.1	187	tgG/tgC	6/24	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.436527035009338	2		587	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0048151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	238	610	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.503653781198206	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.503653781198206	1		610	657	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0048151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	100	282	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.503653781198206	2		282	355	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197257	26197257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	57	596	0	ENST00000356476.2:c.222G>C	p.Glu74Asp	p.E74D	ENST00000356476		74	gaG/gaC	1/1	1	2	FACETS	0.331	0.284	0.384	0.331	0.284	0.384	SUBCLONAL	1	TRUE	1	0.503653781198206	2		596	683	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591238	67591265	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTTTTTCAGGTGGTTGACTCAAAAAGG	TGTTTTTCAGGTGGTTGACTCAAAAAGG	-	novel	NA	P-0048151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	56	325	0	ENST00000274335.5:c.1746-6_1767del		p.X582_splice	ENST00000274335		582		13/15	1	2	FACETS	0.72	0.621	0.826	0.72	0.621	0.826	SUBCLONAL	1	TRUE	1	0.503653781198206	2		325	309	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241956	72241956	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0048151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	47	239	0	ENST00000357731.5:c.434C>G	p.Ser145Ter	p.S145*	ENST00000357731	NM_173808.2	145	tCa/tGa	3/7	1	2	FACETS	0.598	0.507	0.697	0.598	0.507	0.697	SUBCLONAL	1	TRUE	1	0.503653781198206	2		239	312	SUCCESS
CBL	867	MSKCC	GRCh37	11	119145610	119145610	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	138	357	0	ENST00000264033.4:c.816G>T	p.Leu272Phe	p.L272F	ENST00000264033	NM_005188.3	272	ttG/ttT	5/16	0.503653781198206	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.503653781198206	1		357	400	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105238746	105238746	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	181	736	0	ENST00000349310.3:c.1216C>G	p.Arg406Gly	p.R406G	ENST00000349310	NM_001014432.1	406	Cgc/Ggc	13/15	0.190863418533302	0	FACETS	0.496	0.459	0.535			1	INDETERMINATE	1	TRUE	0	0.503653781198206	0		736	719	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244232	41244232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45599040	NA	P-0048151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	47	458	0	ENST00000357654.3:c.3316C>T	p.Pro1106Ser	p.P1106S	ENST00000357654	NM_007294.3	1106	Cct/Tct	10/23	0.419030193194135	3	FACETS	0.381	0.321	0.448	0.191	0.16	0.224	SUBCLONAL	1	TRUE	1	0.503653781198206	3		458	613	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116227	209116227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	45	252	0	ENST00000345146.2:c.49G>A	p.Glu17Lys	p.E17K	ENST00000345146	NM_005896.2	17	Gaa/Aaa	3/10	0.242027294981781	1	FACETS	0.393	0.331	0.461	0.393	0.331	0.461	INDETERMINATE	1	TRUE	0	0.503653781198206	1		252	340	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155227	106155227	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	97	356	0	ENST00000380013.4:c.128G>C	p.Arg43Thr	p.R43T	ENST00000380013	NM_001127208.2	43	aGa/aCa	3/11	0.242027294981781	1	FACETS	0.801	0.72	0.885	0.801	0.72	0.885	INDETERMINATE	1	TRUE	0	0.503653781198206	1		356	360	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155238	106155238	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	92	351	0	ENST00000380013.4:c.139G>C	p.Glu47Gln	p.E47Q	ENST00000380013	NM_001127208.2	47	Gaa/Caa	3/11	0.242027294981781	1	FACETS	0.806	0.723	0.893	0.806	0.723	0.893	INDETERMINATE	1	TRUE	0	0.503653781198206	1		351	339	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155631	106155631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1278235324	NA	P-0048151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	109	319	0	ENST00000380013.4:c.532G>A	p.Glu178Lys	p.E178K	ENST00000380013	NM_001127208.2	178	Gag/Aag	3/11	0.242027294981781	1	FACETS	0.85	0.77	0.933	0.85	0.77	0.933	INDETERMINATE	1	TRUE	0	0.503653781198206	1		319	381	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592168	67592169	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	60	193	0	ENST00000274335.5:c.1985dup	p.Val663GlyfsTer24	p.V663Gfs*24	ENST00000274335		662	gtg/gTtg	14/15	1	2	FACETS	0.913	0.795	1	0.913	0.795	1	CLONAL	1	TRUE	1	0.503653781198206	2		193	261	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6038818	6038818	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	206	563	0	ENST00000265849.7:c.626del	p.Gly209GlufsTer15	p.G209Efs*15	ENST00000265849	NM_000535.5	209	gGa/ga	6/15	0.265885504483021	4	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.503653781198206	4		563	866	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99203949	99203949	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1370549873	NA	P-0048152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	123	267	0	ENST00000074304.5:c.2812C>T	p.Arg938Ter	p.R938*	ENST00000074304	NM_001134224.1	938	Cga/Tga	26/26	0.606609939551705	1	FACETS	0.981	0.902	1	0.981	0.902	1	CLONAL	1	TRUE	0	0.606609939551705	1		267	288	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0048152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	34	461	5	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	0.573023206997019	1	FACETS	0.12	0.097	0.145	0.12	0.097	0.145	SUBCLONAL	1	TRUE	0	0.606609939551705	1		466	653	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577086	7577087	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0048152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	356	594	0	ENST00000269305.4:c.851_852del	p.Thr284ArgfsTer21	p.T284Rfs*21	ENST00000269305	NM_001126112.2	284	aCA/a	8/11	0.606609939551705	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.606609939551705	1		594	719	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211782	2211782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868591504	NA	P-0048152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	348	632	0	ENST00000398665.3:c.1498G>A	p.Ala500Thr	p.A500T	ENST00000398665	NM_032482.2	500	Gca/Aca	16/28	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.606609939551705	2		632	954	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723034	49723034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771296103	NA	P-0048152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	148	377	0	ENST00000449682.2:c.1382G>A	p.Arg461His	p.R461H	ENST00000449682	NM_020998.3	461	cGc/cAc	11/18	0.606609939551705	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.606609939551705	1		377	293	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335064	65335064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	290	452	2	ENST00000342505.4:c.577G>A	p.Ala193Thr	p.A193T	ENST00000342505	NM_002227.2	193	Gct/Act	6/25	0.606609939551705	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.606609939551705	1		454	599	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577206	64577207	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0048152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	364	602	1	ENST00000312049.6:c.375_376del	p.Ile125MetfsTer54	p.I125Mfs*54	ENST00000312049	NM_130799.2	125	atATgg/atgg	2/10	0.606609939551705	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.606609939551705	1		603	734	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289253	33289253	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	249	393	3	ENST00000374542.5:c.299del	p.Leu100TrpfsTer44	p.L100Wfs*44	ENST00000374542	NM_001141970.1	100	tTg/tg	3/8	0.606609939551705	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.606609939551705	1		396	571	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807167	1807167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751635116	NA	P-0048153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	46	916	0	ENST00000260795.2:c.1498G>A	p.Ala500Thr	p.A500T	ENST00000260795		500	Gcc/Acc	10/17	1	2	FACETS	0.417	0.353	0.486	0.417	0.353	0.486	SUBCLONAL	1	TRUE	1	0.771588228583726	2		916	286	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089719	27089722	+	frameshift_variant	Frame_Shift_Del	DEL	GGAA	GGAA	TTC	novel	NA	P-0048153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	95	733	2	ENST00000324856.7:c.2675_2678delinsTTC	p.Arg892LeufsTer27	p.R892Lfs*27	ENST00000324856	NM_006015.4	892	cGGAAa/cTTCa	8/20	1	2	FACETS	0.77	0.693	0.849	0.77	0.693	0.849	SUBCLONAL	1	TRUE	1	0.771588228583726	2		735	320	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0048154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	72	436	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.979	0.853	1	0.979	0.853	1	CLONAL	1	TRUE	1	0.14	2		439	1051	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720808	89720811	+	frameshift_variant	Frame_Shift_Del	DEL	TAAC	TAAC	-	novel	NA	P-0048154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	22	267	0	ENST00000371953.3:c.959_962del	p.Leu320Ter	p.L320*	ENST00000371953	NM_000314.4	320	tTAACa/ta	8/9	1	2	FACETS	0.78	0.603	0.985	0.78	0.603	0.985	CLONAL	1	TRUE	1	0.14	2		267	403	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853181	68853181	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0048154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	47	479	0	ENST00000261769.5:c.1566-2A>T		p.X522_splice	ENST00000261769	NM_004360.3	522			1	2	FACETS	0.986	0.83	1	0.986	0.83	1	CLONAL	1	TRUE	1	0.14	2		479	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1441	48	830	0	ENST00000269305.4:c.470T>G	p.Val157Gly	p.V157G	ENST00000269305	NM_001126112.2	157	gTc/gGc	5/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		830	1489	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631839	90631839	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519906	NA	P-0048156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	41	658	0	ENST00000330062.3:c.514A>G	p.Arg172Gly	p.R172G	ENST00000330062	NM_002168.2	172	Agg/Ggg	4/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		658	1128	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843499	156843499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	49	659	0	ENST00000524377.1:c.925C>T	p.Pro309Ser	p.P309S	ENST00000524377	NM_002529.3	309	Ccg/Tcg	8/17	1	2	FACETS	0.6	0.507	0.702	0.6	0.507	0.702	SUBCLONAL	1	TRUE	1	0.24	2		659	681	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272081	38272081	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	33	595	0	ENST00000425967.3:c.2137G>A	p.Asp713Asn	p.D713N	ENST00000425967	NM_001174067.1	713	Gat/Aat	16/19	1	2	FACETS	0.466	0.379	0.565	0.466	0.379	0.565	SUBCLONAL	1	TRUE	1	0.24	2		595	590	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449845	149449845	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	45	728	0	ENST00000286301.3:c.1219A>T	p.Ile407Leu	p.I407L	ENST00000286301	NM_005211.3	407	Ata/Tta	9/22	1	2	FACETS	0.459	0.384	0.542	0.459	0.384	0.542	SUBCLONAL	1	TRUE	1	0.24	2		728	817	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045742	26045742	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	33	458	0	ENST00000540144.1:c.104G>C	p.Gly35Ala	p.G35A	ENST00000540144	NM_003531.2	35	gGc/gCc	1/1	1	2	FACETS	0.638	0.519	0.772	0.638	0.519	0.772	SUBCLONAL	1	TRUE	1	0.24	2		458	431	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911276	29911276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs45572432	NA	P-0048159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	32	404	1	ENST00000376809.5:c.575T>A	p.Leu192His	p.L192H	ENST00000376809	NM_002116.7	192	cTc/cAc	3/8	1	2	FACETS	0.719	0.584	0.871	0.719	0.584	0.871	SUBCLONAL	1	TRUE	1	0.24	2		405	371	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141549544	141549544	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	31	420	0	ENST00000220592.5:c.2044C>A	p.His682Asn	p.H682N	ENST00000220592	NM_012154.3	682	Cac/Aac	16/19	0.3	3	FACETS	0.573	0.463	0.698	0.286	0.231	0.349	SUBCLONAL	1	TRUE	1	0.24	3		420	505	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412044	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	104	583	0	ENST00000397752.3:c.3028_3028+1insT	p.Asp1010ValfsTer5	p.D1010Vfs*5	ENST00000397752	NM_000245.2	1010	gat/gTat		0.157649727141157	3	FACETS	0.892	0.802	0.988	0.595	0.534	0.659	CLONAL	2	TRUE	0	0.24	3		583	544	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259667	16259667	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0048160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	35	394	0	ENST00000375759.3:c.6932C>G	p.Ser2311Ter	p.S2311*	ENST00000375759	NM_015001.2	2311	tCa/tGa	11/15	0.300515339737132	4	FACETS	0.362	0.296	0.437	0.181	0.148	0.219	SUBCLONAL	1	FALSE	2	0.407994603573296	4		394	667	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242478	+	protein_altering_variant	In_Frame_Del	DEL	GAATTAAGAGAAG	GAATTAAGAGAAG	C	novel	NA	P-0048160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	61	344	0	ENST00000275493.2:c.2236_2248delinsC	p.Glu746_Ala750delinsPro	p.E746_A750delinsP	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGca/Cca	19/28	1	2	FACETS	0.672	0.581	0.77	0.672	0.581	0.77	SUBCLONAL	1	FALSE	1	0.407994603573296	2		344	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0048161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	432	436	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.51964591319333	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.527619227337882	2		439	812	SUCCESS
APC	324	MSKCC	GRCh37	5	112175136	112175136	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0048161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	78	183	0	ENST00000257430.4:c.3845C>G	p.Ser1282Ter	p.S1282*	ENST00000257430	NM_000038.5	1282	tCa/tGa	16/16	NA	2	FACETS	0.758	0.68	0.838			1	INDETERMINATE	2	TRUE	NA	0.527619227337882	2		183	195	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672341	86672342	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1561322357	NA	P-0048161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	66	253	0	ENST00000274376.6:c.2149dup	p.Ile717AsnfsTer9	p.I717Nfs*9	ENST00000274376	NM_002890.2	715	gaa/gAaa	16/25	0.510836960918707	3	FACETS	0.817	0.712	0.929	0.409	0.356	0.465	CLONAL	1	TRUE	1	0.527619227337882	3		253	387	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0048162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	95	418	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	0.793	0.707	0.885	1	0.982	1	SUBCLONAL	2	FALSE	1	0.178508959443607	2		418	671	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519996	NA	P-0048162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	142	886	0	ENST00000269305.4:c.395A>T	p.Lys132Met	p.K132M	ENST00000269305	NM_001126112.2	132	aAg/aTg	5/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.178508959443607	2		886	1242	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256177	133256177	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	65	599	1	ENST00000320574.5:c.484G>T	p.Asp162Tyr	p.D162Y	ENST00000320574	NM_006231.2	162	Gat/Tat	6/49	1	2	FACETS	0.862	0.746	0.988	0.862	0.746	0.988	CLONAL	1	FALSE	1	0.178508959443607	2		600	845	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288925	11288925	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	56	576	1	ENST00000361445.4:c.2830G>T	p.Asp944Tyr	p.D944Y	ENST00000361445	NM_004958.3	944	Gat/Tat	19/58	1	2	FACETS	0.795	0.68	0.922	0.795	0.68	0.922	CLONAL	1	FALSE	1	0.178508959443607	2		577	789	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226568795	226568795	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	59	654	0	ENST00000366794.5:c.1274A>T	p.Lys425Met	p.K425M	ENST00000366794	NM_001618.3	425	aAg/aTg	9/23	1	2	FACETS	0.811	0.696	0.937	0.811	0.696	0.937	CLONAL	1	FALSE	1	0.178508959443607	2		654	815	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742927	17742927	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	71	920	1	ENST00000250003.3:c.835C>A	p.Pro279Thr	p.P279T	ENST00000250003	NM_002478.4	279	Cct/Act	3/3	1	2	FACETS	0.692	0.602	0.79	0.692	0.602	0.79	SUBCLONAL	1	FALSE	1	0.178508959443607	2		921	1150	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625208	69625208	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1152	68	1002	0	ENST00000334134.2:c.585G>C	p.Gln195His	p.Q195H	ENST00000334134	NM_005247.2	195	caG/caC	3/3	1	2	FACETS	0.624	0.541	0.715	0.624	0.541	0.715	SUBCLONAL	1	FALSE	1	0.178508959443607	2		1002	1220	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941471	71941471	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	67	934	0	ENST00000298229.2:c.1156G>T	p.Asp386Tyr	p.D386Y	ENST00000298229	NM_001567.3	386	Gac/Tac	10/28	1	2	FACETS	0.621	0.538	0.713	0.621	0.538	0.713	SUBCLONAL	1	FALSE	1	0.178508959443607	2		934	1208	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21636327	21636327	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	45	328	0	ENST00000421138.2:c.683del	p.Gly228AspfsTer14	p.G228Dfs*14	ENST00000421138		228	gGa/ga	7/16	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	FALSE	1	0.178508959443607	2		328	474	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945046	31945046	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	191	836	0	ENST00000340398.3:c.55A>C	p.Lys19Gln	p.K19Q	ENST00000340398	NM_001013699.2	19	Aaa/Caa	1/1	1	2	FACETS	0.892	0.823	0.963	1	0.992	1	CLONAL	2	FALSE	1	0.178508959443607	2		836	1200	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120921	115120921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	65	739	1	ENST00000257566.3:c.85G>A	p.Ala29Thr	p.A29T	ENST00000257566	NM_016569.3	29	Gcc/Acc	1/8	1	2	FACETS	0.715	0.618	0.821	0.715	0.618	0.821	SUBCLONAL	1	FALSE	1	0.178508959443607	2		740	1019	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826571	50826571	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	42	124	0	ENST00000398568.2:c.2296A>G	p.Ile766Val	p.I766V	ENST00000398568	NM_001042412.1	766	Att/Gtt	15/18	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.178508959443607	2		124	325	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561440	9561442	+	missense_variant	Missense_Mutation	TNP	GCT	GCT	AAG	novel	NA	P-0048162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	59	577	1	ENST00000353224.5:c.340_342delinsCTT	p.Ser114Leu	p.S114L	ENST00000353224	NM_177990.2	114	AGC/CTT	4/10	1	2	FACETS	0.843	0.724	0.974	0.843	0.724	0.974	CLONAL	1	FALSE	1	0.178508959443607	2		578	784	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163062	47163063	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CA	CA	-	novel	NA	P-0048162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	57	307	0	ENST00000409792.3:c.3063_3064del	p.Cys1021Ter	p.C1021*	ENST00000409792	NM_014159.6	1021	tgTGac/tgac	3/21	0.178508959443607	3	FACETS	1	0.96	1	0.675	0.58	0.779	CLONAL	1	FALSE	1	0.178508959443607	3		307	515	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259376	89259376	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	36	387	0	ENST00000336596.2:c.520G>T	p.Val174Phe	p.V174F	ENST00000336596	NM_005233.5	174	Gtc/Ttc	3/17	1	2	FACETS	0.652	0.534	0.784	0.652	0.534	0.784	SUBCLONAL	1	FALSE	1	0.178508959443607	2		387	619	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879672	151879672	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	23	216	0	ENST00000262189.6:c.5273G>T	p.Arg1758Leu	p.R1758L	ENST00000262189	NM_170606.2	1758	cGt/cTt	36/59	1	2	FACETS	0.76	0.593	0.954	0.76	0.593	0.954	CLONAL	1	FALSE	1	0.178508959443607	2		216	339	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220294	98220294	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0048162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	91	341	0	ENST00000331920.6:c.3168+1G>T		p.X1056_splice	ENST00000331920	NM_000264.3	1056			0.178508959443607	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	FALSE	0	0.178508959443607	2		341	449	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039665	47039665	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	88	857	1	ENST00000377604.3:c.1117G>T	p.Asp373Tyr	p.D373Y	ENST00000377604	NM_001204468.1	373	Gac/Tac	11/24	1	2	FACETS	0.912	0.806	1	0.912	0.806	1	CLONAL	1	FALSE	1	0.178508959443607	2		858	1081	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188297	10188297	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs869025653	NA	P-0048163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	150	490	0	ENST00000256474.2:c.444del	p.Phe148LeufsTer11	p.F148Lfs*11	ENST00000256474	NM_000551.3	147	aTt/at	2/3	0.699282744085618	1	FACETS	0.869	0.808	0.931	0.869	0.808	0.931	CLONAL	1	TRUE	0	0.699282744085618	1		490	321	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714436	40714436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1228688924	NA	P-0048163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	29	430	0	ENST00000373198.4:c.3961G>A	p.Glu1321Lys	p.E1321K	ENST00000373198	NM_133170.3	1321	Gag/Aag	29/32	1	2	FACETS	0.147	0.117	0.181	0.147	0.117	0.181	SUBCLONAL	1	TRUE	1	0.699282744085618	2		430	565	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197296	106197296	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1424213081	NA	P-0048163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	112	300	0	ENST00000380013.4:c.5629A>G	p.Lys1877Glu	p.K1877E	ENST00000380013	NM_001127208.2	1877	Aag/Gag	11/11	1	2	FACETS	0.89	0.809	0.974	0.89	0.809	0.974	CLONAL	1	TRUE	1	0.699282744085618	2		300	360	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17940937	17940938	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0048163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	238	837	0	ENST00000458235.1:c.3186_3187delinsAT	p.Pro1063Ser	p.P1063S	ENST00000458235	NM_000215.3	1062	gcGCct/gcATct	23/24	1	2	FACETS	0.941	0.883	1	0.941	0.883	1	CLONAL	1	TRUE	1	0.699282744085618	2		837	723	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584504	52584504	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	192	484	0	ENST00000394830.3:c.4509C>A	p.Tyr1503Ter	p.Y1503*	ENST00000394830	NM_018313.4	1503	taC/taA	29/30	0.699282744085618	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.699282744085618	1		484	347	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	144	349	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.953	0.878	1	0.953	0.878	1	CLONAL	1	TRUE	1	0.71072939202131	2		350	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0048165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	334	643	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.71072939202131	2		643	899	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876449	35876449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2229232	NA	P-0048165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	233	558	0	ENST00000303115.3:c.1241C>T	p.Thr414Met	p.T414M	ENST00000303115	NM_002185.3	414	aCg/aTg	8/8	1	2	FACETS	0.885	0.829	0.942	0.885	0.829	0.942	CLONAL	1	TRUE	1	0.71072939202131	2		558	741	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74000724	74000724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	329	664	0	ENST00000318443.5:c.1414G>A	p.Gly472Arg	p.G472R	ENST00000318443	NM_001024736.1	472	Ggg/Agg	7/10	1	2	FACETS	0.952	0.901	1	0.952	0.901	1	CLONAL	1	TRUE	1	0.71072939202131	2		664	973	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268948	55269237	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGACATGGACGACGTGGTGGATGCCGACGAGTACCTCATCCCACAGCAGGGCTTCTTCAGCAGCCCCTCCACGTCACGGACTCCCCTCCTGAGCTCTCTGGTATGAAATCTCTGTCTCTCTCTCTCTCTCAAGCTGTGTCTACTCATTTGAACAAATTGAATTTTAGGGAAAATAACCATCTAGTGAAACTCACATGGATATGAAGTCAATTTTAACCAAATGGTAAAATCAAAATCAAAATAAATTAAGTGTATTAATTATTTTGTTGCATTGCAACAACTTGATTGT	AAGACATGGACGACGTGGTGGATGCCGACGAGTACCTCATCCCACAGCAGGGCTTCTTCAGCAGCCCCTCCACGTCACGGACTCCCCTCCTGAGCTCTCTGGTATGAAATCTCTGTCTCTCTCTCTCTCTCAAGCTGTGTCTACTCATTTGAACAAATTGAATTTTAGGGAAAATAACCATCTAGTGAAACTCACATGGATATGAAGTCAATTTTAACCAAATGGTAAAATCAAAATCAAAATAAATTAAGTGTATTAATTATTTTGTTGCATTGCAACAACTTGATTGT	-	novel	NA	P-0048165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14355	758	617	0	ENST00000275493.2:c.3017_3115-188del		p.X1006_splice	ENST00000275493	NM_005228.3	1006		25/28	0.71072939202131	22	FACETS	1	0.993	1	0.052	0.049	0.055	CLONAL	1	TRUE	0	0.71072939202131	22		617	15113	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55269468	55269473	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GAAATG	GAAATG	AAATT	novel	NA	P-0048165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14815	1024	642	1	ENST00000275493.2:c.3155_3160delinsAAATT	p.Arg1052LysfsTer26	p.R1052Kfs*26	ENST00000275493	NM_005228.3	1052	aGAAATGgg/aAAATTgg	26/28	0.71072939202131	22	FACETS	1	0.997	1	0.067	0.064	0.07	CLONAL	1	TRUE	0	0.71072939202131	22		643	15839	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	173	376	1	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.696219135280845	2		377	444	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856520	45856520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751318902	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	316	670	0	ENST00000391945.4:c.1738G>A	p.Ala580Thr	p.A580T	ENST00000391945	NM_000400.3	580	Gcc/Acc	18/23	1	2	FACETS	0.946	0.894	0.998	0.946	0.894	0.998	CLONAL	1	TRUE	1	0.696219135280845	2		670	960	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	39	499	3	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.148	0.122	0.178	0.148	0.122	0.178	SUBCLONAL	1	TRUE	1	0.696219135280845	2		502	755	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	425	848	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.998	0.952	1	0.998	0.952	1	CLONAL	1	TRUE	1	0.696219135280845	2		848	1223	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	138	430	3	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.64	0.585	0.699	0.64	0.585	0.699	SUBCLONAL	1	TRUE	1	0.696219135280845	2		433	619	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445149	49445149	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	363	783	1	ENST00000301067.7:c.2317del	p.Gln773SerfsTer157	p.Q773Sfs*157	ENST00000301067	NM_003482.3	773	Cag/ag	10/54	1	2	FACETS	0.999	0.949	1	0.999	0.949	1	CLONAL	1	TRUE	1	0.696219135280845	2		784	1044	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	469	350	10	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	0.689669361510085	4	FACETS	0.968	0.934	1	0.968	0.934	1	CLONAL	3	TRUE	1	0.696219135280845	4		360	787	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	106	318	3	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.795	0.719	0.874	0.795	0.719	0.874	SUBCLONAL	1	TRUE	1	0.696219135280845	2		321	383	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	375	756	0	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.696219135280845	2		756	992	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438316	110438317	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	rs532810290	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	74	161	2	ENST00000375856.3:c.82_84dup	p.Asn28dup	p.N28dup	ENST00000375856	NM_003749.2	28	-/AAC	1/2	1	2	FACETS	0.618	0.545	0.696	0.618	0.545	0.696	SUBCLONAL	1	TRUE	1	0.696219135280845	2		163	344	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169085	119169085	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146517083	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	120	384	0	ENST00000264033.4:c.2269G>A	p.Ala757Thr	p.A757T	ENST00000264033	NM_005188.3	757	Gca/Aca	15/16	1	2	FACETS	0.654	0.593	0.718	0.654	0.593	0.718	SUBCLONAL	1	TRUE	1	0.696219135280845	2		384	527	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	293	608	0	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.696219135280845	2		608	761	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	339	806	2	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	1	2	FACETS	0.976	0.925	1	0.976	0.925	1	CLONAL	1	TRUE	1	0.696219135280845	2		808	998	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55569954	55569954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138585275	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	58	276	0	ENST00000288135.5:c.821C>T	p.Thr274Met	p.T274M	ENST00000288135	NM_000222.2	274	aCg/aTg	5/21	1	2	FACETS	0.761	0.662	0.865	0.761	0.662	0.865	SUBCLONAL	1	TRUE	1	0.696219135280845	2		276	219	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	313	779	11	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	0.796	0.751	0.842	0.796	0.751	0.842	SUBCLONAL	1	TRUE	1	0.696219135280845	2		790	1130	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790455	3790455	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783490	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	232	571	2	ENST00000262367.5:c.4078C>T	p.Arg1360Ter	p.R1360*	ENST00000262367	NM_004380.2	1360	Cga/Tga	24/31	1	2	FACETS	0.876	0.82	0.933	0.876	0.82	0.933	CLONAL	1	TRUE	1	0.696219135280845	2		573	761	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990481	69990481	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs201247895	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	61	203	0	ENST00000394351.3:c.440C>T	p.Thr147Met	p.T147M	ENST00000394351	NM_000248.3	147	aCg/aTg	4/9	1	2	FACETS	0.894	0.784	1	0.894	0.784	1	CLONAL	1	TRUE	1	0.696219135280845	2		203	196	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748480	43748480	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395807781	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	170	254	0	ENST00000523873.1:c.434G>A	p.Arg145Gln	p.R145Q	ENST00000523873		145	cGa/cAa	6/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.696219135280845	2		254	446	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164563	36164563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1340631548	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	169	648	0	ENST00000300305.3:c.1312G>A	p.Gly438Ser	p.G438S	ENST00000300305		438	Ggc/Agc	8/8	0.596696801110749	3	FACETS	0.608	0.558	0.66	0.304	0.279	0.33	SUBCLONAL	1	TRUE	1	0.696219135280845	3		648	1077	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041375	42041375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764277967	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	204	545	0	ENST00000219905.7:c.5570C>T	p.Ser1857Leu	p.S1857L	ENST00000219905	NM_001164273.1	1857	tCg/tTg	17/24	1	2	FACETS	0.913	0.851	0.976	0.913	0.851	0.976	CLONAL	1	TRUE	1	0.696219135280845	2		545	642	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181311	123181311	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs774761933	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	42	105	0	ENST00000218089.9:c.775C>T	p.Arg259Ter	p.R259*	ENST00000218089	NM_001042749.1	259	Cga/Tga	9/35	1	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.696219135280845	1		105	63	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217623	7217623	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	197	418	0	ENST00000380728.2:c.304C>T	p.Arg102Ter	p.R102*	ENST00000380728		102	Cga/Tga	4/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.696219135280845	2		418	536	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128848687	128848687	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1204546630	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	303	610	0	ENST00000249373.3:c.1352G>A	p.Arg451His	p.R451H	ENST00000249373	NM_005631.4	451	cGc/cAc	7/12	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.696219135280845	2		610	866	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957495	175957495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750125741	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	100	434	0	ENST00000367669.3:c.1901G>A	p.Arg634His	p.R634H	ENST00000367669	NM_022457.5	634	cGt/cAt	17/20	1	2	FACETS	0.823	0.742	0.907	0.823	0.742	0.907	CLONAL	1	TRUE	1	0.696219135280845	2		434	349	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609084	43609086	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs377767399	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	383	803	0	ENST00000355710.3:c.1846_1848del	p.Glu616del	p.E616del	ENST00000355710	NM_020975.4	614	GAG/-	10/20	0.696219135280845	3	FACETS	1	0.957	1	0.505	0.479	0.532	CLONAL	1	TRUE	1	0.696219135280845	3		803	1468	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526531	31526531	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs77034974	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	260	559	0	ENST00000344624.3:c.509C>T	p.Pro170Leu	p.P170L	ENST00000344624		170	cCg/cTg	2/33	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.696219135280845	2		559	692	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048667	180048667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749960761	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	442	843	0	ENST00000261937.6:c.1895G>A	p.Arg632His	p.R632H	ENST00000261937	NM_182925.4	632	cGc/cAc	13/30	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.696219135280845	2		843	1187	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942852	68942852	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	123	531	1	ENST00000288368.4:c.664G>A	p.Glu222Lys	p.E222K	ENST00000288368	NM_024870.2	222	Gaa/Aaa	6/40	0.696219135280845	3	FACETS	0.589	0.532	0.648	0.294	0.266	0.324	SUBCLONAL	1	TRUE	1	0.696219135280845	3		532	809	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099262	4099262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730880523	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	304	813	3	ENST00000262948.5:c.856G>A	p.Gly286Arg	p.G286R	ENST00000262948	NM_030662.3	286	Ggg/Agg	7/11	1	2	FACETS	0.824	0.777	0.872	0.824	0.777	0.872	CLONAL	1	TRUE	1	0.696219135280845	2		816	1060	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245026	41245026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80357337	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	179	584	0	ENST00000357654.3:c.2522G>A	p.Arg841Gln	p.R841Q	ENST00000357654	NM_007294.3	841	cGg/cAg	10/23	1	2	FACETS	0.849	0.786	0.913	0.849	0.786	0.913	CLONAL	1	TRUE	1	0.696219135280845	2		584	606	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145672	11145672	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746533073	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	385	764	1	ENST00000358026.2:c.4034C>T	p.Ser1345Leu	p.S1345L	ENST00000358026	NM_001128849.1	1345	tCg/tTg	29/36	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.696219135280845	2		765	1070	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026780	6026780	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138222146	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	28	57	0	ENST00000265849.7:c.1616C>T	p.Ala539Val	p.A539V	ENST00000265849	NM_000535.5	539	gCg/gTg	11/15	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.696219135280845	2		57	68	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101923	11101923	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502063	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	273	821	0	ENST00000358026.2:c.1343G>A	p.Arg448His	p.R448H	ENST00000358026	NM_001128849.1	448	cGc/cAc	8/36	1	2	FACETS	0.703	0.659	0.747	0.703	0.659	0.747	SUBCLONAL	1	TRUE	1	0.696219135280845	2		821	1116	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106558	27106558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	344	747	1	ENST00000324856.7:c.6169C>T	p.Arg2057Trp	p.R2057W	ENST00000324856	NM_006015.4	2057	Cgg/Tgg	20/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.696219135280845	2		748	971	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155386	106155386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1238868376	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	142	385	0	ENST00000380013.4:c.287G>A	p.Arg96His	p.R96H	ENST00000380013	NM_001127208.2	96	cGc/cAc	3/11	1	2	FACETS	0.949	0.873	1	0.949	0.873	1	CLONAL	1	TRUE	1	0.696219135280845	2		385	430	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508786	31508786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	238	550	0	ENST00000344624.3:c.1529G>A	p.Arg510His	p.R510H	ENST00000344624		510	cGc/cAc	7/33	1	2	FACETS	0.938	0.879	0.998	0.938	0.879	0.998	CLONAL	1	TRUE	1	0.696219135280845	2		550	729	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996257	73996257	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775475628	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	47	118	0	ENST00000318443.5:c.991C>T	p.Arg331Cys	p.R331C	ENST00000318443	NM_001024736.1	331	Cgt/Tgt	5/10	1	2	FACETS	0.877	0.754	1	0.877	0.754	1	CLONAL	1	TRUE	1	0.696219135280845	2		118	154	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106592	27106592	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	346	703	1	ENST00000324856.7:c.6203C>T	p.Ser2068Leu	p.S2068L	ENST00000324856	NM_006015.4	2068	tCg/tTg	20/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.696219135280845	2		704	916	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958480	90958480	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	46	132	1	ENST00000265433.3:c.1958del	p.Lys653SerfsTer4	p.K653Sfs*4	ENST00000265433	NM_002485.4	653	aAg/ag	13/16	0.696219135280845	3	FACETS	0.799	0.68	0.927	0.399	0.34	0.464	CLONAL	1	TRUE	1	0.696219135280845	3		133	223	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491375	2491375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760189429	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	477	969	1	ENST00000355716.4:c.418G>A	p.Ala140Thr	p.A140T	ENST00000355716	NM_003820.2	140	Gct/Act	4/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.696219135280845	2		970	1305	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748014	72748014	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1364690756	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	287	659	0	ENST00000357731.5:c.164C>T	p.Thr55Met	p.T55M	ENST00000357731	NM_173808.2	55	aCg/aTg	1/7	1	2	FACETS	0.996	0.94	1	0.996	0.94	1	CLONAL	1	TRUE	1	0.696219135280845	2		659	828	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468261	120468261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587735797	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	341	705	1	ENST00000256646.2:c.4178G>A	p.Arg1393His	p.R1393H	ENST00000256646	NM_024408.3	1393	cGc/cAc	25/34	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.696219135280845	2		706	947	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552736	18552736	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	85	422	0	ENST00000266497.5:c.2147G>T	p.Trp716Leu	p.W716L	ENST00000266497		716	tGg/tTg	14/31	NA	2	FACETS	0.669	0.596	0.746			1	INDETERMINATE	1	TRUE	NA	0.696219135280845	2		422	365	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557604	95557604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	114	383	0	ENST00000393063.1:c.5463G>A	p.Met1821Ile	p.M1821I	ENST00000393063	NM_030621.3	1821	atG/atA	26/28	1	2	FACETS	0.71	0.643	0.78	0.71	0.643	0.78	SUBCLONAL	1	TRUE	1	0.696219135280845	2		383	461	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591612	38591612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057518150	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	72	423	0	ENST00000299084.4:c.71G>A	p.Arg24Gln	p.R24Q	ENST00000299084	NM_152594.2	24	cGa/cAa	2/7	1	2	FACETS	0.433	0.379	0.49	0.433	0.379	0.49	SUBCLONAL	1	TRUE	1	0.696219135280845	2		423	478	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130308	2130308	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1555511520	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	460	832	0	ENST00000219476.3:c.3540G>T	p.Lys1180Asn	p.K1180N	ENST00000219476	NM_000548.3	1180	aaG/aaT	30/42	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.696219135280845	2		832	1269	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81941300	81941300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369542682	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	304	550	0	ENST00000359376.3:c.1478G>A	p.Arg493Gln	p.R493Q	ENST00000359376	NM_002661.3	493	cGg/cAg	16/33	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.696219135280845	2		550	779	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621149	1621149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376498623	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	451	880	1	ENST00000344749.5:c.997G>A	p.Gly333Ser	p.G333S	ENST00000344749	NM_001136139.2	333	Ggc/Agc	12/19	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.696219135280845	2		881	1256	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250476	10250476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	303	635	1	ENST00000340748.4:c.3776G>A	p.Arg1259Gln	p.R1259Q	ENST00000340748		1259	cGg/cAg	33/40	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.696219135280845	2		636	869	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635692	47635692	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	120	167	0	ENST00000233146.2:c.364A>T	p.Lys122Ter	p.K122*	ENST00000233146	NM_000251.2	122	Aag/Tag	2/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.696219135280845	2		167	306	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169361	99169361	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1392799869	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	213	482	1	ENST00000074304.5:c.1291C>T	p.Arg431Trp	p.R431W	ENST00000074304	NM_001134224.1	431	Cgg/Tgg	15/26	1	2	FACETS	0.919	0.858	0.981	0.919	0.858	0.981	CLONAL	1	TRUE	1	0.696219135280845	2		483	666	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713480	40713480	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	216	674	0	ENST00000373198.4:c.4035G>T	p.Gln1345His	p.Q1345H	ENST00000373198	NM_133170.3	1345	caG/caT	30/32	0.279999909910481	5	FACETS	0.95	0.881	1			1	INDETERMINATE	1	TRUE	NA	0.696219135280845	5		674	1335	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566433	41566433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769217956	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	121	292	2	ENST00000263253.7:c.4310C>T	p.Ala1437Val	p.A1437V	ENST00000263253	NM_001429.3	1437	gCa/gTa	27/31	1	2	FACETS	0.903	0.824	0.985	0.903	0.824	0.985	CLONAL	1	TRUE	1	0.696219135280845	2		294	385	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949022	44949022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	80	152	0	ENST00000377967.4:c.3583C>T	p.Pro1195Ser	p.P1195S	ENST00000377967	NM_021140.2	1195	Ccc/Tcc	25/29	1	1	FACETS	0.678	0.607	0.751	0.678	0.607	0.751	SUBCLONAL	1	TRUE	0	0.696219135280845	1		152	221	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0048167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	25	625	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	1	2	FACETS	0.335	0.263	0.418	0.335	0.263	0.418	SUBCLONAL	1	TRUE	1	0.29	2		625	515	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849852	156849852	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	35	600	0	ENST00000524377.1:c.2108A>C	p.Lys703Thr	p.K703T	ENST00000524377	NM_002529.3	703	aAg/aCg	16/17	1	2	FACETS	0.433	0.354	0.522	0.433	0.354	0.522	SUBCLONAL	1	TRUE	1	0.29	2		600	557	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457304	67457304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223765	NA	P-0048167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	33	770	2	ENST00000327367.4:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000327367	NM_005902.3	93	cGa/cAa	2/9	1	2	FACETS	0.348	0.282	0.422	0.348	0.282	0.422	SUBCLONAL	1	TRUE	1	0.29	2		772	654	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001578	150001578	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	17	269	0	ENST00000253339.5:c.2026G>C	p.Asp676His	p.D676H	ENST00000253339		676	Gat/Cat	4/7	1	2	FACETS	0.462	0.345	0.6	0.462	0.345	0.6	SUBCLONAL	1	TRUE	1	0.29	2		269	254	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832810	3832810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	32	517	0	ENST00000262367.5:c.1448G>A	p.Arg483Gln	p.R483Q	ENST00000262367	NM_004380.2	483	cGa/cAa	6/31	1	2	FACETS	0.355	0.287	0.433	0.355	0.287	0.433	SUBCLONAL	1	TRUE	1	0.29	2		517	621	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11297908	11297908	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	25	463	0	ENST00000361445.4:c.2200C>G	p.Leu734Val	p.L734V	ENST00000361445	NM_004958.3	734	Ctc/Gtc	13/58	1	2	FACETS	0.368	0.29	0.459	0.368	0.29	0.459	SUBCLONAL	1	TRUE	1	0.29	2		463	468	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134471	41134471	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0048167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	33	446	0	ENST00000379561.5:c.1157C>G	p.Ser386Ter	p.S386*	ENST00000379561	NM_002015.3	386	tCa/tGa	2/3	1	2	FACETS	0.548	0.447	0.663	0.548	0.447	0.663	SUBCLONAL	1	TRUE	1	0.29	2		446	415	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060869	38060869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	46	749	1	ENST00000250448.2:c.1120C>T	p.His374Tyr	p.H374Y	ENST00000250448	NM_004496.3	374	Cac/Tac	2/2	0.152613026750952	2	FACETS	0.429	0.36	0.506	0.215	0.18	0.253	INDETERMINATE	1	TRUE	0	0.29	2		750	739	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68758609	68758609	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	100	407	0	ENST00000487270.1:c.765G>C	p.Leu255Phe	p.L255F	ENST00000487270	NM_133509.3	255	ttG/ttC	8/11	0.152613026750952	2	FACETS	0.8	0.719	0.885	0.8	0.719	0.885	INDETERMINATE	2	TRUE	0	0.29	2		407	431	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457623	67457623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	39	685	0	ENST00000327367.4:c.433G>A	p.Glu145Lys	p.E145K	ENST00000327367	NM_005902.3	145	Gag/Aag	3/9	1	2	FACETS	0.477	0.394	0.569	0.477	0.394	0.569	SUBCLONAL	1	TRUE	1	0.29	2		685	564	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257883	19257883	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	127	935	0	ENST00000162023.5:c.503C>G	p.Ser168Cys	p.S168C	ENST00000162023		168	tCt/tGt	9/13	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.29	2		935	864	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921500	178921500	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	22	342	0	ENST00000263967.3:c.982T>C	p.Trp328Arg	p.W328R	ENST00000263967	NM_006218.2	328	Tgg/Cgg	5/21	1	2	FACETS	0.446	0.346	0.563	0.446	0.346	0.563	SUBCLONAL	1	TRUE	1	0.29	2		342	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0048168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	56	436	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.131946398096423	2		439	642	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434713	110434713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	147	710	4	ENST00000375856.3:c.3688G>A	p.Gly1230Ser	p.G1230S	ENST00000375856	NM_003749.2	1230	Ggt/Agt	1/2	0.131946398096423	3	FACETS	1	0.916	1	1	0.916	1	CLONAL	3	TRUE	0	0.131946398096423	3		714	790	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916850	48916850	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1131690843	NA	P-0048168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	16	196	0	ENST00000267163.4:c.380G>A	p.Ser127Asn	p.S127N	ENST00000267163	NM_000321.2	127	aGt/aAt	3/27	0.131946398096423	3	FACETS	1	0.867	1	0.435	0.322	0.569	CLONAL	1	TRUE	0	0.131946398096423	3		196	198	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11554273	NA	P-0048168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	31	374	0	ENST00000371085.3:c.601C>A	p.Arg201Ser	p.R201S	ENST00000371085	NM_000516.4	201	Cgt/Agt	8/13	0.131946398096423	3	FACETS	0.982	0.793	1	0.491	0.396	0.599	CLONAL	1	TRUE	1	0.131946398096423	3		374	510	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200690	128200690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	43	663	0	ENST00000341105.2:c.1115C>T	p.Ala372Val	p.A372V	ENST00000341105	NM_032638.4	372	gCc/gTc	5/6	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.131946398096423	2		663	612	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100870	27100870	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	28	442	0	ENST00000324856.7:c.4152C>G	p.His1384Gln	p.H1384Q	ENST00000324856	NM_006015.4	1384	caC/caG	18/20	1	2	FACETS	0.861	0.687	1	0.861	0.687	1	CLONAL	1	TRUE	1	0.131946398096423	2		442	493	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39311689	39311689	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	20	461	0	ENST00000373001.3:c.970A>T	p.Thr324Ser	p.T324S	ENST00000373001	NM_022157.3	324	Act/Tct	6/7	1	2	FACETS	0.835	0.638	1	0.835	0.638	1	CLONAL	1	TRUE	1	0.131946398096423	2		461	363	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276457	115276457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	25	353	0	ENST00000438362.2:c.871G>A	p.Val291Ile	p.V291I	ENST00000438362	NM_001242891.1	291	Gtc/Atc	9/20	1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	1	0.131946398096423	2		353	345	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841454	156841454	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	121	478	0	ENST00000524377.1:c.757A>T	p.Asn253Tyr	p.N253Y	ENST00000524377	NM_002529.3	253	Aat/Tat	7/17	1	2	FACETS	1	0.955	1	1	0.992	1	CLONAL	3	TRUE	1	0.131946398096423	2		478	562	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161293460	161293460	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	35	215	0	ENST00000367975.2:c.77A>T	p.Asn26Ile	p.N26I	ENST00000367975	NM_003001.3	26	aAt/aTt	2/6	1	2	FACETS	0.834	0.686	1	1	0.956	1	CLONAL	2	TRUE	1	0.131946398096423	2		215	318	SUCCESS
RET	5979	MSKCC	GRCh37	10	43613851	43613851	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	64	599	0	ENST00000355710.3:c.2315T>A	p.Leu772Gln	p.L772Q	ENST00000355710	NM_020975.4	772	cTg/cAg	13/20	1	2	FACETS	0.848	0.735	0.971	1	0.976	1	CLONAL	2	TRUE	1	0.131946398096423	2		599	572	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112910808	112910808	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	33	275	0	ENST00000351677.2:c.817A>T	p.Asn273Tyr	p.N273Y	ENST00000351677	NM_002834.3	273	Aac/Tac	7/16	0.131946398096423	1	FACETS	0.831	0.68	1	1	0.953	1	CLONAL	2	TRUE	0	0.131946398096423	1		275	281	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3795278	3795278	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	32	291	0	ENST00000262367.5:c.3914G>T	p.Gly1305Val	p.G1305V	ENST00000262367	NM_004380.2	1305	gGt/gTt	22/31	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.131946398096423	2		291	351	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81916887	81916887	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	43	506	0	ENST00000359376.3:c.707del	p.Pro236ArgfsTer27	p.P236Rfs*27	ENST00000359376	NM_002661.3	236	Ccg/cg	9/33	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.131946398096423	2		506	537	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885935	59885935	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	17	322	0	ENST00000259008.2:c.811G>C	p.Val271Leu	p.V271L	ENST00000259008	NM_032043.2	271	Gtt/Ctt	7/20	1	2	FACETS	0.786	0.586	1	0.786	0.586	1	CLONAL	1	TRUE	1	0.131946398096423	2		322	328	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39573276	39573276	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	20	282	0	ENST00000262039.4:c.757G>A	p.Val253Met	p.V253M	ENST00000262039	NM_002647.2	253	Gtg/Atg	7/25	0.131946398096423	3	FACETS	1	0.799	1	0.525	0.401	0.669	CLONAL	1	TRUE	1	0.131946398096423	3		282	308	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097676	11097676	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	39	643	0	ENST00000358026.2:c.856G>T	p.Glu286Ter	p.E286*	ENST00000358026	NM_001128849.1	286	Gaa/Taa	5/36	0.131946398096423	1	FACETS	0.969	0.802	1	0.969	0.802	1	CLONAL	1	TRUE	0	0.131946398096423	1		643	570	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210812	36210812	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	142	694	0	ENST00000222270.7:c.563G>C	p.Arg188Pro	p.R188P	ENST00000222270	NM_014727.1	188	cGg/cCg	3/37	0.131946398096423	5	FACETS	1	0.953	1	0.641	0.585	0.701	CLONAL	3	TRUE	0	0.131946398096423	5		694	804	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99162431	99162431	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0048168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	34	277	0	ENST00000074304.5:c.950-1G>T		p.X317_splice	ENST00000074304	NM_001134224.1	317			1	2	FACETS	0.876	0.719	1	1	0.957	1	CLONAL	2	TRUE	1	0.131946398096423	2		277	294	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589862	212589862	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	40	341	0	ENST00000342788.4:c.680G>T	p.Ser227Ile	p.S227I	ENST00000342788	NM_005235.2	227	aGt/aTt	6/28	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.131946398096423	2		341	409	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748171	41748171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	24	460	0	ENST00000226382.2:c.598C>T	p.Pro200Ser	p.P200S	ENST00000226382	NM_003924.3	200	Ccc/Tcc	3/3	1	2	FACETS	0.921	0.721	1	0.921	0.721	1	CLONAL	1	TRUE	1	0.131946398096423	2		460	395	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750455	41750455	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	29	469	0	ENST00000226382.2:c.173C>A	p.Pro58His	p.P58H	ENST00000226382	NM_003924.3	58	cCt/cAt	1/3	1	2	FACETS	1	0.834	1	1	0.834	1	CLONAL	1	TRUE	1	0.131946398096423	2		469	421	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535442	66535442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1198132493	NA	P-0048168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	26	544	0	ENST00000273854.3:c.19del	p.Arg7GlyfsTer55	p.R7Gfs*55	ENST00000273854	NM_004439.5	7	Cgg/gg	1/18	1	2	FACETS	0.884	0.699	1	0.884	0.699	1	CLONAL	1	TRUE	1	0.131946398096423	2		544	446	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530360	187530360	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	22	292	0	ENST00000441802.2:c.10183A>T	p.Thr3395Ser	p.T3395S	ENST00000441802	NM_005245.3	3395	Acc/Tcc	16/27	1	2	FACETS	0.99	0.767	1	0.99	0.767	1	CLONAL	1	TRUE	1	0.131946398096423	2		292	337	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293987	1293987	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	403	807	0	ENST00000310581.5:c.1014G>T	p.Lys338Asn	p.K338N	ENST00000310581	NM_198253.2	338	aaG/aaT	2/16	0.131946398096423	10	FACETS	0.955	0.91	1	0.955	0.91	1	CLONAL	9	TRUE	1	0.131946398096423	10		807	1086	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518069	176518069	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	41	553	0	ENST00000292408.4:c.567G>T	p.Gln189His	p.Q189H	ENST00000292408	NM_213647.1	189	caG/caT	5/18	0.131946398096423	3	FACETS	1	0.922	1	0.599	0.498	0.711	CLONAL	1	TRUE	1	0.131946398096423	3		553	553	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552985	106552985	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	39	514	0	ENST00000369096.4:c.950G>T	p.Gly317Val	p.G317V	ENST00000369096	NM_001198.3	317	gGg/gTg	5/7	0.131946398096423	3	FACETS	0.959	0.793	1	0.48	0.396	0.573	CLONAL	1	TRUE	1	0.131946398096423	3		514	657	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031747	69031747	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	23	406	1	ENST00000288368.4:c.3502C>T	p.Gln1168Ter	p.Q1168*	ENST00000288368	NM_024870.2	1168	Cag/Tag	28/40	1	2	FACETS	0.985	0.768	1	0.985	0.768	1	CLONAL	1	TRUE	1	0.131946398096423	2		407	354	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412940	63412940	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	362	679	0	ENST00000330258.3:c.227del	p.Gly76AspfsTer24	p.G76Dfs*24	ENST00000330258	NM_152424.3	76	gGa/ga	2/2	0.228117097725326	1	FACETS	0.563	0.536	0.59	0.563	0.536	0.59	INDETERMINATE	1	TRUE	0	0.853177832030408	1		679	864	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	205	382	0	ENST00000308159.5:c.43C>G	p.Gln15Glu	p.Q15E	ENST00000308159	NM_014669.4	15	Cag/Gag	2/22	1	2	FACETS	0.933	0.874	0.994	0.933	0.874	0.994	CLONAL	1	TRUE	1	0.853177832030408	2		382	515	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342559	118342559	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	71	212	0	ENST00000534358.1:c.685C>T	p.Pro229Ser	p.P229S	ENST00000534358	NM_005933.3	229	Cct/Tct	3/36	1	2	FACETS	0.876	0.78	0.975	0.876	0.78	0.975	CLONAL	1	TRUE	1	0.853177832030408	2		212	190	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196794	106196794	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0048169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	202	343	0	ENST00000380013.4:c.5127T>A	p.Cys1709Ter	p.C1709*	ENST00000380013	NM_001127208.2	1709	tgT/tgA	11/11	1	2	FACETS	0.96	0.899	1	0.96	0.899	1	CLONAL	1	TRUE	1	0.853177832030408	2		343	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579485	7579485	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs869312782	NA	P-0048169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	799	723	0	ENST00000269305.4:c.202G>T	p.Glu68Ter	p.E68*	ENST00000269305	NM_001126112.2	68	Gag/Tag	4/11	0.853177832030408	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.853177832030408	2		723	932	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76931752	76931752	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	161	322	0	ENST00000373344.5:c.3778G>A	p.Asp1260Asn	p.D1260N	ENST00000373344	NM_000489.3	1260	Gat/Aat	10/35	0.228117097725326	1	FACETS	0.466	0.431	0.502	0.466	0.431	0.502	INDETERMINATE	1	TRUE	0	0.853177832030408	1		322	464	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14317331	14317331	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	119	368	0	ENST00000256196.4:c.179G>T	p.Arg60Ile	p.R60I	ENST00000256196		60	aGa/aTa	2/6	0.280344159079004	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.853177832030408	0		368	421	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133912	41133912	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	330	457	0	ENST00000379561.5:c.1716G>T	p.Met572Ile	p.M572I	ENST00000379561	NM_002015.3	572	atG/atT	2/3	0.853177832030408	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.853177832030408	1		457	412	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554360	81554360	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1304759190	NA	P-0048169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	530	337	0	ENST00000298171.2:c.380T>A	p.Leu127His	p.L127H	ENST00000298171	NM_000369.2	127	cTc/cAc	4/10	0.853177832030408	5	FACETS	0.991	0.956	1	0.991	0.956	1	CLONAL	3	TRUE	2	0.853177832030408	5		337	953	SUCCESS
BLM	641	MSKCC	GRCh37	15	91341514	91341514	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	211	383	0	ENST00000355112.3:c.3305A>T	p.His1102Leu	p.H1102L	ENST00000355112	NM_000057.2	1102	cAt/cTt	17/22	0.853177832030408	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.853177832030408	2		383	239	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2125840	2125841	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0048169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	479	688	1	ENST00000219476.3:c.2586_2587delinsTT	p.Glu863Ter	p.E863*	ENST00000219476	NM_000548.3	862	gcGGag/gcTTag	23/42	1	2	FACETS	0.974	0.933	1	0.974	0.933	1	CLONAL	1	TRUE	1	0.853177832030408	2		689	1153	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862821	9862821	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	344	685	1	ENST00000330684.3:c.2482A>T	p.Met828Leu	p.M828L	ENST00000330684	NM_001134407.1	828	Atg/Ttg	12/13	1	2	FACETS	0.95	0.903	0.997	0.95	0.903	0.997	CLONAL	1	TRUE	1	0.853177832030408	2		686	849	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81973550	81973550	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	288	468	0	ENST00000359376.3:c.3367G>C	p.Glu1123Gln	p.E1123Q	ENST00000359376	NM_002661.3	1123	Gaa/Caa	30/33	1	2	FACETS	0.954	0.902	1	0.954	0.902	1	CLONAL	1	TRUE	1	0.853177832030408	2		468	708	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89839793	89839793	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1485075318	NA	P-0048169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	386	595	2	ENST00000389301.3:c.1901-1G>T		p.X634_splice	ENST00000389301	NM_000135.2	634			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.853177832030408	2		597	877	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961224	15961224	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	413	305	0	ENST00000268712.3:c.6165C>G	p.Ile2055Met	p.I2055M	ENST00000268712	NM_006311.3	2055	atC/atG	39/46	0.853177832030408	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.853177832030408	2		305	461	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007234	62007234	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	815	688	0	ENST00000392795.3:c.448G>T	p.Ala150Ser	p.A150S	ENST00000392795	NM_001039933.1	150	Gca/Tca	4/6	0.853177832030408	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.853177832030408	2		688	927	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550313	39550313	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	151	259	0	ENST00000262039.4:c.424G>C	p.Asp142His	p.D142H	ENST00000262039	NM_002647.2	142	Gac/Cac	4/25	1	2	FACETS	0.997	0.925	1	0.997	0.925	1	CLONAL	1	TRUE	1	0.853177832030408	2		259	355	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868389	45868389	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	506	783	0	ENST00000391945.4:c.388G>T	p.Val130Phe	p.V130F	ENST00000391945	NM_000400.3	130	Gtc/Ttc	6/23	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.853177832030408	2		783	1162	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189349	99189350	+	missense_variant	Missense_Mutation	DNP	CG	CG	TT	novel	NA	P-0048169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	340	542	1	ENST00000074304.5:c.2605_2606delinsTT	p.Arg869Leu	p.R869L	ENST00000074304	NM_001134224.1	869	CGg/TTg	24/26	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.853177832030408	2		543	786	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268351	46268351	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	197	362	0	ENST00000371998.3:c.2738A>T	p.Gln913Leu	p.Q913L	ENST00000371998		913	cAg/cTg	15/23	1	2	FACETS	0.954	0.892	1	0.954	0.892	1	CLONAL	1	TRUE	1	0.853177832030408	2		362	484	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106194072	106194072	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	91	215	0	ENST00000380013.4:c.4534G>C	p.Ala1512Pro	p.A1512P	ENST00000380013	NM_001127208.2	1512	Gca/Cca	10/11	1	2	FACETS	0.781	0.704	0.862	0.781	0.704	0.862	SUBCLONAL	1	TRUE	1	0.853177832030408	2		215	273	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189500	56189500	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	189	341	0	ENST00000399503.3:c.4532C>G	p.Thr1511Arg	p.T1511R	ENST00000399503	NM_005921.1	1511	aCa/aGa	20/20	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.853177832030408	2		341	443	SUCCESS
APC	324	MSKCC	GRCh37	5	112176708	112176708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554086711	NA	P-0048169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	79	197	0	ENST00000257430.4:c.5417C>T	p.Ser1806Leu	p.S1806L	ENST00000257430	NM_000038.5	1806	tCa/tTa	16/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.853177832030408	2		197	171	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670922	30670922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	447	704	3	ENST00000376406.3:c.5824G>A	p.Gly1942Arg	p.G1942R	ENST00000376406	NM_014641.2	1942	Ggg/Agg	12/15	0.849437546730442	3	FACETS	0.974	0.928	1	0.487	0.464	0.51	CLONAL	1	TRUE	1	0.853177832030408	3		707	1535	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206818	162206818	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768102678	NA	P-0048169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	205	422	0	ENST00000366898.1:c.857C>A	p.Ser286Tyr	p.S286Y	ENST00000366898	NM_004562.2	286	tCc/tAc	7/12	1	2	FACETS	0.999	0.937	1	0.999	0.937	1	CLONAL	1	TRUE	1	0.853177832030408	2		422	481	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55260483	55260483	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	238	413	0	ENST00000275493.2:c.2650G>T	p.Glu884Ter	p.E884*	ENST00000275493	NM_005228.3	884	Gaa/Taa	22/28	0.228117097725326	1	FACETS	0.527	0.495	0.559	0.527	0.495	0.559	INDETERMINATE	1	TRUE	0	0.853177832030408	1		413	607	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412455	80412455	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	323	295	0	ENST00000286548.4:c.586T>A	p.Leu196Ile	p.L196I	ENST00000286548	NM_002072.3	196	Tta/Ata	4/7	0.853177832030408	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.853177832030408	2		295	368	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918885	76918885	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	188	491	0	ENST00000373344.5:c.4106G>T	p.Arg1369Ile	p.R1369I	ENST00000373344	NM_000489.3	1369	aGa/aTa	12/35	0.228117097725326	1	FACETS	0.504	0.47	0.539	0.504	0.47	0.539	INDETERMINATE	1	TRUE	0	0.853177832030408	1		491	501	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937293	76937293	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs782023982	NA	P-0048169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	71	406	0	ENST00000373344.5:c.3455G>T	p.Gly1152Val	p.G1152V	ENST00000373344	NM_000489.3	1152	gGc/gTc	9/35	0.228117097725326	1	FACETS	0.411	0.364	0.461	0.411	0.364	0.461	INDETERMINATE	1	TRUE	0	0.853177832030408	1		406	232	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123156488	123156488	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	72	261	0	ENST00000218089.9:c.11C>A	p.Ala4Asp	p.A4D	ENST00000218089	NM_001042749.1	4	gCt/gAt	3/35	0.228117097725326	1	FACETS	0.569	0.509	0.63	0.569	0.509	0.63	INDETERMINATE	1	TRUE	0	0.853177832030408	1		261	170	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578204	7578204	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	467	592	0	ENST00000269305.4:c.645T>A	p.Ser215Arg	p.S215R	ENST00000269305	NM_001126112.2	215	agT/agA	6/11	0.845157084395012	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.845157084395012	1		592	630	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22412980	22413009	+	inframe_deletion	In_Frame_Del	DEL	ATGTATTTCTAGTCTGTTTTTCAGTGGTCT	ATGTATTTCTAGTCTGTTTTTCAGTGGTCT	-	novel	NA	P-0048171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	242	131	0	ENST00000344548.3:c.227_256del	p.Asp76_Ser86delinsAla	p.D76_S86delinsA	ENST00000344548	NM_001039802.1	76	gATGTATTTCTAGTCTGTTTTTCAGTGGTCTct/gct	5/7	0.445912540673124	5	FACETS	0.917	0.877	0.956	1	0.993	1	INDETERMINATE	4	TRUE	2	0.845157084395012	5		131	354	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245339	41245339	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1060502333	NA	P-0048171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	303	482	0	ENST00000357654.3:c.2209del	p.Thr737GlnfsTer16	p.T737Qfs*16	ENST00000357654	NM_007294.3	737	Aca/ca	10/23	0.845157084395012	1	FACETS	0.986	0.949	1	0.986	0.949	1	CLONAL	1	TRUE	0	0.845157084395012	1		482	420	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750414	39750414	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	172	375	0	ENST00000361337.2:c.2029G>C	p.Asp677His	p.D677H	ENST00000361337	NM_003286.2	677	Gat/Cat	19/21	0.166060566854425	4	FACETS	1	0.972	1	0.278	0.256	0.3	INDETERMINATE	1	TRUE	0	0.845157084395012	4		375	676	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851673	134851673	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	209	546	1	ENST00000398015.3:c.1079G>T	p.Cys360Phe	p.C360F	ENST00000398015	NM_004441.4	360	tGc/tTc	5/16	0.337198742729816	1	FACETS	0.604	0.567	0.641	0.604	0.567	0.641	INDETERMINATE	1	TRUE	0	0.845157084395012	1		547	473	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805423	1805423	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778617562	NA	P-0048172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	428	615	1	ENST00000260795.2:c.935C>T	p.Ala312Val	p.A312V	ENST00000260795		312	gCg/gTg	7/17	0.658471465427529	3	FACETS	0.976	0.938	1			1	CLONAL	2	TRUE	NA	0.769690593344702	3		616	789	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945147	32945147	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	96	285	0	ENST00000380152.3:c.8542G>T	p.Glu2848Ter	p.E2848*	ENST00000380152		2848	Gaa/Taa	20/27	0.769690593344702	1	FACETS	0.903	0.83	0.974	0.903	0.83	0.974	CLONAL	1	TRUE	0	0.769690593344702	1		285	170	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061192	38061230	+	inframe_deletion	In_Frame_Del	DEL	AAGCGCTTCTGGCGGCGCAAGTAGCAGCCGTTCTCGAAC	AAGCGCTTCTGGCGGCGCAAGTAGCAGCCGTTCTCGAAC	-	novel	NA	P-0048172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	180	487	0	ENST00000250448.2:c.759_797del	p.Met253_Phe266delinsIle	p.M253_F266delinsI	ENST00000250448	NM_004496.3	253	atGTTCGAGAACGGCTGCTACTTGCGCCGCCAGAAGCGCTTc/atc	2/2	1	2	FACETS	0.923	0.858	0.989	0.923	0.858	0.989	CLONAL	1	TRUE	1	0.769690593344702	2		487	507	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677794	58677794	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	250	667	0	ENST00000305921.3:c.19C>G	p.Leu7Val	p.L7V	ENST00000305921	NM_003620.3	7	Ctg/Gtg	1/6	0.769690593344702	3	FACETS	0.965	0.904	1	0.483	0.452	0.514	CLONAL	1	TRUE	1	0.769690593344702	3		667	932	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724541	162724541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759709680	NA	P-0048174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	193	496	4	ENST00000367921.3:c.313C>T	p.Arg105Cys	p.R105C	ENST00000367921	NM_006182.2	105	Cgc/Tgc	5/18	1	2	FACETS	0.988	0.92	1	0.988	0.92	1	CLONAL	1	TRUE	1	0.685708780209281	2		500	570	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533316	29533316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1466678870	NA	P-0048174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	109	246	0	ENST00000356175.3:c.1319G>A	p.Arg440Gln	p.R440Q	ENST00000356175	NM_000267.3	440	cGa/cAa	12/57	0.685708780209281	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.685708780209281	1		246	181	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961059	55961059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530419081	NA	P-0048174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	207	593	0	ENST00000263923.4:c.2881C>T	p.Arg961Trp	p.R961W	ENST00000263923	NM_002253.2	961	Cgg/Tgg	21/30	0.371144726606177	1	FACETS	0.732	0.685	0.78	0.732	0.685	0.78	INDETERMINATE	1	TRUE	0	0.685708780209281	1		593	542	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0048174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	92	426	1	ENST00000311936.3:c.180_181delinsAA	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggAAaa	3/5	0.210116136334937	2	FACETS	0.965	0.87	1	0.483	0.435	0.532	INDETERMINATE	1	TRUE	0	0.685708780209281	2		427	278	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048626	180048626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748514089	NA	P-0048174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	149	760	0	ENST00000261937.6:c.1936G>A	p.Glu646Lys	p.E646K	ENST00000261937	NM_182925.4	646	Gag/Aag	13/30	0.330303269960426	2	FACETS	0.516	0.472	0.563	0.258	0.236	0.282	INDETERMINATE	1	TRUE	0	0.685708780209281	2		760	842	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711359	114711359	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	117	228	0	ENST00000543371.1:c.374C>A	p.Ala125Asp	p.A125D	ENST00000543371	NM_001198531.1	125	gCc/gAc	3/14	0.371144726606177	1	FACETS	0.876	0.806	0.947	0.876	0.806	0.947	INDETERMINATE	1	TRUE	0	0.685708780209281	1		228	256	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436156	56436157	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0048174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	240	561	0	ENST00000407977.2:c.980dup	p.Pro328ThrfsTer115	p.P328Tfs*115	ENST00000407977		327	gga/ggGa	9/10	0.685708780209281	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.685708780209281	1		561	419	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877396	40877396	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	327	511	0	ENST00000373198.4:c.2300C>A	p.Ala767Asp	p.A767D	ENST00000373198	NM_133170.3	767	gCt/gAt	15/32	0.115776763916402	6	FACETS	0.904	0.858	0.951	0.904	0.858	0.951	INDETERMINATE	3	TRUE	3	0.685708780209281	6		511	834	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0048175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	28	566	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.13	2		566	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	85	1084	1	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	0.3	2	FACETS	1	0.967	1			1	CLONAL	1	TRUE	NA	0.13	2		1085	1023	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970830	55970830	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	32	433	0	ENST00000263923.4:c.1967T>C	p.Val656Ala	p.V656A	ENST00000263923	NM_002253.2	656	gTc/gCc	13/30	1	2	FACETS	0.956	0.775	1	0.956	0.775	1	CLONAL	1	TRUE	1	0.13	2		433	515	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17125914	17125914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747675386	NA	P-0048175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	94	640	1	ENST00000285071.4:c.680C>T	p.Thr227Met	p.T227M	ENST00000285071	NM_144997.5	227	aCg/aTg	7/14	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.13	NA		641	925	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974713	21974719	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCAGC	GGGCAGC	-	novel	NA	P-0048175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	34	434	0	ENST00000304494.5:c.108_114del	p.Leu37ThrfsTer14	p.L37Tfs*14	ENST00000304494	NM_000077.4	36	gcGCTGCCC/gc	1/3	1	2	FACETS	0.993	0.81	1	0.993	0.81	1	CLONAL	1	TRUE	1	0.13	2		434	527	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	703	706	8	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.969	0.948	0.989	1	0.998	1	CLONAL	2	TRUE	1	0.812324827390009	2		714	893	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	437	691	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	0.809521200205982	2	FACETS	0.951	0.909	0.994	0.476	0.454	0.497	CLONAL	1	TRUE	0	0.812324827390009	2		692	1131	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	256	660	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.932	0.878	0.987	0.932	0.878	0.987	CLONAL	1	TRUE	1	0.812324827390009	2		660	676	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	274	639	4	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	1	2	FACETS	0.876	0.826	0.927	0.876	0.826	0.927	CLONAL	1	TRUE	1	0.812324827390009	2		643	770	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255248	16255248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752574502	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	90	361	0	ENST00000375759.3:c.2513C>T	p.Thr838Met	p.T838M	ENST00000375759	NM_015001.2	838	aCg/aTg	11/15	1	2	FACETS	0.423	0.376	0.473	0.423	0.376	0.473	SUBCLONAL	1	TRUE	1	0.812324827390009	2		361	524	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106074	27106074	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	245	503	0	ENST00000324856.7:c.5688del	p.Pro1898HisfsTer25	p.P1898Hfs*25	ENST00000324856	NM_006015.4	1895	gaG/ga	20/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.812324827390009	2		503	589	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136244	64136244	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	392	747	0	ENST00000334205.4:c.1403A>G	p.Asn468Ser	p.N468S	ENST00000334205	NM_003942.2	468	aAt/aGt	12/17	1	2	FACETS	0.99	0.944	1	0.99	0.944	1	CLONAL	1	TRUE	1	0.812324827390009	2		747	975	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219177	94219177	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	37	416	0	ENST00000323929.3:c.227T>C	p.Leu76Pro	p.L76P	ENST00000323929	NM_005591.3	76	cTc/cCc	4/20	1	2	FACETS	0.28	0.231	0.335	0.28	0.231	0.335	SUBCLONAL	1	TRUE	1	0.812324827390009	2		416	325	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911916	94911917	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	114	414	0	ENST00000536441.1:c.1013_1014del	p.Phe338CysfsTer32	p.F338Cfs*32	ENST00000536441	NM_144665.3	338	tTT/t	7/10	1	2	FACETS	0.833	0.759	0.909	0.833	0.759	0.909	CLONAL	1	TRUE	1	0.812324827390009	2		414	337	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118370559	118370560	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	135	298	0	ENST00000534358.1:c.6091dup	p.Ile2031AsnfsTer9	p.I2031Nfs*9	ENST00000534358	NM_005933.3	2030	aca/acAa	24/36	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.812324827390009	2		298	326	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231351	46231351	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	104	300	0	ENST00000334344.6:c.1191G>T	p.Gln397His	p.Q397H	ENST00000334344	NM_152641.2	397	caG/caT	10/21	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.812324827390009	2		300	236	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445149	49445149	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	358	783	1	ENST00000301067.7:c.2317del	p.Gln773SerfsTer157	p.Q773Sfs*157	ENST00000301067	NM_003482.3	773	Cag/ag	10/54	1	2	FACETS	0.954	0.907	1	0.954	0.907	1	CLONAL	1	TRUE	1	0.812324827390009	2		784	924	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012452	29012452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	135	431	0	ENST00000282397.4:c.419G>A	p.Ser140Asn	p.S140N	ENST00000282397	NM_002019.4	140	aGt/aAt	4/30	1	2	FACETS	0.95	0.875	1	0.95	0.875	1	CLONAL	1	TRUE	1	0.812324827390009	2		431	350	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037897	49037898	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	68	243	0	ENST00000267163.4:c.2138_2139del	p.Lys713SerfsTer7	p.K713Sfs*7	ENST00000267163	NM_000321.2	713	AAa/a	21/27	0.812324827390009	1	FACETS	0.904	0.822	0.982	0.904	0.822	0.982	CLONAL	1	TRUE	0	0.812324827390009	1		243	110	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061208	38061208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	317	581	0	ENST00000250448.2:c.781C>T	p.Arg261Cys	p.R261C	ENST00000250448	NM_004496.3	261	Cgc/Tgc	2/2	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.812324827390009	2		581	757	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989044	41989044	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	196	442	1	ENST00000219905.7:c.1840del	p.Arg614GlufsTer7	p.R614Efs*7	ENST00000219905	NM_001164273.1	612	ggA/gg	3/24	0.812324827390009	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.812324827390009	1		443	281	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641009	3641009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	421	756	0	ENST00000294008.3:c.2630C>T	p.Ala877Val	p.A877V	ENST00000294008	NM_032444.2	877	gCt/gTt	12/15	1	2	FACETS	0.967	0.923	1	0.967	0.923	1	CLONAL	1	TRUE	1	0.812324827390009	2		756	1072	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3827631	3827631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141098117	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	20	383	0	ENST00000262367.5:c.2141G>A	p.Arg714His	p.R714H	ENST00000262367	NM_004380.2	714	cGc/cAc	11/31	1	2	FACETS	0.129	0.098	0.166	0.129	0.098	0.166	SUBCLONAL	1	TRUE	1	0.812324827390009	2		383	381	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347060	89347060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	331	688	1	ENST00000301030.4:c.5890G>A	p.Gly1964Arg	p.G1964R	ENST00000301030	NM_001256183.1	1964	Ggg/Agg	9/13	1	2	FACETS	0.947	0.898	0.995	0.947	0.898	0.995	CLONAL	1	TRUE	1	0.812324827390009	2		689	861	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696405	47696405	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	218	431	0	ENST00000347630.2:c.418G>T	p.Asp140Tyr	p.D140Y	ENST00000347630	NM_001007230.1	140	Gat/Tat	6/11	1	2	FACETS	0.957	0.897	1	0.957	0.897	1	CLONAL	1	TRUE	1	0.812324827390009	2		431	561	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435788	56435788	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	279	571	0	ENST00000407977.2:c.1349A>G	p.Tyr450Cys	p.Y450C	ENST00000407977		450	tAt/tGt	9/10	1	2	FACETS	0.957	0.904	1	0.957	0.904	1	CLONAL	1	TRUE	1	0.812324827390009	2		571	718	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220070	36220070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	710	672	0	ENST00000222270.7:c.4790G>A	p.Arg1597Gln	p.R1597Q	ENST00000222270	NM_014727.1	1597	cGg/cAg	22/37	0.809521200205982	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.812324827390009	2		672	853	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792068	42792068	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	312	699	0	ENST00000575354.2:c.872G>T	p.Gly291Val	p.G291V	ENST00000575354	NM_015125.3	291	gGg/gTg	6/20	0.809521200205982	2	FACETS	0.912	0.864	0.961	0.456	0.432	0.481	CLONAL	1	TRUE	0	0.812324827390009	2		699	842	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	340	799	4	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			0.809521200205982	2	FACETS	0.971	0.923	1	0.486	0.461	0.51	CLONAL	1	TRUE	0	0.812324827390009	2		803	862	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967157	25967158	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	171	435	0	ENST00000435504.4:c.2046_2048dup	p.Ala684dup	p.A684dup	ENST00000435504		684	gcc/gcAGCc	13/13	1	2	FACETS	0.79	0.732	0.85	0.79	0.732	0.85	SUBCLONAL	1	TRUE	1	0.812324827390009	2		435	533	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607775	46607775	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	408	765	2	ENST00000263734.3:c.1964G>T	p.Gly655Val	p.G655V	ENST00000263734	NM_001430.4	655	gGg/gTg	12/16	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.812324827390009	2		767	1004	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715842	61715842	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	129	374	0	ENST00000401558.2:c.2087T>C	p.Val696Ala	p.V696A	ENST00000401558	NM_003400.3	696	gTg/gCg	18/25	1	2	FACETS	0.895	0.821	0.97	0.895	0.821	0.97	CLONAL	1	TRUE	1	0.812324827390009	2		374	355	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	138	350	10	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	0.963	0.887	1	0.963	0.887	1	CLONAL	1	TRUE	1	0.812324827390009	2		360	353	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162034	22162035	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	199	372	0	ENST00000215832.6:c.220dup	p.Ile74AsnfsTer8	p.I74Nfs*8	ENST00000215832	NM_002745.4	74	atc/aAtc	2/9	1	2	FACETS	0.992	0.928	1	0.992	0.928	1	CLONAL	1	TRUE	1	0.812324827390009	2		372	494	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967309	134967309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs186851943	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	229	505	0	ENST00000398015.3:c.2648G>A	p.Arg883Gln	p.R883Q	ENST00000398015	NM_004441.4	883	cGg/cAg	14/16	1	2	FACETS	0.862	0.808	0.917	0.862	0.808	0.917	CLONAL	1	TRUE	1	0.812324827390009	2		505	654	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1976696	1976696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	363	665	0	ENST00000382891.5:c.3479G>A	p.Arg1160His	p.R1160H	ENST00000382891	NM_133335.3	1160	cGt/cAt	19/22	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.812324827390009	2		665	879	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598153	55598153	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1309976246	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	189	400	0	ENST00000288135.5:c.2350G>A	p.Ala784Thr	p.A784T	ENST00000288135	NM_000222.2	784	Gcc/Acc	16/21	1	2	FACETS	0.931	0.868	0.995	0.931	0.868	0.995	CLONAL	1	TRUE	1	0.812324827390009	2		400	500	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295405	1295405	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	74	176	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.985	0.881	1	0.985	0.881	1	CLONAL	1	TRUE	1	0.812324827390009	2		177	185	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508780	31508780	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	286	535	0	ENST00000344624.3:c.1535del	p.Lys512ArgfsTer19	p.K512Rfs*19	ENST00000344624		512	aAg/ag	7/33	1	2	FACETS	0.907	0.857	0.958	0.907	0.857	0.958	CLONAL	1	TRUE	1	0.812324827390009	2		535	776	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628394	86628394	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	72	283	0	ENST00000274376.6:c.763T>C	p.Tyr255His	p.Y255H	ENST00000274376	NM_002890.2	255	Tat/Cat	3/25	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.812324827390009	2		283	156	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	397	780	1	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	0.981	0.936	1	0.981	0.936	1	CLONAL	1	TRUE	1	0.812324827390009	2		781	996	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903731	41903731	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	435	783	0	ENST00000372991.4:c.826C>T	p.Gln276Ter	p.Q276*	ENST00000372991	NM_001760.3	276	Caa/Taa	5/5	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.812324827390009	2		783	996	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	372	650	2	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.977	0.931	1	0.977	0.931	1	CLONAL	1	TRUE	1	0.812324827390009	2		652	937	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151833995	151834000	+	inframe_deletion	In_Frame_Del	DEL	ATAGTC	ATAGTC	-	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	201	398	0	ENST00000262189.6:c.14653_14658del	p.Asp4885_Tyr4886del	p.D4885_Y4886del	ENST00000262189	NM_170606.2	4885	GACTAT/-	59/59	1	2	FACETS	0.884	0.825	0.944	0.884	0.825	0.944	CLONAL	1	TRUE	1	0.812324827390009	2		398	560	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981872	70981872	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	69	750	2	ENST00000276594.2:c.224C>A	p.Pro75His	p.P75H	ENST00000276594	NM_024504.3	75	cCt/cAt	2/8	1	2	FACETS	0.186	0.161	0.213	0.186	0.161	0.213	SUBCLONAL	1	TRUE	1	0.812324827390009	2		752	913	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518052	8518052	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	195	432	0	ENST00000356435.5:c.1339C>T	p.Gln447Ter	p.Q447*	ENST00000356435		447	Cag/Tag	10/35	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.812324827390009	2		432	477	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs767894241	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	207	476	0	ENST00000358127.4:c.76dup	p.Val26GlyfsTer49	p.V26Gfs*49	ENST00000358127	NM_001280556.1	26	gtt/gGtt	2/10	1	2	FACETS	0.718	0.669	0.768	0.718	0.669	0.768	SUBCLONAL	1	TRUE	1	0.812324827390009	2		476	710	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482251	87482251	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	265	551	0	ENST00000277120.3:c.1538G>A	p.Gly513Asp	p.G513D	ENST00000277120		513	gGc/gAc	14/19	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.812324827390009	2		551	652	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133747514	133747516	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGG	AGG	-	novel	NA	P-0048176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	199	372	0	ENST00000318560.5:c.825_827del		p.X275_splice	ENST00000318560	NM_005157.4	275		5/11	1	2	FACETS	0.984	0.92	1	0.984	0.92	1	CLONAL	1	TRUE	1	0.812324827390009	2		372	498	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0048177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	106	314	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.46	2		314	404	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057976	27057976	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	38	562	0	ENST00000324856.7:c.1684C>T	p.Gln562Ter	p.Q562*	ENST00000324856	NM_006015.4	562	Cag/Tag	3/20	1	2	FACETS	0.263	0.216	0.315	0.263	0.216	0.315	SUBCLONAL	1	TRUE	1	0.46	2		562	629	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519886	NA	P-0048177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	114	324	0	ENST00000349496.5:c.97T>G	p.Ser33Ala	p.S33A	ENST00000349496	NM_001904.3	33	Tct/Gct	3/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.46	2		324	433	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370862	55370862	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs893686270	NA	P-0048177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	72	642	1	ENST00000297316.4:c.164C>T	p.Pro55Leu	p.P55L	ENST00000297316	NM_022454.3	55	cCg/cTg	1/2	1	2	FACETS	0.362	0.316	0.413	0.362	0.316	0.413	SUBCLONAL	1	TRUE	1	0.46	2		643	864	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772290	68772291	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0048177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	82	718	0	ENST00000261769.5:c.144_145del	p.Gly49ProfsTer9	p.G49Pfs*9	ENST00000261769	NM_004360.3	47	GAg/g	2/16	1	2	FACETS	0.41	0.361	0.463	0.41	0.361	0.463	SUBCLONAL	1	TRUE	1	0.46	2		718	869	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591092	67591100	+	inframe_deletion	In_Frame_Del	DEL	GTATGAACA	GTATGAACA	-	novel	NA	P-0048178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	27	172	0	ENST00000274335.5:c.1686_1694del	p.Met563_Ser565del	p.M563_S565del	ENST00000274335		562	cGTATGAACAgc/cgc	12/15	1	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	FALSE	1	0.204219908956838	2		172	249	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082261	16082261	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1204	80	702	0	ENST00000281043.3:c.75G>C	p.Gln25His	p.Q25H	ENST00000281043	NM_005378.4	25	caG/caC	2/3	1	2	FACETS	0.61	0.535	0.692	0.61	0.535	0.692	SUBCLONAL	1	FALSE	1	0.204219908956838	2		702	1284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577144	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs879253942	NA	P-0048214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	582	663	0	ENST00000269305.4:c.794T>C	p.Leu265Pro	p.L265P	ENST00000269305	NM_001126112.2	265	cTg/cCg	8/11	0.746301806022374	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.781489559657522	3		663	683	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137071	64137071	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	128	667	1	ENST00000334205.4:c.1582C>A	p.His528Asn	p.H528N	ENST00000334205	NM_003942.2	528	Cac/Aac	13/17	0.781489559657522	2	FACETS	0.58	0.527	0.634	0.29	0.263	0.317	SUBCLONAL	1	TRUE	0	0.781489559657522	2		668	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	115	512	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.501	0.45	0.555	0.501	0.45	0.555	SUBCLONAL	1	TRUE	1	0.439285611914387	2		512	1045	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115600	108115600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772821016	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	168	372	0	ENST00000278616.4:c.748C>T	p.Arg250Ter	p.R250*	ENST00000278616	NM_000051.3	250	Cga/Tga	7/63	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.439285611914387	2		372	516	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	80	571	0	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	0.478	0.42	0.54	0.478	0.42	0.54	SUBCLONAL	1	TRUE	1	0.439285611914387	2		571	762	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740668	58740668	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs759850701	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	205	530	0	ENST00000305921.3:c.1573G>T	p.Glu525Ter	p.E525*	ENST00000305921	NM_003620.3	525	Gaa/Taa	6/6	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.439285611914387	2		530	633	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410987	31410987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1236254462	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	74	664	0	ENST00000344624.3:c.3533G>A	p.Arg1178Gln	p.R1178Q	ENST00000344624		1178	cGa/cAa	28/33	1	2	FACETS	0.443	0.387	0.503	0.443	0.387	0.503	SUBCLONAL	1	TRUE	1	0.439285611914387	2		664	761	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628125	187628125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1196972484	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	197	715	0	ENST00000441802.2:c.2857G>A	p.Asp953Asn	p.D953N	ENST00000441802	NM_005245.3	953	Gat/Aat	2/27	1	2	FACETS	0.964	0.893	1	0.964	0.893	1	CLONAL	1	TRUE	1	0.439285611914387	2		715	930	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251901	153251901	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	150	385	0	ENST00000281708.4:c.1105G>T	p.Glu369Ter	p.E369*	ENST00000281708	NM_033632.3	369	Gaa/Taa	7/12	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.439285611914387	2		385	525	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443676	29443676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56315533	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	147	705	3	ENST00000389048.3:c.3541C>T	p.Arg1181Cys	p.R1181C	ENST00000389048	NM_004304.4	1181	Cgc/Tgc	23/29	NA	2	FACETS	0.869	0.794	0.947			1	INDETERMINATE	1	TRUE	NA	0.439285611914387	2		708	770	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950493	68950493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760821149	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	79	355	0	ENST00000288368.4:c.805G>A	p.Asp269Asn	p.D269N	ENST00000288368	NM_024870.2	269	Gat/Aat	7/40	0.179576461478298	0	FACETS	0.479	0.423	0.538			1	INDETERMINATE	1	TRUE	0	0.439285611914387	0		355	421	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142447	119142447	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs199739868	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	95	331	0	ENST00000264033.4:c.446G>A	p.Arg149Gln	p.R149Q	ENST00000264033	NM_005188.3	149	cGa/cAa	3/16	1	2	FACETS	0.968	0.866	1	0.968	0.866	1	CLONAL	1	TRUE	1	0.439285611914387	2		331	447	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981172	55981172	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	83	415	0	ENST00000263923.4:c.527G>T	p.Arg176Ile	p.R176I	ENST00000263923	NM_002253.2	176	aGa/aTa	5/30	1	2	FACETS	0.796	0.705	0.892	0.796	0.705	0.892	SUBCLONAL	1	TRUE	1	0.439285611914387	2		415	475	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937850	76937850	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs138256318	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	61	282	0	ENST00000373344.5:c.2898G>T	p.Glu966Asp	p.E966D	ENST00000373344	NM_000489.3	966	gaG/gaT	9/35	1	1	FACETS	0.614	0.532	0.702	0.614	0.532	0.702	SUBCLONAL	1	TRUE	0	0.439285611914387	1		282	353	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961766	55961766	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	131	408	0	ENST00000263923.4:c.2795G>T	p.Arg932Ile	p.R932I	ENST00000263923	NM_002253.2	932	aGa/aTa	20/30	1	2	FACETS	0.994	0.905	1	0.994	0.905	1	CLONAL	1	TRUE	1	0.439285611914387	2		408	600	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133041	30133041	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	38	457	0	ENST00000331968.5:c.560G>T	p.Arg187Ile	p.R187I	ENST00000331968	NM_002742.2	187	aGa/aTa	4/18	1	2	FACETS	0.347	0.286	0.414	0.347	0.286	0.414	SUBCLONAL	1	TRUE	1	0.439285611914387	2		457	499	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661884	227661884	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	129	1092	1	ENST00000305123.5:c.1571G>T	p.Arg524Ile	p.R524I	ENST00000305123	NM_005544.2	524	aGa/aTa	1/2	1	2	FACETS	0.473	0.428	0.522	0.473	0.428	0.522	SUBCLONAL	1	TRUE	1	0.439285611914387	2		1093	1241	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	119	390	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.77	0.695	0.848	0.77	0.695	0.848	SUBCLONAL	1	TRUE	1	0.439285611914387	2		390	704	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	68	277	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.497	0.432	0.567	0.497	0.432	0.567	SUBCLONAL	1	TRUE	1	0.439285611914387	2		277	623	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784865	9784865	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	109	834	0	ENST00000377346.4:c.2868C>A	p.Phe956Leu	p.F956L	ENST00000377346	NM_005026.3	956	ttC/ttA	23/24	1	2	FACETS	0.445	0.398	0.495	0.445	0.398	0.495	SUBCLONAL	1	TRUE	1	0.439285611914387	2		834	1115	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188525	11188525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs922525420	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	133	487	0	ENST00000361445.4:c.5896C>T	p.Arg1966Trp	p.R1966W	ENST00000361445	NM_004958.3	1966	Cgg/Tgg	42/58	1	2	FACETS	0.94	0.856	1	0.94	0.856	1	CLONAL	1	TRUE	1	0.439285611914387	2		487	644	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259486	16259486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759585687	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	61	446	1	ENST00000375759.3:c.6751G>A	p.Ala2251Thr	p.A2251T	ENST00000375759	NM_015001.2	2251	Gca/Aca	11/15	1	2	FACETS	0.429	0.37	0.494	0.429	0.37	0.494	SUBCLONAL	1	TRUE	1	0.439285611914387	2		447	647	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17371320	17371320	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs74315370	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	44	584	1	ENST00000375499.3:c.136C>T	p.Arg46Ter	p.R46*	ENST00000375499	NM_003000.2	46	Cga/Tga	2/8	1	2	FACETS	0.231	0.193	0.273	0.231	0.193	0.273	SUBCLONAL	1	TRUE	1	0.439285611914387	2		585	868	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087503	27087503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	381	923	2	ENST00000324856.7:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000324856	NM_006015.4	693	Cga/Tga	5/20	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.439285611914387	2		925	1158	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28601520	28601520	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	84	761	0	ENST00000253063.3:c.1205G>T	p.Gly402Val	p.G402V	ENST00000253063	NM_031459.4	402	gGc/gTc	8/10	1	2	FACETS	0.357	0.314	0.404	0.357	0.314	0.404	SUBCLONAL	1	TRUE	1	0.439285611914387	2		761	1070	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36808981	36808981	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs534849916	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	123	722	1	ENST00000373129.3:c.1073C>T	p.Ala358Val	p.A358V	ENST00000373129	NM_032017.1	358	gCg/gTg	11/12	1	2	FACETS	0.556	0.501	0.613	0.556	0.501	0.613	SUBCLONAL	1	TRUE	1	0.439285611914387	2		723	1008	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932074	36932074	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	180	746	0	ENST00000361632.4:c.2395A>G	p.Thr799Ala	p.T799A	ENST00000361632		799	Acc/Gcc	16/16	1	2	FACETS	0.885	0.816	0.957	0.885	0.816	0.957	CLONAL	1	TRUE	1	0.439285611914387	2		746	926	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509508	46509508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	75	462	0	ENST00000262741.5:c.1223G>A	p.Ser408Asn	p.S408N	ENST00000262741	NM_003629.3	408	aGc/aAc	10/10	1	2	FACETS	0.503	0.44	0.57	0.503	0.44	0.57	SUBCLONAL	1	TRUE	1	0.439285611914387	2		462	679	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521487	46521487	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	249	479	1	ENST00000262741.5:c.921G>T	p.Lys307Asn	p.K307N	ENST00000262741	NM_003629.3	307	aaG/aaT	7/10	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.439285611914387	2		480	773	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46527637	46527637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778971217	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	69	493	0	ENST00000262741.5:c.728G>A	p.Arg243Gln	p.R243Q	ENST00000262741	NM_003629.3	243	cGa/cAa	6/10	1	2	FACETS	0.43	0.374	0.491	0.43	0.374	0.491	SUBCLONAL	1	TRUE	1	0.439285611914387	2		493	731	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46527713	46527713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	27	318	0	ENST00000262741.5:c.652G>A	p.Ala218Thr	p.A218T	ENST00000262741	NM_003629.3	218	Gct/Act	6/10	1	2	FACETS	0.267	0.212	0.331	0.267	0.212	0.331	SUBCLONAL	1	TRUE	1	0.439285611914387	2		318	460	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46715785	46715785	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	201	463	0	ENST00000371975.4:c.204T>G	p.Ser68Arg	p.S68R	ENST00000371975	NM_003579.3	68	agT/agG	3/18	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.439285611914387	2		463	643	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310563	65310563	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	43	444	1	ENST00000342505.4:c.2125G>T	p.Asp709Tyr	p.D709Y	ENST00000342505	NM_002227.2	709	Gac/Tac	16/25	1	2	FACETS	0.333	0.278	0.394	0.333	0.278	0.394	SUBCLONAL	1	TRUE	1	0.439285611914387	2		445	588	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65323452	65323452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765489448	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	64	495	0	ENST00000342505.4:c.1345G>A	p.Ala449Thr	p.A449T	ENST00000342505	NM_002227.2	449	Gcc/Acc	10/25	1	2	FACETS	0.419	0.362	0.48	0.419	0.362	0.48	SUBCLONAL	1	TRUE	1	0.439285611914387	2		495	696	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332599	65332599	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758451418	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	39	323	0	ENST00000342505.4:c.940G>A	p.Glu314Lys	p.E314K	ENST00000342505	NM_002227.2	314	Gaa/Aaa	7/25	1	2	FACETS	0.432	0.358	0.514	0.432	0.358	0.514	SUBCLONAL	1	TRUE	1	0.439285611914387	2		323	411	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332823	65332823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	27	283	0	ENST00000342505.4:c.716G>A	p.Arg239Gln	p.R239Q	ENST00000342505	NM_002227.2	239	cGg/cAg	7/25	1	2	FACETS	0.304	0.242	0.376	0.304	0.242	0.376	SUBCLONAL	1	TRUE	1	0.439285611914387	2		283	404	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428511	78428511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408536007	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	146	433	1	ENST00000370768.2:c.1288C>T	p.Arg430Cys	p.R430C	ENST00000370768	NM_003902.3	430	Cgt/Tgt	14/20	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.439285611914387	2		434	656	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432754	78432754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	83	350	0	ENST00000370768.2:c.322C>T	p.Pro108Ser	p.P108S	ENST00000370768	NM_003902.3	108	Cca/Tca	5/20	1	2	FACETS	0.919	0.816	1	0.919	0.816	1	CLONAL	1	TRUE	1	0.439285611914387	2		350	411	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263336	115263336	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs562518461	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	56	525	0	ENST00000438362.2:c.2014G>A	p.Asp672Asn	p.D672N	ENST00000438362	NM_001242891.1	672	Gat/Aat	17/20	1	2	FACETS	0.336	0.287	0.39	0.336	0.287	0.39	SUBCLONAL	1	TRUE	1	0.439285611914387	2		525	758	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280616	115280616	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	135	539	0	ENST00000438362.2:c.415G>T	p.Glu139Ter	p.E139*	ENST00000438362	NM_001242891.1	139	Gaa/Taa	4/20	1	2	FACETS	0.799	0.727	0.875	0.799	0.727	0.875	SUBCLONAL	1	TRUE	1	0.439285611914387	2		539	769	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695784	117695784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147263365	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	64	473	0	ENST00000369458.3:c.653C>T	p.Thr218Met	p.T218M	ENST00000369458	NM_024626.3	218	aCg/aTg	4/6	1	2	FACETS	0.525	0.455	0.601	0.525	0.455	0.601	SUBCLONAL	1	TRUE	1	0.439285611914387	2		473	555	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551841	150551841	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	51	244	1	ENST00000369026.2:c.166G>T	p.Val56Leu	p.V56L	ENST00000369026	NM_021960.4	56	Gtg/Ttg	1/3	1	2	FACETS	0.572	0.487	0.664	0.572	0.487	0.664	SUBCLONAL	1	TRUE	1	0.439285611914387	2		245	406	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845433	156845433	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	302	995	0	ENST00000524377.1:c.1476G>T	p.Glu492Asp	p.E492D	ENST00000524377	NM_002529.3	492	gaG/gaT	12/17	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.439285611914387	2		995	1323	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849143	156849143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775191394	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	125	922	4	ENST00000524377.1:c.2035G>A	p.Asp679Asn	p.D679N	ENST00000524377	NM_002529.3	679	Gac/Aac	15/17	1	2	FACETS	0.496	0.448	0.547	0.496	0.448	0.547	SUBCLONAL	1	TRUE	1	0.439285611914387	2		926	1147	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724542	162724542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1041487062	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	93	566	0	ENST00000367921.3:c.314G>A	p.Arg105His	p.R105H	ENST00000367921	NM_006182.2	105	cGc/cAc	5/18	1	2	FACETS	0.571	0.508	0.639	0.571	0.508	0.639	SUBCLONAL	1	TRUE	1	0.439285611914387	2		566	741	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317623	163317623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747173543	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	32	253	0	ENST00000271452.3:c.1019C>T	p.Ser340Leu	p.S340L	ENST00000271452	NM_145697.2	340	tCg/tTg	12/14	1	2	FACETS	0.434	0.352	0.525	0.434	0.352	0.525	SUBCLONAL	1	TRUE	1	0.439285611914387	2		253	336	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218892	193218892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1225502334	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	34	236	0	ENST00000367435.3:c.1450C>T	p.Arg484Cys	p.R484C	ENST00000367435	NM_024529.4	484	Cgt/Tgt	16/17	1	2	FACETS	0.591	0.485	0.708	0.591	0.485	0.708	SUBCLONAL	1	TRUE	1	0.439285611914387	2		236	262	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650027	206650027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201666998	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	63	545	0	ENST00000367120.3:c.547G>A	p.Asp183Asn	p.D183N	ENST00000367120	NM_014002.3	183	Gac/Aac	7/22	1	2	FACETS	0.432	0.373	0.496	0.432	0.373	0.496	SUBCLONAL	1	TRUE	1	0.439285611914387	2		545	664	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945625	206945625	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	64	425	0	ENST00000423557.1:c.156G>T	p.Lys52Asn	p.K52N	ENST00000423557	NM_000572.2	52	aaG/aaT	1/5	1	2	FACETS	0.483	0.418	0.554	0.483	0.418	0.554	SUBCLONAL	1	TRUE	1	0.439285611914387	2		425	603	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945665	206945665	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	53	599	0	ENST00000423557.1:c.116A>C	p.Asn39Thr	p.N39T	ENST00000423557	NM_000572.2	39	aAc/aCc	1/5	1	2	FACETS	0.318	0.271	0.371	0.318	0.271	0.371	SUBCLONAL	1	TRUE	1	0.439285611914387	2		599	758	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567664	226567664	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	96	697	1	ENST00000366794.5:c.1502C>T	p.Ala501Val	p.A501V	ENST00000366794	NM_001618.3	501	gCt/gTt	10/23	1	2	FACETS	0.524	0.466	0.586	0.524	0.466	0.586	SUBCLONAL	1	TRUE	1	0.439285611914387	2		698	834	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612810	228612810	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148579172	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	126	801	1	ENST00000366696.1:c.217C>T	p.Arg73Cys	p.R73C	ENST00000366696	NM_003493.2	73	Cgc/Tgc	1/1	1	2	FACETS	0.592	0.535	0.652	0.592	0.535	0.652	SUBCLONAL	1	TRUE	1	0.439285611914387	2		802	969	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243675668	243675668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	26	249	0	ENST00000263826.5:c.1312G>A	p.Glu438Lys	p.E438K	ENST00000263826	NM_005465.4	438	Gaa/Aaa	12/13	1	2	FACETS	0.333	0.264	0.413	0.333	0.264	0.413	SUBCLONAL	1	TRUE	1	0.439285611914387	2		249	355	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716229	243716229	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	56	471	0	ENST00000263826.5:c.965A>G	p.Asp322Gly	p.D322G	ENST00000263826	NM_005465.4	322	gAc/gGc	10/13	1	2	FACETS	0.418	0.358	0.484	0.418	0.358	0.484	SUBCLONAL	1	TRUE	1	0.439285611914387	2		471	610	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800950	243800950	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	48	357	0	ENST00000263826.5:c.524C>A	p.Ala175Asp	p.A175D	ENST00000263826	NM_005465.4	175	gCt/gAt	5/13	1	2	FACETS	0.44	0.372	0.515	0.44	0.372	0.515	SUBCLONAL	1	TRUE	1	0.439285611914387	2		357	497	SUCCESS
RET	5979	MSKCC	GRCh37	10	43598038	43598038	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	95	905	0	ENST00000355710.3:c.586T>G	p.Leu196Val	p.L196V	ENST00000355710	NM_020975.4	196	Ttg/Gtg	3/20	1	2	FACETS	0.371	0.329	0.416	0.371	0.329	0.416	SUBCLONAL	1	TRUE	1	0.439285611914387	2		905	1165	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601986	43601986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749883001	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	145	1063	1	ENST00000355710.3:c.1030G>A	p.Gly344Ser	p.G344S	ENST00000355710	NM_020975.4	344	Ggc/Agc	5/20	1	2	FACETS	0.496	0.451	0.544	0.496	0.451	0.544	SUBCLONAL	1	TRUE	1	0.439285611914387	2		1064	1331	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606892	43606892	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	279	1126	0	ENST00000355710.3:c.1501C>A	p.Leu501Ile	p.L501I	ENST00000355710	NM_020975.4	501	Ctt/Att	7/20	1	2	FACETS	0.958	0.898	1	0.958	0.898	1	CLONAL	1	TRUE	1	0.439285611914387	2		1126	1326	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609994	43609994	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148935214	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	100	1025	1	ENST00000355710.3:c.1946C>T	p.Ser649Leu	p.S649L	ENST00000355710	NM_020975.4	649	tCg/tTg	11/20	1	2	FACETS	0.379	0.337	0.424	0.379	0.337	0.424	SUBCLONAL	1	TRUE	1	0.439285611914387	2		1026	1201	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622039	43622039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1371891301	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	152	419	0	ENST00000355710.3:c.3056C>T	p.Ala1019Val	p.A1019V	ENST00000355710	NM_020975.4	1019	gCg/gTg	19/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.439285611914387	2		419	540	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333547	70333547	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs538486517	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	45	530	0	ENST00000373644.4:c.1452G>T	p.Glu484Asp	p.E484D	ENST00000373644	NM_030625.2	484	gaG/gaT	2/12	1	2	FACETS	0.354	0.297	0.417	0.354	0.297	0.417	SUBCLONAL	1	TRUE	1	0.439285611914387	2		530	579	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446279	70446279	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763447831	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	80	511	1	ENST00000373644.4:c.5219G>A	p.Arg1740His	p.R1740H	ENST00000373644	NM_030625.2	1740	cGc/cAc	11/12	1	2	FACETS	0.511	0.449	0.577	0.511	0.449	0.577	SUBCLONAL	1	TRUE	1	0.439285611914387	2		512	713	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685294	89685294	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	62	175	0	ENST00000371953.3:c.189C>A	p.Asn63Lys	p.N63K	ENST00000371953	NM_000314.4	63	aaC/aaA	3/9	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.439285611914387	2		175	265	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	116	315	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.909	0.822	1	0.909	0.822	1	CLONAL	1	TRUE	1	0.439285611914387	2		315	581	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692918	89692918	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1114167676	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	122	495	0	ENST00000371953.3:c.402G>T	p.Met134Ile	p.M134I	ENST00000371953	NM_000314.4	134	atG/atT	5/9	1	2	FACETS	0.902	0.817	0.99	0.902	0.817	0.99	CLONAL	1	TRUE	1	0.439285611914387	2		495	616	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724144	112724144	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	22	304	0	ENST00000369452.4:c.28G>T	p.Asp10Tyr	p.D10Y	ENST00000369452	NM_007373.3	10	Gac/Tac	2/9	1	2	FACETS	0.299	0.231	0.378	0.299	0.231	0.378	SUBCLONAL	1	TRUE	1	0.439285611914387	2		304	335	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298139	123298139	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	58	455	0	ENST00000358487.5:c.715T>C	p.Ser239Pro	p.S239P	ENST00000358487	NM_000141.4	239	Tcc/Ccc	6/18	1	2	FACETS	0.416	0.357	0.48	0.416	0.357	0.48	SUBCLONAL	1	TRUE	1	0.439285611914387	2		455	635	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14300921	14300921	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782761955	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	42	327	0	ENST00000256196.4:c.577G>A	p.Glu193Lys	p.E193K	ENST00000256196		193	Gaa/Aaa	6/6	1	2	FACETS	0.382	0.319	0.453	0.382	0.319	0.453	SUBCLONAL	1	TRUE	1	0.439285611914387	2		327	500	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741858	17741858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	32	222	0	ENST00000250003.3:c.529G>A	p.Ala177Thr	p.A177T	ENST00000250003	NM_002478.4	177	Gcc/Acc	1/3	1	2	FACETS	0.56	0.457	0.676	0.56	0.457	0.676	SUBCLONAL	1	TRUE	1	0.439285611914387	2		222	260	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413577	32413577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1037084691	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	46	462	0	ENST00000332351.3:c.1373G>A	p.Arg458Gln	p.R458Q	ENST00000332351	NM_024426.4	458	cGa/cAa	9/10	1	2	FACETS	0.358	0.301	0.421	0.358	0.301	0.421	SUBCLONAL	1	TRUE	1	0.439285611914387	2		462	585	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32449584	32449584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	119	1033	2	ENST00000332351.3:c.790C>T	p.Pro264Ser	p.P264S	ENST00000332351	NM_024426.4	264	Ccg/Tcg	3/10	1	2	FACETS	0.474	0.427	0.524	0.474	0.427	0.524	SUBCLONAL	1	TRUE	1	0.439285611914387	2		1035	1143	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205491	61205491	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	53	390	0	ENST00000301761.2:c.276A>C	p.Glu92Asp	p.E92D	ENST00000301761	NM_017841.2	92	gaA/gaC	3/4	1	2	FACETS	0.408	0.348	0.475	0.408	0.348	0.475	SUBCLONAL	1	TRUE	1	0.439285611914387	2		390	591	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588238	69588238	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	129	573	0	ENST00000168712.1:c.460G>T	p.Glu154Ter	p.E154*	ENST00000168712	NM_002007.2	154	Gag/Tag	3/3	1	2	FACETS	0.812	0.737	0.891	0.812	0.737	0.891	CLONAL	1	TRUE	1	0.439285611914387	2		573	723	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945335	71945335	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs745723030	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	199	844	0	ENST00000298229.2:c.2223G>T	p.Lys741Asn	p.K741N	ENST00000298229	NM_001567.3	741	aaG/aaT	20/28	1	2	FACETS	0.818	0.757	0.882	0.818	0.757	0.882	CLONAL	1	TRUE	1	0.439285611914387	2		844	1107	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103478	77103478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	44	349	0	ENST00000356341.3:c.88G>A	p.Asp30Asn	p.D30N	ENST00000356341	NM_002576.4	30	Gat/Aat	2/15	1	2	FACETS	0.366	0.307	0.432	0.366	0.307	0.432	SUBCLONAL	1	TRUE	1	0.439285611914387	2		349	547	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94153304	94153304	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs750057222	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	36	406	0	ENST00000323929.3:c.2114G>T	p.Arg705Ile	p.R705I	ENST00000323929	NM_005591.3	705	aGa/aTa	20/20	1	2	FACETS	0.397	0.326	0.476	0.397	0.326	0.476	SUBCLONAL	1	TRUE	1	0.439285611914387	2		406	413	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922190	100922190	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	68	362	0	ENST00000325455.5:c.2322G>T	p.Gln774His	p.Q774H	ENST00000325455	NM_001202474.3	774	caG/caT	5/8	1	2	FACETS	0.742	0.648	0.843	0.742	0.648	0.843	SUBCLONAL	1	TRUE	1	0.439285611914387	2		362	417	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076740	102076740	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	84	675	3	ENST00000282441.5:c.919C>T	p.Arg307Ter	p.R307*	ENST00000282441	NM_001130145.2	307	Cga/Tga	5/9	1	2	FACETS	0.45	0.397	0.508	0.45	0.397	0.508	SUBCLONAL	1	TRUE	1	0.439285611914387	2		678	849	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195335	102195335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	55	344	1	ENST00000263464.3:c.95G>A	p.Arg32Gln	p.R32Q	ENST00000263464	NM_001165.4	32	cGa/cAa	2/9	1	2	FACETS	0.463	0.396	0.536	0.463	0.396	0.536	SUBCLONAL	1	TRUE	1	0.439285611914387	2		345	541	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106457	108106457	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1363726955	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	23	198	0	ENST00000278616.4:c.392C>A	p.Ser131Ter	p.S131*	ENST00000278616	NM_000051.3	131	tCa/tAa	5/63	1	2	FACETS	0.424	0.331	0.53	0.424	0.331	0.53	SUBCLONAL	1	TRUE	1	0.439285611914387	2		198	247	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106513	108106513	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	96	244	0	ENST00000278616.4:c.448C>A	p.Leu150Ile	p.L150I	ENST00000278616	NM_000051.3	150	Ctt/Att	5/63	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.439285611914387	2		244	355	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115594	108115594	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730881336	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	129	365	0	ENST00000278616.4:c.742C>T	p.Arg248Ter	p.R248*	ENST00000278616	NM_000051.3	248	Cga/Tga	7/63	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.439285611914387	2		365	517	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139268	108139268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55723361	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	71	.	.	ENST00000278616.4:c.2770C>T	p.Arg924Trp	p.R924W	ENST00000278616	NM_000051.3	924	Cgg/Tgg	18/63	1	2	FACETS	0.36	0.313	0.411	0.36	0.313	0.411	SUBCLONAL	1	TRUE	1	0.439285611914387	2		0	898	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214049	108214049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	104	280	0	ENST00000278616.4:c.8369G>A	p.Arg2790Lys	p.R2790K	ENST00000278616	NM_000051.3	2790	aGa/aAa	57/63	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.439285611914387	2		280	456	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343913	118343913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264831726	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	36	383	0	ENST00000534358.1:c.2039C>T	p.Ser680Leu	p.S680L	ENST00000534358	NM_005933.3	680	tCg/tTg	3/36	1	2	FACETS	0.283	0.232	0.341	0.283	0.232	0.341	SUBCLONAL	1	TRUE	1	0.439285611914387	2		383	579	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344036	118344036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	45	267	0	ENST00000534358.1:c.2162G>A	p.Arg721Gln	p.R721Q	ENST00000534358	NM_005933.3	721	cGa/cAa	3/36	1	2	FACETS	0.407	0.341	0.479	0.407	0.341	0.479	SUBCLONAL	1	TRUE	1	0.439285611914387	2		267	504	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373202	118373202	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	58	460	0	ENST00000534358.1:c.6595A>G	p.Ser2199Gly	p.S2199G	ENST00000534358	NM_005933.3	2199	Agt/Ggt	27/36	1	2	FACETS	0.405	0.347	0.468	0.405	0.347	0.468	SUBCLONAL	1	TRUE	1	0.439285611914387	2		460	652	SUCCESS
CBL	867	MSKCC	GRCh37	11	119158653	119158653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	49	436	0	ENST00000264033.4:c.2033C>T	p.Ala678Val	p.A678V	ENST00000264033	NM_005188.3	678	gCc/gTc	12/16	1	2	FACETS	0.382	0.323	0.447	0.382	0.323	0.447	SUBCLONAL	1	TRUE	1	0.439285611914387	2		436	584	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419064	419064	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	116	406	0	ENST00000399788.2:c.3283G>T	p.Glu1095Ter	p.E1095*	ENST00000399788	NM_001042603.1	1095	Gaa/Taa	22/28	1	2	FACETS	0.87	0.786	0.958	0.87	0.786	0.958	CLONAL	1	TRUE	1	0.439285611914387	2		406	607	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422253	422253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374400044	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	71	590	0	ENST00000399788.2:c.3005G>A	p.Arg1002Gln	p.R1002Q	ENST00000399788	NM_001042603.1	1002	cGa/cAa	20/28	1	2	FACETS	0.406	0.353	0.462	0.406	0.353	0.462	SUBCLONAL	1	TRUE	1	0.439285611914387	2		590	797	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475141	475141	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	49	533	0	ENST00000399788.2:c.496C>A	p.Leu166Ile	p.L166I	ENST00000399788	NM_001042603.1	166	Ctc/Atc	4/28	1	2	FACETS	0.328	0.277	0.384	0.328	0.277	0.384	SUBCLONAL	1	TRUE	1	0.439285611914387	2		533	680	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992143	11992143	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	62	436	0	ENST00000396373.4:c.233C>T	p.Ser78Phe	p.S78F	ENST00000396373	NM_001987.4	78	tCt/tTt	3/8	NA	2	FACETS	0.434	0.375	0.499			1	INDETERMINATE	1	TRUE	NA	0.439285611914387	2		436	650	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443830	18443830	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1235693712	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	40	328	0	ENST00000266497.5:c.803C>A	p.Ser268Tyr	p.S268Y	ENST00000266497		268	tCt/tAt	3/31	1	2	FACETS	0.49	0.407	0.581	0.49	0.407	0.581	SUBCLONAL	1	TRUE	1	0.439285611914387	2		328	372	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691128	18691128	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	100	379	0	ENST00000266497.5:c.3239A>C	p.Tyr1080Ser	p.Y1080S	ENST00000266497		1080	tAc/tCc	23/31	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.439285611914387	2		379	450	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793379	18793379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	38	391	0	ENST00000266497.5:c.4076C>T	p.Ser1359Phe	p.S1359F	ENST00000266497		1359	tCt/tTt	30/31	1	2	FACETS	0.386	0.319	0.461	0.386	0.319	0.461	SUBCLONAL	1	TRUE	1	0.439285611914387	2		391	448	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380283	25380283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913528	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	134	467	0	ENST00000311936.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000311936	NM_004985.3	59	Gca/Aca	3/5	1	2	FACETS	0.965	0.88	1	0.965	0.88	1	CLONAL	1	TRUE	1	0.439285611914387	2		467	632	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944829	31944829	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1270	125	1084	1	ENST00000340398.3:c.272C>T	p.Ala91Val	p.A91V	ENST00000340398	NM_001013699.2	91	gCg/gTg	1/1	1	2	FACETS	0.408	0.368	0.451	0.408	0.368	0.451	SUBCLONAL	1	TRUE	1	0.439285611914387	2		1085	1395	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244476	46244476	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	66	427	0	ENST00000334344.6:c.2570C>A	p.Ser857Tyr	p.S857Y	ENST00000334344	NM_152641.2	857	tCt/tAt	15/21	1	2	FACETS	0.454	0.394	0.519	0.454	0.394	0.519	SUBCLONAL	1	TRUE	1	0.439285611914387	2		427	662	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426313	49426313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1265	131	1189	1	ENST00000301067.7:c.12175G>A	p.Ala4059Thr	p.A4059T	ENST00000301067	NM_003482.3	4059	Gcc/Acc	39/54	1	2	FACETS	0.427	0.386	0.471	0.427	0.386	0.471	SUBCLONAL	1	TRUE	1	0.439285611914387	2		1190	1396	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427701	49427701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532898944	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	127	801	0	ENST00000301067.7:c.10787G>A	p.Arg3596Gln	p.R3596Q	ENST00000301067	NM_003482.3	3596	cGg/cAg	39/54	1	2	FACETS	0.589	0.533	0.649	0.589	0.533	0.649	SUBCLONAL	1	TRUE	1	0.439285611914387	2		801	981	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861838	57861838	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381253752	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	176	694	0	ENST00000228682.2:c.1139G>A	p.Arg380Gln	p.R380Q	ENST00000228682	NM_005269.2	380	cGa/cAa	10/12	1	2	FACETS	0.889	0.819	0.962	0.889	0.819	0.962	CLONAL	1	TRUE	1	0.439285611914387	2		694	901	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57862003	57862003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	61	485	0	ENST00000228682.2:c.1304C>T	p.Ala435Val	p.A435V	ENST00000228682	NM_005269.2	435	gCc/gTc	10/12	1	2	FACETS	0.47	0.405	0.54	0.47	0.405	0.54	SUBCLONAL	1	TRUE	1	0.439285611914387	2		485	591	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145099	58145099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3211612	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	179	686	0	ENST00000257904.6:c.245G>A	p.Arg82Gln	p.R82Q	ENST00000257904	NM_000075.3	82	cGa/cAa	3/8	1	2	FACETS	0.998	0.921	1	0.998	0.921	1	CLONAL	1	TRUE	1	0.439285611914387	2		686	817	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69229721	69229721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	32	309	0	ENST00000462284.1:c.797G>A	p.Ser266Asn	p.S266N	ENST00000462284	NM_002392.5	266	aGc/aAc	9/11	1	2	FACETS	0.354	0.287	0.43	0.354	0.287	0.43	SUBCLONAL	1	TRUE	1	0.439285611914387	2		309	411	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233187	69233187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	23	246	0	ENST00000462284.1:c.1052C>T	p.Ala351Val	p.A351V	ENST00000462284	NM_002392.5	351	gCc/gTc	11/11	1	2	FACETS	0.319	0.249	0.401	0.319	0.249	0.401	SUBCLONAL	1	TRUE	1	0.439285611914387	2		246	328	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856617	111856617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1364785726	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	74	230	1	ENST00000341259.2:c.668C>T	p.Ala223Val	p.A223V	ENST00000341259	NM_005475.2	223	gCg/gTg	2/8	1	2	FACETS	0.916	0.807	1	0.916	0.807	1	CLONAL	1	TRUE	1	0.439285611914387	2		231	368	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112893859	112893859	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	33	388	0	ENST00000351677.2:c.748G>T	p.Glu250Ter	p.E250*	ENST00000351677	NM_002834.3	250	Gaa/Taa	6/16	1	2	FACETS	0.276	0.224	0.335	0.276	0.224	0.335	SUBCLONAL	1	TRUE	1	0.439285611914387	2		388	544	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926960	112926960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770363146	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	55	572	4	ENST00000351677.2:c.1580G>A	p.Arg527His	p.R527H	ENST00000351677	NM_002834.3	527	cGc/cAc	13/16	1	2	FACETS	0.343	0.293	0.398	0.343	0.293	0.398	SUBCLONAL	1	TRUE	1	0.439285611914387	2		576	730	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114226	115114226	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	186	783	0	ENST00000257566.3:c.991A>G	p.Lys331Glu	p.K331E	ENST00000257566	NM_016569.3	331	Aag/Gag	6/8	1	2	FACETS	0.962	0.889	1	0.962	0.889	1	CLONAL	1	TRUE	1	0.439285611914387	2		783	880	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250214	133250214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	358	793	0	ENST00000320574.5:c.1306C>T	p.Pro436Ser	p.P436S	ENST00000320574	NM_006231.2	436	Ccc/Tcc	13/49	1	2	FACETS	0.768	0.729	0.808	1	0.995	1	SUBCLONAL	2	TRUE	1	0.439285611914387	2		793	1061	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619895	21619895	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	91	586	0	ENST00000382592.4:c.271T>C	p.Ser91Pro	p.S91P	ENST00000382592	NM_014572.2	91	Tcg/Ccg	2/8	1	2	FACETS	0.557	0.494	0.624	0.557	0.494	0.624	SUBCLONAL	1	TRUE	1	0.439285611914387	2		586	744	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28885761	28885761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	57	387	0	ENST00000282397.4:c.3601C>T	p.Pro1201Ser	p.P1201S	ENST00000282397	NM_002019.4	1201	Ccg/Tcg	27/30	1	2	FACETS	0.476	0.408	0.55	0.476	0.408	0.55	SUBCLONAL	1	TRUE	1	0.439285611914387	2		387	545	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959145	28959145	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs745886558	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	58	337	0	ENST00000282397.4:c.1993C>T	p.Arg665Ter	p.R665*	ENST00000282397	NM_002019.4	665	Cga/Tga	14/30	1	2	FACETS	0.487	0.419	0.562	0.487	0.419	0.562	SUBCLONAL	1	TRUE	1	0.439285611914387	2		337	542	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001399	29001399	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	113	365	0	ENST00000282397.4:c.1333C>A	p.Pro445Thr	p.P445T	ENST00000282397	NM_002019.4	445	Cca/Aca	10/30	1	2	FACETS	0.978	0.884	1	0.978	0.884	1	CLONAL	1	TRUE	1	0.439285611914387	2		365	526	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32899248	32899248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375125172	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	63	271	0	ENST00000380152.3:c.352C>T	p.Arg118Cys	p.R118C	ENST00000380152		118	Cgc/Tgc	4/27	1	2	FACETS	0.844	0.734	0.961	0.844	0.734	0.961	CLONAL	1	TRUE	1	0.439285611914387	2		271	340	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937655	32937655	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	47	423	0	ENST00000380152.3:c.8316A>C	p.Glu2772Asp	p.E2772D	ENST00000380152		2772	gaA/gaC	18/27	1	2	FACETS	0.412	0.347	0.483	0.412	0.347	0.483	SUBCLONAL	1	TRUE	1	0.439285611914387	2		423	520	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972663	32972663	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	88	406	0	ENST00000380152.3:c.10013C>A	p.Ser3338Ter	p.S3338*	ENST00000380152		3338	tCa/tAa	27/27	1	2	FACETS	0.826	0.735	0.923	0.826	0.735	0.923	CLONAL	1	TRUE	1	0.439285611914387	2		406	485	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134988	41134988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	55	232	0	ENST00000379561.5:c.640C>T	p.Arg214Cys	p.R214C	ENST00000379561	NM_002015.3	214	Cgt/Tgt	2/3	1	2	FACETS	0.852	0.734	0.979	0.852	0.734	0.979	CLONAL	1	TRUE	1	0.439285611914387	2		232	294	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942686	48942686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767011440	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	32	210	0	ENST00000267163.4:c.1073G>A	p.Arg358Gln	p.R358Q	ENST00000267163	NM_000321.2	358	cGa/cAa	11/27	1	2	FACETS	0.448	0.364	0.543	0.448	0.364	0.543	SUBCLONAL	1	TRUE	1	0.439285611914387	2		210	325	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033965	49033965	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	45	400	0	ENST00000267163.4:c.2102A>G	p.Asp701Gly	p.D701G	ENST00000267163	NM_000321.2	701	gAc/gGc	20/27	1	2	FACETS	0.432	0.363	0.508	0.432	0.363	0.508	SUBCLONAL	1	TRUE	1	0.439285611914387	2		400	474	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345122	73345122	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	32	318	0	ENST00000377767.4:c.1675G>A	p.Ala559Thr	p.A559T	ENST00000377767	NM_014953.3	559	Gca/Aca	13/21	1	2	FACETS	0.463	0.376	0.56	0.463	0.376	0.56	SUBCLONAL	1	TRUE	1	0.439285611914387	2		318	315	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046488	30046488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	154	610	0	ENST00000331968.5:c.2695G>A	p.Glu899Lys	p.E899K	ENST00000331968	NM_002742.2	899	Gaa/Aaa	18/18	1	2	FACETS	0.982	0.901	1	0.982	0.901	1	CLONAL	1	TRUE	1	0.439285611914387	2		610	714	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194858	30194858	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771807174	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	58	486	0	ENST00000331968.5:c.287G>A	p.Gly96Glu	p.G96E	ENST00000331968	NM_002742.2	96	gGa/gAa	2/18	1	2	FACETS	0.452	0.388	0.522	0.452	0.388	0.522	SUBCLONAL	1	TRUE	1	0.439285611914387	2		486	584	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061103	38061103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	35	227	0	ENST00000250448.2:c.886G>A	p.Asp296Asn	p.D296N	ENST00000250448	NM_004496.3	296	Gac/Aac	2/2	1	2	FACETS	0.577	0.475	0.691	0.577	0.475	0.691	SUBCLONAL	1	TRUE	1	0.439285611914387	2		227	276	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353772	68353772	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	89	283	0	ENST00000487270.1:c.607G>T	p.Gly203Ter	p.G203*	ENST00000487270	NM_133509.3	203	Gga/Tga	7/11	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.439285611914387	2		283	397	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	69061312	69061312	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	14	163	0	ENST00000487270.1:c.1147A>T	p.Ile383Phe	p.I383F	ENST00000487270	NM_133509.3	383	Att/Ttt	11/11	1	2	FACETS	0.325	0.235	0.434	0.325	0.235	0.434	SUBCLONAL	1	TRUE	1	0.439285611914387	2		163	196	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562470	95562470	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	64	433	0	ENST00000393063.1:c.4787G>T	p.Arg1596Met	p.R1596M	ENST00000393063	NM_030621.3	1596	aGg/aTg	24/28	0.439241486269098	2	FACETS	0.525	0.455	0.601	0.263	0.227	0.301	SUBCLONAL	1	TRUE	0	0.439285611914387	2		433	555	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570090	95570090	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	98	428	0	ENST00000393063.1:c.3643A>G	p.Thr1215Ala	p.T1215A	ENST00000393063	NM_030621.3	1215	Acc/Gcc	22/28	0.439241486269098	2	FACETS	0.898	0.804	0.996	0.449	0.402	0.498	CLONAL	1	TRUE	0	0.439285611914387	2		428	497	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572534	95572534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555370340	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	49	286	0	ENST00000393063.1:c.2831G>A	p.Arg944Gln	p.R944Q	ENST00000393063	NM_030621.3	944	cGa/cAa	19/28	0.439241486269098	2	FACETS	0.72	0.613	0.836	0.36	0.306	0.418	SUBCLONAL	1	TRUE	0	0.439285611914387	2		286	310	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614469	38614469	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	71	333	0	ENST00000299084.4:c.235G>T	p.Asp79Tyr	p.D79Y	ENST00000299084	NM_152594.2	79	Gac/Tac	3/7	1	2	FACETS	0.77	0.674	0.871	0.77	0.674	0.871	SUBCLONAL	1	TRUE	1	0.439285611914387	2		333	420	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643300	38643300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750832911	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	111	379	0	ENST00000299084.4:c.770G>A	p.Arg257His	p.R257H	ENST00000299084	NM_152594.2	257	cGc/cAc	7/7	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.439285611914387	2		379	496	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643315	38643315	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	56	383	0	ENST00000299084.4:c.785G>T	p.Arg262Ile	p.R262I	ENST00000299084	NM_152594.2	262	aGa/aTa	7/7	1	2	FACETS	0.501	0.429	0.579	0.501	0.429	0.579	SUBCLONAL	1	TRUE	1	0.439285611914387	2		383	509	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40683721	40683721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757403176	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	175	737	0	ENST00000249776.8:c.713G>A	p.Arg238Gln	p.R238Q	ENST00000249776	NM_033286.3	238	cGa/cAa	7/9	1	2	FACETS	0.798	0.734	0.864	0.798	0.734	0.864	SUBCLONAL	1	TRUE	1	0.439285611914387	2		737	999	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961791	41961791	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	49	412	0	ENST00000219905.7:c.699C>A	p.Phe233Leu	p.F233L	ENST00000219905	NM_001164273.1	233	ttC/ttA	2/24	1	2	FACETS	0.419	0.355	0.49	0.419	0.355	0.49	SUBCLONAL	1	TRUE	1	0.439285611914387	2		412	532	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035031	42035031	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	78	644	0	ENST00000219905.7:c.4873G>T	p.Glu1625Ter	p.E1625*	ENST00000219905	NM_001164273.1	1625	Gaa/Taa	15/24	1	2	FACETS	0.448	0.393	0.508	0.448	0.393	0.508	SUBCLONAL	1	TRUE	1	0.439285611914387	2		644	792	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713250	43713250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1392592073	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	139	959	1	ENST00000382044.4:c.4223G>A	p.Arg1408His	p.R1408H	ENST00000382044	NM_001141980.1	1408	cGc/cAc	20/28	1	2	FACETS	0.508	0.461	0.558	0.508	0.461	0.558	SUBCLONAL	1	TRUE	1	0.439285611914387	2		960	1246	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43730552	43730552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200776719	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	148	534	0	ENST00000382044.4:c.3161G>A	p.Arg1054Gln	p.R1054Q	ENST00000382044	NM_001141980.1	1054	cGa/cAa	16/28	1	2	FACETS	0.864	0.79	0.941	0.864	0.79	0.941	CLONAL	1	TRUE	1	0.439285611914387	2		534	780	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74000779	74000779	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	83	630	0	ENST00000318443.5:c.1469G>T	p.Arg490Ile	p.R490I	ENST00000318443	NM_001024736.1	490	aGa/aTa	7/10	1	2	FACETS	0.472	0.416	0.533	0.472	0.416	0.533	SUBCLONAL	1	TRUE	1	0.439285611914387	2		630	800	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88428950	88428950	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1331800469	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	35	205	0	ENST00000360948.2:c.2150G>A	p.Gly717Glu	p.G717E	ENST00000360948	NM_001012338.2	717	gGa/gAa	17/19	1	2	FACETS	0.592	0.488	0.709	0.592	0.488	0.709	SUBCLONAL	1	TRUE	1	0.439285611914387	2		205	269	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670407	88670407	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	44	364	0	ENST00000360948.2:c.1279G>T	p.Glu427Ter	p.E427*	ENST00000360948	NM_001012338.2	427	Gaa/Taa	11/19	1	2	FACETS	0.411	0.345	0.485	0.411	0.345	0.485	SUBCLONAL	1	TRUE	1	0.439285611914387	2		364	487	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304045	91304045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	80	535	0	ENST00000355112.3:c.1442C>T	p.Ala481Val	p.A481V	ENST00000355112	NM_000057.2	481	gCc/gTc	7/22	1	2	FACETS	0.51	0.449	0.576	0.51	0.449	0.576	SUBCLONAL	1	TRUE	1	0.439285611914387	2		535	714	SUCCESS
BLM	641	MSKCC	GRCh37	15	91306337	91306337	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	55	349	0	ENST00000355112.3:c.2024C>T	p.Ala675Val	p.A675V	ENST00000355112	NM_000057.2	675	gCg/gTg	8/22	1	2	FACETS	0.474	0.406	0.549	0.474	0.406	0.549	SUBCLONAL	1	TRUE	1	0.439285611914387	2		349	528	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312758	91312758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763918749	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	76	496	0	ENST00000355112.3:c.2497G>A	p.Ala833Thr	p.A833T	ENST00000355112	NM_000057.2	833	Gct/Act	12/22	1	2	FACETS	0.504	0.442	0.572	0.504	0.442	0.572	SUBCLONAL	1	TRUE	1	0.439285611914387	2		496	686	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456496	99456496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223089854	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	59	378	0	ENST00000268035.6:c.1813C>T	p.Arg605Cys	p.R605C	ENST00000268035	NM_000875.3	605	Cgc/Tgc	8/21	1	2	FACETS	0.519	0.446	0.597	0.519	0.446	0.597	SUBCLONAL	1	TRUE	1	0.439285611914387	2		378	518	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465547	99465547	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	77	599	0	ENST00000268035.6:c.2372C>T	p.Ser791Phe	p.S791F	ENST00000268035	NM_000875.3	791	tCt/tTt	11/21	1	2	FACETS	0.461	0.404	0.522	0.461	0.404	0.522	SUBCLONAL	1	TRUE	1	0.439285611914387	2		599	761	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133780	2133780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397515062	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	74	954	1	ENST00000219476.3:c.3968C>T	p.Ala1323Val	p.A1323V	ENST00000219476	NM_000548.3	1323	gCg/gTg	33/42	1	2	FACETS	0.281	0.245	0.321	0.281	0.245	0.321	SUBCLONAL	1	TRUE	1	0.439285611914387	2		955	1197	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658653	3658653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	278	1050	0	ENST00000294008.3:c.313G>A	p.Gly105Ser	p.G105S	ENST00000294008	NM_032444.2	105	Ggc/Agc	2/15	1	2	FACETS	0.915	0.857	0.974	0.915	0.857	0.974	CLONAL	1	TRUE	1	0.439285611914387	2		1050	1384	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777838	3777838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863223334	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1347	192	1222	0	ENST00000262367.5:c.7210G>A	p.Glu2404Lys	p.E2404K	ENST00000262367	NM_004380.2	2404	Gaa/Aaa	31/31	1	2	FACETS	0.568	0.523	0.615	0.568	0.523	0.615	SUBCLONAL	1	TRUE	1	0.439285611914387	2		1222	1539	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820978	3820978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	135	546	1	ENST00000262367.5:c.2473C>T	p.Pro825Ser	p.P825S	ENST00000262367	NM_004380.2	825	Cct/Tct	14/31	1	2	FACETS	0.728	0.662	0.798	0.728	0.662	0.798	SUBCLONAL	1	TRUE	1	0.439285611914387	2		547	844	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830776	3830776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424319951	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	164	553	0	ENST00000262367.5:c.1780G>A	p.Glu594Lys	p.E594K	ENST00000262367	NM_004380.2	594	Gaa/Aaa	8/31	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.439285611914387	2		553	698	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857127	9857127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs976259560	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	90	378	0	ENST00000330684.3:c.4274C>T	p.Ser1425Leu	p.S1425L	ENST00000330684	NM_001134407.1	1425	tCg/tTg	13/13	1	2	FACETS	0.969	0.864	1	0.969	0.864	1	CLONAL	1	TRUE	1	0.439285611914387	2		378	423	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857587	9857587	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	49	518	1	ENST00000330684.3:c.3814G>A	p.Ala1272Thr	p.A1272T	ENST00000330684	NM_001134407.1	1272	Gca/Aca	13/13	1	2	FACETS	0.403	0.341	0.472	0.403	0.341	0.472	SUBCLONAL	1	TRUE	1	0.439285611914387	2		519	553	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858746	9858746	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	68	310	0	ENST00000330684.3:c.2655C>A	p.Phe885Leu	p.F885L	ENST00000330684	NM_001134407.1	885	ttC/ttA	13/13	1	2	FACETS	0.83	0.726	0.941	0.83	0.726	0.941	CLONAL	1	TRUE	1	0.439285611914387	2		310	373	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923392	9923392	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057520116	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	110	558	0	ENST00000330684.3:c.1895C>T	p.Ser632Phe	p.S632F	ENST00000330684	NM_001134407.1	632	tCt/tTt	9/13	1	2	FACETS	0.603	0.542	0.669	0.603	0.542	0.669	SUBCLONAL	1	TRUE	1	0.439285611914387	2		558	830	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23625412	23625412	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	59	425	0	ENST00000261584.4:c.3114G>T	p.Trp1038Cys	p.W1038C	ENST00000261584	NM_024675.3	1038	tgG/tgT	11/13	1	2	FACETS	0.496	0.426	0.571	0.496	0.426	0.571	SUBCLONAL	1	TRUE	1	0.439285611914387	2		425	542	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063643	67063643	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	107	577	0	ENST00000412916.2:c.92G>A	p.Gly31Asp	p.G31D	ENST00000412916		31	gGc/gAc	2/6	1	2	FACETS	0.549	0.492	0.61	0.549	0.492	0.61	SUBCLONAL	1	TRUE	1	0.439285611914387	2		577	887	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842692	68842692	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	268	616	0	ENST00000261769.5:c.628G>T	p.Glu210Ter	p.E210*	ENST00000261769	NM_004360.3	210	Gaa/Taa	5/16	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.439285611914387	2		616	823	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867356	68867356	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369126891	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	82	523	0	ENST00000261769.5:c.2603G>A	p.Arg868His	p.R868H	ENST00000261769	NM_004360.3	868	cGc/cAc	16/16	1	2	FACETS	0.508	0.447	0.573	0.508	0.447	0.573	SUBCLONAL	1	TRUE	1	0.439285611914387	2		523	735	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821365	72821365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745550429	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	81	395	1	ENST00000268489.5:c.10810G>A	p.Ala3604Thr	p.A3604T	ENST00000268489	NM_006885.3	3604	Gcc/Acc	10/10	1	2	FACETS	0.87	0.77	0.976	0.87	0.77	0.976	CLONAL	1	TRUE	1	0.439285611914387	2		396	424	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828024	72828024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200701402	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	128	1006	2	ENST00000268489.5:c.8557G>A	p.Ala2853Thr	p.A2853T	ENST00000268489	NM_006885.3	2853	Gca/Aca	9/10	1	2	FACETS	0.46	0.415	0.507	0.46	0.415	0.507	SUBCLONAL	1	TRUE	1	0.439285611914387	2		1008	1267	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831047	72831047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1396835101	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	64	493	0	ENST00000268489.5:c.5534G>A	p.Ser1845Asn	p.S1845N	ENST00000268489	NM_006885.3	1845	aGc/aAc	9/10	1	2	FACETS	0.498	0.431	0.571	0.498	0.431	0.571	SUBCLONAL	1	TRUE	1	0.439285611914387	2		493	585	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845838	72845838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762268017	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	87	692	1	ENST00000268489.5:c.3629G>A	p.Arg1210Gln	p.R1210Q	ENST00000268489	NM_006885.3	1210	cGa/cAa	6/10	1	2	FACETS	0.474	0.419	0.534	0.474	0.419	0.534	SUBCLONAL	1	TRUE	1	0.439285611914387	2		693	835	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993007	72993008	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	120	1027	0	ENST00000268489.5:c.1037dup	p.Asn346LysfsTer11	p.N346Kfs*11	ENST00000268489	NM_006885.3	346	aac/aaAc	2/10	1	2	FACETS	0.441	0.396	0.487	0.441	0.396	0.487	SUBCLONAL	1	TRUE	1	0.439285611914387	2		1027	1240	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990312	81990312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1212266400	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	53	451	0	ENST00000359376.3:c.3583G>A	p.Glu1195Lys	p.E1195K	ENST00000359376	NM_002661.3	1195	Gaa/Aaa	32/33	1	2	FACETS	0.404	0.344	0.469	0.404	0.344	0.469	SUBCLONAL	1	TRUE	1	0.439285611914387	2		451	598	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350710	89350710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138898373	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	141	857	0	ENST00000301030.4:c.2240C>T	p.Ser747Leu	p.S747L	ENST00000301030	NM_001256183.1	747	tCg/tTg	9/13	1	2	FACETS	0.487	0.442	0.534	0.487	0.442	0.534	SUBCLONAL	1	TRUE	1	0.439285611914387	2		857	1319	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350972	89350972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276054196	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	139	884	0	ENST00000301030.4:c.1978G>A	p.Glu660Lys	p.E660K	ENST00000301030	NM_001256183.1	660	Gaa/Aaa	9/13	1	2	FACETS	0.489	0.444	0.537	0.489	0.444	0.537	SUBCLONAL	1	TRUE	1	0.439285611914387	2		884	1294	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89354953	89354953	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	208	848	2	ENST00000301030.4:c.727A>G	p.Asn243Asp	p.N243D	ENST00000301030	NM_001256183.1	243	Aac/Gac	7/13	1	2	FACETS	0.821	0.761	0.884	0.821	0.761	0.884	CLONAL	1	TRUE	1	0.439285611914387	2		850	1153	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89851353	89851353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	147	679	0	ENST00000389301.3:c.1379G>A	p.Arg460Gln	p.R460Q	ENST00000389301	NM_000135.2	460	cGa/cAa	15/43	1	2	FACETS	0.817	0.746	0.891	0.817	0.746	0.891	CLONAL	1	TRUE	1	0.439285611914387	2		679	819	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7978973	7978973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768093512	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	88	596	1	ENST00000319144.4:c.1594G>A	p.Glu532Lys	p.E532K	ENST00000319144	NM_001139.2	532	Gaa/Aaa	12/15	1	2	FACETS	0.505	0.447	0.568	0.505	0.447	0.568	SUBCLONAL	1	TRUE	1	0.439285611914387	2		597	793	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989466	7989466	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs374767138	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	268	903	0	ENST00000319144.4:c.220T>C	p.Tyr74His	p.Y74H	ENST00000319144	NM_001139.2	74	Tac/Cac	2/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.439285611914387	2		903	1115	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989690	15989690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	70	446	0	ENST00000268712.3:c.3083G>A	p.Arg1028Gln	p.R1028Q	ENST00000268712	NM_006311.3	1028	cGa/cAa	23/46	1	2	FACETS	0.494	0.431	0.563	0.494	0.431	0.563	SUBCLONAL	1	TRUE	1	0.439285611914387	2		446	645	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16022764	16022764	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	90	351	0	ENST00000268712.3:c.1888G>T	p.Glu630Ter	p.E630*	ENST00000268712	NM_006311.3	630	Gaa/Taa	17/46	1	2	FACETS	0.879	0.784	0.981	0.879	0.784	0.981	CLONAL	1	TRUE	1	0.439285611914387	2		351	466	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089907	16089907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	66	332	0	ENST00000268712.3:c.203G>A	p.Arg68Gln	p.R68Q	ENST00000268712	NM_006311.3	68	cGa/cAa	3/46	1	2	FACETS	0.502	0.436	0.574	0.502	0.436	0.574	SUBCLONAL	1	TRUE	1	0.439285611914387	2		332	598	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490382	29490382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754096545	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	53	445	1	ENST00000356175.3:c.467G>A	p.Arg156His	p.R156H	ENST00000356175	NM_000267.3	156	cGc/cAc	4/57	1	2	FACETS	0.354	0.301	0.412	0.354	0.301	0.412	SUBCLONAL	1	TRUE	1	0.439285611914387	2		446	681	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533379	29533379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555611606	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	26	182	0	ENST00000356175.3:c.1382G>A	p.Arg461Gln	p.R461Q	ENST00000356175	NM_000267.3	461	cGa/cAa	12/57	1	2	FACETS	0.418	0.332	0.517	0.418	0.332	0.517	SUBCLONAL	1	TRUE	1	0.439285611914387	2		182	283	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664390	29664390	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	39	385	0	ENST00000356175.3:c.6369G>T	p.Glu2123Asp	p.E2123D	ENST00000356175	NM_000267.3	2123	gaG/gaT	42/57	1	2	FACETS	0.441	0.365	0.524	0.441	0.365	0.524	SUBCLONAL	1	TRUE	1	0.439285611914387	2		385	403	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	25	321	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.3	0.236	0.373	0.3	0.236	0.373	SUBCLONAL	1	TRUE	1	0.439285611914387	2		321	380	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679390	29679390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	73	371	0	ENST00000356175.3:c.7510G>A	p.Asp2504Asn	p.D2504N	ENST00000356175	NM_000267.3	2504	Gac/Aac	50/57	1	2	FACETS	0.59	0.517	0.669	0.59	0.517	0.669	SUBCLONAL	1	TRUE	1	0.439285611914387	2		371	563	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683534	29683534	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	25	284	0	ENST00000356175.3:c.7609G>T	p.Glu2537Ter	p.E2537*	ENST00000356175	NM_000267.3	2537	Gaa/Taa	51/57	1	2	FACETS	0.333	0.262	0.414	0.333	0.262	0.414	SUBCLONAL	1	TRUE	1	0.439285611914387	2		284	342	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264538	30264538	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	73	231	0	ENST00000322652.5:c.273G>T	p.Glu91Asp	p.E91D	ENST00000322652	NM_015355.2	91	gaG/gaT	1/16	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.439285611914387	2		231	322	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627382	37627382	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	148	648	1	ENST00000447079.4:c.1297A>G	p.Ser433Gly	p.S433G	ENST00000447079	NM_015083.1	433	Agt/Ggt	2/14	1	2	FACETS	0.839	0.767	0.915	0.839	0.767	0.915	CLONAL	1	TRUE	1	0.439285611914387	2		649	803	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667783	37667783	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	86	381	0	ENST00000447079.4:c.2668C>T	p.Arg890Cys	p.R890C	ENST00000447079	NM_015083.1	890	Cgc/Tgc	8/14	1	2	FACETS	0.853	0.758	0.954	0.853	0.758	0.954	CLONAL	1	TRUE	1	0.439285611914387	2		381	459	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682537	37682537	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	46	364	0	ENST00000447079.4:c.3728G>T	p.Arg1243Ile	p.R1243I	ENST00000447079	NM_015083.1	1243	aGa/aTa	13/14	1	2	FACETS	0.418	0.352	0.491	0.418	0.352	0.491	SUBCLONAL	1	TRUE	1	0.439285611914387	2		364	501	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881359	37881359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375043510	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	194	901	0	ENST00000269571.5:c.2551G>A	p.Val851Met	p.V851M	ENST00000269571		851	Gtg/Atg	21/27	1	2	FACETS	0.718	0.663	0.775	0.718	0.663	0.775	SUBCLONAL	1	TRUE	1	0.439285611914387	2		901	1230	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474456	40474456	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	62	512	0	ENST00000264657.5:c.1945T>C	p.Ser649Pro	p.S649P	ENST00000264657	NM_139276.2	649	Tca/Cca	21/24	1	2	FACETS	0.4	0.345	0.461	0.4	0.345	0.461	SUBCLONAL	1	TRUE	1	0.439285611914387	2		512	705	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40854561	40854561	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138757221	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	110	863	4	ENST00000428826.2:c.2233G>A	p.Asp745Asn	p.D745N	ENST00000428826		745	Gac/Aac	21/21	1	2	FACETS	0.456	0.409	0.507	0.456	0.409	0.507	SUBCLONAL	1	TRUE	1	0.439285611914387	2		867	1098	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40874827	40874827	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	62	497	0	ENST00000428826.2:c.473T>C	p.Val158Ala	p.V158A	ENST00000428826		158	gTc/gCc	6/21	1	2	FACETS	0.398	0.343	0.458	0.398	0.343	0.458	SUBCLONAL	1	TRUE	1	0.439285611914387	2		497	709	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245143	41245143	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	209	752	0	ENST00000357654.3:c.2405T>C	p.Val802Ala	p.V802A	ENST00000357654	NM_007294.3	802	gTg/gCg	10/23	1	2	FACETS	0.974	0.904	1	0.974	0.904	1	CLONAL	1	TRUE	1	0.439285611914387	2		752	977	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245759	41245759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55650082	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	77	553	0	ENST00000357654.3:c.1789G>A	p.Glu597Lys	p.E597K	ENST00000357654	NM_007294.3	597	Gaa/Aaa	10/23	1	2	FACETS	0.471	0.413	0.534	0.471	0.413	0.534	SUBCLONAL	1	TRUE	1	0.439285611914387	2		553	744	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246152	41246152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80356964	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	144	578	0	ENST00000357654.3:c.1396C>T	p.Arg466Trp	p.R466W	ENST00000357654	NM_007294.3	466	Cgg/Tgg	10/23	1	2	FACETS	0.977	0.893	1	0.977	0.893	1	CLONAL	1	TRUE	1	0.439285611914387	2		578	671	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246282	41246282	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	rs80357417	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	60	523	0	ENST00000357654.3:c.1266T>G	p.Tyr422Ter	p.Y422*	ENST00000357654	NM_007294.3	422	taT/taG	10/23	1	2	FACETS	0.416	0.358	0.479	0.416	0.358	0.479	SUBCLONAL	1	TRUE	1	0.439285611914387	2		523	657	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805457	46805457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780164	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	144	1012	0	ENST00000290295.7:c.499G>A	p.Asp167Asn	p.D167N	ENST00000290295	NM_006361.5	167	Gac/Aac	1/2	1	2	FACETS	0.531	0.483	0.582	0.531	0.483	0.582	SUBCLONAL	1	TRUE	1	0.439285611914387	2		1012	1235	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58701067	58701067	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	73	564	0	ENST00000305921.3:c.658G>T	p.Glu220Ter	p.E220*	ENST00000305921	NM_003620.3	220	Gaa/Taa	2/6	1	2	FACETS	0.432	0.377	0.492	0.432	0.377	0.492	SUBCLONAL	1	TRUE	1	0.439285611914387	2		564	769	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740750	58740750	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760201595	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	148	571	0	ENST00000305921.3:c.1655G>A	p.Arg552Gln	p.R552Q	ENST00000305921	NM_003620.3	552	cGa/cAa	6/6	1	2	FACETS	0.964	0.882	1	0.964	0.882	1	CLONAL	1	TRUE	1	0.439285611914387	2		571	699	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770824	59770824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45572934	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	34	344	0	ENST00000259008.2:c.2542C>T	p.Arg848Cys	p.R848C	ENST00000259008	NM_032043.2	848	Cgc/Tgc	18/20	1	2	FACETS	0.333	0.272	0.402	0.333	0.272	0.402	SUBCLONAL	1	TRUE	1	0.439285611914387	2		344	465	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926512	59926512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61757643	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	98	523	1	ENST00000259008.2:c.485G>A	p.Arg162Gln	p.R162Q	ENST00000259008	NM_032043.2	162	cGa/cAa	5/20	1	2	FACETS	0.676	0.604	0.753	0.676	0.604	0.753	SUBCLONAL	1	TRUE	1	0.439285611914387	2		524	660	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926602	59926602	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs753965650	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	97	384	0	ENST00000259008.2:c.395C>A	p.Thr132Asn	p.T132N	ENST00000259008	NM_032043.2	132	aCc/aAc	5/20	1	2	FACETS	0.979	0.878	1	0.979	0.878	1	CLONAL	1	TRUE	1	0.439285611914387	2		384	451	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007580	62007580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778771873	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	127	968	0	ENST00000392795.3:c.287G>A	p.Arg96His	p.R96H	ENST00000392795	NM_001039933.1	96	cGc/cAc	3/6	1	2	FACETS	0.51	0.461	0.563	0.51	0.461	0.563	SUBCLONAL	1	TRUE	1	0.439285611914387	2		968	1133	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511562	66511562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1224297486	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	49	326	0	ENST00000358598.2:c.22G>A	p.Ala8Thr	p.A8T	ENST00000358598	NM_212471.2	8	Gcc/Acc	2/11	1	2	FACETS	0.514	0.436	0.6	0.514	0.436	0.6	SUBCLONAL	1	TRUE	1	0.439285611914387	2		326	434	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66522028	66522028	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768934933	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	38	255	0	ENST00000358598.2:c.683G>A	p.Arg228Gln	p.R228Q	ENST00000358598	NM_212471.2	228	cGa/cAa	7/11	1	2	FACETS	0.499	0.413	0.594	0.499	0.413	0.594	SUBCLONAL	1	TRUE	1	0.439285611914387	2		255	347	SUCCESS
YES1	7525	MSKCC	GRCh37	18	751726	751726	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1010928891	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	36	359	0	ENST00000314574.4:c.350G>T	p.Arg117Ile	p.R117I	ENST00000314574	NM_005433.3	117	aGa/aTa	3/12	1	2	FACETS	0.337	0.277	0.405	0.337	0.277	0.405	SUBCLONAL	1	TRUE	1	0.439285611914387	2		359	486	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375001	45375001	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	96	417	0	ENST00000262160.6:c.842A>G	p.Glu281Gly	p.E281G	ENST00000262160	NM_005901.5	281	gAa/gGa	8/11	0.439285611914387	1	FACETS	0.81	0.726	0.898	0.81	0.726	0.898	CLONAL	1	TRUE	0	0.439285611914387	1		417	421	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56378177	56378177	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	31	365	0	ENST00000348428.3:c.950G>A	p.Cys317Tyr	p.C317Y	ENST00000348428	NM_006785.3	317	tGc/tAc	7/17	0.439285611914387	1	FACETS	0.253	0.204	0.309	0.253	0.204	0.309	SUBCLONAL	1	TRUE	0	0.439285611914387	1		365	435	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208313	5208313	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	238	920	0	ENST00000357368.4:c.5577C>A	p.Phe1859Leu	p.F1859L	ENST00000357368	NM_002850.3	1859	ttC/ttA	36/38	1	2	FACETS	0.943	0.88	1	0.943	0.88	1	CLONAL	1	TRUE	1	0.439285611914387	2		920	1149	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210755	5210755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1157608522	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	275	1000	0	ENST00000357368.4:c.5296C>T	p.Arg1766Cys	p.R1766C	ENST00000357368	NM_002850.3	1766	Cgc/Tgc	34/38	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.439285611914387	2		1000	1200	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220323	5220323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	176	763	0	ENST00000357368.4:c.3497G>A	p.Gly1166Glu	p.G1166E	ENST00000357368	NM_002850.3	1166	gGa/gAa	21/38	1	2	FACETS	0.909	0.837	0.983	0.909	0.837	0.983	CLONAL	1	TRUE	1	0.439285611914387	2		763	882	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244176	5244176	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767048657	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	100	900	0	ENST00000357368.4:c.1306C>T	p.Arg436Trp	p.R436W	ENST00000357368	NM_002850.3	436	Cgg/Tgg	11/38	1	2	FACETS	0.445	0.396	0.497	0.445	0.396	0.497	SUBCLONAL	1	TRUE	1	0.439285611914387	2		900	1023	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244274	5244274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750721878	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	114	1078	1	ENST00000357368.4:c.1208C>T	p.Ser403Leu	p.S403L	ENST00000357368	NM_002850.3	403	tCg/tTg	11/38	1	2	FACETS	0.453	0.407	0.503	0.453	0.407	0.503	SUBCLONAL	1	TRUE	1	0.439285611914387	2		1079	1145	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244392	5244392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377318412	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	130	837	6	ENST00000357368.4:c.1090G>A	p.Val364Ile	p.V364I	ENST00000357368	NM_002850.3	364	Gtc/Atc	11/38	1	2	FACETS	0.529	0.479	0.583	0.529	0.479	0.583	SUBCLONAL	1	TRUE	1	0.439285611914387	2		843	1118	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265204	5265204	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	111	899	1	ENST00000357368.4:c.383A>G	p.Asp128Gly	p.D128G	ENST00000357368	NM_002850.3	128	gAc/gGc	5/38	1	2	FACETS	0.482	0.432	0.535	0.482	0.432	0.535	SUBCLONAL	1	TRUE	1	0.439285611914387	2		900	1048	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251851	10251851	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	164	633	0	ENST00000340748.4:c.3276G>T	p.Lys1092Asn	p.K1092N	ENST00000340748		1092	aaG/aaT	30/40	1	2	FACETS	0.917	0.843	0.995	0.917	0.843	0.995	CLONAL	1	TRUE	1	0.439285611914387	2		633	814	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10267124	10267124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751093624	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	39	553	1	ENST00000340748.4:c.1294G>A	p.Glu432Lys	p.E432K	ENST00000340748		432	Gaa/Aaa	17/40	1	2	FACETS	0.214	0.177	0.257	0.214	0.177	0.257	SUBCLONAL	1	TRUE	1	0.439285611914387	2		554	828	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271691	15271691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1171	309	1222	1	ENST00000263388.2:c.6748G>A	p.Glu2250Lys	p.E2250K	ENST00000263388	NM_000435.2	2250	Gaa/Aaa	33/33	1	2	FACETS	0.951	0.894	1	0.951	0.894	1	CLONAL	1	TRUE	1	0.439285611914387	2		1223	1480	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276621	15276621	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	246	834	2	ENST00000263388.2:c.5644G>A	p.Ala1882Thr	p.A1882T	ENST00000263388	NM_000435.2	1882	Gcc/Acc	30/33	1	2	FACETS	0.952	0.889	1	0.952	0.889	1	CLONAL	1	TRUE	1	0.439285611914387	2		836	1177	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278086	15278086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771041592	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	114	829	0	ENST00000263388.2:c.5336G>A	p.Gly1779Asp	p.G1779D	ENST00000263388	NM_000435.2	1779	gGc/gAc	29/33	1	2	FACETS	0.484	0.435	0.537	0.484	0.435	0.537	SUBCLONAL	1	TRUE	1	0.439285611914387	2		829	1072	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15280911	15280911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766945667	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	114	938	0	ENST00000263388.2:c.5185G>A	p.Ala1729Thr	p.A1729T	ENST00000263388	NM_000435.2	1729	Gcc/Acc	28/33	1	2	FACETS	0.442	0.397	0.49	0.442	0.397	0.49	SUBCLONAL	1	TRUE	1	0.439285611914387	2		938	1174	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946822	17946822	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	116	914	0	ENST00000458235.1:c.1825G>T	p.Asp609Tyr	p.D609Y	ENST00000458235	NM_000215.3	609	Gac/Tac	14/24	1	2	FACETS	0.474	0.426	0.525	0.474	0.426	0.525	SUBCLONAL	1	TRUE	1	0.439285611914387	2		914	1115	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953881	17953881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767865565	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	280	978	0	ENST00000458235.1:c.521C>T	p.Ala174Val	p.A174V	ENST00000458235	NM_000215.3	174	gCg/gTg	5/24	1	2	FACETS	0.947	0.888	1	0.947	0.888	1	CLONAL	1	TRUE	1	0.439285611914387	2		978	1346	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953956	17953956	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774941503	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	303	955	0	ENST00000458235.1:c.446G>A	p.Arg149His	p.R149H	ENST00000458235	NM_000215.3	149	cGc/cAc	5/24	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.439285611914387	2		955	1346	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266888	18266888	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	120	610	0	ENST00000222254.8:c.199C>T	p.Arg67Ter	p.R67*	ENST00000222254	NM_005027.3	67	Cga/Tga	2/16	1	2	FACETS	0.575	0.518	0.635	0.575	0.518	0.635	SUBCLONAL	1	TRUE	1	0.439285611914387	2		610	950	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256823	19256823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1011118409	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	84	553	0	ENST00000162023.5:c.890G>A	p.Arg297Gln	p.R297Q	ENST00000162023		297	cGa/cAa	13/13	1	2	FACETS	0.466	0.411	0.525	0.466	0.411	0.525	SUBCLONAL	1	TRUE	1	0.439285611914387	2		553	821	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260105	19260105	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	228	931	0	ENST00000162023.5:c.188A>G	p.Asp63Gly	p.D63G	ENST00000162023		63	gAc/gGc	7/13	1	2	FACETS	0.794	0.738	0.851	0.794	0.738	0.851	SUBCLONAL	1	TRUE	1	0.439285611914387	2		931	1308	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218825	36218825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777643588	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	268	1040	1	ENST00000222270.7:c.4436C>T	p.Ser1479Leu	p.S1479L	ENST00000222270	NM_014727.1	1479	tCg/tTg	18/37	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.439285611914387	2		1041	1208	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227822	36227822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	145	1025	1	ENST00000222270.7:c.7307G>A	p.Arg2436Lys	p.R2436K	ENST00000222270	NM_014727.1	2436	aGa/aAa	32/37	1	2	FACETS	0.502	0.457	0.55	0.502	0.457	0.55	SUBCLONAL	1	TRUE	1	0.439285611914387	2		1026	1314	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743874	41743874	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	117	906	4	ENST00000301178.4:c.809G>A	p.Gly270Asp	p.G270D	ENST00000301178	NM_021913.4	270	gGc/gAc	7/20	1	2	FACETS	0.499	0.449	0.552	0.499	0.449	0.552	SUBCLONAL	1	TRUE	1	0.439285611914387	2		910	1068	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758825	41758825	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	113	845	3	ENST00000301178.4:c.1879G>T	p.Asp627Tyr	p.D627Y	ENST00000301178	NM_021913.4	627	Gac/Tac	16/20	1	2	FACETS	0.482	0.432	0.534	0.482	0.432	0.534	SUBCLONAL	1	TRUE	1	0.439285611914387	2		848	1068	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794596	42794596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1353503819	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	63	1056	0	ENST00000575354.2:c.1676C>T	p.Ala559Val	p.A559V	ENST00000575354	NM_015125.3	559	gCc/gTc	10/20	1	2	FACETS	0.233	0.201	0.269	0.233	0.201	0.269	SUBCLONAL	1	TRUE	1	0.439285611914387	2		1056	1230	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794719	42794719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs551970875	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	155	992	0	ENST00000575354.2:c.1799G>A	p.Arg600His	p.R600H	ENST00000575354	NM_015125.3	600	cGc/cAc	10/20	1	2	FACETS	0.582	0.531	0.635	0.582	0.531	0.635	SUBCLONAL	1	TRUE	1	0.439285611914387	2		992	1213	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731692	47731692	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	68	377	3	ENST00000449228.1:c.100C>T	p.Arg34Cys	p.R34C	ENST00000449228	NM_001127240.2	34	Cgc/Tgc	2/4	1	2	FACETS	0.519	0.452	0.592	0.519	0.452	0.592	SUBCLONAL	1	TRUE	1	0.439285611914387	2		380	596	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714594	52714594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	92	885	0	ENST00000322088.6:c.352G>A	p.Glu118Lys	p.E118K	ENST00000322088	NM_014225.5	118	Gag/Aag	4/15	1	2	FACETS	0.394	0.349	0.442	0.394	0.349	0.442	SUBCLONAL	1	TRUE	1	0.439285611914387	2		885	1064	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52729220	52729220	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1043254977	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	75	668	1	ENST00000322088.6:c.1756C>A	p.Leu586Met	p.L586M	ENST00000322088	NM_014225.5	586	Ctg/Atg	15/15	1	2	FACETS	0.418	0.366	0.475	0.418	0.366	0.475	SUBCLONAL	1	TRUE	1	0.439285611914387	2		669	816	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982502	25982502	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	45	228	0	ENST00000435504.4:c.788G>T	p.Arg263Ile	p.R263I	ENST00000435504		263	aGa/aTa	9/13	NA	2	FACETS	0.568	0.478	0.666			1	INDETERMINATE	1	TRUE	NA	0.439285611914387	2		228	361	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416302	29416302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	104	796	1	ENST00000389048.3:c.4651C>A	p.Pro1551Thr	p.P1551T	ENST00000389048	NM_004304.4	1551	Ccg/Acg	29/29	NA	2	FACETS	0.474	0.423	0.528			1	INDETERMINATE	1	TRUE	NA	0.439285611914387	2		797	999	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754847	29754847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	66	565	1	ENST00000389048.3:c.1088C>T	p.Ala363Val	p.A363V	ENST00000389048	NM_004304.4	363	gCc/gTc	4/29	NA	2	FACETS	0.492	0.427	0.562			1	INDETERMINATE	1	TRUE	NA	0.439285611914387	2		566	611	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639587	47639587	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	92	322	0	ENST00000233146.2:c.680G>T	p.Arg227Ile	p.R227I	ENST00000233146	NM_000251.2	227	aGa/aTa	4/16	1	2	FACETS	0.995	0.889	1	0.995	0.889	1	CLONAL	1	TRUE	1	0.439285611914387	2		322	421	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705610	47705610	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502005	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	53	318	1	ENST00000233146.2:c.2410G>A	p.Ala804Thr	p.A804T	ENST00000233146	NM_000251.2	804	Gca/Aca	14/16	1	2	FACETS	0.551	0.471	0.639	0.551	0.471	0.639	SUBCLONAL	1	TRUE	1	0.439285611914387	2		319	438	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027712	48027712	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	39	274	0	ENST00000234420.5:c.2590G>T	p.Gly864Ter	p.G864*	ENST00000234420	NM_000179.2	864	Gga/Tga	4/10	1	2	FACETS	0.507	0.421	0.603	0.507	0.421	0.603	SUBCLONAL	1	TRUE	1	0.439285611914387	2		274	350	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028161	48028161	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1060502920	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	27	333	0	ENST00000234420.5:c.3039G>T	p.Lys1013Asn	p.K1013N	ENST00000234420	NM_000179.2	1013	aaG/aaT	4/10	1	2	FACETS	0.286	0.227	0.353	0.286	0.227	0.353	SUBCLONAL	1	TRUE	1	0.439285611914387	2		333	430	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118821	61118821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146326268	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	25	169	1	ENST00000295025.8:c.14C>T	p.Ala5Val	p.A5V	ENST00000295025	NM_002908.2	5	gCg/gTg	2/11	1	2	FACETS	0.566	0.449	0.699	0.566	0.449	0.699	SUBCLONAL	1	TRUE	1	0.439285611914387	2		170	201	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145357	61145357	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	26	278	0	ENST00000295025.8:c.567T>A	p.Cys189Ter	p.C189*	ENST00000295025	NM_002908.2	189	tgT/tgA	6/11	1	2	FACETS	0.279	0.22	0.346	0.279	0.22	0.346	SUBCLONAL	1	TRUE	1	0.439285611914387	2		278	425	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149129	61149129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144119768	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	57	370	0	ENST00000295025.8:c.1319C>T	p.Ser440Leu	p.S440L	ENST00000295025	NM_002908.2	440	tCg/tTg	11/11	1	2	FACETS	0.465	0.399	0.537	0.465	0.399	0.537	SUBCLONAL	1	TRUE	1	0.439285611914387	2		370	558	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715351	61715351	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	92	647	0	ENST00000401558.2:c.2262A>C	p.Glu754Asp	p.E754D	ENST00000401558	NM_003400.3	754	gaA/gaC	19/25	1	2	FACETS	0.492	0.436	0.551	0.492	0.436	0.551	SUBCLONAL	1	TRUE	1	0.439285611914387	2		647	852	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719307	61719307	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	32	345	1	ENST00000401558.2:c.1750G>A	p.Ala584Thr	p.A584T	ENST00000401558	NM_003400.3	584	Gct/Act	16/25	1	2	FACETS	0.3	0.243	0.364	0.3	0.243	0.364	SUBCLONAL	1	TRUE	1	0.439285611914387	2		346	486	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61720085	61720085	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	119	324	0	ENST00000401558.2:c.1349C>A	p.Ser450Tyr	p.S450Y	ENST00000401558	NM_003400.3	450	tCc/tAc	13/25	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.439285611914387	2		324	423	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724120	61724120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781425578	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	49	277	0	ENST00000401558.2:c.782G>A	p.Arg261Gln	p.R261Q	ENST00000401558	NM_003400.3	261	cGa/cAa	10/25	1	2	FACETS	0.556	0.472	0.648	0.556	0.472	0.648	SUBCLONAL	1	TRUE	1	0.439285611914387	2		277	401	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920736	96920736	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	67	346	0	ENST00000258439.3:c.245-1G>A		p.X82_splice	ENST00000258439	NM_001193304.2	82			1	2	FACETS	0.61	0.531	0.695	0.61	0.531	0.695	SUBCLONAL	1	TRUE	1	0.439285611914387	2		346	500	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160452	99160452	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777449349	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	60	504	0	ENST00000074304.5:c.931G>A	p.Asp311Asn	p.D311N	ENST00000074304	NM_001134224.1	311	Gac/Aac	11/26	1	2	FACETS	0.45	0.387	0.518	0.45	0.387	0.518	SUBCLONAL	1	TRUE	1	0.439285611914387	2		504	607	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182493	99182493	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs375661517	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	97	710	1	ENST00000074304.5:c.2296G>A	p.Asp766Asn	p.D766N	ENST00000074304	NM_001134224.1	766	Gac/Aac	22/26	1	2	FACETS	0.464	0.413	0.519	0.464	0.413	0.519	SUBCLONAL	1	TRUE	1	0.439285611914387	2		711	951	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189367	99189367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	79	685	0	ENST00000074304.5:c.2623G>A	p.Asp875Asn	p.D875N	ENST00000074304	NM_001134224.1	875	Gac/Aac	24/26	1	2	FACETS	0.395	0.347	0.448	0.395	0.347	0.448	SUBCLONAL	1	TRUE	1	0.439285611914387	2		685	910	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038082	128038082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367552856	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	137	451	0	ENST00000285398.2:c.1468G>A	p.Glu490Lys	p.E490K	ENST00000285398	NM_000122.1	490	Gaa/Aaa	9/15	1	2	FACETS	0.955	0.871	1	0.955	0.871	1	CLONAL	1	TRUE	1	0.439285611914387	2		451	653	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872738	136872738	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	55	430	0	ENST00000241393.3:c.760C>T	p.Pro254Ser	p.P254S	ENST00000241393	NM_003467.2	254	Cct/Tct	2/2	1	2	FACETS	0.418	0.357	0.485	0.418	0.357	0.485	SUBCLONAL	1	TRUE	1	0.439285611914387	2		430	599	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738327	190738327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	63	249	0	ENST00000441310.2:c.2579G>A	p.Arg860Lys	p.R860K	ENST00000441310	NM_000534.4	860	aGa/aAa	12/13	1	2	FACETS	0.714	0.619	0.815	0.714	0.619	0.815	SUBCLONAL	1	TRUE	1	0.439285611914387	2		249	402	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149662	202149662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	105	508	0	ENST00000358485.4:c.1103G>A	p.Cys368Tyr	p.C368Y	ENST00000358485	NM_001080125.1	368	tGc/tAc	8/9	1	2	FACETS	0.817	0.734	0.905	0.817	0.734	0.905	CLONAL	1	TRUE	1	0.439285611914387	2		508	585	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150013	202150013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	84	659	0	ENST00000358485.4:c.1454G>A	p.Cys485Tyr	p.C485Y	ENST00000358485	NM_001080125.1	485	tGc/tAc	8/9	1	2	FACETS	0.419	0.369	0.473	0.419	0.369	0.473	SUBCLONAL	1	TRUE	1	0.439285611914387	2		659	913	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737441	204737441	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	58	283	0	ENST00000302823.3:c.578G>T	p.Arg193Ile	p.R193I	ENST00000302823	NM_005214.4	193	aGa/aTa	4/4	1	2	FACETS	0.716	0.618	0.822	0.716	0.618	0.822	SUBCLONAL	1	TRUE	1	0.439285611914387	2		283	369	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	70	229	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.903	0.792	1	0.903	0.792	1	CLONAL	1	TRUE	1	0.439285611914387	2		229	353	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578365	212578365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	83	259	0	ENST00000342788.4:c.892G>A	p.Val298Met	p.V298M	ENST00000342788	NM_005235.2	298	Gtg/Atg	8/28	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.439285611914387	2		259	326	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989562	212989562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755026855	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	53	366	0	ENST00000342788.4:c.149G>A	p.Arg50His	p.R50H	ENST00000342788	NM_005235.2	50	cGc/cAc	2/28	1	2	FACETS	0.55	0.469	0.637	0.55	0.469	0.637	SUBCLONAL	1	TRUE	1	0.439285611914387	2		366	439	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645983	215645984	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1559425604	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	52	435	0	ENST00000260947.4:c.614dup	p.Gln206AlafsTer8	p.Q206Afs*8	ENST00000260947	NM_000465.2	205	aag/aaAg	4/11	1	2	FACETS	0.417	0.354	0.485	0.417	0.354	0.485	SUBCLONAL	1	TRUE	1	0.439285611914387	2		435	568	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646149	215646149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881412	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	100	434	0	ENST00000260947.4:c.449G>A	p.Arg150Gln	p.R150Q	ENST00000260947	NM_000465.2	150	cGa/cAa	4/11	1	2	FACETS	0.817	0.732	0.907	0.817	0.732	0.907	CLONAL	1	TRUE	1	0.439285611914387	2		434	557	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646178	215646178	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs758749603	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	60	342	0	ENST00000260947.4:c.420G>T	p.Lys140Asn	p.K140N	ENST00000260947	NM_000465.2	140	aaG/aaT	4/11	1	2	FACETS	0.644	0.557	0.739	0.644	0.557	0.739	SUBCLONAL	1	TRUE	1	0.439285611914387	2		342	424	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657050	215657050	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781591	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	60	340	0	ENST00000260947.4:c.335G>A	p.Arg112Gln	p.R112Q	ENST00000260947	NM_000465.2	112	cGa/cAa	3/11	1	2	FACETS	0.502	0.433	0.578	0.502	0.433	0.578	SUBCLONAL	1	TRUE	1	0.439285611914387	2		340	544	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225338988	225338988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759758641	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	35	335	0	ENST00000264414.4:c.2281C>T	p.Arg761Cys	p.R761C	ENST00000264414	NM_003590.4	761	Cgc/Tgc	16/16	1	2	FACETS	0.296	0.242	0.356	0.296	0.242	0.356	SUBCLONAL	1	TRUE	1	0.439285611914387	2		335	539	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346699	225346699	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	125	413	0	ENST00000264414.4:c.1939G>T	p.Glu647Ter	p.E647*	ENST00000264414	NM_003590.4	647	Gaa/Taa	14/16	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.439285611914387	2		413	550	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546673	9546673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	37	440	0	ENST00000353224.5:c.1349C>T	p.Ala450Val	p.A450V	ENST00000353224	NM_177990.2	450	gCc/gTc	5/10	1	2	FACETS	0.294	0.242	0.353	0.294	0.242	0.353	SUBCLONAL	1	TRUE	1	0.439285611914387	2		440	573	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561195	9561195	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	45	424	0	ENST00000353224.5:c.587C>T	p.Ser196Phe	p.S196F	ENST00000353224	NM_177990.2	196	tCt/tTt	4/10	1	2	FACETS	0.402	0.337	0.473	0.402	0.337	0.473	SUBCLONAL	1	TRUE	1	0.439285611914387	2		424	510	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023958	31023958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555465153	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	75	699	0	ENST00000375687.4:c.3443G>A	p.Arg1148His	p.R1148H	ENST00000375687	NM_015338.5	1148	cGc/cAc	13/13	1	2	FACETS	0.446	0.39	0.506	0.446	0.39	0.506	SUBCLONAL	1	TRUE	1	0.439285611914387	2		699	766	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733276	40733276	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	75	579	0	ENST00000373198.4:c.3530C>A	p.Ser1177Tyr	p.S1177Y	ENST00000373198	NM_133170.3	1177	tCt/tAt	26/32	0.439285611914387	1	FACETS	0.376	0.329	0.427	0.376	0.329	0.427	SUBCLONAL	1	TRUE	0	0.439285611914387	1		579	708	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739040	40739040	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	72	670	0	ENST00000373198.4:c.3244C>A	p.Leu1082Met	p.L1082M	ENST00000373198	NM_133170.3	1082	Ctg/Atg	24/32	0.439285611914387	1	FACETS	0.335	0.292	0.382	0.335	0.292	0.382	SUBCLONAL	1	TRUE	0	0.439285611914387	1		670	763	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748583	40748583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444440253	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	52	378	1	ENST00000373198.4:c.2933C>T	p.Ala978Val	p.A978V	ENST00000373198	NM_133170.3	978	gCg/gTg	21/32	0.439285611914387	1	FACETS	0.316	0.268	0.368	0.316	0.268	0.368	SUBCLONAL	1	TRUE	0	0.439285611914387	1		379	585	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980918	40980918	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	28	422	0	ENST00000373198.4:c.1568A>G	p.Tyr523Cys	p.Y523C	ENST00000373198	NM_133170.3	523	tAc/tGc	10/32	0.439285611914387	1	FACETS	0.201	0.16	0.248	0.201	0.16	0.248	SUBCLONAL	1	TRUE	0	0.439285611914387	1		422	495	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256758	46256758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	94	347	1	ENST00000371998.3:c.814G>A	p.Asp272Asn	p.D272N	ENST00000371998		272	Gat/Aat	8/23	1	2	FACETS	0.793	0.707	0.883	0.793	0.707	0.883	SUBCLONAL	1	TRUE	1	0.439285611914387	2		348	540	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265474	46265474	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	19	178	0	ENST00000371998.3:c.2344G>T	p.Asp782Tyr	p.D782Y	ENST00000371998		782	Gac/Tac	12/23	1	2	FACETS	0.42	0.32	0.537	0.42	0.32	0.537	SUBCLONAL	1	TRUE	1	0.439285611914387	2		178	206	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319945	62319945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	123	895	0	ENST00000360203.5:c.1787G>A	p.Gly596Asp	p.G596D	ENST00000360203	NM_001283009.1	596	gGc/gAc	21/35	1	2	FACETS	0.482	0.434	0.532	0.482	0.434	0.532	SUBCLONAL	1	TRUE	1	0.439285611914387	2		895	1163	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755516	39755516	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	105	497	0	ENST00000288319.7:c.1249T>C	p.Tyr417His	p.Y417H	ENST00000288319	NM_182918.3	417	Tac/Cac	10/10	1	2	FACETS	0.733	0.658	0.813	0.733	0.658	0.813	SUBCLONAL	1	TRUE	1	0.439285611914387	2		497	652	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651216	45651216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200793282	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	108	731	1	ENST00000407780.3:c.809C>T	p.Ala270Val	p.A270V	ENST00000407780	NM_001283052.1	270	gCg/gTg	5/7	0.181383126436247	3	FACETS	0.601	0.538	0.668	0.2	0.179	0.223	INDETERMINATE	1	TRUE	0	0.439285611914387	3		732	998	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655166	45655166	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	157	547	0	ENST00000407780.3:c.686G>A	p.Gly229Asp	p.G229D	ENST00000407780	NM_001283052.1	229	gGc/gAc	4/7	0.181383126436247	3	FACETS	1	0.972	1	0.378	0.346	0.411	INDETERMINATE	1	TRUE	0	0.439285611914387	3		547	769	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070911	30070911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	94	761	0	ENST00000338641.4:c.1427C>T	p.Ala476Val	p.A476V	ENST00000338641	NM_000268.3	476	gCc/gTc	13/16	1	2	FACETS	0.464	0.412	0.519	0.464	0.412	0.519	SUBCLONAL	1	TRUE	1	0.439285611914387	2		761	923	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536164	41536164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750740148	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	164	429	0	ENST00000263253.7:c.1781C>T	p.Thr594Met	p.T594M	ENST00000263253	NM_001429.3	594	aCg/aTg	9/31	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.439285611914387	2		429	744	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545897	41545897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1215000818	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	143	925	0	ENST00000263253.7:c.2512C>T	p.Arg838Cys	p.R838C	ENST00000263253	NM_001429.3	838	Cgt/Tgt	14/31	1	2	FACETS	0.518	0.471	0.568	0.518	0.471	0.568	SUBCLONAL	1	TRUE	1	0.439285611914387	2		925	1256	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41558740	41558740	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866430850	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	83	301	0	ENST00000263253.7:c.3685G>A	p.Glu1229Lys	p.E1229K	ENST00000263253	NM_001429.3	1229	Gaa/Aaa	21/31	1	2	FACETS	0.933	0.828	1	0.933	0.828	1	CLONAL	1	TRUE	1	0.439285611914387	2		301	405	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458537	12458537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140204299	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	193	662	1	ENST00000287820.6:c.1154G>A	p.Arg385Gln	p.R385Q	ENST00000287820	NM_015869.4	385	cGa/cAa	6/7	1	2	FACETS	0.912	0.843	0.982	0.912	0.843	0.982	CLONAL	1	TRUE	1	0.439285611914387	2		663	964	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050378	37050378	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	99	282	0	ENST00000231790.2:c.527T>G	p.Ile176Ser	p.I176S	ENST00000231790	NM_000249.3	176	aTt/aGt	6/19	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.439285611914387	2		282	395	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182052	38182052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1190702008	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	72	558	1	ENST00000396334.3:c.676G>A	p.Glu226Lys	p.E226K	ENST00000396334	NM_002468.4	226	Gaa/Aaa	3/5	1	2	FACETS	0.452	0.394	0.514	0.452	0.394	0.514	SUBCLONAL	1	TRUE	1	0.439285611914387	2		559	726	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267063	41267063	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	70	320	0	ENST00000349496.5:c.734G>A	p.Gly245Asp	p.G245D	ENST00000349496	NM_001904.3	245	gGt/gAt	5/15	1	2	FACETS	0.648	0.566	0.736	0.648	0.566	0.736	SUBCLONAL	1	TRUE	1	0.439285611914387	2		320	492	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268762	41268762	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1245266458	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	40	386	1	ENST00000349496.5:c.1000G>A	p.Glu334Lys	p.E334K	ENST00000349496	NM_001904.3	334	Gaa/Aaa	7/15	1	2	FACETS	0.36	0.299	0.428	0.36	0.299	0.428	SUBCLONAL	1	TRUE	1	0.439285611914387	2		387	506	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275360	41275360	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs878960699	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	120	303	0	ENST00000349496.5:c.1524+2T>C		p.X508_splice	ENST00000349496	NM_001904.3	508			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.439285611914387	2		303	377	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47061277	47061277	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	186	428	0	ENST00000409792.3:c.7404G>T	p.Lys2468Asn	p.K2468N	ENST00000409792	NM_014159.6	2468	aaG/aaT	19/21	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.439285611914387	2		428	579	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144880	47144880	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	50	392	0	ENST00000409792.3:c.4873C>T	p.Arg1625Cys	p.R1625C	ENST00000409792	NM_014159.6	1625	Cgt/Tgt	7/21	1	2	FACETS	0.399	0.338	0.466	0.399	0.338	0.466	SUBCLONAL	1	TRUE	1	0.439285611914387	2		392	570	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161973	47161973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs912983850	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	48	328	0	ENST00000409792.3:c.4153G>A	p.Glu1385Lys	p.E1385K	ENST00000409792	NM_014159.6	1385	Gaa/Aaa	3/21	1	2	FACETS	0.514	0.435	0.601	0.514	0.435	0.601	SUBCLONAL	1	TRUE	1	0.439285611914387	2		328	425	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442502	52442502	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	43	447	0	ENST00000460680.1:c.243C>A	p.Phe81Leu	p.F81L	ENST00000460680	NM_004656.3	81	ttC/ttA	4/17	1	2	FACETS	0.345	0.288	0.408	0.345	0.288	0.408	SUBCLONAL	1	TRUE	1	0.439285611914387	2		447	568	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643399	52643399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146395938	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	62	430	0	ENST00000394830.3:c.2497C>T	p.Arg833Cys	p.R833C	ENST00000394830	NM_018313.4	833	Cgc/Tgc	17/30	1	2	FACETS	0.472	0.408	0.542	0.472	0.408	0.542	SUBCLONAL	1	TRUE	1	0.439285611914387	2		430	598	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008432	70008432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1195515853	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	32	249	0	ENST00000394351.3:c.719G>A	p.Arg240His	p.R240H	ENST00000394351	NM_000248.3	240	cGc/cAc	8/9	1	2	FACETS	0.463	0.376	0.56	0.463	0.376	0.56	SUBCLONAL	1	TRUE	1	0.439285611914387	2		249	315	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014359	70014359	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	166	668	0	ENST00000394351.3:c.1220G>T	p.Arg407Met	p.R407M	ENST00000394351	NM_000248.3	407	aGg/aTg	9/9	1	2	FACETS	0.906	0.833	0.982	0.906	0.833	0.982	CLONAL	1	TRUE	1	0.439285611914387	2		668	834	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026984	71026984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763413735	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	81	491	1	ENST00000318789.4:c.1343C>T	p.Ser448Leu	p.S448L	ENST00000318789	NM_032682.5	448	tCg/tTg	15/21	1	2	FACETS	0.538	0.474	0.607	0.538	0.474	0.607	SUBCLONAL	1	TRUE	1	0.439285611914387	2		492	685	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799734	72799734	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	155	622	0	ENST00000325599.8:c.1435G>T	p.Glu479Ter	p.E479*	ENST00000325599	NM_018130.2	479	Gaa/Taa	11/11	1	2	FACETS	0.92	0.844	1	0.92	0.844	1	CLONAL	1	TRUE	1	0.439285611914387	2		622	767	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72866502	72866502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757958098	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	32	282	0	ENST00000325599.8:c.761G>A	p.Arg254Gln	p.R254Q	ENST00000325599	NM_018130.2	254	cGa/cAa	7/11	1	2	FACETS	0.356	0.289	0.432	0.356	0.289	0.432	SUBCLONAL	1	TRUE	1	0.439285611914387	2		282	409	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259653	89259653	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	14	245	0	ENST00000336596.2:c.797G>T	p.Arg266Ile	p.R266I	ENST00000336596	NM_005233.5	266	aGa/aTa	3/17	1	2	FACETS	0.228	0.165	0.306	0.228	0.165	0.306	SUBCLONAL	1	TRUE	1	0.439285611914387	2		245	279	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390138	89390138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	81	315	1	ENST00000336596.2:c.887C>T	p.Thr296Ile	p.T296I	ENST00000336596	NM_005233.5	296	aCt/aTt	4/17	1	2	FACETS	0.805	0.712	0.904	0.805	0.712	0.904	CLONAL	1	TRUE	1	0.439285611914387	2		316	458	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390923	89390923	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1559654048	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	34	335	0	ENST00000336596.2:c.989G>T	p.Arg330Ile	p.R330I	ENST00000336596	NM_005233.5	330	aGa/aTa	5/17	1	2	FACETS	0.394	0.322	0.475	0.394	0.322	0.475	SUBCLONAL	1	TRUE	1	0.439285611914387	2		335	393	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462381	89462381	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	86	535	1	ENST00000336596.2:c.1853C>T	p.Ala618Val	p.A618V	ENST00000336596	NM_005233.5	618	gCc/gTc	10/17	1	2	FACETS	0.617	0.546	0.692	0.617	0.546	0.692	SUBCLONAL	1	TRUE	1	0.439285611914387	2		536	635	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499366	89499366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142030914	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	120	418	0	ENST00000336596.2:c.2536C>T	p.Pro846Ser	p.P846S	ENST00000336596	NM_005233.5	846	Ccc/Tcc	15/17	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.439285611914387	2		418	515	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631596	119631596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	86	350	0	ENST00000316626.5:c.670G>A	p.Ala224Thr	p.A224T	ENST00000316626		224	Gca/Aca	6/12	1	2	FACETS	0.814	0.723	0.911	0.814	0.723	0.911	CLONAL	1	TRUE	1	0.439285611914387	2		350	481	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134514513	134514513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758299791	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	160	678	0	ENST00000398015.3:c.40G>A	p.Ala14Thr	p.A14T	ENST00000398015	NM_004441.4	14	Gca/Aca	1/16	1	2	FACETS	0.871	0.799	0.946	0.871	0.799	0.946	CLONAL	1	TRUE	1	0.439285611914387	2		678	836	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138409963	138409963	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	53	283	0	ENST00000289153.2:c.1915C>A	p.Leu639Ile	p.L639I	ENST00000289153	NM_006219.2	639	Ctt/Att	13/22	1	2	FACETS	0.676	0.579	0.781	0.676	0.579	0.781	SUBCLONAL	1	TRUE	1	0.439285611914387	2		283	357	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474703	138474703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1467994756	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	53	457	0	ENST00000289153.2:c.290G>A	p.Arg97Gln	p.R97Q	ENST00000289153	NM_006219.2	97	cGa/cAa	2/22	1	2	FACETS	0.411	0.35	0.478	0.411	0.35	0.478	SUBCLONAL	1	TRUE	1	0.439285611914387	2		457	587	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474772	138474772	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs757588885	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	49	398	0	ENST00000289153.2:c.221A>G	p.Asp74Gly	p.D74G	ENST00000289153	NM_006219.2	74	gAt/gGt	2/22	1	2	FACETS	0.426	0.36	0.498	0.426	0.36	0.498	SUBCLONAL	1	TRUE	1	0.439285611914387	2		398	524	SUCCESS
ATR	545	MSKCC	GRCh37	3	142189026	142189026	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	33	235	0	ENST00000350721.4:c.6222-1G>T		p.X2074_splice	ENST00000350721	NM_001184.3	2074			1	2	FACETS	0.496	0.405	0.598	0.496	0.405	0.598	SUBCLONAL	1	TRUE	1	0.439285611914387	2		235	303	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272744	142272744	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	59	465	0	ENST00000350721.4:c.2455G>A	p.Asp819Asn	p.D819N	ENST00000350721	NM_001184.3	819	Gat/Aat	11/47	1	2	FACETS	0.382	0.328	0.441	0.382	0.328	0.441	SUBCLONAL	1	TRUE	1	0.439285611914387	2		465	704	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281507	142281507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	181	552	0	ENST00000350721.4:c.737C>T	p.Ser246Phe	p.S246F	ENST00000350721	NM_001184.3	246	tCc/tTc	4/47	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.439285611914387	2		552	796	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281802	142281802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	59	440	0	ENST00000350721.4:c.442G>A	p.Glu148Lys	p.E148K	ENST00000350721	NM_001184.3	148	Gaa/Aaa	4/47	1	2	FACETS	0.452	0.389	0.521	0.452	0.389	0.521	SUBCLONAL	1	TRUE	1	0.439285611914387	2		440	594	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260151	149260151	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1307297959	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	247	617	1	ENST00000360632.3:c.742C>T	p.Arg248Ter	p.R248*	ENST00000360632	NM_015472.4	248	Cga/Tga	4/7	1	2	FACETS	0.817	0.768	0.867	1	0.994	1	CLONAL	2	TRUE	1	0.439285611914387	2		618	688	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374688	149374688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	284	805	0	ENST00000360632.3:c.406G>A	p.Ala136Thr	p.A136T	ENST00000360632	NM_015472.4	136	Gcc/Acc	2/7	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.439285611914387	2		805	1184	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	52	447	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.359	0.305	0.418	0.359	0.305	0.418	SUBCLONAL	1	TRUE	1	0.439285611914387	2		447	660	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	75	374	0	ENST00000263967.3:c.333G>T	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaT	2/21	1	2	FACETS	0.825	0.726	0.93	0.825	0.726	0.93	CLONAL	1	TRUE	1	0.439285611914387	2		374	414	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951989	178951989	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	61	337	0	ENST00000263967.3:c.3044C>A	p.Ser1015Tyr	p.S1015Y	ENST00000263967	NM_006218.2	1015	tCt/tAt	21/21	1	2	FACETS	0.548	0.473	0.629	0.548	0.473	0.629	SUBCLONAL	1	TRUE	1	0.439285611914387	2		337	507	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182679136	182679136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202126248	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	34	341	0	ENST00000292782.4:c.398G>A	p.Ser133Asn	p.S133N	ENST00000292782	NM_020640.2	133	aGc/aAc	4/7	1	2	FACETS	0.284	0.231	0.343	0.284	0.231	0.343	SUBCLONAL	1	TRUE	1	0.439285611914387	2		341	545	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504384	186504384	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	37	345	0	ENST00000323963.5:c.721G>A	p.Glu241Lys	p.E241K	ENST00000323963		241	Gaa/Aaa	7/11	1	2	FACETS	0.338	0.278	0.405	0.338	0.278	0.405	SUBCLONAL	1	TRUE	1	0.439285611914387	2		345	499	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443345	187443345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	61	347	1	ENST00000232014.4:c.1781G>A	p.Arg594Gln	p.R594Q	ENST00000232014	NM_001130845.1	594	cGa/cAa	8/10	1	2	FACETS	0.445	0.384	0.512	0.445	0.384	0.512	SUBCLONAL	1	TRUE	1	0.439285611914387	2		348	624	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447195	187447195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	188	757	0	ENST00000232014.4:c.998G>A	p.Ser333Asn	p.S333N	ENST00000232014	NM_001130845.1	333	aGc/aAc	5/10	1	2	FACETS	0.815	0.753	0.88	0.815	0.753	0.88	CLONAL	1	TRUE	1	0.439285611914387	2		757	1050	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806668	1806668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771872811	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	143	1099	0	ENST00000260795.2:c.1384G>A	p.Asp462Asn	p.D462N	ENST00000260795		462	Gac/Aac	9/17	1	2	FACETS	0.493	0.448	0.541	0.493	0.448	0.541	SUBCLONAL	1	TRUE	1	0.439285611914387	2		1099	1320	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1919941	1919941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	206	672	1	ENST00000382891.5:c.1001G>A	p.Ser334Asn	p.S334N	ENST00000382891	NM_133335.3	334	aGc/aAc	5/22	1	2	FACETS	0.932	0.865	1	0.932	0.865	1	CLONAL	1	TRUE	1	0.439285611914387	2		673	1006	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1977026	1977026	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	50	761	0	ENST00000382891.5:c.3520G>A	p.Glu1174Lys	p.E1174K	ENST00000382891	NM_133335.3	1174	Gag/Aag	20/22	1	2	FACETS	0.237	0.2	0.278	0.237	0.2	0.278	SUBCLONAL	1	TRUE	1	0.439285611914387	2		761	959	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747895	41747895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	148	618	3	ENST00000226382.2:c.874G>A	p.Ala292Thr	p.A292T	ENST00000226382	NM_003924.3	292	Gcc/Acc	3/3	1	2	FACETS	0.848	0.775	0.924	0.848	0.775	0.924	CLONAL	1	TRUE	1	0.439285611914387	2		621	795	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748173	41748173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	94	690	0	ENST00000226382.2:c.596G>A	p.Gly199Asp	p.G199D	ENST00000226382	NM_003924.3	199	gGt/gAt	3/3	1	2	FACETS	0.505	0.448	0.565	0.505	0.448	0.565	SUBCLONAL	1	TRUE	1	0.439285611914387	2		690	848	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749376	41749376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	87	362	0	ENST00000226382.2:c.419C>T	p.Ala140Val	p.A140V	ENST00000226382	NM_003924.3	140	gCg/gTg	2/3	1	2	FACETS	0.902	0.803	1	0.902	0.803	1	CLONAL	1	TRUE	1	0.439285611914387	2		362	439	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139837	55139837	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	153	526	3	ENST00000257290.5:c.1498C>T	p.Arg500Ter	p.R500*	ENST00000257290	NM_006206.4	500	Cga/Tga	10/23	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.439285611914387	2		529	662	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144084	55144084	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	121	454	0	ENST00000257290.5:c.1913A>C	p.Lys638Thr	p.K638T	ENST00000257290	NM_006206.4	638	aAa/aCa	14/23	1	2	FACETS	0.935	0.848	1	0.935	0.848	1	CLONAL	1	TRUE	1	0.439285611914387	2		454	589	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156696	55156696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	109	438	0	ENST00000257290.5:c.3097G>A	p.Asp1033Asn	p.D1033N	ENST00000257290	NM_006206.4	1033	Gac/Aac	22/23	1	2	FACETS	0.862	0.776	0.952	0.862	0.776	0.952	CLONAL	1	TRUE	1	0.439285611914387	2		438	576	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565811	55565811	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	69	424	0	ENST00000288135.5:c.635C>A	p.Pro212His	p.P212H	ENST00000288135	NM_000222.2	212	cCt/cAt	4/21	1	2	FACETS	0.502	0.437	0.572	0.502	0.437	0.572	SUBCLONAL	1	TRUE	1	0.439285611914387	2		424	626	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589771	55589771	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	91	392	1	ENST00000288135.5:c.1253A>G	p.Tyr418Cys	p.Y418C	ENST00000288135	NM_000222.2	418	tAc/tGc	8/21	1	2	FACETS	0.847	0.755	0.945	0.847	0.755	0.945	CLONAL	1	TRUE	1	0.439285611914387	2		393	489	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955545	55955545	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	58	411	0	ENST00000263923.4:c.3400G>T	p.Glu1134Ter	p.E1134*	ENST00000263923	NM_002253.2	1134	Gaa/Taa	25/30	1	2	FACETS	0.557	0.479	0.642	0.557	0.479	0.642	SUBCLONAL	1	TRUE	1	0.439285611914387	2		411	474	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961109	55961109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374755237	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	93	740	0	ENST00000263923.4:c.2831G>A	p.Arg944Gln	p.R944Q	ENST00000263923	NM_002253.2	944	cGa/cAa	21/30	1	2	FACETS	0.496	0.441	0.556	0.496	0.441	0.556	SUBCLONAL	1	TRUE	1	0.439285611914387	2		740	853	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964370	55964370	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	105	552	0	ENST00000263923.4:c.2443G>T	p.Glu815Ter	p.E815*	ENST00000263923	NM_002253.2	815	Gaa/Taa	17/30	1	2	FACETS	0.712	0.639	0.79	0.712	0.639	0.79	SUBCLONAL	1	TRUE	1	0.439285611914387	2		552	671	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968610	55968610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374980446	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	89	698	0	ENST00000263923.4:c.2053G>A	p.Glu685Lys	p.E685K	ENST00000263923	NM_002253.2	685	Gaa/Aaa	14/30	1	2	FACETS	0.456	0.404	0.513	0.456	0.404	0.513	SUBCLONAL	1	TRUE	1	0.439285611914387	2		698	888	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970948	55970948	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	66	572	0	ENST00000263923.4:c.1849T>A	p.Phe617Ile	p.F617I	ENST00000263923	NM_002253.2	617	Ttc/Atc	13/30	1	2	FACETS	0.429	0.371	0.491	0.429	0.371	0.491	SUBCLONAL	1	TRUE	1	0.439285611914387	2		572	701	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981572	55981572	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	36	218	0	ENST00000263923.4:c.365G>T	p.Arg122Ile	p.R122I	ENST00000263923	NM_002253.2	122	aGa/aTa	4/30	1	2	FACETS	0.552	0.455	0.659	0.552	0.455	0.659	SUBCLONAL	1	TRUE	1	0.439285611914387	2		218	297	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467838	66467838	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	27	330	0	ENST00000273854.3:c.431T>G	p.Leu144Arg	p.L144R	ENST00000273854	NM_004439.5	144	cTg/cGg	3/18	1	2	FACETS	0.329	0.261	0.406	0.329	0.261	0.406	SUBCLONAL	1	TRUE	1	0.439285611914387	2		330	374	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143226689	143226689	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs149208667	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	43	274	0	ENST00000262992.4:c.425G>A	p.Arg142Gln	p.R142Q	ENST00000262992	NM_001101669.1	142	cGa/cAa	7/24	1	2	FACETS	0.439	0.367	0.518	0.439	0.367	0.518	SUBCLONAL	1	TRUE	1	0.439285611914387	2		274	446	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244184	153244184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759610249	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	56	489	0	ENST00000281708.4:c.1973G>A	p.Arg658Gln	p.R658Q	ENST00000281708	NM_033632.3	658	cGa/cAa	12/12	1	2	FACETS	0.356	0.304	0.412	0.356	0.304	0.412	SUBCLONAL	1	TRUE	1	0.439285611914387	2		489	717	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332915	153332915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200698994	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	46	425	0	ENST00000281708.4:c.41G>A	p.Arg14Gln	p.R14Q	ENST00000281708	NM_033632.3	14	cGa/cAa	2/12	1	2	FACETS	0.392	0.33	0.461	0.392	0.33	0.461	SUBCLONAL	1	TRUE	1	0.439285611914387	2		425	534	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509796	187509796	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777463346	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	65	336	0	ENST00000441802.2:c.13717G>A	p.Glu4573Lys	p.E4573K	ENST00000441802	NM_005245.3	4573	Gaa/Aaa	27/27	1	2	FACETS	0.747	0.651	0.851	0.747	0.651	0.851	SUBCLONAL	1	TRUE	1	0.439285611914387	2		336	396	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518228	187518228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199692977	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	51	418	0	ENST00000441802.2:c.12466G>A	p.Glu4156Lys	p.E4156K	ENST00000441802	NM_005245.3	4156	Gag/Aag	25/27	1	2	FACETS	0.496	0.422	0.577	0.496	0.422	0.577	SUBCLONAL	1	TRUE	1	0.439285611914387	2		418	468	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521187	187521187	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	62	740	1	ENST00000441802.2:c.11968A>C	p.Asn3990His	p.N3990H	ENST00000441802	NM_005245.3	3990	Aac/Cac	22/27	1	2	FACETS	0.333	0.287	0.384	0.333	0.287	0.384	SUBCLONAL	1	TRUE	1	0.439285611914387	2		741	847	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524677	187524677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201075554	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	238	815	0	ENST00000441802.2:c.11003G>A	p.Arg3668Gln	p.R3668Q	ENST00000441802	NM_005245.3	3668	cGg/cAg	19/27	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.439285611914387	2		815	1047	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530342	187530342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	22	266	0	ENST00000441802.2:c.10201G>A	p.Glu3401Lys	p.E3401K	ENST00000441802	NM_005245.3	3401	Gaa/Aaa	16/27	1	2	FACETS	0.249	0.192	0.315	0.249	0.192	0.315	SUBCLONAL	1	TRUE	1	0.439285611914387	2		266	402	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628882	187628882	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	97	610	0	ENST00000441802.2:c.2100G>T	p.Glu700Asp	p.E700D	ENST00000441802	NM_005245.3	700	gaG/gaT	2/27	1	2	FACETS	0.561	0.5	0.626	0.561	0.5	0.626	SUBCLONAL	1	TRUE	1	0.439285611914387	2		610	787	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630114	187630114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561011141	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	160	588	0	ENST00000441802.2:c.868G>A	p.Ala290Thr	p.A290T	ENST00000441802	NM_005245.3	290	Gca/Aca	2/27	1	2	FACETS	0.914	0.839	0.992	0.914	0.839	0.992	CLONAL	1	TRUE	1	0.439285611914387	2		588	797	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228303	228303	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	45	243	0	ENST00000264932.6:c.625C>A	p.Leu209Met	p.L209M	ENST00000264932	NM_004168.2	209	Ctg/Atg	6/15	1	2	FACETS	0.569	0.48	0.667	0.569	0.48	0.667	SUBCLONAL	1	TRUE	1	0.439285611914387	2		243	360	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295210	1295210	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	99	371	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.77	0.689	0.856	0.77	0.689	0.856	SUBCLONAL	1	TRUE	1	0.439285611914387	2		371	585	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31464410	31464410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	94	789	0	ENST00000344624.3:c.2507G>A	p.Arg836Gln	p.R836Q	ENST00000344624		836	cGa/cAa	17/33	1	2	FACETS	0.422	0.375	0.474	0.422	0.375	0.474	SUBCLONAL	1	TRUE	1	0.439285611914387	2		789	1013	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945694	38945694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1175194099	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	31	276	0	ENST00000357387.3:c.4532G>A	p.Gly1511Glu	p.G1511E	ENST00000357387	NM_152756.3	1511	gGa/gAa	34/38	1	2	FACETS	0.401	0.324	0.487	0.401	0.324	0.487	SUBCLONAL	1	TRUE	1	0.439285611914387	2		276	352	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38978694	38978694	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	35	386	0	ENST00000357387.3:c.812G>A	p.Gly271Glu	p.G271E	ENST00000357387	NM_152756.3	271	gGa/gAa	9/38	1	2	FACETS	0.409	0.335	0.491	0.409	0.335	0.491	SUBCLONAL	1	TRUE	1	0.439285611914387	2		386	390	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152566	56152566	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	78	283	0	ENST00000399503.3:c.622C>T	p.Arg208Ter	p.R208*	ENST00000399503	NM_005921.1	208	Cga/Tga	2/20	1	2	FACETS	0.962	0.851	1	0.962	0.851	1	CLONAL	1	TRUE	1	0.439285611914387	2		283	369	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178443	56178443	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	40	255	0	ENST00000399503.3:c.3416C>A	p.Ser1139Tyr	p.S1139Y	ENST00000399503	NM_005921.1	1139	tCt/tAt	14/20	1	2	FACETS	0.484	0.403	0.574	0.484	0.403	0.574	SUBCLONAL	1	TRUE	1	0.439285611914387	2		255	376	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754897	57754897	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	61	283	0	ENST00000274289.3:c.293A>G	p.Glu98Gly	p.E98G	ENST00000274289	NM_006622.3	98	gAg/gGg	2/14	1	2	FACETS	0.745	0.645	0.851	0.745	0.645	0.851	SUBCLONAL	1	TRUE	1	0.439285611914387	2		283	373	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	33	191	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	0.442	0.36	0.533	0.442	0.36	0.533	SUBCLONAL	1	TRUE	1	0.439285611914387	2		191	340	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	35	238	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	0.438	0.359	0.526	0.438	0.359	0.526	SUBCLONAL	1	TRUE	1	0.439285611914387	2		238	364	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79952236	79952236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1445966245	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	39	220	0	ENST00000265081.6:c.244G>A	p.Glu82Lys	p.E82K	ENST00000265081	NM_002439.4	82	Gaa/Aaa	2/24	1	2	FACETS	0.548	0.456	0.65	0.548	0.456	0.65	SUBCLONAL	1	TRUE	1	0.439285611914387	2		220	324	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961018	79961018	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	38	488	0	ENST00000265081.6:c.415G>T	p.Glu139Ter	p.E139*	ENST00000265081	NM_002439.4	139	Gaa/Taa	3/24	1	2	FACETS	0.244	0.201	0.293	0.244	0.201	0.293	SUBCLONAL	1	TRUE	1	0.439285611914387	2		488	708	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79974884	79974884	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	63	424	0	ENST00000265081.6:c.1312G>A	p.Ala438Thr	p.A438T	ENST00000265081	NM_002439.4	438	Gcg/Acg	8/24	1	2	FACETS	0.494	0.427	0.566	0.494	0.427	0.566	SUBCLONAL	1	TRUE	1	0.439285611914387	2		424	581	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064823	80064823	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	24	197	0	ENST00000265081.6:c.2253+1G>A		p.X751_splice	ENST00000265081	NM_002439.4	751			1	2	FACETS	0.446	0.351	0.555	0.446	0.351	0.555	SUBCLONAL	1	TRUE	1	0.439285611914387	2		197	245	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649005	86649005	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	52	263	0	ENST00000274376.6:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000274376	NM_002890.2	429	Gaa/Taa	9/25	1	2	FACETS	0.787	0.674	0.908	0.787	0.674	0.908	CLONAL	1	TRUE	1	0.439285611914387	2		263	301	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	128	248	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.439285611914387	2		248	448	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	90	214	1	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	1	2	FACETS	0.81	0.73	0.892	1	0.984	1	CLONAL	2	TRUE	1	0.439285611914387	2		215	253	SUCCESS
APC	324	MSKCC	GRCh37	5	112178000	112178000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768922431	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	25	374	0	ENST00000257430.4:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000257430	NM_000038.5	2237	Cga/Tga	16/16	1	2	FACETS	0.261	0.205	0.326	0.261	0.205	0.326	SUBCLONAL	1	TRUE	1	0.439285611914387	2		374	436	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911514	131911514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143802516	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	51	344	0	ENST00000265335.6:c.259C>T	p.Arg87Cys	p.R87C	ENST00000265335		87	Cgt/Tgt	3/25	1	2	FACETS	0.472	0.401	0.549	0.472	0.401	0.549	SUBCLONAL	1	TRUE	1	0.439285611914387	2		344	492	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149447843	149447843	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763119382	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	58	927	5	ENST00000286301.3:c.1561G>A	p.Ala521Thr	p.A521T	ENST00000286301	NM_005211.3	521	Gcc/Acc	11/22	1	2	FACETS	0.23	0.197	0.267	0.23	0.197	0.267	SUBCLONAL	1	TRUE	1	0.439285611914387	2		932	1148	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636719	176636719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140095431	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	62	398	0	ENST00000439151.2:c.1319G>A	p.Arg440Gln	p.R440Q	ENST00000439151	NM_022455.4	440	cGa/cAa	5/23	1	2	FACETS	0.455	0.393	0.523	0.455	0.393	0.523	SUBCLONAL	1	TRUE	1	0.439285611914387	2		398	620	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637034	176637034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137993153	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	136	571	0	ENST00000439151.2:c.1634C>T	p.Thr545Met	p.T545M	ENST00000439151	NM_022455.4	545	aCg/aTg	5/23	1	2	FACETS	0.708	0.644	0.776	0.708	0.644	0.776	SUBCLONAL	1	TRUE	1	0.439285611914387	2		571	874	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638875	176638875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137888392	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	301	652	1	ENST00000439151.2:c.3475C>T	p.Arg1159Trp	p.R1159W	ENST00000439151	NM_022455.4	1159	Cgg/Tgg	5/23	1	2	FACETS	0.809	0.765	0.854	1	0.995	1	CLONAL	2	TRUE	1	0.439285611914387	2		653	847	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673790	176673790	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770327039	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	99	372	0	ENST00000439151.2:c.4490G>A	p.Gly1497Asp	p.G1497D	ENST00000439151	NM_022455.4	1497	gGc/gAc	10/23	1	2	FACETS	0.901	0.808	1	0.901	0.808	1	CLONAL	1	TRUE	1	0.439285611914387	2		372	500	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176678848	176678848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764613088	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	29	331	0	ENST00000439151.2:c.4759C>T	p.Arg1587Cys	p.R1587C	ENST00000439151	NM_022455.4	1587	Cgc/Tgc	12/23	1	2	FACETS	0.274	0.22	0.337	0.274	0.22	0.337	SUBCLONAL	1	TRUE	1	0.439285611914387	2		331	481	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687063	176687063	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	104	461	0	ENST00000439151.2:c.5040G>T	p.Lys1680Asn	p.K1680N	ENST00000439151	NM_022455.4	1680	aaG/aaT	14/23	1	2	FACETS	0.635	0.568	0.705	0.635	0.568	0.705	SUBCLONAL	1	TRUE	1	0.439285611914387	2		461	746	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048764	180048764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	100	1123	1	ENST00000261937.6:c.1798G>A	p.Asp600Asn	p.D600N	ENST00000261937	NM_182925.4	600	Gat/Aat	13/30	NA	2	FACETS	0.347	0.309	0.388			1	INDETERMINATE	1	TRUE	NA	0.439285611914387	2		1124	1311	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398855	398855	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	78	605	0	ENST00000380956.4:c.665C>T	p.Ala222Val	p.A222V	ENST00000380956	NM_001195286.1	222	gCt/gTt	6/9	1	2	FACETS	0.49	0.43	0.554	0.49	0.43	0.554	SUBCLONAL	1	TRUE	1	0.439285611914387	2		605	725	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405092	405092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	108	647	0	ENST00000380956.4:c.1174C>T	p.Pro392Ser	p.P392S	ENST00000380956	NM_001195286.1	392	Cca/Tca	8/9	1	2	FACETS	0.595	0.534	0.661	0.595	0.534	0.661	SUBCLONAL	1	TRUE	1	0.439285611914387	2		647	826	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225626	26225626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373685271	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	241	546	0	ENST00000360408.1:c.244G>A	p.Asp82Asn	p.D82N	ENST00000360408	NM_003532.2	82	Gac/Aac	1/1	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.439285611914387	2		546	759	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323362	31323363	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748204482	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	122	399	1	ENST00000412585.2:c.626dup	p.Thr211AspfsTer10	p.T211Dfs*10	ENST00000412585	NM_005514.6	209	cca/ccCa	4/8	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.439285611914387	2		400	519	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165351	32165351	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	140	937	0	ENST00000375023.3:c.4777T>G	p.Ser1593Ala	p.S1593A	ENST00000375023	NM_004557.3	1593	Tca/Gca	27/30	1	2	FACETS	0.525	0.477	0.576	0.525	0.477	0.576	SUBCLONAL	1	TRUE	1	0.439285611914387	2		937	1213	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166770	32166770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs947409717	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	270	954	3	ENST00000375023.3:c.4468C>T	p.Arg1490Trp	p.R1490W	ENST00000375023	NM_004557.3	1490	Cgg/Tgg	24/30	1	2	FACETS	0.958	0.898	1	0.958	0.898	1	CLONAL	1	TRUE	1	0.439285611914387	2		957	1283	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188210	32188210	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	89	770	0	ENST00000375023.3:c.1131C>A	p.Phe377Leu	p.F377L	ENST00000375023	NM_004557.3	377	ttC/ttA	6/30	1	2	FACETS	0.449	0.397	0.505	0.449	0.397	0.505	SUBCLONAL	1	TRUE	1	0.439285611914387	2		770	902	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818836	32818836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1226281975	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	311	704	1	ENST00000354258.4:c.1115G>A	p.Arg372Gln	p.R372Q	ENST00000354258	NM_000593.5	372	cGa/cAa	4/11	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.439285611914387	2		705	999	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64289970	64289970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754493391	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	68	335	0	ENST00000370651.3:c.413G>A	p.Arg138His	p.R138H	ENST00000370651	NM_003463.4	138	cGt/cAt	6/6	1	2	FACETS	0.631	0.55	0.718	0.631	0.55	0.718	SUBCLONAL	1	TRUE	1	0.439285611914387	2		335	491	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955139	93955139	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	56	423	0	ENST00000369303.4:c.2759C>G	p.Pro920Arg	p.P920R	ENST00000369303	NM_004440.3	920	cCt/cGt	16/17	1	2	FACETS	0.52	0.446	0.601	0.52	0.446	0.601	SUBCLONAL	1	TRUE	1	0.439285611914387	2		423	490	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967185	93967185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	74	443	0	ENST00000369303.4:c.2167C>T	p.Leu723Phe	p.L723F	ENST00000369303	NM_004440.3	723	Ctc/Ttc	12/17	1	2	FACETS	0.754	0.662	0.852	0.754	0.662	0.852	SUBCLONAL	1	TRUE	1	0.439285611914387	2		443	447	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93968000	93968000	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	44	338	0	ENST00000369303.4:c.1927G>T	p.Glu643Ter	p.E643*	ENST00000369303	NM_004440.3	643	Gaa/Taa	11/17	1	2	FACETS	0.447	0.375	0.527	0.447	0.375	0.527	SUBCLONAL	1	TRUE	1	0.439285611914387	2		338	448	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974398	93974398	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	37	372	0	ENST00000369303.4:c.1656G>T	p.Gln552His	p.Q552H	ENST00000369303	NM_004440.3	552	caG/caT	8/17	1	2	FACETS	0.413	0.34	0.494	0.413	0.34	0.494	SUBCLONAL	1	TRUE	1	0.439285611914387	2		372	408	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120461	94120461	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	23	319	0	ENST00000369303.4:c.590C>T	p.Ser197Phe	p.S197F	ENST00000369303	NM_004440.3	197	tCt/tTt	3/17	1	2	FACETS	0.286	0.223	0.36	0.286	0.223	0.36	SUBCLONAL	1	TRUE	1	0.439285611914387	2		319	366	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041046	112041046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762290632	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	97	544	0	ENST00000368678.4:c.209C>T	p.Ser70Leu	p.S70L	ENST00000368678		70	tCg/tTg	3/13	1	2	FACETS	0.545	0.486	0.609	0.545	0.486	0.609	SUBCLONAL	1	TRUE	1	0.439285611914387	2		544	810	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642545	117642545	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	184	576	0	ENST00000368508.3:c.5654G>T	p.Arg1885Ile	p.R1885I	ENST00000368508	NM_002944.2	1885	aGa/aTa	35/43	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.439285611914387	2		576	742	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678062	117678062	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754051395	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	38	290	0	ENST00000368508.3:c.3871G>A	p.Glu1291Lys	p.E1291K	ENST00000368508	NM_002944.2	1291	Gaa/Aaa	25/43	1	2	FACETS	0.455	0.377	0.543	0.455	0.377	0.543	SUBCLONAL	1	TRUE	1	0.439285611914387	2		290	380	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686282	117686282	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	35	274	0	ENST00000368508.3:c.3059C>A	p.Pro1020His	p.P1020H	ENST00000368508	NM_002944.2	1020	cCt/cAt	20/43	1	2	FACETS	0.431	0.353	0.517	0.431	0.353	0.517	SUBCLONAL	1	TRUE	1	0.439285611914387	2		274	370	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686839	117686839	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	58	366	0	ENST00000368508.3:c.2878G>T	p.Gly960Ter	p.G960*	ENST00000368508	NM_002944.2	960	Gga/Tga	19/43	1	2	FACETS	0.556	0.478	0.64	0.556	0.478	0.64	SUBCLONAL	1	TRUE	1	0.439285611914387	2		366	475	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700235	117700235	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	81	462	1	ENST00000368508.3:c.2584C>A	p.Leu862Ile	p.L862I	ENST00000368508	NM_002944.2	862	Ctt/Att	17/43	1	2	FACETS	0.739	0.653	0.831	0.739	0.653	0.831	SUBCLONAL	1	TRUE	1	0.439285611914387	2		463	499	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706904	117706904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	70	395	2	ENST00000368508.3:c.2246G>T	p.Gly749Val	p.G749V	ENST00000368508	NM_002944.2	749	gGg/gTg	15/43	1	2	FACETS	0.508	0.443	0.579	0.508	0.443	0.579	SUBCLONAL	1	TRUE	1	0.439285611914387	2		397	627	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525534	137525534	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs771401076	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	96	562	0	ENST00000367739.4:c.481T>C	p.Tyr161His	p.Y161H	ENST00000367739	NM_000416.2	161	Tat/Cat	4/7	1	2	FACETS	0.622	0.554	0.694	0.622	0.554	0.694	SUBCLONAL	1	TRUE	1	0.439285611914387	2		562	703	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527318	137527318	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	177	582	0	ENST00000367739.4:c.328G>T	p.Glu110Ter	p.E110*	ENST00000367739	NM_000416.2	110	Gaa/Taa	3/7	1	2	FACETS	0.92	0.848	0.995	0.92	0.848	0.995	CLONAL	1	TRUE	1	0.439285611914387	2		582	876	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004616	150004616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150904756	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	178	634	2	ENST00000253339.5:c.1609G>A	p.Ala537Thr	p.A537T	ENST00000253339		537	Gct/Act	3/7	1	2	FACETS	0.942	0.869	1	0.942	0.869	1	CLONAL	1	TRUE	1	0.439285611914387	2		636	860	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099529	157099529	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	39	220	1	ENST00000346085.5:c.466C>A	p.Gln156Lys	p.Q156K	ENST00000346085	NM_020732.3	156	Cag/Aag	1/20	1	2	FACETS	0.434	0.36	0.517	0.434	0.36	0.517	SUBCLONAL	1	TRUE	1	0.439285611914387	2		221	409	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528594	157528594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	94	755	0	ENST00000346085.5:c.6319C>T	p.Arg2107Cys	p.R2107C	ENST00000346085	NM_020732.3	2107	Cgt/Tgt	20/20	1	2	FACETS	0.449	0.399	0.503	0.449	0.399	0.503	SUBCLONAL	1	TRUE	1	0.439285611914387	2		755	953	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206852	162206852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34424986	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	59	452	0	ENST00000366898.1:c.823C>T	p.Arg275Trp	p.R275W	ENST00000366898	NM_004562.2	275	Cgg/Tgg	7/12	1	2	FACETS	0.484	0.416	0.558	0.484	0.416	0.558	SUBCLONAL	1	TRUE	1	0.439285611914387	2		452	555	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976742	2976742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1225008718	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	86	983	0	ENST00000396946.4:c.1270C>T	p.Arg424Trp	p.R424W	ENST00000396946	NM_032415.4	424	Cgg/Tgg	9/25	1	2	FACETS	0.333	0.294	0.376	0.333	0.294	0.376	SUBCLONAL	1	TRUE	1	0.439285611914387	2		983	1175	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976745	2976745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748839211	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	125	988	1	ENST00000396946.4:c.1267C>T	p.Arg423Trp	p.R423W	ENST00000396946	NM_032415.4	423	Cgg/Tgg	9/25	1	2	FACETS	0.47	0.424	0.519	0.47	0.424	0.519	SUBCLONAL	1	TRUE	1	0.439285611914387	2		989	1210	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976831	2976831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753594488	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	103	899	0	ENST00000396946.4:c.1181C>T	p.Ser394Leu	p.S394L	ENST00000396946	NM_032415.4	394	tCg/tTg	9/25	1	2	FACETS	0.446	0.398	0.497	0.446	0.398	0.497	SUBCLONAL	1	TRUE	1	0.439285611914387	2		899	1051	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985503	2985503	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	88	480	0	ENST00000396946.4:c.308A>G	p.Tyr103Cys	p.Y103C	ENST00000396946	NM_032415.4	103	tAc/tGc	4/25	1	2	FACETS	0.542	0.48	0.609	0.542	0.48	0.609	SUBCLONAL	1	TRUE	1	0.439285611914387	2		480	739	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2998137	2998137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1247	140	1086	0	ENST00000396946.4:c.4C>T	p.Pro2Ser	p.P2S	ENST00000396946	NM_032415.4	2	Cca/Tca	2/25	1	2	FACETS	0.46	0.417	0.505	0.46	0.417	0.505	SUBCLONAL	1	TRUE	1	0.439285611914387	2		1086	1387	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026709	6026709	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587778618	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1162	109	949	1	ENST00000265849.7:c.1687C>T	p.Arg563Ter	p.R563*	ENST00000265849	NM_000535.5	563	Cga/Tga	11/15	1	2	FACETS	0.39	0.349	0.434	0.39	0.349	0.434	SUBCLONAL	1	TRUE	1	0.439285611914387	2		950	1271	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6438336	6438336	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	88	485	0	ENST00000356142.4:c.269A>G	p.Asp90Gly	p.D90G	ENST00000356142	NM_018890.3	90	gAc/gGc	4/7	1	2	FACETS	0.55	0.487	0.618	0.55	0.487	0.618	SUBCLONAL	1	TRUE	1	0.439285611914387	2		485	728	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729747	41729747	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	127	547	0	ENST00000242208.4:c.782A>C	p.Lys261Thr	p.K261T	ENST00000242208	NM_002192.2	261	aAg/aCg	3/3	1	2	FACETS	0.954	0.867	1	0.954	0.867	1	CLONAL	1	TRUE	1	0.439285611914387	2		547	606	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730107	41730107	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	134	494	0	ENST00000242208.4:c.422C>T	p.Ser141Phe	p.S141F	ENST00000242208	NM_002192.2	141	tCc/tTc	3/3	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.439285611914387	2		494	578	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331991	81331991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1459963778	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	65	267	0	ENST00000222390.5:c.2093C>T	p.Ala698Val	p.A698V	ENST00000222390	NM_000601.4	698	gCc/gTc	18/18	1	2	FACETS	0.848	0.74	0.964	0.848	0.74	0.964	CLONAL	1	TRUE	1	0.439285611914387	2		267	349	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336607	81336607	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	61	228	0	ENST00000222390.5:c.1615C>T	p.Arg539Ter	p.R539*	ENST00000222390	NM_000601.4	539	Cga/Tga	14/18	1	2	FACETS	0.865	0.751	0.987	0.865	0.751	0.987	CLONAL	1	TRUE	1	0.439285611914387	2		228	321	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372710	81372710	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	44	368	0	ENST00000222390.5:c.824A>G	p.Asp275Gly	p.D275G	ENST00000222390	NM_000601.4	275	gAc/gGc	7/18	1	2	FACETS	0.484	0.406	0.57	0.484	0.406	0.57	SUBCLONAL	1	TRUE	1	0.439285611914387	2		368	414	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92404108	92404108	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	54	418	0	ENST00000265734.4:c.271G>T	p.Glu91Ter	p.E91*	ENST00000265734	NM_001259.6	91	Gaa/Taa	3/8	1	2	FACETS	0.416	0.355	0.483	0.416	0.355	0.483	SUBCLONAL	1	TRUE	1	0.439285611914387	2		418	591	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508940	106508940	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	118	484	0	ENST00000359195.3:c.934G>T	p.Asp312Tyr	p.D312Y	ENST00000359195	NM_002649.2	312	Gac/Tac	2/11	1	2	FACETS	0.911	0.824	1	0.911	0.824	1	CLONAL	1	TRUE	1	0.439285611914387	2		484	590	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508955	106508955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759136884	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	57	485	0	ENST00000359195.3:c.949G>A	p.Glu317Lys	p.E317K	ENST00000359195	NM_002649.2	317	Gag/Aag	2/11	1	2	FACETS	0.417	0.357	0.482	0.417	0.357	0.482	SUBCLONAL	1	TRUE	1	0.439285611914387	2		485	622	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509063	106509063	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	69	696	0	ENST00000359195.3:c.1057T>C	p.Ser353Pro	p.S353P	ENST00000359195	NM_002649.2	353	Tcc/Ccc	2/11	1	2	FACETS	0.414	0.36	0.473	0.414	0.36	0.473	SUBCLONAL	1	TRUE	1	0.439285611914387	2		696	759	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509652	106509652	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs776466677	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	82	568	0	ENST00000359195.3:c.1646A>G	p.Asn549Ser	p.N549S	ENST00000359195	NM_002649.2	549	aAc/aGc	2/11	1	2	FACETS	0.556	0.49	0.627	0.556	0.49	0.627	SUBCLONAL	1	TRUE	1	0.439285611914387	2		568	671	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513287	106513287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753731201	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	85	291	0	ENST00000359195.3:c.2191G>A	p.Asp731Asn	p.D731N	ENST00000359195	NM_002649.2	731	Gac/Aac	4/11	1	2	FACETS	0.894	0.794	0.999	0.894	0.794	0.999	CLONAL	1	TRUE	1	0.439285611914387	2		291	433	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397714	116397714	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376459715	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	50	487	0	ENST00000397752.3:c.1988C>T	p.Ser663Leu	p.S663L	ENST00000397752	NM_000245.2	663	tCg/tTg	8/21	1	2	FACETS	0.41	0.348	0.479	0.41	0.348	0.479	SUBCLONAL	1	TRUE	1	0.439285611914387	2		487	555	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418886	116418886	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs745437003	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	49	387	0	ENST00000397752.3:c.3397G>T	p.Asp1133Tyr	p.D1133Y	ENST00000397752	NM_000245.2	1133	Gat/Tat	17/21	1	2	FACETS	0.419	0.354	0.489	0.419	0.354	0.489	SUBCLONAL	1	TRUE	1	0.439285611914387	2		387	533	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829231	128829231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1462673663	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	184	773	1	ENST00000249373.3:c.239G>A	p.Gly80Asp	p.G80D	ENST00000249373	NM_005631.4	80	gGc/gAc	1/12	1	2	FACETS	0.909	0.839	0.981	0.909	0.839	0.981	CLONAL	1	TRUE	1	0.439285611914387	2		774	922	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511205	148511205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	67	588	2	ENST00000320356.2:c.1697G>A	p.Arg566His	p.R566H	ENST00000320356	NM_004456.4	566	cGc/cAc	15/20	1	2	FACETS	0.377	0.327	0.432	0.377	0.327	0.432	SUBCLONAL	1	TRUE	1	0.439285611914387	2		590	809	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523708	148523708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520183	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	67	248	0	ENST00000320356.2:c.745G>A	p.Glu249Lys	p.E249K	ENST00000320356	NM_004456.4	249	Gaa/Aaa	8/20	1	2	FACETS	0.905	0.792	1	0.905	0.792	1	CLONAL	1	TRUE	1	0.439285611914387	2		248	337	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151174419	151174419	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	43	330	0	ENST00000262187.5:c.275G>T	p.Ser92Ile	p.S92I	ENST00000262187	NM_005614.3	92	aGt/aTt	4/8	1	2	FACETS	0.486	0.407	0.573	0.486	0.407	0.573	SUBCLONAL	1	TRUE	1	0.439285611914387	2		330	403	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845973	151845973	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	86	622	0	ENST00000262189.6:c.13039C>T	p.Pro4347Ser	p.P4347S	ENST00000262189	NM_170606.2	4347	Ccg/Tcg	52/59	1	2	FACETS	0.514	0.454	0.578	0.514	0.454	0.578	SUBCLONAL	1	TRUE	1	0.439285611914387	2		622	762	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884466	151884466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1435892915	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	110	317	0	ENST00000262189.6:c.4889C>T	p.Ser1630Leu	p.S1630L	ENST00000262189	NM_170606.2	1630	tCg/tTg	33/59	1	2	FACETS	0.978	0.883	1	0.978	0.883	1	CLONAL	1	TRUE	1	0.439285611914387	2		317	512	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945699	151945699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	143	533	0	ENST00000262189.6:c.1820C>T	p.Ser607Phe	p.S607F	ENST00000262189	NM_170606.2	607	tCc/tTc	14/59	1	2	FACETS	0.945	0.863	1	0.945	0.863	1	CLONAL	1	TRUE	1	0.439285611914387	2		533	689	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151946988	151946988	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	64	349	0	ENST00000262189.6:c.1786C>A	p.Leu596Ile	p.L596I	ENST00000262189	NM_170606.2	596	Ctt/Att	13/59	1	2	FACETS	0.601	0.521	0.687	0.601	0.521	0.687	SUBCLONAL	1	TRUE	1	0.439285611914387	2		349	485	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133386	38133386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	38	333	1	ENST00000317025.8:c.4087C>T	p.Pro1363Ser	p.P1363S	ENST00000317025	NM_023034.1	1363	Ccg/Tcg	24/24	1	2	FACETS	0.4	0.33	0.477	0.4	0.33	0.477	SUBCLONAL	1	TRUE	1	0.439285611914387	2		334	433	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38184331	38184331	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	83	537	0	ENST00000317025.8:c.1625G>T	p.Arg542Met	p.R542M	ENST00000317025	NM_023034.1	542	aGg/aTg	7/24	1	2	FACETS	0.511	0.451	0.576	0.511	0.451	0.576	SUBCLONAL	1	TRUE	1	0.439285611914387	2		537	739	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187330	38187330	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	51	520	0	ENST00000317025.8:c.1147C>T	p.Arg383Ter	p.R383*	ENST00000317025	NM_023034.1	383	Cga/Tga	6/24	1	2	FACETS	0.336	0.285	0.392	0.336	0.285	0.392	SUBCLONAL	1	TRUE	1	0.439285611914387	2		520	691	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272306	38272306	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	94	696	0	ENST00000425967.3:c.2061G>T	p.Lys687Asn	p.K687N	ENST00000425967	NM_001174067.1	687	aaG/aaT	15/19	1	2	FACETS	0.524	0.466	0.587	0.524	0.466	0.587	SUBCLONAL	1	TRUE	1	0.439285611914387	2		696	816	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371683	55371683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753693798	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	122	909	0	ENST00000297316.4:c.373C>T	p.Arg125Cys	p.R125C	ENST00000297316	NM_022454.3	125	Cgc/Tgc	2/2	1	2	FACETS	0.545	0.492	0.602	0.545	0.492	0.602	SUBCLONAL	1	TRUE	1	0.439285611914387	2		909	1019	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931826	68931826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	176	470	0	ENST00000288368.4:c.256G>A	p.Glu86Lys	p.E86K	ENST00000288368	NM_024870.2	86	Gaa/Aaa	3/40	0.179576461478298	0	FACETS	0.771	0.714	0.829			1	INDETERMINATE	1	TRUE	0	0.439285611914387	0		470	583	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69012038	69012038	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	138	559	1	ENST00000288368.4:c.2675G>T	p.Arg892Ile	p.R892I	ENST00000288368	NM_024870.2	892	aGa/aTa	23/40	0.179576461478298	0	FACETS	0.57	0.52	0.622			1	INDETERMINATE	1	TRUE	0	0.439285611914387	0		560	618	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031751	69031751	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	50	540	0	ENST00000288368.4:c.3504+2T>C		p.X1168_splice	ENST00000288368	NM_024870.2	1168			0.179576461478298	0	FACETS	0.181	0.152	0.211			1	INDETERMINATE	1	TRUE	0	0.439285611914387	0		540	707	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69143584	69143584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142298071	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	21	269	0	ENST00000288368.4:c.4792G>A	p.Glu1598Lys	p.E1598K	ENST00000288368	NM_024870.2	1598	Gag/Aag	40/40	0.179576461478298	0	FACETS	0.147	0.113	0.187			1	INDETERMINATE	1	TRUE	0	0.439285611914387	0		269	364	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964514	70964514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762086448	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	79	703	1	ENST00000276594.2:c.1514G>A	p.Arg505His	p.R505H	ENST00000276594	NM_024504.3	505	cGc/cAc	8/8	0.179576461478298	0	FACETS	0.241	0.211	0.273			1	INDETERMINATE	1	TRUE	0	0.439285611914387	0		704	836	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90995064	90995064	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	46	359	0	ENST00000265433.3:c.57G>C	p.Leu19Phe	p.L19F	ENST00000265433	NM_002485.4	19	ttG/ttC	2/16	1	2	FACETS	0.394	0.332	0.464	0.394	0.332	0.464	SUBCLONAL	1	TRUE	1	0.439285611914387	2		359	531	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737651	145737651	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763078132	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	99	1079	1	ENST00000428558.2:c.3112C>T	p.Arg1038Cys	p.R1038C	ENST00000428558	NM_004260.3	1038	Cgc/Tgc	19/22	1	2	FACETS	0.377	0.335	0.422	0.377	0.335	0.422	SUBCLONAL	1	TRUE	1	0.439285611914387	2		1080	1195	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341111	8341111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	102	397	0	ENST00000356435.5:c.5105C>T	p.Ala1702Val	p.A1702V	ENST00000356435		1702	gCc/gTc	30/35	1	2	FACETS	0.944	0.848	1	0.944	0.848	1	CLONAL	1	TRUE	1	0.439285611914387	2		397	492	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404591	8404591	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	28	290	0	ENST00000356435.5:c.4156T>C	p.Tyr1386His	p.Y1386H	ENST00000356435		1386	Tac/Cac	25/35	1	2	FACETS	0.365	0.292	0.449	0.365	0.292	0.449	SUBCLONAL	1	TRUE	1	0.439285611914387	2		290	349	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449746	8449746	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1424143158	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	54	532	0	ENST00000356435.5:c.3967C>T	p.Arg1323Cys	p.R1323C	ENST00000356435		1323	Cgc/Tgc	23/35	1	2	FACETS	0.328	0.279	0.382	0.328	0.279	0.382	SUBCLONAL	1	TRUE	1	0.439285611914387	2		532	749	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500903	8500903	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	106	494	0	ENST00000356435.5:c.1979A>G	p.His660Arg	p.H660R	ENST00000356435		660	cAc/cGc	13/35	1	2	FACETS	0.819	0.736	0.907	0.819	0.736	0.907	CLONAL	1	TRUE	1	0.439285611914387	2		494	589	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528596	8528596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	37	331	0	ENST00000356435.5:c.536G>A	p.Arg179Gln	p.R179Q	ENST00000356435		179	cGa/cAa	4/35	1	2	FACETS	0.39	0.321	0.467	0.39	0.321	0.467	SUBCLONAL	1	TRUE	1	0.439285611914387	2		331	432	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206682	27206682	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	87	478	1	ENST00000380036.4:c.2467G>T	p.Asp823Tyr	p.D823Y	ENST00000380036	NM_000459.3	823	Gac/Tac	15/23	1	2	FACETS	0.58	0.513	0.651	0.58	0.513	0.651	SUBCLONAL	1	TRUE	1	0.439285611914387	2		479	683	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27217701	27217701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772600804	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	80	532	2	ENST00000380036.4:c.3007C>T	p.Arg1003Cys	p.R1003C	ENST00000380036	NM_000459.3	1003	Cgc/Tgc	19/23	1	2	FACETS	0.438	0.385	0.496	0.438	0.385	0.496	SUBCLONAL	1	TRUE	1	0.439285611914387	2		534	831	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570416	87570416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	113	836	0	ENST00000277120.3:c.2156G>A	p.Ser719Asn	p.S719N	ENST00000277120		719	aGc/aAc	17/19	1	2	FACETS	0.469	0.421	0.52	0.469	0.421	0.52	SUBCLONAL	1	TRUE	1	0.439285611914387	2		836	1097	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635175	87635175	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	73	624	0	ENST00000277120.3:c.2227T>C	p.Tyr743His	p.Y743H	ENST00000277120		743	Tac/Cac	18/19	1	2	FACETS	0.42	0.366	0.477	0.42	0.366	0.477	SUBCLONAL	1	TRUE	1	0.439285611914387	2		624	792	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635265	87635265	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	72	542	3	ENST00000277120.3:c.2317C>A	p.Leu773Met	p.L773M	ENST00000277120		773	Ctg/Atg	18/19	1	2	FACETS	0.447	0.39	0.508	0.447	0.39	0.508	SUBCLONAL	1	TRUE	1	0.439285611914387	2		545	734	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97869484	97869484	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	101	797	0	ENST00000289081.3:c.1397A>G	p.Asp466Gly	p.D466G	ENST00000289081	NM_000136.2	466	gAc/gGc	14/15	1	2	FACETS	0.459	0.409	0.512	0.459	0.409	0.512	SUBCLONAL	1	TRUE	1	0.439285611914387	2		797	1002	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97887408	97887408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745910444	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	146	535	0	ENST00000289081.3:c.956C>T	p.Thr319Met	p.T319M	ENST00000289081	NM_000136.2	319	aCg/aTg	10/15	1	2	FACETS	0.892	0.816	0.972	0.892	0.816	0.972	CLONAL	1	TRUE	1	0.439285611914387	2		535	745	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229599	98229599	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	54	379	0	ENST00000331920.6:c.2359G>T	p.Glu787Ter	p.E787*	ENST00000331920	NM_000264.3	787	Gaa/Taa	15/24	1	2	FACETS	0.446	0.381	0.518	0.446	0.381	0.518	SUBCLONAL	1	TRUE	1	0.439285611914387	2		379	551	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891350	101891350	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	50	493	0	ENST00000374994.4:c.311A>G	p.Asp104Gly	p.D104G	ENST00000374994	NM_004612.2	104	gAc/gGc	2/9	1	2	FACETS	0.348	0.294	0.406	0.348	0.294	0.406	SUBCLONAL	1	TRUE	1	0.439285611914387	2		493	655	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128432165	128432165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1371596131	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	45	352	0	ENST00000265960.3:c.281G>A	p.Arg94Gln	p.R94Q	ENST00000265960	NM_001006617.1	94	cGa/cAa	3/12	1	2	FACETS	0.394	0.331	0.464	0.394	0.331	0.464	SUBCLONAL	1	TRUE	1	0.439285611914387	2		352	520	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434778	128434778	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	123	660	0	ENST00000265960.3:c.76A>G	p.Met26Val	p.M26V	ENST00000265960	NM_001006617.1	26	Atg/Gtg	2/12	1	2	FACETS	0.624	0.564	0.688	0.624	0.564	0.688	SUBCLONAL	1	TRUE	1	0.439285611914387	2		660	897	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317422	1317422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759127718	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	76	576	0	ENST00000400841.2:c.643C>T	p.Arg215Trp	p.R215W	ENST00000400841		215	Cgg/Tgg	5/6	1	1	FACETS	0.348	0.305	0.395	0.348	0.305	0.395	SUBCLONAL	1	TRUE	0	0.439285611914387	1		576	775	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321286	1321286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780766655	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	65	565	1	ENST00000400841.2:c.469G>A	p.Asp157Asn	p.D157N	ENST00000400841		157	Gac/Aac	4/6	1	1	FACETS	0.366	0.317	0.419	0.366	0.317	0.419	SUBCLONAL	1	TRUE	0	0.439285611914387	1		566	631	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15822267	15822267	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	16	119	0	ENST00000307771.7:c.346A>G	p.Arg116Gly	p.R116G	ENST00000307771	NM_005089.3	116	Agg/Ggg	5/11	1	1	FACETS	0.296	0.219	0.387	0.296	0.219	0.387	SUBCLONAL	1	TRUE	0	0.439285611914387	1		119	192	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932914	39932914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147493277	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	190	391	0	ENST00000378444.4:c.1685C>T	p.Ser562Leu	p.S562L	ENST00000378444	NM_001123385.1	562	tCg/tTg	4/15	1	1	FACETS	0.767	0.717	0.817	1	0.992	1	SUBCLONAL	2	TRUE	0	0.439285611914387	1		391	440	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44910961	44910961	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	47	116	0	ENST00000377967.4:c.662A>G	p.Tyr221Cys	p.Y221C	ENST00000377967	NM_021140.2	221	tAt/tGt	9/29	1	1	FACETS	0.827	0.706	0.956	0.827	0.706	0.956	CLONAL	1	TRUE	0	0.439285611914387	1		116	202	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938470	44938470	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	29	235	0	ENST00000377967.4:c.3018G>T	p.Gln1006His	p.Q1006H	ENST00000377967	NM_021140.2	1006	caG/caT	20/29	1	1	FACETS	0.362	0.291	0.441	0.362	0.291	0.441	SUBCLONAL	1	TRUE	0	0.439285611914387	1		235	285	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223727	53223727	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	147	595	0	ENST00000375401.3:c.3632G>T	p.Gly1211Val	p.G1211V	ENST00000375401	NM_004187.3	1211	gGg/gTg	23/26	1	1	FACETS	0.746	0.683	0.812	0.746	0.683	0.812	SUBCLONAL	1	TRUE	0	0.439285611914387	1		595	700	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410486	63410486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779325879	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	74	409	1	ENST00000330258.3:c.2681G>A	p.Arg894His	p.R894H	ENST00000330258	NM_152424.3	894	cGc/cAc	2/2	1	1	FACETS	0.587	0.515	0.663	0.587	0.515	0.663	SUBCLONAL	1	TRUE	0	0.439285611914387	1		410	448	SUCCESS
AR	367	MSKCC	GRCh37	X	66765797	66765797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs905313189	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	141	583	1	ENST00000374690.3:c.809C>T	p.Ala270Val	p.A270V	ENST00000374690	NM_000044.3	270	gCc/gTc	1/8	1	1	FACETS	0.735	0.671	0.801	0.735	0.671	0.801	SUBCLONAL	1	TRUE	0	0.439285611914387	1		584	682	SUCCESS
AR	367	MSKCC	GRCh37	X	66765866	66765866	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	150	606	0	ENST00000374690.3:c.878C>A	p.Ser293Tyr	p.S293Y	ENST00000374690	NM_000044.3	293	tCt/tAt	1/8	1	1	FACETS	0.765	0.7	0.832	0.765	0.7	0.832	SUBCLONAL	1	TRUE	0	0.439285611914387	1		606	697	SUCCESS
AR	367	MSKCC	GRCh37	X	66931388	66931388	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	84	335	0	ENST00000374690.3:c.2030T>C	p.Val677Ala	p.V677A	ENST00000374690	NM_000044.3	677	gTc/gCc	4/8	1	1	FACETS	0.737	0.655	0.824	0.737	0.655	0.824	SUBCLONAL	1	TRUE	0	0.439285611914387	1		335	405	SUCCESS
AR	367	MSKCC	GRCh37	X	66943614	66943614	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	35	329	1	ENST00000374690.3:c.2694G>T	p.Glu898Asp	p.E898D	ENST00000374690	NM_000044.3	898	gaG/gaT	8/8	1	1	FACETS	0.325	0.266	0.39	0.325	0.266	0.39	SUBCLONAL	1	TRUE	0	0.439285611914387	1		330	383	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469669	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	193	335	0	ENST00000374080.3:c.130G>A	p.Gly44Ser	p.G44S	ENST00000374080		44	Ggt/Agt	2/45	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.439285611914387	1		335	461	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937984	76937984	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373581602	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	55	248	0	ENST00000373344.5:c.2764G>A	p.Asp922Asn	p.D922N	ENST00000373344	NM_000489.3	922	Gat/Aat	9/35	1	1	FACETS	0.528	0.453	0.609	0.528	0.453	0.609	SUBCLONAL	1	TRUE	0	0.439285611914387	1		248	370	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611795	100611795	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	151	275	0	ENST00000308731.7:c.1326C>A	p.Phe442Leu	p.F442L	ENST00000308731	NM_000061.2	442	ttC/ttA	14/19	1	1	FACETS	0.801	0.744	0.858	1	0.991	1	CLONAL	2	TRUE	0	0.439285611914387	1		275	335	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123026618	123026618	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	70	164	0	ENST00000355640.3:c.1094G>T	p.Arg365Ile	p.R365I	ENST00000355640		365	aGa/aTa	5/7	1	1	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	0	0.439285611914387	1		164	245	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964398	70964398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1289330671	NA	P-0048215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	45	509	0	ENST00000276594.2:c.1630G>A	p.Asp544Asn	p.D544N	ENST00000276594	NM_024504.3	544	Gat/Aat	8/8	0.179576461478298	0	FACETS	0.21	0.176	0.248			1	INDETERMINATE	1	TRUE	0	0.439285611914387	0		509	547	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0048216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	391	436	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.551425619418649	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.551425619418649	1		439	892	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003423	42003423	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs575209923	NA	P-0048216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	33	420	0	ENST00000219905.7:c.2960G>C	p.Gly987Ala	p.G987A	ENST00000219905	NM_001164273.1	987	gGc/gCc	8/24	1	2	FACETS	0.181	0.147	0.22	0.181	0.147	0.22	SUBCLONAL	1	TRUE	1	0.551425619418649	2		420	660	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0048217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	69	684	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.923	0.802	1	0.923	0.802	1	CLONAL	1	TRUE	1	0.18	2		686	831	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652404	206652404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17021877	NA	P-0048217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	62	872	4	ENST00000367120.3:c.1111G>A	p.Ala371Thr	p.A371T	ENST00000367120	NM_014002.3	371	Gcc/Acc	10/22	1	2	FACETS	0.91	0.785	1	0.91	0.785	1	CLONAL	1	TRUE	1	0.18	2		876	757	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70442645	70442645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	49	503	0	ENST00000373644.4:c.4967G>A	p.Arg1656His	p.R1656H	ENST00000373644	NM_030625.2	1656	cGt/cAt	10/12	0.181274291736777	3	FACETS	0.962	0.814	1	0.481	0.407	0.563	CLONAL	1	TRUE	1	0.18	3		503	617	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464892	120464892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745954022	NA	P-0048217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	30	407	1	ENST00000256646.2:c.5180G>A	p.Arg1727His	p.R1727H	ENST00000256646	NM_024408.3	1727	cGt/cAt	28/34	1	2	FACETS	0.664	0.534	0.812	0.664	0.534	0.812	SUBCLONAL	1	TRUE	1	0.18	2		408	502	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830288	72830288	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	37	415	0	ENST00000268489.5:c.6293C>T	p.Ser2098Leu	p.S2098L	ENST00000268489	NM_006885.3	2098	tCg/tTg	9/10	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.18	2		415	289	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097644	8097644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762722802	NA	P-0048217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	29	324	0	ENST00000346208.3:c.26G>A	p.Arg9His	p.R9H	ENST00000346208		9	cGc/cAc	2/6	0.0956254274398237	0	FACETS	0.937	0.754	1			1	INDETERMINATE	1	TRUE	0	0.18	0		324	282	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0048217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	138	550	1	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.18	2		551	1033	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102056857	102056857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	26	358	0	ENST00000282441.5:c.797G>A	p.Arg266His	p.R266H	ENST00000282441	NM_001130145.2	266	cGt/cAt	4/9	0.181274291736777	3	FACETS	0.729	0.577	0.904	0.364	0.288	0.452	CLONAL	1	TRUE	1	0.18	3		358	432	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371737	118371737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	29	167	0	ENST00000534358.1:c.6194G>A	p.Arg2065His	p.R2065H	ENST00000534358	NM_005933.3	2065	cGc/cAc	25/36	0.181274291736777	3	FACETS	1	0.88	1	0.568	0.457	0.694	CLONAL	1	TRUE	1	0.18	3		167	309	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321321	1321321	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	30	594	0	ENST00000400841.2:c.434A>T	p.Asp145Val	p.D145V	ENST00000400841		145	gAt/gTt	4/6	0.3	2	FACETS	0.628	0.505	0.768	0.314	0.252	0.384	SUBCLONAL	1	TRUE	0	0.18	2		594	531	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933839	39933839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749475374	NA	P-0048217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	64	437	0	ENST00000378444.4:c.760G>A	p.Gly254Ser	p.G254S	ENST00000378444	NM_001123385.1	254	Ggt/Agt	4/15	0.3	2	FACETS	0.79	0.686	0.902	0.79	0.686	0.902	CLONAL	2	TRUE	0	0.18	2		437	450	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214046	36214046	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	74	1047	0	ENST00000222270.7:c.2872G>A	p.Gly958Ser	p.G958S	ENST00000222270	NM_014727.1	958	Ggc/Agc	6/37	1	2	FACETS	0.897	0.783	1	0.897	0.783	1	CLONAL	1	TRUE	1	0.18	2		1047	917	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407859	139407859	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756642176	NA	P-0048217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	36	728	0	ENST00000277541.6:c.2338C>T	p.Arg780Trp	p.R780W	ENST00000277541	NM_017617.3	780	Cgg/Tgg	14/34	0.0956254274398237	0	FACETS	0.532	0.436	0.639			1	INDETERMINATE	1	TRUE	0	0.18	0		728	617	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553542	106553542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	45	476	1	ENST00000369096.4:c.1507G>A	p.Ala503Thr	p.A503T	ENST00000369096	NM_001198.3	503	Gcc/Acc	5/7	0.181274291736777	3	FACETS	1	0.928	1	0.595	0.5	0.7	CLONAL	1	TRUE	1	0.18	3		477	458	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431834	49431834	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	31	747	0	ENST00000301067.7:c.9305del	p.Pro3102LeufsTer17	p.P3102Lfs*17	ENST00000301067	NM_003482.3	3102	cCt/ct	34/54	0.181274291736777	4	FACETS	0.66	0.532	0.805	0.33	0.266	0.403	SUBCLONAL	1	TRUE	2	0.18	4		747	616	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249223	133249223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766276875	NA	P-0048217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	38	632	0	ENST00000320574.5:c.1676G>A	p.Arg559Gln	p.R559Q	ENST00000320574	NM_006231.2	559	cGg/cAg	15/49	0.0956254274398237	0	FACETS	0.69	0.57	0.824			1	INDETERMINATE	1	TRUE	0	0.18	0		632	502	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435825	110435825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1380827800	NA	P-0048217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	39	438	0	ENST00000375856.3:c.2576C>T	p.Thr859Met	p.T859M	ENST00000375856	NM_003749.2	859	aCg/aTg	1/2	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.18	2		438	398	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251145	99251145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	47	648	0	ENST00000268035.6:c.449G>A	p.Cys150Tyr	p.C150Y	ENST00000268035	NM_000875.3	150	tGt/tAt	2/21	1	2	FACETS	0.974	0.822	1	0.974	0.822	1	CLONAL	1	TRUE	1	0.18	2		648	536	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647914	3647914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748138902	NA	P-0048217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	79	1102	2	ENST00000294008.3:c.1250C>T	p.Pro417Leu	p.P417L	ENST00000294008	NM_032444.2	417	cCg/cTg	6/15	1	2	FACETS	0.937	0.822	1	0.937	0.822	1	CLONAL	1	TRUE	1	0.18	2		1104	937	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337277	89337277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567537296	NA	P-0048217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	47	763	0	ENST00000301030.4:c.7754G>A	p.Arg2585His	p.R2585H	ENST00000301030	NM_001256183.1	2585	cGc/cAc	12/13	1	2	FACETS	0.785	0.661	0.922	0.785	0.661	0.922	CLONAL	1	TRUE	1	0.18	2		763	665	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533547	63533547	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750084404	NA	P-0048217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	57	975	0	ENST00000307078.5:c.1607C>T	p.Thr536Met	p.T536M	ENST00000307078	NM_004655.3	536	aCg/aTg	6/11	1	2	FACETS	0.85	0.728	0.984	0.85	0.728	0.984	CLONAL	1	TRUE	1	0.18	2		975	745	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210687	2210687	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	54	806	0	ENST00000398665.3:c.1184del	p.Arg395ProfsTer5	p.R395Pfs*5	ENST00000398665	NM_032482.2	395	cGc/cc	14/28	1	2	FACETS	0.812	0.692	0.944	0.812	0.692	0.944	CLONAL	1	TRUE	1	0.18	2		806	739	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976450	25976450	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	37	408	0	ENST00000435504.4:c.1095del	p.Val366TrpfsTer19	p.V366Wfs*19	ENST00000435504		365	aaA/aa	11/13	1	2	FACETS	0.746	0.614	0.894	0.746	0.614	0.894	SUBCLONAL	1	TRUE	1	0.18	2		408	551	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204963	128204963	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	64	864	0	ENST00000341105.2:c.478A>G	p.Thr160Ala	p.T160A	ENST00000341105	NM_032638.4	160	Acc/Gcc	3/6	0.181274291736777	3	FACETS	0.963	0.832	1	0.481	0.416	0.553	CLONAL	1	TRUE	1	0.18	3		864	805	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541003	187541003	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	16	383	0	ENST00000441802.2:c.6737C>T	p.Ala2246Val	p.A2246V	ENST00000441802	NM_005245.3	2246	gCc/gTc	10/27	1	2	FACETS	0.607	0.448	0.797	0.607	0.448	0.797	SUBCLONAL	1	TRUE	1	0.18	2		383	293	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31495409	31495409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868625207	NA	P-0048217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	41	546	0	ENST00000344624.3:c.1739C>T	p.Pro580Leu	p.P580L	ENST00000344624		580	cCg/cTg	9/33	0.181274291736777	0	FACETS	0.666	0.554	0.791			1	SUBCLONAL	1	TRUE	0	0.18	0		546	561	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976810	2976810	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	61	953	0	ENST00000396946.4:c.1202A>G	p.Asp401Gly	p.D401G	ENST00000396946	NM_032415.4	401	gAc/gGc	9/25	0.304570761817408	0	FACETS	0.756	0.651	0.871			1	SUBCLONAL	1	TRUE	0	0.18	0		953	735	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395224	139395224	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	54	1000	0	ENST00000277541.6:c.5714A>G	p.Asp1905Gly	p.D1905G	ENST00000277541	NM_017617.3	1905	gAc/gGc	31/34	0.0956254274398237	0	FACETS	0.629	0.536	0.732			1	INDETERMINATE	1	TRUE	0	0.18	0		1000	782	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578530	7578530	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	257	1320	0	ENST00000269305.4:c.400T>G	p.Phe134Val	p.F134V	ENST00000269305	NM_001126112.2	134	Ttt/Gtt	5/11	0.743603908847894	1	FACETS	0.901	0.855	0.946	0.901	0.855	0.946	CLONAL	1	TRUE	0	0.743603908847894	1		1320	482	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0048218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	116	290	1	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	0.743603908847894	1	FACETS	0.883	0.816	0.95	0.883	0.816	0.95	CLONAL	1	TRUE	0	0.743603908847894	1		291	222	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280109	66280109	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	79	384	1	ENST00000273854.3:c.1580C>A	p.Ala527Glu	p.A527E	ENST00000273854	NM_004439.5	527	gCa/gAa	7/18	0.19579700852847	3	FACETS	1	0.952	1	0.563	0.501	0.627	INDETERMINATE	1	TRUE	1	0.743603908847894	3		385	259	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914949	32914949	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	82	499	0	ENST00000380152.3:c.6457C>A	p.Pro2153Thr	p.P2153T	ENST00000380152		2153	Cca/Aca	11/27	0.743603908847894	1	FACETS	0.976	0.892	1	0.976	0.892	1	CLONAL	1	TRUE	0	0.743603908847894	1		499	142	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0048219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	167	684	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.181698502241463	2	FACETS	0.951	0.873	1	0.951	0.873	1	CLONAL	2	TRUE	0	0.184528311519023	2		686	952	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100015	11100015	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs972341316	NA	P-0048219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	96	681	0	ENST00000358026.2:c.1141C>T	p.Arg381Ter	p.R381*	ENST00000358026	NM_001128849.1	381	Cga/Tga	7/36	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.184528311519023	2		681	982	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984490	72984490	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	97	889	0	ENST00000268489.5:c.3094G>T	p.Val1032Leu	p.V1032L	ENST00000268489	NM_006885.3	1032	Gtg/Ttg	3/10	0.176347139216458	3	FACETS	0.89	0.791	0.997	0.445	0.395	0.499	CLONAL	1	TRUE	1	0.184528311519023	3		889	1290	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	95	331	1	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.874	0.78	0.975	0.874	0.78	0.975	CLONAL	1	TRUE	1	0.348816155929287	2		332	623	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	61	314	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.817	0.707	0.936	0.817	0.707	0.936	CLONAL	1	TRUE	1	0.348816155929287	2		314	428	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128246746	128246746	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	118	591	0	ENST00000265960.3:c.1183C>T	p.Arg395Ter	p.R395*	ENST00000265960	NM_001006617.1	395	Cga/Tga	9/12	1	2	FACETS	0.891	0.805	0.983	0.891	0.805	0.983	CLONAL	1	TRUE	1	0.348816155929287	2		591	759	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	83	277	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.851	0.753	0.957	0.851	0.753	0.957	CLONAL	1	TRUE	1	0.348816155929287	2		277	559	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366939	15366939	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	125	621	1	ENST00000263377.2:c.1687del	p.Ser563AlafsTer21	p.S563Afs*21	ENST00000263377	NM_058243.2	563	Agc/gc	9/20	1	2	FACETS	0.812	0.734	0.894	0.812	0.734	0.894	CLONAL	1	TRUE	1	0.348816155929287	2		622	883	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256769	19256769	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	140	672	1	ENST00000162023.5:c.944del	p.Pro315GlnfsTer?	p.P315Qfs*?	ENST00000162023		315	cCa/ca	13/13	1	2	FACETS	0.899	0.818	0.984	0.899	0.818	0.984	CLONAL	1	TRUE	1	0.348816155929287	2		673	893	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521298	187521299	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	123	594	0	ENST00000441802.2:c.11856dup	p.Gly3953TrpfsTer19	p.G3953Wfs*19	ENST00000441802	NM_005245.3	3952	-/T	22/27	1	2	FACETS	0.873	0.789	0.961	0.873	0.789	0.961	CLONAL	1	TRUE	1	0.348816155929287	2		594	808	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	154	529	1	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.901	0.824	0.982	0.901	0.824	0.982	CLONAL	1	TRUE	1	0.348816155929287	2		530	980	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	61	302	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.73	0.631	0.838	0.73	0.631	0.838	SUBCLONAL	1	TRUE	1	0.348816155929287	2		302	479	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	237	632	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.348816155929287	2		632	1220	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099312	157099312	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	70	443	1	ENST00000346085.5:c.249G>C	p.Gln83His	p.Q83H	ENST00000346085	NM_020732.3	83	caG/caC	1/20	1	2	FACETS	0.675	0.588	0.768	0.675	0.588	0.768	SUBCLONAL	1	TRUE	1	0.348816155929287	2		444	595	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743933	41743933	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778012871	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1152	230	1025	2	ENST00000301178.4:c.874del	p.His292IlefsTer5	p.H292Ifs*5	ENST00000301178	NM_021913.4	290	Ccc/cc	7/20	1	2	FACETS	0.954	0.887	1	0.954	0.887	1	CLONAL	1	TRUE	1	0.348816155929287	2		1027	1382	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262079	10262079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762172122	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	135	567	0	ENST00000340748.4:c.2212G>A	p.Val738Ile	p.V738I	ENST00000340748		738	Gtc/Atc	23/40	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.348816155929287	2		567	773	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39644789	39644789	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	59	229	0	ENST00000262039.4:c.2522del	p.Lys841ArgfsTer8	p.K841Rfs*8	ENST00000262039	NM_002647.2	840	Aaa/aa	23/25	1	2	FACETS	0.95	0.822	1	0.95	0.822	1	CLONAL	1	TRUE	1	0.348816155929287	2		229	356	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	103	499	3	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.778	0.696	0.865	0.778	0.696	0.865	SUBCLONAL	1	TRUE	1	0.348816155929287	2		502	759	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900984	114900984	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778855667	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	145	589	0	ENST00000543371.1:c.598del	p.Leu200SerfsTer25	p.L200Sfs*25	ENST00000543371	NM_001198531.1	198	caC/ca	6/14	1	2	FACETS	0.924	0.843	1	0.924	0.843	1	CLONAL	1	TRUE	1	0.348816155929287	2		589	900	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	86	222	2	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	0.9	0.798	1	0.9	0.798	1	CLONAL	1	TRUE	1	0.348816155929287	2		224	548	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	176	473	6	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.348816155929287	2		479	925	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012773	36012773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	79	246	0	ENST00000358208.4:c.217G>A	p.Val73Ile	p.V73I	ENST00000358208		73	Gtc/Atc	2/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.348816155929287	2		246	304	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954261	32954261	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55933907	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	91	439	2	ENST00000380152.3:c.9235G>A	p.Val3079Ile	p.V3079I	ENST00000380152		3079	Gtt/Att	24/27	1	2	FACETS	0.8	0.711	0.895	0.8	0.711	0.895	SUBCLONAL	1	TRUE	1	0.348816155929287	2		441	652	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100727	8100728	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs771019738	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	140	982	2	ENST00000346208.3:c.708dup	p.Ser237GlnfsTer66	p.S237Qfs*66	ENST00000346208		234	ttc/ttCc	3/6	1	2	FACETS	0.66	0.6	0.724	0.66	0.6	0.724	SUBCLONAL	1	TRUE	1	0.348816155929287	2		984	1216	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214630	133214630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	103	533	0	ENST00000320574.5:c.5648C>T	p.Ala1883Val	p.A1883V	ENST00000320574	NM_006231.2	1883	gCc/gTc	41/49	1	2	FACETS	0.764	0.684	0.85	0.764	0.684	0.85	SUBCLONAL	1	TRUE	1	0.348816155929287	2		533	773	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979319	40979319	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1217327426	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	117	623	3	ENST00000373198.4:c.1814C>T	p.Thr605Met	p.T605M	ENST00000373198	NM_133170.3	605	aCg/aTg	11/32	1	2	FACETS	0.878	0.792	0.969	0.878	0.792	0.969	CLONAL	1	TRUE	1	0.348816155929287	2		626	764	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435293	110435295	+	inframe_deletion	In_Frame_Del	DEL	CGG	CGG	-	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	66	266	0	ENST00000375856.3:c.3106_3108del	p.Pro1036del	p.P1036del	ENST00000375856	NM_003749.2	1036	CCG/-	1/2	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.348816155929287	2		266	329	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	193	809	9	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	1	2	FACETS	0.939	0.867	1	0.939	0.867	1	CLONAL	1	TRUE	1	0.348816155929287	2		818	1179	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629772	187629772	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	129	545	2	ENST00000441802.2:c.1210A>G	p.Ser404Gly	p.S404G	ENST00000441802	NM_005245.3	404	Agt/Ggt	2/27	1	2	FACETS	0.881	0.798	0.967	0.881	0.798	0.967	CLONAL	1	TRUE	1	0.348816155929287	2		547	840	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629770	187629770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	126	536	0	ENST00000441802.2:c.1212del	p.Ser404ArgfsTer10	p.S404Rfs*10	ENST00000441802	NM_005245.3	404	agT/ag	2/27	1	2	FACETS	0.859	0.778	0.945	0.859	0.778	0.945	CLONAL	1	TRUE	1	0.348816155929287	2		536	841	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047959	180047959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs933223149	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	226	1018	0	ENST00000261937.6:c.2216G>A	p.Arg739His	p.R739H	ENST00000261937	NM_182925.4	739	cGc/cAc	15/30	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.348816155929287	2		1018	1257	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259464	89259464	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	106	481	1	ENST00000336596.2:c.608C>A	p.Pro203Gln	p.P203Q	ENST00000336596	NM_005233.5	203	cCa/cAa	3/17	1	2	FACETS	0.917	0.823	1	0.917	0.823	1	CLONAL	1	TRUE	1	0.348816155929287	2		482	663	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984839	11984839	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	85	347	1	ENST00000353533.5:c.385G>A	p.Ala129Thr	p.A129T	ENST00000353533	NM_003010.3	129	Gca/Aca	3/11	1	2	FACETS	0.969	0.859	1	0.969	0.859	1	CLONAL	1	TRUE	1	0.348816155929287	2		348	503	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5239008	5239008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138765579	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	189	867	0	ENST00000357368.4:c.1771G>A	p.Ala591Thr	p.A591T	ENST00000357368	NM_002850.3	591	Gcc/Acc	13/38	1	2	FACETS	0.998	0.921	1	0.998	0.921	1	CLONAL	1	TRUE	1	0.348816155929287	2		867	1086	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125634	47125634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1357325164	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	108	340	1	ENST00000409792.3:c.5636G>A	p.Arg1879His	p.R1879H	ENST00000409792	NM_014159.6	1879	cGc/cAc	12/21	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.348816155929287	2		341	575	SUCCESS
BLM	641	MSKCC	GRCh37	15	91333927	91333927	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775006576	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	116	485	1	ENST00000355112.3:c.2872G>A	p.Val958Met	p.V958M	ENST00000355112	NM_000057.2	958	Gtg/Atg	15/22	1	2	FACETS	0.898	0.809	0.991	0.898	0.809	0.991	CLONAL	1	TRUE	1	0.348816155929287	2		486	741	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612377	1612377	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753978381	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	254	1016	3	ENST00000344749.5:c.1642C>T	p.Arg548Cys	p.R548C	ENST00000344749	NM_001136139.2	548	Cgc/Tgc	18/19	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.348816155929287	2		1019	1315	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845397	42845397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762854045	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	167	787	0	ENST00000398585.3:c.865C>T	p.Arg289Cys	p.R289C	ENST00000398585	NM_001135099.1	289	Cgc/Tgc	9/14	1	2	FACETS	0.946	0.869	1	0.946	0.869	1	CLONAL	1	TRUE	1	0.348816155929287	2		787	1012	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	169	671	0	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	1	2	FACETS	0.784	0.719	0.852	0.784	0.719	0.852	SUBCLONAL	1	TRUE	1	0.348816155929287	2		671	1236	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370754	55370754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	136	564	0	ENST00000297316.4:c.56C>T	p.Ala19Val	p.A19V	ENST00000297316	NM_022454.3	19	gCg/gTg	1/2	1	2	FACETS	0.977	0.889	1	0.977	0.889	1	CLONAL	1	TRUE	1	0.348816155929287	2		564	798	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	269	691	1	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.348816155929287	2		692	1469	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324576	31324576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs151341159	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	91	860	1	ENST00000412585.2:c.232C>T	p.Gln78Ter	p.Q78*	ENST00000412585	NM_005514.6	78	Cag/Tag	2/8	1	2	FACETS	0.47	0.416	0.528	0.47	0.416	0.528	SUBCLONAL	1	TRUE	1	0.348816155929287	2		861	1111	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353965	15353965	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	64	269	0	ENST00000263377.2:c.2915A>T	p.Gln972Leu	p.Q972L	ENST00000263377	NM_058243.2	972	cAg/cTg	14/20	1	2	FACETS	0.981	0.854	1	0.981	0.854	1	CLONAL	1	TRUE	1	0.348816155929287	2		269	374	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229252	36229252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	201	755	0	ENST00000222270.7:c.7942G>A	p.Ala2648Thr	p.A2648T	ENST00000222270	NM_014727.1	2648	Gcc/Acc	37/37	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.348816155929287	2		755	1045	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587160	189587160	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs941268998	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	80	342	0	ENST00000264731.3:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000264731	NM_003722.4	393	Cga/Tga	9/14	1	2	FACETS	0.862	0.761	0.971	0.862	0.761	0.971	CLONAL	1	TRUE	1	0.348816155929287	2		342	532	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1627417	1627417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201841190	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	60	867	0	ENST00000344749.5:c.307G>A	p.Gly103Ser	p.G103S	ENST00000344749	NM_001136139.2	103	Ggt/Agt	6/19	1	2	FACETS	0.298	0.256	0.345	0.298	0.256	0.345	SUBCLONAL	1	TRUE	1	0.348816155929287	2		867	1154	SUCCESS
ATR	545	MSKCC	GRCh37	3	142224106	142224106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1309474194	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	103	324	0	ENST00000350721.4:c.5071G>A	p.Gly1691Arg	p.G1691R	ENST00000350721	NM_001184.3	1691	Gga/Aga	29/47	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.348816155929287	2		324	542	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20486919	20486919	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs376318599	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	51	236	0	ENST00000346618.3:c.885-1C>T		p.X295_splice	ENST00000346618	NM_001949.4	295			1	2	FACETS	0.865	0.739	1	0.865	0.739	1	CLONAL	1	TRUE	1	0.348816155929287	2		236	338	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845958	151845959	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	136	560	0	ENST00000262189.6:c.13053dup	p.Trp4352MetfsTer17	p.W4352Mfs*17	ENST00000262189	NM_170606.2	4351	-/A	52/59	1	2	FACETS	0.874	0.795	0.958	0.874	0.795	0.958	CLONAL	1	TRUE	1	0.348816155929287	2		560	892	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138934	64138934	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	85	434	0	ENST00000334205.4:c.2305del	p.Leu769CysfsTer15	p.L769Cfs*15	ENST00000334205	NM_003942.2	767	ggC/gg	17/17	1	2	FACETS	0.893	0.791	1	0.893	0.791	1	CLONAL	1	TRUE	1	0.348816155929287	2		434	546	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436060	49436060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777415982	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	152	699	1	ENST00000301067.7:c.5921C>T	p.Thr1974Met	p.T1974M	ENST00000301067	NM_003482.3	1974	aCg/aTg	28/54	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.348816155929287	2		700	869	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440135	49440136	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	149	653	0	ENST00000301067.7:c.4490_4491del	p.His1497LeufsTer30	p.H1497Lfs*30	ENST00000301067	NM_003482.3	1497	cAC/c	16/54	1	2	FACETS	0.98	0.895	1	0.98	0.895	1	CLONAL	1	TRUE	1	0.348816155929287	2		653	872	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246416	46246416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140500006	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	65	285	0	ENST00000334344.6:c.4510C>T	p.Arg1504Trp	p.R1504W	ENST00000334344	NM_152641.2	1504	Cgg/Tgg	15/21	1	2	FACETS	0.875	0.761	0.997	0.875	0.761	0.997	CLONAL	1	TRUE	1	0.348816155929287	2		285	426	SUCCESS
APC	324	MSKCC	GRCh37	5	112175015	112175015	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1460397656	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	58	159	0	ENST00000257430.4:c.3724C>T	p.Gln1242Ter	p.Q1242*	ENST00000257430	NM_000038.5	1242	Cag/Tag	16/16	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.348816155929287	2		159	311	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40744850	40744850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1322643388	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	150	804	0	ENST00000392038.2:c.670C>T	p.Arg224Cys	p.R224C	ENST00000392038	NM_001626.4	224	Cgc/Tgc	8/14	1	2	FACETS	0.8	0.73	0.874	0.8	0.73	0.874	SUBCLONAL	1	TRUE	1	0.348816155929287	2		804	1075	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519422	137519422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	69	261	0	ENST00000367739.4:c.1216G>A	p.Asp406Asn	p.D406N	ENST00000367739	NM_000416.2	406	Gat/Aat	7/7	1	2	FACETS	0.989	0.865	1	0.989	0.865	1	CLONAL	1	TRUE	1	0.348816155929287	2		261	400	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858561	57858561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763470494	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	191	795	3	ENST00000228682.2:c.299G>A	p.Arg100His	p.R100H	ENST00000228682	NM_005269.2	100	cGc/cAc	4/12	1	2	FACETS	0.974	0.9	1	0.974	0.9	1	CLONAL	1	TRUE	1	0.348816155929287	2		798	1124	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224088	39224088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	134	541	0	ENST00000402219.2:c.3056G>A	p.Arg1019Gln	p.R1019Q	ENST00000402219	NM_005633.3	1019	cGa/cAa	19/23	0.348816155929287	2	FACETS	0.966	0.879	1	0.483	0.439	0.53	CLONAL	1	TRUE	0	0.348816155929287	2		541	795	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303270	15303270	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	188	1047	0	ENST00000263388.2:c.258del	p.Cys87ValfsTer149	p.C87Vfs*149	ENST00000263388	NM_000435.2	86	ccC/cc	3/33	1	2	FACETS	0.818	0.754	0.885	0.818	0.754	0.885	CLONAL	1	TRUE	1	0.348816155929287	2		1047	1318	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17947980	17947980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs193922361	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	231	933	0	ENST00000458235.1:c.1744C>T	p.Arg582Trp	p.R582W	ENST00000458235	NM_000215.3	582	Cgg/Tgg	13/24	1	2	FACETS	0.988	0.92	1	0.988	0.92	1	CLONAL	1	TRUE	1	0.348816155929287	2		933	1340	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606829	43606829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs537874538	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	228	1000	1	ENST00000355710.3:c.1438G>A	p.Glu480Lys	p.E480K	ENST00000355710	NM_020975.4	480	Gaa/Aaa	7/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.348816155929287	2		1001	1279	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371770	116371770	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs369705803	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	93	347	0	ENST00000397752.3:c.1249C>T	p.Arg417Ter	p.R417*	ENST00000397752	NM_000245.2	417	Cga/Tga	3/21	1	2	FACETS	0.924	0.823	1	0.924	0.823	1	CLONAL	1	TRUE	1	0.348816155929287	2		347	577	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573002	41573002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266719702	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	236	848	0	ENST00000263253.7:c.5287C>T	p.Arg1763Trp	p.R1763W	ENST00000263253	NM_001429.3	1763	Cgg/Tgg	31/31	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.348816155929287	2		848	1176	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073432	8073432	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs779337445	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	140	409	0	ENST00000377482.5:c.1227A>T	p.Lys409Asn	p.K409N	ENST00000377482	NM_018948.3	409	aaA/aaT	4/4	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.348816155929287	2		409	666	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784401	9784401	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773911101	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	157	631	0	ENST00000377346.4:c.2786G>A	p.Arg929His	p.R929H	ENST00000377346	NM_005026.3	929	cGt/cAt	22/24	1	2	FACETS	0.898	0.822	0.978	0.898	0.822	0.978	CLONAL	1	TRUE	1	0.348816155929287	2		631	1002	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089546	27089547	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	204	708	0	ENST00000324856.7:c.2503dup	p.Met835AsnfsTer37	p.M835Nfs*37	ENST00000324856	NM_006015.4	834	-/A	8/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.348816155929287	2		708	1058	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798262	45798262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	198	672	0	ENST00000450313.1:c.674C>T	p.Ser225Phe	p.S225F	ENST00000450313	NM_012222.2	225	tCt/tTt	8/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.348816155929287	2		672	987	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303781	65303781	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	126	401	0	ENST00000342505.4:c.2974G>A	p.Asp992Asn	p.D992N	ENST00000342505	NM_002227.2	992	Gac/Aac	22/25	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.348816155929287	2		401	610	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837964	156837964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	240	1056	1	ENST00000524377.1:c.497G>A	p.Gly166Glu	p.G166E	ENST00000524377	NM_002529.3	166	gGa/gAa	5/17	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.348816155929287	2		1057	1326	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392613	118392613	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	99	397	0	ENST00000534358.1:c.11645G>A	p.Gly3882Asp	p.G3882D	ENST00000534358	NM_005933.3	3882	gGc/gAc	36/36	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.348816155929287	2		397	495	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433721	49433721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374000532	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	259	1089	1	ENST00000301067.7:c.7832G>A	p.Arg2611His	p.R2611H	ENST00000301067	NM_003482.3	2611	cGc/cAc	31/54	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.348816155929287	2		1090	1418	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518693	103518693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142438319	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	67	317	1	ENST00000355739.4:c.2281G>A	p.Ala761Thr	p.A761T	ENST00000355739	NM_000123.3	761	Gct/Act	10/15	1	2	FACETS	0.867	0.756	0.987	0.867	0.756	0.987	CLONAL	1	TRUE	1	0.348816155929287	2		318	443	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061711	38061711	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs567068679	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	82	414	0	ENST00000250448.2:c.278T>C	p.Met93Thr	p.M93T	ENST00000250448	NM_004496.3	93	aTg/aCg	2/2	1	2	FACETS	0.896	0.792	1	0.896	0.792	1	CLONAL	1	TRUE	1	0.348816155929287	2		414	525	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88428929	88428929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	41	291	0	ENST00000360948.2:c.2171G>A	p.Cys724Tyr	p.C724Y	ENST00000360948	NM_001012338.2	724	tGt/tAt	17/19	1	2	FACETS	0.562	0.469	0.666	0.562	0.469	0.666	SUBCLONAL	1	TRUE	1	0.348816155929287	2		291	418	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992246	72992246	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	205	921	0	ENST00000268489.5:c.1799C>T	p.Ala600Val	p.A600V	ENST00000268489	NM_006885.3	600	gCc/gTc	2/10	1	2	FACETS	0.942	0.872	1	0.942	0.872	1	CLONAL	1	TRUE	1	0.348816155929287	2		921	1248	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993363	72993363	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	195	848	0	ENST00000268489.5:c.682C>A	p.Leu228Met	p.L228M	ENST00000268489	NM_006885.3	228	Ctg/Atg	2/10	1	2	FACETS	0.986	0.911	1	0.986	0.911	1	CLONAL	1	TRUE	1	0.348816155929287	2		848	1134	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89815164	89815164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752642945	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	146	712	0	ENST00000389301.3:c.3251G>A	p.Arg1084His	p.R1084H	ENST00000389301	NM_000135.2	1084	cGc/cAc	33/43	1	2	FACETS	0.893	0.815	0.976	0.893	0.815	0.976	CLONAL	1	TRUE	1	0.348816155929287	2		712	937	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441470	40441470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780375123	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	324	815	0	ENST00000345506.4:c.41C>T	p.Ala14Val	p.A14V	ENST00000345506	NM_003152.3	14	gCg/gTg	3/20	0.280246957165635	2	FACETS	0.93	0.88	0.981	0.93	0.88	0.981	CLONAL	2	TRUE	0	0.348816155929287	2		815	999	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216499	2216499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs953702113	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	243	1003	0	ENST00000398665.3:c.2143G>A	p.Gly715Ser	p.G715S	ENST00000398665	NM_032482.2	715	Ggc/Agc	20/28	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.348816155929287	2		1003	1376	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350545	15350545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	206	956	1	ENST00000263377.2:c.3370C>T	p.Pro1124Ser	p.P1124S	ENST00000263377	NM_058243.2	1124	Ccc/Tcc	16/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.348816155929287	2		957	1160	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909688	50909688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	210	951	0	ENST00000440232.2:c.1408C>T	p.Arg470Cys	p.R470C	ENST00000440232	NM_002691.3	470	Cgc/Tgc	12/27	1	2	FACETS	0.977	0.906	1	0.977	0.906	1	CLONAL	1	TRUE	1	0.348816155929287	2		951	1232	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917120	50917120	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1174011798	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	213	1020	0	ENST00000440232.2:c.2372G>A	p.Arg791Gln	p.R791Q	ENST00000440232	NM_002691.3	791	cGg/cAg	19/27	1	2	FACETS	0.92	0.853	0.99	0.92	0.853	0.99	CLONAL	1	TRUE	1	0.348816155929287	2		1020	1327	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082520	16082520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	190	815	1	ENST00000281043.3:c.334C>T	p.Leu112Phe	p.L112F	ENST00000281043	NM_005378.4	112	Ctc/Ttc	2/3	0.348816155929287	2	FACETS	1	0.961	1	0.531	0.49	0.573	CLONAL	1	TRUE	0	0.348816155929287	2		816	1026	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143024	30143024	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1374532256	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	198	1033	0	ENST00000389048.3:c.502T>C	p.Phe168Leu	p.F168L	ENST00000389048	NM_004304.4	168	Ttc/Ctc	1/29	0.348816155929287	2	FACETS	0.881	0.815	0.951	0.441	0.407	0.476	CLONAL	1	TRUE	0	0.348816155929287	2		1033	1288	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61725902	61725902	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	103	351	0	ENST00000401558.2:c.665T>C	p.Val222Ala	p.V222A	ENST00000401558	NM_003400.3	222	gTa/gCa	9/25	0.348816155929287	2	FACETS	0.989	0.887	1	0.495	0.443	0.549	CLONAL	1	TRUE	0	0.348816155929287	2		351	597	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116275	209116275	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	43	210	0	ENST00000345146.2:c.1A>G	p.Met1?	p.M1?	ENST00000345146	NM_005896.2	1	Atg/Gtg	3/10	1	2	FACETS	0.859	0.723	1	0.859	0.723	1	CLONAL	1	TRUE	1	0.348816155929287	2		210	287	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376805	31376805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1357390175	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	120	580	0	ENST00000328111.2:c.800G>A	p.Gly267Asp	p.G267D	ENST00000328111	NM_006892.3	267	gGc/gAc	7/23	1	2	FACETS	0.881	0.796	0.971	0.881	0.796	0.971	CLONAL	1	TRUE	1	0.348816155929287	2		580	781	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980795	40980795	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	120	598	0	ENST00000373198.4:c.1691T>C	p.Phe564Ser	p.F564S	ENST00000373198	NM_133170.3	564	tTc/tCc	10/32	1	2	FACETS	0.861	0.778	0.949	0.861	0.778	0.949	CLONAL	1	TRUE	1	0.348816155929287	2		598	799	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181887	38181887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1224202791	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	86	323	0	ENST00000396334.3:c.511C>T	p.Pro171Ser	p.P171S	ENST00000396334	NM_002468.4	171	Cct/Tct	3/5	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.348816155929287	2		323	461	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026841	71026841	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	70	229	0	ENST00000318789.4:c.1381A>G	p.Asn461Asp	p.N461D	ENST00000318789	NM_032682.5	461	Aac/Gac	16/21	1	2	FACETS	0.944	0.827	1	0.944	0.827	1	CLONAL	1	TRUE	1	0.348816155929287	2		229	425	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825345	134825345	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	111	548	0	ENST00000398015.3:c.864del	p.Ser289ProfsTer66	p.S289Pfs*66	ENST00000398015	NM_004441.4	287	tgC/tg	4/16	1	2	FACETS	0.879	0.791	0.972	0.879	0.791	0.972	CLONAL	1	TRUE	1	0.348816155929287	2		548	724	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431041	181431041	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	162	848	0	ENST00000325404.1:c.893A>G	p.Tyr298Cys	p.Y298C	ENST00000325404	NM_003106.3	298	tAc/tGc	1/1	1	2	FACETS	0.818	0.749	0.89	0.818	0.749	0.89	CLONAL	1	TRUE	1	0.348816155929287	2		848	1136	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356306	66356306	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	116	442	0	ENST00000273854.3:c.1191G>T	p.Lys397Asn	p.K397N	ENST00000273854	NM_004439.5	397	aaG/aaT	5/18	1	2	FACETS	0.967	0.872	1	0.967	0.872	1	CLONAL	1	TRUE	1	0.348816155929287	2		442	688	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155392	106155392	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	94	383	0	ENST00000380013.4:c.293T>C	p.Val98Ala	p.V98A	ENST00000380013	NM_001127208.2	98	gTt/gCt	3/11	1	2	FACETS	0.897	0.799	1	0.897	0.799	1	CLONAL	1	TRUE	1	0.348816155929287	2		383	601	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627206	86627206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	64	237	0	ENST00000274376.6:c.581G>A	p.Arg194His	p.R194H	ENST00000274376	NM_002890.2	194	cGc/cAc	2/25	1	2	FACETS	0.973	0.847	1	0.973	0.847	1	CLONAL	1	TRUE	1	0.348816155929287	2		237	377	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86679535	86679535	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	81	311	0	ENST00000274376.6:c.2696T>C	p.Phe899Ser	p.F899S	ENST00000274376	NM_002890.2	899	tTt/tCt	21/25	1	2	FACETS	0.938	0.829	1	0.938	0.829	1	CLONAL	1	TRUE	1	0.348816155929287	2		311	495	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562840	176562840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1156510513	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	130	444	0	ENST00000439151.2:c.736G>A	p.Gly246Ser	p.G246S	ENST00000439151	NM_022455.4	246	Ggc/Agc	2/23	1	2	FACETS	0.979	0.889	1	0.979	0.889	1	CLONAL	1	TRUE	1	0.348816155929287	2		444	761	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721468	176721468	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	155	647	0	ENST00000439151.2:c.7099G>A	p.Ala2367Thr	p.A2367T	ENST00000439151	NM_022455.4	2367	Gct/Act	23/23	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.348816155929287	2		647	885	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680932	30680932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	161	721	0	ENST00000376406.3:c.787C>T	p.Pro263Ser	p.P263S	ENST00000376406	NM_014641.2	263	Cct/Tct	5/15	1	2	FACETS	0.912	0.836	0.992	0.912	0.836	0.992	CLONAL	1	TRUE	1	0.348816155929287	2		721	1012	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109319951	109319952	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	117	434	0	ENST00000436639.2:c.736_737del	p.Leu246LysfsTer3	p.L246Kfs*3	ENST00000436639	NM_014454.2	246	TTa/a	5/10	1	2	FACETS	0.979	0.884	1	0.979	0.884	1	CLONAL	1	TRUE	1	0.348816155929287	2		434	685	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942878	68942878	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	109	568	0	ENST00000288368.4:c.690C>A	p.His230Gln	p.H230Q	ENST00000288368	NM_024870.2	230	caC/caA	6/40	1	2	FACETS	0.834	0.749	0.924	0.834	0.749	0.924	CLONAL	1	TRUE	1	0.348816155929287	2		568	749	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268745	98268745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	144	538	2	ENST00000331920.6:c.338C>T	p.Ala113Val	p.A113V	ENST00000331920	NM_000264.3	113	gCg/gTg	2/24	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.348816155929287	2		540	803	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802599	135802599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	69	245	0	ENST00000298552.3:c.199C>T	p.Pro67Ser	p.P67S	ENST00000298552	NM_001162426.1	67	Cca/Tca	4/23	1	2	FACETS	0.965	0.844	1	0.965	0.844	1	CLONAL	1	TRUE	1	0.348816155929287	2		245	410	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349653	70349653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	181	634	0	ENST00000374080.3:c.3815C>T	p.Thr1272Ile	p.T1272I	ENST00000374080		1272	aCa/aTa	27/45	0.335084840228874	1	FACETS	0.986	0.91	1	0.986	0.91	1	CLONAL	1	TRUE	0	0.348816155929287	1		634	869	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0048222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4	185	650	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.976740421708903	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.976740421708903	1		650	189	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059244	27059245	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	243	576	0	ENST00000324856.7:c.1882dup	p.Met628AsnfsTer14	p.M628Nfs*14	ENST00000324856	NM_006015.4	627	-/A	4/20	0.976740421708903	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.976740421708903	1		576	250	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004934	16004934	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	273	715	0	ENST00000268712.3:c.2320C>G	p.Pro774Ala	p.P774A	ENST00000268712	NM_006311.3	774	Cca/Gca	20/46	0.976740421708903	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.976740421708903	1		715	279	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349910	15349910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200078058	NA	P-0048222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	101	870	3	ENST00000263377.2:c.3742G>A	p.Ala1248Thr	p.A1248T	ENST00000263377	NM_058243.2	1248	Gct/Act	18/20	0.601915540629199	1	FACETS	0.331	0.299	0.364	0.331	0.299	0.364	SUBCLONAL	1	TRUE	0	0.976740421708903	1		873	320	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609936	43609936	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs377767404	NA	P-0048223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	267	950	0	ENST00000355710.3:c.1888T>C	p.Cys630Arg	p.C630R	ENST00000355710	NM_020975.4	630	Tgc/Cgc	11/20	0.253555156493062	0	FACETS	1	0.955	1			1	CLONAL	1	FALSE	0	0.397684490430128	0		950	795	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0048224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	177	436	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.337070917858533	1	FACETS	0.876	0.807	0.948	0.876	0.807	0.948	CLONAL	1	TRUE	0	0.337070917858533	1		439	997	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202852	16202852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1377681458	NA	P-0048224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	109	621	0	ENST00000375759.3:c.560G>A	p.Arg187Gln	p.R187Q	ENST00000375759	NM_015001.2	187	cGg/cAg	3/15	1	2	FACETS	0.822	0.738	0.911	0.822	0.738	0.911	CLONAL	1	TRUE	1	0.337070917858533	2		621	787	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0048224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	127	497	0	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	0.337070917858533	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.337070917858533	1		497	579	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306996	65306997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	88	388	7	ENST00000342505.4:c.2580dup	p.Pro861ThrfsTer4	p.P861Tfs*4	ENST00000342505	NM_002227.2	860	-/A	19/25	0.326021247620365	1	FACETS	0.926	0.824	1	0.926	0.824	1	CLONAL	1	TRUE	0	0.337070917858533	1		395	469	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625426	69625426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	197	1084	1	ENST00000334134.2:c.367G>A	p.Glu123Lys	p.E123K	ENST00000334134	NM_005247.2	123	Gag/Aag	3/3	1	2	FACETS	0.964	0.891	1	0.964	0.891	1	CLONAL	1	TRUE	1	0.337070917858533	2		1085	1213	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398279	25398279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894365	NA	P-0048224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	112	415	0	ENST00000311936.3:c.40G>A	p.Val14Ile	p.V14I	ENST00000311936	NM_004985.3	14	Gta/Ata	2/5	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.337070917858533	2		415	651	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427984	49427984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	138	821	1	ENST00000301067.7:c.10606C>T	p.Arg3536Cys	p.R3536C	ENST00000301067	NM_003482.3	3536	Cgc/Tgc	38/54	1	2	FACETS	0.824	0.749	0.903	0.824	0.749	0.903	CLONAL	1	TRUE	1	0.337070917858533	2		822	994	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444879	49444879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370622706	NA	P-0048224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	193	1697	1	ENST00000301067.7:c.2587C>T	p.Arg863Trp	p.R863W	ENST00000301067	NM_003482.3	863	Cgg/Tgg	10/54	1	2	FACETS	0.91	0.84	0.983	0.91	0.84	0.983	CLONAL	1	TRUE	1	0.337070917858533	2		1698	1259	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557726	21557726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371745650	NA	P-0048224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	161	781	0	ENST00000382592.4:c.2119C>T	p.Arg707Trp	p.R707W	ENST00000382592	NM_014572.2	707	Cgg/Tgg	5/8	1	2	FACETS	0.985	0.903	1	0.985	0.903	1	CLONAL	1	TRUE	1	0.337070917858533	2		781	970	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606150	81606150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373712078	NA	P-0048224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	100	491	0	ENST00000298171.2:c.820C>T	p.Arg274Trp	p.R274W	ENST00000298171	NM_000369.2	274	Cgg/Tgg	9/10	0.28667903570574	1	FACETS	0.75	0.67	0.834	0.75	0.67	0.834	SUBCLONAL	1	TRUE	0	0.337070917858533	1		491	658	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094668	2094668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766136810	NA	P-0048224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1244	113	1147	2	ENST00000219066.1:c.512C>T	p.Thr171Met	p.T171M	ENST00000219066	NM_002528.5	171	aCg/aTg	3/6	0.28667903570574	1	FACETS	0.411	0.368	0.456	0.411	0.368	0.456	SUBCLONAL	1	TRUE	0	0.337070917858533	1		1149	1357	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14031663	14031663	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373565480	NA	P-0048224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	90	390	0	ENST00000311895.7:c.1852C>T	p.Arg618Cys	p.R618C	ENST00000311895	NM_005236.2	618	Cgc/Tgc	9/11	0.28667903570574	1	FACETS	0.804	0.715	0.899	0.804	0.715	0.899	CLONAL	1	TRUE	0	0.337070917858533	1		390	552	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575159	48575159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	58	326	0	ENST00000342988.3:c.353C>T	p.Ala118Val	p.A118V	ENST00000342988	NM_005359.5	118	gCg/gTg	3/12	0.337070917858533	1	FACETS	0.784	0.677	0.9	0.784	0.677	0.9	SUBCLONAL	1	TRUE	0	0.337070917858533	1		326	365	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226570	1226570	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782364	NA	P-0048224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	209	1053	6	ENST00000326873.7:c.1226G>A	p.Arg409Gln	p.R409Q	ENST00000326873	NM_000455.4	409	cGg/cAg	9/10	0.337070917858533	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.337070917858533	1		1059	1031	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141427	11141427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	176	896	0	ENST00000358026.2:c.3404G>A	p.Arg1135Gln	p.R1135Q	ENST00000358026	NM_001128849.1	1135	cGg/cAg	25/36	0.337070917858533	1	FACETS	0.995	0.917	1	0.995	0.917	1	CLONAL	1	TRUE	0	0.337070917858533	1		896	873	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298005	15298005	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	268	1344	0	ENST00000263388.2:c.1751A>C	p.Asp584Ala	p.D584A	ENST00000263388	NM_000435.2	584	gAc/gCc	11/33	0.337070917858533	1	FACETS	0.928	0.868	0.989	0.928	0.868	0.989	CLONAL	1	TRUE	0	0.337070917858533	1		1344	1425	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798112	42798112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752780532	NA	P-0048224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	180	882	0	ENST00000575354.2:c.4066G>A	p.Glu1356Lys	p.E1356K	ENST00000575354	NM_015125.3	1356	Gaa/Aaa	17/20	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.337070917858533	2		882	1062	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910611	50910611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775434361	NA	P-0048224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	201	980	1	ENST00000440232.2:c.1714G>A	p.Val572Met	p.V572M	ENST00000440232	NM_002691.3	572	Gtg/Atg	14/27	1	2	FACETS	0.872	0.806	0.941	0.872	0.806	0.941	CLONAL	1	TRUE	1	0.337070917858533	2		981	1367	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790143	40790143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368317330	NA	P-0048224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	118	757	0	ENST00000373198.4:c.2588C>T	p.Thr863Met	p.T863M	ENST00000373198	NM_133170.3	863	aCg/aTg	18/32	0.326021247620365	1	FACETS	0.722	0.651	0.797	0.722	0.651	0.797	SUBCLONAL	1	TRUE	0	0.337070917858533	1		757	806	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0048224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	127	317	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.337070917858533	2		317	559	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620470	52620470	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	134	519	0	ENST00000394830.3:c.3283C>T	p.Arg1095Ter	p.R1095*	ENST00000394830	NM_018313.4	1095	Cga/Tga	21/30	0.337070917858533	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.337070917858533	1		519	629	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280027	66280027	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	64	236	0	ENST00000273854.3:c.1662A>T	p.Arg554Ser	p.R554S	ENST00000273854	NM_004439.5	554	agA/agT	7/18	0.337070917858533	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.337070917858533	1		236	274	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397141	397141	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs756699452	NA	P-0048224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	121	512	0	ENST00000380956.4:c.526C>T	p.Arg176Ter	p.R176*	ENST00000380956	NM_001195286.1	176	Cga/Tga	5/9	0.337070917858533	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.337070917858533	1		512	559	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482864	140482864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756851654	NA	P-0048224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	131	583	0	ENST00000288602.6:c.1271G>A	p.Arg424Gln	p.R424Q	ENST00000288602	NM_004333.4	424	cGa/cAa	10/18	1	2	FACETS	0.908	0.824	0.997	0.908	0.824	0.997	CLONAL	1	TRUE	1	0.337070917858533	2		583	856	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0048224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	198	510	1	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.337070917858533	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.337070917858533	1		511	718	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399363	139399363	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1213244424	NA	P-0048224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	232	1197	3	ENST00000277541.6:c.4780C>T	p.Arg1594Trp	p.R1594W	ENST00000277541	NM_017617.3	1594	Cgg/Tgg	26/34	0.337070917858533	1	FACETS	0.934	0.87	1	0.934	0.87	1	CLONAL	1	TRUE	0	0.337070917858533	1		1200	1225	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	47	349	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.23595137873195	2		350	279	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0048225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	149	703	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.23595137873195	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	FALSE	1	0.23595137873195	3		703	596	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0048225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	105	660	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.228879584256116	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	FALSE	1	0.23595137873195	3		660	454	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788617	3788617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519884	NA	P-0048225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	63	405	0	ENST00000262367.5:c.4337G>A	p.Arg1446His	p.R1446H	ENST00000262367	NM_004380.2	1446	cGc/cAc	26/31	0.23595137873195	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	0	0.23595137873195	1		405	373	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425119	49425119	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	118	1148	0	ENST00000301067.7:c.13369G>T	p.Glu4457Ter	p.E4457*	ENST00000301067	NM_003482.3	4457	Gaa/Taa	39/54	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.23595137873195	2		1148	695	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988553	36988553	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	126	955	0	ENST00000354822.5:c.100A>T	p.Ser34Cys	p.S34C	ENST00000354822	NM_001079668.2	34	Agt/Tgt	2/3	0.228879584256116	3	FACETS	1	0.98	1	0.663	0.6	0.73	CLONAL	1	FALSE	1	0.23595137873195	3		955	900	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482843	67482927	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	CCCCAAGCATCCGCTGTTCCAGTGTGTCTTAGAGACATCAAGTATGGTAGGGGAGGGCAGGCTTGGGGAAAATGGCCATGCAGGA	CCCCAAGCATCCGCTGTTCCAGTGTGTCTTAGAGACATCAAGTATGGTAGGGGAGGGCAGGCTTGGGGAAAATGGCCATGCAGGA	-	novel	NA	P-0048225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	38	648	0	ENST00000327367.4:c.1247_*53del		p.*416*	ENST00000327367	NM_005902.3	416		9/9	1	2	FACETS	0.657	0.543	0.785	0.657	0.543	0.785	SUBCLONAL	1	FALSE	1	0.23595137873195	2		648	490	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860773	45860773	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	74	855	0	ENST00000391945.4:c.1336C>G	p.Pro446Ala	p.P446A	ENST00000391945	NM_000400.3	446	Ccc/Gcc	14/23	0.23595137873195	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	0	0.23595137873195	1		855	494	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945154	44945154	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	81	267	0	ENST00000377967.4:c.3478G>C	p.Gly1160Arg	p.G1160R	ENST00000377967	NM_021140.2	1160	Ggc/Cgc	24/29	1	1	FACETS	1	0.966	1	1	0.987	1	CLONAL	2	FALSE	0	0.23595137873195	1		267	251	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179163	123179187	+	frameshift_variant	Frame_Shift_Del	DEL	TACAGGATTGTCTGACTCACAAGTC	TACAGGATTGTCTGACTCACAAGTC	-	novel	NA	P-0048225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	44	262	0	ENST00000218089.9:c.612_636del	p.Thr205GlufsTer12	p.T205Efs*12	ENST00000218089	NM_001042749.1	204	ctTACAGGATTGTCTGACTCACAAGTC/ct	8/35	1	1	FACETS	0.835	0.709	0.971	1	0.967	1	CLONAL	2	FALSE	0	0.23595137873195	1		262	197	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0048226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	262	436	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.496239515919347	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.496239515919347	1		439	785	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0048226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	144	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.357939522066523	1	FACETS	0.951	0.874	1	0.951	0.874	1	CLONAL	1	TRUE	0	0.496239515919347	1		327	459	SUCCESS
APC	324	MSKCC	GRCh37	5	112174043	112174043	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	107	320	0	ENST00000257430.4:c.2752G>T	p.Glu918Ter	p.E918*	ENST00000257430	NM_000038.5	918	Gag/Tag	16/16	0.496239515919347	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.496239515919347	1		320	304	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129867	55129867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373126818	NA	P-0048226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	51	504	2	ENST00000257290.5:c.401C>T	p.Thr134Met	p.T134M	ENST00000257290	NM_006206.4	134	aCg/aTg	4/23	0.289835463941218	2	FACETS	0.372	0.316	0.434	0.186	0.158	0.217	INDETERMINATE	1	TRUE	0	0.496239515919347	2		506	552	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386388	31386388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	312	837	0	ENST00000328111.2:c.1613G>A	p.Arg538His	p.R538H	ENST00000328111	NM_006892.3	538	cGc/cAc	15/23	0.123807011211745	4	FACETS	0.799	0.754	0.846	0.799	0.754	0.846	INDETERMINATE	2	TRUE	2	0.496239515919347	4		837	1177	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338609	70338609	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866295169	NA	P-0048226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	80	739	0	ENST00000374080.3:c.5C>T	p.Ala2Val	p.A2V	ENST00000374080		2	gCg/gTg	1/45	1	2	FACETS	0.304	0.266	0.344	0.304	0.266	0.344	SUBCLONAL	1	TRUE	1	0.496239515919347	2		739	1062	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371800	116371800	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376364468	NA	P-0048226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	196	383	0	ENST00000397752.3:c.1279G>A	p.Val427Ile	p.V427I	ENST00000397752	NM_000245.2	427	Gtt/Att	3/21	0.214026822710498	3	FACETS	1	0.99	1	0.713	0.663	0.765	INDETERMINATE	1	TRUE	1	0.496239515919347	3		383	691	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578188	7578188	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201592	NA	P-0048227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	545	810	0	ENST00000269305.4:c.661G>T	p.Glu221Ter	p.E221*	ENST00000269305	NM_001126112.2	221	Gag/Tag	6/11	0.69295065999552	2	FACETS	0.987	0.959	1	0.987	0.959	1	CLONAL	2	TRUE	0	0.724031008498538	2		810	763	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0048228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	1005	660	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.819425416772824	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.819425416772824	3		660	1137	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0048228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	375	496	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.819425416772824	2		496	850	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0048228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	180	395	1	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.819425416772824	2		396	433	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217229	11217229	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519913	NA	P-0048228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	310	691	0	ENST00000361445.4:c.4449C>G	p.Cys1483Trp	p.C1483W	ENST00000361445	NM_004958.3	1483	tgC/tgG	30/58	1	2	FACETS	0.943	0.894	0.994	0.943	0.894	0.994	CLONAL	1	TRUE	1	0.819425416772824	2		691	802	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0048231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	275	570	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.264313412078934	3	FACETS	0.872	0.822	0.922	0.872	0.822	0.922	CLONAL	3	TRUE	0	0.312116324478422	3		571	779	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36823932	36823932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs945529881	NA	P-0048231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	80	809	0	ENST00000373129.3:c.250C>T	p.Arg84Trp	p.R84W	ENST00000373129	NM_032017.1	84	Cgg/Tgg	5/12	0.241292508201744	4	FACETS	0.726	0.638	0.822	0.242	0.212	0.274	SUBCLONAL	1	TRUE	1	0.312116324478422	4		809	926	SUCCESS
ATR	545	MSKCC	GRCh37	3	142180912	142180924	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTGCATCTTTT	CTCTGCATCTTTT	-	novel	NA	P-0048231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	45	308	0	ENST00000350721.4:c.7050_7062del	p.Arg2350SerfsTer17	p.R2350Sfs*17	ENST00000350721	NM_001184.3	2350	agAAAAGATGCAGAG/ag	42/47	0.245959327712172	3	FACETS	1	0.942	1	0.629	0.532	0.734	CLONAL	1	TRUE	1	0.312116324478422	3		308	265	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0048232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	204	436	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.355867896581884	1	FACETS	0.865	0.802	0.93	0.865	0.802	0.93	CLONAL	1	TRUE	0	0.39248525597449	1		439	966	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0048232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	110	646	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.355867896581884	1	FACETS	0.511	0.459	0.567	0.511	0.459	0.567	SUBCLONAL	1	TRUE	0	0.39248525597449	1		646	881	SUCCESS
APC	324	MSKCC	GRCh37	5	112173283	112173284	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0048232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	27	171	0	ENST00000257430.4:c.1993_1994del	p.Leu665IlefsTer8	p.L665Ifs*8	ENST00000257430	NM_000038.5	664	acTTta/acta	16/16	0.39248525597449	1	FACETS	0.953	0.773	1	0.953	0.773	1	CLONAL	1	TRUE	0	0.39248525597449	1		171	116	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168694	32168694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143040647	NA	P-0048232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	212	1203	2	ENST00000375023.3:c.4229G>A	p.Arg1410His	p.R1410H	ENST00000375023	NM_004557.3	1410	cGc/cAc	23/30	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.39248525597449	2		1205	1011	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982309	201982309	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0048232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	346	1131	0	ENST00000359651.3:c.689-1G>C		p.X230_splice	ENST00000359651		230			0.306451563042406	2	FACETS	0.918	0.872	0.966	0.918	0.872	0.966	CLONAL	2	TRUE	0	0.39248525597449	2		1131	960	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50815172	50815172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	149	577	0	ENST00000398568.2:c.1525G>A	p.Gly509Ser	p.G509S	ENST00000398568	NM_001042412.1	509	Ggc/Agc	9/18	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.39248525597449	2		577	684	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441118	149441118	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	249	1122	0	ENST00000286301.3:c.1794G>T	p.Glu598Asp	p.E598D	ENST00000286301	NM_005211.3	598	gaG/gaT	13/22	0.39248525597449	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.39248525597449	1		1122	810	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0048233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	23	819	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.799739368794513	2	FACETS	0.992	0.87	1	0.992	0.87	1	CLONAL	2	TRUE	0	0.799739368794513	2		819	29	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788651	3788651	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	12	428	0	ENST00000262367.5:c.4303G>T	p.Asp1435Tyr	p.D1435Y	ENST00000262367	NM_004380.2	1435	Gat/Tat	26/31	0.599640622063201	3	FACETS	0.712	0.513	0.944	0.356	0.256	0.472	CLONAL	1	TRUE	1	0.799739368794513	3		428	59	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107212	11107212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	60	711	0	ENST00000358026.2:c.1804G>A	p.Asp602Asn	p.D602N	ENST00000358026	NM_001128849.1	602	Gat/Aat	11/36	0.799739368794513	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	0	0.799739368794513	3		711	66	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540309	187540309	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	18	482	0	ENST00000441802.2:c.7431G>T	p.Gln2477His	p.Q2477H	ENST00000441802	NM_005245.3	2477	caG/caT	10/27	1	2	FACETS	0.834	0.652	1	0.834	0.652	1	CLONAL	1	TRUE	1	0.799739368794513	2		482	54	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873722	151873722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748870708	NA	P-0048233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	35	621	0	ENST00000262189.6:c.8816C>T	p.Pro2939Leu	p.P2939L	ENST00000262189	NM_170606.2	2939	cCa/cTa	38/59	0.443046295364816	5	FACETS	0.844	0.722	0.969	0.844	0.722	0.969	INDETERMINATE	3	TRUE	2	0.799739368794513	5		621	76	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319947	8319947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	85	273	0	ENST00000356435.5:c.5554G>A	p.Gly1852Arg	p.G1852R	ENST00000356435		1852	Gga/Aga	34/35	0.710031481028299	6	FACETS	0.906	0.84	0.968	1	0.975	1	CLONAL	5	TRUE	2	0.799739368794513	6		273	122	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171423	123171423	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs140238058	NA	P-0048233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1	35	509	0	ENST00000218089.9:c.335T>C	p.Ile112Thr	p.I112T	ENST00000218089	NM_001042749.1	112	aTa/aCa	6/35	0.799739368794513	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.799739368794513	2		509	36	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954220	48954237	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTAAATTTTTTACTTTT	GGTAAATTTTTTACTTTT	AA	novel	NA	P-0048233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	30	205	1	ENST00000267163.4:c.1421_1421+17delinsAA		p.X474_splice	ENST00000267163	NM_000321.2	474		15/27	0.799739368794513	2	FACETS	0.962	0.855	1	0.962	0.855	1	CLONAL	2	TRUE	0	0.799739368794513	2		206	39	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0048234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	86	566	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.885	0.784	0.993	0.885	0.784	0.993	CLONAL	1	TRUE	1	0.317120077192445	2		566	613	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591902	48591902	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519740	NA	P-0048234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	108	450	0	ENST00000342988.3:c.1065C>A	p.Asp355Glu	p.D355E	ENST00000342988	NM_005359.5	355	gaC/gaA	9/12	0.317120077192445	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.317120077192445	1		450	544	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566845	212566845	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	70	219	0	ENST00000342788.4:c.1336C>A	p.Gln446Lys	p.Q446K	ENST00000342788	NM_005235.2	446	Cag/Aag	12/28	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.317120077192445	2		219	376	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0048236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	18	566	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.0792955739526207	3	FACETS	0.663	0.498	0.859	0.332	0.249	0.43	INDETERMINATE	1	TRUE	1	0.15	3		566	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578551	7578551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	45	811	0	ENST00000269305.4:c.379T>C	p.Ser127Pro	p.S127P	ENST00000269305	NM_001126112.2	127	Tcc/Ccc	5/11	1	2	FACETS	0.709	0.594	0.837	0.709	0.594	0.837	SUBCLONAL	1	TRUE	1	0.15	2		811	846	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575121	48575122	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	18	244	0	ENST00000342988.3:c.320dup	p.Asn107LysfsTer2	p.N107Kfs*2	ENST00000342988	NM_005359.5	105	-/A	3/12	1	2	FACETS	0.732	0.55	0.946	0.732	0.55	0.946	CLONAL	1	TRUE	1	0.15	2		244	328	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974759	21974759	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	19	315	0	ENST00000304494.5:c.68del	p.Gly23ValfsTer3	p.G23Vfs*3	ENST00000304494	NM_000077.4	23	gGt/gt	1/3	1	2	FACETS	0.997	0.758	1	0.997	0.758	1	CLONAL	1	TRUE	1	0.15	2		315	254	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040891	42040891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753360563	NA	P-0048236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	23	468	0	ENST00000219905.7:c.5269C>T	p.Arg1757Cys	p.R1757C	ENST00000219905	NM_001164273.1	1757	Cgt/Tgt	16/24	1	2	FACETS	0.737	0.574	0.927	0.737	0.574	0.927	CLONAL	1	TRUE	1	0.15	2		468	416	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	113	432	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.861	0.777	0.949	0.861	0.777	0.949	CLONAL	1	TRUE	1	0.458051819651828	2		432	573	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0048240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	126	279	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	0.458051819651828	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.458051819651828	2		279	239	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0048240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	137	288	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	0.458051819651828	2	FACETS	0.89	0.821	0.96	0.89	0.821	0.96	CLONAL	2	TRUE	0	0.458051819651828	2		288	336	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247165	153247165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	48	145	0	ENST00000281708.4:c.1637C>T	p.Ser546Leu	p.S546L	ENST00000281708	NM_033632.3	546	tCa/tTa	10/12	1	2	FACETS	0.862	0.736	0.999	0.862	0.736	0.999	CLONAL	1	TRUE	1	0.458051819651828	2		145	243	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444519	187444519	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	151	451	1	ENST00000232014.4:c.1708G>A	p.Gly570Ser	p.G570S	ENST00000232014	NM_001130845.1	570	Ggt/Agt	7/10	1	2	FACETS	0.804	0.736	0.876	0.804	0.736	0.876	CLONAL	1	TRUE	1	0.458051819651828	2		452	820	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374945	45374945	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	283	299	0	ENST00000262160.6:c.898G>C	p.Asp300His	p.D300H	ENST00000262160	NM_005901.5	300	Gat/Cat	8/11	0.458051819651828	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.458051819651828	2		299	601	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754077	42754077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1381343253	NA	P-0048240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	151	396	0	ENST00000222329.4:c.275G>A	p.Arg92His	p.R92H	ENST00000222329	NM_006494.2	92	cGc/cAc	3/4	1	2	FACETS	0.987	0.905	1	0.987	0.905	1	CLONAL	1	TRUE	1	0.458051819651828	2		396	668	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482861	67482861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	114	342	0	ENST00000327367.4:c.1265C>T	p.Ser422Phe	p.S422F	ENST00000327367	NM_005902.3	422	tCc/tTc	9/9	1	2	FACETS	0.834	0.753	0.919	0.834	0.753	0.919	CLONAL	1	TRUE	1	0.458051819651828	2		342	597	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245547	153245547	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0048240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	64	183	0	ENST00000281708.4:c.1645-1G>C		p.X549_splice	ENST00000281708	NM_033632.3	549			1	2	FACETS	0.984	0.86	1	0.984	0.86	1	CLONAL	1	TRUE	1	0.458051819651828	2		183	284	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519674	176519674	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	200	695	0	ENST00000292408.4:c.946G>A	p.Glu316Lys	p.E316K	ENST00000292408	NM_213647.1	316	Gag/Aag	8/18	0.458051819651828	2	FACETS	0.975	0.904	1	0.487	0.452	0.524	CLONAL	1	TRUE	0	0.458051819651828	2		695	896	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041677	47041677	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	160	475	0	ENST00000377604.3:c.1902G>C	p.Lys634Asn	p.K634N	ENST00000377604	NM_001204468.1	634	aaG/aaC	17/24	1	2	FACETS	0.987	0.907	1	0.987	0.907	1	CLONAL	1	TRUE	1	0.458051819651828	2		475	708	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0048241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	242	643	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.575447971103331	1	FACETS	0.951	0.894	1	0.951	0.894	1	CLONAL	1	TRUE	0	0.575447971103331	1		643	630	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947827	178947827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	187	231	1	ENST00000263967.3:c.2702G>T	p.Cys901Phe	p.C901F	ENST00000263967	NM_006218.2	901	tGt/tTt	19/21	0.417952050323601	4	FACETS	0.971	0.905	1	0.971	0.905	1	CLONAL	2	TRUE	2	0.575447971103331	4		232	527	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246445	105246445	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	312	553	0	ENST00000349310.3:c.155T>G	p.Leu52Arg	p.L52R	ENST00000349310	NM_001014432.1	52	cTc/cGc	4/15	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.575447971103331	2		553	909	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687424	37687424	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	169	371	1	ENST00000447079.4:c.4328T>A	p.Leu1443Gln	p.L1443Q	ENST00000447079	NM_015083.1	1443	cTg/cAg	14/14	NA	2	FACETS	0.863	0.795	0.932			1	INDETERMINATE	1	TRUE	NA	0.575447971103331	2		372	681	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631837	90631837	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	286	684	0	ENST00000330062.3:c.516G>T	p.Arg172Ser	p.R172S	ENST00000330062	NM_002168.2	172	agG/agT	4/11	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.618411792480317	2		684	919	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416757	29416757	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs746970974	NA	P-0048243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	142	358	0	ENST00000389048.3:c.4196T>C	p.Ile1399Thr	p.I1399T	ENST00000389048	NM_004304.4	1399	aTa/aCa	29/29	1	2	FACETS	0.949	0.871	1	0.949	0.871	1	CLONAL	1	TRUE	1	0.618411792480317	2		358	484	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652115	36652116	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	437	849	0	ENST00000244741.5:c.238dup	p.Thr80AsnfsTer9	p.T80Nfs*9	ENST00000244741	NM_000389.4	79	-/A	2/3	0.618411792480317	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.618411792480317	1		849	877	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0048244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	106	491	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.209863045470804	2		491	939	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230571	46230571	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	37	287	1	ENST00000334344.6:c.820C>T	p.Arg274Ter	p.R274*	ENST00000334344	NM_152641.2	274	Cga/Tga	8/21	1	2	FACETS	0.752	0.62	0.9	0.752	0.62	0.9	SUBCLONAL	1	TRUE	1	0.209863045470804	2		288	469	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798324	42798324	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0048244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	126	570	0	ENST00000575354.2:c.4196-1G>A		p.X1399_splice	ENST00000575354	NM_015125.3	1399			1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.209863045470804	2		570	1186	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266050	41266639	+	splice_donor_variant,splice_acceptor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	CAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCAAGATGATG	CAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCAAGATGATG	-	novel	NA	P-0048244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	34	202	0	ENST00000349496.5:c.51_440del		p.X17_splice	ENST00000349496	NM_001904.3	17	cCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAACTATCAAGATGATGca/cca	3-4/15	1	2	FACETS	0.888	0.726	1	0.888	0.726	1	CLONAL	1	TRUE	1	0.209863045470804	2		202	365	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295276	1295276	+	upstream_gene_variant	5'Flank	SNP	C	C	T	rs1278612687	NA	P-0048244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	109	475	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.209863045470804	2		476	963	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869619	117869619	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	43	278	0	ENST00000297338.2:c.575T>G	p.Leu192Arg	p.L192R	ENST00000297338	NM_006265.2	192	cTa/cGa	6/14	0.209863045470804	3	FACETS	0.9	0.753	1	0.45	0.376	0.532	CLONAL	1	TRUE	1	0.209863045470804	3		278	503	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0048245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	518	774	1	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.3	5	FACETS	1	0.985	1			1	CLONAL	5	TRUE	NA	0.16	5		775	1516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579321	7579322	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs587780067	NA	P-0048245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	102	545	0	ENST00000269305.4:c.365_366del	p.Val122AspfsTer26	p.V122Dfs*26	ENST00000269305	NM_001126112.2	122	gTG/g	4/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.16	2		545	866	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76876001	76876001	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0048245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	15	203	0	ENST00000373344.5:c.5135-1G>A		p.X1712_splice	ENST00000373344	NM_000489.3	1712			1	2	FACETS	0.7	0.511	0.926	0.7	0.511	0.926	SUBCLONAL	1	TRUE	1	0.16	2		203	268	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865756	57865756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1349	297	693	0	ENST00000228682.2:c.3233C>T	p.Ser1078Phe	p.S1078F	ENST00000228682	NM_005269.2	1078	tCt/tTt	12/12	0.3	6	FACETS	0.992	0.932	1			1	CLONAL	3	TRUE	NA	0.16	6		693	1646	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181853	56181853	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0048245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	23	244	0	ENST00000399503.3:c.4077T>A	p.Tyr1359Ter	p.Y1359*	ENST00000399503	NM_005921.1	1359	taT/taA	17/20	1	2	FACETS	0.763	0.594	0.958	0.763	0.594	0.958	CLONAL	1	TRUE	1	0.16	2		244	377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0048246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	249	712	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.355660238293081	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.40791791279603	1		712	884	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0048246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	103	246	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	0.397816312359204	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.40791791279603	1		246	351	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273905	10273905	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	212	662	3	ENST00000330684.3:c.364G>A	p.Val122Ile	p.V122I	ENST00000330684	NM_001134407.1	122	Gtc/Atc	2/13	1	2	FACETS	0.996	0.925	1	0.996	0.925	1	CLONAL	1	TRUE	1	0.40791791279603	2		665	1044	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907804	76907804	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	22	110	0	ENST00000373344.5:c.4357G>A	p.Glu1453Lys	p.E1453K	ENST00000373344	NM_000489.3	1453	Gag/Aag	15/35	0.40811721176356	2	FACETS	0.369	0.286	0.466			1	SUBCLONAL	1	TRUE	NA	0.40791791279603	2		110	292	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207817	102207817	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762729326	NA	P-0048246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	67	127	0	ENST00000263464.3:c.1799G>A	p.Arg600His	p.R600H	ENST00000263464	NM_001165.4	600	cGt/cAt	9/9	1	2	FACETS	0.795	0.694	0.904	0.795	0.694	0.904	CLONAL	1	TRUE	1	0.40791791279603	2		127	413	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447415	49447415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778237222	NA	P-0048246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	92	512	2	ENST00000301067.7:c.683G>A	p.Arg228His	p.R228H	ENST00000301067	NM_003482.3	228	cGc/cAc	6/54	1	2	FACETS	0.504	0.447	0.565	0.504	0.447	0.565	SUBCLONAL	1	TRUE	1	0.40791791279603	2		514	895	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80171569	80171569	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs779621335	NA	P-0048246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	24	205	0	ENST00000265081.6:c.3303-1G>A		p.X1101_splice	ENST00000265081	NM_002439.4	1101			0.361264260120541	2	FACETS	0.26	0.203	0.326	0.13	0.101	0.163	SUBCLONAL	1	TRUE	0	0.40791791279603	2		205	452	SUCCESS
APC	324	MSKCC	GRCh37	5	112174476	112174477	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs1060503362	NA	P-0048246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	111	152	0	ENST00000257430.4:c.3186_3187del	p.Ser1063Ter	p.S1063*	ENST00000257430	NM_000038.5	1062	cAA/c	16/16	0.361264260120541	2	FACETS	0.775	0.704	0.849	0.775	0.704	0.849	SUBCLONAL	2	TRUE	0	0.40791791279603	2		152	351	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140508739	140508739	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	43	373	0	ENST00000288602.6:c.561G>A	p.Met187Ile	p.M187I	ENST00000288602	NM_004333.4	187	atG/atA	4/18	0.240184651164989	2	FACETS	0.341	0.284	0.403	0.17	0.142	0.202	INDETERMINATE	1	TRUE	0	0.40791791279603	2		373	619	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0048247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	51	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		327	357	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998898	11998898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	21	52	0	ENST00000353533.5:c.400C>T	p.Arg134Trp	p.R134W	ENST00000353533	NM_003010.3	134	Cgg/Tgg	4/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		52	150	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105767	27105767	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	35	159	0	ENST00000324856.7:c.5378A>T	p.Lys1793Met	p.K1793M	ENST00000324856	NM_006015.4	1793	aAg/aTg	20/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		159	388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0048248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	351	436	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.733466660545552	1	FACETS	0.989	0.949	1	0.989	0.949	1	CLONAL	1	TRUE	0	0.763305425846607	1		439	575	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947852	178947852	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	297	201	0	ENST00000263967.3:c.2727C>A	p.Phe909Leu	p.F909L	ENST00000263967	NM_006218.2	909	ttC/ttA	19/21	0.763305425846607	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.763305425846607	3		201	534	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861143	57861143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772799269	NA	P-0048248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	220	449	1	ENST00000228682.2:c.940C>T	p.Arg314Cys	p.R314C	ENST00000228682	NM_005269.2	314	Cgc/Tgc	9/12	1	2	FACETS	0.765	0.714	0.817	0.765	0.714	0.817	SUBCLONAL	1	TRUE	1	0.763305425846607	2		450	754	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21553871	21553871	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	210	369	0	ENST00000382592.4:c.2731C>T	p.Pro911Ser	p.P911S	ENST00000382592	NM_014572.2	911	Ccg/Tcg	7/8	1	2	FACETS	0.919	0.859	0.98	0.919	0.859	0.98	CLONAL	1	TRUE	1	0.763305425846607	2		369	599	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0048250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	182	566	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.375311497329225	3	FACETS	0.861	0.797	0.926	0.861	0.797	0.926	CLONAL	2	TRUE	1	0.375311497329225	3		566	669	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0048250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	58	314	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.752	0.648	0.865	0.752	0.648	0.865	SUBCLONAL	1	TRUE	1	0.375311497329225	2		314	411	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471800	120471800	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782677147	NA	P-0048250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	130	331	0	ENST00000256646.2:c.3691C>T	p.Arg1231Trp	p.R1231W	ENST00000256646	NM_024408.3	1231	Cgg/Tgg	23/34	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.375311497329225	2		331	622	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508064	106508064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	24	178	0	ENST00000359195.3:c.58C>T	p.Arg20Cys	p.R20C	ENST00000359195	NM_002649.2	20	Cgc/Tgc	2/11	0.375311497329225	3	FACETS	0.357	0.28	0.447	0.179	0.14	0.224	SUBCLONAL	1	TRUE	1	0.375311497329225	3		178	425	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0048250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	132	261	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	0.167154571654883	2	FACETS	1	0.986	1	0.727	0.664	0.792	INDETERMINATE	1	TRUE	0	0.375311497329225	2		261	484	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0048250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	77	227	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.801	0.705	0.904	0.801	0.705	0.904	CLONAL	1	TRUE	1	0.375311497329225	2		227	512	SUCCESS
APC	324	MSKCC	GRCh37	5	112175324	112175324	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1211642532	NA	P-0048250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	135	146	0	ENST00000257430.4:c.4033G>T	p.Glu1345Ter	p.E1345*	ENST00000257430	NM_000038.5	1345	Gaa/Taa	16/16	0.375311497329225	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.375311497329225	2		146	332	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006138	22006138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	229	759	0	ENST00000276925.6:c.265C>T	p.Arg89Trp	p.R89W	ENST00000276925	NM_004936.3	89	Cgg/Tgg	2/2	1	2	FACETS	0.945	0.879	1	0.945	0.879	1	CLONAL	1	TRUE	1	0.375311497329225	2		759	1291	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199974	128199974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781161922	NA	P-0048250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	218	672	0	ENST00000341105.2:c.1331C>T	p.Pro444Leu	p.P444L	ENST00000341105	NM_032638.4	444	cCg/cTg	6/6	1	2	FACETS	0.987	0.917	1	0.987	0.917	1	CLONAL	1	TRUE	1	0.375311497329225	2		672	1177	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663346	67663346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771793540	NA	P-0048250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	88	226	1	ENST00000264010.4:c.1747G>A	p.Val583Ile	p.V583I	ENST00000264010	NM_006565.3	583	Gta/Ata	10/12	1	2	FACETS	0.843	0.749	0.944	0.843	0.749	0.944	CLONAL	1	TRUE	1	0.375311497329225	2		227	556	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120517	70120518	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0048250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	259	675	0	ENST00000245479.2:c.1520dup	p.Arg508SerfsTer70	p.R508Sfs*70	ENST00000245479	NM_000346.3	507	act/aCct	3/3	1	2	FACETS	0.966	0.903	1	0.966	0.903	1	CLONAL	1	TRUE	1	0.375311497329225	2		675	1429	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371747	45371747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	22	258	0	ENST00000262160.6:c.1244G>A	p.Arg415Lys	p.R415K	ENST00000262160	NM_005901.5	415	aGa/aAa	10/11	0.167154571654883	2	FACETS	0.269	0.208	0.34	0.134	0.104	0.17	INDETERMINATE	1	TRUE	0	0.375311497329225	2		258	436	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383804	84383804	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs751068863	NA	P-0048250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	90	394	0	ENST00000321945.7:c.1048G>C	p.Asp350His	p.D350H	ENST00000321945	NM_139076.2	350	Gac/Cac	9/9	1	2	FACETS	0.933	0.831	1	0.933	0.831	1	CLONAL	1	TRUE	1	0.375311497329225	2		394	514	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247175	153247175	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0048250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	86	192	0	ENST00000281708.4:c.1627A>T	p.Arg543Ter	p.R543*	ENST00000281708	NM_033632.3	543	Aga/Tga	10/12	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.375311497329225	2		192	406	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265322	152265322	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	88	257	0	ENST00000206249.3:c.775C>T	p.Arg259Ter	p.R259*	ENST00000206249	NM_000125.3	259	Cga/Tga	4/8	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.375311497329225	2		257	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0048251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	529	507	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.564638656752727	2		507	885	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959044	28959044	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	95	296	0	ENST00000282397.4:c.2094C>A	p.Asn698Lys	p.N698K	ENST00000282397	NM_002019.4	698	aaC/aaA	14/30	1	2	FACETS	0.845	0.758	0.937	0.845	0.758	0.937	CLONAL	1	TRUE	1	0.564638656752727	2		296	398	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423519	88423519	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	304	559	0	ENST00000360948.2:c.2316C>A	p.Phe772Leu	p.F772L	ENST00000360948	NM_001012338.2	772	ttC/ttA	18/19	0.387702504586377	4	FACETS	0.908	0.857	0.959	0.908	0.857	0.959	CLONAL	2	TRUE	2	0.564638656752727	4		559	928	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47127717	47127717	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759310174	NA	P-0048251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	37	439	0	ENST00000409792.3:c.5365G>A	p.Gly1789Ser	p.G1789S	ENST00000409792	NM_014159.6	1789	Ggc/Agc	11/21	0.564638656752727	2	FACETS	0.236	0.194	0.283	0.118	0.097	0.142	SUBCLONAL	1	TRUE	0	0.564638656752727	2		439	556	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2493143	2493143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	195	661	0	ENST00000355716.4:c.583G>A	p.Gly195Arg	p.G195R	ENST00000355716	NM_003820.2	195	Ggg/Agg	6/8	NA	2	FACETS	0.95	0.882	1			1	INDETERMINATE	1	TRUE	NA	0.564638656752727	2		661	727	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435110	49435110	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	570	763	0	ENST00000301067.7:c.6443G>T	p.Gly2148Val	p.G2148V	ENST00000301067	NM_003482.3	2148	gGc/gTc	31/54	0.359019690258769	5	FACETS	0.835	0.803	0.868	0.835	0.803	0.868	CLONAL	3	TRUE	2	0.564638656752727	5		763	1488	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964103	28964103	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs776472661	NA	P-0048251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	112	372	2	ENST00000282397.4:c.1799T>C	p.Met600Thr	p.M600T	ENST00000282397	NM_002019.4	600	aTg/aCg	13/30	1	2	FACETS	0.893	0.809	0.982	0.893	0.809	0.982	CLONAL	1	TRUE	1	0.564638656752727	2		374	444	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335619	73335619	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs764019855	NA	P-0048251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	49	194	0	ENST00000377767.4:c.2552A>G	p.Tyr851Cys	p.Y851C	ENST00000377767	NM_014953.3	851	tAt/tGt	19/21	0.564638656752727	1	FACETS	0.804	0.694	0.918	0.804	0.694	0.918	CLONAL	1	TRUE	0	0.564638656752727	1		194	155	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251019	99251019	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	191	552	0	ENST00000268035.6:c.323G>C	p.Gly108Ala	p.G108A	ENST00000268035	NM_000875.3	108	gGc/gCc	2/21	0.387702504586377	4	FACETS	1	0.946	1	0.514	0.475	0.555	CLONAL	1	TRUE	2	0.564638656752727	4		552	1029	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100642	67100642	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	70	489	0	ENST00000412916.2:c.340A>T	p.Ile114Phe	p.I114F	ENST00000412916		114	Att/Ttt	4/6	1	2	FACETS	0.305	0.265	0.348	0.305	0.265	0.348	SUBCLONAL	1	TRUE	1	0.564638656752727	2		489	813	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068448	16068448	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	16	111	0	ENST00000268712.3:c.463G>T	p.Ala155Ser	p.A155S	ENST00000268712	NM_006311.3	155	Gct/Tct	5/46	0.359019690258769	5	FACETS	0.516	0.382	0.674	0.172	0.127	0.225	SUBCLONAL	1	TRUE	2	0.564638656752727	5		111	203	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653001	29653001	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	260	394	0	ENST00000356175.3:c.4936C>A	p.Pro1646Thr	p.P1646T	ENST00000356175	NM_000267.3	1646	Cct/Act	36/57	0.359019690258769	5	FACETS	1	0.988	1	0.793	0.747	0.84	CLONAL	2	TRUE	2	0.564638656752727	5		394	715	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754910	29754910	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	172	526	0	ENST00000389048.3:c.1025G>C	p.Ser342Thr	p.S342T	ENST00000389048	NM_004304.4	342	aGt/aCt	4/29	1	2	FACETS	0.934	0.863	1	0.934	0.863	1	CLONAL	1	TRUE	1	0.564638656752727	2		526	652	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566504	41566504	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	112	294	0	ENST00000263253.7:c.4381A>C	p.Lys1461Gln	p.K1461Q	ENST00000263253	NM_001429.3	1461	Aag/Cag	27/31	NA	2	FACETS	0.825	0.746	0.907			1	INDETERMINATE	1	TRUE	NA	0.564638656752727	2		294	481	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356113	66356113	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	280	428	0	ENST00000273854.3:c.1384G>T	p.Val462Leu	p.V462L	ENST00000273854	NM_004439.5	462	Gta/Tta	5/18	0.564638656752727	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.564638656752727	2		428	494	SUCCESS
APC	324	MSKCC	GRCh37	5	112173376	112173377	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0048251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	124	268	0	ENST00000257430.4:c.2085_2086delinsTT	p.Gln695_Glu696delinsHisTer	p.Q695_E696delinsH*	ENST00000257430	NM_000038.5	695	caGGaa/caTTaa	16/16	0.564638656752727	2	FACETS	0.819	0.756	0.884	0.819	0.756	0.884	CLONAL	2	TRUE	0	0.564638656752727	2		268	268	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859414	151859414	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	128	411	0	ENST00000262189.6:c.11248del	p.Ala3750ProfsTer28	p.A3750Pfs*28	ENST00000262189	NM_170606.2	3750	Gcc/cc	43/59	0.560129616579428	3	FACETS	0.889	0.807	0.974	0.444	0.403	0.487	CLONAL	1	TRUE	1	0.564638656752727	3		411	654	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518082	8518082	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	242	398	0	ENST00000356435.5:c.1309C>G	p.Gln437Glu	p.Q437E	ENST00000356435		437	Cag/Gag	10/35	0.558751877785624	2	FACETS	0.864	0.817	0.911	0.864	0.817	0.911	CLONAL	2	TRUE	0	0.564638656752727	2		398	496	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185070	123185070	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0048251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	98	183	0	ENST00000218089.9:c.1116+1G>A		p.X372_splice	ENST00000218089	NM_001042749.1	372			0.335842458889118	2	FACETS	0.964	0.868	1			1	INDETERMINATE	1	TRUE	NA	0.564638656752727	2		183	360	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	61	432	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.759	0.655	0.872	1	0.97	1	SUBCLONAL	2	TRUE	1	0.149930795717563	2		432	536	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0048252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	32	483	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.149930795717563	8	FACETS	1	0.886	1	0.19	0.153	0.231	CLONAL	1	TRUE	2	0.149930795717563	8		483	544	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426279	49426279	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	49	934	0	ENST00000301067.7:c.12209C>T	p.Ser4070Phe	p.S4070F	ENST00000301067	NM_003482.3	4070	tCt/tTt	39/54	1	2	FACETS	0.702	0.593	0.823	0.702	0.593	0.823	SUBCLONAL	1	TRUE	1	0.149930795717563	2		934	931	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653811	206653811	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	49	704	0	ENST00000367120.3:c.1362C>A	p.Cys454Ter	p.C454*	ENST00000367120	NM_014002.3	454	tgC/tgA	13/22	0.149930795717563	3	FACETS	0.792	0.669	0.929	0.396	0.334	0.465	CLONAL	1	TRUE	1	0.149930795717563	3		704	887	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961444	41961444	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	35	442	0	ENST00000219905.7:c.352A>G	p.Asn118Asp	p.N118D	ENST00000219905	NM_001164273.1	118	Aat/Gat	2/24	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.149930795717563	2		442	432	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126567	2126567	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1378325757	NA	P-0048252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	53	676	0	ENST00000219476.3:c.2818C>T	p.Leu940Phe	p.L940F	ENST00000219476	NM_000548.3	940	Ctc/Ttc	25/42	0.128162633566754	3	FACETS	1	0.915	1	0.555	0.472	0.646	CLONAL	1	TRUE	1	0.149930795717563	3		676	685	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557245	187557245	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772458984	NA	P-0048252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	36	488	0	ENST00000441802.2:c.4117G>A	p.Val1373Ile	p.V1373I	ENST00000441802	NM_005245.3	1373	Gtt/Att	6/27	0.149930795717563	2	FACETS	0.838	0.688	1	0.419	0.344	0.504	CLONAL	1	TRUE	0	0.149930795717563	2		488	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0048254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	457	494	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.778105217466514	2	FACETS	0.997	0.97	1	0.997	0.97	1	CLONAL	2	TRUE	0	0.77972079033809	2		494	588	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	149	331	1	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.789359716808319	2		332	374	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	81	210	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.789359716808319	2		210	195	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947865	178947865	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776932	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	26	251	0	ENST00000263967.3:c.2740G>A	p.Gly914Arg	p.G914R	ENST00000263967	NM_006218.2	914	Gga/Aga	19/21	1	2	FACETS	0.216	0.171	0.267	0.216	0.171	0.267	SUBCLONAL	1	TRUE	1	0.789359716808319	2		251	305	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	149	371	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.949	0.876	1	0.949	0.876	1	CLONAL	1	TRUE	1	0.789359716808319	2		371	398	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	46	458	3	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.238	0.2	0.28	0.238	0.2	0.28	SUBCLONAL	1	TRUE	1	0.789359716808319	2		461	490	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123760	11123760	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	39	514	0	ENST00000358026.2:c.2410G>A	p.Gly804Arg	p.G804R	ENST00000358026	NM_001128849.1	804	Ggg/Agg	16/36	1	2	FACETS	0.171	0.141	0.204	0.171	0.141	0.204	SUBCLONAL	1	TRUE	1	0.789359716808319	2		514	579	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097621	27097622	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	138	371	0	ENST00000324856.7:c.3216dup	p.Trp1073MetfsTer32	p.W1073Mfs*32	ENST00000324856	NM_006015.4	1070	-/A	12/20	1	2	FACETS	0.777	0.713	0.843	0.777	0.713	0.843	SUBCLONAL	1	TRUE	1	0.789359716808319	2		371	450	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916531	39916531	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	52	635	0	ENST00000378444.4:c.4472A>G	p.Asn1491Ser	p.N1491S	ENST00000378444	NM_001123385.1	1491	aAt/aGt	11/15	NA	2	FACETS	0.177	0.15	0.207			1	INDETERMINATE	1	TRUE	NA	0.789359716808319	2		635	745	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522601	176522601	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	277	900	0	ENST00000292408.4:c.1703del	p.Pro568GlnfsTer53	p.P568Qfs*53	ENST00000292408	NM_213647.1	566	cgC/cg	13/18	1	2	FACETS	0.838	0.789	0.887	0.838	0.789	0.887	CLONAL	1	TRUE	1	0.789359716808319	2		900	838	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	329	578	5	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.9	0.853	0.948	0.9	0.853	0.948	CLONAL	1	TRUE	1	0.789359716808319	2		583	926	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353819	15353819	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	92	366	1	ENST00000263377.2:c.3061del	p.His1021IlefsTer47	p.H1021Ifs*47	ENST00000263377	NM_058243.2	1021	Cat/at	14/20	1	2	FACETS	0.615	0.55	0.683	0.615	0.55	0.683	SUBCLONAL	1	TRUE	1	0.789359716808319	2		367	379	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274794	123274794	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913478	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	164	396	0	ENST00000358487.5:c.1124A>G	p.Tyr375Cys	p.Y375C	ENST00000358487	NM_000141.4	375	tAc/tGc	9/18	1	2	FACETS	0.816	0.755	0.879	0.816	0.755	0.879	CLONAL	1	TRUE	1	0.789359716808319	2		396	509	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772951	135772951	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs118203724	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	136	354	1	ENST00000298552.3:c.2672del	p.Asn891ThrfsTer40	p.N891Tfs*40	ENST00000298552	NM_001162426.1	891	aAc/ac	21/23	1	2	FACETS	0.732	0.67	0.795	0.732	0.67	0.795	SUBCLONAL	1	TRUE	1	0.789359716808319	2		355	471	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	251	883	1	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	0.798	0.749	0.848	0.798	0.749	0.848	SUBCLONAL	1	TRUE	1	0.789359716808319	2		884	797	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653807	89653807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554893782	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	139	267	0	ENST00000371953.3:c.105G>A	p.Met35Ile	p.M35I	ENST00000371953	NM_000314.4	35	atG/atA	2/9	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.789359716808319	2		267	333	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448328	56448328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199909371	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	54	730	0	ENST00000407977.2:c.319G>A	p.Val107Ile	p.V107I	ENST00000407977		107	Gtc/Atc	3/10	1	2	FACETS	0.181	0.154	0.21	0.181	0.154	0.21	SUBCLONAL	1	TRUE	1	0.789359716808319	2		730	757	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663356	67663356	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	31	254	0	ENST00000264010.4:c.1760del	p.Asn587MetfsTer44	p.N587Mfs*44	ENST00000264010	NM_006565.3	586	gAa/ga	10/12	1	2	FACETS	0.196	0.158	0.239	0.196	0.158	0.239	SUBCLONAL	1	TRUE	1	0.789359716808319	2		254	400	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120460319	120460319	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1446995271	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	204	461	1	ENST00000256646.2:c.5996del	p.Asn1999MetfsTer32	p.N1999Mfs*32	ENST00000256646	NM_024408.3	1999	aAt/at	33/34	1	2	FACETS	0.89	0.831	0.95	0.89	0.831	0.95	CLONAL	1	TRUE	1	0.789359716808319	2		462	581	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136120	11136120	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	51	647	0	ENST00000358026.2:c.3104T>C	p.Leu1035Pro	p.L1035P	ENST00000358026	NM_001128849.1	1035	cTg/cCg	22/36	1	2	FACETS	0.196	0.166	0.229	0.196	0.166	0.229	SUBCLONAL	1	TRUE	1	0.789359716808319	2		647	660	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094309	193094309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748952219	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	43	341	0	ENST00000367435.3:c.199G>A	p.Val67Met	p.V67M	ENST00000367435	NM_024529.4	67	Gtg/Atg	2/17	0.789359716808319	4	FACETS	0.247	0.206	0.293	0.082	0.068	0.098	SUBCLONAL	1	TRUE	1	0.789359716808319	4		341	788	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588241	69588241	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs533842802	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	148	440	0	ENST00000168712.1:c.457G>A	p.Asp153Asn	p.D153N	ENST00000168712	NM_002007.2	153	Gat/Aat	3/3	1	2	FACETS	0.839	0.773	0.907	0.839	0.773	0.907	CLONAL	1	TRUE	1	0.789359716808319	2		440	447	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368387	225368388	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	78	223	1	ENST00000264414.4:c.1358dup	p.Asn453LysfsTer5	p.N453Kfs*5	ENST00000264414	NM_003590.4	453	aac/aaAc	9/16	1	2	FACETS	0.62	0.549	0.694	0.62	0.549	0.694	SUBCLONAL	1	TRUE	1	0.789359716808319	2		224	319	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40761117	40761117	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	65	683	0	ENST00000392038.2:c.235C>T	p.Gln79Ter	p.Q79*	ENST00000392038	NM_001626.4	79	Cag/Tag	4/14	1	2	FACETS	0.235	0.203	0.269	0.235	0.203	0.269	SUBCLONAL	1	TRUE	1	0.789359716808319	2		683	702	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	63	848	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.201	0.173	0.231	0.201	0.173	0.231	SUBCLONAL	1	TRUE	1	0.789359716808319	2		848	795	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	329	756	3	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.789359716808319	2		759	797	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53250047	53250047	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	65	582	2	ENST00000375401.3:c.202del	p.Arg68GlufsTer5	p.R68Efs*5	ENST00000375401	NM_004187.3	68	Cga/ga	2/26	1	2	FACETS	0.24	0.208	0.275	0.24	0.208	0.275	SUBCLONAL	1	TRUE	1	0.789359716808319	2		584	686	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266128	198266128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	148	299	2	ENST00000335508.6:c.2492G>A	p.Arg831Gln	p.R831Q	ENST00000335508	NM_012433.2	831	cGa/cAa	17/25	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.789359716808319	2		301	374	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028784	47028784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782008653	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	280	745	0	ENST00000377604.3:c.88C>T	p.Arg30Cys	p.R30C	ENST00000377604	NM_001204468.1	30	Cgc/Tgc	3/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.789359716808319	2		745	668	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243222	123243223	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	272	612	0	ENST00000358487.5:c.2290dup	p.Thr764AsnfsTer4	p.T764Nfs*4	ENST00000358487	NM_000141.4	764	aca/aAca	17/18	1	2	FACETS	0.964	0.91	1	0.964	0.91	1	CLONAL	1	TRUE	1	0.789359716808319	2		612	715	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390715	118390715	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	27	271	0	ENST00000534358.1:c.11365C>T	p.Arg3789Cys	p.R3789C	ENST00000534358	NM_005933.3	3789	Cgt/Tgt	33/36	1	2	FACETS	0.198	0.157	0.244	0.198	0.157	0.244	SUBCLONAL	1	TRUE	1	0.789359716808319	2		271	346	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347627	89347627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559618415	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	46	691	1	ENST00000301030.4:c.5323G>A	p.Ala1775Thr	p.A1775T	ENST00000301030	NM_001256183.1	1775	Gcc/Acc	9/13	1	2	FACETS	0.18	0.151	0.212	0.18	0.151	0.212	SUBCLONAL	1	TRUE	1	0.789359716808319	2		692	647	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485715	40485715	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	37	482	0	ENST00000264657.5:c.1025G>A	p.Gly342Asp	p.G342D	ENST00000264657	NM_139276.2	342	gGc/gAc	10/24	1	2	FACETS	0.177	0.145	0.212	0.177	0.145	0.212	SUBCLONAL	1	TRUE	1	0.789359716808319	2		482	531	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613079	52613079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	160	260	0	ENST00000394830.3:c.3449G>A	p.Arg1150His	p.R1150H	ENST00000394830	NM_018313.4	1150	cGt/cAt	22/30	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.789359716808319	2		260	388	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526312	189526312	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	40	388	0	ENST00000264731.3:c.576G>A	p.Trp192Ter	p.W192*	ENST00000264731	NM_003722.4	192	tgG/tgA	4/14	1	2	FACETS	0.252	0.209	0.299	0.252	0.209	0.299	SUBCLONAL	1	TRUE	1	0.789359716808319	2		388	402	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073280	8073280	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	121	256	0	ENST00000377482.5:c.1379T>C	p.Val460Ala	p.V460A	ENST00000377482	NM_018948.3	460	gTt/gCt	4/4	1	2	FACETS	0.97	0.889	1	0.97	0.889	1	CLONAL	1	TRUE	1	0.789359716808319	2		256	316	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807388	36807388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866820712	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	315	781	1	ENST00000373129.3:c.1276G>A	p.Ala426Thr	p.A426T	ENST00000373129	NM_032017.1	426	Gcc/Acc	12/12	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.789359716808319	2		782	733	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429946	78429946	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	144	311	0	ENST00000370768.2:c.933del	p.Phe311LeufsTer12	p.F311Lfs*12	ENST00000370768	NM_003902.3	311	ttT/tt	11/20	1	2	FACETS	0.97	0.896	1	0.97	0.896	1	CLONAL	1	TRUE	1	0.789359716808319	2		311	376	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120496190	120496190	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	197	427	0	ENST00000256646.2:c.2341T>C	p.Cys781Arg	p.C781R	ENST00000256646	NM_024408.3	781	Tgt/Cgt	14/34	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.789359716808319	2		427	475	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551951	150551951	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1490867890	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	187	498	0	ENST00000369026.2:c.56C>G	p.Ala19Gly	p.A19G	ENST00000369026	NM_021960.4	19	gCc/gGc	1/3	0.789359716808319	4	FACETS	0.834	0.77	0.901	0.278	0.256	0.301	CLONAL	1	TRUE	1	0.789359716808319	4		498	1016	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69456170	69456170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	329	682	0	ENST00000227507.2:c.89C>T	p.Ala30Val	p.A30V	ENST00000227507	NM_053056.2	30	gCc/gTc	1/5	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.789359716808319	2		682	746	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432368	432368	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	93	165	0	ENST00000399788.2:c.2155C>G	p.Arg719Gly	p.R719G	ENST00000399788	NM_001042603.1	719	Cgc/Ggc	16/28	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.789359716808319	2		165	205	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434525	49434525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764884530	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	186	776	1	ENST00000301067.7:c.7028C>T	p.Pro2343Leu	p.P2343L	ENST00000301067	NM_003482.3	2343	cCg/cTg	31/54	1	2	FACETS	0.673	0.624	0.724	0.673	0.624	0.724	SUBCLONAL	1	TRUE	1	0.789359716808319	2		777	700	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435930	49435930	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	258	778	0	ENST00000301067.7:c.6051del	p.Ile2018SerfsTer29	p.I2018Sfs*29	ENST00000301067	NM_003482.3	2017	acC/ac	28/54	1	2	FACETS	0.919	0.866	0.974	0.919	0.866	0.974	CLONAL	1	TRUE	1	0.789359716808319	2		778	711	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123873997	123873997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	29	57	0	ENST00000330479.4:c.28C>T	p.Pro10Ser	p.P10S	ENST00000330479	NM_020382.3	10	Ccc/Tcc	2/9	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.789359716808319	2		57	63	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435250	110435250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	166	364	0	ENST00000375856.3:c.3151G>A	p.Ala1051Thr	p.A1051T	ENST00000375856	NM_003749.2	1051	Gcc/Acc	1/2	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.789359716808319	2		364	392	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586087	29586089	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs267606607	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	23	298	0	ENST00000356175.3:c.4312_4314del	p.Glu1438del	p.E1438del	ENST00000356175	NM_000267.3	1436	aAAGaa/aaa	32/57	1	2	FACETS	0.172	0.134	0.216	0.172	0.134	0.216	SUBCLONAL	1	TRUE	1	0.789359716808319	2		298	339	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296118	15296118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1430165414	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	79	834	0	ENST00000263388.2:c.2246G>A	p.Cys749Tyr	p.C749Y	ENST00000263388	NM_000435.2	749	tGc/tAc	14/33	1	2	FACETS	0.246	0.215	0.278	0.246	0.215	0.278	SUBCLONAL	1	TRUE	1	0.789359716808319	2		834	815	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918181	50918181	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	58	911	0	ENST00000440232.2:c.2498G>A	p.Arg833His	p.R833H	ENST00000440232	NM_002691.3	833	cGc/cAc	20/27	1	2	FACETS	0.188	0.161	0.218	0.188	0.161	0.218	SUBCLONAL	1	TRUE	1	0.789359716808319	2		911	780	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462644	29462644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745499366	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	56	722	3	ENST00000389048.3:c.2257C>T	p.Arg753Trp	p.R753W	ENST00000389048	NM_004304.4	753	Cgg/Tgg	13/29	1	2	FACETS	0.186	0.159	0.217	0.186	0.159	0.217	SUBCLONAL	1	TRUE	1	0.789359716808319	2		725	761	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190742124	190742124	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	123	236	0	ENST00000441310.2:c.2766del	p.His923IlefsTer3	p.H923Ifs*3	ENST00000441310	NM_000534.4	921	Ttt/tt	13/13	1	2	FACETS	0.917	0.839	0.996	0.917	0.839	0.996	CLONAL	1	TRUE	1	0.789359716808319	2		236	340	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191217	185191217	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	27	470	0	ENST00000265026.3:c.2098T>C	p.Ser700Pro	p.S700P	ENST00000265026	NM_004721.4	700	Tcc/Ccc	11/14	1	2	FACETS	0.169	0.134	0.209	0.169	0.134	0.209	SUBCLONAL	1	TRUE	1	0.789359716808319	2		470	404	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527274	187527274	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	35	486	0	ENST00000441802.2:c.10300A>G	p.Asn3434Asp	p.N3434D	ENST00000441802	NM_005245.3	3434	Aat/Gat	17/27	1	2	FACETS	0.148	0.121	0.179	0.148	0.121	0.179	SUBCLONAL	1	TRUE	1	0.789359716808319	2		486	599	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31423000	31423000	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	30	447	0	ENST00000344624.3:c.3313C>T	p.Gln1105Ter	p.Q1105*	ENST00000344624		1105	Caa/Taa	26/33	1	2	FACETS	0.131	0.105	0.161	0.131	0.105	0.161	SUBCLONAL	1	TRUE	1	0.789359716808319	2		447	581	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672384	86672384	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	16	140	0	ENST00000274376.6:c.2184+2T>C		p.X728_splice	ENST00000274376	NM_002890.2	728			1	2	FACETS	0.162	0.12	0.213	0.162	0.12	0.213	SUBCLONAL	1	TRUE	1	0.789359716808319	2		140	250	SUCCESS
APC	324	MSKCC	GRCh37	5	112175114	112175114	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	62	156	0	ENST00000257430.4:c.3823A>G	p.Ser1275Gly	p.S1275G	ENST00000257430	NM_000038.5	1275	Agt/Ggt	16/16	1	2	FACETS	0.924	0.815	1	0.924	0.815	1	CLONAL	1	TRUE	1	0.789359716808319	2		156	170	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730223	133730223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	180	396	0	ENST00000318560.5:c.289G>A	p.Gly97Arg	p.G97R	ENST00000318560	NM_005157.4	97	Ggg/Agg	3/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.789359716808319	2		396	435	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786025	135786025	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	68	668	0	ENST00000298552.3:c.1196del	p.Pro399HisfsTer41	p.P399Hfs*41	ENST00000298552	NM_001162426.1	399	cCa/ca	12/23	1	2	FACETS	0.209	0.181	0.239	0.209	0.181	0.239	SUBCLONAL	1	TRUE	1	0.789359716808319	2		668	826	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798753	135798755	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	92	152	0	ENST00000298552.3:c.488_490del	p.Ser163del	p.S163del	ENST00000298552	NM_001162426.1	163	tCATgg/tgg	6/23	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.789359716808319	2		152	224	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224137	53224137	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	57	776	0	ENST00000375401.3:c.3414G>T	p.Gln1138His	p.Q1138H	ENST00000375401	NM_004187.3	1138	caG/caT	22/26	1	2	FACETS	0.215	0.184	0.249	0.215	0.184	0.249	SUBCLONAL	1	TRUE	1	0.789359716808319	2		776	671	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	122	349	1				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.625048116408952	2		350	352	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725059	89725059	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	66	118	0	ENST00000371953.3:c.1042A>C	p.Thr348Pro	p.T348P	ENST00000371953	NM_000314.4	348	Aca/Cca	9/9	0.625048116408952	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.625048116408952	1		118	116	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708975	117708975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	154	452	0	ENST00000368508.3:c.1982C>T	p.Ser661Leu	p.S661L	ENST00000368508	NM_002944.2	661	tCa/tTa	13/43	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.625048116408952	2		452	458	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	273	706	8	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.986	1	1	0.996	1	CLONAL	2	TRUE	1	0.288978545337587	2		714	828	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	133	648	0	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.288978545337587	2		648	785	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	43	314	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.288978545337587	2		314	272	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	55	347	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.288978545337587	2		347	356	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	58	504	5	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.683	0.586	0.788	0.683	0.586	0.788	SUBCLONAL	1	TRUE	1	0.288978545337587	2		509	588	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	168	348	1	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	1	FACETS	0.987	0.914	1	1	0.993	1	CLONAL	2	TRUE	0	0.288978545337587	1		349	504	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434367	121434367	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	61	739	1	ENST00000257555.6:c.1136del	p.Pro379LeufsTer5	p.P379Lfs*5	ENST00000257555		377	ctC/ct	6/10	1	2	FACETS	0.464	0.399	0.536	0.464	0.399	0.536	SUBCLONAL	1	TRUE	1	0.288978545337587	2		740	909	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681708	78681708	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767783333	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	125	529	2	ENST00000306801.3:c.416G>A	p.Arg139His	p.R139H	ENST00000306801	NM_020761.2	139	cGc/cAc	4/34	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.288978545337587	2		531	765	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	109	494	0	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.288978545337587	2		494	622	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781324	3781326	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs587783502	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	206	730	0	ENST00000262367.5:c.5039_5041del	p.Ser1680del	p.S1680del	ENST00000262367	NM_004380.2	1680	tCCTtg/ttg	30/31	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.288978545337587	2		730	1286	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497245	149497245	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	179	675	0	ENST00000261799.4:c.3073del	p.Leu1025CysfsTer20	p.L1025Cfs*20	ENST00000261799	NM_002609.3	1025	Ctg/tg	22/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.288978545337587	2		675	953	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	185	834	11	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.288978545337587	2		845	1068	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004721	150004721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1034620976	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	30	412	1	ENST00000253339.5:c.1504C>T	p.Arg502Cys	p.R502C	ENST00000253339		502	Cgt/Tgt	3/7	1	2	FACETS	0.375	0.301	0.459	0.375	0.301	0.459	SUBCLONAL	1	TRUE	1	0.288978545337587	2		413	554	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339505	116339505	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760106468	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	25	251	0	ENST00000397752.3:c.367G>A	p.Asp123Asn	p.D123N	ENST00000397752	NM_000245.2	123	Gac/Aac	2/21	1	2	FACETS	0.448	0.353	0.558	0.448	0.353	0.558	SUBCLONAL	1	TRUE	1	0.288978545337587	2		251	386	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053348	37053348	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63751653	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	49	275	0	ENST00000231790.2:c.588del	p.Lys196AsnfsTer6	p.K196Nfs*6	ENST00000231790	NM_000249.3	195	Aaa/aa	7/19	1	2	FACETS	0.774	0.657	0.903	0.774	0.657	0.903	CLONAL	1	TRUE	1	0.288978545337587	2		275	438	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	213403254	213403254	+	frameshift_variant,start_lost,start_retained_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	57	380	2	ENST00000342788.4:c.1del	p.Met1?	p.M1?	ENST00000342788	NM_005235.2	1	Atg/tg	1/28	1	2	FACETS	0.769	0.66	0.887	0.769	0.66	0.887	SUBCLONAL	1	TRUE	1	0.288978545337587	2		382	513	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733223	74733223	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	162	736	0	ENST00000359995.5:c.20del	p.Pro7LeufsTer7	p.P7Lfs*7	ENST00000359995	NM_001195427.1	7	cCt/ct	1/3	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.288978545337587	2		736	795	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647657	3647657	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs774532876	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	138	733	5	ENST00000294008.3:c.1406del	p.Pro469HisfsTer4	p.P469Hfs*4	ENST00000294008	NM_032444.2	469	cCa/ca	7/15	1	2	FACETS	0.92	0.836	1	0.92	0.836	1	CLONAL	1	TRUE	1	0.288978545337587	2		738	1038	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096132	2096133	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs763525759	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	131	674	2	ENST00000219066.1:c.374dup	p.Val127GlyfsTer43	p.V127Gfs*43	ENST00000219066	NM_002528.5	125	cca/ccCa	2/6	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.288978545337587	2		676	833	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432420	49432420	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	159	764	0	ENST00000301067.7:c.8719del	p.Tyr2907ThrfsTer3	p.Y2907Tfs*3	ENST00000301067	NM_003482.3	2907	Tac/ac	34/54	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.288978545337587	2		764	1003	SUCCESS
ATR	545	MSKCC	GRCh37	3	142297533	142297533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200753177	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	153	780	0	ENST00000350721.4:c.14G>A	p.Gly5Asp	p.G5D	ENST00000350721	NM_001184.3	5	gGc/gAc	1/47	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.288978545337587	2		780	879	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639156	3639156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762565535	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	147	848	0	ENST00000294008.3:c.4483G>A	p.Ala1495Thr	p.A1495T	ENST00000294008	NM_032444.2	1495	Gcg/Acg	12/15	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.288978545337587	2		848	976	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272165	15272165	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	162	775	1	ENST00000263388.2:c.6274del	p.Leu2092TrpfsTer57	p.L2092Wfs*57	ENST00000263388	NM_000435.2	2092	Ctg/tg	33/33	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.288978545337587	2		776	933	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778167	3778167	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793091	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	185	872	2	ENST00000262367.5:c.6881G>A	p.Arg2294Gln	p.R2294Q	ENST00000262367	NM_004380.2	2294	cGg/cAg	31/31	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.288978545337587	2		874	1043	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214714	36214714	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	151	669	0	ENST00000222270.7:c.3145del	p.Ala1049ArgfsTer133	p.A1049Rfs*133	ENST00000222270	NM_014727.1	1047	cGg/cg	8/37	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.288978545337587	2		669	744	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125371	7125371	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55882714	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	240	718	1	ENST00000302850.5:c.3181G>A	p.Glu1061Lys	p.E1061K	ENST00000302850	NM_000208.2	1061	Gag/Aag	17/22	0.158099857140304	2	FACETS	0.833	0.778	0.889	0.833	0.778	0.889	INDETERMINATE	2	TRUE	0	0.288978545337587	2		719	997	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244184	133244184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768004570	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	154	496	0	ENST00000320574.5:c.2224C>T	p.Arg742Cys	p.R742C	ENST00000320574	NM_006231.2	742	Cgt/Tgt	20/49	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.288978545337587	2		496	803	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250842	153250842	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	57	266	0	ENST00000281708.4:c.1218G>A	p.Trp406Ter	p.W406*	ENST00000281708	NM_033632.3	406	tgG/tgA	8/12	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.288978545337587	2		266	321	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046350	69046350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	94	391	0	ENST00000288368.4:c.3823G>A	p.Val1275Ile	p.V1275I	ENST00000288368	NM_024870.2	1275	Gtc/Atc	32/40	0.288978545337587	3	FACETS	1	0.957	1	0.575	0.512	0.642	CLONAL	1	TRUE	1	0.288978545337587	3		391	648	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724362	112724362	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	74	422	0	ENST00000369452.4:c.252del	p.Lys84AsnfsTer7	p.K84Nfs*7	ENST00000369452	NM_007373.3	82	agA/ag	2/9	1	2	FACETS	0.885	0.775	1	0.885	0.775	1	CLONAL	1	TRUE	1	0.288978545337587	2		422	579	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016154	31016154	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777619874	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	97	449	1	ENST00000375687.4:c.400G>A	p.Ala134Thr	p.A134T	ENST00000375687	NM_015338.5	134	Gca/Aca	6/13	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.288978545337587	2		450	571	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325212	39325212	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1457027639	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	106	516	0	ENST00000373001.3:c.107A>C	p.Glu36Ala	p.E36A	ENST00000373001	NM_022157.3	36	gAg/gCg	1/7	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.288978545337587	2		516	688	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461131	120461131	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	80	399	0	ENST00000256646.2:c.5827G>T	p.Asp1943Tyr	p.D1943Y	ENST00000256646	NM_024408.3	1943	Gat/Tat	32/34	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.288978545337587	2		399	510	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570883	226570883	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	60	332	0	ENST00000366794.5:c.1013A>T	p.Glu338Val	p.E338V	ENST00000366794	NM_001618.3	338	gAa/gTa	8/23	1	2	FACETS	0.758	0.653	0.871	0.758	0.653	0.871	SUBCLONAL	1	TRUE	1	0.288978545337587	2		332	548	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134267	41134267	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1028000118	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	76	328	0	ENST00000379561.5:c.1361A>G	p.Gln454Arg	p.Q454R	ENST00000379561	NM_002015.3	454	cAg/cGg	2/3	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.288978545337587	2		328	458	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435365	110435367	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	81	505	0	ENST00000375856.3:c.3034_3036del	p.Ser1012del	p.S1012del	ENST00000375856	NM_003749.2	1012	TCC/-	1/2	1	2	FACETS	0.91	0.802	1	0.91	0.802	1	CLONAL	1	TRUE	1	0.288978545337587	2		505	616	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708581	43708582	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	131	438	0	ENST00000382044.4:c.4714dup	p.Glu1572GlyfsTer7	p.E1572Gfs*7	ENST00000382044	NM_001141980.1	1572	gaa/gGaa	22/28	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.288978545337587	2		438	711	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830785	3830785	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	113	428	0	ENST00000262367.5:c.1771G>T	p.Gly591Cys	p.G591C	ENST00000262367	NM_004380.2	591	Ggc/Tgc	8/31	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.288978545337587	2		428	669	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858453	89858453	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	153	477	0	ENST00000389301.3:c.1107G>T	p.Glu369Asp	p.E369D	ENST00000389301	NM_000135.2	369	gaG/gaT	13/43	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.288978545337587	2		477	824	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110207	8110207	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	112	516	0	ENST00000585124.1:c.399-1G>A		p.X133_splice	ENST00000585124	NM_004217.3	133			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.288978545337587	2		516	614	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119743	70119743	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	109	447	0	ENST00000245479.2:c.745A>G	p.Lys249Glu	p.K249E	ENST00000245479	NM_000346.3	249	Aag/Gag	3/3	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.288978545337587	2		447	581	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265705	10265705	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	47	388	0	ENST00000340748.4:c.1472C>T	p.Pro491Leu	p.P491L	ENST00000340748		491	cCc/cTc	19/40	0.158099857140304	2	FACETS	0.574	0.484	0.673	0.287	0.242	0.337	INDETERMINATE	1	TRUE	0	0.288978545337587	2		388	567	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599890	10599890	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	181	788	0	ENST00000171111.5:c.1686C>A	p.His562Gln	p.H562Q	ENST00000171111	NM_203500.1	562	caC/caA	5/6	0.158099857140304	2	FACETS	1	0.92	1	0.5	0.46	0.542	INDETERMINATE	1	TRUE	0	0.288978545337587	2		788	1253	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630344	47630344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56170584	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	164	722	1	ENST00000233146.2:c.14C>T	p.Pro5Leu	p.P5L	ENST00000233146	NM_000251.2	5	cCg/cTg	1/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.288978545337587	2		723	896	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466784	57466784	+	frameshift_variant,start_lost	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	35	145	0	ENST00000371085.3:c.5del	p.Gly2?	p.G2?	ENST00000371085	NM_000516.4	1	atG/at	1/13	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.288978545337587	2		145	213	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574392	41574392	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372813939	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	114	554	0	ENST00000263253.7:c.6677G>A	p.Arg2226Gln	p.R2226Q	ENST00000263253	NM_001429.3	2226	cGg/cAg	31/31	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.288978545337587	2		554	639	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281641	142281641	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	68	362	0	ENST00000350721.4:c.603T>A	p.Asn201Lys	p.N201K	ENST00000350721	NM_001184.3	201	aaT/aaA	4/47	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.288978545337587	2		362	374	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201754	66201754	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	93	389	0	ENST00000273854.3:c.2748G>T	p.Gln916His	p.Q916H	ENST00000273854	NM_004439.5	916	caG/caT	16/18	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.288978545337587	2		389	557	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681151	86681151	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	33	199	0	ENST00000274376.6:c.2792T>A	p.Ile931Lys	p.I931K	ENST00000274376	NM_002890.2	931	aTa/aAa	22/25	1	2	FACETS	0.81	0.662	0.975	0.81	0.662	0.975	CLONAL	1	TRUE	1	0.288978545337587	2		199	282	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149437151	149437151	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	46	546	0	ENST00000286301.3:c.2137A>T	p.Ser713Cys	p.S713C	ENST00000286301	NM_005211.3	713	Agt/Tgt	16/22	1	2	FACETS	0.449	0.377	0.529	0.449	0.377	0.529	SUBCLONAL	1	TRUE	1	0.288978545337587	2		546	709	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520552	176520552	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	196	775	0	ENST00000292408.4:c.1397G>T	p.Arg466Met	p.R466M	ENST00000292408	NM_213647.1	466	aGg/aTg	10/18	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.288978545337587	2		775	1045	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324063	31324063	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151341275	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	182	465	0	ENST00000412585.2:c.500C>T	p.Thr167Ile	p.T167I	ENST00000412585	NM_005514.6	167	aCc/aTc	3/8	1	2	FACETS	1	0.955	1	1	0.993	1	CLONAL	2	TRUE	1	0.288978545337587	2		465	606	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324094	31324094	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs151341247	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	31	291	0	ENST00000412585.2:c.469T>C	p.Trp157Arg	p.W157R	ENST00000412585	NM_005514.6	157	Tgg/Cgg	3/8	1	2	FACETS	0.642	0.52	0.78	0.642	0.52	0.78	SUBCLONAL	1	TRUE	1	0.288978545337587	2		291	334	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32182010	32182010	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	177	718	0	ENST00000375023.3:c.2044G>T	p.Gly682Cys	p.G682C	ENST00000375023	NM_004557.3	682	Ggt/Tgt	13/30	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.288978545337587	2		718	1030	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15840947	15840947	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	81	159	0	ENST00000307771.7:c.1031G>T	p.Arg344Ile	p.R344I	ENST00000307771	NM_005089.3	344	aGa/aTa	11/11	1	1	FACETS	1	0.909	1	1	0.986	1	CLONAL	2	TRUE	0	0.288978545337587	1		159	236	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0048258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	100	494	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.197906908665038	1	FACETS	0.274	0.244	0.306	0.274	0.244	0.306	INDETERMINATE	1	TRUE	0	0.56	1		494	938	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0048258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	117	277	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.856	0.776	0.94	0.856	0.776	0.94	CLONAL	1	TRUE	1	0.56	2		277	488	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0048258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	18	453	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.103	0.077	0.135	0.103	0.077	0.135	SUBCLONAL	1	TRUE	1	0.56	2		453	622	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0048258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	75	189	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.197906908665038	1	FACETS	0.8	0.711	0.893	0.8	0.711	0.893	INDETERMINATE	1	TRUE	0	0.56	1		189	241	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953022	2953022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141681466	NA	P-0048258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	117	790	1	ENST00000396946.4:c.2918G>A	p.Arg973His	p.R973H	ENST00000396946	NM_032415.4	973	cGc/cAc	22/25	1	2	FACETS	0.351	0.315	0.389	0.351	0.315	0.389	SUBCLONAL	1	TRUE	1	0.56	2		791	1190	SUCCESS
APC	324	MSKCC	GRCh37	5	112174241	112174241	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1254176854	NA	P-0048258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	103	228	0	ENST00000257430.4:c.2950G>T	p.Glu984Ter	p.E984*	ENST00000257430	NM_000038.5	984	Gaa/Taa	16/16	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.56	2		228	368	SUCCESS
APC	324	MSKCC	GRCh37	5	112175551	112175552	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0048258-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	90	244	0	ENST00000257430.4:c.4260_4261del	p.Ser1421Ter	p.S1421*	ENST00000257430	NM_000038.5	1420	ccCAgt/ccgt	16/16	1	2	FACETS	0.835	0.746	0.928	0.835	0.746	0.928	CLONAL	1	TRUE	1	0.56	2		244	385	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	196	349	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.918	0.86	0.978	0.918	0.86	0.978	CLONAL	1	TRUE	1	0.93	2		350	459	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0048259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	458	856	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	1	2	FACETS	0.974	0.934	1	0.974	0.934	1	CLONAL	1	TRUE	1	0.93	2		856	1011	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145401	58145401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	365	579	0	ENST00000257904.6:c.100C>T	p.Leu34Phe	p.L34F	ENST00000257904	NM_000075.3	34	Ctc/Ttc	2/8	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.93	2		579	739	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719971	18719971	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1443187096	NA	P-0048259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	148	197	0	ENST00000266497.5:c.3868G>A	p.Val1290Ile	p.V1290I	ENST00000266497		1290	Gta/Ata	27/31	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.93	2		197	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0048260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	629	547	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.820096527733591	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.828170808518591	1		547	795	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495507	56495507	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	69	570	0	ENST00000267101.3:c.3697G>T	p.Ala1233Ser	p.A1233S	ENST00000267101	NM_001982.3	1233	Gcc/Tcc	28/28	0.747716762750185	1	FACETS	0.123	0.106	0.14	0.123	0.106	0.14	SUBCLONAL	1	TRUE	0	0.828170808518591	1		570	796	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026033	48026033	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1481054050	NA	P-0048260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	250	357	0	ENST00000234420.5:c.911T>A	p.Val304Glu	p.V304E	ENST00000234420	NM_000179.2	304	gTg/gAg	4/10	0.696075267330909	1	FACETS	0.912	0.87	0.952	0.912	0.87	0.952	CLONAL	1	TRUE	0	0.828170808518591	1		357	388	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591243	67591393	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCAGGTGGTTGACTCAAAAAGGTGTTCGGCAAAAGAAGTTGAACGAGTGGTTGGGCAATGAAAACACTGAAGAGTAAGTAGTTACTAAAGATGGTGATAGCAGAAGATTTTTCTCATTTTAGGAAAATGCATGACTTGCTTTGTTTTTAG	TTCAGGTGGTTGACTCAAAAAGGTGTTCGGCAAAAGAAGTTGAACGAGTGGTTGGGCAATGAAAACACTGAAGAGTAAGTAGTTACTAAAGATGGTGATAGCAGAAGATTTTTCTCATTTTAGGAAAATGCATGACTTGCTTTGTTTTTAG	-	novel	NA	P-0048260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	12	283	0	ENST00000274335.5:c.1746-5_1814+77del		p.X582_splice	ENST00000274335		582		13/15	0.828170808518591	1	FACETS	0.236	0.168	0.315	0.236	0.168	0.315	SUBCLONAL	1	TRUE	0	0.828170808518591	1		283	72	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0048261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	103	383	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.416296180625682	2		383	474	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0048261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	126	347	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.293565335477443	4	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	TRUE	2	0.416296180625682	4		347	424	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279483	1279483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	169	1146	2	ENST00000310581.5:c.2053G>A	p.Asp685Asn	p.D685N	ENST00000310581	NM_198253.2	685	Gat/Aat	5/16	1	2	FACETS	0.912	0.839	0.989	0.912	0.839	0.989	CLONAL	1	TRUE	1	0.416296180625682	2		1148	890	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917772	29917772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	156	805	0	ENST00000389048.3:c.896C>T	p.Ser299Phe	p.S299F	ENST00000389048	NM_004304.4	299	tCc/tTc	3/29	1	2	FACETS	0.899	0.823	0.977	0.899	0.823	0.977	CLONAL	1	TRUE	1	0.416296180625682	2		805	834	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727805	41727805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	197	868	0	ENST00000301178.4:c.430G>A	p.Glu144Lys	p.E144K	ENST00000301178	NM_021913.4	144	Gag/Aag	4/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.416296180625682	2		868	907	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213539	36213539	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867685821	NA	P-0048261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	223	1080	0	ENST00000222270.7:c.2641C>T	p.Gln881Ter	p.Q881*	ENST00000222270	NM_014727.1	881	Cag/Tag	5/37	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.416296180625682	2		1080	1064	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097766	8097766	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775745771	NA	P-0048261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	125	710	0	ENST00000346208.3:c.148C>T	p.Leu50Phe	p.L50F	ENST00000346208		50	Ctt/Ttt	2/6	1	2	FACETS	0.703	0.636	0.774	0.703	0.636	0.774	SUBCLONAL	1	TRUE	1	0.416296180625682	2		710	854	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77069980	77069980	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	93	479	0	ENST00000356341.3:c.560C>T	p.Pro187Leu	p.P187L	ENST00000356341	NM_002576.4	187	cCa/cTa	6/15	1	2	FACETS	0.788	0.702	0.879	0.788	0.702	0.879	SUBCLONAL	1	TRUE	1	0.416296180625682	2		479	567	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81973631	81973631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762571980	NA	P-0048261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	108	481	0	ENST00000359376.3:c.3448C>T	p.His1150Tyr	p.H1150Y	ENST00000359376	NM_002661.3	1150	Cat/Tat	30/33	1	2	FACETS	0.876	0.789	0.969	0.876	0.789	0.969	CLONAL	1	TRUE	1	0.416296180625682	2		481	592	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462670	29462671	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0048261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	158	786	1	ENST00000389048.3:c.2230_2231delinsAA	p.Gly744Lys	p.G744K	ENST00000389048	NM_004304.4	744	GGg/AAg	13/29	1	2	FACETS	0.862	0.79	0.937	0.862	0.79	0.937	CLONAL	1	TRUE	1	0.416296180625682	2		787	881	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920347	1920347	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	127	552	0	ENST00000382891.5:c.1407T>G	p.Asp469Glu	p.D469E	ENST00000382891	NM_133335.3	469	gaT/gaG	5/22	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.416296180625682	2		552	610	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759730	133759730	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	114	724	0	ENST00000318560.5:c.2053C>T	p.His685Tyr	p.H685Y	ENST00000318560	NM_005157.4	685	Cac/Tac	11/11	0.416296180625682	1	FACETS	0.808	0.73	0.889	0.808	0.73	0.889	CLONAL	1	TRUE	0	0.416296180625682	1		724	537	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061207	38061207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	27	681	2	ENST00000250448.2:c.782G>A	p.Arg261His	p.R261H	ENST00000250448	NM_004496.3	261	cGc/cAc	2/2	0.288431912386666	5	FACETS	1	0.856	1	1	0.856	1	CLONAL	3	FALSE	2	0.315897136855732	5		683	80	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137850	64137850	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	79	1166	0	ENST00000334205.4:c.1951G>T	p.Val651Phe	p.V651F	ENST00000334205	NM_003942.2	651	Gtc/Ttc	15/17	0.315897136855732	4	FACETS	0.837	0.746	0.932	1	0.969	1	CLONAL	3	FALSE	2	0.315897136855732	4		1166	262	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618693	37618694	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0048262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	22	551	0	ENST00000447079.4:c.371_372del	p.Lys124SerfsTer2	p.K124Sfs*2	ENST00000447079	NM_015083.1	123	ctAAaa/ctaa	1/14	1	2	FACETS	0.839	0.667	1	1	0.938	1	CLONAL	2	FALSE	1	0.315897136855732	2		551	83	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37671982	37671982	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0048262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	56	352	0	ENST00000447079.4:c.2769-2A>G		p.X923_splice	ENST00000447079	NM_015083.1	923			1	2	FACETS	0.85	0.748	0.955	1	0.983	1	CLONAL	3	FALSE	1	0.315897136855732	2		352	139	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858363	27858363	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746466177	NA	P-0048262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	77	792	0	ENST00000359303.2:c.208C>T	p.Arg70Cys	p.R70C	ENST00000359303	NM_003535.2	70	Cgc/Tgc	1/1	0.315897136855732	3	FACETS	0.867	0.775	0.962	1	0.973	1	CLONAL	3	FALSE	1	0.315897136855732	3		792	217	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0048263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	32	688	4	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	0.770387988178124	1	FACETS	0.079	0.064	0.097	0.079	0.064	0.097	SUBCLONAL	1	TRUE	0	0.917003255883511	1		692	476	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0048263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	55	703	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.770387988178124	1	FACETS	0.13	0.111	0.151	0.13	0.111	0.151	SUBCLONAL	1	TRUE	0	0.917003255883511	1		703	498	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	52	323	0	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	0.917003255883511	1	FACETS	0.152	0.13	0.177	0.152	0.13	0.177	SUBCLONAL	1	TRUE	0	0.917003255883511	1		323	403	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798148	42798148	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1619	111	811	0	ENST00000575354.2:c.4102G>C	p.Glu1368Gln	p.E1368Q	ENST00000575354	NM_015125.3	1368	Gag/Cag	17/20	0.917003255883511	4	FACETS	0.268	0.24	0.299	0.089	0.08	0.1	SUBCLONAL	1	TRUE	1	0.917003255883511	4		811	1730	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856520	45856520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751318902	NA	P-0048263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	308	670	0	ENST00000391945.4:c.1738G>A	p.Ala580Thr	p.A580T	ENST00000391945	NM_000400.3	580	Gcc/Acc	18/23	0.917003255883511	4	FACETS	0.915	0.861	0.97	0.305	0.287	0.324	CLONAL	1	TRUE	1	0.917003255883511	4		670	1408	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420277	49420277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	382	610	0	ENST00000301067.7:c.15472G>A	p.Glu5158Lys	p.E5158K	ENST00000301067	NM_003482.3	5158	Gag/Aag	48/54	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.917003255883511	2		610	823	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864878	117864878	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1169346397	NA	P-0048263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	47	415	0	ENST00000297338.2:c.1231G>C	p.Asp411His	p.D411H	ENST00000297338	NM_006265.2	411	Gat/Cat	10/14	0.910892002483021	2	FACETS	0.186	0.157	0.219	0.093	0.078	0.11	SUBCLONAL	1	TRUE	0	0.917003255883511	2		415	550	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277972	18277972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1193898416	NA	P-0048263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	53	515	0	ENST00000222254.8:c.1592G>A	p.Arg531His	p.R531H	ENST00000222254	NM_005027.3	531	cGc/cAc	13/16	1	2	FACETS	0.171	0.145	0.199	0.171	0.145	0.199	SUBCLONAL	1	TRUE	1	0.917003255883511	2		515	677	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845262	151845262	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747850540	NA	P-0048263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	233	408	0	ENST00000262189.6:c.13750C>T	p.Arg4584Trp	p.R4584W	ENST00000262189	NM_170606.2	4584	Cgg/Tgg	52/59	1	2	FACETS	0.975	0.919	1	0.975	0.919	1	CLONAL	1	TRUE	1	0.917003255883511	2		408	521	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418690	49418690	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	241	431	0	ENST00000301067.7:c.15824G>C	p.Arg5275Thr	p.R5275T	ENST00000301067	NM_003482.3	5275	aGa/aCa	49/54	1	2	FACETS	0.934	0.88	0.988	0.934	0.88	0.988	CLONAL	1	TRUE	1	0.917003255883511	2		431	563	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41197713	41197713	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659941	NA	P-0048263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	49	789	0	ENST00000357654.3:c.5574C>G	p.Ile1858Met	p.I1858M	ENST00000357654	NM_007294.3	1858	atC/atG	23/23	0.910892002483021	2	FACETS	0.118	0.099	0.139	0.059	0.049	0.07	SUBCLONAL	1	TRUE	0	0.917003255883511	2		789	903	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575210	48575210	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	56	199	0	ENST00000342988.3:c.404G>A	p.Arg135Gln	p.R135Q	ENST00000342988	NM_005359.5	135	cGa/cAa	3/12	1	2	FACETS	0.387	0.333	0.444	0.387	0.333	0.444	SUBCLONAL	1	TRUE	1	0.917003255883511	2		199	316	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798136	42798136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1593	111	784	0	ENST00000575354.2:c.4090G>A	p.Glu1364Lys	p.E1364K	ENST00000575354	NM_015125.3	1364	Gag/Aag	17/20	0.917003255883511	4	FACETS	0.272	0.243	0.303	0.091	0.081	0.101	SUBCLONAL	1	TRUE	1	0.917003255883511	4		784	1704	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428559	72428559	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	29	269	0	ENST00000477973.2:c.445C>T	p.Gln149Ter	p.Q149*	ENST00000477973	NM_012234.5	149	Cag/Tag	2/4	0.917003255883511	2	FACETS	0.155	0.124	0.19	0.078	0.062	0.095	SUBCLONAL	1	TRUE	0	0.917003255883511	2		269	408	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468458	89468458	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	18	213	0	ENST00000336596.2:c.1992G>C	p.Arg664Ser	p.R664S	ENST00000336596	NM_005233.5	664	agG/agC	11/17	0.917003255883511	2	FACETS	0.124	0.093	0.161	0.062	0.046	0.081	SUBCLONAL	1	TRUE	0	0.917003255883511	2		213	317	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149436909	149436909	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217793336	NA	P-0048263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	39	749	0	ENST00000286301.3:c.2260G>A	p.Asp754Asn	p.D754N	ENST00000286301	NM_005211.3	754	Gac/Aac	17/22	NA	2	FACETS	0.11	0.091	0.132			1	INDETERMINATE	1	TRUE	NA	0.917003255883511	2		749	770	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164124	47164124	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	17	258	0	ENST00000409792.3:c.2002C>T	p.Pro668Ser	p.P668S	ENST00000409792	NM_014159.6	668	Ccc/Tcc	3/21	1	2	FACETS	0.717	0.537	0.93	0.717	0.537	0.93	CLONAL	1	FALSE	1	0.244272376702097	2		258	194	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087894	27087901	+	frameshift_variant	Frame_Shift_Del	DEL	GCCACCCA	GCCACCCA	-	novel	NA	P-0048264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	41	589	0	ENST00000324856.7:c.2182_2189del	p.Pro728TrpfsTer86	p.P728Wfs*86	ENST00000324856	NM_006015.4	727	cgGCCACCCAgt/cggt	6/20	1	2	FACETS	0.837	0.698	0.991	0.837	0.698	0.991	CLONAL	1	FALSE	1	0.244272376702097	2		589	401	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15943768	15943768	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	28	277	0	ENST00000268712.3:c.6720del	p.Val2241LeufsTer52	p.V2241Lfs*52	ENST00000268712	NM_006311.3	2240	gcA/gc	43/46	1	2	FACETS	0.816	0.654	0.999	0.816	0.654	0.999	CLONAL	1	FALSE	1	0.244272376702097	2		277	281	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589597	67589599	+	inframe_deletion	In_Frame_Del	DEL	ACT	ACT	-	novel	NA	P-0048264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	15	205	0	ENST00000274335.5:c.1360_1362del	p.Thr454del	p.T454del	ENST00000274335		454	ACT/-	10/15	0.194943770601309	3	FACETS	0.925	0.681	1	0.462	0.34	0.608	CLONAL	1	FALSE	1	0.244272376702097	3		205	149	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739859	145739859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564800052	NA	P-0048264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	47	1042	1	ENST00000428558.2:c.1671G>A	p.Met557Ile	p.M557I	ENST00000428558	NM_004260.3	557	atG/atA	10/22	1	2	FACETS	0.704	0.593	0.825	0.704	0.593	0.825	SUBCLONAL	1	FALSE	1	0.244272376702097	2		1043	547	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0048265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	85	434	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.480332877733693	3	FACETS	0.836	0.762	0.91	0.836	0.762	0.91	CLONAL	3	TRUE	0	0.524789023820585	3		434	163	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508746	38508746	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	67	542	0	ENST00000254066.5:c.794G>T	p.Cys265Phe	p.C265F	ENST00000254066	NM_000964.3	265	tGc/tTc	6/9	1	2	FACETS	0.808	0.72	0.897	1	0.98	1	CLONAL	2	TRUE	1	0.524789023820585	2		542	158	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0048266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	123	512	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.292058383858196	1	FACETS	0.922	0.834	1	0.922	0.834	1	CLONAL	1	TRUE	0	0.292058383858196	1		512	780	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023202	27023202	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	82	218	0	ENST00000324856.7:c.308C>A	p.Ser103Ter	p.S103*	ENST00000324856	NM_006015.4	103	tCg/tAg	1/20	0.274490938505301	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	2	TRUE	0	0.292058383858196	2		218	278	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0048266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	43	276	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	1	2	FACETS	0.811	0.681	0.955	0.811	0.681	0.955	CLONAL	1	TRUE	1	0.292058383858196	2		276	363	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	109	584	0	ENST00000397062.3:c.246A>T	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaT	2/5	1	2	FACETS	0.898	0.806	0.996	0.898	0.806	0.996	CLONAL	1	TRUE	1	0.292058383858196	2		584	831	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs371769427	NA	P-0048266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	42	152	0	ENST00000291552.4:c.101C>A	p.Ser34Tyr	p.S34Y	ENST00000291552	NM_006758.2	34	tCt/tAt	2/8	1	2	FACETS	0.795	0.665	0.937	0.795	0.665	0.937	CLONAL	1	TRUE	1	0.292058383858196	2		152	362	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589561	67589561	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	24	119	0	ENST00000274335.5:c.1324A>T	p.Ile442Phe	p.I442F	ENST00000274335		442	Att/Ttt	10/15	1	2	FACETS	1	0.837	1	1	0.837	1	CLONAL	1	TRUE	1	0.292058383858196	2		119	154	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971104	21971104	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	105	626	1	ENST00000304494.5:c.254C>A	p.Ala85Asp	p.A85D	ENST00000304494	NM_000077.4	85	gCt/gAt	2/3	0.292058383858196	1	FACETS	0.969	0.869	1	0.969	0.869	1	CLONAL	1	TRUE	0	0.292058383858196	1		627	634	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0048267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	42	259	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.663	0.555	0.782	0.663	0.555	0.782	SUBCLONAL	1	FALSE	1	0.369420492567121	2		259	343	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953742	48953742	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	26	177	0	ENST00000267163.4:c.1346del	p.Gly449GlufsTer8	p.G449Efs*8	ENST00000267163	NM_000321.2	449	Gga/ga	14/27	0.36633571238915	1	FACETS	0.565	0.45	0.695	0.565	0.45	0.695	SUBCLONAL	1	FALSE	0	0.369420492567121	1		177	203	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374316	81374316	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	51	213	0	ENST00000222390.5:c.746G>T	p.Arg249Ile	p.R249I	ENST00000222390	NM_000601.4	249	aGa/aTa	6/18	1	2	FACETS	0.812	0.693	0.941	0.812	0.693	0.941	CLONAL	1	FALSE	1	0.369420492567121	2		213	340	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480168	20480168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765868574	NA	P-0048267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	188	249	0	ENST00000346618.3:c.485G>A	p.Arg162Gln	p.R162Q	ENST00000346618	NM_001949.4	162	cGa/cAa	2/7	0.366427374338459	4	FACETS	0.899	0.837	0.961	0.899	0.837	0.961	CLONAL	3	FALSE	1	0.369420492567121	4		249	517	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643214	38643214	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs76128643	NA	P-0048267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	24	220	0	ENST00000299084.4:c.685-1G>T		p.X229_splice	ENST00000299084	NM_152594.2	229			0.192022221028431	0	FACETS	0.414	0.326	0.513			1	INDETERMINATE	1	FALSE	0	0.369420492567121	0		220	198	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679212	88679213	+	missense_variant	Missense_Mutation	DNP	AC	AC	CG	novel	NA	P-0048267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	76	567	0	ENST00000360948.2:c.824_825delinsCG	p.Ser275Thr	p.S275T	ENST00000360948	NM_001012338.2	275	aGT/aCG	8/19	0.192022221028431	0	FACETS	0.397	0.348	0.45			1	INDETERMINATE	1	FALSE	0	0.369420492567121	0		567	653	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021193	31021193	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	102	489	1	ENST00000375687.4:c.1192G>T	p.Gly398Cys	p.G398C	ENST00000375687	NM_015338.5	398	Ggt/Tgt	12/13	1	2	FACETS	0.892	0.799	0.99	0.892	0.799	0.99	CLONAL	1	FALSE	1	0.369420492567121	2		490	619	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385164	41385164	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	177	702	0	ENST00000373198.4:c.797G>C	p.Arg266Pro	p.R266P	ENST00000373198	NM_133170.3	266	cGc/cCc	6/32	1	2	FACETS	0.997	0.919	1	0.997	0.919	1	CLONAL	1	FALSE	1	0.369420492567121	2		702	961	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730212	133730212	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	78	387	0	ENST00000318560.5:c.278A>T	p.Tyr93Phe	p.Y93F	ENST00000318560	NM_005157.4	93	tAt/tTt	3/11	1	2	FACETS	0.746	0.656	0.842	0.746	0.656	0.842	SUBCLONAL	1	FALSE	1	0.369420492567121	2		387	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579538	7579550	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	ATATCGTCCGGGG	ATATCGTCCGGGG	CT	novel	NA	P-0048267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	187	752	2	ENST00000269305.4:c.137_149delinsAG	p.Ser46Ter	p.S46*	ENST00000269305	NM_001126112.2	46	tCCCCGGACGATATt/tAGt	4/11	0.297082989397259	2	FACETS	1	0.988	1	0.678	0.627	0.729	CLONAL	1	FALSE	0	0.369420492567121	2		754	747	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048267-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	115	349	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.966	0.877	1	0.966	0.877	1	CLONAL	1	TRUE	1	0.564047565882613	2		350	422	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0048267-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	80	347	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.906	0.805	1	0.906	0.805	1	CLONAL	1	TRUE	1	0.564047565882613	2		347	313	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572603	64572603	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048267-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	270	773	0	ENST00000312049.6:c.1253A>G	p.Asp418Gly	p.D418G	ENST00000312049	NM_130799.2	418	gAc/gGc	9/10	0.497048403671533	0	FACETS	0.616	0.581	0.651			1	SUBCLONAL	1	TRUE	0	0.564047565882613	0		773	678	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235833	108235833	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048267-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	60	300	0	ENST00000278616.4:c.8875G>C	p.Asp2959His	p.D2959H	ENST00000278616	NM_000051.3	2959	Gac/Cac	62/63	1	2	FACETS	0.854	0.744	0.971	0.854	0.744	0.971	CLONAL	1	TRUE	1	0.564047565882613	2		300	249	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344371	118344371	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048267-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	76	216	0	ENST00000534358.1:c.2497A>G	p.Thr833Ala	p.T833A	ENST00000534358	NM_005933.3	833	Act/Gct	3/36	1	2	FACETS	0.998	0.886	1	0.998	0.886	1	CLONAL	1	TRUE	1	0.564047565882613	2		216	270	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636941	158636941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048267-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	147	473	0	ENST00000263640.3:c.239C>T	p.Thr80Ile	p.T80I	ENST00000263640	NM_001105.4	80	aCc/aTc	4/11	1	2	FACETS	0.863	0.791	0.938	0.863	0.791	0.938	CLONAL	1	TRUE	1	0.564047565882613	2		473	604	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242800967	242800967	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048267-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	261	727	1	ENST00000334409.5:c.24G>A	p.Trp8Ter	p.W8*	ENST00000334409	NM_005018.2	8	tgG/tgA	1/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.564047565882613	2		728	871	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0048268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	45	407	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	1	2	FACETS	0.537	0.45	0.632	0.537	0.45	0.632	SUBCLONAL	1	FALSE	1	0.3	2		407	559	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0048268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	77	509	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	0.847	0.744	0.958	0.847	0.744	0.958	CLONAL	1	FALSE	1	0.3	2		509	606	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0048269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	24	566	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.485	0.379	0.607	0.485	0.379	0.607	SUBCLONAL	1	FALSE	1	0.235217000228305	2		566	421	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0048269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	28	122	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.415	0.331	0.512	0.415	0.331	0.512	SUBCLONAL	1	FALSE	1	0.235217000228305	2		122	573	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28963952	28963952	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	28	286	0	ENST00000282397.4:c.1950G>T	p.Lys650Asn	p.K650N	ENST00000282397	NM_002019.4	650	aaG/aaT	13/30	1	2	FACETS	0.607	0.485	0.747	0.607	0.485	0.747	SUBCLONAL	1	FALSE	1	0.235217000228305	2		286	392	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	127	349	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.500983390518031	2		350	463	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946090	13946090	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1419462186	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	112	326	0	ENST00000405192.2:c.1006C>T	p.Arg336Ter	p.R336*	ENST00000405192	NM_001163147.1	336	Cga/Tga	10/12	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.500983390518031	2		326	414	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424958105	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	128	346	0	ENST00000334344.6:c.940C>T	p.Arg314Cys	p.R314C	ENST00000334344	NM_152641.2	314	Cgt/Tgt	8/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.500983390518031	2		346	434	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801734	3801734	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269891200	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	154	427	0	ENST00000262367.5:c.3772C>T	p.Pro1258Ser	p.P1258S	ENST00000262367	NM_004380.2	1258	Ccc/Tcc	20/31	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.500983390518031	2		427	583	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435490	18435490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760928254	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	44	199	0	ENST00000266497.5:c.475G>A	p.Glu159Lys	p.E159K	ENST00000266497		159	Gaa/Aaa	1/31	1	2	FACETS	0.84	0.713	0.978	0.84	0.713	0.978	CLONAL	1	TRUE	1	0.500983390518031	2		199	209	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913384	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	233	609	0	ENST00000304494.5:c.262G>T	p.Glu88Ter	p.E88*	ENST00000304494	NM_000077.4	88	Gag/Tag	2/3	0.500983390518031	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.500983390518031	1		609	549	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924330	112924330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	278	855	0	ENST00000351677.2:c.1276C>T	p.His426Tyr	p.H426Y	ENST00000351677	NM_002834.3	426	Cac/Tac	11/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.500983390518031	2		855	1067	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874261	155874261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352822	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	158	482	0	ENST00000368323.3:c.270G>A	p.Met90Ile	p.M90I	ENST00000368323	NM_006912.5	90	atG/atA	5/6	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.500983390518031	2		482	623	SUCCESS
AR	367	MSKCC	GRCh37	X	66941766	66941766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	186	543	0	ENST00000374690.3:c.2410G>A	p.Glu804Lys	p.E804K	ENST00000374690	NM_000044.3	804	Gaa/Aaa	6/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.500983390518031	2		543	661	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467663	50467663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	146	568	0	ENST00000331340.3:c.898G>A	p.Glu300Lys	p.E300K	ENST00000331340	NM_006060.4	300	Gag/Aag	8/8	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.500983390518031	2		568	536	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233094	69233094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	81	310	0	ENST00000462284.1:c.959C>T	p.Pro320Leu	p.P320L	ENST00000462284	NM_002392.5	320	cCc/cTc	11/11	1	2	FACETS	0.898	0.797	1	0.898	0.797	1	CLONAL	1	TRUE	1	0.500983390518031	2		310	360	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244913	123244913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1224606327	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	232	845	2	ENST00000358487.5:c.2191G>A	p.Glu731Lys	p.E731K	ENST00000358487	NM_000141.4	731	Gaa/Aaa	16/18	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.500983390518031	2		847	845	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78921067	78921067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	232	660	0	ENST00000306801.3:c.3181C>T	p.His1061Tyr	p.H1061Y	ENST00000306801	NM_020761.2	1061	Cac/Tac	27/34	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.500983390518031	2		660	861	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562641	29562641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854562	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	142	353	0	ENST00000356175.3:c.3721C>T	p.Arg1241Ter	p.R1241*	ENST00000356175	NM_000267.3	1241	Cga/Tga	28/57	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.500983390518031	2		353	503	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066482	94066482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542602078	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	68	313	0	ENST00000369303.4:c.1277G>A	p.Arg426Gln	p.R426Q	ENST00000369303	NM_004440.3	426	cGa/cAa	5/17	1	2	FACETS	0.881	0.773	0.996	0.881	0.773	0.996	CLONAL	1	TRUE	1	0.500983390518031	2		313	308	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576033	29576033	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	107	379	0	ENST00000356175.3:c.4006C>T	p.Gln1336Ter	p.Q1336*	ENST00000356175	NM_000267.3	1336	Cag/Tag	30/57	1	2	FACETS	0.899	0.811	0.992	0.899	0.811	0.992	CLONAL	1	TRUE	1	0.500983390518031	2		379	475	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649565	206649565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	227	685	0	ENST00000367120.3:c.400C>T	p.Arg134Cys	p.R134C	ENST00000367120	NM_014002.3	134	Cgc/Tgc	6/22	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.500983390518031	2		685	811	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733337	40733337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746243026	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	134	436	0	ENST00000373198.4:c.3469G>A	p.Asp1157Asn	p.D1157N	ENST00000373198	NM_133170.3	1157	Gat/Aat	26/32	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.500983390518031	2		436	493	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390191	89390191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483175958	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	105	298	0	ENST00000336596.2:c.940G>A	p.Asp314Asn	p.D314N	ENST00000336596	NM_005233.5	314	Gac/Aac	4/17	1	2	FACETS	0.97	0.875	1	0.97	0.875	1	CLONAL	1	TRUE	1	0.500983390518031	2		298	432	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978703	70978703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	173	583	1	ENST00000276594.2:c.950G>A	p.Gly317Glu	p.G317E	ENST00000276594	NM_024504.3	317	gGa/gAa	5/8	1	2	FACETS	0.997	0.92	1	0.997	0.92	1	CLONAL	1	TRUE	1	0.500983390518031	2		584	693	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005924	69005924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	145	495	0	ENST00000288368.4:c.2335G>A	p.Glu779Lys	p.E779K	ENST00000288368	NM_024870.2	779	Gaa/Aaa	21/40	1	2	FACETS	0.94	0.86	1	0.94	0.86	1	CLONAL	1	TRUE	1	0.500983390518031	2		495	616	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242451	55242451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	132	422	1	ENST00000275493.2:c.2221C>T	p.Pro741Ser	p.P741S	ENST00000275493	NM_005228.3	741	Ccc/Tcc	19/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.500983390518031	2		423	465	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590736	189590736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558374141	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	308	499	2	ENST00000264731.3:c.1301C>T	p.Thr434Met	p.T434M	ENST00000264731	NM_003722.4	434	aCg/aTg	10/14	0.430319364922776	3	FACETS	0.947	0.897	0.998	0.947	0.897	0.998	CLONAL	2	TRUE	1	0.500983390518031	3		501	812	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978383	2978383	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	270	1023	0	ENST00000396946.4:c.947G>A	p.Arg316Lys	p.R316K	ENST00000396946	NM_032415.4	316	aGg/aAg	7/25	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.500983390518031	2		1023	1028	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069604	69069604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777049204	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	117	348	0	ENST00000288368.4:c.4279G>A	p.Glu1427Lys	p.E1427K	ENST00000288368	NM_024870.2	1427	Gaa/Aaa	35/40	1	2	FACETS	0.971	0.881	1	0.971	0.881	1	CLONAL	1	TRUE	1	0.500983390518031	2		348	481	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224393	36224393	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	385	1174	0	ENST00000222270.7:c.6943G>A	p.Gly2315Arg	p.G2315R	ENST00000222270	NM_014727.1	2315	Ggg/Agg	28/37	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.500983390518031	2		1174	1288	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960059	134960059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	232	508	0	ENST00000398015.3:c.2416G>A	p.Asp806Asn	p.D806N	ENST00000398015	NM_004441.4	806	Gac/Aac	13/16	0.430319364922776	3	FACETS	1	0.98	1	0.564	0.526	0.604	CLONAL	1	TRUE	1	0.500983390518031	3		508	1026	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073374	8073374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1204673836	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	159	473	0	ENST00000377482.5:c.1285G>A	p.Asp429Asn	p.D429N	ENST00000377482	NM_018948.3	429	Gac/Aac	4/4	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.500983390518031	2		473	631	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256141	16256141	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	158	433	0	ENST00000375759.3:c.3406C>T	p.Leu1136Phe	p.L1136F	ENST00000375759	NM_015001.2	1136	Ctt/Ttt	11/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.500983390518031	2		433	544	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101349	27101349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326693674	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	230	935	0	ENST00000324856.7:c.4631C>T	p.Ser1544Leu	p.S1544L	ENST00000324856	NM_006015.4	1544	tCg/tTg	18/20	1	2	FACETS	0.989	0.923	1	0.989	0.923	1	CLONAL	1	TRUE	1	0.500983390518031	2		935	928	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310445	65310445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	135	430	0	ENST00000342505.4:c.2243C>T	p.Ser748Phe	p.S748F	ENST00000342505	NM_002227.2	748	tCt/tTt	16/25	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.500983390518031	2		430	529	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65312385	65312385	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	41	565	0	ENST00000342505.4:c.1934T>C	p.Val645Ala	p.V645A	ENST00000342505	NM_002227.2	645	gTc/gCc	14/25	1	2	FACETS	0.216	0.179	0.257	0.216	0.179	0.257	SUBCLONAL	1	TRUE	1	0.500983390518031	2		565	758	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729766	162729766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	161	547	0	ENST00000367921.3:c.852G>A	p.Met284Ile	p.M284I	ENST00000367921	NM_006182.2	284	atG/atA	8/18	1	2	FACETS	0.917	0.843	0.993	0.917	0.843	0.993	CLONAL	1	TRUE	1	0.500983390518031	2		547	701	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091400	193091400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	167	499	1	ENST00000367435.3:c.70G>A	p.Glu24Lys	p.E24K	ENST00000367435	NM_024529.4	24	Gaa/Aaa	1/17	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.500983390518031	2		500	624	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983100	201983100	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	187	706	0	ENST00000359651.3:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000359651		317	Caa/Taa	7/8	1	2	FACETS	0.98	0.907	1	0.98	0.907	1	CLONAL	1	TRUE	1	0.500983390518031	2		706	762	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996788	100996788	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	111	436	0	ENST00000325455.5:c.1739G>A	p.Gly580Asp	p.G580D	ENST00000325455	NM_001202474.3	580	gGt/gAt	2/8	0.500983390518031	1	FACETS	0.888	0.806	0.973	0.888	0.806	0.973	CLONAL	1	TRUE	0	0.500983390518031	1		436	374	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656215	18656215	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	93	301	0	ENST00000266497.5:c.2894G>A	p.Gly965Glu	p.G965E	ENST00000266497		965	gGa/gAa	21/31	1	2	FACETS	0.982	0.88	1	0.982	0.88	1	CLONAL	1	TRUE	1	0.500983390518031	2		301	378	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246389	46246389	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	105	332	0	ENST00000334344.6:c.4483C>T	p.His1495Tyr	p.H1495Y	ENST00000334344	NM_152641.2	1495	Cat/Tat	15/21	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.500983390518031	2		332	375	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885160	111885161	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	184	729	1	ENST00000341259.2:c.1048_1049delinsTT	p.Pro350Leu	p.P350L	ENST00000341259	NM_005475.2	350	CCg/TTg	6/8	1	2	FACETS	0.994	0.92	1	0.994	0.92	1	CLONAL	1	TRUE	1	0.500983390518031	2		730	739	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112910824	112910824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	133	340	0	ENST00000351677.2:c.833G>A	p.Arg278Lys	p.R278K	ENST00000351677	NM_002834.3	278	aGa/aAa	7/16	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.500983390518031	2		340	522	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209285	133209285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500834	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	287	944	0	ENST00000320574.5:c.6101C>T	p.Ser2034Phe	p.S2034F	ENST00000320574	NM_006231.2	2034	tCc/tTc	44/49	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.500983390518031	2		944	1007	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881542	48881543	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	52	192	0	ENST00000267163.4:c.264_264+1delinsAA		p.X88_splice	ENST00000267163	NM_000321.2	88		2/27	1	2	FACETS	0.802	0.688	0.923	0.802	0.688	0.923	CLONAL	1	TRUE	1	0.500983390518031	2		192	259	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42057257	42057258	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	144	377	0	ENST00000219905.7:c.7918_7919delinsTT	p.Pro2640Leu	p.P2640L	ENST00000219905	NM_001164273.1	2640	CCa/TTa	23/24	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.500983390518031	2		377	490	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779608	3779608	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	341	1159	1	ENST00000262367.5:c.5440G>A	p.Gly1814Arg	p.G1814R	ENST00000262367	NM_004380.2	1814	Ggg/Agg	31/31	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.500983390518031	2		1160	1218	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916145	9916145	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	141	473	0	ENST00000330684.3:c.2144A>G	p.Asp715Gly	p.D715G	ENST00000330684	NM_001134407.1	715	gAc/gGc	10/13	1	2	FACETS	0.944	0.864	1	0.944	0.864	1	CLONAL	1	TRUE	1	0.500983390518031	2		473	596	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989475	7989475	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	248	796	0	ENST00000319144.4:c.211A>G	p.Lys71Glu	p.K71E	ENST00000319144	NM_001139.2	71	Aaa/Gaa	2/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.500983390518031	2		796	903	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732457	74732457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	131	407	2	ENST00000359995.5:c.452C>T	p.Ser151Phe	p.S151F	ENST00000359995	NM_001195427.1	151	tCc/tTc	2/3	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.500983390518031	2		409	426	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211766	5211766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	220	738	1	ENST00000357368.4:c.5069C>T	p.Ser1690Phe	p.S1690F	ENST00000357368	NM_002850.3	1690	tCc/tTc	33/38	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.500983390518031	2		739	817	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024651	11024652	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	144	615	1	ENST00000327064.4:c.768_769delinsAA	p.Glu257Lys	p.E257K	ENST00000327064	NM_199141.1	256	tcGGag/tcAAag	6/16	1	2	FACETS	0.861	0.787	0.937	0.861	0.787	0.937	CLONAL	1	TRUE	1	0.500983390518031	2		616	668	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214722	36214722	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	206	790	0	ENST00000222270.7:c.3148G>A	p.Gly1050Arg	p.G1050R	ENST00000222270	NM_014727.1	1050	Gga/Aga	8/37	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.500983390518031	2		790	787	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082277	16082277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	344	1162	0	ENST00000281043.3:c.91G>A	p.Asp31Asn	p.D31N	ENST00000281043	NM_005378.4	31	Gac/Aac	2/3	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.500983390518031	2		1162	1227	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715308	61715308	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754056639	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	190	568	0	ENST00000401558.2:c.2305C>T	p.Pro769Ser	p.P769S	ENST00000401558	NM_003400.3	769	Cca/Tca	19/25	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.500983390518031	2		568	712	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661861	227661862	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	285	894	1	ENST00000305123.5:c.1593_1594delinsTT	p.Pro532Ser	p.P532S	ENST00000305123	NM_005544.2	531	tcCCct/tcTTct	1/2	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.500983390518031	2		895	968	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277903	41277903	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	128	390	0	ENST00000349496.5:c.1867C>A	p.Gln623Lys	p.Q623K	ENST00000349496	NM_001904.3	623	Cag/Aag	12/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.500983390518031	2		390	452	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361250	66361250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	80	284	0	ENST00000273854.3:c.922G>A	p.Gly308Arg	p.G308R	ENST00000273854	NM_004439.5	308	Ggg/Agg	4/18	1	2	FACETS	0.951	0.844	1	0.951	0.844	1	CLONAL	1	TRUE	1	0.500983390518031	2		284	336	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510101	187510101	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	129	446	0	ENST00000441802.2:c.13412C>G	p.Ala4471Gly	p.A4471G	ENST00000441802	NM_005245.3	4471	gCg/gGg	27/27	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.500983390518031	2		446	489	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93607755	93607755	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	94	284	1	ENST00000375746.1:c.457C>T	p.Gln153Ter	p.Q153*	ENST00000375746	NM_001174167.1	153	Cag/Tag	3/14	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.500983390518031	2		285	348	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950037	44950037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	159	473	0	ENST00000377967.4:c.3806C>T	p.Pro1269Leu	p.P1269L	ENST00000377967	NM_021140.2	1269	cCc/cTc	26/29	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.500983390518031	2		473	580	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409775	63409775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	132	487	0	ENST00000330258.3:c.3392G>A	p.Gly1131Glu	p.G1131E	ENST00000330258	NM_152424.3	1131	gGa/gAa	2/2	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.500983390518031	2		487	520	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845361	76845361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	101	269	0	ENST00000373344.5:c.6160C>T	p.Leu2054Phe	p.L2054F	ENST00000373344	NM_000489.3	2054	Ctt/Ttt	27/35	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.500983390518031	2		269	403	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123499672	123499672	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	125	486	0	ENST00000371139.4:c.199G>A	p.Glu67Lys	p.E67K	ENST00000371139	NM_001114937.2	67	Gag/Aag	2/4	1	2	FACETS	0.963	0.876	1	0.963	0.876	1	CLONAL	1	TRUE	1	0.500983390518031	2		486	518	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0048271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	86	706	8	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.14	2		714	1058	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0048271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	73	684	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.14	2		686	1015	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106078	27106078	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	44	499	0	ENST00000324856.7:c.5693del	p.Pro1898HisfsTer25	p.P1898Hfs*25	ENST00000324856	NM_006015.4	1897	Ccc/cc	20/20	1	2	FACETS	0.901	0.754	1	0.901	0.754	1	CLONAL	1	TRUE	1	0.14	2		499	698	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5207955	5207955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1412878073	NA	P-0048271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	63	914	0	ENST00000357368.4:c.5756G>A	p.Arg1919Gln	p.R1919Q	ENST00000357368	NM_002850.3	1919	cGg/cAg	37/38	1	2	FACETS	0.757	0.652	0.872	0.757	0.652	0.872	SUBCLONAL	1	TRUE	1	0.14	2		914	1189	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	36	410	0	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	0.801	0.657	0.963	0.801	0.657	0.963	CLONAL	1	TRUE	1	0.14	2		410	642	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656951	47656951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63749849	NA	P-0048271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	26	262	0	ENST00000233146.2:c.1147C>T	p.Arg383Ter	p.R383*	ENST00000233146	NM_000251.2	383	Cga/Tga	7/16	1	2	FACETS	0.872	0.69	1	0.872	0.69	1	CLONAL	1	TRUE	1	0.14	2		262	426	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913250	NA	P-0048271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	36	320	0	ENST00000369535.4:c.34G>T	p.Gly12Cys	p.G12C	ENST00000369535	NM_002524.4	12	Ggt/Tgt	2/7	1	2	FACETS	0.839	0.688	1	0.839	0.688	1	CLONAL	1	TRUE	1	0.14	2		320	613	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448307	56448307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768842372	NA	P-0048271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	73	803	4	ENST00000407977.2:c.340C>T	p.Arg114Trp	p.R114W	ENST00000407977		114	Cgg/Tgg	3/10	1	2	FACETS	0.934	0.815	1	0.934	0.815	1	CLONAL	1	TRUE	1	0.14	2		807	1116	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855573	45855573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746618110	NA	P-0048271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	65	798	1	ENST00000391945.4:c.2084G>A	p.Arg695His	p.R695H	ENST00000391945	NM_000400.3	695	cGc/cAc	22/23	1	2	FACETS	0.875	0.756	1	0.875	0.756	1	CLONAL	1	TRUE	1	0.14	2		799	1061	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413105	63413105	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374303948	NA	P-0048271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	86	423	1	ENST00000330258.3:c.62G>A	p.Arg21His	p.R21H	ENST00000330258	NM_152424.3	21	cGt/cAt	2/2	1	1	FACETS	0.987	0.874	1	1	0.985	1	CLONAL	2	TRUE	0	0.14	1		424	579	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911508	134911508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201816783	NA	P-0048271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	37	503	1	ENST00000398015.3:c.1973C>T	p.Ser658Leu	p.S658L	ENST00000398015	NM_004441.4	658	tCg/tTg	11/16	1	2	FACETS	0.78	0.641	0.936	0.78	0.641	0.936	CLONAL	1	TRUE	1	0.14	2		504	678	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782062	66782062	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	25	243	1	ENST00000307102.5:c.1034del	p.Asn345ThrfsTer8	p.N345Tfs*8	ENST00000307102	NM_002755.3	343	atA/at	10/11	1	2	FACETS	0.886	0.698	1	0.886	0.698	1	CLONAL	1	TRUE	1	0.14	2		244	403	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699324	18699324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369934938	NA	P-0048271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	20	231	0	ENST00000266497.5:c.3425G>A	p.Arg1142His	p.R1142H	ENST00000266497		1142	cGt/cAt	24/31	1	2	FACETS	0.823	0.629	1	0.823	0.629	1	CLONAL	1	TRUE	1	0.14	2		231	347	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962378	2962378	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1275601330	NA	P-0048271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	56	710	0	ENST00000396946.4:c.2159G>A	p.Arg720Gln	p.R720Q	ENST00000396946	NM_032415.4	720	cGa/cAa	17/25	1	2	FACETS	0.786	0.671	0.912	0.786	0.671	0.912	CLONAL	1	TRUE	1	0.14	2		710	1018	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284906	15284906	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1469453455	NA	P-0048271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1424	83	984	3	ENST00000263388.2:c.4709G>A	p.Arg1570His	p.R1570H	ENST00000263388	NM_000435.2	1570	cGt/cAt	25/33	1	2	FACETS	0.787	0.691	0.89	0.787	0.691	0.89	SUBCLONAL	1	TRUE	1	0.14	2		987	1507	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385105	31385105	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs777301633	NA	P-0048271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	56	613	1	ENST00000328111.2:c.1490G>A	p.Arg497Gln	p.R497Q	ENST00000328111	NM_006892.3	497	cGg/cAg	14/23	1	2	FACETS	0.914	0.781	1	0.914	0.781	1	CLONAL	1	TRUE	1	0.14	2		614	875	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932807	39932807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1160807200	NA	P-0048271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	74	442	0	ENST00000378444.4:c.1792G>A	p.Val598Met	p.V598M	ENST00000378444	NM_001123385.1	598	Gtg/Atg	4/15	1	1	FACETS	0.811	0.71	0.92	1	0.978	1	CLONAL	2	TRUE	0	0.14	1		442	606	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265144	5265144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769916725	NA	P-0048271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	65	961	2	ENST00000357368.4:c.443G>A	p.Arg148Gln	p.R148Q	ENST00000357368	NM_002850.3	148	cGg/cAg	5/38	1	2	FACETS	0.786	0.679	0.903	0.786	0.679	0.903	CLONAL	1	TRUE	1	0.14	2		963	1181	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191047	2191047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886983194	NA	P-0048271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	35	495	2	ENST00000398665.3:c.301C>T	p.Arg101Trp	p.R101W	ENST00000398665	NM_032482.2	101	Cgg/Tgg	5/28	1	2	FACETS	0.716	0.585	0.864	0.716	0.585	0.864	SUBCLONAL	1	TRUE	1	0.14	2		497	698	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705261	52705261	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770424653	NA	P-0048271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	47	468	1	ENST00000322088.6:c.143G>A	p.Arg48Gln	p.R48Q	ENST00000322088	NM_014225.5	48	cGa/cAa	2/15	1	2	FACETS	0.879	0.74	1	0.879	0.74	1	CLONAL	1	TRUE	1	0.14	2		469	764	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636257	87636257	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	40	584	1	ENST00000277120.3:c.2422C>T	p.Arg808Ter	p.R808*	ENST00000277120		808	Cga/Tga	19/19	1	2	FACETS	0.784	0.649	0.934	0.784	0.649	0.934	CLONAL	1	TRUE	1	0.14	2		585	729	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931700	39931700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	52	337	1	ENST00000378444.4:c.2899G>A	p.Ala967Thr	p.A967T	ENST00000378444	NM_001123385.1	967	Gcc/Acc	4/15	1	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.14	1		338	530	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260145	149260145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200641813	NA	P-0048271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	40	463	0	ENST00000360632.3:c.748C>T	p.Arg250Cys	p.R250C	ENST00000360632	NM_015472.4	250	Cgc/Tgc	4/7	1	2	FACETS	0.826	0.684	0.984	0.826	0.684	0.984	CLONAL	1	TRUE	1	0.14	2		463	692	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246078852	246078852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150058397	NA	P-0048271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	57	613	0	ENST00000388985.4:c.793C>T	p.Arg265Cys	p.R265C	ENST00000388985		265	Cgt/Tgt	8/12	1	2	FACETS	0.883	0.756	1	0.883	0.756	1	CLONAL	1	TRUE	1	0.14	2		613	922	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945585	71945585	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	38	426	0	ENST00000298229.2:c.2343del	p.Phe781LeufsTer64	p.F781Lfs*64	ENST00000298229	NM_001567.3	781	Ttt/tt	21/28	1	2	FACETS	0.933	0.77	1	0.933	0.77	1	CLONAL	1	TRUE	1	0.14	2		426	582	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032339	42032339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	51	444	2	ENST00000219905.7:c.4523G>A	p.Gly1508Asp	p.G1508D	ENST00000219905	NM_001164273.1	1508	gGc/gAc	14/24	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.14	2		446	664	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119736	17119737	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0048271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	61	823	0	ENST00000285071.4:c.1257dup	p.Leu420AlafsTer36	p.L420Afs*36	ENST00000285071	NM_144997.5	419	-/G	11/14	1	2	FACETS	0.805	0.692	0.928	0.805	0.692	0.928	CLONAL	1	TRUE	1	0.14	2		823	1083	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231392	5231392	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370330291	NA	P-0048271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	56	906	0	ENST00000357368.4:c.2084C>T	p.Thr695Met	p.T695M	ENST00000357368	NM_002850.3	695	aCg/aTg	14/38	1	2	FACETS	0.741	0.632	0.86	0.741	0.632	0.86	SUBCLONAL	1	TRUE	1	0.14	2		906	1080	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279616	18279616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757901079	NA	P-0048271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	63	820	0	ENST00000222254.8:c.1889C>T	p.Thr630Met	p.T630M	ENST00000222254	NM_005027.3	630	aCg/aTg	15/16	1	2	FACETS	0.794	0.684	0.914	0.794	0.684	0.914	CLONAL	1	TRUE	1	0.14	2		820	1134	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637384	47637384	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	61	619	0	ENST00000233146.2:c.518T>A	p.Leu173Gln	p.L173Q	ENST00000233146	NM_000251.2	173	cTa/cAa	3/16	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.14	2		619	810	SUCCESS
APC	324	MSKCC	GRCh37	5	112177641	112177641	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	23	275	0	ENST00000257430.4:c.6350A>G	p.Gln2117Arg	p.Q2117R	ENST00000257430	NM_000038.5	2117	cAa/cGa	16/16	1	2	FACETS	0.838	0.653	1	0.838	0.653	1	CLONAL	1	TRUE	1	0.14	2		275	392	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026723	6026723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs114037612	NA	P-0048271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	54	628	0	ENST00000265849.7:c.1673C>T	p.Thr558Ile	p.T558I	ENST00000265849	NM_000535.5	558	aCc/aTc	11/15	1	2	FACETS	0.848	0.722	0.986	0.848	0.722	0.986	CLONAL	1	TRUE	1	0.14	2		628	910	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395282	139395282	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	92	913	0	ENST00000277541.6:c.5656A>G	p.Met1886Val	p.M1886V	ENST00000277541	NM_017617.3	1886	Atg/Gtg	31/34	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.14	2		913	1202	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0048272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	115	566	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.263785257309256	2		566	616	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519324	176519324	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs777010660	NA	P-0048272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	137	794	0	ENST00000292408.4:c.730C>T	p.Arg244Trp	p.R244W	ENST00000292408	NM_213647.1	244	Cgg/Tgg	7/18	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.263785257309256	2		794	905	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223957	2223957	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048272-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	151	1013	0	ENST00000326181.6:c.1171A>G	p.Thr391Ala	p.T391A	ENST00000326181	NM_032271.2	391	Acc/Gcc	13/21	1	2	FACETS	0.909	0.829	0.993	0.909	0.829	0.993	CLONAL	1	TRUE	1	0.263785257309256	2		1013	1260	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0048274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	28	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.161254068103913	0	FACETS	0.511	0.408	0.629			1	SUBCLONAL	1	TRUE	0	0.21	0		327	412	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46527668	46527668	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	40	338	0	ENST00000262741.5:c.697C>T	p.Gln233Ter	p.Q233*	ENST00000262741	NM_003629.3	233	Caa/Taa	6/10	1	2	FACETS	0.69	0.573	0.821	0.69	0.573	0.821	SUBCLONAL	1	TRUE	1	0.21	2		338	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578225	7578225	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	77	638	0	ENST00000269305.4:c.624del	p.Asp208GlufsTer39	p.D208Efs*39	ENST00000269305	NM_001126112.2	208	gaC/ga	6/11	1	2	FACETS	0.678	0.594	0.77	0.678	0.594	0.77	SUBCLONAL	1	TRUE	1	0.21	2		638	1081	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	81	432	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.846	0.744	0.955	1	0.98	1	CLONAL	2	TRUE	1	0.12	2		432	798	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0048275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	24	327	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.722	0.564	0.905	0.722	0.564	0.905	CLONAL	1	TRUE	1	0.12	2		327	554	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970971	21970971	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	67	1068	2	ENST00000304494.5:c.387C>A	p.Tyr129Ter	p.Y129*	ENST00000304494	NM_000077.4	129	taC/taA	2/3	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.12	2		1070	1092	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141526	11141526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048275-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	45	864	1	ENST00000358026.2:c.3503C>T	p.Ala1168Val	p.A1168V	ENST00000358026	NM_001128849.1	1168	gCa/gTa	25/36	1	2	FACETS	0.872	0.731	1	0.872	0.731	1	CLONAL	1	TRUE	1	0.12	2		865	860	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247168	153247168	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1560758208	NA	P-0048276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	101	71	0	ENST00000281708.4:c.1634A>G	p.Tyr545Cys	p.Y545C	ENST00000281708	NM_033632.3	545	tAt/tGt	10/12	0.201687396978048	1	FACETS	0.545	0.496	0.594	0.545	0.496	0.594	INDETERMINATE	1	TRUE	0	0.85974231218059	1		71	246	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278352	39278352	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs137852812	NA	P-0048276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	126	173	0	ENST00000402219.2:c.797C>A	p.Thr266Lys	p.T266K	ENST00000402219	NM_005633.3	266	aCa/aAa	6/23	1	2	FACETS	0.928	0.852	1	0.928	0.852	1	CLONAL	1	TRUE	1	0.85974231218059	2		173	316	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576853	7576853	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	287	194	0	ENST00000269305.4:c.993G>C	p.Gln331His	p.Q331H	ENST00000269305	NM_001126112.2	331	caG/caC	9/11	0.852735213250257	1	FACETS	0.969	0.932	1	0.969	0.932	1	CLONAL	1	TRUE	0	0.85974231218059	1		194	393	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714548	52714550	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0048276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	774	211	0	ENST00000322088.6:c.306_308del	p.Val104del	p.V104del	ENST00000322088	NM_014225.5	102	acAGTg/acg	4/15	0.813925326456476	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.85974231218059	3		211	1259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0048278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	470	643	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.637846035081244	2	FACETS	0.924	0.892	0.955	0.924	0.892	0.955	CLONAL	2	TRUE	0	0.666861449400483	2		643	763	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0048278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	85	188	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.969	0.869	1	0.969	0.869	1	CLONAL	1	TRUE	1	0.666861449400483	2		188	263	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514692	103514692	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	107	259	0	ENST00000355739.4:c.1193A>G	p.Asp398Gly	p.D398G	ENST00000355739	NM_000123.3	398	gAc/gGc	8/15	1	2	FACETS	0.831	0.752	0.914	0.831	0.752	0.914	CLONAL	1	TRUE	1	0.666861449400483	2		259	386	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244291	46244307	+	frameshift_variant	Frame_Shift_Del	DEL	TGTCCCACAGAGTCATA	TGTCCCACAGAGTCATA	-	novel	NA	P-0048278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	56	304	0	ENST00000334344.6:c.2388_2404del	p.Pro797TrpfsTer38	p.P797Wfs*38	ENST00000334344	NM_152641.2	795	gcTGTCCCACAGAGTCATAtg/gctg	15/21	1	2	FACETS	0.405	0.347	0.467	0.405	0.347	0.467	SUBCLONAL	1	TRUE	1	0.666861449400483	2		304	415	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0048279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	63	259	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.287350790989474	2		259	371	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604750	48604750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	49	353	0	ENST00000342988.3:c.1572G>T	p.Trp524Cys	p.W524C	ENST00000342988	NM_005359.5	524	tgG/tgT	12/12	0.287350790989474	1	FACETS	0.789	0.671	0.919	0.789	0.671	0.919	CLONAL	1	TRUE	0	0.287350790989474	1		353	370	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593491	48593494	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	rs80338965	NA	P-0048279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	26	242	0	ENST00000342988.3:c.1245_1248del	p.Asp415GlufsTer20	p.D415Efs*20	ENST00000342988	NM_005359.5	414	ttAGAC/tt	10/12	0.287350790989474	1	FACETS	0.458	0.363	0.568	0.458	0.363	0.568	SUBCLONAL	1	TRUE	0	0.287350790989474	1		242	338	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770791	59770791	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	35	235	0	ENST00000259008.2:c.2575G>A	p.Gly859Arg	p.G859R	ENST00000259008	NM_032043.2	859	Gga/Aga	18/20	1	2	FACETS	0.906	0.746	1	0.906	0.746	1	CLONAL	1	TRUE	1	0.287350790989474	2		235	269	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47108581	47108581	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	36	346	1	ENST00000409792.3:c.6088C>T	p.Gln2030Ter	p.Q2030*	ENST00000409792	NM_014159.6	2030	Caa/Taa	13/21	1	2	FACETS	1	0.824	1	1	0.824	1	CLONAL	1	TRUE	1	0.13	2		347	552	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920531	127920531	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	32	303	0	ENST00000373547.4:c.368A>C	p.Tyr123Ser	p.Y123S	ENST00000373547	NM_002721.4	123	tAt/tCt	4/7	1	2	FACETS	0.92	0.746	1	0.92	0.746	1	CLONAL	1	TRUE	1	0.13	2		303	535	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195681	123195681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048279-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	89	490	0	ENST00000218089.9:c.1595C>T	p.Ala532Val	p.A532V	ENST00000218089	NM_001042749.1	532	gCg/gTg	17/35	1	2	FACETS	0.821	0.728	0.92	0.821	0.728	0.92	CLONAL	1	TRUE	1	0.325692862517708	2		490	666	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220494	1220494	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519858	NA	P-0048279-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	165	921	0	ENST00000326873.7:c.587G>T	p.Gly196Val	p.G196V	ENST00000326873	NM_000455.4	196	gGc/gTc	4/10	0.303381364464086	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.325692862517708	1		921	824	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039686	47039686	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048279-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	154	871	0	ENST00000377604.3:c.1138G>T	p.Glu380Ter	p.E380*	ENST00000377604	NM_001204468.1	380	Gag/Tag	11/24	1	2	FACETS	0.993	0.909	1	0.993	0.909	1	CLONAL	1	TRUE	1	0.325692862517708	2		871	952	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335106	65335106	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048279-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	101	471	0	ENST00000342505.4:c.535G>T	p.Glu179Ter	p.E179*	ENST00000342505	NM_002227.2	179	Gag/Tag	6/25	1	2	FACETS	0.895	0.8	0.995	0.895	0.8	0.995	CLONAL	1	TRUE	1	0.325692862517708	2		471	693	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599889	10599889	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048279-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	173	974	0	ENST00000171111.5:c.1687C>T	p.Gln563Ter	p.Q563*	ENST00000171111	NM_203500.1	563	Cag/Tag	5/6	0.325692862517708	1	FACETS	0.905	0.832	0.98	0.905	0.832	0.98	CLONAL	1	TRUE	0	0.325692862517708	1		974	983	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356101	66356101	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048279-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	42	348	0	ENST00000273854.3:c.1396C>A	p.Gln466Lys	p.Q466K	ENST00000273854	NM_004439.5	466	Caa/Aaa	5/18	1	2	FACETS	0.445	0.371	0.528	0.445	0.371	0.528	SUBCLONAL	1	TRUE	1	0.325692862517708	2		348	579	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354574	70354574	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048279-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	28	478	0	ENST00000374080.3:c.4739C>A	p.Thr1580Asn	p.T1580N	ENST00000374080		1580	aCt/aAt	35/45	1	2	FACETS	0.311	0.248	0.383	0.311	0.248	0.383	SUBCLONAL	1	TRUE	1	0.325692862517708	2		478	553	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123199796	123199796	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048279-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	48	244	0	ENST00000218089.9:c.2096A>T	p.Asn699Ile	p.N699I	ENST00000218089	NM_001042749.1	699	aAt/aTt	21/35	1	2	FACETS	0.942	0.8	1	0.942	0.8	1	CLONAL	1	TRUE	1	0.325692862517708	2		244	313	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38954919	38954923	+	frameshift_variant	Frame_Shift_Del	DEL	TGTCC	TGTCC	ATA	novel	NA	P-0048279-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	35	249	0	ENST00000357387.3:c.2650_2654delinsTAT	p.Gly884TyrfsTer6	p.G884Yfs*6	ENST00000357387	NM_152756.3	884	GGACAa/TATa	27/38	1	2	FACETS	0.687	0.564	0.823	0.687	0.564	0.823	SUBCLONAL	1	TRUE	1	0.325692862517708	2		249	313	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599338	55599338	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	314	391	0	ENST00000288135.5:c.2464A>T	p.Asn822Tyr	p.N822Y	ENST00000288135	NM_000222.2	822	Aat/Tat	17/21	0.691323049541052	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.709502097266156	3		391	597	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955580	48955580	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587778857	NA	P-0048280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	79	216	0	ENST00000267163.4:c.1695+1G>A		p.X565_splice	ENST00000267163	NM_000321.2	565			0.709502097266156	1	FACETS	0.998	0.908	1	0.998	0.908	1	CLONAL	1	TRUE	0	0.709502097266156	1		216	144	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262321	115262322	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0048280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	176	356	0	ENST00000438362.2:c.2232_2233del	p.Phe746ProfsTer10	p.F746Pfs*10	ENST00000438362	NM_001242891.1	744	ctCTtt/cttt	18/20	0.709502097266156	1	FACETS	0.912	0.854	0.97	0.912	0.854	0.97	CLONAL	1	TRUE	0	0.709502097266156	1		356	351	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352676	118352676	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	475	479	0	ENST00000534358.1:c.3881C>A	p.Ser1294Ter	p.S1294*	ENST00000534358	NM_005933.3	1294	tCa/tAa	7/36	0.709502097266156	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.709502097266156	2		479	667	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506170	148506171	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs797045568	NA	P-0048281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	93	309	0	ENST00000320356.2:c.2187dup	p.Asp730Ter	p.D730*	ENST00000320356	NM_004456.4	729	-/T	19/20	0.759164745032739	3	FACETS	0.792	0.708	0.88	0.396	0.354	0.44	SUBCLONAL	1	TRUE	1	0.759164745032739	3		309	427	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967067	25967076	+	frameshift_variant	Frame_Shift_Del	DEL	GCCTCCTCTA	GCCTCCTCTA	-	novel	NA	P-0048282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	57	679	0	ENST00000435504.4:c.2130_2139del	p.Arg711ValfsTer85	p.R711Vfs*85	ENST00000435504		710	gcTAGAGGAGGC/gc	13/13	0.449929971438624	1	FACETS	0.415	0.358	0.478	0.415	0.358	0.478	SUBCLONAL	1	TRUE	0	0.539975141758624	1		679	371	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306790	41306790	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200588327	NA	P-0048282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	57	366	0	ENST00000373198.4:c.869C>T	p.Thr290Met	p.T290M	ENST00000373198	NM_133170.3	290	aCg/aTg	7/32	0.380831082799499	1	FACETS	0.741	0.645	0.842	0.741	0.645	0.842	SUBCLONAL	1	TRUE	0	0.539975141758624	1		366	208	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155435	47155446	+	inframe_deletion	In_Frame_Del	DEL	TGCTGTTTTCTC	TGCTGTTTTCTC	-	novel	NA	P-0048282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	90	395	0	ENST00000409792.3:c.4635_4646del	p.Gln1545_Gln1548del	p.Q1545_Q1548del	ENST00000409792	NM_014159.6	1545	caGAGAAAACAGCAt/cat	5/21	0.539975141758624	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.539975141758624	1		395	232	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974227	2974227	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	125	802	0	ENST00000396946.4:c.1378C>T	p.Gln460Ter	p.Q460*	ENST00000396946	NM_032415.4	460	Cag/Tag	10/25	0.326535485674299	1	FACETS	0.851	0.778	0.927	0.851	0.778	0.927	CLONAL	1	TRUE	0	0.539975141758624	1		802	397	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50488275	50488278	+	missense_variant	Missense_Mutation	ONP	GATG	GATG	TATA	novel	NA	P-0048282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	53	507	0	ENST00000394963.4:c.1189_1192delinsTATA	p.Asp397_Asp398delinsTyrAsn	p.D397_D398delinsYN	ENST00000394963	NM_003076.4	397	GATGac/TATAac	10/13	0.326535485674299	1	FACETS	0.481	0.413	0.555	0.481	0.413	0.555	SUBCLONAL	1	TRUE	0	0.539975141758624	1		507	298	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0048283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	29	703	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.349	0.278	0.43	0.349	0.278	0.43	SUBCLONAL	1	TRUE	1	0.14	2		703	1187	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0048283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	42	659	2	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	1	2	FACETS	0.698	0.581	0.83	0.698	0.581	0.83	SUBCLONAL	1	TRUE	1	0.14	2		661	859	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224591	108224591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	20	259	0	ENST00000278616.4:c.8770G>A	p.Glu2924Lys	p.E2924K	ENST00000278616	NM_000051.3	2924	Gaa/Aaa	60/63	1	2	FACETS	0.744	0.568	0.951	0.744	0.568	0.951	CLONAL	1	TRUE	1	0.14	2		259	384	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0048284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	19	566	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.727	0.553	0.93	0.727	0.553	0.93	CLONAL	1	TRUE	1	0.23338072010343	2		566	224	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs760043106	NA	P-0048284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	34	702	1	ENST00000269305.4:c.584T>A	p.Ile195Asn	p.I195N	ENST00000269305	NM_001126112.2	195	aTc/aAc	6/11	0.23338072010343	1	FACETS	0.719	0.588	0.865	0.719	0.588	0.865	SUBCLONAL	1	TRUE	0	0.23338072010343	1		703	358	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970905	21970905	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	35	834	0	ENST00000304494.5:c.453del	p.Ser152GlnfsTer41	p.S152Qfs*41	ENST00000304494	NM_000077.4	151	ccC/cc	2/3	0.19191010378527	2	FACETS	0.914	0.751	1	0.457	0.375	0.548	CLONAL	1	TRUE	0	0.23338072010343	2		834	328	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0048285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	101	483	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.244409245988482	5	FACETS	0.882	0.793	0.975	0.661	0.595	0.731	CLONAL	3	FALSE	1	0.244409245988482	5		483	427	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970971	21970971	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0048285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	108	813	0	ENST00000304494.5:c.387C>G	p.Tyr129Ter	p.Y129*	ENST00000304494	NM_000077.4	129	taC/taG	2/3	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.244409245988482	2		813	733	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019596	42019615	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AATCCTGTGGTAAGTCTGGA	AATCCTGTGGTAAGTCTGGA	-	novel	NA	P-0048285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	40	345	0	ENST00000219905.7:c.3650_3657+12del		p.X1217_splice	ENST00000219905	NM_001164273.1	1217		10/24	0.244409245988482	1	FACETS	0.915	0.763	1	0.915	0.763	1	CLONAL	1	FALSE	0	0.244409245988482	1		345	314	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76764065	76764066	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0048285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	54	447	0	ENST00000373344.5:c.7242_7243delinsAA	p.Gln2415Lys	p.Q2415K	ENST00000373344	NM_000489.3	2414	ctCCag/ctAAag	35/35	0.210319545884829	3	FACETS	0.861	0.735	0.999	0.43	0.367	0.5	CLONAL	1	FALSE	1	0.244409245988482	3		447	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs864622237	NA	P-0048287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	40	481	0	ENST00000269305.4:c.700T>C	p.Tyr234His	p.Y234H	ENST00000269305	NM_001126112.2	234	Tac/Cac	7/11	1	2	FACETS	0.78	0.646	0.93	0.78	0.646	0.93	CLONAL	1	TRUE	1	0.13	2		481	789	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152098	11152098	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1290442223	NA	P-0048287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	43	448	0	ENST00000358026.2:c.4382G>A	p.Arg1461His	p.R1461H	ENST00000358026	NM_001128849.1	1461	cGc/cAc	31/36	1	2	FACETS	1	0.84	1	1	0.84	1	CLONAL	1	TRUE	1	0.13	2		448	658	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050677	30050677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867595517	NA	P-0048288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	182	398	0	ENST00000338641.4:c.479G>A	p.Arg160Gln	p.R160Q	ENST00000338641	NM_000268.3	160	cGg/cAg	5/16	0.86790762281308	2	FACETS	0.877	0.817	0.939	0.439	0.408	0.47	CLONAL	1	TRUE	0	0.86790762281308	2		398	478	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851680	63851680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs553462344	NA	P-0048288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	197	506	1	ENST00000279873.7:c.2458C>T	p.Pro820Ser	p.P820S	ENST00000279873	NM_032199.2	820	Ccc/Tcc	10/10	0.85818034804943	2	FACETS	1	0.957	1	0.514	0.481	0.546	CLONAL	1	TRUE	0	0.86790762281308	2		507	442	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998801	100998801	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	142	966	0	ENST00000325455.5:c.1001G>T	p.Gly334Val	p.G334V	ENST00000325455	NM_001202474.3	334	gGg/gTg	1/8	0.86790762281308	4	FACETS	0.978	0.894	1	0.489	0.447	0.533	CLONAL	1	TRUE	2	0.86790762281308	4		966	625	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0048289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	68	269	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.764	0.673	0.859	0.764	0.673	0.859	SUBCLONAL	1	TRUE	1	0.720881652495113	2		269	247	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0048289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	65	209	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.794	0.698	0.895	0.794	0.698	0.895	SUBCLONAL	1	TRUE	1	0.720881652495113	2		210	227	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850705	63850705	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs201178069	NA	P-0048289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	102	205	0	ENST00000279873.7:c.1489del	p.Ile497Ter	p.I497*	ENST00000279873	NM_032199.2	495	Aaa/aa	10/10	1	2	FACETS	0.95	0.861	1	0.95	0.861	1	CLONAL	1	TRUE	1	0.720881652495113	2		205	298	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574678	41574679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs754418509	NA	P-0048289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	368	616	1	ENST00000263253.7:c.6970dup	p.His2324ProfsTer55	p.H2324Pfs*55	ENST00000263253	NM_001429.3	2321	-/C	31/31	1	2	FACETS	0.895	0.85	0.941	0.895	0.85	0.941	CLONAL	1	TRUE	1	0.720881652495113	2		617	1141	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0048289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	363	659	1	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.720881652495113	2		660	994	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438317	110438322	+	inframe_deletion	In_Frame_Del	DEL	GTTGTT	GTTGTT	-	rs532810290	NA	P-0048289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	101	223	1	ENST00000375856.3:c.79_84del	p.Asn27_Asn28del	p.N27_N28del	ENST00000375856	NM_003749.2	27	AACAAC/-	1/2	1	2	FACETS	0.757	0.683	0.835	0.757	0.683	0.835	SUBCLONAL	1	TRUE	1	0.720881652495113	2		224	370	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183339	56183339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	150	321	0	ENST00000399503.3:c.4249G>A	p.Ala1417Thr	p.A1417T	ENST00000399503	NM_005921.1	1417	Gca/Aca	18/20	1	2	FACETS	0.963	0.889	1	0.963	0.889	1	CLONAL	1	TRUE	1	0.720881652495113	2		321	432	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0048289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	205	430	3	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.720881652495113	2		433	559	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0048289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	145	341	1	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	0.904	0.832	0.978	0.904	0.832	0.978	CLONAL	1	TRUE	1	0.720881652495113	2		342	445	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200026	138200026	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780514490	NA	P-0048289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	266	461	0	ENST00000237289.4:c.1444G>A	p.Gly482Ser	p.G482S	ENST00000237289	NM_001270507.1	482	Ggc/Agc	7/9	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.720881652495113	2		461	731	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797780	42797780	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771163344	NA	P-0048289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	425	820	1	ENST00000575354.2:c.3832G>A	p.Val1278Ile	p.V1278I	ENST00000575354	NM_015125.3	1278	Gtc/Atc	16/20	0.720881652495113	2	FACETS	1	0.983	1	0.529	0.505	0.554	CLONAL	1	TRUE	0	0.720881652495113	2		821	1114	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885939	111885939	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	340	671	0	ENST00000341259.2:c.1566del	p.Glu523SerfsTer25	p.E523Sfs*25	ENST00000341259	NM_005475.2	521	Ccc/cc	8/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.720881652495113	2		671	874	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052633	42052633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	204	380	0	ENST00000219905.7:c.7304G>A	p.Arg2435Gln	p.R2435Q	ENST00000219905	NM_001164273.1	2435	cGg/cAg	20/24	0.720881652495113	1	FACETS	0.955	0.901	1	0.955	0.901	1	CLONAL	1	TRUE	0	0.720881652495113	1		380	379	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	434	903	6	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.720881652495113	2		909	1182	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0048289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	411	918	7	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.961	0.915	1	0.961	0.915	1	CLONAL	1	TRUE	1	0.720881652495113	2		925	1187	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274910	41274910	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	123	335	0	ENST00000349496.5:c.1160A>G	p.Asn387Ser	p.N387S	ENST00000349496	NM_001904.3	387	aAt/aGt	8/15	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.720881652495113	2		335	338	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256250	41256251	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs80357604	NA	P-0048289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	91	252	0	ENST00000357654.3:c.329dup	p.Glu111GlyfsTer3	p.E111Gfs*3	ENST00000357654	NM_007294.3	110	aag/aaAg	6/23	1	2	FACETS	0.918	0.827	1	0.918	0.827	1	CLONAL	1	TRUE	1	0.720881652495113	2		252	275	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056089	26056089	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1018305284	NA	P-0048289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	188	428	0	ENST00000343677.2:c.568G>A	p.Ala190Thr	p.A190T	ENST00000343677	NM_005319.3	190	Gct/Act	1/1	1	2	FACETS	0.988	0.92	1	0.988	0.92	1	CLONAL	1	TRUE	1	0.720881652495113	2		428	528	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937744	76937745	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	21	345	0	ENST00000373344.5:c.3003dup	p.Val1002SerfsTer3	p.V1002Sfs*3	ENST00000373344	NM_000489.3	1001	-/A	9/35	1	2	FACETS	0.189	0.145	0.239	0.189	0.145	0.239	SUBCLONAL	1	TRUE	1	0.720881652495113	2		345	309	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859609	57859610	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	rs1566559797	NA	P-0048289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	247	580	1	ENST00000228682.2:c.671_672dup	p.Glu225ArgfsTer56	p.E225Rfs*56	ENST00000228682	NM_005269.2	221	-/GA	7/12	1	2	FACETS	0.869	0.815	0.924	0.869	0.815	0.924	CLONAL	1	TRUE	1	0.720881652495113	2		581	789	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380309	25380309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1407509439	NA	P-0048289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	120	302	0	ENST00000311936.3:c.149C>T	p.Thr50Ile	p.T50I	ENST00000311936	NM_004985.3	50	aCc/aTc	3/5	1	2	FACETS	0.895	0.817	0.976	0.895	0.817	0.976	CLONAL	1	TRUE	1	0.720881652495113	2		302	372	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427228	49427228	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	275	800	0	ENST00000301067.7:c.11260C>T	p.Gln3754Ter	p.Q3754*	ENST00000301067	NM_003482.3	3754	Cag/Tag	39/54	1	2	FACETS	0.883	0.831	0.936	0.883	0.831	0.936	CLONAL	1	TRUE	1	0.720881652495113	2		800	864	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909490	50909490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774130423	NA	P-0048289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	459	848	2	ENST00000440232.2:c.1294C>T	p.Arg432Trp	p.R432W	ENST00000440232	NM_002691.3	432	Cgg/Tgg	11/27	0.720881652495113	2	FACETS	1	0.965	1	0.505	0.483	0.528	CLONAL	1	TRUE	0	0.720881652495113	2		850	1260	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246091256	246091256	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs566281194	NA	P-0048289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	256	383	1	ENST00000388985.4:c.679C>T	p.Arg227Ter	p.R227*	ENST00000388985		227	Cga/Tga	7/12	0.699568203872265	4	FACETS	1	0.936	1	0.334	0.312	0.356	CLONAL	1	TRUE	1	0.720881652495113	4		384	1221	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137793	64137793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774087398	NA	P-0048289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	528	1103	2	ENST00000334205.4:c.1894C>T	p.Arg632Cys	p.R632C	ENST00000334205	NM_003942.2	632	Cgc/Tgc	15/17	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.720881652495113	2		1105	1455	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102098250	102098250	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	157	431	0	ENST00000282441.5:c.1214G>A	p.Ser405Asn	p.S405N	ENST00000282441	NM_001130145.2	405	aGc/aAc	8/9	1	2	FACETS	0.836	0.771	0.903	0.836	0.771	0.903	CLONAL	1	TRUE	1	0.720881652495113	2		431	521	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343756	118343756	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	155	392	0	ENST00000534358.1:c.1882G>T	p.Glu628Ter	p.E628*	ENST00000534358	NM_005933.3	628	Gag/Tag	3/36	1	2	FACETS	0.935	0.863	1	0.935	0.863	1	CLONAL	1	TRUE	1	0.720881652495113	2		392	460	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811738	102811738	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	256	617	0	ENST00000307046.8:c.446G>T	p.Arg149Met	p.R149M	ENST00000307046	NM_001111285.1	149	aGg/aTg	4/4	1	2	FACETS	0.879	0.826	0.934	0.879	0.826	0.934	CLONAL	1	TRUE	1	0.720881652495113	2		617	808	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220186	36220186	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	593	609	0	ENST00000222270.7:c.4906G>A	p.Gly1636Arg	p.G1636R	ENST00000222270	NM_014727.1	1636	Ggg/Agg	22/37	0.720881652495113	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.720881652495113	2		609	810	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163452	47163452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	67	252	0	ENST00000409792.3:c.2674G>A	p.Val892Met	p.V892M	ENST00000409792	NM_014159.6	892	Gtg/Atg	3/21	1	2	FACETS	0.845	0.745	0.949	0.845	0.745	0.949	CLONAL	1	TRUE	1	0.720881652495113	2		252	220	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515283	31515283	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	222	543	0	ENST00000344624.3:c.1102G>T	p.Glu368Ter	p.E368*	ENST00000344624		368	Gaa/Taa	5/33	1	2	FACETS	0.906	0.847	0.966	0.906	0.847	0.966	CLONAL	1	TRUE	1	0.720881652495113	2		543	680	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	36	349	1				ENST00000310581	NM_198253.2	-/1132			0.147655055254448	1	FACETS	1	0.869	1	1	0.974	1	CLONAL	3	FALSE	0	0.147655055254448	1		350	144	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0048291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	8	314	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.547	0.352	0.8	0.547	0.352	0.8	SUBCLONAL	1	FALSE	1	0.147655055254448	2		314	198	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883554	37883554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs574436396	NA	P-0048291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	26	695	0	ENST00000269571.5:c.3166G>A	p.Gly1056Ser	p.G1056S	ENST00000269571		1056	Ggt/Agt	26/27	1	2	FACETS	0.711	0.562	0.883	0.711	0.562	0.883	SUBCLONAL	1	FALSE	1	0.147655055254448	2		695	495	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206728	36206728	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	90	610	1	ENST00000300305.3:c.784C>T	p.Gln262Ter	p.Q262*	ENST00000300305		262	Cag/Tag	6/8	0.147655055254448	1	FACETS	1	0.915	1	1	0.986	1	CLONAL	2	FALSE	0	0.147655055254448	1		611	546	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812513	43812513	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	26	562	0	ENST00000372470.3:c.1216C>G	p.Leu406Val	p.L406V	ENST00000372470	NM_005373.2	406	Ctg/Gtg	8/12	1	2	FACETS	0.883	0.699	1	0.883	0.699	1	CLONAL	1	FALSE	1	0.147655055254448	2		562	399	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344696	118344696	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	12	274	0	ENST00000534358.1:c.2822C>T	p.Ser941Phe	p.S941F	ENST00000534358	NM_005933.3	941	tCt/tTt	3/36	1	2	FACETS	0.797	0.56	1	0.797	0.56	1	CLONAL	1	FALSE	1	0.147655055254448	2		274	204	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820966	3820966	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	20	544	0	ENST00000262367.5:c.2485C>G	p.Leu829Val	p.L829V	ENST00000262367	NM_004380.2	829	Ctt/Gtt	14/31	0.147655055254448	1	FACETS	0.763	0.583	0.973	0.763	0.583	0.973	CLONAL	1	FALSE	0	0.147655055254448	1		544	329	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554598	29554598	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761023505	NA	P-0048291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	33	192	0	ENST00000356175.3:c.2383C>T	p.Pro795Ser	p.P795S	ENST00000356175	NM_000267.3	795	Cca/Tca	20/57	1	2	FACETS	1	0.883	1	1	0.965	1	CLONAL	2	FALSE	1	0.147655055254448	2		192	203	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37876034	37876063	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGCAGCTGTGTGGACCTGGATGACAAGGG	CTGCAGCTGTGTGGACCTGGATGACAAGGG	-	novel	NA	P-0048291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	54	589	0	ENST00000269571.5:c.1899-2_1926del		p.X633_splice	ENST00000269571		633		16/27	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.147655055254448	2		589	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0048292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	324	625	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.345202343882083	3	FACETS	0.874	0.829	0.919	0.874	0.829	0.919	CLONAL	3	TRUE	0	0.357405589649465	3		625	815	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058575	69058575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	92	424	0	ENST00000288368.4:c.4219C>T	p.Leu1407Phe	p.L1407F	ENST00000288368	NM_024870.2	1407	Ctt/Ttt	34/40	0.311295563180084	3	FACETS	0.885	0.793	0.98	0.59	0.529	0.653	CLONAL	2	TRUE	0	0.357405589649465	3		424	343	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058000	27058000	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	101	444	0	ENST00000324856.7:c.1710del	p.Ser571ArgfsTer48	p.S571Rfs*48	ENST00000324856	NM_006015.4	570	Ccc/cc	3/20	1	2	FACETS	0.82	0.734	0.912	0.82	0.734	0.912	CLONAL	1	TRUE	1	0.357405589649465	2		444	689	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68999967	68999967	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	56	319	0	ENST00000288368.4:c.2036A>T	p.Lys679Ile	p.K679I	ENST00000288368	NM_024870.2	679	aAa/aTa	19/40	0.311295563180084	3	FACETS	0.861	0.739	0.993	0.287	0.246	0.331	CLONAL	1	TRUE	0	0.357405589649465	3		319	429	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981924	70981924	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	146	741	0	ENST00000276594.2:c.172G>T	p.Ala58Ser	p.A58S	ENST00000276594	NM_024504.3	58	Gcc/Tcc	2/8	0.311295563180084	3	FACETS	0.943	0.86	1	0.314	0.286	0.344	CLONAL	1	TRUE	0	0.357405589649465	3		741	1021	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0048293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	168	590	3	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.194917034892071	2	FACETS	1	0.986	1	0.673	0.62	0.728	INDETERMINATE	1	TRUE	0	0.334587659005933	2		593	746	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464881	120464881	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	54	295	0	ENST00000256646.2:c.5191G>T	p.Gly1731Ter	p.G1731*	ENST00000256646	NM_024408.3	1731	Gga/Tga	28/34	1	2	FACETS	0.772	0.661	0.893	0.772	0.661	0.893	SUBCLONAL	1	TRUE	1	0.334587659005933	2		295	418	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28607311	28607311	+	stop_lost	Nonstop_Mutation	SNP	T	T	A	novel	NA	P-0048293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	45	451	0	ENST00000253063.3:c.1441T>A	p.Ter481ArgextTer61	p.*481Rext*61	ENST00000253063	NM_031459.4	481	Tga/Aga	10/10	1	2	FACETS	0.461	0.386	0.543	0.461	0.386	0.543	SUBCLONAL	1	TRUE	1	0.334587659005933	2		451	584	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483295	120483295	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	27	279	0	ENST00000256646.2:c.3066C>A	p.Cys1022Ter	p.C1022*	ENST00000256646	NM_024408.3	1022	tgC/tgA	19/34	1	2	FACETS	0.482	0.383	0.594	0.482	0.383	0.594	SUBCLONAL	1	TRUE	1	0.334587659005933	2		279	335	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724645	112724645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	37	364	0	ENST00000369452.4:c.529C>T	p.Arg177Trp	p.R177W	ENST00000369452	NM_007373.3	177	Cgg/Tgg	2/9	1	2	FACETS	0.42	0.345	0.503	0.42	0.345	0.503	SUBCLONAL	1	TRUE	1	0.334587659005933	2		364	527	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417946	32417946	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	67	354	0	ENST00000332351.3:c.1106G>T	p.Arg369Leu	p.R369L	ENST00000332351	NM_024426.4	369	cGa/cTa	7/10	0.284331799784753	1	FACETS	0.838	0.731	0.952	0.838	0.731	0.952	CLONAL	1	TRUE	0	0.334587659005933	1		354	398	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873200	136873200	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	85	291	0	ENST00000241393.3:c.298del	p.Ala100GlnfsTer68	p.A100Qfs*68	ENST00000241393	NM_003467.2	100	Gca/ca	2/2	0.220731687420379	2	FACETS	1	0.976	1	0.688	0.613	0.768	CLONAL	1	TRUE	0	0.334587659005933	2		291	369	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566878	212566878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	65	180	0	ENST00000342788.4:c.1303C>T	p.Leu435Phe	p.L435F	ENST00000342788	NM_005235.2	435	Ctt/Ttt	12/28	0.220731687420379	2	FACETS	0.803	0.705	0.906	0.803	0.705	0.906	CLONAL	2	TRUE	0	0.334587659005933	2		180	242	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662442	227662442	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	160	580	0	ENST00000305123.5:c.1013G>T	p.Arg338Leu	p.R338L	ENST00000305123	NM_005544.2	338	cGc/cTc	1/2	0.220731687420379	2	FACETS	1	0.989	1	0.739	0.68	0.8	CLONAL	1	TRUE	0	0.334587659005933	2		580	647	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735462	40735462	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	73	611	0	ENST00000373198.4:c.3411G>T	p.Glu1137Asp	p.E1137D	ENST00000373198	NM_133170.3	1137	gaG/gaT	25/32	NA	2	FACETS	0.563	0.492	0.64			1	INDETERMINATE	1	TRUE	NA	0.334587659005933	2		611	775	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743842	40743842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	36	352	0	ENST00000373198.4:c.3153G>T	p.Gln1051His	p.Q1051H	ENST00000373198	NM_133170.3	1051	caG/caT	23/32	NA	2	FACETS	0.454	0.373	0.545			1	INDETERMINATE	1	TRUE	NA	0.334587659005933	2		352	474	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944533	40944533	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	47	431	0	ENST00000373198.4:c.1969del	p.Ser657AlafsTer12	p.S657Afs*12	ENST00000373198	NM_133170.3	657	Agc/gc	12/32	NA	2	FACETS	0.598	0.505	0.7			1	INDETERMINATE	1	TRUE	NA	0.334587659005933	2		431	470	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651383	52651383	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0048293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	58	369	0	ENST00000394830.3:c.1713del	p.Ile571MetfsTer16	p.I571Mfs*16	ENST00000394830	NM_018313.4	571	atT/at	15/30	1	2	FACETS	0.755	0.65	0.869	0.755	0.65	0.869	SUBCLONAL	1	TRUE	1	0.334587659005933	2		369	459	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027100	71027109	+	frameshift_variant	Frame_Shift_Del	DEL	GGTCGTTGGA	GGTCGTTGGA	-	novel	NA	P-0048293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	82	500	0	ENST00000318789.4:c.1218_1227del	p.Pro407GlnfsTer5	p.P407Qfs*5	ENST00000318789	NM_032682.5	406	acTCCAACGACC/ac	15/21	1	2	FACETS	0.928	0.821	1	0.928	0.821	1	CLONAL	1	TRUE	1	0.334587659005933	2		500	528	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278180	142278180	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	44	338	0	ENST00000350721.4:c.1645A>C	p.Ser549Arg	p.S549R	ENST00000350721	NM_001184.3	549	Agt/Cgt	7/47	0.170421866746582	3	FACETS	0.577	0.484	0.681	0.289	0.242	0.341	INDETERMINATE	1	TRUE	1	0.334587659005933	3		338	532	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920264	1920264	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	57	524	0	ENST00000382891.5:c.1324A>G	p.Lys442Glu	p.K442E	ENST00000382891	NM_133335.3	442	Aag/Gag	5/22	NA	2	FACETS	0.55	0.472	0.636			1	INDETERMINATE	1	TRUE	NA	0.334587659005933	2		524	619	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721833	176721842	+	frameshift_variant	Frame_Shift_Del	DEL	AAGTTCATGG	AAGTTCATGG	-	novel	NA	P-0048293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	29	451	1	ENST00000439151.2:c.7464_7473del	p.Ser2489LeufsTer86	p.S2489Lfs*86	ENST00000439151	NM_022455.4	2488	tcAAGTTCATGG/tc	23/23	0.260915540858028	1	FACETS	0.297	0.238	0.365	0.297	0.238	0.365	SUBCLONAL	1	TRUE	0	0.334587659005933	1		452	486	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450358	50450358	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	105	444	2	ENST00000331340.3:c.542C>T	p.Ala181Val	p.A181V	ENST00000331340	NM_006060.4	181	gCc/gTc	5/8	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.334587659005933	2		446	522	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509041	106509041	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	74	521	0	ENST00000359195.3:c.1035C>A	p.Asp345Glu	p.D345E	ENST00000359195	NM_002649.2	345	gaC/gaA	2/11	0.170421866746582	3	FACETS	0.83	0.727	0.941	0.415	0.363	0.471	INDETERMINATE	1	TRUE	1	0.334587659005933	3		521	622	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349643	70349643	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	113	555	0	ENST00000374080.3:c.3805T>A	p.Ser1269Thr	p.S1269T	ENST00000374080		1269	Tct/Act	27/45	0.170421866746582	3	FACETS	1	0.948	1	0.541	0.487	0.598	INDETERMINATE	1	TRUE	1	0.334587659005933	3		555	729	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0048294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	221	466	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.318788521432361	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	FALSE	0	0.331285294550634	2		466	592	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164754	47164754	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	47	290	0	ENST00000409792.3:c.1372A>T	p.Ser458Cys	p.S458C	ENST00000409792	NM_014159.6	458	Agt/Tgt	3/21	0.318788521432361	2	FACETS	0.878	0.745	1	0.439	0.372	0.512	CLONAL	1	FALSE	0	0.331285294550634	2		290	323	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0048295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	197	703	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.590976572056542	2	FACETS	0.832	0.794	0.868	0.832	0.794	0.868	CLONAL	2	TRUE	0	0.87066537036583	2		703	272	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0048295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	52	383	0				ENST00000310581	NM_198253.2	-/1132			0.433744881289194	1	FACETS	0.411	0.357	0.468	0.411	0.357	0.468	INDETERMINATE	1	TRUE	0	0.87066537036583	1		383	164	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793212	33793212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1404014711	NA	P-0048295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	35	83	0	ENST00000498907.2:c.109G>A	p.Ala37Thr	p.A37T	ENST00000498907	NM_004364.3	37	Gcg/Acg	1/1	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.87066537036583	2		83	63	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492308	56492308	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1278635698	NA	P-0048295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	197	429	0	ENST00000267101.3:c.2641G>A	p.Glu881Lys	p.E881K	ENST00000267101	NM_001982.3	881	Gag/Aag	22/28	0.622162650325266	3	FACETS	1	0.976	1	0.551	0.514	0.59	CLONAL	1	TRUE	1	0.87066537036583	3		429	589	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651916	36651931	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCAGCAAGGCCTG	GCGGCAGCAAGGCCTG	-	novel	NA	P-0048295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	88	648	0	ENST00000244741.5:c.38_53del	p.Cys13SerfsTer13	p.C13Sfs*13	ENST00000244741	NM_000389.4	13	tGCGGCAGCAAGGCCTGc/tc	2/3	0.228384612559249	3	FACETS	0.515	0.457	0.577	0.172	0.152	0.193	INDETERMINATE	1	TRUE	0	0.87066537036583	3		648	563	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0048296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	57	383	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.434150510948358	2		383	257	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0048296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	177	622	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.41576717303271	2	FACETS	0.842	0.783	0.903	0.842	0.783	0.903	CLONAL	2	TRUE	0	0.434150510948358	2		622	484	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7163204	7163204	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	96	507	0	ENST00000302850.5:c.1868C>T	p.Ser623Phe	p.S623F	ENST00000302850	NM_000208.2	623	tCt/tTt	9/22	1	2	FACETS	0.966	0.865	1	0.966	0.865	1	CLONAL	1	TRUE	1	0.434150510948358	2		507	458	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430829	181430829	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	153	1123	1	ENST00000325404.1:c.681C>A	p.Tyr227Ter	p.Y227*	ENST00000325404	NM_003106.3	227	taC/taA	1/1	1	2	FACETS	0.905	0.829	0.984	0.905	0.829	0.984	CLONAL	1	TRUE	1	0.434150510948358	2		1124	779	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	83	349	1				ENST00000310581	NM_198253.2	-/1132			0.289338540405956	3	FACETS	0.957	0.852	1	0.957	0.852	1	CLONAL	2	TRUE	1	0.289338540405956	3		350	343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0048297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	48	758	1	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	1	2	FACETS	0.479	0.404	0.562	0.479	0.404	0.562	SUBCLONAL	1	TRUE	1	0.289338540405956	2		759	693	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0048297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	103	731	0	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.289338540405956	2		731	682	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563018	21563018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs577331900	NA	P-0048297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	83	809	2	ENST00000382592.4:c.901G>A	p.Gly301Ser	p.G301S	ENST00000382592	NM_014572.2	301	Ggc/Agc	4/8	0.148307197074656	3	FACETS	0.692	0.609	0.781			1	INDETERMINATE	1	TRUE	NA	0.289338540405956	3		811	949	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343529	118343529	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	72	340	0	ENST00000534358.1:c.1660del	p.Gln554SerfsTer13	p.Q554Sfs*13	ENST00000534358	NM_005933.3	552	gCc/gc	3/36	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.289338540405956	2		340	371	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027178	49027179	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	67	324	0	ENST00000267163.4:c.1747dup	p.Thr583AsnfsTer2	p.T583Nfs*2	ENST00000267163	NM_000321.2	582	cca/ccAa	18/27	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.289338540405956	2		324	370	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630786	187630786	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	68	551	0	ENST00000441802.2:c.196C>T	p.Pro66Ser	p.P66S	ENST00000441802	NM_005245.3	66	Cca/Tca	2/27	1	2	FACETS	0.892	0.777	1	0.892	0.777	1	CLONAL	1	TRUE	1	0.289338540405956	2		551	527	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41209094	41209099	+	frameshift_variant	Frame_Shift_Del	DEL	CGCTTT	CGCTTT	TG	novel	NA	P-0048297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	34	546	1	ENST00000357654.3:c.5247_5252delinsCA	p.Arg1751GlnfsTer13	p.R1751Qfs*13	ENST00000357654	NM_007294.3	1749	ccAAAGCGa/ccCAa	19/23	1	2	FACETS	0.413	0.337	0.499	0.413	0.337	0.499	SUBCLONAL	1	TRUE	1	0.289338540405956	2		547	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	331	512	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.83	0.792	0.868	1	0.996	1	CLONAL	2	TRUE	1	0.62	2		512	643	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102080254	102080254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193100333	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	94	400	0	ENST00000282441.5:c.991C>T	p.Arg331Trp	p.R331W	ENST00000282441	NM_001130145.2	331	Cgg/Tgg	6/9	1	2	FACETS	0.84	0.754	0.93	0.84	0.754	0.93	CLONAL	1	TRUE	1	0.62	2		400	361	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522598	157522598	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554236040	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	175	514	0	ENST00000346085.5:c.4870C>T	p.Arg1624Ter	p.R1624*	ENST00000346085	NM_020732.3	1624	Cga/Tga	18/20	1	2	FACETS	0.896	0.829	0.965	0.896	0.829	0.965	CLONAL	1	TRUE	1	0.62	2		514	630	SUCCESS
B2M	567	MSKCC	GRCh37	15	45008529	45008529	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	52	192	0	ENST00000558401.1:c.349C>T	p.Arg117Ter	p.R117*	ENST00000558401	NM_004048.2	117	Cga/Tga	3/4	1	2	FACETS	0.746	0.642	0.856	0.746	0.642	0.856	SUBCLONAL	1	TRUE	1	0.62	2		192	225	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936983	48936983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690863	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	68	308	0	ENST00000267163.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000267163	NM_000321.2	251	Cga/Tga	8/27	1	2	FACETS	0.803	0.706	0.906	0.803	0.706	0.906	CLONAL	1	TRUE	1	0.62	2		308	273	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918694	44918694	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	86	412	0	ENST00000377967.4:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000377967	NM_021140.2	393	Cga/Tga	12/29	1	2	FACETS	0.746	0.664	0.831	0.746	0.664	0.831	SUBCLONAL	1	TRUE	1	0.62	2		412	372	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546847	9546847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	106	564	0	ENST00000353224.5:c.1175C>T	p.Ser392Leu	p.S392L	ENST00000353224	NM_177990.2	392	tCg/tTg	5/10	1	2	FACETS	0.945	0.855	1	0.945	0.855	1	CLONAL	1	TRUE	1	0.62	2		564	362	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521502	8521502	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	156	531	0	ENST00000356435.5:c.736G>T	p.Glu246Ter	p.E246*	ENST00000356435		246	Gaa/Taa	9/35	1	2	FACETS	0.991	0.914	1	0.991	0.914	1	CLONAL	1	TRUE	1	0.62	2		531	508	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504513	103504513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140917545	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	46	302	0	ENST00000355739.4:c.134G>A	p.Arg45His	p.R45H	ENST00000355739	NM_000123.3	45	cGc/cAc	2/15	1	2	FACETS	0.717	0.611	0.831	0.717	0.611	0.831	SUBCLONAL	1	TRUE	1	0.62	2		302	207	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247039	53247039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556852808	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	181	672	0	ENST00000375401.3:c.461G>A	p.Arg154His	p.R154H	ENST00000375401	NM_004187.3	154	cGc/cAc	4/26	1	2	FACETS	0.967	0.896	1	0.967	0.896	1	CLONAL	1	TRUE	1	0.62	2		672	604	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453486	138453486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451809865	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	53	302	0	ENST00000289153.2:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000289153	NM_006219.2	321	cGa/cAa	5/22	1	2	FACETS	0.731	0.63	0.838	0.731	0.63	0.838	SUBCLONAL	1	TRUE	1	0.62	2		302	234	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333539	70333539	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs570151139	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	116	553	0	ENST00000373644.4:c.1444A>C	p.Asn482His	p.N482H	ENST00000373644	NM_030625.2	482	Aac/Cac	2/12	1	2	FACETS	0.957	0.87	1	0.957	0.87	1	CLONAL	1	TRUE	1	0.62	2		553	391	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416138	416138	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	101	316	0	ENST00000399788.2:c.4048C>T	p.Arg1350Ter	p.R1350*	ENST00000399788	NM_001042603.1	1350	Cga/Tga	24/28	0.3	2	FACETS	0.848	0.765	0.936			1	INDETERMINATE	1	TRUE	NA	0.62	2		316	384	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431664	431664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	124	480	1	ENST00000399788.2:c.2345G>A	p.Arg782Gln	p.R782Q	ENST00000399788	NM_001042603.1	782	cGa/cAa	17/28	0.3	2	FACETS	0.815	0.741	0.891			1	INDETERMINATE	1	TRUE	NA	0.62	2		481	491	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247028	53247028	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	180	664	1	ENST00000375401.3:c.472G>A	p.Glu158Lys	p.E158K	ENST00000375401	NM_004187.3	158	Gaa/Aaa	4/26	1	2	FACETS	0.963	0.893	1	0.963	0.893	1	CLONAL	1	TRUE	1	0.62	2		665	603	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778812	76778812	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	90	383	0	ENST00000373344.5:c.6767C>A	p.Ser2256Tyr	p.S2256Y	ENST00000373344	NM_000489.3	2256	tCt/tAt	31/35	1	2	FACETS	0.885	0.793	0.981	0.885	0.793	0.981	CLONAL	1	TRUE	1	0.62	2		383	328	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606679	29606679	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs865931787	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	135	514	0	ENST00000389048.3:c.1201C>T	p.Arg401Ter	p.R401*	ENST00000389048	NM_004304.4	401	Cga/Tga	5/29	1	2	FACETS	0.931	0.852	1	0.931	0.852	1	CLONAL	1	TRUE	1	0.62	2		514	468	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281802	142281802	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	128	461	0	ENST00000350721.4:c.442G>T	p.Glu148Ter	p.E148*	ENST00000350721	NM_001184.3	148	Gaa/Taa	4/47	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.62	2		461	396	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102874103	102874103	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	48	237	0	ENST00000307046.8:c.57C>A	p.Phe19Leu	p.F19L	ENST00000307046	NM_001111285.1	19	ttC/ttA	1/4	1	2	FACETS	0.679	0.58	0.786	0.679	0.58	0.786	SUBCLONAL	1	TRUE	1	0.62	2		237	228	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941657	48941657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1060503077	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	37	118	0	ENST00000267163.4:c.967G>T	p.Glu323Ter	p.E323*	ENST00000267163	NM_000321.2	323	Gaa/Taa	10/27	1	2	FACETS	0.723	0.605	0.852	0.723	0.605	0.852	SUBCLONAL	1	TRUE	1	0.62	2		118	165	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021785	71021785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs112795301	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	99	229	1	ENST00000318789.4:c.1573C>T	p.Arg525Ter	p.R525*	ENST00000318789	NM_032682.5	525	Cga/Tga	18/21	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.62	2		230	288	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564417	139564417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143123347	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	189	922	5	ENST00000308874.7:c.365G>A	p.Arg122His	p.R122H	ENST00000308874		122	cGc/cAc	6/10	1	2	FACETS	0.881	0.817	0.947	0.881	0.817	0.947	CLONAL	1	TRUE	1	0.62	2		927	692	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491360	18491360	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	50	196	0	ENST00000266497.5:c.1273G>A	p.Glu425Lys	p.E425K	ENST00000266497		425	Gaa/Aaa	8/31	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.62	2		196	157	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546557	9546557	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	114	455	0	ENST00000353224.5:c.1465G>T	p.Glu489Ter	p.E489*	ENST00000353224	NM_177990.2	489	Gaa/Taa	5/10	1	2	FACETS	0.931	0.846	1	0.931	0.846	1	CLONAL	1	TRUE	1	0.62	2		455	395	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24134006	24134006	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	92	340	0	ENST00000263121.7:c.157C>T	p.Arg53Ter	p.R53*	ENST00000263121	NM_003073.3	53	Cga/Tga	2/9	1	2	FACETS	0.886	0.795	0.981	0.886	0.795	0.981	CLONAL	1	TRUE	1	0.62	2		340	335	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111168	193111168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1452051467	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	59	304	0	ENST00000367435.3:c.701G>A	p.Arg234Gln	p.R234Q	ENST00000367435	NM_024529.4	234	cGa/cAa	7/17	1	2	FACETS	0.894	0.78	1	0.894	0.78	1	CLONAL	1	TRUE	1	0.62	2		304	213	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976476	25976476	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	96	329	1	ENST00000435504.4:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000435504		357	Cga/Tga	11/13	1	2	FACETS	0.855	0.769	0.946	0.855	0.769	0.946	CLONAL	1	TRUE	1	0.62	2		330	362	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038418	180038418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530977029	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	249	882	0	ENST00000261937.6:c.3599C>T	p.Ser1200Leu	p.S1200L	ENST00000261937	NM_182925.4	1200	tCg/tTg	27/30	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.62	2		882	717	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950622	38950622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748585755	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	100	374	2	ENST00000357387.3:c.3328C>T	p.Arg1110Cys	p.R1110C	ENST00000357387	NM_152756.3	1110	Cgt/Tgt	31/38	1	2	FACETS	0.927	0.836	1	0.927	0.836	1	CLONAL	1	TRUE	1	0.62	2		376	348	SUCCESS
AR	367	MSKCC	GRCh37	X	66765082	66765082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	51	773	0	ENST00000374690.3:c.94G>A	p.Glu32Lys	p.E32K	ENST00000374690	NM_000044.3	32	Gaa/Aaa	1/8	1	2	FACETS	0.26	0.22	0.303	0.26	0.22	0.303	SUBCLONAL	1	TRUE	1	0.62	2		773	633	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	141	578	0	ENST00000394830.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000394830	NM_018313.4	710	Cga/Tga	17/30	1	2	FACETS	0.88	0.806	0.956	0.88	0.806	0.956	CLONAL	1	TRUE	1	0.62	2		578	517	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430668	80430668	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	86	394	0	ENST00000286548.4:c.340C>T	p.Arg114Ter	p.R114*	ENST00000286548	NM_002072.3	114	Cga/Tga	3/7	1	2	FACETS	0.833	0.744	0.927	0.833	0.744	0.927	CLONAL	1	TRUE	1	0.62	2		394	333	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939417	76939417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781932965	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	129	668	0	ENST00000373344.5:c.1331G>A	p.Arg444Gln	p.R444Q	ENST00000373344	NM_000489.3	444	cGa/cAa	9/35	1	2	FACETS	0.735	0.669	0.804	0.735	0.669	0.804	SUBCLONAL	1	TRUE	1	0.62	2		668	566	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61720080	61720080	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	73	359	0	ENST00000401558.2:c.1354A>C	p.Asn452His	p.N452H	ENST00000401558	NM_003400.3	452	Aat/Cat	13/25	1	2	FACETS	0.863	0.763	0.967	0.863	0.763	0.967	CLONAL	1	TRUE	1	0.62	2		359	273	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557284	187557284	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	39	541	0	ENST00000441802.2:c.4078G>T	p.Glu1360Ter	p.E1360*	ENST00000441802	NM_005245.3	1360	Gaa/Taa	6/27	1	2	FACETS	0.242	0.2	0.289	0.242	0.2	0.289	SUBCLONAL	1	TRUE	1	0.62	2		541	520	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680780	88680780	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	76	658	0	ENST00000360948.2:c.477G>T	p.Gln159His	p.Q159H	ENST00000360948	NM_001012338.2	159	caG/caT	6/19	1	2	FACETS	0.431	0.378	0.487	0.431	0.378	0.487	SUBCLONAL	1	TRUE	1	0.62	2		658	569	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	152	482	0	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	1	2	FACETS	0.985	0.907	1	0.985	0.907	1	CLONAL	1	TRUE	1	0.62	2		482	498	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192545	138192545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs970781981	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	98	364	0	ENST00000237289.4:c.181C>T	p.Arg61Trp	p.R61W	ENST00000237289	NM_001270507.1	61	Cgg/Tgg	2/9	1	2	FACETS	0.891	0.802	0.983	0.891	0.802	0.983	CLONAL	1	TRUE	1	0.62	2		364	355	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023160	150023160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	135	478	0	ENST00000253339.5:c.103C>T	p.Arg35Trp	p.R35W	ENST00000253339		35	Cgg/Tgg	1/7	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.62	2		478	433	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265535	152265535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571716552	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	152	537	1	ENST00000206249.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000206249	NM_000125.3	330	Gag/Aag	4/8	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.62	2		538	466	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772842	135772842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	165	538	0	ENST00000298552.3:c.2781G>T	p.Lys927Asn	p.K927N	ENST00000298552	NM_001162426.1	927	aaG/aaT	21/23	1	2	FACETS	0.944	0.872	1	0.944	0.872	1	CLONAL	1	TRUE	1	0.62	2		538	564	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115600	108115600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772821016	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	98	372	0	ENST00000278616.4:c.748C>T	p.Arg250Ter	p.R250*	ENST00000278616	NM_000051.3	250	Cga/Tga	7/63	1	2	FACETS	0.861	0.775	0.951	0.861	0.775	0.951	CLONAL	1	TRUE	1	0.62	2		372	367	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604790	48604790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	86	348	0	ENST00000342988.3:c.1612G>A	p.Glu538Lys	p.E538K	ENST00000342988	NM_005359.5	538	Gaa/Aaa	12/12	1	2	FACETS	0.898	0.803	0.997	0.898	0.803	0.997	CLONAL	1	TRUE	1	0.62	2		348	309	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937587	76937587	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	71	365	0	ENST00000373344.5:c.3161C>A	p.Ser1054Tyr	p.S1054Y	ENST00000373344	NM_000489.3	1054	tCt/tAt	9/35	1	2	FACETS	0.804	0.709	0.904	0.804	0.709	0.904	CLONAL	1	TRUE	1	0.62	2		365	285	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939761	76939761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	78	563	0	ENST00000373344.5:c.987G>T	p.Lys329Asn	p.K329N	ENST00000373344	NM_000489.3	329	aaG/aaT	9/35	1	2	FACETS	0.502	0.442	0.566	0.502	0.442	0.566	SUBCLONAL	1	TRUE	1	0.62	2		563	501	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041074	42041074	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	189	604	0	ENST00000219905.7:c.5452C>T	p.Arg1818Ter	p.R1818*	ENST00000219905	NM_001164273.1	1818	Cga/Tga	16/24	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.62	2		604	608	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56878418	56878418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374875893	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	106	391	0	ENST00000308159.5:c.2357G>A	p.Arg786Gln	p.R786Q	ENST00000308159	NM_014669.4	786	cGa/cAa	22/22	1	2	FACETS	0.836	0.755	0.921	0.836	0.755	0.921	CLONAL	1	TRUE	1	0.62	2		391	409	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254623	16254623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749814808	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	112	424	0	ENST00000375759.3:c.1888C>T	p.Arg630Cys	p.R630C	ENST00000375759	NM_015001.2	630	Cgt/Tgt	11/15	0.3	3	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.62	3		424	401	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698180	47698180	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63751411	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	57	182	0	ENST00000233146.2:c.1738G>T	p.Glu580Ter	p.E580*	ENST00000233146	NM_000251.2	580	Gaa/Taa	11/16	1	2	FACETS	0.973	0.849	1	0.973	0.849	1	CLONAL	1	TRUE	1	0.62	2		182	189	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347200	347200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	174	744	0	ENST00000262320.3:c.1811G>T	p.Arg604Ile	p.R604I	ENST00000262320	NM_003502.3	604	aGa/aTa	7/11	1	2	FACETS	0.919	0.85	0.99	0.919	0.85	0.99	CLONAL	1	TRUE	1	0.62	2		744	611	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096135	178096135	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	104	458	1	ENST00000397062.3:c.1196C>A	p.Ser399Tyr	p.S399Y	ENST00000397062	NM_006164.4	399	tCt/tAt	5/5	1	2	FACETS	0.795	0.717	0.877	0.795	0.717	0.877	SUBCLONAL	1	TRUE	1	0.62	2		459	422	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952049	178952049	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242945375	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	87	299	0	ENST00000263967.3:c.3104C>T	p.Ala1035Val	p.A1035V	ENST00000263967	NM_006218.2	1035	gCt/gTt	21/21	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.62	2		299	275	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458147	120458147	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1325403451	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	168	681	1	ENST00000256646.2:c.7198C>T	p.Arg2400Ter	p.R2400*	ENST00000256646	NM_024408.3	2400	Cga/Tga	34/34	1	2	FACETS	0.98	0.906	1	0.98	0.906	1	CLONAL	1	TRUE	1	0.62	2		682	553	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165843	47165843	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	111	504	0	ENST00000409792.3:c.283G>T	p.Glu95Ter	p.E95*	ENST00000409792	NM_014159.6	95	Gaa/Taa	3/21	1	2	FACETS	0.819	0.742	0.901	0.819	0.742	0.901	CLONAL	1	TRUE	1	0.62	2		504	437	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554305	81554305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777252114	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	166	350	0	ENST00000298171.2:c.325C>T	p.Arg109Trp	p.R109W	ENST00000298171	NM_000369.2	109	Cgg/Tgg	4/10	1	2	FACETS	0.923	0.867	0.978	1	0.993	1	CLONAL	2	TRUE	1	0.62	2		350	290	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11269467	11269467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	157	493	0	ENST00000361445.4:c.3703C>T	p.Arg1235Trp	p.R1235W	ENST00000361445	NM_004958.3	1235	Cgg/Tgg	25/58	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.62	2		493	476	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	9	571	0	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	0.068	0.044	0.099	0.068	0.044	0.099	SUBCLONAL	1	TRUE	1	0.62	2		571	426	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259409	89259409	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	126	500	0	ENST00000336596.2:c.553G>T	p.Asp185Tyr	p.D185Y	ENST00000336596	NM_005233.5	185	Gat/Tat	3/17	1	2	FACETS	0.92	0.839	1	0.92	0.839	1	CLONAL	1	TRUE	1	0.62	2		500	442	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066675	94066675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	137	473	0	ENST00000369303.4:c.1084G>A	p.Asp362Asn	p.D362N	ENST00000369303	NM_004440.3	362	Gat/Aat	5/17	1	2	FACETS	0.847	0.774	0.922	0.847	0.774	0.922	CLONAL	1	TRUE	1	0.62	2		473	522	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004242	29004242	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766441216	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	84	268	0	ENST00000282397.4:c.1051C>T	p.Arg351Trp	p.R351W	ENST00000282397	NM_002019.4	351	Cgg/Tgg	8/30	1	2	FACETS	0.855	0.762	0.952	0.855	0.762	0.952	CLONAL	1	TRUE	1	0.62	2		268	317	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562982	29562982	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1306237220	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	74	465	0	ENST00000356175.3:c.3917G>A	p.Arg1306Gln	p.R1306Q	ENST00000356175	NM_000267.3	1306	cGa/cAa	29/57	1	2	FACETS	0.686	0.605	0.772	0.686	0.605	0.772	SUBCLONAL	1	TRUE	1	0.62	2		465	348	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692874	89692874	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786204930	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	44	219	0	ENST00000371953.3:c.358G>A	p.Ala120Thr	p.A120T	ENST00000371953	NM_000314.4	120	Gca/Aca	5/9	1	2	FACETS	0.717	0.608	0.834	0.717	0.608	0.834	SUBCLONAL	1	TRUE	1	0.62	2		219	198	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366129	15366129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1468704458	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	158	533	5	ENST00000263377.2:c.2026C>T	p.Arg676Trp	p.R676W	ENST00000263377	NM_058243.2	676	Cgg/Tgg	10/20	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.62	2		538	497	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130163	143130163	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	102	356	0	ENST00000262992.4:c.853G>T	p.Glu285Ter	p.E285*	ENST00000262992	NM_001101669.1	285	Gaa/Taa	11/24	1	2	FACETS	0.882	0.796	0.972	0.882	0.796	0.972	CLONAL	1	TRUE	1	0.62	2		356	373	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163542	32163542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1187763031	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	131	629	0	ENST00000375023.3:c.5684C>T	p.Ser1895Phe	p.S1895F	ENST00000375023	NM_004557.3	1895	tCt/tTt	30/30	1	2	FACETS	0.978	0.895	1	0.978	0.895	1	CLONAL	1	TRUE	1	0.62	2		629	432	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956553	93956553	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1035177735	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	73	293	0	ENST00000369303.4:c.2683C>T	p.Arg895Ter	p.R895*	ENST00000369303	NM_004440.3	895	Cga/Tga	15/17	1	2	FACETS	0.841	0.744	0.944	0.841	0.744	0.944	CLONAL	1	TRUE	1	0.62	2		293	280	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148513849	148513849	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	108	405	0	ENST00000320356.2:c.1432G>T	p.Glu478Ter	p.E478*	ENST00000320356	NM_004456.4	478	Gaa/Taa	12/20	1	2	FACETS	0.889	0.804	0.977	0.889	0.804	0.977	CLONAL	1	TRUE	1	0.62	2		405	392	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412494	80412494	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	96	315	0	ENST00000286548.4:c.547C>T	p.Arg183Ter	p.R183*	ENST00000286548	NM_002072.3	183	Cga/Tga	4/7	1	2	FACETS	0.83	0.746	0.919	0.83	0.746	0.919	CLONAL	1	TRUE	1	0.62	2		315	373	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346314	73346314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs575448022	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	74	243	0	ENST00000377767.4:c.1486G>A	p.Glu496Lys	p.E496K	ENST00000377767	NM_014953.3	496	Gaa/Aaa	10/21	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.62	2		243	236	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727423	66727423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1049040928	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	110	386	1	ENST00000307102.5:c.139C>T	p.Arg47Ter	p.R47*	ENST00000307102	NM_002755.3	47	Cga/Tga	2/11	1	2	FACETS	0.912	0.827	1	0.912	0.827	1	CLONAL	1	TRUE	1	0.62	2		387	389	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236086	108236086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782292	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	100	444	0	ENST00000278616.4:c.9022C>T	p.Arg3008Cys	p.R3008C	ENST00000278616	NM_000051.3	3008	Cgt/Tgt	63/63	1	2	FACETS	0.72	0.647	0.797	0.72	0.647	0.797	SUBCLONAL	1	TRUE	1	0.62	2		444	448	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546725	9546725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210292896	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	63	395	0	ENST00000353224.5:c.1297C>T	p.Arg433Trp	p.R433W	ENST00000353224	NM_177990.2	433	Cgg/Tgg	5/10	1	2	FACETS	0.791	0.691	0.896	0.791	0.691	0.896	SUBCLONAL	1	TRUE	1	0.62	2		395	257	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938406	76938406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	163	618	0	ENST00000373344.5:c.2342G>A	p.Arg781Gln	p.R781Q	ENST00000373344	NM_000489.3	781	cGa/cAa	9/35	1	2	FACETS	0.988	0.913	1	0.988	0.913	1	CLONAL	1	TRUE	1	0.62	2		618	532	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114842	108114842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145355104	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	100	380	0	ENST00000278616.4:c.659C>T	p.Ala220Val	p.A220V	ENST00000278616	NM_000051.3	220	gCg/gTg	6/63	1	2	FACETS	0.853	0.769	0.942	0.853	0.769	0.942	CLONAL	1	TRUE	1	0.62	2		380	378	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101830	11101830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	60	795	0	ENST00000358026.2:c.1250G>A	p.Arg417His	p.R417H	ENST00000358026	NM_001128849.1	417	cGc/cAc	8/36	1	2	FACETS	0.328	0.282	0.378	0.328	0.282	0.378	SUBCLONAL	1	TRUE	1	0.62	2		795	590	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386512	81386512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	71	350	0	ENST00000222390.5:c.475G>A	p.Glu159Lys	p.E159K	ENST00000222390	NM_000601.4	159	Gaa/Aaa	4/18	1	2	FACETS	0.815	0.719	0.917	0.815	0.719	0.917	CLONAL	1	TRUE	1	0.62	2		350	281	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014097	70014097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757354709	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	113	498	0	ENST00000394351.3:c.958G>A	p.Val320Ile	p.V320I	ENST00000394351	NM_000248.3	320	Gtt/Att	9/9	1	2	FACETS	0.787	0.713	0.865	0.787	0.713	0.865	SUBCLONAL	1	TRUE	1	0.62	2		498	463	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461167	120461167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs983208690	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	103	335	0	ENST00000256646.2:c.5791C>T	p.Arg1931Cys	p.R1931C	ENST00000256646	NM_024408.3	1931	Cgc/Tgc	32/34	1	2	FACETS	0.952	0.861	1	0.952	0.861	1	CLONAL	1	TRUE	1	0.62	2		335	349	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868912	117868912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746064262	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	52	278	0	ENST00000297338.2:c.787G>A	p.Asp263Asn	p.D263N	ENST00000297338	NM_006265.2	263	Gat/Aat	7/14	1	2	FACETS	0.614	0.527	0.708	0.614	0.527	0.708	SUBCLONAL	1	TRUE	1	0.62	2		278	273	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201885	152201885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778449608	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	104	289	0	ENST00000206249.3:c.739G>A	p.Glu247Lys	p.E247K	ENST00000206249	NM_000125.3	247	Gaa/Aaa	3/8	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.62	2		289	323	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376627	8376627	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	128	413	0	ENST00000356435.5:c.4486C>T	p.Arg1496Ter	p.R1496*	ENST00000356435		1496	Cga/Tga	27/35	1	2	FACETS	0.951	0.869	1	0.951	0.869	1	CLONAL	1	TRUE	1	0.62	2		413	434	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149516607	149516607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148272095	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	173	750	2	ENST00000261799.4:c.4C>T	p.Arg2Trp	p.R2W	ENST00000261799	NM_002609.3	2	Cgg/Tgg	2/23	1	2	FACETS	0.959	0.887	1	0.959	0.887	1	CLONAL	1	TRUE	1	0.62	2		752	582	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143129648	143129648	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs768272420	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	87	346	0	ENST00000262992.4:c.1002G>T	p.Glu334Asp	p.E334D	ENST00000262992	NM_001101669.1	334	gaG/gaT	12/24	1	2	FACETS	0.759	0.676	0.845	0.759	0.676	0.845	SUBCLONAL	1	TRUE	1	0.62	2		346	370	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672759	86672759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	82	298	0	ENST00000274376.6:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000274376	NM_002890.2	749	cGa/cAa	17/25	1	2	FACETS	0.987	0.882	1	0.987	0.882	1	CLONAL	1	TRUE	1	0.62	2		298	268	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012219	16012219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	79	325	0	ENST00000268712.3:c.2063G>A	p.Arg688Gln	p.R688Q	ENST00000268712	NM_006311.3	688	cGa/cAa	19/46	1	2	FACETS	0.763	0.677	0.854	0.763	0.677	0.854	SUBCLONAL	1	TRUE	1	0.62	2		325	334	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253212	133253212	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	133	548	0	ENST00000320574.5:c.829G>C	p.Glu277Gln	p.E277Q	ENST00000320574	NM_006231.2	277	Gag/Cag	9/49	1	2	FACETS	0.919	0.84	1	0.919	0.84	1	CLONAL	1	TRUE	1	0.62	2		548	467	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740668	58740668	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs759850701	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	137	530	0	ENST00000305921.3:c.1573G>T	p.Glu525Ter	p.E525*	ENST00000305921	NM_003620.3	525	Gaa/Taa	6/6	1	2	FACETS	0.963	0.883	1	0.963	0.883	1	CLONAL	1	TRUE	1	0.62	2		530	459	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273266	198273266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	149	474	0	ENST00000335508.6:c.944G>A	p.Arg315Gln	p.R315Q	ENST00000335508	NM_012433.2	315	cGa/cAa	8/25	1	2	FACETS	0.973	0.895	1	0.973	0.895	1	CLONAL	1	TRUE	1	0.62	2		474	494	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181425	185181425	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1435276633	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	127	368	0	ENST00000265026.3:c.1366C>T	p.Arg456Ter	p.R456*	ENST00000265026	NM_004721.4	456	Cga/Tga	8/14	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.62	2		368	388	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196499	106196499	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs527895107	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	91	428	0	ENST00000380013.4:c.4832C>A	p.Ser1611Tyr	p.S1611Y	ENST00000380013	NM_001127208.2	1611	tCt/tAt	11/11	1	2	FACETS	0.959	0.862	1	0.959	0.862	1	CLONAL	1	TRUE	1	0.62	2		428	306	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124717	108124717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751515818	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	74	349	0	ENST00000278616.4:c.2075G>A	p.Arg692His	p.R692H	ENST00000278616	NM_000051.3	692	cGc/cAc	13/63	1	2	FACETS	0.817	0.723	0.917	0.817	0.723	0.917	CLONAL	1	TRUE	1	0.62	2		349	292	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331962	81331962	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs201768315	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	42	213	0	ENST00000222390.5:c.2122C>T	p.Arg708Ter	p.R708*	ENST00000222390	NM_000601.4	708	Cga/Tga	18/18	1	2	FACETS	0.816	0.692	0.949	0.816	0.692	0.949	CLONAL	1	TRUE	1	0.62	2		213	166	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651331	52651331	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	103	405	0	ENST00000394830.3:c.1765G>A	p.Asp589Asn	p.D589N	ENST00000394830	NM_018313.4	589	Gac/Aac	15/30	1	2	FACETS	0.868	0.783	0.956	0.868	0.783	0.956	CLONAL	1	TRUE	1	0.62	2		405	383	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950099	38950099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757900166	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	104	502	1	ENST00000357387.3:c.3851C>T	p.Ser1284Leu	p.S1284L	ENST00000357387	NM_152756.3	1284	tCg/tTg	31/38	1	2	FACETS	0.826	0.745	0.911	0.826	0.745	0.911	CLONAL	1	TRUE	1	0.62	2		503	406	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709529	176709529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777258117	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	80	283	0	ENST00000439151.2:c.5956C>T	p.Arg1986Cys	p.R1986C	ENST00000439151	NM_022455.4	1986	Cgc/Tgc	19/23	1	2	FACETS	0.928	0.827	1	0.928	0.827	1	CLONAL	1	TRUE	1	0.62	2		283	278	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106162587	106162587	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	54	225	1	ENST00000380013.4:c.3500+1G>A		p.X1167_splice	ENST00000380013	NM_001127208.2	1167			1	2	FACETS	0.912	0.791	1	0.912	0.791	1	CLONAL	1	TRUE	1	0.62	2		226	191	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864002	97864002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369636116	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	50	465	1	ENST00000289081.3:c.1664G>A	p.Arg555Gln	p.R555Q	ENST00000289081	NM_000136.2	555	cGa/cAa	15/15	1	2	FACETS	0.323	0.274	0.377	0.323	0.274	0.377	SUBCLONAL	1	TRUE	1	0.62	2		466	499	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040978	42040978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755286142	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	214	622	0	ENST00000219905.7:c.5356C>T	p.Arg1786Trp	p.R1786W	ENST00000219905	NM_001164273.1	1786	Cgg/Tgg	16/24	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.62	2		622	630	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243774	41243774	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs431825399	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	127	592	0	ENST00000357654.3:c.3774G>T	p.Glu1258Asp	p.E1258D	ENST00000357654	NM_007294.3	1258	gaG/gaT	10/23	1	2	FACETS	0.914	0.835	0.997	0.914	0.835	0.997	CLONAL	1	TRUE	1	0.62	2		592	448	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912075	76912075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782228142	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	87	401	0	ENST00000373344.5:c.4189G>A	p.Glu1397Lys	p.E1397K	ENST00000373344	NM_000489.3	1397	Gaa/Aaa	13/35	1	2	FACETS	0.769	0.686	0.856	0.769	0.686	0.856	SUBCLONAL	1	TRUE	1	0.62	2		401	365	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381567	81381567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370760302	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	67	203	0	ENST00000222390.5:c.494C>T	p.Ser165Leu	p.S165L	ENST00000222390	NM_000601.4	165	tCg/tTg	5/18	1	2	FACETS	0.94	0.828	1	0.94	0.828	1	CLONAL	1	TRUE	1	0.62	2		203	230	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133894	55133894	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	89	319	0	ENST00000257290.5:c.1107G>T	p.Lys369Asn	p.K369N	ENST00000257290	NM_006206.4	369	aaG/aaT	7/23	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.62	2		319	273	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026290	48026290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147737737	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	84	409	2	ENST00000234420.5:c.1168G>A	p.Asp390Asn	p.D390N	ENST00000234420	NM_000179.2	390	Gat/Aat	4/10	1	2	FACETS	0.855	0.762	0.952	0.855	0.762	0.952	CLONAL	1	TRUE	1	0.62	2		411	317	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594066	158594066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769751827	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	82	343	0	ENST00000263640.3:c.1507G>A	p.Asp503Asn	p.D503N	ENST00000263640	NM_001105.4	503	Gac/Aac	11/11	1	2	FACETS	0.829	0.738	0.925	0.829	0.738	0.925	CLONAL	1	TRUE	1	0.62	2		343	319	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521540	46521540	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	143	439	0	ENST00000262741.5:c.868G>T	p.Glu290Ter	p.E290*	ENST00000262741	NM_003629.3	290	Gaa/Taa	7/10	1	2	FACETS	0.963	0.884	1	0.963	0.884	1	CLONAL	1	TRUE	1	0.62	2		439	479	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156894	106156894	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	24	425	0	ENST00000380013.4:c.1795C>A	p.Gln599Lys	p.Q599K	ENST00000380013	NM_001127208.2	599	Caa/Aaa	3/11	1	2	FACETS	0.224	0.176	0.281	0.224	0.176	0.281	SUBCLONAL	1	TRUE	1	0.62	2		425	345	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716359	18716359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	61	296	0	ENST00000266497.5:c.3706G>A	p.Glu1236Lys	p.E1236K	ENST00000266497		1236	Gaa/Aaa	26/31	1	2	FACETS	0.793	0.692	0.901	0.793	0.692	0.901	CLONAL	1	TRUE	1	0.62	2		296	248	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55569904	55569904	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs753318751	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	13	199	0	ENST00000288135.5:c.771G>T	p.Glu257Asp	p.E257D	ENST00000288135	NM_000222.2	257	gaG/gaT	5/21	1	2	FACETS	0.265	0.19	0.357	0.265	0.19	0.357	SUBCLONAL	1	TRUE	1	0.62	2		199	158	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638900	176638900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763399938	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	194	561	0	ENST00000439151.2:c.3500G>A	p.Arg1167His	p.R1167H	ENST00000439151	NM_022455.4	1167	cGc/cAc	5/23	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.62	2		561	572	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912075	56912075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	110	521	2	ENST00000519728.1:c.1303G>A	p.Glu435Lys	p.E435K	ENST00000519728	NM_002350.3	435	Gaa/Aaa	12/13	1	2	FACETS	0.792	0.716	0.871	0.792	0.716	0.871	SUBCLONAL	1	TRUE	1	0.62	2		523	448	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341130	8341130	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	84	380	0	ENST00000356435.5:c.5086G>T	p.Gly1696Ter	p.G1696*	ENST00000356435		1696	Gga/Tga	30/35	1	2	FACETS	0.922	0.823	1	0.922	0.823	1	CLONAL	1	TRUE	1	0.62	2		380	294	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842075	3842075	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1302427305	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	101	334	0	ENST00000262367.5:c.1237C>T	p.Arg413Ter	p.R413*	ENST00000262367	NM_004380.2	413	Cga/Tga	5/31	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.62	2		334	319	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800433	32800433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	264	974	0	ENST00000374899.4:c.1114G>A	p.Glu372Lys	p.E372K	ENST00000374899	NM_018833.2	372	Gaa/Aaa	6/12	1	2	FACETS	0.956	0.898	1	0.956	0.898	1	CLONAL	1	TRUE	1	0.62	2		974	891	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410987	31410987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1236254462	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	163	664	0	ENST00000344624.3:c.3533G>A	p.Arg1178Gln	p.R1178Q	ENST00000344624		1178	cGa/cAa	28/33	1	2	FACETS	0.972	0.898	1	0.972	0.898	1	CLONAL	1	TRUE	1	0.62	2		664	541	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504048	123504048	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	68	285	0	ENST00000371139.4:c.224G>T	p.Arg75Ile	p.R75I	ENST00000371139	NM_001114937.2	75	aGa/aTa	3/4	1	2	FACETS	0.918	0.809	1	0.918	0.809	1	CLONAL	1	TRUE	1	0.62	2		285	239	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024220	31024220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	52	565	0	ENST00000375687.4:c.3705C>A	p.Phe1235Leu	p.F1235L	ENST00000375687	NM_015338.5	1235	ttC/ttA	13/13	1	2	FACETS	0.333	0.283	0.387	0.333	0.283	0.387	SUBCLONAL	1	TRUE	1	0.62	2		565	504	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29106023	29106023	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587782152	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	68	254	0	ENST00000328354.6:c.817G>T	p.Glu273Ter	p.E273*	ENST00000328354	NM_007194.3	273	Gaa/Taa	7/15	1	2	FACETS	0.929	0.82	1	0.929	0.82	1	CLONAL	1	TRUE	1	0.62	2		254	236	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260177	149260177	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	170	577	0	ENST00000360632.3:c.716G>T	p.Arg239Ile	p.R239I	ENST00000360632	NM_015472.4	239	aGa/aTa	4/7	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.62	2		577	531	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128246746	128246746	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	138	591	0	ENST00000265960.3:c.1183C>T	p.Arg395Ter	p.R395*	ENST00000265960	NM_001006617.1	395	Cga/Tga	9/12	1	2	FACETS	0.821	0.751	0.894	0.821	0.751	0.894	CLONAL	1	TRUE	1	0.62	2		591	542	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262885	46262885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761607812	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	103	408	0	ENST00000371998.3:c.1058G>A	p.Arg353Gln	p.R353Q	ENST00000371998		353	cGa/cAa	10/23	1	2	FACETS	0.891	0.804	0.981	0.891	0.804	0.981	CLONAL	1	TRUE	1	0.62	2		408	373	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39762950	39762950	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	68	315	0	ENST00000288319.7:c.886C>A	p.Leu296Ile	p.L296I	ENST00000288319	NM_182918.3	296	Ctt/Att	9/10	1	2	FACETS	0.792	0.696	0.893	0.792	0.696	0.893	SUBCLONAL	1	TRUE	1	0.62	2		315	277	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020225	123020225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	152	584	0	ENST00000355640.3:c.713G>A	p.Arg238Gln	p.R238Q	ENST00000355640		238	cGa/cAa	2/7	1	2	FACETS	0.985	0.907	1	0.985	0.907	1	CLONAL	1	TRUE	1	0.62	2		584	498	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148504755	148504755	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	122	516	0	ENST00000320356.2:c.2239G>T	p.Glu747Ter	p.E747*	ENST00000320356	NM_004456.4	747	Gaa/Taa	20/20	1	2	FACETS	0.839	0.763	0.918	0.839	0.763	0.918	CLONAL	1	TRUE	1	0.62	2		516	469	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80057459	80057459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200337887	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	69	232	0	ENST00000265081.6:c.1858G>A	p.Asp620Asn	p.D620N	ENST00000265081	NM_002439.4	620	Gac/Aac	13/24	1	2	FACETS	0.955	0.844	1	0.955	0.844	1	CLONAL	1	TRUE	1	0.62	2		232	233	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451474	187451474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145456310	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	100	381	1	ENST00000232014.4:c.8C>T	p.Ser3Leu	p.S3L	ENST00000232014	NM_001130845.1	3	tCg/tTg	3/10	1	2	FACETS	0.886	0.799	0.977	0.886	0.799	0.977	CLONAL	1	TRUE	1	0.62	2		382	364	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003374	42003374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372252914	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	146	423	1	ENST00000219905.7:c.2911C>T	p.Arg971Trp	p.R971W	ENST00000219905	NM_001164273.1	971	Cgg/Tgg	8/24	1	2	FACETS	0.996	0.916	1	0.996	0.916	1	CLONAL	1	TRUE	1	0.62	2		424	473	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612095	43612095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	106	687	0	ENST00000355710.3:c.2200G>A	p.Glu734Lys	p.E734K	ENST00000355710	NM_020975.4	734	Gaa/Aaa	12/20	1	2	FACETS	0.781	0.704	0.861	0.781	0.704	0.861	SUBCLONAL	1	TRUE	1	0.62	2		687	438	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215251	123215251	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	90	294	0	ENST00000218089.9:c.2797G>T	p.Glu933Ter	p.E933*	ENST00000218089	NM_001042749.1	933	Gaa/Taa	28/35	1	2	FACETS	0.998	0.896	1	0.998	0.896	1	CLONAL	1	TRUE	1	0.62	2		294	291	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702410	47702410	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs267607986	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	47	194	0	ENST00000233146.2:c.2005+1G>A		p.X669_splice	ENST00000233146	NM_000251.2	669			1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.62	2		194	144	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964903	25964903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561088610	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	104	387	0	ENST00000435504.4:c.4303C>T	p.Arg1435Trp	p.R1435W	ENST00000435504		1435	Cgg/Tgg	13/13	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.62	2		387	333	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628125	187628125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1196972484	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	159	715	0	ENST00000441802.2:c.2857G>A	p.Asp953Asn	p.D953N	ENST00000441802	NM_005245.3	953	Gat/Aat	2/27	1	2	FACETS	0.815	0.75	0.883	0.815	0.75	0.883	CLONAL	1	TRUE	1	0.62	2		715	629	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921447	39921447	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	150	597	0	ENST00000378444.4:c.4373T>C	p.Val1458Ala	p.V1458A	ENST00000378444	NM_001123385.1	1458	gTc/gCc	10/15	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.62	2		597	476	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836804	151836804	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	140	451	0	ENST00000262189.6:c.14416C>T	p.Arg4806Ter	p.R4806*	ENST00000262189	NM_170606.2	4806	Cga/Tga	56/59	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.62	2		451	446	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795032	45795032	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768671057	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	202	555	1	ENST00000450313.1:c.1596C>A	p.Phe532Leu	p.F532L	ENST00000450313	NM_012222.2	532	ttC/ttA	16/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.62	2		556	624	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961137	79961137	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs569679162	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	217	476	0	ENST00000265081.6:c.534G>T	p.Lys178Asn	p.K178N	ENST00000265081	NM_002439.4	178	aaG/aaT	3/24	1	2	FACETS	0.923	0.874	0.972	1	0.995	1	CLONAL	2	TRUE	1	0.62	2		476	379	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907720	76907720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	138	527	0	ENST00000373344.5:c.4441C>T	p.Arg1481Trp	p.R1481W	ENST00000373344	NM_000489.3	1481	Cgg/Tgg	15/35	1	2	FACETS	0.907	0.83	0.985	0.907	0.83	0.985	CLONAL	1	TRUE	1	0.62	2		527	491	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937356	76937356	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	92	370	0	ENST00000373344.5:c.3392G>T	p.Arg1131Ile	p.R1131I	ENST00000373344	NM_000489.3	1131	aGa/aTa	9/35	1	2	FACETS	0.87	0.781	0.964	0.87	0.781	0.964	CLONAL	1	TRUE	1	0.62	2		370	341	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251901	153251901	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	85	385	0	ENST00000281708.4:c.1105G>T	p.Glu369Ter	p.E369*	ENST00000281708	NM_033632.3	369	Gaa/Taa	7/12	1	2	FACETS	0.737	0.656	0.822	0.737	0.656	0.822	SUBCLONAL	1	TRUE	1	0.62	2		385	372	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210116	55210116	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778638117	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	83	396	0	ENST00000275493.2:c.226C>A	p.Leu76Ile	p.L76I	ENST00000275493	NM_005228.3	76	Ctt/Att	2/28	1	2	FACETS	0.706	0.628	0.79	0.706	0.628	0.79	SUBCLONAL	1	TRUE	1	0.62	2		396	379	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889193	76889193	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	63	269	0	ENST00000373344.5:c.4817G>T	p.Ser1606Ile	p.S1606I	ENST00000373344	NM_000489.3	1606	aGt/aTt	18/35	1	2	FACETS	0.797	0.697	0.903	0.797	0.697	0.903	CLONAL	1	TRUE	1	0.62	2		269	255	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861577	152861577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149734965	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	116	737	0	ENST00000406277.2:c.175G>A	p.Glu59Lys	p.E59K	ENST00000406277	NM_152274.4	59	Gag/Aag	4/7	1		FACETS		0.608	0.739				SUBCLONAL	1	TRUE	1	0.62	2		737	557	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850777	63850777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374377066	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	102	431	0	ENST00000279873.7:c.1555G>A	p.Glu519Lys	p.E519K	ENST00000279873	NM_032199.2	519	Gaa/Aaa	10/10	1	2	FACETS	0.922	0.832	1	0.922	0.832	1	CLONAL	1	TRUE	1	0.62	2		431	357	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211219	36211219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765836382	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	305	1086	1	ENST00000222270.7:c.970G>A	p.Glu324Lys	p.E324K	ENST00000222270	NM_014727.1	324	Gaa/Aaa	3/37	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.62	2		1087	930	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557804	187557804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1321370436	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	111	402	0	ENST00000441802.2:c.3907G>A	p.Glu1303Lys	p.E1303K	ENST00000441802	NM_005245.3	1303	Gaa/Aaa	5/27	1	2	FACETS	0.916	0.83	1	0.916	0.83	1	CLONAL	1	TRUE	1	0.62	2		402	391	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803500	32803500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550712305	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	100	732	1	ENST00000374899.4:c.659G>A	p.Arg220Gln	p.R220Q	ENST00000374899	NM_018833.2	220	cGa/cAa	4/12	1	2	FACETS	0.45	0.402	0.501	0.45	0.402	0.501	SUBCLONAL	1	TRUE	1	0.62	2		733	717	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99203949	99203949	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1370549873	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	88	267	0	ENST00000074304.5:c.2812C>T	p.Arg938Ter	p.R938*	ENST00000074304	NM_001134224.1	938	Cga/Tga	26/26	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.62	2		267	274	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015053	27015053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151098324	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	158	422	0	ENST00000335756.4:c.155G>A	p.Arg52Gln	p.R52Q	ENST00000335756	NM_001809.3	52	cGa/cAa	2/5	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.62	2		422	422	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129983	55129983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763718380	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	182	560	1	ENST00000257290.5:c.517G>A	p.Asp173Asn	p.D173N	ENST00000257290	NM_006206.4	173	Gac/Aac	4/23	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.62	2		561	547	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305238	39305238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs890472037	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	162	502	0	ENST00000373001.3:c.1187G>A	p.Arg396Gln	p.R396Q	ENST00000373001	NM_022157.3	396	cGa/cAa	7/7	1	2	FACETS	0.959	0.885	1	0.959	0.885	1	CLONAL	1	TRUE	1	0.62	2		502	545	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443676	29443676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56315533	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	171	705	3	ENST00000389048.3:c.3541C>T	p.Arg1181Cys	p.R1181C	ENST00000389048	NM_004304.4	1181	Cgc/Tgc	23/29	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.62	2		708	540	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187104	38187104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758646155	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	220	802	0	ENST00000317025.8:c.1373C>T	p.Ala458Val	p.A458V	ENST00000317025	NM_023034.1	458	gCg/gTg	6/24	1	2	FACETS	0.886	0.826	0.947	0.886	0.826	0.947	CLONAL	1	TRUE	1	0.62	2		802	801	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533773	41533773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	23	409	1	ENST00000263253.7:c.1739G>A	p.Arg580Gln	p.R580Q	ENST00000263253	NM_001429.3	580	cGa/cAa	8/31	1	2	FACETS	0.188	0.146	0.237	0.188	0.146	0.237	SUBCLONAL	1	TRUE	1	0.62	2		410	394	SUCCESS
APC	324	MSKCC	GRCh37	5	112179582	112179582	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	91	315	0	ENST00000257430.4:c.8291C>A	p.Ser2764Tyr	p.S2764Y	ENST00000257430	NM_000038.5	2764	tCt/tAt	16/16	1	2	FACETS	0.912	0.818	1	0.912	0.818	1	CLONAL	1	TRUE	1	0.62	2		315	322	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439638	51439638	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750990884	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	106	355	0	ENST00000262662.1:c.203G>A	p.Arg68Gln	p.R68Q	ENST00000262662		68	cGa/cAa	4/4	1	2	FACETS	0.974	0.882	1	0.974	0.882	1	CLONAL	1	TRUE	1	0.62	2		355	351	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152120	55152120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745464928	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	160	635	0	ENST00000257290.5:c.2552C>T	p.Ser851Leu	p.S851L	ENST00000257290	NM_006206.4	851	tCg/tTg	18/23	1	2	FACETS	0.887	0.817	0.959	0.887	0.817	0.959	CLONAL	1	TRUE	1	0.62	2		635	582	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433373	49433373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771966959	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	182	797	1	ENST00000301067.7:c.8074C>T	p.Arg2692Trp	p.R2692W	ENST00000301067	NM_003482.3	2692	Cgg/Tgg	32/54	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.62	2		798	555	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042116	6042116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881916	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	74	224	0	ENST00000265849.7:c.505C>T	p.Arg169Cys	p.R169C	ENST00000265849	NM_000535.5	169	Cgc/Tgc	5/15	1	2	FACETS	0.99	0.88	1	0.99	0.88	1	CLONAL	1	TRUE	1	0.62	2		224	241	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277291	41277291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	96	323	1	ENST00000349496.5:c.1760G>A	p.Arg587Gln	p.R587Q	ENST00000349496	NM_001904.3	587	cGa/cAa	11/15	1	2	FACETS	0.924	0.832	1	0.924	0.832	1	CLONAL	1	TRUE	1	0.62	2		324	335	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958874	38958874	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	46	233	0	ENST00000357387.3:c.2238C>A	p.Phe746Leu	p.F746L	ENST00000357387	NM_152756.3	746	ttC/ttA	23/38	1	2	FACETS	0.742	0.633	0.859	0.742	0.633	0.859	SUBCLONAL	1	TRUE	1	0.62	2		233	200	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736388	85736388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs949558985	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	104	335	0	ENST00000370580.1:c.259C>T	p.Arg87Trp	p.R87W	ENST00000370580	NM_003921.4	87	Cgg/Tgg	2/3	1	2	FACETS	0.862	0.779	0.95	0.862	0.779	0.95	CLONAL	1	TRUE	1	0.62	2		335	389	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640689	3640689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750906921	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	198	971	0	ENST00000294008.3:c.2950G>A	p.Glu984Lys	p.E984K	ENST00000294008	NM_032444.2	984	Gaa/Aaa	12/15	1	2	FACETS	0.978	0.91	1	0.978	0.91	1	CLONAL	1	TRUE	1	0.62	2		971	653	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665230	117665230	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1258207555	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	52	218	0	ENST00000368508.3:c.4517G>T	p.Arg1506Ile	p.R1506I	ENST00000368508	NM_002944.2	1506	aGa/aTa	27/43	1	2	FACETS	0.843	0.728	0.965	0.843	0.728	0.965	CLONAL	1	TRUE	1	0.62	2		218	199	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891037	112891037	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	92	330	0	ENST00000351677.2:c.371A>C	p.Lys124Thr	p.K124T	ENST00000351677	NM_002834.3	124	aAa/aCa	4/16	1	2	FACETS	0.908	0.815	1	0.908	0.815	1	CLONAL	1	TRUE	1	0.62	2		330	327	SUCCESS
ATR	545	MSKCC	GRCh37	3	142224146	142224146	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	58	238	0	ENST00000350721.4:c.5032-1G>T		p.X1678_splice	ENST00000350721	NM_001184.3	1678			1	2	FACETS	0.866	0.755	0.984	0.866	0.755	0.984	CLONAL	1	TRUE	1	0.62	2		238	216	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197484	27197484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756064806	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	138	652	1	ENST00000380036.4:c.1796C>T	p.Ser599Leu	p.S599L	ENST00000380036	NM_000459.3	599	tCg/tTg	12/23	1	2	FACETS	0.88	0.805	0.957	0.88	0.805	0.957	CLONAL	1	TRUE	1	0.62	2		653	506	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776955	76776955	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	114	437	0	ENST00000373344.5:c.6997G>T	p.Glu2333Ter	p.E2333*	ENST00000373344	NM_000489.3	2333	Gaa/Taa	33/35	1	2	FACETS	0.931	0.846	1	0.931	0.846	1	CLONAL	1	TRUE	1	0.62	2		437	395	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216627	108216627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786203542	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	54	231	0	ENST00000278616.4:c.8576C>T	p.Ser2859Phe	p.S2859F	ENST00000278616	NM_000051.3	2859	tCt/tTt	58/63	1	2	FACETS	0.889	0.771	1	0.889	0.771	1	CLONAL	1	TRUE	1	0.62	2		231	196	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950493	68950493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760821149	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	107	355	0	ENST00000288368.4:c.805G>A	p.Asp269Asn	p.D269N	ENST00000288368	NM_024870.2	269	Gat/Aat	7/40	1	2	FACETS	0.923	0.835	1	0.923	0.835	1	CLONAL	1	TRUE	1	0.62	2		355	374	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486064	29486064	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782772	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	74	274	0	ENST00000356175.3:c.241C>A	p.Leu81Ile	p.L81I	ENST00000356175	NM_000267.3	81	Ctc/Atc	3/57	1	2	FACETS	0.97	0.861	1	0.97	0.861	1	CLONAL	1	TRUE	1	0.62	2		274	246	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28903838	28903838	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1319953709	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	142	676	0	ENST00000282397.4:c.2621C>T	p.Ala874Val	p.A874V	ENST00000282397	NM_002019.4	874	gCt/gTt	19/30	1	2	FACETS	0.856	0.785	0.93	0.856	0.785	0.93	CLONAL	1	TRUE	1	0.62	2		676	535	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123685	11123685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	190	680	1	ENST00000358026.2:c.2335G>A	p.Asp779Asn	p.D779N	ENST00000358026	NM_001128849.1	779	Gac/Aac	16/36	1	2	FACETS	0.943	0.876	1	0.943	0.876	1	CLONAL	1	TRUE	1	0.62	2		681	650	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233619	233619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457666982	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	75	277	0	ENST00000264932.6:c.923C>T	p.Thr308Met	p.T308M	ENST00000264932	NM_004168.2	308	aCg/aTg	8/15	1	2	FACETS	0.91	0.807	1	0.91	0.807	1	CLONAL	1	TRUE	1	0.62	2		277	266	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435490	18435490	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs760928254	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	39	241	0	ENST00000266497.5:c.475G>T	p.Glu159Ter	p.E159*	ENST00000266497		159	Gaa/Taa	1/31	1	2	FACETS	0.968	0.82	1	0.968	0.82	1	CLONAL	1	TRUE	1	0.62	2		241	130	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242710	46242710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777576250	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	75	270	0	ENST00000334344.6:c.1672C>T	p.Arg558Cys	p.R558C	ENST00000334344	NM_152641.2	558	Cgt/Tgt	13/21	1	2	FACETS	0.877	0.777	0.981	0.877	0.777	0.981	CLONAL	1	TRUE	1	0.62	2		270	276	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749297	43749297	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs748115671	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	166	564	0	ENST00000382044.4:c.1509G>T	p.Lys503Asn	p.K503N	ENST00000382044	NM_001141980.1	503	aaG/aaT	12/28	1	2	FACETS	0.977	0.903	1	0.977	0.903	1	CLONAL	1	TRUE	1	0.62	2		564	548	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938995	76938995	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs886044898	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	141	553	0	ENST00000373344.5:c.1753G>T	p.Glu585Ter	p.E585*	ENST00000373344	NM_000489.3	585	Gaa/Taa	9/35	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.62	2		553	447	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268333	46268333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747268479	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	75	357	0	ENST00000371998.3:c.2720G>A	p.Arg907Gln	p.R907Q	ENST00000371998		907	cGa/cAa	15/23	1	2	FACETS	0.864	0.766	0.967	0.864	0.766	0.967	CLONAL	1	TRUE	1	0.62	2		357	280	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448309	56448309	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781449421	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	220	830	0	ENST00000407977.2:c.338G>A	p.Arg113Gln	p.R113Q	ENST00000407977		113	cGa/cAa	3/10	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.62	2		830	697	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710875	117710875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140178288	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	74	403	0	ENST00000368508.3:c.1397G>A	p.Arg466Gln	p.R466Q	ENST00000368508	NM_002944.2	466	cGa/cAa	12/43	1	2	FACETS	0.71	0.627	0.799	0.71	0.627	0.799	SUBCLONAL	1	TRUE	1	0.62	2		403	336	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707863	43707863	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	272	820	2	ENST00000382044.4:c.5018G>T	p.Arg1673Ile	p.R1673I	ENST00000382044	NM_001141980.1	1673	aGa/aTa	23/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.62	2		822	795	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281637	142281637	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	111	435	0	ENST00000350721.4:c.607G>T	p.Glu203Ter	p.E203*	ENST00000350721	NM_001184.3	203	Gaa/Taa	4/47	1	2	FACETS	0.981	0.891	1	0.981	0.891	1	CLONAL	1	TRUE	1	0.62	2		435	365	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443796	18443796	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1185264920	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	38	234	0	ENST00000266497.5:c.769G>T	p.Glu257Ter	p.E257*	ENST00000266497		257	Gaa/Taa	3/31	1	2	FACETS	0.642	0.536	0.757	0.642	0.536	0.757	SUBCLONAL	1	TRUE	1	0.62	2		234	191	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880126	151880126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146495785	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	100	413	0	ENST00000262189.6:c.5198C>T	p.Ser1733Leu	p.S1733L	ENST00000262189	NM_170606.2	1733	tCg/tTg	35/59	1	2	FACETS	0.922	0.831	1	0.922	0.831	1	CLONAL	1	TRUE	1	0.62	2		413	350	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250350	110250350	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768719572	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	198	960	1	ENST00000374672.4:c.325C>A	p.Leu109Ile	p.L109I	ENST00000374672	NM_004235.4	109	Ctc/Atc	3/5	1	2	FACETS	0.948	0.881	1	0.948	0.881	1	CLONAL	1	TRUE	1	0.62	2		961	674	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776304	76776304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	109	574	0	ENST00000373344.5:c.7162G>A	p.Glu2388Lys	p.E2388K	ENST00000373344	NM_000489.3	2388	Gaa/Aaa	34/35	1	2	FACETS	0.728	0.657	0.802	0.728	0.657	0.802	SUBCLONAL	1	TRUE	1	0.62	2		574	483	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142447	119142447	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs199739868	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	86	331	0	ENST00000264033.4:c.446G>A	p.Arg149Gln	p.R149Q	ENST00000264033	NM_005188.3	149	cGa/cAa	3/16	1	2	FACETS	0.934	0.836	1	0.934	0.836	1	CLONAL	1	TRUE	1	0.62	2		331	297	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3929909	3929909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	134	489	1	ENST00000262367.5:c.9G>T	p.Glu3Asp	p.E3D	ENST00000262367	NM_004380.2	3	gaG/gaT	1/31	1	2	FACETS	0.901	0.824	0.98	0.901	0.824	0.98	CLONAL	1	TRUE	1	0.62	2		490	480	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222962	36222962	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs181607228	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	232	969	2	ENST00000222270.7:c.5591G>A	p.Arg1864Gln	p.R1864Q	ENST00000222270	NM_014727.1	1864	cGa/cAa	27/37	1	2	FACETS	0.919	0.86	0.981	0.919	0.86	0.981	CLONAL	1	TRUE	1	0.62	2		971	814	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005332	29005332	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	78	422	0	ENST00000282397.4:c.929C>A	p.Thr310Asn	p.T310N	ENST00000282397	NM_002019.4	310	aCt/aAt	7/30	1	2	FACETS	0.779	0.691	0.872	0.779	0.691	0.872	SUBCLONAL	1	TRUE	1	0.62	2		422	323	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992274	72992274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767435394	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	243	875	1	ENST00000268489.5:c.1771G>A	p.Ala591Thr	p.A591T	ENST00000268489	NM_006885.3	591	Gct/Act	2/10	1	2	FACETS	0.967	0.906	1	0.967	0.906	1	CLONAL	1	TRUE	1	0.62	2		876	811	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165140	47165140	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540015912	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	56	260	0	ENST00000409792.3:c.986G>A	p.Arg329Gln	p.R329Q	ENST00000409792	NM_014159.6	329	cGg/cAg	3/21	1	2	FACETS	0.692	0.598	0.792	0.692	0.598	0.792	SUBCLONAL	1	TRUE	1	0.62	2		260	261	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680556	241680556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769956664	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	69	413	0	ENST00000366560.3:c.193G>T	p.Asp65Tyr	p.D65Y	ENST00000366560	NM_000143.3	65	Gat/Tat	2/10	1	2	FACETS	0.638	0.559	0.722	0.638	0.559	0.722	SUBCLONAL	1	TRUE	1	0.62	2		413	349	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740814	58740814	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	155	422	0	ENST00000305921.3:c.1719G>T	p.Lys573Asn	p.K573N	ENST00000305921	NM_003620.3	573	aaG/aaT	6/6	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.62	2		422	493	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981172	55981172	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	91	415	0	ENST00000263923.4:c.527G>T	p.Arg176Ile	p.R176I	ENST00000263923	NM_002253.2	176	aGa/aTa	5/30	1	2	FACETS	0.884	0.793	0.98	0.884	0.793	0.98	CLONAL	1	TRUE	1	0.62	2		415	332	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995501	68995501	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1326956245	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	42	489	0	ENST00000288368.4:c.1905G>T	p.Lys635Asn	p.K635N	ENST00000288368	NM_024870.2	635	aaG/aaT	18/40	1	2	FACETS	0.369	0.309	0.436	0.369	0.309	0.436	SUBCLONAL	1	TRUE	1	0.62	2		489	367	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315354	30315354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1480541649	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	109	361	0	ENST00000322652.5:c.1039G>A	p.Glu347Lys	p.E347K	ENST00000322652	NM_015355.2	347	Gaa/Aaa	10/16	1	2	FACETS	0.89	0.806	0.978	0.89	0.806	0.978	CLONAL	1	TRUE	1	0.62	2		361	395	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169036	32169036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745902446	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	221	858	1	ENST00000375023.3:c.3997C>T	p.Arg1333Cys	p.R1333C	ENST00000375023	NM_004557.3	1333	Cgt/Tgt	22/30	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.62	2		859	708	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926518	59926518	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1330277587	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	127	493	0	ENST00000259008.2:c.479G>T	p.Arg160Ile	p.R160I	ENST00000259008	NM_032043.2	160	aGa/aTa	5/20	1	2	FACETS	0.874	0.797	0.953	0.874	0.797	0.953	CLONAL	1	TRUE	1	0.62	2		493	469	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828294	72828294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	154	640	0	ENST00000268489.5:c.8287G>A	p.Asp2763Asn	p.D2763N	ENST00000268489	NM_006885.3	2763	Gat/Aat	9/10	1	2	FACETS	0.92	0.847	0.995	0.92	0.847	0.995	CLONAL	1	TRUE	1	0.62	2		640	540	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105579	30105579	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1036795627	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	190	622	1	ENST00000331968.5:c.1107G>T	p.Glu369Asp	p.E369D	ENST00000331968	NM_002742.2	369	gaG/gaT	7/18	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.62	2		623	607	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923722	72923722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1169589589	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	182	690	0	ENST00000268489.5:c.3356G>A	p.Arg1119Gln	p.R1119Q	ENST00000268489	NM_006885.3	1119	cGa/cAa	4/10	1	2	FACETS	0.982	0.911	1	0.982	0.911	1	CLONAL	1	TRUE	1	0.62	2		690	598	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946090	13946090	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1419462186	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	86	326	0	ENST00000405192.2:c.1006C>T	p.Arg336Ter	p.R336*	ENST00000405192	NM_001163147.1	336	Cga/Tga	10/12	1	2	FACETS	0.854	0.762	0.949	0.854	0.762	0.949	CLONAL	1	TRUE	1	0.62	2		326	325	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841310	15841310	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	149	484	0	ENST00000307771.7:c.1394G>T	p.Gly465Val	p.G465V	ENST00000307771	NM_005089.3	465	gGc/gTc	11/11	1	2	FACETS	0.897	0.824	0.972	0.897	0.824	0.972	CLONAL	1	TRUE	1	0.62	2		484	536	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597525	28597525	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	142	443	0	ENST00000241453.7:c.2380C>A	p.Gln794Lys	p.Q794K	ENST00000241453	NM_004119.2	794	Caa/Aaa	19/24	1	2	FACETS	0.97	0.891	1	0.97	0.891	1	CLONAL	1	TRUE	1	0.62	2		443	472	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611338	28611338	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	91	434	0	ENST00000241453.7:c.1293C>A	p.Phe431Leu	p.F431L	ENST00000241453	NM_004119.2	431	ttC/ttA	10/24	1	2	FACETS	0.818	0.732	0.907	0.818	0.732	0.907	CLONAL	1	TRUE	1	0.62	2		434	359	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032274	10032274	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	164	565	1	ENST00000330684.3:c.549C>A	p.Phe183Leu	p.F183L	ENST00000330684	NM_001134407.1	183	ttC/ttA	3/13	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.62	2		566	516	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191187	2191187	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	70	867	0	ENST00000398665.3:c.441G>T	p.Met147Ile	p.M147I	ENST00000398665	NM_032482.2	147	atG/atT	5/28	1	2	FACETS	0.308	0.268	0.351	0.308	0.268	0.351	SUBCLONAL	1	TRUE	1	0.62	2		867	734	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220483	123220483	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	162	562	0	ENST00000218089.9:c.3140C>A	p.Ser1047Tyr	p.S1047Y	ENST00000218089	NM_001042749.1	1047	tCt/tAt	30/35	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.62	2		562	510	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701889	43701889	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	93	206	0	ENST00000382044.4:c.5356C>T	p.Arg1786Ter	p.R1786*	ENST00000382044	NM_001141980.1	1786	Cga/Tga	25/28	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.62	2		206	263	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146592	55146592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555347387	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	120	385	0	ENST00000257290.5:c.2266G>A	p.Asp756Asn	p.D756N	ENST00000257290	NM_006206.4	756	Gac/Aac	16/23	1	2	FACETS	0.978	0.891	1	0.978	0.891	1	CLONAL	1	TRUE	1	0.62	2		385	396	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937850	76937850	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs138256318	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	94	282	0	ENST00000373344.5:c.2898G>T	p.Glu966Asp	p.E966D	ENST00000373344	NM_000489.3	966	gaG/gaT	9/35	1	2	FACETS	0.72	0.645	0.8	0.72	0.645	0.8	SUBCLONAL	1	TRUE	1	0.62	2		282	421	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50488303	50488303	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs750857733	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	152	510	0	ENST00000394963.4:c.1217C>A	p.Ser406Tyr	p.S406Y	ENST00000394963	NM_003076.4	406	tCt/tAt	10/13	1	2	FACETS	0.945	0.87	1	0.945	0.87	1	CLONAL	1	TRUE	1	0.62	2		510	519	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857757	9857757	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	146	584	0	ENST00000330684.3:c.3644G>T	p.Arg1215Ile	p.R1215I	ENST00000330684	NM_001134407.1	1215	aGa/aTa	13/13	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.62	2		584	444	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240670	133240670	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1208731306	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	159	630	0	ENST00000320574.5:c.2626T>G	p.Phe876Val	p.F876V	ENST00000320574	NM_006231.2	876	Ttt/Gtt	23/49	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.62	2		630	494	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938640	76938640	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	107	562	0	ENST00000373344.5:c.2108C>A	p.Ser703Tyr	p.S703Y	ENST00000373344	NM_000489.3	703	tCt/tAt	9/35	1	2	FACETS	0.779	0.703	0.859	0.779	0.703	0.859	SUBCLONAL	1	TRUE	1	0.62	2		562	443	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249941	39249941	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	26	574	0	ENST00000402219.2:c.1628C>A	p.Ser543Tyr	p.S543Y	ENST00000402219	NM_005633.3	543	tCt/tAt	10/23	1	2	FACETS	0.171	0.135	0.212	0.171	0.135	0.212	SUBCLONAL	1	TRUE	1	0.62	2		574	491	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970985	55970985	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	152	545	0	ENST00000263923.4:c.1812G>T	p.Lys604Asn	p.K604N	ENST00000263923	NM_002253.2	604	aaG/aaT	13/30	1	2	FACETS	0.941	0.866	1	0.941	0.866	1	CLONAL	1	TRUE	1	0.62	2		545	521	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459453	50459453	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	51	240	0	ENST00000331340.3:c.742G>T	p.Glu248Ter	p.E248*	ENST00000331340	NM_006060.4	248	Gaa/Taa	7/8	1	2	FACETS	0.875	0.755	1	0.875	0.755	1	CLONAL	1	TRUE	1	0.62	2		240	188	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593628	55593628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	102	402	0	ENST00000288135.5:c.1694G>A	p.Gly565Glu	p.G565E	ENST00000288135	NM_000222.2	565	gGa/gAa	11/21	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.62	2		402	323	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645414	67645414	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772804334	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	110	412	0	ENST00000264010.4:c.679G>A	p.Asp227Asn	p.D227N	ENST00000264010	NM_006565.3	227	Gat/Aat	3/12	1	2	FACETS	0.988	0.897	1	0.988	0.897	1	CLONAL	1	TRUE	1	0.62	2		412	359	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979589	55979589	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	128	470	0	ENST00000263923.4:c.858G>T	p.Lys286Asn	p.K286N	ENST00000263923	NM_002253.2	286	aaG/aaT	7/30	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.62	2		470	406	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241973	39241973	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	48	253	1	ENST00000402219.2:c.1873C>T	p.Arg625Trp	p.R625W	ENST00000402219	NM_005633.3	625	Cgg/Tgg	11/23	1	2	FACETS	0.656	0.56	0.76	0.656	0.56	0.76	SUBCLONAL	1	TRUE	1	0.62	2		254	236	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353867	68353867	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	117	361	1	ENST00000487270.1:c.702C>A	p.Phe234Leu	p.F234L	ENST00000487270	NM_133509.3	234	ttC/ttA	7/11	1	2	FACETS	0.905	0.823	0.991	0.905	0.823	0.991	CLONAL	1	TRUE	1	0.62	2		362	417	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602916	55602916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372795544	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	105	395	1	ENST00000288135.5:c.2626G>A	p.Asp876Asn	p.D876N	ENST00000288135	NM_000222.2	876	Gat/Aat	19/21	1	2	FACETS	0.92	0.832	1	0.92	0.832	1	CLONAL	1	TRUE	1	0.62	2		396	368	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20486949	20486949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188266138	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	55	234	0	ENST00000346618.3:c.914G>A	p.Arg305Gln	p.R305Q	ENST00000346618	NM_001949.4	305	cGa/cAa	5/7	1	2	FACETS	0.87	0.755	0.991	0.87	0.755	0.991	CLONAL	1	TRUE	1	0.62	2		234	204	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950837	32950837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80359124	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	99	348	1	ENST00000380152.3:c.8663G>A	p.Arg2888His	p.R2888H	ENST00000380152		2888	cGt/cAt	21/27	1	2	FACETS	0.817	0.735	0.903	0.817	0.735	0.903	CLONAL	1	TRUE	1	0.62	2		349	391	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895653	28895653	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	94	458	0	ENST00000282397.4:c.3121T>G	p.Phe1041Val	p.F1041V	ENST00000282397	NM_002019.4	1041	Ttt/Gtt	23/30	1	2	FACETS	0.784	0.702	0.869	0.784	0.702	0.869	SUBCLONAL	1	TRUE	1	0.62	2		458	387	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961766	55961766	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	95	408	0	ENST00000263923.4:c.2795G>T	p.Arg932Ile	p.R932I	ENST00000263923	NM_002253.2	932	aGa/aTa	20/30	1	2	FACETS	0.849	0.762	0.939	0.849	0.762	0.939	CLONAL	1	TRUE	1	0.62	2		408	361	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211894	36211894	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	259	903	0	ENST00000222270.7:c.1645G>T	p.Glu549Ter	p.E549*	ENST00000222270	NM_014727.1	549	Gaa/Taa	3/37	1	2	FACETS	0.977	0.918	1	0.977	0.918	1	CLONAL	1	TRUE	1	0.62	2		903	855	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133041	30133041	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	125	457	0	ENST00000331968.5:c.560G>T	p.Arg187Ile	p.R187I	ENST00000331968	NM_002742.2	187	aGa/aTa	4/18	1	2	FACETS	0.906	0.826	0.989	0.906	0.826	0.989	CLONAL	1	TRUE	1	0.62	2		457	445	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661884	227661884	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	214	1092	1	ENST00000305123.5:c.1571G>T	p.Arg524Ile	p.R524I	ENST00000305123	NM_005544.2	524	aGa/aTa	1/2	1	2	FACETS	0.998	0.931	1	0.998	0.931	1	CLONAL	1	TRUE	1	0.62	2		1093	692	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499611	149499611	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	119	589	0	ENST00000261799.4:c.2662T>C	p.Ser888Pro	p.S888P	ENST00000261799	NM_002609.3	888	Tcc/Ccc	19/23	1	2	FACETS	0.876	0.797	0.959	0.876	0.797	0.959	CLONAL	1	TRUE	1	0.62	2		589	438	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073530	8073530	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs535836763	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	108	424	0	ENST00000377482.5:c.1129C>T	p.Pro377Ser	p.P377S	ENST00000377482	NM_018948.3	377	Cct/Tct	4/4	1	2	FACETS	0.939	0.851	1	0.939	0.851	1	CLONAL	1	TRUE	1	0.62	2		424	371	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272943	11272943	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	79	377	0	ENST00000361445.4:c.3308T>A	p.Phe1103Tyr	p.F1103Y	ENST00000361445	NM_004958.3	1103	tTt/tAt	22/58	1	2	FACETS	0.667	0.59	0.749	0.667	0.59	0.749	SUBCLONAL	1	TRUE	1	0.62	2		377	382	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257033	16257033	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	26	547	0	ENST00000375759.3:c.4298C>A	p.Ser1433Tyr	p.S1433Y	ENST00000375759	NM_015001.2	1433	tCt/tAt	11/15	0.3	3	FACETS	0.228	0.18	0.284			1	INDETERMINATE	1	TRUE	NA	0.62	3		547	481	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058079	27058079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057523568	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	95	445	0	ENST00000324856.7:c.1787G>A	p.Arg596His	p.R596H	ENST00000324856	NM_006015.4	596	cGc/cAc	3/20	1	2	FACETS	0.711	0.637	0.789	0.711	0.637	0.789	SUBCLONAL	1	TRUE	1	0.62	2		445	431	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106582	27106582	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1359226978	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	209	764	0	ENST00000324856.7:c.6193G>A	p.Ala2065Thr	p.A2065T	ENST00000324856	NM_006015.4	2065	Gcc/Acc	20/20	1	2	FACETS	0.984	0.918	1	0.984	0.918	1	CLONAL	1	TRUE	1	0.62	2		764	685	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932167	36932167	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	147	709	0	ENST00000361632.4:c.2302C>A	p.Leu768Ile	p.L768I	ENST00000361632		768	Ctc/Atc	16/16	1	2	FACETS	0.891	0.819	0.967	0.891	0.819	0.967	CLONAL	1	TRUE	1	0.62	2		709	532	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521529	46521529	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	134	442	0	ENST00000262741.5:c.879A>C	p.Lys293Asn	p.K293N	ENST00000262741	NM_003629.3	293	aaA/aaC	7/10	1	2	FACETS	0.879	0.803	0.957	0.879	0.803	0.957	CLONAL	1	TRUE	1	0.62	2		442	492	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726593	46726593	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	123	576	1	ENST00000371975.4:c.672G>T	p.Lys224Asn	p.K224N	ENST00000371975	NM_003579.3	224	aaG/aaT	7/18	1	2	FACETS	0.874	0.796	0.955	0.874	0.796	0.955	CLONAL	1	TRUE	1	0.62	2		577	454	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309886	65309886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	109	458	1	ENST00000342505.4:c.2264G>A	p.Arg755Gln	p.R755Q	ENST00000342505	NM_002227.2	755	cGa/cAa	17/25	1	2	FACETS	0.938	0.85	1	0.938	0.85	1	CLONAL	1	TRUE	1	0.62	2		459	375	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414985	78414985	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	89	333	0	ENST00000370768.2:c.1781G>C	p.Gly594Ala	p.G594A	ENST00000370768	NM_003902.3	594	gGt/gCt	19/20	1	2	FACETS	0.8	0.715	0.889	0.8	0.715	0.889	SUBCLONAL	1	TRUE	1	0.62	2		333	359	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165875	118165875	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	113	430	0	ENST00000369448.3:c.385A>C	p.Ile129Leu	p.I129L	ENST00000369448	NM_017709.3	129	Atc/Ctc	2/2	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.62	2		430	352	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163315554	163315554	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	75	329	0	ENST00000271452.3:c.894G>T	p.Lys298Asn	p.K298N	ENST00000271452	NM_145697.2	298	aaG/aaT	11/14	1	2	FACETS	0.877	0.777	0.981	0.877	0.777	0.981	CLONAL	1	TRUE	1	0.62	2		329	276	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675359	241675359	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	88	364	0	ENST00000366560.3:c.463G>T	p.Glu155Ter	p.E155*	ENST00000366560	NM_000143.3	155	Gaa/Taa	4/10	1	2	FACETS	0.83	0.742	0.922	0.83	0.742	0.922	CLONAL	1	TRUE	1	0.62	2		364	342	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809199	243809199	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	79	340	0	ENST00000263826.5:c.425G>T	p.Arg142Ile	p.R142I	ENST00000263826	NM_005465.4	142	aGa/aTa	4/13	1	2	FACETS	0.923	0.822	1	0.923	0.822	1	CLONAL	1	TRUE	1	0.62	2		340	276	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828186	243828186	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	17	259	0	ENST00000263826.5:c.173-1G>T		p.X58_splice	ENST00000263826	NM_005465.4	58			1	2	FACETS	0.207	0.154	0.27	0.207	0.154	0.27	SUBCLONAL	1	TRUE	1	0.62	2		259	265	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246490625	246490625	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	30	370	0	ENST00000388985.4:c.409A>C	p.Thr137Pro	p.T137P	ENST00000388985		137	Act/Cct	5/12	1	2	FACETS	0.333	0.268	0.405	0.333	0.268	0.405	SUBCLONAL	1	TRUE	1	0.62	2		370	291	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63810678	63810678	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1464829578	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	53	248	0	ENST00000279873.7:c.765G>T	p.Lys255Asn	p.K255N	ENST00000279873	NM_032199.2	255	aaG/aaT	5/10	1	2	FACETS	0.668	0.575	0.768	0.668	0.575	0.768	SUBCLONAL	1	TRUE	1	0.62	2		248	256	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851755	63851755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749293931	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	147	600	2	ENST00000279873.7:c.2533G>A	p.Glu845Lys	p.E845K	ENST00000279873	NM_032199.2	845	Gag/Aag	10/10	1	2	FACETS	0.881	0.809	0.956	0.881	0.809	0.956	CLONAL	1	TRUE	1	0.62	2		602	538	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332336	70332336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775380660	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	123	476	0	ENST00000373644.4:c.241C>T	p.Arg81Cys	p.R81C	ENST00000373644	NM_030625.2	81	Cgc/Tgc	2/12	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.62	2		476	392	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406732	70406732	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768683199	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	100	444	0	ENST00000373644.4:c.4246G>T	p.Asp1416Tyr	p.D1416Y	ENST00000373644	NM_030625.2	1416	Gat/Tat	4/12	1	2	FACETS	0.879	0.792	0.97	0.879	0.792	0.97	CLONAL	1	TRUE	1	0.62	2		444	367	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720816	89720816	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	99	401	0	ENST00000371953.3:c.967A>C	p.Asn323His	p.N323H	ENST00000371953	NM_000314.4	323	Aat/Cat	8/9	1	2	FACETS	0.931	0.84	1	0.931	0.84	1	CLONAL	1	TRUE	1	0.62	2		401	343	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375087	104375087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755390277	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	112	560	0	ENST00000369902.3:c.1085G>A	p.Arg362His	p.R362H	ENST00000369902	NM_016169.3	362	cGc/cAc	9/12	1	2	FACETS	0.632	0.57	0.697	0.632	0.57	0.697	SUBCLONAL	1	TRUE	1	0.62	2		560	572	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161460	2161460	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	186	641	0	ENST00000434045.2:c.67C>A	p.Gln23Lys	p.Q23K	ENST00000434045	NM_001127598.1	23	Caa/Aaa	2/5	1	2	FACETS	0.938	0.87	1	0.938	0.87	1	CLONAL	1	TRUE	1	0.62	2		641	640	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316059	14316059	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	16	340	0	ENST00000256196.4:c.366G>T	p.Met122Ile	p.M122I	ENST00000256196		122	atG/atT	4/6	1	2	FACETS	0.173	0.127	0.227	0.173	0.127	0.227	SUBCLONAL	1	TRUE	1	0.62	2		340	299	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316108	14316108	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	59	299	0	ENST00000256196.4:c.317A>C	p.Lys106Thr	p.K106T	ENST00000256196		106	aAg/aCg	4/6	1	2	FACETS	0.831	0.724	0.944	0.831	0.724	0.944	CLONAL	1	TRUE	1	0.62	2		299	229	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417904	32417904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	135	530	0	ENST00000332351.3:c.1148C>T	p.Ser383Phe	p.S383F	ENST00000332351	NM_024426.4	383	tCt/tTt	7/10	1	2	FACETS	0.951	0.871	1	0.951	0.871	1	CLONAL	1	TRUE	1	0.62	2		530	458	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625333	69625333	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	193	904	0	ENST00000334134.2:c.460T>C	p.Tyr154His	p.Y154H	ENST00000334134	NM_005247.2	154	Tac/Cac	3/3	1	2	FACETS	0.924	0.858	0.991	0.924	0.858	0.991	CLONAL	1	TRUE	1	0.62	2		904	674	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625354	69625354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	208	858	1	ENST00000334134.2:c.439C>T	p.Pro147Ser	p.P147S	ENST00000334134	NM_005247.2	147	Ccc/Tcc	3/3	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.62	2		859	660	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988988	85988988	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	85	238	0	ENST00000263360.6:c.1154A>C	p.Lys385Thr	p.K385T	ENST00000263360	NM_003797.3	385	aAa/aCa	11/12	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.62	2		238	271	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912801	100912801	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	99	374	0	ENST00000325455.5:c.2521T>C	p.Phe841Leu	p.F841L	ENST00000325455	NM_001202474.3	841	Ttt/Ctt	7/8	1	2	FACETS	0.923	0.832	1	0.923	0.832	1	CLONAL	1	TRUE	1	0.62	2		374	346	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100496	102100496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	141	479	0	ENST00000282441.5:c.1340C>T	p.Ala447Val	p.A447V	ENST00000282441	NM_001130145.2	447	gCc/gTc	9/9	1	2	FACETS	0.94	0.862	1	0.94	0.862	1	CLONAL	1	TRUE	1	0.62	2		479	484	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175544	108175544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780628	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	88	352	0	ENST00000278616.4:c.5639C>T	p.Thr1880Met	p.T1880M	ENST00000278616	NM_000051.3	1880	aCg/aTg	37/63	1	2	FACETS	0.759	0.677	0.845	0.759	0.677	0.845	SUBCLONAL	1	TRUE	1	0.62	2		352	374	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118365111	118365111	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs999060359	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	94	337	0	ENST00000534358.1:c.5287C>T	p.Arg1763Trp	p.R1763W	ENST00000534358	NM_005933.3	1763	Cgg/Tgg	17/36	1	2	FACETS	0.835	0.75	0.925	0.835	0.75	0.925	CLONAL	1	TRUE	1	0.62	2		337	363	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514012	125514012	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	111	438	0	ENST00000428830.2:c.950C>A	p.Ser317Tyr	p.S317Y	ENST00000428830	NM_001114121.2	317	tCt/tAt	10/14	1	2	FACETS	0.935	0.848	1	0.935	0.848	1	CLONAL	1	TRUE	1	0.62	2		438	383	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402085	402085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	125	484	0	ENST00000399788.2:c.4706C>T	p.Ala1569Val	p.A1569V	ENST00000399788	NM_001042603.1	1569	gCt/gTt	27/28	0.3	2	FACETS	0.867	0.79	0.947			1	INDETERMINATE	1	TRUE	NA	0.62	2		484	465	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	465601	465601	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	117	500	0	ENST00000399788.2:c.775G>T	p.Glu259Ter	p.E259*	ENST00000399788	NM_001042603.1	259	Gaa/Taa	6/28	0.3	2	FACETS	0.862	0.783	0.944			1	INDETERMINATE	1	TRUE	NA	0.62	2		500	438	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	465607	465607	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	138	537	0	ENST00000399788.2:c.769G>T	p.Asp257Tyr	p.D257Y	ENST00000399788	NM_001042603.1	257	Gat/Tat	6/28	0.3	2	FACETS	0.945	0.866	1			1	INDETERMINATE	1	TRUE	NA	0.62	2		537	471	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385283	4385283	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	138	468	1	ENST00000261254.3:c.308C>T	p.Ala103Val	p.A103V	ENST00000261254	NM_001759.3	103	gCt/gTt	2/5	0.3	2	FACETS	1	0.941	1			1	INDETERMINATE	1	TRUE	NA	0.62	2		469	432	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435588	18435588	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	52	258	0	ENST00000266497.5:c.573G>T	p.Glu191Asp	p.E191D	ENST00000266497		191	gaG/gaT	1/31	1	2	FACETS	0.851	0.735	0.975	0.851	0.735	0.975	CLONAL	1	TRUE	1	0.62	2		258	197	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466933	18466933	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	81	340	0	ENST00000266497.5:c.1072G>T	p.Asp358Tyr	p.D358Y	ENST00000266497		358	Gat/Tat	5/31	1	2	FACETS	0.895	0.797	0.997	0.895	0.797	0.997	CLONAL	1	TRUE	1	0.62	2		340	292	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18473938	18473938	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	60	249	0	ENST00000266497.5:c.1180G>T	p.Glu394Ter	p.E394*	ENST00000266497		394	Gaa/Taa	6/31	1	2	FACETS	0.913	0.798	1	0.913	0.798	1	CLONAL	1	TRUE	1	0.62	2		249	212	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552613	18552613	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1371859788	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	83	347	0	ENST00000266497.5:c.2024G>T	p.Arg675Ile	p.R675I	ENST00000266497		675	aGa/aTa	14/31	1	2	FACETS	0.824	0.734	0.918	0.824	0.734	0.918	CLONAL	1	TRUE	1	0.62	2		347	325	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18762492	18762492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	63	412	0	ENST00000266497.5:c.3988C>T	p.Pro1330Ser	p.P1330S	ENST00000266497		1330	Cct/Tct	29/31	1	2	FACETS	0.649	0.566	0.739	0.649	0.566	0.739	SUBCLONAL	1	TRUE	1	0.62	2		412	313	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123895	46123895	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	108	253	0	ENST00000334344.6:c.161T>G	p.Val54Gly	p.V54G	ENST00000334344	NM_152641.2	54	gTc/gGc	2/21	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.62	2		253	348	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244743	46244743	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	86	501	0	ENST00000334344.6:c.2837T>G	p.Ile946Ser	p.I946S	ENST00000334344	NM_152641.2	946	aTt/aGt	15/21	1	2	FACETS	0.654	0.582	0.731	0.654	0.582	0.731	SUBCLONAL	1	TRUE	1	0.62	2		501	424	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426266	49426266	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	243	955	0	ENST00000301067.7:c.12222A>C	p.Gln4074His	p.Q4074H	ENST00000301067	NM_003482.3	4074	caA/caC	39/54	1	2	FACETS	0.997	0.935	1	0.997	0.935	1	CLONAL	1	TRUE	1	0.62	2		955	786	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432623	49432623	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555191147	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	220	838	0	ENST00000301067.7:c.8516C>G	p.Ser2839Ter	p.S2839*	ENST00000301067	NM_003482.3	2839	tCa/tGa	34/54	1	2	FACETS	0.98	0.916	1	0.98	0.916	1	CLONAL	1	TRUE	1	0.62	2		838	724	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437986	49437986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747363115	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	162	676	1	ENST00000301067.7:c.5185G>A	p.Glu1729Lys	p.E1729K	ENST00000301067	NM_003482.3	1729	Gag/Aag	21/54	1	2	FACETS	0.903	0.832	0.975	0.903	0.832	0.975	CLONAL	1	TRUE	1	0.62	2		677	579	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481824	56481824	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	177	671	0	ENST00000267101.3:c.752A>G	p.Asp251Gly	p.D251G	ENST00000267101	NM_001982.3	251	gAc/gGc	7/28	1	2	FACETS	0.953	0.883	1	0.953	0.883	1	CLONAL	1	TRUE	1	0.62	2		671	599	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857489	57857489	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	220	880	1	ENST00000228682.2:c.15G>T	p.Met5Ile	p.M5I	ENST00000228682	NM_005269.2	5	atG/atT	2/12	1	2	FACETS	0.922	0.86	0.985	0.922	0.86	0.985	CLONAL	1	TRUE	1	0.62	2		881	770	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117320	115117320	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	79	222	0	ENST00000257566.3:c.854A>C	p.Gln285Pro	p.Q285P	ENST00000257566	NM_016569.3	285	cAg/cCg	4/8	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.62	2		222	222	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416625	121416625	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	222	810	0	ENST00000257555.6:c.54G>C	p.Glu18Asp	p.E18D	ENST00000257555		18	gaG/gaC	1/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.62	2		810	606	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245434	133245434	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	173	757	0	ENST00000320574.5:c.1886C>A	p.Ala629Asp	p.A629D	ENST00000320574	NM_006231.2	629	gCc/gAc	17/49	1	2	FACETS	0.906	0.838	0.976	0.906	0.838	0.976	CLONAL	1	TRUE	1	0.62	2		757	616	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252703	133252703	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	149	533	0	ENST00000320574.5:c.997T>A	p.Cys333Ser	p.C333S	ENST00000320574	NM_006231.2	333	Tgt/Agt	10/49	1	2	FACETS	0.923	0.848	0.999	0.923	0.848	0.999	CLONAL	1	TRUE	1	0.62	2		533	521	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253957	133253957	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	154	487	1	ENST00000320574.5:c.793G>A	p.Glu265Lys	p.E265K	ENST00000320574	NM_006231.2	265	Gaa/Aaa	8/49	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.62	2		488	412	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975443	26975443	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	105	392	0	ENST00000381527.3:c.1069G>T	p.Glu357Ter	p.E357*	ENST00000381527	NM_001260.1	357	Gaa/Taa	11/13	1	2	FACETS	0.822	0.742	0.906	0.822	0.742	0.906	CLONAL	1	TRUE	1	0.62	2		392	412	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599042	28599042	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1355239392	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	89	470	0	ENST00000241453.7:c.2246C>T	p.Ser749Leu	p.S749L	ENST00000241453	NM_004119.2	749	tCg/tTg	18/24	1	2	FACETS	0.78	0.697	0.867	0.78	0.697	0.867	SUBCLONAL	1	TRUE	1	0.62	2		470	368	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608270	28608270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	115	499	0	ENST00000241453.7:c.1786G>A	p.Glu596Lys	p.E596K	ENST00000241453	NM_004119.2	596	Gaa/Aaa	14/24	1	2	FACETS	0.89	0.808	0.975	0.89	0.808	0.975	CLONAL	1	TRUE	1	0.62	2		499	417	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609763	28609763	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	149	572	0	ENST00000241453.7:c.1466G>T	p.Arg489Ile	p.R489I	ENST00000241453	NM_004119.2	489	aGa/aTa	12/24	1	2	FACETS	0.956	0.879	1	0.956	0.879	1	CLONAL	1	TRUE	1	0.62	2		572	503	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964128	28964128	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	82	386	0	ENST00000282397.4:c.1774C>A	p.Leu592Met	p.L592M	ENST00000282397	NM_002019.4	592	Ctg/Atg	13/30	1	2	FACETS	0.876	0.781	0.976	0.876	0.781	0.976	CLONAL	1	TRUE	1	0.62	2		386	302	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012437	29012437	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	106	543	0	ENST00000282397.4:c.434T>G	p.Ile145Ser	p.I145S	ENST00000282397	NM_002019.4	145	aTt/aGt	4/30	1	2	FACETS	0.853	0.77	0.939	0.853	0.77	0.939	CLONAL	1	TRUE	1	0.62	2		543	401	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907124	32907124	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	71	391	0	ENST00000380152.3:c.1509G>T	p.Lys503Asn	p.K503N	ENST00000380152		503	aaG/aaT	10/27	1	2	FACETS	0.795	0.701	0.895	0.795	0.701	0.895	SUBCLONAL	1	TRUE	1	0.62	2		391	288	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913062	32913062	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs56386506	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	55	453	0	ENST00000380152.3:c.4570T>G	p.Phe1524Val	p.F1524V	ENST00000380152		1524	Ttt/Gtt	11/27	1	2	FACETS	0.409	0.35	0.472	0.409	0.35	0.472	SUBCLONAL	1	TRUE	1	0.62	2		453	434	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914260	32914260	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	79	452	0	ENST00000380152.3:c.5768A>G	p.Asp1923Gly	p.D1923G	ENST00000380152		1923	gAc/gGc	11/27	1	2	FACETS	0.791	0.702	0.885	0.791	0.702	0.885	SUBCLONAL	1	TRUE	1	0.62	2		452	322	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947550	48947550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	22	286	0	ENST00000267163.4:c.1137G>T	p.Met379Ile	p.M379I	ENST00000267163	NM_000321.2	379	atG/atT	12/27	1	2	FACETS	0.26	0.201	0.328	0.26	0.201	0.328	SUBCLONAL	1	TRUE	1	0.62	2		286	273	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953781	48953781	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	44	153	0	ENST00000267163.4:c.1384A>C	p.Lys462Gln	p.K462Q	ENST00000267163	NM_000321.2	462	Aaa/Caa	14/27	1	2	FACETS	0.946	0.809	1	0.946	0.809	1	CLONAL	1	TRUE	1	0.62	2		153	150	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281206	49281206	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	156	786	0	ENST00000282018.3:c.253C>A	p.Leu85Ile	p.L85I	ENST00000282018	NM_020377.2	85	Ctc/Atc	1/1	1	2	FACETS	0.863	0.794	0.934	0.863	0.794	0.934	CLONAL	1	TRUE	1	0.62	2		786	583	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281447	49281447	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	136	700	0	ENST00000282018.3:c.494T>G	p.Leu165Arg	p.L165R	ENST00000282018	NM_020377.2	165	cTt/cGt	1/1	1	2	FACETS	0.924	0.846	1	0.924	0.846	1	CLONAL	1	TRUE	1	0.62	2		700	475	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73334768	73334768	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	51	210	0	ENST00000377767.4:c.2692G>T	p.Asp898Tyr	p.D898Y	ENST00000377767	NM_014953.3	898	Gat/Tat	20/21	1	2	FACETS	0.81	0.698	0.93	0.81	0.698	0.93	CLONAL	1	TRUE	1	0.62	2		210	203	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345070	73345070	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	81	305	0	ENST00000377767.4:c.1727A>C	p.Lys576Thr	p.K576T	ENST00000377767	NM_014953.3	576	aAg/aCg	13/21	1	2	FACETS	0.923	0.823	1	0.923	0.823	1	CLONAL	1	TRUE	1	0.62	2		305	283	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514595	103514595	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs966111552	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	98	352	0	ENST00000355739.4:c.1096C>T	p.Arg366Ter	p.R366*	ENST00000355739	NM_000123.3	366	Cga/Tga	8/15	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.62	2		352	302	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30095743	30095743	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	78	357	0	ENST00000331968.5:c.1745A>C	p.Gln582Pro	p.Q582P	ENST00000331968	NM_002742.2	582	cAg/cCg	12/18	1	2	FACETS	0.804	0.713	0.9	0.804	0.713	0.9	CLONAL	1	TRUE	1	0.62	2		357	313	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30102098	30102098	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	119	492	0	ENST00000331968.5:c.1369G>T	p.Asp457Tyr	p.D457Y	ENST00000331968	NM_002742.2	457	Gac/Tac	9/18	1	2	FACETS	0.936	0.852	1	0.936	0.852	1	CLONAL	1	TRUE	1	0.62	2		492	410	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353757	68353757	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs774910383	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	64	241	1	ENST00000487270.1:c.592G>T	p.Glu198Ter	p.E198*	ENST00000487270	NM_133509.3	198	Gaa/Taa	7/11	1	2	FACETS	0.89	0.781	1	0.89	0.781	1	CLONAL	1	TRUE	1	0.62	2		242	232	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610270	81610270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	66	462	1	ENST00000298171.2:c.1868C>T	p.Ala623Val	p.A623V	ENST00000298171	NM_000369.2	623	gCc/gTc	10/10	1	2	FACETS	0.554	0.483	0.631	0.554	0.483	0.631	SUBCLONAL	1	TRUE	1	0.62	2		463	384	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557695	95557695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	116	362	0	ENST00000393063.1:c.5372G>A	p.Arg1791Lys	p.R1791K	ENST00000393063	NM_030621.3	1791	aGa/aAa	26/28	1	2	FACETS	0.998	0.908	1	0.998	0.908	1	CLONAL	1	TRUE	1	0.62	2		362	375	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570365	95570365	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	82	281	0	ENST00000393063.1:c.3368A>C	p.Lys1123Thr	p.K1123T	ENST00000393063	NM_030621.3	1123	aAg/aCg	22/28	1	2	FACETS	0.955	0.853	1	0.955	0.853	1	CLONAL	1	TRUE	1	0.62	2		281	277	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000323	42000323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	95	352	0	ENST00000219905.7:c.2342C>A	p.Ser781Tyr	p.S781Y	ENST00000219905	NM_001164273.1	781	tCt/tAt	7/24	1	2	FACETS	0.849	0.762	0.939	0.849	0.762	0.939	CLONAL	1	TRUE	1	0.62	2		352	361	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028765	42028765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	138	541	0	ENST00000219905.7:c.4303G>A	p.Asp1435Asn	p.D1435N	ENST00000219905	NM_001164273.1	1435	Gat/Aat	13/24	1	2	FACETS	0.996	0.914	1	0.996	0.914	1	CLONAL	1	TRUE	1	0.62	2		541	447	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042025	42042025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199971244	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	109	505	0	ENST00000219905.7:c.6220C>T	p.Arg2074Cys	p.R2074C	ENST00000219905	NM_001164273.1	2074	Cgt/Tgt	17/24	1	2	FACETS	0.902	0.817	0.99	0.902	0.817	0.99	CLONAL	1	TRUE	1	0.62	2		505	390	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052661	42052661	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	139	474	0	ENST00000219905.7:c.7332G>T	p.Glu2444Asp	p.E2444D	ENST00000219905	NM_001164273.1	2444	gaG/gaT	20/24	1	2	FACETS	0.936	0.858	1	0.936	0.858	1	CLONAL	1	TRUE	1	0.62	2		474	479	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749137	43749137	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	159	673	0	ENST00000382044.4:c.1669T>C	p.Ser557Pro	p.S557P	ENST00000382044	NM_001141980.1	557	Tct/Cct	12/28	1	2	FACETS	0.825	0.759	0.893	0.825	0.759	0.893	CLONAL	1	TRUE	1	0.62	2		673	622	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358533	67358533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	100	400	0	ENST00000327367.4:c.41G>A	p.Arg14His	p.R14H	ENST00000327367	NM_005902.3	14	cGc/cAc	1/9	1	2	FACETS	0.906	0.817	0.999	0.906	0.817	0.999	CLONAL	1	TRUE	1	0.62	2		400	356	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473770	67473770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	158	668	0	ENST00000327367.4:c.850G>A	p.Glu284Lys	p.E284K	ENST00000327367	NM_005902.3	284	Gag/Aag	6/9	1	2	FACETS	0.951	0.877	1	0.951	0.877	1	CLONAL	1	TRUE	1	0.62	2		668	536	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679159	88679159	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	119	429	0	ENST00000360948.2:c.878G>T	p.Ser293Ile	p.S293I	ENST00000360948	NM_001012338.2	293	aGc/aTc	8/19	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.62	2		429	378	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726674	88726674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	95	468	1	ENST00000360948.2:c.370G>A	p.Ala124Thr	p.A124T	ENST00000360948	NM_001012338.2	124	Gcc/Acc	4/19	1	2	FACETS	0.786	0.705	0.871	0.786	0.705	0.871	SUBCLONAL	1	TRUE	1	0.62	2		469	390	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639238	3639238	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	185	906	0	ENST00000294008.3:c.4401T>G	p.Cys1467Trp	p.C1467W	ENST00000294008	NM_032444.2	1467	tgT/tgG	12/15	1	2	FACETS	0.843	0.781	0.907	0.843	0.781	0.907	CLONAL	1	TRUE	1	0.62	2		906	708	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788659	3788659	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	108	333	0	ENST00000262367.5:c.4295C>A	p.Ser1432Tyr	p.S1432Y	ENST00000262367	NM_004380.2	1432	tCt/tAt	26/31	1	2	FACETS	0.927	0.839	1	0.927	0.839	1	CLONAL	1	TRUE	1	0.62	2		333	376	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858072	9858072	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	144	642	0	ENST00000330684.3:c.3329C>A	p.Ser1110Ter	p.S1110*	ENST00000330684	NM_001134407.1	1110	tCa/tAa	13/13	1	2	FACETS	0.962	0.883	1	0.962	0.883	1	CLONAL	1	TRUE	1	0.62	2		642	483	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923344	9923344	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	122	540	0	ENST00000330684.3:c.1943A>C	p.Asn648Thr	p.N648T	ENST00000330684	NM_001134407.1	648	aAt/aCt	9/13	1	2	FACETS	0.81	0.736	0.886	0.81	0.736	0.886	CLONAL	1	TRUE	1	0.62	2		540	486	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273941	10273941	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	244	903	0	ENST00000330684.3:c.328G>T	p.Ala110Ser	p.A110S	ENST00000330684	NM_001134407.1	110	Gcc/Tcc	2/13	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.62	2		903	783	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783612	50783612	+	start_lost	Translation_Start_Site	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	75	355	0	ENST00000398568.2:c.3G>T	p.Met1?	p.M1?	ENST00000398568	NM_001042412.1	1	atG/atT	3/18	1	2	FACETS	0.768	0.679	0.862	0.768	0.679	0.862	SUBCLONAL	1	TRUE	1	0.62	2		355	315	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50818289	50818289	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	85	335	0	ENST00000398568.2:c.1867G>T	p.Glu623Ter	p.E623*	ENST00000398568	NM_001042412.1	623	Gaa/Taa	11/18	1	2	FACETS	0.876	0.782	0.974	0.876	0.782	0.974	CLONAL	1	TRUE	1	0.62	2		335	313	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132617	67132617	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	116	442	2	ENST00000412916.2:c.500G>T	p.Arg167Ile	p.R167I	ENST00000412916		167	aGa/aTa	6/6	1	2	FACETS	0.845	0.767	0.926	0.845	0.767	0.926	CLONAL	1	TRUE	1	0.62	2		444	443	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835732	68835732	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	213	622	0	ENST00000261769.5:c.323G>T	p.Arg108Ile	p.R108I	ENST00000261769	NM_004360.3	108	aGa/aTa	3/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.62	2		622	664	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992268	72992268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746207124	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	240	890	2	ENST00000268489.5:c.1777G>A	p.Glu593Lys	p.E593K	ENST00000268489	NM_006885.3	593	Gaa/Aaa	2/10	1	2	FACETS	0.958	0.897	1	0.958	0.897	1	CLONAL	1	TRUE	1	0.62	2		892	808	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349532	89349532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369869329	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	232	801	0	ENST00000301030.4:c.3418G>A	p.Ala1140Thr	p.A1140T	ENST00000301030	NM_001256183.1	1140	Gcc/Acc	9/13	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.62	2		801	748	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805570	89805570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs775234845	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	181	628	1	ENST00000389301.3:c.4138G>T	p.Ala1380Ser	p.A1380S	ENST00000389301	NM_000135.2	1380	Gct/Tct	41/43	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.62	2		629	530	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838195	89838195	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	138	549	0	ENST00000389301.3:c.2042C>A	p.Ser681Tyr	p.S681Y	ENST00000389301	NM_000135.2	681	tCt/tAt	23/43	1	2	FACETS	0.892	0.817	0.97	0.892	0.817	0.97	CLONAL	1	TRUE	1	0.62	2		549	499	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16022758	16022758	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	89	305	0	ENST00000268712.3:c.1894G>T	p.Glu632Ter	p.E632*	ENST00000268712	NM_006311.3	632	Gaa/Taa	17/46	1	2	FACETS	0.835	0.747	0.927	0.835	0.747	0.927	CLONAL	1	TRUE	1	0.62	2		305	344	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049769	16049769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	149	400	0	ENST00000268712.3:c.1003G>A	p.Glu335Lys	p.E335K	ENST00000268712	NM_006311.3	335	Gaa/Aaa	10/46	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.62	2		400	467	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068450	16068450	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	33	120	0	ENST00000268712.3:c.461A>G	p.Glu154Gly	p.E154G	ENST00000268712	NM_006311.3	154	gAa/gGa	5/46	1	2	FACETS	0.977	0.815	1	0.977	0.815	1	CLONAL	1	TRUE	1	0.62	2		120	109	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075295	16075295	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	101	322	0	ENST00000268712.3:c.257G>T	p.Arg86Ile	p.R86I	ENST00000268712	NM_006311.3	86	aGa/aTa	4/46	1	2	FACETS	0.939	0.848	1	0.939	0.848	1	CLONAL	1	TRUE	1	0.62	2		322	347	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325698	30325698	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	27	200	0	ENST00000322652.5:c.1896G>T	p.Met632Ile	p.M632I	ENST00000322652	NM_015355.2	632	atG/atT	16/16	1	2	FACETS	0.708	0.573	0.857	0.708	0.573	0.857	SUBCLONAL	1	TRUE	1	0.62	2		200	123	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686970	37686970	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	156	617	0	ENST00000447079.4:c.3874G>A	p.Glu1292Lys	p.E1292K	ENST00000447079	NM_015083.1	1292	Gag/Aag	14/14	1	2	FACETS	0.977	0.901	1	0.977	0.901	1	CLONAL	1	TRUE	1	0.62	2		617	515	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40458275	40458275	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	257	952	0	ENST00000345506.4:c.1490C>A	p.Ala497Asp	p.A497D	ENST00000345506	NM_003152.3	497	gCc/gAc	14/20	1	2	FACETS	0.919	0.862	0.977	0.919	0.862	0.977	CLONAL	1	TRUE	1	0.62	2		952	902	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244826	41244826	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs80356978	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	138	654	0	ENST00000357654.3:c.2722G>T	p.Glu908Ter	p.E908*	ENST00000357654	NM_007294.3	908	Gaa/Taa	10/23	1	2	FACETS	0.782	0.715	0.852	0.782	0.715	0.852	SUBCLONAL	1	TRUE	1	0.62	2		654	569	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244869	41244869	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781771	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	131	612	0	ENST00000357654.3:c.2679G>T	p.Lys893Asn	p.K893N	ENST00000357654	NM_007294.3	893	aaG/aaT	10/23	1	2	FACETS	0.852	0.778	0.929	0.852	0.778	0.929	CLONAL	1	TRUE	1	0.62	2		612	496	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554341	63554341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767445163	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	182	649	0	ENST00000307078.5:c.398C>T	p.Ala133Val	p.A133V	ENST00000307078	NM_004655.3	133	gCg/gTg	2/11	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.62	2		649	586	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78765281	78765281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1361255662	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	103	299	0	ENST00000306801.3:c.862C>T	p.Pro288Ser	p.P288S	ENST00000306801	NM_020761.2	288	Cct/Tct	7/34	1	2	FACETS	0.944	0.853	1	0.944	0.853	1	CLONAL	1	TRUE	1	0.62	2		299	352	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867622	78867622	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	205	805	0	ENST00000306801.3:c.2358G>T	p.Lys786Asn	p.K786N	ENST00000306801	NM_020761.2	786	aaG/aaT	20/34	1	2	FACETS	0.915	0.851	0.98	0.915	0.851	0.98	CLONAL	1	TRUE	1	0.62	2		805	723	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56409133	56409133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	71	309	1	ENST00000348428.3:c.1640C>T	p.Ala547Val	p.A547V	ENST00000348428	NM_006785.3	547	gCt/gTt	14/17	1	2	FACETS	0.905	0.8	1	0.905	0.8	1	CLONAL	1	TRUE	1	0.62	2		310	253	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212111	5212111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	212	825	0	ENST00000357368.4:c.4920C>A	p.Phe1640Leu	p.F1640L	ENST00000357368	NM_002850.3	1640	ttC/ttA	32/38	1	2	FACETS	0.881	0.821	0.943	0.881	0.821	0.943	CLONAL	1	TRUE	1	0.62	2		825	776	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5256124	5256124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	28	190	0	ENST00000357368.4:c.713G>A	p.Arg238Gln	p.R238Q	ENST00000357368	NM_002850.3	238	cGa/cAa	9/38	1	2	FACETS	0.357	0.286	0.437	0.357	0.286	0.437	SUBCLONAL	1	TRUE	1	0.62	2		190	253	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7163175	7163175	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1283232736	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	152	639	0	ENST00000302850.5:c.1897A>G	p.Asn633Asp	p.N633D	ENST00000302850	NM_000208.2	633	Aac/Gac	9/22	1	2	FACETS	0.908	0.835	0.983	0.908	0.835	0.983	CLONAL	1	TRUE	1	0.62	2		639	540	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130361	11130361	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	201	594	0	ENST00000358026.2:c.2600A>C	p.Lys867Thr	p.K867T	ENST00000358026	NM_001128849.1	867	aAg/aCg	18/36	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.62	2		594	646	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15365064	15365064	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	147	563	0	ENST00000263377.2:c.2057T>G	p.Val686Gly	p.V686G	ENST00000263377	NM_058243.2	686	gTt/gGt	11/20	1	2	FACETS	0.877	0.805	0.951	0.877	0.805	0.951	CLONAL	1	TRUE	1	0.62	2		563	541	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950424	17950424	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	201	664	0	ENST00000458235.1:c.1303A>G	p.Thr435Ala	p.T435A	ENST00000458235	NM_000215.3	435	Aca/Gca	10/24	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.62	2		664	615	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954674	17954674	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	229	869	1	ENST00000458235.1:c.220G>T	p.Ala74Ser	p.A74S	ENST00000458235	NM_000215.3	74	Gcc/Tcc	3/24	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.62	2		870	733	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383677	42383677	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1221821073	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	164	753	0	ENST00000221972.3:c.452T>C	p.Ile151Thr	p.I151T	ENST00000221972	NM_021601.3	151	aTc/aCc	3/5	1	2	FACETS	0.882	0.813	0.952	0.882	0.813	0.952	CLONAL	1	TRUE	1	0.62	2		753	600	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966540	25966540	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	143	655	0	ENST00000435504.4:c.2666C>A	p.Ser889Tyr	p.S889Y	ENST00000435504		889	tCt/tAt	13/13	1	2	FACETS	0.854	0.783	0.928	0.854	0.783	0.928	CLONAL	1	TRUE	1	0.62	2		655	540	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449913	29449913	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	266	1020	0	ENST00000389048.3:c.2942T>G	p.Ile981Ser	p.I981S	ENST00000389048	NM_004304.4	981	aTt/aGt	18/29	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.62	2		1020	834	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234311	39234311	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	84	284	0	ENST00000402219.2:c.2534T>G	p.Leu845Ter	p.L845*	ENST00000402219	NM_005633.3	845	tTa/tGa	16/23	1	2	FACETS	0.866	0.772	0.963	0.866	0.772	0.963	CLONAL	1	TRUE	1	0.62	2		284	313	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027750	48027750	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	76	323	0	ENST00000234420.5:c.2628A>C	p.Glu876Asp	p.E876D	ENST00000234420	NM_000179.2	876	gaA/gaC	4/10	1	2	FACETS	0.869	0.771	0.973	0.869	0.771	0.973	CLONAL	1	TRUE	1	0.62	2		323	282	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61706056	61706056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	140	540	0	ENST00000401558.2:c.3115G>A	p.Glu1039Lys	p.E1039K	ENST00000401558	NM_003400.3	1039	Gaa/Aaa	25/25	1	2	FACETS	0.924	0.847	1	0.924	0.847	1	CLONAL	1	TRUE	1	0.62	2		540	489	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715373	61715373	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	116	499	0	ENST00000401558.2:c.2240G>T	p.Ser747Ile	p.S747I	ENST00000401558	NM_003400.3	747	aGt/aTt	19/25	1	2	FACETS	0.906	0.823	0.992	0.906	0.823	0.992	CLONAL	1	TRUE	1	0.62	2		499	413	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719832	61719832	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	117	494	0	ENST00000401558.2:c.1436A>C	p.Lys479Thr	p.K479T	ENST00000401558	NM_003400.3	479	aAg/aCg	14/25	1	2	FACETS	0.862	0.783	0.944	0.862	0.783	0.944	CLONAL	1	TRUE	1	0.62	2		494	438	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726855	61726855	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	63	295	0	ENST00000401558.2:c.583A>C	p.Lys195Gln	p.K195Q	ENST00000401558	NM_003400.3	195	Aaa/Caa	7/25	1	2	FACETS	0.806	0.705	0.913	0.806	0.705	0.913	CLONAL	1	TRUE	1	0.62	2		295	252	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872622	136872622	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	104	415	1	ENST00000241393.3:c.876C>A	p.Phe292Leu	p.F292L	ENST00000241393	NM_003467.2	292	ttC/ttA	2/2	1	2	FACETS	0.892	0.806	0.982	0.892	0.806	0.982	CLONAL	1	TRUE	1	0.62	2		416	376	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873397	136873397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	88	407	0	ENST00000241393.3:c.101C>T	p.Ala34Val	p.A34V	ENST00000241393	NM_003467.2	34	gCt/gTt	2/2	1	2	FACETS	0.931	0.834	1	0.931	0.834	1	CLONAL	1	TRUE	1	0.62	2		407	305	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285193	198285193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	86	386	0	ENST00000335508.6:c.374C>T	p.Thr125Ile	p.T125I	ENST00000335508	NM_012433.2	125	aCc/aTc	4/25	1	2	FACETS	0.756	0.674	0.842	0.756	0.674	0.842	SUBCLONAL	1	TRUE	1	0.62	2		386	367	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136289	202136289	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	131	446	0	ENST00000358485.4:c.533C>A	p.Ser178Tyr	p.S178Y	ENST00000358485	NM_001080125.1	178	tCt/tAt	3/9	1	2	FACETS	0.877	0.801	0.956	0.877	0.801	0.956	CLONAL	1	TRUE	1	0.62	2		446	482	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242800926	242800926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	160	785	0	ENST00000334409.5:c.65G>A	p.Gly22Glu	p.G22E	ENST00000334409	NM_005018.2	22	gGa/gAa	1/5	1	2	FACETS	0.882	0.813	0.954	0.882	0.813	0.954	CLONAL	1	TRUE	1	0.62	2		785	585	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561319	9561319	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs753315436	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	31	459	0	ENST00000353224.5:c.463G>T	p.Asp155Tyr	p.D155Y	ENST00000353224	NM_177990.2	155	Gat/Tat	4/10	1	2	FACETS	0.249	0.201	0.303	0.249	0.201	0.303	SUBCLONAL	1	TRUE	1	0.62	2		459	402	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024197	31024197	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	147	594	0	ENST00000375687.4:c.3682G>T	p.Glu1228Ter	p.E1228*	ENST00000375687	NM_015338.5	1228	Gaa/Taa	13/13	1	2	FACETS	0.958	0.881	1	0.958	0.881	1	CLONAL	1	TRUE	1	0.62	2		594	495	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31390219	31390219	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	44	456	0	ENST00000328111.2:c.2174A>C	p.Lys725Thr	p.K725T	ENST00000328111	NM_006892.3	725	aAa/aCa	20/23	1	2	FACETS	0.268	0.225	0.317	0.268	0.225	0.317	SUBCLONAL	1	TRUE	1	0.62	2		456	529	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39690063	39690063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	49	155	0	ENST00000361337.2:c.88G>A	p.Asp30Asn	p.D30N	ENST00000361337	NM_003286.2	30	Gat/Aat	3/21	1	2	FACETS	0.782	0.671	0.901	0.782	0.671	0.901	CLONAL	1	TRUE	1	0.62	2		155	202	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39726971	39726971	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	41	150	0	ENST00000361337.2:c.969G>T	p.Glu323Asp	p.E323D	ENST00000361337	NM_003286.2	323	gaG/gaT	11/21	1	2	FACETS	0.931	0.791	1	0.931	0.791	1	CLONAL	1	TRUE	1	0.62	2		150	142	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944600	40944600	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	88	377	0	ENST00000373198.4:c.1902G>T	p.Gln634His	p.Q634H	ENST00000373198	NM_133170.3	634	caG/caT	12/32	0.3	0	FACETS	0.364	0.326	0.404			1	INDETERMINATE	1	TRUE	0	0.62	0		377	296	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252889	36252889	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	92	351	0	ENST00000300305.3:c.473T>G	p.Phe158Cys	p.F158C	ENST00000300305		158	tTt/tGt	4/8	1	2	FACETS	0.824	0.739	0.914	0.824	0.739	0.914	CLONAL	1	TRUE	1	0.62	2		351	360	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657017	45657017	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	160	603	0	ENST00000407780.3:c.139T>G	p.Leu47Val	p.L47V	ENST00000407780	NM_001283052.1	47	Tta/Gta	3/7	1	2	FACETS	0.91	0.839	0.984	0.91	0.839	0.984	CLONAL	1	TRUE	1	0.62	2		603	567	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038196	30038196	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	102	364	0	ENST00000338641.4:c.369G>T	p.Lys123Asn	p.K123N	ENST00000338641	NM_000268.3	123	aaG/aaT	4/16	1	2	FACETS	0.904	0.816	0.996	0.904	0.816	0.996	CLONAL	1	TRUE	1	0.62	2		364	364	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37059066	37059066	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	125	374	0	ENST00000231790.2:c.860A>G	p.Asn287Ser	p.N287S	ENST00000231790	NM_000249.3	287	aAc/aGc	10/19	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.62	2		374	382	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266016	41266016	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	33	249	0	ENST00000349496.5:c.14-1G>A		p.X5_splice	ENST00000349496	NM_001904.3	5			1	2	FACETS	0.505	0.414	0.605	0.505	0.414	0.605	SUBCLONAL	1	TRUE	1	0.62	2		249	211	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165167	47165167	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326993979	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	82	260	1	ENST00000409792.3:c.959G>A	p.Gly320Asp	p.G320D	ENST00000409792	NM_014159.6	320	gGt/gAt	3/21	1	2	FACETS	0.98	0.875	1	0.98	0.875	1	CLONAL	1	TRUE	1	0.62	2		261	270	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165465	47165465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	116	421	0	ENST00000409792.3:c.661G>A	p.Val221Ile	p.V221I	ENST00000409792	NM_014159.6	221	Gtt/Att	3/21	1	2	FACETS	0.906	0.823	0.992	0.906	0.823	0.992	CLONAL	1	TRUE	1	0.62	2		421	413	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49929262	49929262	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	155	522	0	ENST00000296474.3:c.3281G>A	p.Gly1094Glu	p.G1094E	ENST00000296474	NM_002447.2	1094	gGa/gAa	15/20	1	2	FACETS	0.938	0.864	1	0.938	0.864	1	CLONAL	1	TRUE	1	0.62	2		522	533	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114601	73114601	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs775783057	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	29	241	0	ENST00000356692.5:c.982G>T	p.Glu328Ter	p.E328*	ENST00000356692		328	Gaa/Taa	9/9	1	2	FACETS	0.463	0.374	0.562	0.463	0.374	0.562	SUBCLONAL	1	TRUE	1	0.62	2		241	202	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670362	134670362	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	108	510	0	ENST00000398015.3:c.273C>A	p.Phe91Leu	p.F91L	ENST00000398015	NM_004441.4	91	ttC/ttA	3/16	0.3	0	FACETS	0.359	0.325	0.394			1	INDETERMINATE	1	TRUE	0	0.62	0		510	369	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474653	138474653	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	25	466	0	ENST00000289153.2:c.340A>G	p.Arg114Gly	p.R114G	ENST00000289153	NM_006219.2	114	Aga/Gga	2/22	1	2	FACETS	0.175	0.138	0.219	0.175	0.138	0.219	SUBCLONAL	1	TRUE	1	0.62	2		466	460	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178201	142178201	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	56	255	0	ENST00000350721.4:c.7217T>G	p.Leu2406Arg	p.L2406R	ENST00000350721	NM_001184.3	2406	cTt/cGt	43/47	1	2	FACETS	0.886	0.77	1	0.886	0.77	1	CLONAL	1	TRUE	1	0.62	2		255	204	SUCCESS
ATR	545	MSKCC	GRCh37	3	142232476	142232476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755364026	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	80	256	0	ENST00000350721.4:c.4508G>A	p.Arg1503Gln	p.R1503Q	ENST00000350721	NM_001184.3	1503	cGa/cAa	26/47	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.62	2		256	241	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259851	142259851	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	106	399	1	ENST00000350721.4:c.3476T>C	p.Met1159Thr	p.M1159T	ENST00000350721	NM_001184.3	1159	aTg/aCg	18/47	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.62	2		400	342	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916651	178916651	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	80	316	0	ENST00000263967.3:c.38T>C	p.Ile13Thr	p.I13T	ENST00000263967	NM_006218.2	13	aTc/aCc	2/21	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.62	2		316	229	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502876	186502876	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	96	333	0	ENST00000323963.5:c.334G>T	p.Glu112Ter	p.E112*	ENST00000323963		112	Gaa/Taa	4/11	1	2	FACETS	0.798	0.716	0.884	0.798	0.716	0.884	SUBCLONAL	1	TRUE	1	0.62	2		333	388	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980404	1980404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	255	930	1	ENST00000382891.5:c.3866G>A	p.Gly1289Asp	p.G1289D	ENST00000382891	NM_133335.3	1289	gGc/gAc	22/22	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.62	2		931	822	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146523	55146523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	61	313	0	ENST00000257290.5:c.2197G>A	p.Asp733Asn	p.D733N	ENST00000257290	NM_006206.4	733	Gac/Aac	16/23	1	2	FACETS	0.82	0.716	0.93	0.82	0.716	0.93	CLONAL	1	TRUE	1	0.62	2		313	240	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564732	55564732	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	34	427	0	ENST00000288135.5:c.619+1G>A		p.X207_splice	ENST00000288135	NM_000222.2	207			1	2	FACETS	0.302	0.247	0.364	0.302	0.247	0.364	SUBCLONAL	1	TRUE	1	0.62	2		427	363	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953804	55953804	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	132	465	0	ENST00000263923.4:c.3632A>C	p.Lys1211Thr	p.K1211T	ENST00000263923	NM_002253.2	1211	aAa/aCa	27/30	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.62	2		465	388	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970882	55970882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	115	481	0	ENST00000263923.4:c.1915G>A	p.Asp639Asn	p.D639N	ENST00000263923	NM_002253.2	639	Gac/Aac	13/30	1	2	FACETS	0.834	0.756	0.915	0.834	0.756	0.915	CLONAL	1	TRUE	1	0.62	2		481	445	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361171	66361171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	83	313	0	ENST00000273854.3:c.1001C>T	p.Thr334Ile	p.T334I	ENST00000273854	NM_004439.5	334	aCc/aTc	4/18	1	2	FACETS	0.967	0.864	1	0.967	0.864	1	CLONAL	1	TRUE	1	0.62	2		313	277	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007320	143007320	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	55	305	0	ENST00000262992.4:c.2464G>T	p.Glu822Ter	p.E822*	ENST00000262992	NM_001101669.1	822	Gaa/Taa	22/24	1	2	FACETS	0.715	0.618	0.819	0.715	0.618	0.819	SUBCLONAL	1	TRUE	1	0.62	2		305	248	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029259	143029259	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	39	221	0	ENST00000262992.4:c.2361G>T	p.Lys787Asn	p.K787N	ENST00000262992	NM_001101669.1	787	aaG/aaT	21/24	1	2	FACETS	0.691	0.58	0.812	0.691	0.58	0.812	SUBCLONAL	1	TRUE	1	0.62	2		221	182	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271212	153271212	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs770911310	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	37	170	0	ENST00000281708.4:c.566A>G	p.Lys189Arg	p.K189R	ENST00000281708	NM_033632.3	189	aAa/aGa	3/12	1	2	FACETS	0.706	0.59	0.832	0.706	0.59	0.832	SUBCLONAL	1	TRUE	1	0.62	2		170	169	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524374	187524374	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	124	495	0	ENST00000441802.2:c.11306T>C	p.Phe3769Ser	p.F3769S	ENST00000441802	NM_005245.3	3769	tTt/tCt	19/27	1	2	FACETS	0.932	0.85	1	0.932	0.85	1	CLONAL	1	TRUE	1	0.62	2		495	429	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540113	187540113	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	112	406	0	ENST00000441802.2:c.7627A>C	p.Asn2543His	p.N2543H	ENST00000441802	NM_005245.3	2543	Aat/Cat	10/27	1	2	FACETS	0.934	0.847	1	0.934	0.847	1	CLONAL	1	TRUE	1	0.62	2		406	387	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540605	187540605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	71	412	0	ENST00000441802.2:c.7135G>A	p.Asp2379Asn	p.D2379N	ENST00000441802	NM_005245.3	2379	Gac/Aac	10/27	1	2	FACETS	0.806	0.711	0.907	0.806	0.711	0.907	CLONAL	1	TRUE	1	0.62	2		412	284	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541943	187541943	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	119	498	0	ENST00000441802.2:c.5797A>G	p.Thr1933Ala	p.T1933A	ENST00000441802	NM_005245.3	1933	Act/Gct	10/27	1	2	FACETS	0.95	0.865	1	0.95	0.865	1	CLONAL	1	TRUE	1	0.62	2		498	404	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874597	35874597	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	129	463	0	ENST00000303115.3:c.753C>A	p.Phe251Leu	p.F251L	ENST00000303115	NM_002185.3	251	ttC/ttA	6/8	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.62	2		463	413	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945727	38945727	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	60	232	0	ENST00000357387.3:c.4499C>T	p.Ala1500Val	p.A1500V	ENST00000357387	NM_152756.3	1500	gCc/gTc	34/38	1	2	FACETS	0.9	0.787	1	0.9	0.787	1	CLONAL	1	TRUE	1	0.62	2		232	215	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947377	38947377	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	35	164	0	ENST00000357387.3:c.4303G>T	p.Asp1435Tyr	p.D1435Y	ENST00000357387	NM_152756.3	1435	Gat/Tat	32/38	1	2	FACETS	0.733	0.61	0.867	0.733	0.61	0.867	SUBCLONAL	1	TRUE	1	0.62	2		164	154	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950364	38950364	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	87	405	0	ENST00000357387.3:c.3586G>T	p.Glu1196Ter	p.E1196*	ENST00000357387	NM_152756.3	1196	Gaa/Taa	31/38	1	2	FACETS	0.791	0.706	0.88	0.791	0.706	0.88	SUBCLONAL	1	TRUE	1	0.62	2		405	355	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959396	38959396	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	60	287	0	ENST00000357387.3:c.2079C>A	p.Asn693Lys	p.N693K	ENST00000357387	NM_152756.3	693	aaC/aaA	22/38	1	2	FACETS	0.82	0.715	0.931	0.82	0.715	0.931	CLONAL	1	TRUE	1	0.62	2		287	236	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962617	38962617	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	45	295	0	ENST00000357387.3:c.1638G>A	p.Trp546Ter	p.W546*	ENST00000357387	NM_152756.3	546	tgG/tgA	18/38	1	2	FACETS	0.657	0.558	0.764	0.657	0.558	0.764	SUBCLONAL	1	TRUE	1	0.62	2		295	221	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38996935	38996935	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	86	413	0	ENST00000357387.3:c.442C>T	p.Arg148Ter	p.R148*	ENST00000357387	NM_152756.3	148	Cga/Tga	6/38	1	2	FACETS	0.826	0.737	0.919	0.826	0.737	0.919	CLONAL	1	TRUE	1	0.62	2		413	336	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39003697	39003697	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	72	276	0	ENST00000357387.3:c.223G>T	p.Glu75Ter	p.E75*	ENST00000357387	NM_152756.3	75	Gaa/Taa	4/38	1	2	FACETS	0.988	0.876	1	0.988	0.876	1	CLONAL	1	TRUE	1	0.62	2		276	235	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575478	67575478	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	123	332	0	ENST00000274335.5:c.551A>C	p.Asp184Ala	p.D184A	ENST00000274335		184	gAc/gCc	4/15	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.62	2		332	390	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79952236	79952236	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	65	223	0	ENST00000265081.6:c.244G>T	p.Glu82Ter	p.E82*	ENST00000265081	NM_002439.4	82	Gaa/Taa	2/24	1	2	FACETS	0.924	0.812	1	0.924	0.812	1	CLONAL	1	TRUE	1	0.62	2		223	227	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80021286	80021286	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	84	340	0	ENST00000265081.6:c.1355G>T	p.Arg452Ile	p.R452I	ENST00000265081	NM_002439.4	452	aGa/aTa	9/24	1	2	FACETS	0.77	0.685	0.859	0.77	0.685	0.859	SUBCLONAL	1	TRUE	1	0.62	2		340	352	SUCCESS
APC	324	MSKCC	GRCh37	5	112090693	112090693	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	35	207	0	ENST00000257430.4:c.106A>C	p.Lys36Gln	p.K36Q	ENST00000257430	NM_000038.5	36	Aaa/Caa	2/16	1	2	FACETS	0.773	0.644	0.913	0.773	0.644	0.913	CLONAL	1	TRUE	1	0.62	2		207	146	SUCCESS
APC	324	MSKCC	GRCh37	5	112176660	112176660	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	54	248	0	ENST00000257430.4:c.5369G>T	p.Arg1790Ile	p.R1790I	ENST00000257430	NM_000038.5	1790	aGa/aTa	16/16	1	2	FACETS	0.842	0.729	0.961	0.842	0.729	0.961	CLONAL	1	TRUE	1	0.62	2		248	207	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925500	131925500	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs867459964	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	80	226	0	ENST00000265335.6:c.1423C>A	p.Leu475Ile	p.L475I	ENST00000265335		475	Ctt/Att	9/25	1	2	FACETS	0.915	0.815	1	0.915	0.815	1	CLONAL	1	TRUE	1	0.62	2		226	282	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131951738	131951738	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs77642085	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	67	197	0	ENST00000265335.6:c.3080G>T	p.Arg1027Ile	p.R1027I	ENST00000265335		1027	aGa/aTa	20/25	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.62	2		197	186	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513278	149513278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	137	647	2	ENST00000261799.4:c.805C>T	p.Pro269Ser	p.P269S	ENST00000261799	NM_002609.3	269	Cct/Tct	6/23	1	2	FACETS	0.948	0.869	1	0.948	0.869	1	CLONAL	1	TRUE	1	0.62	2		649	466	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045921	180045921	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	107	548	0	ENST00000261937.6:c.2851-1G>A		p.X951_splice	ENST00000261937	NM_182925.4	951			1	2	FACETS	0.943	0.854	1	0.943	0.854	1	CLONAL	1	TRUE	1	0.62	2		548	366	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30676062	30676062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	115	469	0	ENST00000376406.3:c.2294C>T	p.Thr765Ile	p.T765I	ENST00000376406	NM_014641.2	765	aCc/aTc	8/15	1	2	FACETS	0.896	0.814	0.982	0.896	0.814	0.982	CLONAL	1	TRUE	1	0.62	2		469	414	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289240	33289240	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	144	578	0	ENST00000374542.5:c.312G>T	p.Glu104Asp	p.E104D	ENST00000374542	NM_001141970.1	104	gaG/gaT	3/8	1	2	FACETS	0.922	0.846	1	0.922	0.846	1	CLONAL	1	TRUE	1	0.62	2		578	504	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609843	117609843	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	163	516	0	ENST00000368508.3:c.6856G>T	p.Glu2286Ter	p.E2286*	ENST00000368508	NM_002944.2	2286	Gaa/Taa	43/43	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.62	2		516	490	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686322	117686322	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141385549	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	39	240	0	ENST00000368508.3:c.3019G>A	p.Gly1007Arg	p.G1007R	ENST00000368508	NM_002944.2	1007	Gga/Aga	20/43	1	2	FACETS	0.635	0.532	0.748	0.635	0.532	0.748	SUBCLONAL	1	TRUE	1	0.62	2		240	198	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686823	117686823	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	74	400	0	ENST00000368508.3:c.2894T>A	p.Phe965Tyr	p.F965Y	ENST00000368508	NM_002944.2	965	tTt/tAt	19/43	1	2	FACETS	0.815	0.72	0.914	0.815	0.72	0.914	CLONAL	1	TRUE	1	0.62	2		400	293	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710882	117710882	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1476515066	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	19	387	0	ENST00000368508.3:c.1390G>T	p.Ala464Ser	p.A464S	ENST00000368508	NM_002944.2	464	Gcc/Tcc	12/43	1	2	FACETS	0.191	0.144	0.246	0.191	0.144	0.246	SUBCLONAL	1	TRUE	1	0.62	2		387	321	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382257	152382257	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	105	274	0	ENST00000206249.3:c.1367C>A	p.Ser456Tyr	p.S456Y	ENST00000206249	NM_000125.3	456	tCt/tAt	6/8	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.62	2		274	310	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100045	157100045	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	12	59	0	ENST00000346085.5:c.982G>T	p.Gly328Ter	p.G328*	ENST00000346085	NM_020732.3	328	Gga/Tga	1/20	1	2	FACETS	1	0.767	1	1	0.767	1	CLONAL	1	TRUE	1	0.62	2		59	37	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100502	157100502	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771204934	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	27	74	0	ENST00000346085.5:c.1439G>A	p.Gly480Asp	p.G480D	ENST00000346085	NM_020732.3	480	gGc/gAc	1/20	1	2	FACETS	0.907	0.74	1	0.907	0.74	1	CLONAL	1	TRUE	1	0.62	2		74	96	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528546	157528546	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	153	693	0	ENST00000346085.5:c.6271A>C	p.Ile2091Leu	p.I2091L	ENST00000346085	NM_020732.3	2091	Atc/Ctc	20/20	1	2	FACETS	0.848	0.779	0.919	0.848	0.779	0.919	CLONAL	1	TRUE	1	0.62	2		693	582	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14027749	14027749	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	88	311	0	ENST00000405192.2:c.95G>T	p.Arg32Ile	p.R32I	ENST00000405192	NM_001163147.1	32	aGa/aTa	3/12	1	2	FACETS	0.94	0.842	1	0.94	0.842	1	CLONAL	1	TRUE	1	0.62	2		311	302	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739642	41739642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	48	634	0	ENST00000242208.4:c.331G>A	p.Ala111Thr	p.A111T	ENST00000242208	NM_002192.2	111	Gca/Aca	2/3	1	2	FACETS	0.323	0.273	0.378	0.323	0.273	0.378	SUBCLONAL	1	TRUE	1	0.62	2		634	479	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481451	140481451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	138	424	0	ENST00000288602.6:c.1357C>T	p.Pro453Ser	p.P453S	ENST00000288602	NM_004333.4	453	Cct/Tct	11/18	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.62	2		424	416	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524317	148524317	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	72	345	0	ENST00000320356.2:c.667A>T	p.Ile223Phe	p.I223F	ENST00000320356	NM_004456.4	223	Att/Ttt	7/20	1	2	FACETS	0.806	0.712	0.906	0.806	0.712	0.906	CLONAL	1	TRUE	1	0.62	2		345	288	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873896	151873896	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	118	476	0	ENST00000262189.6:c.8642G>T	p.Arg2881Ile	p.R2881I	ENST00000262189	NM_170606.2	2881	aGa/aTa	38/59	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.62	2		476	376	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879203	151879203	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	112	538	0	ENST00000262189.6:c.5742T>A	p.Phe1914Leu	p.F1914L	ENST00000262189	NM_170606.2	1914	ttT/ttA	36/59	1	2	FACETS	0.961	0.872	1	0.961	0.872	1	CLONAL	1	TRUE	1	0.62	2		538	376	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132811	152132811	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	187	618	0	ENST00000262189.6:c.61G>T	p.Glu21Ter	p.E21*	ENST00000262189	NM_170606.2	21	Gag/Tag	1/59	1	2	FACETS	0.984	0.914	1	0.984	0.914	1	CLONAL	1	TRUE	1	0.62	2		618	613	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539127	23539127	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	97	457	0	ENST00000380871.4:c.312G>T	p.Leu104Phe	p.L104F	ENST00000380871	NM_006167.3	104	ttG/ttT	2/2	1	2	FACETS	0.802	0.721	0.888	0.802	0.721	0.888	CLONAL	1	TRUE	1	0.62	2		457	390	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931805	68931805	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	89	397	0	ENST00000288368.4:c.235G>T	p.Asp79Tyr	p.D79Y	ENST00000288368	NM_024870.2	79	Gac/Tac	3/40	1	2	FACETS	0.756	0.675	0.841	0.756	0.675	0.841	SUBCLONAL	1	TRUE	1	0.62	2		397	380	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931896	68931896	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	148	464	0	ENST00000288368.4:c.326T>G	p.Phe109Cys	p.F109C	ENST00000288368	NM_024870.2	109	tTt/tGt	3/40	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.62	2		464	457	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021660	69021660	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs554090253	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	94	369	0	ENST00000288368.4:c.2948G>A	p.Ser983Asn	p.S983N	ENST00000288368	NM_024870.2	983	aGc/aAc	25/40	1	2	FACETS	0.82	0.735	0.908	0.82	0.735	0.908	CLONAL	1	TRUE	1	0.62	2		369	370	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028028	69028028	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	65	411	0	ENST00000288368.4:c.3187A>C	p.Lys1063Gln	p.K1063Q	ENST00000288368	NM_024870.2	1063	Aag/Cag	26/40	1	2	FACETS	0.744	0.651	0.842	0.744	0.651	0.842	SUBCLONAL	1	TRUE	1	0.62	2		411	282	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5462929	5462929	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	69	259	2	ENST00000381577.3:c.490G>T	p.Glu164Ter	p.E164*	ENST00000381577	NM_014143.3	164	Gaa/Taa	4/7	1	2	FACETS	0.781	0.687	0.88	0.781	0.687	0.88	SUBCLONAL	1	TRUE	1	0.62	2		261	285	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5563174	5563174	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	91	296	0	ENST00000397747.3:c.779G>T	p.Arg260Ile	p.R260I	ENST00000397747	NM_025239.3	260	aGa/aTa	6/7	1	2	FACETS	0.804	0.72	0.893	0.804	0.72	0.893	CLONAL	1	TRUE	1	0.62	2		296	365	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485858	8485858	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	75	370	0	ENST00000356435.5:c.2959G>T	p.Asp987Tyr	p.D987Y	ENST00000356435		987	Gat/Tat	17/35	1	2	FACETS	0.823	0.728	0.922	0.823	0.728	0.922	CLONAL	1	TRUE	1	0.62	2		370	294	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636723	8636723	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	85	252	0	ENST00000356435.5:c.186G>T	p.Lys62Asn	p.K62N	ENST00000356435		62	aaG/aaT	2/35	1	2	FACETS	0.933	0.834	1	0.933	0.834	1	CLONAL	1	TRUE	1	0.62	2		252	294	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27168511	27168511	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	59	424	0	ENST00000380036.4:c.383C>A	p.Thr128Asn	p.T128N	ENST00000380036	NM_000459.3	128	aCt/aAt	3/23	1	2	FACETS	0.606	0.525	0.693	0.606	0.525	0.693	SUBCLONAL	1	TRUE	1	0.62	2		424	314	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966671	36966671	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	137	502	0	ENST00000358127.4:c.655T>G	p.Phe219Val	p.F219V	ENST00000358127	NM_001280556.1	219	Ttc/Gtc	6/10	1	2	FACETS	0.969	0.888	1	0.969	0.888	1	CLONAL	1	TRUE	1	0.62	2		502	456	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342691	87342691	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	99	513	0	ENST00000277120.3:c.976G>T	p.Glu326Ter	p.E326*	ENST00000277120		326	Gag/Tag	9/19	1	2	FACETS	0.915	0.825	1	0.915	0.825	1	CLONAL	1	TRUE	1	0.62	2		513	349	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342828	87342828	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	89	379	0	ENST00000277120.3:c.1113G>T	p.Glu371Asp	p.E371D	ENST00000277120		371	gaG/gaT	9/19	1	2	FACETS	0.823	0.736	0.914	0.823	0.736	0.914	CLONAL	1	TRUE	1	0.62	2		379	349	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270558	98270558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	68	165	0	ENST00000331920.6:c.86G>A	p.Gly29Glu	p.G29E	ENST00000331920	NM_000264.3	29	gGa/gAa	1/24	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.62	2		165	181	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894935	101894935	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	116	269	0	ENST00000374994.4:c.488A>G	p.Asp163Gly	p.D163G	ENST00000374994	NM_004612.2	163	gAc/gGc	3/9	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.62	2		269	338	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755947	133755947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	199	557	0	ENST00000318560.5:c.1574C>T	p.Ala525Val	p.A525V	ENST00000318560	NM_005157.4	525	gCc/gTc	10/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.62	2		557	592	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393687	139393687	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	198	898	0	ENST00000277541.6:c.5959G>T	p.Asp1987Tyr	p.D1987Y	ENST00000277541	NM_017617.3	1987	Gac/Tac	32/34	1	2	FACETS	0.888	0.826	0.953	0.888	0.826	0.953	CLONAL	1	TRUE	1	0.62	2		898	719	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20150333	20150333	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	95	350	0	ENST00000379607.5:c.304A>T	p.Ser102Cys	p.S102C	ENST00000379607	NM_001412.3	102	Agt/Tgt	5/7	1	2	FACETS	0.891	0.801	0.985	0.891	0.801	0.985	CLONAL	1	TRUE	1	0.62	2		350	344	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932170	39932170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780523057	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	230	882	0	ENST00000378444.4:c.2429G>A	p.Arg810Gln	p.R810Q	ENST00000378444	NM_001123385.1	810	cGa/cAa	4/15	1	2	FACETS	0.93	0.869	0.992	0.93	0.869	0.992	CLONAL	1	TRUE	1	0.62	2		882	798	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932683	39932683	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	220	947	0	ENST00000378444.4:c.1916T>G	p.Phe639Cys	p.F639C	ENST00000378444	NM_001123385.1	639	tTt/tGt	4/15	1	2	FACETS	0.868	0.809	0.928	0.868	0.809	0.928	CLONAL	1	TRUE	1	0.62	2		947	818	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820533	44820533	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	97	356	0	ENST00000377967.4:c.230T>G	p.Val77Gly	p.V77G	ENST00000377967	NM_021140.2	77	gTt/gGt	3/29	1	2	FACETS	0.972	0.876	1	0.972	0.876	1	CLONAL	1	TRUE	1	0.62	2		356	322	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949115	44949115	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	38	476	0	ENST00000377967.4:c.3676C>A	p.His1226Asn	p.H1226N	ENST00000377967	NM_021140.2	1226	Cat/Aat	25/29	1	2	FACETS	0.255	0.211	0.305	0.255	0.211	0.305	SUBCLONAL	1	TRUE	1	0.62	2		476	480	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041645	47041645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782408699	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	168	697	2	ENST00000377604.3:c.1870G>A	p.Asp624Asn	p.D624N	ENST00000377604	NM_001204468.1	624	Gac/Aac	17/24	1	2	FACETS	0.993	0.918	1	0.993	0.918	1	CLONAL	1	TRUE	1	0.62	2		699	546	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411810	63411810	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	204	914	0	ENST00000330258.3:c.1357C>A	p.Leu453Ile	p.L453I	ENST00000330258	NM_152424.3	453	Ctt/Att	2/2	1	2	FACETS	0.939	0.874	1	0.939	0.874	1	CLONAL	1	TRUE	1	0.62	2		914	701	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338650	70338650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	174	741	4	ENST00000374080.3:c.46C>T	p.Arg16Trp	p.R16W	ENST00000374080		16	Cgg/Tgg	1/45	1	2	FACETS	0.947	0.876	1	0.947	0.876	1	CLONAL	1	TRUE	1	0.62	2		745	593	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855046	76855046	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	92	382	0	ENST00000373344.5:c.5790G>T	p.Lys1930Asn	p.K1930N	ENST00000373344	NM_000489.3	1930	aaG/aaT	25/35	1	2	FACETS	0.865	0.776	0.959	0.865	0.776	0.959	CLONAL	1	TRUE	1	0.62	2		382	343	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890192	76890192	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	66	332	0	ENST00000373344.5:c.4702G>A	p.Val1568Ile	p.V1568I	ENST00000373344	NM_000489.3	1568	Gtt/Att	17/35	1	2	FACETS	0.676	0.591	0.766	0.676	0.591	0.766	SUBCLONAL	1	TRUE	1	0.62	2		332	315	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938337	76938337	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	118	601	0	ENST00000373344.5:c.2411C>A	p.Ser804Tyr	p.S804Y	ENST00000373344	NM_000489.3	804	tCt/tAt	9/35	1	2	FACETS	0.793	0.719	0.87	0.793	0.719	0.87	SUBCLONAL	1	TRUE	1	0.62	2		601	480	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613678	100613678	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	125	451	2	ENST00000308731.7:c.901G>T	p.Glu301Ter	p.E301*	ENST00000308731	NM_000061.2	301	Gaa/Taa	11/19	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.62	2		453	371	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034462	123034462	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	65	378	0	ENST00000355640.3:c.1219C>A	p.Leu407Ile	p.L407I	ENST00000355640		407	Ctt/Att	6/7	1	2	FACETS	0.657	0.574	0.746	0.657	0.574	0.746	SUBCLONAL	1	TRUE	1	0.62	2		378	319	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190069	123190069	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	87	351	0	ENST00000218089.9:c.1288G>T	p.Glu430Ter	p.E430*	ENST00000218089	NM_001042749.1	430	Gaa/Taa	14/35	1	2	FACETS	0.861	0.77	0.956	0.861	0.77	0.956	CLONAL	1	TRUE	1	0.62	2		351	326	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202452	123202452	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	97	393	0	ENST00000218089.9:c.2304T>G	p.Phe768Leu	p.F768L	ENST00000218089	NM_001042749.1	768	ttT/ttG	24/35	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.62	2		393	310	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211862	123211862	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	67	409	0	ENST00000218089.9:c.2729T>A	p.Ile910Lys	p.I910K	ENST00000218089	NM_001042749.1	910	aTa/aAa	27/35	1	2	FACETS	0.691	0.605	0.782	0.691	0.605	0.782	SUBCLONAL	1	TRUE	1	0.62	2		409	313	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224466	123224466	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	120	480	0	ENST00000218089.9:c.3319G>T	p.Glu1107Ter	p.E1107*	ENST00000218089	NM_001042749.1	1107	Gaa/Taa	31/35	1	2	FACETS	0.862	0.784	0.943	0.862	0.784	0.943	CLONAL	1	TRUE	1	0.62	2		480	449	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447309	49447310	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	A	novel	NA	P-0048298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	211	609	0	ENST00000301067.7:c.788_789delinsT	p.Arg263LeufsTer41	p.R263Lfs*41	ENST00000301067	NM_003482.3	263	cGC/cT	6/54	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.62	2		609	647	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	317	512	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.93	2		512	623	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102080254	102080254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193100333	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	162	400	0	ENST00000282441.5:c.991C>T	p.Arg331Trp	p.R331W	ENST00000282441	NM_001130145.2	331	Cgg/Tgg	6/9	1	2	FACETS	0.896	0.832	0.96	0.896	0.832	0.96	CLONAL	1	TRUE	1	0.93	2		400	389	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522598	157522598	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554236040	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	225	514	0	ENST00000346085.5:c.4870C>T	p.Arg1624Ter	p.R1624*	ENST00000346085	NM_020732.3	1624	Cga/Tga	18/20	1	2	FACETS	0.922	0.867	0.977	0.922	0.867	0.977	CLONAL	1	TRUE	1	0.93	2		514	525	SUCCESS
B2M	567	MSKCC	GRCh37	15	45008529	45008529	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	89	192	0	ENST00000558401.1:c.349C>T	p.Arg117Ter	p.R117*	ENST00000558401	NM_004048.2	117	Cga/Tga	3/4	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		192	204	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936983	48936983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690863	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	124	308	0	ENST00000267163.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000267163	NM_000321.2	251	Cga/Tga	8/27	0.10198407593633	3	FACETS	1	0.982	1	0.634	0.582	0.687	INDETERMINATE	1	TRUE	1	0.93	3		308	308	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918694	44918694	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	165	412	0	ENST00000377967.4:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000377967	NM_021140.2	393	Cga/Tga	12/29	0.303266542483354	1	FACETS	0.555	0.518	0.592	0.555	0.518	0.592	INDETERMINATE	1	TRUE	0	0.93	1		412	342	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546847	9546847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	141	564	0	ENST00000353224.5:c.1175C>T	p.Ser392Leu	p.S392L	ENST00000353224	NM_177990.2	392	tCg/tTg	5/10	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		564	289	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521502	8521502	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	183	531	0	ENST00000356435.5:c.736G>T	p.Glu246Ter	p.E246*	ENST00000356435		246	Gaa/Taa	9/35	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		531	400	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504513	103504513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140917545	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	108	302	0	ENST00000355739.4:c.134G>A	p.Arg45His	p.R45H	ENST00000355739	NM_000123.3	45	cGc/cAc	2/15	0.10198407593633	3	FACETS	1	0.974	1	0.597	0.544	0.651	INDETERMINATE	1	TRUE	1	0.93	3		302	285	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247039	53247039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556852808	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	243	672	0	ENST00000375401.3:c.461G>A	p.Arg154His	p.R154H	ENST00000375401	NM_004187.3	154	cGc/cAc	4/26	0.303266542483354	1	FACETS	0.613	0.581	0.645	0.613	0.581	0.645	INDETERMINATE	1	TRUE	0	0.93	1		672	456	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453486	138453486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451809865	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	118	302	0	ENST00000289153.2:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000289153	NM_006219.2	321	cGa/cAa	5/22	0.10198407593633	3	FACETS	1	0.975	1	0.588	0.538	0.64	INDETERMINATE	1	TRUE	1	0.93	3		302	316	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333539	70333539	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs570151139	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	86	553	0	ENST00000373644.4:c.1444A>C	p.Asn482His	p.N482H	ENST00000373644	NM_030625.2	482	Aac/Cac	2/12	0.10198407593633	3	FACETS	0.849	0.759	0.944	0.425	0.379	0.472	INDETERMINATE	1	TRUE	1	0.93	3		553	319	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416138	416138	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	180	316	0	ENST00000399788.2:c.4048C>T	p.Arg1350Ter	p.R1350*	ENST00000399788	NM_001042603.1	1350	Cga/Tga	24/28	0.3	3	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.93	3		316	403	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431664	431664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	219	480	1	ENST00000399788.2:c.2345G>A	p.Arg782Gln	p.R782Q	ENST00000399788	NM_001042603.1	782	cGa/cAa	17/28	0.3	3	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.93	3		481	503	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247028	53247028	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	99	664	1	ENST00000375401.3:c.472G>A	p.Glu158Lys	p.E158K	ENST00000375401	NM_004187.3	158	Gaa/Aaa	4/26	0.303266542483354	1	FACETS	0.266	0.238	0.294	0.266	0.238	0.294	INDETERMINATE	1	TRUE	0	0.93	1		665	429	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778812	76778812	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	137	383	0	ENST00000373344.5:c.6767C>A	p.Ser2256Tyr	p.S2256Y	ENST00000373344	NM_000489.3	2256	tCt/tAt	31/35	0.303266542483354	1	FACETS	0.433	0.399	0.468	0.433	0.399	0.468	INDETERMINATE	1	TRUE	0	0.93	1		383	364	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606679	29606679	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs865931787	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	187	514	0	ENST00000389048.3:c.1201C>T	p.Arg401Ter	p.R401*	ENST00000389048	NM_004304.4	401	Cga/Tga	5/29	1	2	FACETS	0.847	0.79	0.904	0.847	0.79	0.904	CLONAL	1	TRUE	1	0.93	2		514	475	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281802	142281802	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	171	461	0	ENST00000350721.4:c.442G>T	p.Glu148Ter	p.E148*	ENST00000350721	NM_001184.3	148	Gaa/Taa	4/47	0.10198407593633	3	FACETS	1	0.985	1	0.608	0.565	0.652	INDETERMINATE	1	TRUE	1	0.93	3		461	443	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102874103	102874103	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	92	237	0	ENST00000307046.8:c.57C>A	p.Phe19Leu	p.F19L	ENST00000307046	NM_001111285.1	19	ttC/ttA	1/4	1	2	FACETS	0.975	0.886	1	0.975	0.886	1	CLONAL	1	TRUE	1	0.93	2		237	203	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941657	48941657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1060503077	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	95	118	0	ENST00000267163.4:c.967G>T	p.Glu323Ter	p.E323*	ENST00000267163	NM_000321.2	323	Gaa/Taa	10/27	0.10198407593633	3	FACETS	1	0.982	1	0.686	0.624	0.75	INDETERMINATE	1	TRUE	1	0.93	3		118	218	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021785	71021785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs112795301	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	124	229	1	ENST00000318789.4:c.1573C>T	p.Arg525Ter	p.R525*	ENST00000318789	NM_032682.5	525	Cga/Tga	18/21	0.10198407593633	3	FACETS	1	0.988	1	0.74	0.683	0.797	INDETERMINATE	1	TRUE	1	0.93	3		230	264	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564417	139564417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143123347	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	269	922	5	ENST00000308874.7:c.365G>A	p.Arg122His	p.R122H	ENST00000308874		122	cGc/cAc	6/10	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		927	591	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491360	18491360	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	70	196	0	ENST00000266497.5:c.1273G>A	p.Glu425Lys	p.E425K	ENST00000266497		425	Gaa/Aaa	8/31	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		196	153	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546557	9546557	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	128	455	0	ENST00000353224.5:c.1465G>T	p.Glu489Ter	p.E489*	ENST00000353224	NM_177990.2	489	Gaa/Taa	5/10	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		455	315	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24134006	24134006	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	158	340	0	ENST00000263121.7:c.157C>T	p.Arg53Ter	p.R53*	ENST00000263121	NM_003073.3	53	Cga/Tga	2/9	1	2	FACETS	0.965	0.898	1	0.965	0.898	1	CLONAL	1	TRUE	1	0.93	2		340	352	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111168	193111168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1452051467	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	100	304	0	ENST00000367435.3:c.701G>A	p.Arg234Gln	p.R234Q	ENST00000367435	NM_024529.4	234	cGa/cAa	7/17	1	2	FACETS	0.892	0.812	0.974	0.892	0.812	0.974	CLONAL	1	TRUE	1	0.93	2		304	241	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976476	25976476	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	172	329	1	ENST00000435504.4:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000435504		357	Cga/Tga	11/13	1	2	FACETS	0.925	0.862	0.988	0.925	0.862	0.988	CLONAL	1	TRUE	1	0.93	2		330	400	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038418	180038418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530977029	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	247	882	0	ENST00000261937.6:c.3599C>T	p.Ser1200Leu	p.S1200L	ENST00000261937	NM_182925.4	1200	tCg/tTg	27/30	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.93	2		882	489	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950622	38950622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748585755	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	144	374	2	ENST00000357387.3:c.3328C>T	p.Arg1110Cys	p.R1110C	ENST00000357387	NM_152756.3	1110	Cgt/Tgt	31/38	0.10198407593633	3	FACETS	1	0.987	1	0.679	0.629	0.73	INDETERMINATE	1	TRUE	1	0.93	3		376	334	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	242	578	0	ENST00000394830.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000394830	NM_018313.4	710	Cga/Tga	17/30	0.10198407593633	3	FACETS	1	0.994	1	0.746	0.705	0.788	INDETERMINATE	1	TRUE	1	0.93	3		578	511	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430668	80430668	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	174	394	0	ENST00000286548.4:c.340C>T	p.Arg114Ter	p.R114*	ENST00000286548	NM_002072.3	114	Cga/Tga	3/7	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		394	392	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939417	76939417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781932965	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	174	668	0	ENST00000373344.5:c.1331G>A	p.Arg444Gln	p.R444Q	ENST00000373344	NM_000489.3	444	cGa/cAa	9/35	0.303266542483354	1	FACETS	0.414	0.385	0.445	0.414	0.385	0.445	INDETERMINATE	1	TRUE	0	0.93	1		668	483	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61720080	61720080	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	148	359	0	ENST00000401558.2:c.1354A>C	p.Asn452His	p.N452H	ENST00000401558	NM_003400.3	452	Aat/Cat	13/25	0.3	4	FACETS	0.858	0.794	0.922			1	INDETERMINATE	2	TRUE	NA	0.93	4		359	358	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925333	114925333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264066389	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	166	482	0	ENST00000543371.1:c.1411C>T	p.Arg471Cys	p.R471C	ENST00000543371	NM_001198531.1	471	Cgc/Tgc	14/14	0.10198407593633	3	FACETS	1	0.989	1	0.679	0.632	0.727	INDETERMINATE	1	TRUE	1	0.93	3		482	385	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192545	138192545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs970781981	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	151	364	0	ENST00000237289.4:c.181C>T	p.Arg61Trp	p.R61W	ENST00000237289	NM_001270507.1	61	Cgg/Tgg	2/9	1	2	FACETS	0.92	0.853	0.987	0.92	0.853	0.987	CLONAL	1	TRUE	1	0.93	2		364	353	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023160	150023160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	217	478	0	ENST00000253339.5:c.103C>T	p.Arg35Trp	p.R35W	ENST00000253339		35	Cgg/Tgg	1/7	1	2	FACETS	0.939	0.882	0.996	0.939	0.882	0.996	CLONAL	1	TRUE	1	0.93	2		478	497	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265535	152265535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571716552	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	179	537	1	ENST00000206249.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000206249	NM_000125.3	330	Gag/Aag	4/8	1	2	FACETS	0.972	0.909	1	0.972	0.909	1	CLONAL	1	TRUE	1	0.93	2		538	396	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772842	135772842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	269	538	0	ENST00000298552.3:c.2781G>T	p.Lys927Asn	p.K927N	ENST00000298552	NM_001162426.1	927	aaG/aaT	21/23	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		538	599	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115600	108115600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772821016	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	156	372	0	ENST00000278616.4:c.748C>T	p.Arg250Ter	p.R250*	ENST00000278616	NM_000051.3	250	Cga/Tga	7/63	1	2	FACETS	0.856	0.793	0.919	0.856	0.793	0.919	CLONAL	1	TRUE	1	0.93	2		372	392	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604790	48604790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	121	348	0	ENST00000342988.3:c.1612G>A	p.Glu538Lys	p.E538K	ENST00000342988	NM_005359.5	538	Gaa/Aaa	12/12	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.93	2		348	258	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937587	76937587	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	102	365	0	ENST00000373344.5:c.3161C>A	p.Ser1054Tyr	p.S1054Y	ENST00000373344	NM_000489.3	1054	tCt/tAt	9/35	0.303266542483354	1	FACETS	0.422	0.383	0.462	0.422	0.383	0.462	INDETERMINATE	1	TRUE	0	0.93	1		365	278	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041074	42041074	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	241	604	0	ENST00000219905.7:c.5452C>T	p.Arg1818Ter	p.R1818*	ENST00000219905	NM_001164273.1	1818	Cga/Tga	16/24	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		604	582	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56878418	56878418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374875893	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	145	391	0	ENST00000308159.5:c.2357G>A	p.Arg786Gln	p.R786Q	ENST00000308159	NM_014669.4	786	cGa/cAa	22/22	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		391	332	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254623	16254623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749814808	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	166	424	0	ENST00000375759.3:c.1888C>T	p.Arg630Cys	p.R630C	ENST00000375759	NM_015001.2	630	Cgt/Tgt	11/15	1	2	FACETS	0.994	0.928	1	0.994	0.928	1	CLONAL	1	TRUE	1	0.93	2		424	359	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698180	47698180	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63751411	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	102	182	0	ENST00000233146.2:c.1738G>T	p.Glu580Ter	p.E580*	ENST00000233146	NM_000251.2	580	Gaa/Taa	11/16	1	2	FACETS	0.954	0.871	1	0.954	0.871	1	CLONAL	1	TRUE	1	0.93	2		182	230	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347200	347200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	216	744	0	ENST00000262320.3:c.1811G>T	p.Arg604Ile	p.R604I	ENST00000262320	NM_003502.3	604	aGa/aTa	7/11	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		744	464	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096135	178096135	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	189	458	1	ENST00000397062.3:c.1196C>A	p.Ser399Tyr	p.S399Y	ENST00000397062	NM_006164.4	399	tCt/tAt	5/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.93	2		459	376	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952049	178952049	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242945375	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	128	299	0	ENST00000263967.3:c.3104C>T	p.Ala1035Val	p.A1035V	ENST00000263967	NM_006218.2	1035	gCt/gTt	21/21	0.10198407593633	3	FACETS	1	0.986	1	0.686	0.632	0.74	INDETERMINATE	1	TRUE	1	0.93	3		299	294	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458147	120458147	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1325403451	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	214	681	1	ENST00000256646.2:c.7198C>T	p.Arg2400Ter	p.R2400*	ENST00000256646	NM_024408.3	2400	Cga/Tga	34/34	1	2	FACETS	0.959	0.901	1	0.959	0.901	1	CLONAL	1	TRUE	1	0.93	2		682	480	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165843	47165843	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	206	504	0	ENST00000409792.3:c.283G>T	p.Glu95Ter	p.E95*	ENST00000409792	NM_014159.6	95	Gaa/Taa	3/21	0.10198407593633	3	FACETS	1	0.991	1	0.696	0.653	0.74	INDETERMINATE	1	TRUE	1	0.93	3		504	466	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554305	81554305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777252114	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	246	350	0	ENST00000298171.2:c.325C>T	p.Arg109Trp	p.R109W	ENST00000298171	NM_000369.2	109	Cgg/Tgg	4/10	1	2	FACETS	0.98	0.956	1	1	0.996	1	CLONAL	2	TRUE	1	0.93	2		350	270	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11269467	11269467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	211	493	0	ENST00000361445.4:c.3703C>T	p.Arg1235Trp	p.R1235W	ENST00000361445	NM_004958.3	1235	Cgg/Tgg	25/58	1	2	FACETS	0.984	0.925	1	0.984	0.925	1	CLONAL	1	TRUE	1	0.93	2		493	461	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259409	89259409	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	149	500	0	ENST00000336596.2:c.553G>T	p.Asp185Tyr	p.D185Y	ENST00000336596	NM_005233.5	185	Gat/Tat	3/17	0.10198407593633	3	FACETS	1	0.988	1	0.682	0.633	0.733	INDETERMINATE	1	TRUE	1	0.93	3		500	344	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066675	94066675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	209	473	0	ENST00000369303.4:c.1084G>A	p.Asp362Asn	p.D362N	ENST00000369303	NM_004440.3	362	Gat/Aat	5/17	1	2	FACETS	0.965	0.906	1	0.965	0.906	1	CLONAL	1	TRUE	1	0.93	2		473	466	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004242	29004242	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766441216	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	131	268	0	ENST00000282397.4:c.1051C>T	p.Arg351Trp	p.R351W	ENST00000282397	NM_002019.4	351	Cgg/Tgg	8/30	0.3	1	FACETS	0.461	0.424	0.498	0.461	0.424	0.498	INDETERMINATE	1	TRUE	0	0.93	1		268	327	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562982	29562982	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1306237220	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	169	465	0	ENST00000356175.3:c.3917G>A	p.Arg1306Gln	p.R1306Q	ENST00000356175	NM_000267.3	1306	cGa/cAa	29/57	1	2	FACETS	0.834	0.775	0.894	0.834	0.775	0.894	CLONAL	1	TRUE	1	0.93	2		465	436	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692874	89692874	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786204930	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	125	219	0	ENST00000371953.3:c.358G>A	p.Ala120Thr	p.A120T	ENST00000371953	NM_000314.4	120	Gca/Aca	5/9	0.10198407593633	3	FACETS	1	0.987	1	0.713	0.658	0.77	INDETERMINATE	1	TRUE	1	0.93	3		219	276	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366129	15366129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1468704458	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	192	533	5	ENST00000263377.2:c.2026C>T	p.Arg676Trp	p.R676W	ENST00000263377	NM_058243.2	676	Cgg/Tgg	10/20	1	2	FACETS	0.945	0.885	1	0.945	0.885	1	CLONAL	1	TRUE	1	0.93	2		538	437	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130163	143130163	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	161	356	0	ENST00000262992.4:c.853G>T	p.Glu285Ter	p.E285*	ENST00000262992	NM_001101669.1	285	Gaa/Taa	11/24	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.93	2		356	341	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163542	32163542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1187763031	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	178	629	0	ENST00000375023.3:c.5684C>T	p.Ser1895Phe	p.S1895F	ENST00000375023	NM_004557.3	1895	tCt/tTt	30/30	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.93	2		629	376	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956553	93956553	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1035177735	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	143	293	0	ENST00000369303.4:c.2683C>T	p.Arg895Ter	p.R895*	ENST00000369303	NM_004440.3	895	Cga/Tga	15/17	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.93	2		293	281	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148513849	148513849	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	160	405	0	ENST00000320356.2:c.1432G>T	p.Glu478Ter	p.E478*	ENST00000320356	NM_004456.4	478	Gaa/Taa	12/20	0.10198407593633	3	FACETS	1	0.989	1	0.698	0.649	0.747	INDETERMINATE	1	TRUE	1	0.93	3		405	361	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412494	80412494	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	166	315	0	ENST00000286548.4:c.547C>T	p.Arg183Ter	p.R183*	ENST00000286548	NM_002072.3	183	Cga/Tga	4/7	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		315	372	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346314	73346314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs575448022	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	147	243	0	ENST00000377767.4:c.1486G>A	p.Glu496Lys	p.E496K	ENST00000377767	NM_014953.3	496	Gaa/Aaa	10/21	0.10198407593633	3	FACETS	1	0.99	1	0.749	0.696	0.803	INDETERMINATE	1	TRUE	1	0.93	3		243	309	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727423	66727423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1049040928	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	191	386	1	ENST00000307102.5:c.139C>T	p.Arg47Ter	p.R47*	ENST00000307102	NM_002755.3	47	Cga/Tga	2/11	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		387	391	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236086	108236086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782292	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	157	444	0	ENST00000278616.4:c.9022C>T	p.Arg3008Cys	p.R3008C	ENST00000278616	NM_000051.3	3008	Cgt/Tgt	63/63	1	2	FACETS	0.864	0.801	0.927	0.864	0.801	0.927	CLONAL	1	TRUE	1	0.93	2		444	391	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546725	9546725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210292896	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	97	395	0	ENST00000353224.5:c.1297C>T	p.Arg433Trp	p.R433W	ENST00000353224	NM_177990.2	433	Cgg/Tgg	5/10	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		395	221	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938406	76938406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	148	618	0	ENST00000373344.5:c.2342G>A	p.Arg781Gln	p.R781Q	ENST00000373344	NM_000489.3	781	cGa/cAa	9/35	0.303266542483354	1	FACETS	0.379	0.349	0.41	0.379	0.349	0.41	INDETERMINATE	1	TRUE	0	0.93	1		618	449	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114842	108114842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145355104	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	155	380	0	ENST00000278616.4:c.659C>T	p.Ala220Val	p.A220V	ENST00000278616	NM_000051.3	220	gCg/gTg	6/63	1	2	FACETS	0.944	0.877	1	0.944	0.877	1	CLONAL	1	TRUE	1	0.93	2		380	353	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386512	81386512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	128	350	0	ENST00000222390.5:c.475G>A	p.Glu159Lys	p.E159K	ENST00000222390	NM_000601.4	159	Gaa/Aaa	4/18	0.10198407593633	3	FACETS	1	0.986	1	0.684	0.63	0.738	INDETERMINATE	1	TRUE	1	0.93	3		350	295	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014097	70014097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757354709	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	192	498	0	ENST00000394351.3:c.958G>A	p.Val320Ile	p.V320I	ENST00000394351	NM_000248.3	320	Gtt/Att	9/9	0.10198407593633	3	FACETS	1	0.991	1	0.7	0.655	0.745	INDETERMINATE	1	TRUE	1	0.93	3		498	432	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461167	120461167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs983208690	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	91	335	0	ENST00000256646.2:c.5791C>T	p.Arg1931Cys	p.R1931C	ENST00000256646	NM_024408.3	1931	Cgc/Tgc	32/34	1	2	FACETS	0.648	0.582	0.717	0.648	0.582	0.717	SUBCLONAL	1	TRUE	1	0.93	2		335	302	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868912	117868912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746064262	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	98	278	0	ENST00000297338.2:c.787G>A	p.Asp263Asn	p.D263N	ENST00000297338	NM_006265.2	263	Gat/Aat	7/14	1	2	FACETS	0.878	0.798	0.96	0.878	0.798	0.96	CLONAL	1	TRUE	1	0.93	2		278	240	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201885	152201885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778449608	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	132	289	0	ENST00000206249.3:c.739G>A	p.Glu247Lys	p.E247K	ENST00000206249	NM_000125.3	247	Gaa/Aaa	3/8	1	2	FACETS	0.982	0.908	1	0.982	0.908	1	CLONAL	1	TRUE	1	0.93	2		289	289	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376627	8376627	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	132	413	0	ENST00000356435.5:c.4486C>T	p.Arg1496Ter	p.R1496*	ENST00000356435		1496	Cga/Tga	27/35	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		413	320	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149516607	149516607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148272095	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	228	750	2	ENST00000261799.4:c.4C>T	p.Arg2Trp	p.R2W	ENST00000261799	NM_002609.3	2	Cgg/Tgg	2/23	1	2	FACETS	0.969	0.913	1	0.969	0.913	1	CLONAL	1	TRUE	1	0.93	2		752	506	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143129648	143129648	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs768272420	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	157	346	0	ENST00000262992.4:c.1002G>T	p.Glu334Asp	p.E334D	ENST00000262992	NM_001101669.1	334	gaG/gaT	12/24	1	2	FACETS	0.965	0.897	1	0.965	0.897	1	CLONAL	1	TRUE	1	0.93	2		346	350	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672759	86672759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	126	298	0	ENST00000274376.6:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000274376	NM_002890.2	749	cGa/cAa	17/25	0.10198407593633	3	FACETS	1	0.979	1	0.605	0.555	0.656	INDETERMINATE	1	TRUE	1	0.93	3		298	328	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012219	16012219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	200	325	0	ENST00000268712.3:c.2063G>A	p.Arg688Gln	p.R688Q	ENST00000268712	NM_006311.3	688	cGa/cAa	19/46	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.93	2		325	406	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253212	133253212	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	162	548	0	ENST00000320574.5:c.829G>C	p.Glu277Gln	p.E277Q	ENST00000320574	NM_006231.2	277	Gag/Cag	9/49	1	2	FACETS	0.891	0.828	0.955	0.891	0.828	0.955	CLONAL	1	TRUE	1	0.93	2		548	391	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740668	58740668	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs759850701	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	239	530	0	ENST00000305921.3:c.1573G>T	p.Glu525Ter	p.E525*	ENST00000305921	NM_003620.3	525	Gaa/Taa	6/6	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.93	2		530	508	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273266	198273266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	171	474	0	ENST00000335508.6:c.944G>A	p.Arg315Gln	p.R315Q	ENST00000335508	NM_012433.2	315	cGa/cAa	8/25	1	2	FACETS	0.867	0.807	0.929	0.867	0.807	0.929	CLONAL	1	TRUE	1	0.93	2		474	424	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181425	185181425	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1435276633	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	165	368	0	ENST00000265026.3:c.1366C>T	p.Arg456Ter	p.R456*	ENST00000265026	NM_004721.4	456	Cga/Tga	8/14	0.10198407593633	3	FACETS	1	0.985	1	0.623	0.579	0.669	INDETERMINATE	1	TRUE	1	0.93	3		368	417	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196499	106196499	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs527895107	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	108	428	0	ENST00000380013.4:c.4832C>A	p.Ser1611Tyr	p.S1611Y	ENST00000380013	NM_001127208.2	1611	tCt/tAt	11/11	1	2	FACETS	0.988	0.906	1	0.988	0.906	1	CLONAL	1	TRUE	1	0.93	2		428	235	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124717	108124717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751515818	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	146	349	0	ENST00000278616.4:c.2075G>A	p.Arg692His	p.R692H	ENST00000278616	NM_000051.3	692	cGc/cAc	13/63	1	2	FACETS	0.963	0.893	1	0.963	0.893	1	CLONAL	1	TRUE	1	0.93	2		349	326	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331962	81331962	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs201768315	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	81	213	0	ENST00000222390.5:c.2122C>T	p.Arg708Ter	p.R708*	ENST00000222390	NM_000601.4	708	Cga/Tga	18/18	0.10198407593633	3	FACETS	1	0.979	1	0.686	0.619	0.754	INDETERMINATE	1	TRUE	1	0.93	3		213	186	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651331	52651331	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	187	405	0	ENST00000394830.3:c.1765G>A	p.Asp589Asn	p.D589N	ENST00000394830	NM_018313.4	589	Gac/Aac	15/30	0.10198407593633	3	FACETS	1	0.992	1	0.738	0.692	0.785	INDETERMINATE	1	TRUE	1	0.93	3		405	399	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950099	38950099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757900166	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	157	502	1	ENST00000357387.3:c.3851C>T	p.Ser1284Leu	p.S1284L	ENST00000357387	NM_152756.3	1284	tCg/tTg	31/38	0.10198407593633	3	FACETS	1	0.988	1	0.672	0.624	0.721	INDETERMINATE	1	TRUE	1	0.93	3		503	368	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709529	176709529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777258117	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	124	283	0	ENST00000439151.2:c.5956C>T	p.Arg1986Cys	p.R1986C	ENST00000439151	NM_022455.4	1986	Cgc/Tgc	19/23	1	2	FACETS	0.936	0.861	1	0.936	0.861	1	CLONAL	1	TRUE	1	0.93	2		283	285	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106162587	106162587	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	108	225	1	ENST00000380013.4:c.3500+1G>A		p.X1167_splice	ENST00000380013	NM_001127208.2	1167			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.93	2		226	217	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040978	42040978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755286142	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	266	622	0	ENST00000219905.7:c.5356C>T	p.Arg1786Trp	p.R1786W	ENST00000219905	NM_001164273.1	1786	Cgg/Tgg	16/24	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		622	580	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243774	41243774	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs431825399	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	211	592	0	ENST00000357654.3:c.3774G>T	p.Glu1258Asp	p.E1258D	ENST00000357654	NM_007294.3	1258	gaG/gaT	10/23	1	2	FACETS	0.995	0.936	1	0.995	0.936	1	CLONAL	1	TRUE	1	0.93	2		592	456	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912075	76912075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782228142	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	221	401	0	ENST00000373344.5:c.4189G>A	p.Glu1397Lys	p.E1397K	ENST00000373344	NM_000489.3	1397	Gaa/Aaa	13/35	0.303266542483354	1	FACETS	0.607	0.573	0.64	0.607	0.573	0.64	INDETERMINATE	1	TRUE	0	0.93	1		401	419	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381567	81381567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370760302	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	97	203	0	ENST00000222390.5:c.494C>T	p.Ser165Leu	p.S165L	ENST00000222390	NM_000601.4	165	tCg/tTg	5/18	0.10198407593633	3	FACETS	1	0.982	1	0.685	0.624	0.748	INDETERMINATE	1	TRUE	1	0.93	3		203	223	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133894	55133894	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	90	319	0	ENST00000257290.5:c.1107G>T	p.Lys369Asn	p.K369N	ENST00000257290	NM_006206.4	369	aaG/aaT	7/23	1	2	FACETS	0.949	0.861	1	0.949	0.861	1	CLONAL	1	TRUE	1	0.93	2		319	204	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026290	48026290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147737737	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	134	409	2	ENST00000234420.5:c.1168G>A	p.Asp390Asn	p.D390N	ENST00000234420	NM_000179.2	390	Gat/Aat	4/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.93	2		411	252	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594066	158594066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769751827	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	126	343	0	ENST00000263640.3:c.1507G>A	p.Asp503Asn	p.D503N	ENST00000263640	NM_001105.4	503	Gac/Aac	11/11	1	2	FACETS	0.866	0.796	0.937	0.866	0.796	0.937	CLONAL	1	TRUE	1	0.93	2		343	313	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521540	46521540	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	217	439	0	ENST00000262741.5:c.868G>T	p.Glu290Ter	p.E290*	ENST00000262741	NM_003629.3	290	Gaa/Taa	7/10	1	2	FACETS	0.97	0.912	1	0.97	0.912	1	CLONAL	1	TRUE	1	0.93	2		439	481	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716359	18716359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	130	296	0	ENST00000266497.5:c.3706G>A	p.Glu1236Lys	p.E1236K	ENST00000266497		1236	Gaa/Aaa	26/31	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		296	282	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638900	176638900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763399938	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	254	561	0	ENST00000439151.2:c.3500G>A	p.Arg1167His	p.R1167H	ENST00000439151	NM_022455.4	1167	cGc/cAc	5/23	1	2	FACETS	0.967	0.914	1	0.967	0.914	1	CLONAL	1	TRUE	1	0.93	2		561	565	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341130	8341130	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	120	380	0	ENST00000356435.5:c.5086G>T	p.Gly1696Ter	p.G1696*	ENST00000356435		1696	Gga/Tga	30/35	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		380	281	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842075	3842075	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1302427305	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	133	334	0	ENST00000262367.5:c.1237C>T	p.Arg413Ter	p.R413*	ENST00000262367	NM_004380.2	413	Cga/Tga	5/31	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		334	339	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800433	32800433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	312	974	0	ENST00000374899.4:c.1114G>A	p.Glu372Lys	p.E372K	ENST00000374899	NM_018833.2	372	Gaa/Aaa	6/12	1	2	FACETS	0.891	0.845	0.937	0.891	0.845	0.937	CLONAL	1	TRUE	1	0.93	2		974	753	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410987	31410987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1236254462	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	196	664	0	ENST00000344624.3:c.3533G>A	p.Arg1178Gln	p.R1178Q	ENST00000344624		1178	cGa/cAa	28/33	0.213346112869584	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		664	457	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504048	123504048	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	106	285	0	ENST00000371139.4:c.224G>T	p.Arg75Ile	p.R75I	ENST00000371139	NM_001114937.2	75	aGa/aTa	3/4	0.303266542483354	1	FACETS	0.575	0.528	0.622	0.575	0.528	0.622	INDETERMINATE	1	TRUE	0	0.93	1		285	212	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29106023	29106023	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587782152	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	100	254	0	ENST00000328354.6:c.817G>T	p.Glu273Ter	p.E273*	ENST00000328354	NM_007194.3	273	Gaa/Taa	7/15	1	2	FACETS	0.765	0.694	0.839	0.765	0.694	0.839	SUBCLONAL	1	TRUE	1	0.93	2		254	281	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260177	149260177	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	209	577	0	ENST00000360632.3:c.716G>T	p.Arg239Ile	p.R239I	ENST00000360632	NM_015472.4	239	aGa/aTa	4/7	0.10198407593633	3	FACETS	1	0.992	1	0.705	0.662	0.748	INDETERMINATE	1	TRUE	1	0.93	3		577	467	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128246746	128246746	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	202	591	0	ENST00000265960.3:c.1183C>T	p.Arg395Ter	p.R395*	ENST00000265960	NM_001006617.1	395	Cga/Tga	9/12	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		591	507	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262885	46262885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761607812	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	167	408	0	ENST00000371998.3:c.1058G>A	p.Arg353Gln	p.R353Q	ENST00000371998		353	cGa/cAa	10/23	1	2	FACETS	0.845	0.785	0.906	0.845	0.785	0.906	CLONAL	1	TRUE	1	0.93	2		408	425	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39762950	39762950	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	116	315	0	ENST00000288319.7:c.886C>A	p.Leu296Ile	p.L296I	ENST00000288319	NM_182918.3	296	Ctt/Att	9/10	0.213346112869584	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		315	298	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020225	123020225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	170	584	0	ENST00000355640.3:c.713G>A	p.Arg238Gln	p.R238Q	ENST00000355640		238	cGa/cAa	2/7	0.303266542483354	1	FACETS	0.434	0.403	0.465	0.434	0.403	0.465	INDETERMINATE	1	TRUE	0	0.93	1		584	451	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148504755	148504755	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	208	516	0	ENST00000320356.2:c.2239G>T	p.Glu747Ter	p.E747*	ENST00000320356	NM_004456.4	747	Gaa/Taa	20/20	0.10198407593633	3	FACETS	1	0.991	1	0.687	0.645	0.73	INDETERMINATE	1	TRUE	1	0.93	3		516	477	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80057459	80057459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200337887	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	90	232	0	ENST00000265081.6:c.1858G>A	p.Asp620Asn	p.D620N	ENST00000265081	NM_002439.4	620	Gac/Aac	13/24	0.10198407593633	3	FACETS	1	0.964	1	0.576	0.52	0.634	INDETERMINATE	1	TRUE	1	0.93	3		232	246	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451474	187451474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145456310	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	157	381	1	ENST00000232014.4:c.8C>T	p.Ser3Leu	p.S3L	ENST00000232014	NM_001130845.1	3	tCg/tTg	3/10	0.10198407593633	3	FACETS	1	0.99	1	0.736	0.685	0.787	INDETERMINATE	1	TRUE	1	0.93	3		382	336	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003374	42003374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372252914	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	189	423	1	ENST00000219905.7:c.2911C>T	p.Arg971Trp	p.R971W	ENST00000219905	NM_001164273.1	971	Cgg/Tgg	8/24	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		424	420	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215251	123215251	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	171	294	0	ENST00000218089.9:c.2797G>T	p.Glu933Ter	p.E933*	ENST00000218089	NM_001042749.1	933	Gaa/Taa	28/35	0.303266542483354	1	FACETS	0.7	0.66	0.74	0.7	0.66	0.74	INDETERMINATE	1	TRUE	0	0.93	1		294	281	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702410	47702410	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs267607986	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	69	194	0	ENST00000233146.2:c.2005+1G>A		p.X669_splice	ENST00000233146	NM_000251.2	669			1	2	FACETS	0.91	0.813	1	0.91	0.813	1	CLONAL	1	TRUE	1	0.93	2		194	163	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964903	25964903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561088610	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	151	387	0	ENST00000435504.4:c.4303C>T	p.Arg1435Trp	p.R1435W	ENST00000435504		1435	Cgg/Tgg	13/13	1	2	FACETS	0.966	0.898	1	0.966	0.898	1	CLONAL	1	TRUE	1	0.93	2		387	336	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628125	187628125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1196972484	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	282	715	0	ENST00000441802.2:c.2857G>A	p.Asp953Asn	p.D953N	ENST00000441802	NM_005245.3	953	Gat/Aat	2/27	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.93	2		715	585	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921447	39921447	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	115	597	0	ENST00000378444.4:c.4373T>C	p.Val1458Ala	p.V1458A	ENST00000378444	NM_001123385.1	1458	gTc/gCc	10/15	0.303266542483354	1	FACETS	0.37	0.336	0.404	0.37	0.336	0.404	INDETERMINATE	1	TRUE	0	0.93	1		597	358	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836804	151836804	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	217	451	0	ENST00000262189.6:c.14416C>T	p.Arg4806Ter	p.R4806*	ENST00000262189	NM_170606.2	4806	Cga/Tga	56/59	0.10198407593633	3	FACETS	0.793	0.748	0.838	0.793	0.748	0.838	INDETERMINATE	2	TRUE	1	0.93	3		451	431	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961137	79961137	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs569679162	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	330	476	0	ENST00000265081.6:c.534G>T	p.Lys178Asn	p.K178N	ENST00000265081	NM_002439.4	178	aaG/aaT	3/24	0.10198407593633	3	FACETS	1	0.995	1	1	0.995	1	INDETERMINATE	2	TRUE	1	0.93	3		476	432	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907720	76907720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	239	527	0	ENST00000373344.5:c.4441C>T	p.Arg1481Trp	p.R1481W	ENST00000373344	NM_000489.3	1481	Cgg/Tgg	15/35	0.303266542483354	1	FACETS	0.593	0.561	0.625	0.593	0.561	0.625	INDETERMINATE	1	TRUE	0	0.93	1		527	464	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937356	76937356	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	162	370	0	ENST00000373344.5:c.3392G>T	p.Arg1131Ile	p.R1131I	ENST00000373344	NM_000489.3	1131	aGa/aTa	9/35	0.303266542483354	1	FACETS	0.595	0.557	0.634	0.595	0.557	0.634	INDETERMINATE	1	TRUE	0	0.93	1		370	313	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251901	153251901	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	168	385	0	ENST00000281708.4:c.1105G>T	p.Glu369Ter	p.E369*	ENST00000281708	NM_033632.3	369	Gaa/Taa	7/12	1	2	FACETS	0.854	0.794	0.915	0.854	0.794	0.915	CLONAL	1	TRUE	1	0.93	2		385	423	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210116	55210116	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778638117	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	184	396	0	ENST00000275493.2:c.226C>A	p.Leu76Ile	p.L76I	ENST00000275493	NM_005228.3	76	Ctt/Att	2/28	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		396	388	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889193	76889193	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	116	269	0	ENST00000373344.5:c.4817G>T	p.Ser1606Ile	p.S1606I	ENST00000373344	NM_000489.3	1606	aGt/aTt	18/35	0.303266542483354	1	FACETS	0.604	0.558	0.65	0.604	0.558	0.65	INDETERMINATE	1	TRUE	0	0.93	1		269	221	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861577	152861577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149734965	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	111	737	0	ENST00000406277.2:c.175G>A	p.Glu59Lys	p.E59K	ENST00000406277	NM_152274.4	59	Gag/Aag	4/7	0.303266542483354		FACETS		0.267	0.324				INDETERMINATE	1	TRUE	0	0.93	1		737	433	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850777	63850777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374377066	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	161	431	0	ENST00000279873.7:c.1555G>A	p.Glu519Lys	p.E519K	ENST00000279873	NM_032199.2	519	Gaa/Aaa	10/10	0.10198407593633	3	FACETS	1	0.988	1	0.664	0.617	0.712	INDETERMINATE	1	TRUE	1	0.93	3		431	382	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211219	36211219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765836382	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	381	1086	1	ENST00000222270.7:c.970G>A	p.Glu324Lys	p.E324K	ENST00000222270	NM_014727.1	324	Gaa/Aaa	3/37	1	2	FACETS	0.978	0.934	1	0.978	0.934	1	CLONAL	1	TRUE	1	0.93	2		1087	838	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557804	187557804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1321370436	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	159	402	0	ENST00000441802.2:c.3907G>A	p.Glu1303Lys	p.E1303K	ENST00000441802	NM_005245.3	1303	Gaa/Aaa	5/27	1	2	FACETS	0.95	0.883	1	0.95	0.883	1	CLONAL	1	TRUE	1	0.93	2		402	360	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99203949	99203949	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1370549873	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	89	267	0	ENST00000074304.5:c.2812C>T	p.Arg938Ter	p.R938*	ENST00000074304	NM_001134224.1	938	Cga/Tga	26/26	1	2	FACETS	0.766	0.69	0.844	0.766	0.69	0.844	SUBCLONAL	1	TRUE	1	0.93	2		267	250	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015053	27015053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151098324	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	162	422	0	ENST00000335756.4:c.155G>A	p.Arg52Gln	p.R52Q	ENST00000335756	NM_001809.3	52	cGa/cAa	2/5	1	2	FACETS	0.862	0.801	0.925	0.862	0.801	0.925	CLONAL	1	TRUE	1	0.93	2		422	404	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129983	55129983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763718380	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	226	560	1	ENST00000257290.5:c.517G>A	p.Asp173Asn	p.D173N	ENST00000257290	NM_006206.4	173	Gac/Aac	4/23	1	2	FACETS	0.946	0.89	1	0.946	0.89	1	CLONAL	1	TRUE	1	0.93	2		561	514	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305238	39305238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs890472037	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	202	502	0	ENST00000373001.3:c.1187G>A	p.Arg396Gln	p.R396Q	ENST00000373001	NM_022157.3	396	cGa/cAa	7/7	1	2	FACETS	0.978	0.918	1	0.978	0.918	1	CLONAL	1	TRUE	1	0.93	2		502	444	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187104	38187104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758646155	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	287	802	0	ENST00000317025.8:c.1373C>T	p.Ala458Val	p.A458V	ENST00000317025	NM_023034.1	458	gCg/gTg	6/24	1	2	FACETS	0.909	0.861	0.958	0.909	0.861	0.958	CLONAL	1	TRUE	1	0.93	2		802	679	SUCCESS
APC	324	MSKCC	GRCh37	5	112179582	112179582	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	112	315	0	ENST00000257430.4:c.8291C>A	p.Ser2764Tyr	p.S2764Y	ENST00000257430	NM_000038.5	2764	tCt/tAt	16/16	0.10198407593633	3	FACETS	1	0.972	1	0.582	0.531	0.635	INDETERMINATE	1	TRUE	1	0.93	3		315	303	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439638	51439638	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750990884	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	136	355	0	ENST00000262662.1:c.203G>A	p.Arg68Gln	p.R68Q	ENST00000262662		68	cGa/cAa	4/4	1	2	FACETS	0.903	0.833	0.973	0.903	0.833	0.973	CLONAL	1	TRUE	1	0.93	2		355	324	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433373	49433373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771966959	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	249	797	1	ENST00000301067.7:c.8074C>T	p.Arg2692Trp	p.R2692W	ENST00000301067	NM_003482.3	2692	Cgg/Tgg	32/54	0.213346112869584	4	FACETS	0.907	0.856	0.958	0.907	0.856	0.958	INDETERMINATE	2	TRUE	2	0.93	4		798	570	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042116	6042116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881916	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	105	224	0	ENST00000265849.7:c.505C>T	p.Arg169Cys	p.R169C	ENST00000265849	NM_000535.5	169	Cgc/Tgc	5/15	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		224	228	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277291	41277291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	165	323	1	ENST00000349496.5:c.1760G>A	p.Arg587Gln	p.R587Q	ENST00000349496	NM_001904.3	587	cGa/cAa	11/15	0.10198407593633	3	FACETS	1	0.99	1	0.714	0.665	0.763	INDETERMINATE	1	TRUE	1	0.93	3		324	364	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958874	38958874	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	115	233	0	ENST00000357387.3:c.2238C>A	p.Phe746Leu	p.F746L	ENST00000357387	NM_152756.3	746	ttC/ttA	23/38	0.10198407593633	3	FACETS	0.791	0.729	0.853	0.791	0.729	0.853	INDETERMINATE	2	TRUE	1	0.93	3		233	229	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736388	85736388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs949558985	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	152	335	0	ENST00000370580.1:c.259C>T	p.Arg87Trp	p.R87W	ENST00000370580	NM_003921.4	87	Cgg/Tgg	2/3	1	2	FACETS	0.95	0.882	1	0.95	0.882	1	CLONAL	1	TRUE	1	0.93	2		335	344	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640689	3640689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750906921	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	247	971	0	ENST00000294008.3:c.2950G>A	p.Glu984Lys	p.E984K	ENST00000294008	NM_032444.2	984	Gaa/Aaa	12/15	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		971	559	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665230	117665230	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1258207555	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	78	218	0	ENST00000368508.3:c.4517G>T	p.Arg1506Ile	p.R1506I	ENST00000368508	NM_002944.2	1506	aGa/aTa	27/43	1	2	FACETS	0.907	0.815	1	0.907	0.815	1	CLONAL	1	TRUE	1	0.93	2		218	185	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891037	112891037	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	135	330	0	ENST00000351677.2:c.371A>C	p.Lys124Thr	p.K124T	ENST00000351677	NM_002834.3	124	aAa/aCa	4/16	1	2	FACETS	0.913	0.843	0.984	0.913	0.843	0.984	CLONAL	1	TRUE	1	0.93	2		330	318	SUCCESS
ATR	545	MSKCC	GRCh37	3	142224146	142224146	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	112	238	0	ENST00000350721.4:c.5032-1G>T		p.X1678_splice	ENST00000350721	NM_001184.3	1678			0.10198407593633	3	FACETS	1	0.985	1	0.697	0.639	0.756	INDETERMINATE	1	TRUE	1	0.93	3		238	253	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197484	27197484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756064806	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	184	652	1	ENST00000380036.4:c.1796C>T	p.Ser599Leu	p.S599L	ENST00000380036	NM_000459.3	599	tCg/tTg	12/23	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		653	405	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776955	76776955	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	126	437	0	ENST00000373344.5:c.6997G>T	p.Glu2333Ter	p.E2333*	ENST00000373344	NM_000489.3	2333	Gaa/Taa	33/35	0.303266542483354	1	FACETS	0.403	0.369	0.438	0.403	0.369	0.438	INDETERMINATE	1	TRUE	0	0.93	1		437	360	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216627	108216627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786203542	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	90	231	0	ENST00000278616.4:c.8576C>T	p.Ser2859Phe	p.S2859F	ENST00000278616	NM_000051.3	2859	tCt/tTt	58/63	1	2	FACETS	0.765	0.69	0.843	0.765	0.69	0.843	SUBCLONAL	1	TRUE	1	0.93	2		231	253	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950493	68950493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760821149	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	110	355	0	ENST00000288368.4:c.805G>A	p.Asp269Asn	p.D269N	ENST00000288368	NM_024870.2	269	Gat/Aat	7/40	0.258321414544118	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		355	262	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486064	29486064	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782772	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	132	274	0	ENST00000356175.3:c.241C>A	p.Leu81Ile	p.L81I	ENST00000356175	NM_000267.3	81	Ctc/Atc	3/57	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.93	2		274	283	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123685	11123685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	252	680	1	ENST00000358026.2:c.2335G>A	p.Asp779Asn	p.D779N	ENST00000358026	NM_001128849.1	779	Gac/Aac	16/36	1	2	FACETS	0.976	0.923	1	0.976	0.923	1	CLONAL	1	TRUE	1	0.93	2		681	555	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233619	233619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457666982	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	111	277	0	ENST00000264932.6:c.923C>T	p.Thr308Met	p.T308M	ENST00000264932	NM_004168.2	308	aCg/aTg	8/15	0.213346112869584	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		277	239	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435490	18435490	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs760928254	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	70	241	0	ENST00000266497.5:c.475G>T	p.Glu159Ter	p.E159*	ENST00000266497		159	Gaa/Taa	1/31	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		241	136	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242710	46242710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777576250	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	119	270	0	ENST00000334344.6:c.1672C>T	p.Arg558Cys	p.R558C	ENST00000334344	NM_152641.2	558	Cgt/Tgt	13/21	0.213346112869584	4	FACETS	0.762	0.697	0.829	0.762	0.697	0.829	INDETERMINATE	2	TRUE	2	0.93	4		270	324	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749297	43749297	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs748115671	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	157	564	0	ENST00000382044.4:c.1509G>T	p.Lys503Asn	p.K503N	ENST00000382044	NM_001141980.1	503	aaG/aaT	12/28	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		564	501	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938995	76938995	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs886044898	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	215	553	0	ENST00000373344.5:c.1753G>T	p.Glu585Ter	p.E585*	ENST00000373344	NM_000489.3	585	Gaa/Taa	9/35	0.303266542483354	1	FACETS	0.623	0.589	0.657	0.623	0.589	0.657	INDETERMINATE	1	TRUE	0	0.93	1		553	397	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268333	46268333	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747268479	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	139	357	0	ENST00000371998.3:c.2720G>A	p.Arg907Gln	p.R907Q	ENST00000371998		907	cGa/cAa	15/23	1	2	FACETS	0.983	0.911	1	0.983	0.911	1	CLONAL	1	TRUE	1	0.93	2		357	304	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710875	117710875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140178288	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	127	403	0	ENST00000368508.3:c.1397G>A	p.Arg466Gln	p.R466Q	ENST00000368508	NM_002944.2	466	cGa/cAa	12/43	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.93	2		403	268	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707863	43707863	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	302	820	2	ENST00000382044.4:c.5018G>T	p.Arg1673Ile	p.R1673I	ENST00000382044	NM_001141980.1	1673	aGa/aTa	23/28	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		822	680	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281637	142281637	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	159	435	0	ENST00000350721.4:c.607G>T	p.Glu203Ter	p.E203*	ENST00000350721	NM_001184.3	203	Gaa/Taa	4/47	0.10198407593633	3	FACETS	1	0.985	1	0.629	0.584	0.676	INDETERMINATE	1	TRUE	1	0.93	3		435	398	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880126	151880126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146495785	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	203	413	0	ENST00000262189.6:c.5198C>T	p.Ser1733Leu	p.S1733L	ENST00000262189	NM_170606.2	1733	tCg/tTg	35/59	0.10198407593633	3	FACETS	0.765	0.719	0.811	0.765	0.719	0.811	INDETERMINATE	2	TRUE	1	0.93	3		413	418	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250350	110250350	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768719572	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	142	960	1	ENST00000374672.4:c.325C>A	p.Leu109Ile	p.L109I	ENST00000374672	NM_004235.4	109	Ctc/Atc	3/5	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		961	534	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776304	76776304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	170	574	0	ENST00000373344.5:c.7162G>A	p.Glu2388Lys	p.E2388K	ENST00000373344	NM_000489.3	2388	Gaa/Aaa	34/35	0.303266542483354	1	FACETS	0.403	0.374	0.433	0.403	0.374	0.433	INDETERMINATE	1	TRUE	0	0.93	1		574	485	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142447	119142447	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs199739868	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	163	331	0	ENST00000264033.4:c.446G>A	p.Arg149Gln	p.R149Q	ENST00000264033	NM_005188.3	149	cGa/cAa	3/16	1	2	FACETS	0.976	0.91	1	0.976	0.91	1	CLONAL	1	TRUE	1	0.93	2		331	359	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3929909	3929909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	18	489	1	ENST00000262367.5:c.9G>T	p.Glu3Asp	p.E3D	ENST00000262367	NM_004380.2	3	gaG/gaT	1/31	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		490	356	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222962	36222962	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs181607228	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	312	969	2	ENST00000222270.7:c.5591G>A	p.Arg1864Gln	p.R1864Q	ENST00000222270	NM_014727.1	1864	cGa/cAa	27/37	1	2	FACETS	0.945	0.898	0.993	0.945	0.898	0.993	CLONAL	1	TRUE	1	0.93	2		971	710	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005332	29005332	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	190	422	0	ENST00000282397.4:c.929C>A	p.Thr310Asn	p.T310N	ENST00000282397	NM_002019.4	310	aCt/aAt	7/30	0.3	1	FACETS	0.583	0.547	0.618	0.583	0.547	0.618	INDETERMINATE	1	TRUE	0	0.93	1		422	375	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992274	72992274	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767435394	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	320	875	1	ENST00000268489.5:c.1771G>A	p.Ala591Thr	p.A591T	ENST00000268489	NM_006885.3	591	Gct/Act	2/10	0.3	3	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.93	3		876	721	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165140	47165140	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540015912	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	112	260	0	ENST00000409792.3:c.986G>A	p.Arg329Gln	p.R329Q	ENST00000409792	NM_014159.6	329	cGg/cAg	3/21	0.10198407593633	3	FACETS	1	0.987	1	0.738	0.678	0.799	INDETERMINATE	1	TRUE	1	0.93	3		260	239	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680556	241680556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769956664	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	21	413	0	ENST00000366560.3:c.193G>T	p.Asp65Tyr	p.D65Y	ENST00000366560	NM_000143.3	65	Gat/Tat	2/10	1	2	FACETS	0.127	0.097	0.162	0.127	0.097	0.162	SUBCLONAL	1	TRUE	1	0.93	2		413	355	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740814	58740814	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	215	422	0	ENST00000305921.3:c.1719G>T	p.Lys573Asn	p.K573N	ENST00000305921	NM_003620.3	573	aaG/aaT	6/6	1	2	FACETS	0.984	0.925	1	0.984	0.925	1	CLONAL	1	TRUE	1	0.93	2		422	470	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981172	55981172	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	150	415	0	ENST00000263923.4:c.527G>T	p.Arg176Ile	p.R176I	ENST00000263923	NM_002253.2	176	aGa/aTa	5/30	1	2	FACETS	0.916	0.85	0.984	0.916	0.85	0.984	CLONAL	1	TRUE	1	0.93	2		415	352	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315354	30315354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1480541649	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	184	361	0	ENST00000322652.5:c.1039G>A	p.Glu347Lys	p.E347K	ENST00000322652	NM_015355.2	347	Gaa/Aaa	10/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.93	2		361	377	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169036	32169036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745902446	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	229	858	1	ENST00000375023.3:c.3997C>T	p.Arg1333Cys	p.R1333C	ENST00000375023	NM_004557.3	1333	Cgt/Tgt	22/30	1	2	FACETS	0.899	0.845	0.953	0.899	0.845	0.953	CLONAL	1	TRUE	1	0.93	2		859	548	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926518	59926518	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1330277587	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	262	493	0	ENST00000259008.2:c.479G>T	p.Arg160Ile	p.R160I	ENST00000259008	NM_032043.2	160	aGa/aTa	5/20	1	2	FACETS	0.995	0.942	1	0.995	0.942	1	CLONAL	1	TRUE	1	0.93	2		493	566	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828294	72828294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	170	640	0	ENST00000268489.5:c.8287G>A	p.Asp2763Asn	p.D2763N	ENST00000268489	NM_006885.3	2763	Gat/Aat	9/10	0.3	3	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.93	3		640	492	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105579	30105579	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1036795627	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	256	622	1	ENST00000331968.5:c.1107G>T	p.Glu369Asp	p.E369D	ENST00000331968	NM_002742.2	369	gaG/gaT	7/18	1	2	FACETS	0.987	0.933	1	0.987	0.933	1	CLONAL	1	TRUE	1	0.93	2		623	558	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923722	72923722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1169589589	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	203	690	0	ENST00000268489.5:c.3356G>A	p.Arg1119Gln	p.R1119Q	ENST00000268489	NM_006885.3	1119	cGa/cAa	4/10	0.3	3	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.93	3		690	460	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946090	13946090	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1419462186	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	103	326	0	ENST00000405192.2:c.1006C>T	p.Arg336Ter	p.R336*	ENST00000405192	NM_001163147.1	336	Cga/Tga	10/12	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		326	296	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841310	15841310	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	197	484	0	ENST00000307771.7:c.1394G>T	p.Gly465Val	p.G465V	ENST00000307771	NM_005089.3	465	gGc/gTc	11/11	0.303266542483354	1	FACETS	0.512	0.479	0.544	0.512	0.479	0.544	INDETERMINATE	1	TRUE	0	0.93	1		484	443	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597525	28597525	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	175	443	0	ENST00000241453.7:c.2380C>A	p.Gln794Lys	p.Q794K	ENST00000241453	NM_004119.2	794	Caa/Aaa	19/24	0.3	1	FACETS	0.483	0.45	0.516	0.483	0.45	0.516	INDETERMINATE	1	TRUE	0	0.93	1		443	417	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611338	28611338	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	53	434	0	ENST00000241453.7:c.1293C>A	p.Phe431Leu	p.F431L	ENST00000241453	NM_004119.2	431	ttC/ttA	10/24	0.3	1	FACETS	0.21	0.18	0.243	0.21	0.18	0.243	INDETERMINATE	1	TRUE	0	0.93	1		434	290	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032274	10032274	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	129	565	1	ENST00000330684.3:c.549C>A	p.Phe183Leu	p.F183L	ENST00000330684	NM_001134407.1	183	ttC/ttA	3/13	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		566	302	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220483	123220483	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	153	562	0	ENST00000218089.9:c.3140C>A	p.Ser1047Tyr	p.S1047Y	ENST00000218089	NM_001042749.1	1047	tCt/tAt	30/35	0.303266542483354	1	FACETS	0.361	0.332	0.39	0.361	0.332	0.39	INDETERMINATE	1	TRUE	0	0.93	1		562	488	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701889	43701889	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	116	206	0	ENST00000382044.4:c.5356C>T	p.Arg1786Ter	p.R1786*	ENST00000382044	NM_001141980.1	1786	Cga/Tga	25/28	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		206	246	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146592	55146592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555347387	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	173	385	0	ENST00000257290.5:c.2266G>A	p.Asp756Asn	p.D756N	ENST00000257290	NM_006206.4	756	Gac/Aac	16/23	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.93	2		385	355	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937850	76937850	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs138256318	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	141	282	0	ENST00000373344.5:c.2898G>T	p.Glu966Asp	p.E966D	ENST00000373344	NM_000489.3	966	gaG/gaT	9/35	0.303266542483354	1	FACETS	0.386	0.355	0.418	0.386	0.355	0.418	INDETERMINATE	1	TRUE	0	0.93	1		282	420	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50488303	50488303	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs750857733	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	216	510	0	ENST00000394963.4:c.1217C>A	p.Ser406Tyr	p.S406Y	ENST00000394963	NM_003076.4	406	tCt/tAt	10/13	0.213346112869584	4	FACETS	0.879	0.825	0.933	0.879	0.825	0.933	INDETERMINATE	2	TRUE	2	0.93	4		510	510	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857757	9857757	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	110	584	0	ENST00000330684.3:c.3644G>T	p.Arg1215Ile	p.R1215I	ENST00000330684	NM_001134407.1	1215	aGa/aTa	13/13	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		584	273	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240670	133240670	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1208731306	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	139	630	0	ENST00000320574.5:c.2626T>G	p.Phe876Val	p.F876V	ENST00000320574	NM_006231.2	876	Ttt/Gtt	23/49	1	2	FACETS	0.681	0.625	0.738	0.681	0.625	0.738	SUBCLONAL	1	TRUE	1	0.93	2		630	439	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938640	76938640	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	123	562	0	ENST00000373344.5:c.2108C>A	p.Ser703Tyr	p.S703Y	ENST00000373344	NM_000489.3	703	tCt/tAt	9/35	0.303266542483354	1	FACETS	0.386	0.352	0.42	0.386	0.352	0.42	INDETERMINATE	1	TRUE	0	0.93	1		562	367	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970985	55970985	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	174	545	0	ENST00000263923.4:c.1812G>T	p.Lys604Asn	p.K604N	ENST00000263923	NM_002253.2	604	aaG/aaT	13/30	1	2	FACETS	0.964	0.9	1	0.964	0.9	1	CLONAL	1	TRUE	1	0.93	2		545	388	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459453	50459453	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	64	240	0	ENST00000331340.3:c.742G>T	p.Glu248Ter	p.E248*	ENST00000331340	NM_006060.4	248	Gaa/Taa	7/8	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		240	169	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593628	55593628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	149	402	0	ENST00000288135.5:c.1694G>A	p.Gly565Glu	p.G565E	ENST00000288135	NM_000222.2	565	gGa/gAa	11/21	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.93	2		402	320	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645414	67645414	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772804334	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	175	412	0	ENST00000264010.4:c.679G>A	p.Asp227Asn	p.D227N	ENST00000264010	NM_006565.3	227	Gat/Aat	3/12	0.3	3	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.93	3		412	388	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979589	55979589	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	161	470	0	ENST00000263923.4:c.858G>T	p.Lys286Asn	p.K286N	ENST00000263923	NM_002253.2	286	aaG/aaT	7/30	1	2	FACETS	0.82	0.761	0.881	0.82	0.761	0.881	CLONAL	1	TRUE	1	0.93	2		470	422	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241973	39241973	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	98	253	1	ENST00000402219.2:c.1873C>T	p.Arg625Trp	p.R625W	ENST00000402219	NM_005633.3	625	Cgg/Tgg	11/23	1	2	FACETS	0.753	0.681	0.826	0.753	0.681	0.826	SUBCLONAL	1	TRUE	1	0.93	2		254	280	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602916	55602916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372795544	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	137	395	1	ENST00000288135.5:c.2626G>A	p.Asp876Asn	p.D876N	ENST00000288135	NM_000222.2	876	Gat/Aat	19/21	1	2	FACETS	0.96	0.888	1	0.96	0.888	1	CLONAL	1	TRUE	1	0.93	2		396	307	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20486949	20486949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188266138	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	120	234	0	ENST00000346618.3:c.914G>A	p.Arg305Gln	p.R305Q	ENST00000346618	NM_001949.4	305	cGa/cAa	5/7	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.93	2		234	258	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950837	32950837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80359124	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	135	348	1	ENST00000380152.3:c.8663G>A	p.Arg2888His	p.R2888H	ENST00000380152		2888	cGt/cAt	21/27	0.10198407593633	3	FACETS	1	0.978	1	0.592	0.545	0.641	INDETERMINATE	1	TRUE	1	0.93	3		349	359	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895653	28895653	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	185	458	0	ENST00000282397.4:c.3121T>G	p.Phe1041Val	p.F1041V	ENST00000282397	NM_002019.4	1041	Ttt/Gtt	23/30	0.3	1	FACETS	0.559	0.524	0.594	0.559	0.524	0.594	INDETERMINATE	1	TRUE	0	0.93	1		458	381	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961766	55961766	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	112	408	0	ENST00000263923.4:c.2795G>T	p.Arg932Ile	p.R932I	ENST00000263923	NM_002253.2	932	aGa/aTa	20/30	1	2	FACETS	0.644	0.585	0.705	0.644	0.585	0.705	SUBCLONAL	1	TRUE	1	0.93	2		408	374	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211894	36211894	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	321	903	0	ENST00000222270.7:c.1645G>T	p.Glu549Ter	p.E549*	ENST00000222270	NM_014727.1	549	Gaa/Taa	3/37	1	2	FACETS	0.996	0.948	1	0.996	0.948	1	CLONAL	1	TRUE	1	0.93	2		903	693	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661884	227661884	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	223	1092	1	ENST00000305123.5:c.1571G>T	p.Arg524Ile	p.R524I	ENST00000305123	NM_005544.2	524	aGa/aTa	1/2	1	2	FACETS	0.9	0.845	0.955	0.9	0.845	0.955	CLONAL	1	TRUE	1	0.93	2		1093	533	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499611	149499611	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	180	589	0	ENST00000261799.4:c.2662T>C	p.Ser888Pro	p.S888P	ENST00000261799	NM_002609.3	888	Tcc/Ccc	19/23	1	2	FACETS	0.928	0.867	0.99	0.928	0.867	0.99	CLONAL	1	TRUE	1	0.93	2		589	417	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073530	8073530	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs535836763	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	160	424	0	ENST00000377482.5:c.1129C>T	p.Pro377Ser	p.P377S	ENST00000377482	NM_018948.3	377	Cct/Tct	4/4	1	2	FACETS	0.894	0.83	0.958	0.894	0.83	0.958	CLONAL	1	TRUE	1	0.93	2		424	385	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272943	11272943	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	149	377	0	ENST00000361445.4:c.3308T>A	p.Phe1103Tyr	p.F1103Y	ENST00000361445	NM_004958.3	1103	tTt/tAt	22/58	1	2	FACETS	0.959	0.89	1	0.959	0.89	1	CLONAL	1	TRUE	1	0.93	2		377	334	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106582	27106582	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1359226978	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	254	764	0	ENST00000324856.7:c.6193G>A	p.Ala2065Thr	p.A2065T	ENST00000324856	NM_006015.4	2065	Gcc/Acc	20/20	1	2	FACETS	0.952	0.899	1	0.952	0.899	1	CLONAL	1	TRUE	1	0.93	2		764	574	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932167	36932167	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	155	709	0	ENST00000361632.4:c.2302C>A	p.Leu768Ile	p.L768I	ENST00000361632		768	Ctc/Atc	16/16	1	2	FACETS	0.887	0.822	0.952	0.887	0.822	0.952	CLONAL	1	TRUE	1	0.93	2		709	376	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521529	46521529	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	222	442	0	ENST00000262741.5:c.879A>C	p.Lys293Asn	p.K293N	ENST00000262741	NM_003629.3	293	aaA/aaC	7/10	1	2	FACETS	0.955	0.898	1	0.955	0.898	1	CLONAL	1	TRUE	1	0.93	2		442	500	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726593	46726593	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	204	576	1	ENST00000371975.4:c.672G>T	p.Lys224Asn	p.K224N	ENST00000371975	NM_003579.3	224	aaG/aaT	7/18	1	2	FACETS	0.999	0.939	1	0.999	0.939	1	CLONAL	1	TRUE	1	0.93	2		577	439	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309886	65309886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	151	458	1	ENST00000342505.4:c.2264G>A	p.Arg755Gln	p.R755Q	ENST00000342505	NM_002227.2	755	cGa/cAa	17/25	1	2	FACETS	0.978	0.909	1	0.978	0.909	1	CLONAL	1	TRUE	1	0.93	2		459	332	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414985	78414985	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	73	333	0	ENST00000370768.2:c.1781G>C	p.Gly594Ala	p.G594A	ENST00000370768	NM_003902.3	594	gGt/gCt	19/20	1	2	FACETS	0.505	0.445	0.568	0.505	0.445	0.568	SUBCLONAL	1	TRUE	1	0.93	2		333	311	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165875	118165875	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	117	430	0	ENST00000369448.3:c.385A>C	p.Ile129Leu	p.I129L	ENST00000369448	NM_017709.3	129	Atc/Ctc	2/2	1	2	FACETS	0.874	0.801	0.948	0.874	0.801	0.948	CLONAL	1	TRUE	1	0.93	2		430	288	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163315554	163315554	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	161	329	0	ENST00000271452.3:c.894G>T	p.Lys298Asn	p.K298N	ENST00000271452	NM_145697.2	298	aaG/aaT	11/14	1	2	FACETS	0.959	0.893	1	0.959	0.893	1	CLONAL	1	TRUE	1	0.93	2		329	361	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675359	241675359	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	76	364	0	ENST00000366560.3:c.463G>T	p.Glu155Ter	p.E155*	ENST00000366560	NM_000143.3	155	Gaa/Taa	4/10	1	2	FACETS	0.545	0.482	0.61	0.545	0.482	0.61	SUBCLONAL	1	TRUE	1	0.93	2		364	300	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809199	243809199	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	51	340	0	ENST00000263826.5:c.425G>T	p.Arg142Ile	p.R142I	ENST00000263826	NM_005465.4	142	aGa/aTa	4/13	1	2	FACETS	0.475	0.408	0.547	0.475	0.408	0.547	SUBCLONAL	1	TRUE	1	0.93	2		340	231	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851755	63851755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749293931	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	256	600	2	ENST00000279873.7:c.2533G>A	p.Glu845Lys	p.E845K	ENST00000279873	NM_032199.2	845	Gag/Aag	10/10	0.10198407593633	3	FACETS	0.765	0.724	0.806	0.765	0.724	0.806	INDETERMINATE	2	TRUE	1	0.93	3		602	527	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332336	70332336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775380660	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	151	476	0	ENST00000373644.4:c.241C>T	p.Arg81Cys	p.R81C	ENST00000373644	NM_030625.2	81	Cgc/Tgc	2/12	0.10198407593633	3	FACETS	1	0.987	1	0.657	0.609	0.706	INDETERMINATE	1	TRUE	1	0.93	3		476	362	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720816	89720816	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	150	401	0	ENST00000371953.3:c.967A>C	p.Asn323His	p.N323H	ENST00000371953	NM_000314.4	323	Aat/Cat	8/9	0.10198407593633	3	FACETS	1	0.986	1	0.64	0.593	0.689	INDETERMINATE	1	TRUE	1	0.93	3		401	369	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161460	2161460	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	217	641	0	ENST00000434045.2:c.67C>A	p.Gln23Lys	p.Q23K	ENST00000434045	NM_001127598.1	23	Caa/Aaa	2/5	1	2	FACETS	0.82	0.769	0.873	0.82	0.769	0.873	CLONAL	1	TRUE	1	0.93	2		641	569	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316108	14316108	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	126	299	0	ENST00000256196.4:c.317A>C	p.Lys106Thr	p.K106T	ENST00000256196		106	aAg/aCg	4/6	1	2	FACETS	0.906	0.834	0.979	0.906	0.834	0.979	CLONAL	1	TRUE	1	0.93	2		299	299	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417904	32417904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	175	530	0	ENST00000332351.3:c.1148C>T	p.Ser383Phe	p.S383F	ENST00000332351	NM_024426.4	383	tCt/tTt	7/10	1	2	FACETS	0.934	0.871	0.997	0.934	0.871	0.997	CLONAL	1	TRUE	1	0.93	2		530	403	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625333	69625333	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	244	904	0	ENST00000334134.2:c.460T>C	p.Tyr154His	p.Y154H	ENST00000334134	NM_005247.2	154	Tac/Cac	3/3	1	2	FACETS	0.956	0.902	1	0.956	0.902	1	CLONAL	1	TRUE	1	0.93	2		904	549	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625354	69625354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	160	858	1	ENST00000334134.2:c.439C>T	p.Pro147Ser	p.P147S	ENST00000334134	NM_005247.2	147	Ccc/Tcc	3/3	1	2	FACETS	0.63	0.581	0.681	0.63	0.581	0.681	SUBCLONAL	1	TRUE	1	0.93	2		859	546	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988988	85988988	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	135	238	0	ENST00000263360.6:c.1154A>C	p.Lys385Thr	p.K385T	ENST00000263360	NM_003797.3	385	aAa/aCa	11/12	1	2	FACETS	0.937	0.865	1	0.937	0.865	1	CLONAL	1	TRUE	1	0.93	2		238	310	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912801	100912801	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	128	374	0	ENST00000325455.5:c.2521T>C	p.Phe841Leu	p.F841L	ENST00000325455	NM_001202474.3	841	Ttt/Ctt	7/8	1	2	FACETS	0.891	0.82	0.963	0.891	0.82	0.963	CLONAL	1	TRUE	1	0.93	2		374	309	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100496	102100496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	218	479	0	ENST00000282441.5:c.1340C>T	p.Ala447Val	p.A447V	ENST00000282441	NM_001130145.2	447	gCc/gTc	9/9	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.93	2		479	445	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175544	108175544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780628	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	144	352	0	ENST00000278616.4:c.5639C>T	p.Thr1880Met	p.T1880M	ENST00000278616	NM_000051.3	1880	aCg/aTg	37/63	1	2	FACETS	0.846	0.782	0.912	0.846	0.782	0.912	CLONAL	1	TRUE	1	0.93	2		352	366	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118365111	118365111	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs999060359	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	133	337	0	ENST00000534358.1:c.5287C>T	p.Arg1763Trp	p.R1763W	ENST00000534358	NM_005933.3	1763	Cgg/Tgg	17/36	1	2	FACETS	0.854	0.786	0.923	0.854	0.786	0.923	CLONAL	1	TRUE	1	0.93	2		337	335	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514012	125514012	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	155	438	0	ENST00000428830.2:c.950C>A	p.Ser317Tyr	p.S317Y	ENST00000428830	NM_001114121.2	317	tCt/tAt	10/14	1	2	FACETS	0.986	0.917	1	0.986	0.917	1	CLONAL	1	TRUE	1	0.93	2		438	338	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402085	402085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	215	484	0	ENST00000399788.2:c.4706C>T	p.Ala1569Val	p.A1569V	ENST00000399788	NM_001042603.1	1569	gCt/gTt	27/28	0.3	3	FACETS	0.754	0.71	0.799			1	INDETERMINATE	2	TRUE	NA	0.93	3		484	449	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	465601	465601	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	265	500	0	ENST00000399788.2:c.775G>T	p.Glu259Ter	p.E259*	ENST00000399788	NM_001042603.1	259	Gaa/Taa	6/28	0.3	3	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.93	3		500	562	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	465607	465607	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	261	537	0	ENST00000399788.2:c.769G>T	p.Asp257Tyr	p.D257Y	ENST00000399788	NM_001042603.1	257	Gat/Tat	6/28	0.3	3	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.93	3		537	613	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385283	4385283	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	166	468	1	ENST00000261254.3:c.308C>T	p.Ala103Val	p.A103V	ENST00000261254	NM_001759.3	103	gCt/gTt	2/5	0.3	3	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.93	3		469	356	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435588	18435588	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	98	258	0	ENST00000266497.5:c.573G>T	p.Glu191Asp	p.E191D	ENST00000266497		191	gaG/gaT	1/31	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		258	213	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466933	18466933	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	122	340	0	ENST00000266497.5:c.1072G>T	p.Asp358Tyr	p.D358Y	ENST00000266497		358	Gat/Tat	5/31	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		340	315	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18473938	18473938	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	86	249	0	ENST00000266497.5:c.1180G>T	p.Glu394Ter	p.E394*	ENST00000266497		394	Gaa/Taa	6/31	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		249	215	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552613	18552613	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1371859788	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	67	347	0	ENST00000266497.5:c.2024G>T	p.Arg675Ile	p.R675I	ENST00000266497		675	aGa/aTa	14/31	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		347	287	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18762492	18762492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	127	412	0	ENST00000266497.5:c.3988C>T	p.Pro1330Ser	p.P1330S	ENST00000266497		1330	Cct/Tct	29/31	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		412	332	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123895	46123895	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	109	253	0	ENST00000334344.6:c.161T>G	p.Val54Gly	p.V54G	ENST00000334344	NM_152641.2	54	gTc/gGc	2/21	0.213346112869584	4	FACETS	0.85	0.777	0.925	0.85	0.777	0.925	INDETERMINATE	2	TRUE	2	0.93	4		253	266	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426266	49426266	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	308	955	0	ENST00000301067.7:c.12222A>C	p.Gln4074His	p.Q4074H	ENST00000301067	NM_003482.3	4074	caA/caC	39/54	0.213346112869584	4	FACETS	0.977	0.929	1	0.977	0.929	1	INDETERMINATE	2	TRUE	2	0.93	4		955	654	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432623	49432623	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555191147	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	285	838	0	ENST00000301067.7:c.8516C>G	p.Ser2839Ter	p.S2839*	ENST00000301067	NM_003482.3	2839	tCa/tGa	34/54	0.213346112869584	4	FACETS	0.974	0.925	1	0.974	0.925	1	INDETERMINATE	2	TRUE	2	0.93	4		838	607	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437986	49437986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747363115	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	210	676	1	ENST00000301067.7:c.5185G>A	p.Glu1729Lys	p.E1729K	ENST00000301067	NM_003482.3	1729	Gag/Aag	21/54	0.213346112869584	4	FACETS	0.899	0.843	0.954	0.899	0.843	0.954	INDETERMINATE	2	TRUE	2	0.93	4		677	485	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481824	56481824	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	220	671	0	ENST00000267101.3:c.752A>G	p.Asp251Gly	p.D251G	ENST00000267101	NM_001982.3	251	gAc/gGc	7/28	0.213346112869584	4	FACETS	0.787	0.738	0.837	0.787	0.738	0.837	INDETERMINATE	2	TRUE	2	0.93	4		671	580	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857489	57857489	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	274	880	1	ENST00000228682.2:c.15G>T	p.Met5Ile	p.M5I	ENST00000228682	NM_005269.2	5	atG/atT	2/12	0.213346112869584	4	FACETS	0.801	0.756	0.846	0.801	0.756	0.846	INDETERMINATE	2	TRUE	2	0.93	4		881	710	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117320	115117320	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	106	222	0	ENST00000257566.3:c.854A>C	p.Gln285Pro	p.Q285P	ENST00000257566	NM_016569.3	285	cAg/cCg	4/8	1	2	FACETS	0.923	0.843	1	0.923	0.843	1	CLONAL	1	TRUE	1	0.93	2		222	247	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416625	121416625	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	207	810	0	ENST00000257555.6:c.54G>C	p.Glu18Asp	p.E18D	ENST00000257555		18	gaG/gaC	1/10	1	2	FACETS	0.966	0.907	1	0.966	0.907	1	CLONAL	1	TRUE	1	0.93	2		810	461	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245434	133245434	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	223	757	0	ENST00000320574.5:c.1886C>A	p.Ala629Asp	p.A629D	ENST00000320574	NM_006231.2	629	gCc/gAc	17/49	1	2	FACETS	0.952	0.895	1	0.952	0.895	1	CLONAL	1	TRUE	1	0.93	2		757	504	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252703	133252703	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	151	533	0	ENST00000320574.5:c.997T>A	p.Cys333Ser	p.C333S	ENST00000320574	NM_006231.2	333	Tgt/Agt	10/49	1	2	FACETS	0.816	0.754	0.879	0.816	0.754	0.879	CLONAL	1	TRUE	1	0.93	2		533	398	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253957	133253957	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	215	487	1	ENST00000320574.5:c.793G>A	p.Glu265Lys	p.E265K	ENST00000320574	NM_006231.2	265	Gaa/Aaa	8/49	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.93	2		488	415	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975443	26975443	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	190	392	0	ENST00000381527.3:c.1069G>T	p.Glu357Ter	p.E357*	ENST00000381527	NM_001260.1	357	Gaa/Taa	11/13	0.3	1	FACETS	0.524	0.491	0.558	0.524	0.491	0.558	INDETERMINATE	1	TRUE	0	0.93	1		392	417	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599042	28599042	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1355239392	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	149	470	0	ENST00000241453.7:c.2246C>T	p.Ser749Leu	p.S749L	ENST00000241453	NM_004119.2	749	tCg/tTg	18/24	0.3	1	FACETS	0.452	0.418	0.487	0.452	0.418	0.487	INDETERMINATE	1	TRUE	0	0.93	1		470	379	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608270	28608270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	163	499	0	ENST00000241453.7:c.1786G>A	p.Glu596Lys	p.E596K	ENST00000241453	NM_004119.2	596	Gaa/Aaa	14/24	0.3	1	FACETS	0.495	0.46	0.53	0.495	0.46	0.53	INDETERMINATE	1	TRUE	0	0.93	1		499	379	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609763	28609763	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	191	572	0	ENST00000241453.7:c.1466G>T	p.Arg489Ile	p.R489I	ENST00000241453	NM_004119.2	489	aGa/aTa	12/24	0.3	1	FACETS	0.551	0.516	0.585	0.551	0.516	0.585	INDETERMINATE	1	TRUE	0	0.93	1		572	399	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964128	28964128	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	125	386	0	ENST00000282397.4:c.1774C>A	p.Leu592Met	p.L592M	ENST00000282397	NM_002019.4	592	Ctg/Atg	13/30	0.3	1	FACETS	0.461	0.423	0.499	0.461	0.423	0.499	INDETERMINATE	1	TRUE	0	0.93	1		386	312	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907124	32907124	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	131	391	0	ENST00000380152.3:c.1509G>T	p.Lys503Asn	p.K503N	ENST00000380152		503	aaG/aaT	10/27	0.10198407593633	3	FACETS	1	0.985	1	0.661	0.61	0.714	INDETERMINATE	1	TRUE	1	0.93	3		391	312	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914260	32914260	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	166	452	0	ENST00000380152.3:c.5768A>G	p.Asp1923Gly	p.D1923G	ENST00000380152		1923	gAc/gGc	11/27	0.10198407593633	3	FACETS	1	0.99	1	0.716	0.668	0.765	INDETERMINATE	1	TRUE	1	0.93	3		452	365	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953781	48953781	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	82	153	0	ENST00000267163.4:c.1384A>C	p.Lys462Gln	p.K462Q	ENST00000267163	NM_000321.2	462	Aaa/Caa	14/27	0.10198407593633	3	FACETS	1	0.981	1	0.722	0.653	0.791	INDETERMINATE	1	TRUE	1	0.93	3		153	179	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281447	49281447	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	180	700	0	ENST00000282018.3:c.494T>G	p.Leu165Arg	p.L165R	ENST00000282018	NM_020377.2	165	cTt/cGt	1/1	0.10198407593633	3	FACETS	1	0.991	1	0.716	0.669	0.763	INDETERMINATE	1	TRUE	1	0.93	3		700	396	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73334768	73334768	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	47	210	0	ENST00000377767.4:c.2692G>T	p.Asp898Tyr	p.D898Y	ENST00000377767	NM_014953.3	898	Gat/Tat	20/21	0.10198407593633	3	FACETS	0.715	0.611	0.828	0.358	0.305	0.414	INDETERMINATE	1	TRUE	1	0.93	3		210	207	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345070	73345070	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	140	305	0	ENST00000377767.4:c.1727A>C	p.Lys576Thr	p.K576T	ENST00000377767	NM_014953.3	576	aAg/aCg	13/21	0.10198407593633	3	FACETS	1	0.986	1	0.662	0.612	0.713	INDETERMINATE	1	TRUE	1	0.93	3		305	333	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514595	103514595	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs966111552	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	125	352	0	ENST00000355739.4:c.1096C>T	p.Arg366Ter	p.R366*	ENST00000355739	NM_000123.3	366	Cga/Tga	8/15	0.10198407593633	3	FACETS	1	0.987	1	0.716	0.66	0.772	INDETERMINATE	1	TRUE	1	0.93	3		352	275	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30095743	30095743	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	151	357	0	ENST00000331968.5:c.1745A>C	p.Gln582Pro	p.Q582P	ENST00000331968	NM_002742.2	582	cAg/cCg	12/18	1	2	FACETS	0.902	0.836	0.969	0.902	0.836	0.969	CLONAL	1	TRUE	1	0.93	2		357	360	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30102098	30102098	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	185	492	0	ENST00000331968.5:c.1369G>T	p.Asp457Tyr	p.D457Y	ENST00000331968	NM_002742.2	457	Gac/Tac	9/18	1	2	FACETS	0.919	0.859	0.98	0.919	0.859	0.98	CLONAL	1	TRUE	1	0.93	2		492	433	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353757	68353757	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs774910383	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	69	241	1	ENST00000487270.1:c.592G>T	p.Glu198Ter	p.E198*	ENST00000487270	NM_133509.3	198	Gaa/Taa	7/11	1	2	FACETS	0.587	0.517	0.66	0.587	0.517	0.66	SUBCLONAL	1	TRUE	1	0.93	2		242	253	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557695	95557695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	138	362	0	ENST00000393063.1:c.5372G>A	p.Arg1791Lys	p.R1791K	ENST00000393063	NM_030621.3	1791	aGa/aAa	26/28	1	2	FACETS	0.939	0.868	1	0.939	0.868	1	CLONAL	1	TRUE	1	0.93	2		362	316	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570365	95570365	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	105	281	0	ENST00000393063.1:c.3368A>C	p.Lys1123Thr	p.K1123T	ENST00000393063	NM_030621.3	1123	aAg/aCg	22/28	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.93	2		281	223	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000323	42000323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	207	352	0	ENST00000219905.7:c.2342C>A	p.Ser781Tyr	p.S781Y	ENST00000219905	NM_001164273.1	781	tCt/tAt	7/24	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		352	460	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028765	42028765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	199	541	0	ENST00000219905.7:c.4303G>A	p.Asp1435Asn	p.D1435N	ENST00000219905	NM_001164273.1	1435	Gat/Aat	13/24	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		541	455	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042025	42042025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199971244	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	221	505	0	ENST00000219905.7:c.6220C>T	p.Arg2074Cys	p.R2074C	ENST00000219905	NM_001164273.1	2074	Cgt/Tgt	17/24	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		505	480	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052661	42052661	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	222	474	0	ENST00000219905.7:c.7332G>T	p.Glu2444Asp	p.E2444D	ENST00000219905	NM_001164273.1	2444	gaG/gaT	20/24	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		474	523	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749137	43749137	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	270	673	0	ENST00000382044.4:c.1669T>C	p.Ser557Pro	p.S557P	ENST00000382044	NM_001141980.1	557	Tct/Cct	12/28	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		673	607	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358533	67358533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	163	400	0	ENST00000327367.4:c.41G>A	p.Arg14His	p.R14H	ENST00000327367	NM_005902.3	14	cGc/cAc	1/9	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		400	355	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473770	67473770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	211	668	0	ENST00000327367.4:c.850G>A	p.Glu284Lys	p.E284K	ENST00000327367	NM_005902.3	284	Gag/Aag	6/9	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		668	461	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679159	88679159	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	99	429	0	ENST00000360948.2:c.878G>T	p.Ser293Ile	p.S293I	ENST00000360948	NM_001012338.2	293	aGc/aTc	8/19	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		429	225	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726674	88726674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	16	468	1	ENST00000360948.2:c.370G>A	p.Ala124Thr	p.A124T	ENST00000360948	NM_001012338.2	124	Gcc/Acc	4/19	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		469	278	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788659	3788659	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	158	333	0	ENST00000262367.5:c.4295C>A	p.Ser1432Tyr	p.S1432Y	ENST00000262367	NM_004380.2	1432	tCt/tAt	26/31	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		333	369	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858072	9858072	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	136	642	0	ENST00000330684.3:c.3329C>A	p.Ser1110Ter	p.S1110*	ENST00000330684	NM_001134407.1	1110	tCa/tAa	13/13	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		642	295	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923344	9923344	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	142	540	0	ENST00000330684.3:c.1943A>C	p.Asn648Thr	p.N648T	ENST00000330684	NM_001134407.1	648	aAt/aCt	9/13	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		540	310	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273941	10273941	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	166	903	0	ENST00000330684.3:c.328G>T	p.Ala110Ser	p.A110S	ENST00000330684	NM_001134407.1	110	Gcc/Tcc	2/13	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		903	458	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783612	50783612	+	start_lost	Translation_Start_Site	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	161	355	0	ENST00000398568.2:c.3G>T	p.Met1?	p.M1?	ENST00000398568	NM_001042412.1	1	atG/atT	3/18	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		355	316	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50818289	50818289	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	146	335	0	ENST00000398568.2:c.1867G>T	p.Glu623Ter	p.E623*	ENST00000398568	NM_001042412.1	623	Gaa/Taa	11/18	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		335	329	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132617	67132617	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	191	442	2	ENST00000412916.2:c.500G>T	p.Arg167Ile	p.R167I	ENST00000412916		167	aGa/aTa	6/6	0.3	3	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.93	3		444	471	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835732	68835732	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	277	622	0	ENST00000261769.5:c.323G>T	p.Arg108Ile	p.R108I	ENST00000261769	NM_004360.3	108	aGa/aTa	3/16	0.3	3	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.93	3		622	622	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992268	72992268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746207124	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	314	890	2	ENST00000268489.5:c.1777G>A	p.Glu593Lys	p.E593K	ENST00000268489	NM_006885.3	593	Gaa/Aaa	2/10	0.3	3	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.93	3		892	708	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349532	89349532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369869329	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	250	801	0	ENST00000301030.4:c.3418G>A	p.Ala1140Thr	p.A1140T	ENST00000301030	NM_001256183.1	1140	Gcc/Acc	9/13	1	2	FACETS	0.952	0.898	1	0.952	0.898	1	CLONAL	1	TRUE	1	0.93	2		801	565	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805570	89805570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs775234845	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	190	628	1	ENST00000389301.3:c.4138G>T	p.Ala1380Ser	p.A1380S	ENST00000389301	NM_000135.2	1380	Gct/Tct	41/43	1	2	FACETS	0.864	0.807	0.922	0.864	0.807	0.922	CLONAL	1	TRUE	1	0.93	2		629	473	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838195	89838195	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	206	549	0	ENST00000389301.3:c.2042C>A	p.Ser681Tyr	p.S681Y	ENST00000389301	NM_000135.2	681	tCt/tAt	23/43	1	2	FACETS	0.998	0.938	1	0.998	0.938	1	CLONAL	1	TRUE	1	0.93	2		549	444	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16022758	16022758	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	175	305	0	ENST00000268712.3:c.1894G>T	p.Glu632Ter	p.E632*	ENST00000268712	NM_006311.3	632	Gaa/Taa	17/46	1	2	FACETS	0.857	0.798	0.917	0.857	0.798	0.917	CLONAL	1	TRUE	1	0.93	2		305	439	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049769	16049769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	151	400	0	ENST00000268712.3:c.1003G>A	p.Glu335Lys	p.E335K	ENST00000268712	NM_006311.3	335	Gaa/Aaa	10/46	1	2	FACETS	0.72	0.664	0.777	0.72	0.664	0.777	SUBCLONAL	1	TRUE	1	0.93	2		400	451	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325698	30325698	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	78	200	0	ENST00000322652.5:c.1896G>T	p.Met632Ile	p.M632I	ENST00000322652	NM_015355.2	632	atG/atT	16/16	1	2	FACETS	0.874	0.785	0.965	0.874	0.785	0.965	CLONAL	1	TRUE	1	0.93	2		200	192	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686970	37686970	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	223	617	0	ENST00000447079.4:c.3874G>A	p.Glu1292Lys	p.E1292K	ENST00000447079	NM_015083.1	1292	Gag/Aag	14/14	1	2	FACETS	0.867	0.814	0.921	0.867	0.814	0.921	CLONAL	1	TRUE	1	0.93	2		617	553	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40458275	40458275	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	320	952	0	ENST00000345506.4:c.1490C>A	p.Ala497Asp	p.A497D	ENST00000345506	NM_003152.3	497	gCc/gAc	14/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.93	2		952	688	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244826	41244826	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs80356978	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	235	654	0	ENST00000357654.3:c.2722G>T	p.Glu908Ter	p.E908*	ENST00000357654	NM_007294.3	908	Gaa/Taa	10/23	1	2	FACETS	0.877	0.825	0.93	0.877	0.825	0.93	CLONAL	1	TRUE	1	0.93	2		654	576	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244869	41244869	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781771	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	210	612	0	ENST00000357654.3:c.2679G>T	p.Lys893Asn	p.K893N	ENST00000357654	NM_007294.3	893	aaG/aaT	10/23	1	2	FACETS	0.916	0.859	0.973	0.916	0.859	0.973	CLONAL	1	TRUE	1	0.93	2		612	493	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554341	63554341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767445163	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	196	649	0	ENST00000307078.5:c.398C>T	p.Ala133Val	p.A133V	ENST00000307078	NM_004655.3	133	gCg/gTg	2/11	1	2	FACETS	0.96	0.9	1	0.96	0.9	1	CLONAL	1	TRUE	1	0.93	2		649	439	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78765281	78765281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1361255662	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	81	299	0	ENST00000306801.3:c.862C>T	p.Pro288Ser	p.P288S	ENST00000306801	NM_020761.2	288	Cct/Tct	7/34	1	2	FACETS	0.512	0.455	0.573	0.512	0.455	0.573	SUBCLONAL	1	TRUE	1	0.93	2		299	340	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867622	78867622	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	261	805	0	ENST00000306801.3:c.2358G>T	p.Lys786Asn	p.K786N	ENST00000306801	NM_020761.2	786	aaG/aaT	20/34	1	2	FACETS	0.892	0.842	0.943	0.892	0.842	0.943	CLONAL	1	TRUE	1	0.93	2		805	629	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56409133	56409133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	129	309	1	ENST00000348428.3:c.1640C>T	p.Ala547Val	p.A547V	ENST00000348428	NM_006785.3	547	gCt/gTt	14/17	1	2	FACETS	0.97	0.895	1	0.97	0.895	1	CLONAL	1	TRUE	1	0.93	2		310	286	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212111	5212111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	291	825	0	ENST00000357368.4:c.4920C>A	p.Phe1640Leu	p.F1640L	ENST00000357368	NM_002850.3	1640	ttC/ttA	32/38	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.93	2		825	619	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7163175	7163175	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1283232736	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	193	639	0	ENST00000302850.5:c.1897A>G	p.Asn633Asp	p.N633D	ENST00000302850	NM_000208.2	633	Aac/Gac	9/22	1	2	FACETS	0.91	0.851	0.97	0.91	0.851	0.97	CLONAL	1	TRUE	1	0.93	2		639	456	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15365064	15365064	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	198	563	0	ENST00000263377.2:c.2057T>G	p.Val686Gly	p.V686G	ENST00000263377	NM_058243.2	686	gTt/gGt	11/20	1	2	FACETS	0.885	0.828	0.943	0.885	0.828	0.943	CLONAL	1	TRUE	1	0.93	2		563	481	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950424	17950424	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	126	664	0	ENST00000458235.1:c.1303A>G	p.Thr435Ala	p.T435A	ENST00000458235	NM_000215.3	435	Aca/Gca	10/24	1	2	FACETS	0.498	0.453	0.545	0.498	0.453	0.545	SUBCLONAL	1	TRUE	1	0.93	2		664	544	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954674	17954674	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	317	869	1	ENST00000458235.1:c.220G>T	p.Ala74Ser	p.A74S	ENST00000458235	NM_000215.3	74	Gcc/Tcc	3/24	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.93	2		870	629	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383677	42383677	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1221821073	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	195	753	0	ENST00000221972.3:c.452T>C	p.Ile151Thr	p.I151T	ENST00000221972	NM_021601.3	151	aTc/aCc	3/5	1	2	FACETS	0.978	0.916	1	0.978	0.916	1	CLONAL	1	TRUE	1	0.93	2		753	429	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966540	25966540	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	242	655	0	ENST00000435504.4:c.2666C>A	p.Ser889Tyr	p.S889Y	ENST00000435504		889	tCt/tAt	13/13	1	2	FACETS	0.891	0.839	0.944	0.891	0.839	0.944	CLONAL	1	TRUE	1	0.93	2		655	584	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449913	29449913	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	359	1020	0	ENST00000389048.3:c.2942T>G	p.Ile981Ser	p.I981S	ENST00000389048	NM_004304.4	981	aTt/aGt	18/29	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.93	2		1020	731	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234311	39234311	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	116	284	0	ENST00000402219.2:c.2534T>G	p.Leu845Ter	p.L845*	ENST00000402219	NM_005633.3	845	tTa/tGa	16/23	1	2	FACETS	0.725	0.661	0.791	0.725	0.661	0.791	SUBCLONAL	1	TRUE	1	0.93	2		284	344	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027750	48027750	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	146	323	0	ENST00000234420.5:c.2628A>C	p.Glu876Asp	p.E876D	ENST00000234420	NM_000179.2	876	gaA/gaC	4/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.93	2		323	288	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61706056	61706056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	265	540	0	ENST00000401558.2:c.3115G>A	p.Glu1039Lys	p.E1039K	ENST00000401558	NM_003400.3	1039	Gaa/Aaa	25/25	0.3	4	FACETS	0.977	0.925	1			1	INDETERMINATE	2	TRUE	NA	0.93	4		540	563	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715373	61715373	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	197	499	0	ENST00000401558.2:c.2240G>T	p.Ser747Ile	p.S747I	ENST00000401558	NM_003400.3	747	aGt/aTt	19/25	0.3	4	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.93	4		499	546	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719832	61719832	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	231	494	0	ENST00000401558.2:c.1436A>C	p.Lys479Thr	p.K479T	ENST00000401558	NM_003400.3	479	aAg/aCg	14/25	0.3	4	FACETS	0.955	0.9	1			1	INDETERMINATE	2	TRUE	NA	0.93	4		494	502	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726855	61726855	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	128	295	0	ENST00000401558.2:c.583A>C	p.Lys195Gln	p.K195Q	ENST00000401558	NM_003400.3	195	Aaa/Caa	7/25	0.3	4	FACETS	0.803	0.737	0.869			1	INDETERMINATE	2	TRUE	NA	0.93	4		295	331	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872622	136872622	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	152	415	1	ENST00000241393.3:c.876C>A	p.Phe292Leu	p.F292L	ENST00000241393	NM_003467.2	292	ttC/ttA	2/2	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.93	2		416	314	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873397	136873397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	129	407	0	ENST00000241393.3:c.101C>T	p.Ala34Val	p.A34V	ENST00000241393	NM_003467.2	34	gCt/gTt	2/2	1	2	FACETS	0.862	0.793	0.932	0.862	0.793	0.932	CLONAL	1	TRUE	1	0.93	2		407	322	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285193	198285193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	190	386	0	ENST00000335508.6:c.374C>T	p.Thr125Ile	p.T125I	ENST00000335508	NM_012433.2	125	aCc/aTc	4/25	1	2	FACETS	0.968	0.907	1	0.968	0.907	1	CLONAL	1	TRUE	1	0.93	2		386	422	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136289	202136289	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	120	446	0	ENST00000358485.4:c.533C>A	p.Ser178Tyr	p.S178Y	ENST00000358485	NM_001080125.1	178	tCt/tAt	3/9	1	2	FACETS	0.587	0.533	0.642	0.587	0.533	0.642	SUBCLONAL	1	TRUE	1	0.93	2		446	440	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242800926	242800926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	214	785	0	ENST00000334409.5:c.65G>A	p.Gly22Glu	p.G22E	ENST00000334409	NM_005018.2	22	gGa/gAa	1/5	1	2	FACETS	0.906	0.85	0.962	0.906	0.85	0.962	CLONAL	1	TRUE	1	0.93	2		785	508	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39690063	39690063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	75	155	0	ENST00000361337.2:c.88G>A	p.Asp30Asn	p.D30N	ENST00000361337	NM_003286.2	30	Gat/Aat	3/21	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		155	186	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39726971	39726971	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	71	150	0	ENST00000361337.2:c.969G>T	p.Glu323Asp	p.E323D	ENST00000361337	NM_003286.2	323	gaG/gaT	11/21	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		150	164	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944600	40944600	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	106	377	0	ENST00000373198.4:c.1902G>T	p.Gln634His	p.Q634H	ENST00000373198	NM_133170.3	634	caG/caT	12/32	0.3	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		377	233	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252889	36252889	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	155	351	0	ENST00000300305.3:c.473T>G	p.Phe158Cys	p.F158C	ENST00000300305		158	tTt/tGt	4/8	0.213346112869584	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		351	368	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657017	45657017	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	205	603	0	ENST00000407780.3:c.139T>G	p.Leu47Val	p.L47V	ENST00000407780	NM_001283052.1	47	Tta/Gta	3/7	0.3	1	FACETS	0.556	0.523	0.59	0.556	0.523	0.59	INDETERMINATE	1	TRUE	0	0.93	1		603	424	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038196	30038196	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	137	364	0	ENST00000338641.4:c.369G>T	p.Lys123Asn	p.K123N	ENST00000338641	NM_000268.3	123	aaG/aaT	4/16	1	2	FACETS	0.856	0.79	0.924	0.856	0.79	0.924	CLONAL	1	TRUE	1	0.93	2		364	344	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37059066	37059066	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	164	374	0	ENST00000231790.2:c.860A>G	p.Asn287Ser	p.N287S	ENST00000231790	NM_000249.3	287	aAc/aGc	10/19	0.10198407593633	3	FACETS	1	0.989	1	0.685	0.638	0.733	INDETERMINATE	1	TRUE	1	0.93	3		374	377	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165167	47165167	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326993979	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	121	260	1	ENST00000409792.3:c.959G>A	p.Gly320Asp	p.G320D	ENST00000409792	NM_014159.6	320	gGt/gAt	3/21	0.10198407593633	3	FACETS	1	0.986	1	0.709	0.652	0.766	INDETERMINATE	1	TRUE	1	0.93	3		261	269	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165465	47165465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	179	421	0	ENST00000409792.3:c.661G>A	p.Val221Ile	p.V221I	ENST00000409792	NM_014159.6	221	Gtt/Att	3/21	0.10198407593633	3	FACETS	1	0.991	1	0.705	0.659	0.752	INDETERMINATE	1	TRUE	1	0.93	3		421	400	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49929262	49929262	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	214	522	0	ENST00000296474.3:c.3281G>A	p.Gly1094Glu	p.G1094E	ENST00000296474	NM_002447.2	1094	gGa/gAa	15/20	0.10198407593633	3	FACETS	1	0.992	1	0.688	0.646	0.73	INDETERMINATE	1	TRUE	1	0.93	3		522	490	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114601	73114601	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs775783057	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	39	241	0	ENST00000356692.5:c.982G>T	p.Glu328Ter	p.E328*	ENST00000356692		328	Gaa/Taa	9/9	0.10198407593633	3	FACETS	0.768	0.646	0.899	0.384	0.323	0.45	INDETERMINATE	1	TRUE	1	0.93	3		241	160	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670362	134670362	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	112	510	0	ENST00000398015.3:c.273C>A	p.Phe91Leu	p.F91L	ENST00000398015	NM_004441.4	91	ttC/ttA	3/16	0.3	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		510	231	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178201	142178201	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	145	255	0	ENST00000350721.4:c.7217T>G	p.Leu2406Arg	p.L2406R	ENST00000350721	NM_001184.3	2406	cTt/cGt	43/47	0.10198407593633	3	FACETS	0.819	0.763	0.874	0.819	0.763	0.874	INDETERMINATE	2	TRUE	1	0.93	3		255	279	SUCCESS
ATR	545	MSKCC	GRCh37	3	142232476	142232476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755364026	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	117	256	0	ENST00000350721.4:c.4508G>A	p.Arg1503Gln	p.R1503Q	ENST00000350721	NM_001184.3	1503	cGa/cAa	26/47	0.10198407593633	3	FACETS	1	0.985	1	0.685	0.629	0.742	INDETERMINATE	1	TRUE	1	0.93	3		256	269	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259851	142259851	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	206	399	1	ENST00000350721.4:c.3476T>C	p.Met1159Thr	p.M1159T	ENST00000350721	NM_001184.3	1159	aTg/aCg	18/47	0.10198407593633	3	FACETS	1	0.992	1	0.712	0.668	0.755	INDETERMINATE	1	TRUE	1	0.93	3		400	456	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916651	178916651	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	136	316	0	ENST00000263967.3:c.38T>C	p.Ile13Thr	p.I13T	ENST00000263967	NM_006218.2	13	aTc/aCc	2/21	0.10198407593633	3	FACETS	0.785	0.728	0.841	0.785	0.728	0.841	INDETERMINATE	2	TRUE	1	0.93	3		316	273	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502876	186502876	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	178	333	0	ENST00000323963.5:c.334G>T	p.Glu112Ter	p.E112*	ENST00000323963		112	Gaa/Taa	4/11	0.10198407593633	3	FACETS	1	0.99	1	0.687	0.641	0.733	INDETERMINATE	1	TRUE	1	0.93	3		333	408	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980404	1980404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	354	930	1	ENST00000382891.5:c.3866G>A	p.Gly1289Asp	p.G1289D	ENST00000382891	NM_133335.3	1289	gGc/gAc	22/22	1	2	FACETS	0.981	0.935	1	0.981	0.935	1	CLONAL	1	TRUE	1	0.93	2		931	776	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146523	55146523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	96	313	0	ENST00000257290.5:c.2197G>A	p.Asp733Asn	p.D733N	ENST00000257290	NM_006206.4	733	Gac/Aac	16/23	1	2	FACETS	0.89	0.808	0.973	0.89	0.808	0.973	CLONAL	1	TRUE	1	0.93	2		313	232	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953804	55953804	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	168	465	0	ENST00000263923.4:c.3632A>C	p.Lys1211Thr	p.K1211T	ENST00000263923	NM_002253.2	1211	aAa/aCa	27/30	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.93	2		465	361	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970882	55970882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	164	481	0	ENST00000263923.4:c.1915G>A	p.Asp639Asn	p.D639N	ENST00000263923	NM_002253.2	639	Gac/Aac	13/30	1	2	FACETS	0.943	0.878	1	0.943	0.878	1	CLONAL	1	TRUE	1	0.93	2		481	374	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361171	66361171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	107	313	0	ENST00000273854.3:c.1001C>T	p.Thr334Ile	p.T334I	ENST00000273854	NM_004439.5	334	aCc/aTc	4/18	1	2	FACETS	0.913	0.834	0.993	0.913	0.834	0.993	CLONAL	1	TRUE	1	0.93	2		313	252	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007320	143007320	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	104	305	0	ENST00000262992.4:c.2464G>T	p.Glu822Ter	p.E822*	ENST00000262992	NM_001101669.1	822	Gaa/Taa	22/24	1	2	FACETS	0.796	0.724	0.87	0.796	0.724	0.87	SUBCLONAL	1	TRUE	1	0.93	2		305	281	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029259	143029259	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	58	221	0	ENST00000262992.4:c.2361G>T	p.Lys787Asn	p.K787N	ENST00000262992	NM_001101669.1	787	aaG/aaT	21/24	1	2	FACETS	0.685	0.6	0.775	0.685	0.6	0.775	SUBCLONAL	1	TRUE	1	0.93	2		221	182	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271212	153271212	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs770911310	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	102	170	0	ENST00000281708.4:c.566A>G	p.Lys189Arg	p.K189R	ENST00000281708	NM_033632.3	189	aAa/aGa	3/12	1	2	FACETS	0.966	0.883	1	0.966	0.883	1	CLONAL	1	TRUE	1	0.93	2		170	227	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524374	187524374	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	143	495	0	ENST00000441802.2:c.11306T>C	p.Phe3769Ser	p.F3769S	ENST00000441802	NM_005245.3	3769	tTt/tCt	19/27	1	2	FACETS	0.82	0.757	0.885	0.82	0.757	0.885	CLONAL	1	TRUE	1	0.93	2		495	375	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540113	187540113	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	115	406	0	ENST00000441802.2:c.7627A>C	p.Asn2543His	p.N2543H	ENST00000441802	NM_005245.3	2543	Aat/Cat	10/27	1	2	FACETS	0.893	0.818	0.969	0.893	0.818	0.969	CLONAL	1	TRUE	1	0.93	2		406	277	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540605	187540605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	150	412	0	ENST00000441802.2:c.7135G>A	p.Asp2379Asn	p.D2379N	ENST00000441802	NM_005245.3	2379	Gac/Aac	10/27	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.93	2		412	312	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541943	187541943	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	159	498	0	ENST00000441802.2:c.5797A>G	p.Thr1933Ala	p.T1933A	ENST00000441802	NM_005245.3	1933	Act/Gct	10/27	1	2	FACETS	0.872	0.81	0.936	0.872	0.81	0.936	CLONAL	1	TRUE	1	0.93	2		498	392	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874597	35874597	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	137	463	0	ENST00000303115.3:c.753C>A	p.Phe251Leu	p.F251L	ENST00000303115	NM_002185.3	251	ttC/ttA	6/8	0.213346112869584	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		463	317	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945727	38945727	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	101	232	0	ENST00000357387.3:c.4499C>T	p.Ala1500Val	p.A1500V	ENST00000357387	NM_152756.3	1500	gCc/gTc	34/38	0.10198407593633	3	FACETS	1	0.985	1	0.73	0.667	0.793	INDETERMINATE	1	TRUE	1	0.93	3		232	218	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947377	38947377	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	78	164	0	ENST00000357387.3:c.4303G>T	p.Asp1435Tyr	p.D1435Y	ENST00000357387	NM_152756.3	1435	Gat/Tat	32/38	0.10198407593633	3	FACETS	1	0.98	1	0.719	0.648	0.79	INDETERMINATE	1	TRUE	1	0.93	3		164	171	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950364	38950364	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	147	405	0	ENST00000357387.3:c.3586G>T	p.Glu1196Ter	p.E1196*	ENST00000357387	NM_152756.3	1196	Gaa/Taa	31/38	0.10198407593633	3	FACETS	1	0.989	1	0.728	0.676	0.781	INDETERMINATE	1	TRUE	1	0.93	3		405	318	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959396	38959396	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	116	287	0	ENST00000357387.3:c.2079C>A	p.Asn693Lys	p.N693K	ENST00000357387	NM_152756.3	693	aaC/aaA	22/38	0.10198407593633	3	FACETS	1	0.983	1	0.653	0.598	0.708	INDETERMINATE	1	TRUE	1	0.93	3		287	280	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962617	38962617	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	112	295	0	ENST00000357387.3:c.1638G>A	p.Trp546Ter	p.W546*	ENST00000357387	NM_152756.3	546	tgG/tgA	18/38	0.10198407593633	3	FACETS	1	0.977	1	0.61	0.557	0.665	INDETERMINATE	1	TRUE	1	0.93	3		295	289	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38996935	38996935	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	189	413	0	ENST00000357387.3:c.442C>T	p.Arg148Ter	p.R148*	ENST00000357387	NM_152756.3	148	Cga/Tga	6/38	0.10198407593633	3	FACETS	1	0.989	1	0.662	0.618	0.705	INDETERMINATE	1	TRUE	1	0.93	3		413	450	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39003697	39003697	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	162	276	0	ENST00000357387.3:c.223G>T	p.Glu75Ter	p.E75*	ENST00000357387	NM_152756.3	75	Gaa/Taa	4/38	0.10198407593633	3	FACETS	0.766	0.715	0.818	0.766	0.715	0.818	INDETERMINATE	2	TRUE	1	0.93	3		276	333	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575478	67575478	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	172	332	0	ENST00000274335.5:c.551A>C	p.Asp184Ala	p.D184A	ENST00000274335		184	gAc/gCc	4/15	0.10198407593633	3	FACETS	1	0.991	1	0.728	0.68	0.777	INDETERMINATE	1	TRUE	1	0.93	3		332	372	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79952236	79952236	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	86	223	0	ENST00000265081.6:c.244G>T	p.Glu82Ter	p.E82*	ENST00000265081	NM_002439.4	82	Gaa/Taa	2/24	0.10198407593633	3	FACETS	1	0.972	1	0.613	0.552	0.675	INDETERMINATE	1	TRUE	1	0.93	3		223	221	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80021286	80021286	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	162	340	0	ENST00000265081.6:c.1355G>T	p.Arg452Ile	p.R452I	ENST00000265081	NM_002439.4	452	aGa/aTa	9/24	0.10198407593633	3	FACETS	1	0.986	1	0.632	0.586	0.678	INDETERMINATE	1	TRUE	1	0.93	3		340	404	SUCCESS
APC	324	MSKCC	GRCh37	5	112090693	112090693	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	79	207	0	ENST00000257430.4:c.106A>C	p.Lys36Gln	p.K36Q	ENST00000257430	NM_000038.5	36	Aaa/Caa	2/16	0.10198407593633	3	FACETS	1	0.971	1	0.625	0.561	0.691	INDETERMINATE	1	TRUE	1	0.93	3		207	199	SUCCESS
APC	324	MSKCC	GRCh37	5	112176660	112176660	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	74	248	0	ENST00000257430.4:c.5369G>T	p.Arg1790Ile	p.R1790I	ENST00000257430	NM_000038.5	1790	aGa/aTa	16/16	0.10198407593633	3	FACETS	1	0.969	1	0.623	0.557	0.691	INDETERMINATE	1	TRUE	1	0.93	3		248	187	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925500	131925500	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs867459964	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	129	226	0	ENST00000265335.6:c.1423C>A	p.Leu475Ile	p.L475I	ENST00000265335		475	Ctt/Att	9/25	0.10198407593633	3	FACETS	1	0.986	1	0.673	0.62	0.726	INDETERMINATE	1	TRUE	1	0.93	3		226	302	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131951738	131951738	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs77642085	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	90	197	0	ENST00000265335.6:c.3080G>T	p.Arg1027Ile	p.R1027I	ENST00000265335		1027	aGa/aTa	20/25	0.10198407593633	3	FACETS	1	0.978	1	0.65	0.589	0.713	INDETERMINATE	1	TRUE	1	0.93	3		197	218	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513278	149513278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	185	647	2	ENST00000261799.4:c.805C>T	p.Pro269Ser	p.P269S	ENST00000261799	NM_002609.3	269	Cct/Tct	6/23	1	2	FACETS	0.992	0.929	1	0.992	0.929	1	CLONAL	1	TRUE	1	0.93	2		649	401	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045921	180045921	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	110	548	0	ENST00000261937.6:c.2851-1G>A		p.X951_splice	ENST00000261937	NM_182925.4	951			1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.93	2		548	229	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30676062	30676062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	176	469	0	ENST00000376406.3:c.2294C>T	p.Thr765Ile	p.T765I	ENST00000376406	NM_014641.2	765	aCc/aTc	8/15	1	2	FACETS	0.939	0.876	1	0.939	0.876	1	CLONAL	1	TRUE	1	0.93	2		469	403	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289240	33289240	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	176	578	0	ENST00000374542.5:c.312G>T	p.Glu104Asp	p.E104D	ENST00000374542	NM_001141970.1	104	gaG/gaT	3/8	1	2	FACETS	0.847	0.788	0.906	0.847	0.788	0.906	CLONAL	1	TRUE	1	0.93	2		578	447	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609843	117609843	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	149	516	0	ENST00000368508.3:c.6856G>T	p.Glu2286Ter	p.E2286*	ENST00000368508	NM_002944.2	2286	Gaa/Taa	43/43	1	2	FACETS	0.815	0.754	0.878	0.815	0.754	0.878	CLONAL	1	TRUE	1	0.93	2		516	393	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686322	117686322	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141385549	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	82	240	0	ENST00000368508.3:c.3019G>A	p.Gly1007Arg	p.G1007R	ENST00000368508	NM_002944.2	1007	Gga/Aga	20/43	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.93	2		240	173	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686823	117686823	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	114	400	0	ENST00000368508.3:c.2894T>A	p.Phe965Tyr	p.F965Y	ENST00000368508	NM_002944.2	965	tTt/tAt	19/43	1	2	FACETS	0.898	0.823	0.975	0.898	0.823	0.975	CLONAL	1	TRUE	1	0.93	2		400	273	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382257	152382257	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	120	274	0	ENST00000206249.3:c.1367C>A	p.Ser456Tyr	p.S456Y	ENST00000206249	NM_000125.3	456	tCt/tAt	6/8	1	2	FACETS	0.846	0.776	0.918	0.846	0.776	0.918	CLONAL	1	TRUE	1	0.93	2		274	305	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528546	157528546	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	203	693	0	ENST00000346085.5:c.6271A>C	p.Ile2091Leu	p.I2091L	ENST00000346085	NM_020732.3	2091	Atc/Ctc	20/20	1	2	FACETS	0.941	0.882	1	0.941	0.882	1	CLONAL	1	TRUE	1	0.93	2		693	464	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14027749	14027749	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	122	311	0	ENST00000405192.2:c.95G>T	p.Arg32Ile	p.R32I	ENST00000405192	NM_001163147.1	32	aGa/aTa	3/12	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		311	324	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481451	140481451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	143	424	0	ENST00000288602.6:c.1357C>T	p.Pro453Ser	p.P453S	ENST00000288602	NM_004333.4	453	Cct/Tct	11/18	0.10198407593633	3	FACETS	0.961	0.883	1	0.48	0.441	0.521	INDETERMINATE	1	TRUE	1	0.93	3		424	469	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524317	148524317	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	142	345	0	ENST00000320356.2:c.667A>T	p.Ile223Phe	p.I223F	ENST00000320356	NM_004456.4	223	Att/Ttt	7/20	0.10198407593633	3	FACETS	1	0.988	1	0.71	0.658	0.763	INDETERMINATE	1	TRUE	1	0.93	3		345	315	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873896	151873896	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	162	476	0	ENST00000262189.6:c.8642G>T	p.Arg2881Ile	p.R2881I	ENST00000262189	NM_170606.2	2881	aGa/aTa	38/59	0.10198407593633	3	FACETS	1	0.989	1	0.684	0.636	0.732	INDETERMINATE	1	TRUE	1	0.93	3		476	373	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879203	151879203	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	156	538	0	ENST00000262189.6:c.5742T>A	p.Phe1914Leu	p.F1914L	ENST00000262189	NM_170606.2	1914	ttT/ttA	36/59	0.10198407593633	3	FACETS	1	0.989	1	0.7	0.651	0.75	INDETERMINATE	1	TRUE	1	0.93	3		538	351	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132811	152132811	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	228	618	0	ENST00000262189.6:c.61G>T	p.Glu21Ter	p.E21*	ENST00000262189	NM_170606.2	21	Gag/Tag	1/59	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		618	520	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539127	23539127	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	137	457	0	ENST00000380871.4:c.312G>T	p.Leu104Phe	p.L104F	ENST00000380871	NM_006167.3	104	ttG/ttT	2/2	1	2	FACETS	0.839	0.774	0.906	0.839	0.774	0.906	CLONAL	1	TRUE	1	0.93	2		457	351	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931805	68931805	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	104	397	0	ENST00000288368.4:c.235G>T	p.Asp79Tyr	p.D79Y	ENST00000288368	NM_024870.2	79	Gac/Tac	3/40	0.258321414544118	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		397	299	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931896	68931896	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	154	464	0	ENST00000288368.4:c.326T>G	p.Phe109Cys	p.F109C	ENST00000288368	NM_024870.2	109	tTt/tGt	3/40	0.258321414544118	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		464	353	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021660	69021660	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs554090253	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	90	369	0	ENST00000288368.4:c.2948G>A	p.Ser983Asn	p.S983N	ENST00000288368	NM_024870.2	983	aGc/aAc	25/40	0.258321414544118	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		369	266	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028028	69028028	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	106	411	0	ENST00000288368.4:c.3187A>C	p.Lys1063Gln	p.K1063Q	ENST00000288368	NM_024870.2	1063	Aag/Cag	26/40	0.258321414544118	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		411	245	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5462929	5462929	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	116	259	2	ENST00000381577.3:c.490G>T	p.Glu164Ter	p.E164*	ENST00000381577	NM_014143.3	164	Gaa/Taa	4/7	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		261	286	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5563174	5563174	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	158	296	0	ENST00000397747.3:c.779G>T	p.Arg260Ile	p.R260I	ENST00000397747	NM_025239.3	260	aGa/aTa	6/7	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		296	371	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966671	36966671	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	179	502	0	ENST00000358127.4:c.655T>G	p.Phe219Val	p.F219V	ENST00000358127	NM_001280556.1	219	Ttc/Gtc	6/10	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		502	394	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342691	87342691	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	135	513	0	ENST00000277120.3:c.976G>T	p.Glu326Ter	p.E326*	ENST00000277120		326	Gag/Tag	9/19	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		513	346	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270558	98270558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	103	165	0	ENST00000331920.6:c.86G>A	p.Gly29Glu	p.G29E	ENST00000331920	NM_000264.3	29	gGa/gAa	1/24	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		165	191	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894935	101894935	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	127	269	0	ENST00000374994.4:c.488A>G	p.Asp163Gly	p.D163G	ENST00000374994	NM_004612.2	163	gAc/gGc	3/9	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		269	312	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755947	133755947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	190	557	0	ENST00000318560.5:c.1574C>T	p.Ala525Val	p.A525V	ENST00000318560	NM_005157.4	525	gCc/gTc	10/11	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		557	474	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393687	139393687	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	275	898	0	ENST00000277541.6:c.5959G>T	p.Asp1987Tyr	p.D1987Y	ENST00000277541	NM_017617.3	1987	Gac/Tac	32/34	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		898	632	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20150333	20150333	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	117	350	0	ENST00000379607.5:c.304A>T	p.Ser102Cys	p.S102C	ENST00000379607	NM_001412.3	102	Agt/Tgt	5/7	0.303266542483354	1	FACETS	0.361	0.328	0.394	0.361	0.328	0.394	INDETERMINATE	1	TRUE	0	0.93	1		350	373	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932170	39932170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780523057	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	174	882	0	ENST00000378444.4:c.2429G>A	p.Arg810Gln	p.R810Q	ENST00000378444	NM_001123385.1	810	cGa/cAa	4/15	0.303266542483354	1	FACETS	0.373	0.345	0.401	0.373	0.345	0.401	INDETERMINATE	1	TRUE	0	0.93	1		882	537	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932683	39932683	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	108	947	0	ENST00000378444.4:c.1916T>G	p.Phe639Cys	p.F639C	ENST00000378444	NM_001123385.1	639	tTt/tGt	4/15	0.303266542483354	1	FACETS	0.228	0.205	0.253	0.228	0.205	0.253	INDETERMINATE	1	TRUE	0	0.93	1		947	544	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820533	44820533	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	138	356	0	ENST00000377967.4:c.230T>G	p.Val77Gly	p.V77G	ENST00000377967	NM_021140.2	77	gTt/gGt	3/29	0.303266542483354	1	FACETS	0.464	0.428	0.501	0.464	0.428	0.501	INDETERMINATE	1	TRUE	0	0.93	1		356	342	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041645	47041645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782408699	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	134	697	2	ENST00000377604.3:c.1870G>A	p.Asp624Asn	p.D624N	ENST00000377604	NM_001204468.1	624	Gac/Aac	17/24	0.303266542483354	1	FACETS	0.367	0.336	0.399	0.367	0.336	0.399	INDETERMINATE	1	TRUE	0	0.93	1		699	420	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411810	63411810	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	180	914	0	ENST00000330258.3:c.1357C>A	p.Leu453Ile	p.L453I	ENST00000330258	NM_152424.3	453	Ctt/Att	2/2	0.303266542483354	1	FACETS	0.515	0.481	0.549	0.515	0.481	0.549	INDETERMINATE	1	TRUE	0	0.93	1		914	402	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338650	70338650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	151	741	4	ENST00000374080.3:c.46C>T	p.Arg16Trp	p.R16W	ENST00000374080		16	Cgg/Tgg	1/45	0.303266542483354	1	FACETS	0.38	0.35	0.411	0.38	0.35	0.411	INDETERMINATE	1	TRUE	0	0.93	1		745	457	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855046	76855046	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	117	382	0	ENST00000373344.5:c.5790G>T	p.Lys1930Asn	p.K1930N	ENST00000373344	NM_000489.3	1930	aaG/aaT	25/35	0.303266542483354	1	FACETS	0.438	0.401	0.477	0.438	0.401	0.477	INDETERMINATE	1	TRUE	0	0.93	1		382	307	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890192	76890192	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	48	332	0	ENST00000373344.5:c.4702G>A	p.Val1568Ile	p.V1568I	ENST00000373344	NM_000489.3	1568	Gtt/Att	17/35	0.303266542483354	1	FACETS	0.187	0.159	0.218	0.187	0.159	0.218	INDETERMINATE	1	TRUE	0	0.93	1		332	295	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613678	100613678	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	160	451	2	ENST00000308731.7:c.901G>T	p.Glu301Ter	p.E301*	ENST00000308731	NM_000061.2	301	Gaa/Taa	11/19	0.303266542483354	1	FACETS	0.628	0.588	0.668	0.628	0.588	0.668	INDETERMINATE	1	TRUE	0	0.93	1		453	293	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034462	123034462	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	117	378	0	ENST00000355640.3:c.1219C>A	p.Leu407Ile	p.L407I	ENST00000355640		407	Ctt/Att	6/7	0.303266542483354	1	FACETS	0.415	0.379	0.453	0.415	0.379	0.453	INDETERMINATE	1	TRUE	0	0.93	1		378	324	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190069	123190069	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	69	351	0	ENST00000218089.9:c.1288G>T	p.Glu430Ter	p.E430*	ENST00000218089	NM_001042749.1	430	Gaa/Taa	14/35	0.303266542483354	1	FACETS	0.216	0.189	0.245	0.216	0.189	0.245	INDETERMINATE	1	TRUE	0	0.93	1		351	367	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202452	123202452	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	113	393	0	ENST00000218089.9:c.2304T>G	p.Phe768Leu	p.F768L	ENST00000218089	NM_001042749.1	768	ttT/ttG	24/35	0.303266542483354	1	FACETS	0.371	0.338	0.406	0.371	0.338	0.406	INDETERMINATE	1	TRUE	0	0.93	1		393	350	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211862	123211862	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	105	409	0	ENST00000218089.9:c.2729T>A	p.Ile910Lys	p.I910K	ENST00000218089	NM_001042749.1	910	aTa/aAa	27/35	0.303266542483354	1	FACETS	0.357	0.323	0.393	0.357	0.323	0.393	INDETERMINATE	1	TRUE	0	0.93	1		409	338	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224466	123224466	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	116	480	0	ENST00000218089.9:c.3319G>T	p.Glu1107Ter	p.E1107*	ENST00000218089	NM_001042749.1	1107	Gaa/Taa	31/35	0.303266542483354	1	FACETS	0.374	0.34	0.408	0.374	0.34	0.408	INDETERMINATE	1	TRUE	0	0.93	1		480	357	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777624	9777624	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	62	784	0	ENST00000377346.4:c.960G>T	p.Glu320Asp	p.E320D	ENST00000377346	NM_005026.3	320	gaG/gaT	8/24	1	2	FACETS	0.203	0.175	0.233	0.203	0.175	0.233	SUBCLONAL	1	TRUE	1	0.93	2		784	658	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63810647	63810647	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	16	181	0	ENST00000279873.7:c.734C>T	p.Ala245Val	p.A245V	ENST00000279873	NM_032199.2	245	gCg/gTg	5/10	0.10198407593633	3	FACETS	0.226	0.167	0.296	0.113	0.083	0.148	INDETERMINATE	1	TRUE	1	0.93	3		181	223	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258036	123258036	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519045	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	11	428	0	ENST00000358487.5:c.1645A>C	p.Asn549His	p.N549H	ENST00000358487	NM_000141.4	549	Aat/Cat	12/18	0.10198407593633	3	FACETS	0.08	0.055	0.112	0.04	0.027	0.056	INDETERMINATE	1	TRUE	1	0.93	3		428	432	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154421	2154421	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	35	877	0	ENST00000434045.2:c.507C>A	p.Phe169Leu	p.F169L	ENST00000434045	NM_001127598.1	169	ttC/ttA	5/5	1	2	FACETS	0.147	0.12	0.177	0.147	0.12	0.177	SUBCLONAL	1	TRUE	1	0.93	2		877	513	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999086	100999086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	73	753	0	ENST00000325455.5:c.716G>A	p.Gly239Asp	p.G239D	ENST00000325455	NM_001202474.3	239	gGc/gAc	1/8	1	2	FACETS	0.4	0.352	0.452	0.4	0.352	0.452	SUBCLONAL	1	TRUE	1	0.93	2		753	392	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435082	18435082	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	18	287	0	ENST00000266497.5:c.67G>T	p.Glu23Ter	p.E23*	ENST00000266497		23	Gaa/Taa	1/31	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		287	249	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800957	18800957	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	14	292	0	ENST00000266497.5:c.4333A>G	p.Ile1445Val	p.I1445V	ENST00000266497		1445	Att/Gtt	31/31	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		292	271	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26970475	26970475	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	16	147	0	ENST00000381527.3:c.844G>T	p.Asp282Tyr	p.D282Y	ENST00000381527	NM_001260.1	282	Gat/Tat	8/13	0.3	1	FACETS	0.106	0.078	0.138	0.106	0.078	0.138	INDETERMINATE	1	TRUE	0	0.93	1		147	174	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911760	32911760	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	57	480	0	ENST00000380152.3:c.3268A>C	p.Met1090Leu	p.M1090L	ENST00000380152		1090	Atg/Ctg	11/27	0.10198407593633	3	FACETS	0.396	0.341	0.457	0.198	0.17	0.229	INDETERMINATE	1	TRUE	1	0.93	3		480	453	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346320	73346320	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	32	248	0	ENST00000377767.4:c.1480G>T	p.Glu494Ter	p.E494*	ENST00000377767	NM_014953.3	494	Gaa/Taa	10/21	0.10198407593633	3	FACETS	0.311	0.253	0.377	0.156	0.126	0.189	INDETERMINATE	1	TRUE	1	0.93	3		248	324	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988353	36988353	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	15	350	0	ENST00000354822.5:c.300G>T	p.Met100Ile	p.M100I	ENST00000354822	NM_001079668.2	100	atG/atT	2/3	1	2	FACETS	0.138	0.101	0.183	0.138	0.101	0.183	SUBCLONAL	1	TRUE	1	0.93	2		350	233	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041753	42041753	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	23	424	0	ENST00000219905.7:c.5948C>A	p.Ser1983Ter	p.S1983*	ENST00000219905	NM_001164273.1	1983	tCa/tAa	17/24	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		424	300	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66679759	66679759	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	33	465	0	ENST00000307102.5:c.74C>A	p.Ser25Tyr	p.S25Y	ENST00000307102	NM_002755.3	25	tCt/tAt	1/11	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		465	411	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440009	99440009	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	28	314	0	ENST00000268035.6:c.977G>C	p.Gly326Ala	p.G326A	ENST00000268035	NM_000875.3	326	gGt/gCt	4/21	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		314	361	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892306	9892306	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	16	394	0	ENST00000330684.3:c.2184C>A	p.Phe728Leu	p.F728L	ENST00000330684	NM_001134407.1	728	ttC/ttA	11/13	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		394	235	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916274	9916274	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	40	341	0	ENST00000330684.3:c.2015G>T	p.Arg672Ile	p.R672I	ENST00000330684	NM_001134407.1	672	aGa/aTa	10/13	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		341	199	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662298	67662298	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	28	408	0	ENST00000264010.4:c.1544G>A	p.Arg515His	p.R515H	ENST00000264010	NM_006565.3	515	cGc/cAc	9/12	0.3	3	FACETS	0.233	0.186	0.287			1	INDETERMINATE	1	TRUE	NA	0.93	3		408	378	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827580	72827580	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	27	470	0	ENST00000268489.5:c.9001G>T	p.Glu3001Ter	p.E3001*	ENST00000268489	NM_006885.3	3001	Gaa/Taa	9/10	0.3	3	FACETS	0.166	0.132	0.206			1	INDETERMINATE	1	TRUE	NA	0.93	3		470	511	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888096	81888096	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	23	432	0	ENST00000359376.3:c.241G>T	p.Asp81Tyr	p.D81Y	ENST00000359376	NM_002661.3	81	Gat/Tat	3/33	1	2	FACETS	0.135	0.105	0.17	0.135	0.105	0.17	SUBCLONAL	1	TRUE	1	0.93	2		432	367	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348079	89348079	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	48	934	2	ENST00000301030.4:c.4871C>T	p.Ala1624Val	p.A1624V	ENST00000301030	NM_001256183.1	1624	gCg/gTg	9/13	1	2	FACETS	0.163	0.137	0.192	0.163	0.137	0.192	SUBCLONAL	1	TRUE	1	0.93	2		936	632	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348669	89348669	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1421678693	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	33	791	0	ENST00000301030.4:c.4281G>T	p.Lys1427Asn	p.K1427N	ENST00000301030	NM_001256183.1	1427	aaG/aaT	9/13	1	2	FACETS	0.114	0.092	0.138	0.114	0.092	0.138	SUBCLONAL	1	TRUE	1	0.93	2		791	624	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572931	7572931	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	96	484	0	ENST00000269305.4:c.1178A>G	p.Asp393Gly	p.D393G	ENST00000269305	NM_001126112.2	393	gAc/gGc	11/11	1	2	FACETS	0.411	0.368	0.457	0.411	0.368	0.457	SUBCLONAL	1	TRUE	1	0.93	2		484	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	110	491	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.4	0.36	0.442	0.4	0.36	0.442	SUBCLONAL	1	TRUE	1	0.93	2		491	591	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998919	11998919	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	12	243	0	ENST00000353533.5:c.421G>T	p.Glu141Ter	p.E141*	ENST00000353533	NM_003010.3	141	Gaa/Taa	4/11	1	2	FACETS	0.113	0.079	0.154	0.113	0.079	0.154	SUBCLONAL	1	TRUE	1	0.93	2		243	229	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024540	16024540	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	40	553	0	ENST00000268712.3:c.1678G>T	p.Glu560Ter	p.E560*	ENST00000268712	NM_006311.3	560	Gaa/Taa	16/46	1	2	FACETS	0.141	0.117	0.168	0.141	0.117	0.168	SUBCLONAL	1	TRUE	1	0.93	2		553	610	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684332	29684332	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	53	449	0	ENST00000356175.3:c.7852C>A	p.Leu2618Ile	p.L2618I	ENST00000356175	NM_000267.3	2618	Ctt/Att	53/57	1	2	FACETS	0.236	0.202	0.275	0.236	0.202	0.275	SUBCLONAL	1	TRUE	1	0.93	2		449	482	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132438	11132438	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794284	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	35	905	3	ENST00000358026.2:c.2654G>A	p.Arg885His	p.R885H	ENST00000358026	NM_001128849.1	885	cGc/cAc	19/36	1	2	FACETS	0.123	0.1	0.149	0.123	0.1	0.149	SUBCLONAL	1	TRUE	1	0.93	2		908	612	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145662	11145662	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770839933	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	63	801	0	ENST00000358026.2:c.4024G>A	p.Glu1342Lys	p.E1342K	ENST00000358026	NM_001128849.1	1342	Gag/Aag	29/36	1	2	FACETS	0.234	0.202	0.269	0.234	0.202	0.269	SUBCLONAL	1	TRUE	1	0.93	2		801	578	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170552	11170552	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568564931	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	33	884	1	ENST00000358026.2:c.4855G>A	p.Glu1619Lys	p.E1619K	ENST00000358026	NM_001128849.1	1619	Gaa/Aaa	34/36	1	2	FACETS	0.117	0.094	0.142	0.117	0.094	0.142	SUBCLONAL	1	TRUE	1	0.93	2		885	608	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469546	25469546	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	71	920	1	ENST00000264709.3:c.1222G>T	p.Glu408Ter	p.E408*	ENST00000264709	NM_175629.2	408	Gaa/Taa	10/23	1	2	FACETS	0.251	0.219	0.286	0.251	0.219	0.286	SUBCLONAL	1	TRUE	1	0.93	2		921	608	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416563	29416563	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs374135358	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	40	655	1	ENST00000389048.3:c.4390C>T	p.Arg1464Ter	p.R1464*	ENST00000389048	NM_004304.4	1464	Cga/Tga	29/29	1	2	FACETS	0.162	0.134	0.193	0.162	0.134	0.193	SUBCLONAL	1	TRUE	1	0.93	2		656	532	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445235	29445235	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	46	721	0	ENST00000389048.3:c.3490T>G	p.Phe1164Val	p.F1164V	ENST00000389048	NM_004304.4	1164	Ttc/Gtc	22/29	1	2	FACETS	0.222	0.187	0.261	0.222	0.187	0.261	SUBCLONAL	1	TRUE	1	0.93	2		721	446	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711231	61711231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	25	333	0	ENST00000401558.2:c.2518G>A	p.Glu840Lys	p.E840K	ENST00000401558	NM_003400.3	840	Gaa/Aaa	21/25	0.3	4	FACETS	0.281	0.221	0.35			1	INDETERMINATE	1	TRUE	NA	0.93	4		333	369	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137487	202137487	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	33	413	0	ENST00000358485.4:c.715G>T	p.Glu239Ter	p.E239*	ENST00000358485	NM_001080125.1	239	Gaa/Taa	4/9	1	2	FACETS	0.194	0.158	0.235	0.194	0.158	0.235	SUBCLONAL	1	TRUE	1	0.93	2		413	366	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440076	220440076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770572812	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	42	894	1	ENST00000243786.2:c.929C>T	p.Ala310Val	p.A310V	ENST00000243786	NM_002191.3	310	gCt/gTt	2/2	1	2	FACETS	0.154	0.128	0.183	0.154	0.128	0.183	SUBCLONAL	1	TRUE	1	0.93	2		895	586	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023108	31023108	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147895689	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	25	563	0	ENST00000375687.4:c.2593G>A	p.Glu865Lys	p.E865K	ENST00000375687	NM_015338.5	865	Gaa/Aaa	13/13	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		563	407	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162066	47162066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138005965	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	27	399	0	ENST00000409792.3:c.4060G>A	p.Asp1354Asn	p.D1354N	ENST00000409792	NM_014159.6	1354	Gat/Aat	3/21	0.10198407593633	3	FACETS	0.231	0.183	0.285	0.115	0.091	0.143	INDETERMINATE	1	TRUE	1	0.93	3		399	369	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164327	47164327	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	20	320	0	ENST00000409792.3:c.1799T>G	p.Leu600Ter	p.L600*	ENST00000409792	NM_014159.6	600	tTa/tGa	3/21	0.10198407593633	3	FACETS	0.205	0.157	0.262	0.103	0.078	0.131	INDETERMINATE	1	TRUE	1	0.93	3		320	307	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927995	49927995	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759230802	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	28	635	0	ENST00000296474.3:c.3733C>T	p.Arg1245Cys	p.R1245C	ENST00000296474	NM_002447.2	1245	Cgc/Tgc	18/20	0.10198407593633	3	FACETS	0.16	0.127	0.198	0.08	0.063	0.099	INDETERMINATE	1	TRUE	1	0.93	3		635	551	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670643	134670643	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	26	740	0	ENST00000398015.3:c.554C>A	p.Ser185Tyr	p.S185Y	ENST00000398015	NM_004441.4	185	tCt/tAt	3/16	0.3	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		740	459	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433417	138433417	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	35	350	0	ENST00000289153.2:c.1195C>T	p.Arg399Ter	p.R399*	ENST00000289153	NM_006219.2	399	Cga/Tga	7/22	0.10198407593633	3	FACETS	0.235	0.192	0.283	0.117	0.096	0.142	INDETERMINATE	1	TRUE	1	0.93	3		350	470	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	31	390	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.10198407593633	3	FACETS	0.151	0.122	0.185	0.076	0.061	0.093	INDETERMINATE	1	TRUE	1	0.93	3		390	645	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146636	55146636	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	91	480	0	ENST00000257290.5:c.2310G>T	p.Lys770Asn	p.K770N	ENST00000257290	NM_006206.4	770	aaG/aaT	16/23	1	2	FACETS	0.416	0.371	0.464	0.416	0.371	0.464	SUBCLONAL	1	TRUE	1	0.93	2		480	470	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956198	55956198	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	41	514	0	ENST00000263923.4:c.3117G>T	p.Lys1039Asn	p.K1039N	ENST00000263923	NM_002253.2	1039	aaG/aaT	23/30	1	2	FACETS	0.179	0.149	0.213	0.179	0.149	0.213	SUBCLONAL	1	TRUE	1	0.93	2		514	493	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557242	187557242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	30	476	0	ENST00000441802.2:c.4120G>A	p.Ala1374Thr	p.A1374T	ENST00000441802	NM_005245.3	1374	Gct/Act	6/27	1	2	FACETS	0.156	0.125	0.191	0.156	0.125	0.191	SUBCLONAL	1	TRUE	1	0.93	2		476	414	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251119	251119	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	17	248	0	ENST00000264932.6:c.1564C>A	p.His522Asn	p.H522N	ENST00000264932	NM_004168.2	522	Cat/Aat	12/15	0.213346112869584	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		248	217	SUCCESS
APC	324	MSKCC	GRCh37	5	112177901	112177901	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs752654519	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	34	299	0	ENST00000257430.4:c.6610C>T	p.Arg2204Ter	p.R2204*	ENST00000257430	NM_000038.5	2204	Cga/Tga	16/16	0.10198407593633	3	FACETS	0.375	0.307	0.45	0.187	0.153	0.225	INDETERMINATE	1	TRUE	1	0.93	3		299	286	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658382	117658382	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	38	646	0	ENST00000368508.3:c.5201A>C	p.Lys1734Thr	p.K1734T	ENST00000368508	NM_002944.2	1734	aAg/aCg	31/43	1	2	FACETS	0.172	0.141	0.205	0.172	0.141	0.205	SUBCLONAL	1	TRUE	1	0.93	2		646	476	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687431	117687431	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	28	295	1	ENST00000368508.3:c.2620G>T	p.Glu874Ter	p.E874*	ENST00000368508	NM_002944.2	874	Gaa/Taa	18/43	1	2	FACETS	0.189	0.151	0.233	0.189	0.151	0.233	SUBCLONAL	1	TRUE	1	0.93	2		296	318	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211097	55211097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219568637	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	26	410	0	ENST00000275493.2:c.340G>A	p.Glu114Lys	p.E114K	ENST00000275493	NM_005228.3	114	Gaa/Aaa	3/28	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		410	341	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411728	116411728	+	intron_variant	Intron	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	63	861	0	ENST00000397752.3:c.2887+20C>A		p.*963*	ENST00000397752	NM_000245.2	-/1390			0.10198407593633	3	FACETS	0.232	0.2	0.267	0.116	0.1	0.134	INDETERMINATE	1	TRUE	1	0.93	3		861	855	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845426	151845426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1342954023	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	26	677	1	ENST00000262189.6:c.13586G>A	p.Arg4529His	p.R4529H	ENST00000262189	NM_170606.2	4529	cGt/cAt	52/59	0.10198407593633	3	FACETS	0.181	0.143	0.225	0.091	0.071	0.113	INDETERMINATE	1	TRUE	1	0.93	3		678	452	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864758	68864758	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	18	495	0	ENST00000288368.4:c.129G>T	p.Glu43Asp	p.E43D	ENST00000288368	NM_024870.2	43	gaG/gaT	1/40	0.258321414544118	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		495	337	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021764	69021764	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	30	457	0	ENST00000288368.4:c.3052G>T	p.Glu1018Ter	p.E1018*	ENST00000288368	NM_024870.2	1018	Gaa/Taa	25/40	0.258321414544118	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		457	357	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141569503	141569503	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	35	440	0	ENST00000220592.5:c.781G>T	p.Glu261Ter	p.E261*	ENST00000220592	NM_012154.3	261	Gaa/Taa	6/19	1	2	FACETS	0.202	0.166	0.243	0.202	0.166	0.243	SUBCLONAL	1	TRUE	1	0.93	2		440	372	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341119	8341119	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	14	400	1	ENST00000356435.5:c.5097C>A	p.Tyr1699Ter	p.Y1699*	ENST00000356435		1699	taC/taA	30/35	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		401	271	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341925	8341925	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	18	364	0	ENST00000356435.5:c.4715G>T	p.Arg1572Ile	p.R1572I	ENST00000356435		1572	aGa/aTa	29/35	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		364	213	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485254	8485254	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	25	412	0	ENST00000356435.5:c.3126G>T	p.Glu1042Asp	p.E1042D	ENST00000356435		1042	gaG/gaT	18/35	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		412	300	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128206860	128206860	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	19	363	0	ENST00000265960.3:c.1363C>T	p.Leu455Phe	p.L455F	ENST00000265960	NM_001006617.1	455	Ctc/Ttc	11/12	0.10198407593633	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		363	325	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447310	49447310	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	254	610	0	ENST00000301067.7:c.788G>T	p.Arg263Leu	p.R263L	ENST00000301067	NM_003482.3	263	cGc/cTc	6/54	0.213346112869584	4	FACETS	0.854	0.806	0.903	0.854	0.806	0.903	INDETERMINATE	2	TRUE	2	0.93	4		610	617	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447309	49447309	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048298-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	252	609	0	ENST00000301067.7:c.789del	p.Lys264AsnfsTer40	p.K264Nfs*40	ENST00000301067	NM_003482.3	263	cgC/cg	6/54	0.213346112869584	4	FACETS	0.845	0.796	0.894	0.845	0.796	0.894	INDETERMINATE	2	TRUE	2	0.93	4		609	619	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0048301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	149	249	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.434235319368059	3	FACETS	0.83	0.763	0.898	0.83	0.763	0.898	CLONAL	2	TRUE	1	0.439889807765485	3		249	498	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0048301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	28	293	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.36	0.287	0.442	0.36	0.287	0.442	SUBCLONAL	1	TRUE	1	0.439889807765485	2		293	354	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842471	68842471	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1131690808	NA	P-0048301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	222	489	0	ENST00000261769.5:c.531+1G>A		p.X177_splice	ENST00000261769	NM_004360.3	177			0.340491664270565	4	FACETS	0.997	0.931	1	0.997	0.931	1	CLONAL	2	TRUE	2	0.439889807765485	4		489	729	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466018	69466018	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	451	928	0	ENST00000227507.2:c.856A>G	p.Thr286Ala	p.T286A	ENST00000227507	NM_053056.2	286	Aca/Gca	5/5	0.439889807765485	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.439889807765485	2		928	1004	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105859	27105860	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	256	552	0	ENST00000324856.7:c.5471dup	p.Val1825GlyfsTer6	p.V1825Gfs*6	ENST00000324856	NM_006015.4	1824	gtg/gTtg	20/20	0.439889807765485	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.439889807765485	2		552	567	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867234	68867234	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	248	541	0	ENST00000261769.5:c.2481del	p.Tyr827Ter	p.Y827*	ENST00000261769	NM_004360.3	827	taT/ta	16/16	0.340491664270565	4	FACETS	0.944	0.885	1	0.944	0.885	1	CLONAL	2	TRUE	2	0.439889807765485	4		541	860	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752636	42752636	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	323	697	0	ENST00000222329.4:c.1628T>A	p.Leu543Gln	p.L543Q	ENST00000222329	NM_006494.2	543	cTg/cAg	4/4	0.434235319368059	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.439889807765485	3		697	881	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115750	8115750	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs104894164	NA	P-0048302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	236	575	0	ENST00000346208.3:c.1096C>T	p.Arg366Ter	p.R366*	ENST00000346208		366	Cga/Tga	6/6	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.688694107671623	2		575	654	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0048302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	293	699	0	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	0.688694107671623	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.688694107671623	1		699	549	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263941	104263941	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1227379293	NA	P-0048302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	62	133	0	ENST00000369902.3:c.32G>A	p.Gly11Asp	p.G11D	ENST00000369902	NM_016169.3	11	gGc/gAc	1/12	1	2	FACETS	0.948	0.833	1	0.948	0.833	1	CLONAL	1	TRUE	1	0.688694107671623	2		133	190	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871147	12871148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	181	369	0	ENST00000228872.4:c.375dup	p.Glu126Ter	p.E126*	ENST00000228872	NM_004064.3	125	tct/tcTt	1/3	1	2	FACETS	0.935	0.868	1	0.935	0.868	1	CLONAL	1	TRUE	1	0.688694107671623	2		369	562	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829463	72829471	+	inframe_deletion	In_Frame_Del	DEL	TCCATGGCA	TCCATGGCA	-	rs746065760	NA	P-0048302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	297	743	1	ENST00000268489.5:c.7110_7118del	p.Asp2370_Met2372del	p.D2370_M2372del	ENST00000268489	NM_006885.3	2370	gaTGCCATGGAa/gaa	9/10	0.688694107671623	1	FACETS	0.968	0.921	1	0.968	0.921	1	CLONAL	1	TRUE	0	0.688694107671623	1		744	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0048305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	432	491	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.670521418690903	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	FALSE	0	0.664977927975015	2		491	649	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076758	72076758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	159	526	0	ENST00000357731.5:c.739G>A	p.Gly247Ser	p.G247S	ENST00000357731	NM_173808.2	247	Ggt/Agt	5/7	0.670521418690903	4	FACETS	1	0.966	1	0.548	0.503	0.594	CLONAL	1	FALSE	2	0.664977927975015	4		526	727	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966872	25966873	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0048305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	180	663	2	ENST00000435504.4:c.2333dup	p.Val779SerfsTer25	p.V779Sfs*25	ENST00000435504		778	cca/ccCa	13/13	NA	2	FACETS	0.865	0.801	0.93			1	INDETERMINATE	1	FALSE	NA	0.664977927975015	2		665	626	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944441	40944441	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	105	569	0	ENST00000373198.4:c.2061C>A	p.Tyr687Ter	p.Y687*	ENST00000373198	NM_133170.3	687	taC/taA	12/32	0.641014740781175	3	FACETS	0.511	0.457	0.568			1	SUBCLONAL	1	FALSE	NA	0.664977927975015	3		569	824	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506296	120506296	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	93	443	0	ENST00000256646.2:c.1816G>C	p.Asp606His	p.D606H	ENST00000256646	NM_024408.3	606	Gac/Cac	11/34	0.670521418690903	4	FACETS	0.57	0.506	0.638	0.285	0.253	0.319	SUBCLONAL	1	FALSE	2	0.664977927975015	4		443	817	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150549964	150549964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	70	211	0	ENST00000369026.2:c.940G>A	p.Gly314Arg	p.G314R	ENST00000369026	NM_021960.4	314	Ggg/Agg	3/3	0.664977927975015	5	FACETS	0.889	0.777	1	0.296	0.259	0.337	CLONAL	1	FALSE	2	0.664977927975015	5		211	473	SUCCESS
ATM	472	MSKCC	GRCh37	11	108183140	108183140	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	52	218	0	ENST00000278616.4:c.5921G>A	p.Ser1974Asn	p.S1974N	ENST00000278616	NM_000051.3	1974	aGt/aAt	40/63	0.670521418690903	3	FACETS	0.894	0.77	1	0.447	0.385	0.514	CLONAL	1	FALSE	1	0.664977927975015	3		218	233	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3094774	3094774	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	98	304	0	ENST00000078429.4:c.125T>A	p.Leu42Gln	p.L42Q	ENST00000078429	NM_002067.2	42	cTg/cAg	1/7	0.251163630308935	3	FACETS	1	0.913	1	0.509	0.457	0.563	INDETERMINATE	1	FALSE	1	0.664977927975015	3		304	386	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150014	202150014	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	53	611	0	ENST00000358485.4:c.1455C>G	p.Cys485Trp	p.C485W	ENST00000358485	NM_001080125.1	485	tgC/tgG	8/9	0.5563327133741	4	FACETS	0.31	0.263	0.361			1	SUBCLONAL	1	FALSE	NA	0.664977927975015	4		611	857	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196828	138196828	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	54	206	0	ENST00000237289.4:c.490T>C	p.Trp164Arg	p.W164R	ENST00000237289	NM_001270507.1	164	Tgg/Cgg	4/9	0.670521418690903	4	FACETS	0.653	0.559	0.755			1	SUBCLONAL	1	FALSE	NA	0.664977927975015	4		206	414	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932623	39932623	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	107	995	0	ENST00000378444.4:c.1976del	p.Pro659LeufsTer10	p.P659Lfs*10	ENST00000378444	NM_001123385.1	659	cCt/ct	4/15	0.161218563614891	1	FACETS	0.239	0.214	0.266	0.239	0.214	0.266	INDETERMINATE	1	FALSE	0	0.664977927975015	1		995	899	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950064	44950064	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	37	426	0	ENST00000377967.4:c.3833C>G	p.Ala1278Gly	p.A1278G	ENST00000377967	NM_021140.2	1278	gCa/gGa	26/29	0.161218563614891	1	FACETS	0.205	0.169	0.245	0.205	0.169	0.245	INDETERMINATE	1	FALSE	0	0.664977927975015	1		426	362	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53254022	53254039	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	AACACCGGGCACTCCGGT	AACACCGGGCACTCCGGT	TCGGAAATCAGCTACAGCTA	novel	NA	P-0048305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	241	852	2	ENST00000375401.3:c.33_50delinsTAGCTGTAGCTGATTTCCGA	p.Pro12SerfsTer4	p.P12Sfs*4	ENST00000375401	NM_004187.3	11	ccACCGGAGTGCCCGGTGTTc/ccTAGCTGTAGCTGATTTCCGAc	1/26	0.670521418690903	3	FACETS	0.888	0.829	0.949	0.444	0.414	0.475	CLONAL	1	FALSE	1	0.664977927975015	3		854	1088	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	70	432	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.424299046270406	5	FACETS	0.72	0.627	0.821	0.24	0.209	0.274	SUBCLONAL	1	TRUE	2	0.424299046270406	5		432	750	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0048306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	301	621	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.330843147397285	2	FACETS	0.914	0.865	0.964	0.914	0.865	0.964	CLONAL	2	TRUE	0	0.424299046270406	2		621	776	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748481	162748481	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	56	370	0	ENST00000367921.3:c.2395G>A	p.Glu799Lys	p.E799K	ENST00000367921	NM_006182.2	799	Gag/Aag	17/18	0.424299046270406	8	FACETS	0.622	0.531	0.722	0.078	0.066	0.091	SUBCLONAL	1	TRUE	0	0.424299046270406	8		370	965	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910647	29910647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1630	164	1249	0	ENST00000376809.5:c.187G>A	p.Asp63Asn	p.D63N	ENST00000376809	NM_002116.7	63	Gac/Aac	2/8	0.36806360596502	5	FACETS	0.705	0.644	0.769	0.235	0.214	0.257	SUBCLONAL	1	TRUE	2	0.424299046270406	5		1249	1794	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772290	68772290	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	574	942	0	ENST00000261769.5:c.139G>A	p.Glu47Lys	p.E47K	ENST00000261769	NM_004360.3	47	Gag/Aag	2/16	0.265458017693798	5	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	2	0.424299046270406	5		942	1314	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205323	38205323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	137	773	0	ENST00000317025.8:c.367G>A	p.Glu123Lys	p.E123K	ENST00000317025	NM_023034.1	123	Gaa/Aaa	2/24	0.209782258983656	4	FACETS	0.944	0.858	1	0.315	0.286	0.345	INDETERMINATE	1	TRUE	1	0.424299046270406	4		773	974	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034489	47034489	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	117	367	0	ENST00000377604.3:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000377604	NM_001204468.1	192	Cag/Tag	6/24	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.424299046270406	1		367	334	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282512	115282512	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0048306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	45	306	0	ENST00000438362.2:c.139-1G>C		p.X47_splice	ENST00000438362	NM_001242891.1	47			0.209782258983656	4	FACETS	0.849	0.715	0.995	0.283	0.238	0.332	INDETERMINATE	1	TRUE	1	0.424299046270406	4		306	356	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439518	220439518	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540215120	NA	P-0048306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	102	779	0	ENST00000243786.2:c.371G>A	p.Arg124His	p.R124H	ENST00000243786	NM_002191.3	124	cGc/cAc	2/2	0.420067506059711	2	FACETS	0.914	0.82	1	0.457	0.41	0.507	CLONAL	1	TRUE	0	0.424299046270406	2		779	526	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416091	49416091	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	201	592	0	ENST00000301067.7:c.16384G>C	p.Asp5462His	p.D5462H	ENST00000301067	NM_003482.3	5462	Gat/Cat	52/54	0.265458017693798	5	FACETS	0.947	0.879	1	0.631	0.586	0.678	CLONAL	2	TRUE	2	0.424299046270406	5		592	819	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95579443	95579443	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	36	253	0	ENST00000393063.1:c.2026C>G	p.Arg676Gly	p.R676G	ENST00000393063	NM_030621.3	676	Cga/Gga	13/28	0.424299046270406	3	FACETS	0.729	0.602	0.87	0.365	0.301	0.435	SUBCLONAL	1	TRUE	1	0.424299046270406	3		253	282	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260190	10260190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	86	672	0	ENST00000340748.4:c.2477C>T	p.Ser826Leu	p.S826L	ENST00000340748		826	tCa/tTa	25/40	0.209782258983656	4	FACETS	0.696	0.614	0.783	0.232	0.204	0.261	INDETERMINATE	1	TRUE	1	0.424299046270406	4		672	830	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387343	17387343	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs775834500	NA	P-0048306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	140	921	0	ENST00000359435.4:c.609G>C	p.Gln203His	p.Q203H	ENST00000359435	NM_001033549.1	203	caG/caC	7/9	NA	2	FACETS	0.704	0.641	0.771			1	INDETERMINATE	1	TRUE	NA	0.424299046270406	2		921	937	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190708696	190708696	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	54	303	0	ENST00000441310.2:c.589A>G	p.Ile197Val	p.I197V	ENST00000441310	NM_000534.4	197	Att/Gtt	6/13	0.424299046270406	4	FACETS	1	0.894	1			1	CLONAL	1	TRUE	NA	0.424299046270406	4		303	345	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645910	215645910	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	62	595	0	ENST00000260947.4:c.688G>C	p.Asp230His	p.D230H	ENST00000260947	NM_000465.2	230	Gac/Cac	4/11	0.420067506059711	2	FACETS	0.669	0.579	0.765	0.334	0.289	0.383	SUBCLONAL	1	TRUE	0	0.424299046270406	2		595	437	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598231	52598231	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	55	372	0	ENST00000394830.3:c.3635C>A	p.Ser1212Ter	p.S1212*	ENST00000394830	NM_018313.4	1212	tCa/tAa	24/30	1	2	FACETS	0.779	0.67	0.896	0.779	0.67	0.896	SUBCLONAL	1	TRUE	1	0.424299046270406	2		372	333	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127357	55127357	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	159	538	0	ENST00000257290.5:c.145T>C	p.Cys49Arg	p.C49R	ENST00000257290	NM_006206.4	49	Tgc/Cgc	3/23	0.156255952648533	2	FACETS	1	0.989	1	0.749	0.692	0.809	INDETERMINATE	1	TRUE	0	0.424299046270406	2		538	500	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323207	31323207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	329	732	1	ENST00000412585.2:c.782G>A	p.Gly261Glu	p.G261E	ENST00000412585	NM_005514.6	261	gGa/gAa	4/8	0.424299046270406	3	FACETS	1	0.992	1	0.803	0.763	0.844	CLONAL	2	TRUE	0	0.424299046270406	3		733	780	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324140	31324385	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCGTACTGGTCATGCCCGCGGAGGAGGCGCCCGTCCGGCCCCACGTCGCAGCCGTACATGCTCTGGAGGGTGTGAGACCCTGGCCCCGGCCCCGCGGTCAGCCCAGTCCCCCGAGCCCCGCCCCGCCCCGACCAACCCGCGGGGATTTTGGCCTCAACTGAAAATGAAACCGGGTAAACGCGCCTGGGGCTCTCGCCGGTCGAGGGTCTGGGCGGGTCCCGCGGCCTCAGGGAGGCGGATCTCGG	GGCGTACTGGTCATGCCCGCGGAGGAGGCGCCCGTCCGGCCCCACGTCGCAGCCGTACATGCTCTGGAGGGTGTGAGACCCTGGCCCCGGCCCCGCGGTCAGCCCAGTCCCCCGAGCCCCGCCCCGCCCCGACCAACCCGCGGGGATTTTGGCCTCAACTGAAAATGAAACCGGGTAAACGCGCCTGGGGCTCTCGCCGGTCGAGGGTCTGGGCGGGTCCCGCGGCCTCAGGGAGGCGGATCTCGG	-	novel	NA	P-0048306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	120	459	0	ENST00000412585.2:c.343+80_423del		p.X115_splice	ENST00000412585	NM_005514.6	115		3/8	0.424299046270406	3	FACETS	0.818	0.745	0.894	0.545	0.496	0.596	CLONAL	2	TRUE	0	0.424299046270406	3		459	419	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332049	81332049	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	38	213	0	ENST00000222390.5:c.2035T>C	p.Cys679Arg	p.C679R	ENST00000222390	NM_000601.4	679	Tgt/Cgt	18/18	0.424299046270406	3	FACETS	0.832	0.692	0.986	0.416	0.346	0.493	CLONAL	1	TRUE	1	0.424299046270406	3		213	261	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281061	49281061	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	86	543	0	ENST00000282018.3:c.108C>G	p.Phe36Leu	p.F36L	ENST00000282018	NM_020377.2	36	ttC/ttG	1/1	0.352261075966778	3	FACETS	0.924	0.819	1	0.308	0.273	0.345	CLONAL	1	TRUE	0	0.424299046270406	3		543	532	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554299	81554299	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	14	269	0	ENST00000298171.2:c.319G>C	p.Glu107Gln	p.E107Q	ENST00000298171	NM_000369.2	107	Gaa/Caa	4/10	0.424299046270406	3	FACETS	0.289	0.208	0.386	0.144	0.104	0.193	SUBCLONAL	1	TRUE	1	0.424299046270406	3		269	277	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78797016	78797016	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	62	522	0	ENST00000306801.3:c.1129G>C	p.Ala377Pro	p.A377P	ENST00000306801	NM_020761.2	377	Gcc/Ccc	9/34	0.308085660420181	3	FACETS	0.554	0.478	0.637	0.277	0.239	0.319	SUBCLONAL	1	TRUE	1	0.424299046270406	3		522	639	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971723	18971723	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	128	723	0	ENST00000262803.5:c.2389G>A	p.Glu797Lys	p.E797K	ENST00000262803	NM_002911.3	797	Gag/Aag	17/24	NA	2	FACETS	0.783	0.71	0.859			1	INDETERMINATE	1	TRUE	NA	0.424299046270406	2		723	771	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264275	46264275	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200950152	NA	P-0048306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	70	283	0	ENST00000371998.3:c.1322C>T	p.Ser441Leu	p.S441L	ENST00000371998		441	tCa/tTa	11/23	0.0886487753855112	4	FACETS	1	0.893	1			1	INDETERMINATE	1	TRUE	NA	0.424299046270406	4		283	459	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447612	187447612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	125	680	0	ENST00000232014.4:c.581C>T	p.Ser194Phe	p.S194F	ENST00000232014	NM_001130845.1	194	tCt/tTt	5/10	0.344749986240721	4	FACETS	1	0.935	1			1	CLONAL	1	TRUE	NA	0.424299046270406	4		680	806	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250683	26250683	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	139	562	0	ENST00000446824.2:c.151G>C	p.Glu51Gln	p.E51Q	ENST00000446824	NM_021018.2	51	Gaa/Caa	1/1	0.424299046270406	8	FACETS	1	0.975	1	0.242	0.219	0.265	CLONAL	1	TRUE	3	0.424299046270406	8		562	1233	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	452	621	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.757148724680482	2	FACETS	0.901	0.873	0.927	0.901	0.873	0.927	CLONAL	2	TRUE	0	0.803002142283137	2		621	625	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910647	29910647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	243	1249	0	ENST00000376809.5:c.187G>A	p.Asp63Asn	p.D63N	ENST00000376809	NM_002116.7	63	Gac/Aac	2/8	0.72030016477924	4	FACETS	0.786	0.733	0.842	0.262	0.244	0.281	SUBCLONAL	1	TRUE	1	0.803002142283137	4		1249	1388	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772290	68772290	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	439	942	0	ENST00000261769.5:c.139G>A	p.Glu47Lys	p.E47K	ENST00000261769	NM_004360.3	47	Gag/Aag	2/16	0.803002142283137	3	FACETS	0.928	0.891	0.964	0.928	0.891	0.964	CLONAL	2	TRUE	1	0.803002142283137	3		942	826	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205323	38205323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1444	208	773	0	ENST00000317025.8:c.367G>A	p.Glu123Lys	p.E123K	ENST00000317025	NM_023034.1	123	Gaa/Aaa	2/24	0.803002142283137	7	FACETS	0.943	0.872	1			1	CLONAL	1	TRUE	NA	0.803002142283137	7		773	1652	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034489	47034489	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	426	367	0	ENST00000377604.3:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000377604	NM_001204468.1	192	Cag/Tag	6/24	0.690079053550978	2	FACETS	1	0.99	1			1	CLONAL	2	TRUE	NA	0.803002142283137	2		367	514	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282512	115282512	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	64	306	0	ENST00000438362.2:c.139-1G>C		p.X47_splice	ENST00000438362	NM_001242891.1	47			0.789913262423935	3	FACETS	0.894	0.783	1	0.447	0.391	0.506	CLONAL	1	TRUE	1	0.803002142283137	3		306	250	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439518	220439518	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540215120	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	174	779	0	ENST00000243786.2:c.371G>A	p.Arg124His	p.R124H	ENST00000243786	NM_002191.3	124	cGc/cAc	2/2	0.757148724680482	2	FACETS	0.948	0.882	1	0.474	0.441	0.508	CLONAL	1	TRUE	0	0.803002142283137	2		779	457	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416091	49416091	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	684	592	0	ENST00000301067.7:c.16384G>C	p.Asp5462His	p.D5462H	ENST00000301067	NM_003482.3	5462	Gat/Cat	52/54	0.803002142283137	6	FACETS	0.933	0.905	0.961			1	CLONAL	4	TRUE	NA	0.803002142283137	6		592	1189	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95579443	95579443	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	80	253	0	ENST00000393063.1:c.2026C>G	p.Arg676Gly	p.R676G	ENST00000393063	NM_030621.3	676	Cga/Gga	13/28	0.803002142283137	6	FACETS	1	0.971	1	0.443	0.392	0.497	CLONAL	1	TRUE	3	0.803002142283137	6		253	391	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260190	10260190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	218	672	0	ENST00000340748.4:c.2477C>T	p.Ser826Leu	p.S826L	ENST00000340748		826	tCa/tTa	25/40	0.778988873751403	5	FACETS	1	0.97	1	0.36	0.335	0.387	CLONAL	1	TRUE	2	0.803002142283137	5		672	1107	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387343	17387343	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs775834500	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	235	921	0	ENST00000359435.4:c.609G>C	p.Gln203His	p.Q203H	ENST00000359435	NM_001033549.1	203	caG/caC	7/9	0.722139935215493	3	FACETS	0.887	0.828	0.947	0.296	0.276	0.316	CLONAL	1	TRUE	0	0.803002142283137	3		921	925	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190708696	190708696	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	52	303	0	ENST00000441310.2:c.589A>G	p.Ile197Val	p.I197V	ENST00000441310	NM_000534.4	197	Att/Gtt	6/13	0.803002142283137	4	FACETS	0.679	0.58	0.786			1	SUBCLONAL	1	TRUE	NA	0.803002142283137	4		303	344	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645910	215645910	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	97	595	0	ENST00000260947.4:c.688G>C	p.Asp230His	p.D230H	ENST00000260947	NM_000465.2	230	Gac/Cac	4/11	0.757148724680482	2	FACETS	0.767	0.692	0.845	0.383	0.346	0.423	SUBCLONAL	1	TRUE	0	0.803002142283137	2		595	315	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598231	52598231	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	84	372	0	ENST00000394830.3:c.3635C>A	p.Ser1212Ter	p.S1212*	ENST00000394830	NM_018313.4	1212	tCa/tAa	24/30	1	2	FACETS	0.697	0.623	0.776	0.697	0.623	0.776	SUBCLONAL	1	TRUE	1	0.803002142283137	2		372	300	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127357	55127357	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	318	538	0	ENST00000257290.5:c.145T>C	p.Cys49Arg	p.C49R	ENST00000257290	NM_006206.4	49	Tgc/Cgc	3/23	0.789913262423935	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.803002142283137	3		538	543	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323207	31323207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	584	732	1	ENST00000412585.2:c.782G>A	p.Gly261Glu	p.G261E	ENST00000412585	NM_005514.6	261	gGa/gAa	4/8	0.722139935215493	3	FACETS	0.981	0.961	0.999	0.981	0.961	0.999	CLONAL	3	TRUE	0	0.803002142283137	3		733	693	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324140	31324385	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCGTACTGGTCATGCCCGCGGAGGAGGCGCCCGTCCGGCCCCACGTCGCAGCCGTACATGCTCTGGAGGGTGTGAGACCCTGGCCCCGGCCCCGCGGTCAGCCCAGTCCCCCGAGCCCCGCCCCGCCCCGACCAACCCGCGGGGATTTTGGCCTCAACTGAAAATGAAACCGGGTAAACGCGCCTGGGGCTCTCGCCGGTCGAGGGTCTGGGCGGGTCCCGCGGCCTCAGGGAGGCGGATCTCGG	GGCGTACTGGTCATGCCCGCGGAGGAGGCGCCCGTCCGGCCCCACGTCGCAGCCGTACATGCTCTGGAGGGTGTGAGACCCTGGCCCCGGCCCCGCGGTCAGCCCAGTCCCCCGAGCCCCGCCCCGCCCCGACCAACCCGCGGGGATTTTGGCCTCAACTGAAAATGAAACCGGGTAAACGCGCCTGGGGCTCTCGCCGGTCGAGGGTCTGGGCGGGTCCCGCGGCCTCAGGGAGGCGGATCTCGG	-	novel	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	129	459	0	ENST00000412585.2:c.343+80_423del		p.X115_splice	ENST00000412585	NM_005514.6	115		3/8	0.722139935215493	3	FACETS	1	0.936	1	0.67	0.624	0.715	CLONAL	2	TRUE	0	0.803002142283137	3		459	224	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332049	81332049	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	58	213	0	ENST00000222390.5:c.2035T>C	p.Cys679Arg	p.C679R	ENST00000222390	NM_000601.4	679	Tgt/Cgt	18/18	0.803002142283137	3	FACETS	0.997	0.87	1	0.499	0.435	0.566	CLONAL	1	TRUE	1	0.803002142283137	3		213	203	SUCCESS
AR	367	MSKCC	GRCh37	X	66766450	66766450	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	122	215	0	ENST00000374690.3:c.1462C>T	p.Gln488Ter	p.Q488*	ENST00000374690	NM_000044.3	488	Cag/Tag	1/8	0.690079053550978	2	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.803002142283137	2		215	257	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069345	30069345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	188	688	0	ENST00000338641.4:c.1210G>A	p.Glu404Lys	p.E404K	ENST00000338641	NM_000268.3	404	Gag/Aag	12/16	0.803002142283137	6	FACETS	0.947	0.873	1	0.189	0.174	0.205	CLONAL	1	TRUE	1	0.803002142283137	6		688	1288	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512242	120512242	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	155	482	0	ENST00000256646.2:c.1000G>C	p.Asp334His	p.D334H	ENST00000256646	NM_024408.3	334	Gac/Cac	6/34	0.611132908830245	5	FACETS	0.95	0.87	1			1	CLONAL	1	TRUE	NA	0.803002142283137	5		482	896	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49449083	49449083	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	132	435	1	ENST00000301067.7:c.25G>A	p.Glu9Lys	p.E9K	ENST00000301067	NM_003482.3	9	Gag/Aag	1/54	0.803002142283137	6	FACETS	0.87	0.789	0.955			1	CLONAL	1	TRUE	NA	0.803002142283137	6		436	985	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459264	99459264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1469887199	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	170	651	0	ENST00000268035.6:c.1900C>T	p.Pro634Ser	p.P634S	ENST00000268035	NM_000875.3	634	Ccc/Tcc	9/21	1	2	FACETS	0.905	0.84	0.971	0.905	0.84	0.971	CLONAL	1	TRUE	1	0.803002142283137	2		651	468	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663410	67663410	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	72	254	0	ENST00000264010.4:c.1811C>G	p.Ser604Cys	p.S604C	ENST00000264010	NM_006565.3	604	tCt/tGt	10/12	0.803002142283137	3	FACETS	0.888	0.784	0.998	0.444	0.392	0.499	CLONAL	1	TRUE	1	0.803002142283137	3		254	283	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670670	67670670	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1314705510	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	167	508	0	ENST00000264010.4:c.1915C>G	p.Gln639Glu	p.Q639E	ENST00000264010	NM_006565.3	639	Cag/Gag	11/12	0.803002142283137	3	FACETS	1	0.928	1	0.503	0.464	0.542	CLONAL	1	TRUE	1	0.803002142283137	3		508	580	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33446176	33446176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	116	477	0	ENST00000345365.6:c.98C>T	p.Ser33Phe	p.S33F	ENST00000345365	NM_002878.3	33	tCt/tTt	2/10	NA	2	FACETS	0.686	0.623	0.752			1	INDETERMINATE	1	TRUE	NA	0.803002142283137	2		477	421	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627430	14627430	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	194	691	0	ENST00000254322.2:c.640G>C	p.Glu214Gln	p.E214Q	ENST00000254322	NM_006145.1	214	Gaa/Caa	2/3	0.778988873751403	5	FACETS	0.962	0.889	1	0.321	0.296	0.346	CLONAL	1	TRUE	2	0.803002142283137	5		691	1107	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627571	14627571	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	162	657	0	ENST00000254322.2:c.499G>A	p.Asp167Asn	p.D167N	ENST00000254322	NM_006145.1	167	Gac/Aac	2/3	0.778988873751403	5	FACETS	0.898	0.823	0.976	0.299	0.274	0.326	CLONAL	1	TRUE	2	0.803002142283137	5		657	991	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47735854	47735854	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	181	643	0	ENST00000449228.1:c.6del	p.Lys2AsnfsTer227	p.K2Nfs*227	ENST00000449228	NM_001127240.2	2	aaA/aa	1/4	0.614854163973622	4	FACETS	0.825	0.761	0.892			1	CLONAL	1	TRUE	NA	0.803002142283137	4		643	985	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46275943	46275943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	132	497	0	ENST00000371998.3:c.3379C>T	p.His1127Tyr	p.H1127Y	ENST00000371998		1127	Cat/Tat	18/23	0.614854163973622	4	FACETS	0.923	0.84	1			1	CLONAL	1	TRUE	NA	0.803002142283137	4		497	642	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121232	29121232	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	515	569	0	ENST00000328354.6:c.443G>C	p.Arg148Thr	p.R148T	ENST00000328354	NM_007194.3	148	aGg/aCg	3/15	0.803002142283137	6	FACETS	0.962	0.929	0.994	0.769	0.743	0.795	CLONAL	4	TRUE	1	0.803002142283137	6		569	869	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098778	47098778	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	165	693	0	ENST00000409792.3:c.6496G>A	p.Gly2166Ser	p.G2166S	ENST00000409792	NM_014159.6	2166	Ggt/Agt	15/21	1	2	FACETS	0.897	0.832	0.964	0.897	0.832	0.964	CLONAL	1	TRUE	1	0.803002142283137	2		693	458	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808367	1808367	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs755495007	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	221	1141	0	ENST00000260795.2:c.2125G>C	p.Glu709Gln	p.E709Q	ENST00000260795		709	Gag/Cag	15/17	0.789913262423935	3	FACETS	0.995	0.929	1	0.498	0.464	0.532	CLONAL	1	TRUE	1	0.803002142283137	3		1141	775	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166809	32166809	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	258	928	0	ENST00000375023.3:c.4429G>C	p.Glu1477Gln	p.E1477Q	ENST00000375023	NM_004557.3	1477	Gag/Cag	24/30	0.722139935215493	3	FACETS	1	0.953	1	0.339	0.318	0.361	CLONAL	1	TRUE	0	0.803002142283137	3		928	885	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933749	39933749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs977644059	NA	P-0048306-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	156	362	0	ENST00000378444.4:c.850G>A	p.Asp284Asn	p.D284N	ENST00000378444	NM_001123385.1	284	Gac/Aac	4/15	0.690079053550978	2	FACETS	0.994	0.921	1			1	CLONAL	1	TRUE	NA	0.803002142283137	2		362	391	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0048307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	116	386	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.69710823046999	1	FACETS	0.999	0.924	1	0.999	0.924	1	CLONAL	1	TRUE	0	0.69710823046999	1		386	217	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578476	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTGCCGGGCGG	GGGTGCCGGGCGG	-	rs876659215	NA	P-0048307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	260	880	60	ENST00000269305.4:c.454_466del	p.Pro152AlafsTer14	p.P152Afs*14	ENST00000269305	NM_001126112.2	152	CCGCCCGGCACCCgc/gc	5/11	0.69710823046999	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.69710823046999	1		940	486	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487295	56487295	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1488014391	NA	P-0048307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	120	422	0	ENST00000267101.3:c.1441C>T	p.Arg481Ter	p.R481*	ENST00000267101	NM_001982.3	481	Cga/Tga	12/28	0.69710823046999	1	FACETS	0.95	0.878	1	0.95	0.878	1	CLONAL	1	TRUE	0	0.69710823046999	1		422	236	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772809	135772809	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0048307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	179	508	0	ENST00000298552.3:c.2813+1G>A		p.X938_splice	ENST00000298552	NM_001162426.1	938			0.69710823046999	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.69710823046999	1		508	262	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0048308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	47	405	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.232	0.195	0.273	0.232	0.195	0.273	SUBCLONAL	1	TRUE	1	0.668756028768026	2		405	605	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665045	138665045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	82	129	0	ENST00000330315.3:c.520G>A	p.Gly174Ser	p.G174S	ENST00000330315	NM_023067.3	174	Ggc/Agc	1/1	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.668756028768026	2		129	181	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829039	128829040	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs570242755	NA	P-0048308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	19	36	1	ENST00000249373.3:c.67_69dup	p.Leu23dup	p.L23dup	ENST00000249373	NM_005631.4	23	ggg/ggGCTg	1/12	1	2	FACETS	0.552	0.425	0.695	0.552	0.425	0.695	SUBCLONAL	1	TRUE	1	0.668756028768026	2		37	103	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568590	41568590	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	206	445	0	ENST00000263253.7:c.4540G>A	p.Glu1514Lys	p.E1514K	ENST00000263253	NM_001429.3	1514	Gaa/Aaa	28/31	1	2	FACETS	0.939	0.876	1	0.939	0.876	1	CLONAL	1	TRUE	1	0.668756028768026	2		445	656	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223533	53223533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	355	751	0	ENST00000375401.3:c.3826G>A	p.Glu1276Lys	p.E1276K	ENST00000375401	NM_004187.3	1276	Gag/Aag	23/26	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.668756028768026	2		751	918	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279932	18279932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1423694208	NA	P-0048308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	379	773	0	ENST00000222254.8:c.2015G>A	p.Arg672His	p.R672H	ENST00000222254	NM_005027.3	672	cGc/cAc	16/16	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.668756028768026	2		773	1131	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562237	21562237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751564042	NA	P-0048308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	380	1069	0	ENST00000382592.4:c.1682C>T	p.Ala561Val	p.A561V	ENST00000382592	NM_014572.2	561	gCc/gTc	4/8	0.668756028768026	1	FACETS	0.799	0.761	0.837	0.799	0.761	0.837	SUBCLONAL	1	TRUE	0	0.668756028768026	1		1069	947	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658911	3658911	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	255	482	0	ENST00000294008.3:c.55C>T	p.His19Tyr	p.H19Y	ENST00000294008	NM_032444.2	19	Cat/Tat	2/15	1	2	FACETS	0.999	0.939	1	0.999	0.939	1	CLONAL	1	TRUE	1	0.668756028768026	2		482	763	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167585	24167585	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	239	518	0	ENST00000263121.7:c.969G>C	p.Gln323His	p.Q323H	ENST00000263121	NM_003073.3	323	caG/caC	7/9	1	2	FACETS	0.939	0.88	1	0.939	0.88	1	CLONAL	1	TRUE	1	0.668756028768026	2		518	761	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598199	52598199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	224	412	0	ENST00000394830.3:c.3667G>A	p.Glu1223Lys	p.E1223K	ENST00000394830	NM_018313.4	1223	Gaa/Aaa	24/30	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.668756028768026	2		412	629	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176700738	176700738	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	414	325	1	ENST00000439151.2:c.5575G>T	p.Glu1859Ter	p.E1859*	ENST00000439151	NM_022455.4	1859	Gaa/Taa	17/23	0.668756028768026	3	FACETS	0.987	0.957	1	0.987	0.957	1	CLONAL	3	TRUE	0	0.668756028768026	3		326	558	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057710	180057710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs578179579	NA	P-0048308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	414	954	0	ENST00000261937.6:c.245G>A	p.Arg82Gln	p.R82Q	ENST00000261937	NM_182925.4	82	cGa/cAa	3/30	0.668756028768026	3	FACETS	1	0.978	1	0.35	0.332	0.368	CLONAL	1	TRUE	0	0.668756028768026	3		954	1573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0048309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	134	634	0	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	0.3	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.29	1		634	661	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979368	40979368	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	66	347	0	ENST00000373198.4:c.1765C>G	p.Pro589Ala	p.P589A	ENST00000373198	NM_133170.3	589	Cca/Gca	11/32	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.29	2		347	420	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778004	27778004	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	41	511	0	ENST00000369163.2:c.153G>T	p.Glu51Asp	p.E51D	ENST00000369163	NM_003536.2	51	gaG/gaT	1/1	1	2	FACETS	0.593	0.494	0.703	0.593	0.494	0.703	SUBCLONAL	1	TRUE	1	0.29	2		511	477	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950716	79950733	+	inframe_deletion	In_Frame_Del	DEL	CCGCAGCGGCCGCAGCGC	CCGCAGCGGCCGCAGCGC	-	novel	NA	P-0048309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	96	166	0	ENST00000265081.6:c.172_189del	p.Ala58_Pro63del	p.A58_P63del	ENST00000265081	NM_002439.4	57	gCCGCAGCGGCCGCAGCGCcc/gcc	1/24	1	2	FACETS	1	0.96	1	1	0.988	1	CLONAL	2	TRUE	1	0.29	2		166	294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0048313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	150	743	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.645501634104087	2	FACETS	1	0.992	1	0.744	0.704	0.783	CLONAL	1	FALSE	0	0.941693031279757	2		744	214	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1321583762	NA	P-0048313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	33	214	1	ENST00000257430.4:c.3925G>T	p.Glu1309Ter	p.E1309*	ENST00000257430	NM_000038.5	1309	Gaa/Taa	16/16	0.665514981763269	3	FACETS	1	0.899	1	0.687	0.602	0.766	CLONAL	2	FALSE	0	0.941693031279757	3		215	50	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968597	55968597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34038364	NA	P-0048313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	35	649	3	ENST00000263923.4:c.2066C>T	p.Thr689Met	p.T689M	ENST00000263923	NM_002253.2	689	aCg/aTg	14/30	0.576669138652008	3	FACETS	0.578	0.479	0.688	0.289	0.239	0.344	SUBCLONAL	1	FALSE	1	0.941693031279757	3		652	189	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32439147	32439147	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	70	525	0	ENST00000332351.3:c.926T>A	p.Met309Lys	p.M309K	ENST00000332351	NM_024426.4	309	aTg/aAg	4/10	0.505148701664752	4	FACETS	0.764	0.679	0.851	0.764	0.679	0.851	INDETERMINATE	2	FALSE	2	0.941693031279757	4		525	189	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0048314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	171	610	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.427091709109405	1	FACETS	0.972	0.898	1	0.972	0.898	1	CLONAL	1	FALSE	0	0.427091709109405	1		610	648	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0048314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	139	660	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.427091709109405	2		660	561	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443595	52443595	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	115	510	0	ENST00000460680.1:c.97T>C	p.Tyr33His	p.Y33H	ENST00000460680	NM_004656.3	33	Tac/Cac	3/17	0.427091709109405	1	FACETS	0.958	0.869	1	0.958	0.869	1	CLONAL	1	FALSE	0	0.427091709109405	1		510	442	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117811	70117812	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGT	novel	NA	P-0048314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	110	609	0	ENST00000245479.2:c.281_282insTCG	p.Arg94dup	p.R94dup	ENST00000245479	NM_000346.3	94	-/CGT	1/3	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.427091709109405	2		609	477	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793287	242793287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146642159	NA	P-0048314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	153	825	1	ENST00000334409.5:c.790C>T	p.Arg264Cys	p.R264C	ENST00000334409	NM_005018.2	264	Cgc/Tgc	5/5	0.427091709109405	1	FACETS	0.814	0.747	0.885	0.814	0.747	0.885	CLONAL	1	FALSE	0	0.427091709109405	1		826	692	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739669	41739669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	50	653	0	ENST00000242208.4:c.304G>A	p.Glu102Lys	p.E102K	ENST00000242208	NM_002192.2	102	Gag/Aag	2/3	0.193433963140261	3	FACETS	0.894	0.758	1	0.447	0.379	0.523	CLONAL	1	TRUE	1	0.193433963140261	3		653	634	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373380	118373380	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	44	475	0	ENST00000534358.1:c.6773G>C	p.Ser2258Thr	p.S2258T	ENST00000534358	NM_005933.3	2258	aGt/aCt	27/36	1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.193433963140261	2		475	453	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877195	151877195	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	62	403	0	ENST00000262189.6:c.7166A>C	p.Glu2389Ala	p.E2389A	ENST00000262189	NM_170606.2	2389	gAa/gCa	37/59	0.193433963140261	3	FACETS	1	0.88	1	1	0.88	1	CLONAL	2	TRUE	1	0.193433963140261	3		403	347	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242483	+	protein_altering_variant	In_Frame_Del	DEL	ATTAAGAGAAGCAACA	ATTAAGAGAAGCAACA	C	novel	NA	P-0048315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	30	363	2	ENST00000275493.2:c.2238_2253delinsC	p.Glu746_Thr751delinsAsp	p.E746_T751delinsD	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACA/gaC	19/28	0.193433963140261	3	FACETS	0.893	0.72	1	0.446	0.36	0.545	CLONAL	1	TRUE	1	0.193433963140261	3		365	381	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736290	243736290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	29	436	0	ENST00000263826.5:c.757G>A	p.Ala253Thr	p.A253T	ENST00000263826	NM_005465.4	253	Gca/Aca	8/13	0.302607786184243	5	FACETS	0.803	0.656	0.964	0.535	0.437	0.643	CLONAL	2	FALSE	2	0.502979873724066	5		436	126	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800837	18800837	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	19	318	0	ENST00000266497.5:c.4213C>A	p.Gln1405Lys	p.Q1405K	ENST00000266497		1405	Caa/Aaa	31/31	NA	2	FACETS	1	0.854	1			1	INDETERMINATE	1	FALSE	NA	0.502979873724066	2		318	67	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574029	7574030	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	114	665	1	ENST00000269305.4:c.997_998insA	p.Arg333GlnfsTer4	p.R333Qfs*4	ENST00000269305	NM_001126112.2	333	cgt/cAgt	10/11	0.464869945087968	2	FACETS	1	0.986	1	0.748	0.683	0.814	CLONAL	1	FALSE	0	0.502979873724066	2		666	303	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736290	243736290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048316-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	98	436	0	ENST00000263826.5:c.757G>A	p.Ala253Thr	p.A253T	ENST00000263826	NM_005465.4	253	Gca/Aca	8/13	1	2	FACETS	0.998	0.9	1	0.998	0.9	1	CLONAL	1	TRUE	1	0.572390273237245	2		436	343	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800837	18800837	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048316-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	65	318	0	ENST00000266497.5:c.4213C>A	p.Gln1405Lys	p.Q1405K	ENST00000266497		1405	Caa/Aaa	31/31	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.572390273237245	2		318	226	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574029	7574030	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048316-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	347	665	1	ENST00000269305.4:c.997_998insA	p.Arg333GlnfsTer4	p.R333Qfs*4	ENST00000269305	NM_001126112.2	333	cgt/cAgt	10/11	0.572390273237245	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.572390273237245	2		666	559	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43773213	43773213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048316-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	101	363	0	ENST00000382044.4:c.379G>A	p.Gly127Arg	p.G127R	ENST00000382044	NM_001141980.1	127	Gga/Aga	5/28	0.572390273237245	2	FACETS	1	0.945	1	0.533	0.482	0.587	CLONAL	1	TRUE	0	0.572390273237245	2		363	331	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512424	38512424	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048316-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	179	1057	0	ENST00000254066.5:c.1335C>A	p.Ser445Arg	p.S445R	ENST00000254066	NM_000964.3	445	agC/agA	9/9	0.572390273237245	2	FACETS	0.974	0.902	1	0.487	0.451	0.525	CLONAL	1	TRUE	0	0.572390273237245	2		1057	642	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0048317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	308	314	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.494510605745495	6	FACETS	1	0.971	1	1	0.971	1	CLONAL	6	TRUE	0	0.494510605745495	6		314	410	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916747	48916747	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690915	NA	P-0048317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	60	318	0	ENST00000267163.4:c.277C>T	p.Gln93Ter	p.Q93*	ENST00000267163	NM_000321.2	93	Caa/Taa	3/27	0.494510605745495	2	FACETS	0.926	0.823	1	0.926	0.823	1	CLONAL	2	TRUE	0	0.494510605745495	2		318	131	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280679	115280679	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	151	431	0	ENST00000438362.2:c.352G>C	p.Glu118Gln	p.E118Q	ENST00000438362	NM_001242891.1	118	Gaa/Caa	4/20	0.490501925809698	2	FACETS	0.911	0.847	0.977	0.911	0.847	0.977	CLONAL	2	TRUE	0	0.494510605745495	2		431	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519998	NA	P-0048320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	275	657	0	ENST00000269305.4:c.581T>A	p.Leu194His	p.L194H	ENST00000269305	NM_001126112.2	194	cTt/cAt	6/11	0.585391379236546	1	FACETS	0.803	0.761	0.846	0.803	0.761	0.846	CLONAL	1	TRUE	0	0.73280791751303	1		657	592	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273416	38273416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765629435	NA	P-0048320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	217	943	1	ENST00000425967.3:c.1919G>A	p.Arg640Gln	p.R640Q	ENST00000425967	NM_001174067.1	640	cGa/cAa	14/19	1	2	FACETS	0.567	0.527	0.609	0.567	0.527	0.609	SUBCLONAL	1	TRUE	1	0.73280791751303	2		944	1044	SUCCESS
APC	324	MSKCC	GRCh37	5	112175247	112175248	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0048320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	162	196	0	ENST00000257430.4:c.3959_3960dup	p.Ser1321Ter	p.S1321*	ENST00000257430	NM_000038.5	1319	cct/ccTGt	16/16	0.619491011279393	2	FACETS	0.787	0.739	0.834	0.787	0.739	0.834	SUBCLONAL	2	TRUE	0	0.73280791751303	2		196	281	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0048321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	194	314	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.462528882527576	3	FACETS	0.916	0.861	0.97	0.916	0.861	0.97	CLONAL	3	TRUE	0	0.462528882527576	3		314	376	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161677	56161678	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0048321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	206	350	0	ENST00000399503.3:c.1175dup	p.Tyr392Ter	p.Y392*	ENST00000399503	NM_005921.1	392	tat/tAat	6/20	0.179524371152747	6	FACETS	1	0.984	1	0.793	0.738	0.849	INDETERMINATE	2	TRUE	3	0.462528882527576	6		350	721	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178550	56178550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	113	174	0	ENST00000399503.3:c.3523C>T	p.Gln1175Ter	p.Q1175*	ENST00000399503	NM_005921.1	1175	Caa/Taa	14/20	0.179524371152747	6	FACETS	0.861	0.783	0.942	0.861	0.783	0.942	INDETERMINATE	3	TRUE	3	0.462528882527576	6		174	364	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	protein_altering_variant	In_Frame_Ins	INS	T	T	AGGG	novel	NA	P-0048321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	126	607	0	ENST00000206249.3:c.1607delinsAGGG	p.Leu536delinsGlnGly	p.L536delinsQG	ENST00000206249	NM_000125.3	536	cTc/cAGGGc	8/8	0.462528882527576	3	FACETS	0.814	0.737	0.895	0.407	0.368	0.448	CLONAL	1	TRUE	1	0.462528882527576	3		607	824	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	118	349	1				ENST00000310581	NM_198253.2	-/1132			0.335211981600305	3	FACETS	0.98	0.893	1	0.98	0.893	1	CLONAL	2	TRUE	1	0.364934831169134	3		350	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0048322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	201	684	2	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.364934831169134	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.364934831169134	1		686	731	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123260409	123260409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	122	555	0	ENST00000358487.5:c.1492G>A	p.Ala498Thr	p.A498T	ENST00000358487	NM_000141.4	498	Gcg/Acg	11/18	1	2	FACETS	0.896	0.811	0.986	0.896	0.811	0.986	CLONAL	1	TRUE	1	0.364934831169134	2		555	746	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425329	49425329	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	160	806	0	ENST00000301067.7:c.13159del	p.Gln4387ArgfsTer16	p.Q4387Rfs*16	ENST00000301067	NM_003482.3	4387	Cag/ag	39/54	1	2	FACETS	0.894	0.819	0.972	0.894	0.819	0.972	CLONAL	1	TRUE	1	0.364934831169134	2		806	981	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096243	178096243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	84	427	0	ENST00000397062.3:c.1088C>T	p.Ser363Phe	p.S363F	ENST00000397062	NM_006164.4	363	tCt/tTt	5/5	0.186350714886249	3	FACETS	0.993	0.879	1	0.497	0.439	0.558	INDETERMINATE	1	TRUE	1	0.364934831169134	3		427	548	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971179	21971180	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCACT	novel	NA	P-0048322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	111	364	0	ENST00000304494.5:c.174_178dup	p.Ala60GlufsTer88	p.A60Efs*88	ENST00000304494	NM_000077.4	60	gcg/gAGTGGcg	2/3	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.364934831169134	2		364	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0048353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	169	436	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.421198430353255	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.421198430353255	1		439	568	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741492	17741492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	130	408	0	ENST00000250003.3:c.163G>A	p.Ala55Thr	p.A55T	ENST00000250003	NM_002478.4	55	Gcg/Acg	1/3	1	2	FACETS	0.937	0.852	1	0.937	0.852	1	CLONAL	1	TRUE	1	0.421198430353255	2		408	659	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105809	27105810	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	117	329	0	ENST00000324856.7:c.5421dup	p.Lys1808Ter	p.K1808*	ENST00000324856	NM_006015.4	1807	agt/agTt	20/20	0.218229869452872	1	FACETS	0.981	0.891	1	0.981	0.891	1	INDETERMINATE	1	TRUE	0	0.421198430353255	1		329	447	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089478	27089478	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	71	444	1	ENST00000324856.7:c.2434C>T	p.Gln812Ter	p.Q812*	ENST00000324856	NM_006015.4	812	Cag/Tag	8/20	0.218229869452872	1	FACETS	0.438	0.383	0.499	0.438	0.383	0.499	INDETERMINATE	1	TRUE	0	0.421198430353255	1		445	607	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256557	133256563	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGGAC	TGGGGAC	-	novel	NA	P-0048353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	67	272	0	ENST00000320574.5:c.400_406del	p.Val134LysfsTer13	p.V134Kfs*13	ENST00000320574	NM_006231.2	134	GTCCCCAaa/aa	5/49	1	2	FACETS	0.713	0.622	0.812	0.713	0.622	0.812	SUBCLONAL	1	TRUE	1	0.421198430353255	2		272	446	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557630	21557630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	144	467	1	ENST00000382592.4:c.2215G>A	p.Asp739Asn	p.D739N	ENST00000382592	NM_014572.2	739	Gac/Aac	5/8	1	2	FACETS	0.975	0.891	1	0.975	0.891	1	CLONAL	1	TRUE	1	0.421198430353255	2		468	701	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046506	30046506	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1418111788	NA	P-0048353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	57	368	0	ENST00000331968.5:c.2677G>A	p.Asp893Asn	p.D893N	ENST00000331968	NM_002742.2	893	Gac/Aac	18/18	0.218229869452872	1	FACETS	0.368	0.316	0.426	0.368	0.316	0.426	INDETERMINATE	1	TRUE	0	0.421198430353255	1		368	580	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517400	157517400	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	161	373	0	ENST00000346085.5:c.3964G>C	p.Gly1322Arg	p.G1322R	ENST00000346085	NM_020732.3	1322	Ggc/Cgc	16/20	0.218229869452872	1	FACETS	1	0.942	1	1	0.942	1	INDETERMINATE	1	TRUE	0	0.421198430353255	1		373	588	SUCCESS
ALK	238	MSKCC	GRCh37	2	29497983	29497983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1469128263	NA	P-0048354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	142	410	0	ENST00000389048.3:c.2023C>T	p.Pro675Ser	p.P675S	ENST00000389048	NM_004304.4	675	Ccc/Tcc	11/29	NA	2	FACETS	0.895	0.823	0.969			1	INDETERMINATE	1	TRUE	NA	0.722752542201473	2		410	439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578267	7578267	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1567552031	NA	P-0048354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	540	524	0	ENST00000269305.4:c.582del	p.Ile195SerfsTer52	p.I195Sfs*52	ENST00000269305	NM_001126112.2	194	ctT/ct	6/11	0.718354245816258	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.722752542201473	2		524	733	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222720	5222720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752731468	NA	P-0048354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	184	646	1	ENST00000357368.4:c.3083G>A	p.Arg1028Gln	p.R1028Q	ENST00000357368	NM_002850.3	1028	cGg/cAg	18/38	1	2	FACETS	0.791	0.733	0.85	0.791	0.733	0.85	SUBCLONAL	1	TRUE	1	0.722752542201473	2		647	644	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0048355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	51	383	0				ENST00000310581	NM_198253.2	-/1132			0.078945572927368	0	FACETS	0.656	0.56	0.761			1	INDETERMINATE	1	TRUE	0	0.31	0		383	346	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0048355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	45	303	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.31	2		303	270	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652147	36652148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	121	596	0	ENST00000244741.5:c.270dup	p.Gly91ArgfsTer38	p.G91Rfs*38	ENST00000244741	NM_000389.4	90	gga/ggAa	2/3	1	2	FACETS	0.986	0.891	1	0.986	0.891	1	CLONAL	1	TRUE	1	0.31	2		596	792	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39239481	39239481	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	29	218	0	ENST00000402219.2:c.2176A>G	p.Met726Val	p.M726V	ENST00000402219	NM_005633.3	726	Atg/Gtg	14/23	1	2	FACETS	0.55	0.442	0.673	0.55	0.442	0.673	SUBCLONAL	1	TRUE	1	0.31	2		218	340	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950110	44950110	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0048355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	15	127	0	ENST00000377967.4:c.3878+1G>A		p.X1293_splice	ENST00000377967	NM_021140.2	1293			1	1	FACETS	0.629	0.464	0.824	0.629	0.464	0.824	SUBCLONAL	1	TRUE	0	0.31	1		127	130	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	33	349	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.427	0.347	0.517	0.427	0.347	0.517	SUBCLONAL	1	TRUE	1	0.31	2		350	499	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0048356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	68	317	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	0.693	0.603	0.791	0.693	0.603	0.791	SUBCLONAL	1	TRUE	1	0.31	2		317	633	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0048356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	28	222	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	1	2	FACETS	0.789	0.634	0.964	0.789	0.634	0.964	CLONAL	1	TRUE	1	0.31	2		222	229	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100451	8100451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266983268	NA	P-0048356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	66	837	0	ENST00000346208.3:c.425C>T	p.Ser142Leu	p.S142L	ENST00000346208		142	tCg/tTg	3/6	1	2	FACETS	0.406	0.351	0.466	0.406	0.351	0.466	SUBCLONAL	1	TRUE	1	0.31	2		837	1049	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508823	106508823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	97	559	0	ENST00000359195.3:c.817C>T	p.Arg273Cys	p.R273C	ENST00000359195	NM_002649.2	273	Cgc/Tgc	2/11	0.164166807640152	3	FACETS	1	0.896	1	0.503	0.448	0.561	INDETERMINATE	1	TRUE	1	0.31	3		559	719	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477861	140477861	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs397507474	NA	P-0048356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	22	417	0	ENST00000288602.6:c.1447A>G	p.Lys483Glu	p.K483E	ENST00000288602	NM_004333.4	483	Aaa/Gaa	12/18	0.164166807640152	3	FACETS	0.707	0.549	0.888	0.353	0.274	0.444	INDETERMINATE	1	TRUE	1	0.31	3		417	232	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748296	41748296	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	86	751	0	ENST00000226382.2:c.473G>A	p.Arg158His	p.R158H	ENST00000226382	NM_003924.3	158	cGc/cAc	3/3	0.3	1	FACETS	0.475	0.419	0.535	0.475	0.419	0.535	SUBCLONAL	1	TRUE	0	0.31	1		751	988	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81941371	81941371	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	85	486	0	ENST00000359376.3:c.1549G>T	p.Val517Leu	p.V517L	ENST00000359376	NM_002661.3	517	Gtg/Ttg	16/33	1	2	FACETS	0.928	0.821	1	0.928	0.821	1	CLONAL	1	TRUE	1	0.31	2		486	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576716	7576923	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGCCATTGTCTTTGAGGCATCACTGCCCCCTGATGGCAAATGCCCCAATTGCAGGTAAAACAGTCAAGAAGAAAACGGCATTTTGAGTGTTAGACTGGAAACTTTCCACTTGATAAGAGGTCCCAAGACTTAGTACCTGAAGGGTGAAATATTCTCCATCCAGTGGTTTCTTCTTTGGCTGGGGAGAGGAGCTGGTGTTGTTGGGCA	GAGCCATTGTCTTTGAGGCATCACTGCCCCCTGATGGCAAATGCCCCAATTGCAGGTAAAACAGTCAAGAAGAAAACGGCATTTTGAGTGTTAGACTGGAAACTTTCCACTTGATAAGAGGTCCCAAGACTTAGTACCTGAAGGGTGAAATATTCTCCATCCAGTGGTTTCTTCTTTGGCTGGGGAGAGGAGCTGGTGTTGTTGGGCA	-	novel	NA	P-0048356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	50	366	1	ENST00000269305.4:c.923_993+137del		p.X308_splice	ENST00000269305	NM_001126112.2	308		9/11	1	2	FACETS	0.978	0.833	1	0.978	0.833	1	CLONAL	1	TRUE	1	0.31	2		367	330	SUCCESS
APC	324	MSKCC	GRCh37	5	112175525	112175526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAAT	novel	NA	P-0048356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	21	308	0	ENST00000257430.4:c.4236_4239dup	p.Val1414AsnfsTer10	p.V1414Nfs*10	ENST00000257430	NM_000038.5	1412	gga/gGAATga	16/16	1	2	FACETS	0.374	0.288	0.475	0.374	0.288	0.475	SUBCLONAL	1	TRUE	1	0.31	2		308	362	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932140	39932140	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	48	297	0	ENST00000378444.4:c.2459del	p.Asn820ThrfsTer36	p.N820Tfs*36	ENST00000378444	NM_001123385.1	820	aAc/ac	4/15	1	1	FACETS	0.683	0.579	0.797	0.683	0.579	0.797	SUBCLONAL	1	TRUE	0	0.31	1		297	383	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274911	41274911	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	204	332	0	ENST00000349496.5:c.1161T>G	p.Asn387Lys	p.N387K	ENST00000349496	NM_001904.3	387	aaT/aaG	8/15	0.547057740920588	3	FACETS	0.802	0.749	0.857	0.802	0.749	0.857	CLONAL	2	TRUE	1	0.547057740920588	3		332	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934575	NA	P-0048358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	153	404	0	ENST00000269305.4:c.733G>C	p.Gly245Arg	p.G245R	ENST00000269305	NM_001126112.2	245	Ggc/Cgc	7/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.601841524562388	2		404	467	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0048358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	107	397	0	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	0.909	0.823	1	0.909	0.823	1	CLONAL	1	TRUE	1	0.601841524562388	2		397	391	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057296	180057296	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	297	634	0	ENST00000261937.6:c.442G>T	p.Val148Phe	p.V148F	ENST00000261937	NM_182925.4	148	Gtc/Ttc	4/30	0.827452713638905	3	FACETS	1	0.975	1	0.529	0.499	0.56	CLONAL	1	FALSE	1	0.828344995813615	3		634	959	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0048361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	223	643	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.765208839106772	2		643	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0048361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	183	607	1	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.765208839106772	2		608	463	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0048361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	82	188	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.765208839106772	2		188	199	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540515	187540515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769335147	NA	P-0048361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	18	347	1	ENST00000441802.2:c.7225G>A	p.Val2409Met	p.V2409M	ENST00000441802	NM_005245.3	2409	Gtg/Atg	10/27	0.160973969357638	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.765208839106772	0		348	266	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939657	131939657	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0048361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	18	270	0	ENST00000265335.6:c.2443A>C	p.Lys815Gln	p.K815Q	ENST00000265335		815	Aag/Cag	15/25	1	2	FACETS	0.15	0.112	0.194	0.15	0.112	0.194	SUBCLONAL	1	TRUE	1	0.765208839106772	2		270	314	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937761	76937761	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0048361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	168	181	0	ENST00000373344.5:c.2987C>G	p.Ser996Ter	p.S996*	ENST00000373344	NM_000489.3	996	tCa/tGa	9/35	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.765208839106772	1		181	234	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	91	349	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.969	0.871	1	0.969	0.871	1	CLONAL	1	TRUE	1	0.641229522968945	2		350	293	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503838	149503838	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs864309711	NA	P-0048371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	184	597	0	ENST00000261799.4:c.1998C>A	p.Asn666Lys	p.N666K	ENST00000261799	NM_002609.3	666	aaC/aaA	14/23	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.641229522968945	2		597	566	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462588	92462589	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0048371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	232	343	1	ENST00000265734.4:c.49_50delinsAA	p.Ala17Lys	p.A17K	ENST00000265734	NM_001259.6	17	GCg/AAg	2/8	0.641229522968945	3	FACETS	0.977	0.922	1	0.977	0.922	1	CLONAL	2	TRUE	1	0.641229522968945	3		344	489	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444984	49444999	+	frameshift_variant	Frame_Shift_Del	DEL	GTTGGGGGGACAAGCA	GTTGGGGGGACAAGCA	-	novel	NA	P-0048371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	203	326	0	ENST00000301067.7:c.2467_2482del	p.Cys823LeufsTer102	p.C823Lfs*102	ENST00000301067	NM_003482.3	823	TGCTTGTCCCCCCAACct/ct	10/54	1	2	FACETS	0.752	0.707	0.797	1	0.993	1	SUBCLONAL	2	TRUE	1	0.641229522968945	2		326	421	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512324	38512324	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	326	445	0	ENST00000254066.5:c.1235A>T	p.Glu412Val	p.E412V	ENST00000254066	NM_000964.3	412	gAa/gTa	9/9	0.641229522968945	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.641229522968945	3		445	664	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505109	149505113	+	protein_altering_variant	In_Frame_Del	DEL	ATCAC	ATCAC	GG	novel	NA	P-0048371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	197	411	1	ENST00000261799.4:c.1702_1706delinsCC	p.Val568_Ile569delinsPro	p.V568_I569delinsP	ENST00000261799	NM_002609.3	568	GTGATt/CCt	12/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.641229522968945	2		412	557	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652243	36652243	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	173	517	0	ENST00000244741.5:c.365G>T	p.Arg122Leu	p.R122L	ENST00000244741	NM_000389.4	122	cGc/cTc	2/3	1	2	FACETS	0.861	0.796	0.928	0.861	0.796	0.928	CLONAL	1	TRUE	1	0.641229522968945	2		517	627	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878938	117878938	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	258	249	0	ENST00000297338.2:c.31A>G	p.Arg11Gly	p.R11G	ENST00000297338	NM_006265.2	11	Aga/Gga	2/14	0.632185536748287	4	FACETS	0.879	0.833	0.924	0.879	0.833	0.924	CLONAL	3	TRUE	1	0.641229522968945	4		249	501	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861508	152861508	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0048371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	133	282	0	ENST00000406277.2:c.244del	p.Glu82LysfsTer46	p.E82Kfs*46	ENST00000406277	NM_152274.4	82	Gaa/aa	4/7	1		FACETS		0.976	1				CLONAL	1	TRUE	1	0.641229522968945	2		282	356	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0048373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	23	215	0	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	0.0943591004143909	4	FACETS	1	0.883	1	1	0.946	1	INDETERMINATE	3	TRUE	2	0.292750521458049	4		215	60	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972649	25972649	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1162036867	NA	P-0048373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	42	322	1	ENST00000435504.4:c.1776G>T	p.Gln592His	p.Q592H	ENST00000435504		592	caG/caT	12/13	0.292750521458049	4	FACETS	0.647	0.54	0.767	0.216	0.18	0.256	SUBCLONAL	1	TRUE	1	0.292750521458049	4		323	573	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979338	40979338	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	194	434	0	ENST00000373198.4:c.1795C>A	p.Pro599Thr	p.P599T	ENST00000373198	NM_133170.3	599	Cca/Aca	11/32	0.171947860884304	5	FACETS	0.845	0.784	0.908	0.845	0.784	0.908	INDETERMINATE	3	TRUE	2	0.292750521458049	5		434	752	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380051	116380052	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0048373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	102	412	1	ENST00000397752.3:c.1440_1441delinsAA	p.Leu481Met	p.L481M	ENST00000397752	NM_000245.2	480	ctCCtg/ctAAtg	4/21	0.217235227747321	4	FACETS	0.975	0.877	1	0.975	0.877	1	CLONAL	2	TRUE	2	0.292750521458049	4		413	462	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317440	1317440	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	100	470	1	ENST00000400841.2:c.625T>A	p.Trp209Arg	p.W209R	ENST00000400841		209	Tgg/Agg	5/6	0.292750521458049	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.292750521458049	1		471	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578486	7578491	+	frameshift_variant	Frame_Shift_Del	DEL	ATCAAC	ATCAAC	G	novel	NA	P-0048373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	487	701	0	ENST00000269305.4:c.439_444delinsC	p.Val147LeufsTer32	p.V147Lfs*32	ENST00000269305	NM_001126112.2	147	GTTGAT/C	5/11	0.292750521458049	4	FACETS	0.9	0.863	0.937	1	0.994	1	CLONAL	4	TRUE	1	0.292750521458049	4		701	1195	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0048374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	116	424	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.167904717700755	3	FACETS	0.872	0.788	0.961	0.872	0.788	0.961	CLONAL	3	TRUE	0	0.160391302752404	3		424	597	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196059	67196059	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	87	541	0	ENST00000312629.5:c.43A>G	p.Ser15Gly	p.S15G	ENST00000312629	NM_003952.2	15	Agc/Ggc	1/15	1	2	FACETS	0.837	0.742	0.939	1	0.982	1	CLONAL	2	TRUE	1	0.160391302752404	2		541	648	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15938117	15938117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769360451	NA	P-0048374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	88	240	0	ENST00000268712.3:c.7097C>T	p.Thr2366Met	p.T2366M	ENST00000268712	NM_006311.3	2366	aCg/aTg	45/46	0.167904717700755	3	FACETS	0.988	0.885	1	1	0.975	1	CLONAL	4	TRUE	0	0.160391302752404	3		240	300	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437370	110437370	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	16	168	0	ENST00000375856.3:c.1031C>T	p.Thr344Ile	p.T344I	ENST00000375856	NM_003749.2	344	aCc/aTc	1/2	0.160391302752404	5	FACETS	1	0.863	1	0.322	0.239	0.421	CLONAL	1	TRUE	1	0.160391302752404	5		168	192	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	33	323	0	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	1	2	FACETS	0.709	0.579	0.853	0.709	0.579	0.853	SUBCLONAL	1	TRUE	1	0.336210122435458	2		323	277	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0048375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	25	275	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.214402126648395	3	FACETS	0.661	0.522	0.819	0.33	0.261	0.41	SUBCLONAL	1	TRUE	1	0.336210122435458	3		275	263	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0048375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	21	228	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.698	0.541	0.878	0.698	0.541	0.878	SUBCLONAL	1	TRUE	1	0.336210122435458	2		228	179	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412110	63412110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852216	NA	P-0048375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	115	548	0	ENST00000330258.3:c.1057C>T	p.Arg353Ter	p.R353*	ENST00000330258	NM_152424.3	353	Cga/Tga	2/2	0.336210122435458	1	FACETS	0.976	0.882	1	0.976	0.882	1	CLONAL	1	TRUE	0	0.336210122435458	1		548	583	SUCCESS
APC	324	MSKCC	GRCh37	5	112174502	112174502	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876659539	NA	P-0048375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	28	205	0	ENST00000257430.4:c.3211C>T	p.Gln1071Ter	p.Q1071*	ENST00000257430	NM_000038.5	1071	Caa/Taa	16/16	1	2	FACETS	1	0.811	1	1	0.811	1	CLONAL	1	TRUE	1	0.336210122435458	2		205	166	SUCCESS
APC	324	MSKCC	GRCh37	5	112175642	112175642	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	40	237	1	ENST00000257430.4:c.4351G>T	p.Glu1451Ter	p.E1451*	ENST00000257430	NM_000038.5	1451	Gaa/Taa	16/16	1	2	FACETS	0.763	0.636	0.902	0.763	0.636	0.902	CLONAL	1	TRUE	1	0.336210122435458	2		238	312	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982653	90982653	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	54	233	0	ENST00000265433.3:c.835C>T	p.Gln279Ter	p.Q279*	ENST00000265433	NM_002485.4	279	Cag/Tag	7/16	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.336210122435458	2		233	281	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120130	70120130	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	74	175	0	ENST00000245479.2:c.1132C>T	p.Gln378Ter	p.Q378*	ENST00000245479	NM_000346.3	378	Cag/Tag	3/3	0.336210122435458	2	FACETS	0.895	0.804	0.986	1	0.976	1	CLONAL	3	TRUE	0	0.336210122435458	2		175	164	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981212	201981212	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	277	567	0	ENST00000359651.3:c.292del	p.Asp98MetfsTer57	p.D98Mfs*57	ENST00000359651		97	atG/at	2/8	0.214402126648395	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.336210122435458	3		567	910	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132896	64132896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	111	580	0	ENST00000334205.4:c.1030C>T	p.Pro344Ser	p.P344S	ENST00000334205	NM_003942.2	344	Ccc/Tcc	9/17	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.336210122435458	2		580	605	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637674	23637674	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	45	380	0	ENST00000261584.4:c.2631G>C	p.Trp877Cys	p.W877C	ENST00000261584	NM_024675.3	877	tgG/tgC	7/13	1	2	FACETS	0.65	0.547	0.763	0.65	0.547	0.763	SUBCLONAL	1	TRUE	1	0.336210122435458	2		380	412	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822452	72822456	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTA	CTTTA	-	novel	NA	P-0048375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	107	604	0	ENST00000268489.5:c.9719_9723del	p.Val3240GlyfsTer189	p.V3240Gfs*189	ENST00000268489	NM_006885.3	3240	gTAAAG/g	10/10	1	2	FACETS	0.987	0.887	1	0.987	0.887	1	CLONAL	1	TRUE	1	0.336210122435458	2		604	645	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0048376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	348	494	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.575016465239318	2	FACETS	0.915	0.877	0.954	0.915	0.877	0.954	CLONAL	2	TRUE	0	0.616186640945984	2		494	617	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755607	39755607	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0048376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	68	518	0	ENST00000288319.7:c.1158C>G	p.Tyr386Ter	p.Y386*	ENST00000288319	NM_182918.3	386	taC/taG	10/10	0.358668115524238	6	FACETS	0.435	0.377	0.499	0.109	0.094	0.125	INDETERMINATE	1	TRUE	2	0.616186640945984	6		518	1132	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	69061264	69061264	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	41	157	0	ENST00000487270.1:c.1099C>T	p.Gln367Ter	p.Q367*	ENST00000487270	NM_133509.3	367	Cag/Tag	11/11	0.616186640945984	2	FACETS	0.512	0.429	0.603	0.256	0.214	0.302	SUBCLONAL	1	TRUE	0	0.616186640945984	2		157	260	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349259	89349259	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	115	664	0	ENST00000301030.4:c.3691G>C	p.Asp1231His	p.D1231H	ENST00000301030	NM_001256183.1	1231	Gat/Cat	9/13	0.301058547600509	1	FACETS	0.438	0.396	0.483	0.438	0.396	0.483	INDETERMINATE	1	TRUE	0	0.616186640945984	1		664	589	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288519	15288519	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1278093299	NA	P-0048376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	25	219	0	ENST00000263388.2:c.4220G>T	p.Ser1407Ile	p.S1407I	ENST00000263388	NM_000435.2	1407	aGc/aTc	24/33	0.478809891372307	1	FACETS	0.252	0.199	0.312	0.252	0.199	0.312	SUBCLONAL	1	TRUE	0	0.616186640945984	1		219	223	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243940	53243940	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	82	649	0	ENST00000375401.3:c.1053C>G	p.Ile351Met	p.I351M	ENST00000375401	NM_004187.3	351	atC/atG	8/26	NA	2	FACETS	0.328	0.289	0.371			1	INDETERMINATE	1	TRUE	NA	0.616186640945984	2		649	811	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411009	63411010	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	AG	novel	NA	P-0048376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	57	587	0	ENST00000330258.3:c.2157_2158delinsCT	p.Met719_Gln720delinsIleTer	p.M719_Q720delinsI*	ENST00000330258	NM_152424.3	719	atGCag/atCTag	2/2	NA	2	FACETS	0.289	0.247	0.334			1	INDETERMINATE	1	TRUE	NA	0.616186640945984	2		587	641	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0048378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	27	259	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.270487759273187	3	FACETS	1	0.806	1	0.504	0.403	0.618	CLONAL	1	TRUE	1	0.270487759273187	3		259	225	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0048378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	84	436	3	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.253764386046274	1	FACETS	0.894	0.79	1	0.894	0.79	1	CLONAL	1	TRUE	0	0.270487759273187	1		439	601	SUCCESS
APC	324	MSKCC	GRCh37	5	112175147	112175147	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	33	153	0	ENST00000257430.4:c.3856G>T	p.Glu1286Ter	p.E1286*	ENST00000257430	NM_000038.5	1286	Gaa/Taa	16/16	0.129229261406505	3	FACETS	0.923	0.763	1	0.923	0.763	1	INDETERMINATE	2	TRUE	1	0.270487759273187	3		153	150	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805441	46805441	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	84	579	0	ENST00000290295.7:c.515G>T	p.Trp172Leu	p.W172L	ENST00000290295	NM_006361.5	172	tGg/tTg	1/2	1	2	FACETS	0.866	0.765	0.975	0.866	0.765	0.975	CLONAL	1	TRUE	1	0.270487759273187	2		579	717	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089622	27089623	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0048379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	83	560	0	ENST00000324856.7:c.2579dup	p.His860GlnfsTer12	p.H860Qfs*12	ENST00000324856	NM_006015.4	860	cac/cAac	8/20	0.198365241425688	3	FACETS	0.646	0.569	0.729	0.323	0.284	0.365	SUBCLONAL	1	TRUE	1	0.32253631535005	3		560	925	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0048379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	103	277	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.198365241425688	3	FACETS	0.889	0.801	0.981	0.889	0.801	0.981	CLONAL	2	TRUE	1	0.32253631535005	3		277	417	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679216	88679216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs187007070	NA	P-0048379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	38	500	1	ENST00000360948.2:c.821C>T	p.Thr274Met	p.T274M	ENST00000360948	NM_001012338.2	274	aCg/aTg	8/19	1	2	FACETS	0.405	0.334	0.484	0.405	0.334	0.484	SUBCLONAL	1	TRUE	1	0.32253631535005	2		501	582	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0048379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	314	712	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.270100254610312	3	FACETS	0.936	0.887	0.986	0.936	0.887	0.986	CLONAL	3	TRUE	0	0.32253631535005	3		712	805	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120407	70120408	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0048379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	263	655	0	ENST00000245479.2:c.1413dup	p.Ala472ArgfsTer106	p.A472Rfs*106	ENST00000245479	NM_000346.3	470	aac/aaCc	3/3	0.286000347945779	3	FACETS	0.895	0.839	0.953	0.895	0.839	0.953	CLONAL	2	TRUE	1	0.32253631535005	3		655	1058	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672758	86672758	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1204340475	NA	P-0048379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	62	260	0	ENST00000274376.6:c.2245C>T	p.Arg749Ter	p.R749*	ENST00000274376	NM_002890.2	749	Cga/Tga	17/25	0.178277704582324	4	FACETS	0.787	0.684	0.897	0.787	0.684	0.897	INDETERMINATE	2	TRUE	2	0.32253631535005	4		260	323	SUCCESS
APC	324	MSKCC	GRCh37	5	112174349	112174349	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	50	208	0	ENST00000257430.4:c.3058G>T	p.Glu1020Ter	p.E1020*	ENST00000257430	NM_000038.5	1020	Gaa/Taa	16/16	0.178277704582324	4	FACETS	0.884	0.758	1	0.884	0.758	1	INDETERMINATE	2	TRUE	2	0.32253631535005	4		208	232	SUCCESS
APC	324	MSKCC	GRCh37	5	112175761	112175761	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	62	275	0	ENST00000257430.4:c.4473del	p.Phe1491LeufsTer16	p.F1491Lfs*16	ENST00000257430	NM_000038.5	1490	caT/ca	16/16	0.178277704582324	4	FACETS	1	0.966	1	0.691	0.6	0.789	INDETERMINATE	1	TRUE	2	0.32253631535005	4		275	368	SUCCESS
AR	367	MSKCC	GRCh37	X	66765746	66765746	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769445750	NA	P-0048379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	57	363	0	ENST00000374690.3:c.758C>T	p.Ala253Val	p.A253V	ENST00000374690	NM_000044.3	253	gCg/gTg	1/8	0.32253631535005	2	FACETS	0.526	0.451	0.608			1	SUBCLONAL	1	TRUE	NA	0.32253631535005	2		363	672	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952074	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913283	NA	P-0048386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	15	322	0	ENST00000263967.3:c.3129G>A	p.Met1043Ile	p.M1043I	ENST00000263967	NM_006218.2	1043	atG/atA	21/21	1	2	FACETS	0.28	0.204	0.372	0.28	0.204	0.372	SUBCLONAL	1	FALSE	1	0.305020102675201	2		322	351	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720808	89720808	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	37	229	0	ENST00000371953.3:c.959T>C	p.Leu320Ser	p.L320S	ENST00000371953	NM_000314.4	320	tTa/tCa	8/9	0.234144026397532	2	FACETS	0.822	0.681	0.979	0.411	0.34	0.49	CLONAL	1	FALSE	0	0.305020102675201	2		229	295	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120645	115120646	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0048386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	132	680	0	ENST00000257566.3:c.359_360dup	p.Thr121AlafsTer19	p.T121Afs*19	ENST00000257566	NM_016569.3	120	-/GC	1/8	0.305020102675201	0	FACETS	0.972	0.885	1			1	CLONAL	1	FALSE	0	0.305020102675201	0		680	619	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885921	111885921	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs768764036	NA	P-0048386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	23	562	0	ENST00000341259.2:c.1543C>A	p.Leu515Ile	p.L515I	ENST00000341259	NM_005475.2	515	Ctc/Atc	8/8	0.305020102675201	3	FACETS	0.406	0.316	0.511	0.203	0.158	0.256	SUBCLONAL	1	FALSE	1	0.305020102675201	3		562	428	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862075	68862075	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0048386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	62	369	0	ENST00000261769.5:c.2165-2A>G		p.X722_splice	ENST00000261769	NM_004360.3	722			0.305020102675201	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	0	0.305020102675201	1		369	286	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42057168	42057168	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	53	557	0	ENST00000219905.7:c.7829C>T	p.Pro2610Leu	p.P2610L	ENST00000219905	NM_001164273.1	2610	cCc/cTc	23/24	1	2	FACETS	0.712	0.608	0.827	0.712	0.608	0.827	SUBCLONAL	1	TRUE	1	0.287790606155232	2		557	517	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213960	2213960	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	69	757	0	ENST00000398665.3:c.1772C>G	p.Ala591Gly	p.A591G	ENST00000398665	NM_032482.2	591	gCg/gGg	18/28	1	2	FACETS	0.89	0.776	1	0.89	0.776	1	CLONAL	1	TRUE	1	0.287790606155232	2		757	539	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	29	349	1				ENST00000310581	NM_198253.2	-/1132			0.213035354186534	4	FACETS	0.946	0.786	1	0.946	0.786	1	INDETERMINATE	2	TRUE	2	0.647491579972871	4		350	78	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743909	46743909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	37	527	2	ENST00000371975.4:c.2199C>A	p.Phe733Leu	p.F733L	ENST00000371975	NM_003579.3	733	ttC/ttA	18/18	1	2	FACETS	0.945	0.797	1	0.945	0.797	1	CLONAL	1	TRUE	1	0.647491579972871	2		529	121	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166802	32166802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	58	767	0	ENST00000375023.3:c.4436G>A	p.Gly1479Glu	p.G1479E	ENST00000375023	NM_004557.3	1479	gGa/gAa	24/30	0.147785480875203	4	FACETS	1	0.915	1	1	0.915	1	INDETERMINATE	2	TRUE	2	0.647491579972871	4		767	141	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	53	349	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.56276949676651	2		350	188	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0048389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	299	712	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.547855106103182	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.56276949676651	2		712	515	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690819	89690820	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0048389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	93	242	1	ENST00000371953.3:c.227_228del	p.Tyr76Ter	p.Y76*	ENST00000371953	NM_000314.4	76	TAt/t	4/9	0.56276949676651	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.56276949676651	1		243	185	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953760	48953760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913302	NA	P-0048389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	56	166	0	ENST00000267163.4:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000267163	NM_000321.2	455	Cga/Tga	14/27	0.56276949676651	1	FACETS	0.867	0.758	0.98	0.867	0.758	0.98	CLONAL	1	TRUE	0	0.56276949676651	1		166	165	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858119	152858119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370810560	NA	P-0048389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	126	628	1	ENST00000406277.2:c.496G>A	p.Val166Ile	p.V166I	ENST00000406277	NM_152274.4	166	Gtc/Atc	6/7	1	2	FACETS	0.941	0.857	1	0.941	0.857	1	CLONAL	1	TRUE	1	0.56276949676651	2		629	476	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559859	29559862	+	frameshift_variant	Frame_Shift_Del	DEL	ACTC	ACTC	-	rs1321848637	NA	P-0048389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	109	208	0	ENST00000356175.3:c.3457_3460del	p.Leu1153MetfsTer4	p.L1153Mfs*4	ENST00000356175	NM_000267.3	1152	ttACTC/tt	26/57	0.547855106103182	2	FACETS	0.876	0.806	0.947	0.876	0.806	0.947	CLONAL	2	TRUE	0	0.56276949676651	2		208	221	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62311287	62311287	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376411169	NA	P-0048389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	45	306	0	ENST00000360203.5:c.1123C>T	p.His375Tyr	p.H375Y	ENST00000360203	NM_001283009.1	375	Cac/Tac	13/35	1	2	FACETS	0.617	0.523	0.721	0.617	0.523	0.721	SUBCLONAL	1	TRUE	1	0.56276949676651	2		306	259	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0048391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	161	314	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.729889209847683	2		314	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0048391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	278	511	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	0.729889209847683	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.729889209847683	1		511	462	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039505	49039505	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0048391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	142	396	2	ENST00000267163.4:c.2489+1G>T		p.X830_splice	ENST00000267163	NM_000321.2	830			0.729889209847683	1	FACETS	0.861	0.8	0.922	0.861	0.8	0.922	CLONAL	1	TRUE	0	0.729889209847683	1		398	287	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204495560	204495560	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	140	261	0	ENST00000367182.3:c.151G>A	p.Glu51Lys	p.E51K	ENST00000367182	NM_001278516.1	51	Gag/Aag	3/11	0.672615345974698	3	FACETS	1	0.97	1	0.561	0.514	0.609	CLONAL	1	TRUE	1	0.729889209847683	3		261	467	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914715	32915737	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAGTTAAGGGAGTGTTAGAGGAATTTGATTTAATCAGAACTGAGCATAGTCTTCACTATTCACCTACGTCTAGACAAAATGTATCAAAAATACTTCCTCGTGTTGATAAGAGAAACCCAGAGCACTGTGTAAACTCAGAAATGGAAAAAACCTGCAGTAAAGAATTTAAATTATCAAATAACTTAAATGTTGAAGGTGGTTCTTCAGAAAATAATCACTCTATTAAAGTTTCTCCATATCTCTCTCAATTTCAACAAGACAAACAACAGTTGGTATTAGGAACCAAAGTGTCACTTGTTGAGAACATTCATGTTTTGGGAAAAGAACAGGCTTCACCTAAAAACGTAAAAATGGAAATTGGTAAAACTGAAACTTTTTCTGATGTTCCTGTGAAAACAAATATAGAAGTTTGTTCTACTTACTCCAAAGATTCAGAAAACTACTTTGAAACAGAAGCAGTAGAAATTGCTAAAGCTTTTATGGAAGATGATGAACTGACAGATTCTAAACTGCCAAGTCATGCCACACATTCTCTTTTTACATGTCCCGAAAATGAGGAAATGGTTTTGTCAAATTCAAGAATTGGAAAAAGAAGAGGAGAGCCCCTTATCTTAGTGGGTAAGTGTTCATTTTTACCTTTCGTGTTGCCAATCACTATTTTTAAAGTGTTTATTCAGTAGACTTGGTATGCTAACAATTAAGAGTGTTATAAACTATGTCTTTTCAGCCATTTTTGTGTAGTCAGTTTGGGGGAGTATGGTTTGATATACAGATACACAGATTCAGTATTCGTATACAGATTTGATATCTTGGTATACAGATTCGATATCTCTGAATCTGTATACCAAGAAATCATGTTTTAAGGGTCTCAATATATTTTCAAAAAGATTATTAGTATAATAATTGAGAAATTACTGTTAAAAAGTTTTGAGTTTCTCTAGAAAATTTGAAACTCTTAACAAAACCTGCATAATACTAACTTAACTGTTTTCATATACATAGCAAGTTCAGACTCTGACTTA	AAAGTTAAGGGAGTGTTAGAGGAATTTGATTTAATCAGAACTGAGCATAGTCTTCACTATTCACCTACGTCTAGACAAAATGTATCAAAAATACTTCCTCGTGTTGATAAGAGAAACCCAGAGCACTGTGTAAACTCAGAAATGGAAAAAACCTGCAGTAAAGAATTTAAATTATCAAATAACTTAAATGTTGAAGGTGGTTCTTCAGAAAATAATCACTCTATTAAAGTTTCTCCATATCTCTCTCAATTTCAACAAGACAAACAACAGTTGGTATTAGGAACCAAAGTGTCACTTGTTGAGAACATTCATGTTTTGGGAAAAGAACAGGCTTCACCTAAAAACGTAAAAATGGAAATTGGTAAAACTGAAACTTTTTCTGATGTTCCTGTGAAAACAAATATAGAAGTTTGTTCTACTTACTCCAAAGATTCAGAAAACTACTTTGAAACAGAAGCAGTAGAAATTGCTAAAGCTTTTATGGAAGATGATGAACTGACAGATTCTAAACTGCCAAGTCATGCCACACATTCTCTTTTTACATGTCCCGAAAATGAGGAAATGGTTTTGTCAAATTCAAGAATTGGAAAAAGAAGAGGAGAGCCCCTTATCTTAGTGGGTAAGTGTTCATTTTTACCTTTCGTGTTGCCAATCACTATTTTTAAAGTGTTTATTCAGTAGACTTGGTATGCTAACAATTAAGAGTGTTATAAACTATGTCTTTTCAGCCATTTTTGTGTAGTCAGTTTGGGGGAGTATGGTTTGATATACAGATACACAGATTCAGTATTCGTATACAGATTTGATATCTTGGTATACAGATTCGATATCTCTGAATCTGTATACCAAGAAATCATGTTTTAAGGGTCTCAATATATTTTCAAAAAGATTATTAGTATAATAATTGAGAAATTACTGTTAAAAAGTTTTGAGTTTCTCTAGAAAATTTGAAACTCTTAACAAAACCTGCATAATACTAACTTAACTGTTTTCATATACATAGCAAGTTCAGACTCTGACTTA	-	novel	NA	P-0048391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	102	396	0	ENST00000380152.3:c.6223_6841+404del		p.X2075_splice	ENST00000380152		2075		11/27	0.729889209847683	1	FACETS	0.66	0.6	0.722	0.66	0.6	0.722	SUBCLONAL	1	TRUE	0	0.729889209847683	1		396	269	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222252	2222252	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0048391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	292	746	0	ENST00000326181.6:c.536A>T	p.Glu179Val	p.E179V	ENST00000326181	NM_032271.2	179	gAg/gTg	8/21	0.728685887875797	2	FACETS	0.914	0.863	0.967	0.457	0.431	0.484	CLONAL	1	TRUE	0	0.729889209847683	2		746	875	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041815	14041815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	149	366	0	ENST00000311895.7:c.2362C>T	p.Leu788Phe	p.L788F	ENST00000311895	NM_005236.2	788	Ctc/Ttc	11/11	1	2	FACETS	0.793	0.729	0.859	0.793	0.729	0.859	SUBCLONAL	1	TRUE	1	0.729889209847683	2		366	515	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56872781	56872919	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTAAATGCTATTCCACTGTTACGGATTACACAGAAATTCCTGATACACTCTTACTACCCCCACCCCGTTTTTGTCTTTCAGGTATAGGGCTCAAGGAATAAGCGCAAATAAATTTGTGGACTCCACGTTCTATCTTC	TTTTAAATGCTATTCCACTGTTACGGATTACACAGAAATTCCTGATACACTCTTACTACCCCCACCCCGTTTTTGTCTTTCAGGTATAGGGCTCAAGGAATAAGCGCAAATAAATTTGTGGACTCCACGTTCTATCTTC	-	novel	NA	P-0048391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	55	82	0	ENST00000308159.5:c.2019-79_2078del		p.X673_splice	ENST00000308159	NM_014669.4	673		19/22	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.729889209847683	2		82	129	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918989	50919002	+	frameshift_variant	Frame_Shift_Del	DEL	AGCGGGACCCCGGG	AGCGGGACCCCGGG	-	novel	NA	P-0048391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	218	544	0	ENST00000440232.2:c.2728_2741del	p.Arg910CysfsTer39	p.R910Cfs*39	ENST00000440232	NM_002691.3	909	aAGCGGGACCCCGGG/a	22/27	NA	2	FACETS	0.912	0.853	0.973			1	INDETERMINATE	1	TRUE	NA	0.729889209847683	2		544	655	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956976	2956976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1455337069	NA	P-0048391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	257	520	0	ENST00000396946.4:c.2651G>A	p.Arg884Gln	p.R884Q	ENST00000396946	NM_032415.4	884	cGg/cAg	20/25	0.538266407897703	4	FACETS	0.912	0.852	0.974	0.456	0.426	0.487	CLONAL	1	TRUE	2	0.729889209847683	4		520	1336	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874329	76874329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	228	522	0	ENST00000373344.5:c.5393G>A	p.Arg1798Lys	p.R1798K	ENST00000373344	NM_000489.3	1798	aGa/aAa	21/35	1	2	FACETS	0.902	0.844	0.96	0.902	0.844	0.96	CLONAL	1	TRUE	1	0.729889209847683	2		522	693	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0048392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	105	314	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.260525094716358	3	FACETS	1	0.965	1	0.764	0.69	0.841	CLONAL	2	TRUE	0	0.27001339349891	3		314	385	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922364	178922364	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	108	330	0	ENST00000263967.3:c.1133G>T	p.Cys378Phe	p.C378F	ENST00000263967	NM_006218.2	378	tGt/tTt	6/21	0.260525094716358	3	FACETS	1	0.967	1	0.772	0.699	0.848	CLONAL	2	TRUE	0	0.27001339349891	3		330	392	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738304	145738304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1206178457	NA	P-0048392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	86	886	0	ENST00000428558.2:c.2681G>A	p.Arg894Lys	p.R894K	ENST00000428558	NM_004260.3	894	aGa/aAa	16/22	0.251568580432864	3	FACETS	0.848	0.749	0.954	0.424	0.374	0.477	CLONAL	1	TRUE	1	0.27001339349891	3		886	853	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577600	7577601	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0048392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	161	486	0	ENST00000269305.4:c.680_681del	p.Ser227Ter	p.S227*	ENST00000269305	NM_001126112.2	227	tCT/t	7/11	0.233077175818432	3	FACETS	1	0.983	1			1	CLONAL	2	TRUE	NA	0.27001339349891	3		486	544	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221481	36221481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	63	743	1	ENST00000222270.7:c.5240C>T	p.Ser1747Leu	p.S1747L	ENST00000222270	NM_014727.1	1747	tCg/tTg	25/37	0.251568580432864	3	FACETS	0.718	0.62	0.824	0.359	0.31	0.412	SUBCLONAL	1	TRUE	1	0.27001339349891	3		744	738	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339153	65339153	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1456317552	NA	P-0048392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	52	454	0	ENST00000342505.4:c.383G>A	p.Arg128His	p.R128H	ENST00000342505	NM_002227.2	128	cGt/cAt	5/25	1	2	FACETS	0.837	0.714	0.972	0.837	0.714	0.972	CLONAL	1	TRUE	1	0.27001339349891	2		454	460	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073938	8073938	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	54	406	0	ENST00000377482.5:c.721C>T	p.Gln241Ter	p.Q241*	ENST00000377482	NM_018948.3	241	Cag/Tag	4/4	1	2	FACETS	0.866	0.741	1	0.866	0.741	1	CLONAL	1	TRUE	1	0.27001339349891	2		406	462	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143416	30143416	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1437432300	NA	P-0048392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	156	623	1	ENST00000389048.3:c.110C>T	p.Pro37Leu	p.P37L	ENST00000389048	NM_004304.4	37	cCg/cTg	1/29	0.251568580432864	3	FACETS	0.991	0.91	1	0.991	0.91	1	CLONAL	2	TRUE	1	0.27001339349891	3		624	662	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170009715	170009717	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0048392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	27	281	0	ENST00000295797.4:c.1280_1282del	p.Gly427del	p.G427del	ENST00000295797	NM_002740.5	426	aGAGga/aga	13/18	0.260525094716358	3	FACETS	0.701	0.558	0.863	0.234	0.186	0.288	SUBCLONAL	1	TRUE	0	0.27001339349891	3		281	324	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739747	145739747	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0048392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	106	666	0	ENST00000428558.2:c.1705-1G>C		p.X569_splice	ENST00000428558	NM_004260.3	569			0.251568580432864	3	FACETS	1	0.973	1	0.628	0.563	0.696	CLONAL	1	TRUE	1	0.27001339349891	3		666	710	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0048393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	26	534	0	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	1	2	FACETS	0.487	0.385	0.605	0.487	0.385	0.605	SUBCLONAL	1	TRUE	1	0.21	2		534	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0048394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	183	587	1	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.367866566741819	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	0	0.373149927851618	2		588	488	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903718	114903718	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241370314	NA	P-0048394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	139	451	0	ENST00000543371.1:c.722C>T	p.Pro241Leu	p.P241L	ENST00000543371	NM_001198531.1	241	cCg/cTg	7/14	0.26519180492749	2	FACETS	0.881	0.809	0.954	0.881	0.809	0.954	CLONAL	2	TRUE	0	0.373149927851618	2		451	423	SUCCESS
APC	324	MSKCC	GRCh37	5	112175223	112175224	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGGAACTAGGTCAGCTGAAGATC	novel	NA	P-0048394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	42	208	0	ENST00000257430.4:c.3933_3955dup	p.Pro1319LeufsTer10	p.P1319Lfs*10	ENST00000257430	NM_000038.5	1311	att/atTGGAACTAGGTCAGCTGAAGATCt	16/16	0.367866566741819	2	FACETS	1	0.939	1	0.618	0.523	0.721	CLONAL	1	TRUE	0	0.373149927851618	2		208	182	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816539	32816539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	169	625	0	ENST00000354258.4:c.1636C>T	p.Pro546Ser	p.P546S	ENST00000354258	NM_000593.5	546	Cct/Tct	7/11	0.321539393482482	3	FACETS	0.92	0.851	0.992	0.92	0.851	0.992	CLONAL	2	TRUE	1	0.373149927851618	3		625	584	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0048401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	35	566	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.547	0.45	0.656	0.547	0.45	0.656	SUBCLONAL	1	TRUE	1	0.414045683096536	2		566	309	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778294	3778294	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	281	603	0	ENST00000262367.5:c.6754C>A	p.Gln2252Lys	p.Q2252K	ENST00000262367	NM_004380.2	2252	Cag/Aag	31/31	0.414045683096536	3	FACETS	0.807	0.759	0.856			1	CLONAL	2	TRUE	NA	0.414045683096536	3		603	1015	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221939	1221953	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTCCTCAGGGATGC	TCTCCTCAGGGATGC	-	novel	NA	P-0048401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	163	546	0	ENST00000326873.7:c.863-8_869del		p.X288_splice	ENST00000326873	NM_000455.4	288		7/10	0.203019206733558	2	FACETS	0.931	0.855	1	0.465	0.427	0.505	INDETERMINATE	1	TRUE	0	0.414045683096536	2		546	846	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0048402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	149	494	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.398587551385082	2		494	629	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	126	349	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.931	0.855	1	0.931	0.855	1	CLONAL	1	TRUE	1	0.802844237458024	2		350	337	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0048403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	224	703	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.803	0.751	0.856	0.803	0.751	0.856	CLONAL	1	TRUE	1	0.802844237458024	2		703	695	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828812	72828812	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	209	405	0	ENST00000268489.5:c.7769C>G	p.Ser2590Cys	p.S2590C	ENST00000268489	NM_006885.3	2590	tCt/tGt	9/10	1	2	FACETS	0.955	0.894	1	0.955	0.894	1	CLONAL	1	TRUE	1	0.802844237458024	2		405	545	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349447	73349447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	143	333	0	ENST00000377767.4:c.889C>T	p.Leu297Phe	p.L297F	ENST00000377767	NM_014953.3	297	Ctc/Ttc	6/21	0.802844237458024	3	FACETS	0.859	0.787	0.935	0.43	0.393	0.468	CLONAL	1	TRUE	1	0.802844237458024	3		333	581	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022253	31022271	+	frameshift_variant	Frame_Shift_Del	DEL	AAACCACCCTGGGTGGTTA	AAACCACCCTGGGTGGTTA	-	novel	NA	P-0048403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	105	245	0	ENST00000375687.4:c.1740_1758del	p.Pro581ValfsTer116	p.P581Vfs*116	ENST00000375687	NM_015338.5	580	AAACCACCCTGGGTGGTTAaa/aa	13/13	0.802844237458024	3	FACETS	0.919	0.83	1	0.459	0.415	0.506	CLONAL	1	TRUE	1	0.802844237458024	3		245	399	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556659	41556659	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	315	323	0	ENST00000263253.7:c.3604G>T	p.Glu1202Ter	p.E1202*	ENST00000263253	NM_001429.3	1202	Gag/Tag	20/31	0.74913418606237	3	FACETS	0.89	0.848	0.932	0.89	0.848	0.932	CLONAL	2	TRUE	1	0.802844237458024	3		323	618	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067252	37067252	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	175	303	0	ENST00000231790.2:c.1163C>A	p.Ser388Tyr	p.S388Y	ENST00000231790	NM_000249.3	388	tCc/tAc	12/19	1	2	FACETS	0.877	0.815	0.941	0.877	0.815	0.941	CLONAL	1	TRUE	1	0.802844237458024	2		303	497	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004221	150004221	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	79	143	0	ENST00000253339.5:c.2004G>C	p.Met668Ile	p.M668I	ENST00000253339		668	atG/atC	3/7	1	2	FACETS	0.965	0.866	1	0.965	0.866	1	CLONAL	1	TRUE	1	0.802844237458024	2		143	204	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949083	44949083	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	184	202	0	ENST00000377967.4:c.3644G>T	p.Gly1215Val	p.G1215V	ENST00000377967	NM_021140.2	1215	gGa/gTa	25/29	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.802844237458024	1		202	235	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0048404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	149	240	2				ENST00000310581	NM_198253.2	-/1132			0.644928878562655	3	FACETS	0.985	0.903	1	0.492	0.451	0.535	CLONAL	1	TRUE	1	0.677658048833311	3		242	598	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0048404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	244	347	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.677658048833311	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	1	0.677658048833311	4		347	389	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424958105	NA	P-0048404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	111	346	0	ENST00000334344.6:c.940C>T	p.Arg314Cys	p.R314C	ENST00000334344	NM_152641.2	314	Cgt/Tgt	8/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.677658048833311	2		346	296	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857524	9857524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778230379	NA	P-0048404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	142	421	1	ENST00000330684.3:c.3877G>A	p.Asp1293Asn	p.D1293N	ENST00000330684	NM_001134407.1	1293	Gat/Aat	13/13	1	2	FACETS	0.877	0.805	0.951	0.877	0.805	0.951	CLONAL	1	TRUE	1	0.677658048833311	2		422	478	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686267	117686267	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	131	203	0	ENST00000368508.3:c.3074G>A	p.Gly1025Glu	p.G1025E	ENST00000368508	NM_002944.2	1025	gGa/gAa	20/43	0.644928878562655	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.677658048833311	3		203	234	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0048404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	105	299	0	ENST00000304494.5:c.151-1G>A		p.X51_splice	ENST00000304494	NM_000077.4	51			0.677658048833311	1	FACETS	0.67	0.608	0.733	0.67	0.608	0.733	SUBCLONAL	1	TRUE	0	0.677658048833311	1		299	306	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121566	2121566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750663771	NA	P-0048404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	322	533	0	ENST00000219476.3:c.1895C>T	p.Pro632Leu	p.P632L	ENST00000219476	NM_000548.3	632	cCc/cTc	18/42	1	2	FACETS	0.922	0.872	0.973	0.922	0.872	0.973	CLONAL	1	TRUE	1	0.677658048833311	2		533	1031	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612015	189612016	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0048404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	146	289	0	ENST00000264731.3:c.1767_1768delinsTT	p.Pro590Ser	p.P590S	ENST00000264731	NM_003722.4	589	atCCct/atTTct	14/14	1	2	FACETS	0.862	0.792	0.934	0.862	0.792	0.934	CLONAL	1	TRUE	1	0.677658048833311	2		289	500	SUCCESS
APC	324	MSKCC	GRCh37	5	112174563	112174563	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	113	249	0	ENST00000257430.4:c.3272C>A	p.Pro1091Gln	p.P1091Q	ENST00000257430	NM_000038.5	1091	cCa/cAa	16/16	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.677658048833311	2		249	331	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543672	148543672	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1199671048	NA	P-0048404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	101	216	1	ENST00000320356.2:c.136C>T	p.Arg46Cys	p.R46C	ENST00000320356	NM_004456.4	46	Cgt/Tgt	3/20	0.677658048833311	4	FACETS	0.958	0.859	1	0.319	0.286	0.354	CLONAL	1	TRUE	1	0.677658048833311	4		217	522	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939141	36939141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757569036	NA	P-0048405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	141	672	2	ENST00000361632.4:c.568C>T	p.Arg190Cys	p.R190C	ENST00000361632		190	Cgc/Tgc	5/16	0.260192739989806	3	FACETS	1	0.972	1	1	0.99	1	CLONAL	3	FALSE	1	0.260192739989806	3		674	366	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949177	44949177	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0048405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	67	127	0	ENST00000377967.4:c.3736+2T>A		p.X1246_splice	ENST00000377967	NM_021140.2	1246			0.260192739989806	2	FACETS	0.923	0.85	0.991			1	CLONAL	6	FALSE	NA	0.260192739989806	2		127	93	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	19	349	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.954	0.723	1	0.954	0.723	1	CLONAL	1	TRUE	1	0.12	2		350	332	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0048406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	23	703	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.587	0.456	0.74	0.587	0.456	0.74	SUBCLONAL	1	TRUE	1	0.12	2		703	653	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949754	151949754	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	45	242	0	ENST00000262189.6:c.1346G>A	p.Trp449Ter	p.W449*	ENST00000262189	NM_170606.2	449	tGg/tAg	10/59	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.12	2		242	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577569	7577569	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519981	NA	P-0048407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	324	527	3	ENST00000269305.4:c.712T>A	p.Cys238Ser	p.C238S	ENST00000269305	NM_001126112.2	238	Tgt/Agt	7/11	0.523746857856103	3	FACETS	0.897	0.858	0.936	0.897	0.858	0.936	CLONAL	3	TRUE	0	0.537003460786385	3		530	569	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122300	2122300	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	279	702	1	ENST00000219476.3:c.2156A>G	p.Tyr719Cys	p.Y719C	ENST00000219476	NM_000548.3	719	tAt/tGt	20/42	0.528585662210714	2	FACETS	0.992	0.943	1	0.992	0.943	1	CLONAL	2	TRUE	0	0.537003460786385	2		703	524	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989661	15989661	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	90	359	0	ENST00000268712.3:c.3112C>G	p.Pro1038Ala	p.P1038A	ENST00000268712	NM_006311.3	1038	Ccg/Gcg	23/46	0.523746857856103	3	FACETS	0.926	0.826	1	0.309	0.275	0.345	CLONAL	1	TRUE	0	0.537003460786385	3		359	459	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39214679	39214679	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	190	478	1	ENST00000402219.2:c.3445G>T	p.Val1149Phe	p.V1149F	ENST00000402219	NM_005633.3	1149	Gtc/Ttc	22/23	0.536109264109651	4	FACETS	0.846	0.785	0.908	0.846	0.785	0.908	CLONAL	2	TRUE	2	0.537003460786385	4		479	643	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165845	47165845	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	181	440	0	ENST00000409792.3:c.281del	p.Asn94MetfsTer17	p.N94Mfs*17	ENST00000409792	NM_014159.6	94	aAt/at	3/21	0.496290189150569	2	FACETS	0.955	0.896	1	0.955	0.896	1	CLONAL	2	TRUE	0	0.537003460786385	2		440	353	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410017	139410017	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	542	919	0	ENST00000277541.6:c.1821C>A	p.Cys607Ter	p.C607*	ENST00000277541	NM_017617.3	607	tgC/tgA	11/34	0.523746857856103	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.537003460786385	3		919	824	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0048408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	352	330	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.881316695294656	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.881316695294656	1		330	432	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186895	142186895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866304619	NA	P-0048408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	33	131	0	ENST00000350721.4:c.6568C>T	p.Arg2190Cys	p.R2190C	ENST00000350721	NM_001184.3	2190	Cgt/Tgt	39/47	0.839959333367654	3	FACETS	0.21	0.17	0.255	0.105	0.085	0.128	SUBCLONAL	1	TRUE	1	0.881316695294656	3		131	514	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692816	89692817	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554898084	NA	P-0048408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	37	120	0	ENST00000371953.3:c.301dup	p.Ile101AsnfsTer6	p.I101Nfs*6	ENST00000371953	NM_000314.4	100	-/A	5/9	0.444542831676577	1	FACETS	0.206	0.171	0.245	0.206	0.171	0.245	INDETERMINATE	1	TRUE	0	0.881316695294656	1		120	228	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127911953	127911953	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0048408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	349	138	0	ENST00000373547.4:c.917G>C	p.Ter306SerextTer7	p.*306Sext*7	ENST00000373547	NM_002721.4	306	tGa/tCa	7/7	0.881316695294656	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.881316695294656	2		138	384	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321328	65321328	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	349	251	0	ENST00000342505.4:c.1512G>T	p.Lys504Asn	p.K504N	ENST00000342505	NM_002227.2	504	aaG/aaT	11/25	1	2	FACETS	0.912	0.868	0.958	0.912	0.868	0.958	CLONAL	1	TRUE	1	0.881316695294656	2		251	868	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429286	78429286	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	186	201	0	ENST00000370768.2:c.1156G>T	p.Gly386Trp	p.G386W	ENST00000370768	NM_003902.3	386	Ggg/Tgg	13/20	1	2	FACETS	0.823	0.766	0.881	0.823	0.766	0.881	CLONAL	1	TRUE	1	0.881316695294656	2		201	513	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989061	41989067	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAATT	GAAAATT	-	novel	NA	P-0048408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	37	255	0	ENST00000219905.7:c.1857_1863del	p.Lys619AsnfsTer16	p.K619Nfs*16	ENST00000219905	NM_001164273.1	618	cGAAAATTg/cg	3/24	0.881316695294656	1	FACETS	0.167	0.138	0.199	0.167	0.138	0.199	SUBCLONAL	1	TRUE	0	0.881316695294656	1		255	282	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379775	17379775	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	552	357	0	ENST00000359435.4:c.160G>T	p.Glu54Ter	p.E54*	ENST00000359435	NM_001033549.1	54	Gag/Tag	2/9	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.881316695294656	2		357	1157	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314645	30314645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	3284	277	0	ENST00000262643.3:c.1194G>T	p.Gln398His	p.Q398H	ENST00000262643	NM_001238.2	398	caG/caT	12/12	0.881316695294656	11	FACETS	1	0.993	1			1	CLONAL	10	TRUE	NA	0.881316695294656	11		277	3698	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561520	9561520	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	194	245	1	ENST00000353224.5:c.262G>T	p.Asp88Tyr	p.D88Y	ENST00000353224	NM_177990.2	88	Gat/Tat	4/10	1	2	FACETS	0.778	0.725	0.832	0.778	0.725	0.832	SUBCLONAL	1	TRUE	1	0.881316695294656	2		246	566	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730767	40730767	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	262	250	0	ENST00000373198.4:c.3768G>T	p.Met1256Ile	p.M1256I	ENST00000373198	NM_133170.3	1256	atG/atT	27/32	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.881316695294656	2		250	577	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374814	149374818	+	frameshift_variant	Frame_Shift_Del	DEL	GGGAC	GGGAC	-	novel	NA	P-0048408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	289	197	0	ENST00000360632.3:c.276_280del	p.Ser93AlafsTer11	p.S93Afs*11	ENST00000360632	NM_015472.4	92	gcGTCCCtg/gctg	2/7	0.839959333367654	3	FACETS	1	0.96	1	0.511	0.482	0.541	CLONAL	1	TRUE	1	0.881316695294656	3		197	924	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797714	32797714	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0048408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	315	261	0	ENST00000374899.4:c.1788A>G	p.Ile596Met	p.I596M	ENST00000374899	NM_018833.2	596	atA/atG	10/12	1	2	FACETS	0.997	0.947	1	0.997	0.947	1	CLONAL	1	TRUE	1	0.881316695294656	2		261	717	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522604	106522604	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	171	237	0	ENST00000359195.3:c.2581G>C	p.Asp861His	p.D861H	ENST00000359195	NM_002649.2	861	Gat/Cat	7/11	1	2	FACETS	0.8	0.742	0.859	0.8	0.742	0.859	SUBCLONAL	1	TRUE	1	0.881316695294656	2		237	485	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27220135	27220135	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	346	227	0	ENST00000380036.4:c.3192T>A	p.Asp1064Glu	p.D1064E	ENST00000380036	NM_000459.3	1064	gaT/gaA	21/23	0.881316695294656	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.881316695294656	1		227	431	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396302	139396302	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	984	354	0	ENST00000277541.6:c.5536C>T	p.Gln1846Ter	p.Q1846*	ENST00000277541	NM_017617.3	1846	Cag/Tag	30/34	0.881316695294656	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.881316695294656	2		354	1067	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412725	63412725	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	243	248	0	ENST00000330258.3:c.442G>C	p.Ala148Pro	p.A148P	ENST00000330258	NM_152424.3	148	Gct/Cct	2/2	0.826796740663189	3	FACETS	1	0.962	1	0.518	0.485	0.551	CLONAL	1	TRUE	1	0.881316695294656	3		248	767	SUCCESS
AR	367	MSKCC	GRCh37	X	66766141	66766141	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200067740	NA	P-0048408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	313	242	0	ENST00000374690.3:c.1153G>T	p.Ala385Ser	p.A385S	ENST00000374690	NM_000044.3	385	Gct/Tct	1/8	0.826796740663189	3	FACETS	0.988	0.933	1	0.494	0.466	0.522	CLONAL	1	TRUE	1	0.881316695294656	3		242	1036	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0048410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	130	432	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.779	0.709	0.851	0.779	0.709	0.851	SUBCLONAL	1	TRUE	1	0.597230533802906	2		432	559	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0048410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	126	383	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.597230533802906	2		383	382	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380277	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913238	NA	P-0048410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	190	305	0	ENST00000311936.3:c.181C>G	p.Gln61Glu	p.Q61E	ENST00000311936	NM_004985.3	61	Caa/Gaa	3/5	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.597230533802906	2		305	620	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717715	89717715	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs1057519368	NA	P-0048410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	23	295	0	ENST00000371953.3:c.740T>G	p.Leu247Ter	p.L247*	ENST00000371953	NM_000314.4	247	tTa/tGa	7/9	0.597230533802906	1	FACETS	0.133	0.103	0.168	0.133	0.103	0.168	SUBCLONAL	1	TRUE	0	0.597230533802906	1		295	406	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846206	128846206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761081288	NA	P-0048410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	155	440	0	ENST00000249373.3:c.1136C>T	p.Ala379Val	p.A379V	ENST00000249373	NM_005631.4	379	gCg/gTg	5/12	1	2	FACETS	0.733	0.673	0.796	0.733	0.673	0.796	SUBCLONAL	1	TRUE	1	0.597230533802906	2		440	708	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874237	155874237	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs541801566	NA	P-0048410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	182	388	0	ENST00000368323.3:c.294C>G	p.Ile98Met	p.I98M	ENST00000368323	NM_006912.5	98	atC/atG	5/6	1	2	FACETS	0.963	0.892	1	0.963	0.892	1	CLONAL	1	TRUE	1	0.597230533802906	2		388	633	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0048431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	347	512	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.356541183135035	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	0	0.356541183135035	3		512	701	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0048431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	147	249	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	NA	2	FACETS	0.848	0.787	0.91			1	INDETERMINATE	3	TRUE	NA	0.356541183135035	2		249	324	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575195	48575195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	112	218	0	ENST00000342988.3:c.389C>T	p.Pro130Leu	p.P130L	ENST00000342988	NM_005359.5	130	cCa/cTa	3/12	0.356541183135035	3	FACETS	0.979	0.898	1	0.979	0.898	1	CLONAL	3	TRUE	0	0.356541183135035	3		218	252	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120675	115120675	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	198	685	0	ENST00000257566.3:c.331G>T	p.Glu111Ter	p.E111*	ENST00000257566	NM_016569.3	111	Gaa/Taa	1/8	0.267122399486638	4	FACETS	0.751	0.695	0.809	0.501	0.463	0.539	SUBCLONAL	2	TRUE	1	0.356541183135035	4		685	1003	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266002	41266229	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTC	GTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTC	-	novel	NA	P-0048431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	31	162	0	ENST00000349496.5:c.14-15_226del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.356541183135035	4	FACETS	1	0.832	1	0.504	0.416	0.599	CLONAL	2	TRUE	0	0.356541183135035	4		162	117	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180258	27180258	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	230	455	0	ENST00000380036.4:c.922G>C	p.Gly308Arg	p.G308R	ENST00000380036	NM_000459.3	308	Ggg/Cgg	7/23	0.356541183135035	5	FACETS	0.884	0.827	0.942	0.884	0.827	0.942	CLONAL	3	TRUE	2	0.356541183135035	5		455	747	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814535	43814535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1400122324	NA	P-0048432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	156	519	2	ENST00000372470.3:c.1330G>A	p.Ala444Thr	p.A444T	ENST00000372470	NM_005373.2	444	Gcc/Acc	9/12	1	2	FACETS	0.931	0.855	1	0.931	0.855	1	CLONAL	1	TRUE	1	0.469329335284022	2		521	714	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39763605	39763605	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	88	307	0	ENST00000288319.7:c.847del	p.Thr283LeufsTer8	p.T283Lfs*8	ENST00000288319	NM_182918.3	283	Act/ct	8/10	1	2	FACETS	0.997	0.89	1	0.997	0.89	1	CLONAL	1	TRUE	1	0.469329335284022	2		307	376	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188286	10188286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs773556807	NA	P-0048432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	145	538	0	ENST00000256474.2:c.429C>G	p.Asp143Glu	p.D143E	ENST00000256474	NM_000551.3	143	gaC/gaG	2/3	0.431100811067954	1	FACETS	0.83	0.76	0.901	0.83	0.76	0.901	CLONAL	1	TRUE	0	0.469329335284022	1		538	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0048435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	383	491	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.675408605353635	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.675408605353635	2		491	557	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0048435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	95	267	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.675408605353635	2		267	273	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0048435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	54	147	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.874	0.759	0.995	0.874	0.759	0.995	CLONAL	1	TRUE	1	0.675408605353635	2		147	183	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43699721	43699721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	305	478	0	ENST00000382044.4:c.5794C>T	p.Pro1932Ser	p.P1932S	ENST00000382044	NM_001141980.1	1932	Cca/Tca	28/28	0.675408605353635	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.675408605353635	3		478	574	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554416	63554416	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0048435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	211	629	0	ENST00000307078.5:c.323T>C	p.Leu108Ser	p.L108S	ENST00000307078	NM_004655.3	108	tTa/tCa	2/11	0.675408605353635	3	FACETS	0.932	0.866	0.999	0.466	0.433	0.5	CLONAL	1	TRUE	1	0.675408605353635	3		629	897	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561124	9561124	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	221	355	0	ENST00000353224.5:c.658C>A	p.Gln220Lys	p.Q220K	ENST00000353224	NM_177990.2	220	Cag/Aag	4/10	0.675408605353635	6	FACETS	1	0.947	1	0.508	0.474	0.543	CLONAL	2	TRUE	2	0.675408605353635	6		355	757	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944386	40944386	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	153	445	0	ENST00000373198.4:c.2116C>A	p.Gln706Lys	p.Q706K	ENST00000373198	NM_133170.3	706	Cag/Aag	12/32	0.675408605353635	6	FACETS	1	0.964	1	0.275	0.251	0.3	CLONAL	1	TRUE	2	0.675408605353635	6		445	969	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969122	93969122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0048435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	112	347	0	ENST00000369303.4:c.1874C>T	p.Ala625Val	p.A625V	ENST00000369303	NM_004440.3	625	gCc/gTc	10/17	0.675408605353635	2	FACETS	1	0.948	1	0.528	0.481	0.576	CLONAL	1	TRUE	0	0.675408605353635	2		347	314	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285494	38285494	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778166317	NA	P-0048435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	213	627	1	ENST00000425967.3:c.659G>A	p.Arg220His	p.R220H	ENST00000425967	NM_001174067.1	220	cGc/cAc	6/19	0.675408605353635	3	FACETS	0.96	0.893	1	0.48	0.446	0.515	CLONAL	1	TRUE	1	0.675408605353635	3		628	879	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579406	7579406	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0048436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	488	792	0	ENST00000269305.4:c.281C>A	p.Ser94Ter	p.S94*	ENST00000269305	NM_001126112.2	94	tCa/tAa	4/11	0.646502958897307	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.646502958897307	2		792	734	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230872	66230873	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0048436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	50	269	0	ENST00000273854.3:c.2098dup	p.Arg700LysfsTer11	p.R700Kfs*11	ENST00000273854	NM_004439.5	700	aga/aAga	12/18	0.606643082033508	1	FACETS	0.406	0.347	0.469	0.406	0.347	0.469	SUBCLONAL	1	TRUE	0	0.646502958897307	1		269	258	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933189	100933189	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0048436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	18	312	0	ENST00000325455.5:c.2201A>C	p.Lys734Thr	p.K734T	ENST00000325455	NM_001202474.3	734	aAa/aCa	4/8	0.314115978263685	1	FACETS	0.127	0.095	0.165	0.127	0.095	0.165	INDETERMINATE	1	TRUE	0	0.646502958897307	1		312	296	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041653	42041653	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	142	486	0	ENST00000219905.7:c.5848C>G	p.Pro1950Ala	p.P1950A	ENST00000219905	NM_001164273.1	1950	Cca/Gca	17/24	NA	2	FACETS	0.771	0.705	0.838			1	INDETERMINATE	1	TRUE	NA	0.646502958897307	2		486	570	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0048439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	45	349	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.789	0.663	0.928	0.789	0.663	0.928	CLONAL	1	TRUE	1	0.230979167109801	2		350	494	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0048439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	148	277	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.188650645371647	4	FACETS	0.896	0.822	0.973			1	CLONAL	3	TRUE	NA	0.230979167109801	4		277	587	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597869	43597869	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0048439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	105	740	0	ENST00000355710.3:c.417G>A	p.Trp139Ter	p.W139*	ENST00000355710	NM_020975.4	139	tgG/tgA	3/20	1	2	FACETS	0.817	0.73	0.91	0.817	0.73	0.91	CLONAL	1	TRUE	1	0.230979167109801	2		740	1113	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742519	17742519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	108	600	0	ENST00000250003.3:c.701C>T	p.Ala234Val	p.A234V	ENST00000250003	NM_002478.4	234	gCg/gTg	2/3	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.230979167109801	2		600	932	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942027	81942027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1231256206	NA	P-0048439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	55	340	0	ENST00000359376.3:c.1564C>T	p.Pro522Ser	p.P522S	ENST00000359376	NM_002661.3	522	Ccc/Tcc	17/33	1	2	FACETS	0.914	0.782	1	0.914	0.782	1	CLONAL	1	TRUE	1	0.230979167109801	2		340	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0048439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	253	743	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.222038078586101	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.230979167109801	2		744	1070	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593406	48593406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912580	NA	P-0048439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	38	217	0	ENST00000342988.3:c.1157G>A	p.Gly386Asp	p.G386D	ENST00000342988	NM_005359.5	386	gGt/gAt	10/12	0.159414353279458	2	FACETS	0.873	0.723	1	0.436	0.361	0.52	CLONAL	1	TRUE	0	0.230979167109801	2		217	377	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218659	36218659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555731093	NA	P-0048439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	121	775	1	ENST00000222270.7:c.4363C>T	p.Arg1455Cys	p.R1455C	ENST00000222270	NM_014727.1	1455	Cgc/Tgc	17/37	1	2	FACETS	0.879	0.792	0.971	0.879	0.792	0.971	CLONAL	1	TRUE	1	0.230979167109801	2		776	1192	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374245	138374245	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	62	371	0	ENST00000289153.2:c.3199G>C	p.Asp1067His	p.D1067H	ENST00000289153	NM_006219.2	1067	Gac/Cac	22/22	1	2	FACETS	0.898	0.775	1	0.898	0.775	1	CLONAL	1	TRUE	1	0.230979167109801	2		371	598	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056403	180056403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149373386	NA	P-0048439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	97	661	0	ENST00000261937.6:c.841G>A	p.Glu281Lys	p.E281K	ENST00000261937	NM_182925.4	281	Gag/Aag	7/30	1	2	FACETS	0.892	0.794	0.996	0.892	0.794	0.996	CLONAL	1	TRUE	1	0.230979167109801	2		661	942	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902289	151902289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1345303559	NA	P-0048439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	22	64	1	ENST00000262189.6:c.3863G>A	p.Arg1288Gln	p.R1288Q	ENST00000262189	NM_170606.2	1288	cGg/cAg	25/59	1	2	FACETS	0.774	0.608	0.961	1	0.928	1	CLONAL	2	TRUE	1	0.230979167109801	2		65	123	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157250	106157250	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0048470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	26	299	0	ENST00000380013.4:c.2151C>G	p.His717Gln	p.H717Q	ENST00000380013	NM_001127208.2	717	caC/caG	3/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		299	355	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469564	25469564	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs796065342	NA	P-0048470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	423	832	2	ENST00000264709.3:c.1204C>T	p.Gln402Ter	p.Q402*	ENST00000264709	NM_175629.2	402	Cag/Tag	10/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		834	1088	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562982	21562982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0048470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	268	958	0	ENST00000382592.4:c.937G>A	p.Val313Met	p.V313M	ENST00000382592	NM_014572.2	313	Gtg/Atg	4/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		958	528	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25536802	25536802	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0048470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	438	957	0	ENST00000264709.3:c.52G>T	p.Glu18Ter	p.E18*	ENST00000264709	NM_175629.2	18	Gag/Tag	2/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		957	1295	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090415	37090415	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0048470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	28	421	1	ENST00000231790.2:c.2010G>T	p.Lys670Asn	p.K670N	ENST00000231790	NM_000249.3	670	aaG/aaT	18/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		422	379	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361239	66361239	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0048470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	59	236	0	ENST00000273854.3:c.933A>T	p.Lys311Asn	p.K311N	ENST00000273854	NM_004439.5	311	aaA/aaT	4/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		236	336	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440844	52440844	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0048472-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	58	636	0	ENST00000460680.1:c.659+1G>T		p.X220_splice	ENST00000460680	NM_004656.3	220			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		636	770	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549376	5549376	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0048473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	162	571	0	ENST00000397747.3:c.403G>C	p.Glu135Gln	p.E135Q	ENST00000397747	NM_025239.3	135	Gaa/Caa	4/7	0.667111792391622	3	FACETS	1	0.982	1	0.61	0.563	0.658	CLONAL	1	TRUE	1	0.662371747918037	3		571	534	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0048474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	234	703	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.307688701115804	3	FACETS	0.928	0.867	0.991			1	CLONAL	2	TRUE	NA	0.325043858142374	3		703	902	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0048474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	148	610	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.325043858142374	1	FACETS	0.969	0.886	1	0.969	0.886	1	CLONAL	1	TRUE	0	0.325043858142374	1		610	787	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0048474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	63	282	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.325043858142374	2		282	381	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114905820	114905821	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0048474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	115	540	0	ENST00000543371.1:c.843dup	p.Thr282HisfsTer46	p.T282Hfs*46	ENST00000543371	NM_001198531.1	280	tac/taCc	8/14	0.325043858142374	1	FACETS	0.945	0.853	1	0.945	0.853	1	CLONAL	1	TRUE	0	0.325043858142374	1		540	627	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729864	41729864	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0048474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	74	496	0	ENST00000242208.4:c.665del	p.Pro222LeufsTer137	p.P222Lfs*137	ENST00000242208	NM_002192.2	222	cCt/ct	3/3	1	2	FACETS	0.9	0.79	1	0.9	0.79	1	CLONAL	1	TRUE	1	0.325043858142374	2		496	506	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913172	44913173	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0048474-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	72	520	0	ENST00000377967.4:c.848_849del	p.Ser283TrpfsTer29	p.S283Wfs*29	ENST00000377967	NM_021140.2	283	TCt/t	10/29	0.325043858142374	1	FACETS	0.873	0.766	0.988	0.873	0.766	0.988	CLONAL	1	TRUE	0	0.325043858142374	1		520	425	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0048476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	110	290	1	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	0.749905825606563	1	FACETS	0.684	0.625	0.744	0.684	0.625	0.744	SUBCLONAL	1	TRUE	0	0.749905825606563	1		291	268	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514495	NA	P-0048476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	236	699	1	ENST00000269305.4:c.542G>A	p.Arg181His	p.R181H	ENST00000269305	NM_001126112.2	181	cGc/cAc	5/11	0.749905825606563	1	FACETS	0.752	0.709	0.796	0.752	0.709	0.796	SUBCLONAL	1	TRUE	0	0.749905825606563	1		700	523	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097200	11097205	+	inframe_deletion	In_Frame_Del	DEL	GGCCCT	GGCCCT	-	rs372601826	NA	P-0048476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	156	795	0	ENST00000358026.2:c.708_713del	p.Gly243_Pro244del	p.G243_P244del	ENST00000358026	NM_001128849.1	231	GGCCCT/-	4/36	0.381170026237296	1	FACETS	0.308	0.282	0.335	0.308	0.282	0.335	INDETERMINATE	1	TRUE	0	0.749905825606563	1		795	845	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922973	44922973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0048476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	241	259	0	ENST00000377967.4:c.1834C>T	p.Arg612Ter	p.R612*	ENST00000377967	NM_021140.2	612	Cga/Tga	16/29	0.749905825606563	1	FACETS	0.818	0.774	0.863	0.818	0.774	0.863	CLONAL	1	TRUE	0	0.749905825606563	1		259	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138729528	NA	P-0048476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	314	736	0	ENST00000269305.4:c.523C>T	p.Arg175Cys	p.R175C	ENST00000269305	NM_001126112.2	175	Cgc/Tgc	5/11	0.749905825606563	1	FACETS	0.918	0.877	0.96	0.918	0.877	0.96	CLONAL	1	TRUE	0	0.749905825606563	1		736	570	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890150	76890150	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0048476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	211	388	1	ENST00000373344.5:c.4744del	p.Thr1582GlnfsTer24	p.T1582Qfs*24	ENST00000373344	NM_000489.3	1582	Aca/ca	17/35	0.749905825606563	1	FACETS	0.884	0.834	0.933	0.884	0.834	0.933	CLONAL	1	TRUE	0	0.749905825606563	1		389	398	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4388007	4388007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775067994	NA	P-0048476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	194	437	0	ENST00000261254.3:c.493C>T	p.Arg165Cys	p.R165C	ENST00000261254	NM_001759.3	165	Cgc/Tgc	3/5	1	2	FACETS	0.871	0.811	0.933	0.871	0.811	0.933	CLONAL	1	TRUE	1	0.749905825606563	2		437	594	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182071	11182073	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1196560364	NA	P-0048476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	30	560	0	ENST00000361445.4:c.6773_6775del	p.Lys2258del	p.K2258del	ENST00000361445	NM_004958.3	2258	aAGAtc/atc	48/58	0.749905825606563	1	FACETS	0.109	0.088	0.134	0.109	0.088	0.134	SUBCLONAL	1	TRUE	0	0.749905825606563	1		560	457	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371948	55371948	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0048476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	257	477	0	ENST00000297316.4:c.638C>A	p.Pro213Gln	p.P213Q	ENST00000297316	NM_022454.3	213	cCg/cAg	2/2	1	2	FACETS	0.953	0.897	1	0.953	0.897	1	CLONAL	1	TRUE	1	0.749905825606563	2		477	719	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383350	42383350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144006380	NA	P-0048476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	162	522	0	ENST00000221972.3:c.370C>T	p.Arg124Cys	p.R124C	ENST00000221972	NM_021601.3	124	Cgc/Tgc	2/5	0.381170026237296	1	FACETS	0.454	0.418	0.491	0.454	0.418	0.491	INDETERMINATE	1	TRUE	0	0.749905825606563	1		522	595	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555752	21555752	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200852337	NA	P-0048476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	266	565	0	ENST00000382592.4:c.2518G>A	p.Asp840Asn	p.D840N	ENST00000382592	NM_014572.2	840	Gac/Aac	6/8	0.749905825606563	1	FACETS	0.84	0.797	0.883	0.84	0.797	0.883	CLONAL	1	TRUE	0	0.749905825606563	1		565	528	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670882	134670882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200018500	NA	P-0048476-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	117	315	0	ENST00000398015.3:c.793G>A	p.Val265Met	p.V265M	ENST00000398015	NM_004441.4	265	Gtg/Atg	3/16	0.749905825606563	1	FACETS	0.826	0.762	0.891	0.826	0.762	0.891	CLONAL	1	TRUE	0	0.749905825606563	1		315	236	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0001694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	32	353	0	ENST00000269305.4:c.96+1G>A		p.X32_splice	ENST00000269305	NM_001126112.2	32			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		353	607	SUCCESS
AR	367	MSKCC	GRCh37	X	66766357	66766398	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC	-	rs746853821	NA	P-0007324-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	209	176	0	ENST00000374690.3:c.1379_1420del	p.Gly460_Gly473del	p.G460_G473del	ENST00000374690	NM_000044.3	457	GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC/-	1/8	1	2	FACETS	0.926	0.873	0.979	1	0.996	1	CLONAL	4	TRUE	1	0.281366284045862	2		176	401	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046281	180046281	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007324-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	286	688	0	ENST00000261937.6:c.2733C>A	p.Asn911Lys	p.N911K	ENST00000261937	NM_182925.4	911	aaC/aaA	19/30	0.281366284045862	1	FACETS	1	0.971	1	1	0.996	1	CLONAL	2	TRUE	0	0.281366284045862	1		688	836	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30133009	30133009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760058972	NA	P-0007324-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	42	524	1	ENST00000331968.5:c.592G>A	p.Gly198Ser	p.G198S	ENST00000331968	NM_002742.2	198	Ggt/Agt	4/18	1	2	FACETS	0.42	0.349	0.498	0.42	0.349	0.498	SUBCLONAL	1	TRUE	1	0.281366284045862	2		525	711	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578376	7578379	+	frameshift_variant	Frame_Shift_Del	DEL	CTAT	CTAT	-	novel	NA	P-0007343-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	394	559	0	ENST00000269305.4:c.551_554del	p.Asp184AlafsTer62	p.D184Afs*62	ENST00000269305	NM_001126112.2	184	gATAGc/gc	5/11	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.776097017404848	2		559	499	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303679	65303679	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0007343-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	329	515	0	ENST00000342505.4:c.3076A>T	p.Lys1026Ter	p.K1026*	ENST00000342505	NM_002227.2	1026	Aaa/Taa	22/25	NA	2	FACETS	0.968	0.935	0.999			1	INDETERMINATE	2	TRUE	NA	0.776097017404848	2		515	438	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720857	89721263	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTTTCTCCAAATTTTAAGGTCAGTTAAATTAAACATTTTGTGGGGGTTGTTGACTTGTATGTATGTGATGTGTGTTTAATTCTAGGAGTACAGCTGATGAAGAACTTGCTTGACAAGTTTTTAACTTATGTATTATTTCGAAGCAGTGTTTACGTAGCAGTAACATGAAAGTTTCTAATAAAATACCCAATGTACACAGCGTCAAAAAAGCTGCATTTTTCCTTTTCCTAATTCTTCGTTGTTTGCTGAAATCTGGGGCAAAGGTGCGGGAGGGGGCTAAATGACTGGGATATGAAGTAGGAATGGGAGAGGAAAGAAATAGATGGGAACTCAGTCATTTGGGAATGATTCATATGGAATGTTTTTACTGCTTCCACTCCTGTCTGCCTTCCAATTTATTCTCAAT	CTTTTCTCCAAATTTTAAGGTCAGTTAAATTAAACATTTTGTGGGGGTTGTTGACTTGTATGTATGTGATGTGTGTTTAATTCTAGGAGTACAGCTGATGAAGAACTTGCTTGACAAGTTTTTAACTTATGTATTATTTCGAAGCAGTGTTTACGTAGCAGTAACATGAAAGTTTCTAATAAAATACCCAATGTACACAGCGTCAAAAAAGCTGCATTTTTCCTTTTCCTAATTCTTCGTTGTTTGCTGAAATCTGGGGCAAAGGTGCGGGAGGGGGCTAAATGACTGGGATATGAAGTAGGAATGGGAGAGGAAAGAAATAGATGGGAACTCAGTCATTTGGGAATGATTCATATGGAATGTTTTTACTGCTTCCACTCCTGTCTGCCTTCCAATTTATTCTCAAT	-	novel	NA	P-0007343-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	62	296	0	ENST00000371953.3:c.1009_1026+389del		p.X337_splice	ENST00000371953	NM_000314.4	337		8/9	0.75964017693098	2	FACETS	0.783	0.708	0.856	0.783	0.708	0.856	SUBCLONAL	2	TRUE	0	0.776097017404848	2		296	102	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951062	48951091	+	inframe_deletion	In_Frame_Del	DEL	AGTGAATCCAAAAGAAAGTATACTGAAAAG	AGTGAATCCAAAAGAAAGTATACTGAAAAG	-	novel	NA	P-0007343-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	73	181	0	ENST00000267163.4:c.1230_1259del	p.Asn410_Val419del	p.N410_V419del	ENST00000267163	NM_000321.2	408	acAGTGAATCCAAAAGAAAGTATACTGAAAAGa/aca	13/27	0.747536872352445	2	FACETS	0.863	0.792	0.93	0.863	0.792	0.93	CLONAL	2	TRUE	0	0.776097017404848	2		181	109	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430729	47430729	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007343-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	384	364	0	ENST00000377045.4:c.1694C>G	p.Ala565Gly	p.A565G	ENST00000377045	NM_001654.4	565	gCc/gGc	16/16	0.776097017404848	2	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.776097017404848	2		364	458	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0009261-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	1455	530	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.563665432633886	10	FACETS	1	0.996	1			1	CLONAL	8	TRUE	NA	0.563665432633886	10		530	2020	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953228	81953228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369760877	NA	P-0009261-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	89	371	0	ENST00000359376.3:c.2194C>T	p.Arg732Cys	p.R732C	ENST00000359376	NM_002661.3	732	Cgc/Tgc	20/33	1	2	FACETS	0.902	0.807	1	0.902	0.807	1	CLONAL	1	TRUE	1	0.563665432633886	2		371	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009261-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	336	951	0	ENST00000269305.4:c.380C>A	p.Ser127Tyr	p.S127Y	ENST00000269305	NM_001126112.2	127	tCc/tAc	5/11	0.476506497858011	2	FACETS	0.854	0.814	0.894	0.854	0.814	0.894	CLONAL	2	TRUE	0	0.563665432633886	2		951	698	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009261-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	1646	768	0	ENST00000269571.5:c.829G>T	p.Asp277Tyr	p.D277Y	ENST00000269571		277	Gac/Tac	7/27	0.563665432633886	10	FACETS	1	0.993	1			1	CLONAL	8	TRUE	NA	0.563665432633886	10		768	2332	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224496	224496	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009261-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	34	193	0	ENST00000264932.6:c.172G>C	p.Val58Leu	p.V58L	ENST00000264932	NM_004168.2	58	Gtg/Ctg	3/15	0.533539842588911	3	FACETS	0.733	0.604	0.876	0.366	0.302	0.438	SUBCLONAL	1	TRUE	1	0.563665432633886	3		193	211	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864368	162864368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009261-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	274	456	0	ENST00000366898.1:c.145G>A	p.Glu49Lys	p.E49K	ENST00000366898	NM_004562.2	49	Gag/Aag	2/12	0.563665432633886	4	FACETS	0.915	0.868	0.961	0.915	0.868	0.961	CLONAL	3	TRUE	1	0.563665432633886	4		456	554	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534564	140534564	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009261-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	122	377	0	ENST00000288602.6:c.349A>T	p.Met117Leu	p.M117L	ENST00000288602	NM_004333.4	117	Atg/Ttg	3/18	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.563665432633886	2		377	413	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967262	38967262	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0009261-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	37	200	0	ENST00000357387.3:c.1218+1G>T		p.X406_splice	ENST00000357387	NM_152756.3	406			0.533539842588911	3	FACETS	0.681	0.565	0.809	0.341	0.282	0.405	SUBCLONAL	1	TRUE	1	0.563665432633886	3		200	247	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14015942	14015942	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009261-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	40	248	0	ENST00000311895.7:c.262G>C	p.Val88Leu	p.V88L	ENST00000311895	NM_005236.2	88	Gta/Cta	2/11	0.563665432633886	6	FACETS	0.565	0.469	0.673			1	SUBCLONAL	1	TRUE	NA	0.563665432633886	6		248	534	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86627245	86627245	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009261-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	62	289	0	ENST00000274376.6:c.620G>C	p.Arg207Thr	p.R207T	ENST00000274376	NM_002890.2	207	aGa/aCa	2/25	0.533539842588911	3	FACETS	0.81	0.704	0.924	0.405	0.352	0.462	CLONAL	1	TRUE	1	0.563665432633886	3		289	348	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011095-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	14	516	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.452	0.327	0.604	0.452	0.327	0.604	SUBCLONAL	1	TRUE	1	0.261152582010213	2		516	237	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0011095-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	55	433	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	0.9	0.771	1	0.9	0.771	1	CLONAL	1	TRUE	1	0.261152582010213	2		433	468	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501449	149501449	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011095-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	41	632	0	ENST00000261799.4:c.2338C>T	p.Pro780Ser	p.P780S	ENST00000261799	NM_002609.3	780	Ccc/Tcc	16/23	1	2	FACETS	0.479	0.398	0.569	0.479	0.398	0.569	SUBCLONAL	1	TRUE	1	0.261152582010213	2		632	656	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518099	8518099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764400127	NA	P-0011095-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	17	396	1	ENST00000356435.5:c.1292C>T	p.Ser431Leu	p.S431L	ENST00000356435		431	tCg/tTg	10/35	0.250645234963131	0	FACETS	0.308	0.23	0.402			1	SUBCLONAL	1	TRUE	0	0.261152582010213	0		397	312	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097628	11097628	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011095-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	56	977	0	ENST00000358026.2:c.808C>T	p.Pro270Ser	p.P270S	ENST00000358026	NM_001128849.1	270	Ccc/Tcc	5/36	1	2	FACETS	0.41	0.35	0.477	0.41	0.35	0.477	SUBCLONAL	1	TRUE	1	0.261152582010213	2		977	1045	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0011095-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	56	537	1	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			1	2	FACETS	0.788	0.676	0.911	0.788	0.676	0.911	CLONAL	1	TRUE	1	0.261152582010213	2		538	544	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004277	29004277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370686484	NA	P-0011095-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	23	287	0	ENST00000282397.4:c.1016G>A	p.Arg339Gln	p.R339Q	ENST00000282397	NM_002019.4	339	cGa/cAa	8/30	1	2	FACETS	0.595	0.464	0.746	0.595	0.464	0.746	SUBCLONAL	1	TRUE	1	0.261152582010213	2		287	296	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144107	11144107	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011095-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	50	776	1	ENST00000358026.2:c.3688C>T	p.Gln1230Ter	p.Q1230*	ENST00000358026	NM_001128849.1	1230	Cag/Tag	26/36	1	2	FACETS	0.433	0.366	0.507	0.433	0.366	0.507	SUBCLONAL	1	TRUE	1	0.261152582010213	2		777	884	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858351	9858351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011095-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	22	410	0	ENST00000330684.3:c.3050C>T	p.Ser1017Phe	p.S1017F	ENST00000330684	NM_001134407.1	1017	tCc/tTc	13/13	1	2	FACETS	0.52	0.403	0.656	0.52	0.403	0.656	SUBCLONAL	1	TRUE	1	0.261152582010213	2		410	324	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851903	63851903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776160603	NA	P-0011095-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	57	517	2	ENST00000279873.7:c.2681C>T	p.Ser894Leu	p.S894L	ENST00000279873	NM_032199.2	894	tCg/tTg	10/10	1	2	FACETS	0.893	0.767	1	0.893	0.767	1	CLONAL	1	TRUE	1	0.261152582010213	2		519	489	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944412	40944412	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011095-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	39	411	0	ENST00000373198.4:c.2090C>T	p.Pro697Leu	p.P697L	ENST00000373198	NM_133170.3	697	cCc/cTc	12/32	0.261152582010213	1	FACETS	0.547	0.453	0.651	0.547	0.453	0.651	SUBCLONAL	1	TRUE	0	0.261152582010213	1		411	475	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650843	93650843	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748067972	NA	P-0011095-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	62	350	0	ENST00000375746.1:c.1769G>A	p.Arg590Gln	p.R590Q	ENST00000375746	NM_001174167.1	590	cGg/cAg	13/14	0.261152582010213	1	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	0	0.261152582010213	1		350	395	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808937	1808937	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868538559	NA	P-0011095-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	45	789	2	ENST00000260795.2:c.2369C>T	p.Ala790Val	p.A790V	ENST00000260795		790	gCc/gTc	17/17	0.261152582010213	1	FACETS	0.376	0.315	0.444	0.376	0.315	0.444	SUBCLONAL	1	TRUE	0	0.261152582010213	1		791	797	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261308	16261308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011095-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	128	576	0	ENST00000375759.3:c.8573C>T	p.Pro2858Leu	p.P2858L	ENST00000375759	NM_015001.2	2858	cCt/cTt	11/15	0.168982653659892	5	FACETS	0.966	0.877	1	0.644	0.584	0.707	CLONAL	2	TRUE	2	0.261152582010213	5		576	706	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78435656	78435656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011095-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	59	243	0	ENST00000370768.2:c.164C>T	p.Ser55Leu	p.S55L	ENST00000370768	NM_003902.3	55	tCa/tTa	2/20	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.261152582010213	2		243	402	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573924	18573924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779347644	NA	P-0011095-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	16	229	0	ENST00000266497.5:c.2242C>T	p.Leu748Phe	p.L748F	ENST00000266497		748	Ctc/Ttc	15/31	1	2	FACETS	0.513	0.379	0.672	0.513	0.379	0.672	SUBCLONAL	1	TRUE	1	0.261152582010213	2		229	239	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205238	46205238	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011095-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	30	283	0	ENST00000334344.6:c.322G>A	p.Glu108Lys	p.E108K	ENST00000334344	NM_152641.2	108	Gag/Aag	4/21	1	2	FACETS	0.714	0.576	0.869	0.714	0.576	0.869	SUBCLONAL	1	TRUE	1	0.261152582010213	2		283	322	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669526	88669526	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011095-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	57	360	0	ENST00000360948.2:c.1372C>T	p.Arg458Ter	p.R458*	ENST00000360948	NM_001012338.2	458	Cga/Tga	12/19	1	2	FACETS	0.927	0.797	1	0.927	0.797	1	CLONAL	1	TRUE	1	0.261152582010213	2		360	471	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347782	347782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011095-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	142	1008	0	ENST00000262320.3:c.1724C>T	p.Ser575Phe	p.S575F	ENST00000262320	NM_003502.3	575	tCc/tTc	6/11	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.261152582010213	2		1008	1078	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897370	78897370	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776223335	NA	P-0011095-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	52	930	0	ENST00000306801.3:c.2705C>T	p.Pro902Leu	p.P902L	ENST00000306801	NM_020761.2	902	cCt/cTt	23/34	1	2	FACETS	0.43	0.365	0.502	0.43	0.365	0.502	SUBCLONAL	1	TRUE	1	0.261152582010213	2		930	926	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291551	15291551	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011095-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	48	886	0	ENST00000263388.2:c.3083G>A	p.Trp1028Ter	p.W1028*	ENST00000263388	NM_000435.2	1028	tGg/tAg	19/33	1	2	FACETS	0.408	0.343	0.479	0.408	0.343	0.479	SUBCLONAL	1	TRUE	1	0.261152582010213	2		886	902	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086038	16086038	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011095-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	78	578	0	ENST00000281043.3:c.1214G>A	p.Arg405Lys	p.R405K	ENST00000281043	NM_005378.4	405	aGg/aAg	3/3	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.261152582010213	2		578	559	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932723	49932723	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011095-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	55	745	2	ENST00000296474.3:c.3148C>T	p.Pro1050Ser	p.P1050S	ENST00000296474	NM_002447.2	1050	Cca/Tca	14/20	1	2	FACETS	0.562	0.48	0.653	0.562	0.48	0.653	SUBCLONAL	1	TRUE	1	0.261152582010213	2		747	749	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515273	31515273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372990492	NA	P-0011095-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	38	563	0	ENST00000344624.3:c.1112G>A	p.Arg371His	p.R371H	ENST00000344624		371	cGt/cAt	5/33	1	2	FACETS	0.465	0.383	0.556	0.465	0.383	0.556	SUBCLONAL	1	TRUE	1	0.261152582010213	2		563	626	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622214	117622214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1351695625	NA	P-0011095-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	23	279	1	ENST00000368508.3:c.6656G>A	p.Arg2219Lys	p.R2219K	ENST00000368508	NM_002944.2	2219	aGa/aAa	42/43	1	2	FACETS	0.535	0.417	0.672	0.535	0.417	0.672	SUBCLONAL	1	TRUE	1	0.261152582010213	2		280	329	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527502	157527502	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554237157	NA	P-0011095-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	37	353	0	ENST00000346085.5:c.5227G>T	p.Glu1743Ter	p.E1743*	ENST00000346085	NM_020732.3	1743	Gaa/Taa	20/20	0.261152582010213	1	FACETS	0.787	0.651	0.938	0.787	0.651	0.938	CLONAL	1	TRUE	0	0.261152582010213	1		353	313	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739953	41739953	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011095-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	42	378	0	ENST00000242208.4:c.20G>C	p.Arg7Thr	p.R7T	ENST00000242208	NM_002192.2	7	aGa/aCa	2/3	1	2	FACETS	0.825	0.69	0.974	0.825	0.69	0.974	CLONAL	1	TRUE	1	0.261152582010213	2		378	390	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539050	23539050	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011095-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	42	521	0	ENST00000380871.4:c.389C>T	p.Ala130Val	p.A130V	ENST00000380871	NM_006167.3	130	gCc/gTc	2/2	1	2	FACETS	0.69	0.576	0.817	0.69	0.576	0.817	SUBCLONAL	1	TRUE	1	0.261152582010213	2		521	466	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005916	69005916	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011095-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	25	388	0	ENST00000288368.4:c.2327C>T	p.Pro776Leu	p.P776L	ENST00000288368	NM_024870.2	776	cCt/cTt	21/40	1	2	FACETS	0.465	0.366	0.579	0.465	0.366	0.579	SUBCLONAL	1	TRUE	1	0.261152582010213	2		388	412	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163758	152163758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011373-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	125	422	0	ENST00000206249.3:c.479G>A	p.Gly160Asp	p.G160D	ENST00000206249	NM_000125.3	160	gGt/gAt	2/8	1	2	FACETS	0.973	0.889	1	0.973	0.889	1	CLONAL	1	TRUE	1	0.659147281307286	2		422	390	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936073	44936073	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0011373-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	99	337	0	ENST00000377967.4:c.2832+2T>C		p.X944_splice	ENST00000377967	NM_021140.2	944			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.659147281307286	2		337	265	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55228032	55229054	+	splice_donor_variant,intron_variant	Splice_Site	DEL	GTAAGTCACCGCTTTCTGTTTAGTTTATGGAGTTGGTTCTAATGGGTCCTTTATTTGTATTTAGAATATTGAAGGGCTATTCCCATTTAAATTACTTTTTTCAGTTCCTTAAGAAGCAAATTAAAATCTTAAGATTCCTAACTGTGAAATTACCATGTGAATTCCATTAAAACTTTTTCCAGATCATTACCATTCAATGGGATGAATTTACCCTGAGGTTTAGGCTACCAATTATTTGTAATGTAAGTAACTAAATTTAGTATTAGTTATATTACCTTTTAGTTGTAGGTCACTCTCTGCTCATTTCAGCCTGTAAAGACTACAGCTACACACATACACACACAGAGGAATGGAATGAGCACTTTACATCAACACTTCCTGTTCTGGCTCTAGAGCCTCAGCTTTTGAAGCTGGTGAGAGCCTGGCCTGTGCTGGGCCTTGGCCACGGGCAGCGTCAGCTTTGAGTCAAGTGCTGGTCTGGCCTCCCTAGCTTTGAGCCTCTGTCAATTCCCTTAATCTGTTTAGGCTTTGGCTTCCTCATCCATAGAATGGAGATATGAATGATTCCTACGCCGTAGTGCTTTGAGAGAATTCAGTGAAATTCCTGTGTGTAAAACCCTTCCATGGTGCCTAGCACACAGCACACAGCCAATGGCCCAATGGCTCCTATCAGCTGTGGGATTTGTCATCAGAACACCACCAGCTCTGCTCCAGGCTGCCCTGGGTACCATCAAAACACACCCTGTGCCCAGCAGCACCTGCTCCTCTGCACACCTGGTTCCTTCAGCAGGGGCAGTGGCCGTGGGAGCACAGAAAACATGGAGTCCCATCTGGTTTAATTGATGCCATTGCCAAAGGGGAGGACTCACGGCACCCCCTCTCGGGTGCCAGGGTGCCTGGCTCCCACCAGGAGGAAGACCTGTCCTCCACTGTCAGGCACATTTCAGTCTTCCCAGCAGCCAGCACAACTACTTTGTCCTTCCAGTCACGGTCGGCCTCTGGGAAGCCCAGTCTGTGTCCTCC	GTAAGTCACCGCTTTCTGTTTAGTTTATGGAGTTGGTTCTAATGGGTCCTTTATTTGTATTTAGAATATTGAAGGGCTATTCCCATTTAAATTACTTTTTTCAGTTCCTTAAGAAGCAAATTAAAATCTTAAGATTCCTAACTGTGAAATTACCATGTGAATTCCATTAAAACTTTTTCCAGATCATTACCATTCAATGGGATGAATTTACCCTGAGGTTTAGGCTACCAATTATTTGTAATGTAAGTAACTAAATTTAGTATTAGTTATATTACCTTTTAGTTGTAGGTCACTCTCTGCTCATTTCAGCCTGTAAAGACTACAGCTACACACATACACACACAGAGGAATGGAATGAGCACTTTACATCAACACTTCCTGTTCTGGCTCTAGAGCCTCAGCTTTTGAAGCTGGTGAGAGCCTGGCCTGTGCTGGGCCTTGGCCACGGGCAGCGTCAGCTTTGAGTCAAGTGCTGGTCTGGCCTCCCTAGCTTTGAGCCTCTGTCAATTCCCTTAATCTGTTTAGGCTTTGGCTTCCTCATCCATAGAATGGAGATATGAATGATTCCTACGCCGTAGTGCTTTGAGAGAATTCAGTGAAATTCCTGTGTGTAAAACCCTTCCATGGTGCCTAGCACACAGCACACAGCCAATGGCCCAATGGCTCCTATCAGCTGTGGGATTTGTCATCAGAACACCACCAGCTCTGCTCCAGGCTGCCCTGGGTACCATCAAAACACACCCTGTGCCCAGCAGCACCTGCTCCTCTGCACACCTGGTTCCTTCAGCAGGGGCAGTGGCCGTGGGAGCACAGAAAACATGGAGTCCCATCTGGTTTAATTGATGCCATTGCCAAAGGGGAGGACTCACGGCACCCCCTCTCGGGTGCCAGGGTGCCTGGCTCCCACCAGGAGGAAGACCTGTCCTCCACTGTCAGGCACATTTCAGTCTTCCCAGCAGCCAGCACAACTACTTTGTCCTTCCAGTCACGGTCGGCCTCTGGGAAGCCCAGTCTGTGTCCTCC	-	novel	NA	P-0011373-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	18	200	0	ENST00000275493.2:c.1498+1_1499-138del		p.X500_splice	ENST00000275493	NM_005228.3	500			1	2	FACETS	0.259	0.195	0.334	0.259	0.195	0.334	SUBCLONAL	1	TRUE	1	0.659147281307286	2		200	211	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505014	186505014	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0011373-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	105	283	0	ENST00000323963.5:c.870del	p.Glu291ArgfsTer26	p.E291Rfs*26	ENST00000323963		290	acT/ac	8/11	1	2	FACETS	0.883	0.798	0.97	0.883	0.798	0.97	CLONAL	1	TRUE	1	0.659147281307286	2		283	361	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412045	116412045	+	splice_donor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0012149-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	20	604	0	ENST00000397752.3:c.3028+2del		p.X1010_splice	ENST00000397752	NM_000245.2	1010			NA	2	FACETS	0.706	0.542	0.898			1	INDETERMINATE	1	FALSE	NA	0.247305317680167	2		604	229	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420262	88420262	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012149-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	13	430	0	ENST00000360948.2:c.2424G>C	p.Gln808His	p.Q808H	ENST00000360948	NM_001012338.2	808	caG/caC	19/19	1	2	FACETS	0.476	0.339	0.642	0.476	0.339	0.642	SUBCLONAL	1	FALSE	1	0.247305317680167	2		430	221	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0013375-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	884	1078	6	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.720253341814064	2		1084	1166	SUCCESS
APC	324	MSKCC	GRCh37	5	112137082	112137082	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0013375-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	190	490	0	ENST00000257430.4:c.834+2T>C		p.X278_splice	ENST00000257430	NM_000038.5	278			0.720253341814064	1	FACETS	0.984	0.927	1	0.984	0.927	1	CLONAL	1	TRUE	0	0.720253341814064	1		490	343	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933200	100933202	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	novel	NA	P-0013375-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	465	1135	3	ENST00000325455.5:c.2188_2190del	p.Val730del	p.V730del	ENST00000325455	NM_001202474.3	730	GTC/-	4/8	1	2	FACETS	0.959	0.916	1	0.959	0.916	1	CLONAL	1	TRUE	1	0.720253341814064	2		1138	1347	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0014496-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	91	396	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.44970877438913	2		396	389	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610498	10610498	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014496-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	155	782	0	ENST00000171111.5:c.212G>T	p.Arg71Leu	p.R71L	ENST00000171111	NM_203500.1	71	cGg/cTg	2/6	0.44970877438913	1	FACETS	0.926	0.852	1	0.926	0.852	1	CLONAL	1	TRUE	0	0.44970877438913	1		782	577	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193172940	193172940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1244272523	NA	P-0014496-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	72	311	0	ENST00000367435.3:c.988C>T	p.Arg330Trp	p.R330W	ENST00000367435	NM_024529.4	330	Cgg/Tgg	11/17	0.4136446659298	3	FACETS	1	0.922	1	0.533	0.468	0.602	CLONAL	1	TRUE	1	0.44970877438913	3		311	368	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472548	88472548	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0014496-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	138	703	0	ENST00000360948.2:c.2007C>G	p.Tyr669Ter	p.Y669*	ENST00000360948	NM_001012338.2	669	taC/taG	16/19	1	2	FACETS	0.998	0.911	1	0.998	0.911	1	CLONAL	1	TRUE	1	0.44970877438913	2		703	615	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221929	1221960	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCGCCGGCTTCTCCTCAGGGATGCTTGAGTA	CTCGCCGGCTTCTCCTCAGGGATGCTTGAGTA	-	novel	NA	P-0014496-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	143	737	0	ENST00000326873.7:c.863-18_876del		p.X288_splice	ENST00000326873	NM_000455.4	288		7/10	0.44970877438913	1	FACETS	0.965	0.885	1	0.965	0.885	1	CLONAL	1	TRUE	0	0.44970877438913	1		737	511	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497370	149497370	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014496-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	118	584	0	ENST00000261799.4:c.2948C>G	p.Pro983Arg	p.P983R	ENST00000261799	NM_002609.3	983	cCa/cGa	22/23	0.239136997066592	1	FACETS	0.799	0.724	0.877	0.799	0.724	0.877	INDETERMINATE	1	TRUE	0	0.44970877438913	1		584	509	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001492	150001493	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATAG	novel	NA	P-0014496-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	40	517	0	ENST00000253339.5:c.2108_2111dup	p.Met704IlefsTer16	p.M704Ifs*16	ENST00000253339		704	atg/atCTATg	4/7	1	2	FACETS	0.359	0.298	0.428	0.359	0.298	0.428	SUBCLONAL	1	TRUE	1	0.44970877438913	2		517	495	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015067-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	1011	516	0				ENST00000310581	NM_198253.2	-/1132			0.677749429869084	6	FACETS	1	0.996	1	1	0.996	1	CLONAL	6	TRUE	0	0.677749429869084	6		516	1141	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0015067-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	378	429	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.677749429869084	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.677749429869084	2		429	558	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248409	59248409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184098204	NA	P-0015067-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	588	630	0	ENST00000371222.2:c.334G>A	p.Glu112Lys	p.E112K	ENST00000371222	NM_002228.3	112	Gag/Aag	1/1	0.677749429869084	3	FACETS	0.963	0.929	0.997	0.963	0.929	0.997	CLONAL	2	TRUE	1	0.677749429869084	3		630	1206	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0015067-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	400	531	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.677749429869084	2	FACETS	0.929	0.895	0.963	0.929	0.895	0.963	CLONAL	2	TRUE	0	0.677749429869084	2		531	635	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652035	36652035	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015067-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	1524	960	0	ENST00000244741.5:c.159del	p.Phe53LeufsTer95	p.F53Lfs*95	ENST00000244741	NM_000389.4	53	Ttt/tt	2/3	0.677749429869084	4	FACETS	0.943	0.929	0.957	0.943	0.929	0.957	CLONAL	4	TRUE	0	0.677749429869084	4		960	2000	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983222	149983223	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015067-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	378	497	0	ENST00000253339.5:c.3035dup	p.Ile1013AsnfsTer2	p.I1013Nfs*2	ENST00000253339		1012	aca/acCa	7/7	0.677749429869084	2	FACETS	0.985	0.95	1	0.985	0.95	1	CLONAL	2	TRUE	0	0.677749429869084	2		497	566	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983350	149983350	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015067-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	297	458	0	ENST00000253339.5:c.2908C>A	p.His970Asn	p.H970N	ENST00000253339		970	Cac/Aac	7/7	0.677749429869084	2	FACETS	0.965	0.926	1	0.965	0.926	1	CLONAL	2	TRUE	0	0.677749429869084	2		458	454	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889108	76889108	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015067-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	223	151	0	ENST00000373344.5:c.4902G>T	p.Trp1634Cys	p.W1634C	ENST00000373344	NM_000489.3	1634	tgG/tgT	18/35	0.677749429869084	2	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.677749429869084	2		151	301	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872961	35872961	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015067-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	481	517	0	ENST00000216797.5:c.271A>T	p.Met91Leu	p.M91L	ENST00000216797	NM_020529.2	91	Atg/Ttg	2/6	0.559169861951121	4	FACETS	0.919	0.88	0.959	0.919	0.88	0.959	CLONAL	2	TRUE	2	0.677749429869084	4		517	1295	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438168	56438168	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0015067-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	594	877	1	ENST00000407977.2:c.825T>A	p.Cys275Ter	p.C275*	ENST00000407977		275	tgT/tgA	7/10	0.326230303235081	6	FACETS	0.911	0.876	0.946	0.911	0.876	0.946	INDETERMINATE	3	TRUE	3	0.677749429869084	6		878	1511	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0016050-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	31	206	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.32033317225185	1	FACETS	0.642	0.522	0.777	0.642	0.522	0.777	SUBCLONAL	1	TRUE	0	0.325863686241906	1		206	248	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389236	8389236	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016050-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	71	373	1	ENST00000356435.5:c.4382C>A	p.Ser1461Ter	p.S1461*	ENST00000356435		1461	tCa/tAa	26/35	0.325863686241906	1	FACETS	0.803	0.703	0.911	0.803	0.703	0.911	CLONAL	1	TRUE	0	0.325863686241906	1		374	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0016050-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	137	858	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.32033317225185	1	FACETS	0.854	0.777	0.935	0.854	0.777	0.935	CLONAL	1	TRUE	0	0.325863686241906	1		858	824	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932410	36932410	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016050-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	113	632	0	ENST00000361632.4:c.2059G>C	p.Gly687Arg	p.G687R	ENST00000361632		687	Ggc/Cgc	16/16	0.325863686241906	3	FACETS	0.973	0.875	1	0.486	0.437	0.538	CLONAL	1	TRUE	1	0.325863686241906	3		632	829	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111454	8111455	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0016050-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	77	463	0	ENST00000346208.3:c.940_941delinsTT	p.Gly314Leu	p.G314L	ENST00000346208		314	GGg/TTg	5/6	1	2	FACETS	0.761	0.668	0.86	0.761	0.668	0.86	SUBCLONAL	1	TRUE	1	0.325863686241906	2		463	621	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333795	70333795	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016050-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	78	556	0	ENST00000373644.4:c.1700C>T	p.Pro567Leu	p.P567L	ENST00000373644	NM_030625.2	567	cCa/cTa	2/12	1	2	FACETS	0.81	0.712	0.915	0.81	0.712	0.915	CLONAL	1	TRUE	1	0.325863686241906	2		556	591	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2111885	2111885	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016050-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	163	633	0	ENST00000219476.3:c.1133C>A	p.Pro378Gln	p.P378Q	ENST00000219476	NM_000548.3	378	cCg/cAg	12/42	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.325863686241906	2		633	803	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78935249	78935249	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016050-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	124	817	0	ENST00000306801.3:c.3661A>C	p.Lys1221Gln	p.K1221Q	ENST00000306801	NM_020761.2	1221	Aag/Cag	31/34	1	2	FACETS	0.985	0.891	1	0.985	0.891	1	CLONAL	1	TRUE	1	0.325863686241906	2		817	773	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943691	17943691	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016050-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	102	864	0	ENST00000458235.1:c.2398G>T	p.Asp800Tyr	p.D800Y	ENST00000458235	NM_000215.3	800	Gat/Tat	18/24	1	2	FACETS	0.699	0.624	0.778	0.699	0.624	0.778	SUBCLONAL	1	TRUE	1	0.325863686241906	2		864	896	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224171	36224171	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs779883307	NA	P-0016050-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	62	686	0	ENST00000222270.7:c.6721G>C	p.Gly2241Arg	p.G2241R	ENST00000222270	NM_014727.1	2241	Ggc/Cgc	28/37	0.206480530819314	1	FACETS	0.492	0.424	0.565	0.492	0.424	0.565	SUBCLONAL	1	TRUE	0	0.325863686241906	1		686	648	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272116	142272116	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1295857035	NA	P-0016050-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	91	382	0	ENST00000350721.4:c.2758G>A	p.Val920Ile	p.V920I	ENST00000350721	NM_001184.3	920	Gtt/Att	13/47	1	2	FACETS	0.899	0.8	1	0.899	0.8	1	CLONAL	1	TRUE	1	0.325863686241906	2		382	621	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138642	55138642	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016050-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	94	390	0	ENST00000257290.5:c.1319C>A	p.Thr440Lys	p.T440K	ENST00000257290	NM_006206.4	440	aCg/aAg	9/23	1	2	FACETS	0.998	0.89	1	0.998	0.89	1	CLONAL	1	TRUE	1	0.325863686241906	2		390	578	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270095	66270095	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016050-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	57	311	0	ENST00000273854.3:c.1787G>C	p.Gly596Ala	p.G596A	ENST00000273854	NM_004439.5	596	gGa/gCa	8/18	1	2	FACETS	0.823	0.708	0.948	0.823	0.708	0.948	CLONAL	1	TRUE	1	0.325863686241906	2		311	425	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264658	1264658	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0016050-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	109	803	1	ENST00000310581.5:c.2704A>T	p.Lys902Ter	p.K902*	ENST00000310581	NM_198253.2	902	Aag/Tag	11/16	0.293685796291349	4	FACETS	0.935	0.838	1	0.312	0.279	0.346	CLONAL	1	TRUE	1	0.325863686241906	4		804	949	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055994	180055994	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016050-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	113	715	0	ENST00000261937.6:c.991C>A	p.Pro331Thr	p.P331T	ENST00000261937	NM_182925.4	331	Ccc/Acc	8/30	0.325863686241906	1	FACETS	0.968	0.873	1	0.968	0.873	1	CLONAL	1	TRUE	0	0.325863686241906	1		715	600	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395910	395910	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016050-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	80	484	1	ENST00000380956.4:c.467C>A	p.Thr156Lys	p.T156K	ENST00000380956	NM_001195286.1	156	aCg/aAg	4/9	NA	2	FACETS	0.795	0.7	0.896			1	INDETERMINATE	1	TRUE	NA	0.325863686241906	2		485	618	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778248	27778248	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016050-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	86	547	0	ENST00000369163.2:c.397G>T	p.Gly133Cys	p.G133C	ENST00000369163	NM_003536.2	133	Ggc/Tgc	1/1	0.325863686241906	5	FACETS	1	0.971	1			1	CLONAL	1	TRUE	NA	0.325863686241906	5		547	597	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527803	157527803	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs758748419	NA	P-0016050-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	76	404	0	ENST00000346085.5:c.5528G>T	p.Arg1843Leu	p.R1843L	ENST00000346085	NM_020732.3	1843	cGc/cTc	20/20	0.219158661374856	3	FACETS	1	0.94	1	0.557	0.49	0.629	CLONAL	1	TRUE	1	0.325863686241906	3		404	487	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635166	87635166	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016050-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	96	440	0	ENST00000277120.3:c.2218A>T	p.Ser740Cys	p.S740C	ENST00000277120		740	Agc/Tgc	18/19	0.325863686241906	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.325863686241906	1		440	462	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426121	47426121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519786	NA	P-0016050-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	182	796	1	ENST00000377045.4:c.641C>T	p.Ser214Phe	p.S214F	ENST00000377045	NM_001654.4	214	tCc/tTc	7/16	0.206480530819314	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.325863686241906	1		797	878	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650527	48650527	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016050-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	107	731	1	ENST00000376670.3:c.497C>A	p.Pro166His	p.P166H	ENST00000376670	NM_002049.3	166	cCt/cAt	3/6	0.206480530819314	1	FACETS	0.713	0.639	0.791	0.713	0.639	0.791	SUBCLONAL	1	TRUE	0	0.325863686241906	1		732	771	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352357	70352357	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016050-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	57	522	0	ENST00000374080.3:c.4384C>A	p.Arg1462Ser	p.R1462S	ENST00000374080		1462	Cgc/Agc	31/45	0.206480530819314	1	FACETS	0.479	0.411	0.554	0.479	0.411	0.554	SUBCLONAL	1	TRUE	0	0.325863686241906	1		522	611	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890135	76890135	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016050-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	112	434	1	ENST00000373344.5:c.4759G>T	p.Gly1587Cys	p.G1587C	ENST00000373344	NM_000489.3	1587	Ggt/Tgt	17/35	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.325863686241906	2		435	648	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937089	76937089	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016050-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	59	374	0	ENST00000373344.5:c.3659G>T	p.Ser1220Ile	p.S1220I	ENST00000373344	NM_000489.3	1220	aGc/aTc	9/35	1	2	FACETS	0.779	0.671	0.895	0.779	0.671	0.895	SUBCLONAL	1	TRUE	1	0.325863686241906	2		374	465	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938647	76938647	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016050-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	101	478	0	ENST00000373344.5:c.2101C>A	p.Arg701Ser	p.R701S	ENST00000373344	NM_000489.3	701	Cgt/Agt	9/35	1	2	FACETS	0.908	0.812	1	0.908	0.812	1	CLONAL	1	TRUE	1	0.325863686241906	2		478	683	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016050-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	19	349	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.284	0.215	0.366	0.284	0.215	0.366	SUBCLONAL	1	FALSE	1	0.320726928549343	2		349	417	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453148	140453148	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs397507483	NA	P-0016050-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	21	191	0	ENST00000288602.6:c.1787G>T	p.Gly596Val	p.G596V	ENST00000288602	NM_004333.4	596	gGt/gTt	15/18	1	2	FACETS	0.346	0.266	0.44	0.346	0.266	0.44	SUBCLONAL	1	FALSE	1	0.320726928549343	2		191	378	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942535	17942535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753577833	NA	P-0016050-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	86	705	0	ENST00000458235.1:c.2753G>A	p.Arg918His	p.R918H	ENST00000458235	NM_000215.3	918	cGc/cAc	20/24	1	2	FACETS	0.668	0.59	0.751	0.668	0.59	0.751	SUBCLONAL	1	FALSE	1	0.320726928549343	2		705	803	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524183	187524183	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016050-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	23	279	0	ENST00000441802.2:c.11356A>T	p.Arg3786Trp	p.R3786W	ENST00000441802	NM_005245.3	3786	Agg/Tgg	20/27	1	2	FACETS	0.377	0.294	0.474	0.377	0.294	0.474	SUBCLONAL	1	FALSE	1	0.320726928549343	2		279	380	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182259	38182259	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016050-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	52	373	0	ENST00000396334.3:c.695T>C	p.Met232Thr	p.M232T	ENST00000396334	NM_002468.4	232	aTg/aCg	4/5	1	2	FACETS	0.654	0.557	0.76	0.654	0.557	0.76	SUBCLONAL	1	FALSE	1	0.320726928549343	2		373	496	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112360	115112360	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016050-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	26	510	0	ENST00000257566.3:c.1380G>T	p.Glu460Asp	p.E460D	ENST00000257566	NM_016569.3	460	gaG/gaT	7/8	1	2	FACETS	0.326	0.257	0.404	0.326	0.257	0.404	SUBCLONAL	1	FALSE	1	0.320726928549343	2		510	498	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845528	128845528	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016050-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	36	562	0	ENST00000249373.3:c.825T>G	p.Phe275Leu	p.F275L	ENST00000249373	NM_005631.4	275	ttT/ttG	4/12	1	2	FACETS	0.323	0.264	0.389	0.323	0.264	0.389	SUBCLONAL	1	FALSE	1	0.320726928549343	2		562	695	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971039	21971039	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554654024	NA	P-0016050-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	74	577	0	ENST00000304494.5:c.319C>A	p.Arg107Ser	p.R107S	ENST00000304494	NM_000077.4	107	Cgc/Agc	2/3	1	2	FACETS	0.665	0.582	0.755	0.665	0.582	0.755	SUBCLONAL	1	FALSE	1	0.320726928549343	2		577	694	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027060	71027084	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAGGGGCCTTGGGTGACGGGAGT	CAGAGGGGCCTTGGGTGACGGGAGT	-	novel	NA	P-0016961-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	78	265	0	ENST00000318789.4:c.1243_1267del	p.Thr415SerfsTer51	p.T415Sfs*51	ENST00000318789	NM_032682.5	415	ACTCCCGTCACCCAAGGCCCCTCTGtc/tc	15/21	0.132525374620818	4	FACETS	1	0.977	1	0.717	0.637	0.801	INDETERMINATE	1	TRUE	2	0.60313665879997	4		265	289	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28929495	NA	P-0017319-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	184	534	0	ENST00000275493.2:c.2155G>T	p.Gly719Cys	p.G719C	ENST00000275493	NM_005228.3	719	Ggc/Tgc	18/28	0.595360526545521	3	FACETS	0.961	0.908	1	0.961	0.908	1	CLONAL	2	TRUE	1	0.928140275879755	3		534	302	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0017319-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	223	593	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.595360526545521	3	FACETS	0.928	0.88	0.975	0.928	0.88	0.975	CLONAL	2	TRUE	1	0.928140275879755	3		593	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577521	7577521	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017319-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	83	570	0	ENST00000269305.4:c.760A>T	p.Ile254Phe	p.I254F	ENST00000269305	NM_001126112.2	254	Atc/Ttc	7/11	0.928140275879755	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.928140275879755	1		570	92	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242742	46242742	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0017319-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	35	247	1	ENST00000334344.6:c.1704T>A	p.Tyr568Ter	p.Y568*	ENST00000334344	NM_152641.2	568	taT/taA	13/21	0.921936140140526	2	FACETS	0.517	0.43	0.61	0.258	0.215	0.305	SUBCLONAL	1	TRUE	0	0.928140275879755	2		248	146	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772349	56772349	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017319-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	39	318	0	ENST00000337432.4:c.203G>T	p.Cys68Phe	p.C68F	ENST00000337432	NM_058216.2	68	tGt/tTt	2/9	0.475755152369054	1	FACETS	0.421	0.359	0.486	0.421	0.359	0.486	INDETERMINATE	1	TRUE	0	0.928140275879755	1		318	107	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782329	NA	P-0017325-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	73	566	0	ENST00000269305.4:c.746G>A	p.Arg249Lys	p.R249K	ENST00000269305	NM_001126112.2	249	aGg/aAg	7/11	1	2	FACETS	0.855	0.746	0.973	0.855	0.746	0.973	CLONAL	1	TRUE	1	0.18	2		566	949	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495686	56495686	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017325-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	22	405	0	ENST00000267101.3:c.3876G>A	p.Met1292Ile	p.M1292I	ENST00000267101	NM_001982.3	1292	atG/atA	28/28	1	2	FACETS	0.323	0.249	0.41	0.323	0.249	0.41	SUBCLONAL	1	TRUE	1	0.18	2		405	756	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970831	55970831	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017325-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	17	451	0	ENST00000263923.4:c.1966G>T	p.Val656Phe	p.V656F	ENST00000263923	NM_002253.2	656	Gtc/Ttc	13/30	1	2	FACETS	0.271	0.201	0.356	0.271	0.201	0.356	SUBCLONAL	1	TRUE	1	0.18	2		451	696	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120163	70120163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017325-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	33	409	2	ENST00000245479.2:c.1165C>T	p.Pro389Ser	p.P389S	ENST00000245479	NM_000346.3	389	Ccg/Tcg	3/3	1	2	FACETS	0.602	0.489	0.73	0.602	0.489	0.73	SUBCLONAL	1	TRUE	1	0.18	2		411	609	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0017386-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	1229	424	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.677788619465441	15	FACETS	0.98	0.962	0.997			1	CLONAL	12	TRUE	NA	0.677788619465441	15		424	1667	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577088	7577088	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1204379654	NA	P-0017386-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	922	809	0	ENST00000269305.4:c.850A>C	p.Thr284Pro	p.T284P	ENST00000269305	NM_001126112.2	284	Aca/Cca	8/11	0.68100888133863	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.677788619465441	3		809	1186	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521327	8521327	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017386-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	283	389	0	ENST00000356435.5:c.911C>G	p.Ala304Gly	p.A304G	ENST00000356435		304	gCt/gGt	9/35	0.68100888133863	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.677788619465441	2		389	403	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143087	7143087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017386-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	252	656	0	ENST00000302850.5:c.2282G>A	p.Arg761His	p.R761H	ENST00000302850	NM_000208.2	761	cGc/cAc	12/22	0.666631446817511	4	FACETS	1	0.97	1			1	CLONAL	1	TRUE	NA	0.677788619465441	4		656	1173	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402238	402238	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017386-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	204	511	0	ENST00000399788.2:c.4553G>C	p.Gly1518Ala	p.G1518A	ENST00000399788	NM_001042603.1	1518	gGa/gCa	27/28	0.670614432496977	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.677788619465441	1		511	398	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021110	31021110	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017386-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	90	542	0	ENST00000375687.4:c.1109C>A	p.Ser370Ter	p.S370*	ENST00000375687	NM_015338.5	370	tCa/tAa	12/13	0.68100888133863	3	FACETS	0.432	0.383	0.485			1	SUBCLONAL	1	TRUE	NA	0.677788619465441	3		542	823	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62320870	62320870	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017386-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	367	1095	0	ENST00000360203.5:c.1894G>C	p.Asp632His	p.D632H	ENST00000360203	NM_001283009.1	632	Gac/Cac	23/35	0.552867171270387	3	FACETS	1	0.961	1			1	CLONAL	1	TRUE	NA	0.677788619465441	3		1095	1424	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018541-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	75	516	0				ENST00000310581	NM_198253.2	-/1132			0.323462936542202	0	FACETS	0.844	0.756	0.934			1	CLONAL	2	FALSE	0	0.321025092253193	0		516	188	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857925	9857925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs534440095	NA	P-0018541-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	43	584	0	ENST00000330684.3:c.3476G>A	p.Arg1159His	p.R1159H	ENST00000330684	NM_001134407.1	1159	cGc/cAc	13/13	0.323462936542202	0	FACETS	0.652	0.549	0.765			1	SUBCLONAL	1	FALSE	0	0.321025092253193	0		584	279	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0018541-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	477	898	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.321025092253193	5	FACETS	0.949	0.913	0.985			1	CLONAL	5	FALSE	NA	0.321025092253193	5		898	928	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523588	41523588	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018541-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	49	618	0	ENST00000263253.7:c.1004G>A	p.Arg335His	p.R335H	ENST00000263253	NM_001429.3	335	cGc/cAc	4/31	1	2	FACETS	0.585	0.495	0.683	0.585	0.495	0.683	SUBCLONAL	1	FALSE	1	0.321025092253193	2		618	522	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047305	77047305	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018541-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	27	449	0	ENST00000356341.3:c.1239G>C	p.Gln413His	p.Q413H	ENST00000356341	NM_002576.4	413	caG/caC	13/15	0.252505256478399	3	FACETS	0.646	0.515	0.796			1	SUBCLONAL	1	FALSE	NA	0.321025092253193	3		449	302	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879855	37879855	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018541-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	393	841	0	ENST00000269571.5:c.2150A>T	p.Glu717Val	p.E717V	ENST00000269571		717	gAg/gTg	18/27	0.321025092253193	5	FACETS	0.9	0.861	0.939			1	CLONAL	5	FALSE	NA	0.321025092253193	5		841	806	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47168147	47168147	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018541-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	58	323	0	ENST00000409792.3:c.78A>T	p.Glu26Asp	p.E26D	ENST00000409792	NM_014159.6	26	gaA/gaT	2/21	0.300000381012843	5	FACETS	1	0.967	1			1	CLONAL	1	FALSE	NA	0.321025092253193	5		323	369	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652056	36652056	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018541-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	182	1078	0	ENST00000244741.5:c.178G>T	p.Glu60Ter	p.E60*	ENST00000244741	NM_000389.4	60	Gag/Tag	2/3	0.321025092253193	10	FACETS	1	0.982	1			1	CLONAL	2	FALSE	NA	0.321025092253193	10		1078	1066	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0018869-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	169	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.282955193138844	5	FACETS	1	0.981	1	0.785	0.727	0.844	INDETERMINATE	2	TRUE	2	0.504035040435182	5		511	500	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275842	38275842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367715495	NA	P-0018869-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	346	625	0	ENST00000425967.3:c.1427G>A	p.Arg476Gln	p.R476Q	ENST00000425967	NM_001174067.1	476	cGg/cAg	11/19	0.504035040435182	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.504035040435182	2		625	598	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112287	115112287	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018869-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	18	55	0	ENST00000257566.3:c.1453C>T	p.Gln485Ter	p.Q485*	ENST00000257566	NM_016569.3	485	Cag/Tag	7/8	0.282955193138844	5	FACETS	1	0.827	1	1	0.924	1	INDETERMINATE	4	TRUE	2	0.504035040435182	5		55	31	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849628	68849628	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690810	NA	P-0018869-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	241	616	0	ENST00000261769.5:c.1531C>T	p.Gln511Ter	p.Q511*	ENST00000261769	NM_004360.3	511	Cag/Tag	10/16	0.504035040435182	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.504035040435182	2		616	464	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125513702	125513702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775245290	NA	P-0018869-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	81	291	0	ENST00000428830.2:c.830G>A	p.Arg277Gln	p.R277Q	ENST00000428830	NM_001114121.2	277	cGa/cAa	9/14	0.482340126359778	2	FACETS	1	0.938	1	0.539	0.48	0.601	CLONAL	1	TRUE	0	0.504035040435182	2		291	298	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138855	64138855	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs755269861	NA	P-0018869-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	78	438	0	ENST00000334205.4:c.2222C>A	p.Ser741Tyr	p.S741Y	ENST00000334205	NM_003942.2	741	tCc/tAc	17/17	0.282955193138844	5	FACETS	0.781	0.691	0.876	0.521	0.461	0.584	INDETERMINATE	2	TRUE	2	0.504035040435182	5		438	348	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021128	31021128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020052-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	197	575	0	ENST00000375687.4:c.1127G>A	p.Gly376Asp	p.G376D	ENST00000375687	NM_015338.5	376	gGc/gAc	12/13	0.415088850401652	5	FACETS	0.849	0.785	0.916	0.283	0.261	0.306	INDETERMINATE	1	TRUE	2	0.936440452024313	5		575	1191	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265696	41266154	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTTTCTGCTCACTCCTCCTAATGGCTTGGTGAAATAGCAAACAAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCA	ATTTTCTGCTCACTCCTCCTAATGGCTTGGTGAAATAGCAAACAAGCCACCAGCAGGAATCTAGTCTGGATGACTGCTTCTGGAGCCTGGATGCAGTACCATTCTTCCACTGATTCAGTGAGTAACTGTTAGGTGGTTCCCTAAGGGATTAGGTATTTCATCACTGAGCTAACCCTGGCTATCATTCTGCTTTTCTTGGCTGTCTTTCAGATTTGACTTTATTTCTAAAAATATTTCAATGGGTCATATCACAGATTCTTTTTTTTTAAATTAAAGTAACATTTCCAATCTACTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCA	-	novel	NA	P-0020052-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	50	89	0	ENST00000349496.5:c.13+126_153del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	1	2	FACETS	0.861	0.752	0.974	0.861	0.752	0.974	CLONAL	1	TRUE	1	0.936440452024313	2		89	124	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188760	32188760	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020052-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	161	709	0	ENST00000375023.3:c.794C>T	p.Pro265Leu	p.P265L	ENST00000375023	NM_004557.3	265	cCc/cTc	4/30	0.528613709102014	3	FACETS	0.575	0.527	0.625	0.288	0.263	0.313	INDETERMINATE	1	TRUE	1	0.936440452024313	3		709	878	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807987	3807988	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0020052-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	150	549	0	ENST00000262367.5:c.3431_3432del	p.Thr1144ArgfsTer24	p.T1144Rfs*24	ENST00000262367	NM_004380.2	1144	aCA/a	18/31	0.75011057079739	3	FACETS	0.528	0.483	0.576	0.264	0.241	0.288	SUBCLONAL	1	TRUE	1	0.936440452024313	3		549	890	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262480	16262480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761074906	NA	P-0020052-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	45	208	0	ENST00000375759.3:c.9745C>T	p.Pro3249Ser	p.P3249S	ENST00000375759	NM_015001.2	3249	Ccc/Tcc	11/15	0.450960231713177	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.936440452024313	0		208	107	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262652	16262652	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020052-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	117	424	0	ENST00000375759.3:c.9917A>T	p.Tyr3306Phe	p.Y3306F	ENST00000375759	NM_015001.2	3306	tAc/tTc	11/15	0.450960231713177	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.936440452024313	0		424	262	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36823901	36823901	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020052-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	237	680	1	ENST00000373129.3:c.281A>C	p.Tyr94Ser	p.Y94S	ENST00000373129	NM_032017.1	94	tAc/tCc	5/12	0.461833969100854	1	FACETS	0.404	0.379	0.429	0.404	0.379	0.429	INDETERMINATE	1	TRUE	0	0.936440452024313	1		681	667	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518197	103518197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020052-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	39	245	0	ENST00000355739.4:c.2135G>A	p.Gly712Asp	p.G712D	ENST00000355739	NM_000123.3	712	gGt/gAt	9/15	0.618230538338773	1	FACETS	0.193	0.161	0.229	0.193	0.161	0.229	SUBCLONAL	1	TRUE	0	0.936440452024313	1		245	229	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371912	55371912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020052-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	63	518	1	ENST00000297316.4:c.602G>A	p.Gly201Asp	p.G201D	ENST00000297316	NM_022454.3	201	gGc/gAc	2/2	0.515901868411503	3	FACETS	0.235	0.203	0.271			1	INDETERMINATE	1	TRUE	NA	0.936440452024313	3		519	840	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606593	93606593	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020052-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	73	510	0	ENST00000375746.1:c.413T>A	p.Leu138Gln	p.L138Q	ENST00000375746	NM_001174167.1	138	cTg/cAg	2/14	0.445673714092722	1	FACETS	0.227	0.2	0.256	0.227	0.2	0.256	INDETERMINATE	1	TRUE	0	0.936440452024313	1		510	365	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390797	139390797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020052-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	269	995	0	ENST00000277541.6:c.7394C>T	p.Pro2465Leu	p.P2465L	ENST00000277541	NM_017617.3	2465	cCc/cTc	34/34	0.15204895037969	4	FACETS	0.96	0.9	1	0.48	0.45	0.511	INDETERMINATE	1	TRUE	2	0.936440452024313	4		995	1159	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624274	89624274	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs587782187	NA	P-0021823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	106	154	0	ENST00000371953.3:c.48T>A	p.Tyr16Ter	p.Y16*	ENST00000371953	NM_000314.4	16	taT/taA	1/9	1	2	FACETS	0.931	0.842	1	1	0.992	1	CLONAL	6	TRUE	1	0.100957629105251	2		154	376	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589663	67589663	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587777709	NA	P-0021823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	35	75	0	ENST00000274335.5:c.1425+1G>A		p.X475_splice	ENST00000274335		475			0.100957629105251	0	FACETS	1	0.855	1			1	CLONAL	5	TRUE	0	0.100957629105251	0		75	122	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115463	115115463	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0021823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	140	136	0	ENST00000257566.3:c.865-2A>G		p.X289_splice	ENST00000257566	NM_016569.3	289			1	2	FACETS	0.959	0.879	1	1	0.994	1	CLONAL	6	TRUE	1	0.100957629105251	2		136	482	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1620978	1620979	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0021823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	251	447	0	ENST00000344749.5:c.1081dup	p.Gln361ProfsTer32	p.Q361Pfs*32	ENST00000344749	NM_001136139.2	361	cag/cCag	13/19	1	2	FACETS	0.998	0.932	1	1	0.996	1	CLONAL	4	TRUE	1	0.100957629105251	2		447	1246	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29106010	29106010	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	67	102	0	ENST00000328354.6:c.830del	p.Leu277Ter	p.L277*	ENST00000328354	NM_007194.3	277	tTg/tg	7/15	0.100957629105251	1	FACETS	0.964	0.85	1	1	0.988	1	CLONAL	6	TRUE	0	0.100957629105251	1		102	218	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578266	+	missense_variant	Missense_Mutation	ONP	CGGAT	CGGAT	GAAGG	novel	NA	P-0021823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	33	249	0	ENST00000269305.4:c.583_587delinsCCTTC	p.Ile195_Arg196delinsProSer	p.I195_R196delinsPS	ENST00000269305	NM_001126112.2	195	ATCCGa/CCTTCa	6/11	0.100957629105251	3	FACETS	0.832	0.675	1	0.416	0.337	0.506	CLONAL	1	TRUE	1	0.100957629105251	3		249	825	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780684	9780684	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022075-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	88	988	1	ENST00000377346.4:c.1486C>T	p.Arg496Ter	p.R496*	ENST00000377346	NM_005026.3	496	Cga/Tga	12/24	1	2	FACETS	0.557	0.492	0.627	0.557	0.492	0.627	SUBCLONAL	1	TRUE	1	0.288117031121539	2		989	1097	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322590	30322590	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022075-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	42	246	0	ENST00000322652.5:c.1603C>T	p.Arg535Ter	p.R535*	ENST00000322652	NM_015355.2	535	Cga/Tga	14/16	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.288117031121539	2		246	250	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0022184-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	61	336	1	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	1	2	FACETS	0.977	0.845	1	0.977	0.845	1	CLONAL	1	TRUE	1	0.28	2		337	446	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248153	59248154	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGGCC	novel	NA	P-0022184-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	18	172	0	ENST00000371222.2:c.585_589dup	p.Phe197TrpfsTer31	p.F197Wfs*31	ENST00000371222	NM_002228.3	197	ttt/tGGCCTtt	1/1	1	2	FACETS	0.656	0.496	0.844	0.656	0.496	0.844	SUBCLONAL	1	TRUE	1	0.28	2		172	196	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019410	42019410	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs528009988	NA	P-0022184-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	97	497	0	ENST00000219905.7:c.3463C>T	p.Arg1155Ter	p.R1155*	ENST00000219905	NM_001164273.1	1155	Cga/Tga	10/24	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.28	2		497	684	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241993	105241993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060503071	NA	P-0022184-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	128	764	1	ENST00000349310.3:c.431G>A	p.Arg144His	p.R144H	ENST00000349310	NM_001014432.1	144	cGc/cAc	6/15	1	2	FACETS	0.945	0.856	1	0.945	0.856	1	CLONAL	1	TRUE	1	0.28	2		765	967	SUCCESS
FH	2271	MSKCC	GRCh37	1	241672081	241672081	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123166	NA	P-0022184-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	60	352	0	ENST00000366560.3:c.560C>T	p.Ser187Leu	p.S187L	ENST00000366560	NM_000143.3	187	tCa/tTa	5/10	0.297713875120092	4	FACETS	0.935	0.805	1	0.234	0.201	0.269	CLONAL	1	TRUE	0	0.28	4		352	587	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436101	116436101	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022184-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	88	433	0	ENST00000397752.3:c.4096C>G	p.Pro1366Ala	p.P1366A	ENST00000397752	NM_000245.2	1366	Cct/Gct	21/21	0.277162532674771	3	FACETS	1	0.928	1			1	CLONAL	1	TRUE	NA	0.28	3		433	674	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933284	39933287	+	frameshift_variant	Frame_Shift_Del	DEL	TATC	TATC	-	novel	NA	P-0022184-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	153	753	0	ENST00000378444.4:c.1312_1315del	p.Asp438SerfsTer3	p.D438Sfs*3	ENST00000378444	NM_001123385.1	438	GATAag/ag	4/15	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.28	2		753	1025	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410279	63410279	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022184-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	126	788	0	ENST00000330258.3:c.2888C>A	p.Pro963His	p.P963H	ENST00000330258	NM_152424.3	963	cCc/cAc	2/2	1	2	FACETS	0.938	0.849	1	0.938	0.849	1	CLONAL	1	TRUE	1	0.28	2		788	959	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0022294-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	63	309	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.665	0.577	0.76	0.665	0.577	0.76	SUBCLONAL	1	FALSE	1	0.45213356007095	2		309	419	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573586	48573586	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022294-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	54	223	0	ENST00000342988.3:c.170T>C	p.Leu57Ser	p.L57S	ENST00000342988	NM_005359.5	57	tTa/tCa	2/12	0.45213356007095	1	FACETS	0.889	0.77	1	0.889	0.77	1	CLONAL	1	FALSE	0	0.45213356007095	1		223	208	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915334	32915335	+	splice_donor_variant	Splice_Site	INS	-	-	GC	novel	NA	P-0022294-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	110	587	0	ENST00000380152.3:c.6841+1_6841+2insGC		p.X2281_splice	ENST00000380152		2281			1	2	FACETS	0.835	0.752	0.922	0.835	0.752	0.922	CLONAL	1	FALSE	1	0.45213356007095	2		587	583	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937477	32937477	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022294-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	123	541	0	ENST00000380152.3:c.8140del	p.Gln2714LysfsTer19	p.Q2714Kfs*19	ENST00000380152		2713	aCc/ac	18/27	1	2	FACETS	0.862	0.782	0.947	0.862	0.782	0.947	CLONAL	1	FALSE	1	0.45213356007095	2		541	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578518	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGTCTTGGC	CAGGTCTTGGC	-	novel	NA	P-0022294-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	256	994	0	ENST00000269305.4:c.412_422del	p.Ala138ProfsTer7	p.A138Pfs*7	ENST00000269305	NM_001126112.2	138	GCCAAGACCTGc/c	5/11	0.221909314231112	1	FACETS	0.856	0.802	0.912	0.856	0.802	0.912	INDETERMINATE	1	FALSE	0	0.45213356007095	1		994	1024	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471000	8471000	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022294-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	65	283	0	ENST00000356435.5:c.3499G>C	p.Asp1167His	p.D1167H	ENST00000356435		1167	Gat/Cat	20/35	0.45213356007095	1	FACETS	0.897	0.787	1	0.897	0.787	1	CLONAL	1	FALSE	0	0.45213356007095	1		283	248	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0022719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	204	773	1	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.179893336292235	2	FACETS	0.832	0.77	0.896	0.832	0.77	0.896	CLONAL	2	TRUE	0	0.201255948588447	2		774	1219	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074238	39074240	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0022719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	144	706	0	ENST00000357387.3:c.70_72del	p.Glu24del	p.E24del	ENST00000357387	NM_152756.3	24	GAG/-	2/38	0.201255948588447	4	FACETS	1	0.983	1	0.676	0.615	0.741	CLONAL	1	TRUE	2	0.201255948588447	4		706	1271	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76890108	76890108	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	142	653	0	ENST00000373344.5:c.4786A>T	p.Met1596Leu	p.M1596L	ENST00000373344	NM_000489.3	1596	Atg/Ttg	17/35	0.201255948588447	3	FACETS	0.983	0.897	1	0.983	0.897	1	CLONAL	2	TRUE	1	0.201255948588447	3		653	790	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026132	71026132	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0023036-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	120	269	0	ENST00000318789.4:c.1490del	p.Arg497GlnfsTer30	p.R497Qfs*30	ENST00000318789	NM_032682.5	497	cGa/ca	17/21	0.163873958746464	4	FACETS	1	0.97	1	0.582	0.528	0.639	INDETERMINATE	1	FALSE	2	0.64389149207748	4		269	526	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0024300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	405	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.3464097316075	6	FACETS	0.914	0.872	0.956	0.685	0.654	0.717	INDETERMINATE	3	TRUE	2	0.688487351567462	6		511	1020	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324537	62324537	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs778531697	NA	P-0024300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1305	73	1065	0	ENST00000360203.5:c.2893G>C	p.Glu965Gln	p.E965Q	ENST00000360203	NM_001283009.1	965	Gag/Cag	30/35	0.603821523904491	4	FACETS	0.26	0.226	0.297	0.13	0.113	0.149	SUBCLONAL	1	TRUE	2	0.688487351567462	4		1065	1378	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981238	201981239	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0024300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	78	916	0	ENST00000359651.3:c.318_319del	p.Leu107Ter	p.L107*	ENST00000359651		106	gCC/g	2/8	0.681571413852953	3	FACETS	0.252	0.22	0.286	0.126	0.11	0.143	SUBCLONAL	1	TRUE	1	0.688487351567462	3		916	1211	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871650	35871650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	155	558	0	ENST00000216797.5:c.856G>A	p.Glu286Lys	p.E286K	ENST00000216797	NM_020529.2	286	Gag/Aag	5/6	0.603821523904491	4	FACETS	0.966	0.885	1	0.483	0.442	0.525	CLONAL	1	TRUE	2	0.688487351567462	4		558	787	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66679702	66679702	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	238	685	0	ENST00000307102.5:c.17C>T	p.Pro6Leu	p.P6L	ENST00000307102	NM_002755.3	6	cCg/cTg	1/11	0.603821523904491	4	FACETS	1	0.957	1	0.517	0.482	0.553	CLONAL	1	TRUE	2	0.688487351567462	4		685	1129	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211660	36211660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	163	649	1	ENST00000222270.7:c.1411C>T	p.Arg471Trp	p.R471W	ENST00000222270	NM_014727.1	471	Cgg/Tgg	3/37	0.603821523904491	4	FACETS	0.999	0.918	1	0.5	0.459	0.542	CLONAL	1	TRUE	2	0.688487351567462	4		650	800	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50916699	50916699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	195	692	1	ENST00000440232.2:c.2171G>A	p.Gly724Glu	p.G724E	ENST00000440232	NM_002691.3	724	gGa/gAa	18/27	0.603821523904491	4	FACETS	0.896	0.829	0.967	0.448	0.414	0.484	CLONAL	1	TRUE	2	0.688487351567462	4		693	1067	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519786	29519786	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	255	796	0	ENST00000389048.3:c.1785G>A	p.Trp595Ter	p.W595*	ENST00000389048	NM_004304.4	595	tgG/tgA	9/29	0.603821523904491	4	FACETS	1	0.974	1	0.54	0.505	0.576	CLONAL	1	TRUE	2	0.688487351567462	4		796	1159	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920164	76920164	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0024300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	266	849	1	ENST00000373344.5:c.3913A>T	p.Lys1305Ter	p.K1305*	ENST00000373344	NM_000489.3	1305	Aaa/Taa	11/35	0.603821523904491	4	FACETS	1	0.958	1	0.515	0.482	0.549	CLONAL	1	TRUE	2	0.688487351567462	4		850	1266	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105682	27105685	+	missense_variant	Missense_Mutation	ONP	GAAG	GAAG	AAAA	novel	NA	P-0024300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	134	499	0	ENST00000324856.7:c.5293_5296delinsAAAA	p.Glu1765_Glu1766delinsLysLys	p.E1765_E1766delinsKK	ENST00000324856	NM_006015.4	1765	GAAGaa/AAAAaa	20/20	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.688487351567462	2		499	384	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44515836	44515836	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	257	687	0	ENST00000291552.4:c.217G>C	p.Glu73Gln	p.E73Q	ENST00000291552	NM_006758.2	73	Gag/Cag	4/8	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.913001368205	2		687	533	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240215	5240215	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141697567	NA	P-0024528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	292	853	0	ENST00000357368.4:c.1699C>T	p.Arg567Trp	p.R567W	ENST00000357368	NM_002850.3	567	Cgg/Tgg	12/38	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.913001368205	2		853	597	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169988339	169988339	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	127	298	0	ENST00000295797.4:c.581C>A	p.Ser194Tyr	p.S194Y	ENST00000295797	NM_002740.5	194	tCt/tAt	6/18	0.510589597007209	6	FACETS	1	0.986	1	0.495	0.451	0.542	INDETERMINATE	1	TRUE	3	0.913001368205	6		298	529	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176931	56176934	+	frameshift_variant	Frame_Shift_Del	DEL	TTGA	TTGA	-	novel	NA	P-0024528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	129	369	0	ENST00000399503.3:c.2203_2206del	p.Asp735MetfsTer3	p.D735Mfs*3	ENST00000399503	NM_005921.1	734	gTTGAt/gt	13/20	0.913001368205	1	FACETS	0.966	0.92	1	0.966	0.92	1	CLONAL	1	TRUE	0	0.913001368205	1		369	159	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0025128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	210	470	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.956	0.9	1			1	INDETERMINATE	3	TRUE	NA	0.342321146184467	2		470	428	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259234	16259234	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	80	910	0	ENST00000375759.3:c.6499A>C	p.Lys2167Gln	p.K2167Q	ENST00000375759	NM_015001.2	2167	Aag/Cag	11/15	0.342321146184467	5	FACETS	0.622	0.546	0.705			1	SUBCLONAL	1	TRUE	NA	0.342321146184467	5		910	1137	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094345	27094346	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0025128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	265	1010	0	ENST00000324856.7:c.3054dup	p.Glu1019Ter	p.E1019*	ENST00000324856	NM_006015.4	1018	cct/ccTt	11/20	1	2	FACETS	0.82	0.77	0.871	1	0.994	1	CLONAL	2	TRUE	1	0.342321146184467	2		1010	944	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46597561	46597562	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	50	933	0	ENST00000262741.5:c.63dup	p.Tyr22LeufsTer10	p.Y22Lfs*10	ENST00000262741	NM_003629.3	21	-/C	1/10	NA	2	FACETS	0.292	0.247	0.343			1	INDETERMINATE	1	TRUE	NA	0.342321146184467	2		933	999	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115961	8115972	+	inframe_deletion	In_Frame_Del	DEL	CCAGCATGGTCA	CCAGCATGGTCA	-	novel	NA	P-0025128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	234	803	0	ENST00000346208.3:c.1309_1320del	p.Ser437_Thr440del	p.S437_T440del	ENST00000346208		436	tCCAGCATGGTCAcc/tcc	6/6	0.342321146184467	5	FACETS	1	0.955	1	0.687	0.641	0.734	CLONAL	2	TRUE	2	0.342321146184467	5		803	1004	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114901013	114901013	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs778461209	NA	P-0025128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	78	1115	0	ENST00000543371.1:c.623A>G	p.Asn208Ser	p.N208S	ENST00000543371	NM_001198531.1	208	aAt/aGt	6/14	0.209779029589361	2	FACETS	0.541	0.475	0.613	0.271	0.237	0.307	SUBCLONAL	1	TRUE	0	0.342321146184467	2		1115	842	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457722	67457722	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	53	822	1	ENST00000327367.4:c.532G>A	p.Glu178Lys	p.E178K	ENST00000327367	NM_005902.3	178	Gag/Aag	3/9	1	2	FACETS	0.463	0.394	0.539	0.463	0.394	0.539	SUBCLONAL	1	TRUE	1	0.342321146184467	2		823	669	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996276	73996276	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	18	30	0	ENST00000318443.5:c.1010G>C	p.Ser337Thr	p.S337T	ENST00000318443	NM_001024736.1	337	aGc/aCc	5/10	1	2	FACETS	0.876	0.699	1	1	0.95	1	CLONAL	3	TRUE	1	0.342321146184467	2		30	40	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	153	842	0	ENST00000335508.6:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000335508	NM_012433.2	902	Gaa/Aaa	18/25	0.234892926233969	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.342321146184467	1		842	626	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209106832	209106832	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs373048968	NA	P-0025128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	357	1086	1	ENST00000345146.2:c.736T>C	p.Tyr246His	p.Y246H	ENST00000345146	NM_005896.2	246	Tat/Cat	7/10	0.234892926233969	1	FACETS	1	0.98	1	1	0.997	1	CLONAL	2	TRUE	0	0.342321146184467	1		1087	823	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164691	36164691	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	275	1173	0	ENST00000300305.3:c.1184del	p.Pro395ArgfsTer199	p.P395Rfs*199	ENST00000300305		395	cCg/cg	8/8	0.214621813508074	2	FACETS	0.865	0.813	0.917	0.865	0.813	0.917	CLONAL	2	TRUE	0	0.342321146184467	2		1173	929	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119585476	119585476	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0025128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	89	591	0	ENST00000316626.5:c.910-1G>A		p.X304_splice	ENST00000316626		304			0.329974670137605	3	FACETS	0.947	0.84	1	0.474	0.42	0.531	CLONAL	1	TRUE	1	0.342321146184467	3		591	643	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272097	142272097	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	52	826	0	ENST00000350721.4:c.2777T>C	p.Phe926Ser	p.F926S	ENST00000350721	NM_001184.3	926	tTc/tCc	13/47	0.329974670137605	3	FACETS	0.409	0.347	0.477	0.204	0.173	0.239	SUBCLONAL	1	TRUE	1	0.342321146184467	3		826	870	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538297	187538297	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0025128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	86	926	0	ENST00000441802.2:c.8937T>G	p.Tyr2979Ter	p.Y2979*	ENST00000441802	NM_005245.3	2979	taT/taG	11/27	0.227310561522515	1	FACETS	0.525	0.464	0.591	0.525	0.464	0.591	SUBCLONAL	1	TRUE	0	0.342321146184467	1		926	793	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925491	131925491	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	45	634	0	ENST00000265335.6:c.1414G>C	p.Asp472His	p.D472H	ENST00000265335		472	Gac/Cac	9/25	0.234892926233969	1	FACETS	0.416	0.349	0.49	0.416	0.349	0.49	SUBCLONAL	1	TRUE	0	0.342321146184467	1		634	524	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460576	149460576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757795589	NA	P-0025128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	60	998	0	ENST00000286301.3:c.61C>T	p.Pro21Ser	p.P21S	ENST00000286301	NM_005211.3	21	Cca/Tca	3/22	0.234892926233969	1	FACETS	0.343	0.294	0.396	0.343	0.294	0.396	SUBCLONAL	1	TRUE	0	0.342321146184467	1		998	848	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106543497	106543497	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	29	500	0	ENST00000369096.4:c.299G>C	p.Gly100Ala	p.G100A	ENST00000369096	NM_001198.3	100	gGa/gCa	3/7	1	2	FACETS	0.39	0.313	0.479	0.39	0.313	0.479	SUBCLONAL	1	TRUE	1	0.342321146184467	2		500	434	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035212	6035212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	44	801	0	ENST00000265849.7:c.856G>A	p.Asp286Asn	p.D286N	ENST00000265849	NM_000535.5	286	Gac/Aac	8/15	0.342321146184467	3	FACETS	0.355	0.296	0.42	0.118	0.098	0.14	SUBCLONAL	1	TRUE	0	0.342321146184467	3		801	848	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484310	8484310	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	39	878	0	ENST00000356435.5:c.3222C>A	p.Asn1074Lys	p.N1074K	ENST00000356435		1074	aaC/aaA	19/35	0.234892926233969	1	FACETS	0.313	0.259	0.374	0.313	0.259	0.374	SUBCLONAL	1	TRUE	0	0.342321146184467	1		878	603	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342723	70342723	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	59	682	1	ENST00000374080.3:c.1484A>T	p.Glu495Val	p.E495V	ENST00000374080		495	gAg/gTg	10/45	0.342321146184467	2	FACETS	0.668	0.575	0.769			1	SUBCLONAL	1	TRUE	NA	0.342321146184467	2		683	516	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020196	123020196	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	224	942	0	ENST00000355640.3:c.684C>G	p.Phe228Leu	p.F228L	ENST00000355640		228	ttC/ttG	2/7	1	1	FACETS	0.774	0.724	0.825	1	0.993	1	SUBCLONAL	2	TRUE	0	0.342321146184467	1		942	701	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020270	123020270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	201	846	0	ENST00000355640.3:c.758C>T	p.Ser253Leu	p.S253L	ENST00000355640		253	tCa/tTa	2/7	1	1	FACETS	0.823	0.768	0.88	1	0.993	1	CLONAL	2	TRUE	0	0.342321146184467	1		846	591	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211837	123211837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	152	575	2	ENST00000218089.9:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000218089	NM_001042749.1	902	Gaa/Aaa	27/35	0.342321146184467	3	FACETS	0.97	0.893	1			1	CLONAL	2	TRUE	NA	0.342321146184467	3		577	536	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361172	70361172	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs779631682	NA	P-0025128-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	45	859	3	ENST00000374080.3:c.6360G>C	p.Gln2120His	p.Q2120H	ENST00000374080		2120	caG/caC	43/45	0.342321146184467	2	FACETS	0.529	0.444	0.622			1	SUBCLONAL	1	TRUE	NA	0.342321146184467	2		862	497	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0026989-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	93	396	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.319730116166904	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.327357280991117	1		396	400	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0026989-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	326	828	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.319730116166904	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.327357280991117	1		828	1389	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482607	56482607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs993665271	NA	P-0026989-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	154	527	0	ENST00000267101.3:c.1064C>T	p.Thr355Ile	p.T355I	ENST00000267101	NM_001982.3	355	aCc/aTc	9/28	0.327357280991117	2	FACETS	0.904	0.826	0.985	0.452	0.413	0.493	CLONAL	1	TRUE	0	0.327357280991117	2		527	1041	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125088	46125089	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0026989-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	67	172	0	ENST00000334344.6:c.277dup	p.Tyr93LeufsTer18	p.Y93Lfs*18	ENST00000334344	NM_152641.2	92	tat/taTt	3/21	0.327357280991117	2	FACETS	0.764	0.671	0.862	0.764	0.671	0.862	SUBCLONAL	2	TRUE	0	0.327357280991117	2		172	268	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986656	36986657	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026989-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	35	108	0	ENST00000354822.5:c.1032dup	p.Ala345ArgfsTer94	p.A345Rfs*94	ENST00000354822	NM_001079668.2	344	-/C	3/3	0.319730116166904	1	FACETS	0.999	0.828	1	0.999	0.828	1	CLONAL	1	TRUE	0	0.327357280991117	1		108	179	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870055	40870055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026989-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	71	315	0	ENST00000428826.2:c.962G>A	p.Arg321His	p.R321H	ENST00000428826		321	cGc/cAc	10/21	0.319730116166904	1	FACETS	0.78	0.683	0.884	0.78	0.683	0.884	SUBCLONAL	1	TRUE	0	0.327357280991117	1		315	465	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431031	49431031	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0026989-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	83	636	1	ENST00000301067.7:c.10108del	p.Gln3370SerfsTer22	p.Q3370Sfs*22	ENST00000301067	NM_003482.3	3370	Cag/ag	34/54	0.327357280991117	2	FACETS	0.429	0.377	0.485	0.215	0.188	0.243	SUBCLONAL	1	TRUE	0	0.327357280991117	2		637	1182	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135345	30135345	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	96	318	0	ENST00000331968.5:c.473C>G	p.Ala158Gly	p.A158G	ENST00000331968	NM_002742.2	158	gCt/gGt	3/18	0.539859572578706	4	FACETS	0.936	0.836	1	0.468	0.418	0.521	CLONAL	1	TRUE	2	0.539859572578706	4		318	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577157	7577157	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1060501207	NA	P-0027242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	383	445	0	ENST00000269305.4:c.783-2A>G		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.436692337527745	4	FACETS	0.881	0.848	0.914	0.881	0.848	0.914	CLONAL	4	TRUE	0	0.539859572578706	4		445	620	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627319	37627319	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	121	381	0	ENST00000447079.4:c.1234G>C	p.Ala412Pro	p.A412P	ENST00000447079	NM_015083.1	412	Gca/Cca	2/14	0.539859572578706	3	FACETS	0.968	0.878	1	0.484	0.439	0.532	CLONAL	1	TRUE	1	0.539859572578706	3		381	588	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201791	66201791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	105	356	0	ENST00000273854.3:c.2711C>T	p.Pro904Leu	p.P904L	ENST00000273854	NM_004439.5	904	cCt/cTt	16/18	0.515649436394923	4	FACETS	0.927	0.832	1	0.464	0.416	0.514	CLONAL	1	TRUE	2	0.539859572578706	4		356	646	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0027242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	198	498	0				ENST00000310581	NM_198253.2	-/1132			0.539859572578706	4	FACETS	1	0.991	1	0.747	0.694	0.802	CLONAL	1	TRUE	2	0.539859572578706	4		498	756	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56859019	56859019	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	76	364	0	ENST00000519728.1:c.145C>T	p.Gln49Ter	p.Q49*	ENST00000519728	NM_002350.3	49	Cag/Tag	3/13	0.539859572578706	3	FACETS	0.612	0.537	0.693	0.306	0.268	0.347	SUBCLONAL	1	TRUE	1	0.539859572578706	3		364	584	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949002	44949003	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0027242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	151	126	0	ENST00000377967.4:c.3565dup	p.Leu1189ProfsTer10	p.L1189Pfs*10	ENST00000377967	NM_021140.2	1188	ttc/ttCc	25/29	0.539859572578706	2	FACETS	1	0.971	1			1	CLONAL	2	TRUE	NA	0.539859572578706	2		126	263	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889184	76889184	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs122445093	NA	P-0027242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	117	137	0	ENST00000373344.5:c.4826A>G	p.His1609Arg	p.H1609R	ENST00000373344	NM_000489.3	1609	cAt/cGt	18/35	0.539859572578706	2	FACETS	1	0.985	1			1	CLONAL	2	TRUE	NA	0.539859572578706	2		137	177	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0027633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	83	396	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.366554767050798	2	FACETS	1	0.97	1	0.632	0.563	0.704	CLONAL	1	TRUE	0	0.411970963856675	2		396	319	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11276228	11276228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	45	461	0	ENST00000361445.4:c.3094G>A	p.Asp1032Asn	p.D1032N	ENST00000361445	NM_004958.3	1032	Gat/Aat	20/58	1	2	FACETS	0.681	0.574	0.797	0.681	0.574	0.797	SUBCLONAL	1	TRUE	1	0.411970963856675	2		461	321	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400822	72400822	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	43	413	0	ENST00000357731.5:c.349A>G	p.Thr117Ala	p.T117A	ENST00000357731	NM_173808.2	117	Acg/Gcg	2/7	1	2	FACETS	0.715	0.601	0.839	0.715	0.601	0.839	SUBCLONAL	1	TRUE	1	0.411970963856675	2		413	292	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649891	88649891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368595543	NA	P-0027633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	26	383	0	ENST00000372037.3:c.140G>A	p.Gly47Glu	p.G47E	ENST00000372037	NM_004329.2	47	gGa/gAa	4/13	0.216061896377315	1	FACETS	0.364	0.289	0.45	0.364	0.289	0.45	INDETERMINATE	1	TRUE	0	0.411970963856675	1		383	275	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104353466	104353466	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	50	878	1	ENST00000369902.3:c.671G>T	p.Arg224Leu	p.R224L	ENST00000369902	NM_016169.3	224	cGg/cTg	5/12	0.216061896377315	1	FACETS	0.513	0.436	0.596	0.513	0.436	0.596	INDETERMINATE	1	TRUE	0	0.411970963856675	1		879	376	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589729	69589729	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	12	91	0	ENST00000168712.1:c.124G>T	p.Glu42Ter	p.E42*	ENST00000168712	NM_002007.2	42	Gag/Tag	1/3	0.188903030049064	1	FACETS	0.812	0.585	1	0.812	0.585	1	INDETERMINATE	1	TRUE	0	0.411970963856675	1		91	57	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922274	100922274	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	49	396	0	ENST00000325455.5:c.2238C>G	p.Asp746Glu	p.D746E	ENST00000325455	NM_001202474.3	746	gaC/gaG	5/8	0.188903030049064	1	FACETS	0.665	0.567	0.771	0.665	0.567	0.771	INDETERMINATE	1	TRUE	0	0.411970963856675	1		396	284	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478882	56478882	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	153	812	1	ENST00000267101.3:c.338G>T	p.Gly113Val	p.G113V	ENST00000267101	NM_001982.3	113	gGg/gTg	3/28	0.366554767050798	2	FACETS	0.856	0.79	0.922	0.856	0.79	0.922	CLONAL	2	TRUE	0	0.411970963856675	2		813	434	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233524	69233536	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTATGGCCTGC	TCTTATGGCCTGC	-	novel	NA	P-0027633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	138	416	0	ENST00000462284.1:c.1390_1402del	p.Met465HisfsTer6	p.M465Hfs*6	ENST00000462284	NM_002392.5	463	caTCTTATGGCCTGC/ca	11/11	0.366554767050798	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	0	0.411970963856675	2		416	331	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879747	123879747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1235814187	NA	P-0027633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	36	142	0	ENST00000330479.4:c.443C>T	p.Thr148Ile	p.T148I	ENST00000330479	NM_020382.3	148	aCc/aTc	4/9	0.366554767050798	2	FACETS	0.857	0.725	0.995	0.857	0.725	0.995	CLONAL	2	TRUE	0	0.411970963856675	2		142	102	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225522	133225522	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	158	780	0	ENST00000320574.5:c.4142A>C	p.Tyr1381Ser	p.Y1381S	ENST00000320574	NM_006231.2	1381	tAt/tCt	32/49	0.366554767050798	2	FACETS	0.966	0.896	1	0.966	0.896	1	CLONAL	2	TRUE	0	0.411970963856675	2		780	397	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626686	28626686	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	61	499	0	ENST00000241453.7:c.610G>T	p.Glu204Ter	p.E204*	ENST00000241453	NM_004119.2	204	Gaa/Taa	5/24	0.411970963856675	1	FACETS	0.822	0.715	0.936	0.822	0.715	0.936	CLONAL	1	TRUE	0	0.411970963856675	1		499	286	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961683	41961683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	59	525	0	ENST00000219905.7:c.591G>A	p.Met197Ile	p.M197I	ENST00000219905	NM_001164273.1	197	atG/atA	2/24	0.411970963856675	1	FACETS	0.776	0.673	0.887	0.776	0.673	0.887	SUBCLONAL	1	TRUE	0	0.411970963856675	1		525	293	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726682	88726682	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	55	532	0	ENST00000360948.2:c.362G>T	p.Arg121Ile	p.R121I	ENST00000360948	NM_001012338.2	121	aGa/aTa	4/19	0.411970963856675	1	FACETS	0.815	0.704	0.935	0.815	0.704	0.935	CLONAL	1	TRUE	0	0.411970963856675	1		532	260	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969980	81969980	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	42	471	1	ENST00000359376.3:c.3049G>T	p.Ala1017Ser	p.A1017S	ENST00000359376	NM_002661.3	1017	Gca/Tca	27/33	0.188903030049064	1	FACETS	0.618	0.519	0.726	0.618	0.519	0.726	INDETERMINATE	1	TRUE	0	0.411970963856675	1		472	262	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0027633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	104	911	1	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.377485384923725	1	FACETS	0.95	0.856	1	0.95	0.856	1	CLONAL	1	TRUE	0	0.411970963856675	1		912	422	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562762	29562762	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1060500341	NA	P-0027633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	80	436	0	ENST00000356175.3:c.3842C>G	p.Ala1281Gly	p.A1281G	ENST00000356175	NM_000267.3	1281	gCc/gGc	28/57	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.411970963856675	2		436	333	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575055	48575055	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs1555685149	NA	P-0027633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	32	347	0	ENST00000342988.3:c.250-1G>C		p.X84_splice	ENST00000342988	NM_005359.5	84			0.188903030049064	1	FACETS	0.436	0.355	0.527	0.436	0.355	0.527	INDETERMINATE	1	TRUE	0	0.411970963856675	1		347	283	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602721	10602721	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	113	1045	0	ENST00000171111.5:c.857A>T	p.Gln286Leu	p.Q286L	ENST00000171111	NM_203500.1	286	cAg/cTg	3/6	0.411970963856675	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.411970963856675	1		1045	421	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505417	25505418	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1553423604	NA	P-0027633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	94	887	0	ENST00000264709.3:c.340dup	p.Ala114GlyfsTer10	p.A114Gfs*10	ENST00000264709	NM_175629.2	114	gcc/gGcc	4/23	0.181289654126208	2	FACETS	1	0.949	1	0.55	0.492	0.61	INDETERMINATE	1	TRUE	0	0.411970963856675	2		887	415	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728682	190728682	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	33	443	0	ENST00000441310.2:c.2070G>T	p.Arg690Ser	p.R690S	ENST00000441310	NM_000534.4	690	agG/agT	10/13	0.227085565354304	2	FACETS	0.481	0.392	0.581	0.241	0.196	0.291	INDETERMINATE	1	TRUE	0	0.411970963856675	2		443	333	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730916	40730916	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	34	690	0	ENST00000373198.4:c.3619C>A	p.Arg1207Ser	p.R1207S	ENST00000373198	NM_133170.3	1207	Cgt/Agt	27/32	0.188903030049064	1	FACETS	0.371	0.304	0.447	0.371	0.304	0.447	INDETERMINATE	1	TRUE	0	0.411970963856675	1		690	353	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427702	72427702	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	61	468	0	ENST00000477973.2:c.788A>T	p.Lys263Met	p.K263M	ENST00000477973	NM_012234.5	263	aAg/aTg	4/4	NA	2	FACETS	0.955	0.83	1			1	INDETERMINATE	1	TRUE	NA	0.411970963856675	2		468	310	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390928	89390928	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	48	404	0	ENST00000336596.2:c.994G>T	p.Val332Phe	p.V332F	ENST00000336596	NM_005233.5	332	Gtt/Ttt	5/17	NA	2	FACETS	0.793	0.674	0.921			1	INDETERMINATE	1	TRUE	NA	0.411970963856675	2		404	294	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967293	134967293	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	33	686	1	ENST00000398015.3:c.2632C>A	p.Leu878Ile	p.L878I	ENST00000398015	NM_004441.4	878	Cta/Ata	14/16	0.377485384923725	1	FACETS	0.37	0.301	0.447	0.37	0.301	0.447	SUBCLONAL	1	TRUE	0	0.411970963856675	1		687	344	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593617	55593617	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	76	436	0	ENST00000288135.5:c.1683G>T	p.Glu561Asp	p.E561D	ENST00000288135	NM_000222.2	561	gaG/gaT	11/21	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.411970963856675	2		436	351	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149450021	149450021	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs775029262	NA	P-0027633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	83	695	0	ENST00000286301.3:c.1196G>A	p.Arg399Gln	p.R399Q	ENST00000286301	NM_005211.3	399	cGa/cAa	8/22	0.216061896377315	1	FACETS	0.944	0.84	1	0.944	0.84	1	INDETERMINATE	1	TRUE	0	0.411970963856675	1		695	339	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171552	32171552	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	120	724	0	ENST00000375023.3:c.3226C>A	p.Pro1076Thr	p.P1076T	ENST00000375023	NM_004557.3	1076	Ccc/Acc	20/30	0.285307251822424	3	FACETS	0.775	0.705	0.849	0.775	0.705	0.849	SUBCLONAL	2	TRUE	1	0.411970963856675	3		724	453	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066704	94066704	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	61	569	0	ENST00000369303.4:c.1055G>T	p.Ser352Ile	p.S352I	ENST00000369303	NM_004440.3	352	aGt/aTt	5/17	0.297687853253157	1	FACETS	0.822	0.715	0.936	0.822	0.715	0.936	CLONAL	1	TRUE	0	0.411970963856675	1		569	286	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509769	106509769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178692056	NA	P-0027633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	34	621	0	ENST00000359195.3:c.1763C>T	p.Ala588Val	p.A588V	ENST00000359195	NM_002649.2	588	gCa/gTa	2/11	1	2	FACETS	0.47	0.385	0.566	0.47	0.385	0.566	SUBCLONAL	1	TRUE	1	0.411970963856675	2		621	351	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874863	151874863	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	52	414	0	ENST00000262189.6:c.7675A>G	p.Ile2559Val	p.I2559V	ENST00000262189	NM_170606.2	2559	Att/Gtt	38/59	1	2	FACETS	0.77	0.659	0.89	0.77	0.659	0.89	SUBCLONAL	1	TRUE	1	0.411970963856675	2		414	328	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430289	47430289	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027633-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	89	853	2	ENST00000377045.4:c.1564G>T	p.Val522Leu	p.V522L	ENST00000377045	NM_001654.4	522	Gtg/Ttg	15/16	0.411970963856675	1	FACETS	0.945	0.845	1	0.945	0.845	1	CLONAL	1	TRUE	0	0.411970963856675	1		855	363	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0027861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	927	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.773695190944524	6	FACETS	0.924	0.9	0.948			1	CLONAL	4	TRUE	NA	0.773695190944524	6		511	1652	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0027861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	316	898	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.773695190944524	2		898	770	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281617	49281617	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs953527715	NA	P-0027861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	284	536	0	ENST00000282018.3:c.664C>G	p.Leu222Val	p.L222V	ENST00000282018	NM_020377.2	222	Ctg/Gtg	1/1	1	2	FACETS	0.969	0.915	1	0.969	0.915	1	CLONAL	1	TRUE	1	0.773695190944524	2		536	758	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129650	11129672	+	frameshift_variant	Frame_Shift_Del	DEL	CGTACGAGTTTGACAAGTGGGCC	CGTACGAGTTTGACAAGTGGGCC	-	novel	NA	P-0027861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	198	640	0	ENST00000358026.2:c.2457_2479del	p.Tyr820LeufsTer117	p.Y820Lfs*117	ENST00000358026	NM_001128849.1	819	gCGTACGAGTTTGACAAGTGGGCC/g	17/36	0.773695190944524	1	FACETS	0.791	0.743	0.838	0.791	0.743	0.838	SUBCLONAL	1	TRUE	0	0.773695190944524	1		640	397	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097182	178097182	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	227	423	0	ENST00000397062.3:c.532G>A	p.Asp178Asn	p.D178N	ENST00000397062	NM_006164.4	178	Gac/Aac	4/5	1	2	FACETS	0.798	0.747	0.851	0.798	0.747	0.851	SUBCLONAL	1	TRUE	1	0.773695190944524	2		423	735	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949126	151949126	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	280	473	0	ENST00000262189.6:c.1519C>T	p.Gln507Ter	p.Q507*	ENST00000262189	NM_170606.2	507	Cag/Tag	11/59	1	2	FACETS	0.981	0.926	1	0.981	0.926	1	CLONAL	1	TRUE	1	0.773695190944524	2		473	738	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131375	202131375	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	243	563	0	ENST00000358485.4:c.343G>T	p.Glu115Ter	p.E115*	ENST00000358485	NM_001080125.1	115	Gaa/Taa	2/9	0.146229272369212	2	FACETS	1	0.991	1	0.675	0.632	0.719	INDETERMINATE	1	TRUE	0	0.410565035996832	2		563	877	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220698	1220698	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	277	601	0	ENST00000326873.7:c.716G>A	p.Trp239Ter	p.W239*	ENST00000326873	NM_000455.4	239	tGg/tAg	5/10	0.333824554091066	2	FACETS	0.784	0.738	0.83	0.784	0.738	0.83	SUBCLONAL	2	TRUE	0	0.410565035996832	2		601	861	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55963836	55963836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	112	455	3	ENST00000263923.4:c.2607G>A	p.Met869Ile	p.M869I	ENST00000263923	NM_002253.2	869	atG/atA	18/30	1	2	FACETS	0.709	0.637	0.784	0.709	0.637	0.784	SUBCLONAL	1	TRUE	1	0.410565035996832	2		458	770	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907807	76907807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028763-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	20	246	0	ENST00000373344.5:c.4354G>A	p.Glu1452Lys	p.E1452K	ENST00000373344	NM_000489.3	1452	Gag/Aag	15/35	0.275185301142092	2	FACETS	0.274	0.209	0.35	0.137	0.104	0.175	SUBCLONAL	1	TRUE	0	0.410565035996832	2		246	356	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0029532-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	46	164	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.37472620791075	3	FACETS	0.63	0.53	0.739	0.21	0.176	0.247	SUBCLONAL	1	TRUE	0	0.37472620791075	3		164	463	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0029532-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	162	322	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.182081879545258	4	FACETS	1	0.97	1			1	INDETERMINATE	2	TRUE	NA	0.37472620791075	4		322	539	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0029532-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	131	467	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	0.337500777822934	2	FACETS	0.985	0.905	1	0.985	0.905	1	CLONAL	2	TRUE	0	0.37472620791075	2		467	355	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560493	65560493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029532-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	61	653	0	ENST00000358664.4:c.104G>T	p.Arg35Leu	p.R35L	ENST00000358664	NM_002382.4	35	cGt/cTt	3/5	0.190862695769239	2	FACETS	0.602	0.519	0.691	0.301	0.259	0.346	INDETERMINATE	1	TRUE	0	0.37472620791075	2		653	541	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031999	26031999	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1411351920	NA	P-0029532-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	88	479	0	ENST00000244661.2:c.290G>C	p.Cys97Ser	p.C97S	ENST00000244661	NM_003537.3	97	tGt/tCt	1/1	0.271799018253835	3	FACETS	0.829	0.734	0.929	0.414	0.367	0.465	CLONAL	1	TRUE	1	0.37472620791075	3		479	673	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165688	47165688	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029532-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	190	649	2	ENST00000409792.3:c.438A>T	p.Lys146Asn	p.K146N	ENST00000409792	NM_014159.6	146	aaA/aaT	3/21	0.337500777822934	2	FACETS	0.924	0.86	0.989	0.924	0.86	0.989	CLONAL	2	TRUE	0	0.37472620791075	2		651	549	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017736	31017746	+	protein_altering_variant	In_Frame_Del	DEL	GGCAGCCCGTC	GGCAGCCCGTC	AG	novel	NA	P-0029532-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	53	844	3	ENST00000375687.4:c.598_608delinsAG	p.Gly200_Pro202del	p.G200_P202del	ENST00000375687	NM_015338.5	200	GGCAGCCCGTCc/AGc	8/13	0.37472620791075	5	FACETS	0.438	0.372	0.511			1	SUBCLONAL	1	TRUE	NA	0.37472620791075	5		847	1008	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163711	32163712	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029532-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	129	507	0	ENST00000375023.3:c.5514_5515insA	p.Pro1839ThrfsTer77	p.P1839Tfs*77	ENST00000375023	NM_004557.3	1838	-/A	30/30	0.306122439613966	4	FACETS	1	0.979	1	0.634	0.575	0.695	CLONAL	1	TRUE	2	0.37472620791075	4		507	747	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151167739	151167739	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0029532-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	29	253	0	ENST00000262187.5:c.381-1G>A		p.X127_splice	ENST00000262187	NM_005614.3	127			0.127420300258226	6	FACETS	0.833	0.67	1			1	INDETERMINATE	1	TRUE	NA	0.37472620791075	6		253	325	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120820	115120821	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030240-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	546	448	0	ENST00000257566.3:c.185dup	p.Pro63AlafsTer48	p.P63Afs*48	ENST00000257566	NM_016569.3	62	aag/aaAg	1/8	0.700404461917384	4	FACETS	0.931	0.895	0.968	0.931	0.895	0.968	CLONAL	2	TRUE	2	0.773708506917931	4		448	1344	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541523	29541523	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030240-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	66	368	0	ENST00000356175.3:c.1447G>T	p.Asp483Tyr	p.D483Y	ENST00000356175	NM_000267.3	483	Gac/Tac	13/57	0.700404461917384	4	FACETS	0.548	0.476	0.626	0.274	0.238	0.313	SUBCLONAL	1	TRUE	2	0.773708506917931	4		368	552	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825395	134825395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371780361	NA	P-0030240-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	324	597	0	ENST00000398015.3:c.911G>A	p.Arg304Gln	p.R304Q	ENST00000398015	NM_004441.4	304	cGg/cAg	4/16	0.773708506917931	3	FACETS	1	0.958	1	0.508	0.48	0.537	CLONAL	1	TRUE	1	0.773708506917931	3		597	1143	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031216-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	32	349	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.619	0.502	0.751	0.619	0.502	0.751	SUBCLONAL	1	FALSE	1	0.22728363230076	2		349	455	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0031216-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	54	340	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.22728363230076	1	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	FALSE	0	0.22728363230076	1		341	417	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143985	11143985	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031216-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	56	677	0	ENST00000358026.2:c.3566G>T	p.Arg1189Leu	p.R1189L	ENST00000358026	NM_001128849.1	1189	cGa/cTa	26/36	0.22728363230076	3	FACETS	0.71	0.607	0.823	0.355	0.303	0.412	SUBCLONAL	1	FALSE	1	0.22728363230076	3		677	773	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30102152	30102152	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs775376594	NA	P-0031216-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	40	364	0	ENST00000331968.5:c.1315C>T	p.Arg439Trp	p.R439W	ENST00000331968	NM_002742.2	439	Cgg/Tgg	9/18	0.21880308262799	1	FACETS	0.763	0.635	0.905	0.763	0.635	0.905	CLONAL	1	FALSE	0	0.22728363230076	1		364	409	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0031240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	19	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.752	0.575	0.956	1	0.911	1	CLONAL	2	TRUE	1	0.16	2		511	158	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0031240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	99	530	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.162350971079396	3	FACETS	0.755	0.673	0.843	0.755	0.673	0.843	SUBCLONAL	2	TRUE	1	0.16	3		530	885	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205277	61205277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	96	559	1	ENST00000301761.2:c.217G>A	p.Glu73Lys	p.E73K	ENST00000301761	NM_017841.2	73	Gag/Aag	2/4	1	2	FACETS	0.871	0.776	0.971	1	0.984	1	CLONAL	2	TRUE	1	0.16	2		560	689	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396835	396835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	124	566	0	ENST00000262320.3:c.191C>T	p.Ser64Leu	p.S64L	ENST00000262320	NM_003502.3	64	tCg/tTg	2/11	1	2	FACETS	0.992	0.898	1	1	0.989	1	CLONAL	2	TRUE	1	0.16	2		566	781	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953288	17953288	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs941028266	NA	P-0031240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	103	597	0	ENST00000458235.1:c.698C>G	p.Ser233Trp	p.S233W	ENST00000458235	NM_000215.3	233	tCg/tGg	6/24	1	2	FACETS	0.787	0.704	0.875	1	0.983	1	SUBCLONAL	2	TRUE	1	0.16	2		597	818	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300137	137300137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540273274	NA	P-0031240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	93	544	4	ENST00000481739.1:c.422G>A	p.Arg141His	p.R141H	ENST00000481739	NM_002957.4	141	cGc/cAc	3/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.16	2		548	835	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814825	139814825	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	98	670	0	ENST00000247668.2:c.818A>C	p.Glu273Ala	p.E273A	ENST00000247668	NM_021138.3	273	gAg/gCg	8/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.16	2		670	885	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346861	70346861	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0031240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	63	548	0	ENST00000374080.3:c.2728A>T	p.Lys910Ter	p.K910*	ENST00000374080		910	Aaa/Taa	20/45	0.165306627054951	2	FACETS	1	0.871	1	0.505	0.436	0.58	CLONAL	1	TRUE	0	0.16	2		548	780	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764146326	NA	P-0032057-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	351	883	0	ENST00000269305.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000269305	NM_001126112.2	281	Gac/Aac	8/11	1	2	FACETS	0.922	0.876	0.969	0.922	0.876	0.969	CLONAL	1	TRUE	1	0.794867235324084	2		883	958	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123885	46123885	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032057-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	154	357	0	ENST00000334344.6:c.151del	p.Tyr51ThrfsTer7	p.Y51Tfs*7	ENST00000334344	NM_152641.2	51	Tac/ac	2/21	1	2	FACETS	0.952	0.881	1	0.952	0.881	1	CLONAL	1	TRUE	1	0.794867235324084	2		357	407	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937670	36937670	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032466-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	319	657	0	ENST00000361632.4:c.1068G>C	p.Trp356Cys	p.W356C	ENST00000361632		356	tgG/tgC	8/16	0.389152383808767	3	FACETS	1	0.978	1	0.704	0.667	0.741	CLONAL	2	TRUE	0	0.442540724591807	3		657	834	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446079	49446079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032466-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	188	872	0	ENST00000301067.7:c.1387G>A	p.Glu463Lys	p.E463K	ENST00000301067	NM_003482.3	463	Gag/Aag	10/54	0.442850723955352	4	FACETS	0.93	0.857	1	0.31	0.285	0.336	CLONAL	1	TRUE	1	0.442540724591807	4		872	1318	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714152	43714152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032466-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	165	630	0	ENST00000382044.4:c.4001G>A	p.Ser1334Asn	p.S1334N	ENST00000382044	NM_001141980.1	1334	aGc/aAc	19/28	0.251209932324211	5	FACETS	1	0.97	1	0.373	0.342	0.406	INDETERMINATE	1	TRUE	2	0.442540724591807	5		630	1108	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349651	89349651	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032466-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	121	557	0	ENST00000301030.4:c.3299C>G	p.Ser1100Cys	p.S1100C	ENST00000301030	NM_001256183.1	1100	tCt/tGt	9/13	0.415290319364835	2	FACETS	0.898	0.814	0.986	0.449	0.407	0.493	CLONAL	1	TRUE	0	0.442540724591807	2		557	609	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0032466-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	135	567	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	0.442850723955352	3	FACETS	0.862	0.784	0.945	0.431	0.392	0.473	CLONAL	1	TRUE	1	0.442540724591807	3		567	864	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579585	7579585	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032466-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	340	465	1	ENST00000269305.4:c.102del	p.Leu35CysfsTer9	p.L35Cfs*9	ENST00000269305	NM_001126112.2	34	ccC/cc	4/11	0.442850723955352	3	FACETS	0.892	0.851	0.934	1	0.994	1	CLONAL	3	TRUE	1	0.442540724591807	3		466	701	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732969	30732969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893810	NA	P-0032466-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	206	306	0	ENST00000295754.5:c.1582C>T	p.Arg528Cys	p.R528C	ENST00000295754	NM_003242.5	528	Cgt/Tgt	7/7	0.411424712884675	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.442540724591807	2		306	446	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0032466-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	454	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.442540724591807	11	FACETS	0.931	0.89	0.974	0.466	0.445	0.487	CLONAL	5	TRUE	1	0.442540724591807	11		511	1318	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945162	38945162	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032466-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	41	138	0	ENST00000357387.3:c.4642G>C	p.Asp1548His	p.D1548H	ENST00000357387	NM_152756.3	1548	Gat/Cat	35/38	0.442540724591807	8	FACETS	0.958	0.799	1			1	CLONAL	1	TRUE	NA	0.442540724591807	8		138	450	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433730	149433730	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032466-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	278	639	0	ENST00000286301.3:c.2821G>T	p.Glu941Ter	p.E941*	ENST00000286301	NM_005211.3	941	Gag/Tag	22/22	0.379514907327349	2	FACETS	0.903	0.853	0.953	0.903	0.853	0.953	CLONAL	2	TRUE	0	0.442540724591807	2		639	696	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397813	116397813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750276956	NA	P-0032466-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	70	370	0	ENST00000397752.3:c.2087C>T	p.Thr696Ile	p.T696I	ENST00000397752	NM_000245.2	696	aCa/aTa	8/21	0.415290319364835	2	FACETS	0.855	0.75	0.967	0.428	0.375	0.484	CLONAL	1	TRUE	0	0.442540724591807	2		370	370	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611828	100611828	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032466-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	100	376	0	ENST00000308731.7:c.1293G>A	p.Met431Ile	p.M431I	ENST00000308731	NM_000061.2	431	atG/atA	14/19	0.442850723955352	1	FACETS	0.811	0.729	0.897	0.811	0.729	0.897	CLONAL	1	TRUE	0	0.442540724591807	1		376	434	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	122	516	0				ENST00000310581	NM_198253.2	-/1132			0.192078020216494	4	FACETS	0.853	0.775	0.934	0.853	0.775	0.934	CLONAL	3	TRUE	1	0.229461724802296	4		516	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0034211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	189	757	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	1	2	FACETS	0.866	0.801	0.934	1	0.992	1	CLONAL	2	TRUE	1	0.229461724802296	2		757	951	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879854	37879854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	185	667	0	ENST00000269571.5:c.2149G>A	p.Glu717Lys	p.E717K	ENST00000269571		717	Gag/Aag	18/27	0.194845110654029	4	FACETS	0.863	0.795	0.933			1	CLONAL	2	TRUE	NA	0.229461724802296	4		667	1149	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256566	115256566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746572499	NA	P-0034211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	44	316	0	ENST00000369535.4:c.145G>A	p.Glu49Lys	p.E49K	ENST00000369535	NM_002524.4	49	Gaa/Aaa	3/7	0.199336304946347	3	FACETS	0.9	0.755	1	0.45	0.377	0.53	CLONAL	1	TRUE	1	0.229461724802296	3		316	475	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43730547	43730547	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	39	429	0	ENST00000382044.4:c.3166G>A	p.Glu1056Lys	p.E1056K	ENST00000382044	NM_001141980.1	1056	Gag/Aag	16/28	1	2	FACETS	0.483	0.399	0.577	0.483	0.399	0.577	SUBCLONAL	1	TRUE	1	0.229461724802296	2		429	704	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43730590	43730590	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	40	386	0	ENST00000382044.4:c.3123G>C	p.Leu1041Phe	p.L1041F	ENST00000382044	NM_001141980.1	1041	ttG/ttC	16/28	1	2	FACETS	0.561	0.465	0.669	0.561	0.465	0.669	SUBCLONAL	1	TRUE	1	0.229461724802296	2		386	621	SUCCESS
BLM	641	MSKCC	GRCh37	15	91334054	91334054	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	28	274	0	ENST00000355112.3:c.2999G>C	p.Arg1000Thr	p.R1000T	ENST00000355112	NM_000057.2	1000	aGa/aCa	15/22	1	2	FACETS	0.626	0.5	0.769	0.626	0.5	0.769	SUBCLONAL	1	TRUE	1	0.229461724802296	2		274	390	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2114378	2114378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	96	784	0	ENST00000219476.3:c.1549G>A	p.Glu517Lys	p.E517K	ENST00000219476	NM_000548.3	517	Gag/Aag	15/42	1	2	FACETS	0.823	0.731	0.921	0.823	0.731	0.921	CLONAL	1	TRUE	1	0.229461724802296	2		784	1017	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129612	2129619	+	frameshift_variant	Frame_Shift_Del	DEL	GTCCCAGG	GTCCCAGG	-	novel	NA	P-0034211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	90	908	0	ENST00000219476.3:c.3339_3346del	p.Glu1113AspfsTer52	p.E1113Dfs*52	ENST00000219476	NM_000548.3	1113	gaGTCCCAGGct/gact	29/42	1	2	FACETS	0.686	0.606	0.771	0.686	0.606	0.771	SUBCLONAL	1	TRUE	1	0.229461724802296	2		908	1144	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861786	59861786	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0034211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	30	225	0	ENST00000259008.2:c.1474-1G>T		p.X492_splice	ENST00000259008	NM_032043.2	492			0.207684255084327	2	FACETS	1	0.917	1	0.629	0.51	0.761	CLONAL	1	TRUE	0	0.229461724802296	2		225	208	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792752	33792752	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	28	75	0	ENST00000498907.2:c.569C>G	p.Ser190Trp	p.S190W	ENST00000498907	NM_004364.3	190	tCg/tGg	1/1	0.229461724802296	7	FACETS	0.877	0.71	1			1	CLONAL	3	TRUE	NA	0.229461724802296	7		75	146	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41558776	41558776	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	47	292	0	ENST00000263253.7:c.3721C>G	p.Pro1241Ala	p.P1241A	ENST00000263253	NM_001429.3	1241	Cct/Gct	21/31	NA	2	FACETS	1	0.948	1			1	INDETERMINATE	1	TRUE	NA	0.229461724802296	2		292	317	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948799	55948799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	26	263	0	ENST00000263923.4:c.3666G>T	p.Gln1222His	p.Q1222H	ENST00000263923	NM_002253.2	1222	caG/caT	28/30	1	2	FACETS	0.623	0.493	0.771	0.623	0.493	0.771	SUBCLONAL	1	TRUE	1	0.229461724802296	2		263	364	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942803	44942808	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	GCATGA	GCATGA	TATG	novel	NA	P-0034211-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	65	262	0	ENST00000377967.4:c.3383_3388delinsTATG	p.Gly1128ValfsTer2	p.G1128Vfs*2	ENST00000377967	NM_021140.2	1128	gGCATGAac/gTATGac	23/29	0.15710317291387	2	FACETS	0.891	0.778	1			1	CLONAL	2	TRUE	NA	0.229461724802296	2		262	318	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099008	27099008	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	94	459	0	ENST00000324856.7:c.3424C>T	p.Gln1142Ter	p.Q1142*	ENST00000324856	NM_006015.4	1142	Cag/Tag	13/20	0.678222540227247	3	FACETS	0.882	0.789	0.979	0.441	0.394	0.49	CLONAL	1	TRUE	1	0.678222540227247	3		459	421	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916640	178916666	+	inframe_deletion	In_Frame_Del	DEL	ACTGTGGGGCATCCACTTGATGCCCCC	ACTGTGGGGCATCCACTTGATGCCCCC	-	novel	NA	P-0034561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	93	203	0	ENST00000263967.3:c.28_54del	p.Leu10_Pro18del	p.L10_P18del	ENST00000263967	NM_006218.2	9	gaACTGTGGGGCATCCACTTGATGCCCCCa/gaa	2/21	0.678222540227247	3	FACETS	0.914	0.832	0.996	0.914	0.832	0.996	CLONAL	2	TRUE	1	0.678222540227247	3		203	201	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527703	157527703	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554237318	NA	P-0034561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	219	460	0	ENST00000346085.5:c.5428C>T	p.Gln1810Ter	p.Q1810*	ENST00000346085	NM_020732.3	1810	Cag/Tag	20/20	0.433211461430897	4	FACETS	1	0.952	1			1	CLONAL	2	TRUE	NA	0.678222540227247	4		460	533	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057766	27057766	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	391	672	0	ENST00000324856.7:c.1474C>T	p.Gln492Ter	p.Q492*	ENST00000324856	NM_006015.4	492	Cag/Tag	3/20	0.678222540227247	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	1	0.678222540227247	3		672	659	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955040	55955040	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	70	349	0	ENST00000263923.4:c.3505C>G	p.Gln1169Glu	p.Q1169E	ENST00000263923	NM_002253.2	1169	Cag/Gag	26/30	0.59241587382749	1	FACETS	0.696	0.618	0.776	0.696	0.618	0.776	SUBCLONAL	1	TRUE	0	0.678222540227247	1		349	196	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373221	118373221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1456050279	NA	P-0034561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	36	343	1	ENST00000534358.1:c.6614C>T	p.Pro2205Leu	p.P2205L	ENST00000534358	NM_005933.3	2205	cCc/cTc	27/36	0.678222540227247	2	FACETS	0.423	0.35	0.504	0.211	0.175	0.252	SUBCLONAL	1	TRUE	0	0.678222540227247	2		344	251	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569306	67569306	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	60	287	0	ENST00000274335.5:c.423G>T	p.Lys141Asn	p.K141N	ENST00000274335		141	aaG/aaT	2/15	0.678222540227247	3	FACETS	1	0.893	1	0.513	0.447	0.582	CLONAL	1	TRUE	1	0.678222540227247	3		287	231	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0035180-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	15	1013	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.267	0.195	0.354	0.267	0.195	0.354	SUBCLONAL	1	FALSE	1	0.452498293486369	2		1013	248	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0035180-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	15	593	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.28	0.204	0.37	0.28	0.204	0.37	SUBCLONAL	1	FALSE	1	0.452498293486369	2		593	237	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0035180-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	11	282	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	0.316248041085706	1	FACETS	0.198	0.137	0.274	0.198	0.137	0.274	SUBCLONAL	1	FALSE	0	0.452498293486369	1		282	190	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562657	29562660	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs1064794276	NA	P-0035180-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	31	374	0	ENST00000356175.3:c.3739_3742del	p.Phe1247IlefsTer18	p.F1247Ifs*18	ENST00000356175	NM_000267.3	1246	cTGTTt/ct	28/57	1	2	FACETS	0.557	0.453	0.674	0.557	0.453	0.674	SUBCLONAL	1	FALSE	1	0.452498293486369	2		374	246	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851717	134851717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150028142	NA	P-0035180-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	15	649	0	ENST00000398015.3:c.1123G>A	p.Asp375Asn	p.D375N	ENST00000398015	NM_004441.4	375	Gac/Aac	5/16	1	2	FACETS	0.34	0.249	0.449	0.34	0.249	0.449	SUBCLONAL	1	FALSE	1	0.452498293486369	2		649	195	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245759	41245759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55650082	NA	P-0035180-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	16	412	0	ENST00000357654.3:c.1789G>A	p.Glu597Lys	p.E597K	ENST00000357654	NM_007294.3	597	Gaa/Aaa	10/23	1	2	FACETS	0.28	0.206	0.367	0.28	0.206	0.367	SUBCLONAL	1	FALSE	1	0.452498293486369	2		412	253	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56871587	56871587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758034157	NA	P-0035180-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	29	490	0	ENST00000308159.5:c.1967C>T	p.Pro656Leu	p.P656L	ENST00000308159	NM_014669.4	656	cCg/cTg	18/22	1	2	FACETS	0.408	0.328	0.499	0.408	0.328	0.499	SUBCLONAL	1	FALSE	1	0.452498293486369	2		490	314	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470498	25470498	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747448117	NA	P-0035180-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	15	701	0	ENST00000264709.3:c.976C>T	p.Arg326Cys	p.R326C	ENST00000264709	NM_175629.2	326	Cgc/Tgc	8/23	1	2	FACETS	0.248	0.181	0.329	0.248	0.181	0.329	SUBCLONAL	1	FALSE	1	0.452498293486369	2		701	267	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579365	7579365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782461	NA	P-0035180-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	24	717	0	ENST00000269305.4:c.322G>A	p.Gly108Ser	p.G108S	ENST00000269305	NM_001126112.2	108	Ggt/Agt	4/11	1	2	FACETS	0.314	0.246	0.392	0.314	0.246	0.392	SUBCLONAL	1	FALSE	1	0.452498293486369	2		717	338	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858201	9858201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035180-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	23	515	0	ENST00000330684.3:c.3200G>A	p.Arg1067Gln	p.R1067Q	ENST00000330684	NM_001134407.1	1067	cGg/cAg	13/13	1	2	FACETS	0.466	0.365	0.582	0.466	0.365	0.582	SUBCLONAL	1	FALSE	1	0.452498293486369	2		515	218	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041026	112041026	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746134687	NA	P-0035180-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	20	460	0	ENST00000368678.4:c.229C>T	p.Arg77Cys	p.R77C	ENST00000368678		77	Cgt/Tgt	3/13	1	2	FACETS	0.359	0.275	0.457	0.359	0.275	0.457	SUBCLONAL	1	FALSE	1	0.452498293486369	2		460	246	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198888	67198888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751194292	NA	P-0035180-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	27	493	0	ENST00000312629.5:c.359G>A	p.Arg120Gln	p.R120Q	ENST00000312629	NM_003952.2	120	cGg/cAg	5/15	1	2	FACETS	0.31	0.246	0.383	0.31	0.246	0.383	SUBCLONAL	1	FALSE	1	0.452498293486369	2		493	385	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568636	41568636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035180-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	17	260	0	ENST00000263253.7:c.4586G>A	p.Arg1529Gln	p.R1529Q	ENST00000263253	NM_001429.3	1529	cGa/cAa	28/31	1	2	FACETS	0.228	0.17	0.298	0.228	0.17	0.298	SUBCLONAL	1	FALSE	1	0.452498293486369	2		260	329	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306549	163306549	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753469318	NA	P-0035180-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	18	243	1	ENST00000271452.3:c.346C>T	p.Arg116Trp	p.R116W	ENST00000271452	NM_145697.2	116	Cgg/Tgg	6/14	1	2	FACETS	0.296	0.222	0.382	0.296	0.222	0.382	SUBCLONAL	1	FALSE	1	0.452498293486369	2		244	269	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277291	41277291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035180-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	17	255	0	ENST00000349496.5:c.1760G>A	p.Arg587Gln	p.R587Q	ENST00000349496	NM_001904.3	587	cGa/cAa	11/15	1	2	FACETS	0.37	0.277	0.48	0.37	0.277	0.48	SUBCLONAL	1	FALSE	1	0.452498293486369	2		255	203	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860908	151860908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035180-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	22	230	0	ENST00000262189.6:c.9754C>T	p.Arg3252Cys	p.R3252C	ENST00000262189	NM_170606.2	3252	Cgt/Tgt	43/59	1	2	FACETS	0.463	0.36	0.581	0.463	0.36	0.581	SUBCLONAL	1	FALSE	1	0.452498293486369	2		230	210	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420190	49420190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775954885	NA	P-0035180-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	10	622	1	ENST00000301067.7:c.15559G>A	p.Ala5187Thr	p.A5187T	ENST00000301067	NM_003482.3	5187	Gcc/Acc	48/54	1	2	FACETS	0.242	0.163	0.339	0.242	0.163	0.339	SUBCLONAL	1	FALSE	1	0.452498293486369	2		623	183	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039222	49039223	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0035180-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	22	322	0	ENST00000267163.4:c.2302_2303del	p.Ile768PhefsTer26	p.I768Ffs*26	ENST00000267163	NM_000321.2	767	aAT/a	22/27	1	2	FACETS	0.523	0.408	0.655	0.523	0.408	0.655	SUBCLONAL	1	FALSE	1	0.452498293486369	2		322	186	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254461	10254461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144533539	NA	P-0035180-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	26	460	2	ENST00000340748.4:c.3049C>T	p.Arg1017Trp	p.R1017W	ENST00000340748		1017	Cgg/Tgg	28/40	1	2	FACETS	0.359	0.284	0.444	0.359	0.284	0.444	SUBCLONAL	1	FALSE	1	0.452498293486369	2		462	320	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943480	17943480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035180-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	19	691	2	ENST00000458235.1:c.2528C>T	p.Pro843Leu	p.P843L	ENST00000458235	NM_000215.3	843	cCg/cTg	19/24	1	2	FACETS	0.285	0.216	0.366	0.285	0.216	0.366	SUBCLONAL	1	FALSE	1	0.452498293486369	2		693	295	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293643	1293643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035180-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	19	959	2	ENST00000310581.5:c.1358G>A	p.Arg453His	p.R453H	ENST00000310581	NM_198253.2	453	cGc/cAc	2/16	1	2	FACETS	0.236	0.178	0.304	0.236	0.178	0.304	SUBCLONAL	1	FALSE	1	0.452498293486369	2		961	356	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76812968	76812968	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035180-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	21	166	0	ENST00000373344.5:c.6653del	p.Pro2218LeufsTer32	p.P2218Lfs*32	ENST00000373344	NM_000489.3	2218	cCt/ct	30/35	1	1	FACETS	0.495	0.385	0.621	0.495	0.385	0.621	SUBCLONAL	1	FALSE	0	0.452498293486369	1		166	145	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440206	49440206	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	54	526	0	ENST00000301067.7:c.4420T>C	p.Cys1474Arg	p.C1474R	ENST00000301067	NM_003482.3	1474	Tgt/Cgt	16/54	1	2	FACETS	0.555	0.474	0.644	0.555	0.474	0.644	SUBCLONAL	1	TRUE	1	0.355687489442179	2		526	547	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412952	49412952	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	73	773	0	ENST00000418115.1:c.71T>A	p.Val24Asp	p.V24D	ENST00000418115	NM_001664.2	24	gTc/gAc	2/5	1	2	FACETS	0.443	0.387	0.505	0.443	0.387	0.505	SUBCLONAL	1	TRUE	1	0.355687489442179	2		773	926	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0037226-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	72	349	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.191307341456558	3	FACETS	0.851	0.745	0.964	0.851	0.745	0.964	CLONAL	2	TRUE	1	0.193343135478468	3		349	480	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618616	37618616	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037226-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	65	413	0	ENST00000447079.4:c.292G>T	p.Glu98Ter	p.E98*	ENST00000447079	NM_015083.1	98	Gaa/Taa	1/14	0.191307341456558	3	FACETS	1	0.934	1	0.565	0.49	0.648	CLONAL	1	TRUE	1	0.193343135478468	3		413	652	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0037226-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	166	628	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.193343135478468	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	0	0.193343135478468	2		628	838	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544705	65544705	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037226-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	134	496	0	ENST00000358664.4:c.221del	p.Met74SerfsTer96	p.M74Sfs*96	ENST00000358664	NM_002382.4	74	aTg/ag	4/5	0.193343135478468	2	FACETS	0.916	0.833	1	0.916	0.833	1	CLONAL	2	TRUE	0	0.193343135478468	2		496	757	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470539	25470539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037226-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	78	582	0	ENST00000264709.3:c.935C>T	p.Ser312Phe	p.S312F	ENST00000264709	NM_175629.2	312	tCt/tTt	8/23	0.191307341456558	3	FACETS	1	0.89	1	0.508	0.445	0.576	CLONAL	1	TRUE	1	0.193343135478468	3		582	871	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513238	44513238	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037226-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	57	332	0	ENST00000291552.4:c.697G>T	p.Asp233Tyr	p.D233Y	ENST00000291552	NM_006758.2	233	Gat/Tat	8/8	0.191307341456558	3	FACETS	1	0.91	1	0.542	0.464	0.626	CLONAL	1	TRUE	1	0.193343135478468	3		332	597	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401453	401453	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1407719860	NA	P-0037226-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	44	216	0	ENST00000380956.4:c.775C>T	p.Arg259Trp	p.R259W	ENST00000380956	NM_001195286.1	259	Cgg/Tgg	7/9	0.17148455149101	4	FACETS	0.911	0.768	1	0.911	0.768	1	CLONAL	2	TRUE	2	0.193343135478468	4		216	298	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0037957-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	307	1013	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.300154225841869	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.354436349892522	2		1013	838	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0037957-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	42	353	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.305653582711859	3	FACETS	0.894	0.75	1	0.447	0.375	0.527	CLONAL	1	TRUE	1	0.354436349892522	3		353	312	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0037957-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	177	419	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.322057451942882	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.354436349892522	4		419	591	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0037957-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	95	281	0	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	0.305653582711859	3	FACETS	0.891	0.801	0.986	0.891	0.801	0.986	CLONAL	2	TRUE	1	0.354436349892522	3		281	354	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827886	40827886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201911869	NA	P-0037957-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	73	415	0	ENST00000373198.4:c.2542G>A	p.Gly848Arg	p.G848R	ENST00000373198	NM_133170.3	848	Gga/Aga	17/32	0.354436349892522	5	FACETS	0.778	0.679	0.885	0.259	0.226	0.295	SUBCLONAL	1	TRUE	2	0.354436349892522	5		415	811	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199670	11199670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766533620	NA	P-0037957-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	86	625	2	ENST00000361445.4:c.4918C>T	p.Arg1640Trp	p.R1640W	ENST00000361445	NM_004958.3	1640	Cgg/Tgg	35/58	0.305653582711859	3	FACETS	0.735	0.65	0.827	0.368	0.325	0.414	SUBCLONAL	1	TRUE	1	0.354436349892522	3		627	777	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589648	69589648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037957-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	21	179	0	ENST00000168712.1:c.205G>A	p.Val69Ile	p.V69I	ENST00000168712	NM_002007.2	69	Gtc/Atc	1/3	0.305653582711859	3	FACETS	0.601	0.464	0.76	0.301	0.232	0.38	SUBCLONAL	1	TRUE	1	0.354436349892522	3		179	232	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435111	110435111	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037957-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	137	773	0	ENST00000375856.3:c.3290G>C	p.Arg1097Pro	p.R1097P	ENST00000375856	NM_003749.2	1097	cGc/cCc	1/2	0.354436349892522	4	FACETS	0.864	0.784	0.949	0.288	0.261	0.317	CLONAL	1	TRUE	1	0.354436349892522	4		773	1212	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120471	70120472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0037957-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	181	949	2	ENST00000245479.2:c.1474_1475dup	p.His493ProfsTer31	p.H493Pfs*31	ENST00000245479	NM_000346.3	491	-/AC	3/3	0.349572702248021	3	FACETS	0.862	0.793	0.934	0.431	0.396	0.467	CLONAL	1	TRUE	1	0.354436349892522	3		951	1395	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	175	277	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.157795916937382	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.824554430244013	0		277	359	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	397	717	1	ENST00000267101.3:c.273G>A	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atA	3/28	0.707222619073327	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.824554430244013	4		718	860	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105237170	105237170	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	109	579	0	ENST00000349310.3:c.1275C>G	p.Phe425Leu	p.F425L	ENST00000349310	NM_001014432.1	425	ttC/ttG	14/15	0.216581036930052	3	FACETS	1	0.978	1	0.419	0.381	0.458	INDETERMINATE	1	TRUE	0	0.824554430244013	3		579	297	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341568	70341568	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	261	712	1	ENST00000374080.3:c.1003C>T	p.Gln335Ter	p.Q335*	ENST00000374080		335	Cag/Tag	7/45	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.824554430244013	2		713	505	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161350	185161350	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	75	772	0	ENST00000265026.3:c.777G>C	p.Trp259Cys	p.W259C	ENST00000265026	NM_004721.4	259	tgG/tgC	4/14	1	2	FACETS	0.139	0.121	0.158	0.139	0.121	0.158	SUBCLONAL	1	FALSE	1	0.975875374802155	2		772	1107	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637558	23637558	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	47	643	0	ENST00000261584.4:c.2747A>T	p.Glu916Val	p.E916V	ENST00000261584	NM_024675.3	916	gAg/gTg	7/13	1	2	FACETS	0.109	0.092	0.129	0.109	0.092	0.129	SUBCLONAL	1	FALSE	1	0.975875374802155	2		643	881	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15280918	15280918	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	489	1085	0	ENST00000263388.2:c.5178C>A	p.Cys1726Ter	p.C1726*	ENST00000263388	NM_000435.2	1726	tgC/tgA	28/33	1	2	FACETS	0.942	0.905	0.979	0.942	0.905	0.979	CLONAL	1	FALSE	1	0.975875374802155	2		1085	1064	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962662	38962662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039221-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	105	413	0	ENST00000357387.3:c.1593C>A	p.Asn531Lys	p.N531K	ENST00000357387	NM_152756.3	531	aaC/aaA	18/38	1	2	FACETS	0.382	0.343	0.423	0.382	0.343	0.423	SUBCLONAL	1	FALSE	1	0.975875374802155	2		413	563	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224558	108224558	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	14	312	0	ENST00000278616.4:c.8737G>A	p.Asp2913Asn	p.D2913N	ENST00000278616	NM_000051.3	2913	Gat/Aat	60/63	0.220111589488475	3	FACETS	1	0.778	1	1	0.778	1	CLONAL	2	TRUE	1	0.09	3		312	150	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749098	43749098	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	30	708	0	ENST00000382044.4:c.1708G>C	p.Asp570His	p.D570H	ENST00000382044	NM_001141980.1	570	Gat/Cat	12/28	0.144913785012516	3	FACETS	0.886	0.717	1	1	0.926	1	CLONAL	3	TRUE	1	0.09	3		708	262	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321286	1321286	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	19	451	0	ENST00000400841.2:c.469G>T	p.Asp157Tyr	p.D157Y	ENST00000400841		157	Gac/Tac	4/6	1	2	FACETS	0.926	0.705	1	1	0.929	1	CLONAL	2	TRUE	1	0.09	2		451	228	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039285-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	85	277	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.256378967963486	2		277	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579329	7579332	+	frameshift_variant	Frame_Shift_Del	DEL	TGGC	TGGC	-	novel	NA	P-0039285-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	69	602	0	ENST00000269305.4:c.355_358del	p.Ala119SerfsTer3	p.A119Sfs*3	ENST00000269305	NM_001126112.2	119	GCCAag/ag	4/11	1	2	FACETS	0.697	0.606	0.796	0.697	0.606	0.796	SUBCLONAL	1	TRUE	1	0.256378967963486	2		602	772	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215553	5215553	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1394993665	NA	P-0039285-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	100	851	1	ENST00000357368.4:c.4150C>T	p.Arg1384Trp	p.R1384W	ENST00000357368	NM_002850.3	1384	Cgg/Tgg	27/38	1	2	FACETS	0.661	0.589	0.739	0.661	0.589	0.739	SUBCLONAL	1	TRUE	1	0.256378967963486	2		852	1180	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026139	71026139	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039285-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	32	344	0	ENST00000318789.4:c.1483T>A	p.Phe495Ile	p.F495I	ENST00000318789	NM_032682.5	495	Ttc/Atc	17/21	1	2	FACETS	0.432	0.35	0.525	0.432	0.35	0.525	SUBCLONAL	1	TRUE	1	0.256378967963486	2		344	578	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157256651	157256651	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs573836252	NA	P-0039285-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	35	254	0	ENST00000346085.5:c.1978G>T	p.Gly660Ter	p.G660*	ENST00000346085	NM_020732.3	660	Gga/Tga	5/20	1	2	FACETS	0.726	0.596	0.872	0.726	0.596	0.872	SUBCLONAL	1	TRUE	1	0.256378967963486	2		254	376	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0039352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	65	396	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.167017103394186	3	FACETS	0.976	0.849	1	0.976	0.849	1	CLONAL	2	TRUE	1	0.167017103394186	3		396	432	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435125	18435125	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	25	332	0	ENST00000266497.5:c.110G>T	p.Ser37Ile	p.S37I	ENST00000266497		37	aGt/aTt	1/31	0.167017103394186	3	FACETS	0.843	0.664	1	0.421	0.332	0.524	CLONAL	1	TRUE	1	0.167017103394186	3		332	385	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180981	108180981	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	50	326	0	ENST00000278616.4:c.5857A>G	p.Thr1953Ala	p.T1953A	ENST00000278616	NM_000051.3	1953	Aca/Gca	39/63	0.167017103394186	2	FACETS	0.916	0.781	1	0.916	0.781	1	CLONAL	2	TRUE	0	0.167017103394186	2		326	327	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988873	41988882	+	frameshift_variant	Frame_Shift_Del	DEL	TATATCTGAC	TATATCTGAC	-	novel	NA	P-0039352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	34	477	0	ENST00000219905.7:c.1665_1674del	p.Asp555GlufsTer42	p.D555Efs*42	ENST00000219905	NM_001164273.1	555	gaTATATCTGAC/ga	3/24	1	2	FACETS	0.897	0.732	1	0.897	0.732	1	CLONAL	1	TRUE	1	0.167017103394186	2		477	454	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122357	2122357	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	101	662	0	ENST00000219476.3:c.2213G>T	p.Cys738Phe	p.C738F	ENST00000219476	NM_000548.3	738	tGc/tTc	20/42	0.167017103394186	3	FACETS	0.997	0.893	1	0.997	0.893	1	CLONAL	2	TRUE	1	0.167017103394186	3		662	657	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143235875	143235875	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	33	347	0	ENST00000262992.4:c.413C>T	p.Pro138Leu	p.P138L	ENST00000262992	NM_001101669.1	138	cCa/cTa	6/24	0.167017103394186	3	FACETS	1	0.908	1	0.598	0.488	0.722	CLONAL	1	TRUE	1	0.167017103394186	3		347	358	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341776	8341776	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	106	530	1	ENST00000356435.5:c.4864G>T	p.Ala1622Ser	p.A1622S	ENST00000356435		1622	Gct/Tct	29/35	0.167017103394186	4	FACETS	1	0.973	1	0.828	0.744	0.917	CLONAL	2	TRUE	1	0.167017103394186	4		531	596	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028875	47028875	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0039352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	85	685	0	ENST00000377604.3:c.179C>G	p.Ser60Ter	p.S60*	ENST00000377604	NM_001204468.1	60	tCa/tGa	3/24	0.167017103394186	3	FACETS	0.768	0.679	0.864	0.768	0.679	0.864	SUBCLONAL	2	TRUE	1	0.167017103394186	3		685	718	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944337	76944337	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039352-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	57	391	0	ENST00000373344.5:c.568C>A	p.Pro190Thr	p.P190T	ENST00000373344	NM_000489.3	190	Cct/Act	7/35	0.167017103394186	3	FACETS	0.769	0.66	0.887	0.769	0.66	0.887	SUBCLONAL	2	TRUE	1	0.167017103394186	3		391	481	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001304	150001304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779067408	NA	P-0039373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	123	620	0	ENST00000253339.5:c.2300G>A	p.Arg767His	p.R767H	ENST00000253339		767	cGt/cAt	4/7	1	2	FACETS	0.656	0.593	0.722	0.656	0.593	0.722	SUBCLONAL	1	TRUE	1	0.489030913550529	2		620	767	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	203	569	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.489030913550529	2		569	828	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624840	9624840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1184049921	NA	P-0039373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	195	503	0	ENST00000353224.5:c.137C>T	p.Thr46Met	p.T46M	ENST00000353224	NM_177990.2	46	aCg/aTg	3/10	1	2	FACETS	0.89	0.824	0.958	0.89	0.824	0.958	CLONAL	1	TRUE	1	0.489030913550529	2		503	896	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444304	49444304	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	457	985	1	ENST00000301067.7:c.3067C>T	p.Gln1023Ter	p.Q1023*	ENST00000301067	NM_003482.3	1023	Cag/Tag	11/54	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.489030913550529	2		986	1594	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982339	201982339	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	452	891	2	ENST00000359651.3:c.720del	p.Lys241SerfsTer13	p.K241Sfs*13	ENST00000359651		240	Ccc/cc	6/8	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.489030913550529	2		893	1459	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593520	48593520	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	78	332	0	ENST00000342988.3:c.1271A>C	p.Asp424Ala	p.D424A	ENST00000342988	NM_005359.5	424	gAt/gCt	10/12	0.458204315303535	1	FACETS	0.671	0.594	0.753	0.671	0.594	0.753	SUBCLONAL	1	TRUE	0	0.489030913550529	1		332	359	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040109-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	236	516	0				ENST00000310581	NM_198253.2	-/1132			0.424133061448784	12	FACETS	0.907	0.847	0.969			1	CLONAL	4	TRUE	NA	0.424133061448784	12		516	957	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0040109-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	474	706	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.424133061448784	3	FACETS	0.947	0.91	0.983	0.947	0.91	0.983	CLONAL	3	TRUE	0	0.424133061448784	3		706	954	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225341	2225341	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753585181	NA	P-0040109-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	146	785	1	ENST00000326181.6:c.1426C>T	p.Arg476Trp	p.R476W	ENST00000326181	NM_032271.2	476	Cgg/Tgg	16/21	1	2	FACETS	0.974	0.891	1	0.974	0.891	1	CLONAL	1	TRUE	1	0.424133061448784	2		786	707	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121744	108121744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040109-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	266	426	0	ENST00000278616.4:c.1552G>A	p.Glu518Lys	p.E518K	ENST00000278616	NM_000051.3	518	Gag/Aag	10/63	0.424133061448784	3	FACETS	1	0.991	1	0.832	0.787	0.878	CLONAL	2	TRUE	0	0.424133061448784	3		426	609	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942124	81942125	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040109-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	128	575	0	ENST00000359376.3:c.1667dup	p.Lys557GlnfsTer16	p.K557Qfs*16	ENST00000359376	NM_002661.3	554	acg/acGg	17/33	0.424133061448784	3	FACETS	0.949	0.861	1	0.474	0.43	0.521	CLONAL	1	TRUE	1	0.424133061448784	3		575	771	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917673	178917673	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040109-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	77	208	0	ENST00000263967.3:c.548A>C	p.Asn183Thr	p.N183T	ENST00000263967	NM_006218.2	183	aAt/aCt	3/21	0.392156308205213	4	FACETS	0.853	0.757	0.955	0.427	0.378	0.478	CLONAL	2	TRUE	0	0.424133061448784	4		208	303	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682152	37682152	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040109-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	86	454	0	ENST00000447079.4:c.3343G>A	p.Glu1115Lys	p.E1115K	ENST00000447079	NM_015083.1	1115	Gaa/Aaa	13/14	1	2	FACETS	0.88	0.781	0.984	0.88	0.781	0.984	CLONAL	1	TRUE	1	0.424133061448784	2		454	461	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259130	16259130	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1017059236	NA	P-0040109-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	73	543	1	ENST00000375759.3:c.6395G>A	p.Gly2132Asp	p.G2132D	ENST00000375759	NM_015001.2	2132	gGt/gAt	11/15	0.372608107220391	2	FACETS	0.678	0.594	0.768	0.339	0.297	0.384	SUBCLONAL	1	TRUE	0	0.424133061448784	2		544	508	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670516	246670516	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040109-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	74	411	0	ENST00000388985.4:c.4G>C	p.Glu2Gln	p.E2Q	ENST00000388985		2	Gag/Cag	1/12	1	2	FACETS	0.815	0.717	0.921	0.815	0.717	0.921	CLONAL	1	TRUE	1	0.424133061448784	2		411	428	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209306	133209306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479792502	NA	P-0040109-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	261	791	0	ENST00000320574.5:c.6080G>A	p.Arg2027Lys	p.R2027K	ENST00000320574	NM_006231.2	2027	aGg/aAg	44/49	1	2	FACETS	0.756	0.711	0.802	1	0.993	1	SUBCLONAL	2	TRUE	1	0.424133061448784	2		791	814	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991596	72991596	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040109-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	144	706	0	ENST00000268489.5:c.2449A>G	p.Arg817Gly	p.R817G	ENST00000268489	NM_006885.3	817	Agg/Ggg	2/10	0.424133061448784	3	FACETS	0.909	0.829	0.994	0.455	0.414	0.497	CLONAL	1	TRUE	1	0.424133061448784	3		706	905	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049826	16049826	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040109-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	220	315	0	ENST00000268712.3:c.946G>T	p.Glu316Ter	p.E316*	ENST00000268712	NM_006311.3	316	Gag/Tag	10/46	0.424133061448784	3	FACETS	0.942	0.888	0.996	0.942	0.888	0.996	CLONAL	3	TRUE	0	0.424133061448784	3		315	445	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948753	55948753	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040109-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	114	420	0	ENST00000263923.4:c.3712A>G	p.Thr1238Ala	p.T1238A	ENST00000263923	NM_002253.2	1238	Aca/Gca	28/30	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.424133061448784	2		420	537	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539600	187539600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040109-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	74	369	0	ENST00000441802.2:c.8140G>A	p.Glu2714Lys	p.E2714K	ENST00000441802	NM_005245.3	2714	Gag/Aag	10/27	NA	2	FACETS	1	0.882	1			1	INDETERMINATE	1	TRUE	NA	0.424133061448784	2		369	349	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169020	32169020	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs778683490	NA	P-0040109-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	108	824	0	ENST00000375023.3:c.4013T>A	p.Met1338Lys	p.M1338K	ENST00000375023	NM_004557.3	1338	aTg/aAg	22/30	0.351573040818583	3	FACETS	0.743	0.666	0.824	0.248	0.222	0.275	SUBCLONAL	1	TRUE	0	0.424133061448784	3		824	831	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443650	49443651	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0040109-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	101	725	0	ENST00000301067.7:c.3720_3721delinsTT	p.Met1240_Glu1241delinsIleTer	p.M1240_E1241delinsI*	ENST00000301067	NM_003482.3	1240	atGGag/atTTag	11/54	1	2	FACETS	0.743	0.665	0.826	0.743	0.665	0.826	SUBCLONAL	1	TRUE	1	0.424133061448784	2		725	641	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28883005	28883026	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAGTTCTTCAAAGGTTTTGA	AAAAGTTCTTCAAAGGTTTTGA	-	novel	NA	P-0040109-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	56	484	0	ENST00000282397.4:c.3674_3695del	p.Ile1225AsnfsTer24	p.I1225Nfs*24	ENST00000282397	NM_002019.4	1225	aTCAAAACCTTTGAAGAACTTTTa/aa	28/30	0.424133061448784	3	FACETS	0.535	0.458	0.619			1	SUBCLONAL	1	TRUE	NA	0.424133061448784	3		484	598	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009417	69009417	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040109-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	83	403	0	ENST00000288368.4:c.2534T>C	p.Phe845Ser	p.F845S	ENST00000288368	NM_024870.2	845	tTc/tCc	22/40	0.206089952086832	3	FACETS	0.81	0.715	0.91	0.405	0.357	0.455	INDETERMINATE	1	TRUE	1	0.424133061448784	3		403	586	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0040655-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	81	550	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	0.788	0.696	0.885	1	0.979	1	SUBCLONAL	2	TRUE	1	0.216924615814717	2		550	474	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988182	85988182	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0040655-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	41	457	1	ENST00000263360.6:c.1125+2T>C		p.X375_splice	ENST00000263360	NM_003797.3	375			0.216924615814717	3	FACETS	0.925	0.771	1			1	CLONAL	1	TRUE	NA	0.216924615814717	3		458	453	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254728	46254728	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040655-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	67	401	0	ENST00000334344.6:c.4918A>G	p.Lys1640Glu	p.K1640E	ENST00000334344	NM_152641.2	1640	Aaa/Gaa	16/21	1	2	FACETS	0.809	0.706	0.918	1	0.976	1	CLONAL	2	TRUE	1	0.216924615814717	2		401	382	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112580	115112581	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0040655-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	118	1074	2	ENST00000257566.3:c.1159_1160delinsAA	p.Pro387Asn	p.P387N	ENST00000257566	NM_016569.3	387	CCc/AAc	7/8	1	2	FACETS	0.993	0.894	1	0.993	0.894	1	CLONAL	1	TRUE	1	0.216924615814717	2		1076	1096	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959073	28959073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761475937	NA	P-0040655-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	47	552	0	ENST00000282397.4:c.2065G>A	p.Glu689Lys	p.E689K	ENST00000282397	NM_002019.4	689	Gag/Aag	14/30	0.216924615814717	1	FACETS	0.69	0.582	0.809	0.69	0.582	0.809	SUBCLONAL	1	TRUE	0	0.216924615814717	1		552	560	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060973	38060973	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040655-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	55	619	0	ENST00000250448.2:c.1016G>T	p.Gly339Val	p.G339V	ENST00000250448	NM_004496.3	339	gGg/gTg	2/2	0.168087579359845	3	FACETS	0.889	0.76	1	0.445	0.38	0.516	CLONAL	1	TRUE	1	0.216924615814717	3		619	632	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239294	105239294	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040655-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	55	1044	0	ENST00000349310.3:c.1093G>T	p.Glu365Ter	p.E365*	ENST00000349310	NM_001014432.1	365	Gag/Tag	12/15	0.168087579359845	3	FACETS	0.596	0.508	0.693	0.298	0.254	0.347	SUBCLONAL	1	TRUE	1	0.216924615814717	3		1044	943	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040655-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	144	1176	0	ENST00000269305.4:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000269305	NM_001126112.2	136	Caa/Taa	5/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.216924615814717	2		1176	1052	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145589	11145589	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0040655-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	98	689	0	ENST00000358026.2:c.3952-1G>A		p.X1318_splice	ENST00000358026	NM_001128849.1	1318			0.216924615814717	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.216924615814717	1		689	697	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660280	227660280	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040655-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	109	867	1	ENST00000305123.5:c.3175C>A	p.Leu1059Met	p.L1059M	ENST00000305123	NM_005544.2	1059	Ctg/Atg	1/2	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.216924615814717	2		868	761	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098556	47098562	+	frameshift_variant	Frame_Shift_Del	DEL	ACTGGGA	ACTGGGA	-	novel	NA	P-0040655-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	36	646	0	ENST00000409792.3:c.6712_6718del	p.Ser2238MetfsTer8	p.S2238Mfs*8	ENST00000409792	NM_014159.6	2238	TCCCAGTat/at	15/21	1	2	FACETS	0.538	0.441	0.647	0.538	0.441	0.647	SUBCLONAL	1	TRUE	1	0.216924615814717	2		646	617	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879391	56879391	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040655-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	59	850	0	ENST00000519728.1:c.908T>C	p.Val303Ala	p.V303A	ENST00000519728	NM_002350.3	303	gTg/gCg	9/13	0.216924615814717	1	FACETS	0.508	0.436	0.588	0.508	0.436	0.588	SUBCLONAL	1	TRUE	0	0.216924615814717	1		850	954	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964388	70964388	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040655-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	103	572	0	ENST00000276594.2:c.1640C>A	p.Ser547Ter	p.S547*	ENST00000276594	NM_024504.3	547	tCa/tAa	8/8	0.216924615814717	6	FACETS	0.904	0.809	1	0.452	0.404	0.503	CLONAL	2	TRUE	2	0.216924615814717	6		572	753	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039883	47039883	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040655-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	105	1038	0	ENST00000377604.3:c.1226C>A	p.Ala409Glu	p.A409E	ENST00000377604	NM_001204468.1	409	gCg/gAg	12/24	0.168087579359845	3	FACETS	1	0.917	1	0.515	0.46	0.573	CLONAL	1	TRUE	1	0.216924615814717	3		1038	1042	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0040770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	356	682	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.347695990298507	1	FACETS	0.986	0.938	1	0.986	0.938	1	CLONAL	1	TRUE	0	0.568877401084434	1		684	908	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0040770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	141	643	0	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.347695990298507	1	FACETS	0.359	0.326	0.393	0.359	0.326	0.393	SUBCLONAL	1	TRUE	0	0.568877401084434	1		643	989	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0040770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	49	276	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.296264585690373	0	FACETS	0.229	0.195	0.267			1	INDETERMINATE	1	TRUE	0	0.568877401084434	0		276	324	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0040770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	99	428	0	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	0.250201719784027	1	FACETS	0.497	0.445	0.552	0.497	0.445	0.552	INDETERMINATE	1	TRUE	0	0.568877401084434	1		428	501	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0040770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	99	716	3	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	0.347695990298507	1	FACETS	0.283	0.252	0.316	0.283	0.252	0.316	SUBCLONAL	1	TRUE	0	0.568877401084434	1		719	879	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936995	48936995	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778842	NA	P-0040770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	158	432	0	ENST00000267163.4:c.763C>T	p.Arg255Ter	p.R255*	ENST00000267163	NM_000321.2	255	Cga/Tga	8/27	0.568877401084434	1	FACETS	0.872	0.806	0.939	0.872	0.806	0.939	CLONAL	1	TRUE	0	0.568877401084434	1		432	456	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912359	97912359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554302947	NA	P-0040770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	64	437	0	ENST00000289081.3:c.532G>A	p.Glu178Lys	p.E178K	ENST00000289081	NM_000136.2	178	Gag/Aag	7/15	1	2	FACETS	0.396	0.343	0.454	0.396	0.343	0.454	SUBCLONAL	1	TRUE	1	0.568877401084434	2		437	568	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37083821	37083821	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs56185292	NA	P-0040770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	102	434	0	ENST00000231790.2:c.1730C>T	p.Ser577Leu	p.S577L	ENST00000231790	NM_000249.3	577	tCg/tTg	15/19	0.568877401084434	3	FACETS	0.528	0.471	0.588	0.264	0.235	0.294	SUBCLONAL	1	TRUE	1	0.568877401084434	3		434	873	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661663	227661664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761880048	NA	P-0040770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	210	1044	17	ENST00000305123.5:c.1791dup	p.His598AlafsTer13	p.H598Afs*13	ENST00000305123	NM_005544.2	597	-/G	1/2	1	2	FACETS	0.915	0.851	0.98	0.915	0.851	0.98	CLONAL	1	TRUE	1	0.568877401084434	2		1061	807	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813031	76813031	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	242	586	0	ENST00000373344.5:c.6590G>A	p.Arg2197His	p.R2197H	ENST00000373344	NM_000489.3	2197	cGt/cAt	30/35	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.568877401084434	2		586	769	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775583	39775583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369318352	NA	P-0040770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	93	583	3	ENST00000288319.7:c.437C>T	p.Ala146Val	p.A146V	ENST00000288319	NM_182918.3	146	gCg/gTg	4/10	1	2	FACETS	0.416	0.369	0.466	0.416	0.369	0.466	SUBCLONAL	1	TRUE	1	0.568877401084434	2		586	786	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599048	28599048	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781675235	NA	P-0040770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	239	718	0	ENST00000241453.7:c.2240C>T	p.Pro747Leu	p.P747L	ENST00000241453	NM_004119.2	747	cCg/cTg	18/24	0.568877401084434	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.568877401084434	1		718	538	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111012	193111012	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	37	258	0	ENST00000367435.3:c.545T>A	p.Ile182Asn	p.I182N	ENST00000367435	NM_024529.4	182	aTt/aAt	7/17	0.568877401084434	3	FACETS	0.426	0.352	0.51	0.213	0.176	0.255	SUBCLONAL	1	TRUE	1	0.568877401084434	3		258	392	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591739	38591739	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	87	475	0	ENST00000299084.4:c.198G>T	p.Arg66Ser	p.R66S	ENST00000299084	NM_152594.2	66	agG/agT	2/7	1	2	FACETS	0.479	0.425	0.538	0.479	0.425	0.538	SUBCLONAL	1	TRUE	1	0.568877401084434	2		475	638	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354452	91354452	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	30	404	2	ENST00000355112.3:c.3892G>T	p.Gly1298Trp	p.G1298W	ENST00000355112	NM_000057.2	1298	Ggg/Tgg	21/22	1	2	FACETS	0.184	0.148	0.226	0.184	0.148	0.226	SUBCLONAL	1	TRUE	1	0.568877401084434	2		406	572	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652263	3652263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750475726	NA	P-0040770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	156	868	0	ENST00000294008.3:c.806C>T	p.Ala269Val	p.A269V	ENST00000294008	NM_032444.2	269	gCc/gTc	4/15	1	2	FACETS	0.47	0.429	0.512	0.47	0.429	0.512	SUBCLONAL	1	TRUE	1	0.568877401084434	2		868	1168	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118604	17118604	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs535236784	NA	P-0040770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	52	707	0	ENST00000285071.4:c.1327G>A	p.Ala443Thr	p.A443T	ENST00000285071	NM_144997.5	443	Gca/Aca	12/14	1	2	FACETS	0.199	0.168	0.233	0.199	0.168	0.233	SUBCLONAL	1	TRUE	1	0.568877401084434	2		707	919	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220175	36220175	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	49	741	0	ENST00000222270.7:c.4895C>T	p.Ala1632Val	p.A1632V	ENST00000222270	NM_014727.1	1632	gCt/gTt	22/37	1	2	FACETS	0.178	0.15	0.209	0.178	0.15	0.209	SUBCLONAL	1	TRUE	1	0.568877401084434	2		741	968	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940517	49940517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151106960	NA	P-0040770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1280	389	1012	0	ENST00000296474.3:c.526G>A	p.Asp176Asn	p.D176N	ENST00000296474	NM_002447.2	176	Gac/Aac	1/20	0.568877401084434	3	FACETS	1	0.977	1	0.526	0.499	0.555	CLONAL	1	TRUE	1	0.568877401084434	3		1012	1669	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141565999	141565999	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040770-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	69	474	0	ENST00000220592.5:c.1265del	p.Gly422AlafsTer46	p.G422Afs*46	ENST00000220592	NM_012154.3	422	gGc/gc	10/19	1	2	FACETS	0.4	0.348	0.456	0.4	0.348	0.456	SUBCLONAL	1	TRUE	1	0.568877401084434	2		474	607	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207021	1207021	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913324	NA	P-0040984-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	342	778	0	ENST00000326873.7:c.109C>T	p.Gln37Ter	p.Q37*	ENST00000326873	NM_000455.4	37	Cag/Tag	1/10	0.267435806814076	2	FACETS	0.928	0.877	0.98	0.928	0.877	0.98	CLONAL	2	TRUE	0	0.283097253898708	2		778	1302	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0040984-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	137	387	2	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.267435806814076	2	FACETS	0.955	0.874	1	0.955	0.874	1	CLONAL	2	TRUE	0	0.283097253898708	2		389	507	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs869025608	NA	P-0040984-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	310	586	0	ENST00000307102.5:c.171G>T	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaT	2/11	0.283097253898708	5	FACETS	0.932	0.879	0.986	0.932	0.879	0.986	CLONAL	3	TRUE	2	0.283097253898708	5		586	1116	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602698	10602698	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040984-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	345	913	1	ENST00000171111.5:c.880G>T	p.Asp294Tyr	p.D294Y	ENST00000171111	NM_203500.1	294	Gac/Tac	3/6	0.267435806814076	2	FACETS	0.94	0.889	0.992	0.94	0.889	0.992	CLONAL	2	TRUE	0	0.283097253898708	2		914	1296	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994779	73994779	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040984-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	457	809	0	ENST00000318443.5:c.263C>G	p.Ala88Gly	p.A88G	ENST00000318443	NM_001024736.1	88	gCc/gGc	3/10	0.283097253898708	5	FACETS	0.992	0.946	1	0.992	0.946	1	CLONAL	3	TRUE	2	0.283097253898708	5		809	1545	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762459	41762497	+	inframe_deletion	In_Frame_Del	DEL	CAAGTGGATTGCCATTGAGAGTCTAGCTGACCGTGTCTA	CAAGTGGATTGCCATTGAGAGTCTAGCTGACCGTGTCTA	-	novel	NA	P-0040984-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	97	671	0	ENST00000301178.4:c.2141_2179del	p.Lys714_Tyr726del	p.K714_Y726del	ENST00000301178	NM_021913.4	713	gtCAAGTGGATTGCCATTGAGAGTCTAGCTGACCGTGTCTAc/gtc	18/20	0.267435806814076	2	FACETS	0.741	0.659	0.828	0.37	0.329	0.414	SUBCLONAL	1	TRUE	0	0.283097253898708	2		671	925	SUCCESS
APC	324	MSKCC	GRCh37	5	112173673	112173673	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040984-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	70	404	0	ENST00000257430.4:c.2382T>A	p.Ser794Arg	p.S794R	ENST00000257430	NM_000038.5	794	agT/agA	16/16	0.267435806814076	2	FACETS	1	0.908	1	0.524	0.458	0.595	CLONAL	1	TRUE	0	0.283097253898708	2		404	472	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236107	108236107	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042086-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	80	584	0	ENST00000278616.4:c.9043G>A	p.Glu3015Lys	p.E3015K	ENST00000278616	NM_000051.3	3015	Gag/Aag	63/63	0.212408719474608	3	FACETS	0.997	0.882	1	0.664	0.588	0.746	CLONAL	2	TRUE	0	0.212408719474608	3		584	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0042157-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	307	1080	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.310005591525206	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.310005591525206	1		1080	1164	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0042157-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	241	552	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.310005591525206	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.310005591525206	1		553	1075	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976872	55976872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs551579207	NA	P-0042157-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	120	656	0	ENST00000263923.4:c.1040G>A	p.Arg347His	p.R347H	ENST00000263923	NM_002253.2	347	cGt/cAt	8/30	1	2	FACETS	0.771	0.695	0.852	0.771	0.695	0.852	SUBCLONAL	1	TRUE	1	0.310005591525206	2		656	1004	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591888	48591888	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519739	NA	P-0042157-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	72	623	0	ENST00000342988.3:c.1051G>C	p.Asp351His	p.D351H	ENST00000342988	NM_005359.5	351	Gat/Cat	9/12	0.249675986267148	2	FACETS	0.624	0.544	0.709	0.312	0.272	0.355	SUBCLONAL	1	TRUE	0	0.310005591525206	2		623	745	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910685	29910685	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs199474408	NA	P-0042157-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1878	165	1494	0	ENST00000376809.5:c.225G>A	p.Trp75Ter	p.W75*	ENST00000376809	NM_002116.7	75	tgG/tgA	2/8	0.254667337102602	4	FACETS	0.683	0.624	0.745	0.341	0.312	0.373	SUBCLONAL	1	TRUE	2	0.310005591525206	4		1494	2043	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339974	116339974	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042157-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	155	498	0	ENST00000397752.3:c.836T>C	p.Ile279Thr	p.I279T	ENST00000397752	NM_000245.2	279	aTc/aCc	2/21	0.246448322032643	3	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	1	0.310005591525206	3		498	563	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827310	72827310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042157-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	89	874	0	ENST00000268489.5:c.9271C>T	p.Leu3091Phe	p.L3091F	ENST00000268489	NM_006885.3	3091	Ctt/Ttt	9/10	0.310005591525206	2	FACETS	0.483	0.426	0.543	0.241	0.213	0.272	SUBCLONAL	1	TRUE	0	0.310005591525206	2		874	1190	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100108	11100108	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042157-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	110	705	0	ENST00000358026.2:c.1234T>G	p.Phe412Val	p.F412V	ENST00000358026	NM_001128849.1	412	Ttc/Gtc	7/36	0.249675986267148	2	FACETS	0.737	0.661	0.818	0.368	0.33	0.409	SUBCLONAL	1	TRUE	0	0.310005591525206	2		705	963	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467877	66467877	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042157-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	55	444	0	ENST00000273854.3:c.392A>C	p.Lys131Thr	p.K131T	ENST00000273854	NM_004439.5	131	aAa/aCa	3/18	1	2	FACETS	0.723	0.619	0.836	0.723	0.619	0.836	SUBCLONAL	1	TRUE	1	0.310005591525206	2		444	491	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155986	106155986	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042157-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	69	418	0	ENST00000380013.4:c.887G>A	p.Cys296Tyr	p.C296Y	ENST00000380013	NM_001127208.2	296	tGt/tAt	3/11	1	2	FACETS	0.961	0.84	1	0.961	0.84	1	CLONAL	1	TRUE	1	0.310005591525206	2		418	463	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176700673	176700673	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042157-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	73	477	0	ENST00000439151.2:c.5510C>G	p.Ala1837Gly	p.A1837G	ENST00000439151	NM_022455.4	1837	gCt/gGt	17/23	0.310005591525206	3	FACETS	0.733	0.64	0.833	0.367	0.32	0.417	SUBCLONAL	1	TRUE	1	0.310005591525206	3		477	742	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0042517-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	52	323	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.789	0.672	0.917	1	0.967	1	CLONAL	2	TRUE	1	0.13	2		323	507	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0042517-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	31	277	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	TRUE	1	0.13	2		277	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0042517-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	51	593	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.13	2		593	658	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971167	21971167	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042517-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	24	400	0	ENST00000304494.5:c.191T>C	p.Leu64Pro	p.L64P	ENST00000304494	NM_000077.4	64	cTg/cCg	2/3	1	2	FACETS	0.786	0.615	0.984	0.786	0.615	0.984	CLONAL	1	TRUE	1	0.13	2		400	470	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974776	21974794	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCAGCCAGTCAGCCGAA	GGCCAGCCAGTCAGCCGAA	-	novel	NA	P-0042517-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	7	271	0	ENST00000304494.5:c.33_51del	p.Ser12ArgfsTer8	p.S12Rfs*8	ENST00000304494	NM_000077.4	11	ccTTCGGCTGACTGGCTGGCC/cc	1/3	1	2	FACETS	0.483	0.3	0.725	0.483	0.3	0.725	SUBCLONAL	1	TRUE	1	0.13	2		271	223	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81534602	81534602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151211603	NA	P-0042517-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	23	305	0	ENST00000298171.2:c.247G>A	p.Val83Ile	p.V83I	ENST00000298171	NM_000369.2	83	Gta/Ata	3/10	1	2	FACETS	0.956	0.745	1	0.956	0.745	1	CLONAL	1	TRUE	1	0.13	2		305	370	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859921	151859922	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0042517-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	23	402	0	ENST00000262189.6:c.10740_10741del	p.His3580GlnfsTer15	p.H3580Qfs*15	ENST00000262189	NM_170606.2	3580	caCAgt/cagt	43/59	1	2	FACETS	0.912	0.71	1	0.912	0.71	1	CLONAL	1	TRUE	1	0.13	2		402	388	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	67	516	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.991	0.863	1	0.991	0.863	1	CLONAL	1	TRUE	1	0.28	2		516	483	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0042865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	84	1065	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	0.668	0.589	0.753	0.668	0.589	0.753	SUBCLONAL	1	TRUE	1	0.28	2		1065	898	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0042865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	154	1080	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.28	2		1080	978	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724339	52724339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs969720045	NA	P-0042865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	49	716	0	ENST00000322088.6:c.1471G>A	p.Gly491Arg	p.G491R	ENST00000322088	NM_014225.5	491	Gga/Aga	12/15	0.138062215478413	3	FACETS	0.534	0.451	0.626	0.267	0.225	0.313	INDETERMINATE	1	TRUE	1	0.28	3		716	747	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038859	12038859	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0042865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	29	296	0	ENST00000396373.4:c.1153-1G>A		p.X385_splice	ENST00000396373	NM_001987.4	385			0.138062215478413	3	FACETS	0.61	0.49	0.747	0.305	0.245	0.374	INDETERMINATE	1	TRUE	1	0.28	3		296	387	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106973	27106973	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	45	688	1	ENST00000324856.7:c.6584T>A	p.Leu2195His	p.L2195H	ENST00000324856	NM_006015.4	2195	cTc/cAc	20/20	1	2	FACETS	0.516	0.433	0.608	0.516	0.433	0.608	SUBCLONAL	1	TRUE	1	0.28	2		689	623	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050980	49050981	+	splice_donor_variant	Splice_Site	DEL	GT	GT	-	novel	NA	P-0042865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	24	246	0	ENST00000267163.4:c.2663+1_2663+2del		p.X888_splice	ENST00000267163	NM_000321.2	888			1	2	FACETS	0.506	0.396	0.632	0.506	0.396	0.632	SUBCLONAL	1	TRUE	1	0.28	2		246	339	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061558	38061559	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0042865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	34	445	0	ENST00000250448.2:c.430dup	p.Ala144GlyfsTer83	p.A144Gfs*83	ENST00000250448	NM_004496.3	144	gcg/gGcg	2/2	1	2	FACETS	0.637	0.521	0.768	0.637	0.521	0.768	SUBCLONAL	1	TRUE	1	0.28	2		445	381	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0042865-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	28	530	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		530	971	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0042865-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	49	1080	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		1080	985	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0043094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	186	470	0				ENST00000310581	NM_198253.2	-/1132			0.145325119431852	3	FACETS	1	0.971	1	0.363	0.337	0.39	INDETERMINATE	1	TRUE	0	0.783880560434138	3		470	607	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0043094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	209	164	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.246270482437192	3	FACETS	0.81	0.761	0.86	0.81	0.761	0.86	INDETERMINATE	2	TRUE	1	0.783880560434138	3		164	458	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980844	40980844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	204	668	0	ENST00000373198.4:c.1642G>A	p.Glu548Lys	p.E548K	ENST00000373198	NM_133170.3	548	Gaa/Aaa	10/32	1	2	FACETS	0.933	0.872	0.995	0.933	0.872	0.995	CLONAL	1	TRUE	1	0.783880560434138	2		668	558	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812260	212812260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751175543	NA	P-0043094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	142	113	0	ENST00000342788.4:c.316C>T	p.Arg106Cys	p.R106C	ENST00000342788	NM_005235.2	106	Cgt/Tgt	3/28	1	2	FACETS	0.998	0.921	1	0.998	0.921	1	CLONAL	1	TRUE	1	0.783880560434138	2		113	363	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720803	89720804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs786204892	NA	P-0043094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	98	72	0	ENST00000371953.3:c.955dup	p.Thr319AsnfsTer6	p.T319Nfs*6	ENST00000371953	NM_000314.4	318	-/A	8/9	0.783880560434138	1	FACETS	0.768	0.703	0.833	0.768	0.703	0.833	SUBCLONAL	1	TRUE	0	0.783880560434138	1		72	198	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0043094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	838	965	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	0.762698851928844	3	FACETS	0.98	0.953	1	0.98	0.953	1	CLONAL	2	TRUE	1	0.783880560434138	3		965	1518	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716366	18716366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs935135637	NA	P-0043094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	151	187	0	ENST00000266497.5:c.3713C>T	p.Ser1238Leu	p.S1238L	ENST00000266497		1238	tCa/tTa	26/31	1	2	FACETS	0.922	0.851	0.993	0.922	0.851	0.993	CLONAL	1	TRUE	1	0.783880560434138	2		187	418	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955149	93955149	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	203	131	0	ENST00000369303.4:c.2749C>T	p.Gln917Ter	p.Q917*	ENST00000369303	NM_004440.3	917	Caa/Taa	16/17	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.783880560434138	2		131	509	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93640037	93640037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	110	345	0	ENST00000375746.1:c.1366C>T	p.Leu456Phe	p.L456F	ENST00000375746	NM_001174167.1	456	Ctc/Ttc	10/14	1	2	FACETS	0.995	0.908	1	0.995	0.908	1	CLONAL	1	TRUE	1	0.783880560434138	2		345	282	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139721	55139721	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	180	413	0	ENST00000257290.5:c.1382C>T	p.Ser461Phe	p.S461F	ENST00000257290	NM_006206.4	461	tCc/tTc	10/23	1	2	FACETS	0.979	0.912	1	0.979	0.912	1	CLONAL	1	TRUE	1	0.783880560434138	2		413	469	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073655	8073656	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0043094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	183	484	0	ENST00000377482.5:c.1003_1004delinsTT	p.Pro335Phe	p.P335F	ENST00000377482	NM_018948.3	335	CCc/TTc	4/4	1	2	FACETS	0.959	0.893	1	0.959	0.893	1	CLONAL	1	TRUE	1	0.783880560434138	2		484	487	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243102	105243102	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	264	901	0	ENST00000349310.3:c.181C>T	p.Gln61Ter	p.Q61*	ENST00000349310	NM_001014432.1	61	Cag/Tag	5/15	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.783880560434138	2		901	673	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99163051	99163051	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	186	371	0	ENST00000074304.5:c.1057C>T	p.Gln353Ter	p.Q353*	ENST00000074304	NM_001134224.1	353	Cag/Tag	13/26	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.783880560434138	2		371	435	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728857	190728857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	139	95	0	ENST00000441310.2:c.2245C>T	p.Pro749Ser	p.P749S	ENST00000441310	NM_000534.4	749	Cca/Tca	10/13	1	2	FACETS	0.974	0.898	1	0.974	0.898	1	CLONAL	1	TRUE	1	0.783880560434138	2		95	364	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520219	9520219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867360779	NA	P-0043094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	216	458	0	ENST00000353224.5:c.2050G>A	p.Glu684Lys	p.E684K	ENST00000353224	NM_177990.2	684	Gag/Aag	10/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.783880560434138	2		458	511	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566516	41566516	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	169	275	1	ENST00000263253.7:c.4393G>A	p.Glu1465Lys	p.E1465K	ENST00000263253	NM_001429.3	1465	Gaa/Aaa	27/31	1	2	FACETS	0.991	0.921	1	0.991	0.921	1	CLONAL	1	TRUE	1	0.783880560434138	2		276	435	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090558	71090558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369057936	NA	P-0043094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	208	439	0	ENST00000318789.4:c.790C>T	p.Pro264Ser	p.P264S	ENST00000318789	NM_032682.5	264	Cct/Tct	11/21	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.783880560434138	2		439	509	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665387	117665387	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	156	144	0	ENST00000368508.3:c.4360C>G	p.Pro1454Ala	p.P1454A	ENST00000368508	NM_002944.2	1454	Cca/Gca	27/43	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.783880560434138	2		144	337	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709191	117709191	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	106	234	0	ENST00000368508.3:c.1766T>A	p.Ile589Asn	p.I589N	ENST00000368508	NM_002944.2	589	aTc/aAc	13/43	1	2	FACETS	0.933	0.848	1	0.933	0.848	1	CLONAL	1	TRUE	1	0.783880560434138	2		234	290	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005563	150005563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043094-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	171	349	0	ENST00000253339.5:c.662C>T	p.Ser221Leu	p.S221L	ENST00000253339		221	tCa/tTa	3/7	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.783880560434138	2		349	427	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0043100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	80	309	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.179205714100122	3	FACETS	1	0.97	1	0.646	0.574	0.722	INDETERMINATE	1	TRUE	1	0.479862227743757	3		309	320	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0043100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	66	323	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.315383428903517	1	FACETS	0.55	0.48	0.626	0.55	0.48	0.626	SUBCLONAL	1	TRUE	0	0.479862227743757	1		323	380	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0043100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	61	353	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.479862227743757	2		353	248	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0043100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	33	206	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.936	0.774	1	0.936	0.774	1	CLONAL	1	TRUE	1	0.479862227743757	2		206	147	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1627369	1627369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35936626	NA	P-0043100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	156	672	0	ENST00000344749.5:c.355G>A	p.Gly119Ser	p.G119S	ENST00000344749	NM_001136139.2	119	Ggc/Agc	6/19	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.479862227743757	2		672	583	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314638	30314638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	99	496	1	ENST00000262643.3:c.1187C>T	p.Pro396Leu	p.P396L	ENST00000262643	NM_001238.2	396	cCg/cTg	12/12	1	2	FACETS	0.856	0.768	0.949	0.856	0.768	0.949	CLONAL	1	TRUE	1	0.479862227743757	2		497	482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577796	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTCCAGTGTGATGATGGTGAGGATGGGCCTCCGGTTCATGCCGCCCATGCAGGAACTGTTACACATGTAGTTGTAGTGGATGGTGGTACAGTCAGAGCCAACCTAGGAGATAACACAGGCCCAAGATGAGGCCAGTGCGCCTTGGGGAGACCTGTGGCAAGCAGGGGAGGCCTTTTTTTTTTTTTTTTGAGATGGAATCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGTGATCTCAGCTCACTGCAAGCTCCACCGCCCAGGTTCACGCCATTCTCCTTCCTCAGC	CTTCCAGTGTGATGATGGTGAGGATGGGCCTCCGGTTCATGCCGCCCATGCAGGAACTGTTACACATGTAGTTGTAGTGGATGGTGGTACAGTCAGAGCCAACCTAGGAGATAACACAGGCCCAAGATGAGGCCAGTGCGCCTTGGGGAGACCTGTGGCAAGCAGGGGAGGCCTTTTTTTTTTTTTTTTGAGATGGAATCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGTGATCTCAGCTCACTGCAAGCTCCACCGCCCAGGTTCACGCCATTCTCCTTCCTCAGC	-	novel	NA	P-0043100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	27	549	0	ENST00000269305.4:c.673-188_775del		p.X225_splice	ENST00000269305	NM_001126112.2	225		7/11	0.476758316610893	1	FACETS	0.29	0.231	0.357	0.29	0.231	0.357	SUBCLONAL	1	TRUE	0	0.479862227743757	1		549	295	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212269	36212269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767783057	NA	P-0043100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	98	730	0	ENST00000222270.7:c.2020C>T	p.Pro674Ser	p.P674S	ENST00000222270	NM_014727.1	674	Cct/Tct	3/37	1	2	FACETS	0.847	0.759	0.94	0.847	0.759	0.94	CLONAL	1	TRUE	1	0.479862227743757	2		730	482	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510915	157510915	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0043100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	113	370	0	ENST00000346085.5:c.3689+1G>A		p.X1230_splice	ENST00000346085	NM_020732.3	1230			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.479862227743757	2		370	365	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229269	123229269	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043100-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	53	218	0	ENST00000218089.9:c.3753C>A	p.Phe1251Leu	p.F1251L	ENST00000218089	NM_001042749.1	1251	ttC/ttA	34/35	0.380189399067094	1	FACETS	0.651	0.56	0.748	0.651	0.56	0.748	SUBCLONAL	1	TRUE	0	0.479862227743757	1		218	258	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578341	212578341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1216559792	NA	P-0043500-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	37	360	3	ENST00000342788.4:c.916C>T	p.Arg306Cys	p.R306C	ENST00000342788	NM_005235.2	306	Cgt/Tgt	8/28	1	2	FACETS	0.924	0.774	1	0.924	0.774	1	CLONAL	1	TRUE	1	0.52336709274686	2		363	153	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170345	32170345	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761015481	NA	P-0043500-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	43	959	0	ENST00000375023.3:c.3263C>T	p.Ala1088Val	p.A1088V	ENST00000375023	NM_004557.3	1088	gCc/gTc	21/30	0.329567406532175	1	FACETS	0.564	0.477	0.659	0.564	0.477	0.659	SUBCLONAL	1	TRUE	0	0.52336709274686	1		959	215	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220502	1220502	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043500-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	56	952	1	ENST00000326873.7:c.595del	p.Glu199ArgfsTer88	p.E199Rfs*88	ENST00000326873	NM_000455.4	199	Gag/ag	4/10	0.52336709274686	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.52336709274686	1		953	140	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0043769-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	170	277	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.518929219624174	3	FACETS	0.992	0.923	1	0.992	0.923	1	CLONAL	2	TRUE	1	0.518929219624174	3		277	416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0043769-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	557	976	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	0.518929219624174	2	FACETS	0.975	0.94	1	0.975	0.94	1	CLONAL	2	TRUE	0	0.518929219624174	2		976	1101	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045684	26045684	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1428894577	NA	P-0043769-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	100	365	0	ENST00000540144.1:c.46G>A	p.Ala16Thr	p.A16T	ENST00000540144	NM_003531.2	16	Gct/Act	1/1	0.518929219624174	3	FACETS	0.985	0.883	1	0.492	0.441	0.546	CLONAL	1	TRUE	1	0.518929219624174	3		365	493	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730140	41730140	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043769-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	238	400	0	ENST00000242208.4:c.389G>A	p.Gly130Glu	p.G130E	ENST00000242208	NM_002192.2	130	gGa/gAa	3/3	0.475725214830489	4	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	2	0.518929219624174	4		400	672	SUCCESS
APC	324	MSKCC	GRCh37	5	112175429	112175430	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0043769-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	158	342	0	ENST00000257430.4:c.4142dup	p.Leu1382ThrfsTer4	p.L1382Tfs*4	ENST00000257430	NM_000038.5	1380	acc/aCcc	16/16	0.518929219624174	3	FACETS	0.949	0.88	1	0.949	0.88	1	CLONAL	2	TRUE	1	0.518929219624174	3		342	404	SUCCESS
APC	324	MSKCC	GRCh37	5	112174424	112174424	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043769-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	32	180	0	ENST00000257430.4:c.3133C>T	p.Gln1045Ter	p.Q1045*	ENST00000257430	NM_000038.5	1045	Cag/Tag	16/16	0.518929219624174	3	FACETS	0.672	0.549	0.81	0.336	0.274	0.405	SUBCLONAL	1	TRUE	1	0.518929219624174	3		180	231	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119914	70119915	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043769-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	153	783	0	ENST00000245479.2:c.917dup	p.Pro307AlafsTer271	p.P307Afs*271	ENST00000245479	NM_000346.3	306	gtg/gTtg	3/3	0.518929219624174	2	FACETS	0.715	0.654	0.778	0.357	0.327	0.389	SUBCLONAL	1	TRUE	0	0.518929219624174	2		783	825	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606293	93606294	+	missense_variant	Missense_Mutation	DNP	TT	TT	AA	novel	NA	P-0043769-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1436	248	1087	1	ENST00000375746.1:c.113_114inv	p.Leu38Gln	p.L38Q	ENST00000375746	NM_001174167.1	38	cTT/cAA	2/14	0.475725214830489	4	FACETS	0.862	0.803	0.923	0.431	0.401	0.462	CLONAL	1	TRUE	2	0.518929219624174	4		1088	1684	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429353	47429353	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043769-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	180	1095	0	ENST00000377045.4:c.1482del	p.Tyr495ThrfsTer9	p.Y495Tfs*9	ENST00000377045	NM_001654.4	494	gCc/gc	14/16	0.518929219624174	3	FACETS	0.639	0.588	0.693	0.32	0.294	0.347	SUBCLONAL	1	TRUE	1	0.518929219624174	3		1095	1367	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0043949-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	138	553	0	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.782910349328763	2		553	349	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197793	123197794	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043949-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	78	185	0	ENST00000218089.9:c.1918dup	p.Cys640LeufsTer2	p.C640Lfs*2	ENST00000218089	NM_001042749.1	639	-/T	20/35	1	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.782910349328763	1		185	109	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044466-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	26	516	0				ENST00000310581	NM_198253.2	-/1132			0.719162360810426	1	FACETS	0.908	0.761	1	0.908	0.761	1	CLONAL	1	TRUE	0	0.719162360810426	1		516	51	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95556989	95556989	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044466-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	19	407	0	ENST00000393063.1:c.5615G>T	p.Arg1872Ile	p.R1872I	ENST00000393063	NM_030621.3	1872	aGa/aTa	28/28	NA	2	FACETS	0.184	0.139	0.237			1	INDETERMINATE	1	TRUE	NA	0.719162360810426	2		407	287	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43742119	43742119	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044466-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	222	722	0	ENST00000523873.1:c.108T>A	p.Asn36Lys	p.N36K	ENST00000523873		36	aaT/aaA	2/8	0.718995253372995	4	FACETS	0.777	0.727	0.828	0.777	0.727	0.828	SUBCLONAL	2	TRUE	2	0.719162360810426	4		722	683	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044554-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	103	516	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.647059428875006	2		516	262	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0044554-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	110	258	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.647059428875006	2		258	253	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0044554-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	138	467	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	FALSE	1	0.647059428875006	2		467	423	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591891	48591891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912581	NA	P-0044554-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	158	338	0	ENST00000342988.3:c.1054G>A	p.Gly352Arg	p.G352R	ENST00000342988	NM_005359.5	352	Gga/Aga	9/12	0.647059428875006	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	FALSE	0	0.647059428875006	2		338	211	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733044	74733044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044554-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	174	465	0	ENST00000359995.5:c.199G>A	p.Asp67Asn	p.D67N	ENST00000359995	NM_001195427.1	67	Gac/Aac	1/3	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	FALSE	1	0.647059428875006	2		465	528	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741925	162741925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044554-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	110	342	0	ENST00000367921.3:c.1616C>T	p.Ser539Leu	p.S539L	ENST00000367921	NM_006182.2	539	tCa/tTa	13/18	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.647059428875006	2		342	288	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478795	56478795	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1425922004	NA	P-0044554-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	173	419	0	ENST00000267101.3:c.251C>G	p.Thr84Arg	p.T84R	ENST00000267101	NM_001982.3	84	aCa/aGa	3/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.647059428875006	2		419	448	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428216	72428216	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044554-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	91	310	0	ENST00000477973.2:c.676A>G	p.Thr226Ala	p.T226A	ENST00000477973	NM_012234.5	226	Acc/Gcc	3/4	0.394798084012752	1	FACETS	0.831	0.742	0.926	0.831	0.742	0.926	CLONAL	1	FALSE	0	0.394798084012752	1		310	445	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778781	76778781	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044984-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	106	200	0	ENST00000373344.5:c.6798G>C	p.Leu2266Phe	p.L2266F	ENST00000373344	NM_000489.3	2266	ttG/ttC	31/35	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.727729320768679	1		200	149	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0045209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	42	671	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	1	2	FACETS	0.913	0.763	1	0.913	0.763	1	CLONAL	1	TRUE	1	0.2	2		671	460	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0045209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	65	708	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.2	2		708	548	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0045209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	9	274	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	0.738	0.491	1	0.738	0.491	1	CLONAL	1	TRUE	1	0.2	2		274	122	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186757	108186757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs864622251	NA	P-0045209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	22	437	0	ENST00000278616.4:c.6115G>A	p.Glu2039Lys	p.E2039K	ENST00000278616	NM_000051.3	2039	Gaa/Aaa	42/63	1	2	FACETS	0.671	0.52	0.846	0.671	0.52	0.846	SUBCLONAL	1	TRUE	1	0.2	2		437	328	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs199469672	NA	P-0045387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	224	548	0	ENST00000374080.3:c.131G>C	p.Gly44Ala	p.G44A	ENST00000374080		44	gGt/gCt	2/45	0.703474076295349	3	FACETS	0.961	0.907	1	0.961	0.907	1	CLONAL	2	TRUE	1	0.703474076295349	3		548	448	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500488	149500488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1060499540	NA	P-0045387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	155	651	0	ENST00000261799.4:c.2549A>T	p.Asp850Val	p.D850V	ENST00000261799	NM_002609.3	850	gAc/gTc	18/23	0.703474076295349	3	FACETS	0.98	0.901	1	0.49	0.45	0.531	CLONAL	1	TRUE	1	0.703474076295349	3		651	608	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813023	89813023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142833057	NA	P-0045387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	122	304	0	ENST00000389301.3:c.3482C>T	p.Thr1161Met	p.T1161M	ENST00000389301	NM_000135.2	1161	aCg/aTg	35/43	1	2	FACETS	0.932	0.873	0.99	1	0.992	1	CLONAL	2	TRUE	1	0.703474076295349	2		304	186	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39311685	39311685	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	116	567	0	ENST00000373001.3:c.974T>G	p.Val325Gly	p.V325G	ENST00000373001	NM_022157.3	325	gTc/gGc	6/7	0.60333488759209	4	FACETS	0.722	0.651	0.797	0.361	0.325	0.399	SUBCLONAL	1	TRUE	2	0.703474076295349	4		567	778	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844801	156844801	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs764771898	NA	P-0045387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	131	599	0	ENST00000524377.1:c.1354+1G>A		p.X452_splice	ENST00000524377	NM_002529.3	452			0.703474076295349	3	FACETS	1	0.914	1	0.5	0.457	0.546	CLONAL	1	TRUE	1	0.703474076295349	3		599	503	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999598	100999598	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	345	986	0	ENST00000325455.5:c.204C>G	p.Asp68Glu	p.D68E	ENST00000325455	NM_001202474.3	68	gaC/gaG	1/8	0.681721710857158	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.703474076295349	2		986	452	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836665	89836665	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	122	751	2	ENST00000389301.3:c.2225A>G	p.Gln742Arg	p.Q742R	ENST00000389301	NM_000135.2	742	cAg/cGg	25/43	1	2	FACETS	0.961	0.878	1	0.961	0.878	1	CLONAL	1	TRUE	1	0.703474076295349	2		753	361	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31020721	31020721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1180014276	NA	P-0045387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	139	258	0	ENST00000375687.4:c.1018G>A	p.Glu340Lys	p.E340K	ENST00000375687	NM_015338.5	340	Gaa/Aaa	11/13	0.651012499108445	4	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	2	0.703474076295349	4		258	331	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574131	41574131	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	88	534	0	ENST00000263253.7:c.6416G>A	p.Gly2139Asp	p.G2139D	ENST00000263253	NM_001429.3	2139	gGc/gAc	31/31	1	2	FACETS	0.973	0.876	1	0.973	0.876	1	CLONAL	1	TRUE	1	0.703474076295349	2		534	257	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50358672	50358672	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs374267123	NA	P-0045387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	15	179	0	ENST00000331340.3:c.15G>C	p.Glu5Asp	p.E5D	ENST00000331340	NM_006060.4	5	gaG/gaC	2/8	0.651012499108445	4	FACETS	0.265	0.193	0.351	0.133	0.096	0.176	SUBCLONAL	1	TRUE	2	0.703474076295349	4		179	274	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845575	128845575	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs948837758	NA	P-0045387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	55	624	0	ENST00000249373.3:c.872G>A	p.Arg291Gln	p.R291Q	ENST00000249373	NM_005631.4	291	cGa/cAa	4/12	0.651012499108445	4	FACETS	0.426	0.364	0.494	0.213	0.182	0.247	SUBCLONAL	1	TRUE	2	0.703474076295349	4		624	625	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974762	21974763	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	T	novel	NA	P-0045387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	104	269	0	ENST00000304494.5:c.64_65delinsA	p.Gly23ValfsTer3	p.G23Vfs*3	ENST00000304494	NM_000077.4	22	CGg/Ag	1/3	0.703474076295349	2	FACETS	0.817	0.754	0.878	0.817	0.754	0.878	CLONAL	2	TRUE	0	0.703474076295349	2		269	181	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500452	149500456	+	protein_altering_variant,splice_region_variant	In_Frame_Del	DEL	CTGCC	CTGCC	AA	novel	NA	P-0045387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	120	468	0	ENST00000261799.4:c.2581_2585delinsTT	p.Gly861_Ser862delinsPhe	p.G861_S862delinsF	ENST00000261799	NM_002609.3	861	GGCAGc/TTc	18/23	0.703474076295349	3	FACETS	0.917	0.832	1	0.458	0.416	0.503	CLONAL	1	TRUE	1	0.703474076295349	3		468	503	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045684-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	34	516	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.994	0.814	1	0.994	0.814	1	CLONAL	1	TRUE	1	0.2	2		516	342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0045684-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	74	1013	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.695	0.607	0.792	0.695	0.607	0.792	SUBCLONAL	1	TRUE	1	0.2	2		1013	1064	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0045684-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	124	277	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.966	1	1	0.991	1	CLONAL	2	TRUE	1	0.2	2		277	547	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933761	39933761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763713717	NA	P-0045684-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	50	871	3	ENST00000378444.4:c.838G>A	p.Val280Ile	p.V280I	ENST00000378444	NM_001123385.1	280	Gtc/Atc	4/15	1	2	FACETS	0.608	0.515	0.712	0.608	0.515	0.712	SUBCLONAL	1	TRUE	1	0.2	2		874	822	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495336	56495336	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045684-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	46	581	0	ENST00000267101.3:c.3526A>G	p.Thr1176Ala	p.T1176A	ENST00000267101	NM_001982.3	1176	Acc/Gcc	28/28	1	2	FACETS	0.557	0.467	0.656	0.557	0.467	0.656	SUBCLONAL	1	TRUE	1	0.2	2		581	826	SUCCESS
APC	324	MSKCC	GRCh37	5	112178462	112178462	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1554088100	NA	P-0045684-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	31	161	0	ENST00000257430.4:c.7171A>G	p.Ile2391Val	p.I2391V	ENST00000257430	NM_000038.5	2391	Att/Gtt	16/16	1	2	FACETS	0.934	0.757	1	0.934	0.757	1	CLONAL	1	TRUE	1	0.2	2		161	332	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0045905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	22	470	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.657	0.509	0.829	0.657	0.509	0.829	SUBCLONAL	1	TRUE	1	0.2	2		470	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0045905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	61	597	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	1	2	FACETS	0.91	0.785	1	0.91	0.785	1	CLONAL	1	TRUE	1	0.2	2		597	670	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679762	30679762	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	41	567	0	ENST00000376406.3:c.1957G>C	p.Asp653His	p.D653H	ENST00000376406	NM_014641.2	653	Gac/Cac	5/15	0.476842158133182	3	FACETS	0.741	0.616	0.88	0.37	0.308	0.44	SUBCLONAL	1	TRUE	1	0.2	3		567	609	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40371821	40371821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1326533398	NA	P-0045905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	30	661	1	ENST00000293328.3:c.590G>A	p.Arg197His	p.R197H	ENST00000293328	NM_012448.3	197	cGt/cAt	6/19	0.19111935896234	1	FACETS	0.479	0.385	0.586	0.479	0.385	0.586	SUBCLONAL	1	TRUE	0	0.2	1		662	564	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424968	49424969	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0045905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	37	596	0	ENST00000301067.7:c.13519dup	p.Ser4507LysfsTer68	p.S4507Kfs*68	ENST00000301067	NM_003482.3	4507	agc/aAgc	39/54	1	2	FACETS	0.608	0.5	0.729	0.608	0.5	0.729	SUBCLONAL	1	TRUE	1	0.2	2		596	609	SUCCESS
APC	324	MSKCC	GRCh37	5	112178367	112178367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1411349043	NA	P-0045905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	21	325	0	ENST00000257430.4:c.7076C>T	p.Ser2359Leu	p.S2359L	ENST00000257430	NM_000038.5	2359	tCa/tTa	16/16	1	2	FACETS	0.585	0.45	0.743	0.585	0.45	0.743	SUBCLONAL	1	TRUE	1	0.2	2		325	359	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679865	30679865	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	24	522	0	ENST00000376406.3:c.1854G>C	p.Glu618Asp	p.E618D	ENST00000376406	NM_014641.2	618	gaG/gaC	5/15	0.476842158133182	3	FACETS	0.555	0.434	0.695	0.277	0.217	0.348	SUBCLONAL	1	TRUE	1	0.2	3		522	476	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679975	30679975	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	34	519	0	ENST00000376406.3:c.1744G>C	p.Glu582Gln	p.E582Q	ENST00000376406	NM_014641.2	582	Gag/Cag	5/15	0.476842158133182	3	FACETS	0.786	0.641	0.948	0.393	0.32	0.474	CLONAL	1	TRUE	1	0.2	3		519	476	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679987	30679987	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045905-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	34	542	0	ENST00000376406.3:c.1732G>T	p.Glu578Ter	p.E578*	ENST00000376406	NM_014641.2	578	Gaa/Taa	5/15	0.476842158133182	3	FACETS	0.753	0.614	0.909	0.376	0.307	0.455	CLONAL	1	TRUE	1	0.2	3		542	497	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782191	9782191	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs755934302	NA	P-0045936-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	53	828	0	ENST00000377346.4:c.2214C>A	p.Ser738Arg	p.S738R	ENST00000377346	NM_005026.3	738	agC/agA	17/24	0.238557355120696	2	FACETS	0.179	0.152	0.209	0.09	0.076	0.105	INDETERMINATE	1	TRUE	0	0.715479647189917	2		828	826	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400358	225400358	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045936-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	28	234	0	ENST00000264414.4:c.265G>T	p.Val89Leu	p.V89L	ENST00000264414	NM_003590.4	89	Gtg/Ttg	3/16	0.238557355120696	2	FACETS	0.301	0.241	0.369	0.151	0.12	0.185	INDETERMINATE	1	TRUE	0	0.715479647189917	2		234	260	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0045946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	441	658	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.604023983341151	3	FACETS	0.885	0.856	0.914	0.885	0.856	0.914	CLONAL	3	TRUE	0	0.67816591331558	3		658	656	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858039	152858039	+	synonymous_variant	Silent	SNP	C	C	T	rs781829925	NA	P-0045946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	120	482	0	ENST00000406277.2:c.576G>A	p.Ala192=	p.A192=	ENST00000406277	NM_152274.4	192	gcG/gcA	6/7	0.341239484401562	1	FACETS	0.79	0.725	0.857	0.79	0.725	0.857	INDETERMINATE	1	TRUE	0	0.67816591331558	1		482	296	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99472785	99472785	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0045946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	89	472	1	ENST00000268035.6:c.2783-2A>G		p.X928_splice	ENST00000268035	NM_000875.3	928			1	2	FACETS	0.969	0.871	1	0.969	0.871	1	CLONAL	1	TRUE	1	0.67816591331558	2		473	271	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41222997	41222998	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	G	novel	NA	P-0045946-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	159	774	0	ENST00000357654.3:c.4933_4934delinsC	p.Val1646SerfsTer12	p.V1646Sfs*12	ENST00000357654	NM_007294.3	1645	AGg/Cg	15/23	0.67816591331558	1	FACETS	0.931	0.868	0.994	0.931	0.868	0.994	CLONAL	1	TRUE	0	0.67816591331558	1		774	333	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0046077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	415	470	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.835458928151998	2		470	864	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0046077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1698	13558	756	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.835458928151998	31	FACETS	0.996	0.993	1	0.93	0.926	0.934	CLONAL	28	TRUE	1	0.835458928151998	31		756	15256	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217011	2217026	+	frameshift_variant	Frame_Shift_Del	DEL	CATGAAGCTGAGCCCT	CATGAAGCTGAGCCCT	-	novel	NA	P-0046077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1797	640	1164	0	ENST00000398665.3:c.2468_2483del	p.Met823ArgfsTer23	p.M823Rfs*23	ENST00000398665	NM_032482.2	822	agCATGAAGCTGAGCCCT/ag	21/28	0.835458928151998	3	FACETS	0.891	0.855	0.928	0.297	0.285	0.31	CLONAL	1	TRUE	0	0.835458928151998	3		1164	2437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0046131-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	153	665	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	1	2	FACETS	0.969	0.885	1	0.969	0.885	1	CLONAL	1	FALSE	1	0.3	2		665	1053	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0046262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	595	1078	6	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.921531447124075	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.921531447124075	1		1084	671	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041439	47041439	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	556	293	0	ENST00000377604.3:c.1783C>T	p.Gln595Ter	p.Q595*	ENST00000377604	NM_001204468.1	595	Cag/Tag	16/24	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.921531447124075	1		293	605	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652250	36652251	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGC	novel	NA	P-0046262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	609	618	0	ENST00000244741.5:c.373_376dup	p.Gln126ArgfsTer4	p.Q126Rfs*4	ENST00000244741	NM_000389.4	124	-/GAGC	2/3	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	1	TRUE	NA	0.921531447124075	2		618	1082	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433527	49433527	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	776	884	0	ENST00000301067.7:c.8026G>C	p.Glu2676Gln	p.E2676Q	ENST00000301067	NM_003482.3	2676	Gag/Cag	31/54	1	2	FACETS	0.997	0.965	1	0.997	0.965	1	CLONAL	1	TRUE	1	0.921531447124075	2		884	1690	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69203049	69203049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	254	378	0	ENST00000462284.1:c.76C>T	p.Pro26Ser	p.P26S	ENST00000462284	NM_002392.5	26	Cca/Tca	2/11	1	2	FACETS	0.923	0.871	0.976	0.923	0.871	0.976	CLONAL	1	TRUE	1	0.921531447124075	2		378	597	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527680	103527680	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	53	208	0	ENST00000355739.4:c.2988C>G	p.Phe996Leu	p.F996L	ENST00000355739	NM_000123.3	996	ttC/ttG	15/15	1	2	FACETS	0.481	0.415	0.553	0.481	0.415	0.553	SUBCLONAL	1	TRUE	1	0.921531447124075	2		208	239	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708587	43708587	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	202	462	0	ENST00000382044.4:c.4709C>G	p.Ser1570Cys	p.S1570C	ENST00000382044	NM_001141980.1	1570	tCt/tGt	22/28	0.480162416165839	1	FACETS	0.355	0.331	0.381	0.355	0.331	0.381	INDETERMINATE	1	TRUE	0	0.921531447124075	1		462	665	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198272733	198272733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	236	416	0	ENST00000335508.6:c.1228G>A	p.Glu410Lys	p.E410K	ENST00000335508	NM_012433.2	410	Gaa/Aaa	9/25	0.480162416165839	1	FACETS	0.712	0.677	0.746	0.712	0.677	0.746	INDETERMINATE	1	TRUE	0	0.921531447124075	1		416	388	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295219	1295222	+	upstream_gene_variant	5'Flank	DEL	GGGC	GGGC	-	novel	NA	P-0046262-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	121	269	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.45	0.408	0.495			1	INDETERMINATE	1	TRUE	NA	0.921531447124075	2		269	583	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0046331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	402	691	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.567544569205479	2	FACETS	0.882	0.847	0.917	0.882	0.847	0.917	CLONAL	2	TRUE	0	0.643671411317529	2		691	708	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950818	32950818	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	130	295	0	ENST00000380152.3:c.8644A>G	p.Lys2882Glu	p.K2882E	ENST00000380152		2882	Aaa/Gaa	21/27	1	2	FACETS	0.948	0.867	1	0.948	0.867	1	CLONAL	1	TRUE	1	0.643671411317529	2		295	426	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30310116	30310116	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	14	51	0	ENST00000322652.5:c.1016A>G	p.Asp339Gly	p.D339G	ENST00000322652	NM_015355.2	339	gAt/gGt	9/16	NA	2	FACETS	0.68	0.503	0.881			1	INDETERMINATE	1	TRUE	NA	0.643671411317529	2		51	64	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348289	70348289	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046331-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	283	528	0	ENST00000374080.3:c.3353A>G	p.Asp1118Gly	p.D1118G	ENST00000374080		1118	gAt/gGt	23/45	0.643671411317529	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.643671411317529	1		528	559	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39708807	39708807	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	80	241	0	ENST00000361337.2:c.418C>G	p.Arg140Gly	p.R140G	ENST00000361337	NM_003286.2	140	Cga/Gga	6/21	1	2	FACETS	0.912	0.811	1	0.912	0.811	1	CLONAL	1	TRUE	1	0.571412518799445	2		241	307	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037865	49037865	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0046437-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	244	261	0	ENST00000267163.4:c.2107-2A>G		p.X703_splice	ENST00000267163	NM_000321.2	703			0.48574356826546	3	FACETS	0.946	0.898	0.994	0.946	0.898	0.994	CLONAL	3	TRUE	0	0.48574356826546	3		261	440	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046437-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	499	745	0	ENST00000269305.4:c.329del	p.Arg110LeufsTer13	p.R110Lfs*13	ENST00000269305	NM_001126112.2	110	cGt/ct	4/11	0.37370952250192	3	FACETS	0.838	0.806	0.87	0.838	0.806	0.87	CLONAL	3	TRUE	0	0.48574356826546	3		745	1016	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151871270	151871270	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046437-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	277	446	0	ENST00000262189.6:c.9320T>C	p.Ile3107Thr	p.I3107T	ENST00000262189	NM_170606.2	3107	aTa/aCa	39/59	0.425764300349107	3	FACETS	0.889	0.838	0.941	0.889	0.838	0.941	CLONAL	2	TRUE	1	0.48574356826546	3		446	797	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5258067	5258067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046437-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	146	638	1	ENST00000357368.4:c.667G>A	p.Gly223Ser	p.G223S	ENST00000357368	NM_002850.3	223	Ggc/Agc	8/38	0.444922723624003	3	FACETS	0.858	0.783	0.936	0.286	0.261	0.312	CLONAL	1	TRUE	0	0.48574356826546	3		639	871	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132428	11132428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	298	1004	0	ENST00000358026.2:c.2644G>A	p.Glu882Lys	p.E882K	ENST00000358026	NM_001128849.1	882	Gaa/Aaa	19/36	0.40580431161925	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.40580431161925	1		1004	930	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894916	101894916	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060502040	NA	P-0046476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	107	363	0	ENST00000374994.4:c.469C>T	p.Arg157Ter	p.R157*	ENST00000374994	NM_004612.2	157	Cga/Tga	3/9	0.40580431161925	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	0	0.40580431161925	1		363	417	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880219	37880220	+	missense_variant	Missense_Mutation	DNP	TT	TT	CC	rs121913469	NA	P-0046476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	141	686	0	ENST00000269571.5:c.2263_2264delinsCC	p.Leu755Pro	p.L755P	ENST00000269571		755	TTg/CCg	19/27	1	2	FACETS	0.821	0.748	0.898	0.821	0.748	0.898	CLONAL	1	TRUE	1	0.40580431161925	2		686	846	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610131	10610131	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	232	915	0	ENST00000171111.5:c.579G>C	p.Gln193His	p.Q193H	ENST00000171111	NM_203500.1	193	caG/caC	2/6	0.40580431161925	1	FACETS	0.973	0.908	1	0.973	0.908	1	CLONAL	1	TRUE	0	0.40580431161925	1		915	937	SUCCESS
APC	324	MSKCC	GRCh37	5	112164587	112164587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1371086615	NA	P-0046476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	60	250	0	ENST00000257430.4:c.1661G>A	p.Arg554Gln	p.R554Q	ENST00000257430	NM_000038.5	554	cGa/cAa	14/16	0.40580431161925	1	FACETS	0.97	0.845	1	0.97	0.845	1	CLONAL	1	TRUE	0	0.40580431161925	1		250	243	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610076	10610076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	106	811	0	ENST00000171111.5:c.634G>A	p.Gly212Arg	p.G212R	ENST00000171111	NM_203500.1	212	Ggg/Agg	2/6	0.40580431161925	1	FACETS	0.552	0.494	0.612	0.552	0.494	0.612	SUBCLONAL	1	TRUE	0	0.40580431161925	1		811	755	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610334	10610334	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	339	1100	0	ENST00000171111.5:c.376G>A	p.Glu126Lys	p.E126K	ENST00000171111	NM_203500.1	126	Gag/Aag	2/6	0.40580431161925	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.40580431161925	1		1100	1164	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50827523	50827523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779374474	NA	P-0046476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	139	426	1	ENST00000398568.2:c.2408C>T	p.Pro803Leu	p.P803L	ENST00000398568	NM_001042412.1	803	cCg/cTg	16/18	1	2	FACETS	0.933	0.851	1	0.933	0.851	1	CLONAL	1	TRUE	1	0.40580431161925	2		427	734	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101179	41101179	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046476-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	190	773	0	ENST00000373198.4:c.1177G>T	p.Val393Leu	p.V393L	ENST00000373198	NM_133170.3	393	Gtg/Ttg	8/32	1	2	FACETS	0.953	0.88	1	0.953	0.88	1	CLONAL	1	TRUE	1	0.40580431161925	2		773	983	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0046477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	592	541	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.696215799740067	3	FACETS	0.957	0.934	0.98	0.957	0.934	0.98	CLONAL	3	TRUE	0	0.735073115444811	3		542	767	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0046477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	212	322	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.332783433664681	4	FACETS	0.975	0.915	1	0.975	0.915	1	INDETERMINATE	2	TRUE	2	0.735073115444811	4		322	513	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871749	35871749	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046477-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1174	274	518	0	ENST00000216797.5:c.757C>G	p.Pro253Ala	p.P253A	ENST00000216797	NM_020529.2	253	Ccc/Gcc	5/6	0.735073115444811	5	FACETS	1	0.976	1	0.361	0.338	0.385	CLONAL	1	TRUE	2	0.735073115444811	5		518	1448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0046489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	468	858	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.714530080430875	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.714530080430875	1		858	791	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161193	56161193	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	218	454	0	ENST00000399503.3:c.1062C>G	p.Phe354Leu	p.F354L	ENST00000399503	NM_005921.1	354	ttC/ttG	5/20	1	2	FACETS	0.94	0.879	1	0.94	0.879	1	CLONAL	1	TRUE	1	0.714530080430875	2		454	649	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	23	277	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.427	0.332	0.538	0.427	0.332	0.538	SUBCLONAL	1	FALSE	1	0.232624976136488	2		277	463	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593533	48593533	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046572-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	22	182	0	ENST00000342988.3:c.1284G>T	p.Lys428Asn	p.K428N	ENST00000342988	NM_005359.5	428	aaG/aaT	10/12	1	2	FACETS	0.643	0.499	0.811	0.643	0.499	0.811	SUBCLONAL	1	FALSE	1	0.232624976136488	2		182	294	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045888	47045888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782671192	NA	P-0046590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	99	397	1	ENST00000377604.3:c.2683C>T	p.Arg895Trp	p.R895W	ENST00000377604	NM_001204468.1	895	Cgg/Tgg	24/24	0.262332037494177	2	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.279874722128462	2		398	498	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0046590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	200	634	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.279874722128462	3	FACETS	0.941	0.873	1	0.941	0.873	1	CLONAL	2	TRUE	1	0.279874722128462	3		634	866	SUCCESS
AR	367	MSKCC	GRCh37	X	66943543	66943543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137852581	NA	P-0046590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	77	238	0	ENST00000374690.3:c.2623C>T	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	875	Cat/Tat	8/8	0.262332037494177	2	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.279874722128462	2		238	379	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389135	31389135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1165118132	NA	P-0046590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	100	627	0	ENST00000328111.2:c.2048G>A	p.Arg683His	p.R683H	ENST00000328111	NM_006892.3	683	cGc/cAc	19/23	0.279874722128462	2	FACETS	1	0.926	1	0.522	0.467	0.581	CLONAL	1	TRUE	0	0.279874722128462	2		627	684	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022388	31022388	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs868446207	NA	P-0046590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	65	433	0	ENST00000375687.4:c.1873C>T	p.Arg625Ter	p.R625*	ENST00000375687	NM_015338.5	625	Cga/Tga	13/13	0.279874722128462	2	FACETS	0.929	0.807	1	0.464	0.403	0.531	CLONAL	1	TRUE	0	0.279874722128462	2		433	500	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349730	15349730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750347317	NA	P-0046590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	115	744	0	ENST00000263377.2:c.3844C>T	p.Arg1282Cys	p.R1282C	ENST00000263377	NM_058243.2	1282	Cgc/Tgc	19/20	0.279874722128462	3	FACETS	1	0.943	1	0.534	0.481	0.591	CLONAL	1	TRUE	1	0.279874722128462	3		744	877	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165687	185165687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	150	440	0	ENST00000265026.3:c.962C>T	p.Ala321Val	p.A321V	ENST00000265026	NM_004721.4	321	gCg/gTg	5/14	0.279874722128462	4	FACETS	0.997	0.914	1	0.997	0.914	1	CLONAL	2	TRUE	2	0.279874722128462	4		440	688	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779343	3779343	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1369215188	NA	P-0046590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	344	802	1	ENST00000262367.5:c.5705C>T	p.Thr1902Met	p.T1902M	ENST00000262367	NM_004380.2	1902	aCg/aTg	31/31	0.264052715296474	4	FACETS	0.963	0.912	1	0.963	0.912	1	CLONAL	3	TRUE	1	0.279874722128462	4		803	1089	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911508	134911508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201816783	NA	P-0046590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	59	686	0	ENST00000398015.3:c.1973C>T	p.Ser658Leu	p.S658L	ENST00000398015	NM_004441.4	658	tCg/tTg	11/16	0.279874722128462	4	FACETS	0.608	0.521	0.702	0.304	0.26	0.351	SUBCLONAL	1	TRUE	2	0.279874722128462	4		686	888	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0046590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	242	1187	3	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	0.279874722128462	3	FACETS	0.921	0.86	0.984	0.921	0.86	0.984	CLONAL	2	TRUE	1	0.279874722128462	3		1190	1070	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0046590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	92	695	5	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	0.279874722128462	3	FACETS	0.723	0.641	0.812	0.362	0.32	0.406	SUBCLONAL	1	TRUE	1	0.279874722128462	3		700	1036	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134569	2134569	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs397514939	NA	P-0046590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	122	831	4	ENST00000219476.3:c.4351del	p.Arg1451AlafsTer25	p.R1451Afs*25	ENST00000219476	NM_000548.3	1449	tCc/tc	34/42	0.264052715296474	4	FACETS	1	0.905	1	0.334	0.301	0.37	CLONAL	1	TRUE	1	0.279874722128462	4		835	1112	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625302	69625302	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782573423	NA	P-0046590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	99	842	0	ENST00000334134.2:c.491G>A	p.Arg164His	p.R164H	ENST00000334134	NM_005247.2	164	cGc/cAc	3/3	0.279874722128462	3	FACETS	0.808	0.72	0.902	0.404	0.36	0.451	CLONAL	1	TRUE	1	0.279874722128462	3		842	998	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475282	40475282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064796762	NA	P-0046590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	203	606	1	ENST00000264657.5:c.1744G>A	p.Glu582Lys	p.E582K	ENST00000264657	NM_139276.2	582	Gaa/Aaa	19/24	0.279874722128462	3	FACETS	0.985	0.915	1	0.985	0.915	1	CLONAL	2	TRUE	1	0.279874722128462	3		607	839	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40491387	40491387	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	101	760	1	ENST00000264657.5:c.413C>T	p.Thr138Met	p.T138M	ENST00000264657	NM_139276.2	138	aCg/aTg	5/24	0.279874722128462	3	FACETS	0.861	0.768	0.96	0.43	0.384	0.48	CLONAL	1	TRUE	1	0.279874722128462	3		761	956	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098489	11098489	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765058736	NA	P-0046590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	127	348	1	ENST00000358026.2:c.1007C>T	p.Pro336Leu	p.P336L	ENST00000358026	NM_001128849.1	336	cCg/cTg	6/36	0.279874722128462	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.279874722128462	3		349	433	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461984	120461984	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1216790064	NA	P-0046590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	185	620	1	ENST00000256646.2:c.5732G>A	p.Arg1911His	p.R1911H	ENST00000256646	NM_024408.3	1911	cGc/cAc	31/34	0.279874722128462	3	FACETS	0.993	0.919	1	0.993	0.919	1	CLONAL	2	TRUE	1	0.279874722128462	3		621	759	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042145	14042145	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	185	368	0	ENST00000311895.7:c.2692T>A	p.Tyr898Asn	p.Y898N	ENST00000311895	NM_005236.2	898	Tat/Aat	11/11	0.264052715296474	4	FACETS	1	0.946	1	1	0.946	1	CLONAL	3	TRUE	1	0.279874722128462	4		368	553	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656981	47656984	+	frameshift_variant	Frame_Shift_Del	DEL	AAGT	AAGT	-	novel	NA	P-0046590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	85	424	0	ENST00000233146.2:c.1177_1180del	p.Lys393PhefsTer18	p.K393Ffs*18	ENST00000233146	NM_000251.2	393	AAGTtt/tt	7/16	0.279874722128462	2	FACETS	1	0.977	1	0.711	0.632	0.795	CLONAL	1	TRUE	0	0.279874722128462	2		424	427	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128036864	128036865	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	106	722	0	ENST00000285398.2:c.1614dup	p.Asn539GlnfsTer4	p.N539Qfs*4	ENST00000285398	NM_000122.1	538	-/C	10/15	0.279874722128462	3	FACETS	0.96	0.86	1	0.48	0.43	0.534	CLONAL	1	TRUE	1	0.279874722128462	3		722	899	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979283	40979283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146000056	NA	P-0046590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	92	620	0	ENST00000373198.4:c.1850G>A	p.Arg617Gln	p.R617Q	ENST00000373198	NM_133170.3	617	cGg/cAg	11/32	0.279874722128462	3	FACETS	0.89	0.79	0.997	0.445	0.395	0.499	CLONAL	1	TRUE	1	0.279874722128462	3		620	842	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295168	1295168	+	upstream_gene_variant	5'Flank	DEL	C	C	-	novel	NA	P-0046590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	50	172	0				ENST00000310581	NM_198253.2	-/1132			0.279874722128462	3	FACETS	0.984	0.846	1	0.984	0.846	1	CLONAL	2	TRUE	1	0.279874722128462	3		172	207	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80063779	80063779	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	57	513	0	ENST00000265081.6:c.1924G>A	p.Val642Ile	p.V642I	ENST00000265081	NM_002439.4	642	Gtc/Atc	14/24	0.279874722128462	3	FACETS	0.944	0.811	1	0.472	0.405	0.544	CLONAL	1	TRUE	1	0.279874722128462	3		513	492	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410990	63410990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	132	386	0	ENST00000330258.3:c.2177C>T	p.Ala726Val	p.A726V	ENST00000330258	NM_152424.3	726	gCc/gTc	2/2	0.262332037494177	2	FACETS	0.895	0.817	0.976			1	CLONAL	2	TRUE	NA	0.279874722128462	2		386	527	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0046620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	99	588	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.96	0.859	1	1	0.986	1	CLONAL	2	TRUE	1	0.19	2		588	543	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858129	40858129	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	58	560	0	ENST00000428826.2:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000428826		579	Cga/Tga	16/21	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.19	2		560	608	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607547	46607547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375648855	NA	P-0046620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	52	732	0	ENST00000263734.3:c.1736C>T	p.Pro579Leu	p.P579L	ENST00000263734	NM_001430.4	579	cCg/cTg	12/16	0.18657726659475	3	FACETS	0.695	0.59	0.811			1	SUBCLONAL	1	TRUE	NA	0.19	3		732	862	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031676	69031676	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	18	244	0	ENST00000288368.4:c.3431T>G	p.Leu1144Arg	p.L1144R	ENST00000288368	NM_024870.2	1144	cTt/cGt	28/40	1	2	FACETS	0.712	0.537	0.92	0.712	0.537	0.92	CLONAL	1	TRUE	1	0.19	2		244	266	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	42	515	6	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	0.493123219071842	4	FACETS	0.609	0.51	0.719	0.305	0.255	0.36	SUBCLONAL	1	TRUE	2	0.61	4		521	364	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	49	889	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.263790914556283	3	FACETS	0.525	0.446	0.612	0.263	0.223	0.306	INDETERMINATE	1	TRUE	1	0.61	3		895	399	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946143	13946143	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	87	479	2	ENST00000405192.2:c.953del	p.Leu318TrpfsTer2	p.L318Wfs*2	ENST00000405192	NM_001163147.1	318	tTg/tg	10/12	0.493123219071842	4	FACETS	0.844	0.749	0.945	0.422	0.374	0.473	CLONAL	1	TRUE	2	0.61	4		481	544	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119910	70119910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1297203260	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	61	707	0	ENST00000245479.2:c.916del	p.Val306CysfsTer77	p.V306Cfs*77	ENST00000245479	NM_000346.3	304	ccG/cc	3/3	0.263790914556283	3	FACETS	0.627	0.543	0.719	0.314	0.271	0.36	INDETERMINATE	1	TRUE	1	0.61	3		707	416	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045799	26045799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	66	723	0	ENST00000540144.1:c.161G>A	p.Arg54His	p.R54H	ENST00000540144	NM_003531.2	54	cGc/cAc	1/1	0.493123219071842	11	FACETS	1	0.942	1			1	CLONAL	1	TRUE	NA	0.61	11		723	698	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	31	383	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	0.263790914556283	4	FACETS	0.685	0.557	0.828	0.342	0.278	0.414	INDETERMINATE	1	TRUE	2	0.61	4		384	239	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	59	1144	2	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	1	2	FACETS	0.54	0.467	0.619	0.54	0.467	0.619	SUBCLONAL	1	TRUE	1	0.61	2		1146	358	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106228	27106228	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	31	641	1	ENST00000324856.7:c.5839C>T	p.Gln1947Ter	p.Q1947*	ENST00000324856	NM_006015.4	1947	Cag/Tag	20/20	0.263790914556283	4	FACETS	0.56	0.454	0.679	0.28	0.227	0.34	INDETERMINATE	1	TRUE	2	0.61	4		642	292	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741507	17741507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	22	779	2	ENST00000250003.3:c.178G>A	p.Glu60Lys	p.E60K	ENST00000250003	NM_002478.4	60	Gaa/Aaa	1/3	1	2	FACETS	0.35	0.272	0.439	0.35	0.272	0.439	SUBCLONAL	1	TRUE	1	0.61	2		781	206	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998598	100998598	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1279278874	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	35	935	0	ENST00000325455.5:c.1204C>T	p.Arg402Cys	p.R402C	ENST00000325455	NM_001202474.3	402	Cgt/Tgt	1/8	0.567798209235905	4	FACETS	0.515	0.422	0.618	0.257	0.211	0.309	SUBCLONAL	1	TRUE	2	0.61	4		935	359	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425787	49425788	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	20	925	0	ENST00000301067.7:c.12700_12701del	p.Gln4235GlyfsTer98	p.Q4235Gfs*98	ENST00000301067	NM_003482.3	4234	AGt/t	39/54	0.493123219071842	4	FACETS	0.525	0.403	0.667	0.263	0.201	0.334	SUBCLONAL	1	TRUE	2	0.61	4		925	201	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	24	810	2	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	0.493123219071842	4	FACETS	0.432	0.339	0.539	0.216	0.169	0.27	SUBCLONAL	1	TRUE	2	0.61	4		812	293	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799167	88799167	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	28	618	0	ENST00000360948.2:c.218T>C	p.Ile73Thr	p.I73T	ENST00000360948	NM_001012338.2	73	aTc/aCc	2/19	1	2	FACETS	0.394	0.316	0.482	0.394	0.316	0.482	SUBCLONAL	1	TRUE	1	0.61	2		618	233	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500472	99500472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	57	913	0	ENST00000268035.6:c.3905G>A	p.Ser1302Asn	p.S1302N	ENST00000268035	NM_000875.3	1302	aGc/aAc	21/21	1	2	FACETS	0.497	0.428	0.572	0.497	0.428	0.572	SUBCLONAL	1	TRUE	1	0.61	2		913	376	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50816329	50816329	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	28	361	0	ENST00000398568.2:c.1769G>T	p.Gly590Val	p.G590V	ENST00000398568	NM_001042412.1	590	gGc/gTc	10/18	0.263790914556283	4	FACETS	0.513	0.411	0.629	0.257	0.205	0.315	INDETERMINATE	1	TRUE	2	0.61	4		361	288	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844190	68844190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567505715	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	39	616	0	ENST00000261769.5:c.778C>T	p.Pro260Ser	p.P260S	ENST00000261769	NM_004360.3	260	Ccc/Tcc	6/16	0.493123219071842	1	FACETS	0.302	0.251	0.358	0.302	0.251	0.358	SUBCLONAL	1	TRUE	0	0.61	1		616	294	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847399	68847399	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	37	501	0	ENST00000261769.5:c.1320+1G>T		p.X440_splice	ENST00000261769	NM_004360.3	440			0.493123219071842	1	FACETS	0.437	0.364	0.517	0.437	0.364	0.517	SUBCLONAL	1	TRUE	0	0.61	1		501	193	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828029	72828029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	71	874	0	ENST00000268489.5:c.8552G>A	p.Gly2851Asp	p.G2851D	ENST00000268489	NM_006885.3	2851	gGc/gAc	9/10	0.493123219071842	5	FACETS	0.857	0.75	0.973			1	CLONAL	1	TRUE	NA	0.61	5		874	520	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59878688	59878688	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730881633	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	29	365	0	ENST00000259008.2:c.1066C>T	p.Arg356Ter	p.R356*	ENST00000259008	NM_032043.2	356	Cga/Tga	8/20	0.263790914556283	3	FACETS	0.333	0.267	0.407	0.166	0.133	0.204	INDETERMINATE	1	TRUE	1	0.61	3		365	373	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222030	2222031	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	25	1221	0	ENST00000398665.3:c.2867_2868del	p.Leu956HisfsTer11	p.L956Hfs*11	ENST00000398665	NM_032482.2	954	gcCTct/gcct	24/28	0.263790914556283	0	FACETS	0.151	0.119	0.187			1	INDETERMINATE	1	TRUE	0	0.61	0		1221	212	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243984	5243984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173811578	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	12	993	1	ENST00000357368.4:c.1498C>T	p.Arg500Trp	p.R500W	ENST00000357368	NM_002850.3	500	Cgg/Tgg	11/38	0.263790914556283	0	FACETS	0.074	0.052	0.102			1	INDETERMINATE	1	TRUE	0	0.61	0		994	206	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096993	11096993	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	31	1076	0	ENST00000358026.2:c.484T>G	p.Leu162Val	p.L162V	ENST00000358026	NM_001128849.1	162	Ttg/Gtg	4/36	1	2	FACETS	0.466	0.379	0.563	0.466	0.379	0.563	SUBCLONAL	1	TRUE	1	0.61	2		1076	218	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256768	19256769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1202792889	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	11	935	2	ENST00000162023.5:c.944dup	p.Val316SerfsTer6	p.V316Sfs*6	ENST00000162023		315	cca/ccCa	13/13	1	2	FACETS	0.173	0.119	0.24	0.173	0.119	0.24	SUBCLONAL	1	TRUE	1	0.61	2		937	208	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210725	36210725	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	52	1064	0	ENST00000222270.7:c.481del	p.Leu161PhefsTer6	p.L161Ffs*6	ENST00000222270	NM_014727.1	159	aCc/ac	3/37	1	2	FACETS	0.442	0.377	0.512	0.442	0.377	0.512	SUBCLONAL	1	TRUE	1	0.61	2		1064	386	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982440	25982440	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	31	332	2	ENST00000435504.4:c.850C>T	p.Arg284Ter	p.R284*	ENST00000435504		284	Cga/Tga	9/13	1	2	FACETS	0.395	0.321	0.479	0.395	0.321	0.479	SUBCLONAL	1	TRUE	1	0.61	2		334	257	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292682	62292682	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	33	826	2	ENST00000360203.5:c.134G>A	p.Gly45Asp	p.G45D	ENST00000360203	NM_001283009.1	45	gGt/gAt	3/35	0.263790914556283	4	FACETS	0.601	0.491	0.724	0.3	0.245	0.362	INDETERMINATE	1	TRUE	2	0.61	4		828	290	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651261	45651261	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	45	787	0	ENST00000407780.3:c.764C>A	p.Ala255Asp	p.A255D	ENST00000407780	NM_001283052.1	255	gCc/gAc	5/7	0.263790914556283	4	FACETS	0.642	0.541	0.753	0.321	0.27	0.377	INDETERMINATE	1	TRUE	2	0.61	4		787	370	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437677	52437677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	31	978	2	ENST00000460680.1:c.1484C>T	p.Thr495Met	p.T495M	ENST00000460680	NM_004656.3	495	aCg/aTg	13/17	0.263790914556283	4	FACETS	0.564	0.458	0.684	0.282	0.229	0.342	INDETERMINATE	1	TRUE	2	0.61	4		980	290	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439262	52439262	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	45	926	0	ENST00000460680.1:c.980G>T	p.Ser327Ile	p.S327I	ENST00000460680	NM_004656.3	327	aGc/aTc	11/17	0.263790914556283	4	FACETS	0.675	0.569	0.791	0.337	0.284	0.396	INDETERMINATE	1	TRUE	2	0.61	4		926	352	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664528	138664528	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	28	432	0	ENST00000330315.3:c.1037C>T	p.Ala346Val	p.A346V	ENST00000330315	NM_023067.3	346	gCt/gTt	1/1	0.263790914556283	4	FACETS	0.875	0.706	1	0.437	0.353	0.531	INDETERMINATE	1	TRUE	2	0.61	4		432	169	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456532	189456532	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	58	397	0	ENST00000264731.3:c.293T>C	p.Met98Thr	p.M98T	ENST00000264731	NM_003722.4	98	aTg/aCg	3/14	0.263790914556283	4	FACETS	0.707	0.609	0.813	0.354	0.304	0.407	INDETERMINATE	1	TRUE	2	0.61	4		397	433	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970922	79970922	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs71539687	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	72	563	1	ENST00000265081.6:c.1148A>G	p.Lys383Arg	p.K383R	ENST00000265081	NM_002439.4	383	aAg/aGg	7/24	0.567798209235905	4	FACETS	0.671	0.587	0.762	0.336	0.293	0.381	SUBCLONAL	1	TRUE	2	0.61	4		564	566	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048568	180048568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	23	1131	2	ENST00000261937.6:c.1994G>A	p.Cys665Tyr	p.C665Y	ENST00000261937	NM_182925.4	665	tGc/tAc	13/30	1	2	FACETS	0.351	0.274	0.438	0.351	0.274	0.438	SUBCLONAL	1	TRUE	1	0.61	2		1133	215	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672843	30672843	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	28	915	0	ENST00000376406.3:c.4117C>A	p.Leu1373Ile	p.L1373I	ENST00000376406	NM_014641.2	1373	Ctc/Atc	10/15	0.567798209235905	4	FACETS	0.349	0.279	0.43	0.175	0.139	0.215	SUBCLONAL	1	TRUE	2	0.61	4		915	423	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55269455	55269455	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	60	818	0	ENST00000275493.2:c.3142G>T	p.Ala1048Ser	p.A1048S	ENST00000275493	NM_005228.3	1048	Gct/Tct	26/28	0.493123219071842	4	FACETS	0.745	0.644	0.855	0.373	0.322	0.428	SUBCLONAL	1	TRUE	2	0.61	4		818	425	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436092	116436092	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	49	434	0	ENST00000397752.3:c.4087G>T	p.Ala1363Ser	p.A1363S	ENST00000397752	NM_000245.2	1363	Gct/Tct	21/21	0.493123219071842	4	FACETS	0.772	0.657	0.898	0.386	0.328	0.449	SUBCLONAL	1	TRUE	2	0.61	4		434	335	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501350	140501350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906660	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	27	254	0	ENST00000288602.6:c.722C>T	p.Thr241Met	p.T241M	ENST00000288602	NM_004333.4	241	aCg/aTg	6/18	0.493123219071842	4	FACETS	0.609	0.487	0.747	0.305	0.243	0.374	SUBCLONAL	1	TRUE	2	0.61	4		254	234	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300900	137300900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148741267	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	22	1069	3	ENST00000481739.1:c.545G>A	p.Arg182Gln	p.R182Q	ENST00000481739	NM_002957.4	182	cGg/cAg	4/10	1	2	FACETS	0.24	0.185	0.302	0.24	0.185	0.302	SUBCLONAL	1	TRUE	1	0.61	2		1072	301	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928872	44928872	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs755440519	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	43	203	0	ENST00000377967.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000377967	NM_021140.2	658	Cga/Tga	17/29	0.493123219071842	3	FACETS	1	0.944	1	0.414	0.353	0.479	CLONAL	1	TRUE	0	0.61	3		203	148	SUCCESS
AR	367	MSKCC	GRCh37	X	66766339	66766350	+	inframe_deletion	In_Frame_Del	DEL	GGTGGTGGTGGG	GGTGGTGGTGGG	-	novel	NA	P-0046653-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	10	97	0	ENST00000374690.3:c.1359_1370del	p.Gly470_Gly473del	p.G470_G473del	ENST00000374690	NM_000044.3	451	GGTGGTGGTGGG/-	1/8	0.493123219071842	3	FACETS	0.792	0.55	1	0.264	0.183	0.361	CLONAL	1	TRUE	0	0.61	3		97	54	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	19	277	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.81	0.613	1	0.81	0.613	1	CLONAL	1	TRUE	1	0.1	2		277	469	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971167	21971167	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	31	400	0	ENST00000304494.5:c.191T>C	p.Leu64Pro	p.L64P	ENST00000304494	NM_000077.4	64	cTg/cCg	2/3	1	2	FACETS	1	0.819	1	1	0.819	1	CLONAL	1	TRUE	1	0.1	2		400	610	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0046674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	30	400	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.912	0.732	1	0.912	0.732	1	CLONAL	1	TRUE	1	0.1	2		400	658	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683697	162683697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528661586	NA	P-0046674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	36	477	1	ENST00000366898.1:c.272C>T	p.Ala91Val	p.A91V	ENST00000366898	NM_004562.2	91	gCg/gTg	3/12	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.1	2		478	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs530941076	NA	P-0046674-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	45	645	0	ENST00000269305.4:c.658T>A	p.Tyr220Asn	p.Y220N	ENST00000269305	NM_001126112.2	220	Tat/Aat	6/11	1	2	FACETS	0.974	0.816	1	0.974	0.816	1	CLONAL	1	TRUE	1	0.1	2		645	924	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0046745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	240	655	1	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	0.596855156594516	3	FACETS	0.886	0.846	0.924			1	CLONAL	3	FALSE	NA	0.669861362325811	3		656	360	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147751	61147751	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs531828152	NA	P-0046745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	79	166	0	ENST00000295025.8:c.1061T>C	p.Ile354Thr	p.I354T	ENST00000295025	NM_002908.2	354	aTt/aCt	10/11	0.669861362325811	3	FACETS	0.963	0.893	1	0.963	0.893	1	CLONAL	3	FALSE	0	0.669861362325811	3		166	109	SUCCESS
APC	324	MSKCC	GRCh37	5	112176821	112176821	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	18	252	1	ENST00000257430.4:c.5530C>T	p.His1844Tyr	p.H1844Y	ENST00000257430	NM_000038.5	1844	Cat/Tat	16/16	0.440724651648668	3	FACETS	0.834	0.641	1	0.417	0.32	0.526	CLONAL	1	FALSE	1	0.669861362325811	3		253	86	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715435	117715435	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	18	243	0	ENST00000368508.3:c.1054A>G	p.Asn352Asp	p.N352D	ENST00000368508	NM_002944.2	352	Aac/Gac	10/43	0.214953141166297	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.669861362325811	0		243	92	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268906	55268906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	79	540	0	ENST00000275493.2:c.2972G>A	p.Ser991Asn	p.S991N	ENST00000275493	NM_005228.3	991	aGt/aAt	25/28	0.319682870587243	4	FACETS	1	0.916	1	0.347	0.307	0.39	INDETERMINATE	1	FALSE	1	0.669861362325811	4		540	378	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525867	148525890	+	inframe_deletion	In_Frame_Del	DEL	TCTCTTTCTTCAGGATCGTCTCCA	TCTCTTTCTTCAGGATCGTCTCCA	-	novel	NA	P-0046745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	72	222	0	ENST00000320356.2:c.567_590del	p.Asp189_Arg196del	p.D189_R196del	ENST00000320356	NM_004456.4	189	gaTGGAGACGATCCTGAAGAAAGAGAa/gaa	6/20	0.669861362325811	3	FACETS	1	0.976	1	0.71	0.632	0.791	CLONAL	1	FALSE	1	0.669861362325811	3		222	202	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412962	63412962	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046745-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	80	658	0	ENST00000330258.3:c.205C>G	p.Leu69Val	p.L69V	ENST00000330258	NM_152424.3	69	Ctg/Gtg	2/2	0.669861362325811	1	FACETS	0.659	0.589	0.732	0.659	0.589	0.732	SUBCLONAL	1	FALSE	0	0.669861362325811	1		658	241	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599338	55599338	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046781-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	132	422	0	ENST00000288135.5:c.2464A>T	p.Asn822Tyr	p.N822Y	ENST00000288135	NM_000222.2	822	Aat/Tat	17/21	0.39822622826387	4	FACETS	0.775	0.711	0.841	0.775	0.711	0.841	INDETERMINATE	2	TRUE	2	0.744723806102269	4		422	399	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528596	8528596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046781-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	116	302	0	ENST00000356435.5:c.536G>A	p.Arg179Gln	p.R179Q	ENST00000356435		179	cGa/cAa	4/35	0.744723806102269	6	FACETS	0.934	0.842	1	0.234	0.21	0.258	CLONAL	1	TRUE	2	0.744723806102269	6		302	830	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599266	55599266	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046781-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	144	431	0	ENST00000288135.5:c.2392A>G	p.Ile798Val	p.I798V	ENST00000288135	NM_000222.2	798	Atc/Gtc	17/21	0.39822622826387	4	FACETS	0.854	0.788	0.922	0.854	0.788	0.922	INDETERMINATE	2	TRUE	2	0.744723806102269	4		431	395	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913906	32913906	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs80358765	NA	P-0046781-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	203	379	0	ENST00000380152.3:c.5414A>G	p.Asn1805Ser	p.N1805S	ENST00000380152		1805	aAt/aGt	11/27	0.609928964867004	4	FACETS	0.983	0.921	1	0.983	0.921	1	CLONAL	2	TRUE	2	0.744723806102269	4		379	484	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29579964	29579964	+	intron_variant	Intron	SNP	C	C	A	novel	NA	P-0046781-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	220	382	0	ENST00000356175.3:c.4110+3827C>A		p.*1370*	ENST00000356175	NM_000267.3	1373/2839			0.744336332914083	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.744723806102269	2		382	290	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533093	63533094	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046781-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	208	740	0	ENST00000307078.5:c.1800dup	p.Gly601ArgfsTer27	p.G601Rfs*27	ENST00000307078	NM_004655.3	600	-/C	7/11	0.744723806102269	3	FACETS	1	0.942	1	0.506	0.471	0.543	CLONAL	1	TRUE	1	0.744723806102269	3		740	757	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267385	198267385	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046781-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	218	443	0	ENST00000335508.6:c.1972T>C	p.Trp658Arg	p.W658R	ENST00000335508	NM_012433.2	658	Tgg/Cgg	14/25	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.744723806102269	2		443	504	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729355	41729355	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046781-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	179	636	1	ENST00000242208.4:c.1174G>T	p.Val392Leu	p.V392L	ENST00000242208	NM_002192.2	392	Gtg/Ttg	3/3	0.486088282039059	4	FACETS	0.946	0.872	1	0.473	0.436	0.511	CLONAL	1	TRUE	2	0.744723806102269	4		637	887	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046822-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	27	516	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.54	0.429	0.666	0.54	0.429	0.666	SUBCLONAL	1	TRUE	1	0.263983540842276	2		516	379	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046822-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	120	277	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.195537882475053	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	1	0.263983540842276	4		277	338	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035169	30035169	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046822-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	82	434	0	ENST00000338641.4:c.331C>T	p.Gln111Ter	p.Q111*	ENST00000338641	NM_000268.3	111	Cag/Tag	3/16	0.237904941785565	2	FACETS	0.941	0.837	1	0.941	0.837	1	CLONAL	2	TRUE	0	0.263983540842276	2		434	330	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551085	41551085	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046822-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	118	548	0	ENST00000263253.7:c.3229C>T	p.Gln1077Ter	p.Q1077*	ENST00000263253	NM_001429.3	1077	Caa/Taa	17/31	0.237904941785565	2	FACETS	0.871	0.79	0.957	0.871	0.79	0.957	CLONAL	2	TRUE	0	0.263983540842276	2		548	513	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871813	12871813	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046822-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	140	265	0	ENST00000228872.4:c.530G>T	p.Gly177Val	p.G177V	ENST00000228872	NM_004064.3	177	gGt/gTt	2/3	0.195537882475053	4	FACETS	0.931	0.854	1	0.931	0.854	1	CLONAL	3	TRUE	1	0.263983540842276	4		265	480	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435721	110435769	+	frameshift_variant	Frame_Shift_Del	DEL	ACAGGCGCGTGGGCCTCACCGCCCGGCCGCGCTGGCCCAAGAAGCCCTC	ACAGGCGCGTGGGCCTCACCGCCCGGCCGCGCTGGCCCAAGAAGCCCTC	-	novel	NA	P-0046822-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	76	300	0	ENST00000375856.3:c.2632_2680del	p.Glu878ProfsTer86	p.E878Pfs*86	ENST00000375856	NM_003749.2	878	GAGGGCTTCTTGGGCCAGCGCGGCCGGGCGGTGAGGCCCACGCGCCTGTcc/cc	1/2	0.263983540842276	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.263983540842276	1		300	443	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991122	41991122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs996180092	NA	P-0046822-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	19	363	0	ENST00000219905.7:c.2075C>T	p.Ser692Leu	p.S692L	ENST00000219905	NM_001164273.1	692	tCa/tTa	4/24	0.263983540842276	1	FACETS	0.735	0.561	0.936	0.735	0.561	0.936	CLONAL	1	TRUE	0	0.263983540842276	1		363	170	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354433	91354433	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs150421256	NA	P-0046822-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	24	361	0	ENST00000355112.3:c.3875-2A>G		p.X1292_splice	ENST00000355112	NM_000057.2	1292			0.263983540842276	1	FACETS	0.357	0.279	0.447	0.357	0.279	0.447	SUBCLONAL	1	TRUE	0	0.263983540842276	1		361	442	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678062	58678062	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046822-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	91	305	0	ENST00000305921.3:c.287C>A	p.Ser96Tyr	p.S96Y	ENST00000305921	NM_003620.3	96	tCc/tAc	1/6	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.263983540842276	2		305	591	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248672	212248672	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs780519461	NA	P-0046822-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	64	451	0	ENST00000342788.4:c.3595G>C	p.Glu1199Gln	p.E1199Q	ENST00000342788	NM_005235.2	1199	Gag/Cag	28/28	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.263983540842276	2		451	464	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916669	178916669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046822-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	17	295	0	ENST00000263967.3:c.56G>A	p.Arg19Lys	p.R19K	ENST00000263967	NM_006218.2	19	aGa/aAa	2/21	1	2	FACETS	0.864	0.65	1	0.864	0.65	1	CLONAL	1	TRUE	1	0.263983540842276	2		295	149	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970834	55970834	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046822-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	53	467	0	ENST00000263923.4:c.1963G>T	p.Val655Leu	p.V655L	ENST00000263923	NM_002253.2	655	Gtg/Ttg	13/30	1	2	FACETS	0.915	0.782	1	0.915	0.782	1	CLONAL	1	TRUE	1	0.263983540842276	2		467	439	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270102	66270102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046822-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	22	286	0	ENST00000273854.3:c.1780C>T	p.Leu594Phe	p.L594F	ENST00000273854	NM_004439.5	594	Ctc/Ttc	8/18	1	2	FACETS	0.548	0.425	0.691	0.548	0.425	0.691	SUBCLONAL	1	TRUE	1	0.263983540842276	2		286	304	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950249	38950249	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0046822-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	33	327	0	ENST00000357387.3:c.3701C>G	p.Ser1234Ter	p.S1234*	ENST00000357387	NM_152756.3	1234	tCa/tGa	31/38	1	2	FACETS	1	0.832	1	1	0.832	1	CLONAL	1	TRUE	1	0.263983540842276	2		327	246	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672392	30672392	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046822-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	190	698	1	ENST00000376406.3:c.4568C>A	p.Ser1523Tyr	p.S1523Y	ENST00000376406	NM_014641.2	1523	tCt/tAt	10/15	0.110055385025824	4	FACETS	1	0.939	1	1	0.939	1	INDETERMINATE	2	TRUE	2	0.263983540842276	4		699	895	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0046824-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	127	396	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.605098247715247	3	FACETS	1	0.966	1	0.561	0.511	0.613	CLONAL	1	TRUE	1	0.605098247715247	3		396	487	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0046824-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	274	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.605098247715247	3	FACETS	0.932	0.882	0.982	0.932	0.882	0.982	CLONAL	2	TRUE	1	0.605098247715247	3		511	633	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222006	1222006	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0046824-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	355	795	1	ENST00000326873.7:c.920+1G>T		p.X307_splice	ENST00000326873	NM_000455.4	307			0.605098247715247	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.605098247715247	2		796	556	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602887	55602887	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046824-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	112	362	0	ENST00000288135.5:c.2597G>A	p.Gly866Glu	p.G866E	ENST00000288135	NM_000222.2	866	gGa/gAa	19/21	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.605098247715247	2		362	348	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602822	10602822	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046824-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	581	1113	1	ENST00000171111.5:c.756G>T	p.Trp252Cys	p.W252C	ENST00000171111	NM_203500.1	252	tgG/tgT	3/6	0.605098247715247	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.605098247715247	2		1114	860	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256179	123256179	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046824-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	164	577	0	ENST00000358487.5:c.1730G>T	p.Arg577Leu	p.R577L	ENST00000358487	NM_000141.4	577	cGa/cTa	13/18	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.605098247715247	2		577	501	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224270	98224270	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046824-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	60	335	0	ENST00000331920.6:c.2571T>A	p.Asp857Glu	p.D857E	ENST00000331920	NM_000264.3	857	gaT/gaA	16/24	1	2	FACETS	0.972	0.851	1	0.972	0.851	1	CLONAL	1	TRUE	1	0.605098247715247	2		335	204	SUCCESS
AR	367	MSKCC	GRCh37	X	66931343	66931343	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046824-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	174	695	1	ENST00000374690.3:c.1985T>A	p.Val662Glu	p.V662E	ENST00000374690	NM_000044.3	662	gTg/gAg	4/8	0.543623103502636	5	FACETS	1	0.978	1	0.292	0.269	0.317	CLONAL	1	TRUE	1	0.605098247715247	5		696	939	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134240	11134240	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046824-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	364	778	0	ENST00000358026.2:c.2906A>G	p.His969Arg	p.H969R	ENST00000358026	NM_001128849.1	969	cAc/cGc	20/36	0.605098247715247	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.605098247715247	2		778	594	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599260	28599260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046824-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	488	1101	0	ENST00000253063.3:c.706G>A	p.Glu236Lys	p.E236K	ENST00000253063	NM_031459.4	236	Gaa/Aaa	5/10	0.605098247715247	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.605098247715247	2		1101	800	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118857	115118857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046824-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	96	552	0	ENST00000257566.3:c.484C>T	p.Arg162Cys	p.R162C	ENST00000257566	NM_016569.3	162	Cgt/Tgt	2/8	0.605098247715247	3	FACETS	0.761	0.68	0.847	0.381	0.34	0.424	SUBCLONAL	1	TRUE	1	0.605098247715247	3		552	543	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210931	133210931	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046824-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	199	773	0	ENST00000320574.5:c.5845G>T	p.Glu1949Ter	p.E1949*	ENST00000320574	NM_006231.2	1949	Gag/Tag	43/49	0.605098247715247	3	FACETS	1	0.973	1	0.547	0.508	0.588	CLONAL	1	TRUE	1	0.605098247715247	3		773	783	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108268	8108268	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046824-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	245	956	0	ENST00000585124.1:c.956C>G	p.Ala319Gly	p.A319G	ENST00000585124	NM_004217.3	319	gCc/gGc	9/9	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.605098247715247	2		956	774	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313452	30313452	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046824-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	188	671	0	ENST00000262643.3:c.1052G>T	p.Gly351Val	p.G351V	ENST00000262643	NM_001238.2	351	gGc/gTc	11/12	0.605098247715247	3	FACETS	1	0.95	1	0.517	0.478	0.557	CLONAL	1	TRUE	1	0.605098247715247	3		671	783	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223932	36223932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747873093	NA	P-0046824-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	245	1062	4	ENST00000222270.7:c.6482G>A	p.Arg2161His	p.R2161H	ENST00000222270	NM_014727.1	2161	cGc/cAc	28/37	0.605098247715247	3	FACETS	1	0.961	1	0.519	0.485	0.554	CLONAL	1	TRUE	1	0.605098247715247	3		1066	1016	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877396	40877396	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046824-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	338	696	0	ENST00000373198.4:c.2300C>G	p.Ala767Gly	p.A767G	ENST00000373198	NM_133170.3	767	gCt/gGt	15/32	0.605098247715247	3	FACETS	0.957	0.911	1	0.957	0.911	1	CLONAL	2	TRUE	1	0.605098247715247	3		696	760	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130595	29130595	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060502696	NA	P-0046824-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	153	727	0	ENST00000328354.6:c.115T>C	p.Ser39Pro	p.S39P	ENST00000328354	NM_007194.3	39	Tcc/Ccc	2/15	1	2	FACETS	0.951	0.875	1	0.951	0.875	1	CLONAL	1	TRUE	1	0.605098247715247	2		727	532	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430723	181430723	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750656301	NA	P-0046824-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	397	836	2	ENST00000325404.1:c.575C>T	p.Ala192Val	p.A192V	ENST00000325404	NM_003106.3	192	gCg/gTg	1/1	0.605098247715247	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.605098247715247	3		838	745	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029297	143029297	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046824-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	82	327	0	ENST00000262992.4:c.2323G>T	p.Glu775Ter	p.E775*	ENST00000262992	NM_001101669.1	775	Gaa/Taa	21/24	1	2	FACETS	0.919	0.819	1	0.919	0.819	1	CLONAL	1	TRUE	1	0.605098247715247	2		327	295	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509440	149509440	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046824-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	213	1036	2	ENST00000261799.4:c.1459C>A	p.Gln487Lys	p.Q487K	ENST00000261799	NM_002609.3	487	Cag/Aag	10/23	0.605098247715247	3	FACETS	1	0.954	1	0.517	0.481	0.554	CLONAL	1	TRUE	1	0.605098247715247	3		1038	887	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341543	70341543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046824-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	758	937	1	ENST00000374080.3:c.978C>A	p.Ser326Arg	p.S326R	ENST00000374080		326	agC/agA	7/45	0.543623103502636	5	FACETS	0.953	0.927	0.979	0.953	0.927	0.979	CLONAL	4	TRUE	1	0.605098247715247	5		938	1254	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852245	63852245	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1376484834	NA	P-0046827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	628	590	3	ENST00000279873.7:c.3023C>T	p.Ala1008Val	p.A1008V	ENST00000279873	NM_032199.2	1008	gCg/gTg	10/10	0.460425725306809	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	1	0.460425725306809	4		593	1301	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602329	10602329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	490	1063	1	ENST00000171111.5:c.1249G>A	p.Gly417Arg	p.G417R	ENST00000171111	NM_203500.1	417	Ggg/Agg	3/6	0.434369371327504	2	FACETS	0.984	0.944	1	0.984	0.944	1	CLONAL	2	TRUE	0	0.460425725306809	2		1064	1082	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0046827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	410	792	0	ENST00000269305.4:c.560-2A>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.440506550172563	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.460425725306809	2		792	847	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748512	162748512	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	124	602	0	ENST00000367921.3:c.2426G>T	p.Gly809Val	p.G809V	ENST00000367921	NM_006182.2	809	gGg/gTg	17/18	0.441613012123085	4	FACETS	0.882	0.797	0.971	0.294	0.265	0.324	CLONAL	1	TRUE	1	0.460425725306809	4		602	892	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435017	18435017	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0046827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	146	208	0	ENST00000266497.5:c.2T>C	p.Met1?	p.M1?	ENST00000266497		1	aTg/aCg	1/31	0.434369371327504	2	FACETS	0.843	0.779	0.909	0.843	0.779	0.909	CLONAL	2	TRUE	0	0.460425725306809	2		208	376	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942181	17942181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	384	852	0	ENST00000458235.1:c.2834G>A	p.Cys945Tyr	p.C945Y	ENST00000458235	NM_000215.3	945	tGc/tAc	21/24	0.440506550172563	2	FACETS	0.958	0.914	1	0.958	0.914	1	CLONAL	2	TRUE	0	0.460425725306809	2		852	871	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31435925	31435929	+	frameshift_variant	Frame_Shift_Del	DEL	CTAAT	CTAAT	-	novel	NA	P-0046827-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	221	580	0	ENST00000344624.3:c.2985_2989del	p.Leu996AsnfsTer20	p.L996Nfs*20	ENST00000344624		995	ggATTAGca/ggca	22/33	0.295371080566232	4	FACETS	1	0.991	1	0.713	0.664	0.764	CLONAL	1	TRUE	2	0.460425725306809	4		580	983	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0046841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	373	305	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	0.555797271178717	5	FACETS	1	0.975	1	1	0.975	1	CLONAL	4	TRUE	1	0.555797271178717	5		305	604	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984408	201984408	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0046841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	163	566	0	ENST00000359651.3:c.1073C>G	p.Ser358Ter	p.S358*	ENST00000359651		358	tCa/tGa	8/8	0.555797271178717	4	FACETS	0.76	0.696	0.827	0.19	0.174	0.207	SUBCLONAL	1	TRUE	0	0.555797271178717	4		566	1201	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866654	117866654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3227	198	342	0	ENST00000297338.2:c.991G>A	p.Glu331Lys	p.E331K	ENST00000297338	NM_006265.2	331	Gag/Aag	9/14	0.555797271178717	26	FACETS	0.798	0.734	0.865			1	SUBCLONAL	2	TRUE	NA	0.555797271178717	26		342	3425	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367066	40367066	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	229	665	0	ENST00000397332.2:c.131A>T	p.Asp44Val	p.D44V	ENST00000397332	NM_001033082.2	44	gAc/gTc	2/3	0.555797271178717	2	FACETS	0.974	0.91	1	0.487	0.455	0.52	CLONAL	1	TRUE	0	0.555797271178717	2		665	846	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404793	70404793	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	232	299	0	ENST00000373644.4:c.2307A>T	p.Glu769Asp	p.E769D	ENST00000373644	NM_030625.2	769	gaA/gaT	4/12	0.423529548912508	4	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	2	0.555797271178717	4		299	642	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112940037	112940038	+	missense_variant	Missense_Mutation	DNP	TA	TA	CC	novel	NA	P-0046841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	171	545	0	ENST00000351677.2:c.1689_1690delinsCC	p.Thr564Pro	p.T564P	ENST00000351677	NM_002834.3	563	tgTAct/tgCCct	14/16	0.448743131612946	5	FACETS	0.901	0.826	0.978			1	CLONAL	1	TRUE	NA	0.555797271178717	5		545	1253	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56381333	56381333	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	44	144	0	ENST00000348428.3:c.977G>C	p.Gly326Ala	p.G326A	ENST00000348428	NM_006785.3	326	gGt/gCt	8/17	0.555797271178717	3	FACETS	0.822	0.695	0.961	0.411	0.347	0.481	CLONAL	1	TRUE	1	0.555797271178717	3		144	246	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505672	186505672	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0046841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	64	163	0	ENST00000323963.5:c.1079+1G>C		p.X360_splice	ENST00000323963		360			0.555797271178717	5	FACETS	0.862	0.748	0.985	0.215	0.187	0.247	CLONAL	1	TRUE	1	0.555797271178717	5		163	490	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509879	187509879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	101	318	0	ENST00000441802.2:c.13634C>T	p.Ser4545Phe	p.S4545F	ENST00000441802	NM_005245.3	4545	tCc/tTc	27/27	0.555797271178717	3	FACETS	0.88	0.789	0.975	0.44	0.394	0.488	CLONAL	1	TRUE	1	0.555797271178717	3		318	528	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884915	151884928	+	frameshift_variant	Frame_Shift_Del	DEL	GCATCCGTGAAAAA	GCATCCGTGAAAAA	-	novel	NA	P-0046841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	23	202	0	ENST00000262189.6:c.4665_4678del	p.Phe1556SerfsTer15	p.F1556Sfs*15	ENST00000262189	NM_170606.2	1555	gcTTTTTCACGGATGCct/gcct	32/59	0.555797271178717	3	FACETS	0.314	0.244	0.394	0.157	0.122	0.197	SUBCLONAL	1	TRUE	1	0.555797271178717	3		202	337	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868489	117868489	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3275	206	342	0	ENST00000297338.2:c.853G>A	p.Glu285Lys	p.E285K	ENST00000297338	NM_006265.2	285	Gaa/Aaa	8/14	0.555797271178717	26	FACETS	0.817	0.753	0.884			1	CLONAL	2	TRUE	NA	0.555797271178717	26		342	3481	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27218785	27218785	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	130	396	0	ENST00000380036.4:c.3073G>T	p.Gly1025Cys	p.G1025C	ENST00000380036	NM_000459.3	1025	Ggt/Tgt	20/23	1	2	FACETS	0.886	0.808	0.967	0.886	0.808	0.967	CLONAL	1	TRUE	1	0.555797271178717	2		396	528	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	157	638	9	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.31535747952767	2		647	806	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	80	502	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.941	0.83	1	0.941	0.83	1	CLONAL	1	TRUE	1	0.31535747952767	2		507	539	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	72	340	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.917	0.803	1	0.917	0.803	1	CLONAL	1	TRUE	1	0.31535747952767	2		341	498	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	195	535	2	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.31535747952767	2		537	870	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39644789	39644789	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	61	254	0	ENST00000262039.4:c.2522del	p.Lys841ArgfsTer8	p.K841Rfs*8	ENST00000262039	NM_002647.2	840	Aaa/aa	23/25	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.31535747952767	2		254	380	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	40	222	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.94	0.785	1	0.94	0.785	1	CLONAL	1	TRUE	1	0.31535747952767	2		222	270	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161938	47161939	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	73	306	1	ENST00000409792.3:c.4187dup	p.Asn1396LysfsTer2	p.N1396Kfs*2	ENST00000409792	NM_014159.6	1396	aat/aaAt	3/21	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.31535747952767	2		307	425	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	83	394	0	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.31535747952767	2		394	374	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007753	45007753	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	77	356	0	ENST00000558401.1:c.204del	p.Val69TrpfsTer34	p.V69Wfs*34	ENST00000558401	NM_004048.2	67	gAa/ga	2/4	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.31535747952767	2		356	472	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	212	758	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.31535747952767	2		758	1162	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882049	36882050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs780753361	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	71	821	4	ENST00000358127.4:c.963dup	p.Ala322ArgfsTer19	p.A322Rfs*19	ENST00000358127	NM_001280556.1	321	-/C	8/10	1	2	FACETS	0.355	0.309	0.406	0.355	0.309	0.406	SUBCLONAL	1	TRUE	1	0.31535747952767	2		825	1267	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	65	250	0	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.31535747952767	2		250	388	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208051	5208051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1477222866	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	132	693	0	ENST00000357368.4:c.5660C>T	p.Thr1887Met	p.T1887M	ENST00000357368	NM_002850.3	1887	aCg/aTg	37/38	1	2	FACETS	0.994	0.903	1	0.994	0.903	1	CLONAL	1	TRUE	1	0.31535747952767	2		693	842	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261555	142261555	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	66	299	0	ENST00000350721.4:c.3402del	p.Phe1134LeufsTer6	p.F1134Lfs*6	ENST00000350721	NM_001184.3	1134	ttT/tt	17/47	1	2	FACETS	0.945	0.823	1	0.945	0.823	1	CLONAL	1	TRUE	1	0.31535747952767	2		299	443	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645499	67645500	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	49	212	0	ENST00000264010.4:c.769dup	p.Ile257AsnfsTer2	p.I257Nfs*2	ENST00000264010	NM_006565.3	255	aca/acAa	3/12	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.31535747952767	2		212	279	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058747	180058748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755445139	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	167	780	1	ENST00000261937.6:c.89dup	p.Thr31AspfsTer15	p.T31Dfs*15	ENST00000261937	NM_182925.4	30	ccg/ccCg	2/30	1	2	FACETS	0.946	0.868	1	0.946	0.868	1	CLONAL	1	TRUE	1	0.31535747952767	2		781	1119	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178258	56178258	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	68	287	0	ENST00000399503.3:c.3236del	p.Asn1079IlefsTer3	p.N1079Ifs*3	ENST00000399503	NM_005921.1	1077	tcA/tc	14/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.31535747952767	2		287	351	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638900	176638900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763399938	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	175	532	0	ENST00000439151.2:c.3500G>A	p.Arg1167His	p.R1167H	ENST00000439151	NM_022455.4	1167	cGc/cAc	5/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.31535747952767	2		532	846	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020769	37020769	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	189	539	1	ENST00000358127.4:c.76G>T	p.Val26Phe	p.V26F	ENST00000358127	NM_001280556.1	26	Gtt/Ttt	2/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.31535747952767	2		540	857	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957837	1957837	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	178	600	0	ENST00000382891.5:c.2803C>T	p.Arg935Ter	p.R935*	ENST00000382891	NM_133335.3	935	Cga/Tga	15/22	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.31535747952767	2		600	958	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211899	36211899	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	227	778	8	ENST00000222270.7:c.1656del	p.Lys553AsnfsTer52	p.K553Nfs*52	ENST00000222270	NM_014727.1	550	gaC/ga	3/37	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.31535747952767	2		786	1121	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346058	152346058	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	109	502	0	ENST00000359321.1:c.512C>T	p.Ser171Phe	p.S171F	ENST00000359321	NM_005431.1	171	tCt/tTt	3/3	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.31535747952767	2		502	600	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141567244	141567244	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	328	731	0	ENST00000220592.5:c.970del	p.His324ThrfsTer33	p.H324Tfs*33	ENST00000220592	NM_012154.3	324	Cac/ac	8/19	0.215542249679427	3	FACETS	0.923	0.871	0.976	0.923	0.871	0.976	CLONAL	2	TRUE	1	0.31535747952767	3		731	1305	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78425912	78425913	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	92	403	0	ENST00000370768.2:c.1532dup	p.Asn512LysfsTer13	p.N512Kfs*13	ENST00000370768	NM_003902.3	511	gga/ggGa	16/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.31535747952767	2		403	489	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120043	70120043	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	13	34	0	ENST00000245479.2:c.1049del	p.Pro350HisfsTer33	p.P350Hfs*33	ENST00000245479	NM_000346.3	349	Ccc/cc	3/3	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.31535747952767	2		34	56	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805787	32805788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1174402903	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	215	887	0	ENST00000374899.4:c.223dup	p.Leu75ProfsTer92	p.L75Pfs*92	ENST00000374899	NM_018833.2	75	ctg/cCtg	2/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.31535747952767	2		887	1158	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194904	29194904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372203752	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	386	900	1	ENST00000240100.2:c.824G>A	p.Arg275His	p.R275H	ENST00000240100	NM_001394.6	275	cGc/cAc	4/4	0.215542249679427	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.31535747952767	3		901	1358	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591712	38591713	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	115	454	0	ENST00000299084.4:c.177dup	p.Ile60TyrfsTer18	p.I60Yfs*18	ENST00000299084	NM_152594.2	57	-/T	2/7	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.31535747952767	2		454	655	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	360054	360055	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	134	739	0	ENST00000262320.3:c.1034dup	p.Tyr346IlefsTer5	p.Y346Ifs*5	ENST00000262320	NM_003502.3	345	cca/ccCa	4/11	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.31535747952767	2		739	839	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532659	46532659	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	83	378	0	ENST00000262741.5:c.419A>T	p.Tyr140Phe	p.Y140F	ENST00000262741	NM_003629.3	140	tAt/tTt	4/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.31535747952767	2		378	463	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121589	108121589	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs770028453	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	134	479	0	ENST00000278616.4:c.1397A>G	p.Gln466Arg	p.Q466R	ENST00000278616	NM_000051.3	466	cAa/cGa	10/63	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.31535747952767	2		479	686	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472209	472209	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	146	470	0	ENST00000399788.2:c.592A>G	p.Ser198Gly	p.S198G	ENST00000399788	NM_001042603.1	198	Agc/Ggc	5/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.31535747952767	2		470	803	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244866	46244866	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	146	563	0	ENST00000334344.6:c.2960C>T	p.Ala987Val	p.A987V	ENST00000334344	NM_152641.2	987	gCc/gTc	15/21	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.31535747952767	2		563	844	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434004	49434005	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750341925	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	157	908	0	ENST00000301067.7:c.7548dup	p.Asn2517GlnfsTer138	p.N2517Qfs*138	ENST00000301067	NM_003482.3	2516	-/C	31/54	1	2	FACETS	0.897	0.82	0.978	0.897	0.82	0.978	CLONAL	1	TRUE	1	0.31535747952767	2		908	1110	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864381	57864381	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	182	817	0	ENST00000228682.2:c.1858T>C	p.Trp620Arg	p.W620R	ENST00000228682	NM_005269.2	620	Tgg/Cgg	12/12	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.31535747952767	2		817	979	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120696	115120697	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	218	698	0	ENST00000257566.3:c.309dup	p.Lys104GlnfsTer7	p.K104Qfs*7	ENST00000257566	NM_016569.3	103	-/C	1/8	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.31535747952767	2		698	1096	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828435	72828435	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	107	682	0	ENST00000268489.5:c.8146del	p.Cys2716AlafsTer30	p.C2716Afs*30	ENST00000268489	NM_006885.3	2716	Tgc/gc	9/10	1	2	FACETS	0.692	0.62	0.77	0.692	0.62	0.77	SUBCLONAL	1	TRUE	1	0.31535747952767	2		682	980	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845902	72845902	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	139	501	0	ENST00000268489.5:c.3565T>C	p.Ser1189Pro	p.S1189P	ENST00000268489	NM_006885.3	1189	Tct/Cct	6/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.31535747952767	2		501	776	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346236	89346236	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	120	507	1	ENST00000301030.4:c.6714C>A	p.Ser2238Arg	p.S2238R	ENST00000301030	NM_001256183.1	2238	agC/agA	9/13	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.31535747952767	2		508	608	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877432	89877432	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	233	657	0	ENST00000389301.3:c.331A>G	p.Ile111Val	p.I111V	ENST00000389301	NM_000135.2	111	Att/Gtt	4/43	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.31535747952767	2		657	1116	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219376	1219376	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1380135986	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	188	671	0	ENST00000326873.7:c.428T>C	p.Val143Ala	p.V143A	ENST00000326873	NM_000455.4	143	gTg/gCg	3/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.31535747952767	2		671	996	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15379792	15379792	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	117	483	0	ENST00000263377.2:c.347del	p.Asn116ThrfsTer31	p.N116Tfs*31	ENST00000263377	NM_058243.2	116	aAc/ac	3/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.31535747952767	2		483	637	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912050	50912050	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	275	803	0	ENST00000440232.2:c.1784A>G	p.Asp595Gly	p.D595G	ENST00000440232	NM_002691.3	595	gAc/gGc	15/27	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.31535747952767	2		803	1222	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181358	185181359	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1560126178	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	82	300	0	ENST00000265026.3:c.1305dup	p.His436ThrfsTer3	p.H436Tfs*3	ENST00000265026	NM_004721.4	433	-/A	8/14	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.31535747952767	2		300	436	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980558	1980559	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCC	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	98	725	0	ENST00000382891.5:c.4026_4028dup	p.Pro1343dup	p.P1343dup	ENST00000382891	NM_133335.3	1343	-/CCC	22/22	1	2	FACETS	0.6	0.534	0.671	0.6	0.534	0.671	SUBCLONAL	1	TRUE	1	0.31535747952767	2		725	1035	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540916	187540916	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	81	343	0	ENST00000441802.2:c.6824A>G	p.Asp2275Gly	p.D2275G	ENST00000441802	NM_005245.3	2275	gAc/gGc	10/27	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.31535747952767	2		343	451	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590988	67590988	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	21	137	0	ENST00000274335.5:c.1581T>G	p.Asn527Lys	p.N527K	ENST00000274335		527	aaT/aaG	12/15	1	2	FACETS	0.925	0.719	1	0.925	0.719	1	CLONAL	1	TRUE	1	0.31535747952767	2		137	144	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910653	29910653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11539961	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1500	82	1338	2	ENST00000376809.5:c.193G>A	p.Ala65Thr	p.A65T	ENST00000376809	NM_002116.7	65	Gcg/Acg	2/8	1	2	FACETS	0.329	0.288	0.373	0.329	0.288	0.373	SUBCLONAL	1	TRUE	1	0.31535747952767	2		1340	1582	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911318	29911319	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	54	503	0	ENST00000376809.5:c.619+1dup		p.T206fs	ENST00000376809	NM_002116.7	206	acg/acGg	3/8	1	2	FACETS	0.65	0.555	0.753	0.65	0.555	0.753	SUBCLONAL	1	TRUE	1	0.31535747952767	2		503	527	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502199	157502199	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	127	574	0	ENST00000346085.5:c.3232A>G	p.Thr1078Ala	p.T1078A	ENST00000346085	NM_020732.3	1078	Acc/Gcc	12/20	1	2	FACETS	0.958	0.867	1	0.958	0.867	1	CLONAL	1	TRUE	1	0.31535747952767	2		574	841	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930330	39930330	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	98	325	0	ENST00000378444.4:c.3134A>G	p.Lys1045Arg	p.K1045R	ENST00000378444	NM_001123385.1	1045	aAa/aGa	6/15	1	1	FACETS	0.871	0.779	0.969	0.871	0.779	0.969	CLONAL	1	TRUE	0	0.31535747952767	1		325	601	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226228	53226228	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0046844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	164	297	0	ENST00000375401.3:c.2623-2A>C		p.X875_splice	ENST00000375401	NM_004187.3	875			1	1	FACETS	1	0.936	1	1	0.993	1	CLONAL	2	TRUE	0	0.31535747952767	1		297	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0046854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	311	524	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.617687152496242	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.617687152496242	1		524	571	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911016	32911016	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587782454	NA	P-0046854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	30	330	0	ENST00000380152.3:c.2524G>C	p.Val842Leu	p.V842L	ENST00000380152		842	Gta/Cta	11/27	0.33234994612257	1	FACETS	0.162	0.13	0.198	0.162	0.13	0.198	INDETERMINATE	1	TRUE	0	0.617687152496242	1		330	415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0046903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	116	557	1	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.26649233334419	3	FACETS	1	0.98	1	0.68	0.614	0.751	CLONAL	1	TRUE	1	0.268600114595035	3		558	720	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	373	539	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.268600114595035	7	FACETS	1	0.986	1	0.878	0.834	0.921	CLONAL	4	TRUE	2	0.268600114595035	7		539	1058	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621875	1621875	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	77	653	0	ENST00000344749.5:c.917G>A	p.Ser306Asn	p.S306N	ENST00000344749	NM_001136139.2	306	aGc/aAc	11/19	0.189488704122674	2	FACETS	0.831	0.729	0.94	0.415	0.364	0.47	CLONAL	1	TRUE	0	0.268600114595035	2		653	690	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136330	202136330	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	93	330	0	ENST00000358485.4:c.574del	p.Leu192TrpfsTer5	p.L192Wfs*5	ENST00000358485	NM_001080125.1	192	Ctg/tg	3/9	0.268600114595035	5	FACETS	1	0.964	1	0.786	0.703	0.873	CLONAL	2	TRUE	2	0.268600114595035	5		330	412	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600417	10600417	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	166	482	0	ENST00000171111.5:c.1438G>T	p.Gly480Trp	p.G480W	ENST00000171111	NM_203500.1	480	Ggg/Tgg	4/6	0.187487379065287	2	FACETS	0.777	0.713	0.844	0.777	0.713	0.844	SUBCLONAL	2	FALSE	0	0.197109843055604	2		482	1084	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579396	7579405	+	frameshift_variant	Frame_Shift_Del	DEL	GACAGAAGAT	GACAGAAGAT	-	novel	NA	P-0046927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	122	538	0	ENST00000269305.4:c.282_291del	p.Ser95LeufsTer25	p.S95Lfs*25	ENST00000269305	NM_001126112.2	94	tcATCTTCTGTC/tc	4/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.197109843055604	2		538	923	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426126	47426126	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	188	595	0	ENST00000377045.4:c.646C>G	p.Pro216Ala	p.P216A	ENST00000377045	NM_001654.4	216	Ccc/Gcc	7/16	0.197109843055604	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	0	0.197109843055604	1		595	1150	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643248	38643248	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	16	202	0	ENST00000299084.4:c.718C>T	p.Gln240Ter	p.Q240*	ENST00000299084	NM_152594.2	240	Caa/Taa	7/7	1	2	FACETS	1	0.745	1	1	0.745	1	CLONAL	1	FALSE	1	0.197109843055604	2		202	162	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562742	21562743	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	rs1309929430	NA	P-0046927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	211	402	0	ENST00000382592.4:c.1176_1177del	p.His393ArgfsTer6	p.H393Rfs*6	ENST00000382592	NM_014572.2	392	gcGCac/gcac	4/8	1	2	FACETS	1	0.982	1	1	0.994	1	CLONAL	2	FALSE	1	0.197109843055604	2		402	916	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163307822	163307822	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	19	162	0	ENST00000271452.3:c.448G>T	p.Asp150Tyr	p.D150Y	ENST00000271452	NM_145697.2	150	Gac/Tac	7/14	0.166954483465064	3	FACETS	1	0.82	1	0.546	0.416	0.697	CLONAL	1	FALSE	1	0.197109843055604	3		162	194	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800918	243800918	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	43	179	0	ENST00000263826.5:c.556G>T	p.Ala186Ser	p.A186S	ENST00000263826	NM_005465.4	186	Gca/Tca	5/13	0.166954483465064	3	FACETS	0.918	0.78	1	1	0.955	1	CLONAL	3	FALSE	1	0.197109843055604	3		179	174	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606910	43606910	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	156	547	0	ENST00000355710.3:c.1519T>C	p.Ser507Pro	p.S507P	ENST00000355710	NM_020975.4	507	Tca/Cca	7/20	1	2	FACETS	0.832	0.762	0.906	1	0.99	1	CLONAL	2	FALSE	1	0.197109843055604	2		547	951	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656244	18656244	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	23	259	0	ENST00000266497.5:c.2923A>T	p.Thr975Ser	p.T975S	ENST00000266497		975	Acc/Tcc	21/31	0.166954483465064	3	FACETS	1	0.809	1	0.519	0.406	0.649	CLONAL	1	FALSE	1	0.197109843055604	3		259	247	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40371810	40371810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	54	387	1	ENST00000293328.3:c.601G>A	p.Glu201Lys	p.E201K	ENST00000293328	NM_012448.3	201	Gag/Aag	6/19	1	2	FACETS	0.725	0.618	0.842	0.725	0.618	0.842	SUBCLONAL	1	FALSE	1	0.197109843055604	2		388	756	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46275983	46275983	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	76	334	0	ENST00000371998.3:c.3419A>G	p.Asn1140Ser	p.N1140S	ENST00000371998		1140	aAt/aGt	18/23	1	2	FACETS	1	0.892	1	1	0.983	1	CLONAL	2	FALSE	1	0.197109843055604	2		334	381	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739866	41739866	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	69	335	1	ENST00000242208.4:c.107C>A	p.Pro36Gln	p.P36Q	ENST00000242208	NM_002192.2	36	cCg/cAg	2/3	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.197109843055604	2		336	503	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781466	135781466	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	58	284	0	ENST00000298552.3:c.1499G>T	p.Arg500Leu	p.R500L	ENST00000298552	NM_001162426.1	500	cGa/cTa	15/23	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.197109843055604	2		284	456	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342362	70342364	+	missense_variant	Missense_Mutation	TNP	GTG	GTG	TTT	novel	NA	P-0046927-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	76	328	0	ENST00000374080.3:c.1253_1255delinsTTT	p.Arg418_Ala419delinsLeuSer	p.R418_A419delinsLS	ENST00000374080		418	cGTGca/cTTTca	9/45	0.197109843055604	1	FACETS	0.971	0.851	1	0.971	0.851	1	CLONAL	1	FALSE	0	0.197109843055604	1		328	716	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604789	48604789	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046931-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	180	384	0	ENST00000342988.3:c.1611C>A	p.Asp537Glu	p.D537E	ENST00000342988	NM_005359.5	537	gaC/gaA	12/12	0.322880865676111	2	FACETS	0.928	0.861	0.996	0.928	0.861	0.996	CLONAL	2	TRUE	0	0.354059019514958	2		384	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0046931-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	363	709	5	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.354059019514958	2	FACETS	0.977	0.928	1	0.977	0.928	1	CLONAL	2	TRUE	0	0.354059019514958	2		714	1049	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0046931-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	57	308	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.354059019514958	3	FACETS	0.68	0.584	0.786	0.34	0.292	0.393	SUBCLONAL	1	TRUE	1	0.354059019514958	3		308	557	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054377	42054377	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046931-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	147	296	0	ENST00000219905.7:c.7561C>T	p.Gln2521Ter	p.Q2521*	ENST00000219905	NM_001164273.1	2521	Cag/Tag	22/24	0.354059019514958	2	FACETS	0.961	0.886	1	0.961	0.886	1	CLONAL	2	TRUE	0	0.354059019514958	2		296	432	SUCCESS
APC	324	MSKCC	GRCh37	5	112170717	112170718	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATAT	novel	NA	P-0046931-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	270	501	1	ENST00000257430.4:c.1816_1819dup	p.Cys607TyrfsTer28	p.C607Yfs*28	ENST00000257430	NM_000038.5	605	gat/gATATat	15/16	0.354059019514958	3	FACETS	0.971	0.913	1	0.971	0.913	1	CLONAL	2	TRUE	1	0.354059019514958	3		502	924	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0046939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	292	682	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.571070245340639	2	FACETS	0.834	0.795	0.874	0.834	0.795	0.874	CLONAL	2	TRUE	0	0.637411059862482	2		684	549	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0046939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	59	353	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.246283002097092	3	FACETS	1	0.915	1	0.533	0.464	0.606	INDETERMINATE	1	TRUE	1	0.637411059862482	3		353	229	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0046939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	18	471	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.464257328164171	3	FACETS	0.192	0.144	0.249	0.096	0.072	0.125	SUBCLONAL	1	TRUE	1	0.637411059862482	3		471	388	SUCCESS
APC	324	MSKCC	GRCh37	5	112175788	112175788	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	74	215	0	ENST00000257430.4:c.4497del	p.Ser1501LeufsTer6	p.S1501Lfs*6	ENST00000257430	NM_000038.5	1499	ggA/gg	16/16	0.246283002097092	3	FACETS	1	0.971	1	0.657	0.584	0.733	INDETERMINATE	1	TRUE	1	0.637411059862482	3		215	233	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123784	11123784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	81	464	0	ENST00000358026.2:c.2434C>T	p.Leu812Phe	p.L812F	ENST00000358026	NM_001128849.1	812	Ctc/Ttc	16/36	0.464257328164171	3	FACETS	0.673	0.595	0.757	0.336	0.297	0.379	SUBCLONAL	1	TRUE	1	0.637411059862482	3		464	498	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450243	50450243	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757521297	NA	P-0046939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	257	394	0	ENST00000331340.3:c.427C>T	p.Arg143Trp	p.R143W	ENST00000331340	NM_006060.4	143	Cgg/Tgg	5/8	0.474286384390838	5	FACETS	0.884	0.835	0.933	0.884	0.835	0.933	CLONAL	3	TRUE	2	0.637411059862482	5		394	595	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188210	32188210	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	35	739	0	ENST00000375023.3:c.1131C>A	p.Phe377Leu	p.F377L	ENST00000375023	NM_004557.3	377	ttC/ttA	6/30	0.541347525094205	3	FACETS	0.214	0.174	0.258	0.107	0.087	0.129	SUBCLONAL	1	TRUE	1	0.637411059862482	3		739	677	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868928	117868928	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	61	271	0	ENST00000297338.2:c.771G>C	p.Glu257Asp	p.E257D	ENST00000297338	NM_006265.2	257	gaG/gaC	7/14	0.637411059862482	3	FACETS	0.76	0.66	0.868	0.38	0.33	0.434	SUBCLONAL	1	TRUE	1	0.637411059862482	3		271	332	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412472	63412473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046939-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	326	387	0	ENST00000330258.3:c.694dup	p.Gln232ProfsTer20	p.Q232Pfs*20	ENST00000330258	NM_152424.3	232	caa/cCaa	2/2	0.618943629499291	2	FACETS	0.989	0.949	1			1	CLONAL	2	TRUE	NA	0.637411059862482	2		387	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0046940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	632	1013	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.881913690893726	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.881913690893726	1		1013	719	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355374	15355374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781044333	NA	P-0046940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	102	470	0	ENST00000263377.2:c.2249C>T	p.Pro750Leu	p.P750L	ENST00000263377	NM_058243.2	750	cCg/cTg	13/20	0.518679813613707	6	FACETS	0.584	0.521	0.652			1	INDETERMINATE	1	TRUE	NA	0.881913690893726	6		470	1094	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40451808	40451808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766259233	NA	P-0046940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	144	717	1	ENST00000345506.4:c.590G>A	p.Arg197His	p.R197H	ENST00000345506	NM_003152.3	197	cGt/cAt	7/20	0.881913690893726	1	FACETS	0.28	0.256	0.305	0.28	0.256	0.305	SUBCLONAL	1	TRUE	0	0.881913690893726	1		718	652	SUCCESS
ATM	472	MSKCC	GRCh37	11	108126946	108126946	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1565394456	NA	P-0046940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	41	354	0	ENST00000278616.4:c.2129C>A	p.Thr710Lys	p.T710K	ENST00000278616	NM_000051.3	710	aCa/aAa	14/63	1	2	FACETS	0.237	0.198	0.281	0.237	0.198	0.281	SUBCLONAL	1	TRUE	1	0.881913690893726	2		354	392	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496957	29496957	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046941-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	77	137	0	ENST00000356175.3:c.528del	p.Asp176GlufsTer2	p.D176Efs*2	ENST00000356175	NM_000267.3	176	gaT/ga	5/57	NA	2	FACETS	0.942	0.841	1			1	INDETERMINATE	2	TRUE	NA	0.352217680222151	2		137	232	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0046942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	25	239	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	0.855	0.673	1	0.855	0.673	1	CLONAL	1	TRUE	1	0.15	2		239	390	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624239	89624272	+	frameshift_variant	Frame_Shift_Del	DEL	ATCAAAGAGATCGTTAGCAGAAACAAAAGGAGAT	ATCAAAGAGATCGTTAGCAGAAACAAAAGGAGAT	-	novel	NA	P-0046942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	45	150	0	ENST00000371953.3:c.18_51del	p.Glu7ArgfsTer6	p.E7Rfs*6	ENST00000371953	NM_000314.4	5	ATCAAAGAGATCGTTAGCAGAAACAAAAGGAGATat/at	1/9	1	2	FACETS	0.897	0.761	1	1	0.977	1	CLONAL	3	TRUE	1	0.15	2		150	223	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923738	72923738	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	38	542	0	ENST00000268489.5:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000268489	NM_006885.3	1114	Cga/Tga	4/10	1	2	FACETS	0.797	0.657	0.953	0.797	0.657	0.953	CLONAL	1	TRUE	1	0.15	2		542	636	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339230	70339230	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	20	393	0	ENST00000374080.3:c.107T>C	p.Leu36Pro	p.L36P	ENST00000374080		36	cTg/cCg	2/45	1	2	FACETS	0.506	0.385	0.648	0.506	0.385	0.648	SUBCLONAL	1	TRUE	1	0.15	2		393	527	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699498	117699498	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs761558645	NA	P-0046942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	29	245	0	ENST00000369458.3:c.143T>C	p.Ile48Thr	p.I48T	ENST00000369458	NM_024626.3	48	aTt/aCt	3/6	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.15	2		245	352	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485058	57485058	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1802356	NA	P-0046942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	26	274	1	ENST00000371085.3:c.892G>T	p.Ala298Ser	p.A298S	ENST00000371085	NM_000516.4	298	Gct/Tct	11/13	1	2	FACETS	0.932	0.738	1	0.932	0.738	1	CLONAL	1	TRUE	1	0.15	2		275	372	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349258	70349258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519912	NA	P-0046943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	240	332	0	ENST00000374080.3:c.3670C>T	p.Leu1224Phe	p.L1224F	ENST00000374080		1224	Ctc/Ttc	26/45	0.0795286504249586	2	FACETS	1	0.978	1			1	INDETERMINATE	4	FALSE	NA	0.260475185202489	2		332	435	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353879	15353879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753808683	NA	P-0046943-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	152	468	0	ENST00000263377.2:c.3001C>T	p.Pro1001Ser	p.P1001S	ENST00000263377	NM_058243.2	1001	Ccc/Tcc	14/20	1	2	FACETS	0.958	0.88	1	1	0.991	1	CLONAL	2	FALSE	1	0.260475185202489	2		468	609	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40368097	40368097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555548681	NA	P-0046944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	197	422	0	ENST00000293328.3:c.1408G>A	p.Val470Ile	p.V470I	ENST00000293328	NM_012448.3	470	Gtt/Att	12/19	0.546364245525695	1	FACETS	0.338	0.314	0.363	0.338	0.314	0.363	INDETERMINATE	1	TRUE	0	0.932448476943338	1		422	667	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740642	58740642	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs772936724	NA	P-0046944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	127	374	0	ENST00000305921.3:c.1547C>A	p.Ser516Ter	p.S516*	ENST00000305921	NM_003620.3	516	tCa/tAa	6/6	0.546364245525695	1	FACETS	0.28	0.255	0.307	0.28	0.255	0.307	INDETERMINATE	1	TRUE	0	0.932448476943338	1		374	519	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882319	89882320	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0046944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	178	440	1	ENST00000389301.3:c.154_155del	p.Arg52LysfsTer11	p.R52Kfs*11	ENST00000389301	NM_000135.2	52	CGa/a	2/43	0.491399419295522	1	FACETS	0.286	0.264	0.309	0.286	0.264	0.309	INDETERMINATE	1	TRUE	0	0.932448476943338	1		441	712	SUCCESS
APC	324	MSKCC	GRCh37	5	112151290	112151291	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	CT	novel	NA	P-0046944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	137	180	1	ENST00000257430.4:c.933_933+1delinsCT		p.X311_splice	ENST00000257430	NM_000038.5	311		9/16	0.932448476943338	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.932448476943338	1		181	152	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38135369	38135840	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GATAAGCCCAGCTGATGACCCACAAACTAATCCAGGTGCCCAATTGCCAGCAGGTTCCTGAGATGGTCACAAACACACAAACAGACTTCTTTTTTTTTTTTTTTTTGAGATAGAGTCTTGCACTGTCACCCAGGCTGGAGTGCAGTGGTGCGATCTTGGCTCACTGCAAGCTCCGCATCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCACCCATCACCATGCCCAGCTAATTTTTTGTATTTTTAGTAGAGATGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCTGCCCGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCGCGCCCGGCCAAACAGACTTCTTAACAGCCCTACTCCTTATCGCCTGTTGACTGGGGGCGCTCCCCTGCAAGACTGACCTTTGGCCGCACTCCTA	GATAAGCCCAGCTGATGACCCACAAACTAATCCAGGTGCCCAATTGCCAGCAGGTTCCTGAGATGGTCACAAACACACAAACAGACTTCTTTTTTTTTTTTTTTTTGAGATAGAGTCTTGCACTGTCACCCAGGCTGGAGTGCAGTGGTGCGATCTTGGCTCACTGCAAGCTCCGCATCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCACCCATCACCATGCCCAGCTAATTTTTTGTATTTTTAGTAGAGATGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCTGCCCGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCGCGCCCGGCCAAACAGACTTCTTAACAGCCCTACTCCTTATCGCCTGTTGACTGGGGGCGCTCCCCTGCAAGACTGACCTTTGGCCGCACTCCTA	-	novel	NA	P-0046944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	1625	0	0	ENST00000317025.8:c.3851_3867+455del		p.X1284_splice	ENST00000317025	NM_023034.1	1284		22/24	0.932448476943338	13	FACETS	0.977	0.971	0.983			1	CLONAL	13	TRUE	NA	0.932448476943338	13		0	1681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0046945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	184	557	1	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.238758985844559	2	FACETS	0.866	0.8	0.935	0.866	0.8	0.935	CLONAL	2	TRUE	0	0.238758985844559	2		558	890	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168992	11168992	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	217	648	0	ENST00000358026.2:c.4582G>T	p.Glu1528Ter	p.E1528*	ENST00000358026	NM_001128849.1	1528	Gag/Tag	32/36	0.238758985844559	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.238758985844559	2		648	856	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494692	2494692	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	91	721	0	ENST00000355716.4:c.832G>T	p.Gly278Trp	p.G278W	ENST00000355716	NM_003820.2	278	Ggg/Tgg	8/8	0.176196023101666	1	FACETS	0.802	0.711	0.899	0.802	0.711	0.899	CLONAL	1	TRUE	0	0.238758985844559	1		721	837	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245528	153245528	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	96	272	0	ENST00000281708.4:c.1663G>A	p.Val555Met	p.V555M	ENST00000281708	NM_033632.3	555	Gtg/Atg	11/12	0.238758985844559	3	FACETS	0.843	0.753	0.938	0.843	0.753	0.938	CLONAL	2	TRUE	1	0.238758985844559	3		272	534	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961219	41961219	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	219	307	0	ENST00000219905.7:c.127A>T	p.Thr43Ser	p.T43S	ENST00000219905	NM_001164273.1	43	Act/Tct	2/24	0.238758985844559	4	FACETS	0.988	0.926	1	0.988	0.926	1	CLONAL	4	TRUE	0	0.238758985844559	4		307	575	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923488	9923488	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	163	375	0	ENST00000330684.3:c.1799C>G	p.Thr600Arg	p.T600R	ENST00000330684	NM_001134407.1	600	aCa/aGa	9/13	0.220894654143899	5	FACETS	0.961	0.886	1	0.961	0.886	1	CLONAL	3	TRUE	2	0.238758985844559	5		375	643	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584525	48584525	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	46	337	0	ENST00000342988.3:c.698A>T	p.His233Leu	p.H233L	ENST00000342988	NM_005359.5	233	cAt/cTt	6/12	0.238758985844559	3	FACETS	0.759	0.639	0.893	0.38	0.319	0.447	SUBCLONAL	1	TRUE	1	0.238758985844559	3		337	568	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217771	2217771	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	233	671	0	ENST00000398665.3:c.2545G>T	p.Gly849Cys	p.G849C	ENST00000398665	NM_032482.2	849	Ggc/Tgc	22/28	0.238758985844559	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.238758985844559	2		671	944	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257890	19257890	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	296	965	0	ENST00000162023.5:c.496C>G	p.Arg166Gly	p.R166G	ENST00000162023		166	Cgc/Ggc	9/13	0.238758985844559	2	FACETS	0.913	0.858	0.969	0.913	0.858	0.969	CLONAL	2	TRUE	0	0.238758985844559	2		965	1358	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61722607	61722607	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	68	114	0	ENST00000401558.2:c.1030A>G	p.Arg344Gly	p.R344G	ENST00000401558	NM_003400.3	344	Agg/Ggg	11/25	0.238758985844559	4	FACETS	0.997	0.872	1	0.997	0.872	1	CLONAL	2	TRUE	2	0.238758985844559	4		114	354	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41554484	41554484	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	125	401	1	ENST00000263253.7:c.3571del	p.Tyr1191IlefsTer36	p.Y1191Ifs*36	ENST00000263253	NM_001429.3	1190	acT/ac	19/31	0.238758985844559	2	FACETS	0.85	0.771	0.932	0.85	0.771	0.932	CLONAL	2	TRUE	0	0.238758985844559	2		402	616	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231217	142231217	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	76	349	0	ENST00000350721.4:c.4737G>C	p.Gln1579His	p.Q1579H	ENST00000350721	NM_001184.3	1579	caG/caC	27/47	0.238758985844559	6	FACETS	1	0.915	1	0.265	0.231	0.301	CLONAL	1	TRUE	2	0.238758985844559	6		349	889	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818789	170818789	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	53	231	0	ENST00000296930.5:c.338G>C	p.Gly113Ala	p.G113A	ENST00000296930	NM_002520.6	113	gGa/gCa	4/11	0.229551079135344	3	FACETS	1	0.876	1	0.514	0.439	0.597	CLONAL	1	TRUE	1	0.238758985844559	3		231	483	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522034	157522034	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	77	500	1	ENST00000346085.5:c.4306G>A	p.Gly1436Arg	p.G1436R	ENST00000346085	NM_020732.3	1436	Ggg/Agg	18/20	0.229551079135344	3	FACETS	0.941	0.826	1	0.471	0.413	0.533	CLONAL	1	TRUE	1	0.238758985844559	3		501	767	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950434	68950434	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	37	342	0	ENST00000288368.4:c.746G>C	p.Cys249Ser	p.C249S	ENST00000288368	NM_024870.2	249	tGt/tCt	7/40	0.238758985844559	3	FACETS	0.596	0.49	0.715	0.298	0.245	0.358	SUBCLONAL	1	TRUE	1	0.238758985844559	3		342	582	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225362535	225362540	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGTC	GCTGTC	T	novel	NA	P-0046945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	72	298	0	ENST00000264414.4:c.1637_1642delinsA	p.Arg546HisfsTer21	p.R546Hfs*21	ENST00000264414	NM_003590.4	546	cGACAGCtc/cAtc	12/16	0.230008931243373	3	FACETS	1	0.969	1			1	CLONAL	1	TRUE	NA	0.238758985844559	3		298	497	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	12	516	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.826	0.585	1	0.826	0.585	1	CLONAL	1	TRUE	1	0.266640244897919	2		516	109	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610073	10610073	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	73	507	0	ENST00000171111.5:c.637G>T	p.Glu213Ter	p.E213*	ENST00000171111	NM_203500.1	213	Gag/Tag	2/6	0.198140070636527	2	FACETS	1	0.975	1	0.734	0.646	0.828	CLONAL	1	TRUE	0	0.266640244897919	2		507	373	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921499	39921499	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	59	242	0	ENST00000378444.4:c.4321C>T	p.Gln1441Ter	p.Q1441*	ENST00000378444	NM_001123385.1	1441	Cag/Tag	10/15	0.264248136966938	2	FACETS	0.946	0.824	1			1	CLONAL	2	TRUE	NA	0.266640244897919	2		242	234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579312	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0046946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	70	472	0	ENST00000269305.4:c.375_375+1delinsTT		p.X125_splice	ENST00000269305	NM_001126112.2	125		4/11	0.266640244897919	3	FACETS	0.791	0.694	0.895	0.528	0.462	0.597	SUBCLONAL	2	TRUE	0	0.266640244897919	3		472	376	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450158	32450158	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	63	552	2	ENST00000332351.3:c.654C>A	p.Ser218Arg	p.S218R	ENST00000332351	NM_024426.4	218	agC/agA	2/10	0.198140070636527	2	FACETS	1	0.959	1	0.639	0.555	0.728	CLONAL	1	TRUE	0	0.266640244897919	2		554	370	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588111	69588111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	64	450	0	ENST00000168712.1:c.587C>T	p.Thr196Ile	p.T196I	ENST00000168712	NM_002007.2	196	aCc/aTc	3/3	0.178323792088972	4	FACETS	1	0.965	1	0.676	0.587	0.772	CLONAL	1	TRUE	2	0.266640244897919	4		450	450	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204894	94204894	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1481968823	NA	P-0046946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	17	249	0	ENST00000323929.3:c.691G>C	p.Glu231Gln	p.E231Q	ENST00000323929	NM_005591.3	231	Gaa/Caa	8/20	0.178323792088972	4	FACETS	1	0.893	1	0.702	0.53	0.901	CLONAL	1	TRUE	2	0.266640244897919	4		249	115	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164837	47164837	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	47	197	0	ENST00000409792.3:c.1289C>G	p.Ser430Cys	p.S430C	ENST00000409792	NM_014159.6	430	tCt/tGt	3/21	0.266640244897919	3	FACETS	0.965	0.824	1	0.643	0.549	0.744	CLONAL	2	TRUE	0	0.266640244897919	3		197	207	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52649448	52649448	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	72	329	0	ENST00000394830.3:c.1843G>T	p.Glu615Ter	p.E615*	ENST00000394830	NM_018313.4	615	Gag/Tag	16/30	0.266640244897919	3	FACETS	1	0.939	1	0.734	0.648	0.824	CLONAL	2	TRUE	0	0.266640244897919	3		329	278	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902728	1902728	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	73	437	0	ENST00000382891.5:c.347C>G	p.Pro116Arg	p.P116R	ENST00000382891	NM_133335.3	116	cCt/cGt	2/22	0.156010972725795	3	FACETS	1	0.971	1	0.699	0.613	0.79	INDETERMINATE	1	TRUE	1	0.266640244897919	3		437	444	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127397	55127397	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	42	379	0	ENST00000257290.5:c.185C>A	p.Ser62Tyr	p.S62Y	ENST00000257290	NM_006206.4	62	tCt/tAt	3/23	0.156010972725795	3	FACETS	0.834	0.697	0.986	0.417	0.348	0.493	INDETERMINATE	1	TRUE	1	0.266640244897919	3		379	428	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127409	55127409	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	54	381	0	ENST00000257290.5:c.197G>A	p.Ser66Asn	p.S66N	ENST00000257290	NM_006206.4	66	aGc/aAc	3/23	0.156010972725795	3	FACETS	1	0.899	1	0.531	0.455	0.615	INDETERMINATE	1	TRUE	1	0.266640244897919	3		381	432	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526521	31526523	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0046946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	31	531	0	ENST00000344624.3:c.517_519del	p.Ser173del	p.S173del	ENST00000344624		173	TCT/-	2/33	1	2	FACETS	0.614	0.496	0.746	0.614	0.496	0.746	SUBCLONAL	1	TRUE	1	0.266640244897919	2		531	379	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045730	26045730	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	76	302	0	ENST00000540144.1:c.92C>A	p.Pro31Gln	p.P31Q	ENST00000540144	NM_003531.2	31	cCg/cAg	1/1	0.266640244897919	5	FACETS	1	0.964	1	0.618	0.546	0.693	CLONAL	2	TRUE	1	0.266640244897919	5		302	323	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683662	162683662	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	24	208	0	ENST00000366898.1:c.307A>G	p.Thr103Ala	p.T103A	ENST00000366898	NM_004562.2	103	Act/Gct	3/12	0.197809639987769	2	FACETS	0.9	0.71	1	0.45	0.355	0.559	CLONAL	1	TRUE	0	0.266640244897919	2		208	200	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350087	81350087	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	24	246	0	ENST00000222390.5:c.1245G>A	p.Trp415Ter	p.W415*	ENST00000222390	NM_000601.4	415	tgG/tgA	10/18	0.266640244897919	5	FACETS	1	0.899	1	0.63	0.497	0.782	CLONAL	1	TRUE	3	0.266640244897919	5		246	200	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534951	5534951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	53	334	0	ENST00000397747.3:c.262C>T	p.His88Tyr	p.H88Y	ENST00000397747	NM_025239.3	88	Cac/Tac	3/7	0.20712803154688	2	FACETS	1	0.944	1	0.606	0.519	0.7	CLONAL	1	TRUE	0	0.266640244897919	2		334	328	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555731	21555732	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	226	880	0	ENST00000382592.4:c.2538dup	p.Asn847Ter	p.N847*	ENST00000382592	NM_014572.2	846	-/T	6/8	0.470009543226474	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.470009543226474	1		880	635	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005717	150005717	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	63	316	0	ENST00000253339.5:c.508C>T	p.Gln170Ter	p.Q170*	ENST00000253339		170	Caa/Taa	3/7	0.470009543226474	1	FACETS	0.844	0.739	0.955	0.844	0.739	0.955	CLONAL	1	TRUE	0	0.470009543226474	1		316	243	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436306	52436306	+	stop_lost	Nonstop_Mutation	SNP	A	A	T	novel	NA	P-0046948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	159	927	0	ENST00000460680.1:c.2188T>A	p.Ter730ArgextTer205	p.*730Rext*205	ENST00000460680	NM_004656.3	730	Tga/Aga	17/17	0.470009543226474	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.470009543226474	1		927	490	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0046950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	376	349	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.709797081507156	4	FACETS	0.851	0.815	0.887	1	0.995	1	CLONAL	3	TRUE	2	0.712113452348773	4		349	708	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578393	7578393	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876660821	NA	P-0046950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	262	943	0	ENST00000269305.4:c.537T>G	p.His179Gln	p.H179Q	ENST00000269305	NM_001126112.2	179	caT/caG	5/11	0.608125133815078	2	FACETS	0.823	0.784	0.862	0.823	0.784	0.862	CLONAL	2	TRUE	0	0.712113452348773	2		943	447	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106182985	106182998	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CCTGATGCATATAA	CCTGATGCATATAA	TAG	novel	NA	P-0046950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	65	273	0	ENST00000380013.4:c.4024_4037delinsTAG	p.Pro1342Ter	p.P1342*	ENST00000380013	NM_001127208.2	1342	CCTGATGCATATAAt/TAGt	8/11	1	2	FACETS	0.956	0.844	1	0.956	0.844	1	CLONAL	1	TRUE	1	0.712113452348773	2		273	191	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696450	47696450	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	165	466	0	ENST00000347630.2:c.373T>C	p.Phe125Leu	p.F125L	ENST00000347630	NM_001007230.1	125	Ttt/Ctt	6/11	0.340315213197074	1	FACETS	0.941	0.869	1	0.941	0.869	1	CLONAL	1	TRUE	0	0.487634832819215	1		466	544	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246405	46246405	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0046951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	104	315	0	ENST00000334344.6:c.4499C>G	p.Ser1500Ter	p.S1500*	ENST00000334344	NM_152641.2	1500	tCa/tGa	15/21	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.487634832819215	2		315	372	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353791	40353791	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs765607800	NA	P-0046951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	58	768	0	ENST00000293328.3:c.2329A>G	p.Met777Val	p.M777V	ENST00000293328	NM_012448.3	777	Atg/Gtg	19/19	0.340315213197074	1	FACETS	0.223	0.191	0.258	0.223	0.191	0.258	SUBCLONAL	1	TRUE	0	0.487634832819215	1		768	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0046952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	525	757	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.559500209840229	4	FACETS	0.923	0.899	0.947	0.923	0.899	0.947	CLONAL	4	TRUE	0	0.682423611183073	4		757	701	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0046952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	41	204	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.576918678470653	3	FACETS	0.814	0.686	0.953			1	CLONAL	1	TRUE	NA	0.682423611183073	3		204	198	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492861	8492861	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0046952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	113	463	0	ENST00000356435.5:c.2467+1G>T		p.X823_splice	ENST00000356435		823			0.30682017754726	1	FACETS	0.598	0.543	0.654	0.598	0.543	0.654	INDETERMINATE	1	TRUE	0	0.682423611183073	1		463	365	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115972	8115973	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0046953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	155	375	0	ENST00000346208.3:c.1320dup	p.Ala441ArgfsTer66	p.A441Rfs*66	ENST00000346208		440	acc/aCcc	6/6	0.249411600732205	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.249411600732205	3		375	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0046954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3	24	552	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.749017885447645	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.802503823955571	1		553	27	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974771	21974771	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	27	351	0	ENST00000304494.5:c.56C>G	p.Ala19Gly	p.A19G	ENST00000304494	NM_000077.4	19	gCc/gGc	1/3	1	2	FACETS	0.922	0.76	1	0.922	0.76	1	CLONAL	1	TRUE	1	0.802503823955571	2		351	73	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711017	114711018	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	59	327	0	ENST00000543371.1:c.244dup	p.Ser82LysfsTer15	p.S82Kfs*15	ENST00000543371	NM_001198531.1	81	gaa/gAaa	2/14	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.802503823955571	2		327	117	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256200	41256200	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs80357189	NA	P-0046954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	16	553	0	ENST00000357654.3:c.380G>T	p.Ser127Ile	p.S127I	ENST00000357654	NM_007294.3	127	aGt/aTt	6/23	1	2	FACETS	0.886	0.685	1	0.886	0.685	1	CLONAL	1	TRUE	1	0.802503823955571	2		553	45	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256210	41256210	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs80357448	NA	P-0046954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	14	512	0	ENST00000357654.3:c.370A>G	p.Ile124Val	p.I124V	ENST00000357654	NM_007294.3	124	Atc/Gtc	6/23	1	2	FACETS	0.895	0.679	1	0.895	0.679	1	CLONAL	1	TRUE	1	0.802503823955571	2		512	39	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660664	190660664	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773719324	NA	P-0046954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	13	343	0	ENST00000441310.2:c.302G>A	p.Cys101Tyr	p.C101Y	ENST00000441310	NM_000534.4	101	tGt/tAt	3/13	0.802503823955571	3	FACETS	0.631	0.458	0.831	0.315	0.229	0.416	SUBCLONAL	1	TRUE	1	0.802503823955571	3		343	72	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031284	36031284	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0046954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	55	603	1	ENST00000358208.4:c.1402+1G>A		p.X468_splice	ENST00000358208		468			0.802503823955571	5	FACETS	1	0.969	1	0.491	0.426	0.56	CLONAL	1	TRUE	2	0.802503823955571	5		604	205	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528313	157528313	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	42	859	0	ENST00000346085.5:c.6038G>A	p.Trp2013Ter	p.W2013*	ENST00000346085	NM_020732.3	2013	tGg/tAg	20/20	0.527932713506948	4	FACETS	1	0.857	1	0.338	0.286	0.395	CLONAL	1	TRUE	1	0.802503823955571	4		859	186	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459535	50459535	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	21	307	0	ENST00000331340.3:c.824A>T	p.Lys275Met	p.K275M	ENST00000331340	NM_006060.4	275	aAg/aTg	7/8	0.802503823955571	4	FACETS	1	0.914	1	0.449	0.357	0.55	CLONAL	1	TRUE	1	0.802503823955571	4		307	70	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146093	38146093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	45	761	0	ENST00000317025.8:c.3413G>A	p.Cys1138Tyr	p.C1138Y	ENST00000317025	NM_023034.1	1138	tGc/tAc	19/24	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.802503823955571	2		761	91	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911543	39911543	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	77	617	0	ENST00000378444.4:c.5087A>C	p.Glu1696Ala	p.E1696A	ENST00000378444	NM_001123385.1	1696	gAa/gCa	15/15	0.672790965678829	3	FACETS	0.944	0.885	0.995	1	0.987	1	CLONAL	3	TRUE	1	0.802503823955571	3		617	95	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0046955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	42	349	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.87	0.726	1	0.87	0.726	1	CLONAL	1	TRUE	1	0.19	2		349	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0046955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	55	683	0	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	1	2	FACETS	0.871	0.744	1	0.871	0.744	1	CLONAL	1	TRUE	1	0.19	2		683	665	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853077	151853077	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	47	388	0	ENST00000262189.6:c.11878C>T	p.Arg3960Ter	p.R3960*	ENST00000262189	NM_170606.2	3960	Cga/Tga	46/59	1	2	FACETS	0.948	0.8	1	0.948	0.8	1	CLONAL	1	TRUE	1	0.19	2		388	522	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593484	48593484	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	54	291	0	ENST00000342988.3:c.1235del	p.Tyr412SerfsTer3	p.Y412Sfs*3	ENST00000342988	NM_005359.5	412	tAc/tc	10/12	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.19	2		291	465	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227915	123227915	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	34	372	0	ENST00000218089.9:c.3626A>T	p.Glu1209Val	p.E1209V	ENST00000218089	NM_001042749.1	1209	gAa/gTa	33/35	1	2	FACETS	0.808	0.66	0.974	0.808	0.66	0.974	CLONAL	1	TRUE	1	0.19	2		372	443	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215595215	215595215	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	16	288	0	ENST00000260947.4:c.1921del	p.Arg641GlufsTer73	p.R641Efs*73	ENST00000260947	NM_000465.2	641	Cga/ga	10/11	1	2	FACETS	0.604	0.449	0.787	0.604	0.449	0.787	SUBCLONAL	1	FALSE	1	0.333092971133051	2		288	159	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145481	24145481	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0046956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	61	551	0	ENST00000263121.7:c.501-1G>A		p.X167_splice	ENST00000263121	NM_003073.3	167			0.333092971133051	1	FACETS	0.672	0.581	0.771	0.672	0.581	0.771	SUBCLONAL	1	FALSE	0	0.333092971133051	1		551	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934573	NA	P-0046957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	237	708	1	ENST00000269305.4:c.722C>A	p.Ser241Tyr	p.S241Y	ENST00000269305	NM_001126112.2	241	tCc/tAc	7/11	0.312899969465878	1	FACETS	0.775	0.726	0.827	1	0.993	1	SUBCLONAL	2	TRUE	0	0.312899969465878	1		709	824	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913428	32913428	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs886038111	NA	P-0046957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	60	340	0	ENST00000380152.3:c.4936G>T	p.Glu1646Ter	p.E1646*	ENST00000380152		1646	Gaa/Taa	11/27	0.312899969465878	1	FACETS	0.763	0.659	0.875	0.763	0.659	0.875	SUBCLONAL	1	TRUE	0	0.312899969465878	1		340	424	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729975	41729979	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCC	CTGCC	-	novel	NA	P-0046957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	98	803	0	ENST00000242208.4:c.550_554del	p.Gly184LeufsTer18	p.G184Lfs*18	ENST00000242208	NM_002192.2	184	GGCAGc/c	3/3	1	2	FACETS	0.986	0.881	1	0.986	0.881	1	CLONAL	1	TRUE	1	0.312899969465878	2		803	635	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0046960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	91	164	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.716028612702411	3	FACETS	0.888	0.796	0.985	0.444	0.398	0.493	CLONAL	1	TRUE	1	0.817727161078559	3		164	353	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411818	116412557	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCATGAGTTCTGGGCACTGGGTCAAAGTCTCCTGGGGCCCATGATAGCCGTCTTTAACAAGCTCTTTCTTTCTCTCTGTTTTAAGATCTGGGCAGTGAATTAGTTCGCTACGATGCAAGAGTACACACTCCTCATTTGGATAGGCTTGTAAGTGCCCGAAGTGTAAGCCCAACTACAGAAATGGTTTCAAATGAATCTGTAGACTACCGAGCTACTTTTCCAGAAGGTATATTTCAGTTTATTGTTCTGAGAAATACCTATACATATACCTCAGTGGGTTGTGACATTGTTGTTTATTTTTGGTTTTGCATTTATATTTTTATAAAAACCTAAAGGAAGTATTTACCTCTGCCAAGTAAGTATTTGACACAAAATTACATGGCTCTTAATTTTAAAAGAACCCATGTATATATTACATTATGATTTTAGAGTCCATAAGCTCTCATTTCACAAAAAGGTTAATTTGAGCAAAAGTAATTTGTTTATCATCTAAGTGCAATAGTAAGAAATTGCGAAGCTCTCTTTTACAATCCAGGAAGAGTTAAGTTACAAAATATACTTATTTAAATGTAAGTTGGAACTGCTACATTTTTTACCTGTTGAAGCCCAAACATTGAAATTATACTGTTAGTAATTCTTCGAAGTGTTTTCAATGAACTGTTAGTACACAGCCTTTTTCCCACCATATTCTAGGACTTGAATGTATTTTGAGACTTAGCCAAGGAAAACCTTCAATTATG	CCATGAGTTCTGGGCACTGGGTCAAAGTCTCCTGGGGCCCATGATAGCCGTCTTTAACAAGCTCTTTCTTTCTCTCTGTTTTAAGATCTGGGCAGTGAATTAGTTCGCTACGATGCAAGAGTACACACTCCTCATTTGGATAGGCTTGTAAGTGCCCGAAGTGTAAGCCCAACTACAGAAATGGTTTCAAATGAATCTGTAGACTACCGAGCTACTTTTCCAGAAGGTATATTTCAGTTTATTGTTCTGAGAAATACCTATACATATACCTCAGTGGGTTGTGACATTGTTGTTTATTTTTGGTTTTGCATTTATATTTTTATAAAAACCTAAAGGAAGTATTTACCTCTGCCAAGTAAGTATTTGACACAAAATTACATGGCTCTTAATTTTAAAAGAACCCATGTATATATTACATTATGATTTTAGAGTCCATAAGCTCTCATTTCACAAAAAGGTTAATTTGAGCAAAAGTAATTTGTTTATCATCTAAGTGCAATAGTAAGAAATTGCGAAGCTCTCTTTTACAATCCAGGAAGAGTTAAGTTACAAAATATACTTATTTAAATGTAAGTTGGAACTGCTACATTTTTTACCTGTTGAAGCCCAAACATTGAAATTATACTGTTAGTAATTCTTCGAAGTGTTTTCAATGAACTGTTAGTACACAGCCTTTTTCCCACCATATTCTAGGACTTGAATGTATTTTGAGACTTAGCCAAGGAAAACCTTCAATTATG	-	novel	NA	P-0046961-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	227	785	0	ENST00000397752.3:c.2888-79_3028+520del		p.X963_splice	ENST00000397752	NM_000245.2	963		14/21	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		785	1135	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0046962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	39	1013	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.1	0.082	0.12	0.1	0.082	0.12	SUBCLONAL	1	TRUE	1	0.707630469265711	2		1013	1104	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467823	50467823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	69	683	0	ENST00000331340.3:c.1058C>T	p.Pro353Leu	p.P353L	ENST00000331340	NM_006060.4	353	cCg/cTg	8/8	0.707630469265711	3	FACETS	0.268	0.232	0.307	0.134	0.116	0.154	SUBCLONAL	1	TRUE	1	0.707630469265711	3		683	985	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441813	49441813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	287	800	1	ENST00000301067.7:c.4171G>A	p.Glu1391Lys	p.E1391K	ENST00000301067	NM_003482.3	1391	Gag/Aag	14/54	1	2	FACETS	0.947	0.893	1	0.947	0.893	1	CLONAL	1	TRUE	1	0.707630469265711	2		801	857	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860599	45860599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1381	449	1742	0	ENST00000391945.4:c.1408A>G	p.Ile470Val	p.I470V	ENST00000391945	NM_000400.3	470	Atc/Gtc	15/23	1	2	FACETS	0.693	0.66	0.728	0.693	0.66	0.728	SUBCLONAL	1	TRUE	1	0.707630469265711	2		1742	1830	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023080	31023081	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGCCTGCAGAACAGAGC	novel	NA	P-0046962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	243	566	0	ENST00000375687.4:c.2566_2582dup	p.Phe862AlafsTer11	p.F862Afs*11	ENST00000375687	NM_015338.5	855	-/TGCCTGCAGAACAGAGC	13/13	0.707630469265711	3	FACETS	0.895	0.836	0.955	0.447	0.418	0.478	CLONAL	1	TRUE	1	0.707630469265711	3		566	1039	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0046963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	23	396	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.746	0.581	0.936	0.746	0.581	0.936	CLONAL	1	TRUE	1	0.179813798886198	2		396	343	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602329	10602329	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	178	1194	0	ENST00000171111.5:c.1249G>T	p.Gly417Trp	p.G417W	ENST00000171111	NM_203500.1	417	Ggg/Tgg	3/6	0.179813798886198	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.179813798886198	1		1194	1232	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218415	1218415	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs112675807	NA	P-0046963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	78	493	0	ENST00000326873.7:c.291-1G>A		p.X97_splice	ENST00000326873	NM_000455.4	97			0.179813798886198	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.179813798886198	1		493	576	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220720	2220720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	43	559	1	ENST00000326181.6:c.337G>A	p.Glu113Lys	p.E113K	ENST00000326181	NM_032271.2	113	Gag/Aag	5/21	1	2	FACETS	0.757	0.632	0.895	0.757	0.632	0.895	SUBCLONAL	1	TRUE	1	0.179813798886198	2		560	632	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831475	89831475	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0046963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	53	513	0	ENST00000389301.3:c.2602-1G>C		p.X868_splice	ENST00000389301	NM_000135.2	868			1	2	FACETS	0.951	0.81	1	0.951	0.81	1	CLONAL	1	TRUE	1	0.179813798886198	2		513	620	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039609	47039609	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0046963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	62	301	0	ENST00000377604.3:c.1063-2A>T		p.X355_splice	ENST00000377604	NM_001204468.1	355			1	1	FACETS	0.897	0.779	1	1	0.977	1	CLONAL	2	TRUE	0	0.179813798886198	1		301	350	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0046964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	54	193	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.255570256573045	5	FACETS	1	0.955	1	0.826	0.719	0.938	CLONAL	2	TRUE	2	0.424504328724627	5		193	168	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	262	1078	6	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.957	1	1	0.995	1	CLONAL	2	TRUE	1	0.287821569681062	2		1084	890	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587777894	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	25	445	1	ENST00000361445.4:c.6644C>A	p.Ser2215Tyr	p.S2215Y	ENST00000361445	NM_004958.3	2215	tCt/tAt	47/58	0.287821569681062	3	FACETS	0.24	0.188	0.301	0.12	0.094	0.151	SUBCLONAL	1	TRUE	1	0.287821569681062	3		446	827	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	387	436	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	0.287821569681062	3	FACETS	0.934	0.893	0.976	1	0.997	1	CLONAL	4	TRUE	1	0.287821569681062	3		436	823	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	77	295	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.889	0.788	0.995	1	0.982	1	CLONAL	2	TRUE	1	0.287821569681062	2		295	301	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139794123	139794123	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs200834553	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	125	347	0	ENST00000247668.2:c.266C>T	p.Ser89Leu	p.S89L	ENST00000247668	NM_021138.3	89	tCg/tTg	3/11	1	2	FACETS	1	0.967	1	1	0.991	1	CLONAL	2	TRUE	1	0.287821569681062	2		347	389	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277291	41277291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	115	255	0	ENST00000349496.5:c.1760G>A	p.Arg587Gln	p.R587Q	ENST00000349496	NM_001904.3	587	cGa/cAa	11/15	1	2	FACETS	1	0.963	1	1	0.99	1	CLONAL	2	TRUE	1	0.287821569681062	2		255	359	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	23	193	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.929	0.743	1	1	0.947	1	CLONAL	2	TRUE	1	0.287821569681062	2		193	86	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104712	193104712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	61	188	0	ENST00000367435.3:c.416G>A	p.Arg139Gln	p.R139Q	ENST00000367435	NM_024529.4	139	cGa/cAa	5/17	0.287821569681062	3	FACETS	0.911	0.811	1	1	0.981	1	CLONAL	4	TRUE	1	0.287821569681062	3		188	133	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182637	38182637	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs748659894	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	36	253	1	ENST00000396334.3:c.790C>T	p.Arg264Ter	p.R264*	ENST00000396334	NM_002468.4	264	Cga/Tga	5/5	1	2	FACETS	0.669	0.551	0.801	0.669	0.551	0.801	SUBCLONAL	1	TRUE	1	0.287821569681062	2		254	374	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504401	8504401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757922864	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	109	331	0	ENST00000356435.5:c.1682G>A	p.Arg561Gln	p.R561Q	ENST00000356435		561	cGa/cAa	12/35	1	2	FACETS	1	0.944	1	1	0.989	1	CLONAL	2	TRUE	1	0.287821569681062	2		331	358	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232132	98232132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778627715	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	118	215	0	ENST00000331920.6:c.1810G>A	p.Glu604Lys	p.E604K	ENST00000331920	NM_000264.3	604	Gag/Aag	13/24	1	2	FACETS	1	0.977	1	1	0.991	1	CLONAL	2	TRUE	1	0.287821569681062	2		215	338	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568563	41568563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555911574	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	48	419	0	ENST00000263253.7:c.4513G>A	p.Glu1505Lys	p.E1505K	ENST00000263253	NM_001429.3	1505	Gag/Aag	28/31	0.287821569681062	1	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	0	0.287821569681062	1		419	272	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509637	106509637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766453335	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	120	393	0	ENST00000359195.3:c.1631G>A	p.Arg544Gln	p.R544Q	ENST00000359195	NM_002649.2	544	cGa/cAa	2/11	0.280185935080151	3	FACETS	1	0.979	1	0.439	0.397	0.484	CLONAL	1	TRUE	0	0.287821569681062	3		393	724	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961336	15961336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200722329	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	176	397	0	ENST00000268712.3:c.6053G>A	p.Arg2018Gln	p.R2018Q	ENST00000268712	NM_006311.3	2018	cGa/cAa	39/46	1	2	FACETS	1	0.976	1	1	0.993	1	CLONAL	2	TRUE	1	0.287821569681062	2		397	546	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922896	39922896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs892857458	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	325	551	1	ENST00000378444.4:c.3812C>T	p.Ser1271Leu	p.S1271L	ENST00000378444	NM_001123385.1	1271	tCg/tTg	8/15	0.265499264737894	1	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	0	0.287821569681062	1		552	853	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111958593	111958593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555186772	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	153	321	1	ENST00000375549.3:c.65G>A	p.Arg22Gln	p.R22Q	ENST00000375549	NM_003002.3	22	cGa/cAa	2/4	1	2	FACETS	1	0.967	1	1	0.992	1	CLONAL	2	TRUE	1	0.287821569681062	2		322	488	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549428	187549428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2304867	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	266	450	1	ENST00000441802.2:c.4690G>A	p.Ala1564Thr	p.A1564T	ENST00000441802	NM_005245.3	1564	Gct/Act	9/27	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.287821569681062	2		451	763	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259477	89259477	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200567888	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	56	368	0	ENST00000336596.2:c.621G>T	p.Lys207Asn	p.K207N	ENST00000336596	NM_005233.5	207	aaG/aaT	3/17	1	2	FACETS	0.859	0.737	0.991	0.859	0.737	0.991	CLONAL	1	TRUE	1	0.287821569681062	2		368	453	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576801	212576801	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	31	284	0	ENST00000342788.4:c.1098G>T	p.Leu366Phe	p.L366F	ENST00000342788	NM_005235.2	366	ttG/ttT	9/28	0.196589372134191	2	FACETS	1	0.905	1	0.592	0.483	0.712	CLONAL	1	TRUE	0	0.287821569681062	2		284	182	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793710	89793710	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	84	216	0	ENST00000336032.3:c.779A>C	p.Lys260Thr	p.K260T	ENST00000336032	NM_006813.2	260	aAa/aCa	2/2	1	2	FACETS	0.888	0.8	0.98	1	0.988	1	CLONAL	3	TRUE	1	0.287821569681062	2		216	219	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431664	431664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	157	335	0	ENST00000399788.2:c.2345G>A	p.Arg782Gln	p.R782Q	ENST00000399788	NM_001042603.1	782	cGa/cAa	17/28	1	2	FACETS	1	0.981	1	1	0.993	1	CLONAL	2	TRUE	1	0.287821569681062	2		335	460	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	190	393	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	1	0.982	1	1	0.994	1	CLONAL	2	TRUE	1	0.287821569681062	2		393	570	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335121	65335121	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	176	384	0	ENST00000342505.4:c.520C>T	p.Arg174Ter	p.R174*	ENST00000342505	NM_002227.2	174	Cga/Tga	6/25	0.287821569681062	3	FACETS	0.989	0.914	1	0.989	0.914	1	CLONAL	2	TRUE	1	0.287821569681062	3		384	707	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641904	12641904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752713997	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	102	185	0	ENST00000251849.4:c.845G>A	p.Arg282Gln	p.R282Q	ENST00000251849	NM_002880.3	282	cGa/cAa	8/17	1	2	FACETS	0.844	0.766	0.924	1	0.99	1	CLONAL	3	TRUE	1	0.287821569681062	2		185	280	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573894	18573894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759658584	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	40	239	0	ENST00000266497.5:c.2212C>T	p.Arg738Cys	p.R738C	ENST00000266497		738	Cgt/Tgt	15/31	1	2	FACETS	1	0.899	1	1	0.972	1	CLONAL	2	TRUE	1	0.287821569681062	2		239	129	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941657	48941657	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1060503077	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	15	144	0	ENST00000267163.4:c.967G>T	p.Glu323Ter	p.E323*	ENST00000267163	NM_000321.2	323	Gaa/Taa	10/27	0.265499264737894	1	FACETS	0.797	0.601	1	1	0.907	1	CLONAL	2	TRUE	0	0.287821569681062	1		144	56	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001303	29001303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201407326	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	91	200	1	ENST00000282397.4:c.1429G>A	p.Glu477Lys	p.E477K	ENST00000282397	NM_002019.4	477	Gaa/Aaa	10/30	0.265499264737894	1	FACETS	0.963	0.867	1	1	0.986	1	CLONAL	2	TRUE	0	0.287821569681062	1		201	281	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740216	162740216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775098890	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	351	388	1	ENST00000367921.3:c.1418G>A	p.Arg473His	p.R473H	ENST00000367921	NM_006182.2	473	cGc/cAc	12/18	0.287821569681062	3	FACETS	0.981	0.937	1	1	0.996	1	CLONAL	4	TRUE	1	0.287821569681062	3		389	711	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026752	48026752	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	90	296	0	ENST00000234420.5:c.1630G>T	p.Glu544Ter	p.E544*	ENST00000234420	NM_000179.2	544	Gaa/Taa	4/10	0.265499264737894	1	FACETS	0.839	0.752	0.93	1	0.984	1	CLONAL	2	TRUE	0	0.287821569681062	1		296	319	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649686	48649686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	198	820	1	ENST00000376670.3:c.170C>T	p.Ala57Val	p.A57V	ENST00000376670	NM_002049.3	57	gCt/gTt	2/6	0.265499264737894	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.287821569681062	1		821	1100	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374881	45374881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	61	388	0	ENST00000262160.6:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000262160	NM_005901.5	321	cGa/cAa	8/11	0.287821569681062	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.287821569681062	1		388	323	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267600319	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	121	234	0	ENST00000257430.4:c.4199C>T	p.Ser1400Leu	p.S1400L	ENST00000257430	NM_000038.5	1400	tCg/tTg	16/16	1	2	FACETS	0.842	0.77	0.915	1	0.991	1	CLONAL	3	TRUE	1	0.287821569681062	2		234	333	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218483	1218483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775595174	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	184	476	1	ENST00000326873.7:c.358G>A	p.Glu120Lys	p.E120K	ENST00000326873	NM_000455.4	120	Gaa/Aaa	2/10	1	2	FACETS	1	0.982	1	1	0.994	1	CLONAL	2	TRUE	1	0.287821569681062	2		477	546	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004222	29004222	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	147	297	0	ENST00000282397.4:c.1071G>T	p.Met357Ile	p.M357I	ENST00000282397	NM_002019.4	357	atG/atT	8/30	0.265499264737894	1	FACETS	0.938	0.864	1	1	0.991	1	CLONAL	2	TRUE	0	0.287821569681062	1		297	466	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6036981	6036981	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777286241	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	310	287	0	ENST00000265849.7:c.779C>T	p.Ser260Phe	p.S260F	ENST00000265849	NM_000535.5	260	tCc/tTc	7/15	0.280185935080151	3	FACETS	1	0.986	1	1	0.995	1	CLONAL	4	TRUE	0	0.287821569681062	3		287	568	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389203	31389203	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs996239307	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	233	410	0	ENST00000328111.2:c.2116G>A	p.Asp706Asn	p.D706N	ENST00000328111	NM_006892.3	706	Gac/Aac	19/23	1	2	FACETS	1	0.989	1	1	0.995	1	CLONAL	2	TRUE	1	0.287821569681062	2		410	657	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953890	55953890	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	97	306	0	ENST00000263923.4:c.3546G>T	p.Glu1182Asp	p.E1182D	ENST00000263923	NM_002253.2	1182	gaG/gaT	27/30	1	2	FACETS	1	0.954	1	1	0.988	1	CLONAL	2	TRUE	1	0.287821569681062	2		306	307	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733503	85733503	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	125	330	1	ENST00000370580.1:c.509C>A	p.Ser170Tyr	p.S170Y	ENST00000370580	NM_003921.4	170	tCt/tAt	3/3	0.287821569681062	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	1	0.287821569681062	3		331	466	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851255	156851255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1480681042	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	269	675	1	ENST00000524377.1:c.2212G>A	p.Asp738Asn	p.D738N	ENST00000524377	NM_002529.3	738	Gac/Aac	17/17	0.287821569681062	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.287821569681062	3		676	997	SUCCESS
APC	324	MSKCC	GRCh37	5	112176873	112176873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	63	237	0	ENST00000257430.4:c.5582C>A	p.Ser1861Tyr	p.S1861Y	ENST00000257430	NM_000038.5	1861	tCt/tAt	16/16	1	2	FACETS	0.948	0.841	1	1	0.985	1	CLONAL	3	TRUE	1	0.287821569681062	2		237	154	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258036	123258036	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519045	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	138	359	0	ENST00000358487.5:c.1645A>C	p.Asn549His	p.N549H	ENST00000358487	NM_000141.4	549	Aat/Cat	12/18	1	2	FACETS	1	0.966	1	1	0.992	1	CLONAL	2	TRUE	1	0.287821569681062	2		359	436	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115600	108115600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772821016	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	74	321	0	ENST00000278616.4:c.748C>T	p.Arg250Ter	p.R250*	ENST00000278616	NM_000051.3	250	Cga/Tga	7/63	1	2	FACETS	0.857	0.765	0.952	1	0.987	1	CLONAL	3	TRUE	1	0.287821569681062	2		321	200	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589298	28589298	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	84	244	0	ENST00000241453.7:c.2749G>T	p.Glu917Ter	p.E917*	ENST00000241453	NM_004119.2	917	Gaa/Taa	22/24	0.265499264737894	1	FACETS	0.915	0.829	1	1	0.989	1	CLONAL	3	TRUE	0	0.287821569681062	1		244	182	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351986	89351986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1407933251	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	417	704	0	ENST00000301030.4:c.964G>A	p.Glu322Lys	p.E322K	ENST00000301030	NM_001256183.1	322	Gag/Aag	9/13	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	1	0.287821569681062	2		704	1209	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161380	55161380	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376544204	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	195	338	0	ENST00000257290.5:c.3211G>A	p.Asp1071Asn	p.D1071N	ENST00000257290	NM_006206.4	1071	Gac/Aac	23/23	1	2	FACETS	1	0.982	1	1	0.994	1	CLONAL	2	TRUE	1	0.287821569681062	2		338	583	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914743	39914743	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	167	329	0	ENST00000378444.4:c.4619A>G	p.Asn1540Ser	p.N1540S	ENST00000378444	NM_001123385.1	1540	aAc/aGc	12/15	0.265499264737894	1	FACETS	0.978	0.905	1	1	0.992	1	CLONAL	2	TRUE	0	0.287821569681062	1		329	508	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131412	202131412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1339962485	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	264	366	0	ENST00000358485.4:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000358485	NM_001080125.1	127	cGa/cAa	2/9	0.196589372134191	2	FACETS	0.934	0.894	0.972	1	0.996	1	CLONAL	5	TRUE	0	0.287821569681062	2		366	393	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898755	134898755	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs546798910	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	126	253	0	ENST00000398015.3:c.1813G>A	p.Glu605Lys	p.E605K	ENST00000398015	NM_004441.4	605	Gaa/Aaa	10/16	1	2	FACETS	1	0.974	1	1	0.991	1	CLONAL	2	TRUE	1	0.287821569681062	2		253	376	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961867	41961867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	97	275	0	ENST00000219905.7:c.775C>T	p.Arg259Trp	p.R259W	ENST00000219905	NM_001164273.1	259	Cgg/Tgg	2/24	0.265499264737894	1	FACETS	1	0.944	1	1	0.988	1	CLONAL	2	TRUE	0	0.287821569681062	1		275	272	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245326	41245326	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	22	464	1	ENST00000357654.3:c.2222C>A	p.Ser741Tyr	p.S741Y	ENST00000357654	NM_007294.3	741	tCt/tAt	10/23	1	2	FACETS	0.413	0.32	0.522	0.413	0.32	0.522	SUBCLONAL	1	TRUE	1	0.287821569681062	2		465	370	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675571	30675571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772732783	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	305	612	1	ENST00000376406.3:c.2785G>A	p.Asp929Asn	p.D929N	ENST00000376406	NM_014641.2	929	Gat/Aat	8/15	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.287821569681062	2		613	894	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500882	8500882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs191877533	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	146	342	0	ENST00000356435.5:c.2000C>T	p.Ser667Leu	p.S667L	ENST00000356435		667	tCg/tTg	13/35	1	2	FACETS	0.995	0.914	1	1	0.991	1	CLONAL	2	TRUE	1	0.287821569681062	2		342	510	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66468014	66468014	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	42	144	0	ENST00000273854.3:c.255G>T	p.Glu85Asp	p.E85D	ENST00000273854	NM_004439.5	85	gaG/gaT	3/18	1	2	FACETS	0.909	0.782	1	1	0.978	1	CLONAL	3	TRUE	1	0.287821569681062	2		144	107	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259967	16259967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	199	489	0	ENST00000375759.3:c.7232C>T	p.Ser2411Leu	p.S2411L	ENST00000375759	NM_015001.2	2411	tCg/tTg	11/15	0.287821569681062	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.287821569681062	3		489	755	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447384	187447384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780987785	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	138	529	0	ENST00000232014.4:c.809G>A	p.Arg270Gln	p.R270Q	ENST00000232014	NM_001130845.1	270	cGa/cAa	5/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.287821569681062	2		529	764	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971370	13971370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748346103	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	220	244	0	ENST00000405192.2:c.559C>T	p.Arg187Cys	p.R187C	ENST00000405192	NM_001163147.1	187	Cgc/Tgc	8/12	0.280185935080151	3	FACETS	1	0.975	1	1	0.993	1	CLONAL	4	TRUE	0	0.287821569681062	3		244	414	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687122	176687122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	159	338	1	ENST00000439151.2:c.5099G>A	p.Arg1700Gln	p.R1700Q	ENST00000439151	NM_022455.4	1700	cGa/cAa	14/23	1	2	FACETS	1	0.984	1	1	0.993	1	CLONAL	2	TRUE	1	0.287821569681062	2		339	447	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359740	40359740	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	97	264	0	ENST00000293328.3:c.1913G>T	p.Arg638Ile	p.R638I	ENST00000293328	NM_012448.3	638	aGa/aTa	16/19	1	2	FACETS	1	0.953	1	1	0.988	1	CLONAL	2	TRUE	1	0.287821569681062	2		264	308	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66521949	66521949	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	100	212	1	ENST00000358598.2:c.604G>T	p.Glu202Ter	p.E202*	ENST00000358598	NM_212471.2	202	Gaa/Taa	7/11	1	2	FACETS	1	0.971	1	1	0.989	1	CLONAL	2	TRUE	1	0.287821569681062	2		213	293	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121280	29121280	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs750393263	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	62	506	1	ENST00000328354.6:c.395G>T	p.Arg132Ile	p.R132I	ENST00000328354	NM_007194.3	132	aGa/aTa	3/15	0.287821569681062	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.287821569681062	1		507	294	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546725	9546725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210292896	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	117	275	0	ENST00000353224.5:c.1297C>T	p.Arg433Trp	p.R433W	ENST00000353224	NM_177990.2	433	Cgg/Tgg	5/10	1	2	FACETS	1	0.958	1	1	0.99	1	CLONAL	2	TRUE	1	0.287821569681062	2		275	373	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435837	56435837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	260	509	0	ENST00000407977.2:c.1300C>T	p.Pro434Ser	p.P434S	ENST00000407977		434	Ccc/Tcc	9/10	1	2	FACETS	0.888	0.837	0.94	1	0.996	1	CLONAL	3	TRUE	1	0.287821569681062	2		509	678	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729394	41729394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	203	460	0	ENST00000242208.4:c.1135C>T	p.Arg379Trp	p.R379W	ENST00000242208	NM_002192.2	379	Cgg/Tgg	3/3	0.280185935080151	3	FACETS	0.852	0.79	0.916	0.568	0.527	0.611	CLONAL	2	TRUE	0	0.287821569681062	3		460	947	SUCCESS
APC	324	MSKCC	GRCh37	5	112177587	112177587	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	45	219	0	ENST00000257430.4:c.6296T>G	p.Phe2099Cys	p.F2099C	ENST00000257430	NM_000038.5	2099	tTt/tGt	16/16	1	2	FACETS	0.99	0.847	1	1	0.973	1	CLONAL	2	TRUE	1	0.287821569681062	2		219	158	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646744	23646744	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs373298267	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	136	415	0	ENST00000261584.4:c.1123C>A	p.Leu375Ile	p.L375I	ENST00000261584	NM_024675.3	375	Cta/Ata	4/13	1	2	FACETS	1	0.982	1	1	0.992	1	CLONAL	2	TRUE	1	0.287821569681062	2		415	379	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1315001	1315001	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs199680740	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	285	452	0	ENST00000400841.2:c.660G>T	p.Glu220Asp	p.E220D	ENST00000400841		220	gaG/gaT	6/6	0.265499264737894	1	FACETS	1	0.982	1	1	0.996	1	CLONAL	2	TRUE	0	0.287821569681062	1		452	776	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984860	9984860	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	194	362	0	ENST00000330684.3:c.1105G>T	p.Asp369Tyr	p.D369Y	ENST00000330684	NM_001134407.1	369	Gac/Tac	4/13	1	2	FACETS	1	0.976	1	1	0.994	1	CLONAL	2	TRUE	1	0.287821569681062	2		362	609	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220477	123220477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1372684971	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	214	431	0	ENST00000218089.9:c.3134G>A	p.Arg1045Gln	p.R1045Q	ENST00000218089	NM_001042749.1	1045	cGa/cAa	30/35	0.265499264737894	1	FACETS	1	0.985	1	1	0.995	1	CLONAL	2	TRUE	0	0.287821569681062	1		431	547	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285669	46285669	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1368075571	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	33	295	0	ENST00000334344.6:c.5029C>T	p.Arg1677Ter	p.R1677*	ENST00000334344	NM_152641.2	1677	Cga/Tga	17/21	1	2	FACETS	0.583	0.475	0.705	0.583	0.475	0.705	SUBCLONAL	1	TRUE	1	0.287821569681062	2		295	393	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984651	72984651	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750714180	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	385	747	0	ENST00000268489.5:c.2933C>T	p.Ala978Val	p.A978V	ENST00000268489	NM_006885.3	978	gCg/gTg	3/10	1	2	FACETS	0.873	0.832	0.916	1	0.997	1	CLONAL	3	TRUE	1	0.287821569681062	2		747	1021	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143129648	143129648	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs768272420	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	57	305	0	ENST00000262992.4:c.1002G>T	p.Glu334Asp	p.E334D	ENST00000262992	NM_001101669.1	334	gaG/gaT	12/24	1	2	FACETS	1	0.945	1	1	0.981	1	CLONAL	2	TRUE	1	0.287821569681062	2		305	172	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624245	89624245	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554890335	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	89	152	0	ENST00000371953.3:c.19G>T	p.Glu7Ter	p.E7*	ENST00000371953	NM_000314.4	7	Gag/Tag	1/9	1	2	FACETS	1	0.92	1	1	0.99	1	CLONAL	3	TRUE	1	0.287821569681062	2		152	203	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857334	9857334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	198	406	0	ENST00000330684.3:c.4067C>T	p.Ser1356Phe	p.S1356F	ENST00000330684	NM_001134407.1	1356	tCt/tTt	13/13	1	2	FACETS	0.91	0.851	0.97	1	0.995	1	CLONAL	3	TRUE	1	0.287821569681062	2		406	504	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740668	58740668	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs759850701	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	130	356	0	ENST00000305921.3:c.1573G>T	p.Glu525Ter	p.E525*	ENST00000305921	NM_003620.3	525	Gaa/Taa	6/6	1	2	FACETS	1	0.975	1	1	0.992	1	CLONAL	2	TRUE	1	0.287821569681062	2		356	386	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291528	10291528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755995375	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	91	359	0	ENST00000340748.4:c.151G>A	p.Glu51Lys	p.E51K	ENST00000340748		51	Gaa/Aaa	3/40	1	2	FACETS	1	0.957	1	1	0.988	1	CLONAL	2	TRUE	1	0.287821569681062	2		359	282	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181425	185181425	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1435276633	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	130	324	0	ENST00000265026.3:c.1366C>T	p.Arg456Ter	p.R456*	ENST00000265026	NM_004721.4	456	Cga/Tga	8/14	1	2	FACETS	1	0.973	1	1	0.991	1	CLONAL	2	TRUE	1	0.287821569681062	2		324	392	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28963966	28963966	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	56	233	0	ENST00000282397.4:c.1936G>T	p.Glu646Ter	p.E646*	ENST00000282397	NM_002019.4	646	Gaa/Taa	13/30	0.265499264737894	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.287821569681062	1		233	227	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65300295	65300295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	62	199	0	ENST00000342505.4:c.3415C>T	p.Arg1139Trp	p.R1139W	ENST00000342505	NM_002227.2	1139	Cgg/Tgg	25/25	0.287821569681062	3	FACETS	1	0.952	1	1	0.98	1	CLONAL	3	TRUE	1	0.287821569681062	3		199	144	SUCCESS
APC	324	MSKCC	GRCh37	5	112177359	112177359	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	62	217	0	ENST00000257430.4:c.6068G>T	p.Arg2023Ile	p.R2023I	ENST00000257430	NM_000038.5	2023	aGa/aTa	16/16	1	2	FACETS	1	0.934	1	1	0.982	1	CLONAL	2	TRUE	1	0.287821569681062	2		217	196	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720928	176720928	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784209	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	205	376	0	ENST00000439151.2:c.6559C>T	p.Arg2187Ter	p.R2187*	ENST00000439151	NM_022455.4	2187	Cga/Tga	23/23	1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	1	0.287821569681062	2		376	580	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710578	117710578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142303126	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	129	193	0	ENST00000368508.3:c.1694C>T	p.Ser565Leu	p.S565L	ENST00000368508	NM_002944.2	565	tCg/tTg	12/43	1	2	FACETS	0.892	0.82	0.966	1	0.992	1	CLONAL	3	TRUE	1	0.287821569681062	2		193	335	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192594	94192594	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104895016	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	179	417	1	ENST00000323929.3:c.1480G>A	p.Glu494Lys	p.E494K	ENST00000323929	NM_005591.3	494	Gaa/Aaa	13/20	1	2	FACETS	1	0.979	1	1	0.995	1	CLONAL	4	TRUE	1	0.287821569681062	2		418	289	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395686	45395686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200841904	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	100	268	0	ENST00000262160.6:c.448G>A	p.Glu150Lys	p.E150K	ENST00000262160	NM_005901.5	150	Gaa/Aaa	4/11	0.287821569681062	1	FACETS	1	0.972	1	1	0.99	1	CLONAL	2	TRUE	0	0.287821569681062	1		268	252	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267638	7267638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs896894246	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	310	533	0	ENST00000302850.5:c.370G>A	p.Glu124Lys	p.E124K	ENST00000302850	NM_000208.2	124	Gag/Aag	2/22	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.287821569681062	2		533	897	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467948	66467948	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	75	204	0	ENST00000273854.3:c.321G>T	p.Gln107His	p.Q107H	ENST00000273854	NM_004439.5	107	caG/caT	3/18	1	2	FACETS	1	0.967	1	1	0.986	1	CLONAL	2	TRUE	1	0.287821569681062	2		204	212	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409167	4409167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1261984704	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	185	345	0	ENST00000261254.3:c.862G>A	p.Asp288Asn	p.D288N	ENST00000261254	NM_001759.3	288	Gac/Aac	5/5	1	2	FACETS	1	0.979	1	1	0.994	1	CLONAL	2	TRUE	1	0.287821569681062	2		345	564	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727174	40727174	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200157212	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	240	471	0	ENST00000373198.4:c.3790G>A	p.Ala1264Thr	p.A1264T	ENST00000373198	NM_133170.3	1264	Gcc/Acc	28/32	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.287821569681062	2		471	732	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265007	198265007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773349667	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	121	217	0	ENST00000335508.6:c.2870G>A	p.Arg957Gln	p.R957Q	ENST00000335508	NM_012433.2	957	cGa/cAa	19/25	0.196589372134191	2	FACETS	0.95	0.872	1	1	0.986	1	CLONAL	3	TRUE	0	0.287821569681062	2		217	295	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916669	178916669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	66	233	0	ENST00000263967.3:c.56G>T	p.Arg19Ile	p.R19I	ENST00000263967	NM_006218.2	19	aGa/aTa	2/21	1	2	FACETS	1	0.939	1	1	0.983	1	CLONAL	2	TRUE	1	0.287821569681062	2		233	208	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115747	108115747	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	17	109	0	ENST00000278616.4:c.895G>T	p.Glu299Ter	p.E299*	ENST00000278616	NM_000051.3	299	Gaa/Taa	7/63	1	2	FACETS	1	0.867	1	1	0.942	1	CLONAL	2	TRUE	1	0.287821569681062	2		109	50	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045799	26045799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	238	723	0	ENST00000540144.1:c.161G>A	p.Arg54His	p.R54H	ENST00000540144	NM_003531.2	54	cGc/cAc	1/1	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.287821569681062	2		723	726	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170373	119170373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	148	276	0	ENST00000264033.4:c.2603G>A	p.Gly868Glu	p.G868E	ENST00000264033	NM_005188.3	868	gGg/gAg	16/16	1	2	FACETS	1	0.974	1	1	0.992	1	CLONAL	2	TRUE	1	0.287821569681062	2		276	452	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934931	9934931	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	90	222	0	ENST00000330684.3:c.1359G>T	p.Lys453Asn	p.K453N	ENST00000330684	NM_001134407.1	453	aaG/aaT	6/13	1	2	FACETS	0.887	0.801	0.975	1	0.989	1	CLONAL	3	TRUE	1	0.287821569681062	2		222	235	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100016	11100016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749059769	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	341	556	1	ENST00000358026.2:c.1142G>A	p.Arg381Gln	p.R381Q	ENST00000358026	NM_001128849.1	381	cGa/cAa	7/36	1	2	FACETS	0.863	0.819	0.908	1	0.997	1	CLONAL	3	TRUE	1	0.287821569681062	2		557	915	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248560	212248560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763559555	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	67	466	0	ENST00000342788.4:c.3707C>T	p.Ala1236Val	p.A1236V	ENST00000342788	NM_005235.2	1236	gCg/gTg	28/28	0.196589372134191	2	FACETS	0.704	0.612	0.805	0.352	0.306	0.403	SUBCLONAL	1	TRUE	0	0.287821569681062	2		466	661	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670598	134670598	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs563780078	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	300	613	0	ENST00000398015.3:c.509G>A	p.Arg170Gln	p.R170Q	ENST00000398015	NM_004441.4	170	cGg/cAg	3/16	1	2	FACETS	0.842	0.796	0.889	1	0.996	1	CLONAL	3	TRUE	1	0.287821569681062	2		613	825	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465467	8465467	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	51	238	0	ENST00000356435.5:c.3713C>A	p.Ser1238Tyr	p.S1238Y	ENST00000356435		1238	tCt/tAt	21/35	1	2	FACETS	0.895	0.771	1	1	0.974	1	CLONAL	2	TRUE	1	0.287821569681062	2		238	198	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	28	205	0	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	0.265499264737894	1	FACETS	1	0.837	1	1	0.96	1	CLONAL	2	TRUE	0	0.287821569681062	1		205	82	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750596	41750596	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	161	429	0	ENST00000226382.2:c.32C>T	p.Ser11Phe	p.S11F	ENST00000226382	NM_003924.3	11	tCc/tTc	1/3	1	2	FACETS	1	0.981	1	1	0.993	1	CLONAL	2	TRUE	1	0.287821569681062	2		429	471	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398665	116398665	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1351264833	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	95	242	0	ENST00000397752.3:c.2255C>A	p.Ser752Tyr	p.S752Y	ENST00000397752	NM_000245.2	752	tCt/tAt	9/21	0.280185935080151	3	FACETS	1	0.97	1	1	0.986	1	CLONAL	4	TRUE	0	0.287821569681062	3		242	168	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584578	187584578	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	110	290	0	ENST00000441802.2:c.3455C>A	p.Ser1152Tyr	p.S1152Y	ENST00000441802	NM_005245.3	1152	tCt/tAt	3/27	1	2	FACETS	1	0.968	1	1	0.99	1	CLONAL	2	TRUE	1	0.287821569681062	2		290	334	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020225	123020225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	177	463	1	ENST00000355640.3:c.713G>A	p.Arg238Gln	p.R238Q	ENST00000355640		238	cGa/cAa	2/7	0.265499264737894	1	FACETS	1	0.98	1	1	0.994	1	CLONAL	2	TRUE	0	0.287821569681062	1		464	461	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342775	118342775	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	66	167	0	ENST00000534358.1:c.901C>T	p.Arg301Ter	p.R301*	ENST00000534358	NM_005933.3	301	Cga/Tga	3/36	1	2	FACETS	1	0.917	1	1	0.983	1	CLONAL	2	TRUE	1	0.287821569681062	2		167	218	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322748	30322748	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	23	236	0	ENST00000322652.5:c.1761G>T	p.Lys587Asn	p.K587N	ENST00000322652	NM_015355.2	587	aaG/aaT	14/16	1	2	FACETS	0.828	0.65	1	0.828	0.65	1	CLONAL	1	TRUE	1	0.287821569681062	2		236	193	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371707	118371707	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	65	163	0	ENST00000534358.1:c.6164C>T	p.Ser2055Phe	p.S2055F	ENST00000534358	NM_005933.3	2055	tCc/tTc	25/36	1	2	FACETS	1	0.947	1	1	0.983	1	CLONAL	2	TRUE	1	0.287821569681062	2		163	199	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271304	18271304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs553673157	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	388	694	0	ENST00000222254.8:c.346G>A	p.Glu116Lys	p.E116K	ENST00000222254	NM_005027.3	116	Gag/Aag	3/16	1	2	FACETS	1	0.993	1	1	0.997	1	CLONAL	2	TRUE	1	0.287821569681062	2		694	1082	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728891	190728891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	23	184	0	ENST00000441310.2:c.2279G>T	p.Arg760Ile	p.R760I	ENST00000441310	NM_000534.4	760	aGa/aTa	10/13	0.196589372134191	2	FACETS	1	0.893	1	0.615	0.485	0.76	CLONAL	1	TRUE	0	0.287821569681062	2		184	130	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515335	103515335	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	17	179	0	ENST00000355739.4:c.1836G>T	p.Glu612Asp	p.E612D	ENST00000355739	NM_000123.3	612	gaG/gaT	8/15	0.265499264737894	1	FACETS	0.458	0.342	0.594	0.458	0.342	0.594	SUBCLONAL	1	TRUE	0	0.287821569681062	1		179	221	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412470	80412470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28764015	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	138	271	0	ENST00000286548.4:c.571G>A	p.Glu191Lys	p.E191K	ENST00000286548	NM_002072.3	191	Gaa/Aaa	4/7	1	2	FACETS	1	0.979	1	1	0.992	1	CLONAL	2	TRUE	1	0.287821569681062	2		271	401	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79961137	79961137	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs569679162	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	104	331	1	ENST00000265081.6:c.534G>T	p.Lys178Asn	p.K178N	ENST00000265081	NM_002439.4	178	aaG/aaT	3/24	1	2	FACETS	0.882	0.803	0.964	1	0.99	1	CLONAL	3	TRUE	1	0.287821569681062	2		332	273	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184669	185184669	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202042288	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	134	252	0	ENST00000265026.3:c.1561C>T	p.Arg521Cys	p.R521C	ENST00000265026	NM_004721.4	521	Cgt/Tgt	10/14	1	2	FACETS	0.954	0.872	1	1	0.99	1	CLONAL	2	TRUE	1	0.287821569681062	2		252	488	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259533	55259533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	152	524	1	ENST00000275493.2:c.2591C>T	p.Ala864Val	p.A864V	ENST00000275493	NM_005228.3	864	gCg/gTg	21/28	0.280185935080151	3	FACETS	1	0.986	1	0.462	0.423	0.504	CLONAL	1	TRUE	0	0.287821569681062	3		525	871	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650051	206650051	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs782081148	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	445	550	0	ENST00000367120.3:c.571C>T	p.Arg191Ter	p.R191*	ENST00000367120	NM_014002.3	191	Cga/Tga	7/22	0.287821569681062	3	FACETS	0.901	0.864	0.939	1	0.997	1	CLONAL	4	TRUE	1	0.287821569681062	3		550	981	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321717	62321717	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761805038	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	327	557	1	ENST00000360203.5:c.2336C>T	p.Ser779Leu	p.S779L	ENST00000360203	NM_001283009.1	779	tCg/tTg	26/35	1	2	FACETS	0.917	0.87	0.964	1	0.997	1	CLONAL	3	TRUE	1	0.287821569681062	2		558	826	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996231	73996231	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1186699933	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	195	379	0	ENST00000318443.5:c.965A>G	p.Asn322Ser	p.N322S	ENST00000318443	NM_001024736.1	322	aAt/aGt	5/10	0.265499264737894	1	FACETS	1	0.983	1	1	0.994	1	CLONAL	2	TRUE	0	0.287821569681062	1		379	502	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748962	43748962	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141222111	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	102	680	0	ENST00000382044.4:c.1844C>T	p.Thr615Met	p.T615M	ENST00000382044	NM_001141980.1	615	aCg/aTg	12/28	0.265499264737894	1	FACETS	0.671	0.599	0.748	0.671	0.599	0.748	SUBCLONAL	1	TRUE	0	0.287821569681062	1		680	904	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845395	156845395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139731614	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	391	775	0	ENST00000524377.1:c.1438G>A	p.Glu480Lys	p.E480K	ENST00000524377	NM_002529.3	480	Gag/Aag	12/17	0.287821569681062	3	FACETS	0.835	0.794	0.877	1	0.993	1	CLONAL	3	TRUE	1	0.287821569681062	3		775	1240	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590694	189590694	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	169	385	0	ENST00000264731.3:c.1259C>T	p.Ser420Phe	p.S420F	ENST00000264731	NM_003722.4	420	tCc/tTc	10/14	1	2	FACETS	1	0.973	1	1	0.993	1	CLONAL	2	TRUE	1	0.287821569681062	2		385	529	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966566	36966566	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	87	631	0	ENST00000358127.4:c.760G>T	p.Glu254Ter	p.E254*	ENST00000358127	NM_001280556.1	254	Gag/Tag	6/10	1	2	FACETS	0.669	0.592	0.753	0.669	0.592	0.753	SUBCLONAL	1	TRUE	1	0.287821569681062	2		631	903	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784525	43784525	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1048972918	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	33	403	0	ENST00000382044.4:c.149G>A	p.Arg50Gln	p.R50Q	ENST00000382044	NM_001141980.1	50	cGa/cAa	2/28	0.265499264737894	1	FACETS	0.507	0.413	0.613	0.507	0.413	0.613	SUBCLONAL	1	TRUE	0	0.287821569681062	1		403	387	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256831	16256831	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	289	420	0	ENST00000375759.3:c.4096C>T	p.Arg1366Ter	p.R1366*	ENST00000375759	NM_015001.2	1366	Cga/Tga	11/15	0.287821569681062	3	FACETS	1	0.988	1	1	0.995	1	CLONAL	3	TRUE	1	0.287821569681062	3		420	668	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656338	18656338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	47	252	0	ENST00000266497.5:c.3017C>T	p.Ala1006Val	p.A1006V	ENST00000266497		1006	gCa/gTa	21/31	1	2	FACETS	0.842	0.72	0.972	1	0.969	1	CLONAL	2	TRUE	1	0.287821569681062	2		252	194	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530154	212530154	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	62	240	0	ENST00000342788.4:c.1765T>G	p.Cys589Gly	p.C589G	ENST00000342788	NM_005235.2	589	Tgt/Ggt	15/28	0.196589372134191	2	FACETS	0.767	0.668	0.871	0.767	0.668	0.871	SUBCLONAL	2	TRUE	0	0.287821569681062	2		240	281	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245009	41245009	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555589446	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	140	469	0	ENST00000357654.3:c.2539A>G	p.Met847Val	p.M847V	ENST00000357654	NM_007294.3	847	Atg/Gtg	10/23	1	2	FACETS	1	0.971	1	1	0.992	1	CLONAL	2	TRUE	1	0.287821569681062	2		469	433	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999317	100999317	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	162	921	0	ENST00000325455.5:c.485C>A	p.Ser162Tyr	p.S162Y	ENST00000325455	NM_001202474.3	162	tCc/tAc	1/8	1	2	FACETS	0.844	0.772	0.919	0.844	0.772	0.919	CLONAL	1	TRUE	1	0.287821569681062	2		921	1334	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418986	116418986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199763277	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	179	197	0	ENST00000397752.3:c.3497G>A	p.Arg1166Gln	p.R1166Q	ENST00000397752	NM_000245.2	1166	cGa/cAa	17/21	0.280185935080151	3	FACETS	0.909	0.856	0.962	1	0.992	1	CLONAL	5	TRUE	0	0.287821569681062	3		197	313	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922938	44922938	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	188	396	0	ENST00000377967.4:c.1799G>A	p.Gly600Glu	p.G600E	ENST00000377967	NM_021140.2	600	gGa/gAa	16/29	0.265499264737894	1	FACETS	0.953	0.886	1	1	0.993	1	CLONAL	2	TRUE	0	0.287821569681062	1		396	587	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122771	7122771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202160383	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	236	558	0	ENST00000302850.5:c.3383G>A	p.Arg1128His	p.R1128H	ENST00000302850	NM_000208.2	1128	cGc/cAc	19/22	1	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	2	TRUE	1	0.287821569681062	2		558	709	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458329	12458329	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1364613522	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	205	432	0	ENST00000287820.6:c.946C>T	p.Arg316Cys	p.R316C	ENST00000287820	NM_015869.4	316	Cgc/Tgc	6/7	1	2	FACETS	1	0.969	1	1	0.994	1	CLONAL	2	TRUE	1	0.287821569681062	2		432	666	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682664	86682664	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	24	125	0	ENST00000274376.6:c.2869A>G	p.Asn957Asp	p.N957D	ENST00000274376	NM_002890.2	957	Aat/Gat	23/25	1	2	FACETS	1	0.868	1	1	0.956	1	CLONAL	2	TRUE	1	0.287821569681062	2		125	76	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020790	37020790	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	186	376	0	ENST00000358127.4:c.55G>T	p.Gly19Ter	p.G19*	ENST00000358127	NM_001280556.1	19	Gga/Tga	2/10	1	2	FACETS	1	0.983	1	1	0.994	1	CLONAL	2	TRUE	1	0.287821569681062	2		376	547	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201838	152201838	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	156	288	0	ENST00000206249.3:c.692A>C	p.Lys231Thr	p.K231T	ENST00000206249	NM_000125.3	231	aAa/aCa	3/8	1	2	FACETS	0.862	0.798	0.928	1	0.993	1	CLONAL	3	TRUE	1	0.287821569681062	2		288	419	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106063	8106063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	205	412	1	ENST00000346208.3:c.883G>A	p.Gly295Arg	p.G295R	ENST00000346208		295	Gga/Aga	4/6	1	2	FACETS	1	0.981	1	1	0.994	1	CLONAL	2	TRUE	1	0.287821569681062	2		413	624	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300846	137300846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	401	776	1	ENST00000481739.1:c.491G>A	p.Arg164His	p.R164H	ENST00000481739	NM_002957.4	164	cGc/cAc	4/10	1	2	FACETS	0.853	0.813	0.894	1	0.997	1	CLONAL	3	TRUE	1	0.287821569681062	2		777	1089	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884076	37884076	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	228	782	0	ENST00000269571.5:c.3547G>T	p.Asp1183Tyr	p.D1183Y	ENST00000269571		1183	Gac/Tac	27/27	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.287821569681062	2		782	1202	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349471	73349471	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777245855	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	114	307	0	ENST00000377767.4:c.865G>A	p.Glu289Lys	p.E289K	ENST00000377767	NM_014953.3	289	Gaa/Aaa	6/21	0.265499264737894	1	FACETS	0.974	0.887	1	1	0.989	1	CLONAL	2	TRUE	0	0.287821569681062	1		307	348	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405743	70405743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	87	274	0	ENST00000373644.4:c.3257C>T	p.Ser1086Leu	p.S1086L	ENST00000373644	NM_030625.2	1086	tCg/tTg	4/12	1	2	FACETS	1	0.942	1	1	0.987	1	CLONAL	2	TRUE	1	0.287821569681062	2		274	281	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46271087	46271087	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	174	343	0	ENST00000371998.3:c.3211G>T	p.Glu1071Ter	p.E1071*	ENST00000371998		1071	Gaa/Taa	17/23	1	2	FACETS	1	0.981	1	1	0.994	1	CLONAL	2	TRUE	1	0.287821569681062	2		343	515	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054752	5054752	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	61	225	0	ENST00000381652.3:c.804G>T	p.Glu268Asp	p.E268D	ENST00000381652	NM_004972.3	268	gaG/gaT	7/25	1	2	FACETS	0.872	0.77	0.978	1	0.984	1	CLONAL	3	TRUE	1	0.287821569681062	2		225	162	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170011280	170011280	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	131	324	1	ENST00000295797.4:c.1401G>T	p.Glu467Asp	p.E467D	ENST00000295797	NM_002740.5	467	gaG/gaT	14/18	1	2	FACETS	1	0.965	1	1	0.991	1	CLONAL	2	TRUE	1	0.287821569681062	2		325	413	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230632	46230632	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	89	328	1	ENST00000334344.6:c.881G>T	p.Arg294Ile	p.R294I	ENST00000334344	NM_152641.2	294	aGa/aTa	8/21	1	2	FACETS	1	0.916	1	1	0.987	1	CLONAL	2	TRUE	1	0.287821569681062	2		329	302	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3824685	3824685	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	191	380	1	ENST00000262367.5:c.2168C>A	p.Ser723Ter	p.S723*	ENST00000262367	NM_004380.2	723	tCa/tAa	12/31	1	2	FACETS	1	0.98	1	1	0.994	1	CLONAL	2	TRUE	1	0.287821569681062	2		381	580	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934583	9934583	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	206	430	0	ENST00000330684.3:c.1572C>A	p.Phe524Leu	p.F524L	ENST00000330684	NM_001134407.1	524	ttC/ttA	7/13	1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	1	0.287821569681062	2		430	587	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729932	30729932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	199	301	0	ENST00000295754.5:c.1453G>A	p.Glu485Lys	p.E485K	ENST00000295754	NM_003242.5	485	Gaa/Aaa	6/7	1	2	FACETS	1	0.982	1	1	0.994	1	CLONAL	2	TRUE	1	0.287821569681062	2		301	601	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240738	53240738	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	240	503	0	ENST00000375401.3:c.1342G>T	p.Glu448Ter	p.E448*	ENST00000375401	NM_004187.3	448	Gaa/Taa	10/26	0.265499264737894	1	FACETS	1	0.963	1	1	0.995	1	CLONAL	2	TRUE	0	0.287821569681062	1		503	689	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915579	131915579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28903087	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	18	137	1	ENST00000265335.6:c.577C>T	p.Arg193Trp	p.R193W	ENST00000265335		193	Cgg/Tgg	5/25	1	2	FACETS	0.948	0.735	1	1	0.934	1	CLONAL	2	TRUE	1	0.287821569681062	2		138	66	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347850	128347850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771286674	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	244	477	0	ENST00000265960.3:c.655C>T	p.Arg219Trp	p.R219W	ENST00000265960	NM_001006617.1	219	Cgg/Tgg	5/12	1	2	FACETS	1	0.982	1	1	0.995	1	CLONAL	2	TRUE	1	0.287821569681062	2		477	756	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625162	69625162	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554980307	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	355	847	3	ENST00000334134.2:c.631C>T	p.Arg211Trp	p.R211W	ENST00000334134	NM_005247.2	211	Cgg/Tgg	3/3	1	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	2	TRUE	1	0.287821569681062	2		850	1068	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622622	158622622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	114	324	0	ENST00000263640.3:c.877G>A	p.Asp293Asn	p.D293N	ENST00000263640	NM_001105.4	293	Gac/Aac	8/11	0.265499264737894	1	FACETS	1	0.955	1	1	0.99	1	CLONAL	2	TRUE	0	0.287821569681062	1		324	316	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281838	39281838	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	46	312	0	ENST00000402219.2:c.637C>T	p.Arg213Ter	p.R213*	ENST00000402219	NM_005633.3	213	Cga/Tga	5/23	0.265499264737894	1	FACETS	0.931	0.8	1	1	0.973	1	CLONAL	2	TRUE	0	0.287821569681062	1		312	147	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233540	69233540	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	95	268	0	ENST00000462284.1:c.1405A>G	p.Thr469Ala	p.T469A	ENST00000462284	NM_002392.5	469	Aca/Gca	11/11	1	2	FACETS	0.925	0.839	1	1	0.99	1	CLONAL	3	TRUE	1	0.287821569681062	2		268	238	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031893	10031893	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	96	569	1	ENST00000330684.3:c.930C>A	p.Phe310Leu	p.F310L	ENST00000330684	NM_001134407.1	310	ttC/ttA	3/13	1	2	FACETS	0.933	0.831	1	0.933	0.831	1	CLONAL	1	TRUE	1	0.287821569681062	2		570	715	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465627	8465627	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	24	309	0	ENST00000356435.5:c.3553G>T	p.Glu1185Ter	p.E1185*	ENST00000356435		1185	Gaa/Taa	21/35	1	2	FACETS	0.583	0.458	0.727	0.583	0.458	0.727	SUBCLONAL	1	TRUE	1	0.287821569681062	2		309	286	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611388	28611388	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	51	308	0	ENST00000241453.7:c.1243G>T	p.Glu415Ter	p.E415*	ENST00000241453	NM_004119.2	415	Gaa/Taa	10/24	0.265499264737894	1	FACETS	0.82	0.708	0.939	1	0.971	1	CLONAL	2	TRUE	0	0.287821569681062	1		308	185	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211487	98211487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769287098	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	285	583	0	ENST00000331920.6:c.3668C>T	p.Ser1223Leu	p.S1223L	ENST00000331920	NM_000264.3	1223	tCg/tTg	22/24	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.287821569681062	2		583	815	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437879	52437879	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371601284	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	371	698	0	ENST00000460680.1:c.1282G>A	p.Ala428Thr	p.A428T	ENST00000460680	NM_004656.3	428	Gca/Aca	13/17	1	2	FACETS	0.853	0.811	0.895	1	0.997	1	CLONAL	3	TRUE	1	0.287821569681062	2		698	1008	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951962	178951962	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	109	282	0	ENST00000263967.3:c.3017T>G	p.Leu1006Arg	p.L1006R	ENST00000263967	NM_006218.2	1006	cTt/cGt	21/21	1	2	FACETS	1	0.939	1	1	0.991	1	CLONAL	3	TRUE	1	0.287821569681062	2		282	245	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27190529	27190529	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	143	398	0	ENST00000380036.4:c.1330C>A	p.Leu444Ile	p.L444I	ENST00000380036	NM_000459.3	444	Ctt/Att	10/23	1	2	FACETS	1	0.966	1	1	0.992	1	CLONAL	2	TRUE	1	0.287821569681062	2		398	454	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38616972	38616972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764823722	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	10	225	0	ENST00000299084.4:c.385G>A	p.Glu129Lys	p.E129K	ENST00000299084	NM_152594.2	129	Gaa/Aaa	4/7	0.265499264737894	1	FACETS	0.496	0.338	0.692	0.496	0.338	0.692	SUBCLONAL	1	TRUE	0	0.287821569681062	1		225	120	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349099	11349099	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	179	277	0	ENST00000332029.2:c.237C>A	p.Phe79Leu	p.F79L	ENST00000332029	NM_003745.1	79	ttC/ttA	2/2	1	2	FACETS	0.864	0.804	0.925	1	0.994	1	CLONAL	3	TRUE	1	0.287821569681062	2		277	480	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152446	56152446	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	52	129	0	ENST00000399503.3:c.502G>T	p.Glu168Ter	p.E168*	ENST00000399503	NM_005921.1	168	Gaa/Taa	2/20	1	2	FACETS	1	0.921	1	1	0.979	1	CLONAL	2	TRUE	1	0.287821569681062	2		129	166	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912291	32912291	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	40	288	0	ENST00000380152.3:c.3799G>T	p.Asp1267Tyr	p.D1267Y	ENST00000380152		1267	Gat/Tat	11/27	0.265499264737894	1	FACETS	0.773	0.653	0.901	1	0.961	1	CLONAL	2	TRUE	0	0.287821569681062	1		288	154	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942524	17942524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763951351	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	200	847	0	ENST00000458235.1:c.2764G>A	p.Asp922Asn	p.D922N	ENST00000458235	NM_000215.3	922	Gat/Aat	20/24	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.287821569681062	2		847	1052	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867477	35867477	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	56	180	0	ENST00000303115.3:c.291G>T	p.Lys97Asn	p.K97N	ENST00000303115	NM_002185.3	97	aaG/aaT	3/8	1	2	FACETS	0.859	0.753	0.968	1	0.982	1	CLONAL	3	TRUE	1	0.287821569681062	2		180	151	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478122	99478122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1470161328	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	88	397	1	ENST00000268035.6:c.3026C>T	p.Ser1009Leu	p.S1009L	ENST00000268035	NM_000875.3	1009	tCg/tTg	16/21	0.280185935080151	3	FACETS	0.822	0.727	0.924	0.274	0.242	0.308	CLONAL	1	TRUE	0	0.287821569681062	3		398	851	SUCCESS
AR	367	MSKCC	GRCh37	X	66905929	66905929	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555990485	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	20	343	1	ENST00000374690.3:c.1846C>T	p.Arg616Cys	p.R616C	ENST00000374690	NM_000044.3	616	Cgt/Tgt	3/8	0.265499264737894	1	FACETS	0.398	0.304	0.508	0.398	0.304	0.508	SUBCLONAL	1	TRUE	0	0.287821569681062	1		344	299	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528185	103528185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781355194	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	130	261	0	ENST00000355739.4:c.3493G>A	p.Ala1165Thr	p.A1165T	ENST00000355739	NM_000123.3	1165	Gcc/Acc	15/15	0.265499264737894	1	FACETS	1	0.939	1	1	0.991	1	CLONAL	2	TRUE	0	0.287821569681062	1		261	376	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931321	131931321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773761143	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	154	338	0	ENST00000265335.6:c.2026G>A	p.Glu676Lys	p.E676K	ENST00000265335		676	Gaa/Aaa	13/25	1	2	FACETS	1	0.971	1	1	0.993	1	CLONAL	2	TRUE	1	0.287821569681062	2		338	483	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286951	33286951	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1453165364	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	114	547	0	ENST00000374542.5:c.1986G>T	p.Lys662Asn	p.K662N	ENST00000374542	NM_001141970.1	662	aaG/aaT	7/8	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.287821569681062	2		547	752	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76949328	76949328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	57	290	0	ENST00000373344.5:c.469C>T	p.Leu157Phe	p.L157F	ENST00000373344	NM_000489.3	157	Ctc/Ttc	6/35	0.265499264737894	1	FACETS	1	0.883	1	1	0.98	1	CLONAL	2	TRUE	0	0.287821569681062	1		290	168	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670256	134670256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	182	360	3	ENST00000398015.3:c.167G>A	p.Arg56His	p.R56H	ENST00000398015	NM_004441.4	56	cGc/cAc	3/16	1	2	FACETS	0.852	0.793	0.912	1	0.994	1	CLONAL	3	TRUE	1	0.287821569681062	2		363	495	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955551	48955551	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773116120	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	33	190	0	ENST00000267163.4:c.1667G>A	p.Arg556Gln	p.R556Q	ENST00000267163	NM_000321.2	556	cGa/cAa	17/27	0.265499264737894	1	FACETS	1	0.864	1	1	0.967	1	CLONAL	2	TRUE	0	0.287821569681062	1		190	95	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980728	40980728	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	176	324	0	ENST00000373198.4:c.1758T>G	p.Ile586Met	p.I586M	ENST00000373198	NM_133170.3	586	atT/atG	10/32	1	2	FACETS	0.848	0.788	0.908	1	0.994	1	CLONAL	3	TRUE	1	0.287821569681062	2		324	481	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190436	32190436	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs758283279	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	337	798	0	ENST00000375023.3:c.303C>A	p.Phe101Leu	p.F101L	ENST00000375023	NM_004557.3	101	ttC/ttA	3/30	1	2	FACETS	1	0.991	1	1	0.997	1	CLONAL	2	TRUE	1	0.287821569681062	2		798	970	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001539	150001539	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	27	293	0	ENST00000253339.5:c.2065G>T	p.Glu689Ter	p.E689*	ENST00000253339		689	Gaa/Taa	4/7	1	2	FACETS	0.993	0.796	1	0.993	0.796	1	CLONAL	1	TRUE	1	0.287821569681062	2		293	189	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565867	55565867	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	42	357	0	ENST00000288135.5:c.691G>T	p.Val231Leu	p.V231L	ENST00000288135	NM_000222.2	231	Gtg/Ttg	4/21	1	2	FACETS	0.674	0.563	0.797	0.674	0.563	0.797	SUBCLONAL	1	TRUE	1	0.287821569681062	2		357	433	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533379	29533379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555611606	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	59	153	0	ENST00000356175.3:c.1382G>A	p.Arg461Gln	p.R461Q	ENST00000356175	NM_000267.3	461	cGa/cAa	12/57	1	2	FACETS	1	0.937	1	1	0.982	1	CLONAL	2	TRUE	1	0.287821569681062	2		153	184	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880980	134880980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771555643	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	225	479	1	ENST00000398015.3:c.1543G>A	p.Gly515Ser	p.G515S	ENST00000398015	NM_004441.4	515	Ggc/Agc	7/16	1	2	FACETS	1	0.972	1	1	0.995	1	CLONAL	2	TRUE	1	0.287821569681062	2		480	730	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509561	106509561	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	109	382	0	ENST00000359195.3:c.1555C>A	p.Leu519Ile	p.L519I	ENST00000359195	NM_002649.2	519	Ctt/Att	2/11	0.280185935080151	3	FACETS	1	0.97	1	0.404	0.363	0.448	CLONAL	1	TRUE	0	0.287821569681062	3		382	715	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267839	7267839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886044001	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	174	370	0	ENST00000302850.5:c.169G>A	p.Glu57Lys	p.E57K	ENST00000302850	NM_000208.2	57	Gaa/Aaa	2/22	1	2	FACETS	1	0.966	1	1	0.993	1	CLONAL	2	TRUE	1	0.287821569681062	2		370	564	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25462004	25462004	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	101	469	0	ENST00000264709.3:c.2403G>T	p.Met801Ile	p.M801I	ENST00000264709	NM_175629.2	801	atG/atT	20/23	0.265499264737894	1	FACETS	0.769	0.687	0.856	0.769	0.687	0.856	SUBCLONAL	1	TRUE	0	0.287821569681062	1		469	781	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740750	58740750	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs760201595	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	157	391	0	ENST00000305921.3:c.1655G>T	p.Arg552Leu	p.R552L	ENST00000305921	NM_003620.3	552	cGa/cTa	6/6	1	2	FACETS	1	0.953	1	1	0.992	1	CLONAL	2	TRUE	1	0.287821569681062	2		391	521	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165003	47165003	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	43	199	0	ENST00000409792.3:c.1123G>T	p.Asp375Tyr	p.D375Y	ENST00000409792	NM_014159.6	375	Gat/Tat	3/21	1	2	FACETS	1	0.891	1	1	0.974	1	CLONAL	2	TRUE	1	0.287821569681062	2		199	142	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608234	28608234	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	84	385	0	ENST00000241453.7:c.1822G>T	p.Glu608Ter	p.E608*	ENST00000241453	NM_004119.2	608	Gaa/Taa	14/24	0.265499264737894	1	FACETS	0.912	0.816	1	1	0.985	1	CLONAL	2	TRUE	0	0.287821569681062	1		385	274	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702632	52702632	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779102269	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	50	302	0	ENST00000394830.3:c.266C>A	p.Ser89Tyr	p.S89Y	ENST00000394830	NM_018313.4	89	tCt/tAt	4/30	1	2	FACETS	1	0.943	1	1	0.979	1	CLONAL	2	TRUE	1	0.287821569681062	2		302	148	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983213	149983213	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	133	381	0	ENST00000253339.5:c.3045C>A	p.Phe1015Leu	p.F1015L	ENST00000253339		1015	ttC/ttA	7/7	1	2	FACETS	1	0.982	1	1	0.992	1	CLONAL	2	TRUE	1	0.287821569681062	2		381	370	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115803	8115803	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	221	390	0	ENST00000346208.3:c.1149G>T	p.Glu383Asp	p.E383D	ENST00000346208		383	gaG/gaT	6/6	1	2	FACETS	1	0.982	1	1	0.995	1	CLONAL	2	TRUE	1	0.287821569681062	2		390	677	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519179	137519179	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1562281992	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	39	141	0	ENST00000367739.4:c.1459G>T	p.Glu487Ter	p.E487*	ENST00000367739	NM_000416.2	487	Gaa/Taa	7/7	1	2	FACETS	0.975	0.824	1	1	0.969	1	CLONAL	2	TRUE	1	0.287821569681062	2		141	139	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019669	123019669	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	183	395	0	ENST00000355640.3:c.157C>A	p.Leu53Ile	p.L53I	ENST00000355640		53	Ctt/Att	2/7	0.265499264737894	1	FACETS	0.981	0.911	1	1	0.993	1	CLONAL	2	TRUE	0	0.287821569681062	1		395	555	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115267948	115267948	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	113	286	0	ENST00000438362.2:c.1785C>A	p.Phe595Leu	p.F595L	ENST00000438362	NM_001242891.1	595	ttC/ttA	15/20	0.287821569681062	3	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	1	0.287821569681062	3		286	429	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319038	62319038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219409480	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	236	868	0	ENST00000360203.5:c.1396G>A	p.Glu466Lys	p.E466K	ENST00000360203	NM_001283009.1	466	Gag/Aag	17/35	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.287821569681062	2		868	1285	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94906475	94906475	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs759770944	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	67	301	1	ENST00000536441.1:c.1423C>T	p.Arg475Ter	p.R475*	ENST00000536441	NM_144665.3	475	Cga/Tga	10/10	1	2	FACETS	0.935	0.823	1	1	0.981	1	CLONAL	2	TRUE	1	0.287821569681062	2		302	249	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726716	88726716	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	150	321	0	ENST00000360948.2:c.328A>G	p.Ile110Val	p.I110V	ENST00000360948	NM_001012338.2	110	Atc/Gtc	4/19	0.280185935080151	3	FACETS	1	0.937	1	0.683	0.627	0.741	CLONAL	2	TRUE	0	0.287821569681062	3		321	582	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233171	69233171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	50	189	0	ENST00000462284.1:c.1036G>A	p.Glu346Lys	p.E346K	ENST00000462284	NM_002392.5	346	Gaa/Aaa	11/11	1	2	FACETS	0.869	0.747	0.998	1	0.972	1	CLONAL	2	TRUE	1	0.287821569681062	2		189	200	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112365	115112365	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751549922	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	171	301	0	ENST00000257566.3:c.1375C>T	p.Arg459Cys	p.R459C	ENST00000257566	NM_016569.3	459	Cgc/Tgc	7/8	1	2	FACETS	1	0.981	1	1	0.993	1	CLONAL	2	TRUE	1	0.287821569681062	2		301	505	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159059	143159059	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	31	231	0	ENST00000262992.4:c.794C>A	p.Pro265His	p.P265H	ENST00000262992	NM_001101669.1	265	cCt/cAt	10/24	1	2	FACETS	1	0.833	1	1	0.963	1	CLONAL	2	TRUE	1	0.287821569681062	2		231	107	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224374	36224374	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	436	841	0	ENST00000222270.7:c.6924G>T	p.Glu2308Asp	p.E2308D	ENST00000222270	NM_014727.1	2308	gaG/gaT	28/37	1	2	FACETS	1	0.993	1	1	0.997	1	CLONAL	2	TRUE	1	0.287821569681062	2		841	1256	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164388	47164388	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	50	207	0	ENST00000409792.3:c.1738G>T	p.Glu580Ter	p.E580*	ENST00000409792	NM_014159.6	580	Gaa/Taa	3/21	1	2	FACETS	0.884	0.77	1	1	0.981	1	CLONAL	3	TRUE	1	0.287821569681062	2		207	131	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373178	118373178	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200497972	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	81	280	0	ENST00000534358.1:c.6571C>T	p.Arg2191Ter	p.R2191*	ENST00000534358	NM_005933.3	2191	Cga/Tga	27/36	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.287821569681062	2		280	462	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436851	110436851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761099871	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	450	725	1	ENST00000375856.3:c.1550G>A	p.Arg517Gln	p.R517Q	ENST00000375856	NM_003749.2	517	cGa/cAa	1/2	0.265499264737894	1	FACETS	1	0.993	1	1	0.997	1	CLONAL	2	TRUE	0	0.287821569681062	1		726	1135	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174912	11174912	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	131	413	0	ENST00000361445.4:c.7122G>T	p.Lys2374Asn	p.K2374N	ENST00000361445	NM_004958.3	2374	aaG/aaT	52/58	0.287821569681062	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.287821569681062	3		413	477	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057660	27057660	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	286	401	0	ENST00000324856.7:c.1368A>C	p.Gln456His	p.Q456H	ENST00000324856	NM_006015.4	456	caA/caC	3/20	0.287821569681062	3	FACETS	0.918	0.871	0.966	1	0.996	1	CLONAL	4	TRUE	1	0.287821569681062	3		401	619	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092983	27092983	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	121	240	0	ENST00000324856.7:c.2914G>A	p.Asp972Asn	p.D972N	ENST00000324856	NM_006015.4	972	Gat/Aat	10/20	0.287821569681062	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.287821569681062	3		240	441	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105957	27105957	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	109	412	0	ENST00000324856.7:c.5568G>T	p.Gln1856His	p.Q1856H	ENST00000324856	NM_006015.4	1856	caG/caT	20/20	0.287821569681062	3	FACETS	1	0.975	1	0.641	0.576	0.709	CLONAL	1	TRUE	1	0.287821569681062	3		412	676	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812182	43812182	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	233	387	0	ENST00000372470.3:c.1047C>A	p.Phe349Leu	p.F349L	ENST00000372470	NM_005373.2	349	ttC/ttA	7/12	0.287821569681062	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.287821569681062	3		387	767	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818313	43818313	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs781682729	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	504	601	0	ENST00000372470.3:c.1778G>T	p.Arg593Ile	p.R593I	ENST00000372470	NM_005373.2	593	aGa/aTa	12/12	0.287821569681062	3	FACETS	0.921	0.886	0.957	1	0.997	1	CLONAL	4	TRUE	1	0.287821569681062	3		601	1087	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247836	59247836	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	655	683	0	ENST00000371222.2:c.907G>T	p.Glu303Ter	p.E303*	ENST00000371222	NM_002228.3	303	Gaa/Taa	1/1	0.287821569681062	3	FACETS	0.917	0.886	0.949	1	0.998	1	CLONAL	4	TRUE	1	0.287821569681062	3		683	1419	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335153	65335153	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	33	286	0	ENST00000342505.4:c.488A>G	p.Gln163Arg	p.Q163R	ENST00000342505	NM_002227.2	163	cAg/cGg	6/25	0.287821569681062	3	FACETS	0.514	0.418	0.623	0.257	0.209	0.312	SUBCLONAL	1	TRUE	1	0.287821569681062	3		286	510	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241938	72241938	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs370438310	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	105	230	0	ENST00000357731.5:c.452A>G	p.Asn151Ser	p.N151S	ENST00000357731	NM_173808.2	151	aAt/aGt	3/7	0.287821569681062	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.287821569681062	3		230	365	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491668	120491668	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	188	250	0	ENST00000256646.2:c.2561T>G	p.Phe854Cys	p.F854C	ENST00000256646	NM_024408.3	854	tTt/tGt	16/34	0.287821569681062	3	FACETS	0.898	0.841	0.956	1	0.993	1	CLONAL	4	TRUE	1	0.287821569681062	3		250	416	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550820	150550820	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	52	302	0	ENST00000369026.2:c.836A>G	p.Lys279Arg	p.K279R	ENST00000369026	NM_021960.4	279	aAg/aGg	2/3	0.287821569681062	3	FACETS	0.681	0.579	0.793	0.34	0.289	0.397	SUBCLONAL	1	TRUE	1	0.287821569681062	3		302	607	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156836704	156836704	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	79	658	0	ENST00000524377.1:c.362A>C	p.Asn121Thr	p.N121T	ENST00000524377	NM_002529.3	121	aAt/aCt	4/17	0.287821569681062	3	FACETS	0.515	0.451	0.584	0.257	0.225	0.292	SUBCLONAL	1	TRUE	1	0.287821569681062	3		658	1220	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162688912	162688912	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	274	355	0	ENST00000367921.3:c.59C>A	p.Ser20Tyr	p.S20Y	ENST00000367921	NM_006182.2	20	tCt/tAt	3/18	0.287821569681062	3	FACETS	0.937	0.888	0.986	1	0.995	1	CLONAL	4	TRUE	1	0.287821569681062	3		355	581	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724987	162724987	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1291613281	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	139	288	0	ENST00000367921.3:c.459G>T	p.Lys153Asn	p.K153N	ENST00000367921	NM_006182.2	153	aaG/aaT	6/18	0.287821569681062	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.287821569681062	3		288	508	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725003	162725003	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1337564334	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	159	300	0	ENST00000367921.3:c.475A>G	p.Ile159Val	p.I159V	ENST00000367921	NM_006182.2	159	Att/Gtt	6/18	0.287821569681062	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.287821569681062	3		300	568	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163310194	163310194	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	27	276	0	ENST00000271452.3:c.647T>G	p.Ile216Ser	p.I216S	ENST00000271452	NM_145697.2	216	aTt/aGt	9/14	0.287821569681062	3	FACETS	1	0.834	1	0.523	0.419	0.641	CLONAL	1	TRUE	1	0.287821569681062	3		276	205	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163325134	163325134	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	18	160	0	ENST00000271452.3:c.1270C>A	p.Leu424Ile	p.L424I	ENST00000271452	NM_145697.2	424	Cta/Ata	14/14	0.287821569681062	3	FACETS	0.973	0.739	1	0.487	0.369	0.623	CLONAL	1	TRUE	1	0.287821569681062	3		160	147	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012376	176012376	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	117	258	0	ENST00000367669.3:c.1558G>T	p.Asp520Tyr	p.D520Y	ENST00000367669	NM_022457.5	520	Gac/Tac	14/20	0.287821569681062	3	FACETS	1	0.96	1	1	0.988	1	CLONAL	3	TRUE	1	0.287821569681062	3		258	287	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193181588	193181588	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs971586985	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	18	219	0	ENST00000367435.3:c.1135G>T	p.Asp379Tyr	p.D379Y	ENST00000367435	NM_024529.4	379	Gac/Tac	13/17	0.287821569681062	3	FACETS	1	0.858	1	0.596	0.454	0.76	CLONAL	1	TRUE	1	0.287821569681062	3		219	120	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809277	243809277	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	111	307	0	ENST00000263826.5:c.347G>T	p.Arg116Ile	p.R116I	ENST00000263826	NM_005465.4	116	aGa/aTa	4/13	0.287821569681062	3	FACETS	1	0.943	1	1	0.987	1	CLONAL	3	TRUE	1	0.287821569681062	3		307	282	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759937	63759937	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	151	263	0	ENST00000279873.7:c.590A>C	p.Lys197Thr	p.K197T	ENST00000279873	NM_032199.2	197	aAg/aCg	4/10	1	2	FACETS	0.864	0.798	0.93	1	0.993	1	CLONAL	3	TRUE	1	0.287821569681062	2		263	405	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63760053	63760053	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	117	249	0	ENST00000279873.7:c.706G>T	p.Glu236Ter	p.E236*	ENST00000279873	NM_032199.2	236	Gaa/Taa	4/10	1	2	FACETS	1	0.972	1	1	0.991	1	CLONAL	2	TRUE	1	0.287821569681062	2		249	350	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332654	70332654	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	137	389	0	ENST00000373644.4:c.559G>A	p.Glu187Lys	p.E187K	ENST00000373644	NM_030625.2	187	Gag/Aag	2/12	1	2	FACETS	1	0.977	1	1	0.992	1	CLONAL	2	TRUE	1	0.287821569681062	2		389	405	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405608	70405608	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	73	326	0	ENST00000373644.4:c.3122G>T	p.Arg1041Ile	p.R1041I	ENST00000373644	NM_030625.2	1041	aGa/aTa	4/12	1	2	FACETS	0.999	0.885	1	1	0.983	1	CLONAL	2	TRUE	1	0.287821569681062	2		326	254	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711983	89711983	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554900638	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	70	237	1	ENST00000371953.3:c.601G>T	p.Glu201Ter	p.E201*	ENST00000371953	NM_000314.4	201	Gaa/Taa	6/9	1	2	FACETS	1	0.953	1	1	0.985	1	CLONAL	2	TRUE	1	0.287821569681062	2		238	212	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104268963	104268963	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	311	499	0	ENST00000369902.3:c.220T>C	p.Tyr74His	p.Y74H	ENST00000369902	NM_016169.3	74	Tac/Cac	2/12	1	2	FACETS	0.85	0.805	0.896	1	0.996	1	CLONAL	3	TRUE	1	0.287821569681062	2		499	847	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112760262	112760262	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	108	235	0	ENST00000369452.4:c.931G>T	p.Glu311Ter	p.E311*	ENST00000369452	NM_007373.3	311	Gaa/Taa	4/9	1	2	FACETS	1	0.968	1	1	0.992	1	CLONAL	4	TRUE	1	0.287821569681062	2		235	174	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154865	2154865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	362	767	0	ENST00000434045.2:c.356G>A	p.Ser119Asn	p.S119N	ENST00000434045	NM_001127598.1	119	aGc/aAc	4/5	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	1	0.287821569681062	2		767	1046	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316365	14316365	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	148	401	0	ENST00000256196.4:c.240A>C	p.Glu80Asp	p.E80D	ENST00000256196		80	gaA/gaC	3/6	1	2	FACETS	1	0.98	1	1	0.993	1	CLONAL	2	TRUE	1	0.287821569681062	2		401	431	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741928	17741928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	138	219	0	ENST00000250003.3:c.599C>T	p.Ser200Phe	p.S200F	ENST00000250003	NM_002478.4	200	tCc/tTc	1/3	1	2	FACETS	0.957	0.884	1	1	0.993	1	CLONAL	3	TRUE	1	0.287821569681062	2		219	334	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945342	71945342	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	294	553	0	ENST00000298229.2:c.2230G>T	p.Asp744Tyr	p.D744Y	ENST00000298229	NM_001567.3	744	Gac/Tac	20/28	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.287821569681062	2		553	884	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946733	71946733	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	254	515	0	ENST00000298229.2:c.2674G>T	p.Asp892Tyr	p.D892Y	ENST00000298229	NM_001567.3	892	Gat/Tat	24/28	1	2	FACETS	0.866	0.816	0.918	1	0.996	1	CLONAL	3	TRUE	1	0.287821569681062	2		515	679	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988989	85988989	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	30	206	0	ENST00000263360.6:c.1155A>C	p.Lys385Asn	p.K385N	ENST00000263360	NM_003797.3	385	aaA/aaC	11/12	1	2	FACETS	0.993	0.819	1	1	0.961	1	CLONAL	2	TRUE	1	0.287821569681062	2		206	105	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94211999	94211999	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	96	268	0	ENST00000323929.3:c.446T>G	p.Phe149Cys	p.F149C	ENST00000323929	NM_005591.3	149	tTt/tGt	6/20	1	2	FACETS	1	0.973	1	1	0.989	1	CLONAL	2	TRUE	1	0.287821569681062	2		268	272	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917722	94917722	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	10	297	0	ENST00000536441.1:c.799G>T	p.Glu267Ter	p.E267*	ENST00000536441	NM_144665.3	267	Gaa/Taa	6/10	1	2	FACETS	0.378	0.256	0.531	0.378	0.256	0.531	SUBCLONAL	1	TRUE	1	0.287821569681062	2		297	184	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94923016	94923016	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	23	319	0	ENST00000536441.1:c.452G>T	p.Arg151Ile	p.R151I	ENST00000536441	NM_144665.3	151	aGa/aTa	4/10	1	2	FACETS	0.545	0.426	0.684	0.545	0.426	0.684	SUBCLONAL	1	TRUE	1	0.287821569681062	2		319	293	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920761	100920761	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	28	267	0	ENST00000325455.5:c.2387C>A	p.Ser796Ter	p.S796*	ENST00000325455	NM_001202474.3	796	tCa/tAa	6/8	1	2	FACETS	0.797	0.64	0.975	0.797	0.64	0.975	CLONAL	1	TRUE	1	0.287821569681062	2		267	244	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115702	108115702	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	29	182	1	ENST00000278616.4:c.850C>A	p.Gln284Lys	p.Q284K	ENST00000278616	NM_000051.3	284	Caa/Aaa	7/63	1	2	FACETS	0.84	0.697	0.99	1	0.966	1	CLONAL	3	TRUE	1	0.287821569681062	2		183	80	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117822	108117822	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	34	228	0	ENST00000278616.4:c.1033T>G	p.Leu345Val	p.L345V	ENST00000278616	NM_000051.3	345	Ttg/Gtg	8/63	1	2	FACETS	1	0.899	1	1	0.968	1	CLONAL	2	TRUE	1	0.287821569681062	2		228	107	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155078	108155078	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	30	303	0	ENST00000278616.4:c.3871C>A	p.Leu1291Ile	p.L1291I	ENST00000278616	NM_000051.3	1291	Ctt/Att	26/63	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.287821569681062	2		303	205	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170546	108170546	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	29	273	0	ENST00000278616.4:c.5111A>G	p.Glu1704Gly	p.E1704G	ENST00000278616	NM_000051.3	1704	gAa/gGa	34/63	1	2	FACETS	0.854	0.699	1	1	0.953	1	CLONAL	2	TRUE	1	0.287821569681062	2		273	118	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205739	108205739	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	63	225	0	ENST00000278616.4:c.8054C>A	p.Ser2685Ter	p.S2685*	ENST00000278616	NM_000051.3	2685	tCa/tAa	55/63	1	2	FACETS	1	0.961	1	1	0.984	1	CLONAL	2	TRUE	1	0.287821569681062	2		225	178	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118339501	118339501	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	136	256	0	ENST00000534358.1:c.444C>A	p.Phe148Leu	p.F148L	ENST00000534358	NM_005933.3	148	ttC/ttA	2/36	1	2	FACETS	1	0.982	1	1	0.992	1	CLONAL	2	TRUE	1	0.287821569681062	2		256	381	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359367	118359367	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	137	260	1	ENST00000534358.1:c.4371G>T	p.Lys1457Asn	p.K1457N	ENST00000534358	NM_005933.3	1457	aaG/aaT	11/36	1	2	FACETS	1	0.982	1	1	0.992	1	CLONAL	2	TRUE	1	0.287821569681062	2		261	381	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373907	118373907	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	55	191	0	ENST00000534358.1:c.7300A>C	p.Lys2434Gln	p.K2434Q	ENST00000534358	NM_005933.3	2434	Aaa/Caa	27/36	1	2	FACETS	1	0.955	1	1	0.981	1	CLONAL	2	TRUE	1	0.287821569681062	2		191	157	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376541	118376541	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	152	257	0	ENST00000534358.1:c.9934A>G	p.Thr3312Ala	p.T3312A	ENST00000534358	NM_005933.3	3312	Act/Gct	27/36	1	2	FACETS	0.941	0.872	1	1	0.993	1	CLONAL	3	TRUE	1	0.287821569681062	2		257	374	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103374	119103374	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	56	253	0	ENST00000264033.4:c.412G>T	p.Glu138Ter	p.E138*	ENST00000264033	NM_005188.3	138	Gaa/Taa	2/16	1	2	FACETS	0.876	0.769	0.987	1	0.983	1	CLONAL	3	TRUE	1	0.287821569681062	2		253	148	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416137	416137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1449032009	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	43	274	1	ENST00000399788.2:c.4049G>A	p.Arg1350Gln	p.R1350Q	ENST00000399788	NM_001042603.1	1350	cGa/cAa	24/28	1	2	FACETS	0.903	0.758	1	0.903	0.758	1	CLONAL	1	TRUE	1	0.287821569681062	2		275	331	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	461452	461452	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	100	306	0	ENST00000399788.2:c.1068A>C	p.Gln356His	p.Q356H	ENST00000399788	NM_001042603.1	356	caA/caC	9/28	1	2	FACETS	0.987	0.89	1	1	0.988	1	CLONAL	2	TRUE	1	0.287821569681062	2		306	352	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435245	18435245	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	85	214	0	ENST00000266497.5:c.230C>A	p.Ser77Ter	p.S77*	ENST00000266497		77	tCa/tAa	1/31	1	2	FACETS	0.841	0.757	0.929	1	0.988	1	CLONAL	3	TRUE	1	0.287821569681062	2		214	234	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466994	18466994	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs773615749	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	19	235	0	ENST00000266497.5:c.1133G>T	p.Arg378Leu	p.R378L	ENST00000266497		378	cGa/cTa	5/31	1	2	FACETS	0.62	0.472	0.792	0.62	0.472	0.792	SUBCLONAL	1	TRUE	1	0.287821569681062	2		235	213	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715797	18715797	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	55	220	0	ENST00000266497.5:c.3628A>C	p.Ile1210Leu	p.I1210L	ENST00000266497		1210	Att/Ctt	25/31	1	2	FACETS	1	0.936	1	1	0.98	1	CLONAL	2	TRUE	1	0.287821569681062	2		220	170	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800949	18800949	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs12816860	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	21	223	0	ENST00000266497.5:c.4325A>G	p.Asn1442Ser	p.N1442S	ENST00000266497		1442	aAc/aGc	31/31	1	2	FACETS	1	0.822	1	1	0.822	1	CLONAL	1	TRUE	1	0.287821569681062	2		223	137	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624485	21624485	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	104	463	0	ENST00000421138.2:c.1544T>G	p.Leu515Arg	p.L515R	ENST00000421138		515	cTg/cGg	14/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.287821569681062	2		463	602	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245505	46245505	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	126	264	0	ENST00000334344.6:c.3599G>T	p.Gly1200Val	p.G1200V	ENST00000334344	NM_152641.2	1200	gGa/gTa	15/21	1	2	FACETS	1	0.979	1	1	0.992	1	CLONAL	2	TRUE	1	0.287821569681062	2		264	357	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415648	49415648	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1383821738	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	131	273	0	ENST00000301067.7:c.16529A>G	p.Tyr5510Cys	p.Y5510C	ENST00000301067	NM_003482.3	5510	tAt/tGt	54/54	1	2	FACETS	0.845	0.776	0.916	1	0.992	1	CLONAL	3	TRUE	1	0.287821569681062	2		273	359	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484117	50484117	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	241	434	0	ENST00000394963.4:c.967A>C	p.Ile323Leu	p.I323L	ENST00000394963	NM_003076.4	323	Att/Ctt	8/13	1	2	FACETS	0.859	0.807	0.911	1	0.995	1	CLONAL	3	TRUE	1	0.287821569681062	2		434	650	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482610	56482610	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	320	545	0	ENST00000267101.3:c.1067A>C	p.Lys356Thr	p.K356T	ENST00000267101	NM_001982.3	356	aAg/aCg	9/28	1	2	FACETS	0.891	0.845	0.938	1	0.997	1	CLONAL	3	TRUE	1	0.287821569681062	2		545	832	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487316	56487316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1394170153	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	154	280	0	ENST00000267101.3:c.1462C>T	p.Arg488Trp	p.R488W	ENST00000267101	NM_001982.3	488	Cgg/Tgg	12/28	1	2	FACETS	1	0.98	1	1	0.993	1	CLONAL	2	TRUE	1	0.287821569681062	2		280	454	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811655	102811655	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	238	542	0	ENST00000307046.8:c.529G>T	p.Glu177Ter	p.E177*	ENST00000307046	NM_001111285.1	177	Gag/Tag	4/4	1	2	FACETS	1	0.97	1	1	0.995	1	CLONAL	2	TRUE	1	0.287821569681062	2		542	781	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102874129	102874129	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	45	232	0	ENST00000307046.8:c.31T>G	p.Leu11Val	p.L11V	ENST00000307046	NM_001111285.1	11	Tta/Gta	1/4	1	2	FACETS	1	0.925	1	1	0.976	1	CLONAL	2	TRUE	1	0.287821569681062	2		232	139	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102874153	102874153	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	37	221	0	ENST00000307046.8:c.7A>C	p.Lys3Gln	p.K3Q	ENST00000307046	NM_001111285.1	3	Aaa/Caa	1/4	1	2	FACETS	0.893	0.749	1	1	0.964	1	CLONAL	2	TRUE	1	0.287821569681062	2		221	144	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888252	112888252	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	136	318	0	ENST00000351677.2:c.268G>T	p.Glu90Ter	p.E90*	ENST00000351677	NM_002834.3	90	Gag/Tag	3/16	1	2	FACETS	0.842	0.775	0.911	1	0.992	1	CLONAL	3	TRUE	1	0.287821569681062	2		318	374	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112942506	112942506	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	18	160	0	ENST00000351677.2:c.1720G>T	p.Glu574Ter	p.E574*	ENST00000351677	NM_002834.3	574	Gaa/Taa	15/16	1	2	FACETS	0.549	0.414	0.707	0.549	0.414	0.707	SUBCLONAL	1	TRUE	1	0.287821569681062	2		160	228	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118838	115118838	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	158	309	0	ENST00000257566.3:c.503C>A	p.Ser168Tyr	p.S168Y	ENST00000257566	NM_016569.3	168	tCt/tAt	2/8	1	2	FACETS	1	0.973	1	1	0.993	1	CLONAL	2	TRUE	1	0.287821569681062	2		309	490	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133234459	133234459	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs139603739	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	164	339	0	ENST00000320574.5:c.3373C>T	p.Arg1125Ter	p.R1125*	ENST00000320574	NM_006231.2	1125	Cga/Tga	27/49	1	2	FACETS	1	0.98	1	1	0.993	1	CLONAL	2	TRUE	1	0.287821569681062	2		339	488	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563387	21563387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528026146	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1217	176	960	0	ENST00000382592.4:c.532G>A	p.Asp178Asn	p.D178N	ENST00000382592	NM_014572.2	178	Gat/Aat	4/8	0.265499264737894	1	FACETS	0.752	0.69	0.816	0.752	0.69	0.816	SUBCLONAL	1	TRUE	0	0.287821569681062	1		960	1393	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592719	28592719	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	205	316	0	ENST00000241453.7:c.2426A>G	p.His809Arg	p.H809R	ENST00000241453	NM_004119.2	809	cAc/cGc	20/24	0.265499264737894	1	FACETS	1	0.962	1	1	0.994	1	CLONAL	2	TRUE	0	0.287821569681062	1		316	584	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880820	28880820	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	246	468	0	ENST00000282397.4:c.3810G>T	p.Lys1270Asn	p.K1270N	ENST00000282397	NM_002019.4	1270	aaG/aaT	29/30	0.265499264737894	1	FACETS	1	0.972	1	1	0.995	1	CLONAL	2	TRUE	0	0.287821569681062	1		468	692	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28883015	28883015	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	122	356	0	ENST00000282397.4:c.3685G>T	p.Glu1229Ter	p.E1229*	ENST00000282397	NM_002019.4	1229	Gaa/Taa	28/30	0.265499264737894	1	FACETS	0.926	0.845	1	1	0.989	1	CLONAL	2	TRUE	0	0.287821569681062	1		356	392	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895653	28895653	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	51	343	0	ENST00000282397.4:c.3121T>G	p.Phe1041Val	p.F1041V	ENST00000282397	NM_002019.4	1041	Ttt/Gtt	23/30	0.265499264737894	1	FACETS	0.852	0.727	0.988	0.852	0.727	0.988	CLONAL	1	TRUE	0	0.287821569681062	1		343	356	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28903839	28903839	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	78	580	0	ENST00000282397.4:c.2620G>A	p.Ala874Thr	p.A874T	ENST00000282397	NM_002019.4	874	Gct/Act	19/30	0.265499264737894	1	FACETS	0.599	0.526	0.679	0.599	0.526	0.679	SUBCLONAL	1	TRUE	0	0.287821569681062	1		580	774	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931696	28931696	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	141	298	0	ENST00000282397.4:c.2243T>C	p.Val748Ala	p.V748A	ENST00000282397	NM_002019.4	748	gTt/gCt	15/30	0.265499264737894	1	FACETS	1	0.96	1	1	0.992	1	CLONAL	2	TRUE	0	0.287821569681062	1		298	393	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005342	29005342	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	71	370	0	ENST00000282397.4:c.919G>T	p.Gly307Ter	p.G307*	ENST00000282397	NM_002019.4	307	Gga/Tga	7/30	0.265499264737894	1	FACETS	0.96	0.851	1	1	0.983	1	CLONAL	2	TRUE	0	0.287821569681062	1		370	220	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906541	32906541	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs886038059	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	34	243	0	ENST00000380152.3:c.926C>A	p.Ser309Ter	p.S309*	ENST00000380152		309	tCa/tAa	10/27	0.265499264737894	1	FACETS	1	0.849	1	1	0.967	1	CLONAL	2	TRUE	0	0.287821569681062	1		243	100	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912918	32912918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1380537823	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	45	264	0	ENST00000380152.3:c.4426G>A	p.Asp1476Asn	p.D1476N	ENST00000380152		1476	Gac/Aac	11/27	0.265499264737894	1	FACETS	0.869	0.744	1	1	0.97	1	CLONAL	2	TRUE	0	0.287821569681062	1		264	154	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914386	32914386	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	73	338	0	ENST00000380152.3:c.5894T>G	p.Leu1965Arg	p.L1965R	ENST00000380152		1965	cTt/cGt	11/27	0.265499264737894	1	FACETS	1	0.946	1	1	0.985	1	CLONAL	2	TRUE	0	0.287821569681062	1		338	197	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73334017	73334017	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	32	211	0	ENST00000377767.4:c.2794-1G>T		p.X932_splice	ENST00000377767	NM_014953.3	932			0.265499264737894	1	FACETS	0.898	0.747	1	1	0.96	1	CLONAL	2	TRUE	0	0.287821569681062	1		211	106	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515291	103515291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	79	194	1	ENST00000355739.4:c.1792G>A	p.Asp598Asn	p.D598N	ENST00000355739	NM_000123.3	598	Gat/Aat	8/15	0.265499264737894	1	FACETS	1	0.905	1	1	0.985	1	CLONAL	2	TRUE	0	0.287821569681062	1		195	232	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524615	103524615	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	130	201	0	ENST00000355739.4:c.2746A>C	p.Lys916Gln	p.K916Q	ENST00000355739	NM_000123.3	916	Aaa/Caa	13/15	0.265499264737894	1	FACETS	1	0.96	1	1	0.991	1	CLONAL	2	TRUE	0	0.287821569681062	1		201	359	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100225	30100225	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	73	221	0	ENST00000331968.5:c.1395A>C	p.Glu465Asp	p.E465D	ENST00000331968	NM_002742.2	465	gaA/gaC	10/18	1	2	FACETS	1	0.955	1	1	0.985	1	CLONAL	2	TRUE	1	0.287821569681062	2		221	221	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352635	68352635	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	71	223	1	ENST00000487270.1:c.502G>T	p.Glu168Ter	p.E168*	ENST00000487270	NM_133509.3	168	Gaa/Taa	6/11	1	2	FACETS	1	0.898	1	1	0.987	1	CLONAL	3	TRUE	1	0.287821569681062	2		224	164	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81557420	81557420	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	44	219	0	ENST00000298171.2:c.400T>C	p.Phe134Leu	p.F134L	ENST00000298171	NM_000369.2	134	Ttc/Ctc	5/10	1	2	FACETS	0.91	0.775	1	1	0.97	1	CLONAL	2	TRUE	1	0.287821569681062	2		219	168	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606108	81606108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs567674408	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	288	407	0	ENST00000298171.2:c.778C>A	p.Leu260Ile	p.L260I	ENST00000298171	NM_000369.2	260	Ctt/Att	9/10	1	2	FACETS	0.945	0.894	0.996	1	0.996	1	CLONAL	3	TRUE	1	0.287821569681062	2		407	706	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606113	81606113	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	85	410	0	ENST00000298171.2:c.783G>T	p.Lys261Asn	p.K261N	ENST00000298171	NM_000369.2	261	aaG/aaT	9/10	1	2	FACETS	0.856	0.757	0.962	0.856	0.757	0.962	CLONAL	1	TRUE	1	0.287821569681062	2		410	690	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569787	95569787	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs771037069	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	102	200	0	ENST00000393063.1:c.3946G>T	p.Glu1316Ter	p.E1316*	ENST00000393063	NM_030621.3	1316	Gaa/Taa	22/28	1	2	FACETS	0.902	0.82	0.985	1	0.99	1	CLONAL	3	TRUE	1	0.287821569681062	2		200	262	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022972	33022972	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	63	374	0	ENST00000300177.4:c.81A>C	p.Lys27Asn	p.K27N	ENST00000300177	NM_001191322.1	27	aaA/aaC	2/2	0.265499264737894	1	FACETS	0.787	0.682	0.901	0.787	0.682	0.901	CLONAL	1	TRUE	0	0.287821569681062	1		374	476	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961840	41961840	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	34	272	0	ENST00000219905.7:c.748G>T	p.Asp250Tyr	p.D250Y	ENST00000219905	NM_001164273.1	250	Gat/Tat	2/24	0.265499264737894	1	FACETS	0.707	0.58	0.849	0.707	0.58	0.849	SUBCLONAL	1	TRUE	0	0.287821569681062	1		272	286	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035031	42035031	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	55	425	0	ENST00000219905.7:c.4873G>T	p.Glu1625Ter	p.E1625*	ENST00000219905	NM_001164273.1	1625	Gaa/Taa	15/24	0.265499264737894	1	FACETS	0.612	0.523	0.708	0.612	0.523	0.708	SUBCLONAL	1	TRUE	0	0.287821569681062	1		425	535	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293279	91293279	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	64	202	0	ENST00000355112.3:c.781C>A	p.His261Asn	p.H261N	ENST00000355112	NM_000057.2	261	Cat/Aat	3/22	0.280185935080151	3	FACETS	0.982	0.86	1	0.655	0.573	0.741	CLONAL	2	TRUE	0	0.287821569681062	3		202	259	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303963	91303963	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	151	458	0	ENST00000355112.3:c.1360A>G	p.Asn454Asp	p.N454D	ENST00000355112	NM_000057.2	454	Aat/Gat	7/22	0.280185935080151	3	FACETS	1	0.943	1	0.689	0.632	0.747	CLONAL	2	TRUE	0	0.287821569681062	3		458	581	SUCCESS
BLM	641	MSKCC	GRCh37	15	91341477	91341477	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	27	238	0	ENST00000355112.3:c.3268G>T	p.Glu1090Ter	p.E1090*	ENST00000355112	NM_000057.2	1090	Gaa/Taa	17/22	0.280185935080151	3	FACETS	0.887	0.718	1	0.591	0.479	0.715	CLONAL	2	TRUE	0	0.287821569681062	3		238	121	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251261	99251261	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	54	458	0	ENST00000268035.6:c.565A>G	p.Lys189Glu	p.K189E	ENST00000268035	NM_000875.3	189	Aag/Gag	2/21	0.280185935080151	3	FACETS	0.586	0.5	0.682	0.195	0.166	0.228	SUBCLONAL	1	TRUE	0	0.287821569681062	3		458	732	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99482573	99482573	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	191	437	0	ENST00000268035.6:c.3441C>A	p.Phe1147Leu	p.F1147L	ENST00000268035	NM_000875.3	1147	ttC/ttA	18/21	0.280185935080151	3	FACETS	0.892	0.826	0.961	0.595	0.55	0.641	CLONAL	2	TRUE	0	0.287821569681062	3		437	851	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641021	3641021	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	413	754	3	ENST00000294008.3:c.2618C>T	p.Ala873Val	p.A873V	ENST00000294008	NM_032444.2	873	gCc/gTc	12/15	1	2	FACETS	0.844	0.804	0.883	1	0.997	1	CLONAL	3	TRUE	1	0.287821569681062	2		757	1134	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860752	3860752	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	197	354	0	ENST00000262367.5:c.827T>G	p.Phe276Cys	p.F276C	ENST00000262367	NM_004380.2	276	tTt/tGt	3/31	1	2	FACETS	1	0.983	1	1	0.994	1	CLONAL	2	TRUE	1	0.287821569681062	2		354	586	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858137	9858137	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	239	503	0	ENST00000330684.3:c.3264G>T	p.Arg1088Ser	p.R1088S	ENST00000330684	NM_001134407.1	1088	agG/agT	13/13	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	1	0.287821569681062	2		503	684	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862914	9862914	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	220	507	0	ENST00000330684.3:c.2389A>G	p.Thr797Ala	p.T797A	ENST00000330684	NM_001134407.1	797	Act/Gct	12/13	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.287821569681062	2		507	657	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934869	9934869	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	48	340	0	ENST00000330684.3:c.1421C>A	p.Thr474Asn	p.T474N	ENST00000330684	NM_001134407.1	474	aCt/aAt	6/13	1	2	FACETS	0.924	0.784	1	0.924	0.784	1	CLONAL	1	TRUE	1	0.287821569681062	2		340	361	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273892	10273892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	320	741	0	ENST00000330684.3:c.377G>A	p.Gly126Asp	p.G126D	ENST00000330684	NM_001134407.1	126	gGc/gAc	2/13	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.287821569681062	2		741	946	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641656	23641656	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1567218740	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	73	344	0	ENST00000261584.4:c.1819C>A	p.Leu607Ile	p.L607I	ENST00000261584	NM_024675.3	607	Ctc/Atc	5/13	1	2	FACETS	0.903	0.798	1	1	0.982	1	CLONAL	2	TRUE	1	0.287821569681062	2		344	281	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647328	23647328	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	36	400	0	ENST00000261584.4:c.539A>T	p.Glu180Val	p.E180V	ENST00000261584	NM_024675.3	180	gAa/gTa	4/13	1	2	FACETS	0.691	0.569	0.827	0.691	0.569	0.827	SUBCLONAL	1	TRUE	1	0.287821569681062	2		400	362	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50821710	50821710	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	26	270	0	ENST00000398568.2:c.2046C>A	p.Phe682Leu	p.F682L	ENST00000398568	NM_001042412.1	682	ttC/ttA	13/18	1	2	FACETS	1	0.825	1	1	0.956	1	CLONAL	2	TRUE	1	0.287821569681062	2		270	89	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644754	67644754	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	166	304	0	ENST00000264010.4:c.19G>T	p.Glu7Ter	p.E7*	ENST00000264010	NM_006565.3	7	Gaa/Taa	3/12	1	2	FACETS	1	0.984	1	1	0.993	1	CLONAL	2	TRUE	1	0.287821569681062	2		304	473	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888069	81888069	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	120	254	0	ENST00000359376.3:c.214G>T	p.Glu72Ter	p.E72*	ENST00000359376	NM_002661.3	72	Gaa/Taa	3/33	1	2	FACETS	1	0.97	1	1	0.991	1	CLONAL	2	TRUE	1	0.287821569681062	2		254	365	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81927396	81927396	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	89	532	1	ENST00000359376.3:c.1069G>T	p.Glu357Ter	p.E357*	ENST00000359376	NM_002661.3	357	Gaa/Taa	12/33	1	2	FACETS	0.664	0.588	0.746	0.664	0.588	0.746	SUBCLONAL	1	TRUE	1	0.287821569681062	2		533	931	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349930	89349930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs919092415	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	381	716	0	ENST00000301030.4:c.3020G>A	p.Arg1007Gln	p.R1007Q	ENST00000301030	NM_001256183.1	1007	cGa/cAa	9/13	1	2	FACETS	0.847	0.806	0.888	1	0.997	1	CLONAL	3	TRUE	1	0.287821569681062	2		716	1042	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350144	89350144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	368	713	0	ENST00000301030.4:c.2806G>A	p.Glu936Lys	p.E936K	ENST00000301030	NM_001256183.1	936	Gaa/Aaa	9/13	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	1	0.287821569681062	2		713	1059	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831335	89831335	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	299	534	0	ENST00000389301.3:c.2741G>T	p.Arg914Ile	p.R914I	ENST00000389301	NM_000135.2	914	aGa/aTa	28/43	1	2	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	TRUE	1	0.287821569681062	2		534	846	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217835	7217835	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	84	535	0	ENST00000380728.2:c.176G>T	p.Arg59Ile	p.R59I	ENST00000380728		59	aGa/aTa	3/11	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.287821569681062	2		535	569	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217872	7217872	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	150	422	0	ENST00000380728.2:c.139G>T	p.Glu47Ter	p.E47*	ENST00000380728		47	Gaa/Taa	3/11	1	2	FACETS	1	0.98	1	1	0.993	1	CLONAL	2	TRUE	1	0.287821569681062	2		422	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572931	7572931	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	201	430	0	ENST00000269305.4:c.1178A>G	p.Asp393Gly	p.D393G	ENST00000269305	NM_001126112.2	393	gAc/gGc	11/11	1	2	FACETS	1	0.984	1	1	0.994	1	CLONAL	2	TRUE	1	0.287821569681062	2		430	592	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942924	15942924	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	161	321	0	ENST00000268712.3:c.6778A>C	p.Asn2260His	p.N2260H	ENST00000268712	NM_006311.3	2260	Aat/Cat	44/46	1	2	FACETS	0.857	0.794	0.922	1	0.993	1	CLONAL	3	TRUE	1	0.287821569681062	2		321	435	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973823	15973823	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	49	293	0	ENST00000268712.3:c.4169T>G	p.Phe1390Cys	p.F1390C	ENST00000268712	NM_006311.3	1390	tTt/tGt	31/46	1	2	FACETS	0.882	0.749	1	0.882	0.749	1	CLONAL	1	TRUE	1	0.287821569681062	2		293	386	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029434	16029434	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	46	249	0	ENST00000268712.3:c.1596G>T	p.Lys532Asn	p.K532N	ENST00000268712	NM_006311.3	532	aaG/aaT	15/46	1	2	FACETS	1	0.899	1	1	0.976	1	CLONAL	2	TRUE	1	0.287821569681062	2		249	151	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049769	16049769	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	68	345	0	ENST00000268712.3:c.1003G>T	p.Glu335Ter	p.E335*	ENST00000268712	NM_006311.3	335	Gaa/Taa	10/46	1	2	FACETS	1	0.91	1	1	0.983	1	CLONAL	2	TRUE	1	0.287821569681062	2		345	228	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089943	16089943	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	158	227	0	ENST00000268712.3:c.167T>G	p.Leu56Arg	p.L56R	ENST00000268712	NM_006311.3	56	cTt/cGt	3/46	1	2	FACETS	1	0.979	1	1	0.993	1	CLONAL	2	TRUE	1	0.287821569681062	2		227	471	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556856	29556856	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	21	217	0	ENST00000356175.3:c.2854T>G	p.Leu952Val	p.L952V	ENST00000356175	NM_000267.3	952	Tta/Gta	22/57	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.287821569681062	2		217	126	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588776	29588776	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	124	246	0	ENST00000356175.3:c.4562T>G	p.Leu1521Arg	p.L1521R	ENST00000356175	NM_000267.3	1521	cTt/cGt	34/57	1	2	FACETS	0.895	0.821	0.97	1	0.992	1	CLONAL	3	TRUE	1	0.287821569681062	2		246	321	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627509	37627509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371684674	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	102	306	0	ENST00000447079.4:c.1424C>T	p.Ser475Phe	p.S475F	ENST00000447079	NM_015083.1	475	tCt/tTt	2/14	1	2	FACETS	1	0.971	1	1	0.99	1	CLONAL	2	TRUE	1	0.287821569681062	2		306	299	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362502	40362502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	61	418	0	ENST00000293328.3:c.1694G>A	p.Gly565Glu	p.G565E	ENST00000293328	NM_012448.3	565	gGa/gAa	14/19	1	2	FACETS	0.95	0.822	1	0.95	0.822	1	CLONAL	1	TRUE	1	0.287821569681062	2		418	446	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246218	41246218	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	67	342	0	ENST00000357654.3:c.1330A>C	p.Ser444Arg	p.S444R	ENST00000357654	NM_007294.3	444	Agt/Cgt	10/23	1	2	FACETS	1	0.921	1	1	0.983	1	CLONAL	2	TRUE	1	0.287821569681062	2		342	220	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805936	46805936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	151	338	0	ENST00000290295.7:c.20C>T	p.Ala7Val	p.A7V	ENST00000290295	NM_006361.5	7	gCc/gTc	1/2	1	2	FACETS	1	0.98	1	1	0.993	1	CLONAL	2	TRUE	1	0.287821569681062	2		338	443	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438226	56438226	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755996999	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	334	665	0	ENST00000407977.2:c.767G>A	p.Arg256Gln	p.R256Q	ENST00000407977		256	cGg/cAg	7/10	1	2	FACETS	0.857	0.813	0.901	1	0.997	1	CLONAL	3	TRUE	1	0.287821569681062	2		665	903	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58725354	58725354	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	140	341	0	ENST00000305921.3:c.928A>C	p.Ile310Leu	p.I310L	ENST00000305921	NM_003620.3	310	Ata/Cta	4/6	1	2	FACETS	0.851	0.784	0.92	1	0.993	1	CLONAL	3	TRUE	1	0.287821569681062	2		341	381	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796930	78796930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	202	402	0	ENST00000306801.3:c.1043G>A	p.Arg348Gln	p.R348Q	ENST00000306801	NM_020761.2	348	cGa/cAa	9/34	1	2	FACETS	1	0.98	1	1	0.994	1	CLONAL	2	TRUE	1	0.287821569681062	2		402	619	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586287	48586287	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	35	244	0	ENST00000342988.3:c.955+1G>A		p.X319_splice	ENST00000342988	NM_005359.5	319			0.287821569681062	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.287821569681062	1		244	178	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56367721	56367721	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	98	222	0	ENST00000348428.3:c.547A>C	p.Lys183Gln	p.K183Q	ENST00000348428	NM_006785.3	183	Aaa/Caa	4/17	0.287821569681062	1	FACETS	1	0.965	1	1	0.989	1	CLONAL	2	TRUE	0	0.287821569681062	1		222	257	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56411617	56411617	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	27	242	0	ENST00000348428.3:c.1801C>A	p.Gln601Lys	p.Q601K	ENST00000348428	NM_006785.3	601	Caa/Aaa	15/17	0.287821569681062	1	FACETS	0.828	0.675	0.994	1	0.949	1	CLONAL	2	TRUE	0	0.287821569681062	1		242	97	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56412970	56412970	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	37	259	0	ENST00000348428.3:c.1984G>A	p.Asp662Asn	p.D662N	ENST00000348428	NM_006785.3	662	Gat/Aat	16/17	0.287821569681062	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.287821569681062	1		259	190	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254535	10254535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746527645	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	282	496	0	ENST00000340748.4:c.2975G>A	p.Arg992Gln	p.R992Q	ENST00000340748		992	cGa/cAa	28/40	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.287821569681062	2		496	829	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10259583	10259583	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs530293931	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	335	576	0	ENST00000340748.4:c.2649G>T	p.Gln883His	p.Q883H	ENST00000340748		883	caG/caT	26/40	1	2	FACETS	0.871	0.826	0.916	1	0.997	1	CLONAL	3	TRUE	1	0.287821569681062	2		576	891	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169030	11169030	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	129	577	1	ENST00000358026.2:c.4620G>T	p.Lys1540Asn	p.K1540N	ENST00000358026	NM_001128849.1	1540	aaG/aaT	32/36	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.287821569681062	2		578	872	SUCCESS
CALR	811	MSKCC	GRCh37	19	13049518	13049543	+	frameshift_variant	Frame_Shift_Del	DEL	CTCGGCCTCCTCGGCCTGGCCGTCGC	CTCGGCCTCCTCGGCCTGGCCGTCGC	-	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	412	608	0	ENST00000316448.5:c.26_51del	p.Leu9ArgfsTer42	p.L9Rfs*42	ENST00000316448	NM_004343.3	9	CTCGGCCTCCTCGGCCTGGCCGTCGCc/c	1/9	1	2	FACETS	0.968	0.925	1	1	0.997	1	CLONAL	3	TRUE	1	0.287821569681062	2		608	986	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375447	15375447	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	181	719	0	ENST00000263377.2:c.980C>A	p.Pro327His	p.P327H	ENST00000263377	NM_058243.2	327	cCt/cAt	6/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.287821569681062	2		719	1073	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18943153	18943153	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	40	182	0	ENST00000262803.5:c.135G>T	p.Gln45His	p.Q45H	ENST00000262803	NM_002911.3	45	caG/caT	1/24	1	2	FACETS	0.894	0.746	1	0.894	0.746	1	CLONAL	1	TRUE	1	0.287821569681062	2		182	311	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965491	18965491	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	369	649	0	ENST00000262803.5:c.1238T>G	p.Phe413Cys	p.F413C	ENST00000262803	NM_002911.3	413	tTt/tGt	9/24	1	2	FACETS	0.834	0.793	0.876	1	0.997	1	CLONAL	3	TRUE	1	0.287821569681062	2		649	1025	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313153	30313153	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775361688	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	194	387	0	ENST00000262643.3:c.847G>A	p.Asp283Asn	p.D283N	ENST00000262643	NM_001238.2	283	Gat/Aat	10/12	1	2	FACETS	1	0.983	1	1	0.994	1	CLONAL	2	TRUE	1	0.287821569681062	2		387	572	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214378	36214378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	233	460	0	ENST00000222270.7:c.3032G>A	p.Arg1011Gln	p.R1011Q	ENST00000222270	NM_014727.1	1011	cGg/cAg	7/37	1	2	FACETS	1	0.969	1	1	0.995	1	CLONAL	2	TRUE	1	0.287821569681062	2		460	765	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910608	50910608	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	169	723	1	ENST00000440232.2:c.1711C>T	p.Pro571Ser	p.P571S	ENST00000440232	NM_002691.3	571	Ccc/Tcc	14/27	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.287821569681062	2		724	1124	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965031	25965031	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	226	386	0	ENST00000435504.4:c.4175G>A	p.Ser1392Asn	p.S1392N	ENST00000435504		1392	aGc/aAc	13/13	0.265499264737894	1	FACETS	1	0.98	1	1	0.995	1	CLONAL	2	TRUE	0	0.287821569681062	1		386	608	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39251178	39251178	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	53	329	0	ENST00000402219.2:c.1175C>A	p.Ser392Tyr	p.S392Y	ENST00000402219	NM_005633.3	392	tCt/tAt	9/23	0.265499264737894	1	FACETS	0.991	0.863	1	1	0.978	1	CLONAL	2	TRUE	0	0.287821569681062	1		329	159	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39294829	39294829	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	34	242	1	ENST00000402219.2:c.153A>T	p.Leu51Phe	p.L51F	ENST00000402219	NM_005633.3	51	ttA/ttT	2/23	0.265499264737894	1	FACETS	0.924	0.76	1	0.924	0.76	1	CLONAL	1	TRUE	0	0.287821569681062	1		243	219	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47600969	47600969	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	187	390	0	ENST00000263735.4:c.207G>T	p.Met69Ile	p.M69I	ENST00000263735	NM_002354.2	69	atG/atT	3/9	0.265499264737894	1	FACETS	1	0.973	1	1	0.994	1	CLONAL	2	TRUE	0	0.287821569681062	1		390	512	SUCCESS
REL	5966	MSKCC	GRCh37	2	61144017	61144018	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	58	232	0	ENST00000295025.8:c.405dup	p.Gln136ThrfsTer4	p.Q136Tfs*4	ENST00000295025	NM_002908.2	134	gaa/gAaa	5/11	0.265499264737894	1	FACETS	1	0.879	1	1	0.98	1	CLONAL	2	TRUE	0	0.287821569681062	1		232	172	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170758	99170758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199795768	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	81	423	0	ENST00000074304.5:c.1387G>A	p.Asp463Asn	p.D463N	ENST00000074304	NM_001134224.1	463	Gac/Aac	16/26	0.265499264737894	1	FACETS	0.864	0.762	0.972	0.864	0.762	0.972	CLONAL	1	TRUE	0	0.287821569681062	1		423	558	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095513	178095513	+	stop_lost	Nonstop_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	21	169	0	ENST00000397062.3:c.1818G>T	p.Ter606TyrextTer2	p.*606Yext*2	ENST00000397062	NM_006164.4	606	taG/taT	5/5	0.196589372134191	2	FACETS	1	0.884	1	0.613	0.479	0.765	CLONAL	1	TRUE	0	0.287821569681062	2		169	119	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098867	178098867	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1333348595	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	198	422	0	ENST00000397062.3:c.178G>T	p.Glu60Ter	p.E60*	ENST00000397062	NM_006164.4	60	Gaa/Taa	2/5	0.196589372134191	2	FACETS	1	0.963	1	1	0.993	1	CLONAL	3	TRUE	0	0.287821569681062	2		422	442	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265494	198265494	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	37	353	0	ENST00000335508.6:c.2663T>G	p.Leu888Arg	p.L888R	ENST00000335508	NM_012433.2	888	cTt/cGt	18/25	0.196589372134191	2	FACETS	1	0.952	1	0.726	0.606	0.857	CLONAL	1	TRUE	0	0.287821569681062	2		353	177	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204737449	204737449	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	41	206	0	ENST00000302823.3:c.586C>A	p.Leu196Ile	p.L196I	ENST00000302823	NM_005214.4	196	Ctt/Att	4/4	0.196589372134191	2	FACETS	1	0.939	1	0.633	0.532	0.743	CLONAL	1	TRUE	0	0.287821569681062	2		206	225	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251787	212251787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	204	287	0	ENST00000342788.4:c.3272C>T	p.Ala1091Val	p.A1091V	ENST00000342788	NM_005235.2	1091	gCt/gTt	27/28	0.196589372134191	2	FACETS	1	0.983	1	1	0.994	1	CLONAL	3	TRUE	0	0.287821569681062	2		287	422	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288952	212288952	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	163	332	0	ENST00000342788.4:c.2794T>G	p.Leu932Val	p.L932V	ENST00000342788	NM_005235.2	932	Tta/Gta	23/28	0.196589372134191	2	FACETS	1	0.981	1	1	0.992	1	CLONAL	3	TRUE	0	0.287821569681062	2		332	332	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770557	40770557	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	65	327	0	ENST00000373198.4:c.2825C>A	p.Ser942Tyr	p.S942Y	ENST00000373198	NM_133170.3	942	tCc/tAc	19/32	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.287821569681062	2		327	443	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256717	46256717	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	81	284	0	ENST00000371998.3:c.773G>T	p.Arg258Ile	p.R258I	ENST00000371998		258	aGa/aTa	8/23	1	2	FACETS	1	0.951	1	1	0.986	1	CLONAL	2	TRUE	1	0.287821569681062	2		284	253	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262299	46262299	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	21	289	1	ENST00000371998.3:c.883G>T	p.Asp295Tyr	p.D295Y	ENST00000371998		295	Gat/Tat	9/23	1	2	FACETS	0.503	0.388	0.638	0.503	0.388	0.638	SUBCLONAL	1	TRUE	1	0.287821569681062	2		290	290	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537109	41537109	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	146	219	1	ENST00000263253.7:c.1936G>T	p.Glu646Ter	p.E646*	ENST00000263253	NM_001429.3	646	Gaa/Taa	10/31	0.287821569681062	1	FACETS	0.934	0.867	1	1	0.993	1	CLONAL	3	TRUE	0	0.287821569681062	1		220	310	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41558740	41558740	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	33	223	0	ENST00000263253.7:c.3685G>T	p.Glu1229Ter	p.E1229*	ENST00000263253	NM_001429.3	1229	Gaa/Taa	21/31	0.287821569681062	1	FACETS	0.825	0.686	0.974	1	0.957	1	CLONAL	2	TRUE	0	0.287821569681062	1		223	119	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641654	12641654	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	83	401	0	ENST00000251849.4:c.987A>C	p.Lys329Asn	p.K329N	ENST00000251849	NM_002880.3	329	aaA/aaC	9/17	1	2	FACETS	0.932	0.823	1	0.932	0.823	1	CLONAL	1	TRUE	1	0.287821569681062	2		401	619	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163935	47163935	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs933495344	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	56	260	0	ENST00000409792.3:c.2191G>T	p.Asp731Tyr	p.D731Y	ENST00000409792	NM_014159.6	731	Gac/Tac	3/21	1	2	FACETS	0.963	0.838	1	1	0.978	1	CLONAL	2	TRUE	1	0.287821569681062	2		260	202	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164411	47164411	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1425320029	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	57	221	0	ENST00000409792.3:c.1715C>A	p.Ser572Tyr	p.S572Y	ENST00000409792	NM_014159.6	572	tCt/tAt	3/21	1	2	FACETS	0.943	0.831	1	1	0.984	1	CLONAL	3	TRUE	1	0.287821569681062	2		221	140	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165752	47165752	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	36	359	0	ENST00000409792.3:c.374C>A	p.Ser125Tyr	p.S125Y	ENST00000409792	NM_014159.6	125	tCt/tAt	3/21	1	2	FACETS	0.621	0.511	0.744	0.621	0.511	0.744	SUBCLONAL	1	TRUE	1	0.287821569681062	2		359	403	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47205382	47205382	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	104	411	0	ENST00000409792.3:c.33G>T	p.Lys11Asn	p.K11N	ENST00000409792	NM_014159.6	11	aaG/aaT	1/21	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.287821569681062	2		411	700	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397782	49397782	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	92	392	0	ENST00000418115.1:c.442G>T	p.Ala148Ser	p.A148S	ENST00000418115	NM_001664.2	148	Gca/Tca	5/5	1	2	FACETS	0.958	0.852	1	0.958	0.852	1	CLONAL	1	TRUE	1	0.287821569681062	2		392	667	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933713	49933713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	371	709	0	ENST00000296474.3:c.2564C>T	p.Pro855Leu	p.P855L	ENST00000296474	NM_002447.2	855	cCt/cTt	10/20	1	2	FACETS	0.906	0.863	0.95	1	0.997	1	CLONAL	3	TRUE	1	0.287821569681062	2		709	948	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008509	70008509	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	137	251	0	ENST00000394351.3:c.796G>T	p.Glu266Ter	p.E266*	ENST00000394351	NM_000248.3	266	Gaa/Taa	8/9	1	2	FACETS	1	0.965	1	1	0.992	1	CLONAL	2	TRUE	1	0.287821569681062	2		251	434	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114163	73114163	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	120	256	0	ENST00000356692.5:c.799G>T	p.Glu267Ter	p.E267*	ENST00000356692		267	Gaa/Taa	8/9	1	2	FACETS	1	0.973	1	1	0.991	1	CLONAL	2	TRUE	1	0.287821569681062	2		256	358	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259325	89259325	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	24	272	0	ENST00000336596.2:c.469C>A	p.Leu157Ile	p.L157I	ENST00000336596	NM_005233.5	157	Ctt/Att	3/17	1	2	FACETS	0.681	0.535	0.847	0.681	0.535	0.847	SUBCLONAL	1	TRUE	1	0.287821569681062	2		272	245	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390084	89390084	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	81	219	0	ENST00000336596.2:c.833A>T	p.Tyr278Phe	p.Y278F	ENST00000336596	NM_005233.5	278	tAc/tTc	4/17	1	2	FACETS	1	0.916	1	1	0.985	1	CLONAL	2	TRUE	1	0.287821569681062	2		219	273	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582343	119582343	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	183	285	0	ENST00000316626.5:c.1058T>G	p.Phe353Cys	p.F353C	ENST00000316626		353	tTt/tGt	10/12	1	2	FACETS	0.853	0.794	0.913	1	0.994	1	CLONAL	3	TRUE	1	0.287821569681062	2		285	497	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582425	119582425	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	41	208	0	ENST00000316626.5:c.976G>A	p.Ala326Thr	p.A326T	ENST00000316626		326	Gca/Aca	10/12	1	2	FACETS	0.826	0.69	0.976	0.826	0.69	0.976	CLONAL	1	TRUE	1	0.287821569681062	2		208	345	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670212	134670212	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	109	278	0	ENST00000398015.3:c.124-1G>A		p.X42_splice	ENST00000398015	NM_004441.4	42			1	2	FACETS	1	0.963	1	1	0.99	1	CLONAL	2	TRUE	1	0.287821569681062	2		278	339	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670334	134670334	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	198	360	1	ENST00000398015.3:c.245C>G	p.Ala82Gly	p.A82G	ENST00000398015	NM_004441.4	82	gCc/gGc	3/16	1	2	FACETS	0.905	0.845	0.965	1	0.995	1	CLONAL	3	TRUE	1	0.287821569681062	2		361	507	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260306	149260306	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	138	638	0	ENST00000360632.3:c.587A>C	p.Gln196Pro	p.Q196P	ENST00000360632	NM_015472.4	196	cAg/cCg	4/7	1	2	FACETS	0.995	0.904	1	0.995	0.904	1	CLONAL	1	TRUE	1	0.287821569681062	2		638	964	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683387	182683387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1298281414	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	39	284	0	ENST00000292782.4:c.158G>A	p.Arg53Gln	p.R53Q	ENST00000292782	NM_020640.2	53	cGa/cAa	2/7	1	2	FACETS	0.928	0.783	1	1	0.968	1	CLONAL	2	TRUE	1	0.287821569681062	2		284	146	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612110	189612110	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	308	461	0	ENST00000264731.3:c.1862G>T	p.Ser621Ile	p.S621I	ENST00000264731	NM_003722.4	621	aGc/aTc	14/14	1	2	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	TRUE	1	0.287821569681062	2		461	868	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807888	1807888	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	124	807	0	ENST00000260795.2:c.1947G>T	p.Lys649Asn	p.K649N	ENST00000260795		649	aaG/aaT	13/17	1	2	FACETS	0.76	0.686	0.839	0.76	0.686	0.839	SUBCLONAL	1	TRUE	1	0.287821569681062	2		807	1133	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1977029	1977029	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs112199742	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	305	521	0	ENST00000382891.5:c.3523C>A	p.Leu1175Met	p.L1175M	ENST00000382891	NM_133335.3	1175	Ctg/Atg	20/22	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.287821569681062	2		521	911	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139876	55139876	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	168	310	0	ENST00000257290.5:c.1537G>T	p.Glu513Ter	p.E513*	ENST00000257290	NM_006206.4	513	Gag/Tag	10/23	1	2	FACETS	1	0.966	1	1	0.993	1	CLONAL	2	TRUE	1	0.287821569681062	2		310	543	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156479	55156479	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	140	274	0	ENST00000257290.5:c.2881-1G>T		p.X961_splice	ENST00000257290	NM_006206.4	961			1	2	FACETS	0.869	0.801	0.939	1	0.993	1	CLONAL	3	TRUE	1	0.287821569681062	2		274	373	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953773	55953773	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	127	357	0	ENST00000263923.4:c.3662+1G>T		p.X1221_splice	ENST00000263923	NM_002253.2	1221			1	2	FACETS	1	0.962	1	1	0.991	1	CLONAL	2	TRUE	1	0.287821569681062	2		357	403	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961766	55961766	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	120	321	0	ENST00000263923.4:c.2795G>T	p.Arg932Ile	p.R932I	ENST00000263923	NM_002253.2	932	aGa/aTa	20/30	1	2	FACETS	1	0.978	1	1	0.991	1	CLONAL	2	TRUE	1	0.287821569681062	2		321	342	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976604	55976604	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	109	371	0	ENST00000263923.4:c.1221G>T	p.Glu407Asp	p.E407D	ENST00000263923	NM_002253.2	407	gaG/gaT	9/30	1	2	FACETS	1	0.931	1	1	0.989	1	CLONAL	2	TRUE	1	0.287821569681062	2		371	367	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984855	55984855	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	43	403	0	ENST00000263923.4:c.274A>G	p.Lys92Glu	p.K92E	ENST00000263923	NM_002253.2	92	Aaa/Gaa	3/30	1	2	FACETS	0.496	0.415	0.587	0.496	0.415	0.587	SUBCLONAL	1	TRUE	1	0.287821569681062	2		403	602	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231664	66231664	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	46	268	0	ENST00000273854.3:c.2036G>T	p.Arg679Ile	p.R679I	ENST00000273854	NM_004439.5	679	aGa/aTa	11/18	1	2	FACETS	0.963	0.825	1	1	0.973	1	CLONAL	2	TRUE	1	0.287821569681062	2		268	166	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66468015	66468015	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	40	145	0	ENST00000273854.3:c.254A>C	p.Glu85Ala	p.E85A	ENST00000273854	NM_004439.5	85	gAg/gCg	3/18	1	2	FACETS	0.874	0.748	1	1	0.976	1	CLONAL	3	TRUE	1	0.287821569681062	2		145	106	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157424	106157424	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	50	190	0	ENST00000380013.4:c.2325C>A	p.Phe775Leu	p.F775L	ENST00000380013	NM_001127208.2	775	ttC/ttA	3/11	1	2	FACETS	1	0.872	1	1	0.976	1	CLONAL	2	TRUE	1	0.287821569681062	2		190	172	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193764	106193764	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	106	217	0	ENST00000380013.4:c.4226A>C	p.Lys1409Thr	p.K1409T	ENST00000380013	NM_001127208.2	1409	aAa/aCa	10/11	1	2	FACETS	1	0.975	1	1	0.99	1	CLONAL	2	TRUE	1	0.287821569681062	2		217	301	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197090	106197090	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	113	226	0	ENST00000380013.4:c.5423G>T	p.Arg1808Ile	p.R1808I	ENST00000380013	NM_001127208.2	1808	aGa/aTa	11/11	1	2	FACETS	0.881	0.805	0.959	1	0.991	1	CLONAL	3	TRUE	1	0.287821569681062	2		226	297	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197584	106197584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs982791029	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	79	211	0	ENST00000380013.4:c.5917G>A	p.Glu1973Lys	p.E1973K	ENST00000380013	NM_001127208.2	1973	Gaa/Aaa	11/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.287821569681062	2		211	381	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143129607	143129607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	50	277	0	ENST00000262992.4:c.1043G>A	p.Arg348Lys	p.R348K	ENST00000262992	NM_001101669.1	348	aGa/aAa	12/24	1	2	FACETS	1	0.911	1	1	0.978	1	CLONAL	2	TRUE	1	0.287821569681062	2		277	162	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332864	153332864	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	200	303	0	ENST00000281708.4:c.92A>C	p.Glu31Ala	p.E31A	ENST00000281708	NM_033632.3	31	gAa/gCa	2/12	1	2	FACETS	0.847	0.791	0.904	1	0.995	1	CLONAL	3	TRUE	1	0.287821569681062	2		303	547	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521237	187521237	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	227	524	0	ENST00000441802.2:c.11918T>C	p.Phe3973Ser	p.F3973S	ENST00000441802	NM_005245.3	3973	tTc/tCc	22/27	1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	1	0.287821569681062	2		524	652	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540782	187540782	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	100	262	0	ENST00000441802.2:c.6958T>G	p.Tyr2320Asp	p.Y2320D	ENST00000441802	NM_005245.3	2320	Tac/Gac	10/27	1	2	FACETS	0.848	0.77	0.929	1	0.99	1	CLONAL	3	TRUE	1	0.287821569681062	2		262	273	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630948	187630948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	165	337	0	ENST00000441802.2:c.34C>T	p.Leu12Phe	p.L12F	ENST00000441802	NM_005245.3	12	Ctc/Ttc	2/27	1	2	FACETS	1	0.98	1	1	0.993	1	CLONAL	2	TRUE	1	0.287821569681062	2		337	489	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224506	224506	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	149	223	0	ENST00000264932.6:c.182A>C	p.Glu61Ala	p.E61A	ENST00000264932	NM_004168.2	61	gAa/gCa	3/15	1	2	FACETS	0.911	0.842	0.98	1	0.993	1	CLONAL	3	TRUE	1	0.287821569681062	2		223	379	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871284	35871284	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	40	184	0	ENST00000303115.3:c.506A>G	p.Tyr169Cys	p.Y169C	ENST00000303115	NM_002185.3	169	tAc/tGc	4/8	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.287821569681062	2		184	215	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945595	38945595	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	20	180	0	ENST00000357387.3:c.4631C>T	p.Ser1544Leu	p.S1544L	ENST00000357387	NM_152756.3	1544	tCa/tTa	34/38	1	2	FACETS	0.794	0.611	1	0.794	0.611	1	CLONAL	1	TRUE	1	0.287821569681062	2		180	175	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38949979	38949979	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	37	265	0	ENST00000357387.3:c.3971C>A	p.Ser1324Tyr	p.S1324Y	ENST00000357387	NM_152756.3	1324	tCt/tAt	31/38	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.287821569681062	2		265	215	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38975702	38975702	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	118	276	0	ENST00000357387.3:c.826G>A	p.Asp276Asn	p.D276N	ENST00000357387	NM_152756.3	276	Gac/Aac	10/38	1	2	FACETS	1	0.974	1	1	0.991	1	CLONAL	2	TRUE	1	0.287821569681062	2		276	347	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750785	57750785	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	27	303	0	ENST00000274289.3:c.1819A>C	p.Lys607Gln	p.K607Q	ENST00000274289	NM_006622.3	607	Aaa/Caa	13/14	1	2	FACETS	0.542	0.432	0.669	0.542	0.432	0.669	SUBCLONAL	1	TRUE	1	0.287821569681062	2		303	346	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79952313	79952313	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	108	291	0	ENST00000265081.6:c.321G>T	p.Lys107Asn	p.K107N	ENST00000265081	NM_002439.4	107	aaG/aaT	2/24	1	2	FACETS	1	0.947	1	1	0.989	1	CLONAL	2	TRUE	1	0.287821569681062	2		291	352	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80024704	80024704	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	44	286	0	ENST00000265081.6:c.1488G>T	p.Glu496Asp	p.E496D	ENST00000265081	NM_002439.4	496	gaG/gaT	10/24	1	2	FACETS	1	0.859	1	1	0.973	1	CLONAL	2	TRUE	1	0.287821569681062	2		286	152	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80160737	80160737	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	51	367	0	ENST00000265081.6:c.3106G>T	p.Glu1036Ter	p.E1036*	ENST00000265081	NM_002439.4	1036	Gag/Tag	22/24	1	2	FACETS	0.935	0.797	1	0.935	0.797	1	CLONAL	1	TRUE	1	0.287821569681062	2		367	379	SUCCESS
APC	324	MSKCC	GRCh37	5	112175103	112175103	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	40	121	0	ENST00000257430.4:c.3812T>G	p.Phe1271Cys	p.F1271C	ENST00000257430	NM_000038.5	1271	tTt/tGt	16/16	1	2	FACETS	1	0.865	1	1	0.971	1	CLONAL	2	TRUE	1	0.287821569681062	2		121	136	SUCCESS
APC	324	MSKCC	GRCh37	5	112179171	112179171	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	42	215	0	ENST00000257430.4:c.7880C>A	p.Ser2627Tyr	p.S2627Y	ENST00000257430	NM_000038.5	2627	tCt/tAt	16/16	1	2	FACETS	0.954	0.811	1	1	0.971	1	CLONAL	2	TRUE	1	0.287821569681062	2		215	153	SUCCESS
APC	324	MSKCC	GRCh37	5	112179297	112179297	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	37	243	0	ENST00000257430.4:c.8006C>A	p.Pro2669His	p.P2669H	ENST00000257430	NM_000038.5	2669	cCt/cAt	16/16	1	2	FACETS	0.963	0.798	1	0.963	0.798	1	CLONAL	1	TRUE	1	0.287821569681062	2		243	267	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131893024	131893024	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1277596729	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	93	259	0	ENST00000265335.6:c.8G>T	p.Arg3Leu	p.R3L	ENST00000265335		3	cGg/cTg	1/25	1	2	FACETS	1	0.922	1	1	0.987	1	CLONAL	2	TRUE	1	0.287821569681062	2		259	314	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502739	149502739	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	126	492	0	ENST00000261799.4:c.2049C>A	p.Tyr683Ter	p.Y683*	ENST00000261799	NM_002609.3	683	taC/taA	15/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.287821569681062	2		492	749	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170832372	170832372	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs760598971	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	11	202	0	ENST00000296930.5:c.736G>T	p.Asp246Tyr	p.D246Y	ENST00000296930	NM_002520.6	246	Gac/Tac	9/11	1	2	FACETS	0.91	0.637	1	0.91	0.637	1	CLONAL	1	TRUE	1	0.287821569681062	2		202	84	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053020	180053020	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	142	884	0	ENST00000261937.6:c.1270A>C	p.Ile424Leu	p.I424L	ENST00000261937	NM_182925.4	424	Ata/Cta	10/30	1	2	FACETS	0.988	0.899	1	0.988	0.899	1	CLONAL	1	TRUE	1	0.287821569681062	2		884	999	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670589	30670589	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	106	434	0	ENST00000376406.3:c.5931G>T	p.Lys1977Asn	p.K1977N	ENST00000376406	NM_014641.2	1977	aaG/aaT	13/15	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.287821569681062	2		434	663	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672698	30672698	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	318	737	0	ENST00000376406.3:c.4262A>G	p.Asp1421Gly	p.D1421G	ENST00000376406	NM_014641.2	1421	gAc/gGc	10/15	1	2	FACETS	1	0.984	1	1	0.996	1	CLONAL	2	TRUE	1	0.287821569681062	2		737	1002	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675685	30675685	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	61	572	0	ENST00000376406.3:c.2671A>C	p.Lys891Gln	p.K891Q	ENST00000376406	NM_014641.2	891	Aag/Cag	8/15	1	2	FACETS	0.697	0.601	0.802	0.697	0.601	0.802	SUBCLONAL	1	TRUE	1	0.287821569681062	2		572	608	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166718	32166718	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	439	830	0	ENST00000375023.3:c.4520A>G	p.Asp1507Gly	p.D1507G	ENST00000375023	NM_004557.3	1507	gAc/gGc	24/30	1	2	FACETS	0.841	0.803	0.88	1	0.997	1	CLONAL	3	TRUE	1	0.287821569681062	2		830	1209	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184727	32184727	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	90	493	0	ENST00000375023.3:c.1856T>G	p.Phe619Cys	p.F619C	ENST00000375023	NM_004557.3	619	tTc/tGc	11/30	1	2	FACETS	0.76	0.673	0.852	0.76	0.673	0.852	SUBCLONAL	1	TRUE	1	0.287821569681062	2		493	823	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793507	89793507	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	53	162	0	ENST00000336032.3:c.576T>G	p.Ile192Met	p.I192M	ENST00000336032	NM_006813.2	192	atT/atG	2/2	1	2	FACETS	0.907	0.784	1	1	0.975	1	CLONAL	2	TRUE	1	0.287821569681062	2		162	203	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554799	106554799	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	58	235	0	ENST00000369096.4:c.1916G>T	p.Arg639Ile	p.R639I	ENST00000369096	NM_001198.3	639	aGa/aTa	7/7	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.287821569681062	2		235	364	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112035567	112035567	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	28	219	0	ENST00000368678.4:c.327T>G	p.Phe109Leu	p.F109L	ENST00000368678		109	ttT/ttG	4/13	1	2	FACETS	0.614	0.491	0.753	0.614	0.491	0.753	SUBCLONAL	1	TRUE	1	0.287821569681062	2		219	317	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157495145	157495145	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	145	253	0	ENST00000346085.5:c.3029C>T	p.Ser1010Phe	p.S1010F	ENST00000346085	NM_020732.3	1010	tCt/tTt	11/20	1	2	FACETS	1	0.982	1	1	0.993	1	CLONAL	2	TRUE	1	0.287821569681062	2		253	407	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962800	2962800	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	133	696	0	ENST00000396946.4:c.2108A>C	p.Lys703Thr	p.K703T	ENST00000396946	NM_032415.4	703	aAa/aCa	16/25	0.280185935080151	3	FACETS	0.829	0.751	0.912	0.276	0.25	0.304	CLONAL	1	TRUE	0	0.287821569681062	3		696	1275	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210033	55210033	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1263793183	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	61	338	0	ENST00000275493.2:c.143T>C	p.Phe48Ser	p.F48S	ENST00000275493	NM_005228.3	48	tTt/tCt	2/28	0.280185935080151	3	FACETS	0.796	0.687	0.915	0.265	0.229	0.305	CLONAL	1	TRUE	0	0.287821569681062	3		338	609	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220245	55220245	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	146	656	0	ENST00000275493.2:c.635A>C	p.Lys212Thr	p.K212T	ENST00000275493	NM_005228.3	212	aAa/aCa	6/28	0.280185935080151	3	FACETS	0.9	0.819	0.986	0.3	0.273	0.329	CLONAL	1	TRUE	0	0.287821569681062	3		656	1289	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266551	55266551	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	70	376	0	ENST00000275493.2:c.2843T>G	p.Val948Gly	p.V948G	ENST00000275493	NM_005228.3	948	gTc/gGc	23/28	0.280185935080151	3	FACETS	0.772	0.672	0.88	0.257	0.224	0.294	SUBCLONAL	1	TRUE	0	0.287821569681062	3		376	721	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332001	81332001	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1351384112	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	114	185	0	ENST00000222390.5:c.2083C>T	p.Arg695Cys	p.R695C	ENST00000222390	NM_000601.4	695	Cgt/Tgt	18/18	0.280185935080151	3	FACETS	0.956	0.88	1	1	0.983	1	CLONAL	4	TRUE	0	0.287821569681062	3		185	237	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359023	81359023	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	101	384	0	ENST00000222390.5:c.938A>G	p.Tyr313Cys	p.Y313C	ENST00000222390	NM_000601.4	313	tAc/tGc	8/18	0.280185935080151	3	FACETS	1	0.979	1	0.464	0.415	0.515	CLONAL	1	TRUE	0	0.287821569681062	3		384	577	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526603	106526603	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1277491292	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	169	264	0	ENST00000359195.3:c.2896G>A	p.Gly966Arg	p.G966R	ENST00000359195	NM_002649.2	966	Ggg/Agg	10/11	0.280185935080151	3	FACETS	1	0.982	1	1	0.992	1	CLONAL	4	TRUE	0	0.287821569681062	3		264	300	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339953	116339953	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	53	240	0	ENST00000397752.3:c.815A>G	p.Gln272Arg	p.Q272R	ENST00000397752	NM_000245.2	272	cAg/cGg	2/21	0.280185935080151	3	FACETS	0.813	0.7	0.935	0.542	0.466	0.624	CLONAL	2	TRUE	0	0.287821569681062	3		240	259	SUCCESS
MET	4233	MSKCC	GRCh37	7	116422052	116422052	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	24	232	0	ENST00000397752.3:c.3533T>C	p.Val1178Ala	p.V1178A	ENST00000397752	NM_000245.2	1178	gTa/gCa	18/21	0.280185935080151	3	FACETS	0.852	0.671	1	0.284	0.223	0.353	CLONAL	1	TRUE	0	0.287821569681062	3		232	224	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148504766	148504766	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	401	423	1	ENST00000320356.2:c.2228G>A	p.Gly743Asp	p.G743D	ENST00000320356	NM_004456.4	743	gGc/gAc	20/20	0.280185935080151	3	FACETS	1	0.986	1	1	0.996	1	CLONAL	4	TRUE	0	0.287821569681062	3		424	750	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874344	151874344	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	36	271	0	ENST00000262189.6:c.8194T>G	p.Leu2732Val	p.L2732V	ENST00000262189	NM_170606.2	2732	Ttg/Gtg	38/59	0.280185935080151	3	FACETS	1	0.936	1	0.434	0.359	0.516	CLONAL	1	TRUE	0	0.287821569681062	3		271	220	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874869	151874869	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	41	266	0	ENST00000262189.6:c.7669G>A	p.Ala2557Thr	p.A2557T	ENST00000262189	NM_170606.2	2557	Gca/Aca	38/59	0.280185935080151	3	FACETS	0.731	0.609	0.866	0.244	0.203	0.289	SUBCLONAL	1	TRUE	0	0.287821569681062	3		266	446	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884899	151884899	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	59	222	0	ENST00000262189.6:c.4694T>G	p.Leu1565Arg	p.L1565R	ENST00000262189	NM_170606.2	1565	cTt/cGt	32/59	0.280185935080151	3	FACETS	1	0.968	1	0.484	0.419	0.554	CLONAL	1	TRUE	0	0.287821569681062	3		222	323	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132768	152132768	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	188	469	0	ENST00000262189.6:c.104G>T	p.Arg35Ile	p.R35I	ENST00000262189	NM_170606.2	35	aGa/aTa	1/59	0.280185935080151	3	FACETS	0.754	0.696	0.814	0.503	0.464	0.543	SUBCLONAL	2	TRUE	0	0.287821569681062	3		469	991	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345764	152345764	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	55	186	0	ENST00000359321.1:c.806T>G	p.Phe269Cys	p.F269C	ENST00000359321	NM_005431.1	269	tTt/tGt	3/3	0.280185935080151	3	FACETS	0.861	0.743	0.986	0.574	0.495	0.657	CLONAL	2	TRUE	0	0.287821569681062	3		186	254	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133957	38133957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758159008	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	188	488	1	ENST00000317025.8:c.3929G>A	p.Arg1310Gln	p.R1310Q	ENST00000317025	NM_023034.1	1310	cGa/cAa	23/24	1	2	FACETS	0.979	0.909	1	1	0.993	1	CLONAL	2	TRUE	1	0.287821569681062	2		489	667	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38153361	38153361	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	133	443	0	ENST00000317025.8:c.2868G>T	p.Lys956Asn	p.K956N	ENST00000317025	NM_023034.1	956	aaG/aaT	16/24	1	2	FACETS	0.903	0.824	0.984	1	0.99	1	CLONAL	2	TRUE	1	0.287821569681062	2		443	512	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187278	38187278	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	214	457	0	ENST00000317025.8:c.1199A>C	p.Glu400Ala	p.E400A	ENST00000317025	NM_023034.1	400	gAa/gCa	6/24	1	2	FACETS	1	0.982	1	1	0.995	1	CLONAL	2	TRUE	1	0.287821569681062	2		457	654	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205317	38205317	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	299	631	0	ENST00000317025.8:c.373C>A	p.Leu125Met	p.L125M	ENST00000317025	NM_023034.1	125	Ctg/Atg	2/24	1	2	FACETS	0.88	0.833	0.928	1	0.996	1	CLONAL	3	TRUE	1	0.287821569681062	2		631	787	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56854431	56854431	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	48	207	0	ENST00000519728.1:c.13A>C	p.Lys5Gln	p.K5Q	ENST00000519728	NM_002350.3	5	Aaa/Caa	2/13	1	2	FACETS	1	0.87	1	1	0.976	1	CLONAL	2	TRUE	1	0.287821569681062	2		207	165	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56860253	56860253	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	166	332	1	ENST00000519728.1:c.255G>T	p.Lys85Asn	p.K85N	ENST00000519728	NM_002350.3	85	aaG/aaT	4/13	1	2	FACETS	1	0.982	1	1	0.993	1	CLONAL	2	TRUE	1	0.287821569681062	2		333	483	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950417	68950417	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	25	271	0	ENST00000288368.4:c.729C>A	p.Cys243Ter	p.C243*	ENST00000288368	NM_024870.2	243	tgC/tgA	7/40	1	2	FACETS	0.575	0.454	0.714	0.575	0.454	0.714	SUBCLONAL	1	TRUE	1	0.287821569681062	2		271	302	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976724	90976724	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	43	224	1	ENST00000265433.3:c.908G>T	p.Arg303Ile	p.R303I	ENST00000265433	NM_002485.4	303	aGa/aTa	8/16	1	2	FACETS	0.928	0.79	1	1	0.97	1	CLONAL	2	TRUE	1	0.287821569681062	2		225	161	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389236	8389236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	83	277	0	ENST00000356435.5:c.4382C>T	p.Ser1461Leu	p.S1461L	ENST00000356435		1461	tCa/tTa	26/35	1	2	FACETS	1	0.968	1	1	0.987	1	CLONAL	2	TRUE	1	0.287821569681062	2		277	238	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460424	8460424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	104	259	0	ENST00000356435.5:c.3862C>A	p.Leu1288Ile	p.L1288I	ENST00000356435		1288	Ctt/Att	22/35	1	2	FACETS	0.906	0.824	0.988	1	0.991	1	CLONAL	3	TRUE	1	0.287821569681062	2		259	266	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486124	8486124	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	96	422	0	ENST00000356435.5:c.2693G>T	p.Arg898Ile	p.R898I	ENST00000356435		898	aGa/aTa	17/35	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.287821569681062	2		422	507	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504273	8504273	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	149	319	1	ENST00000356435.5:c.1810A>G	p.Thr604Ala	p.T604A	ENST00000356435		604	Acc/Gcc	12/35	1	2	FACETS	1	0.974	1	1	0.992	1	CLONAL	2	TRUE	1	0.287821569681062	2		320	456	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518286	8518286	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	110	227	0	ENST00000356435.5:c.1105G>T	p.Glu369Ter	p.E369*	ENST00000356435		369	Gaa/Taa	10/35	1	2	FACETS	1	0.974	1	1	0.99	1	CLONAL	2	TRUE	1	0.287821569681062	2		227	319	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8733804	8733804	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	130	440	0	ENST00000356435.5:c.40T>G	p.Phe14Val	p.F14V	ENST00000356435		14	Ttc/Gtc	1/35	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.287821569681062	2		440	651	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970924	21970924	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	157	685	0	ENST00000304494.5:c.434T>G	p.Ile145Arg	p.I145R	ENST00000304494	NM_000077.4	145	aTa/aGa	2/3	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.287821569681062	2		685	1056	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202945	27202945	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	108	357	0	ENST00000380036.4:c.2037G>T	p.Lys679Asn	p.K679N	ENST00000380036	NM_000459.3	679	aaG/aaT	13/23	1	2	FACETS	1	0.935	1	1	0.989	1	CLONAL	2	TRUE	1	0.287821569681062	2		357	361	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015112	37015112	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	276	553	0	ENST00000358127.4:c.292A>C	p.Lys98Gln	p.K98Q	ENST00000358127	NM_001280556.1	98	Aaa/Caa	3/10	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.287821569681062	2		553	775	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537219	80537219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	169	298	1	ENST00000286548.4:c.179G>A	p.Arg60Lys	p.R60K	ENST00000286548	NM_002072.3	60	aGa/aAa	2/7	1	2	FACETS	0.981	0.914	1	1	0.994	1	CLONAL	3	TRUE	1	0.287821569681062	2		299	399	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317102	87317102	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	102	288	0	ENST00000277120.3:c.241A>C	p.Ile81Leu	p.I81L	ENST00000277120		81	Atc/Ctc	3/19	1	2	FACETS	1	0.904	1	1	0.988	1	CLONAL	2	TRUE	1	0.287821569681062	2		288	354	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87475991	87475991	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	112	608	0	ENST00000277120.3:c.1433G>T	p.Arg478Ile	p.R478I	ENST00000277120		478	aGa/aTa	13/19	1	2	FACETS	1	0.972	1	1	0.99	1	CLONAL	2	TRUE	1	0.287821569681062	2		608	332	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563376	87563376	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	75	337	0	ENST00000277120.3:c.1765-1G>T		p.X589_splice	ENST00000277120		589			1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.287821569681062	2		337	484	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891164	101891164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1345066131	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	72	222	0	ENST00000374994.4:c.125C>T	p.Thr42Ile	p.T42I	ENST00000374994	NM_004612.2	42	aCa/aTa	2/9	1	2	FACETS	1	0.941	1	1	0.985	1	CLONAL	2	TRUE	1	0.287821569681062	2		222	228	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412610	139412610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1392094557	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	410	778	0	ENST00000277541.6:c.1234G>A	p.Asp412Asn	p.D412N	ENST00000277541	NM_017617.3	412	Gac/Aac	7/34	1	2	FACETS	1	0.993	1	1	0.997	1	CLONAL	2	TRUE	1	0.287821569681062	2		778	1155	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815611	139815611	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	100	607	0	ENST00000247668.2:c.1082T>G	p.Phe361Cys	p.F361C	ENST00000247668	NM_021138.3	361	tTc/tGc	9/11	1	2	FACETS	0.822	0.734	0.917	0.822	0.734	0.917	CLONAL	1	TRUE	1	0.287821569681062	2		607	845	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911509	39911509	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	214	472	0	ENST00000378444.4:c.5121C>A	p.Phe1707Leu	p.F1707L	ENST00000378444	NM_001123385.1	1707	ttC/ttA	15/15	0.265499264737894	1	FACETS	0.984	0.919	1	1	0.994	1	CLONAL	2	TRUE	0	0.287821569681062	1		472	647	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922160	39922160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	372	596	0	ENST00000378444.4:c.4012G>A	p.Glu1338Lys	p.E1338K	ENST00000378444	NM_001123385.1	1338	Gaa/Aaa	9/15	0.265499264737894	1	FACETS	1	0.987	1	1	0.997	1	CLONAL	2	TRUE	0	0.287821569681062	1		596	1004	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934418	39934418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	234	467	0	ENST00000378444.4:c.181G>A	p.Ala61Thr	p.A61T	ENST00000378444	NM_001123385.1	61	Gcc/Acc	4/15	0.265499264737894	1	FACETS	1	0.937	1	1	0.995	1	CLONAL	2	TRUE	0	0.287821569681062	1		467	696	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44733201	44733201	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	229	337	0	ENST00000377967.4:c.193G>T	p.Asp65Tyr	p.D65Y	ENST00000377967	NM_021140.2	65	Gat/Tat	2/29	0.265499264737894	1	FACETS	1	0.981	1	1	0.995	1	CLONAL	2	TRUE	0	0.287821569681062	1		337	611	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650446	48650446	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	388	778	0	ENST00000376670.3:c.416A>C	p.Glu139Ala	p.E139A	ENST00000376670	NM_002049.3	139	gAg/gCg	3/6	0.265499264737894	1	FACETS	1	0.99	1	1	0.997	1	CLONAL	2	TRUE	0	0.287821569681062	1		778	1013	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354570	70354570	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	210	339	0	ENST00000374080.3:c.4735T>G	p.Phe1579Val	p.F1579V	ENST00000374080		1579	Ttc/Gtc	35/45	0.265499264737894	1	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	0	0.287821569681062	1		339	512	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360487	70360487	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	135	627	0	ENST00000374080.3:c.6047T>G	p.Phe2016Cys	p.F2016C	ENST00000374080		2016	tTt/tGt	42/45	0.265499264737894	1	FACETS	0.83	0.753	0.91	0.83	0.753	0.91	CLONAL	1	TRUE	0	0.287821569681062	1		627	968	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912126	76912126	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	16	248	0	ENST00000373344.5:c.4138G>T	p.Glu1380Ter	p.E1380*	ENST00000373344	NM_000489.3	1380	Gaa/Taa	13/35	0.265499264737894	1	FACETS	0.738	0.55	0.957	0.738	0.55	0.957	CLONAL	1	TRUE	0	0.287821569681062	1		248	129	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918920	76918920	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	28	474	0	ENST00000373344.5:c.4071G>T	p.Lys1357Asn	p.K1357N	ENST00000373344	NM_000489.3	1357	aaG/aaT	12/35	0.265499264737894	1	FACETS	0.371	0.296	0.457	0.371	0.296	0.457	SUBCLONAL	1	TRUE	0	0.287821569681062	1		474	449	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937011	76937011	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	19	195	0	ENST00000373344.5:c.3736+1G>A		p.X1246_splice	ENST00000373344	NM_000489.3	1246			0.265499264737894	1	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	0	0.287821569681062	1		195	99	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937738	76937738	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	13	354	0	ENST00000373344.5:c.3010A>C	p.Lys1004Gln	p.K1004Q	ENST00000373344	NM_000489.3	1004	Aaa/Caa	9/35	0.265499264737894	1	FACETS	0.447	0.32	0.601	0.447	0.32	0.601	SUBCLONAL	1	TRUE	0	0.287821569681062	1		354	173	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938604	76938604	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	64	374	0	ENST00000373344.5:c.2144A>C	p.Lys715Thr	p.K715T	ENST00000373344	NM_000489.3	715	aAa/aCa	9/35	0.265499264737894	1	FACETS	0.869	0.764	0.98	1	0.979	1	CLONAL	2	TRUE	0	0.287821569681062	1		374	219	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939409	76939409	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	75	485	0	ENST00000373344.5:c.1339G>T	p.Glu447Ter	p.E447*	ENST00000373344	NM_000489.3	447	Gaa/Taa	9/35	0.265499264737894	1	FACETS	0.805	0.714	0.902	1	0.98	1	CLONAL	2	TRUE	0	0.287821569681062	1		485	277	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940496	76940496	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	24	236	0	ENST00000373344.5:c.597T>A	p.Asn199Lys	p.N199K	ENST00000373344	NM_000489.3	199	aaT/aaA	8/35	0.265499264737894	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.287821569681062	1		236	113	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952119	76952119	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	50	266	0	ENST00000373344.5:c.316G>T	p.Asp106Tyr	p.D106Y	ENST00000373344	NM_000489.3	106	Gat/Tat	5/35	0.265499264737894	1	FACETS	1	0.93	1	1	0.979	1	CLONAL	2	TRUE	0	0.287821569681062	1		266	134	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972640	76972640	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	79	340	0	ENST00000373344.5:c.101C>A	p.Ser34Tyr	p.S34Y	ENST00000373344	NM_000489.3	34	tCt/tAt	2/35	0.265499264737894	1	FACETS	0.845	0.752	0.942	1	0.982	1	CLONAL	2	TRUE	0	0.287821569681062	1		340	278	SUCCESS
BTK	695	MSKCC	GRCh37	X	100609664	100609664	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	90	311	1	ENST00000308731.7:c.1585G>T	p.Val529Leu	p.V529L	ENST00000308731	NM_000061.2	529	Gta/Tta	16/19	0.265499264737894	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.287821569681062	1		312	497	SUCCESS
BTK	695	MSKCC	GRCh37	X	100609675	100609675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs128620183	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	142	288	0	ENST00000308731.7:c.1574G>A	p.Arg525Gln	p.R525Q	ENST00000308731	NM_000061.2	525	cGa/cAa	16/19	0.265499264737894	1	FACETS	0.893	0.82	0.968	1	0.99	1	CLONAL	2	TRUE	0	0.287821569681062	1		288	473	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020344	123020344	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	19	308	0	ENST00000355640.3:c.832T>C	p.Ser278Pro	p.S278P	ENST00000355640		278	Tca/Cca	2/7	0.265499264737894	1	FACETS	0.533	0.406	0.682	0.533	0.406	0.682	SUBCLONAL	1	TRUE	0	0.287821569681062	1		308	212	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123022559	123022559	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	33	330	0	ENST00000355640.3:c.968G>T	p.Trp323Leu	p.W323L	ENST00000355640		323	tGg/tTg	3/7	0.265499264737894	1	FACETS	0.642	0.524	0.773	0.642	0.524	0.773	SUBCLONAL	1	TRUE	0	0.287821569681062	1		330	306	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191795	123191795	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	19	295	0	ENST00000218089.9:c.1384A>G	p.Lys462Glu	p.K462E	ENST00000218089	NM_001042749.1	462	Aag/Gag	15/35	0.265499264737894	1	FACETS	0.557	0.424	0.711	0.557	0.424	0.711	SUBCLONAL	1	TRUE	0	0.287821569681062	1		295	203	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195143	123195143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	102	362	0	ENST00000218089.9:c.1486G>A	p.Glu496Lys	p.E496K	ENST00000218089	NM_001042749.1	496	Gaa/Aaa	16/35	0.265499264737894	1	FACETS	0.867	0.783	0.954	1	0.986	1	CLONAL	2	TRUE	0	0.287821569681062	1		362	350	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123499646	123499646	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	29	455	0	ENST00000371139.4:c.173A>C	p.Gln58Pro	p.Q58P	ENST00000371139	NM_001114937.2	58	cAg/cCg	2/4	0.265499264737894	1	FACETS	0.577	0.464	0.705	0.577	0.464	0.705	SUBCLONAL	1	TRUE	0	0.287821569681062	1		455	299	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0046968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	102	519	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		519	329	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223933	2223933	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	125	617	0	ENST00000326181.6:c.1147C>G	p.Gln383Glu	p.Q383E	ENST00000326181	NM_032271.2	383	Cag/Gag	13/21	0.137333717898402	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		617	343	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182641	38182641	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs387907272	NA	P-0046969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	11	262	0	ENST00000396334.3:c.794T>C	p.Leu265Pro	p.L265P	ENST00000396334	NM_002468.4	265	cTg/cCg	5/5	0.327141601485688	1	FACETS	0.149	0.103	0.208	0.149	0.103	0.208	SUBCLONAL	1	TRUE	0	0.388995230888327	1		262	305	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870324	155870324	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	112	377	0	ENST00000368323.3:c.515A>T	p.Asp172Val	p.D172V	ENST00000368323	NM_006912.5	172	gAt/gTt	6/6	1	2	FACETS	0.874	0.787	0.965	0.874	0.787	0.965	CLONAL	1	TRUE	1	0.388995230888327	2		377	659	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201952	102201952	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	12	166	0	ENST00000263464.3:c.1304del	p.Ala435GlufsTer12	p.A435Efs*12	ENST00000263464	NM_001165.4	435	gCa/ga	6/9	1	2	FACETS	0.291	0.204	0.398	0.291	0.204	0.398	SUBCLONAL	1	TRUE	1	0.388995230888327	2		166	212	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352567	118352567	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	72	415	0	ENST00000534358.1:c.3772A>G	p.Ser1258Gly	p.S1258G	ENST00000534358	NM_005933.3	1258	Agt/Ggt	7/36	1	2	FACETS	0.603	0.527	0.685	0.603	0.527	0.685	SUBCLONAL	1	TRUE	1	0.388995230888327	2		415	614	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210829	133210829	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	113	648	0	ENST00000320574.5:c.5947T>A	p.Leu1983Met	p.L1983M	ENST00000320574	NM_006231.2	1983	Ttg/Atg	43/49	1	2	FACETS	0.701	0.63	0.776	0.701	0.63	0.776	SUBCLONAL	1	TRUE	1	0.388995230888327	2		648	829	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138122	2138122	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	140	845	0	ENST00000219476.3:c.5142G>T	p.Gln1714His	p.Q1714H	ENST00000219476	NM_000548.3	1714	caG/caT	40/42	1	2	FACETS	0.718	0.653	0.786	0.718	0.653	0.786	SUBCLONAL	1	TRUE	1	0.388995230888327	2		845	1003	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50815160	50815160	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763885572	NA	P-0046969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	76	324	0	ENST00000398568.2:c.1513G>A	p.Asp505Asn	p.D505N	ENST00000398568	NM_001042412.1	505	Gat/Aat	9/18	1	2	FACETS	0.637	0.559	0.721	0.637	0.559	0.721	SUBCLONAL	1	TRUE	1	0.388995230888327	2		324	613	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346978	89346978	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	88	544	0	ENST00000301030.4:c.5972C>G	p.Pro1991Arg	p.P1991R	ENST00000301030	NM_001256183.1	1991	cCa/cGa	9/13	1	2	FACETS	0.784	0.696	0.878	0.784	0.696	0.878	SUBCLONAL	1	TRUE	1	0.388995230888327	2		544	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577113	+	inframe_deletion	In_Frame_Del	DEL	CGCCGGTCTCTCCCAGGACAGGCA	CGCCGGTCTCTCCCAGGACAGGCA	-	novel	NA	P-0046969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	134	687	0	ENST00000269305.4:c.825_848del	p.Ala276_Arg283del	p.A276_R283del	ENST00000269305	NM_001126112.2	275	tgTGCCTGTCCTGGGAGAGACCGGCGc/tgc	8/11	0.327141601485688	1	FACETS	0.716	0.651	0.784	0.716	0.651	0.784	SUBCLONAL	1	TRUE	0	0.388995230888327	1		687	775	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696742	47696742	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	66	214	0	ENST00000347630.2:c.206T>C	p.Leu69Ser	p.L69S	ENST00000347630	NM_001007230.1	69	tTg/tCg	5/11	0.327141601485688	1	FACETS	0.811	0.709	0.92	0.811	0.709	0.92	CLONAL	1	TRUE	0	0.388995230888327	1		214	337	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281491	15281491	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	112	654	0	ENST00000263388.2:c.4882G>T	p.Asp1628Tyr	p.D1628Y	ENST00000263388	NM_000435.2	1628	Gac/Tac	26/33	0.327141601485688	1	FACETS	0.759	0.684	0.838	0.759	0.684	0.838	SUBCLONAL	1	TRUE	0	0.388995230888327	1		654	611	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213166	39213166	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	277	846	1	ENST00000402219.2:c.3801C>A	p.His1267Gln	p.H1267Q	ENST00000402219	NM_005633.3	1267	caC/caA	23/23	0.180073842498903	3	FACETS	1	0.993	1	0.481	0.452	0.512	INDETERMINATE	1	TRUE	0	0.388995230888327	3		847	1178	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755409	39755409	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1240625071	NA	P-0046969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	106	531	0	ENST00000288319.7:c.1356C>A	p.Tyr452Ter	p.Y452*	ENST00000288319	NM_182918.3	452	taC/taA	10/10	0.327141601485688	1	FACETS	0.735	0.661	0.814	0.735	0.661	0.814	SUBCLONAL	1	TRUE	0	0.388995230888327	1		531	597	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978658	70978658	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs772975291	NA	P-0046969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	138	521	0	ENST00000276594.2:c.995G>T	p.Arg332Leu	p.R332L	ENST00000276594	NM_024504.3	332	cGc/cTc	5/8	1	2	FACETS	0.86	0.783	0.941	0.86	0.783	0.941	CLONAL	1	TRUE	1	0.388995230888327	2		521	825	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409988	63409988	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	103	257	0	ENST00000330258.3:c.3179G>C	p.Cys1060Ser	p.C1060S	ENST00000330258	NM_152424.3	1060	tGc/tCc	2/2	1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.388995230888327	1		257	321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0046971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	73	682	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.773	0.674	0.881	0.773	0.674	0.881	SUBCLONAL	1	TRUE	1	0.16	2		684	1180	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0046971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	43	349	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.16	2		349	505	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0046971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1188	52	759	2	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.524	0.444	0.613	0.524	0.444	0.613	SUBCLONAL	1	TRUE	1	0.16	2		761	1240	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	101	539	2	ENST00000304494.5:c.143C>T	p.Pro48Leu	p.P48L	ENST00000304494	NM_000077.4	48	cCg/cTg	1/3	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.16	2		541	1025	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928512	69928512	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1269	81	757	0	ENST00000352241.4:c.332A>G	p.Gln111Arg	p.Q111R	ENST00000352241	NM_198159.2	111	cAg/cGg	2/10	1	2	FACETS	0.75	0.658	0.849	0.75	0.658	0.849	SUBCLONAL	1	TRUE	1	0.16	2		757	1350	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0046972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	87	259	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.49315058501969	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.489672945029727	1		259	189	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405215	139405215	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371050668	NA	P-0046972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	314	880	0	ENST00000277541.6:c.2630C>T	p.Pro877Leu	p.P877L	ENST00000277541	NM_017617.3	877	cCg/cTg	17/34	0.151947366916108	3	FACETS	0.856	0.815	0.896	0.856	0.815	0.896	INDETERMINATE	3	TRUE	0	0.489672945029727	3		880	622	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600434	10600434	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	279	712	0	ENST00000171111.5:c.1421C>A	p.Ala474Asp	p.A474D	ENST00000171111	NM_203500.1	474	gCc/gAc	4/6	0.49315058501969	1	FACETS	0.777	0.738	0.816	1	0.995	1	SUBCLONAL	2	TRUE	0	0.489672945029727	1		712	554	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521744	89521744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	18	328	1	ENST00000336596.2:c.2821G>A	p.Asp941Asn	p.D941N	ENST00000336596	NM_005233.5	941	Gac/Aac	16/17	NA	2	FACETS	0.299	0.225	0.386			1	INDETERMINATE	1	TRUE	NA	0.489672945029727	2		329	246	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193920	106193920	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	68	269	0	ENST00000380013.4:c.4382T>G	p.Val1461Gly	p.V1461G	ENST00000380013	NM_001127208.2	1461	gTc/gGc	10/11	0.736227419424146	3	FACETS	0.919	0.808	1	0.46	0.404	0.519	CLONAL	1	TRUE	1	0.72878309280128	3		269	277	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741704	145741713	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCGTTCCA	CCTCGTTCCA	-	novel	NA	P-0046973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	137	950	0	ENST00000428558.2:c.790_799del	p.Trp264SerfsTer26	p.W264Sfs*26	ENST00000428558	NM_004260.3	264	TGGAACGAGGag/ag	5/22	0.736227419424146	3	FACETS	1	0.924	1	0.337	0.308	0.367	CLONAL	1	TRUE	0	0.72878309280128	3		950	508	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	136	424	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	0.665200874212314	4	FACETS	1	0.923	1	0.506	0.461	0.552	CLONAL	1	TRUE	2	0.867754901282358	4		424	579	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	100	676	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	1	2	FACETS	0.436	0.39	0.484	0.436	0.39	0.484	SUBCLONAL	1	TRUE	1	0.867754901282358	2		676	529	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265569	152265569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	153	480	0	ENST00000206249.3:c.1022C>T	p.Ser341Leu	p.S341L	ENST00000206249	NM_000125.3	341	tCg/tTg	4/8	0.867754901282358	3	FACETS	0.961	0.885	1	0.481	0.442	0.52	CLONAL	1	TRUE	1	0.867754901282358	3		480	526	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077543	30077543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	99	416	0	ENST00000338641.4:c.1690G>A	p.Glu564Lys	p.E564K	ENST00000338641	NM_000268.3	564	Gag/Aag	15/16	0.630043980962529	4	FACETS	0.881	0.79	0.976			1	CLONAL	1	TRUE	NA	0.867754901282358	4		416	484	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751931	57751931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55768901	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	190	499	0	ENST00000274289.3:c.1306G>A	p.Glu436Lys	p.E436K	ENST00000274289	NM_006622.3	436	Gaa/Aaa	10/14	0.867754901282358	4	FACETS	0.838	0.775	0.904			1	CLONAL	1	TRUE	NA	0.867754901282358	4		499	976	SUCCESS
YES1	7525	MSKCC	GRCh37	18	732848	732848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755971181	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	144	567	0	ENST00000314574.4:c.1409G>A	p.Arg470Gln	p.R470Q	ENST00000314574	NM_005433.3	470	cGa/cAa	11/12	0.3392966010944	3	FACETS	1	0.987	1	0.457	0.423	0.492	INDETERMINATE	1	TRUE	0	0.867754901282358	3		567	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	432	636	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.853722457871448	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.867754901282358	2		636	491	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870260	44870260	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	116	397	0	ENST00000377967.4:c.439C>T	p.Gln147Ter	p.Q147*	ENST00000377967	NM_021140.2	147	Cag/Tag	5/29	0.663476859766419	3	FACETS	0.867	0.787	0.951			1	CLONAL	1	TRUE	NA	0.867754901282358	3		397	442	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729400	41729400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	157	577	0	ENST00000242208.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000242208	NM_002192.2	377	Cgc/Tgc	3/3	0.790492287000057	4	FACETS	0.87	0.798	0.945	0.435	0.399	0.473	CLONAL	1	TRUE	2	0.867754901282358	4		577	777	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42840456	42840456	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	123	474	0	ENST00000398585.3:c.1292C>T	p.Ser431Leu	p.S431L	ENST00000398585	NM_001135099.1	431	tCa/tTa	12/14	0.867754901282358	3	FACETS	0.861	0.784	0.942	0.431	0.392	0.471	CLONAL	1	TRUE	1	0.867754901282358	3		474	472	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729866	39729866	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs990347811	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	130	410	0	ENST00000361337.2:c.1181C>T	p.Ser394Phe	p.S394F	ENST00000361337	NM_003286.2	394	tCt/tTt	13/21	0.867754901282358	5	FACETS	1	0.966	1	0.375	0.341	0.411	CLONAL	1	TRUE	2	0.867754901282358	5		410	613	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023030	27023030	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	22	63	0	ENST00000324856.7:c.136G>T	p.Glu46Ter	p.E46*	ENST00000324856	NM_006015.4	46	Gag/Tag	1/20	NA	2	FACETS	0.746	0.597	0.905			1	INDETERMINATE	1	TRUE	NA	0.867754901282358	2		63	68	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755705	39755705	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs547051424	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	191	591	0	ENST00000288319.7:c.1060C>T	p.Arg354Trp	p.R354W	ENST00000288319	NM_182918.3	354	Cgg/Tgg	10/10	1	2	FACETS	0.996	0.932	1	0.996	0.932	1	CLONAL	1	TRUE	1	0.867754901282358	2		591	442	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961237	1961237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	145	453	1	ENST00000382891.5:c.3025G>A	p.Asp1009Asn	p.D1009N	ENST00000382891	NM_133335.3	1009	Gat/Aat	17/22	0.760578294995341	4	FACETS	0.943	0.863	1			1	CLONAL	1	TRUE	NA	0.867754901282358	4		454	662	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040727	16040727	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	76	185	0	ENST00000268712.3:c.1408-1G>C		p.X470_splice	ENST00000268712	NM_006311.3	470			0.853722457871448	2	FACETS	1	0.914	1	0.509	0.458	0.561	CLONAL	1	TRUE	0	0.867754901282358	2		185	172	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56882350	56882350	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	140	469	0	ENST00000519728.1:c.1048C>T	p.Gln350Ter	p.Q350*	ENST00000519728	NM_002350.3	350	Cag/Tag	10/13	0.867754901282358	6	FACETS	0.733	0.665	0.803	0.183	0.166	0.201	SUBCLONAL	1	TRUE	2	0.867754901282358	6		469	1205	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427912	49427912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	200	684	0	ENST00000301067.7:c.10678G>A	p.Asp3560Asn	p.D3560N	ENST00000301067	NM_003482.3	3560	Gat/Aat	38/54	0.790492287000057	4	FACETS	0.904	0.838	0.973	0.452	0.419	0.487	CLONAL	1	TRUE	2	0.867754901282358	4		684	952	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256219	16256219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	138	436	0	ENST00000375759.3:c.3484G>A	p.Asp1162Asn	p.D1162N	ENST00000375759	NM_015001.2	1162	Gac/Aac	11/15	0.867754901282358	3	FACETS	0.867	0.793	0.944	0.434	0.396	0.472	CLONAL	1	TRUE	1	0.867754901282358	3		436	526	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981276	201981276	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	246	912	0	ENST00000359651.3:c.355G>T	p.Asp119Tyr	p.D119Y	ENST00000359651		119	Gac/Tac	2/8	0.867754901282358	5	FACETS	0.924	0.862	0.989			1	CLONAL	1	TRUE	NA	0.867754901282358	5		912	1412	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206918	102206918	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	91	238	0	ENST00000263464.3:c.1546G>C	p.Glu516Gln	p.E516Q	ENST00000263464	NM_001165.4	516	Gaa/Caa	7/9	0.867754901282358	3	FACETS	0.925	0.83	1	0.463	0.415	0.513	CLONAL	1	TRUE	1	0.867754901282358	3		238	325	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871770	12871770	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	84	182	0	ENST00000228872.4:c.487C>G	p.Gln163Glu	p.Q163E	ENST00000228872	NM_004064.3	163	Caa/Gaa	2/3	0.861225693913554	2	FACETS	1	0.966	1	0.569	0.517	0.622	CLONAL	1	TRUE	0	0.867754901282358	2		182	170	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21626529	21626529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	106	455	0	ENST00000421138.2:c.1403C>T	p.Ser468Leu	p.S468L	ENST00000421138		468	tCa/tTa	13/16	0.861225693913554	2	FACETS	0.882	0.803	0.963	0.441	0.401	0.482	CLONAL	1	TRUE	0	0.867754901282358	2		455	277	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448094	49448094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	175	547	0	ENST00000301067.7:c.506C>T	p.Ser169Leu	p.S169L	ENST00000301067	NM_003482.3	169	tCa/tTa	4/54	0.790492287000057	4	FACETS	0.972	0.897	1	0.486	0.448	0.525	CLONAL	1	TRUE	2	0.867754901282358	4		547	775	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864378	57864378	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	258	877	0	ENST00000228682.2:c.1855C>A	p.Pro619Thr	p.P619T	ENST00000228682	NM_005269.2	619	Cct/Act	12/12	0.790492287000057	4	FACETS	1	0.985	1	0.577	0.541	0.614	CLONAL	1	TRUE	2	0.867754901282358	4		877	962	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42002948	42002948	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	139	404	0	ENST00000219905.7:c.2485G>C	p.Glu829Gln	p.E829Q	ENST00000219905	NM_001164273.1	829	Gaa/Caa	8/24	0.577255917456001	4	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.867754901282358	4		404	512	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865899	56865899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779103749	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	99	313	1	ENST00000308159.5:c.1231G>A	p.Glu411Lys	p.E411K	ENST00000308159	NM_014669.4	411	Gag/Aag	11/22	0.665200874212314	4	FACETS	0.931	0.835	1	0.465	0.417	0.516	CLONAL	1	TRUE	2	0.867754901282358	4		314	458	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761247	59761247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	326	580	0	ENST00000259008.2:c.3160G>A	p.Glu1054Lys	p.E1054K	ENST00000259008	NM_032043.2	1054	Gaa/Aaa	20/20	0.867754901282358	4	FACETS	0.897	0.852	0.943	0.449	0.426	0.472	CLONAL	2	TRUE	0	0.867754901282358	4		580	782	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78865595	78865595	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	193	538	0	ENST00000306801.3:c.2059G>C	p.Glu687Gln	p.E687Q	ENST00000306801	NM_020761.2	687	Gaa/Caa	18/34	0.867754901282358	5	FACETS	0.973	0.9	1	0.195	0.18	0.21	CLONAL	1	TRUE	0	0.867754901282358	5		538	1052	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189334	99189334	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	166	510	0	ENST00000074304.5:c.2590C>T	p.Gln864Ter	p.Q864*	ENST00000074304	NM_001134224.1	864	Cag/Tag	24/26	0.867754901282358	3	FACETS	0.898	0.829	0.969	0.449	0.414	0.485	CLONAL	1	TRUE	1	0.867754901282358	3		510	611	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096592	178096592	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	86	233	0	ENST00000397062.3:c.739C>T	p.Leu247Phe	p.L247F	ENST00000397062	NM_006164.4	247	Ctt/Ttt	5/5	0.867754901282358	3	FACETS	1	0.911	1	0.509	0.456	0.565	CLONAL	1	TRUE	1	0.867754901282358	3		233	279	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051626	30051626	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	107	314	0	ENST00000338641.4:c.560G>C	p.Arg187Thr	p.R187T	ENST00000338641	NM_000268.3	187	aGa/aCa	6/16	0.630043980962529	4	FACETS	1	0.94	1			1	CLONAL	1	TRUE	NA	0.867754901282358	4		314	436	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127539	55127539	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	102	326	0	ENST00000257290.5:c.327G>C	p.Glu109Asp	p.E109D	ENST00000257290	NM_006206.4	109	gaG/gaC	3/23	0.867754901282358	3	FACETS	0.887	0.8	0.978	0.444	0.4	0.489	CLONAL	1	TRUE	1	0.867754901282358	3		326	380	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176619009	176619009	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	130	402	0	ENST00000439151.2:c.1052C>T	p.Ser351Leu	p.S351L	ENST00000439151	NM_022455.4	351	tCa/tTa	3/23	0.622564034022321	5	FACETS	1	0.964	1			1	CLONAL	1	TRUE	NA	0.867754901282358	5		402	617	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839889	27839889	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	212	710	0	ENST00000328488.2:c.205C>T	p.Gln69Ter	p.Q69*	ENST00000328488	NM_003533.2	69	Cag/Tag	1/1	0.665200874212314	4	FACETS	0.935	0.869	1	0.468	0.434	0.502	CLONAL	1	TRUE	2	0.867754901282358	4		710	976	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32191635	32191635	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	183	770	0	ENST00000375023.3:c.71G>A	p.Arg24Lys	p.R24K	ENST00000375023	NM_004557.3	24	aGa/aAa	1/30	0.665200874212314	4	FACETS	0.823	0.76	0.889	0.412	0.38	0.445	CLONAL	1	TRUE	2	0.867754901282358	4		770	957	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32191641	32191641	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	181	786	0	ENST00000375023.3:c.65G>C	p.Arg22Thr	p.R22T	ENST00000375023	NM_004557.3	22	aGa/aCa	1/30	0.665200874212314	4	FACETS	0.818	0.755	0.885	0.409	0.377	0.443	CLONAL	1	TRUE	2	0.867754901282358	4		786	952	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414370	6414370	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	97	238	0	ENST00000356142.4:c.4C>T	p.Gln2Ter	p.Q2*	ENST00000356142	NM_018890.3	2	Cag/Tag	1/7	0.790492287000057	4	FACETS	1	0.964	1	0.578	0.52	0.639	CLONAL	1	TRUE	2	0.867754901282358	4		238	361	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949054	151949054	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	171	426	0	ENST00000262189.6:c.1591G>C	p.Glu531Gln	p.E531Q	ENST00000262189	NM_170606.2	531	Gag/Cag	11/59	0.867754901282358	3	FACETS	1	0.979	1	0.572	0.53	0.615	CLONAL	1	TRUE	1	0.867754901282358	3		426	494	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224729	123224729	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	68	349	0	ENST00000218089.9:c.3493C>T	p.Gln1165Ter	p.Q1165*	ENST00000218089	NM_001042749.1	1165	Caa/Taa	32/35	0.260903975952617	1	FACETS	0.305	0.267	0.345	0.305	0.267	0.345	INDETERMINATE	1	TRUE	0	0.867754901282358	1		349	291	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	112	516	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.53	2		516	416	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0046975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	241	164	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.514751659669682	4	FACETS	0.935	0.884	0.986	0.935	0.884	0.986	CLONAL	3	TRUE	1	0.53	4		164	496	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812583	43812583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	168	617	2	ENST00000372470.3:c.1286G>A	p.Gly429Glu	p.G429E	ENST00000372470	NM_005373.2	429	gGa/gAa	8/12	1	2	FACETS	0.952	0.878	1	0.952	0.878	1	CLONAL	1	TRUE	1	0.53	2		619	666	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70441155	70441155	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0046975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	75	130	0	ENST00000373644.4:c.4825-1G>A		p.X1609_splice	ENST00000373644	NM_030625.2	1609			1	2	FACETS	0.793	0.699	0.892	0.793	0.699	0.892	SUBCLONAL	1	TRUE	1	0.53	2		130	357	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66679750	66679750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	133	641	1	ENST00000307102.5:c.65G>A	p.Gly22Glu	p.G22E	ENST00000307102	NM_002755.3	22	gGg/gAg	1/11	1	2	FACETS	0.828	0.755	0.905	0.828	0.755	0.905	CLONAL	1	TRUE	1	0.53	2		642	606	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149770	202149770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	35	544	1	ENST00000358485.4:c.1211G>A	p.Cys404Tyr	p.C404Y	ENST00000358485	NM_001080125.1	404	tGc/tAc	8/9	1	2	FACETS	0.19	0.155	0.229	0.19	0.155	0.229	SUBCLONAL	1	TRUE	1	0.53	2		545	696	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268766	41268766	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	119	286	0	ENST00000349496.5:c.1004A>C	p.Lys335Thr	p.K335T	ENST00000349496	NM_001904.3	335	aAa/aCa	7/15	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.53	2		286	448	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171933	32171933	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	158	565	0	ENST00000375023.3:c.3099G>C	p.Gln1033His	p.Q1033H	ENST00000375023	NM_004557.3	1033	caG/caC	19/30	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.53	2		565	560	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715464	117715464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	60	156	0	ENST00000368508.3:c.1025G>A	p.Gly342Glu	p.G342E	ENST00000368508	NM_002944.2	342	gGa/gAa	10/43	1	2	FACETS	0.786	0.683	0.896	0.786	0.683	0.896	SUBCLONAL	1	TRUE	1	0.53	2		156	288	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913384	NA	P-0046975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	205	705	0	ENST00000304494.5:c.262G>T	p.Glu88Ter	p.E88*	ENST00000304494	NM_000077.4	88	Gag/Tag	2/3	0.535287694244493	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.53	1		705	538	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894962	101894962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	81	195	0	ENST00000374994.4:c.515C>T	p.Ser172Leu	p.S172L	ENST00000374994	NM_004612.2	172	tCa/tTa	3/9	0.535287694244493	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.53	1		195	208	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564626	139564626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1207929986	NA	P-0046975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	282	1025	0	ENST00000308874.7:c.415G>A	p.Asp139Asn	p.D139N	ENST00000308874		139	Gat/Aat	7/10	0.535287694244493	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.53	1		1025	736	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0046983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	130	519	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.54573203856738	1	FACETS	0.99	0.909	1	0.99	0.909	1	CLONAL	1	TRUE	0	0.54573203856738	1		519	350	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0046983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	115	430	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.539159377691999	1	FACETS	0.788	0.716	0.862	0.788	0.716	0.862	SUBCLONAL	1	TRUE	0	0.54573203856738	1		430	389	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	106	419	0	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	0.54573203856738	1	FACETS	0.977	0.889	1	0.977	0.889	1	CLONAL	1	TRUE	0	0.54573203856738	1		419	289	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877366	28877366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1392528455	NA	P-0046983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	131	428	0	ENST00000282397.4:c.3955G>A	p.Ala1319Thr	p.A1319T	ENST00000282397	NM_002019.4	1319	Gcg/Acg	30/30	1	2	FACETS	0.954	0.871	1	0.954	0.871	1	CLONAL	1	TRUE	1	0.54573203856738	2		428	503	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265313	152265313	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	80	305	0	ENST00000206249.3:c.766C>T	p.Arg256Ter	p.R256*	ENST00000206249	NM_000125.3	256	Cga/Tga	4/8	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.54573203856738	2		305	292	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368252	45368252	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	77	390	0	ENST00000262160.6:c.1350C>G	p.Asp450Glu	p.D450E	ENST00000262160	NM_005901.5	450	gaC/gaG	11/11	0.54573203856738	1	FACETS	0.881	0.785	0.979	0.881	0.785	0.979	CLONAL	1	TRUE	0	0.54573203856738	1		390	233	SUCCESS
APC	324	MSKCC	GRCh37	5	112175551	112175552	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0046983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	74	315	0	ENST00000257430.4:c.4260_4261del	p.Ser1421Ter	p.S1421*	ENST00000257430	NM_000038.5	1420	ccCAgt/ccgt	16/16	0.54573203856738	1	FACETS	0.888	0.79	0.99	0.888	0.79	0.99	CLONAL	1	TRUE	0	0.54573203856738	1		315	222	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226349	133226349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	176	787	0	ENST00000320574.5:c.3709G>A	p.Glu1237Lys	p.E1237K	ENST00000320574	NM_006231.2	1237	Gag/Aag	30/49	1	2	FACETS	0.868	0.802	0.937	0.868	0.802	0.937	CLONAL	1	TRUE	1	0.54573203856738	2		787	743	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972432	32972432	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	83	542	0	ENST00000380152.3:c.9782A>G	p.Asp3261Gly	p.D3261G	ENST00000380152		3261	gAc/gGc	27/27	1	2	FACETS	0.602	0.533	0.676	0.602	0.533	0.676	SUBCLONAL	1	TRUE	1	0.54573203856738	2		542	505	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533793	63533793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	177	648	0	ENST00000307078.5:c.1361C>T	p.Ser454Phe	p.S454F	ENST00000307078	NM_004655.3	454	tCt/tTt	6/11	1	2	FACETS	0.998	0.923	1	0.998	0.923	1	CLONAL	1	TRUE	1	0.54573203856738	2		648	650	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139010	50139010	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	214	809	0	ENST00000246792.3:c.553C>A	p.Gln185Lys	p.Q185K	ENST00000246792	NM_006270.3	185	Cag/Aag	5/6	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.54573203856738	2		809	769	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662283	227662283	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	163	618	0	ENST00000305123.5:c.1172G>C	p.Ser391Thr	p.S391T	ENST00000305123	NM_005544.2	391	aGt/aCt	1/2	1	2	FACETS	0.938	0.864	1	0.938	0.864	1	CLONAL	1	TRUE	1	0.54573203856738	2		618	637	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172008	32172008	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	236	670	1	ENST00000375023.3:c.3024C>A	p.Asp1008Glu	p.D1008E	ENST00000375023	NM_004557.3	1008	gaC/gaA	19/30	0.371054484317741	2	FACETS	0.785	0.739	0.831	0.785	0.739	0.831	SUBCLONAL	2	TRUE	0	0.54573203856738	2		671	551	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0046984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	36	164	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		164	210	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0046985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	169	557	1	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.520204020082935	3	FACETS	0.935	0.879	0.99	0.935	0.879	0.99	CLONAL	3	TRUE	0	0.520204020082935	3		558	292	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039505	49039505	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs764754259	NA	P-0046985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	131	217	0	ENST00000267163.4:c.2489+1G>C		p.X830_splice	ENST00000267163	NM_000321.2	830			0.520204020082935	3	FACETS	0.932	0.869	0.994	0.932	0.869	0.994	CLONAL	3	TRUE	0	0.520204020082935	3		217	227	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870933	12870933	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	161	272	0	ENST00000228872.4:c.160G>T	p.Glu54Ter	p.E54*	ENST00000228872	NM_004064.3	54	Gag/Tag	1/3	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.712944764019118	2		272	381	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242705	46242705	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0046987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	90	267	0	ENST00000334344.6:c.1667T>G	p.Leu556Ter	p.L556*	ENST00000334344	NM_152641.2	556	tTa/tGa	13/21	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.712944764019118	2		267	249	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033857	49033857	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs483352689	NA	P-0046987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	141	285	0	ENST00000267163.4:c.1994T>G	p.Leu665Arg	p.L665R	ENST00000267163	NM_000321.2	665	cTt/cGt	20/27	0.712944764019118	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.712944764019118	1		285	237	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281342	142281342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	139	321	0	ENST00000350721.4:c.902C>T	p.Thr301Ile	p.T301I	ENST00000350721	NM_001184.3	301	aCa/aTa	4/47	0.712944764019118	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.712944764019118	1		321	243	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0046988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	215	432	0	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	0.682448718778265	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.686054071338285	2		432	313	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433349	49433349	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046988-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	214	497	0	ENST00000301067.7:c.8098C>G	p.Leu2700Val	p.L2700V	ENST00000301067	NM_003482.3	2700	Ctg/Gtg	32/54	0.682448718778265	2	FACETS	0.931	0.885	0.976	0.931	0.885	0.976	CLONAL	2	TRUE	0	0.686054071338285	2		497	335	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971121	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0046989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	105	313	2	ENST00000304494.5:c.237_238delinsTT	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	79	acCCga/acTTga	2/3	0.334013209425992	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.334013209425992	1		315	443	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031230	36031230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	103	611	1	ENST00000358208.4:c.1349C>T	p.Ser450Phe	p.S450F	ENST00000358208		450	tCc/tTc	11/12	1	2	FACETS	0.754	0.674	0.839	0.754	0.674	0.839	SUBCLONAL	1	TRUE	1	0.334013209425992	2		612	818	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089726	27089727	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	114	644	0	ENST00000324856.7:c.2682_2683delinsTT	p.Gln895Ter	p.Q895*	ENST00000324856	NM_006015.4	894	acCCaa/acTTaa	8/20	1	2	FACETS	0.803	0.723	0.888	0.803	0.723	0.888	CLONAL	1	TRUE	1	0.334013209425992	2		644	850	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480615	120480615	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	67	278	0	ENST00000256646.2:c.3202A>C	p.Ser1068Arg	p.S1068R	ENST00000256646	NM_024408.3	1068	Agt/Cgt	20/34	1	2	FACETS	0.85	0.74	0.968	0.85	0.74	0.968	CLONAL	1	TRUE	1	0.334013209425992	2		278	472	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176050291	176050291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	26	224	0	ENST00000367669.3:c.1274C>T	p.Ser425Phe	p.S425F	ENST00000367669	NM_022457.5	425	tCt/tTt	11/20	0.240918340614629	3	FACETS	0.715	0.568	0.882	0.358	0.284	0.441	SUBCLONAL	1	TRUE	1	0.334013209425992	3		224	254	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256558	133256559	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0046989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	113	374	0	ENST00000320574.5:c.404_405delinsTT	p.Pro135Leu	p.P135L	ENST00000320574	NM_006231.2	135	cCC/cTT	5/49	0.275853486411763	3	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.334013209425992	3		374	607	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56415064	56415064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	29	260	0	ENST00000348428.3:c.2465C>T	p.Ser822Phe	p.S822F	ENST00000348428	NM_006785.3	822	tCt/tTt	17/17	1	2	FACETS	0.583	0.469	0.712	0.583	0.469	0.712	SUBCLONAL	1	TRUE	1	0.334013209425992	2		260	298	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225449685	225449686	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0046989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	64	395	0	ENST00000264414.4:c.41_42delinsTT	p.Thr14Ile	p.T14I	ENST00000264414	NM_003590.4	14	aCC/aTT	1/16	1	2	FACETS	0.711	0.616	0.814	0.711	0.616	0.814	SUBCLONAL	1	TRUE	1	0.334013209425992	2		395	539	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538371	9538371	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	38	230	0	ENST00000353224.5:c.1627G>A	p.Glu543Lys	p.E543K	ENST00000353224	NM_177990.2	543	Gaa/Aaa	7/10	1	2	FACETS	0.798	0.663	0.948	0.798	0.663	0.948	CLONAL	1	TRUE	1	0.334013209425992	2		230	285	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537169	41537169	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	105	490	1	ENST00000263253.7:c.1996C>T	p.Pro666Ser	p.P666S	ENST00000263253	NM_001429.3	666	Cca/Tca	10/31	1	2	FACETS	0.934	0.838	1	0.934	0.838	1	CLONAL	1	TRUE	1	0.334013209425992	2		491	673	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630710	187630711	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	47	531	0	ENST00000441802.2:c.271_272delinsAA	p.Gly91Lys	p.G91K	ENST00000441802	NM_005245.3	91	GGa/AAa	2/27	1	2	FACETS	0.53	0.447	0.622	0.53	0.447	0.622	SUBCLONAL	1	TRUE	1	0.334013209425992	2		531	531	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043405	180043405	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	981	620	0	ENST00000261937.6:c.3181G>C	p.Asp1061His	p.D1061H	ENST00000261937	NM_182925.4	1061	Gac/Cac	23/30	0.334013209425992	8	FACETS	1	0.994	1	0.918	0.894	0.942	CLONAL	6	TRUE	1	0.334013209425992	8		620	1831	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431648	6431649	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	novel	NA	P-0046989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	79	453	0	ENST00000356142.4:c.201_202delinsTT	p.Leu67_Arg68delinsPheCys	p.L67_R68delinsFC	ENST00000356142	NM_018890.3	67	ttACgc/ttTTgc	3/7	1	2	FACETS	0.908	0.8	1	0.908	0.8	1	CLONAL	1	TRUE	1	0.334013209425992	2		453	521	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136795	69136795	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	56	316	0	ENST00000288368.4:c.4709G>A	p.Gly1570Glu	p.G1570E	ENST00000288368	NM_024870.2	1570	gGa/gAa	39/40	1	2	FACETS	0.748	0.642	0.864	0.748	0.642	0.864	SUBCLONAL	1	TRUE	1	0.334013209425992	2		316	448	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563485	87563485	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	99	497	0	ENST00000277120.3:c.1873G>A	p.Glu625Lys	p.E625K	ENST00000277120		625	Gag/Aag	16/19	1	2	FACETS	0.911	0.814	1	0.911	0.814	1	CLONAL	1	TRUE	1	0.334013209425992	2		497	651	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916947	178916952	+	inframe_deletion	In_Frame_Del	DEL	ATCCTC	ATCCTC	-	novel	NA	P-0046990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	72	430	0	ENST00000263967.3:c.335_340del	p.Ile112_Leu113del	p.I112_L113del	ENST00000263967	NM_006218.2	112	ATCCTC/-	2/21	0.415366842825766	4	FACETS	0.945	0.828	1	0.315	0.276	0.358	CLONAL	1	TRUE	1	0.415366842825766	4		430	519	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782329	NA	P-0046990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	515	754	1	ENST00000269305.4:c.746G>C	p.Arg249Thr	p.R249T	ENST00000269305	NM_001126112.2	249	aGg/aCg	7/11	0.415366842825766	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.415366842825766	2		755	1150	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052629	42052629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	256	527	1	ENST00000219905.7:c.7300C>T	p.Arg2434Trp	p.R2434W	ENST00000219905	NM_001164273.1	2434	Cgg/Tgg	20/24	0.38191325898559	3	FACETS	0.892	0.838	0.948	0.892	0.838	0.948	CLONAL	2	TRUE	1	0.415366842825766	3		528	834	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943628	9943628	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	217	754	0	ENST00000330684.3:c.1313A>C	p.Lys438Thr	p.K438T	ENST00000330684	NM_001134407.1	438	aAg/aCg	5/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.415366842825766	2		754	956	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809332	243809332	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	109	371	0	ENST00000263826.5:c.292T>C	p.Trp98Arg	p.W98R	ENST00000263826	NM_005465.4	98	Tgg/Cgg	4/13	0.415366842825766	2	FACETS	1	0.965	1	0.574	0.519	0.632	CLONAL	1	TRUE	0	0.415366842825766	2		371	457	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210905	133210905	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1255	235	856	0	ENST00000320574.5:c.5871G>T	p.Glu1957Asp	p.E1957D	ENST00000320574	NM_006231.2	1957	gaG/gaT	43/49	0.410016881533574	3	FACETS	0.917	0.853	0.984	0.459	0.426	0.492	CLONAL	1	TRUE	1	0.415366842825766	3		856	1490	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38506073	38506073	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2969	199	744	0	ENST00000254066.5:c.365A>G	p.Tyr122Cys	p.Y122C	ENST00000254066	NM_000964.3	122	tAc/tGc	4/9	0.415366842825766	11	FACETS	0.868	0.799	0.94			1	CLONAL	1	TRUE	NA	0.415366842825766	11		744	3168	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728814	39728814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	97	390	0	ENST00000361337.2:c.1094G>A	p.Gly365Asp	p.G365D	ENST00000361337	NM_003286.2	365	gGc/gAc	12/21	0.415366842825766	5	FACETS	0.899	0.801	1	0.3	0.267	0.335	CLONAL	1	TRUE	2	0.415366842825766	5		390	843	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138681	55138698	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTAAGAAGTATGGAAAAC	TTAAGAAGTATGGAAAAC	-	novel	NA	P-0046990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	120	417	0	ENST00000257290.5:c.1358_1364+11del		p.X453_splice	ENST00000257290	NM_006206.4	453		9/23	0.415366842825766	2	FACETS	1	0.927	1	0.513	0.465	0.564	CLONAL	1	TRUE	0	0.415366842825766	2		417	563	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369182	118369182	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	137	415	0	ENST00000534358.1:c.5900G>T	p.Cys1967Phe	p.C1967F	ENST00000534358	NM_005933.3	1967	tGt/tTt	22/36	0.328211267948615	3	FACETS	1	0.982	1	0.64	0.586	0.696	INDETERMINATE	1	TRUE	1	0.56460425092512	3		415	486	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061139	38061198	+	inframe_deletion	In_Frame_Del	DEL	CCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCT	CCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCT	-	novel	NA	P-0046991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	229	463	2	ENST00000250448.2:c.791_850del	p.Lys264_Gly284delinsSer	p.K264_G284delinsS	ENST00000250448	NM_004496.3	264	aAGCGCTTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGgc/agc	2/2	0.101633327763037	3	FACETS	0.976	0.918	1	0.976	0.918	1	INDETERMINATE	2	TRUE	1	0.56460425092512	3		465	533	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	22	272	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.132	0.102	0.168	0.132	0.102	0.168	SUBCLONAL	1	TRUE	1	0.752191370554651	2		272	442	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	193	438	2	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.671	0.622	0.721	0.671	0.622	0.721	SUBCLONAL	1	TRUE	1	0.752191370554651	2		440	765	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	154	419	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.727712779354591	1	FACETS	0.626	0.579	0.674	0.626	0.579	0.674	SUBCLONAL	1	TRUE	0	0.752191370554651	1		419	408	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	202	515	6	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.654	0.607	0.703	0.654	0.607	0.703	SUBCLONAL	1	TRUE	1	0.752191370554651	2		521	821	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	215	502	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.625	0.581	0.67	0.625	0.581	0.67	SUBCLONAL	1	TRUE	1	0.752191370554651	2		507	915	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1162	267	1010	1	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	1	2	FACETS	0.497	0.465	0.53	0.497	0.465	0.53	SUBCLONAL	1	TRUE	1	0.752191370554651	2		1011	1429	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	121	806	1	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.276	0.249	0.306	0.276	0.249	0.306	SUBCLONAL	1	TRUE	1	0.752191370554651	2		807	1164	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438316	110438317	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	rs532810290	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	298	257	0	ENST00000375856.3:c.82_84dup	p.Asn28dup	p.N28dup	ENST00000375856	NM_003749.2	28	-/AAC	1/2	0.752191370554651	4	FACETS	0.767	0.724	0.811	0.511	0.483	0.541	SUBCLONAL	2	TRUE	1	0.752191370554651	4		257	905	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	69	222	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.6	0.527	0.677	0.6	0.527	0.677	SUBCLONAL	1	TRUE	1	0.752191370554651	2		222	306	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119910	70119910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1297203260	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	60	707	0	ENST00000245479.2:c.916del	p.Val306CysfsTer77	p.V306Cfs*77	ENST00000245479	NM_000346.3	304	ccG/cc	3/3	1	2	FACETS	0.147	0.126	0.171	0.147	0.126	0.171	SUBCLONAL	1	TRUE	1	0.752191370554651	2		707	1082	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332337	70332337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761821309	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	177	506	0	ENST00000373644.4:c.242G>A	p.Arg81His	p.R81H	ENST00000373644	NM_030625.2	81	cGc/cAc	2/12	1	2	FACETS	0.651	0.601	0.702	0.651	0.601	0.702	SUBCLONAL	1	TRUE	1	0.752191370554651	2		506	723	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743932	41743933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs778012871	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1440	135	1100	4	ENST00000301178.4:c.874dup	p.His292ProfsTer47	p.H292Pfs*47	ENST00000301178	NM_021913.4	289	-/C	7/20	1	2	FACETS	0.228	0.206	0.251	0.228	0.206	0.251	SUBCLONAL	1	TRUE	1	0.752191370554651	2		1104	1575	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	95	394	0	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.516	0.461	0.573	0.516	0.461	0.573	SUBCLONAL	1	TRUE	1	0.752191370554651	2		394	490	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1294	416	1232	5	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.647	0.614	0.68	0.647	0.614	0.68	SUBCLONAL	1	TRUE	1	0.752191370554651	2		1237	1710	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874637	35874637	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	139	412	1	ENST00000303115.3:c.799del	p.Arg267GlyfsTer28	p.R267Gfs*28	ENST00000303115	NM_002185.3	265	Aaa/aa	6/8	1	2	FACETS	0.543	0.495	0.593	0.543	0.495	0.593	SUBCLONAL	1	TRUE	1	0.752191370554651	2		413	681	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944913	31944913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	150	341	1	ENST00000340398.3:c.188G>A	p.Arg63Gln	p.R63Q	ENST00000340398	NM_001013699.2	63	cGg/cAg	1/1	1	2	FACETS	0.695	0.638	0.754	0.695	0.638	0.754	SUBCLONAL	1	TRUE	1	0.752191370554651	2		342	574	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740623	58740624	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs763475304	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	197	525	2	ENST00000305921.3:c.1535dup	p.Asn512LysfsTer16	p.N512Kfs*16	ENST00000305921	NM_003620.3	510	caa/cAaa	6/6	1	2	FACETS	0.655	0.607	0.704	0.655	0.607	0.704	SUBCLONAL	1	TRUE	1	0.752191370554651	2		527	800	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117594	70117594	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	333	996	0	ENST00000245479.2:c.66del	p.Ser23AlafsTer38	p.S23Afs*38	ENST00000245479	NM_000346.3	21	gCc/gc	1/3	1	2	FACETS	0.64	0.604	0.677	0.64	0.604	0.677	SUBCLONAL	1	TRUE	1	0.752191370554651	2		996	1384	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681119	117681120	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs748436511	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	148	482	0	ENST00000368508.3:c.3500dup	p.Leu1167PhefsTer26	p.L1167Ffs*26	ENST00000368508	NM_002944.2	1167	tta/ttTa	23/43	1	2	FACETS	0.643	0.589	0.699	0.643	0.589	0.699	SUBCLONAL	1	TRUE	1	0.752191370554651	2		482	612	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126729	5126729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774469142	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	89	455	0	ENST00000381652.3:c.3337C>T	p.Arg1113Cys	p.R1113C	ENST00000381652	NM_004972.3	1113	Cgc/Tgc	25/25	1	2	FACETS	0.626	0.559	0.697	0.626	0.559	0.697	SUBCLONAL	1	TRUE	1	0.752191370554651	2		455	378	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147770	61147771	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	104	214	0	ENST00000295025.8:c.1086dup	p.Glu363ArgfsTer8	p.E363Rfs*8	ENST00000295025	NM_002908.2	360	-/A	10/11	1	2	FACETS	0.645	0.581	0.711	0.645	0.581	0.711	SUBCLONAL	1	TRUE	1	0.752191370554651	2		214	429	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416952	416953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs771545848	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	189	488	12	ENST00000399788.2:c.3597dup	p.Gly1200ArgfsTer7	p.G1200Rfs*7	ENST00000399788	NM_001042603.1	1199	-/A	23/28	1	2	FACETS	0.646	0.598	0.695	0.646	0.598	0.695	SUBCLONAL	1	TRUE	1	0.752191370554651	2		500	778	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911288	29911288	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs45552635	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	29	393	3	ENST00000376809.5:c.587T>C	p.Leu196Pro	p.L196P	ENST00000376809	NM_002116.7	196	cTg/cCg	3/8	1	2	FACETS	0.141	0.113	0.174	0.141	0.113	0.174	SUBCLONAL	1	TRUE	1	0.752191370554651	2		396	546	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434959	49434959	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555192751	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	68	894	1	ENST00000301067.7:c.6594del	p.Tyr2199IlefsTer65	p.Y2199Ifs*65	ENST00000301067	NM_003482.3	2198	ccC/cc	31/54	1	2	FACETS	0.153	0.132	0.176	0.153	0.132	0.176	SUBCLONAL	1	TRUE	1	0.752191370554651	2		895	1180	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793676	89793677	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	106	298	1	ENST00000336032.3:c.752dup	p.Pro252AlafsTer3	p.P252Afs*3	ENST00000336032	NM_006813.2	249	gaa/gAaa	2/2	1	2	FACETS	0.58	0.522	0.64	0.58	0.522	0.64	SUBCLONAL	1	TRUE	1	0.752191370554651	2		299	486	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161390	2161390	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	283	696	0	ENST00000434045.2:c.137G>A	p.Arg46His	p.R46H	ENST00000434045	NM_001127598.1	46	cGc/cAc	2/5	1	2	FACETS	0.672	0.632	0.714	0.672	0.632	0.714	SUBCLONAL	1	TRUE	1	0.752191370554651	2		696	1119	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931451	131931452	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	106	418	3	ENST00000265335.6:c.2164_2165dup	p.Glu723ArgfsTer14	p.E723Rfs*14	ENST00000265335		719	cta/ctAAa	13/25	1	2	FACETS	0.442	0.397	0.49	0.442	0.397	0.49	SUBCLONAL	1	TRUE	1	0.752191370554651	2		421	637	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502662	149502662	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759436020	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	320	700	0	ENST00000261799.4:c.2126G>A	p.Arg709His	p.R709H	ENST00000261799	NM_002609.3	709	cGc/cAc	15/23	1	2	FACETS	0.719	0.678	0.76	0.719	0.678	0.76	SUBCLONAL	1	TRUE	1	0.752191370554651	2		700	1184	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647423	3647423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755156257	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	309	956	1	ENST00000294008.3:c.1640C>T	p.Thr547Met	p.T547M	ENST00000294008	NM_032444.2	547	aCg/aTg	7/15	1	2	FACETS	0.592	0.557	0.627	0.592	0.557	0.627	SUBCLONAL	1	TRUE	1	0.752191370554651	2		957	1389	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361097	70361098	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAG	rs766775649	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	170	343	0	ENST00000374080.3:c.6306_6308dup	p.Gln2115dup	p.Q2115dup	ENST00000374080		2115	-/CAG	43/45	1	1	FACETS	0.629	0.585	0.675	0.629	0.585	0.675	SUBCLONAL	1	TRUE	0	0.752191370554651	1		343	448	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944931	31944931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	152	340	0	ENST00000340398.3:c.170C>T	p.Ser57Leu	p.S57L	ENST00000340398	NM_001013699.2	57	tCg/tTg	1/1	1	2	FACETS	0.736	0.677	0.797	0.736	0.677	0.797	SUBCLONAL	1	TRUE	1	0.752191370554651	2		340	549	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198264796	198264796	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	61	457	0	ENST00000335508.6:c.2996C>A	p.Ala999Asp	p.A999D	ENST00000335508	NM_012433.2	999	gCc/gAc	20/25	1	2	FACETS	0.25	0.215	0.288	0.25	0.215	0.288	SUBCLONAL	1	TRUE	1	0.752191370554651	2		457	648	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127733	64127733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	404	1005	0	ENST00000334205.4:c.226G>A	p.Ala76Thr	p.A76T	ENST00000334205	NM_003942.2	76	Gcc/Acc	3/17	1	2	FACETS	0.735	0.698	0.772	0.735	0.698	0.772	SUBCLONAL	1	TRUE	1	0.752191370554651	2		1005	1462	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121037	3121037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772471502	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	121	961	0	ENST00000078429.4:c.940G>A	p.Val314Met	p.V314M	ENST00000078429	NM_002067.2	314	Gtg/Atg	7/7	1	2	FACETS	0.258	0.232	0.286	0.258	0.232	0.286	SUBCLONAL	1	TRUE	1	0.752191370554651	2		961	1245	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411771	63411772	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	291	473	0	ENST00000330258.3:c.1395dup	p.Asn466GlnfsTer2	p.N466Qfs*2	ENST00000330258	NM_152424.3	465	-/C	2/2	1	1	FACETS	0.791	0.751	0.831	0.791	0.751	0.831	SUBCLONAL	1	TRUE	0	0.752191370554651	1		473	610	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127991	64127991	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	348	943	0	ENST00000334205.4:c.389G>A	p.Arg130His	p.R130H	ENST00000334205	NM_003942.2	130	cGc/cAc	4/17	1	2	FACETS	0.644	0.609	0.681	0.644	0.609	0.681	SUBCLONAL	1	TRUE	1	0.752191370554651	2		943	1436	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418412	49418412	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1201302456	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	113	719	0	ENST00000301067.7:c.16001A>G	p.Asn5334Ser	p.N5334S	ENST00000301067	NM_003482.3	5334	aAc/aGc	50/54	1	2	FACETS	0.283	0.254	0.314	0.283	0.254	0.314	SUBCLONAL	1	TRUE	1	0.752191370554651	2		719	1061	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434673	49434673	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1416	102	1146	0	ENST00000301067.7:c.6880del	p.Ala2294HisfsTer28	p.A2294Hfs*28	ENST00000301067	NM_003482.3	2294	Gca/ca	31/54	1	2	FACETS	0.179	0.159	0.2	0.179	0.159	0.2	SUBCLONAL	1	TRUE	1	0.752191370554651	2		1146	1518	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864249	57864249	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1565601582	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	108	829	0	ENST00000228682.2:c.1726T>C	p.Ser576Pro	p.S576P	ENST00000228682	NM_005269.2	576	Tcc/Ccc	12/12	1	2	FACETS	0.251	0.225	0.28	0.251	0.225	0.28	SUBCLONAL	1	TRUE	1	0.752191370554651	2		829	1143	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41011056	41011056	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	93	663	0	ENST00000267868.3:c.489G>T	p.Glu163Asp	p.E163D	ENST00000267868	NM_002875.4	163	gaG/gaT	6/10	0.589321182270255	1	FACETS	0.173	0.153	0.194	0.173	0.153	0.194	SUBCLONAL	1	TRUE	0	0.752191370554651	1		663	891	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467213	99467213	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	153	391	0	ENST00000268035.6:c.2594A>G	p.Tyr865Cys	p.Y865C	ENST00000268035	NM_000875.3	865	tAt/tGt	12/21	1	2	FACETS	0.721	0.663	0.781	0.721	0.663	0.781	SUBCLONAL	1	TRUE	1	0.752191370554651	2		391	564	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640656	3640656	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1337	83	1099	0	ENST00000294008.3:c.2983T>A	p.Ser995Thr	p.S995T	ENST00000294008	NM_032444.2	995	Tca/Aca	12/15	1	2	FACETS	0.155	0.136	0.176	0.155	0.136	0.176	SUBCLONAL	1	TRUE	1	0.752191370554651	2		1099	1420	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37863374	37863374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1421	95	1003	0	ENST00000269571.5:c.205G>A	p.Ala69Thr	p.A69T	ENST00000269571		69	Gcc/Acc	2/27	1	2	FACETS	0.167	0.147	0.187	0.167	0.147	0.187	SUBCLONAL	1	TRUE	1	0.752191370554651	2		1003	1516	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678100	58678100	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	277	707	0	ENST00000305921.3:c.325G>A	p.Gly109Arg	p.G109R	ENST00000305921	NM_003620.3	109	Ggg/Agg	1/6	1	2	FACETS	0.636	0.597	0.676	0.636	0.597	0.676	SUBCLONAL	1	TRUE	1	0.752191370554651	2		707	1158	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226919	2226919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	130	725	1	ENST00000398665.3:c.4399C>T	p.Pro1467Ser	p.P1467S	ENST00000398665	NM_032482.2	1467	Ccc/Tcc	27/28	1	2	FACETS	0.314	0.284	0.346	0.314	0.284	0.346	SUBCLONAL	1	TRUE	1	0.752191370554651	2		726	1101	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303323	15303323	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1455	90	984	0	ENST00000263388.2:c.205C>T	p.Pro69Ser	p.P69S	ENST00000263388	NM_000435.2	69	Cct/Tct	3/33	1	2	FACETS	0.155	0.136	0.175	0.155	0.136	0.175	SUBCLONAL	1	TRUE	1	0.752191370554651	2		984	1545	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224301	36224301	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1518	92	1082	0	ENST00000222270.7:c.6851T>C	p.Phe2284Ser	p.F2284S	ENST00000222270	NM_014727.1	2284	tTc/tCc	28/37	1	2	FACETS	0.152	0.134	0.171	0.152	0.134	0.171	SUBCLONAL	1	TRUE	1	0.752191370554651	2		1082	1610	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149917	202149917	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	250	746	0	ENST00000358485.4:c.1358C>A	p.Pro453Gln	p.P453Q	ENST00000358485	NM_001080125.1	453	cCg/cAg	8/9	0.461903941765006	1	FACETS	0.502	0.471	0.534	0.502	0.471	0.534	SUBCLONAL	1	TRUE	0	0.752191370554651	1		746	826	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817418	39817418	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	222	616	2	ENST00000288319.7:c.145C>A	p.Pro49Thr	p.P49T	ENST00000288319	NM_182918.3	49	Cca/Aca	2/10	1	2	FACETS	0.626	0.583	0.67	0.626	0.583	0.67	SUBCLONAL	1	TRUE	1	0.752191370554651	2		618	943	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71064752	71064752	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	65	484	0	ENST00000318789.4:c.922T>C	p.Cys308Arg	p.C308R	ENST00000318789	NM_032682.5	308	Tgc/Cgc	12/21	1	2	FACETS	0.226	0.195	0.259	0.226	0.195	0.259	SUBCLONAL	1	TRUE	1	0.752191370554651	2		484	766	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433536	138433536	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	31	447	0	ENST00000289153.2:c.1076A>G	p.His359Arg	p.H359R	ENST00000289153	NM_006219.2	359	cAt/cGt	7/22	1	2	FACETS	0.164	0.132	0.2	0.164	0.132	0.2	SUBCLONAL	1	TRUE	1	0.752191370554651	2		447	503	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806197	1806197	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	275	1049	0	ENST00000260795.2:c.1216C>A	p.Leu406Met	p.L406M	ENST00000260795		406	Ctg/Atg	8/17	1	2	FACETS	0.513	0.48	0.546	0.513	0.48	0.546	SUBCLONAL	1	TRUE	1	0.752191370554651	2		1049	1426	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143181645	143181645	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	37	381	0	ENST00000262992.4:c.688G>T	p.Val230Leu	p.V230L	ENST00000262992	NM_001101669.1	230	Gtg/Ttg	9/24	1	2	FACETS	0.178	0.146	0.213	0.178	0.146	0.213	SUBCLONAL	1	TRUE	1	0.752191370554651	2		381	554	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31437407	31437407	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	75	456	0	ENST00000344624.3:c.2883-2A>T		p.X961_splice	ENST00000344624		961			1	2	FACETS	0.278	0.243	0.316	0.278	0.243	0.316	SUBCLONAL	1	TRUE	1	0.752191370554651	2		456	717	SUCCESS
APC	324	MSKCC	GRCh37	5	112175398	112175399	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	91	290	0	ENST00000257430.4:c.4111dup	p.Ser1371LysfsTer4	p.S1371Kfs*4	ENST00000257430	NM_000038.5	1369	-/A	16/16	1	2	FACETS	0.609	0.545	0.678	0.609	0.545	0.678	SUBCLONAL	1	TRUE	1	0.752191370554651	2		290	397	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915153	131915153	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	127	473	0	ENST00000265335.6:c.510G>T	p.Lys170Asn	p.K170N	ENST00000265335		170	aaG/aaT	4/25	1	2	FACETS	0.591	0.538	0.648	0.591	0.538	0.648	SUBCLONAL	1	TRUE	1	0.752191370554651	2		473	571	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517514	176517514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373397427	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1463	128	1138	3	ENST00000292408.4:c.215G>A	p.Arg72His	p.R72H	ENST00000292408	NM_213647.1	72	cGc/cAc	3/18	1	2	FACETS	0.214	0.193	0.236	0.214	0.193	0.236	SUBCLONAL	1	TRUE	1	0.752191370554651	2		1141	1591	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048844	180048844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1366	123	1130	0	ENST00000261937.6:c.1718C>T	p.Pro573Leu	p.P573L	ENST00000261937	NM_182925.4	573	cCg/cTg	13/30	1	2	FACETS	0.22	0.197	0.243	0.22	0.197	0.243	SUBCLONAL	1	TRUE	1	0.752191370554651	2		1130	1489	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250449	26250449	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	221	710	0	ENST00000446824.2:c.385C>T	p.Arg129Cys	p.R129C	ENST00000446824	NM_021018.2	129	Cgc/Tgc	1/1	1	2	FACETS	0.605	0.563	0.648	0.605	0.563	0.648	SUBCLONAL	1	TRUE	1	0.752191370554651	2		710	972	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680349	30680349	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	279	661	0	ENST00000376406.3:c.1370T>C	p.Val457Ala	p.V457A	ENST00000376406	NM_014641.2	457	gTg/gCg	5/15	1	2	FACETS	0.694	0.652	0.737	0.694	0.652	0.737	SUBCLONAL	1	TRUE	1	0.752191370554651	2		661	1069	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803007	32803007	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	237	679	2	ENST00000374899.4:c.869C>A	p.Pro290His	p.P290H	ENST00000374899	NM_018833.2	290	cCt/cAt	5/12	1	2	FACETS	0.655	0.612	0.7	0.655	0.612	0.7	SUBCLONAL	1	TRUE	1	0.752191370554651	2		681	962	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411611	116411611	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	202	452	0	ENST00000397752.3:c.2790T>A	p.Asn930Lys	p.N930K	ENST00000397752	NM_000245.2	930	aaT/aaA	13/21	1	2	FACETS	0.781	0.727	0.836	0.781	0.727	0.836	SUBCLONAL	1	TRUE	1	0.752191370554651	2		452	688	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249740	110249740	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1412	112	1077	1	ENST00000374672.4:c.935C>A	p.Pro312His	p.P312H	ENST00000374672	NM_004235.4	312	cCc/cAc	3/5	1	2	FACETS	0.195	0.175	0.218	0.195	0.175	0.218	SUBCLONAL	1	TRUE	1	0.752191370554651	2		1078	1524	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395022	139395022	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	94	806	0	ENST00000277541.6:c.5916C>A	p.Asp1972Glu	p.D1972E	ENST00000277541	NM_017617.3	1972	gaC/gaA	31/34	1	2	FACETS	0.214	0.189	0.24	0.214	0.189	0.24	SUBCLONAL	1	TRUE	1	0.752191370554651	2		806	1170	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0046992-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	271	671	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.631363953609706	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.632335606862764	1		671	554	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0046992-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	21	297	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.671	0.526	0.832	0.671	0.526	0.832	SUBCLONAL	1	TRUE	1	0.632335606862764	2		297	99	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0046992-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	12	439	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.631363953609706	1	FACETS	0.175	0.123	0.239	0.175	0.123	0.239	SUBCLONAL	1	TRUE	0	0.632335606862764	1		439	148	SUCCESS
APC	324	MSKCC	GRCh37	5	112175411	112175411	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046992-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	70	298	0	ENST00000257430.4:c.4120G>T	p.Glu1374Ter	p.E1374*	ENST00000257430	NM_000038.5	1374	Gaa/Taa	16/16	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.632335606862764	2		298	201	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380276	+	missense_variant	Missense_Mutation	DNP	TT	TT	GA	novel	NA	P-0046992-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	93	543	0	ENST00000311936.3:c.182_183delinsTC	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAA/cTC	3/5	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.632335606862764	2		543	245	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061352	38061352	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	139	1023	1	ENST00000250448.2:c.637C>T	p.Arg213Cys	p.R213C	ENST00000250448	NM_004496.3	213	Cgc/Tgc	2/2	0.576770182045601	2	FACETS	0.514	0.468	0.563	0.257	0.234	0.282	SUBCLONAL	1	TRUE	0	0.641105282907165	2		1024	843	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579346	7579348	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs764486868	NA	P-0046993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	699	949	0	ENST00000269305.4:c.339_341del	p.Phe113del	p.F113del	ENST00000269305	NM_001126112.2	113	ttCTTg/ttg	4/11	0.51304876055539	3	FACETS	0.871	0.847	0.895	0.871	0.847	0.895	CLONAL	3	TRUE	0	0.641105282907165	3		949	1102	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939094	76939114	+	frameshift_variant	Frame_Shift_Del	DEL	TTCCACTGCTGCCATCCCCTT	TTCCACTGCTGCCATCCCCTT	GG	novel	NA	P-0046993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	109	607	2	ENST00000373344.5:c.1634_1654delinsCC	p.Gln545ProfsTer11	p.Q545Pfs*11	ENST00000373344	NM_000489.3	545	cAAGGGGATGGCAGCAGTGGAAct/cCCct	9/35	0.560851025641117	2	FACETS	1	0.978	1	0.621	0.566	0.676	CLONAL	1	TRUE	0	0.641105282907165	2		609	274	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1442	80	729	0	ENST00000269305.4:c.880del	p.Glu294SerfsTer51	p.E294Sfs*51	ENST00000269305	NM_001126112.2	294	Gag/ag	8/11	1	2	FACETS	0.611	0.535	0.693	0.611	0.535	0.693	SUBCLONAL	1	TRUE	1	0.172113561810007	2		729	1522	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604784	48604807	+	inframe_deletion	In_Frame_Del	DEL	CTAGACGAAGTACTTCATACCATG	CTAGACGAAGTACTTCATACCATG	-	novel	NA	P-0046994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	27	307	0	ENST00000342988.3:c.1607_1630del	p.Leu536_Met543del	p.L536_M543del	ENST00000342988	NM_005359.5	536	CTAGACGAAGTACTTCATACCATG/-	12/12	0.0737904884999496	3	FACETS	0.741	0.589	0.915	0.37	0.294	0.458	INDETERMINATE	1	TRUE	1	0.172113561810007	3		307	460	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0046995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	186	209	0	ENST00000288602.6:c.1397G>T	p.Gly466Val	p.G466V	ENST00000288602	NM_004333.4	466	gGa/gTa	11/18	1	2	FACETS	0.918	0.856	0.98	0.918	0.856	0.98	CLONAL	1	TRUE	1	0.855184191447477	2		209	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579440	7579440	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs867725248	NA	P-0046995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	559	1133	0	ENST00000269305.4:c.247del	p.Ala83ArgfsTer40	p.A83Rfs*40	ENST00000269305	NM_001126112.2	83	Gcg/cg	4/11	0.855184191447477	1	FACETS	0.996	0.97	1	0.996	0.97	1	CLONAL	1	TRUE	0	0.855184191447477	1		1133	751	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936266	78936266	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs142332444	NA	P-0046995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	416	901	0	ENST00000306801.3:c.3698A>G	p.Asn1233Ser	p.N1233S	ENST00000306801	NM_020761.2	1233	aAt/aGt	32/34	0.510467526032121	1	FACETS	0.654	0.627	0.682	0.654	0.627	0.682	INDETERMINATE	1	TRUE	0	0.855184191447477	1		901	851	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12632423	12632423	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	474	879	0	ENST00000251849.4:c.1244A>G	p.Asp415Gly	p.D415G	ENST00000251849	NM_002880.3	415	gAc/gGc	12/17	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.855184191447477	2		879	1100	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245373	153245373	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	223	273	0	ENST00000281708.4:c.1818G>A	p.Trp606Ter	p.W606*	ENST00000281708	NM_033632.3	606	tgG/tgA	11/12	0.322068751026184	1	FACETS	0.524	0.491	0.557	0.524	0.491	0.557	INDETERMINATE	1	TRUE	0	0.855184191447477	1		273	570	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055948	180055948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1309857166	NA	P-0046995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	538	1316	3	ENST00000261937.6:c.1037C>T	p.Thr346Met	p.T346M	ENST00000261937	NM_182925.4	346	aCg/aTg	8/30	0.322068751026184	1	FACETS	0.551	0.529	0.573	0.551	0.529	0.573	INDETERMINATE	1	TRUE	0	0.855184191447477	1		1319	1307	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730008	41730008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537531066	NA	P-0046995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	414	833	0	ENST00000242208.4:c.521G>A	p.Arg174His	p.R174H	ENST00000242208	NM_002192.2	174	cGc/cAc	3/3	0.322068751026184	1	FACETS	0.532	0.508	0.556	0.532	0.508	0.556	INDETERMINATE	1	TRUE	0	0.855184191447477	1		833	1042	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194543	29194543	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0046995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	553	1324	0	ENST00000240100.2:c.1185G>C	p.Ter395TyrextTer16	p.*395Yext*16	ENST00000240100	NM_001394.6	395	taG/taC	4/4	0.619166891912857	1	FACETS	0.857	0.83	0.883	0.857	0.83	0.883	CLONAL	1	TRUE	0	0.855184191447477	1		1324	864	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280068	18280083	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCCCGGGCCCCGGC	CGCCCCGGGCCCCGGC	-	novel	NA	P-0046995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	264	329	0	ENST00000222254.8:c.2152_2167del	p.Ala718ArgfsTer151	p.A718Rfs*151	ENST00000222254	NM_005027.3	717	cgCGCCCCGGGCCCCGGC/cg	16/16	0.322068751026184	1	FACETS	0.796	0.759	0.833	0.796	0.759	0.833	INDETERMINATE	1	TRUE	0	0.855184191447477	1		329	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0046996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	248	593	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.236142941132045	2	FACETS	0.802	0.749	0.856	0.802	0.749	0.856	CLONAL	2	TRUE	0	0.284356371967237	2		593	1088	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130235	2130235	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1252	188	1247	0	ENST00000219476.3:c.3467C>G	p.Pro1156Arg	p.P1156R	ENST00000219476	NM_000548.3	1156	cCa/cGa	30/42	1	2	FACETS	0.918	0.846	0.994	0.918	0.846	0.994	CLONAL	1	TRUE	1	0.284356371967237	2		1247	1440	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288415	15288415	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	89	802	0	ENST00000263388.2:c.4324T>G	p.Cys1442Gly	p.C1442G	ENST00000263388	NM_000435.2	1442	Tgc/Ggc	24/33	1	2	FACETS	0.811	0.718	0.91	0.811	0.718	0.91	CLONAL	1	TRUE	1	0.284356371967237	2		802	772	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	67	516	0				ENST00000310581	NM_198253.2	-/1132			0.40276268755427	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.594038460726425	1		516	129	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	293	709	5	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.502250175046203	5	FACETS	0.947	0.913	0.98	1	0.996	1	CLONAL	5	TRUE	2	0.594038460726425	5		714	394	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750394	133750394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	134	632	2	ENST00000318560.5:c.1225G>A	p.Glu409Lys	p.E409K	ENST00000318560	NM_005157.4	409	Gag/Aag	7/11	0.205280788460559	4	FACETS	0.999	0.919	1	0.999	0.919	1	INDETERMINATE	2	TRUE	2	0.594038460726425	4		634	360	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129420	2129420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781774	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	214	816	0	ENST00000219476.3:c.3275C>T	p.Pro1092Leu	p.P1092L	ENST00000219476	NM_000548.3	1092	cCg/cTg	28/42	0.304602583035213	3	FACETS	0.944	0.887	1	0.944	0.887	1	INDETERMINATE	2	TRUE	1	0.594038460726425	3		816	495	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272140	15272140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	58	1131	0	ENST00000263388.2:c.6299C>T	p.Ser2100Leu	p.S2100L	ENST00000263388	NM_000435.2	2100	tCg/tTg	33/33	0.249192774286564	3	FACETS	0.942	0.817	1	0.314	0.272	0.359	INDETERMINATE	1	TRUE	0	0.594038460726425	3		1131	269	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435828	56435828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs995358248	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	15	723	2	ENST00000407977.2:c.1309C>T	p.Arg437Trp	p.R437W	ENST00000407977		437	Cgg/Tgg	9/10	0.346087519655941	1	FACETS	0.172	0.125	0.227	0.172	0.125	0.227	INDETERMINATE	1	TRUE	0	0.594038460726425	1		725	207	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622138	1622138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370087169	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	64	1017	2	ENST00000344749.5:c.737C>T	p.Pro246Leu	p.P246L	ENST00000344749	NM_001136139.2	246	cCg/cTg	10/19	0.249192774286564	3	FACETS	0.751	0.654	0.856	0.25	0.218	0.286	INDETERMINATE	1	TRUE	0	0.594038460726425	3		1019	372	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094997	11094997	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568417458	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	185	1117	0	ENST00000358026.2:c.170C>T	p.Pro57Leu	p.P57L	ENST00000358026	NM_001128849.1	57	cCc/cTc	2/36	0.249192774286564	3	FACETS	0.844	0.796	0.892	0.844	0.796	0.892	INDETERMINATE	3	TRUE	0	0.594038460726425	3		1117	319	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509619	106509619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142822484	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	71	564	0	ENST00000359195.3:c.1613C>T	p.Pro538Leu	p.P538L	ENST00000359195	NM_002649.2	538	cCg/cTg	2/11	0.594038460726425	5	FACETS	0.81	0.715	0.911	0.54	0.476	0.607	CLONAL	2	TRUE	2	0.594038460726425	5		564	279	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022616	31022616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	153	656	1	ENST00000375687.4:c.2101C>T	p.Pro701Ser	p.P701S	ENST00000375687	NM_015338.5	701	Cct/Tct	13/13	0.594038460726425	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.594038460726425	3		657	276	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476382	88476382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	31	626	0	ENST00000360948.2:c.1750G>A	p.Asp584Asn	p.D584N	ENST00000360948	NM_001012338.2	584	Gat/Aat	15/19	0.471663923377651	0	FACETS	0.441	0.367	0.521			1	SUBCLONAL	1	TRUE	0	0.594038460726425	0		626	96	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585494	29585494	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660428	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	36	259	0	ENST00000356175.3:c.4243G>A	p.Glu1415Lys	p.E1415K	ENST00000356175	NM_000267.3	1415	Gaa/Aaa	31/57	0.594038460726425	5	FACETS	1	0.941	1	0.83	0.706	0.96	CLONAL	2	TRUE	2	0.594038460726425	5		259	92	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317926	8317926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	16	344	0	ENST00000356435.5:c.5687C>T	p.Ser1896Phe	p.S1896F	ENST00000356435		1896	tCc/tTc	35/35	0.594038460726425	1	FACETS	0.971	0.758	1	0.971	0.758	1	CLONAL	1	TRUE	0	0.594038460726425	1		344	39	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68982089	68982089	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	26	499	0	ENST00000288368.4:c.1463G>C	p.Arg488Pro	p.R488P	ENST00000288368	NM_024870.2	488	cGt/cCt	13/40	0.594038460726425	1	FACETS	0.81	0.663	0.966	0.81	0.663	0.966	CLONAL	1	TRUE	0	0.594038460726425	1		499	76	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610068	81610068	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	17	502	0	ENST00000298171.2:c.1666C>T	p.Pro556Ser	p.P556S	ENST00000298171	NM_000369.2	556	Cct/Tct	10/10	0.594038460726425	3	FACETS	0.516	0.388	0.665	0.258	0.194	0.333	SUBCLONAL	1	TRUE	1	0.594038460726425	3		502	144	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118370615	118370615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	79	261	0	ENST00000534358.1:c.6145C>T	p.Pro2049Ser	p.P2049S	ENST00000534358	NM_005933.3	2049	Cct/Tct	24/36	0.379244970047942	5	FACETS	1	0.941	1	1	0.941	1	CLONAL	3	TRUE	2	0.594038460726425	5		261	159	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400039	139400039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780500109	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	174	978	1	ENST00000277541.6:c.4309G>A	p.Gly1437Arg	p.G1437R	ENST00000277541	NM_017617.3	1437	Ggg/Agg	25/34	0.205280788460559	4	FACETS	1	0.954	1	1	0.954	1	INDETERMINATE	2	TRUE	2	0.594038460726425	4		979	452	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375438	15375438	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	219	923	0	ENST00000263377.2:c.989C>T	p.Pro330Leu	p.P330L	ENST00000263377	NM_058243.2	330	cCt/cTt	6/20	0.249192774286564	3	FACETS	1	0.991	1	0.828	0.784	0.871	INDETERMINATE	2	TRUE	0	0.594038460726425	3		923	385	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964454	70964454	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	11	662	0	ENST00000276594.2:c.1574C>A	p.Ser525Tyr	p.S525Y	ENST00000276594	NM_024504.3	525	tCt/tAt	8/8	0.594038460726425	1	FACETS	0.299	0.209	0.408	0.299	0.209	0.408	SUBCLONAL	1	TRUE	0	0.594038460726425	1		662	87	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639407	3639407	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	151	882	1	ENST00000294008.3:c.4232G>A	p.Arg1411Lys	p.R1411K	ENST00000294008	NM_032444.2	1411	aGa/aAa	12/15	0.304602583035213	3	FACETS	0.911	0.844	0.978	0.911	0.844	0.978	INDETERMINATE	2	TRUE	1	0.594038460726425	3		883	362	SUCCESS
AR	367	MSKCC	GRCh37	X	66942737	66942737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1419690127	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	22	236	0	ENST00000374690.3:c.2518G>A	p.Asp840Asn	p.D840N	ENST00000374690	NM_000044.3	840	Gat/Aat	7/8	1	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.594038460726425	1		236	39	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858448	9858448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	35	535	0	ENST00000330684.3:c.2953C>T	p.Pro985Ser	p.P985S	ENST00000330684	NM_001134407.1	985	Cct/Tct	13/13	0.304602583035213	3	FACETS	0.967	0.804	1	0.484	0.402	0.572	INDETERMINATE	1	TRUE	1	0.594038460726425	3		535	158	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955383	48955383	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	16	158	0	ENST00000267163.4:c.1499G>A	p.Arg500Lys	p.R500K	ENST00000267163	NM_000321.2	500	aGa/aAa	17/27	0.517612823977124	4	FACETS	0.753	0.575	0.95			1	CLONAL	2	TRUE	NA	0.594038460726425	4		158	57	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553435	106553435	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs77256382	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	93	455	1	ENST00000369096.4:c.1400C>T	p.Pro467Leu	p.P467L	ENST00000369096	NM_001198.3	467	cCg/cTg	5/7	0.511259904633881	5	FACETS	0.894	0.803	0.989			1	CLONAL	2	TRUE	NA	0.594038460726425	5		456	331	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528570	89528570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	14	252	0	ENST00000336596.2:c.2870C>T	p.Thr957Ile	p.T957I	ENST00000336596	NM_005233.5	957	aCc/aTc	17/17	NA	2	FACETS	0.628	0.463	0.82			1	INDETERMINATE	1	TRUE	NA	0.594038460726425	2		252	75	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2225413	2225413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	164	409	0	ENST00000398665.3:c.3623C>T	p.Ser1208Phe	p.S1208F	ENST00000398665	NM_032482.2	1208	tCc/tTc	26/28	0.249192774286564	3	FACETS	1	0.957	1	0.69	0.644	0.736	INDETERMINATE	2	TRUE	0	0.594038460726425	3		409	346	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073274	8073274	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	150	316	0	ENST00000377482.5:c.1385C>T	p.Pro462Leu	p.P462L	ENST00000377482	NM_018948.3	462	cCt/cTt	4/4	0.496696706780739	3	FACETS	1	0.965	1			1	CLONAL	2	TRUE	NA	0.594038460726425	3		316	309	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258508	16258508	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199583436	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	91	647	0	ENST00000375759.3:c.5773G>A	p.Glu1925Lys	p.E1925K	ENST00000375759	NM_015001.2	1925	Gag/Aag	11/15	0.594038460726425	6	FACETS	0.816	0.729	0.907			1	CLONAL	2	TRUE	NA	0.594038460726425	6		647	411	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261651	16261652	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	180	651	0	ENST00000375759.3:c.8916_8917delinsTT	p.Leu2973Phe	p.L2973F	ENST00000375759	NM_015001.2	2972	gtCCtt/gtTTtt	11/15	0.594038460726425	6	FACETS	1	0.984	1			1	CLONAL	3	TRUE	NA	0.594038460726425	6		651	380	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809239	243809239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	23	403	0	ENST00000263826.5:c.385G>A	p.Gly129Arg	p.G129R	ENST00000263826	NM_005465.4	129	Gga/Aga	4/13	0.434004735660897	1	FACETS	0.801	0.646	0.965	0.801	0.646	0.965	CLONAL	1	TRUE	0	0.594038460726425	1		403	68	SUCCESS
EED	8726	MSKCC	GRCh37	11	85979520	85979520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746020326	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	41	334	0	ENST00000263360.6:c.883C>T	p.His295Tyr	p.H295Y	ENST00000263360	NM_003797.3	295	Cat/Tat	9/12	0.363422067347226	4	FACETS	1	0.96	1	0.743	0.631	0.864	CLONAL	1	TRUE	2	0.594038460726425	4		334	148	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416899	416900	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	63	461	0	ENST00000399788.2:c.3650_3651delinsAA	p.Arg1217Gln	p.R1217Q	ENST00000399788	NM_001042603.1	1217	cGG/cAA	23/28	0.363422067347226	4	FACETS	0.79	0.694	0.891	0.79	0.694	0.891	SUBCLONAL	2	TRUE	2	0.594038460726425	4		461	214	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022459	12022459	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	72	873	0	ENST00000396373.4:c.565A>T	p.Asn189Tyr	p.N189Y	ENST00000396373	NM_001987.4	189	Aat/Tat	5/8	0.363422067347226	4	FACETS	1	0.971	1	0.68	0.6	0.764	CLONAL	1	TRUE	2	0.594038460726425	4		873	284	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416660	49416660	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	162	418	0	ENST00000301067.7:c.16053-2A>G		p.X5351_splice	ENST00000301067	NM_003482.3	5351			0.594038460726425	5	FACETS	0.982	0.915	1	0.982	0.915	1	CLONAL	3	TRUE	2	0.594038460726425	5		418	350	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420111	49420111	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	64	665	0	ENST00000301067.7:c.15638C>G	p.Thr5213Arg	p.T5213R	ENST00000301067	NM_003482.3	5213	aCg/aGg	48/54	0.594038460726425	5	FACETS	1	0.902	1	0.348	0.303	0.397	CLONAL	1	TRUE	2	0.594038460726425	5		665	390	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433899	49433899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	88	1135	0	ENST00000301067.7:c.7654C>T	p.Pro2552Ser	p.P2552S	ENST00000301067	NM_003482.3	2552	Cct/Tct	31/54	0.594038460726425	5	FACETS	1	0.954	1	0.38	0.337	0.425	CLONAL	1	TRUE	2	0.594038460726425	5		1135	492	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912228	32912228	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	26	480	0	ENST00000380152.3:c.3736A>T	p.Asn1246Tyr	p.N1246Y	ENST00000380152		1246	Aat/Tat	11/27	0.299553646071474	4	FACETS	1	0.869	1			1	INDETERMINATE	1	TRUE	NA	0.594038460726425	4		480	126	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590792	95590792	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	17	347	0	ENST00000393063.1:c.1117del	p.Val373Ter	p.V373*	ENST00000393063	NM_030621.3	373	Gta/ta	9/28	0.594038460726425	3	FACETS	0.728	0.551	0.931	0.364	0.275	0.466	CLONAL	1	TRUE	1	0.594038460726425	3		347	102	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646235	3646235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1379412301	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	147	1085	0	ENST00000294008.3:c.1843C>T	p.Leu615Phe	p.L615F	ENST00000294008	NM_032444.2	615	Ctc/Ttc	8/15	0.304602583035213	3	FACETS	0.933	0.864	1	0.933	0.864	1	INDETERMINATE	2	TRUE	1	0.594038460726425	3		1085	344	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14031642	14031643	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TA	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	62	402	1	ENST00000311895.7:c.1831_1832delinsTA	p.Gly611Ter	p.G611*	ENST00000311895	NM_005236.2	611	GGa/TAa	9/11	0.304602583035213	3	FACETS	1	0.97	1	0.698	0.613	0.786	INDETERMINATE	1	TRUE	1	0.594038460726425	3		403	194	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863639	68863639	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1357766058	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	148	722	0	ENST00000261769.5:c.2378G>A	p.Ser793Asn	p.S793N	ENST00000261769	NM_004360.3	793	aGt/aAt	15/16	0.304602583035213	3	FACETS	0.923	0.855	0.992	0.923	0.855	0.992	INDETERMINATE	2	TRUE	1	0.594038460726425	3		722	350	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993833	72993834	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	33	694	0	ENST00000268489.5:c.211_212delinsTT	p.Pro71Phe	p.P71F	ENST00000268489	NM_006885.3	71	CCc/TTc	2/10	0.304602583035213	3	FACETS	0.833	0.686	0.994	0.416	0.343	0.497	INDETERMINATE	1	TRUE	1	0.594038460726425	3		694	173	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664428	29664428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774161532	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	64	481	0	ENST00000356175.3:c.6407C>T	p.Ser2136Leu	p.S2136L	ENST00000356175	NM_000267.3	2136	tCa/tTa	42/57	0.594038460726425	5	FACETS	0.961	0.845	1	0.641	0.563	0.722	CLONAL	2	TRUE	2	0.594038460726425	5		481	212	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763346	59763346	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	41	627	0	ENST00000259008.2:c.2756C>T	p.Ser919Leu	p.S919L	ENST00000259008	NM_032043.2	919	tCa/tTa	19/20	0.530100327334605	3	FACETS	1	0.893	1	0.536	0.453	0.625	CLONAL	1	TRUE	1	0.594038460726425	3		627	167	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120235	70120235	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	103	789	0	ENST00000245479.2:c.1237C>T	p.His413Tyr	p.H413Y	ENST00000245479	NM_000346.3	413	Cac/Tac	3/3	0.530100327334605	3	FACETS	0.83	0.755	0.907	0.83	0.755	0.907	CLONAL	2	TRUE	1	0.594038460726425	3		789	271	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212296	36212297	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	69	787	1	ENST00000222270.7:c.2047_2048delinsTT	p.Pro683Phe	p.P683F	ENST00000222270	NM_014727.1	683	CCt/TTt	3/37	0.249192774286564	3	FACETS	0.656	0.573	0.746	0.219	0.191	0.249	INDETERMINATE	1	TRUE	0	0.594038460726425	3		788	459	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794850	42794850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761981948	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	225	810	0	ENST00000575354.2:c.1930G>A	p.Gly644Arg	p.G644R	ENST00000575354	NM_015125.3	644	Gga/Aga	10/20	0.594038460726425	4	FACETS	0.892	0.842	0.943			1	CLONAL	3	TRUE	NA	0.594038460726425	4		810	451	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905321	50905321	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760402496	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	56	1137	0	ENST00000440232.2:c.529C>T	p.Arg177Cys	p.R177C	ENST00000440232	NM_002691.3	177	Cgc/Tgc	5/27	NA	2	FACETS	0.496	0.426	0.572			1	INDETERMINATE	1	TRUE	NA	0.594038460726425	2		1137	380	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464523	25464523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	201	840	0	ENST00000264709.3:c.1990G>A	p.Glu664Lys	p.E664K	ENST00000264709	NM_175629.2	664	Gag/Aag	17/23	0.434004735660897	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.594038460726425	1		840	367	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966102	25966102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	34	678	1	ENST00000435504.4:c.3104C>T	p.Pro1035Leu	p.P1035L	ENST00000435504		1035	cCc/cTc	13/13	0.434004735660897	1	FACETS	0.345	0.284	0.414	0.345	0.284	0.414	SUBCLONAL	1	TRUE	0	0.594038460726425	1		679	233	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794961	242794961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	263	1053	1	ENST00000334409.5:c.248C>T	p.Pro83Leu	p.P83L	ENST00000334409	NM_005018.2	83	cCc/cTc	2/5	0.249192774286564	3	FACETS	1	0.981	1	0.714	0.677	0.752	INDETERMINATE	2	TRUE	0	0.594038460726425	3		1054	536	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265034	46265034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781339192	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	67	475	0	ENST00000371998.3:c.1904C>T	p.Ser635Phe	p.S635F	ENST00000371998		635	tCc/tTc	12/23	0.594038460726425	5	FACETS	0.767	0.673	0.867	0.511	0.449	0.578	SUBCLONAL	2	TRUE	2	0.594038460726425	5		475	278	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145509	24145510	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	139	723	2	ENST00000263121.7:c.528_529delinsTT	p.His177Tyr	p.H177Y	ENST00000263121	NM_003073.3	176	atCCat/atTTat	5/9	0.430502012251151	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	2	0.594038460726425	4		725	350	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182315	38182315	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	32	494	0	ENST00000396334.3:c.751A>G	p.Lys251Glu	p.K251E	ENST00000396334	NM_002468.4	251	Aaa/Gaa	4/5	0.594038460726425	3	FACETS	0.656	0.536	0.789	0.328	0.268	0.395	SUBCLONAL	1	TRUE	1	0.594038460726425	3		494	213	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588740	52588741	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	26	629	1	ENST00000394830.3:c.4287_4288delinsAA	p.Gly1430Ser	p.G1430S	ENST00000394830	NM_018313.4	1429	ccGGgt/ccAAgt	27/30	0.594038460726425	3	FACETS	0.487	0.387	0.6	0.244	0.193	0.3	SUBCLONAL	1	TRUE	1	0.594038460726425	3		630	233	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167709	185167710	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	11	502	0	ENST00000265026.3:c.1032_1033delinsAA	p.Trp344_Glu345delinsTer	p.W344_E345delins*	ENST00000265026	NM_004721.4	344	tgGGag/tgAAag	6/14	0.364903108411514	1	FACETS	0.219	0.152	0.301	0.219	0.152	0.301	SUBCLONAL	1	TRUE	0	0.594038460726425	1		502	119	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584528	189584528	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	50	402	0	ENST00000264731.3:c.824A>T	p.Tyr275Phe	p.Y275F	ENST00000264731	NM_003722.4	275	tAt/tTt	6/14	0.364903108411514	1	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	0	0.594038460726425	1		402	118	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807690	1807995	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTGGAGTAGGCTGGGCCCTGCCCTGAGATGCTGGGAGCAGCGGGGAGAGGTGGAGAGGCTTCAGCCCTGCCTCCCACCCCTTCCCCAGTGCATCCACAGGGACCTGGCTGCCCGCAATGTGCTGGTGACCGAGGACAACGTGATGAAGATCGCAGACTTCGGGCTGGCCCGGGACGTGCACAACCTCGACTACTACAAGAAGACGACCAACGTGAGCCCGGCCCTGGGGTGCGGGGGTGGGGGTCATGCCAGTAGGACGCCTGGCGCCAACACCGCCTTCCCACACCCTCCCAGGGCCGGCTGCCC	GTGGAGTAGGCTGGGCCCTGCCCTGAGATGCTGGGAGCAGCGGGGAGAGGTGGAGAGGCTTCAGCCCTGCCTCCCACCCCTTCCCCAGTGCATCCACAGGGACCTGGCTGCCCGCAATGTGCTGGTGACCGAGGACAACGTGATGAAGATCGCAGACTTCGGGCTGGCCCGGGACGTGCACAACCTCGACTACTACAAGAAGACGACCAACGTGAGCCCGGCCCTGGGGTGCGGGGGTGGGGGTCATGCCAGTAGGACGCCTGGCGCCAACACCGCCTTCCCACACCCTCCCAGGGCCGGCTGCCC	-	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	157	908	0	ENST00000260795.2:c.1836+26_1974del		p.X612_splice	ENST00000260795		612		13-14/17	0.238396867284379	2	FACETS	0.796	0.741	0.851	0.796	0.741	0.851	INDETERMINATE	2	TRUE	0	0.594038460726425	2		908	332	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808046	1808052	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GAGTGAC	GAGTGAC	-	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	165	1106	0	ENST00000260795.2:c.2023_2029del	p.Asp676GlyfsTer30	p.D676Gfs*30	ENST00000260795		674	caGAGTGAC/ca	14/17	0.238396867284379	2	FACETS	0.852	0.797	0.907	0.852	0.797	0.907	INDETERMINATE	2	TRUE	0	0.594038460726425	2		1106	326	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518848	187518848	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	60	344	0	ENST00000441802.2:c.12356T>G	p.Phe4119Cys	p.F4119C	ENST00000441802	NM_005245.3	4119	tTt/tGt	24/27	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.594038460726425	2		344	158	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522427	187522427	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	31	393	0	ENST00000441802.2:c.11636T>A	p.Leu3879Ter	p.L3879*	ENST00000441802	NM_005245.3	3879	tTg/tAg	21/27	1	2	FACETS	0.863	0.711	1	0.863	0.711	1	CLONAL	1	TRUE	1	0.594038460726425	2		393	121	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532921	187532921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	21	252	0	ENST00000441802.2:c.9472C>T	p.Arg3158Trp	p.R3158W	ENST00000441802	NM_005245.3	3158	Cgg/Tgg	14/27	1	2	FACETS	0.93	0.736	1	0.93	0.736	1	CLONAL	1	TRUE	1	0.594038460726425	2		252	76	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394911	394911	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	94	515	0	ENST00000380956.4:c.307A>T	p.Lys103Ter	p.K103*	ENST00000380956	NM_001195286.1	103	Aag/Tag	3/9	0.346087519655941	1	FACETS	0.959	0.87	1	0.959	0.87	1	INDETERMINATE	1	TRUE	0	0.594038460726425	1		515	232	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977548	2977548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751008087	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	91	662	1	ENST00000396946.4:c.1136G>A	p.Arg379Gln	p.R379Q	ENST00000396946	NM_032415.4	379	cGg/cAg	8/25	0.304602583035213	3	FACETS	1	0.976	1	0.656	0.589	0.725	INDETERMINATE	1	TRUE	1	0.594038460726425	3		663	303	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435713	116435714	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	72	340	0	ENST00000397752.3:c.3803_3804delinsTT	p.Ser1268Phe	p.S1268F	ENST00000397752	NM_000245.2	1268	tCC/tTT	20/21	0.594038460726425	5	FACETS	1	0.966	1	0.817	0.729	0.908	CLONAL	2	TRUE	2	0.594038460726425	5		340	187	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453094	140453094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	11	337	0	ENST00000288602.6:c.1841C>T	p.Ser614Phe	p.S614F	ENST00000288602	NM_004333.4	614	tCt/tTt	15/18	0.530100327334605	3	FACETS	0.372	0.258	0.512	0.186	0.129	0.256	SUBCLONAL	1	TRUE	1	0.594038460726425	3		337	129	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132757	152132758	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	235	543	2	ENST00000262189.6:c.114_115delinsTT	p.Arg39Trp	p.R39W	ENST00000262189	NM_170606.2	38	ggCCgg/ggTTgg	1/59	0.530100327334605	3	FACETS	0.989	0.932	1	0.989	0.932	1	CLONAL	2	TRUE	1	0.594038460726425	3		545	519	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38315038	38315038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1445177402	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	88	639	0	ENST00000425967.3:c.26G>A	p.Arg9Lys	p.R9K	ENST00000425967	NM_001174067.1	9	aGg/aAg	3/19	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.594038460726425	2		639	203	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971104	21971104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	112	747	0	ENST00000304494.5:c.254del	p.Ala85ValfsTer61	p.A85Vfs*61	ENST00000304494	NM_000077.4	85	gCt/gt	2/3	0.594038460726425	1	FACETS	0.762	0.71	0.812	1	0.989	1	SUBCLONAL	2	TRUE	0	0.594038460726425	1		747	174	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391110	139391111	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	130	1049	1	ENST00000277541.6:c.7080_7081delinsTT	p.Gln2361Ter	p.Q2361*	ENST00000277541	NM_017617.3	2360	tcCCag/tcTTag	34/34	0.205280788460559	4	FACETS	1	0.921	1	1	0.921	1	INDETERMINATE	2	TRUE	2	0.594038460726425	4		1050	348	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395153	139395153	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	152	1157	1	ENST00000277541.6:c.5785G>A	p.Glu1929Lys	p.E1929K	ENST00000277541	NM_017617.3	1929	Gag/Aag	31/34	0.205280788460559	4	FACETS	0.843	0.777	0.911	0.843	0.777	0.911	INDETERMINATE	2	TRUE	2	0.594038460726425	4		1158	484	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412446	63412446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1271751294	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	45	498	1	ENST00000330258.3:c.721C>T	p.Pro241Ser	p.P241S	ENST00000330258	NM_152424.3	241	Cca/Tca	2/2	1	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.594038460726425	1		499	83	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611256	100611256	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	48	240	0	ENST00000308731.7:c.1350G>A	p.Met450Ile	p.M450I	ENST00000308731	NM_000061.2	450	atG/atA	15/19	1	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.594038460726425	1		240	84	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099959	27099962	+	frameshift_variant	Frame_Shift_Del	DEL	CCCT	CCCT	TTC	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	90	843	1	ENST00000324856.7:c.3838_3841delinsTTC	p.Pro1280PhefsTer9	p.P1280Ffs*9	ENST00000324856	NM_006015.4	1280	CCCTat/TTCat	15/20	0.530100327334605	3	FACETS	1	0.932	1	0.528	0.472	0.587	CLONAL	1	TRUE	1	0.594038460726425	3		844	372	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976853	2976855	+	missense_variant	Missense_Mutation	TNP	CTC	CTC	TTT	novel	NA	P-0046997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	60	657	0	ENST00000396946.4:c.1157_1159delinsAAA	p.Arg386_Asp387delinsGlnAsn	p.R386_D387delinsQN	ENST00000396946	NM_032415.4	386	cGAGat/cAAAat	9/25	0.304602583035213	3	FACETS	1	0.912	1	0.53	0.462	0.603	INDETERMINATE	1	TRUE	1	0.594038460726425	3		657	247	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140507849	140507849	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs727504571	NA	P-0046998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	38	462	0	ENST00000288602.6:c.622A>G	p.Ile208Val	p.I208V	ENST00000288602	NM_004333.4	208	Att/Gtt	5/18	1	2	FACETS	0.51	0.422	0.61	0.51	0.422	0.61	SUBCLONAL	1	FALSE	1	0.308891635437778	2		462	482	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559090	29559090	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1223905930	NA	P-0047000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	46	85	0	ENST00000356175.3:c.3198-1G>A		p.X1066_splice	ENST00000356175	NM_000267.3	1066			0.392469566956875	1	FACETS	0.849	0.737	0.963	1	0.973	1	CLONAL	2	TRUE	0	0.392469566956875	1		85	111	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162735805	162735805	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	39	440	0	ENST00000367921.3:c.1114A>G	p.Asn372Asp	p.N372D	ENST00000367921	NM_006182.2	372	Aac/Gac	10/18	1	2	FACETS	0.295	0.243	0.352	0.295	0.243	0.352	SUBCLONAL	1	TRUE	1	0.392469566956875	2		440	674	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303838	91303838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775209685	NA	P-0047000-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	57	302	0	ENST00000355112.3:c.1235C>T	p.Thr412Met	p.T412M	ENST00000355112	NM_000057.2	412	aCg/aTg	7/22	1	2	FACETS	0.905	0.781	1	0.905	0.781	1	CLONAL	1	TRUE	1	0.392469566956875	2		302	321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0047008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	64	852	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.29205776540623	1	FACETS	0.581	0.503	0.666	0.581	0.503	0.666	SUBCLONAL	1	FALSE	0	0.29205776540623	1		852	644	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0047009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	204	883	1	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	0.979	0.91	1	0.979	0.91	1	CLONAL	1	TRUE	1	0.524472922138949	2		884	795	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441414	52441414	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1553645838	NA	P-0047009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	137	502	0	ENST00000460680.1:c.437+1G>T		p.X146_splice	ENST00000460680	NM_004656.3	146			0.51680826998811	1	FACETS	0.981	0.902	1	0.981	0.902	1	CLONAL	1	TRUE	0	0.524472922138949	1		502	393	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374293	138374293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	34	537	0	ENST00000289153.2:c.3151G>A	p.Glu1051Lys	p.E1051K	ENST00000289153	NM_006219.2	1051	Gaa/Aaa	22/22	1	2	FACETS	0.261	0.213	0.315	0.261	0.213	0.315	SUBCLONAL	1	TRUE	1	0.610417945199175	2		537	427	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141427	11141427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	142	719	1	ENST00000358026.2:c.3404G>A	p.Arg1135Gln	p.R1135Q	ENST00000358026	NM_001128849.1	1135	cGg/cAg	25/36	0.199752644562288	2	FACETS	0.611	0.557	0.667	0.305	0.278	0.334	INDETERMINATE	1	TRUE	0	0.610417945199175	2		720	762	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24133942	24133942	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0047011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	78	223	0	ENST00000263121.7:c.94-1G>A		p.X32_splice	ENST00000263121	NM_003073.3	32			0.201225173894808	3	FACETS	1	0.952	1	0.379	0.337	0.424	INDETERMINATE	1	TRUE	0	0.610417945199175	3		223	293	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159091	24159091	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	375	480	0	ENST00000263121.7:c.763G>T	p.Glu255Ter	p.E255*	ENST00000263121	NM_003073.3	255	Gag/Tag	6/9	0.201225173894808	3	FACETS	1	0.994	1	0.803	0.77	0.835	INDETERMINATE	2	TRUE	0	0.610417945199175	3		480	666	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0047012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	137	272	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.456878481427058	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.456878481427058	2		272	277	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	rs786202799	NA	P-0047012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	363	720	0	ENST00000269305.4:c.376-2A>T		p.X126_splice	ENST00000269305	NM_001126112.2	126			NA	2	FACETS	0.982	0.937	1			1	INDETERMINATE	2	TRUE	NA	0.456878481427058	2		720	809	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158132	27158132	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773256013	NA	P-0047012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	73	333	0	ENST00000380036.4:c.356G>A	p.Arg119His	p.R119H	ENST00000380036	NM_000459.3	119	cGt/cAt	2/23	0.387535420916624	5	FACETS	0.955	0.836	1	0.318	0.278	0.361	CLONAL	1	TRUE	2	0.456878481427058	5		333	564	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16001703	16001703	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1176533842	NA	P-0047012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	94	274	0	ENST00000268712.3:c.2798G>A	p.Arg933Gln	p.R933Q	ENST00000268712	NM_006311.3	933	cGa/cAa	21/46	0.411921916306369	1	FACETS	0.833	0.747	0.924	0.833	0.747	0.924	CLONAL	1	TRUE	0	0.456878481427058	1		274	381	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061086	38061186	+	frameshift_variant	Frame_Shift_Del	DEL	AGAGGCGCCAGAGGGGTCCTTGCGGCTCTCAGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGC	AGAGGCGCCAGAGGGGTCCTTGCGGCTCTCAGGGCCGCCCTTGGCGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGC	-	novel	NA	P-0047012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	143	335	0	ENST00000250448.2:c.803_903del	p.Cys268Ter	p.C268*	ENST00000250448	NM_004496.3	268	tGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGGCGCCAAGGGCGGCCCTGAGAGCCGCAAGGACCCCTCTGGCGCCTCT/t	2/2	0.294495011481864	2	FACETS	1	0.984	1	0.652	0.599	0.707	CLONAL	1	TRUE	0	0.456878481427058	2		335	480	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0047028-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	135	336	1	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	0.44809704808371	3	FACETS	0.966	0.887	1	0.966	0.887	1	CLONAL	2	TRUE	1	0.447979396879314	3		337	382	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910797	29910797	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs41559912	NA	P-0047028-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	159	619	1	ENST00000376809.5:c.337G>T	p.Glu113Ter	p.E113*	ENST00000376809	NM_002116.7	113	Gag/Tag	2/8	0.378199423448119	4	FACETS	1	0.964	1	0.548	0.502	0.596	CLONAL	1	TRUE	2	0.447979396879314	4		620	938	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599994	10599994	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047028-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	382	745	1	ENST00000171111.5:c.1582C>T	p.Gln528Ter	p.Q528*	ENST00000171111	NM_203500.1	528	Cag/Tag	5/6	0.421099561705329	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.447979396879314	2		746	849	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647264	2647264	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1291358013	NA	P-0047028-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	98	429	0	ENST00000342085.4:c.1542C>G	p.Phe514Leu	p.F514L	ENST00000342085	NM_002613.4	514	ttC/ttG	13/14	1	2	FACETS	0.891	0.798	0.989	0.891	0.798	0.989	CLONAL	1	TRUE	1	0.447979396879314	2		429	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579854	7579854	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0047028-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	313	665	0	ENST00000269305.4:c.59C>G	p.Ser20Ter	p.S20*	ENST00000269305	NM_001126112.2	20	tCa/tGa	2/11	0.421099561705329	2	FACETS	0.96	0.911	1	0.96	0.911	1	CLONAL	2	TRUE	0	0.447979396879314	2		665	728	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295347	1295348	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0047028-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2238	383	474	5				ENST00000310581	NM_198253.2	-/1132			0.447979396879314	18	FACETS	0.997	0.942	1			1	CLONAL	3	TRUE	NA	0.447979396879314	18		479	2621	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2493210	2493210	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047028-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	151	506	1	ENST00000355716.4:c.650C>G	p.Ser217Cys	p.S217C	ENST00000355716	NM_003820.2	217	tCc/tGc	6/8	0.44809704808371	3	FACETS	1	0.938	1	0.515	0.471	0.561	CLONAL	1	TRUE	1	0.447979396879314	3		507	801	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918464	94918464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047028-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	66	365	0	ENST00000536441.1:c.718G>A	p.Asp240Asn	p.D240N	ENST00000536441	NM_144665.3	240	Gac/Aac	5/10	0.421099561705329	2	FACETS	0.65	0.566	0.741	0.325	0.283	0.371	SUBCLONAL	1	TRUE	0	0.447979396879314	2		365	453	SUCCESS
BLM	641	MSKCC	GRCh37	15	91290647	91290647	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047028-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	57	247	0	ENST00000355112.3:c.25C>G	p.Leu9Val	p.L9V	ENST00000355112	NM_000057.2	9	Cta/Gta	2/22	0.44809704808371	3	FACETS	0.754	0.649	0.868	0.377	0.324	0.434	SUBCLONAL	1	TRUE	1	0.447979396879314	3		247	413	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858241	9858241	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047028-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	92	372	0	ENST00000330684.3:c.3160G>C	p.Glu1054Gln	p.E1054Q	ENST00000330684	NM_001134407.1	1054	Gaa/Caa	13/13	1	2	FACETS	0.992	0.887	1	0.992	0.887	1	CLONAL	1	TRUE	1	0.447979396879314	2		372	414	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989592	212989592	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047028-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	62	250	0	ENST00000342788.4:c.119C>G	p.Ser40Cys	p.S40C	ENST00000342788	NM_005235.2	40	tCt/tGt	2/28	0.44809704808371	3	FACETS	1	0.886	1	0.51	0.443	0.582	CLONAL	1	TRUE	1	0.447979396879314	3		250	332	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250668	26250668	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047028-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	115	585	0	ENST00000446824.2:c.166C>G	p.Gln56Glu	p.Q56E	ENST00000446824	NM_021018.2	56	Cag/Gag	1/1	0.378199423448119	4	FACETS	0.874	0.786	0.966	0.437	0.393	0.483	CLONAL	1	TRUE	2	0.447979396879314	4		585	851	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527493	157527493	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047028-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	73	337	0	ENST00000346085.5:c.5218G>T	p.Asp1740Tyr	p.D1740Y	ENST00000346085	NM_020732.3	1740	Gac/Tac	20/20	0.34254619334495	4	FACETS	0.942	0.826	1	0.471	0.413	0.534	CLONAL	1	TRUE	2	0.447979396879314	4		337	501	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683617	162683617	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047028-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	254	531	0	ENST00000366898.1:c.352G>T	p.Gly118Trp	p.G118W	ENST00000366898	NM_004562.2	118	Ggg/Tgg	3/12	0.34254619334495	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.447979396879314	4		531	787	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508010	106508010	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs777512949	NA	P-0047028-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	84	139	0	ENST00000359195.3:c.4G>C	p.Glu2Gln	p.E2Q	ENST00000359195	NM_002649.2	2	Gag/Cag	2/11	0.44809704808371	3	FACETS	1	0.916	1	1	0.916	1	CLONAL	2	TRUE	1	0.447979396879314	3		139	225	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396781	139396781	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047028-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	132	814	0	ENST00000277541.6:c.5327C>T	p.Ser1776Phe	p.S1776F	ENST00000277541	NM_017617.3	1776	tCt/tTt	28/34	0.44809704808371	5	FACETS	0.763	0.691	0.84	0.254	0.23	0.28	SUBCLONAL	1	TRUE	2	0.447979396879314	5		814	1291	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20153875	20153875	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047028-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	74	164	0	ENST00000379607.5:c.185G>C	p.Arg62Thr	p.R62T	ENST00000379607	NM_001412.3	62	aGa/aCa	3/7	1	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.447979396879314	1		164	188	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873715	37873715	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	204	812	1	ENST00000269571.5:c.1880C>T	p.Pro627Leu	p.P627L	ENST00000269571		627	cCc/cTc	15/27	1	2	FACETS	1	0.976	1	1	0.995	1	CLONAL	3	FALSE	1	0.191393612314602	2		813	644	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0047031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	71	209	0	ENST00000288602.6:c.1397G>T	p.Gly466Val	p.G466V	ENST00000288602	NM_004333.4	466	gGa/gTa	11/18	1	2	FACETS	0.909	0.808	1	1	0.987	1	CLONAL	4	FALSE	1	0.191393612314602	2		209	204	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0047031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	163	907	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.191393612314602	1	FACETS	1	0.945	1	1	0.994	1	CLONAL	3	FALSE	0	0.191393612314602	1		907	500	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913237	NA	P-0047031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	96	521	1	ENST00000369535.4:c.35G>T	p.Gly12Val	p.G12V	ENST00000369535	NM_002524.4	12	gGt/gTt	2/7	1	2	FACETS	0.939	0.844	1	1	0.989	1	CLONAL	3	FALSE	1	0.191393612314602	2		522	356	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041007	47041007	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	115	436	0	ENST00000377604.3:c.1537G>T	p.Glu513Ter	p.E513*	ENST00000377604	NM_001204468.1	513	Gag/Tag	14/24	0.179176255002232	2	FACETS	1	0.926	1			1	CLONAL	5	FALSE	NA	0.191393612314602	2		436	239	SUCCESS
AR	367	MSKCC	GRCh37	X	66942786	66942786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs9332971	NA	P-0047031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	100	310	1	ENST00000374690.3:c.2567G>A	p.Arg856His	p.R856H	ENST00000374690	NM_000044.3	856	cGc/cAc	7/8	0.179176255002232	2	FACETS	1	0.949	1			1	CLONAL	5	FALSE	NA	0.191393612314602	2		311	199	SUCCESS
RET	5979	MSKCC	GRCh37	10	43613888	43613888	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	73	855	1	ENST00000355710.3:c.2354del	p.Pro785HisfsTer84	p.P785Hfs*84	ENST00000355710	NM_020975.4	784	caC/ca	13/20	1	2	FACETS	1	0.941	1	1	0.984	1	CLONAL	2	FALSE	1	0.191393612314602	2		856	343	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769051	112769051	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	11	611	1	ENST00000369452.4:c.1330C>T	p.Leu444Phe	p.L444F	ENST00000369452	NM_007373.3	444	Ctt/Ttt	7/9	1	2	FACETS	0.635	0.439	0.878	0.635	0.439	0.878	SUBCLONAL	1	FALSE	1	0.191393612314602	2		612	181	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204925	94204925	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	26	507	0	ENST00000323929.3:c.660G>T	p.Arg220Ser	p.R220S	ENST00000323929	NM_005591.3	220	agG/agT	8/20	1	2	FACETS	0.854	0.684	1	1	0.945	1	CLONAL	2	FALSE	1	0.191393612314602	2		507	159	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319080	62319080	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	143	944	0	ENST00000360203.5:c.1438G>T	p.Gly480Cys	p.G480C	ENST00000360203	NM_001283009.1	480	Ggc/Tgc	17/35	0.143478082932258	0	FACETS	1	0.938	1			1	CLONAL	2	FALSE	0	0.191393612314602	0		944	587	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508695	106508695	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047031-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	99	682	1	ENST00000359195.3:c.689G>T	p.Ser230Ile	p.S230I	ENST00000359195	NM_002649.2	230	aGc/aTc	2/11	1	2	FACETS	1	0.965	1	1	0.989	1	CLONAL	2	FALSE	1	0.191393612314602	2		683	442	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0047047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	80	220	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.98	0.879	1	1	0.985	1	CLONAL	2	TRUE	1	0.381651405446452	2		221	214	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750600586	NA	P-0047047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	384	850	0	ENST00000269305.4:c.413C>T	p.Ala138Val	p.A138V	ENST00000269305	NM_001126112.2	138	gCc/gTc	5/11	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	2	TRUE	NA	0.381651405446452	2		850	963	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0047047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	245	547	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	NA	2	FACETS	0.962	0.905	1			1	INDETERMINATE	2	TRUE	NA	0.381651405446452	2		547	667	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918920	76918921	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	52	219	0	ENST00000373344.5:c.4070dup	p.Thr1358AspfsTer4	p.T1358Dfs*4	ENST00000373344	NM_000489.3	1357	aag/aaAg	12/35	1	1	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	0	0.381651405446452	1		219	212	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907844	76907844	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0047047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	19	62	1	ENST00000373344.5:c.4318-1G>T		p.X1440_splice	ENST00000373344	NM_000489.3	1440			1	1	FACETS	0.79	0.626	0.963	1	0.93	1	CLONAL	2	TRUE	0	0.381651405446452	1		63	51	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972664	76972664	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0047047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	59	198	0	ENST00000373344.5:c.77C>G	p.Ser26Ter	p.S26*	ENST00000373344	NM_000489.3	26	tCa/tGa	2/35	1	1	FACETS	1	0.897	1	1	0.982	1	CLONAL	2	TRUE	0	0.381651405446452	1		198	124	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132561	11132561	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555778797	NA	P-0047048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	155	853	0	ENST00000358026.2:c.2777A>G	p.Asn926Ser	p.N926S	ENST00000358026	NM_001128849.1	926	aAc/aGc	19/36	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.500779346482788	2		853	599	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574919	64575049	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGAGGGGAAGCTGAAGCTCAGGAAGGGAAAGTGCCCCTGCCCAGGGTCCCACAGCAAGTCAAGTCTGGCCTAGCCCAGTCCTGCCCCATTGGCTCAGCCCTCACCTGCTGCAGCTGCAGAAGCTCCAGCG	AGGAGGGGAAGCTGAAGCTCAGGAAGGGAAAGTGCCCCTGCCCAGGGTCCCACAGCAAGTCAAGTCTGGCCTAGCCCAGTCCTGCCCCATTGGCTCAGCCCTCACCTGCTGCAGCTGCAGAAGCTCCAGCG	-	novel	NA	P-0047048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	84	249	1	ENST00000312049.6:c.758_783+105del		p.X253_splice	ENST00000312049	NM_130799.2	253		4/10	1	2	FACETS	1	0.978	1	1	0.989	1	CLONAL	2	TRUE	1	0.500779346482788	2		250	137	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577278	64577278	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	115	776	0	ENST00000312049.6:c.304G>T	p.Asp102Tyr	p.D102Y	ENST00000312049	NM_130799.2	102	Gac/Tac	2/10	1	2	FACETS	0.955	0.865	1	0.955	0.865	1	CLONAL	1	TRUE	1	0.500779346482788	2		776	481	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380243	25380244	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGTACTGGTCCCTCATTGCAC	novel	NA	P-0047048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	56	452	0	ENST00000311936.3:c.194_214dup	p.Ser65_Tyr71dup	p.S65_Y71dup	ENST00000311936	NM_004985.3	65	atg/aGTGCAATGAGGGACCAGTACAtg	3/5	0.139539208391277	0	FACETS	0.222	0.19	0.257			1	INDETERMINATE	1	TRUE	0	0.500779346482788	0		452	502	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440733	56440733	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047048-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	85	623	0	ENST00000407977.2:c.485T>C	p.Val162Ala	p.V162A	ENST00000407977		162	gTg/gCg	5/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.500779346482788	2		623	260	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0047049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	476	430	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.544248794789414	3	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.544248794789414	3		430	1029	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023209	27023225	+	frameshift_variant	Frame_Shift_Del	DEL	GAACGCGGGCCCTAGGC	GAACGCGGGCCCTAGGC	AACG	novel	NA	P-0047049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	62	141	0	ENST00000324856.7:c.315_331delinsAACG	p.Asn106ThrfsTer4	p.N106Tfs*4	ENST00000324856	NM_006015.4	105	ggGAACGCGGGCCCTAGGCcc/ggAACGcc	1/20	0.544248794789414	1	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	0	0.544248794789414	1		141	159	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858349	9858349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775756583	NA	P-0047050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	83	434	3	ENST00000330684.3:c.3052G>A	p.Val1018Met	p.V1018M	ENST00000330684	NM_001134407.1	1018	Gtg/Atg	13/13	1	2	FACETS	0.92	0.815	1	0.92	0.815	1	CLONAL	1	TRUE	1	0.371096917435482	2		437	486	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	51	516	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.72182436886677	2		516	140	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937694	76937694	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1184990999	NA	P-0047051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	27	252	0	ENST00000373344.5:c.3054G>T	p.Lys1018Asn	p.K1018N	ENST00000373344	NM_000489.3	1018	aaG/aaT	9/35	1	2	FACETS	0.157	0.124	0.194	0.157	0.124	0.194	SUBCLONAL	1	TRUE	1	0.72182436886677	2		252	478	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720671	89720671	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587782607	NA	P-0047051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	118	137	0	ENST00000371953.3:c.822G>A	p.Trp274Ter	p.W274*	ENST00000371953	NM_000314.4	274	tgG/tgA	8/9	0.72182436886677	1	FACETS	0.832	0.767	0.899	0.832	0.767	0.899	CLONAL	1	TRUE	0	0.72182436886677	1		137	251	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654643	67654643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs968244943	NA	P-0047051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	17	447	0	ENST00000264010.4:c.1130G>A	p.Arg377His	p.R377H	ENST00000264010	NM_006565.3	377	cGt/cAt	6/12	0.72182436886677	1	FACETS	0.099	0.073	0.129	0.099	0.073	0.129	SUBCLONAL	1	TRUE	0	0.72182436886677	1		447	305	SUCCESS
APC	324	MSKCC	GRCh37	5	112176752	112176752	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	110	125	0	ENST00000257430.4:c.5462del	p.Lys1821ArgfsTer42	p.K1821Rfs*42	ENST00000257430	NM_000038.5	1821	Aag/ag	16/16	1	2	FACETS	0.929	0.845	1	0.929	0.845	1	CLONAL	1	TRUE	1	0.72182436886677	2		125	328	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0047052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	369	277	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.789031424544619	2		277	681	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0047053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	257	731	7	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	NA	2	FACETS	0.902	0.852	0.952			1	INDETERMINATE	2	TRUE	NA	0.494689632981523	2		738	576	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223640	55223663	+	splice_donor_variant,intron_variant	Splice_Site	DEL	GTAGGAAGCCCGCCGGTGTGCGGA	GTAGGAAGCCCGCCGGTGTGCGGA	-	novel	NA	P-0047053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	70	509	0	ENST00000275493.2:c.1006+1_1006+24del		p.X336_splice	ENST00000275493	NM_005228.3	336			0.494689632981523	3	FACETS	0.776	0.678	0.88	0.388	0.339	0.44	SUBCLONAL	1	TRUE	1	0.494689632981523	3		509	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0047055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	119	593	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.317198725451829	1	FACETS	0.763	0.69	0.839	0.763	0.69	0.839	SUBCLONAL	1	TRUE	0	0.402013120345117	1		593	620	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	203	481	0	ENST00000397752.3:c.3028G>A	p.Asp1010Asn	p.D1010N	ENST00000397752	NM_000245.2	1010	Gat/Aat	14/21	0.241502353482011	2	FACETS	1	0.989	1	0.661	0.614	0.709	CLONAL	1	TRUE	0	0.402013120345117	2		481	764	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675310	241675310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157774951	NA	P-0047055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	113	355	0	ENST00000366560.3:c.512G>A	p.Ser171Asn	p.S171N	ENST00000366560	NM_000143.3	171	aGc/aAc	4/10	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.402013120345117	2		355	527	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479844	67479844	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	69	571	0	ENST00000327367.4:c.1151A>G	p.Tyr384Cys	p.Y384C	ENST00000327367	NM_005902.3	384	tAc/tGc	8/9	0.402013120345117	1	FACETS	0.552	0.481	0.628	0.552	0.481	0.628	SUBCLONAL	1	TRUE	0	0.402013120345117	1		571	497	SUCCESS
MET	4233	MSKCC	GRCh37	7	116409777	116409777	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	76	209	0	ENST00000397752.3:c.2662C>A	p.His888Asn	p.H888N	ENST00000397752	NM_000245.2	888	Cat/Aat	12/21	0.241502353482011	2	FACETS	1	0.956	1	0.585	0.518	0.657	CLONAL	1	TRUE	0	0.402013120345117	2		209	323	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	86	438	2	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.907	0.814	1	1	0.988	1	CLONAL	3	FALSE	1	0.24315853980844	2		440	260	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	166	638	9	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	1	2	FACETS	1	0.982	1	1	0.993	1	CLONAL	2	FALSE	1	0.24315853980844	2		647	562	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	28	214	2	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	1	2	FACETS	0.972	0.803	1	1	0.967	1	CLONAL	3	FALSE	1	0.24315853980844	2		216	79	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	110	502	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.969	1	1	0.992	1	CLONAL	4	FALSE	1	0.24315853980844	2		507	205	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	403	763	8	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	0.24315853980844	5	FACETS	0.989	0.945	1	1	0.994	1	CLONAL	5	FALSE	1	0.24315853980844	5		771	915	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	37	259	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.885	0.757	1	1	0.977	1	CLONAL	4	FALSE	1	0.24315853980844	2		259	86	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	63	580	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.914	1	1	0.981	1	CLONAL	2	FALSE	1	0.24315853980844	2		580	245	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007825	45007825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	50	333	0	ENST00000558401.1:c.276del	p.Thr93LeufsTer10	p.T93Lfs*10	ENST00000558401	NM_004048.2	91	aCc/ac	2/4	0.24315853980844	0	FACETS	0.935	0.82	1			1	CLONAL	3	FALSE	0	0.24315853980844	0		333	111	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	194	336	0	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	1	0.983	1	1	0.996	1	CLONAL	5	FALSE	1	0.24315853980844	2		336	294	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396234	396234	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	222	838	1	ENST00000262320.3:c.792del	p.Gly265GlufsTer149	p.G265Efs*149	ENST00000262320	NM_003502.3	264	ccC/cc	2/11	1	2	FACETS	0.9	0.842	0.96	1	0.995	1	CLONAL	3	FALSE	1	0.24315853980844	2		839	676	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	260	1187	3	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	1	0.982	1	1	0.995	1	CLONAL	2	FALSE	1	0.24315853980844	2		1190	955	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	66	457	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	0.22434571803634	3	FACETS	1	0.882	1	1	0.882	1	CLONAL	2	FALSE	1	0.24315853980844	3		457	302	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	208	1048	7	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	0.24315853980844	6	FACETS	1	0.984	1	0.483	0.448	0.519	CLONAL	2	FALSE	1	0.24315853980844	6		1055	1053	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	79	394	0	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	0.24315853980844	3	FACETS	0.996	0.889	1	0.996	0.889	1	CLONAL	3	FALSE	0	0.24315853980844	3		394	244	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494324	2494324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143033733	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	180	926	3	ENST00000355716.4:c.715G>A	p.Val239Ile	p.V239I	ENST00000355716	NM_003820.2	239	Gtc/Atc	7/8	1	2	FACETS	1	0.983	1	1	0.994	1	CLONAL	2	FALSE	1	0.24315853980844	2		929	617	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073877	8073877	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	53	408	0	ENST00000377482.5:c.782C>T	p.Ala261Val	p.A261V	ENST00000377482	NM_018948.3	261	gCc/gTc	4/4	1	2	FACETS	0.87	0.756	0.989	1	0.981	1	CLONAL	3	FALSE	1	0.24315853980844	2		408	167	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023144	27023144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868822840	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	26	36	0	ENST00000324856.7:c.250G>A	p.Gly84Ser	p.G84S	ENST00000324856	NM_006015.4	84	Ggc/Agc	1/20	1	2	FACETS	1	0.891	1	1	0.967	1	CLONAL	3	FALSE	1	0.24315853980844	2		36	64	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023542	27023542	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	176	520	0	ENST00000324856.7:c.651del	p.Asn218ThrfsTer14	p.N218Tfs*14	ENST00000324856	NM_006015.4	216	taC/ta	1/20	1	2	FACETS	1	0.982	1	1	0.994	1	CLONAL	2	FALSE	1	0.24315853980844	2		520	607	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057739	27057739	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	221	820	0	ENST00000324856.7:c.1447C>T	p.Pro483Ser	p.P483S	ENST00000324856	NM_006015.4	483	Cca/Tca	3/20	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	FALSE	1	0.24315853980844	2		820	753	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598940	28598940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886369318	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	246	981	1	ENST00000253063.3:c.500C>T	p.Ala167Val	p.A167V	ENST00000253063	NM_031459.4	167	gCg/gTg	4/10	1	2	FACETS	0.878	0.824	0.934	1	0.996	1	CLONAL	3	FALSE	1	0.24315853980844	2		982	768	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46733195	46733195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269019049	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	164	631	0	ENST00000371975.4:c.956G>A	p.Arg319Gln	p.R319Q	ENST00000371975	NM_003579.3	319	cGg/cAg	9/18	1	2	FACETS	1	0.981	1	1	0.993	1	CLONAL	2	FALSE	1	0.24315853980844	2		631	566	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	47	383	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.885	1	1	0.975	1	CLONAL	2	FALSE	1	0.24315853980844	2		384	186	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258733	115258733	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	95	404	0	ENST00000369535.4:c.49A>G	p.Ser17Gly	p.S17G	ENST00000369535	NM_002524.4	17	Agc/Ggc	2/7	1	2	FACETS	0.84	0.757	0.927	1	0.989	1	CLONAL	3	FALSE	1	0.24315853980844	2		404	310	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275425	115275425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	38	359	1	ENST00000438362.2:c.988C>T	p.Pro330Ser	p.P330S	ENST00000438362	NM_001242891.1	330	Cca/Tca	10/20	1	2	FACETS	0.906	0.768	1	1	0.975	1	CLONAL	3	FALSE	1	0.24315853980844	2		360	115	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458306	120458306	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370648780	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	166	820	2	ENST00000256646.2:c.7039C>T	p.Arg2347Cys	p.R2347C	ENST00000256646	NM_024408.3	2347	Cgt/Tgt	34/34	1	2	FACETS	1	0.984	1	1	0.993	1	CLONAL	2	FALSE	1	0.24315853980844	2		822	553	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462204	120462204	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs766543218	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	75	517	0	ENST00000256646.2:c.5512C>T	p.Arg1838Ter	p.R1838*	ENST00000256646	NM_024408.3	1838	Cga/Tga	31/34	1	2	FACETS	0.918	0.818	1	1	0.987	1	CLONAL	3	FALSE	1	0.24315853980844	2		517	224	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193181525	193181525	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs771907995	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	19	240	0	ENST00000367435.3:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000367435	NM_024529.4	358	Cga/Tga	13/17	1	2	FACETS	1	0.826	1	1	0.942	1	CLONAL	2	FALSE	1	0.24315853980844	2		240	73	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652330	206652330	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	242	1035	3	ENST00000367120.3:c.1042del	p.Arg348AspfsTer32	p.R348Dfs*32	ENST00000367120	NM_014002.3	346	gCc/gc	10/22	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	FALSE	1	0.24315853980844	2		1038	844	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852118	63852118	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	118	619	0	ENST00000279873.7:c.2901del	p.Lys967AsnfsTer15	p.K967Nfs*15	ENST00000279873	NM_032199.2	966	Aaa/aa	10/10	1	2	FACETS	0.949	0.866	1	1	0.992	1	CLONAL	3	FALSE	1	0.24315853980844	2		619	341	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332273	70332273	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	40	299	2	ENST00000373644.4:c.184del	p.Thr62GlnfsTer13	p.T62Qfs*13	ENST00000373644	NM_030625.2	60	Aaa/aa	2/12	1	2	FACETS	0.971	0.828	1	1	0.977	1	CLONAL	3	FALSE	1	0.24315853980844	2		301	113	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741882	17741882	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1179926739	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	38	106	2	ENST00000250003.3:c.557del	p.Pro186ArgfsTer25	p.P186Rfs*25	ENST00000250003	NM_002478.4	185	Ccc/cc	1/3	1	2	FACETS	1	0.902	1	1	0.971	1	CLONAL	2	FALSE	1	0.24315853980844	2		108	142	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998373	100998373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	49	88	0	ENST00000325455.5:c.1429C>T	p.Pro477Ser	p.P477S	ENST00000325455	NM_001202474.3	477	Ccg/Tcg	1/8	1	2	FACETS	0.916	0.802	1	1	0.983	1	CLONAL	4	FALSE	1	0.24315853980844	2		88	110	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999149	100999149	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	56	947	1	ENST00000325455.5:c.653C>T	p.Ala218Val	p.A218V	ENST00000325455	NM_001202474.3	218	gCg/gTg	1/8	1	2	FACETS	0.699	0.598	0.809	0.699	0.598	0.809	SUBCLONAL	1	FALSE	1	0.24315853980844	2		948	659	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870978	12870978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388968180	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	151	473	1	ENST00000228872.4:c.205C>T	p.Pro69Ser	p.P69S	ENST00000228872	NM_004064.3	69	Ccc/Tcc	1/3	0.24315853980844	6	FACETS	1	0.943	1	1	0.943	1	CLONAL	5	FALSE	1	0.24315853980844	6		474	362	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436109	49436109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755573725	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	100	523	1	ENST00000301067.7:c.5872C>T	p.Arg1958Cys	p.R1958C	ENST00000301067	NM_003482.3	1958	Cgc/Tgc	28/54	0.24315853980844	6	FACETS	1	0.93	1	0.625	0.563	0.691	CLONAL	3	FALSE	1	0.24315853980844	6		524	391	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445500	49445500	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs886042284	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	521	760	3	ENST00000301067.7:c.1966del	p.Leu656CysfsTer274	p.L656Cfs*274	ENST00000301067	NM_003482.3	656	Ctg/tg	10/54	0.24315853980844	6	FACETS	1	0.973	1	1	0.995	1	CLONAL	6	FALSE	1	0.24315853980844	6		763	1048	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486785	56486785	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	167	638	0	ENST00000267101.3:c.1199A>G	p.Gln400Arg	p.Q400R	ENST00000267101	NM_001982.3	400	cAg/cGg	11/28	0.24315853980844	6	FACETS	1	0.966	1	0.65	0.6	0.702	CLONAL	3	FALSE	1	0.24315853980844	6		638	628	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863319	57863319	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	243	925	1	ENST00000228682.2:c.1418del	p.Gly473AlafsTer40	p.G473Afs*40	ENST00000228682	NM_005269.2	472	Ggg/gg	11/12	0.24315853980844	6	FACETS	1	0.978	1	0.66	0.618	0.704	CLONAL	3	FALSE	1	0.24315853980844	6		926	900	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112910749	112910749	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	83	319	0	ENST00000351677.2:c.758C>T	p.Thr253Ile	p.T253I	ENST00000351677	NM_002834.3	253	aCa/aTa	7/16	0.24315853980844	6	FACETS	0.94	0.85	1	1	0.962	1	CLONAL	6	FALSE	1	0.24315853980844	6		319	180	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431332	121431332	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760869012	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	137	468	0	ENST00000257555.6:c.536A>G	p.His179Arg	p.H179R	ENST00000257555		179	cAt/cGt	3/10	0.24315853980844	6	FACETS	0.887	0.813	0.964	0.71	0.65	0.771	CLONAL	4	FALSE	1	0.24315853980844	6		468	472	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435295	121435296	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs776793516	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	245	1032	0	ENST00000257555.6:c.1330_1331del	p.Gln444GlufsTer104	p.Q444Efs*104	ENST00000257555		443	gCA/g	7/10	0.24315853980844	6	FACETS	1	0.968	1	0.633	0.592	0.675	CLONAL	3	FALSE	1	0.24315853980844	6		1032	947	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557684	21557684	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	151	808	0	ENST00000382592.4:c.2161G>A	p.Ala721Thr	p.A721T	ENST00000382592	NM_014572.2	721	Gcc/Acc	5/8	1	2	FACETS	1	0.973	1	1	0.992	1	CLONAL	2	FALSE	1	0.24315853980844	2		808	546	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608318	28608318	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	46	439	1	ENST00000241453.7:c.1738C>T	p.Gln580Ter	p.Q580*	ENST00000241453	NM_004119.2	580	Cag/Tag	14/24	1	2	FACETS	1	0.936	1	1	0.977	1	CLONAL	2	FALSE	1	0.24315853980844	2		440	161	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911074	32911074	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	19	272	0	ENST00000380152.3:c.2588del	p.Asn863IlefsTer11	p.N863Ifs*11	ENST00000380152		861	cAa/ca	11/27	1	2	FACETS	0.914	0.72	1	1	0.951	1	CLONAL	3	FALSE	1	0.24315853980844	2		272	57	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435129	110435129	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	295	782	4	ENST00000375856.3:c.3272del	p.Pro1091ArgfsTer15	p.P1091Rfs*15	ENST00000375856	NM_003749.2	1091	cCg/cg	1/2	1	2	FACETS	0.896	0.845	0.947	1	0.996	1	CLONAL	3	FALSE	1	0.24315853980844	2		786	903	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871728	35871728	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528542318	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	177	757	0	ENST00000216797.5:c.778C>T	p.Arg260Cys	p.R260C	ENST00000216797	NM_020529.2	260	Cgc/Tgc	5/6	1	2	FACETS	1	0.974	1	1	0.993	1	CLONAL	2	FALSE	1	0.24315853980844	2		757	654	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961687	41961687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	53	458	0	ENST00000219905.7:c.595C>T	p.Arg199Cys	p.R199C	ENST00000219905	NM_001164273.1	199	Cgt/Tgt	2/24	0.24315853980844	0	FACETS	0.84	0.736	0.946			1	CLONAL	3	FALSE	0	0.24315853980844	0		458	131	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708603	43708603	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	37	536	0	ENST00000382044.4:c.4693G>T	p.Gly1565Ter	p.G1565*	ENST00000382044	NM_001141980.1	1565	Gga/Tga	22/28	0.24315853980844	0	FACETS	0.776	0.659	0.897			1	SUBCLONAL	3	FALSE	0	0.24315853980844	0		536	99	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748607	43748608	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	83	750	0	ENST00000382044.4:c.2198dup	p.Gln734SerfsTer7	p.Q734Sfs*7	ENST00000382044	NM_001141980.1	733	cct/ccCt	12/28	0.24315853980844	0	FACETS	1	0.908	1			1	CLONAL	3	FALSE	0	0.24315853980844	0		750	172	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774194	66774194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	214	1101	3	ENST00000307102.5:c.670G>A	p.Val224Met	p.V224M	ENST00000307102	NM_002755.3	224	Gtg/Atg	6/11	0.106591269764354	0	FACETS	0.8	0.744	0.856			1	INDETERMINATE	2	FALSE	0	0.24315853980844	0		1104	833	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303500	91303500	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776516663	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	25	258	1	ENST00000355112.3:c.1211G>A	p.Arg404Gln	p.R404Q	ENST00000355112	NM_000057.2	404	cGg/cAg	6/22	0.106591269764354	0	FACETS	1	0.91	1			1	INDETERMINATE	1	FALSE	0	0.24315853980844	0		259	122	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310208	91310208	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs747341586	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	28	185	0	ENST00000355112.3:c.2268del	p.Asp757ThrfsTer4	p.D757Tfs*4	ENST00000355112	NM_000057.2	754	tcA/tc	10/22	0.106591269764354	0	FACETS	0.842	0.7	0.989			1	INDETERMINATE	3	FALSE	0	0.24315853980844	0		185	69	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456274	99456274	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	49	286	0	ENST00000268035.6:c.1591C>T	p.Pro531Ser	p.P531S	ENST00000268035	NM_000875.3	531	Ccc/Tcc	8/21	0.106591269764354	0	FACETS	0.897	0.773	1			1	INDETERMINATE	2	FALSE	0	0.24315853980844	0		286	170	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096132	2096133	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs763525759	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	146	866	4	ENST00000219066.1:c.374dup	p.Val127GlyfsTer43	p.V127Gfs*43	ENST00000219066	NM_002528.5	125	cca/ccCa	2/6	1	2	FACETS	1	0.982	1	1	0.993	1	CLONAL	2	FALSE	1	0.24315853980844	2		870	482	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647564	3647564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377440877	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	161	956	2	ENST00000294008.3:c.1499C>T	p.Thr500Met	p.T500M	ENST00000294008	NM_032444.2	500	aCg/aTg	7/15	1	2	FACETS	1	0.959	1	1	0.992	1	CLONAL	2	FALSE	1	0.24315853980844	2		958	623	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032118	10032118	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	58	670	0	ENST00000330684.3:c.705G>T	p.Glu235Asp	p.E235D	ENST00000330684	NM_001134407.1	235	gaG/gaT	3/13	1	2	FACETS	0.777	0.672	0.889	1	0.971	1	SUBCLONAL	2	FALSE	1	0.24315853980844	2		670	307	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644874	67644874	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	164	632	0	ENST00000264010.4:c.143del	p.Gly48ValfsTer14	p.G48Vfs*14	ENST00000264010	NM_006565.3	47	Ggg/gg	3/12	1	2	FACETS	0.894	0.827	0.963	1	0.994	1	CLONAL	3	FALSE	1	0.24315853980844	2		632	503	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992127	72992127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748545102	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	196	939	2	ENST00000268489.5:c.1918G>A	p.Val640Met	p.V640M	ENST00000268489	NM_006885.3	640	Gtg/Atg	2/10	1	2	FACETS	0.834	0.776	0.894	1	0.994	1	CLONAL	3	FALSE	1	0.24315853980844	2		941	644	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89335041	89335041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	138	434	0	ENST00000301030.4:c.7837G>A	p.Ala2613Thr	p.A2613T	ENST00000301030	NM_001256183.1	2613	Gcc/Acc	13/13	1	2	FACETS	1	0.979	1	1	0.992	1	CLONAL	2	FALSE	1	0.24315853980844	2		434	469	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15967385	15967385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1006410157	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	195	494	0	ENST00000268712.3:c.5218C>T	p.Pro1740Ser	p.P1740S	ENST00000268712	NM_006311.3	1740	Cca/Tca	35/46	1	2	FACETS	0.931	0.868	0.996	1	0.995	1	CLONAL	3	FALSE	1	0.24315853980844	2		494	574	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131231	17131231	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	301	1033	1	ENST00000285071.4:c.221C>A	p.Pro74Gln	p.P74Q	ENST00000285071	NM_144997.5	74	cCg/cAg	4/14	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	FALSE	1	0.24315853980844	2		1034	1017	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512402	38512402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	163	807	3	ENST00000254066.5:c.1319del	p.Pro440ArgfsTer203	p.P440Rfs*203	ENST00000254066	NM_000964.3	438	gCc/gc	9/9	1	2	FACETS	1	0.979	1	1	0.993	1	CLONAL	2	FALSE	1	0.24315853980844	2		810	574	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40457683	40457683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs893730531	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	207	840	0	ENST00000345506.4:c.1436C>T	p.Thr479Met	p.T479M	ENST00000345506	NM_003152.3	479	aCg/aTg	13/20	1	2	FACETS	1	0.984	1	1	0.994	1	CLONAL	2	FALSE	1	0.24315853980844	2		840	721	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865350	40865350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	183	685	0	ENST00000428826.2:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000428826		361	Cgc/Tgc	11/21	1	2	FACETS	1	0.965	1	1	0.993	1	CLONAL	2	FALSE	1	0.24315853980844	2		685	702	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58711260	58711260	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	59	468	1	ENST00000305921.3:c.748C>T	p.Arg250Ter	p.R250*	ENST00000305921	NM_003620.3	250	Cga/Tga	3/6	1	2	FACETS	1	0.943	1	1	0.982	1	CLONAL	2	FALSE	1	0.24315853980844	2		469	211	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554517	63554518	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	186	808	0	ENST00000307078.5:c.221dup	p.Leu75SerfsTer66	p.L75Sfs*66	ENST00000307078	NM_004655.3	74	cct/ccCt	2/11	1	2	FACETS	0.973	0.906	1	1	0.995	1	CLONAL	3	FALSE	1	0.24315853980844	2		808	524	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120031	70120031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	26	35	0	ENST00000245479.2:c.1037del	p.Pro346ArgfsTer37	p.P346Rfs*37	ENST00000245479	NM_000346.3	345	Ccc/cc	3/3	1	2	FACETS	1	0.867	1	1	0.958	1	CLONAL	2	FALSE	1	0.24315853980844	2		35	98	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858943	78858943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	134	672	0	ENST00000306801.3:c.1978C>T	p.Arg660Trp	p.R660W	ENST00000306801	NM_020761.2	660	Cgg/Tgg	17/34	1	2	FACETS	1	0.968	1	1	0.991	1	CLONAL	2	FALSE	1	0.24315853980844	2		672	492	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622410	1622410	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	191	682	0	ENST00000344749.5:c.554A>G	p.Tyr185Cys	p.Y185C	ENST00000344749	NM_001136139.2	185	tAc/tGc	9/19	1	2	FACETS	1	0.964	1	1	0.995	1	CLONAL	3	FALSE	1	0.24315853980844	2		682	499	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223460	2223460	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	123	614	0	ENST00000398665.3:c.3571T>G	p.Ser1191Ala	p.S1191A	ENST00000398665	NM_032482.2	1191	Tct/Gct	25/28	1	2	FACETS	0.964	0.882	1	1	0.992	1	CLONAL	3	FALSE	1	0.24315853980844	2		614	350	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3113445	3113445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767809613	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	209	783	0	ENST00000078429.4:c.439C>T	p.Arg147Cys	p.R147C	ENST00000078429	NM_002067.2	147	Cgc/Tgc	3/7	1	2	FACETS	0.851	0.794	0.91	1	0.995	1	CLONAL	3	FALSE	1	0.24315853980844	2		783	673	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214618	5214618	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767215087	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	252	1061	0	ENST00000357368.4:c.4448G>A	p.Arg1483Gln	p.R1483Q	ENST00000357368	NM_002850.3	1483	cGg/cAg	29/38	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	FALSE	1	0.24315853980844	2		1061	846	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262139	10262139	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	130	730	3	ENST00000340748.4:c.2152del	p.Met718CysfsTer59	p.M718Cfs*59	ENST00000340748		718	Atg/tg	23/40	1	2	FACETS	1	0.969	1	1	0.991	1	CLONAL	2	FALSE	1	0.24315853980844	2		733	471	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270561	10270561	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	268	871	0	ENST00000340748.4:c.1079T>C	p.Leu360Pro	p.L360P	ENST00000340748		360	cTg/cCg	15/40	1	2	FACETS	0.909	0.856	0.964	1	0.996	1	CLONAL	3	FALSE	1	0.24315853980844	2		871	808	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024656	11024656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	154	719	0	ENST00000327064.4:c.773C>T	p.Pro258Leu	p.P258L	ENST00000327064	NM_199141.1	258	cCc/cTc	6/16	1	2	FACETS	0.863	0.796	0.933	1	0.993	1	CLONAL	3	FALSE	1	0.24315853980844	2		719	489	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050873	13050873	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	94	494	0	ENST00000316448.5:c.404A>G	p.Asp135Gly	p.D135G	ENST00000316448	NM_004343.3	135	gAc/gGc	4/9	1	2	FACETS	0.892	0.804	0.983	1	0.989	1	CLONAL	3	FALSE	1	0.24315853980844	2		494	289	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952540	17952540	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	226	824	1	ENST00000458235.1:c.893T>C	p.Ile298Thr	p.I298T	ENST00000458235	NM_000215.3	298	aTc/aCc	7/24	1	2	FACETS	0.857	0.802	0.914	1	0.995	1	CLONAL	3	FALSE	1	0.24315853980844	2		825	723	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214866	36214866	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568372429	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	265	992	7	ENST00000222270.7:c.3296del	p.Gly1099AlafsTer83	p.G1099Afs*83	ENST00000222270	NM_014727.1	1098	Ggg/gg	8/37	1	2	FACETS	0.865	0.813	0.918	1	0.996	1	CLONAL	3	FALSE	1	0.24315853980844	2		999	840	SUCCESS
AXL	558	MSKCC	GRCh37	19	41737127	41737127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767654945	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	295	1050	2	ENST00000301178.4:c.707G>A	p.Arg236His	p.R236H	ENST00000301178	NM_021913.4	236	cGc/cAc	6/20	1	2	FACETS	0.869	0.82	0.919	1	0.996	1	CLONAL	3	FALSE	1	0.24315853980844	2		1052	931	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795609	42795609	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	250	1059	3	ENST00000575354.2:c.2694del	p.Ala900ProfsTer24	p.A900Pfs*24	ENST00000575354	NM_015125.3	897	Ccc/cc	10/20	1	2	FACETS	0.891	0.837	0.947	1	0.996	1	CLONAL	3	FALSE	1	0.24315853980844	2		1062	769	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856520	45856520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751318902	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	210	901	1	ENST00000391945.4:c.1738G>A	p.Ala580Thr	p.A580T	ENST00000391945	NM_000400.3	580	Gcc/Acc	18/23	1	2	FACETS	0.914	0.853	0.976	1	0.995	1	CLONAL	3	FALSE	1	0.24315853980844	2		902	630	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902293	50902293	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1224431670	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	276	1022	0	ENST00000440232.2:c.185T>C	p.Leu62Pro	p.L62P	ENST00000440232	NM_002691.3	62	cTg/cCg	2/27	1	2	FACETS	0.914	0.861	0.968	1	0.996	1	CLONAL	3	FALSE	1	0.24315853980844	2		1022	828	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	215	1073	5	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	0.863	0.806	0.922	1	0.995	1	CLONAL	3	FALSE	1	0.24315853980844	2		1078	683	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142900	30142900	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	258	1002	0	ENST00000389048.3:c.626G>A	p.Arg209His	p.R209H	ENST00000389048	NM_004304.4	209	cGc/cAc	1/29	1	2	FACETS	0.853	0.801	0.906	1	0.996	1	CLONAL	3	FALSE	1	0.24315853980844	2		1002	829	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574172	46574172	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	195	774	1	ENST00000263734.3:c.187T>A	p.Phe63Ile	p.F63I	ENST00000263734	NM_001430.4	63	Ttc/Atc	2/16	1	2	FACETS	0.871	0.81	0.933	1	0.994	1	CLONAL	3	FALSE	1	0.24315853980844	2		775	614	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607783	46607783	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766696421	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	270	1013	2	ENST00000263734.3:c.1972C>T	p.Arg658Cys	p.R658C	ENST00000263734	NM_001430.4	658	Cgc/Tgc	12/16	1	2	FACETS	0.888	0.835	0.941	1	0.996	1	CLONAL	3	FALSE	1	0.24315853980844	2		1015	834	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630543	47630543	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	123	784	0	ENST00000233146.2:c.211+2T>G		p.X71_splice	ENST00000233146	NM_000251.2	71			1	2	FACETS	1	0.978	1	1	0.991	1	CLONAL	2	FALSE	1	0.24315853980844	2		784	413	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437288	220437288	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1190141661	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	228	1178	0	ENST00000243786.2:c.197del	p.Gly66AlafsTer61	p.G66Afs*61	ENST00000243786	NM_002191.3	64	ctG/ct	1/2	1	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	2	FALSE	1	0.24315853980844	2		1178	800	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662137	227662137	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs768016050	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	207	833	0	ENST00000305123.5:c.1318A>G	p.Ser440Gly	p.S440G	ENST00000305123	NM_005544.2	440	Agt/Ggt	1/2	1	2	FACETS	0.973	0.91	1	1	0.995	1	CLONAL	3	FALSE	1	0.24315853980844	2		833	583	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	42	897	0	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	1	2	FACETS	0.492	0.41	0.584	0.492	0.41	0.584	SUBCLONAL	1	FALSE	1	0.24315853980844	2		897	702	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662692	227662692	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1242850490	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	209	915	0	ENST00000305123.5:c.763G>T	p.Glu255Ter	p.E255*	ENST00000305123	NM_005544.2	255	Gag/Tag	1/2	1	2	FACETS	1	0.982	1	1	0.994	1	CLONAL	2	FALSE	1	0.24315853980844	2		915	747	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275688	41275688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	128	505	0	ENST00000349496.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000349496	NM_001904.3	528	cGt/cAt	10/15	1	2	FACETS	0.882	0.807	0.959	1	0.992	1	CLONAL	3	FALSE	1	0.24315853980844	2		505	398	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163320	47163320	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	36	333	0	ENST00000409792.3:c.2806C>A	p.Leu936Ile	p.L936I	ENST00000409792	NM_014159.6	936	Ctt/Att	3/21	1	2	FACETS	0.889	0.75	1	1	0.973	1	CLONAL	3	FALSE	1	0.24315853980844	2		333	111	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47205386	47205386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773221585	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	202	467	0	ENST00000409792.3:c.29C>T	p.Pro10Leu	p.P10L	ENST00000409792	NM_014159.6	10	cCg/cTg	1/21	1	2	FACETS	1	0.954	1	1	0.995	1	CLONAL	3	FALSE	1	0.24315853980844	2		467	540	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412907	49412907	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	83	689	0	ENST00000418115.1:c.116T>C	p.Phe39Ser	p.F39S	ENST00000418115	NM_001664.2	39	tTt/tCt	2/5	1	2	FACETS	1	0.932	1	1	0.986	1	CLONAL	2	FALSE	1	0.24315853980844	2		689	321	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52661367	52661367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762715677	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	48	325	1	ENST00000394830.3:c.1463C>T	p.Ala488Val	p.A488V	ENST00000394830	NM_018313.4	488	gCc/gTc	14/30	1	2	FACETS	1	0.911	1	1	0.976	1	CLONAL	2	FALSE	1	0.24315853980844	2		326	182	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272521	142272521	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	66	487	0	ENST00000350721.4:c.2594T>C	p.Leu865Pro	p.L865P	ENST00000350721	NM_001184.3	865	cTg/cCg	12/47	1	2	FACETS	0.994	0.881	1	1	0.986	1	CLONAL	3	FALSE	1	0.24315853980844	2		487	182	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447282	187447284	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1350754735	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	142	711	0	ENST00000232014.4:c.909_911del	p.Glu304del	p.E304del	ENST00000232014	NM_001130845.1	303	gaAGAg/gag	5/10	1	2	FACETS	1	0.964	1	1	0.992	1	CLONAL	2	FALSE	1	0.24315853980844	2		711	534	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920312	1920312	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	178	701	0	ENST00000382891.5:c.1372T>C	p.Ser458Pro	p.S458P	ENST00000382891	NM_133335.3	458	Tcc/Ccc	5/22	1	2	FACETS	0.982	0.913	1	1	0.994	1	CLONAL	3	FALSE	1	0.24315853980844	2		701	497	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980560	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	206	869	0	ENST00000382891.5:c.4027_4028del	p.Pro1343ArgfsTer91	p.P1343Rfs*91	ENST00000382891	NM_133335.3	1341	CCc/c	22/22	1	2	FACETS	0.87	0.812	0.93	1	0.995	1	CLONAL	3	FALSE	1	0.24315853980844	2		869	649	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197733	66197733	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	57	388	0	ENST00000273854.3:c.2966del	p.Asn989MetfsTer12	p.N989Mfs*12	ENST00000273854	NM_004439.5	989	aAt/at	17/18	1	2	FACETS	1	0.909	1	1	0.984	1	CLONAL	3	FALSE	1	0.24315853980844	2		388	150	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467482	66467482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371073025	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	61	377	0	ENST00000273854.3:c.787G>A	p.Val263Ile	p.V263I	ENST00000273854	NM_004439.5	263	Gtc/Atc	3/18	1	2	FACETS	1	0.929	1	1	0.981	1	CLONAL	2	FALSE	1	0.24315853980844	2		377	229	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526601	31526601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1464818570	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	113	426	0	ENST00000344624.3:c.439C>T	p.Pro147Ser	p.P147S	ENST00000344624		147	Ccc/Tcc	2/33	1	2	FACETS	1	0.933	1	1	0.992	1	CLONAL	4	FALSE	1	0.24315853980844	2		426	229	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35857099	35857100	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	26	247	0	ENST00000303115.3:c.24dup	p.Gly9TrpfsTer29	p.G9Wfs*29	ENST00000303115	NM_002185.3	7	act/acTt	1/8	1	2	FACETS	1	0.882	1	1	0.959	1	CLONAL	2	FALSE	1	0.24315853980844	2		247	95	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873708	35873708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1394251315	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	17	328	0	ENST00000303115.3:c.664C>T	p.Pro222Ser	p.P222S	ENST00000303115	NM_002185.3	222	Cca/Tca	5/8	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	FALSE	1	0.24315853980844	2		328	99	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38964892	38964892	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	17	131	0	ENST00000357387.3:c.1400+2T>C		p.X467_splice	ENST00000357387	NM_152756.3	467			1	2	FACETS	0.951	0.741	1	1	0.946	1	CLONAL	3	FALSE	1	0.24315853980844	2		131	49	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755537	57755537	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	162	717	0	ENST00000274289.3:c.250C>G	p.Arg84Gly	p.R84G	ENST00000274289	NM_006622.3	84	Cgg/Ggg	1/14	1	2	FACETS	1	0.975	1	1	0.993	1	CLONAL	2	FALSE	1	0.24315853980844	2		717	585	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165354	32165354	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	186	997	0	ENST00000375023.3:c.4774A>G	p.Met1592Val	p.M1592V	ENST00000375023	NM_004557.3	1592	Atg/Gtg	27/30	0.22434571803634	3	FACETS	1	0.969	1	1	0.992	1	CLONAL	3	FALSE	1	0.24315853980844	3		997	534	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32182015	32182016	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	rs760466471	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	172	838	1	ENST00000375023.3:c.2037_2038dup	p.Asp680ValfsTer14	p.D680Vfs*14	ENST00000375023	NM_004557.3	680	gac/gTGac	13/30	0.22434571803634	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	FALSE	1	0.24315853980844	3		839	653	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322667	109322667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376950903	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	50	416	1	ENST00000436639.2:c.370G>A	p.Ala124Thr	p.A124T	ENST00000436639	NM_014454.2	124	Gca/Aca	3/10	0.22434571803634	3	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	FALSE	1	0.24315853980844	3		417	204	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710594	117710594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768790336	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	94	334	0	ENST00000368508.3:c.1678C>T	p.Arg560Cys	p.R560C	ENST00000368508	NM_002944.2	560	Cgc/Tgc	12/43	0.22434571803634	3	FACETS	0.973	0.877	1	1	0.982	1	CLONAL	3	FALSE	1	0.24315853980844	3		334	297	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983227	149983228	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	31	407	0	ENST00000253339.5:c.3030dup	p.Lys1011Ter	p.K1011*	ENST00000253339		1010	-/T	7/7	0.22434571803634	3	FACETS	1	0.858	1	1	0.858	1	CLONAL	2	FALSE	1	0.24315853980844	3		407	136	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977573	2977573	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	369	832	1	ENST00000396946.4:c.1111C>T	p.Gln371Ter	p.Q371*	ENST00000396946	NM_032415.4	371	Cag/Tag	8/25	0.24315853980844	5	FACETS	0.969	0.924	1	1	0.993	1	CLONAL	5	FALSE	1	0.24315853980844	5		833	855	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207409	29207409	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	233	659	0	ENST00000240100.2:c.387G>T	p.Gln129His	p.Q129H	ENST00000240100	NM_001394.6	129	caG/caT	1/4	1	2	FACETS	1	0.975	1	1	0.996	1	CLONAL	3	FALSE	1	0.24315853980844	2		659	598	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271528	38271528	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1329256283	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	138	899	1	ENST00000425967.3:c.2293C>T	p.Arg765Trp	p.R765W	ENST00000425967	NM_001174067.1	765	Cgg/Tgg	18/19	1	2	FACETS	1	0.964	1	1	0.991	1	CLONAL	2	FALSE	1	0.24315853980844	2		900	516	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737323	145737323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369843844	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	312	1129	1	ENST00000428558.2:c.3364G>A	p.Ala1122Thr	p.A1122T	ENST00000428558	NM_004260.3	1122	Gca/Aca	20/22	1	2	FACETS	0.894	0.845	0.944	1	0.996	1	CLONAL	3	FALSE	1	0.24315853980844	2		1130	957	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	167	853	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	1	0.973	1	1	0.993	1	CLONAL	2	FALSE	1	0.24315853980844	2		853	614	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133761012	133761012	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	220	891	0	ENST00000318560.5:c.3335A>G	p.Gln1112Arg	p.Q1112R	ENST00000318560	NM_005157.4	1112	cAg/cGg	11/11	1	2	FACETS	0.877	0.819	0.935	1	0.995	1	CLONAL	3	FALSE	1	0.24315853980844	2		891	688	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137321023	137321023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	297	1095	2	ENST00000481739.1:c.980C>T	p.Ala327Val	p.A327V	ENST00000481739	NM_002957.4	327	gCc/gTc	7/10	1	2	FACETS	0.856	0.808	0.906	1	0.996	1	CLONAL	3	FALSE	1	0.24315853980844	2		1097	951	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815530	139815530	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528114067	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	219	931	2	ENST00000247668.2:c.1001C>T	p.Ala334Val	p.A334V	ENST00000247668	NM_021138.3	334	gCg/gTg	9/11	1	2	FACETS	0.844	0.789	0.902	1	0.995	1	CLONAL	3	FALSE	1	0.24315853980844	2		933	711	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346924	70346924	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	226	372	0	ENST00000374080.3:c.2791C>T	p.Arg931Trp	p.R931W	ENST00000374080		931	Cgg/Tgg	20/45	0.24315853980844	2	FACETS	0.945	0.902	0.986			1	CLONAL	6	FALSE	NA	0.24315853980844	2		372	328	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	160	516	0				ENST00000310581	NM_198253.2	-/1132			0.759647346166139	3	FACETS	1	0.962	1	0.535	0.494	0.578	CLONAL	1	TRUE	1	0.759647346166139	3		516	543	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100485	2100485	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	199	384	0	ENST00000219476.3:c.223G>T	p.Glu75Ter	p.E75*	ENST00000219476	NM_000548.3	75	Gag/Tag	3/42	0.759647346166139	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.759647346166139	1		384	312	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603116	48603116	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	219	466	0	ENST00000342988.3:c.1417G>T	p.Gly473Ter	p.G473*	ENST00000342988	NM_005359.5	473	Gga/Tga	11/12	0.759647346166139	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.759647346166139	1		466	334	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183707	10183731	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGGCCCGTGCTGCGCTCGGTGAA	CGCGGCCCGTGCTGCGCTCGGTGAA	-	novel	NA	P-0047074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	136	733	0	ENST00000256474.2:c.177_201del	p.Pro61AlafsTer90	p.P61Afs*90	ENST00000256474	NM_000551.3	59	cCGCGGCCCGTGCTGCGCTCGGTGAAc/cc	1/3	0.404931404369714	1	FACETS	0.948	0.866	1	0.948	0.866	1	CLONAL	1	TRUE	0	0.404931404369714	1		733	565	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441189	52441189	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0047074-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	78	348	0	ENST00000460680.1:c.580+1G>T		p.X194_splice	ENST00000460680	NM_004656.3	194			0.404931404369714	1	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	0	0.404931404369714	1		348	307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0047075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	86	709	5	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.202528445440022	2	FACETS	1	0.963	1	0.602	0.535	0.672	CLONAL	1	TRUE	0	0.327912790187199	2		714	436	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437508	49437508	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	75	605	0	ENST00000301067.7:c.5377G>C	p.Gly1793Arg	p.G1793R	ENST00000301067	NM_003482.3	1793	Ggg/Cgg	23/54	0.327912790187199	3	FACETS	0.832	0.729	0.943	0.416	0.364	0.472	CLONAL	1	TRUE	1	0.327912790187199	3		605	640	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0047077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	118	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.753366371822105	2	FACETS	0.958	0.876	1	0.479	0.438	0.521	CLONAL	1	TRUE	0	0.767069378276781	2		511	321	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0047077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	90	424	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.35133523706379	6	FACETS	0.819	0.733	0.91	0.546	0.488	0.607	INDETERMINATE	2	TRUE	3	0.767069378276781	6		424	363	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502662	149502662	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759436020	NA	P-0047077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	155	700	0	ENST00000261799.4:c.2126G>A	p.Arg709His	p.R709H	ENST00000261799	NM_002609.3	709	cGc/cAc	15/23	0.767069378276781	3	FACETS	0.978	0.899	1	0.326	0.299	0.353	CLONAL	1	TRUE	0	0.767069378276781	3		700	572	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0047077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	374	380	1	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.767069378276781	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	0	0.767069378276781	3		381	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578509	7578509	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519978	NA	P-0047077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	228	883	0	ENST00000269305.4:c.421T>G	p.Cys141Gly	p.C141G	ENST00000269305	NM_001126112.2	141	Tgc/Ggc	5/11	0.767069378276781	2	FACETS	0.89	0.85	0.929	0.89	0.85	0.929	CLONAL	2	TRUE	0	0.767069378276781	2		883	334	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466769	25466769	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	290	639	0	ENST00000264709.3:c.1934C>G	p.Thr645Arg	p.T645R	ENST00000264709	NM_175629.2	645	aCa/aGa	16/23	0.753366371822105	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.767069378276781	2		639	376	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	80	516	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.876	0.784	0.972	0.876	0.784	0.972	CLONAL	1	TRUE	1	0.763926973748307	2		516	239	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0047078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	197	620	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	0.986	0.921	1	0.986	0.921	1	CLONAL	1	TRUE	1	0.763926973748307	2		620	523	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463566	25463566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	89	513	0	ENST00000264709.3:c.2116G>A	p.Gly706Arg	p.G706R	ENST00000264709	NM_175629.2	706	Ggg/Agg	18/23	1	2	FACETS	0.426	0.378	0.477	0.426	0.378	0.477	SUBCLONAL	1	TRUE	1	0.763926973748307	2		513	547	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797146	42797146	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	136	814	1	ENST00000575354.2:c.3508C>T	p.Gln1170Ter	p.Q1170*	ENST00000575354	NM_015125.3	1170	Cag/Tag	15/20	0.763926973748307	1	FACETS	0.439	0.402	0.478	0.439	0.402	0.478	SUBCLONAL	1	TRUE	0	0.763926973748307	1		815	501	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422435	225422435	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	53	382	1	ENST00000264414.4:c.205C>A	p.His69Asn	p.H69N	ENST00000264414	NM_003590.4	69	Cat/Aat	2/16	1	2	FACETS	0.402	0.344	0.465	0.402	0.344	0.465	SUBCLONAL	1	TRUE	1	0.763926973748307	2		383	345	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0047079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	43	396	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.956	0.8	1	0.956	0.8	1	CLONAL	1	TRUE	1	0.18	2		396	500	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189926	66189926	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	27	249	0	ENST00000273854.3:c.3020G>T	p.Arg1007Leu	p.R1007L	ENST00000273854	NM_004439.5	1007	cGg/cTg	18/18	1	2	FACETS	0.741	0.589	0.914	0.741	0.589	0.914	CLONAL	1	TRUE	1	0.18	2		249	405	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908218	28908218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	40	416	0	ENST00000282397.4:c.2537C>T	p.Ala846Val	p.A846V	ENST00000282397	NM_002019.4	846	gCa/gTa	18/30	1	2	FACETS	0.719	0.596	0.856	0.719	0.596	0.856	SUBCLONAL	1	TRUE	1	0.18	2		416	618	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290896	15290896	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	79	807	0	ENST00000263388.2:c.3314G>T	p.Gly1105Val	p.G1105V	ENST00000263388	NM_000435.2	1105	gGc/gTc	20/33	1	2	FACETS	0.938	0.823	1	0.938	0.823	1	CLONAL	1	TRUE	1	0.18	2		807	936	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961615	18961615	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	78	686	0	ENST00000262803.5:c.748G>T	p.Glu250Ter	p.E250*	ENST00000262803	NM_002911.3	250	Gag/Tag	5/24	1	2	FACETS	0.976	0.856	1	0.976	0.856	1	CLONAL	1	TRUE	1	0.18	2		686	888	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271387	26271387	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	33	559	0	ENST00000305910.3:c.226G>C	p.Ala76Pro	p.A76P	ENST00000305910	NM_003534.2	76	Gct/Cct	1/1	1	2	FACETS	0.619	0.503	0.751	0.619	0.503	0.751	SUBCLONAL	1	TRUE	1	0.18	2		559	592	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005888	69005888	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	35	383	0	ENST00000288368.4:c.2299G>A	p.Asp767Asn	p.D767N	ENST00000288368	NM_024870.2	767	Gac/Aac	21/40	1	2	FACETS	0.718	0.587	0.864	0.718	0.587	0.864	SUBCLONAL	1	TRUE	1	0.18	2		383	542	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524949	8524949	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	36	341	0	ENST00000356435.5:c.655G>C	p.Ala219Pro	p.A219P	ENST00000356435		219	Gct/Cct	7/35	1	2	FACETS	0.909	0.747	1	0.909	0.747	1	CLONAL	1	TRUE	1	0.18	2		341	440	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	194	349	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.579125127482729	3	FACETS	0.886	0.829	0.944	0.886	0.829	0.944	CLONAL	2	TRUE	1	0.621003258712387	3		349	462	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007443	62007443	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	346	600	0	ENST00000392795.3:c.424C>T	p.Arg142Ter	p.R142*	ENST00000392795	NM_001039933.1	142	Cga/Tga	3/6	0.613844281959839	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.621003258712387	2		600	549	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653437	206653437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782340929	NA	P-0047080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	479	654	2	ENST00000367120.3:c.1321C>T	p.Arg441Trp	p.R441W	ENST00000367120	NM_014002.3	441	Cgg/Tgg	12/22	0.588051775474496	5	FACETS	0.933	0.895	0.97	0.933	0.895	0.97	CLONAL	3	TRUE	2	0.621003258712387	5		656	1065	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911266	29911266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41562120	NA	P-0047080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	50	471	3	ENST00000376809.5:c.565G>A	p.Val189Met	p.V189M	ENST00000376809	NM_002116.7	189	Gtg/Atg	3/8	0.529760843725721	3	FACETS	0.437	0.371	0.509	0.218	0.185	0.255	SUBCLONAL	1	TRUE	1	0.621003258712387	3		474	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579401	7579401	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	400	799	0	ENST00000269305.4:c.286del	p.Ser96LeufsTer27	p.S96Lfs*27	ENST00000269305	NM_001126112.2	96	Tct/ct	4/11	0.613844281959839	2	FACETS	0.929	0.893	0.965	0.929	0.893	0.965	CLONAL	2	TRUE	0	0.621003258712387	2		799	693	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135303	30135303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1174219763	NA	P-0047080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	158	355	0	ENST00000331968.5:c.515G>A	p.Arg172His	p.R172H	ENST00000331968	NM_002742.2	172	cGt/cAt	3/18	0.418949685190563	4	FACETS	0.863	0.797	0.93	0.863	0.797	0.93	CLONAL	2	TRUE	2	0.621003258712387	4		355	478	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857710	59857710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	70	325	0	ENST00000259008.2:c.1847C>T	p.Thr616Ile	p.T616I	ENST00000259008	NM_032043.2	616	aCa/aTa	13/20	0.613844281959839	2	FACETS	0.723	0.635	0.815	0.361	0.317	0.408	SUBCLONAL	1	TRUE	0	0.621003258712387	2		325	312	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436018	116436018	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	291	581	1	ENST00000397752.3:c.4013C>T	p.Ser1338Leu	p.S1338L	ENST00000397752	NM_000245.2	1338	tCa/tTa	21/21	0.529760843725721	3	FACETS	0.957	0.907	1	0.957	0.907	1	CLONAL	2	TRUE	1	0.621003258712387	3		582	642	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411885	116411901	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTTTCTCTCTGTTTTAA	CTTTCTCTCTGTTTTAA	-	novel	NA	P-0047082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	200	696	0	ENST00000397752.3:c.2888-18_2888-2del		p.X963_splice	ENST00000397752	NM_000245.2	963			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		696	967	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	125	516	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.803631948649209	2		516	279	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519337	176519337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758837002	NA	P-0047084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	314	805	2	ENST00000292408.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000292408	NM_213647.1	248	cGg/cAg	7/18	1	2	FACETS	0.848	0.802	0.894	0.848	0.802	0.894	CLONAL	1	TRUE	1	0.803631948649209	2		807	922	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882025	NA	P-0047084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	373	703	0	ENST00000269305.4:c.646G>T	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ttg	6/11	1	2	FACETS	0.938	0.892	0.984	0.938	0.892	0.984	CLONAL	1	TRUE	1	0.803631948649209	2		703	990	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845750	151845750	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs886331780	NA	P-0047084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	313	705	0	ENST00000262189.6:c.13262A>G	p.Asn4421Ser	p.N4421S	ENST00000262189	NM_170606.2	4421	aAc/aGc	52/59	1	2	FACETS	0.914	0.866	0.964	0.914	0.866	0.964	CLONAL	1	TRUE	1	0.803631948649209	2		705	852	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	36	516	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.831	1	1	0.831	1	CLONAL	1	TRUE	1	0.311951422771803	2		516	230	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0047085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	136	735	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.311951422771803	2		735	753	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579591	7579591	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0047089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	137	686	0	ENST00000269305.4:c.97-1G>A		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.196775401575781	3	FACETS	0.854	0.78	0.931	0.854	0.78	0.931	CLONAL	3	TRUE	0	0.196775401575781	3		686	597	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176145102	176145102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	45	338	0	ENST00000367669.3:c.509G>A	p.Cys170Tyr	p.C170Y	ENST00000367669	NM_022457.5	170	tGt/tAt	3/20	0.196775401575781	3	FACETS	1	0.945	1	0.647	0.545	0.76	CLONAL	1	TRUE	1	0.196775401575781	3		338	388	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67197025	67197025	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	43	449	0	ENST00000312629.5:c.268A>G	p.Thr90Ala	p.T90A	ENST00000312629	NM_003952.2	90	Acc/Gcc	4/15	0.196775401575781	4	FACETS	0.876	0.732	1	0.438	0.366	0.518	CLONAL	1	TRUE	2	0.196775401575781	4		449	597	SUCCESS
ATM	472	MSKCC	GRCh37	11	108126983	108126996	+	frameshift_variant	Frame_Shift_Del	DEL	GGTGGGTGTCCTTG	GGTGGGTGTCCTTG	-	novel	NA	P-0047089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	40	523	0	ENST00000278616.4:c.2167_2180del	p.Val723LeufsTer10	p.V723Lfs*10	ENST00000278616	NM_000051.3	722	ttGGTGGGTGTCCTTGgc/ttgc	14/63	0.196775401575781	5	FACETS	1	0.91	1	0.576	0.479	0.685	CLONAL	1	TRUE	3	0.196775401575781	5		523	457	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0047090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	96	442	0	ENST00000304494.5:c.151-1G>A		p.X51_splice	ENST00000304494	NM_000077.4	51			0.52942195719735	1	FACETS	0.599	0.538	0.663	0.599	0.538	0.663	SUBCLONAL	1	TRUE	0	0.610151586425213	1		442	365	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148875	119148875	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs397517076	NA	P-0047090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	73	224	0	ENST00000264033.4:c.1096-1G>T		p.X366_splice	ENST00000264033	NM_005188.3	366			0.450821749137872	2	FACETS	1	0.977	1	0.7	0.627	0.774	CLONAL	1	TRUE	0	0.610151586425213	2		224	171	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475063	40475063	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	312	683	0	ENST00000264657.5:c.1847A>G	p.Glu616Gly	p.E616G	ENST00000264657	NM_139276.2	616	gAa/gGa	20/24	0.436553005471235	3	FACETS	1	0.994	1	0.721	0.681	0.761	CLONAL	1	TRUE	1	0.610151586425213	3		683	926	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133553	55133553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	102	504	1	ENST00000257290.5:c.857G>A	p.Gly286Glu	p.G286E	ENST00000257290	NM_006206.4	286	gGa/gAa	6/23	1	2	FACETS	0.669	0.6	0.74	0.669	0.6	0.74	SUBCLONAL	1	TRUE	1	0.610151586425213	2		505	500	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602619	10602619	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	365	894	0	ENST00000171111.5:c.959G>C	p.Arg320Pro	p.R320P	ENST00000171111	NM_203500.1	320	cGg/cCg	3/6	0.454408244157809	2	FACETS	1	0.995	1	0.721	0.687	0.755	CLONAL	1	TRUE	0	0.610151586425213	2		894	830	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221293	1221293	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs9282859	NA	P-0047090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	384	843	0	ENST00000326873.7:c.816C>G	p.Tyr272Ter	p.Y272*	ENST00000326873	NM_000455.4	272	taC/taG	6/10	0.454408244157809	2	FACETS	1	0.995	1	0.71	0.677	0.742	CLONAL	1	TRUE	0	0.610151586425213	2		843	887	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450100	32450101	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0047090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	341	797	1	ENST00000332351.3:c.711_712del	p.Gln238ValfsTer9	p.Q238Vfs*9	ENST00000332351	NM_024426.4	237	gcGCag/gcag	2/10	0.450821749137872	2	FACETS	1	0.995	1	0.723	0.688	0.758	CLONAL	1	TRUE	0	0.610151586425213	2		798	773	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096367	178096367	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	176	462	0	ENST00000397062.3:c.964C>A	p.Leu322Ile	p.L322I	ENST00000397062	NM_006164.4	322	Cta/Ata	5/5	0.363448392094264	3	FACETS	1	0.985	1	0.631	0.584	0.679	INDETERMINATE	1	TRUE	1	0.610151586425213	3		462	597	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038815	47038824	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCTACCAG	GCCCTACCAG	-	novel	NA	P-0047090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	149	525	0	ENST00000377604.3:c.826_835del	p.Tyr276ArgfsTer29	p.Y276Rfs*29	ENST00000377604	NM_001204468.1	274	caGCCCTACCAG/ca	9/24	1	1	FACETS	0.838	0.774	0.903	0.838	0.774	0.903	CLONAL	1	TRUE	0	0.610151586425213	1		525	405	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	317	349	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.464657680655277	4	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.699141154114058	4		349	684	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578485	7578485	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1064793929	NA	P-0047091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	565	718	0	ENST00000269305.4:c.445del	p.Ser149ProfsTer21	p.S149Pfs*21	ENST00000269305	NM_001126112.2	149	Tcc/cc	5/11	0.323658504129196	1	FACETS	1	0.996	1	1	0.996	1	INDETERMINATE	1	TRUE	0	0.699141154114058	1		718	903	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981882	70981882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	232	632	0	ENST00000276594.2:c.214C>T	p.Arg72Trp	p.R72W	ENST00000276594	NM_024504.3	72	Cgg/Tgg	2/8	1	2	FACETS	0.973	0.912	1	0.973	0.912	1	CLONAL	1	TRUE	1	0.699141154114058	2		632	682	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498116	498116	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1479374937	NA	P-0047091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	691	328	0	ENST00000399788.2:c.142A>G	p.Ile48Val	p.I48V	ENST00000399788	NM_001042603.1	48	Atc/Gtc	1/28	0.36362887514527	4	FACETS	0.913	0.891	0.933			1	INDETERMINATE	4	TRUE	NA	0.699141154114058	4		328	920	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0047092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	672	792	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	0.750373652813555	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.750373652813555	2		792	828	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141507	11141507	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	492	764	1	ENST00000358026.2:c.3484G>T	p.Gly1162Cys	p.G1162C	ENST00000358026	NM_001128849.1	1162	Ggc/Tgc	25/36	0.750373652813555	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.750373652813555	2		765	645	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256235	16256236	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0047092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	137	540	0	ENST00000375759.3:c.3502_3503del	p.Ser1168LeufsTer10	p.S1168Lfs*10	ENST00000375759	NM_015001.2	1167	cAG/c	11/15	1	2	FACETS	0.871	0.8	0.945	0.871	0.8	0.945	CLONAL	1	TRUE	1	0.750373652813555	2		540	419	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858797	9858797	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	151	227	0	ENST00000330684.3:c.2604C>A	p.Tyr868Ter	p.Y868*	ENST00000330684	NM_001134407.1	868	taC/taA	13/13	0.750373652813555	3	FACETS	0.999	0.934	1	0.999	0.934	1	CLONAL	2	TRUE	1	0.750373652813555	3		227	277	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6038842	6038842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	66	624	0	ENST00000265849.7:c.602G>A	p.Ser201Asn	p.S201N	ENST00000265849	NM_000535.5	201	aGt/aAt	6/15	0.57089855569325	5	FACETS	0.343	0.296	0.394	0.114	0.098	0.132	SUBCLONAL	1	TRUE	2	0.750373652813555	5		624	1090	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851197	63851197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1405883740	NA	P-0047092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	670	687	0	ENST00000279873.7:c.1975G>A	p.Asp659Asn	p.D659N	ENST00000279873	NM_032199.2	659	Gac/Aac	10/10	0.750373652813555	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	1	0.750373652813555	4		687	1014	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484185	50484185	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	192	566	0	ENST00000394963.4:c.1035G>T	p.Gln345His	p.Q345H	ENST00000394963	NM_003076.4	345	caG/caT	8/13	0.750373652813555	3	FACETS	0.972	0.902	1	0.486	0.451	0.522	CLONAL	1	TRUE	1	0.750373652813555	3		566	724	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254239	133254239	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	398	542	0	ENST00000320574.5:c.645G>T	p.Leu215Phe	p.L215F	ENST00000320574	NM_006231.2	215	ttG/ttT	7/49	0.750373652813555	3	FACETS	0.99	0.95	1	0.99	0.95	1	CLONAL	2	TRUE	1	0.750373652813555	3		542	737	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96930986	96930986	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	239	583	0	ENST00000258439.3:c.134G>T	p.Cys45Phe	p.C45F	ENST00000258439	NM_001193304.2	45	tGc/tTc	2/4	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.750373652813555	2		583	582	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527460	41527460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151308825	NA	P-0047092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	208	621	0	ENST00000263253.7:c.1351C>T	p.Pro451Ser	p.P451S	ENST00000263253	NM_001429.3	451	Ccc/Tcc	6/31	1	2	FACETS	0.951	0.889	1	0.951	0.889	1	CLONAL	1	TRUE	1	0.750373652813555	2		621	583	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524723	187524723	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	249	719	0	ENST00000441802.2:c.10957G>T	p.Glu3653Ter	p.E3653*	ENST00000441802	NM_005245.3	3653	Gaa/Taa	19/27	0.750373652813555	3	FACETS	0.965	0.903	1	0.482	0.451	0.514	CLONAL	1	TRUE	1	0.750373652813555	3		719	946	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891316	101891316	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	359	508	1	ENST00000374994.4:c.277G>T	p.Gly93Trp	p.G93W	ENST00000374994	NM_004612.2	93	Ggg/Tgg	2/9	0.750373652813555	3	FACETS	0.995	0.953	1	0.995	0.953	1	CLONAL	2	TRUE	1	0.750373652813555	3		509	661	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934349	39934349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	252	335	0	ENST00000378444.4:c.250G>T	p.Val84Phe	p.V84F	ENST00000378444	NM_001123385.1	84	Gtc/Ttc	4/15	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.750373652813555	1		335	325	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	56	516	0				ENST00000310581	NM_198253.2	-/1132			0.246987108499022	0	FACETS	0.34	0.294	0.388			1	INDETERMINATE	1	TRUE	0	0.58797124102774	0		516	231	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0047099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	498	530	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.328337273238624	6	FACETS	0.947	0.912	0.982			1	INDETERMINATE	4	TRUE	NA	0.58797124102774	6		530	973	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	414	486	0	ENST00000269305.4:c.859G>T	p.Glu287Ter	p.E287*	ENST00000269305	NM_001126112.2	287	Gag/Tag	8/11	0.581790595978085	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.58797124102774	2		486	701	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352697	NA	P-0047099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	294	501	0	ENST00000269305.4:c.587G>A	p.Arg196Gln	p.R196Q	ENST00000269305	NM_001126112.2	196	cGa/cAa	6/11	0.581790595978085	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.58797124102774	2		501	487	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405188	70405188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	33	374	0	ENST00000373644.4:c.2702C>T	p.Ser901Leu	p.S901L	ENST00000373644	NM_030625.2	901	tCa/tTa	4/12	0.208867737339913	2	FACETS	0.567	0.466	0.679	0.283	0.233	0.34	INDETERMINATE	1	TRUE	0	0.58797124102774	2		374	198	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112035575	112035575	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1159797492	NA	P-0047099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	27	276	0	ENST00000368678.4:c.319G>C	p.Glu107Gln	p.E107Q	ENST00000368678		107	Gaa/Caa	4/13	0.396734848184907	1	FACETS	0.63	0.512	0.757	0.63	0.512	0.757	SUBCLONAL	1	TRUE	0	0.58797124102774	1		276	103	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430342	78430342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	11	338	0	ENST00000370768.2:c.826G>A	p.Glu276Lys	p.E276K	ENST00000370768	NM_003902.3	276	Gaa/Aaa	10/20	0.305278893719284	1	FACETS	0.4	0.282	0.541	0.4	0.282	0.541	INDETERMINATE	1	TRUE	0	0.58797124102774	1		338	66	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596088	43596088	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	117	522	0	ENST00000355710.3:c.255G>C	p.Trp85Cys	p.W85C	ENST00000355710	NM_020975.4	85	tgG/tgC	2/20	0.208867737339913	2	FACETS	0.816	0.739	0.895	0.408	0.369	0.448	INDETERMINATE	1	TRUE	0	0.58797124102774	2		522	488	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129762	108129762	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0047099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	22	292	0	ENST00000278616.4:c.2426C>G	p.Ser809Ter	p.S809*	ENST00000278616	NM_000051.3	809	tCa/tGa	16/63	0.189515077438394	2	FACETS	0.713	0.562	0.881	0.356	0.281	0.441	INDETERMINATE	1	TRUE	0	0.58797124102774	2		292	105	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881467	48881468	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	13	217	0	ENST00000267163.4:c.191dup	p.Leu64PhefsTer46	p.L64Ffs*46	ENST00000267163	NM_000321.2	63	-/T	2/27	1	2	FACETS	0.819	0.629	1	1	0.912	1	CLONAL	2	TRUE	1	0.58797124102774	2		217	27	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665728	29665728	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	10	177	0	ENST00000356175.3:c.6763G>C	p.Glu2255Gln	p.E2255Q	ENST00000356175	NM_000267.3	2255	Gag/Cag	45/57	0.316629122974495	4	FACETS	1	0.848	1			1	INDETERMINATE	1	TRUE	NA	0.58797124102774	4		177	38	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190708742	190708742	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0047099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	40	298	0	ENST00000441310.2:c.635C>G	p.Ser212Ter	p.S212*	ENST00000441310	NM_000534.4	212	tCa/tGa	6/13	0.305278893719284	1	FACETS	0.924	0.791	1	0.924	0.791	1	INDETERMINATE	1	TRUE	0	0.58797124102774	1		298	104	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278816	1278826	+	frameshift_variant	Frame_Shift_Del	DEL	ACGCACGCAGT	ACGCACGCAGT	-	novel	NA	P-0047099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	101	579	0	ENST00000310581.5:c.2216_2226del	p.Tyr739SerfsTer58	p.Y739Sfs*58	ENST00000310581	NM_198253.2	739	tACTGCGTGCGT/t	6/16	0.246987108499022	0	FACETS	0.306	0.274	0.339			1	INDETERMINATE	1	TRUE	0	0.58797124102774	0		579	463	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089755	5089755	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	29	186	0	ENST00000381652.3:c.2653C>T	p.Gln885Ter	p.Q885*	ENST00000381652	NM_004972.3	885	Cag/Tag	20/25	0.189515077438394	2	FACETS	1	0.924	1	0.617	0.512	0.727	INDETERMINATE	1	TRUE	0	0.58797124102774	2		186	80	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212883	27212883	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	73	527	0	ENST00000380036.4:c.2865G>C	p.Leu955Phe	p.L955F	ENST00000380036	NM_000459.3	955	ttG/ttC	17/23	0.189515077438394	2	FACETS	0.54	0.473	0.611	0.27	0.236	0.306	INDETERMINATE	1	TRUE	0	0.58797124102774	2		527	460	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339250	70339253	+	protein_altering_variant	In_Frame_Del	DEL	CAAG	CAAG	T	novel	NA	P-0047099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	173	236	0	ENST00000374080.3:c.127_130delinsT	p.Gln43_Gly44delinsCys	p.Q43_G44delinsC	ENST00000374080		43	CAAGgt/Tgt	2/45	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.58797124102774	1		236	303	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0047100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	341	665	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.262583951189203	3	FACETS	0.842	0.8	0.885	0.842	0.8	0.885	CLONAL	3	TRUE	0	0.350127301154084	3		665	906	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0047100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	46	176	0	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	0.350127301154084	5	FACETS	1	0.952	1	0.675	0.571	0.787	CLONAL	1	TRUE	3	0.350127301154084	5		176	297	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268156	153268156	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	195	332	0	ENST00000281708.4:c.652C>T	p.Gln218Ter	p.Q218*	ENST00000281708	NM_033632.3	218	Caa/Taa	4/12	0.350127301154084	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	1	0.350127301154084	3		332	644	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117083	7117083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs52826008	NA	P-0047100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	193	422	0	ENST00000302850.5:c.4133G>A	p.Arg1378Gln	p.R1378Q	ENST00000302850	NM_000208.2	1378	cGg/cAg	22/22	1	2	FACETS	0.817	0.759	0.876	1	0.992	1	CLONAL	2	TRUE	1	0.350127301154084	2		422	675	SUCCESS
APC	324	MSKCC	GRCh37	5	112173665	112173665	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0047100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	73	242	0	ENST00000257430.4:c.2374A>T	p.Lys792Ter	p.K792*	ENST00000257430	NM_000038.5	792	Aag/Tag	16/16	0.350127301154084	5	FACETS	0.874	0.769	0.985	0.874	0.769	0.985	CLONAL	2	TRUE	3	0.350127301154084	5		242	364	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	93	516	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.700716048224247	2		516	250	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692802	89692802	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123320	NA	P-0047101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	48	251	0	ENST00000371953.3:c.286C>T	p.Pro96Ser	p.P96S	ENST00000371953	NM_000314.4	96	Cca/Tca	5/9	0.700716048224247	1	FACETS	0.365	0.311	0.423	0.365	0.311	0.423	SUBCLONAL	1	TRUE	0	0.700716048224247	1		251	244	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945948	17945948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373027121	NA	P-0047101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	226	646	0	ENST00000458235.1:c.1991C>T	p.Pro664Leu	p.P664L	ENST00000458235	NM_000215.3	664	cCg/cTg	15/24	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.700716048224247	2		646	643	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266638	142266638	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1176218951	NA	P-0047101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	170	276	0	ENST00000350721.4:c.3286A>G	p.Ile1096Val	p.I1096V	ENST00000350721	NM_001184.3	1096	Ata/Gta	16/47	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.700716048224247	2		276	483	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916614	178916614	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0047101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	134	230	1	ENST00000263967.3:c.1A>G	p.Met1?	p.M1?	ENST00000263967	NM_006218.2	1	Atg/Gtg	2/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.700716048224247	2		231	347	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	124	349	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.2840580600276	1	FACETS	0.752	0.685	0.822	0.752	0.685	0.822	INDETERMINATE	1	TRUE	0	0.526948891596706	1		349	461	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968840	32968840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80359194	NA	P-0047104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	49	164	0	ENST00000380152.3:c.9271G>A	p.Val3091Ile	p.V3091I	ENST00000380152		3091	Gtc/Atc	25/27	1	2	FACETS	0.525	0.446	0.611	0.525	0.446	0.611	SUBCLONAL	1	TRUE	1	0.526948891596706	2		164	354	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670641	134670641	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	103	523	2	ENST00000398015.3:c.552G>T	p.Met184Ile	p.M184I	ENST00000398015	NM_004441.4	184	atG/atT	3/16	0.526948891596706	1	FACETS	0.419	0.375	0.466	0.419	0.375	0.466	SUBCLONAL	1	TRUE	0	0.526948891596706	1		525	687	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040923	47040923	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	211	309	1	ENST00000377604.3:c.1453G>T	p.Glu485Ter	p.E485*	ENST00000377604	NM_001204468.1	485	Gag/Tag	14/24	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.526948891596706	1		310	442	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0047105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	116	272	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.798244103745587	4	FACETS	0.996	0.933	1	0.996	0.933	1	CLONAL	3	TRUE	1	0.831593985873715	4		272	171	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0047105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	100	376	0	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	1	2	FACETS	0.908	0.824	0.993	0.908	0.824	0.993	CLONAL	1	TRUE	1	0.831593985873715	2		376	265	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115435	115115437	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	rs1319662056	NA	P-0047105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	103	420	0	ENST00000257566.3:c.889_891del	p.Asn297del	p.N297del	ENST00000257566	NM_016569.3	297	AAC/-	5/8	0.751341090025248	2	FACETS	0.904	0.849	0.955	0.904	0.849	0.955	CLONAL	2	TRUE	0	0.831593985873715	2		420	137	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636970	158636970	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	113	399	0	ENST00000263640.3:c.210C>A	p.Cys70Ter	p.C70*	ENST00000263640	NM_001105.4	70	tgC/tgA	4/11	1	2	FACETS	0.88	0.802	0.958	0.88	0.802	0.958	CLONAL	1	TRUE	1	0.831593985873715	2		399	309	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057519990	NA	P-0047106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	31	460	0	ENST00000269305.4:c.796G>T	p.Gly266Ter	p.G266*	ENST00000269305	NM_001126112.2	266	Gga/Tga	8/11	1	2	FACETS	0.608	0.489	0.743	0.608	0.489	0.743	SUBCLONAL	1	TRUE	1	0.11	2		460	927	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	86	349	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.283242481940873	2	FACETS	0.76	0.677	0.847	0.76	0.677	0.847	SUBCLONAL	2	TRUE	0	0.307411741502198	2		349	368	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163315498	163315498	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	55	381	2	ENST00000271452.3:c.838G>T	p.Gly280Ter	p.G280*	ENST00000271452	NM_145697.2	280	Gga/Tga	11/14	0.307411741502198	3	FACETS	0.843	0.721	0.974	0.421	0.36	0.487	CLONAL	1	TRUE	1	0.307411741502198	3		383	490	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476310	88476310	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	77	639	0	ENST00000360948.2:c.1822G>T	p.Gly608Cys	p.G608C	ENST00000360948	NM_001012338.2	608	Ggc/Tgc	15/19	1	2	FACETS	0.715	0.627	0.809	0.715	0.627	0.809	SUBCLONAL	1	TRUE	1	0.307411741502198	2		639	701	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892139	9892139	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	112	476	1	ENST00000330684.3:c.2351G>T	p.Gly784Val	p.G784V	ENST00000330684	NM_001134407.1	784	gGt/gTt	11/13	0.195640190573958	2	FACETS	1	0.978	1	0.656	0.592	0.724	CLONAL	1	TRUE	0	0.307411741502198	2		477	555	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207009	1207009	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	227	770	0	ENST00000326873.7:c.97G>T	p.Glu33Ter	p.E33*	ENST00000326873	NM_000455.4	33	Gag/Tag	1/10	0.283242481940873	2	FACETS	0.936	0.875	0.999	0.936	0.875	0.999	CLONAL	2	TRUE	0	0.307411741502198	2		770	789	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602746	10602746	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	356	810	0	ENST00000171111.5:c.832C>G	p.Pro278Ala	p.P278A	ENST00000171111	NM_203500.1	278	Ccg/Gcg	3/6	0.283242481940873	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.307411741502198	2		810	1118	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578332	212578332	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	44	372	0	ENST00000342788.4:c.925C>A	p.Pro309Thr	p.P309T	ENST00000342788	NM_005235.2	309	Cct/Act	8/28	1	2	FACETS	0.77	0.647	0.904	0.77	0.647	0.904	CLONAL	1	TRUE	1	0.307411741502198	2		372	372	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715678	30715678	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886039551	NA	P-0047108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	39	335	0	ENST00000295754.5:c.1336G>A	p.Asp446Asn	p.D446N	ENST00000295754	NM_003242.5	446	Gat/Aat	5/7	0.307411741502198	1	FACETS	0.617	0.513	0.733	0.617	0.513	0.733	SUBCLONAL	1	TRUE	0	0.307411741502198	1		335	348	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390834	139390835	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0047108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	147	943	3	ENST00000277541.6:c.7356_7357delinsTT	p.Val2453Leu	p.V2453L	ENST00000277541	NM_017617.3	2452	gcGGtg/gcTTtg	34/34	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.307411741502198	2		946	943	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813074	76813074	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	46	495	0	ENST00000373344.5:c.6547C>G	p.Gln2183Glu	p.Q2183E	ENST00000373344	NM_000489.3	2183	Cag/Gag	30/35	1	2	FACETS	0.579	0.487	0.68	0.579	0.487	0.68	SUBCLONAL	1	TRUE	1	0.307411741502198	2		495	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0047114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	212	682	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.855995672748638	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.857062729250969	1		684	264	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032847	48032847	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0047114-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	108	310	1	ENST00000234420.5:c.3646+1G>A		p.X1216_splice	ENST00000234420	NM_000179.2	1216			0.186364348617858	3	FACETS	1	0.986	1	0.744	0.681	0.807	INDETERMINATE	1	TRUE	1	0.857062729250969	3		311	242	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047115-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	18	516	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		516	220	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047115-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	104	516	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		516	309	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	89	274	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	0.36989840762621	2	FACETS	1	0.92	1			1	CLONAL	2	TRUE	NA	0.412555756420513	2		274	212	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480435	50480435	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	22	544	0	ENST00000394963.4:c.397C>G	p.Leu133Val	p.L133V	ENST00000394963	NM_003076.4	133	Cta/Gta	3/13	1	2	FACETS	0.256	0.198	0.324	0.256	0.198	0.324	SUBCLONAL	1	TRUE	1	0.412555756420513	2		544	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520000	NA	P-0047116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	179	996	0	ENST00000269305.4:c.452C>A	p.Pro151His	p.P151H	ENST00000269305	NM_001126112.2	151	cCc/cAc	5/11	0.407728033445021	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.412555756420513	1		996	626	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179050	123179050	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	109	344	0	ENST00000218089.9:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000218089	NM_001042749.1	167	Cag/Tag	8/35	0.36989840762621	2	FACETS	0.899	0.819	0.98			1	CLONAL	2	TRUE	NA	0.412555756420513	2		344	294	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056464	26056465	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	75	455	0	ENST00000343677.2:c.192dup	p.Ala65SerfsTer8	p.A65Sfs*8	ENST00000343677	NM_005319.3	64	-/A	1/1	0.11128888670071	4	FACETS	1	0.976	1	0.734	0.647	0.825	INDETERMINATE	1	TRUE	2	0.412555756420513	4		455	350	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230371	46230371	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0047116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	63	342	0	ENST00000334344.6:c.706-1G>A		p.X236_splice	ENST00000334344	NM_152641.2	236			1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.412555756420513	2		342	299	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170046	32170046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768387019	NA	P-0047116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	135	1034	0	ENST00000375023.3:c.3562G>A	p.Asp1188Asn	p.D1188N	ENST00000375023	NM_004557.3	1188	Gat/Aat	21/30	0.11128888670071	4	FACETS	1	0.985	1	0.714	0.651	0.781	INDETERMINATE	1	TRUE	2	0.412555756420513	4		1034	647	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363382	40363382	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	64	790	0	ENST00000397332.2:c.847G>C	p.Glu283Gln	p.E283Q	ENST00000397332	NM_001033082.2	283	Gag/Cag	3/3	1	2	FACETS	0.629	0.546	0.72	0.629	0.546	0.72	SUBCLONAL	1	TRUE	1	0.412555756420513	2		790	493	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406303	406303	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	105	642	0	ENST00000399788.2:c.4138C>G	p.Pro1380Ala	p.P1380A	ENST00000399788	NM_001042603.1	1380	Ccc/Gcc	25/28	NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.412555756420513	2		642	467	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151866298	151866298	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	38	379	0	ENST00000262189.6:c.9490C>T	p.Pro3164Ser	p.P3164S	ENST00000262189	NM_170606.2	3164	Cct/Tct	41/59	0.138770819145846	6	FACETS	0.668	0.552	0.799	0.223	0.184	0.267	INDETERMINATE	1	TRUE	3	0.412555756420513	6		379	503	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0047117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	187	615	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	1	2	FACETS	0.805	0.742	0.871	1	0.991	1	CLONAL	2	TRUE	1	0.187280372361247	2		615	1240	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0047118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	129	519	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	NA	2	FACETS	1	0.953	1			1	INDETERMINATE	1	TRUE	NA	0.364866991057637	2		519	656	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256190	133256190	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	63	578	0	ENST00000320574.5:c.471C>A	p.Phe157Leu	p.F157L	ENST00000320574	NM_006231.2	157	ttC/ttA	6/49	0.0748252501133972	3	FACETS	0.566	0.488	0.65			1	INDETERMINATE	1	TRUE	NA	0.364866991057637	3		578	722	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	15	353	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.328	0.239	0.434	0.328	0.239	0.434	SUBCLONAL	1	TRUE	1	0.340038563122082	2		353	269	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	20	580	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.231	0.176	0.296	0.231	0.176	0.296	SUBCLONAL	1	TRUE	1	0.340038563122082	2		580	509	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	11	222	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.325	0.224	0.45	0.325	0.224	0.45	SUBCLONAL	1	TRUE	1	0.340038563122082	2		222	199	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	52	428	2	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.109770388975837	3	FACETS	0.875	0.747	1	0.437	0.373	0.508	INDETERMINATE	1	TRUE	1	0.340038563122082	3		430	409	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739030	145739030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199562131	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	44	739	0	ENST00000428558.2:c.2125C>T	p.Arg709Trp	p.R709W	ENST00000428558	NM_004260.3	709	Cgg/Tgg	13/22	1	2	FACETS	0.352	0.294	0.416	0.352	0.294	0.416	SUBCLONAL	1	TRUE	1	0.340038563122082	2		739	736	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	70	1009	0	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	0.484	0.421	0.553	0.484	0.421	0.553	SUBCLONAL	1	TRUE	1	0.340038563122082	2		1009	850	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851848	134851848	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	38	732	0	ENST00000398015.3:c.1259del	p.Pro420HisfsTer28	p.P420Hfs*28	ENST00000398015	NM_004441.4	418	ttC/tt	5/16	1	2	FACETS	0.323	0.266	0.387	0.323	0.266	0.387	SUBCLONAL	1	TRUE	1	0.340038563122082	2		732	692	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686901	37686901	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	48	552	2	ENST00000447079.4:c.3810del	p.Gly1271AspfsTer23	p.G1271Dfs*23	ENST00000447079	NM_015083.1	1269	Ccc/cc	14/14	1	2	FACETS	0.474	0.4	0.555	0.474	0.4	0.555	SUBCLONAL	1	TRUE	1	0.340038563122082	2		554	596	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687472	37687472	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	24	446	3	ENST00000447079.4:c.4382del	p.Gly1461AlafsTer38	p.G1461Afs*38	ENST00000447079	NM_015083.1	1459	tGg/tg	14/14	1	2	FACETS	0.365	0.285	0.456	0.365	0.285	0.456	SUBCLONAL	1	TRUE	1	0.340038563122082	2		449	387	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411678	63411678	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	33	396	0	ENST00000330258.3:c.1489C>T	p.Arg497Ter	p.R497*	ENST00000330258	NM_152424.3	497	Cga/Tga	2/2	NA	2	FACETS	0.568	0.463	0.685			1	INDETERMINATE	1	TRUE	NA	0.340038563122082	2		396	342	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182145	11182145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1238905384	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	45	780	0	ENST00000361445.4:c.6701C>T	p.Ser2234Leu	p.S2234L	ENST00000361445	NM_004958.3	2234	tCg/tTg	48/58	1	2	FACETS	0.362	0.303	0.427	0.362	0.303	0.427	SUBCLONAL	1	TRUE	1	0.340038563122082	2		780	731	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910708	29910708	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	71	1131	0	ENST00000376809.5:c.248A>G	p.Tyr83Cys	p.Y83C	ENST00000376809	NM_002116.7	83	tAt/tGt	2/8	1	2	FACETS	0.399	0.347	0.456	0.399	0.347	0.456	SUBCLONAL	1	TRUE	1	0.340038563122082	2		1131	1046	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619216	1619216	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	52	761	0	ENST00000344749.5:c.1344del	p.Glu449ArgfsTer37	p.E449Rfs*37	ENST00000344749	NM_001136139.2	448	ccC/cc	16/19	1	2	FACETS	0.418	0.355	0.488	0.418	0.355	0.488	SUBCLONAL	1	TRUE	1	0.340038563122082	2		761	731	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	77	751	5	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	1	2	FACETS	0.681	0.598	0.771	0.681	0.598	0.771	SUBCLONAL	1	TRUE	1	0.340038563122082	2		756	665	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	51	1144	2	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	1	2	FACETS	0.402	0.34	0.469	0.402	0.34	0.469	SUBCLONAL	1	TRUE	1	0.340038563122082	2		1146	747	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803571	1803571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs4647924	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	26	477	1	ENST00000260795.2:c.749C>T	p.Pro250Leu	p.P250L	ENST00000260795		250	cCg/cTg	6/17	1	2	FACETS	0.344	0.272	0.428	0.344	0.272	0.428	SUBCLONAL	1	TRUE	1	0.340038563122082	2		478	444	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599271	28599271	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs770146088	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	53	927	0	ENST00000253063.3:c.722del	p.Pro241GlnfsTer6	p.P241Qfs*6	ENST00000253063	NM_031459.4	239	agC/ag	5/10	1	2	FACETS	0.352	0.299	0.41	0.352	0.299	0.41	SUBCLONAL	1	TRUE	1	0.340038563122082	2		927	886	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015025	27015025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754932895	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	30	434	0	ENST00000335756.4:c.127C>T	p.Arg43Trp	p.R43W	ENST00000335756	NM_001809.3	43	Cgg/Tgg	2/5	1	2	FACETS	0.352	0.283	0.431	0.352	0.283	0.431	SUBCLONAL	1	TRUE	1	0.340038563122082	2		434	501	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129351	64129351	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	61	983	2	ENST00000334205.4:c.788del	p.Pro263LeufsTer112	p.P263Lfs*112	ENST00000334205	NM_003942.2	261	ttC/tt	8/17	1	2	FACETS	0.491	0.423	0.566	0.491	0.423	0.566	SUBCLONAL	1	TRUE	1	0.340038563122082	2		985	730	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197435	106197435	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	30	338	0	ENST00000380013.4:c.5772del	p.Ala1925ProfsTer25	p.A1925Pfs*25	ENST00000380013	NM_001127208.2	1923	gAa/ga	11/11	1	2	FACETS	0.58	0.469	0.707	0.58	0.469	0.707	SUBCLONAL	1	TRUE	1	0.340038563122082	2		338	304	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214313	55214313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs532655845	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	49	681	0	ENST00000275493.2:c.439G>A	p.Ala147Thr	p.A147T	ENST00000275493	NM_005228.3	147	Gcc/Acc	4/28	1	2	FACETS	0.465	0.393	0.544	0.465	0.393	0.544	SUBCLONAL	1	TRUE	1	0.340038563122082	2		681	620	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846014	128846014	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	39	647	0	ENST00000249373.3:c.944T>C	p.Val315Ala	p.V315A	ENST00000249373	NM_005631.4	315	gTc/gCc	5/12	1	2	FACETS	0.389	0.322	0.465	0.389	0.322	0.465	SUBCLONAL	1	TRUE	1	0.340038563122082	2		647	589	SUCCESS
ATM	472	MSKCC	GRCh37	11	108183191	108183191	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	16	249	0	ENST00000278616.4:c.5977del	p.Ser1993ValfsTer7	p.S1993Vfs*7	ENST00000278616	NM_000051.3	1991	gAa/ga	40/63	1	2	FACETS	0.379	0.28	0.498	0.379	0.28	0.498	SUBCLONAL	1	TRUE	1	0.340038563122082	2		249	248	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434905	110434905	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	44	688	1	ENST00000375856.3:c.3496G>A	p.Ala1166Thr	p.A1166T	ENST00000375856	NM_003749.2	1166	Gcc/Acc	1/2	1	2	FACETS	0.327	0.273	0.387	0.327	0.273	0.387	SUBCLONAL	1	TRUE	1	0.340038563122082	2		689	792	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278755	1278755	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	42	721	1	ENST00000310581.5:c.2286+1G>A		p.X762_splice	ENST00000310581	NM_198253.2	762			1	2	FACETS	0.421	0.351	0.499	0.421	0.351	0.499	SUBCLONAL	1	TRUE	1	0.340038563122082	2		722	587	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187202	11187202	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	23	544	0	ENST00000361445.4:c.6217-1G>T		p.X2073_splice	ENST00000361445	NM_004958.3	2073			1	2	FACETS	0.316	0.246	0.398	0.316	0.246	0.398	SUBCLONAL	1	TRUE	1	0.340038563122082	2		544	428	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652414	206652414	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782715972	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	43	779	3	ENST00000367120.3:c.1121C>T	p.Thr374Met	p.T374M	ENST00000367120	NM_014002.3	374	aCg/aTg	10/22	1	2	FACETS	0.325	0.271	0.386	0.325	0.271	0.386	SUBCLONAL	1	TRUE	1	0.340038563122082	2		782	777	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360585	118360587	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	23	441	0	ENST00000534358.1:c.4566_4568del	p.Lys1523del	p.K1523del	ENST00000534358	NM_005933.3	1520	AAG/-	12/36	1	2	FACETS	0.305	0.237	0.384	0.305	0.237	0.384	SUBCLONAL	1	TRUE	1	0.340038563122082	2		441	443	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896548	78896548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242627252	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	57	826	2	ENST00000306801.3:c.2545C>T	p.Arg849Cys	p.R849C	ENST00000306801	NM_020761.2	849	Cgc/Tgc	22/34	1	2	FACETS	0.43	0.368	0.498	0.43	0.368	0.498	SUBCLONAL	1	TRUE	1	0.340038563122082	2		828	779	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100034	11100034	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	49	755	0	ENST00000358026.2:c.1160A>G	p.Asn387Ser	p.N387S	ENST00000358026	NM_001128849.1	387	aAc/aGc	7/36	1	2	FACETS	0.402	0.339	0.471	0.402	0.339	0.471	SUBCLONAL	1	TRUE	1	0.340038563122082	2		755	717	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279585	18279585	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766061667	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	48	820	0	ENST00000222254.8:c.1858C>T	p.Arg620Cys	p.R620C	ENST00000222254	NM_005027.3	620	Cgc/Tgc	15/16	1	2	FACETS	0.358	0.302	0.421	0.358	0.302	0.421	SUBCLONAL	1	TRUE	1	0.340038563122082	2		820	788	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213366	36213366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866223177	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	54	978	1	ENST00000222270.7:c.2563C>T	p.Arg855Trp	p.R855W	ENST00000222270	NM_014727.1	855	Cgg/Tgg	4/37	1	2	FACETS	0.376	0.32	0.437	0.376	0.32	0.437	SUBCLONAL	1	TRUE	1	0.340038563122082	2		979	845	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223619	36223619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769427218	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	68	1079	2	ENST00000222270.7:c.6169C>T	p.Arg2057Cys	p.R2057C	ENST00000222270	NM_014727.1	2057	Cgc/Tgc	28/37	1	2	FACETS	0.504	0.437	0.576	0.504	0.437	0.576	SUBCLONAL	1	TRUE	1	0.340038563122082	2		1081	794	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663357	227663357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	63	663	0	ENST00000305123.5:c.98G>A	p.Arg33His	p.R33H	ENST00000305123	NM_005544.2	33	cGc/cAc	1/2	1	2	FACETS	0.674	0.583	0.772	0.674	0.583	0.772	SUBCLONAL	1	TRUE	1	0.340038563122082	2		663	550	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945676	54945677	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	20	373	0	ENST00000312783.6:c.893dup	p.Glu299Ter	p.E299*	ENST00000312783	NM_198436.1	298	cct/ccCt	9/10	1	2	FACETS	0.368	0.281	0.469	0.368	0.281	0.469	SUBCLONAL	1	TRUE	1	0.340038563122082	2		373	320	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532542	187532543	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	15	306	0	ENST00000441802.2:c.9850dup	p.Thr3284AsnfsTer8	p.T3284Nfs*8	ENST00000441802	NM_005245.3	3284	aca/aAca	14/27	1	2	FACETS	0.317	0.232	0.42	0.317	0.232	0.42	SUBCLONAL	1	TRUE	1	0.340038563122082	2		306	278	SUCCESS
APC	324	MSKCC	GRCh37	5	112116551	112116551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748193367	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	15	376	1	ENST00000257430.4:c.596C>T	p.Ala199Val	p.A199V	ENST00000257430	NM_000038.5	199	gCg/gTg	6/16	1	2	FACETS	0.307	0.224	0.407	0.307	0.224	0.407	SUBCLONAL	1	TRUE	1	0.340038563122082	2		377	287	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517531	176517531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	47	1000	1	ENST00000292408.4:c.232C>T	p.Arg78Cys	p.R78C	ENST00000292408	NM_213647.1	78	Cgt/Tgt	3/18	1	2	FACETS	0.363	0.305	0.427	0.363	0.305	0.427	SUBCLONAL	1	TRUE	1	0.340038563122082	2		1001	761	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805885	32805885	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	50	944	0	ENST00000374899.4:c.126del	p.Thr43ProfsTer11	p.T43Pfs*11	ENST00000374899	NM_018833.2	42	ggG/gg	2/12	1	2	FACETS	0.364	0.307	0.426	0.364	0.307	0.426	SUBCLONAL	1	TRUE	1	0.340038563122082	2		944	809	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737596	145737596	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs773143092	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	49	1017	0	ENST00000428558.2:c.3167A>G	p.Tyr1056Cys	p.Y1056C	ENST00000428558	NM_004260.3	1056	tAt/tGt	19/22	1	2	FACETS	0.356	0.301	0.418	0.356	0.301	0.418	SUBCLONAL	1	TRUE	1	0.340038563122082	2		1017	809	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041199	47041199	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	24	447	0	ENST00000377604.3:c.1627A>G	p.Thr543Ala	p.T543A	ENST00000377604	NM_001204468.1	543	Acc/Gcc	15/24	NA	2	FACETS	0.408	0.32	0.51			1	INDETERMINATE	1	TRUE	NA	0.340038563122082	2		447	346	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0047123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	194	374	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.778248377173078	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.778248377173078	1		374	271	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0047123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	290	663	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.778248377173078	2		663	652	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637631	23637631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45476495	NA	P-0047123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	263	571	1	ENST00000261584.4:c.2674G>A	p.Glu892Lys	p.E892K	ENST00000261584	NM_024675.3	892	Gaa/Aaa	7/13	0.350158843709307	3	FACETS	1	0.993	1	0.718	0.677	0.759	INDETERMINATE	1	TRUE	1	0.778248377173078	3		572	654	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578189	7578190	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0047123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	344	656	0	ENST00000269305.4:c.659dup	p.Tyr220Ter	p.Y220*	ENST00000269305	NM_001126112.2	220	tat/taAt	6/11	0.778248377173078	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.778248377173078	1		656	476	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46588099	46588100	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0047123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	255	719	0	ENST00000263734.3:c.651_652del	p.Leu218AlafsTer9	p.L218Afs*9	ENST00000263734	NM_001430.4	217	CCc/c	6/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.778248377173078	2		719	639	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192550	138192550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	99	398	0	ENST00000237289.4:c.186G>T	p.Glu62Asp	p.E62D	ENST00000237289	NM_001270507.1	62	gaG/gaT	2/9	1	2	FACETS	0.487	0.436	0.541	0.487	0.436	0.541	SUBCLONAL	1	TRUE	1	0.778248377173078	2		398	522	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0047124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	26	578	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	1	2	FACETS	0.323	0.255	0.403	0.323	0.255	0.403	SUBCLONAL	1	TRUE	1	0.17	2		578	946	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0047124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	47	803	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	1	2	FACETS	0.603	0.507	0.71	0.603	0.507	0.71	SUBCLONAL	1	TRUE	1	0.17	2		803	917	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760817	59760817	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	66	496	2	ENST00000259008.2:c.3590G>T	p.Gly1197Val	p.G1197V	ENST00000259008	NM_032043.2	1197	gGa/gTa	20/20	1	2	FACETS	0.847	0.733	0.971	0.847	0.733	0.971	CLONAL	1	TRUE	1	0.17	2		498	917	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430296	181430296	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	33	377	0	ENST00000325404.1:c.148G>T	p.Val50Leu	p.V50L	ENST00000325404	NM_003106.3	50	Gtg/Ttg	1/1	0.17135055960264	3	FACETS	0.892	0.726	1	0.446	0.363	0.54	CLONAL	1	TRUE	1	0.17	3		377	472	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047125-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	188	349	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.358467152294325	3	FACETS	0.978	0.916	1	1	0.992	1	CLONAL	3	TRUE	1	0.382791400450068	3		349	399	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206667323	206667323	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs782670085	NA	P-0047126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1606	167	741	3	ENST00000367120.3:c.2116C>T	p.Arg706Trp	p.R706W	ENST00000367120	NM_014002.3	706	Cgg/Tgg	21/22	0.715189225314777	4	FACETS	0.4	0.366	0.436	0.133	0.122	0.146	SUBCLONAL	1	TRUE	1	0.888687073803228	4		744	1773	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117439	4117439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202220799	NA	P-0047126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	224	698	1	ENST00000262948.5:c.281C>T	p.Ser94Leu	p.S94L	ENST00000262948	NM_030662.3	94	tCg/tTg	2/11	0.598384296371061	1	FACETS	0.395	0.369	0.421	0.395	0.369	0.421	SUBCLONAL	1	TRUE	0	0.888687073803228	1		699	710	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056039	26056039	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs61742488	NA	P-0047126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	113	451	0	ENST00000343677.2:c.618G>C	p.Lys206Asn	p.K206N	ENST00000343677	NM_005319.3	206	aaG/aaC	1/1	0.396741963287419	3	FACETS	0.602	0.543	0.664	0.301	0.271	0.332	INDETERMINATE	1	TRUE	1	0.888687073803228	3		451	610	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197129	26197129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	147	645	0	ENST00000356476.2:c.350G>A	p.Arg117Gln	p.R117Q	ENST00000356476		117	cGa/cAa	1/1	0.396741963287419	3	FACETS	0.548	0.5	0.598	0.274	0.25	0.299	INDETERMINATE	1	TRUE	1	0.888687073803228	3		645	872	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609052	43609052	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	198	785	0	ENST00000355710.3:c.1808A>T	p.Lys603Ile	p.K603I	ENST00000355710	NM_020975.4	603	aAa/aTa	10/20	1	2	FACETS	0.546	0.506	0.587	0.546	0.506	0.587	SUBCLONAL	1	TRUE	1	0.888687073803228	2		785	816	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446346	70446346	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	321	575	1	ENST00000373644.4:c.5286G>T	p.Met1762Ile	p.M1762I	ENST00000373644	NM_030625.2	1762	atG/atT	11/12	0.315170085721109	1	FACETS	0.694	0.663	0.725	0.694	0.663	0.725	INDETERMINATE	1	TRUE	0	0.888687073803228	1		576	578	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905488	11905489	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCG	novel	NA	P-0047126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	128	445	0	ENST00000396373.4:c.139_141dup	p.Ser47dup	p.S47dup	ENST00000396373	NM_001987.4	47	-/TCG	2/8	1	2	FACETS	0.479	0.435	0.524	0.479	0.435	0.524	SUBCLONAL	1	TRUE	1	0.888687073803228	2		445	602	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250256	133250256	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs745356467	NA	P-0047126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	284	801	0	ENST00000320574.5:c.1264C>G	p.His422Asp	p.H422D	ENST00000320574	NM_006231.2	422	Cat/Gat	13/49	NA	2	FACETS	0.56	0.526	0.595			1	INDETERMINATE	1	TRUE	NA	0.888687073803228	2		801	1141	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857262	9857262	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	197	647	0	ENST00000330684.3:c.4139G>A	p.Gly1380Glu	p.G1380E	ENST00000330684	NM_001134407.1	1380	gGg/gAg	13/13	0.642779315336082	1	FACETS	0.374	0.347	0.401	0.374	0.347	0.401	SUBCLONAL	1	TRUE	0	0.888687073803228	1		647	659	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973617	15973617	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	122	470	0	ENST00000268712.3:c.4375C>G	p.Leu1459Val	p.L1459V	ENST00000268712	NM_006311.3	1459	Ctt/Gtt	31/46	1	2	FACETS	0.417	0.378	0.459	0.417	0.378	0.459	SUBCLONAL	1	TRUE	1	0.888687073803228	2		470	658	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664565	29664565	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	102	498	0	ENST00000356175.3:c.6544G>C	p.Glu2182Gln	p.E2182Q	ENST00000356175	NM_000267.3	2182	Gaa/Caa	42/57	0.642779315336082	1	FACETS	0.285	0.256	0.316	0.285	0.256	0.316	SUBCLONAL	1	TRUE	0	0.888687073803228	1		498	447	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468358	89468400	+	frameshift_variant	Frame_Shift_Del	DEL	AATTTGGAGAGGTGTGCAGTGGTCGCTTAAAACTTCCTTCAAA	AATTTGGAGAGGTGTGCAGTGGTCGCTTAAAACTTCCTTCAAA	-	novel	NA	P-0047126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	21	221	0	ENST00000336596.2:c.1894_1936del	p.Phe632LysfsTer10	p.F632Kfs*10	ENST00000336596	NM_005233.5	631	gAATTTGGAGAGGTGTGCAGTGGTCGCTTAAAACTTCCTTCAAAa/ga	11/17	0.877973069609293	1	FACETS	0.161	0.125	0.203	0.161	0.125	0.203	SUBCLONAL	1	TRUE	0	0.888687073803228	1		221	163	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001343	150001343	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	109	589	0	ENST00000253339.5:c.2261G>C	p.Arg754Thr	p.R754T	ENST00000253339		754	aGa/aCa	4/7	0.40183736612276	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.888687073803228	0		589	389	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518324	8518325	+	missense_variant	Missense_Mutation	DNP	AT	AT	CA	novel	NA	P-0047126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	71	362	0	ENST00000356435.5:c.1066_1067delinsTG	p.Ile356Cys	p.I356C	ENST00000356435		356	ATt/TGt	10/35	0.642779315336082	1	FACETS	0.3	0.264	0.338	0.3	0.264	0.338	SUBCLONAL	1	TRUE	0	0.888687073803228	1		362	296	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27220100	27220100	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	187	701	0	ENST00000380036.4:c.3157C>A	p.Gln1053Lys	p.Q1053K	ENST00000380036	NM_000459.3	1053	Cag/Aag	21/23	0.642779315336082	1	FACETS	0.336	0.311	0.361	0.336	0.311	0.361	SUBCLONAL	1	TRUE	0	0.888687073803228	1		701	697	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0047133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	71	419	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.312616321774799	1	FACETS	0.514	0.456	0.575	0.514	0.456	0.575	INDETERMINATE	1	TRUE	0	0.786414960753781	1		419	213	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951891	2951891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs116583746	NA	P-0047133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	292	583	1	ENST00000396946.4:c.3059C>T	p.Thr1020Met	p.T1020M	ENST00000396946	NM_032415.4	1020	aCg/aTg	23/25	0.786414960753781	4	FACETS	1	0.968	1	0.348	0.327	0.37	CLONAL	1	TRUE	1	0.786414960753781	4		584	1270	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278106	41278106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	154	330	0	ENST00000349496.5:c.1982G>A	p.Arg661Gln	p.R661Q	ENST00000349496	NM_001904.3	661	cGa/cAa	13/15	0.786414960753781	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.786414960753781	1		330	223	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0047133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	178	367	0	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	0.786414960753781	1	FACETS	0.985	0.931	1	0.985	0.931	1	CLONAL	1	TRUE	0	0.786414960753781	1		367	279	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944273	81944273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	342	651	0	ENST00000359376.3:c.1882G>A	p.Glu628Lys	p.E628K	ENST00000359376	NM_002661.3	628	Gag/Aag	18/33	0.786414960753781	3	FACETS	1	0.983	1	0.545	0.516	0.575	CLONAL	1	TRUE	1	0.786414960753781	3		651	1112	SUCCESS
ATM	472	MSKCC	GRCh37	11	108099930	108099930	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	31	143	0	ENST00000278616.4:c.211G>T	p.Glu71Ter	p.E71*	ENST00000278616	NM_000051.3	71	Gaa/Taa	4/63	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.786414960753781	2		143	76	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442925	49442925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375635160	NA	P-0047133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	298	563	0	ENST00000301067.7:c.3983G>A	p.Arg1328Gln	p.R1328Q	ENST00000301067	NM_003482.3	1328	cGg/cAg	12/54	0.45181037975719	4	FACETS	1	0.991	1	0.417	0.393	0.442	INDETERMINATE	1	TRUE	1	0.786414960753781	4		563	1082	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578535	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTG	novel	NA	P-0047133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	422	773	0	ENST00000269305.4:c.393_395dup	p.Asn131dup	p.N131dup	ENST00000269305	NM_001126112.2	131	aag/aaCAAg	5/11	0.786414960753781	1	FACETS	0.981	0.946	1	0.981	0.946	1	CLONAL	1	TRUE	0	0.786414960753781	1		773	664	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41265988	41266211	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGAT	CTAATGCTAATACTGTTTCGTATTTATAGCTGATTTGATGGAGTTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGAT	-	novel	NA	P-0047133-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	14	170	0	ENST00000349496.5:c.14-29_208del		p.X5_splice	ENST00000349496	NM_001904.3	5		3/15	0.786414960753781	1	FACETS	0.527	0.398	0.666	0.527	0.398	0.666	SUBCLONAL	1	TRUE	0	0.786414960753781	1		170	41	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0047135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	54	187	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.484178712550155	1	FACETS	0.272	0.234	0.313	0.272	0.234	0.313	INDETERMINATE	1	TRUE	0	0.871414020847153	1		187	257	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144148	55144148	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519700	NA	P-0047135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	28	393	0	ENST00000257290.5:c.1977C>G	p.Asn659Lys	p.N659K	ENST00000257290	NM_006206.4	659	aaC/aaG	14/23	1	2	FACETS	0.087	0.069	0.108	0.087	0.069	0.108	SUBCLONAL	1	TRUE	1	0.871414020847153	2		393	735	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0047135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	720	639	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.871414020847153	2	FACETS	0.995	0.979	1	0.995	0.979	1	CLONAL	2	TRUE	0	0.871414020847153	2		639	830	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413070	139413072	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0047135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	597	609	0	ENST00000277541.6:c.1070_1072del	p.Phe357del	p.F357del	ENST00000277541	NM_017617.3	357	tTCTac/tac	6/34	0.647267023351768	2	FACETS	0.772	0.75	0.793	0.772	0.75	0.793	SUBCLONAL	2	TRUE	0	0.871414020847153	2		609	888	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730876	40730876	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372862828	NA	P-0047135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	238	702	0	ENST00000373198.4:c.3659G>A	p.Arg1220Gln	p.R1220Q	ENST00000373198	NM_133170.3	1220	cGg/cAg	27/32	1	2	FACETS	0.633	0.592	0.675	0.633	0.592	0.675	SUBCLONAL	1	TRUE	1	0.871414020847153	2		702	863	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993737	72993737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776936617	NA	P-0047135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	349	581	0	ENST00000268489.5:c.308G>A	p.Arg103His	p.R103H	ENST00000268489	NM_006885.3	103	cGc/cAc	2/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.871414020847153	2		581	747	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17354304	17354306	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1173714647	NA	P-0047135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	214	347	0	ENST00000375499.3:c.478_480del	p.Lys160del	p.K160del	ENST00000375499	NM_003000.2	160	AAG/-	5/8	1	2	FACETS	0.823	0.77	0.877	0.823	0.77	0.877	CLONAL	1	TRUE	1	0.871414020847153	2		347	597	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374588	118374589	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0047135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	219	341	0	ENST00000534358.1:c.7981_7982del	p.Lys2661GlufsTer4	p.K2661Efs*4	ENST00000534358	NM_005933.3	2661	AAg/g	27/36	0.871414020847153	3	FACETS	0.983	0.918	1	0.492	0.459	0.525	CLONAL	1	TRUE	1	0.871414020847153	3		341	734	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220687	2220688	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0047135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	246	635	0	ENST00000326181.6:c.307_308del	p.Leu103AlafsTer49	p.L103Afs*49	ENST00000326181	NM_032271.2	102	TCt/t	5/21	1	2	FACETS	0.657	0.616	0.7	0.657	0.616	0.7	SUBCLONAL	1	TRUE	1	0.871414020847153	2		635	859	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450333	50450333	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	275	603	0	ENST00000331340.3:c.517T>C	p.Phe173Leu	p.F173L	ENST00000331340	NM_006060.4	173	Ttc/Ctc	5/8	0.71157539515755	3	FACETS	0.869	0.816	0.923	0.434	0.408	0.462	CLONAL	1	TRUE	1	0.871414020847153	3		603	1043	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0047137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	386	652	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.609579821598691	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.724470577279246	1		653	668	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685316	89685316	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0047137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	134	230	0	ENST00000371953.3:c.209+2T>G		p.X70_splice	ENST00000371953	NM_000314.4	70			0.685144263469091	1	FACETS	0.967	0.9	1	0.967	0.9	1	CLONAL	1	TRUE	0	0.724470577279246	1		230	244	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030468	49030468	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	166	267	0	ENST00000267163.4:c.1943C>A	p.Ser648Ter	p.S648*	ENST00000267163	NM_000321.2	648	tCa/tAa	19/27	0.685144263469091	1	FACETS	0.842	0.786	0.898	0.842	0.786	0.898	CLONAL	1	TRUE	0	0.724470577279246	1		267	347	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428224	33428224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761290755	NA	P-0047137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	167	452	1	ENST00000345365.6:c.899G>A	p.Arg300Gln	p.R300Q	ENST00000345365	NM_002878.3	300	cGa/cAa	9/10	0.280141559661593	1	FACETS	0.69	0.641	0.74	0.69	0.641	0.74	INDETERMINATE	1	TRUE	0	0.724470577279246	1		453	426	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	232	516	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.973	0.915	1	0.973	0.915	1	CLONAL	1	TRUE	1	0.839707249248426	2		516	568	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0047138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	302	430	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.839707249248426	2		430	675	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720862	89720868	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCAAA	CTCCAAA	-	novel	NA	P-0047138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	91	278	0	ENST00000371953.3:c.1013_1019del	p.Ser338PhefsTer4	p.S338Ffs*4	ENST00000371953	NM_000314.4	338	tCTCCAAAt/tt	8/9	0.403915161416159	2	FACETS	0.907	0.82	0.996	0.453	0.41	0.498	INDETERMINATE	1	TRUE	0	0.839707249248426	2		278	239	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484784	57484784	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	50	554	0	ENST00000371085.3:c.764T>C	p.Met255Thr	p.M255T	ENST00000371085	NM_000516.4	255	aTg/aCg	10/13	1	2	FACETS	0.147	0.124	0.172	0.147	0.124	0.172	SUBCLONAL	1	TRUE	1	0.839707249248426	2		554	812	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	213	516	0				ENST00000310581	NM_198253.2	-/1132			0.56953279206445	3	FACETS	0.91	0.858	0.961	0.91	0.858	0.961	CLONAL	2	TRUE	1	0.780604541463683	3		516	417	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0047139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	26	898	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	0.154297783724064	3	FACETS	0.081	0.063	0.101	0.04	0.031	0.051	INDETERMINATE	1	TRUE	1	0.780604541463683	3		898	1149	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0047139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	378	682	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.248461219036679	1	FACETS	0.644	0.614	0.674	0.644	0.614	0.674	INDETERMINATE	1	TRUE	0	0.780604541463683	1		682	917	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577543	7577543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1019340046	NA	P-0047139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	237	584	0	ENST00000269305.4:c.738G>A	p.Met246Ile	p.M246I	ENST00000269305	NM_001126112.2	246	atG/atA	7/11	0.248461219036679	1	FACETS	0.521	0.488	0.554	0.521	0.488	0.554	INDETERMINATE	1	TRUE	0	0.780604541463683	1		584	711	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727077	41727077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35202236	NA	P-0047139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	77	660	0	ENST00000301178.4:c.335C>T	p.Thr112Met	p.T112M	ENST00000301178	NM_021913.4	112	aCg/aTg	3/20	1	2	FACETS	0.2	0.175	0.228	0.2	0.175	0.228	SUBCLONAL	1	TRUE	1	0.780604541463683	2		660	984	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075157	16075157	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	35	274	0	ENST00000268712.3:c.395C>G	p.Pro132Arg	p.P132R	ENST00000268712	NM_006311.3	132	cCg/cGg	4/46	0.248461219036679	1	FACETS	0.134	0.11	0.162	0.134	0.11	0.162	INDETERMINATE	1	TRUE	0	0.780604541463683	1		274	407	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412575	63412575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774927630	NA	P-0047139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	20	313	1	ENST00000330258.3:c.592G>A	p.Glu198Lys	p.E198K	ENST00000330258	NM_152424.3	198	Gag/Aag	2/2	1	1	FACETS	0.079	0.06	0.102	0.079	0.06	0.102	SUBCLONAL	1	TRUE	0	0.780604541463683	1		314	395	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338683	70338683	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	60	285	0	ENST00000374080.3:c.79C>T	p.Gln27Ter	p.Q27*	ENST00000374080		27	Cag/Tag	1/45	1	1	FACETS	0.231	0.2	0.266	0.231	0.2	0.266	SUBCLONAL	1	TRUE	0	0.780604541463683	1		285	405	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729693	162729693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139577393	NA	P-0047139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	67	489	0	ENST00000367921.3:c.779G>A	p.Arg260Gln	p.R260Q	ENST00000367921	NM_006182.2	260	cGg/cAg	8/18	0.660488637188454	3	FACETS	0.244	0.211	0.28			1	SUBCLONAL	1	TRUE	NA	0.780604541463683	3		489	978	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023622	27023624	+	frameshift_variant	Frame_Shift_Del	DEL	CGG	CGG	GT	novel	NA	P-0047139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	266	339	2	ENST00000324856.7:c.728_730delinsGT	p.Ala243GlyfsTer120	p.A243Gfs*120	ENST00000324856	NM_006015.4	243	gCGGcg/gGTcg	1/20	0.154297783724064	3	FACETS	0.808	0.765	0.852	0.808	0.765	0.852	INDETERMINATE	2	TRUE	1	0.780604541463683	3		341	586	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166313	118166313	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	138	355	0	ENST00000369448.3:c.824del	p.Phe275SerfsTer34	p.F275Sfs*34	ENST00000369448	NM_017709.3	275	Ttc/tc	2/2	1	2	FACETS	0.886	0.815	0.959	0.886	0.815	0.959	CLONAL	1	TRUE	1	0.780604541463683	2		355	399	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948773	71948773	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs757808454	NA	P-0047139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	304	758	0	ENST00000298229.2:c.3485A>G	p.Tyr1162Cys	p.Y1162C	ENST00000298229	NM_001567.3	1162	tAt/tGt	26/28	NA	2	FACETS	0.969	0.917	1			1	INDETERMINATE	1	TRUE	NA	0.780604541463683	2		758	804	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245543	46245543	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1416414304	NA	P-0047139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	38	309	0	ENST00000334344.6:c.3638del	p.Pro1213GlnfsTer30	p.P1213Qfs*30	ENST00000334344	NM_152641.2	1213	Cca/ca	15/21	0.241039738124053	4	FACETS	0.333	0.274	0.398	0.166	0.137	0.199	INDETERMINATE	1	TRUE	2	0.780604541463683	4		309	521	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443940	49443940	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	427	668	0	ENST00000301067.7:c.3431del	p.Leu1144TrpfsTer20	p.L1144Wfs*20	ENST00000301067	NM_003482.3	1144	tTg/tg	11/54	0.241039738124053	4	FACETS	0.905	0.865	0.946	0.905	0.865	0.946	INDETERMINATE	2	TRUE	2	0.780604541463683	4		668	1076	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111886101	111886101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1200233231	NA	P-0047139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	46	385	0	ENST00000341259.2:c.1723C>T	p.Leu575Phe	p.L575F	ENST00000341259	NM_005475.2	575	Ctc/Ttc	8/8	0.154297783724064	3	FACETS	0.257	0.216	0.302	0.128	0.108	0.151	INDETERMINATE	1	TRUE	1	0.780604541463683	3		385	638	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060712	38060712	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1566823601	NA	P-0047139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	927	834	0	ENST00000250448.2:c.1277A>C	p.Tyr426Ser	p.Y426S	ENST00000250448	NM_004496.3	426	tAc/tCc	2/2	0.780604541463683	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.780604541463683	1		834	1192	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614577	38614577	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	342	443	0	ENST00000299084.4:c.343G>T	p.Gly115Cys	p.G115C	ENST00000299084	NM_152594.2	115	Ggt/Tgt	3/7	0.154297783724064	3	FACETS	1	0.995	1	0.746	0.709	0.782	INDETERMINATE	1	TRUE	1	0.780604541463683	3		443	817	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828795	3828795	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	278	523	0	ENST00000262367.5:c.1847C>T	p.Pro616Leu	p.P616L	ENST00000262367	NM_004380.2	616	cCt/cTt	9/31	0.248461219036679	1	FACETS	0.653	0.618	0.689	0.653	0.618	0.689	INDETERMINATE	1	TRUE	0	0.780604541463683	1		523	665	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965950	18965951	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0047139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	73	642	0	ENST00000262803.5:c.1445_1446del	p.Val482AlafsTer68	p.V482Afs*68	ENST00000262803	NM_002911.3	481	acTGtg/actg	11/24	NA	2	FACETS	0.221	0.192	0.252			1	INDETERMINATE	1	TRUE	NA	0.780604541463683	2		642	847	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40740960	40740960	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	324	733	0	ENST00000392038.2:c.1358C>T	p.Pro453Leu	p.P453L	ENST00000392038	NM_001626.4	453	cCt/cTt	13/14	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.780604541463683	2		733	822	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860620	45860620	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	382	753	0	ENST00000391945.4:c.1387C>A	p.Pro463Thr	p.P463T	ENST00000391945	NM_000400.3	463	Ccg/Acg	15/23	1	2	FACETS	0.937	0.892	0.983	0.937	0.892	0.983	CLONAL	1	TRUE	1	0.780604541463683	2		753	1044	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389089	31389089	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	265	334	0	ENST00000328111.2:c.2002A>G	p.Thr668Ala	p.T668A	ENST00000328111	NM_006892.3	668	Aca/Gca	19/23	0.164913813065451	4	FACETS	0.964	0.911	1	0.964	0.911	1	INDETERMINATE	2	TRUE	2	0.780604541463683	4		334	627	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458322	12458322	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	514	526	0	ENST00000287820.6:c.939C>G	p.Cys313Trp	p.C313W	ENST00000287820	NM_015869.4	313	tgC/tgG	6/7	0.56953279206445	3	FACETS	0.909	0.876	0.943	0.909	0.876	0.943	CLONAL	2	TRUE	1	0.780604541463683	3		526	1007	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440379	52440379	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	270	473	1	ENST00000460680.1:c.673G>T	p.Asp225Tyr	p.D225Y	ENST00000460680	NM_004656.3	225	Gac/Tac	9/17	0.376411149238998	1	FACETS	0.774	0.734	0.814	0.774	0.734	0.814	INDETERMINATE	1	TRUE	0	0.780604541463683	1		474	545	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442599	52442599	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	77	270	0	ENST00000460680.1:c.146T>A	p.Leu49Gln	p.L49Q	ENST00000460680	NM_004656.3	49	cTg/cAg	4/17	0.376411149238998	1	FACETS	0.351	0.31	0.394	0.351	0.31	0.394	INDETERMINATE	1	TRUE	0	0.780604541463683	1		270	343	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955965	55955965	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754208569	NA	P-0047139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	31	316	1	ENST00000263923.4:c.3197G>A	p.Arg1066His	p.R1066H	ENST00000263923	NM_002253.2	1066	cGc/cAc	24/30	0.248461219036679	1	FACETS	0.093	0.074	0.113	0.093	0.074	0.113	INDETERMINATE	1	TRUE	0	0.780604541463683	1		317	523	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332595	153332595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	50	341	0	ENST00000281708.4:c.361G>A	p.Glu121Lys	p.E121K	ENST00000281708	NM_033632.3	121	Gag/Aag	2/12	0.510593877342651	1	FACETS	0.163	0.138	0.191	0.163	0.138	0.191	SUBCLONAL	1	TRUE	0	0.780604541463683	1		341	478	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332681	153332681	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	33	351	0	ENST00000281708.4:c.275C>T	p.Ser92Leu	p.S92L	ENST00000281708	NM_033632.3	92	tCa/tTa	2/12	0.510593877342651	1	FACETS	0.086	0.069	0.105	0.086	0.069	0.105	SUBCLONAL	1	TRUE	0	0.780604541463683	1		351	599	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393168	393169	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0047139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	57	398	0	ENST00000380956.4:c.16_17delinsAA	p.Gly6Asn	p.G6N	ENST00000380956	NM_001195286.1	6	GGc/AAc	2/9	NA	2	FACETS	0.32	0.275	0.369			1	INDETERMINATE	1	TRUE	NA	0.780604541463683	2		398	456	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339212	87339212	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	28	411	0	ENST00000277120.3:c.794C>G	p.Ser265Cys	p.S265C	ENST00000277120		265	tCt/tGt	8/19	0.780604541463683	1	FACETS	0.079	0.062	0.097	0.079	0.062	0.097	SUBCLONAL	1	TRUE	0	0.780604541463683	1		411	557	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772082	135772082	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	63	448	0	ENST00000298552.3:c.3035C>G	p.Ser1012Cys	p.S1012C	ENST00000298552	NM_001162426.1	1012	tCt/tGt	23/23	0.750006143142852	2	FACETS	0.293	0.253	0.336	0.146	0.126	0.168	SUBCLONAL	1	TRUE	0	0.780604541463683	2		448	551	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922734	44922759	+	frameshift_variant	Frame_Shift_Del	DEL	CACTGCCTACAAACTCAGTCTCTGGC	CACTGCCTACAAACTCAGTCTCTGGC	-	novel	NA	P-0047139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	287	187	0	ENST00000377967.4:c.1597_1622del	p.Leu533AlafsTer11	p.L533Afs*11	ENST00000377967	NM_021140.2	532	tCACTGCCTACAAACTCAGTCTCTGGC/t	16/29	0.660488637188454	2	FACETS	1	0.978	1			1	CLONAL	2	TRUE	NA	0.780604541463683	2		187	362	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575520	64575524	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCA	TGGCA	C	novel	NA	P-0047139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	340	517	0	ENST00000312049.6:c.493_497delinsG	p.Cys165GlyfsTer19	p.C165Gfs*19	ENST00000312049	NM_130799.2	165	TGCCAg/Gg	3/10	0.248461219036679	1	FACETS	0.685	0.652	0.719	0.685	0.652	0.719	INDETERMINATE	1	TRUE	0	0.780604541463683	1		517	775	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0047140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	77	272	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.310403048482256	2		272	382	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0047140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	232	659	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	0.761	0.71	0.814	1	0.992	1	SUBCLONAL	2	TRUE	1	0.310403048482256	2		659	982	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426492	47426492	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765113993	NA	P-0047140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	154	558	0	ENST00000377045.4:c.835C>T	p.Arg279Cys	p.R279C	ENST00000377045	NM_001654.4	279	Cgc/Tgc	9/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.310403048482256	2		558	805	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916643	178916666	+	inframe_deletion	In_Frame_Del	DEL	GTGGGGCATCCACTTGATGCCCCC	GTGGGGCATCCACTTGATGCCCCC	-	novel	NA	P-0047140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	34	257	0	ENST00000263967.3:c.30_53del	p.Trp11_Pro18del	p.W11_P18del	ENST00000263967	NM_006218.2	10	ctGTGGGGCATCCACTTGATGCCCCCa/cta	2/21	1	2	FACETS	0.66	0.54	0.794	0.66	0.54	0.794	SUBCLONAL	1	TRUE	1	0.310403048482256	2		257	332	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0047140-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	57	272	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.366437372563936	2		272	254	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0047140-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	199	659	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.366437372563936	2		659	1029	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426492	47426492	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765113993	NA	P-0047140-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	148	558	0	ENST00000377045.4:c.835C>T	p.Arg279Cys	p.R279C	ENST00000377045	NM_001654.4	279	Cgc/Tgc	9/16	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.366437372563936	2		558	803	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916643	178916666	+	inframe_deletion	In_Frame_Del	DEL	GTGGGGCATCCACTTGATGCCCCC	GTGGGGCATCCACTTGATGCCCCC	-	novel	NA	P-0047140-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	49	257	0	ENST00000263967.3:c.30_53del	p.Trp11_Pro18del	p.W11_P18del	ENST00000263967	NM_006218.2	10	ctGTGGGGCATCCACTTGATGCCCCCa/cta	2/21	1	2	FACETS	0.942	0.803	1	0.942	0.803	1	CLONAL	1	TRUE	1	0.366437372563936	2		257	284	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225938	2225938	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047140-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	105	573	0	ENST00000326181.6:c.1730A>C	p.Tyr577Ser	p.Y577S	ENST00000326181	NM_032271.2	577	tAc/tCc	18/21	1	2	FACETS	0.691	0.619	0.768	0.691	0.619	0.768	SUBCLONAL	1	TRUE	1	0.366437372563936	2		573	829	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926900	112926900	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs886039463	NA	P-0047141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	73	423	1	ENST00000351677.2:c.1520C>A	p.Thr507Lys	p.T507K	ENST00000351677	NM_002834.3	507	aCa/aAa	13/16	0.624847361551005	2	FACETS	0.492	0.431	0.557	0.246	0.215	0.279	SUBCLONAL	1	FALSE	0	0.624847361551005	2		424	475	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0047142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	174	731	7	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.335707413115902	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.335707413115902	1		738	790	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0047142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	77	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.886	0.779	0.999	0.886	0.779	0.999	CLONAL	1	TRUE	1	0.335707413115902	2		511	518	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0047142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	121	276	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.335707413115902	2	FACETS	0.998	0.912	1	0.998	0.912	1	CLONAL	2	TRUE	0	0.335707413115902	2		276	361	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256441	16256441	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	42	518	0	ENST00000375759.3:c.3706G>C	p.Asp1236His	p.D1236H	ENST00000375759	NM_015001.2	1236	Gat/Cat	11/15	1	2	FACETS	0.584	0.487	0.693	0.584	0.487	0.693	SUBCLONAL	1	TRUE	1	0.230433235692369	2		518	624	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0047144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	80	658	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.297557143906557	1	FACETS	0.871	0.77	0.979	0.871	0.77	0.979	CLONAL	1	TRUE	0	0.337015366615317	1		658	453	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0047144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	196	580	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.170664258103277	2	FACETS	0.771	0.716	0.828	0.771	0.716	0.828	INDETERMINATE	2	TRUE	0	0.337015366615317	2		580	754	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835780	68835781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0047144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	53	506	0	ENST00000261769.5:c.377dup	p.Pro127AlafsTer41	p.P127Afs*41	ENST00000261769	NM_004360.3	124	cgc/cgCc	3/16	0.297557143906557	1	FACETS	0.627	0.536	0.726	0.627	0.536	0.726	SUBCLONAL	1	TRUE	0	0.337015366615317	1		506	417	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917681	178917681	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	67	159	0	ENST00000263967.3:c.556G>C	p.Asp186His	p.D186H	ENST00000263967	NM_006218.2	186	Gat/Cat	3/21	0.170664258103277	2	FACETS	0.768	0.675	0.866	0.768	0.675	0.866	INDETERMINATE	2	TRUE	0	0.337015366615317	2		159	259	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462869	69462869	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	87	826	1	ENST00000227507.2:c.682C>G	p.Arg228Gly	p.R228G	ENST00000227507	NM_053056.2	228	Cgc/Ggc	4/5	1	2	FACETS	0.853	0.756	0.957	0.853	0.756	0.957	CLONAL	1	TRUE	1	0.337015366615317	2		827	605	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117383	115117384	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0047144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	130	354	4	ENST00000257566.3:c.790_791del	p.Pro264LeufsTer2	p.P264Lfs*2	ENST00000257566	NM_016569.3	264	CCt/t	4/8	0.307207534180272	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.337015366615317	2		358	352	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436722	110436722	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	117	866	0	ENST00000375856.3:c.1679C>G	p.Ser560Trp	p.S560W	ENST00000375856	NM_003749.2	560	tCg/tGg	1/2	1	2	FACETS	0.958	0.864	1	0.958	0.864	1	CLONAL	1	TRUE	1	0.337015366615317	2		866	725	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919287	178919287	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	81	160	0	ENST00000263967.3:c.772G>C	p.Asp258His	p.D258H	ENST00000263967	NM_006218.2	258	Gat/Cat	4/21	0.170664258103277	2	FACETS	1	0.979	1	0.746	0.664	0.833	INDETERMINATE	1	TRUE	0	0.337015366615317	2		160	322	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176579	56176579	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	65	423	0	ENST00000399503.3:c.2129G>A	p.Cys710Tyr	p.C710Y	ENST00000399503	NM_005921.1	710	tGc/tAc	12/20	0.337015366615317	3	FACETS	0.854	0.741	0.975	0.427	0.37	0.488	CLONAL	1	TRUE	1	0.337015366615317	3		423	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0047147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	256	658	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.995	0.938	1	0.995	0.938	1	CLONAL	1	TRUE	1	0.786655680643477	2		658	654	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0047147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	108	220	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.786655680643477	2		221	235	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0047147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	226	577	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.786655680643477	2		577	544	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138431133	138431133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	84	309	1	ENST00000289153.2:c.1316C>T	p.Ala439Val	p.A439V	ENST00000289153	NM_006219.2	439	gCg/gTg	8/22	1	2	FACETS	0.971	0.874	1	0.971	0.874	1	CLONAL	1	TRUE	1	0.786655680643477	2		310	220	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938858	76938859	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	115	288	0	ENST00000373344.5:c.1889_1890insT	p.Gln631ThrfsTer5	p.Q631Tfs*5	ENST00000373344	NM_000489.3	630	gga/ggTa	9/35	0.638585547220488	0	FACETS		NA	1			1	NA	1	TRUE	NA	0.786655680643477	0		288	153	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459290	120459290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1430961661	NA	P-0047149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	159	468	0	ENST00000256646.2:c.6055C>T	p.Arg2019Trp	p.R2019W	ENST00000256646	NM_024408.3	2019	Cgg/Tgg	34/34	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.491093543016797	2		468	614	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827295	72827295	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	47	811	0	ENST00000268489.5:c.9286C>T	p.Gln3096Ter	p.Q3096*	ENST00000268489	NM_006885.3	3096	Cag/Tag	9/10	0.491093543016797	1	FACETS	0.213	0.179	0.251	0.213	0.179	0.251	SUBCLONAL	1	TRUE	0	0.491093543016797	1		811	678	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576867	7576868	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	451	694	0	ENST00000269305.4:c.978dup	p.Tyr327IlefsTer10	p.Y327Ifs*10	ENST00000269305	NM_001126112.2	326	-/A	9/11	NA	2	FACETS	0.954	0.915	0.993			1	INDETERMINATE	2	TRUE	NA	0.491093543016797	2		694	963	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0047150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	40	552	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.765	0.634	0.913	0.765	0.634	0.913	CLONAL	1	TRUE	1	0.13	2		553	804	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311619	15311621	+	inframe_deletion	In_Frame_Del	DEL	AGC	AGC	-	rs746497955	NA	P-0047150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	10	146	0	ENST00000263388.2:c.96_98del	p.Leu33del	p.L33del	ENST00000263388	NM_000435.2	32	ctGCTa/cta	1/33	1	2	FACETS	0.855	0.58	1	0.855	0.58	1	CLONAL	1	TRUE	1	0.13	2		146	180	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324651	31324651	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	42	544	0	ENST00000412585.2:c.157G>C	p.Asp53His	p.D53H	ENST00000412585	NM_005514.6	53	Gac/Cac	2/8	0.265881958099362	4	FACETS	0.889	0.74	1	0.445	0.37	0.528	CLONAL	1	TRUE	2	0.13	4		544	821	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0047151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	403	1013	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.737248068779845	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.747020276892446	1		1013	666	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	120	349	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.813	0.741	0.888	0.813	0.741	0.888	CLONAL	1	TRUE	1	0.747020276892446	2		349	395	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466994	18466994	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773615749	NA	P-0047151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	130	241	1	ENST00000266497.5:c.1133G>A	p.Arg378Gln	p.R378Q	ENST00000266497		378	cGa/cAa	5/31	1	2	FACETS	0.941	0.863	1	0.941	0.863	1	CLONAL	1	TRUE	1	0.747020276892446	2		242	370	SUCCESS
APC	324	MSKCC	GRCh37	5	112173668	112173668	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	127	270	0	ENST00000257430.4:c.2377C>T	p.Gln793Ter	p.Q793*	ENST00000257430	NM_000038.5	793	Caa/Taa	16/16	1	2	FACETS	0.997	0.915	1	0.997	0.915	1	CLONAL	1	TRUE	1	0.747020276892446	2		270	341	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262204	10262204	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	299	545	3	ENST00000340748.4:c.2087T>C	p.Met696Thr	p.M696T	ENST00000340748		696	aTg/aCg	23/40	1	2	FACETS	0.964	0.912	1	0.964	0.912	1	CLONAL	1	TRUE	1	0.747020276892446	2		548	830	SUCCESS
APC	324	MSKCC	GRCh37	5	112175770	112175771	+	frameshift_variant	Frame_Shift_Ins	INS	GG	GG	AGA	novel	NA	P-0047151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	109	229	1	ENST00000257430.4:c.4479_4480delinsAGA	p.Ser1495LysfsTer19	p.S1495Kfs*19	ENST00000257430	NM_000038.5	1493	acGGaa/acAGAaa	16/16	1	2	FACETS	0.929	0.845	1	0.929	0.845	1	CLONAL	1	TRUE	1	0.747020276892446	2		230	314	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371712	45371712	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	152	262	1	ENST00000262160.6:c.1279C>T	p.Arg427Ter	p.R427*	ENST00000262160	NM_005901.5	427	Cga/Tga	10/11	0.74155708220588	1	FACETS	0.973	0.912	1	0.973	0.912	1	CLONAL	1	TRUE	0	0.747020276892446	1		263	262	SUCCESS
APC	324	MSKCC	GRCh37	5	112173657	112173657	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	129	264	0	ENST00000257430.4:c.2366A>G	p.Gln789Arg	p.Q789R	ENST00000257430	NM_000038.5	789	cAg/cGg	16/16	1	2	FACETS	0.973	0.893	1	0.973	0.893	1	CLONAL	1	TRUE	1	0.747020276892446	2		264	355	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0047152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	959	593	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.312923182506992	8	FACETS	1	0.982	1	1	0.997	1	CLONAL	7	TRUE	2	0.312923182506992	8		593	1681	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469672	NA	P-0047152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	172	527	0	ENST00000374080.3:c.131G>A	p.Gly44Asp	p.G44D	ENST00000374080		44	gGt/gAt	2/45	0.312923182506992	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.312923182506992	1		527	807	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937519	76937520	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0047152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	56	398	0	ENST00000373344.5:c.3228_3229del	p.Ser1077ArgfsTer3	p.S1077Rfs*3	ENST00000373344	NM_000489.3	1076	tcTTca/tcca	9/35	0.312923182506992	1	FACETS	0.807	0.703	0.917	1	0.974	1	CLONAL	2	TRUE	0	0.312923182506992	1		398	187	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0047153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	55	507	0	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		507	718	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0047154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	53	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.961	0.833	1	0.961	0.833	1	CLONAL	1	TRUE	1	0.593162681238282	2		511	186	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0047154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	419	759	2	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.586584988853648	2	FACETS	0.928	0.892	0.964	0.928	0.892	0.964	CLONAL	2	TRUE	0	0.593162681238282	2		761	761	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0047154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	779	709	5	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.593162681238282	6	FACETS	0.972	0.952	0.991			1	CLONAL	6	TRUE	NA	0.593162681238282	6		714	985	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469669	NA	P-0047154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	125	488	0	ENST00000374080.3:c.130G>A	p.Gly44Ser	p.G44S	ENST00000374080		44	Ggt/Agt	2/45	0.593162681238282	1	FACETS	0.869	0.797	0.944	0.869	0.797	0.944	CLONAL	1	TRUE	0	0.593162681238282	1		488	341	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380254	25380254	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	96	409	0	ENST00000311936.3:c.204G>T	p.Arg68Ser	p.R68S	ENST00000311936	NM_004985.3	68	agG/agT	3/5	0.127508863767909	0	FACETS	0.442	0.398	0.487			1	INDETERMINATE	1	TRUE	0	0.593162681238282	0		409	298	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030325	180030325	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115824945	NA	P-0047154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	192	681	0	ENST00000261937.6:c.3959G>A	p.Arg1320Gln	p.R1320Q	ENST00000261937	NM_182925.4	1320	cGg/cAg	30/30	0.21545425195849	0	FACETS	0.353	0.327	0.38			1	INDETERMINATE	1	TRUE	0	0.593162681238282	0		681	746	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	139	355	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	0.901	0.825	0.98	0.901	0.825	0.98	CLONAL	1	TRUE	1	0.593162681238282	2		355	520	SUCCESS
APC	324	MSKCC	GRCh37	5	112173975	112173975	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0047154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	57	242	0	ENST00000257430.4:c.2684C>G	p.Ser895Ter	p.S895*	ENST00000257430	NM_000038.5	895	tCa/tGa	16/16	1	2	FACETS	0.839	0.729	0.956	0.839	0.729	0.956	CLONAL	1	TRUE	1	0.593162681238282	2		242	229	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120244	70120244	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	541	682	1	ENST00000245479.2:c.1246C>T	p.Gln416Ter	p.Q416*	ENST00000245479	NM_000346.3	416	Caa/Taa	3/3	0.586584988853648	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.593162681238282	2		683	909	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178340	56178341	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	47	219	0	ENST00000399503.3:c.3315dup	p.Ile1106TyrfsTer4	p.I1106Yfs*4	ENST00000399503	NM_005921.1	1105	gtt/gTtt	14/20	1	2	FACETS	0.796	0.681	0.92	0.796	0.681	0.92	CLONAL	1	TRUE	1	0.593162681238282	2		219	199	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30095727	30095727	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	13	305	0	ENST00000331968.5:c.1761A>C	p.Glu587Asp	p.E587D	ENST00000331968	NM_002742.2	587	gaA/gaC	12/18	1	2	FACETS	0.262	0.187	0.353	0.262	0.187	0.353	SUBCLONAL	1	TRUE	1	0.593162681238282	2		305	167	SUCCESS
APC	324	MSKCC	GRCh37	5	112175756	112175759	+	frameshift_variant	Frame_Shift_Del	DEL	TTAC	TTAC	-	novel	NA	P-0047154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	34	237	0	ENST00000257430.4:c.4465_4468del	p.Leu1489IlefsTer17	p.L1489Ifs*17	ENST00000257430	NM_000038.5	1489	TTACat/at	16/16	1	2	FACETS	0.603	0.498	0.719	0.603	0.498	0.719	SUBCLONAL	1	TRUE	1	0.593162681238282	2		237	190	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	132	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.635379923796427	2		511	396	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	120	318	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.928	0.845	1	0.928	0.845	1	CLONAL	1	TRUE	1	0.635379923796427	2		318	407	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	88	277	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.757	0.676	0.842	0.757	0.676	0.842	SUBCLONAL	1	TRUE	1	0.635379923796427	2		277	366	SUCCESS
APC	324	MSKCC	GRCh37	5	112178449	112178449	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	118	283	0	ENST00000257430.4:c.7158G>C	p.Lys2386Asn	p.K2386N	ENST00000257430	NM_000038.5	2386	aaG/aaC	16/16	1	2	FACETS	0.967	0.881	1	0.967	0.881	1	CLONAL	1	TRUE	1	0.635379923796427	2		283	384	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263850	133263850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	126	371	1	ENST00000320574.5:c.52G>A	p.Glu18Lys	p.E18K	ENST00000320574	NM_006231.2	18	Gag/Aag	1/49	1	2	FACETS	0.935	0.854	1	0.935	0.854	1	CLONAL	1	TRUE	1	0.635379923796427	2		372	424	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163720	32163720	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	265	689	0	ENST00000375023.3:c.5506G>C	p.Glu1836Gln	p.E1836Q	ENST00000375023	NM_004557.3	1836	Gag/Cag	30/30	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.635379923796427	2		689	727	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031885	26031885	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	91	258	0	ENST00000244661.2:c.404G>C	p.Arg135Thr	p.R135T	ENST00000244661	NM_003537.3	135	aGa/aCa	1/1	1	2	FACETS	0.968	0.87	1	0.968	0.87	1	CLONAL	1	TRUE	1	0.635379923796427	2		258	296	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981761	101981761	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	213	660	0	ENST00000282441.5:c.182C>G	p.Ser61Trp	p.S61W	ENST00000282441	NM_001130145.2	61	tCg/tGg	1/9	1	2	FACETS	0.959	0.895	1	0.959	0.895	1	CLONAL	1	TRUE	1	0.635379923796427	2		660	699	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	394	508	0	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	0.635379923796427	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.635379923796427	2		508	591	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774181	56774181	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	178	462	0	ENST00000337432.4:c.532C>G	p.Gln178Glu	p.Q178E	ENST00000337432	NM_058216.2	178	Cag/Gag	3/9	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.635379923796427	2		462	480	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678029	58678029	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567962294	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	166	412	0	ENST00000305921.3:c.254C>T	p.Ser85Leu	p.S85L	ENST00000305921	NM_003620.3	85	tCg/tTg	1/6	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.635379923796427	2		412	458	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202178	108202178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	44	221	0	ENST00000278616.4:c.7523G>A	p.Gly2508Glu	p.G2508E	ENST00000278616	NM_000051.3	2508	gGa/gAa	51/63	1	2	FACETS	0.778	0.662	0.902	0.778	0.662	0.902	CLONAL	1	TRUE	1	0.635379923796427	2		221	178	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441226	52441226	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	171	465	0	ENST00000460680.1:c.544G>C	p.Glu182Gln	p.E182Q	ENST00000460680	NM_004656.3	182	Gag/Cag	7/17	1	2	FACETS	0.961	0.89	1	0.961	0.89	1	CLONAL	1	TRUE	1	0.635379923796427	2		465	560	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296095	15296095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	364	1072	1	ENST00000263388.2:c.2269C>T	p.His757Tyr	p.H757Y	ENST00000263388	NM_000435.2	757	Cac/Tac	14/33	1	2	FACETS	0.947	0.898	0.997	0.947	0.898	0.997	CLONAL	1	TRUE	1	0.635379923796427	2		1073	1210	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219785	36219785	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	323	871	0	ENST00000222270.7:c.4682C>G	p.Ser1561Ter	p.S1561*	ENST00000222270	NM_014727.1	1561	tCa/tGa	20/37	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.635379923796427	2		871	962	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526993	31526993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769152940	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	242	636	0	ENST00000344624.3:c.47G>A	p.Arg16Gln	p.R16Q	ENST00000344624		16	cGa/cAa	2/33	1	2	FACETS	0.977	0.915	1	0.977	0.915	1	CLONAL	1	TRUE	1	0.635379923796427	2		636	780	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617564	100617564	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	189	616	0	ENST00000308731.7:c.505G>A	p.Glu169Lys	p.E169K	ENST00000308731	NM_000061.2	169	Gag/Aag	6/19	1	2	FACETS	0.831	0.77	0.893	0.831	0.77	0.893	CLONAL	1	TRUE	1	0.635379923796427	2		616	716	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705404	43705404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	276	918	0	ENST00000382044.4:c.5218C>T	p.Leu1740Phe	p.L1740F	ENST00000382044	NM_001141980.1	1740	Ctc/Ttc	24/28	1	2	FACETS	0.947	0.891	1	0.947	0.891	1	CLONAL	1	TRUE	1	0.635379923796427	2		918	917	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845536	63845537	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	79	203	0	ENST00000279873.7:c.1278_1279dup	p.Asn427ArgfsTer53	p.N427Rfs*53	ENST00000279873	NM_032199.2	425	-/GA	9/10	1	2	FACETS	0.863	0.768	0.964	0.863	0.768	0.964	CLONAL	1	TRUE	1	0.635379923796427	2		203	288	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514488	125514488	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	97	336	0	ENST00000428830.2:c.1183G>C	p.Glu395Gln	p.E395Q	ENST00000428830	NM_001114121.2	395	Gag/Cag	11/14	1	2	FACETS	0.839	0.754	0.927	0.839	0.754	0.927	CLONAL	1	TRUE	1	0.635379923796427	2		336	364	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865314	57865314	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	291	828	0	ENST00000228682.2:c.2791C>G	p.Leu931Val	p.L931V	ENST00000228682	NM_005269.2	931	Ctg/Gtg	12/12	1	2	FACETS	0.927	0.873	0.982	0.927	0.873	0.982	CLONAL	1	TRUE	1	0.635379923796427	2		828	988	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253212	133253212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	200	619	0	ENST00000320574.5:c.829G>A	p.Glu277Lys	p.E277K	ENST00000320574	NM_006231.2	277	Gag/Aag	9/49	1	2	FACETS	0.908	0.845	0.974	0.908	0.845	0.974	CLONAL	1	TRUE	1	0.635379923796427	2		619	693	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643799	38643799	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	263	738	0	ENST00000299084.4:c.1269G>C	p.Leu423Phe	p.L423F	ENST00000299084	NM_152594.2	423	ttG/ttC	7/7	1	2	FACETS	0.894	0.839	0.95	0.894	0.839	0.95	CLONAL	1	TRUE	1	0.635379923796427	2		738	926	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42053967	42053967	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1317613647	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	55	271	0	ENST00000219905.7:c.7429C>G	p.Gln2477Glu	p.Q2477E	ENST00000219905	NM_001164273.1	2477	Cag/Gag	21/24	1	2	FACETS	0.802	0.695	0.915	0.802	0.695	0.915	CLONAL	1	TRUE	1	0.635379923796427	2		271	216	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654637	67654637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	217	508	0	ENST00000264010.4:c.1124G>A	p.Gly375Glu	p.G375E	ENST00000264010	NM_006565.3	375	gGa/gAa	6/12	0.635379923796427	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.635379923796427	1		508	463	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649003	37649003	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	104	260	0	ENST00000447079.4:c.2109-1G>C		p.X703_splice	ENST00000447079	NM_015083.1	703			1	2	FACETS	0.897	0.811	0.987	0.897	0.811	0.987	CLONAL	1	TRUE	1	0.635379923796427	2		260	365	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796923	78796923	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	184	559	0	ENST00000306801.3:c.1036C>G	p.Leu346Val	p.L346V	ENST00000306801	NM_020761.2	346	Ctg/Gtg	9/34	1	2	FACETS	0.933	0.865	1	0.933	0.865	1	CLONAL	1	TRUE	1	0.635379923796427	2		559	621	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198260784	198260784	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	103	314	0	ENST00000335508.6:c.3535G>C	p.Asp1179His	p.D1179H	ENST00000335508	NM_012433.2	1179	Gat/Cat	23/25	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.635379923796427	2		314	323	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209106850	209106850	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	177	441	1	ENST00000345146.2:c.718G>T	p.Glu240Ter	p.E240*	ENST00000345146	NM_005896.2	240	Gaa/Taa	7/10	1	2	FACETS	0.988	0.916	1	0.988	0.916	1	CLONAL	1	TRUE	1	0.635379923796427	2		442	564	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24129362	24129362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	161	456	0	ENST00000263121.7:c.6G>A	p.Met2Ile	p.M2I	ENST00000263121	NM_003073.3	2	atG/atA	1/9	0.635379923796427	1	FACETS	0.91	0.846	0.975	0.91	0.846	0.975	CLONAL	1	TRUE	0	0.635379923796427	1		456	380	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799465	72799465	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	243	654	0	ENST00000325599.8:c.1704G>C	p.Glu568Asp	p.E568D	ENST00000325599	NM_018130.2	568	gaG/gaC	11/11	1	2	FACETS	0.966	0.905	1	0.966	0.905	1	CLONAL	1	TRUE	1	0.635379923796427	2		654	792	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39002660	39002660	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	96	314	0	ENST00000357387.3:c.369G>T	p.Leu123Phe	p.L123F	ENST00000357387	NM_152756.3	123	ttG/ttT	5/38	1	2	FACETS	0.93	0.837	1	0.93	0.837	1	CLONAL	1	TRUE	1	0.635379923796427	2		314	325	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967971	93967971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1206076675	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	132	441	0	ENST00000369303.4:c.1956G>C	p.Leu652Phe	p.L652F	ENST00000369303	NM_004440.3	652	ttG/ttC	11/17	1	2	FACETS	0.985	0.902	1	0.985	0.902	1	CLONAL	1	TRUE	1	0.635379923796427	2		441	422	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845772	151845772	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	254	597	0	ENST00000262189.6:c.13240G>A	p.Asp4414Asn	p.D4414N	ENST00000262189	NM_170606.2	4414	Gat/Aat	52/59	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.635379923796427	2		597	783	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22008895	22008925	+	frameshift_variant	Frame_Shift_Del	DEL	TGGCCAGACCCTCATCGCTGCCGCCCCCACT	TGGCCAGACCCTCATCGCTGCCGCCCCCACT	-	novel	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	223	795	0	ENST00000276925.6:c.28_58del	p.Ser10AlafsTer7	p.S10Afs*7	ENST00000276925	NM_004936.3	10	AGTGGGGGCGGCAGCGATGAGGGTCTGGCCAgc/gc	1/2	1	2	FACETS	0.799	0.745	0.854	0.799	0.745	0.854	SUBCLONAL	1	TRUE	1	0.635379923796427	2		795	879	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128432108	128432108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	98	325	0	ENST00000265960.3:c.338C>T	p.Ser113Phe	p.S113F	ENST00000265960	NM_001006617.1	113	tCt/tTt	3/12	1	2	FACETS	0.961	0.867	1	0.961	0.867	1	CLONAL	1	TRUE	1	0.635379923796427	2		325	321	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922749	44922749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	169	442	0	ENST00000377967.4:c.1610C>T	p.Ser537Leu	p.S537L	ENST00000377967	NM_021140.2	537	tCa/tTa	16/29	1	2	FACETS	0.991	0.917	1	0.991	0.917	1	CLONAL	1	TRUE	1	0.635379923796427	2		442	537	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195183	123195183	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	143	395	0	ENST00000218089.9:c.1526G>C	p.Gly509Ala	p.G509A	ENST00000218089	NM_001042749.1	509	gGa/gCa	16/35	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.635379923796427	2		395	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	129	523	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	1	2	FACETS	0.989	0.898	1	0.989	0.898	1	CLONAL	1	TRUE	1	0.374805013373837	2		523	696	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0047156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	157	735	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	1	2	FACETS	0.94	0.861	1	0.94	0.861	1	CLONAL	1	TRUE	1	0.374805013373837	2		735	891	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732318	74732318	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	82	339	0	ENST00000359995.5:c.591G>C	p.Lys197Asn	p.K197N	ENST00000359995	NM_001195427.1	197	aaG/aaC	2/3	1	2	FACETS	0.937	0.829	1	0.937	0.829	1	CLONAL	1	TRUE	1	0.374805013373837	2		339	467	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535450	66535450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	78	400	0	ENST00000273854.3:c.11C>T	p.Ser4Leu	p.S4L	ENST00000273854	NM_004439.5	4	tCg/tTg	1/18	1	2	FACETS	0.935	0.825	1	0.935	0.825	1	CLONAL	1	TRUE	1	0.374805013373837	2		400	445	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105685	27105685	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	95	299	0	ENST00000324856.7:c.5296G>T	p.Glu1766Ter	p.E1766*	ENST00000324856	NM_006015.4	1766	Gaa/Taa	20/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.374805013373837	2		299	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579418	7579418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526625	NA	P-0047156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	152	679	0	ENST00000269305.4:c.269C>T	p.Ser90Phe	p.S90F	ENST00000269305	NM_001126112.2	90	tCc/tTc	4/11	1	2	FACETS	0.998	0.913	1	0.998	0.913	1	CLONAL	1	TRUE	1	0.374805013373837	2		679	813	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139650	202139650	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	70	249	0	ENST00000358485.4:c.811C>G	p.Pro271Ala	p.P271A	ENST00000358485	NM_001080125.1	271	Cca/Gca	6/9	0.327840478751387	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.374805013373837	1		249	288	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259172	36259172	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	143	629	0	ENST00000300305.3:c.319C>G	p.Arg107Gly	p.R107G	ENST00000300305		107	Cgc/Ggc	3/8	1	2	FACETS	0.912	0.831	0.996	0.912	0.831	0.996	CLONAL	1	TRUE	1	0.374805013373837	2		629	837	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106387	27106387	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	106	464	0	ENST00000324856.7:c.5998G>C	p.Glu2000Gln	p.E2000Q	ENST00000324856	NM_006015.4	2000	Gag/Cag	20/20	1	2	FACETS	0.941	0.846	1	0.941	0.846	1	CLONAL	1	TRUE	1	0.374805013373837	2		464	601	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39321501	39321501	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	77	401	0	ENST00000373001.3:c.520G>A	p.Glu174Lys	p.E174K	ENST00000373001	NM_022157.3	174	Gag/Aag	3/7	1	2	FACETS	0.809	0.712	0.913	0.809	0.712	0.913	CLONAL	1	TRUE	1	0.374805013373837	2		401	508	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310500	65310500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	98	465	0	ENST00000342505.4:c.2188G>A	p.Glu730Lys	p.E730K	ENST00000342505	NM_002227.2	730	Gag/Aag	16/25	1	2	FACETS	0.882	0.788	0.981	0.882	0.788	0.981	CLONAL	1	TRUE	1	0.374805013373837	2		465	593	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176176059	176176059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	148	532	0	ENST00000367669.3:c.56C>T	p.Ser19Leu	p.S19L	ENST00000367669	NM_022457.5	19	tCg/tTg	1/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.374805013373837	2		532	762	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325023	123325023	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	100	525	0	ENST00000358487.5:c.305C>G	p.Ser102Cys	p.S102C	ENST00000358487	NM_000141.4	102	tCc/tGc	3/18	1	2	FACETS	0.895	0.801	0.995	0.895	0.801	0.995	CLONAL	1	TRUE	1	0.374805013373837	2		525	596	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955539	48955539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146236493	NA	P-0047156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	32	270	0	ENST00000267163.4:c.1655G>A	p.Arg552Gln	p.R552Q	ENST00000267163	NM_000321.2	552	cGa/cAa	17/27	0.219767072664953	1	FACETS	0.503	0.409	0.607	0.503	0.409	0.607	INDETERMINATE	1	TRUE	0	0.374805013373837	1		270	276	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41022122	41022122	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	118	500	0	ENST00000267868.3:c.846T>A	p.Asp282Glu	p.D282E	ENST00000267868	NM_002875.4	282	gaT/gaA	9/10	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.374805013373837	2		500	611	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875655	56875655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	80	456	0	ENST00000308159.5:c.2259G>A	p.Met753Ile	p.M753I	ENST00000308159	NM_014669.4	753	atG/atA	21/22	1	2	FACETS	0.778	0.686	0.876	0.778	0.686	0.876	SUBCLONAL	1	TRUE	1	0.374805013373837	2		456	549	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645927	67645927	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	103	464	0	ENST00000264010.4:c.855G>T	p.Met285Ile	p.M285I	ENST00000264010	NM_006565.3	285	atG/atT	4/12	1	2	FACETS	0.949	0.852	1	0.949	0.852	1	CLONAL	1	TRUE	1	0.374805013373837	2		464	579	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348701	89348701	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs151040526	NA	P-0047156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	147	757	0	ENST00000301030.4:c.4249G>C	p.Asp1417His	p.D1417H	ENST00000301030	NM_001256183.1	1417	Gat/Cat	9/13	1	2	FACETS	0.84	0.766	0.917	0.84	0.766	0.917	CLONAL	1	TRUE	1	0.374805013373837	2		757	934	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349070	89349070	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs144053389	NA	P-0047156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	201	780	0	ENST00000301030.4:c.3880G>C	p.Glu1294Gln	p.E1294Q	ENST00000301030	NM_001256183.1	1294	Gaa/Caa	9/13	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.374805013373837	2		780	1033	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349405	89349405	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	181	843	0	ENST00000301030.4:c.3545G>C	p.Arg1182Thr	p.R1182T	ENST00000301030	NM_001256183.1	1182	aGa/aCa	9/13	1	2	FACETS	0.855	0.788	0.926	0.855	0.788	0.926	CLONAL	1	TRUE	1	0.374805013373837	2		843	1129	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350609	89350609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	189	727	1	ENST00000301030.4:c.2341G>A	p.Asp781Asn	p.D781N	ENST00000301030	NM_001256183.1	781	Gat/Aat	9/13	1	2	FACETS	0.937	0.865	1	0.937	0.865	1	CLONAL	1	TRUE	1	0.374805013373837	2		728	1076	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125671	47125671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	81	312	0	ENST00000409792.3:c.5599G>A	p.Glu1867Lys	p.E1867K	ENST00000409792	NM_014159.6	1867	Gaa/Aaa	12/21	1	2	FACETS	0.944	0.835	1	0.944	0.835	1	CLONAL	1	TRUE	1	0.374805013373837	2		312	458	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522556	187522556	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	90	338	0	ENST00000441802.2:c.11507G>C	p.Gly3836Ala	p.G3836A	ENST00000441802	NM_005245.3	3836	gGa/gCa	21/27	0.354676963326038	1	FACETS	0.971	0.867	1	0.971	0.867	1	CLONAL	1	TRUE	0	0.374805013373837	1		338	402	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250101	110250101	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1169388589	NA	P-0047156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	115	652	0	ENST00000374672.4:c.574G>T	p.Asp192Tyr	p.D192Y	ENST00000374672	NM_004235.4	192	Gac/Tac	3/5	1	2	FACETS	0.817	0.736	0.902	0.817	0.736	0.902	CLONAL	1	TRUE	1	0.374805013373837	2		652	751	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	119	349	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.461455805172011	3	FACETS	0.968	0.885	1	0.968	0.885	1	CLONAL	2	TRUE	1	0.461455805172011	3		349	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0047157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	168	630	1	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.460310294739225	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.461455805172011	2		631	347	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208064	5208064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753044393	NA	P-0047157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	93	489	0	ENST00000357368.4:c.5647G>A	p.Gly1883Ser	p.G1883S	ENST00000357368	NM_002850.3	1883	Ggc/Agc	37/38	0.204872561961279	4	FACETS	0.89	0.799	0.984	0.89	0.799	0.984	INDETERMINATE	2	TRUE	2	0.461455805172011	4		489	331	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426649	212426649	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	129	403	0	ENST00000342788.4:c.2466C>G	p.Asn822Lys	p.N822K	ENST00000342788	NM_005235.2	822	aaC/aaG	20/28	0.461455805172011	3	FACETS	0.869	0.796	0.944	0.869	0.796	0.944	CLONAL	2	TRUE	1	0.461455805172011	3		403	396	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940508	49940508	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1323633773	NA	P-0047157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	83	799	0	ENST00000296474.3:c.535G>T	p.Ala179Ser	p.A179S	ENST00000296474	NM_002447.2	179	Gcc/Tcc	1/20	0.461455805172011	3	FACETS	0.909	0.805	1	0.455	0.402	0.51	CLONAL	1	TRUE	1	0.461455805172011	3		799	487	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	34	516	0				ENST00000310581	NM_198253.2	-/1132			0.3	2	FACETS	1	0.898	1			1	CLONAL	1	TRUE	NA	0.12	2		516	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0047158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	43	634	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	1	2	FACETS	0.989	0.825	1	0.989	0.825	1	CLONAL	1	TRUE	1	0.12	2		634	725	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39240663	39240663	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	21	357	0	ENST00000402219.2:c.2105A>T	p.Tyr702Phe	p.Y702F	ENST00000402219	NM_005633.3	702	tAt/tTt	13/23	1	2	FACETS	1	0.772	1	1	0.772	1	CLONAL	1	TRUE	1	0.12	2		357	349	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916861	178916861	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1560137208	NA	P-0047158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	48	490	1	ENST00000263967.3:c.248T>C	p.Phe83Ser	p.F83S	ENST00000263967	NM_006218.2	83	tTt/tCt	2/21	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.12	2		491	618	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947865	178947865	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	16	294	0	ENST00000263967.3:c.2740G>C	p.Gly914Arg	p.G914R	ENST00000263967	NM_006218.2	914	Gga/Cga	19/21	1	2	FACETS	0.866	0.639	1	0.866	0.639	1	CLONAL	1	TRUE	1	0.12	2		294	308	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCCA	novel	NA	P-0047159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	147	376	0	ENST00000288135.5:c.1506_1507insCATGCC	p.Ala502_Tyr503insHisAla	p.A502_Y503insHA	ENST00000288135	NM_000222.2	501	tct/tcTGCCCAt	9/21	1	2	FACETS	0.784	0.719	0.852	0.784	0.719	0.852	SUBCLONAL	1	TRUE	1	0.616704024845437	2		376	608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0047174-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	291	652	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.351018906637191	3	FACETS	1	0.992	1	0.825	0.785	0.866	CLONAL	2	TRUE	0	0.522876648864703	3		653	567	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0047174-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	113	303	1	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.270695021619089	4	FACETS	1	0.966	1	1	0.966	1	INDETERMINATE	2	TRUE	2	0.522876648864703	4		304	295	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999454	100999454	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047174-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	130	1201	0	ENST00000325455.5:c.348C>G	p.Asp116Glu	p.D116E	ENST00000325455	NM_001202474.3	116	gaC/gaG	1/8	0.270695021619089	4	FACETS	0.751	0.685	0.82	0.751	0.685	0.82	INDETERMINATE	2	TRUE	2	0.522876648864703	4		1201	504	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793343	242793343	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047174-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	80	1089	0	ENST00000334409.5:c.734A>T	p.Gln245Leu	p.Q245L	ENST00000334409	NM_005018.2	245	cAg/cTg	5/5	0.411488311103925	3	FACETS	0.935	0.827	1	0.467	0.413	0.525	CLONAL	1	TRUE	1	0.522876648864703	3		1089	413	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266501	55266501	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047174-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	143	732	0	ENST00000275493.2:c.2793A>T	p.Glu931Asp	p.E931D	ENST00000275493	NM_005228.3	931	gaA/gaT	23/28	0.522876648864703	7	FACETS	1	0.975	1	0.239	0.217	0.262	CLONAL	1	TRUE	2	0.522876648864703	7		732	1057	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249016	55249017	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCCACG	rs397517114	NA	P-0047183-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	266	676	0	ENST00000275493.2:c.2315_2320dup	p.His773_Val774insAlaHis	p.H773_V774insAH	ENST00000275493	NM_005228.3	772	ccc/cCCCACGcc	20/28	0.214998672197765	8	FACETS	0.886	0.83	0.943	0.59	0.553	0.629	CLONAL	4	TRUE	2	0.214998672197765	8		676	1149	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106538	108106538	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047183-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	51	229	0	ENST00000278616.4:c.473A>T	p.Glu158Val	p.E158V	ENST00000278616	NM_000051.3	158	gAa/gTa	5/63	0.196293246721226	4	FACETS	0.796	0.679	0.923	0.796	0.679	0.923	CLONAL	2	TRUE	2	0.214998672197765	4		229	362	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682964	241682964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047183-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1256	78	670	1	ENST00000366560.3:c.59C>T	p.Ala20Val	p.A20V	ENST00000366560	NM_000143.3	20	gCa/gTa	1/10	0.214998672197765	8	FACETS	0.895	0.783	1			1	CLONAL	1	TRUE	NA	0.214998672197765	8		671	1334	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751131	57751131	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047183-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	24	243	0	ENST00000274289.3:c.1736T>C	p.Met579Thr	p.M579T	ENST00000274289	NM_006622.3	579	aTg/aCg	12/14	0.196293246721226	4	FACETS	0.835	0.655	1	0.417	0.327	0.521	CLONAL	1	TRUE	2	0.214998672197765	4		243	325	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	52	349	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.51	0.437	0.588	0.51	0.437	0.588	SUBCLONAL	1	TRUE	1	0.736618236713148	2		349	277	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0047184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	156	592	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.698560322456768	3	FACETS	1	0.981	1	0.599	0.552	0.646	CLONAL	1	TRUE	1	0.736618236713148	3		592	484	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519922	NA	P-0047184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	229	542	0	ENST00000397062.3:c.235G>A	p.Glu79Lys	p.E79K	ENST00000397062	NM_006164.4	79	Gag/Aag	2/5	0.361724726649744	3	FACETS	0.76	0.714	0.806	0.76	0.714	0.806	INDETERMINATE	2	TRUE	1	0.736618236713148	3		542	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579582	7579583	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	260	654	0	ENST00000269305.4:c.104dup	p.Leu35PhefsTer8	p.L35Ffs*8	ENST00000269305	NM_001126112.2	35	ttg/ttTg	4/11	0.698560322456768	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.736618236713148	3		654	477	SUCCESS
ATR	545	MSKCC	GRCh37	3	142183937	142183937	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0047184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	116	213	0	ENST00000350721.4:c.7041+2T>C		p.X2347_splice	ENST00000350721	NM_001184.3	2347			0.736618236713148	3	FACETS	0.958	0.884	1	0.958	0.884	1	CLONAL	2	TRUE	1	0.736618236713148	3		213	225	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852416	63852416	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	145	575	0	ENST00000279873.7:c.3194G>T	p.Gly1065Val	p.G1065V	ENST00000279873	NM_032199.2	1065	gGa/gTa	10/10	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.736618236713148	2		575	358	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81904455	81904455	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0047184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	86	222	0	ENST00000359376.3:c.565-2A>G		p.X189_splice	ENST00000359376	NM_002661.3	189			0.389688037597788	1	FACETS	0.883	0.805	0.962	0.883	0.805	0.962	INDETERMINATE	1	TRUE	0	0.736618236713148	1		222	167	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098599	11098599	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	145	722	0	ENST00000358026.2:c.1117A>T	p.Arg373Trp	p.R373W	ENST00000358026	NM_001128849.1	373	Agg/Tgg	6/36	0.361724726649744	3	FACETS	1	0.986	1	0.662	0.61	0.715	INDETERMINATE	1	TRUE	1	0.736618236713148	3		722	407	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522186	157522186	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	120	610	0	ENST00000346085.5:c.4459del	p.Ala1487ArgfsTer7	p.A1487Rfs*7	ENST00000346085	NM_020732.3	1486	caG/ca	18/20	0.736618236713148	1	FACETS	0.923	0.855	0.99	0.923	0.855	0.99	CLONAL	1	TRUE	0	0.736618236713148	1		610	223	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370837	55370837	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	54	834	0	ENST00000297316.4:c.139G>T	p.Glu47Ter	p.E47*	ENST00000297316	NM_022454.3	47	Gag/Tag	1/2	0.410694699926514	1	FACETS	0.349	0.301	0.402	0.349	0.301	0.402	INDETERMINATE	1	TRUE	0	0.736618236713148	1		834	265	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992821	68992821	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0047184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	43	353	0	ENST00000288368.4:c.1785+1G>T		p.X595_splice	ENST00000288368	NM_024870.2	595			0.410694699926514	1	FACETS	0.442	0.375	0.513	0.442	0.375	0.513	INDETERMINATE	1	TRUE	0	0.736618236713148	1		353	167	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047189-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	66	349	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.853	0.751	0.961	1	0.979	1	CLONAL	2	TRUE	1	0.333506022894325	2		349	232	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0047189-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	29	458	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.326249500384408	0	FACETS	0.633	0.513	0.768			1	SUBCLONAL	1	TRUE	0	0.333506022894325	0		458	183	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0047189-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	55	652	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.325861804945659	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	0	0.333506022894325	1		653	258	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0047189-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	53	439	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.325861804945659	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.333506022894325	1		439	224	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871640	35871640	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs957688002	NA	P-0047189-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	41	314	0	ENST00000216797.5:c.866A>G	p.Tyr289Cys	p.Y289C	ENST00000216797	NM_020529.2	289	tAt/tGt	5/6	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.333506022894325	2		314	232	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0047195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	62	374	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.906	0.792	1	0.906	0.792	1	CLONAL	1	TRUE	1	0.565415784323936	2		374	242	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0047195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	158	552	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.511625825815557	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.565415784323936	1		553	379	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0047195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	64	308	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.565415784323936	2		308	198	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	42	643	0	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	1	2	FACETS	0.897	0.753	1	0.897	0.753	1	CLONAL	1	TRUE	1	0.31	2		643	302	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	140	889	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.95	0.879	1	1	0.993	1	CLONAL	3	TRUE	1	0.31	2		895	317	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753452	42753452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	48	838	3	ENST00000222329.4:c.812C>T	p.Thr271Met	p.T271M	ENST00000222329	NM_006494.2	271	aCg/aTg	4/4	1	2	FACETS	0.863	0.732	1	0.863	0.732	1	CLONAL	1	TRUE	1	0.31	2		841	359	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	17	457	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	0.118374646999404	3	FACETS	1	0.866	1	0.621	0.47	0.794	INDETERMINATE	1	TRUE	1	0.31	3		457	102	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233090	69233090	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746910913	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	16	216	1	ENST00000462284.1:c.961del	p.Leu321PhefsTer52	p.L321Ffs*52	ENST00000462284	NM_002392.5	319	Ccc/cc	11/11	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.31	2		217	78	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	26	816	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.927	0.74	1	0.927	0.74	1	CLONAL	1	TRUE	1	0.31	2		817	181	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49413010	49413010	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519952	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	17	452	1	ENST00000418115.1:c.13C>T	p.Arg5Trp	p.R5W	ENST00000418115	NM_001664.2	5	Cgg/Tgg	2/5	1	2	FACETS	0.669	0.502	0.864	0.669	0.502	0.864	SUBCLONAL	1	TRUE	1	0.31	2		453	164	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	43	248	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.878	0.747	1	1	0.969	1	CLONAL	2	TRUE	1	0.31	2		248	158	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533905	63533905	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	14	506	1	ENST00000307078.5:c.1249del	p.Ala417ArgfsTer41	p.A417Rfs*41	ENST00000307078	NM_004655.3	417	Gcg/cg	6/11	1	2	FACETS	0.428	0.31	0.571	0.428	0.31	0.571	SUBCLONAL	1	TRUE	1	0.31	2		507	211	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349090	11349090	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	40	366	0	ENST00000332029.2:c.246del	p.Leu84Ter	p.L84*	ENST00000332029	NM_003745.1	82	ggG/gg	2/2	1	2	FACETS	0.866	0.723	1	0.866	0.723	1	CLONAL	1	TRUE	1	0.31	2		366	298	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	34	1048	7	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.31	2		1055	198	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911116	29911116	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs199474504	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	38	899	0	ENST00000376809.5:c.415C>T	p.Gln139Ter	p.Q139*	ENST00000376809	NM_002116.7	139	Cag/Tag	3/8	0.118374646999404	3	FACETS	1	0.882	1	0.538	0.447	0.639	INDETERMINATE	1	TRUE	1	0.31	3		899	263	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346158	89346158	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs878855327	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	12	360	0	ENST00000301030.4:c.6792del	p.Ala2265ProfsTer72	p.A2265Pfs*72	ENST00000301030	NM_001256183.1	2264	ccC/cc	9/13	1	2	FACETS	0.717	0.508	0.968	0.717	0.508	0.968	CLONAL	1	TRUE	1	0.31	2		360	108	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	55	456	0	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.31	2		456	341	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436026	56436026	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771831816	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	23	435	0	ENST00000407977.2:c.1111C>T	p.Arg371Ter	p.R371*	ENST00000407977		371	Cga/Tga	9/10	1	2	FACETS	0.933	0.734	1	0.933	0.734	1	CLONAL	1	TRUE	1	0.31	2		435	159	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713414	40713414	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	22	647	1	ENST00000373198.4:c.4101del	p.Ser1368ProfsTer31	p.S1368Pfs*31	ENST00000373198	NM_133170.3	1367	ccC/cc	30/32	0.118374646999404	0	FACETS	0.608	0.475	0.76			1	INDETERMINATE	1	TRUE	0	0.31	0		648	161	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45864886	45864886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200043231	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	29	720	1	ENST00000391945.4:c.1133G>A	p.Arg378His	p.R378H	ENST00000391945	NM_000400.3	378	cGc/cAc	12/23	1	2	FACETS	0.783	0.631	0.953	0.783	0.631	0.953	CLONAL	1	TRUE	1	0.31	2		721	239	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999560	100999560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778465984	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	19	825	1	ENST00000325455.5:c.242C>T	p.Ser81Leu	p.S81L	ENST00000325455	NM_001202474.3	81	tCg/tTg	1/8	1	2	FACETS	0.581	0.442	0.743	0.581	0.442	0.743	SUBCLONAL	1	TRUE	1	0.31	2		826	211	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798450	42798450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142012810	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	26	619	0	ENST00000575354.2:c.4321C>T	p.Arg1441Cys	p.R1441C	ENST00000575354	NM_015125.3	1441	Cgt/Tgt	18/20	1	2	FACETS	0.883	0.704	1	0.883	0.704	1	CLONAL	1	TRUE	1	0.31	2		619	190	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225574	133225574	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	13	643	0	ENST00000320574.5:c.4090del	p.Arg1364ValfsTer5	p.R1364Vfs*5	ENST00000320574	NM_006231.2	1364	Cgt/gt	32/49	1	2	FACETS	0.332	0.236	0.448	0.332	0.236	0.448	SUBCLONAL	1	TRUE	1	0.31	2		643	253	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461508	138461508	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	10	380	2	ENST00000289153.2:c.513G>A	p.Trp171Ter	p.W171*	ENST00000289153	NM_006219.2	171	tgG/tgA	3/22	1	2	FACETS	0.529	0.36	0.738	0.529	0.36	0.738	SUBCLONAL	1	TRUE	1	0.31	2		382	122	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746075	162746075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	14	261	0	ENST00000367921.3:c.2198G>A	p.Arg733Lys	p.R733K	ENST00000367921	NM_006182.2	733	aGg/aAg	16/18	1	2	FACETS	0.706	0.514	0.934	0.706	0.514	0.934	CLONAL	1	TRUE	1	0.31	2		261	128	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158026	27158026	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	12	451	0	ENST00000380036.4:c.255del	p.Val86LeufsTer31	p.V86Lfs*31	ENST00000380036	NM_000459.3	84	Aaa/aa	2/23	1	2	FACETS	0.49	0.345	0.667	0.49	0.345	0.667	SUBCLONAL	1	TRUE	1	0.31	2		451	158	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215621	36215621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1268488101	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	26	694	0	ENST00000222270.7:c.3418C>T	p.Arg1140Cys	p.R1140C	ENST00000222270	NM_014727.1	1140	Cgc/Tgc	9/37	1	2	FACETS	0.645	0.513	0.796	0.645	0.513	0.796	SUBCLONAL	1	TRUE	1	0.31	2		694	260	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595382	141595382	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	15	557	0	ENST00000220592.5:c.51del	p.Ile18SerfsTer121	p.I18Sfs*121	ENST00000220592	NM_012154.3	17	ccC/cc	2/19	1	2	FACETS	0.365	0.267	0.484	0.365	0.267	0.484	SUBCLONAL	1	TRUE	1	0.31	2		557	265	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324221	31324221	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	18	622	0	ENST00000412585.2:c.344-2A>G		p.X115_splice	ENST00000412585	NM_005514.6	115			0.118374646999404	3	FACETS	0.702	0.531	0.903	0.351	0.265	0.452	INDETERMINATE	1	TRUE	1	0.31	3		622	191	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271919	15271919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376494303	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	12	919	1	ENST00000263388.2:c.6520C>T	p.Arg2174Trp	p.R2174W	ENST00000263388	NM_000435.2	2174	Cgg/Tgg	33/33	1	2	FACETS	0.367	0.258	0.501	0.367	0.258	0.501	SUBCLONAL	1	TRUE	1	0.31	2		920	211	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861563	152861563	+	synonymous_variant	Silent	SNP	G	G	A	rs139660436	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	16	610	0	ENST00000406277.2:c.189C>T	p.Asp63=	p.D63=	ENST00000406277	NM_152274.4	63	gaC/gaT	4/7	0.118374646999404		FACETS		0.285	0.503				INDETERMINATE	1	TRUE	0	0.31	0		610	185	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600036	10600036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371976438	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	32	632	0	ENST00000171111.5:c.1540G>A	p.Val514Ile	p.V514I	ENST00000171111	NM_203500.1	514	Gtc/Atc	5/6	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.31	2		632	186	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778839	9778839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143521812	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	39	644	1	ENST00000377346.4:c.1108G>A	p.Val370Met	p.V370M	ENST00000377346	NM_005026.3	370	Gtg/Atg	9/24	1	2	FACETS	0.877	0.73	1	0.877	0.73	1	CLONAL	1	TRUE	1	0.31	2		645	287	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484606	57484606	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	26	409	0	ENST00000371085.3:c.690A>T	p.Glu230Asp	p.E230D	ENST00000371085	NM_000516.4	230	gaA/gaT	9/13	0.118374646999404	0	FACETS	0.567	0.452	0.698			1	INDETERMINATE	1	TRUE	0	0.31	0		409	204	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261154	16261154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764040616	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	28	360	3	ENST00000375759.3:c.8419C>T	p.Arg2807Cys	p.R2807C	ENST00000375759	NM_015001.2	2807	Cgt/Tgt	11/15	1	2	FACETS	0.877	0.706	1	0.877	0.706	1	CLONAL	1	TRUE	1	0.31	2		363	206	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246126	46246126	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	13	248	0	ENST00000334344.6:c.4220C>T	p.Ala1407Val	p.A1407V	ENST00000334344	NM_152641.2	1407	gCc/gTc	15/21	1	2	FACETS	1	0.788	1	1	0.788	1	CLONAL	1	TRUE	1	0.31	2		248	76	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762168	43762168	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	17	572	0	ENST00000382044.4:c.1277del	p.Pro426LeufsTer65	p.P426Lfs*65	ENST00000382044	NM_001141980.1	426	cCt/ct	11/28	1	2	FACETS	0.699	0.525	0.902	0.699	0.525	0.902	SUBCLONAL	1	TRUE	1	0.31	2		572	157	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43771659	43771659	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	20	446	1	ENST00000382044.4:c.724C>A	p.Pro242Thr	p.P242T	ENST00000382044	NM_001141980.1	242	Cct/Act	7/28	1	2	FACETS	0.849	0.655	1	0.849	0.655	1	CLONAL	1	TRUE	1	0.31	2		447	152	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215920	41215920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28897696	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	14	349	0	ENST00000357654.3:c.5123C>T	p.Ala1708Val	p.A1708V	ENST00000357654	NM_007294.3	1708	gCg/gTg	17/23	1	2	FACETS	0.792	0.578	1	0.792	0.578	1	CLONAL	1	TRUE	1	0.31	2		349	114	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131238	202131238	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	11	259	0	ENST00000358485.4:c.206T>C	p.Ile69Thr	p.I69T	ENST00000358485	NM_001080125.1	69	aTt/aCt	2/9	1	2	FACETS	0.639	0.445	0.877	0.639	0.445	0.877	SUBCLONAL	1	TRUE	1	0.31	2		259	111	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466785	57466785	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	13	104	0	ENST00000371085.3:c.4G>T	p.Gly2Cys	p.G2C	ENST00000371085	NM_000516.4	2	Ggc/Tgc	1/13	0.118374646999404	0	FACETS	0.658	0.476	0.872			1	INDETERMINATE	1	TRUE	0	0.31	0		104	88	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562747	176562747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	27	359	1	ENST00000439151.2:c.643C>T	p.Pro215Ser	p.P215S	ENST00000439151	NM_022455.4	215	Cca/Tca	2/23	1	2	FACETS	0.871	0.698	1	0.871	0.698	1	CLONAL	1	TRUE	1	0.31	2		360	200	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056312	180056312	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	11	754	1	ENST00000261937.6:c.932A>C	p.Lys311Thr	p.K311T	ENST00000261937	NM_182925.4	311	aAg/aCg	7/30	1	2	FACETS	0.37	0.255	0.511	0.37	0.255	0.511	SUBCLONAL	1	TRUE	1	0.31	2		755	192	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271491	26271491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	77	453	0	ENST00000305910.3:c.122G>A	p.Arg41His	p.R41H	ENST00000305910	NM_003534.2	41	cGc/cAc	1/1	0.3	14	FACETS	1	0.915	1			1	CLONAL	4	TRUE	NA	0.31	14		453	341	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778069	27778069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1290595614	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	69	546	0	ENST00000369163.2:c.218G>A	p.Arg73His	p.R73H	ENST00000369163	NM_003536.2	73	cGt/cAt	1/1	0.3	14	FACETS	1	0.932	1			1	CLONAL	3	TRUE	NA	0.31	14		546	386	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165266	32165266	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	35	809	0	ENST00000375023.3:c.4862A>G	p.Asp1621Gly	p.D1621G	ENST00000375023	NM_004557.3	1621	gAt/gGt	27/30	0.118374646999404	3	FACETS	0.855	0.703	1	0.428	0.351	0.512	INDETERMINATE	1	TRUE	1	0.31	3		809	305	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570289	87570289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1406280648	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	11	526	0	ENST00000277120.3:c.2029G>A	p.Ala677Thr	p.A677T	ENST00000277120		677	Gcc/Acc	17/19	1	2	FACETS	0.335	0.231	0.464	0.335	0.231	0.464	SUBCLONAL	1	TRUE	1	0.31	2		526	212	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411777	63411777	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	12	628	0	ENST00000330258.3:c.1390G>C	p.Ala464Pro	p.A464P	ENST00000330258	NM_152424.3	464	Gcc/Ccc	2/2	0.118374646999404	0	FACETS	0.399	0.281	0.541			1	INDETERMINATE	1	TRUE	0	0.31	0		628	134	SUCCESS
AR	367	MSKCC	GRCh37	X	66766114	66766114	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	20	609	0	ENST00000374690.3:c.1126C>A	p.Pro376Thr	p.P376T	ENST00000374690	NM_000044.3	376	Ccc/Acc	1/8	0.118374646999404	0	FACETS	0.45	0.345	0.571			1	INDETERMINATE	1	TRUE	0	0.31	0		609	198	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76777820	76777820	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	20	424	0	ENST00000373344.5:c.6896del	p.Pro2299LeufsTer21	p.P2299Lfs*21	ENST00000373344	NM_000489.3	2299	cCt/ct	32/35	0.118374646999404	0	FACETS	0.701	0.542	0.882			1	INDETERMINATE	1	TRUE	0	0.31	0		424	127	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0047198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	451	277	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.591876364023888	6	FACETS	0.973	0.941	1			1	CLONAL	5	TRUE	NA	0.591876364023888	6		277	684	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306937	65306937	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	96	280	0	ENST00000342505.4:c.2640del	p.Leu881TrpfsTer30	p.L881Wfs*30	ENST00000342505	NM_002227.2	880	gaC/ga	19/25	0.591876364023888	4	FACETS	0.946	0.845	1	0.315	0.281	0.351	CLONAL	1	TRUE	1	0.591876364023888	4		280	546	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445218	49445218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	200	934	1	ENST00000301067.7:c.2248C>T	p.Pro750Ser	p.P750S	ENST00000301067	NM_003482.3	750	Ccg/Tcg	10/54	0.51489468605325	5	FACETS	0.956	0.884	1	0.239	0.221	0.258	CLONAL	1	TRUE	1	0.591876364023888	5		935	1334	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492721	56492722	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0047198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	428	447	0	ENST00000407977.2:c.217dup	p.Ala73GlyfsTer2	p.A73Gfs*2	ENST00000407977		73	gct/gGct	2/10	0.591876364023888	3	FACETS	0.935	0.903	0.967	0.935	0.903	0.967	CLONAL	3	TRUE	0	0.591876364023888	3		447	668	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904872	101904872	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863223832	NA	P-0047198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	166	295	0	ENST00000374994.4:c.860C>A	p.Ser287Tyr	p.S287Y	ENST00000374994	NM_004612.2	287	tCc/tAc	5/9	0.574695379117581	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.591876364023888	2		295	270	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0047199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	263	164	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.495625489694128	5	FACETS	0.942	0.89	0.994	0.942	0.89	0.994	CLONAL	3	TRUE	2	0.576561983844348	5		164	602	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101985	11101985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502079	NA	P-0047199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	241	728	0	ENST00000358026.2:c.1405C>T	p.Arg469Trp	p.R469W	ENST00000358026	NM_001128849.1	469	Cgg/Tgg	8/36	0.478930733906293	1	FACETS	0.811	0.76	0.862	0.811	0.76	0.862	CLONAL	1	TRUE	0	0.576561983844348	1		728	734	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792461	33792461	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	233	702	0	ENST00000498907.2:c.860T>A	p.Val287Glu	p.V287E	ENST00000498907	NM_004364.3	287	gTg/gAg	1/1	1	2	FACETS	0.912	0.852	0.974	0.912	0.852	0.974	CLONAL	1	TRUE	1	0.576561983844348	2		702	886	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0047200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	50	349	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.915	0.777	1	0.915	0.777	1	CLONAL	1	TRUE	1	0.23	2		349	475	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0047200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	92	709	5	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.23	2		714	715	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0047200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	45	258	1	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.957	0.806	1	0.957	0.806	1	CLONAL	1	TRUE	1	0.23	2		259	409	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508389	106508389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758375337	NA	P-0047200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	45	316	1	ENST00000359195.3:c.383C>T	p.Thr128Met	p.T128M	ENST00000359195	NM_002649.2	128	aCg/aTg	2/11	1	2	FACETS	0.902	0.759	1	0.902	0.759	1	CLONAL	1	TRUE	1	0.23	2		317	434	SUCCESS
APC	324	MSKCC	GRCh37	5	112175358	112175358	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	16	183	1	ENST00000257430.4:c.4067C>A	p.Ser1356Ter	p.S1356*	ENST00000257430	NM_000038.5	1356	tCa/tAa	16/16	1	2	FACETS	0.502	0.371	0.659	0.502	0.371	0.659	SUBCLONAL	1	TRUE	1	0.23	2		184	277	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248242	59248243	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0047200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	18	72	0	ENST00000371222.2:c.500dup	p.Pro168AlafsTer142	p.P168Afs*142	ENST00000371222	NM_002228.3	167	ccg/ccCg	1/1	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.23	2		72	111	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43773107	43773108	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	88	532	0	ENST00000382044.4:c.484dup	p.Ser162PhefsTer5	p.S162Ffs*5	ENST00000382044	NM_001141980.1	162	tcc/tTcc	5/28	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.23	2		532	764	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858179	40858179	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	67	545	0	ENST00000428826.2:c.1685G>A	p.Arg562His	p.R562H	ENST00000428826		562	cGc/cAc	16/21	1	2	FACETS	0.65	0.564	0.745	0.65	0.564	0.745	SUBCLONAL	1	TRUE	1	0.23	2		545	896	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0047202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	279	396	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.640427291189296	3	FACETS	0.991	0.94	1	0.991	0.94	1	CLONAL	2	TRUE	1	0.651641348411393	3		396	573	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021818	71021818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869025203	NA	P-0047202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	156	217	0	ENST00000318789.4:c.1540C>T	p.Arg514Cys	p.R514C	ENST00000318789	NM_032682.5	514	Cgt/Tgt	18/21	0.651641348411393	2	FACETS	0.965	0.909	1	0.965	0.909	1	CLONAL	2	TRUE	0	0.651641348411393	2		217	248	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435420	110435420	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1049519615	NA	P-0047202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	219	724	0	ENST00000375856.3:c.2981C>T	p.Pro994Leu	p.P994L	ENST00000375856	NM_003749.2	994	cCg/cTg	1/2	1	2	FACETS	0.994	0.93	1	0.994	0.93	1	CLONAL	1	TRUE	1	0.651641348411393	2		724	676	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207203	1207203	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0047202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	429	649	0	ENST00000326873.7:c.290+1G>T		p.X97_splice	ENST00000326873	NM_000455.4	97			NA	2	FACETS	0.946	0.912	0.979			1	INDETERMINATE	2	TRUE	NA	0.651641348411393	2		649	696	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625652	1625652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533848977	NA	P-0047202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	283	973	1	ENST00000344749.5:c.422C>T	p.Ser141Leu	p.S141L	ENST00000344749	NM_001136139.2	141	tCg/tTg	7/19	NA	2	FACETS	0.91	0.856	0.964			1	INDETERMINATE	1	TRUE	NA	0.651641348411393	2		974	955	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518415	8518415	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	80	264	0	ENST00000356435.5:c.976C>T	p.Pro326Ser	p.P326S	ENST00000356435		326	Cca/Tca	10/35	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.651641348411393	2		264	235	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442080	52442080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	364	466	0	ENST00000460680.1:c.269C>T	p.Ser90Phe	p.S90F	ENST00000460680	NM_004656.3	90	tCt/tTt	5/17	0.651641348411393	2	FACETS	0.942	0.905	0.978	0.942	0.905	0.978	CLONAL	2	TRUE	0	0.651641348411393	2		466	593	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130682	29130682	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1064793817	NA	P-0047202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	151	393	0	ENST00000328354.6:c.28C>T	p.Gln10Ter	p.Q10*	ENST00000328354	NM_007194.3	10	Cag/Tag	2/15	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.651641348411393	2		393	459	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857965	9857965	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	157	577	0	ENST00000330684.3:c.3436del	p.Asp1146ThrfsTer22	p.D1146Tfs*22	ENST00000330684	NM_001134407.1	1146	Gac/ac	13/13	1	2	FACETS	0.813	0.748	0.88	0.813	0.748	0.88	CLONAL	1	TRUE	1	0.651641348411393	2		577	593	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100119	11100119	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	418	581	0	ENST00000358026.2:c.1245G>T	p.Gln415His	p.Q415H	ENST00000358026	NM_001128849.1	415	caG/caT	7/36	0.651641348411393	2	FACETS	0.978	0.943	1	0.978	0.943	1	CLONAL	2	TRUE	0	0.651641348411393	2		581	656	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525696	187525696	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	128	404	0	ENST00000441802.2:c.10383G>T	p.Gln3461His	p.Q3461H	ENST00000441802	NM_005245.3	3461	caG/caT	18/27	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.651641348411393	2		404	393	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149511631	149511631	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	349	574	1	ENST00000261799.4:c.1154G>T	p.Arg385Leu	p.R385L	ENST00000261799	NM_002609.3	385	cGc/cTc	8/23	0.640427291189296	3	FACETS	0.974	0.929	1	0.974	0.929	1	CLONAL	2	TRUE	1	0.651641348411393	3		575	729	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570289	87570289	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	177	701	0	ENST00000277120.3:c.2029G>T	p.Ala677Ser	p.A677S	ENST00000277120		677	Gcc/Tcc	17/19	1	2	FACETS	0.915	0.847	0.984	0.915	0.847	0.984	CLONAL	1	TRUE	1	0.651641348411393	2		701	594	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412045	116412049	+	splice_donor_variant,intron_variant	Splice_Site	DEL	TATAT	TATAT	-	novel	NA	P-0047203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	91	573	0	ENST00000397752.3:c.3028+3_3028+7del		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.186667087513953	2	FACETS	1	0.968	1	0.62	0.551	0.693	CLONAL	1	TRUE	0	0.246853058416628	2		573	595	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953779	48953779	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	42	164	0	ENST00000267163.4:c.1382T>C	p.Leu461Pro	p.L461P	ENST00000267163	NM_000321.2	461	cTt/cCt	14/27	0.246853058416628	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.246853058416628	1		164	222	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375931	8375935	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CTTAC	CTTAC	-	novel	NA	P-0047203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	24	308	0	ENST00000356435.5:c.4661+1_4661+5del		p.X1554_splice	ENST00000356435		1554			0.143952578973385	0	FACETS	0.563	0.443	0.702			1	INDETERMINATE	1	TRUE	0	0.246853058416628	0		308	260	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	595	845	0	ENST00000269305.4:c.472C>G	p.Arg158Gly	p.R158G	ENST00000269305	NM_001126112.2	158	Cgc/Ggc	5/11	0.934354859950732	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.934354859950732	1		845	617	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941654	48941654	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs776534331	NA	P-0047204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	269	154	0	ENST00000267163.4:c.964G>T	p.Glu322Ter	p.E322*	ENST00000267163	NM_000321.2	322	Gaa/Taa	10/27	0.934354859950732	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.934354859950732	2		154	274	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161293408	161293408	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs774768866	NA	P-0047204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	257	322	0	ENST00000367975.2:c.25G>T	p.Val9Phe	p.V9F	ENST00000367975	NM_003001.3	9	Gtt/Ttt	2/6	1	2	FACETS	0.988	0.934	1	0.988	0.934	1	CLONAL	1	TRUE	1	0.934354859950732	2		322	557	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120496168	120496168	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	271	387	0	ENST00000256646.2:c.2363A>T	p.Lys788Ile	p.K788I	ENST00000256646	NM_024408.3	788	aAa/aTa	14/34	1	2	FACETS	0.975	0.923	1	0.975	0.923	1	CLONAL	1	TRUE	1	0.934354859950732	2		387	595	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665866	241665866	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	248	322	0	ENST00000366560.3:c.1113G>T	p.Lys371Asn	p.K371N	ENST00000366560	NM_000143.3	371	aaG/aaT	8/10	1	2	FACETS	0.983	0.929	1	0.983	0.929	1	CLONAL	1	TRUE	1	0.934354859950732	2		322	540	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720694	89720694	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	201	245	0	ENST00000371953.3:c.845G>T	p.Gly282Val	p.G282V	ENST00000371953	NM_000314.4	282	gGa/gTa	8/9	0.934354859950732	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.934354859950732	1		245	208	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154407	2154407	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	474	862	0	ENST00000434045.2:c.521C>A	p.Thr174Asn	p.T174N	ENST00000434045	NM_001127598.1	174	aCc/aAc	5/5	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.934354859950732	2		862	1014	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32903606	32903606	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	344	271	0	ENST00000380152.3:c.658G>T	p.Val220Leu	p.V220L	ENST00000380152		220	Gta/Tta	8/27	0.934354859950732	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.934354859950732	2		271	353	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858783	9858784	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0047204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	125	182	0	ENST00000330684.3:c.2617_2618delinsTT	p.Gly873Leu	p.G873L	ENST00000330684	NM_001134407.1	873	GGa/TTa	13/13	NA	2	FACETS	1	0.95	1			1	INDETERMINATE	1	TRUE	NA	0.934354859950732	2		182	258	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917797	29917797	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	461	717	3	ENST00000389048.3:c.871C>A	p.Arg291Ser	p.R291S	ENST00000389048	NM_004304.4	291	Cgc/Agc	3/29	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.934354859950732	2		720	927	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188940	142188940	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	244	312	0	ENST00000350721.4:c.6307G>A	p.Glu2103Lys	p.E2103K	ENST00000350721	NM_001184.3	2103	Gaa/Aaa	37/47	0.925105963816456	3	FACETS	0.948	0.889	1	0.474	0.444	0.505	CLONAL	1	TRUE	1	0.934354859950732	3		312	808	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980310	55980310	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	289	377	0	ENST00000263923.4:c.781G>T	p.Glu261Ter	p.E261*	ENST00000263923	NM_002253.2	261	Gaa/Taa	6/30	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.934354859950732	2		377	560	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517486	176517486	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	508	966	0	ENST00000292408.4:c.187G>T	p.Gly63Cys	p.G63C	ENST00000292408	NM_213647.1	63	Ggt/Tgt	3/18	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.934354859950732	2		966	1080	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653865	89653866	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AG	AG	T	novel	NA	P-0047204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	35	271	0	ENST00000371953.3:c.163_164delinsT	p.Arg55CysfsTer44	p.R55Cfs*44	ENST00000371953	NM_000314.4	55	AGg/Tg	2/9	0.934354859950732	1	FACETS	0.154	0.127	0.185	0.154	0.127	0.185	SUBCLONAL	1	TRUE	0	0.934354859950732	1		271	259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0047205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	138	682	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.198006872038524	1	FACETS	0.776	0.707	0.849	1	0.987	1	SUBCLONAL	2	TRUE	0	0.198006872038524	1		684	809	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0047205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	65	353	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.751	0.653	0.857	1	0.972	1	SUBCLONAL	2	TRUE	1	0.198006872038524	2		353	437	SUCCESS
APC	324	MSKCC	GRCh37	5	112175548	112175548	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	34	270	0	ENST00000257430.4:c.4260del	p.Ser1421ValfsTer52	p.S1421Vfs*52	ENST00000257430	NM_000038.5	1419	agC/ag	16/16	1	2	FACETS	0.781	0.638	0.941	0.781	0.638	0.941	CLONAL	1	TRUE	1	0.198006872038524	2		270	440	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912182	114912182	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	67	511	2	ENST00000543371.1:c.1252T>C	p.Ser418Pro	p.S418P	ENST00000543371	NM_001198531.1	418	Tcc/Ccc	11/14	1	2	FACETS	0.877	0.761	1	0.877	0.761	1	CLONAL	1	TRUE	1	0.198006872038524	2		513	772	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426256	49426256	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	164	844	0	ENST00000301067.7:c.12232G>A	p.Val4078Ile	p.V4078I	ENST00000301067	NM_003482.3	4078	Gtc/Atc	39/54	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.198006872038524	2		844	1221	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347071	347071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751506537	NA	P-0047205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	59	879	2	ENST00000262320.3:c.1940G>A	p.Arg647His	p.R647H	ENST00000262320	NM_003502.3	647	cGc/cAc	7/11	1	2	FACETS	0.548	0.469	0.634	0.548	0.469	0.634	SUBCLONAL	1	TRUE	1	0.198006872038524	2		881	1088	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	459	516	0				ENST00000310581	NM_198253.2	-/1132			0.73504718170976	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	1	0.73504718170976	4		516	712	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0047206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	775	858	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.73504718170976	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.73504718170976	2		858	1014	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245913	5245913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	365	947	1	ENST00000357368.4:c.862G>A	p.Glu288Lys	p.E288K	ENST00000357368	NM_002850.3	288	Gag/Aag	10/38	0.727221673400483	3	FACETS	0.991	0.938	1	0.495	0.469	0.522	CLONAL	1	TRUE	1	0.73504718170976	3		948	1371	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938079	76938079	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	256	396	0	ENST00000373344.5:c.2669C>T	p.Ser890Leu	p.S890L	ENST00000373344	NM_000489.3	890	tCa/tTa	9/35	0.73504718170976	5	FACETS	1	0.972	1	0.357	0.334	0.382	CLONAL	1	TRUE	2	0.73504718170976	5		396	1366	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350504	89350504	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1183047246	NA	P-0047206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	237	555	0	ENST00000301030.4:c.2446G>A	p.Glu816Lys	p.E816K	ENST00000301030	NM_001256183.1	816	Gaa/Aaa	9/13	0.73504718170976	3	FACETS	0.95	0.888	1	0.317	0.296	0.338	CLONAL	1	TRUE	0	0.73504718170976	3		555	928	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056617	26056617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751385999	NA	P-0047206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	124	250	0	ENST00000343677.2:c.40C>T	p.Pro14Ser	p.P14S	ENST00000343677	NM_005319.3	14	Cct/Tct	1/1	0.314505665431981	5	FACETS	1	0.984	1	0.475	0.432	0.52	INDETERMINATE	1	TRUE	2	0.73504718170976	5		250	498	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037492	12037492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	54	261	0	ENST00000396373.4:c.1123G>A	p.Gly375Arg	p.G375R	ENST00000396373	NM_001987.4	375	Gga/Aga	6/8	0.727221673400483	3	FACETS	0.373	0.319	0.433	0.187	0.159	0.217	SUBCLONAL	1	TRUE	1	0.73504718170976	3		261	538	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795022	45795022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746159001	NA	P-0047206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	246	514	0	ENST00000450313.1:c.1606C>T	p.His536Tyr	p.H536Y	ENST00000450313	NM_012222.2	536	Cac/Tac	16/16	0.73504718170976	3	FACETS	0.917	0.858	0.978	0.459	0.429	0.489	CLONAL	1	TRUE	1	0.73504718170976	3		514	998	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714239	43714239	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1404522384	NA	P-0047206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	130	687	0	ENST00000382044.4:c.3914G>A	p.Gly1305Glu	p.G1305E	ENST00000382044	NM_001141980.1	1305	gGg/gAg	19/28	0.688698313051297	3	FACETS	0.434	0.392	0.478	0.217	0.196	0.239	SUBCLONAL	1	TRUE	1	0.73504718170976	3		687	1115	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993440	72993440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	391	794	0	ENST00000268489.5:c.605C>T	p.Ser202Leu	p.S202L	ENST00000268489	NM_006885.3	202	tCa/tTa	2/10	0.71413278877738	3	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.73504718170976	3		794	1349	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492710	56492710	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1403944234	NA	P-0047206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	171	405	0	ENST00000407977.2:c.229C>G	p.Pro77Ala	p.P77A	ENST00000407977		77	Cca/Gca	2/10	0.73504718170976	3	FACETS	0.909	0.839	0.982	0.454	0.419	0.491	CLONAL	1	TRUE	1	0.73504718170976	3		405	700	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644690	134644690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	175	359	0	ENST00000398015.3:c.91G>A	p.Glu31Lys	p.E31K	ENST00000398015	NM_004441.4	31	Gag/Aag	2/16	0.688698313051297	3	FACETS	0.959	0.886	1	0.479	0.443	0.517	CLONAL	1	TRUE	1	0.73504718170976	3		359	679	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961105	55961105	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	414	564	1	ENST00000263923.4:c.2835C>A	p.Phe945Leu	p.F945L	ENST00000263923	NM_002253.2	945	ttC/ttA	21/30	0.560452090681399	3	FACETS	0.949	0.91	0.987	0.949	0.91	0.987	CLONAL	2	TRUE	1	0.73504718170976	3		565	812	SUCCESS
APC	324	MSKCC	GRCh37	5	112179072	112179072	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs543396310	NA	P-0047206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	80	169	0	ENST00000257430.4:c.7781C>G	p.Ser2594Cys	p.S2594C	ENST00000257430	NM_000038.5	2594	tCt/tGt	16/16	1	2	FACETS	0.985	0.883	1	0.985	0.883	1	CLONAL	1	TRUE	1	0.73504718170976	2		169	221	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517446	157517446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761133847	NA	P-0047206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	184	323	1	ENST00000346085.5:c.4010G>A	p.Arg1337Gln	p.R1337Q	ENST00000346085	NM_020732.3	1337	cGa/cAa	16/20	0.44846627041505	2	FACETS	0.954	0.887	1	0.477	0.443	0.511	CLONAL	1	TRUE	0	0.73504718170976	2		324	525	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331946	81331946	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	62	158	0	ENST00000222390.5:c.2138C>G	p.Ala713Gly	p.A713G	ENST00000222390	NM_000601.4	713	gCa/gGa	18/18	0.73504718170976	4	FACETS	0.82	0.712	0.936	0.273	0.237	0.312	CLONAL	1	TRUE	1	0.73504718170976	4		158	357	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939259	76939259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	371	488	0	ENST00000373344.5:c.1489G>A	p.Asp497Asn	p.D497N	ENST00000373344	NM_000489.3	497	Gat/Aat	9/35	0.73504718170976	5	FACETS	1	0.995	1	0.498	0.472	0.525	CLONAL	1	TRUE	2	0.73504718170976	5		488	1421	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185026	123185026	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	55	328	0	ENST00000218089.9:c.1073A>T	p.Lys358Ile	p.K358I	ENST00000218089	NM_001042749.1	358	aAa/aTa	12/35	0.73504718170976	5	FACETS	0.347	0.295	0.403	0.116	0.098	0.135	SUBCLONAL	1	TRUE	2	0.73504718170976	5		328	908	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	201	349	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.456201377658346	2	FACETS	0.817	0.763	0.871	0.817	0.763	0.871	CLONAL	2	TRUE	0	0.473356685888472	2		349	520	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0047207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	181	992	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.473356685888472	1	FACETS	0.848	0.785	0.914	0.848	0.785	0.914	CLONAL	1	TRUE	0	0.473356685888472	1		992	688	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482368	56482368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	277	602	0	ENST00000267101.3:c.916C>T	p.Pro306Ser	p.P306S	ENST00000267101	NM_001982.3	306	Cct/Tct	8/28	0.456201377658346	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.473356685888472	2		602	562	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604655	48604655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	74	289	0	ENST00000342988.3:c.1477G>A	p.Asp493Asn	p.D493N	ENST00000342988	NM_005359.5	493	Gat/Aat	12/12	0.473356685888472	1	FACETS	0.79	0.698	0.887	0.79	0.698	0.887	SUBCLONAL	1	TRUE	0	0.473356685888472	1		289	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578538	7578538	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	736	890	0	ENST00000269305.4:c.392A>G	p.Asn131Ser	p.N131S	ENST00000269305	NM_001126112.2	131	aAc/aGc	5/11	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.935700111480896	2		890	784	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100172	157100172	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1235492881	NA	P-0047209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	10	94	0	ENST00000346085.5:c.1114del	p.Arg372GlyfsTer7	p.R372Gfs*7	ENST00000346085	NM_020732.3	370	tCc/tc	1/20	1	2	FACETS	0.107	0.072	0.151	0.107	0.072	0.151	SUBCLONAL	1	TRUE	1	0.935700111480896	2		94	199	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063628	67063628	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0047209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	271	378	0	ENST00000412916.2:c.79-2A>T		p.X27_splice	ENST00000412916		27			0.935700111480896	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.935700111480896	1		378	306	SUCCESS
AR	367	MSKCC	GRCh37	X	66943542	66943543	+	missense_variant	Missense_Mutation	DNP	GC	GC	CT	novel	NA	P-0047211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	69	177	0	ENST00000374690.3:c.2622_2623delinsCT	p.His875Tyr	p.H875Y	ENST00000374690	NM_000044.3	874	ctGCat/ctCTat	8/8	0.737122109060606	4	FACETS	1	0.957	1			1	CLONAL	3	FALSE	NA	0.737122109060606	4		177	101	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0047212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	185	1080	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.372292078347939	1	FACETS	0.394	0.364	0.426	0.394	0.364	0.426	INDETERMINATE	1	TRUE	0	0.659143421694344	1		1080	955	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0047212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	409	612	2	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.372292078347939	1	FACETS	0.898	0.859	0.938	0.898	0.859	0.938	INDETERMINATE	1	TRUE	0	0.659143421694344	1		614	926	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258744	115258744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434596	NA	P-0047212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	25	286	0	ENST00000369535.4:c.38G>A	p.Gly13Asp	p.G13D	ENST00000369535	NM_002524.4	13	gGt/gAt	2/7	1	2	FACETS	0.117	0.092	0.147	0.117	0.092	0.147	SUBCLONAL	1	TRUE	1	0.659143421694344	2		286	647	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440943	56440943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786205215	NA	P-0047212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	47	462	1	ENST00000407977.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000407977		132	Cga/Tga	4/10	0.372292078347939	1	FACETS	0.103	0.086	0.121	0.103	0.086	0.121	INDETERMINATE	1	TRUE	0	0.659143421694344	1		463	931	SUCCESS
APC	324	MSKCC	GRCh37	5	112177968	112177968	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1246580689	NA	P-0047212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	31	230	0	ENST00000257430.4:c.6677G>A	p.Arg2226Gln	p.R2226Q	ENST00000257430	NM_000038.5	2226	cGa/cAa	16/16	0.659143421694344	1	FACETS	0.245	0.199	0.297	0.245	0.199	0.297	SUBCLONAL	1	TRUE	0	0.659143421694344	1		230	257	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151850009	151850009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1221667616	NA	P-0047212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	21	233	0	ENST00000262189.6:c.12307G>A	p.Asp4103Asn	p.D4103N	ENST00000262189	NM_170606.2	4103	Gac/Aac	49/59	0.245929285676515	3	FACETS	0.207	0.159	0.264	0.069	0.053	0.088	INDETERMINATE	1	TRUE	0	0.659143421694344	3		233	409	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115450	115115450	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	136	354	0	ENST00000257566.3:c.876A>T	p.Leu292Phe	p.L292F	ENST00000257566	NM_016569.3	292	ttA/ttT	5/8	1	2	FACETS	0.577	0.525	0.631	0.577	0.525	0.631	SUBCLONAL	1	TRUE	1	0.659143421694344	2		354	715	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508629	106508629	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	40	414	0	ENST00000359195.3:c.623C>A	p.Pro208Gln	p.P208Q	ENST00000359195	NM_002649.2	208	cCg/cAg	2/11	0.245929285676515	3	FACETS	0.202	0.167	0.242	0.067	0.055	0.081	INDETERMINATE	1	TRUE	0	0.659143421694344	3		414	798	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118934	70118934	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	84	628	0	ENST00000245479.2:c.506A>C	p.His169Pro	p.H169P	ENST00000245479	NM_000346.3	169	cAc/cCc	2/3	0.372292078347939	1	FACETS	0.194	0.171	0.22	0.194	0.171	0.22	INDETERMINATE	1	TRUE	0	0.659143421694344	1		628	879	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0047213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	45	323	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.13	2		323	590	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0047213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	15	277	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.432	0.314	0.575	0.432	0.314	0.575	SUBCLONAL	1	TRUE	1	0.13	2		277	534	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0047214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	451	593	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.642974394635505	4	FACETS	1	0.977	1			1	CLONAL	4	TRUE	NA	0.65430689254048	4		593	568	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741466	17741466	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	246	724	0	ENST00000250003.3:c.137T>G	p.Leu46Arg	p.L46R	ENST00000250003	NM_002478.4	46	cTg/cGg	1/3	0.65430689254048	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.65430689254048	2		724	357	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059390	42059390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	73	312	0	ENST00000219905.7:c.9110G>A	p.Gly3037Asp	p.G3037D	ENST00000219905	NM_001164273.1	3037	gGc/gAc	24/24	0.335729339136487	4	FACETS	0.875	0.779	0.974			1	INDETERMINATE	2	TRUE	NA	0.65430689254048	4		312	211	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39239392	39239392	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	21	402	0	ENST00000402219.2:c.2265G>T	p.Gln755His	p.Q755H	ENST00000402219	NM_005633.3	755	caG/caT	14/23	0.446233955092554	4	FACETS	0.303	0.232	0.384	0.151	0.116	0.192	SUBCLONAL	1	TRUE	2	0.65430689254048	4		402	351	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281210	142281210	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	40	274	0	ENST00000350721.4:c.1034C>G	p.Ala345Gly	p.A345G	ENST00000350721	NM_001184.3	345	gCt/gGt	4/47	0.65430689254048	5	FACETS	1	0.858	1	0.342	0.286	0.403	CLONAL	1	TRUE	2	0.65430689254048	5		274	236	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479784	67479784	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs886039177	NA	P-0047215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	235	631	0	ENST00000327367.4:c.1091A>G	p.Tyr364Cys	p.Y364C	ENST00000327367	NM_005902.3	364	tAc/tGc	8/9	1	2	FACETS	0.922	0.864	0.983	0.922	0.864	0.983	CLONAL	1	TRUE	1	0.662561554272431	2		631	769	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653051	29653051	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	157	287	0	ENST00000356175.3:c.4986C>A	p.Asn1662Lys	p.N1662K	ENST00000356175	NM_000267.3	1662	aaC/aaA	36/57	0.643230911486305	1	FACETS	0.972	0.906	1	0.972	0.906	1	CLONAL	1	TRUE	0	0.662561554272431	1		287	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0047216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	152	592	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	1	2	FACETS	0.805	0.74	0.871	1	0.99	1	CLONAL	2	TRUE	1	0.354347492600821	2		592	533	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420213	49420213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267607237	NA	P-0047216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	185	683	0	ENST00000301067.7:c.15536G>A	p.Arg5179His	p.R5179H	ENST00000301067	NM_003482.3	5179	cGt/cAt	48/54	0.20726343481868	4	FACETS	0.831	0.768	0.896	0.554	0.512	0.598	INDETERMINATE	2	TRUE	1	0.354347492600821	4		683	851	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660033	12660033	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	40	380	0	ENST00000251849.4:c.188C>G	p.Pro63Arg	p.P63R	ENST00000251849	NM_002880.3	63	cCg/cGg	2/17	0.354347492600821	3	FACETS	0.648	0.539	0.769	0.324	0.269	0.385	SUBCLONAL	1	TRUE	1	0.354347492600821	3		380	410	SUCCESS
ATR	545	MSKCC	GRCh37	3	142184028	142184028	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	30	309	0	ENST00000350721.4:c.6952G>C	p.Asp2318His	p.D2318H	ENST00000350721	NM_001184.3	2318	Gat/Cat	41/47	0.354347492600821	5	FACETS	0.864	0.698	1	0.288	0.232	0.351	CLONAL	1	TRUE	2	0.354347492600821	5		309	300	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55143603	55143603	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	76	348	0	ENST00000257290.5:c.1835C>G	p.Ala612Gly	p.A612G	ENST00000257290	NM_006206.4	612	gCc/gGc	13/23	0.274410253724545	3	FACETS	1	0.974	1	0.469	0.414	0.527	CLONAL	1	TRUE	0	0.354347492600821	3		348	359	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672779	30672779	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1218	67	699	0	ENST00000376406.3:c.4181del	p.Gly1394GlufsTer49	p.G1394Efs*49	ENST00000376406	NM_014641.2	1394	gGa/ga	10/15	0.354347492600821	8	FACETS	0.607	0.525	0.696			1	SUBCLONAL	1	TRUE	NA	0.354347492600821	8		699	1285	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673271	30673271	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	62	558	0	ENST00000376406.3:c.3689G>C	p.Gly1230Ala	p.G1230A	ENST00000376406	NM_014641.2	1230	gGa/gCa	10/15	0.354347492600821	8	FACETS	0.592	0.509	0.682			1	SUBCLONAL	1	TRUE	NA	0.354347492600821	8		558	1220	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324916	31324916	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1265822237	NA	P-0047216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1955	262	1064	0	ENST00000412585.2:c.20G>T	p.Arg7Leu	p.R7L	ENST00000412585	NM_005514.6	7	cGa/cTa	1/8	0.354347492600821	8	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.354347492600821	8		1064	2217	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309006	137309006	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	78	786	1	ENST00000481739.1:c.613G>T	p.Val205Leu	p.V205L	ENST00000481739	NM_002957.4	205	Gtg/Ttg	5/10	0.354347492600821	1	FACETS	0.539	0.473	0.61	0.539	0.473	0.61	SUBCLONAL	1	TRUE	0	0.354347492600821	1		787	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0047230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	77	682	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.966	0.848	1	0.966	0.848	1	CLONAL	1	TRUE	1	0.23	2		684	693	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0047230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	39	272	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.23	2		272	291	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0047230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	30	285	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	0.615	0.495	0.751	0.615	0.495	0.751	SUBCLONAL	1	TRUE	1	0.23	2		285	424	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690810	89690813	+	frameshift_variant	Frame_Shift_Del	DEL	GAAA	GAAA	-	novel	NA	P-0047230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	28	182	0	ENST00000371953.3:c.219_222del	p.Glu73AspfsTer25	p.E73Dfs*25	ENST00000371953	NM_000314.4	73	GAAAga/ga	4/9	1	2	FACETS	0.962	0.772	1	0.962	0.772	1	CLONAL	1	TRUE	1	0.23	2		182	253	SUCCESS
AR	367	MSKCC	GRCh37	X	66766050	66766050	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs759716252	NA	P-0047230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	52	667	0	ENST00000374690.3:c.1062C>A	p.Asp354Glu	p.D354E	ENST00000374690	NM_000044.3	354	gaC/gaA	1/8	1	2	FACETS	0.456	0.386	0.532	0.456	0.386	0.532	SUBCLONAL	1	TRUE	1	0.23	2		667	992	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	38	516	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.668	0.554	0.794	0.668	0.554	0.794	SUBCLONAL	1	TRUE	1	0.362346735300461	2		516	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	79	523	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	1	2	FACETS	0.789	0.695	0.889	0.789	0.695	0.889	SUBCLONAL	1	TRUE	1	0.362346735300461	2		523	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780071	NA	P-0047232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	90	697	0	ENST00000269305.4:c.580C>T	p.Leu194Phe	p.L194F	ENST00000269305	NM_001126112.2	194	Ctt/Ttt	6/11	1	2	FACETS	0.838	0.744	0.937	0.838	0.744	0.937	CLONAL	1	TRUE	1	0.362346735300461	2		697	593	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287229	46287229	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0047232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	46	346	0	ENST00000334344.6:c.5174C>G	p.Ser1725Ter	p.S1725*	ENST00000334344	NM_152641.2	1725	tCa/tGa	19/21	1	2	FACETS	0.618	0.521	0.724	0.618	0.521	0.724	SUBCLONAL	1	TRUE	1	0.362346735300461	2		346	411	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135385	30135385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	45	322	0	ENST00000331968.5:c.433C>T	p.Arg145Cys	p.R145C	ENST00000331968	NM_002742.2	145	Cgt/Tgt	3/18	1	2	FACETS	0.603	0.507	0.708	0.603	0.507	0.708	SUBCLONAL	1	TRUE	1	0.362346735300461	2		322	412	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524687	187524687	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs928653182	NA	P-0047232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	120	756	1	ENST00000441802.2:c.10993C>T	p.Arg3665Ter	p.R3665*	ENST00000441802	NM_005245.3	3665	Cga/Tga	19/27	0.358330492087515	1	FACETS	0.851	0.771	0.936	0.851	0.771	0.936	CLONAL	1	TRUE	0	0.362346735300461	1		757	637	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748128	43748128	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	58	500	0	ENST00000382044.4:c.2678C>G	p.Ser893Cys	p.S893C	ENST00000382044	NM_001141980.1	893	tCt/tGt	12/28	1	2	FACETS	0.745	0.641	0.856	0.745	0.641	0.856	SUBCLONAL	1	TRUE	1	0.362346735300461	2		500	430	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348650	89348650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	91	839	0	ENST00000301030.4:c.4300G>A	p.Glu1434Lys	p.E1434K	ENST00000301030	NM_001256183.1	1434	Gag/Aag	9/13	1	2	FACETS	0.727	0.646	0.814	0.727	0.646	0.814	SUBCLONAL	1	TRUE	1	0.362346735300461	2		839	691	SUCCESS
AR	367	MSKCC	GRCh37	X	66765400	66765400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	42	809	1	ENST00000374690.3:c.412G>A	p.Ala138Thr	p.A138T	ENST00000374690	NM_000044.3	138	Gcc/Acc	1/8	0.273506631676002	2	FACETS	0.298	0.248	0.355	0.149	0.124	0.178	SUBCLONAL	1	TRUE	0	0.362346735300461	2		810	777	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189097	38189097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775871355	NA	P-0047232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	139	374	0	ENST00000317025.8:c.917G>A	p.Arg306Gln	p.R306Q	ENST00000317025	NM_023034.1	306	cGa/cAa	5/24	0.291468779024335	3	FACETS	0.827	0.756	0.9	0.827	0.756	0.9	CLONAL	2	TRUE	1	0.362346735300461	3		374	548	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245486	46245486	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	54	297	0	ENST00000334344.6:c.3580C>T	p.Gln1194Ter	p.Q1194*	ENST00000334344	NM_152641.2	1194	Cag/Tag	15/21	1	2	FACETS	0.852	0.731	0.983	0.852	0.731	0.983	CLONAL	1	TRUE	1	0.362346735300461	2		297	350	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347462	89347462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	103	800	0	ENST00000301030.4:c.5488G>A	p.Glu1830Lys	p.E1830K	ENST00000301030	NM_001256183.1	1830	Gaa/Aaa	9/13	1	2	FACETS	0.868	0.778	0.964	0.868	0.778	0.964	CLONAL	1	TRUE	1	0.362346735300461	2		800	655	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348125	89348125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	102	877	0	ENST00000301030.4:c.4825G>A	p.Glu1609Lys	p.E1609K	ENST00000301030	NM_001256183.1	1609	Gag/Aag	9/13	1	2	FACETS	0.874	0.783	0.971	0.874	0.783	0.971	CLONAL	1	TRUE	1	0.362346735300461	2		877	644	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348541	89348541	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	113	923	0	ENST00000301030.4:c.4409G>C	p.Arg1470Thr	p.R1470T	ENST00000301030	NM_001256183.1	1470	aGa/aCa	9/13	1	2	FACETS	0.77	0.693	0.852	0.77	0.693	0.852	SUBCLONAL	1	TRUE	1	0.362346735300461	2		923	810	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349048	89349048	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	78	875	0	ENST00000301030.4:c.3902G>C	p.Ser1301Thr	p.S1301T	ENST00000301030	NM_001256183.1	1301	aGc/aCc	9/13	1	2	FACETS	0.576	0.505	0.651	0.576	0.505	0.651	SUBCLONAL	1	TRUE	1	0.362346735300461	2		875	748	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349232	89349232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	122	925	1	ENST00000301030.4:c.3718G>A	p.Glu1240Lys	p.E1240K	ENST00000301030	NM_001256183.1	1240	Gag/Aag	9/13	1	2	FACETS	0.846	0.765	0.932	0.846	0.765	0.932	CLONAL	1	TRUE	1	0.362346735300461	2		926	796	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383714	84383714	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	83	505	0	ENST00000321945.7:c.1138G>C	p.Asp380His	p.D380H	ENST00000321945	NM_139076.2	380	Gat/Cat	9/9	1	2	FACETS	0.871	0.771	0.978	0.871	0.771	0.978	CLONAL	1	TRUE	1	0.362346735300461	2		505	526	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249486	153249487	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0047232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	82	425	0	ENST00000281708.4:c.1291_1292del	p.Asp431GlnfsTer5	p.D431Qfs*5	ENST00000281708	NM_033632.3	431	GAc/c	9/12	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.362346735300461	NA		425	488	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449389	31449389	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	23	343	0	ENST00000344624.3:c.2820A>T	p.Lys940Asn	p.K940N	ENST00000344624		940	aaA/aaT	19/33	1	2	FACETS	0.379	0.295	0.476	0.379	0.295	0.476	SUBCLONAL	1	TRUE	1	0.362346735300461	2		343	335	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680431	30680431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	61	534	0	ENST00000376406.3:c.1288G>A	p.Asp430Asn	p.D430N	ENST00000376406	NM_014641.2	430	Gat/Aat	5/15	0.29655940698063	3	FACETS	0.766	0.662	0.88	0.383	0.331	0.44	SUBCLONAL	1	TRUE	1	0.362346735300461	3		534	519	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866562	117866562	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	57	395	0	ENST00000297338.2:c.1083G>C	p.Met361Ile	p.M361I	ENST00000297338	NM_006265.2	361	atG/atC	9/14	0.216636176933399	4	FACETS	0.778	0.668	0.898	0.389	0.334	0.449	INDETERMINATE	1	TRUE	2	0.362346735300461	4		395	551	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0047233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	144	396	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.456053135447207	4	FACETS	1	0.976	1	0.766	0.706	0.828	CLONAL	2	TRUE	1	0.456053135447207	4		396	400	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0047233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	60	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.455942179845831	3	FACETS	0.808	0.699	0.926	0.404	0.349	0.463	CLONAL	1	TRUE	1	0.456053135447207	3		511	400	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542201	187542201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs189523191	NA	P-0047233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	67	399	0	ENST00000441802.2:c.5539G>A	p.Val1847Ile	p.V1847I	ENST00000441802	NM_005245.3	1847	Gtc/Atc	10/27	0.455942179845831	3	FACETS	0.902	0.787	1	0.451	0.393	0.513	CLONAL	1	TRUE	1	0.456053135447207	3		399	400	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212252718	212252718	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0047233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	18	121	0	ENST00000342788.4:c.3136-1G>C		p.X1046_splice	ENST00000342788	NM_005235.2	1046			0.456053135447207	4	FACETS	0.714	0.541	0.915	0.238	0.18	0.305	CLONAL	1	TRUE	1	0.456053135447207	4		121	161	SUCCESS
APC	324	MSKCC	GRCh37	5	112173798	112173798	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	174	254	0	ENST00000257430.4:c.2507del	p.Ser836TyrfsTer6	p.S836Yfs*6	ENST00000257430	NM_000038.5	836	tCa/ta	16/16	0.456053135447207	3	FACETS	0.985	0.926	1	0.985	0.926	1	CLONAL	3	TRUE	0	0.456053135447207	3		254	317	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531007	187531007	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	86	321	0	ENST00000441802.2:c.10016C>A	p.Thr3339Asn	p.T3339N	ENST00000441802	NM_005245.3	3339	aCc/aAc	15/27	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.573247232963688	2		321	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519985	NA	P-0047238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	125	654	0	ENST00000269305.4:c.857A>C	p.Glu286Ala	p.E286A	ENST00000269305	NM_001126112.2	286	gAa/gCa	8/11	0.19664913349025	3	FACETS	1	0.972	1	0.755	0.693	0.818	INDETERMINATE	2	TRUE	0	0.423134052819453	3		654	316	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918424	94918424	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	20	232	0	ENST00000536441.1:c.758T>G	p.Phe253Cys	p.F253C	ENST00000536441	NM_144665.3	253	tTt/tGt	5/10	0.345915483389392	2	FACETS	0.473	0.363	0.6	0.236	0.181	0.3	SUBCLONAL	1	TRUE	0	0.423134052819453	2		232	200	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524705	106524705	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	10	162	0	ENST00000359195.3:c.2866G>C	p.Glu956Gln	p.E956Q	ENST00000359195	NM_002649.2	956	Gag/Cag	9/11	0.300598979258766	4	FACETS	0.372	0.252	0.522	0.186	0.126	0.261	SUBCLONAL	1	TRUE	2	0.423134052819453	4		162	181	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020501	69020501	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1240011031	NA	P-0047238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	11	457	0	ENST00000288368.4:c.2873T>A	p.Phe958Tyr	p.F958Y	ENST00000288368	NM_024870.2	958	tTt/tAt	24/40	0.414422098319013	1	FACETS	0.259	0.179	0.358	0.259	0.179	0.358	SUBCLONAL	1	TRUE	0	0.423134052819453	1		457	158	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424399	47424399	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	21	574	0	ENST00000377045.4:c.319T>G	p.Phe107Val	p.F107V	ENST00000377045	NM_001654.4	107	Ttc/Gtc	5/16	0.242690433042339	2	FACETS	0.369	0.284	0.467	0.184	0.142	0.234	INDETERMINATE	1	TRUE	0	0.423134052819453	2		574	269	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0047239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	97	419	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.265535695338757	1	FACETS	0.782	0.704	0.864	0.782	0.704	0.864	INDETERMINATE	1	TRUE	0	0.526577547623535	1		419	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578509	7578509	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519978	NA	P-0047239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	385	760	0	ENST00000269305.4:c.421T>C	p.Cys141Arg	p.C141R	ENST00000269305	NM_001126112.2	141	Tgc/Cgc	5/11	0.526577547623535	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.526577547623535	1		760	1003	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175217	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	21	143	0	ENST00000257430.4:c.3929dup	p.Ile1311AspfsTer4	p.I1311Dfs*4	ENST00000257430	NM_000038.5	1309	gaa/gAaa	16/16	0.297048924273616	2	FACETS	0.453	0.351	0.57	0.227	0.175	0.285	INDETERMINATE	1	TRUE	0	0.526577547623535	2		143	176	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912186	114912186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	187	411	0	ENST00000543371.1:c.1256C>T	p.Ala419Val	p.A419V	ENST00000543371	NM_001198531.1	419	gCg/gTg	11/14	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.526577547623535	2		411	603	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120449	70120450	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0047239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	364	800	0	ENST00000245479.2:c.1452_1453dup	p.Gly485ValfsTer39	p.G485Vfs*39	ENST00000245479	NM_000346.3	484	tct/tcTGt	3/3	0.162305607173511	2	FACETS	1	0.992	1	0.613	0.581	0.645	INDETERMINATE	1	TRUE	0	0.526577547623535	2		800	1128	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1646426	1646426	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	222	501	0	ENST00000344749.5:c.73A>G	p.Met25Val	p.M25V	ENST00000344749	NM_001136139.2	25	Atg/Gtg	3/19	0.526577547623535	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.526577547623535	1		501	527	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221033	5221033	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765371680	NA	P-0047239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	187	501	2	ENST00000357368.4:c.3433G>A	p.Gly1145Ser	p.G1145S	ENST00000357368	NM_002850.3	1145	Ggc/Agc	20/38	0.526577547623535	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.526577547623535	1		503	463	SUCCESS
APC	324	MSKCC	GRCh37	5	112173840	112173847	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGTTTG	GAAGTTTG	-	novel	NA	P-0047239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	92	247	0	ENST00000257430.4:c.2551_2558del	p.Ser851GlufsTer58	p.S851Efs*58	ENST00000257430	NM_000038.5	850	aGAAGTTTG/a	16/16	0.297048924273616	2	FACETS	1	0.979	1	0.68	0.614	0.748	INDETERMINATE	1	TRUE	0	0.526577547623535	2		247	257	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	126	516	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.96	0.883	1	0.96	0.883	1	CLONAL	1	FALSE	1	0.852485516728917	2		516	308	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0047240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	63	220	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.728	0.64	0.82	0.728	0.64	0.82	SUBCLONAL	1	FALSE	1	0.852485516728917	2		221	203	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791757	42791757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568504941	NA	P-0047240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	138	613	2	ENST00000575354.2:c.643C>T	p.Arg215Trp	p.R215W	ENST00000575354	NM_015125.3	215	Cgg/Tgg	5/20	0.852485516728917	1	FACETS	0.522	0.481	0.564	0.522	0.481	0.564	SUBCLONAL	1	FALSE	0	0.852485516728917	1		615	356	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107105	27107105	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	15	466	0	ENST00000324856.7:c.6716T>C	p.Leu2239Pro	p.L2239P	ENST00000324856	NM_006015.4	2239	cTt/cCt	20/20	0.852485516728917	1	FACETS	0.076	0.055	0.101	0.076	0.055	0.101	SUBCLONAL	1	FALSE	0	0.852485516728917	1		466	265	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432732	78432732	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0047240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	62	266	1	ENST00000370768.2:c.343+1G>T		p.X115_splice	ENST00000370768	NM_003902.3	115			0.852485516728917	1	FACETS	0.385	0.337	0.435	0.385	0.337	0.435	SUBCLONAL	1	FALSE	0	0.852485516728917	1		267	217	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791736	42791738	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	novel	NA	P-0047240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	114	573	0	ENST00000575354.2:c.624_626del	p.Met208del	p.M208del	ENST00000575354	NM_015125.3	208	ATG/-	5/20	0.852485516728917	1	FACETS	0.451	0.411	0.493	0.451	0.411	0.493	SUBCLONAL	1	FALSE	0	0.852485516728917	1		573	340	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412332	139412332	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	47	794	0	ENST00000277541.6:c.1313G>C	p.Cys438Ser	p.C438S	ENST00000277541	NM_017617.3	438	tGc/tCc	8/34	NA	2	FACETS	0.131	0.11	0.155			1	INDETERMINATE	1	FALSE	NA	0.852485516728917	2		794	841	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0047241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	43	274	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.288109580716346	2		274	218	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207058	1207069	+	inframe_deletion	In_Frame_Del	DEL	ACCTGATGGGGG	ACCTGATGGGGG	-	rs1131690916	NA	P-0047241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	93	719	0	ENST00000326873.7:c.151_162del	p.Met51_Leu54del	p.M51_L54del	ENST00000326873	NM_000455.4	49	tACCTGATGGGGGac/tac	1/10	0.277661941350707	1	FACETS	0.634	0.563	0.711	0.634	0.563	0.711	SUBCLONAL	1	TRUE	0	0.288109580716346	1		719	871	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439886	51439886	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	37	274	0	ENST00000262662.1:c.451G>T	p.Glu151Ter	p.E151*	ENST00000262662		151	Gag/Tag	4/4	1	2	FACETS	0.606	0.499	0.725	0.606	0.499	0.725	SUBCLONAL	1	TRUE	1	0.288109580716346	2		274	424	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211546	46211559	+	frameshift_variant	Frame_Shift_Del	DEL	ATGAAGTGGACTTT	ATGAAGTGGACTTT	-	novel	NA	P-0047241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	68	176	0	ENST00000334344.6:c.512_525del	p.Asn171SerfsTer3	p.N171Sfs*3	ENST00000334344	NM_152641.2	171	aATGAAGTGGACTTT/a	5/21	0.247159763792307	2	FACETS	0.975	0.86	1	0.975	0.86	1	CLONAL	2	TRUE	0	0.288109580716346	2		176	242	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	110	516	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.949	0.856	1	0.949	0.856	1	CLONAL	1	TRUE	1	0.434983752479804	2		516	533	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0047254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	167	324	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	0.434983752479804	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	3	TRUE	1	0.434983752479804	4		324	350	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099309	4099309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	263	1096	2	ENST00000262948.5:c.809C>T	p.Pro270Leu	p.P270L	ENST00000262948	NM_030662.3	270	cCc/cTc	7/11	1	2	FACETS	0.917	0.858	0.979	0.917	0.858	0.979	CLONAL	1	TRUE	1	0.434983752479804	2		1098	1318	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211622	5211622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	127	453	0	ENST00000357368.4:c.5213C>T	p.Ala1738Val	p.A1738V	ENST00000357368	NM_002850.3	1738	gCc/gTc	33/38	1	2	FACETS	0.991	0.901	1	0.991	0.901	1	CLONAL	1	TRUE	1	0.434983752479804	2		453	589	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89869695	89869695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	128	492	0	ENST00000389301.3:c.764G>A	p.Arg255Lys	p.R255K	ENST00000389301	NM_000135.2	255	aGa/aAa	8/43	0.434983752479804	1	FACETS	0.965	0.881	1	0.965	0.881	1	CLONAL	1	TRUE	0	0.434983752479804	1		492	477	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058575	69058575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	63	498	0	ENST00000288368.4:c.4219C>T	p.Leu1407Phe	p.L1407F	ENST00000288368	NM_024870.2	1407	Ctt/Ttt	34/40	0.427396537263149	3	FACETS	0.777	0.674	0.888	0.388	0.337	0.444	SUBCLONAL	1	TRUE	1	0.434983752479804	3		498	454	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974393	93974393	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	35	285	0	ENST00000369303.4:c.1661C>T	p.Pro554Leu	p.P554L	ENST00000369303	NM_004440.3	554	cCt/cTt	8/17	1	2	FACETS	0.756	0.624	0.9	0.756	0.624	0.9	SUBCLONAL	1	TRUE	1	0.434983752479804	2		285	213	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435269	18435269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	41	262	0	ENST00000266497.5:c.254C>T	p.Ser85Phe	p.S85F	ENST00000266497		85	tCc/tTc	1/31	0.262410888109266	1	FACETS	0.911	0.771	1	0.911	0.771	1	CLONAL	1	TRUE	0	0.434983752479804	1		262	162	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287412	46287412	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0047254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	32	260	0	ENST00000334344.6:c.5272-1G>A		p.X1758_splice	ENST00000334344	NM_152641.2	1758			NA	2	FACETS	0.937	0.771	1			1	INDETERMINATE	1	TRUE	NA	0.434983752479804	2		260	157	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445335	49445335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	303	1029	1	ENST00000301067.7:c.2131C>T	p.Pro711Ser	p.P711S	ENST00000301067	NM_003482.3	711	Ccg/Tcg	10/54	NA	2	FACETS	0.918	0.863	0.975			1	INDETERMINATE	1	TRUE	NA	0.434983752479804	2		1030	1517	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117369	115117369	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1198837775	NA	P-0047254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	57	224	0	ENST00000257566.3:c.805C>T	p.Arg269Trp	p.R269W	ENST00000257566	NM_016569.3	269	Cgg/Tgg	4/8	1	2	FACETS	0.898	0.776	1	0.898	0.776	1	CLONAL	1	TRUE	1	0.434983752479804	2		224	292	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524577	103524577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	28	192	0	ENST00000355739.4:c.2708C>T	p.Pro903Leu	p.P903L	ENST00000355739	NM_000123.3	903	cCa/cTa	13/15	0.434983752479804	1	FACETS	0.763	0.619	0.921	0.763	0.619	0.921	CLONAL	1	TRUE	0	0.434983752479804	1		192	132	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483853	88483853	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0047254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	519	585	0	ENST00000360948.2:c.1716+1G>A		p.X572_splice	ENST00000360948	NM_001012338.2	572			0.434983752479804	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	1	0.434983752479804	4		585	1132	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669553	88669553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	63	332	0	ENST00000360948.2:c.1345C>T	p.Leu449Phe	p.L449F	ENST00000360948	NM_001012338.2	449	Ctc/Ttc	12/19	0.434983752479804	4	FACETS	0.767	0.664	0.879	0.256	0.221	0.293	SUBCLONAL	1	TRUE	1	0.434983752479804	4		332	542	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829776	72829776	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	163	630	0	ENST00000268489.5:c.6805G>A	p.Asp2269Asn	p.D2269N	ENST00000268489	NM_006885.3	2269	Gat/Aat	9/10	0.434983752479804	1	FACETS	0.86	0.792	0.931	0.86	0.792	0.931	CLONAL	1	TRUE	0	0.434983752479804	1		630	682	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456462	29456463	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0047254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	140	667	0	ENST00000389048.3:c.2455_2456delinsAA	p.Gly819Lys	p.G819K	ENST00000389048	NM_004304.4	819	GGa/AAa	14/29	1	2	FACETS	0.805	0.733	0.88	0.805	0.733	0.88	CLONAL	1	TRUE	1	0.434983752479804	2		667	800	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309777	30309778	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0047254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	144	551	0	ENST00000307677.4:c.244_245delinsTT	p.Pro82Phe	p.P82F	ENST00000307677	NM_138578.1	82	CCc/TTc	2/3	1	2	FACETS	0.918	0.839	1	0.918	0.839	1	CLONAL	1	TRUE	1	0.434983752479804	2		551	721	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655229	45655229	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs900588921	NA	P-0047254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	195	694	0	ENST00000407780.3:c.623C>T	p.Thr208Ile	p.T208I	ENST00000407780	NM_001283052.1	208	aCc/aTc	4/7	1	2	FACETS	0.935	0.865	1	0.935	0.865	1	CLONAL	1	TRUE	1	0.434983752479804	2		694	959	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545921	41545921	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886057560	NA	P-0047254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	216	603	0	ENST00000263253.7:c.2536C>T	p.Pro846Ser	p.P846S	ENST00000263253	NM_001429.3	846	Ccc/Tcc	14/31	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.434983752479804	2		603	910	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84406201	84406202	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0047254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	176	484	2	ENST00000321945.7:c.24_25delinsAA	p.Val9Met	p.V9M	ENST00000321945	NM_139076.2	8	gcGGtg/gcAAtg	1/9	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.434983752479804	2		486	802	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211513	46211516	+	frameshift_variant	Frame_Shift_Del	DEL	AATT	AATT	TA	novel	NA	P-0047254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	29	204	1	ENST00000334344.6:c.479_482delinsTA	p.Lys160IlefsTer12	p.K160Ifs*12	ENST00000334344	NM_152641.2	160	aAATTg/aTAg	5/21	0.262410888109266	1	FACETS	0.61	0.495	0.738	0.61	0.495	0.738	SUBCLONAL	1	TRUE	0	0.434983752479804	1		205	171	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0047255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	19	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.0971137345316411	3	FACETS	0.283	0.214	0.364	0.141	0.107	0.182	INDETERMINATE	1	TRUE	1	0.398150042870202	3		511	405	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	136	349	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	1	0.938	1			1	INDETERMINATE	2	TRUE	NA	0.398150042870202	2		349	335	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0047255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	21	280	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.463	0.357	0.585	0.463	0.357	0.585	SUBCLONAL	1	TRUE	1	0.398150042870202	2		280	228	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913286	NA	P-0047255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	27	422	0	ENST00000263967.3:c.1636C>G	p.Gln546Glu	p.Q546E	ENST00000263967	NM_006218.2	546	Cag/Gag	10/21	0.0971137345316411	3	FACETS	0.383	0.304	0.473	0.191	0.152	0.237	INDETERMINATE	1	TRUE	1	0.398150042870202	3		422	425	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717715	89717716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587782341	NA	P-0047255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	21	328	1	ENST00000371953.3:c.741dup	p.Pro248ThrfsTer5	p.P248Tfs*5	ENST00000371953	NM_000314.4	247	tta/ttAa	7/9	1	2	FACETS	0.398	0.307	0.504	0.398	0.307	0.504	SUBCLONAL	1	TRUE	1	0.398150042870202	2		329	265	SUCCESS
APC	324	MSKCC	GRCh37	5	112175789	112175789	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	61	156	0	ENST00000257430.4:c.4501del	p.Ser1501LeufsTer6	p.S1501Lfs*6	ENST00000257430	NM_000038.5	1500	Ttt/tt	16/16	0.0141555025531528	3	FACETS	0.998	0.878	1	0.998	0.878	1	INDETERMINATE	2	TRUE	1	0.398150042870202	3		156	184	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717743	89717744	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	22	283	0	ENST00000371953.3:c.770dup	p.Phe258LeufsTer40	p.F258Lfs*40	ENST00000371953	NM_000314.4	256	-/T	7/9	1	2	FACETS	0.493	0.384	0.62	0.493	0.384	0.62	SUBCLONAL	1	TRUE	1	0.398150042870202	2		283	224	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632753	23632753	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	14	341	0	ENST00000261584.4:c.3043A>T	p.Thr1015Ser	p.T1015S	ENST00000261584	NM_024675.3	1015	Act/Tct	10/13	1	2	FACETS	0.251	0.181	0.336	0.251	0.181	0.336	SUBCLONAL	1	TRUE	1	0.398150042870202	2		341	280	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371774	45371774	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	12	270	0	ENST00000262160.6:c.1217A>G	p.Tyr406Cys	p.Y406C	ENST00000262160	NM_005901.5	406	tAt/tGt	10/11	0.398150042870202	1	FACETS	0.326	0.23	0.443	0.326	0.23	0.443	SUBCLONAL	1	TRUE	0	0.398150042870202	1		270	148	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395691	45395691	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	15	251	0	ENST00000262160.6:c.443del	p.Asn148ThrfsTer15	p.N148Tfs*15	ENST00000262160	NM_005901.5	148	aAc/ac	4/11	0.398150042870202	1	FACETS	0.29	0.212	0.383	0.29	0.212	0.383	SUBCLONAL	1	TRUE	0	0.398150042870202	1		251	208	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210421	2210421	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	114	826	0	ENST00000398665.3:c.1028G>T	p.Arg343Leu	p.R343L	ENST00000398665	NM_032482.2	343	cGc/cTc	13/28	0.398150042870202	1	FACETS	0.739	0.666	0.815	0.739	0.666	0.815	SUBCLONAL	1	TRUE	0	0.398150042870202	1		826	621	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254554	10254554	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	59	494	0	ENST00000340748.4:c.2956G>C	p.Asp986His	p.D986H	ENST00000340748		986	Gat/Cat	28/40	0.398150042870202	1	FACETS	0.588	0.507	0.674	0.588	0.507	0.674	SUBCLONAL	1	TRUE	0	0.398150042870202	1		494	404	SUCCESS
APC	324	MSKCC	GRCh37	5	112137045	112137045	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	109	229	0	ENST00000257430.4:c.799G>T	p.Gly267Ter	p.G267*	ENST00000257430	NM_000038.5	267	Gga/Tga	8/16	0.0141555025531528	3	FACETS	1	0.937	1	1	0.937	1	INDETERMINATE	2	TRUE	1	0.398150042870202	3		229	316	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250590	26250590	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	139	540	0	ENST00000446824.2:c.244G>T	p.Asp82Tyr	p.D82Y	ENST00000446824	NM_021018.2	82	Gac/Tac	1/1	0.398150042870202	6	FACETS	1	0.95	1			1	CLONAL	2	TRUE	NA	0.398150042870202	6		540	594	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738850	145738850	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047255-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	89	919	0	ENST00000428558.2:c.2215A>G	p.Thr739Ala	p.T739A	ENST00000428558	NM_004260.3	739	Acc/Gcc	14/22	1	2	FACETS	0.496	0.439	0.558	0.496	0.439	0.558	SUBCLONAL	1	TRUE	1	0.398150042870202	2		919	901	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	126	652	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.976	0.884	1	0.976	0.884	1	CLONAL	1	TRUE	1	0.32	2		653	807	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	113	436	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.32	2		436	597	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	83	466	0	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	NA	2	FACETS	0.894	0.79	1			1	INDETERMINATE	1	TRUE	NA	0.32	2		466	580	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066739	5066739	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1340580425	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	34	260	0	ENST00000381652.3:c.1276C>T	p.Arg426Ter	p.R426*	ENST00000381652	NM_004972.3	426	Cga/Tga	10/25	1	2	FACETS	0.672	0.551	0.808	0.672	0.551	0.808	SUBCLONAL	1	TRUE	1	0.32	2		260	316	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11168277	11168277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	101	503	0	ENST00000361445.4:c.7595C>T	p.Ala2532Val	p.A2532V	ENST00000361445	NM_004958.3	2532	gCg/gTg	57/58	1	2	FACETS	0.974	0.872	1	0.974	0.872	1	CLONAL	1	TRUE	1	0.32	2		503	648	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264627	11264627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	86	569	0	ENST00000361445.4:c.3935C>T	p.Pro1312Leu	p.P1312L	ENST00000361445	NM_004958.3	1312	cCg/cTg	26/58	1	2	FACETS	0.893	0.791	1	0.893	0.791	1	CLONAL	1	TRUE	1	0.32	2		569	602	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316111	11316111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	79	567	0	ENST00000361445.4:c.643G>A	p.Ala215Thr	p.A215T	ENST00000361445	NM_004958.3	215	Gcc/Acc	5/58	1	2	FACETS	0.721	0.634	0.814	0.721	0.634	0.814	SUBCLONAL	1	TRUE	1	0.32	2		567	685	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245539	16245539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1471081719	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	29	274	0	ENST00000375759.3:c.1514G>A	p.Arg505His	p.R505H	ENST00000375759	NM_015001.2	505	cGc/cAc	7/15	1	2	FACETS	0.497	0.399	0.608	0.497	0.399	0.608	SUBCLONAL	1	TRUE	1	0.32	2		274	365	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255346	16255346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151043425	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	74	409	0	ENST00000375759.3:c.2611C>T	p.Arg871Cys	p.R871C	ENST00000375759	NM_015001.2	871	Cgc/Tgc	11/15	1	2	FACETS	0.898	0.788	1	0.898	0.788	1	CLONAL	1	TRUE	1	0.32	2		409	515	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255862	16255862	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	60	295	0	ENST00000375759.3:c.3127G>T	p.Glu1043Ter	p.E1043*	ENST00000375759	NM_015001.2	1043	Gaa/Taa	11/15	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.32	2		295	367	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257841	16257842	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	74	468	0	ENST00000375759.3:c.5111dup	p.Gly1705ArgfsTer6	p.G1705Rfs*6	ENST00000375759	NM_015001.2	1702	-/C	11/15	1	2	FACETS	0.787	0.689	0.891	0.787	0.689	0.891	SUBCLONAL	1	TRUE	1	0.32	2		468	588	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258070	16258070	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140024761	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	82	377	3	ENST00000375759.3:c.5335G>A	p.Ala1779Thr	p.A1779T	ENST00000375759	NM_015001.2	1779	Gcc/Acc	11/15	1	2	FACETS	0.978	0.865	1	0.978	0.865	1	CLONAL	1	TRUE	1	0.32	2		380	524	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258557	16258557	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	76	576	0	ENST00000375759.3:c.5822C>T	p.Ala1941Val	p.A1941V	ENST00000375759	NM_015001.2	1941	gCt/gTt	11/15	1	2	FACETS	0.859	0.755	0.971	0.859	0.755	0.971	CLONAL	1	TRUE	1	0.32	2		576	553	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057711	27057711	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	109	632	1	ENST00000324856.7:c.1419G>T	p.Gln473His	p.Q473H	ENST00000324856	NM_006015.4	473	caG/caT	3/20	1	2	FACETS	0.852	0.764	0.944	0.852	0.764	0.944	CLONAL	1	TRUE	1	0.32	2		633	800	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099958	27099959	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	56	728	0	ENST00000324856.7:c.3839_3840dup	p.Tyr1281ProfsTer9	p.Y1281Pfs*9	ENST00000324856	NM_006015.4	1279	-/CC	15/20	1	2	FACETS	0.417	0.356	0.484	0.417	0.356	0.484	SUBCLONAL	1	TRUE	1	0.32	2		728	839	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941085	36941085	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	152	753	0	ENST00000361632.4:c.254C>A	p.Ser85Tyr	p.S85Y	ENST00000361632		85	tCt/tAt	3/16	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.32	2		753	879	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941110	36941110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	140	765	1	ENST00000361632.4:c.229C>T	p.Arg77Cys	p.R77C	ENST00000361632		77	Cgt/Tgt	3/16	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.32	2		766	859	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45800107	45800107	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	108	589	0	ENST00000450313.1:c.113A>G	p.Lys38Arg	p.K38R	ENST00000450313	NM_012222.2	38	aAg/aGg	2/16	1	2	FACETS	0.927	0.833	1	0.927	0.833	1	CLONAL	1	TRUE	1	0.32	2		589	728	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509404	46509404	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs746874311	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	36	561	0	ENST00000262741.5:c.1327T>C	p.Ser443Pro	p.S443P	ENST00000262741	NM_003629.3	443	Tcc/Ccc	10/10	1	2	FACETS	0.319	0.261	0.384	0.319	0.261	0.384	SUBCLONAL	1	TRUE	1	0.32	2		561	705	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46546362	46546362	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	61	327	0	ENST00000262741.5:c.167G>T	p.Ser56Ile	p.S56I	ENST00000262741	NM_003629.3	56	aGt/aTt	2/10	1	2	FACETS	0.97	0.84	1	0.97	0.84	1	CLONAL	1	TRUE	1	0.32	2		327	393	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65312368	65312368	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149968614	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	72	551	0	ENST00000342505.4:c.1951G>A	p.Val651Met	p.V651M	ENST00000342505	NM_002227.2	651	Gtg/Atg	14/25	1	2	FACETS	0.74	0.647	0.841	0.74	0.647	0.841	SUBCLONAL	1	TRUE	1	0.32	2		551	608	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468333	120468333	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	77	725	0	ENST00000256646.2:c.4106C>A	p.Pro1369His	p.P1369H	ENST00000256646	NM_024408.3	1369	cCc/cAc	25/34	0.204171348728106	1	FACETS	0.547	0.48	0.62	0.547	0.48	0.62	SUBCLONAL	1	TRUE	0	0.32	1		725	739	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491093	120491093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	42	415	0	ENST00000256646.2:c.2696G>A	p.Cys899Tyr	p.C899Y	ENST00000256646	NM_024408.3	899	tGt/tAt	17/34	0.204171348728106	1	FACETS	0.445	0.372	0.527	0.445	0.372	0.527	SUBCLONAL	1	TRUE	0	0.32	1		415	495	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874259	155874259	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	90	459	0	ENST00000368323.3:c.272G>T	p.Arg91Met	p.R91M	ENST00000368323	NM_006912.5	91	aGg/aTg	5/6	1	2	FACETS	0.942	0.837	1	0.942	0.837	1	CLONAL	1	TRUE	1	0.32	2		459	597	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161298248	161298248	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	73	336	0	ENST00000367975.2:c.140G>A	p.Gly47Asp	p.G47D	ENST00000367975	NM_003001.3	47	gGt/gAt	3/6	1	2	FACETS	0.967	0.848	1	0.967	0.848	1	CLONAL	1	TRUE	1	0.32	2		336	472	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111132	193111132	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	47	263	0	ENST00000367435.3:c.665G>A	p.Arg222Gln	p.R222Q	ENST00000367435	NM_024529.4	222	cGa/cAa	7/17	1	2	FACETS	0.83	0.703	0.969	0.83	0.703	0.969	CLONAL	1	TRUE	1	0.32	2		263	354	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648329	206648329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55721947	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	58	647	0	ENST00000367120.3:c.350G>A	p.Arg117His	p.R117H	ENST00000367120	NM_014002.3	117	cGc/cAc	5/22	1	2	FACETS	0.413	0.354	0.478	0.413	0.354	0.478	SUBCLONAL	1	TRUE	1	0.32	2		647	878	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666660	206666660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782760912	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	63	656	1	ENST00000367120.3:c.1994C>T	p.Pro665Leu	p.P665L	ENST00000367120	NM_014002.3	665	cCg/cTg	20/22	1	2	FACETS	0.453	0.391	0.521	0.453	0.391	0.521	SUBCLONAL	1	TRUE	1	0.32	2		657	869	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226566895	226566895	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	53	538	0	ENST00000366794.5:c.1693G>T	p.Gly565Ter	p.G565*	ENST00000366794	NM_001618.3	565	Gga/Tga	12/23	1	2	FACETS	0.476	0.405	0.554	0.476	0.405	0.554	SUBCLONAL	1	TRUE	1	0.32	2		538	696	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226579931	226579931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765535441	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	118	541	0	ENST00000366794.5:c.371C>T	p.Thr124Met	p.T124M	ENST00000366794	NM_001618.3	124	aCg/aTg	3/23	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.32	2		541	736	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736245	243736245	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	70	299	0	ENST00000263826.5:c.802G>A	p.Val268Met	p.V268M	ENST00000263826	NM_005465.4	268	Gtg/Atg	8/13	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.32	2		299	392	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405557	70405557	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	75	400	0	ENST00000373644.4:c.3071G>T	p.Gly1024Val	p.G1024V	ENST00000373644	NM_030625.2	1024	gGg/gTg	4/12	1	2	FACETS	0.86	0.755	0.973	0.86	0.755	0.973	CLONAL	1	TRUE	1	0.32	2		400	545	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446390	70446390	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	55	377	0	ENST00000373644.4:c.5330C>A	p.Pro1777His	p.P1777H	ENST00000373644	NM_030625.2	1777	cCt/cAt	11/12	1	2	FACETS	0.694	0.595	0.803	0.694	0.595	0.803	SUBCLONAL	1	TRUE	1	0.32	2		377	495	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450655	70450656	+	missense_variant	Missense_Mutation	DNP	CG	CG	TA	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	56	374	2	ENST00000373644.4:c.5495_5496delinsTA	p.Ser1832Leu	p.S1832L	ENST00000373644	NM_030625.2	1832	tCG/tTA	12/12	1	2	FACETS	0.726	0.623	0.839	0.726	0.623	0.839	SUBCLONAL	1	TRUE	1	0.32	2		376	482	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911590	114911590	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	54	406	0	ENST00000543371.1:c.1108G>A	p.Ala370Thr	p.A370T	ENST00000543371	NM_001198531.1	370	Gct/Act	10/14	1	2	FACETS	0.72	0.615	0.833	0.72	0.615	0.833	SUBCLONAL	1	TRUE	1	0.32	2		406	469	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279521	123279521	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	102	576	0	ENST00000358487.5:c.911A>G	p.Asp304Gly	p.D304G	ENST00000358487	NM_000141.4	304	gAc/gGc	7/18	1	2	FACETS	0.931	0.833	1	0.931	0.833	1	CLONAL	1	TRUE	1	0.32	2		576	685	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205265	61205265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532255760	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	93	474	0	ENST00000301761.2:c.205C>T	p.Arg69Cys	p.R69C	ENST00000301761	NM_017841.2	69	Cgc/Tgc	2/4	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.32	2		474	540	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136051	64136051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	49	857	2	ENST00000334205.4:c.1312G>A	p.Ala438Thr	p.A438T	ENST00000334205	NM_003942.2	438	Gca/Aca	11/17	1	2	FACETS	0.325	0.274	0.381	0.325	0.274	0.381	SUBCLONAL	1	TRUE	1	0.32	2		859	943	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462870	69462870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200179137	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	119	766	0	ENST00000227507.2:c.683G>A	p.Arg228His	p.R228H	ENST00000227507	NM_053056.2	228	cGc/cAc	4/5	1	2	FACETS	0.895	0.808	0.987	0.895	0.808	0.987	CLONAL	1	TRUE	1	0.32	2		766	831	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940249	71940249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17847214	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	56	754	1	ENST00000298229.2:c.634G>A	p.Ala212Thr	p.A212T	ENST00000298229	NM_001567.3	212	Gct/Act	5/28	1	2	FACETS	0.417	0.356	0.483	0.417	0.356	0.483	SUBCLONAL	1	TRUE	1	0.32	2		755	840	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942616	71942616	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	118	551	0	ENST00000298229.2:c.1572T>G	p.His524Gln	p.H524Q	ENST00000298229	NM_001567.3	524	caT/caG	13/28	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.32	2		551	715	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949114	71949114	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	139	857	0	ENST00000298229.2:c.3581G>T	p.Ser1194Ile	p.S1194I	ENST00000298229	NM_001567.3	1194	aGc/aTc	27/28	1	2	FACETS	0.948	0.863	1	0.948	0.863	1	CLONAL	1	TRUE	1	0.32	2		857	916	SUCCESS
EED	8726	MSKCC	GRCh37	11	85975286	85975286	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	37	242	0	ENST00000263360.6:c.707G>T	p.Arg236Ile	p.R236I	ENST00000263360	NM_003797.3	236	aGa/aTa	7/12	1	2	FACETS	0.838	0.694	0.997	0.838	0.694	0.997	CLONAL	1	TRUE	1	0.32	2		242	276	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180463	94180463	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	91	529	0	ENST00000323929.3:c.1705G>T	p.Gly569Ter	p.G569*	ENST00000323929	NM_005591.3	569	Gga/Tga	15/20	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.32	2		529	556	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163375	108163375	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201594549	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	55	360	0	ENST00000278616.4:c.4466G>A	p.Arg1489His	p.R1489H	ENST00000278616	NM_000051.3	1489	cGt/cAt	30/63	1	2	FACETS	0.749	0.642	0.866	0.749	0.642	0.866	SUBCLONAL	1	TRUE	1	0.32	2		360	459	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196878	108196878	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501668	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	50	269	0	ENST00000278616.4:c.6901G>A	p.Ala2301Thr	p.A2301T	ENST00000278616	NM_000051.3	2301	Gca/Aca	47/63	1	2	FACETS	0.833	0.709	0.969	0.833	0.709	0.969	CLONAL	1	TRUE	1	0.32	2		269	375	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202276	108202276	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	42	221	0	ENST00000278616.4:c.7621C>A	p.Leu2541Ile	p.L2541I	ENST00000278616	NM_000051.3	2541	Ctc/Atc	51/63	1	2	FACETS	0.795	0.667	0.937	0.795	0.667	0.937	CLONAL	1	TRUE	1	0.32	2		221	330	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111965564	111965564	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	32	191	0	ENST00000375549.3:c.350G>A	p.Gly117Glu	p.G117E	ENST00000375549	NM_003002.3	117	gGg/gAg	4/4	1	2	FACETS	0.922	0.754	1	0.922	0.754	1	CLONAL	1	TRUE	1	0.32	2		191	217	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363941	118363941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	66	263	0	ENST00000534358.1:c.5174C>T	p.Ser1725Phe	p.S1725F	ENST00000534358	NM_005933.3	1725	tCt/tTt	16/36	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.32	2		263	358	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375803	118375803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	69	394	1	ENST00000534358.1:c.9196G>A	p.Ala3066Thr	p.A3066T	ENST00000534358	NM_005933.3	3066	Gct/Act	27/36	1	2	FACETS	0.933	0.815	1	0.933	0.815	1	CLONAL	1	TRUE	1	0.32	2		395	462	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392061	118392061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	41	361	0	ENST00000534358.1:c.11572G>A	p.Val3858Met	p.V3858M	ENST00000534358	NM_005933.3	3858	Gtg/Atg	35/36	1	2	FACETS	0.48	0.399	0.57	0.48	0.399	0.57	SUBCLONAL	1	TRUE	1	0.32	2		361	534	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385377	4385377	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	25	270	0	ENST00000261254.3:c.402G>T	p.Gln134His	p.Q134H	ENST00000261254	NM_001759.3	134	caG/caT	2/5	1	2	FACETS	0.539	0.425	0.669	0.539	0.425	0.669	SUBCLONAL	1	TRUE	1	0.32	2		270	290	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18576933	18576933	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs994054948	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	66	426	0	ENST00000266497.5:c.2341C>T	p.Arg781Cys	p.R781C	ENST00000266497		781	Cgc/Tgc	16/31	1	2	FACETS	0.814	0.707	0.928	0.814	0.707	0.928	CLONAL	1	TRUE	1	0.32	2		426	507	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21623977	21623977	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	44	154	0	ENST00000421138.2:c.1723A>G	p.Lys575Glu	p.K575E	ENST00000421138		575	Aaa/Gaa	15/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.32	2		154	212	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944947	31944947	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868835690	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	95	402	1	ENST00000340398.3:c.154C>T	p.Arg52Cys	p.R52C	ENST00000340398	NM_001013699.2	52	Cgt/Tgt	1/1	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.32	2		403	539	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230720	46230720	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	51	285	0	ENST00000334344.6:c.972del	p.Phe324LeufsTer4	p.F324Lfs*4	ENST00000334344	NM_152641.2	323	caT/ca	8/21	1	2	FACETS	0.883	0.753	1	0.883	0.753	1	CLONAL	1	TRUE	1	0.32	2		285	361	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244872	46244872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766470086	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	103	467	1	ENST00000334344.6:c.2966C>T	p.Ser989Leu	p.S989L	ENST00000334344	NM_152641.2	989	tCg/tTg	15/21	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.32	2		468	632	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416133	49416133	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1422752351	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	75	361	0	ENST00000301067.7:c.16342C>T	p.Arg5448Ter	p.R5448*	ENST00000301067	NM_003482.3	5448	Cga/Tga	52/54	1	2	FACETS	0.991	0.871	1	0.991	0.871	1	CLONAL	1	TRUE	1	0.32	2		361	473	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416600	49416600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	91	557	0	ENST00000301067.7:c.16111G>A	p.Glu5371Lys	p.E5371K	ENST00000301067	NM_003482.3	5371	Gag/Aag	51/54	1	2	FACETS	0.964	0.857	1	0.964	0.857	1	CLONAL	1	TRUE	1	0.32	2		557	590	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420147	49420147	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	110	673	0	ENST00000301067.7:c.15602G>T	p.Ser5201Ile	p.S5201I	ENST00000301067	NM_003482.3	5201	aGt/aTt	48/54	1	2	FACETS	0.989	0.89	1	0.989	0.89	1	CLONAL	1	TRUE	1	0.32	2		673	695	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445244	49445244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778453	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	155	969	2	ENST00000301067.7:c.2222C>T	p.Pro741Leu	p.P741L	ENST00000301067	NM_003482.3	741	cCg/cTg	10/54	1	2	FACETS	0.874	0.799	0.953	0.874	0.799	0.953	CLONAL	1	TRUE	1	0.32	2		971	1108	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446824	49446824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	105	581	1	ENST00000301067.7:c.986G>A	p.Gly329Asp	p.G329D	ENST00000301067	NM_003482.3	329	gGc/gAc	8/54	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.32	2		582	635	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447917	49447917	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	89	517	0	ENST00000301067.7:c.517T>C	p.Ser173Pro	p.S173P	ENST00000301067	NM_003482.3	173	Tcc/Ccc	5/54	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.32	2		517	554	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486604	56486604	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	35	484	1	ENST00000267101.3:c.1183G>A	p.Gly395Ser	p.G395S	ENST00000267101	NM_001982.3	395	Ggt/Agt	10/28	1	2	FACETS	0.377	0.308	0.455	0.377	0.308	0.455	SUBCLONAL	1	TRUE	1	0.32	2		485	580	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495604	56495604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142809206	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	89	520	1	ENST00000267101.3:c.3794G>A	p.Arg1265Gln	p.R1265Q	ENST00000267101	NM_001982.3	1265	cGg/cAg	28/28	1	2	FACETS	0.943	0.837	1	0.943	0.837	1	CLONAL	1	TRUE	1	0.32	2		521	590	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864391	57864391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753413155	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	114	796	1	ENST00000228682.2:c.1868G>A	p.Arg623Gln	p.R623Q	ENST00000228682	NM_005269.2	623	cGa/cAa	12/12	1	2	FACETS	0.768	0.69	0.85	0.768	0.69	0.85	SUBCLONAL	1	TRUE	1	0.32	2		797	928	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118902	115118903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	44	272	0	ENST00000257566.3:c.438dup	p.Ala147SerfsTer13	p.A147Sfs*13	ENST00000257566	NM_016569.3	146	-/A	2/8	NA	2	FACETS	0.816	0.687	0.958			1	INDETERMINATE	1	TRUE	NA	0.32	2		272	337	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123875183	123875183	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751091053	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	66	405	0	ENST00000330479.4:c.139G>A	p.Val47Ile	p.V47I	ENST00000330479	NM_020382.3	47	Gta/Ata	3/9	NA	2	FACETS	0.95	0.828	1			1	INDETERMINATE	1	TRUE	NA	0.32	2		405	434	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209011	133209011	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	86	587	0	ENST00000320574.5:c.6220G>A	p.Val2074Ile	p.V2074I	ENST00000320574	NM_006231.2	2074	Gtc/Atc	45/49	NA	2	FACETS	0.866	0.766	0.971			1	INDETERMINATE	1	TRUE	NA	0.32	2		587	621	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214718	133214718	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs557167678	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	73	441	2	ENST00000320574.5:c.5560G>A	p.Ala1854Thr	p.A1854T	ENST00000320574	NM_006231.2	1854	Gct/Act	41/49	NA	2	FACETS	0.854	0.748	0.968			1	INDETERMINATE	1	TRUE	NA	0.32	2		443	534	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219823	133219823	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	95	582	0	ENST00000320574.5:c.4538T>C	p.Phe1513Ser	p.F1513S	ENST00000320574	NM_006231.2	1513	tTt/tCt	35/49	NA	2	FACETS	0.978	0.872	1			1	INDETERMINATE	1	TRUE	NA	0.32	2		582	607	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233945	133233945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	61	605	1	ENST00000320574.5:c.3449C>T	p.Ala1150Val	p.A1150V	ENST00000320574	NM_006231.2	1150	gCc/gTc	28/49	NA	2	FACETS	0.508	0.437	0.585			1	INDETERMINATE	1	TRUE	NA	0.32	2		606	751	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235897	133235897	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	115	620	0	ENST00000320574.5:c.3259T>A	p.Ser1087Thr	p.S1087T	ENST00000320574	NM_006231.2	1087	Tcc/Acc	26/49	NA	2	FACETS	0.956	0.861	1			1	INDETERMINATE	1	TRUE	NA	0.32	2		620	752	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975447	26975447	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	69	326	0	ENST00000381527.3:c.1073T>G	p.Phe358Cys	p.F358C	ENST00000381527	NM_001260.1	358	tTt/tGt	11/13	1	2	FACETS	0.987	0.863	1	0.987	0.863	1	CLONAL	1	TRUE	1	0.32	2		326	437	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877476	28877476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773736576	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	54	424	0	ENST00000282397.4:c.3845C>T	p.Ser1282Leu	p.S1282L	ENST00000282397	NM_002019.4	1282	tCg/tTg	30/30	1	2	FACETS	0.727	0.622	0.842	0.727	0.622	0.842	SUBCLONAL	1	TRUE	1	0.32	2		424	464	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28886229	28886229	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	69	362	0	ENST00000282397.4:c.3393G>T	p.Gln1131His	p.Q1131H	ENST00000282397	NM_002019.4	1131	caG/caT	26/30	1	2	FACETS	0.923	0.807	1	0.923	0.807	1	CLONAL	1	TRUE	1	0.32	2		362	467	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913036	32913036	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	61	397	0	ENST00000380152.3:c.4544A>C	p.Lys1515Thr	p.K1515T	ENST00000380152		1515	aAg/aCg	11/27	1	2	FACETS	0.7	0.604	0.804	0.7	0.604	0.804	SUBCLONAL	1	TRUE	1	0.32	2		397	545	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133907	41133907	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	77	453	0	ENST00000379561.5:c.1721C>A	p.Ala574Asp	p.A574D	ENST00000379561	NM_002015.3	574	gCc/gAc	2/3	1	2	FACETS	0.963	0.847	1	0.963	0.847	1	CLONAL	1	TRUE	1	0.32	2		453	500	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134988	41134988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	50	194	0	ENST00000379561.5:c.640C>T	p.Arg214Cys	p.R214C	ENST00000379561	NM_002015.3	214	Cgt/Tgt	2/3	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.32	2		194	258	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916834	48916834	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	43	268	0	ENST00000267163.4:c.368del	p.Asn123ThrfsTer2	p.N123Tfs*2	ENST00000267163	NM_000321.2	122	Aaa/aa	3/27	1	2	FACETS	0.774	0.65	0.911	0.774	0.65	0.911	CLONAL	1	TRUE	1	0.32	2		268	347	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937070	48937070	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	40	174	0	ENST00000267163.4:c.838G>T	p.Glu280Ter	p.E280*	ENST00000267163	NM_000321.2	280	Gaa/Taa	8/27	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.32	2		174	239	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335624	73335624	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	44	189	0	ENST00000377767.4:c.2547A>C	p.Glu849Asp	p.E849D	ENST00000377767	NM_014953.3	849	gaA/gaC	19/21	1	2	FACETS	0.982	0.829	1	0.982	0.829	1	CLONAL	1	TRUE	1	0.32	2		189	280	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103508437	103508437	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	24	142	0	ENST00000355739.4:c.503G>T	p.Arg168Ile	p.R168I	ENST00000355739	NM_000123.3	168	aGa/aTa	5/15	1	2	FACETS	0.746	0.588	0.926	0.746	0.588	0.926	CLONAL	1	TRUE	1	0.32	2		142	201	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514788	103514788	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs746036033	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	46	334	0	ENST00000355739.4:c.1289A>T	p.Glu430Val	p.E430V	ENST00000355739	NM_000123.3	430	gAa/gTa	8/15	1	2	FACETS	0.853	0.721	0.997	0.853	0.721	0.997	CLONAL	1	TRUE	1	0.32	2		334	337	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107713	30107713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1160777726	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	63	393	1	ENST00000331968.5:c.967G>A	p.Glu323Lys	p.E323K	ENST00000331968	NM_002742.2	323	Gaa/Aaa	6/18	1	2	FACETS	0.674	0.583	0.773	0.674	0.583	0.773	SUBCLONAL	1	TRUE	1	0.32	2		394	584	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061352	38061352	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	114	1023	1	ENST00000250448.2:c.637C>T	p.Arg213Cys	p.R213C	ENST00000250448	NM_004496.3	213	Cgc/Tgc	2/2	1	2	FACETS	0.776	0.698	0.859	0.776	0.698	0.859	SUBCLONAL	1	TRUE	1	0.32	2		1024	918	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061877	38061877	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	83	821	0	ENST00000250448.2:c.112C>A	p.Leu38Met	p.L38M	ENST00000250448	NM_004496.3	38	Ctg/Atg	2/2	1	2	FACETS	0.558	0.492	0.63	0.558	0.492	0.63	SUBCLONAL	1	TRUE	1	0.32	2		821	929	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81528536	81528536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1348276163	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	48	226	0	ENST00000298171.2:c.215T>C	p.Phe72Ser	p.F72S	ENST00000298171	NM_000369.2	72	tTt/tCt	2/10	1	2	FACETS	0.971	0.825	1	0.971	0.825	1	CLONAL	1	TRUE	1	0.32	2		226	309	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105240286	105240286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369698909	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	156	824	0	ENST00000349310.3:c.665G>A	p.Arg222His	p.R222H	ENST00000349310	NM_001014432.1	222	cGc/cAc	9/15	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.32	2		824	920	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40681731	40681731	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	54	263	0	ENST00000249776.8:c.510A>C	p.Lys170Asn	p.K170N	ENST00000249776	NM_033286.3	170	aaA/aaC	5/9	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.32	2		263	295	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003386	42003386	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	81	436	0	ENST00000219905.7:c.2923C>T	p.Gln975Ter	p.Q975*	ENST00000219905	NM_001164273.1	975	Cag/Tag	8/24	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.32	2		436	501	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042425	42042425	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	97	375	0	ENST00000219905.7:c.6620C>T	p.Thr2207Ile	p.T2207I	ENST00000219905	NM_001164273.1	2207	aCa/aTa	17/24	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.32	2		375	515	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701197	43701197	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	36	484	0	ENST00000382044.4:c.5498A>G	p.His1833Arg	p.H1833R	ENST00000382044	NM_001141980.1	1833	cAt/cGt	26/28	1	2	FACETS	0.363	0.297	0.437	0.363	0.297	0.437	SUBCLONAL	1	TRUE	1	0.32	2		484	620	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708453	43708453	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	53	537	0	ENST00000382044.4:c.4843C>T	p.Pro1615Ser	p.P1615S	ENST00000382044	NM_001141980.1	1615	Cct/Tct	22/28	1	2	FACETS	0.526	0.448	0.611	0.526	0.448	0.611	SUBCLONAL	1	TRUE	1	0.32	2		537	630	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43771698	43771698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767165113	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	114	450	0	ENST00000382044.4:c.685G>A	p.Glu229Lys	p.E229K	ENST00000382044	NM_001141980.1	229	Gaa/Aaa	7/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.32	2		450	599	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729187	66729187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	91	528	1	ENST00000307102.5:c.395C>T	p.Ala132Val	p.A132V	ENST00000307102	NM_002755.3	132	gCg/gTg	3/11	1	2	FACETS	0.868	0.772	0.971	0.868	0.772	0.971	CLONAL	1	TRUE	1	0.32	2		529	655	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631593	90631593	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs576407061	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	88	487	1	ENST00000330062.3:c.676G>A	p.Glu226Lys	p.E226K	ENST00000330062	NM_002168.2	226	Gag/Aag	5/11	1	2	FACETS	0.902	0.8	1	0.902	0.8	1	CLONAL	1	TRUE	1	0.32	2		488	610	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121796	2121796	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	168	1022	2	ENST00000219476.3:c.1958G>T	p.Arg653Ile	p.R653I	ENST00000219476	NM_000548.3	653	aGa/aTa	19/42	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.32	2		1024	1040	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121888	2121888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779275341	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	67	1088	1	ENST00000219476.3:c.2050G>A	p.Val684Met	p.V684M	ENST00000219476	NM_000548.3	684	Gtg/Atg	19/42	1	2	FACETS	0.387	0.335	0.444	0.387	0.335	0.444	SUBCLONAL	1	TRUE	1	0.32	2		1089	1082	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632381	3632381	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771230395	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	186	1023	1	ENST00000294008.3:c.5467C>T	p.Arg1823Trp	p.R1823W	ENST00000294008	NM_032444.2	1823	Cgg/Tgg	15/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.32	2		1024	1022	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632566	3632566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1205902549	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	204	1026	0	ENST00000294008.3:c.5282G>A	p.Arg1761His	p.R1761H	ENST00000294008	NM_032444.2	1761	cGc/cAc	15/15	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.32	2		1026	1139	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640689	3640689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750906921	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	161	836	0	ENST00000294008.3:c.2950G>A	p.Glu984Lys	p.E984K	ENST00000294008	NM_032444.2	984	Gaa/Aaa	12/15	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.32	2		836	940	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641010	3641010	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761296000	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	152	920	0	ENST00000294008.3:c.2629G>A	p.Ala877Thr	p.A877T	ENST00000294008	NM_032444.2	877	Gct/Act	12/15	1	2	FACETS	0.921	0.841	1	0.921	0.841	1	CLONAL	1	TRUE	1	0.32	2		920	1032	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652273	3652273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543071212	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	111	685	0	ENST00000294008.3:c.796G>A	p.Ala266Thr	p.A266T	ENST00000294008	NM_032444.2	266	Gct/Act	4/15	1	2	FACETS	0.872	0.783	0.965	0.872	0.783	0.965	CLONAL	1	TRUE	1	0.32	2		685	796	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658692	3658692	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	125	791	0	ENST00000294008.3:c.274A>G	p.Arg92Gly	p.R92G	ENST00000294008	NM_032444.2	92	Agg/Ggg	2/15	1	2	FACETS	0.812	0.734	0.895	0.812	0.734	0.895	CLONAL	1	TRUE	1	0.32	2		791	962	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778813	3778813	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	135	946	0	ENST00000262367.5:c.6235T>C	p.Ser2079Pro	p.S2079P	ENST00000262367	NM_004380.2	2079	Tcc/Ccc	31/31	1	2	FACETS	0.911	0.828	0.999	0.911	0.828	0.999	CLONAL	1	TRUE	1	0.32	2		946	926	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820578	3820578	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1356131652	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	118	708	0	ENST00000262367.5:c.2873G>A	p.Gly958Asp	p.G958D	ENST00000262367	NM_004380.2	958	gGc/gAc	14/31	1	2	FACETS	0.889	0.801	0.981	0.889	0.801	0.981	CLONAL	1	TRUE	1	0.32	2		708	830	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031850	10031850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	97	595	0	ENST00000330684.3:c.973G>A	p.Glu325Lys	p.E325K	ENST00000330684	NM_001134407.1	325	Gag/Aag	3/13	1	2	FACETS	0.866	0.772	0.966	0.866	0.772	0.966	CLONAL	1	TRUE	1	0.32	2		595	700	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032006	10032006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	74	602	2	ENST00000330684.3:c.817C>T	p.Pro273Ser	p.P273S	ENST00000330684	NM_001134407.1	273	Cca/Tca	3/13	1	2	FACETS	0.69	0.604	0.783	0.69	0.604	0.783	SUBCLONAL	1	TRUE	1	0.32	2		604	670	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274115	10274115	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555491518	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	44	802	0	ENST00000330684.3:c.154C>T	p.Arg52Ter	p.R52*	ENST00000330684	NM_001134407.1	52	Cga/Tga	2/13	1	2	FACETS	0.335	0.279	0.396	0.335	0.279	0.396	SUBCLONAL	1	TRUE	1	0.32	2		802	822	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646465	23646465	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	99	575	0	ENST00000261584.4:c.1402A>G	p.Thr468Ala	p.T468A	ENST00000261584	NM_024675.3	468	Aca/Gca	4/13	1	2	FACETS	0.893	0.798	0.994	0.893	0.798	0.994	CLONAL	1	TRUE	1	0.32	2		575	693	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128261	30128261	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1329197803	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	114	769	0	ENST00000263025.4:c.971C>T	p.Ala324Val	p.A324V	ENST00000263025	NM_002746.2	324	gCg/gTg	7/9	1	2	FACETS	0.822	0.739	0.909	0.822	0.739	0.909	CLONAL	1	TRUE	1	0.32	2		769	867	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56862975	56862975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	38	409	0	ENST00000308159.5:c.881G>A	p.Arg294Gln	p.R294Q	ENST00000308159	NM_014669.4	294	cGa/cAa	9/22	1	2	FACETS	0.446	0.368	0.533	0.446	0.368	0.533	SUBCLONAL	1	TRUE	1	0.32	2		409	533	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822031	72822031	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	55	453	0	ENST00000268489.5:c.10144C>T	p.Gln3382Ter	p.Q3382*	ENST00000268489	NM_006885.3	3382	Caa/Taa	10/10	1	2	FACETS	0.652	0.558	0.755	0.652	0.558	0.755	SUBCLONAL	1	TRUE	1	0.32	2		453	527	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822273	72822273	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	125	746	0	ENST00000268489.5:c.9902C>A	p.Ala3301Glu	p.A3301E	ENST00000268489	NM_006885.3	3301	gCa/gAa	10/10	1	2	FACETS	0.853	0.771	0.939	0.853	0.771	0.939	CLONAL	1	TRUE	1	0.32	2		746	916	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828461	72828461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139821312	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	91	642	0	ENST00000268489.5:c.8120C>T	p.Ala2707Val	p.A2707V	ENST00000268489	NM_006885.3	2707	gCg/gTg	9/10	1	2	FACETS	0.787	0.698	0.881	0.787	0.698	0.881	SUBCLONAL	1	TRUE	1	0.32	2		642	723	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992355	72992355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	121	809	0	ENST00000268489.5:c.1690G>A	p.Ala564Thr	p.A564T	ENST00000268489	NM_006885.3	564	Gcg/Acg	2/10	1	2	FACETS	0.789	0.711	0.87	0.789	0.711	0.87	SUBCLONAL	1	TRUE	1	0.32	2		809	959	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81934353	81934353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	115	582	0	ENST00000359376.3:c.1330C>T	p.Pro444Ser	p.P444S	ENST00000359376	NM_002661.3	444	Ccc/Tcc	14/33	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.32	2		582	709	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942036	81942036	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	69	341	0	ENST00000359376.3:c.1573G>T	p.Glu525Ter	p.E525*	ENST00000359376	NM_002661.3	525	Gaa/Taa	17/33	1	2	FACETS	0.92	0.803	1	0.92	0.803	1	CLONAL	1	TRUE	1	0.32	2		341	469	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351923	89351923	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147744268	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	119	878	1	ENST00000301030.4:c.1027G>A	p.Val343Ile	p.V343I	ENST00000301030	NM_001256183.1	343	Gtc/Atc	9/13	1	2	FACETS	0.795	0.716	0.878	0.795	0.716	0.878	SUBCLONAL	1	TRUE	1	0.32	2		879	936	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89833635	89833635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	39	187	0	ENST00000389301.3:c.2515G>A	p.Ala839Thr	p.A839T	ENST00000389301	NM_000135.2	839	Gca/Aca	27/43	1	2	FACETS	0.975	0.814	1	0.975	0.814	1	CLONAL	1	TRUE	1	0.32	2		187	250	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576858	7576858	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	97	552	0	ENST00000269305.4:c.988C>A	p.Leu330Ile	p.L330I	ENST00000269305	NM_001126112.2	330	Ctt/Att	9/11	1	2	FACETS	0.871	0.777	0.971	0.871	0.777	0.971	CLONAL	1	TRUE	1	0.32	2		552	696	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519999	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	90	546	0	ENST00000269305.4:c.716A>G	p.Asn239Ser	p.N239S	ENST00000269305	NM_001126112.2	239	aAc/aGc	7/11	1	2	FACETS	0.882	0.783	0.987	0.882	0.783	0.987	CLONAL	1	TRUE	1	0.32	2		546	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781845	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	29	774	0	ENST00000269305.4:c.511G>A	p.Glu171Lys	p.E171K	ENST00000269305	NM_001126112.2	171	Gag/Aag	5/11	1	2	FACETS	0.2	0.16	0.247	0.2	0.16	0.247	SUBCLONAL	1	TRUE	1	0.32	2		774	904	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028632	12028632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753665559	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	31	298	0	ENST00000353533.5:c.835G>A	p.Ala279Thr	p.A279T	ENST00000353533	NM_003010.3	279	Gca/Aca	8/11	1	2	FACETS	0.469	0.379	0.571	0.469	0.379	0.571	SUBCLONAL	1	TRUE	1	0.32	2		298	413	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971357	15971357	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151311067	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	75	562	0	ENST00000268712.3:c.4592C>T	p.Ala1531Val	p.A1531V	ENST00000268712	NM_006311.3	1531	gCg/gTg	32/46	1	2	FACETS	0.691	0.606	0.784	0.691	0.606	0.784	SUBCLONAL	1	TRUE	1	0.32	2		562	678	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004811	16004811	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	67	524	0	ENST00000268712.3:c.2443C>T	p.Pro815Ser	p.P815S	ENST00000268712	NM_006311.3	815	Ccc/Tcc	20/46	1	2	FACETS	0.608	0.528	0.695	0.608	0.528	0.695	SUBCLONAL	1	TRUE	1	0.32	2		524	689	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004951	16004951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148612896	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	105	594	1	ENST00000268712.3:c.2303C>T	p.Ala768Val	p.A768V	ENST00000268712	NM_006311.3	768	gCa/gTa	20/46	1	2	FACETS	0.824	0.738	0.916	0.824	0.738	0.916	CLONAL	1	TRUE	1	0.32	2		595	796	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508180	38508180	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	85	456	0	ENST00000254066.5:c.488A>G	p.Asn163Ser	p.N163S	ENST00000254066	NM_000964.3	163	aAc/aGc	5/9	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.32	2		456	483	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456552	40456552	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	55	648	0	ENST00000345506.4:c.1262T>G	p.Leu421Arg	p.L421R	ENST00000345506	NM_003152.3	421	cTg/cGg	12/20	1	2	FACETS	0.468	0.4	0.544	0.468	0.4	0.544	SUBCLONAL	1	TRUE	1	0.32	2		648	734	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40498723	40498723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868859792	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	31	343	0	ENST00000264657.5:c.137C>T	p.Ala46Val	p.A46V	ENST00000264657	NM_139276.2	46	gCg/gTg	3/24	1	2	FACETS	0.397	0.32	0.484	0.397	0.32	0.484	SUBCLONAL	1	TRUE	1	0.32	2		343	488	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215357	41215357	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	51	364	0	ENST00000357654.3:c.5186T>C	p.Leu1729Pro	p.L1729P	ENST00000357654	NM_007294.3	1729	cTg/cCg	18/23	1	2	FACETS	0.705	0.6	0.82	0.705	0.6	0.82	SUBCLONAL	1	TRUE	1	0.32	2		364	452	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245617	41245617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	92	516	0	ENST00000357654.3:c.1931G>A	p.Cys644Tyr	p.C644Y	ENST00000357654	NM_007294.3	644	tGt/tAt	10/23	1	2	FACETS	0.863	0.768	0.965	0.863	0.768	0.965	CLONAL	1	TRUE	1	0.32	2		516	666	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805933	46805933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747307642	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	56	505	0	ENST00000290295.7:c.23C>T	p.Thr8Ile	p.T8I	ENST00000290295	NM_006361.5	8	aCc/aTc	1/2	1	2	FACETS	0.662	0.567	0.765	0.662	0.567	0.765	SUBCLONAL	1	TRUE	1	0.32	2		505	529	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734155	58734155	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	84	450	0	ENST00000305921.3:c.1213G>T	p.Glu405Ter	p.E405*	ENST00000305921	NM_003620.3	405	Gaa/Taa	5/6	1	2	FACETS	0.813	0.718	0.914	0.813	0.718	0.914	CLONAL	1	TRUE	1	0.32	2		450	646	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120032	70120032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	22	84	0	ENST00000245479.2:c.1034C>T	p.Pro345Leu	p.P345L	ENST00000245479	NM_000346.3	345	cCc/cTc	3/3	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.32	2		84	102	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617659	39617659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	30	217	0	ENST00000262039.4:c.1843G>A	p.Ala615Thr	p.A615T	ENST00000262039	NM_002647.2	615	Gcc/Acc	17/25	1	2	FACETS	0.679	0.549	0.826	0.679	0.549	0.826	SUBCLONAL	1	TRUE	1	0.32	2		217	276	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617683	39617683	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	37	248	0	ENST00000262039.4:c.1867T>G	p.Phe623Val	p.F623V	ENST00000262039	NM_002647.2	623	Ttt/Gtt	17/25	1	2	FACETS	0.734	0.607	0.875	0.734	0.607	0.875	SUBCLONAL	1	TRUE	1	0.32	2		248	315	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372160	45372160	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1040132520	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	59	332	1	ENST00000262160.6:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000262160	NM_005901.5	337	Cgc/Tgc	9/11	1	2	FACETS	0.908	0.784	1	0.908	0.784	1	CLONAL	1	TRUE	1	0.32	2		333	406	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45423102	45423102	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749758342	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	23	187	0	ENST00000262160.6:c.26C>T	p.Pro9Leu	p.P9L	ENST00000262160	NM_005901.5	9	cCg/cTg	2/11	1	2	FACETS	0.601	0.47	0.752	0.601	0.47	0.752	SUBCLONAL	1	TRUE	1	0.32	2		187	239	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575209	48575209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767326	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	21	234	1	ENST00000342988.3:c.403C>T	p.Arg135Ter	p.R135*	ENST00000342988	NM_005359.5	135	Cga/Tga	3/12	1	2	FACETS	0.451	0.347	0.572	0.451	0.347	0.572	SUBCLONAL	1	TRUE	1	0.32	2		235	291	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56412897	56412897	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	16	113	0	ENST00000348428.3:c.1912-1G>T		p.X638_splice	ENST00000348428	NM_006785.3	638			1	2	FACETS	0.529	0.392	0.691	0.529	0.392	0.691	SUBCLONAL	1	TRUE	1	0.32	2		113	189	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56413018	56413018	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	40	260	0	ENST00000348428.3:c.2032T>G	p.Leu678Val	p.L678V	ENST00000348428	NM_006785.3	678	Tta/Gta	16/17	1	2	FACETS	0.887	0.741	1	0.887	0.741	1	CLONAL	1	TRUE	1	0.32	2		260	282	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611846	1611846	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	88	552	1	ENST00000344749.5:c.1816C>T	p.Arg606Trp	p.R606W	ENST00000344749	NM_001136139.2	606	Cgg/Tgg	19/19	1	2	FACETS	0.866	0.768	0.971	0.866	0.768	0.971	CLONAL	1	TRUE	1	0.32	2		553	635	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119235	3119235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529942770	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	91	701	0	ENST00000078429.4:c.767G>A	p.Arg256Gln	p.R256Q	ENST00000078429	NM_002067.2	256	cGg/cAg	6/7	1	2	FACETS	0.74	0.656	0.829	0.74	0.656	0.829	SUBCLONAL	1	TRUE	1	0.32	2		701	769	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121110	3121110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	116	651	0	ENST00000078429.4:c.1013G>A	p.Arg338His	p.R338H	ENST00000078429	NM_002067.2	338	cGc/cAc	7/7	1	2	FACETS	0.917	0.826	1	0.917	0.826	1	CLONAL	1	TRUE	1	0.32	2		651	791	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4090642	4090642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	130	766	1	ENST00000262948.5:c.1157C>T	p.Thr386Ile	p.T386I	ENST00000262948	NM_030662.3	386	aCc/aTc	11/11	1	2	FACETS	0.892	0.808	0.98	0.892	0.808	0.98	CLONAL	1	TRUE	1	0.32	2		767	911	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208016	5208016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1042776388	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	93	707	1	ENST00000357368.4:c.5695C>T	p.Arg1899Trp	p.R1899W	ENST00000357368	NM_002850.3	1899	Cgg/Tgg	37/38	1	2	FACETS	0.694	0.617	0.778	0.694	0.617	0.778	SUBCLONAL	1	TRUE	1	0.32	2		708	837	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222735	5222735	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	84	863	0	ENST00000357368.4:c.3068C>A	p.Pro1023His	p.P1023H	ENST00000357368	NM_002850.3	1023	cCc/cAc	18/38	1	2	FACETS	0.541	0.477	0.611	0.541	0.477	0.611	SUBCLONAL	1	TRUE	1	0.32	2		863	970	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274223	5274223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	109	750	0	ENST00000357368.4:c.224C>T	p.Ser75Phe	p.S75F	ENST00000357368	NM_002850.3	75	tCt/tTt	3/38	1	2	FACETS	0.804	0.722	0.892	0.804	0.722	0.892	CLONAL	1	TRUE	1	0.32	2		750	847	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7126594	7126594	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	96	547	1	ENST00000302850.5:c.3013+1G>A		p.X1005_splice	ENST00000302850	NM_000208.2	1005			1	2	FACETS	0.912	0.813	1	0.912	0.813	1	CLONAL	1	TRUE	1	0.32	2		548	658	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265344	10265344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1227919940	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	74	669	2	ENST00000340748.4:c.1702G>A	p.Gly568Arg	p.G568R	ENST00000340748		568	Ggg/Agg	20/40	1	2	FACETS	0.55	0.48	0.625	0.55	0.48	0.625	SUBCLONAL	1	TRUE	1	0.32	2		671	841	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10271084	10271084	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	74	400	0	ENST00000340748.4:c.971G>T	p.Arg324Ile	p.R324I	ENST00000340748		324	aGa/aTa	13/40	1	2	FACETS	0.898	0.788	1	0.898	0.788	1	CLONAL	1	TRUE	1	0.32	2		400	515	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600476	10600476	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	131	621	0	ENST00000171111.5:c.1379G>T	p.Arg460Met	p.R460M	ENST00000171111	NM_203500.1	460	aGg/aTg	4/6	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.32	2		621	780	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121131	11121131	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	44	705	2	ENST00000358026.2:c.2198C>T	p.Ala733Val	p.A733V	ENST00000358026	NM_001128849.1	733	gCc/gTc	15/36	1	2	FACETS	0.34	0.284	0.402	0.34	0.284	0.402	SUBCLONAL	1	TRUE	1	0.32	2		707	810	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054565	13054565	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	82	388	0	ENST00000316448.5:c.1092G>T	p.Glu364Asp	p.E364D	ENST00000316448	NM_004343.3	364	gaG/gaT	9/9	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.32	2		388	471	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276665	15276665	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	127	896	0	ENST00000263388.2:c.5600C>T	p.Ala1867Val	p.A1867V	ENST00000263388	NM_000435.2	1867	gCc/gTc	30/33	1	2	FACETS	0.848	0.767	0.933	0.848	0.767	0.933	CLONAL	1	TRUE	1	0.32	2		896	936	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15280904	15280904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1251693132	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	130	804	2	ENST00000263388.2:c.5192G>A	p.Arg1731Gln	p.R1731Q	ENST00000263388	NM_000435.2	1731	cGg/cAg	28/33	1	2	FACETS	0.963	0.873	1	0.963	0.873	1	CLONAL	1	TRUE	1	0.32	2		806	844	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273825	18273825	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	70	660	0	ENST00000222254.8:c.1158C>A	p.His386Gln	p.H386Q	ENST00000222254	NM_005027.3	386	caC/caA	10/16	1	2	FACETS	0.534	0.464	0.609	0.534	0.464	0.609	SUBCLONAL	1	TRUE	1	0.32	2		660	820	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974263	18974263	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	54	536	0	ENST00000262803.5:c.2617G>C	p.Val873Leu	p.V873L	ENST00000262803	NM_002911.3	873	Gtg/Ctg	19/24	1	2	FACETS	0.551	0.47	0.64	0.551	0.47	0.64	SUBCLONAL	1	TRUE	1	0.32	2		536	612	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258632	19258632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757401725	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	48	738	1	ENST00000162023.5:c.268C>T	p.Arg90Trp	p.R90W	ENST00000162023		90	Cgg/Tgg	8/13	1	2	FACETS	0.45	0.379	0.528	0.45	0.379	0.528	SUBCLONAL	1	TRUE	1	0.32	2		739	667	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221726	36221728	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	132	801	0	ENST00000222270.7:c.5398_5400del	p.Glu1800del	p.E1800del	ENST00000222270	NM_014727.1	1799	GAG/-	26/37	1	2	FACETS	0.859	0.779	0.944	0.859	0.779	0.944	CLONAL	1	TRUE	1	0.32	2		801	960	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383653	42383653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555843732	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	128	712	0	ENST00000221972.3:c.428G>A	p.Arg143Gln	p.R143Q	ENST00000221972	NM_021601.3	143	cGa/cAa	3/5	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.32	2		712	761	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42788920	42788920	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	132	668	1	ENST00000575354.2:c.64T>C	p.Phe22Leu	p.F22L	ENST00000575354	NM_015125.3	22	Ttc/Ctc	1/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.32	2		669	765	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856532	45856532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201165309	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	126	658	1	ENST00000391945.4:c.1726G>A	p.Glu576Lys	p.E576K	ENST00000391945	NM_000400.3	576	Gaa/Aaa	18/23	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.32	2		659	737	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867583	45867583	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	168	955	0	ENST00000391945.4:c.725T>C	p.Val242Ala	p.V242A	ENST00000391945	NM_000400.3	242	gTc/gCc	9/23	1	2	FACETS	0.974	0.894	1	0.974	0.894	1	CLONAL	1	TRUE	1	0.32	2		955	1078	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140378	50140378	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368625677	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	79	466	0	ENST00000246792.3:c.163G>A	p.Val55Met	p.V55M	ENST00000246792	NM_006270.3	55	Gtg/Atg	2/6	1	2	FACETS	0.896	0.79	1	0.896	0.79	1	CLONAL	1	TRUE	1	0.32	2		466	551	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910297	50910297	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs149043082	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	151	801	0	ENST00000440232.2:c.1552C>A	p.Leu518Met	p.L518M	ENST00000440232	NM_002691.3	518	Ctg/Atg	13/27	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.32	2		801	926	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716212	52716212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555791268	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	142	674	1	ENST00000322088.6:c.656C>T	p.Ser219Leu	p.S219L	ENST00000322088	NM_014225.5	219	tCg/tTg	6/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.32	2		675	783	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716329	52716329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863225094	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	124	664	0	ENST00000322088.6:c.773G>A	p.Arg258His	p.R258H	ENST00000322088	NM_014225.5	258	cGc/cAc	6/15	1	2	FACETS	0.987	0.894	1	0.987	0.894	1	CLONAL	1	TRUE	1	0.32	2		664	785	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25459872	25459872	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs750597155	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	99	535	0	ENST00000264709.3:c.2411C>T	p.Pro804Leu	p.P804L	ENST00000264709	NM_175629.2	804	cCg/cTg	21/23	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.32	2		535	596	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467089	25467089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	128	814	2	ENST00000264709.3:c.1786C>T	p.Arg596Trp	p.R596W	ENST00000264709	NM_175629.2	596	Cgg/Tgg	15/23	1	2	FACETS	0.995	0.902	1	0.995	0.902	1	CLONAL	1	TRUE	1	0.32	2		816	804	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972866	25972866	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	61	349	1	ENST00000435504.4:c.1559C>A	p.Ser520Tyr	p.S520Y	ENST00000435504		520	tCt/tAt	12/13	1	2	FACETS	0.755	0.652	0.866	0.755	0.652	0.866	SUBCLONAL	1	TRUE	1	0.32	2		350	505	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635547	47635547	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	52	238	0	ENST00000233146.2:c.219G>T	p.Lys73Asn	p.K73N	ENST00000233146	NM_000251.2	73	aaG/aaT	2/16	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.32	2		238	307	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656951	47656951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63749849	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	20	239	0	ENST00000233146.2:c.1147C>T	p.Arg383Ter	p.R383*	ENST00000233146	NM_000251.2	383	Cga/Tga	7/16	1	2	FACETS	0.357	0.273	0.456	0.357	0.273	0.456	SUBCLONAL	1	TRUE	1	0.32	2		239	350	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690230	47690230	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63749947	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	78	306	0	ENST00000233146.2:c.1447G>T	p.Glu483Ter	p.E483*	ENST00000233146	NM_000251.2	483	Gaa/Taa	9/16	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.32	2		306	442	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698180	47698180	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63751411	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	42	200	0	ENST00000233146.2:c.1738G>T	p.Glu580Ter	p.E580*	ENST00000233146	NM_000251.2	580	Gaa/Taa	11/16	1	2	FACETS	0.976	0.82	1	0.976	0.82	1	CLONAL	1	TRUE	1	0.32	2		200	269	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47710037	47710037	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1553370893	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	27	169	0	ENST00000233146.2:c.2754G>T	p.Lys918Asn	p.K918N	ENST00000233146	NM_000251.2	918	aaG/aaT	16/16	1	2	FACETS	0.609	0.486	0.749	0.609	0.486	0.749	SUBCLONAL	1	TRUE	1	0.32	2		169	277	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018091	48018092	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	83	557	0	ENST00000234420.5:c.289dup	p.Trp97LeufsTer20	p.W97Lfs*20	ENST00000234420	NM_000179.2	96	gtt/gTtt	2/10	1	2	FACETS	0.719	0.635	0.811	0.719	0.635	0.811	SUBCLONAL	1	TRUE	1	0.32	2		557	721	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027199	48027199	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	49	351	0	ENST00000234420.5:c.2077A>T	p.Lys693Ter	p.K693*	ENST00000234420	NM_000179.2	693	Aaa/Taa	4/10	1	2	FACETS	0.711	0.603	0.829	0.711	0.603	0.829	SUBCLONAL	1	TRUE	1	0.32	2		351	431	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	66	369	2	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	0.863	0.751	0.984	0.863	0.751	0.984	CLONAL	1	TRUE	1	0.32	2		371	478	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921749	111921749	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	59	359	0	ENST00000393256.3:c.538C>T	p.Arg180Ter	p.R180*	ENST00000393256	NM_006538.4	180	Cga/Tga	4/4	1	2	FACETS	0.786	0.678	0.904	0.786	0.678	0.904	CLONAL	1	TRUE	1	0.32	2		359	469	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634689	158634689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	67	341	0	ENST00000263640.3:c.497C>T	p.Thr166Ile	p.T166I	ENST00000263640	NM_001105.4	166	aCt/aTt	5/11	1	2	FACETS	0.926	0.807	1	0.926	0.807	1	CLONAL	1	TRUE	1	0.32	2		341	452	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267472	198267472	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	61	279	0	ENST00000335508.6:c.1885G>T	p.Ala629Ser	p.A629S	ENST00000335508	NM_012433.2	629	Gct/Tct	14/25	1	2	FACETS	0.97	0.84	1	0.97	0.84	1	CLONAL	1	TRUE	1	0.32	2		279	393	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293162	212293162	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	53	304	0	ENST00000342788.4:c.2690T>C	p.Phe897Ser	p.F897S	ENST00000342788	NM_005235.2	897	tTc/tCc	22/28	1	2	FACETS	0.834	0.714	0.966	0.834	0.714	0.966	CLONAL	1	TRUE	1	0.32	2		304	397	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645649	215645649	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	77	380	0	ENST00000260947.4:c.949G>T	p.Glu317Ter	p.E317*	ENST00000260947	NM_000465.2	317	Gaa/Taa	4/11	1	2	FACETS	0.968	0.852	1	0.968	0.852	1	CLONAL	1	TRUE	1	0.32	2		380	497	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437193	220437193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301689911	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	214	1112	1	ENST00000243786.2:c.97G>A	p.Val33Met	p.V33M	ENST00000243786	NM_002191.3	33	Gtg/Atg	1/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.32	2		1113	1139	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440193	220440193	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	148	781	0	ENST00000243786.2:c.1046C>A	p.Ser349Tyr	p.S349Y	ENST00000243786	NM_002191.3	349	tCt/tAt	2/2	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.32	2		781	876	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225338988	225338988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759758641	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	46	313	0	ENST00000264414.4:c.2281C>T	p.Arg761Cys	p.R761C	ENST00000264414	NM_003590.4	761	Cgc/Tgc	16/16	1	2	FACETS	0.779	0.658	0.912	0.779	0.658	0.912	CLONAL	1	TRUE	1	0.32	2		313	369	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342921	225342921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766952042	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	36	340	0	ENST00000264414.4:c.2171C>T	p.Ala724Val	p.A724V	ENST00000264414	NM_003590.4	724	gCg/gTg	15/16	1	2	FACETS	0.571	0.47	0.684	0.571	0.47	0.684	SUBCLONAL	1	TRUE	1	0.32	2		340	394	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368506	225368506	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	56	290	0	ENST00000264414.4:c.1240A>G	p.Lys414Glu	p.K414E	ENST00000264414	NM_003590.4	414	Aaa/Gaa	9/16	1	2	FACETS	0.799	0.686	0.922	0.799	0.686	0.922	CLONAL	1	TRUE	1	0.32	2		290	438	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383281	31383281	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751976489	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	104	506	0	ENST00000328111.2:c.1193G>A	p.Arg398His	p.R398H	ENST00000328111	NM_006892.3	398	cGc/cAc	11/23	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.32	2		506	566	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384655	31384655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	108	667	0	ENST00000328111.2:c.1357G>A	p.Gly453Arg	p.G453R	ENST00000328111	NM_006892.3	453	Ggg/Agg	13/23	1	2	FACETS	0.843	0.756	0.935	0.843	0.756	0.935	CLONAL	1	TRUE	1	0.32	2		667	801	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012672	36012672	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	44	219	0	ENST00000358208.4:c.116G>T	p.Ser39Ile	p.S39I	ENST00000358208		39	aGc/aTc	2/12	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.32	2		219	244	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264985	46264985	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	48	405	0	ENST00000371998.3:c.1860del	p.Lys620AsnfsTer18	p.K620Nfs*18	ENST00000371998		619	Aaa/aa	12/23	1	2	FACETS	0.62	0.524	0.725	0.62	0.524	0.725	SUBCLONAL	1	TRUE	1	0.32	2		405	484	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57474013	57474013	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140388147	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	60	252	0	ENST00000371085.3:c.230C>T	p.Pro77Leu	p.P77L	ENST00000371085	NM_000516.4	77	cCg/cTg	3/13	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.32	2		252	367	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62311299	62311299	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs201938707	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	70	368	0	ENST00000360203.5:c.1135C>T	p.Arg379Cys	p.R379C	ENST00000360203	NM_001283009.1	379	Cgt/Tgt	13/35	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.32	2		368	370	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321674	62321674	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	188	726	0	ENST00000360203.5:c.2293G>A	p.Ala765Thr	p.A765T	ENST00000360203	NM_001283009.1	765	Gca/Aca	26/35	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.32	2		726	871	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130699	29130699	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	61	355	0	ENST00000328354.6:c.11A>C	p.Glu4Ala	p.E4A	ENST00000328354	NM_007194.3	4	gAg/gCg	2/15	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.32	2		355	363	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070869	30070869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373650983	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	94	587	1	ENST00000338641.4:c.1385G>A	p.Arg462His	p.R462H	ENST00000338641	NM_000268.3	462	cGc/cAc	13/16	1	2	FACETS	0.792	0.704	0.885	0.792	0.704	0.885	SUBCLONAL	1	TRUE	1	0.32	2		588	742	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543927	41543927	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	99	635	0	ENST00000263253.7:c.2218G>A	p.Ala740Thr	p.A740T	ENST00000263253	NM_001429.3	740	Gct/Act	12/31	1	2	FACETS	0.848	0.757	0.944	0.848	0.757	0.944	CLONAL	1	TRUE	1	0.32	2		635	730	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546045	41546045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs953108559	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	107	659	0	ENST00000263253.7:c.2660C>T	p.Thr887Ile	p.T887I	ENST00000263253	NM_001429.3	887	aCa/aTa	14/31	1	2	FACETS	0.873	0.783	0.968	0.873	0.783	0.968	CLONAL	1	TRUE	1	0.32	2		659	766	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458204	12458204	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs200116144	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	55	338	0	ENST00000287820.6:c.821C>T	p.Pro274Leu	p.P274L	ENST00000287820	NM_015869.4	274	cCa/cTa	6/7	1	2	FACETS	0.853	0.732	0.984	0.853	0.732	0.984	CLONAL	1	TRUE	1	0.32	2		338	403	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182772	38182772	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	97	478	0	ENST00000396334.3:c.925C>T	p.Pro309Ser	p.P309S	ENST00000396334	NM_002468.4	309	Ccc/Tcc	5/5	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.32	2		478	575	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939934	49939934	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	157	911	1	ENST00000296474.3:c.1109C>A	p.Pro370His	p.P370H	ENST00000296474	NM_002447.2	370	cCc/cAc	1/20	1	2	FACETS	0.925	0.846	1	0.925	0.846	1	CLONAL	1	TRUE	1	0.32	2		912	1061	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438494	52438494	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756443059	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	41	486	0	ENST00000460680.1:c.1225G>A	p.Val409Met	p.V409M	ENST00000460680	NM_004656.3	409	Gtg/Atg	12/17	1	2	FACETS	0.404	0.335	0.48	0.404	0.335	0.48	SUBCLONAL	1	TRUE	1	0.32	2		486	635	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637625	52637625	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	62	350	0	ENST00000394830.3:c.2691T>G	p.His897Gln	p.H897Q	ENST00000394830	NM_018313.4	897	caT/caG	18/30	1	2	FACETS	0.775	0.67	0.888	0.775	0.67	0.888	SUBCLONAL	1	TRUE	1	0.32	2		350	500	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	85	483	0	ENST00000394830.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000394830	NM_018313.4	710	Cga/Tga	17/30	1	2	FACETS	0.882	0.781	0.991	0.882	0.781	0.991	CLONAL	1	TRUE	1	0.32	2		483	602	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643788	52643788	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	81	468	0	ENST00000394830.3:c.2108C>A	p.Pro703His	p.P703H	ENST00000394830	NM_018313.4	703	cCc/cAc	17/30	1	2	FACETS	0.86	0.758	0.968	0.86	0.758	0.968	CLONAL	1	TRUE	1	0.32	2		468	589	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582383	119582383	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	23	319	0	ENST00000316626.5:c.1018G>A	p.Ala340Thr	p.A340T	ENST00000316626		340	Gcc/Acc	10/12	1	2	FACETS	0.363	0.282	0.456	0.363	0.282	0.456	SUBCLONAL	1	TRUE	1	0.32	2		319	396	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873105	134873105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749312347	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	51	507	0	ENST00000398015.3:c.1409G>A	p.Arg470Gln	p.R470Q	ENST00000398015	NM_004441.4	470	cGg/cAg	6/16	1	2	FACETS	0.607	0.516	0.707	0.607	0.516	0.707	SUBCLONAL	1	TRUE	1	0.32	2		507	525	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453511	138453511	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	50	354	0	ENST00000289153.2:c.937C>A	p.Leu313Ile	p.L313I	ENST00000289153	NM_006219.2	313	Ctt/Att	5/22	1	2	FACETS	0.799	0.68	0.929	0.799	0.68	0.929	CLONAL	1	TRUE	1	0.32	2		354	391	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260135	149260135	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	71	424	1	ENST00000360632.3:c.758A>G	p.Glu253Gly	p.E253G	ENST00000360632	NM_015472.4	253	gAg/gGg	4/7	1	2	FACETS	0.844	0.738	0.958	0.844	0.738	0.958	CLONAL	1	TRUE	1	0.32	2		425	526	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155301	185155301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140999720	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	36	392	0	ENST00000265026.3:c.542C>T	p.Ala181Val	p.A181V	ENST00000265026	NM_004721.4	181	gCg/gTg	3/14	1	2	FACETS	0.447	0.367	0.537	0.447	0.367	0.537	SUBCLONAL	1	TRUE	1	0.32	2		392	503	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502464	186502464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	46	238	0	ENST00000323963.5:c.187G>A	p.Ala63Thr	p.A63T	ENST00000323963		63	Gct/Act	3/11	1	2	FACETS	0.896	0.758	1	0.896	0.758	1	CLONAL	1	TRUE	1	0.32	2		238	321	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440335	187440335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	111	466	2	ENST00000232014.4:c.2032C>T	p.Arg678Cys	p.R678C	ENST00000232014	NM_001130845.1	678	Cgc/Tgc	10/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.32	2		468	584	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442757	187442757	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	93	479	0	ENST00000232014.4:c.1949G>A	p.Arg650Gln	p.R650Q	ENST00000232014	NM_001130845.1	650	cGa/cAa	9/10	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.32	2		479	559	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447449	187447449	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	115	668	0	ENST00000232014.4:c.744G>T	p.Glu248Asp	p.E248D	ENST00000232014	NM_001130845.1	248	gaG/gaT	5/10	1	2	FACETS	0.946	0.852	1	0.946	0.852	1	CLONAL	1	TRUE	1	0.32	2		668	760	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152011	55152011	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	61	380	0	ENST00000257290.5:c.2443G>T	p.Val815Phe	p.V815F	ENST00000257290	NM_006206.4	815	Gtc/Ttc	18/23	1	2	FACETS	0.923	0.799	1	0.923	0.799	1	CLONAL	1	TRUE	1	0.32	2		380	413	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953822	55953822	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	28	442	0	ENST00000263923.4:c.3614A>G	p.Glu1205Gly	p.E1205G	ENST00000263923	NM_002253.2	1205	gAg/gGg	27/30	1	2	FACETS	0.328	0.262	0.405	0.328	0.262	0.405	SUBCLONAL	1	TRUE	1	0.32	2		442	533	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081539	143081539	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	75	358	0	ENST00000262992.4:c.1535A>G	p.His512Arg	p.H512R	ENST00000262992	NM_001101669.1	512	cAt/cGt	15/24	1	2	FACETS	0.989	0.869	1	0.989	0.869	1	CLONAL	1	TRUE	1	0.32	2		358	474	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244091	153244091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	68	424	1	ENST00000281708.4:c.2066G>A	p.Arg689Gln	p.R689Q	ENST00000281708	NM_033632.3	689	cGg/cAg	12/12	1	2	FACETS	0.8	0.697	0.912	0.8	0.697	0.912	CLONAL	1	TRUE	1	0.32	2		425	531	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249520	153249520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	58	387	0	ENST00000281708.4:c.1258C>T	p.His420Tyr	p.H420Y	ENST00000281708	NM_033632.3	420	Cat/Tat	9/12	1	2	FACETS	0.765	0.658	0.881	0.765	0.658	0.881	SUBCLONAL	1	TRUE	1	0.32	2		387	474	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268152	153268152	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	63	338	0	ENST00000281708.4:c.656G>T	p.Gly219Val	p.G219V	ENST00000281708	NM_033632.3	219	gGg/gTg	4/12	1	2	FACETS	0.922	0.8	1	0.922	0.8	1	CLONAL	1	TRUE	1	0.32	2		338	427	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332499	153332499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs950959848	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	45	313	0	ENST00000281708.4:c.457C>T	p.Pro153Ser	p.P153S	ENST00000281708	NM_033632.3	153	Ccc/Tcc	2/12	1	2	FACETS	0.641	0.539	0.753	0.641	0.539	0.753	SUBCLONAL	1	TRUE	1	0.32	2		313	439	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525049	187525049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	50	423	0	ENST00000441802.2:c.10631C>T	p.Ala3544Val	p.A3544V	ENST00000441802	NM_005245.3	3544	gCg/gTg	19/27	1	2	FACETS	0.574	0.487	0.67	0.574	0.487	0.67	SUBCLONAL	1	TRUE	1	0.32	2		423	544	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532587	187532587	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	63	290	0	ENST00000441802.2:c.9806T>C	p.Ile3269Thr	p.I3269T	ENST00000441802	NM_005245.3	3269	aTa/aCa	14/27	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.32	2		290	363	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532645	187532645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	67	322	0	ENST00000441802.2:c.9748C>A	p.Leu3250Ile	p.L3250I	ENST00000441802	NM_005245.3	3250	Ctt/Att	14/27	1	2	FACETS	0.916	0.799	1	0.916	0.799	1	CLONAL	1	TRUE	1	0.32	2		322	457	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540324	187540324	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	61	331	0	ENST00000441802.2:c.7416del	p.Phe2472LeufsTer9	p.F2472Lfs*9	ENST00000441802	NM_005245.3	2472	ttT/tt	10/27	1	2	FACETS	0.823	0.712	0.944	0.823	0.712	0.944	CLONAL	1	TRUE	1	0.32	2		331	463	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224637	224637	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	51	109	0	ENST00000264932.6:c.312+1G>T		p.X104_splice	ENST00000264932	NM_004168.2	104			1	2	FACETS	0.966	0.837	1	1	0.976	1	CLONAL	2	TRUE	1	0.32	2		109	165	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449475	31449475	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	60	340	0	ENST00000344624.3:c.2734C>A	p.His912Asn	p.H912N	ENST00000344624		912	Cat/Aat	19/33	1	2	FACETS	0.85	0.735	0.976	0.85	0.735	0.976	CLONAL	1	TRUE	1	0.32	2		340	441	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526647	31526648	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	112	643	2	ENST00000344624.3:c.392dup	p.Val132SerfsTer34	p.V132Sfs*34	ENST00000344624		131	cca/ccCa	2/33	1	2	FACETS	0.938	0.844	1	0.938	0.844	1	CLONAL	1	TRUE	1	0.32	2		645	746	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867530	35867530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	25	201	1	ENST00000303115.3:c.344G>A	p.Ser115Asn	p.S115N	ENST00000303115	NM_002185.3	115	aGt/aAt	3/8	1	2	FACETS	0.562	0.444	0.697	0.562	0.444	0.697	SUBCLONAL	1	TRUE	1	0.32	2		202	278	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873752	35873752	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	40	208	0	ENST00000303115.3:c.706+2T>C		p.X236_splice	ENST00000303115	NM_002185.3	236			1	2	FACETS	0.853	0.712	1	0.853	0.712	1	CLONAL	1	TRUE	1	0.32	2		208	293	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39002727	39002727	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	20	263	0	ENST00000357387.3:c.302C>T	p.Ala101Val	p.A101V	ENST00000357387	NM_152756.3	101	gCa/gTa	5/38	1	2	FACETS	0.326	0.248	0.416	0.326	0.248	0.416	SUBCLONAL	1	TRUE	1	0.32	2		263	384	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160643	56160643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375262853	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	61	250	0	ENST00000399503.3:c.917G>A	p.Arg306His	p.R306H	ENST00000399503	NM_005921.1	306	cGc/cAc	4/20	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.32	2		250	370	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56171126	56171126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376758896	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	22	249	0	ENST00000399503.3:c.1954G>A	p.Val652Ile	p.V652I	ENST00000399503	NM_005921.1	652	Gtt/Att	10/20	1	2	FACETS	0.418	0.324	0.527	0.418	0.324	0.527	SUBCLONAL	1	TRUE	1	0.32	2		249	329	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178670	56178670	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	23	155	0	ENST00000399503.3:c.3643G>T	p.Asp1215Tyr	p.D1215Y	ENST00000399503	NM_005921.1	1215	Gat/Tat	14/20	1	2	FACETS	0.946	0.745	1	0.946	0.745	1	CLONAL	1	TRUE	1	0.32	2		155	152	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755641	57755641	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	155	828	0	ENST00000274289.3:c.146C>T	p.Ala49Val	p.A49V	ENST00000274289	NM_006622.3	49	gCg/gTg	1/14	1	2	FACETS	0.951	0.869	1	0.951	0.869	1	CLONAL	1	TRUE	1	0.32	2		828	1019	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589618	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519838	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	37	177	0	ENST00000274335.5:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000274335		461	Cga/Tga	10/15	1	2	FACETS	0.988	0.821	1	0.988	0.821	1	CLONAL	1	TRUE	1	0.32	2		177	234	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950676	79950676	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	57	458	0	ENST00000265081.6:c.130G>T	p.Ala44Ser	p.A44S	ENST00000265081	NM_002439.4	44	Gcc/Tcc	1/24	1	2	FACETS	0.632	0.542	0.73	0.632	0.542	0.73	SUBCLONAL	1	TRUE	1	0.32	2		458	564	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645121	86645121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	45	249	0	ENST00000274376.6:c.1193G>A	p.Arg398Gln	p.R398Q	ENST00000274376	NM_002890.2	398	cGa/cAa	8/25	1	2	FACETS	0.919	0.776	1	0.919	0.776	1	CLONAL	1	TRUE	1	0.32	2		249	306	SUCCESS
APC	324	MSKCC	GRCh37	5	112164554	112164554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	21	158	0	ENST00000257430.4:c.1628T>C	p.Val543Ala	p.V543A	ENST00000257430	NM_000038.5	543	gTt/gCt	14/16	1	2	FACETS	0.677	0.524	0.853	0.677	0.524	0.853	SUBCLONAL	1	TRUE	1	0.32	2		158	194	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131951822	131951822	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	37	147	0	ENST00000265335.6:c.3164G>T	p.Ser1055Ile	p.S1055I	ENST00000265335		1055	aGt/aTt	20/25	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.32	2		147	224	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149434801	149434801	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1455721054	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	74	520	0	ENST00000286301.3:c.2653A>G	p.Ile885Val	p.I885V	ENST00000286301	NM_005211.3	885	Ata/Gta	20/22	1	2	FACETS	0.814	0.714	0.922	0.814	0.714	0.922	CLONAL	1	TRUE	1	0.32	2		520	568	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441061	149441061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	84	548	0	ENST00000286301.3:c.1851G>A	p.Met617Ile	p.M617I	ENST00000286301	NM_005211.3	617	atG/atA	13/22	1	2	FACETS	0.894	0.791	1	0.894	0.791	1	CLONAL	1	TRUE	1	0.32	2		548	587	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497323	149497323	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1561984776	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	121	650	1	ENST00000261799.4:c.2995C>T	p.Arg999Ter	p.R999*	ENST00000261799	NM_002609.3	999	Cga/Tga	22/23	1	2	FACETS	0.986	0.891	1	0.986	0.891	1	CLONAL	1	TRUE	1	0.32	2		651	767	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504391	149504391	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752228799	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	143	619	1	ENST00000261799.4:c.1811G>A	p.Arg604His	p.R604H	ENST00000261799	NM_002609.3	604	cGc/cAc	13/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.32	2		620	747	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513317	149513317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147568171	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	91	485	2	ENST00000261799.4:c.766C>T	p.Arg256Trp	p.R256W	ENST00000261799	NM_002609.3	256	Cgg/Tgg	6/23	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.32	2		487	551	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637435	176637435	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	34	374	0	ENST00000439151.2:c.2035C>T	p.Gln679Ter	p.Q679*	ENST00000439151	NM_022455.4	679	Cag/Tag	5/23	1	2	FACETS	0.507	0.414	0.612	0.507	0.414	0.612	SUBCLONAL	1	TRUE	1	0.32	2		374	419	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687031	176687031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1164947711	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	77	378	0	ENST00000439151.2:c.5008G>A	p.Ala1670Thr	p.A1670T	ENST00000439151	NM_022455.4	1670	Gcc/Acc	14/23	1	2	FACETS	0.972	0.856	1	0.972	0.856	1	CLONAL	1	TRUE	1	0.32	2		378	495	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048881	180048881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751002839	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	131	946	0	ENST00000261937.6:c.1681G>A	p.Glu561Lys	p.E561K	ENST00000261937	NM_182925.4	561	Gaa/Aaa	13/30	1	2	FACETS	0.823	0.746	0.904	0.823	0.746	0.904	CLONAL	1	TRUE	1	0.32	2		946	995	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490594	20490594	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	53	454	0	ENST00000346618.3:c.1331T>C	p.Ile444Thr	p.I444T	ENST00000346618	NM_001949.4	444	aTc/aCc	7/7	1	2	FACETS	0.53	0.451	0.616	0.53	0.451	0.616	SUBCLONAL	1	TRUE	1	0.32	2		454	625	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056602	26056602	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200705328	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	75	305	0	ENST00000343677.2:c.55C>A	p.Pro19Thr	p.P19T	ENST00000343677	NM_005319.3	19	Cct/Act	1/1	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.32	2		305	359	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912355	29912355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	172	709	0	ENST00000376809.5:c.974C>T	p.Ala325Val	p.A325V	ENST00000376809	NM_002116.7	325	gCt/gTt	5/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.32	2		709	893	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672399	30672399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754933032	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	112	571	0	ENST00000376406.3:c.4561C>T	p.Arg1521Trp	p.R1521W	ENST00000376406	NM_014641.2	1521	Cgg/Tgg	10/15	1	2	FACETS	0.922	0.83	1	0.922	0.83	1	CLONAL	1	TRUE	1	0.32	2		571	759	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675417	30675417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753904353	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	144	688	0	ENST00000376406.3:c.2939C>T	p.Thr980Ile	p.T980I	ENST00000376406	NM_014641.2	980	aCc/aTc	8/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.32	2		688	837	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675500	30675500	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	79	852	0	ENST00000376406.3:c.2856G>T	p.Glu952Asp	p.E952D	ENST00000376406	NM_014641.2	952	gaG/gaT	8/15	1	2	FACETS	0.5	0.439	0.567	0.5	0.439	0.567	SUBCLONAL	1	TRUE	1	0.32	2		852	987	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903745	41903745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764155094	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	171	794	0	ENST00000372991.4:c.812G>A	p.Arg271Gln	p.R271Q	ENST00000372991	NM_001760.3	271	cGg/cAg	5/5	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.32	2		794	999	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956675	93956675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776802108	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	65	307	0	ENST00000369303.4:c.2561G>A	p.Arg854His	p.R854H	ENST00000369303	NM_004440.3	854	cGt/cAt	15/17	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.32	2		307	404	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536269	106536269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1427730094	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	76	350	0	ENST00000369096.4:c.236C>T	p.Ala79Val	p.A79V	ENST00000369096	NM_001198.3	79	gCg/gTg	2/7	1	2	FACETS	0.847	0.744	0.957	0.847	0.744	0.957	CLONAL	1	TRUE	1	0.32	2		350	561	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020771	112020771	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374907658	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	68	291	0	ENST00000368678.4:c.800C>T	p.Ser267Leu	p.S267L	ENST00000368678		267	tCg/tTg	8/13	1	2	FACETS	0.932	0.813	1	0.932	0.813	1	CLONAL	1	TRUE	1	0.32	2		291	456	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678001	117678001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs62430836	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	83	356	0	ENST00000368508.3:c.3932G>A	p.Arg1311Gln	p.R1311Q	ENST00000368508	NM_002944.2	1311	cGa/cAa	25/43	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.32	2		356	474	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001362	150001362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	125	450	0	ENST00000253339.5:c.2242G>A	p.Ala748Thr	p.A748T	ENST00000253339		748	Gct/Act	4/7	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.32	2		450	583	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163807	152163807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	32	419	0	ENST00000206249.3:c.528G>T	p.Met176Ile	p.M176I	ENST00000206249	NM_000125.3	176	atG/atT	2/8	1	2	FACETS	0.379	0.307	0.461	0.379	0.307	0.461	SUBCLONAL	1	TRUE	1	0.32	2		419	528	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099072	157099072	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1015147137	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	28	268	0	ENST00000346085.5:c.9T>A	p.His3Gln	p.H3Q	ENST00000346085	NM_020732.3	3	caT/caA	1/20	1	2	FACETS	0.581	0.466	0.713	0.581	0.466	0.713	SUBCLONAL	1	TRUE	1	0.32	2		268	301	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962849	2962849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs562372731	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	109	861	1	ENST00000396946.4:c.2059G>A	p.Ala687Thr	p.A687T	ENST00000396946	NM_032415.4	687	Gcg/Acg	16/25	1	2	FACETS	0.696	0.624	0.773	0.696	0.624	0.773	SUBCLONAL	1	TRUE	1	0.32	2		862	979	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6031649	6031649	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs200640585	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	79	373	0	ENST00000265849.7:c.943C>T	p.Arg315Ter	p.R315*	ENST00000265849	NM_000535.5	315	Cga/Tga	9/15	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.32	2		373	488	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729290	41729290	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	74	393	0	ENST00000242208.4:c.1239G>T	p.Lys413Asn	p.K413N	ENST00000242208	NM_002192.2	413	aaG/aaT	3/3	1	2	FACETS	0.925	0.812	1	0.925	0.812	1	CLONAL	1	TRUE	1	0.32	2		393	500	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509676	106509676	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139426517	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	40	459	0	ENST00000359195.3:c.1670C>T	p.Ala557Val	p.A557V	ENST00000359195	NM_002649.2	557	gCg/gTg	2/11	1	2	FACETS	0.405	0.336	0.483	0.405	0.336	0.483	SUBCLONAL	1	TRUE	1	0.32	2		459	617	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845178	128845178	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs148484943	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	98	813	0	ENST00000249373.3:c.672G>T	p.Glu224Asp	p.E224D	ENST00000249373	NM_005631.4	224	gaG/gaT	3/12	1	2	FACETS	0.733	0.653	0.818	0.733	0.653	0.818	SUBCLONAL	1	TRUE	1	0.32	2		813	836	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506223	148506223	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	55	367	0	ENST00000320356.2:c.2135G>T	p.Arg712Met	p.R712M	ENST00000320356	NM_004456.4	712	aGg/aTg	19/20	1	2	FACETS	0.647	0.554	0.749	0.647	0.554	0.749	SUBCLONAL	1	TRUE	1	0.32	2		367	531	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845504	151845504	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	109	570	0	ENST00000262189.6:c.13508G>A	p.Cys4503Tyr	p.C4503Y	ENST00000262189	NM_170606.2	4503	tGc/tAc	52/59	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.32	2		570	674	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151850021	151850021	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	36	237	0	ENST00000262189.6:c.12295G>T	p.Ala4099Ser	p.A4099S	ENST00000262189	NM_170606.2	4099	Gct/Tct	49/59	1	2	FACETS	0.708	0.583	0.846	0.708	0.583	0.846	SUBCLONAL	1	TRUE	1	0.32	2		237	318	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896364	151896364	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs746270757	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	48	314	0	ENST00000262189.6:c.4273G>A	p.Gly1425Ser	p.G1425S	ENST00000262189	NM_170606.2	1425	Ggt/Agt	27/59	1	2	FACETS	0.824	0.699	0.961	0.824	0.699	0.961	CLONAL	1	TRUE	1	0.32	2		314	364	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162828	38162828	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754800291	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	89	505	1	ENST00000317025.8:c.2378G>A	p.Arg793His	p.R793H	ENST00000317025	NM_023034.1	793	cGc/cAc	13/24	1	2	FACETS	0.924	0.82	1	0.924	0.82	1	CLONAL	1	TRUE	1	0.32	2		506	602	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273432	38273432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1412996644	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	99	961	0	ENST00000425967.3:c.1903G>A	p.Ala635Thr	p.A635T	ENST00000425967	NM_001174067.1	635	Gcc/Acc	14/19	1	2	FACETS	0.523	0.465	0.585	0.523	0.465	0.585	SUBCLONAL	1	TRUE	1	0.32	2		961	1183	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279443	38279443	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	97	475	3	ENST00000425967.3:c.1046C>T	p.Thr349Ile	p.T349I	ENST00000425967	NM_001174067.1	349	aCc/aTc	9/19	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.32	2		478	530	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864681	68864681	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	91	461	0	ENST00000288368.4:c.52G>A	p.Glu18Lys	p.E18K	ENST00000288368	NM_024870.2	18	Gag/Aag	1/40	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.32	2		461	544	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738660	145738660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs897118164	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	155	988	0	ENST00000428558.2:c.2404G>A	p.Val802Met	p.V802M	ENST00000428558	NM_004260.3	802	Gtg/Atg	15/22	1	2	FACETS	0.88	0.804	0.959	0.88	0.804	0.959	CLONAL	1	TRUE	1	0.32	2		988	1101	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044458	5044458	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	81	380	0	ENST00000381652.3:c.406A>C	p.Ile136Leu	p.I136L	ENST00000381652	NM_004972.3	136	Ata/Cta	5/25	1	2	FACETS	0.927	0.819	1	0.927	0.819	1	CLONAL	1	TRUE	1	0.32	2		380	546	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089758	5089758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	31	167	0	ENST00000381652.3:c.2656C>T	p.His886Tyr	p.H886Y	ENST00000381652	NM_004972.3	886	Cat/Tat	20/25	1	2	FACETS	0.828	0.674	1	0.828	0.674	1	CLONAL	1	TRUE	1	0.32	2		167	234	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521547	8521547	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	60	318	0	ENST00000356435.5:c.692-1G>A		p.X231_splice	ENST00000356435		231			1	2	FACETS	0.83	0.716	0.952	0.83	0.716	0.952	CLONAL	1	TRUE	1	0.32	2		318	452	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27205049	27205049	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	74	470	0	ENST00000380036.4:c.2350G>T	p.Ala784Ser	p.A784S	ENST00000380036	NM_000459.3	784	Gcc/Tcc	14/23	1	2	FACETS	0.816	0.715	0.924	0.816	0.715	0.924	CLONAL	1	TRUE	1	0.32	2		470	567	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020790	37020790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	77	414	0	ENST00000358127.4:c.55G>A	p.Gly19Arg	p.G19R	ENST00000358127	NM_001280556.1	19	Gga/Aga	2/10	1	2	FACETS	0.998	0.879	1	0.998	0.879	1	CLONAL	1	TRUE	1	0.32	2		414	482	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97933362	97933362	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs781542763	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	45	270	0	ENST00000289081.3:c.520C>T	p.Arg174Ter	p.R174*	ENST00000289081	NM_000136.2	174	Cga/Tga	6/15	1	2	FACETS	0.764	0.644	0.896	0.764	0.644	0.896	SUBCLONAL	1	TRUE	1	0.32	2		270	368	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232135	98232135	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	49	270	0	ENST00000331920.6:c.1807C>T	p.Arg603Cys	p.R603C	ENST00000331920	NM_000264.3	603	Cgc/Tgc	13/24	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.32	2		270	284	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907028	101907028	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	33	204	0	ENST00000374994.4:c.988G>A	p.Ala330Thr	p.A330T	ENST00000374994	NM_004612.2	330	Gct/Act	6/9	1	2	FACETS	0.818	0.67	0.984	0.818	0.67	0.984	CLONAL	1	TRUE	1	0.32	2		204	252	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249866	110249866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	65	902	0	ENST00000374672.4:c.809C>T	p.Pro270Leu	p.P270L	ENST00000374672	NM_004235.4	270	cCg/cTg	3/5	1	2	FACETS	0.437	0.377	0.502	0.437	0.377	0.502	SUBCLONAL	1	TRUE	1	0.32	2		902	930	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920545	127920545	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	70	336	0	ENST00000373547.4:c.354G>T	p.Gln118His	p.Q118H	ENST00000373547	NM_002721.4	118	caG/caT	4/7	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.32	2		336	430	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759820	133759820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778014	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	134	745	1	ENST00000318560.5:c.2143C>T	p.Arg715Cys	p.R715C	ENST00000318560	NM_005157.4	715	Cgc/Tgc	11/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.32	2		746	779	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782694	135782694	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	64	332	0	ENST00000298552.3:c.1327G>T	p.Gly443Ter	p.G443*	ENST00000298552	NM_001162426.1	443	Gga/Tga	13/23	1	2	FACETS	0.901	0.782	1	0.901	0.782	1	CLONAL	1	TRUE	1	0.32	2		332	444	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137326053	137326053	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	138	873	0	ENST00000481739.1:c.1241G>A	p.Arg414Lys	p.R414K	ENST00000481739	NM_002957.4	414	aGg/aAg	9/10	1	2	FACETS	0.905	0.823	0.992	0.905	0.823	0.992	CLONAL	1	TRUE	1	0.32	2		873	953	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391143	139391143	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	184	974	1	ENST00000277541.6:c.7048C>A	p.Leu2350Met	p.L2350M	ENST00000277541	NM_017617.3	2350	Ctg/Atg	34/34	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.32	2		975	1042	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407897	139407897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1439517621	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	49	795	0	ENST00000277541.6:c.2300C>T	p.Thr767Ile	p.T767I	ENST00000277541	NM_017617.3	767	aCc/aTc	14/34	1	2	FACETS	0.316	0.266	0.371	0.316	0.266	0.371	SUBCLONAL	1	TRUE	1	0.32	2		795	970	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793242	139793242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	155	762	0	ENST00000247668.2:c.50C>T	p.Pro17Leu	p.P17L	ENST00000247668	NM_021138.3	17	cCc/cTc	2/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.32	2		762	875	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139794123	139794123	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs200834553	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	66	347	0	ENST00000247668.2:c.266C>T	p.Ser89Leu	p.S89L	ENST00000247668	NM_021138.3	89	tCg/tTg	3/11	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.32	2		347	406	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802577	139802577	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	166	916	0	ENST00000247668.2:c.422G>A	p.Gly141Asp	p.G141D	ENST00000247668	NM_021138.3	141	gGc/gAc	5/11	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.32	2		916	1020	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913212	39913212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367883774	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	25	399	0	ENST00000378444.4:c.4903G>A	p.Asp1635Asn	p.D1635N	ENST00000378444	NM_001123385.1	1635	Gat/Aat	14/15	1	2	FACETS	0.327	0.257	0.408	0.327	0.257	0.408	SUBCLONAL	1	TRUE	1	0.32	2		399	478	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931652	39931652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	45	595	0	ENST00000378444.4:c.2947G>A	p.Glu983Lys	p.E983K	ENST00000378444	NM_001123385.1	983	Gaa/Aaa	4/15	1	2	FACETS	0.416	0.349	0.491	0.416	0.349	0.491	SUBCLONAL	1	TRUE	1	0.32	2		595	676	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931967	39931967	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768022261	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	51	757	1	ENST00000378444.4:c.2632G>A	p.Val878Ile	p.V878I	ENST00000378444	NM_001123385.1	878	Gta/Ata	4/15	1	2	FACETS	0.387	0.328	0.452	0.387	0.328	0.452	SUBCLONAL	1	TRUE	1	0.32	2		758	824	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932783	39932783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	178	811	1	ENST00000378444.4:c.1816G>A	p.Ala606Thr	p.A606T	ENST00000378444	NM_001123385.1	606	Gcc/Acc	4/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.32	2		812	961	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040949	47040949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781934331	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	69	996	1	ENST00000377604.3:c.1479G>A	p.Met493Ile	p.M493I	ENST00000377604	NM_001204468.1	493	atG/atA	14/24	1	2	FACETS	0.42	0.365	0.481	0.42	0.365	0.481	SUBCLONAL	1	TRUE	1	0.32	2		997	1026	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041371	47041371	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	108	675	0	ENST00000377604.3:c.1715A>G	p.Tyr572Cys	p.Y572C	ENST00000377604	NM_001204468.1	572	tAc/tGc	16/24	1	2	FACETS	0.863	0.775	0.957	0.863	0.775	0.957	CLONAL	1	TRUE	1	0.32	2		675	782	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422655	47422655	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1569319031	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	105	602	1	ENST00000377045.4:c.127G>A	p.Asp43Asn	p.D43N	ENST00000377045	NM_001654.4	43	Gac/Aac	3/16	1	2	FACETS	0.971	0.871	1	0.971	0.871	1	CLONAL	1	TRUE	1	0.32	2		603	676	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426420	47426420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1020990103	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	122	783	0	ENST00000377045.4:c.763C>T	p.Arg255Trp	p.R255W	ENST00000377045	NM_001654.4	255	Cgg/Tgg	9/16	1	2	FACETS	0.846	0.764	0.933	0.846	0.764	0.933	CLONAL	1	TRUE	1	0.32	2		783	901	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410481	63410481	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	106	735	1	ENST00000330258.3:c.2686C>A	p.Leu896Ile	p.L896I	ENST00000330258	NM_152424.3	896	Ctc/Atc	2/2	1	2	FACETS	0.817	0.732	0.907	0.817	0.732	0.907	CLONAL	1	TRUE	1	0.32	2		736	811	SUCCESS
AR	367	MSKCC	GRCh37	X	66765067	66765067	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1257545761	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	101	747	0	ENST00000374690.3:c.79T>C	p.Phe27Leu	p.F27L	ENST00000374690	NM_000044.3	27	Ttc/Ctc	1/8	1	2	FACETS	0.782	0.699	0.871	0.782	0.699	0.871	SUBCLONAL	1	TRUE	1	0.32	2		747	807	SUCCESS
AR	367	MSKCC	GRCh37	X	66766492	66766492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	111	666	1	ENST00000374690.3:c.1504G>A	p.Val502Met	p.V502M	ENST00000374690	NM_000044.3	502	Gtg/Atg	1/8	1	2	FACETS	0.901	0.81	0.997	0.901	0.81	0.997	CLONAL	1	TRUE	1	0.32	2		667	770	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339704	70339704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	88	596	0	ENST00000374080.3:c.373C>T	p.Pro125Ser	p.P125S	ENST00000374080		125	Cca/Tca	3/45	1	2	FACETS	0.77	0.682	0.864	0.77	0.682	0.864	SUBCLONAL	1	TRUE	1	0.32	2		596	714	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347221	70347221	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	77	539	0	ENST00000374080.3:c.2885C>T	p.Ser962Phe	p.S962F	ENST00000374080		962	tCc/tTc	21/45	1	2	FACETS	0.739	0.649	0.836	0.739	0.649	0.836	SUBCLONAL	1	TRUE	1	0.32	2		539	651	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354226	70354226	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1423751717	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	100	712	2	ENST00000374080.3:c.4637C>T	p.Thr1546Met	p.T1546M	ENST00000374080		1546	aCg/aTg	34/45	1	2	FACETS	0.768	0.685	0.856	0.768	0.685	0.856	SUBCLONAL	1	TRUE	1	0.32	2		714	814	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356808	70356808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	105	692	1	ENST00000374080.3:c.5480G>A	p.Gly1827Asp	p.G1827D	ENST00000374080		1827	gGt/gAt	38/45	1	2	FACETS	0.792	0.709	0.88	0.792	0.709	0.88	SUBCLONAL	1	TRUE	1	0.32	2		693	829	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937989	76937989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	61	456	0	ENST00000373344.5:c.2759G>A	p.Gly920Asp	p.G920D	ENST00000373344	NM_000489.3	920	gGt/gAt	9/35	1	2	FACETS	0.713	0.615	0.818	0.713	0.615	0.818	SUBCLONAL	1	TRUE	1	0.32	2		456	535	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184052	123184052	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	58	289	0	ENST00000218089.9:c.910A>C	p.Ile304Leu	p.I304L	ENST00000218089	NM_001042749.1	304	Att/Ctt	11/35	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.32	2		289	348	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196786	123196786	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	52	361	0	ENST00000218089.9:c.1673A>C	p.Asp558Ala	p.D558A	ENST00000218089	NM_001042749.1	558	gAt/gCt	18/35	1	2	FACETS	0.721	0.614	0.837	0.721	0.614	0.837	SUBCLONAL	1	TRUE	1	0.32	2		361	451	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205096	123205096	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	65	428	0	ENST00000218089.9:c.2456C>A	p.Ser819Tyr	p.S819Y	ENST00000218089	NM_001042749.1	819	tCt/tAt	25/35	1	2	FACETS	0.848	0.737	0.968	0.848	0.737	0.968	CLONAL	1	TRUE	1	0.32	2		428	479	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224734	123224734	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	74	372	0	ENST00000218089.9:c.3498A>C	p.Arg1166Ser	p.R1166S	ENST00000218089	NM_001042749.1	1166	agA/agC	32/35	1	2	FACETS	0.992	0.872	1	0.992	0.872	1	CLONAL	1	TRUE	1	0.32	2		372	466	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224774	123224774	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	84	382	0	ENST00000218089.9:c.3538A>C	p.Met1180Leu	p.M1180L	ENST00000218089	NM_001042749.1	1180	Atg/Ctg	32/35	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.32	2		382	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577525	7577527	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0047259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	252	543	0	ENST00000269305.4:c.754_756del	p.Leu252del	p.L252del	ENST00000269305	NM_001126112.2	252	CTC/-	7/11	0.325397040139511	2	FACETS	0.816	0.765	0.869	0.816	0.765	0.869	CLONAL	2	TRUE	0	0.333802330103563	2		543	925	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0047260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	25	309	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.796	0.626	0.993	0.796	0.626	0.993	CLONAL	1	TRUE	1	0.13	2		309	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0047260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	44	541	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	0.967	0.809	1	0.967	0.809	1	CLONAL	1	TRUE	1	0.13	2		542	700	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360929	118360929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	38	463	0	ENST00000534358.1:c.4661C>T	p.Ser1554Leu	p.S1554L	ENST00000534358	NM_005933.3	1554	tCa/tTa	13/36	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.13	2		463	565	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417834	138417834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs912490737	NA	P-0047270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	122	386	0	ENST00000289153.2:c.1685G>A	p.Arg562Gln	p.R562Q	ENST00000289153	NM_006219.2	562	cGa/cAa	11/22	0.362747798913281	3	FACETS	1	0.956	1	0.55	0.497	0.605	CLONAL	1	TRUE	1	0.362747798913281	3		386	723	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0047284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	55	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.238562450206115	4	FACETS	0.975	0.841	1	0.975	0.841	1	CLONAL	2	FALSE	2	0.265409658368754	4		511	269	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0047284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	101	277	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.863	0.782	0.946	1	0.99	1	CLONAL	3	FALSE	1	0.265409658368754	2		277	294	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615036	43615036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1345166214	NA	P-0047284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	92	905	2	ENST00000355710.3:c.2450G>A	p.Arg817His	p.R817H	ENST00000355710	NM_020975.4	817	cGc/cAc	14/20	0.265409658368754	0	FACETS	0.707	0.64	0.777			1	SUBCLONAL	3	FALSE	0	0.265409658368754	0		907	240	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89846310	89846310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148154682	NA	P-0047284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	38	682	2	ENST00000389301.3:c.1682C>T	p.Thr561Met	p.T561M	ENST00000389301	NM_000135.2	561	aCg/aTg	18/43	0.142259102615612	4	FACETS	0.995	0.825	1	0.498	0.412	0.593	INDETERMINATE	1	FALSE	2	0.265409658368754	4		684	364	SUCCESS
REL	5966	MSKCC	GRCh37	2	61128198	61128198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	36	221	0	ENST00000295025.8:c.374C>T	p.Ala125Val	p.A125V	ENST00000295025	NM_002908.2	125	gCa/gTa	4/11	0.142259102615612	4	FACETS	1	0.845	1	1	0.845	1	INDETERMINATE	2	FALSE	2	0.265409658368754	4		221	169	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044506	128044506	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	72	668	0	ENST00000285398.2:c.1115A>T	p.Glu372Val	p.E372V	ENST00000285398	NM_000122.1	372	gAg/gTg	8/15	NA	2	FACETS	0.939	0.828	1			1	INDETERMINATE	2	FALSE	NA	0.265409658368754	2		668	289	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136292	202136292	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	87	499	0	ENST00000358485.4:c.536T>C	p.Phe179Ser	p.F179S	ENST00000358485	NM_001080125.1	179	tTt/tCt	3/9	0.142259102615612	4	FACETS	0.878	0.785	0.975	1	0.975	1	INDETERMINATE	3	FALSE	2	0.265409658368754	4		499	315	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430227	181430227	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	11	489	0	ENST00000325404.1:c.79G>A	p.Ala27Thr	p.A27T	ENST00000325404	NM_003106.3	27	Gcg/Acg	1/1	0.238562450206115	4	FACETS	0.593	0.41	0.819	0.296	0.205	0.41	SUBCLONAL	1	FALSE	2	0.265409658368754	4		489	177	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0047284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	48	222	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	NA	2	FACETS	1	0.949	1			1	INDETERMINATE	2	FALSE	NA	0.265409658368754	2		222	147	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453149	140453149	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913361	NA	P-0047284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	62	328	0	ENST00000288602.6:c.1786G>T	p.Gly596Cys	p.G596C	ENST00000288602	NM_004333.4	596	Ggt/Tgt	15/18	NA	2	FACETS	1	0.92	1			1	INDETERMINATE	2	FALSE	NA	0.265409658368754	2		328	219	SUCCESS
APC	324	MSKCC	GRCh37	5	112137009	112137011	+	frameshift_variant	Frame_Shift_Del	DEL	CAT	CAT	G	novel	NA	P-0047284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	96	407	0	ENST00000257430.4:c.763_765delinsG	p.His255GlyfsTer3	p.H255Gfs*3	ENST00000257430	NM_000038.5	255	CAT/G	8/16	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	2	FALSE	NA	0.265409658368754	2		407	295	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	134	516	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.951	0.872	1	0.951	0.872	1	CLONAL	1	TRUE	1	0.67742435127595	2		516	416	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479193	50479193	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	75	490	0	ENST00000394963.4:c.41G>C	p.Gly14Ala	p.G14A	ENST00000394963	NM_003076.4	14	gGc/gCc	1/13	0.477275848445699	1	FACETS	0.283	0.248	0.32	0.283	0.248	0.32	SUBCLONAL	1	TRUE	0	0.67742435127595	1		490	518	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56376756	56376756	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	24	339	0	ENST00000348428.3:c.796C>A	p.Pro266Thr	p.P266T	ENST00000348428	NM_006785.3	266	Cca/Aca	5/17	1	2	FACETS	0.204	0.159	0.255	0.204	0.159	0.255	SUBCLONAL	1	TRUE	1	0.53	2		339	445	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228280	53228280	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	23	367	0	ENST00000375401.3:c.2122A>T	p.Ile708Phe	p.I708F	ENST00000375401	NM_004187.3	708	Atc/Ttc	15/26	1	1	FACETS	0.211	0.164	0.265	0.211	0.164	0.265	SUBCLONAL	1	TRUE	0	0.53	1		367	302	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528075	157528075	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	156	618	0	ENST00000346085.5:c.5800A>G	p.Ile1934Val	p.I1934V	ENST00000346085	NM_020732.3	1934	Atc/Gtc	20/20	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.612263155627216	2		618	502	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155695	56155695	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	110	418	0	ENST00000399503.3:c.789del	p.Lys263AsnfsTer7	p.K263Nfs*7	ENST00000399503	NM_005921.1	263	Aaa/aa	3/20	1	2	FACETS	0.938	0.851	1	0.938	0.851	1	CLONAL	1	TRUE	1	0.612263155627216	2		418	383	SUCCESS
APC	324	MSKCC	GRCh37	5	112175882	112175890	+	frameshift_variant	Frame_Shift_Del	DEL	AATGACAAT	AATGACAAT	G	novel	NA	P-0047288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	49	264	0	ENST00000257430.4:c.4591_4599delinsG	p.Asn1531GlyfsTer3	p.N1531Gfs*3	ENST00000257430	NM_000038.5	1531	AATGACAAT/G	16/16	0.612263155627216	1	FACETS	0.957	0.836	1	0.957	0.836	1	CLONAL	1	TRUE	0	0.612263155627216	1		264	116	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433847	78433848	+	splice_donor_variant	Splice_Site	DEL	AC	AC	-	rs1477051807	NA	P-0047289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	41	313	1	ENST00000370768.2:c.250+1_250+2del		p.X84_splice	ENST00000370768	NM_003902.3	84			1	2	FACETS	0.635	0.532	0.749	0.635	0.532	0.749	SUBCLONAL	1	TRUE	1	0.451246774832872	2		314	286	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591901	48591901	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	64	458	0	ENST00000342988.3:c.1064A>T	p.Asp355Val	p.D355V	ENST00000342988	NM_005359.5	355	gAc/gTc	9/12	0.341897993169965	1	FACETS	0.495	0.429	0.565	0.495	0.429	0.565	SUBCLONAL	1	TRUE	0	0.451246774832872	1		458	444	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156037	106156037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	98	326	0	ENST00000380013.4:c.938C>T	p.Thr313Ile	p.T313I	ENST00000380013	NM_001127208.2	313	aCc/aTc	3/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.451246774832872	2		326	383	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641096	93641096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	62	554	0	ENST00000375746.1:c.1442G>A	p.Gly481Asp	p.G481D	ENST00000375746	NM_001174167.1	481	gGc/gAc	11/14	0.374660557528266	2	FACETS	0.476	0.411	0.547	0.238	0.205	0.274	SUBCLONAL	1	TRUE	0	0.451246774832872	2		554	577	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932447	39932447	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	33	377	0	ENST00000378444.4:c.2152G>A	p.Asp718Asn	p.D718N	ENST00000378444	NM_001123385.1	718	Gat/Aat	4/15	0.427979949419933	2	FACETS	0.229	0.186	0.278			1	SUBCLONAL	1	TRUE	NA	0.451246774832872	2		377	638	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398285	+	missense_variant	Missense_Mutation	ONP	CACC	CACC	AACA	novel	NA	P-0047289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	169	448	0	ENST00000311936.3:c.34_37delinsTGTT	p.Gly12_Gly13delinsCysCys	p.G12_G13delinsCC	ENST00000311936	NM_004985.3	12	GGTGgc/TGTTgc	2/5	0.443108983592543	2	FACETS	0.932	0.867	0.997	0.932	0.867	0.997	CLONAL	2	TRUE	0	0.451246774832872	2		448	402	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	68	516	0				ENST00000310581	NM_198253.2	-/1132			0.394235068367446	4	FACETS	0.864	0.764	0.968	0.864	0.764	0.968	CLONAL	2	TRUE	2	0.595229733884063	4		516	211	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0047290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	175	258	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.449552873781083	6	FACETS	0.878	0.816	0.942	0.878	0.816	0.942	CLONAL	3	TRUE	3	0.595229733884063	6		258	489	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0047290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	229	467	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.377839808527308	3	FACETS	0.883	0.839	0.926	0.883	0.839	0.926	CLONAL	3	TRUE	0	0.595229733884063	3		467	377	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457716	149457716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	205	636	1	ENST00000286301.3:c.688G>A	p.Asp230Asn	p.D230N	ENST00000286301	NM_005211.3	230	Gat/Aat	5/22	0.571997465108252	2	FACETS	0.928	0.877	0.98	0.928	0.877	0.98	CLONAL	2	TRUE	0	0.595229733884063	2		637	371	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437766	52437766	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	134	729	0	ENST00000460680.1:c.1395C>G	p.Ile465Met	p.I465M	ENST00000460680	NM_004656.3	465	atC/atG	13/17	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.595229733884063	2		729	321	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	162	274	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	0.595229733884063	2	FACETS	0.852	0.812	0.89			1	CLONAL	3	TRUE	NA	0.595229733884063	2		274	213	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944562	40944562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868189942	NA	P-0047290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	230	451	1	ENST00000373198.4:c.1940C>T	p.Ser647Leu	p.S647L	ENST00000373198	NM_133170.3	647	tCg/tTg	12/32	0.349831633693119	6	FACETS	0.926	0.875	0.977	0.926	0.875	0.977	INDETERMINATE	4	TRUE	2	0.595229733884063	6		452	457	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066739	5066739	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1340580425	NA	P-0047290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	93	260	0	ENST00000381652.3:c.1276C>T	p.Arg426Ter	p.R426*	ENST00000381652	NM_004972.3	426	Cga/Tga	10/25	0.595229733884063	2	FACETS	0.755	0.686	0.824	0.755	0.686	0.824	SUBCLONAL	2	TRUE	0	0.595229733884063	2		260	207	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307520	118307520	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	71	549	0	ENST00000534358.1:c.293C>A	p.Ser98Ter	p.S98*	ENST00000534358	NM_005933.3	98	tCa/tAa	1/36	0.595229733884063	3	FACETS	0.741	0.649	0.838	0.37	0.324	0.419	SUBCLONAL	1	TRUE	1	0.595229733884063	3		549	418	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272363	15272363	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1409708568	NA	P-0047290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	205	844	0	ENST00000263388.2:c.6076C>G	p.Gln2026Glu	p.Q2026E	ENST00000263388	NM_000435.2	2026	Caa/Gaa	33/33	0.313095190324475	5	FACETS	1	0.967	1	0.707	0.659	0.755	INDETERMINATE	2	TRUE	2	0.595229733884063	5		844	615	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40742259	40742259	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	182	671	0	ENST00000392038.2:c.865A>G	p.Ile289Val	p.I289V	ENST00000392038	NM_001626.4	289	Atc/Gtc	10/14	0.313095190324475	5	FACETS	1	0.978	1	0.752	0.699	0.806	INDETERMINATE	2	TRUE	2	0.595229733884063	5		671	513	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920683	96920683	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	145	423	0	ENST00000258439.3:c.297C>G	p.Phe99Leu	p.F99L	ENST00000258439	NM_001193304.2	99	ttC/ttG	3/4	0.365163794455864	5	FACETS	0.917	0.842	0.994	0.611	0.561	0.663	CLONAL	2	TRUE	2	0.595229733884063	5		423	503	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437298	52437299	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0047290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	161	631	0	ENST00000460680.1:c.1745_1746delinsTT	p.Ser582Phe	p.S582F	ENST00000460680	NM_004656.3	582	tCC/tTT	14/17	NA	2	FACETS	0.942	0.884	1			1	INDETERMINATE	2	TRUE	NA	0.595229733884063	2		631	287	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230889	66230889	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	58	319	0	ENST00000273854.3:c.2082G>C	p.Leu694Phe	p.L694F	ENST00000273854	NM_004439.5	694	ttG/ttC	12/18	0.113573435706159	4	FACETS	0.972	0.853	1	0.972	0.853	1	INDETERMINATE	2	TRUE	2	0.595229733884063	4		319	160	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207546	29207546	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	93	723	1	ENST00000240100.2:c.250G>A	p.Glu84Lys	p.E84K	ENST00000240100	NM_001394.6	84	Gag/Aag	1/4	0.179334836503152	3	FACETS	0.885	0.791	0.985	0.295	0.263	0.329	INDETERMINATE	1	TRUE	0	0.595229733884063	3		724	458	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225109	53225109	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	202	280	0	ENST00000375401.3:c.3109G>A	p.Asp1037Asn	p.D1037N	ENST00000375401	NM_004187.3	1037	Gat/Aat	20/26	0.595229733884063	2	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.595229733884063	2		280	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781504	NA	P-0047292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	54	840	0	ENST00000269305.4:c.314G>T	p.Gly105Val	p.G105V	ENST00000269305	NM_001126112.2	105	gGc/gTc	4/11	1	2	FACETS	0.4	0.34	0.465	0.4	0.34	0.465	SUBCLONAL	1	TRUE	1	0.28	2		840	965	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139794922	139794922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs551577118	NA	P-0047292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	46	653	1	ENST00000247668.2:c.316G>A	p.Val106Ile	p.V106I	ENST00000247668	NM_021138.3	106	Gtc/Atc	4/11	1	2	FACETS	0.412	0.346	0.486	0.412	0.346	0.486	SUBCLONAL	1	TRUE	1	0.28	2		654	797	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130279	2130279	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	62	895	0	ENST00000219476.3:c.3511G>C	p.Ala1171Pro	p.A1171P	ENST00000219476	NM_000548.3	1171	Gct/Cct	30/42	0.164773291582243	2	FACETS	0.419	0.36	0.483	0.209	0.18	0.242	INDETERMINATE	1	TRUE	0	0.28	2		895	1058	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223716	36223716	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	65	1059	0	ENST00000222270.7:c.6266G>T	p.Gly2089Val	p.G2089V	ENST00000222270	NM_014727.1	2089	gGa/gTa	28/37	1	2	FACETS	0.446	0.385	0.512	0.446	0.385	0.512	SUBCLONAL	1	TRUE	1	0.28	2		1059	1042	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661182	227661182	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	60	841	0	ENST00000305123.5:c.2273A>G	p.His758Arg	p.H758R	ENST00000305123	NM_005544.2	758	cAc/cGc	1/2	1	2	FACETS	0.398	0.341	0.46	0.398	0.341	0.46	SUBCLONAL	1	TRUE	1	0.28	2		841	1077	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572604	64572604	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894264	NA	P-0047293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	293	794	1	ENST00000312049.6:c.1252G>T	p.Asp418Tyr	p.D418Y	ENST00000312049	NM_130799.2	418	Gac/Tac	9/10	0.822677479708692	1	FACETS	0.947	0.908	0.984	0.947	0.908	0.984	CLONAL	1	TRUE	0	0.822677479708692	1		795	443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs786203436	NA	P-0047304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	275	948	1	ENST00000269305.4:c.487T>G	p.Tyr163Asp	p.Y163D	ENST00000269305	NM_001126112.2	163	Tac/Gac	5/11	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.677270031714346	2		949	334	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486192	99486192	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	79	576	0	ENST00000268035.6:c.3498C>A	p.Tyr1166Ter	p.Y1166*	ENST00000268035	NM_000875.3	1166	taC/taA	19/21	NA	2	FACETS	1	0.957	1			1	INDETERMINATE	1	TRUE	NA	0.677270031714346	2		576	206	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938292	76938292	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	89	469	0	ENST00000373344.5:c.2456C>A	p.Ser819Ter	p.S819*	ENST00000373344	NM_000489.3	819	tCa/tAa	9/35	0.615812601711699	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.677270031714346	1		469	173	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0047306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	370	658	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.364985906329018	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.364985906329018	2		658	996	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350146	89350146	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs575811373	NA	P-0047306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	274	780	0	ENST00000301030.4:c.2804C>T	p.Ser935Leu	p.S935L	ENST00000301030	NM_001256183.1	935	tCg/tTg	9/13	0.312221497061437	2	FACETS	0.854	0.804	0.905	0.854	0.804	0.905	CLONAL	2	TRUE	0	0.364985906329018	2		780	879	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612061	189612061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777373892	NA	P-0047306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	61	538	0	ENST00000264731.3:c.1813C>T	p.Arg605Trp	p.R605W	ENST00000264731	NM_003722.4	605	Cgg/Tgg	14/14	0.364985906329018	3	FACETS	0.403	0.346	0.464	0.201	0.173	0.232	SUBCLONAL	1	TRUE	1	0.364985906329018	3		538	982	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214636	5214636	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532712500	NA	P-0047306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	171	950	0	ENST00000357368.4:c.4430G>A	p.Arg1477His	p.R1477H	ENST00000357368	NM_002850.3	1477	cGt/cAt	29/38	0.364985906329018	1	FACETS	0.841	0.774	0.911	0.841	0.774	0.911	CLONAL	1	TRUE	0	0.364985906329018	1		950	911	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180357	27180357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	84	323	0	ENST00000380036.4:c.1021G>A	p.Glu341Lys	p.E341K	ENST00000380036	NM_000459.3	341	Gag/Aag	7/23	0.305132639088065	1	FACETS	0.787	0.698	0.882	0.787	0.698	0.882	SUBCLONAL	1	TRUE	0	0.364985906329018	1		323	478	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612905	228612905	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	276	662	0	ENST00000366696.1:c.122G>A	p.Arg41His	p.R41H	ENST00000366696	NM_003493.2	41	cGc/cAc	1/1	0.364985906329018	3	FACETS	0.933	0.878	0.99	0.622	0.585	0.66	CLONAL	2	TRUE	0	0.364985906329018	3		662	958	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259306	36259307	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCGC	novel	NA	P-0047306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	90	369	0	ENST00000300305.3:c.184_185insGCGG	p.Asp62GlyfsTer77	p.D62Gfs*77	ENST00000300305		62	gac/gGCGGac	3/8	0.364985906329018	2	FACETS	1	0.968	1	0.615	0.549	0.684	CLONAL	1	TRUE	0	0.364985906329018	2		369	401	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615635	100615635	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	40	512	0	ENST00000308731.7:c.697C>G	p.Leu233Val	p.L233V	ENST00000308731	NM_000061.2	233	Cta/Gta	8/19	0.287476655018013	1	FACETS	0.259	0.214	0.308	0.259	0.214	0.308	SUBCLONAL	1	TRUE	0	0.364985906329018	1		512	693	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0047307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	89	592	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.400989001424012	2	FACETS	1	0.952	1	0.555	0.497	0.616	CLONAL	1	TRUE	0	0.482863657269844	2		592	332	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711891	89711891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	58	406	0	ENST00000371953.3:c.509G>A	p.Ser170Asn	p.S170N	ENST00000371953	NM_000314.4	170	aGt/aAt	6/9	0.400989001424012	2	FACETS	1	0.949	1	0.592	0.516	0.671	CLONAL	1	TRUE	0	0.482863657269844	2		406	203	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589600	67589601	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0047307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	21	147	0	ENST00000274335.5:c.1363_1364del	p.Gln455ValfsTer9	p.Q455Vfs*9	ENST00000274335		455	CAg/g	10/15	0.29571202514303	2	FACETS	0.713	0.556	0.89	0.356	0.278	0.445	SUBCLONAL	1	TRUE	0	0.482863657269844	2		147	122	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675082	40675082	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1307486609	NA	P-0047307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	144	820	0	ENST00000249776.8:c.46A>G	p.Thr16Ala	p.T16A	ENST00000249776	NM_033286.3	16	Aca/Gca	1/9	0.41474257204356	3	FACETS	1	0.986	1	0.467	0.428	0.507	CLONAL	1	TRUE	0	0.482863657269844	3		820	529	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868115	56868115	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	100	625	0	ENST00000308159.5:c.1613A>C	p.Lys538Thr	p.K538T	ENST00000308159	NM_014669.4	538	aAg/aCg	14/22	0.384404510734926	3	FACETS	1	0.938	1	0.354	0.317	0.393	CLONAL	1	TRUE	0	0.482863657269844	3		625	484	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748473	43748476	+	frameshift_variant	Frame_Shift_Del	DEL	TCAG	TCAG	-	novel	NA	P-0047307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	30	243	0	ENST00000523873.1:c.428_431del	p.Ser143PhefsTer30	p.S143Ffs*30	ENST00000523873		143	TCAGtt/tt	6/8	0.482863657269844	5	FACETS	0.821	0.664	0.997	0.41	0.332	0.499	CLONAL	1	TRUE	3	0.482863657269844	5		243	261	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6438311	6438311	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	72	457	0	ENST00000356142.4:c.244A>G	p.Lys82Glu	p.K82E	ENST00000356142	NM_018890.3	82	Aag/Gag	4/7	0.351290063357891	5	FACETS	1	0.958	1	0.406	0.356	0.46	CLONAL	1	TRUE	2	0.482863657269844	5		457	422	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741782	145741782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	209	931	0	ENST00000428558.2:c.721G>A	p.Ala241Thr	p.A241T	ENST00000428558	NM_004260.3	241	Gcc/Acc	5/22	0.393731097744242	4	FACETS	0.856	0.802	0.91	0.856	0.802	0.91	CLONAL	3	TRUE	1	0.482863657269844	4		931	500	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061141	38061144	+	frameshift_variant	Frame_Shift_Del	DEL	CCGC	CCGC	TT	novel	NA	P-0047307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	44	227	0	ENST00000250448.2:c.845_848delinsAA	p.Ser282LysfsTer10	p.S282Kfs*10	ENST00000250448	NM_004496.3	282	aGCGGg/aAAg	2/2	0.463076951805475	4	FACETS	0.79	0.673	0.915	0.395	0.336	0.458	CLONAL	2	TRUE	0	0.482863657269844	4		227	171	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867546	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs11466445	NA	P-0047308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	18	7	0	ENST00000374994.4:c.70_78del	p.Ala24_Ala26del	p.A24_A26del	ENST00000374994	NM_004612.2	17	ctGGCGGCGGCg/ctg	1/9	1	2	FACETS	0.807	0.635	0.99	0.807	0.635	0.99	CLONAL	1	TRUE	1	0.91	2		7	49	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132644	11132644	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0047308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	707	876	0	ENST00000358026.2:c.2859+1G>A		p.X953_splice	ENST00000358026	NM_001128849.1	953			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.91	2		876	1545	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135032	11135033	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0047308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	607	767	30	ENST00000358026.2:c.3000dup	p.Ser1001ValfsTer20	p.S1001Vfs*20	ENST00000358026	NM_001128849.1	1000	atg/atGg	21/36	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.91	2		797	1332	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144049	11144051	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0047310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	91	656	1	ENST00000358026.2:c.3634_3636del	p.Glu1212del	p.E1212del	ENST00000358026	NM_001128849.1	1210	gtGGAg/gtg	26/36	1	2	FACETS	0.717	0.641	0.798	0.717	0.641	0.798	SUBCLONAL	1	TRUE	1	0.625088361366475	2		657	406	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919601	96919601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144326855	NA	P-0047310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	79	575	0	ENST00000258439.3:c.662C>T	p.Pro221Leu	p.P221L	ENST00000258439	NM_001193304.2	221	cCg/cTg	4/4	1	2	FACETS	0.667	0.59	0.748	0.667	0.59	0.748	SUBCLONAL	1	TRUE	1	0.625088361366475	2		575	379	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188207	10188207	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs869025640	NA	P-0047310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	89	449	0	ENST00000256474.2:c.351del	p.Trp117CysfsTer42	p.W117Cfs*42	ENST00000256474	NM_000551.3	117	tGg/tg	2/3	0.49803159397924	1	FACETS	0.739	0.664	0.816	0.739	0.664	0.816	SUBCLONAL	1	TRUE	0	0.625088361366475	1		449	265	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637717	52637717	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	16	395	0	ENST00000394830.3:c.2599G>T	p.Glu867Ter	p.E867*	ENST00000394830	NM_018313.4	867	Gaa/Taa	18/30	1	2	FACETS	1	0.831	1	1	0.948	1	CLONAL	3	TRUE	1	0.327114383457406	2		395	31	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578232	7578232	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0047311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	17	830	0	ENST00000269305.4:c.617T>A	p.Leu206Ter	p.L206*	ENST00000269305	NM_001126112.2	206	tTg/tAg	6/11	0.327114383457406	1	FACETS	1	0.83	1	1	0.83	1	CLONAL	1	TRUE	0	0.327114383457406	1		830	78	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661201	227661201	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	27	1153	1	ENST00000305123.5:c.2254G>T	p.Gly752Cys	p.G752C	ENST00000305123	NM_005544.2	752	Ggc/Tgc	1/2	1	2	FACETS	0.943	0.758	1	0.943	0.758	1	CLONAL	1	TRUE	1	0.327114383457406	2		1154	175	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0047312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	67	277	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.259753950887087	1	FACETS	0.698	0.609	0.792	0.698	0.609	0.792	SUBCLONAL	1	TRUE	0	0.40781342246381	1		277	375	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0047312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	68	336	1	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.40781342246381	2		337	304	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0047312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	101	798	2	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.78	0.698	0.867	0.78	0.698	0.867	SUBCLONAL	1	TRUE	1	0.40781342246381	2		800	635	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	89	419	0	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	0.40781342246381	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.40781342246381	1		419	306	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900984	114900984	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs778855667	NA	P-0047312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	122	692	1	ENST00000543371.1:c.598del	p.Leu200SerfsTer25	p.L200Sfs*25	ENST00000543371	NM_001198531.1	198	caC/ca	6/14	1	2	FACETS	0.932	0.844	1	0.932	0.844	1	CLONAL	1	TRUE	1	0.40781342246381	2		693	642	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905960	50905960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777944185	NA	P-0047312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	181	1149	0	ENST00000440232.2:c.932G>A	p.Arg311His	p.R311H	ENST00000440232	NM_002691.3	311	cGc/cAc	8/27	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.40781342246381	2		1149	845	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035986	47035986	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0047312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	265	398	0	ENST00000377604.3:c.663+1G>T		p.X221_splice	ENST00000377604	NM_001204468.1	221			0.390112275567929	2	FACETS	0.908	0.864	0.952			1	CLONAL	3	TRUE	NA	0.40781342246381	2		398	477	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105921	27105921	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	114	608	0	ENST00000324856.7:c.5532G>A	p.Trp1844Ter	p.W1844*	ENST00000324856	NM_006015.4	1844	tgG/tgA	20/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.40781342246381	2		608	517	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118907	70118907	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	136	871	0	ENST00000245479.2:c.479G>A	p.Arg160Gln	p.R160Q	ENST00000245479	NM_000346.3	160	cGg/cAg	2/3	1	2	FACETS	0.949	0.864	1	0.949	0.864	1	CLONAL	1	TRUE	1	0.40781342246381	2		871	703	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450390	50450390	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	78	620	0	ENST00000331340.3:c.574C>A	p.Leu192Met	p.L192M	ENST00000331340	NM_006060.4	192	Ctg/Atg	5/8	0.40781342246381	3	FACETS	0.795	0.7	0.898	0.398	0.35	0.449	SUBCLONAL	1	TRUE	1	0.40781342246381	3		620	579	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0047313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	189	805	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.394398547445099	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.394398547445099	1		805	677	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0047313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	163	930	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.394398547445099	1	FACETS	0.947	0.871	1	0.947	0.871	1	CLONAL	1	TRUE	0	0.394398547445099	1		930	701	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39311710	39311710	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs151267022	NA	P-0047313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	120	790	0	ENST00000373001.3:c.949A>G	p.Ile317Val	p.I317V	ENST00000373001	NM_022157.3	317	Att/Gtt	6/7	0.235998391784873	3	FACETS	0.858	0.775	0.946	0.429	0.387	0.473	INDETERMINATE	1	TRUE	1	0.394398547445099	3		790	849	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979345	93979345	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	59	466	0	ENST00000369303.4:c.1483A>T	p.Thr495Ser	p.T495S	ENST00000369303	NM_004440.3	495	Acc/Tcc	7/17	1	2	FACETS	0.883	0.764	1	0.883	0.764	1	CLONAL	1	TRUE	1	0.394398547445099	2		466	339	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357218	70357220	+	frameshift_variant	Frame_Shift_Del	DEL	TCG	TCG	C	novel	NA	P-0047313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	167	729	0	ENST00000374080.3:c.5733_5735delinsC	p.Arg1912ProfsTer138	p.R1912Pfs*138	ENST00000374080		1911	ctTCGc/ctCc	39/45	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.394398547445099	2		729	708	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0047314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	149	470	0				ENST00000310581	NM_198253.2	-/1132			0.397970807536774	1	FACETS	0.612	0.569	0.654	0.612	0.569	0.654	INDETERMINATE	1	FALSE	0	0.891291717826919	1		470	303	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0047314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16522	409	758	0	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.891291717826919	29	FACETS	0.706	0.666	0.748	0.025	0.023	0.027	SUBCLONAL	1	FALSE	1	0.891291717826919	29		758	16931	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276477	115276477	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	278	392	0	ENST00000438362.2:c.851G>T	p.Gly284Val	p.G284V	ENST00000438362	NM_001242891.1	284	gGt/gTt	9/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.891291717826919	2		392	613	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100093	11100093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502078	NA	P-0047314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	266	641	0	ENST00000358026.2:c.1219C>T	p.Leu407Phe	p.L407F	ENST00000358026	NM_001128849.1	407	Ctc/Ttc	7/36	0.388985734824482	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.891291717826919	0		641	530	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0047315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	149	164	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.411901423770569	3	FACETS	0.999	0.922	1	0.999	0.922	1	CLONAL	2	TRUE	1	0.450265587139026	3		164	406	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444401	50444401	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	106	475	1	ENST00000331340.3:c.331C>T	p.Arg111Ter	p.R111*	ENST00000331340	NM_006060.4	111	Cga/Tga	4/8	0.411901423770569	3	FACETS	1	0.954	1	0.551	0.496	0.61	CLONAL	1	TRUE	1	0.450265587139026	3		476	523	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336095	73336095	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780575971	NA	P-0047315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	92	227	0	ENST00000377767.4:c.2308C>T	p.Pro770Ser	p.P770S	ENST00000377767	NM_014953.3	770	Cca/Tca	17/21	0.450265587139026	5	FACETS	1	0.952	1	0.734	0.659	0.811	CLONAL	2	TRUE	2	0.450265587139026	5		227	311	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372693	81372693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	144	327	0	ENST00000222390.5:c.841G>A	p.Glu281Lys	p.E281K	ENST00000222390	NM_000601.4	281	Gag/Aag	7/18	0.411901423770569	3	FACETS	0.931	0.857	1	0.931	0.857	1	CLONAL	2	TRUE	1	0.450265587139026	3		327	421	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295217	1295217	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs796849347	NA	P-0047315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	274	279	0				ENST00000310581	NM_198253.2	-/1132			0.450265587139026	3	FACETS	1	0.986	1	1	0.995	1	CLONAL	3	TRUE	1	0.450265587139026	3		279	457	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813330	102813330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	255	749	1	ENST00000307046.8:c.359C>T	p.Ser120Phe	p.S120F	ENST00000307046	NM_001111285.1	120	tCt/tTt	3/4	0.411901423770569	3	FACETS	0.97	0.913	1	0.97	0.913	1	CLONAL	2	TRUE	1	0.450265587139026	3		750	715	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875711	56875711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	118	615	0	ENST00000308159.5:c.2315C>T	p.Ser772Phe	p.S772F	ENST00000308159	NM_014669.4	772	tCc/tTc	21/22	0.392873541167708	3	FACETS	0.887	0.801	0.978	0.443	0.4	0.489	CLONAL	1	TRUE	1	0.450265587139026	3		615	724	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992192	72992192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	132	951	0	ENST00000268489.5:c.1853C>T	p.Pro618Leu	p.P618L	ENST00000268489	NM_006885.3	618	cCc/cTc	2/10	0.392873541167708	3	FACETS	0.817	0.742	0.897	0.409	0.371	0.449	CLONAL	1	TRUE	1	0.450265587139026	3		951	879	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131398	202131399	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0047315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	77	530	0	ENST00000358485.4:c.366_367delinsAA	p.Glu123Lys	p.E123K	ENST00000358485	NM_001080125.1	122	aaGGag/aaAAag	2/9	0.411901423770569	3	FACETS	0.831	0.732	0.938	0.416	0.366	0.469	CLONAL	1	TRUE	1	0.450265587139026	3		530	504	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643972	52643972	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0047315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	108	251	0	ENST00000394830.3:c.1925-1G>A		p.X642_splice	ENST00000394830	NM_018313.4	642			0.450265587139026	2	FACETS	0.983	0.9	1	0.983	0.9	1	CLONAL	2	TRUE	0	0.450265587139026	2		251	244	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384688	84384688	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs114513239	NA	P-0047315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	252	432	0	ENST00000321945.7:c.755G>A	p.Arg252Gln	p.R252Q	ENST00000321945	NM_139076.2	252	cGa/cAa	8/9	0.303664608841421	4	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	2	0.450265587139026	4		432	808	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591128	67591128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	94	293	0	ENST00000274335.5:c.1721G>A	p.Arg574Lys	p.R574K	ENST00000274335		574	aGa/aAa	12/15	0.179171599824575	4	FACETS	0.917	0.825	1	0.612	0.55	0.676	INDETERMINATE	2	TRUE	1	0.450265587139026	4		293	330	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	234	349	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.265559083952232	5	FACETS	1	0.987	1	0.694	0.655	0.732	INDETERMINATE	3	TRUE	0	0.500274722750015	5		349	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0047318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	720	855	23	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.500274722750015	3	FACETS	0.99	0.962	1	0.99	0.962	1	CLONAL	3	TRUE	0	0.500274722750015	3		878	1211	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604789	48604789	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	124	384	0	ENST00000342988.3:c.1611C>A	p.Asp537Glu	p.D537E	ENST00000342988	NM_005359.5	537	gaC/gaA	12/12	0.490857087245584	1	FACETS	0.913	0.834	0.996	0.913	0.834	0.996	CLONAL	1	TRUE	0	0.500274722750015	1		384	407	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18962992	18962992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	271	1036	15	ENST00000262803.5:c.859G>A	p.Glu287Lys	p.E287K	ENST00000262803	NM_002911.3	287	Gag/Aag	6/24	0.481916613175442	3	FACETS	1	0.94	1	0.502	0.47	0.535	CLONAL	1	TRUE	1	0.500274722750015	3		1051	1350	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971015	21971015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779913365	NA	P-0047318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	193	472	3	ENST00000304494.5:c.343G>A	p.Val115Met	p.V115M	ENST00000304494	NM_000077.4	115	Gtg/Atg	2/3	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.500274722750015	2		475	652	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0047319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	18	164	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.477	0.357	0.619	0.477	0.357	0.619	SUBCLONAL	1	TRUE	1	0.13	2		164	581	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653841	89653841	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	31	153	0	ENST00000371953.3:c.139A>T	p.Arg47Trp	p.R47W	ENST00000371953	NM_000314.4	47	Agg/Tgg	2/9	1	2	FACETS	0.885	0.714	1	0.885	0.714	1	CLONAL	1	TRUE	1	0.13	2		153	539	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084162	47084162	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0047319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	52	188	0	ENST00000409792.3:c.7127T>A	p.Leu2376Ter	p.L2376*	ENST00000409792	NM_014159.6	2376	tTg/tAg	17/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.13	2		188	648	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	123	516	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		516	448	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0047321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	105	164	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		164	341	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762959	40762959	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs387906659	NA	P-0047321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	243	643	0	ENST00000392038.2:c.49G>A	p.Glu17Lys	p.E17K	ENST00000392038	NM_001626.4	17	Gaa/Aaa	3/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		643	849	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89862377	89862377	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757389865	NA	P-0047321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	350	757	1	ENST00000389301.3:c.943C>T	p.Pro315Ser	p.P315S	ENST00000389301	NM_000135.2	315	Cct/Tct	11/43	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		758	1089	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625468	69625468	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	300	718	0	ENST00000334134.2:c.325G>C	p.Glu109Gln	p.E109Q	ENST00000334134	NM_005247.2	109	Gag/Cag	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		718	959	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478182	99478182	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	230	610	0	ENST00000268035.6:c.3086G>C	p.Arg1029Thr	p.R1029T	ENST00000268035	NM_000875.3	1029	aGa/aCa	16/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		610	800	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349872	15349872	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	145	768	0	ENST00000263377.2:c.3780G>A	p.Met1260Ile	p.M1260I	ENST00000263377	NM_058243.2	1260	atG/atA	18/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		768	988	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053316	37053316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064796057	NA	P-0047321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	105	369	0	ENST00000231790.2:c.551C>T	p.Ser184Leu	p.S184L	ENST00000231790	NM_000249.3	184	tCa/tTa	7/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		369	362	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572092	64572093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767319284	NA	P-0047323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	518	677	1	ENST00000312049.6:c.1546dup	p.Arg516ProfsTer15	p.R516Pfs*15	ENST00000312049	NM_130799.2	516	cgg/cCgg	10/10	0.786487604206655	1	FACETS	0.811	0.781	0.84	0.811	0.781	0.84	CLONAL	1	TRUE	0	0.786487604206655	1		678	986	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0047324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	129	272	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.310665340439348	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.310665340439348	3		272	438	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156740	20156740	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	79	482	0	ENST00000379607.5:c.17G>A	p.Gly6Asp	p.G6D	ENST00000379607	NM_001412.3	6	gGt/gAt	2/7	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.310665340439348	2		482	456	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692792	89692792	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs779530981	NA	P-0047324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	198	462	0	ENST00000371953.3:c.276C>A	p.Asp92Glu	p.D92E	ENST00000371953	NM_000314.4	92	gaC/gaA	5/9	0.166698976893183	4	FACETS	1	0.976	1			1	INDETERMINATE	3	TRUE	NA	0.310665340439348	4		462	509	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160489	108160489	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	74	620	0	ENST00000278616.4:c.4397G>C	p.Arg1466Pro	p.R1466P	ENST00000278616	NM_000051.3	1466	cGa/cCa	29/63	0.310665340439348	1	FACETS	0.864	0.758	0.976	0.864	0.758	0.976	CLONAL	1	TRUE	0	0.310665340439348	1		620	466	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971175	21971182	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCGCCA	CTCCGCCA	-	novel	NA	P-0047324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	212	557	0	ENST00000304494.5:c.176_183del	p.Val59AlafsTer58	p.V59Afs*58	ENST00000304494	NM_000077.4	59	gTGGCGGAG/g	2/3	0.310665340439348	2	FACETS	0.998	0.931	1	0.998	0.931	1	CLONAL	2	TRUE	0	0.310665340439348	2		557	684	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566036	95566185	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTTGGCTCACCGAAAAGTAAATCCCTCCAGTTACACACACACACACACACACACACACACACACACACACACAAACTTACCATTTCATCTTTTTCCCATTTATCTGTGTTGCTTTTGTCTTGATTTACTACATAACCAGGAGGAAGCCA	ATTTGGCTCACCGAAAAGTAAATCCCTCCAGTTACACACACACACACACACACACACACACACACACACACACAAACTTACCATTTCATCTTTTTCCCATTTATCTGTGTTGCTTTTGTCTTGATTTACTACATAACCAGGAGGAAGCCA	-	novel	NA	P-0047324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	39	175	0	ENST00000393063.1:c.4138_4206+81del		p.X1380_splice	ENST00000393063	NM_030621.3	1380		23/28	1	2	FACETS	0.831	0.701	0.971	1	0.963	1	CLONAL	2	TRUE	1	0.310665340439348	2		175	151	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677932	58677932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047324-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	75	367	1	ENST00000305921.3:c.157C>T	p.Pro53Ser	p.P53S	ENST00000305921	NM_003620.3	53	Ccg/Tcg	1/6	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.310665340439348	2		368	435	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110795	2110795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1800725	NA	P-0047325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	298	985	0	ENST00000219476.3:c.1100G>A	p.Arg367Gln	p.R367Q	ENST00000219476	NM_000548.3	367	cGg/cAg	11/42	0.892731364402503	3	FACETS	1	0.975	1	0.528	0.498	0.558	CLONAL	1	TRUE	1	0.892731364402503	3		985	915	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033971	49033971	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0047325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	943	539	1	ENST00000267163.4:c.2106+2T>A		p.X702_splice	ENST00000267163	NM_000321.2	702			0.892731364402503	6	FACETS	0.931	0.919	0.943	0.931	0.919	0.943	CLONAL	6	TRUE	0	0.892731364402503	6		540	1053	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679748	88679748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	233	788	1	ENST00000360948.2:c.715C>T	p.Pro239Ser	p.P239S	ENST00000360948	NM_001012338.2	239	Cct/Tct	7/19	0.892731364402503	3	FACETS	0.897	0.838	0.957	0.448	0.419	0.479	CLONAL	1	TRUE	1	0.892731364402503	3		789	842	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197399	26197399	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	244	454	0	ENST00000356476.2:c.80G>C	p.Arg27Pro	p.R27P	ENST00000356476		27	cGa/cCa	1/1	0.698900231172691	4	FACETS	0.917	0.865	0.97	0.917	0.865	0.97	CLONAL	2	TRUE	2	0.892731364402503	4		454	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577157	7577157	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0047325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	654	669	0	ENST00000269305.4:c.783-2A>C		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.759661552877844	3	FACETS	0.931	0.914	0.947	0.931	0.914	0.947	CLONAL	3	TRUE	0	0.892731364402503	3		669	759	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612056	43612056	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	289	1012	0	ENST00000355710.3:c.2161C>G	p.Arg721Gly	p.R721G	ENST00000355710	NM_020975.4	721	Cgg/Ggg	12/20	0.787721060282291	3	FACETS	0.946	0.891	1	0.473	0.445	0.501	CLONAL	1	TRUE	1	0.892731364402503	3		1012	990	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578241	28578241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1775	269	732	0	ENST00000241453.7:c.2930G>A	p.Arg977Lys	p.R977K	ENST00000241453	NM_004119.2	977	aGa/aAa	24/24	0.892731364402503	6	FACETS	0.821	0.767	0.878	0.137	0.127	0.147	CLONAL	1	TRUE	0	0.892731364402503	6		732	2044	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872559	37872559	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	290	644	0	ENST00000269571.5:c.1519G>T	p.Glu507Ter	p.E507*	ENST00000269571		507	Gag/Tag	13/27	0.82423910595228	4	FACETS	1	0.993	1	0.692	0.653	0.733	CLONAL	1	TRUE	2	0.892731364402503	4		644	888	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683718	162683718	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	223	824	1	ENST00000366898.1:c.251G>T	p.Gly84Val	p.G84V	ENST00000366898	NM_004562.2	84	gGa/gTa	3/12	0.803085424291905	3	FACETS	0.792	0.738	0.848	0.264	0.246	0.283	SUBCLONAL	1	TRUE	0	0.892731364402503	3		825	912	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960129	151960129	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0047325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	122	633	0	ENST00000262189.6:c.1271C>G	p.Ser424Ter	p.S424*	ENST00000262189	NM_170606.2	424	tCa/tGa	9/59	0.787721060282291	3	FACETS	0.714	0.647	0.783	0.357	0.323	0.392	SUBCLONAL	1	TRUE	1	0.892731364402503	3		633	554	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0047326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	254	477	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.236650862336006	2	FACETS	0.837	0.784	0.893	0.837	0.784	0.893	CLONAL	2	TRUE	0	0.280367462327836	2		477	1082	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038893	12038894	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0047326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	67	208	0	ENST00000396373.4:c.1188_1189del	p.Arg396SerfsTer29	p.R396Sfs*29	ENST00000396373	NM_001987.4	396	AGa/a	7/8	1	2	FACETS	0.883	0.769	1	0.883	0.769	1	CLONAL	1	TRUE	1	0.280367462327836	2		208	541	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525569	187525569	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0047326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	99	319	0	ENST00000441802.2:c.10510A>T	p.Lys3504Ter	p.K3504*	ENST00000441802	NM_005245.3	3504	Aag/Tag	18/27	0.280367462327836	1	FACETS	0.892	0.797	0.993	0.892	0.797	0.993	CLONAL	1	TRUE	0	0.280367462327836	1		319	681	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0047327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	147	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.770490084935334	2		511	355	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0047327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	106	272	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.770490084935334	2		272	270	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254846	16254846	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	127	536	0	ENST00000375759.3:c.2111G>C	p.Arg704Thr	p.R704T	ENST00000375759	NM_015001.2	704	aGa/aCa	11/15	1	2	FACETS	0.958	0.879	1	0.958	0.879	1	CLONAL	1	TRUE	1	0.770490084935334	2		536	344	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736540	85736544	+	missense_variant	Missense_Mutation	ONP	CTCTC	CTCTC	TTCTG	novel	NA	P-0047327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	71	296	0	ENST00000370580.1:c.103_107delinsCAGAA	p.Glu35_Arg36delinsGlnLys	p.E35_R36delinsQK	ENST00000370580	NM_003921.4	35	GAGAGa/CAGAAa	2/3	1	2	FACETS	0.67	0.591	0.753	0.67	0.591	0.753	SUBCLONAL	1	TRUE	1	0.770490084935334	2		296	275	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165957	118165957	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	131	518	0	ENST00000369448.3:c.467C>T	p.Ser156Phe	p.S156F	ENST00000369448	NM_017709.3	156	tCc/tTc	2/2	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.770490084935334	2		518	335	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106058	8106058	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	153	567	0	ENST00000346208.3:c.878T>A	p.Met293Lys	p.M293K	ENST00000346208		293	aTg/aAg	4/6	1	2	FACETS	0.976	0.903	1	0.976	0.903	1	CLONAL	1	TRUE	1	0.770490084935334	2		567	407	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243214	123243214	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	198	731	1	ENST00000358487.5:c.2299G>A	p.Glu767Lys	p.E767K	ENST00000358487	NM_000141.4	767	Gag/Aag	17/18	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.770490084935334	2		732	470	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375357	118375357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	102	405	0	ENST00000534358.1:c.8750C>T	p.Ser2917Phe	p.S2917F	ENST00000534358	NM_005933.3	2917	tCt/tTt	27/36	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.770490084935334	2		405	261	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061288	38061288	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	152	789	1	ENST00000250448.2:c.701C>T	p.Ser234Phe	p.S234F	ENST00000250448	NM_004496.3	234	tCc/tTc	2/2	1	2	FACETS	0.849	0.782	0.916	0.849	0.782	0.916	CLONAL	1	TRUE	1	0.770490084935334	2		790	465	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354594	91354594	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	91	521	0	ENST00000355112.3:c.4034C>G	p.Ser1345Cys	p.S1345C	ENST00000355112	NM_000057.2	1345	tCt/tGt	21/22	1	2	FACETS	0.725	0.65	0.803	0.725	0.65	0.803	SUBCLONAL	1	TRUE	1	0.770490084935334	2		521	326	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0047327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	71	424	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	0.770490084935334	1	FACETS	0.606	0.54	0.674	0.606	0.54	0.674	SUBCLONAL	1	TRUE	0	0.770490084935334	1		424	187	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16001793	16001793	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0047327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	88	476	0	ENST00000268712.3:c.2708C>G	p.Ser903Ter	p.S903*	ENST00000268712	NM_006311.3	903	tCa/tGa	21/46	1	2	FACETS	0.619	0.552	0.689	0.619	0.552	0.689	SUBCLONAL	1	TRUE	1	0.770490084935334	2		476	369	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30302690	30302690	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	93	454	0	ENST00000322652.5:c.781G>C	p.Glu261Gln	p.E261Q	ENST00000322652	NM_015355.2	261	Gag/Cag	7/16	1	2	FACETS	0.802	0.722	0.885	0.802	0.722	0.885	CLONAL	1	TRUE	1	0.770490084935334	2		454	301	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619076	37619076	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	143	668	1	ENST00000447079.4:c.752C>A	p.Ser251Ter	p.S251*	ENST00000447079	NM_015083.1	251	tCa/tAa	1/14	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.770490084935334	2		669	369	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385215	41385215	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	182	794	1	ENST00000373198.4:c.746C>A	p.Ser249Ter	p.S249*	ENST00000373198	NM_133170.3	249	tCa/tAa	6/32	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.770490084935334	2		795	465	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49724654	49724654	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1559656920	NA	P-0047327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	96	617	0	ENST00000449682.2:c.535G>A	p.Gly179Arg	p.G179R	ENST00000449682	NM_020998.3	179	Gga/Aga	5/18	1	2	FACETS	0.893	0.807	0.982	0.893	0.807	0.982	CLONAL	1	TRUE	1	0.770490084935334	2		617	279	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204928	128204928	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	176	1003	0	ENST00000341105.2:c.513C>A	p.Phe171Leu	p.F171L	ENST00000341105	NM_032638.4	171	ttC/ttA	3/6	1	2	FACETS	0.958	0.89	1	0.958	0.89	1	CLONAL	1	TRUE	1	0.770490084935334	2		1003	477	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179468	56179468	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	118	295	0	ENST00000399503.3:c.3781C>T	p.Gln1261Ter	p.Q1261*	ENST00000399503	NM_005921.1	1261	Caa/Taa	15/20	0.706250942427048	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.770490084935334	1		295	188	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163687	32163688	+	missense_variant	Missense_Mutation	DNP	AC	AC	GT	novel	NA	P-0047327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	119	503	0	ENST00000375023.3:c.5538_5539inv	p.Ser1847Pro	p.S1847P	ENST00000375023	NM_004557.3	1846	gtGTca/gtACca	30/30	0.108313055797514	4	FACETS	0.959	0.881	1	0.959	0.881	1	INDETERMINATE	2	TRUE	2	0.770490084935334	4		503	285	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545821	106545821	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	99	348	1	ENST00000359195.3:c.3298C>T	p.His1100Tyr	p.H1100Y	ENST00000359195	NM_002649.2	1100	Cat/Tat	11/11	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.770490084935334	2		349	254	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38135864	38135864	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	23	585	0	ENST00000317025.8:c.3827G>C	p.Gly1276Ala	p.G1276A	ENST00000317025	NM_023034.1	1276	gGa/gCa	22/24	1	2	FACETS	0.137	0.106	0.173	0.137	0.106	0.173	SUBCLONAL	1	TRUE	1	0.770490084935334	2		585	436	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38137127	38137127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	162	698	0	ENST00000317025.8:c.3691G>A	p.Glu1231Lys	p.E1231K	ENST00000317025	NM_023034.1	1231	Gaa/Aaa	21/24	1	2	FACETS	0.826	0.763	0.891	0.826	0.763	0.891	CLONAL	1	TRUE	1	0.770490084935334	2		698	509	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38157004	38157004	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	153	596	0	ENST00000317025.8:c.2716A>G	p.Met906Val	p.M906V	ENST00000317025	NM_023034.1	906	Atg/Gtg	15/24	1	2	FACETS	0.886	0.818	0.956	0.886	0.818	0.956	CLONAL	1	TRUE	1	0.770490084935334	2		596	448	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801012	135801012	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	67	437	0	ENST00000298552.3:c.325C>A	p.Gln109Lys	p.Q109K	ENST00000298552	NM_001162426.1	109	Caa/Aaa	5/23	1	2	FACETS	0.565	0.495	0.639	0.565	0.495	0.639	SUBCLONAL	1	TRUE	1	0.770490084935334	2		437	308	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937536	76937536	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	148	477	0	ENST00000373344.5:c.3212G>A	p.Gly1071Glu	p.G1071E	ENST00000373344	NM_000489.3	1071	gGa/gAa	9/35	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.770490084935334	2		477	321	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0047328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	268	561	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.47465739542049	2		561	884	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577560	7577566	+	frameshift_variant	Frame_Shift_Del	DEL	AACTGTT	AACTGTT	-	novel	NA	P-0047328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	192	610	0	ENST00000269305.4:c.715_721del	p.Asn239ProfsTer6	p.N239Pfs*6	ENST00000269305	NM_001126112.2	239	AACAGTTcc/cc	7/11	0.47465739542049	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.47465739542049	1		610	601	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117650575	117650575	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	133	439	0	ENST00000368508.3:c.5283A>C	p.Leu1761Phe	p.L1761F	ENST00000368508	NM_002944.2	1761	ttA/ttC	32/43	0.368365451384153	1	FACETS	0.738	0.673	0.806	0.738	0.673	0.806	SUBCLONAL	1	TRUE	0	0.47465739542049	1		439	579	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	50	164	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	FALSE	1	0.358288028132739	2		164	232	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	60	612	2	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	0.181119454246704	4	FACETS	1	0.932	1	0.564	0.488	0.647	INDETERMINATE	1	FALSE	2	0.358288028132739	4		614	403	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	66	465	1	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	0.108030442050458	0	FACETS	0.913	0.801	1			1	INDETERMINATE	1	FALSE	0	0.358288028132739	0		466	259	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	134	889	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.852	0.78	0.926	1	0.989	1	CLONAL	2	FALSE	1	0.358288028132739	2		895	439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	65	805	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.358288028132739	2		805	293	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	44	421	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	0.10757007654599	4	FACETS	1	0.947	1	0.652	0.55	0.762	INDETERMINATE	1	FALSE	2	0.358288028132739	4		421	256	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053022	180053023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750808726	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	43	1008	3	ENST00000261937.6:c.1267dup	p.Gln423ProfsTer4	p.Q423Pfs*4	ENST00000261937	NM_182925.4	423	cag/cCag	10/30	0.358288028132739	0	FACETS	0.697	0.589	0.814			1	SUBCLONAL	1	FALSE	0	0.358288028132739	0		1011	221	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	235	889	1	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	1	2	FACETS	0.952	0.893	1	1	0.994	1	CLONAL	2	FALSE	1	0.358288028132739	2		890	689	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	55	870	8	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	0.358288028132739	0	FACETS	0.9	0.779	1			1	CLONAL	1	FALSE	0	0.358288028132739	0		878	219	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611336	28611336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201905189	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	43	440	0	ENST00000241453.7:c.1295C>T	p.Thr432Met	p.T432M	ENST00000241453	NM_004119.2	432	aCg/aTg	10/24	0.272628321567264	1	FACETS	0.835	0.705	0.976	0.835	0.705	0.976	CLONAL	1	FALSE	0	0.358288028132739	1		440	236	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272337	15272337	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs771517374	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	80	1034	5	ENST00000263388.2:c.6102del	p.Gly2035ValfsTer50	p.G2035Vfs*50	ENST00000263388	NM_000435.2	2034	ccC/cc	33/33	1	2	FACETS	0.812	0.723	0.904	1	0.981	1	CLONAL	2	FALSE	1	0.358288028132739	2		1039	275	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985473	2985473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	34	483	2	ENST00000396946.4:c.338G>A	p.Arg113Gln	p.R113Q	ENST00000396946	NM_032415.4	113	cGg/cAg	4/25	0.358288028132739	0	FACETS	0.47	0.386	0.564			1	SUBCLONAL	1	FALSE	0	0.358288028132739	0		485	259	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733513	85733513	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs387906350	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	75	483	3	ENST00000370580.1:c.499del	p.Ser167LeufsTer6	p.S167Lfs*6	ENST00000370580	NM_003921.4	167	Tct/ct	3/3	0.181119454246704	4	FACETS	0.831	0.734	0.935	0.831	0.734	0.935	INDETERMINATE	2	FALSE	2	0.358288028132739	4		486	342	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107008	27107008	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	65	695	0	ENST00000324856.7:c.6619C>T	p.Gln2207Ter	p.Q2207*	ENST00000324856	NM_006015.4	2207	Cag/Tag	20/20	0.181119454246704	4	FACETS	1	0.959	1	0.632	0.55	0.72	INDETERMINATE	1	FALSE	2	0.358288028132739	4		695	390	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119910	70119910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1297203260	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	200	707	0	ENST00000245479.2:c.916del	p.Val306CysfsTer77	p.V306Cfs*77	ENST00000245479	NM_000346.3	304	ccG/cc	3/3	1	2	FACETS	1	0.98	1	1	0.994	1	CLONAL	2	FALSE	1	0.358288028132739	2		707	500	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932084	39932085	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1394942244	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	11	386	0	ENST00000378444.4:c.2514dup	p.Lys839GlnfsTer5	p.K839Qfs*5	ENST00000378444	NM_001123385.1	838	-/C	4/15	0.289974007371346	2	FACETS	0.3	0.207	0.415			1	SUBCLONAL	1	FALSE	NA	0.358288028132739	2		386	205	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99163087	99163087	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	46	526	0	ENST00000074304.5:c.1093G>A	p.Ala365Thr	p.A365T	ENST00000074304	NM_001134224.1	365	Gca/Aca	13/26	1	2	FACETS	0.882	0.747	1	0.882	0.747	1	CLONAL	1	FALSE	1	0.358288028132739	2		526	291	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265386	10265386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1003447106	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	112	827	1	ENST00000340748.4:c.1660G>A	p.Ala554Thr	p.A554T	ENST00000340748		554	Gcg/Acg	20/40	1	2	FACETS	0.781	0.709	0.857	1	0.986	1	SUBCLONAL	2	FALSE	1	0.358288028132739	2		828	400	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120511	94120511	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	32	393	2	ENST00000369303.4:c.540G>T	p.Lys180Asn	p.K180N	ENST00000369303	NM_004440.3	180	aaG/aaT	3/17	0.251748674740349	4	FACETS	1	0.927	1	0.642	0.526	0.77	CLONAL	1	FALSE	2	0.358288028132739	4		395	189	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064779	80064780	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	52	350	0	ENST00000265081.6:c.2216dup	p.Asn739LysfsTer29	p.N739Kfs*29	ENST00000265081	NM_002439.4	737	cta/ctAa	15/24	0.181119454246704	4	FACETS	1	0.964	1	0.719	0.617	0.83	INDETERMINATE	1	FALSE	2	0.358288028132739	4		350	274	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324463	31324463	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	75	296	0	ENST00000412585.2:c.343+2T>C		p.X115_splice	ENST00000412585	NM_005514.6	115			0.358288028132739	6	FACETS	1	0.9	1	1	0.975	1	CLONAL	4	FALSE	3	0.358288028132739	6		296	179	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617690	39617690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141329274	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	47	339	1	ENST00000262039.4:c.1874C>T	p.Thr625Met	p.T625M	ENST00000262039	NM_002647.2	625	aCg/aTg	17/25	0.10757007654599	4	FACETS	0.792	0.675	0.918	0.792	0.675	0.918	INDETERMINATE	2	FALSE	2	0.358288028132739	4		340	225	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967156	25967156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201808592	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	33	553	1	ENST00000435504.4:c.2050G>A	p.Ala684Thr	p.A684T	ENST00000435504		684	Gcc/Acc	13/13	1	2	FACETS	1	0.824	1	1	0.824	1	CLONAL	1	FALSE	1	0.358288028132739	2		554	184	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639380	3639380	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs781663547	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	73	873	0	ENST00000294008.3:c.4259del	p.Pro1420GlnfsTer30	p.P1420Qfs*30	ENST00000294008	NM_032444.2	1420	cCa/ca	12/15	0.108030442050458	0	FACETS	0.797	0.703	0.897			1	INDETERMINATE	1	FALSE	0	0.358288028132739	0		873	328	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389236	8389236	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	30	373	1	ENST00000356435.5:c.4382C>A	p.Ser1461Ter	p.S1461*	ENST00000356435		1461	tCa/tAa	26/35	0.108030442050458	0	FACETS	0.581	0.472	0.702			1	INDETERMINATE	1	FALSE	0	0.358288028132739	0		374	185	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263964	16263964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	109	866	1	ENST00000375759.3:c.10333G>A	p.Val3445Ile	p.V3445I	ENST00000375759	NM_015001.2	3445	Gtc/Atc	12/15	0.181119454246704	4	FACETS	0.836	0.755	0.922	0.836	0.755	0.922	INDETERMINATE	2	FALSE	2	0.358288028132739	4		867	494	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943764	71943764	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	77	810	0	ENST00000298229.2:c.1807T>G	p.Phe603Val	p.F603V	ENST00000298229	NM_001567.3	603	Ttc/Gtc	15/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.358288028132739	2		810	309	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446859	18446859	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs369352037	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	40	284	0	ENST00000266497.5:c.944T>C	p.Ile315Thr	p.I315T	ENST00000266497		315	aTt/aCt	4/31	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	FALSE	1	0.358288028132739	2		284	203	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610116	81610116	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs987282140	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	45	492	0	ENST00000298171.2:c.1714A>G	p.Met572Val	p.M572V	ENST00000298171	NM_000369.2	572	Atg/Gtg	10/10	0.10757007654599	4	FACETS	1	0.941	1	0.625	0.529	0.73	INDETERMINATE	1	FALSE	2	0.358288028132739	4		492	273	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779476	3779476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1204228560	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	71	1158	0	ENST00000262367.5:c.5572C>T	p.Arg1858Cys	p.R1858C	ENST00000262367	NM_004380.2	1858	Cgc/Tgc	31/31	0.108030442050458	0	FACETS	0.845	0.744	0.951			1	INDETERMINATE	1	FALSE	0	0.358288028132739	0		1158	301	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857373	9857373	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	32	514	0	ENST00000330684.3:c.4028T>C	p.Leu1343Pro	p.L1343P	ENST00000330684	NM_001134407.1	1343	cTt/cCt	13/13	0.108030442050458	0	FACETS	0.637	0.522	0.763			1	INDETERMINATE	1	FALSE	0	0.358288028132739	0		514	180	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39623700	39623700	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	25	285	0	ENST00000262039.4:c.2112del	p.Phe704LeufsTer31	p.F704Lfs*31	ENST00000262039	NM_002647.2	703	Ttt/tt	20/25	0.10757007654599	4	FACETS	1	0.916	1	0.663	0.529	0.813	INDETERMINATE	1	FALSE	2	0.358288028132739	4		285	143	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1627416	1627416	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	80	875	0	ENST00000344749.5:c.308G>A	p.Gly103Asp	p.G103D	ENST00000344749	NM_001136139.2	103	gGt/gAt	6/19	0.149218980406112	0	FACETS	0.933	0.83	1			1	INDETERMINATE	1	FALSE	0	0.358288028132739	0		875	307	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982526	10982526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	111	201	1	ENST00000327064.4:c.148C>T	p.His50Tyr	p.H50Y	ENST00000327064	NM_199141.1	50	Cac/Tac	1/16	1	2	FACETS	0.917	0.834	1	1	0.988	1	CLONAL	2	FALSE	1	0.358288028132739	2		202	338	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637437	47637437	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	64	555	0	ENST00000233146.2:c.571C>A	p.Leu191Ile	p.L191I	ENST00000233146	NM_000251.2	191	Ctc/Atc	3/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.358288028132739	2		555	269	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149703	202149703	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	89	613	1	ENST00000358485.4:c.1144A>T	p.Ile382Phe	p.I382F	ENST00000358485	NM_001080125.1	382	Atc/Ttc	8/9	0.10757007654599	4	FACETS	1	0.96	1	1	0.96	1	INDETERMINATE	2	FALSE	2	0.358288028132739	4		614	295	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280110	66280110	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	44	378	0	ENST00000273854.3:c.1579G>A	p.Ala527Thr	p.A527T	ENST00000273854	NM_004439.5	527	Gca/Aca	7/18	0.108030442050458	0	FACETS	0.788	0.669	0.917			1	INDETERMINATE	1	FALSE	0	0.358288028132739	0		378	200	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820216	32820216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	210	694	1	ENST00000354258.4:c.842C>T	p.Ala281Val	p.A281V	ENST00000354258	NM_000593.5	281	gCc/gTc	2/11	0.358288028132739	9	FACETS	0.984	0.915	1	0.59	0.549	0.634	CLONAL	3	FALSE	4	0.358288028132739	9		695	895	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198245	138198245	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150198888	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	34	276	0	ENST00000237289.4:c.838C>T	p.Arg280Trp	p.R280W	ENST00000237289	NM_001270507.1	280	Cgg/Tgg	6/9	0.251748674740349	4	FACETS	0.64	0.523	0.771	0.32	0.261	0.386	SUBCLONAL	1	FALSE	2	0.358288028132739	4		276	403	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864646	68864646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	20	274	0	ENST00000288368.4:c.17G>A	p.Arg6His	p.R6H	ENST00000288368	NM_024870.2	6	cGc/cAc	1/40	0.108030442050458	0	FACETS	0.602	0.466	0.756			1	INDETERMINATE	1	FALSE	0	0.358288028132739	0		274	119	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339254	87339254	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	45	478	0	ENST00000277120.3:c.836T>C	p.Val279Ala	p.V279A	ENST00000277120		279	gTc/gCc	8/19	0.108030442050458	0	FACETS	0.844	0.719	0.978			1	INDETERMINATE	1	FALSE	0	0.358288028132739	0		478	191	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879965	44879965	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	12	218	0	ENST00000377967.4:c.554C>T	p.Ser185Phe	p.S185F	ENST00000377967	NM_021140.2	185	tCt/tTt	6/29	0.289974007371346	2	FACETS	0.532	0.376	0.72			1	SUBCLONAL	1	FALSE	NA	0.358288028132739	2		218	126	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163315571	163315571	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	78	278	0	ENST00000271452.3:c.911C>A	p.Ser304Ter	p.S304*	ENST00000271452	NM_145697.2	304	tCa/tAa	11/14	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.32	2		278	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587780070	NA	P-0047332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	100	804	0	ENST00000269305.4:c.535C>A	p.His179Asn	p.H179N	ENST00000269305	NM_001126112.2	179	Cat/Aat	5/11	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	2	TRUE	NA	0.452200385432991	2		804	201	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550728	150550734	+	frameshift_variant	Frame_Shift_Del	DEL	TTTGTTT	TTTGTTT	CA	novel	NA	P-0047332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	57	407	1	ENST00000369026.2:c.922_928delinsTG	p.Lys308TrpfsTer46	p.K308Wfs*46	ENST00000369026	NM_021960.4	308	AAACAAAga/TGga	2/3	0.452200385432991	16	FACETS	0.956	0.818	1			1	CLONAL	1	TRUE	NA	0.452200385432991	16		408	1098	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579369	7579369	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555526581	NA	P-0047334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	83	719	0	ENST00000269305.4:c.318C>G	p.Ser106Arg	p.S106R	ENST00000269305	NM_001126112.2	106	agC/agG	4/11	0.233785721977957	3	FACETS	0.951	0.856	1	1	0.98	1	CLONAL	3	TRUE	1	0.323433687030039	3		719	209	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188252	10188252	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1347416980	NA	P-0047334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	20	593	0	ENST00000256474.2:c.395A>C	p.Gln132Pro	p.Q132P	ENST00000256474	NM_000551.3	132	cAa/cCa	2/3	0.262061040307213	2	FACETS	1	0.83	1	0.542	0.421	0.68	CLONAL	1	TRUE	0	0.323433687030039	2		593	114	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47079180	47079181	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0047334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	27	560	0	ENST00000409792.3:c.7325dup	p.Thr2443AsnfsTer3	p.T2443Nfs*3	ENST00000409792	NM_014159.6	2442	cca/ccCa	18/21	0.262061040307213	2	FACETS	1	0.933	1	0.707	0.573	0.855	CLONAL	1	TRUE	0	0.323433687030039	2		560	118	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057682	27057682	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520585	NA	P-0047335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	624	621	1	ENST00000324856.7:c.1390C>T	p.Gln464Ter	p.Q464*	ENST00000324856	NM_006015.4	464	Caa/Taa	3/20	0.146342157970523	5	FACETS	1	0.994	1			1	INDETERMINATE	4	TRUE	NA	0.625759813714947	5		622	894	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098973	178098973	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	215	159	0	ENST00000397062.3:c.72G>C	p.Trp24Cys	p.W24C	ENST00000397062	NM_006164.4	24	tgG/tgC	2/5	0.590256606545805	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.625759813714947	2		159	329	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499354	89499354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	117	415	0	ENST00000336596.2:c.2524C>T	p.Arg842Ter	p.R842*	ENST00000336596	NM_005233.5	842	Cga/Tga	15/17	0.625759813714947	1	FACETS	0.842	0.771	0.916	0.842	0.771	0.916	CLONAL	1	TRUE	0	0.625759813714947	1		415	305	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0047335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	357	666	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.38678702626418	5	FACETS	1	0.979	1	0.705	0.669	0.741	CLONAL	2	TRUE	2	0.625759813714947	5		666	1046	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733480	85733480	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	139	320	0	ENST00000370580.1:c.532G>C	p.Glu178Gln	p.E178Q	ENST00000370580	NM_003921.4	178	Gaa/Caa	3/3	0.590256606545805	2	FACETS	0.889	0.814	0.966	0.444	0.407	0.483	CLONAL	1	TRUE	0	0.625759813714947	2		320	500	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21627813	21627813	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	310	481	1	ENST00000421138.2:c.1317G>T	p.Lys439Asn	p.K439N	ENST00000421138		439	aaG/aaT	12/16	0.38678702626418	5	FACETS	1	0.96	1	0.68	0.642	0.718	CLONAL	2	TRUE	2	0.625759813714947	5		482	942	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272321	15272321	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs748286003	NA	P-0047335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	510	882	0	ENST00000263388.2:c.6118G>T	p.Gly2040Trp	p.G2040W	ENST00000263388	NM_000435.2	2040	Ggg/Tgg	33/33	0.622324277528439	3	FACETS	0.996	0.958	1	0.996	0.958	1	CLONAL	2	TRUE	1	0.625759813714947	3		882	1074	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165113	47165113	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	163	149	0	ENST00000409792.3:c.1013A>T	p.Asp338Val	p.D338V	ENST00000409792	NM_014159.6	338	gAt/gTt	3/21	0.590256606545805	2	FACETS	0.865	0.811	0.92	0.865	0.811	0.92	CLONAL	2	TRUE	0	0.625759813714947	2		149	301	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602711	55602711	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0047335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	247	321	0	ENST00000288135.5:c.2532T>A	p.Cys844Ter	p.C844*	ENST00000288135	NM_000222.2	844	tgT/tgA	18/21	0.448111382818351	4	FACETS	0.962	0.905	1			1	CLONAL	2	TRUE	NA	0.625759813714947	4		321	667	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190848	106190848	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	293	497	0	ENST00000380013.4:c.4126G>C	p.Asp1376His	p.D1376H	ENST00000380013	NM_001127208.2	1376	Gac/Cac	9/11	0.55947129136047	3	FACETS	0.871	0.825	0.917	0.871	0.825	0.917	CLONAL	2	TRUE	1	0.625759813714947	3		497	706	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38153468	38153468	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	281	333	0	ENST00000317025.8:c.2761G>T	p.Gly921Ter	p.G921*	ENST00000317025	NM_023034.1	921	Gga/Tga	16/24	0.503040590816654	4	FACETS	1	0.956	1			1	CLONAL	2	TRUE	NA	0.625759813714947	4		333	721	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56882324	56882324	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	539	497	0	ENST00000519728.1:c.1022T>C	p.Leu341Pro	p.L341P	ENST00000519728	NM_002350.3	341	cTt/cCt	10/13	0.578117729276084	3	FACETS	0.938	0.91	0.965	0.938	0.91	0.965	CLONAL	3	TRUE	0	0.625759813714947	3		497	804	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932189	39932189	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	249	419	0	ENST00000378444.4:c.2410G>A	p.Val804Ile	p.V804I	ENST00000378444	NM_001123385.1	804	Gtc/Atc	4/15	0.448111382818351	2	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.625759813714947	2		419	648	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971196	21971199	+	frameshift_variant	Frame_Shift_Del	DEL	CATC	CATC	ATT	novel	NA	P-0047335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	145	461	1	ENST00000304494.5:c.159_162delinsAAT	p.Met53IlefsTer93	p.M53Ifs*93	ENST00000304494	NM_000077.4	53	atGATG/atAAT	2/3	0.625759813714947	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.625759813714947	1		462	309	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0047336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	113	323	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.22	2		323	924	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0047336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1348	146	636	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.888	0.808	0.973	0.888	0.808	0.973	CLONAL	1	TRUE	1	0.22	2		636	1494	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0047336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1410	114	991	6	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	0.187505878858216	3	FACETS	0.755	0.677	0.838	0.377	0.338	0.419	SUBCLONAL	1	TRUE	1	0.22	3		997	1524	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0047336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	89	262	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.876	0.78	0.977	1	0.984	1	CLONAL	2	TRUE	1	0.22	2		262	462	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417596	139417596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372660483	NA	P-0047336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1433	179	1049	1	ENST00000277541.6:c.448G>A	p.Ala150Thr	p.A150T	ENST00000277541	NM_017617.3	150	Gcc/Acc	4/34	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.22	2		1050	1612	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184750	185184750	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs752255390	NA	P-0047336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	38	315	1	ENST00000265026.3:c.1642C>T	p.Arg548Trp	p.R548W	ENST00000265026	NM_004721.4	548	Cgg/Tgg	10/14	1	2	FACETS	0.652	0.538	0.779	0.652	0.538	0.779	SUBCLONAL	1	TRUE	1	0.22	2		316	530	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188200	10188200	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs5030811	NA	P-0047336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	80	523	0	ENST00000256474.2:c.343C>T	p.His115Tyr	p.H115Y	ENST00000256474	NM_000551.3	115	Cac/Tac	2/3	0.3	2	FACETS	0.854	0.75	0.965			1	CLONAL	1	TRUE	NA	0.22	2		523	852	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029193	26029195	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0047336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	49	298	0	ENST00000435504.4:c.155_157del	p.Pro52del	p.P52del	ENST00000435504		52	cCTCtt/ctt	4/13	1	2	FACETS	0.844	0.714	0.986	0.844	0.714	0.986	CLONAL	1	TRUE	1	0.22	2		298	528	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903755	114903755	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	95	554	0	ENST00000543371.1:c.763del	p.His255IlefsTer3	p.H255Ifs*3	ENST00000543371	NM_001198531.1	253	atC/at	7/14	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.22	2		554	862	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939260	71939260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	146	840	0	ENST00000298229.2:c.209G>A	p.Arg70His	p.R70H	ENST00000298229	NM_001567.3	70	cGc/cAc	2/28	1	2	FACETS	0.939	0.855	1	0.939	0.855	1	CLONAL	1	TRUE	1	0.22	2		840	1413	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647657	3647657	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs774532876	NA	P-0047336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	118	886	2	ENST00000294008.3:c.1406del	p.Pro469HisfsTer4	p.P469Hfs*4	ENST00000294008	NM_032444.2	469	cCa/ca	7/15	1	2	FACETS	0.81	0.728	0.896	0.81	0.728	0.896	CLONAL	1	TRUE	1	0.22	2		888	1325	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161938	47161939	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	47	306	1	ENST00000409792.3:c.4187dup	p.Asn1396LysfsTer2	p.N1396Kfs*2	ENST00000409792	NM_014159.6	1396	aat/aaAt	3/21	1	2	FACETS	0.856	0.723	1	0.856	0.723	1	CLONAL	1	TRUE	1	0.22	2		307	499	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228265	53228265	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	109	756	0	ENST00000375401.3:c.2137A>G	p.Thr713Ala	p.T713A	ENST00000375401	NM_004187.3	713	Acg/Gcg	15/26	1	2	FACETS	0.856	0.767	0.952	0.856	0.767	0.952	CLONAL	1	TRUE	1	0.22	2		756	1157	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976876	55976876	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	84	648	0	ENST00000263923.4:c.1036del	p.Glu346SerfsTer17	p.E346Sfs*17	ENST00000263923	NM_002253.2	346	Gag/ag	8/30	1	2	FACETS	0.819	0.722	0.924	0.819	0.722	0.924	CLONAL	1	TRUE	1	0.22	2		648	932	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760966	59760967	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs753683450	NA	P-0047336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	65	518	0	ENST00000259008.2:c.3440dup	p.Asn1147LysfsTer2	p.N1147Kfs*2	ENST00000259008	NM_032043.2	1147	aat/aaAt	20/20	1	2	FACETS	0.786	0.68	0.901	0.786	0.68	0.901	CLONAL	1	TRUE	1	0.22	2		518	752	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945054	31945054	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766952582	NA	P-0047336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1339	125	814	1	ENST00000340398.3:c.47C>T	p.Ala16Val	p.A16V	ENST00000340398	NM_001013699.2	16	gCc/gTc	1/1	0.187505878858216	3	FACETS	0.862	0.777	0.952	0.431	0.388	0.476	CLONAL	1	TRUE	1	0.22	3		815	1464	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436113	49436113	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	77	446	1	ENST00000301067.7:c.5868G>T	p.Arg1956Ser	p.R1956S	ENST00000301067	NM_003482.3	1956	agG/agT	28/54	0.187505878858216	3	FACETS	0.94	0.824	1	0.47	0.412	0.533	CLONAL	1	TRUE	1	0.22	3		447	827	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830526	72830526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	91	642	2	ENST00000268489.5:c.6055G>A	p.Ala2019Thr	p.A2019T	ENST00000268489	NM_006885.3	2019	Gcc/Acc	9/10	1	2	FACETS	0.731	0.647	0.821	0.731	0.647	0.821	SUBCLONAL	1	TRUE	1	0.22	2		644	1132	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993371	72993371	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	134	848	0	ENST00000268489.5:c.674G>T	p.Ser225Ile	p.S225I	ENST00000268489	NM_006885.3	225	aGc/aTc	2/10	1	2	FACETS	0.914	0.828	1	0.914	0.828	1	CLONAL	1	TRUE	1	0.22	2		848	1333	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350679	89350679	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1206	131	798	0	ENST00000301030.4:c.2271del	p.Lys757AsnfsTer2	p.K757Nfs*2	ENST00000301030	NM_001256183.1	757	aaA/aa	9/13	1	2	FACETS	0.891	0.806	0.981	0.891	0.806	0.981	CLONAL	1	TRUE	1	0.22	2		798	1337	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252751	10252751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776461147	NA	P-0047336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1226	134	848	3	ENST00000340748.4:c.3214G>A	p.Val1072Ile	p.V1072I	ENST00000340748		1072	Gtc/Atc	29/40	1	2	FACETS	0.896	0.811	0.985	0.896	0.811	0.985	CLONAL	1	TRUE	1	0.22	2		851	1360	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042521	37042522	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0047336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	46	474	0	ENST00000231790.2:c.284_285del	p.Ser95TyrfsTer7	p.S95Yfs*7	ENST00000231790	NM_000249.3	95	TCt/t	3/19	1	2	FACETS	0.692	0.582	0.814	0.692	0.582	0.814	SUBCLONAL	1	TRUE	1	0.22	2		474	604	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620686	52620686	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	34	315	0	ENST00000394830.3:c.3067C>T	p.Pro1023Ser	p.P1023S	ENST00000394830	NM_018313.4	1023	Cca/Tca	21/30	1	2	FACETS	0.685	0.56	0.827	0.685	0.56	0.827	SUBCLONAL	1	TRUE	1	0.22	2		315	451	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38943020	38943020	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	63	304	0	ENST00000357387.3:c.4967T>C	p.Val1656Ala	p.V1656A	ENST00000357387	NM_152756.3	1656	gTt/gCt	37/38	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.22	2		304	490	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638240	176638240	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	100	752	0	ENST00000439151.2:c.2840A>T	p.Asn947Ile	p.N947I	ENST00000439151	NM_022455.4	947	aAt/aTt	5/23	0.187505878858216	3	FACETS	0.877	0.782	0.98	0.439	0.391	0.49	CLONAL	1	TRUE	1	0.22	3		752	1150	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800185	32800185	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	70	424	0	ENST00000374899.4:c.1197G>A	p.Met399Ile	p.M399I	ENST00000374899	NM_018833.2	399	atG/atA	7/12	1	2	FACETS	0.753	0.655	0.859	0.753	0.655	0.859	SUBCLONAL	1	TRUE	1	0.22	2		424	845	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813561	32813561	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	91	441	0	ENST00000354258.4:c.2222T>C	p.Val741Ala	p.V741A	ENST00000354258	NM_000593.5	741	gTg/gCg	11/11	0.187505878858216	3	FACETS	1	0.943	1	0.551	0.489	0.618	CLONAL	1	TRUE	1	0.22	3		441	833	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32816782	32816782	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	94	674	0	ENST00000354258.4:c.1542C>A	p.Phe514Leu	p.F514L	ENST00000354258	NM_000593.5	514	ttC/ttA	6/11	0.187505878858216	3	FACETS	0.794	0.705	0.891	0.397	0.352	0.446	SUBCLONAL	1	TRUE	1	0.22	3		674	1194	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046345	69046345	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775225179	NA	P-0047336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	77	518	0	ENST00000288368.4:c.3818C>T	p.Ala1273Val	p.A1273V	ENST00000288368	NM_024870.2	1273	gCc/gTc	32/40	0.187505878858216	3	FACETS	0.85	0.745	0.964	0.425	0.372	0.482	CLONAL	1	TRUE	1	0.22	3		518	914	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339212	87339212	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	73	509	1	ENST00000277120.3:c.794C>A	p.Ser265Tyr	p.S265Y	ENST00000277120		265	tCt/tAt	8/19	1	2	FACETS	0.788	0.688	0.897	0.788	0.688	0.897	SUBCLONAL	1	TRUE	1	0.22	2		510	842	SUCCESS
AR	367	MSKCC	GRCh37	X	66942755	66942755	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	65	493	0	ENST00000374690.3:c.2539del	p.Arg847GlufsTer36	p.R847Efs*36	ENST00000374690	NM_000044.3	846	Aaa/aa	7/8	1	2	FACETS	0.703	0.608	0.806	0.703	0.608	0.806	SUBCLONAL	1	TRUE	1	0.22	2		493	841	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436371	52436383	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCCGATGCTGA	CGGCCGATGCTGA	TGG	novel	NA	P-0047336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	127	908	3	ENST00000460680.1:c.2111_2123delinsCCA	p.Val704AlafsTer29	p.V704Afs*29	ENST00000460680	NM_004656.3	704	gTCAGCATCGGCCGg/gCCAg	17/17	1	2	FACETS	0.939	0.849	1	0.939	0.849	1	CLONAL	1	TRUE	1	0.22	2		911	1229	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0047338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	580	396	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.401937433511663	4	FACETS	0.905	0.878	0.932	1	0.995	1	CLONAL	5	TRUE	0	0.401937433511663	4		396	894	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467924	50467924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	108	753	0	ENST00000331340.3:c.1159G>A	p.Glu387Lys	p.E387K	ENST00000331340	NM_006060.4	387	Gag/Aag	8/8	0.401937433511663	4	FACETS	0.936	0.84	1	0.468	0.42	0.519	CLONAL	1	TRUE	2	0.401937433511663	4		753	805	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991329	72991329	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs143561313	NA	P-0047338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	131	592	0	ENST00000268489.5:c.2716C>G	p.Leu906Val	p.L906V	ENST00000268489	NM_006885.3	906	Cta/Gta	2/10	0.401937433511663	3	FACETS	1	0.97	1	0.576	0.524	0.631	CLONAL	1	TRUE	1	0.401937433511663	3		592	679	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488715	212488715	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747184711	NA	P-0047338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	203	564	0	ENST00000342788.4:c.2134A>G	p.Ile712Val	p.I712V	ENST00000342788	NM_005235.2	712	Att/Gtt	18/28	0.401937433511663	3	FACETS	0.815	0.758	0.874	0.815	0.758	0.874	CLONAL	2	TRUE	1	0.401937433511663	3		564	744	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444387	50444387	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	172	492	0	ENST00000331340.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000331340	NM_006060.4	106	gGa/gTa	4/8	0.401937433511663	4	FACETS	0.895	0.827	0.966	0.895	0.827	0.966	CLONAL	2	TRUE	2	0.401937433511663	4		492	670	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859462	151859462	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	114	542	0	ENST00000262189.6:c.11200C>G	p.Pro3734Ala	p.P3734A	ENST00000262189	NM_170606.2	3734	Cct/Gct	43/59	0.401937433511663	4	FACETS	0.913	0.821	1	0.457	0.41	0.505	CLONAL	1	TRUE	2	0.401937433511663	4		542	871	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0047339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	274	1013	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.611945259886852	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.611945259886852	1		1013	600	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0047339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	205	303	1	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.495401737538055	3	FACETS	0.977	0.917	1	0.977	0.917	1	CLONAL	2	TRUE	1	0.611945259886852	3		304	448	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510573	38510573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	210	735	2	ENST00000254066.5:c.827G>A	p.Arg276Gln	p.R276Q	ENST00000254066	NM_000964.3	276	cGg/cAg	7/9	0.611945259886852	4	FACETS	0.926	0.858	0.996			1	CLONAL	1	TRUE	NA	0.611945259886852	4		737	1195	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	86	516	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.779	0.693	0.871	0.779	0.693	0.871	SUBCLONAL	1	TRUE	1	0.50494863313668	2		516	437	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968610	55968610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374980446	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	280	572	0	ENST00000263923.4:c.2053G>A	p.Glu685Lys	p.E685K	ENST00000263923	NM_002253.2	685	Gaa/Aaa	14/30	1	2	FACETS	0.936	0.879	0.995	0.936	0.879	0.995	CLONAL	1	TRUE	1	0.50494863313668	2		572	1185	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	252	520	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.50494863313668	2		520	873	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457192	25457192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771922296	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	319	611	0	ENST00000264709.3:c.2695C>T	p.Arg899Cys	p.R899C	ENST00000264709	NM_175629.2	899	Cgc/Tgc	23/23	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.50494863313668	2		611	1136	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	365	788	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.50494863313668	2		788	1364	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	321	593	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.50494863313668	2		593	1219	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650109	93650109	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	231	550	1	ENST00000375746.1:c.1660G>A	p.Asp554Asn	p.D554N	ENST00000375746	NM_001174167.1	554	Gat/Aat	12/14	1	2	FACETS	0.947	0.884	1	0.947	0.884	1	CLONAL	1	TRUE	1	0.50494863313668	2		551	966	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100375	27100375	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	238	580	0	ENST00000324856.7:c.4087C>T	p.Gln1363Ter	p.Q1363*	ENST00000324856	NM_006015.4	1363	Caa/Taa	17/20	0.256871110724455	3	FACETS	1	0.97	1	0.534	0.498	0.571	INDETERMINATE	1	TRUE	1	0.50494863313668	3		580	1106	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164268	47164268	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	88	245	0	ENST00000409792.3:c.1858C>T	p.Arg620Ter	p.R620*	ENST00000409792	NM_014159.6	620	Cga/Tga	3/21	1	2	FACETS	0.789	0.702	0.88	0.789	0.702	0.88	SUBCLONAL	1	TRUE	1	0.50494863313668	2		245	442	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561352	9561352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773981325	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	216	505	0	ENST00000353224.5:c.430G>A	p.Glu144Lys	p.E144K	ENST00000353224	NM_177990.2	144	Gaa/Aaa	4/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.50494863313668	2		505	814	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729679	41729679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1488698571	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	274	724	1	ENST00000242208.4:c.850G>A	p.Glu284Lys	p.E284K	ENST00000242208	NM_002192.2	284	Gaa/Aaa	3/3	1	2	FACETS	0.928	0.871	0.987	0.928	0.871	0.987	CLONAL	1	TRUE	1	0.50494863313668	2		725	1169	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622630	158622630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	182	430	1	ENST00000263640.3:c.869C>T	p.Ser290Leu	p.S290L	ENST00000263640	NM_001105.4	290	tCg/tTg	8/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.50494863313668	2		431	692	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793483	18793483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603405	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	119	244	1	ENST00000266497.5:c.4180G>A	p.Glu1394Lys	p.E1394K	ENST00000266497		1394	Gaa/Aaa	30/31	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.50494863313668	2		245	409	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066501	94066501	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	143	343	0	ENST00000369303.4:c.1258G>A	p.Gly420Arg	p.G420R	ENST00000369303	NM_004440.3	420	Gga/Aga	5/17	1	2	FACETS	0.921	0.843	1	0.921	0.843	1	CLONAL	1	TRUE	1	0.50494863313668	2		343	615	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341914	8341914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	123	349	0	ENST00000356435.5:c.4726G>A	p.Glu1576Lys	p.E1576K	ENST00000356435		1576	Gaa/Aaa	29/35	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.50494863313668	2		349	482	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120377	94120377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	137	252	0	ENST00000369303.4:c.674C>T	p.Ser225Phe	p.S225F	ENST00000369303	NM_004440.3	225	tCc/tTc	3/17	1	2	FACETS	0.94	0.859	1	0.94	0.859	1	CLONAL	1	TRUE	1	0.50494863313668	2		252	577	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829797	72829797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs953863150	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	335	643	0	ENST00000268489.5:c.6784G>A	p.Asp2262Asn	p.D2262N	ENST00000268489	NM_006885.3	2262	Gat/Aat	9/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.50494863313668	2		643	1142	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278890	1278890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	327	838	0	ENST00000310581.5:c.2152G>A	p.Asp718Asn	p.D718N	ENST00000310581	NM_198253.2	718	Gac/Aac	6/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.50494863313668	2		838	1247	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811603	102811603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	215	540	0	ENST00000307046.8:c.581G>A	p.Gly194Glu	p.G194E	ENST00000307046	NM_001111285.1	194	gGa/gAa	4/4	1	2	FACETS	0.975	0.908	1	0.975	0.908	1	CLONAL	1	TRUE	1	0.50494863313668	2		540	873	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857425	9857425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1268143219	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	197	491	0	ENST00000330684.3:c.3976G>A	p.Gly1326Ser	p.G1326S	ENST00000330684	NM_001134407.1	1326	Ggc/Agc	13/13	1	2	FACETS	0.934	0.867	1	0.934	0.867	1	CLONAL	1	TRUE	1	0.50494863313668	2		491	835	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518175	8518175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1354824749	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	200	473	0	ENST00000356435.5:c.1216G>A	p.Glu406Lys	p.E406K	ENST00000356435		406	Gaa/Aaa	10/35	1	2	FACETS	0.922	0.856	0.991	0.922	0.856	0.991	CLONAL	1	TRUE	1	0.50494863313668	2		473	859	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595553	55595553	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs878853763	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	137	315	0	ENST00000288135.5:c.2043T>G	p.Phe681Leu	p.F681L	ENST00000288135	NM_000222.2	681	ttT/ttG	14/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.50494863313668	2		315	506	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1268704	1268704	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	336	949	3	ENST00000310581.5:c.2513C>T	p.Ser838Phe	p.S838F	ENST00000310581	NM_198253.2	838	tCc/tTc	9/16	1	2	FACETS	0.951	0.898	1	0.951	0.898	1	CLONAL	1	TRUE	1	0.50494863313668	2		952	1400	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930595	131930595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	109	213	0	ENST00000265335.6:c.1828C>T	p.His610Tyr	p.H610Y	ENST00000265335		610	Cat/Tat	12/25	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.50494863313668	2		213	410	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857172	9857172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555481986	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	182	498	0	ENST00000330684.3:c.4229C>T	p.Ser1410Leu	p.S1410L	ENST00000330684	NM_001134407.1	1410	tCg/tTg	13/13	1	2	FACETS	0.89	0.822	0.96	0.89	0.822	0.96	CLONAL	1	TRUE	1	0.50494863313668	2		498	810	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392143	81392143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	73	211	0	ENST00000222390.5:c.134C>T	p.Ser45Leu	p.S45L	ENST00000222390	NM_000601.4	45	tCa/tTa	2/18	1	2	FACETS	0.808	0.711	0.91	0.808	0.711	0.91	CLONAL	1	TRUE	1	0.50494863313668	2		211	358	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050711	69050711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	136	325	0	ENST00000288368.4:c.4046C>T	p.Ser1349Phe	p.S1349F	ENST00000288368	NM_024870.2	1349	tCc/tTc	33/40	1	2	FACETS	0.998	0.912	1	0.998	0.912	1	CLONAL	1	TRUE	1	0.50494863313668	2		325	540	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790031	40790031	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	280	612	0	ENST00000373198.4:c.2700G>A	p.Met900Ile	p.M900I	ENST00000373198	NM_133170.3	900	atG/atA	18/32	NA	2	FACETS	0.767	0.719	0.817			1	INDETERMINATE	1	TRUE	NA	0.50494863313668	2		612	1446	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30090763	30090763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761191666	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	270	712	0	ENST00000338641.4:c.1760C>T	p.Ser587Phe	p.S587F	ENST00000338641	NM_000268.3	587	tCc/tTc	16/16	1	2	FACETS	0.91	0.853	0.969	0.91	0.853	0.969	CLONAL	1	TRUE	1	0.50494863313668	2		712	1175	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610228	81610228	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139352934	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	214	445	0	ENST00000298171.2:c.1826G>A	p.Arg609Gln	p.R609Q	ENST00000298171	NM_000369.2	609	cGa/cAa	10/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.50494863313668	2		445	768	SUCCESS
CBL	867	MSKCC	GRCh37	11	119077192	119077192	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	563	677	0	ENST00000264033.4:c.65C>T	p.Ser22Leu	p.S22L	ENST00000264033	NM_005188.3	22	tCg/tTg	1/16	0.358339020905293	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.50494863313668	2		677	1059	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652995	29652996	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1135402867	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	199	446	0	ENST00000356175.3:c.4935dup	p.Pro1646SerfsTer15	p.P1646Sfs*15	ENST00000356175	NM_000267.3	1644	gtt/gTtt	36/57	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.50494863313668	2		446	780	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322511	109322511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769935193	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	183	426	0	ENST00000436639.2:c.526C>T	p.Arg176Cys	p.R176C	ENST00000436639	NM_014454.2	176	Cgt/Tgt	3/10	1	2	FACETS	0.895	0.827	0.965	0.895	0.827	0.965	CLONAL	1	TRUE	1	0.50494863313668	2		426	810	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396184	396184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	259	662	0	ENST00000262320.3:c.842C>T	p.Ser281Phe	p.S281F	ENST00000262320	NM_003502.3	281	tCc/tTc	2/11	1	2	FACETS	0.911	0.853	0.971	0.911	0.853	0.971	CLONAL	1	TRUE	1	0.50494863313668	2		662	1126	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961526	54961526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1211313151	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	218	447	0	ENST00000312783.6:c.106C>T	p.Pro36Ser	p.P36S	ENST00000312783	NM_198436.1	36	Cca/Tca	4/10	0.50494863313668	3	FACETS	0.989	0.919	1	0.494	0.459	0.531	CLONAL	1	TRUE	1	0.50494863313668	3		447	1094	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609027	43609027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483605155	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	255	687	1	ENST00000355710.3:c.1783G>A	p.Glu595Lys	p.E595K	ENST00000355710	NM_020975.4	595	Gag/Aag	10/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.50494863313668	2		688	929	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604206	189604206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	148	475	0	ENST00000264731.3:c.1373C>T	p.Ser458Leu	p.S458L	ENST00000264731	NM_003722.4	458	tCa/tTa	11/14	1	2	FACETS	0.776	0.71	0.846	0.776	0.71	0.846	SUBCLONAL	1	TRUE	1	0.50494863313668	2		475	755	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427387	49427387	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	303	803	0	ENST00000301067.7:c.11101C>T	p.Pro3701Ser	p.P3701S	ENST00000301067	NM_003482.3	3701	Cct/Tct	39/54	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.50494863313668	2		803	1162	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275843	38275843	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781608303	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	292	748	1	ENST00000425967.3:c.1426C>T	p.Arg476Trp	p.R476W	ENST00000425967	NM_001174067.1	476	Cgg/Tgg	11/19	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.50494863313668	2		749	1143	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532683	46532683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	252	320	0	ENST00000262741.5:c.395C>T	p.Ser132Phe	p.S132F	ENST00000262741	NM_003629.3	132	tCc/tTc	4/10	0.256871110724455	3	FACETS	0.852	0.8	0.904	0.852	0.8	0.904	INDETERMINATE	2	TRUE	1	0.50494863313668	3		320	734	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085797	16085797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	245	611	0	ENST00000281043.3:c.973C>T	p.Pro325Ser	p.P325S	ENST00000281043	NM_005378.4	325	Ccc/Tcc	3/3	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.50494863313668	2		611	929	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298476	11298476	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1276797201	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	381	530	0	ENST00000361445.4:c.1985T>C	p.Val662Ala	p.V662A	ENST00000361445	NM_004958.3	662	gTt/gCt	12/58	0.256871110724455	3	FACETS	0.876	0.833	0.919	0.876	0.833	0.919	INDETERMINATE	2	TRUE	1	0.50494863313668	3		530	1079	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818302	43818302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	514	738	1	ENST00000372470.3:c.1767G>A	p.Met589Ile	p.M589I	ENST00000372470	NM_005373.2	589	atG/atA	12/12	0.256871110724455	3	FACETS	0.871	0.835	0.909	0.871	0.835	0.909	INDETERMINATE	2	TRUE	1	0.50494863313668	3		739	1463	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725087	89725087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	33	108	0	ENST00000371953.3:c.1070C>T	p.Pro357Leu	p.P357L	ENST00000371953	NM_000314.4	357	cCa/cTa	9/9	1	2	FACETS	0.817	0.674	0.973	0.817	0.674	0.973	CLONAL	1	TRUE	1	0.50494863313668	2		108	160	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32439144	32439144	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	170	475	0	ENST00000332351.3:c.929A>G	p.Asn310Ser	p.N310S	ENST00000332351	NM_024426.4	310	aAc/aGc	4/10	1	2	FACETS	0.958	0.883	1	0.958	0.883	1	CLONAL	1	TRUE	1	0.50494863313668	2		475	703	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102033218	102033218	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	293	537	0	ENST00000282441.5:c.604C>T	p.Pro202Ser	p.P202S	ENST00000282441	NM_001130145.2	202	Ccc/Tcc	3/9	0.358339020905293	2	FACETS	1	0.988	1	0.583	0.549	0.617	CLONAL	1	TRUE	0	0.50494863313668	2		537	996	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149247	119149247	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	476	545	0	ENST00000264033.4:c.1255T>C	p.Cys419Arg	p.C419R	ENST00000264033	NM_005188.3	419	Tgc/Cgc	9/16	0.358339020905293	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.50494863313668	2		545	931	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623604	28623604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	141	486	0	ENST00000241453.7:c.953C>T	p.Ser318Leu	p.S318L	ENST00000241453	NM_004119.2	318	tCa/tTa	8/24	1	2	FACETS	0.844	0.771	0.92	0.844	0.771	0.92	CLONAL	1	TRUE	1	0.50494863313668	2		486	662	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41023376	41023376	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	162	382	0	ENST00000267868.3:c.1020A>G	p.Ter340TrpextTer8	p.*340Wext*8	ENST00000267868	NM_002875.4	340	tgA/tgG	10/10	1	2	FACETS	0.972	0.895	1	0.972	0.895	1	CLONAL	1	TRUE	1	0.50494863313668	2		382	660	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576241	88576241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	252	562	0	ENST00000360948.2:c.1432G>A	p.Ala478Thr	p.A478T	ENST00000360948	NM_001012338.2	478	Gcc/Acc	13/19	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.50494863313668	2		562	958	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639564	3639564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772219842	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	356	964	1	ENST00000294008.3:c.4075C>T	p.Pro1359Ser	p.P1359S	ENST00000294008	NM_032444.2	1359	Cca/Tca	12/15	1	2	FACETS	0.962	0.91	1	0.962	0.91	1	CLONAL	1	TRUE	1	0.50494863313668	2		965	1465	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3651032	3651032	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	311	536	0	ENST00000294008.3:c.1111G>C	p.Val371Leu	p.V371L	ENST00000294008	NM_032444.2	371	Gtg/Ctg	5/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.50494863313668	2		536	1092	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652855	29652859	+	frameshift_variant	Frame_Shift_Del	DEL	TCAAT	TCAAT	-	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	79	216	0	ENST00000356175.3:c.4790_4794del	p.Ile1597ArgfsTer2	p.I1597Rfs*2	ENST00000356175	NM_000267.3	1597	aTCAAT/a	36/57	1	2	FACETS	0.886	0.785	0.993	0.886	0.785	0.993	CLONAL	1	TRUE	1	0.50494863313668	2		216	353	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649081	37649083	+	missense_variant	Missense_Mutation	TNP	TTA	TTA	CAT	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	124	385	0	ENST00000447079.4:c.2186_2188delinsCAT	p.Ile729_Ile730delinsThrPhe	p.I729_I730delinsTF	ENST00000447079	NM_015083.1	729	aTTAtt/aCATtt	4/14	1	2	FACETS	0.772	0.7	0.848	0.772	0.7	0.848	SUBCLONAL	1	TRUE	1	0.50494863313668	2		385	636	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872593	37872593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	282	814	0	ENST00000269571.5:c.1553G>A	p.Gly518Glu	p.G518E	ENST00000269571		518	gGg/gAg	13/27	1	2	FACETS	0.955	0.897	1	0.955	0.897	1	CLONAL	1	TRUE	1	0.50494863313668	2		814	1169	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37882836	37882836	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	241	762	1	ENST00000269571.5:c.2894G>T	p.Cys965Phe	p.C965F	ENST00000269571		965	tGt/tTt	24/27	1	2	FACETS	0.923	0.862	0.986	0.923	0.862	0.986	CLONAL	1	TRUE	1	0.50494863313668	2		763	1034	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40857184	40857185	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	187	330	1	ENST00000428826.2:c.1856_1857delinsTT	p.Pro619Leu	p.P619L	ENST00000428826		619	cCC/cTT	17/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.50494863313668	2		331	649	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39617720	39617720	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	106	318	0	ENST00000262039.4:c.1904T>A	p.Phe635Tyr	p.F635Y	ENST00000262039	NM_002647.2	635	tTt/tAt	17/25	1	2	FACETS	0.83	0.747	0.917	0.83	0.747	0.917	CLONAL	1	TRUE	1	0.50494863313668	2		318	506	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123764	11123764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	232	649	0	ENST00000358026.2:c.2414C>T	p.Pro805Leu	p.P805L	ENST00000358026	NM_001128849.1	805	cCc/cTc	16/36	1	2	FACETS	0.873	0.814	0.934	0.873	0.814	0.934	CLONAL	1	TRUE	1	0.50494863313668	2		649	1053	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272213	15272213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	269	619	0	ENST00000263388.2:c.6226G>A	p.Gly2076Arg	p.G2076R	ENST00000263388	NM_000435.2	2076	Ggg/Agg	33/33	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.50494863313668	2		619	919	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954592	17954592	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	317	789	0	ENST00000458235.1:c.302G>A	p.Arg101Lys	p.R101K	ENST00000458235	NM_000215.3	101	aGg/aAg	3/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.50494863313668	2		789	1213	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220926	36220926	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	163	445	0	ENST00000222270.7:c.4976T>A	p.Leu1659His	p.L1659H	ENST00000222270	NM_014727.1	1659	cTc/cAc	23/37	1	2	FACETS	0.893	0.821	0.967	0.893	0.821	0.967	CLONAL	1	TRUE	1	0.50494863313668	2		445	723	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727836	41727836	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs765828639	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	327	887	1	ENST00000301178.4:c.461C>A	p.Thr154Asn	p.T154N	ENST00000301178	NM_021913.4	154	aCc/aAc	4/20	1	2	FACETS	0.991	0.935	1	0.991	0.935	1	CLONAL	1	TRUE	1	0.50494863313668	2		888	1307	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752765	42752765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	335	898	0	ENST00000222329.4:c.1499C>T	p.Pro500Leu	p.P500L	ENST00000222329	NM_006494.2	500	cCc/cTc	4/4	1	2	FACETS	0.976	0.922	1	0.976	0.922	1	CLONAL	1	TRUE	1	0.50494863313668	2		898	1359	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795736	42795736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465588621	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	333	946	0	ENST00000575354.2:c.2725C>T	p.Pro909Ser	p.P909S	ENST00000575354	NM_015125.3	909	Ccg/Tcg	11/20	1	2	FACETS	0.925	0.873	0.978	0.925	0.873	0.978	CLONAL	1	TRUE	1	0.50494863313668	2		946	1426	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910370	50910370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	310	894	0	ENST00000440232.2:c.1625C>T	p.Pro542Leu	p.P542L	ENST00000440232	NM_002691.3	542	cCc/cTc	13/27	1	2	FACETS	0.889	0.837	0.943	0.889	0.837	0.943	CLONAL	1	TRUE	1	0.50494863313668	2		894	1381	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918834	50918834	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	339	903	0	ENST00000440232.2:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000440232	NM_002691.3	902	Gag/Aag	21/27	1	2	FACETS	0.932	0.88	0.985	0.932	0.88	0.985	CLONAL	1	TRUE	1	0.50494863313668	2		903	1441	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416427	29416427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	337	763	0	ENST00000389048.3:c.4526C>T	p.Ser1509Phe	p.S1509F	ENST00000389048	NM_004304.4	1509	tCc/tTc	29/29	1	2	FACETS	0.992	0.937	1	0.992	0.937	1	CLONAL	1	TRUE	1	0.50494863313668	2		763	1345	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917802	29917802	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs112782816	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	306	817	0	ENST00000389048.3:c.866C>T	p.Ser289Phe	p.S289F	ENST00000389048	NM_004304.4	289	tCc/tTc	3/29	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.50494863313668	2		817	1212	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589842	212589842	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	229	506	0	ENST00000342788.4:c.700T>C	p.Cys234Arg	p.C234R	ENST00000342788	NM_005235.2	234	Tgt/Cgt	6/28	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.50494863313668	2		506	905	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727095	40727095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	259	638	1	ENST00000373198.4:c.3869C>T	p.Ser1290Phe	p.S1290F	ENST00000373198	NM_133170.3	1290	tCt/tTt	28/32	NA	2	FACETS	0.808	0.755	0.862			1	INDETERMINATE	1	TRUE	NA	0.50494863313668	2		639	1270	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264907	46264907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	170	379	1	ENST00000371998.3:c.1777C>T	p.Leu593Phe	p.L593F	ENST00000371998		593	Ctc/Ttc	12/23	0.50494863313668	3	FACETS	1	0.924	1	0.502	0.462	0.544	CLONAL	1	TRUE	1	0.50494863313668	3		380	840	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324567	62324567	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs754293748	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1355	377	905	0	ENST00000360203.5:c.2923G>C	p.Gly975Arg	p.G975R	ENST00000360203	NM_001283009.1	975	Ggc/Cgc	30/35	0.50494863313668	3	FACETS	1	0.982	1	0.54	0.511	0.57	CLONAL	1	TRUE	1	0.50494863313668	3		905	1732	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665354	182665354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	81	183	0	ENST00000292782.4:c.587G>A	p.Trp196Ter	p.W196*	ENST00000292782	NM_020640.2	196	tGg/tAg	5/7	1	2	FACETS	0.946	0.841	1	0.946	0.841	1	CLONAL	1	TRUE	1	0.50494863313668	2		183	339	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526224	189526224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	321	800	0	ENST00000264731.3:c.488C>T	p.Pro163Leu	p.P163L	ENST00000264731	NM_003722.4	163	cCc/cTc	4/14	1	2	FACETS	0.971	0.916	1	0.971	0.916	1	CLONAL	1	TRUE	1	0.50494863313668	2		800	1309	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807548	1807549	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	335	810	1	ENST00000260795.2:c.1717_1718delinsTT	p.Pro573Leu	p.P573L	ENST00000260795		573	CCg/TTg	12/17	1	2	FACETS	0.983	0.928	1	0.983	0.928	1	CLONAL	1	TRUE	1	0.50494863313668	2		811	1350	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193959	106193959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	147	244	0	ENST00000380013.4:c.4421C>T	p.Ala1474Val	p.A1474V	ENST00000380013	NM_001127208.2	1474	gCt/gTt	10/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.50494863313668	2		244	549	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460555	149460555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	338	790	0	ENST00000286301.3:c.82C>T	p.Pro28Ser	p.P28S	ENST00000286301	NM_005211.3	28	Cct/Tct	3/22	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.50494863313668	2		790	1223	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057075	180057075	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	288	846	1	ENST00000261937.6:c.544G>A	p.Glu182Lys	p.E182K	ENST00000261937	NM_182925.4	182	Gag/Aag	5/30	1	2	FACETS	0.951	0.894	1	0.951	0.894	1	CLONAL	1	TRUE	1	0.50494863313668	2		847	1199	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188361	32188361	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	283	813	0	ENST00000375023.3:c.980G>A	p.Arg327Lys	p.R327K	ENST00000375023	NM_004557.3	327	aGa/aAa	6/30	1	2	FACETS	0.898	0.843	0.955	0.898	0.843	0.955	CLONAL	1	TRUE	1	0.50494863313668	2		813	1248	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120681	94120681	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	161	341	0	ENST00000369303.4:c.370A>G	p.Asn124Asp	p.N124D	ENST00000369303	NM_004440.3	124	Aat/Gat	3/17	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.50494863313668	2		341	634	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109315685	109315688	+	frameshift_variant	Frame_Shift_Del	DEL	CTCT	CTCT	-	rs751167597	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	177	352	0	ENST00000436639.2:c.1097_1100del	p.Glu366ValfsTer57	p.E366Vfs*57	ENST00000436639	NM_014454.2	366	gAGAGt/gt	6/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.50494863313668	2		352	685	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469871	157469871	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs138254872	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	273	695	1	ENST00000346085.5:c.2665C>T	p.Gln889Ter	p.Q889*	ENST00000346085	NM_020732.3	889	Cag/Tag	9/20	1	2	FACETS	0.967	0.908	1	0.967	0.908	1	CLONAL	1	TRUE	1	0.50494863313668	2		696	1118	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963978	2963978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	310	740	0	ENST00000396946.4:c.1829C>T	p.Ser610Phe	p.S610F	ENST00000396946	NM_032415.4	610	tCc/tTc	15/25	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.50494863313668	2		740	1200	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6045616	6045616	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	114	215	0	ENST00000265849.7:c.70C>T	p.His24Tyr	p.H24Y	ENST00000265849	NM_000535.5	24	Cat/Tat	2/15	1	2	FACETS	0.912	0.825	1	0.912	0.825	1	CLONAL	1	TRUE	1	0.50494863313668	2		215	495	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468300	50468300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	266	662	0	ENST00000331340.3:c.1535G>A	p.Gly512Glu	p.G512E	ENST00000331340	NM_006060.4	512	gGg/gAg	8/8	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.50494863313668	2		662	1048	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878754	151878754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367655701	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	165	407	0	ENST00000262189.6:c.6191C>T	p.Ser2064Leu	p.S2064L	ENST00000262189	NM_170606.2	2064	tCa/tTa	36/59	1	2	FACETS	0.943	0.869	1	0.943	0.869	1	CLONAL	1	TRUE	1	0.50494863313668	2		407	693	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29196000	29196000	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	282	725	0	ENST00000240100.2:c.598del	p.Leu200PhefsTer27	p.L200Ffs*27	ENST00000240100	NM_001394.6	200	Ctt/tt	3/4	1	2	FACETS	0.952	0.894	1	0.952	0.894	1	CLONAL	1	TRUE	1	0.50494863313668	2		725	1173	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341712	8341712	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	160	446	0	ENST00000356435.5:c.4928G>A	p.Gly1643Glu	p.G1643E	ENST00000356435		1643	gGa/gAa	29/35	1	2	FACETS	0.867	0.797	0.94	0.867	0.797	0.94	CLONAL	1	TRUE	1	0.50494863313668	2		446	731	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521522	8521522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	197	440	0	ENST00000356435.5:c.716C>T	p.Ser239Phe	p.S239F	ENST00000356435		239	tCt/tTt	9/35	1	2	FACETS	0.871	0.807	0.937	0.871	0.807	0.937	CLONAL	1	TRUE	1	0.50494863313668	2		440	896	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970899	21970899	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	277	685	0	ENST00000304494.5:c.457+2T>G		p.X153_splice	ENST00000304494	NM_000077.4	153			1	2	FACETS	0.915	0.859	0.973	0.915	0.859	0.973	CLONAL	1	TRUE	1	0.50494863313668	2		685	1199	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185483	27185483	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	175	353	1	ENST00000380036.4:c.1183C>T	p.Pro395Ser	p.P395S	ENST00000380036	NM_000459.3	395	Cca/Tca	9/23	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.50494863313668	2		354	665	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755485	133755485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	280	624	0	ENST00000318560.5:c.1454C>T	p.Ser485Phe	p.S485F	ENST00000318560	NM_005157.4	485	tCc/tTc	9/11	1	2	FACETS	0.978	0.919	1	0.978	0.919	1	CLONAL	1	TRUE	1	0.50494863313668	2		624	1134	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405110	139405125	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCAGTCGTCGATGT	CGGCAGTCGTCGATGT	-	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	313	846	0	ENST00000277541.6:c.2720_2735del	p.Asp907GlyfsTer267	p.D907Gfs*267	ENST00000277541	NM_017617.3	907	gACATCGACGACTGCCGg/gg	17/34	1	2	FACETS	0.91	0.857	0.964	0.91	0.857	0.964	CLONAL	1	TRUE	1	0.50494863313668	2		846	1363	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221614	36221615	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	T	novel	NA	P-0047341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	316	861	0	ENST00000222270.7:c.5283_5284delinsT	p.Arg1762ValfsTer133	p.R1762Vfs*133	ENST00000222270	NM_014727.1	1761	tcCCgt/tcTgt	26/37	1	2	FACETS	0.955	0.9	1	0.955	0.9	1	CLONAL	1	TRUE	1	0.50494863313668	2		861	1311	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0047343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	141	889	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.979	0.892	1	0.979	0.892	1	CLONAL	1	TRUE	1	0.32	2		895	900	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0047343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	116	695	5	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.937	0.844	1	0.937	0.844	1	CLONAL	1	TRUE	1	0.32	2		700	774	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467828	50467828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1040607869	NA	P-0047343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	103	743	0	ENST00000331340.3:c.1063G>A	p.Ala355Thr	p.A355T	ENST00000331340	NM_006060.4	355	Gcg/Acg	8/8	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.32	2		743	643	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517413	157517413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370064281	NA	P-0047343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	100	605	0	ENST00000346085.5:c.3977G>A	p.Arg1326His	p.R1326H	ENST00000346085	NM_020732.3	1326	cGc/cAc	16/20	1	2	FACETS	0.906	0.81	1	0.906	0.81	1	CLONAL	1	TRUE	1	0.32	2		605	690	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211270	36211270	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	137	1034	1	ENST00000222270.7:c.1021C>T	p.Gln341Ter	p.Q341*	ENST00000222270	NM_014727.1	341	Caa/Taa	3/37	1	2	FACETS	0.885	0.805	0.971	0.885	0.805	0.971	CLONAL	1	TRUE	1	0.32	2		1035	967	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	147	971	0	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.96	0.876	1	0.96	0.876	1	CLONAL	1	TRUE	1	0.32	2		971	957	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435199	49435199	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	82	794	0	ENST00000301067.7:c.6354del	p.Ala2119LeufsTer25	p.A2119Lfs*25	ENST00000301067	NM_003482.3	2118	ccC/cc	31/54	1	2	FACETS	0.765	0.675	0.862	0.765	0.675	0.862	SUBCLONAL	1	TRUE	1	0.32	2		794	670	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879801	123879801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150318048	NA	P-0047343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	75	451	0	ENST00000330479.4:c.497C>T	p.Ala166Val	p.A166V	ENST00000330479	NM_020382.3	166	gCc/gTc	4/9	1	2	FACETS	0.898	0.788	1	0.898	0.788	1	CLONAL	1	TRUE	1	0.32	2		451	522	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690823	89690824	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CACCG	novel	NA	P-0047343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	77	381	0	ENST00000371953.3:c.232_236dup	p.Lys80ProfsTer21	p.K80Pfs*21	ENST00000371953	NM_000314.4	77	gac/gaCACCGc	4/9	0.3	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.32	2		381	220	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130637	29130638	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0047343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	99	645	0	ENST00000328354.6:c.72_73del	p.Val25TyrfsTer51	p.V25Yfs*51	ENST00000328354	NM_007194.3	24	agCGtt/agtt	2/15	1	2	FACETS	0.813	0.726	0.906	0.813	0.726	0.906	CLONAL	1	TRUE	1	0.32	2		645	761	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591225	67591255	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCTTTTCAAAACTGTTTTTCAGGTGGTTGA	CTCTTTTCAAAACTGTTTTTCAGGTGGTTGA	-	novel	NA	P-0047343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	29	373	0	ENST00000274335.5:c.1746-20_1756del		p.X582_splice	ENST00000274335		582		13/15	1	2	FACETS	0.906	0.733	1	0.906	0.733	1	CLONAL	1	TRUE	1	0.32	2		373	200	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149498321	149498321	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	114	676	0	ENST00000261799.4:c.2893G>T	p.Gly965Cys	p.G965C	ENST00000261799	NM_002609.3	965	Ggt/Tgt	21/23	1	2	FACETS	0.88	0.792	0.973	0.88	0.792	0.973	CLONAL	1	TRUE	1	0.32	2		676	810	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217230	11217230	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786205165	NA	P-0047344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	181	603	0	ENST00000361445.4:c.4448G>T	p.Cys1483Phe	p.C1483F	ENST00000361445	NM_004958.3	1483	tGc/tTc	30/58	1	2	FACETS	0.939	0.867	1	0.939	0.867	1	CLONAL	1	TRUE	1	0.462790638721977	2		603	833	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268931	115268931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	111	440	0	ENST00000438362.2:c.1679C>T	p.Ser560Phe	p.S560F	ENST00000438362	NM_001242891.1	560	tCt/tTt	14/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.462790638721977	2		440	420	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805038	89805038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1203903110	NA	P-0047344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	217	783	0	ENST00000389301.3:c.4339G>A	p.Asp1447Asn	p.D1447N	ENST00000389301	NM_000135.2	1447	Gac/Aac	43/43	1	2	FACETS	0.935	0.869	1	0.935	0.869	1	CLONAL	1	TRUE	1	0.462790638721977	2		783	1003	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40497588	40497588	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	240	586	0	ENST00000264657.5:c.361del	p.Thr121LeufsTer17	p.T121Lfs*17	ENST00000264657	NM_139276.2	121	Act/ct	4/24	1	2	FACETS	0.928	0.866	0.992	0.928	0.866	0.992	CLONAL	1	TRUE	1	0.462790638721977	2		586	1118	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184360	7184360	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	248	654	0	ENST00000302850.5:c.941A>G	p.Glu314Gly	p.E314G	ENST00000302850	NM_000208.2	314	gAg/gGg	3/22	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.462790638721977	2		654	1067	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610581	52610581	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	57	348	0	ENST00000394830.3:c.3592del	p.Thr1198ProfsTer4	p.T1198Pfs*4	ENST00000394830	NM_018313.4	1198	Acc/cc	23/30	0.462790638721977	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.462790638721977	1		348	175	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0047345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	95	824	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	2	TRUE	NA	0.544693976019622	2		824	157	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	22	465	0	ENST00000304494.5:c.250G>C	p.Asp84His	p.D84H	ENST00000304494	NM_000077.4	84	Gac/Cac	2/3	0.490281172257096	3	FACETS	0.871	0.685	1	0.436	0.342	0.54	CLONAL	1	TRUE	1	0.544693976019622	3		465	118	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462635	29462635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747611056	NA	P-0047345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	38	959	1	ENST00000389048.3:c.2266G>A	p.Gly756Ser	p.G756S	ENST00000389048	NM_004304.4	756	Ggc/Agc	13/29	0.342313133112749	0	FACETS	0.496	0.419	0.579			1	SUBCLONAL	1	TRUE	0	0.544693976019622	0		960	128	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78935260	78935260	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	36	940	0	ENST00000306801.3:c.3672C>G	p.Asp1224Glu	p.D1224E	ENST00000306801	NM_020761.2	1224	gaC/gaG	31/34	0.544693976019622	2	FACETS	0.994	0.833	1	0.497	0.416	0.583	CLONAL	1	TRUE	0	0.544693976019622	2		940	133	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217715	7217715	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	48	532	0	ENST00000380728.2:c.212A>C	p.Lys71Thr	p.K71T	ENST00000380728		71	aAg/aCg	4/11	0.460802045634845	4	FACETS	1	0.962	1			1	CLONAL	1	TRUE	NA	0.544693976019622	4		532	190	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414875	56414875	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	38	701	0	ENST00000348428.3:c.2276G>A	p.Gly759Asp	p.G759D	ENST00000348428	NM_006785.3	759	gGt/gAt	17/17	0.264732565292535	3	FACETS	0.906	0.757	1	0.453	0.378	0.534	INDETERMINATE	1	TRUE	1	0.544693976019622	3		701	196	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308344	30308344	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	30	600	1	ENST00000262643.3:c.358A>G	p.Met120Val	p.M120V	ENST00000262643	NM_001238.2	120	Atg/Gtg	6/12	0.260639249271738	5	FACETS	0.958	0.777	1			1	INDETERMINATE	1	TRUE	NA	0.544693976019622	5		601	209	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399338	139399338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	25	914	0	ENST00000277541.6:c.4805C>T	p.Thr1602Ile	p.T1602I	ENST00000277541	NM_017617.3	1602	aCc/aTc	26/34	0.544693976019622	2	FACETS	0.701	0.56	0.857	0.35	0.28	0.429	SUBCLONAL	1	TRUE	0	0.544693976019622	2		914	131	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0047346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	237	705	0	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	0.301038152133297	1	FACETS	1	0.977	1	1	0.995	1	CLONAL	2	TRUE	0	0.15	1		705	1322	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265404	152265404	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	65	487	0	ENST00000206249.3:c.857T>C	p.Met286Thr	p.M286T	ENST00000206249	NM_000125.3	286	aTg/aCg	4/8	1	2	FACETS	0.959	0.829	1	0.959	0.829	1	CLONAL	1	TRUE	1	0.15	2		487	904	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577123	7577123	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876660333	NA	P-0047347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	425	675	0	ENST00000269305.4:c.815T>A	p.Val272Glu	p.V272E	ENST00000269305	NM_001126112.2	272	gTg/gAg	8/11	0.734046853580575	2	FACETS	0.815	0.787	0.842	0.815	0.787	0.842	CLONAL	2	TRUE	0	0.81249704636878	2		675	642	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528237	103528237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	39	258	0	ENST00000355739.4:c.3545G>A	p.Arg1182Lys	p.R1182K	ENST00000355739	NM_000123.3	1182	aGa/aAa	15/15	1	2	FACETS	0.33	0.274	0.391	0.33	0.274	0.391	SUBCLONAL	1	TRUE	1	0.81249704636878	2		258	291	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871765	35871772	+	frameshift_variant	Frame_Shift_Del	DEL	GGTAACTC	GGTAACTC	TTCTGA	novel	NA	P-0047347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	100	640	1	ENST00000216797.5:c.734_741delinsTCAGAA	p.Arg245IlefsTer39	p.R245Ifs*39	ENST00000216797	NM_020529.2	245	aGAGTTACC/aTCAGAA	5/6	0.366277874205326	1	FACETS	0.253	0.226	0.281	0.253	0.226	0.281	INDETERMINATE	1	TRUE	0	0.81249704636878	1		641	578	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	152	516	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.752860008453006	2		516	395	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624840	9624840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1184049921	NA	P-0047354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	250	503	0	ENST00000353224.5:c.137C>T	p.Thr46Met	p.T46M	ENST00000353224	NM_177990.2	46	aCg/aTg	3/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.752860008453006	2		503	581	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0047354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	254	472	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.752860008453006	3	FACETS	1	0.954	1	0.511	0.479	0.544	CLONAL	1	TRUE	1	0.752860008453006	3		472	909	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467645	50467645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773981346	NA	P-0047354-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	180	486	0	ENST00000331340.3:c.880G>A	p.Asp294Asn	p.D294N	ENST00000331340	NM_006060.4	294	Gac/Aac	8/8	0.752860008453006	3	FACETS	1	0.947	1	0.513	0.475	0.553	CLONAL	1	TRUE	1	0.752860008453006	3		486	641	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414399	6414399	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	76	194	0	ENST00000356142.4:c.33C>A	p.Asp11Glu	p.D11E	ENST00000356142	NM_018890.3	11	gaC/gaA	1/7	0.261010964072805	5	FACETS	0.793	0.7	0.89	0.528	0.467	0.594	INDETERMINATE	2	TRUE	2	0.465137615181516	5		194	350	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222593	69222593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1194693256	NA	P-0047355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	70	322	1	ENST00000462284.1:c.566G>A	p.Arg189His	p.R189H	ENST00000462284	NM_002392.5	189	cGc/cAc	8/11	1	2	FACETS	0.993	0.874	1	0.993	0.874	1	CLONAL	1	TRUE	1	0.465137615181516	2		323	303	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566521	41566521	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	76	291	0	ENST00000263253.7:c.4398G>C	p.Trp1466Cys	p.W1466C	ENST00000263253	NM_001429.3	1466	tgG/tgC	27/31	0.465137615181516	1	FACETS	0.965	0.857	1	0.965	0.857	1	CLONAL	1	TRUE	0	0.465137615181516	1		291	260	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151882717	151882717	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0047355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	23	196	0	ENST00000262189.6:c.5009-1G>C		p.X1670_splice	ENST00000262189	NM_170606.2	1670			1	2	FACETS	0.622	0.489	0.772	0.622	0.489	0.772	SUBCLONAL	1	TRUE	1	0.465137615181516	2		196	159	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430854	78430854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1203134411	NA	P-0047355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	135	368	0	ENST00000370768.2:c.535C>T	p.His179Tyr	p.H179Y	ENST00000370768	NM_003902.3	179	Cat/Tat	8/20	0.465137615181516	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.465137615181516	1		368	406	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779698	3779698	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	156	690	0	ENST00000262367.5:c.5350C>T	p.Gln1784Ter	p.Q1784*	ENST00000262367	NM_004380.2	1784	Cag/Tag	31/31	0.465137615181516	3	FACETS	0.954	0.874	1	0.477	0.437	0.519	CLONAL	1	TRUE	1	0.465137615181516	3		690	867	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781273	3781273	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	242	868	0	ENST00000262367.5:c.5092C>G	p.Gln1698Glu	p.Q1698E	ENST00000262367	NM_004380.2	1698	Cag/Gag	30/31	0.465137615181516	3	FACETS	1	0.979	1	0.557	0.52	0.596	CLONAL	1	TRUE	1	0.465137615181516	3		868	1151	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074308	30074308	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	80	291	0	ENST00000338641.4:c.1570G>T	p.Glu524Ter	p.E524*	ENST00000338641	NM_000268.3	524	Gaa/Taa	14/16	0.465137615181516	1	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	0	0.465137615181516	1		291	259	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028871	47028871	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047355-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	139	527	0	ENST00000377604.3:c.175G>T	p.Asp59Tyr	p.D59Y	ENST00000377604	NM_001204468.1	59	Gac/Tac	3/24	1	2	FACETS	0.937	0.855	1	0.937	0.855	1	CLONAL	1	TRUE	1	0.465137615181516	2		527	638	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566521	41566521	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047355-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	77	291	0	ENST00000263253.7:c.4398G>C	p.Trp1466Cys	p.W1466C	ENST00000263253	NM_001429.3	1466	tgG/tgC	27/31	0.302088779528648	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.3	1		291	345	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151882717	151882717	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0047355-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	23	196	0	ENST00000262189.6:c.5009-1G>C		p.X1670_splice	ENST00000262189	NM_170606.2	1670			1	2	FACETS	0.941	0.74	1	0.941	0.74	1	CLONAL	1	TRUE	1	0.3	2		196	163	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430854	78430854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1203134411	NA	P-0047355-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	86	368	0	ENST00000370768.2:c.535C>T	p.His179Tyr	p.H179Y	ENST00000370768	NM_003902.3	179	Cat/Tat	8/20	0.28772056462869	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.3	1		368	424	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074308	30074308	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047355-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	85	291	0	ENST00000338641.4:c.1570G>T	p.Glu524Ter	p.E524*	ENST00000338641	NM_000268.3	524	Gaa/Taa	14/16	0.302088779528648	1	FACETS	0.767	0.685	0.853	1	0.981	1	SUBCLONAL	2	TRUE	0	0.3	1		291	314	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0047356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	139	470	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.705436713113151	2		470	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0047356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	73	509	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	1	2	FACETS	0.358	0.313	0.406	0.358	0.313	0.406	SUBCLONAL	1	TRUE	1	0.705436713113151	2		509	578	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	42	516	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.218624163218515	2		516	350	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0047357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	119	430	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.20827556555335	2	FACETS	0.823	0.745	0.906	0.823	0.745	0.906	CLONAL	2	TRUE	0	0.218624163218515	2		430	661	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0047357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	95	520	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.218624163218515	2		520	764	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980844	40980844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	67	668	0	ENST00000373198.4:c.1642G>A	p.Glu548Lys	p.E548K	ENST00000373198	NM_133170.3	548	Gaa/Aaa	10/32	1	2	FACETS	0.896	0.778	1	0.896	0.778	1	CLONAL	1	TRUE	1	0.218624163218515	2		668	684	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	90	527	0	ENST00000304494.5:c.262G>A	p.Glu88Lys	p.E88K	ENST00000304494	NM_000077.4	88	Gag/Aag	2/3	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.218624163218515	2		527	657	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005419	29005419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55687105	NA	P-0047357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	31	288	0	ENST00000282397.4:c.842G>A	p.Arg281Gln	p.R281Q	ENST00000282397	NM_002019.4	281	cGa/cAa	7/30	1	2	FACETS	0.7	0.566	0.852	0.7	0.566	0.852	SUBCLONAL	1	TRUE	1	0.218624163218515	2		288	405	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022962	33022962	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	54	429	2	ENST00000300177.4:c.71G>A	p.Gly24Glu	p.G24E	ENST00000300177	NM_001191322.1	24	gGg/gAg	2/2	1	2	FACETS	0.937	0.801	1	0.937	0.801	1	CLONAL	1	TRUE	1	0.218624163218515	2		431	527	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245381	153245381	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	55	496	0	ENST00000281708.4:c.1810A>G	p.Lys604Glu	p.K604E	ENST00000281708	NM_033632.3	604	Aaa/Gaa	11/12	1	2	FACETS	0.886	0.758	1	0.886	0.758	1	CLONAL	1	TRUE	1	0.218624163218515	2		496	568	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058515	69058515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	69	470	0	ENST00000288368.4:c.4159C>T	p.His1387Tyr	p.H1387Y	ENST00000288368	NM_024870.2	1387	Cat/Tat	34/40	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.218624163218515	2		470	516	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332598	153332598	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	30	312	0	ENST00000281708.4:c.358C>T	p.Gln120Ter	p.Q120*	ENST00000281708	NM_033632.3	120	Cag/Tag	2/12	1	2	FACETS	0.624	0.502	0.762	0.624	0.502	0.762	SUBCLONAL	1	TRUE	1	0.218624163218515	2		312	440	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719930	18719930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	32	283	0	ENST00000266497.5:c.3827G>A	p.Arg1276Lys	p.R1276K	ENST00000266497		1276	aGa/aAa	27/31	1	2	FACETS	0.681	0.552	0.826	0.681	0.552	0.826	SUBCLONAL	1	TRUE	1	0.218624163218515	2		283	430	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2218087	2218087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	122	760	0	ENST00000326181.6:c.149C>T	p.Thr50Ile	p.T50I	ENST00000326181	NM_032271.2	50	aCc/aTc	4/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.218624163218515	2		760	975	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114824	108114824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	41	368	0	ENST00000278616.4:c.641C>T	p.Ser214Phe	p.S214F	ENST00000278616	NM_000051.3	214	tCc/tTc	6/63	0.218443610062312	1	FACETS	0.792	0.66	0.938	0.792	0.66	0.938	CLONAL	1	TRUE	0	0.218624163218515	1		368	422	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246264	46246264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	55	335	0	ENST00000334344.6:c.4358C>T	p.Ala1453Val	p.A1453V	ENST00000334344	NM_152641.2	1453	gCt/gTt	15/21	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.218624163218515	2		335	458	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912975	32912975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358680	NA	P-0047357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	46	349	1	ENST00000380152.3:c.4483G>A	p.Val1495Ile	p.V1495I	ENST00000380152		1495	Gtc/Atc	11/27	1	2	FACETS	0.799	0.672	0.938	0.799	0.672	0.938	CLONAL	1	TRUE	1	0.218624163218515	2		350	527	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639981	3639982	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0047357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	75	726	2	ENST00000294008.3:c.3657_3658delinsAA	p.Gly1220Arg	p.G1220R	ENST00000294008	NM_032444.2	1219	gaGGgg/gaAAgg	12/15	1	2	FACETS	0.812	0.71	0.922	0.812	0.71	0.922	CLONAL	1	TRUE	1	0.218624163218515	2		728	845	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032058	10032058	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555455645	NA	P-0047357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	67	506	0	ENST00000330684.3:c.765G>A	p.Trp255Ter	p.W255*	ENST00000330684	NM_001134407.1	255	tgG/tgA	3/13	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.218624163218515	2		506	612	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014127	70014128	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGCATCAT	novel	NA	P-0047357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	68	453	0	ENST00000394351.3:c.989_996dup	p.Ala333SerfsTer6	p.A333Sfs*6	ENST00000394351	NM_000248.3	330	cag/cAGCATCATag	9/9	1	2	FACETS	0.991	0.862	1	0.991	0.862	1	CLONAL	1	TRUE	1	0.218624163218515	2		453	628	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876434	35876434	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	96	592	1	ENST00000303115.3:c.1226G>A	p.Gly409Glu	p.G409E	ENST00000303115	NM_002185.3	409	gGg/gAg	8/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.218624163218515	2		593	687	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710554	117710554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	23	208	0	ENST00000368508.3:c.1718C>T	p.Ala573Val	p.A573V	ENST00000368508	NM_002944.2	573	gCt/gTt	12/43	1	2	FACETS	0.704	0.549	0.882	0.704	0.549	0.882	SUBCLONAL	1	TRUE	1	0.218624163218515	2		208	299	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194917	29194917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	86	671	0	ENST00000240100.2:c.811G>A	p.Asp271Asn	p.D271N	ENST00000240100	NM_001394.6	271	Gac/Aac	4/4	1	2	FACETS	0.873	0.771	0.983	0.873	0.771	0.983	CLONAL	1	TRUE	1	0.218624163218515	2		671	901	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971075	21971076	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0047357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	82	567	0	ENST00000304494.5:c.282_283delinsAA	p.Val95Met	p.V95M	ENST00000304494	NM_000077.4	94	ctGGtg/ctAAtg	2/3	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.218624163218515	2		567	680	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239078	98239078	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	40	383	0	ENST00000331920.6:c.1565T>G	p.Phe522Cys	p.F522C	ENST00000331920	NM_000264.3	522	tTc/tGc	11/24	0.218624163218515	1	FACETS	0.691	0.574	0.821	0.691	0.574	0.821	SUBCLONAL	1	TRUE	0	0.218624163218515	1		383	472	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	119	349	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.295377457464884	3	FACETS	0.908	0.827	0.991	0.908	0.827	0.991	CLONAL	2	TRUE	1	0.418271735569417	3		349	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0047358-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	118	424	2	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.385748351382079	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.418271735569417	1		426	437	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711893	89711893	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204864	NA	P-0047361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	57	293	0	ENST00000371953.3:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000371953	NM_000314.4	171	Cag/Tag	6/9	1	2	FACETS	0.966	0.839	1	0.966	0.839	1	CLONAL	1	TRUE	1	0.513046145048914	2		293	230	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0047361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	147	686	0	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	0.465460505123481	1	FACETS	0.862	0.793	0.934	0.862	0.793	0.934	CLONAL	1	TRUE	0	0.513046145048914	1		686	494	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844166	68844167	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	135	516	0	ENST00000261769.5:c.755dup	p.Thr253AsnfsTer5	p.T253Nfs*5	ENST00000261769	NM_004360.3	252	gta/gTta	6/16	0.465460505123481	1	FACETS	0.957	0.878	1	0.957	0.878	1	CLONAL	1	TRUE	0	0.513046145048914	1		516	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579366	7579366	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs770776262	NA	P-0047362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	459	569	1	ENST00000269305.4:c.321C>A	p.Tyr107Ter	p.Y107*	ENST00000269305	NM_001126112.2	107	taC/taA	4/11	0.703600081011045	2	FACETS	0.982	0.952	1	0.982	0.952	1	CLONAL	2	TRUE	0	0.704673674531903	2		570	663	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94201032	94201032	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs570102851	NA	P-0047362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	78	253	0	ENST00000323929.3:c.1045C>T	p.Arg349Trp	p.R349W	ENST00000323929	NM_005591.3	349	Cgg/Tgg	10/20	0.702709146147453	3	FACETS	0.853	0.755	0.956	0.426	0.377	0.478	CLONAL	1	TRUE	1	0.704673674531903	3		253	351	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444803	49444829	+	inframe_deletion	In_Frame_Del	DEL	TCCCCAGGGGGAGGGAACAAGGGCAGC	TCCCCAGGGGGAGGGAACAAGGGCAGC	-	novel	NA	P-0047362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	183	651	0	ENST00000301067.7:c.2637_2663del	p.Leu880_Glu888del	p.L880_E888del	ENST00000301067	NM_003482.3	879	gaGCTGCCCTTGTTCCCTCCCCCTGGGGAa/gaa	10/54	0.702709146147453	3	FACETS	0.779	0.719	0.841	0.389	0.359	0.421	SUBCLONAL	1	TRUE	1	0.704673674531903	3		651	902	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468316	50468316	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	73	474	0	ENST00000331340.3:c.1551del	p.His517GlnfsTer2	p.H517Qfs*2	ENST00000331340	NM_006060.4	517	caC/ca	8/8	0.395033347655859	3	FACETS	0.513	0.449	0.582	0.257	0.224	0.291	INDETERMINATE	1	TRUE	1	0.704673674531903	3		474	546	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517901	8517901	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	97	249	0	ENST00000356435.5:c.1490C>A	p.Ser497Ter	p.S497*	ENST00000356435		497	tCa/tAa	10/35	0.704673674531903	2	FACETS	0.994	0.899	1	0.497	0.449	0.546	CLONAL	1	TRUE	0	0.704673674531903	2		249	277	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	83	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.365471673006317	3	FACETS	1	0.978	1	0.702	0.629	0.779	CLONAL	1	TRUE	1	0.606377829711002	3		511	254	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	217	438	2	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.606377829711002	3	FACETS	0.773	0.724	0.824	0.773	0.724	0.824	SUBCLONAL	2	TRUE	1	0.606377829711002	3		440	603	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	206	502	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.606377829711002	2		507	477	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	151	763	8	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	NA	2	FACETS	0.666	0.61	0.725			1	INDETERMINATE	1	TRUE	NA	0.606377829711002	2		771	748	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	144	654	0	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	0.606377829711002	3	FACETS	0.509	0.463	0.558	0.17	0.154	0.186	SUBCLONAL	1	TRUE	0	0.606377829711002	3		654	1215	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	139	771	3	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.59	0.537	0.645	0.59	0.537	0.645	SUBCLONAL	1	TRUE	1	0.606377829711002	2		774	777	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	394	889	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.839	0.804	0.875	1	0.996	1	CLONAL	2	TRUE	1	0.606377829711002	2		895	774	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188125	11188125	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	90	464	2	ENST00000361445.4:c.5969C>T	p.Ala1990Val	p.A1990V	ENST00000361445	NM_004958.3	1990	gCa/gTa	43/58	NA	2	FACETS	0.502	0.446	0.562			1	INDETERMINATE	1	TRUE	NA	0.606377829711002	2		466	591	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023290	27023290	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	74	131	0	ENST00000324856.7:c.400del	p.Ala134ArgfsTer98	p.A134Rfs*98	ENST00000324856	NM_006015.4	132	gtG/gt	1/20	1	2	FACETS	0.884	0.783	0.991	0.884	0.783	0.991	CLONAL	1	TRUE	1	0.606377829711002	2		131	276	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	180	633	2	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.931	0.862	1	0.931	0.862	1	CLONAL	1	TRUE	1	0.606377829711002	2		635	638	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807505	36807505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200986219	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	77	652	1	ENST00000373129.3:c.1159G>A	p.Glu387Lys	p.E387K	ENST00000373129	NM_032017.1	387	Gag/Aag	12/12	1	2	FACETS	0.28	0.245	0.317	0.28	0.245	0.317	SUBCLONAL	1	TRUE	1	0.606377829711002	2		653	908	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814661	43814661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777700319	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	163	423	1	ENST00000372470.3:c.1456G>A	p.Ala486Thr	p.A486T	ENST00000372470	NM_005373.2	486	Gcc/Acc	9/12	1	2	FACETS	0.843	0.776	0.911	0.843	0.776	0.911	CLONAL	1	TRUE	1	0.606377829711002	2		424	638	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797138	45797138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748700385	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	108	769	0	ENST00000450313.1:c.1277G>A	p.Arg426His	p.R426H	ENST00000450313	NM_012222.2	426	cGt/cAt	13/16	1	2	FACETS	0.356	0.318	0.396	0.356	0.318	0.396	SUBCLONAL	1	TRUE	1	0.606377829711002	2		769	1001	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521525	46521525	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	161	422	1	ENST00000262741.5:c.883del	p.Met295Ter	p.M295*	ENST00000262741	NM_003629.3	295	Atg/tg	7/10	1	2	FACETS	0.982	0.906	1	0.982	0.906	1	CLONAL	1	TRUE	1	0.606377829711002	2		423	541	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430401	78430401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs548529194	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	53	308	0	ENST00000370768.2:c.767G>A	p.Arg256His	p.R256H	ENST00000370768	NM_003902.3	256	cGt/cAt	10/20	1	2	FACETS	0.439	0.375	0.509	0.439	0.375	0.509	SUBCLONAL	1	TRUE	1	0.606377829711002	2		308	398	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091353	193091353	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	33	311	0	ENST00000367435.3:c.23T>G	p.Leu8Arg	p.L8R	ENST00000367435	NM_024529.4	8	cTg/cGg	1/17	1	2	FACETS	0.28	0.228	0.338	0.28	0.228	0.338	SUBCLONAL	1	TRUE	1	0.606377829711002	2		311	389	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858937	243858937	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	14	331	0	ENST00000263826.5:c.128A>G	p.Gln43Arg	p.Q43R	ENST00000263826	NM_005465.4	43	cAa/cGa	2/13	1	2	FACETS	0.262	0.19	0.349	0.262	0.19	0.349	SUBCLONAL	1	TRUE	1	0.606377829711002	2		331	176	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100456	8100456	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	240	744	0	ENST00000346208.3:c.430G>A	p.Gly144Ser	p.G144S	ENST00000346208		144	Ggc/Agc	3/6	0.365471673006317	3	FACETS	0.982	0.917	1	0.491	0.458	0.525	CLONAL	1	TRUE	1	0.606377829711002	3		744	1050	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88677064	88677064	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	45	378	0	ENST00000372037.3:c.849G>A	p.Met283Ile	p.M283I	ENST00000372037	NM_004329.2	283	atG/atA	9/13	0.606377829711002	3	FACETS	0.321	0.269	0.379	0.161	0.134	0.19	SUBCLONAL	1	TRUE	1	0.606377829711002	3		378	602	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724362	112724362	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	79	366	0	ENST00000369452.4:c.252del	p.Lys84AsnfsTer7	p.K84Nfs*7	ENST00000369452	NM_007373.3	82	agA/ag	2/9	0.606377829711002	3	FACETS	0.484	0.425	0.547	0.242	0.212	0.274	SUBCLONAL	1	TRUE	1	0.606377829711002	3		366	702	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741936	17741936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	96	281	1	ENST00000250003.3:c.607C>T	p.Arg203Cys	p.R203C	ENST00000250003	NM_002478.4	203	Cgc/Tgc	1/3	0.200087538181165	0	FACETS	0.335	0.301	0.371			1	INDETERMINATE	1	TRUE	0	0.606377829711002	0		282	372	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200877	67200877	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	190	595	0	ENST00000312629.5:c.870del	p.Tyr291ThrfsTer14	p.Y291Tfs*14	ENST00000312629	NM_003952.2	289	Ccc/cc	10/15	1	2	FACETS	0.858	0.796	0.923	0.858	0.796	0.923	CLONAL	1	TRUE	1	0.606377829711002	2		595	730	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201717	67201717	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772467031	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	92	585	0	ENST00000312629.5:c.1018C>T	p.Arg340Cys	p.R340C	ENST00000312629	NM_003952.2	340	Cgt/Tgt	12/15	1	2	FACETS	0.371	0.329	0.415	0.371	0.329	0.415	SUBCLONAL	1	TRUE	1	0.606377829711002	2		585	819	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998718	100998718	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	152	670	0	ENST00000325455.5:c.1084G>A	p.Ala362Thr	p.A362T	ENST00000325455	NM_001202474.3	362	Gcg/Acg	1/8	1	2	FACETS	0.785	0.72	0.852	0.785	0.72	0.852	SUBCLONAL	1	TRUE	1	0.606377829711002	2		670	639	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999041	100999041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	122	626	0	ENST00000325455.5:c.761C>T	p.Ala254Val	p.A254V	ENST00000325455	NM_001202474.3	254	gCg/gTg	1/8	1	2	FACETS	0.632	0.572	0.694	0.632	0.572	0.694	SUBCLONAL	1	TRUE	1	0.606377829711002	2		626	637	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448476	49448476	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	89	572	1	ENST00000301067.7:c.235C>T	p.Gln79Ter	p.Q79*	ENST00000301067	NM_003482.3	79	Cag/Tag	3/54	1	2	FACETS	0.371	0.328	0.416	0.371	0.328	0.416	SUBCLONAL	1	TRUE	1	0.606377829711002	2		573	792	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50483719	50483719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746898820	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	184	449	1	ENST00000394963.4:c.824C>T	p.Pro275Leu	p.P275L	ENST00000394963	NM_003076.4	275	cCg/cTg	7/13	1	2	FACETS	0.992	0.92	1	0.992	0.92	1	CLONAL	1	TRUE	1	0.606377829711002	2		450	612	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478922	56478922	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	252	560	0	ENST00000267101.3:c.378C>A	p.Asn126Lys	p.N126K	ENST00000267101	NM_001982.3	126	aaC/aaA	3/28	1	2	FACETS	0.963	0.903	1	0.963	0.903	1	CLONAL	1	TRUE	1	0.606377829711002	2		560	863	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914046	32914046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358777	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	64	349	0	ENST00000380152.3:c.5554G>A	p.Val1852Ile	p.V1852I	ENST00000380152		1852	Gtt/Att	11/27	1	2	FACETS	0.986	0.867	1	0.986	0.867	1	CLONAL	1	TRUE	1	0.606377829711002	2		349	214	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436217	110436217	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	131	515	0	ENST00000375856.3:c.2184G>T	p.Lys728Asn	p.K728N	ENST00000375856	NM_003749.2	728	aaG/aaT	1/2	1	2	FACETS	0.749	0.682	0.818	0.749	0.682	0.818	SUBCLONAL	1	TRUE	1	0.606377829711002	2		515	577	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436315	110436315	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	138	291	1	ENST00000375856.3:c.2086G>A	p.Ala696Thr	p.A696T	ENST00000375856	NM_003749.2	696	Gcc/Acc	1/2	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.606377829711002	2		292	390	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873807	35873807	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768610997	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	146	321	0	ENST00000216797.5:c.44G>A	p.Gly15Asp	p.G15D	ENST00000216797	NM_020529.2	15	gGc/gAc	1/6	0.383218616512957	4	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.606377829711002	4		321	555	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42057092	42057092	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	40	374	0	ENST00000219905.7:c.7753T>C	p.Ser2585Pro	p.S2585P	ENST00000219905	NM_001164273.1	2585	Tca/Cca	23/24	1	2	FACETS	0.271	0.225	0.322	0.271	0.225	0.322	SUBCLONAL	1	TRUE	1	0.606377829711002	2		374	487	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	109	636	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.458	0.411	0.508	0.458	0.411	0.508	SUBCLONAL	1	TRUE	1	0.606377829711002	2		636	785	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007825	45007825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	69	333	0	ENST00000558401.1:c.276del	p.Thr93LeufsTer10	p.T93Lfs*10	ENST00000558401	NM_004048.2	91	aCc/ac	2/4	1	2	FACETS	0.513	0.448	0.582	0.513	0.448	0.582	SUBCLONAL	1	TRUE	1	0.606377829711002	2		333	444	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347722	347722	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	205	603	0	ENST00000262320.3:c.1784G>T	p.Ser595Ile	p.S595I	ENST00000262320	NM_003502.3	595	aGt/aTt	6/11	1	2	FACETS	0.888	0.826	0.952	0.888	0.826	0.952	CLONAL	1	TRUE	1	0.606377829711002	2		603	761	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2114373	2114373	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	241	769	0	ENST00000219476.3:c.1544T>C	p.Leu515Pro	p.L515P	ENST00000219476	NM_000548.3	515	cTg/cCg	15/42	1	2	FACETS	0.919	0.86	0.979	0.919	0.86	0.979	CLONAL	1	TRUE	1	0.606377829711002	2		769	865	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778599	3778599	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587783512	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	215	595	0	ENST00000262367.5:c.6449C>T	p.Pro2150Leu	p.P2150L	ENST00000262367	NM_004380.2	2150	cCg/cTg	31/31	1	2	FACETS	0.956	0.891	1	0.956	0.891	1	CLONAL	1	TRUE	1	0.606377829711002	2		595	742	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862712	9862712	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	104	388	1	ENST00000330684.3:c.2591G>A	p.Ser864Asn	p.S864N	ENST00000330684	NM_001134407.1	864	aGc/aAc	12/13	1	2	FACETS	0.796	0.717	0.878	0.796	0.717	0.878	SUBCLONAL	1	TRUE	1	0.606377829711002	2		389	431	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67646013	67646014	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs1470210640	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	52	328	0	ENST00000264010.4:c.950_951del	p.Thr317ArgfsTer91	p.T317Rfs*91	ENST00000264010	NM_006565.3	314	aAC/a	4/12	1	2	FACETS	0.314	0.267	0.366	0.314	0.267	0.366	SUBCLONAL	1	TRUE	1	0.606377829711002	2		328	546	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821959	72821960	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762108866	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	64	345	1	ENST00000268489.5:c.10215dup	p.Gly3406ArgfsTer25	p.G3406Rfs*25	ENST00000268489	NM_006885.3	3405	-/C	10/10	1	2	FACETS	0.448	0.389	0.512	0.448	0.389	0.512	SUBCLONAL	1	TRUE	1	0.606377829711002	2		346	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	53	535	2	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	1	2	FACETS	0.299	0.254	0.348	0.299	0.254	0.348	SUBCLONAL	1	TRUE	1	0.606377829711002	2		537	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577111	7577111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	50	543	1	ENST00000269305.4:c.827C>T	p.Ala276Val	p.A276V	ENST00000269305	NM_001126112.2	276	gCc/gTc	8/11	1	2	FACETS	0.22	0.186	0.258	0.22	0.186	0.258	SUBCLONAL	1	TRUE	1	0.606377829711002	2		544	748	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782177	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	67	515	1	ENST00000269305.4:c.644G>T	p.Ser215Ile	p.S215I	ENST00000269305	NM_001126112.2	215	aGt/aTt	6/11	1	2	FACETS	0.334	0.29	0.382	0.334	0.29	0.382	SUBCLONAL	1	TRUE	1	0.606377829711002	2		516	662	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578214	7578214	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	71	523	1	ENST00000269305.4:c.635T>A	p.Phe212Tyr	p.F212Y	ENST00000269305	NM_001126112.2	212	tTt/tAt	6/11	1	2	FACETS	0.347	0.303	0.396	0.347	0.303	0.396	SUBCLONAL	1	TRUE	1	0.606377829711002	2		524	674	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	168	436	0	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	0.885	0.817	0.956	0.885	0.817	0.956	CLONAL	1	TRUE	1	0.606377829711002	2		436	626	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732390	74732395	+	inframe_deletion	In_Frame_Del	DEL	GGACTT	GGACTT	-	rs746260518	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	141	422	1	ENST00000359995.5:c.514_519del	p.Lys172_Ser173del	p.K172_S173del	ENST00000359995	NM_001195427.1	172	AAGTCC/-	2/3	1	2	FACETS	0.703	0.642	0.766	0.703	0.642	0.766	SUBCLONAL	1	TRUE	1	0.606377829711002	2		423	662	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573556	48573556	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	24	156	0	ENST00000342988.3:c.140T>C	p.Leu47Pro	p.L47P	ENST00000342988	NM_005359.5	47	cTg/cCg	2/12	0.192094492944988	2	FACETS	0.386	0.304	0.479	0.193	0.152	0.24	INDETERMINATE	1	TRUE	0	0.606377829711002	2		156	205	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603031	48603031	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	149	259	0	ENST00000342988.3:c.1332T>G	p.His444Gln	p.H444Q	ENST00000342988	NM_005359.5	444	caT/caG	11/12	0.192094492944988	2	FACETS	1	0.988	1	0.69	0.639	0.742	INDETERMINATE	1	TRUE	0	0.606377829711002	2		259	356	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214717	5214717	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	38	617	0	ENST00000357368.4:c.4349A>G	p.Asn1450Ser	p.N1450S	ENST00000357368	NM_002850.3	1450	aAc/aGc	29/38	0.407751808369256	1	FACETS	0.131	0.108	0.158	0.131	0.108	0.158	SUBCLONAL	1	TRUE	0	0.606377829711002	1		617	665	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117126	7117127	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	242	573	0	ENST00000302850.5:c.4089_4090del	p.Met1364GlufsTer39	p.M1364Efs*39	ENST00000302850	NM_000208.2	1363	caCAtg/catg	22/22	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.606377829711002	NA		573	686	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247809	10247809	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1368186167	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	91	697	1	ENST00000340748.4:c.4393G>A	p.Gly1465Ser	p.G1465S	ENST00000340748		1465	Ggc/Agc	36/40	0.355519051871702	2	FACETS	0.324	0.287	0.364	0.162	0.143	0.182	INDETERMINATE	1	TRUE	0	0.606377829711002	2		698	926	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602652	10602652	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	100	801	0	ENST00000171111.5:c.926C>T	p.Thr309Ile	p.T309I	ENST00000171111	NM_203500.1	309	aCc/aTc	3/6	0.355519051871702	2	FACETS	0.336	0.299	0.375	0.168	0.149	0.188	INDETERMINATE	1	TRUE	0	0.606377829711002	2		801	983	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610241	10610241	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	108	689	0	ENST00000171111.5:c.469A>G	p.Asn157Asp	p.N157D	ENST00000171111	NM_203500.1	157	Aac/Gac	2/6	0.355519051871702	2	FACETS	0.383	0.343	0.426	0.192	0.171	0.213	INDETERMINATE	1	TRUE	0	0.606377829711002	2		689	930	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130334	11130334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1480398200	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	330	587	1	ENST00000358026.2:c.2573C>T	p.Thr858Met	p.T858M	ENST00000358026	NM_001128849.1	858	aCg/aTg	18/36	NA	2	FACETS	0.807	0.77	0.845			1	INDETERMINATE	2	TRUE	NA	0.606377829711002	2		588	674	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273228	18273228	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	227	528	0	ENST00000222254.8:c.1021A>G	p.Asn341Asp	p.N341D	ENST00000222254	NM_005027.3	341	Aac/Gac	9/16	1	2	FACETS	0.927	0.866	0.989	0.927	0.866	0.989	CLONAL	1	TRUE	1	0.606377829711002	2		528	808	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211694	36211694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764859385	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	76	556	0	ENST00000222270.7:c.1445G>A	p.Arg482Gln	p.R482Q	ENST00000222270	NM_014727.1	482	cGg/cAg	3/37	1	2	FACETS	0.342	0.3	0.388	0.342	0.3	0.388	SUBCLONAL	1	TRUE	1	0.606377829711002	2		556	732	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	52	1010	1	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	1	2	FACETS	0.188	0.159	0.22	0.188	0.159	0.22	SUBCLONAL	1	TRUE	1	0.606377829711002	2		1011	912	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213545	36213545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762042908	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	282	821	0	ENST00000222270.7:c.2647C>T	p.Arg883Trp	p.R883W	ENST00000222270	NM_014727.1	883	Cgg/Tgg	5/37	1	2	FACETS	0.914	0.859	0.969	0.914	0.859	0.969	CLONAL	1	TRUE	1	0.606377829711002	2		821	1018	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223997	36223997	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	93	747	0	ENST00000222270.7:c.6552del	p.Lys2185AsnfsTer18	p.K2185Nfs*18	ENST00000222270	NM_014727.1	2183	Ccc/cc	28/37	1	2	FACETS	0.329	0.291	0.369	0.329	0.291	0.369	SUBCLONAL	1	TRUE	1	0.606377829711002	2		747	933	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753478	42753479	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	270	767	0	ENST00000222329.4:c.785dup	p.Gln263SerfsTer46	p.Q263Sfs*46	ENST00000222329	NM_006494.2	262	cct/ccCt	4/4	1	2	FACETS	0.87	0.816	0.924	0.87	0.816	0.924	CLONAL	1	TRUE	1	0.606377829711002	2		767	1024	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46587791	46587791	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1170479651	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	117	378	0	ENST00000263734.3:c.469A>G	p.Lys157Glu	p.K157E	ENST00000263734	NM_001430.4	157	Aaa/Gaa	5/16	1	2	FACETS	0.982	0.893	1	0.982	0.893	1	CLONAL	1	TRUE	1	0.606377829711002	2		378	393	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639588	47639588	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63749897	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	21	227	0	ENST00000233146.2:c.687del	p.Ala230LeufsTer16	p.A230Lfs*16	ENST00000233146	NM_000251.2	227	agA/ag	4/16	1	2	FACETS	0.228	0.175	0.289	0.228	0.175	0.289	SUBCLONAL	1	TRUE	1	0.606377829711002	2		227	304	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907683	111907683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146318804	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	40	367	0	ENST00000393256.3:c.457C>T	p.Arg153Trp	p.R153W	ENST00000393256	NM_006538.4	153	Cgg/Tgg	3/4	NA	2	FACETS	0.251	0.208	0.299			1	INDETERMINATE	1	TRUE	NA	0.606377829711002	2		367	526	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149799	202149799	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	107	424	0	ENST00000358485.4:c.1245del	p.Phe415LeufsTer26	p.F415Lfs*26	ENST00000358485	NM_001080125.1	414	Ttt/tt	8/9	0.248595985093767	3	FACETS	0.765	0.688	0.847			1	INDETERMINATE	1	TRUE	NA	0.606377829711002	3		424	601	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36014498	36014498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	197	532	0	ENST00000358208.4:c.271G>A	p.Ala91Thr	p.A91T	ENST00000358208		91	Gcc/Acc	3/12	1	2	FACETS	0.907	0.843	0.974	0.907	0.843	0.974	CLONAL	1	TRUE	1	0.606377829711002	2		532	716	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57474003	57474003	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	37	260	0	ENST00000371085.3:c.220G>A	p.Glu74Lys	p.E74K	ENST00000371085	NM_000516.4	74	Gaa/Aaa	3/13	1	2	FACETS	0.302	0.249	0.361	0.302	0.249	0.361	SUBCLONAL	1	TRUE	1	0.606377829711002	2		260	404	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319354	62319354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748223349	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	200	743	1	ENST00000360203.5:c.1546G>A	p.Val516Ile	p.V516I	ENST00000360203	NM_001283009.1	516	Gtc/Atc	18/35	1	2	FACETS	0.742	0.688	0.798	0.742	0.688	0.798	SUBCLONAL	1	TRUE	1	0.606377829711002	2		744	889	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067255	37067255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750361	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	98	377	0	ENST00000231790.2:c.1166G>A	p.Arg389Gln	p.R389Q	ENST00000231790	NM_000249.3	389	cGg/cAg	12/19	1	2	FACETS	0.6	0.536	0.666	0.6	0.536	0.666	SUBCLONAL	1	TRUE	1	0.606377829711002	2		377	539	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582243	52582243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1163354335	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	55	226	0	ENST00000394830.3:c.4585C>T	p.Arg1529Cys	p.R1529C	ENST00000394830	NM_018313.4	1529	Cgc/Tgc	30/30	1	2	FACETS	0.637	0.549	0.731	0.637	0.549	0.731	SUBCLONAL	1	TRUE	1	0.606377829711002	2		226	285	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884858	134884858	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774975718	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	129	421	1	ENST00000398015.3:c.1634C>T	p.Ser545Leu	p.S545L	ENST00000398015	NM_004441.4	545	tCg/tTg	8/16	0.177003980388084	0	FACETS	0.34	0.31	0.372			1	INDETERMINATE	1	TRUE	0	0.606377829711002	0		422	492	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274802	142274802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	89	376	1	ENST00000350721.4:c.2258G>A	p.Cys753Tyr	p.C753Y	ENST00000350721	NM_001184.3	753	tGt/tAt	10/47	0.365471673006317	3	FACETS	1	0.968	1	0.607	0.544	0.673	CLONAL	1	TRUE	1	0.606377829711002	3		377	315	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281435	142281435	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	116	430	3	ENST00000350721.4:c.809del	p.Phe270SerfsTer8	p.F270Sfs*8	ENST00000350721	NM_001184.3	270	tTc/tc	4/47	0.365471673006317	3	FACETS	1	0.959	1	0.552	0.5	0.605	CLONAL	1	TRUE	1	0.606377829711002	3		433	452	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	24	254	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	0.365471673006317	3	FACETS	0.357	0.28	0.445	0.178	0.14	0.223	SUBCLONAL	1	TRUE	1	0.606377829711002	3		254	289	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183567	185183567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199572011	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	222	349	0	ENST00000265026.3:c.1421G>A	p.Arg474Gln	p.R474Q	ENST00000265026	NM_004721.4	474	cGg/cAg	9/14	0.365471673006317	3	FACETS	0.864	0.811	0.918	0.864	0.811	0.918	CLONAL	2	TRUE	1	0.606377829711002	3		349	552	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980559	1980559	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs752037034	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	187	663	6	ENST00000382891.5:c.4028del	p.Pro1343GlnfsTer49	p.P1343Qfs*49	ENST00000382891	NM_133335.3	1341	Ccc/cc	22/22	NA	2	FACETS	0.781	0.723	0.841			1	INDETERMINATE	1	TRUE	NA	0.606377829711002	2		669	790	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980601	1980601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201148179	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	119	565	2	ENST00000382891.5:c.4063C>T	p.Arg1355Trp	p.R1355W	ENST00000382891	NM_133335.3	1355	Cgg/Tgg	22/22	NA	2	FACETS	0.595	0.538	0.655			1	INDETERMINATE	1	TRUE	NA	0.606377829711002	2		567	660	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747996	41747996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	25	61	3	ENST00000226382.2:c.773C>T	p.Ala258Val	p.A258V	ENST00000226382	NM_003924.3	258	gCg/gTg	3/3	0.177003980388084	0	FACETS	0.382	0.309	0.461			1	INDETERMINATE	1	TRUE	0	0.606377829711002	0		64	85	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196397	106196397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	78	340	0	ENST00000380013.4:c.4730G>A	p.Ser1577Asn	p.S1577N	ENST00000380013	NM_001127208.2	1577	aGt/aAt	11/11	1	2	FACETS	0.663	0.586	0.745	0.663	0.586	0.745	SUBCLONAL	1	TRUE	1	0.606377829711002	2		340	388	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007332	143007332	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	69	241	0	ENST00000262992.4:c.2452del	p.Arg818GlufsTer4	p.R818Efs*4	ENST00000262992	NM_001101669.1	818	Aga/ga	22/24	1	2	FACETS	0.816	0.718	0.919	0.816	0.718	0.919	CLONAL	1	TRUE	1	0.606377829711002	2		241	279	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278814	1278814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768168259	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	209	659	1	ENST00000310581.5:c.2228G>A	p.Arg743Gln	p.R743Q	ENST00000310581	NM_198253.2	743	cGg/cAg	6/16	0.144033473397125	0	FACETS	0.349	0.325	0.374			1	INDETERMINATE	1	TRUE	0	0.606377829711002	0		660	777	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295195	1295195	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	35	229	0				ENST00000310581	NM_198253.2	-/1132			0.144033473397125	0	FACETS	0.154	0.126	0.185			1	INDETERMINATE	1	TRUE	0	0.606377829711002	0		229	295	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752812	57752812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	79	287	0	ENST00000274289.3:c.1116del	p.Phe372LeufsTer31	p.F372Lfs*31	ENST00000274289	NM_006622.3	372	ttT/tt	8/14	1	2	FACETS	0.937	0.834	1	0.937	0.834	1	CLONAL	1	TRUE	1	0.606377829711002	2		287	278	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517552	176517552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs569265847	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	191	783	2	ENST00000292408.4:c.253C>T	p.Arg85Cys	p.R85C	ENST00000292408	NM_213647.1	85	Cgc/Tgc	3/18	1	2	FACETS	0.752	0.696	0.81	0.752	0.696	0.81	SUBCLONAL	1	TRUE	1	0.606377829711002	2		785	838	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522424	176522424	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	53	676	0	ENST00000292408.4:c.1613G>A	p.Gly538Asp	p.G538D	ENST00000292408	NM_213647.1	538	gGt/gAt	12/18	1	2	FACETS	0.243	0.207	0.283	0.243	0.207	0.283	SUBCLONAL	1	TRUE	1	0.606377829711002	2		676	719	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522720	176522720	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757092386	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	167	617	2	ENST00000292408.4:c.1817G>A	p.Arg606Gln	p.R606Q	ENST00000292408	NM_213647.1	606	cGg/cAg	13/18	1	2	FACETS	0.893	0.824	0.964	0.893	0.824	0.964	CLONAL	1	TRUE	1	0.606377829711002	2		619	617	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	57	336	0	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.522	0.45	0.6	0.522	0.45	0.6	SUBCLONAL	1	TRUE	1	0.606377829711002	2		336	360	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051053	180051053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755736057	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	207	595	0	ENST00000261937.6:c.1430G>A	p.Arg477Gln	p.R477Q	ENST00000261937	NM_182925.4	477	cGg/cAg	11/30	0.251524792024461	0	FACETS	0.429	0.4	0.459			1	INDETERMINATE	1	TRUE	0	0.606377829711002	0		595	626	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402538	20402540	+	inframe_deletion	In_Frame_Del	DEL	CGC	CGC	-	rs775820172	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	124	378	1	ENST00000346618.3:c.84_86del	p.Ala31del	p.A31del	ENST00000346618	NM_001949.4	25	gtCGCc/gtc	1/7	NA	2	FACETS	0.706	0.641	0.775			1	INDETERMINATE	1	TRUE	NA	0.606377829711002	2		379	579	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911072	29911072	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	45	452	0	ENST00000376809.5:c.371G>A	p.Gly124Asp	p.G124D	ENST00000376809	NM_002116.7	124	gGc/gAc	3/8	1	2	FACETS	0.237	0.198	0.279	0.237	0.198	0.279	SUBCLONAL	1	TRUE	1	0.606377829711002	2		452	627	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322914	31322914	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1273680566	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	173	482	2	ENST00000412585.2:c.982G>A	p.Ala328Thr	p.A328T	ENST00000412585	NM_005514.6	328	Gct/Act	5/8	0.136053749331391	4	FACETS	1	0.988	1	0.692	0.639	0.747	INDETERMINATE	1	TRUE	2	0.606377829711002	4		484	662	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324642	31324642	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	45	230	0	ENST00000412585.2:c.166del	p.Gln56SerfsTer3	p.Q56Sfs*3	ENST00000412585	NM_005514.6	56	Cag/ag	2/8	0.136053749331391	4	FACETS	1	0.906	1	0.547	0.464	0.636	INDETERMINATE	1	TRUE	2	0.606377829711002	4		230	218	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32191659	32191664	+	inframe_deletion	In_Frame_Del	DEL	AGCAGC	AGCAGC	-	rs35795312	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	145	507	3	ENST00000375023.3:c.42_47del	p.Leu15_Leu16del	p.L15_L16del	ENST00000375023	NM_004557.3	14	ctGCTGCTa/cta	1/30	1	2	FACETS	0.692	0.633	0.754	0.692	0.633	0.754	SUBCLONAL	1	TRUE	1	0.606377829711002	2		510	691	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800564	32800564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148663600	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	143	608	1	ENST00000374899.4:c.983C>T	p.Ala328Val	p.A328V	ENST00000374899	NM_018833.2	328	gCg/gTg	6/12	1	2	FACETS	0.578	0.527	0.631	0.578	0.527	0.631	SUBCLONAL	1	TRUE	1	0.606377829711002	2		609	816	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908277	41908277	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	231	563	0	ENST00000372991.4:c.245T>C	p.Met82Thr	p.M82T	ENST00000372991	NM_001760.3	82	aTg/aCg	2/5	0.365471673006317	3	FACETS	1	0.983	1	0.575	0.537	0.614	CLONAL	1	TRUE	1	0.606377829711002	3		563	864	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112025282	112025282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370545141	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	105	384	1	ENST00000368678.4:c.467G>A	p.Arg156Gln	p.R156Q	ENST00000368678		156	cGa/cAa	6/13	0.248595985093767	3	FACETS	1	0.935	1			1	INDETERMINATE	1	TRUE	NA	0.606377829711002	3		385	431	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200309	138200309	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773410176	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	106	452	0	ENST00000237289.4:c.1727C>T	p.Pro576Leu	p.P576L	ENST00000237289	NM_001270507.1	576	cCg/cTg	7/9	1	2	FACETS	0.595	0.534	0.658	0.595	0.534	0.658	SUBCLONAL	1	TRUE	1	0.606377829711002	2		452	588	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997769	149997769	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200080860	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	62	412	0	ENST00000253339.5:c.2698C>T	p.Arg900Cys	p.R900C	ENST00000253339		900	Cgc/Tgc	5/7	1	2	FACETS	0.353	0.305	0.406	0.353	0.305	0.406	SUBCLONAL	1	TRUE	1	0.606377829711002	2		412	579	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405954	157405954	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	56	510	0	ENST00000346085.5:c.2201del	p.Gly734AlafsTer11	p.G734Afs*11	ENST00000346085	NM_020732.3	732	ccG/cc	6/20	1	2	FACETS	0.258	0.22	0.299	0.258	0.22	0.299	SUBCLONAL	1	TRUE	1	0.606377829711002	2		510	716	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946143	13946143	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	71	479	2	ENST00000405192.2:c.953del	p.Leu318TrpfsTer2	p.L318Wfs*2	ENST00000405192	NM_001163147.1	318	tTg/tg	10/12	0.479384804237445	3	FACETS	0.553	0.483	0.628	0.276	0.241	0.314	SUBCLONAL	1	TRUE	1	0.606377829711002	3		481	552	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509135	106509135	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs752883989	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	57	517	0	ENST00000359195.3:c.1129A>G	p.Thr377Ala	p.T377A	ENST00000359195	NM_002649.2	377	Acc/Gcc	2/11	0.365471673006317	3	FACETS	0.302	0.259	0.351	0.151	0.129	0.176	SUBCLONAL	1	TRUE	1	0.606377829711002	3		517	810	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509636	106509636	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867282260	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	298	453	0	ENST00000359195.3:c.1630C>T	p.Arg544Ter	p.R544*	ENST00000359195	NM_002649.2	544	Cga/Tga	2/11	0.365471673006317	3	FACETS	0.868	0.822	0.914	0.868	0.822	0.914	CLONAL	2	TRUE	1	0.606377829711002	3		453	738	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371770	116371770	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs369705803	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	243	318	0	ENST00000397752.3:c.1249C>T	p.Arg417Ter	p.R417*	ENST00000397752	NM_000245.2	417	Cga/Tga	3/21	0.606377829711002	3	FACETS	0.956	0.902	1	0.956	0.902	1	CLONAL	2	TRUE	1	0.606377829711002	3		318	546	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851177	151851177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141966811	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	116	361	2	ENST00000262189.6:c.12194C>T	p.Ala4065Val	p.A4065V	ENST00000262189	NM_170606.2	4065	gCg/gTg	48/59	0.606377829711002	3	FACETS	0.923	0.847	1	0.923	0.847	1	CLONAL	2	TRUE	1	0.606377829711002	3		363	270	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345760	152345760	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	58	186	0	ENST00000359321.1:c.810del	p.Phe270LeufsTer27	p.F270Lfs*27	ENST00000359321	NM_005431.1	270	ttT/tt	3/3	0.248595985093767	3	FACETS	0.92	0.798	1			1	INDETERMINATE	1	TRUE	NA	0.606377829711002	3		186	271	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370876	55370876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	64	586	0	ENST00000297316.4:c.178G>A	p.Gly60Ser	p.G60S	ENST00000297316	NM_022454.3	60	Ggc/Agc	1/2	NA	2	FACETS	0.25	0.215	0.287			1	INDETERMINATE	1	TRUE	NA	0.606377829711002	2		586	845	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863054	56863054	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1266824391	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	111	387	1	ENST00000519728.1:c.327del	p.Glu110LysfsTer15	p.E110Kfs*15	ENST00000519728	NM_002350.3	107	acA/ac	5/13	NA	2	FACETS	0.697	0.629	0.769			1	INDETERMINATE	1	TRUE	NA	0.606377829711002	2		388	525	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922484	56922484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	106	352	0	ENST00000519728.1:c.1354G>A	p.Val452Met	p.V452M	ENST00000519728	NM_002350.3	452	Gtg/Atg	13/13	NA	2	FACETS	0.714	0.643	0.788			1	INDETERMINATE	1	TRUE	NA	0.606377829711002	2		352	490	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950509	68950509	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs753865918	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	39	259	0	ENST00000288368.4:c.821A>G	p.Tyr274Cys	p.Y274C	ENST00000288368	NM_024870.2	274	tAc/tGc	7/40	NA	2	FACETS	0.447	0.372	0.529			1	INDETERMINATE	1	TRUE	NA	0.606377829711002	2		259	288	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209616	98209617	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761353734	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	88	567	0	ENST00000331920.6:c.3921dup	p.Arg1308GlnfsTer17	p.R1308Qfs*17	ENST00000331920	NM_000264.3	1307	-/C	23/24	0.479384804237445	3	FACETS	0.522	0.462	0.586	0.261	0.231	0.293	SUBCLONAL	1	TRUE	1	0.606377829711002	3		567	725	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923700	39923700	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372187961	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	208	661	0	ENST00000378444.4:c.3391C>T	p.Arg1131Trp	p.R1131W	ENST00000378444	NM_001123385.1	1131	Cgg/Tgg	7/15	1	2	FACETS	0.844	0.785	0.905	0.844	0.785	0.905	CLONAL	1	TRUE	1	0.606377829711002	2		661	813	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411104	63411104	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	119	570	0	ENST00000330258.3:c.2063C>A	p.Thr688Asn	p.T688N	ENST00000330258	NM_152424.3	688	aCt/aAt	2/2	NA	2	FACETS	0.654	0.592	0.719			1	INDETERMINATE	1	TRUE	NA	0.606377829711002	2		570	600	SUCCESS
AR	367	MSKCC	GRCh37	X	66766348	66766348	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	23	106	0	ENST00000374690.3:c.1364del	p.Gly455ValfsTer24	p.G455Vfs*24	ENST00000374690	NM_000044.3	454	Ggg/gg	1/8	NA	2	FACETS	0.486	0.383	0.604			1	INDETERMINATE	1	TRUE	NA	0.606377829711002	2		106	156	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939502	76939502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782253905	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	100	415	0	ENST00000373344.5:c.1246G>A	p.Glu416Lys	p.E416K	ENST00000373344	NM_000489.3	416	Gag/Aag	9/35	NA	2	FACETS	0.767	0.689	0.848			1	INDETERMINATE	1	TRUE	NA	0.606377829711002	2		415	430	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615679	100615679	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1569292813	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	54	495	0	ENST00000308731.7:c.653del	p.Lys218ArgfsTer11	p.K218Rfs*11	ENST00000308731	NM_000061.2	218	aAg/ag	8/19	0.606377829711002	1	FACETS	0.285	0.244	0.33	0.285	0.244	0.33	SUBCLONAL	1	TRUE	0	0.606377829711002	1		495	435	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991711	72991712	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCC	rs757794567	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	30	356	1	ENST00000268489.5:c.2331_2333dup	p.Ala784dup	p.A784dup	ENST00000268489	NM_006885.3	784	gct/gcGGCt	2/10	1	2	FACETS	0.276	0.222	0.336	0.276	0.222	0.336	SUBCLONAL	1	TRUE	1	0.606377829711002	2		357	359	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349640	89349641	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs772267579	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	129	539	20	ENST00000301030.4:c.3309dup	p.Asp1104ArgfsTer2	p.D1104Rfs*2	ENST00000301030	NM_001256183.1	1103	-/A	9/13	1	2	FACETS	0.644	0.585	0.705	0.644	0.585	0.705	SUBCLONAL	1	TRUE	1	0.606377829711002	2		559	661	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324892	31324892	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs765875917	NA	P-0047363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	83	225	0	ENST00000412585.2:c.44del	p.Ala15GlyfsTer5	p.A15Gfs*5	ENST00000412585	NM_005514.6	15	gCg/gg	1/8	0.136053749331391	4	FACETS	1	0.967	1	0.618	0.549	0.69	INDETERMINATE	1	TRUE	2	0.606377829711002	4		225	356	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047365-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	84	516	0				ENST00000310581	NM_198253.2	-/1132			0.3	2	FACETS	1	0.929	1			1	CLONAL	1	TRUE	NA	0.3	2		516	525	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476387	88476387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202056599	NA	P-0047365-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	107	718	2	ENST00000360948.2:c.1745G>A	p.Arg582Gln	p.R582Q	ENST00000360948	NM_001012338.2	582	cGg/cAg	15/19	1	2	FACETS	0.863	0.773	0.957	0.863	0.773	0.957	CLONAL	1	TRUE	1	0.3	2		720	827	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266111	41266493	+	splice_donor_variant,splice_acceptor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	TTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGC	TTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGC	-	novel	NA	P-0047365-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	84	431	0	ENST00000349496.5:c.109_291del		p.X37_splice	ENST00000349496	NM_001904.3	37	caTTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCt/cat	3-4/15	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.3	2		431	505	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0047371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	49	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.695	0.587	0.812	0.695	0.587	0.812	SUBCLONAL	1	FALSE	1	0.232849419895337	2		511	606	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0047371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	49	272	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	FALSE	1	0.232849419895337	2		272	405	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0047371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1561	485	759	2	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.232849419895337	6	FACETS	0.995	0.948	1			1	CLONAL	3	FALSE	NA	0.232849419895337	6		761	2046	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0047371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	41	331	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.887	0.74	1	0.887	0.74	1	CLONAL	1	FALSE	1	0.232849419895337	2		331	397	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519998	NA	P-0047371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	155	754	0	ENST00000269305.4:c.581T>A	p.Leu194His	p.L194H	ENST00000269305	NM_001126112.2	194	cTt/cAt	6/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.232849419895337	2		754	1048	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0047371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	175	775	1	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.232849419895337	2		776	1278	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778363	3778363	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139688311	NA	P-0047371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	89	878	1	ENST00000262367.5:c.6685G>A	p.Gly2229Ser	p.G2229S	ENST00000262367	NM_004380.2	2229	Ggc/Agc	31/31	1	2	FACETS	0.944	0.836	1	0.944	0.836	1	CLONAL	1	FALSE	1	0.232849419895337	2		879	810	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101238	27101239	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	92	727	0	ENST00000324856.7:c.4522dup	p.Tyr1508LeufsTer24	p.Y1508Lfs*24	ENST00000324856	NM_006015.4	1507	aat/aaTt	18/20	1	2	FACETS	0.941	0.835	1	0.941	0.835	1	CLONAL	1	FALSE	1	0.232849419895337	2		727	840	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617416	43617416	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74799832	NA	P-0047372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	126	571	0	ENST00000355710.3:c.2753T>C	p.Met918Thr	p.M918T	ENST00000355710	NM_020975.4	918	aTg/aCg	16/20	0.26591553515165	3	FACETS	0.873	0.803	0.945	1	0.984	1	CLONAL	3	TRUE	1	0.37	3		571	308	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867546	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs11466445	NA	P-0047373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	11	7	0	ENST00000374994.4:c.70_78del	p.Ala24_Ala26del	p.A24_A26del	ENST00000374994	NM_004612.2	17	ctGGCGGCGGCg/ctg	1/9	1	2	FACETS	0.887	0.637	1	1	0.891	1	CLONAL	2	TRUE	1	0.31	2		7	40	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	224	771	3	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.69	0.643	0.739	0.69	0.643	0.739	SUBCLONAL	1	TRUE	1	0.653825123991689	2		774	993	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	663	889	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.924	0.896	0.95	1	0.998	1	CLONAL	2	TRUE	1	0.653825123991689	2		895	1098	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852245	63852245	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1376484834	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	335	590	3	ENST00000279873.7:c.3023C>T	p.Ala1008Val	p.A1008V	ENST00000279873	NM_032199.2	1008	gCg/gTg	10/10	1	2	FACETS	0.996	0.943	1	0.996	0.943	1	CLONAL	1	TRUE	1	0.653825123991689	2		593	1029	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057936	27057937	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1415146710	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	351	796	0	ENST00000324856.7:c.1650dup	p.Tyr551LeufsTer72	p.Y551Lfs*72	ENST00000324856	NM_006015.4	548	-/C	3/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.653825123991689	2		796	1069	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099361	27099361	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	295	616	0	ENST00000324856.7:c.3598C>T	p.Gln1200Ter	p.Q1200*	ENST00000324856	NM_006015.4	1200	Cag/Tag	14/20	1	2	FACETS	0.958	0.904	1	0.958	0.904	1	CLONAL	1	TRUE	1	0.653825123991689	2		616	942	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36826926	36826926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769201571	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	307	641	0	ENST00000373129.3:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000373129	NM_032017.1	3	cGg/cAg	3/12	1	2	FACETS	0.869	0.819	0.919	0.869	0.819	0.919	CLONAL	1	TRUE	1	0.653825123991689	2		641	1081	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306959	65306959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358494508	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	151	473	0	ENST00000342505.4:c.2618G>A	p.Arg873His	p.R873H	ENST00000342505	NM_002227.2	873	cGc/cAc	19/25	1	2	FACETS	0.663	0.607	0.721	0.663	0.607	0.721	SUBCLONAL	1	TRUE	1	0.653825123991689	2		473	697	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306996	65306997	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	180	405	5	ENST00000342505.4:c.2580dup	p.Pro861ThrfsTer4	p.P861Tfs*4	ENST00000342505	NM_002227.2	860	-/A	19/25	1	2	FACETS	0.841	0.778	0.905	0.841	0.778	0.905	CLONAL	1	TRUE	1	0.653825123991689	2		410	655	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653236	206653236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143491598	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	286	756	1	ENST00000367120.3:c.1207G>A	p.Val403Ile	p.V403I	ENST00000367120	NM_014002.3	403	Gtc/Atc	11/22	1	2	FACETS	0.814	0.765	0.863	0.814	0.765	0.863	CLONAL	1	TRUE	1	0.653825123991689	2		757	1075	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945647	206945647	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550164520	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	281	564	1	ENST00000423557.1:c.134G>A	p.Arg45Gln	p.R45Q	ENST00000423557	NM_000572.2	45	cGa/cAa	1/5	1	2	FACETS	0.926	0.872	0.982	0.926	0.872	0.982	CLONAL	1	TRUE	1	0.653825123991689	2		565	928	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692961	89692961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060500122	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	194	510	0	ENST00000371953.3:c.445C>T	p.Gln149Ter	p.Q149*	ENST00000371953	NM_000314.4	149	Caa/Taa	5/9	1	2	FACETS	0.913	0.849	0.979	0.913	0.849	0.979	CLONAL	1	TRUE	1	0.653825123991689	2		510	650	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	427	606	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.825	0.792	0.857	1	0.997	1	CLONAL	2	TRUE	1	0.653825123991689	2		606	792	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572228	64572228	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	159	528	0	ENST00000312049.6:c.1411T>C	p.Trp471Arg	p.W471R	ENST00000312049	NM_130799.2	471	Tgg/Cgg	10/10	1	2	FACETS	0.767	0.706	0.831	0.767	0.706	0.831	SUBCLONAL	1	TRUE	1	0.653825123991689	2		528	634	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202491	67202491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375129435	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	410	861	1	ENST00000312629.5:c.1300C>T	p.Arg434Trp	p.R434W	ENST00000312629	NM_003952.2	434	Cgg/Tgg	15/15	1	2	FACETS	0.996	0.948	1	0.996	0.948	1	CLONAL	1	TRUE	1	0.653825123991689	2		862	1259	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943359	71943359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775327646	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	292	714	0	ENST00000298229.2:c.1691C>T	p.Ser564Leu	p.S564L	ENST00000298229	NM_001567.3	564	tCg/tTg	14/28	1	2	FACETS	0.898	0.846	0.951	0.898	0.846	0.951	CLONAL	1	TRUE	1	0.653825123991689	2		714	995	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	324	816	1	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.913	0.863	0.964	0.913	0.863	0.964	CLONAL	1	TRUE	1	0.653825123991689	2		817	1085	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156010	119156010	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs779425249	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	412	834	1	ENST00000264033.4:c.1675C>T	p.Arg559Ter	p.R559*	ENST00000264033	NM_005188.3	559	Cga/Tga	11/16	1	2	FACETS	0.918	0.873	0.963	0.918	0.873	0.963	CLONAL	1	TRUE	1	0.653825123991689	2		835	1373	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445403	49445403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368472158	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	419	991	0	ENST00000301067.7:c.2063G>A	p.Arg688His	p.R688H	ENST00000301067	NM_003482.3	688	cGc/cAc	10/54	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.653825123991689	2		991	1223	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562372	21562372	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775535885	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	130	702	0	ENST00000382592.4:c.1547C>T	p.Pro516Leu	p.P516L	ENST00000382592	NM_014572.2	516	cCg/cTg	4/8	1	2	FACETS	0.413	0.374	0.455	0.413	0.374	0.455	SUBCLONAL	1	TRUE	1	0.653825123991689	2		702	962	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562708	21562708	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	218	427	0	ENST00000382592.4:c.1211G>C	p.Ser404Thr	p.S404T	ENST00000382592	NM_014572.2	404	aGc/aCc	4/8	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.653825123991689	2		427	581	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434889	110434889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1021457672	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	325	752	0	ENST00000375856.3:c.3512G>A	p.Arg1171His	p.R1171H	ENST00000375856	NM_003749.2	1171	cGc/cAc	1/2	1	2	FACETS	0.96	0.908	1	0.96	0.908	1	CLONAL	1	TRUE	1	0.653825123991689	2		752	1036	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105512	30105512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768104173	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	336	772	0	ENST00000331968.5:c.1174G>A	p.Ala392Thr	p.A392T	ENST00000331968	NM_002742.2	392	Gcc/Acc	7/18	1	2	FACETS	0.949	0.898	1	0.949	0.898	1	CLONAL	1	TRUE	1	0.653825123991689	2		772	1083	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465636	99465636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775915596	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	233	543	0	ENST00000268035.6:c.2461G>A	p.Val821Ile	p.V821I	ENST00000268035	NM_000875.3	821	Gtc/Atc	11/21	1	2	FACETS	0.852	0.796	0.909	0.852	0.796	0.909	CLONAL	1	TRUE	1	0.653825123991689	2		543	837	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789591	3789591	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	230	521	0	ENST00000262367.5:c.4268del	p.Pro1423LeufsTer36	p.P1423Lfs*36	ENST00000262367	NM_004380.2	1423	cCt/ct	25/31	1	2	FACETS	0.92	0.86	0.981	0.92	0.86	0.981	CLONAL	1	TRUE	1	0.653825123991689	2		521	765	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	224	574	2	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.848	0.792	0.906	0.848	0.792	0.906	CLONAL	1	TRUE	1	0.653825123991689	2		576	808	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17124911	17124911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	315	742	0	ENST00000285071.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000285071	NM_144997.5	271	Gag/Aag	8/14	1	2	FACETS	0.876	0.827	0.926	0.876	0.827	0.926	CLONAL	1	TRUE	1	0.653825123991689	2		742	1100	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	221	534	0	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	0.823	0.768	0.88	0.823	0.768	0.88	CLONAL	1	TRUE	1	0.653825123991689	2		534	821	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805404	46805404	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1188	67	849	0	ENST00000290295.7:c.552C>A	p.Cys184Ter	p.C184*	ENST00000290295	NM_006361.5	184	tgC/tgA	1/2	1	2	FACETS	0.163	0.141	0.188	0.163	0.141	0.188	SUBCLONAL	1	TRUE	1	0.653825123991689	2		849	1255	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885955	59885955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758360637	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	294	584	0	ENST00000259008.2:c.791G>A	p.Arg264Gln	p.R264Q	ENST00000259008	NM_032043.2	264	cGg/cAg	7/20	1	2	FACETS	0.955	0.9	1	0.955	0.9	1	CLONAL	1	TRUE	1	0.653825123991689	2		584	942	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59924571	59924571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761432927	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	93	309	0	ENST00000259008.2:c.518G>A	p.Arg173His	p.R173H	ENST00000259008	NM_032043.2	173	cGt/cAt	6/20	1	2	FACETS	0.806	0.723	0.893	0.806	0.723	0.893	CLONAL	1	TRUE	1	0.653825123991689	2		309	353	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78811741	78811741	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	298	682	0	ENST00000306801.3:c.1156G>A	p.Val386Ile	p.V386I	ENST00000306801	NM_020761.2	386	Gtt/Att	10/34	1	2	FACETS	0.904	0.853	0.957	0.904	0.853	0.957	CLONAL	1	TRUE	1	0.653825123991689	2		682	1008	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274219	5274219	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	349	730	0	ENST00000357368.4:c.228G>T	p.Gln76His	p.Q76H	ENST00000357368	NM_002850.3	76	caG/caT	3/38	1	2	FACETS	0.949	0.899	1	0.949	0.899	1	CLONAL	1	TRUE	1	0.653825123991689	2		730	1125	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602347	10602347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	448	826	2	ENST00000171111.5:c.1231G>A	p.Val411Met	p.V411M	ENST00000171111	NM_203500.1	411	Gtg/Atg	3/6	1	2	FACETS	0.98	0.934	1	0.98	0.934	1	CLONAL	1	TRUE	1	0.653825123991689	2		828	1399	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11018790	11018790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	452	958	1	ENST00000327064.4:c.422C>T	p.Thr141Met	p.T141M	ENST00000327064	NM_199141.1	141	aCg/aTg	3/16	1	2	FACETS	0.996	0.951	1	0.996	0.951	1	CLONAL	1	TRUE	1	0.653825123991689	2		959	1388	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132467	11132467	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	63	780	0	ENST00000358026.2:c.2683C>T	p.Gln895Ter	p.Q895*	ENST00000358026	NM_001128849.1	895	Cag/Tag	19/36	1	2	FACETS	0.16	0.138	0.185	0.16	0.138	0.185	SUBCLONAL	1	TRUE	1	0.653825123991689	2		780	1203	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051222	13051222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	217	638	0	ENST00000316448.5:c.658G>A	p.Asp220Asn	p.D220N	ENST00000316448	NM_004343.3	220	Gat/Aat	5/9	1	2	FACETS	0.749	0.697	0.803	0.749	0.697	0.803	SUBCLONAL	1	TRUE	1	0.653825123991689	2		638	886	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289907	15289907	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265324934	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	391	924	1	ENST00000263388.2:c.3647C>T	p.Ala1216Val	p.A1216V	ENST00000263388	NM_000435.2	1216	gCg/gTg	22/33	1	2	FACETS	0.93	0.884	0.977	0.93	0.884	0.977	CLONAL	1	TRUE	1	0.653825123991689	2		925	1286	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223175	36223175	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1242	173	955	3	ENST00000222270.7:c.5730del	p.Arg1911AspfsTer23	p.R1911Dfs*23	ENST00000222270	NM_014727.1	1909	Ccc/cc	28/37	1	2	FACETS	0.374	0.343	0.407	0.374	0.343	0.407	SUBCLONAL	1	TRUE	1	0.653825123991689	2		958	1415	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765474	41765474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763936923	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	291	736	0	ENST00000301178.4:c.2350C>T	p.Arg784Trp	p.R784W	ENST00000301178	NM_021913.4	784	Cgg/Tgg	20/20	1	2	FACETS	0.863	0.813	0.915	0.863	0.813	0.915	CLONAL	1	TRUE	1	0.653825123991689	2		736	1031	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796483	42796483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751173226	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	395	889	0	ENST00000575354.2:c.3040G>A	p.Ala1014Thr	p.A1014T	ENST00000575354	NM_015125.3	1014	Gcg/Acg	13/20	1	2	FACETS	0.989	0.941	1	0.989	0.941	1	CLONAL	1	TRUE	1	0.653825123991689	2		889	1222	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867268	45867268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395652548	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	378	772	1	ENST00000391945.4:c.925G>A	p.Val309Met	p.V309M	ENST00000391945	NM_000400.3	309	Gtg/Atg	10/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.653825123991689	2		773	1058	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	333	798	2	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.928	0.878	0.979	0.928	0.878	0.979	CLONAL	1	TRUE	1	0.653825123991689	2		800	1098	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466773	25466773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1431156021	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	284	593	1	ENST00000264709.3:c.1930G>A	p.Ala644Thr	p.A644T	ENST00000264709	NM_175629.2	644	Gct/Act	16/23	0.653825123991689	2	FACETS	0.902	0.849	0.956	0.451	0.424	0.478	CLONAL	1	TRUE	0	0.653825123991689	2		594	963	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467482	25467482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs951361433	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	331	760	1	ENST00000264709.3:c.1594G>A	p.Gly532Ser	p.G532S	ENST00000264709	NM_175629.2	532	Ggc/Agc	14/23	0.653825123991689	2	FACETS	0.885	0.837	0.934	0.443	0.418	0.467	CLONAL	1	TRUE	0	0.653825123991689	2		761	1144	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662682	227662682	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	255	782	2	ENST00000305123.5:c.773G>T	p.Arg258Leu	p.R258L	ENST00000305123	NM_005544.2	258	cGg/cTg	1/2	1	2	FACETS	0.76	0.711	0.809	0.76	0.711	0.809	SUBCLONAL	1	TRUE	1	0.653825123991689	2		784	1027	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067870	30067870	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764441073	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	256	588	0	ENST00000338641.4:c.1055C>T	p.Thr352Met	p.T352M	ENST00000338641	NM_000268.3	352	aCg/aTg	11/16	1	2	FACETS	0.907	0.852	0.965	0.907	0.852	0.965	CLONAL	1	TRUE	1	0.653825123991689	2		588	863	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713702	30713702	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs758614833	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	46	586	0	ENST00000295754.5:c.1027A>G	p.Ser343Gly	p.S343G	ENST00000295754	NM_003242.5	343	Agc/Ggc	4/7	1	2	FACETS	0.166	0.139	0.196	0.166	0.139	0.196	SUBCLONAL	1	TRUE	1	0.653825123991689	2		586	846	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267296	41267296	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	44	392	0	ENST00000349496.5:c.880T>G	p.Leu294Val	p.L294V	ENST00000349496	NM_001904.3	294	Ttg/Gtg	6/15	1	2	FACETS	0.208	0.174	0.246	0.208	0.174	0.246	SUBCLONAL	1	TRUE	1	0.653825123991689	2		392	646	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021728	71021728	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1559602356	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	219	443	0	ENST00000318789.4:c.1630C>T	p.Arg544Ter	p.R544*	ENST00000318789	NM_032682.5	544	Cga/Tga	18/21	1	2	FACETS	0.894	0.835	0.956	0.894	0.835	0.956	CLONAL	1	TRUE	1	0.653825123991689	2		443	749	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217557	142217557	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1268253442	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	167	487	3	ENST00000350721.4:c.5440del	p.Arg1814GlufsTer10	p.R1814Efs*10	ENST00000350721	NM_001184.3	1814	Aga/ga	32/47	1	2	FACETS	0.769	0.709	0.832	0.769	0.709	0.832	SUBCLONAL	1	TRUE	1	0.653825123991689	2		490	664	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442853	187442853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766041104	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	189	402	0	ENST00000232014.4:c.1853G>A	p.Arg618His	p.R618H	ENST00000232014	NM_001130845.1	618	cGt/cAt	9/10	1	2	FACETS	0.937	0.871	1	0.937	0.871	1	CLONAL	1	TRUE	1	0.653825123991689	2		402	617	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444650	187444650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1246753673	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	234	525	0	ENST00000232014.4:c.1577G>A	p.Arg526His	p.R526H	ENST00000232014	NM_001130845.1	526	cGc/cAc	7/10	1	2	FACETS	0.973	0.911	1	0.973	0.911	1	CLONAL	1	TRUE	1	0.653825123991689	2		525	736	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447328	187447328	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	324	628	1	ENST00000232014.4:c.865C>T	p.Arg289Ter	p.R289*	ENST00000232014	NM_001130845.1	289	Cga/Tga	5/10	1	2	FACETS	0.965	0.913	1	0.965	0.913	1	CLONAL	1	TRUE	1	0.653825123991689	2		629	1027	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541124	187541124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1466632971	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	233	414	1	ENST00000441802.2:c.6616G>A	p.Ala2206Thr	p.A2206T	ENST00000441802	NM_005245.3	2206	Gct/Act	10/27	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.653825123991689	2		415	684	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592144	67592144	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	136	270	0	ENST00000274335.5:c.1960C>T	p.Gln654Ter	p.Q654*	ENST00000274335		654	Cag/Tag	14/15	1	2	FACETS	0.954	0.875	1	0.954	0.875	1	CLONAL	1	TRUE	1	0.653825123991689	2		270	436	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79966025	79966025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763873895	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	167	514	0	ENST00000265081.6:c.689C>T	p.Thr230Met	p.T230M	ENST00000265081	NM_002439.4	230	aCg/aTg	4/24	1	2	FACETS	0.739	0.681	0.799	0.739	0.681	0.799	SUBCLONAL	1	TRUE	1	0.653825123991689	2		514	691	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131893105	131893105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	162	316	0	ENST00000265335.6:c.89C>T	p.Pro30Leu	p.P30L	ENST00000265335		30	cCc/cTc	1/25	1	2	FACETS	0.853	0.787	0.921	0.853	0.787	0.921	CLONAL	1	TRUE	1	0.653825123991689	2		316	581	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519337	176519337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758837002	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	292	805	2	ENST00000292408.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000292408	NM_213647.1	248	cGg/cAg	7/18	1	2	FACETS	0.955	0.901	1	0.955	0.901	1	CLONAL	1	TRUE	1	0.653825123991689	2		807	935	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398937	398937	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	125	590	0	ENST00000380956.4:c.745+2T>G		p.X249_splice	ENST00000380956	NM_001195286.1	249			1	2	FACETS	0.492	0.445	0.541	0.492	0.445	0.541	SUBCLONAL	1	TRUE	1	0.653825123991689	2		590	777	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680239	30680239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	253	859	0	ENST00000376406.3:c.1480G>A	p.Asp494Asn	p.D494N	ENST00000376406	NM_014641.2	494	Gac/Aac	5/15	1	2	FACETS	0.63	0.588	0.672	0.63	0.588	0.672	SUBCLONAL	1	TRUE	1	0.653825123991689	2		859	1229	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631362	117631362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150262256	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	224	497	1	ENST00000368508.3:c.6316G>A	p.Ala2106Thr	p.A2106T	ENST00000368508	NM_002944.2	2106	Gcc/Acc	40/43	1	2	FACETS	0.969	0.906	1	0.969	0.906	1	CLONAL	1	TRUE	1	0.653825123991689	2		498	707	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150410	157150410	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs141260832	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	279	715	0	ENST00000346085.5:c.1592T>C	p.Met531Thr	p.M531T	ENST00000346085	NM_020732.3	531	aTg/aCg	2/20	1	2	FACETS	0.919	0.865	0.974	0.919	0.865	0.974	CLONAL	1	TRUE	1	0.653825123991689	2		715	929	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026721	6026721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751153838	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	333	576	2	ENST00000265849.7:c.1675G>A	p.Gly559Arg	p.G559R	ENST00000265849	NM_000535.5	559	Gga/Aga	11/15	1	2	FACETS	0.998	0.945	1	0.998	0.945	1	CLONAL	1	TRUE	1	0.653825123991689	2		578	1021	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229246	55229246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564398642	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	312	593	0	ENST00000275493.2:c.1553C>T	p.Pro518Leu	p.P518L	ENST00000275493	NM_005228.3	518	cCg/cTg	13/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.653825123991689	2		593	882	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172977	38172977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs185827074	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	300	599	0	ENST00000317025.8:c.2072C>T	p.Ser691Leu	p.S691L	ENST00000317025	NM_023034.1	691	tCg/tTg	11/24	1	2	FACETS	0.956	0.902	1	0.956	0.902	1	CLONAL	1	TRUE	1	0.653825123991689	2		599	960	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970930	70970930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1308927556	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	330	784	1	ENST00000276594.2:c.1331G>A	p.Arg444Gln	p.R444Q	ENST00000276594	NM_024504.3	444	cGg/cAg	6/8	1	2	FACETS	0.953	0.902	1	0.953	0.902	1	CLONAL	1	TRUE	1	0.653825123991689	2		785	1059	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128268614	128268614	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	340	795	0	ENST00000265960.3:c.1041G>T	p.Trp347Cys	p.W347C	ENST00000265960	NM_001006617.1	347	tgG/tgT	8/12	1	2	FACETS	0.855	0.808	0.902	0.855	0.808	0.902	CLONAL	1	TRUE	1	0.653825123991689	2		795	1217	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424664	47424664	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	347	815	0	ENST00000377045.4:c.472G>A	p.Val158Ile	p.V158I	ENST00000377045	NM_001654.4	158	Gtc/Atc	6/16	1	2	FACETS	0.99	0.939	1	0.99	0.939	1	CLONAL	1	TRUE	1	0.653825123991689	2		815	1072	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222484	53222484	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	352	899	1	ENST00000375401.3:c.4348G>A	p.Ala1450Thr	p.A1450T	ENST00000375401	NM_004187.3	1450	Gct/Act	26/26	1	2	FACETS	0.912	0.865	0.961	0.912	0.865	0.961	CLONAL	1	TRUE	1	0.653825123991689	2		900	1180	SUCCESS
AR	367	MSKCC	GRCh37	X	66765778	66765779	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1555969694	NA	P-0047374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	307	911	0	ENST00000374690.3:c.796dup	p.Asp266GlyfsTer39	p.D266Gfs*39	ENST00000374690	NM_000044.3	264	cgg/cGgg	1/8	1	2	FACETS	0.703	0.662	0.746	0.703	0.662	0.746	SUBCLONAL	1	TRUE	1	0.653825123991689	2		911	1335	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55087020	55087020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180577495	NA	P-0047375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	55	494	0	ENST00000275493.2:c.50C>T	p.Ala17Val	p.A17V	ENST00000275493	NM_005228.3	17	gCg/gTg	1/28	1	2	FACETS	0.281	0.24	0.326	0.281	0.24	0.326	SUBCLONAL	1	TRUE	1	0.596884088882518	2		494	656	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354437	354437	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs538987269	NA	P-0047375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1441	310	849	1	ENST00000262320.3:c.1121C>T	p.Thr374Met	p.T374M	ENST00000262320	NM_003502.3	374	aCg/aTg	5/11	0.30145198289726	5	FACETS	1	0.984	1	0.375	0.352	0.398	INDETERMINATE	1	TRUE	2	0.596884088882518	5		850	1751	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967176	134967176	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	156	575	0	ENST00000398015.3:c.2515C>A	p.Gln839Lys	p.Q839K	ENST00000398015	NM_004441.4	839	Cag/Aag	14/16	0.433446579496301	1	FACETS	0.519	0.477	0.564	0.519	0.477	0.564	SUBCLONAL	1	TRUE	0	0.596884088882518	1		575	706	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115898	8115899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0047376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	254	508	0	ENST00000346208.3:c.1245dup	p.Leu416AlafsTer91	p.L416Afs*91	ENST00000346208		415	atg/atGg	6/6	1	2	FACETS	0.938	0.878	1	1	0.994	1	CLONAL	2	TRUE	1	0.257090723816802	2		508	1053	SUCCESS
EED	8726	MSKCC	GRCh37	11	85979544	85979544	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	71	351	0	ENST00000263360.6:c.907G>A	p.Asp303Asn	p.D303N	ENST00000263360	NM_003797.3	303	Gac/Aac	9/12	0.224024982180223	1	FACETS	0.769	0.671	0.874	0.769	0.671	0.874	SUBCLONAL	1	TRUE	0	0.257090723816802	1		351	626	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260254	10260254	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	328	586	0	ENST00000340748.4:c.2413C>A	p.Leu805Ile	p.L805I	ENST00000340748		805	Ctc/Atc	25/40	0.257090723816802	1	FACETS	0.99	0.936	1	1	0.996	1	CLONAL	2	TRUE	0	0.257090723816802	1		586	1123	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115898	8115899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0047376-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	104	508	0	ENST00000346208.3:c.1245dup	p.Leu416AlafsTer91	p.L416Afs*91	ENST00000346208		415	atg/atGg	6/6	1	2	FACETS	0.771	0.691	0.856	1	0.983	1	SUBCLONAL	2	TRUE	1	0.198608534386637	2		508	679	SUCCESS
EED	8726	MSKCC	GRCh37	11	85979544	85979544	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047376-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	36	351	0	ENST00000263360.6:c.907G>A	p.Asp303Asn	p.D303N	ENST00000263360	NM_003797.3	303	Gac/Aac	9/12	1	2	FACETS	0.737	0.605	0.885	0.737	0.605	0.885	SUBCLONAL	1	TRUE	1	0.198608534386637	2		351	492	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260254	10260254	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047376-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	146	586	0	ENST00000340748.4:c.2413C>A	p.Leu805Ile	p.L805I	ENST00000340748		805	Ctc/Atc	25/40	0.198608534386637	1	FACETS	0.921	0.842	1	1	0.99	1	CLONAL	2	TRUE	0	0.198608534386637	1		586	719	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0047377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	61	340	1	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.849	0.732	0.976	0.849	0.732	0.976	CLONAL	1	TRUE	1	0.233412068432687	2		341	616	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0047377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	187	793	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.201208683050076	2	FACETS	0.852	0.787	0.92	0.852	0.787	0.92	CLONAL	2	TRUE	0	0.233412068432687	2		793	940	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	66	412	0	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.233412068432687	2		412	541	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795388	39795388	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	74	842	0	ENST00000288319.7:c.332A>T	p.Lys111Met	p.K111M	ENST00000288319	NM_182918.3	111	aAg/aTg	3/10	1	2	FACETS	0.586	0.511	0.667	0.586	0.511	0.667	SUBCLONAL	1	TRUE	1	0.233412068432687	2		842	1082	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0047379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	79	272	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.48	2		272	297	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0047379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	102	502	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.988	0.89	1	0.988	0.89	1	CLONAL	1	TRUE	1	0.48	2		507	430	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0047379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	347	889	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.825	0.784	0.866	1	0.996	1	CLONAL	2	TRUE	1	0.48	2		895	876	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913403	NA	P-0047379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	114	417	0	ENST00000349496.5:c.110C>A	p.Ser37Tyr	p.S37Y	ENST00000349496	NM_001904.3	37	tCt/tAt	3/15	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.48	2		417	470	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101099	27101099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	211	885	0	ENST00000324856.7:c.4381C>T	p.Arg1461Ter	p.R1461*	ENST00000324856	NM_006015.4	1461	Cga/Tga	18/20	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.48	2		885	866	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577138	7577138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780075	NA	P-0047379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	26	761	1	ENST00000269305.4:c.800G>A	p.Arg267Gln	p.R267Q	ENST00000269305	NM_001126112.2	267	cGg/cAg	8/11	1	2	FACETS	0.147	0.116	0.184	0.147	0.116	0.184	SUBCLONAL	1	TRUE	1	0.48	2		762	735	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560464	95560464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	145	618	0	ENST00000393063.1:c.5125G>A	p.Asp1709Asn	p.D1709N	ENST00000393063	NM_030621.3	1709	Gat/Aat	25/28	1	2	FACETS	0.885	0.809	0.963	0.885	0.809	0.963	CLONAL	1	TRUE	1	0.48	2		618	683	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748451	40748451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867449500	NA	P-0047379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	165	844	1	ENST00000392038.2:c.431G>A	p.Arg144Gln	p.R144Q	ENST00000392038	NM_001626.4	144	cGg/cAg	5/14	1	2	FACETS	0.968	0.892	1	0.968	0.892	1	CLONAL	1	TRUE	1	0.48	2		845	710	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653807	89653807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554893782	NA	P-0047379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	140	444	0	ENST00000371953.3:c.105G>A	p.Met35Ile	p.M35I	ENST00000371953	NM_000314.4	35	atG/atA	2/9	0.3	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.48	2		444	238	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497566	125497566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771939046	NA	P-0047379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	33	377	0	ENST00000428830.2:c.130C>T	p.Arg44Cys	p.R44C	ENST00000428830	NM_001114121.2	44	Cgt/Tgt	3/14	1	2	FACETS	0.705	0.58	0.844	0.705	0.58	0.844	SUBCLONAL	1	TRUE	1	0.48	2		377	195	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562840	95562840	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	81	413	4	ENST00000393063.1:c.4417del	p.Ser1473GlnfsTer17	p.S1473Qfs*17	ENST00000393063	NM_030621.3	1473	Tca/ca	24/28	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.48	2		417	308	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948208	71948209	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs749079348	NA	P-0047379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	83	1037	1	ENST00000298229.2:c.2927dup	p.Pro977ThrfsTer7	p.P977Tfs*7	ENST00000298229	NM_001567.3	974	gcc/gCcc	26/28	1	2	FACETS	0.367	0.323	0.415	0.367	0.323	0.415	SUBCLONAL	1	TRUE	1	0.48	2		1038	942	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023715	27023716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0047379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	134	456	0	ENST00000324856.7:c.827dup	p.Gly277ArgfsTer123	p.G277Rfs*123	ENST00000324856	NM_006015.4	274	atg/atGg	1/20	1	2	FACETS	0.921	0.84	1	0.921	0.84	1	CLONAL	1	TRUE	1	0.48	2		456	606	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221726	36221726	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	184	1052	1	ENST00000222270.7:c.5395G>T	p.Glu1799Ter	p.E1799*	ENST00000222270	NM_014727.1	1799	Gag/Tag	26/37	1	2	FACETS	0.804	0.743	0.869	0.804	0.743	0.869	CLONAL	1	TRUE	1	0.48	2		1053	953	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430981	181430982	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0047379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	111	882	0	ENST00000325404.1:c.837dup	p.Gly280ArgfsTer30	p.G280Rfs*30	ENST00000325404	NM_003106.3	278	ctc/ctCc	1/1	1	2	FACETS	0.424	0.38	0.471	0.424	0.38	0.471	SUBCLONAL	1	TRUE	1	0.48	2		882	1090	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589588	67589608	+	inframe_deletion	In_Frame_Del	DEL	GAATATAACACTCAGTTTCAA	GAATATAACACTCAGTTTCAA	-	novel	NA	P-0047379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	45	250	0	ENST00000274335.5:c.1354_1374del	p.Tyr452_Glu458del	p.Y452_E458del	ENST00000274335		451	GAATATAACACTCAGTTTCAA/-	10/15	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.48	2		250	153	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661663	227661664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761880048	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	162	1044	17	ENST00000305123.5:c.1791dup	p.His598AlafsTer13	p.H598Afs*13	ENST00000305123	NM_005544.2	597	-/G	1/2	1	2	FACETS	0.751	0.691	0.812	0.751	0.691	0.812	SUBCLONAL	1	TRUE	1	0.657085001371118	2		1061	657	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	236	612	2	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.944	0.884	1	0.944	0.884	1	CLONAL	1	TRUE	1	0.657085001371118	2		614	761	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967091	18967092	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1384543747	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	92	1160	1	ENST00000262803.5:c.1814_1815del	p.Glu605AlafsTer17	p.E605Afs*17	ENST00000262803	NM_002911.3	602	gcAGag/gcag	13/24	1	2	FACETS	0.31	0.275	0.348	0.31	0.275	0.348	SUBCLONAL	1	TRUE	1	0.657085001371118	2		1161	902	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	160	515	6	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.72	0.662	0.781	0.72	0.662	0.781	SUBCLONAL	1	TRUE	1	0.657085001371118	2		521	676	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	258	502	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.653772960166482	2	FACETS	0.96	0.902	1	0.48	0.451	0.51	CLONAL	1	TRUE	0	0.657085001371118	2		507	818	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	283	763	8	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	0.654266156709829	3	FACETS	0.976	0.917	1	0.488	0.458	0.519	CLONAL	1	TRUE	1	0.657085001371118	3		771	1172	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	271	889	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.657085001371118	2		895	790	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851177	151851177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141966811	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	106	361	2	ENST00000262189.6:c.12194C>T	p.Ala4065Val	p.A4065V	ENST00000262189	NM_170606.2	4065	gCg/gTg	48/59	0.654266156709829	3	FACETS	0.871	0.785	0.962	0.436	0.392	0.481	CLONAL	1	TRUE	1	0.657085001371118	3		363	492	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776016	9776016	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	218	1086	1	ENST00000377346.4:c.480G>T	p.Glu160Asp	p.E160D	ENST00000377346	NM_005026.3	160	gaG/gaT	5/24	1	2	FACETS	0.909	0.849	0.971	0.909	0.849	0.971	CLONAL	1	TRUE	1	0.657085001371118	2		1087	730	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	190	723	0	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	0.959	0.892	1	0.959	0.892	1	CLONAL	1	TRUE	1	0.657085001371118	2		723	603	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598267	28598267	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	54	1155	0	ENST00000253063.3:c.239C>A	p.Ala80Glu	p.A80E	ENST00000253063	NM_031459.4	80	gCa/gAa	3/10	1	2	FACETS	0.16	0.136	0.187	0.16	0.136	0.187	SUBCLONAL	1	TRUE	1	0.657085001371118	2		1155	1027	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599958	28599958	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	313	1199	0	ENST00000253063.3:c.840G>T	p.Gln280His	p.Q280H	ENST00000253063	NM_031459.4	280	caG/caT	6/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.657085001371118	2		1199	837	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807415	36807415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759242925	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	294	1200	5	ENST00000373129.3:c.1249G>A	p.Ala417Thr	p.A417T	ENST00000373129	NM_032017.1	417	Gca/Aca	12/12	1	2	FACETS	0.991	0.935	1	0.991	0.935	1	CLONAL	1	TRUE	1	0.657085001371118	2		1205	903	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303646	65303646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	176	891	2	ENST00000342505.4:c.3109G>A	p.Val1037Ile	p.V1037I	ENST00000342505	NM_002227.2	1037	Gtc/Atc	22/25	1	2	FACETS	0.743	0.686	0.802	0.743	0.686	0.802	SUBCLONAL	1	TRUE	1	0.657085001371118	2		893	721	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115260812	115260812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375339756	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	167	746	0	ENST00000438362.2:c.2513G>A	p.Arg838His	p.R838H	ENST00000438362	NM_001242891.1	838	cGt/cAt	20/20	1	2	FACETS	0.835	0.77	0.901	0.835	0.77	0.901	CLONAL	1	TRUE	1	0.657085001371118	2		746	609	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699279	117699279	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	52	663	0	ENST00000369458.3:c.362A>G	p.Gln121Arg	p.Q121R	ENST00000369458	NM_024626.3	121	cAa/cGa	3/6	1	2	FACETS	0.242	0.206	0.283	0.242	0.206	0.283	SUBCLONAL	1	TRUE	1	0.657085001371118	2		663	653	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099361	193099361	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	141	353	0	ENST00000367435.3:c.295A>G	p.Asn99Asp	p.N99D	ENST00000367435	NM_024529.4	99	Aat/Gat	3/17	1	2	FACETS	0.878	0.805	0.953	0.878	0.805	0.953	CLONAL	1	TRUE	1	0.657085001371118	2		353	489	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111145	193111146	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	rs760591174	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	103	462	0	ENST00000367435.3:c.687_688dup	p.Val230GlufsTer28	p.V230Efs*28	ENST00000367435	NM_024529.4	226	-/AG	7/17	1	2	FACETS	0.883	0.798	0.972	0.883	0.798	0.972	CLONAL	1	TRUE	1	0.657085001371118	2		462	355	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619156	43619156	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	216	1128	0	ENST00000355710.3:c.2839C>A	p.Leu947Ile	p.L947I	ENST00000355710	NM_020975.4	947	Cta/Ata	17/20	1	2	FACETS	0.914	0.853	0.977	0.914	0.853	0.977	CLONAL	1	TRUE	1	0.657085001371118	2		1128	719	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653833	89653833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1085308042	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	117	420	0	ENST00000371953.3:c.131G>A	p.Gly44Asp	p.G44D	ENST00000371953	NM_000314.4	44	gGc/gAc	2/9	1	2	FACETS	0.864	0.786	0.946	0.864	0.786	0.946	CLONAL	1	TRUE	1	0.657085001371118	2		420	412	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913476	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	194	776	0	ENST00000358487.5:c.1647T>G	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaG	12/18	1	2	FACETS	0.984	0.916	1	0.984	0.916	1	CLONAL	1	TRUE	1	0.657085001371118	2		776	600	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123353249	123353249	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	208	822	0	ENST00000358487.5:c.83T>C	p.Val28Ala	p.V28A	ENST00000358487	NM_000141.4	28	gTt/gCt	2/18	1	2	FACETS	0.959	0.895	1	0.959	0.895	1	CLONAL	1	TRUE	1	0.657085001371118	2		822	660	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	82	472	1	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	0.73	0.649	0.815	0.73	0.649	0.815	SUBCLONAL	1	TRUE	1	0.657085001371118	2		473	342	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	68	998	8	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	1	2	FACETS	0.253	0.22	0.29	0.253	0.22	0.29	SUBCLONAL	1	TRUE	1	0.657085001371118	2		1006	817	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999260	100999260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	263	1154	0	ENST00000325455.5:c.542C>T	p.Ala181Val	p.A181V	ENST00000325455	NM_001202474.3	181	gCc/gTc	1/8	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.657085001371118	2		1154	784	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216477	108216477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587782558	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	59	235	0	ENST00000278616.4:c.8432del	p.Lys2811SerfsTer46	p.K2811Sfs*46	ENST00000278616	NM_000051.3	2809	cAa/ca	58/63	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.657085001371118	2		235	178	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125507352	125507352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs975304527	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	119	439	0	ENST00000428830.2:c.727C>T	p.His243Tyr	p.H243Y	ENST00000428830	NM_001114121.2	243	Cat/Tat	8/14	1	2	FACETS	0.946	0.862	1	0.946	0.862	1	CLONAL	1	TRUE	1	0.657085001371118	2		439	383	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416125	416125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746295514	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	292	587	0	ENST00000399788.2:c.4061G>A	p.Gly1354Asp	p.G1354D	ENST00000399788	NM_001042603.1	1354	gGc/gAc	24/28	0.556434695187936	3	FACETS	0.847	0.802	0.892			1	CLONAL	2	TRUE	NA	0.657085001371118	3		587	697	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432289	432289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376128815	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	230	832	0	ENST00000399788.2:c.2234G>A	p.Arg745His	p.R745H	ENST00000399788	NM_001042603.1	745	cGt/cAt	16/28	0.556434695187936	3	FACETS	1	0.94	1			1	CLONAL	1	TRUE	NA	0.657085001371118	3		832	923	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424442	49424443	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs797044740	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	497	1074	0	ENST00000301067.7:c.13780dup	p.Ala4594GlyfsTer12	p.A4594Gfs*12	ENST00000301067	NM_003482.3	4594	gcc/gGcc	41/54	0.654266156709829	3	FACETS	0.939	0.902	0.976	0.939	0.902	0.976	CLONAL	2	TRUE	1	0.657085001371118	3		1074	1070	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426753	49426754	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTTGCT	rs398123709	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	136	524	0	ENST00000301067.7:c.11729_11734dup	p.Gln3910_Gln3911dup	p.Q3910_Q3911dup	ENST00000301067	NM_003482.3	3910	ctt/cAGCAACtt	39/54	0.654266156709829	3	FACETS	1	0.977	1	0.596	0.546	0.648	CLONAL	1	TRUE	1	0.657085001371118	3		524	461	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433586	49433586	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1014845953	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	343	1408	0	ENST00000301067.7:c.7967T>C	p.Leu2656Ser	p.L2656S	ENST00000301067	NM_003482.3	2656	tTg/tCg	31/54	0.654266156709829	3	FACETS	0.968	0.914	1	0.484	0.457	0.512	CLONAL	1	TRUE	1	0.657085001371118	3		1408	1433	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	318	1257	3	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.654266156709829	3	FACETS	1	0.976	1	0.53	0.5	0.561	CLONAL	1	TRUE	1	0.657085001371118	3		1260	1213	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480010	50480010	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	246	1172	2	ENST00000394963.4:c.249del	p.Asn84ThrfsTer79	p.N84Tfs*79	ENST00000394963	NM_003076.4	82	Ggg/gg	2/13	0.654266156709829	3	FACETS	0.908	0.849	0.97	0.454	0.424	0.485	CLONAL	1	TRUE	1	0.657085001371118	3		1174	1095	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	365	991	6	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	0.654266156709829	3	FACETS	1	0.977	1	0.527	0.499	0.555	CLONAL	1	TRUE	1	0.657085001371118	3		997	1401	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864655	57864655	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	594	1251	2	ENST00000228682.2:c.2132C>T	p.Thr711Ile	p.T711I	ENST00000228682	NM_005269.2	711	aCc/aTc	12/12	0.654266156709829	3	FACETS	0.962	0.927	0.996	0.962	0.927	0.996	CLONAL	2	TRUE	1	0.657085001371118	3		1253	1249	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915706	112915706	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	204	591	0	ENST00000351677.2:c.979T>C	p.Tyr327His	p.Y327H	ENST00000351677	NM_002834.3	327	Tac/Cac	9/16	0.654266156709829	3	FACETS	0.981	0.911	1	0.49	0.455	0.527	CLONAL	1	TRUE	1	0.657085001371118	3		591	841	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109962	115109962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	98	990	2	ENST00000257566.3:c.1916G>A	p.Arg639His	p.R639H	ENST00000257566	NM_016569.3	639	cGc/cAc	8/8	0.654266156709829	3	FACETS	0.366	0.325	0.409	0.183	0.162	0.205	SUBCLONAL	1	TRUE	1	0.657085001371118	3		992	1084	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133773	41133773	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1164031879	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	146	626	2	ENST00000379561.5:c.1855C>T	p.Arg619Trp	p.R619W	ENST00000379561	NM_002015.3	619	Cgg/Tgg	2/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.657085001371118	2		628	396	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435088	110435088	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1258579269	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	63	997	1	ENST00000375856.3:c.3313G>A	p.Val1105Met	p.V1105M	ENST00000375856	NM_003749.2	1105	Gtg/Atg	1/2	1	2	FACETS	0.264	0.227	0.303	0.264	0.227	0.303	SUBCLONAL	1	TRUE	1	0.657085001371118	2		998	727	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066832	30066832	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	208	743	0	ENST00000331968.5:c.2299T>C	p.Trp767Arg	p.W767R	ENST00000331968	NM_002742.2	767	Tgg/Cgg	16/18	1	2	FACETS	0.91	0.848	0.973	0.91	0.848	0.973	CLONAL	1	TRUE	1	0.657085001371118	2		743	696	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059170	42059170	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs756744691	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	179	656	2	ENST00000219905.7:c.8895del	p.Thr2966ProfsTer4	p.T2966Pfs*4	ENST00000219905	NM_001164273.1	2964	Ccc/cc	24/24	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.657085001371118	2		658	545	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457696	67457696	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772034969	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	48	959	0	ENST00000327367.4:c.506G>A	p.Gly169Asp	p.G169D	ENST00000327367	NM_005902.3	169	gGc/gAc	3/9	1	2	FACETS	0.185	0.156	0.218	0.185	0.156	0.218	SUBCLONAL	1	TRUE	1	0.657085001371118	2		959	789	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473728	67473728	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	248	1115	0	ENST00000327367.4:c.808T>C	p.Cys270Arg	p.C270R	ENST00000327367	NM_005902.3	270	Tgc/Cgc	6/9	1	2	FACETS	0.928	0.871	0.987	0.928	0.871	0.987	CLONAL	1	TRUE	1	0.657085001371118	2		1115	813	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354421	354421	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	70	1167	0	ENST00000262320.3:c.1137G>T	p.Lys379Asn	p.K379N	ENST00000262320	NM_003502.3	379	aaG/aaT	5/11	0.653772960166482	2	FACETS	0.194	0.168	0.221	0.097	0.084	0.111	SUBCLONAL	1	TRUE	0	0.657085001371118	2		1167	1101	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396234	396234	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	653	838	1	ENST00000262320.3:c.792del	p.Gly265GlufsTer149	p.G265Efs*149	ENST00000262320	NM_003502.3	264	ccC/cc	2/11	0.653772960166482	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.657085001371118	2		839	973	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103416	2103416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375824753	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	675	1261	1	ENST00000219476.3:c.299C>T	p.Ala100Val	p.A100V	ENST00000219476	NM_000548.3	100	gCg/gTg	4/42	0.653772960166482	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.657085001371118	2		1262	977	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133751	2133752	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	572	1271	0	ENST00000219476.3:c.3944dup	p.Gly1316ArgfsTer6	p.G1316Rfs*6	ENST00000219476	NM_000548.3	1313	-/C	33/42	0.653772960166482	2	FACETS	0.927	0.898	0.956	0.927	0.898	0.956	CLONAL	2	TRUE	0	0.657085001371118	2		1271	939	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781435	3781435	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	234	985	0	ENST00000262367.5:c.4930A>G	p.Asn1644Asp	p.N1644D	ENST00000262367	NM_004380.2	1644	Aac/Gac	30/31	0.653772960166482	2	FACETS	1	0.955	1	0.512	0.479	0.545	CLONAL	1	TRUE	0	0.657085001371118	2		985	696	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032147	10032147	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	228	1055	0	ENST00000330684.3:c.676G>T	p.Val226Phe	p.V226F	ENST00000330684	NM_001134407.1	226	Gtc/Ttc	3/13	1	2	FACETS	0.935	0.875	0.997	0.935	0.875	0.997	CLONAL	1	TRUE	1	0.657085001371118	2		1055	742	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647607	23647607	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	182	521	0	ENST00000261584.4:c.260A>G	p.His87Arg	p.H87R	ENST00000261584	NM_024675.3	87	cAt/cGt	4/13	1	2	FACETS	0.953	0.885	1	0.953	0.885	1	CLONAL	1	TRUE	1	0.657085001371118	2		521	581	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825519	50825519	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	136	426	0	ENST00000398568.2:c.2156del	p.Asn719MetfsTer13	p.N719Mfs*13	ENST00000398568	NM_001042412.1	717	gAa/ga	14/18	1	2	FACETS	0.922	0.845	1	0.922	0.845	1	CLONAL	1	TRUE	1	0.657085001371118	2		426	449	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822036	72822036	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs780296945	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	162	672	1	ENST00000268489.5:c.10139A>G	p.Gln3380Arg	p.Q3380R	ENST00000268489	NM_006885.3	3380	cAg/cGg	10/10	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.657085001371118	2		673	487	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831987	72831987	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs561343106	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	268	900	0	ENST00000268489.5:c.4594A>G	p.Asn1532Asp	p.N1532D	ENST00000268489	NM_006885.3	1532	Aat/Gat	9/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.657085001371118	2		900	791	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858458	89858458	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	255	968	2	ENST00000389301.3:c.1102G>A	p.Ala368Thr	p.A368T	ENST00000389301	NM_000135.2	368	Gca/Aca	13/43	1	2	FACETS	0.982	0.923	1	0.982	0.923	1	CLONAL	1	TRUE	1	0.657085001371118	2		970	790	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572966	+	frameshift_variant	Frame_Shift_Del	DEL	TTTT	TTTT	-	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	208	823	0	ENST00000269305.4:c.1143_1146del	p.Lys381AsnfsTer40	p.K381Nfs*40	ENST00000269305	NM_001126112.2	381	aaAAAA/aa	11/11	1	2	FACETS	0.86	0.801	0.921	0.86	0.801	0.921	CLONAL	1	TRUE	1	0.657085001371118	2		823	736	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110582	8110582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	273	987	0	ENST00000585124.1:c.310G>A	p.Ala104Thr	p.A104T	ENST00000585124	NM_004217.3	104	Gcg/Acg	5/9	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.657085001371118	2		987	818	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024495	16024495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	43	822	1	ENST00000268712.3:c.1723G>A	p.Ala575Thr	p.A575T	ENST00000268712	NM_006311.3	575	Gcc/Acc	16/46	1	2	FACETS	0.166	0.138	0.197	0.166	0.138	0.197	SUBCLONAL	1	TRUE	1	0.657085001371118	2		823	789	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	266	1281	15	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	0.931	0.875	0.988	0.931	0.875	0.988	CLONAL	1	TRUE	1	0.657085001371118	2		1296	870	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245131	41245131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555589705	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	226	1010	0	ENST00000357654.3:c.2417C>T	p.Ala806Val	p.A806V	ENST00000357654	NM_007294.3	806	gCa/gTa	10/23	1	2	FACETS	0.949	0.887	1	0.949	0.887	1	CLONAL	1	TRUE	1	0.657085001371118	2		1010	725	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245587	41245587	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357522	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	42	845	3	ENST00000357654.3:c.1961del	p.Lys654SerfsTer47	p.K654Sfs*47	ENST00000357654	NM_007294.3	654	aAg/ag	10/23	1	2	FACETS	0.166	0.138	0.197	0.166	0.138	0.197	SUBCLONAL	1	TRUE	1	0.657085001371118	2		848	771	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	434	1232	3	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.657085001371118	2		1235	1005	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533939	63533940	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs771001164	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	66	846	2	ENST00000307078.5:c.1214_1215del	p.Glu405GlyfsTer56	p.E405Gfs*56	ENST00000307078	NM_004655.3	405	gAG/g	6/11	1	2	FACETS	0.317	0.275	0.363	0.317	0.275	0.363	SUBCLONAL	1	TRUE	1	0.657085001371118	2		848	633	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745962	745963	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	95	531	0	ENST00000314574.4:c.559_560del	p.Ser187Ter	p.S187*	ENST00000314574	NM_005433.3	187	AGt/t	5/12	1	2	FACETS	0.73	0.655	0.809	0.73	0.655	0.809	SUBCLONAL	1	TRUE	1	0.657085001371118	2		531	396	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39644789	39644789	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	23	254	0	ENST00000262039.4:c.2522del	p.Lys841ArgfsTer8	p.K841Rfs*8	ENST00000262039	NM_002647.2	840	Aaa/aa	23/25	1	2	FACETS	0.19	0.147	0.239	0.19	0.147	0.239	SUBCLONAL	1	TRUE	1	0.657085001371118	2		254	369	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612230	1612230	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	72	896	1	ENST00000344749.5:c.1789C>A	p.Leu597Met	p.L597M	ENST00000344749	NM_001136139.2	597	Ctg/Atg	18/19	1	2	FACETS	0.365	0.319	0.415	0.365	0.319	0.415	SUBCLONAL	1	TRUE	1	0.657085001371118	2		897	600	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2220191	2220191	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	329	1171	1	ENST00000398665.3:c.2776G>A	p.Gly926Arg	p.G926R	ENST00000398665	NM_032482.2	926	Ggg/Agg	23/28	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.657085001371118	2		1172	975	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4102415	4102415	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	66	1277	0	ENST00000262948.5:c.487A>G	p.Lys163Glu	p.K163E	ENST00000262948	NM_030662.3	163	Aag/Gag	4/11	1	2	FACETS	0.212	0.183	0.243	0.212	0.183	0.243	SUBCLONAL	1	TRUE	1	0.657085001371118	2		1277	948	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210796	5210796	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758652323	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	316	1032	0	ENST00000357368.4:c.5255C>T	p.Ala1752Val	p.A1752V	ENST00000357368	NM_002850.3	1752	gCg/gTg	34/38	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.657085001371118	2		1032	821	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222790	5222790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	227	839	1	ENST00000357368.4:c.3013G>A	p.Ala1005Thr	p.A1005T	ENST00000357368	NM_002850.3	1005	Gcc/Acc	18/38	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.657085001371118	2		840	669	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229575	5229575	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	12	203	0	ENST00000357368.4:c.2276A>G	p.His759Arg	p.H759R	ENST00000357368	NM_002850.3	759	cAc/cGc	15/38	1	2	FACETS	0.171	0.12	0.233	0.171	0.12	0.233	SUBCLONAL	1	TRUE	1	0.657085001371118	2		203	214	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243966	5243966	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	321	1077	2	ENST00000357368.4:c.1516T>C	p.Ser506Pro	p.S506P	ENST00000357368	NM_002850.3	506	Tcc/Ccc	11/38	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.657085001371118	2		1079	931	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117155	7117155	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	57	1110	1	ENST00000302850.5:c.4061G>A	p.Ser1354Asn	p.S1354N	ENST00000302850	NM_000208.2	1354	aGc/aAc	22/22	1	2	FACETS	0.18	0.154	0.209	0.18	0.154	0.209	SUBCLONAL	1	TRUE	1	0.657085001371118	2		1111	963	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260611	10260611	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	195	870	0	ENST00000340748.4:c.2251T>C	p.Cys751Arg	p.C751R	ENST00000340748		751	Tgc/Cgc	24/40	1	2	FACETS	0.929	0.864	0.995	0.929	0.864	0.995	CLONAL	1	TRUE	1	0.657085001371118	2		870	639	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031532	11031532	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	326	1313	0	ENST00000327064.4:c.1451del	p.Pro484HisfsTer37	p.P484Hfs*37	ENST00000327064	NM_199141.1	483	Ccc/cc	13/16	1	2	FACETS	0.992	0.939	1	0.992	0.939	1	CLONAL	1	TRUE	1	0.657085001371118	2		1313	1000	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280000	18280000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	259	884	0	ENST00000222254.8:c.2083C>T	p.His695Tyr	p.H695Y	ENST00000222254	NM_005027.3	695	Cac/Tac	16/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.657085001371118	2		884	768	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214077	36214077	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1264213973	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	341	1338	0	ENST00000222270.7:c.2903A>G	p.His968Arg	p.H968R	ENST00000222270	NM_014727.1	968	cAc/cGc	6/37	1	2	FACETS	0.955	0.904	1	0.955	0.904	1	CLONAL	1	TRUE	1	0.657085001371118	2		1338	1087	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214714	36214714	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	202	1010	4	ENST00000222270.7:c.3145del	p.Ala1049ArgfsTer133	p.A1049Rfs*133	ENST00000222270	NM_014727.1	1047	cGg/cg	8/37	1	2	FACETS	0.923	0.86	0.988	0.923	0.86	0.988	CLONAL	1	TRUE	1	0.657085001371118	2		1014	666	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214871	36214871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	296	1208	10	ENST00000222270.7:c.3302del	p.Pro1101LeufsTer81	p.P1101Lfs*81	ENST00000222270	NM_014727.1	1099	ggC/gg	8/37	1	2	FACETS	0.865	0.815	0.916	0.865	0.815	0.916	CLONAL	1	TRUE	1	0.657085001371118	2		1218	1042	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228055	36228055	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1279392856	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	323	1243	1	ENST00000222270.7:c.7441G>A	p.Gly2481Arg	p.G2481R	ENST00000222270	NM_014727.1	2481	Gga/Aga	33/37	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.657085001371118	2		1244	921	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754491	41754491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	368	1188	0	ENST00000301178.4:c.1610C>T	p.Ala537Val	p.A537V	ENST00000301178	NM_021913.4	537	gCc/gTc	13/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.657085001371118	2		1188	1017	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457192	25457192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771922296	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	321	611	0	ENST00000264709.3:c.2695C>T	p.Arg899Cys	p.R899C	ENST00000264709	NM_175629.2	899	Cgc/Tgc	23/23	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.657085001371118	2		611	965	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009113	27009118	+	inframe_deletion	In_Frame_Del	DEL	AGCCCG	AGCCCG	-	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	31	172	0	ENST00000335756.4:c.56_61del	p.Ser19_Pro20del	p.S19_P20del	ENST00000335756	NM_001809.3	17	AGCCCG/-	1/5	1	2	FACETS	0.709	0.583	0.847	0.709	0.583	0.847	SUBCLONAL	1	TRUE	1	0.657085001371118	2		172	133	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27016049	27016049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756721845	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	228	961	0	ENST00000335756.4:c.325G>A	p.Ala109Thr	p.A109T	ENST00000335756	NM_001809.3	109	Gcc/Acc	4/5	1	2	FACETS	0.898	0.839	0.958	0.898	0.839	0.958	CLONAL	1	TRUE	1	0.657085001371118	2		961	773	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519818	29519818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772496459	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	258	1044	1	ENST00000389048.3:c.1753G>A	p.Ala585Thr	p.A585T	ENST00000389048	NM_004304.4	585	Gcc/Acc	9/29	1	2	FACETS	0.999	0.939	1	0.999	0.939	1	CLONAL	1	TRUE	1	0.657085001371118	2		1045	786	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116263	209116263	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	71	284	0	ENST00000345146.2:c.13del	p.Ile5SerfsTer7	p.I5Sfs*7	ENST00000345146	NM_005896.2	5	Atc/tc	3/10	1	2	FACETS	0.748	0.659	0.841	0.748	0.659	0.841	SUBCLONAL	1	TRUE	1	0.657085001371118	2		284	289	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439778	220439778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	55	1311	1	ENST00000243786.2:c.631G>A	p.Ala211Thr	p.A211T	ENST00000243786	NM_002191.3	211	Gcc/Acc	2/2	1	2	FACETS	0.171	0.145	0.199	0.171	0.145	0.199	SUBCLONAL	1	TRUE	1	0.657085001371118	2		1312	980	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660639	227660639	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	37	1060	1	ENST00000305123.5:c.2816A>T	p.Glu939Val	p.E939V	ENST00000305123	NM_005544.2	939	gAg/gTg	1/2	1	2	FACETS	0.155	0.127	0.187	0.155	0.127	0.187	SUBCLONAL	1	TRUE	1	0.657085001371118	2		1061	725	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662817	227662817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1273995645	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	281	1120	1	ENST00000305123.5:c.638G>A	p.Arg213His	p.R213H	ENST00000305123	NM_005544.2	213	cGc/cAc	1/2	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.657085001371118	2		1121	832	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793385	242793385	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750496363	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	327	1288	1	ENST00000334409.5:c.692G>A	p.Arg231Gln	p.R231Q	ENST00000334409	NM_005018.2	231	cGa/cAa	5/5	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.657085001371118	2		1289	965	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31015949	31015949	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	197	635	0	ENST00000375687.4:c.271T>A	p.Ser91Thr	p.S91T	ENST00000375687	NM_015338.5	91	Tct/Act	5/13	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.657085001371118	2		635	575	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395615	31395615	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	326	1058	1	ENST00000328111.2:c.2468G>A	p.Arg823His	p.R823H	ENST00000328111	NM_006892.3	823	cGt/cAt	23/23	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.657085001371118	2		1059	981	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	63	822	1	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	1	2	FACETS	0.29	0.25	0.333	0.29	0.25	0.333	SUBCLONAL	1	TRUE	1	0.657085001371118	2		823	662	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306550	41306550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760520624	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	184	979	4	ENST00000373198.4:c.1109C>T	p.Thr370Met	p.T370M	ENST00000373198	NM_133170.3	370	aCg/aTg	7/32	1	2	FACETS	0.82	0.76	0.882	0.82	0.76	0.882	CLONAL	1	TRUE	1	0.657085001371118	2		983	683	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306593	41306593	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	238	1223	0	ENST00000373198.4:c.1066T>C	p.Tyr356His	p.Y356H	ENST00000373198	NM_133170.3	356	Tat/Cat	7/32	1	2	FACETS	0.946	0.886	1	0.946	0.886	1	CLONAL	1	TRUE	1	0.657085001371118	2		1223	766	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262885	46262885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761607812	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	157	612	0	ENST00000371998.3:c.1058G>A	p.Arg353Gln	p.R353Q	ENST00000371998		353	cGa/cAa	10/23	1	2	FACETS	0.93	0.858	1	0.93	0.858	1	CLONAL	1	TRUE	1	0.657085001371118	2		612	514	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961396	54961396	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	198	513	0	ENST00000312783.6:c.236T>C	p.Leu79Ser	p.L79S	ENST00000312783	NM_198436.1	79	tTg/tCg	4/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.657085001371118	2		513	490	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57470684	57470684	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	122	471	0	ENST00000371085.3:c.160del	p.Ser54AlafsTer4	p.S54Afs*4	ENST00000371085	NM_000516.4	53	Aaa/aa	2/13	1	2	FACETS	0.99	0.904	1	0.99	0.904	1	CLONAL	1	TRUE	1	0.657085001371118	2		471	375	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755554	39755554	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	191	777	3	ENST00000288319.7:c.1211del	p.Pro404ArgfsTer25	p.P404Rfs*25	ENST00000288319	NM_182918.3	404	cCg/cg	10/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.657085001371118	2		780	563	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162017	22162017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	144	782	0	ENST00000215832.6:c.238C>T	p.His80Tyr	p.H80Y	ENST00000215832	NM_002745.4	80	Cat/Tat	2/9	1	2	FACETS	0.768	0.703	0.834	0.768	0.703	0.834	SUBCLONAL	1	TRUE	1	0.657085001371118	2		782	571	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551023	41551023	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	248	557	0	ENST00000263253.7:c.3167A>G	p.Gln1056Arg	p.Q1056R	ENST00000263253	NM_001429.3	1056	cAg/cGg	17/31	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.657085001371118	2		557	689	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266201	41266201	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886041553	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	141	477	0	ENST00000349496.5:c.198G>A	p.Trp66Ter	p.W66*	ENST00000349496	NM_001904.3	66	tgG/tgA	3/15	1	2	FACETS	0.987	0.907	1	0.987	0.907	1	CLONAL	1	TRUE	1	0.657085001371118	2		477	435	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161907	47161907	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	36	500	2	ENST00000409792.3:c.4219del	p.Arg1407GlyfsTer5	p.R1407Gfs*5	ENST00000409792	NM_014159.6	1407	Agg/gg	3/21	1	2	FACETS	0.192	0.157	0.231	0.192	0.157	0.231	SUBCLONAL	1	TRUE	1	0.657085001371118	2		502	571	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70001016	70001016	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	134	438	0	ENST00000394351.3:c.617del	p.Lys206ArgfsTer6	p.K206Rfs*6	ENST00000394351	NM_000248.3	205	Aaa/aa	6/9	1	2	FACETS	0.908	0.832	0.987	0.908	0.832	0.987	CLONAL	1	TRUE	1	0.657085001371118	2		438	449	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204656	128204656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	69	1236	0	ENST00000341105.2:c.785G>A	p.Ser262Asn	p.S262N	ENST00000341105	NM_032638.4	262	aGc/aAc	3/6	1	2	FACETS	0.244	0.212	0.28	0.244	0.212	0.28	SUBCLONAL	1	TRUE	1	0.657085001371118	2		1236	859	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825440	134825440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	174	724	1	ENST00000398015.3:c.956G>A	p.Cys319Tyr	p.C319Y	ENST00000398015	NM_004441.4	319	tGc/tAc	4/16	1	2	FACETS	0.854	0.79	0.92	0.854	0.79	0.92	CLONAL	1	TRUE	1	0.657085001371118	2		725	620	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	220	687	1	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	1	2	FACETS	0.934	0.872	0.997	0.934	0.872	0.997	CLONAL	1	TRUE	1	0.657085001371118	2		688	717	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664989	138664989	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	87	390	0	ENST00000330315.3:c.576del	p.Lys193SerfsTer78	p.K193Sfs*78	ENST00000330315	NM_023067.3	192	ccC/cc	1/1	1	2	FACETS	0.759	0.677	0.844	0.759	0.677	0.844	SUBCLONAL	1	TRUE	1	0.657085001371118	2		390	349	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922310	178922310	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	94	401	0	ENST00000263967.3:c.1079T>C	p.Ile360Thr	p.I360T	ENST00000263967	NM_006218.2	360	aTc/aCc	6/21	1	2	FACETS	0.694	0.622	0.771	0.694	0.622	0.771	SUBCLONAL	1	TRUE	1	0.657085001371118	2		401	412	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183618	185183618	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	46	703	0	ENST00000265026.3:c.1472T>C	p.Leu491Pro	p.L491P	ENST00000265026	NM_004721.4	491	cTg/cCg	9/14	1	2	FACETS	0.242	0.203	0.285	0.242	0.203	0.285	SUBCLONAL	1	TRUE	1	0.657085001371118	2		703	578	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142950056	142950056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568595082	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	81	436	0	ENST00000262992.4:c.2654G>A	p.Arg885His	p.R885H	ENST00000262992	NM_001101669.1	885	cGc/cAc	24/24	1	2	FACETS	0.71	0.631	0.794	0.71	0.631	0.794	SUBCLONAL	1	TRUE	1	0.657085001371118	2		436	347	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31466363	31466363	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	202	927	0	ENST00000344624.3:c.2392G>A	p.Val798Met	p.V798M	ENST00000344624		798	Gtg/Atg	16/33	0.653772960166482	2	FACETS	0.849	0.79	0.91	0.425	0.395	0.455	CLONAL	1	TRUE	0	0.657085001371118	2		927	724	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945092	38945092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769767383	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	148	467	0	ENST00000357387.3:c.4712C>T	p.Ser1571Leu	p.S1571L	ENST00000357387	NM_152756.3	1571	tCg/tTg	35/38	0.653772960166482	2	FACETS	0.952	0.877	1	0.476	0.438	0.515	CLONAL	1	TRUE	0	0.657085001371118	2		467	473	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176973	56176973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	104	500	0	ENST00000399503.3:c.2243C>T	p.Ser748Leu	p.S748L	ENST00000399503	NM_005921.1	748	tCa/tTa	13/20	0.653772960166482	2	FACETS	0.745	0.671	0.822	0.372	0.335	0.411	SUBCLONAL	1	TRUE	0	0.657085001371118	2		500	425	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592097	67592097	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	33	483	0	ENST00000274335.5:c.1913T>C	p.Leu638Ser	p.L638S	ENST00000274335		638	tTg/tCg	14/15	0.653772960166482	2	FACETS	0.215	0.174	0.26	0.107	0.087	0.13	SUBCLONAL	1	TRUE	0	0.657085001371118	2		483	468	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682722	86682722	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	80	211	0	ENST00000274376.6:c.2925+2T>C		p.X975_splice	ENST00000274376	NM_002890.2	975			0.653772960166482	2	FACETS	1	0.943	1	0.541	0.484	0.6	CLONAL	1	TRUE	0	0.657085001371118	2		211	225	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149447842	149447842	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	287	1080	0	ENST00000286301.3:c.1562C>T	p.Ala521Val	p.A521V	ENST00000286301	NM_005211.3	521	gCc/gTc	11/22	0.653772960166482	2	FACETS	1	0.981	1	0.541	0.511	0.572	CLONAL	1	TRUE	0	0.657085001371118	2		1080	807	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524623	176524623	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	309	1333	1	ENST00000292408.4:c.2359del	p.Leu787CysfsTer90	p.L787Cfs*90	ENST00000292408	NM_213647.1	785	gaC/ga	18/18	0.653772960166482	2	FACETS	0.941	0.889	0.995	0.471	0.444	0.498	CLONAL	1	TRUE	0	0.657085001371118	2		1334	999	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707723	176707723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	243	717	0	ENST00000439151.2:c.5780C>T	p.Ala1927Val	p.A1927V	ENST00000439151	NM_022455.4	1927	gCc/gTc	18/23	0.653772960166482	2	FACETS	0.993	0.931	1	0.496	0.465	0.528	CLONAL	1	TRUE	0	0.657085001371118	2		717	745	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046682	180046682	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	325	1331	0	ENST00000261937.6:c.2630C>T	p.Ala877Val	p.A877V	ENST00000261937	NM_182925.4	877	gCc/gTc	18/30	0.653772960166482	2	FACETS	0.954	0.902	1	0.477	0.451	0.504	CLONAL	1	TRUE	0	0.657085001371118	2		1331	1037	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673051	30673051	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	282	1182	0	ENST00000376406.3:c.3909del	p.Lys1304SerfsTer57	p.K1304Sfs*57	ENST00000376406	NM_014641.2	1303	ccC/cc	10/15	1	2	FACETS	0.88	0.828	0.933	0.88	0.828	0.933	CLONAL	1	TRUE	1	0.657085001371118	2		1182	975	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166303	32166303	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	370	1154	1	ENST00000375023.3:c.4651C>T	p.Leu1551Phe	p.L1551F	ENST00000375023	NM_004557.3	1551	Ctc/Ttc	26/30	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.657085001371118	2		1155	1047	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188297	32188297	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs753855314	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	55	1171	3	ENST00000375023.3:c.1044del	p.Gly349AlafsTer49	p.G349Afs*49	ENST00000375023	NM_004557.3	348	ggC/gg	6/30	1	2	FACETS	0.164	0.14	0.192	0.164	0.14	0.192	SUBCLONAL	1	TRUE	1	0.657085001371118	2		1174	1018	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288985	33288985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	53	881	1	ENST00000374542.5:c.567G>C	p.Gln189His	p.Q189H	ENST00000374542	NM_001141970.1	189	caG/caC	3/8	1	2	FACETS	0.22	0.187	0.256	0.22	0.187	0.256	SUBCLONAL	1	TRUE	1	0.657085001371118	2		882	734	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662735	117662735	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	116	524	0	ENST00000368508.3:c.4730C>T	p.Ser1577Phe	p.S1577F	ENST00000368508	NM_002944.2	1577	tCt/tTt	29/43	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.657085001371118	2		524	343	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199837	138199837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	208	810	0	ENST00000237289.4:c.1255C>T	p.Pro419Ser	p.P419S	ENST00000237289	NM_001270507.1	419	Cca/Tca	7/9	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.657085001371118	2		810	613	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683632	162683632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	239	895	1	ENST00000366898.1:c.337C>T	p.Pro113Ser	p.P113S	ENST00000366898	NM_004562.2	113	Cca/Tca	3/12	1	2	FACETS	0.998	0.936	1	0.998	0.936	1	CLONAL	1	TRUE	1	0.657085001371118	2		896	729	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971174	13971174	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	136	563	0	ENST00000405192.2:c.755del	p.Pro252LeufsTer3	p.P252Lfs*3	ENST00000405192	NM_001163147.1	252	cCt/ct	8/12	0.654266156709829	3	FACETS	0.862	0.786	0.941	0.431	0.393	0.471	CLONAL	1	TRUE	1	0.657085001371118	3		563	638	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	128	504	3	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	0.654266156709829	3	FACETS	0.767	0.696	0.841	0.383	0.348	0.421	SUBCLONAL	1	TRUE	1	0.657085001371118	3		507	675	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381528	81381528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776090604	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	116	451	0	ENST00000222390.5:c.533G>A	p.Arg178Gln	p.R178Q	ENST00000222390	NM_000601.4	178	cGa/cAa	5/18	0.654266156709829	3	FACETS	0.888	0.804	0.977	0.444	0.402	0.489	CLONAL	1	TRUE	1	0.657085001371118	3		451	528	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624404	140624409	+	inframe_deletion	In_Frame_Del	DEL	CGGCGC	CGGCGC	-	rs397507458	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	45	198	0	ENST00000288602.6:c.95_100del	p.Gly32_Ala33del	p.G32_A33del	ENST00000288602	NM_004333.4	32	gGCGCCGcg/gcg	1/18	0.654266156709829	3	FACETS	0.938	0.799	1	0.469	0.399	0.544	CLONAL	1	TRUE	1	0.657085001371118	3		198	194	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372364	55372364	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1193005049	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	287	1045	2	ENST00000297316.4:c.1054G>A	p.Ala352Thr	p.A352T	ENST00000297316	NM_022454.3	352	Gcc/Acc	2/2	0.654266156709829	3	FACETS	1	0.968	1	0.522	0.491	0.554	CLONAL	1	TRUE	1	0.657085001371118	3		1047	1111	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002852	69002852	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	36	489	0	ENST00000288368.4:c.2152T>C	p.Cys718Arg	p.C718R	ENST00000288368	NM_024870.2	718	Tgc/Cgc	20/40	0.654266156709829	3	FACETS	0.285	0.234	0.343	0.143	0.117	0.172	SUBCLONAL	1	TRUE	1	0.657085001371118	3		489	510	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141569579	141569582	+	frameshift_variant	Frame_Shift_Del	DEL	ACAA	ACAA	-	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	169	634	0	ENST00000220592.5:c.702_705del	p.Cys235LysfsTer15	p.C235Kfs*15	ENST00000220592	NM_012154.3	234	gtTTGT/gt	6/19	0.654266156709829	3	FACETS	0.785	0.722	0.85	0.392	0.361	0.425	SUBCLONAL	1	TRUE	1	0.657085001371118	3		634	871	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27190576	27190576	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	95	1001	0	ENST00000380036.4:c.1377C>A	p.Asn459Lys	p.N459K	ENST00000380036	NM_000459.3	459	aaC/aaA	10/23	0.605284153235727	3	FACETS	0.392	0.348	0.439	0.131	0.116	0.147	SUBCLONAL	1	TRUE	0	0.657085001371118	3		1001	980	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882050	36882050	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs780753361	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	309	1085	6	ENST00000358127.4:c.963del	p.Ala322LeufsTer11	p.A322Lfs*11	ENST00000358127	NM_001280556.1	321	ccC/cc	8/10	0.657085001371118	3	FACETS	0.841	0.792	0.893	0.28	0.263	0.298	CLONAL	1	TRUE	0	0.657085001371118	3		1091	1485	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342841	87342841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	51	668	1	ENST00000277120.3:c.1126G>A	p.Ala376Thr	p.A376T	ENST00000277120		376	Gct/Act	9/19	0.657085001371118	3	FACETS	0.329	0.279	0.384	0.11	0.093	0.128	SUBCLONAL	1	TRUE	0	0.657085001371118	3		669	627	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650080	93650080	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	250	861	0	ENST00000375746.1:c.1631T>A	p.Ile544Asn	p.I544N	ENST00000375746	NM_001174167.1	544	aTc/aAc	12/14	0.657085001371118	3	FACETS	1	0.95	1	0.339	0.317	0.362	CLONAL	1	TRUE	0	0.657085001371118	3		861	994	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211415	98211415	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	58	1097	1	ENST00000331920.6:c.3740C>T	p.Ala1247Val	p.A1247V	ENST00000331920	NM_000264.3	1247	gCg/gTg	22/24	0.657085001371118	3	FACETS	0.205	0.175	0.237	0.068	0.058	0.079	SUBCLONAL	1	TRUE	0	0.657085001371118	3		1098	1146	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	86	806	1	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	0.657085001371118	3	FACETS	0.346	0.305	0.39	0.115	0.101	0.13	SUBCLONAL	1	TRUE	0	0.657085001371118	3		807	1005	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922258	39922258	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	191	783	0	ENST00000378444.4:c.3914del	p.Lys1305SerfsTer64	p.K1305Sfs*64	ENST00000378444	NM_001123385.1	1305	aAg/ag	9/15	1	2	FACETS	0.906	0.841	0.972	0.906	0.841	0.972	CLONAL	1	TRUE	1	0.657085001371118	2		783	642	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945198	44945198	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	206	724	0	ENST00000377967.4:c.3522G>T	p.Trp1174Cys	p.W1174C	ENST00000377967	NM_021140.2	1174	tgG/tgT	24/29	1	2	FACETS	0.978	0.912	1	0.978	0.912	1	CLONAL	1	TRUE	1	0.657085001371118	2		724	641	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428394	47428394	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	260	1103	2	ENST00000377045.4:c.1262A>G	p.His421Arg	p.H421R	ENST00000377045	NM_001654.4	421	cAt/cGt	12/16	1	2	FACETS	0.913	0.857	0.97	0.913	0.857	0.97	CLONAL	1	TRUE	1	0.657085001371118	2		1105	867	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430332	47430332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	319	1167	0	ENST00000377045.4:c.1607G>A	p.Ser536Asn	p.S536N	ENST00000377045	NM_001654.4	536	aGc/aAc	15/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.657085001371118	2		1167	910	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164942	123164942	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	97	445	0	ENST00000218089.9:c.255T>A	p.Phe85Leu	p.F85L	ENST00000218089	NM_001042749.1	85	ttT/ttA	5/35	NA	2	FACETS	0.753	0.676	0.834			1	INDETERMINATE	1	TRUE	NA	0.657085001371118	2		445	392	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134504	30134504	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	25	385	0	ENST00000263025.4:c.27del	p.Gly11AlafsTer21	p.G11Afs*21	ENST00000263025	NM_002746.2	9	ggC/gg	1/9	1	2	FACETS	0.3	0.237	0.371	0.3	0.237	0.371	SUBCLONAL	1	TRUE	1	0.657085001371118	2		385	254	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740698	58740698	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	139	567	0	ENST00000305921.3:c.1606del	p.Arg536GlyfsTer3	p.R536Gfs*3	ENST00000305921	NM_003620.3	535	Aaa/aa	6/6	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.359402881563599	2		567	751	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183872	10183872	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs730882032	NA	P-0047381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	169	574	0	ENST00000256474.2:c.340+1G>T		p.X114_splice	ENST00000256474	NM_000551.3	114			0.359402881563599	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.359402881563599	1		574	606	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442591	52442595	+	frameshift_variant	Frame_Shift_Del	DEL	ATTTG	ATTTG	-	novel	NA	P-0047381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	66	440	0	ENST00000460680.1:c.150_154del	p.Phe50LeufsTer17	p.F50Lfs*17	ENST00000460680	NM_004656.3	50	ttCAAATgg/ttgg	4/17	0.359402881563599	1	FACETS	0.524	0.455	0.599	0.524	0.455	0.599	SUBCLONAL	1	TRUE	0	0.359402881563599	1		440	575	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966584	36966584	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	228	781	1	ENST00000358127.4:c.742G>A	p.Asp248Asn	p.D248N	ENST00000358127	NM_001280556.1	248	Gac/Aac	6/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.359402881563599	2		782	1101	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0047382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	175	1013	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.299545950310505	2	FACETS	1	0.985	1	0.631	0.582	0.681	CLONAL	1	FALSE	0	0.378012381489111	2		1013	734	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0047382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	24	419	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.858	0.694	1	1	0.946	1	CLONAL	2	FALSE	1	0.378012381489111	2		419	74	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	26	794	3	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	1	2	FACETS	0.876	0.702	1	0.876	0.702	1	CLONAL	1	FALSE	1	0.378012381489111	2		797	157	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247243	153247243	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	18	564	0	ENST00000281708.4:c.1559A>T	p.Asp520Val	p.D520V	ENST00000281708	NM_033632.3	520	gAt/gTt	10/12	1	2	FACETS	0.85	0.649	1	0.85	0.649	1	CLONAL	1	FALSE	1	0.378012381489111	2		564	112	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508257	106508257	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766854286	NA	P-0047382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	108	577	1	ENST00000359195.3:c.251C>T	p.Ala84Val	p.A84V	ENST00000359195	NM_002649.2	84	gCg/gTg	2/11	0.156943216498965	3	FACETS	1	0.977	1	0.431	0.388	0.476	INDETERMINATE	1	FALSE	0	0.378012381489111	3		578	525	SUCCESS
APC	324	MSKCC	GRCh37	5	112151291	112151291	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs876660765	NA	P-0047382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	17	387	0	ENST00000257430.4:c.933+1G>A		p.X311_splice	ENST00000257430	NM_000038.5	311			0.329426011590365	1	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	FALSE	0	0.378012381489111	1		387	63	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62298844	62298844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560281693	NA	P-0047382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	81	1011	0	ENST00000360203.5:c.637C>T	p.Arg213Trp	p.R213W	ENST00000360203	NM_001283009.1	213	Cgg/Tgg	8/35	0.156943216498965	3	FACETS	0.734	0.647	0.828	0.245	0.215	0.276	INDETERMINATE	1	FALSE	0	0.378012381489111	3		1011	694	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753452	42753452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	247	838	3	ENST00000222329.4:c.812C>T	p.Thr271Met	p.T271M	ENST00000222329	NM_006494.2	271	aCg/aTg	4/4	0.187784363297555	4	FACETS	1	0.991	1	0.701	0.654	0.75	INDETERMINATE	1	FALSE	2	0.378012381489111	4		841	1284	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014383	70014383	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780036017	NA	P-0047382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	63	804	0	ENST00000394351.3:c.1244C>T	p.Thr415Met	p.T415M	ENST00000394351	NM_000248.3	415	aCg/aTg	9/9	1	2	FACETS	0.792	0.687	0.905	0.792	0.687	0.905	CLONAL	1	FALSE	1	0.378012381489111	2		804	421	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681425	88681425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	39	702	0	ENST00000372037.3:c.1315G>A	p.Glu439Lys	p.E439K	ENST00000372037	NM_004329.2	439	Gag/Aag	11/13	1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	FALSE	1	0.378012381489111	2		702	204	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589528	69589528	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	72	138	2	ENST00000168712.1:c.325G>A	p.Ala109Thr	p.A109T	ENST00000168712	NM_002007.2	109	Gcg/Acg	1/3	1	2	FACETS	0.528	0.46	0.6	0.528	0.46	0.6	SUBCLONAL	1	FALSE	1	0.378012381489111	2		140	722	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112226	115112226	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	92	395	2	ENST00000257566.3:c.1514C>T	p.Pro505Leu	p.P505L	ENST00000257566	NM_016569.3	505	cCg/cTg	7/8	0.121452843833845	4	FACETS	1	0.97	1	0.627	0.558	0.699	INDETERMINATE	1	FALSE	2	0.378012381489111	4		397	535	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155847	106155847	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	14	580	0	ENST00000380013.4:c.748A>G	p.Asn250Asp	p.N250D	ENST00000380013	NM_001127208.2	250	Aat/Gat	3/11	1	2	FACETS	1	0.786	1	1	0.786	1	CLONAL	1	FALSE	1	0.378012381489111	2		580	69	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557630	95557630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	150	611	0	ENST00000393063.1:c.5437G>A	p.Glu1813Lys	p.E1813K	ENST00000393063	NM_030621.3	1813	Gag/Aag	26/28	1	2	FACETS	0.933	0.854	1	0.933	0.854	1	CLONAL	1	TRUE	1	0.43	2		611	748	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0047383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	114	533	0	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	1	2	FACETS	0.916	0.827	1	0.916	0.827	1	CLONAL	1	TRUE	1	0.43	2		533	579	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685269	89685269	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0047383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	30	173	0	ENST00000371953.3:c.165-1G>T		p.X55_splice	ENST00000371953	NM_000314.4	55			1	2	FACETS	0.674	0.547	0.816	0.674	0.547	0.816	SUBCLONAL	1	TRUE	1	0.43	2		173	207	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106064	27106064	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	161	819	0	ENST00000324856.7:c.5675del	p.Thr1892LysfsTer31	p.T1892Kfs*31	ENST00000324856	NM_006015.4	1892	aCa/aa	20/20	1	2	FACETS	0.92	0.845	0.998	0.92	0.845	0.998	CLONAL	1	TRUE	1	0.43	2		819	814	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692778	89692778	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	97	438	0	ENST00000371953.3:c.262del	p.Tyr88IlefsTer11	p.Y88Ifs*11	ENST00000371953	NM_000314.4	88	Tat/at	5/9	1	2	FACETS	0.902	0.808	1	0.902	0.808	1	CLONAL	1	TRUE	1	0.43	2		438	500	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571513	95571513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1413756805	NA	P-0047383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	158	657	0	ENST00000393063.1:c.3164C>T	p.Pro1055Leu	p.P1055L	ENST00000393063	NM_030621.3	1055	cCc/cTc	21/28	1	2	FACETS	0.964	0.885	1	0.964	0.885	1	CLONAL	1	TRUE	1	0.43	2		657	762	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821638	72821638	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047383-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	32	137	0	ENST00000268489.5:c.10537del	p.Ser3513ValfsTer32	p.S3513Vfs*32	ENST00000268489	NM_006885.3	3513	Agt/gt	10/10	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.43	2		137	138	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0047384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	21	277	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.237416453554029	6	FACETS	1	0.918	1	0.5	0.387	0.629	CLONAL	1	TRUE	3	0.237416453554029	6		277	174	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0047384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	86	329	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.237416453554029	5	FACETS	0.898	0.796	1	0.898	0.796	1	CLONAL	2	TRUE	3	0.237416453554029	5		329	547	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368208	45368208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	56	493	0	ENST00000262160.6:c.1394G>A	p.Ser465Asn	p.S465N	ENST00000262160	NM_005901.5	465	aGc/aAc	11/11	0.237416453554029	6	FACETS	0.911	0.793	1	0.729	0.634	0.828	CLONAL	4	TRUE	1	0.237416453554029	6		493	191	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204681	108204681	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs745775382	NA	P-0047384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	36	238	0	ENST00000278616.4:c.7996A>G	p.Thr2666Ala	p.T2666A	ENST00000278616	NM_000051.3	2666	Act/Gct	54/63	NA	2	FACETS	0.849	0.714	0.993			1	INDETERMINATE	3	TRUE	NA	0.237416453554029	2		238	119	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793043	42793043	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	124	792	0	ENST00000575354.2:c.935C>A	p.Ser312Tyr	p.S312Y	ENST00000575354	NM_015125.3	312	tCc/tAc	7/20	0.237416453554029	5	FACETS	0.96	0.869	1	0.64	0.579	0.704	CLONAL	2	TRUE	2	0.237416453554029	5		792	738	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579315	7579316	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1267047192	NA	P-0047385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	692	495	0	ENST00000269305.4:c.371dup	p.Cys124TrpfsTer25	p.C124Wfs*25	ENST00000269305	NM_001126112.2	124	tgc/tgGc	4/11	0.61214503292674	3	FACETS	0.971	0.945	0.995	0.971	0.945	0.995	CLONAL	3	TRUE	0	0.61214503292674	3		495	1014	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0047386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	204	470	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.996	0.935	1	0.996	0.935	1	CLONAL	1	TRUE	1	0.908583199526475	2		470	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0047386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	450	673	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.906244211059174	1	FACETS	0.992	0.968	1	0.992	0.968	1	CLONAL	1	TRUE	0	0.908583199526475	1		673	545	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233041	55233043	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0047386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1235	13161	605	0	ENST00000275493.2:c.1793_1795del	p.Gly598del	p.G598del	ENST00000275493	NM_005228.3	597	gcAGGa/gca	15/28	0.908583199526475	32	FACETS	1	0.999	1	0.95	0.946	0.953	CLONAL	29	TRUE	1	0.908583199526475	32		605	14396	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233048	55233048	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs746395542	NA	P-0047386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	14230	628	0	ENST00000275493.2:c.1798A>T	p.Met600Leu	p.M600L	ENST00000275493	NM_005228.3	600	Atg/Ttg	15/28	0.908583199526475	32	FACETS	0.997	0.994	0.999	0.997	0.994	0.999	CLONAL	31	TRUE	1	0.908583199526475	32		628	14827	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0047386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	209	442	0	ENST00000304494.5:c.151-1G>A		p.X51_splice	ENST00000304494	NM_000077.4	51			0.908583199526475	1	FACETS	0.951	0.914	0.986	0.951	0.914	0.986	CLONAL	1	TRUE	0	0.908583199526475	1		442	264	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0047387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	78	775	3	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	0.378	0.331	0.428	0.378	0.331	0.428	SUBCLONAL	1	TRUE	1	0.471565967245767	2		778	876	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206892	36206893	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0047387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	133	473	0	ENST00000300305.3:c.619dup	p.Arg207ProfsTer6	p.R207Pfs*6	ENST00000300305		207	cgg/cCgg	6/8	0.173682728425208	2	FACETS	0.881	0.803	0.964	0.441	0.401	0.482	INDETERMINATE	1	TRUE	0	0.471565967245767	2		473	640	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	123	516	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.902	0.821	0.987	0.902	0.821	0.987	CLONAL	1	TRUE	1	0.563232187847414	2		516	484	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0047388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	382	467	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.133285657437008	5	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.563232187847414	5		467	1124	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670391	88670391	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0047388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	103	484	0	ENST00000360948.2:c.1293+2T>C		p.X431_splice	ENST00000360948	NM_001012338.2	431			0.520916980320788	3	FACETS	0.734	0.657	0.814	0.367	0.328	0.407	SUBCLONAL	1	TRUE	1	0.563232187847414	3		484	639	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10259657	10259657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749258509	NA	P-0047388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	184	601	1	ENST00000340748.4:c.2575G>A	p.Asp859Asn	p.D859N	ENST00000340748		859	Gac/Aac	26/40	1	2	FACETS	0.783	0.724	0.845	0.783	0.724	0.845	SUBCLONAL	1	TRUE	1	0.563232187847414	2		602	834	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41558754	41558756	+	missense_variant	Missense_Mutation	TNP	GAG	GAG	TAA	novel	NA	P-0047388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	87	450	1	ENST00000263253.7:c.3699_3701delinsTAA	p.Lys1233_Arg1234delinsAsnLys	p.K1233_R1234delinsNK	ENST00000263253	NM_001429.3	1233	aaGAGa/aaTAAa	21/31	1	2	FACETS	0.508	0.45	0.57	0.508	0.45	0.57	SUBCLONAL	1	TRUE	1	0.563232187847414	2		451	608	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41558764	41558766	+	stop_gained	Nonsense_Mutation	TNP	GAC	GAC	TAA	novel	NA	P-0047388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	86	467	0	ENST00000263253.7:c.3709_3711delinsTAA	p.Asp1237Ter	p.D1237*	ENST00000263253	NM_001429.3	1237	GAC/TAA	21/31	1	2	FACETS	0.495	0.438	0.556	0.495	0.438	0.556	SUBCLONAL	1	TRUE	1	0.563232187847414	2		467	617	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188187	32188187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754712190	NA	P-0047389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	350	607	0	ENST00000375023.3:c.1154G>A	p.Arg385His	p.R385H	ENST00000375023	NM_004557.3	385	cGc/cAc	6/30	0.474384526530913	1	FACETS	0.754	0.72	0.789	0.754	0.72	0.789	SUBCLONAL	1	TRUE	0	0.781155066177197	1		607	724	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27168576	27168576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753021890	NA	P-0047389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	134	533	0	ENST00000380036.4:c.448G>A	p.Glu150Lys	p.E150K	ENST00000380036	NM_000459.3	150	Gaa/Aaa	3/23	0.39974833697681	1	FACETS	0.352	0.321	0.385	0.352	0.321	0.385	INDETERMINATE	1	TRUE	0	0.781155066177197	1		533	594	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835697	68835697	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	448	696	0	ENST00000261769.5:c.289del	p.His97IlefsTer20	p.H97Ifs*20	ENST00000261769	NM_004360.3	96	atC/at	3/16	0.781155066177197	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.781155066177197	1		696	692	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435071	18435071	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1217978720	NA	P-0047390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	30	424	0	ENST00000266497.5:c.56A>G	p.Tyr19Cys	p.Y19C	ENST00000266497		19	tAt/tGt	1/31	1	2	FACETS	0.684	0.55	0.837	0.684	0.55	0.837	SUBCLONAL	1	TRUE	1	0.16	2		424	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579316	7579322	+	frameshift_variant	Frame_Shift_Del	DEL	CAAGTCA	CAAGTCA	-	novel	NA	P-0047390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	61	753	0	ENST00000269305.4:c.365_371del	p.Val122AlafsTer46	p.V122Afs*46	ENST00000269305	NM_001126112.2	122	gTGACTTGc/gc	4/11	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.16	2		753	739	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246271	41246271	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs886039939	NA	P-0047390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	47	710	0	ENST00000357654.3:c.1277C>G	p.Ser426Ter	p.S426*	ENST00000357654	NM_007294.3	426	tCa/tGa	10/23	1	2	FACETS	0.751	0.632	0.883	0.751	0.632	0.883	SUBCLONAL	1	TRUE	1	0.16	2		710	782	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018165	48018165	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	65	855	0	ENST00000234420.5:c.361del	p.Arg121AlafsTer28	p.R121Afs*28	ENST00000234420	NM_000179.2	120	atC/at	2/10	1	2	FACETS	0.8	0.692	0.919	0.8	0.692	0.919	CLONAL	1	TRUE	1	0.16	2		855	1015	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	42	516	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	0.701	0.589	0.824	0.701	0.589	0.824	SUBCLONAL	1	TRUE	0	0.36	1		516	273	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0047391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	83	164	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.977	0.865	1	0.977	0.865	1	CLONAL	1	TRUE	1	0.36	2		164	472	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881129	37881129	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	150	833	0	ENST00000269571.5:c.2458C>G	p.Gln820Glu	p.Q820E	ENST00000269571		820	Cag/Gag	20/27	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.36	2		833	806	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0047392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	293	419	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.432933640961014	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.4339876648417	2		419	636	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0047392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	421	552	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.432933640961014	2	FACETS	0.907	0.866	0.948	0.907	0.866	0.948	CLONAL	2	TRUE	0	0.4339876648417	2		553	1070	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0047392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	155	652	1	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.4339876648417	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.4339876648417	1		653	545	SUCCESS
APC	324	MSKCC	GRCh37	5	112175328	112175328	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0047392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	201	361	0	ENST00000257430.4:c.4037C>G	p.Ser1346Ter	p.S1346*	ENST00000257430	NM_000038.5	1346	tCa/tGa	16/16	0.4339876648417	3	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	1	0.4339876648417	3		361	559	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0047392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	74	297	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.4339876648417	3	FACETS	0.766	0.671	0.867	0.383	0.335	0.434	SUBCLONAL	1	TRUE	1	0.4339876648417	3		297	542	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394052	31394052	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	135	574	2	ENST00000328111.2:c.2339C>T	p.Ser780Leu	p.S780L	ENST00000328111	NM_006892.3	780	tCg/tTg	22/23	0.4339876648417	5	FACETS	0.834	0.756	0.916	0.278	0.252	0.306	CLONAL	1	TRUE	2	0.4339876648417	5		576	1232	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639237	3639237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760497928	NA	P-0047392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1236	479	1196	0	ENST00000294008.3:c.4402C>T	p.Arg1468Cys	p.R1468C	ENST00000294008	NM_032444.2	1468	Cgc/Tgc	12/15	0.360361085086007	4	FACETS	0.923	0.881	0.966	0.923	0.881	0.966	CLONAL	2	TRUE	2	0.4339876648417	4		1196	1715	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	105	516	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.28390418894634	2		516	539	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0047394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	106	396	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.28390418894634	2		396	703	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0047394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	73	375	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	1	2	FACETS	0.938	0.822	1	0.938	0.822	1	CLONAL	1	TRUE	1	0.28390418894634	2		375	548	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0047394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	102	280	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.28390418894634	1	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	0	0.28390418894634	1		280	612	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392143	81392143	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	66	337	0	ENST00000222390.5:c.134C>A	p.Ser45Ter	p.S45*	ENST00000222390	NM_000601.4	45	tCa/tAa	2/18	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.28390418894634	2		337	454	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912198	114912198	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	187	635	0	ENST00000543371.1:c.1268A>G	p.Tyr423Cys	p.Y423C	ENST00000543371	NM_001198531.1	423	tAt/tGt	11/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.28390418894634	2		635	1114	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122691	108122691	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	100	468	0	ENST00000278616.4:c.1735T>C	p.Trp579Arg	p.W579R	ENST00000278616	NM_000051.3	579	Tgg/Cgg	11/63	1	2	FACETS	0.973	0.869	1	0.973	0.869	1	CLONAL	1	TRUE	1	0.28390418894634	2		468	724	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39623766	39623767	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs1449755492	NA	P-0047394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	115	465	0	ENST00000262039.4:c.2174dup	p.Tyr725Ter	p.Y725*	ENST00000262039	NM_002647.2	725	tac/tAac	20/25	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.28390418894634	2		465	695	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589881	212589881	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	144	651	0	ENST00000342788.4:c.661T>A	p.Cys221Ser	p.C221S	ENST00000342788	NM_005235.2	221	Tgc/Agc	6/28	1	2	FACETS	0.923	0.84	1	0.923	0.84	1	CLONAL	1	TRUE	1	0.28390418894634	2		651	1099	SUCCESS
APC	324	MSKCC	GRCh37	5	112137018	112137018	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	102	493	0	ENST00000257430.4:c.772del	p.Glu258SerfsTer35	p.E258Sfs*35	ENST00000257430	NM_000038.5	258	Gag/ag	8/16	1	2	FACETS	0.944	0.844	1	0.944	0.844	1	CLONAL	1	TRUE	1	0.28390418894634	2		493	761	SUCCESS
APC	324	MSKCC	GRCh37	5	112173510	112173510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	82	403	0	ENST00000257430.4:c.2219C>T	p.Ala740Val	p.A740V	ENST00000257430	NM_000038.5	740	gCc/gTc	16/16	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.28390418894634	2		403	574	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268105	55268105	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	190	858	0	ENST00000275493.2:c.2945A>G	p.Gln982Arg	p.Q982R	ENST00000275493	NM_005228.3	982	cAg/cGg	24/28	1	2	FACETS	0.987	0.91	1	0.987	0.91	1	CLONAL	1	TRUE	1	0.28390418894634	2		858	1356	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22008928	22008928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	185	671	1	ENST00000276925.6:c.25C>T	p.Pro9Ser	p.P9S	ENST00000276925	NM_004936.3	9	Ccc/Tcc	1/2	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.28390418894634	2		672	1174	SUCCESS
AR	367	MSKCC	GRCh37	X	66941715	66941715	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555997580	NA	P-0047394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	177	757	0	ENST00000374690.3:c.2359C>T	p.Arg787Ter	p.R787*	ENST00000374690	NM_000044.3	787	Cga/Tga	6/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.28390418894634	2		757	1166	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0047395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	72	204	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.293926608776218	1	FACETS	0.851	0.746	0.963	0.851	0.746	0.963	CLONAL	1	TRUE	0	0.325154211924963	1		204	436	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043377	180043377	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771345898	NA	P-0047395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	175	639	4	ENST00000261937.6:c.3209G>A	p.Arg1070His	p.R1070H	ENST00000261937	NM_182925.4	1070	cGc/cAc	23/30	1	2	FACETS	0.996	0.916	1	0.996	0.916	1	CLONAL	1	TRUE	1	0.325154211924963	2		643	1081	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0047395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	158	607	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.325154211924963	2		607	884	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274568	198274568	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746956131	NA	P-0047395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	167	595	0	ENST00000335508.6:c.830C>T	p.Ala277Val	p.A277V	ENST00000335508	NM_012433.2	277	gCg/gTg	7/25	1	2	FACETS	0.932	0.855	1	0.932	0.855	1	CLONAL	1	TRUE	1	0.325154211924963	2		595	1102	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920450	114920450	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	129	547	0	ENST00000543371.1:c.1391G>A	p.Arg464Lys	p.R464K	ENST00000543371	NM_001198531.1	464	aGg/aAg	13/14	1	2	FACETS	0.833	0.754	0.916	0.833	0.754	0.916	CLONAL	1	TRUE	1	0.325154211924963	2		547	953	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456366	32456366	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	176	714	0	ENST00000332351.3:c.526C>T	p.Arg176Cys	p.R176C	ENST00000332351	NM_024426.4	176	Cgc/Tgc	1/10	1	2	FACETS	0.964	0.887	1	0.964	0.887	1	CLONAL	1	TRUE	1	0.325154211924963	2		714	1123	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267295	41267295	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	88	379	1	ENST00000349496.5:c.879C>A	p.Phe293Leu	p.F293L	ENST00000349496	NM_001904.3	293	ttC/ttA	6/15	1	2	FACETS	0.902	0.8	1	0.902	0.8	1	CLONAL	1	TRUE	1	0.325154211924963	2		380	600	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0047396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	101	550	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.562537043670068	2	FACETS	0.853	0.784	0.921	0.853	0.784	0.921	CLONAL	2	TRUE	0	0.630081720261141	2		550	188	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	35	457	1	ENST00000288602.6:c.1780G>T	p.Asp594Tyr	p.D594Y	ENST00000288602	NM_004333.4	594	Gat/Tat	15/18	1	2	FACETS	0.661	0.549	0.784	0.661	0.549	0.784	SUBCLONAL	1	TRUE	1	0.630081720261141	2		458	168	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200990	108200990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755418571	NA	P-0047396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	56	514	0	ENST00000278616.4:c.7357C>T	p.Arg2453Cys	p.R2453C	ENST00000278616	NM_000051.3	2453	Cgt/Tgt	50/63	0.33954997216374	1	FACETS	0.628	0.546	0.713	0.628	0.546	0.713	INDETERMINATE	1	TRUE	0	0.630081720261141	1		514	194	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871617	35871617	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	138	398	1	ENST00000216797.5:c.889G>T	p.Glu297Ter	p.E297*	ENST00000216797	NM_020529.2	297	Gag/Tag	5/6	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.630081720261141	2		399	347	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66525014	66525014	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	75	329	0	ENST00000358598.2:c.773C>G	p.Ser258Cys	p.S258C	ENST00000358598	NM_212471.2	258	tCt/tGt	9/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.630081720261141	2		329	200	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602584	10602585	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0047396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	198	863	3	ENST00000171111.5:c.993_994delinsTT	p.Gly332Cys	p.G332C	ENST00000171111	NM_203500.1	331	gcGGgc/gcTTgc	3/6	0.630081720261141	1	FACETS	0.981	0.92	1	0.981	0.92	1	CLONAL	1	TRUE	0	0.630081720261141	1		866	439	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463247	25463248	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0047396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	78	736	3	ENST00000264709.3:c.2245_2246delinsTT	p.Arg749Phe	p.R749F	ENST00000264709	NM_175629.2	749	CGc/TTc	19/23	0.314650289104712	3	FACETS	0.479	0.42	0.542	0.16	0.14	0.181	INDETERMINATE	1	TRUE	0	0.630081720261141	3		739	680	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437823	52437832	+	frameshift_variant	Frame_Shift_Del	DEL	GTTGATGGTG	GTTGATGGTG	-	novel	NA	P-0047396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	188	940	0	ENST00000460680.1:c.1329_1338del	p.Asn443LysfsTer125	p.N443Kfs*125	ENST00000460680	NM_004656.3	443	aaCACCATCAAC/aa	13/17	0.579376737620231	1	FACETS	0.955	0.893	1	0.955	0.893	1	CLONAL	1	TRUE	0	0.630081720261141	1		940	428	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412623	63412630	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTCCGG	TCTTCCGG	-	novel	NA	P-0047396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	119	768	0	ENST00000330258.3:c.537_544del	p.His179GlnfsTer7	p.H179Qfs*7	ENST00000330258	NM_152424.3	179	caCCGGAAGAgc/cagc	2/2	0.630081720261141	1	FACETS	0.804	0.735	0.874	0.804	0.735	0.874	CLONAL	1	TRUE	0	0.630081720261141	1		768	322	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741949	17741949	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	85	282	0	ENST00000250003.3:c.620C>T	p.Ser207Phe	p.S207F	ENST00000250003	NM_002478.4	207	tCc/tTc	1/3	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.509220764239325	2		282	276	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432310	49432310	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	227	828	1	ENST00000301067.7:c.8829del	p.Asn2943LysfsTer61	p.N2943Kfs*61	ENST00000301067	NM_003482.3	2943	aaC/aa	34/54	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.509220764239325	2		829	859	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862752	9862752	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	131	519	0	ENST00000330684.3:c.2551G>T	p.Gly851Cys	p.G851C	ENST00000330684	NM_001134407.1	851	Ggc/Tgc	12/13	0.509220764239325	3	FACETS	0.9	0.818	0.987	0.45	0.409	0.494	CLONAL	1	TRUE	1	0.509220764239325	3		519	717	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098480	11098480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	134	524	0	ENST00000358026.2:c.998C>T	p.Pro333Leu	p.P333L	ENST00000358026	NM_001128849.1	333	cCc/cTc	6/36	0.509220764239325	1	FACETS	0.952	0.873	1	0.952	0.873	1	CLONAL	1	TRUE	0	0.509220764239325	1		524	412	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713931	30713931	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0047419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	76	367	0	ENST00000295754.5:c.1254+2T>G		p.X418_splice	ENST00000295754	NM_003242.5	418			0.509220764239325	1	FACETS	0.759	0.673	0.85	0.759	0.673	0.85	SUBCLONAL	1	TRUE	0	0.509220764239325	1		367	293	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673400	30673400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	48	645	0	ENST00000376406.3:c.3560C>T	p.Thr1187Ile	p.T1187I	ENST00000376406	NM_014641.2	1187	aCt/aTt	10/15	0.509220764239325	2	FACETS	0.246	0.207	0.289	0.123	0.103	0.145	SUBCLONAL	1	TRUE	0	0.509220764239325	2		645	766	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352312	70352312	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	183	630	1	ENST00000374080.3:c.4339G>T	p.Ala1447Ser	p.A1447S	ENST00000374080		1447	Gct/Tct	31/45	0.509220764239325	3	FACETS	1	0.966	1	0.539	0.498	0.582	CLONAL	1	TRUE	1	0.509220764239325	3		631	836	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252878	36252878	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519751	NA	P-0047420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	28	286	0	ENST00000300305.3:c.484A>G	p.Arg162Gly	p.R162G	ENST00000300305		162	Agg/Ggg	4/8	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		286	94	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331742	68331742	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	11	216	0	ENST00000487270.1:c.338G>T	p.Gly113Val	p.G113V	ENST00000487270	NM_133509.3	113	gGa/gTa	5/11	0.123591566262368	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		216	58	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	93	516	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.235518509737779	2		516	567	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670597	134670597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1330628001	NA	P-0047421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	99	735	0	ENST00000398015.3:c.508C>T	p.Arg170Trp	p.R170W	ENST00000398015	NM_004441.4	170	Cgg/Tgg	3/16	1	2	FACETS	0.856	0.763	0.956	0.856	0.763	0.956	CLONAL	1	TRUE	1	0.235518509737779	2		735	982	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286812	212286812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	26	337	0	ENST00000342788.4:c.2884G>A	p.Asp962Asn	p.D962N	ENST00000342788	NM_005235.2	962	Gac/Aac	24/28	1	2	FACETS	0.51	0.403	0.633	0.51	0.403	0.633	SUBCLONAL	1	TRUE	1	0.235518509737779	2		337	433	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056294	27056294	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	82	535	0	ENST00000324856.7:c.1292del	p.Pro431ArgfsTer2	p.P431Rfs*2	ENST00000324856	NM_006015.4	430	taC/ta	2/20	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.235518509737779	2		535	690	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938499	44938505	+	frameshift_variant	Frame_Shift_Del	DEL	GAACAAA	GAACAAA	-	novel	NA	P-0047421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	35	225	0	ENST00000377967.4:c.3050_3056del	p.Thr1017LysfsTer29	p.T1017Kfs*29	ENST00000377967	NM_021140.2	1016	gGAACAAAg/gg	20/29	1	1	FACETS	0.84	0.691	1	0.84	0.691	1	CLONAL	1	TRUE	0	0.235518509737779	1		225	312	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047421-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	79	516	0				ENST00000310581	NM_198253.2	-/1132			0.134464820636429	3	FACETS	0.867	0.767	0.975	0.867	0.767	0.975	INDETERMINATE	2	TRUE	1	0.24	3		516	425	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670597	134670597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1330628001	NA	P-0047421-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	76	735	0	ENST00000398015.3:c.508C>T	p.Arg170Trp	p.R170W	ENST00000398015	NM_004441.4	170	Cgg/Tgg	3/16	1	2	FACETS	0.725	0.634	0.822	0.725	0.634	0.822	SUBCLONAL	1	TRUE	1	0.24	2		735	874	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286812	212286812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047421-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	32	337	0	ENST00000342788.4:c.2884G>A	p.Asp962Asn	p.D962N	ENST00000342788	NM_005235.2	962	Gac/Aac	24/28	1	2	FACETS	0.803	0.653	0.972	0.803	0.653	0.972	CLONAL	1	TRUE	1	0.24	2		337	332	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056294	27056294	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047421-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	71	535	0	ENST00000324856.7:c.1292del	p.Pro431ArgfsTer2	p.P431Rfs*2	ENST00000324856	NM_006015.4	430	taC/ta	2/20	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.24	2		535	575	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938499	44938505	+	frameshift_variant	Frame_Shift_Del	DEL	GAACAAA	GAACAAA	-	novel	NA	P-0047421-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	62	225	0	ENST00000377967.4:c.3050_3056del	p.Thr1017LysfsTer29	p.T1017Kfs*29	ENST00000377967	NM_021140.2	1016	gGAACAAAg/gg	20/29	1	1	FACETS	0.795	0.693	0.904	1	0.974	1	CLONAL	2	TRUE	0	0.24	1		225	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577508	7577508	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060501201	NA	P-0047422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	372	601	0	ENST00000269305.4:c.773A>G	p.Glu258Gly	p.E258G	ENST00000269305	NM_001126112.2	258	gAa/gGa	7/11	0.457265526495532	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.457265526495532	2		601	788	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246344	46246344	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	171	299	0	ENST00000334344.6:c.4438G>T	p.Gly1480Ter	p.G1480*	ENST00000334344	NM_152641.2	1480	Gga/Tga	15/21	NA	2	FACETS	0.976	0.911	1			1	INDETERMINATE	2	TRUE	NA	0.457265526495532	2		299	383	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691936	30691938	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	novel	NA	P-0047422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	208	287	0	ENST00000295754.5:c.442_444del	p.Ile148del	p.I148del	ENST00000295754	NM_003242.5	146	aaCATc/aac	3/7	0.457265526495532	3	FACETS	1	0.987	1	0.796	0.747	0.845	CLONAL	2	TRUE	0	0.457265526495532	3		287	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0047423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	237	624	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	NA	2	FACETS	0.906	0.849	0.963			1	INDETERMINATE	2	TRUE	NA	0.362974723652816	2		624	721	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023114	31023114	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	155	535	1	ENST00000375687.4:c.2599G>A	p.Gly867Arg	p.G867R	ENST00000375687	NM_015338.5	867	Ggg/Agg	13/13	0.0766776047890816	4	FACETS	0.98	0.901	1	0.98	0.901	1	INDETERMINATE	2	TRUE	2	0.362974723652816	4		536	594	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0047424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	541	541	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.72677937659332	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.72677937659332	2		542	733	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531800	46531800	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	42	229	0	ENST00000262741.5:c.547G>C	p.Glu183Gln	p.E183Q	ENST00000262741	NM_003629.3	183	Gaa/Caa	5/10	0.72677937659332	3	FACETS	0.28	0.234	0.333	0.14	0.117	0.167	SUBCLONAL	1	TRUE	1	0.72677937659332	3		229	562	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941675	48941676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTTT	novel	NA	P-0047424-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	121	146	0	ENST00000267163.4:c.985_986insTTTT	p.Lys329IlefsTer13	p.K329Ifs*13	ENST00000267163	NM_000321.2	329	aaa/aTTTTaa	10/27	0.72677937659332	2	FACETS	0.785	0.729	0.84	0.785	0.729	0.84	SUBCLONAL	2	TRUE	0	0.72677937659332	2		146	212	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0047431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	15	303	1	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.218011434531851	3	FACETS	1	0.747	1	0.509	0.373	0.669	CLONAL	1	TRUE	1	0.19	3		304	170	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0047431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	161	759	2	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.298960750433059	1	FACETS	0.931	0.854	1	1	0.991	1	CLONAL	2	TRUE	0	0.19	1		761	824	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0047431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	62	428	2	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.227193925740861	3	FACETS	1	0.924	1	1	0.924	1	CLONAL	3	TRUE	0	0.19	3		430	221	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0047431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	184	691	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.298960750433059	1	FACETS	0.941	0.869	1	1	0.992	1	CLONAL	2	TRUE	0	0.19	1		691	931	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0047431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	143	642	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.298960750433059	1	FACETS	0.865	0.79	0.945	1	0.989	1	CLONAL	2	TRUE	0	0.19	1		642	787	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099479	27099479	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0047431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	48	320	0	ENST00000324856.7:c.3715+1G>A		p.X1239_splice	ENST00000324856	NM_006015.4	1239			0.197795096504305	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	2	TRUE	0	0.19	2		320	233	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593466	48593466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064796102	NA	P-0047431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	36	296	0	ENST00000342988.3:c.1217C>T	p.Ala406Val	p.A406V	ENST00000342988	NM_005359.5	406	gCg/gTg	10/12	0.12580282248693	0	FACETS	0.843	0.694	1			1	CLONAL	1	TRUE	0	0.19	0		296	364	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816306	89816306	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	51	402	0	ENST00000389301.3:c.3071T>C	p.Met1024Thr	p.M1024T	ENST00000389301	NM_000135.2	1024	aTg/aCg	32/43	0.286284649073538	3	FACETS	1	0.897	1	0.535	0.455	0.624	CLONAL	1	TRUE	1	0.19	3		402	549	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217080	2217080	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	68	667	0	ENST00000398665.3:c.2535del	p.Ser845ArgfsTer6	p.S845Rfs*6	ENST00000398665	NM_032482.2	845	agC/ag	21/28	1	2	FACETS	0.998	0.868	1	0.998	0.868	1	CLONAL	1	TRUE	1	0.19	2		667	717	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024254	31024254	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	34	498	0	ENST00000375687.4:c.3739C>G	p.Arg1247Gly	p.R1247G	ENST00000375687	NM_015338.5	1247	Cgt/Ggt	13/13	0.177667931480172	4	FACETS	0.832	0.679	1	0.416	0.339	0.502	CLONAL	1	TRUE	2	0.19	4		498	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0047432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	88	541	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.404939016597042	4	FACETS	0.904	0.835	0.971			1	CLONAL	4	FALSE	NA	0.55717307478551	4		542	136	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739743	145739743	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373178405	NA	P-0047432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	11	624	0	ENST00000428558.2:c.1708C>T	p.Arg570Trp	p.R570W	ENST00000428558	NM_004260.3	570	Cgg/Tgg	11/22	0.326452935154605	5	FACETS	0.483	0.335	0.666	0.161	0.111	0.222	INDETERMINATE	1	FALSE	2	0.55717307478551	5		624	150	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056424	26056424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs556238695	NA	P-0047432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	38	261	0	ENST00000343677.2:c.233G>A	p.Ser78Asn	p.S78N	ENST00000343677	NM_005319.3	78	aGc/aAc	1/1	0.55717307478551	16	FACETS	0.956	0.797	1	0.261	0.217	0.309	CLONAL	3	FALSE	5	0.55717307478551	16		261	233	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140341	50140341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778415296	NA	P-0047432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	10	497	2	ENST00000246792.3:c.200C>T	p.Thr67Met	p.T67M	ENST00000246792	NM_006270.3	67	aCg/aTg	2/6	0.436334750181733	3	FACETS	0.249	0.169	0.351	0.125	0.084	0.176	SUBCLONAL	1	FALSE	1	0.55717307478551	3		499	184	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840580	36840580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146173797	NA	P-0047432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	38	750	0	ENST00000358127.4:c.1153G>A	p.Ala385Thr	p.A385T	ENST00000358127	NM_001280556.1	385	Gcc/Acc	10/10	0.159317167350888	5	FACETS	1	0.859	1	0.259	0.215	0.307	INDETERMINATE	1	FALSE	1	0.55717307478551	5		750	242	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261326	16261326	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	172	431	0	ENST00000375759.3:c.8591C>G	p.Ser2864Trp	p.S2864W	ENST00000375759	NM_015001.2	2864	tCg/tGg	11/15	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.484288958815238	2		431	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578369	7578369	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0047433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	354	538	0	ENST00000269305.4:c.559+2T>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.484405216174624	2	FACETS	0.995	0.949	1	0.995	0.949	1	CLONAL	2	TRUE	0	0.484288958815238	2		538	735	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876536	35876536	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0047433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	139	386	0	ENST00000303115.3:c.1328C>G	p.Ser443Ter	p.S443*	ENST00000303115	NM_002185.3	443	tCa/tGa	8/8	0.484405216174624	3	FACETS	0.973	0.887	1	0.486	0.443	0.532	CLONAL	1	TRUE	1	0.484288958815238	3		386	733	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486049	29486049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	78	194	0	ENST00000356175.3:c.226G>A	p.Glu76Lys	p.E76K	ENST00000356175	NM_000267.3	76	Gaa/Aaa	3/57	0.484405216174624	2	FACETS	0.95	0.842	1	0.475	0.421	0.533	CLONAL	1	TRUE	0	0.484288958815238	2		194	339	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211437	36211437	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	1492	692	0	ENST00000222270.7:c.1188G>C	p.Lys396Asn	p.K396N	ENST00000222270	NM_014727.1	396	aaG/aaC	3/37	0.484288958815238	7	FACETS	0.991	0.973	1			1	CLONAL	6	TRUE	NA	0.484288958815238	7		692	2290	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467039	25467039	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	181	504	0	ENST00000264709.3:c.1836C>G	p.Asn612Lys	p.N612K	ENST00000264709	NM_175629.2	612	aaC/aaG	15/23	0.484405216174624	2	FACETS	1	0.961	1	0.53	0.49	0.571	CLONAL	1	TRUE	0	0.484288958815238	2		504	705	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459493	50459493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	82	173	0	ENST00000331340.3:c.782C>T	p.Ser261Phe	p.S261F	ENST00000331340	NM_006060.4	261	tCt/tTt	7/8	0.465984261382063	1	FACETS	0.891	0.795	0.992	0.891	0.795	0.992	CLONAL	1	TRUE	0	0.484288958815238	1		173	288	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258723	115258723	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	143	197	1	ENST00000369535.4:c.59C>T	p.Thr20Ile	p.T20I	ENST00000369535	NM_002524.4	20	aCa/aTa	2/7	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.51	2		198	506	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205270	46205270	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	160	256	0	ENST00000334344.6:c.356del	p.Lys119SerfsTer96	p.K119Sfs*96	ENST00000334344	NM_152641.2	118	ccA/cc	4/21	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.51	2		256	592	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281739	46281739	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	202	424	0	ENST00000371998.3:c.4187del	p.Asn1396MetfsTer10	p.N1396Mfs*10	ENST00000371998		1396	Aat/at	22/23	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.51	2		424	772	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183792	10183805	+	frameshift_variant	Frame_Shift_Del	DEL	ATGGCTCAACTTCG	ATGGCTCAACTTCG	-	novel	NA	P-0047434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	220	547	0	ENST00000256474.2:c.262_275del	p.Trp88ArgfsTer39	p.W88Rfs*39	ENST00000256474	NM_000551.3	87	gtATGGCTCAACTTCGac/gtac	1/3	0.3	1	FACETS	0.993	0.93	1	0.993	0.93	1	INDETERMINATE	1	TRUE	0	0.51	1		547	647	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247562	53247562	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	148	141	0	ENST00000375401.3:c.247del	p.Leu83Ter	p.L83*	ENST00000375401	NM_004187.3	83	Ctg/tg	3/26	1	1	FACETS	0.751	0.7	0.802	1	0.99	1	SUBCLONAL	2	TRUE	0	0.51	1		141	288	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187791	11187791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	84	449	1	ENST00000361445.4:c.6106C>T	p.Arg2036Cys	p.R2036C	ENST00000361445	NM_004958.3	2036	Cgt/Tgt	44/58	0.121512954512892	4	FACETS	1	0.975	1	0.708	0.627	0.796	INDETERMINATE	1	TRUE	2	0.261505101497661	4		450	572	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	58	470	0				ENST00000310581	NM_198253.2	-/1132			0.121512954512892	4	FACETS	0.788	0.68	0.904	0.788	0.68	0.904	INDETERMINATE	2	TRUE	2	0.261505101497661	4		470	355	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	40	593	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.555	0.461	0.661	0.555	0.461	0.661	SUBCLONAL	1	TRUE	1	0.261505101497661	2		593	551	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259951	16259951	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777364899	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	85	442	0	ENST00000375759.3:c.7216C>T	p.Pro2406Ser	p.P2406S	ENST00000375759	NM_015001.2	2406	Ccc/Tcc	11/15	0.121512954512892	4	FACETS	1	0.974	1	0.688	0.609	0.772	INDETERMINATE	1	TRUE	2	0.261505101497661	4		442	596	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106207	27106207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	37	465	0	ENST00000324856.7:c.5818C>T	p.Pro1940Ser	p.P1940S	ENST00000324856	NM_006015.4	1940	Cca/Tca	20/20	0.121512954512892	4	FACETS	0.636	0.524	0.763	0.318	0.262	0.382	INDETERMINATE	1	TRUE	2	0.261505101497661	4		465	561	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076718	72076718	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	49	375	0	ENST00000357731.5:c.779G>A	p.Gly260Glu	p.G260E	ENST00000357731	NM_173808.2	260	gGa/gAa	5/7	0.121512954512892	4	FACETS	0.965	0.818	1	0.482	0.409	0.564	INDETERMINATE	1	TRUE	2	0.261505101497661	4		375	490	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400902	72400902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1450443698	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	39	244	1	ENST00000357731.5:c.269G>A	p.Arg90Gln	p.R90Q	ENST00000357731	NM_173808.2	90	cGa/cAa	2/7	0.121512954512892	4	FACETS	1	0.874	1	0.531	0.441	0.631	INDETERMINATE	1	TRUE	2	0.261505101497661	4		245	354	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094286	193094286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	33	281	0	ENST00000367435.3:c.176C>T	p.Ser59Phe	p.S59F	ENST00000367435	NM_024529.4	59	tCc/tTc	2/17	1	2	FACETS	0.789	0.644	0.951	0.789	0.644	0.951	CLONAL	1	TRUE	1	0.261505101497661	2		281	320	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608363	43608363	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750958377	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	101	817	1	ENST00000355710.3:c.1711G>A	p.Asp571Asn	p.D571N	ENST00000355710	NM_020975.4	571	Gat/Aat	9/20	1	2	FACETS	0.96	0.857	1	0.96	0.857	1	CLONAL	1	TRUE	1	0.261505101497661	2		818	805	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114799823	114799823	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	81	388	0	ENST00000543371.1:c.490G>A	p.Gly164Arg	p.G164R	ENST00000543371	NM_001198531.1	164	Ggg/Agg	5/14	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.261505101497661	2		388	484	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742814	17742814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	56	733	0	ENST00000250003.3:c.722G>A	p.Gly241Glu	p.G241E	ENST00000250003	NM_002478.4	241	gGg/gAg	3/3	0.261505101497661	1	FACETS	0.601	0.515	0.696	0.601	0.515	0.696	SUBCLONAL	1	TRUE	0	0.261505101497661	1		733	619	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912831	100912831	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	31	238	0	ENST00000325455.5:c.2491C>T	p.Pro831Ser	p.P831S	ENST00000325455	NM_001202474.3	831	Cct/Tct	7/8	1	2	FACETS	0.885	0.718	1	0.885	0.718	1	CLONAL	1	TRUE	1	0.261505101497661	2		238	268	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344839	118344839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139989306	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	24	252	0	ENST00000534358.1:c.2965C>T	p.Leu989Phe	p.L989F	ENST00000534358	NM_005933.3	989	Ctc/Ttc	3/36	1	2	FACETS	0.572	0.448	0.714	0.572	0.448	0.714	SUBCLONAL	1	TRUE	1	0.261505101497661	2		252	321	SUCCESS
CBL	867	MSKCC	GRCh37	11	119168170	119168170	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	60	285	0	ENST00000264033.4:c.2230A>T	p.Ile744Phe	p.I744F	ENST00000264033	NM_005188.3	744	Atc/Ttc	14/16	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.261505101497661	2		285	393	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	459938	459938	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	66	354	0	ENST00000399788.2:c.1157C>T	p.Pro386Leu	p.P386L	ENST00000399788	NM_001042603.1	386	cCc/cTc	10/28	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.261505101497661	2		354	403	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650670	18650671	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	36	258	1	ENST00000266497.5:c.2881_2882delinsAA	p.Gly961Lys	p.G961K	ENST00000266497		961	GGa/AAa	20/31	1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	TRUE	1	0.261505101497661	2		259	269	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243947	46243947	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	56	336	0	ENST00000334344.6:c.2041G>T	p.Val681Phe	p.V681F	ENST00000334344	NM_152641.2	681	Gtt/Ttt	15/21	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.261505101497661	2		336	397	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285690	46285690	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	51	273	0	ENST00000334344.6:c.5050A>T	p.Thr1684Ser	p.T1684S	ENST00000334344	NM_152641.2	1684	Acc/Tcc	17/21	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.261505101497661	2		273	381	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426069	49426069	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	114	637	0	ENST00000301067.7:c.12419C>T	p.Ser4140Phe	p.S4140F	ENST00000301067	NM_003482.3	4140	tCc/tTc	39/54	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.261505101497661	2		637	795	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432441	49432441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	101	657	0	ENST00000301067.7:c.8698C>T	p.Pro2900Ser	p.P2900S	ENST00000301067	NM_003482.3	2900	Cca/Tca	34/54	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.261505101497661	2		657	762	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432459	49432459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	104	615	0	ENST00000301067.7:c.8680C>T	p.Pro2894Ser	p.P2894S	ENST00000301067	NM_003482.3	2894	Ccg/Tcg	34/54	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.261505101497661	2		615	732	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433351	49433351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	92	586	0	ENST00000301067.7:c.8096C>T	p.Thr2699Ile	p.T2699I	ENST00000301067	NM_003482.3	2699	aCc/aTc	32/54	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.261505101497661	2		586	658	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434090	49434090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779629382	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	109	572	0	ENST00000301067.7:c.7463C>T	p.Ser2488Leu	p.S2488L	ENST00000301067	NM_003482.3	2488	tCg/tTg	31/54	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.261505101497661	2		572	709	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443703	49443703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	95	650	0	ENST00000301067.7:c.3668C>T	p.Ser1223Leu	p.S1223L	ENST00000301067	NM_003482.3	1223	tCa/tTa	11/54	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.261505101497661	2		650	699	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445991	49445991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265398099	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	128	847	0	ENST00000301067.7:c.1475C>T	p.Ser492Leu	p.S492L	ENST00000301067	NM_003482.3	492	tCg/tTg	10/54	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.261505101497661	2		847	855	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482577	56482577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762035321	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	89	478	0	ENST00000267101.3:c.1034C>T	p.Ser345Leu	p.S345L	ENST00000267101	NM_001982.3	345	tCg/tTg	9/28	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.261505101497661	2		478	627	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112445	115112445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	34	620	0	ENST00000257566.3:c.1295C>T	p.Ser432Leu	p.S432L	ENST00000257566	NM_016569.3	432	tCg/tTg	7/8	1	2	FACETS	0.404	0.329	0.489	0.404	0.329	0.489	SUBCLONAL	1	TRUE	1	0.261505101497661	2		620	643	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794768	120794768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750439002	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	87	676	0	ENST00000257552.2:c.589C>T	p.Arg197Trp	p.R197W	ENST00000257552	NM_002442.3	197	Cgg/Tgg	9/15	1	2	FACETS	0.805	0.711	0.905	0.805	0.711	0.905	CLONAL	1	TRUE	1	0.261505101497661	2		676	827	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911770	32911770	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	43	370	0	ENST00000380152.3:c.3278C>T	p.Ser1093Phe	p.S1093F	ENST00000380152		1093	tCc/tTc	11/27	0.261505101497661	1	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	0	0.261505101497661	1		370	277	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134288	41134288	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1005190964	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	67	350	0	ENST00000379561.5:c.1340C>T	p.Ser447Leu	p.S447L	ENST00000379561	NM_002015.3	447	tCg/tTg	2/3	0.261505101497661	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.261505101497661	1		350	401	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954199	48954199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	15	178	0	ENST00000267163.4:c.1400G>A	p.Arg467Gln	p.R467Q	ENST00000267163	NM_000321.2	467	cGa/cAa	15/27	0.261505101497661	1	FACETS	0.639	0.47	0.84	0.639	0.47	0.84	SUBCLONAL	1	TRUE	0	0.261505101497661	1		178	156	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047519	49047519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	15	169	0	ENST00000267163.4:c.2513C>T	p.Ser838Leu	p.S838L	ENST00000267163	NM_000321.2	838	tCa/tTa	24/27	0.261505101497661	1	FACETS	0.968	0.717	1	0.968	0.717	1	CLONAL	1	TRUE	0	0.261505101497661	1		169	103	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435364	110435364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	56	483	0	ENST00000375856.3:c.3037C>T	p.Pro1013Ser	p.P1013S	ENST00000375856	NM_003749.2	1013	Ccg/Tcg	1/2	0.261505101497661	1	FACETS	0.928	0.798	1	0.928	0.798	1	CLONAL	1	TRUE	0	0.261505101497661	1		483	401	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353772	68353772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	41	271	0	ENST00000487270.1:c.607G>A	p.Gly203Arg	p.G203R	ENST00000487270	NM_133509.3	203	Gga/Aga	7/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.261505101497661	2		271	220	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560405	95560406	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	26	383	2	ENST00000393063.1:c.5183_5184delinsTT	p.Ser1728Phe	p.S1728F	ENST00000393063	NM_030621.3	1728	tCC/tTT	25/28	1	2	FACETS	0.424	0.335	0.526	0.424	0.335	0.526	SUBCLONAL	1	TRUE	1	0.261505101497661	2		385	469	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988830	41988830	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	56	343	0	ENST00000219905.7:c.1622A>G	p.Gln541Arg	p.Q541R	ENST00000219905	NM_001164273.1	541	cAa/cGa	3/24	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.261505101497661	2		343	379	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477138	67477139	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	97	513	3	ENST00000327367.4:c.945_946delinsTT	p.Gln316Ter	p.Q316*	ENST00000327367	NM_005902.3	315	gtCCag/gtTTag	7/9	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.261505101497661	2		516	626	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996209	73996210	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	81	461	0	ENST00000318443.5:c.943_944delinsTT	p.Pro315Leu	p.P315L	ENST00000318443	NM_001024736.1	315	CCg/TTg	5/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.261505101497661	2		461	473	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434776	99434776	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	73	571	0	ENST00000268035.6:c.863C>T	p.Ala288Val	p.A288V	ENST00000268035	NM_000875.3	288	gCc/gTc	3/21	1	2	FACETS	0.774	0.677	0.88	0.774	0.677	0.88	SUBCLONAL	1	TRUE	1	0.261505101497661	2		571	721	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	397000	397000	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	108	600	0	ENST00000262320.3:c.26C>T	p.Pro9Leu	p.P9L	ENST00000262320	NM_003502.3	9	cCc/cTc	2/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.261505101497661	NA		600	597	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639159	3639159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	50	695	1	ENST00000294008.3:c.4480G>A	p.Gly1494Ser	p.G1494S	ENST00000294008	NM_032444.2	1494	Ggc/Agc	12/15	1	2	FACETS	0.521	0.441	0.609	0.521	0.441	0.609	SUBCLONAL	1	TRUE	1	0.261505101497661	2		696	734	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778284	3778284	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1191357764	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	115	648	0	ENST00000262367.5:c.6764C>T	p.Pro2255Leu	p.P2255L	ENST00000262367	NM_004380.2	2255	cCc/cTc	31/31	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.261505101497661	2		648	705	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858184	9858184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	57	423	0	ENST00000330684.3:c.3217G>A	p.Glu1073Lys	p.E1073K	ENST00000330684	NM_001134407.1	1073	Gaa/Aaa	13/13	1	2	FACETS	0.823	0.706	0.949	0.823	0.706	0.949	CLONAL	1	TRUE	1	0.261505101497661	2		423	530	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858327	9858327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	56	343	1	ENST00000330684.3:c.3074C>T	p.Ser1025Leu	p.S1025L	ENST00000330684	NM_001134407.1	1025	tCa/tTa	13/13	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.261505101497661	2		344	403	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862896	9862896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1198247451	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	42	478	0	ENST00000330684.3:c.2407G>A	p.Glu803Lys	p.E803K	ENST00000330684	NM_001134407.1	803	Gag/Aag	12/13	1	2	FACETS	0.614	0.512	0.727	0.614	0.512	0.727	SUBCLONAL	1	TRUE	1	0.261505101497661	2		478	523	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134469	30134470	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	56	434	1	ENST00000263025.4:c.61_62delinsAA	p.Gly21Asn	p.G21N	ENST00000263025	NM_002746.2	21	GGc/AAc	1/9	1	2	FACETS	0.876	0.751	1	0.876	0.751	1	CLONAL	1	TRUE	1	0.261505101497661	2		435	489	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813768	50813768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	33	531	0	ENST00000398568.2:c.1322C>T	p.Ser441Phe	p.S441F	ENST00000398568	NM_001042412.1	441	tCt/tTt	8/18	0.170307475186121	1	FACETS	0.415	0.337	0.503	0.415	0.337	0.503	SUBCLONAL	1	TRUE	0	0.261505101497661	1		531	529	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132676	67132676	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536749790	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	25	360	0	ENST00000412916.2:c.559C>T	p.Arg187Cys	p.R187C	ENST00000412916		187	Cgt/Tgt	6/6	0.170307475186121	1	FACETS	0.42	0.33	0.523	0.42	0.33	0.523	SUBCLONAL	1	TRUE	0	0.261505101497661	1		360	396	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828675	72828677	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs747990539	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	40	517	0	ENST00000268489.5:c.7904_7906del	p.Gly2635del	p.G2635del	ENST00000268489	NM_006885.3	2635	gGAGaa/gaa	9/10	0.170307475186121	1	FACETS	0.478	0.397	0.569	0.478	0.397	0.569	SUBCLONAL	1	TRUE	0	0.261505101497661	1		517	556	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832062	72832062	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	39	412	1	ENST00000268489.5:c.4519G>A	p.Gly1507Ser	p.G1507S	ENST00000268489	NM_006885.3	1507	Ggc/Agc	9/10	0.170307475186121	1	FACETS	0.561	0.465	0.668	0.561	0.465	0.668	SUBCLONAL	1	TRUE	0	0.261505101497661	1		413	462	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992819	72992819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370750954	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	38	588	0	ENST00000268489.5:c.1226C>T	p.Ser409Leu	p.S409L	ENST00000268489	NM_006885.3	409	tCg/tTg	2/10	0.170307475186121	1	FACETS	0.464	0.382	0.554	0.464	0.382	0.554	SUBCLONAL	1	TRUE	0	0.261505101497661	1		588	545	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993399	72993399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243611387	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	56	681	1	ENST00000268489.5:c.646C>T	p.Pro216Ser	p.P216S	ENST00000268489	NM_006885.3	216	Ccg/Tcg	2/10	0.170307475186121	1	FACETS	0.558	0.477	0.647	0.558	0.477	0.647	SUBCLONAL	1	TRUE	0	0.261505101497661	1		682	667	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81960726	81960727	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	32	428	1	ENST00000359376.3:c.2457_2458delinsTT	p.Pro820Ser	p.P820S	ENST00000359376	NM_002661.3	819	ttCCca/ttTTca	23/33	0.170307475186121	1	FACETS	0.463	0.376	0.563	0.463	0.376	0.563	SUBCLONAL	1	TRUE	0	0.261505101497661	1		429	459	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81979836	81979836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	48	411	0	ENST00000359376.3:c.3538C>T	p.Leu1180Phe	p.L1180F	ENST00000359376	NM_002661.3	1180	Ctc/Ttc	31/33	0.170307475186121	1	FACETS	0.7	0.592	0.818	0.7	0.592	0.818	SUBCLONAL	1	TRUE	0	0.261505101497661	1		411	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	88	523	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.261505101497661	2		523	557	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119808	17119808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	75	578	0	ENST00000285071.4:c.1186C>T	p.Pro396Ser	p.P396S	ENST00000285071	NM_144997.5	396	Ccc/Tcc	11/14	1	2	FACETS	0.969	0.85	1	0.969	0.85	1	CLONAL	1	TRUE	1	0.261505101497661	2		578	592	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685536	29685536	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	26	274	0	ENST00000356175.3:c.7946C>T	p.Ser2649Leu	p.S2649L	ENST00000356175	NM_000267.3	2649	tCa/tTa	54/57	1	2	FACETS	0.67	0.531	0.827	0.67	0.531	0.827	SUBCLONAL	1	TRUE	1	0.261505101497661	2		274	297	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508280	38508281	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	90	487	0	ENST00000254066.5:c.588_589delinsAA	p.Glu197Lys	p.E197K	ENST00000254066	NM_000964.3	196	caGGaa/caAAaa	5/9	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.261505101497661	2		487	645	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508617	38508617	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	39	529	0	ENST00000254066.5:c.665T>A	p.Ile222Asn	p.I222N	ENST00000254066	NM_000964.3	222	aTt/aAt	6/9	1	2	FACETS	0.499	0.412	0.595	0.499	0.412	0.595	SUBCLONAL	1	TRUE	1	0.261505101497661	2		529	598	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40483533	40483533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1456534236	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	31	250	0	ENST00000264657.5:c.1066C>T	p.Pro356Ser	p.P356S	ENST00000264657	NM_139276.2	356	Cct/Tct	11/24	1	2	FACETS	1	0.821	1	1	0.821	1	CLONAL	1	TRUE	1	0.261505101497661	2		250	235	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858062	40858062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	84	538	0	ENST00000428826.2:c.1802C>T	p.Ser601Phe	p.S601F	ENST00000428826		601	tCc/tTc	16/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.261505101497661	2		538	579	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870606	40870606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	76	478	0	ENST00000428826.2:c.797C>T	p.Pro266Leu	p.P266L	ENST00000428826		266	cCc/cTc	9/21	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.261505101497661	2		478	518	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734180	58734180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	45	370	0	ENST00000305921.3:c.1238C>T	p.Pro413Leu	p.P413L	ENST00000305921	NM_003620.3	413	cCa/cTa	5/6	1	2	FACETS	0.812	0.683	0.953	0.812	0.683	0.953	CLONAL	1	TRUE	1	0.261505101497661	2		370	424	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222481	2222481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	47	671	0	ENST00000398665.3:c.3313C>T	p.Pro1105Ser	p.P1105S	ENST00000398665	NM_032482.2	1105	Ccc/Tcc	24/28	1	2	FACETS	0.478	0.402	0.562	0.478	0.402	0.562	SUBCLONAL	1	TRUE	1	0.261505101497661	2		671	752	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218470	5218471	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	77	541	0	ENST00000357368.4:c.4008_4009delinsAA	p.Asp1337Asn	p.D1337N	ENST00000357368	NM_002850.3	1336	aaGGac/aaAAac	25/38	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.261505101497661	2		541	583	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170656	7170656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	64	570	1	ENST00000302850.5:c.1375C>T	p.Pro459Ser	p.P459S	ENST00000302850	NM_000208.2	459	Ccc/Tcc	6/22	1	2	FACETS	0.821	0.711	0.941	0.821	0.711	0.941	CLONAL	1	TRUE	1	0.261505101497661	2		571	596	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376283	15376284	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	91	697	1	ENST00000263377.2:c.730_731delinsTT	p.Pro244Phe	p.P244F	ENST00000263377	NM_058243.2	244	CCc/TTc	5/20	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.261505101497661	2		698	659	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953133	17953133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568406966	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	48	636	1	ENST00000458235.1:c.853G>A	p.Glu285Lys	p.E285K	ENST00000458235	NM_000215.3	285	Gaa/Aaa	6/24	1	2	FACETS	0.615	0.519	0.721	0.615	0.519	0.721	SUBCLONAL	1	TRUE	1	0.261505101497661	2		637	597	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383120	42383120	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1390442945	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	30	513	0	ENST00000221972.3:c.140G>A	p.Gly47Glu	p.G47E	ENST00000221972	NM_021601.3	47	gGg/gAg	2/5	1	2	FACETS	0.457	0.367	0.559	0.457	0.367	0.559	SUBCLONAL	1	TRUE	1	0.261505101497661	2		513	502	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867714	45867714	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763125782	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	165	747	1	ENST00000391945.4:c.686C>T	p.Ala229Val	p.A229V	ENST00000391945	NM_000400.3	229	gCc/gTc	8/23	1	2	FACETS	0.837	0.77	0.906	1	0.991	1	CLONAL	2	TRUE	1	0.261505101497661	2		748	754	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715975	52715976	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	37	547	0	ENST00000322088.6:c.540_541delinsAA	p.Met180_Val181delinsIleMet	p.M180_V181delinsIM	ENST00000322088	NM_014225.5	180	atGGtg/atAAtg	5/15	1	2	FACETS	0.449	0.369	0.539	0.449	0.369	0.539	SUBCLONAL	1	TRUE	1	0.261505101497661	2		547	630	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919835	96919836	+	missense_variant	Missense_Mutation	DNP	AC	AC	CT	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	76	326	0	ENST00000258439.3:c.427_428delinsAG	p.Val143Ser	p.V143S	ENST00000258439	NM_001193304.2	143	GTc/AGc	4/4	0.261505101497661	3	FACETS	0.796	0.701	0.896	0.796	0.701	0.896	SUBCLONAL	2	TRUE	1	0.261505101497661	3		326	413	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169254	99169254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	59	330	0	ENST00000074304.5:c.1184C>T	p.Ser395Leu	p.S395L	ENST00000074304	NM_001134224.1	395	tCa/tTa	15/26	0.261505101497661	3	FACETS	1	0.952	1	0.619	0.534	0.711	CLONAL	1	TRUE	1	0.261505101497661	3		330	412	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872585	136872585	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	21	261	0	ENST00000241393.3:c.913C>T	p.Leu305Phe	p.L305F	ENST00000241393	NM_003467.2	305	Ctt/Ttt	2/2	1	2	FACETS	0.395	0.303	0.502	0.395	0.303	0.502	SUBCLONAL	1	TRUE	1	0.261505101497661	2		261	407	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732541	190732541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	25	229	0	ENST00000441310.2:c.2359C>T	p.His787Tyr	p.H787Y	ENST00000441310	NM_000534.4	787	Cat/Tat	11/13	1	2	FACETS	0.981	0.778	1	0.981	0.778	1	CLONAL	1	TRUE	1	0.261505101497661	2		229	195	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131271	202131271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	55	329	0	ENST00000358485.4:c.239C>T	p.Ser80Phe	p.S80F	ENST00000358485	NM_001080125.1	80	tCc/tTc	2/9	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.261505101497661	2		329	389	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286748	212286748	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	15	211	0	ENST00000342788.4:c.2948G>A	p.Arg983Lys	p.R983K	ENST00000342788	NM_005235.2	983	aGa/aAa	24/28	1	2	FACETS	0.443	0.324	0.586	0.443	0.324	0.586	SUBCLONAL	1	TRUE	1	0.261505101497661	2		211	259	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288946	212288946	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	57	305	0	ENST00000342788.4:c.2800G>T	p.Glu934Ter	p.E934*	ENST00000342788	NM_005235.2	934	Gag/Tag	23/28	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.261505101497661	2		305	321	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293165	212293165	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	39	253	0	ENST00000342788.4:c.2687A>T	p.Lys896Ile	p.K896I	ENST00000342788	NM_005235.2	896	aAa/aTa	22/28	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.261505101497661	2		253	220	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215674247	215674247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1326565823	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	93	662	0	ENST00000260947.4:c.47C>T	p.Ser16Phe	p.S16F	ENST00000260947	NM_000465.2	16	tCc/tTc	1/11	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.261505101497661	2		662	655	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523329	9523329	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867092977	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	76	378	0	ENST00000353224.5:c.1908G>A	p.Met636Ile	p.M636I	ENST00000353224	NM_177990.2	636	atG/atA	9/10	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.261505101497661	2		378	504	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40738997	40738997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	89	441	1	ENST00000373198.4:c.3287C>T	p.Ala1096Val	p.A1096V	ENST00000373198	NM_133170.3	1096	gCt/gTt	24/32	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.261505101497661	2		442	497	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845289	42845289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	64	663	0	ENST00000398585.3:c.973C>T	p.Pro325Ser	p.P325S	ENST00000398585	NM_001135099.1	325	Ccc/Tcc	9/14	1	2	FACETS	0.77	0.666	0.882	0.77	0.666	0.882	SUBCLONAL	1	TRUE	1	0.261505101497661	2		663	636	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272245	21272245	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	43	367	0	ENST00000354336.3:c.23C>T	p.Ser8Phe	p.S8F	ENST00000354336	NM_005207.3	8	tCc/tTc	1/3	1	2	FACETS	0.688	0.576	0.812	0.688	0.576	0.812	SUBCLONAL	1	TRUE	1	0.261505101497661	2		367	478	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574737	41574737	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	56	685	0	ENST00000263253.7:c.7022C>T	p.Ser2341Phe	p.S2341F	ENST00000263253	NM_001429.3	2341	tCc/tTc	31/31	1	2	FACETS	0.584	0.5	0.677	0.584	0.5	0.677	SUBCLONAL	1	TRUE	1	0.261505101497661	2		685	733	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183592	10183592	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	53	753	2	ENST00000256474.2:c.61G>A	p.Glu21Lys	p.E21K	ENST00000256474	NM_000551.3	21	Gaa/Aaa	1/3	1	2	FACETS	0.586	0.499	0.682	0.586	0.499	0.682	SUBCLONAL	1	TRUE	1	0.261505101497661	2		755	692	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37059018	37059018	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	50	283	0	ENST00000231790.2:c.812C>T	p.Ser271Phe	p.S271F	ENST00000231790	NM_000249.3	271	tCc/tTc	10/19	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.261505101497661	2		283	325	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651444	52651444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	75	402	0	ENST00000394830.3:c.1652C>T	p.Ser551Phe	p.S551F	ENST00000394830	NM_018313.4	551	tCc/tTc	15/30	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.261505101497661	2		402	408	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651505	52651505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	31	361	0	ENST00000394830.3:c.1591C>T	p.Leu531Phe	p.L531F	ENST00000394830	NM_018313.4	531	Ctt/Ttt	15/30	1	2	FACETS	0.627	0.507	0.763	0.627	0.507	0.763	SUBCLONAL	1	TRUE	1	0.261505101497661	2		361	378	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427700	72427701	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	54	307	0	ENST00000477973.2:c.787_788delinsAA	p.Glu264Lys	p.E264K	ENST00000477973	NM_012234.5	263	aaGGaa/aaAAaa	4/4	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.261505101497661	2		307	338	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468364	89468364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	12	136	0	ENST00000336596.2:c.1898G>A	p.Gly633Glu	p.G633E	ENST00000336596	NM_005233.5	633	gGa/gAa	11/17	1	2	FACETS	0.534	0.376	0.727	0.534	0.376	0.727	SUBCLONAL	1	TRUE	1	0.261505101497661	2		136	172	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468393	89468393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	15	173	0	ENST00000336596.2:c.1927C>T	p.Pro643Ser	p.P643S	ENST00000336596	NM_005233.5	643	Cct/Tct	11/17	1	2	FACETS	0.574	0.42	0.757	0.574	0.42	0.757	SUBCLONAL	1	TRUE	1	0.261505101497661	2		173	200	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498489	89498489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758657242	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	16	214	0	ENST00000336596.2:c.2461G>A	p.Gly821Arg	p.G821R	ENST00000336596	NM_005233.5	821	Gga/Aga	14/17	1	2	FACETS	0.462	0.341	0.606	0.462	0.341	0.606	SUBCLONAL	1	TRUE	1	0.261505101497661	2		214	265	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204921	128204921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1487820188	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	55	620	1	ENST00000341105.2:c.520C>T	p.Pro174Ser	p.P174S	ENST00000341105	NM_032638.4	174	Cca/Tca	3/6	1	2	FACETS	0.613	0.524	0.711	0.613	0.524	0.711	SUBCLONAL	1	TRUE	1	0.261505101497661	2		621	686	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825400	134825401	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	51	468	1	ENST00000398015.3:c.916_917delinsAA	p.Gly306Asn	p.G306N	ENST00000398015	NM_004441.4	306	GGt/AAt	4/16	1	2	FACETS	0.747	0.635	0.87	0.747	0.635	0.87	SUBCLONAL	1	TRUE	1	0.261505101497661	2		469	522	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851627	134851627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	68	444	0	ENST00000398015.3:c.1033C>T	p.Pro345Ser	p.P345S	ENST00000398015	NM_004441.4	345	Cca/Tca	5/16	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.261505101497661	2		444	482	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898705	134898705	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	16	217	0	ENST00000398015.3:c.1763C>A	p.Ser588Tyr	p.S588Y	ENST00000398015	NM_004441.4	588	tCc/tAc	10/16	1	2	FACETS	0.445	0.329	0.584	0.445	0.329	0.584	SUBCLONAL	1	TRUE	1	0.261505101497661	2		217	275	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960013	134960013	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	53	364	0	ENST00000398015.3:c.2370G>A	p.Trp790Ter	p.W790*	ENST00000398015	NM_004441.4	790	tgG/tgA	13/16	1	2	FACETS	0.829	0.708	0.962	0.829	0.708	0.962	CLONAL	1	TRUE	1	0.261505101497661	2		364	489	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683508	182683508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	29	356	0	ENST00000292782.4:c.37C>T	p.Arg13Cys	p.R13C	ENST00000292782	NM_020640.2	13	Cgt/Tgt	2/7	1	2	FACETS	0.948	0.765	1	0.948	0.765	1	CLONAL	1	TRUE	1	0.261505101497661	2		356	234	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957917	1957917	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	28	321	0	ENST00000382891.5:c.2881+2T>C		p.X961_splice	ENST00000382891	NM_133335.3	961			1	2	FACETS	0.671	0.537	0.824	0.671	0.537	0.824	SUBCLONAL	1	TRUE	1	0.261505101497661	2		321	319	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141065	55141065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	56	291	0	ENST00000257290.5:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000257290	NM_006206.4	571	Gaa/Aaa	12/23	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.261505101497661	2		291	405	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561704	55561704	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	34	222	0	ENST00000288135.5:c.94G>A	p.Gly32Arg	p.G32R	ENST00000288135	NM_000222.2	32	Ggg/Agg	2/21	1	2	FACETS	0.894	0.733	1	0.894	0.733	1	CLONAL	1	TRUE	1	0.261505101497661	2		222	291	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604629	55604629	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779103998	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	39	432	0	ENST00000288135.5:c.2837G>A	p.Arg946Gln	p.R946Q	ENST00000288135	NM_000222.2	946	cGa/cAa	21/21	1	2	FACETS	0.552	0.457	0.659	0.552	0.457	0.659	SUBCLONAL	1	TRUE	1	0.261505101497661	2		432	540	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984810	55984810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	66	398	0	ENST00000263923.4:c.319G>A	p.Glu107Lys	p.E107K	ENST00000263923	NM_002253.2	107	Gaa/Aaa	3/30	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.261505101497661	2		398	438	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213909	66213909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	33	208	0	ENST00000273854.3:c.2521C>T	p.Pro841Ser	p.P841S	ENST00000273854	NM_004439.5	841	Cca/Tca	15/18	1	2	FACETS	0.918	0.751	1	0.918	0.751	1	CLONAL	1	TRUE	1	0.261505101497661	2		208	275	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213917	66213917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	15	199	0	ENST00000273854.3:c.2513G>A	p.Gly838Glu	p.G838E	ENST00000273854	NM_004439.5	838	gGa/gAa	15/18	1	2	FACETS	0.461	0.337	0.61	0.461	0.337	0.61	SUBCLONAL	1	TRUE	1	0.261505101497661	2		199	249	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356139	66356139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	27	337	0	ENST00000273854.3:c.1358G>A	p.Gly453Glu	p.G453E	ENST00000273854	NM_004439.5	453	gGa/gAa	5/18	1	2	FACETS	0.462	0.367	0.571	0.462	0.367	0.571	SUBCLONAL	1	TRUE	1	0.261505101497661	2		337	447	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356216	66356216	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	66	383	0	ENST00000273854.3:c.1281G>A	p.Met427Ile	p.M427I	ENST00000273854	NM_004439.5	427	atG/atA	5/18	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.261505101497661	2		383	504	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467388	66467388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	34	163	0	ENST00000273854.3:c.881G>A	p.Gly294Glu	p.G294E	ENST00000273854	NM_004439.5	294	gGa/gAa	3/18	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.261505101497661	2		163	235	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467924	66467925	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	17	217	0	ENST00000273854.3:c.344_345delinsTT	p.Thr115Ile	p.T115I	ENST00000273854	NM_004439.5	115	aCC/aTT	3/18	1	2	FACETS	0.435	0.324	0.566	0.435	0.324	0.566	SUBCLONAL	1	TRUE	1	0.261505101497661	2		217	299	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268213	153268213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	28	201	0	ENST00000281708.4:c.595C>T	p.Leu199Phe	p.L199F	ENST00000281708	NM_033632.3	199	Ctt/Ttt	4/12	1	2	FACETS	0.943	0.758	1	0.943	0.758	1	CLONAL	1	TRUE	1	0.261505101497661	2		201	227	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525670	187525670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	35	336	0	ENST00000441802.2:c.10409C>T	p.Ser3470Phe	p.S3470F	ENST00000441802	NM_005245.3	3470	tCc/tTc	18/27	1	2	FACETS	0.683	0.56	0.82	0.683	0.56	0.82	SUBCLONAL	1	TRUE	1	0.261505101497661	2		336	392	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538346	187538346	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	21	242	0	ENST00000441802.2:c.8888C>T	p.Pro2963Leu	p.P2963L	ENST00000441802	NM_005245.3	2963	cCt/cTt	11/27	1	2	FACETS	0.678	0.523	0.857	0.678	0.523	0.857	SUBCLONAL	1	TRUE	1	0.261505101497661	2		242	237	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540799	187540799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	45	280	0	ENST00000441802.2:c.6941C>T	p.Pro2314Leu	p.P2314L	ENST00000441802	NM_005245.3	2314	cCa/cTa	10/27	1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	1	0.261505101497661	2		280	343	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271312	1271312	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	93	598	0	ENST00000310581.5:c.2390C>T	p.Ser797Phe	p.S797F	ENST00000310581	NM_198253.2	797	tCc/tTc	8/16	0.121512954512892	4	FACETS	1	0.978	1	0.711	0.633	0.794	INDETERMINATE	1	TRUE	2	0.261505101497661	4		598	631	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873648	35873648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867618621	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	44	223	0	ENST00000303115.3:c.604G>A	p.Glu202Lys	p.E202K	ENST00000303115	NM_002185.3	202	Gag/Aag	5/8	0.121512954512892	4	FACETS	1	0.953	1	0.694	0.584	0.813	INDETERMINATE	1	TRUE	2	0.261505101497661	4		223	306	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178253	56178253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	45	202	0	ENST00000399503.3:c.3226C>T	p.Pro1076Ser	p.P1076S	ENST00000399503	NM_005921.1	1076	Ccc/Tcc	14/20	0.121512954512892	4	FACETS	1	0.949	1	0.666	0.562	0.78	INDETERMINATE	1	TRUE	2	0.261505101497661	4		202	326	SUCCESS
APC	324	MSKCC	GRCh37	5	112154675	112154675	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	35	314	0	ENST00000257430.4:c.946T>G	p.Tyr316Asp	p.Y316D	ENST00000257430	NM_000038.5	316	Tat/Gat	10/16	0.121512954512892	4	FACETS	0.889	0.729	1	0.444	0.364	0.534	INDETERMINATE	1	TRUE	2	0.261505101497661	4		314	380	SUCCESS
APC	324	MSKCC	GRCh37	5	112173824	112173824	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554084249	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	37	231	0	ENST00000257430.4:c.2533C>T	p.Arg845Cys	p.R845C	ENST00000257430	NM_000038.5	845	Cgt/Tgt	16/16	0.121512954512892	4	FACETS	1	0.91	1	0.581	0.481	0.693	INDETERMINATE	1	TRUE	2	0.261505101497661	4		231	307	SUCCESS
APC	324	MSKCC	GRCh37	5	112177205	112177205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1222940653	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	28	198	0	ENST00000257430.4:c.5914C>T	p.Leu1972Phe	p.L1972F	ENST00000257430	NM_000038.5	1972	Ctc/Ttc	16/16	0.121512954512892	4	FACETS	0.955	0.765	1	0.477	0.382	0.585	INDETERMINATE	1	TRUE	2	0.261505101497661	4		198	283	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460546	149460546	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	102	629	0	ENST00000286301.3:c.91G>A	p.Val31Ile	p.V31I	ENST00000286301	NM_005211.3	31	Gtc/Atc	3/22	0.121512954512892	4	FACETS	1	0.978	1	0.691	0.618	0.768	INDETERMINATE	1	TRUE	2	0.261505101497661	4		629	712	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394996	394996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	92	322	0	ENST00000380956.4:c.392G>A	p.Gly131Glu	p.G131E	ENST00000380956	NM_001195286.1	131	gGa/gAa	3/9	0.261505101497661	3	FACETS	0.915	0.817	1	0.915	0.817	1	CLONAL	2	TRUE	1	0.261505101497661	3		322	435	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271398	26271398	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	129	513	0	ENST00000305910.3:c.215T>A	p.Val72Glu	p.V72E	ENST00000305910	NM_003534.2	72	gTg/gAg	1/1	0.261505101497661	3	FACETS	0.954	0.868	1	0.954	0.868	1	CLONAL	2	TRUE	1	0.261505101497661	3		513	585	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911275	29911275	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199474569	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	32	535	0	ENST00000376809.5:c.574C>T	p.Leu192Phe	p.L192F	ENST00000376809	NM_002116.7	192	Ctc/Ttc	3/8	0.261505101497661	3	FACETS	0.471	0.381	0.572	0.235	0.19	0.286	SUBCLONAL	1	TRUE	1	0.261505101497661	3		535	588	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163671	32163671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	154	525	1	ENST00000375023.3:c.5555C>T	p.Pro1852Leu	p.P1852L	ENST00000375023	NM_004557.3	1852	cCg/cTg	30/30	NA	2	FACETS	0.832	0.763	0.903			1	INDETERMINATE	2	TRUE	NA	0.261505101497661	2		526	708	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908197	41908197	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	46	645	0	ENST00000372991.4:c.325C>G	p.Leu109Val	p.L109V	ENST00000372991	NM_001760.3	109	Ctg/Gtg	2/5	0.261505101497661	3	FACETS	0.514	0.431	0.606	0.257	0.215	0.303	SUBCLONAL	1	TRUE	1	0.261505101497661	3		645	774	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120689	94120689	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	25	309	0	ENST00000369303.4:c.362A>G	p.Glu121Gly	p.E121G	ENST00000369303	NM_004440.3	121	gAa/gGa	3/17	0.261505101497661	3	FACETS	0.527	0.415	0.657	0.264	0.207	0.329	SUBCLONAL	1	TRUE	1	0.261505101497661	3		309	410	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710617	117710617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769974183	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	68	228	0	ENST00000368508.3:c.1655C>T	p.Ser552Phe	p.S552F	ENST00000368508	NM_002944.2	552	tCc/tTc	12/43	0.219467485990582	2	FACETS	0.783	0.686	0.887	0.783	0.686	0.887	SUBCLONAL	2	TRUE	0	0.261505101497661	2		228	332	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163790	152163790	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	31	363	0	ENST00000206249.3:c.511A>C	p.Lys171Gln	p.K171Q	ENST00000206249	NM_000125.3	171	Aag/Cag	2/8	0.219467485990582	2	FACETS	0.519	0.419	0.632	0.259	0.209	0.316	SUBCLONAL	1	TRUE	0	0.261505101497661	2		363	457	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358993	81358993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	70	358	0	ENST00000222390.5:c.968G>A	p.Gly323Glu	p.G323E	ENST00000222390	NM_000601.4	323	gGa/gAa	8/18	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.261505101497661	2		358	432	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381514	81381514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	48	227	0	ENST00000222390.5:c.547G>A	p.Glu183Lys	p.E183K	ENST00000222390	NM_000601.4	183	Gaa/Aaa	5/18	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.261505101497661	2		227	346	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873758	151873758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	44	366	0	ENST00000262189.6:c.8780C>T	p.Ser2927Phe	p.S2927F	ENST00000262189	NM_170606.2	2927	tCt/tTt	38/59	1	2	FACETS	0.705	0.592	0.831	0.705	0.592	0.831	SUBCLONAL	1	TRUE	1	0.261505101497661	2		366	477	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370865	55370865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	88	592	0	ENST00000297316.4:c.167C>T	p.Ala56Val	p.A56V	ENST00000297316	NM_022454.3	56	gCc/gTc	1/2	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.261505101497661	2		592	614	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372029	55372029	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1332803887	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	52	551	0	ENST00000297316.4:c.719C>T	p.Pro240Leu	p.P240L	ENST00000297316	NM_022454.3	240	cCg/cTg	2/2	1	2	FACETS	0.823	0.702	0.957	0.823	0.702	0.957	CLONAL	1	TRUE	1	0.261505101497661	2		551	483	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995620	68995620	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761696818	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	20	352	0	ENST00000288368.4:c.2024G>A	p.Arg675Lys	p.R675K	ENST00000288368	NM_024870.2	675	aGa/aAa	18/40	1	2	FACETS	0.522	0.399	0.666	0.522	0.399	0.666	SUBCLONAL	1	TRUE	1	0.261505101497661	2		352	293	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69011995	69011995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	36	423	0	ENST00000288368.4:c.2632C>T	p.Pro878Ser	p.P878S	ENST00000288368	NM_024870.2	878	Cct/Tct	23/40	1	2	FACETS	0.715	0.588	0.857	0.715	0.588	0.857	SUBCLONAL	1	TRUE	1	0.261505101497661	2		423	385	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69012043	69012043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	36	393	0	ENST00000288368.4:c.2680G>A	p.Glu894Lys	p.E894K	ENST00000288368	NM_024870.2	894	Gaa/Aaa	23/40	1	2	FACETS	0.791	0.652	0.947	0.791	0.652	0.947	CLONAL	1	TRUE	1	0.261505101497661	2		393	348	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69027992	69027992	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	27	222	0	ENST00000288368.4:c.3151C>A	p.Leu1051Met	p.L1051M	ENST00000288368	NM_024870.2	1051	Ctg/Atg	26/40	1	2	FACETS	0.979	0.784	1	0.979	0.784	1	CLONAL	1	TRUE	1	0.261505101497661	2		222	211	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033209	69033209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	54	375	0	ENST00000288368.4:c.3649C>T	p.His1217Tyr	p.H1217Y	ENST00000288368	NM_024870.2	1217	Cat/Tat	30/40	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.261505101497661	2		375	406	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129904	69129904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	45	282	0	ENST00000288368.4:c.4658G>A	p.Gly1553Glu	p.G1553E	ENST00000288368	NM_024870.2	1553	gGa/gAa	38/40	1	2	FACETS	0.92	0.775	1	0.92	0.775	1	CLONAL	1	TRUE	1	0.261505101497661	2		282	374	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868510	117868510	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	81	335	1	ENST00000297338.2:c.832C>T	p.Pro278Ser	p.P278S	ENST00000297338	NM_006265.2	278	Cct/Tct	8/14	1	2	FACETS	0.78	0.691	0.874	1	0.979	1	SUBCLONAL	2	TRUE	1	0.261505101497661	2		336	397	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5456116	5456116	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs111401207	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	20	156	0	ENST00000381577.3:c.3G>A	p.Met1?	p.M1?	ENST00000381577	NM_014143.3	1	atG/atA	2/7	1	2	FACETS	0.987	0.761	1	0.987	0.761	1	CLONAL	1	TRUE	1	0.261505101497661	2		156	155	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319917	8319917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	34	184	0	ENST00000356435.5:c.5584G>A	p.Glu1862Lys	p.E1862K	ENST00000356435		1862	Gaa/Aaa	34/35	1	2	FACETS	0.935	0.768	1	0.935	0.768	1	CLONAL	1	TRUE	1	0.261505101497661	2		184	278	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331603	8331603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	60	432	0	ENST00000356435.5:c.5513G>A	p.Gly1838Glu	p.G1838E	ENST00000356435		1838	gGa/gAa	33/35	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.261505101497661	2		432	456	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341713	8341713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866358279	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	57	352	0	ENST00000356435.5:c.4927G>A	p.Gly1643Arg	p.G1643R	ENST00000356435		1643	Gga/Aga	29/35	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.261505101497661	2		352	424	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465522	8465522	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	56	373	0	ENST00000356435.5:c.3658C>T	p.Gln1220Ter	p.Q1220*	ENST00000356435		1220	Caa/Taa	21/35	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.261505101497661	2		373	387	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465621	8465621	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	60	282	0	ENST00000356435.5:c.3559G>A	p.Glu1187Lys	p.E1187K	ENST00000356435		1187	Gaa/Aaa	21/35	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.261505101497661	2		282	368	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471012	8471012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	40	266	0	ENST00000356435.5:c.3487G>A	p.Glu1163Lys	p.E1163K	ENST00000356435		1163	Gaa/Aaa	20/35	1	2	FACETS	0.981	0.818	1	0.981	0.818	1	CLONAL	1	TRUE	1	0.261505101497661	2		266	312	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484167	8484167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	36	355	0	ENST00000356435.5:c.3365G>A	p.Gly1122Asp	p.G1122D	ENST00000356435		1122	gGc/gAc	19/35	1	2	FACETS	0.685	0.563	0.821	0.685	0.563	0.821	SUBCLONAL	1	TRUE	1	0.261505101497661	2		355	402	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486082	8486082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	54	440	0	ENST00000356435.5:c.2735C>T	p.Ser912Phe	p.S912F	ENST00000356435		912	tCc/tTc	17/35	1	2	FACETS	0.855	0.731	0.99	0.855	0.731	0.99	CLONAL	1	TRUE	1	0.261505101497661	2		440	483	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486347	8486347	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	15	184	0	ENST00000356435.5:c.2470C>T	p.Pro824Ser	p.P824S	ENST00000356435		824	Cca/Tca	17/35	1	2	FACETS	0.425	0.31	0.563	0.425	0.31	0.563	SUBCLONAL	1	TRUE	1	0.261505101497661	2		184	270	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8497265	8497265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1270795879	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	28	139	0	ENST00000356435.5:c.2326G>A	p.Glu776Lys	p.E776K	ENST00000356435		776	Gaa/Aaa	15/35	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.261505101497661	2		139	147	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499838	8499838	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	53	296	0	ENST00000356435.5:c.2131C>T	p.Pro711Ser	p.P711S	ENST00000356435		711	Cct/Tct	14/35	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.261505101497661	2		296	367	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8501048	8501048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	53	210	0	ENST00000356435.5:c.1834C>T	p.Pro612Ser	p.P612S	ENST00000356435		612	Cct/Tct	13/35	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.261505101497661	2		210	309	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517990	8517990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	51	309	0	ENST00000356435.5:c.1401G>A	p.Met467Ile	p.M467I	ENST00000356435		467	atG/atA	10/35	1	2	FACETS	0.98	0.835	1	0.98	0.835	1	CLONAL	1	TRUE	1	0.261505101497661	2		309	398	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218658	98218658	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	82	313	0	ENST00000331920.6:c.3206G>A	p.Gly1069Asp	p.G1069D	ENST00000331920	NM_000264.3	1069	gGc/gAc	19/24	0.219467485990582	2	FACETS	0.866	0.769	0.968	0.866	0.769	0.968	CLONAL	2	TRUE	0	0.261505101497661	2		313	362	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412261	139412261	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	162	733	1	ENST00000277541.6:c.1384C>T	p.Gln462Ter	p.Q462*	ENST00000277541	NM_017617.3	462	Cag/Tag	8/34	0.219467485990582	2	FACETS	0.856	0.787	0.927	0.856	0.787	0.927	CLONAL	2	TRUE	0	0.261505101497661	2		734	724	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929355	44929355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	42	283	0	ENST00000377967.4:c.2455C>T	p.Pro819Ser	p.P819S	ENST00000377967	NM_021140.2	819	Cca/Tca	17/29	0.18171731811993	0	FACETS	0.847	0.711	0.996			1	CLONAL	1	TRUE	NA	0.261505101497661	0		283	280	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649520	48649520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	63	300	0	ENST00000376670.3:c.4G>A	p.Glu2Lys	p.E2K	ENST00000376670	NM_002049.3	2	Gag/Aag	2/6	0.18171731811993	0	FACETS	1	0.923	1			1	CLONAL	1	TRUE	NA	0.261505101497661	0		300	328	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939069	76939069	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	37	166	0	ENST00000373344.5:c.1679C>T	p.Ser560Phe	p.S560F	ENST00000373344	NM_000489.3	560	tCt/tTt	9/35	0.179086462163414	0	FACETS	1	0.913	1			1	CLONAL	1	TRUE	NA	0.261505101497661	0		166	181	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627664	37627664	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	84	541	0	ENST00000447079.4:c.1580del	p.Pro527HisfsTer83	p.P527Hfs*83	ENST00000447079	NM_015083.1	527	Cca/ca	2/14	1	2	FACETS	0.758	0.674	0.847	1	0.979	1	SUBCLONAL	2	FALSE	1	0.285604089733106	2		541	388	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139938	50139938	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	205	773	0	ENST00000246792.3:c.391G>T	p.Asp131Tyr	p.D131Y	ENST00000246792	NM_006270.3	131	Gac/Tac	4/6	1	2	FACETS	0.998	0.929	1	1	0.994	1	CLONAL	2	FALSE	1	0.285604089733106	2		773	719	SUCCESS
APC	324	MSKCC	GRCh37	5	112177280	112177280	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	16	274	0	ENST00000257430.4:c.5989G>T	p.Gly1997Ter	p.G1997*	ENST00000257430	NM_000038.5	1997	Gga/Tga	16/16	0.285604089733106	3	FACETS	1	0.79	1	0.534	0.398	0.691	CLONAL	1	FALSE	1	0.285604089733106	3		274	120	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	74	516	0				ENST00000310581	NM_198253.2	-/1132			0.252552557501673	3	FACETS	0.77	0.679	0.867	0.77	0.679	0.867	SUBCLONAL	2	TRUE	1	0.31	3		516	358	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0047438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	67	655	1	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	0.249640203061932	3	FACETS	0.678	0.589	0.776	0.339	0.294	0.388	SUBCLONAL	1	TRUE	1	0.31	3		656	736	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963988	2963988	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755527825	NA	P-0047438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	131	627	0	ENST00000396946.4:c.1819G>A	p.Glu607Lys	p.E607K	ENST00000396946	NM_032415.4	607	Gaa/Aaa	15/25	0.232521810446713	2	FACETS	1	0.984	1	0.703	0.64	0.769	CLONAL	1	TRUE	0	0.31	2		627	601	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101309	27101309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772281669	NA	P-0047438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	68	802	0	ENST00000324856.7:c.4591G>A	p.Glu1531Lys	p.E1531K	ENST00000324856	NM_006015.4	1531	Gaa/Aaa	18/20	0.3	3	FACETS	0.611	0.531	0.699			1	SUBCLONAL	1	TRUE	NA	0.31	3		802	829	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983129	201983129	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	140	559	2	ENST00000359651.3:c.978C>A	p.Tyr326Ter	p.Y326*	ENST00000359651		326	taC/taA	7/8	1	2	FACETS	0.884	0.81	0.96	1	0.99	1	CLONAL	2	TRUE	1	0.31	2		561	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577527	+	frameshift_variant	Frame_Shift_Del	DEL	AGTGTGATGATGGTGAG	AGTGTGATGATGGTGAG	-	novel	NA	P-0047438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	76	620	0	ENST00000269305.4:c.754_770del	p.Leu252GlyfsTer6	p.L252Gfs*6	ENST00000269305	NM_001126112.2	252	CTCACCATCATCACACTg/g	7/11	0.249640203061932	3	FACETS	0.861	0.755	0.974	0.43	0.377	0.487	CLONAL	1	TRUE	1	0.31	3		620	658	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136998	11136998	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	74	701	0	ENST00000358026.2:c.3191G>A	p.Gly1064Glu	p.G1064E	ENST00000358026	NM_001128849.1	1064	gGg/gAg	23/36	0.252552557501673	3	FACETS	0.749	0.655	0.851	0.375	0.327	0.426	SUBCLONAL	1	TRUE	1	0.31	3		701	736	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719184	61719184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	20	280	0	ENST00000401558.2:c.1873C>T	p.Leu625Phe	p.L625F	ENST00000401558	NM_003400.3	625	Ctt/Ttt	16/25	0.252552557501673	3	FACETS	0.464	0.355	0.593	0.232	0.177	0.297	SUBCLONAL	1	TRUE	1	0.31	3		280	321	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727101	40727101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1302171855	NA	P-0047438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	39	571	0	ENST00000373198.4:c.3863G>A	p.Cys1288Tyr	p.C1288Y	ENST00000373198	NM_133170.3	1288	tGc/tAc	28/32	0.277880588125802	1	FACETS	0.505	0.419	0.601	0.505	0.419	0.601	SUBCLONAL	1	TRUE	0	0.31	1		571	421	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448542	89448542	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	69	391	0	ENST00000336596.2:c.1506C>A	p.Asp502Glu	p.D502E	ENST00000336596	NM_005233.5	502	gaC/gaA	7/17	0.182215333761902	4	FACETS	1	0.947	1	0.583	0.509	0.663	INDETERMINATE	1	TRUE	2	0.31	4		391	500	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041442	47041442	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0047438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	109	314	1	ENST00000377604.3:c.1785+1G>A		p.X595_splice	ENST00000377604	NM_001204468.1	595			0.3	2	FACETS	0.974	0.883	1			1	CLONAL	2	TRUE	NA	0.31	2		315	361	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	102	550	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.390762193391631	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.390762193391631	1		550	360	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987031	36987031	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	38	529	0	ENST00000354822.5:c.658G>A	p.Glu220Lys	p.E220K	ENST00000354822	NM_001079668.2	220	Gag/Aag	3/3	0.306886363480557	4	FACETS	1	0.924	1	0.601	0.501	0.711	CLONAL	1	TRUE	2	0.390762193391631	4		529	225	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690593	88690593	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	73	346	0	ENST00000360948.2:c.437T>A	p.Leu146His	p.L146H	ENST00000360948	NM_001012338.2	146	cTc/cAc	5/19	0.369106437914771	4	FACETS	0.769	0.677	0.866	0.769	0.677	0.866	SUBCLONAL	2	TRUE	2	0.390762193391631	4		346	338	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900350	3900386	+	frameshift_variant	Frame_Shift_Del	DEL	TGCGGGGAAACCTGCGTTAGGGTCTCAGCCAGCACGC	TGCGGGGAAACCTGCGTTAGGGTCTCAGCCAGCACGC	-	novel	NA	P-0047442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	181	697	0	ENST00000262367.5:c.710_746del	p.Ser237LysfsTer2	p.S237Kfs*2	ENST00000262367	NM_004380.2	237	aGCGTGCTGGCTGAGACCCTAACGCAGGTTTCCCCGCAa/aa	2/31	0.382038716627431	4	FACETS	0.845	0.786	0.906	0.845	0.786	0.906	CLONAL	3	TRUE	1	0.390762193391631	4		697	508	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78933987	78933987	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047442-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	75	689	0	ENST00000306801.3:c.3588del	p.Met1197TrpfsTer9	p.M1197Wfs*9	ENST00000306801	NM_020761.2	1196	aGg/ag	30/34	0.369106437914771	4	FACETS	1	0.886	1	0.505	0.443	0.571	CLONAL	1	TRUE	2	0.390762193391631	4		689	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0047443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	851	911	1	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.952240527115826	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.962500261043558	1		912	898	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279521	1279521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1353891039	NA	P-0047443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1786	936	889	1	ENST00000310581.5:c.2015G>A	p.Arg672His	p.R672H	ENST00000310581	NM_198253.2	672	cGc/cAc	5/16	0.501328944276372	4	FACETS	1	0.998	1	0.467	0.452	0.483	INDETERMINATE	1	TRUE	1	0.962500261043558	4		890	2722	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196207	108196207	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	386	411	0	ENST00000278616.4:c.6743A>T	p.Lys2248Met	p.K2248M	ENST00000278616	NM_000051.3	2248	aAg/aTg	46/63	1	2	FACETS	0.999	0.955	1	0.999	0.955	1	CLONAL	1	TRUE	1	0.962500261043558	2		411	803	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027169	49027169	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	278	341	0	ENST00000267163.4:c.1736del	p.Arg579GlnfsTer32	p.R579Qfs*32	ENST00000267163	NM_000321.2	579	cGa/ca	18/27	0.962500261043558	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.962500261043558	1		341	297	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858901	78858901	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	818	775	0	ENST00000306801.3:c.1936A>G	p.Met646Val	p.M646V	ENST00000306801	NM_020761.2	646	Atg/Gtg	17/34	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.962500261043558	2		775	1689	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021092	31021092	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	442	416	0	ENST00000375687.4:c.1091G>T	p.Gly364Val	p.G364V	ENST00000375687	NM_015338.5	364	gGt/gTt	12/13	1	2	FACETS	0.982	0.942	1	0.982	0.942	1	CLONAL	1	TRUE	1	0.962500261043558	2		416	935	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036987	180036987	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	618	676	1	ENST00000261937.6:c.3725G>T	p.Arg1242Ile	p.R1242I	ENST00000261937	NM_182925.4	1242	aGa/aTa	28/30	0.962500261043558	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.962500261043558	1		677	657	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933967	39933967	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1403354721	NA	P-0047443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	696	331	0	ENST00000378444.4:c.632A>G	p.Asn211Ser	p.N211S	ENST00000378444	NM_001123385.1	211	aAt/aGt	4/15	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.962500261043558	1		331	727	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0047444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	124	272	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.378352019392724	3	FACETS	0.945	0.871	1	1	0.987	1	CLONAL	3	TRUE	1	0.378352019392724	3		272	275	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0047444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	217	633	2	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.933	0.873	0.994	1	0.994	1	CLONAL	2	TRUE	1	0.378352019392724	2		635	615	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0047444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	135	282	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	0.378352019392724	1	FACETS	0.952	0.88	1	1	0.991	1	CLONAL	2	TRUE	0	0.378352019392724	1		282	304	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210482	5210482	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs147647579	NA	P-0047444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	160	429	0	ENST00000357368.4:c.5485C>T	p.Arg1829Trp	p.R1829W	ENST00000357368	NM_002850.3	1829	Cgg/Tgg	35/38	0.266673009225838	3	FACETS	0.8	0.736	0.865	0.8	0.736	0.865	SUBCLONAL	2	TRUE	1	0.378352019392724	3		429	629	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351208	89351208	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	292	625	0	ENST00000301030.4:c.1742C>G	p.Ser581Cys	p.S581C	ENST00000301030	NM_001256183.1	581	tCt/tGt	9/13	1	2	FACETS	1	0.964	1	1	0.996	1	CLONAL	2	TRUE	1	0.378352019392724	2		625	753	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099864	27099864	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0047444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	213	513	0	ENST00000324856.7:c.3743C>G	p.Ser1248Ter	p.S1248*	ENST00000324856	NM_006015.4	1248	tCa/tGa	15/20	1	2	FACETS	0.823	0.768	0.879	1	0.993	1	CLONAL	2	TRUE	1	0.378352019392724	2		513	684	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475083	40475085	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0047444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	230	564	0	ENST00000264657.5:c.1825_1827del	p.Arg609del	p.R609del	ENST00000264657	NM_139276.2	609	AGA/-	20/24	0.378352019392724	3	FACETS	0.939	0.878	1	0.939	0.878	1	CLONAL	2	TRUE	1	0.378352019392724	3		564	770	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231869	36231870	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	195	385	0	ENST00000300305.3:c.514dup	p.Ser172LysfsTer41	p.S172Kfs*41	ENST00000300305		172	agc/aAgc	5/8	1	2	FACETS	0.899	0.838	0.962	1	0.993	1	CLONAL	2	TRUE	1	0.378352019392724	2		385	573	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152857994	152857994	+	synonymous_variant	Silent	SNP	G	G	A	rs139186601	NA	P-0047444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	94	302	0	ENST00000406277.2:c.621C>T	p.Ala207=	p.A207=	ENST00000406277	NM_152274.4	207	gcC/gcT	6/7	0.378352019392724	1	FACETS	0.854	0.774	0.935	1	0.986	1	CLONAL	2	TRUE	0	0.378352019392724	1		302	236	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0047446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	648	671	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.609285615474575	3	FACETS	0.979	0.953	1			1	CLONAL	3	TRUE	NA	0.609285615474575	3		671	945	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484206	8484206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768568228	NA	P-0047446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	172	409	0	ENST00000356435.5:c.3326G>A	p.Arg1109His	p.R1109H	ENST00000356435		1109	cGt/cAt	19/35	0.59302275891742	1	FACETS	0.937	0.872	1	0.937	0.872	1	CLONAL	1	TRUE	0	0.609285615474575	1		409	419	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453531	138453531	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372119491	NA	P-0047446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	166	269	0	ENST00000289153.2:c.917G>A	p.Arg306Gln	p.R306Q	ENST00000289153	NM_006219.2	306	cGa/cAa	5/22	0.565100185615417	5	FACETS	0.955	0.883	1	0.637	0.588	0.686	CLONAL	2	TRUE	2	0.609285615474575	5		269	546	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729259	41729259	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs894989688	NA	P-0047446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	251	321	0	ENST00000242208.4:c.1270G>T	p.Gly424Trp	p.G424W	ENST00000242208	NM_002192.2	424	Ggg/Tgg	3/3	0.609285615474575	4	FACETS	0.913	0.858	0.969	0.913	0.858	0.969	CLONAL	2	TRUE	2	0.609285615474575	4		321	726	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450876	70450876	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	215	466	0	ENST00000373644.4:c.5716G>T	p.Glu1906Ter	p.E1906*	ENST00000373644	NM_030625.2	1906	Gaa/Taa	12/12	0.609285615474575	3	FACETS	1	0.977	1	0.553	0.515	0.593	CLONAL	1	TRUE	1	0.609285615474575	3		466	832	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100600	102100600	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	169	334	0	ENST00000282441.5:c.1444A>G	p.Ile482Val	p.I482V	ENST00000282441	NM_001130145.2	482	Atc/Gtc	9/9	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.609285615474575	2		334	510	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3645673	3645673	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	534	672	0	ENST00000294008.3:c.1946G>T	p.Gly649Val	p.G649V	ENST00000294008	NM_032444.2	649	gGc/gTc	9/15	0.609285615474575	3	FACETS	0.956	0.919	0.993	0.956	0.919	0.993	CLONAL	2	TRUE	1	0.609285615474575	3		672	1196	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309634	30309634	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	610	540	0	ENST00000307677.4:c.388C>T	p.Leu130Phe	p.L130F	ENST00000307677	NM_138578.1	130	Ctc/Ttc	2/3	0.46253176665518	5	FACETS	1	0.995	1	0.816	0.785	0.847	CLONAL	2	TRUE	2	0.609285615474575	5		540	1566	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564449	55564449	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0047446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2806	203	297	0	ENST00000288135.5:c.338-1G>T		p.X113_splice	ENST00000288135	NM_000222.2	113			0.609285615474575	22	FACETS	0.785	0.724	0.85			1	SUBCLONAL	2	TRUE	NA	0.609285615474575	22		297	3009	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411396	63411396	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	276	366	0	ENST00000330258.3:c.1771A>G	p.Arg591Gly	p.R591G	ENST00000330258	NM_152424.3	591	Agg/Ggg	2/2	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.609285615474575	1		366	435	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007809	45007810	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACTACA	novel	NA	P-0047447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	47	379	0	ENST00000558401.1:c.257_262dup	p.Tyr87_Thr88insAsnTyr	p.Y87_T88insNY	ENST00000558401	NM_004048.2	86	tac/tACTACAac	2/4	0.32094563245296	1	FACETS	0.472	0.398	0.554	0.472	0.398	0.554	SUBCLONAL	1	TRUE	0	0.32094563245296	1		379	521	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400269	225400269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	38	168	0	ENST00000264414.4:c.354G>A	p.Met118Ile	p.M118I	ENST00000264414	NM_003590.4	118	atG/atA	3/16	1	2	FACETS	0.94	0.782	1	0.94	0.782	1	CLONAL	1	TRUE	1	0.32094563245296	2		168	252	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575451	67575451	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	137	265	0	ENST00000274335.5:c.526del	p.Met176Ter	p.M176*	ENST00000274335		175	gAa/ga	4/15	0.274266594555016	3	FACETS	0.922	0.843	1	0.922	0.843	1	CLONAL	2	TRUE	1	0.32094563245296	3		265	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0047449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	354	1013	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.3839464310704	2	FACETS	0.994	0.946	1	0.994	0.946	1	CLONAL	2	TRUE	0	0.417554072868056	2		1013	853	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786038	135786038	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1280	113	750	1	ENST00000298552.3:c.1183C>T	p.Pro395Ser	p.P395S	ENST00000298552	NM_001162426.1	395	Cct/Tct	12/23	0.235634831239398	5	FACETS	0.632	0.566	0.702	0.211	0.188	0.234	INDETERMINATE	1	TRUE	2	0.417554072868056	5		751	1393	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786446	135786446	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	70	502	0	ENST00000298552.3:c.1084C>G	p.Pro362Ala	p.P362A	ENST00000298552	NM_001162426.1	362	Cct/Gct	11/23	0.235634831239398	5	FACETS	0.599	0.52	0.683	0.2	0.173	0.228	INDETERMINATE	1	TRUE	2	0.417554072868056	5		502	911	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0047450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	601	396	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.590464408840229	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.590464408840229	3		396	838	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0047450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	281	564	1	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.590464408840229	2		565	941	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0047450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	318	706	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.549223142193478	1	FACETS	0.921	0.873	0.97	0.921	0.873	0.97	CLONAL	1	TRUE	0	0.590464408840229	1		706	824	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880257	37880257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	179	453	0	ENST00000269571.5:c.2301C>G	p.Ile767Met	p.I767M	ENST00000269571		767	atC/atG	19/27	0.588299877640282	3	FACETS	0.938	0.866	1	0.469	0.433	0.507	CLONAL	1	TRUE	1	0.590464408840229	3		453	837	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293875	1293875	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1737	335	1039	0	ENST00000310581.5:c.1126C>T	p.Pro376Ser	p.P376S	ENST00000310581	NM_198253.2	376	Ccc/Tcc	2/16	0.590464408840229	4	FACETS	0.871	0.82	0.924	0.29	0.273	0.308	CLONAL	1	TRUE	1	0.590464408840229	4		1039	2072	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874031	123874031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1447464550	NA	P-0047450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	10	29	0	ENST00000330479.4:c.62C>T	p.Ala21Val	p.A21V	ENST00000330479	NM_020382.3	21	gCg/gTg	2/9	0.590464408840229	3	FACETS	0.482	0.33	0.669			1	SUBCLONAL	1	TRUE	NA	0.590464408840229	3		29	91	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042214	42042214	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	167	401	0	ENST00000219905.7:c.6409G>T	p.Glu2137Ter	p.E2137*	ENST00000219905	NM_001164273.1	2137	Gaa/Taa	17/24	0.590464408840229	1	FACETS	0.921	0.855	0.987	0.921	0.855	0.987	CLONAL	1	TRUE	0	0.590464408840229	1		401	433	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254583	46254583	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0047450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	318	349	0	ENST00000334344.6:c.4774-1G>T		p.X1592_splice	ENST00000334344	NM_152641.2	1592			0.531090678238676	2	FACETS	0.93	0.888	0.972	0.93	0.888	0.972	CLONAL	2	TRUE	0	0.590464408840229	2		349	579	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436101	56436101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	499	660	0	ENST00000407977.2:c.1036C>T	p.Pro346Ser	p.P346S	ENST00000407977		346	Ccc/Tcc	9/10	0.588299877640282	3	FACETS	0.955	0.917	0.994	0.955	0.917	0.994	CLONAL	2	TRUE	1	0.590464408840229	3		660	1146	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974986	18974986	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	169	500	0	ENST00000262803.5:c.2783G>T	p.Arg928Leu	p.R928L	ENST00000262803	NM_002911.3	928	cGc/cTc	20/24	1	2	FACETS	0.751	0.692	0.813	0.751	0.692	0.813	SUBCLONAL	1	TRUE	1	0.590464408840229	2		500	762	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867374	45867374	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	1205	854	0	ENST00000391945.4:c.819C>G	p.Ile273Met	p.I273M	ENST00000391945	NM_000400.3	273	atC/atG	10/23	0.334315485159583	6	FACETS	0.91	0.89	0.93			1	INDETERMINATE	5	TRUE	NA	0.590464408840229	6		854	1956	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045504	47045504	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	265	322	0	ENST00000377604.3:c.2471A>T	p.Lys824Met	p.K824M	ENST00000377604	NM_001204468.1	824	aAg/aTg	22/24	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.590464408840229	1		322	514	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0047451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	102	220	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.632487777632931	2		221	268	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	711	813	0	ENST00000269305.4:c.470T>G	p.Val157Gly	p.V157G	ENST00000269305	NM_001126112.2	157	gTc/gGc	5/11	0.632487777632931	2	FACETS	0.855	0.837	0.871	1	0.998	1	CLONAL	3	TRUE	0	0.632487777632931	2		813	877	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123697	46123697	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	44	290	0	ENST00000334344.6:c.79del	p.His27ThrfsTer31	p.H27Tfs*31	ENST00000334344	NM_152641.2	26	ttC/tt	1/21	1	2	FACETS	0.517	0.436	0.605	0.517	0.436	0.605	SUBCLONAL	1	TRUE	1	0.632487777632931	2		290	269	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910605	32910605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	59	290	0	ENST00000380152.3:c.2113G>A	p.Glu705Lys	p.E705K	ENST00000380152		705	Gaa/Aaa	11/27	1	2	FACETS	0.506	0.437	0.58	0.506	0.437	0.58	SUBCLONAL	1	TRUE	1	0.632487777632931	2		290	369	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937933	76937934	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0047451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	37	249	0	ENST00000373344.5:c.2813_2814dup	p.Val939LysfsTer32	p.V939Kfs*32	ENST00000373344	NM_000489.3	938	-/AA	9/35	1	1	FACETS	0.261	0.216	0.312	0.261	0.216	0.312	SUBCLONAL	1	TRUE	0	0.632487777632931	1		249	306	SUCCESS
APC	324	MSKCC	GRCh37	5	112175240	112175240	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	63	220	0	ENST00000257430.4:c.3949G>T	p.Glu1317Ter	p.E1317*	ENST00000257430	NM_000038.5	1317	Gaa/Taa	16/16	0.225554429620926	2	FACETS	0.864	0.756	0.979	0.864	0.756	0.979	CLONAL	2	TRUE	0	0.283694432765045	2		220	257	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003749	45003749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368160918	NA	P-0047452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	73	505	0	ENST00000558401.1:c.5C>T	p.Ser2Phe	p.S2F	ENST00000558401	NM_004048.2	2	tCt/tTt	1/4	1	2	FACETS	0.671	0.586	0.763	0.671	0.586	0.763	SUBCLONAL	1	TRUE	1	0.283694432765045	2		505	767	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578393	7578395	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	novel	NA	P-0047452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	76	731	0	ENST00000269305.4:c.535_537del	p.His179del	p.H179del	ENST00000269305	NM_001126112.2	179	CAT/-	5/11	1	2	FACETS	0.551	0.482	0.625	0.551	0.482	0.625	SUBCLONAL	1	TRUE	1	0.283694432765045	2		731	973	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577508	7577510	+	frameshift_variant	Frame_Shift_Del	DEL	TCC	TCC	GG	novel	NA	P-0047452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	147	601	0	ENST00000269305.4:c.771_773delinsCC	p.Glu258GlnfsTer87	p.E258Qfs*87	ENST00000269305	NM_001126112.2	257	ctGGAa/ctCCa	7/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.283694432765045	2		601	913	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578429	7578429	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1567553148	NA	P-0047453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	747	687	0	ENST00000269305.4:c.501del	p.Gln167HisfsTer3	p.Q167Hfs*3	ENST00000269305	NM_001126112.2	167	caG/ca	5/11	0.893295392260875	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.893295392260875	2		687	805	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292416	15292416	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	293	725	0	ENST00000263388.2:c.2763C>A	p.Cys921Ter	p.C921*	ENST00000263388	NM_000435.2	921	tgC/tgA	17/33	0.893295392260875	4	FACETS	0.937	0.881	0.996	0.234	0.22	0.249	CLONAL	1	TRUE	0	0.893295392260875	4		725	1325	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543552	9543552	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	177	349	0	ENST00000353224.5:c.1602T>G	p.Ile534Met	p.I534M	ENST00000353224	NM_177990.2	534	atT/atG	6/10	0.893295392260875	3	FACETS	0.983	0.911	1	0.492	0.455	0.529	CLONAL	1	TRUE	1	0.893295392260875	3		349	583	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182638	38182638	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	100	286	0	ENST00000396334.3:c.791G>T	p.Arg264Leu	p.R264L	ENST00000396334	NM_002468.4	264	cGa/cTa	5/5	0.893295392260875	3	FACETS	0.81	0.729	0.895	0.405	0.364	0.448	CLONAL	1	TRUE	1	0.893295392260875	3		286	400	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591128	67591129	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAAGAC	novel	NA	P-0047453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	122	197	1	ENST00000274335.5:c.1722_1727dup	p.Lys575_Thr576dup	p.K575_T576dup	ENST00000274335		575	aga/agAAAGACa	12/15	1	2	FACETS	0.846	0.775	0.918	0.846	0.775	0.918	CLONAL	1	TRUE	1	0.893295392260875	2		198	323	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467905	50467905	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	146	471	0	ENST00000331340.3:c.1140G>C	p.Lys380Asn	p.K380N	ENST00000331340	NM_006060.4	380	aaG/aaC	8/8	0.893295392260875	3	FACETS	0.993	0.914	1	0.497	0.457	0.538	CLONAL	1	TRUE	1	0.893295392260875	3		471	476	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224442	123224442	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	151	360	0	ENST00000218089.9:c.3295A>C	p.Ser1099Arg	p.S1099R	ENST00000218089	NM_001042749.1	1099	Agt/Cgt	31/35	1	2	FACETS	0.569	0.522	0.618	0.569	0.522	0.618	SUBCLONAL	1	TRUE	1	0.893295392260875	2		360	594	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	13	516	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.837	1			1	INDETERMINATE	1	TRUE	NA	0.483197822245211	2		516	45	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750269	133750269	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	13	438	1	ENST00000318560.5:c.1100G>T	p.Arg367Leu	p.R367L	ENST00000318560	NM_005157.4	367	cGa/cTa	7/11	1	2	FACETS	0.758	0.551	0.998	0.758	0.551	0.998	CLONAL	1	TRUE	1	0.483197822245211	2		439	71	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148511	119148511	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	14	340	0	ENST00000264033.4:c.1052G>T	p.Gly351Val	p.G351V	ENST00000264033	NM_005188.3	351	gGc/gTc	7/16	1	2	FACETS	1	0.769	1	1	0.769	1	CLONAL	1	TRUE	1	0.483197822245211	2		340	56	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0047455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	88	164	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.3431265634076	2		164	425	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125006	46125013	+	frameshift_variant	Frame_Shift_Del	DEL	GAGAAGAA	GAGAAGAA	-	novel	NA	P-0047455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	43	210	0	ENST00000334344.6:c.193_200del	p.Glu65SerfsTer7	p.E65Sfs*7	ENST00000334344	NM_152641.2	65	GAGAAGAAt/t	3/21	1	2	FACETS	0.798	0.671	0.938	0.798	0.671	0.938	CLONAL	1	TRUE	1	0.3431265634076	2		210	314	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0047456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	91	146	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.634217046489341	3	FACETS	1	0.966	1			1	CLONAL	1	TRUE	NA	0.634217046489341	3		146	319	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227926	55227926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	72	246	0	ENST00000275493.2:c.1393G>A	p.Gly465Arg	p.G465R	ENST00000275493	NM_005228.3	465	Gga/Aga	12/28	0.37704885901052	5	FACETS	0.713	0.623	0.811	0.238	0.207	0.271	INDETERMINATE	1	TRUE	2	0.634217046489341	5		246	621	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741414	17741414	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	88	566	0	ENST00000250003.3:c.85T>G	p.Phe29Val	p.F29V	ENST00000250003	NM_002478.4	29	Ttc/Gtc	1/3	0.634217046489341	2	FACETS	0.274	0.242	0.309	0.137	0.121	0.155	SUBCLONAL	1	TRUE	0	0.634217046489341	2		566	1011	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199836	108199836	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1555122073	NA	P-0047456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	147	152	0	ENST00000278616.4:c.7178T>G	p.Phe2393Cys	p.F2393C	ENST00000278616	NM_000051.3	2393	tTt/tGt	49/63	0.634217046489341	2	FACETS	0.954	0.895	1	0.954	0.895	1	CLONAL	2	TRUE	0	0.634217046489341	2		152	243	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61713061	61713061	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	103	216	0	ENST00000401558.2:c.2350G>T	p.Val784Phe	p.V784F	ENST00000401558	NM_003400.3	784	Gtt/Ttt	20/25	0.634217046489341	3	FACETS	0.775	0.696	0.859	0.388	0.348	0.43	SUBCLONAL	1	TRUE	1	0.634217046489341	3		216	552	SUCCESS
APC	324	MSKCC	GRCh37	5	112174266	112174266	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	161	257	0	ENST00000257430.4:c.2975del	p.Ser992IlefsTer13	p.S992Ifs*13	ENST00000257430	NM_000038.5	992	aGt/at	16/16	0.634217046489341	3	FACETS	0.82	0.76	0.88			1	CLONAL	2	TRUE	NA	0.634217046489341	3		257	408	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197144	26197144	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	118	476	0	ENST00000356476.2:c.335C>T	p.Ala112Val	p.A112V	ENST00000356476		112	gCc/gTc	1/1	0.294580597535564	4	FACETS	0.629	0.566	0.695	0.314	0.283	0.348	INDETERMINATE	1	TRUE	2	0.634217046489341	4		476	967	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127923136	127923136	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	141	326	0	ENST00000373547.4:c.221C>G	p.Thr74Arg	p.T74R	ENST00000373547	NM_002721.4	74	aCa/aGa	3/7	1	2	FACETS	0.934	0.857	1	0.934	0.857	1	CLONAL	1	TRUE	1	0.634217046489341	2		326	476	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467669	50467669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	328	507	0	ENST00000331340.3:c.904G>A	p.Glu302Lys	p.E302K	ENST00000331340	NM_006060.4	302	Gag/Aag	8/8	0.339845142232996	6	FACETS	0.864	0.82	0.908	0.864	0.82	0.908	INDETERMINATE	3	TRUE	3	0.73879686616294	6		507	849	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164832	47164832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1017636782	NA	P-0047457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	335	295	0	ENST00000409792.3:c.1294C>T	p.Arg432Cys	p.R432C	ENST00000409792	NM_014159.6	432	Cgt/Tgt	3/21	0.73639221680846	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	2	0.73879686616294	4		295	654	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101358	27101358	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	585	816	0	ENST00000324856.7:c.4640C>T	p.Ser1547Phe	p.S1547F	ENST00000324856	NM_006015.4	1547	tCc/tTc	18/20	0.73879686616294	3	FACETS	0.983	0.95	1	0.983	0.95	1	CLONAL	2	TRUE	1	0.73879686616294	3		816	1103	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274104	10274104	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057521810	NA	P-0047457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	316	811	0	ENST00000330684.3:c.165G>A	p.Trp55Ter	p.W55*	ENST00000330684	NM_001134407.1	55	tgG/tgA	2/13	0.73879686616294	3	FACETS	1	0.974	1	0.527	0.498	0.558	CLONAL	1	TRUE	1	0.73879686616294	3		811	1111	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244942	123244942	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	244	633	1	ENST00000358487.5:c.2162G>A	p.Arg721Lys	p.R721K	ENST00000358487	NM_000141.4	721	aGa/aAa	16/18	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.73879686616294	2		634	656	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295230	+	upstream_gene_variant	5'Flank	TNP	GGG	GGG	AGA	novel	NA	P-0047457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	411	334	0				ENST00000310581	NM_198253.2	-/1132			0.73879686616294	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	4	TRUE	0	0.73879686616294	4		334	476	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148874	119148874	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0047457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	215	222	0	ENST00000264033.4:c.1096-2A>T		p.X366_splice	ENST00000264033	NM_005188.3	366			0.73879686616294	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.73879686616294	2		222	288	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934623	9934623	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267604688	NA	P-0047457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	191	428	0	ENST00000330684.3:c.1532C>T	p.Ser511Leu	p.S511L	ENST00000330684	NM_001134407.1	511	tCg/tTg	7/13	0.73879686616294	3	FACETS	1	0.97	1	0.541	0.502	0.58	CLONAL	1	TRUE	1	0.73879686616294	3		428	655	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111516	8111517	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0047457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	192	551	2	ENST00000346208.3:c.1002_1003delinsAA	p.Asp335Asn	p.D335N	ENST00000346208		334	ggGGac/ggAAac	5/6	1	2	FACETS	0.893	0.831	0.956	0.893	0.831	0.956	CLONAL	1	TRUE	1	0.73879686616294	2		553	582	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333131	70333131	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	260	598	0	ENST00000373644.4:c.1036C>T	p.Gln346Ter	p.Q346*	ENST00000373644	NM_030625.2	346	Caa/Taa	2/12	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.73879686616294	2		598	699	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155087	108155087	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1478504213	NA	P-0047457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	376	409	0	ENST00000278616.4:c.3880A>T	p.Ile1294Phe	p.I1294F	ENST00000278616	NM_000051.3	1294	Att/Ttt	26/63	0.73879686616294	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.73879686616294	2		409	476	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857528	57857528	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0047457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	602	710	0	ENST00000228682.2:c.54T>A	p.Cys18Ter	p.C18*	ENST00000228682	NM_005269.2	18	tgT/tgA	2/12	0.73879686616294	2	FACETS	0.992	0.967	1	0.992	0.967	1	CLONAL	2	TRUE	0	0.73879686616294	2		710	821	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434110	121434110	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	497	706	0	ENST00000257555.6:c.1001C>T	p.Pro334Leu	p.P334L	ENST00000257555		334	cCc/cTc	5/10	0.73879686616294	2	FACETS	0.947	0.919	0.975	0.947	0.919	0.975	CLONAL	2	TRUE	0	0.73879686616294	2		706	710	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295112	91295112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1243827792	NA	P-0047457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	404	297	0	ENST00000355112.3:c.895G>A	p.Asp299Asn	p.D299N	ENST00000355112	NM_000057.2	299	Gat/Aat	4/22	0.73879686616294	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.73879686616294	3		297	486	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81891889	81891889	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	347	435	0	ENST00000359376.3:c.359T>A	p.Val120Asp	p.V120D	ENST00000359376	NM_002661.3	120	gTt/gAt	4/33	0.629988973130176	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.73879686616294	3		435	626	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838130	89838130	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555548512	NA	P-0047457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	351	576	1	ENST00000389301.3:c.2107C>T	p.Gln703Ter	p.Q703*	ENST00000389301	NM_000135.2	703	Cag/Tag	23/43	0.629988973130176	3	FACETS	0.891	0.85	0.932	0.891	0.85	0.932	CLONAL	2	TRUE	1	0.73879686616294	3		577	730	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554544	29554545	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGGAAGA	novel	NA	P-0047457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	165	201	0	ENST00000356175.3:c.2330_2336dup	p.Asp779GlufsTer17	p.D779Efs*17	ENST00000356175	NM_000267.3	777	tgg/tGGGAAGAgg	20/57	0.73879686616294	4	FACETS	0.867	0.804	0.931	0.867	0.804	0.931	CLONAL	2	TRUE	2	0.73879686616294	4		201	448	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556849	29556853	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTAGG	TTAGG	-	novel	NA	P-0047457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	246	260	0	ENST00000356175.3:c.2851-2_2853del		p.X951_splice	ENST00000356175	NM_000267.3	951		22/57	0.73879686616294	4	FACETS	0.919	0.865	0.974	0.919	0.865	0.974	CLONAL	2	TRUE	2	0.73879686616294	4		260	630	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320342	30320342	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	200	244	0	ENST00000322652.5:c.1283T>C	p.Ile428Thr	p.I428T	ENST00000322652	NM_015355.2	428	aTa/aCa	11/16	0.73879686616294	4	FACETS	0.877	0.819	0.935	0.877	0.819	0.935	CLONAL	2	TRUE	2	0.73879686616294	4		244	537	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885893	59885893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	499	470	0	ENST00000259008.2:c.853C>T	p.His285Tyr	p.H285Y	ENST00000259008	NM_032043.2	285	Cat/Tat	7/20	0.51349279835966	6	FACETS	0.973	0.934	1	0.973	0.934	1	CLONAL	3	TRUE	3	0.73879686616294	6		470	1147	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216602	2216603	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0047457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	656	1019	0	ENST00000398665.3:c.2246_2247delinsTT	p.Pro749Leu	p.P749L	ENST00000398665	NM_032482.2	749	cCC/cTT	20/28	0.73879686616294	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.73879686616294	2		1019	887	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211208	36211208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	732	980	1	ENST00000222270.7:c.959C>T	p.Ser320Phe	p.S320F	ENST00000222270	NM_014727.1	320	tCc/tTc	3/37	0.73879686616294	4	FACETS	1	0.972	1			1	CLONAL	2	TRUE	NA	0.73879686616294	4		981	1713	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966544	25966544	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	452	636	0	ENST00000435504.4:c.2662A>G	p.Thr888Ala	p.T888A	ENST00000435504		888	Aca/Gca	13/13	0.73879686616294	3	FACETS	0.904	0.867	0.94	0.904	0.867	0.94	CLONAL	2	TRUE	1	0.73879686616294	3		636	927	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391240	89391240	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	245	279	1	ENST00000336596.2:c.1306G>A	p.Ala436Thr	p.A436T	ENST00000336596	NM_005233.5	436	Gct/Act	5/17	0.73639221680846	4	FACETS	0.923	0.868	0.978	0.923	0.868	0.978	CLONAL	2	TRUE	2	0.73879686616294	4		280	625	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467487	66467487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1202947730	NA	P-0047457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	258	323	1	ENST00000273854.3:c.782C>T	p.Ser261Phe	p.S261F	ENST00000273854	NM_004439.5	261	tCc/tTc	3/18	0.738429112049683	2	FACETS	0.946	0.907	0.984	0.946	0.907	0.984	CLONAL	2	TRUE	0	0.73879686616294	2		324	369	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156451	106156451	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	108	319	0	ENST00000380013.4:c.1352T>C	p.Ile451Thr	p.I451T	ENST00000380013	NM_001127208.2	451	aTa/aCa	3/11	0.73879686616294	2	FACETS	0.713	0.645	0.784	0.357	0.322	0.392	SUBCLONAL	1	TRUE	0	0.73879686616294	2		319	410	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513170	149513170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	436	631	0	ENST00000261799.4:c.913G>A	p.Ala305Thr	p.A305T	ENST00000261799	NM_002609.3	305	Gcc/Acc	6/23	0.73879686616294	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.73879686616294	2		631	588	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412063	116412063	+	intron_variant	Intron	SNP	T	T	A	novel	NA	P-0047457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1504	643	630	0	ENST00000397752.3:c.3028+20T>A		p.*1010*	ENST00000397752	NM_000245.2	-/1390			0.73879686616294	6	FACETS	1	0.965	1	0.502	0.482	0.522	CLONAL	2	TRUE	2	0.73879686616294	6		630	2147	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15827356	15827356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	224	218	0	ENST00000307771.7:c.472C>T	p.Pro158Ser	p.P158S	ENST00000307771	NM_005089.3	158	Cca/Tca	7/11	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.73879686616294	1		218	297	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	33	516	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.622	0.51	0.747	0.622	0.51	0.747	SUBCLONAL	1	TRUE	1	0.461272448761562	2		516	230	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0047458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	234	992	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.461272448761562	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.461272448761562	1		992	626	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941638	48941641	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	rs1566194323	NA	P-0047458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	38	181	0	ENST00000267163.4:c.951_954del	p.Ser318AsnfsTer13	p.S318Nfs*13	ENST00000267163	NM_000321.2	316	aaTCTT/aa	10/27	0.461272448761562	1	FACETS	0.899	0.757	1	0.899	0.757	1	CLONAL	1	TRUE	0	0.461272448761562	1		181	141	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743648	46743648	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	104	564	0	ENST00000371975.4:c.2029G>C	p.Asp677His	p.D677H	ENST00000371975	NM_003579.3	677	Gac/Cac	17/18	1	2	FACETS	0.964	0.867	1	0.964	0.867	1	CLONAL	1	TRUE	1	0.461272448761562	2		564	468	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591070	67591071	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGTATCGAGAAATTGACA	novel	NA	P-0047458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	39	198	0	ENST00000274335.5:c.1665_1682dup	p.Tyr556_Lys561dup	p.Y556_K561dup	ENST00000274335		556	gag/gAGTATCGAGAAATTGACAag	12/15	1	2	FACETS	0.786	0.658	0.927	0.786	0.658	0.927	CLONAL	1	TRUE	1	0.461272448761562	2		198	215	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358936	81358936	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	62	371	1	ENST00000222390.5:c.1025A>G	p.Glu342Gly	p.E342G	ENST00000222390	NM_000601.4	342	gAa/gGa	8/18	0.408934386493333	3	FACETS	0.831	0.721	0.95	0.416	0.36	0.475	CLONAL	1	TRUE	1	0.461272448761562	3		372	398	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501357	140501357	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	51	201	0	ENST00000288602.6:c.715C>T	p.Arg239Ter	p.R239*	ENST00000288602	NM_004333.4	239	Cga/Tga	6/18	0.25124264258781	6	FACETS	1	0.941	1			1	INDETERMINATE	1	TRUE	NA	0.461272448761562	6		201	351	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0047459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	44	322	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	0.731	0.614	0.86	0.731	0.614	0.86	SUBCLONAL	1	TRUE	1	0.283336079351149	2		322	425	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11172458	11172458	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0047459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	56	672	0	ENST00000358026.2:c.5008-2A>C		p.X1670_splice	ENST00000358026	NM_001128849.1	1670			1	2	FACETS	0.52	0.445	0.603	0.52	0.445	0.603	SUBCLONAL	1	TRUE	1	0.283336079351149	2		672	760	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338641	70338641	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	88	376	0	ENST00000374080.3:c.40del	p.Leu14Ter	p.L14*	ENST00000374080		13	Ccc/cc	1/45	1	1	FACETS	0.823	0.736	0.913	1	0.983	1	CLONAL	2	TRUE	0	0.283336079351149	1		376	324	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0047460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	58	633	2	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.438	0.375	0.506	0.438	0.375	0.506	SUBCLONAL	1	TRUE	1	0.339674908353889	2		635	780	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0047460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	68	665	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.312450767409327	1	FACETS	0.353	0.306	0.404	0.353	0.306	0.404	SUBCLONAL	1	TRUE	0	0.339674908353889	1		665	942	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870996	12871174	+	frameshift_variant	Frame_Shift_Del	DEL	GAGTGGCAAGAGGTGGAGAAGGGCAGCTTGCCCGAGTTCTACTACAGACCCCCGCGGCCCCCCAAAGGTGCCTGCAAGGTGCCGGCGCAGGAGAGCCAGGATGTCAGCGGGAGCCGCCCGGCGGCGCCTTTAATTGGGGCTCCGGCTAACTCTGAGGACACGCATTTGGTGGACCCAAA	GAGTGGCAAGAGGTGGAGAAGGGCAGCTTGCCCGAGTTCTACTACAGACCCCCGCGGCCCCCCAAAGGTGCCTGCAAGGTGCCGGCGCAGGAGAGCCAGGATGTCAGCGGGAGCCGCCCGGCGGCGCCTTTAATTGGGGCTCCGGCTAACTCTGAGGACACGCATTTGGTGGACCCAAA	-	novel	NA	P-0047460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	57	420	0	ENST00000228872.4:c.225_403del	p.Glu75AspfsTer2	p.E75Dfs*2	ENST00000228872	NM_004064.3	75	GAGTGGCAAGAGGTGGAGAAGGGCAGCTTGCCCGAGTTCTACTACAGACCCCCGCGGCCCCCCAAAGGTGCCTGCAAGGTGCCGGCGCAGGAGAGCCAGGATGTCAGCGGGAGCCGCCCGGCGGCGCCTTTAATTGGGGCTCCGGCTAACTCTGAGGACACGCATTTGGTGGACCCAAAg/g	1/3	0.333056407626853	3	FACETS	0.726	0.623	0.838	0.363	0.311	0.419	SUBCLONAL	1	TRUE	1	0.339674908353889	3		420	541	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0047461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	23	277	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.842	0.656	1	0.842	0.656	1	CLONAL	1	TRUE	1	0.14	2		277	390	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593491	48593494	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	rs80338965	NA	P-0047461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	27	268	0	ENST00000342988.3:c.1245_1248del	p.Asp415GlufsTer20	p.D415Efs*20	ENST00000342988	NM_005359.5	414	ttAGAC/tt	10/12	1	2	FACETS	0.916	0.728	1	0.916	0.728	1	CLONAL	1	TRUE	1	0.14	2		268	421	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031708	36031708	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	77	898	1	ENST00000358208.4:c.1537G>A	p.Glu513Lys	p.E513K	ENST00000358208		513	Gag/Aag	12/12	1	2	FACETS	0.93	0.814	1	0.93	0.814	1	CLONAL	1	TRUE	1	0.14	2		899	1183	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898818	134898818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1387550343	NA	P-0047461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	25	242	0	ENST00000398015.3:c.1876G>A	p.Gly626Arg	p.G626R	ENST00000398015	NM_004441.4	626	Gga/Aga	10/16	1	2	FACETS	1	0.799	1	1	0.799	1	CLONAL	1	TRUE	1	0.14	2		242	352	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412599	63412599	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	58	661	0	ENST00000330258.3:c.568del	p.Ser190ValfsTer19	p.S190Vfs*19	ENST00000330258	NM_152424.3	190	Agt/gt	2/2	1	2	FACETS	0.905	0.775	1	0.905	0.775	1	CLONAL	1	TRUE	1	0.14	2		661	916	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253176	133253176	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	37	530	0	ENST00000320574.5:c.865G>A	p.Glu289Lys	p.E289K	ENST00000320574	NM_006231.2	289	Gag/Aag	9/49	1	2	FACETS	0.562	0.462	0.673	0.562	0.462	0.673	SUBCLONAL	1	FALSE	1	0.253438300696053	2		530	520	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262160	16262160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	28	322	0	ENST00000375759.3:c.9425C>T	p.Pro3142Leu	p.P3142L	ENST00000375759	NM_015001.2	3142	cCa/cTa	11/15	1	2	FACETS	0.639	0.511	0.784	0.639	0.511	0.784	SUBCLONAL	1	FALSE	1	0.253438300696053	2		322	346	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106559	27106559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	53	805	1	ENST00000324856.7:c.6170G>A	p.Arg2057Gln	p.R2057Q	ENST00000324856	NM_006015.4	2057	cGg/cAg	20/20	1	2	FACETS	0.604	0.514	0.702	0.604	0.514	0.702	SUBCLONAL	1	FALSE	1	0.253438300696053	2		806	693	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137205	64137205	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	43	852	2	ENST00000334205.4:c.1637C>A	p.Pro546Gln	p.P546Q	ENST00000334205	NM_003942.2	546	cCg/cAg	14/17	1	2	FACETS	0.503	0.42	0.595	0.503	0.42	0.595	SUBCLONAL	1	FALSE	1	0.253438300696053	2		854	675	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668625	52668625	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	28	353	0	ENST00000394830.3:c.1294C>T	p.Gln432Ter	p.Q432*	ENST00000394830	NM_018313.4	432	Cag/Tag	12/30	1	2	FACETS	0.68	0.544	0.834	0.68	0.544	0.834	SUBCLONAL	1	FALSE	1	0.253438300696053	2		353	325	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169195	32169195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	46	850	1	ENST00000375023.3:c.3838G>A	p.Asp1280Asn	p.D1280N	ENST00000375023	NM_004557.3	1280	Gat/Aat	22/30	NA	2	FACETS	0.547	0.459	0.643			1	INDETERMINATE	1	FALSE	NA	0.253438300696053	2		851	664	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509387	106509387	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1056639757	NA	P-0047463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	367	578	0	ENST00000359195.3:c.1381C>G	p.Leu461Val	p.L461V	ENST00000359195	NM_002649.2	461	Ctc/Gtc	2/11	0.253438300696053	7	FACETS	1	0.985	1			1	CLONAL	5	FALSE	NA	0.253438300696053	7		578	878	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0047464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	30	242	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	1	2	FACETS	1	0.811	1	1	0.811	1	CLONAL	1	FALSE	1	0.25082700068931	2		242	239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578264	7578268	+	frameshift_variant	Frame_Shift_Del	DEL	GATAA	GATAA	-	novel	NA	P-0047464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	39	589	0	ENST00000269305.4:c.581_585del	p.Leu194ProfsTer13	p.L194Pfs*13	ENST00000269305	NM_001126112.2	194	cTTATC/c	6/11	0.226900014710908	3	FACETS	0.936	0.777	1	0.468	0.388	0.556	CLONAL	1	FALSE	1	0.25082700068931	3		589	374	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219364	5219364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	54	715	0	ENST00000357368.4:c.3880G>A	p.Val1294Ile	p.V1294I	ENST00000357368	NM_002850.3	1294	Gtc/Atc	23/38	0.25082700068931	3	FACETS	1	0.888	1	0.522	0.446	0.605	CLONAL	1	FALSE	1	0.25082700068931	3		715	464	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0047465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	232	424	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.193122700719491	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	0	0.193122700719491	3		424	782	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0047465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	136	1078	6	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.15053030421465	2	FACETS	0.764	0.694	0.837	0.764	0.694	0.837	SUBCLONAL	2	TRUE	0	0.193122700719491	2		1084	922	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097624	11097625	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1165714406	NA	P-0047465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	162	993	1	ENST00000358026.2:c.810dup	p.Gly271ArgfsTer16	p.G271Rfs*16	ENST00000358026	NM_001128849.1	268	-/C	5/36	0.15053030421465	2	FACETS	1	0.986	1	0.69	0.632	0.752	CLONAL	1	TRUE	0	0.193122700719491	2		994	1215	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339071	225339071	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	36	282	0	ENST00000264414.4:c.2198G>T	p.Arg733Leu	p.R733L	ENST00000264414	NM_003590.4	733	cGa/cTa	16/16	1	2	FACETS	0.89	0.732	1	0.89	0.732	1	CLONAL	1	TRUE	1	0.193122700719491	2		282	419	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834543	156834543	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	319	825	0	ENST00000524377.1:c.311G>T	p.Arg104Leu	p.R104L	ENST00000524377	NM_002529.3	104	cGt/cTt	3/17	0.193122700719491	3	FACETS	0.996	0.94	1	0.996	0.94	1	CLONAL	3	TRUE	0	0.193122700719491	3		825	1212	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445091	49445091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1417735119	NA	P-0047465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	186	589	1	ENST00000301067.7:c.2375C>T	p.Ala792Val	p.A792V	ENST00000301067	NM_003482.3	792	gCt/gTt	10/54	0.193122700719491	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	0	0.193122700719491	2		590	963	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727516	88727516	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	82	439	0	ENST00000360948.2:c.263G>T	p.Trp88Leu	p.W88L	ENST00000360948	NM_001012338.2	88	tGg/tTg	3/19	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.193122700719491	2		439	683	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552122	29552140	+	frameshift_variant	Frame_Shift_Del	DEL	AGAAGTTCCTGTCACTTTC	AGAAGTTCCTGTCACTTTC	-	novel	NA	P-0047465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	17	190	0	ENST00000356175.3:c.1855_1873del	p.Arg619SerfsTer6	p.R619Sfs*6	ENST00000356175	NM_000267.3	619	AGAAGTTCCTGTCACTTTCtc/tc	17/57	1	2	FACETS	0.851	0.637	1	0.851	0.637	1	CLONAL	1	TRUE	1	0.193122700719491	2		190	207	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560127	29560127	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs146641724	NA	P-0047465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	51	273	0	ENST00000356175.3:c.3604G>T	p.Ala1202Ser	p.A1202S	ENST00000356175	NM_000267.3	1202	Gct/Tct	27/57	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.193122700719491	2		273	463	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495222	212495222	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	31	402	0	ENST00000342788.4:c.2044A>G	p.Lys682Glu	p.K682E	ENST00000342788	NM_005235.2	682	Aag/Gag	17/28	1	2	FACETS	0.614	0.495	0.748	0.614	0.495	0.748	SUBCLONAL	1	TRUE	1	0.193122700719491	2		402	523	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038335	180038335	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	43	630	0	ENST00000261937.6:c.3682G>T	p.Ala1228Ser	p.A1228S	ENST00000261937	NM_182925.4	1228	Gcc/Tcc	27/30	1	2	FACETS	0.584	0.488	0.692	0.584	0.488	0.692	SUBCLONAL	1	TRUE	1	0.193122700719491	2		630	762	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450237	50450237	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0047465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	37	390	0	ENST00000331340.3:c.422-1G>T		p.X141_splice	ENST00000331340	NM_006060.4	141			1	2	FACETS	0.678	0.558	0.813	0.678	0.558	0.813	SUBCLONAL	1	TRUE	1	0.193122700719491	2		390	565	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932470	39932470	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	68	726	0	ENST00000378444.4:c.2129G>T	p.Arg710Leu	p.R710L	ENST00000378444	NM_001123385.1	710	cGt/cTt	4/15	0.172774016050979	1	FACETS	0.604	0.523	0.691	0.604	0.523	0.691	SUBCLONAL	1	TRUE	0	0.193122700719491	1		726	1054	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158357	108158357	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555095899	NA	P-0047468-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	62	341	0	ENST00000278616.4:c.4024G>A	p.Glu1342Lys	p.E1342K	ENST00000278616	NM_000051.3	1342	Gag/Aag	27/63	0.241215234535966	3	FACETS	1	0.961	1	0.653	0.567	0.746	CLONAL	1	FALSE	1	0.3	3		341	364	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487160	56487160	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047468-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	190	422	0	ENST00000267101.3:c.1306T>A	p.Leu436Met	p.L436M	ENST00000267101	NM_001982.3	436	Ttg/Atg	12/28	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.3	NA		422	540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0047468-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	247	934	0	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	0.29813795611206	2	FACETS	0.956	0.896	1	0.956	0.896	1	CLONAL	2	FALSE	0	0.3	2		934	861	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118613	17118614	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AT	novel	NA	P-0047468-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	150	537	2	ENST00000285071.4:c.1317_1318delinsAT	p.Glu440Ter	p.E440*	ENST00000285071	NM_144997.5	439	gtGGag/gtATag	12/14	0.29813795611206	2	FACETS	0.99	0.911	1	0.99	0.911	1	CLONAL	2	FALSE	0	0.3	2		539	505	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223162	5223162	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs771623625	NA	P-0047468-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	272	1163	0	ENST00000357368.4:c.2641C>G	p.Leu881Val	p.L881V	ENST00000357368	NM_002850.3	881	Ctg/Gtg	18/38	0.258326787378621	2	FACETS	0.958	0.901	1	0.958	0.901	1	CLONAL	2	FALSE	0	0.3	2		1163	946	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399543	139399543	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047468-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	249	899	0	ENST00000277541.6:c.4600C>G	p.Gln1534Glu	p.Q1534E	ENST00000277541	NM_017617.3	1534	Cag/Gag	26/34	0.29813795611206	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	FALSE	0	0.3	2		899	781	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966768	44966768	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047468-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	56	234	0	ENST00000377967.4:c.3992G>T	p.Cys1331Phe	p.C1331F	ENST00000377967	NM_021140.2	1331	tGt/tTt	27/29	1	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	0	0.3	1		234	222	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913250	NA	P-0047471-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	80	532	0	ENST00000369535.4:c.34G>T	p.Gly12Cys	p.G12C	ENST00000369535	NM_002524.4	12	Ggt/Tgt	2/7	0.327175003942049	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.327175003942049	1		532	285	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984450	201984450	+	stop_lost	Nonstop_Mutation	SNP	G	G	T	novel	NA	P-0047471-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	116	438	0	ENST00000359651.3:c.1115G>T	p.Ter372LeuextTer43	p.*372Lext*43	ENST00000359651		372	tGa/tTa	8/8	0.327175003942049	6	FACETS	0.974	0.881	1	0.487	0.44	0.537	CLONAL	2	TRUE	2	0.327175003942049	6		438	602	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446338	70446345	+	frameshift_variant	Frame_Shift_Ins	INS	GCGATGAT	GCGATGAT	TTCACGTTCTGGAAA	novel	NA	P-0047471-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	31	453	0	ENST00000373644.4:c.5278_5285delinsTTCACGTTCTGGAAA	p.Ala1760PhefsTer12	p.A1760Ffs*12	ENST00000373644	NM_030625.2	1760	GCGATGATg/TTCACGTTCTGGAAAg	11/12	0.327175003942049	2	FACETS	0.621	0.504	0.754	0.311	0.252	0.377	SUBCLONAL	1	TRUE	0	0.327175003942049	2		453	305	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0047471-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	103	671	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.259256671552366	3	FACETS	0.829	0.746	0.915	0.553	0.497	0.61	CLONAL	2	TRUE	0	0.327175003942049	3		671	442	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1646421	1646421	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047471-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	131	481	0	ENST00000344749.5:c.78C>G	p.Phe26Leu	p.F26L	ENST00000344749	NM_001136139.2	26	ttC/ttG	3/19	0.218000171372944	4	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	2	0.327175003942049	4		481	516	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182292	38182292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1353791431	NA	P-0047471-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	10	439	1	ENST00000396334.3:c.728G>A	p.Ser243Asn	p.S243N	ENST00000396334	NM_002468.4	243	aGc/aAc	4/5	0.322329091199243	2	FACETS	0.167	0.112	0.236	0.084	0.056	0.118	SUBCLONAL	1	TRUE	0	0.327175003942049	2		440	366	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141051	55141051	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1560480581	NA	P-0047471-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	43	301	0	ENST00000257290.5:c.1697G>T	p.Ser566Ile	p.S566I	ENST00000257290	NM_006206.4	566	aGc/aTc	12/23	0.25616697550377	4	FACETS	0.758	0.64	0.887	0.758	0.64	0.887	SUBCLONAL	2	TRUE	2	0.327175003942049	4		301	230	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295407	1295407	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0047471-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	35	119	0				ENST00000310581	NM_198253.2	-/1132			0.327175003942049	5	FACETS	0.967	0.803	1	0.644	0.535	0.763	CLONAL	2	TRUE	2	0.327175003942049	5		119	165	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858201	27858201	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047471-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	87	489	1	ENST00000359303.2:c.370G>T	p.Asp124Tyr	p.D124Y	ENST00000359303	NM_003535.2	124	Gac/Tac	1/1	0.327175003942049	4	FACETS	0.85	0.757	0.949	0.85	0.757	0.949	CLONAL	2	TRUE	2	0.327175003942049	4		490	415	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005245	150005245	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047471-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	63	352	0	ENST00000253339.5:c.980G>C	p.Arg327Thr	p.R327T	ENST00000253339		327	aGa/aCa	3/7	0.327175003942049	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.327175003942049	4		352	208	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730074	41730074	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs377167564	NA	P-0047471-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	91	423	0	ENST00000242208.4:c.455G>T	p.Arg152Leu	p.R152L	ENST00000242208	NM_002192.2	152	cGt/cTt	3/3	0.327175003942049	4	FACETS	0.939	0.84	1	0.939	0.84	1	CLONAL	2	TRUE	2	0.327175003942049	4		423	393	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29195970	29195970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1172464424	NA	P-0047471-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	129	709	0	ENST00000240100.2:c.628C>T	p.His210Tyr	p.H210Y	ENST00000240100	NM_001394.6	210	Cat/Tat	3/4	0.327175003942049	3	FACETS	0.881	0.803	0.962	0.881	0.803	0.962	CLONAL	2	TRUE	1	0.327175003942049	3		709	521	SUCCESS
ATR	545	MSKCC	GRCh37	3	142253951	142253951	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	16	358	0	ENST00000350721.4:c.3916A>C	p.Ser1306Arg	p.S1306R	ENST00000350721	NM_001184.3	1306	Agc/Cgc	21/47	1	2	FACETS	1	0.818	1	1	0.951	1	CLONAL	5	FALSE	1	0.126867207209232	2		358	47	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366803	40366803	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	26	853	0	ENST00000397332.2:c.394del	p.Arg132GlyfsTer8	p.R132Gfs*8	ENST00000397332	NM_001033082.2	132	Cgg/gg	2/3	1	2	FACETS	0.967	0.782	1	1	0.967	1	CLONAL	4	FALSE	1	0.126867207209232	2		853	106	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615592	43615592	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs75234356	NA	P-0047484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	59	636	0	ENST00000355710.3:c.2671T>G	p.Ser891Ala	p.S891A	ENST00000355710	NM_020975.4	891	Tcg/Gcg	15/20	0.126867207209232	12	FACETS	1	0.912	1	1	0.98	1	CLONAL	12	FALSE	5	0.126867207209232	12		636	123	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0047486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	197	664	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.243040008418198	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.28	2		664	677	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098950	178098950	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	78	283	0	ENST00000397062.3:c.95T>G	p.Val32Gly	p.V32G	ENST00000397062	NM_006164.4	32	gTa/gGa	2/5	0.299219706007928	3	FACETS	1	0.949	1			1	CLONAL	2	TRUE	NA	0.28	3		283	283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576851	7576851	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0047486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	100	501	0	ENST00000269305.4:c.993+2T>C		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.284928850974325	2	FACETS	0.873	0.785	0.965	0.873	0.785	0.965	CLONAL	2	TRUE	0	0.28	2		501	409	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023183	150023183	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	94	441	0	ENST00000253339.5:c.80G>T	p.Ser27Ile	p.S27I	ENST00000253339		27	aGc/aTc	1/7	0.227890416035942	3	FACETS	1	0.915	1	0.682	0.612	0.756	CLONAL	2	TRUE	0	0.28	3		441	374	SUCCESS
AR	367	MSKCC	GRCh37	X	66766462	66766462	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	99	509	1	ENST00000374690.3:c.1474G>T	p.Gly492Cys	p.G492C	ENST00000374690	NM_000044.3	492	Ggc/Tgc	1/8	0.178380927704568	3	FACETS	1	0.981	1	0.733	0.656	0.814	CLONAL	1	TRUE	1	0.28	3		510	550	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937996	76937996	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	82	508	0	ENST00000373344.5:c.2752A>T	p.Thr918Ser	p.T918S	ENST00000373344	NM_000489.3	918	Act/Tct	9/35	0.178380927704568	3	FACETS	1	0.968	1	0.638	0.564	0.718	CLONAL	1	TRUE	1	0.28	3		508	523	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0047488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	57	396	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.154234348566743	2	FACETS	1	0.965	1	0.709	0.611	0.816	CLONAL	1	TRUE	0	0.21088894875818	2		396	381	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612623	228612623	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	25	580	0	ENST00000366696.1:c.404G>T	p.Arg135Leu	p.R135L	ENST00000366696	NM_003493.2	135	cGg/cTg	1/1	0.199242842410857	3	FACETS	0.633	0.498	0.788	0.317	0.249	0.394	SUBCLONAL	1	TRUE	1	0.21088894875818	3		580	414	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236117	108236117	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	86	458	2	ENST00000278616.4:c.9053A>T	p.Lys3018Ile	p.K3018I	ENST00000278616	NM_000051.3	3018	aAa/aTa	63/63	0.154234348566743	2	FACETS	0.89	0.791	0.996	0.89	0.791	0.996	CLONAL	2	TRUE	0	0.21088894875818	2		460	458	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108074	30108074	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0047488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	75	513	0	ENST00000331968.5:c.733A>T	p.Lys245Ter	p.K245*	ENST00000331968	NM_002742.2	245	Aag/Tag	5/18	0.21088894875818	3	FACETS	1	0.972	1	0.702	0.616	0.794	CLONAL	1	TRUE	1	0.21088894875818	3		513	560	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043477	180043477	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	56	680	0	ENST00000261937.6:c.3109G>C	p.Asp1037His	p.D1037H	ENST00000261937	NM_182925.4	1037	Gac/Cac	23/30	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.21088894875818	2		680	380	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004558	150004558	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	24	669	2	ENST00000253339.5:c.1667C>T	p.Pro556Leu	p.P556L	ENST00000253339		556	cCa/cTa	3/7	1	2	FACETS	0.477	0.373	0.598	0.477	0.373	0.598	SUBCLONAL	1	TRUE	1	0.21088894875818	2		671	477	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111495	8111496	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGGA	novel	NA	P-0047489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	30	610	0	ENST00000346208.3:c.982_985dup	p.Arg329MetfsTer24	p.R329Mfs*24	ENST00000346208		327	-/TGGA	5/6	0.212722327946416	1	FACETS	0.568	0.457	0.694	0.568	0.457	0.694	SUBCLONAL	1	FALSE	0	0.212722327946416	1		610	444	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577176	64577177	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTTG	novel	NA	P-0047489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	35	878	0	ENST00000312049.6:c.402_405dup	p.Asp136GlnfsTer45	p.D136Qfs*45	ENST00000312049	NM_130799.2	135	-/CAAG	2/10	0.212722327946416	1	FACETS	0.609	0.498	0.733	0.609	0.498	0.733	SUBCLONAL	1	FALSE	0	0.212722327946416	1		878	483	SUCCESS
ALK	238	MSKCC	GRCh37	2	29541222	29541222	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	19	558	1	ENST00000389048.3:c.1595C>A	p.Ala532Asp	p.A532D	ENST00000389048	NM_004304.4	532	gCt/gAt	8/29	1	2	FACETS	0.672	0.51	0.861	0.672	0.51	0.861	SUBCLONAL	1	FALSE	1	0.212722327946416	2		559	266	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	26	279	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	0.141331130604489	3	FACETS	0.876	0.696	1	0.438	0.348	0.54	INDETERMINATE	1	FALSE	1	0.274536095321475	3		279	246	SUCCESS
APC	324	MSKCC	GRCh37	5	112116601	112116601	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs863225370	NA	P-0047490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	32	255	0	ENST00000257430.4:c.645+1G>A		p.X215_splice	ENST00000257430	NM_000038.5	215			0.141331130604489	3	FACETS	1	0.885	1	0.559	0.457	0.674	INDETERMINATE	1	FALSE	1	0.274536095321475	3		255	237	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261773	16261773	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	34	518	0	ENST00000375759.3:c.9038T>C	p.Val3013Ala	p.V3013A	ENST00000375759	NM_015001.2	3013	gTc/gCc	11/15	1	2	FACETS	0.477	0.389	0.577	0.477	0.389	0.577	SUBCLONAL	1	FALSE	1	0.274536095321475	2		518	519	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118865	70118865	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	132	585	0	ENST00000245479.2:c.437T>G	p.Leu146Arg	p.L146R	ENST00000245479	NM_000346.3	146	cTg/cGg	2/3	0.177846305831073	3	FACETS	1	0.945	1	0.698	0.637	0.762	CLONAL	2	FALSE	0	0.274536095321475	3		585	522	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483982	212483982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	21	367	0	ENST00000342788.4:c.2221G>T	p.Gly741Ter	p.G741*	ENST00000342788	NM_005235.2	741	Gga/Tga	19/28	0.141331130604489	3	FACETS	0.526	0.404	0.667	0.263	0.202	0.334	INDETERMINATE	1	FALSE	1	0.274536095321475	3		367	331	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739028	40739028	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757894088	NA	P-0047490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	35	621	0	ENST00000373198.4:c.3256C>T	p.Arg1086Cys	p.R1086C	ENST00000373198	NM_133170.3	1086	Cgc/Tgc	24/32	1	2	FACETS	0.461	0.377	0.556	0.461	0.377	0.556	SUBCLONAL	1	FALSE	1	0.274536095321475	2		621	553	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946234	55946234	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	43	379	0	ENST00000263923.4:c.3945C>A	p.Asp1315Glu	p.D1315E	ENST00000263923	NM_002253.2	1315	gaC/gaA	30/30	1	2	FACETS	0.684	0.573	0.807	0.684	0.573	0.807	SUBCLONAL	1	FALSE	1	0.274536095321475	2		379	458	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456600	32456600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	27	277	1	ENST00000332351.3:c.292G>A	p.Gly98Ser	p.G98S	ENST00000332351	NM_024426.4	98	Ggc/Agc	1/10	1	2	FACETS	0.459	0.365	0.566	0.459	0.365	0.566	SUBCLONAL	1	TRUE	1	0.33316399485914	2		278	353	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106331	27106331	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	295	682	0	ENST00000324856.7:c.5942G>A	p.Cys1981Tyr	p.C1981Y	ENST00000324856	NM_006015.4	1981	tGc/tAc	20/20	0.33316399485914	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.33316399485914	2		682	805	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273543	38273543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	164	651	0	ENST00000425967.3:c.1792G>A	p.Gly598Ser	p.G598S	ENST00000425967	NM_001174067.1	598	Ggc/Agc	14/19	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.33316399485914	2		651	806	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220409	123220409	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	42	429	0	ENST00000218089.9:c.3066G>T	p.Leu1022Phe	p.L1022F	ENST00000218089	NM_001042749.1	1022	ttG/ttT	30/35	NA	2	FACETS	0.448	0.373	0.531			1	INDETERMINATE	1	TRUE	NA	0.33316399485914	2		429	563	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0047493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	41	272	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.832	0.694	0.984	0.832	0.694	0.984	CLONAL	1	TRUE	1	0.254807278827874	2		272	387	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588751	29588751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760703505	NA	P-0047493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	108	322	0	ENST00000356175.3:c.4537C>T	p.Arg1513Ter	p.R1513*	ENST00000356175	NM_000267.3	1513	Cga/Tga	34/57	1	2	FACETS	1	0.971	1	1	0.99	1	CLONAL	2	TRUE	1	0.254807278827874	2		322	358	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805473	1805473	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188723332	NA	P-0047493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	112	951	2	ENST00000260795.2:c.985G>A	p.Val329Ile	p.V329I	ENST00000260795		329	Gtc/Atc	7/17	1	2	FACETS	0.947	0.851	1	0.947	0.851	1	CLONAL	1	TRUE	1	0.254807278827874	2		953	928	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032206	26032206	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	134	379	0	ENST00000244661.2:c.83A>T	p.Lys28Met	p.K28M	ENST00000244661	NM_003537.3	28	aAg/aTg	1/1	1	2	FACETS	0.901	0.828	0.977	1	0.992	1	CLONAL	3	TRUE	1	0.254807278827874	2		379	389	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665107	29665107	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0047493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	201	657	0	ENST00000356175.3:c.6706A>T	p.Lys2236Ter	p.K2236*	ENST00000356175	NM_000267.3	2236	Aaa/Taa	44/57	1	2	FACETS	0.931	0.869	0.994	1	0.995	1	CLONAL	3	TRUE	1	0.254807278827874	2		657	565	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032186	26032186	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	145	369	0	ENST00000244661.2:c.103G>C	p.Gly35Arg	p.G35R	ENST00000244661	NM_003537.3	35	Ggc/Cgc	1/1	1	2	FACETS	0.953	0.879	1	1	0.993	1	CLONAL	3	TRUE	1	0.254807278827874	2		369	398	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829825	76829825	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0047493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	118	252	1	ENST00000373344.5:c.6218-2A>G		p.X2073_splice	ENST00000373344	NM_000489.3	2073			1	1	FACETS	1	0.967	1	1	0.993	1	CLONAL	5	TRUE	0	0.254807278827874	1		253	156	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	97	797	0	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.261839367041218	1	FACETS	0.825	0.736	0.919	0.825	0.736	0.919	CLONAL	1	TRUE	0	0.308339217126621	1		797	645	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43700174	43700174	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	29	578	0	ENST00000382044.4:c.5713G>C	p.Val1905Leu	p.V1905L	ENST00000382044	NM_001141980.1	1905	Gtg/Ctg	27/28	1	2	FACETS	0.394	0.316	0.484	0.394	0.316	0.484	SUBCLONAL	1	TRUE	1	0.308339217126621	2		578	477	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974404	93974404	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	31	427	0	ENST00000369303.4:c.1650T>G	p.Ser550Arg	p.S550R	ENST00000369303	NM_004440.3	550	agT/agG	8/17	0.261839367041218	1	FACETS	0.649	0.527	0.786	0.649	0.527	0.786	SUBCLONAL	1	TRUE	0	0.308339217126621	1		427	262	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44896923	44896923	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	39	265	0	ENST00000377967.4:c.643T>A	p.Tyr215Asn	p.Y215N	ENST00000377967	NM_021140.2	215	Tat/Aat	8/29	0.253778921629544	0	FACETS	0.741	0.619	0.875			1	SUBCLONAL	1	TRUE	NA	0.308339217126621	0		265	236	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	142	575	3	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	0.209971393800247	5	FACETS	1	0.982	1	0.44	0.4	0.481	INDETERMINATE	1	TRUE	2	0.390973756035716	5		578	874	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0047495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	348	715	1	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.271879855759511	3	FACETS	1	0.989	1	0.761	0.723	0.8	CLONAL	2	TRUE	0	0.390973756035716	3		716	932	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992526	72992526	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	57	894	0	ENST00000268489.5:c.1519C>G	p.Pro507Ala	p.P507A	ENST00000268489	NM_006885.3	507	Ccc/Gcc	2/10	0.173582993628592	4	FACETS	0.36	0.307	0.417	0.18	0.153	0.209	INDETERMINATE	1	TRUE	2	0.390973756035716	4		894	1128	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409934	139409934	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0047495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	83	837	0	ENST00000277541.6:c.1903+1G>T		p.X635_splice	ENST00000277541	NM_017617.3	635			0.346489590849701	4	FACETS	0.529	0.465	0.597			1	SUBCLONAL	1	TRUE	NA	0.390973756035716	4		837	1117	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222632	53222632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782413552	NA	P-0047495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	105	443	1	ENST00000375401.3:c.4304G>A	p.Arg1435His	p.R1435H	ENST00000375401	NM_004187.3	1435	cGc/cAc	25/26	0.247306810465591	2	FACETS	0.858	0.77	0.951			1	CLONAL	1	TRUE	NA	0.390973756035716	2		444	626	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	588	349	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.267690936348701	9	FACETS	1	0.989	1			1	CLONAL	8	TRUE	NA	0.267690936348701	9		349	1014	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961399	41961399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748756129	NA	P-0047496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	71	457	1	ENST00000219905.7:c.307C>T	p.Arg103Cys	p.R103C	ENST00000219905	NM_001164273.1	103	Cgc/Tgc	2/24	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.267690936348701	2		458	461	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347811	70347811	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	69	614	0	ENST00000374080.3:c.3050G>T	p.Trp1017Leu	p.W1017L	ENST00000374080		1017	tGg/tTg	22/45	1	2	FACETS	0.821	0.715	0.935	0.821	0.715	0.935	CLONAL	1	TRUE	1	0.267690936348701	2		614	628	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998388	100998388	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	47	203	0	ENST00000325455.5:c.1414C>A	p.Gln472Lys	p.Q472K	ENST00000325455	NM_001202474.3	472	Cag/Aag	1/8	1	2	FACETS	0.891	0.762	1	1	0.971	1	CLONAL	2	TRUE	1	0.267690936348701	2		203	197	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061517	38061519	+	inframe_deletion	In_Frame_Del	DEL	CGC	CGC	-	novel	NA	P-0047496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	61	504	3	ENST00000250448.2:c.470_472del	p.Gly157del	p.G157del	ENST00000250448	NM_004496.3	157	gGCGac/gac	2/2	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.267690936348701	2		507	433	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058498	42058498	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	52	402	0	ENST00000219905.7:c.8218C>G	p.Gln2740Glu	p.Q2740E	ENST00000219905	NM_001164273.1	2740	Caa/Gaa	24/24	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.267690936348701	2		402	383	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467556	66467556	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	48	333	0	ENST00000273854.3:c.713G>T	p.Arg238Leu	p.R238L	ENST00000273854	NM_004439.5	238	cGa/cTa	3/18	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.267690936348701	2		333	353	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509993	187509993	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	81	467	0	ENST00000441802.2:c.13520G>T	p.Gly4507Val	p.G4507V	ENST00000441802	NM_005245.3	4507	gGt/gTt	27/27	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.267690936348701	2		467	439	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946168	13946168	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573599843	NA	P-0047496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	96	641	0	ENST00000405192.2:c.928G>A	p.Gly310Arg	p.G310R	ENST00000405192	NM_001163147.1	310	Gga/Aga	10/12	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.267690936348701	2		641	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0047498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	831	634	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.759373837642827	3	FACETS	0.988	0.97	1	0.988	0.97	1	CLONAL	3	TRUE	0	0.76183608640512	3		634	1016	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338656	70338656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	233	702	1	ENST00000374080.3:c.52C>T	p.Arg18Trp	p.R18W	ENST00000374080		18	Cgg/Tgg	1/45	0.317017573440201	5	FACETS	1	0.982	1	0.384	0.357	0.411	INDETERMINATE	1	TRUE	2	0.76183608640512	5		703	1139	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249510	153249510	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1157879635	NA	P-0047498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	234	541	0	ENST00000281708.4:c.1268G>T	p.Gly423Val	p.G423V	ENST00000281708	NM_033632.3	423	gGa/gTa	9/12	0.730970153623025	3	FACETS	0.924	0.874	0.974	0.924	0.874	0.974	CLONAL	2	TRUE	1	0.76183608640512	3		541	459	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054650	13054658	+	inframe_deletion	In_Frame_Del	DEL	GAGGATGAG	GAGGATGAG	-	rs550353351	NA	P-0047498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	137	603	0	ENST00000316448.5:c.1191_1199del	p.Glu398_Asp400del	p.E398_D400del	ENST00000316448	NM_004343.3	393	GAGGATGAG/-	9/9	0.76183608640512	3	FACETS	0.661	0.602	0.723	0.331	0.301	0.362	SUBCLONAL	1	TRUE	1	0.76183608640512	3		603	751	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456363	32456363	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1467	550	892	0	ENST00000332351.3:c.529T>G	p.Tyr177Asp	p.Y177D	ENST00000332351	NM_024426.4	177	Tac/Gac	1/10	0.548249680401014	6	FACETS	0.903	0.864	0.943			1	CLONAL	2	TRUE	NA	0.76183608640512	6		892	2017	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591075	67591075	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0047498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	70	246	0	ENST00000274335.5:c.1668T>G	p.Tyr556Ter	p.Y556*	ENST00000274335		556	taT/taG	12/15	0.730970153623025	3	FACETS	1	0.908	1	0.516	0.455	0.579	CLONAL	1	TRUE	1	0.76183608640512	3		246	246	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591131	67591142	+	inframe_deletion	In_Frame_Del	DEL	AGACGAGAGACC	AGACGAGAGACC	-	novel	NA	P-0047498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	125	287	0	ENST00000274335.5:c.1725_1736del	p.Thr576_Gln579del	p.T576_Q579del	ENST00000274335		575	aAGACGAGAGACCaa/aaa	12/15	0.730970153623025	3	FACETS	0.871	0.805	0.938	0.871	0.805	0.938	CLONAL	2	TRUE	1	0.76183608640512	3		287	260	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577205	64577205	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	144	823	0	ENST00000312049.6:c.377G>A	p.Trp126Ter	p.W126*	ENST00000312049	NM_130799.2	126	tGg/tAg	2/10	0.569485600401899	1	FACETS	0.526	0.48	0.573	0.526	0.48	0.573	SUBCLONAL	1	TRUE	0	0.569485600401899	1		823	688	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875981	76875984	+	frameshift_variant	Frame_Shift_Del	DEL	ACAA	ACAA	-	novel	NA	P-0047499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	26	171	0	ENST00000373344.5:c.5151_5154del	p.Cys1718MetfsTer6	p.C1718Mfs*6	ENST00000373344	NM_000489.3	1717	gtTTGT/gt	20/35	1	1	FACETS	0.228	0.181	0.282	0.228	0.181	0.282	SUBCLONAL	1	TRUE	0	0.569485600401899	1		171	286	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161751	47161751	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	55	346	0	ENST00000409792.3:c.4375C>T	p.Arg1459Ter	p.R1459*	ENST00000409792	NM_014159.6	1459	Cga/Tga	3/21	0.569485600401899	1	FACETS	0.365	0.313	0.421	0.365	0.313	0.421	SUBCLONAL	1	TRUE	0	0.569485600401899	1		346	379	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982975	201982982	+	frameshift_variant	Frame_Shift_Del	DEL	TGTGGGAG	TGTGGGAG	-	novel	NA	P-0047499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	172	815	0	ENST00000359651.3:c.825_832del	p.Trp276HisfsTer22	p.W276Hfs*22	ENST00000359651		275	cTGTGGGAG/c	7/8	0.569485600401899	1	FACETS	0.668	0.617	0.72	0.668	0.617	0.72	SUBCLONAL	1	TRUE	0	0.569485600401899	1		815	647	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572212	64572242	+	frameshift_variant	Frame_Shift_Del	DEL	CGGGCTTCCTCGCCCCACGGCTCCTCGGCCT	CGGGCTTCCTCGCCCCACGGCTCCTCGGCCT	-	novel	NA	P-0047499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	54	701	0	ENST00000312049.6:c.1397_1427del	p.Glu466GlyfsTer83	p.E466Gfs*83	ENST00000312049	NM_130799.2	466	gAGGCCGAGGAGCCGTGGGGCGAGGAAGCCCGg/gg	10/10	0.569485600401899	1	FACETS	0.255	0.218	0.296	0.255	0.218	0.296	SUBCLONAL	1	TRUE	0	0.569485600401899	1		701	531	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577298	64577305	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGTGAA	GCGGTGAA	-	novel	NA	P-0047499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	46	861	0	ENST00000312049.6:c.277_284del	p.Phe93ProfsTer21	p.F93Pfs*21	ENST00000312049	NM_130799.2	93	TTCACCGCc/c	2/10	0.569485600401899	1	FACETS	0.195	0.164	0.229	0.195	0.164	0.229	SUBCLONAL	1	TRUE	0	0.569485600401899	1		861	593	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891468	76891484	+	frameshift_variant	Frame_Shift_Del	DEL	TTGGTTTCTTCATCTTC	TTGGTTTCTTCATCTTC	-	novel	NA	P-0047499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	144	346	0	ENST00000373344.5:c.4621_4637del	p.Glu1541ArgfsTer8	p.E1541Rfs*8	ENST00000373344	NM_000489.3	1541	GAAGATGAAGAAACCAAa/a	16/35	1	1	FACETS	0.87	0.801	0.94	0.87	0.801	0.94	CLONAL	1	TRUE	0	0.569485600401899	1		346	416	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0047500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	48	396	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.462	0.39	0.541	0.462	0.39	0.541	SUBCLONAL	1	TRUE	1	0.37	2		396	562	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120502076	120502076	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047500-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	27	455	0	ENST00000256646.2:c.1965C>G	p.Ile655Met	p.I655M	ENST00000256646	NM_024408.3	655	atC/atG	12/34	1	2	FACETS	0.281	0.223	0.347	0.281	0.223	0.347	SUBCLONAL	1	TRUE	1	0.37	2		455	520	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057988	27057988	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	156	732	0	ENST00000324856.7:c.1696C>T	p.Gln566Ter	p.Q566*	ENST00000324856	NM_006015.4	566	Cag/Tag	3/20	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.341987859903735	2		732	902	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197187	26197187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	114	594	0	ENST00000356476.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000356476		98	Gag/Aag	1/1	1	2	FACETS	0.988	0.891	1	0.988	0.891	1	CLONAL	1	TRUE	1	0.341987859903735	2		594	675	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953090	38953090	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	31	210	0	ENST00000357387.3:c.2894G>A	p.Arg965Lys	p.R965K	ENST00000357387	NM_152756.3	965	aGa/aAa	29/38	0.314405176903128	3	FACETS	0.807	0.656	0.977	0.404	0.328	0.489	CLONAL	1	TRUE	1	0.341987859903735	3		210	263	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519920	NA	P-0047504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	85	314	1	ENST00000397062.3:c.85G>T	p.Asp29Tyr	p.D29Y	ENST00000397062	NM_006164.4	29	Gat/Tat	2/5	1	2	FACETS	0.869	0.771	0.972	0.869	0.771	0.972	CLONAL	1	TRUE	1	0.430196728735586	2		315	455	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989060	41989060	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	154	468	0	ENST00000219905.7:c.1852C>T	p.Arg618Ter	p.R618*	ENST00000219905	NM_001164273.1	618	Cga/Tga	3/24	1	2	FACETS	0.921	0.844	1	0.921	0.844	1	CLONAL	1	TRUE	1	0.430196728735586	2		468	777	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106237	27106237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1003835206	NA	P-0047505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	202	544	1	ENST00000324856.7:c.5848C>T	p.Arg1950Trp	p.R1950W	ENST00000324856	NM_006015.4	1950	Cgg/Tgg	20/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		545	883	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579874	7579875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1555527002	NA	P-0047505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	266	653	0	ENST00000269305.4:c.38dup	p.Leu14SerfsTer15	p.L14Sfs*15	ENST00000269305	NM_001126112.2	13	cct/ccCt	2/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		653	808	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098423	11098423	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs549254467	NA	P-0047505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	238	491	1	ENST00000358026.2:c.941C>T	p.Ala314Val	p.A314V	ENST00000358026	NM_001128849.1	314	gCg/gTg	6/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		492	839	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568668	41568668	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0047505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	202	272	0	ENST00000263253.7:c.4617+1G>C		p.X1539_splice	ENST00000263253	NM_001429.3	1539			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		272	420	SUCCESS
MET	4233	MSKCC	GRCh37	7	116422151	116422151	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	125	300	0	ENST00000397752.3:c.3632T>C	p.Met1211Thr	p.M1211T	ENST00000397752	NM_000245.2	1211	aTg/aCg	18/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		300	533	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413894	139413894	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0047505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	165	567	0	ENST00000277541.6:c.865+1G>A		p.X289_splice	ENST00000277541	NM_017617.3	289			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		567	790	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0047506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	196	834	1	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	1	2	FACETS	0.919	0.855	0.985	0.919	0.855	0.985	CLONAL	1	TRUE	1	0.66	2		835	646	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253753	153253754	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	106	334	0	ENST00000281708.4:c.979_980insT	p.Glu327ValfsTer5	p.E327Vfs*5	ENST00000281708	NM_033632.3	327	gaa/gTaa	6/12	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.66	2		334	320	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44896907	44896917	+	frameshift_variant	Frame_Shift_Del	DEL	TCACATTGCCC	TCACATTGCCC	-	novel	NA	P-0047506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	98	534	0	ENST00000377967.4:c.627_637del	p.Phe209LeufsTer4	p.F209Lfs*4	ENST00000377967	NM_021140.2	209	ttTCACATTGCCCac/ttac	8/29	1	2	FACETS	0.733	0.659	0.811	0.733	0.659	0.811	SUBCLONAL	1	TRUE	1	0.66	2		534	405	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402602	20402602	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	129	584	0	ENST00000346618.3:c.139G>C	p.Ala47Pro	p.A47P	ENST00000346618	NM_001949.4	47	Gcc/Ccc	1/7	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.414579318716432	2		584	581	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061136	38061202	+	frameshift_variant	Frame_Shift_Del	DEL	TGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTG	TGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGCTTCTG	-	novel	NA	P-0047509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	424	310	0	ENST00000250448.2:c.787_853del	p.Gln263AlafsTer36	p.Q263Afs*36	ENST00000250448	NM_004496.3	263	CAGAAGCGCTTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAgc/gc	2/2	0.478142823059625	12	FACETS	1	0.985	1			1	CLONAL	11	FALSE	NA	0.478142823059625	12		310	536	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649080	37649082	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	novel	NA	P-0047509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	44	453	0	ENST00000447079.4:c.2188_2190del	p.Ile730del	p.I730del	ENST00000447079	NM_015083.1	729	ATT/-	4/14	0.18231832953668	3	FACETS	0.884	0.759	1	0.884	0.759	1	INDETERMINATE	2	FALSE	1	0.478142823059625	3		453	129	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099247	4099247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	37	823	1	ENST00000262948.5:c.871C>T	p.Pro291Ser	p.P291S	ENST00000262948	NM_030662.3	291	Cct/Tct	7/11	0.131140056449513	5	FACETS	0.898	0.743	1	0.299	0.247	0.357	INDETERMINATE	1	FALSE	2	0.478142823059625	5		824	296	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619352	37619354	+	frameshift_variant	Frame_Shift_Del	DEL	GTC	GTC	A	novel	NA	P-0047509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	60	389	1	ENST00000447079.4:c.1028_1030delinsA	p.Ser343LysfsTer7	p.S343Kfs*7	ENST00000447079	NM_015083.1	343	aGTCgg/aAgg	1/14	0.18231832953668	3	FACETS	1	0.967	1	0.682	0.595	0.774	INDETERMINATE	1	FALSE	1	0.478142823059625	3		390	228	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0047510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	65	277	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	FALSE	1	0.201023521880604	2		277	611	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0047510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	92	685	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.188761610455005	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	FALSE	0	0.201023521880604	1		685	739	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0047511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	210	349	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.320677229825459	3	FACETS	0.931	0.871	0.992	0.931	0.871	0.992	CLONAL	2	TRUE	1	0.498931116950429	3		349	565	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976873	55976873	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	250	654	0	ENST00000263923.4:c.1039C>A	p.Arg347Ser	p.R347S	ENST00000263923	NM_002253.2	347	Cgt/Agt	8/30	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.498931116950429	2		654	855	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370818	225370818	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs983814335	NA	P-0047511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	66	432	0	ENST00000264414.4:c.1061G>T	p.Arg354Leu	p.R354L	ENST00000264414	NM_003590.4	354	cGc/cTc	8/16	1	2	FACETS	0.501	0.435	0.572	0.501	0.435	0.572	SUBCLONAL	1	TRUE	1	0.498931116950429	2		432	528	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470597	25470597	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	237	772	0	ENST00000264709.3:c.877G>T	p.Gly293Trp	p.G293W	ENST00000264709	NM_175629.2	293	Ggg/Tgg	8/23	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.498931116950429	2		772	827	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740163	162740163	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	116	575	0	ENST00000367921.3:c.1365C>A	p.Asn455Lys	p.N455K	ENST00000367921	NM_006182.2	455	aaC/aaA	12/18	1	2	FACETS	0.61	0.55	0.674	0.61	0.55	0.674	SUBCLONAL	1	TRUE	1	0.498931116950429	2		575	762	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857437	9857437	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1555482135	NA	P-0047511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	165	619	0	ENST00000330684.3:c.3964G>T	p.Gly1322Ter	p.G1322*	ENST00000330684	NM_001134407.1	1322	Gga/Tga	13/13	0.498931116950429	3	FACETS	0.958	0.88	1	0.479	0.44	0.52	CLONAL	1	TRUE	1	0.498931116950429	3		619	863	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857958	9857958	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs140536516	NA	P-0047511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	515	719	0	ENST00000330684.3:c.3443C>A	p.Pro1148Gln	p.P1148Q	ENST00000330684	NM_001134407.1	1148	cCg/cAg	13/13	0.498931116950429	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	1	0.498931116950429	3		719	1050	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299832	15299832	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	194	895	0	ENST00000263388.2:c.1346G>T	p.Arg449Leu	p.R449L	ENST00000263388	NM_000435.2	449	cGc/cTc	8/33	0.383536710578259	0	FACETS	0.527	0.489	0.567			1	SUBCLONAL	1	TRUE	0	0.498931116950429	0		895	739	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156648	55156648	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	230	540	0	ENST00000257290.5:c.3049G>T	p.Gly1017Cys	p.G1017C	ENST00000257290	NM_006206.4	1017	Ggc/Tgc	22/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.498931116950429	2		540	779	SUCCESS
APC	324	MSKCC	GRCh37	5	112177495	112177495	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554087277	NA	P-0047511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	109	355	0	ENST00000257430.4:c.6204G>T	p.Met2068Ile	p.M2068I	ENST00000257430	NM_000038.5	2068	atG/atT	16/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.498931116950429	2		355	362	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150548	157150548	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	205	547	0	ENST00000346085.5:c.1730A>T	p.Gln577Leu	p.Q577L	ENST00000346085	NM_020732.3	577	cAg/cTg	2/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.498931116950429	2		547	626	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030493	47030496	+	frameshift_variant	Frame_Shift_Del	DEL	CCCA	CCCA	-	novel	NA	P-0047511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	259	846	0	ENST00000377604.3:c.270_273del	p.Thr91AlafsTer42	p.T91Afs*42	ENST00000377604	NM_001204468.1	90	CCCAcc/cc	4/24	0.498931116950429	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.498931116950429	1		846	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579707	7579707	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	74	771	0	ENST00000269305.4:c.89del	p.Asn30ThrfsTer14	p.N30Tfs*14	ENST00000269305	NM_001126112.2	30	aAc/ac	3/11	1	2	FACETS	0.805	0.704	0.915	0.805	0.704	0.915	CLONAL	1	TRUE	1	0.23	2		771	799	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630804	187630804	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	48	736	0	ENST00000441802.2:c.178G>A	p.Gly60Ser	p.G60S	ENST00000441802	NM_005245.3	60	Ggt/Agt	2/27	1	2	FACETS	0.628	0.53	0.736	0.628	0.53	0.736	SUBCLONAL	1	TRUE	1	0.23	2		736	665	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0047514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	95	277	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.267944100331939	3	FACETS	0.929	0.832	1	0.929	0.832	1	CLONAL	2	TRUE	1	0.267944100331939	3		277	433	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042266	6042266	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs587781913	NA	P-0047514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	43	566	0	ENST00000265849.7:c.355G>A	p.Asp119Asn	p.D119N	ENST00000265849	NM_000535.5	119	Gat/Aat	5/15	0.249753134295444	4	FACETS	0.526	0.439	0.624	0.263	0.219	0.312	SUBCLONAL	1	TRUE	2	0.267944100331939	4		566	773	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577059	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0047514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	288	972	0	ENST00000269305.4:c.879_880del	p.Glu294AlafsTer11	p.E294Afs*11	ENST00000269305	NM_001126112.2	293	ggGGag/ggag	8/11	0.267944100331939	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.267944100331939	2		972	1045	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404545	8404545	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	50	266	0	ENST00000356435.5:c.4202C>G	p.Ala1401Gly	p.A1401G	ENST00000356435		1401	gCt/gGt	25/35	0.267944100331939	2	FACETS	0.998	0.86	1	0.998	0.86	1	CLONAL	2	TRUE	0	0.267944100331939	2		266	187	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974701	21974876	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	ATTCGGTGCGTTGGGCAGCGCCCCCGCCTCCAGCAGCGCCCGCACCTCCTCTACCCGACCCCGGGCCGCGGCCGTGGCCAGCCAGTCAGCCGAAGGCTCCATGCTGCTCCCCGCCGCCGGCTCCATGCTGCTCCCCGCCGCCCGCTGCCTGCTCTCCCCCTCTCCGCAGCCGCCGA	ATTCGGTGCGTTGGGCAGCGCCCCCGCCTCCAGCAGCGCCCGCACCTCCTCTACCCGACCCCGGGCCGCGGCCGTGGCCAGCCAGTCAGCCGAAGGCTCCATGCTGCTCCCCGCCGCCGGCTCCATGCTGCTCCCCGCCGCCCGCTGCCTGCTCTCCCCCTCTCCGCAGCCGCCGA	-	novel	NA	P-0047514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	186	560	0	ENST00000304494.5:c.-50_126del		p.*17*	ENST00000304494	NM_000077.4	?-42/156		1/3	0.267944100331939	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.267944100331939	2		560	643	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420618	49420618	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	191	646	0	ENST00000301067.7:c.15131A>T	p.Asp5044Val	p.D5044V	ENST00000301067	NM_003482.3	5044	gAt/gTt	48/54	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.424567564605467	2		646	865	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0047541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	107	280	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.765259132922559	1	FACETS	0.918	0.849	0.987	0.918	0.849	0.987	CLONAL	1	TRUE	0	0.765259132922559	1		280	188	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922123	39922124	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0047541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	314	349	0	ENST00000378444.4:c.4048_4049insC	p.Tyr1350SerfsTer59	p.Y1350Sfs*59	ENST00000378444	NM_001123385.1	1350	tac/tCac	9/15	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.765259132922559	1		349	386	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0047542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	14	258	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.25254027881437	2		258	81	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178197	56178198	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	20	212	0	ENST00000399503.3:c.3171dup	p.His1058ThrfsTer7	p.H1058Tfs*7	ENST00000399503	NM_005921.1	1057	ata/atAa	14/20	0.25254027881437	1	FACETS	0.954	0.737	1	0.954	0.737	1	CLONAL	1	TRUE	0	0.25254027881437	1		212	145	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0047543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	115	272	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.627761754397958	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.627761754397958	3		272	216	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879885	37879885	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	222	905	0	ENST00000269571.5:c.2180G>C	p.Gly727Ala	p.G727A	ENST00000269571		727	gGa/gCa	18/27	0.485549379174567	4	FACETS	0.955	0.887	1	0.477	0.443	0.513	CLONAL	1	TRUE	2	0.627761754397958	4		905	1206	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218205	69218205	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs759861388	NA	P-0047543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	99	254	0	ENST00000462284.1:c.421C>G	p.Gln141Glu	p.Q141E	ENST00000462284	NM_002392.5	141	Caa/Gaa	6/11	0.627761754397958	3	FACETS	1	0.933	1	0.525	0.472	0.58	CLONAL	1	TRUE	1	0.627761754397958	3		254	395	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913471	NA	P-0047543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	581	889	0	ENST00000269571.5:c.2329G>C	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ctg	20/27	0.485549379174567	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.627761754397958	4		889	1407	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245733	46245733	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	101	381	0	ENST00000334344.6:c.3827C>A	p.Thr1276Lys	p.T1276K	ENST00000334344	NM_152641.2	1276	aCa/aAa	15/21	0.627761754397958	3	FACETS	1	0.948	1	0.541	0.487	0.597	CLONAL	1	TRUE	1	0.627761754397958	3		381	391	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160565	56160565	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	149	215	0	ENST00000399503.3:c.839A>G	p.Gln280Arg	p.Q280R	ENST00000399503	NM_005921.1	280	cAg/cGg	4/20	0.627761754397958	4	FACETS	0.998	0.935	1	0.998	0.935	1	CLONAL	3	TRUE	1	0.627761754397958	4		215	258	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167802	56167802	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	123	332	0	ENST00000399503.3:c.1368del	p.Thr457GlnfsTer30	p.T457Qfs*30	ENST00000399503	NM_005921.1	456	cTt/ct	7/20	0.627761754397958	4	FACETS	1	0.911	1	0.335	0.303	0.368	CLONAL	1	TRUE	1	0.627761754397958	4		332	635	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569238	67569242	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGA	GCAGA	-	novel	NA	P-0047543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	90	329	1	ENST00000274335.5:c.359_363del	p.Glu120ValfsTer5	p.E120Vfs*5	ENST00000274335		119	GCAGAg/g	2/15	0.627761754397958	4	FACETS	0.823	0.732	0.92	0.274	0.244	0.307	CLONAL	1	TRUE	1	0.627761754397958	4		330	567	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371981	55371981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1472360404	NA	P-0047543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	204	510	0	ENST00000297316.4:c.671C>T	p.Thr224Met	p.T224M	ENST00000297316	NM_022454.3	224	aCg/aTg	2/2	0.627761754397958	3	FACETS	1	0.981	1	0.575	0.535	0.617	CLONAL	1	TRUE	1	0.627761754397958	3		510	742	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0047544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	440	986	4	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.390467209642208	2	FACETS	0.857	0.822	0.892	1	0.995	1	CLONAL	3	TRUE	0	0.382378434089943	2		990	895	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0047544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	74	228	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.382378434089943	5	FACETS	0.797	0.702	0.899	0.531	0.468	0.599	SUBCLONAL	2	TRUE	2	0.382378434089943	5		228	382	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3634797	3634797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765601038	NA	P-0047544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	320	773	0	ENST00000294008.3:c.4712C>T	p.Thr1571Met	p.T1571M	ENST00000294008	NM_032444.2	1571	aCg/aTg	13/15	0.390467209642208	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.382378434089943	3		773	819	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209679	98209679	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	134	880	3	ENST00000331920.6:c.3859C>A	p.His1287Asn	p.H1287N	ENST00000331920	NM_000264.3	1287	Cac/Aac	23/24	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.382378434089943	2		883	610	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0047546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	28	456	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	0.651	0.521	0.798	0.651	0.521	0.798	SUBCLONAL	1	TRUE	1	0.276731842182945	2		456	311	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0047546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	81	389	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.276731842182945	2		389	441	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606709	29606709	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	48	490	0	ENST00000389048.3:c.1171G>C	p.Gly391Arg	p.G391R	ENST00000389048	NM_004304.4	391	Gga/Cga	5/29	1	2	FACETS	0.766	0.648	0.895	0.766	0.648	0.895	SUBCLONAL	1	TRUE	1	0.276731842182945	2		490	453	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0047548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	83	419	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.524257341984716	2		419	307	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0047548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	163	658	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.524257341984716	1	FACETS	0.901	0.833	0.971	0.901	0.833	0.971	CLONAL	1	TRUE	0	0.524257341984716	1		658	509	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0047548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	87	258	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.89	0.794	0.991	0.89	0.794	0.991	CLONAL	1	TRUE	1	0.524257341984716	2		258	373	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11205059	11205059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	257	461	1	ENST00000361445.4:c.4730C>T	p.Ala1577Val	p.A1577V	ENST00000361445	NM_004958.3	1577	gCg/gTg	33/58	0.517118123318757	2	FACETS	0.921	0.872	0.971	0.921	0.872	0.971	CLONAL	2	TRUE	0	0.524257341984716	2		462	532	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375023	45375023	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	61	278	0	ENST00000262160.6:c.820T>C	p.Trp274Arg	p.W274R	ENST00000262160	NM_005901.5	274	Tgg/Cgg	8/11	0.524257341984716	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.524257341984716	1		278	162	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033483	48033483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367912290	NA	P-0047548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	79	330	1	ENST00000234420.5:c.3787C>T	p.Arg1263Cys	p.R1263C	ENST00000234420	NM_000179.2	1263	Cgc/Tgc	8/10	1	2	FACETS	0.979	0.869	1	0.979	0.869	1	CLONAL	1	TRUE	1	0.524257341984716	2		331	308	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651278	52651294	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CTGGGAGCCCTCCTCAT	CTGGGAGCCCTCCTCAT	-	novel	NA	P-0047548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	58	286	0	ENST00000394830.3:c.1802_1818del	p.Asn601SerfsTer3	p.N601Sfs*3	ENST00000394830	NM_018313.4	601	aATGAGGAGGGCTCCCAG/a	15/30	1	2	FACETS	0.802	0.695	0.916	0.802	0.695	0.916	CLONAL	1	TRUE	1	0.524257341984716	2		286	276	SUCCESS
APC	324	MSKCC	GRCh37	5	112175863	112175863	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	80	175	0	ENST00000257430.4:c.4573del	p.Met1525CysfsTer40	p.M1525Cfs*40	ENST00000257430	NM_000038.5	1524	atA/at	16/16	0.524257341984716	2	FACETS	0.936	0.848	1	0.936	0.848	1	CLONAL	2	TRUE	0	0.524257341984716	2		175	163	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829756	76829756	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	89	375	0	ENST00000373344.5:c.6285G>T	p.Arg2095Ser	p.R2095S	ENST00000373344	NM_000489.3	2095	agG/agT	28/35	0.524257341984716	3	FACETS	0.889	0.791	0.993	0.445	0.395	0.497	CLONAL	1	TRUE	1	0.524257341984716	3		375	482	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0047549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	71	456	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	0.8	0.707	0.898	0.8	0.707	0.898	SUBCLONAL	1	TRUE	1	0.682450699327967	2		456	260	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0047549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	174	349	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.682450699327967	2	FACETS	0.924	0.873	0.974	0.924	0.873	0.974	CLONAL	2	TRUE	0	0.682450699327967	2		349	276	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560113	29560113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs370820478	NA	P-0047549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	72	296	0	ENST00000356175.3:c.3590C>G	p.Ala1197Gly	p.A1197G	ENST00000356175	NM_000267.3	1197	gCa/gGa	27/57	0.682450699327967	1	FACETS	0.574	0.509	0.643	0.574	0.509	0.643	SUBCLONAL	1	TRUE	0	0.682450699327967	1		296	242	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0047550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	103	349	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.233475579778834	3	FACETS	1	0.967	1			1	CLONAL	2	TRUE	NA	0.320644750886924	3		349	323	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042235	42042235	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	37	394	1	ENST00000219905.7:c.6430G>T	p.Gly2144Ter	p.G2144*	ENST00000219905	NM_001164273.1	2144	Gga/Tga	17/24	1	2	FACETS	0.774	0.641	0.922	0.774	0.641	0.922	CLONAL	1	TRUE	1	0.320644750886924	2		395	298	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218485	1218486	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0047550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	46	518	0	ENST00000326873.7:c.363_364del	p.Lys122AlafsTer40	p.K122Afs*40	ENST00000326873	NM_000455.4	120	gaAGag/gaag	2/10	0.320644750886924	1	FACETS	0.909	0.771	1	0.909	0.771	1	CLONAL	1	TRUE	0	0.320644750886924	1		518	265	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710653	40710653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	42	442	0	ENST00000373198.4:c.4198G>A	p.Gly1400Arg	p.G1400R	ENST00000373198	NM_133170.3	1400	Ggg/Agg	31/32	1	2	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	1	0.320644750886924	2		442	258	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843293	128843293	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	129	1069	1	ENST00000249373.3:c.400T>A	p.Cys134Ser	p.C134S	ENST00000249373	NM_005631.4	134	Tgt/Agt	2/12	0.183695295206981	3	FACETS	0.808	0.735	0.883	0.808	0.735	0.883	INDETERMINATE	2	TRUE	1	0.320644750886924	3		1070	578	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945121	151945121	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1232843333	NA	P-0047550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	14	384	0	ENST00000262189.6:c.2398T>A	p.Tyr800Asn	p.Y800N	ENST00000262189	NM_170606.2	800	Tac/Aac	14/59	0.183695295206981	3	FACETS	0.502	0.363	0.669	0.251	0.181	0.335	INDETERMINATE	1	TRUE	1	0.320644750886924	3		384	202	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0047551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	142	1080	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.599830392573626	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.599830392573626	1		1080	256	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39251221	39251221	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	19	472	0	ENST00000402219.2:c.1132A>T	p.Thr378Ser	p.T378S	ENST00000402219	NM_005633.3	378	Aca/Tca	9/23	1	2	FACETS	0.946	0.74	1	0.946	0.74	1	CLONAL	1	TRUE	1	0.599830392573626	2		472	67	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281857	49281857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	44	627	0	ENST00000282018.3:c.904C>T	p.Pro302Ser	p.P302S	ENST00000282018	NM_020377.2	302	Cct/Tct	1/1	1	2	FACETS	0.965	0.825	1	0.965	0.825	1	CLONAL	1	TRUE	1	0.599830392573626	2		627	152	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216959	7216968	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCACCACC	AGGCACCACC	-	novel	NA	P-0047551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	73	665	0	ENST00000380728.2:c.553_562del	p.Gly185MetfsTer157	p.G185Mfs*157	ENST00000380728		185	GGTGGTGCCTat/at	7/11	0.599830392573626	1	FACETS	0.921	0.823	1	0.921	0.823	1	CLONAL	1	TRUE	0	0.599830392573626	1		665	185	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227017	2227017	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs370187220	NA	P-0047551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	30	999	0	ENST00000398665.3:c.4497C>G	p.Ser1499Arg	p.S1499R	ENST00000398665	NM_032482.2	1499	agC/agG	27/28	0.599830392573626	1	FACETS	0.313	0.253	0.379	0.313	0.253	0.379	SUBCLONAL	1	TRUE	0	0.599830392573626	1		999	224	SUCCESS
AR	367	MSKCC	GRCh37	X	66905906	66905906	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137852573	NA	P-0047555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	155	388	0	ENST00000374690.3:c.1823G>A	p.Arg608Gln	p.R608Q	ENST00000374690	NM_000044.3	608	cGa/cAa	3/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.66644561646866	2		388	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579529	7579529	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658483	NA	P-0047556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	399	858	0	ENST00000269305.4:c.158G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tGg/tAg	4/11	0.74983769836077	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.80623881358259	1		858	579	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71064764	71065786	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CATAGAGAGGATGGCTATGGGGGTGCTCCTCATGGGACAAACTGAAAGAAAACACACAGAAGACCAGAGAATGAATTTGCTGCCAAGAACCATTCCACCAGACGAGGATAAAAAAGGCAGGAGGAGCCCACATGGCCAAATGTGGACAAGACAAATCTGTGATTTCCCCCATCCCATGTAATTGACTAATTAATTCTGCATTGTTGCCTAAAAGCAAGAGTTAAATTGTACCTAAGTGTATTTAGTCAAATGTTAGAAATGTACATCTATGTATGAAAAAGTGTTTGACAGGCTTTTGTTAGATGCAAAGCTCTTTACTCAGACTGCGAAGGAGTCTTTAAAAAGCTAGAACTTATTTAATCTACATAATGAAAATTATAAAATCTGTACTTGATTTTGAGATTTTCTTGCTACATCTACAAGGAATATTATCCATTTTCTCCTCTTCCCTTCCCCCAGAAACTGCTTTCATATAATCACATATTTTTTCCCAAGTTAATTTTATCCAGCAAAGAGGAGTACAATTAAATAATTTGGAATAATACCAAAATAATTTAGGAAGACAAATGTATCCAAGCAGATGATTCGTGTTTTTTTTAAAAAAGCTAATAATGGCAAGAAGATTATATTCCTAAAATTCCTAACACCAACAGTGAGAGAAAATTTGGCATGAACACGAAGGGGTTAATCCTCCAGTGGGGTTCCAATCAATACGTAATGATCTGGCCACACGGATCCAAGTCATGGGATGCTTTGATCCGCACCATGTGGTGCTCGGGGAAGAGTATCTGTTGCACTCACCGATGAACCATATTCTCAAATATTTTCTCTATTATATTTCTGCATCCAGACTTCTTTCAGACAAATTATTTTTACAGTTGTTTCCATAACCTTAAATTCCATCAGATAGAAATGTAAAGCTAACATTGAGAGTTCTGTTTCGTACTCAAGTGCATTCCCTTCCCGGGAAGGGCTATTTTGCAACTTACTCGACTGTCTCTGCCTGACTTTGAACTTCAAGCA	CATAGAGAGGATGGCTATGGGGGTGCTCCTCATGGGACAAACTGAAAGAAAACACACAGAAGACCAGAGAATGAATTTGCTGCCAAGAACCATTCCACCAGACGAGGATAAAAAAGGCAGGAGGAGCCCACATGGCCAAATGTGGACAAGACAAATCTGTGATTTCCCCCATCCCATGTAATTGACTAATTAATTCTGCATTGTTGCCTAAAAGCAAGAGTTAAATTGTACCTAAGTGTATTTAGTCAAATGTTAGAAATGTACATCTATGTATGAAAAAGTGTTTGACAGGCTTTTGTTAGATGCAAAGCTCTTTACTCAGACTGCGAAGGAGTCTTTAAAAAGCTAGAACTTATTTAATCTACATAATGAAAATTATAAAATCTGTACTTGATTTTGAGATTTTCTTGCTACATCTACAAGGAATATTATCCATTTTCTCCTCTTCCCTTCCCCCAGAAACTGCTTTCATATAATCACATATTTTTTCCCAAGTTAATTTTATCCAGCAAAGAGGAGTACAATTAAATAATTTGGAATAATACCAAAATAATTTAGGAAGACAAATGTATCCAAGCAGATGATTCGTGTTTTTTTTAAAAAAGCTAATAATGGCAAGAAGATTATATTCCTAAAATTCCTAACACCAACAGTGAGAGAAAATTTGGCATGAACACGAAGGGGTTAATCCTCCAGTGGGGTTCCAATCAATACGTAATGATCTGGCCACACGGATCCAAGTCATGGGATGCTTTGATCCGCACCATGTGGTGCTCGGGGAAGAGTATCTGTTGCACTCACCGATGAACCATATTCTCAAATATTTTCTCTATTATATTTCTGCATCCAGACTTCTTTCAGACAAATTATTTTTACAGTTGTTTCCATAACCTTAAATTCCATCAGATAGAAATGTAAAGCTAACATTGAGAGTTCTGTTTCGTACTCAAGTGCATTCCCTTCCCGGGAAGGGCTATTTTGCAACTTACTCGACTGTCTCTGCCTGACTTTGAACTTCAAGCA	-	novel	NA	P-0047556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	109	427	0	ENST00000318789.4:c.870-982_910del		p.X290_splice	ENST00000318789	NM_032682.5	290		12/21	1	2	FACETS	0.63	0.57	0.693	0.63	0.57	0.693	SUBCLONAL	1	TRUE	1	0.80623881358259	2		427	429	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680383	30680383	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	269	628	0	ENST00000376406.3:c.1336C>G	p.Gln446Glu	p.Q446E	ENST00000376406	NM_014641.2	446	Caa/Gaa	5/15	1	2	FACETS	0.863	0.813	0.914	0.863	0.813	0.914	CLONAL	1	TRUE	1	0.80623881358259	2		628	773	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	113	516	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.965	0.882	1	0.965	0.882	1	CLONAL	1	TRUE	1	0.813018423405417	2		516	288	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606382	93606382	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764942726	NA	P-0047557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	217	687	0	ENST00000375746.1:c.202C>T	p.Arg68Trp	p.R68W	ENST00000375746	NM_001174167.1	68	Cgg/Tgg	2/14	1	2	FACETS	0.914	0.856	0.973	0.914	0.856	0.973	CLONAL	1	TRUE	1	0.813018423405417	2		687	584	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953228	81953228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369760877	NA	P-0047557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	114	371	0	ENST00000359376.3:c.2194C>T	p.Arg732Cys	p.R732C	ENST00000359376	NM_002661.3	732	Cgc/Tgc	20/33	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.813018423405417	2		371	265	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817414	39817414	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542019196	NA	P-0047557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	139	425	0	ENST00000288319.7:c.149G>A	p.Arg50His	p.R50H	ENST00000288319	NM_182918.3	50	cGc/cAc	2/10	1	2	FACETS	0.905	0.833	0.978	0.905	0.833	0.978	CLONAL	1	TRUE	1	0.813018423405417	2		425	378	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980353	201980353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	237	711	0	ENST00000359651.3:c.89C>T	p.Pro30Leu	p.P30L	ENST00000359651		30	cCc/cTc	1/8	1	2	FACETS	0.962	0.905	1	0.962	0.905	1	CLONAL	1	TRUE	1	0.813018423405417	2		711	606	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	160	516	0				ENST00000310581	NM_198253.2	-/1132			0.519485679280327	1	FACETS	0.494	0.459	0.528	0.494	0.459	0.528	INDETERMINATE	1	TRUE	0	0.944932866525553	1		516	362	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0047558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	231	424	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.961	0.905	1	0.961	0.905	1	CLONAL	1	TRUE	1	0.944932866525553	2		424	509	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0047559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	209	561	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.526027700926526	2		561	597	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039505	49039505	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs764754259	NA	P-0047560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	106	289	0	ENST00000267163.4:c.2489+1G>A		p.X830_splice	ENST00000267163	NM_000321.2	830			0.71544617935316	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.71544617935316	1		289	190	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs863224499	NA	P-0047560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	180	503	0	ENST00000269305.4:c.672+1G>A		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.71544617935316	1	FACETS	0.903	0.846	0.959	0.903	0.846	0.959	CLONAL	1	TRUE	0	0.71544617935316	1		503	358	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402523	139402523	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769854763	NA	P-0047560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	345	884	0	ENST00000277541.6:c.3394C>T	p.Arg1132Cys	p.R1132C	ENST00000277541	NM_017617.3	1132	Cgc/Tgc	21/34	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.71544617935316	2		884	942	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724646	162724646	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0047560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	128	293	0	ENST00000367921.3:c.417+1G>T		p.X139_splice	ENST00000367921	NM_006182.2	139			1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.71544617935316	2		293	348	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855772	45855772	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	218	673	0	ENST00000391945.4:c.2038G>T	p.Ala680Ser	p.A680S	ENST00000391945	NM_000400.3	680	Gcc/Tcc	21/23	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.71544617935316	2		673	601	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39002755	39002755	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	69	183	0	ENST00000357387.3:c.274T>G	p.Leu92Val	p.L92V	ENST00000357387	NM_152756.3	92	Tta/Gta	5/38	1	2	FACETS	0.807	0.712	0.906	0.807	0.712	0.906	CLONAL	1	TRUE	1	0.71544617935316	2		183	239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0047561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	206	1013	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.238256152400735	2	FACETS	0.879	0.817	0.943	0.879	0.817	0.943	CLONAL	2	TRUE	0	0.28	2		1013	837	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0047561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	120	277	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.299179902745556	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.28	2		277	382	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971066	21971067	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0047561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	146	726	0	ENST00000304494.5:c.291dup	p.His98AlafsTer22	p.H98Afs*22	ENST00000304494	NM_000077.4	97	-/G	2/3	0.299179902745556	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.28	1		726	650	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	87	676	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.259012612735132	2		676	573	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252865	36252865	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	20	308	0	ENST00000300305.3:c.497G>T	p.Arg166Leu	p.R166L	ENST00000300305		166	cGa/cTa	4/8	1	2	FACETS	0.497	0.38	0.634	0.497	0.38	0.634	SUBCLONAL	1	TRUE	1	0.259012612735132	2		308	311	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21643132	21643132	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1237988770	NA	P-0047562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	41	377	0	ENST00000421138.2:c.394+1G>A		p.X132_splice	ENST00000421138		132			0.166060414970846	3	FACETS	1	0.944	1	0.657	0.551	0.774	CLONAL	1	TRUE	1	0.259012612735132	3		377	272	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907481	32907481	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	20	228	0	ENST00000380152.3:c.1868del	p.Asn623MetfsTer21	p.N623Mfs*21	ENST00000380152		622	gcA/gc	10/27	0.259012612735132	1	FACETS	0.996	0.77	1	0.996	0.77	1	CLONAL	1	TRUE	0	0.259012612735132	1		228	135	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923282	9923282	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	37	486	1	ENST00000330684.3:c.2005A>C	p.Lys669Gln	p.K669Q	ENST00000330684	NM_001134407.1	669	Aag/Cag	9/13	1	2	FACETS	0.925	0.765	1	0.925	0.765	1	CLONAL	1	TRUE	1	0.259012612735132	2		487	309	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626892	158626892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	31	374	0	ENST00000263640.3:c.778G>A	p.Glu260Lys	p.E260K	ENST00000263640	NM_001105.4	260	Gaa/Aaa	7/11	1	2	FACETS	0.678	0.549	0.824	0.678	0.549	0.824	SUBCLONAL	1	TRUE	1	0.259012612735132	2		374	353	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161678	56161678	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	20	368	0	ENST00000399503.3:c.1175A>G	p.Tyr392Cys	p.Y392C	ENST00000399503	NM_005921.1	392	tAt/tGt	6/20	0.219585408610424	4	FACETS	0.775	0.593	0.986	0.258	0.197	0.329	CLONAL	1	TRUE	1	0.259012612735132	4		368	251	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760063	133760063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	71	748	0	ENST00000318560.5:c.2386G>A	p.Glu796Lys	p.E796K	ENST00000318560	NM_005157.4	796	Gag/Aag	11/11	0.259012612735132	1	FACETS	0.739	0.645	0.84	0.739	0.645	0.84	SUBCLONAL	1	TRUE	0	0.259012612735132	1		748	646	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24145483	24145483	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	135	481	0	ENST00000263121.7:c.504del	p.Phe168LeufsTer8	p.F168Lfs*8	ENST00000263121	NM_003073.3	168	Ttt/tt	5/9	0.437955146424018	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.437955146424018	1		481	452	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0047564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	85	396	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.428004952658684	3	FACETS	0.938	0.841	1	0.938	0.841	1	CLONAL	2	TRUE	1	0.428004952658684	3		396	257	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101057	41101057	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	177	632	0	ENST00000373198.4:c.1299G>T	p.Gln433His	p.Q433H	ENST00000373198	NM_133170.3	433	caG/caT	8/32	0.132375977448029	6	FACETS	1	0.981	1	0.785	0.726	0.846	INDETERMINATE	2	TRUE	3	0.428004952658684	6		632	652	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741955	162741955	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	231	390	0	ENST00000367921.3:c.1646C>A	p.Ser549Ter	p.S549*	ENST00000367921	NM_006182.2	549	tCa/tAa	13/18	0.428004952658684	5	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	TRUE	2	0.428004952658684	5		390	552	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434694	49434694	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	137	939	1	ENST00000301067.7:c.6859G>T	p.Val2287Leu	p.V2287L	ENST00000301067	NM_003482.3	2287	Gtg/Ttg	31/54	0.428004952658684	3	FACETS	0.999	0.909	1	0.499	0.454	0.547	CLONAL	1	TRUE	1	0.428004952658684	3		940	778	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109776	115109776	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	133	726	1	ENST00000257566.3:c.2102C>A	p.Ser701Tyr	p.S701Y	ENST00000257566	NM_016569.3	701	tCc/tAc	8/8	0.428004952658684	3	FACETS	1	0.942	1	0.523	0.476	0.573	CLONAL	1	TRUE	1	0.428004952658684	3		727	721	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685585	29685585	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	69	347	0	ENST00000356175.3:c.7995G>C	p.Gln2665His	p.Q2665H	ENST00000356175	NM_000267.3	2665	caG/caC	54/57	0.132375977448029	6	FACETS	0.935	0.821	1	0.623	0.547	0.704	INDETERMINATE	2	TRUE	3	0.428004952658684	6		347	320	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221295	1221299	+	frameshift_variant	Frame_Shift_Del	DEL	CCATC	CCATC	-	novel	NA	P-0047564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	212	663	0	ENST00000326873.7:c.820_824del	p.Ile274GlyfsTer9	p.I274Gfs*9	ENST00000326873	NM_000455.4	273	gCCATC/g	6/10	0.428004952658684	2	FACETS	0.933	0.874	0.992	0.933	0.874	0.992	CLONAL	2	TRUE	0	0.428004952658684	2		663	531	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610550	10610550	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	273	859	0	ENST00000171111.5:c.160T>G	p.Tyr54Asp	p.Y54D	ENST00000171111	NM_203500.1	54	Tac/Gac	2/6	0.428004952658684	2	FACETS	0.977	0.923	1	0.977	0.923	1	CLONAL	2	TRUE	0	0.428004952658684	2		859	653	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872497	136872497	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	106	225	0	ENST00000241393.3:c.1001G>T	p.Arg334Leu	p.R334L	ENST00000241393	NM_003467.2	334	cGa/cTa	2/2	0.411769701380527	4	FACETS	0.962	0.88	1	0.962	0.88	1	CLONAL	3	TRUE	1	0.428004952658684	4		225	245	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946181	55946181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	114	332	0	ENST00000263923.4:c.3998G>A	p.Gly1333Glu	p.G1333E	ENST00000263923	NM_002253.2	1333	gGa/gAa	30/30	0.415554283781193	4	FACETS	0.868	0.787	0.953	0.868	0.787	0.953	CLONAL	2	TRUE	2	0.428004952658684	4		332	438	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033177	69033177	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	46	297	0	ENST00000288368.4:c.3617C>G	p.Pro1206Arg	p.P1206R	ENST00000288368	NM_024870.2	1206	cCa/cGa	30/40	0.428004952658684	4	FACETS	0.726	0.612	0.851	0.181	0.153	0.213	SUBCLONAL	1	TRUE	0	0.428004952658684	4		297	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0047565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	711	1080	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.902433982797445	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.902433982797445	2		1080	766	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0047565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	185	331	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.820004193233161	4	FACETS	0.931	0.87	0.992	0.931	0.87	0.992	CLONAL	2	TRUE	2	0.902433982797445	4		331	419	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222920	36222920	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	971	986	0	ENST00000222270.7:c.5549G>T	p.Gly1850Val	p.G1850V	ENST00000222270	NM_014727.1	1850	gGc/gTc	27/37	0.428699584725211	5	FACETS	0.93	0.905	0.954	0.93	0.905	0.954	INDETERMINATE	3	TRUE	2	0.902433982797445	5		986	1816	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197447	26197447	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	59	368	0	ENST00000356476.2:c.32C>A	p.Ser11Tyr	p.S11Y	ENST00000356476		11	tCc/tAc	1/1	0.406325015146262	5	FACETS	0.685	0.591	0.788	0.228	0.197	0.263	INDETERMINATE	1	TRUE	2	0.902433982797445	5		368	449	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0047566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	79	277	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.875	0.773	0.985	0.875	0.773	0.985	CLONAL	1	TRUE	1	0.392366889418744	2		277	460	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0047566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	106	380	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.392366889418744	2		380	495	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725042	89725042	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1085308041	NA	P-0047566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	79	212	0	ENST00000371953.3:c.1027-2A>G		p.X343_splice	ENST00000371953	NM_000314.4	343			0.392366889418744	3	FACETS	0.873	0.777	0.973	0.873	0.777	0.973	CLONAL	2	TRUE	1	0.392366889418744	3		212	276	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916725	178916725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749415085	NA	P-0047566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	77	278	0	ENST00000263967.3:c.112C>T	p.Arg38Cys	p.R38C	ENST00000263967	NM_006218.2	38	Cgt/Tgt	2/21	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.392366889418744	2		278	359	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711887	89711887	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776673	NA	P-0047566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	100	379	0	ENST00000371953.3:c.507del	p.Ser170ValfsTer13	p.S170Vfs*13	ENST00000371953	NM_000314.4	169	Ccc/cc	6/9	0.392366889418744	3	FACETS	0.969	0.867	1	0.485	0.433	0.539	CLONAL	1	TRUE	1	0.392366889418744	3		379	629	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645069	67645069	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	73	649	0	ENST00000264010.4:c.334G>T	p.Glu112Ter	p.E112*	ENST00000264010	NM_006565.3	112	Gaa/Taa	3/12	1	2	FACETS	0.465	0.406	0.529	0.465	0.406	0.529	SUBCLONAL	1	TRUE	1	0.392366889418744	2		649	800	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0047566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	68	595	0	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	1	2	FACETS	0.529	0.46	0.604	0.529	0.46	0.604	SUBCLONAL	1	TRUE	1	0.392366889418744	2		595	655	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057811	27057811	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	100	936	1	ENST00000324856.7:c.1519C>T	p.Gln507Ter	p.Q507*	ENST00000324856	NM_006015.4	507	Caa/Taa	3/20	1	2	FACETS	0.472	0.421	0.528	0.472	0.421	0.528	SUBCLONAL	1	TRUE	1	0.392366889418744	2		937	1079	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188078	11188078	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	37	501	0	ENST00000361445.4:c.6016G>C	p.Val2006Leu	p.V2006L	ENST00000361445	NM_004958.3	2006	Gtc/Ctc	43/58	1	2	FACETS	0.35	0.288	0.42	0.35	0.288	0.42	SUBCLONAL	1	TRUE	1	0.392366889418744	2		501	539	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429354	78429354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	118	498	0	ENST00000370768.2:c.1088G>A	p.Arg363Lys	p.R363K	ENST00000370768	NM_003902.3	363	aGa/aAa	13/20	1	2	FACETS	0.955	0.863	1	0.955	0.863	1	CLONAL	1	TRUE	1	0.392366889418744	2		498	630	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670854	134670854	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	46	463	0	ENST00000398015.3:c.765C>A	p.Cys255Ter	p.C255*	ENST00000398015	NM_004441.4	255	tgC/tgA	3/16	1	2	FACETS	0.492	0.414	0.577	0.492	0.414	0.577	SUBCLONAL	1	TRUE	1	0.392366889418744	2		463	477	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218783	66218783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	27	216	0	ENST00000273854.3:c.2275G>A	p.Gly759Ser	p.G759S	ENST00000273854	NM_004439.5	759	Ggc/Agc	13/18	1	2	FACETS	0.583	0.466	0.716	0.583	0.466	0.716	SUBCLONAL	1	TRUE	1	0.392366889418744	2		216	236	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0047567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	18	277	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.951	0.715	1	0.951	0.715	1	CLONAL	1	TRUE	1	0.11	2		277	344	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220687	1220687	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	37	1162	0	ENST00000326873.7:c.706del	p.Val236TrpfsTer51	p.V236Wfs*51	ENST00000326873	NM_000455.4	235	aaG/aa	5/10	1	2	FACETS	0.984	0.809	1	0.984	0.809	1	CLONAL	1	TRUE	1	0.11	2		1162	684	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271322	18271322	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	62	1074	1	ENST00000222254.8:c.364G>A	p.Asp122Asn	p.D122N	ENST00000222254	NM_005027.3	122	Gat/Aat	3/16	0.158349873973244	0	FACETS	0.48	0.416	0.55			1	INDETERMINATE	1	TRUE	0	0.376867475039047	0		1075	427	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0047568-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	98	470	0				ENST00000310581	NM_198253.2	-/1132			0.154052612392791	4	FACETS	1	0.933	1	1	0.933	1	CLONAL	2	TRUE	2	0.231512710225085	4		470	494	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935768	15935768	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047568-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	59	313	0	ENST00000268712.3:c.7165A>G	p.Thr2389Ala	p.T2389A	ENST00000268712	NM_006311.3	2389	Act/Gct	46/46	0.231512710225085	5	FACETS	1	0.953	1			1	CLONAL	1	TRUE	NA	0.231512710225085	5		313	543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579716	7579716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1192416464	NA	P-0047571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	57	657	0	ENST00000269305.4:c.80del	p.Pro27LeufsTer17	p.P27Lfs*17	ENST00000269305	NM_001126112.2	27	cCt/ct	3/11	1	2	FACETS	0.94	0.809	1	1	0.976	1	CLONAL	2	TRUE	1	0.14	2		657	433	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295795	212295795	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369248674	NA	P-0047571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	52	510	0	ENST00000342788.4:c.2518G>A	p.Val840Ile	p.V840I	ENST00000342788	NM_005235.2	840	Gtt/Att	21/28	1	2	FACETS	0.802	0.684	0.932	1	0.968	1	CLONAL	2	TRUE	1	0.14	2		510	463	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215591	5215591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760885887	NA	P-0047571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	46	963	0	ENST00000357368.4:c.4112C>T	p.Pro1371Leu	p.P1371L	ENST00000357368	NM_002850.3	1371	cCg/cTg	27/38	0.3	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.14	1		963	496	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912079	127912079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	30	312	2	ENST00000373547.4:c.791G>A	p.Arg264His	p.R264H	ENST00000373547	NM_002721.4	264	cGt/cAt	7/7	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.14	2		314	310	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468934	25468934	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0047571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	59	762	0	ENST00000264709.3:c.1430-1G>A		p.X477_splice	ENST00000264709	NM_175629.2	477			0.3	1	FACETS	0.754	0.649	0.868	1	0.969	1	SUBCLONAL	2	TRUE	0	0.14	1		762	520	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998286	100998288	+	inframe_deletion	In_Frame_Del	DEL	CGG	CGG	-	rs766303231	NA	P-0047571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	10	279	0	ENST00000325455.5:c.1514_1516del	p.Ala505del	p.A505del	ENST00000325455	NM_001202474.3	505	gCCGgg/ggg	1/8	0.15907430098988	3	FACETS	0.809	0.548	1	0.404	0.274	0.568	CLONAL	1	TRUE	1	0.14	3		279	189	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	261	516	0				ENST00000310581	NM_198253.2	-/1132			0.612926782407262	3	FACETS	0.962	0.911	1	0.962	0.911	1	CLONAL	2	TRUE	1	0.690075238699868	3		516	529	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0047573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	49	258	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.439831195084941	3	FACETS	0.451	0.382	0.526	0.225	0.191	0.263	SUBCLONAL	1	TRUE	1	0.690075238699868	3		258	424	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446124	49446125	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	240	965	0	ENST00000301067.7:c.1341dup	p.Pro448ThrfsTer7	p.P448Tfs*7	ENST00000301067	NM_003482.3	447	-/A	10/54	1	2	FACETS	0.826	0.773	0.88	0.826	0.773	0.88	CLONAL	1	TRUE	1	0.690075238699868	2		965	842	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937509	32937509	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	154	557	0	ENST00000380152.3:c.8170G>C	p.Gly2724Arg	p.G2724R	ENST00000380152		2724	Ggg/Cgg	18/27	1	2	FACETS	0.96	0.886	1	0.96	0.886	1	CLONAL	1	TRUE	1	0.690075238699868	2		557	465	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817832	3817832	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	187	522	0	ENST00000262367.5:c.3139G>T	p.Glu1047Ter	p.E1047*	ENST00000262367	NM_004380.2	1047	Gaa/Taa	16/31	0.690075238699868	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.690075238699868	1		522	349	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632707	23632707	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	91	432	0	ENST00000261584.4:c.3089C>G	p.Thr1030Ser	p.T1030S	ENST00000261584	NM_024675.3	1030	aCt/aGt	10/13	1	2	FACETS	0.799	0.717	0.885	0.799	0.717	0.885	SUBCLONAL	1	TRUE	1	0.690075238699868	2		432	330	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022252	31022252	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	91	417	0	ENST00000375687.4:c.1737C>G	p.Ile579Met	p.I579M	ENST00000375687	NM_015338.5	579	atC/atG	13/13	1	2	FACETS	0.593	0.529	0.66	0.593	0.529	0.66	SUBCLONAL	1	TRUE	1	0.690075238699868	2		417	445	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69788762	69788762	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1413689457	NA	P-0047573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	124	387	1	ENST00000352241.4:c.14C>T	p.Ser5Leu	p.S5L	ENST00000352241	NM_198159.2	5	tCg/tTg	1/10	0.412745849368163	1	FACETS	0.594	0.543	0.648	0.594	0.543	0.648	INDETERMINATE	1	TRUE	0	0.690075238699868	1		388	396	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975425	13975425	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	198	424	0	ENST00000405192.2:c.462C>A	p.Asn154Lys	p.N154K	ENST00000405192	NM_001163147.1	154	aaC/aaA	7/12	0.309106342030888	2	FACETS	1	0.989	1	0.631	0.591	0.671	INDETERMINATE	1	TRUE	0	0.690075238699868	2		424	455	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220528	123220529	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	165	270	0	ENST00000218089.9:c.3187dup	p.Ile1063AsnfsTer11	p.I1063Nfs*11	ENST00000218089	NM_001042749.1	1062	gga/ggAa	30/35	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.690075238699868	1		270	270	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0047574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	23	624	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	1	2	FACETS	0.298	0.232	0.373	0.298	0.232	0.373	SUBCLONAL	1	TRUE	1	0.55	2		624	281	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0047574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	32	659	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	0.278	0.225	0.337	0.278	0.225	0.337	SUBCLONAL	1	TRUE	1	0.55	2		659	419	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860138	57860138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	84	699	1	ENST00000228682.2:c.878G>A	p.Arg293His	p.R293H	ENST00000228682	NM_005269.2	293	cGc/cAc	8/12	1	2	FACETS	0.865	0.764	0.973	0.865	0.764	0.973	CLONAL	1	TRUE	1	0.28	2		700	694	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199442	16199442	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	33	304	0	ENST00000375759.3:c.215G>C	p.Arg72Thr	p.R72T	ENST00000375759	NM_015001.2	72	aGa/aCa	2/15	0.189704787415934	2	FACETS	0.702	0.572	0.846	0.351	0.286	0.423	SUBCLONAL	1	TRUE	0	0.28	2		304	336	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858973	57858973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867870031	NA	P-0047575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	52	765	0	ENST00000228682.2:c.469C>T	p.His157Tyr	p.H157Y	ENST00000228682	NM_005269.2	157	Cat/Tat	5/12	1	2	FACETS	0.505	0.429	0.588	0.505	0.429	0.588	SUBCLONAL	1	TRUE	1	0.28	2		765	736	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562899	21562899	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	70	888	0	ENST00000382592.4:c.1020C>G	p.Ser340Arg	p.S340R	ENST00000382592	NM_014572.2	340	agC/agG	4/8	1	2	FACETS	0.662	0.577	0.755	0.662	0.577	0.755	SUBCLONAL	1	TRUE	1	0.28	2		888	755	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314568	30314568	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	42	533	0	ENST00000262643.3:c.1117G>C	p.Ala373Pro	p.A373P	ENST00000262643	NM_001238.2	373	Gcc/Ccc	12/12	1	2	FACETS	0.465	0.387	0.552	0.465	0.387	0.552	SUBCLONAL	1	TRUE	1	0.28	2		533	645	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030672	48030672	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	38	383	0	ENST00000234420.5:c.3286C>A	p.His1096Asn	p.H1096N	ENST00000234420	NM_000179.2	1096	Cat/Aat	5/10	0.257489969991343	3	FACETS	0.616	0.509	0.736	0.308	0.254	0.368	SUBCLONAL	1	TRUE	1	0.28	3		383	502	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794406	242794406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	78	926	0	ENST00000334409.5:c.536G>A	p.Gly179Asp	p.G179D	ENST00000334409	NM_005018.2	179	gGc/gAc	3/5	0.257489969991343	3	FACETS	0.795	0.698	0.9	0.397	0.349	0.45	SUBCLONAL	1	TRUE	1	0.28	3		926	799	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0047577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	438	898	1	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.689400734950219	2	FACETS	0.91	0.879	0.939	0.91	0.879	0.939	CLONAL	2	TRUE	0	0.73063849995869	2		899	659	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189909	66189909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	21	362	0	ENST00000273854.3:c.3037G>T	p.Val1013Phe	p.V1013F	ENST00000273854	NM_004439.5	1013	Gtc/Ttc	18/18	0.249678066112093	3	FACETS	0.191	0.147	0.244	0.064	0.049	0.082	INDETERMINATE	1	TRUE	0	0.73063849995869	3		362	410	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443585	52443585	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	194	607	0	ENST00000460680.1:c.107A>G	p.Gln36Arg	p.Q36R	ENST00000460680	NM_004656.3	36	cAg/cGg	3/17	0.274028587076391	3	FACETS	1	0.988	1	0.427	0.398	0.457	INDETERMINATE	1	TRUE	0	0.73063849995869	3		607	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0047578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	627	1080	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.68308520729468	3	FACETS	0.997	0.974	1	0.997	0.974	1	CLONAL	3	TRUE	0	0.68308520729468	3		1080	823	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40376853	40376853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1177773526	NA	P-0047578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	156	502	0	ENST00000293328.3:c.319C>T	p.Arg107Cys	p.R107C	ENST00000293328	NM_012448.3	107	Cgc/Tgc	4/19	0.435521198794202	5	FACETS	1	0.987	1	0.468	0.43	0.508	CLONAL	1	TRUE	2	0.68308520729468	5		502	658	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808045	3808045	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	84	271	0	ENST00000262367.5:c.3374A>G	p.Tyr1125Cys	p.Y1125C	ENST00000262367	NM_004380.2	1125	tAt/tGt	18/31	0.68308520729468	3	FACETS	0.959	0.854	1	0.48	0.427	0.535	CLONAL	1	TRUE	1	0.68308520729468	3		271	344	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661616	227661616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	225	728	0	ENST00000305123.5:c.1839G>A	p.Met613Ile	p.M613I	ENST00000305123	NM_005544.2	613	atG/atA	1/2	0.209406476602289	4	FACETS	0.912	0.855	0.97	0.912	0.855	0.97	INDETERMINATE	2	TRUE	2	0.68308520729468	4		728	608	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023017	27023027	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCAGCGG	GGCGGCAGCGG	-	novel	NA	P-0047578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	61	33	0	ENST00000324856.7:c.123_133del	p.Ala42ArgfsTer65	p.A42Rfs*65	ENST00000324856	NM_006015.4	41	gcGGCGGCAGCGGcc/gccc	1/20	0.61337486953841	2	FACETS		NA	1	1	0.984	1	NA	3	TRUE	0	0.68308520729468	2		33	69	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670755	67670755	+	splice_donor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0047578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	288	345	0	ENST00000264010.4:c.1999+1del		p.X667_splice	ENST00000264010	NM_006565.3	667			0.68308520729468	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.68308520729468	3		345	523	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349756	15349756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868319763	NA	P-0047578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	256	825	2	ENST00000263377.2:c.3818G>A	p.Arg1273Gln	p.R1273Q	ENST00000263377	NM_058243.2	1273	cGg/cAg	19/20	0.505701548023305	5	FACETS	1	0.982	1	0.736	0.693	0.78	CLONAL	2	TRUE	2	0.68308520729468	5		827	687	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916780	178916780	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	97	305	0	ENST00000263967.3:c.167A>G	p.Tyr56Cys	p.Y56C	ENST00000263967	NM_006218.2	56	tAc/tGc	2/21	0.136854057470266	3	FACETS	1	0.978	1	0.652	0.589	0.718	INDETERMINATE	1	TRUE	1	0.68308520729468	3		305	292	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538787	23538787	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	255	364	0	ENST00000380871.4:c.652C>A	p.Pro218Thr	p.P218T	ENST00000380871	NM_006167.3	218	Cct/Act	2/2	0.68308520729468	3	FACETS	0.954	0.916	0.99	0.954	0.916	0.99	CLONAL	3	TRUE	0	0.68308520729468	3		364	350	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197353	27197353	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	93	436	0	ENST00000380036.4:c.1665T>G	p.Ser555Arg	p.S555R	ENST00000380036	NM_000459.3	555	agT/agG	12/23	1	2	FACETS	0.83	0.746	0.918	0.83	0.746	0.918	CLONAL	1	TRUE	1	0.68308520729468	2		436	328	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747089	40747089	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	50	543	0	ENST00000373198.4:c.2993A>C	p.Asn998Thr	p.N998T	ENST00000373198	NM_133170.3	998	aAc/aCc	22/32	0.68308520729468	6	FACETS	0.409	0.346	0.479	0.102	0.086	0.12	SUBCLONAL	1	TRUE	2	0.68308520729468	6		543	846	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729579	41729579	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	157	561	0	ENST00000242208.4:c.950A>C	p.Lys317Thr	p.K317T	ENST00000242208	NM_002192.2	317	aAg/aCg	3/3	0.68308520729468	3	FACETS	0.92	0.846	0.998	0.46	0.423	0.499	CLONAL	1	TRUE	1	0.68308520729468	3		561	670	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0047578-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	262	1080	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.240958625471577	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	FALSE	0	0.240958625471577	3		1080	761	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40376853	40376853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1177773526	NA	P-0047578-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	70	502	0	ENST00000293328.3:c.319C>T	p.Arg107Cys	p.R107C	ENST00000293328	NM_012448.3	107	Cgc/Tgc	4/19	0.240958625471577	3	FACETS	1	0.91	1	0.528	0.46	0.601	CLONAL	1	FALSE	1	0.240958625471577	3		502	617	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808045	3808045	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047578-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	36	271	0	ENST00000262367.5:c.3374A>G	p.Tyr1125Cys	p.Y1125C	ENST00000262367	NM_004380.2	1125	tAt/tGt	18/31	0.240958625471577	3	FACETS	1	0.895	1	0.562	0.463	0.671	CLONAL	1	FALSE	1	0.240958625471577	3		271	298	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661616	227661616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047578-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	97	728	0	ENST00000305123.5:c.1839G>A	p.Met613Ile	p.M613I	ENST00000305123	NM_005544.2	613	atG/atA	1/2	0.240958625471577	3	FACETS	1	0.979	1	0.715	0.638	0.796	CLONAL	1	FALSE	1	0.240958625471577	3		728	631	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023017	27023027	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGGCAGCGG	GGCGGCAGCGG	-	novel	NA	P-0047578-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	35	33	0	ENST00000324856.7:c.123_133del	p.Ala42ArgfsTer65	p.A42Rfs*65	ENST00000324856	NM_006015.4	41	gcGGCGGCAGCGGcc/gccc	1/20	0.240958625471577	2	FACETS	1	0.924	1	1	0.976	1	CLONAL	5	FALSE	0	0.240958625471577	2		33	54	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670755	67670755	+	splice_donor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0047578-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	129	345	0	ENST00000264010.4:c.1999+1del		p.X667_splice	ENST00000264010	NM_006565.3	667			0.240958625471577	3	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	FALSE	1	0.240958625471577	3		345	568	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349756	15349756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868319763	NA	P-0047578-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	108	825	2	ENST00000263377.2:c.3818G>A	p.Arg1273Gln	p.R1273Q	ENST00000263377	NM_058243.2	1273	cGg/cAg	19/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	1	0.240958625471577	2		827	809	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916780	178916780	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047578-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	87	305	0	ENST00000263967.3:c.167A>G	p.Tyr56Cys	p.Y56C	ENST00000263967	NM_006218.2	56	tAc/tGc	2/21	0.240958625471577	4	FACETS	0.876	0.782	0.974	0.876	0.782	0.974	CLONAL	3	FALSE	1	0.240958625471577	4		305	341	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538787	23538787	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047578-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	82	364	0	ENST00000380871.4:c.652C>A	p.Pro218Thr	p.P218T	ENST00000380871	NM_006167.3	218	Cct/Act	2/2	0.240958625471577	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	FALSE	0	0.240958625471577	2		364	308	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197353	27197353	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047578-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	47	436	0	ENST00000380036.4:c.1665T>G	p.Ser555Arg	p.S555R	ENST00000380036	NM_000459.3	555	agT/agG	12/23	1	2	FACETS	0.911	0.77	1	0.911	0.77	1	CLONAL	1	FALSE	1	0.240958625471577	2		436	428	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0047595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	83	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.351617119048019	4	FACETS	1	0.971	1	0.441	0.391	0.495	CLONAL	1	TRUE	1	0.351617119048019	4		511	482	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0047595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	223	470	0				ENST00000310581	NM_198253.2	-/1132			0.351617119048019	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	3	TRUE	1	0.351617119048019	4		470	560	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855971	76855971	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	84	631	0	ENST00000373344.5:c.5629C>T	p.Gln1877Ter	p.Q1877*	ENST00000373344	NM_000489.3	1877	Cag/Tag	23/35	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.351617119048019	2		631	418	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100075	27100075	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	162	715	1	ENST00000324856.7:c.3871G>T	p.Glu1291Ter	p.E1291*	ENST00000324856	NM_006015.4	1291	Gag/Tag	16/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.351617119048019	2		716	887	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40789994	40789994	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs746391800	NA	P-0047595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	93	538	2	ENST00000373198.4:c.2737G>A	p.Glu913Lys	p.E913K	ENST00000373198	NM_133170.3	913	Gag/Aag	18/32	0.351617119048019	3	FACETS	0.742	0.659	0.831	0.371	0.329	0.416	SUBCLONAL	1	TRUE	1	0.351617119048019	3		540	838	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415628	49415628	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	29	463	0	ENST00000301067.7:c.16549G>C	p.Glu5517Gln	p.E5517Q	ENST00000301067	NM_003482.3	5517	Gag/Cag	54/54	1	2	FACETS	0.318	0.255	0.391	0.318	0.255	0.391	SUBCLONAL	1	TRUE	1	0.351617119048019	2		463	518	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5225855	5225855	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	135	627	0	ENST00000357368.4:c.2377G>A	p.Glu793Lys	p.E793K	ENST00000357368	NM_002850.3	793	Gag/Aag	17/38	1	2	FACETS	0.854	0.776	0.936	0.854	0.776	0.936	CLONAL	1	TRUE	1	0.351617119048019	2		627	899	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099050	27099050	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	136	559	0	ENST00000324856.7:c.3466G>C	p.Glu1156Gln	p.E1156Q	ENST00000324856	NM_006015.4	1156	Gaa/Caa	13/20	1	2	FACETS	0.897	0.816	0.983	0.897	0.816	0.983	CLONAL	1	TRUE	1	0.351617119048019	2		559	862	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099340	27099340	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	113	649	0	ENST00000324856.7:c.3577G>C	p.Asp1193His	p.D1193H	ENST00000324856	NM_006015.4	1193	Gat/Cat	14/20	1	2	FACETS	0.909	0.819	1	0.909	0.819	1	CLONAL	1	TRUE	1	0.351617119048019	2		649	707	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870356	155870356	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	126	585	0	ENST00000368323.3:c.483T>G	p.Phe161Leu	p.F161L	ENST00000368323	NM_006912.5	161	ttT/ttG	6/6	0.351617119048019	3	FACETS	1	0.966	1	0.569	0.516	0.626	CLONAL	1	TRUE	1	0.351617119048019	3		585	740	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132935	64132935	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	120	486	0	ENST00000334205.4:c.1069C>T	p.Gln357Ter	p.Q357*	ENST00000334205	NM_003942.2	357	Cag/Tag	9/17	1	2	FACETS	0.922	0.834	1	0.922	0.834	1	CLONAL	1	TRUE	1	0.351617119048019	2		486	740	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298056	15298056	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0047595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	193	831	1	ENST00000263388.2:c.1700C>G	p.Ser567Ter	p.S567*	ENST00000263388	NM_000435.2	567	tCa/tGa	11/33	1	2	FACETS	0.997	0.921	1	0.997	0.921	1	CLONAL	1	TRUE	1	0.351617119048019	2		832	1101	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905057	50905062	+	inframe_deletion	In_Frame_Del	DEL	GGGGCC	GGGGCC	-	novel	NA	P-0047595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	150	675	0	ENST00000440232.2:c.339_344del	p.Gly114_Pro115del	p.G114_P115del	ENST00000440232	NM_002691.3	113	ggGGGGCCc/ggc	4/27	0.334474294552086	3	FACETS	1	0.918	1	0.503	0.459	0.549	CLONAL	1	TRUE	1	0.351617119048019	3		675	998	SUCCESS
ATR	545	MSKCC	GRCh37	3	142168420	142168420	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	81	458	0	ENST00000350721.4:c.7786G>C	p.Glu2596Gln	p.E2596Q	ENST00000350721	NM_001184.3	2596	Gag/Cag	47/47	0.351617119048019	4	FACETS	1	0.969	1	0.432	0.382	0.486	CLONAL	1	TRUE	1	0.351617119048019	4		458	480	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342123	70342123	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	142	607	0	ENST00000374080.3:c.1175C>T	p.Ser392Leu	p.S392L	ENST00000374080		392	tCa/tTa	8/45	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.351617119048019	2		607	792	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70343561	70343561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	123	621	0	ENST00000374080.3:c.1735C>T	p.Pro579Ser	p.P579S	ENST00000374080		579	Ccc/Tcc	12/45	1	2	FACETS	0.948	0.858	1	0.948	0.858	1	CLONAL	1	TRUE	1	0.351617119048019	2		621	738	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0047596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	74	470	0				ENST00000310581	NM_198253.2	-/1132			0.323314590563495	1	FACETS	0.527	0.472	0.583	0.527	0.472	0.583	INDETERMINATE	1	TRUE	0	0.876583845787292	1		470	180	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0047596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	507	430	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.876583845787292	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.876583845787292	3		430	552	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032120	10032120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	111	542	1	ENST00000330684.3:c.703G>A	p.Glu235Lys	p.E235K	ENST00000330684	NM_001134407.1	235	Gag/Aag	3/13	1	2	FACETS	0.892	0.814	0.971	0.892	0.814	0.971	CLONAL	1	TRUE	1	0.876583845787292	2		543	284	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0047596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	259	788	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	1	2	FACETS	0.872	0.821	0.923	0.872	0.821	0.923	CLONAL	1	TRUE	1	0.876583845787292	2		788	678	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932479	39932479	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	169	308	0	ENST00000378444.4:c.2120C>T	p.Pro707Leu	p.P707L	ENST00000378444	NM_001123385.1	707	cCc/cTc	4/15	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.876583845787292	1		308	206	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874407	76874407	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	67	175	0	ENST00000373344.5:c.5315C>T	p.Ser1772Phe	p.S1772F	ENST00000373344	NM_000489.3	1772	tCc/tTc	21/35	1	1	FACETS	0.965	0.892	1	0.965	0.892	1	CLONAL	1	TRUE	0	0.876583845787292	1		175	89	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196370	106196370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	84	316	0	ENST00000380013.4:c.4703C>T	p.Pro1568Leu	p.P1568L	ENST00000380013	NM_001127208.2	1568	cCa/cTa	11/11	1	2	FACETS	0.939	0.847	1	0.939	0.847	1	CLONAL	1	TRUE	1	0.876583845787292	2		316	204	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325189	123325189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1367082521	NA	P-0047596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	125	482	0	ENST00000358487.5:c.139C>T	p.Pro47Ser	p.P47S	ENST00000358487	NM_000141.4	47	Cca/Tca	3/18	0.716061217042506	1	FACETS	0.467	0.428	0.507	0.467	0.428	0.507	SUBCLONAL	1	TRUE	0	0.876583845787292	1		482	343	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133234501	133234502	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0047596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	141	525	1	ENST00000320574.5:c.3330_3331delinsTT	p.Arg1111Trp	p.R1111W	ENST00000320574	NM_006231.2	1110	ctCCgg/ctTTgg	27/49	1	2	FACETS	0.987	0.913	1	0.987	0.913	1	CLONAL	1	TRUE	1	0.876583845787292	2		526	326	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588644	28588644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	106	371	0	ENST00000241453.7:c.2804C>T	p.Ser935Phe	p.S935F	ENST00000241453	NM_004119.2	935	tCc/tTc	23/24	0.716061217042506	1	FACETS	0.641	0.589	0.693	0.641	0.589	0.693	SUBCLONAL	1	TRUE	0	0.876583845787292	1		371	212	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380979	116380979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	251	550	1	ENST00000397752.3:c.1601C>T	p.Pro534Leu	p.P534L	ENST00000397752	NM_000245.2	534	cCc/cTc	5/21	0.876583845787292	3	FACETS	1	0.961	1	0.515	0.484	0.548	CLONAL	1	TRUE	1	0.876583845787292	3		551	799	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539042	23539042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	73	504	0	ENST00000380871.4:c.397C>T	p.His133Tyr	p.H133Y	ENST00000380871	NM_006167.3	133	Cac/Tac	2/2	0.469201859179204	1	FACETS	0.317	0.28	0.357	0.317	0.28	0.357	INDETERMINATE	1	TRUE	0	0.876583845787292	1		504	295	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	119	575	3	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.387712799401611	2		578	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0047598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	498	682	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	NA	2	FACETS	0.881	0.847	0.914			1	INDETERMINATE	2	TRUE	NA	0.570031801635191	2		684	992	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166118	118166118	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	144	450	0	ENST00000369448.3:c.628G>A	p.Val210Met	p.V210M	ENST00000369448	NM_017709.3	210	Gtg/Atg	2/2	0.513737154139504	4	FACETS	0.902	0.823	0.986	0.451	0.411	0.493	CLONAL	1	TRUE	2	0.570031801635191	4		450	879	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	443406	443406	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0047598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	107	275	0	ENST00000399788.2:c.1490+1G>C		p.X497_splice	ENST00000399788	NM_001042603.1	497			0.570031801635191	3	FACETS	0.903	0.813	0.998			1	CLONAL	1	TRUE	NA	0.570031801635191	3		275	534	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38153464	38153464	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	70	365	0	ENST00000317025.8:c.2765G>T	p.Arg922Ile	p.R922I	ENST00000317025	NM_023034.1	922	aGa/aTa	16/24	0.570031801635191	3	FACETS	0.413	0.359	0.471			1	SUBCLONAL	1	TRUE	NA	0.570031801635191	3		365	765	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862850	9862850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751455326	NA	P-0047600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	332	666	0	ENST00000330684.3:c.2453C>T	p.Ala818Val	p.A818V	ENST00000330684	NM_001134407.1	818	gCg/gTg	12/13	0.314488986869391	1	FACETS	0.563	0.536	0.59	0.563	0.536	0.59	INDETERMINATE	1	TRUE	0	0.903452876834921	1		666	716	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401817	139401817	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs777194812	NA	P-0047600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	246	764	3	ENST00000277541.6:c.3583G>T	p.Gly1195Trp	p.G1195W	ENST00000277541	NM_017617.3	1195	Ggg/Tgg	22/34	0.903452876834921	1	FACETS	0.992	0.958	1	0.992	0.958	1	CLONAL	1	TRUE	0	0.903452876834921	1		767	301	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593586	55593604	+	protein_altering_variant	In_Frame_Del	DEL	CCATGTATGAAGTACAGTG	CCATGTATGAAGTACAGTG	T	novel	NA	P-0047600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	290	385	0	ENST00000288135.5:c.1652_1670delinsT	p.Pro551_Trp557delinsLeu	p.P551_W557delinsL	ENST00000288135	NM_000222.2	551	cCCATGTATGAAGTACAGTGg/cTg	11/21	0.903452876834921	3	FACETS	1	0.992	1			1	CLONAL	1	TRUE	NA	0.903452876834921	3		385	733	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	63	164	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.283199084601795	3	FACETS	0.713	0.616	0.819	0.357	0.308	0.41	SUBCLONAL	1	TRUE	1	0.283199084601795	3		164	712	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	116	525	1	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.283199084601795	2		526	800	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	91	258	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.283199084601795	2		258	597	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804953	43804953	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	48	517	1	ENST00000372470.3:c.408del	p.Ser137ValfsTer29	p.S137Vfs*29	ENST00000372470	NM_005373.2	135	Ccc/cc	4/12	1	2	FACETS	0.705	0.596	0.824	0.705	0.596	0.824	SUBCLONAL	1	TRUE	1	0.283199084601795	2		518	481	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023327	27023327	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	26	112	0	ENST00000324856.7:c.437del	p.Pro146GlnfsTer86	p.P146Qfs*86	ENST00000324856	NM_006015.4	145	Ccc/cc	1/20	1	2	FACETS	0.883	0.714	1	1	0.949	1	CLONAL	2	TRUE	1	0.283199084601795	2		112	104	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438316	110438317	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	rs532810290	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	30	257	0	ENST00000375856.3:c.82_84dup	p.Asn28dup	p.N28dup	ENST00000375856	NM_003749.2	28	-/AAC	1/2	1	2	FACETS	0.788	0.637	0.957	0.788	0.637	0.957	CLONAL	1	TRUE	1	0.283199084601795	2		257	269	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930634	32930634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56070345	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	31	405	0	ENST00000380152.3:c.7505G>A	p.Arg2502His	p.R2502H	ENST00000380152		2502	cGc/cAc	15/27	1	2	FACETS	0.362	0.292	0.442	0.362	0.292	0.442	SUBCLONAL	1	TRUE	1	0.283199084601795	2		405	604	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221131	5221131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201447856	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	133	1068	3	ENST00000357368.4:c.3335C>T	p.Thr1112Met	p.T1112M	ENST00000357368	NM_002850.3	1112	aCg/aTg	20/38	1	2	FACETS	0.968	0.878	1	0.968	0.878	1	CLONAL	1	TRUE	1	0.283199084601795	2		1071	970	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291083	10291084	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755889652	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	106	902	7	ENST00000340748.4:c.387dup	p.Lys130GlnfsTer19	p.K130Qfs*19	ENST00000340748		129	-/C	4/40	1	2	FACETS	0.727	0.65	0.809	0.727	0.65	0.809	SUBCLONAL	1	TRUE	1	0.283199084601795	2		909	1030	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737820	145737820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs36023964	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	129	1124	1	ENST00000428558.2:c.3010C>T	p.Arg1004Trp	p.R1004W	ENST00000428558	NM_004260.3	1004	Cgg/Tgg	18/22	1	2	FACETS	0.964	0.873	1	0.964	0.873	1	CLONAL	1	TRUE	1	0.283199084601795	2		1125	945	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424734	47424734	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	106	880	1	ENST00000377045.4:c.547del	p.Gln183ArgfsTer109	p.Q183Rfs*109	ENST00000377045	NM_001654.4	181	aCc/ac	6/16	1	2	FACETS	0.905	0.811	1	0.905	0.811	1	CLONAL	1	TRUE	1	0.283199084601795	2		881	827	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188853	32188853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs192478549	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	85	1011	0	ENST00000375023.3:c.701G>A	p.Arg234Gln	p.R234Q	ENST00000375023	NM_004557.3	234	cGg/cAg	4/30	1	2	FACETS	0.669	0.59	0.754	0.669	0.59	0.754	SUBCLONAL	1	TRUE	1	0.283199084601795	2		1011	897	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467573	66467573	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	37	430	0	ENST00000273854.3:c.696del	p.Lys232AsnfsTer36	p.K232Nfs*36	ENST00000273854	NM_004439.5	232	aaA/aa	3/18	1	2	FACETS	0.567	0.467	0.678	0.567	0.467	0.678	SUBCLONAL	1	TRUE	1	0.283199084601795	2		430	461	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955112	17955112	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755706305	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	127	1016	3	ENST00000458235.1:c.115del	p.Gln39SerfsTer108	p.Q39Sfs*108	ENST00000458235	NM_000215.3	39	Cag/ag	2/24	1	2	FACETS	0.886	0.802	0.976	0.886	0.802	0.976	CLONAL	1	TRUE	1	0.283199084601795	2		1019	1012	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933013	39933013	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	51	1021	1	ENST00000378444.4:c.1586del	p.Asn529ThrfsTer60	p.N529Tfs*60	ENST00000378444	NM_001123385.1	529	aAc/ac	4/15	1	2	FACETS	0.389	0.329	0.454	0.389	0.329	0.454	SUBCLONAL	1	TRUE	1	0.283199084601795	2		1022	927	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255694	16255694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376676096	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	83	530	0	ENST00000375759.3:c.2959C>T	p.Arg987Cys	p.R987C	ENST00000375759	NM_015001.2	987	Cgc/Tgc	11/15	1	2	FACETS	0.966	0.853	1	0.966	0.853	1	CLONAL	1	TRUE	1	0.283199084601795	2		530	607	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255563	16255563	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	38	569	2	ENST00000375759.3:c.2828A>G	p.Lys943Arg	p.K943R	ENST00000375759	NM_015001.2	943	aAg/aGg	11/15	1	2	FACETS	0.414	0.341	0.495	0.414	0.341	0.495	SUBCLONAL	1	TRUE	1	0.283199084601795	2		571	649	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241276	105241276	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	116	989	0	ENST00000349310.3:c.632C>T	p.Thr211Ile	p.T211I	ENST00000349310	NM_001014432.1	211	aCa/aTa	8/15	1	2	FACETS	0.914	0.823	1	0.914	0.823	1	CLONAL	1	TRUE	1	0.283199084601795	2		989	896	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123040864	123040864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1489246570	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	121	679	0	ENST00000355640.3:c.1327C>T	p.Arg443Cys	p.R443C	ENST00000355640		443	Cgc/Tgc	7/7	1	2	FACETS	0.848	0.765	0.936	0.848	0.765	0.936	CLONAL	1	TRUE	1	0.283199084601795	2		679	1008	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	48	457	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	0.468	0.395	0.55	0.468	0.395	0.55	SUBCLONAL	1	TRUE	1	0.283199084601795	2		457	724	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	82	811	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	0.283199084601795	3	FACETS	0.697	0.613	0.788	0.349	0.306	0.394	SUBCLONAL	1	TRUE	1	0.283199084601795	3		811	948	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441816	49441816	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	52	852	2	ENST00000301067.7:c.4168del	p.Ala1390GlnfsTer27	p.A1390Qfs*27	ENST00000301067	NM_003482.3	1390	Gca/ca	14/54	1	2	FACETS	0.4	0.339	0.467	0.4	0.339	0.467	SUBCLONAL	1	TRUE	1	0.283199084601795	2		854	919	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444933	49444933	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767415197	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	50	909	4	ENST00000301067.7:c.2533del	p.Arg845GlyfsTer85	p.R845Gfs*85	ENST00000301067	NM_003482.3	845	Cgg/gg	10/54	1	2	FACETS	0.435	0.368	0.51	0.435	0.368	0.51	SUBCLONAL	1	TRUE	1	0.283199084601795	2		913	811	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197307	94197308	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	86	391	0	ENST00000323929.3:c.1196dup	p.Arg400GlnfsTer3	p.R400Qfs*3	ENST00000323929	NM_005591.3	399	ttc/ttTc	11/20	1	2	FACETS	0.869	0.769	0.976	0.869	0.769	0.976	CLONAL	1	TRUE	1	0.283199084601795	2		391	699	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323268	31323268	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1322740343	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	37	624	0	ENST00000412585.2:c.721T>C	p.Trp241Arg	p.W241R	ENST00000412585	NM_005514.6	241	Tgg/Cgg	4/8	1	2	FACETS	0.424	0.349	0.509	0.424	0.349	0.509	SUBCLONAL	1	TRUE	1	0.283199084601795	2		624	616	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714412	40714412	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	92	745	0	ENST00000373198.4:c.3985G>A	p.Glu1329Lys	p.E1329K	ENST00000373198	NM_133170.3	1329	Gag/Aag	29/32	0.270640891498751	1	FACETS	0.717	0.636	0.803	0.717	0.636	0.803	SUBCLONAL	1	TRUE	0	0.283199084601795	1		745	778	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370847	55370847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	61	545	2	ENST00000297316.4:c.149C>T	p.Ala50Val	p.A50V	ENST00000297316	NM_022454.3	50	gCg/gTg	1/2	1	2	FACETS	0.894	0.772	1	0.894	0.772	1	CLONAL	1	TRUE	1	0.283199084601795	2		547	482	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765647	41765647	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1181583644	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	151	1072	2	ENST00000301178.4:c.2528del	p.Pro843GlnfsTer113	p.P843Qfs*113	ENST00000301178	NM_021913.4	841	gaC/ga	20/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.283199084601795	2		1074	941	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43815020	43815041	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCACACTACAGGTACCGCCCCC	GCACACTACAGGTACCGCCCCC	-	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	114	761	0	ENST00000372470.3:c.1557_1565+13del		p.X519_splice	ENST00000372470	NM_005373.2	519		10/12	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.283199084601795	2		761	788	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099341	193099341	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	79	281	0	ENST00000367435.3:c.275A>G	p.Lys92Arg	p.K92R	ENST00000367435	NM_024529.4	92	aAa/aGa	3/17	1	2	FACETS	0.861	0.757	0.972	0.861	0.757	0.972	CLONAL	1	TRUE	1	0.283199084601795	2		281	648	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982157	201982157	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	140	1010	0	ENST00000359651.3:c.681C>A	p.Phe227Leu	p.F227L	ENST00000359651		227	ttC/ttA	5/8	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.283199084601795	2		1010	980	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667515	241667515	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	58	226	0	ENST00000366560.3:c.935T>C	p.Phe312Ser	p.F312S	ENST00000366560	NM_000143.3	312	tTt/tCt	7/10	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.283199084601795	2		226	356	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347526	118347527	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	105	442	0	ENST00000534358.1:c.3166dup	p.Ser1056LysfsTer2	p.S1056Kfs*2	ENST00000534358	NM_005933.3	1055	gaa/gAaa	4/36	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.283199084601795	2		442	681	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445238	49445238	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	109	1247	0	ENST00000301067.7:c.2228T>C	p.Leu743Pro	p.L743P	ENST00000301067	NM_003482.3	743	cTg/cCg	10/54	1	2	FACETS	0.695	0.623	0.773	0.695	0.623	0.773	SUBCLONAL	1	TRUE	1	0.283199084601795	2		1247	1107	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194790	30194791	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	124	626	0	ENST00000331968.5:c.354dup	p.Ala119SerfsTer4	p.A119Sfs*4	ENST00000331968	NM_002742.2	118	-/A	2/18	1	2	FACETS	0.958	0.866	1	0.958	0.866	1	CLONAL	1	TRUE	1	0.283199084601795	2		626	914	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43699749	43699750	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	76	533	0	ENST00000382044.4:c.5765_5766del	p.Phe1922Ter	p.F1922*	ENST00000382044	NM_001141980.1	1922	tTT/t	28/28	1	2	FACETS	0.828	0.727	0.938	0.828	0.727	0.938	CLONAL	1	TRUE	1	0.283199084601795	2		533	648	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122362	17122362	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	68	836	0	ENST00000285071.4:c.1033G>T	p.Val345Phe	p.V345F	ENST00000285071	NM_144997.5	345	Gtc/Ttc	9/14	1	2	FACETS	0.674	0.586	0.77	0.674	0.586	0.77	SUBCLONAL	1	TRUE	1	0.283199084601795	2		836	712	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756562	756562	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	137	395	0	ENST00000314574.4:c.266T>C	p.Leu89Ser	p.L89S	ENST00000314574	NM_005433.3	89	tTa/tCa	2/12	0.238213721495353	2	FACETS	0.776	0.709	0.847	0.776	0.709	0.847	SUBCLONAL	2	TRUE	0	0.283199084601795	2		395	623	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221126	5221126	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	114	1058	0	ENST00000357368.4:c.3340A>G	p.Thr1114Ala	p.T1114A	ENST00000357368	NM_002850.3	1114	Acc/Gcc	20/38	1	2	FACETS	0.848	0.763	0.939	0.848	0.763	0.939	CLONAL	1	TRUE	1	0.283199084601795	2		1058	949	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311608	15311608	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	24	193	1	ENST00000263388.2:c.109G>T	p.Gly37Trp	p.G37W	ENST00000263388	NM_000435.2	37	Ggg/Tgg	1/33	1	2	FACETS	1	0.798	1	1	0.798	1	CLONAL	1	TRUE	1	0.283199084601795	2		194	168	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714693	52714693	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	157	1045	0	ENST00000322088.6:c.451T>A	p.Phe151Ile	p.F151I	ENST00000322088	NM_014225.5	151	Ttc/Atc	4/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.283199084601795	2		1045	1011	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206707	36206707	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	72	1074	0	ENST00000300305.3:c.805G>T	p.Asp269Tyr	p.D269Y	ENST00000300305		269	Gat/Tat	6/8	1	2	FACETS	0.47	0.409	0.537	0.47	0.409	0.537	SUBCLONAL	1	TRUE	1	0.283199084601795	2		1074	1081	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098538	47098538	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	42	699	0	ENST00000409792.3:c.6736G>A	p.Gly2246Ser	p.G2246S	ENST00000409792	NM_014159.6	2246	Ggt/Agt	15/21	1	2	FACETS	0.444	0.37	0.527	0.444	0.37	0.527	SUBCLONAL	1	TRUE	1	0.283199084601795	2		699	668	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162778	47162778	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	70	422	0	ENST00000409792.3:c.3348del	p.Lys1116AsnfsTer5	p.K1116Nfs*5	ENST00000409792	NM_014159.6	1116	aaA/aa	3/21	1	2	FACETS	0.801	0.699	0.912	0.801	0.699	0.912	CLONAL	1	TRUE	1	0.283199084601795	2		422	617	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928438	69928438	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	60	812	0	ENST00000352241.4:c.258G>A	p.Met86Ile	p.M86I	ENST00000352241	NM_198159.2	86	atG/atA	2/10	1	2	FACETS	0.548	0.471	0.632	0.548	0.471	0.632	SUBCLONAL	1	TRUE	1	0.283199084601795	2		812	773	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873118	134873118	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	84	759	0	ENST00000398015.3:c.1422G>T	p.Lys474Asn	p.K474N	ENST00000398015	NM_004441.4	474	aaG/aaT	6/16	0.148481537823146	1	FACETS	0.756	0.667	0.85	0.756	0.667	0.85	INDETERMINATE	1	TRUE	0	0.283199084601795	1		759	674	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916904	178916905	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	53	503	0	ENST00000263967.3:c.296dup	p.Leu99PhefsTer5	p.L99Ffs*5	ENST00000263967	NM_006218.2	97	-/T	2/21	1	2	FACETS	0.476	0.404	0.554	0.476	0.404	0.554	SUBCLONAL	1	TRUE	1	0.283199084601795	2		503	787	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323979	31323979	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	71	732	0	ENST00000412585.2:c.584A>G	p.Tyr195Cys	p.Y195C	ENST00000412585	NM_005514.6	195	tAc/tGc	3/8	1	2	FACETS	0.688	0.6	0.783	0.688	0.6	0.783	SUBCLONAL	1	TRUE	1	0.283199084601795	2		732	729	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522125	157522125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	113	865	3	ENST00000346085.5:c.4397C>T	p.Ala1466Val	p.A1466V	ENST00000346085	NM_020732.3	1466	gCa/gTa	18/20	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.283199084601795	2		868	778	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146133	38146133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	131	918	1	ENST00000317025.8:c.3373C>T	p.Pro1125Ser	p.P1125S	ENST00000317025	NM_023034.1	1125	Ccg/Tcg	19/24	1	2	FACETS	0.911	0.826	1	0.911	0.826	1	CLONAL	1	TRUE	1	0.283199084601795	2		919	1015	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	322	1080	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.380352292847509	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	FALSE	0	0.380352292847509	1		1080	974	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435631	149435631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs690016557	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	146	628	0	ENST00000286301.3:c.2512G>A	p.Val838Ile	p.V838I	ENST00000286301	NM_005211.3	838	Gtc/Atc	19/22	0.132610281937033	0	FACETS	0.553	0.505	0.604			1	INDETERMINATE	1	FALSE	0	0.380352292847509	0		628	860	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987025	69987025	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750608171	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	63	551	0	ENST00000394351.3:c.86G>A	p.Arg29Gln	p.R29Q	ENST00000394351	NM_000248.3	29	cGg/cAg	2/9	1	2	FACETS	0.392	0.338	0.451	0.392	0.338	0.451	SUBCLONAL	1	FALSE	1	0.380352292847509	2		551	845	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557909	187557909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564430066	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	155	537	2	ENST00000441802.2:c.3802C>T	p.Arg1268Trp	p.R1268W	ENST00000441802	NM_005245.3	1268	Cgg/Tgg	5/27	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.380352292847509	2		539	766	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020775	112020775	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369151232	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	130	434	0	ENST00000368678.4:c.796C>T	p.Arg266Cys	p.R266C	ENST00000368678		266	Cgt/Tgt	8/13	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	FALSE	1	0.380352292847509	2		434	674	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233090	69233090	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746910913	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	48	216	1	ENST00000462284.1:c.961del	p.Leu321PhefsTer52	p.L321Ffs*52	ENST00000462284	NM_002392.5	319	Ccc/cc	11/11	1	2	FACETS	0.421	0.355	0.493	0.421	0.355	0.493	SUBCLONAL	1	FALSE	1	0.380352292847509	2		217	600	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572261	64572261	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs104894267	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	133	455	2	ENST00000312049.6:c.1378C>T	p.Arg460Ter	p.R460*	ENST00000312049	NM_130799.2	460	Cga/Tga	10/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.380352292847509	2		457	551	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097630	27097630	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	206	535	0	ENST00000324856.7:c.3219G>A	p.Trp1073Ter	p.W1073*	ENST00000324856	NM_006015.4	1073	tgG/tgA	12/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.380352292847509	2		535	878	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924822	49924822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202007332	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	92	822	0	ENST00000296474.3:c.4121G>A	p.Arg1374His	p.R1374H	ENST00000296474	NM_002447.2	1374	cGt/cAt	20/20	1	2	FACETS	0.425	0.377	0.478	0.425	0.377	0.478	SUBCLONAL	1	FALSE	1	0.380352292847509	2		822	1137	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723126	49723128	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs751306787	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	64	483	0	ENST00000449682.2:c.1288_1290del	p.Glu430del	p.E430del	ENST00000449682	NM_020998.3	430	GAG/-	11/18	1	2	FACETS	0.479	0.414	0.549	0.479	0.414	0.549	SUBCLONAL	1	FALSE	1	0.380352292847509	2		483	703	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651096	206651096	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868911910	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	91	620	0	ENST00000367120.3:c.706C>T	p.Arg236Trp	p.R236W	ENST00000367120	NM_014002.3	236	Cgg/Tgg	8/22	1	2	FACETS	0.463	0.41	0.52	0.463	0.41	0.52	SUBCLONAL	1	FALSE	1	0.380352292847509	2		620	1034	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851456	63851456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201542647	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	320	500	1	ENST00000279873.7:c.2234C>T	p.Ala745Val	p.A745V	ENST00000279873	NM_032199.2	745	gCg/gTg	10/10	0.0990754804915412	6	FACETS	0.939	0.887	0.991			1	INDETERMINATE	3	FALSE	NA	0.380352292847509	6		501	1052	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855831	45855831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747646421	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	310	688	0	ENST00000391945.4:c.1979C>T	p.Ala660Val	p.A660V	ENST00000391945	NM_000400.3	660	gCg/gTg	21/23	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	FALSE	1	0.380352292847509	2		688	1140	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446279	70446279	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763447831	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	172	553	0	ENST00000373644.4:c.5219G>A	p.Arg1740His	p.R1740H	ENST00000373644	NM_030625.2	1740	cGc/cAc	11/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.380352292847509	2		553	798	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425644	49425644	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057517992	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	253	796	0	ENST00000301067.7:c.12844C>T	p.Arg4282Ter	p.R4282*	ENST00000301067	NM_003482.3	4282	Cga/Tga	39/54	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.380352292847509	2		796	1051	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008324	29008324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770377283	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	124	338	0	ENST00000282397.4:c.547C>T	p.Arg183Cys	p.R183C	ENST00000282397	NM_002019.4	183	Cgc/Tgc	5/30	0.380352292847509	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	0	0.380352292847509	1		338	496	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163309260	163309260	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	35	343	1	ENST00000271452.3:c.604del	p.Thr202ArgfsTer2	p.T202Rfs*2	ENST00000271452	NM_145697.2	200	cAa/ca	8/14	1	2	FACETS	0.287	0.234	0.347	0.287	0.234	0.347	SUBCLONAL	1	FALSE	1	0.380352292847509	2		344	641	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342776	118342776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781978595	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	25	310	0	ENST00000534358.1:c.902G>A	p.Arg301Gln	p.R301Q	ENST00000534358	NM_005933.3	301	cGa/cAa	3/36	0.132610281937033	0	FACETS	0.174	0.137	0.217			1	INDETERMINATE	1	FALSE	0	0.380352292847509	0		310	468	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917610	151917610	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	67	529	0	ENST00000262189.6:c.3710G>A	p.Arg1237Gln	p.R1237Q	ENST00000262189	NM_170606.2	1237	cGa/cAa	23/59	1	2	FACETS	0.425	0.368	0.487	0.425	0.368	0.487	SUBCLONAL	1	FALSE	1	0.380352292847509	2		529	829	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261683	16261683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149575630	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	244	599	0	ENST00000375759.3:c.8948C>T	p.Thr2983Met	p.T2983M	ENST00000375759	NM_015001.2	2983	aCg/aTg	11/15	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.380352292847509	2		599	920	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914152	32914152	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507795	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	154	477	1	ENST00000380152.3:c.5660C>T	p.Thr1887Met	p.T1887M	ENST00000380152		1887	aCg/aTg	11/27	0.380352292847509	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	0	0.380352292847509	1		478	587	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865611	57865611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1027428919	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	283	831	0	ENST00000228682.2:c.3088G>A	p.Glu1030Lys	p.E1030K	ENST00000228682	NM_005269.2	1030	Gaa/Aaa	12/12	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.380352292847509	2		831	1280	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777801	3777801	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1213	99	880	0	ENST00000262367.5:c.7247G>A	p.Ser2416Asn	p.S2416N	ENST00000262367	NM_004380.2	2416	aGc/aAc	31/31	1	2	FACETS	0.397	0.353	0.444	0.397	0.353	0.444	SUBCLONAL	1	FALSE	1	0.380352292847509	2		880	1312	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845261	151845261	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	195	473	0	ENST00000262189.6:c.13751G>A	p.Arg4584Gln	p.R4584Q	ENST00000262189	NM_170606.2	4584	cGg/cAg	52/59	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.380352292847509	2		473	796	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061593	38061622	+	inframe_deletion	In_Frame_Del	DEL	GGCCGCGTAGGGGCCCAGGCCATTCATGGA	GGCCGCGTAGGGGCCCAGGCCATTCATGGA	-	novel	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	19	90	0	ENST00000250448.2:c.367_396del	p.Ser123_Ala132del	p.S123_A132del	ENST00000250448	NM_004496.3	123	TCCATGAATGGCCTGGGCCCCTACGCGGCC/-	2/2	1	2	FACETS	0.628	0.48	0.8	0.628	0.48	0.8	SUBCLONAL	1	FALSE	1	0.380352292847509	2		90	159	SUCCESS
APC	324	MSKCC	GRCh37	5	112102982	112102982	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201764637	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	159	453	1	ENST00000257430.4:c.317G>A	p.Arg106His	p.R106H	ENST00000257430	NM_000038.5	106	cGt/cAt	4/16	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.380352292847509	2		454	808	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362545	118362545	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	114	456	0	ENST00000534358.1:c.4906C>T	p.Arg1636Ter	p.R1636*	ENST00000534358	NM_005933.3	1636	Cga/Tga	15/36	0.132610281937033	0	FACETS	0.538	0.485	0.595			1	INDETERMINATE	1	FALSE	0	0.380352292847509	0		456	690	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2492147	2492147	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	140	627	0	ENST00000355716.4:c.545A>G	p.Gln182Arg	p.Q182R	ENST00000355716	NM_003820.2	182	cAg/cGg	5/8	1	2	FACETS	0.822	0.748	0.899	0.822	0.748	0.899	CLONAL	1	FALSE	1	0.380352292847509	2		627	896	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939141	36939141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757569036	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	307	791	0	ENST00000361632.4:c.568C>T	p.Arg190Cys	p.R190C	ENST00000361632		190	Cgc/Tgc	5/16	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	FALSE	1	0.380352292847509	2		791	1193	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332611	65332611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568014073	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	39	382	0	ENST00000342505.4:c.928G>A	p.Val310Ile	p.V310I	ENST00000342505	NM_002227.2	310	Gtt/Att	7/25	1	2	FACETS	0.328	0.271	0.392	0.328	0.271	0.392	SUBCLONAL	1	FALSE	1	0.380352292847509	2		382	625	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984347	201984361	+	inframe_deletion	In_Frame_Del	DEL	AAACGGGAGATCCTG	AAACGGGAGATCCTG	-	novel	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	183	630	0	ENST00000359651.3:c.1012_1026del	p.Lys338_Leu342del	p.K338_L342del	ENST00000359651		338	AAACGGGAGATCCTG/-	8/8	1	2	FACETS	0.995	0.918	1	0.995	0.918	1	CLONAL	1	FALSE	1	0.380352292847509	2		630	967	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332981	70332981	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	77	734	0	ENST00000373644.4:c.886T>C	p.Cys296Arg	p.C296R	ENST00000373644	NM_030625.2	296	Tgc/Cgc	2/12	1	2	FACETS	0.378	0.33	0.429	0.378	0.33	0.429	SUBCLONAL	1	FALSE	1	0.380352292847509	2		734	1072	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589636	69589636	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	42	115	0	ENST00000168712.1:c.217G>A	p.Ala73Thr	p.A73T	ENST00000168712	NM_002007.2	73	Gcc/Acc	1/3	0.380352292847509	9	FACETS	0.943	0.787	1			1	CLONAL	1	FALSE	NA	0.380352292847509	9		115	546	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420688	49420688	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783695	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	227	579	1	ENST00000301067.7:c.15061C>T	p.Arg5021Ter	p.R5021*	ENST00000301067	NM_003482.3	5021	Cga/Tga	48/54	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.380352292847509	2		580	1060	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428240	49428240	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	112	715	2	ENST00000301067.7:c.10460C>A	p.Pro3487His	p.P3487H	ENST00000301067	NM_003482.3	3487	cCc/cAc	37/54	1	2	FACETS	0.482	0.432	0.535	0.482	0.432	0.535	SUBCLONAL	1	FALSE	1	0.380352292847509	2		717	1222	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440161	49440161	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	60	608	0	ENST00000301067.7:c.4465T>C	p.Cys1489Arg	p.C1489R	ENST00000301067	NM_003482.3	1489	Tgt/Cgt	16/54	1	2	FACETS	0.287	0.246	0.332	0.287	0.246	0.332	SUBCLONAL	1	FALSE	1	0.380352292847509	2		608	1099	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479307	50479307	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	36	319	0	ENST00000394963.4:c.155C>G	p.Pro52Arg	p.P52R	ENST00000394963	NM_003076.4	52	cCg/cGg	1/13	1	2	FACETS	0.325	0.266	0.391	0.325	0.266	0.391	SUBCLONAL	1	FALSE	1	0.380352292847509	2		319	583	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214639	133214639	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	49	571	0	ENST00000320574.5:c.5639T>C	p.Val1880Ala	p.V1880A	ENST00000320574	NM_006231.2	1880	gTg/gCg	41/49	1	2	FACETS	0.281	0.237	0.329	0.281	0.237	0.329	SUBCLONAL	1	FALSE	1	0.380352292847509	2		571	918	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632602	3632602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377329498	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	66	769	1	ENST00000294008.3:c.5246C>T	p.Ala1749Val	p.A1749V	ENST00000294008	NM_032444.2	1749	gCg/gTg	15/15	1	2	FACETS	0.322	0.278	0.37	0.322	0.278	0.37	SUBCLONAL	1	FALSE	1	0.380352292847509	2		770	1077	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772297	68772297	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	129	697	2	ENST00000261769.5:c.146G>A	p.Gly49Asp	p.G49D	ENST00000261769	NM_004360.3	49	gGc/gAc	2/16	0.380352292847509	1	FACETS	0.573	0.519	0.63	0.573	0.519	0.63	SUBCLONAL	1	FALSE	0	0.380352292847509	1		699	959	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371698	89371698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1366375142	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	290	734	0	ENST00000301030.4:c.142G>A	p.Gly48Arg	p.G48R	ENST00000301030	NM_001256183.1	48	Ggg/Agg	4/13	0.380352292847509	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	0	0.380352292847509	1		734	1060	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273533	5273533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	105	655	0	ENST00000357368.4:c.299G>A	p.Arg100Gln	p.R100Q	ENST00000357368	NM_002850.3	100	cGg/cAg	4/38	1	2	FACETS	0.536	0.479	0.596	0.536	0.479	0.596	SUBCLONAL	1	FALSE	1	0.380352292847509	2		655	1031	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15273340	15273340	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	68	700	0	ENST00000263388.2:c.5849A>G	p.Asn1950Ser	p.N1950S	ENST00000263388	NM_000435.2	1950	aAc/aGc	32/33	1	2	FACETS	0.315	0.273	0.361	0.315	0.273	0.361	SUBCLONAL	1	FALSE	1	0.380352292847509	2		700	1136	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943675	17943675	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	63	755	0	ENST00000458235.1:c.2414G>T	p.Gly805Val	p.G805V	ENST00000458235	NM_000215.3	805	gGt/gTt	18/24	1	2	FACETS	0.301	0.259	0.346	0.301	0.259	0.346	SUBCLONAL	1	FALSE	1	0.380352292847509	2		755	1102	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026705	48026706	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	180	544	0	ENST00000234420.5:c.1583_1584del	p.Glu528GlyfsTer2	p.E528Gfs*2	ENST00000234420	NM_000179.2	528	gAA/g	4/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.380352292847509	2		544	735	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376214	225376214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	175	576	0	ENST00000264414.4:c.740G>A	p.Arg247Gln	p.R247Q	ENST00000264414	NM_003590.4	247	cGa/cAa	6/16	NA	2	FACETS	0.996	0.917	1			1	INDETERMINATE	1	FALSE	NA	0.380352292847509	2		576	924	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405949	49405949	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	67	546	1	ENST00000418115.1:c.189G>T	p.Gln63His	p.Q63H	ENST00000418115	NM_001664.2	63	caG/caT	3/5	1	2	FACETS	0.376	0.326	0.431	0.376	0.326	0.431	SUBCLONAL	1	FALSE	1	0.380352292847509	2		547	936	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014110	70014110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	62	590	1	ENST00000394351.3:c.971G>A	p.Cys324Tyr	p.C324Y	ENST00000394351	NM_000248.3	324	tGc/tAc	9/9	1	2	FACETS	0.384	0.331	0.442	0.384	0.331	0.442	SUBCLONAL	1	FALSE	1	0.380352292847509	2		591	849	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751570	57751570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	38	330	0	ENST00000274289.3:c.1421C>T	p.Thr474Ile	p.T474I	ENST00000274289	NM_006622.3	474	aCa/aTa	11/14	1	2	FACETS	0.369	0.304	0.441	0.369	0.304	0.441	SUBCLONAL	1	FALSE	1	0.380352292847509	2		330	542	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631153	176631153	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1172667661	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	54	534	0	ENST00000439151.2:c.1096G>A	p.Val366Met	p.V366M	ENST00000439151	NM_022455.4	366	Gtg/Atg	4/23	0.132610281937033	0	FACETS	0.201	0.17	0.234			1	INDETERMINATE	1	FALSE	0	0.380352292847509	0		534	877	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146046	38146046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1387874215	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	95	673	1	ENST00000317025.8:c.3460C>T	p.Arg1154Trp	p.R1154W	ENST00000317025	NM_023034.1	1154	Cgg/Tgg	19/24	0.30272155127808	1	FACETS	0.371	0.33	0.416	0.371	0.33	0.416	SUBCLONAL	1	FALSE	0	0.380352292847509	1		674	1089	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391467	139391467	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	90	752	1	ENST00000277541.6:c.6724C>A	p.Leu2242Met	p.L2242M	ENST00000277541	NM_017617.3	2242	Ctg/Atg	34/34	1	2	FACETS	0.39	0.345	0.439	0.39	0.345	0.439	SUBCLONAL	1	FALSE	1	0.380352292847509	2		753	1212	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410063	139410063	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544117297	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	341	747	3	ENST00000277541.6:c.1775G>A	p.Arg592His	p.R592H	ENST00000277541	NM_017617.3	592	cGc/cAc	11/34	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	FALSE	1	0.380352292847509	2		750	1257	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932303	39932303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1025284999	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	105	460	1	ENST00000378444.4:c.2296G>A	p.Glu766Lys	p.E766K	ENST00000378444	NM_001123385.1	766	Gag/Aag	4/15	0.337075088055205	2	FACETS	0.637	0.57	0.708			1	SUBCLONAL	1	FALSE	NA	0.380352292847509	2		461	867	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228289	53228289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	413	351	0	ENST00000375401.3:c.2113C>T	p.Arg705Cys	p.R705C	ENST00000375401	NM_004187.3	705	Cgc/Tgc	15/26	0.337075088055205	2	FACETS	1	0.984	1			1	CLONAL	3	FALSE	NA	0.380352292847509	2		351	695	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519920	NA	P-0047603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	164	399	0	ENST00000397062.3:c.85G>C	p.Asp29His	p.D29H	ENST00000397062	NM_006164.4	29	Gat/Cat	2/5	0.701562309639268	3	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.701562309639268	3		399	518	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059132	47059132	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	278	603	0	ENST00000409792.3:c.7529G>T	p.Arg2510Leu	p.R2510L	ENST00000409792	NM_014159.6	2510	cGc/cTc	20/21	0.677052455363546	3	FACETS	0.949	0.901	0.997	0.949	0.901	0.997	CLONAL	2	TRUE	1	0.701562309639268	3		603	564	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155478	47155478	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	107	412	0	ENST00000409792.3:c.4603A>G	p.Asn1535Asp	p.N1535D	ENST00000409792	NM_014159.6	1535	Aat/Gat	5/21	0.677052455363546	3	FACETS	0.974	0.88	1	0.487	0.44	0.536	CLONAL	1	TRUE	1	0.701562309639268	3		412	423	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176700671	176700671	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0047603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	372	445	0	ENST00000439151.2:c.5510-2A>G		p.X1837_splice	ENST00000439151	NM_022455.4	1837			0.679789371353387	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	0	0.701562309639268	3		445	467	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652025	36652025	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	459	922	0	ENST00000244741.5:c.147G>A	p.Trp49Ter	p.W49*	ENST00000244741	NM_000389.4	49	tgG/tgA	2/3	1	2	FACETS	0.979	0.936	1	0.979	0.936	1	CLONAL	1	TRUE	1	0.789398818463719	2		922	1188	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257854	19257854	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752421135	NA	P-0047604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	399	839	0	ENST00000162023.5:c.532G>A	p.Gly178Arg	p.G178R	ENST00000162023		178	Ggg/Agg	9/13	1	2	FACETS	0.966	0.921	1	0.966	0.921	1	CLONAL	1	TRUE	1	0.789398818463719	2		839	1047	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573537	48573537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	180	345	0	ENST00000342988.3:c.121G>A	p.Glu41Lys	p.E41K	ENST00000342988	NM_005359.5	41	Gaa/Aaa	2/12	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.789398818463719	2		345	454	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105505	11105516	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	AATACCTCAATA	AATACCTCAATA	-	novel	NA	P-0047604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	252	568	0	ENST00000358026.2:c.1421_1432del	p.Glu474_Ser478delinsGly	p.E474_S478delinsG	ENST00000358026	NM_001128849.1	474	gAATACCTCAATAgc/ggc	9/36	1	2	FACETS	0.939	0.884	0.995	0.939	0.884	0.995	CLONAL	1	TRUE	1	0.789398818463719	2		568	680	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193967	106193967	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	191	297	0	ENST00000380013.4:c.4429G>C	p.Glu1477Gln	p.E1477Q	ENST00000380013	NM_001127208.2	1477	Gaa/Caa	10/11	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.789398818463719	2		297	470	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652025	36652025	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047604-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	384	922	0	ENST00000244741.5:c.147G>A	p.Trp49Ter	p.W49*	ENST00000244741	NM_000389.4	49	tgG/tgA	2/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.796049536988771	2		922	939	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257854	19257854	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752421135	NA	P-0047604-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	235	839	0	ENST00000162023.5:c.532G>A	p.Gly178Arg	p.G178R	ENST00000162023		178	Ggg/Agg	9/13	1	2	FACETS	0.962	0.904	1	0.962	0.904	1	CLONAL	1	FALSE	1	0.796049536988771	2		839	614	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573537	48573537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047604-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	81	345	0	ENST00000342988.3:c.121G>A	p.Glu41Lys	p.E41K	ENST00000342988	NM_005359.5	41	Gaa/Aaa	2/12	1	2	FACETS	0.921	0.826	1	0.921	0.826	1	CLONAL	1	FALSE	1	0.796049536988771	2		345	221	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105505	11105516	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	AATACCTCAATA	AATACCTCAATA	-	novel	NA	P-0047604-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	151	568	0	ENST00000358026.2:c.1421_1432del	p.Glu474_Ser478delinsGly	p.E474_S478delinsG	ENST00000358026	NM_001128849.1	474	gAATACCTCAATAgc/ggc	9/36	1	2	FACETS	0.978	0.905	1	0.978	0.905	1	CLONAL	1	FALSE	1	0.796049536988771	2		568	388	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193967	106193967	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047604-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	110	297	0	ENST00000380013.4:c.4429G>C	p.Glu1477Gln	p.E1477Q	ENST00000380013	NM_001127208.2	1477	Gaa/Caa	10/11	1	2	FACETS	0.891	0.812	0.973	0.891	0.812	0.973	CLONAL	1	FALSE	1	0.796049536988771	2		297	310	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0047608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	43	519	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.313	0.261	0.37	0.313	0.261	0.37	SUBCLONAL	1	TRUE	1	0.471229135783713	2		519	584	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0047608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	171	580	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.911	0.839	0.985	0.911	0.839	0.985	CLONAL	1	TRUE	1	0.471229135783713	2		580	797	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0047608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	139	454	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.471229135783713	2		454	552	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440713	56440713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779337229	NA	P-0047608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	152	591	0	ENST00000407977.2:c.505G>A	p.Ala169Thr	p.A169T	ENST00000407977		169	Gct/Act	5/10	0.471229135783713	1	FACETS	0.745	0.683	0.809	0.745	0.683	0.809	SUBCLONAL	1	TRUE	0	0.471229135783713	1		591	662	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258035	123258035	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	168	517	0	ENST00000358487.5:c.1646A>C	p.Asn549Thr	p.N549T	ENST00000358487	NM_000141.4	549	aAt/aCt	12/18	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.471229135783713	2		517	653	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371810	55371831	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGCCCCGAGGGCGGCCGCGT	TGGGCCCCGAGGGCGGCCGCGT	-	novel	NA	P-0047608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	58	62	0	ENST00000297316.4:c.500_521del	p.Leu167ArgfsTer213	p.L167Rfs*213	ENST00000297316	NM_022454.3	167	cTGGGCCCCGAGGGCGGCCGCGTg/cg	2/2	1	2	FACETS	0.826	0.727	0.928	1	0.977	1	CLONAL	2	TRUE	1	0.471229135783713	2		62	149	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89335044	89335044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	47	319	0	ENST00000301030.4:c.7834G>A	p.Glu2612Lys	p.E2612K	ENST00000301030	NM_001256183.1	2612	Gag/Aag	13/13	1	2	FACETS	0.57	0.483	0.666	0.57	0.483	0.666	SUBCLONAL	1	TRUE	1	0.471229135783713	2		319	350	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439945	56439945	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	73	577	1	ENST00000407977.2:c.647C>A	p.Ser216Ter	p.S216*	ENST00000407977		216	tCg/tAg	6/10	0.471229135783713	1	FACETS	0.277	0.242	0.316	0.277	0.242	0.316	SUBCLONAL	1	TRUE	0	0.471229135783713	1		578	854	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440698	56440698	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	43	621	0	ENST00000407977.2:c.520G>T	p.Glu174Ter	p.E174*	ENST00000407977		174	Gag/Tag	5/10	0.471229135783713	1	FACETS	0.197	0.164	0.234	0.197	0.164	0.234	SUBCLONAL	1	TRUE	0	0.471229135783713	1		621	708	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131478	202131478	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	64	428	0	ENST00000358485.4:c.446T>C	p.Leu149Pro	p.L149P	ENST00000358485	NM_001080125.1	149	cTt/cCt	2/9	1	2	FACETS	0.49	0.425	0.561	0.49	0.425	0.561	SUBCLONAL	1	TRUE	1	0.471229135783713	2		428	554	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948134	178948134	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	87	222	0	ENST00000263967.3:c.2906A>G	p.Gln969Arg	p.Q969R	ENST00000263967	NM_006218.2	969	cAa/cGa	20/21	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.471229135783713	2		222	338	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100324	157100324	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	26	216	0	ENST00000346085.5:c.1261C>T	p.Gln421Ter	p.Q421*	ENST00000346085	NM_020732.3	421	Cag/Tag	1/20	1	2	FACETS	0.311	0.246	0.385	0.311	0.246	0.385	SUBCLONAL	1	TRUE	1	0.471229135783713	2		216	355	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339327	70339327	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	124	427	0	ENST00000374080.3:c.204+1del		p.K68fs	ENST00000374080		68	aaG/aa	2/45	1	2	FACETS	0.95	0.863	1	0.95	0.863	1	CLONAL	1	TRUE	1	0.471229135783713	2		427	554	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0047609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	138	334	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.155746531346041	2	FACETS	1	0.985	1	0.694	0.633	0.756	INDETERMINATE	1	TRUE	0	0.324600561778862	2		334	613	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0047609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	127	744	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	0.901	0.816	0.991	0.901	0.816	0.991	CLONAL	1	TRUE	1	0.324600561778862	2		744	868	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	150	815	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.257269890291021	1	FACETS	0.97	0.888	1	0.97	0.888	1	CLONAL	1	TRUE	0	0.324600561778862	1		815	798	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0047609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	80	456	0	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.827	0.729	0.932	0.827	0.729	0.932	CLONAL	1	TRUE	1	0.324600561778862	2		456	596	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217652	7217653	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0047609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	88	596	0	ENST00000380728.2:c.274_275insTA	p.Lys92IlefsTer18	p.K92Ifs*18	ENST00000380728		92	aaa/aTAaa	4/11	1	2	FACETS	0.656	0.581	0.738	0.656	0.581	0.738	SUBCLONAL	1	TRUE	1	0.324600561778862	2		596	826	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0047610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	93	1080	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.2265565698664	2	FACETS	0.626	0.556	0.701	0.313	0.278	0.351	SUBCLONAL	1	TRUE	0	0.369966210648575	2		1080	803	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56798164	56798164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	64	459	0	ENST00000337432.4:c.895C>T	p.Pro299Ser	p.P299S	ENST00000337432	NM_058216.2	299	Cct/Tct	6/9	0.2265565698664	2	FACETS	1	0.897	1	0.516	0.45	0.587	CLONAL	1	TRUE	0	0.369966210648575	2		459	335	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37672045	37672045	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	88	693	0	ENST00000447079.4:c.2830C>T	p.Gln944Ter	p.Q944*	ENST00000447079	NM_015083.1	944	Cag/Tag	9/14	0.2265565698664	2	FACETS	0.936	0.832	1	0.468	0.416	0.524	CLONAL	1	TRUE	0	0.369966210648575	2		693	508	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451812	29451812	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	55	770	0	ENST00000389048.3:c.2753G>C	p.Arg918Thr	p.R918T	ENST00000389048	NM_004304.4	918	aGa/aCa	16/29	1	2	FACETS	0.453	0.387	0.526	0.453	0.387	0.526	SUBCLONAL	1	TRUE	1	0.369966210648575	2		770	656	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401156	139401169	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGCGGCACCCACCG	CGCGGCACCCACCG	TGT	novel	NA	P-0047610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	84	865	3	ENST00000277541.6:c.3900_3901+12delinsACA		p.X1300_splice	ENST00000277541	NM_017617.3	1300		23/34	0.2265565698664	2	FACETS	0.554	0.489	0.625	0.277	0.244	0.313	SUBCLONAL	1	TRUE	0	0.369966210648575	2		868	819	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786201059	NA	P-0047612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	313	878	0	ENST00000269305.4:c.856G>C	p.Glu286Gln	p.E286Q	ENST00000269305	NM_001126112.2	286	Gaa/Caa	8/11	0.359123651110022	2	FACETS	0.941	0.89	0.993	0.941	0.89	0.993	CLONAL	2	TRUE	0	0.359123651110022	2		878	926	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021818	71021818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869025203	NA	P-0047612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	58	217	0	ENST00000318789.4:c.1540C>T	p.Arg514Cys	p.R514C	ENST00000318789	NM_032682.5	514	Cgt/Tgt	18/21	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.359123651110022	2		217	284	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11114030	11114030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774927302	NA	P-0047612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	99	527	0	ENST00000358026.2:c.1958C>T	p.Pro653Leu	p.P653L	ENST00000358026	NM_001128849.1	653	cCg/cTg	13/36	0.10732692636481	3	FACETS	0.84	0.75	0.936	0.28	0.25	0.312	INDETERMINATE	1	TRUE	0	0.359123651110022	3		527	774	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448705	49448705	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	242	495	0	ENST00000301067.7:c.154C>T	p.Gln52Ter	p.Q52*	ENST00000301067	NM_003482.3	52	Cag/Tag	2/54	0.359123651110022	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	1	0.359123651110022	3		495	783	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	67	516	0				ENST00000310581	NM_198253.2	-/1132			0.319917540716018	3	FACETS	1	0.945	1	0.573	0.502	0.648	CLONAL	1	TRUE	1	0.486456451322179	3		516	299	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0047613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	152	511	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.459419665244272	3	FACETS	0.941	0.869	1	0.941	0.869	1	CLONAL	2	TRUE	1	0.486456451322179	3		511	413	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414397	6414397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	64	176	0	ENST00000356142.4:c.31G>A	p.Asp11Asn	p.D11N	ENST00000356142	NM_018890.3	11	Gac/Aac	1/7	0.486456451322179	3	FACETS	0.935	0.814	1	0.467	0.407	0.532	CLONAL	1	TRUE	1	0.486456451322179	3		176	350	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933186	36933186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	164	788	2	ENST00000361632.4:c.1931G>A	p.Gly644Glu	p.G644E	ENST00000361632		644	gGa/gAa	14/16	1	2	FACETS	0.826	0.759	0.896	0.826	0.759	0.896	CLONAL	1	TRUE	1	0.486456451322179	2		790	816	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131740	2131740	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs45517309	NA	P-0047613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	195	1039	0	ENST00000219476.3:c.3755C>G	p.Ser1252Ter	p.S1252*	ENST00000219476	NM_000548.3	1252	tCa/tGa	31/42	0.473013507246555	3	FACETS	0.874	0.807	0.942	0.437	0.403	0.471	CLONAL	1	TRUE	1	0.486456451322179	3		1039	1141	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55729472	55729472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753961064	NA	P-0047613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	223	935	0	ENST00000284073.2:c.740C>T	p.Ala247Val	p.A247V	ENST00000284073	NM_138962.2	247	gCg/gTg	11/14	0.486456451322179	3	FACETS	0.851	0.791	0.914	0.426	0.395	0.457	CLONAL	1	TRUE	1	0.486456451322179	3		935	1339	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035170	30035173	+	frameshift_variant	Frame_Shift_Del	DEL	AGGA	AGGA	-	novel	NA	P-0047613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	247	549	0	ENST00000338641.4:c.332_335del	p.Gln111ArgfsTer11	p.Q111Rfs*11	ENST00000338641	NM_000268.3	111	cAGGAg/cg	3/16	0.486456451322179	2	FACETS	0.888	0.837	0.939	0.888	0.837	0.939	CLONAL	2	TRUE	0	0.486456451322179	2		549	572	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251990	153251990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	99	311	0	ENST00000281708.4:c.1016G>A	p.Arg339Lys	p.R339K	ENST00000281708	NM_033632.3	339	aGa/aAa	7/12	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.486456451322179	2		311	388	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845251	151845251	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	326	542	0	ENST00000262189.6:c.13761G>A	p.Trp4587Ter	p.W4587*	ENST00000262189	NM_170606.2	4587	tgG/tgA	52/59	0.444888751624788	3	FACETS	0.914	0.872	0.955	0.914	0.872	0.955	CLONAL	3	TRUE	0	0.486456451322179	3		542	608	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	114	516	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.551177809883683	2		516	404	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0047614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	331	564	1	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	0.547699295187022	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.551177809883683	2		565	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	496	729	0	ENST00000269305.4:c.799C>G	p.Arg267Gly	p.R267G	ENST00000269305	NM_001126112.2	267	Cgg/Ggg	8/11	0.547699295187022	2	FACETS	0.961	0.926	0.997	0.961	0.926	0.997	CLONAL	2	TRUE	0	0.551177809883683	2		729	936	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451121	70451121	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	248	751	2	ENST00000373644.4:c.5961G>T	p.Leu1987Phe	p.L1987F	ENST00000373644	NM_030625.2	1987	ttG/ttT	12/12	1	2	FACETS	0.965	0.903	1	0.965	0.903	1	CLONAL	1	TRUE	1	0.551177809883683	2		753	933	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445026	49445029	+	frameshift_variant	Frame_Shift_Del	DEL	GCGG	GCGG	-	novel	NA	P-0047614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	187	866	0	ENST00000301067.7:c.2437_2440del	p.Pro813ThrfsTer116	p.P813Tfs*116	ENST00000301067	NM_003482.3	813	CCGCac/ac	10/54	1	2	FACETS	0.814	0.753	0.877	0.814	0.753	0.877	CLONAL	1	TRUE	1	0.551177809883683	2		866	834	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966751	18966752	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	293	1070	0	ENST00000262803.5:c.1563dup	p.Pro522SerfsTer29	p.P522Sfs*29	ENST00000262803	NM_002911.3	521	gct/gcTt	12/24	1	2	FACETS	0.984	0.926	1	0.984	0.926	1	CLONAL	1	TRUE	1	0.551177809883683	2		1070	1081	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359903	87359903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs556985581	NA	P-0047614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	169	416	1	ENST00000277120.3:c.1211C>T	p.Ala404Val	p.A404V	ENST00000277120		404	gCg/gTg	11/19	0.547699295187022	2	FACETS	0.983	0.908	1	0.491	0.454	0.53	CLONAL	1	TRUE	0	0.551177809883683	2		417	624	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396314	139396314	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	622	995	2	ENST00000277541.6:c.5524C>T	p.Gln1842Ter	p.Q1842*	ENST00000277541	NM_017617.3	1842	Cag/Tag	30/34	0.547699295187022	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.551177809883683	2		997	1015	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0047615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	224	424	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.129520793398038	5	FACETS	0.977	0.911	1			1	INDETERMINATE	3	TRUE	NA	0.247920676936984	5		424	846	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0047615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	223	1080	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.230639977044776	3	FACETS	1	0.982	1	0.766	0.714	0.819	CLONAL	2	TRUE	0	0.247920676936984	3		1080	880	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944310	206944310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755490123	NA	P-0047615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	83	770	0	ENST00000423557.1:c.320C>T	p.Ala107Val	p.A107V	ENST00000423557	NM_000572.2	107	gCg/gTg	3/5	0.247920676936984	5	FACETS	0.912	0.803	1	0.304	0.267	0.344	CLONAL	1	TRUE	2	0.247920676936984	5		770	1007	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448310	56448310	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567880628	NA	P-0047615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	132	873	0	ENST00000407977.2:c.337C>T	p.Arg113Ter	p.R113*	ENST00000407977		113	Cga/Tga	3/10	0.245578095634306	3	FACETS	1	0.966	1	0.569	0.516	0.626	CLONAL	1	TRUE	1	0.247920676936984	3		873	1051	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484206	8484206	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768568228	NA	P-0047615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	94	409	0	ENST00000356435.5:c.3326G>A	p.Arg1109His	p.R1109H	ENST00000356435		1109	cGt/cAt	19/35	1	2	FACETS	0.946	0.841	1	0.946	0.841	1	CLONAL	1	TRUE	1	0.247920676936984	2		409	802	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274133	10274133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs796052542	NA	P-0047615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	88	750	0	ENST00000330684.3:c.136G>A	p.Val46Met	p.V46M	ENST00000330684	NM_001134407.1	46	Gtg/Atg	2/13	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.247920676936984	2		750	638	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435945	56435945	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760806622	NA	P-0047615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	45	622	1	ENST00000407977.2:c.1192G>A	p.Ala398Thr	p.A398T	ENST00000407977		398	Gct/Act	9/10	0.245578095634306	3	FACETS	0.655	0.549	0.772	0.327	0.274	0.386	SUBCLONAL	1	TRUE	1	0.247920676936984	3		623	623	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913250	NA	P-0047617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	2668	532	0	ENST00000369535.4:c.34G>T	p.Gly12Cys	p.G12C	ENST00000369535	NM_002524.4	12	Ggt/Tgt	2/7	0.3	25	FACETS	1	0.996	1			1	CLONAL	24	FALSE	NA	0.3	25		532	3253	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857925	9857925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs534440095	NA	P-0047617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	116	584	0	ENST00000330684.3:c.3476G>A	p.Arg1159His	p.R1159H	ENST00000330684	NM_001134407.1	1159	cGc/cAc	13/13	0.134984111067116	4	FACETS	1	0.972	1	0.61	0.549	0.674	INDETERMINATE	1	FALSE	2	0.3	4		584	824	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041561	14041561	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs774900622	NA	P-0047617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	126	592	0	ENST00000311895.7:c.2108G>T	p.Gly703Val	p.G703V	ENST00000311895	NM_005236.2	703	gGc/gTc	11/11	0.3	5	FACETS	0.77	0.697	0.846			1	SUBCLONAL	2	FALSE	NA	0.3	5		592	791	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905718	50905718	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs746195458	NA	P-0047617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	60	953	0	ENST00000440232.2:c.766G>C	p.Val256Leu	p.V256L	ENST00000440232	NM_002691.3	256	Gtg/Ctg	7/27	1	2	FACETS	0.546	0.47	0.63	0.546	0.47	0.63	SUBCLONAL	1	FALSE	1	0.3	2		953	732	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249013	55249014	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACCCCC	novel	NA	P-0047618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	106	660	0	ENST00000275493.2:c.2314_2319dup	p.Pro772_His773dup	p.P772_H773dup	ENST00000275493	NM_005228.3	772	aac/aACCCCCac	20/28	NA	2	FACETS	0.936	0.85	1			1	INDETERMINATE	1	TRUE	NA	0.757871255571694	2		660	299	SUCCESS
APC	324	MSKCC	GRCh37	5	112176212	112176212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755126540	NA	P-0047618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	44	490	0	ENST00000257430.4:c.4921G>A	p.Val1641Met	p.V1641M	ENST00000257430	NM_000038.5	1641	Gtg/Atg	16/16	0.313387159981431	1	FACETS	0.451	0.384	0.521	0.451	0.384	0.521	INDETERMINATE	1	TRUE	0	0.757871255571694	1		490	160	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600549	43600549	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1216449106	NA	P-0047618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	59	664	0	ENST00000355710.3:c.775C>T	p.Pro259Ser	p.P259S	ENST00000355710	NM_020975.4	259	Ccg/Tcg	4/20	0.174981254015339	5	FACETS	1	0.967	1	0.462	0.402	0.526	INDETERMINATE	1	TRUE	2	0.757871255571694	5		664	240	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620377	43620377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	51	591	0	ENST00000355710.3:c.2986C>T	p.Pro996Ser	p.P996S	ENST00000355710	NM_020975.4	996	Ccg/Tcg	18/20	0.174981254015339	5	FACETS	0.94	0.804	1	0.313	0.268	0.363	INDETERMINATE	1	TRUE	2	0.757871255571694	5		591	306	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42026793	42026793	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0047618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	50	370	0	ENST00000219905.7:c.3916+1G>A		p.X1306_splice	ENST00000219905	NM_001164273.1	1306			0.757871255571694	1	FACETS	0.468	0.404	0.536	0.468	0.404	0.536	SUBCLONAL	1	TRUE	0	0.757871255571694	1		370	175	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038638	14038638	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	111	414	0	ENST00000311895.7:c.1963G>T	p.Asp655Tyr	p.D655Y	ENST00000311895	NM_005236.2	655	Gac/Tac	10/11	0.745225370225681	3	FACETS	1	0.951	1	0.537	0.487	0.589	CLONAL	1	TRUE	1	0.757871255571694	3		414	376	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164596	36164605	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCGGCGA	GCGGCGGCGA	-	novel	NA	P-0047618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	29	543	0	ENST00000300305.3:c.1270_1279del	p.Ser424AlafsTer167	p.S424Afs*167	ENST00000300305		424	TCGCCGCCGCgc/gc	8/8	0.372644730223272	1	FACETS	0.534	0.441	0.633	0.534	0.441	0.633	INDETERMINATE	1	TRUE	0	0.757871255571694	1		543	89	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143226611	143226611	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	60	409	0	ENST00000262992.4:c.503G>A	p.Arg168Lys	p.R168K	ENST00000262992	NM_001101669.1	168	aGa/aAa	7/24	0.737180621917856	1	FACETS	0.435	0.38	0.494	0.435	0.38	0.494	SUBCLONAL	1	TRUE	0	0.757871255571694	1		409	226	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045979	26045979	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	45	493	0	ENST00000540144.1:c.341A>C	p.His114Pro	p.H114P	ENST00000540144	NM_003531.2	114	cAc/cCc	1/1	0.316278551762989	2	FACETS	0.663	0.566	0.768	0.332	0.283	0.384	INDETERMINATE	1	TRUE	0	0.757871255571694	2		493	179	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336607	81336607	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	48	375	0	ENST00000222390.5:c.1615C>T	p.Arg539Ter	p.R539*	ENST00000222390	NM_000601.4	539	Cga/Tga	14/18	0.303423311437062	5	FACETS	0.991	0.844	1	0.33	0.281	0.384	INDETERMINATE	1	TRUE	2	0.757871255571694	5		375	273	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499808	8499808	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1415574662	NA	P-0047618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	76	531	0	ENST00000356435.5:c.2161G>C	p.Glu721Gln	p.E721Q	ENST00000356435		721	Gag/Cag	14/35	1	2	FACETS	0.513	0.452	0.577	0.513	0.452	0.577	SUBCLONAL	1	TRUE	1	0.757871255571694	2		531	391	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218397	36218429	+	protein_altering_variant	In_Frame_Del	DEL	GTGTGCTGGGGCAGCGCAGCCCCGCTGGCGAGA	GTGTGCTGGGGCAGCGCAGCCCCGCTGGCGAGA	AGG	novel	NA	P-0047618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	75	808	6	ENST00000222270.7:c.4176_4208delinsAGG	p.Cys1393_Glu1403delinsGly	p.C1393_E1403delinsG	ENST00000222270	NM_014727.1	1392	ccGTGTGCTGGGGCAGCGCAGCCCCGCTGGCGAGAg/ccAGGg	16/37	0.355908176939686	3	FACETS	0.992	0.88	1	0.496	0.44	0.556	INDETERMINATE	1	TRUE	1	0.757871255571694	3		814	275	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0047619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	337	708	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.39974678271932	6	FACETS	0.921	0.874	0.969	0.921	0.874	0.969	CLONAL	3	TRUE	3	0.576009790034355	6		708	911	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0047619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	370	541	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.555799518757397	2	FACETS	0.97	0.93	1	0.97	0.93	1	CLONAL	2	TRUE	0	0.576009790034355	2		542	662	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604790	48604790	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1568211615	NA	P-0047620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	27	417	1	ENST00000342988.3:c.1612G>T	p.Glu538Ter	p.E538*	ENST00000342988	NM_005359.5	538	Gaa/Taa	12/12	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		418	480	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510305	187510305	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs758757364	NA	P-0047620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	30	484	0	ENST00000441802.2:c.13208A>G	p.Tyr4403Cys	p.Y4403C	ENST00000441802	NM_005245.3	4403	tAt/tGt	27/27	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		484	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0047622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	133	652	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.24716596235088	2	FACETS	0.82	0.746	0.897	0.82	0.746	0.897	CLONAL	2	TRUE	0	0.249599847578246	2		653	650	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099403	157099429	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAGCAACAG	CAGCAGCAGCAGCAGCAGCAGCAACAG	-	rs910569810	NA	P-0047622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	24	292	0	ENST00000346085.5:c.360_386del	p.Gln123_Gln131del	p.Q123_Q131del	ENST00000346085	NM_020732.3	114	CAGCAGCAGCAGCAGCAGCAGCAACAG/-	1/20	0.171380227572431	3	FACETS	1	0.873	1	0.578	0.456	0.717	CLONAL	1	TRUE	1	0.249599847578246	3		292	187	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36823941	36823941	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	50	917	0	ENST00000373129.3:c.241C>T	p.Gln81Ter	p.Q81*	ENST00000373129	NM_032017.1	81	Cag/Tag	5/12	0.222228923451128	3	FACETS	0.607	0.513	0.709	0.202	0.171	0.237	SUBCLONAL	1	TRUE	0	0.249599847578246	3		917	743	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44527585	44527585	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	54	473	0	ENST00000291552.4:c.20C>T	p.Ser7Phe	p.S7F	ENST00000291552	NM_006758.2	7	tCc/tTc	1/8	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.249599847578246	2		473	421	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0047623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	37	456	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	0.0981446213053498	6	FACETS	0.907	0.748	1	0.605	0.498	0.725	CLONAL	2	FALSE	3	0.0981446213053498	6		456	497	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	46	575	3	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	0.0981446213053498	10	FACETS	0.894	0.751	1	0.358	0.3	0.421	CLONAL	2	FALSE	5	0.0981446213053498	10		578	730	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526456	66526456	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	42	611	0	ENST00000358598.2:c.1012A>G	p.Thr338Ala	p.T338A	ENST00000358598	NM_212471.2	338	Aca/Gca	11/11	0.0693211420300246	3	FACETS	1	0.942	1	0.661	0.551	0.784	CLONAL	1	FALSE	1	0.0981446213053498	3		611	679	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260900	16260900	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	275	401	0	ENST00000375759.3:c.8165C>T	p.Pro2722Leu	p.P2722L	ENST00000375759	NM_015001.2	2722	cCa/cTa	11/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.556428985658793	2		401	891	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	314	612	2	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.556428985658793	2		614	909	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247894	59247894	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	364	688	2	ENST00000371222.2:c.849del	p.Val284Ter	p.V284*	ENST00000371222	NM_002228.3	283	aaA/aa	1/1	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.556428985658793	2		690	1299	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	221	264	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.926	0.874	0.977	1	0.995	1	CLONAL	2	TRUE	1	0.556428985658793	2		264	429	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	420	438	2	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.993	1	1	0.997	1	CLONAL	2	TRUE	1	0.556428985658793	2		440	675	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948484	71948484	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1358	475	867	0	ENST00000298229.2:c.3201del	p.Ser1068AlafsTer63	p.S1068Afs*63	ENST00000298229	NM_001567.3	1066	Ccc/cc	26/28	1	2	FACETS	0.931	0.888	0.976	0.931	0.888	0.976	CLONAL	1	TRUE	1	0.556428985658793	2		867	1833	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373709	118373709	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	166	273	0	ENST00000534358.1:c.7102C>A	p.Leu2368Ile	p.L2368I	ENST00000534358	NM_005933.3	2368	Ctc/Atc	27/36	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.556428985658793	2		273	576	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	159	305	0	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	0.964	0.888	1	0.964	0.888	1	CLONAL	1	TRUE	1	0.556428985658793	2		305	593	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628716	21628716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755679996	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	94	334	0	ENST00000421138.2:c.992C>T	p.Thr331Met	p.T331M	ENST00000421138		331	aCg/aTg	10/16	0.260056988573864	1	FACETS	0.611	0.547	0.678	0.611	0.547	0.678	INDETERMINATE	1	TRUE	0	0.556428985658793	1		334	399	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	141	419	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	NA	2	FACETS	1	0.95	1			1	INDETERMINATE	1	TRUE	NA	0.556428985658793	2		419	483	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243365	46243365	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs76994389	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	80	173	0	ENST00000334344.6:c.1718C>T	p.Thr573Met	p.T573M	ENST00000334344	NM_152641.2	573	aCg/aTg	14/21	NA	2	FACETS	1	0.958	1			1	INDETERMINATE	1	TRUE	NA	0.556428985658793	2		173	250	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421039	49421039	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs398123721	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	281	443	0	ENST00000301067.7:c.14710C>T	p.Arg4904Ter	p.R4904*	ENST00000301067	NM_003482.3	4904	Cga/Tga	48/54	NA	2	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.556428985658793	2		443	986	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434829	49434829	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1344298960	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1217	497	772	1	ENST00000301067.7:c.6724G>A	p.Asp2242Asn	p.D2242N	ENST00000301067	NM_003482.3	2242	Gac/Aac	31/54	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.556428985658793	2		773	1714	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885145	111885145	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs892433462	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	284	491	0	ENST00000341259.2:c.1038del	p.Leu347CysfsTer26	p.L347Cfs*26	ENST00000341259	NM_005475.2	345	Ggg/gg	6/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.556428985658793	2		491	979	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924349	112924349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	363	628	1	ENST00000351677.2:c.1295C>T	p.Pro432Leu	p.P432L	ENST00000351677	NM_002834.3	432	cCt/cTt	11/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.556428985658793	2		629	1230	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549170	21549170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1009657720	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	337	621	1	ENST00000382592.4:c.3106G>A	p.Ala1036Thr	p.A1036T	ENST00000382592	NM_014572.2	1036	Gca/Aca	8/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.556428985658793	2		622	1126	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562919	21562919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770192145	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	466	754	0	ENST00000382592.4:c.1000C>T	p.Arg334Cys	p.R334C	ENST00000382592	NM_014572.2	334	Cgc/Tgc	4/8	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.556428985658793	2		754	1482	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528182	103528182	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	112	279	0	ENST00000355739.4:c.3490A>G	p.Thr1164Ala	p.T1164A	ENST00000355739	NM_000123.3	1164	Acc/Gcc	15/15	1	2	FACETS	0.818	0.74	0.901	0.818	0.74	0.901	CLONAL	1	TRUE	1	0.556428985658793	2		279	492	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353863	68353863	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	146	236	0	ENST00000487270.1:c.698A>T	p.Lys233Met	p.K233M	ENST00000487270	NM_133509.3	233	aAg/aTg	7/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.556428985658793	2		236	505	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994829	73994829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751833994	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	168	286	1	ENST00000318443.5:c.313G>A	p.Ala105Thr	p.A105T	ENST00000318443	NM_001024736.1	105	Gca/Aca	3/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.556428985658793	2		287	554	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	338151	338153	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1204980787	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	357	592	0	ENST00000262320.3:c.2558_2560del	p.Lys853del	p.K853del	ENST00000262320	NM_003502.3	853	aAGAtc/atc	11/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.556428985658793	2		592	1199	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222500	2222500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766165474	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	486	774	1	ENST00000326181.6:c.694C>T	p.Arg232Trp	p.R232W	ENST00000326181	NM_032271.2	232	Cgg/Tgg	9/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.556428985658793	2		775	1651	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225603	2225603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	400	651	2	ENST00000326181.6:c.1606G>A	p.Gly536Ser	p.G536S	ENST00000326181	NM_032271.2	536	Ggc/Agc	17/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.556428985658793	2		653	1359	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349186	11349186	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1429369206	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	69	125	2	ENST00000332029.2:c.150del	p.Gly51AlafsTer34	p.G51Afs*34	ENST00000332029	NM_003745.1	50	ccC/cc	2/2	1	2	FACETS	0.936	0.824	1	0.936	0.824	1	CLONAL	1	TRUE	1	0.556428985658793	2		127	265	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835781	68835781	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060501215	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	249	429	0	ENST00000261769.5:c.377del	p.Pro126ArgfsTer89	p.P126Rfs*89	ENST00000261769	NM_004360.3	124	cgC/cg	3/16	0.556428985658793	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.556428985658793	1		429	620	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991704	72991704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	250	282	0	ENST00000268489.5:c.2341G>A	p.Ala781Thr	p.A781T	ENST00000268489	NM_006885.3	781	Gcg/Acg	2/10	0.556428985658793	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.556428985658793	1		282	513	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993624	72993624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs997674247	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	328	634	0	ENST00000268489.5:c.421G>A	p.Ala141Thr	p.A141T	ENST00000268489	NM_006885.3	141	Gcg/Acg	2/10	0.556428985658793	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.556428985658793	1		634	826	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352037	89352037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138353708	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	383	578	1	ENST00000301030.4:c.913G>A	p.Ala305Thr	p.A305T	ENST00000301030	NM_001256183.1	305	Gca/Aca	9/13	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.556428985658793	2		579	1231	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89846290	89846290	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778754162	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	283	474	1	ENST00000389301.3:c.1702G>A	p.Val568Ile	p.V568I	ENST00000389301	NM_000135.2	568	Gtc/Atc	18/43	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.556428985658793	2		475	1008	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578425	7578425	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	463	735	0	ENST00000269305.4:c.505A>G	p.Met169Val	p.M169V	ENST00000269305	NM_001126112.2	169	Atg/Gtg	5/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.556428985658793	2		735	1562	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	119	253	0	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.556428985658793	2		253	406	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	297	638	9	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	1	2	FACETS	0.914	0.86	0.969	0.914	0.86	0.969	CLONAL	1	TRUE	1	0.556428985658793	2		647	1168	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553493	29553493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786201768	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	346	619	0	ENST00000356175.3:c.2042G>A	p.Arg681Gln	p.R681Q	ENST00000356175	NM_000267.3	681	cGa/cAa	18/57	1	2	FACETS	0.999	0.945	1	0.999	0.945	1	CLONAL	1	TRUE	1	0.556428985658793	2		619	1245	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649111	37649111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	138	234	0	ENST00000447079.4:c.2216G>A	p.Gly739Asp	p.G739D	ENST00000447079	NM_015083.1	739	gGc/gAc	4/14	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.556428985658793	2		234	478	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581268	48581268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752575871	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	226	532	0	ENST00000342988.3:c.572C>T	p.Ser191Leu	p.S191L	ENST00000342988	NM_005359.5	191	tCg/tTg	5/12	1	2	FACETS	0.727	0.676	0.779	0.727	0.676	0.779	SUBCLONAL	1	TRUE	1	0.556428985658793	2		532	1118	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2194571	2194571	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	216	301	0	ENST00000398665.3:c.646T>C	p.Tyr216His	p.Y216H	ENST00000398665	NM_032482.2	216	Tac/Cac	7/28	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.556428985658793	2		301	698	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222313	2222313	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1314918641	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	477	732	0	ENST00000398665.3:c.3145A>G	p.Ile1049Val	p.I1049V	ENST00000398665	NM_032482.2	1049	Atc/Gtc	24/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.556428985658793	2		732	1671	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110607	4110607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370559062	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	447	563	0	ENST00000262948.5:c.350G>A	p.Arg117His	p.R117H	ENST00000262948	NM_030662.3	117	cGc/cAc	3/11	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.556428985658793	2		563	1439	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967091	18967092	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1384543747	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	318	1160	1	ENST00000262803.5:c.1814_1815del	p.Glu605AlafsTer17	p.E605Afs*17	ENST00000262803	NM_002911.3	602	gcAGag/gcag	13/24	1	2	FACETS	0.854	0.805	0.905	0.854	0.805	0.905	CLONAL	1	TRUE	1	0.556428985658793	2		1161	1338	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213611	36213611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757982914	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1262	484	818	0	ENST00000222270.7:c.2713G>A	p.Ala905Thr	p.A905T	ENST00000222270	NM_014727.1	905	Gcc/Acc	5/37	1	2	FACETS	0.996	0.951	1	0.996	0.951	1	CLONAL	1	TRUE	1	0.556428985658793	2		818	1746	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224339	36224340	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1228	340	819	4	ENST00000222270.7:c.6895dup	p.Arg2299ProfsTer4	p.R2299Pfs*4	ENST00000222270	NM_014727.1	2297	gcc/gCcc	28/37	1	2	FACETS	0.779	0.735	0.825	0.779	0.735	0.825	SUBCLONAL	1	TRUE	1	0.556428985658793	2		823	1568	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754583	42754583	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	427	750	2	ENST00000222329.4:c.157G>A	p.Gly53Arg	p.G53R	ENST00000222329	NM_006494.2	53	Ggg/Agg	2/4	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.556428985658793	2		752	1492	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902182	50902182	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	454	708	0	ENST00000440232.2:c.74A>G	p.Asp25Gly	p.D25G	ENST00000440232	NM_002691.3	25	gAt/gGt	2/27	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.556428985658793	2		708	1447	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085995	16085995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	256	417	0	ENST00000281043.3:c.1171C>T	p.Arg391Cys	p.R391C	ENST00000281043	NM_005378.4	391	Cgc/Tgc	3/3	0.556428985658793	2	FACETS	1	0.978	1	0.543	0.51	0.577	CLONAL	1	TRUE	0	0.556428985658793	2		417	847	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497874	25497874	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	384	634	0	ENST00000264709.3:c.575C>A	p.Ala192Glu	p.A192E	ENST00000264709	NM_175629.2	192	gCg/gAg	6/23	0.556428985658793	2	FACETS	1	0.984	1	0.541	0.514	0.569	CLONAL	1	TRUE	0	0.556428985658793	2		634	1275	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497944	25497944	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1203651882	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	282	483	0	ENST00000264709.3:c.505C>T	p.Arg169Trp	p.R169W	ENST00000264709	NM_175629.2	169	Cgg/Tgg	6/23	0.556428985658793	2	FACETS	1	0.964	1	0.517	0.486	0.548	CLONAL	1	TRUE	0	0.556428985658793	2		483	981	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446389	29446389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774836034	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	410	697	0	ENST00000389048.3:c.3178C>T	p.Arg1060Cys	p.R1060C	ENST00000389048	NM_004304.4	1060	Cgc/Tgc	20/29	0.556428985658793	2	FACETS	1	0.988	1	0.554	0.527	0.582	CLONAL	1	TRUE	0	0.556428985658793	2		697	1329	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	147	515	6	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	0.556428985658793	2	FACETS	0.82	0.751	0.892	0.41	0.375	0.446	CLONAL	1	TRUE	0	0.556428985658793	2		521	644	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098891	178098892	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	186	350	0	ENST00000397062.3:c.153_154del	p.Lys53ThrfsTer2	p.K53Tfs*2	ENST00000397062	NM_006164.4	51	caGAaa/caaa	2/5	1	2	FACETS	0.935	0.866	1	0.935	0.866	1	CLONAL	1	TRUE	1	0.556428985658793	2		350	715	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39772564	39772564	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	136	218	0	ENST00000288319.7:c.677del	p.Gly226ValfsTer65	p.G226Vfs*65	ENST00000288319	NM_182918.3	226	gGt/gt	6/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.556428985658793	2		218	461	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795373	39795373	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	314	607	0	ENST00000288319.7:c.347del	p.Pro116GlnfsTer3	p.P116Qfs*3	ENST00000288319	NM_182918.3	116	cCa/ca	3/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.556428985658793	2		607	1066	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574678	41574679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs754418509	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	409	707	1	ENST00000263253.7:c.6970dup	p.His2324ProfsTer55	p.H2324Pfs*55	ENST00000263253	NM_001429.3	2321	-/C	31/31	1	2	FACETS	0.941	0.894	0.989	0.941	0.894	0.989	CLONAL	1	TRUE	1	0.556428985658793	2		708	1563	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	305	244	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.556428985658793	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.556428985658793	2		244	493	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933438	49933438	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	408	630	3	ENST00000296474.3:c.2752del	p.Leu918CysfsTer18	p.L918Cfs*18	ENST00000296474	NM_002447.2	918	Ctg/tg	11/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.556428985658793	2		633	1406	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439887	52439887	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	285	403	0	ENST00000460680.1:c.825G>T	p.Lys275Asn	p.K275N	ENST00000460680	NM_004656.3	275	aaG/aaT	10/17	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.556428985658793	2		403	917	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799959	72799959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1486066559	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	61	235	0	ENST00000325599.8:c.1210G>A	p.Ala404Thr	p.A404T	ENST00000325599	NM_018130.2	404	Gcc/Acc	11/11	1	2	FACETS	0.486	0.42	0.557	0.486	0.42	0.557	SUBCLONAL	1	TRUE	1	0.556428985658793	2		235	451	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169999051	169999051	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	85	145	0	ENST00000295797.4:c.980G>T	p.Arg327Ile	p.R327I	ENST00000295797	NM_002740.5	327	aGa/aTa	10/18	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.556428985658793	2		145	273	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509085	66509085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	41	170	0	ENST00000273854.3:c.242del	p.Asn81MetfsTer24	p.N81Mfs*24	ENST00000273854	NM_004439.5	81	aAt/at	2/18	1	2	FACETS	0.67	0.563	0.786	0.67	0.563	0.786	SUBCLONAL	1	TRUE	1	0.556428985658793	2		170	220	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509127	66509127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145126637	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	38	181	0	ENST00000273854.3:c.200G>A	p.Arg67His	p.R67H	ENST00000273854	NM_004439.5	67	cGc/cAc	2/18	1	2	FACETS	0.635	0.53	0.751	0.635	0.53	0.751	SUBCLONAL	1	TRUE	1	0.556428985658793	2		181	215	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540670	187540670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530876083	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	172	279	0	ENST00000441802.2:c.7070C>T	p.Thr2357Met	p.T2357M	ENST00000441802	NM_005245.3	2357	aCg/aTg	10/27	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.556428985658793	2		279	555	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280299	1280299	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs761603068	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	513	751	0	ENST00000310581.5:c.1924G>T	p.Ala642Ser	p.A642S	ENST00000310581	NM_198253.2	642	Gcc/Tcc	4/16	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.556428985658793	2		751	1627	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	81	214	2	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.556428985658793	2		216	279	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753348	57753348	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	130	293	0	ENST00000274289.3:c.776G>T	p.Cys259Phe	p.C259F	ENST00000274289	NM_006622.3	259	tGt/tTt	6/14	1	2	FACETS	0.944	0.861	1	0.944	0.861	1	CLONAL	1	TRUE	1	0.556428985658793	2		293	495	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	228	502	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.556428985658793	2		507	744	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564300	86564300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	190	376	0	ENST00000274376.6:c.32G>A	p.Gly11Asp	p.G11D	ENST00000274376	NM_002890.2	11	gGc/gAc	1/25	1	2	FACETS	0.971	0.901	1	0.971	0.901	1	CLONAL	1	TRUE	1	0.556428985658793	2		376	703	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047631	180047631	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	289	456	0	ENST00000261937.6:c.2384T>A	p.Leu795His	p.L795H	ENST00000261937	NM_182925.4	795	cTc/cAc	16/30	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.556428985658793	2		456	923	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956682	93956682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	111	241	0	ENST00000369303.4:c.2554G>A	p.Gly852Ser	p.G852S	ENST00000369303	NM_004440.3	852	Ggt/Agt	15/17	1	2	FACETS	0.971	0.879	1	0.971	0.879	1	CLONAL	1	TRUE	1	0.556428985658793	2		241	411	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554937	106554937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs565965311	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	256	387	1	ENST00000369096.4:c.2054G>A	p.Arg685Gln	p.R685Q	ENST00000369096	NM_001198.3	685	cGg/cAg	7/7	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.556428985658793	2		388	793	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202370	138202370	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867951430	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	275	553	1	ENST00000237289.4:c.2287C>T	p.Arg763Trp	p.R763W	ENST00000237289	NM_001270507.1	763	Cgg/Tgg	9/9	1	2	FACETS	0.964	0.906	1	0.964	0.906	1	CLONAL	1	TRUE	1	0.556428985658793	2		554	1025	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129307	152129307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1267605861	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	400	666	1	ENST00000206249.3:c.260C>T	p.Ala87Val	p.A87V	ENST00000206249	NM_000125.3	87	gCg/gTg	1/8	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.556428985658793	2		667	1219	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	717	763	8	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	1	0.992	1	1	0.998	1	CLONAL	2	TRUE	1	0.556428985658793	2		771	1217	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214367	55214367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778252	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	248	532	0	ENST00000275493.2:c.493C>T	p.Arg165Trp	p.R165W	ENST00000275493	NM_005228.3	165	Cgg/Tgg	4/28	1	2	FACETS	0.907	0.849	0.967	0.907	0.849	0.967	CLONAL	1	TRUE	1	0.556428985658793	2		532	983	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526647	106526648	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	144	328	0	ENST00000359195.3:c.2946_2947del	p.Arg982SerfsTer8	p.R982Sfs*8	ENST00000359195	NM_002649.2	980	aaAGag/aaag	10/11	1	2	FACETS	0.95	0.871	1	0.95	0.871	1	CLONAL	1	TRUE	1	0.556428985658793	2		328	545	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	431	766	0	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.556428985658793	2		766	1474	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	247	323	12	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	1	2	FACETS	0.959	0.909	1	1	0.995	1	CLONAL	2	TRUE	1	0.556428985658793	2		335	463	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950480	68950481	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	163	288	0	ENST00000288368.4:c.798dup	p.Leu267SerfsTer4	p.L267Sfs*4	ENST00000288368	NM_024870.2	264	-/T	7/40	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.556428985658793	2		288	510	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1201	421	654	0	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	1	2	FACETS	0.933	0.887	0.98	0.933	0.887	0.98	CLONAL	1	TRUE	1	0.556428985658793	2		654	1622	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5064997	5064997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	106	217	0	ENST00000381652.3:c.1171G>A	p.Ala391Thr	p.A391T	ENST00000381652	NM_004972.3	391	Gcc/Acc	9/25	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.556428985658793	2		217	315	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242281	98242281	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	221	430	0	ENST00000331920.6:c.1037del	p.Thr346LysfsTer21	p.T346Kfs*21	ENST00000331920	NM_000264.3	346	aCa/aa	7/24	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.556428985658793	2		430	741	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969407	44969407	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	180	152	0	ENST00000377967.4:c.4093del	p.Thr1365GlnfsTer11	p.T1365Qfs*11	ENST00000377967	NM_021140.2	1363	cgA/cg	28/29	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.556428985658793	1		152	316	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	375	550	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.285787462589941	5	FACETS	0.981	0.938	1			1	CLONAL	4	TRUE	NA	0.401937932878694	5		550	762	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857648	59857648	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs541203428	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	63	243	0	ENST00000259008.2:c.1909G>T	p.Ala637Ser	p.A637S	ENST00000259008	NM_032043.2	637	Gct/Tct	13/20	0.209961165060349	4	FACETS	0.99	0.859	1			1	INDETERMINATE	1	TRUE	NA	0.401937932878694	4		243	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578470	7578471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	505	821	0	ENST00000269305.4:c.459dup	p.Gly154ArgfsTer27	p.G154Rfs*27	ENST00000269305	NM_001126112.2	153	-/C	5/11	0.387399144220157	2	FACETS	0.941	0.902	0.981	0.941	0.902	0.981	CLONAL	2	TRUE	0	0.401937932878694	2		821	1335	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148876	119148876	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	132	169	0	ENST00000264033.4:c.1096G>T	p.Glu366Ter	p.E366*	ENST00000264033	NM_005188.3	366	Gaa/Taa	8/16	0.401937932878694	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.401937932878694	3		169	379	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307593	118307593	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	242	757	0	ENST00000534358.1:c.366C>G	p.Ile122Met	p.I122M	ENST00000534358	NM_005933.3	122	atC/atG	1/36	0.401937932878694	3	FACETS	1	0.973	1	0.542	0.505	0.58	CLONAL	1	TRUE	1	0.401937932878694	3		757	1335	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317592	163317592	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	47	219	1	ENST00000271452.3:c.988G>T	p.Glu330Ter	p.E330*	ENST00000271452	NM_145697.2	330	Gaa/Taa	12/14	0.387399144220157	2	FACETS	0.735	0.623	0.858	0.368	0.311	0.429	SUBCLONAL	1	TRUE	0	0.401937932878694	2		220	318	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106230	27106230	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	163	464	0	ENST00000324856.7:c.5841G>T	p.Gln1947His	p.Q1947H	ENST00000324856	NM_006015.4	1947	caG/caT	20/20	0.393875923925253	3	FACETS	1	0.97	1	0.56	0.514	0.608	CLONAL	1	TRUE	1	0.401937932878694	3		464	870	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551366	150551366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	549	906	0	ENST00000369026.2:c.641G>A	p.Arg214Gln	p.R214Q	ENST00000369026	NM_021960.4	214	cGa/cAa	1/3	0.260674344847865	4	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.401937932878694	4		906	1655	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606880	43606880	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1258	361	836	1	ENST00000355710.3:c.1489C>A	p.Gln497Lys	p.Q497K	ENST00000355710	NM_020975.4	497	Cag/Aag	7/20	0.401937932878694	3	FACETS	1	0.993	1	0.666	0.63	0.704	CLONAL	1	TRUE	1	0.401937932878694	3		837	1619	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343396	118343396	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781978013	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	72	276	0	ENST00000534358.1:c.1522G>A	p.Glu508Lys	p.E508K	ENST00000534358	NM_005933.3	508	Gaa/Aaa	3/36	0.401937932878694	3	FACETS	0.774	0.677	0.878	0.387	0.338	0.439	SUBCLONAL	1	TRUE	1	0.401937932878694	3		276	556	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435232	110435232	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	287	431	0	ENST00000375856.3:c.3169G>T	p.Gly1057Cys	p.G1057C	ENST00000375856	NM_003749.2	1057	Ggc/Tgc	1/2	0.387399144220157	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	0	0.401937932878694	2		431	707	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242086	105242086	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	214	711	0	ENST00000349310.3:c.338A>T	p.Gln113Leu	p.Q113L	ENST00000349310	NM_001014432.1	113	cAg/cTg	6/15	0.401937932878694	1	FACETS	0.971	0.904	1	0.971	0.904	1	CLONAL	1	TRUE	0	0.401937932878694	1		711	876	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838182	89838182	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	169	419	0	ENST00000389301.3:c.2055G>T	p.Arg685Ser	p.R685S	ENST00000389301	NM_000135.2	685	agG/agT	23/43	0.397318287887162	2	FACETS	1	0.97	1	0.554	0.51	0.6	CLONAL	1	TRUE	0	0.401937932878694	2		419	759	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511619	38511619	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs954829630	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	210	641	0	ENST00000254066.5:c.1117A>G	p.Met373Val	p.M373V	ENST00000254066	NM_000964.3	373	Atg/Gtg	8/9	NA	2	FACETS	0.985	0.914	1			1	INDETERMINATE	1	TRUE	NA	0.401937932878694	2		641	1061	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40457655	40457655	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1351526729	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	190	627	0	ENST00000345506.4:c.1408G>A	p.Val470Ile	p.V470I	ENST00000345506	NM_003152.3	470	Gtc/Atc	13/20	0.393875923925253	3	FACETS	0.979	0.903	1	0.489	0.451	0.529	CLONAL	1	TRUE	1	0.401937932878694	3		627	1160	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795136	42795136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	437	885	0	ENST00000575354.2:c.2216C>T	p.Ser739Leu	p.S739L	ENST00000575354	NM_015125.3	739	tCa/tTa	10/20	0.401937932878694	2	FACETS	1	0.996	1	0.746	0.71	0.782	CLONAL	1	TRUE	0	0.401937932878694	2		885	1458	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46603714	46603714	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	317	562	0	ENST00000263734.3:c.1071C>G	p.Asp357Glu	p.D357E	ENST00000263734	NM_001430.4	357	gaC/gaG	9/16	0.362988755228092	4	FACETS	0.9	0.849	0.953	0.9	0.849	0.953	CLONAL	2	TRUE	2	0.401937932878694	4		562	1228	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713349	40713349	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	152	633	0	ENST00000373198.4:c.4166G>C	p.Arg1389Thr	p.R1389T	ENST00000373198	NM_133170.3	1389	aGg/aCg	30/32	0.18472397144107	3	FACETS	0.856	0.782	0.934			1	INDETERMINATE	1	TRUE	NA	0.401937932878694	3		633	1061	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733243	40733244	+	missense_variant	Missense_Mutation	DNP	TG	TG	CT	novel	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	117	446	0	ENST00000373198.4:c.3562_3563delinsAG	p.Gln1188Arg	p.Q1188R	ENST00000373198	NM_133170.3	1188	CAg/AGg	26/32	0.18472397144107	3	FACETS	0.873	0.787	0.964			1	INDETERMINATE	1	TRUE	NA	0.401937932878694	3		446	801	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204115	142204115	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs201091477	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	87	286	0	ENST00000350721.4:c.6088G>T	p.Ala2030Ser	p.A2030S	ENST00000350721	NM_001184.3	2030	Gcg/Tcg	36/47	0.401937932878694	3	FACETS	0.835	0.74	0.936	0.417	0.37	0.468	CLONAL	1	TRUE	1	0.401937932878694	3		286	623	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564561	55564561	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	138	432	0	ENST00000288135.5:c.449G>T	p.Gly150Val	p.G150V	ENST00000288135	NM_000222.2	150	gGg/gTg	3/21	0.387399144220157	2	FACETS	1	0.936	1	0.516	0.47	0.563	CLONAL	1	TRUE	0	0.401937932878694	2		432	666	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459827	149459827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	212	769	0	ENST00000286301.3:c.380G>A	p.Cys127Tyr	p.C127Y	ENST00000286301	NM_005211.3	127	tGt/tAt	4/22	0.259391240983904	1	FACETS	0.75	0.696	0.806	0.75	0.696	0.806	SUBCLONAL	1	TRUE	0	0.401937932878694	1		769	1124	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271325	26271326	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	285	480	0	ENST00000305910.3:c.287_288delinsAG	p.Ala96Glu	p.A96E	ENST00000305910	NM_003534.2	96	gCC/gAG	1/1	0.401937932878694	5	FACETS	0.93	0.874	0.988	0.62	0.582	0.659	CLONAL	2	TRUE	2	0.401937932878694	5		480	1222	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163592	32163592	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs779655015	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1202	362	588	0	ENST00000375023.3:c.5634G>T	p.Gln1878His	p.Q1878H	ENST00000375023	NM_004557.3	1878	caG/caT	30/30	0.401937932878694	5	FACETS	0.923	0.873	0.974	0.615	0.582	0.65	CLONAL	2	TRUE	2	0.401937932878694	5		588	1564	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202433	138202433	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	207	600	1	ENST00000237289.4:c.2350C>T	p.Gln784Ter	p.Q784*	ENST00000237289	NM_001270507.1	784	Cag/Tag	9/9	0.387399144220157	2	FACETS	1	0.978	1	0.566	0.525	0.608	CLONAL	1	TRUE	0	0.401937932878694	2		601	910	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978873	13978873	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	64	264	0	ENST00000405192.2:c.236-2A>T		p.X79_splice	ENST00000405192	NM_001163147.1	79			0.401937932878694	3	FACETS	0.694	0.601	0.794	0.347	0.3	0.397	SUBCLONAL	1	TRUE	1	0.401937932878694	3		264	551	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355274	81355274	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	64	230	0	ENST00000222390.5:c.1100C>A	p.Thr367Asn	p.T367N	ENST00000222390	NM_000601.4	367	aCc/aAc	9/18	0.393875923925253	3	FACETS	0.844	0.733	0.964	0.422	0.366	0.482	CLONAL	1	TRUE	1	0.401937932878694	3		230	453	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398637	116398637	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	83	316	0	ENST00000397752.3:c.2227A>G	p.Ile743Val	p.I743V	ENST00000397752	NM_000245.2	743	Att/Gtt	9/21	0.393875923925253	3	FACETS	0.838	0.74	0.942	0.419	0.37	0.471	CLONAL	1	TRUE	1	0.401937932878694	3		316	592	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501222	140501222	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	163	294	0	ENST00000288602.6:c.850G>C	p.Asp284His	p.D284H	ENST00000288602	NM_004333.4	284	Gac/Cac	6/18	0.393875923925253	3	FACETS	0.966	0.894	1	0.966	0.894	1	CLONAL	2	TRUE	1	0.401937932878694	3		294	504	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389324	8389324	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	168	416	0	ENST00000356435.5:c.4294C>T	p.Leu1432Phe	p.L1432F	ENST00000356435		1432	Ctc/Ttc	26/35	0.397318287887162	2	FACETS	0.796	0.737	0.857	0.796	0.737	0.857	SUBCLONAL	2	TRUE	0	0.401937932878694	2		416	525	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499712	8499712	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	273	410	0	ENST00000356435.5:c.2257A>T	p.Arg753Trp	p.R753W	ENST00000356435		753	Agg/Tgg	14/35	0.397318287887162	2	FACETS	0.972	0.918	1	0.972	0.918	1	CLONAL	2	TRUE	0	0.401937932878694	2		410	699	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636827	8636827	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	155	313	0	ENST00000356435.5:c.82C>G	p.Arg28Gly	p.R28G	ENST00000356435		28	Cga/Gga	2/35	0.397318287887162	2	FACETS	0.905	0.837	0.975	0.905	0.837	0.975	CLONAL	2	TRUE	0	0.401937932878694	2		313	426	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410144	63410144	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	65	705	0	ENST00000330258.3:c.3023C>A	p.Pro1008Gln	p.P1008Q	ENST00000330258	NM_152424.3	1008	cCa/cAa	2/2	0.401937932878694	1	FACETS	0.31	0.268	0.356	0.31	0.268	0.356	SUBCLONAL	1	TRUE	0	0.401937932878694	1		705	834	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920251	76920251	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	70	231	0	ENST00000373344.5:c.3826C>T	p.Leu1276Phe	p.L1276F	ENST00000373344	NM_000489.3	1276	Ctt/Ttt	11/35	0.401937932878694	1	FACETS	0.819	0.719	0.925	0.819	0.719	0.925	CLONAL	1	TRUE	0	0.401937932878694	1		231	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0047634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	284	591	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.383425004796933	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.383425004796933	2		591	728	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188136	108188136	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1800060	NA	P-0047634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	45	214	0	ENST00000278616.4:c.6235G>A	p.Val2079Ile	p.V2079I	ENST00000278616	NM_000051.3	2079	Gtc/Atc	43/63	0.367299158475448	3	FACETS	0.758	0.639	0.889	0.379	0.319	0.445	SUBCLONAL	1	TRUE	1	0.383425004796933	3		214	369	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021817	71021817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs797045586	NA	P-0047634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	49	185	0	ENST00000318789.4:c.1541G>A	p.Arg514His	p.R514H	ENST00000318789	NM_032682.5	514	cGt/cAt	18/21	0.367299158475448	3	FACETS	0.97	0.826	1	0.485	0.413	0.564	CLONAL	1	TRUE	1	0.383425004796933	3		185	314	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609990	43609990	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs77711105	NA	P-0047634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	176	817	1	ENST00000355710.3:c.1942G>A	p.Val648Ile	p.V648I	ENST00000355710	NM_020975.4	648	Gtc/Atc	11/20	0.367299158475448	3	FACETS	0.982	0.903	1	0.491	0.451	0.532	CLONAL	1	TRUE	1	0.383425004796933	3		818	1114	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494908	56494908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs551223118	NA	P-0047634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	159	502	0	ENST00000267101.3:c.3265C>T	p.Arg1089Trp	p.R1089W	ENST00000267101	NM_001982.3	1089	Cgg/Tgg	27/28	0.367299158475448	3	FACETS	1	0.977	1	0.59	0.541	0.641	CLONAL	1	TRUE	1	0.383425004796933	3		502	838	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623858	28623858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	74	389	0	ENST00000241453.7:c.796G>A	p.Glu266Lys	p.E266K	ENST00000241453	NM_004119.2	266	Gaa/Aaa	7/24	0.383425004796933	6	FACETS	0.703	0.614	0.8	0.176	0.153	0.2	SUBCLONAL	1	TRUE	2	0.383425004796933	6		389	970	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097796	27097796	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0047634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	246	351	0	ENST00000324856.7:c.3385A>T	p.Lys1129Ter	p.K1129*	ENST00000324856	NM_006015.4	1129	Aag/Tag	12/20	0.352900481239737	4	FACETS	0.859	0.807	0.911	0.859	0.807	0.911	CLONAL	3	TRUE	1	0.383425004796933	4		351	689	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28883002	28883002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs115595062	NA	P-0047634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	408	410	0	ENST00000282397.4:c.3698C>T	p.Pro1233Leu	p.P1233L	ENST00000282397	NM_002019.4	1233	cCg/cTg	28/30	0.383425004796933	6	FACETS	1	0.978	1	1	0.978	1	CLONAL	4	TRUE	2	0.383425004796933	6		410	908	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701190	43701190	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	136	445	0	ENST00000382044.4:c.5505G>A	p.Trp1835Ter	p.W1835*	ENST00000382044	NM_001141980.1	1835	tgG/tgA	26/28	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.383425004796933	2		445	622	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215597	5215597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	164	718	0	ENST00000357368.4:c.4106G>A	p.Ser1369Asn	p.S1369N	ENST00000357368	NM_002850.3	1369	aGc/aAc	27/38	0.253461674666373	3	FACETS	1	0.974	1	0.571	0.525	0.62	CLONAL	1	TRUE	1	0.383425004796933	3		718	892	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0047635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	224	424	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.87	0.814	0.926	0.87	0.814	0.926	CLONAL	1	TRUE	1	0.772348538063257	2		424	667	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0047635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	114	259	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.906	0.826	0.988	0.906	0.826	0.988	CLONAL	1	TRUE	1	0.772348538063257	2		259	326	SUCCESS
APC	324	MSKCC	GRCh37	5	112174113	112174113	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554084511	NA	P-0047635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	115	181	0	ENST00000257430.4:c.2825del	p.Asn942IlefsTer13	p.N942Ifs*13	ENST00000257430	NM_000038.5	941	gAa/ga	16/16	1	2	FACETS	0.871	0.794	0.95	0.871	0.794	0.95	CLONAL	1	TRUE	1	0.772348538063257	2		181	342	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866393	37866393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	881	727	0	ENST00000269571.5:c.698C>T	p.Thr233Ile	p.T233I	ENST00000269571		233	aCt/aTt	6/27	0.765851976554585	2	FACETS	0.993	0.973	1	0.993	0.973	1	CLONAL	2	TRUE	0	0.772348538063257	2		727	1149	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411576	63411576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	294	557	0	ENST00000330258.3:c.1591C>T	p.Arg531Ter	p.R531*	ENST00000330258	NM_152424.3	531	Cga/Tga	2/2	0.522883546187584	3	FACETS	0.937	0.882	0.994	0.469	0.441	0.497	CLONAL	1	TRUE	1	0.772348538063257	3		557	1126	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579568	7579568	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	655	487	0	ENST00000269305.4:c.119del	p.Met40ArgfsTer4	p.M40Rfs*4	ENST00000269305	NM_001126112.2	40	aTg/ag	4/11	0.765851976554585	2	FACETS	0.965	0.942	0.987	0.965	0.942	0.987	CLONAL	2	TRUE	0	0.772348538063257	2		487	879	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149865	202149865	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	46	372	0	ENST00000358485.4:c.1306G>T	p.Glu436Ter	p.E436*	ENST00000358485	NM_001080125.1	436	Gag/Tag	8/9	1	2	FACETS	0.181	0.152	0.213	0.181	0.152	0.213	SUBCLONAL	1	TRUE	1	0.772348538063257	2		372	658	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	223	516	0				ENST00000310581	NM_198253.2	-/1132			0.523903109882172	4	FACETS	0.904	0.846	0.962	0.904	0.846	0.962	CLONAL	2	TRUE	2	0.616663080275809	4		516	647	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546919	9546919	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0047636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	143	437	0	ENST00000353224.5:c.1103C>G	p.Ser368Ter	p.S368*	ENST00000353224	NM_177990.2	368	tCa/tGa	5/10	0.278767167254476	4	FACETS	0.983	0.897	1			1	INDETERMINATE	1	TRUE	NA	0.616663080275809	4		437	763	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725039	162725039	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778072557	NA	P-0047636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1521	133	385	1	ENST00000367921.3:c.511G>A	p.Asp171Asn	p.D171N	ENST00000367921	NM_006182.2	171	Gac/Aac	6/18	0.616663080275809	10	FACETS	0.904	0.818	0.996			1	CLONAL	1	TRUE	NA	0.616663080275809	10		386	1654	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551100	41551100	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	189	435	0	ENST00000263253.7:c.3244C>T	p.Gln1082Ter	p.Q1082*	ENST00000263253	NM_001429.3	1082	Cag/Tag	17/31	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.616663080275809	2		435	595	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437669	52437669	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	265	693	0	ENST00000460680.1:c.1492G>C	p.Glu498Gln	p.E498Q	ENST00000460680	NM_004656.3	498	Gag/Cag	13/17	0.320669306636332	6	FACETS	1	0.99	1	0.442	0.413	0.472	INDETERMINATE	1	TRUE	3	0.616663080275809	6		693	1448	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069387	30069387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765540111	NA	P-0047636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	232	625	1	ENST00000338641.4:c.1252C>T	p.Arg418Cys	p.R418C	ENST00000338641	NM_000268.3	418	Cgc/Tgc	12/16	1	2	FACETS	0.908	0.848	0.968	0.908	0.848	0.968	CLONAL	1	TRUE	1	0.616663080275809	2		626	829	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185023	32185023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762392289	NA	P-0047636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	267	638	0	ENST00000375023.3:c.1645G>A	p.Glu549Lys	p.E549K	ENST00000375023	NM_004557.3	549	Gag/Aag	10/30	0.605844049489029	3	FACETS	0.972	0.911	1	0.486	0.455	0.518	CLONAL	1	TRUE	1	0.616663080275809	3		638	1166	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28607258	28607258	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1438624951	NA	P-0047636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1791	236	566	2	ENST00000253063.3:c.1388G>A	p.Arg463His	p.R463H	ENST00000253063	NM_031459.4	463	cGc/cAc	10/10	0.616663080275809	8	FACETS	1	0.969	1			1	CLONAL	1	TRUE	NA	0.616663080275809	8		568	2027	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739322	46739322	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	145	381	0	ENST00000371975.4:c.1513C>G	p.Leu505Val	p.L505V	ENST00000371975	NM_003579.3	505	Ctg/Gtg	14/18	0.605844049489029	3	FACETS	0.884	0.808	0.963	0.442	0.404	0.482	CLONAL	1	TRUE	1	0.616663080275809	3		381	696	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946892	71946892	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1313734902	NA	P-0047636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	310	722	1	ENST00000298229.2:c.2741C>T	p.Ser914Leu	p.S914L	ENST00000298229	NM_001567.3	914	tCa/tTa	25/28	0.616663080275809	3	FACETS	1	0.974	1	0.529	0.498	0.56	CLONAL	1	TRUE	1	0.616663080275809	3		723	1244	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946937	71946937	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	324	869	0	ENST00000298229.2:c.2786C>T	p.Ser929Phe	p.S929F	ENST00000298229	NM_001567.3	929	tCc/tTc	25/28	0.616663080275809	3	FACETS	0.986	0.93	1	0.493	0.465	0.522	CLONAL	1	TRUE	1	0.616663080275809	3		869	1394	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344813	118344813	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	102	217	0	ENST00000534358.1:c.2942del	p.Pro981HisfsTer26	p.P981Hfs*26	ENST00000534358	NM_005933.3	980	gCc/gc	3/36	0.616663080275809	3	FACETS	0.979	0.881	1	0.49	0.44	0.541	CLONAL	1	TRUE	1	0.616663080275809	3		217	442	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953727	48953728	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	novel	NA	P-0047636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	150	148	0	ENST00000267163.4:c.1333-2dup		p.X445_splice	ENST00000267163	NM_000321.2	445			NA	2	FACETS	1	0.954	1			1	INDETERMINATE	2	TRUE	NA	0.616663080275809	2		148	239	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687538	37687539	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	346	311	0	ENST00000447079.4:c.4443dup	p.Gly1482ArgfsTer31	p.G1482Rfs*31	ENST00000447079	NM_015083.1	1481	aga/agAa	14/14	0.559191047154914	4	FACETS	0.892	0.852	0.932	0.892	0.852	0.932	CLONAL	3	TRUE	1	0.616663080275809	4		311	678	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965722	18965722	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1465	295	812	0	ENST00000262803.5:c.1300G>A	p.Glu434Lys	p.E434K	ENST00000262803	NM_002911.3	434	Gag/Aag	10/24	0.590217508802467	4	FACETS	0.879	0.824	0.935	0.439	0.412	0.468	CLONAL	1	TRUE	2	0.616663080275809	4		812	1760	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752902	42752902	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2175	796	950	0	ENST00000222329.4:c.1362C>G	p.Phe454Leu	p.F454L	ENST00000222329	NM_006494.2	454	ttC/ttG	4/4	0.616663080275809	7	FACETS	1	0.993	1	0.552	0.532	0.573	CLONAL	2	TRUE	3	0.616663080275809	7		950	2971	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715331	61715331	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	144	500	0	ENST00000401558.2:c.2282G>C	p.Gly761Ala	p.G761A	ENST00000401558	NM_003400.3	761	gGt/gCt	19/25	0.616663080275809	3	FACETS	0.727	0.663	0.794	0.364	0.331	0.397	SUBCLONAL	1	TRUE	1	0.616663080275809	3		500	840	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553318	41553318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	173	413	0	ENST00000263253.7:c.3407C>T	p.Ser1136Leu	p.S1136L	ENST00000263253	NM_001429.3	1136	tCa/tTa	18/31	1	2	FACETS	0.956	0.885	1	0.956	0.885	1	CLONAL	1	TRUE	1	0.616663080275809	2		413	587	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556696	41556696	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	144	345	0	ENST00000263253.7:c.3641C>G	p.Ser1214Cys	p.S1214C	ENST00000263253	NM_001429.3	1214	tCt/tGt	20/31	1	2	FACETS	0.983	0.903	1	0.983	0.903	1	CLONAL	1	TRUE	1	0.616663080275809	2		345	475	SUCCESS
ATR	545	MSKCC	GRCh37	3	142189021	142189021	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs372864251	NA	P-0047636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	67	179	0	ENST00000350721.4:c.6226C>G	p.Leu2076Val	p.L2076V	ENST00000350721	NM_001184.3	2076	Cta/Gta	37/47	0.616663080275809	3	FACETS	0.856	0.749	0.97	0.428	0.374	0.485	CLONAL	1	TRUE	1	0.616663080275809	3		179	332	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183153	32183153	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	272	784	0	ENST00000375023.3:c.1871G>C	p.Cys624Ser	p.C624S	ENST00000375023	NM_004557.3	624	tGt/tCt	12/30	0.605844049489029	3	FACETS	0.908	0.851	0.967	0.454	0.425	0.484	CLONAL	1	TRUE	1	0.616663080275809	3		784	1271	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732954	44732954	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	173	508	0	ENST00000377967.4:c.157G>C	p.Asp53His	p.D53H	ENST00000377967	NM_021140.2	53	Gac/Cac	1/29	0.333523427351552	5	FACETS	1	0.972	1	0.373	0.343	0.404	INDETERMINATE	1	TRUE	2	0.616663080275809	5		508	965	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41554426	41554428	+	missense_variant	Missense_Mutation	TNP	CTC	CTC	TTA	novel	NA	P-0047636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	181	397	0	ENST00000263253.7:c.3512_3514delinsTTA	p.Ser1171_Pro1172delinsPheThr	p.S1171_P1172delinsFT	ENST00000263253	NM_001429.3	1171	tCTCca/tTTAca	19/31	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.616663080275809	2		397	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0047637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	282	588	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.321944502370366	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.321944502370366	1		588	1072	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913315	NA	P-0047637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	351	761	0	ENST00000326873.7:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000326873	NM_000455.4	194	Gac/Tac	4/10	0.321944502370366	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.321944502370366	1		761	1270	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699237	117699237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	61	320	0	ENST00000369458.3:c.404C>T	p.Ser135Phe	p.S135F	ENST00000369458	NM_024626.3	135	tCt/tTt	3/6	0.177231017105351	1	FACETS	0.626	0.54	0.718	0.626	0.54	0.718	INDETERMINATE	1	TRUE	0	0.321944502370366	1		320	508	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052917	180052917	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	458	846	0	ENST00000261937.6:c.1373G>T	p.Trp458Leu	p.W458L	ENST00000261937	NM_182925.4	458	tGg/tTg	10/30	0.321944502370366	1	FACETS	0.766	0.73	0.802	1	0.996	1	SUBCLONAL	2	TRUE	0	0.321944502370366	1		846	1559	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435146	18435146	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	54	265	0	ENST00000266497.5:c.131T>C	p.Val44Ala	p.V44A	ENST00000266497		44	gTa/gCa	1/31	0.321944502370366	1	FACETS	0.813	0.698	0.938	0.813	0.698	0.938	CLONAL	1	TRUE	0	0.321944502370366	1		265	346	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679173	88679173	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	94	430	0	ENST00000360948.2:c.864C>A	p.Asn288Lys	p.N288K	ENST00000360948	NM_001012338.2	288	aaC/aaA	8/19	1	2	FACETS	0.782	0.695	0.874	0.782	0.695	0.874	SUBCLONAL	1	TRUE	1	0.321944502370366	2		430	747	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321353	65321353	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	122	518	0	ENST00000342505.4:c.1487A>T	p.Lys496Met	p.K496M	ENST00000342505	NM_002227.2	496	aAg/aTg	11/25	0.177231017105351	1	FACETS	0.784	0.709	0.864	0.784	0.709	0.864	INDETERMINATE	1	TRUE	0	0.321944502370366	1		518	811	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567713	226567713	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	197	553	1	ENST00000366794.5:c.1453G>T	p.Val485Leu	p.V485L	ENST00000366794	NM_001618.3	485	Gtg/Ttg	10/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.321944502370366	2		554	1061	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416864	121416864	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1304	178	835	0	ENST00000257555.6:c.293C>A	p.Ala98Asp	p.A98D	ENST00000257555		98	gCc/gAc	1/10	1	2	FACETS	0.746	0.685	0.81	0.746	0.685	0.81	SUBCLONAL	1	TRUE	1	0.321944502370366	2		835	1482	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623615	28623615	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	41	419	0	ENST00000241453.7:c.942T>A	p.Phe314Leu	p.F314L	ENST00000241453	NM_004119.2	314	ttT/ttA	8/24	0.185520985599228	2	FACETS	0.408	0.339	0.485	0.204	0.169	0.243	INDETERMINATE	1	TRUE	0	0.321944502370366	2		419	624	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582969	95582969	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	91	210	0	ENST00000393063.1:c.1573G>C	p.Gly525Arg	p.G525R	ENST00000393063	NM_030621.3	525	Ggt/Cgt	11/28	0.321944502370366	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.321944502370366	1		210	362	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438164	56438164	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	295	766	0	ENST00000407977.2:c.829G>T	p.Glu277Ter	p.E277*	ENST00000407977		277	Gag/Tag	7/10	0.321944502370366	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.321944502370366	1		766	1168	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144113	11144113	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	340	694	1	ENST00000358026.2:c.3694G>T	p.Gly1232Cys	p.G1232C	ENST00000358026	NM_001128849.1	1232	Ggc/Tgc	26/36	0.321944502370366	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.321944502370366	1		695	1245	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752639	42752639	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1178888044	NA	P-0047637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	273	633	0	ENST00000222329.4:c.1625C>T	p.Ser542Phe	p.S542F	ENST00000222329	NM_006494.2	542	tCc/tTc	4/4	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.321944502370366	2		633	1263	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022714	31022714	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs768911270	NA	P-0047637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	208	535	1	ENST00000375687.4:c.2199G>T	p.Gln733His	p.Q733H	ENST00000375687	NM_015338.5	733	caG/caT	13/13	0.142831601204956	4	FACETS	0.776	0.719	0.834	0.776	0.719	0.834	INDETERMINATE	2	TRUE	2	0.321944502370366	4		536	1101	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672380	86672380	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	48	208	0	ENST00000274376.6:c.2182G>T	p.Glu728Ter	p.E728*	ENST00000274376	NM_002890.2	728	Gag/Tag	16/25	0.321944502370366	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.321944502370366	1		208	221	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942864	68942864	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	165	424	1	ENST00000288368.4:c.676G>T	p.Glu226Ter	p.E226*	ENST00000288368	NM_024870.2	226	Gaa/Taa	6/40	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.321944502370366	2		425	798	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971042	21971042	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	136	575	0	ENST00000304494.5:c.316del	p.Val106CysfsTer40	p.V106Cfs*40	ENST00000304494	NM_000077.4	106	Gtg/tg	2/3	0.321944502370366	1	FACETS	0.804	0.73	0.881	0.804	0.73	0.881	CLONAL	1	TRUE	0	0.321944502370366	1		575	882	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716344	18716344	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778895247	NA	P-0047638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	27	243	0	ENST00000266497.5:c.3691G>A	p.Glu1231Lys	p.E1231K	ENST00000266497		1231	Gaa/Aaa	26/31	0.3	1	FACETS	0.847	0.674	1	0.847	0.674	1	CLONAL	1	TRUE	0	0.15	1		243	393	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0047638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	23	240	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	1	2	FACETS	0.992	0.774	1	0.992	0.774	1	CLONAL	1	TRUE	1	0.15	2		240	309	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121835	2121835	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1515	91	829	0	ENST00000219476.3:c.1997C>T	p.Pro666Leu	p.P666L	ENST00000219476	NM_000548.3	666	cCc/cTc	19/42	1	2	FACETS	0.756	0.668	0.85	0.756	0.668	0.85	SUBCLONAL	1	TRUE	1	0.15	2		829	1606	SUCCESS
BTK	695	MSKCC	GRCh37	X	100629571	100629571	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	24	193	0	ENST00000308731.7:c.193G>A	p.Glu65Lys	p.E65K	ENST00000308731	NM_000061.2	65	Gaa/Aaa	3/19	1	1	FACETS	1	0.801	1	1	0.801	1	CLONAL	1	TRUE	0	0.15	1		193	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0047639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	357	652	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.186334508108032	4	FACETS	0.877	0.833	0.922	0.877	0.833	0.922	CLONAL	4	TRUE	0	0.243273091039037	4		653	1040	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899060	40899060	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	106	573	0	ENST00000373198.4:c.2210C>A	p.Thr737Asn	p.T737N	ENST00000373198	NM_133170.3	737	aCt/aAt	14/32	0.195256496130342	5	FACETS	0.757	0.678	0.84	0.504	0.452	0.56	SUBCLONAL	2	TRUE	2	0.243273091039037	5		573	786	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23640563	23640563	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	83	412	0	ENST00000261584.4:c.2548A>G	p.Ile850Val	p.I850V	ENST00000261584	NM_024675.3	850	Ata/Gta	6/13	0.118777033999268	4	FACETS	0.862	0.763	0.967	0.862	0.763	0.967	INDETERMINATE	2	TRUE	2	0.243273091039037	4		412	492	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688737	47688737	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	90	367	0	ENST00000347630.2:c.563A>G	p.Asp188Gly	p.D188G	ENST00000347630	NM_001007230.1	188	gAt/gGt	7/11	0.0651134593597895	4	FACETS	0.808	0.719	0.904	0.808	0.719	0.904	INDETERMINATE	2	TRUE	2	0.243273091039037	4		367	569	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871271	35871271	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	58	275	0	ENST00000303115.3:c.493C>A	p.His165Asn	p.H165N	ENST00000303115	NM_002185.3	165	Cac/Aac	4/8	0.243273091039037	7	FACETS	0.826	0.711	0.951	0.331	0.284	0.381	CLONAL	2	TRUE	2	0.243273091039037	7		275	464	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652429	48652429	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	175	1133	2	ENST00000376670.3:c.1100T>A	p.Leu367Gln	p.L367Q	ENST00000376670	NM_002049.3	367	cTg/cAg	6/6	0.0484179202572101	4	FACETS	0.953	0.878	1	0.953	0.878	1	INDETERMINATE	2	TRUE	2	0.243273091039037	4		1135	938	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937561	76937561	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	37	293	0	ENST00000373344.5:c.3187T>A	p.Tyr1063Asn	p.Y1063N	ENST00000373344	NM_000489.3	1063	Tat/Aat	9/35	0.0484179202572101	4	FACETS	1	0.95	1	0.736	0.61	0.874	INDETERMINATE	1	TRUE	2	0.243273091039037	4		293	257	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs760043106	NA	P-0047640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	359	581	0	ENST00000269305.4:c.584T>A	p.Ile195Asn	p.I195N	ENST00000269305	NM_001126112.2	195	aTc/aAc	6/11	0.899259645516675	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.911747598746144	1		581	419	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564441	139564441	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780383344	NA	P-0047640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2074	474	807	1	ENST00000308874.7:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000308874		130	cGg/cAg	6/10	0.911747598746144	5	FACETS	0.966	0.919	1	0.322	0.306	0.338	CLONAL	1	TRUE	2	0.911747598746144	5		808	2548	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612035	189612035	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	206	413	0	ENST00000264731.3:c.1787del	p.Ala596GlyfsTer108	p.A596Gfs*108	ENST00000264731	NM_003722.4	596	gCg/gg	14/14	0.814417103475573	5	FACETS	0.929	0.861	1			1	CLONAL	1	TRUE	NA	0.911747598746144	5		413	1152	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420005	152420005	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	150	508	1	ENST00000206249.3:c.1692C>G	p.Asp564Glu	p.D564E	ENST00000206249	NM_000125.3	564	gaC/gaG	8/8	0.436669970438651	3	FACETS	0.583	0.533	0.635	0.194	0.177	0.212	INDETERMINATE	1	TRUE	0	0.911747598746144	3		509	822	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0047641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	398	731	7	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.308837543310806	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.327030644451212	2		738	1073	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0047641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	33	353	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.327030644451212	2		353	167	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177584	56177584	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368201444	NA	P-0047641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	44	244	0	ENST00000399503.3:c.2557C>T	p.Arg853Cys	p.R853C	ENST00000399503	NM_005921.1	853	Cgt/Tgt	14/20	1	2	FACETS	0.619	0.519	0.728	0.619	0.519	0.728	SUBCLONAL	1	TRUE	1	0.327030644451212	2		244	435	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0047641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	36	375	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	1	2	FACETS	0.781	0.645	0.932	0.781	0.645	0.932	CLONAL	1	TRUE	1	0.327030644451212	2		375	282	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143043354	143043354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	27	191	0	ENST00000262992.4:c.2062G>A	p.Asp688Asn	p.D688N	ENST00000262992	NM_001101669.1	688	Gat/Aat	19/24	0.327030644451212	3	FACETS	0.535	0.426	0.66	0.268	0.213	0.33	SUBCLONAL	1	TRUE	1	0.327030644451212	3		191	359	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711258	114711258	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	106	319	0	ENST00000543371.1:c.273del	p.Asp91GlufsTer17	p.D91Efs*17	ENST00000543371	NM_001198531.1	91	gaT/ga	3/14	0.327030644451212	3	FACETS	1	0.948	1	0.546	0.49	0.605	CLONAL	1	TRUE	1	0.327030644451212	3		319	691	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248454	212248454	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	58	242	0	ENST00000342788.4:c.3813T>A	p.Asn1271Lys	p.N1271K	ENST00000342788	NM_005235.2	1271	aaT/aaA	28/28	0.285481559414455	4	FACETS	0.89	0.765	1	0.445	0.382	0.513	CLONAL	1	TRUE	2	0.327030644451212	4		242	529	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268726	41268726	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	40	173	0	ENST00000349496.5:c.964C>T	p.Gln322Ter	p.Q322*	ENST00000349496	NM_001904.3	322	Caa/Taa	7/15	0.327030644451212	4	FACETS	1	0.868	1	0.349	0.291	0.413	CLONAL	1	TRUE	1	0.327030644451212	4		173	310	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200769	128200769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1559985135	NA	P-0047641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	276	510	0	ENST00000341105.2:c.1036G>A	p.Gly346Ser	p.G346S	ENST00000341105	NM_032638.4	346	Ggc/Agc	5/6	0.325059614801957	4	FACETS	0.918	0.861	0.977	0.918	0.861	0.977	CLONAL	2	TRUE	2	0.327030644451212	4		510	1220	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845406	151845406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	102	445	1	ENST00000262189.6:c.13606G>A	p.Ala4536Thr	p.A4536T	ENST00000262189	NM_170606.2	4536	Gct/Act	52/59	0.325059614801957	4	FACETS	0.852	0.76	0.949	0.426	0.38	0.475	CLONAL	1	TRUE	2	0.327030644451212	4		446	972	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339192	70339239	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAACAACTAAACGCCGCTTTCCTGCCTCAGGATGAACTGACGGCCTT	AAAACAACTAAACGCCGCTTTCCTGCCTCAGGATGAACTGACGGCCTT	-	novel	NA	P-0047641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	93	142	1	ENST00000374080.3:c.100-31_116del		p.X34_splice	ENST00000374080		34		2/45	0.248972885017822	2	FACETS	1	0.906	1			1	CLONAL	2	TRUE	NA	0.327030644451212	2		143	283	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0047646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	518	322	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.432584646589365	8	FACETS	1	0.991	1	0.775	0.747	0.804	CLONAL	5	TRUE	1	0.432584646589365	8		322	1014	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576911	7576912	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0047646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	120	651	0	ENST00000269305.4:c.934_935del	p.Thr312GlnfsTer24	p.T312Qfs*24	ENST00000269305	NM_001126112.2	312	ACc/c	9/11	1	2	FACETS	0.519	0.468	0.574	0.519	0.468	0.574	SUBCLONAL	1	TRUE	1	0.432584646589365	2		651	1068	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576853	7576853	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs11575996	NA	P-0047647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	52	457	0	ENST00000269305.4:c.993G>T	p.Gln331His	p.Q331H	ENST00000269305	NM_001126112.2	331	caG/caT	9/11	0.247090916571303	1	FACETS	0.559	0.475	0.651	0.559	0.475	0.651	SUBCLONAL	1	TRUE	0	0.247090916571302	1		457	660	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031691	69031691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748595305	NA	P-0047647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	33	340	0	ENST00000288368.4:c.3446G>A	p.Arg1149His	p.R1149H	ENST00000288368	NM_024870.2	1149	cGc/cAc	28/40	1	2	FACETS	0.586	0.477	0.709	0.586	0.477	0.709	SUBCLONAL	1	TRUE	1	0.247090916571302	2		340	456	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842433	68842433	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	151	391	0	ENST00000261769.5:c.494A>G	p.Glu165Gly	p.E165G	ENST00000261769	NM_004360.3	165	gAa/gGa	4/16	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.247090916571302	NA		391	701	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412007	63412007	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	134	514	0	ENST00000330258.3:c.1160A>T	p.Glu387Val	p.E387V	ENST00000330258	NM_152424.3	387	gAg/gTg	2/2	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.247090916571302	2		514	829	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788617	3788617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519884	NA	P-0047648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	14	295	1	ENST00000262367.5:c.4337G>A	p.Arg1446His	p.R1446H	ENST00000262367	NM_004380.2	1446	cGc/cAc	26/31	0.259117982083449	1	FACETS	0.097	0.07	0.131	0.097	0.07	0.131	INDETERMINATE	1	TRUE	0	0.513395603938485	1		296	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574005	7574005	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	744	655	0	ENST00000269305.4:c.1022T>C	p.Phe341Ser	p.F341S	ENST00000269305	NM_001126112.2	341	tTc/tCc	10/11	0.491920870998159	3	FACETS	1	0.983	1			1	CLONAL	3	TRUE	NA	0.513395603938485	3		655	1197	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910570	29910570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199474358	NA	P-0047648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	109	792	0	ENST00000376809.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000376809	NM_002116.7	37	tCc/tTc	2/8	0.458769006598159	2	FACETS	0.583	0.524	0.646	0.292	0.262	0.323	SUBCLONAL	1	TRUE	0	0.513395603938485	2		792	728	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986598	36986598	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	46	434	0	ENST00000354822.5:c.1091C>T	p.Ala364Val	p.A364V	ENST00000354822	NM_001079668.2	364	gCc/gTc	3/3	0.346001103250313	1	FACETS	0.265	0.223	0.311	0.265	0.223	0.311	SUBCLONAL	1	TRUE	0	0.513395603938485	1		434	503	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918984	50918984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	101	622	0	ENST00000440232.2:c.2721G>A	p.Met907Ile	p.M907I	ENST00000440232	NM_002691.3	907	atG/atA	22/27	0.458769006598159	2	FACETS	0.554	0.495	0.617	0.277	0.247	0.309	SUBCLONAL	1	TRUE	0	0.513395603938485	2		622	710	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545172	41545182	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTCTCAAGTA	TGTCTCAAGTA	-	novel	NA	P-0047648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	43	419	0	ENST00000263253.7:c.2379_2379+10del		p.X793_splice	ENST00000263253	NM_001429.3	793		13/31	0.513395603938485	1	FACETS	0.308	0.258	0.364	0.308	0.258	0.364	SUBCLONAL	1	TRUE	0	0.513395603938485	1		419	404	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97876993	97876993	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0047648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	132	349	0	ENST00000289081.3:c.1073-1G>A		p.X358_splice	ENST00000289081	NM_000136.2	358			1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.513395603938485	2		349	510	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361107	70361127	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAACAGCAA	CAGCAGCAGCAGCAACAGCAA	-	novel	NA	P-0047648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	19	278	0	ENST00000374080.3:c.6318_6338del	p.Gln2109_Gln2115del	p.Q2109_Q2115del	ENST00000374080		2099	CAGCAGCAGCAGCAACAGCAA/-	43/45	1	1	FACETS	0.164	0.124	0.211	0.164	0.124	0.211	SUBCLONAL	1	TRUE	0	0.513395603938485	1		278	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0047651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	201	1078	6	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.28550326911517	2	FACETS	0.872	0.81	0.937	0.872	0.81	0.937	CLONAL	2	TRUE	0	0.28550326911517	2		1084	807	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0047651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	20	336	1	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.28550326911517	3	FACETS	0.465	0.355	0.594	0.233	0.177	0.297	SUBCLONAL	1	TRUE	1	0.28550326911517	3		337	344	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259489	89259489	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	44	310	0	ENST00000336596.2:c.633G>T	p.Met211Ile	p.M211I	ENST00000336596	NM_005233.5	211	atG/atT	3/17	0.28550326911517	3	FACETS	0.709	0.594	0.835	0.354	0.297	0.418	SUBCLONAL	1	TRUE	1	0.28550326911517	3		310	497	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587118	212587118	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs74898139	NA	P-0047651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	66	199	0	ENST00000342788.4:c.883C>T	p.His295Tyr	p.H295Y	ENST00000342788	NM_005235.2	295	Cat/Tat	7/28	0.2029259466547	4	FACETS	0.864	0.755	0.981	0.864	0.755	0.981	CLONAL	2	TRUE	2	0.28550326911517	4		199	344	SUCCESS
APC	324	MSKCC	GRCh37	5	112174774	112174774	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0047651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	49	118	0	ENST00000257430.4:c.3484del	p.Tyr1162IlefsTer3	p.Y1162Ifs*3	ENST00000257430	NM_000038.5	1161	aaT/aa	16/16	0.28550326911517	3	FACETS	0.934	0.801	1	0.934	0.801	1	CLONAL	2	TRUE	1	0.28550326911517	3		118	210	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822299	72822299	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	140	626	0	ENST00000268489.5:c.9876G>T	p.Gln3292His	p.Q3292H	ENST00000268489	NM_006885.3	3292	caG/caT	10/10	0.245625666897846	4	FACETS	1	0.967	1	0.378	0.343	0.414	CLONAL	1	TRUE	1	0.28550326911517	4		626	1113	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0047652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	176	1013	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.893	0.822	0.967	0.893	0.822	0.967	CLONAL	1	TRUE	1	0.396552632149356	2		1013	994	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0047652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	462	470	0				ENST00000310581	NM_198253.2	-/1132			0.368404962383837	4	FACETS	0.892	0.857	0.927	0.892	0.857	0.927	CLONAL	4	TRUE	0	0.396552632149356	4		470	912	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0047652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	202	658	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.967	0.895	1	0.967	0.895	1	CLONAL	1	TRUE	1	0.396552632149356	2		658	1054	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0047652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	204	664	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.396552632149356	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.396552632149356	1		664	727	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867546	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs11466445	NA	P-0047652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	17	7	0	ENST00000374994.4:c.70_78del	p.Ala24_Ala26del	p.A24_A26del	ENST00000374994	NM_004612.2	17	ctGGCGGCGGCg/ctg	1/9	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.396552632149356	2		7	64	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413072	139413072	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	360	569	0	ENST00000277541.6:c.1070T>C	p.Phe357Ser	p.F357S	ENST00000277541	NM_017617.3	357	tTc/tCc	6/34	0.313130429913304	3	FACETS	1	0.992	1	0.797	0.758	0.836	CLONAL	2	TRUE	0	0.396552632149356	3		569	910	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910349	29910349	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1381	211	1007	1	ENST00000376809.5:c.19C>T	p.Arg7Ter	p.R7*	ENST00000376809	NM_002116.7	7	Cga/Tga	1/8	0.187172134968601	3	FACETS	0.801	0.741	0.863	0.4	0.37	0.432	INDETERMINATE	1	TRUE	1	0.396552632149356	3		1008	1592	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256765	46256765	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs757864008	NA	P-0047652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	21	229	0	ENST00000371998.3:c.821C>T	p.Ser274Leu	p.S274L	ENST00000371998		274	tCa/tTa	8/23	0.187172134968601	3	FACETS	1	0.918	1	0.713	0.561	0.881	INDETERMINATE	1	TRUE	1	0.396552632149356	3		229	89	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121438937	121438937	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	214	725	0	ENST00000257555.6:c.1838C>G	p.Ser613Cys	p.S613C	ENST00000257555		613	tCc/tGc	10/10	0.137941666553635	4	FACETS	1	0.989	1	0.667	0.619	0.717	INDETERMINATE	1	TRUE	2	0.396552632149356	4		725	1130	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245752	41245752	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1174268388	NA	P-0047652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	29	401	0	ENST00000357654.3:c.1796A>G	p.Asn599Ser	p.N599S	ENST00000357654	NM_007294.3	599	aAt/aGt	10/23	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.396552632149356	2		401	128	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523752	41523752	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	118	460	0	ENST00000263253.7:c.1168G>A	p.Val390Met	p.V390M	ENST00000263253	NM_001429.3	390	Gtg/Atg	4/31	1	2	FACETS	0.974	0.881	1	0.974	0.881	1	CLONAL	1	TRUE	1	0.396552632149356	2		460	611	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259382	89259382	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs755222529	NA	P-0047652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	51	306	0	ENST00000336596.2:c.526A>G	p.Lys176Glu	p.K176E	ENST00000336596	NM_005233.5	176	Aag/Gag	3/17	0.277146512049567	3	FACETS	1	0.963	1	0.704	0.605	0.809	CLONAL	1	TRUE	1	0.396552632149356	3		306	219	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549397	187549397	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	158	416	0	ENST00000441802.2:c.4721C>A	p.Ser1574Ter	p.S1574*	ENST00000441802	NM_005245.3	1574	tCg/tAg	9/27	1	2	FACETS	0.95	0.871	1	0.95	0.871	1	CLONAL	1	TRUE	1	0.396552632149356	2		416	839	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910379	29910386	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGCCCT	CTGGCCCT	-	novel	NA	P-0047652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1391	185	1026	0	ENST00000376809.5:c.49_56del	p.Leu17AspfsTer79	p.L17Dfs*79	ENST00000376809	NM_002116.7	17	CTGGCCCTg/g	1/8	0.187172134968601	3	FACETS	0.709	0.653	0.769	0.355	0.326	0.385	INDETERMINATE	1	TRUE	1	0.396552632149356	3		1026	1576	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587777894	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	126	445	1	ENST00000361445.4:c.6644C>A	p.Ser2215Tyr	p.S2215Y	ENST00000361445	NM_004958.3	2215	tCt/tAt	47/58	1	2	FACETS	0.887	0.805	0.972	0.887	0.805	0.972	CLONAL	1	TRUE	1	0.44	2		446	646	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	147	436	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.44	2		436	645	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521619	46521619	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	82	268	0	ENST00000262741.5:c.789G>T	p.Leu263Phe	p.L263F	ENST00000262741	NM_003629.3	263	ttG/ttT	7/10	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.44	2		268	360	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745466	162745466	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	46	267	0	ENST00000367921.3:c.1881G>T	p.Lys627Asn	p.K627N	ENST00000367921	NM_006182.2	627	aaG/aaT	15/18	1	2	FACETS	0.786	0.667	0.916	0.786	0.667	0.916	CLONAL	1	TRUE	1	0.44	2		267	266	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944372	206944372	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	107	374	0	ENST00000423557.1:c.258G>T	p.Met86Ile	p.M86I	ENST00000423557	NM_000572.2	86	atG/atT	3/5	1	2	FACETS	0.873	0.786	0.965	0.873	0.786	0.965	CLONAL	1	TRUE	1	0.44	2		374	557	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850948	63850948	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	54	388	0	ENST00000279873.7:c.1726G>T	p.Glu576Ter	p.E576*	ENST00000279873	NM_032199.2	576	Gaa/Taa	10/10	1	2	FACETS	0.409	0.349	0.475	0.409	0.349	0.475	SUBCLONAL	1	TRUE	1	0.44	2		388	600	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332788	70332788	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	113	481	0	ENST00000373644.4:c.693G>T	p.Glu231Asp	p.E231D	ENST00000373644	NM_030625.2	231	gaG/gaT	2/12	1	2	FACETS	0.948	0.856	1	0.948	0.856	1	CLONAL	1	TRUE	1	0.44	2		481	542	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653838	89653838	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	59	271	0	ENST00000371953.3:c.136T>C	p.Tyr46His	p.Y46H	ENST00000371953	NM_000314.4	46	Tac/Cac	2/9	1	2	FACETS	0.76	0.657	0.87	0.76	0.657	0.87	SUBCLONAL	1	TRUE	1	0.44	2		271	353	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	81	330	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.87	0.771	0.976	0.87	0.771	0.976	CLONAL	1	TRUE	1	0.44	2		330	423	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692940	89692940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746152219	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	103	385	0	ENST00000371953.3:c.424C>T	p.Arg142Trp	p.R142W	ENST00000371953	NM_000314.4	142	Cgg/Tgg	5/9	1	2	FACETS	0.946	0.85	1	0.946	0.85	1	CLONAL	1	TRUE	1	0.44	2		385	495	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247515	123247515	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	97	329	0	ENST00000358487.5:c.1976A>C	p.Lys659Thr	p.K659T	ENST00000358487	NM_000141.4	659	aAg/aCg	14/18	1	2	FACETS	0.893	0.799	0.991	0.893	0.799	0.991	CLONAL	1	TRUE	1	0.44	2		329	494	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410705	32410705	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1315549918	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	79	336	0	ENST00000332351.3:c.1453C>T	p.Arg485Trp	p.R485W	ENST00000332351	NM_024426.4	485	Cgg/Tgg	10/10	1	2	FACETS	0.8	0.706	0.899	0.8	0.706	0.899	SUBCLONAL	1	TRUE	1	0.44	2		336	449	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417887	32417887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1564972874	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	112	461	0	ENST00000332351.3:c.1165C>T	p.Arg389Cys	p.R389C	ENST00000332351	NM_024426.4	389	Cgc/Tgc	7/10	1	2	FACETS	0.907	0.819	1	0.907	0.819	1	CLONAL	1	TRUE	1	0.44	2		461	561	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207817	102207817	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762729326	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	58	174	0	ENST00000263464.3:c.1799G>A	p.Arg600His	p.R600H	ENST00000263464	NM_001165.4	600	cGt/cAt	9/9	0.103178102445733	3	FACETS	1	0.943	1	0.585	0.507	0.668	INDETERMINATE	1	TRUE	1	0.44	3		174	275	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433357	49433357	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774178055	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	175	637	0	ENST00000301067.7:c.8090G>A	p.Arg2697His	p.R2697H	ENST00000301067	NM_003482.3	2697	cGc/cAc	32/54	1	2	FACETS	0.988	0.911	1	0.988	0.911	1	CLONAL	1	TRUE	1	0.44	2		637	805	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	70	466	0	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	1	2	FACETS	0.68	0.594	0.772	0.68	0.594	0.772	SUBCLONAL	1	TRUE	1	0.44	2		466	468	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910464	32910464	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	72	277	0	ENST00000380152.3:c.1972T>C	p.Ser658Pro	p.S658P	ENST00000380152		658	Tcc/Ccc	11/27	1	2	FACETS	0.882	0.775	0.996	0.882	0.775	0.996	CLONAL	1	TRUE	1	0.44	2		277	371	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953748	48953748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759079385	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	46	143	0	ENST00000267163.4:c.1351C>T	p.Arg451Cys	p.R451C	ENST00000267163	NM_000321.2	451	Cgc/Tgc	14/27	1	2	FACETS	0.875	0.743	1	0.875	0.743	1	CLONAL	1	TRUE	1	0.44	2		143	239	SUCCESS
BLM	641	MSKCC	GRCh37	15	91290720	91290720	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs139282091	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	43	180	0	ENST00000355112.3:c.98C>T	p.Ser33Leu	p.S33L	ENST00000355112	NM_000057.2	33	tCa/tTa	2/22	1	2	FACETS	0.719	0.605	0.843	0.719	0.605	0.843	SUBCLONAL	1	TRUE	1	0.44	2		180	272	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442819	99442819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1365982598	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	57	411	1	ENST00000268035.6:c.1216C>T	p.Arg406Cys	p.R406C	ENST00000268035	NM_000875.3	406	Cgc/Tgc	5/21	1	2	FACETS	0.46	0.395	0.532	0.46	0.395	0.532	SUBCLONAL	1	TRUE	1	0.44	2		412	563	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828804	3828804	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	140	458	0	ENST00000262367.5:c.1838T>C	p.Phe613Ser	p.F613S	ENST00000262367	NM_004380.2	613	tTc/tCc	9/31	1	2	FACETS	0.957	0.874	1	0.957	0.874	1	CLONAL	1	TRUE	1	0.44	2		458	665	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020583	14020583	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	70	269	0	ENST00000311895.7:c.554T>G	p.Leu185Arg	p.L185R	ENST00000311895	NM_005236.2	185	cTt/cGt	3/11	1	2	FACETS	0.822	0.72	0.931	0.822	0.72	0.931	CLONAL	1	TRUE	1	0.44	2		269	387	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654624	67654624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	108	302	0	ENST00000264010.4:c.1111C>T	p.Arg371Cys	p.R371C	ENST00000264010	NM_006565.3	371	Cgc/Tgc	6/12	1	2	FACETS	0.944	0.851	1	0.944	0.851	1	CLONAL	1	TRUE	1	0.44	2		302	520	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828383	72828383	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1277890729	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	138	527	1	ENST00000268489.5:c.8198G>A	p.Arg2733His	p.R2733H	ENST00000268489	NM_006885.3	2733	cGt/cAt	9/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.44	2		528	591	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993035	72993035	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	198	710	0	ENST00000268489.5:c.1010T>C	p.Val337Ala	p.V337A	ENST00000268489	NM_006885.3	337	gTa/gCa	2/10	1	2	FACETS	0.959	0.889	1	0.959	0.889	1	CLONAL	1	TRUE	1	0.44	2		710	938	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033970	48033970	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782309	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	64	276	0	ENST00000234420.5:c.4054A>G	p.Lys1352Glu	p.K1352E	ENST00000234420	NM_000179.2	1352	Aaa/Gaa	10/10	0.103178102445733	3	FACETS	0.941	0.819	1	0.471	0.409	0.537	INDETERMINATE	1	TRUE	1	0.44	3		276	377	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873391	136873391	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	90	258	0	ENST00000241393.3:c.107T>C	p.Phe36Ser	p.F36S	ENST00000241393	NM_003467.2	36	tTc/tCc	2/2	1	2	FACETS	0.919	0.82	1	0.919	0.82	1	CLONAL	1	TRUE	1	0.44	2		258	445	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266137	198266137	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	79	260	0	ENST00000335508.6:c.2483G>T	p.Arg828Ile	p.R828I	ENST00000335508	NM_012433.2	828	aGa/aTa	17/25	1	2	FACETS	0.867	0.767	0.974	0.867	0.767	0.974	CLONAL	1	TRUE	1	0.44	2		260	414	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632204	215632204	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1553619196	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	43	237	0	ENST00000260947.4:c.1568+2T>C		p.X523_splice	ENST00000260947	NM_000465.2	523			1	2	FACETS	0.654	0.55	0.768	0.654	0.55	0.768	SUBCLONAL	1	TRUE	1	0.44	2		237	299	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275126	41275126	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	53	262	0	ENST00000349496.5:c.1292A>C	p.Asn431Thr	p.N431T	ENST00000349496	NM_001904.3	431	aAt/aCt	9/15	1	2	FACETS	0.746	0.639	0.861	0.746	0.639	0.861	SUBCLONAL	1	TRUE	1	0.44	2		262	323	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158233	47158233	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	53	214	0	ENST00000409792.3:c.4466A>C	p.Lys1489Thr	p.K1489T	ENST00000409792	NM_014159.6	1489	aAa/aCa	4/21	1	2	FACETS	0.673	0.576	0.778	0.673	0.576	0.778	SUBCLONAL	1	TRUE	1	0.44	2		214	358	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916860	178916860	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	66	366	0	ENST00000263967.3:c.247T>G	p.Phe83Val	p.F83V	ENST00000263967	NM_006218.2	83	Ttt/Gtt	2/21	1	2	FACETS	0.549	0.477	0.628	0.549	0.477	0.628	SUBCLONAL	1	TRUE	1	0.44	2		366	546	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	78	580	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.632	0.556	0.713	0.632	0.556	0.713	SUBCLONAL	1	TRUE	1	0.44	2		580	561	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131112	55131112	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	115	397	0	ENST00000257290.5:c.655G>T	p.Glu219Ter	p.E219*	ENST00000257290	NM_006206.4	219	Gaa/Taa	5/23	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.44	2		397	505	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575630	55575630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	60	296	0	ENST00000288135.5:c.1156G>A	p.Glu386Lys	p.E386K	ENST00000288135	NM_000222.2	386	Gaa/Aaa	7/21	1	2	FACETS	0.705	0.61	0.807	0.705	0.61	0.807	SUBCLONAL	1	TRUE	1	0.44	2		296	387	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968610	55968610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374980446	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	125	572	0	ENST00000263923.4:c.2053G>A	p.Glu685Lys	p.E685K	ENST00000263923	NM_002253.2	685	Gaa/Aaa	14/30	1	2	FACETS	0.884	0.802	0.97	0.884	0.802	0.97	CLONAL	1	TRUE	1	0.44	2		572	643	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	66	525	1	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.804	0.702	0.914	0.804	0.702	0.914	CLONAL	1	TRUE	1	0.44	2		526	373	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271223	153271223	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	19	176	0	ENST00000281708.4:c.555G>T	p.Lys185Asn	p.K185N	ENST00000281708	NM_033632.3	185	aaG/aaT	3/12	1	2	FACETS	0.368	0.279	0.471	0.368	0.279	0.471	SUBCLONAL	1	TRUE	1	0.44	2		176	235	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539951	187539951	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs777631605	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	76	323	0	ENST00000441802.2:c.7789C>T	p.Arg2597Ter	p.R2597*	ENST00000441802	NM_005245.3	2597	Cga/Tga	10/27	1	2	FACETS	0.769	0.677	0.868	0.769	0.677	0.868	SUBCLONAL	1	TRUE	1	0.44	2		323	449	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589552	67589552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	32	110	0	ENST00000274335.5:c.1315G>A	p.Glu439Lys	p.E439K	ENST00000274335		439	Gaa/Aaa	10/15	1	2	FACETS	0.703	0.575	0.845	0.703	0.575	0.845	SUBCLONAL	1	TRUE	1	0.44	2		110	207	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590445	67590445	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	40	85	0	ENST00000274335.5:c.1507C>T	p.Arg503Trp	p.R503W	ENST00000274335		503	Cgg/Tgg	11/15	1	2	FACETS	0.937	0.788	1	0.937	0.788	1	CLONAL	1	TRUE	1	0.44	2		85	194	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	38	374	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.535	0.443	0.636	0.535	0.443	0.636	SUBCLONAL	1	TRUE	1	0.44	2		374	323	SUCCESS
APC	324	MSKCC	GRCh37	5	112175897	112175897	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	40	143	0	ENST00000257430.4:c.4606G>T	p.Glu1536Ter	p.E1536*	ENST00000257430	NM_000038.5	1536	Gaa/Taa	16/16	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.44	2		143	179	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939071	131939071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369996457	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	61	227	1	ENST00000265335.6:c.2287C>T	p.Arg763Cys	p.R763C	ENST00000265335		763	Cgc/Tgc	14/25	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.44	2		228	265	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163827	152163827	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373558014	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	135	344	0	ENST00000206249.3:c.548G>A	p.Arg183His	p.R183H	ENST00000206249	NM_000125.3	183	cGc/cAc	2/8	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.44	2		344	594	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729927	41729927	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	130	564	0	ENST00000242208.4:c.602G>T	p.Arg201Met	p.R201M	ENST00000242208	NM_002192.2	201	aGg/aTg	3/3	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.44	2		564	588	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132745	152132745	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1327515855	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	107	392	0	ENST00000262189.6:c.127G>T	p.Asp43Tyr	p.D43Y	ENST00000262189	NM_170606.2	43	Gat/Tat	1/59	1	2	FACETS	0.752	0.675	0.833	0.752	0.675	0.833	SUBCLONAL	1	TRUE	1	0.44	2		392	647	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370997	55370997	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	153	591	0	ENST00000297316.4:c.299A>C	p.Lys100Thr	p.K100T	ENST00000297316	NM_022454.3	100	aAg/aCg	1/2	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.44	2		591	667	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27190544	27190544	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	119	445	0	ENST00000380036.4:c.1345A>C	p.Asn449His	p.N449H	ENST00000380036	NM_000459.3	449	Aat/Cat	10/23	1	2	FACETS	0.941	0.852	1	0.941	0.852	1	CLONAL	1	TRUE	1	0.44	2		445	575	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426069	47426069	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	132	691	0	ENST00000377045.4:c.589T>G	p.Phe197Val	p.F197V	ENST00000377045	NM_001654.4	197	Ttc/Gtc	7/16	0.103178102445733	0	FACETS	0.444	0.403	0.487			1	INDETERMINATE	1	TRUE	0	0.44	0		691	757	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs199469669	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	65	421	0	ENST00000374080.3:c.130G>C	p.Gly44Arg	p.G44R	ENST00000374080		44	Ggt/Cgt	2/45	0.103178102445733	0	FACETS	0.265	0.229	0.303			1	INDETERMINATE	1	TRUE	0	0.44	0		421	625	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888715	76888715	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs782709380	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	43	327	0	ENST00000373344.5:c.5114A>G	p.Asn1705Ser	p.N1705S	ENST00000373344	NM_000489.3	1705	aAc/aGc	19/35	0.103178102445733	0	FACETS	0.31	0.26	0.365			1	INDETERMINATE	1	TRUE	0	0.44	0		327	353	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939017	76939017	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	120	461	0	ENST00000373344.5:c.1731A>C	p.Lys577Asn	p.K577N	ENST00000373344	NM_000489.3	577	aaA/aaC	9/35	0.103178102445733	0	FACETS	0.639	0.58	0.7			1	INDETERMINATE	1	TRUE	0	0.44	0		461	478	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868346	45868346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776313922	NA	P-0047666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	179	793	1	ENST00000391945.4:c.431C>T	p.Ala144Val	p.A144V	ENST00000391945	NM_000400.3	144	gCg/gTg	6/23	1	2	FACETS	0.88	0.811	0.951	1	0.992	1	CLONAL	2	FALSE	1	0.224871985883746	2		794	905	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0047666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	34	220	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	FALSE	1	0.224871985883746	2		221	249	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578368	7578369	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	novel	NA	P-0047666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	208	569	1	ENST00000269305.4:c.559+2_559+3del		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.224871985883746	2	FACETS	1	0.946	1	1	0.992	1	CLONAL	3	FALSE	0	0.224871985883746	2		570	608	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0047667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	30	308	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.78	0.627	0.954	0.78	0.627	0.954	CLONAL	1	TRUE	1	0.15	2		308	513	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	110	438	2	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.10942140221945	4	FACETS	1	0.965	1	1	0.965	1	INDETERMINATE	2	TRUE	2	0.530355728901221	4		440	285	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	29	214	2	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.530355728901221	2		216	102	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023765	27023765	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	120	349	3	ENST00000324856.7:c.871G>C	p.Ala291Pro	p.A291P	ENST00000324856	NM_006015.4	291	Gcc/Ccc	1/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.530355728901221	2		352	339	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088787	27088788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	133	475	0	ENST00000324856.7:c.2402dup	p.Gln802SerfsTer15	p.Q802Sfs*15	ENST00000324856	NM_006015.4	799	cag/caGg	7/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.530355728901221	2		475	450	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	196	517	1	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.767	0.717	0.817	1	0.992	1	SUBCLONAL	2	TRUE	1	0.530355728901221	2		518	482	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803902	43803902	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs368753117	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	174	452	2	ENST00000372470.3:c.212G>A	p.Arg71Gln	p.R71Q	ENST00000372470	NM_005373.2	71	cGg/cAg	2/12	1	2	FACETS	0.777	0.724	0.831	1	0.991	1	SUBCLONAL	2	TRUE	1	0.530355728901221	2		454	422	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154241	2154242	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755455183	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	176	707	2	ENST00000434045.2:c.686dup	p.Glu230ArgfsTer50	p.E230Rfs*50	ENST00000434045	NM_001127598.1	229	cca/ccCa	5/5	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.530355728901221	2		709	631	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945008	31945008	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	285	698	0	ENST00000340398.3:c.93del	p.Ser32LeufsTer5	p.S32Lfs*5	ENST00000340398	NM_001013699.2	31	ccC/cc	1/1	0.157091795821078	4	FACETS	1	0.968	1	1	0.968	1	INDETERMINATE	2	TRUE	2	0.530355728901221	4		698	793	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438235	49438236	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	311	554	2	ENST00000301067.7:c.5033_5034del	p.Lys1678ArgfsTer12	p.K1678Rfs*12	ENST00000301067	NM_003482.3	1678	aAA/a	20/54	0.157091795821078	4	FACETS	1	0.992	1	1	0.992	1	INDETERMINATE	2	TRUE	2	0.530355728901221	4		556	725	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	169	771	3	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	0.157091795821078	4	FACETS	0.999	0.927	1	0.999	0.927	1	INDETERMINATE	2	TRUE	2	0.530355728901221	4		774	488	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856274	111856274	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	48	48	0	ENST00000341259.2:c.325G>A	p.Gly109Ser	p.G109S	ENST00000341259	NM_005475.2	109	Ggc/Agc	2/8	0.157091795821078	4	FACETS	0.879	0.77	0.99	1	0.963	1	INDETERMINATE	3	TRUE	2	0.530355728901221	4		48	105	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930730	32930730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs74047012	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	101	348	2	ENST00000380152.3:c.7601C>T	p.Ala2534Val	p.A2534V	ENST00000380152		2534	gCg/gTg	15/27	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.530355728901221	2		350	283	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042709	42042711	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs1159823543	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	60	320	0	ENST00000219905.7:c.6909_6911del	p.Glu2303del	p.E2303del	ENST00000219905	NM_001164273.1	2302	GAA/-	17/24	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.530355728901221	2		320	165	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120557	2120557	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	363	847	0	ENST00000219476.3:c.1817T>C	p.Ile606Thr	p.I606T	ENST00000219476	NM_000548.3	606	aTc/aCc	17/42	1	2	FACETS	0.805	0.767	0.844	1	0.996	1	CLONAL	2	TRUE	1	0.530355728901221	2		847	850	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	132	465	1	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.87	0.805	0.936	1	0.991	1	CLONAL	2	TRUE	1	0.530355728901221	2		466	286	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	203	889	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.530355728901221	2		895	548	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733022	74733022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	216	500	3	ENST00000359995.5:c.221C>T	p.Ala74Val	p.A74V	ENST00000359995	NM_001195427.1	74	gCc/gTc	1/3	1	2	FACETS	0.761	0.714	0.809	1	0.993	1	SUBCLONAL	2	TRUE	1	0.530355728901221	2		503	535	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222816	5222816	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775778266	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	283	717	0	ENST00000357368.4:c.2987C>T	p.Thr996Met	p.T996M	ENST00000357368	NM_002850.3	996	aCg/aTg	18/38	1	2	FACETS	0.792	0.749	0.835	1	0.995	1	SUBCLONAL	2	TRUE	1	0.530355728901221	2		717	674	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384783	17384783	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772589405	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	235	657	1	ENST00000359435.4:c.415G>A	p.Asp139Asn	p.D139N	ENST00000359435	NM_001033549.1	139	Gac/Aac	4/9	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.530355728901221	2		658	613	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968144	18968144	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	236	595	1	ENST00000262803.5:c.1984G>A	p.Asp662Asn	p.D662N	ENST00000262803	NM_002911.3	662	Gac/Aac	15/24	1	2	FACETS	0.818	0.771	0.866	1	0.994	1	CLONAL	2	TRUE	1	0.530355728901221	2		596	544	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224512	36224512	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	113	822	0	ENST00000222270.7:c.6974G>A	p.Arg2325Lys	p.R2325K	ENST00000222270	NM_014727.1	2325	aGg/aAg	29/37	1	2	FACETS	0.532	0.478	0.589	0.532	0.478	0.589	SUBCLONAL	1	TRUE	1	0.530355728901221	2		822	801	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439680	220439680	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	223	826	0	ENST00000243786.2:c.533T>C	p.Val178Ala	p.V178A	ENST00000243786	NM_002191.3	178	gTg/gCg	2/2	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.530355728901221	2		826	597	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	69	255	10	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	0.834	0.746	0.923	1	0.981	1	CLONAL	2	TRUE	1	0.530355728901221	2		265	156	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	84	276	1	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.530355728901221	2		277	241	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920469	134920469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	167	555	2	ENST00000398015.3:c.2284G>A	p.Asp762Asn	p.D762N	ENST00000398015	NM_004441.4	762	Gac/Aac	12/16	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.530355728901221	2		557	442	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	204	646	0	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	0.84	0.788	0.892	1	0.993	1	CLONAL	2	TRUE	1	0.530355728901221	2		646	458	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	65	295	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.530355728901221	2		295	178	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542762	187542762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	56	325	0	ENST00000441802.2:c.4978G>A	p.Ala1660Thr	p.A1660T	ENST00000441802	NM_005245.3	1660	Gct/Act	10/27	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.530355728901221	2		325	173	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048772	180048772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758587669	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	159	770	2	ENST00000261937.6:c.1790C>T	p.Thr597Met	p.T597M	ENST00000261937	NM_182925.4	597	aCg/aTg	13/30	1	2	FACETS	0.95	0.874	1	0.95	0.874	1	CLONAL	1	TRUE	1	0.530355728901221	2		772	631	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402523	20402523	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770338281	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	303	464	0	ENST00000346618.3:c.64del	p.Ala22ArgfsTer18	p.A22Rfs*18	ENST00000346618	NM_001949.4	20	gaG/ga	1/7	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.530355728901221	2		464	799	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189085	32189085	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762851866	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	128	439	0	ENST00000375023.3:c.469C>T	p.Arg157Trp	p.R157W	ENST00000375023	NM_004557.3	157	Cgg/Tgg	4/30	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.530355728901221	2		439	330	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729357	41729357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	177	461	0	ENST00000242208.4:c.1172G>A	p.Cys391Tyr	p.C391Y	ENST00000242208	NM_002192.2	391	tGt/tAt	3/3	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.530355728901221	2		461	473	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524966	8524966	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764474694	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	66	275	0	ENST00000356435.5:c.638C>T	p.Ala213Val	p.A213V	ENST00000356435		213	gCg/gTg	7/35	1	2	FACETS	0.929	0.815	1	0.929	0.815	1	CLONAL	1	TRUE	1	0.530355728901221	2		275	268	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8525033	8525033	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	46	211	0	ENST00000356435.5:c.571G>A	p.Ala191Thr	p.A191T	ENST00000356435		191	Gcc/Acc	7/35	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.530355728901221	2		211	147	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940012	76940012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs122445105	NA	P-0047668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	97	237	1	ENST00000373344.5:c.736C>T	p.Arg246Cys	p.R246C	ENST00000373344	NM_000489.3	246	Cgc/Tgc	9/35	1	1	FACETS	1	0.976	1	1	0.991	1	CLONAL	2	TRUE	0	0.530355728901221	1		238	124	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0047669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	38	309	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.948	0.784	1	0.948	0.784	1	CLONAL	1	TRUE	1	0.2	2		309	401	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236081	108236081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1319582645	NA	P-0047669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	30	344	0	ENST00000278616.4:c.9017C>T	p.Ala3006Val	p.A3006V	ENST00000278616	NM_000051.3	3006	gCt/gTt	63/63	1	2	FACETS	0.781	0.63	0.953	0.781	0.63	0.953	CLONAL	1	TRUE	1	0.2	2		344	384	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066889	30066889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1303923680	NA	P-0047669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	63	355	0	ENST00000331968.5:c.2242G>A	p.Ala748Thr	p.A748T	ENST00000331968	NM_002742.2	748	Gct/Act	16/18	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.2	2		355	508	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900262	101900263	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0047669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	34	243	0	ENST00000374994.4:c.699_700dup	p.Phe234TyrfsTer20	p.F234Yfs*20	ENST00000374994	NM_004612.2	232	-/AT	4/9	0.161560190153556	1	FACETS	0.981	0.804	1	0.981	0.804	1	CLONAL	1	TRUE	0	0.2	1		243	312	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	135	636	0	ENST00000269571.5:c.829G>C	p.Asp277His	p.D277H	ENST00000269571		277	Gac/Cac	7/27	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.21	2		636	929	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0047670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	111	530	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.21	2		530	825	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339981	70339981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	38	239	0	ENST00000374080.3:c.514G>A	p.Glu172Lys	p.E172K	ENST00000374080		172	Gag/Aag	4/45	1	1	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	0	0.21	1		239	282	SUCCESS
FH	2271	MSKCC	GRCh37	1	241683007	241683007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	45	490	0	ENST00000366560.3:c.16C>T	p.Arg6Trp	p.R6W	ENST00000366560	NM_000143.3	6	Cgg/Tgg	1/10	1	2	FACETS	0.767	0.644	0.903	0.767	0.644	0.903	CLONAL	1	TRUE	1	0.21	2		490	559	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0047670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	28	267	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	0.745	0.596	0.915	0.745	0.596	0.915	CLONAL	1	TRUE	1	0.21	2		267	358	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022992	33022992	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	27	397	0	ENST00000300177.4:c.101C>T	p.Pro34Leu	p.P34L	ENST00000300177	NM_001191322.1	34	cCc/cTc	2/2	1	2	FACETS	0.541	0.43	0.669	0.541	0.43	0.669	SUBCLONAL	1	TRUE	1	0.21	2		397	475	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045024	47045024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	91	428	0	ENST00000377604.3:c.2350C>T	p.His784Tyr	p.H784Y	ENST00000377604	NM_001204468.1	784	Cac/Tac	20/24	1	1	FACETS	0.854	0.762	0.952	1	0.984	1	CLONAL	2	TRUE	0	0.21	1		428	454	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903779	41903779	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	74	801	0	ENST00000372991.4:c.778C>T	p.Gln260Ter	p.Q260*	ENST00000372991	NM_001760.3	260	Cag/Tag	5/5	1	2	FACETS	0.843	0.737	0.958	0.843	0.737	0.958	CLONAL	1	TRUE	1	0.21	2		801	836	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106649	27106649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	72	614	0	ENST00000324856.7:c.6260G>A	p.Gly2087Glu	p.G2087E	ENST00000324856	NM_006015.4	2087	gGa/gAa	20/20	1	2	FACETS	0.978	0.854	1	0.978	0.854	1	CLONAL	1	TRUE	1	0.21	2		614	701	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465527	8465527	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	30	406	0	ENST00000356435.5:c.3653A>G	p.Gln1218Arg	p.Q1218R	ENST00000356435		1218	cAa/cGa	21/35	1	2	FACETS	0.674	0.543	0.823	0.674	0.543	0.823	SUBCLONAL	1	TRUE	1	0.21	2		406	424	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660441	227660441	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373248004	NA	P-0047670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	42	592	0	ENST00000305123.5:c.3014C>T	p.Ser1005Leu	p.S1005L	ENST00000305123	NM_005544.2	1005	tCg/tTg	1/2	1	2	FACETS	0.697	0.581	0.826	0.697	0.581	0.826	SUBCLONAL	1	TRUE	1	0.21	2		592	574	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382128	152382128	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	50	236	0	ENST00000206249.3:c.1238A>G	p.Asn413Ser	p.N413S	ENST00000206249	NM_000125.3	413	aAc/aGc	6/8	1	2	FACETS	0.863	0.737	0.998	1	0.971	1	CLONAL	2	TRUE	1	0.21	2		236	276	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256591	16256591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	31	393	0	ENST00000375759.3:c.3856G>A	p.Gly1286Arg	p.G1286R	ENST00000375759	NM_015001.2	1286	Ggg/Agg	11/15	1	2	FACETS	0.705	0.57	0.857	0.705	0.57	0.857	SUBCLONAL	1	TRUE	1	0.21	2		393	419	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112578	115112578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	118	782	0	ENST00000257566.3:c.1162G>A	p.Glu388Lys	p.E388K	ENST00000257566	NM_016569.3	388	Gag/Aag	7/8	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.21	2		782	1000	SUCCESS
APC	324	MSKCC	GRCh37	5	112173992	112173992	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	16	257	0	ENST00000257430.4:c.2701C>G	p.Gln901Glu	p.Q901E	ENST00000257430	NM_000038.5	901	Cag/Gag	16/16	1	2	FACETS	0.546	0.403	0.717	0.546	0.403	0.717	SUBCLONAL	1	TRUE	1	0.21	2		257	279	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163689	72163689	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0047670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	15	288	0	ENST00000357731.5:c.667+2T>C		p.X223_splice	ENST00000357731	NM_173808.2	223			1	2	FACETS	0.56	0.41	0.741	0.56	0.41	0.741	SUBCLONAL	1	TRUE	1	0.21	2		288	255	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282430	115282430	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	21	351	0	ENST00000438362.2:c.220G>T	p.Gly74Trp	p.G74W	ENST00000438362	NM_001242891.1	74	Ggg/Tgg	3/20	1	2	FACETS	0.581	0.447	0.738	0.581	0.447	0.738	SUBCLONAL	1	TRUE	1	0.21	2		351	344	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863434	57863434	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	76	568	0	ENST00000228682.2:c.1529G>T	p.Arg510Leu	p.R510L	ENST00000228682	NM_005269.2	510	cGg/cTg	11/12	1	2	FACETS	0.917	0.804	1	0.917	0.804	1	CLONAL	1	TRUE	1	0.21	2		568	789	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060928	38060928	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1319052552	NA	P-0047670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	38	607	0	ENST00000250448.2:c.1061C>T	p.Ser354Phe	p.S354F	ENST00000250448	NM_004496.3	354	tCc/tTc	2/2	1	2	FACETS	0.73	0.603	0.872	0.73	0.603	0.872	SUBCLONAL	1	TRUE	1	0.21	2		607	496	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15938127	15938127	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	17	261	0	ENST00000268712.3:c.7087C>T	p.His2363Tyr	p.H2363Y	ENST00000268712	NM_006311.3	2363	Cat/Tat	45/46	1	2	FACETS	0.482	0.359	0.628	0.482	0.359	0.628	SUBCLONAL	1	TRUE	1	0.21	2		261	336	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281272	15281272	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	95	959	0	ENST00000263388.2:c.4984G>A	p.Val1662Ile	p.V1662I	ENST00000263388	NM_000435.2	1662	Gtc/Atc	27/33	1	2	FACETS	0.877	0.779	0.982	0.877	0.779	0.982	CLONAL	1	TRUE	1	0.21	2		959	1032	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976465	18976465	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	129	1038	0	ENST00000262803.5:c.3115C>A	p.Gln1039Lys	p.Q1039K	ENST00000262803	NM_002911.3	1039	Caa/Aaa	22/24	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.21	2		1038	1106	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855787	45855787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	66	708	0	ENST00000391945.4:c.2023G>A	p.Gly675Ser	p.G675S	ENST00000391945	NM_000400.3	675	Ggc/Agc	21/23	1	2	FACETS	0.758	0.657	0.869	0.758	0.657	0.869	SUBCLONAL	1	TRUE	1	0.21	2		708	829	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44527589	44527589	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868676340	NA	P-0047670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	46	435	0	ENST00000291552.4:c.16G>A	p.Ala6Thr	p.A6T	ENST00000291552	NM_006758.2	6	Gcc/Acc	1/8	1	2	FACETS	0.802	0.675	0.943	0.802	0.675	0.943	CLONAL	1	TRUE	1	0.21	2		435	546	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183589	10183589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	77	859	0	ENST00000256474.2:c.58G>A	p.Val20Ile	p.V20I	ENST00000256474	NM_000551.3	20	Gtc/Atc	1/3	1	2	FACETS	0.874	0.766	0.991	0.874	0.766	0.991	CLONAL	1	TRUE	1	0.21	2		859	839	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69998222	69998222	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	54	383	0	ENST00000394351.3:c.462G>C	p.Leu154Phe	p.L154F	ENST00000394351	NM_000248.3	154	ttG/ttC	5/9	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.21	2		383	505	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443269	187443285	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CCTGCCCACTCTGCTCA	CCTGCCCACTCTGCTCA	-	novel	NA	P-0047670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	19	199	0	ENST00000232014.4:c.1839+2_1839+18del		p.X613_splice	ENST00000232014	NM_001130845.1	613			1	2	FACETS	0.696	0.529	0.892	0.696	0.529	0.892	SUBCLONAL	1	TRUE	1	0.21	2		199	260	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189585727	189585727	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	34	344	0	ENST00000264731.3:c.988A>G	p.Arg330Gly	p.R330G	ENST00000264731	NM_003722.4	330	Aga/Gga	7/14	1	2	FACETS	0.743	0.607	0.896	0.743	0.607	0.896	SUBCLONAL	1	TRUE	1	0.21	2		344	436	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532888	187532888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	27	289	0	ENST00000441802.2:c.9505G>A	p.Asp3169Asn	p.D3169N	ENST00000441802	NM_005245.3	3169	Gat/Aat	14/27	1	2	FACETS	0.838	0.668	1	0.838	0.668	1	CLONAL	1	TRUE	1	0.21	2		289	307	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514451	149514451	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	61	519	0	ENST00000261799.4:c.493G>T	p.Gly165Trp	p.G165W	ENST00000261799	NM_002609.3	165	Ggg/Tgg	4/23	1	2	FACETS	0.825	0.711	0.95	0.825	0.711	0.95	CLONAL	1	TRUE	1	0.21	2		519	704	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324587	31324587	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs151341140	NA	P-0047670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	117	1170	1	ENST00000412585.2:c.221C>G	p.Pro74Arg	p.P74R	ENST00000412585	NM_005514.6	74	cCg/cGg	2/8	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.21	2		1171	1050	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035222	6035222	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	39	320	0	ENST00000265849.7:c.846G>C	p.Arg282Ser	p.R282S	ENST00000265849	NM_000535.5	282	agG/agC	8/15	1	2	FACETS	0.769	0.637	0.916	0.769	0.637	0.916	CLONAL	1	TRUE	1	0.21	2		320	483	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380944	116380944	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0047670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	72	582	0	ENST00000397752.3:c.1566T>A	p.His522Gln	p.H522Q	ENST00000397752	NM_000245.2	522	caT/caA	5/21	1	2	FACETS	0.868	0.757	0.988	0.868	0.757	0.988	CLONAL	1	TRUE	1	0.21	2		582	790	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0047671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	201	553	1	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	1	2	FACETS	0.803	0.745	0.863	0.803	0.745	0.863	CLONAL	1	TRUE	1	0.569726459989281	2		554	879	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0047671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	74	424	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	1	2	FACETS	0.626	0.55	0.707	0.626	0.55	0.707	SUBCLONAL	1	TRUE	1	0.569726459989281	2		424	415	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591902	48591902	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519740	NA	P-0047671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	113	327	0	ENST00000342988.3:c.1065C>A	p.Asp355Glu	p.D355E	ENST00000342988	NM_005359.5	355	gaC/gaA	9/12	0.569726459989281	1	FACETS	0.715	0.648	0.783	0.715	0.648	0.783	SUBCLONAL	1	TRUE	0	0.569726459989281	1		327	397	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874092	151874092	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0047671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	144	405	0	ENST00000262189.6:c.8446T>A	p.Ser2816Thr	p.S2816T	ENST00000262189	NM_170606.2	2816	Tcc/Acc	38/59	1	2	FACETS	0.881	0.807	0.957	0.881	0.807	0.957	CLONAL	1	TRUE	1	0.569726459989281	2		405	574	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94908802	94908802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	106	293	0	ENST00000536441.1:c.1252G>A	p.Asp418Asn	p.D418N	ENST00000536441	NM_144665.3	418	Gat/Aat	9/10	0.270217611748742	3	FACETS	0.936	0.842	1	0.468	0.421	0.517	INDETERMINATE	1	TRUE	1	0.569726459989281	3		293	511	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986511	36986511	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	138	679	1	ENST00000354822.5:c.1178C>T	p.Ser393Phe	p.S393F	ENST00000354822	NM_001079668.2	393	tCc/tTc	3/3	0.255075628513321	2	FACETS	0.468	0.425	0.513	0.234	0.212	0.257	INDETERMINATE	1	TRUE	0	0.569726459989281	2		680	1036	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249076	55249076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	207	542	1	ENST00000275493.2:c.2374C>T	p.Leu792Phe	p.L792F	ENST00000275493	NM_005228.3	792	Ctc/Ttc	20/28	1	2	FACETS	0.83	0.772	0.891	0.83	0.772	0.891	CLONAL	1	TRUE	1	0.569726459989281	2		543	875	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115670	108115670	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	61	293	0	ENST00000278616.4:c.818A>G	p.Asp273Gly	p.D273G	ENST00000278616	NM_000051.3	273	gAt/gGt	7/63	0.56137032431851	4	FACETS	0.822	0.712	0.94	0.411	0.356	0.47	CLONAL	1	TRUE	2	0.641428168341211	4		293	380	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0047742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	650	519	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.593983667577656	4	FACETS	0.958	0.935	0.98	0.958	0.935	0.98	CLONAL	4	TRUE	0	0.641428168341211	4		519	868	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577095	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519984	NA	P-0047742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	459	721	1	ENST00000269305.4:c.843C>A	p.Asp281Glu	p.D281E	ENST00000269305	NM_001126112.2	281	gaC/gaA	8/11	0.577794482960685	2	FACETS	0.893	0.861	0.926	0.893	0.861	0.926	CLONAL	2	TRUE	0	0.641428168341211	2		722	801	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521729	89521729	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369167718	NA	P-0047742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	103	353	0	ENST00000336596.2:c.2806G>A	p.Glu936Lys	p.E936K	ENST00000336596	NM_005233.5	936	Gag/Aag	16/17	0.572897944927914	3	FACETS	0.878	0.79	0.971	0.439	0.395	0.486	CLONAL	1	TRUE	1	0.641428168341211	3		353	483	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161739	56161751	+	frameshift_variant	Frame_Shift_Del	DEL	TTCACGCATGTCA	TTCACGCATGTCA	-	novel	NA	P-0047742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	162	346	0	ENST00000399503.3:c.1236_1248del	p.Ser413IlefsTer19	p.S413Ifs*19	ENST00000399503	NM_005921.1	412	gtTTCACGCATGTCA/gt	6/20	0.56137032431851	4	FACETS	1	0.987	1	0.687	0.634	0.743	CLONAL	1	TRUE	2	0.641428168341211	4		346	603	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189433	56189439	+	frameshift_variant	Frame_Shift_Del	DEL	TTAGAAC	TTAGAAC	-	novel	NA	P-0047742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	242	425	2	ENST00000399503.3:c.4467_4473del	p.Leu1489PhefsTer13	p.L1489Ffs*13	ENST00000399503	NM_005921.1	1489	TTAGAACtt/tt	20/20	0.56137032431851	4	FACETS	0.845	0.793	0.898	0.845	0.793	0.898	CLONAL	2	TRUE	2	0.641428168341211	4		427	733	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	115	516	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.996	0.904	1	0.996	0.904	1	CLONAL	1	TRUE	1	0.567599917163729	2		516	407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0047743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	229	532	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.567599917163729	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.567599917163729	1		532	563	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652147	36652148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0047743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	273	883	0	ENST00000244741.5:c.270dup	p.Gly91ArgfsTer38	p.G91Rfs*38	ENST00000244741	NM_000389.4	90	gga/ggAa	2/3	0.383524680256879	1	FACETS	0.724	0.68	0.768	0.724	0.68	0.768	SUBCLONAL	1	TRUE	0	0.567599917163729	1		883	952	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942685	48942685	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913301	NA	P-0047743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	35	233	0	ENST00000267163.4:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000267163	NM_000321.2	358	Cga/Tga	11/27	0.567599917163729	1	FACETS	0.94	0.795	1	0.94	0.795	1	CLONAL	1	TRUE	0	0.567599917163729	1		233	94	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0047743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	354	1065	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.567599917163729	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.567599917163729	1		1065	793	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385257	41385257	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	144	606	0	ENST00000373198.4:c.704C>A	p.Thr235Lys	p.T235K	ENST00000373198	NM_133170.3	235	aCg/aAg	6/32	1	2	FACETS	0.72	0.658	0.785	0.72	0.658	0.785	SUBCLONAL	1	TRUE	1	0.567599917163729	2		606	705	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119595282	119595282	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0047743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	19	202	0	ENST00000316626.5:c.887T>G	p.Ile296Ser	p.I296S	ENST00000316626		296	aTt/aGt	8/12	1	2	FACETS	0.847	0.659	1	0.847	0.659	1	CLONAL	1	TRUE	1	0.567599917163729	2		202	79	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651961	36651962	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCAGC	novel	NA	P-0047743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	206	764	0	ENST00000244741.5:c.84_88dup	p.Leu30ArgfsTer3	p.L30Rfs*3	ENST00000244741	NM_000389.4	28	gag/gaGCAGCg	2/3	0.383524680256879	1	FACETS	0.596	0.554	0.64	0.596	0.554	0.64	SUBCLONAL	1	TRUE	0	0.567599917163729	1		764	872	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0047746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	381	1013	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.596155728290359	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.596155728290359	1		1013	740	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871182	12871182	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1328655695	NA	P-0047746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	129	382	0	ENST00000228872.4:c.410del	p.Pro137ArgfsTer8	p.P137Rfs*8	ENST00000228872	NM_004064.3	137	Ccg/cg	1/3	0.258643119221492	3	FACETS	1	0.98	1	0.626	0.571	0.682	INDETERMINATE	1	TRUE	1	0.596155728290359	3		382	449	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651621	206651621	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149987336	NA	P-0047746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	254	1127	1	ENST00000367120.3:c.931G>A	p.Val311Ile	p.V311I	ENST00000367120	NM_014002.3	311	Gtc/Atc	9/22	1	2	FACETS	0.777	0.727	0.829	0.777	0.727	0.829	SUBCLONAL	1	TRUE	1	0.596155728290359	2		1128	1096	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153252022	153252022	+	splice_acceptor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0047746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	121	424	0	ENST00000281708.4:c.986-2del		p.X329_splice	ENST00000281708	NM_033632.3	329			0.355426277287892	1	FACETS	0.824	0.753	0.896	0.824	0.753	0.896	INDETERMINATE	1	TRUE	0	0.596155728290359	1		424	346	SUCCESS
APC	324	MSKCC	GRCh37	5	112174882	112174882	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	58	294	0	ENST00000257430.4:c.3591del	p.Ser1198GlnfsTer67	p.S1198Qfs*67	ENST00000257430	NM_000038.5	1197	ttC/tt	16/16	1	2	FACETS	0.861	0.749	0.979	0.861	0.749	0.979	CLONAL	1	TRUE	1	0.596155728290359	2		294	226	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0047748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	61	280	0	ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	4/10	1	2	FACETS	0.943	0.822	1	0.943	0.822	1	CLONAL	1	TRUE	1	0.505501521151567	2		280	256	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0047748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	233	731	7	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.505501521151567	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.505501521151567	1		738	688	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274803	123274803	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913477	NA	P-0047748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	138	552	0	ENST00000358487.5:c.1115C>G	p.Ser372Cys	p.S372C	ENST00000358487	NM_000141.4	372	tCc/tGc	9/18	1	2	FACETS	0.984	0.9	1	0.984	0.9	1	CLONAL	1	TRUE	1	0.505501521151567	2		552	555	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033844	49033844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853294	NA	P-0047751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	148	388	0	ENST00000267163.4:c.1981C>T	p.Arg661Trp	p.R661W	ENST00000267163	NM_000321.2	661	Cgg/Tgg	20/27	0.452286710142956	2	FACETS	0.927	0.859	0.996	0.927	0.859	0.996	CLONAL	2	TRUE	0	0.452286710142956	2		388	353	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0047751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	40	383	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.452286710142956	1	FACETS	0.681	0.572	0.8	0.681	0.572	0.8	SUBCLONAL	1	TRUE	0	0.452286710142956	1		383	201	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426123	138426123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217537873	NA	P-0047751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	20	364	0	ENST00000289153.2:c.1408G>A	p.Glu470Lys	p.E470K	ENST00000289153	NM_006219.2	470	Gaa/Aaa	9/22	0.156740083560394	5	FACETS	0.48	0.367	0.613	0.16	0.122	0.205	INDETERMINATE	1	TRUE	2	0.452286710142956	5		364	309	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26978124	26978124	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	302	680	0	ENST00000381527.3:c.1301C>G	p.Pro434Arg	p.P434R	ENST00000381527	NM_001260.1	434	cCt/cGt	13/13	0.182456582643233	6	FACETS	1	0.945	1	1	0.945	1	INDETERMINATE	3	TRUE	3	0.452286710142956	6		680	848	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31372634	31372634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201395541	NA	P-0047751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	325	591	0	ENST00000328111.2:c.275G>A	p.Arg92Gln	p.R92Q	ENST00000328111	NM_006892.3	92	cGg/cAg	4/23	0.207764155776914	4	FACETS	0.877	0.833	0.922	0.877	0.833	0.922	INDETERMINATE	3	TRUE	1	0.452286710142956	4		591	793	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151927366	151927366	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0047751-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	26	47	0	ENST00000262189.6:c.2810A>C	p.Glu937Ala	p.E937A	ENST00000262189	NM_170606.2	937	gAa/gCa	17/59	0.452286710142956	4	FACETS	0.96	0.797	1	0.96	0.797	1	CLONAL	3	TRUE	1	0.452286710142956	4		47	58	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	62	516	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.2	2		516	552	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0047752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	37	396	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.564	0.464	0.677	0.564	0.464	0.677	SUBCLONAL	1	TRUE	1	0.2	2		396	656	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361088	70361088	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	28	444	0	ENST00000374080.3:c.6276G>T	p.Gln2092His	p.Q2092H	ENST00000374080		2092	caG/caT	43/45	1	2	FACETS	0.521	0.416	0.643	0.521	0.416	0.643	SUBCLONAL	1	TRUE	1	0.2	2		444	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782620	NA	P-0047753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	523	1018	0	ENST00000269305.4:c.427G>A	p.Val143Met	p.V143M	ENST00000269305	NM_001126112.2	143	Gtg/Atg	5/11	0.740050100517155	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.740050100517155	1		1018	830	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0047753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	82	146	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.398148230521795	1	FACETS	0.739	0.667	0.812	0.739	0.667	0.812	INDETERMINATE	1	TRUE	0	0.740050100517155	1		146	189	SUCCESS
APC	324	MSKCC	GRCh37	5	112137024	112137024	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	54	329	1	ENST00000257430.4:c.778C>T	p.Gln260Ter	p.Q260*	ENST00000257430	NM_000038.5	260	Cag/Tag	8/16	0.398148230521795	1	FACETS	0.253	0.217	0.293	0.253	0.217	0.293	INDETERMINATE	1	TRUE	0	0.740050100517155	1		330	363	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577563	64577587	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	GGGCGGCCTTCAGCCCCATGGCGGC	GGGCGGCCTTCAGCCCCATGGCGGC	-	novel	NA	P-0047754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	82	358	0	ENST00000312049.6:c.-6_19del		p.*2*	ENST00000312049	NM_130799.2	?-7/615		2/10	0.858036409155658	1	FACETS	0.758	0.692	0.822	0.758	0.692	0.822	SUBCLONAL	1	TRUE	0	0.858036409155658	1		358	144	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359378	118359378	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	237	403	0	ENST00000534358.1:c.4382A>G	p.Glu1461Gly	p.E1461G	ENST00000534358	NM_005933.3	1461	gAg/gGg	11/36	0.858036409155658	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.858036409155658	1		403	301	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287314	33287314	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0047754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	233	535	0	ENST00000374542.5:c.1783G>T	p.Glu595Ter	p.E595*	ENST00000374542	NM_001141970.1	595	Gag/Tag	6/8	0.857773485369369	1	FACETS	0.966	0.926	1	0.966	0.926	1	CLONAL	1	TRUE	0	0.858036409155658	1		535	321	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494152	140494152	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	301	715	0	ENST00000288602.6:c.1096G>C	p.Ala366Pro	p.A366P	ENST00000288602	NM_004333.4	366	Gct/Cct	8/18	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.858036409155658	2		715	685	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0047755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	142	272	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.639980193113026	4	FACETS	0.893	0.823	0.964	0.893	0.823	0.964	CLONAL	2	TRUE	2	0.709876754978041	4		272	383	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670840	134670840	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	97	407	0	ENST00000398015.3:c.751G>T	p.Gly251Trp	p.G251W	ENST00000398015	NM_004441.4	251	Ggg/Tgg	3/16	0.639980193113026	4	FACETS	0.906	0.81	1	0.453	0.405	0.503	CLONAL	1	TRUE	2	0.709876754978041	4		407	516	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045882	26045882	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0047755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	101	482	0	ENST00000540144.1:c.244del	p.Asp82ThrfsTer9	p.D82Tfs*9	ENST00000540144	NM_003531.2	82	Gac/ac	1/1	0.663260455377779	4	FACETS	0.639	0.571	0.712			1	SUBCLONAL	1	TRUE	NA	0.709876754978041	4		482	761	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0047757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	431	470	0				ENST00000310581	NM_198253.2	-/1132			0.157403864789814	6	FACETS	0.93	0.896	0.964			1	INDETERMINATE	4	TRUE	NA	0.871978408810075	6		470	729	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0047757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	266	164	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.855304112497385	3	FACETS	0.961	0.915	1	0.961	0.915	1	CLONAL	2	TRUE	1	0.871978408810075	3		164	456	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220715	1220715	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	297	577	0	ENST00000326873.7:c.733C>A	p.Leu245Ile	p.L245I	ENST00000326873	NM_000455.4	245	Ctc/Atc	5/10	1	2	FACETS	0.928	0.879	0.978	0.928	0.879	0.978	CLONAL	1	TRUE	1	0.871978408810075	2		577	734	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943632	9943632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	290	393	0	ENST00000330684.3:c.1309C>T	p.Arg437Trp	p.R437W	ENST00000330684	NM_001134407.1	437	Cgg/Tgg	5/13	1	2	FACETS	0.949	0.898	1	0.949	0.898	1	CLONAL	1	TRUE	1	0.871978408810075	2		393	701	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256530	+	missense_variant	Missense_Mutation	DNP	TG	TG	CT	rs1057519834	NA	P-0047757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	205	321	1	ENST00000369535.4:c.181_182delinsAG	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	CAa/AGa	3/7	0.871978408810075	1	FACETS	0.914	0.872	0.955	0.914	0.872	0.955	CLONAL	1	TRUE	0	0.871978408810075	1		322	290	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638770	176638770	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0047757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	490	323	0	ENST00000439151.2:c.3370G>T	p.Glu1124Ter	p.E1124*	ENST00000439151	NM_022455.4	1124	Gaa/Taa	5/23	0.871978408810075	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.871978408810075	2		323	547	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125789	47125789	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	166	215	0	ENST00000409792.3:c.5481G>A	p.Trp1827Ter	p.W1827*	ENST00000409792	NM_014159.6	1827	tgG/tgA	12/21	1	2	FACETS	0.979	0.911	1	0.979	0.911	1	CLONAL	1	TRUE	1	0.871978408810075	2		215	389	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053355	37053355	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0047757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	122	230	0	ENST00000231790.2:c.588+2T>C		p.X196_splice	ENST00000231790	NM_000249.3	196			1	2	FACETS	0.823	0.753	0.895	0.823	0.753	0.895	CLONAL	1	TRUE	1	0.871978408810075	2		230	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0047758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	412	406	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.74955565789047	2	FACETS	0.998	0.967	1	0.998	0.967	1	CLONAL	2	TRUE	0	0.74955565789047	2		406	551	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915788	112915788	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	137	232	0	ENST00000351677.2:c.1061T>C	p.Val354Ala	p.V354A	ENST00000351677	NM_002834.3	354	gTc/gCc	9/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.74955565789047	2		232	338	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729909	30729909	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	111	242	0	ENST00000295754.5:c.1430A>G	p.Lys477Arg	p.K477R	ENST00000295754	NM_003242.5	477	aAg/aGg	6/7	1	2	FACETS	0.987	0.9	1	0.987	0.9	1	CLONAL	1	TRUE	1	0.74955565789047	2		242	300	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189037	32189037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1482319808	NA	P-0047758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	176	582	0	ENST00000375023.3:c.517G>A	p.Ala173Thr	p.A173T	ENST00000375023	NM_004557.3	173	Gcc/Acc	4/30	0.704705960675645	3	FACETS	0.902	0.833	0.973	0.451	0.416	0.487	CLONAL	1	TRUE	1	0.74955565789047	3		582	716	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0047759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	362	470	0				ENST00000310581	NM_198253.2	-/1132			0.380085703162103	3	FACETS	0.929	0.886	0.973	0.929	0.886	0.973	CLONAL	3	TRUE	0	0.380085703162103	3		470	813	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508803	29508803	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1567826188	NA	P-0047759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	95	213	1	ENST00000356175.3:c.730G>A	p.Glu244Lys	p.E244K	ENST00000356175	NM_000267.3	244	Gaa/Aaa	7/57	0.380085703162103	2	FACETS	0.916	0.827	1	0.916	0.827	1	CLONAL	2	TRUE	0	0.380085703162103	2		214	273	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758766	41758766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	333	619	0	ENST00000301178.4:c.1820G>A	p.Gly607Asp	p.G607D	ENST00000301178	NM_021913.4	607	gGt/gAt	16/20	0.380085703162103	2	FACETS	0.943	0.894	0.993	0.943	0.894	0.993	CLONAL	2	TRUE	0	0.380085703162103	2		619	929	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965706	93965706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	52	199	0	ENST00000369303.4:c.2222G>A	p.Gly741Glu	p.G741E	ENST00000369303	NM_004440.3	741	gGa/gAa	13/17	0.335340828330305	3	FACETS	0.925	0.791	1	0.463	0.395	0.536	CLONAL	1	TRUE	1	0.380085703162103	3		199	352	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120845	94120845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465346253	NA	P-0047759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	175	284	0	ENST00000369303.4:c.206G>A	p.Arg69Gln	p.R69Q	ENST00000369303	NM_004440.3	69	cGa/cAa	3/17	0.335340828330305	3	FACETS	0.927	0.858	0.998	0.927	0.858	0.998	CLONAL	2	TRUE	1	0.380085703162103	3		284	591	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436016	56436016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	273	429	0	ENST00000407977.2:c.1121C>T	p.Pro374Leu	p.P374L	ENST00000407977		374	cCc/cTc	9/10	0.380085703162103	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.380085703162103	2		429	608	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111519	8111519	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1238949082	NA	P-0047759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	120	406	0	ENST00000346208.3:c.1005C>A	p.Asp335Glu	p.D335E	ENST00000346208		335	gaC/gaA	5/6	0.335340828330305	3	FACETS	1	0.925	1	0.513	0.464	0.566	CLONAL	1	TRUE	1	0.380085703162103	3		406	732	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262905	46262905	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867083206	NA	P-0047759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	99	252	0	ENST00000371998.3:c.1078C>T	p.Arg360Ter	p.R360*	ENST00000371998		360	Cga/Tga	10/23	0.380085703162103	3	FACETS	1	0.935	1	0.531	0.475	0.59	CLONAL	1	TRUE	1	0.380085703162103	3		252	584	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36653561	36653561	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs981464191	NA	P-0047759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	375	432	0	ENST00000244741.5:c.479C>T	p.Ser160Phe	p.S160F	ENST00000244741	NM_000389.4	160	tCc/tTc	3/3	0.380085703162103	5	FACETS	1	0.96	1	1	0.96	1	CLONAL	3	TRUE	2	0.380085703162103	5		432	1022	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31429584	31429584	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1354342796	NA	P-0047759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	101	222	0	ENST00000344624.3:c.3214C>T	p.Pro1072Ser	p.P1072S	ENST00000344624		1072	Ccg/Tcg	24/33	0.292362343587917	2	FACETS	0.828	0.749	0.91	0.828	0.749	0.91	CLONAL	2	TRUE	0	0.380085703162103	2		222	321	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597513	28597513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	198	305	0	ENST00000241453.7:c.2392G>A	p.Gly798Arg	p.G798R	ENST00000241453	NM_004119.2	798	Gga/Aga	19/24	0.380085703162103	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.380085703162103	2		305	497	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390793	139390793	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	415	833	0	ENST00000277541.6:c.7398del	p.Ser2467ArgfsTer10	p.S2467Rfs*10	ENST00000277541	NM_017617.3	2466	acG/ac	34/34	0.380085703162103	3	FACETS	0.958	0.911	1	0.958	0.911	1	CLONAL	2	TRUE	1	0.380085703162103	3		833	1357	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050933	49050933	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0047759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	144	216	0	ENST00000267163.4:c.2617A>G	p.Lys873Glu	p.K873E	ENST00000267163	NM_000321.2	873	Aaa/Gaa	25/27	0.380085703162103	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.380085703162103	2		216	351	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073797	8073797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	127	238	0	ENST00000377482.5:c.862C>T	p.Pro288Ser	p.P288S	ENST00000377482	NM_018948.3	288	Ccc/Tcc	4/4	0.380085703162103	2	FACETS	0.875	0.801	0.951	0.875	0.801	0.951	CLONAL	2	TRUE	0	0.380085703162103	2		238	382	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206617	108206617	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	129	191	0	ENST00000278616.4:c.8197C>T	p.Gln2733Ter	p.Q2733*	ENST00000278616	NM_000051.3	2733	Cag/Tag	56/63	0.380085703162103	2	FACETS	0.91	0.834	0.988	0.91	0.834	0.988	CLONAL	2	TRUE	0	0.380085703162103	2		191	373	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435133	110435133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778534422	NA	P-0047759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	355	747	0	ENST00000375856.3:c.3268C>T	p.Pro1090Ser	p.P1090S	ENST00000375856	NM_003749.2	1090	Ccc/Tcc	1/2	0.350516953275734	4	FACETS	0.998	0.945	1	0.998	0.945	1	CLONAL	2	TRUE	2	0.380085703162103	4		747	1291	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022991	33022991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	87	345	0	ENST00000300177.4:c.100C>T	p.Pro34Ser	p.P34S	ENST00000300177	NM_001191322.1	34	Ccc/Tcc	2/2	NA	2	FACETS	0.775	0.687	0.868			1	INDETERMINATE	1	TRUE	NA	0.380085703162103	2		345	591	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828095	72828095	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	286	528	0	ENST00000268489.5:c.8486A>G	p.Lys2829Arg	p.K2829R	ENST00000268489	NM_006885.3	2829	aAg/aGg	9/10	0.380085703162103	2	FACETS	0.928	0.876	0.981	0.928	0.876	0.981	CLONAL	2	TRUE	0	0.380085703162103	2		528	811	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965526	25965526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	261	419	0	ENST00000435504.4:c.3680C>T	p.Ala1227Val	p.A1227V	ENST00000435504		1227	gCt/gTt	13/13	0.363523544260353	4	FACETS	1	0.961	1			1	CLONAL	2	TRUE	NA	0.380085703162103	4		419	918	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872917	136872918	+	missense_variant	Missense_Mutation	DNP	AA	AA	GT	rs867008465	NA	P-0047759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	144	255	0	ENST00000241393.3:c.580_581delinsAC	p.Leu194Thr	p.L194T	ENST00000241393	NM_003467.2	194	TTg/ACg	2/2	0.380085703162103	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.380085703162103	2		255	351	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520241	9520241	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	173	381	0	ENST00000353224.5:c.2028C>G	p.Phe676Leu	p.F676L	ENST00000353224	NM_177990.2	676	ttC/ttG	10/10	0.380085703162103	3	FACETS	0.818	0.756	0.883	0.818	0.756	0.883	CLONAL	2	TRUE	1	0.380085703162103	3		381	662	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420070	41420070	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144120350	NA	P-0047759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	169	318	0	ENST00000373198.4:c.251C>T	p.Ser84Phe	p.S84F	ENST00000373198	NM_133170.3	84	tCt/tTt	3/32	0.146949080770272	3	FACETS	0.928	0.858	1	0.619	0.572	0.667	INDETERMINATE	2	TRUE	0	0.380085703162103	3		318	570	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555149	106555149	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	87	377	0	ENST00000369096.4:c.2266G>A	p.Glu756Lys	p.E756K	ENST00000369096	NM_001198.3	756	Gag/Aag	7/7	0.335340828330305	3	FACETS	0.841	0.745	0.943	0.42	0.372	0.472	CLONAL	1	TRUE	1	0.380085703162103	3		377	648	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109319927	109319927	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	55	378	0	ENST00000436639.2:c.761C>T	p.Ser254Phe	p.S254F	ENST00000436639	NM_014454.2	254	tCc/tTc	5/10	0.335340828330305	3	FACETS	0.534	0.456	0.619	0.267	0.228	0.31	SUBCLONAL	1	TRUE	1	0.380085703162103	3		378	645	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020760	112020760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	154	216	0	ENST00000368678.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000368678		271	Gag/Aag	8/13	0.335340828330305	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.380085703162103	3		216	436	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0047760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	264	516	0				ENST00000310581	NM_198253.2	-/1132			0.445436310821113	5	FACETS	0.952	0.898	1	0.952	0.898	1	CLONAL	3	TRUE	2	0.445436310821113	5		516	692	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058033	27058033	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0047760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	48	363	0	ENST00000324856.7:c.1741C>T	p.Gln581Ter	p.Q581*	ENST00000324856	NM_006015.4	581	Cag/Tag	3/20	0.16913365520295	6	FACETS	0.582	0.491	0.683	0.194	0.163	0.228	INDETERMINATE	1	TRUE	3	0.445436310821113	6		363	700	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	221	389	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	0.251958295103223	5	FACETS	1	0.976	1	0.645	0.606	0.685	INDETERMINATE	3	TRUE	0	0.445436310821113	5		389	513	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653860	89653860	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0047760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	12	219	0	ENST00000371953.3:c.158T>C	p.Val53Ala	p.V53A	ENST00000371953	NM_000314.4	53	gTa/gCa	2/9	1	2	FACETS	0.657	0.469	0.881	0.657	0.469	0.881	SUBCLONAL	1	TRUE	1	0.445436310821113	2		219	82	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481882	56481882	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	127	525	0	ENST00000267101.3:c.810C>G	p.Phe270Leu	p.F270L	ENST00000267101	NM_001982.3	270	ttC/ttG	7/28	0.251958295103223	5	FACETS	1	0.977	1	0.25	0.226	0.275	INDETERMINATE	1	TRUE	0	0.445436310821113	5		525	761	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1131691023	NA	P-0047760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	165	729	0	ENST00000269305.4:c.470T>A	p.Val157Asp	p.V157D	ENST00000269305	NM_001126112.2	157	gTc/gAc	5/11	0.218389233593693	4	FACETS	1	0.971	1	0.282	0.258	0.306	INDETERMINATE	1	TRUE	0	0.445436310821113	4		729	950	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0047760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	140	852	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.218389233593693	4	FACETS	1	0.933	1	0.257	0.234	0.282	INDETERMINATE	1	TRUE	0	0.445436310821113	4		852	883	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743919	41743919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201003955	NA	P-0047760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	47	788	1	ENST00000301178.4:c.854C>T	p.Ser285Leu	p.S285L	ENST00000301178	NM_021913.4	285	tCg/tTg	7/20	0.0903863417516184	4	FACETS	0.365	0.307	0.43	0.183	0.153	0.215	INDETERMINATE	1	TRUE	2	0.445436310821113	4		789	835	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569841	95569841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	16	231	0	ENST00000393063.1:c.3892C>T	p.Leu1298Phe	p.L1298F	ENST00000393063	NM_030621.3	1298	Ctt/Ttt	22/28	0.445436310821113	3	FACETS	0.295	0.217	0.387	0.147	0.108	0.194	SUBCLONAL	1	TRUE	1	0.445436310821113	3		231	298	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107100	27107366	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	GCTGCTTGCCTTGGCCAAGGTGGACGAGAACCACTCAGAGTTTACTCTGTACGAATCACGGCTGTTGGACATCTCGGTATCACCGTTGATGAACTCATTGGTTTCACAAGTCATTTGTGATGTACTGTTTTTGATTGGCCAGTCATGACAGCCGTGGGACACCTCCCCCCCCCGTGTGTGTGTGCGTGTGTGGAGAACTTAGAAACTGACTGTTGCCCTTTATTTATGCAAAACCACCTCAGAATCCAGTTTACCCTGTGCTGTCCA	GCTGCTTGCCTTGGCCAAGGTGGACGAGAACCACTCAGAGTTTACTCTGTACGAATCACGGCTGTTGGACATCTCGGTATCACCGTTGATGAACTCATTGGTTTCACAAGTCATTTGTGATGTACTGTTTTTGATTGGCCAGTCATGACAGCCGTGGGACACCTCCCCCCCCCGTGTGTGTGTGCGTGTGTGGAGAACTTAGAAACTGACTGTTGCCCTTTATTTATGCAAAACCACCTCAGAATCCAGTTTACCCTGTGCTGTCCA	-	novel	NA	P-0047760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	76	418	0	ENST00000324856.7:c.6714_*122del		p.*2238*	ENST00000324856	NM_006015.4	2237		20/20	0.16913365520295	6	FACETS	1	0.943	1	0.377	0.33	0.426	INDETERMINATE	1	TRUE	3	0.445436310821113	6		418	571	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343179	118343179	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	57	188	0	ENST00000534358.1:c.1307del	p.Pro436LeufsTer8	p.P436Lfs*8	ENST00000534358	NM_005933.3	435	gaC/ga	3/36	0.445436310821113	4	FACETS	1	0.909	1	0.357	0.308	0.411	CLONAL	1	TRUE	1	0.445436310821113	4		188	345	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362557	118362557	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0047760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	107	326	0	ENST00000534358.1:c.4918G>C	p.Glu1640Gln	p.E1640Q	ENST00000534358	NM_005933.3	1640	Gaa/Caa	15/36	0.445436310821113	4	FACETS	1	0.972	1	0.41	0.369	0.454	CLONAL	1	TRUE	1	0.445436310821113	4		326	564	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21630818	21630818	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	25	339	0	ENST00000421138.2:c.786G>C	p.Leu262Phe	p.L262F	ENST00000421138		262	ttG/ttC	8/16	0.173849213493095	3	FACETS	0.352	0.277	0.438	0.176	0.138	0.219	INDETERMINATE	1	TRUE	1	0.445436310821113	3		339	390	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591671	38591671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0047760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	145	419	0	ENST00000299084.4:c.130G>T	p.Val44Phe	p.V44F	ENST00000299084	NM_152594.2	44	Gtc/Ttc	2/7	1	2	FACETS	0.773	0.712	0.836	1	0.989	1	SUBCLONAL	2	TRUE	1	0.445436310821113	2		419	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578260	7578260	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0047760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	219	538	0	ENST00000269305.4:c.589del	p.Val197TrpfsTer50	p.V197Wfs*50	ENST00000269305	NM_001126112.2	197	Gtg/tg	6/11	0.218389233593693	4	FACETS	1	0.988	1	0.616	0.577	0.655	INDETERMINATE	2	TRUE	0	0.445436310821113	4		538	577	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995247	15995247	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	37	308	0	ENST00000268712.3:c.2946G>C	p.Gln982His	p.Q982H	ENST00000268712	NM_006311.3	982	caG/caC	22/46	0.218389233593693	4	FACETS	0.518	0.426	0.62	0.129	0.106	0.155	INDETERMINATE	1	TRUE	0	0.445436310821113	4		308	464	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184568	7184568	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0047760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	33	426	0	ENST00000302850.5:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000302850	NM_000208.2	245	Cag/Tag	3/22	0.18302263421297	3	FACETS	0.312	0.253	0.378	0.104	0.084	0.126	INDETERMINATE	1	TRUE	0	0.445436310821113	3		426	581	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267229	41267229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0047760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	23	294	0	ENST00000349496.5:c.813G>A	p.Met271Ile	p.M271I	ENST00000349496	NM_001904.3	271	atG/atA	6/15	0.445436310821113	4	FACETS	0.399	0.311	0.502	0.133	0.103	0.168	SUBCLONAL	1	TRUE	1	0.445436310821113	4		294	374	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517751	187517751	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs376695610	NA	P-0047760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	12	183	0	ENST00000441802.2:c.12943A>G	p.Asn4315Asp	p.N4315D	ENST00000441802	NM_005245.3	4315	Aac/Gac	25/27	1	2	FACETS	0.298	0.209	0.406	0.298	0.209	0.406	SUBCLONAL	1	TRUE	1	0.445436310821113	2		183	181	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753933	57753933	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0047760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	35	280	0	ENST00000274289.3:c.691G>C	p.Glu231Gln	p.E231Q	ENST00000274289	NM_006622.3	231	Gaa/Caa	5/14	NA	2	FACETS	0.557	0.459	0.667			1	INDETERMINATE	1	TRUE	NA	0.445436310821113	2		280	282	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335642	81335642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0047760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	19	243	1	ENST00000222390.5:c.1718G>A	p.Gly573Asp	p.G573D	ENST00000222390	NM_000601.4	573	gGc/gAc	15/18	0.246678047192611	5	FACETS	0.455	0.345	0.584	0.152	0.115	0.195	INDETERMINATE	1	TRUE	2	0.445436310821113	5		244	313	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913233	NA	P-0047761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	248	769	0	ENST00000451590.1:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000451590	NM_001130442.1	61	cAg/cTg	3/5	0.290219900866187	3	FACETS	1	0.991	1	0.695	0.649	0.743	CLONAL	1	TRUE	1	0.33	3		769	1260	SUCCESS
AR	367	MSKCC	GRCh37	X	66765845	66765845	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0047761-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	157	933	0	ENST00000374690.3:c.857C>A	p.Pro286Gln	p.P286Q	ENST00000374690	NM_000044.3	286	cCa/cAa	1/8	1	2	FACETS	0.795	0.727	0.867	0.795	0.727	0.867	SUBCLONAL	1	TRUE	1	0.33	2		933	1197	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0000112-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	271	131	0	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.46609019297427	2		131	527	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187682	11187682	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000112-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	226	280	2	ENST00000361445.4:c.6215A>G	p.Gln2072Arg	p.Q2072R	ENST00000361445	NM_004958.3	2072	cAg/cGg	44/58	0.46609019297427	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.46609019297427	1		282	648	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588770	52588770	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143564112	NA	P-0000112-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	149	171	0	ENST00000394830.3:c.4258G>A	p.Val1420Met	p.V1420M	ENST00000394830	NM_018313.4	1420	Gtg/Atg	27/30	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.46609019297427	2		171	571	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90990461	90990461	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000112-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	183	436	2	ENST00000265433.3:c.571C>G	p.Pro191Ala	p.P191A	ENST00000265433	NM_002485.4	191	Cca/Gca	5/16	0.46609019297427	3	FACETS	0.975	0.9	1	0.325	0.3	0.352	CLONAL	1	TRUE	0	0.46609019297427	3		438	993	SUCCESS
AXL	558	MSKCC	GRCh37	19	41736935	41736935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776682499	NA	P-0000112-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	328	212	3	ENST00000301178.4:c.650G>A	p.Arg217His	p.R217H	ENST00000301178	NM_021913.4	217	cGc/cAc	5/20	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.46609019297427	2		215	662	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156719	20156719	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000112-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	221	243	0	ENST00000379607.5:c.38G>T	p.Arg13Leu	p.R13L	ENST00000379607	NM_001412.3	13	cGc/cTc	2/7	0.339489281073355	2	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.46609019297427	2		243	726	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120000	70120001	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000112-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	41	21	0	ENST00000245479.2:c.1003dup	p.Trp335LeufsTer243	p.W335Lfs*243	ENST00000245479	NM_000346.3	334	-/T	3/3	0.46274964153345	3	FACETS	1	0.948	1	0.657	0.556	0.766	CLONAL	1	TRUE	1	0.46609019297427	3		21	165	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603062	48603063	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000112-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	107	152	0	ENST00000342988.3:c.1365dup	p.Ala456SerfsTer38	p.A456Sfs*38	ENST00000342988	NM_005359.5	455	caa/cAaa	11/12	0.46609019297427	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.46609019297427	1		152	343	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000358-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	272	697	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.449262127424771	1	FACETS	0.961	0.919	1	1	0.996	1	CLONAL	2	TRUE	0	0.505040903402675	1		697	419	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606826	43606826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000358-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	35	295	0	ENST00000355710.3:c.1435G>A	p.Ala479Thr	p.A479T	ENST00000355710	NM_020975.4	479	Gcc/Acc	7/20	0.234153011550948	3	FACETS	0.933	0.773	1	0.467	0.386	0.555	INDETERMINATE	1	TRUE	1	0.505040903402675	3		295	186	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0000397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	49	109	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.877	0.747	1	0.877	0.747	1	CLONAL	1	TRUE	1	0.355750649728507	2		109	314	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0000397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	77	258	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.548	0.48	0.621	0.548	0.48	0.621	SUBCLONAL	1	TRUE	1	0.355750649728507	2		258	790	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0000397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	119	269	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	1	2	FACETS	0.85	0.767	0.937	0.85	0.767	0.937	CLONAL	1	TRUE	1	0.355750649728507	2		269	787	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	90	938	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.290598883239509	0	FACETS	0.533	0.473	0.596			1	SUBCLONAL	1	TRUE	0	0.355750649728507	0		938	612	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138375049	138375049	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	79	181	0	ENST00000289153.2:c.3010T>A	p.Phe1004Ile	p.F1004I	ENST00000289153	NM_006219.2	1004	Ttt/Att	21/22	0.230049222237067	1	FACETS	0.526	0.462	0.595	0.526	0.462	0.595	SUBCLONAL	1	TRUE	0	0.355750649728507	1		181	694	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564731	86564731	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1647	493	467	1	ENST00000274376.6:c.463G>T	p.Glu155Ter	p.E155*	ENST00000274376	NM_002890.2	155	Gaa/Taa	1/25	0.197050343582433	4	FACETS	0.878	0.837	0.92	0.878	0.837	0.92	INDETERMINATE	2	TRUE	2	0.355750649728507	4		468	2140	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671462	30671462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	129	419	0	ENST00000376406.3:c.5498C>T	p.Ser1833Phe	p.S1833F	ENST00000376406	NM_014641.2	1833	tCc/tTc	10/15	0.158921883249532	1	FACETS	0.594	0.538	0.654	0.594	0.538	0.654	INDETERMINATE	1	TRUE	0	0.355750649728507	1		419	1003	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370945	55370945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	66	231	0	ENST00000297316.4:c.247C>T	p.Arg83Cys	p.R83C	ENST00000297316	NM_022454.3	83	Cgc/Tgc	1/2	1	2	FACETS	0.683	0.594	0.78	0.683	0.594	0.78	SUBCLONAL	1	TRUE	1	0.355750649728507	2		231	543	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485288	8485288	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	93	260	0	ENST00000356435.5:c.3092A>C	p.Lys1031Thr	p.K1031T	ENST00000356435		1031	aAg/aCg	18/35	1	2	FACETS	0.664	0.59	0.744	0.664	0.59	0.744	SUBCLONAL	1	TRUE	1	0.355750649728507	2		260	787	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254247	133254247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	132	418	0	ENST00000320574.5:c.637G>A	p.Asp213Asn	p.D213N	ENST00000320574	NM_006231.2	213	Gac/Aac	7/49	0.355750649728507	1	FACETS	0.57	0.516	0.626	0.57	0.516	0.626	SUBCLONAL	1	TRUE	0	0.355750649728507	1		418	1071	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436921	110436921	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	53	87	0	ENST00000375856.3:c.1480G>T	p.Asp494Tyr	p.D494Y	ENST00000375856	NM_003749.2	494	Gac/Tac	1/2	0.287828851931645	1	FACETS	0.968	0.834	1	0.968	0.834	1	CLONAL	1	TRUE	0	0.355750649728507	1		87	253	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528054	29528054	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs1555610955	NA	P-0000397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	31	61	0	ENST00000356175.3:c.1063-1G>C		p.X355_splice	ENST00000356175	NM_000267.3	355			0.276590207857394	1	FACETS	0.901	0.738	1	0.901	0.738	1	CLONAL	1	TRUE	0	0.355750649728507	1		61	159	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356426	70356426	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	103	466	2	ENST00000374080.3:c.5321C>A	p.Ala1774Asp	p.A1774D	ENST00000374080		1774	gCt/gAt	37/45	0.355750649728507	1	FACETS	0.441	0.394	0.492	0.441	0.394	0.492	SUBCLONAL	1	TRUE	0	0.355750649728507	1		468	1079	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844109	68844110	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000397-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	93	251	0	ENST00000261769.5:c.698dup	p.His233GlnfsTer11	p.H233Qfs*11	ENST00000261769	NM_004360.3	233	cac/cAac	6/16	0.355750649728507	1	FACETS	0.709	0.632	0.792	0.709	0.632	0.792	SUBCLONAL	1	TRUE	0	0.355750649728507	1		251	606	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732724	204732724	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000509-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	109	481	0	ENST00000302823.3:c.59G>A	p.Trp20Ter	p.W20*	ENST00000302823	NM_005214.4	20	tGg/tAg	1/4	1	2	FACETS	0.883	0.795	0.976	0.883	0.795	0.976	CLONAL	1	TRUE	1	0.427842086427443	2		481	577	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474637	138474651	+	inframe_deletion	In_Frame_Del	DEL	CCTGGGTCACAACTT	CCTGGGTCACAACTT	-	novel	NA	P-0000509-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	76	419	0	ENST00000289153.2:c.342_356del	p.Ser115_Gly119del	p.S115_G119del	ENST00000289153	NM_006219.2	114	agAAGTTGTGACCCAGGg/agg	2/22	1	2	FACETS	0.618	0.542	0.699	0.618	0.542	0.699	SUBCLONAL	1	TRUE	1	0.427842086427443	2		419	575	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859653	151859653	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000509-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	101	400	0	ENST00000262189.6:c.11009A>C	p.Asn3670Thr	p.N3670T	ENST00000262189	NM_170606.2	3670	aAt/aCt	43/59	1	2	FACETS	0.871	0.781	0.966	0.871	0.781	0.966	CLONAL	1	TRUE	1	0.427842086427443	2		400	542	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310871	123310871	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs755793	NA	P-0000789-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	25	441	0	ENST00000358487.5:c.557T>C	p.Met186Thr	p.M186T	ENST00000358487	NM_000141.4	186	aTg/aCg	5/18	0.541885941818643	2	FACETS	0.243	0.191	0.302	0.121	0.095	0.151	SUBCLONAL	1	TRUE	0	0.546658939804528	2		441	377	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994806	73994806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs7173448	NA	P-0000789-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	13	253	2	ENST00000318443.5:c.290C>T	p.Pro97Leu	p.P97L	ENST00000318443	NM_001024736.1	97	cCg/cTg	3/10	0.492784271476028	3	FACETS	0.28	0.2	0.378	0.14	0.1	0.189	SUBCLONAL	1	TRUE	1	0.546658939804528	3		255	216	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805698	43805698	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs141311765	NA	P-0000789-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	28	312	1	ENST00000372470.3:c.754T>C	p.Tyr252His	p.Y252H	ENST00000372470	NM_005373.2	252	Tac/Cac	5/12	0.492784271476028	3	FACETS	0.389	0.311	0.478	0.195	0.155	0.239	SUBCLONAL	1	TRUE	1	0.546658939804528	3		313	335	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743501	46743501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000789-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	17	182	0	ENST00000371975.4:c.1882G>A	p.Glu628Lys	p.E628K	ENST00000371975	NM_003579.3	628	Gag/Aag	17/18	0.492784271476028	3	FACETS	0.311	0.232	0.404	0.155	0.116	0.202	SUBCLONAL	1	TRUE	1	0.546658939804528	3		182	255	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293955	1293955	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs904848231	NA	P-0000789-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	56	300	0	ENST00000310581.5:c.1046C>G	p.Ser349Cys	p.S349C	ENST00000310581	NM_198253.2	349	tCt/tGt	2/16	0.303934489298587	5	FACETS	1	0.934	1			1	INDETERMINATE	1	TRUE	NA	0.546658939804528	5		300	325	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039583	180039583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs75614493	NA	P-0000789-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	19	439	0	ENST00000261937.6:c.3460G>A	p.Gly1154Arg	p.G1154R	ENST00000261937	NM_182925.4	1154	Gga/Aga	26/30	0.309772878029435	4	FACETS	0.284	0.215	0.366	0.142	0.107	0.183	INDETERMINATE	1	TRUE	2	0.546658939804528	4		439	378	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522223	157522223	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs34870395	NA	P-0000789-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	18	194	0	ENST00000346085.5:c.4495A>T	p.Met1499Leu	p.M1499L	ENST00000346085	NM_020732.3	1499	Atg/Ttg	18/20	0.546658939804528	1	FACETS	0.283	0.214	0.364	0.283	0.214	0.364	SUBCLONAL	1	TRUE	0	0.546658939804528	1		194	169	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38318621	38318621	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000789-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	10	323	0	ENST00000425967.3:c.4G>C	p.Glu2Gln	p.E2Q	ENST00000425967	NM_001174067.1	2	Gag/Cag	2/19	0.546658939804528	1	FACETS	0.136	0.092	0.192	0.136	0.092	0.192	SUBCLONAL	1	TRUE	0	0.546658939804528	1		323	195	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739679	145739679	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs2721191	NA	P-0000789-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	26	222	0	ENST00000428558.2:c.1772C>T	p.Pro591Leu	p.P591L	ENST00000428558	NM_004260.3	591	cCt/cTt	11/22	0.402756265404448	6	FACETS	0.6	0.475	0.742			1	SUBCLONAL	1	TRUE	NA	0.546658939804528	6		222	332	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456500	32456500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000789-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	10	31	0	ENST00000332351.3:c.392C>T	p.Pro131Leu	p.P131L	ENST00000332351	NM_024426.4	131	cCc/cTc	1/10	0.396922368249935	4	FACETS	0.808	0.572	1	0.808	0.572	1	CLONAL	2	TRUE	2	0.546658939804528	4		31	35	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343304	118343304	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000789-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	41	236	0	ENST00000534358.1:c.1430C>G	p.Ser477Cys	p.S477C	ENST00000534358	NM_005933.3	477	tCt/tGt	3/36	0.266155239933647	3	FACETS	0.637	0.533	0.751			1	INDETERMINATE	1	TRUE	NA	0.546658939804528	3		236	300	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112554	115112554	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs78115331	NA	P-0000789-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	18	416	0	ENST00000257566.3:c.1186T>A	p.Ser396Thr	p.S396T	ENST00000257566	NM_016569.3	396	Tcc/Acc	7/8	0.247474870489651	4	FACETS	0.299	0.224	0.387	0.149	0.112	0.194	INDETERMINATE	1	TRUE	2	0.546658939804528	4		416	341	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578209	28578209	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs74041526	NA	P-0000789-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	28	411	0	ENST00000241453.7:c.2962G>C	p.Ala988Pro	p.A988P	ENST00000241453	NM_004119.2	988	Gct/Cct	24/24	0.189283661898766	3	FACETS	0.289	0.231	0.356	0.096	0.077	0.119	INDETERMINATE	1	TRUE	0	0.546658939804528	3		411	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0000789-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	108	196	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	NA	2	FACETS	1	0.926	1			1	INDETERMINATE	2	TRUE	NA	0.546658939804528	2		196	197	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769970658	NA	P-0000789-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	16	188	0	ENST00000407977.2:c.1976G>A	p.Gly659Asp	p.G659D	ENST00000407977		659	gGt/gAt	9/10	0.346019716009737	6	FACETS	0.439	0.324	0.577			1	SUBCLONAL	1	TRUE	NA	0.546658939804528	6		188	279	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223059	1223059	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913325	NA	P-0000789-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	128	381	0	ENST00000326873.7:c.996G>A	p.Trp332Ter	p.W332*	ENST00000326873	NM_000455.4	332	tgG/tgA	8/10	0.541885941818643	2	FACETS	0.874	0.808	0.94	0.874	0.808	0.94	CLONAL	2	TRUE	0	0.546658939804528	2		381	268	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214724	5214724	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000789-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	107	291	0	ENST00000357368.4:c.4342A>T	p.Asn1448Tyr	p.N1448Y	ENST00000357368	NM_002850.3	1448	Aat/Tat	29/38	0.541885941818643	2	FACETS	0.829	0.76	0.9	0.829	0.76	0.9	CLONAL	2	TRUE	0	0.546658939804528	2		291	236	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375067	31375067	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000789-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	130	295	2	ENST00000328111.2:c.464G>T	p.Gly155Val	p.G155V	ENST00000328111	NM_006892.3	155	gGa/gTa	6/23	0.492784271476028	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	1	0.546658939804528	3		297	286	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599938	10599938	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000789-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	218	578	0	ENST00000171111.5:c.1638del	p.Phe546LeufsTer2	p.F546Lfs*2	ENST00000171111	NM_203500.1	546	ttC/tt	5/6	0.541885941818643	2	FACETS	0.787	0.739	0.835	0.787	0.739	0.835	SUBCLONAL	2	TRUE	0	0.546658939804528	2		578	507	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720658	89720658	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001055-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	62	288	0	ENST00000371953.3:c.809T>C	p.Met270Thr	p.M270T	ENST00000371953	NM_000314.4	270	aTg/aCg	8/9	0.578520315845145	1	FACETS	0.819	0.721	0.921	0.819	0.721	0.921	CLONAL	1	TRUE	0	0.578520315845145	1		288	186	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500549	99500549	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs531850849	NA	P-0001055-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	174	669	0	ENST00000268035.6:c.3982G>A	p.Gly1328Ser	p.G1328S	ENST00000268035	NM_000875.3	1328	Ggc/Agc	21/21	1	2	FACETS	0.911	0.842	0.983	0.911	0.842	0.983	CLONAL	1	TRUE	1	0.578520315845145	2		669	660	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198262752	198262752	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001055-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	164	464	0	ENST00000335508.6:c.3223A>G	p.Arg1075Gly	p.R1075G	ENST00000335508	NM_012433.2	1075	Aga/Gga	22/25	1	2	FACETS	0.901	0.831	0.974	0.901	0.831	0.974	CLONAL	1	TRUE	1	0.578520315845145	2		464	629	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251749	212251749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001309-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	50	151	0	ENST00000342788.4:c.3310G>A	p.Asp1104Asn	p.D1104N	ENST00000342788	NM_005235.2	1104	Gac/Aac	27/28	0.481832986886783	1	FACETS	0.352	0.3	0.407	0.352	0.3	0.407	SUBCLONAL	1	TRUE	0	0.683388173169752	1		151	274	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259324	89259324	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001309-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	49	216	0	ENST00000336596.2:c.468T>A	p.Asp156Glu	p.D156E	ENST00000336596	NM_005233.5	156	gaT/gaA	3/17	0.683388173169752	1	FACETS	0.356	0.304	0.413	0.356	0.304	0.413	SUBCLONAL	1	TRUE	0	0.683388173169752	1		216	265	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55987327	55987327	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001309-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	28	171	0	ENST00000263923.4:c.98G>T	p.Arg33Met	p.R33M	ENST00000263923	NM_002253.2	33	aGg/aTg	2/30	0.260917915280362	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.683388173169752	0		171	180	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752871	57752871	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001309-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	115	131	0	ENST00000274289.3:c.1057G>C	p.Asp353His	p.D353H	ENST00000274289	NM_006622.3	353	Gat/Cat	8/14	0.683388173169752	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.683388173169752	1		131	214	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754920	57754920	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0001309-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	143	158	0	ENST00000274289.3:c.271-1G>A		p.X91_splice	ENST00000274289	NM_006622.3	91			0.683388173169752	1	FACETS	0.953	0.886	1	0.953	0.886	1	CLONAL	1	TRUE	0	0.683388173169752	1		158	289	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129123	152129123	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001309-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	150	371	0	ENST00000206249.3:c.76C>A	p.Leu26Met	p.L26M	ENST00000206249	NM_000125.3	26	Ctg/Atg	1/8	0.260917915280362	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.683388173169752	0		371	416	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432038	121432038	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001309-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	311	228	0	ENST00000257555.6:c.785T>A	p.Val262Glu	p.V262E	ENST00000257555		262	gTg/gAg	4/10	0.214184936894531	3	FACETS	0.774	0.733	0.815	0.774	0.733	0.815	INDETERMINATE	2	TRUE	1	0.683388173169752	3		228	789	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352498	73352498	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001309-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	101	232	0	ENST00000377767.4:c.407A>T	p.Glu136Val	p.E136V	ENST00000377767	NM_014953.3	136	gAa/gTa	3/21	0.650593087098359	1	FACETS	0.857	0.782	0.933	0.857	0.782	0.933	CLONAL	1	TRUE	0	0.683388173169752	1		232	227	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273853	10273853	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0001309-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	43	128	0	ENST00000330684.3:c.414+2T>G		p.X138_splice	ENST00000330684	NM_001134407.1	138			0.429155798500879	1	FACETS	0.269	0.226	0.316	0.269	0.226	0.316	SUBCLONAL	1	TRUE	0	0.683388173169752	1		128	308	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220370	1220370	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0001309-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	352	170	0	ENST00000326873.7:c.465-2A>T		p.X155_splice	ENST00000326873	NM_000455.4	155			0.683388173169752	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.683388173169752	1		170	655	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713345	40713345	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001309-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	137	162	0	ENST00000373198.4:c.4170G>T	p.Glu1390Asp	p.E1390D	ENST00000373198	NM_133170.3	1390	gaG/gaT	30/32	1	2	FACETS	0.905	0.83	0.982	0.905	0.83	0.982	CLONAL	1	TRUE	1	0.683388173169752	2		162	443	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743895	40743895	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001309-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	152	170	0	ENST00000373198.4:c.3100C>A	p.Leu1034Met	p.L1034M	ENST00000373198	NM_133170.3	1034	Ctg/Atg	23/32	1	2	FACETS	0.925	0.852	0.999	0.925	0.852	0.999	CLONAL	1	TRUE	1	0.683388173169752	2		170	481	SUCCESS
APC	324	MSKCC	GRCh37	5	112179012	112179013	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0001309-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	122	127	0	ENST00000257430.4:c.7722_7723del	p.Ser2575CysfsTer7	p.S2575Cfs*7	ENST00000257430	NM_000038.5	2574	cTT/c	16/16	0.683388173169752	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.683388173169752	1		127	226	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602354	10602354	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001309-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	322	281	0	ENST00000171111.5:c.1224del	p.Met409Ter	p.M409*	ENST00000171111	NM_203500.1	408	ccC/cc	3/6	0.683388173169752	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.683388173169752	1		281	556	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562482	21562483	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGGCG	rs550642106	NA	P-0001447-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	13	15	0	ENST00000382592.4:c.1431_1436dup	p.Pro479_Ala480dup	p.P479_A480dup	ENST00000382592	NM_014572.2	479	ccg/ccCGCCCCg	4/8	NA	2	FACETS	1	0.822	1			1	INDETERMINATE	1	TRUE	NA	0.404492305765948	2		15	55	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852029	63852029	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001447-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	27	135	0	ENST00000279873.7:c.2807G>T	p.Gly936Val	p.G936V	ENST00000279873	NM_032199.2	936	gGc/gTc	10/10	0.305857583129176	5	FACETS	0.953	0.785	1	0.953	0.785	1	CLONAL	3	TRUE	2	0.404492305765948	5		135	75	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044572	47044572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001447-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	14	378	0	ENST00000377604.3:c.2069C>T	p.Ala690Val	p.A690V	ENST00000377604	NM_001204468.1	690	gCa/gTa	18/24	0.322348138414075	1	FACETS	0.383	0.279	0.509	0.383	0.279	0.509	SUBCLONAL	1	TRUE	0	0.404492305765948	1		378	144	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0003499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	30	363	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA	2	FACETS	0.805	0.652	0.975			1	INDETERMINATE	1	TRUE	NA	0.334441350853776	2		363	223	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0003499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	106	390	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.334441350853776	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.334441350853776	1		390	388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0003499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	273	350	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.334441350853776	3	FACETS	0.954	0.896	1			1	CLONAL	2	TRUE	NA	0.334441350853776	3		350	999	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247168	153247168	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1560758208	NA	P-0003499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	61	301	0	ENST00000281708.4:c.1634A>G	p.Tyr545Cys	p.Y545C	ENST00000281708	NM_033632.3	545	tAt/tGt	10/12	0.255830572157473	2	FACETS	0.786	0.687	0.891	0.786	0.687	0.891	SUBCLONAL	2	TRUE	0	0.334441350853776	2		301	232	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143043369	143043369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	24	314	2	ENST00000262992.4:c.2047G>A	p.Ala683Thr	p.A683T	ENST00000262992	NM_001101669.1	683	Gcc/Acc	19/24	0.255830572157473	2	FACETS	0.854	0.676	1	0.427	0.338	0.528	CLONAL	1	TRUE	0	0.334441350853776	2		316	168	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162475170	162475170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763650901	NA	P-0003499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	29	445	0	ENST00000366898.1:c.571C>T	p.Arg191Trp	p.R191W	ENST00000366898	NM_004562.2	191	Cgg/Tgg	5/12	1	2	FACETS	0.842	0.681	1	0.842	0.681	1	CLONAL	1	TRUE	1	0.334441350853776	2		445	206	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956956	2956956	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs750486472	NA	P-0003499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	129	195	0	ENST00000396946.4:c.2671C>T	p.Arg891Ter	p.R891*	ENST00000396946	NM_032415.4	891	Cga/Tga	20/25	1	2	FACETS	0.943	0.855	1	0.943	0.855	1	CLONAL	1	TRUE	1	0.334441350853776	2		195	818	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584572	48584572	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	59	301	0	ENST00000342988.3:c.745C>T	p.Gln249Ter	p.Q249*	ENST00000342988	NM_005359.5	249	Cag/Tag	6/12	1	2	FACETS	0.924	0.798	1	0.924	0.798	1	CLONAL	1	TRUE	1	0.334441350853776	2		301	382	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	212	427	0				ENST00000310581	NM_198253.2	-/1132			0.177428485338786	1	FACETS	0.613	0.576	0.65	0.613	0.576	0.65	INDETERMINATE	1	TRUE	0	0.857511118846649	1		427	461	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0004226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	80	594	1	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.616	0.547	0.687	0.616	0.547	0.687	SUBCLONAL	1	TRUE	1	0.857511118846649	2		595	303	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398262	25398262	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913538	NA	P-0004226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	93	393	0	ENST00000311936.3:c.57G>C	p.Leu19Phe	p.L19F	ENST00000311936	NM_004985.3	19	ttG/ttC	2/5	1	2	FACETS	0.647	0.581	0.717	0.647	0.581	0.717	SUBCLONAL	1	TRUE	1	0.857511118846649	2		393	335	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158626	26158626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772836222	NA	P-0004226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	160	278	1	ENST00000289316.2:c.229G>A	p.Glu77Lys	p.E77K	ENST00000289316	NM_138720.2	77	Gag/Aag	1/2	1	2	FACETS	0.842	0.78	0.906	0.842	0.78	0.906	CLONAL	1	TRUE	1	0.857511118846649	2		279	443	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645693	12645693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397516827	NA	P-0004226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	191	204	0	ENST00000251849.4:c.776C>T	p.Ser259Phe	p.S259F	ENST00000251849	NM_002880.3	259	tCc/tTc	7/17	1	2	FACETS	0.977	0.913	1	0.977	0.913	1	CLONAL	1	TRUE	1	0.857511118846649	2		204	456	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230772	46230772	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	93	264	0	ENST00000334344.6:c.1021G>C	p.Glu341Gln	p.E341Q	ENST00000334344	NM_152641.2	341	Gag/Cag	8/21	1	2	FACETS	0.893	0.808	0.98	0.893	0.808	0.98	CLONAL	1	TRUE	1	0.857511118846649	2		264	243	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588849	69588849	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2329	599	979	1	ENST00000168712.1:c.387C>A	p.Phe129Leu	p.F129L	ENST00000168712	NM_002007.2	129	ttC/ttA	2/3	0.857511118846649	4	FACETS	0.886	0.848	0.925			1	CLONAL	1	TRUE	NA	0.857511118846649	4		980	2928	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298501	11298501	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	67	581	0	ENST00000361445.4:c.1960G>A	p.Asp654Asn	p.D654N	ENST00000361445	NM_004958.3	654	Gat/Aat	12/58	1	2	FACETS	0.185	0.16	0.213	0.185	0.16	0.213	SUBCLONAL	1	TRUE	1	0.857511118846649	2		581	843	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112919902	112919902	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	40	214	0	ENST00000351677.2:c.1117G>C	p.Asp373His	p.D373H	ENST00000351677	NM_002834.3	373	Gat/Cat	10/16	1	2	FACETS	0.321	0.267	0.379	0.321	0.267	0.379	SUBCLONAL	1	TRUE	1	0.857511118846649	2		214	291	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844122	68844122	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	86	568	0	ENST00000261769.5:c.710C>G	p.Ser237Cys	p.S237C	ENST00000261769	NM_004360.3	237	tCc/tGc	6/16	1	2	FACETS	0.239	0.211	0.269	0.239	0.211	0.269	SUBCLONAL	1	TRUE	1	0.857511118846649	2		568	839	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89818628	89818628	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0004226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	42	344	0	ENST00000389301.3:c.2984C>G	p.Ser995Ter	p.S995*	ENST00000389301	NM_000135.2	995	tCa/tGa	31/43	1	2	FACETS	0.202	0.168	0.239	0.202	0.168	0.239	SUBCLONAL	1	TRUE	1	0.857511118846649	2		344	485	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168983	11168983	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	426	710	0	ENST00000358026.2:c.4573G>C	p.Glu1525Gln	p.E1525Q	ENST00000358026	NM_001128849.1	1525	Gag/Cag	32/36	1	2	FACETS	0.959	0.917	1	0.959	0.917	1	CLONAL	1	TRUE	1	0.857511118846649	2		710	1036	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170834	11170834	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	429	803	0	ENST00000358026.2:c.4978G>A	p.Asp1660Asn	p.D1660N	ENST00000358026	NM_001128849.1	1660	Gac/Aac	35/36	1	2	FACETS	0.917	0.876	0.958	0.917	0.876	0.958	CLONAL	1	TRUE	1	0.857511118846649	2		803	1091	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170861	11170861	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1298648044	NA	P-0004226-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	338	658	1	ENST00000358026.2:c.5005G>A	p.Glu1669Lys	p.E1669K	ENST00000358026	NM_001128849.1	1669	Gag/Aag	35/36	1	2	FACETS	0.904	0.859	0.95	0.904	0.859	0.95	CLONAL	1	TRUE	1	0.857511118846649	2		659	872	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511172	148511172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554486390	NA	P-0005978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	49	577	1	ENST00000320356.2:c.1730C>T	p.Pro577Leu	p.P577L	ENST00000320356	NM_004456.4	577	cCg/cTg	15/20	0.261447823465776	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.261447823465776	1		578	274	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933800	39933819	+	frameshift_variant	Frame_Shift_Del	DEL	GCCTCATGGGTGATGCCAAG	GCCTCATGGGTGATGCCAAG	-	novel	NA	P-0005978-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	21	414	0	ENST00000378444.4:c.780_799del	p.Ala262AspfsTer32	p.A262Dfs*32	ENST00000378444	NM_001123385.1	260	tcCTTGGCATCACCCATGAGGCtc/tctc	4/15	0.119975959009515	0	FACETS	0.702	0.544	0.883			1	INDETERMINATE	1	TRUE	NA	0.261447823465776	0		414	169	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0006304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	79	361	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.373461554380228	2		361	304	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608282	28608282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773466203	NA	P-0006304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	77	120	0	ENST00000241453.7:c.1774G>A	p.Val592Ile	p.V592I	ENST00000241453	NM_004119.2	592	Gtt/Att	14/24	1	2	FACETS	0.914	0.806	1	0.914	0.806	1	CLONAL	1	TRUE	1	0.373461554380228	2		120	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572935	7572935	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	177	133	0	ENST00000269305.4:c.1174T>C	p.Ser392Pro	p.S392P	ENST00000269305	NM_001126112.2	392	Tca/Cca	11/11	0.27816415800787	2	FACETS	0.981	0.912	1	0.981	0.912	1	CLONAL	2	TRUE	0	0.373461554380228	2		133	483	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587782289	NA	P-0006304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	208	178	0	ENST00000269305.4:c.706T>A	p.Tyr236Asn	p.Y236N	ENST00000269305	NM_001126112.2	236	Tac/Aac	7/11	0.27816415800787	2	FACETS	0.949	0.887	1	0.949	0.887	1	CLONAL	2	TRUE	0	0.373461554380228	2		178	587	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033822	49033822	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0006304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	57	83	0	ENST00000267163.4:c.1961-2A>G		p.X654_splice	ENST00000267163	NM_000321.2	654			1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.373461554380228	2		83	242	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148919	119148919	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1377506801	NA	P-0006304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	12	87	0	ENST00000264033.4:c.1139T>C	p.Leu380Pro	p.L380P	ENST00000264033	NM_005188.3	380	cTa/cCa	8/16	1	2	FACETS	0.163	0.114	0.224	0.163	0.114	0.224	SUBCLONAL	1	TRUE	1	0.373461554380228	2		87	395	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274091	18274091	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	37	169	1	ENST00000222254.8:c.1309G>T	p.Asp437Tyr	p.D437Y	ENST00000222254	NM_005027.3	437	Gac/Tac	11/16	1	2	FACETS	0.325	0.267	0.39	0.325	0.267	0.39	SUBCLONAL	1	TRUE	1	0.373461554380228	2		170	609	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133748324	133748324	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	100	191	0	ENST00000318560.5:c.985G>C	p.Glu329Gln	p.E329Q	ENST00000318560	NM_005157.4	329	Gag/Cag	6/11	1	2	FACETS	0.875	0.783	0.972	0.875	0.783	0.972	CLONAL	1	TRUE	1	0.373461554380228	2		191	612	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	54	427	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.834	0.719	0.959	1	0.972	1	CLONAL	2	TRUE	1	0.241467380352534	2		427	268	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0007574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	100	390	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.239938070693572	2	FACETS	0.986	0.894	1	1	0.984	1	CLONAL	3	TRUE	0	0.241467380352534	2		390	280	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412905	49412905	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519951	NA	P-0007574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	96	511	0	ENST00000418115.1:c.118G>C	p.Glu40Gln	p.E40Q	ENST00000418115	NM_001664.2	40	Gag/Cag	2/5	0.241467380352534	1	FACETS	0.885	0.788	0.988	0.885	0.788	0.988	CLONAL	1	TRUE	0	0.241467380352534	1		511	790	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578530	7578530	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs267605077	NA	P-0007574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	103	304	0	ENST00000269305.4:c.400T>A	p.Phe134Ile	p.F134I	ENST00000269305	NM_001126112.2	134	Ttt/Att	5/11	1	2	FACETS	0.845	0.759	0.935	1	0.985	1	CLONAL	2	TRUE	1	0.241467380352534	2		304	505	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149794	202149794	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	90	356	0	ENST00000358485.4:c.1235A>G	p.Lys412Arg	p.K412R	ENST00000358485	NM_001080125.1	412	aAa/aGa	8/9	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.241467380352534	2		356	646	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395927	395927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	25	319	0	ENST00000380956.4:c.484C>T	p.Pro162Ser	p.P162S	ENST00000380956	NM_001195286.1	162	Cca/Tca	4/9	1	2	FACETS	0.422	0.331	0.526	0.422	0.331	0.526	SUBCLONAL	1	TRUE	1	0.241467380352534	2		319	491	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912276	29912276	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0007574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	64	218	0	ENST00000376809.5:c.896-1G>C		p.X299_splice	ENST00000376809	NM_002116.7	299			1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.241467380352534	2		218	447	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270496	98270496	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	102	303	0	ENST00000331920.6:c.148C>A	p.Leu50Met	p.L50M	ENST00000331920	NM_000264.3	50	Ctg/Atg	1/24	1	2	FACETS	0.895	0.804	0.99	1	0.986	1	CLONAL	2	TRUE	1	0.241467380352534	2		303	472	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907297	32907297	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	49	376	0	ENST00000380152.3:c.1682G>T	p.Gly561Val	p.G561V	ENST00000380152		561	gGa/gTa	10/27	0.241467380352534	1	FACETS	0.596	0.504	0.697	0.596	0.504	0.697	SUBCLONAL	1	TRUE	0	0.241467380352534	1		376	599	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185238	123185238	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	59	413	0	ENST00000218089.9:c.1190T>A	p.Val397Asp	p.V397D	ENST00000218089	NM_001042749.1	397	gTt/gAt	13/35	1	2	FACETS	0.584	0.501	0.675	0.584	0.501	0.675	SUBCLONAL	1	TRUE	1	0.241467380352534	2		413	837	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333991	70333993	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	rs903550402	NA	P-0007574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	45	204	0	ENST00000373644.4:c.1902_1904del	p.Val635del	p.V635del	ENST00000373644	NM_030625.2	632	tcTGTt/tct	2/12	1	2	FACETS	0.971	0.818	1	0.971	0.818	1	CLONAL	1	TRUE	1	0.241467380352534	2		204	384	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183728	10183729	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0008592-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	48	815	0	ENST00000256474.2:c.197_198insA	p.Asn67GlufsTer65	p.N67Efs*65	ENST00000256474	NM_000551.3	66	gtg/gtAg	1/3	1	2	FACETS	0.671	0.566	0.789	0.671	0.566	0.789	SUBCLONAL	1	TRUE	1	0.17	2		815	841	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0009346-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1663	434	121	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.721105388273169	10	FACETS	1	0.988	1			1	CLONAL	2	FALSE	NA	0.721105388273169	10		121	2097	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937070	48937093	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	GAACATGAATGTAATATAGATGAG	GAACATGAATGTAATATAGATGAG	-	novel	NA	P-0009346-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	174	49	0	ENST00000267163.4:c.839_861+1del		p.EHECNIDEdel	ENST00000267163	NM_000321.2	280	GAACATGAATGTAATATAGATGAG/-	8/27	0.721105388273169	3	FACETS	0.968	0.925	1			1	CLONAL	3	FALSE	NA	0.721105388273169	3		49	226	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073546	8073547	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0009346-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	292	74	0	ENST00000377482.5:c.1112dup	p.Ser372IlefsTer4	p.S372Ifs*4	ENST00000377482	NM_018948.3	371	gga/ggGa	4/4	0.381056644266056	2	FACETS	1	0.99	1	1	0.99	1	INDETERMINATE	2	FALSE	0	0.721105388273169	2		74	377	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242481	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAA	AATTAAGAGAAGCAA	TCC	novel	NA	P-0009346-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	422	76	1	ENST00000275493.2:c.2237_2251delinsTCC	p.Glu746_Thr751delinsValPro	p.E746_T751delinsVP	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAAca/gTCCca	19/28	0.721105388273169	10	FACETS	0.941	0.9	0.982			1	CLONAL	5	FALSE	NA	0.721105388273169	10		77	966	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249092	55249092	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009346-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1940	228	123	0	ENST00000275493.2:c.2390G>C	p.Cys797Ser	p.C797S	ENST00000275493	NM_005228.3	797	tGc/tCc	20/28	0.721105388273169	10	FACETS	1	0.978	1			1	CLONAL	1	FALSE	NA	0.721105388273169	10		123	2168	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211810	36211810	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009346-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	443	177	0	ENST00000222270.7:c.1561C>G	p.Leu521Val	p.L521V	ENST00000222270	NM_014727.1	521	Ctg/Gtg	3/37	0.680758403126373	4	FACETS	0.955	0.913	0.997	0.955	0.913	0.997	CLONAL	2	FALSE	2	0.721105388273169	4		177	1107	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346878	91346878	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009346-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	126	92	0	ENST00000355112.3:c.3486T>A	p.Asn1162Lys	p.N1162K	ENST00000355112	NM_000057.2	1162	aaT/aaA	18/22	0.148393707364032	5	FACETS	0.838	0.765	0.914			1	INDETERMINATE	2	FALSE	NA	0.721105388273169	5		92	434	SUCCESS
REL	5966	MSKCC	GRCh37	2	61121568	61121568	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009346-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	80	57	0	ENST00000295025.8:c.190A>G	p.Thr64Ala	p.T64A	ENST00000295025	NM_002908.2	64	Aca/Gca	3/11	0.680758403126373	4	FACETS	0.88	0.778	0.988	0.44	0.389	0.494	CLONAL	1	FALSE	2	0.721105388273169	4		57	434	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143043377	143043383	+	frameshift_variant	Frame_Shift_Del	DEL	TCTAGCA	TCTAGCA	-	novel	NA	P-0009346-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	73	57	0	ENST00000262992.4:c.2033_2039del	p.Met678ArgfsTer10	p.M678Rfs*10	ENST00000262992	NM_001101669.1	678	aTGCTAGAg/ag	19/24	0.606822573545453	4	FACETS	0.922	0.811	1	0.461	0.405	0.52	CLONAL	1	FALSE	2	0.721105388273169	4		57	378	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609942	43609942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767407	NA	P-0012439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	65	845	0	ENST00000355710.3:c.1894G>A	p.Glu632Lys	p.E632K	ENST00000355710	NM_020975.4	632	Gag/Aag	11/20	0.220546632576299	5	FACETS	1	0.929	1	0.371	0.321	0.426	CLONAL	1	FALSE	2	0.220546632576299	5		845	704	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209302	133209302	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	110	763	2	ENST00000320574.5:c.6084G>T	p.Arg2028Ser	p.R2028S	ENST00000320574	NM_006231.2	2028	agG/agT	44/49	0.185234430781025	3	FACETS	1	0.975	1	0.831	0.752	0.915	CLONAL	2	FALSE	0	0.220546632576299	3		765	444	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241692	55241692	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	101	611	0	ENST00000275493.2:c.2140A>G	p.Lys714Glu	p.K714E	ENST00000275493	NM_005228.3	714	Aag/Gag	18/28	0.220546632576299	5	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	FALSE	3	0.220546632576299	5		611	572	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0012439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	100	598	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	0.220546632576299	5	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	FALSE	3	0.220546632576299	5		598	553	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044581	47044581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012439-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	44	847	0	ENST00000377604.3:c.2078G>A	p.Gly693Asp	p.G693D	ENST00000377604	NM_001204468.1	693	gGc/gAc	18/24	0.220546632576299	4	FACETS	0.802	0.672	0.947	0.401	0.336	0.474	CLONAL	1	FALSE	2	0.220546632576299	4		847	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs786203436	NA	P-0012674-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	349	1055	0	ENST00000269305.4:c.487T>G	p.Tyr163Asp	p.Y163D	ENST00000269305	NM_001126112.2	163	Tac/Gac	5/11	0.83854140058052	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.83122738911418	3		1055	374	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495315	212495315	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012674-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	77	414	0	ENST00000342788.4:c.1951C>G	p.Pro651Ala	p.P651A	ENST00000342788	NM_005235.2	651	Ccc/Gcc	17/28	0.83854140058052	2	FACETS	0.813	0.725	0.903	0.406	0.362	0.452	CLONAL	1	TRUE	0	0.83122738911418	2		414	228	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753187	128753193	+	frameshift_variant	Frame_Shift_Del	DEL	CGGAACT	CGGAACT	-	novel	NA	P-0012674-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	102	283	0	ENST00000377970.2:c.1349_1355del	p.Arg450LeufsTer7	p.R450Lfs*7	ENST00000377970	NM_002467.4	450	CGGAACTct/ct	3/3	0.83122738911418	11	FACETS	0.82	0.734	0.912			1	CLONAL	2	TRUE	NA	0.83122738911418	11		283	709	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023105	48023116	+	inframe_deletion	In_Frame_Del	DEL	AACGTGCAGATG	AACGTGCAGATG	-	novel	NA	P-0012674-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	91	373	0	ENST00000234420.5:c.532_543del	p.Arg178_Glu181del	p.R178_E181del	ENST00000234420	NM_000179.2	177	cAACGTGCAGATGaa/caa	3/10	0.279838330329293	3	FACETS	0.871	0.795	0.946	0.871	0.795	0.946	INDETERMINATE	2	TRUE	1	0.83122738911418	3		373	178	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450401	50450401	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012674-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	192	548	1	ENST00000331340.3:c.585C>A	p.His195Gln	p.H195Q	ENST00000331340	NM_006060.4	195	caC/caA	5/8	0.83854140058052	5	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.83122738911418	5		549	794	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711275	114711275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012674-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	34	452	0	ENST00000543371.1:c.290G>A	p.Gly97Glu	p.G97E	ENST00000543371	NM_001198531.1	97	gGg/gAg	3/14	0.83854140058052	3	FACETS	0.541	0.446	0.647	0.18	0.148	0.216	SUBCLONAL	1	TRUE	0	0.83122738911418	3		452	214	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756763	756763	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012674-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	106	520	3	ENST00000314574.4:c.65C>A	p.Pro22Gln	p.P22Q	ENST00000314574	NM_005433.3	22	cCa/cAa	2/12	0.776452027197264	6	FACETS	0.899	0.806	0.998	0.3	0.268	0.333	CLONAL	1	TRUE	3	0.83122738911418	6		523	755	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728899	190728899	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012674-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	60	294	0	ENST00000441310.2:c.2287G>C	p.Glu763Gln	p.E763Q	ENST00000441310	NM_000534.4	763	Gag/Cag	10/13	0.83854140058052	2	FACETS	0.914	0.806	1	0.457	0.403	0.513	CLONAL	1	TRUE	0	0.83122738911418	2		294	158	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189400	56189400	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012674-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	110	589	0	ENST00000399503.3:c.4432T>G	p.Ser1478Ala	p.S1478A	ENST00000399503	NM_005921.1	1478	Tct/Gct	20/20	0.83854140058052	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.83122738911418	1		589	128	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982029	93982029	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012674-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	101	348	0	ENST00000369303.4:c.1436A>C	p.Lys479Thr	p.K479T	ENST00000369303	NM_004440.3	479	aAg/aCg	6/17	0.83854140058052	3	FACETS	0.991	0.895	1	0.496	0.447	0.546	CLONAL	1	TRUE	1	0.83122738911418	3		348	347	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860434	151860461	+	frameshift_variant	Frame_Shift_Del	DEL	TCTCTTGCTGTTCTCGTAAACGTTCCTT	TCTCTTGCTGTTCTCGTAAACGTTCCTT	-	novel	NA	P-0012674-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	61	601	0	ENST00000262189.6:c.10201_10228del	p.Lys3401AspfsTer10	p.K3401Dfs*10	ENST00000262189	NM_170606.2	3401	AAGGAACGTTTACGAGAACAGCAAGAGAga/ga	43/59	0.537030916835961	6	FACETS	0.851	0.736	0.976	0.284	0.245	0.326	CLONAL	1	TRUE	3	0.83122738911418	6		601	459	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751004	128751004	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772094171	NA	P-0012674-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	129	596	0	ENST00000377970.2:c.541C>T	p.Arg181Cys	p.R181C	ENST00000377970	NM_002467.4	181	Cgc/Tgc	2/3	0.83122738911418	11	FACETS	1	0.956	1			1	CLONAL	1	TRUE	NA	0.83122738911418	11		596	1336	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012705-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	20	427	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		427	359	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0012705-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	21	232	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		233	274	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645683	12645683	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs397516829	NA	P-0012705-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	27	272	0	ENST00000251849.4:c.786T>A	p.Asn262Lys	p.N262K	ENST00000251849	NM_002880.3	262	aaT/aaA	7/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		272	304	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430361	78430361	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012705-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	26	430	0	ENST00000370768.2:c.807del	p.Ser270GlnfsTer3	p.S270Qfs*3	ENST00000370768	NM_003902.3	269	ggG/gg	10/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		430	470	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0013550-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	49	572	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.289346966506748	3	FACETS	0.881	0.755	1	0.881	0.755	1	CLONAL	2	TRUE	1	0.289346966506748	3		572	220	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0013550-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	48	321	1	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	0.128205984365015	3	FACETS	1	0.928	1	0.581	0.493	0.676	INDETERMINATE	1	TRUE	1	0.289346966506748	3		322	327	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259477	89259477	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200567888	NA	P-0013550-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	42	378	0	ENST00000336596.2:c.621G>T	p.Lys207Asn	p.K207N	ENST00000336596	NM_005233.5	207	aaG/aaT	3/17	0.18424795820124	1	FACETS	0.728	0.61	0.859	0.728	0.61	0.859	SUBCLONAL	1	TRUE	0	0.289346966506748	1		378	341	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259236	89259236	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013550-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	35	330	0	ENST00000336596.2:c.380C>G	p.Ser127Cys	p.S127C	ENST00000336596	NM_005233.5	127	tCt/tGt	3/17	0.18424795820124	1	FACETS	0.802	0.661	0.959	0.802	0.661	0.959	CLONAL	1	TRUE	0	0.289346966506748	1		330	258	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462400	89462400	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1162005172	NA	P-0013550-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	26	483	0	ENST00000336596.2:c.1872T>A	p.Asp624Glu	p.D624E	ENST00000336596	NM_005233.5	624	gaT/gaA	10/17	0.18424795820124	1	FACETS	0.557	0.442	0.688	0.557	0.442	0.688	SUBCLONAL	1	TRUE	0	0.289346966506748	1		483	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0013713-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	451	803	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	0.888	0.852	0.925			1	INDETERMINATE	2	TRUE	NA	0.533191652479844	2		803	952	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0013713-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	6175	552	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.533191652479844	30	FACETS	1	0.998	1			1	CLONAL	28	TRUE	NA	0.533191652479844	30		552	6938	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46215271	46215271	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0013713-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	147	146	0	ENST00000334344.6:c.705+1G>T		p.X235_splice	ENST00000334344	NM_152641.2	235			0.513776036409016	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	4	TRUE	0	0.533191652479844	4		146	194	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791695	42791695	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0013713-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	387	494	0	ENST00000575354.2:c.583-2A>T		p.X195_splice	ENST00000575354	NM_015125.3	195			0.490858674757753	4	FACETS	0.868	0.825	0.912	0.868	0.825	0.912	CLONAL	2	TRUE	2	0.533191652479844	4		494	1282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs530941076	NA	P-0015027-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	428	697	0	ENST00000269305.4:c.658T>C	p.Tyr220His	p.Y220H	ENST00000269305	NM_001126112.2	220	Tat/Cat	6/11	0.733795587980976	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.733795587980976	1		697	581	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163309245	163309245	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs891356338	NA	P-0015027-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	155	334	0	ENST00000271452.3:c.584A>G	p.Asn195Ser	p.N195S	ENST00000271452	NM_145697.2	195	aAt/aGt	8/14	0.733795587980976	3	FACETS	1	0.952	1	0.523	0.481	0.566	CLONAL	1	TRUE	1	0.733795587980976	3		334	552	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996254	73996254	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs769691860	NA	P-0015027-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	70	155	0	ENST00000318443.5:c.988G>T	p.Val330Leu	p.V330L	ENST00000318443	NM_001024736.1	330	Gtg/Ttg	5/10	1	2	FACETS	0.959	0.852	1	0.959	0.852	1	CLONAL	1	TRUE	1	0.733795587980976	2		155	199	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0015489-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	135	409	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA	2	FACETS	0.901	0.824	0.98			1	INDETERMINATE	1	TRUE	NA	0.615360108208632	2		410	487	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0015489-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	153	362	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.615360108208632	2		362	482	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047034	128047034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1249110579	NA	P-0015489-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	217	570	1	ENST00000285398.2:c.701G>A	p.Arg234Gln	p.R234Q	ENST00000285398	NM_000122.1	234	cGa/cAa	6/15	1	2	FACETS	0.942	0.879	1	0.942	0.879	1	CLONAL	1	TRUE	1	0.615360108208632	2		571	749	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308353	30308353	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015489-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	190	552	0	ENST00000262643.3:c.367A>G	p.Lys123Glu	p.K123E	ENST00000262643	NM_001238.2	123	Aag/Gag	6/12	1	2	FACETS	0.904	0.839	0.971	0.904	0.839	0.971	CLONAL	1	TRUE	1	0.615360108208632	2		552	683	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221996	1221996	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs376280361	NA	P-0015489-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	251	646	0	ENST00000326873.7:c.911G>C	p.Arg304Pro	p.R304P	ENST00000326873	NM_000455.4	304	cGg/cCg	7/10	0.615360108208632	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.615360108208632	1		646	515	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812477	43812477	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015489-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	190	493	0	ENST00000372470.3:c.1180C>G	p.Pro394Ala	p.P394A	ENST00000372470	NM_005373.2	394	Cca/Gca	8/12	0.597715917399696	3	FACETS	0.953	0.882	1	0.477	0.441	0.514	CLONAL	1	TRUE	1	0.615360108208632	3		493	847	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256048	123256048	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0015489-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	172	463	0	ENST00000358487.5:c.1861A>T	p.Lys621Ter	p.K621*	ENST00000358487	NM_000141.4	621	Aaa/Taa	13/18	1	2	FACETS	0.927	0.857	0.999	0.927	0.857	0.999	CLONAL	1	TRUE	1	0.615360108208632	2		463	603	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279603	123279603	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015489-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	253	620	0	ENST00000358487.5:c.829G>T	p.Val277Phe	p.V277F	ENST00000358487	NM_000141.4	277	Gtc/Ttc	7/18	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.615360108208632	2		620	773	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524625	103524625	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015489-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	131	296	0	ENST00000355739.4:c.2756G>T	p.Arg919Leu	p.R919L	ENST00000355739	NM_000123.3	919	cGg/cTg	13/15	0.615360108208632	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.615360108208632	1		296	293	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018107	48018107	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015489-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	268	617	0	ENST00000234420.5:c.302A>T	p.Glu101Val	p.E101V	ENST00000234420	NM_000179.2	101	gAg/gTg	2/10	1	2	FACETS	0.975	0.917	1	0.975	0.917	1	CLONAL	1	TRUE	1	0.615360108208632	2		617	893	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271225	26271225	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015489-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	179	464	0	ENST00000305910.3:c.388C>A	p.Arg130Ser	p.R130S	ENST00000305910	NM_003534.2	130	Cgc/Agc	1/1	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.615360108208632	2		464	580	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74868211	74868211	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015489-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1635	135	215	0	ENST00000284811.8:c.83A>C	p.Glu28Ala	p.E28A	ENST00000284811		28	gAa/gCa	3/4	0.615360108208632	13	FACETS	1	0.953	1			1	CLONAL	1	TRUE	NA	0.615360108208632	13		215	1770	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400076	139400076	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015489-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	285	796	0	ENST00000277541.6:c.4272G>T	p.Leu1424Phe	p.L1424F	ENST00000277541	NM_017617.3	1424	ttG/ttT	25/34	1	2	FACETS	0.967	0.911	1	0.967	0.911	1	CLONAL	1	TRUE	1	0.615360108208632	2		796	958	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0017367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	90	325	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.48819892213315	2	FACETS	0.91	0.813	1	0.455	0.406	0.507	CLONAL	1	TRUE	0	0.48819892213315	2		325	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0017367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	346	649	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.356662744146456	3	FACETS	1	0.992	1	0.79	0.753	0.827	CLONAL	2	TRUE	0	0.48819892213315	3		649	744	SUCCESS
APC	324	MSKCC	GRCh37	5	112174152	112174152	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0017367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	67	237	0	ENST00000257430.4:c.2861T>A	p.Leu954Ter	p.L954*	ENST00000257430	NM_000038.5	954	tTa/tAa	16/16	1	2	FACETS	0.888	0.778	1	0.888	0.778	1	CLONAL	1	TRUE	1	0.48819892213315	2		237	309	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0017367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	83	232	0	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.48819892213315	2		232	330	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339071	225339071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017367-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	52	249	0	ENST00000264414.4:c.2198G>A	p.Arg733Gln	p.R733Q	ENST00000264414	NM_003590.4	733	cGa/cAa	16/16	0.48819892213315	3	FACETS	0.642	0.548	0.744	0.321	0.274	0.372	SUBCLONAL	1	TRUE	1	0.48819892213315	3		249	413	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0017604-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	177	363	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.54763679382671	4	FACETS	0.842	0.78	0.906	0.842	0.78	0.906	CLONAL	2	TRUE	2	0.54763679382671	4		363	594	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0017604-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	351	109	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.54763679382671	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	1	0.54763679382671	4		109	613	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017604-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	180	525	0	ENST00000206249.3:c.1607T>A	p.Leu536His	p.L536H	ENST00000206249	NM_000125.3	536	cTc/cAc	8/8	0.54763679382671	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.54763679382671	1		525	447	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968878	32968878	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017604-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	81	271	0	ENST00000380152.3:c.9311del	p.Lys3104SerfsTer4	p.K3104Sfs*4	ENST00000380152		3103	atA/at	25/27	1	2	FACETS	0.845	0.75	0.945	0.845	0.75	0.945	CLONAL	1	TRUE	1	0.54763679382671	2		271	350	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932666	39932666	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017604-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	234	853	0	ENST00000378444.4:c.1933G>C	p.Ala645Pro	p.A645P	ENST00000378444	NM_001123385.1	645	Gca/Cca	4/15	0.54763679382671	1	FACETS	0.911	0.855	0.969	0.911	0.855	0.969	CLONAL	1	TRUE	0	0.54763679382671	1		853	681	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957132	81957132	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1567534502	NA	P-0017604-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	182	472	0	ENST00000359376.3:c.2350C>T	p.Arg784Ter	p.R784*	ENST00000359376	NM_002661.3	784	Cga/Tga	22/33	0.54763679382671	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.54763679382671	1		472	418	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812272	43812272	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1441446586	NA	P-0017604-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	181	486	0	ENST00000372470.3:c.1139del	p.Gly380AlafsTer116	p.G380Afs*116	ENST00000372470	NM_005373.2	379	ctG/ct	7/12	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.54763679382671	2		486	593	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14303168	14303179	+	inframe_deletion	In_Frame_Del	DEL	ATGGAAAGCTTG	ATGGAAAGCTTG	-	novel	NA	P-0017604-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	132	374	0	ENST00000256196.4:c.496_507del	p.Gln166_His169del	p.Q166_H169del	ENST00000256196		166	CAAGCTTTCCAT/-	5/6	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.54763679382671	2		374	466	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409164	4409164	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017604-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	224	368	0	ENST00000261254.3:c.859A>G	p.Ile287Val	p.I287V	ENST00000261254	NM_001759.3	287	Atc/Gtc	5/5	0.54763679382671	4	FACETS	0.878	0.821	0.936	0.878	0.821	0.936	CLONAL	2	TRUE	2	0.54763679382671	4		368	721	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870825	12870838	+	frameshift_variant	Frame_Shift_Del	DEL	GCCAGGCAGGCGGA	GCCAGGCAGGCGGA	-	novel	NA	P-0017604-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	137	205	0	ENST00000228872.4:c.54_67del	p.Arg19ProfsTer101	p.R19Pfs*101	ENST00000228872	NM_004064.3	18	GCCAGGCAGGCGGAg/g	1/3	0.54763679382671	4	FACETS	0.937	0.861	1	0.937	0.861	1	CLONAL	2	TRUE	2	0.54763679382671	4		205	413	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0020566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	250	774	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.658450005792223	4	FACETS	1	0.992	1	0.863	0.827	0.897	CLONAL	3	FALSE	0	0.713442725819868	4		774	348	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0020566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	176	589	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.713442725819868	4	FACETS	0.839	0.787	0.89	0.839	0.787	0.89	CLONAL	3	FALSE	1	0.713442725819868	4		589	336	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0020566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	47	109	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.690317904816232	5	FACETS	0.909	0.831	0.977	1	0.965	1	CLONAL	5	FALSE	1	0.713442725819868	5		109	60	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167804	56167805	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0020566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	232	471	0	ENST00000399503.3:c.1370_1371del	p.Thr457SerfsTer3	p.T457Sfs*3	ENST00000399503	NM_005921.1	457	ACa/a	7/20	0.713442725819868	8	FACETS	1	0.987	1	1	0.987	1	CLONAL	7	FALSE	1	0.713442725819868	8		471	279	SUCCESS
YES1	7525	MSKCC	GRCh37	18	739800	739800	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	20	387	0	ENST00000314574.4:c.1072G>A	p.Asp358Asn	p.D358N	ENST00000314574	NM_005433.3	358	Gat/Aat	9/12	0.679822770598411	3	FACETS	0.963	0.755	1	0.481	0.377	0.597	CLONAL	1	FALSE	1	0.713442725819868	3		387	79	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0020820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	87	512	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	0.584738899106977	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.584738899106977	1		512	170	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0020820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	68	509	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.287539084988942	4	FACETS	0.912	0.808	1	0.912	0.808	1	INDETERMINATE	2	TRUE	2	0.584738899106977	4		509	202	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	75	868	2	ENST00000326873.7:c.667G>T	p.Glu223Ter	p.E223*	ENST00000326873	NM_000455.4	223	Gag/Tag	5/10	0.584738899106977	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.584738899106977	1		870	143	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782144	NA	P-0020820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	100	904	0	ENST00000269305.4:c.473G>C	p.Arg158Pro	p.R158P	ENST00000269305	NM_001126112.2	158	cGc/cCc	5/11	0.584738899106977	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.584738899106977	1		904	194	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602763	10602763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774469695	NA	P-0020820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	83	1005	1	ENST00000171111.5:c.815G>A	p.Arg272His	p.R272H	ENST00000171111	NM_203500.1	272	cGc/cAc	3/6	0.584738899106977	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.584738899106977	1		1006	178	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097782	27097782	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	96	427	0	ENST00000324856.7:c.3371A>T	p.Lys1124Met	p.K1124M	ENST00000324856	NM_006015.4	1124	aAg/aTg	12/20	0.584738899106977	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.584738899106977	1		427	181	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120460387	120460387	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0020820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	68	401	0	ENST00000256646.2:c.5930-2A>T		p.X1977_splice	ENST00000256646	NM_024408.3	1977			0.584738899106977	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.584738899106977	1		401	125	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999347	100999347	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	60	972	1	ENST00000325455.5:c.455C>A	p.Pro152Gln	p.P152Q	ENST00000325455	NM_001202474.3	152	cCg/cAg	1/8	0.584738899106977	1	FACETS	0.975	0.861	1	0.975	0.861	1	CLONAL	1	TRUE	0	0.584738899106977	1		973	149	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499689	18499689	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	26	419	0	ENST00000266497.5:c.1544C>G	p.Ser515Cys	p.S515C	ENST00000266497		515	tCc/tGc	10/31	0.229182291961072	3	FACETS	0.618	0.493	0.758	0.309	0.246	0.379	INDETERMINATE	1	TRUE	1	0.584738899106977	3		419	186	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434067	49434067	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	70	788	1	ENST00000301067.7:c.7486G>T	p.Ala2496Ser	p.A2496S	ENST00000301067	NM_003482.3	2496	Gca/Tca	31/54	0.287539084988942	4	FACETS	0.912	0.809	1	0.912	0.809	1	INDETERMINATE	2	TRUE	2	0.584738899106977	4		789	208	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446430	49446430	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	81	637	0	ENST00000301067.7:c.1175G>T	p.Cys392Phe	p.C392F	ENST00000301067	NM_003482.3	392	tGc/tTc	9/54	0.287539084988942	4	FACETS	1	0.903	1	1	0.903	1	INDETERMINATE	2	TRUE	2	0.584738899106977	4		637	218	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479833	67479833	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	57	580	0	ENST00000327367.4:c.1140G>T	p.Trp380Cys	p.W380C	ENST00000327367	NM_005902.3	380	tgG/tgT	8/9	0.283636310184008	1	FACETS	0.683	0.595	0.776	0.683	0.595	0.776	INDETERMINATE	1	TRUE	0	0.584738899106977	1		580	202	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251761	212251761	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	52	372	0	ENST00000342788.4:c.3298G>T	p.Glu1100Ter	p.E1100*	ENST00000342788	NM_005235.2	1100	Gag/Tag	27/28	0.268146495767518	3	FACETS	0.995	0.857	1	0.498	0.428	0.572	INDETERMINATE	1	TRUE	1	0.584738899106977	3		372	231	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750473	41750473	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	33	563	0	ENST00000226382.2:c.155G>C	p.Gly52Ala	p.G52A	ENST00000226382	NM_003924.3	52	gGg/gCg	1/3	0.158079500205125	2	FACETS	0.537	0.441	0.644	0.269	0.22	0.322	INDETERMINATE	1	TRUE	0	0.584738899106977	2		563	210	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038562	47038562	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	90	855	0	ENST00000377604.3:c.724G>T	p.Glu242Ter	p.E242*	ENST00000377604	NM_001204468.1	242	Gag/Tag	8/24	0.584738899106977	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.584738899106977	1		855	175	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938611	76938611	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	18	484	0	ENST00000373344.5:c.2137C>A	p.Pro713Thr	p.P713T	ENST00000373344	NM_000489.3	713	Cct/Act	9/35	0.283636310184008	1	FACETS	0.272	0.206	0.349	0.272	0.206	0.349	INDETERMINATE	1	TRUE	0	0.584738899106977	1		484	160	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200032	123200032	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	18	252	0	ENST00000218089.9:c.2104G>C	p.Asp702His	p.D702H	ENST00000218089	NM_001042749.1	702	Gac/Cac	22/35	0.283636310184008	1	FACETS	0.419	0.32	0.532	0.419	0.32	0.532	INDETERMINATE	1	TRUE	0	0.584738899106977	1		252	104	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933371	39933371	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020820-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	41	830	0	ENST00000378444.4:c.1228G>C	p.Ala410Pro	p.A410P	ENST00000378444	NM_001123385.1	410	Gcc/Ccc	4/15	0.584738899106977	1	FACETS	0.539	0.455	0.63	0.539	0.455	0.63	SUBCLONAL	1	TRUE	0	0.584738899106977	1		830	184	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715389	117715389	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	83	224	0	ENST00000368508.3:c.1100G>A	p.Gly367Glu	p.G367E	ENST00000368508	NM_002944.2	367	gGa/gAa	10/43	0.749528897293476	1	FACETS	0.523	0.467	0.58	0.523	0.467	0.58	SUBCLONAL	1	TRUE	0	0.749528897293476	1		224	265	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	156	427	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.749528897293476	2		427	412	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	130	199	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	0.567721086956725	3	FACETS	1	0.915	1	0.501	0.457	0.546	CLONAL	1	TRUE	1	0.749528897293476	3		199	476	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310896	123310896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs974173968	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	106	386	0	ENST00000358487.5:c.532C>T	p.Arg178Cys	p.R178C	ENST00000358487	NM_000141.4	178	Cgc/Tgc	5/18	0.401640544597909	1	FACETS	0.368	0.332	0.407	0.368	0.332	0.407	INDETERMINATE	1	TRUE	0	0.749528897293476	1		386	480	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	162	306	0	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	0.265055310111436	3	FACETS	0.99	0.913	1	0.495	0.456	0.535	INDETERMINATE	1	TRUE	1	0.749528897293476	3		306	600	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	86	172	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	0.345441927800824	1	FACETS	0.455	0.407	0.506	0.455	0.407	0.506	INDETERMINATE	1	TRUE	0	0.749528897293476	1		172	315	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341925	8341925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	62	280	0	ENST00000356435.5:c.4715G>A	p.Arg1572Lys	p.R1572K	ENST00000356435		1572	aGa/aAa	29/35	0.375608704646058	1	FACETS	0.321	0.279	0.366	0.321	0.279	0.366	INDETERMINATE	1	TRUE	0	0.749528897293476	1		280	322	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929432	81929432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775728338	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	75	379	0	ENST00000359376.3:c.1093G>A	p.Asp365Asn	p.D365N	ENST00000359376	NM_002661.3	365	Gat/Aat	13/33	0.375608704646058	1	FACETS	0.31	0.272	0.349	0.31	0.272	0.349	INDETERMINATE	1	TRUE	0	0.749528897293476	1		379	404	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556852	29556852	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	159	192	0	ENST00000356175.3:c.2851-1G>A		p.X951_splice	ENST00000356175	NM_000267.3	951			0.345441927800824	1	FACETS	0.767	0.714	0.82	0.767	0.714	0.82	INDETERMINATE	1	TRUE	0	0.749528897293476	1		192	346	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560970	9560970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781706438	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	95	336	0	ENST00000353224.5:c.812C>T	p.Ser271Leu	p.S271L	ENST00000353224	NM_177990.2	271	tCg/tTg	4/10	1	2	FACETS	0.538	0.481	0.598	0.538	0.481	0.598	SUBCLONAL	1	TRUE	1	0.749528897293476	2		336	471	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420082	41420082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	125	241	0	ENST00000373198.4:c.239C>T	p.Ser80Phe	p.S80F	ENST00000373198	NM_133170.3	80	tCt/tTt	3/32	1	2	FACETS	0.999	0.916	1	0.999	0.916	1	CLONAL	1	TRUE	1	0.749528897293476	2		241	334	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923328	9923328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	106	388	0	ENST00000330684.3:c.1959G>A	p.Met653Ile	p.M653I	ENST00000330684	NM_001134407.1	653	atG/atA	9/13	0.375608704646058	1	FACETS	0.368	0.331	0.406	0.368	0.331	0.406	INDETERMINATE	1	TRUE	0	0.749528897293476	1		388	481	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858394	9858394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	76	333	0	ENST00000330684.3:c.3007G>A	p.Glu1003Lys	p.E1003K	ENST00000330684	NM_001134407.1	1003	Gaa/Aaa	13/13	0.375608704646058	1	FACETS	0.369	0.325	0.414	0.369	0.325	0.414	INDETERMINATE	1	TRUE	0	0.749528897293476	1		333	344	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631183	69631183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	99	322	0	ENST00000334134.2:c.229G>A	p.Glu77Lys	p.E77K	ENST00000334134	NM_005247.2	77	Gag/Aag	2/3	0.265055310111436	3	FACETS	0.643	0.575	0.714	0.321	0.287	0.357	INDETERMINATE	1	TRUE	1	0.749528897293476	3		322	565	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244973	123244973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	125	471	0	ENST00000358487.5:c.2131G>A	p.Glu711Lys	p.E711K	ENST00000358487	NM_000141.4	711	Gaa/Aaa	16/18	0.401640544597909	1	FACETS	0.377	0.342	0.413	0.377	0.342	0.413	INDETERMINATE	1	TRUE	0	0.749528897293476	1		471	553	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435313	18435313	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	132	226	0	ENST00000266497.5:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000266497		100	Caa/Taa	1/31	1	2	FACETS	0.924	0.848	1	0.924	0.848	1	CLONAL	1	TRUE	1	0.749528897293476	2		226	381	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691122	18691122	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	88	250	0	ENST00000266497.5:c.3233T>G	p.Met1078Arg	p.M1078R	ENST00000266497		1078	aTg/aGg	23/31	1	2	FACETS	0.502	0.446	0.561	0.502	0.446	0.561	SUBCLONAL	1	TRUE	1	0.749528897293476	2		250	468	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556190	29556190	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	40	118	0	ENST00000356175.3:c.2557C>T	p.Gln853Ter	p.Q853*	ENST00000356175	NM_000267.3	853	Cag/Tag	21/57	0.345441927800824	1	FACETS	0.454	0.384	0.529	0.454	0.384	0.529	INDETERMINATE	1	TRUE	0	0.749528897293476	1		118	147	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533887	63533887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376630432	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	84	352	0	ENST00000307078.5:c.1267C>T	p.Leu423Phe	p.L423F	ENST00000307078	NM_004655.3	423	Ctc/Ttc	6/11	0.345441927800824	1	FACETS	0.321	0.284	0.359	0.321	0.284	0.359	INDETERMINATE	1	TRUE	0	0.749528897293476	1		352	437	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743053	743053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	278	424	0	ENST00000314574.4:c.925C>T	p.Pro309Ser	p.P309S	ENST00000314574	NM_005433.3	309	Cca/Tca	8/12	1	2	FACETS	0.975	0.92	1	0.975	0.92	1	CLONAL	1	TRUE	1	0.749528897293476	2		424	761	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756559	756559	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	147	264	0	ENST00000314574.4:c.269C>T	p.Thr90Ile	p.T90I	ENST00000314574	NM_005433.3	90	aCa/aTa	2/12	1	2	FACETS	0.988	0.912	1	0.988	0.912	1	CLONAL	1	TRUE	1	0.749528897293476	2		264	397	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223009	5223009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	263	437	0	ENST00000357368.4:c.2794C>T	p.Pro932Ser	p.P932S	ENST00000357368	NM_002850.3	932	Ccg/Tcg	18/38	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.749528897293476	2		437	696	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257451	19257451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	191	975	0	ENST00000162023.5:c.682C>T	p.Leu228Phe	p.L228F	ENST00000162023		228	Ctc/Ttc	11/13	1	2	FACETS	0.535	0.495	0.577	0.535	0.495	0.577	SUBCLONAL	1	TRUE	1	0.749528897293476	2		975	952	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213971	36213971	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	177	641	0	ENST00000222270.7:c.2797G>T	p.Gly933Trp	p.G933W	ENST00000222270	NM_014727.1	933	Ggg/Tgg	6/37	1	2	FACETS	0.513	0.473	0.556	0.513	0.473	0.556	SUBCLONAL	1	TRUE	1	0.749528897293476	2		641	920	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743906	41743906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	152	642	0	ENST00000301178.4:c.841G>A	p.Glu281Lys	p.E281K	ENST00000301178	NM_021913.4	281	Gag/Aag	7/20	1	2	FACETS	0.478	0.437	0.521	0.478	0.437	0.521	SUBCLONAL	1	TRUE	1	0.749528897293476	2		642	848	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793162	42793162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	133	534	0	ENST00000575354.2:c.1054C>T	p.Pro352Ser	p.P352S	ENST00000575354	NM_015125.3	352	Ccc/Tcc	7/20	1	2	FACETS	0.427	0.388	0.469	0.427	0.388	0.469	SUBCLONAL	1	TRUE	1	0.749528897293476	2		534	831	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460345	149460345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	175	318	0	ENST00000286301.3:c.292C>T	p.His98Tyr	p.H98Y	ENST00000286301	NM_005211.3	98	Cac/Tac	3/22	0.401640544597909	1	FACETS	0.8	0.748	0.852	0.8	0.748	0.852	INDETERMINATE	1	TRUE	0	0.749528897293476	1		318	365	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642486	117642486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	305	492	0	ENST00000368508.3:c.5713G>A	p.Glu1905Lys	p.E1905K	ENST00000368508	NM_002944.2	1905	Gag/Aag	35/43	0.749528897293476	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.749528897293476	1		492	483	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345809	152345809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	87	318	0	ENST00000359321.1:c.761C>T	p.Ser254Leu	p.S254L	ENST00000359321	NM_005431.1	254	tCa/tTa	3/3	0.567721086956725	3	FACETS	0.549	0.487	0.616	0.275	0.243	0.308	SUBCLONAL	1	TRUE	1	0.749528897293476	3		318	581	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486155	8486155	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	78	308	0	ENST00000356435.5:c.2662G>A	p.Gly888Arg	p.G888R	ENST00000356435		888	Gga/Aga	17/35	0.375608704646058	1	FACETS	0.322	0.284	0.362	0.322	0.284	0.362	INDETERMINATE	1	TRUE	0	0.749528897293476	1		308	404	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626629	100626629	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	174	129	0	ENST00000308731.7:c.301C>T	p.Pro101Ser	p.P101S	ENST00000308731	NM_000061.2	101	Ccc/Tcc	4/19	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.749528897293476	1		129	246	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117874083	117874094	+	frameshift_variant	Frame_Shift_Del	DEL	AAGTCAGGCAGT	AAGTCAGGCAGT	G	novel	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	112	199	0	ENST00000297338.2:c.360_371delinsC	p.Leu121ArgfsTer2	p.L121Rfs*2	ENST00000297338	NM_006265.2	120	ccACTGCCTGACTTa/ccCa	4/14	1	2	FACETS	0.864	0.786	0.944	0.864	0.786	0.944	CLONAL	1	TRUE	1	0.749528897293476	2		199	346	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797951	45797951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769237459	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	140	445	1	ENST00000450313.1:c.820C>T	p.Arg274Trp	p.R274W	ENST00000450313	NM_012222.2	274	Cgg/Tgg	10/16	0.375608704646058	1	FACETS	0.38	0.347	0.415	0.38	0.347	0.415	INDETERMINATE	1	TRUE	0	0.749528897293476	1		446	614	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939505	68939505	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777220819	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	79	257	0	ENST00000288368.4:c.490G>A	p.Gly164Arg	p.G164R	ENST00000288368	NM_024870.2	164	Gga/Aga	5/40	1	2	FACETS	0.436	0.385	0.492	0.436	0.385	0.492	SUBCLONAL	1	TRUE	1	0.749528897293476	2		257	483	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666693	206666693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782183853	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	149	356	0	ENST00000367120.3:c.2027G>A	p.Arg676Gln	p.R676Q	ENST00000367120	NM_014002.3	676	cGa/cAa	20/22	0.74963093724844	3	FACETS	0.572	0.522	0.624	0.286	0.261	0.312	SUBCLONAL	1	TRUE	1	0.749528897293476	3		356	956	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732890	74732890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs931513044	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	44	88	1	ENST00000359995.5:c.353G>A	p.Arg118Gln	p.R118Q	ENST00000359995	NM_001195427.1	118	cGg/cAg	1/3	0.345441927800824	1	FACETS	0.328	0.277	0.382	0.328	0.277	0.382	INDETERMINATE	1	TRUE	0	0.749528897293476	1		89	224	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622586	158622586	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	96	387	0	ENST00000263640.3:c.913T>G	p.Cys305Gly	p.C305G	ENST00000263640	NM_001105.4	305	Tgc/Ggc	8/11	0.375608704646058	1	FACETS	0.342	0.306	0.38	0.342	0.306	0.38	INDETERMINATE	1	TRUE	0	0.749528897293476	1		387	468	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155373	106155373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	77	332	0	ENST00000380013.4:c.274G>A	p.Gly92Arg	p.G92R	ENST00000380013	NM_001127208.2	92	Gga/Aga	3/11	1	2	FACETS	0.439	0.386	0.495	0.439	0.386	0.495	SUBCLONAL	1	TRUE	1	0.749528897293476	2		332	468	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285684	87285684	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs76318698	NA	P-0021847-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	101	325	0	ENST00000277120.3:c.21G>A	p.Trp7Ter	p.W7*	ENST00000277120		7	tgG/tgA	2/19	0.375608704646058	1	FACETS	0.349	0.313	0.387	0.349	0.313	0.387	INDETERMINATE	1	TRUE	0	0.749528897293476	1		325	483	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163405	47163405	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021937-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	242	179	0	ENST00000409792.3:c.2721del	p.Leu908TrpfsTer5	p.L908Wfs*5	ENST00000409792	NM_014159.6	907	gtT/gt	3/21	0.455234542343099	2	FACETS	0.915	0.862	0.969	0.915	0.862	0.969	CLONAL	2	TRUE	0	0.455234542343099	2		179	581	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0022232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	188	693	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.901	0.834	0.971	0.901	0.834	0.971	CLONAL	1	TRUE	1	0.527399753437083	2		693	791	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592192	55592192	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	147	499	0	ENST00000288135.5:c.1516T>C	p.Phe506Leu	p.F506L	ENST00000288135	NM_000222.2	506	Ttt/Ctt	9/21	1	2	FACETS	0.868	0.795	0.944	0.868	0.795	0.944	CLONAL	1	TRUE	1	0.527399753437083	2		499	642	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552823	106552823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1042709746	NA	P-0022232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	270	694	0	ENST00000369096.4:c.788G>A	p.Gly263Glu	p.G263E	ENST00000369096	NM_001198.3	263	gGa/gAa	5/7	1	2	FACETS	0.971	0.912	1	0.971	0.912	1	CLONAL	1	TRUE	1	0.527399753437083	2		694	1054	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0022232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	552	850	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.527399753437083	5	FACETS	1	0.978	1			1	CLONAL	4	TRUE	NA	0.527399753437083	5		850	925	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032279	10032279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	239	607	0	ENST00000330684.3:c.544G>A	p.Glu182Lys	p.E182K	ENST00000330684	NM_001134407.1	182	Gaa/Aaa	3/13	1	2	FACETS	0.975	0.911	1	0.975	0.911	1	CLONAL	1	TRUE	1	0.527399753437083	2		607	930	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246091330	246091330	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1437168377	NA	P-0022232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	353	413	1	ENST00000388985.4:c.605C>T	p.Ser202Phe	p.S202F	ENST00000388985		202	tCt/tTt	7/12	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	2	TRUE	NA	0.527399753437083	2		414	650	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717633	89717634	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0022232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	156	450	0	ENST00000371953.3:c.659dup	p.Val222GlyfsTer21	p.V222Gfs*21	ENST00000371953	NM_000314.4	220	cta/cTta	7/9	0.527399753437083	1	FACETS	0.917	0.847	0.989	0.917	0.847	0.989	CLONAL	1	TRUE	0	0.527399753437083	1		450	475	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560403	95560404	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0022232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	283	528	2	ENST00000393063.1:c.5185_5186delinsTT	p.Pro1729Leu	p.P1729L	ENST00000393063	NM_030621.3	1729	CCg/TTg	25/28	0.239348953033931	1	FACETS	0.751	0.706	0.797	0.751	0.706	0.797	INDETERMINATE	1	TRUE	0	0.527399753437083	1		530	1052	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40678608	40678608	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	271	611	0	ENST00000249776.8:c.350C>T	p.Ser117Phe	p.S117F	ENST00000249776	NM_033286.3	117	tCc/tTc	3/9	1	2	FACETS	0.996	0.935	1	0.996	0.935	1	CLONAL	1	TRUE	1	0.527399753437083	2		611	1032	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958155	54958155	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	200	580	0	ENST00000312783.6:c.452G>A	p.Arg151Lys	p.R151K	ENST00000312783	NM_198436.1	151	aGa/aAa	6/10	1	2	FACETS	0.895	0.831	0.962	0.895	0.831	0.962	CLONAL	1	TRUE	1	0.527399753437083	2		580	847	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050310	37050310	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	125	422	0	ENST00000231790.2:c.459G>C	p.Glu153Asp	p.E153D	ENST00000231790	NM_000249.3	153	gaG/gaC	6/19	1	2	FACETS	0.985	0.898	1	0.985	0.898	1	CLONAL	1	TRUE	1	0.527399753437083	2		422	481	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953780	55953780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	118	497	0	ENST00000263923.4:c.3656G>A	p.Gly1219Glu	p.G1219E	ENST00000263923	NM_002253.2	1219	gGa/gAa	27/30	1	2	FACETS	0.773	0.699	0.85	0.773	0.699	0.85	SUBCLONAL	1	TRUE	1	0.527399753437083	2		497	579	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981894	70981894	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1292	330	685	0	ENST00000276594.2:c.202C>T	p.Pro68Ser	p.P68S	ENST00000276594	NM_024504.3	68	Ccc/Tcc	2/8	0.524431671196099	4	FACETS	1	0.988	1	0.393	0.37	0.416	CLONAL	1	TRUE	1	0.527399753437083	4		685	1622	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974676	21974676	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0022232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	245	559	0	ENST00000304494.5:c.150+1G>A		p.X50_splice	ENST00000304494	NM_000077.4	50			0.527399753437083	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.527399753437083	1		559	658	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041167	47041167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	331	726	1	ENST00000377604.3:c.1595C>T	p.Pro532Leu	p.P532L	ENST00000377604	NM_001204468.1	532	cCc/cTc	15/24	0.527399753437083	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.527399753437083	1		727	875	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	184	427	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.50580252299332	2		427	650	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0022308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	229	292	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.50580252299332	3	FACETS	0.938	0.88	0.996	0.938	0.88	0.996	CLONAL	2	TRUE	1	0.50580252299332	3		292	605	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765576	41765576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763066660	NA	P-0022308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	210	866	0	ENST00000301178.4:c.2452G>A	p.Glu818Lys	p.E818K	ENST00000301178	NM_021913.4	818	Gaa/Aaa	20/20	1	2	FACETS	0.937	0.871	1	0.937	0.871	1	CLONAL	1	TRUE	1	0.50580252299332	2		866	886	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164529	47164529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301833521	NA	P-0022308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	126	516	0	ENST00000409792.3:c.1597C>T	p.Pro533Ser	p.P533S	ENST00000409792	NM_014159.6	533	Ccc/Tcc	3/21	0.11791618634924	3	FACETS	1	0.976	1	0.607	0.553	0.664	INDETERMINATE	1	TRUE	1	0.50580252299332	3		516	514	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534921	5534921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	185	572	0	ENST00000397747.3:c.232G>A	p.Glu78Lys	p.E78K	ENST00000397747	NM_025239.3	78	Gag/Aag	3/7	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.50580252299332	2		572	729	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88635833	88635833	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1472397694	NA	P-0022308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	192	852	0	ENST00000372037.3:c.58C>T	p.Arg20Cys	p.R20C	ENST00000372037	NM_004329.2	20	Cgt/Tgt	3/13	0.50580252299332	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.50580252299332	1		852	538	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609621	81609621	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	225	688	0	ENST00000298171.2:c.1219C>T	p.Pro407Ser	p.P407S	ENST00000298171	NM_000369.2	407	Ccg/Tcg	10/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.50580252299332	2		688	845	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39772529	39772529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	170	623	1	ENST00000288319.7:c.712C>T	p.Pro238Ser	p.P238S	ENST00000288319	NM_182918.3	238	Cct/Tct	6/10	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.50580252299332	2		624	663	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002840	69002840	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	101	363	0	ENST00000288368.4:c.2140C>T	p.His714Tyr	p.H714Y	ENST00000288368	NM_024870.2	714	Cac/Tac	20/40	0.251602994924533	1	FACETS	0.785	0.708	0.866	0.785	0.708	0.866	INDETERMINATE	1	TRUE	0	0.50580252299332	1		363	380	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812293	212812293	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569995088	NA	P-0022384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	112	629	2	ENST00000342788.4:c.283C>T	p.Arg95Cys	p.R95C	ENST00000342788	NM_005235.2	95	Cgt/Tgt	3/28	1	2	FACETS	0.801	0.727	0.877	0.801	0.727	0.877	CLONAL	1	TRUE	1	0.744030279754881	2		631	376	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0022384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	8	286	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.055	0.035	0.081	0.055	0.035	0.081	SUBCLONAL	1	TRUE	1	0.744030279754881	2		286	390	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0022384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	188	693	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.744030279754881	2		693	498	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0022384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	444	1143	1	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.744030279754881	2	FACETS	0.922	0.893	0.951	0.922	0.893	0.951	CLONAL	2	TRUE	0	0.744030279754881	2		1144	647	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770594	40770594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	195	854	0	ENST00000373198.4:c.2788G>A	p.Glu930Lys	p.E930K	ENST00000373198	NM_133170.3	930	Gaa/Aaa	19/32	1	2	FACETS	0.854	0.795	0.914	0.854	0.795	0.914	CLONAL	1	TRUE	1	0.744030279754881	2		854	614	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156732	20156732	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	190	415	0	ENST00000379607.5:c.25G>C	p.Gly9Arg	p.G9R	ENST00000379607	NM_001412.3	9	Ggt/Cgt	2/7	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.744030279754881	1		415	268	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	220	768	1	ENST00000304494.5:c.143C>T	p.Pro48Leu	p.P48L	ENST00000304494	NM_000077.4	48	cCg/cTg	1/3	0.744030279754881	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.744030279754881	1		769	361	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898732	134898732	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	165	612	0	ENST00000398015.3:c.1790C>T	p.Pro597Leu	p.P597L	ENST00000398015	NM_004441.4	597	cCc/cTc	10/16	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.744030279754881	2		612	433	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253844	153253844	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0022384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	140	682	0	ENST00000281708.4:c.889G>T	p.Glu297Ter	p.E297*	ENST00000281708	NM_033632.3	297	Gaa/Taa	6/12	1	2	FACETS	0.938	0.864	1	0.938	0.864	1	CLONAL	1	TRUE	1	0.744030279754881	2		682	401	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907162	32907162	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs768641298	NA	P-0022384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	148	681	1	ENST00000380152.3:c.1547T>A	p.Phe516Tyr	p.F516Y	ENST00000380152		516	tTc/tAc	10/27	1	2	FACETS	0.968	0.893	1	0.968	0.893	1	CLONAL	1	TRUE	1	0.744030279754881	2		682	411	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519100	103519100	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	247	940	0	ENST00000355739.4:c.2438T>C	p.Ile813Thr	p.I813T	ENST00000355739	NM_000123.3	813	aTc/aCc	11/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.744030279754881	2		940	631	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312675	91312675	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	126	531	0	ENST00000355112.3:c.2414A>G	p.His805Arg	p.H805R	ENST00000355112	NM_000057.2	805	cAt/cGt	12/22	1	2	FACETS	0.973	0.892	1	0.973	0.892	1	CLONAL	1	TRUE	1	0.744030279754881	2		531	348	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346247	89346247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	155	496	3	ENST00000301030.4:c.6703C>T	p.Pro2235Ser	p.P2235S	ENST00000301030	NM_001256183.1	2235	Ccg/Tcg	9/13	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.744030279754881	2		499	365	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244303	153244303	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0022384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	74	335	0	ENST00000281708.4:c.1856-2A>G		p.X619_splice	ENST00000281708	NM_033632.3	619			1	2	FACETS	0.888	0.79	0.99	0.888	0.79	0.99	CLONAL	1	TRUE	1	0.744030279754881	2		335	224	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672488	30672488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	356	1176	1	ENST00000376406.3:c.4472C>T	p.Pro1491Leu	p.P1491L	ENST00000376406	NM_014641.2	1491	cCc/cTc	10/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.744030279754881	2		1177	874	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553422	106553422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1280567332	NA	P-0022384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	108	525	0	ENST00000369096.4:c.1387C>T	p.Pro463Ser	p.P463S	ENST00000369096	NM_001198.3	463	Ccc/Tcc	5/7	1	2	FACETS	0.818	0.741	0.897	0.818	0.741	0.897	CLONAL	1	TRUE	1	0.744030279754881	2		525	355	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500768	8500768	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757479150	NA	P-0022384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	165	619	0	ENST00000356435.5:c.2114G>A	p.Arg705Gln	p.R705Q	ENST00000356435		705	cGa/cAa	13/35	0.744030279754881	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.744030279754881	1		619	277	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27183477	27183477	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	180	838	2	ENST00000380036.4:c.1051A>C	p.Lys351Gln	p.K351Q	ENST00000380036	NM_000459.3	351	Aag/Cag	8/23	0.744030279754881	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.744030279754881	1		840	298	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231215	98231215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750970743	NA	P-0022384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	348	1001	3	ENST00000331920.6:c.2068G>A	p.Val690Ile	p.V690I	ENST00000331920	NM_000264.3	690	Gtc/Atc	14/24	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.744030279754881	2		1004	844	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15821917	15821917	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022384-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	203	339	0	ENST00000307771.7:c.310G>A	p.Glu104Lys	p.E104K	ENST00000307771	NM_005089.3	104	Gag/Aag	4/11	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.744030279754881	1		339	269	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0022396-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	84	346	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.15363222036105	3	FACETS	1	0.955	1	0.767	0.681	0.859	CLONAL	2	FALSE	0	0.184525913895786	3		346	432	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	353	427	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.988	0.939	1	0.988	0.939	1	CLONAL	1	TRUE	1	0.78	2		427	916	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59820400	59820400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	366	586	0	ENST00000259008.2:c.2353C>T	p.Pro785Ser	p.P785S	ENST00000259008	NM_032043.2	785	Cct/Tct	16/20	1	2	FACETS	0.948	0.901	0.995	0.948	0.901	0.995	CLONAL	1	TRUE	1	0.78	2		586	990	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875645	35875645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201449880	NA	P-0022570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	334	565	1	ENST00000303115.3:c.832G>A	p.Asp278Asn	p.D278N	ENST00000303115	NM_002185.3	278	Gat/Aat	7/8	1	2	FACETS	0.875	0.829	0.921	0.875	0.829	0.921	CLONAL	1	TRUE	1	0.78	2		566	979	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692971	89693004	+	frameshift_variant	Frame_Shift_Del	DEL	TAGATTTCTATGGGGAAGTAAGGACCAGAGACAA	TAGATTTCTATGGGGAAGTAAGGACCAGAGACAA	-	novel	NA	P-0022570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	287	561	1	ENST00000371953.3:c.455_488del	p.Leu152GlnfsTer4	p.L152Qfs*4	ENST00000371953	NM_000314.4	152	cTAGATTTCTATGGGGAAGTAAGGACCAGAGACAAa/ca	5/9	0.769931478937125	1	FACETS	0.844	0.803	0.884	0.844	0.803	0.884	CLONAL	1	TRUE	0	0.78	1		562	532	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563438	21563438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	649	920	0	ENST00000382592.4:c.481G>A	p.Gly161Arg	p.G161R	ENST00000382592	NM_014572.2	161	Ggg/Agg	4/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.78	2		920	1610	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790011	40790011	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	324	550	0	ENST00000373198.4:c.2720G>A	p.Gly907Glu	p.G907E	ENST00000373198	NM_133170.3	907	gGg/gAg	18/32	0.769931478937125	2	FACETS	0.895	0.848	0.943			1	CLONAL	1	TRUE	NA	0.78	2		550	928	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846390	128846390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	428	710	1	ENST00000249373.3:c.1226G>A	p.Gly409Asp	p.G409D	ENST00000249373	NM_005631.4	409	gGc/gAc	6/12	1	2	FACETS	0.916	0.874	0.959	0.916	0.874	0.959	CLONAL	1	TRUE	1	0.78	2		711	1198	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317933	8317933	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	271	460	0	ENST00000356435.5:c.5680C>T	p.Gln1894Ter	p.Q1894*	ENST00000356435		1894	Cag/Tag	35/35	0.769931478937125	1	FACETS	0.961	0.918	1	0.961	0.918	1	CLONAL	1	TRUE	0	0.78	1		460	441	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351967	70351968	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0022570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	470	411	0	ENST00000374080.3:c.4164_4165delinsAA	p.Val1389Ile	p.V1389I	ENST00000374080		1388	gaGGtt/gaAAtt	30/45	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.78	1		411	646	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248193	59248193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	81	109	0	ENST00000371222.2:c.550G>A	p.Gly184Ser	p.G184S	ENST00000371222	NM_002228.3	184	Ggc/Agc	1/1	0.384076405086917	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	2	0.384076405086917	4		109	255	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148560	119149582	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTGTTTCACATGATAACCATATCACTGGACACAAGCTTTAGTATATTCTTTATAGAACTGACAGCATAATTGAATTCATTGGAACCCATTGACTAGATTAGTGAATTTGTGTGTATGTGGTTTCACTTTAAACCCTGGAGCTTAAAATAGGACCCAGACTAGATGCTTTCTGGTTTAATAAAAAATAAACCACTGTTGTGACATTTTTATATAAGCAAAATTTGTATAGGAAACAAGTCTTCACTTTTTCTGTTAACATTTATAATTGCAGTTATTTATTCAACTAATAGTCTTTTAATTTTTTTTAATCAAAGGAACAATATGAATTATACTGTGAGATGGGCTCCACATTCCAACTATGTAAAATATGTGCTGAAAATGATAAGGATGTAAAGATTGAGCCCTGTGGACACCTCATGTGCACATCCTGTCTTACATCCTGGCAGGTACGGATCTAAACAGCGACTTTTTTCAGCTATGTAATAACCTTGGAAAATTCGGTATTATATAGCCTTTACTGATACAAGGGGTGGCCTGGCTTTTGGGGTTAGGTTTAAACTTTTACTTTTTTTTGATCTCTAGGAAATGTATTTTCTAGTAGATTAATATTTTAAGTATTTTCAGATGCATCTGTTACTATCTTTTGCTTCTTCTGCAGGAATCAGAAGGTCAGGGCTGTCCTTTCTGCCGATGTGAAATTAAAGGTACTGAACCCATCGTGGTAGATCCGTTTGATCCTAGAGGGAGTGGCAGCCTGTTGAGGCAAGGAGCAGAGGGAGCTCCCTCCCCAAATTATGATGATGATGATGATGAACGAGCTGATGATACTCTCTTCATGATGAAGGAATTGGCTGGTGCCAAGGTAAGATGGCAGTTTAGGAGACTGGCAAAATCCATTGTGAGTTGTCTTCTAAAGCCGTAAAACACTTAACGATATCCAAACTACAATGATAGGTAGTATTAATAGCTAATATTTATTGAGCATTTACTATATGACAGATATTGTGTTAAGCACTTTACT	TTTTGTTTCACATGATAACCATATCACTGGACACAAGCTTTAGTATATTCTTTATAGAACTGACAGCATAATTGAATTCATTGGAACCCATTGACTAGATTAGTGAATTTGTGTGTATGTGGTTTCACTTTAAACCCTGGAGCTTAAAATAGGACCCAGACTAGATGCTTTCTGGTTTAATAAAAAATAAACCACTGTTGTGACATTTTTATATAAGCAAAATTTGTATAGGAAACAAGTCTTCACTTTTTCTGTTAACATTTATAATTGCAGTTATTTATTCAACTAATAGTCTTTTAATTTTTTTTAATCAAAGGAACAATATGAATTATACTGTGAGATGGGCTCCACATTCCAACTATGTAAAATATGTGCTGAAAATGATAAGGATGTAAAGATTGAGCCCTGTGGACACCTCATGTGCACATCCTGTCTTACATCCTGGCAGGTACGGATCTAAACAGCGACTTTTTTCAGCTATGTAATAACCTTGGAAAATTCGGTATTATATAGCCTTTACTGATACAAGGGGTGGCCTGGCTTTTGGGGTTAGGTTTAAACTTTTACTTTTTTTTGATCTCTAGGAAATGTATTTTCTAGTAGATTAATATTTTAAGTATTTTCAGATGCATCTGTTACTATCTTTTGCTTCTTCTGCAGGAATCAGAAGGTCAGGGCTGTCCTTTCTGCCGATGTGAAATTAAAGGTACTGAACCCATCGTGGTAGATCCGTTTGATCCTAGAGGGAGTGGCAGCCTGTTGAGGCAAGGAGCAGAGGGAGCTCCCTCCCCAAATTATGATGATGATGATGATGAACGAGCTGATGATACTCTCTTCATGATGAAGGAATTGGCTGGTGCCAAGGTAAGATGGCAGTTTAGGAGACTGGCAAAATCCATTGTGAGTTGTCTTCTAAAGCCGTAAAACACTTAACGATATCCAAACTACAATGATAGGTAGTATTAATAGCTAATATTTATTGAGCATTTACTATATGACAGATATTGTGTTAAGCACTTTACT	-	novel	NA	P-0022658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	171	370	0	ENST00000264033.4:c.1095+7_1431+160del		p.X365_splice	ENST00000264033	NM_005188.3	365		8-9/16	0.384076405086917	2	FACETS	0.878	0.822	0.934	1	0.989	1	CLONAL	3	TRUE	0	0.384076405086917	2		370	338	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294348	1294348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	479	776	2	ENST00000310581.5:c.653C>T	p.Ala218Val	p.A218V	ENST00000310581	NM_198253.2	218	gCc/gTc	2/16	0.384076405086917	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.384076405086917	3		778	1467	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295294	1295294	+	upstream_gene_variant	5'Flank	SNP	G	G	C	novel	NA	P-0022658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	372	758	0				ENST00000310581	NM_198253.2	-/1132			0.384076405086917	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.384076405086917	3		758	1132	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934278	68934278	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	52	570	0	ENST00000288368.4:c.344A>C	p.Lys115Thr	p.K115T	ENST00000288368	NM_024870.2	115	aAg/aCg	4/40	0.384076405086917	3	FACETS	0.787	0.672	0.913	0.394	0.336	0.457	CLONAL	1	TRUE	1	0.384076405086917	3		570	410	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0022670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	308	292	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.223966463323092	3	FACETS	0.897	0.85	0.945	0.897	0.85	0.945	INDETERMINATE	2	TRUE	1	0.548363686991802	3		292	798	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0022670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	144	389	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.548363686991802	2		389	494	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692800	89692800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204856	NA	P-0022670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	51	471	0	ENST00000371953.3:c.284C>T	p.Pro95Leu	p.P95L	ENST00000371953	NM_000314.4	95	cCa/cTa	5/9	0.254058298351009	2	FACETS	0.353	0.3	0.411	0.176	0.15	0.206	INDETERMINATE	1	TRUE	0	0.548363686991802	2		471	527	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117632187	117632187	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	69	677	0	ENST00000368508.3:c.6229C>T	p.His2077Tyr	p.H2077Y	ENST00000368508	NM_002944.2	2077	Cac/Tac	39/43	0.548363686991802	1	FACETS	0.332	0.289	0.378	0.332	0.289	0.378	SUBCLONAL	1	TRUE	0	0.548363686991802	1		677	551	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0022689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	9	292	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.726	1	1	0.726	1	CLONAL	1	TRUE	1	0.17	2		292	96	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913409	NA	P-0022689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	9	431	0	ENST00000349496.5:c.134C>G	p.Ser45Cys	p.S45C	ENST00000349496	NM_001904.3	45	tCt/tGt	3/15	1	2	FACETS	0.875	0.582	1	0.875	0.582	1	CLONAL	1	TRUE	1	0.17	2		431	121	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139822	55139822	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868384918	NA	P-0022689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	25	702	2	ENST00000257290.5:c.1483G>A	p.Glu495Lys	p.E495K	ENST00000257290	NM_006206.4	495	Gag/Aag	10/23	1	2	FACETS	0.897	0.707	1	0.897	0.707	1	CLONAL	1	TRUE	1	0.17	2		704	328	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859797	151859797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	18	502	0	ENST00000262189.6:c.10865C>T	p.Pro3622Leu	p.P3622L	ENST00000262189	NM_170606.2	3622	cCa/cTa	43/59	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.17	2		502	179	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532837	187532837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	14	833	0	ENST00000441802.2:c.9556C>T	p.Pro3186Ser	p.P3186S	ENST00000441802	NM_005245.3	3186	Cct/Tct	14/27	1	2	FACETS	0.905	0.656	1	0.905	0.656	1	CLONAL	1	TRUE	1	0.17	2		833	182	SUCCESS
APC	324	MSKCC	GRCh37	5	112170762	112170765	+	frameshift_variant	Frame_Shift_Del	DEL	CTTA	CTTA	-	novel	NA	P-0022689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	12	897	0	ENST00000257430.4:c.1863_1866del	p.Tyr622GlyfsTer7	p.Y622Gfs*7	ENST00000257430	NM_000038.5	620	CTTAct/ct	15/16	1	2	FACETS	0.793	0.558	1	0.793	0.558	1	CLONAL	1	TRUE	1	0.17	2		897	178	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209312	98209312	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	25	995	0	ENST00000331920.6:c.4226T>A	p.Phe1409Tyr	p.F1409Y	ENST00000331920	NM_000264.3	1409	tTt/tAt	23/24	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.17	2		995	255	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20152120	20152120	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	47	281	0	ENST00000379607.5:c.210G>T	p.Trp70Cys	p.W70C	ENST00000379607	NM_001412.3	70	tgG/tgT	4/7	1	1	FACETS	0.569	0.491	0.652	0.569	0.491	0.652	SUBCLONAL	1	TRUE	0	0.725434920974335	1		281	145	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441261	52441261	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	131	663	0	ENST00000460680.1:c.509T>G	p.Phe170Cys	p.F170C	ENST00000460680	NM_004656.3	170	tTt/tGt	7/17	0.725434920974335	1	FACETS	0.518	0.474	0.564	0.518	0.474	0.564	SUBCLONAL	1	TRUE	0	0.725434920974335	1		663	444	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226551675	226551675	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1470565638	NA	P-0022726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	168	749	1	ENST00000366794.5:c.2755A>G	p.Ile919Val	p.I919V	ENST00000366794	NM_001618.3	919	Atc/Gtc	20/23	1	2	FACETS	0.898	0.831	0.966	0.898	0.831	0.966	CLONAL	1	TRUE	1	0.725434920974335	2		750	516	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442086	52442108	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTATCAGCTGTGAAACCAAGAA	GGTATCAGCTGTGAAACCAAGAA	-	novel	NA	P-0022726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	94	704	0	ENST00000460680.1:c.256-15_263del		p.X86_splice	ENST00000460680	NM_004656.3	86		5/17	0.725434920974335	1	FACETS	0.404	0.361	0.448	0.404	0.361	0.448	SUBCLONAL	1	TRUE	0	0.725434920974335	1		704	409	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	25	427	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.878	0.691	1	0.878	0.691	1	CLONAL	1	TRUE	1	0.13	2		427	438	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166491	118166491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	33	517	0	ENST00000369448.3:c.1001C>T	p.Ser334Phe	p.S334F	ENST00000369448	NM_017709.3	334	tCc/tTc	2/2	1	2	FACETS	0.856	0.696	1	0.856	0.696	1	CLONAL	1	TRUE	1	0.13	2		517	593	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	42	987	0	ENST00000269305.4:c.1045del	p.Glu349AsnfsTer21	p.E349Nfs*21	ENST00000269305	NM_001126112.2	349	Gaa/aa	10/11	1	2	FACETS	0.809	0.673	0.96	0.809	0.673	0.96	CLONAL	1	TRUE	1	0.13	2		987	799	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292390	15292390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	28	833	0	ENST00000263388.2:c.2789C>T	p.Pro930Leu	p.P930L	ENST00000263388	NM_000435.2	930	cCc/cTc	17/33	1	2	FACETS	0.807	0.643	0.994	0.807	0.643	0.994	CLONAL	1	TRUE	1	0.13	2		833	534	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546085	29546086	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0022743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	50	680	1	ENST00000356175.3:c.1590_1591delinsTT	p.Gln531Ter	p.Q531*	ENST00000356175	NM_000267.3	530	gtCCaa/gtTTaa	14/57	1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	1	0.13	2		681	760	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292389	15292390	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0022743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	29	830	3	ENST00000263388.2:c.2789_2790delinsTT	p.Pro930Leu	p.P930L	ENST00000263388	NM_000435.2	930	cCC/cTT	17/33	1	2	FACETS	0.822	0.658	1	0.822	0.658	1	CLONAL	1	TRUE	1	0.13	2		833	543	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031600	36031600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	42	892	2	ENST00000358208.4:c.1429C>T	p.Gln477Ter	p.Q477*	ENST00000358208		477	Cag/Tag	12/12	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.13	2		894	622	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	29	427	0				ENST00000310581	NM_198253.2	-/1132			0.204885461267068	0	FACETS	0.996	0.816	1			1	CLONAL	2	FALSE	0	0.204885461267068	0		427	113	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0022807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	72	484	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.204885461267068	2		484	572	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0022807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	56	377	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.204885461267068	2		377	419	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663425	67663425	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	32	201	0	ENST00000264010.4:c.1826C>T	p.Ser609Phe	p.S609F	ENST00000264010	NM_006565.3	609	tCc/tTc	10/12	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	FALSE	1	0.204885461267068	2		201	255	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120360	94120360	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs749418654	NA	P-0022807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	14	278	0	ENST00000369303.4:c.691C>T	p.Arg231Ter	p.R231*	ENST00000369303	NM_004440.3	231	Cga/Tga	3/17	0.204885461267068	0	FACETS	0.632	0.458	0.84			1	SUBCLONAL	1	FALSE	0	0.204885461267068	0		278	172	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331729	68331729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	26	208	0	ENST00000487270.1:c.325C>T	p.Pro109Ser	p.P109S	ENST00000487270	NM_133509.3	109	Cca/Tca	5/11	0.204885461267068	5	FACETS	0.993	0.795	1			1	CLONAL	2	FALSE	NA	0.204885461267068	5		208	167	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292713	91292713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866358637	NA	P-0022807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	75	400	1	ENST00000355112.3:c.215C>T	p.Ser72Phe	p.S72F	ENST00000355112	NM_000057.2	72	tCc/tTc	3/22	NA	2	FACETS	0.878	0.773	0.99			1	INDETERMINATE	2	FALSE	NA	0.204885461267068	2		401	417	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188404	32188404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763926116	NA	P-0022807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	30	472	0	ENST00000375023.3:c.937G>A	p.Glu313Lys	p.E313K	ENST00000375023	NM_004557.3	313	Gaa/Aaa	6/30	0.204885461267068	6	FACETS	1	0.91	1	0.413	0.333	0.504	CLONAL	1	FALSE	3	0.204885461267068	6		472	333	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999743	100999743	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774399131	NA	P-0022807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	36	648	0	ENST00000325455.5:c.59C>T	p.Ser20Phe	p.S20F	ENST00000325455	NM_001202474.3	20	tCc/tTc	1/8	0.204885461267068	0	FACETS	1	0.886	1			1	CLONAL	1	FALSE	0	0.204885461267068	0		648	255	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436461	110436461	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	89	814	0	ENST00000375856.3:c.1940T>C	p.Leu647Pro	p.L647P	ENST00000375856	NM_003749.2	647	cTg/cCg	1/2	0.150774740938142	0	FACETS	0.815	0.726	0.908			1	CLONAL	2	FALSE	0	0.204885461267068	0		814	424	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609638	81609638	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200182253	NA	P-0022807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	71	529	0	ENST00000298171.2:c.1236G>A	p.Met412Ile	p.M412I	ENST00000298171	NM_000369.2	412	atG/atA	10/10	1	2	FACETS	0.893	0.784	1	1	0.98	1	CLONAL	2	FALSE	1	0.204885461267068	2		529	388	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56852601	56852601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	87	512	0	ENST00000308159.5:c.515C>T	p.Pro172Leu	p.P172L	ENST00000308159	NM_014669.4	172	cCc/cTc	6/22	1	2	FACETS	0.838	0.744	0.937	1	0.982	1	CLONAL	2	FALSE	1	0.204885461267068	2		512	507	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346954	89346954	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756815181	NA	P-0022807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	31	299	0	ENST00000301030.4:c.5996C>T	p.Pro1999Leu	p.P1999L	ENST00000301030	NM_001256183.1	1999	cCc/cTc	9/13	1	2	FACETS	1	0.838	1	1	0.962	1	CLONAL	2	FALSE	1	0.204885461267068	2		299	148	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110557	4110558	+	missense_variant	Missense_Mutation	DNP	AG	AG	GA	novel	NA	P-0022807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	118	599	1	ENST00000262948.5:c.399_400delinsTC	p.Tyr134His	p.Y134H	ENST00000262948	NM_030662.3	133	ttCTac/ttTCac	3/11	1	2	FACETS	0.948	0.863	1	1	0.991	1	CLONAL	3	FALSE	1	0.204885461267068	2		600	405	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267915	46267915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	60	536	0	ENST00000371998.3:c.2676G>A	p.Met892Ile	p.M892I	ENST00000371998		892	atG/atA	14/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	1	0.204885461267068	2		536	412	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149452874	149452874	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	62	489	0	ENST00000286301.3:c.1072G>A	p.Asp358Asn	p.D358N	ENST00000286301	NM_005211.3	358	Gac/Aac	7/22	1	2	FACETS	0.822	0.714	0.939	1	0.975	1	CLONAL	2	FALSE	1	0.204885461267068	2		489	368	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965635	93965635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	18	445	0	ENST00000369303.4:c.2293C>T	p.Leu765Phe	p.L765F	ENST00000369303	NM_004440.3	765	Ctt/Ttt	13/17	0.204885461267068	0	FACETS	0.519	0.391	0.671			1	SUBCLONAL	1	FALSE	0	0.204885461267068	0		445	269	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339782	116339782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	65	439	0	ENST00000397752.3:c.644C>T	p.Ser215Leu	p.S215L	ENST00000397752	NM_000245.2	215	tCa/tTa	2/21	0.204885461267068	3	FACETS	0.835	0.726	0.951			1	CLONAL	2	FALSE	NA	0.204885461267068	3		439	419	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484259	8484260	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	novel	NA	P-0022807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	59	549	0	ENST00000356435.5:c.3272_3273delinsAA	p.Ser1091Lys	p.S1091K	ENST00000356435		1091	aGT/aAA	19/35	0.204885461267068	0	FACETS	0.675	0.584	0.773			1	SUBCLONAL	2	FALSE	0	0.204885461267068	0		549	339	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928948	44928948	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022807-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	10	211	0	ENST00000377967.4:c.2048C>T	p.Pro683Leu	p.P683L	ENST00000377967	NM_021140.2	683	cCc/cTc	17/29	1	1	FACETS	0.471	0.319	0.662	0.471	0.319	0.662	SUBCLONAL	1	FALSE	0	0.204885461267068	1		211	186	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0022885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	441	292	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.587690702296632	7	FACETS	0.943	0.907	0.978	0.943	0.907	0.978	CLONAL	5	TRUE	2	0.587690702296632	7		292	786	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0022885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	158	693	0				ENST00000310581	NM_198253.2	-/1132			0.587690702296632	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.587690702296632	3		693	324	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996338	73996338	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs146707793	NA	P-0022885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	92	359	1	ENST00000318443.5:c.1072G>A	p.Ala358Thr	p.A358T	ENST00000318443	NM_001024736.1	358	Gct/Act	5/10	0.52775416995571	4	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	2	0.587690702296632	4		360	229	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557881	187557881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	336	714	0	ENST00000441802.2:c.3830C>T	p.Thr1277Ile	p.T1277I	ENST00000441802	NM_005245.3	1277	aCc/aTc	5/27	0.587690702296632	5	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	TRUE	2	0.587690702296632	5		714	698	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217306	123217306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768937075	NA	P-0022885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	535	859	0	ENST00000218089.9:c.2960C>T	p.Pro987Leu	p.P987L	ENST00000218089	NM_001042749.1	987	cCg/cTg	29/35	0.587690702296632	5	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	2	0.587690702296632	5		859	1065	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276376	115276376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	467	878	0	ENST00000438362.2:c.952C>T	p.Pro318Ser	p.P318S	ENST00000438362	NM_001242891.1	318	Cca/Tca	9/20	0.587690702296632	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	1	0.587690702296632	4		878	823	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412088	63412088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs943717871	NA	P-0022885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	507	1329	0	ENST00000330258.3:c.1079C>T	p.Ser360Phe	p.S360F	ENST00000330258	NM_152424.3	360	tCc/tTc	2/2	0.587690702296632	5	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	2	0.587690702296632	5		1329	1030	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940571	71940571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760513714	NA	P-0022885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	300	981	1	ENST00000298229.2:c.722C>T	p.Ser241Leu	p.S241L	ENST00000298229	NM_001567.3	241	tCg/tTg	6/28	0.587690702296632	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.587690702296632	4		982	747	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437115	121437115	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	311	1225	0	ENST00000257555.6:c.1546G>A	p.Gly516Ser	p.G516S	ENST00000257555		516	Ggc/Agc	8/10	0.587690702296632	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.587690702296632	2		1225	436	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940142	31940142	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	520	1335	1	ENST00000375333.2:c.284C>T	p.Ser95Phe	p.S95F	ENST00000375333	NM_032454.1	95	tCt/tTt	2/8	0.587690702296632	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	1	0.587690702296632	4		1336	914	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117746795	117746795	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	112	574	1	ENST00000368508.3:c.25C>T	p.Pro9Ser	p.P9S	ENST00000368508	NM_002944.2	9	Ccg/Tcg	1/43	0.587690702296632	4	FACETS	1	0.962	1	0.377	0.34	0.416	CLONAL	1	TRUE	1	0.587690702296632	4		575	535	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860796	151860796	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144248018	NA	P-0022885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	81	550	1	ENST00000262189.6:c.9866C>T	p.Pro3289Leu	p.P3289L	ENST00000262189	NM_170606.2	3289	cCc/cTc	43/59	0.587690702296632	4	FACETS	1	0.924	1	0.529	0.468	0.593	CLONAL	1	TRUE	2	0.587690702296632	4		551	414	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879357	151879357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	197	558	0	ENST00000262189.6:c.5588C>T	p.Pro1863Leu	p.P1863L	ENST00000262189	NM_170606.2	1863	cCc/cTc	36/59	0.587690702296632	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.587690702296632	4		558	432	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538874	23538874	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748311757	NA	P-0022885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	268	534	1	ENST00000380871.4:c.565G>A	p.Gly189Arg	p.G189R	ENST00000380871	NM_006167.3	189	Gga/Aga	2/2	0.587690702296632	5	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	2	0.587690702296632	5		535	511	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123159721	123159721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022885-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	271	679	0	ENST00000218089.9:c.76G>A	p.Asp26Asn	p.D26N	ENST00000218089	NM_001042749.1	26	Gat/Aat	4/35	0.587690702296632	5	FACETS	1	0.985	1	0.755	0.712	0.799	CLONAL	2	TRUE	2	0.587690702296632	5		679	766	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722761	49722761	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs62262682	NA	P-0022886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	22	61	1	ENST00000449682.2:c.1478G>T	p.Arg493Leu	p.R493L	ENST00000449682	NM_020998.3	493	cGt/cTt	13/18	1	2	FACETS	0.698	0.554	0.856	0.698	0.554	0.856	SUBCLONAL	1	TRUE	1	0.741322311480449	2		62	85	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519886	NA	P-0022886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	10	368	0	ENST00000349496.5:c.97T>C	p.Ser33Pro	p.S33P	ENST00000349496	NM_001904.3	33	Tct/Cct	3/15	1	2	FACETS	0.123	0.083	0.174	0.123	0.083	0.174	SUBCLONAL	1	TRUE	1	0.741322311480449	2		368	219	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551502	150551502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	446	1368	0	ENST00000369026.2:c.505G>A	p.Glu169Lys	p.E169K	ENST00000369026	NM_021960.4	169	Gag/Aag	1/3	0.741322311480449	3	FACETS	0.79	0.756	0.824	0.79	0.756	0.824	SUBCLONAL	2	TRUE	1	0.741322311480449	3		1368	1044	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042451	42042451	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	134	798	1	ENST00000219905.7:c.6646C>T	p.Gln2216Ter	p.Q2216*	ENST00000219905	NM_001164273.1	2216	Cag/Tag	17/24	1	2	FACETS	0.908	0.834	0.985	0.908	0.834	0.985	CLONAL	1	TRUE	1	0.741322311480449	2		799	398	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755732	39755732	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	125	675	0	ENST00000288319.7:c.1033G>A	p.Asp345Asn	p.D345N	ENST00000288319	NM_182918.3	345	Gac/Aac	10/10	0.381813993358949	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.741322311480449	0		675	349	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922871	44922871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	112	315	0	ENST00000377967.4:c.1732C>T	p.Pro578Ser	p.P578S	ENST00000377967	NM_021140.2	578	Ccc/Tcc	16/29	1	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.741322311480449	1		315	176	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730107	41730107	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	214	543	0	ENST00000242208.4:c.422C>T	p.Ser141Phe	p.S141F	ENST00000242208	NM_002192.2	141	tCc/tTc	3/3	0.741322311480449	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.741322311480449	3		543	394	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100756	8100756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140982061	NA	P-0022886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	141	1010	1	ENST00000346208.3:c.730C>T	p.Pro244Ser	p.P244S	ENST00000346208		244	Ccc/Tcc	3/6	0.68306880468766	1	FACETS	0.977	0.913	1	0.977	0.913	1	CLONAL	1	TRUE	0	0.741322311480449	1		1011	245	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433955	49433955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	177	1057	1	ENST00000301067.7:c.7598C>T	p.Pro2533Leu	p.P2533L	ENST00000301067	NM_003482.3	2533	cCc/cTc	31/54	0.154465895160455	4	FACETS	0.843	0.784	0.904	0.843	0.784	0.904	INDETERMINATE	2	TRUE	2	0.741322311480449	4		1058	493	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991359	41991359	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0022886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	129	638	0	ENST00000219905.7:c.2188+2T>C		p.X730_splice	ENST00000219905	NM_001164273.1	730			1	2	FACETS	0.868	0.794	0.944	0.868	0.794	0.944	CLONAL	1	TRUE	1	0.741322311480449	2		638	401	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220920	36220920	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	75	420	0	ENST00000222270.7:c.4970C>T	p.Ser1657Phe	p.S1657F	ENST00000222270	NM_014727.1	1657	tCc/tTc	23/37	1	2	FACETS	0.92	0.82	1	0.92	0.82	1	CLONAL	1	TRUE	1	0.741322311480449	2		420	220	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39214652	39214652	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1396062382	NA	P-0022886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	143	801	0	ENST00000402219.2:c.3472C>T	p.Arg1158Ter	p.R1158*	ENST00000402219	NM_005633.3	1158	Cga/Tga	22/23	1	2	FACETS	0.712	0.652	0.773	0.712	0.652	0.773	SUBCLONAL	1	TRUE	1	0.741322311480449	2		801	542	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574655	41574655	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	208	1352	0	ENST00000263253.7:c.6940C>T	p.Pro2314Ser	p.P2314S	ENST00000263253	NM_001429.3	2314	Cct/Tct	31/31	0.160814320103805	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.741322311480449	0		1352	582	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644705	134644705	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772984614	NA	P-0022886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	144	748	2	ENST00000398015.3:c.106G>A	p.Ala36Thr	p.A36T	ENST00000398015	NM_004441.4	36	Gcc/Acc	2/16	0.741322311480449	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.741322311480449	1		750	231	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526308	189526308	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	98	498	1	ENST00000264731.3:c.572C>A	p.Thr191Asn	p.T191N	ENST00000264731	NM_003722.4	191	aCc/aAc	4/14	1	2	FACETS	0.867	0.783	0.954	0.867	0.783	0.954	CLONAL	1	TRUE	1	0.741322311480449	2		499	305	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803099	1803099	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	154	1049	1	ENST00000260795.2:c.451C>T	p.Pro151Ser	p.P151S	ENST00000260795		151	Cct/Tct	4/17	1	2	FACETS	0.907	0.837	0.979	0.907	0.837	0.979	CLONAL	1	TRUE	1	0.741322311480449	2		1050	458	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518844	187518844	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	75	566	0	ENST00000441802.2:c.12360G>T	p.Arg4120Ser	p.R4120S	ENST00000441802	NM_005245.3	4120	agG/agT	24/27	1	2	FACETS	0.688	0.609	0.771	0.688	0.609	0.771	SUBCLONAL	1	TRUE	1	0.741322311480449	2		566	294	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518854	187518854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1263240063	NA	P-0022886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	89	608	0	ENST00000441802.2:c.12350C>T	p.Ser4117Leu	p.S4117L	ENST00000441802	NM_005245.3	4117	tCg/tTg	24/27	1	2	FACETS	0.725	0.649	0.805	0.725	0.649	0.805	SUBCLONAL	1	TRUE	1	0.741322311480449	2		608	331	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665499	176665499	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	115	541	0	ENST00000439151.2:c.4183A>G	p.Lys1395Glu	p.K1395E	ENST00000439151	NM_022455.4	1395	Aaa/Gaa	7/23	1	2	FACETS	0.825	0.751	0.902	0.825	0.751	0.902	CLONAL	1	TRUE	1	0.741322311480449	2		541	376	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185819	32185819	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	211	1028	0	ENST00000375023.3:c.1577C>G	p.Ala526Gly	p.A526G	ENST00000375023	NM_004557.3	526	gCg/gGg	9/30	0.117283734872434	4	FACETS	0.836	0.781	0.891	0.836	0.781	0.891	INDETERMINATE	2	TRUE	2	0.741322311480449	4		1028	593	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956625	93956625	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	74	636	0	ENST00000369303.4:c.2611G>A	p.Asp871Asn	p.D871N	ENST00000369303	NM_004440.3	871	Gat/Aat	15/17	0.68306880468766	1	FACETS	0.8	0.721	0.881	0.8	0.721	0.881	SUBCLONAL	1	TRUE	0	0.741322311480449	1		636	157	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444330	50444330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	159	458	0	ENST00000331340.3:c.260C>T	p.Ala87Val	p.A87V	ENST00000331340	NM_006060.4	87	gCc/gTc	4/8	0.741322311480449	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.741322311480449	3		458	286	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021663	69021663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	62	590	0	ENST00000288368.4:c.2951C>T	p.Pro984Leu	p.P984L	ENST00000288368	NM_024870.2	984	cCt/cTt	25/40	1	2	FACETS	0.867	0.762	0.976	0.867	0.762	0.976	CLONAL	1	TRUE	1	0.741322311480449	2		590	193	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0022986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	11	454	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	0.34	0.234	0.473	0.34	0.234	0.473	SUBCLONAL	1	TRUE	1	0.21	2		454	308	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270593	98270595	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs756897237	NA	P-0022986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	10	101	2	ENST00000331920.6:c.49_51del	p.Gly17del	p.G17del	ENST00000331920	NM_000264.3	17	GGC/-	1/24	1	2	FACETS	1	0.714	1	1	0.714	1	CLONAL	1	TRUE	1	0.21	2		103	91	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100117	157100119	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs797045268	NA	P-0022986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	12	83	0	ENST00000346085.5:c.1069_1071del	p.Gly357del	p.G357del	ENST00000346085	NM_020732.3	352	GGC/-	1/20	1	2	FACETS	0.866	0.621	1	1	0.891	1	CLONAL	2	TRUE	1	0.21	2		83	66	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453135	140453136	+	missense_variant	Missense_Mutation	DNP	CA	CA	TT	rs121913377	NA	P-0022986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	15	555	1	ENST00000288602.6:c.1799_1800delinsAA	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTG/gAA	15/18	1	2	FACETS	0.661	0.484	0.873	0.661	0.484	0.873	SUBCLONAL	1	TRUE	1	0.21	2		556	216	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174875	11174875	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	46	804	0	ENST00000361445.4:c.7159A>G	p.Met2387Val	p.M2387V	ENST00000361445	NM_004958.3	2387	Atg/Gtg	52/58	1	2	FACETS	0.993	0.838	1	0.993	0.838	1	CLONAL	1	TRUE	1	0.21	2		804	441	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259580	16259580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	51	632	0	ENST00000375759.3:c.6845C>T	p.Ser2282Phe	p.S2282F	ENST00000375759	NM_015001.2	2282	tCt/tTt	11/15	1	2	FACETS	0.93	0.791	1	0.93	0.791	1	CLONAL	1	TRUE	1	0.21	2		632	522	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285647	46285647	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	40	576	0	ENST00000334344.6:c.5007G>A	p.Trp1669Ter	p.W1669*	ENST00000334344	NM_152641.2	1669	tgG/tgA	17/21	0.245202455161057	3	FACETS	1	0.943	1	0.666	0.555	0.788	CLONAL	1	TRUE	1	0.21	3		576	316	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437520	49437520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	58	712	1	ENST00000301067.7:c.5365C>T	p.Leu1789Phe	p.L1789F	ENST00000301067	NM_003482.3	1789	Ctt/Ttt	23/54	0.245202455161057	3	FACETS	0.8	0.686	0.925	0.4	0.343	0.463	CLONAL	1	TRUE	1	0.21	3		713	763	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81939023	81939023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	32	467	0	ENST00000359376.3:c.1378C>T	p.Pro460Ser	p.P460S	ENST00000359376	NM_002661.3	460	Ccc/Tcc	15/33	0.245202455161057	3	FACETS	0.71	0.576	0.863	0.355	0.288	0.432	SUBCLONAL	1	TRUE	1	0.21	3		467	474	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965212	81965212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	70	755	1	ENST00000359376.3:c.2692G>A	p.Glu898Lys	p.E898K	ENST00000359376	NM_002661.3	898	Gag/Aag	25/33	0.245202455161057	3	FACETS	1	0.922	1	0.541	0.471	0.616	CLONAL	1	TRUE	1	0.21	3		756	681	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762883	40762883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	77	790	1	ENST00000392038.2:c.125C>T	p.Pro42Leu	p.P42L	ENST00000392038	NM_001626.4	42	cCc/cTc	3/14	1	2	FACETS	0.996	0.874	1	0.996	0.874	1	CLONAL	1	TRUE	1	0.21	2		791	736	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731701	47731701	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	51	386	0	ENST00000449228.1:c.91C>T	p.Pro31Ser	p.P31S	ENST00000449228	NM_001127240.2	31	Ccc/Tcc	2/4	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.21	2		386	357	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295220	1295221	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0022986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	23	557	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.513	0.399	0.645	0.513	0.399	0.645	SUBCLONAL	1	TRUE	1	0.21	2		558	427	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227989	123227989	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	13	526	0	ENST00000218089.9:c.3700G>C	p.Asp1234His	p.D1234H	ENST00000218089	NM_001042749.1	1234	Gat/Cat	33/35	1	2	FACETS	0.595	0.425	0.803	0.595	0.425	0.803	SUBCLONAL	1	TRUE	1	0.21	2		526	208	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	238	693	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.874	0.827	0.92	1	0.996	1	CLONAL	3	FALSE	1	0.394820360385643	2		693	460	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2969666	2969666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747866557	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	109	1223	1	ENST00000396946.4:c.1613C>T	p.Ser538Phe	p.S538F	ENST00000396946	NM_032415.4	538	tCc/tTc	12/25	0.394820360385643	3	FACETS	0.66	0.592	0.733	0.33	0.296	0.367	SUBCLONAL	1	FALSE	1	0.394820360385643	3		1224	1001	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419926	41419926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	90	741	1	ENST00000373198.4:c.395G>A	p.Gly132Glu	p.G132E	ENST00000373198	NM_133170.3	132	gGg/gAg	3/32	0.343871711386998	4	FACETS	0.897	0.796	1	0.448	0.398	0.503	CLONAL	1	FALSE	2	0.394820360385643	4		742	709	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306689	41306689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868376470	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	140	940	0	ENST00000373198.4:c.970G>A	p.Glu324Lys	p.E324K	ENST00000373198	NM_133170.3	324	Gaa/Aaa	7/32	0.343871711386998	4	FACETS	0.862	0.788	0.938	0.862	0.788	0.938	CLONAL	2	FALSE	2	0.394820360385643	4		940	574	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371749	55371749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138778434	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	338	742	1	ENST00000297316.4:c.439C>T	p.Arg147Trp	p.R147W	ENST00000297316	NM_022454.3	147	Cgg/Tgg	2/2	0.360109215097307	3	FACETS	0.988	0.942	1	0.988	0.942	1	CLONAL	3	FALSE	0	0.394820360385643	3		743	692	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876305	35876305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778728560	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	171	660	1	ENST00000303115.3:c.1097C>T	p.Ser366Phe	p.S366F	ENST00000303115	NM_002185.3	366	tCc/tTc	8/8	0.326248462918924	4	FACETS	0.905	0.841	0.97	1	0.989	1	CLONAL	3	FALSE	2	0.394820360385643	4		661	445	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502728	149502728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	113	847	0	ENST00000261799.4:c.2060G>A	p.Gly687Glu	p.G687E	ENST00000261799	NM_002609.3	687	gGa/gAa	15/23	0.326248462918924	4	FACETS	0.783	0.703	0.867	0.391	0.351	0.434	SUBCLONAL	1	FALSE	2	0.394820360385643	4		847	1020	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383635	42383635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	379	769	0	ENST00000221972.3:c.410G>A	p.Gly137Glu	p.G137E	ENST00000221972	NM_021601.3	137	gGg/gAg	3/5	0.394820360385643	3	FACETS	0.878	0.837	0.918	1	0.994	1	CLONAL	3	FALSE	1	0.394820360385643	3		769	873	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862887	9862887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868222927	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	75	840	0	ENST00000330684.3:c.2416G>A	p.Glu806Lys	p.E806K	ENST00000330684	NM_001134407.1	806	Gag/Aag	12/13	1	2	FACETS	0.677	0.594	0.766	0.677	0.594	0.766	SUBCLONAL	1	FALSE	1	0.394820360385643	2		840	561	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559101	29559101	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202023	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	38	245	0	ENST00000356175.3:c.3208C>T	p.Gln1070Ter	p.Q1070*	ENST00000356175	NM_000267.3	1070	Cag/Tag	25/57	0.337876951774394	1	FACETS	0.936	0.785	1	0.936	0.785	1	CLONAL	1	FALSE	0	0.394820360385643	1		245	165	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194616	29194616	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	385	1408	0	ENST00000240100.2:c.1112C>T	p.Ser371Phe	p.S371F	ENST00000240100	NM_001394.6	371	tCc/tTc	4/4	0.394820360385643	0	FACETS	0.829	0.795	0.863			1	CLONAL	2	FALSE	0	0.394820360385643	0		1408	712	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526580	106526580	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	135	518	0	ENST00000359195.3:c.2873G>A	p.Gly958Glu	p.G958E	ENST00000359195	NM_002649.2	958	gGa/gAa	10/11	0.372556800584498	4	FACETS	1	0.919	1	1	0.919	1	CLONAL	2	FALSE	2	0.394820360385643	4		518	475	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652446	206652446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	256	781	0	ENST00000367120.3:c.1153G>A	p.Ala385Thr	p.A385T	ENST00000367120	NM_014002.3	385	Gcc/Acc	10/22	0.394820360385643	3	FACETS	1	0.992	1	0.722	0.675	0.769	CLONAL	1	FALSE	1	0.394820360385643	3		781	1076	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982123	93982123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769773179	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	62	522	0	ENST00000369303.4:c.1342G>A	p.Gly448Arg	p.G448R	ENST00000369303	NM_004440.3	448	Gga/Aga	6/17	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	FALSE	1	0.394820360385643	2		522	278	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570084	212570084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1366336180	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	160	667	0	ENST00000342788.4:c.1157C>T	p.Pro386Leu	p.P386L	ENST00000342788	NM_005235.2	386	cCa/cTa	10/28	1	2	FACETS	1	0.971	1	1	0.993	1	CLONAL	2	FALSE	1	0.394820360385643	2		667	373	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1952803	1952803	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144714547	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	199	510	2	ENST00000382891.5:c.1886C>T	p.Ser629Leu	p.S629L	ENST00000382891	NM_133335.3	629	tCg/tTg	10/22	1	2	FACETS	0.883	0.823	0.943	1	0.993	1	CLONAL	2	FALSE	1	0.394820360385643	2		512	571	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344888	118344888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	91	373	0	ENST00000534358.1:c.3014C>T	p.Ser1005Phe	p.S1005F	ENST00000534358	NM_005933.3	1005	tCc/tTc	3/36	1	2	FACETS	0.826	0.743	0.912	1	0.984	1	CLONAL	2	FALSE	1	0.394820360385643	2		373	279	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198262794	198262794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	142	555	0	ENST00000335508.6:c.3181G>A	p.Glu1061Lys	p.E1061K	ENST00000335508	NM_012433.2	1061	Gag/Aag	22/25	1	2	FACETS	0.962	0.887	1	1	0.991	1	CLONAL	2	FALSE	1	0.394820360385643	2		555	374	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341587	89341587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	217	715	0	ENST00000301030.4:c.7483C>T	p.Pro2495Ser	p.P2495S	ENST00000301030	NM_001256183.1	2495	Ccc/Tcc	10/13	0.394820360385643	1	FACETS	0.845	0.803	0.887	1	0.996	1	CLONAL	3	FALSE	0	0.394820360385643	1		715	348	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189880	11189880	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	198	578	0	ENST00000361445.4:c.5629C>T	p.Leu1877Phe	p.L1877F	ENST00000361445	NM_004958.3	1877	Ctc/Ttc	40/58	0.356123279050223	3	FACETS	0.914	0.85	0.979	0.914	0.85	0.979	CLONAL	2	FALSE	1	0.394820360385643	3		578	657	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255216	16255216	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs924209244	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	205	516	1	ENST00000375759.3:c.2481G>T	p.Lys827Asn	p.K827N	ENST00000375759	NM_015001.2	827	aaG/aaT	11/15	0.356123279050223	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	FALSE	1	0.394820360385643	3		517	517	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262225	16262225	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1340812093	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	24	249	0	ENST00000375759.3:c.9490C>T	p.Leu3164Phe	p.L3164F	ENST00000375759	NM_015001.2	3164	Ctt/Ttt	11/15	0.356123279050223	3	FACETS	0.758	0.598	0.94	0.379	0.299	0.47	CLONAL	1	FALSE	1	0.394820360385643	3		249	192	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17359614	17359614	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	96	664	0	ENST00000375499.3:c.227T>A	p.Leu76Ter	p.L76*	ENST00000375499	NM_003000.2	76	tTa/tAa	3/8	0.356123279050223	3	FACETS	1	0.977	1	0.679	0.608	0.753	CLONAL	1	FALSE	1	0.394820360385643	3		664	429	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807487	36807487	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	356	1082	1	ENST00000373129.3:c.1177C>T	p.His393Tyr	p.H393Y	ENST00000373129	NM_032017.1	393	Cat/Tat	12/12	0.356123279050223	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	FALSE	1	0.394820360385643	3		1083	974	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726657	46726658	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	69	607	1	ENST00000371975.4:c.736_737delinsAA	p.Gly246Lys	p.G246K	ENST00000371975	NM_003579.3	246	GGa/AAa	7/18	0.356123279050223	3	FACETS	0.825	0.72	0.939	0.413	0.36	0.47	CLONAL	1	FALSE	1	0.394820360385643	3		608	507	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46738354	46738354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	204	778	1	ENST00000371975.4:c.1255C>T	p.Leu419Phe	p.L419F	ENST00000371975	NM_003579.3	419	Ctt/Ttt	12/18	0.356123279050223	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	FALSE	1	0.394820360385643	3		779	515	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571818	64571820	+	frameshift_variant	Frame_Shift_Del	DEL	GCG	GCG	CA	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1378	112	1232	2	ENST00000312049.6:c.1819_1821delinsTG	p.Arg607Ter	p.R607*	ENST00000312049	NM_130799.2	607	CGC/TG	10/10	1	2	FACETS	0.381	0.341	0.423	0.381	0.341	0.423	SUBCLONAL	1	FALSE	1	0.394820360385643	2		1234	1490	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192597	94192597	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	141	853	0	ENST00000323929.3:c.1477C>T	p.Leu493Phe	p.L493F	ENST00000323929	NM_005591.3	493	Ctc/Ttc	13/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.394820360385643	2		853	492	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106419	108106419	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	23	245	0	ENST00000278616.4:c.354A>C	p.Gln118His	p.Q118H	ENST00000278616	NM_000051.3	118	caA/caC	5/63	1	2	FACETS	0.857	0.676	1	0.857	0.676	1	CLONAL	1	FALSE	1	0.394820360385643	2		245	136	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202220	108202220	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555124039	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	40	644	0	ENST00000278616.4:c.7565A>G	p.Gln2522Arg	p.Q2522R	ENST00000278616	NM_000051.3	2522	cAa/cGa	51/63	1	2	FACETS	0.542	0.451	0.642	0.542	0.451	0.642	SUBCLONAL	1	FALSE	1	0.394820360385643	2		644	374	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343640	118343640	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	148	648	2	ENST00000534358.1:c.1766C>T	p.Thr589Ile	p.T589I	ENST00000534358	NM_005933.3	589	aCa/aTa	3/36	1	2	FACETS	0.951	0.879	1	1	0.992	1	CLONAL	2	FALSE	1	0.394820360385643	2		650	394	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375896	118375896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	127	615	0	ENST00000534358.1:c.9289C>T	p.Leu3097Phe	p.L3097F	ENST00000534358	NM_005933.3	3097	Ctt/Ttt	27/36	1	2	FACETS	0.886	0.812	0.962	1	0.99	1	CLONAL	2	FALSE	1	0.394820360385643	2		615	363	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897016	28897016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	203	757	0	ENST00000282397.4:c.2864C>T	p.Pro955Leu	p.P955L	ENST00000282397	NM_002019.4	955	cCa/cTa	21/30	0.337876951774394	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	0	0.394820360385643	1		757	743	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73350109	73350109	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	187	763	0	ENST00000377767.4:c.776T>C	p.Leu259Ser	p.L259S	ENST00000377767	NM_014953.3	259	tTg/tCg	5/21	0.372556800584498	4	FACETS	0.841	0.783	0.9	1	0.987	1	CLONAL	3	FALSE	2	0.394820360385643	4		763	524	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034749	42034749	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	132	399	0	ENST00000219905.7:c.4591C>T	p.Arg1531Ter	p.R1531*	ENST00000219905	NM_001164273.1	1531	Cga/Tga	15/24	0.394820360385643	1	FACETS	0.84	0.786	0.893	1	0.993	1	CLONAL	3	FALSE	0	0.394820360385643	1		399	213	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762171	43762171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196486842	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	297	1079	0	ENST00000382044.4:c.1274C>T	p.Pro425Leu	p.P425L	ENST00000382044	NM_001141980.1	425	cCc/cTc	11/28	1	2	FACETS	0.951	0.9	1	1	0.996	1	CLONAL	2	FALSE	1	0.394820360385643	2		1079	791	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916206	9916206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	89	727	0	ENST00000330684.3:c.2083C>T	p.Arg695Trp	p.R695W	ENST00000330684	NM_001134407.1	695	Cgg/Tgg	10/13	1	2	FACETS	0.811	0.729	0.896	1	0.984	1	CLONAL	2	FALSE	1	0.394820360385643	2		727	278	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992756	72992756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1178788473	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	223	870	0	ENST00000268489.5:c.1289C>T	p.Ser430Phe	p.S430F	ENST00000268489	NM_006885.3	430	tCc/tTc	2/10	1	2	FACETS	0.941	0.883	1	1	0.994	1	CLONAL	2	FALSE	1	0.394820360385643	2		870	600	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592261	29592262	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	79	304	1	ENST00000356175.3:c.4679_4680del	p.Lys1560ArgfsTer40	p.K1560Rfs*40	ENST00000356175	NM_000267.3	1559	gAA/g	35/57	0.337876951774394	1	FACETS	1	0.937	1	1	0.987	1	CLONAL	2	FALSE	0	0.394820360385643	1		305	154	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30323816	30323816	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	74	334	0	ENST00000322652.5:c.1795-1G>A		p.X599_splice	ENST00000322652	NM_015355.2	599			0.337876951774394	1	FACETS	0.779	0.696	0.865	1	0.98	1	SUBCLONAL	2	FALSE	0	0.394820360385643	1		334	193	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267791	7267791	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	83	942	0	ENST00000302850.5:c.217T>A	p.Phe73Ile	p.F73I	ENST00000302850	NM_000208.2	73	Ttc/Atc	2/22	0.394820360385643	3	FACETS	0.621	0.547	0.7	0.31	0.273	0.35	SUBCLONAL	1	FALSE	1	0.394820360385643	3		942	811	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265709	10265709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	103	704	0	ENST00000340748.4:c.1468G>A	p.Asp490Asn	p.D490N	ENST00000340748		490	Gat/Aat	19/40	0.394820360385643	3	FACETS	0.926	0.829	1	0.463	0.414	0.514	CLONAL	1	FALSE	1	0.394820360385643	3		704	675	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602408	10602409	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1587	241	1339	2	ENST00000171111.5:c.1169_1170delinsTT	p.Ser390Phe	p.S390F	ENST00000171111	NM_203500.1	390	tCC/tTT	3/6	0.394820360385643	3	FACETS	0.8	0.744	0.858	0.4	0.372	0.429	SUBCLONAL	1	FALSE	1	0.394820360385643	3		1341	1828	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11137006	11137006	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	177	1069	0	ENST00000358026.2:c.3199G>T	p.Gly1067Cys	p.G1067C	ENST00000358026	NM_001128849.1	1067	Ggc/Tgc	23/36	0.394820360385643	3	FACETS	0.909	0.836	0.985	0.455	0.418	0.493	CLONAL	1	FALSE	1	0.394820360385643	3		1069	1181	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284919	15284919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	213	1408	1	ENST00000263388.2:c.4696G>A	p.Glu1566Lys	p.E1566K	ENST00000263388	NM_000435.2	1566	Gaa/Aaa	25/33	0.394820360385643	3	FACETS	0.949	0.88	1	0.475	0.44	0.511	CLONAL	1	FALSE	1	0.394820360385643	3		1409	1361	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971718	18971718	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1431948871	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	398	1052	0	ENST00000262803.5:c.2384C>T	p.Pro795Leu	p.P795L	ENST00000262803	NM_002911.3	795	cCc/cTc	17/24	0.394820360385643	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	FALSE	1	0.394820360385643	3		1052	1207	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257968	19257968	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767215450	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1394	123	1674	0	ENST00000162023.5:c.418C>T	p.Pro140Ser	p.P140S	ENST00000162023		140	Cca/Tca	9/13	0.394820360385643	3	FACETS	0.492	0.443	0.544	0.246	0.221	0.272	SUBCLONAL	1	FALSE	1	0.394820360385643	3		1674	1517	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455272	29455272	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	182	743	0	ENST00000389048.3:c.2530G>A	p.Gly844Ser	p.G844S	ENST00000389048	NM_004304.4	844	Ggt/Agt	15/29	1	2	FACETS	0.809	0.751	0.868	1	0.992	1	CLONAL	2	FALSE	1	0.394820360385643	2		743	570	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537939	212537939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	177	652	0	ENST00000342788.4:c.1666G>A	p.Asp556Asn	p.D556N	ENST00000342788	NM_005235.2	556	Gac/Aac	14/28	1	2	FACETS	1	0.97	1	1	0.994	1	CLONAL	2	FALSE	1	0.394820360385643	2		652	418	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566728	212566728	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	133	493	0	ENST00000342788.4:c.1453A>G	p.Ile485Val	p.I485V	ENST00000342788	NM_005235.2	485	Ata/Gta	12/28	1	2	FACETS	1	0.974	1	1	0.992	1	CLONAL	2	FALSE	1	0.394820360385643	2		493	300	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525123	9525123	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	136	592	0	ENST00000353224.5:c.1762G>A	p.Gly588Ser	p.G588S	ENST00000353224	NM_177990.2	588	Ggt/Agt	8/10	0.343871711386998	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	FALSE	2	0.394820360385643	4		592	413	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420106	41420106	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	76	340	0	ENST00000373198.4:c.215G>A	p.Gly72Glu	p.G72E	ENST00000373198	NM_133170.3	72	gGa/gAa	3/32	0.343871711386998	4	FACETS	0.909	0.813	1	1	0.976	1	CLONAL	3	FALSE	2	0.394820360385643	4		340	197	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434218	12434218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	228	710	0	ENST00000287820.6:c.586C>T	p.Gln196Ter	p.Q196*	ENST00000287820	NM_015869.4	196	Cag/Tag	4/7	NA	2	FACETS	0.823	0.77	0.876			1	INDETERMINATE	2	FALSE	NA	0.394820360385643	2		710	702	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623223	52623224	+	missense_variant	Missense_Mutation	DNP	AA	AA	GG	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	158	595	0	ENST00000394830.3:c.2827_2828delinsCC	p.Leu943Pro	p.L943P	ENST00000394830	NM_018313.4	943	TTa/CCa	19/30	0.244639961933329	4	FACETS	0.908	0.841	0.975	1	0.988	1	CLONAL	3	FALSE	2	0.394820360385643	4		595	410	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114745	73114745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	38	313	1	ENST00000356692.5:c.1126G>A	p.Asp376Asn	p.D376N	ENST00000356692		376	Gac/Aac	9/9	0.244639961933329	4	FACETS	1	0.908	1	0.571	0.476	0.676	CLONAL	1	FALSE	2	0.394820360385643	4		314	235	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670546	134670546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	188	1034	0	ENST00000398015.3:c.457G>A	p.Gly153Arg	p.G153R	ENST00000398015	NM_004441.4	153	Gga/Aga	3/16	1	2	FACETS	0.887	0.826	0.949	1	0.993	1	CLONAL	2	FALSE	1	0.394820360385643	2		1034	537	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279184	142279184	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	158	720	0	ENST00000350721.4:c.1462G>C	p.Glu488Gln	p.E488Q	ENST00000350721	NM_001184.3	488	Gag/Cag	6/47	1	2	FACETS	0.907	0.84	0.977	1	0.992	1	CLONAL	2	FALSE	1	0.394820360385643	2		720	441	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295219	1295219	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	97	682	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.751	0.677	0.829	1	0.983	1	SUBCLONAL	2	FALSE	1	0.394820360385643	2		683	327	SUCCESS
APC	324	MSKCC	GRCh37	5	112176077	112176077	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	224	518	0	ENST00000257430.4:c.4786C>G	p.Gln1596Glu	p.Q1596E	ENST00000257430	NM_000038.5	1596	Cag/Gag	16/16	0.326248462918924	4	FACETS	0.942	0.891	0.993	1	0.995	1	CLONAL	4	FALSE	2	0.394820360385643	4		518	420	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190812	32190812	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	779	1352	0	ENST00000375023.3:c.125T>A	p.Leu42Gln	p.L42Q	ENST00000375023	NM_004557.3	42	cTg/cAg	2/30	0.394820360385643	5	FACETS	1	0.993	1	1	0.998	1	CLONAL	4	FALSE	2	0.394820360385643	5		1352	1472	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715844	117715844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	170	667	1	ENST00000368508.3:c.914C>T	p.Ser305Phe	p.S305F	ENST00000368508	NM_002944.2	305	tCt/tTt	9/43	1	2	FACETS	0.999	0.929	1	1	0.993	1	CLONAL	2	FALSE	1	0.394820360385643	2		668	431	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962358	2962359	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	195	939	3	ENST00000396946.4:c.2178_2179delinsTT	p.Pro727Ser	p.P727S	ENST00000396946	NM_032415.4	726	gtCCcg/gtTTcg	17/25	0.394820360385643	3	FACETS	0.833	0.774	0.894	0.833	0.774	0.894	CLONAL	2	FALSE	1	0.394820360385643	3		942	710	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878667	151878667	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs558139040	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	87	578	0	ENST00000262189.6:c.6278C>T	p.Pro2093Leu	p.P2093L	ENST00000262189	NM_170606.2	2093	cCa/cTa	36/59	0.372556800584498	4	FACETS	0.931	0.832	1	0.931	0.832	1	CLONAL	2	FALSE	2	0.394820360385643	4		578	330	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021843	69021843	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1328974208	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	331	650	0	ENST00000288368.4:c.3131T>C	p.Val1044Ala	p.V1044A	ENST00000288368	NM_024870.2	1044	gTt/gCt	25/40	0.360109215097307	3	FACETS	0.965	0.927	1	1	0.995	1	CLONAL	4	FALSE	0	0.394820360385643	3		650	520	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69032513	69032513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	217	814	0	ENST00000288368.4:c.3587G>A	p.Gly1196Glu	p.G1196E	ENST00000288368	NM_024870.2	1196	gGa/gAa	29/40	0.360109215097307	3	FACETS	0.862	0.81	0.915	0.862	0.81	0.915	CLONAL	3	FALSE	0	0.394820360385643	3		814	509	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5557638	5557638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	235	756	0	ENST00000397747.3:c.652C>T	p.His218Tyr	p.H218Y	ENST00000397747	NM_025239.3	218	Cat/Tat	5/7	1	2	FACETS	0.788	0.738	0.84	1	0.993	1	SUBCLONAL	2	FALSE	1	0.394820360385643	2		756	755	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485782	8485782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	56	335	0	ENST00000356435.5:c.3035G>A	p.Arg1012Lys	p.R1012K	ENST00000356435		1012	aGg/aAg	17/35	1	2	FACETS	0.921	0.807	1	1	0.978	1	CLONAL	2	FALSE	1	0.394820360385643	2		335	154	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157829	27157829	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	124	590	0	ENST00000380036.4:c.53G>A	p.Gly18Glu	p.G18E	ENST00000380036	NM_000459.3	18	gGa/gAa	2/23	1	2	FACETS	1	0.929	1	1	0.991	1	CLONAL	2	FALSE	1	0.394820360385643	2		590	310	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211440	98211440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758411912	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	108	766	1	ENST00000331920.6:c.3715C>T	p.Arg1239Trp	p.R1239W	ENST00000331920	NM_000264.3	1239	Cgg/Tgg	22/24	1	2	FACETS	0.942	0.847	1	0.942	0.847	1	CLONAL	1	FALSE	1	0.394820360385643	2		767	581	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044853	47044853	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	247	684	1	ENST00000377604.3:c.2179G>A	p.Gly727Arg	p.G727R	ENST00000377604	NM_001204468.1	727	Gga/Aga	20/24	1	1	FACETS	0.814	0.766	0.862	1	0.994	1	CLONAL	2	FALSE	0	0.394820360385643	1		685	617	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0023050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	179	556	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	1	2	FACETS	0.977	0.907	1	0.977	0.907	1	CLONAL	1	TRUE	1	0.666148820952956	2		556	550	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579469	7579470	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CG	novel	NA	P-0023050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	185	963	0	ENST00000269305.4:c.216_217dup	p.Val73AlafsTer51	p.V73Afs*51	ENST00000269305	NM_001126112.2	73	gtg/gCGtg	4/11	1	2	FACETS	0.961	0.893	1	0.961	0.893	1	CLONAL	1	TRUE	1	0.666148820952956	2		963	578	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78931508	78931508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1010687194	NA	P-0023050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	139	775	1	ENST00000306801.3:c.3455C>T	p.Thr1152Ile	p.T1152I	ENST00000306801	NM_020761.2	1152	aCa/aTa	29/34	1	2	FACETS	0.989	0.909	1	0.989	0.909	1	CLONAL	1	TRUE	1	0.666148820952956	2		776	422	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344116	70344116	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	580	1068	0	ENST00000374080.3:c.1852C>G	p.Leu618Val	p.L618V	ENST00000374080		618	Ctc/Gtc	13/45	0.337663853181927	3	FACETS	1	0.983	1			1	INDETERMINATE	3	TRUE	NA	0.666148820952956	3		1068	766	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0023092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	162	333	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.645242998250392	2		333	473	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0023092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	319	591	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.645242998250392	2		591	835	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0023092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	102	510	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.676	0.607	0.747	0.676	0.607	0.747	SUBCLONAL	1	TRUE	1	0.645242998250392	2		510	468	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0023092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	178	693	0				ENST00000310581	NM_198253.2	-/1132			0.145780416130245	0	FACETS	0.375	0.348	0.403			1	INDETERMINATE	1	TRUE	0	0.645242998250392	0		693	522	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561418	9561418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	195	471	0	ENST00000353224.5:c.364G>A	p.Glu122Lys	p.E122K	ENST00000353224	NM_177990.2	122	Gaa/Aaa	4/10	1	2	FACETS	0.973	0.906	1	0.973	0.906	1	CLONAL	1	TRUE	1	0.645242998250392	2		471	621	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306721	41306721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	191	544	1	ENST00000373198.4:c.938C>T	p.Ser313Phe	p.S313F	ENST00000373198	NM_133170.3	313	tCc/tTc	7/32	NA	2	FACETS	0.912	0.847	0.979			1	INDETERMINATE	1	TRUE	NA	0.645242998250392	2		545	649	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612028	189612028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs900140738	NA	P-0023092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	159	439	1	ENST00000264731.3:c.1780C>T	p.Arg594Ter	p.R594*	ENST00000264731	NM_003722.4	594	Cga/Tga	14/14	1	2	FACETS	0.988	0.912	1	0.988	0.912	1	CLONAL	1	TRUE	1	0.645242998250392	2		440	499	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633430	8633430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	104	383	1	ENST00000356435.5:c.239C>T	p.Ser80Leu	p.S80L	ENST00000356435		80	tCa/tTa	3/35	1	2	FACETS	0.728	0.655	0.803	0.728	0.655	0.803	SUBCLONAL	1	TRUE	1	0.645242998250392	2		384	443	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486082	8486082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	209	438	1	ENST00000356435.5:c.2735C>T	p.Ser912Phe	p.S912F	ENST00000356435		912	tCc/tTc	17/35	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.645242998250392	2		439	569	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967255	134967255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751581569	NA	P-0023092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	207	542	0	ENST00000398015.3:c.2594G>A	p.Arg865Gln	p.R865Q	ENST00000398015	NM_004441.4	865	cGg/cAg	14/16	NA	2	FACETS	1	0.948	1			1	INDETERMINATE	1	TRUE	NA	0.645242998250392	2		542	630	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69011995	69011995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	213	650	0	ENST00000288368.4:c.2632C>T	p.Pro878Ser	p.P878S	ENST00000288368	NM_024870.2	878	Cct/Tct	23/40	0.272451907433902	0	FACETS	0.35	0.327	0.374			1	INDETERMINATE	1	TRUE	0	0.645242998250392	0		650	669	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550298	39550298	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749558522	NA	P-0023092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	21	268	0	ENST00000262039.4:c.409C>T	p.Arg137Cys	p.R137C	ENST00000262039	NM_002647.2	137	Cgc/Tgc	4/25	1	2	FACETS	0.189	0.145	0.24	0.189	0.145	0.24	SUBCLONAL	1	TRUE	1	0.645242998250392	2		268	345	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633539	69633539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	155	392	0	ENST00000334134.2:c.163C>T	p.His55Tyr	p.H55Y	ENST00000334134	NM_005247.2	55	Cac/Tac	1/3	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.645242998250392	2		392	474	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281249	49281249	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	331	579	0	ENST00000282018.3:c.296T>C	p.Leu99Pro	p.L99P	ENST00000282018	NM_020377.2	99	cTt/cCt	1/1	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.645242998250392	2		579	833	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701154	29701154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	164	328	0	ENST00000356175.3:c.8438G>A	p.Ser2813Asn	p.S2813N	ENST00000356175	NM_000267.3	2813	aGc/aAc	57/57	1	2	FACETS	0.987	0.913	1	0.987	0.913	1	CLONAL	1	TRUE	1	0.645242998250392	2		328	515	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40447646	40447646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	228	474	0	ENST00000345506.4:c.385C>T	p.Pro129Ser	p.P129S	ENST00000345506	NM_003152.3	129	Ccg/Tcg	6/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.645242998250392	2		474	666	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172313	7172313	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	35	414	0	ENST00000302850.5:c.1256C>T	p.Thr419Ile	p.T419I	ENST00000302850	NM_000208.2	419	aCc/aTc	5/22	1	2	FACETS	0.169	0.138	0.204	0.169	0.138	0.204	SUBCLONAL	1	TRUE	1	0.645242998250392	2		414	642	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014100	70014100	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	39	502	0	ENST00000394351.3:c.961C>T	p.Leu321Phe	p.L321F	ENST00000394351	NM_000248.3	321	Ctt/Ttt	9/9	1	2	FACETS	0.178	0.147	0.213	0.178	0.147	0.213	SUBCLONAL	1	TRUE	1	0.645242998250392	2		502	680	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590717	189590717	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1361527608	NA	P-0023092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	231	507	1	ENST00000264731.3:c.1282C>T	p.Pro428Ser	p.P428S	ENST00000264731	NM_003722.4	428	Cct/Tct	10/14	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.645242998250392	2		508	688	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748210	41748210	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263398908	NA	P-0023092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	259	539	0	ENST00000226382.2:c.559G>A	p.Ala187Thr	p.A187T	ENST00000226382	NM_003924.3	187	Gcc/Acc	3/3	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.645242998250392	2		539	743	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976878	55976879	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0023092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	214	554	1	ENST00000263923.4:c.1033_1034delinsAA	p.Gly345Lys	p.G345K	ENST00000263923	NM_002253.2	345	GGg/AAg	8/30	1	2	FACETS	0.96	0.896	1	0.96	0.896	1	CLONAL	1	TRUE	1	0.645242998250392	2		555	691	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293829	1293829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1314611158	NA	P-0023092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	215	727	0	ENST00000310581.5:c.1172C>T	p.Pro391Leu	p.P391L	ENST00000310581	NM_198253.2	391	cCc/cTc	2/16	0.145780416130245	0	FACETS	0.271	0.252	0.291			1	INDETERMINATE	1	TRUE	0	0.645242998250392	0		727	872	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876281	35876281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	178	460	1	ENST00000303115.3:c.1073C>T	p.Pro358Leu	p.P358L	ENST00000303115	NM_002185.3	358	cCa/cTa	8/8	1	2	FACETS	0.942	0.873	1	0.942	0.873	1	CLONAL	1	TRUE	1	0.645242998250392	2		461	586	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803418	32803418	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0023092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	209	514	0	ENST00000374899.4:c.739+2T>C		p.X247_splice	ENST00000374899	NM_018833.2	247			0.645242998250392	4	FACETS	0.876	0.812	0.942	0.292	0.27	0.314	CLONAL	1	TRUE	1	0.645242998250392	4		514	1217	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739834	41739834	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	191	452	0	ENST00000242208.4:c.139G>T	p.Val47Leu	p.V47L	ENST00000242208	NM_002192.2	47	Gta/Tta	2/3	0.145780416130245	0	FACETS	0.375	0.349	0.402			1	INDETERMINATE	1	TRUE	0	0.645242998250392	0		452	560	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046482	69046482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	200	942	1	ENST00000288368.4:c.3955C>T	p.His1319Tyr	p.H1319Y	ENST00000288368	NM_024870.2	1319	Cac/Tac	32/40	0.272451907433902	0	FACETS	0.334	0.31	0.358			1	INDETERMINATE	1	TRUE	0	0.645242998250392	0		943	659	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93640035	93640035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	118	332	0	ENST00000375746.1:c.1364C>T	p.Pro455Leu	p.P455L	ENST00000375746	NM_001174167.1	455	cCc/cTc	10/14	1	2	FACETS	0.97	0.884	1	0.97	0.884	1	CLONAL	1	TRUE	1	0.645242998250392	2		332	377	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	223	427	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.874424418711696	2		427	507	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0023139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	252	850	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	1	2	FACETS	0.94	0.887	0.995	0.94	0.887	0.995	CLONAL	1	TRUE	1	0.874424418711696	2		850	613	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046482	69046482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	384	942	1	ENST00000288368.4:c.3955C>T	p.His1319Tyr	p.H1319Y	ENST00000288368	NM_024870.2	1319	Cac/Tac	32/40	1	2	FACETS	0.963	0.919	1	0.963	0.919	1	CLONAL	1	TRUE	1	0.874424418711696	2		943	912	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201008	108201008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881383	NA	P-0023139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	211	807	0	ENST00000278616.4:c.7375C>T	p.Arg2459Cys	p.R2459C	ENST00000278616	NM_000051.3	2459	Cgt/Tgt	50/63	0.306353210116298	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.874424418711696	0		807	611	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46215202	46215202	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0023139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	146	506	0	ENST00000334344.6:c.638-1G>A		p.X213_splice	ENST00000334344	NM_152641.2	213			1	2	FACETS	0.93	0.86	1	0.93	0.86	1	CLONAL	1	TRUE	1	0.874424418711696	2		506	359	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607257	189607257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	478	913	0	ENST00000264731.3:c.1636G>A	p.Asp546Asn	p.D546N	ENST00000264731	NM_003722.4	546	Gat/Aat	12/14	0.462126826588785	1	FACETS	0.694	0.669	0.72	0.694	0.669	0.72	INDETERMINATE	1	TRUE	0	0.874424418711696	1		913	886	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144679	55144679	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367722824	NA	P-0023139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	288	612	1	ENST00000257290.5:c.2153G>A	p.Arg718Gln	p.R718Q	ENST00000257290	NM_006206.4	718	cGg/cAg	15/23	1	2	FACETS	0.979	0.927	1	0.979	0.927	1	CLONAL	1	TRUE	1	0.874424418711696	2		613	673	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534464	187534464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	318	675	1	ENST00000441802.2:c.9262G>A	p.Glu3088Lys	p.E3088K	ENST00000441802	NM_005245.3	3088	Gag/Aag	13/27	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.874424418711696	2		676	701	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873670	35873670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	310	760	1	ENST00000303115.3:c.626C>T	p.Pro209Leu	p.P209L	ENST00000303115	NM_002185.3	209	cCt/cTt	5/8	1	2	FACETS	0.958	0.909	1	0.958	0.909	1	CLONAL	1	TRUE	1	0.874424418711696	2		761	740	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372744	81372744	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	277	678	0	ENST00000222390.5:c.790G>C	p.Asp264His	p.D264H	ENST00000222390	NM_000601.4	264	Gat/Cat	7/18	1	2	FACETS	0.947	0.896	0.999	0.947	0.896	0.999	CLONAL	1	TRUE	1	0.874424418711696	2		678	669	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0023252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	329	544	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	0.941	0.892	0.991	0.941	0.892	0.991	CLONAL	1	TRUE	1	0.735218029216771	2		544	951	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2224042	2224042	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	341	737	0	ENST00000326181.6:c.1256C>G	p.Thr419Ser	p.T419S	ENST00000326181	NM_032271.2	419	aCc/aGc	13/21	1	2	FACETS	0.901	0.854	0.948	0.901	0.854	0.948	CLONAL	1	TRUE	1	0.735218029216771	2		737	1030	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443729	52443729	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0023252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	475	941	0	ENST00000460680.1:c.67+1G>T		p.X23_splice	ENST00000460680	NM_004656.3	23			0.735218029216771	1	FACETS	0.95	0.915	0.985	0.95	0.915	0.985	CLONAL	1	TRUE	0	0.735218029216771	1		941	860	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913492	NA	P-0023343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	57	555	0	ENST00000286548.4:c.626A>G	p.Gln209Arg	p.Q209R	ENST00000286548	NM_002072.3	209	cAa/cGa	5/7	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.358541373250145	2		555	281	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443710	52443729	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CAGGGAGAAAAGGCTCTTAC	CAGGGAGAAAAGGCTCTTAC	-	novel	NA	P-0023343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	62	787	0	ENST00000460680.1:c.67+1_67+20del		p.X23_splice	ENST00000460680	NM_004656.3	23			0.358541373250145	1	FACETS	0.946	0.824	1	0.946	0.824	1	CLONAL	1	TRUE	0	0.358541373250145	1		787	300	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	129	427	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.898	0.816	0.983	0.898	0.816	0.983	CLONAL	1	TRUE	1	0.462869199707	2		427	621	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059260	27059260	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	80	533	0	ENST00000324856.7:c.1897C>T	p.Gln633Ter	p.Q633*	ENST00000324856	NM_006015.4	633	Cag/Tag	4/20	0.251641891621725	1	FACETS	0.385	0.339	0.435	0.385	0.339	0.435	INDETERMINATE	1	TRUE	0	0.462869199707	1		533	690	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266100	41266100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519886	NA	P-0023378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	28	368	0	ENST00000349496.5:c.97T>C	p.Ser33Pro	p.S33P	ENST00000349496	NM_001904.3	33	Tct/Cct	3/15	0.208111003905442	3	FACETS	0.335	0.267	0.412	0.167	0.133	0.206	INDETERMINATE	1	TRUE	1	0.462869199707	3		368	445	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546847	9546847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	132	508	0	ENST00000353224.5:c.1175C>T	p.Ser392Leu	p.S392L	ENST00000353224	NM_177990.2	392	tCg/tTg	5/10	0.208111003905442	3	FACETS	1	0.981	1	0.637	0.581	0.696	INDETERMINATE	1	TRUE	1	0.462869199707	3		508	551	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132428	11132428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	122	663	0	ENST00000358026.2:c.2644G>A	p.Glu882Lys	p.E882K	ENST00000358026	NM_001128849.1	882	Gaa/Aaa	19/36	0.208111003905442	3	FACETS	0.685	0.619	0.756	0.343	0.309	0.378	INDETERMINATE	1	TRUE	1	0.462869199707	3		663	947	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164773	106164773	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765414159	NA	P-0023378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	130	488	0	ENST00000380013.4:c.3641G>A	p.Arg1214Gln	p.R1214Q	ENST00000380013	NM_001127208.2	1214	cGg/cAg	6/11	1	2	FACETS	0.886	0.806	0.97	0.886	0.806	0.97	CLONAL	1	TRUE	1	0.462869199707	2		488	634	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197443	106197443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1452689450	NA	P-0023378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	32	301	0	ENST00000380013.4:c.5776C>T	p.Arg1926Cys	p.R1926C	ENST00000380013	NM_001127208.2	1926	Cgt/Tgt	11/11	1	2	FACETS	0.376	0.305	0.455	0.376	0.305	0.455	SUBCLONAL	1	TRUE	1	0.462869199707	2		301	368	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483911	88483911	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	191	700	0	ENST00000360948.2:c.1659C>A	p.Phe553Leu	p.F553L	ENST00000360948	NM_001012338.2	553	ttC/ttA	14/19	1	2	FACETS	0.991	0.917	1	0.991	0.917	1	CLONAL	1	TRUE	1	0.462869199707	2		700	833	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944716	206944742	+	inframe_deletion	In_Frame_Del	DEL	CAAGGACTCCTTTAACAACAAGTTGTC	CAAGGACTCCTTTAACAACAAGTTGTC	-	novel	NA	P-0023378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	169	541	0	ENST00000423557.1:c.184_210del	p.Asp62_Leu70del	p.D62_L70del	ENST00000423557	NM_000572.2	62	GACAACTTGTTGTTAAAGGAGTCCTTG/-	2/5	1	2	FACETS	0.975	0.898	1	0.975	0.898	1	CLONAL	1	TRUE	1	0.462869199707	2		541	749	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165708	108165708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	191	447	1	ENST00000278616.4:c.4831C>T	p.Leu1611Phe	p.L1611F	ENST00000278616	NM_000051.3	1611	Ctt/Ttt	32/63	0.19080803968061	4	FACETS	0.885	0.822	0.951	0.885	0.822	0.951	INDETERMINATE	2	TRUE	2	0.462869199707	4		448	682	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514488	125514488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	179	446	0	ENST00000428830.2:c.1183G>A	p.Glu395Lys	p.E395K	ENST00000428830	NM_001114121.2	395	Gag/Aag	11/14	0.19080803968061	4	FACETS	0.805	0.744	0.867	0.805	0.744	0.867	INDETERMINATE	2	TRUE	2	0.462869199707	4		446	703	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433543	49433544	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0023378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	103	873	2	ENST00000301067.7:c.8009_8010delinsTT	p.Ser2670Phe	p.S2670F	ENST00000301067	NM_003482.3	2670	tCC/tTT	31/54	0.251641891621725	1	FACETS	0.344	0.307	0.383	0.344	0.307	0.383	INDETERMINATE	1	TRUE	0	0.462869199707	1		875	995	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623673	28623673	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs559157798	NA	P-0023378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	113	615	0	ENST00000241453.7:c.884G>A	p.Gly295Asp	p.G295D	ENST00000241453	NM_004119.2	295	gGc/gAc	8/24	0.19080803968061	4	FACETS	0.924	0.832	1	0.462	0.416	0.511	INDETERMINATE	1	TRUE	2	0.462869199707	4		615	773	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004984	16004984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141130092	NA	P-0023378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	205	718	3	ENST00000268712.3:c.2270C>T	p.Thr757Met	p.T757M	ENST00000268712	NM_006311.3	757	aCg/aTg	20/46	1	2	FACETS	0.996	0.925	1	0.996	0.925	1	CLONAL	1	TRUE	1	0.462869199707	2		721	889	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752480	55752480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	175	786	5	ENST00000284073.2:c.938G>A	p.Gly313Asp	p.G313D	ENST00000284073	NM_138962.2	313	gGc/gAc	12/14	1	2	FACETS	0.793	0.73	0.858	0.793	0.73	0.858	SUBCLONAL	1	TRUE	1	0.462869199707	2		791	954	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740836	58740836	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs747668756	NA	P-0023378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	70	503	0	ENST00000305921.3:c.1741C>T	p.Arg581Ter	p.R581*	ENST00000305921	NM_003620.3	581	Cga/Tga	6/6	1	2	FACETS	0.427	0.372	0.487	0.427	0.372	0.487	SUBCLONAL	1	TRUE	1	0.462869199707	2		503	708	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350527	15350527	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs376162076	NA	P-0023378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	95	682	0	ENST00000263377.2:c.3388C>G	p.Arg1130Gly	p.R1130G	ENST00000263377	NM_058243.2	1130	Cgg/Ggg	16/20	0.208111003905442	3	FACETS	0.503	0.447	0.563	0.251	0.223	0.282	INDETERMINATE	1	TRUE	1	0.462869199707	3		682	1005	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943385	17943385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	112	781	1	ENST00000458235.1:c.2623C>T	p.Leu875Phe	p.L875F	ENST00000458235	NM_000215.3	875	Ctc/Ttc	19/24	0.208111003905442	3	FACETS	0.552	0.495	0.612	0.276	0.247	0.306	INDETERMINATE	1	TRUE	1	0.462869199707	3		782	1080	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753369	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0023378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	84	860	1	ENST00000222329.4:c.895_896delinsAA	p.Gly299Lys	p.G299K	ENST00000222329	NM_006494.2	299	GGa/AAa	4/4	0.208111003905442	3	FACETS	0.388	0.341	0.438	0.194	0.17	0.219	INDETERMINATE	1	TRUE	1	0.462869199707	3		861	1152	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845256	42845256	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	65	510	0	ENST00000398585.3:c.1006G>A	p.Glu336Lys	p.E336K	ENST00000398585	NM_001135099.1	336	Gaa/Aaa	9/14	1	2	FACETS	0.452	0.391	0.517	0.452	0.391	0.517	SUBCLONAL	1	TRUE	1	0.462869199707	2		510	622	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462588	92462589	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0023378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	314	498	1	ENST00000265734.4:c.49_50delinsAA	p.Ala17Lys	p.A17K	ENST00000265734	NM_001259.6	17	GCg/AAg	2/8	0.225006061629444	3	FACETS	1	0.989	1	0.767	0.728	0.806	INDETERMINATE	2	TRUE	0	0.462869199707	3		499	726	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0023552-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	40	109	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.946	0.79	1	0.946	0.79	1	CLONAL	1	TRUE	1	0.3	2		109	282	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0023552-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	146	538	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.3	3	FACETS	0.97	0.889	1	0.647	0.593	0.703	CLONAL	2	TRUE	0	0.3	3		538	577	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7141702	7141702	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1568440846	NA	P-0023552-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	45	410	0	ENST00000302850.5:c.2668C>T	p.Arg890Ter	p.R890*	ENST00000302850	NM_000208.2	890	Cga/Tga	13/22	0.3	3	FACETS	0.662	0.556	0.779	0.331	0.278	0.39	SUBCLONAL	1	TRUE	1	0.3	3		410	521	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0023610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	150	572	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.947847514837156	36	FACETS	1	0.932	1	0.471	0.437	0.507	CLONAL	15	FALSE	4	0.947847514837156	36		572	359	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120196	70120196	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	268	546	0	ENST00000245479.2:c.1198G>C	p.Glu400Gln	p.E400Q	ENST00000245479	NM_000346.3	400	Gag/Cag	3/3	0.947847514837156	28	FACETS	0.974	0.919	1	0.447	0.421	0.472	CLONAL	11	FALSE	4	0.947847514837156	28		546	703	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144810	11144810	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	282	605	0	ENST00000358026.2:c.3886del	p.Val1296CysfsTer10	p.V1296Cfs*10	ENST00000358026	NM_001128849.1	1295	gaG/ga	28/36	0.947847514837156	20	FACETS	1	0.966	1	0.699	0.666	0.732	CLONAL	11	FALSE	4	0.947847514837156	20		605	507	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15280916	15280916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs989373826	NA	P-0023610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	39	749	0	ENST00000263388.2:c.5180C>T	p.Pro1727Leu	p.P1727L	ENST00000263388	NM_000435.2	1727	cCa/cTa	28/33	0.947847514837156	20	FACETS	1	0.951	1	0.092	0.076	0.11	CLONAL	1	FALSE	4	0.947847514837156	20		749	533	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647488	117647488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	30	549	2	ENST00000368508.3:c.5456C>T	p.Ser1819Phe	p.S1819F	ENST00000368508	NM_002944.2	1819	tCc/tTc	33/43	0.947847514837156	30	FACETS	1	0.902	1	0.093	0.074	0.113	CLONAL	2	FALSE	4	0.947847514837156	30		551	375	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989661	68989661	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	158	689	0	ENST00000288368.4:c.1599G>A	p.Met533Ile	p.M533I	ENST00000288368	NM_024870.2	533	atG/atA	15/40	0.947847514837156	28	FACETS	1	0.946	1	0.302	0.277	0.327	CLONAL	7	FALSE	4	0.947847514837156	28		689	613	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	37	427	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.827	0.687	0.981			1	INDETERMINATE	1	TRUE	NA	0.390744520867002	2		427	229	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0023733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	108	292	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.390744520867002	2		292	544	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819752	81819753	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0023733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	60	560	1	ENST00000359376.3:c.158_159delinsTT	p.Ala53Val	p.A53V	ENST00000359376	NM_002661.3	53	gCC/gTT	2/33	0.390744520867002	1	FACETS	0.647	0.56	0.741	0.647	0.56	0.741	SUBCLONAL	1	TRUE	0	0.390744520867002	1		561	382	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718264	117718264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1302819459	NA	P-0023733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	83	469	0	ENST00000368508.3:c.593C>T	p.Pro198Leu	p.P198L	ENST00000368508	NM_002944.2	198	cCt/cTt	7/43	0.390744520867002	1	FACETS	0.89	0.791	0.995	0.89	0.791	0.995	CLONAL	1	TRUE	0	0.390744520867002	1		469	384	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0023734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	2407	292	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.746589436900044	36	FACETS	0.99	0.982	0.997			1	CLONAL	34	FALSE	NA	0.746589436900044	36		292	2624	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0023734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	59	693	0				ENST00000310581	NM_198253.2	-/1132			0.746589436900044	3	FACETS	0.952	0.879	1	0.952	0.879	1	CLONAL	3	FALSE	0	0.746589436900044	3		693	76	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913250	NA	P-0023734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	35	520	2	ENST00000369535.4:c.34G>T	p.Gly12Cys	p.G12C	ENST00000369535	NM_002524.4	12	Ggt/Tgt	2/7	0.740410845355933	4	FACETS	0.585	0.481	0.7	0.146	0.12	0.175	SUBCLONAL	1	FALSE	0	0.746589436900044	4		522	280	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577106	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0023734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	311	757	0	ENST00000269305.4:c.832_833delinsTT	p.Pro278Phe	p.P278F	ENST00000269305	NM_001126112.2	278	CCt/TTt	8/11	0.740410845355933	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	4	FALSE	0	0.746589436900044	4		757	360	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178712	108178712	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs869312756	NA	P-0023734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	74	388	1	ENST00000278616.4:c.5762+1G>A		p.X1921_splice	ENST00000278616	NM_000051.3	1921			0.734481850917103	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	FALSE	0	0.746589436900044	2		389	96	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431903	49431903	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	147	800	0	ENST00000301067.7:c.9236A>C	p.Lys3079Thr	p.K3079T	ENST00000301067	NM_003482.3	3079	aAg/aCg	34/54	0.746589436900044	4	FACETS	1	0.959	1			1	CLONAL	2	FALSE	NA	0.746589436900044	4		800	328	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42384776	42384776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	151	597	0	ENST00000221972.3:c.538G>A	p.Asp180Asn	p.D180N	ENST00000221972	NM_021601.3	180	Gat/Aat	4/5	0.746589436900044	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	FALSE	0	0.746589436900044	3		597	182	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801109	1801109	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	180	788	0	ENST00000260795.2:c.238G>A	p.Gly80Arg	p.G80R	ENST00000260795		80	Ggg/Agg	2/17	0.568154824045024	3	FACETS	1	0.985	1			1	CLONAL	3	FALSE	NA	0.746589436900044	3		788	211	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974723	21974723	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746834149	NA	P-0023734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	151	425	0	ENST00000304494.5:c.104G>A	p.Gly35Glu	p.G35E	ENST00000304494	NM_000077.4	35	gGg/gAg	1/3	0.746589436900044	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	FALSE	0	0.746589436900044	3		425	173	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	63	390	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.389476348730756	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.389476348730756	1		390	243	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	41	246	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.389476348730756	2		247	179	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645693	12645693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397516827	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	29	204	0	ENST00000251849.4:c.776C>T	p.Ser259Phe	p.S259F	ENST00000251849	NM_002880.3	259	tCc/tTc	7/17	0.0821482119879249	3	FACETS	0.978	0.792	1	0.489	0.396	0.592	INDETERMINATE	1	TRUE	1	0.389476348730756	3		204	182	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858517	9858517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765370528	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	46	375	1	ENST00000330684.3:c.2884G>A	p.Glu962Lys	p.E962K	ENST00000330684	NM_001134407.1	962	Gaa/Aaa	13/13	1	2	FACETS	0.952	0.809	1	0.952	0.809	1	CLONAL	1	TRUE	1	0.389476348730756	2		376	248	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552648	18552648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	62	425	0	ENST00000266497.5:c.2059G>A	p.Glu687Lys	p.E687K	ENST00000266497		687	Gaa/Aaa	14/31	0.157745092300077	3	FACETS	1	0.964	1	0.66	0.575	0.751	INDETERMINATE	1	TRUE	1	0.389476348730756	3		425	288	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593603	55593603	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913235	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	32	313	0	ENST00000288135.5:c.1669T>G	p.Trp557Gly	p.W557G	ENST00000288135	NM_000222.2	557	Tgg/Ggg	11/21	1	2	FACETS	0.775	0.634	0.932	0.775	0.634	0.932	CLONAL	1	TRUE	1	0.389476348730756	2		313	212	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665752	29665755	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1555535032	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	57	246	0	ENST00000356175.3:c.6789_6792del	p.Tyr2264ThrfsTer5	p.Y2264Tfs*5	ENST00000356175	NM_000267.3	2263	ACTTac/ac	45/57	0.389476348730756	2	FACETS	1	0.964	1	0.678	0.589	0.771	CLONAL	1	TRUE	0	0.389476348730756	2		246	216	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641144	117641144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866970127	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	58	413	2	ENST00000368508.3:c.5827G>A	p.Glu1943Lys	p.E1943K	ENST00000368508	NM_002944.2	1943	Gaa/Aaa	36/43	1	2	FACETS	0.9	0.778	1	0.9	0.778	1	CLONAL	1	TRUE	1	0.389476348730756	2		415	331	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678460	88678460	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	63	414	0	ENST00000360948.2:c.1076C>T	p.Ser359Phe	p.S359F	ENST00000360948	NM_001012338.2	359	tCc/tTc	9/19	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.389476348730756	2		414	268	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976476	25976476	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	42	331	0	ENST00000435504.4:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000435504		357	Cga/Tga	11/13	1	2	FACETS	0.967	0.815	1	0.967	0.815	1	CLONAL	1	TRUE	1	0.389476348730756	2		331	223	SUCCESS
APC	324	MSKCC	GRCh37	5	112178000	112178000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768922431	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	32	285	1	ENST00000257430.4:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000257430	NM_000038.5	2237	Cga/Tga	16/16	1	2	FACETS	0.809	0.662	0.972	0.809	0.662	0.972	CLONAL	1	TRUE	1	0.389476348730756	2		286	203	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245411	153245411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	65	416	0	ENST00000281708.4:c.1780C>T	p.Leu594Phe	p.L594F	ENST00000281708	NM_033632.3	594	Ctt/Ttt	11/12	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.389476348730756	2		416	309	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211055	55211055	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866460345	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	41	368	0	ENST00000275493.2:c.298C>T	p.Pro100Ser	p.P100S	ENST00000275493	NM_005228.3	100	Cct/Tct	3/28	0.244479439407033	5	FACETS	1	0.84	1	0.335	0.28	0.396	CLONAL	1	TRUE	2	0.389476348730756	5		368	332	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912191	114912191	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	64	400	0	ENST00000543371.1:c.1261G>A	p.Asp421Asn	p.D421N	ENST00000543371	NM_001198531.1	421	Gat/Aat	11/14	1	2	FACETS	0.865	0.752	0.986	0.865	0.752	0.986	CLONAL	1	TRUE	1	0.389476348730756	2		400	380	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386512	81386512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	45	230	0	ENST00000222390.5:c.475G>A	p.Glu159Lys	p.E159K	ENST00000222390	NM_000601.4	159	Gaa/Aaa	4/18	0.244479439407033	5	FACETS	0.75	0.636	0.874	0.5	0.424	0.583	SUBCLONAL	2	TRUE	2	0.389476348730756	5		230	244	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982021	93982021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867625037	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	26	215	0	ENST00000369303.4:c.1444G>A	p.Glu482Lys	p.E482K	ENST00000369303	NM_004440.3	482	Gag/Aag	6/17	1	2	FACETS	0.814	0.651	0.997	0.814	0.651	0.997	CLONAL	1	TRUE	1	0.389476348730756	2		215	164	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519886	29519886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	74	374	0	ENST00000389048.3:c.1685G>A	p.Gly562Glu	p.G562E	ENST00000389048	NM_004304.4	562	gGa/gAa	9/29	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.389476348730756	2		374	342	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733337	40733337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746243026	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	60	300	0	ENST00000373198.4:c.3469G>A	p.Asp1157Asn	p.D1157N	ENST00000373198	NM_133170.3	1157	Gat/Aat	26/32	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.389476348730756	2		300	262	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779181	135779181	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202241429	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	71	324	0	ENST00000298552.3:c.2065C>T	p.Arg689Cys	p.R689C	ENST00000298552	NM_001162426.1	689	Cgc/Tgc	17/23	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.389476348730756	2		324	309	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248617	212248617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765120252	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	37	385	0	ENST00000342788.4:c.3650G>A	p.Gly1217Glu	p.G1217E	ENST00000342788	NM_005235.2	1217	gGa/gAa	28/28	1	2	FACETS	0.736	0.611	0.875	0.736	0.611	0.875	SUBCLONAL	1	TRUE	1	0.389476348730756	2		385	258	SUCCESS
APC	324	MSKCC	GRCh37	5	112128185	112128185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779805	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	39	302	0	ENST00000257430.4:c.688C>T	p.Arg230Cys	p.R230C	ENST00000257430	NM_000038.5	230	Cgt/Tgt	7/16	1	2	FACETS	0.672	0.559	0.796	0.672	0.559	0.796	SUBCLONAL	1	TRUE	1	0.389476348730756	2		302	298	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187558040	187558040	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746739063	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	15	188	1	ENST00000441802.2:c.3671C>T	p.Pro1224Leu	p.P1224L	ENST00000441802	NM_005245.3	1224	cCc/cTc	5/27	1	2	FACETS	0.514	0.378	0.675	0.514	0.378	0.675	SUBCLONAL	1	TRUE	1	0.389476348730756	2		189	150	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715333	117715333	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	25	256	0	ENST00000368508.3:c.1156G>A	p.Asp386Asn	p.D386N	ENST00000368508	NM_002944.2	386	Gat/Aat	10/43	1	2	FACETS	0.873	0.696	1	0.873	0.696	1	CLONAL	1	TRUE	1	0.389476348730756	2		256	147	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651124	206651124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	67	512	1	ENST00000367120.3:c.734C>T	p.Ala245Val	p.A245V	ENST00000367120	NM_014002.3	245	gCc/gTc	8/22	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.389476348730756	2		513	295	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100959	41100959	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	46	375	0	ENST00000373198.4:c.1397A>G	p.Asn466Ser	p.N466S	ENST00000373198	NM_133170.3	466	aAc/aGc	8/32	1	2	FACETS	0.707	0.598	0.827	0.707	0.598	0.827	SUBCLONAL	1	TRUE	1	0.389476348730756	2		375	334	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418373	139418373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	77	502	0	ENST00000277541.6:c.199C>T	p.Pro67Ser	p.P67S	ENST00000277541	NM_017617.3	67	Ccc/Tcc	3/34	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.389476348730756	2		502	353	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383230	42383230	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	53	383	1	ENST00000221972.3:c.250G>A	p.Gly84Ser	p.G84S	ENST00000221972	NM_021601.3	84	Ggc/Agc	2/5	1	2	FACETS	0.895	0.768	1	0.895	0.768	1	CLONAL	1	TRUE	1	0.389476348730756	2		384	304	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790129	40790129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	46	426	0	ENST00000373198.4:c.2602C>T	p.Pro868Ser	p.P868S	ENST00000373198	NM_133170.3	868	Ccc/Tcc	18/32	1	2	FACETS	0.691	0.584	0.808	0.691	0.584	0.808	SUBCLONAL	1	TRUE	1	0.389476348730756	2		426	342	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031230	36031230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	73	458	0	ENST00000358208.4:c.1349C>T	p.Ser450Phe	p.S450F	ENST00000358208		450	tCc/tTc	11/12	1	2	FACETS	0.994	0.875	1	0.994	0.875	1	CLONAL	1	TRUE	1	0.389476348730756	2		458	377	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752817	42752817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	57	486	1	ENST00000222329.4:c.1447C>T	p.Arg483Cys	p.R483C	ENST00000222329	NM_006494.2	483	Cgc/Tgc	4/4	1	2	FACETS	0.841	0.725	0.966	0.841	0.725	0.966	CLONAL	1	TRUE	1	0.389476348730756	2		487	348	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243777028	243777028	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	49	336	0	ENST00000263826.5:c.641C>T	p.Ser214Phe	p.S214F	ENST00000263826	NM_005465.4	214	tCc/tTc	7/13	1	2	FACETS	0.791	0.674	0.919	0.791	0.674	0.919	CLONAL	1	TRUE	1	0.389476348730756	2		336	318	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864355	57864355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765569651	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	43	447	0	ENST00000228682.2:c.1832G>A	p.Arg611Gln	p.R611Q	ENST00000228682	NM_005269.2	611	cGg/cAg	12/12	0.157745092300077	3	FACETS	0.859	0.722	1	0.43	0.361	0.505	INDETERMINATE	1	TRUE	1	0.389476348730756	3		447	307	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444082	49444082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	54	402	0	ENST00000301067.7:c.3289C>T	p.Pro1097Ser	p.P1097S	ENST00000301067	NM_003482.3	1097	Cca/Tca	11/54	0.157745092300077	3	FACETS	0.82	0.71	0.936	0.82	0.71	0.936	INDETERMINATE	2	TRUE	1	0.389476348730756	3		402	202	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149260	119149260	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	65	389	0	ENST00000264033.4:c.1268T>C	p.Ile423Thr	p.I423T	ENST00000264033	NM_005188.3	423	aTt/aCt	9/16	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.389476348730756	2		389	315	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119562156	119562156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772550262	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	93	295	0	ENST00000316626.5:c.1180C>T	p.His394Tyr	p.H394Y	ENST00000316626		394	Cat/Tat	11/12	0.389476348730756	1	FACETS	0.772	0.698	0.848	1	0.984	1	SUBCLONAL	2	TRUE	0	0.389476348730756	1		295	249	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106808	27106808	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	66	406	0	ENST00000324856.7:c.6419C>T	p.Pro2140Leu	p.P2140L	ENST00000324856	NM_006015.4	2140	cCc/cTc	20/20	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.389476348730756	2		406	303	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288735	11288735	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	61	351	0	ENST00000361445.4:c.3020C>T	p.Ala1007Val	p.A1007V	ENST00000361445	NM_004958.3	1007	gCc/gTc	19/58	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.389476348730756	2		351	294	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258601	16258607	+	frameshift_variant	Frame_Shift_Del	DEL	ACACGCC	ACACGCC	CT	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	43	326	2	ENST00000375759.3:c.5866_5872delinsCT	p.Thr1956LeufsTer5	p.T1956Lfs*5	ENST00000375759	NM_015001.2	1956	ACACGCCgg/CTgg	11/15	1	2	FACETS	0.928	0.783	1	0.928	0.783	1	CLONAL	1	TRUE	1	0.389476348730756	2		328	238	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261949	16261949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772442954	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	41	370	0	ENST00000375759.3:c.9214C>T	p.His3072Tyr	p.H3072Y	ENST00000375759	NM_015001.2	3072	Cac/Tac	11/15	1	2	FACETS	0.915	0.769	1	0.915	0.769	1	CLONAL	1	TRUE	1	0.389476348730756	2		370	230	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532699	46532699	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	30	277	0	ENST00000262741.5:c.379C>G	p.Pro127Ala	p.P127A	ENST00000262741	NM_003629.3	127	Cct/Gct	4/10	1	2	FACETS	0.748	0.607	0.905	0.748	0.607	0.905	CLONAL	1	TRUE	1	0.389476348730756	2		277	206	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726621	46726621	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	42	369	0	ENST00000371975.4:c.700C>T	p.Leu234Phe	p.L234F	ENST00000371975	NM_003579.3	234	Ctc/Ttc	7/18	1	2	FACETS	0.773	0.649	0.909	0.773	0.649	0.909	CLONAL	1	TRUE	1	0.389476348730756	2		369	279	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282358	115282359	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	49	362	2	ENST00000438362.2:c.291_292delinsTT	p.His98Tyr	p.H98Y	ENST00000438362	NM_001242891.1	97	ttCCac/ttTTac	3/20	1	2	FACETS	0.871	0.742	1	0.871	0.742	1	CLONAL	1	TRUE	1	0.389476348730756	2		364	289	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468189	120468189	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	58	434	0	ENST00000256646.2:c.4250C>T	p.Pro1417Leu	p.P1417L	ENST00000256646	NM_024408.3	1417	cCc/cTc	25/34	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.389476348730756	2		434	274	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844416	156844416	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	73	510	1	ENST00000524377.1:c.1249G>A	p.Gly417Arg	p.G417R	ENST00000524377	NM_002529.3	417	Ggg/Agg	10/17	1	2	FACETS	0.897	0.788	1	0.897	0.788	1	CLONAL	1	TRUE	1	0.389476348730756	2		511	418	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332178	70332178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773402594	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	33	231	0	ENST00000373644.4:c.83G>A	p.Arg28Gln	p.R28Q	ENST00000373644	NM_030625.2	28	cGa/cAa	2/12	1	2	FACETS	0.831	0.682	0.995	0.831	0.682	0.995	CLONAL	1	TRUE	1	0.389476348730756	2		231	204	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446317	70446317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1371245854	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	66	374	0	ENST00000373644.4:c.5257C>T	p.Arg1753Cys	p.R1753C	ENST00000373644	NM_030625.2	1753	Cgt/Tgt	11/12	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.389476348730756	2		374	313	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88677078	88677078	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	52	356	0	ENST00000372037.3:c.863T>C	p.Ile288Thr	p.I288T	ENST00000372037	NM_004329.2	288	aTa/aCa	9/13	1	2	FACETS	0.785	0.672	0.909	0.785	0.672	0.909	CLONAL	1	TRUE	1	0.389476348730756	2		356	340	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456585	32456585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	24	58	0	ENST00000332351.3:c.307G>A	p.Ala103Thr	p.A103T	ENST00000332351	NM_024426.4	103	Gcg/Acg	1/10	1	2	FACETS	0.948	0.772	1	1	0.952	1	CLONAL	2	TRUE	1	0.389476348730756	2		58	65	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588130	69588130	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	73	424	0	ENST00000168712.1:c.568G>A	p.Gly190Arg	p.G190R	ENST00000168712	NM_002007.2	190	Ggg/Agg	3/3	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.389476348730756	2		424	326	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77043864	77043864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	73	452	0	ENST00000356341.3:c.1462G>A	p.Glu488Lys	p.E488K	ENST00000356341	NM_002576.4	488	Gag/Aag	14/15	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.389476348730756	2		452	375	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342451	118342451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1330801496	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	35	215	0	ENST00000534358.1:c.577C>T	p.Pro193Ser	p.P193S	ENST00000534358	NM_005933.3	193	Cca/Tca	3/36	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.389476348730756	2		215	147	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342545	118342545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	14	206	0	ENST00000534358.1:c.671G>A	p.Arg224Lys	p.R224K	ENST00000534358	NM_005933.3	224	aGa/aAa	3/36	1	2	FACETS	0.58	0.422	0.767	0.58	0.422	0.767	SUBCLONAL	1	TRUE	1	0.389476348730756	2		206	124	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343913	118343913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264831726	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	49	291	0	ENST00000534358.1:c.2039C>T	p.Ser680Leu	p.S680L	ENST00000534358	NM_005933.3	680	tCg/tTg	3/36	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.389476348730756	2		291	228	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343994	118343997	+	frameshift_variant	Frame_Shift_Del	DEL	CTCA	CTCA	-	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	24	275	0	ENST00000534358.1:c.2123_2126del	p.His708LeufsTer7	p.H708Lfs*7	ENST00000534358	NM_005933.3	707	gCTCAc/gc	3/36	1	2	FACETS	0.639	0.504	0.792	0.639	0.504	0.792	SUBCLONAL	1	TRUE	1	0.389476348730756	2		275	193	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118355589	118355589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	51	385	0	ENST00000534358.1:c.4231G>A	p.Ala1411Thr	p.A1411T	ENST00000534358	NM_005933.3	1411	Gca/Aca	10/36	1	2	FACETS	0.885	0.757	1	0.885	0.757	1	CLONAL	1	TRUE	1	0.389476348730756	2		385	296	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699356	18699356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	30	232	0	ENST00000266497.5:c.3457C>T	p.His1153Tyr	p.H1153Y	ENST00000266497		1153	Cat/Tat	24/31	0.157745092300077	3	FACETS	0.99	0.805	1	0.495	0.402	0.598	INDETERMINATE	1	TRUE	1	0.389476348730756	3		232	186	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432348	49432348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	73	423	1	ENST00000301067.7:c.8791C>T	p.Pro2931Ser	p.P2931S	ENST00000301067	NM_003482.3	2931	Cca/Tca	34/54	0.157745092300077	3	FACETS	1	0.966	1	0.642	0.565	0.723	INDETERMINATE	1	TRUE	1	0.389476348730756	3		424	349	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446167	49446168	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	87	421	1	ENST00000301067.7:c.1298_1299delinsTT	p.Pro433Leu	p.P433L	ENST00000301067	NM_003482.3	433	cCC/cTT	10/54	0.157745092300077	3	FACETS	0.89	0.797	0.987	0.89	0.797	0.987	INDETERMINATE	2	TRUE	1	0.389476348730756	3		422	300	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495826	56495826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	27	247	0	ENST00000267101.3:c.4016C>T	p.Ala1339Val	p.A1339V	ENST00000267101	NM_001982.3	1339	gCc/gTc	28/28	0.157745092300077	3	FACETS	1	0.875	1	0.56	0.451	0.681	INDETERMINATE	1	TRUE	1	0.389476348730756	3		247	148	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623794	28623794	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	57	384	0	ENST00000241453.7:c.860T>C	p.Leu287Ser	p.L287S	ENST00000241453	NM_004119.2	287	tTa/tCa	7/24	1	2	FACETS	0.941	0.813	1	0.941	0.813	1	CLONAL	1	TRUE	1	0.389476348730756	2		384	311	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29007982	29007982	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	43	258	0	ENST00000282397.4:c.787C>T	p.Gln263Ter	p.Q263*	ENST00000282397	NM_002019.4	263	Caa/Taa	6/30	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.389476348730756	2		258	193	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972704	32972704	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1475702169	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	74	333	0	ENST00000380152.3:c.10054C>G	p.Leu3352Val	p.L3352V	ENST00000380152		3352	Ctt/Gtt	27/27	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.389476348730756	2		333	313	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562489	95562489	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	41	332	0	ENST00000393063.1:c.4768G>A	p.Val1590Met	p.V1590M	ENST00000393063	NM_030621.3	1590	Gtg/Atg	24/28	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.389476348730756	2		332	190	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019419	42019419	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	71	390	0	ENST00000219905.7:c.3472C>A	p.Pro1158Thr	p.P1158T	ENST00000219905	NM_001164273.1	1158	Cca/Aca	10/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.389476348730756	2		390	281	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714168	43714168	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs752288363	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	70	495	0	ENST00000382044.4:c.3985A>G	p.Met1329Val	p.M1329V	ENST00000382044	NM_001141980.1	1329	Atg/Gtg	19/28	1	2	FACETS	0.868	0.76	0.984	0.868	0.76	0.984	CLONAL	1	TRUE	1	0.389476348730756	2		495	414	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726697	88726697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754131028	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	43	311	0	ENST00000360948.2:c.347G>A	p.Arg116Gln	p.R116Q	ENST00000360948	NM_001012338.2	116	cGg/cAg	4/19	1	2	FACETS	0.932	0.786	1	0.932	0.786	1	CLONAL	1	TRUE	1	0.389476348730756	2		311	237	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396427	396427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	48	553	0	ENST00000262320.3:c.599C>T	p.Ser200Phe	p.S200F	ENST00000262320	NM_003502.3	200	tCc/tTc	2/11	1	2	FACETS	0.734	0.623	0.854	0.734	0.623	0.854	SUBCLONAL	1	TRUE	1	0.389476348730756	2		553	336	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396436	396436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773096813	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	49	553	0	ENST00000262320.3:c.590C>T	p.Thr197Ile	p.T197I	ENST00000262320	NM_003502.3	197	aCc/aTc	2/11	1	2	FACETS	0.695	0.591	0.809	0.695	0.591	0.809	SUBCLONAL	1	TRUE	1	0.389476348730756	2		553	362	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222206	2222206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	67	374	0	ENST00000326181.6:c.490G>A	p.Asp164Asn	p.D164N	ENST00000326181	NM_032271.2	164	Gac/Aac	8/21	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.389476348730756	2		374	338	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2224258	2224258	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1345441201	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	63	466	0	ENST00000326181.6:c.1270G>A	p.Asp424Asn	p.D424N	ENST00000326181	NM_032271.2	424	Gac/Aac	14/21	1	2	FACETS	0.952	0.828	1	0.952	0.828	1	CLONAL	1	TRUE	1	0.389476348730756	2		466	340	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225402	2225402	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	65	450	0	ENST00000326181.6:c.1487C>T	p.Ser496Phe	p.S496F	ENST00000326181	NM_032271.2	496	tCc/tTc	16/21	1	2	FACETS	0.951	0.829	1	0.951	0.829	1	CLONAL	1	TRUE	1	0.389476348730756	2		450	351	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50816367	50816368	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	25	282	0	ENST00000398568.2:c.1807_1808delinsTT	p.Thr603Phe	p.T603F	ENST00000398568	NM_001042412.1	603	ACc/TTc	10/18	1	2	FACETS	0.544	0.43	0.673	0.544	0.43	0.673	SUBCLONAL	1	TRUE	1	0.389476348730756	2		282	236	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72863710	72863710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	88	448	1	ENST00000268489.5:c.3497C>T	p.Pro1166Leu	p.P1166L	ENST00000268489	NM_006885.3	1166	cCa/cTa	5/10	1	2	FACETS	0.991	0.882	1	0.991	0.882	1	CLONAL	1	TRUE	1	0.389476348730756	2		449	456	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993732	72993732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	44	321	0	ENST00000268489.5:c.313C>T	p.Pro105Ser	p.P105S	ENST00000268489	NM_006885.3	105	Ccg/Tcg	2/10	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.389476348730756	2		321	219	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877440	89877440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs926971713	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	67	388	1	ENST00000389301.3:c.323C>T	p.Pro108Leu	p.P108L	ENST00000389301	NM_000135.2	108	cCc/cTc	4/43	1	2	FACETS	0.98	0.857	1	0.98	0.857	1	CLONAL	1	TRUE	1	0.389476348730756	2		389	351	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979512	7979512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749294264	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	47	380	1	ENST00000319144.4:c.1513G>A	p.Val505Met	p.V505M	ENST00000319144	NM_001139.2	505	Gtg/Atg	11/15	1	2	FACETS	0.774	0.656	0.902	0.774	0.656	0.902	CLONAL	1	TRUE	1	0.389476348730756	2		381	312	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12043169	12043169	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	45	202	0	ENST00000353533.5:c.1054G>A	p.Glu352Lys	p.E352K	ENST00000353533	NM_003010.3	352	Gaa/Aaa	10/11	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.389476348730756	2		202	205	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30302513	30302513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	23	89	0	ENST00000322652.5:c.604C>T	p.Pro202Ser	p.P202S	ENST00000322652	NM_015355.2	202	Cca/Tca	7/16	0.389476348730756	2	FACETS	1	0.923	1	0.695	0.555	0.847	CLONAL	1	TRUE	0	0.389476348730756	2		89	85	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881303	37881303	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	36	446	0	ENST00000269571.5:c.2495G>A	p.Gly832Glu	p.G832E	ENST00000269571		832	gGg/gAg	21/27	0.389476348730756	2	FACETS	0.698	0.576	0.832	0.349	0.288	0.416	SUBCLONAL	1	TRUE	0	0.389476348730756	2		446	265	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752378	55752378	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	93	515	0	ENST00000284073.2:c.836C>T	p.Pro279Leu	p.P279L	ENST00000284073	NM_138962.2	279	cCa/cTa	12/14	0.389476348730756	2	FACETS	1	0.962	1	0.582	0.521	0.647	CLONAL	1	TRUE	0	0.389476348730756	2		515	410	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390406	56390406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	43	269	1	ENST00000348428.3:c.1145C>T	p.Ser382Leu	p.S382L	ENST00000348428	NM_006785.3	382	tCa/tTa	10/17	1	2	FACETS	0.956	0.807	1	0.956	0.807	1	CLONAL	1	TRUE	1	0.389476348730756	2		270	231	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226260	2226261	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	59	450	3	ENST00000398665.3:c.3740_3741delinsTT	p.Pro1247Leu	p.P1247L	ENST00000398665	NM_032482.2	1247	cCC/cTT	27/28	1	2	FACETS	0.873	0.755	1	0.873	0.755	1	CLONAL	1	TRUE	1	0.389476348730756	2		453	347	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226995	2226996	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	55	379	3	ENST00000398665.3:c.4475_4476delinsTT	p.Ser1492Phe	p.S1492F	ENST00000398665	NM_032482.2	1492	tCC/tTT	27/28	1	2	FACETS	0.926	0.797	1	0.926	0.797	1	CLONAL	1	TRUE	1	0.389476348730756	2		382	305	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11018777	11018777	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	96	512	1	ENST00000327064.4:c.409T>C	p.Phe137Leu	p.F137L	ENST00000327064	NM_199141.1	137	Ttc/Ctc	3/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.389476348730756	2		513	419	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271781	15271781	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	57	473	0	ENST00000263388.2:c.6658G>A	p.Glu2220Lys	p.E2220K	ENST00000263388	NM_000435.2	2220	Gag/Aag	33/33	1	2	FACETS	0.853	0.736	0.98	0.853	0.736	0.98	CLONAL	1	TRUE	1	0.389476348730756	2		473	343	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272152	15272152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745724101	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	53	417	0	ENST00000263388.2:c.6287C>T	p.Ser2096Leu	p.S2096L	ENST00000263388	NM_000435.2	2096	tCg/tTg	33/33	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.389476348730756	2		417	264	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350596	15350596	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200882606	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	63	501	0	ENST00000263377.2:c.3319C>T	p.Leu1107Phe	p.L1107F	ENST00000263377	NM_058243.2	1107	Ctc/Ttc	16/20	1	2	FACETS	0.865	0.752	0.987	0.865	0.752	0.987	CLONAL	1	TRUE	1	0.389476348730756	2		501	374	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355040	15355040	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	74	510	0	ENST00000263377.2:c.2581+2T>G		p.X861_splice	ENST00000263377	NM_058243.2	861			1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.389476348730756	2		510	365	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223001	36223001	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	65	482	0	ENST00000222270.7:c.5630T>C	p.Leu1877Ser	p.L1877S	ENST00000222270	NM_014727.1	1877	tTg/tCg	27/37	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.389476348730756	2		482	333	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906325	50906325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	42	430	0	ENST00000440232.2:c.986C>T	p.Pro329Leu	p.P329L	ENST00000440232	NM_002691.3	329	cCt/cTt	9/27	1	2	FACETS	0.998	0.842	1	0.998	0.842	1	CLONAL	1	TRUE	1	0.389476348730756	2		430	216	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224158	39224158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	38	299	0	ENST00000402219.2:c.2986C>T	p.Pro996Ser	p.P996S	ENST00000402219	NM_005633.3	996	Ccg/Tcg	19/23	1	2	FACETS	0.668	0.555	0.794	0.668	0.555	0.794	SUBCLONAL	1	TRUE	1	0.389476348730756	2		299	292	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698196	47698196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1280971849	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	39	220	0	ENST00000233146.2:c.1754C>T	p.Ser585Phe	p.S585F	ENST00000233146	NM_000251.2	585	tCt/tTt	11/16	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.389476348730756	2		220	182	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543814	212543814	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	75	321	0	ENST00000342788.4:c.1585G>A	p.Gly529Arg	p.G529R	ENST00000342788	NM_005235.2	529	Gga/Aga	13/28	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.389476348730756	2		321	326	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560854	9560854	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	80	372	0	ENST00000353224.5:c.928G>A	p.Gly310Arg	p.G310R	ENST00000353224	NM_177990.2	310	Gga/Aga	4/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.389476348730756	2		372	360	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561247	9561248	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	45	382	0	ENST00000353224.5:c.534_535delinsAA	p.Glu179Lys	p.E179K	ENST00000353224	NM_177990.2	178	ggGGag/ggAAag	4/10	1	2	FACETS	0.943	0.799	1	0.943	0.799	1	CLONAL	1	TRUE	1	0.389476348730756	2		382	245	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710526	40710526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	50	383	0	ENST00000373198.4:c.4325C>T	p.Thr1442Ile	p.T1442I	ENST00000373198	NM_133170.3	1442	aCc/aTc	31/32	1	2	FACETS	0.876	0.748	1	0.876	0.748	1	CLONAL	1	TRUE	1	0.389476348730756	2		383	293	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733238	40733238	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	43	399	0	ENST00000373198.4:c.3568A>T	p.Asn1190Tyr	p.N1190Y	ENST00000373198	NM_133170.3	1190	Aac/Tac	26/32	1	2	FACETS	0.669	0.562	0.787	0.669	0.562	0.787	SUBCLONAL	1	TRUE	1	0.389476348730756	2		399	330	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743953	40743954	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CA	CA	TT	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	44	317	1	ENST00000373198.4:c.3041_3042delinsAA	p.Val1014Glu	p.V1014E	ENST00000373198	NM_133170.3	1014	gTG/gAA	23/32	1	2	FACETS	0.89	0.752	1	0.89	0.752	1	CLONAL	1	TRUE	1	0.389476348730756	2		318	254	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790066	40790066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1357627666	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	86	396	1	ENST00000373198.4:c.2665C>T	p.Arg889Trp	p.R889W	ENST00000373198	NM_133170.3	889	Cgg/Tgg	18/32	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.389476348730756	2		397	356	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961435	54961435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	43	156	0	ENST00000312783.6:c.197C>T	p.Ser66Phe	p.S66F	ENST00000312783	NM_198436.1	66	tCc/tTc	4/10	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.389476348730756	2		156	192	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164637	36164637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	80	432	0	ENST00000300305.3:c.1238C>T	p.Ser413Phe	p.S413F	ENST00000300305		413	tCc/tTc	8/8	0.389476348730756	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.389476348730756	1		432	263	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36421166	36421166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766610477	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	38	283	1	ENST00000300305.3:c.31C>T	p.Pro11Ser	p.P11S	ENST00000300305		11	Cct/Tct	1/8	0.389476348730756	1	FACETS	0.593	0.493	0.703	0.593	0.493	0.703	SUBCLONAL	1	TRUE	0	0.389476348730756	1		284	265	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038261	30038261	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	52	356	0	ENST00000338641.4:c.434C>T	p.Ala145Val	p.A145V	ENST00000338641	NM_000268.3	145	gCc/gTc	4/16	0.157745092300077	3	FACETS	1	0.925	1	0.564	0.483	0.65	INDETERMINATE	1	TRUE	1	0.389476348730756	3		356	283	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627989	37627989	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868625507	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	103	407	1	ENST00000249071.6:c.271G>A	p.Glu91Lys	p.E91K	ENST00000249071	NM_002872.4	91	Gag/Aag	4/7	0.157745092300077	3	FACETS	0.79	0.712	0.871	0.79	0.712	0.871	INDETERMINATE	2	TRUE	1	0.389476348730756	3		408	400	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47088087	47088087	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	71	313	0	ENST00000409792.3:c.6988T>G	p.Tyr2330Asp	p.Y2330D	ENST00000409792	NM_014159.6	2330	Tat/Gat	16/21	0.0821482119879249	3	FACETS	1	0.969	1	0.67	0.589	0.756	INDETERMINATE	1	TRUE	1	0.389476348730756	3		313	325	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165819	47165819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1285112235	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	45	323	1	ENST00000409792.3:c.307C>T	p.Pro103Ser	p.P103S	ENST00000409792	NM_014159.6	103	Cct/Tct	3/21	0.0821482119879249	3	FACETS	0.857	0.724	1	0.429	0.362	0.502	INDETERMINATE	1	TRUE	1	0.389476348730756	3		324	322	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259104	89259104	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	30	247	0	ENST00000336596.2:c.248G>A	p.Arg83Lys	p.R83K	ENST00000336596	NM_005233.5	83	aGa/aAa	3/17	0.0821482119879249	3	FACETS	0.959	0.779	1	0.479	0.389	0.579	INDETERMINATE	1	TRUE	1	0.389476348730756	3		247	192	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608612	189608612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	134	441	0	ENST00000264731.3:c.1687G>A	p.Asp563Asn	p.D563N	ENST00000264731	NM_003722.4	563	Gac/Aac	13/14	0.389476348730756	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.389476348730756	1		441	381	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749368	41749369	+	stop_gained,splice_region_variant	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	28	255	0	ENST00000226382.2:c.426_427delinsTT	p.Gln143Ter	p.Q143*	ENST00000226382	NM_003924.3	142	gtCCag/gtTTag	2/3	1	2	FACETS	0.888	0.717	1	0.888	0.717	1	CLONAL	1	TRUE	1	0.389476348730756	2		255	162	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604668	55604668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	72	375	0	ENST00000288135.5:c.2876C>T	p.Ser959Phe	p.S959F	ENST00000288135	NM_000222.2	959	tCt/tTt	21/21	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.389476348730756	2		375	315	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189846	66189846	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	31	316	0	ENST00000273854.3:c.3100A>G	p.Met1034Val	p.M1034V	ENST00000273854	NM_004439.5	1034	Atg/Gtg	18/18	1	2	FACETS	0.704	0.573	0.851	0.704	0.573	0.851	SUBCLONAL	1	TRUE	1	0.389476348730756	2		316	226	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280008	66280008	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	29	152	0	ENST00000273854.3:c.1681C>T	p.Pro561Ser	p.P561S	ENST00000273854	NM_004439.5	561	Cca/Tca	7/18	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.389476348730756	2		152	134	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521067	187521067	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	36	265	0	ENST00000441802.2:c.12088C>T	p.Pro4030Ser	p.P4030S	ENST00000441802	NM_005245.3	4030	Ccg/Tcg	22/27	1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	TRUE	1	0.389476348730756	2		265	182	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539513	187539513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	40	311	0	ENST00000441802.2:c.8227C>T	p.Pro2743Ser	p.P2743S	ENST00000441802	NM_005245.3	2743	Cca/Tca	10/27	1	2	FACETS	0.905	0.758	1	0.905	0.758	1	CLONAL	1	TRUE	1	0.389476348730756	2		311	227	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539696	187539696	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs377061753	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	28	277	0	ENST00000441802.2:c.8044T>A	p.Ser2682Thr	p.S2682T	ENST00000441802	NM_005245.3	2682	Tca/Aca	10/27	1	2	FACETS	0.549	0.44	0.672	0.549	0.44	0.672	SUBCLONAL	1	TRUE	1	0.389476348730756	2		277	262	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945793	38945793	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	34	203	0	ENST00000357387.3:c.4433A>T	p.Asn1478Ile	p.N1478I	ENST00000357387	NM_152756.3	1478	aAt/aTt	34/38	1	2	FACETS	0.934	0.771	1	0.934	0.771	1	CLONAL	1	TRUE	1	0.389476348730756	2		203	187	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950783	38950783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	15	193	0	ENST00000357387.3:c.3167C>T	p.Ser1056Phe	p.S1056F	ENST00000357387	NM_152756.3	1056	tCt/tTt	31/38	1	2	FACETS	0.626	0.462	0.819	0.626	0.462	0.819	SUBCLONAL	1	TRUE	1	0.389476348730756	2		193	123	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564674	86564674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	60	476	0	ENST00000274376.6:c.406C>T	p.Pro136Ser	p.P136S	ENST00000274376	NM_002890.2	136	Cct/Tct	1/25	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.389476348730756	2		476	258	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818325	170818325	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372208958	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	55	335	0	ENST00000296930.5:c.155G>A	p.Gly52Asp	p.G52D	ENST00000296930	NM_002520.6	52	gGt/gAt	3/11	1	2	FACETS	0.923	0.795	1	0.923	0.795	1	CLONAL	1	TRUE	1	0.389476348730756	2		335	306	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671005	30671005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	71	474	1	ENST00000376406.3:c.5741G>A	p.Gly1914Glu	p.G1914E	ENST00000376406	NM_014641.2	1914	gGa/gAa	12/15	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.389476348730756	2		475	341	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120407	94120407	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	27	221	0	ENST00000369303.4:c.644T>C	p.Phe215Ser	p.F215S	ENST00000369303	NM_004440.3	215	tTt/tCt	3/17	1	2	FACETS	0.9	0.725	1	0.9	0.725	1	CLONAL	1	TRUE	1	0.389476348730756	2		221	154	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631325	117631325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	37	322	0	ENST00000368508.3:c.6353G>A	p.Arg2118Lys	p.R2118K	ENST00000368508	NM_002944.2	2118	aGa/aAa	40/43	1	2	FACETS	0.772	0.641	0.917	0.772	0.641	0.917	CLONAL	1	TRUE	1	0.389476348730756	2		322	246	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700301	117700301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1484966865	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	21	327	0	ENST00000368508.3:c.2518C>T	p.Leu840Phe	p.L840F	ENST00000368508	NM_002944.2	840	Ctc/Ttc	17/43	1	2	FACETS	0.562	0.435	0.708	0.562	0.435	0.708	SUBCLONAL	1	TRUE	1	0.389476348730756	2		327	192	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710717	117710717	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	40	266	0	ENST00000368508.3:c.1555C>T	p.Gln519Ter	p.Q519*	ENST00000368508	NM_002944.2	519	Caa/Taa	12/43	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.389476348730756	2		266	193	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157454236	157454236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	42	354	0	ENST00000346085.5:c.2446C>T	p.Pro816Ser	p.P816S	ENST00000346085	NM_020732.3	816	Cct/Tct	8/20	1	2	FACETS	0.749	0.629	0.881	0.749	0.629	0.881	SUBCLONAL	1	TRUE	1	0.389476348730756	2		354	288	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984154	2984154	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	56	266	0	ENST00000396946.4:c.376G>C	p.Gly126Arg	p.G126R	ENST00000396946	NM_032415.4	126	Ggc/Cgc	5/25	0.244479439407033	5	FACETS	0.995	0.863	1	0.663	0.575	0.757	CLONAL	2	TRUE	2	0.389476348730756	5		266	229	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444362	50444362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	80	260	1	ENST00000331340.3:c.292G>A	p.Asp98Asn	p.D98N	ENST00000331340	NM_006060.4	98	Gac/Aac	4/8	0.244479439407033	5	FACETS	1	0.966	1	0.809	0.722	0.901	CLONAL	2	TRUE	2	0.389476348730756	5		261	268	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55225380	55225380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	95	363	0	ENST00000275493.2:c.1232C>T	p.Pro411Leu	p.P411L	ENST00000275493	NM_005228.3	411	cCt/cTt	11/28	0.244479439407033	5	FACETS	0.903	0.809	1	0.602	0.539	0.668	CLONAL	2	TRUE	2	0.389476348730756	5		363	428	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335712	81335712	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	46	233	0	ENST00000222390.5:c.1648A>G	p.Ile550Val	p.I550V	ENST00000222390	NM_000601.4	550	Att/Gtt	15/18	0.244479439407033	5	FACETS	1	0.929	1	0.392	0.332	0.458	CLONAL	1	TRUE	2	0.389476348730756	5		233	318	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381506	81381507	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	72	255	1	ENST00000222390.5:c.554_555delinsAA	p.Gly185Glu	p.G185E	ENST00000222390	NM_000601.4	185	gGG/gAA	5/18	0.244479439407033	5	FACETS	0.879	0.774	0.991	0.586	0.516	0.661	CLONAL	2	TRUE	2	0.389476348730756	5		256	333	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523482	106523482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762208681	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	49	162	0	ENST00000359195.3:c.2634G>A	p.Met878Ile	p.M878I	ENST00000359195	NM_002649.2	878	atG/atA	8/11	0.244479439407033	5	FACETS	0.91	0.78	1	0.607	0.52	0.7	CLONAL	2	TRUE	2	0.389476348730756	5		162	219	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850885	128850885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61740964	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	87	448	0	ENST00000249373.3:c.1732G>A	p.Glu578Lys	p.E578K	ENST00000249373	NM_005631.4	578	Gag/Aag	10/12	0.244479439407033	5	FACETS	0.839	0.746	0.936	0.559	0.497	0.624	CLONAL	2	TRUE	2	0.389476348730756	5		448	422	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874926	151874926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1335592152	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	71	283	0	ENST00000262189.6:c.7612C>T	p.Pro2538Ser	p.P2538S	ENST00000262189	NM_170606.2	2538	Cct/Tct	38/59	0.244479439407033	5	FACETS	0.926	0.815	1	0.617	0.543	0.695	CLONAL	2	TRUE	2	0.389476348730756	5		283	312	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931880	68931880	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	60	427	0	ENST00000288368.4:c.310G>A	p.Glu104Lys	p.E104K	ENST00000288368	NM_024870.2	104	Gaa/Aaa	3/40	1	2	FACETS	0.763	0.659	0.874	0.763	0.659	0.874	SUBCLONAL	1	TRUE	1	0.389476348730756	2		427	404	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965479	68965479	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	58	446	0	ENST00000288368.4:c.1091A>C	p.Lys364Thr	p.K364T	ENST00000288368	NM_024870.2	364	aAa/aCa	9/40	1	2	FACETS	0.782	0.674	0.898	0.782	0.674	0.898	SUBCLONAL	1	TRUE	1	0.389476348730756	2		446	381	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002901	69002901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	38	294	0	ENST00000288368.4:c.2201G>A	p.Ser734Asn	p.S734N	ENST00000288368	NM_024870.2	734	aGt/aAt	20/40	1	2	FACETS	0.952	0.795	1	0.952	0.795	1	CLONAL	1	TRUE	1	0.389476348730756	2		294	205	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341880	8341880	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	46	402	0	ENST00000356435.5:c.4760T>C	p.Leu1587Ser	p.L1587S	ENST00000356435		1587	tTa/tCa	29/35	0.389476348730756	1	FACETS	0.729	0.618	0.849	0.729	0.618	0.849	SUBCLONAL	1	TRUE	0	0.389476348730756	1		402	261	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27183486	27183486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	35	311	0	ENST00000380036.4:c.1060G>A	p.Asp354Asn	p.D354N	ENST00000380036	NM_000459.3	354	Gat/Aat	8/23	0.389476348730756	1	FACETS	0.774	0.641	0.92	0.774	0.641	0.92	CLONAL	1	TRUE	0	0.389476348730756	1		311	187	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93627369	93627369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	43	385	0	ENST00000375746.1:c.836C>T	p.Ser279Phe	p.S279F	ENST00000375746	NM_001174167.1	279	tCc/tTc	6/14	1	2	FACETS	0.88	0.742	1	0.88	0.742	1	CLONAL	1	TRUE	1	0.389476348730756	2		385	251	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209694	98209694	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	97	499	0	ENST00000331920.6:c.3844C>T	p.Pro1282Ser	p.P1282S	ENST00000331920	NM_000264.3	1282	Ccg/Tcg	23/24	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.389476348730756	2		499	382	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035930	47035930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1308446046	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	75	227	0	ENST00000377604.3:c.608C>T	p.Ser203Leu	p.S203L	ENST00000377604	NM_001204468.1	203	tCg/tTg	7/24	1	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.389476348730756	1		227	207	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041409	47041409	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	65	269	0	ENST00000377604.3:c.1753C>T	p.Gln585Ter	p.Q585*	ENST00000377604	NM_001204468.1	585	Cag/Tag	16/24	1	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.389476348730756	1		269	194	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652416	48652416	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	57	242	0	ENST00000376670.3:c.1087C>T	p.Leu363Phe	p.L363F	ENST00000376670	NM_002049.3	363	Ctc/Ttc	6/6	1	1	FACETS	0.83	0.731	0.932	1	0.977	1	CLONAL	2	TRUE	0	0.389476348730756	1		242	142	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410310	63410310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374610712	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	48	242	0	ENST00000330258.3:c.2857C>T	p.Pro953Ser	p.P953S	ENST00000330258	NM_152424.3	953	Cca/Tca	2/2	1	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.389476348730756	1		242	139	SUCCESS
AR	367	MSKCC	GRCh37	X	66943649	66943649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	65	233	0	ENST00000374690.3:c.2729G>A	p.Gly910Glu	p.G910E	ENST00000374690	NM_000044.3	910	gGg/gAg	8/8	1	1	FACETS	0.764	0.676	0.854	1	0.977	1	SUBCLONAL	2	TRUE	0	0.389476348730756	1		233	176	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1022604	1022604	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0023765-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	49	397	0	ENST00000358495.3:c.1210del	p.His404IlefsTer7	p.H404Ifs*7	ENST00000358495	NM_134424.2	404	Cat/at	12/12	NA	2	FACETS	0.918	0.784	1			1	INDETERMINATE	1	TRUE	NA	0.389476348730756	2		397	274	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	142	246	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	1	0.698920532913028	2		247	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	358	386	0	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	0.655160379256527	2	FACETS	0.95	0.915	0.985	0.95	0.915	0.985	CLONAL	2	FALSE	0	0.698920532913028	2		386	539	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	2414	356	0	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	0.698920532913028	14	FACETS	0.967	0.96	0.975			1	CLONAL	14	FALSE	NA	0.698920532913028	14		356	2649	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969933	81969933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752209691	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	192	395	0	ENST00000359376.3:c.3002G>A	p.Arg1001His	p.R1001H	ENST00000359376	NM_002661.3	1001	cGc/cAc	27/33	0.698920532913028	1	FACETS	0.961	0.903	1	0.961	0.903	1	CLONAL	1	FALSE	0	0.698920532913028	1		395	372	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829040	128829042	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	rs570242755	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	11	47	0	ENST00000249373.3:c.67_69del	p.Leu23del	p.L23del	ENST00000249373	NM_005631.4	16	ggGCTg/ggg	1/12	1	2	FACETS	0.276	0.192	0.379	0.276	0.192	0.379	SUBCLONAL	1	FALSE	1	0.698920532913028	2		47	114	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293431	1293431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	186	350	0	ENST00000310581.5:c.1570C>T	p.Pro524Ser	p.P524S	ENST00000310581	NM_198253.2	524	Cca/Tca	2/16	1	2	FACETS	0.973	0.905	1	0.973	0.905	1	CLONAL	1	FALSE	1	0.698920532913028	2		350	547	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs984459719	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	148	456	2	ENST00000324856.7:c.2291C>T	p.Ser764Phe	p.S764F	ENST00000324856	NM_006015.4	764	tCc/tTc	7/20	1	2	FACETS	0.593	0.543	0.646	0.593	0.543	0.646	SUBCLONAL	1	FALSE	1	0.698920532913028	2		458	714	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874636	35874636	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	154	279	0	ENST00000303115.3:c.792G>A	p.Trp264Ter	p.W264*	ENST00000303115	NM_002185.3	264	tgG/tgA	6/8	1	2	FACETS	0.984	0.909	1	0.984	0.909	1	CLONAL	1	FALSE	1	0.698920532913028	2		279	448	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873223	136873223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	75	239	0	ENST00000241393.3:c.275C>T	p.Pro92Leu	p.P92L	ENST00000241393	NM_003467.2	92	cCc/cTc	2/2	1	2	FACETS	0.552	0.486	0.622	0.552	0.486	0.622	SUBCLONAL	1	FALSE	1	0.698920532913028	2		239	389	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724308	117724308	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	171	310	0	ENST00000368508.3:c.571C>T	p.His191Tyr	p.H191Y	ENST00000368508	NM_002944.2	191	Cat/Tat	6/43	0.476669153386787	1	FACETS	0.719	0.668	0.77	0.719	0.668	0.77	SUBCLONAL	1	FALSE	0	0.698920532913028	1		310	443	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802565	139802565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	264	477	1	ENST00000247668.2:c.410C>T	p.Pro137Leu	p.P137L	ENST00000247668	NM_021138.3	137	cCc/cTc	5/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.698920532913028	2		478	680	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561325	9561325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	112	338	0	ENST00000353224.5:c.457G>A	p.Gly153Arg	p.G153R	ENST00000353224	NM_177990.2	153	Gga/Aga	4/10	1	2	FACETS	0.585	0.528	0.645	0.585	0.528	0.645	SUBCLONAL	1	FALSE	1	0.698920532913028	2		338	548	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38632044	38632044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs553832516	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	207	364	0	ENST00000299084.4:c.530C>T	p.Pro177Leu	p.P177L	ENST00000299084	NM_152594.2	177	cCc/cTc	5/7	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	FALSE	1	0.698920532913028	2		364	592	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295204	1295204	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs2735943	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	140	214	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.698920532913028	2		214	359	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109927	115109927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	108	415	1	ENST00000257566.3:c.1951G>A	p.Asp651Asn	p.D651N	ENST00000257566	NM_016569.3	651	Gac/Aac	8/8	0.370364546359535	1	FACETS	0.405	0.364	0.447	0.405	0.364	0.447	INDETERMINATE	1	FALSE	0	0.698920532913028	1		416	497	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918843	50918843	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759530743	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	222	381	0	ENST00000440232.2:c.2713G>A	p.Glu905Lys	p.E905K	ENST00000440232	NM_002691.3	905	Gag/Aag	21/27	0.370364546359535	1	FACETS	0.843	0.794	0.893	0.843	0.794	0.893	INDETERMINATE	1	FALSE	0	0.698920532913028	1		381	490	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490396	29490396	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	269	284	0	ENST00000356175.3:c.479+2T>C		p.X160_splice	ENST00000356175	NM_000267.3	160			0.655160379256527	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	FALSE	0	0.698920532913028	2		284	374	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762085	43762085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	236	342	0	ENST00000382044.4:c.1360C>T	p.Pro454Ser	p.P454S	ENST00000382044	NM_001141980.1	454	Cct/Tct	11/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.698920532913028	2		342	609	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055937	180055937	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766452541	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	210	413	1	ENST00000261937.6:c.1048G>A	p.Glu350Lys	p.E350K	ENST00000261937	NM_182925.4	350	Gag/Aag	8/30	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.698920532913028	2		414	584	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186697	11186698	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	189	388	0	ENST00000361445.4:c.6507_6508delinsTT	p.Arg2170Trp	p.R2170W	ENST00000361445	NM_004958.3	2169	ccCCgg/ccTTgg	46/58	1	2	FACETS	0.959	0.892	1	0.959	0.892	1	CLONAL	1	FALSE	1	0.698920532913028	2		388	564	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845329	156845329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	217	454	0	ENST00000524377.1:c.1372C>T	p.Pro458Ser	p.P458S	ENST00000524377	NM_002529.3	458	Cca/Tca	12/17	1	2	FACETS	0.941	0.879	1	0.941	0.879	1	CLONAL	1	FALSE	1	0.698920532913028	2		454	660	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333593	70333605	+	frameshift_variant	Frame_Shift_Del	DEL	GAGAAGCAGGTTC	GAGAAGCAGGTTC	-	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	169	345	0	ENST00000373644.4:c.1498_1510del	p.Glu500IlefsTer2	p.E500Ifs*2	ENST00000373644	NM_030625.2	500	GAGAAGCAGGTTCat/at	2/12	0.698920532913028	1	FACETS	0.992	0.93	1	0.992	0.93	1	CLONAL	1	FALSE	0	0.698920532913028	1		345	317	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903681	114903681	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	212	364	0	ENST00000543371.1:c.686-1G>A		p.X229_splice	ENST00000543371	NM_001198531.1	229			0.698920532913028	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	0	0.698920532913028	1		364	351	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413602	32413602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	182	353	0	ENST00000332351.3:c.1348C>T	p.Pro450Ser	p.P450S	ENST00000332351	NM_024426.4	450	Cca/Tca	9/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.698920532913028	2		353	478	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207671	102207671	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	139	228	0	ENST00000263464.3:c.1653del	p.Gln552LysfsTer16	p.Q552Kfs*16	ENST00000263464	NM_001165.4	551	ctA/ct	9/9	1	2	FACETS	0.992	0.912	1	0.992	0.912	1	CLONAL	1	FALSE	1	0.698920532913028	2		228	401	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944821	31944821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs563005029	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	135	412	0	ENST00000340398.3:c.280G>A	p.Glu94Lys	p.E94K	ENST00000340398	NM_001013699.2	94	Gag/Aag	1/1	0.370364546359535	1	FACETS	0.454	0.415	0.496	0.454	0.415	0.496	INDETERMINATE	1	FALSE	0	0.698920532913028	1		412	553	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495074	56495074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	114	420	0	ENST00000267101.3:c.3431C>T	p.Thr1144Ile	p.T1144I	ENST00000267101	NM_001982.3	1144	aCc/aTc	27/28	0.370364546359535	1	FACETS	0.381	0.344	0.42	0.381	0.344	0.42	INDETERMINATE	1	FALSE	0	0.698920532913028	1		420	557	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223799	2223799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	136	408	0	ENST00000326181.6:c.1097C>T	p.Ser366Phe	p.S366F	ENST00000326181	NM_032271.2	366	tCc/tTc	12/21	1	2	FACETS	0.598	0.545	0.653	0.598	0.545	0.653	SUBCLONAL	1	FALSE	1	0.698920532913028	2		408	651	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633155	3633155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs184699331	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	279	452	0	ENST00000294008.3:c.5096C>T	p.Ser1699Phe	p.S1699F	ENST00000294008	NM_032444.2	1699	tCt/tTt	14/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.698920532913028	2		452	733	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216083	7216083	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	210	230	0	ENST00000380728.2:c.976C>T	p.His326Tyr	p.H326Y	ENST00000380728		326	Cac/Tac	11/11	0.655160379256527	2	FACETS	0.954	0.908	0.998	0.954	0.908	0.998	CLONAL	2	FALSE	0	0.698920532913028	2		230	315	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936733	78936733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	212	409	1	ENST00000306801.3:c.3815C>T	p.Ser1272Phe	p.S1272F	ENST00000306801	NM_020761.2	1272	tCc/tTc	33/34	0.387200975020296	3	FACETS	1	0.978	1	0.558	0.52	0.597	INDETERMINATE	1	FALSE	1	0.698920532913028	3		410	733	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3120990	3120990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1259650887	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	144	317	0	ENST00000078429.4:c.893C>T	p.Pro298Leu	p.P298L	ENST00000078429	NM_002067.2	298	cCc/cTc	7/7	0.370364546359535	1	FACETS	0.777	0.719	0.836	0.777	0.719	0.836	INDETERMINATE	1	FALSE	0	0.698920532913028	1		317	345	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245915	5245915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs724159894	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	261	489	1	ENST00000357368.4:c.860C>T	p.Pro287Leu	p.P287L	ENST00000357368	NM_002850.3	287	cCc/cTc	10/38	0.370364546359535	1	FACETS	0.821	0.776	0.866	0.821	0.776	0.866	INDETERMINATE	1	FALSE	0	0.698920532913028	1		490	592	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291218	10291218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	99	338	0	ENST00000340748.4:c.253C>T	p.Leu85Phe	p.L85F	ENST00000340748		85	Ctt/Ttt	4/40	0.370364546359535	1	FACETS	0.378	0.339	0.42	0.378	0.339	0.42	INDETERMINATE	1	FALSE	0	0.698920532913028	1		338	487	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279655	18279655	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	91	359	0	ENST00000222254.8:c.1928C>T	p.Thr643Ile	p.T643I	ENST00000222254	NM_005027.3	643	aCc/aTc	15/16	0.370364546359535	1	FACETS	0.417	0.373	0.464	0.417	0.373	0.464	INDETERMINATE	1	FALSE	0	0.698920532913028	1		359	406	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519916	29519916	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	185	286	0	ENST00000389048.3:c.1655T>C	p.Met552Thr	p.M552T	ENST00000389048	NM_004304.4	552	aTg/aCg	9/29	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.698920532913028	2		286	490	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281915	39281915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	216	307	1	ENST00000402219.2:c.560C>T	p.Ser187Phe	p.S187F	ENST00000402219	NM_005633.3	187	tCt/tTt	5/23	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.698920532913028	2		308	550	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285173	212285173	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754420079	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	139	272	0	ENST00000342788.4:c.3128C>T	p.Ser1043Leu	p.S1043L	ENST00000342788	NM_005235.2	1043	tCg/tTg	25/28	1	2	FACETS	0.888	0.815	0.963	0.888	0.815	0.963	CLONAL	1	FALSE	1	0.698920532913028	2		272	448	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525080	9525080	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	101	417	0	ENST00000353224.5:c.1805C>G	p.Ser602Ter	p.S602*	ENST00000353224	NM_177990.2	602	tCa/tGa	8/10	1	2	FACETS	0.519	0.465	0.576	0.519	0.465	0.576	SUBCLONAL	1	FALSE	1	0.698920532913028	2		417	557	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713666	30713666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759215875	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	170	320	0	ENST00000295754.5:c.991G>A	p.Gly331Ser	p.G331S	ENST00000295754	NM_003242.5	331	Ggc/Agc	4/7	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.698920532913028	2		320	466	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067233	37067233	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	135	282	0	ENST00000231790.2:c.1144C>T	p.Gln382Ter	p.Q382*	ENST00000231790	NM_000249.3	382	Cag/Tag	12/19	1	2	FACETS	0.822	0.752	0.894	0.822	0.752	0.894	CLONAL	1	FALSE	1	0.698920532913028	2		282	470	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665109	138665110	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	80	245	1	ENST00000330315.3:c.455_456delinsTT	p.Pro152Leu	p.P152L	ENST00000330315	NM_023067.3	152	cCC/cTT	1/1	1	2	FACETS	0.683	0.606	0.764	0.683	0.606	0.764	SUBCLONAL	1	FALSE	1	0.698920532913028	2		246	335	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260316	149260316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1184903351	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	134	443	1	ENST00000360632.3:c.577C>T	p.His193Tyr	p.H193Y	ENST00000360632	NM_015472.4	193	Cac/Tac	4/7	1	2	FACETS	0.564	0.513	0.617	0.564	0.513	0.617	SUBCLONAL	1	FALSE	1	0.698920532913028	2		444	680	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961757	55961757	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs770009278	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	2803	313	0	ENST00000263923.4:c.2804T>G	p.Phe935Cys	p.F935C	ENST00000263923	NM_002253.2	935	tTt/tGt	20/30	0.698920532913028	14	FACETS	0.975	0.968	0.981			1	CLONAL	14	FALSE	NA	0.698920532913028	14		313	3052	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197107	106197107	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	48	225	0	ENST00000380013.4:c.5440G>A	p.Gly1814Arg	p.G1814R	ENST00000380013	NM_001127208.2	1814	Gga/Aga	11/11	0.276418882301155	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.698920532913028	0		225	275	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720929	176720929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1471211571	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	206	318	1	ENST00000439151.2:c.6560G>A	p.Arg2187Gln	p.R2187Q	ENST00000439151	NM_022455.4	2187	cGa/cAa	23/23	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.698920532913028	2		319	543	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469929	157469929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	196	387	0	ENST00000346085.5:c.2723C>T	p.Pro908Leu	p.P908L	ENST00000346085	NM_020732.3	908	cCa/cTa	9/20	0.476669153386787	1	FACETS	0.783	0.733	0.834	0.783	0.733	0.834	SUBCLONAL	1	FALSE	0	0.698920532913028	1		387	466	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206941	162206941	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	56	186	0	ENST00000366898.1:c.735-1G>A		p.X245_splice	ENST00000366898	NM_004562.2	245			0.476669153386787	1	FACETS	0.463	0.402	0.529	0.463	0.402	0.529	SUBCLONAL	1	FALSE	0	0.698920532913028	1		186	225	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042178	6042178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	230	334	0	ENST00000265849.7:c.443C>T	p.Pro148Leu	p.P148L	ENST00000265849	NM_000535.5	148	cCc/cTc	5/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.698920532913028	2		334	606	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435746	116435746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	151	321	0	ENST00000397752.3:c.3836G>A	p.Arg1279Lys	p.R1279K	ENST00000397752	NM_000245.2	1279	aGa/aAa	20/21	1	2	FACETS	0.864	0.796	0.935	0.864	0.796	0.935	CLONAL	1	FALSE	1	0.698920532913028	2		321	500	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172977	38172977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs185827074	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	290	467	1	ENST00000317025.8:c.2072C>T	p.Ser691Leu	p.S691L	ENST00000317025	NM_023034.1	691	tCg/tTg	11/24	0.404254163491301	1	FACETS	0.842	0.799	0.886	0.842	0.799	0.886	INDETERMINATE	1	FALSE	0	0.698920532913028	1		468	641	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8338947	8338947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	217	374	0	ENST00000356435.5:c.5354G>A	p.Arg1785Lys	p.R1785K	ENST00000356435		1785	aGg/aAg	32/35	0.698920532913028	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	0	0.698920532913028	1		374	345	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471006	8471006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	99	324	0	ENST00000356435.5:c.3493G>A	p.Glu1165Lys	p.E1165K	ENST00000356435		1165	Gaa/Aaa	20/35	0.698920532913028	1	FACETS	0.501	0.451	0.553	0.501	0.451	0.553	SUBCLONAL	1	FALSE	0	0.698920532913028	1		324	368	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934346	39934346	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	174	177	0	ENST00000378444.4:c.253C>T	p.Pro85Ser	p.P85S	ENST00000378444	NM_001123385.1	85	Ccg/Tcg	4/15	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	0	0.698920532913028	1		177	279	SUCCESS
BTK	695	MSKCC	GRCh37	X	100612562	100612562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	158	149	1	ENST00000308731.7:c.1112C>T	p.Ser371Phe	p.S371F	ENST00000308731	NM_000061.2	371	tCc/tTc	13/19	1	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	0	0.698920532913028	1		150	270	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996839	100996841	+	missense_variant	Missense_Mutation	TNP	GGT	GGT	AGA	novel	NA	P-0023777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	85	372	0	ENST00000325455.5:c.1686_1688delinsTCT	p.Leu562_Pro563delinsPheLeu	p.L562_P563delinsFL	ENST00000325455	NM_001202474.3	562	ttACCt/ttTCTt	2/8	1	2	FACETS	0.474	0.42	0.532	0.474	0.42	0.532	SUBCLONAL	1	FALSE	1	0.698920532913028	2		372	513	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0023993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	84	693	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.928	0.825	1	0.928	0.825	1	CLONAL	1	TRUE	1	0.463045447441345	2		693	391	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46240662	46240663	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0023993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	73	612	0	ENST00000334344.6:c.1523_1524dup	p.Val509MetfsTer8	p.V509Mfs*8	ENST00000334344	NM_152641.2	508	cat/cATat	12/21	1	2	FACETS	0.982	0.866	1	0.982	0.866	1	CLONAL	1	TRUE	1	0.463045447441345	2		612	321	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352675	68352675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1416106631	NA	P-0023993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	102	694	0	ENST00000487270.1:c.542G>A	p.Arg181Gln	p.R181Q	ENST00000487270	NM_133509.3	181	cGg/cAg	6/11	1	2	FACETS	0.937	0.843	1	0.937	0.843	1	CLONAL	1	TRUE	1	0.463045447441345	2		694	470	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007688	45007688	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	89	614	0	ENST00000558401.1:c.135C>G	p.Cys45Trp	p.C45W	ENST00000558401	NM_004048.2	45	tgC/tgG	2/4	0.42454864386438	1	FACETS	0.884	0.792	0.982	0.884	0.792	0.982	CLONAL	1	TRUE	0	0.463045447441345	1		614	334	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911135	29911135	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0023993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	135	884	0	ENST00000376809.5:c.434A>C	p.Lys145Thr	p.K145T	ENST00000376809	NM_002116.7	145	aAg/aCg	3/8	1	2	FACETS	0.855	0.779	0.935	0.855	0.779	0.935	CLONAL	1	TRUE	1	0.463045447441345	2		884	682	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983275	149983275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	262	967	4	ENST00000253339.5:c.2983C>T	p.Arg995Cys	p.R995C	ENST00000253339		995	Cgc/Tgc	7/7	0.465739433476924	3	FACETS	1	0.985	1	0.572	0.538	0.607	INDETERMINATE	1	TRUE	1	0.801480468293016	3		971	800	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	73	427	0				ENST00000310581	NM_198253.2	-/1132			0.604520334988162	3	FACETS	0.918	0.83	1	0.918	0.83	1	CLONAL	2	TRUE	1	0.801480468293016	3		427	139	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445244	29445244	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145194836	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	239	1051	1	ENST00000389048.3:c.3481G>A	p.Glu1161Lys	p.E1161K	ENST00000389048	NM_004304.4	1161	Gaa/Aaa	22/29	0.740598387747101	4	FACETS	1	0.962	1	0.348	0.325	0.372	CLONAL	1	TRUE	1	0.801480468293016	4		1052	1029	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	604	938	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.801480468293016	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.801480468293016	2		938	728	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057869	27057869	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753919975	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	357	1113	2	ENST00000324856.7:c.1577C>T	p.Pro526Leu	p.P526L	ENST00000324856	NM_006015.4	526	cCa/cTa	3/20	0.655343409139029	4	FACETS	1	0.993	1	0.424	0.402	0.447	CLONAL	1	TRUE	1	0.801480468293016	4		1115	1261	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743790	46743790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140793609	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	666	1003	0	ENST00000371975.4:c.2080C>T	p.Pro694Ser	p.P694S	ENST00000371975	NM_003579.3	694	Cct/Tct	18/18	0.655343409139029	4	FACETS	0.925	0.898	0.951	0.925	0.898	0.951	CLONAL	3	TRUE	1	0.801480468293016	4		1003	1079	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170612	108170612	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	85	590	1	ENST00000278616.4:c.5177G>A	p.Cys1726Tyr	p.C1726Y	ENST00000278616	NM_000051.3	1726	tGt/tAt	34/63	0.314228343089202	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.801480468293016	0		591	282	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343319	118343319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	100	584	2	ENST00000534358.1:c.1445C>T	p.Pro482Leu	p.P482L	ENST00000534358	NM_005933.3	482	cCc/cTc	3/36	0.314228343089202	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.801480468293016	0		586	291	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170274	119170274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057518072	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	76	521	0	ENST00000264033.4:c.2504G>A	p.Arg835Gln	p.R835Q	ENST00000264033	NM_005188.3	835	cGg/cAg	16/16	0.314228343089202	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.801480468293016	0		521	251	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658352	18658353	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	308	777	2	ENST00000266497.5:c.3157_3158delinsAA	p.Gly1053Lys	p.G1053K	ENST00000266497		1053	GGa/AAa	22/31	0.477529661735358	5	FACETS	1	0.99	1	0.776	0.736	0.816	INDETERMINATE	2	TRUE	2	0.801480468293016	5		779	727	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120950	115120950	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	413	661	3	ENST00000257566.3:c.56C>T	p.Pro19Leu	p.P19L	ENST00000257566	NM_016569.3	19	cCg/cTg	1/8	0.783454767279886	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.801480468293016	3		664	467	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416785	121416785	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747159467	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	585	1044	1	ENST00000257555.6:c.214G>A	p.Asp72Asn	p.D72N	ENST00000257555		72	Gac/Aac	1/10	0.783454767279886	3	FACETS	0.999	0.98	1	0.999	0.98	1	CLONAL	3	TRUE	0	0.801480468293016	3		1045	682	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039374	49039374	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853293	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	138	1152	0	ENST00000267163.4:c.2359C>T	p.Arg787Ter	p.R787*	ENST00000267163	NM_000321.2	787	Cga/Tga	23/27	0.801480468293016	1	FACETS	0.761	0.708	0.815	0.761	0.708	0.815	SUBCLONAL	1	TRUE	0	0.801480468293016	1		1152	271	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459909	99459909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	103	671	1	ENST00000268035.6:c.2005C>T	p.Pro669Ser	p.P669S	ENST00000268035	NM_000875.3	669	Ccc/Tcc	10/21	0.801480468293016	3	FACETS	0.496	0.444	0.551	0.248	0.222	0.276	SUBCLONAL	1	TRUE	1	0.801480468293016	3		672	726	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862944	9862944	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	489	758	1	ENST00000330684.3:c.2359G>A	p.Glu787Lys	p.E787K	ENST00000330684	NM_001134407.1	787	Gag/Aag	12/13	0.796406445563277	3	FACETS	0.971	0.948	0.992	0.971	0.948	0.992	CLONAL	3	TRUE	0	0.801480468293016	3		759	587	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552143	29552144	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1555613558	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	200	400	1	ENST00000356175.3:c.1882dup	p.Tyr628LeufsTer6	p.Y628Lfs*6	ENST00000356175	NM_000267.3	626	ctt/cTtt	17/57	0.801480468293016	2	FACETS	0.938	0.898	0.976	0.938	0.898	0.976	CLONAL	2	TRUE	0	0.801480468293016	2		401	266	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359593	40359593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	582	990	1	ENST00000293328.3:c.2060C>T	p.Pro687Leu	p.P687L	ENST00000293328	NM_012448.3	687	cCc/cTc	16/19	0.801480468293016	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.801480468293016	3		991	994	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295806	15295806	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757980886	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	452	1227	0	ENST00000263388.2:c.2321C>T	p.Pro774Leu	p.P774L	ENST00000263388	NM_000435.2	774	cCc/cTc	15/33	0.407154853660504	2	FACETS	0.814	0.786	0.841	0.814	0.786	0.841	INDETERMINATE	2	TRUE	0	0.801480468293016	2		1227	693	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302789	15302789	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs530724830	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	430	999	1	ENST00000263388.2:c.661G>A	p.Asp221Asn	p.D221N	ENST00000263388	NM_000435.2	221	Gac/Aac	4/33	0.407154853660504	2	FACETS	0.838	0.81	0.866	0.838	0.81	0.866	INDETERMINATE	2	TRUE	0	0.801480468293016	2		1000	640	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946006	17946007	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	116	994	2	ENST00000458235.1:c.1932_1933delinsTT	p.His645Tyr	p.H645Y	ENST00000458235	NM_000215.3	644	ccCCat/ccTTat	15/24	0.407154853660504	2	FACETS	0.501	0.453	0.551	0.25	0.226	0.276	INDETERMINATE	1	TRUE	0	0.801480468293016	2		996	578	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965743	25965743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	278	1064	0	ENST00000435504.4:c.3463C>T	p.Pro1155Ser	p.P1155S	ENST00000435504		1155	Ccc/Tcc	13/13	0.740598387747101	4	FACETS	1	0.957	1	0.341	0.32	0.363	CLONAL	1	TRUE	1	0.801480468293016	4		1064	1220	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519919	29519919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374136388	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	206	644	0	ENST00000389048.3:c.1652G>A	p.Arg551Gln	p.R551Q	ENST00000389048	NM_004304.4	551	cGa/cAa	9/29	0.740598387747101	4	FACETS	1	0.985	1	0.402	0.374	0.432	CLONAL	1	TRUE	1	0.801480468293016	4		644	767	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561340	9561340	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	531	838	0	ENST00000353224.5:c.442G>A	p.Glu148Lys	p.E148K	ENST00000353224	NM_177990.2	148	Gag/Aag	4/10	0.801480468293016	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.801480468293016	3		838	911	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713416	40713416	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs539998222	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	261	991	1	ENST00000373198.4:c.4099C>T	p.Pro1367Ser	p.P1367S	ENST00000373198	NM_133170.3	1367	Ccc/Tcc	30/32	0.801480468293016	3	FACETS	1	0.958	1	0.513	0.482	0.545	CLONAL	1	TRUE	1	0.801480468293016	3		992	889	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755662	39755662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	271	966	3	ENST00000288319.7:c.1103C>T	p.Ala368Val	p.A368V	ENST00000288319	NM_182918.3	368	gCc/gTc	10/10	0.421307249120052	1	FACETS	0.77	0.732	0.809	0.77	0.732	0.809	INDETERMINATE	1	TRUE	0	0.801480468293016	1		969	526	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795473	39795473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	106	859	0	ENST00000288319.7:c.247G>A	p.Asp83Asn	p.D83N	ENST00000288319	NM_182918.3	83	Gat/Aat	3/10	0.421307249120052	1	FACETS	0.335	0.302	0.37	0.335	0.302	0.37	INDETERMINATE	1	TRUE	0	0.801480468293016	1		859	473	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574631	41574631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	818	1211	2	ENST00000263253.7:c.6916C>T	p.Gln2306Ter	p.Q2306*	ENST00000263253	NM_001429.3	2306	Caa/Taa	31/31	0.801480468293016	5	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	2	0.801480468293016	5		1213	1490	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927934	49927934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764547217	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	450	914	3	ENST00000296474.3:c.3794C>T	p.Thr1265Ile	p.T1265I	ENST00000296474	NM_002447.2	1265	aCc/aTc	18/20	0.635055799758681	3	FACETS	1	0.996	1	0.809	0.783	0.834	CLONAL	2	TRUE	0	0.801480468293016	3		917	648	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526122	189526122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193287780	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	281	949	0	ENST00000264731.3:c.386C>T	p.Ser129Leu	p.S129L	ENST00000264731	NM_003722.4	129	tCg/tTg	4/14	0.801480468293016	3	FACETS	1	0.97	1	0.524	0.493	0.556	CLONAL	1	TRUE	1	0.801480468293016	3		949	937	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604263	189604263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	539	947	0	ENST00000264731.3:c.1430C>T	p.Ser477Phe	p.S477F	ENST00000264731	NM_003722.4	477	tCt/tTt	11/14	0.801480468293016	3	FACETS	0.997	0.963	1	0.997	0.963	1	CLONAL	2	TRUE	1	0.801480468293016	3		947	945	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801073	1801073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	243	1047	0	ENST00000260795.2:c.202C>T	p.Pro68Ser	p.P68S	ENST00000260795		68	Ccc/Tcc	2/17	1	2	FACETS	0.972	0.914	1	0.972	0.914	1	CLONAL	1	TRUE	1	0.801480468293016	2		1047	624	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84390291	84390292	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	213	757	0	ENST00000321945.7:c.489_490delinsAA	p.Val164Ile	p.V164I	ENST00000321945	NM_139076.2	163	agGGta/agAAta	6/9	1	2	FACETS	0.915	0.856	0.975	0.915	0.856	0.975	CLONAL	1	TRUE	1	0.801480468293016	2		757	581	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196361	106196362	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	209	614	2	ENST00000380013.4:c.4694_4695delinsAT	p.Ser1565Tyr	p.S1565Y	ENST00000380013	NM_001127208.2	1565	tCC/tAT	11/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.801480468293016	2		616	511	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524147	187524147	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	264	761	0	ENST00000441802.2:c.11392C>T	p.Pro3798Ser	p.P3798S	ENST00000441802	NM_005245.3	3798	Ccg/Tcg	20/27	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.801480468293016	2		761	629	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557744	187557744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	174	537	0	ENST00000441802.2:c.3967C>T	p.Leu1323Phe	p.L1323F	ENST00000441802	NM_005245.3	1323	Ctt/Ttt	5/27	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.801480468293016	2		537	394	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279569	1279570	+	missense_variant	Missense_Mutation	DNP	GA	GA	AC	novel	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	202	1074	3	ENST00000310581.5:c.1966_1967delinsGT	p.Ser656Val	p.S656V	ENST00000310581	NM_198253.2	656	TCg/GTg	5/16	0.604520334988162	3	FACETS	1	0.963	1	0.526	0.49	0.564	CLONAL	1	TRUE	1	0.801480468293016	3		1077	671	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460399	149460399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	339	905	0	ENST00000286301.3:c.238G>A	p.Gly80Arg	p.G80R	ENST00000286301	NM_005211.3	80	Ggg/Agg	3/22	0.604520334988162	3	FACETS	0.844	0.805	0.883	0.844	0.805	0.883	CLONAL	2	TRUE	1	0.801480468293016	3		905	702	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681675	30681675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373360750	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	285	832	2	ENST00000376406.3:c.422C>T	p.Ser141Phe	p.S141F	ENST00000376406	NM_014641.2	141	tCc/tTc	3/15	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.801480468293016	2		834	609	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178569	32178569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1252701920	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	240	971	3	ENST00000375023.3:c.2825G>A	p.Gly942Glu	p.G942E	ENST00000375023	NM_004557.3	942	gGg/gAg	18/30	1	2	FACETS	0.96	0.902	1	0.96	0.902	1	CLONAL	1	TRUE	1	0.801480468293016	2		974	624	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066599	94066599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	229	831	2	ENST00000369303.4:c.1160G>A	p.Gly387Glu	p.G387E	ENST00000369303	NM_004440.3	387	gGa/gAa	5/17	0.465739433476924	3	FACETS	1	0.985	1	0.58	0.543	0.618	INDETERMINATE	1	TRUE	1	0.801480468293016	3		833	690	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068042	94068042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	313	797	0	ENST00000369303.4:c.920C>T	p.Ser307Phe	p.S307F	ENST00000369303	NM_004440.3	307	tCc/tTc	4/17	0.465739433476924	3	FACETS	0.933	0.891	0.976	0.933	0.891	0.976	INDETERMINATE	2	TRUE	1	0.801480468293016	3		797	586	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547271	106547271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	307	667	0	ENST00000369096.4:c.508G>A	p.Glu170Lys	p.E170K	ENST00000369096	NM_001198.3	170	Gag/Aag	4/7	0.465739433476924	3	FACETS	0.941	0.898	0.985	0.941	0.898	0.985	INDETERMINATE	2	TRUE	1	0.801480468293016	3		667	570	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459558	50459558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	157	477	0	ENST00000331340.3:c.847C>T	p.Leu283Phe	p.L283F	ENST00000331340	NM_006060.4	283	Ctt/Ttt	7/8	0.41006316912428	5	FACETS	1	0.986	1	0.45	0.414	0.488	INDETERMINATE	1	TRUE	2	0.801480468293016	5		477	639	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878458	151878458	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	421	1021	1	ENST00000262189.6:c.6487C>T	p.Pro2163Ser	p.P2163S	ENST00000262189	NM_170606.2	2163	Cct/Tct	36/59	0.41006316912428	5	FACETS	1	0.993	1	0.793	0.758	0.827	INDETERMINATE	2	TRUE	2	0.801480468293016	5		1022	973	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884370	151884370	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	247	577	0	ENST00000262189.6:c.4985C>T	p.Pro1662Leu	p.P1662L	ENST00000262189	NM_170606.2	1662	cCc/cTc	33/59	0.41006316912428	5	FACETS	1	0.983	1	0.743	0.7	0.787	INDETERMINATE	2	TRUE	2	0.801480468293016	5		577	609	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965339	68965340	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	197	834	1	ENST00000288368.4:c.951_952delinsTT	p.His318Tyr	p.H318Y	ENST00000288368	NM_024870.2	317	ttCCat/ttTTat	9/40	0.801480468293016	3	FACETS	1	0.948	1	0.512	0.476	0.549	CLONAL	1	TRUE	1	0.801480468293016	3		835	673	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738689	145738689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1471609431	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	418	986	0	ENST00000428558.2:c.2375C>T	p.Pro792Leu	p.P792L	ENST00000428558	NM_004260.3	792	cCc/cTc	15/22	0.801480468293016	3	FACETS	0.991	0.953	1	0.991	0.953	1	CLONAL	2	TRUE	1	0.801480468293016	3		986	737	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517993	8517993	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	232	842	0	ENST00000356435.5:c.1398G>A	p.Trp466Ter	p.W466*	ENST00000356435		466	tgG/tgA	10/35	0.423141301413219	1	FACETS	0.781	0.739	0.824	0.781	0.739	0.824	INDETERMINATE	1	TRUE	0	0.801480468293016	1		842	444	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27228298	27228298	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	118	794	0	ENST00000380036.4:c.3295C>T	p.Arg1099Ter	p.R1099*	ENST00000380036	NM_000459.3	1099	Cga/Tga	22/23	0.423141301413219	1	FACETS	0.387	0.351	0.424	0.387	0.351	0.424	INDETERMINATE	1	TRUE	0	0.801480468293016	1		794	456	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411527	63411527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	334	547	1	ENST00000330258.3:c.1640C>T	p.Ser547Phe	p.S547F	ENST00000330258	NM_152424.3	547	tCc/tTc	2/2	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.801480468293016	1		548	391	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0024235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	338	488	1	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	0.516505925263492	5	FACETS	0.92	0.88	0.961	0.92	0.88	0.961	CLONAL	4	FALSE	1	0.516505925263492	5		489	631	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0024235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	345	497	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	0.482603205477945	3	FACETS	1	0.993	1			1	CLONAL	2	FALSE	NA	0.516505925263492	3		497	685	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70411647	70411647	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	34	624	0	ENST00000373644.4:c.4321G>T	p.Gly1441Trp	p.G1441W	ENST00000373644	NM_030625.2	1441	Ggg/Tgg	5/12	0.224243546289149	5	FACETS	0.348	0.283	0.421			1	INDETERMINATE	1	FALSE	NA	0.516505925263492	5		624	672	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560902	9560902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756198440	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	110	659	1	ENST00000353224.5:c.880G>A	p.Glu294Lys	p.E294K	ENST00000353224	NM_177990.2	294	Gaa/Aaa	4/10	0.227704794989168	4	FACETS	1	0.978	1	0.659	0.593	0.728	CLONAL	1	TRUE	2	0.368391579985632	4		660	620	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190873	185190873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144909413	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	213	907	1	ENST00000265026.3:c.1754G>A	p.Arg585Gln	p.R585Q	ENST00000265026	NM_004721.4	585	cGa/cAa	11/14	0.368391579985632	3	FACETS	0.84	0.782	0.9	0.84	0.782	0.9	CLONAL	2	TRUE	1	0.368391579985632	3		908	815	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074195	8074195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1299729594	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	75	483	2	ENST00000377482.5:c.464C>T	p.Pro155Leu	p.P155L	ENST00000377482	NM_018948.3	155	cCg/cTg	4/4	0.368391579985632	3	FACETS	0.847	0.743	0.959	0.424	0.371	0.48	CLONAL	1	TRUE	1	0.368391579985632	3		485	569	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778776	9778776	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	74	718	0	ENST00000377346.4:c.1045C>T	p.His349Tyr	p.H349Y	ENST00000377346	NM_005026.3	349	Cac/Tac	9/24	0.368391579985632	3	FACETS	0.732	0.641	0.83	0.366	0.32	0.415	SUBCLONAL	1	TRUE	1	0.368391579985632	3		718	650	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184652	11184652	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	85	655	0	ENST00000361445.4:c.6565C>T	p.His2189Tyr	p.H2189Y	ENST00000361445	NM_004958.3	2189	Cat/Tat	47/58	0.368391579985632	3	FACETS	0.859	0.76	0.965	0.43	0.38	0.483	CLONAL	1	TRUE	1	0.368391579985632	3		655	636	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255047	16255047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761816625	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	40	413	0	ENST00000375759.3:c.2312C>T	p.Pro771Leu	p.P771L	ENST00000375759	NM_015001.2	771	cCt/cTt	11/15	0.317503702836696	4	FACETS	0.721	0.6	0.856	0.24	0.2	0.286	SUBCLONAL	1	TRUE	1	0.368391579985632	4		413	412	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17349134	17349134	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	51	745	0	ENST00000375499.3:c.734C>T	p.Thr245Ile	p.T245I	ENST00000375499	NM_003000.2	245	aCc/aTc	7/8	0.317503702836696	4	FACETS	0.494	0.419	0.577	0.165	0.139	0.193	SUBCLONAL	1	TRUE	1	0.368391579985632	4		745	767	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099325	27099325	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	275	737	2	ENST00000324856.7:c.3562C>T	p.Gln1188Ter	p.Q1188*	ENST00000324856	NM_006015.4	1188	Cag/Tag	14/20	0.317503702836696	4	FACETS	0.93	0.878	0.983	0.93	0.878	0.983	CLONAL	3	TRUE	1	0.368391579985632	4		739	732	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804269	43804269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766638870	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	261	729	0	ENST00000372470.3:c.269G>A	p.Arg90Gln	p.R90Q	ENST00000372470	NM_005373.2	90	cGa/cAa	3/12	0.317503702836696	4	FACETS	0.887	0.835	0.939	0.887	0.835	0.939	CLONAL	3	TRUE	1	0.368391579985632	4		729	729	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46511683	46511683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	88	915	1	ENST00000262741.5:c.1094G>A	p.Arg365Gln	p.R365Q	ENST00000262741	NM_003629.3	365	cGa/cAa	9/10	0.317503702836696	4	FACETS	0.712	0.63	0.801	0.237	0.21	0.267	SUBCLONAL	1	TRUE	1	0.368391579985632	4		916	918	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726971	46726971	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	251	664	1	ENST00000371975.4:c.805C>T	p.Pro269Ser	p.P269S	ENST00000371975	NM_003579.3	269	Ccc/Tcc	8/18	0.317503702836696	4	FACETS	0.861	0.809	0.914	0.861	0.809	0.914	CLONAL	3	TRUE	1	0.368391579985632	4		665	722	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444662	78444663	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	55	564	1	ENST00000370768.2:c.26_27delinsTT	p.Pro9Leu	p.P9L	ENST00000370768	NM_003902.3	9	cCC/cTT	1/20	0.317503702836696	4	FACETS	0.552	0.471	0.641	0.184	0.157	0.214	SUBCLONAL	1	TRUE	1	0.368391579985632	4		565	740	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699325	117699325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	173	670	1	ENST00000369458.3:c.316G>A	p.Asp106Asn	p.D106N	ENST00000369458	NM_024626.3	106	Gat/Aat	3/6	0.368391579985632	5	FACETS	0.897	0.826	0.97	0.598	0.551	0.647	CLONAL	2	TRUE	2	0.368391579985632	5		671	813	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162735832	162735832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	105	713	0	ENST00000367921.3:c.1141C>T	p.Pro381Ser	p.P381S	ENST00000367921	NM_006182.2	381	Cct/Tct	10/18	0.368391579985632	3	FACETS	0.865	0.775	0.961	0.433	0.387	0.481	CLONAL	1	TRUE	1	0.368391579985632	3		713	780	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981285	201981285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	97	853	0	ENST00000359651.3:c.364C>T	p.His122Tyr	p.H122Y	ENST00000359651		122	Cat/Tat	2/8	0.368391579985632	3	FACETS	0.928	0.828	1	0.464	0.414	0.517	CLONAL	1	TRUE	1	0.368391579985632	3		853	672	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609036	43609036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	113	746	0	ENST00000355710.3:c.1792G>A	p.Glu598Lys	p.E598K	ENST00000355710	NM_020975.4	598	Gag/Aag	10/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.368391579985632	2		746	484	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333555	70333555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150689919	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	169	676	0	ENST00000373644.4:c.1460C>T	p.Ser487Leu	p.S487L	ENST00000373644	NM_030625.2	487	tCa/tTa	2/12	0.368391579985632	3	FACETS	0.997	0.922	1	0.997	0.922	1	CLONAL	2	TRUE	1	0.368391579985632	3		676	545	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405515	70405515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747672308	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	194	761	0	ENST00000373644.4:c.3029C>T	p.Ser1010Leu	p.S1010L	ENST00000373644	NM_030625.2	1010	tCa/tTa	4/12	0.368391579985632	3	FACETS	0.982	0.913	1	0.982	0.913	1	CLONAL	2	TRUE	1	0.368391579985632	3		761	635	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405923	70405923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	213	917	1	ENST00000373644.4:c.3437C>T	p.Thr1146Ile	p.T1146I	ENST00000373644	NM_030625.2	1146	aCc/aTc	4/12	0.368391579985632	3	FACETS	0.913	0.851	0.977	0.913	0.851	0.977	CLONAL	2	TRUE	1	0.368391579985632	3		918	750	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70432683	70432683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	106	759	0	ENST00000373644.4:c.4705G>A	p.Glu1569Lys	p.E1569K	ENST00000373644	NM_030625.2	1569	Gag/Aag	8/12	0.368391579985632	3	FACETS	1	0.92	1	0.515	0.462	0.571	CLONAL	1	TRUE	1	0.368391579985632	3		759	662	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256157	123256158	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	102	809	1	ENST00000358487.5:c.1751_1752delinsCT	p.Met584Thr	p.M584T	ENST00000358487	NM_000141.4	584	aTG/aCT	13/18	NA	2	FACETS	0.801	0.717	0.891			1	INDETERMINATE	1	TRUE	NA	0.368391579985632	2		810	691	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414292	32414292	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	66	603	0	ENST00000332351.3:c.1259C>T	p.Pro420Leu	p.P420L	ENST00000332351	NM_024426.4	420	cCa/cTa	8/10	0.317503702836696	4	FACETS	0.759	0.659	0.868	0.253	0.219	0.29	SUBCLONAL	1	TRUE	1	0.368391579985632	4		603	646	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417928	32417928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	83	676	0	ENST00000332351.3:c.1124C>T	p.Ala375Val	p.A375V	ENST00000332351	NM_024426.4	375	gCc/gTc	7/10	0.317503702836696	4	FACETS	0.911	0.804	1	0.304	0.268	0.342	CLONAL	1	TRUE	1	0.368391579985632	4		676	677	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466022	69466022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	181	929	2	ENST00000227507.2:c.860C>T	p.Pro287Leu	p.P287L	ENST00000227507	NM_053056.2	287	cCc/cTc	5/5	0.317503702836696	4	FACETS	0.839	0.775	0.906	0.56	0.517	0.604	CLONAL	2	TRUE	1	0.368391579985632	4		931	801	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588211	69588211	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	55	759	1	ENST00000168712.1:c.487C>T	p.Pro163Ser	p.P163S	ENST00000168712	NM_002007.2	163	Ccc/Tcc	3/3	0.317503702836696	4	FACETS	0.668	0.571	0.774	0.223	0.19	0.258	SUBCLONAL	1	TRUE	1	0.368391579985632	4		760	612	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633608	69633608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	36	169	2	ENST00000334134.2:c.94C>T	p.Arg32Cys	p.R32C	ENST00000334134	NM_005247.2	32	Cgt/Tgt	1/3	0.317503702836696	4	FACETS	0.942	0.788	1	0.628	0.525	0.738	CLONAL	2	TRUE	1	0.368391579985632	4		171	142	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212866	94212866	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	188	660	0	ENST00000323929.3:c.376C>A	p.His126Asn	p.H126N	ENST00000323929	NM_005591.3	126	Cat/Aat	5/20	0.330349031116346	2	FACETS	0.92	0.856	0.985	0.92	0.856	0.985	CLONAL	2	TRUE	0	0.368391579985632	2		660	555	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18576896	18576896	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs753453484	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	193	742	1	ENST00000266497.5:c.2304G>A	p.Trp768Ter	p.W768*	ENST00000266497		768	tgG/tgA	16/31	0.368391579985632	3	FACETS	0.795	0.737	0.855	0.795	0.737	0.855	SUBCLONAL	2	TRUE	1	0.368391579985632	3		743	780	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650671	18650671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	58	505	1	ENST00000266497.5:c.2882G>A	p.Gly961Glu	p.G961E	ENST00000266497		961	gGa/gAa	20/31	0.368391579985632	3	FACETS	0.734	0.631	0.846	0.367	0.315	0.423	SUBCLONAL	1	TRUE	1	0.368391579985632	3		506	508	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628690	21628690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	237	798	0	ENST00000421138.2:c.1018C>T	p.His340Tyr	p.H340Y	ENST00000421138		340	Cat/Tat	10/16	0.368391579985632	3	FACETS	0.918	0.859	0.978	0.918	0.859	0.978	CLONAL	2	TRUE	1	0.368391579985632	3		798	830	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432350	49432350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777025180	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	125	887	0	ENST00000301067.7:c.8789C>T	p.Pro2930Leu	p.P2930L	ENST00000301067	NM_003482.3	2930	cCc/cTc	34/54	0.368391579985632	3	FACETS	1	0.947	1	0.534	0.483	0.587	CLONAL	1	TRUE	1	0.368391579985632	3		887	753	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443901	49443901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	121	955	1	ENST00000301067.7:c.3470C>T	p.Pro1157Leu	p.P1157L	ENST00000301067	NM_003482.3	1157	cCc/cTc	11/54	0.368391579985632	3	FACETS	1	0.928	1	0.516	0.466	0.568	CLONAL	1	TRUE	1	0.368391579985632	3		956	754	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444974	49444974	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	80	743	0	ENST00000301067.7:c.2492C>T	p.Ser831Leu	p.S831L	ENST00000301067	NM_003482.3	831	tCa/tTa	10/54	0.368391579985632	3	FACETS	0.97	0.856	1	0.485	0.428	0.546	CLONAL	1	TRUE	1	0.368391579985632	3		743	530	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448290	49448336	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGCCCCATTCTCCTCACTCACCTCCAGGTTCTCCTAGGTGGGCAGGT	TGCCCCATTCTCCTCACTCACCTCCAGGTTCTCCTAGGTGGGCAGGT	-	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	150	712	0	ENST00000301067.7:c.375_400+21del		p.X125_splice	ENST00000301067	NM_003482.3	125		3/54	0.368391579985632	3	FACETS	0.816	0.749	0.885	0.816	0.749	0.885	CLONAL	2	TRUE	1	0.368391579985632	3		712	591	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864817	57864817	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1191551029	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	94	820	0	ENST00000228682.2:c.2294C>T	p.Pro765Leu	p.P765L	ENST00000228682	NM_005269.2	765	cCc/cTc	12/12	0.191946804621492	3	FACETS	0.986	0.879	1	0.493	0.439	0.55	INDETERMINATE	1	TRUE	1	0.368391579985632	3		820	613	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209020	133209020	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	72	831	2	ENST00000320574.5:c.6211C>T	p.Gln2071Ter	p.Q2071*	ENST00000320574	NM_006231.2	2071	Cag/Tag	45/49	1	2	FACETS	0.739	0.647	0.838	0.739	0.647	0.838	SUBCLONAL	1	TRUE	1	0.368391579985632	2		833	529	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549251	21549251	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1160850771	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	148	1138	0	ENST00000382592.4:c.3025A>G	p.Ser1009Gly	p.S1009G	ENST00000382592	NM_014572.2	1009	Agc/Ggc	8/8	0.191946804621492	3	FACETS	1	0.98	1	0.618	0.565	0.673	INDETERMINATE	1	TRUE	1	0.368391579985632	3		1138	770	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893575	28893575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	87	541	0	ENST00000282397.4:c.3271G>A	p.Glu1091Lys	p.E1091K	ENST00000282397	NM_002019.4	1091	Gaa/Aaa	24/30	0.191946804621492	3	FACETS	1	0.959	1	0.585	0.52	0.654	INDETERMINATE	1	TRUE	1	0.368391579985632	3		541	478	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28971169	28971169	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	89	569	0	ENST00000282397.4:c.1588T>A	p.Ser530Thr	p.S530T	ENST00000282397	NM_002019.4	530	Tct/Act	12/30	0.191946804621492	3	FACETS	1	0.959	1	0.583	0.518	0.651	INDETERMINATE	1	TRUE	1	0.368391579985632	3		569	491	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004206	29004206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	46	476	0	ENST00000282397.4:c.1087C>T	p.Pro363Ser	p.P363S	ENST00000282397	NM_002019.4	363	Ccc/Tcc	8/30	0.191946804621492	3	FACETS	0.797	0.673	0.933	0.399	0.336	0.467	INDETERMINATE	1	TRUE	1	0.368391579985632	3		476	371	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041725	29041725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	82	602	0	ENST00000282397.4:c.94C>T	p.Pro32Ser	p.P32S	ENST00000282397	NM_002019.4	32	Cct/Tct	2/30	0.191946804621492	3	FACETS	0.889	0.785	1	0.445	0.392	0.5	INDETERMINATE	1	TRUE	1	0.368391579985632	3		602	593	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912904	32912904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	93	545	0	ENST00000380152.3:c.4412G>A	p.Arg1471Lys	p.R1471K	ENST00000380152		1471	aGa/aAa	11/27	0.191946804621492	3	FACETS	1	0.964	1	0.593	0.529	0.661	INDETERMINATE	1	TRUE	1	0.368391579985632	3		545	504	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32931942	32931942	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs80358994	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	80	545	1	ENST00000380152.3:c.7681C>T	p.Gln2561Ter	p.Q2561*	ENST00000380152		2561	Cag/Tag	16/27	0.191946804621492	3	FACETS	1	0.91	1	0.518	0.458	0.583	INDETERMINATE	1	TRUE	1	0.368391579985632	3		546	496	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281927	49281927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	116	872	0	ENST00000282018.3:c.974C>T	p.Pro325Leu	p.P325L	ENST00000282018	NM_020377.2	325	cCa/cTa	1/1	0.191946804621492	3	FACETS	0.937	0.844	1	0.468	0.422	0.518	INDETERMINATE	1	TRUE	1	0.368391579985632	3		872	796	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574662	95574662	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	114	451	0	ENST00000393063.1:c.2435A>T	p.Gln812Leu	p.Q812L	ENST00000393063	NM_030621.3	812	cAg/cTg	16/28	0.368391579985632	3	FACETS	0.825	0.748	0.906	0.825	0.748	0.906	CLONAL	2	TRUE	1	0.368391579985632	3		451	444	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729163	66729163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516792	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	174	944	0	ENST00000307102.5:c.371C>T	p.Pro124Leu	p.P124L	ENST00000307102	NM_002755.3	124	cCg/cTg	3/11	0.324452173376508	4	FACETS	0.756	0.696	0.818	0.378	0.348	0.409	SUBCLONAL	2	TRUE	0	0.368391579985632	4		944	855	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420231	88420231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	65	674	1	ENST00000360948.2:c.2455G>A	p.Glu819Lys	p.E819K	ENST00000360948	NM_001012338.2	819	Gag/Aag	19/19	0.324452173376508	4	FACETS	0.721	0.624	0.825	0.18	0.156	0.207	SUBCLONAL	1	TRUE	0	0.368391579985632	4		675	670	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124271	2124271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	294	1031	1	ENST00000219476.3:c.2426C>T	p.Ser809Phe	p.S809F	ENST00000219476	NM_000548.3	809	tCc/tTc	22/42	0.366147283641563	4	FACETS	1	0.988	1	0.581	0.548	0.615	CLONAL	2	TRUE	0	0.368391579985632	4		1032	940	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222275	2222275	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149059378	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	425	1007	1	ENST00000326181.6:c.559C>T	p.His187Tyr	p.H187Y	ENST00000326181	NM_032271.2	187	Cac/Tac	8/21	0.366147283641563	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	4	TRUE	0	0.368391579985632	4		1008	743	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640061	3640061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368695839	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	220	1159	0	ENST00000294008.3:c.3578C>T	p.Ser1193Phe	p.S1193F	ENST00000294008	NM_032444.2	1193	tCc/tTc	12/15	0.366147283641563	4	FACETS	0.768	0.714	0.824	0.384	0.357	0.412	SUBCLONAL	2	TRUE	0	0.368391579985632	4		1159	1064	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777961	3777961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	267	1248	1	ENST00000262367.5:c.7087C>T	p.Pro2363Ser	p.P2363S	ENST00000262367	NM_004380.2	2363	Ccg/Tcg	31/31	0.366147283641563	4	FACETS	0.823	0.771	0.877	0.412	0.385	0.439	CLONAL	2	TRUE	0	0.368391579985632	4		1249	1205	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934581	9934581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	209	734	0	ENST00000330684.3:c.1574C>T	p.Ser525Phe	p.S525F	ENST00000330684	NM_001134407.1	525	tCt/tTt	7/13	0.366147283641563	4	FACETS	1	0.986	1	0.6	0.56	0.641	CLONAL	2	TRUE	0	0.368391579985632	4		734	647	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576873	7576873	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs863224500	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	197	879	0	ENST00000269305.4:c.973G>T	p.Gly325Ter	p.G325*	ENST00000269305	NM_001126112.2	325	Gga/Tga	9/11	0.333764321992287	2	FACETS	0.86	0.8	0.921	0.86	0.8	0.921	CLONAL	2	TRUE	0	0.368391579985632	2		879	622	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665053	29665053	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691093	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	189	725	2	ENST00000356175.3:c.6652C>T	p.Gln2218Ter	p.Q2218*	ENST00000356175	NM_000267.3	2218	Caa/Taa	44/57	0.333764321992287	2	FACETS	0.889	0.827	0.953	0.889	0.827	0.953	CLONAL	2	TRUE	0	0.368391579985632	2		727	577	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872646	37872646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	117	1055	1	ENST00000269571.5:c.1606C>T	p.Arg536Trp	p.R536W	ENST00000269571		536	Cgg/Tgg	13/27	0.333764321992287	2	FACETS	0.871	0.786	0.961	0.436	0.393	0.481	CLONAL	1	TRUE	0	0.368391579985632	2		1056	729	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40491367	40491367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	205	886	1	ENST00000264657.5:c.433G>A	p.Glu145Lys	p.E145K	ENST00000264657	NM_139276.2	145	Gag/Aag	5/24	0.333764321992287	2	FACETS	0.852	0.794	0.911	0.852	0.794	0.911	CLONAL	2	TRUE	0	0.368391579985632	2		887	653	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40871210	40871210	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	149	662	0	ENST00000428826.2:c.680C>T	p.Ser227Phe	p.S227F	ENST00000428826		227	tCc/tTc	8/21	0.333764321992287	2	FACETS	0.887	0.817	0.959	0.887	0.817	0.959	CLONAL	2	TRUE	0	0.368391579985632	2		662	456	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39644757	39644757	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	150	521	0	ENST00000262039.4:c.2486C>T	p.Pro829Leu	p.P829L	ENST00000262039	NM_002647.2	829	cCa/cTa	23/25	0.330349031116346	2	FACETS	0.881	0.812	0.952	0.881	0.812	0.952	CLONAL	2	TRUE	0	0.368391579985632	2		521	462	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56376664	56376664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	122	825	0	ENST00000348428.3:c.704C>T	p.Ser235Phe	p.S235F	ENST00000348428	NM_006785.3	235	tCc/tTc	5/17	0.330349031116346	2	FACETS	0.986	0.892	1	0.493	0.446	0.542	CLONAL	1	TRUE	0	0.368391579985632	2		825	672	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210784	5210784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762745270	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	77	901	1	ENST00000357368.4:c.5267C>T	p.Pro1756Leu	p.P1756L	ENST00000357368	NM_002850.3	1756	cCg/cTg	34/38	0.202275222787739	2	FACETS	0.703	0.617	0.794	0.351	0.308	0.397	INDETERMINATE	1	TRUE	0	0.368391579985632	2		902	595	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229591	5229592	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	36	219	0	ENST00000357368.4:c.2259_2260delinsTT	p.Arg754Cys	p.R754C	ENST00000357368	NM_002850.3	753	atCCgc/atTTgc	15/38	0.202275222787739	2	FACETS	1	0.899	1	0.558	0.465	0.661	INDETERMINATE	1	TRUE	0	0.368391579985632	2		219	175	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125532	7125532	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	48	728	1	ENST00000302850.5:c.3020C>T	p.Pro1007Leu	p.P1007L	ENST00000302850	NM_000208.2	1007	cCa/cTa	17/22	0.202275222787739	2	FACETS	0.592	0.501	0.692	0.296	0.25	0.346	INDETERMINATE	1	TRUE	0	0.368391579985632	2		729	440	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172370	7172370	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	69	767	0	ENST00000302850.5:c.1199C>T	p.Ser400Phe	p.S400F	ENST00000302850	NM_000208.2	400	tCc/tTc	5/22	0.202275222787739	2	FACETS	0.732	0.638	0.832	0.366	0.319	0.416	INDETERMINATE	1	TRUE	0	0.368391579985632	2		767	512	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7174711	7174711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	121	747	0	ENST00000302850.5:c.1006C>T	p.Pro336Ser	p.P336S	ENST00000302850	NM_000208.2	336	Ccc/Tcc	4/22	0.202275222787739	2	FACETS	1	0.976	1	0.617	0.56	0.677	INDETERMINATE	1	TRUE	0	0.368391579985632	2		747	532	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051631	13051631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	179	828	0	ENST00000316448.5:c.890C>T	p.Pro297Leu	p.P297L	ENST00000316448	NM_004343.3	297	cCc/cTc	7/9	0.323604517760739	3	FACETS	0.773	0.715	0.834	0.773	0.715	0.834	SUBCLONAL	2	TRUE	1	0.368391579985632	3		828	744	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968249	18968249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	100	829	0	ENST00000262803.5:c.2089C>T	p.Arg697Cys	p.R697C	ENST00000262803	NM_002911.3	697	Cgc/Tgc	15/24	0.323604517760739	3	FACETS	0.977	0.874	1	0.489	0.437	0.544	CLONAL	1	TRUE	1	0.368391579985632	3		829	658	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257164	19257164	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	101	696	0	ENST00000162023.5:c.799C>T	p.Pro267Ser	p.P267S	ENST00000162023		267	Cct/Tct	12/13	0.323604517760739	3	FACETS	1	0.926	1	0.521	0.466	0.579	CLONAL	1	TRUE	1	0.368391579985632	3		696	623	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257881	19257881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	106	1076	0	ENST00000162023.5:c.505C>T	p.Pro169Ser	p.P169S	ENST00000162023		169	Ccc/Tcc	9/13	0.323604517760739	3	FACETS	0.907	0.814	1	0.454	0.407	0.504	CLONAL	1	TRUE	1	0.368391579985632	3		1076	751	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224181	36224182	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	160	829	2	ENST00000222270.7:c.6731_6732delinsAT	p.Pro2244His	p.P2244H	ENST00000222270	NM_014727.1	2244	cCC/cAT	28/37	0.323604517760739	3	FACETS	0.779	0.717	0.844	0.779	0.717	0.844	SUBCLONAL	2	TRUE	1	0.368391579985632	3		831	660	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227851	36227851	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	226	1177	0	ENST00000222270.7:c.7336C>G	p.Arg2446Gly	p.R2446G	ENST00000222270	NM_014727.1	2446	Cga/Gga	32/37	0.323604517760739	3	FACETS	0.818	0.763	0.875	0.818	0.763	0.875	CLONAL	2	TRUE	1	0.368391579985632	3		1177	888	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744057	41744057	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	68	711	0	ENST00000301178.4:c.992G>A	p.Gly331Glu	p.G331E	ENST00000301178	NM_021913.4	331	gGa/gAa	7/20	0.323604517760739	3	FACETS	0.775	0.675	0.883	0.388	0.337	0.442	SUBCLONAL	1	TRUE	1	0.368391579985632	3		711	564	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754650	41754650	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	180	848	0	ENST00000301178.4:c.1636G>A	p.Glu546Lys	p.E546K	ENST00000301178	NM_021913.4	546	Gag/Aag	14/20	0.323604517760739	3	FACETS	0.894	0.828	0.962	0.894	0.828	0.962	CLONAL	2	TRUE	1	0.368391579985632	3		848	647	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085773	16085773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	79	622	0	ENST00000281043.3:c.949G>A	p.Glu317Lys	p.E317K	ENST00000281043	NM_005378.4	317	Gag/Aag	3/3	0.368391579985632	3	FACETS	1	0.903	1	0.513	0.452	0.578	CLONAL	1	TRUE	1	0.368391579985632	3		622	495	SUCCESS
ALK	238	MSKCC	GRCh37	2	29419721	29419721	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	120	511	1	ENST00000389048.3:c.4079G>T	p.Arg1360Leu	p.R1360L	ENST00000389048	NM_004304.4	1360	cGg/cTg	28/29	0.368391579985632	4	FACETS	1	0.983	1	0.718	0.65	0.789	CLONAL	1	TRUE	2	0.368391579985632	4		512	621	SUCCESS
ALK	238	MSKCC	GRCh37	2	29420472	29420472	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	251	725	2	ENST00000389048.3:c.4009G>A	p.Glu1337Lys	p.E1337K	ENST00000389048	NM_004304.4	1337	Gaa/Aaa	27/29	0.368391579985632	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.368391579985632	4		727	803	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432701	29432701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	236	715	0	ENST00000389048.3:c.3787G>A	p.Gly1263Arg	p.G1263R	ENST00000389048	NM_004304.4	1263	Gga/Aga	25/29	0.368391579985632	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.368391579985632	4		715	770	SUCCESS
ALK	238	MSKCC	GRCh37	2	29541246	29541246	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	165	658	0	ENST00000389048.3:c.1571C>T	p.Thr524Ile	p.T524I	ENST00000389048	NM_004304.4	524	aCt/aTt	8/29	0.368391579985632	4	FACETS	0.915	0.843	0.989	0.915	0.843	0.989	CLONAL	2	TRUE	2	0.368391579985632	4		658	670	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872881	136872881	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	117	443	0	ENST00000241393.3:c.617T>C	p.Val206Ala	p.V206A	ENST00000241393	NM_003467.2	206	gTt/gCt	2/2	0.368391579985632	4	FACETS	0.776	0.702	0.853	0.776	0.702	0.853	SUBCLONAL	2	TRUE	2	0.368391579985632	4		443	560	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488679	212488679	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	175	651	1	ENST00000342788.4:c.2170C>A	p.Leu724Ile	p.L724I	ENST00000342788	NM_005235.2	724	Ctt/Att	18/28	0.368391579985632	4	FACETS	0.782	0.721	0.846	0.782	0.721	0.846	SUBCLONAL	2	TRUE	2	0.368391579985632	4		652	831	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538263	9538263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748547848	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	206	777	1	ENST00000353224.5:c.1735G>A	p.Asp579Asn	p.D579N	ENST00000353224	NM_177990.2	579	Gat/Aat	7/10	0.227704794989168	4	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	2	0.368391579985632	4		778	759	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624936	9624936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760501160	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	93	526	1	ENST00000353224.5:c.41C>T	p.Pro14Leu	p.P14L	ENST00000353224	NM_177990.2	14	cCg/cTg	3/10	0.227704794989168	4	FACETS	1	0.976	1	0.68	0.607	0.758	CLONAL	1	TRUE	2	0.368391579985632	4		527	508	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024180	31024180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	197	758	0	ENST00000375687.4:c.3665C>T	p.Ser1222Phe	p.S1222F	ENST00000375687	NM_015338.5	1222	tCc/tTc	13/13	0.227704794989168	4	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	2	0.368391579985632	4		758	732	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376789	31376789	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	111	697	0	ENST00000328111.2:c.784C>T	p.Gln262Ter	p.Q262*	ENST00000328111	NM_006892.3	262	Cag/Tag	7/23	0.227704794989168	4	FACETS	1	0.982	1	0.715	0.644	0.789	CLONAL	1	TRUE	2	0.368391579985632	4		697	577	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744976	39744976	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	169	718	0	ENST00000361337.2:c.1766T>C	p.Phe589Ser	p.F589S	ENST00000361337	NM_003286.2	589	tTc/tCc	17/21	0.227704794989168	4	FACETS	0.858	0.79	0.927	0.858	0.79	0.927	CLONAL	2	TRUE	2	0.368391579985632	4		718	732	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770575	40770575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1294592345	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	149	686	1	ENST00000373198.4:c.2807G>A	p.Arg936Gln	p.R936Q	ENST00000373198	NM_133170.3	936	cGa/cAa	19/32	0.227704794989168	4	FACETS	0.867	0.795	0.943	0.867	0.795	0.943	CLONAL	2	TRUE	2	0.368391579985632	4		687	638	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400142	41400142	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	70	742	1	ENST00000373198.4:c.617G>A	p.Gly206Glu	p.G206E	ENST00000373198	NM_133170.3	206	gGg/gAg	5/32	0.227704794989168	4	FACETS	0.697	0.607	0.795	0.349	0.303	0.398	SUBCLONAL	1	TRUE	2	0.368391579985632	4		743	746	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281275	46281275	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	41	458	0	ENST00000371998.3:c.4072C>T	p.Gln1358Ter	p.Q1358*	ENST00000371998		1358	Cag/Tag	21/23	0.227704794989168	4	FACETS	0.648	0.54	0.768	0.324	0.27	0.384	SUBCLONAL	1	TRUE	2	0.368391579985632	4		458	470	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775521	39775522	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AT	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	123	785	1	ENST00000288319.7:c.498_499delinsAT	p.Glu167Ter	p.E167*	ENST00000288319	NM_182918.3	166	aaGGaa/aaATaa	4/10	0.227704794989168	4	FACETS	1	0.985	1	0.735	0.666	0.807	CLONAL	1	TRUE	2	0.368391579985632	4		786	622	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651316	45651316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756890702	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	147	861	0	ENST00000407780.3:c.709G>A	p.Gly237Arg	p.G237R	ENST00000407780	NM_001283052.1	237	Gga/Aga	5/7	0.227704794989168	4	FACETS	0.811	0.743	0.883	0.811	0.743	0.883	CLONAL	2	TRUE	2	0.368391579985632	4		861	673	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272398	21272398	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	235	1033	1	ENST00000354336.3:c.176C>T	p.Ser59Phe	p.S59F	ENST00000354336	NM_005207.3	59	tCc/tTc	1/3	0.323604517760739	3	FACETS	0.838	0.783	0.895	0.838	0.783	0.895	CLONAL	2	TRUE	1	0.368391579985632	3		1034	901	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458240	12458240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	90	699	1	ENST00000287820.6:c.857G>A	p.Gly286Glu	p.G286E	ENST00000287820	NM_015869.4	286	gGa/gAa	6/7	0.368391579985632	3	FACETS	0.921	0.818	1	0.461	0.409	0.516	CLONAL	1	TRUE	1	0.368391579985632	3		700	628	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458537	12458537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140204299	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	106	877	3	ENST00000287820.6:c.1154G>A	p.Arg385Gln	p.R385Q	ENST00000287820	NM_015869.4	385	cGa/cAa	6/7	0.368391579985632	3	FACETS	0.791	0.709	0.879	0.396	0.354	0.44	SUBCLONAL	1	TRUE	1	0.368391579985632	3		880	861	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723525	49723525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568019355	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	16	80	1	ENST00000449682.2:c.1117C>T	p.Arg373Trp	p.R373W	ENST00000449682	NM_020998.3	373	Cgg/Tgg	9/18	0.368391579985632	3	FACETS	1	0.903	1	0.745	0.565	0.949	CLONAL	1	TRUE	1	0.368391579985632	3		81	69	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637717	52637717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	85	772	2	ENST00000394830.3:c.2599G>A	p.Glu867Lys	p.E867K	ENST00000394830	NM_018313.4	867	Gaa/Aaa	18/30	0.368391579985632	3	FACETS	0.905	0.801	1	0.452	0.4	0.508	CLONAL	1	TRUE	1	0.368391579985632	3		774	604	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72861888	72861888	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	192	866	0	ENST00000325599.8:c.994C>T	p.Pro332Ser	p.P332S	ENST00000325599	NM_018130.2	332	Cca/Tca	9/11	0.368391579985632	4	FACETS	0.815	0.754	0.878	0.815	0.754	0.878	CLONAL	2	TRUE	2	0.368391579985632	4		866	875	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391097	89391097	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	201	868	0	ENST00000336596.2:c.1163G>A	p.Gly388Glu	p.G388E	ENST00000336596	NM_005233.5	388	gGa/gAa	5/17	0.368391579985632	4	FACETS	0.902	0.837	0.968	0.902	0.837	0.968	CLONAL	2	TRUE	2	0.368391579985632	4		868	828	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521711	89521711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	125	623	0	ENST00000336596.2:c.2788G>A	p.Glu930Lys	p.E930K	ENST00000336596	NM_005233.5	930	Gaa/Aaa	16/17	0.368391579985632	4	FACETS	1	0.979	1	0.642	0.582	0.706	CLONAL	1	TRUE	2	0.368391579985632	4		623	723	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644711	134644711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	70	749	1	ENST00000398015.3:c.112C>T	p.Pro38Ser	p.P38S	ENST00000398015	NM_004441.4	38	Cct/Tct	2/16	0.368391579985632	3	FACETS	0.735	0.641	0.837	0.368	0.32	0.419	SUBCLONAL	1	TRUE	1	0.368391579985632	3		750	612	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178942511	178942511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	84	545	0	ENST00000263967.3:c.2318C>T	p.Ser773Phe	p.S773F	ENST00000263967	NM_006218.2	773	tCc/tTc	16/21	0.368391579985632	3	FACETS	0.963	0.852	1	0.481	0.426	0.541	CLONAL	1	TRUE	1	0.368391579985632	3		545	561	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665116	182665116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772065612	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	150	576	1	ENST00000292782.4:c.610C>T	p.His204Tyr	p.H204Y	ENST00000292782	NM_020640.2	204	Cat/Tat	6/7	0.368391579985632	3	FACETS	0.812	0.745	0.881	0.812	0.745	0.881	CLONAL	2	TRUE	1	0.368391579985632	3		577	594	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444525	187444525	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	99	747	0	ENST00000232014.4:c.1702C>T	p.His568Tyr	p.H568Y	ENST00000232014	NM_001130845.1	568	Cat/Tat	7/10	0.368391579985632	3	FACETS	0.882	0.787	0.982	0.441	0.393	0.491	CLONAL	1	TRUE	1	0.368391579985632	3		747	722	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803244	1803244	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	139	904	0	ENST00000260795.2:c.596A>C	p.His199Pro	p.H199P	ENST00000260795		199	cAc/cCc	4/17	0.205026546924489	3	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.368391579985632	3		904	597	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803246	1803246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886043613	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	140	900	0	ENST00000260795.2:c.598C>T	p.Arg200Cys	p.R200C	ENST00000260795		200	Cgc/Tgc	4/17	0.205026546924489	3	FACETS	0.75	0.686	0.817			1	INDETERMINATE	2	TRUE	NA	0.368391579985632	3		900	600	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133733	55133733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	203	657	0	ENST00000257290.5:c.946G>A	p.Glu316Lys	p.E316K	ENST00000257290	NM_006206.4	316	Gaa/Aaa	7/23	0.368391579985632	5	FACETS	1	0.964	1	0.706	0.656	0.758	CLONAL	2	TRUE	2	0.368391579985632	5		657	808	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139895	55139895	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	58	432	0	ENST00000257290.5:c.1556C>T	p.Pro519Leu	p.P519L	ENST00000257290	NM_006206.4	519	cCc/cTc	10/23	0.368391579985632	5	FACETS	1	0.903	1	0.354	0.305	0.408	CLONAL	1	TRUE	2	0.368391579985632	5		432	460	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141059	55141059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	191	560	0	ENST00000257290.5:c.1705G>A	p.Gly569Arg	p.G569R	ENST00000257290	NM_006206.4	569	Gga/Aga	12/23	0.368391579985632	5	FACETS	1	0.974	1	0.738	0.685	0.793	CLONAL	2	TRUE	2	0.368391579985632	5		560	727	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964326	55964327	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	212	546	2	ENST00000263923.4:c.2486_2487delinsAT	p.Phe829Tyr	p.F829Y	ENST00000263923	NM_002253.2	829	tTC/tAT	17/30	0.368391579985632	5	FACETS	1	0.982	1	0.771	0.718	0.825	CLONAL	2	TRUE	2	0.368391579985632	5		548	773	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157551	106157551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757207662	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	71	435	0	ENST00000380013.4:c.2452C>T	p.Pro818Ser	p.P818S	ENST00000380013	NM_001127208.2	818	Cct/Tct	3/11	0.317503702836696	4	FACETS	0.997	0.872	1	0.332	0.29	0.378	CLONAL	1	TRUE	1	0.368391579985632	4		435	529	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534340	187534341	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	79	787	2	ENST00000441802.2:c.9385_9386delinsTT	p.Pro3129Phe	p.P3129F	ENST00000441802	NM_005245.3	3129	CCt/TTt	13/27	0.191946804621492	3	FACETS	0.894	0.788	1	0.447	0.394	0.504	INDETERMINATE	1	TRUE	1	0.368391579985632	3		789	568	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526371	31526371	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	194	1361	1	ENST00000344624.3:c.669A>T	p.Glu223Asp	p.E223D	ENST00000344624		223	gaA/gaT	2/33	0.368391579985632	3	FACETS	1	0.939	1	0.509	0.47	0.55	CLONAL	1	TRUE	1	0.368391579985632	3		1362	1224	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526631	31526631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269978298	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	96	772	0	ENST00000344624.3:c.409C>T	p.Pro137Ser	p.P137S	ENST00000344624		137	Cct/Tct	2/33	0.368391579985632	3	FACETS	0.852	0.76	0.951	0.426	0.38	0.476	CLONAL	1	TRUE	1	0.368391579985632	3		772	724	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871199	35871199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	65	474	0	ENST00000303115.3:c.421G>A	p.Glu141Lys	p.E141K	ENST00000303115	NM_002185.3	141	Gaa/Aaa	4/8	0.368391579985632	3	FACETS	0.778	0.675	0.889	0.389	0.337	0.445	SUBCLONAL	1	TRUE	1	0.368391579985632	3		474	537	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876133	35876133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867328876	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	194	672	0	ENST00000303115.3:c.925C>T	p.His309Tyr	p.H309Y	ENST00000303115	NM_002185.3	309	Cat/Tat	8/8	0.368391579985632	3	FACETS	0.961	0.893	1	0.961	0.893	1	CLONAL	2	TRUE	1	0.368391579985632	3		672	649	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950648	38950648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776074870	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	150	575	0	ENST00000357387.3:c.3302C>T	p.Ser1101Leu	p.S1101L	ENST00000357387	NM_152756.3	1101	tCg/tTg	31/38	0.368391579985632	3	FACETS	0.808	0.741	0.877	0.808	0.741	0.877	CLONAL	2	TRUE	1	0.368391579985632	3		575	597	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149452999	149453000	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	144	640	1	ENST00000286301.3:c.946_947delinsAA	p.Gly316Lys	p.G316K	ENST00000286301	NM_005211.3	316	GGg/AAg	7/22	0.368391579985632	3	FACETS	0.83	0.76	0.901	0.83	0.76	0.901	CLONAL	2	TRUE	1	0.368391579985632	3		641	558	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460362	149460362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	137	599	0	ENST00000286301.3:c.275G>A	p.Gly92Glu	p.G92E	ENST00000286301	NM_005211.3	92	gGa/gAa	3/22	0.368391579985632	3	FACETS	0.805	0.736	0.877	0.805	0.736	0.877	CLONAL	2	TRUE	1	0.368391579985632	3		599	547	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500563	149500563	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	80	811	0	ENST00000261799.4:c.2474G>A	p.Arg825Lys	p.R825K	ENST00000261799	NM_002609.3	825	aGa/aAa	18/23	0.368391579985632	3	FACETS	0.847	0.747	0.955	0.424	0.373	0.478	CLONAL	1	TRUE	1	0.368391579985632	3		811	607	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500827	149500827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748872294	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	232	896	1	ENST00000261799.4:c.2403G>A	p.Met801Ile	p.M801I	ENST00000261799	NM_002609.3	801	atG/atA	17/23	0.368391579985632	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.368391579985632	3		897	705	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520253	176520253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375466821	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	104	893	1	ENST00000292408.4:c.1172G>A	p.Arg391Gln	p.R391Q	ENST00000292408	NM_213647.1	391	cGa/cAa	9/18	0.368391579985632	3	FACETS	0.957	0.857	1	0.478	0.428	0.531	CLONAL	1	TRUE	1	0.368391579985632	3		894	699	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046746	180046746	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	162	928	0	ENST00000261937.6:c.2566T>C	p.Phe856Leu	p.F856L	ENST00000261937	NM_182925.4	856	Ttc/Ctc	18/30	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.368391579985632	2		928	623	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048881	180048881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751002839	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	190	1157	0	ENST00000261937.6:c.1681G>A	p.Glu561Lys	p.E561K	ENST00000261937	NM_182925.4	561	Gaa/Aaa	13/30	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.368391579985632	2		1157	716	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051017	180051017	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	78	980	1	ENST00000261937.6:c.1466G>A	p.Trp489Ter	p.W489*	ENST00000261937	NM_182925.4	489	tGg/tAg	11/30	NA	2	FACETS	0.628	0.552	0.71			1	INDETERMINATE	1	TRUE	NA	0.368391579985632	2		981	674	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056291	180056291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199942873	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	203	1099	0	ENST00000261937.6:c.953G>A	p.Arg318Gln	p.R318Q	ENST00000261937	NM_182925.4	318	cGa/cAa	7/30	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.368391579985632	2		1099	846	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490458	20490458	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	184	749	1	ENST00000346618.3:c.1195C>T	p.Pro399Ser	p.P399S	ENST00000346618	NM_001949.4	399	Cct/Tct	7/7	0.368391579985632	5	FACETS	0.995	0.921	1	0.664	0.614	0.715	CLONAL	2	TRUE	2	0.368391579985632	5		750	779	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181926	32181926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	108	860	1	ENST00000375023.3:c.2128C>T	p.Pro710Ser	p.P710S	ENST00000375023	NM_004557.3	710	Ccc/Tcc	13/30	0.317503702836696	4	FACETS	1	0.913	1	0.34	0.305	0.377	CLONAL	1	TRUE	1	0.368391579985632	4		861	787	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956523	93956523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	67	520	0	ENST00000369303.4:c.2713G>A	p.Gly905Arg	p.G905R	ENST00000369303	NM_004440.3	905	Gga/Aga	15/17	0.368391579985632	3	FACETS	0.886	0.772	1	0.443	0.386	0.505	CLONAL	1	TRUE	1	0.368391579985632	3		520	486	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969189	93969189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868510824	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	62	493	0	ENST00000369303.4:c.1807C>T	p.Pro603Ser	p.P603S	ENST00000369303	NM_004440.3	603	Cca/Tca	10/17	0.368391579985632	3	FACETS	0.832	0.72	0.953	0.416	0.36	0.477	CLONAL	1	TRUE	1	0.368391579985632	3		493	479	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117650525	117650525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	244	970	1	ENST00000368508.3:c.5333G>A	p.Gly1778Glu	p.G1778E	ENST00000368508	NM_002944.2	1778	gGa/gAa	32/43	0.368391579985632	3	FACETS	0.821	0.768	0.876	0.821	0.768	0.876	CLONAL	2	TRUE	1	0.368391579985632	3		971	955	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710750	117710750	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	70	509	0	ENST00000368508.3:c.1522G>A	p.Asp508Asn	p.D508N	ENST00000368508	NM_002944.2	508	Gac/Aac	12/43	0.368391579985632	3	FACETS	0.924	0.808	1	0.462	0.404	0.525	CLONAL	1	TRUE	1	0.368391579985632	3		509	487	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725504	117725504	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	93	713	1	ENST00000368508.3:c.377G>A	p.Gly126Glu	p.G126E	ENST00000368508	NM_002944.2	126	gGa/gAa	5/43	0.368391579985632	3	FACETS	0.946	0.842	1	0.473	0.421	0.528	CLONAL	1	TRUE	1	0.368391579985632	3		714	632	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519343	137519343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	108	429	2	ENST00000367739.4:c.1295C>T	p.Pro432Leu	p.P432L	ENST00000367739	NM_000416.2	432	cCa/cTa	7/7	0.368391579985632	3	FACETS	0.833	0.753	0.916	0.833	0.753	0.916	CLONAL	2	TRUE	1	0.368391579985632	3		431	417	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016306	150016306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	113	764	0	ENST00000253339.5:c.400G>A	p.Ala134Thr	p.A134T	ENST00000253339		134	Gca/Aca	2/7	0.368391579985632	3	FACETS	0.918	0.826	1	0.459	0.413	0.508	CLONAL	1	TRUE	1	0.368391579985632	3		764	791	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023244	150023244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	64	614	0	ENST00000253339.5:c.19C>T	p.Pro7Ser	p.P7S	ENST00000253339		7	Cca/Tca	1/7	0.368391579985632	3	FACETS	0.818	0.709	0.935	0.409	0.354	0.468	CLONAL	1	TRUE	1	0.368391579985632	3		614	503	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771153	161771153	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751485437	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	148	741	0	ENST00000366898.1:c.1376G>A	p.Gly459Glu	p.G459E	ENST00000366898	NM_004562.2	459	gGg/gAg	12/12	0.368391579985632	3	FACETS	1	0.986	1	0.701	0.641	0.762	CLONAL	1	TRUE	1	0.368391579985632	3		741	679	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683745	162683745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759650233	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	65	736	0	ENST00000366898.1:c.224G>A	p.Arg75Lys	p.R75K	ENST00000366898	NM_004562.2	75	aGa/aAa	3/12	0.368391579985632	3	FACETS	0.681	0.59	0.779	0.34	0.295	0.39	SUBCLONAL	1	TRUE	1	0.368391579985632	3		736	614	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2949757	2949757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358903936	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	120	941	0	ENST00000396946.4:c.3187G>A	p.Asp1063Asn	p.D1063N	ENST00000396946	NM_032415.4	1063	Gac/Aac	24/25	0.368391579985632	3	FACETS	0.901	0.813	0.994	0.451	0.406	0.497	CLONAL	1	TRUE	1	0.368391579985632	3		941	856	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956940	2956940	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	88	771	0	ENST00000396946.4:c.2687T>A	p.Phe896Tyr	p.F896Y	ENST00000396946	NM_032415.4	896	tTt/tAt	20/25	0.368391579985632	3	FACETS	0.887	0.786	0.994	0.443	0.393	0.497	CLONAL	1	TRUE	1	0.368391579985632	3		771	638	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983953	2983953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	115	1016	2	ENST00000396946.4:c.577G>A	p.Glu193Lys	p.E193K	ENST00000396946	NM_032415.4	193	Gag/Aag	5/25	0.368391579985632	3	FACETS	0.752	0.676	0.833	0.376	0.338	0.417	SUBCLONAL	1	TRUE	1	0.368391579985632	3		1018	983	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392156	81392156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376573289	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	71	512	0	ENST00000222390.5:c.121G>A	p.Glu41Lys	p.E41K	ENST00000222390	NM_000601.4	41	Gaa/Aaa	2/18	0.368391579985632	4	FACETS	0.903	0.789	1	0.301	0.263	0.342	CLONAL	1	TRUE	1	0.368391579985632	4		512	584	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509117	106509117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	100	737	0	ENST00000359195.3:c.1111C>T	p.Pro371Ser	p.P371S	ENST00000359195	NM_002649.2	371	Ccc/Tcc	2/11	0.368391579985632	4	FACETS	0.939	0.839	1	0.313	0.279	0.349	CLONAL	1	TRUE	1	0.368391579985632	4		737	791	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520081	106520081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	105	482	0	ENST00000359195.3:c.2509G>A	p.Asp837Asn	p.D837N	ENST00000359195	NM_002649.2	837	Gat/Aat	6/11	0.368391579985632	4	FACETS	0.771	0.693	0.852	0.514	0.462	0.568	SUBCLONAL	2	TRUE	1	0.368391579985632	4		482	506	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526694	106526694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772274649	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	98	643	1	ENST00000359195.3:c.2987G>A	p.Gly996Glu	p.G996E	ENST00000359195	NM_002649.2	996	gGa/gAa	10/11	0.368391579985632	4	FACETS	0.977	0.872	1	0.326	0.29	0.363	CLONAL	1	TRUE	1	0.368391579985632	4		644	745	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340054	116340054	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	118	379	0	ENST00000397752.3:c.916A>T	p.Lys306Ter	p.K306*	ENST00000397752	NM_000245.2	306	Aag/Tag	2/21	0.368391579985632	4	FACETS	0.915	0.83	1	0.61	0.553	0.669	CLONAL	2	TRUE	1	0.368391579985632	4		379	479	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397692	116397692	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	165	560	0	ENST00000397752.3:c.1966G>A	p.Asp656Asn	p.D656N	ENST00000397752	NM_000245.2	656	Gat/Aat	8/21	0.368391579985632	4	FACETS	1	0.931	1	0.673	0.621	0.727	CLONAL	2	TRUE	1	0.368391579985632	4		560	607	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876977	151876977	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	55	510	1	ENST00000262189.6:c.7384C>T	p.Gln2462Ter	p.Q2462*	ENST00000262189	NM_170606.2	2462	Cag/Tag	37/59	0.368391579985632	4	FACETS	0.955	0.819	1	0.318	0.273	0.368	CLONAL	1	TRUE	1	0.368391579985632	4		511	428	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031690	69031690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371787029	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	93	772	2	ENST00000288368.4:c.3445C>T	p.Arg1149Cys	p.R1149C	ENST00000288368	NM_024870.2	1149	Cgc/Tgc	28/40	0.330349031116346	2	FACETS	0.84	0.748	0.938	0.42	0.374	0.469	CLONAL	1	TRUE	0	0.368391579985632	2		774	601	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572607	141572607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	244	788	0	ENST00000220592.5:c.463C>T	p.Pro155Ser	p.P155S	ENST00000220592	NM_012154.3	155	Cct/Tct	4/19	0.368391579985632	3	FACETS	0.839	0.79	0.889	0.839	0.79	0.889	CLONAL	3	TRUE	0	0.368391579985632	3		788	623	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521384	8521384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777779009	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	285	826	0	ENST00000356435.5:c.854G>A	p.Gly285Glu	p.G285E	ENST00000356435		285	gGa/gAa	9/35	0.237168315037292	3	FACETS	0.84	0.794	0.887	0.84	0.794	0.887	CLONAL	3	TRUE	0	0.368391579985632	3		826	727	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521505	8521505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	219	729	0	ENST00000356435.5:c.733C>T	p.His245Tyr	p.H245Y	ENST00000356435		245	Cat/Tat	9/35	0.237168315037292	3	FACETS	1	0.981	1	0.746	0.698	0.795	CLONAL	2	TRUE	0	0.368391579985632	3		729	629	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197468	27197468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	94	965	0	ENST00000380036.4:c.1780C>T	p.Pro594Ser	p.P594S	ENST00000380036	NM_000459.3	594	Cca/Tca	12/23	0.237168315037292	3	FACETS	0.666	0.591	0.745	0.222	0.197	0.249	SUBCLONAL	1	TRUE	0	0.368391579985632	3		965	908	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27203010	27203010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	64	758	1	ENST00000380036.4:c.2102G>A	p.Gly701Asp	p.G701D	ENST00000380036	NM_000459.3	701	gGc/gAc	13/23	0.237168315037292	3	FACETS	0.617	0.534	0.707	0.206	0.178	0.236	SUBCLONAL	1	TRUE	0	0.368391579985632	3		759	667	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637034	93637034	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	64	598	0	ENST00000375746.1:c.1084G>A	p.Glu362Lys	p.E362K	ENST00000375746	NM_001174167.1	362	Gag/Aag	9/14	0.317503702836696	4	FACETS	0.776	0.672	0.889	0.259	0.224	0.297	SUBCLONAL	1	TRUE	1	0.368391579985632	4		598	613	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641110	93641110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	76	904	1	ENST00000375746.1:c.1456G>A	p.Glu486Lys	p.E486K	ENST00000375746	NM_001174167.1	486	Gag/Aag	11/14	0.317503702836696	4	FACETS	0.687	0.601	0.779	0.229	0.2	0.26	SUBCLONAL	1	TRUE	1	0.368391579985632	4		905	822	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209525	98209525	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771238114	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	96	722	1	ENST00000331920.6:c.4013G>A	p.Arg1338His	p.R1338H	ENST00000331920	NM_000264.3	1338	cGc/cAc	23/24	0.317503702836696	4	FACETS	1	0.937	1	0.357	0.318	0.399	CLONAL	1	TRUE	1	0.368391579985632	4		723	665	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209616	98209617	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761353734	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	58	651	1	ENST00000331920.6:c.3921dup	p.Arg1308GlnfsTer17	p.R1308Qfs*17	ENST00000331920	NM_000264.3	1307	-/C	23/24	0.317503702836696	4	FACETS	0.713	0.613	0.823	0.238	0.204	0.275	SUBCLONAL	1	TRUE	1	0.368391579985632	4		652	604	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220422	98220422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1404012576	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	270	776	0	ENST00000331920.6:c.3041C>T	p.Pro1014Leu	p.P1014L	ENST00000331920	NM_000264.3	1014	cCc/cTc	18/24	0.317503702836696	4	FACETS	0.95	0.896	1	0.95	0.896	1	CLONAL	3	TRUE	1	0.368391579985632	4		776	704	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249911	110249911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753243501	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	251	724	0	ENST00000374672.4:c.764C>T	p.Pro255Leu	p.P255L	ENST00000374672	NM_004235.4	255	cCt/cTt	3/5	0.317503702836696	4	FACETS	0.922	0.868	0.977	0.922	0.868	0.977	CLONAL	3	TRUE	1	0.368391579985632	4		724	674	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738328	133738329	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	110	601	2	ENST00000318560.5:c.728_729delinsTT	p.Thr243Ile	p.T243I	ENST00000318560	NM_005157.4	243	aCC/aTT	4/11	0.175097231639311	2	FACETS	1	0.978	1	0.645	0.583	0.71	INDETERMINATE	1	TRUE	0	0.368391579985632	2		603	463	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293646	137293646	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1308326616	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	174	1144	2	ENST00000481739.1:c.197C>T	p.Ser66Leu	p.S66L	ENST00000481739	NM_002957.4	66	tCg/tTg	2/10	0.175097231639311	2	FACETS	1	0.987	1	0.678	0.626	0.731	INDETERMINATE	1	TRUE	0	0.368391579985632	2		1146	697	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400192	139400192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776239050	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	93	892	0	ENST00000277541.6:c.4156C>T	p.Pro1386Ser	p.P1386S	ENST00000277541	NM_017617.3	1386	Ccg/Tcg	25/34	0.175097231639311	2	FACETS	0.763	0.679	0.852	0.381	0.339	0.426	INDETERMINATE	1	TRUE	0	0.368391579985632	2		892	662	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321375	1321375	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	69	437	0	ENST00000400841.2:c.380T>G	p.Phe127Cys	p.F127C	ENST00000400841		127	tTt/tGt	4/6	0.230450148688509	2	FACETS	0.886	0.774	1			1	CLONAL	1	TRUE	NA	0.368391579985632	2		437	423	SUCCESS
AR	367	MSKCC	GRCh37	X	66766286	66766286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	75	291	1	ENST00000374690.3:c.1298C>T	p.Ser433Leu	p.S433L	ENST00000374690	NM_000044.3	433	tCa/tTa	1/8	0.368391579985632	2	FACETS	1	0.974	1			1	CLONAL	1	TRUE	NA	0.368391579985632	2		292	290	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813008	76813008	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	235	370	0	ENST00000373344.5:c.6613A>C	p.Thr2205Pro	p.T2205P	ENST00000373344	NM_000489.3	2205	Act/Cct	30/35	0.368391579985632	2	FACETS	0.856	0.808	0.904			1	CLONAL	3	TRUE	NA	0.368391579985632	2		370	497	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034363	123034363	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	78	292	1	ENST00000355640.3:c.1120C>T	p.Pro374Ser	p.P374S	ENST00000355640		374	Cct/Tct	6/7	0.205026546924489	2	FACETS	0.941	0.841	1			1	INDETERMINATE	2	TRUE	NA	0.368391579985632	2		293	225	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775521	39775521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	121	785	0	ENST00000288319.7:c.499G>T	p.Glu167Ter	p.E167*	ENST00000288319	NM_182918.3	167	Gaa/Taa	4/10	0.227704794989168	4	FACETS	1	0.984	1	0.732	0.663	0.804	CLONAL	1	TRUE	2	0.368391579985632	4		785	614	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149452999	149452999	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752720838	NA	P-0024262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	144	640	1	ENST00000286301.3:c.947G>A	p.Gly316Glu	p.G316E	ENST00000286301	NM_005211.3	316	gGg/gAg	7/22	0.368391579985632	3	FACETS	0.83	0.76	0.901	0.83	0.76	0.901	CLONAL	2	TRUE	1	0.368391579985632	3		641	558	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573672	41573672	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144626200	NA	P-0024422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	137	491	0	ENST00000263253.7:c.5957C>T	p.Pro1986Leu	p.P1986L	ENST00000263253	NM_001429.3	1986	cCg/cTg	31/31	0.548992081260348	5	FACETS	1	0.956	1	0.361	0.328	0.395	CLONAL	1	TRUE	2	0.606274734528201	5		491	797	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101031	4101031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375843855	NA	P-0024422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	180	437	0	ENST00000262948.5:c.691C>T	p.Arg231Cys	p.R231C	ENST00000262948	NM_030662.3	231	Cgc/Tgc	6/11	0.416551221405072	5	FACETS	1	0.959	1	0.699	0.649	0.75	CLONAL	2	TRUE	2	0.606274734528201	5		437	541	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258744	115258744	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121434596	NA	P-0024422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	140	345	0	ENST00000369535.4:c.38G>T	p.Gly13Val	p.G13V	ENST00000369535	NM_002524.4	13	gGt/gTt	2/7	0.572796119145255	3	FACETS	1	0.964	1	0.367	0.335	0.399	CLONAL	1	TRUE	0	0.606274734528201	3		345	547	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656319	18656319	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	113	374	0	ENST00000266497.5:c.2998C>A	p.Gln1000Lys	p.Q1000K	ENST00000266497		1000	Cag/Aag	21/31	0.606274734528201	7	FACETS	0.84	0.754	0.932	0.14	0.125	0.156	CLONAL	1	TRUE	1	0.606274734528201	7		374	1116	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614558	38614559	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0024422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	288	518	0	ENST00000299084.4:c.325_326dup	p.Arg110LeufsTer12	p.R110Lfs*12	ENST00000299084	NM_152594.2	108	-/GC	3/7	NA	2	FACETS	0.809	0.769	0.85			1	INDETERMINATE	2	TRUE	NA	0.606274734528201	2		518	587	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965958	18965958	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	239	550	0	ENST00000262803.5:c.1451A>G	p.Gln484Arg	p.Q484R	ENST00000262803	NM_002911.3	484	cAa/cGa	11/24	0.436357305845408	4	FACETS	0.797	0.747	0.849	0.797	0.747	0.849	SUBCLONAL	2	TRUE	2	0.606274734528201	4		550	794	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0024744-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	42	409	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.95	0.795	1	0.95	0.795	1	CLONAL	1	TRUE	1	0.222645601442373	2		410	397	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584560	48584560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0024744-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	49	401	0	ENST00000342988.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000342988	NM_005359.5	245	Cag/Tag	6/12	0.222645601442373	1	FACETS	0.943	0.8	1	0.943	0.8	1	CLONAL	1	TRUE	0	0.222645601442373	1		401	415	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024744-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	95	412	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.972	0.87	1	1	0.986	1	CLONAL	2	TRUE	1	0.222645601442373	2		412	439	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150217	108150217	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0024744-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	29	314	0	ENST00000278616.4:c.3285-1G>T		p.X1095_splice	ENST00000278616	NM_000051.3	1095			1	2	FACETS	0.854	0.687	1	0.854	0.687	1	CLONAL	1	TRUE	1	0.222645601442373	2		314	305	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	182	427	0				ENST00000310581	NM_198253.2	-/1132			0.53951316279238	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	4	TRUE	0	0.53951316279238	4		427	255	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0024771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	510	292	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.53951316279238	6	FACETS	0.904	0.873	0.934	1	0.994	1	CLONAL	5	TRUE	2	0.53951316279238	6		292	870	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249230	133249230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754985761	NA	P-0024771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	293	686	0	ENST00000320574.5:c.1669C>T	p.Pro557Ser	p.P557S	ENST00000320574	NM_006231.2	557	Cct/Tct	15/49	0.53951316279238	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.53951316279238	3		686	671	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298175	123298175	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	329	512	0	ENST00000358487.5:c.679G>A	p.Gly227Arg	p.G227R	ENST00000358487	NM_000141.4	227	Gga/Aga	6/18	0.53951316279238	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.53951316279238	3		512	713	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572997	7572997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	255	470	0	ENST00000269305.4:c.1112C>T	p.Ser371Phe	p.S371F	ENST00000269305	NM_001126112.2	371	tCc/tTc	11/11	0.53951316279238	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.53951316279238	3		470	536	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146502	55146502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	193	346	0	ENST00000257290.5:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000257290	NM_006206.4	726	Gaa/Aaa	16/23	0.47497373549652	3	FACETS	0.99	0.926	1	0.99	0.926	1	CLONAL	2	TRUE	1	0.53951316279238	3		346	459	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240692	53240692	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	289	628	1	ENST00000375401.3:c.1388C>T	p.Thr463Ile	p.T463I	ENST00000375401	NM_004187.3	463	aCc/aTc	10/26	0.36281178100705	4	FACETS	0.905	0.853	0.958	0.905	0.853	0.958	CLONAL	2	TRUE	2	0.53951316279238	4		629	911	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	63	427	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.682	0.592	0.778	0.682	0.592	0.778	SUBCLONAL	1	TRUE	1	0.464332517882428	2		427	398	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0024994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	59	292	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.934	0.811	1	0.934	0.811	1	CLONAL	1	TRUE	1	0.464332517882428	2		292	272	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400190	41400190	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	68	368	0	ENST00000373198.4:c.569G>A	p.Arg190Lys	p.R190K	ENST00000373198	NM_133170.3	190	aGa/aAa	5/32	0.257696396345583	2	FACETS	0.469	0.408	0.536	0.235	0.204	0.268	INDETERMINATE	1	TRUE	0	0.464332517882428	2		368	624	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37628840	37628840	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs193920791	NA	P-0024994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	354	278	0	ENST00000249071.6:c.225+1G>A		p.X75_splice	ENST00000249071	NM_002872.4	75			0.464332517882428	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.464332517882428	3		278	841	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974702	21974702	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	104	219	0	ENST00000304494.5:c.125A>T	p.Asn42Ile	p.N42I	ENST00000304494	NM_000077.4	42	aAt/aTt	1/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.464332517882428	2		219	333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0025064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	182	630	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.51368248084499	3	FACETS	0.921	0.85	0.995	0.461	0.425	0.498	CLONAL	1	TRUE	1	0.51368248084499	3		630	967	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0025064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	378	742	1	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	0.51368248084499	3	FACETS	0.934	0.89	0.979	0.934	0.89	0.979	CLONAL	2	TRUE	1	0.51368248084499	3		743	990	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797777	42797777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778206	NA	P-0025064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	476	615	0	ENST00000575354.2:c.3829C>T	p.Arg1277Cys	p.R1277C	ENST00000575354	NM_015125.3	1277	Cgc/Tgc	16/20	0.507462708240459	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	TRUE	0	0.51368248084499	3		615	773	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164586	36164586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253570532	NA	P-0025064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	105	433	0	ENST00000300305.3:c.1289C>T	p.Pro430Leu	p.P430L	ENST00000300305		430	cCg/cTg	8/8	0.51368248084499	2	FACETS	0.925	0.834	1	0.462	0.417	0.51	CLONAL	1	TRUE	0	0.51368248084499	2		433	442	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937519	76937520	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0025064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	143	243	0	ENST00000373344.5:c.3228_3229del	p.Ser1077ArgfsTer3	p.S1077Rfs*3	ENST00000373344	NM_000489.3	1076	tcTTca/tcca	9/35	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.51368248084499	1		243	307	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0025065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	149	497	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	0.871	0.799	0.946	0.871	0.799	0.946	CLONAL	1	TRUE	1	0.578853327945557	2		497	591	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440334	52440334	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0025065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	177	458	0	ENST00000460680.1:c.718A>T	p.Lys240Ter	p.K240*	ENST00000460680	NM_004656.3	240	Aag/Tag	9/17	0.578853327945557	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.578853327945557	1		458	423	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0025093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	102	292	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.732109512645966	2		292	271	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0025093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	161	340	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.901	0.833	0.971	0.901	0.833	0.971	CLONAL	1	TRUE	1	0.732109512645966	2		340	488	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400190	41400190	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	205	368	0	ENST00000373198.4:c.569G>A	p.Arg190Lys	p.R190K	ENST00000373198	NM_133170.3	190	aGa/aAa	5/32	1	2	FACETS	0.917	0.855	0.979	0.917	0.855	0.979	CLONAL	1	TRUE	1	0.732109512645966	2		368	611	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201900	67201900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375294282	NA	P-0025093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	336	487	1	ENST00000312629.5:c.1100C>T	p.Pro367Leu	p.P367L	ENST00000312629	NM_003952.2	367	cCg/cTg	13/15	1	2	FACETS	0.994	0.943	1	0.994	0.943	1	CLONAL	1	TRUE	1	0.732109512645966	2		488	923	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340201	116340201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561295443	NA	P-0025093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	164	226	0	ENST00000397752.3:c.1063G>A	p.Glu355Lys	p.E355K	ENST00000397752	NM_000245.2	355	Gaa/Aaa	2/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.732109512645966	2		226	425	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40461481	40461481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	411	672	0	ENST00000345506.4:c.2201C>T	p.Pro734Leu	p.P734L	ENST00000345506	NM_003152.3	734	cCc/cTc	19/20	1	2	FACETS	0.931	0.887	0.976	0.931	0.887	0.976	CLONAL	1	TRUE	1	0.732109512645966	2		672	1206	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218985	193218985	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	53	260	0	ENST00000367435.3:c.1543T>C	p.Trp515Arg	p.W515R	ENST00000367435	NM_024529.4	515	Tgg/Cgg	16/17	1	2	FACETS	0.922	0.803	1	0.922	0.803	1	CLONAL	1	TRUE	1	0.732109512645966	2		260	157	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850723	63850723	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	159	313	0	ENST00000279873.7:c.1501C>T	p.Gln501Ter	p.Q501*	ENST00000279873	NM_032199.2	501	Cag/Tag	10/10	1	2	FACETS	0.953	0.881	1	0.953	0.881	1	CLONAL	1	TRUE	1	0.732109512645966	2		313	456	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642706	3642706	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	268	478	0	ENST00000294008.3:c.2321C>T	p.Ala774Val	p.A774V	ENST00000294008	NM_032444.2	774	gCc/gTc	11/15	1	2	FACETS	0.945	0.89	1	0.945	0.89	1	CLONAL	1	TRUE	1	0.732109512645966	2		478	775	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143021	47143021	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	138	516	0	ENST00000409792.3:c.4942G>T	p.Val1648Phe	p.V1648F	ENST00000409792	NM_014159.6	1648	Gtt/Ttt	8/21	1	2	FACETS	0.774	0.709	0.841	0.774	0.709	0.841	SUBCLONAL	1	TRUE	1	0.732109512645966	2		516	487	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161984	47161984	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0025093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	140	322	0	ENST00000409792.3:c.4142T>G	p.Leu1381Ter	p.L1381*	ENST00000409792	NM_014159.6	1381	tTa/tGa	3/21	1	2	FACETS	0.968	0.891	1	0.968	0.891	1	CLONAL	1	TRUE	1	0.732109512645966	2		322	395	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047230	180047230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	339	622	3	ENST00000261937.6:c.2485G>A	p.Glu829Lys	p.E829K	ENST00000261937	NM_182925.4	829	Gaa/Aaa	17/30	1	2	FACETS	0.922	0.874	0.971	0.922	0.874	0.971	CLONAL	1	TRUE	1	0.732109512645966	2		625	1004	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374338	81374338	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202185530	NA	P-0025093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	129	339	0	ENST00000222390.5:c.724C>T	p.Arg242Trp	p.R242W	ENST00000222390	NM_000601.4	242	Cgg/Tgg	6/18	1	2	FACETS	0.96	0.881	1	0.96	0.881	1	CLONAL	1	TRUE	1	0.732109512645966	2		339	367	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518120	8518121	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	novel	NA	P-0025093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	182	341	0	ENST00000356435.5:c.1270_1271delinsAA	p.Val424Asn	p.V424N	ENST00000356435		424	GTc/AAc	10/35	1	2	FACETS	0.84	0.779	0.902	0.84	0.779	0.902	CLONAL	1	TRUE	1	0.732109512645966	2		341	592	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593662	55593664	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0025131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	276	465	0	ENST00000288135.5:c.1729_1731del	p.Pro577del	p.P577del	ENST00000288135	NM_000222.2	576	ctTCCt/ctt	11/21	0.718164708031512	3	FACETS	0.893	0.846	0.939			1	CLONAL	2	TRUE	NA	0.718164708031512	3		465	585	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692816	89692817	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554898084	NA	P-0025131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	179	285	0	ENST00000371953.3:c.301dup	p.Ile101AsnfsTer6	p.I101Nfs*6	ENST00000371953	NM_000314.4	100	-/A	5/9	0.697755805018947	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.718164708031512	2		285	238	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248101	59248124	+	inframe_deletion	In_Frame_Del	DEL	CTGCTGGGGCAGGTGGTGCGGCGG	CTGCTGGGGCAGGTGGTGCGGCGG	-	novel	NA	P-0025131-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	41	184	0	ENST00000371222.2:c.619_642del	p.Pro207_Gln214del	p.P207_Q214del	ENST00000371222	NM_002228.3	207	CCGCCGCACCACCTGCCCCAGCAG/-	1/1	1	2	FACETS	0.714	0.604	0.831	0.714	0.604	0.831	SUBCLONAL	1	TRUE	1	0.718164708031512	2		184	160	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0025283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	160	594	1	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.136053634822368	1	FACETS	0.912	0.84	0.986	1	0.991	1	INDETERMINATE	2	TRUE	0	0.258952831291511	1		595	590	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857020	9857020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555481892	NA	P-0025283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	60	249	0	ENST00000330684.3:c.4381G>A	p.Glu1461Lys	p.E1461K	ENST00000330684	NM_001134407.1	1461	Gaa/Aaa	13/13	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.258952831291511	2		249	377	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610473	81610473	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	104	324	0	ENST00000298171.2:c.2071A>G	p.Ile691Val	p.I691V	ENST00000298171	NM_000369.2	691	Atc/Gtc	10/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.258952831291511	2		324	702	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0026571-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	133	684	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.3591011730498	3	FACETS	0.923	0.856	0.991	0.923	0.856	0.991	CLONAL	3	TRUE	0	0.434709241758012	3		684	269	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248980	55248981	+	splice_region_variant,intron_variant	In_Frame_Ins	INS	-	-	TCCAGGAAGCCT	rs397517106	NA	P-0026571-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	214	513	0	ENST00000275493.2:c.2284-5_2290dup		p.A763_Y764insFQEA	ENST00000275493	NM_005228.3	763			0.434709241758012	8	FACETS	0.951	0.894	1	0.793	0.745	0.841	CLONAL	5	TRUE	2	0.434709241758012	8		513	477	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623170	52623170	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026571-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	23	491	0	ENST00000394830.3:c.2881G>C	p.Gly961Arg	p.G961R	ENST00000394830	NM_018313.4	961	Gga/Cga	19/30	0.331283643202795	2	FACETS	0.615	0.483	0.765	0.308	0.241	0.383	SUBCLONAL	1	TRUE	0	0.434709241758012	2		491	172	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7978925	7978925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397514532	NA	P-0026698-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	167	447	3	ENST00000319144.4:c.1642C>T	p.Arg548Trp	p.R548W	ENST00000319144	NM_001139.2	548	Cgg/Tgg	12/15	1	2	FACETS	0.878	0.813	0.945	0.878	0.813	0.945	CLONAL	1	TRUE	1	0.742589341228854	2		450	512	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56857674	56857674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144804729	NA	P-0026698-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	251	567	0	ENST00000308159.5:c.710C>T	p.Pro237Leu	p.P237L	ENST00000308159	NM_014669.4	237	cCg/cTg	8/22	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.742589341228854	2		567	649	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877859	151877860	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0026698-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	281	346	0	ENST00000262189.6:c.7085dup	p.Gly2363ArgfsTer4	p.G2363Rfs*4	ENST00000262189	NM_170606.2	2362	tca/tcCa	36/59	0.73038414364085	3	FACETS	0.863	0.819	0.908	0.863	0.819	0.908	CLONAL	2	TRUE	1	0.742589341228854	3		346	601	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	45	350	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.474049403589151	2	FACETS	0.43	0.361	0.505	0.215	0.18	0.253	SUBCLONAL	1	TRUE	0	0.49500792036324	2		350	423	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147721	61147721	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	19	174	0	ENST00000295025.8:c.1031A>T	p.Glu344Val	p.E344V	ENST00000295025	NM_002908.2	344	gAg/gTg	10/11	0.271863678519387	3	FACETS	0.509	0.388	0.65	0.17	0.129	0.217	INDETERMINATE	1	TRUE	0	0.49500792036324	3		174	188	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0026710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	109	389	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	1	2	FACETS	0.888	0.801	0.979	0.888	0.801	0.979	CLONAL	1	TRUE	1	0.49500792036324	2		389	496	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646198	3646198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774683778	NA	P-0026710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	309	676	1	ENST00000294008.3:c.1880C>T	p.Pro627Leu	p.P627L	ENST00000294008	NM_032444.2	627	cCg/cTg	8/15	0.49500792036324	4	FACETS	0.944	0.891	0.997	0.944	0.891	0.997	CLONAL	2	TRUE	2	0.49500792036324	4		677	989	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371900	55371900	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	98	364	0	ENST00000297316.4:c.590C>T	p.Pro197Leu	p.P197L	ENST00000297316	NM_022454.3	197	cCg/cTg	2/2	0.49500792036324	5	FACETS	1	0.957	1	0.38	0.339	0.423	CLONAL	1	TRUE	2	0.49500792036324	5		364	605	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593405	48593405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519962	NA	P-0027325-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	28	210	0	ENST00000342988.3:c.1156G>A	p.Gly386Ser	p.G386S	ENST00000342988	NM_005359.5	386	Ggt/Agt	10/12	1	2	FACETS	0.808	0.647	0.992	0.808	0.647	0.992	CLONAL	1	TRUE	1	0.21	2		210	330	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057901	27057901	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027325-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	97	522	1	ENST00000324856.7:c.1609C>T	p.Gln537Ter	p.Q537*	ENST00000324856	NM_006015.4	537	Cag/Tag	3/20	1	2	FACETS	0.855	0.765	0.951	1	0.984	1	CLONAL	2	TRUE	1	0.21	2		523	540	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009305	69009305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196832669	NA	P-0027325-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	21	313	0	ENST00000288368.4:c.2422G>A	p.Val808Met	p.V808M	ENST00000288368	NM_024870.2	808	Gtg/Atg	22/40	0.3	3	FACETS	0.538	0.413	0.683	0.269	0.206	0.342	SUBCLONAL	1	TRUE	1	0.21	3		313	411	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740620	145740620	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs386833844	NA	P-0027325-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	124	659	0	ENST00000428558.2:c.1397C>T	p.Pro466Leu	p.P466L	ENST00000428558	NM_004260.3	466	cCg/cTg	8/22	0.3	3	FACETS	0.936	0.848	1	0.936	0.848	1	CLONAL	2	TRUE	1	0.21	3		659	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0027755-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	267	823	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.42543456408913	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	0	0.42543456408913	1		823	959	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033934	49033934	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027755-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	81	393	0	ENST00000267163.4:c.2071G>T	p.Glu691Ter	p.E691*	ENST00000267163	NM_000321.2	691	Gag/Tag	20/27	0.326666679700433	0	FACETS	0.622	0.552	0.695			1	SUBCLONAL	1	FALSE	0	0.42543456408913	0		393	352	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217230	11217230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205165	NA	P-0027755-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	188	566	0	ENST00000361445.4:c.4448G>A	p.Cys1483Tyr	p.C1483Y	ENST00000361445	NM_004958.3	1483	tGc/tAc	30/58	1	2	FACETS	0.978	0.904	1	0.978	0.904	1	CLONAL	1	FALSE	1	0.42543456408913	2		566	904	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982016	70982017	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0027755-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1372	236	915	0	ENST00000276594.2:c.79_80del	p.Ala27ArgfsTer100	p.A27Rfs*100	ENST00000276594	NM_024504.3	27	GCc/c	2/8	NA	2	FACETS	0.69	0.642	0.74			1	INDETERMINATE	1	FALSE	NA	0.42543456408913	2		915	1608	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751109	128751109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs577698378	NA	P-0027755-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	146	637	1	ENST00000377970.2:c.646G>A	p.Asp216Asn	p.D216N	ENST00000377970	NM_002467.4	216	Gac/Aac	2/3	0.42543456408913	4	FACETS	0.751	0.684	0.823	0.25	0.228	0.275	SUBCLONAL	1	FALSE	1	0.42543456408913	4		638	1302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0028499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	302	812	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.59817626362145	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.59817626362145	1		812	661	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910333	29910333	+	start_lost	Translation_Start_Site	SNP	G	G	T	novel	NA	P-0028499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	336	750	0	ENST00000376809.5:c.3G>T	p.Met1?	p.M1?	ENST00000376809	NM_002116.7	1	atG/atT	1/8	0.136614256394837	4	FACETS	0.827	0.783	0.872	0.827	0.783	0.872	INDETERMINATE	2	TRUE	2	0.59817626362145	4		750	1085	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680186	30680186	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	316	729	0	ENST00000376406.3:c.1533G>C	p.Glu511Asp	p.E511D	ENST00000376406	NM_014641.2	511	gaG/gaC	5/15	0.136614256394837	4	FACETS	0.799	0.754	0.844	0.799	0.754	0.844	INDETERMINATE	2	TRUE	2	0.59817626362145	4		729	1057	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263201	115263202	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0028893-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	72	394	0	ENST00000438362.2:c.2148dup	p.Thr717HisfsTer19	p.T717Hfs*19	ENST00000438362	NM_001242891.1	716	-/C	17/20	1	2	FACETS	0.828	0.724	0.939	0.828	0.724	0.939	CLONAL	1	TRUE	1	0.313405162734865	2		394	555	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725054	89725061	+	frameshift_variant	Frame_Shift_Del	DEL	ACTTCACA	ACTTCACA	-	novel	NA	P-0028893-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	14	132	0	ENST00000371953.3:c.1038_1045del	p.Tyr346Ter	p.Y346*	ENST00000371953	NM_000314.4	346	tACTTCACA/t	9/9	0.313405162734865	1	FACETS	0.618	0.45	0.816	0.618	0.45	0.816	SUBCLONAL	1	TRUE	0	0.313405162734865	1		132	122	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039339	49039339	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0028893-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	40	393	1	ENST00000267163.4:c.2326-2A>T		p.X776_splice	ENST00000267163	NM_000321.2	776			0.313405162734865	1	FACETS	0.629	0.524	0.746	0.629	0.524	0.746	SUBCLONAL	1	TRUE	0	0.313405162734865	1		394	342	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0028893-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	73	569	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	1	2	FACETS	0.76	0.665	0.862	0.76	0.665	0.862	SUBCLONAL	1	TRUE	1	0.313405162734865	2		569	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0028893-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	72	480	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	1	2	FACETS	0.772	0.675	0.877	0.772	0.675	0.877	SUBCLONAL	1	TRUE	1	0.313405162734865	2		480	595	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098959	178098959	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028893-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	30	194	0	ENST00000397062.3:c.86A>C	p.Asp29Ala	p.D29A	ENST00000397062	NM_006164.4	29	gAt/gCt	2/5	0.258143504069566	1	FACETS	0.676	0.547	0.819	0.676	0.547	0.819	SUBCLONAL	1	TRUE	0	0.313405162734865	1		194	239	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478020	138478020	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0028893-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	66	224	0	ENST00000289153.2:c.166A>T	p.Lys56Ter	p.K56*	ENST00000289153	NM_006219.2	56	Aag/Tag	1/22	0.17299157287358	3	FACETS	0.978	0.86	1			1	INDETERMINATE	2	TRUE	NA	0.313405162734865	3		224	249	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972063	55972063	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028893-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	56	298	0	ENST00000263923.4:c.1581G>T	p.Leu527Phe	p.L527F	ENST00000263923	NM_002253.2	527	ttG/ttT	12/30	0.313405162734865	1	FACETS	0.819	0.705	0.943	0.819	0.705	0.943	CLONAL	1	TRUE	0	0.313405162734865	1		298	368	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	32	361	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.933	0.757	1	0.933	0.757	1	CLONAL	1	TRUE	1	0.164128564034065	2		361	418	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622162	1622162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	90	952	0	ENST00000344749.5:c.713C>T	p.Pro238Leu	p.P238L	ENST00000344749	NM_001136139.2	238	cCc/cTc	10/19	0.164128564034065	1	FACETS	0.922	0.816	1	0.922	0.816	1	CLONAL	1	TRUE	0	0.164128564034065	1		952	1092	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372040	45372040	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	30	360	0	ENST00000262160.6:c.1129C>T	p.Pro377Ser	p.P377S	ENST00000262160	NM_005901.5	377	Cca/Tca	9/11	1	2	FACETS	0.707	0.569	0.865	0.707	0.569	0.865	SUBCLONAL	1	TRUE	1	0.164128564034065	2		360	517	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686267	117686267	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	38	305	0	ENST00000368508.3:c.3074G>A	p.Gly1025Glu	p.G1025E	ENST00000368508	NM_002944.2	1025	gGa/gAa	20/43	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.164128564034065	2		305	400	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58701074	58701074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	52	572	0	ENST00000305921.3:c.665C>T	p.Pro222Leu	p.P222L	ENST00000305921	NM_003620.3	222	cCc/cTc	2/6	1	2	FACETS	0.811	0.689	0.946	0.811	0.689	0.946	CLONAL	1	TRUE	1	0.164128564034065	2		572	781	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136004	64136004	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	85	985	0	ENST00000334205.4:c.1265T>G	p.Phe422Cys	p.F422C	ENST00000334205	NM_003942.2	422	tTt/tGt	11/17	1	2	FACETS	0.886	0.781	1	0.886	0.781	1	CLONAL	1	TRUE	1	0.164128564034065	2		985	1169	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306761	41306761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	45	523	0	ENST00000373198.4:c.898G>T	p.Val300Leu	p.V300L	ENST00000373198	NM_133170.3	300	Gtg/Ttg	7/32	1	2	FACETS	0.868	0.728	1	0.868	0.728	1	CLONAL	1	TRUE	1	0.164128564034065	2		523	632	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445230	49445230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201896284	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	89	1006	0	ENST00000301067.7:c.2236C>T	p.Arg746Trp	p.R746W	ENST00000301067	NM_003482.3	746	Cgg/Tgg	10/54	1	2	FACETS	0.822	0.726	0.926	0.822	0.726	0.926	CLONAL	1	TRUE	1	0.164128564034065	2		1006	1319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579312	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	80	597	1	ENST00000269305.4:c.375_375+1delinsAA		p.X125_splice	ENST00000269305	NM_001126112.2	125		4/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.164128564034065	2		598	714	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866441	42866441	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770444484	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1227	108	901	0	ENST00000398585.3:c.191C>T	p.Pro64Leu	p.P64L	ENST00000398585	NM_001135099.1	64	cCc/cTc	3/14	1	2	FACETS	0.986	0.882	1	0.986	0.882	1	CLONAL	1	TRUE	1	0.164128564034065	2		901	1335	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940093	31940093	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	87	801	0	ENST00000375333.2:c.235G>A	p.Glu79Lys	p.E79K	ENST00000375333	NM_032454.1	79	Gag/Aag	2/8	1	2	FACETS	0.894	0.789	1	0.894	0.789	1	CLONAL	1	TRUE	1	0.164128564034065	2		801	1186	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263863	16263864	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	59	695	1	ENST00000375759.3:c.10232_10233delinsAA	p.Arg3411Lys	p.R3411K	ENST00000375759	NM_015001.2	3411	aGG/aAA	12/15	1	2	FACETS	0.771	0.662	0.892	0.771	0.662	0.892	SUBCLONAL	1	TRUE	1	0.164128564034065	2		696	932	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532596	46532596	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	29	260	0	ENST00000262741.5:c.482C>T	p.Ser161Phe	p.S161F	ENST00000262741	NM_003629.3	161	tCc/tTc	4/10	1	2	FACETS	0.789	0.632	0.967	0.789	0.632	0.967	CLONAL	1	TRUE	1	0.164128564034065	2		260	448	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551637	150551637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771094920	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	59	587	0	ENST00000369026.2:c.370G>A	p.Glu124Lys	p.E124K	ENST00000369026	NM_021960.4	124	Gag/Aag	1/3	1	2	FACETS	0.907	0.778	1	0.907	0.778	1	CLONAL	1	TRUE	1	0.164128564034065	2		587	793	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606815	43606816	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	83	928	2	ENST00000355710.3:c.1424_1425delinsAA	p.Arg475Gln	p.R475Q	ENST00000355710	NM_020975.4	475	cGG/cAA	7/20	1	2	FACETS	0.889	0.782	1	0.889	0.782	1	CLONAL	1	TRUE	1	0.164128564034065	2		930	1138	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615126	43615126	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	104	930	0	ENST00000355710.3:c.2540C>T	p.Thr847Ile	p.T847I	ENST00000355710	NM_020975.4	847	aCc/aTc	14/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.164128564034065	2		930	1161	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342599	118342599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	21	187	0	ENST00000534358.1:c.725C>T	p.Ser242Leu	p.S242L	ENST00000534358	NM_005933.3	242	tCa/tTa	3/36	1	2	FACETS	0.867	0.668	1	0.867	0.668	1	CLONAL	1	TRUE	1	0.164128564034065	2		187	295	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155963	119155963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	77	658	0	ENST00000264033.4:c.1628C>T	p.Pro543Leu	p.P543L	ENST00000264033	NM_005188.3	543	cCa/cTa	11/16	1	2	FACETS	0.964	0.845	1	0.964	0.845	1	CLONAL	1	TRUE	1	0.164128564034065	2		658	973	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748789	43748790	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	89	695	0	ENST00000382044.4:c.2016_2017delinsTT	p.Pro673Ser	p.P673S	ENST00000382044	NM_001141980.1	672	atCCct/atTTct	12/28	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.164128564034065	2		695	1009	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934839	9934839	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	36	410	0	ENST00000330684.3:c.1451A>T	p.Lys484Met	p.K484M	ENST00000330684	NM_001134407.1	484	aAg/aTg	6/13	1	2	FACETS	0.774	0.635	0.93	0.774	0.635	0.93	CLONAL	1	TRUE	1	0.164128564034065	2		410	567	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649442	23649442	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	35	218	0	ENST00000261584.4:c.57G>C	p.Glu19Asp	p.E19D	ENST00000261584	NM_024675.3	19	gaG/gaC	2/13	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.164128564034065	2		218	388	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132631	67132631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	43	462	0	ENST00000412916.2:c.514C>T	p.Pro172Ser	p.P172S	ENST00000412916		172	Cct/Tct	6/6	1	2	FACETS	0.768	0.641	0.91	0.768	0.641	0.91	CLONAL	1	TRUE	1	0.164128564034065	2		462	682	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687598	29687598	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	55	484	0	ENST00000356175.3:c.8191G>A	p.Glu2731Lys	p.E2731K	ENST00000356175	NM_000267.3	2731	Gaa/Aaa	56/57	1	2	FACETS	0.969	0.827	1	0.969	0.827	1	CLONAL	1	TRUE	1	0.164128564034065	2		484	692	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245092	41245092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	77	638	0	ENST00000357654.3:c.2456C>T	p.Ser819Phe	p.S819F	ENST00000357654	NM_007294.3	819	tCc/tTc	10/23	1	2	FACETS	0.945	0.827	1	0.945	0.827	1	CLONAL	1	TRUE	1	0.164128564034065	2		638	993	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584495	39584496	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	33	264	0	ENST00000262039.4:c.1160_1161delinsTT	p.Ala387Val	p.A387V	ENST00000262039	NM_002647.2	387	gCC/gTT	10/25	1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	1	0.164128564034065	2		264	385	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919719	96919719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	52	560	0	ENST00000258439.3:c.544G>A	p.Gly182Arg	p.G182R	ENST00000258439	NM_001193304.2	182	Gga/Aga	4/4	1	2	FACETS	0.891	0.757	1	0.891	0.757	1	CLONAL	1	TRUE	1	0.164128564034065	2		560	711	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164277	47164277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372521251	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	28	276	0	ENST00000409792.3:c.1849C>T	p.Pro617Ser	p.P617S	ENST00000409792	NM_014159.6	617	Cca/Tca	3/21	0.164128564034065	1	FACETS	0.785	0.627	0.965	0.785	0.627	0.965	CLONAL	1	TRUE	0	0.164128564034065	1		276	399	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445016	89445016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	41	354	0	ENST00000336596.2:c.1336G>A	p.Asp446Asn	p.D446N	ENST00000336596	NM_005233.5	446	Gat/Aat	6/17	0.164128564034065	1	FACETS	0.817	0.68	0.971	0.817	0.68	0.971	CLONAL	1	TRUE	0	0.164128564034065	1		354	561	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961237	1961237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	52	435	0	ENST00000382891.5:c.3025G>A	p.Asp1009Asn	p.D1009N	ENST00000382891	NM_133335.3	1009	Gat/Aat	17/22	1	2	FACETS	0.963	0.819	1	0.963	0.819	1	CLONAL	1	TRUE	1	0.164128564034065	2		435	658	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638204	176638204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	65	583	1	ENST00000439151.2:c.2804C>T	p.Ser935Phe	p.S935F	ENST00000439151	NM_022455.4	935	tCt/tTt	5/23	1	2	FACETS	0.909	0.787	1	0.909	0.787	1	CLONAL	1	TRUE	1	0.164128564034065	2		584	871	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066608	94066608	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	43	475	0	ENST00000369303.4:c.1151G>C	p.Ser384Thr	p.S384T	ENST00000369303	NM_004440.3	384	aGt/aCt	5/17	1	2	FACETS	0.821	0.686	0.972	0.821	0.686	0.972	CLONAL	1	TRUE	1	0.164128564034065	2		475	638	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023060	150023060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	65	599	0	ENST00000253339.5:c.203C>T	p.Pro68Leu	p.P68L	ENST00000253339		68	cCa/cTa	1/7	1	2	FACETS	0.977	0.845	1	0.977	0.845	1	CLONAL	1	TRUE	1	0.164128564034065	2		599	811	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515111	148515111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	58	472	0	ENST00000320356.2:c.1098C>A	p.Asn366Lys	p.N366K	ENST00000320356	NM_004456.4	366	aaC/aaA	10/20	0.164128564034065	1	FACETS	0.947	0.813	1	0.947	0.813	1	CLONAL	1	TRUE	0	0.164128564034065	1		472	685	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912066	56912066	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	72	560	0	ENST00000519728.1:c.1294C>T	p.Leu432Phe	p.L432F	ENST00000519728	NM_002350.3	432	Ctc/Ttc	12/13	1	2	FACETS	0.962	0.839	1	0.962	0.839	1	CLONAL	1	TRUE	1	0.164128564034065	2		560	912	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220410	98220410	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	65	615	0	ENST00000331920.6:c.3053G>A	p.Trp1018Ter	p.W1018*	ENST00000331920	NM_000264.3	1018	tGg/tAg	18/24	0.164128564034065	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.164128564034065	1		615	669	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874407	76874407	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	50	182	0	ENST00000373344.5:c.5315C>T	p.Ser1772Phe	p.S1772F	ENST00000373344	NM_000489.3	1772	tCc/tTc	21/35	1	1	FACETS	1	0.896	1	1	0.976	1	CLONAL	2	TRUE	0	0.164128564034065	1		182	264	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751513	57751513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	42	347	0	ENST00000274289.3:c.1478C>T	p.Pro493Leu	p.P493L	ENST00000274289	NM_006622.3	493	cCc/cTc	11/14	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.164128564034065	2		347	469	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517996	176517996	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1263120442	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	81	749	0	ENST00000292408.4:c.494G>A	p.Gly165Glu	p.G165E	ENST00000292408	NM_213647.1	165	gGg/gAg	5/18	1	2	FACETS	0.968	0.85	1	0.968	0.85	1	CLONAL	1	TRUE	1	0.164128564034065	2		749	1020	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043963	180043963	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	73	774	0	ENST00000261937.6:c.3033G>C	p.Met1011Ile	p.M1011I	ENST00000261937	NM_182925.4	1011	atG/atC	22/30	1	2	FACETS	0.959	0.836	1	0.959	0.836	1	CLONAL	1	TRUE	1	0.164128564034065	2		774	928	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0033566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	346	743	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.415143383138051	2	FACETS	0.928	0.882	0.974	0.928	0.882	0.974	CLONAL	2	TRUE	0	0.429240228502315	2		743	869	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0033566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	122	429	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.340514377080248	3	FACETS	1	0.984	1	0.715	0.65	0.782	CLONAL	1	TRUE	1	0.429240228502315	3		429	483	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0033566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	174	326	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.429240228502315	2	FACETS	0.921	0.857	0.986	0.921	0.857	0.986	CLONAL	2	TRUE	0	0.429240228502315	2		326	440	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933406	100933406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150584881	NA	P-0033566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	123	353	0	ENST00000325455.5:c.1984G>A	p.Val662Ile	p.V662I	ENST00000325455	NM_001202474.3	662	Gtt/Att	4/8	0.41088936141066	3	FACETS	1	0.957	1	0.547	0.496	0.601	CLONAL	1	TRUE	1	0.429240228502315	3		353	636	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218623	98218623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778629	NA	P-0033566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	92	464	0	ENST00000331920.6:c.3241G>A	p.Val1081Met	p.V1081M	ENST00000331920	NM_000264.3	1081	Gtg/Atg	19/24	1	2	FACETS	0.899	0.802	1	0.899	0.802	1	CLONAL	1	TRUE	1	0.429240228502315	2		464	477	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194905	29194905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375453930	NA	P-0033566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	193	769	0	ENST00000240100.2:c.823C>T	p.Arg275Cys	p.R275C	ENST00000240100	NM_001394.6	275	Cgc/Tgc	4/4	0.429990585706813	3	FACETS	1	0.934	1	0.506	0.467	0.546	CLONAL	1	TRUE	1	0.429240228502315	3		769	1080	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39709868	39709870	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs748165145	NA	P-0033566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	40	166	1	ENST00000361337.2:c.504_506del	p.Glu169del	p.E169del	ENST00000361337	NM_003286.2	165	ctAGAa/cta	7/21	0.429990585706813	5	FACETS	0.861	0.717	1	0.287	0.239	0.34	CLONAL	1	TRUE	2	0.429240228502315	5		167	356	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779184	3779184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	119	538	0	ENST00000262367.5:c.5864C>T	p.Ala1955Val	p.A1955V	ENST00000262367	NM_004380.2	1955	gCg/gTg	31/31	0.41088936141066	3	FACETS	0.831	0.75	0.917	0.416	0.375	0.459	CLONAL	1	TRUE	1	0.429240228502315	3		538	810	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094272	193094272	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs121434265	NA	P-0033566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	110	386	0	ENST00000367435.3:c.162C>G	p.Tyr54Ter	p.Y54*	ENST00000367435	NM_024529.4	54	taC/taG	2/17	0.340514377080248	3	FACETS	1	0.945	1	0.537	0.483	0.593	CLONAL	1	TRUE	1	0.429240228502315	3		386	580	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411510	63411510	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	470	775	1	ENST00000330258.3:c.1657del	p.Ala553GlnfsTer9	p.A553Qfs*9	ENST00000330258	NM_152424.3	553	Gca/ca	2/2	0.385713979042623	4	FACETS	0.891	0.853	0.929	0.891	0.853	0.929	CLONAL	3	TRUE	1	0.429240228502315	4		776	1171	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872097	76872097	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0033566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	83	360	0	ENST00000373344.5:c.5550C>G	p.Tyr1850Ter	p.Y1850*	ENST00000373344	NM_000489.3	1850	taC/taG	22/35	0.385713979042623	4	FACETS	0.831	0.734	0.936	0.277	0.244	0.312	CLONAL	1	TRUE	1	0.429240228502315	4		360	665	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78831644	78831644	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	170	634	0	ENST00000306801.3:c.1453C>T	p.Arg485Ter	p.R485*	ENST00000306801	NM_020761.2	485	Cga/Tga	13/34	0.41088936141066	3	FACETS	0.951	0.874	1	0.475	0.437	0.516	CLONAL	1	TRUE	1	0.429240228502315	3		634	1012	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354985	70354985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs968428355	NA	P-0033566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	190	655	1	ENST00000374080.3:c.4907G>A	p.Arg1636His	p.R1636H	ENST00000374080		1636	cGc/cAc	36/45	0.385713979042623	4	FACETS	1	0.964	1	0.358	0.33	0.387	CLONAL	1	TRUE	1	0.429240228502315	4		656	1178	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0034062-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	289	593	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.343912823889526	2	FACETS	0.963	0.908	1	0.963	0.908	1	CLONAL	2	TRUE	0	0.343912823889526	2		593	873	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0034062-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	806	494	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.343912823889526	8	FACETS	1	0.992	1	1	0.992	1	CLONAL	6	TRUE	2	0.343912823889526	8		494	1498	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0034062-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	152	689	0	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.343912823889526	2		689	852	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552152	29552152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199474738	NA	P-0034062-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	142	277	0	ENST00000356175.3:c.1885G>A	p.Gly629Arg	p.G629R	ENST00000356175	NM_000267.3	629	Ggg/Agg	17/57	0.343912823889526	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.343912823889526	2		277	385	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589591	67589592	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATA	novel	NA	P-0034062-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	236	252	0	ENST00000274335.5:c.1356_1358dup	p.Asn453dup	p.N453dup	ENST00000274335		453	tat/tATAat	10/15	0.343912823889526	7	FACETS	0.93	0.873	0.989			1	CLONAL	4	TRUE	NA	0.343912823889526	7		252	686	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845699	68845700	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034155-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	99	519	0	ENST00000261769.5:c.946dup	p.Met316AsnfsTer5	p.M316Nfs*5	ENST00000261769	NM_004360.3	315	-/A	7/16	0.255319058271061	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.255319058271061	1		519	511	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758774	41758774	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs758985963	NA	P-0034155-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	93	728	0	ENST00000301178.4:c.1828C>T	p.Arg610Ter	p.R610*	ENST00000301178	NM_021913.4	610	Cga/Tga	16/20	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.255319058271061	2		728	704	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112505	115112506	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0034155-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	81	635	0	ENST00000257566.3:c.1234dup	p.Val412GlyfsTer9	p.V412Gfs*9	ENST00000257566	NM_016569.3	412	gtc/gGtc	7/8	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.255319058271061	2		635	617	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579557	7579558	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CAAATCA	novel	NA	P-0034155-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	90	689	0	ENST00000269305.4:c.123_129dup	p.Met44Ter	p.M44*	ENST00000269305	NM_001126112.2	43	-/TGATTTG	4/11	0.255319058271061	1	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	0	0.255319058271061	1		689	610	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011106	12011107	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	CT	novel	NA	P-0034155-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	22	301	0	ENST00000353533.5:c.514-1_514delinsCT		p.X172_splice	ENST00000353533	NM_003010.3	172		5/11	0.255319058271061	1	FACETS	0.759	0.592	0.952	0.759	0.592	0.952	CLONAL	1	TRUE	0	0.255319058271061	1		301	198	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194839	29194847	+	frameshift_variant	Frame_Shift_Del	DEL	TCATCAGGT	TCATCAGGT	A	novel	NA	P-0034155-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	99	849	0	ENST00000240100.2:c.881_889delinsT	p.Tyr294PhefsTer15	p.Y294Ffs*15	ENST00000240100	NM_001394.6	294	tACCTGATGAtg/tTtg	4/4	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.255319058271061	2		849	742	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0034163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	95	363	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.205078993524751	4	FACETS	0.988	0.883	1	0.988	0.883	1	CLONAL	2	TRUE	2	0.236325574416941	4		363	503	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221320	1221320	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587776656	NA	P-0034163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	250	816	0	ENST00000326873.7:c.843del	p.Leu282SerfsTer5	p.L282Sfs*5	ENST00000326873	NM_000455.4	281	ccG/cc	6/10	0.236325574416941	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.236325574416941	2		816	1016	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390995	89390995	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	116	483	0	ENST00000336596.2:c.1061G>T	p.Arg354Leu	p.R354L	ENST00000336596	NM_005233.5	354	cGg/cTg	5/17	0.156511648636326	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	2	0.236325574416941	4		483	529	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134512	30134512	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	86	302	0	ENST00000263025.4:c.19C>A	p.Gln7Lys	p.Q7K	ENST00000263025	NM_002746.2	7	Cag/Aag	1/9	0.205078993524751	4	FACETS	1	0.89	1	1	0.89	1	CLONAL	2	TRUE	2	0.236325574416941	4		302	449	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610358	10610358	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	268	1059	2	ENST00000171111.5:c.352C>T	p.Gln118Ter	p.Q118*	ENST00000171111	NM_203500.1	118	Cag/Tag	2/6	0.236325574416941	2	FACETS	0.969	0.908	1	0.969	0.908	1	CLONAL	2	TRUE	0	0.236325574416941	2		1061	1170	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103792	47103792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766552660	NA	P-0034163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	56	489	0	ENST00000409792.3:c.6154C>T	p.Pro2052Ser	p.P2052S	ENST00000409792	NM_014159.6	2052	Cct/Tct	14/21	0.156511648636326	4	FACETS	0.796	0.681	0.923	0.398	0.34	0.462	CLONAL	1	TRUE	2	0.236325574416941	4		489	736	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0035237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	18	359	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.287388557548109	6	FACETS	0.599	0.452	0.773	0.1	0.075	0.129	INDETERMINATE	1	TRUE	0	0.485081074645365	6		359	244	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7120734	7120734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	123	551	0	ENST00000302850.5:c.3556G>A	p.Glu1186Lys	p.E1186K	ENST00000302850	NM_000208.2	1186	Gaa/Aaa	20/22	0.377093849605347	2	FACETS	1	0.985	1	0.708	0.648	0.77	CLONAL	1	TRUE	0	0.485081074645365	2		551	358	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874151	155874151	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	32	402	0	ENST00000368323.3:c.380C>G	p.Thr127Arg	p.T127R	ENST00000368323	NM_006912.5	127	aCa/aGa	5/6	0.327467796142342	6	FACETS	0.412	0.333	0.501	0.103	0.083	0.126	SUBCLONAL	1	TRUE	2	0.485081074645365	6		402	631	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579564	7579565	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0035237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	153	486	0	ENST00000269305.4:c.122_123del	p.Asp41GlyfsTer10	p.D41Gfs*10	ENST00000269305	NM_001126112.2	41	gAT/g	4/11	0.39244896588978	3	FACETS	1	0.962	1	0.706	0.655	0.758	CLONAL	2	TRUE	0	0.485081074645365	3		486	370	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905321	50905321	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	56	873	0	ENST00000440232.2:c.529C>G	p.Arg177Gly	p.R177G	ENST00000440232	NM_002691.3	177	Cgc/Ggc	5/27	0.138129449151306	3	FACETS	0.519	0.444	0.6			1	INDETERMINATE	1	TRUE	NA	0.485081074645365	3		873	553	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71064711	71064711	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	19	230	2	ENST00000318789.4:c.963A>T	p.Gln321His	p.Q321H	ENST00000318789	NM_032682.5	321	caA/caT	12/21	0.39244896588978	3	FACETS	0.431	0.328	0.551	0.144	0.109	0.184	SUBCLONAL	1	TRUE	0	0.485081074645365	3		232	226	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798562	32798562	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0035237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	35	415	0	ENST00000374899.4:c.1294del	p.Asp432IlefsTer37	p.D432Ifs*37	ENST00000374899	NM_018833.2	432	Gat/at	8/12	0.485081074645365	4	FACETS	0.446	0.365	0.538	0.223	0.182	0.269	SUBCLONAL	1	TRUE	2	0.485081074645365	4		415	480	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426686	47426686	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	34	547	1	ENST00000377045.4:c.931C>T	p.Gln311Ter	p.Q311*	ENST00000377045	NM_001654.4	311	Cag/Tag	10/16	0.485081074645365	1	FACETS	0.373	0.305	0.447	0.373	0.305	0.447	SUBCLONAL	1	TRUE	0	0.485081074645365	1		548	285	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0036397-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	1950	494	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.223070354302971	21	FACETS	0.978	0.963	0.993			1	CLONAL	20	TRUE	NA	0.223070354302971	21		494	2788	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944686	32944686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202484	NA	P-0036397-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	28	317	0	ENST00000380152.3:c.8479C>T	p.Pro2827Ser	p.P2827S	ENST00000380152		2827	Cct/Tct	19/27	0.223070354302971	1	FACETS	0.422	0.337	0.521	0.422	0.337	0.521	SUBCLONAL	1	TRUE	0	0.223070354302971	1		317	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577585	7577586	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0036397-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	154	538	1	ENST00000269305.4:c.695_696delinsAT	p.Ile232Asn	p.I232N	ENST00000269305	NM_001126112.2	232	aTC/aAT	7/11	1	2	FACETS	0.828	0.758	0.901	1	0.99	1	CLONAL	2	TRUE	1	0.223070354302971	2		539	834	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	131	610	3	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.944	0.861	1	0.944	0.861	1	CLONAL	1	TRUE	1	0.51	2		613	544	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	10	150	0	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	0.3	2	FACETS	0.306	0.208	0.428	0.153	0.104	0.214	INDETERMINATE	1	TRUE	0	0.51	2		150	128	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	160	486	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.889	0.817	0.963	0.889	0.817	0.963	CLONAL	1	TRUE	1	0.51	2		489	706	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	51	483	2	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.309	0.262	0.36	0.309	0.262	0.36	SUBCLONAL	1	TRUE	1	0.51	2		485	648	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	232	778	1	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	1	2	FACETS	0.97	0.905	1	0.97	0.905	1	CLONAL	1	TRUE	1	0.51	2		779	938	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	140	630	3	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.51	2		633	524	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	129	368	0	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	0.984	0.897	1	0.984	0.897	1	CLONAL	1	TRUE	1	0.51	2		368	514	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059207	27059207	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	54	463	0	ENST00000324856.7:c.1848del	p.Ser617GlnfsTer2	p.S617Qfs*2	ENST00000324856	NM_006015.4	615	gCc/gc	4/20	1	2	FACETS	0.32	0.273	0.372	0.32	0.273	0.372	SUBCLONAL	1	TRUE	1	0.51	2		463	662	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428542	78428543	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	121	437	0	ENST00000370768.2:c.1256dup	p.Asn419LysfsTer5	p.N419Kfs*5	ENST00000370768	NM_003902.3	419	aat/aaAt	14/20	1	2	FACETS	0.79	0.715	0.867	0.79	0.715	0.867	SUBCLONAL	1	TRUE	1	0.51	2		437	601	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468219	120468219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395144495	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	93	669	0	ENST00000256646.2:c.4220C>T	p.Ser1407Leu	p.S1407L	ENST00000256646	NM_024408.3	1407	tCg/tTg	25/34	1	2	FACETS	0.5	0.445	0.56	0.5	0.445	0.56	SUBCLONAL	1	TRUE	1	0.51	2		669	729	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443943	18443943	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1454100925	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	66	238	0	ENST00000266497.5:c.916T>C	p.Cys306Arg	p.C306R	ENST00000266497		306	Tgt/Cgt	3/31	0.0883842408271464	0	FACETS	0.437	0.383	0.495			1	INDETERMINATE	1	TRUE	0	0.51	0		238	290	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424178	49424178	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs886040960	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	136	386	2	ENST00000301067.7:c.13884del	p.Thr4629ProfsTer11	p.T4629Pfs*11	ENST00000301067	NM_003482.3	4628	ccC/cc	42/54	0.140862576394589	4	FACETS	0.763	0.697	0.831	0.763	0.697	0.831	INDETERMINATE	2	TRUE	2	0.51	4		388	528	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434246	49434247	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	268	853	0	ENST00000301067.7:c.7306dup	p.Cys2436LeufsTer13	p.C2436Lfs*13	ENST00000301067	NM_003482.3	2436	tgc/tTgc	31/54	0.140862576394589	4	FACETS	1	0.992	1	0.683	0.64	0.728	INDETERMINATE	1	TRUE	2	0.51	4		853	1161	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134987	41134987	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	28	217	1	ENST00000379561.5:c.641G>A	p.Arg214His	p.R214H	ENST00000379561	NM_002015.3	214	cGt/cAt	2/3	1	2	FACETS	0.29	0.231	0.356	0.29	0.231	0.356	SUBCLONAL	1	TRUE	1	0.51	2		218	379	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43699735	43699735	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137879443	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	137	477	0	ENST00000382044.4:c.5780C>T	p.Thr1927Met	p.T1927M	ENST00000382044	NM_001141980.1	1927	aCg/aTg	28/28	1	2	FACETS	0.931	0.851	1	0.931	0.851	1	CLONAL	1	TRUE	1	0.51	2		477	577	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708473	43708473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	197	606	1	ENST00000382044.4:c.4823G>A	p.Gly1608Asp	p.G1608D	ENST00000382044	NM_001141980.1	1608	gGc/gAc	22/28	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.51	2		607	720	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472603	88472603	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	110	454	0	ENST00000360948.2:c.1952T>G	p.Leu651Arg	p.L651R	ENST00000360948	NM_001012338.2	651	cTg/cGg	16/19	1	2	FACETS	0.994	0.899	1	0.994	0.899	1	CLONAL	1	TRUE	1	0.51	2		454	434	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	140	510	2	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.893	0.816	0.973	0.893	0.816	0.973	CLONAL	1	TRUE	1	0.51	2		512	615	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346637	89346637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755913170	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	109	502	1	ENST00000301030.4:c.6313G>A	p.Gly2105Ser	p.G2105S	ENST00000301030	NM_001256183.1	2105	Ggc/Agc	9/13	1	2	FACETS	0.894	0.807	0.985	0.894	0.807	0.985	CLONAL	1	TRUE	1	0.51	2		503	478	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881332	37881332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519738	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	200	703	1	ENST00000269571.5:c.2524G>A	p.Val842Ile	p.V842I	ENST00000269571		842	Gta/Ata	21/27	1	2	FACETS	0.918	0.852	0.987	0.918	0.852	0.987	CLONAL	1	TRUE	1	0.51	2		704	854	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533066	63533066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776445861	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	149	634	1	ENST00000307078.5:c.1828C>T	p.Arg610Trp	p.R610W	ENST00000307078	NM_004655.3	610	Cgg/Tgg	7/11	1	2	FACETS	0.979	0.898	1	0.979	0.898	1	CLONAL	1	TRUE	1	0.51	2		635	597	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144049	11144051	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	191	657	0	ENST00000358026.2:c.3634_3636del	p.Glu1212del	p.E1212del	ENST00000358026	NM_001128849.1	1210	gtGGAg/gtg	26/36	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.51	2		657	735	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285008	15285008	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	79	648	0	ENST00000263388.2:c.4607G>A	p.Ser1536Asn	p.S1536N	ENST00000263388	NM_000435.2	1536	aGc/aAc	25/33	1	2	FACETS	0.472	0.415	0.533	0.472	0.415	0.533	SUBCLONAL	1	TRUE	1	0.51	2		648	657	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795609	42795609	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	186	710	2	ENST00000575354.2:c.2694del	p.Ala900ProfsTer24	p.A900Pfs*24	ENST00000575354	NM_015125.3	897	Ccc/cc	10/20	1	2	FACETS	0.946	0.876	1	0.946	0.876	1	CLONAL	1	TRUE	1	0.51	2		712	771	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909698	50909698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	79	741	0	ENST00000440232.2:c.1418C>T	p.Thr473Met	p.T473M	ENST00000440232	NM_002691.3	473	aCg/aTg	12/27	1	2	FACETS	0.457	0.402	0.516	0.457	0.402	0.516	SUBCLONAL	1	TRUE	1	0.51	2		741	678	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634719	158634719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755732603	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	134	375	0	ENST00000263640.3:c.467G>A	p.Arg156His	p.R156H	ENST00000263640	NM_001105.4	156	cGc/cAc	5/11	1	2	FACETS	0.991	0.906	1	0.991	0.906	1	CLONAL	1	TRUE	1	0.51	2		375	530	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368388	225368388	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1366667901	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	111	249	1	ENST00000264414.4:c.1358del	p.Asn453ThrfsTer2	p.N453Tfs*2	ENST00000264414	NM_003590.4	453	aAc/ac	9/16	1	2	FACETS	0.963	0.871	1	0.963	0.871	1	CLONAL	1	TRUE	1	0.51	2		250	452	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164486	36164486	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	65	453	1	ENST00000300305.3:c.1389del	p.Thr464ProfsTer130	p.T464Pfs*130	ENST00000300305		463	ccC/cc	8/8	1	2	FACETS	0.45	0.39	0.514	0.45	0.39	0.514	SUBCLONAL	1	TRUE	1	0.51	2		454	567	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37055922	37055922	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs267607784	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	72	236	0	ENST00000231790.2:c.678-1G>A		p.X226_splice	ENST00000231790	NM_000249.3	226			1	2	FACETS	0.994	0.878	1	0.994	0.878	1	CLONAL	1	TRUE	1	0.51	2		236	284	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286237	66286238	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	32	320	0	ENST00000273854.3:c.1448dup	p.Asn483LysfsTer21	p.N483Kfs*21	ENST00000273854	NM_004439.5	483	aac/aaAc	6/18	1	2	FACETS	0.296	0.24	0.359	0.296	0.24	0.359	SUBCLONAL	1	TRUE	1	0.51	2		320	424	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	112	428	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.75	0.676	0.827	0.75	0.676	0.827	SUBCLONAL	1	TRUE	1	0.51	2		428	586	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131978039	131978039	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	107	330	0	ENST00000265335.6:c.3922G>T	p.Gly1308Ter	p.G1308*	ENST00000265335		1308	Gga/Tga	25/25	1	2	FACETS	0.912	0.823	1	0.912	0.823	1	CLONAL	1	TRUE	1	0.51	2		330	460	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710638	117710638	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs991227380	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	77	319	0	ENST00000368508.3:c.1634T>C	p.Leu545Ser	p.L545S	ENST00000368508	NM_002944.2	545	tTg/tCg	12/43	0.140862576394589	3	FACETS	1	0.901	1	0.511	0.451	0.574	INDETERMINATE	1	TRUE	1	0.51	3		319	371	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528372	157528372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	197	661	0	ENST00000346085.5:c.6097G>A	p.Gly2033Arg	p.G2033R	ENST00000346085	NM_020732.3	2033	Ggg/Agg	20/20	0.140862576394589	3	FACETS	1	0.983	1	0.596	0.552	0.64	INDETERMINATE	1	TRUE	1	0.51	3		661	814	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845645	151845647	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	169	480	0	ENST00000262189.6:c.13365_13367del	p.Arg4456del	p.R4456del	ENST00000262189	NM_170606.2	4455	agGAGa/aga	52/59	0.140862576394589	3	FACETS	1	0.987	1	0.665	0.614	0.718	INDETERMINATE	1	TRUE	1	0.51	3		480	625	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020373	69020373	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs781779558	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	121	393	0	ENST00000288368.4:c.2745G>A	p.Trp915Ter	p.W915*	ENST00000288368	NM_024870.2	915	tgG/tgA	24/40	1	2	FACETS	0.884	0.802	0.969	0.884	0.802	0.969	CLONAL	1	TRUE	1	0.51	2		393	537	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981903	70981903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747860295	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	180	735	0	ENST00000276594.2:c.193G>A	p.Ala65Thr	p.A65T	ENST00000276594	NM_024504.3	65	Gcc/Acc	2/8	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.51	2		735	672	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639901	93639901	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	33	245	0	ENST00000375746.1:c.1233del	p.Ala412LeufsTer7	p.A412Lfs*7	ENST00000375746	NM_001174167.1	410	gaC/ga	10/14	1	2	FACETS	0.385	0.314	0.465	0.385	0.314	0.465	SUBCLONAL	1	TRUE	1	0.51	2		245	336	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417562	139417562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	193	759	0	ENST00000277541.6:c.482C>T	p.Ser161Phe	p.S161F	ENST00000277541	NM_017617.3	161	tCc/tTc	4/34	1	2	FACETS	0.972	0.901	1	0.972	0.901	1	CLONAL	1	TRUE	1	0.51	2		759	779	SUCCESS
AR	367	MSKCC	GRCh37	X	66766424	66766424	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036882-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	59	113	0	ENST00000374690.3:c.1440del	p.Tyr481ThrfsTer29	p.Y481Tfs*29	ENST00000374690	NM_000044.3	479	gCc/gc	1/8	0.3	2	FACETS	1	0.919	1	1	0.919	1	INDETERMINATE	2	TRUE	0	0.51	2		113	112	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0037133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	39	361	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.281375667279563	2		361	266	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552630	18552630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200787716	NA	P-0037133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	35	392	1	ENST00000266497.5:c.2041C>T	p.Arg681Cys	p.R681C	ENST00000266497		681	Cgc/Tgc	14/31	1	2	FACETS	0.655	0.537	0.786	0.655	0.537	0.786	SUBCLONAL	1	TRUE	1	0.281375667279563	2		393	380	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266713	198266713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776846119	NA	P-0037133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	49	439	1	ENST00000335508.6:c.2219G>A	p.Gly740Glu	p.G740E	ENST00000335508	NM_012433.2	740	gGa/gAa	15/25	1	2	FACETS	0.804	0.682	0.938	0.804	0.682	0.938	CLONAL	1	TRUE	1	0.281375667279563	2		440	433	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272140	15272140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	62	500	0	ENST00000263388.2:c.6299C>T	p.Ser2100Leu	p.S2100L	ENST00000263388	NM_000435.2	2100	tCg/tTg	33/33	1	2	FACETS	0.72	0.622	0.827	0.72	0.622	0.827	SUBCLONAL	1	TRUE	1	0.281375667279563	2		500	612	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264412	46264412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746670862	NA	P-0037133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	48	380	0	ENST00000371998.3:c.1459C>T	p.Arg487Cys	p.R487C	ENST00000371998		487	Cgt/Tgt	11/23	1	2	FACETS	0.828	0.701	0.967	0.828	0.701	0.967	CLONAL	1	TRUE	1	0.281375667279563	2		380	412	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214899	36214899	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	69	666	0	ENST00000222270.7:c.3325C>T	p.Arg1109Ter	p.R1109*	ENST00000222270	NM_014727.1	1109	Cga/Tga	8/37	1	2	FACETS	0.805	0.702	0.917	0.805	0.702	0.917	CLONAL	1	TRUE	1	0.281375667279563	2		666	609	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933770	39933770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	77	672	0	ENST00000378444.4:c.829C>T	p.Pro277Ser	p.P277S	ENST00000378444	NM_001123385.1	277	Ccg/Tcg	4/15	1	2	FACETS	0.849	0.745	0.96	0.849	0.745	0.96	CLONAL	1	TRUE	1	0.281375667279563	2		672	645	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12393134	12393134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs943725719	NA	P-0037133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	55	470	0	ENST00000287820.6:c.43G>A	p.Asp15Asn	p.D15N	ENST00000287820	NM_015869.4	15	Gat/Aat	1/7	1	2	FACETS	0.844	0.723	0.976	0.844	0.723	0.976	CLONAL	1	TRUE	1	0.281375667279563	2		470	463	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163446	32163446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	119	674	0	ENST00000375023.3:c.5780C>T	p.Pro1927Leu	p.P1927L	ENST00000375023	NM_004557.3	1927	cCt/cTt	30/30	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.281375667279563	2		674	782	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931412	131931412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773566981	NA	P-0037133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	44	341	0	ENST00000265335.6:c.2117G>A	p.Arg706Gln	p.R706Q	ENST00000265335		706	cGa/cAa	13/25	1	2	FACETS	0.776	0.652	0.913	0.776	0.652	0.913	CLONAL	1	TRUE	1	0.281375667279563	2		341	403	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809800	36809800	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	91	691	1	ENST00000373129.3:c.805T>G	p.Tyr269Asp	p.Y269D	ENST00000373129	NM_032017.1	269	Tat/Gat	9/12	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.281375667279563	2		692	639	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425689	49425689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1259726868	NA	P-0037133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	84	758	0	ENST00000301067.7:c.12799C>T	p.Pro4267Ser	p.P4267S	ENST00000301067	NM_003482.3	4267	Cct/Tct	39/54	1	2	FACETS	0.767	0.677	0.864	0.767	0.677	0.864	SUBCLONAL	1	TRUE	1	0.281375667279563	2		758	778	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908260	28908260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	47	346	0	ENST00000282397.4:c.2495C>T	p.Ser832Leu	p.S832L	ENST00000282397	NM_002019.4	832	tCa/tTa	18/30	1	2	FACETS	0.983	0.832	1	0.983	0.832	1	CLONAL	1	TRUE	1	0.281375667279563	2		346	340	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130202	2130202	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397515162	NA	P-0037133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	76	756	3	ENST00000219476.3:c.3434C>T	p.Pro1145Leu	p.P1145L	ENST00000219476	NM_000548.3	1145	cCg/cTg	30/42	0.244478222440947	1	FACETS	0.692	0.607	0.784	0.692	0.607	0.784	SUBCLONAL	1	TRUE	0	0.281375667279563	1		759	671	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830305	72830305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	34	427	0	ENST00000268489.5:c.6276G>A	p.Met2092Ile	p.M2092I	ENST00000268489	NM_006885.3	2092	atG/atA	9/10	1	2	FACETS	0.558	0.456	0.673	0.558	0.456	0.673	SUBCLONAL	1	TRUE	1	0.281375667279563	2		427	433	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636874	158636874	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	47	432	0	ENST00000263640.3:c.306C>A	p.Asn102Lys	p.N102K	ENST00000263640	NM_001105.4	102	aaC/aaA	4/11	1	2	FACETS	0.679	0.573	0.796	0.679	0.573	0.796	SUBCLONAL	1	TRUE	1	0.281375667279563	2		432	492	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660046	12660046	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	50	398	0	ENST00000251849.4:c.175C>T	p.Arg59Cys	p.R59C	ENST00000251849	NM_002880.3	59	Cgt/Tgt	2/17	1	2	FACETS	0.836	0.711	0.973	0.836	0.711	0.973	CLONAL	1	TRUE	1	0.281375667279563	2		398	425	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266140	41266140	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	21	320	1	ENST00000349496.5:c.137T>C	p.Leu46Pro	p.L46P	ENST00000349496	NM_001904.3	46	cTg/cCg	3/15	1	2	FACETS	0.402	0.309	0.511	0.402	0.309	0.511	SUBCLONAL	1	TRUE	1	0.281375667279563	2		321	371	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593612	55593613	+	missense_variant	Missense_Mutation	DNP	GT	GT	AA	novel	NA	P-0037133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	160	343	1	ENST00000288135.5:c.1678_1679delinsAA	p.Val560Asn	p.V560N	ENST00000288135	NM_000222.2	560	GTt/AAt	11/21	0.281375667279563	4	FACETS	0.972	0.897	1			1	CLONAL	3	TRUE	NA	0.281375667279563	4		344	500	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557197	187557198	+	missense_variant	Missense_Mutation	DNP	GG	GG	TA	novel	NA	P-0037133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	37	398	1	ENST00000441802.2:c.4164_4165delinsTA	p.Leu1389Ile	p.L1389I	ENST00000441802	NM_005245.3	1388	ccCCtt/ccTAtt	6/27	1	2	FACETS	0.626	0.516	0.749	0.626	0.516	0.749	SUBCLONAL	1	TRUE	1	0.281375667279563	2		399	420	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273008	55273008	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	75	542	0	ENST00000275493.2:c.3331C>T	p.His1111Tyr	p.H1111Y	ENST00000275493	NM_005228.3	1111	Cac/Tac	28/28	1	2	FACETS	0.861	0.755	0.975	0.861	0.755	0.975	CLONAL	1	TRUE	1	0.281375667279563	2		542	619	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371863	116371863	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	40	335	0	ENST00000397752.3:c.1342G>A	p.Gly448Arg	p.G448R	ENST00000397752	NM_000245.2	448	Gga/Aga	3/21	1	2	FACETS	0.677	0.563	0.804	0.677	0.563	0.804	SUBCLONAL	1	TRUE	1	0.281375667279563	2		335	420	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465494	8465494	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	38	418	0	ENST00000356435.5:c.3686T>A	p.Val1229Glu	p.V1229E	ENST00000356435		1229	gTg/gAg	21/35	0.158252230563505	1	FACETS	0.703	0.583	0.837	0.703	0.583	0.837	INDETERMINATE	1	TRUE	0	0.281375667279563	1		418	330	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028813	47028813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1482080375	NA	P-0037133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	54	738	0	ENST00000377604.3:c.117G>A	p.Met39Ile	p.M39I	ENST00000377604	NM_001204468.1	39	atG/atA	3/24	1	2	FACETS	0.609	0.52	0.707	0.609	0.52	0.707	SUBCLONAL	1	TRUE	1	0.281375667279563	2		738	630	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181281	123181281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	26	244	0	ENST00000218089.9:c.745G>A	p.Glu249Lys	p.E249K	ENST00000218089	NM_001042749.1	249	Gaa/Aaa	9/35	1	2	FACETS	0.78	0.62	0.961	0.78	0.62	0.961	CLONAL	1	TRUE	1	0.281375667279563	2		244	237	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	172	427	0				ENST00000310581	NM_198253.2	-/1132			0.594717386687656	1	FACETS	0.717	0.673	0.761	0.717	0.673	0.761	SUBCLONAL	1	TRUE	0	0.867596301648065	1		427	313	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0037711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	424	292	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.368686702169571	5	FACETS	1	0.986	1	0.785	0.756	0.814	INDETERMINATE	3	TRUE	1	0.867596301648065	5		292	716	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247618	123247618	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1466101220	NA	P-0037711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	242	414	0	ENST00000358487.5:c.1873C>T	p.Arg625Ter	p.R625*	ENST00000358487	NM_000141.4	625	Cga/Tga	14/18	0.867596301648065	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.867596301648065	1		414	299	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505595	186505595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	240	398	0	ENST00000323963.5:c.1003C>T	p.Arg335Cys	p.R335C	ENST00000323963		335	Cgc/Tgc	10/11	0.462312905282226	1	FACETS	0.739	0.701	0.776	0.739	0.701	0.776	INDETERMINATE	1	TRUE	0	0.867596301648065	1		398	424	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508905	106508905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755134917	NA	P-0037711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	417	549	0	ENST00000359195.3:c.899G>A	p.Gly300Glu	p.G300E	ENST00000359195	NM_002649.2	300	gGa/gAa	2/11	0.368686702169571	5	FACETS	1	0.976	1	0.765	0.736	0.794	INDETERMINATE	3	TRUE	1	0.867596301648065	5		549	723	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157539	106157539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs192553789	NA	P-0037711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	229	345	0	ENST00000380013.4:c.2440C>T	p.Arg814Cys	p.R814C	ENST00000380013	NM_001127208.2	814	Cgt/Tgt	3/11	0.428656111764885	2	FACETS	1	0.994	1	0.713	0.678	0.748	INDETERMINATE	1	TRUE	0	0.867596301648065	2		345	370	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857745	9857745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs909465034	NA	P-0037711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	111	625	0	ENST00000330684.3:c.3656C>T	p.Ser1219Phe	p.S1219F	ENST00000330684	NM_001134407.1	1219	tCc/tTc	13/13	0.562092483824412	1	FACETS	0.36	0.325	0.395	0.36	0.325	0.395	SUBCLONAL	1	TRUE	0	0.867596301648065	1		625	403	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50830258	50830258	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	221	499	0	ENST00000398568.2:c.2701C>T	p.Pro901Ser	p.P901S	ENST00000398568	NM_001042412.1	901	Cct/Tct	18/18	0.562092483824412	1	FACETS	0.719	0.681	0.758	0.719	0.681	0.758	SUBCLONAL	1	TRUE	0	0.867596301648065	1		499	401	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051148	13051148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	353	726	0	ENST00000316448.5:c.584C>T	p.Ser195Phe	p.S195F	ENST00000316448	NM_004343.3	195	tCc/tTc	5/9	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.867596301648065	2		726	811	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103264	119103264	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	459	538	0	ENST00000264033.4:c.302G>A	p.Arg101Lys	p.R101K	ENST00000264033	NM_005188.3	101	aGa/aAa	2/16	0.859647137719532	2	FACETS	0.991	0.969	1	0.991	0.969	1	CLONAL	2	TRUE	0	0.867596301648065	2		538	534	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36945084	36945084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528738573	NA	P-0037711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	199	851	0	ENST00000361632.4:c.14G>A	p.Gly5Glu	p.G5E	ENST00000361632		5	gGa/gAa	2/16	0.562092483824412	1	FACETS	0.38	0.353	0.408	0.38	0.353	0.408	SUBCLONAL	1	TRUE	0	0.867596301648065	1		851	683	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420826	49420827	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0037711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	222	719	1	ENST00000301067.7:c.14922_14923delinsTT	p.Arg4975Cys	p.R4975C	ENST00000301067	NM_003482.3	4974	tcCCgt/tcTTgt	48/54	1	2	FACETS	0.831	0.778	0.884	0.831	0.778	0.884	CLONAL	1	TRUE	1	0.867596301648065	2		720	616	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30098264	30098264	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs765965096	NA	P-0037711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	163	202	0	ENST00000331968.5:c.1708C>T	p.Gln570Ter	p.Q570*	ENST00000331968	NM_002742.2	570	Cag/Tag	11/18	0.867596301648065	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.867596301648065	1		202	202	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004814	16004814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	195	761	0	ENST00000268712.3:c.2440C>T	p.Pro814Ser	p.P814S	ENST00000268712	NM_006311.3	814	Cca/Tca	20/46	0.448309125457464	1	FACETS	0.439	0.409	0.47	0.439	0.409	0.47	INDETERMINATE	1	TRUE	0	0.867596301648065	1		761	580	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222703	5222703	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	219	759	0	ENST00000357368.4:c.3100C>T	p.Gln1034Ter	p.Q1034*	ENST00000357368	NM_002850.3	1034	Caa/Taa	18/38	1	2	FACETS	0.836	0.783	0.89	0.836	0.783	0.89	CLONAL	1	TRUE	1	0.867596301648065	2		759	604	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141425	11141426	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0037711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	275	844	1	ENST00000358026.2:c.3402_3403delinsTT	p.Arg1135Trp	p.R1135W	ENST00000358026	NM_001128849.1	1134	gaCCgg/gaTTgg	25/36	1	2	FACETS	0.915	0.864	0.966	0.915	0.864	0.966	CLONAL	1	TRUE	1	0.867596301648065	2		845	693	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257937	19257937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140321393	NA	P-0037711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	452	1153	0	ENST00000162023.5:c.449C>T	p.Pro150Leu	p.P150L	ENST00000162023		150	cCa/cTa	9/13	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.867596301648065	2		1153	952	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795490	42795491	+	missense_variant	Missense_Mutation	DNP	CA	CA	TT	novel	NA	P-0037711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	299	887	1	ENST00000575354.2:c.2570_2571delinsTT	p.Ala857Val	p.A857V	ENST00000575354	NM_015125.3	857	gCA/gTT	10/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.867596301648065	2		888	672	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023702	31023702	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	172	795	0	ENST00000375687.4:c.3187C>G	p.Gln1063Glu	p.Q1063E	ENST00000375687	NM_015338.5	1063	Cag/Gag	13/13	0.107682319607457	3	FACETS	0.566	0.52	0.613	0.189	0.173	0.205	INDETERMINATE	1	TRUE	0	0.867596301648065	3		795	1005	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733250	40733250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	133	721	1	ENST00000373198.4:c.3556G>A	p.Asp1186Asn	p.D1186N	ENST00000373198	NM_133170.3	1186	Gac/Aac	26/32	0.107682319607457	3	FACETS	0.566	0.515	0.621	0.189	0.171	0.207	INDETERMINATE	1	TRUE	0	0.867596301648065	3		722	776	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49724603	49724603	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	202	563	0	ENST00000449682.2:c.586G>C	p.Gly196Arg	p.G196R	ENST00000449682	NM_020998.3	196	Ggc/Cgc	5/18	0.448309125457464	1	FACETS	0.697	0.657	0.737	0.697	0.657	0.737	INDETERMINATE	1	TRUE	0	0.867596301648065	1		563	378	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190308	32190308	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765965167	NA	P-0037711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	211	636	0	ENST00000375023.3:c.431C>T	p.Ser144Phe	p.S144F	ENST00000375023	NM_004557.3	144	tCc/tTc	3/30	0.573330404822036	3	FACETS	1	0.983	1	0.574	0.536	0.612	CLONAL	1	TRUE	1	0.867596301648065	3		636	608	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98002965	98002965	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	210	283	0	ENST00000289081.3:c.311A>T	p.Asn104Ile	p.N104I	ENST00000289081	NM_000136.2	104	aAt/aTt	4/15	1	2	FACETS	0.866	0.81	0.923	0.866	0.81	0.923	CLONAL	1	TRUE	1	0.867596301648065	2		283	559	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039230-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	212	561	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.425331970491114	3	FACETS	0.95	0.888	1	0.95	0.888	1	CLONAL	2	TRUE	1	0.425331970491114	3		561	636	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0039230-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	150	355	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	0.425331970491114	4	FACETS	1	0.981	1	0.804	0.742	0.867	CLONAL	2	TRUE	1	0.425331970491114	4		355	417	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0039980-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	95	359	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.417519264154884	4	FACETS	1	0.95	1	0.554	0.495	0.618	CLONAL	1	TRUE	2	0.459802777914321	4		359	544	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0039980-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	1193	429	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.459802777914321	15	FACETS	0.991	0.974	1			1	CLONAL	13	TRUE	NA	0.459802777914321	15		429	1606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0039980-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	525	1019	1	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.459802777914321	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.459802777914321	2		1020	1061	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439494	220439494	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764382434	NA	P-0039980-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	318	755	0	ENST00000243786.2:c.347G>A	p.Arg116Gln	p.R116Q	ENST00000243786	NM_002191.3	116	cGg/cAg	2/2	0.349645890542284	4	FACETS	0.99	0.936	1	0.99	0.936	1	CLONAL	2	TRUE	2	0.459802777914321	4		755	1020	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986820	36986821	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0039980-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	120	222	0	ENST00000354822.5:c.868dup	p.Val290GlyfsTer149	p.V290Gfs*149	ENST00000354822	NM_001079668.2	290	gtg/gGtg	3/3	NA	2	FACETS	1	0.921	1			1	INDETERMINATE	2	TRUE	NA	0.459802777914321	2		222	261	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652087	36652087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769049147	NA	P-0039980-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	222	952	1	ENST00000244741.5:c.209G>A	p.Gly70Asp	p.G70D	ENST00000244741	NM_000389.4	70	gGc/gAc	2/3	0.308411029350682	4	FACETS	1	0.985	1	0.603	0.56	0.647	CLONAL	1	TRUE	2	0.459802777914321	4		953	1169	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550535	29550537	+	frameshift_variant	Frame_Shift_Ins	INS	TGG	TGG	GTGT	novel	NA	P-0039980-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	21	348	2	ENST00000356175.3:c.1795_1797delinsGTGT	p.Trp599ValfsTer11	p.W599Vfs*11	ENST00000356175	NM_000267.3	599	TGG/GTGT	16/57	0.459802777914321	3	FACETS	0.302	0.232	0.384	0.151	0.116	0.192	SUBCLONAL	1	TRUE	1	0.459802777914321	3		350	372	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675287	176675287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	147	379	1	ENST00000439151.2:c.4603C>T	p.Arg1535Cys	p.R1535C	ENST00000439151	NM_022455.4	1535	Cgc/Tgc	11/23	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.564658725846469	2		380	490	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040120-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	59	427	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.763948921631336	2		427	140	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0040120-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	254	649	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.763948921631336	NA		649	680	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720679	89720679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123329	NA	P-0040120-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	182	312	0	ENST00000371953.3:c.830C>T	p.Thr277Ile	p.T277I	ENST00000371953	NM_000314.4	277	aCa/aTa	8/9	0.763948921631336	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.763948921631336	1		312	285	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209390	98209390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571030658	NA	P-0040120-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	214	755	0	ENST00000331920.6:c.4148C>T	p.Pro1383Leu	p.P1383L	ENST00000331920	NM_000264.3	1383	cCg/cTg	23/24	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.763948921631336	2		755	551	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489220	2489220	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040120-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	252	747	0	ENST00000355716.4:c.125G>T	p.Cys42Phe	p.C42F	ENST00000355716	NM_003820.2	42	tGc/tTc	2/8	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.763948921631336	2		747	648	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	480	427	0				ENST00000310581	NM_198253.2	-/1132			0.554166624594147	4	FACETS	1	0.995	1	0.797	0.767	0.827	CLONAL	2	TRUE	1	0.808792502404274	4		427	898	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0040569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	8	572	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.067	0.042	0.098	0.067	0.042	0.098	SUBCLONAL	1	TRUE	1	0.808792502404274	2		572	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0040569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	433	646	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	1	2	FACETS	0.906	0.865	0.947	0.906	0.865	0.947	CLONAL	1	TRUE	1	0.808792502404274	2		646	1182	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0040569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	503	838	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.808792502404274	2		838	1229	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30061031	30061031	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0040569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	17	371	0	ENST00000338641.4:c.863C>G	p.Ser288Ter	p.S288*	ENST00000338641	NM_000268.3	288	tCa/tGa	9/16	0.808792502404274	1	FACETS	0.082	0.061	0.107	0.082	0.061	0.107	SUBCLONAL	1	TRUE	0	0.808792502404274	1		371	305	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0040569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	447	751	0	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	1	2	FACETS	0.918	0.877	0.959	0.918	0.877	0.959	CLONAL	1	TRUE	1	0.808792502404274	2		751	1204	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251620	212251620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	30	358	0	ENST00000342788.4:c.3439G>A	p.Glu1147Lys	p.E1147K	ENST00000342788	NM_005235.2	1147	Gag/Aag	27/28	0.676942456244098	1	FACETS	0.102	0.082	0.125	0.102	0.082	0.125	SUBCLONAL	1	TRUE	0	0.808792502404274	1		358	433	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047519	49047519	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1131690908	NA	P-0040569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	47	255	0	ENST00000267163.4:c.2513C>G	p.Ser838Ter	p.S838*	ENST00000267163	NM_000321.2	838	tCa/tGa	24/27	0.808792502404274	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.808792502404274	1		255	65	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772254	68772254	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	110	960	1	ENST00000261769.5:c.103G>T	p.Glu35Ter	p.E35*	ENST00000261769	NM_004360.3	35	Gag/Tag	2/16	0.732107793783903	1	FACETS	0.146	0.13	0.162	0.146	0.13	0.162	SUBCLONAL	1	TRUE	0	0.808792502404274	1		961	1112	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434618	49434618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs949690934	NA	P-0040569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1398	123	937	0	ENST00000301067.7:c.6935C>T	p.Ser2312Leu	p.S2312L	ENST00000301067	NM_003482.3	2312	tCa/tTa	31/54	1	2	FACETS	0.2	0.18	0.221	0.2	0.18	0.221	SUBCLONAL	1	TRUE	1	0.808792502404274	2		937	1521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579563	7579563	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	407	754	0	ENST00000269305.4:c.124G>T	p.Asp42Tyr	p.D42Y	ENST00000269305	NM_001126112.2	42	Gat/Tat	4/11	1	2	FACETS	0.872	0.831	0.914	0.872	0.831	0.914	CLONAL	1	TRUE	1	0.808792502404274	2		754	1154	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572022239	NA	P-0040569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1468	122	967	0	ENST00000301067.7:c.7061C>T	p.Pro2354Leu	p.P2354L	ENST00000301067	NM_003482.3	2354	cCt/cTt	31/54	1	2	FACETS	0.19	0.17	0.21	0.19	0.17	0.21	SUBCLONAL	1	TRUE	1	0.808792502404274	2		967	1590	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519938	66519938	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	203	323	0	ENST00000358598.2:c.421C>A	p.Leu141Ile	p.L141I	ENST00000358598	NM_212471.2	141	Ctt/Att	4/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.808792502404274	2		323	483	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349205	15349205	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	38	366	0	ENST00000263377.2:c.4072G>C	p.Glu1358Gln	p.E1358Q	ENST00000263377	NM_058243.2	1358	Gaa/Caa	20/20	1	2	FACETS	0.146	0.12	0.175	0.146	0.12	0.175	SUBCLONAL	1	TRUE	1	0.808792502404274	2		366	644	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143514	30143514	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	29	275	0	ENST00000389048.3:c.12C>G	p.Ile4Met	p.I4M	ENST00000389048	NM_004304.4	4	atC/atG	1/29	1	2	FACETS	0.145	0.116	0.179	0.145	0.116	0.179	SUBCLONAL	1	TRUE	1	0.808792502404274	2		275	493	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288946	212288946	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	19	376	0	ENST00000342788.4:c.2800G>C	p.Glu934Gln	p.E934Q	ENST00000342788	NM_005235.2	934	Gag/Cag	23/28	0.676942456244098	1	FACETS	0.104	0.079	0.134	0.104	0.079	0.134	SUBCLONAL	1	TRUE	0	0.808792502404274	1		376	269	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651987	36651988	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0040569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	523	855	0	ENST00000244741.5:c.110_111dup	p.Met38Ter	p.M38*	ENST00000244741	NM_000389.4	37	cta/cTAta	2/3	0.102854369415657	4	FACETS	0.805	0.772	0.839	0.805	0.772	0.839	INDETERMINATE	2	TRUE	2	0.808792502404274	4		855	1453	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652250	36652251	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGC	novel	NA	P-0040569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	487	742	0	ENST00000244741.5:c.373_376dup	p.Gln126ArgfsTer4	p.Q126Rfs*4	ENST00000244741	NM_000389.4	124	-/GAGC	2/3	0.102854369415657	4	FACETS	0.834	0.798	0.87	0.834	0.798	0.87	INDETERMINATE	2	TRUE	2	0.808792502404274	4		742	1306	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93640016	93640016	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	31	309	0	ENST00000375746.1:c.1345G>C	p.Glu449Gln	p.E449Q	ENST00000375746	NM_001174167.1	449	Gag/Cag	10/14	1	2	FACETS	0.133	0.107	0.162	0.133	0.107	0.162	SUBCLONAL	1	TRUE	1	0.808792502404274	2		309	577	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923064	39923064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	65	334	0	ENST00000378444.4:c.3644G>A	p.Arg1215Lys	p.R1215K	ENST00000378444	NM_001123385.1	1215	aGa/aAa	8/15	0.579885273988744	2	FACETS	0.218	0.188	0.25			1	SUBCLONAL	1	TRUE	NA	0.808792502404274	2		334	737	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937678	76937678	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	22	193	0	ENST00000373344.5:c.3070G>C	p.Glu1024Gln	p.E1024Q	ENST00000373344	NM_000489.3	1024	Gaa/Caa	9/35	0.579885273988744	2	FACETS	0.197	0.153	0.249			1	SUBCLONAL	1	TRUE	NA	0.808792502404274	2		193	276	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938716	76938716	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	49	239	0	ENST00000373344.5:c.2032G>T	p.Asp678Tyr	p.D678Y	ENST00000373344	NM_000489.3	678	Gat/Tat	9/35	0.579885273988744	2	FACETS	0.244	0.207	0.286			1	SUBCLONAL	1	TRUE	NA	0.808792502404274	2		239	496	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748174	72748174	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779210726	NA	P-0040569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	185	343	0	ENST00000357731.5:c.4G>A	p.Asp2Asn	p.D2N	ENST00000357731	NM_173808.2	2	Gac/Aac	1/7	1	2	FACETS	0.805	0.748	0.864	0.805	0.748	0.864	CLONAL	1	TRUE	1	0.808792502404274	2		343	568	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727571	66727571	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040569-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	29	353	0	ENST00000307102.5:c.287G>T	p.Arg96Ile	p.R96I	ENST00000307102	NM_002755.3	96	aGa/aTa	2/11	0.280450068394692	1	FACETS	0.092	0.074	0.114	0.092	0.074	0.114	INDETERMINATE	1	TRUE	0	0.808792502404274	1		353	462	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416881	121416881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040863-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	155	919	0	ENST00000257555.6:c.310G>A	p.Val104Met	p.V104M	ENST00000257555		104	Gtg/Atg	1/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.484454978582538	2		919	587	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041649-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	23	427	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.904	0.707	1	0.904	0.707	1	CLONAL	1	FALSE	1	0.198017280266328	2		427	257	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653805	89653805	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659443	NA	P-0041649-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	34	205	0	ENST00000371953.3:c.103A>G	p.Met35Val	p.M35V	ENST00000371953	NM_000314.4	35	Atg/Gtg	2/9	0.198017280266328	1	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	FALSE	0	0.198017280266328	1		205	284	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048756	180048756	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1297327643	NA	P-0041649-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	40	695	0	ENST00000261937.6:c.1806C>G	p.His602Gln	p.H602Q	ENST00000261937	NM_182925.4	602	caC/caG	13/30	1	2	FACETS	0.658	0.546	0.784	0.658	0.546	0.784	SUBCLONAL	1	FALSE	1	0.198017280266328	2		695	614	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862752	9862752	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1328846513	NA	P-0042060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	28	600	0	ENST00000330684.3:c.2551G>C	p.Gly851Arg	p.G851R	ENST00000330684	NM_001134407.1	851	Ggc/Cgc	12/13	1	2	FACETS	0.559	0.446	0.689	0.559	0.446	0.689	SUBCLONAL	1	TRUE	1	0.184357282348867	2		600	543	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40447796	40447796	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	88	647	0	ENST00000345506.4:c.535A>T	p.Ser179Cys	p.S179C	ENST00000345506	NM_003152.3	179	Agc/Tgc	6/20	1	2	FACETS	0.92	0.817	1	1	0.984	1	CLONAL	2	TRUE	1	0.184357282348867	2		647	519	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188207	10188207	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	93	579	0	ENST00000256474.2:c.350G>C	p.Trp117Ser	p.W117S	ENST00000256474	NM_000551.3	117	tGg/tCg	2/3	0.184357282348867	1	FACETS	1	0.924	1	1	0.987	1	CLONAL	2	TRUE	0	0.184357282348867	1		579	440	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263339	115263339	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0042260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	207	652	1	ENST00000438362.2:c.2012-1G>T		p.X671_splice	ENST00000438362	NM_001242891.1	671			0.669204820261344	1	FACETS	0.931	0.875	0.987	0.931	0.875	0.987	CLONAL	1	TRUE	0	0.669204820261344	1		653	442	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593664	55593665	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTATGA	novel	NA	P-0042260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	165	545	0	ENST00000288135.5:c.1732_1737dup	p.Tyr578_Asp579dup	p.Y578_D579dup	ENST00000288135	NM_000222.2	578	cct/ccTTATGAt	11/21	1	2	FACETS	0.804	0.742	0.869	0.804	0.742	0.869	CLONAL	1	TRUE	1	0.669204820261344	2		545	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519986	NA	P-0042717-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	157	604	0	ENST00000269305.4:c.809T>C	p.Phe270Ser	p.F270S	ENST00000269305	NM_001126112.2	270	tTt/tCt	8/11	0.243848424975516	2	FACETS	0.954	0.878	1	0.954	0.878	1	CLONAL	2	TRUE	0	0.287777792985315	2		604	572	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503831	149503831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042717-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	50	506	0	ENST00000261799.4:c.2005G>A	p.Gly669Arg	p.G669R	ENST00000261799	NM_002609.3	669	Ggg/Agg	14/23	1	2	FACETS	0.662	0.562	0.772	0.662	0.562	0.772	SUBCLONAL	1	TRUE	1	0.287777792985315	2		506	525	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259514	55259515	+	missense_variant	Missense_Mutation	DNP	CT	CT	AG	rs1057519847	NA	P-0042717-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	182	473	0	ENST00000275493.2:c.2572_2573inv	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	CTg/AGg	21/28	0.287777792985315	4	FACETS	0.794	0.732	0.858	0.794	0.732	0.858	SUBCLONAL	2	TRUE	2	0.287777792985315	4		473	1026	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0043747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	423	882	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	2	TRUE	NA	0.492732200974165	2		882	854	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231106	53231106	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	165	275	0	ENST00000375401.3:c.1796G>T	p.Arg599Leu	p.R599L	ENST00000375401	NM_004187.3	599	cGt/cTt	13/26	0.323278585537206	2	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.492732200974165	2		275	550	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215376	41215376	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	164	330	0	ENST00000357654.3:c.5167A>T	p.Ile1723Phe	p.I1723F	ENST00000357654	NM_007294.3	1723	Att/Ttt	18/23	0.155019735121052	6	FACETS	0.847	0.783	0.913	0.847	0.783	0.913	INDETERMINATE	3	TRUE	3	0.492732200974165	6		330	520	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456320	32456320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	183	745	1	ENST00000332351.3:c.572G>T	p.Gly191Val	p.G191V	ENST00000332351	NM_024426.4	191	gGc/gTc	1/10	0.492732200974165	3	FACETS	0.837	0.771	0.906	0.419	0.385	0.453	CLONAL	1	TRUE	1	0.492732200974165	3		746	1106	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661605	227661605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1205996251	NA	P-0043747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	313	756	0	ENST00000305123.5:c.1850C>T	p.Pro617Leu	p.P617L	ENST00000305123	NM_005544.2	617	cCa/cTa	1/2	0.492732200974165	3	FACETS	1	0.975	1	0.696	0.661	0.733	CLONAL	2	TRUE	0	0.492732200974165	3		756	758	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204000	142204000	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	79	297	0	ENST00000350721.4:c.6203T>C	p.Ile2068Thr	p.I2068T	ENST00000350721	NM_001184.3	2068	aTa/aCa	36/47	0.492732200974165	5	FACETS	1	0.882	1	0.25	0.22	0.283	CLONAL	1	TRUE	1	0.492732200974165	5		297	557	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274743	142274743	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0043747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	241	242	0	ENST00000350721.4:c.2317A>T	p.Lys773Ter	p.K773*	ENST00000350721	NM_001184.3	773	Aaa/Taa	10/47	0.492732200974165	5	FACETS	1	0.983	1	1	0.983	1	CLONAL	4	TRUE	1	0.492732200974165	5		242	397	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322873	31322915	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCTTCCCTACCTGAACTCTTCCTCCTACACATCACAGCAGCG	CCCTTCCCTACCTGAACTCTTCCTCCTACACATCACAGCAGCG	-	novel	NA	P-0043747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	151	490	0	ENST00000412585.2:c.981_1012+11del		p.X327_splice	ENST00000412585	NM_005514.6	327		5/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.492732200974165	2		490	430	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850814	128850814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	74	531	0	ENST00000249373.3:c.1661G>A	p.Gly554Glu	p.G554E	ENST00000249373	NM_005631.4	554	gGg/gAg	10/12	0.492732200974165	3	FACETS	0.541	0.473	0.614	0.27	0.236	0.307	SUBCLONAL	1	TRUE	1	0.492732200974165	3		531	692	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5029907	5029907	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0043747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	127	285	0	ENST00000381652.3:c.350+1G>A		p.X117_splice	ENST00000381652	NM_004972.3	117			0.492732200974165	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.492732200974165	2		285	252	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1331479	1331479	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	149	540	0	ENST00000400841.2:c.49G>T	p.Gly17Cys	p.G17C	ENST00000400841		17	Ggc/Tgc	1/6	0.359001266570846	2	FACETS	0.807	0.739	0.879			1	CLONAL	1	TRUE	NA	0.492732200974165	2		540	749	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148681	20148681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	88	161	0	ENST00000379607.5:c.382G>A	p.Glu128Lys	p.E128K	ENST00000379607	NM_001412.3	128	Gaa/Aaa	6/7	0.359001266570846	2	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.492732200974165	2		161	261	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0044019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	39	292	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.648036448062012	3	FACETS	1	0.854	1	0.508	0.427	0.594	CLONAL	1	TRUE	1	0.648036448062012	3		292	157	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0044019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	84	279	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.894	0.799	0.993	0.894	0.799	0.993	CLONAL	1	TRUE	1	0.648036448062012	2		279	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578240	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0044019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	246	551	2	ENST00000269305.4:c.608_609dup	p.Glu204TrpfsTer44	p.E204Wfs*44	ENST00000269305	NM_001126112.2	203	-/TG	6/11	0.648036448062012	1	FACETS	0.959	0.906	1	0.959	0.906	1	CLONAL	1	TRUE	0	0.648036448062012	1		553	535	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260064	19260064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774866350	NA	P-0044019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	458	701	1	ENST00000162023.5:c.229G>A	p.Glu77Lys	p.E77K	ENST00000162023		77	Gag/Aag	7/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.648036448062012	2		702	1370	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066687	94066687	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	154	372	1	ENST00000369303.4:c.1072G>T	p.Gly358Trp	p.G358W	ENST00000369303	NM_004440.3	358	Ggg/Tgg	5/17	1	2	FACETS	0.978	0.902	1	0.978	0.902	1	CLONAL	1	TRUE	1	0.648036448062012	2		373	486	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539725	187539725	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	55	299	0	ENST00000441802.2:c.8015T>G	p.Phe2672Cys	p.F2672C	ENST00000441802	NM_005245.3	2672	tTt/tGt	10/27	1	2	FACETS	0.797	0.691	0.909	0.797	0.691	0.909	CLONAL	1	TRUE	1	0.648036448062012	2		299	213	SUCCESS
APC	324	MSKCC	GRCh37	5	112162919	112162919	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0044019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	18	305	0	ENST00000257430.4:c.1523T>A	p.Leu508Ter	p.L508*	ENST00000257430	NM_000038.5	508	tTg/tAg	12/16	1	2	FACETS	0.772	0.596	0.967	0.772	0.596	0.967	CLONAL	1	TRUE	1	0.648036448062012	2		305	72	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660160	12660160	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752484962	NA	P-0044088-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	22	478	0	ENST00000251849.4:c.61G>A	p.Val21Met	p.V21M	ENST00000251849	NM_002880.3	21	Gtg/Atg	2/17	0.0858990955114127	4	FACETS	0.305	0.236	0.386	0.153	0.118	0.193	INDETERMINATE	1	TRUE	2	0.661806174655556	4		478	362	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469672	NA	P-0044109-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	283	367	0	ENST00000374080.3:c.131G>A	p.Gly44Asp	p.G44D	ENST00000374080		44	gGt/gAt	2/45	1	2	FACETS	0.949	0.894	1	0.949	0.894	1	CLONAL	1	TRUE	1	0.684963753850878	2		367	871	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937684	76937684	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044109-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	169	492	0	ENST00000373344.5:c.3064C>T	p.Arg1022Ter	p.R1022*	ENST00000373344	NM_000489.3	1022	Cga/Tga	9/35	1	2	FACETS	0.94	0.87	1	0.94	0.87	1	CLONAL	1	TRUE	1	0.684963753850878	2		492	525	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041062	42041062	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044109-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	187	731	0	ENST00000219905.7:c.5440T>G	p.Leu1814Val	p.L1814V	ENST00000219905	NM_001164273.1	1814	Ttg/Gtg	16/24	0.391603143210043	1	FACETS	0.408	0.376	0.44	0.408	0.376	0.44	INDETERMINATE	1	TRUE	0	0.684963753850878	1		731	881	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044395-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	163	427	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	0.924	0.857	0.992	0.924	0.857	0.992	INDETERMINATE	1	TRUE	0	0.58	1		427	432	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0044395-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	221	320	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.182293766337634	4	FACETS	1	0.949	1	0.676	0.633	0.719	INDETERMINATE	2	TRUE	1	0.58	4		320	594	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872559	37872559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293998208	NA	P-0044395-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	35	424	0	ENST00000269571.5:c.1519G>A	p.Glu507Lys	p.E507K	ENST00000269571		507	Gag/Aag	13/27	1	2	FACETS	0.25	0.204	0.301	0.25	0.204	0.301	SUBCLONAL	1	TRUE	1	0.58	2		424	483	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168682	32168682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs935064991	NA	P-0044395-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	207	643	1	ENST00000375023.3:c.4241C>T	p.Ala1414Val	p.A1414V	ENST00000375023	NM_004557.3	1414	gCg/gTg	23/30	1	2	FACETS	0.849	0.789	0.91	0.849	0.789	0.91	CLONAL	1	TRUE	1	0.58	2		644	841	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523088	25523088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758534627	NA	P-0044395-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	52	630	1	ENST00000264709.3:c.97C>T	p.Arg33Cys	p.R33C	ENST00000264709	NM_175629.2	33	Cgt/Tgt	3/23	1	2	FACETS	0.217	0.184	0.253	0.217	0.184	0.253	SUBCLONAL	1	TRUE	1	0.58	2		631	827	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89828391	89828391	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1185836546	NA	P-0044395-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	157	467	0	ENST00000389301.3:c.2818C>G	p.Gln940Glu	p.Q940E	ENST00000389301	NM_000135.2	940	Caa/Gaa	29/43	1	2	FACETS	0.907	0.834	0.982	0.907	0.834	0.982	CLONAL	1	TRUE	1	0.58	2		467	597	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435759	56435759	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044395-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	154	523	0	ENST00000407977.2:c.1378G>C	p.Asp460His	p.D460H	ENST00000407977		460	Gat/Cat	9/10	1	2	FACETS	0.973	0.895	1	0.973	0.895	1	CLONAL	1	TRUE	1	0.58	2		523	546	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110556	4110556	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs727504370	NA	P-0044395-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	214	689	0	ENST00000262948.5:c.401A>G	p.Tyr134Cys	p.Y134C	ENST00000262948	NM_030662.3	134	tAc/tGc	3/11	0.3	1	FACETS	0.75	0.699	0.801	0.75	0.699	0.801	INDETERMINATE	1	TRUE	0	0.58	1		689	699	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651426	52651426	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044395-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	222	487	0	ENST00000394830.3:c.1670A>T	p.Asp557Val	p.D557V	ENST00000394830	NM_018313.4	557	gAt/gTt	15/30	0.3	1	FACETS	0.918	0.861	0.976	0.918	0.861	0.976	INDETERMINATE	1	TRUE	0	0.58	1		487	592	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481457	140481457	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044395-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	323	464	0	ENST00000288602.6:c.1351G>C	p.Glu451Gln	p.E451Q	ENST00000288602	NM_004333.4	451	Gag/Cag	11/18	0.182293766337634	4	FACETS	1	0.989	1	0.763	0.724	0.802	INDETERMINATE	2	TRUE	1	0.58	4		464	769	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	124	630	3	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	0.446946452715659	1	FACETS	0.824	0.765	0.881	1	0.99	1	CLONAL	2	FALSE	0	0.508209529535662	1		633	221	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	42	382	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.675	0.568	0.791	0.675	0.568	0.791	SUBCLONAL	1	FALSE	1	0.508209529535662	2		382	245	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143994	11143994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	104	655	1	ENST00000358026.2:c.3575G>A	p.Arg1192His	p.R1192H	ENST00000358026	NM_001128849.1	1192	cGc/cAc	26/36	0.508209529535662	3	FACETS	0.974	0.875	1	0.487	0.437	0.539	CLONAL	1	FALSE	1	0.508209529535662	3		656	527	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	68	368	0	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	0.146640708906831	0	FACETS	0.377	0.33	0.427			1	INDETERMINATE	1	FALSE	0	0.508209529535662	0		368	349	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442579	52442579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1312611941	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	171	491	1	ENST00000460680.1:c.166C>T	p.Arg56Cys	p.R56C	ENST00000460680	NM_004656.3	56	Cgc/Tgc	4/17	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.508209529535662	2		492	555	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743943	40743943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763964405	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	23	524	0	ENST00000373198.4:c.3052C>T	p.Arg1018Ter	p.R1018*	ENST00000373198	NM_133170.3	1018	Cga/Tga	23/32	0.508209529535662	0	FACETS	0.169	0.132	0.212			1	SUBCLONAL	1	FALSE	0	0.508209529535662	0		524	263	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216560	2216560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777525091	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	181	874	0	ENST00000398665.3:c.2204C>T	p.Thr735Met	p.T735M	ENST00000398665	NM_032482.2	735	aCg/aTg	20/28	1	2	FACETS	0.784	0.731	0.839	1	0.992	1	SUBCLONAL	2	FALSE	1	0.508209529535662	2		874	454	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	102	689	0	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	0.508209529535662	3	FACETS	0.997	0.895	1	0.498	0.447	0.552	CLONAL	1	FALSE	1	0.508209529535662	3		689	505	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220476	123220476	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	126	351	0	ENST00000218089.9:c.3133C>T	p.Arg1045Ter	p.R1045*	ENST00000218089	NM_001042749.1	1045	Cga/Tga	30/35	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	0	0.508209529535662	1		351	271	SUCCESS
APC	324	MSKCC	GRCh37	5	112154969	112154969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137854567	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	113	708	0	ENST00000257430.4:c.1240C>T	p.Arg414Cys	p.R414C	ENST00000257430	NM_000038.5	414	Cgc/Tgc	10/16	1	2	FACETS	0.874	0.79	0.961	0.874	0.79	0.961	CLONAL	1	FALSE	1	0.508209529535662	2		708	509	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746002	162746002	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1056323839	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	53	496	0	ENST00000367921.3:c.2125C>T	p.Arg709Ter	p.R709*	ENST00000367921	NM_006182.2	709	Cga/Tga	16/18	0.508209529535662	3	FACETS	0.615	0.526	0.713	0.308	0.263	0.357	SUBCLONAL	1	FALSE	1	0.508209529535662	3		496	425	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242904	142242904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	80	569	0	ENST00000350721.4:c.4083G>T	p.Leu1361Phe	p.L1361F	ENST00000350721	NM_001184.3	1361	ttG/ttT	22/47	1	2	FACETS	0.753	0.666	0.845	0.753	0.666	0.845	SUBCLONAL	1	FALSE	1	0.508209529535662	2		569	418	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200961	108200961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782310	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	54	428	1	ENST00000278616.4:c.7328G>A	p.Arg2443Gln	p.R2443Q	ENST00000278616	NM_000051.3	2443	cGa/cAa	50/63	1	2	FACETS	0.681	0.585	0.785	0.681	0.585	0.785	SUBCLONAL	1	FALSE	1	0.508209529535662	2		429	312	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820836	36820836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1452017656	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	58	687	1	ENST00000373129.3:c.541G>A	p.Val181Met	p.V181M	ENST00000373129	NM_032017.1	181	Gtg/Atg	6/12	1	2	FACETS	0.732	0.633	0.838	0.732	0.633	0.838	SUBCLONAL	1	FALSE	1	0.508209529535662	2		688	312	SUCCESS
APC	324	MSKCC	GRCh37	5	112173495	112173495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147655929	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	47	350	0	ENST00000257430.4:c.2204C>T	p.Ala735Val	p.A735V	ENST00000257430	NM_000038.5	735	gCg/gTg	16/16	1	2	FACETS	0.864	0.738	1	0.864	0.738	1	CLONAL	1	FALSE	1	0.508209529535662	2		350	214	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197448	26197448	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	29	387	0	ENST00000356476.2:c.31T>C	p.Ser11Pro	p.S11P	ENST00000356476		11	Tcc/Ccc	1/1	0.508209529535662	6	FACETS	0.446	0.357	0.548	0.089	0.071	0.11	SUBCLONAL	1	FALSE	1	0.508209529535662	6		387	516	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285059	15285059	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs367543285	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	130	814	0	ENST00000263388.2:c.4556T>C	p.Leu1519Pro	p.L1519P	ENST00000263388	NM_000435.2	1519	cTg/cCg	25/33	0.508209529535662	3	FACETS	1	0.962	1	0.552	0.503	0.604	CLONAL	1	FALSE	1	0.508209529535662	3		814	581	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041242	112041242	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	56	418	0	ENST00000368678.4:c.13C>T	p.Gln5Ter	p.Q5*	ENST00000368678		5	Caa/Taa	3/13	1	2	FACETS	0.641	0.552	0.737	0.641	0.552	0.737	SUBCLONAL	1	FALSE	1	0.508209529535662	2		418	344	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233024	55233024	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144943614	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	59	598	1	ENST00000275493.2:c.1774G>A	p.Val592Ile	p.V592I	ENST00000275493	NM_005228.3	592	Gtc/Atc	15/28	1	2	FACETS	0.673	0.582	0.771	0.673	0.582	0.771	SUBCLONAL	1	FALSE	1	0.508209529535662	2		599	345	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186757	108186757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs864622251	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	54	551	0	ENST00000278616.4:c.6115G>A	p.Glu2039Lys	p.E2039K	ENST00000278616	NM_000051.3	2039	Gaa/Aaa	42/63	1	2	FACETS	0.781	0.673	0.898	0.781	0.673	0.898	SUBCLONAL	1	FALSE	1	0.508209529535662	2		551	272	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866710	37866710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258412021	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	145	839	2	ENST00000269571.5:c.877G>A	p.Ala293Thr	p.A293T	ENST00000269571		293	Gcc/Acc	7/27	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	1	0.508209529535662	2		841	540	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349964	15349964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1411701353	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	65	849	2	ENST00000263377.2:c.3688G>A	p.Ala1230Thr	p.A1230T	ENST00000263377	NM_058243.2	1230	Gcc/Acc	18/20	0.508209529535662	3	FACETS	0.571	0.495	0.653	0.285	0.247	0.327	SUBCLONAL	1	FALSE	1	0.508209529535662	3		851	562	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258595	19258595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377026490	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	118	903	3	ENST00000162023.5:c.305C>T	p.Pro102Leu	p.P102L	ENST00000162023		102	cCg/cTg	8/13	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	FALSE	1	0.508209529535662	2		906	450	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11019828	11019828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	118	711	0	ENST00000327064.4:c.503G>A	p.Arg168Gln	p.R168Q	ENST00000327064	NM_199141.1	168	cGg/cAg	4/16	0.508209529535662	3	FACETS	1	0.923	1	0.511	0.462	0.562	CLONAL	1	FALSE	1	0.508209529535662	3		711	570	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514775	103514775	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603745	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	24	500	1	ENST00000355739.4:c.1276G>A	p.Glu426Lys	p.E426K	ENST00000355739	NM_000123.3	426	Gag/Aag	8/15	0.154021330632408	4	FACETS	0.493	0.387	0.615	0.246	0.193	0.308	INDETERMINATE	1	FALSE	2	0.508209529535662	4		501	289	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420670	49420670	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs797045659	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	97	721	0	ENST00000301067.7:c.15079C>T	p.Arg5027Ter	p.R5027*	ENST00000301067	NM_003482.3	5027	Cga/Tga	48/54	0.45501973939108	4	FACETS	1	0.943	1	0.541	0.484	0.602	CLONAL	1	FALSE	2	0.508209529535662	4		721	532	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928292	69928292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752026814	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	102	510	1	ENST00000352241.4:c.112G>A	p.Ala38Thr	p.A38T	ENST00000352241	NM_198159.2	38	Gcc/Acc	2/10	1	2	FACETS	0.963	0.867	1	0.963	0.867	1	CLONAL	1	FALSE	1	0.508209529535662	2		511	417	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433388	49433388	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555191598	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	86	839	0	ENST00000301067.7:c.8059C>T	p.Arg2687Ter	p.R2687*	ENST00000301067	NM_003482.3	2687	Cga/Tga	32/54	0.45501973939108	4	FACETS	1	0.929	1	0.532	0.472	0.595	CLONAL	1	FALSE	2	0.508209529535662	4		839	480	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602443	10602443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1321752702	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	119	766	2	ENST00000171111.5:c.1135G>A	p.Gly379Ser	p.G379S	ENST00000171111	NM_203500.1	379	Ggc/Agc	3/6	0.508209529535662	3	FACETS	0.919	0.831	1	0.46	0.415	0.506	CLONAL	1	FALSE	1	0.508209529535662	3		768	639	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416115	49416115	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs267607239	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	210	560	1	ENST00000301067.7:c.16360C>T	p.Arg5454Ter	p.R5454*	ENST00000301067	NM_003482.3	5454	Cga/Tga	52/54	0.45501973939108	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	FALSE	2	0.508209529535662	4		561	527	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56857716	56857716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370111038	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	80	605	0	ENST00000308159.5:c.752G>A	p.Arg251His	p.R251H	ENST00000308159	NM_014669.4	251	cGc/cAc	8/22	0.146640708906831	0	FACETS	0.406	0.36	0.456			1	INDETERMINATE	1	FALSE	0	0.508209529535662	0		605	381	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455533	189455533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144315591	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	73	504	0	ENST00000264731.3:c.67G>A	p.Val23Ile	p.V23I	ENST00000264731	NM_003722.4	23	Gta/Ata	2/14	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	1	0.508209529535662	2		504	269	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521177	187521177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778434346	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	82	681	0	ENST00000441802.2:c.11978C>T	p.Pro3993Leu	p.P3993L	ENST00000441802	NM_005245.3	3993	cCc/cTc	22/27	1	2	FACETS	0.865	0.768	0.968	0.865	0.768	0.968	CLONAL	1	FALSE	1	0.508209529535662	2		681	373	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526271	31526271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545917535	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	140	959	1	ENST00000344624.3:c.769G>A	p.Asp257Asn	p.D257N	ENST00000344624		257	Gac/Aac	2/33	0.293239746625843	0	FACETS	0.465	0.425	0.506			1	INDETERMINATE	1	FALSE	0	0.508209529535662	0		960	583	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190873	185190873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144909413	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	40	907	1	ENST00000265026.3:c.1754G>A	p.Arg585Gln	p.R585Q	ENST00000265026	NM_004721.4	585	cGa/cAa	11/14	1	2	FACETS	0.345	0.287	0.41	0.345	0.287	0.41	SUBCLONAL	1	FALSE	1	0.508209529535662	2		908	456	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59871074	59871074	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780227	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	47	370	0	ENST00000259008.2:c.1357G>A	p.Ala453Thr	p.A453T	ENST00000259008	NM_032043.2	453	Gct/Act	10/20	1	2	FACETS	0.811	0.691	0.94	0.811	0.691	0.94	CLONAL	1	FALSE	1	0.508209529535662	2		370	228	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100143	30100143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs191202207	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	94	740	0	ENST00000331968.5:c.1477G>A	p.Glu493Lys	p.E493K	ENST00000331968	NM_002742.2	493	Gaa/Aaa	10/18	1	2	FACETS	0.877	0.785	0.973	0.877	0.785	0.973	CLONAL	1	FALSE	1	0.508209529535662	2		740	422	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568635	41568635	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1569118537	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	62	466	0	ENST00000263253.7:c.4585C>T	p.Arg1529Ter	p.R1529*	ENST00000263253	NM_001429.3	1529	Cga/Tga	28/31	1	2	FACETS	0.928	0.81	1	0.928	0.81	1	CLONAL	1	FALSE	1	0.508209529535662	2		466	263	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7168037	7168037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866529817	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	116	696	2	ENST00000302850.5:c.1552C>T	p.Pro518Ser	p.P518S	ENST00000302850	NM_000208.2	518	Ccg/Tcg	7/22	1	2	FACETS	0.685	0.619	0.756	0.685	0.619	0.756	SUBCLONAL	1	FALSE	1	0.508209529535662	2		698	666	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553308	41553308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1203250209	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	58	672	0	ENST00000263253.7:c.3397C>T	p.Arg1133Trp	p.R1133W	ENST00000263253	NM_001429.3	1133	Cgg/Tgg	18/31	1	2	FACETS	0.716	0.619	0.82	0.716	0.619	0.82	SUBCLONAL	1	FALSE	1	0.508209529535662	2		672	319	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752347	55752347	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1485302383	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	44	793	1	ENST00000284073.2:c.805C>T	p.Arg269Trp	p.R269W	ENST00000284073	NM_138962.2	269	Cgg/Tgg	12/14	1	2	FACETS	0.424	0.356	0.5	0.424	0.356	0.5	SUBCLONAL	1	FALSE	1	0.508209529535662	2		794	408	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262663	16262663	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747459170	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	74	529	1	ENST00000375759.3:c.9928G>A	p.Asp3310Asn	p.D3310N	ENST00000375759	NM_015001.2	3310	Gac/Aac	11/15	1	2	FACETS	0.971	0.858	1	0.971	0.858	1	CLONAL	1	FALSE	1	0.508209529535662	2		530	300	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65311209	65311209	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs117679986	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	47	513	0	ENST00000342505.4:c.2102C>T	p.Ala701Val	p.A701V	ENST00000342505	NM_002227.2	701	gCc/gTc	15/25	1	2	FACETS	0.755	0.643	0.876	0.755	0.643	0.876	SUBCLONAL	1	FALSE	1	0.508209529535662	2		513	245	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325882	65325882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1490560356	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	60	639	1	ENST00000342505.4:c.1240C>T	p.Arg414Trp	p.R414W	ENST00000342505	NM_002227.2	414	Cgg/Tgg	9/25	1	2	FACETS	0.694	0.602	0.794	0.694	0.602	0.794	SUBCLONAL	1	FALSE	1	0.508209529535662	2		640	340	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846355	156846355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775718859	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	231	781	2	ENST00000524377.1:c.1796G>A	p.Arg599His	p.R599H	ENST00000524377	NM_002529.3	599	cGc/cAc	14/17	0.508209529535662	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	FALSE	1	0.508209529535662	3		783	462	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348808	118348808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1131691799	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	68	407	0	ENST00000534358.1:c.3461G>A	p.Arg1154Gln	p.R1154Q	ENST00000534358	NM_005933.3	1154	cGg/cAg	5/36	1	2	FACETS	0.847	0.743	0.958	0.847	0.743	0.958	CLONAL	1	FALSE	1	0.508209529535662	2		407	316	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719895	18719895	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	61	495	0	ENST00000266497.5:c.3792G>A	p.Trp1264Ter	p.W1264*	ENST00000266497		1264	tgG/tgA	27/31	0.45501973939108	4	FACETS	1	0.906	1	0.528	0.458	0.603	CLONAL	1	FALSE	2	0.508209529535662	4		495	343	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918750	32918750	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	51	290	0	ENST00000380152.3:c.6897T>A	p.Asn2299Lys	p.N2299K	ENST00000380152		2299	aaT/aaA	12/27	0.154021330632408	4	FACETS	1	0.96	1	0.682	0.586	0.784	INDETERMINATE	1	FALSE	2	0.508209529535662	4		290	222	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370284	40370284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	95	876	0	ENST00000293328.3:c.1054G>A	p.Val352Met	p.V352M	ENST00000293328	NM_012448.3	352	Gtg/Atg	9/19	1	2	FACETS	0.836	0.749	0.929	0.836	0.749	0.929	CLONAL	1	FALSE	1	0.508209529535662	2		876	447	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250809	10250809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	95	793	2	ENST00000340748.4:c.3671C>T	p.Pro1224Leu	p.P1224L	ENST00000340748		1224	cCg/cTg	32/40	0.508209529535662	3	FACETS	0.919	0.822	1	0.46	0.411	0.512	CLONAL	1	FALSE	1	0.508209529535662	3		795	510	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11027439	11027439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	269	828	0	ENST00000327064.4:c.1006C>T	p.Arg336Trp	p.R336W	ENST00000327064	NM_199141.1	336	Cgg/Tgg	8/16	0.508209529535662	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	FALSE	1	0.508209529535662	3		828	597	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030692	48030693	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	rs267608092	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	64	511	0	ENST00000234420.5:c.3311_3312del	p.Phe1104TrpfsTer3	p.F1104Wfs*3	ENST00000234420	NM_000179.2	1102	acTTtt/actt	5/10	1	2	FACETS	0.84	0.733	0.953	0.84	0.733	0.953	CLONAL	1	FALSE	1	0.508209529535662	2		511	300	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539294	187539294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	49	527	0	ENST00000441802.2:c.8446G>A	p.Ala2816Thr	p.A2816T	ENST00000441802	NM_005245.3	2816	Gca/Aca	10/27	1	2	FACETS	0.817	0.699	0.944	0.817	0.699	0.944	CLONAL	1	FALSE	1	0.508209529535662	2		527	236	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407587	407587	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	116	373	0	ENST00000380956.4:c.1345A>G	p.Ile449Val	p.I449V	ENST00000380956	NM_001195286.1	449	Att/Gtt	9/9	0.508209529535662	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	0	0.508209529535662	1		373	237	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841838	151841838	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	61	416	0	ENST00000262189.6:c.14303A>G	p.Glu4768Gly	p.E4768G	ENST00000262189	NM_170606.2	4768	gAa/gGa	55/59	1	2	FACETS	0.941	0.821	1	0.941	0.821	1	CLONAL	1	FALSE	1	0.508209529535662	2		416	255	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942801	44942829	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCATGAACACAGTTCAACTATACATGA	GGGCATGAACACAGTTCAACTATACATGA	-	novel	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	78	351	0	ENST00000377967.4:c.3381_3409del	p.Gly1128SerfsTer13	p.G1128Sfs*13	ENST00000377967	NM_021140.2	1127	ttGGGCATGAACACAGTTCAACTATACATGAaa/ttaa	23/29	1	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	0	0.508209529535662	1		351	174	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55693418	55693418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769598215	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	93	798	3	ENST00000284073.2:c.625G>A	p.Ala209Thr	p.A209T	ENST00000284073	NM_138962.2	209	Gcg/Acg	9/14	1	2	FACETS	0.784	0.7	0.872	0.784	0.7	0.872	SUBCLONAL	1	FALSE	1	0.508209529535662	2		801	467	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843577	156843577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	61	815	1	ENST00000524377.1:c.1003C>T	p.Pro335Ser	p.P335S	ENST00000524377	NM_002529.3	335	Ccg/Tcg	8/17	0.508209529535662	3	FACETS	0.482	0.415	0.554	0.241	0.207	0.277	SUBCLONAL	1	FALSE	1	0.508209529535662	3		816	625	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219092	133219092	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	43	754	0	ENST00000320574.5:c.4952G>T	p.Arg1651Met	p.R1651M	ENST00000320574	NM_006231.2	1651	aGg/aTg	37/49	0.205465173269331	2	FACETS	0.59	0.496	0.692	0.295	0.248	0.346	INDETERMINATE	1	FALSE	0	0.508209529535662	2		754	287	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110408657	110408657	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	24	371	0	ENST00000375856.3:c.4013-2A>T		p.X1338_splice	ENST00000375856	NM_003749.2	1338			0.154021330632408	4	FACETS	0.663	0.522	0.823	0.331	0.261	0.412	INDETERMINATE	1	FALSE	2	0.508209529535662	4		371	215	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110129	8110129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746973523	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	142	629	0	ENST00000585124.1:c.476G>A	p.Arg159His	p.R159H	ENST00000585124	NM_004217.3	159	cGc/cAc	6/9	1	2	FACETS	0.861	0.787	0.938	0.861	0.787	0.938	CLONAL	1	FALSE	1	0.508209529535662	2		629	649	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191039	2191039	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	44	504	0	ENST00000398665.3:c.293T>C	p.Leu98Pro	p.L98P	ENST00000398665	NM_032482.2	98	cTg/cCg	5/28	1	2	FACETS	0.589	0.496	0.69	0.589	0.496	0.69	SUBCLONAL	1	FALSE	1	0.508209529535662	2		504	294	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246473	10246473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	52	865	1	ENST00000340748.4:c.4664G>A	p.Arg1555His	p.R1555H	ENST00000340748		1555	cGc/cAc	38/40	0.508209529535662	3	FACETS	0.575	0.491	0.668	0.288	0.245	0.334	SUBCLONAL	1	FALSE	1	0.508209529535662	3		866	446	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218353	36218353	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	110	872	0	ENST00000222270.7:c.4132A>G	p.Ile1378Val	p.I1378V	ENST00000222270	NM_014727.1	1378	Atc/Gtc	16/37	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	FALSE	1	0.508209529535662	2		872	424	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467925	50467925	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	53	619	0	ENST00000331340.3:c.1160A>G	p.Glu387Gly	p.E387G	ENST00000331340	NM_006060.4	387	gAg/gGg	8/8	1	2	FACETS	0.719	0.618	0.829	0.719	0.618	0.829	SUBCLONAL	1	FALSE	1	0.508209529535662	2		619	290	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411305	63411305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	17	417	0	ENST00000330258.3:c.1862G>A	p.Arg621Lys	p.R621K	ENST00000330258	NM_152424.3	621	aGg/aAg	2/2	1	1	FACETS	0.312	0.234	0.403	0.312	0.234	0.403	SUBCLONAL	1	FALSE	0	0.508209529535662	1		417	160	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0044470-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	265	357	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.403688772377248	5	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.403688772377248	5		357	879	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0044470-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	421	684	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.169863936819708	4	FACETS	1	0.992	1	0.59	0.562	0.618	INDETERMINATE	2	TRUE	0	0.403688772377248	4		684	1241	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435386	56435386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372159496	NA	P-0044470-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	244	799	0	ENST00000407977.2:c.1751G>A	p.Arg584Gln	p.R584Q	ENST00000407977		584	cGg/cAg	9/10	0.358993289602402	3	FACETS	1	0.97	1	0.535	0.499	0.573	CLONAL	1	TRUE	1	0.403688772377248	3		799	1357	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981298	201981298	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044470-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	110	665	0	ENST00000359651.3:c.377G>C	p.Arg126Pro	p.R126P	ENST00000359651		126	cGa/cCa	2/8	0.403688772377248	2	FACETS	0.443	0.396	0.492	0.221	0.198	0.246	SUBCLONAL	1	TRUE	0	0.403688772377248	2		665	1231	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804367	46804367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1187061907	NA	P-0044470-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	208	593	0	ENST00000290295.7:c.640C>T	p.Arg214Cys	p.R214C	ENST00000290295	NM_006361.5	214	Cgt/Tgt	2/2	0.358993289602402	3	FACETS	1	0.982	1	0.591	0.549	0.636	CLONAL	1	TRUE	1	0.403688772377248	3		593	1047	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492853	56492853	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044470-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	149	484	0	ENST00000407977.2:c.86del	p.Gly29AspfsTer22	p.G29Dfs*22	ENST00000407977		29	gGa/ga	2/10	0.358993289602402	3	FACETS	1	0.914	1	0.5	0.457	0.546	CLONAL	1	TRUE	1	0.403688772377248	3		484	887	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633382	8633382	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044470-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	119	433	0	ENST00000356435.5:c.287A>T	p.Tyr96Phe	p.Y96F	ENST00000356435		96	tAt/tTt	3/35	0.403688772377248	2	FACETS	0.84	0.759	0.925	0.42	0.379	0.463	CLONAL	1	TRUE	0	0.403688772377248	2		433	702	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348848	89348849	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0044470-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	70	722	0	ENST00000301030.4:c.4101_4102del	p.Lys1368ArgfsTer17	p.K1368Rfs*17	ENST00000301030	NM_001256183.1	1367	aaGAaa/aaaa	9/13	0.211585850487511	1	FACETS	0.25	0.217	0.286	0.25	0.217	0.286	INDETERMINATE	1	TRUE	0	0.403688772377248	1		722	1106	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044491-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	348	427	0				ENST00000310581	NM_198253.2	-/1132			0.630588927978446	4	FACETS	0.901	0.863	0.938	0.901	0.863	0.938	CLONAL	3	TRUE	1	0.736854914950284	4		427	607	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0044491-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	591	667	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.709161724565551	3	FACETS	0.938	0.915	0.961	0.938	0.915	0.961	CLONAL	3	TRUE	0	0.736854914950284	3		667	780	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044491-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	361	494	0	ENST00000335508.6:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000335508	NM_012433.2	902	Gaa/Aaa	18/25	0.672752728239529	2	FACETS	0.894	0.861	0.926	0.894	0.861	0.926	CLONAL	2	TRUE	0	0.736854914950284	2		494	548	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057835	27057835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044491-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	585	869	0	ENST00000324856.7:c.1543C>T	p.Gln515Ter	p.Q515*	ENST00000324856	NM_006015.4	515	Cag/Tag	3/20	0.124557469446647	5	FACETS	0.883	0.851	0.915			1	INDETERMINATE	3	TRUE	NA	0.736854914950284	5		869	1262	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50784085	50784085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044491-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	98	606	0	ENST00000398568.2:c.476C>T	p.Ser159Phe	p.S159F	ENST00000398568	NM_001042412.1	159	tCc/tTc	3/18	0.246578881970379	2	FACETS	0.326	0.29	0.364	0.163	0.145	0.182	INDETERMINATE	1	TRUE	0	0.736854914950284	2		606	817	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632513	3632513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs973283650	NA	P-0044491-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	310	813	3	ENST00000294008.3:c.5335C>T	p.Arg1779Trp	p.R1779W	ENST00000294008	NM_032444.2	1779	Cgg/Tgg	15/15	0.246578881970379	2	FACETS	0.827	0.78	0.874	0.413	0.39	0.437	INDETERMINATE	1	TRUE	0	0.736854914950284	2		816	1018	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290207	15290207	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144559574	NA	P-0044491-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	466	775	1	ENST00000263388.2:c.3428G>A	p.Arg1143His	p.R1143H	ENST00000263388	NM_000435.2	1143	cGc/cAc	21/33	0.25035691800128	3	FACETS	0.752	0.72	0.784	0.752	0.72	0.784	INDETERMINATE	2	TRUE	1	0.736854914950284	3		776	1151	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057775	27057775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044491-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	612	918	2	ENST00000324856.7:c.1483C>T	p.His495Tyr	p.H495Y	ENST00000324856	NM_006015.4	495	Cat/Tat	3/20	0.124557469446647	5	FACETS	0.886	0.855	0.917			1	INDETERMINATE	3	TRUE	NA	0.736854914950284	5		920	1316	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059213	27059213	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044491-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	368	494	0	ENST00000324856.7:c.1850C>A	p.Ser617Ter	p.S617*	ENST00000324856	NM_006015.4	617	tCa/tAa	4/20	0.124557469446647	5	FACETS	0.892	0.851	0.932			1	INDETERMINATE	3	TRUE	NA	0.736854914950284	5		494	786	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546128	41546128	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377517076	NA	P-0044491-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	361	473	0	ENST00000263253.7:c.2743C>T	p.Arg915Cys	p.R915C	ENST00000263253	NM_001429.3	915	Cgc/Tgc	14/31	0.25125769259001	2	FACETS	1	0.994	1	0.648	0.619	0.678	INDETERMINATE	1	TRUE	0	0.736854914950284	2		473	756	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86676334	86676334	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044491-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	78	244	0	ENST00000274376.6:c.2612G>C	p.Arg871Thr	p.R871T	ENST00000274376	NM_002890.2	871	aGa/aCa	20/25	0.664024224380906	1	FACETS	0.836	0.756	0.916	0.836	0.756	0.916	CLONAL	1	TRUE	0	0.736854914950284	1		244	160	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941877	44941878	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044491-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	217	187	0	ENST00000377967.4:c.3202dup	p.Ser1068PhefsTer3	p.S1068Ffs*3	ENST00000377967	NM_021140.2	1067	-/T	21/29	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.736854914950284	1		187	344	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21623910	21623910	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044491-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	134	100	0	ENST00000421138.2:c.1790C>G	p.Ser597Cys	p.S597C	ENST00000421138		597	tCt/tGt	15/16	0.736854914950284	16	FACETS	0.994	0.904	1			1	CLONAL	3	TRUE	NA	0.736854914950284	16		100	751	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624363	21624363	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044491-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2574	834	409	0	ENST00000421138.2:c.1666A>C	p.Lys556Gln	p.K556Q	ENST00000421138		556	Aaa/Caa	14/16	0.736854914950284	16	FACETS	1	0.98	1			1	CLONAL	4	TRUE	NA	0.736854914950284	16		409	3408	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733204	74733204	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044491-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	62	629	0	ENST00000359995.5:c.39G>C	p.Met13Ile	p.M13I	ENST00000359995	NM_001195427.1	13	atG/atC	1/3	0.262748570244209	4	FACETS	0.242	0.207	0.279	0.121	0.103	0.14	INDETERMINATE	1	TRUE	2	0.736854914950284	4		629	1210	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164750	32164750	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044491-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	125	703	1	ENST00000375023.3:c.5152G>A	p.Glu1718Lys	p.E1718K	ENST00000375023	NM_004557.3	1718	Gaa/Aaa	28/30	NA	2	FACETS	0.285	0.257	0.315			1	INDETERMINATE	1	TRUE	NA	0.736854914950284	2		704	1191	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044554-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	23	427	0				ENST00000310581	NM_198253.2	-/1132			0.235940572152799	0	FACETS	0.745	0.584	0.929			1	CLONAL	1	TRUE	0	0.235940572152799	0		427	200	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0044554-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	38	667	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.959	0.795	1	0.959	0.795	1	CLONAL	1	TRUE	1	0.235940572152799	2		667	336	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0044554-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	96	109	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.153491270979677	4	FACETS	0.774	0.69	0.863	0.774	0.69	0.863	SUBCLONAL	2	TRUE	2	0.235940572152799	4		109	650	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591891	48591891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912581	NA	P-0044554-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	195	428	0	ENST00000342988.3:c.1054G>A	p.Gly352Arg	p.G352R	ENST00000342988	NM_005359.5	352	Gga/Aga	9/12	0.233707938254833	4	FACETS	0.908	0.843	0.975	0.908	0.843	0.975	CLONAL	3	TRUE	1	0.235940572152799	4		428	750	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733044	74733044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044554-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	67	167	0	ENST00000359995.5:c.199G>A	p.Asp67Asn	p.D67N	ENST00000359995	NM_001195427.1	67	Gac/Aac	1/3	0.0892098875572103	3	FACETS	1	0.937	1	0.566	0.492	0.646	INDETERMINATE	1	TRUE	1	0.235940572152799	3		167	561	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741925	162741925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044554-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	79	131	0	ENST00000367921.3:c.1616C>T	p.Ser539Leu	p.S539L	ENST00000367921	NM_006182.2	539	tCa/tTa	13/18	0.173171607622147	3	FACETS	1	0.976	1	0.743	0.655	0.837	CLONAL	1	TRUE	1	0.235940572152799	3		131	504	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478795	56478795	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1425922004	NA	P-0044554-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	87	163	0	ENST00000267101.3:c.251C>G	p.Thr84Arg	p.T84R	ENST00000267101	NM_001982.3	84	aCa/aGa	3/28	0.228171579330717	4	FACETS	1	0.974	1	0.685	0.607	0.769	CLONAL	1	TRUE	2	0.235940572152799	4		163	665	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794460	42794460	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044554-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	106	280	0	ENST00000575354.2:c.1540C>A	p.Pro514Thr	p.P514T	ENST00000575354	NM_015125.3	514	Ccc/Acc	10/20	0.158499830835775	3	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.235940572152799	3		280	724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0044577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	180	803	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.365471614984325	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.365471614984325	1		803	768	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161284210	161284210	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	116	469	0	ENST00000367975.2:c.15G>C	p.Leu5Phe	p.L5F	ENST00000367975	NM_003001.3	5	ttG/ttC	1/6	1	2	FACETS	0.853	0.769	0.942	0.853	0.769	0.942	CLONAL	1	TRUE	1	0.365471614984325	2		469	744	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333347	70333347	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	160	576	0	ENST00000373644.4:c.1252A>T	p.Thr418Ser	p.T418S	ENST00000373644	NM_030625.2	418	Act/Tct	2/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.365471614984325	2		576	795	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419049	419049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044705-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	19	315	0	ENST00000399788.2:c.3298G>A	p.Glu1100Lys	p.E1100K	ENST00000399788	NM_001042603.1	1100	Gaa/Aaa	22/28	NA	2	FACETS	0.191	0.145	0.246			1	INDETERMINATE	1	TRUE	NA	0.525523602702003	2		315	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0044705-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	547	529	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.29603544041296	3	FACETS	0.993	0.954	1	0.993	0.954	1	INDETERMINATE	2	TRUE	1	0.525523602702003	3		529	1324	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249012	55249013	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGTTT	novel	NA	P-0044705-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2528	913	557	0	ENST00000275493.2:c.2310_2311insGGGTTT	p.Asp770_Asn771insGlyPhe	p.D770_N771insGF	ENST00000275493	NM_005228.3	770	-/GGGTTT	20/28	0.525523602702003	5	FACETS	0.903	0.872	0.934	0.602	0.581	0.623	CLONAL	2	TRUE	2	0.525523602702003	5		557	3441	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274133	10274133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs796052542	NA	P-0044705-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4246	1726	617	1	ENST00000330684.3:c.136G>A	p.Val46Met	p.V46M	ENST00000330684	NM_001134407.1	46	Gtg/Atg	2/13	0.527758185839991	5	FACETS	0.983	0.96	1	0.656	0.64	0.672	CLONAL	2	TRUE	2	0.525523602702003	5		618	5972	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044707-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	122	363	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.550799233996118	2		363	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578232	7578232	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0044707-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	246	585	3	ENST00000269305.4:c.617T>A	p.Leu206Ter	p.L206*	ENST00000269305	NM_001126112.2	206	tTg/tAg	6/11	0.535719471210133	1	FACETS	0.979	0.921	1	0.979	0.921	1	CLONAL	1	TRUE	0	0.550799233996118	1		588	661	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271393	26271393	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044707-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	283	594	1	ENST00000305910.3:c.220G>T	p.Glu74Ter	p.E74*	ENST00000305910	NM_003534.2	74	Gaa/Taa	1/1	0.535719471210133	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.550799233996118	1		595	708	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986989	36986990	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	AA	novel	NA	P-0044707-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	678	484	1	ENST00000354822.5:c.699_700delinsTT	p.Gln234Ter	p.Q234*	ENST00000354822	NM_001079668.2	233	acGCag/acTTag	3/3	0.550799233996118	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.550799233996118	3		485	1001	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935516	13935516	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045227-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	45	440	0	ENST00000405192.2:c.1340C>T	p.Pro447Leu	p.P447L	ENST00000405192	NM_001163147.1	447	cCc/cTc	12/12	1	2	FACETS	0.251	0.21	0.295	0.251	0.21	0.295	SUBCLONAL	1	TRUE	1	0.763968034395085	2		440	470	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045949	26045949	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045227-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	236	570	0	ENST00000540144.1:c.311T>G	p.Leu104Arg	p.L104R	ENST00000540144	NM_003531.2	104	cTc/cGc	1/1	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.763968034395085	2		570	612	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0045258-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	238	424	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.073714848409391	3	FACETS	1	0.97	1	1	0.994	1	INDETERMINATE	3	TRUE	1	0.34726706145863	3		424	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0045258-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	163	670	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.34726706145863	2		670	752	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797482	45797482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778538	NA	P-0045258-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	179	901	0	ENST00000450313.1:c.1037C>T	p.Ser346Leu	p.S346L	ENST00000450313	NM_012222.2	346	tCg/tTg	12/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.34726706145863	2		901	866	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971104	21971105	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGT	novel	NA	P-0045258-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	100	561	0	ENST00000304494.5:c.251_253dup	p.Asp84dup	p.D84dup	ENST00000304494	NM_000077.4	84	gct/gACGct	2/3	0.31051937902267	0	FACETS	0.814	0.731	0.901			1	CLONAL	1	TRUE	0	0.34726706145863	0		561	462	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099315	27099316	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	T	novel	NA	P-0045258-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	77	458	0	ENST00000324856.7:c.3552_3553delinsT	p.Val1185LeufsTer21	p.V1185Lfs*21	ENST00000324856	NM_006015.4	1184	tcAGtt/tcTtt	14/20	0.180038918812497	3	FACETS	0.953	0.838	1	0.477	0.419	0.538	INDETERMINATE	1	TRUE	1	0.34726706145863	3		458	546	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0045435-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	17	359	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.161508714383978	1	FACETS	0.867	0.656	1	1	0.919	1	CLONAL	2	FALSE	0	0.163588497524284	1		359	110	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0045435-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	27	610	3	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	0.161508714383978	1	FACETS	0.876	0.704	1	1	0.948	1	CLONAL	2	FALSE	0	0.163588497524284	1		613	173	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0045435-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	22	391	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.161508714383978	1	FACETS	0.95	0.746	1	1	0.942	1	CLONAL	2	FALSE	0	0.163588497524284	1		391	130	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711947	89711947	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1554900615	NA	P-0045435-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	16	557	0	ENST00000371953.3:c.565A>T	p.Arg189Ter	p.R189*	ENST00000371953	NM_000314.4	189	Aga/Tga	6/9	0.142814543121554	3	FACETS	0.814	0.607	1	0.814	0.607	1	CLONAL	2	FALSE	1	0.163588497524284	3		557	130	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717650	89717650	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs1057520900	NA	P-0045435-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	12	605	0	ENST00000371953.3:c.675T>G	p.Tyr225Ter	p.Y225*	ENST00000371953	NM_000314.4	225	taT/taG	7/9	0.142814543121554	3	FACETS	0.767	0.539	1	0.383	0.269	0.523	CLONAL	1	FALSE	1	0.163588497524284	3		605	207	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200720	128200720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867160952	NA	P-0045435-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	9	961	1	ENST00000341105.2:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000341105	NM_032638.4	362	cGa/cAa	5/6	0.161508714383978	1	FACETS	0.23	0.151	0.332	0.23	0.151	0.332	SUBCLONAL	1	FALSE	0	0.163588497524284	1		962	439	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023182	27023188	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGCCG	GGAGCCG	-	novel	NA	P-0045435-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	33	109	0	ENST00000324856.7:c.289_295del	p.Glu97ThrfsTer2	p.E97Tfs*2	ENST00000324856	NM_006015.4	96	gcGGAGCCG/gc	1/20	0.163588497524284	1	FACETS	1	0.871	1	1	0.972	1	CLONAL	3	FALSE	0	0.163588497524284	1		109	117	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	95	687	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.261509415011302	4	FACETS	1	0.963	1	0.596	0.53	0.667	CLONAL	1	TRUE	2	0.24	4		687	823	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	94	405	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.917	1	1	0.987	1	CLONAL	2	TRUE	1	0.24	2		408	382	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	36	790	2	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	0.122635987936675	0	FACETS	0.333	0.273	0.401			1	INDETERMINATE	1	TRUE	0	0.24	0		792	684	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	43	485	2	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	0.122635987936675	0	FACETS	0.515	0.43	0.609			1	INDETERMINATE	1	TRUE	0	0.24	0		487	529	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100728	8100728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs771019738	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	51	585	0	ENST00000346208.3:c.708del	p.Ser237AlafsTer28	p.S237Afs*28	ENST00000346208		234	ttC/tt	3/6	0.122635987936675	0	FACETS	0.575	0.488	0.67			1	INDETERMINATE	1	TRUE	0	0.24	0		585	562	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835781	68835781	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060501215	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	43	463	3	ENST00000261769.5:c.377del	p.Pro126ArgfsTer89	p.P126Rfs*89	ENST00000261769	NM_004360.3	124	cgC/cg	3/16	0.0782087148446676	0	FACETS	0.452	0.378	0.535			1	INDETERMINATE	1	TRUE	0	0.24	0		466	602	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	94	286	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	0.987	0.884	1	1	0.987	1	CLONAL	2	TRUE	1	0.24	2		286	397	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	51	377	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.771	0.655	0.899	0.771	0.655	0.899	SUBCLONAL	1	TRUE	1	0.24	2		379	551	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	91	274	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.868	0.774	0.966	1	0.984	1	CLONAL	2	TRUE	1	0.24	2		275	437	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967305	25967305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766049052	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	46	310	0	ENST00000435504.4:c.1901C>T	p.Ser634Leu	p.S634L	ENST00000435504		634	tCg/tTg	13/13	0.122635987936675	0	FACETS	0.639	0.538	0.75			1	INDETERMINATE	1	TRUE	0	0.24	0		310	456	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198193	185198193	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544421900	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	49	441	1	ENST00000265026.3:c.2675C>T	p.Thr892Met	p.T892M	ENST00000265026	NM_004721.4	892	aCg/aTg	13/14	1	2	FACETS	0.727	0.615	0.849	0.727	0.615	0.849	SUBCLONAL	1	TRUE	1	0.24	2		442	562	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193202211	193202211	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	58	339	0	ENST00000367435.3:c.1247del	p.Gly416AlafsTer12	p.G416Afs*12	ENST00000367435	NM_024529.4	415	Ggg/gg	14/17	1	2	FACETS	0.882	0.758	1	0.882	0.758	1	CLONAL	1	TRUE	1	0.24	2		339	548	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726051	61726052	+	splice_region_variant,intron_variant	Splice_Region	DEL	AA	AA	-	rs372688892	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	30	191	0	ENST00000401558.2:c.591-4_591-3del		p.X197_splice	ENST00000401558	NM_003400.3	197			1	2	FACETS	0.853	0.689	1	0.853	0.689	1	CLONAL	1	TRUE	1	0.24	2		191	293	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805731	32805731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	74	605	0	ENST00000374899.4:c.280G>A	p.Val94Ile	p.V94I	ENST00000374899	NM_018833.2	94	Gtc/Atc	2/12	1	2	FACETS	0.862	0.754	0.979	0.862	0.754	0.979	CLONAL	1	TRUE	1	0.24	2		605	715	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022586	31022586	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	48	417	0	ENST00000375687.4:c.2071C>A	p.Leu691Ile	p.L691I	ENST00000375687	NM_015338.5	691	Cta/Ata	13/13	0.157144816808014	0	FACETS	0.617	0.521	0.721			1	SUBCLONAL	1	TRUE	0	0.24	0		417	493	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223725	53223725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	79	728	1	ENST00000375401.3:c.3634C>T	p.Arg1212Trp	p.R1212W	ENST00000375401	NM_004187.3	1212	Cgg/Tgg	23/26	0.122635987936675	0	FACETS	0.816	0.718	0.921			1	INDETERMINATE	1	TRUE	0	0.24	0		729	613	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471679	120471679	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	40	442	0	ENST00000256646.2:c.3812A>G	p.Asn1271Ser	p.N1271S	ENST00000256646	NM_024408.3	1271	aAc/aGc	23/34	1	2	FACETS	0.714	0.593	0.848	0.714	0.593	0.848	SUBCLONAL	1	TRUE	1	0.24	2		442	467	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610467	215610468	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	31	310	1	ENST00000260947.4:c.1788dup	p.Tyr597IlefsTer3	p.Y597Ifs*3	ENST00000260947	NM_000465.2	596	-/A	8/11	1	2	FACETS	0.608	0.491	0.74	0.608	0.491	0.74	SUBCLONAL	1	TRUE	1	0.24	2		311	425	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032092	10032092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201674066	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	49	456	0	ENST00000330684.3:c.731G>A	p.Arg244His	p.R244H	ENST00000330684	NM_001134407.1	244	cGc/cAc	3/13	0.0782087148446676	0	FACETS	0.828	0.703	0.964			1	INDETERMINATE	1	TRUE	0	0.24	0		456	375	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400312	225400312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768929186	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	39	195	0	ENST00000264414.4:c.311C>T	p.Thr104Met	p.T104M	ENST00000264414	NM_003590.4	104	aCg/aTg	3/16	1	2	FACETS	0.988	0.821	1	0.988	0.821	1	CLONAL	1	TRUE	1	0.24	2		195	329	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923037	39923037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	69	559	1	ENST00000378444.4:c.3671C>T	p.Ala1224Val	p.A1224V	ENST00000378444	NM_001123385.1	1224	gCa/gTa	8/15	0.122635987936675	0	FACETS	0.751	0.654	0.855			1	INDETERMINATE	1	TRUE	0	0.24	0		560	582	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909490	50909490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774130423	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	93	729	0	ENST00000440232.2:c.1294C>T	p.Arg432Trp	p.R432W	ENST00000440232	NM_002691.3	432	Cgg/Tgg	11/27	0.0782087148446676	0	FACETS	0.874	0.777	0.977			1	INDETERMINATE	1	TRUE	0	0.24	0		729	674	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982996	201982998	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	114	628	0	ENST00000359651.3:c.847_849del	p.Leu283del	p.L283del	ENST00000359651		282	aTCCtc/atc	7/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.24	2		628	719	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435258	49435258	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1452715535	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	169	653	1	ENST00000301067.7:c.6295C>T	p.Arg2099Ter	p.R2099*	ENST00000301067	NM_003482.3	2099	Cga/Tga	31/54	0.261509415011302	4	FACETS	0.976	0.897	1	0.976	0.897	1	CLONAL	2	TRUE	2	0.24	4		654	895	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842662	68842662	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	40	559	0	ENST00000261769.5:c.602del	p.Pro201LeufsTer14	p.P201Lfs*14	ENST00000261769	NM_004360.3	200	Ccc/cc	5/16	0.0782087148446676	0	FACETS	0.365	0.302	0.435			1	INDETERMINATE	1	TRUE	0	0.24	0		559	695	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510660	38510660	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	74	563	0	ENST00000254066.5:c.914T>A	p.Leu305His	p.L305H	ENST00000254066	NM_000964.3	305	cTc/cAc	7/9	1	2	FACETS	0.839	0.734	0.953	0.839	0.734	0.953	CLONAL	1	TRUE	1	0.24	2		563	735	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512323	38512324	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	41	532	0	ENST00000254066.5:c.1237dup	p.Met413AsnfsTer33	p.M413Nfs*33	ENST00000254066	NM_000964.3	412	gaa/gAaa	9/9	1	2	FACETS	0.52	0.432	0.618	0.52	0.432	0.618	SUBCLONAL	1	TRUE	1	0.24	2		532	657	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40458406	40458406	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	28	157	0	ENST00000345506.4:c.1621A>G	p.Ser541Gly	p.S541G	ENST00000345506	NM_003152.3	541	Agc/Ggc	14/20	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.24	2		157	188	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117800	70117800	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	27	610	0	ENST00000245479.2:c.270del	p.Met91CysfsTer19	p.M91Cfs*19	ENST00000245479	NM_000346.3	90	Ccc/cc	1/3	1	2	FACETS	0.447	0.355	0.553	0.447	0.355	0.553	SUBCLONAL	1	TRUE	1	0.24	2		610	503	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297973	15297973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770146452	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	35	775	0	ENST00000263388.2:c.1783G>A	p.Gly595Ser	p.G595S	ENST00000263388	NM_000435.2	595	Ggc/Agc	11/33	0.0782087148446676	0	FACETS	0.339	0.277	0.409			1	INDETERMINATE	1	TRUE	0	0.24	0		775	654	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349706	15349711	+	inframe_deletion	In_Frame_Del	DEL	GCTGCT	GCTGCT	-	rs748141481	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	44	652	2	ENST00000263377.2:c.3863_3868del	p.Gln1288_Gln1289del	p.Q1288_Q1289del	ENST00000263377	NM_058243.2	1288	cAGCAGCgc/cgc	19/20	0.0782087148446676	0	FACETS	0.557	0.467	0.657			1	INDETERMINATE	1	TRUE	0	0.24	0		654	500	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103827	209103827	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	55	352	0	ENST00000345146.2:c.1122G>T	p.Lys374Asn	p.K374N	ENST00000345146	NM_005896.2	374	aaG/aaT	9/10	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.24	2		352	457	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675472	30675472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775063662	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	107	657	1	ENST00000376406.3:c.2884G>A	p.Ala962Thr	p.A962T	ENST00000376406	NM_014641.2	962	Gcc/Acc	8/15	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.24	2		658	844	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741892	145741892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757780731	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	94	705	0	ENST00000428558.2:c.611C>T	p.Ala204Val	p.A204V	ENST00000428558	NM_004260.3	204	gCc/gTc	5/22	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.24	2		705	715	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938413	76938413	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	36	434	0	ENST00000373344.5:c.2335del	p.Arg779GlyfsTer24	p.R779Gfs*24	ENST00000373344	NM_000489.3	779	Agg/gg	9/35	0.122635987936675	0	FACETS	0.517	0.425	0.62			1	INDETERMINATE	1	TRUE	0	0.24	0		434	441	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123246905	123246905	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	31	338	1	ENST00000358487.5:c.2020G>A	p.Ala674Thr	p.A674T	ENST00000358487	NM_000141.4	674	Gcc/Acc	15/18	1	2	FACETS	0.773	0.629	0.932	0.773	0.629	0.932	CLONAL	1	FALSE	1	0.369841845163014	2		339	217	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990711	7990711	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	52	516	0	ENST00000319144.4:c.50G>C	p.Gly17Ala	p.G17A	ENST00000319144	NM_001139.2	17	gGa/gCa	1/15	0.195516279772996	3	FACETS	0.715	0.609	0.83	0.238	0.203	0.277	INDETERMINATE	1	FALSE	0	0.369841845163014	3		516	466	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386417	31386417	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	50	572	0	ENST00000328111.2:c.1642G>C	p.Ala548Pro	p.A548P	ENST00000328111	NM_006892.3	548	Gcc/Ccc	15/23	0.199976915268575	3	FACETS	0.655	0.556	0.764	0.328	0.278	0.382	INDETERMINATE	1	FALSE	1	0.369841845163014	3		572	489	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477830	140477844	+	inframe_deletion	In_Frame_Del	DEL	TGAGGTGTAGGTGCT	TGAGGTGTAGGTGCT	-	novel	NA	P-0045710-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	26	363	0	ENST00000288602.6:c.1464_1478del	p.Ala489_Gln493del	p.A489_Q493del	ENST00000288602	NM_004333.4	488	acAGCACCTACACCTCAg/acg	12/18	0.363386323699368	4	FACETS	0.678	0.538	0.838	0.339	0.269	0.419	SUBCLONAL	1	FALSE	2	0.369841845163014	4		363	284	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0045735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	186	239	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.461482104872578	3	FACETS	0.982	0.926	1	0.982	0.926	1	CLONAL	3	TRUE	0	0.484012025801827	3		239	324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs864622237	NA	P-0045735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	245	426	3	ENST00000269305.4:c.700T>C	p.Tyr234His	p.Y234H	ENST00000269305	NM_001126112.2	234	Tac/Cac	7/11	0.480780533942843	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.484012025801827	2		429	488	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639422	3639422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	323	571	1	ENST00000294008.3:c.4217C>T	p.Ser1406Phe	p.S1406F	ENST00000294008	NM_032444.2	1406	tCc/tTc	12/15	0.431366870734312	4	FACETS	0.999	0.946	1	0.999	0.946	1	CLONAL	2	TRUE	2	0.484012025801827	4		572	991	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223292	36223292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749284326	NA	P-0045735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	235	758	8	ENST00000222270.7:c.5842G>A	p.Val1948Ile	p.V1948I	ENST00000222270	NM_014727.1	1948	Gtc/Atc	28/37	0.48461146943379	3	FACETS	1	0.936	1	0.335	0.312	0.359	CLONAL	1	TRUE	0	0.484012025801827	3		766	1200	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176176097	176176097	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	151	555	0	ENST00000367669.3:c.18G>T	p.Gln6His	p.Q6H	ENST00000367669	NM_022457.5	6	caG/caT	1/20	0.417072912837822	3	FACETS	1	0.925	1	0.506	0.463	0.551	CLONAL	1	TRUE	1	0.484012025801827	3		555	766	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222114	5222135	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGCTGGCTGGGCAGTCGCACCT	TGCTGGCTGGGCAGTCGCACCT	-	novel	NA	P-0045735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	176	302	1	ENST00000357368.4:c.3200_3201+20del		p.X1067_splice	ENST00000357368	NM_002850.3	1067		19/38	0.480780533942843	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.484012025801827	2		303	347	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599984	10599984	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	350	668	1	ENST00000171111.5:c.1592T>C	p.Leu531Pro	p.L531P	ENST00000171111	NM_203500.1	531	cTg/cCg	5/6	0.480780533942843	2	FACETS	0.984	0.939	1	0.984	0.939	1	CLONAL	2	TRUE	0	0.484012025801827	2		669	735	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138536	11138536	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	201	446	0	ENST00000358026.2:c.3294del	p.Val1099CysfsTer7	p.V1099Cfs*7	ENST00000358026	NM_001128849.1	1098	Aaa/aa	24/36	0.480780533942843	2	FACETS	0.853	0.798	0.908	0.853	0.798	0.908	CLONAL	2	TRUE	0	0.484012025801827	2		446	487	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050734	5050734	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	101	273	0	ENST00000381652.3:c.517G>T	p.Glu173Ter	p.E173*	ENST00000381652	NM_004972.3	173	Gaa/Taa	6/25	0.455381993673696	2	FACETS	0.831	0.756	0.908	0.831	0.756	0.908	CLONAL	2	TRUE	0	0.484012025801827	2		273	251	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0045807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	22	391	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.350011937585878	1	FACETS	0.622	0.486	0.777	0.622	0.486	0.777	SUBCLONAL	1	TRUE	0	0.365669578816783	1		391	158	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572588	64572588	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	54	1010	0	ENST00000312049.6:c.1268G>A	p.Trp423Ter	p.W423*	ENST00000312049	NM_130799.2	423	tGg/tAg	9/10	0.265136114945635	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	0	0.365669578816783	1		1010	228	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577537	7577538	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0045807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	37	912	1	ENST00000269305.4:c.743_744delinsAA	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGG/cAA	7/11	0.350011937585878	1	FACETS	0.784	0.652	0.928	0.784	0.652	0.928	CLONAL	1	TRUE	0	0.365669578816783	1		913	211	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207064	1207065	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1131690917	NA	P-0045807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	62	1188	0	ENST00000326873.7:c.157dup	p.Asp53GlyfsTer110	p.D53Gfs*110	ENST00000326873	NM_000455.4	51	atg/atGg	1/10	0.365669578816783	1	FACETS	0.93	0.81	1	0.93	0.81	1	CLONAL	1	TRUE	0	0.365669578816783	1		1188	298	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602692	10602692	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	60	1063	1	ENST00000171111.5:c.886del	p.Arg296AlafsTer21	p.R296Afs*21	ENST00000171111	NM_203500.1	296	Cgc/gc	3/6	0.365669578816783	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.365669578816783	1		1064	232	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739392	145739392	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	33	984	0	ENST00000428558.2:c.1978G>C	p.Glu660Gln	p.E660Q	ENST00000428558	NM_004260.3	660	Gaa/Caa	12/22	0.28473794488895	3	FACETS	0.673	0.55	0.812	0.337	0.275	0.406	SUBCLONAL	1	TRUE	1	0.365669578816783	3		984	317	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859702	151859702	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	20	486	0	ENST00000262189.6:c.10960C>T	p.Gln3654Ter	p.Q3654*	ENST00000262189	NM_170606.2	3654	Caa/Taa	43/59	NA	2	FACETS	0.573	0.44	0.726			1	INDETERMINATE	1	TRUE	NA	0.365669578816783	2		486	191	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256591	16256591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	19	638	0	ENST00000375759.3:c.3856G>A	p.Gly1286Arg	p.G1286R	ENST00000375759	NM_015001.2	1286	Ggg/Agg	11/15	0.265136114945635	1	FACETS	0.586	0.448	0.744	0.586	0.448	0.744	SUBCLONAL	1	TRUE	0	0.365669578816783	1		638	145	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832863	3832863	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	20	643	0	ENST00000262367.5:c.1395G>C	p.Gln465His	p.Q465H	ENST00000262367	NM_004380.2	465	caG/caC	6/31	1	2	FACETS	0.493	0.378	0.626	0.493	0.378	0.626	SUBCLONAL	1	TRUE	1	0.365669578816783	2		643	222	SUCCESS
APC	324	MSKCC	GRCh37	5	112174622	112174622	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	12	467	0	ENST00000257430.4:c.3331G>C	p.Glu1111Gln	p.E1111Q	ENST00000257430	NM_000038.5	1111	Gaa/Caa	16/16	0.178874815778701	1	FACETS	0.536	0.381	0.723	0.536	0.381	0.723	INDETERMINATE	1	TRUE	0	0.365669578816783	1		467	100	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665213	138665213	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	29	983	1	ENST00000330315.3:c.352G>T	p.Glu118Ter	p.E118*	ENST00000330315	NM_023067.3	118	Gag/Tag	1/1	1	2	FACETS	0.605	0.488	0.738	0.605	0.488	0.738	SUBCLONAL	1	TRUE	1	0.365669578816783	2		984	262	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742942	17742942	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	18	816	0	ENST00000250003.3:c.850G>C	p.Glu284Gln	p.E284Q	ENST00000250003	NM_002478.4	284	Gag/Cag	3/3	0.265136114945635	1	FACETS	0.428	0.323	0.55	0.428	0.323	0.55	SUBCLONAL	1	TRUE	0	0.365669578816783	1		816	188	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69458693	69458693	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	73	662	0	ENST00000227507.2:c.508G>C	p.Glu170Gln	p.E170Q	ENST00000227507	NM_053056.2	170	Gag/Cag	3/5	0.265136114945635	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.365669578816783	1		662	281	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865426	57865426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	36	1073	1	ENST00000228682.2:c.2903C>T	p.Ser968Leu	p.S968L	ENST00000228682	NM_005269.2	968	tCa/tTa	12/12	1	2	FACETS	0.8	0.662	0.953	0.8	0.662	0.953	CLONAL	1	TRUE	1	0.365669578816783	2		1074	246	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726714	88726714	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	38	567	0	ENST00000360948.2:c.330C>G	p.Ile110Met	p.I110M	ENST00000360948	NM_001012338.2	110	atC/atG	4/19	0.265136114945635	1	FACETS	0.982	0.823	1	0.982	0.823	1	CLONAL	1	TRUE	0	0.365669578816783	1		567	173	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348719	11348719	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs769665959	NA	P-0045807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	27	844	0	ENST00000332029.2:c.617C>G	p.Ser206Cys	p.S206C	ENST00000332029	NM_003745.1	206	tCc/tGc	2/2	1	2	FACETS	0.579	0.462	0.711	0.579	0.462	0.711	SUBCLONAL	1	TRUE	1	0.365669578816783	2		844	255	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221489	36221489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1331677016	NA	P-0045807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	85	1142	0	ENST00000222270.7:c.5248G>A	p.Glu1750Lys	p.E1750K	ENST00000222270	NM_014727.1	1750	Gag/Aag	25/37	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.365669578816783	2		1142	408	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526907	31526907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	48	1005	0	ENST00000344624.3:c.133C>T	p.Gln45Ter	p.Q45*	ENST00000344624		45	Cag/Tag	2/33	0.278792714212605	3	FACETS	1	0.896	1	0.534	0.454	0.62	CLONAL	1	TRUE	1	0.365669578816783	3		1005	291	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679893	30679910	+	inframe_deletion	In_Frame_Del	DEL	TCTGCCCCAGCATCCCCT	TCTGCCCCAGCATCCCCT	-	novel	NA	P-0045807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	80	616	0	ENST00000376406.3:c.1809_1826del	p.Gly604_Glu609del	p.G604_E609del	ENST00000376406	NM_014641.2	603	gaAGGGGATGCTGGGGCAGAg/gag	5/15	0.365669578816783	10	FACETS	1	0.937	1			1	CLONAL	2	TRUE	NA	0.365669578816783	10		616	492	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371791	55371791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045807-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	11	210	0	ENST00000297316.4:c.481G>A	p.Glu161Lys	p.E161K	ENST00000297316	NM_022454.3	161	Gag/Aag	2/2	0.265136114945635	1	FACETS	0.424	0.295	0.582	0.424	0.295	0.582	SUBCLONAL	1	TRUE	0	0.365669578816783	1		210	116	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0045809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	191	494	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.258074853736026	2	FACETS	0.965	0.895	1	0.965	0.895	1	CLONAL	2	TRUE	0	0.26	2		494	761	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0045809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	118	495	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.26	2		495	828	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783730	50783730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	40	488	0	ENST00000398568.2:c.121G>A	p.Val41Ile	p.V41I	ENST00000398568	NM_001042412.1	41	Gta/Ata	3/18	0.114517719000477	4	FACETS	0.498	0.413	0.594	0.249	0.206	0.297	INDETERMINATE	1	TRUE	2	0.26	4		488	778	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79974795	79974795	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	47	508	0	ENST00000265081.6:c.1223C>G	p.Ser408Cys	p.S408C	ENST00000265081	NM_002439.4	408	tCt/tGt	8/24	1	2	FACETS	0.415	0.349	0.489	0.415	0.349	0.489	SUBCLONAL	1	TRUE	1	0.26	2		508	871	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0045810-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	59	357	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.397486042291441	3	FACETS	0.486	0.417	0.561	0.243	0.208	0.281	SUBCLONAL	1	TRUE	1	0.397486042291441	3		357	732	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579536	7579536	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045810-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	128	746	0	ENST00000269305.4:c.151del	p.Glu51AsnfsTer72	p.E51Nfs*72	ENST00000269305	NM_001126112.2	51	Gaa/aa	4/11	1	2	FACETS	0.599	0.541	0.659	0.599	0.541	0.659	SUBCLONAL	1	TRUE	1	0.397486042291441	2		746	1076	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779860	3779860	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045810-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	120	736	0	ENST00000262367.5:c.5188A>T	p.Ile1730Phe	p.I1730F	ENST00000262367	NM_004380.2	1730	Atc/Ttc	31/31	1	2	FACETS	0.56	0.505	0.619	0.56	0.505	0.619	SUBCLONAL	1	TRUE	1	0.397486042291441	2		736	1078	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0045872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	251	593	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.863	0.812	0.916	0.863	0.812	0.916	CLONAL	1	TRUE	1	0.840156102216502	2		593	692	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0045872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	96	232	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.866	0.783	0.95	0.866	0.783	0.95	CLONAL	1	TRUE	1	0.840156102216502	2		233	264	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0045872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	156	361	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.840156102216502	2		361	329	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215787	98215787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376844749	NA	P-0045872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	169	528	0	ENST00000331920.6:c.3422C>T	p.Ala1141Val	p.A1141V	ENST00000331920	NM_000264.3	1141	gCg/gTg	20/24	1	2	FACETS	0.61	0.562	0.658	0.61	0.562	0.658	SUBCLONAL	1	TRUE	1	0.840156102216502	2		528	660	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799060	42799060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	232	848	1	ENST00000575354.2:c.4544G>A	p.Arg1515His	p.R1515H	ENST00000575354	NM_015125.3	1515	cGc/cAc	20/20	0.840156102216502	1	FACETS	0.713	0.674	0.752	0.713	0.674	0.752	SUBCLONAL	1	TRUE	0	0.840156102216502	1		849	449	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344077	70344077	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	257	706	0	ENST00000374080.3:c.1813C>T	p.Arg605Ter	p.R605*	ENST00000374080		605	Cga/Tga	13/45	1	2	FACETS	0.831	0.782	0.881	0.831	0.782	0.881	CLONAL	1	TRUE	1	0.840156102216502	2		706	736	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956553	93956553	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1035177735	NA	P-0045872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	141	318	0	ENST00000369303.4:c.2683C>T	p.Arg895Ter	p.R895*	ENST00000369303	NM_004440.3	895	Cga/Tga	15/17	1	2	FACETS	0.93	0.858	1	0.93	0.858	1	CLONAL	1	TRUE	1	0.840156102216502	2		318	361	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429758	78429758	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	124	242	0	ENST00000370768.2:c.1030C>T	p.Arg344Ter	p.R344*	ENST00000370768	NM_003902.3	344	Cga/Tga	12/20	0.840156102216502	1	FACETS	0.915	0.858	0.971	0.915	0.858	0.971	CLONAL	1	TRUE	0	0.840156102216502	1		242	187	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793386	242793386	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs756100729	NA	P-0045872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	245	820	1	ENST00000334409.5:c.691C>T	p.Arg231Ter	p.R231*	ENST00000334409	NM_005018.2	231	Cga/Tga	5/5	1	2	FACETS	0.877	0.825	0.93	0.877	0.825	0.93	CLONAL	1	TRUE	1	0.840156102216502	2		821	665	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249857	133249857	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1565972665	NA	P-0045872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	124	342	0	ENST00000320574.5:c.1366G>C	p.Ala456Pro	p.A456P	ENST00000320574	NM_006231.2	456	Gcc/Ccc	14/49	1	2	FACETS	0.931	0.855	1	0.931	0.855	1	CLONAL	1	TRUE	1	0.840156102216502	2		342	317	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798242	42798242	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0045872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	78	687	0	ENST00000575354.2:c.4195+1G>A		p.X1399_splice	ENST00000575354	NM_015125.3	1399			0.840156102216502	1	FACETS	0.295	0.261	0.331	0.295	0.261	0.331	SUBCLONAL	1	TRUE	0	0.840156102216502	1		687	365	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096364	2096364	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375615004	NA	P-0045872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	194	640	1	ENST00000219066.1:c.143C>T	p.Ala48Val	p.A48V	ENST00000219066	NM_002528.5	48	gCg/gTg	2/6	1	2	FACETS	0.642	0.596	0.69	0.642	0.596	0.69	SUBCLONAL	1	TRUE	1	0.840156102216502	2		641	719	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279590	123279590	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	200	584	0	ENST00000358487.5:c.842A>C	p.Tyr281Ser	p.Y281S	ENST00000358487	NM_000141.4	281	tAc/tCc	7/18	1	2	FACETS	0.71	0.66	0.76	0.71	0.66	0.76	SUBCLONAL	1	TRUE	1	0.840156102216502	2		584	671	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245618	46245618	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	108	293	0	ENST00000334344.6:c.3712A>G	p.Lys1238Glu	p.K1238E	ENST00000334344	NM_152641.2	1238	Aaa/Gaa	15/21	1	2	FACETS	0.874	0.796	0.955	0.874	0.796	0.955	CLONAL	1	TRUE	1	0.840156102216502	2		293	294	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32932056	32932056	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs41293509	NA	P-0045872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	49	231	0	ENST00000380152.3:c.7795G>T	p.Glu2599Ter	p.E2599*	ENST00000380152		2599	Gaa/Taa	16/27	1	2	FACETS	0.496	0.424	0.574	0.496	0.424	0.574	SUBCLONAL	1	TRUE	1	0.840156102216502	2		231	235	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16097876	16097876	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	54	144	0	ENST00000268712.3:c.8G>T	p.Ser3Ile	p.S3I	ENST00000268712	NM_006311.3	3	aGt/aTt	2/46	1	2	FACETS	0.63	0.546	0.72	0.63	0.546	0.72	SUBCLONAL	1	TRUE	1	0.840156102216502	2		144	204	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948743	17948743	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	213	626	0	ENST00000458235.1:c.1699G>C	p.Glu567Gln	p.E567Q	ENST00000458235	NM_000215.3	567	Gag/Cag	12/24	1	2	FACETS	0.796	0.744	0.849	0.796	0.744	0.849	SUBCLONAL	1	TRUE	1	0.840156102216502	2		626	637	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47061267	47061267	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	172	394	0	ENST00000409792.3:c.7414G>T	p.Glu2472Ter	p.E2472*	ENST00000409792	NM_014159.6	2472	Gaa/Taa	19/21	1	2	FACETS	0.881	0.818	0.944	0.881	0.818	0.944	CLONAL	1	TRUE	1	0.840156102216502	2		394	465	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72866422	72866422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	127	318	0	ENST00000325599.8:c.841G>A	p.Ala281Thr	p.A281T	ENST00000325599	NM_018130.2	281	Gca/Aca	7/11	1	2	FACETS	0.874	0.802	0.948	0.874	0.802	0.948	CLONAL	1	TRUE	1	0.840156102216502	2		318	346	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499459	89499459	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	220	440	0	ENST00000336596.2:c.2629A>C	p.Ile877Leu	p.I877L	ENST00000336596	NM_005233.5	877	Att/Ctt	15/17	1	2	FACETS	0.922	0.865	0.98	0.922	0.865	0.98	CLONAL	1	TRUE	1	0.840156102216502	2		440	568	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587156	189587156	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	175	315	0	ENST00000264731.3:c.1173G>T	p.Lys391Asn	p.K391N	ENST00000264731	NM_003722.4	391	aaG/aaT	9/14	1	2	FACETS	0.89	0.828	0.954	0.89	0.828	0.954	CLONAL	1	TRUE	1	0.840156102216502	2		315	468	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213902	66214232	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGATTGGAATTTTTCCTCCCTAAAATTGAAAAAGATTTAAAAAACTTCCTACATACTTCAAATGTGCCTAGGGACAGTGTTGCCTCACTGAAAAGATCTAGACAGAGATGTAGCATTTTTAAGTGAATCTGTTTGACAGCGCGCAGTGTCTTTTCAAATCTCTCAGCCCATAAGCAGTTGTAGACTACTAATTGGCTGTCTAGAAGGTTTCTAGTTTAAATTCTGTGTGACTACTGAAATACATACAGAAACCACATCTCAATTACAGTCCTCAGTATAGCAGCTCTAAGTAAGGGAAAGCAGGCAGTCAAGCAAACCAATAAGGTATAC	CTGATTGGAATTTTTCCTCCCTAAAATTGAAAAAGATTTAAAAAACTTCCTACATACTTCAAATGTGCCTAGGGACAGTGTTGCCTCACTGAAAAGATCTAGACAGAGATGTAGCATTTTTAAGTGAATCTGTTTGACAGCGCGCAGTGTCTTTTCAAATCTCTCAGCCCATAAGCAGTTGTAGACTACTAATTGGCTGTCTAGAAGGTTTCTAGTTTAAATTCTGTGTGACTACTGAAATACATACAGAAACCACATCTCAATTACAGTCCTCAGTATAGCAGCTCTAAGTAAGGGAAAGCAGGCAGTCAAGCAAACCAATAAGGTATAC	-	novel	NA	P-0045872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	24	336	0	ENST00000273854.3:c.2509-311_2528del		p.X837_splice	ENST00000273854	NM_004439.5	837		15/18	1	2	FACETS	0.152	0.118	0.19	0.152	0.118	0.19	SUBCLONAL	1	TRUE	1	0.840156102216502	2		336	377	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588942	67588942	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	61	237	0	ENST00000274335.5:c.1033G>T	p.Glu345Ter	p.E345*	ENST00000274335		345	Gaa/Taa	8/15	1	2	FACETS	0.745	0.653	0.84	0.745	0.653	0.84	SUBCLONAL	1	TRUE	1	0.840156102216502	2		237	195	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841058	15841058	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	158	532	0	ENST00000307771.7:c.1142G>T	p.Arg381Ile	p.R381I	ENST00000307771	NM_005089.3	381	aGa/aTa	11/11	1	2	FACETS	0.611	0.562	0.661	0.611	0.562	0.661	SUBCLONAL	1	TRUE	1	0.840156102216502	2		532	616	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028862	47028862	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	43	641	0	ENST00000377604.3:c.166G>C	p.Asp56His	p.D56H	ENST00000377604	NM_001204468.1	56	Gac/Cac	3/24	1	2	FACETS	0.156	0.13	0.185	0.156	0.13	0.185	SUBCLONAL	1	TRUE	1	0.840156102216502	2		641	657	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0045898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	93	325	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.176866798469329	1	FACETS	0.666	0.594	0.742	0.666	0.594	0.742	INDETERMINATE	1	TRUE	0	0.429929337807835	1		325	510	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591891	48591891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912581	NA	P-0045898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	135	428	0	ENST00000342988.3:c.1054G>A	p.Gly352Arg	p.G352R	ENST00000342988	NM_005359.5	352	Gga/Aga	9/12	0.390574845399606	1	FACETS	0.892	0.814	0.972	0.892	0.814	0.972	CLONAL	1	TRUE	0	0.429929337807835	1		428	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs886039483	NA	P-0045898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	171	577	0	ENST00000269305.4:c.376T>G	p.Tyr126Asp	p.Y126D	ENST00000269305	NM_001126112.2	126	Tac/Gac	5/11	0.390574845399606	1	FACETS	0.817	0.753	0.884	0.817	0.753	0.884	CLONAL	1	TRUE	0	0.429929337807835	1		577	764	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120460349	120460349	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045898-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	122	437	0	ENST00000256646.2:c.5966A>C	p.Asn1989Thr	p.N1989T	ENST00000256646	NM_024408.3	1989	aAt/aCt	33/34	1	2	FACETS	0.841	0.761	0.924	0.841	0.761	0.924	CLONAL	1	TRUE	1	0.429929337807835	2		437	675	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519998	NA	P-0045941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	557	612	0	ENST00000269305.4:c.581T>A	p.Leu194His	p.L194H	ENST00000269305	NM_001126112.2	194	cTt/cAt	6/11	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.710358940895558	2		612	768	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098953	178098953	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	40	271	0	ENST00000397062.3:c.92G>C	p.Gly31Ala	p.G31A	ENST00000397062	NM_006164.4	31	gGa/gCa	2/5	0.612555945796537	4	FACETS	0.9	0.755	1	0.45	0.377	0.529	CLONAL	1	TRUE	2	0.710358940895558	4		271	214	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749400	43749400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749361637	NA	P-0045941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	80	237	0	ENST00000382044.4:c.1406C>T	p.Ser469Phe	p.S469F	ENST00000382044	NM_001141980.1	469	tCc/tTc	12/28	0.612555945796537	4	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	2	0.710358940895558	4		237	181	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607802	46607802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1367	159	931	0	ENST00000263734.3:c.1991C>T	p.Ala664Val	p.A664V	ENST00000263734	NM_001430.4	664	gCa/gTa	12/16	0.265853949606097	5	FACETS	0.606	0.553	0.661	0.202	0.184	0.221	INDETERMINATE	1	TRUE	2	0.710358940895558	5		931	1526	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710542	40710542	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	375	570	0	ENST00000373198.4:c.4309T>C	p.Ser1437Pro	p.S1437P	ENST00000373198	NM_133170.3	1437	Tcc/Ccc	31/32	0.612555945796537	4	FACETS	0.995	0.949	1	0.995	0.949	1	CLONAL	2	TRUE	2	0.710358940895558	4		570	907	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266906	41266906	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	161	359	0	ENST00000349496.5:c.577C>T	p.Gln193Ter	p.Q193*	ENST00000349496	NM_001904.3	193	Cag/Tag	5/15	0.710358940895558	2	FACETS	0.918	0.866	0.967	0.918	0.866	0.967	CLONAL	2	TRUE	0	0.710358940895558	2		359	247	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867550	35867550	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1434346021	NA	P-0045941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	57	207	0	ENST00000303115.3:c.364G>C	p.Asp122His	p.D122H	ENST00000303115	NM_002185.3	122	Gac/Cac	3/8	0.705867017357963	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	3	TRUE	0	0.710358940895558	3		207	69	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962592	38962592	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	15	148	0	ENST00000357387.3:c.1663C>G	p.Leu555Val	p.L555V	ENST00000357387	NM_152756.3	555	Ctt/Gtt	18/38	0.705867017357963	3	FACETS	0.894	0.671	1	0.298	0.223	0.382	CLONAL	1	TRUE	0	0.710358940895558	3		148	64	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335625	81335625	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	77	336	0	ENST00000222390.5:c.1735C>G	p.Leu579Val	p.L579V	ENST00000222390	NM_000601.4	579	Ctg/Gtg	15/18	0.649614943781458	5	FACETS	0.937	0.835	1	0.625	0.556	0.695	CLONAL	2	TRUE	2	0.710358940895558	5		336	239	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	33	424	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.83	1	1	0.83	1	CLONAL	1	TRUE	1	0.17	2		424	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579362	7579362	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057523496	NA	P-0046062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	68	985	0	ENST00000269305.4:c.325T>G	p.Phe109Val	p.F109V	ENST00000269305	NM_001126112.2	109	Ttc/Gtc	4/11	1	2	FACETS	0.916	0.795	1	0.916	0.795	1	CLONAL	1	TRUE	1	0.17	2		985	873	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603147	48603147	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0046062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	43	459	0	ENST00000342988.3:c.1447+1G>C		p.X483_splice	ENST00000342988	NM_005359.5	483			1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.17	2		459	482	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524698	187524698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367980391	NA	P-0046067-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	34	738	1	ENST00000441802.2:c.10982G>A	p.Arg3661His	p.R3661H	ENST00000441802	NM_005245.3	3661	cGc/cAc	19/27	0.12495297751481	7	FACETS	1	0.88	1	0.185	0.15	0.224	CLONAL	1	FALSE	1	0.12495297751481	7		739	644	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0046068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	53	572	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	FALSE	1	0.383789809664306	2		572	245	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440943	56440943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786205215	NA	P-0046068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	197	800	0	ENST00000407977.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000407977		132	Cga/Tga	4/10	0.383789809664306	2	FACETS	0.835	0.784	0.886	1	0.989	1	CLONAL	3	FALSE	0	0.383789809664306	2		800	410	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286237	66286238	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	39	320	0	ENST00000273854.3:c.1448dup	p.Asn483LysfsTer21	p.N483Kfs*21	ENST00000273854	NM_004439.5	483	aac/aaAc	6/18	1	2	FACETS	0.941	0.787	1	0.941	0.787	1	CLONAL	1	FALSE	1	0.383789809664306	2		320	216	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727451	66727451	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519729	NA	P-0046068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	74	569	0	ENST00000307102.5:c.167A>C	p.Gln56Pro	p.Q56P	ENST00000307102	NM_002755.3	56	cAg/cCg	2/11	1	2	FACETS	0.756	0.671	0.846	1	0.978	1	SUBCLONAL	2	FALSE	1	0.383789809664306	2		569	255	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511578	66511578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	54	404	0	ENST00000358598.2:c.38G>A	p.Arg13His	p.R13H	ENST00000358598	NM_212471.2	13	cGc/cAc	2/11	0.383789809664306	2	FACETS	1	0.897	1	0.525	0.452	0.603	CLONAL	1	FALSE	0	0.383789809664306	2		404	268	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119910	70119910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1297203260	NA	P-0046068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	88	800	2	ENST00000245479.2:c.916del	p.Val306CysfsTer77	p.V306Cfs*77	ENST00000245479	NM_000346.3	304	ccG/cc	3/3	0.383789809664306	2	FACETS	1	0.964	1	0.597	0.533	0.665	CLONAL	1	FALSE	0	0.383789809664306	2		802	384	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740438	58740439	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs758630849	NA	P-0046068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	50	622	0	ENST00000305921.3:c.1349dup	p.Leu450PhefsTer6	p.L450Ffs*6	ENST00000305921	NM_003620.3	448	aat/aaTt	6/6	0.383789809664306	2	FACETS	0.983	0.841	1	0.492	0.42	0.569	CLONAL	1	FALSE	0	0.383789809664306	2		622	265	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432116	121432116	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1565885932	NA	P-0046068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	81	1072	1	ENST00000257555.6:c.863G>C	p.Gly288Ala	p.G288A	ENST00000257555		288	gGg/gCg	4/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	1	0.383789809664306	2		1073	379	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432116	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0046068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	44	1073	0	ENST00000257555.6:c.862_863insC	p.Gly288AlafsTer29	p.G288Afs*29	ENST00000257555		288	ggg/gCgg	4/10	1	2	FACETS	0.605	0.508	0.711	0.605	0.508	0.711	SUBCLONAL	1	FALSE	1	0.383789809664306	2		1073	379	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850750	63850750	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	30	416	0	ENST00000279873.7:c.1528T>C	p.Ser510Pro	p.S510P	ENST00000279873	NM_032199.2	510	Tcc/Ccc	10/10	1	2	FACETS	0.704	0.571	0.853	0.704	0.571	0.853	SUBCLONAL	1	FALSE	1	0.383789809664306	2		416	222	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852365	63852365	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	51	714	0	ENST00000279873.7:c.3143A>C	p.Glu1048Ala	p.E1048A	ENST00000279873	NM_032199.2	1048	gAg/gCg	10/10	1	2	FACETS	0.833	0.712	0.965	0.833	0.712	0.965	CLONAL	1	FALSE	1	0.383789809664306	2		714	319	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114724345	114724345	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	44	515	0	ENST00000543371.1:c.412T>C	p.Ser138Pro	p.S138P	ENST00000543371	NM_001198531.1	138	Tct/Cct	4/14	1	2	FACETS	0.566	0.475	0.666	0.566	0.475	0.666	SUBCLONAL	1	FALSE	1	0.383789809664306	2		515	405	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885877	111885877	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	80	1024	0	ENST00000341259.2:c.1499A>G	p.His500Arg	p.H500R	ENST00000341259	NM_005475.2	500	cAc/cGc	8/8	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	FALSE	1	0.383789809664306	2		1024	415	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915197	32915197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	54	405	0	ENST00000380152.3:c.6705G>A	p.Met2235Ile	p.M2235I	ENST00000380152		2235	atG/atA	11/27	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.383789809664306	2		405	217	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066830	30066830	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	30	594	0	ENST00000331968.5:c.2301G>A	p.Trp767Ter	p.W767*	ENST00000331968	NM_002742.2	767	tgG/tgA	16/18	1	2	FACETS	0.668	0.541	0.81	0.668	0.541	0.81	SUBCLONAL	1	FALSE	1	0.383789809664306	2		594	234	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38641625	38641625	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	43	349	0	ENST00000299084.4:c.585A>G	p.Ile195Met	p.I195M	ENST00000299084	NM_152594.2	195	atA/atG	6/7	1	2	FACETS	0.954	0.805	1	0.954	0.805	1	CLONAL	1	FALSE	1	0.383789809664306	2		349	235	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827890	72827891	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	47	770	0	ENST00000268489.5:c.8690dup	p.Ala2898GlyfsTer6	p.A2898Gfs*6	ENST00000268489	NM_006885.3	2897	ccg/ccCg	9/10	1	2	FACETS	0.783	0.664	0.912	0.783	0.664	0.912	CLONAL	1	FALSE	1	0.383789809664306	2		770	313	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117848	70117848	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs886042523	NA	P-0046068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	87	782	0	ENST00000245479.2:c.316A>G	p.Lys106Glu	p.K106E	ENST00000245479	NM_000346.3	106	Aag/Gag	1/3	0.383789809664306	2	FACETS	1	0.979	1	0.715	0.639	0.794	CLONAL	1	FALSE	0	0.383789809664306	2		782	317	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223140	5223140	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	65	1289	0	ENST00000357368.4:c.2663A>G	p.Asp888Gly	p.D888G	ENST00000357368	NM_002850.3	888	gAc/gGc	18/38	1	2	FACETS	0.847	0.737	0.964	0.847	0.737	0.964	CLONAL	1	FALSE	1	0.383789809664306	2		1289	400	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353818	15353819	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	33	544	2	ENST00000263377.2:c.3061dup	p.His1021ProfsTer72	p.H1021Pfs*72	ENST00000263377	NM_058243.2	1021	cat/cCat	14/20	1	2	FACETS	0.644	0.527	0.775	0.644	0.527	0.775	SUBCLONAL	1	FALSE	1	0.383789809664306	2		546	267	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791040	42791040	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	69	761	0	ENST00000575354.2:c.185C>A	p.Ala62Asp	p.A62D	ENST00000575354	NM_015125.3	62	gCc/gAc	2/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.383789809664306	2		761	292	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994404	25994404	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	49	351	0	ENST00000435504.4:c.409T>C	p.Ser137Pro	p.S137P	ENST00000435504		137	Tcg/Ccg	6/13	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.383789809664306	2		351	200	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288270	21288270	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	85	787	0	ENST00000354336.3:c.515T>C	p.Met172Thr	p.M172T	ENST00000354336	NM_005207.3	172	aTg/aCg	2/3	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	FALSE	1	0.383789809664306	2		787	442	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713876	30713876	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	101	820	0	ENST00000295754.5:c.1201T>C	p.Ser401Pro	p.S401P	ENST00000295754	NM_003242.5	401	Tcc/Ccc	4/7	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.383789809664306	2		820	430	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275719	41275719	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	98	659	0	ENST00000349496.5:c.1614G>C	p.Gln538His	p.Q538H	ENST00000349496	NM_001904.3	538	caG/caC	10/15	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.383789809664306	2		659	398	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323300	31323300	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	17	320	0	ENST00000412585.2:c.689T>C	p.Leu230Pro	p.L230P	ENST00000412585	NM_005514.6	230	cTg/cCg	4/8	1	2	FACETS	0.692	0.522	0.89	0.692	0.522	0.89	SUBCLONAL	1	FALSE	1	0.383789809664306	2		320	128	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419965	152419965	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200128829	NA	P-0046068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	76	782	1	ENST00000206249.3:c.1652C>T	p.Ala551Val	p.A551V	ENST00000206249	NM_000125.3	551	gCg/gTg	8/8	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	FALSE	1	0.383789809664306	2		783	363	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422713	47422713	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	22	770	0	ENST00000377045.4:c.185A>G	p.Tyr62Cys	p.Y62C	ENST00000377045	NM_001654.4	62	tAc/tGc	3/16	0.234190498345115	1	FACETS	0.299	0.231	0.377	0.299	0.231	0.377	SUBCLONAL	1	FALSE	0	0.383789809664306	1		770	310	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323288	31323291	+	missense_variant	Missense_Mutation	ONP	GGGT	GGGT	AGGC	novel	NA	P-0046068-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	33	342	0	ENST00000412585.2:c.698_701delinsGCCT	p.Tyr233_Pro234delinsCysLeu	p.Y233_P234delinsCL	ENST00000412585	NM_005514.6	233	tACCCt/tGCCTt	4/8	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	1	0.383789809664306	2		342	136	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578501	7578518	+	inframe_deletion	In_Frame_Del	DEL	CACAGGGCAGGTCTTGGC	CACAGGGCAGGTCTTGGC	-	novel	NA	P-0046137-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	331	1065	0	ENST00000269305.4:c.412_429del	p.Ala138_Val143del	p.A138_V143del	ENST00000269305	NM_001126112.2	138	GCCAAGACCTGCCCTGTG/-	5/11	0.306595963533456	2	FACETS	0.83	0.784	0.878	0.83	0.784	0.878	CLONAL	2	TRUE	0	0.30830346538396	2		1065	1293	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	41	424	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.898	0.748	1	0.898	0.748	1	CLONAL	1	TRUE	1	0.21	2		424	435	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060499964	NA	P-0046180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	149	925	1	ENST00000326873.7:c.667G>A	p.Glu223Lys	p.E223K	ENST00000326873	NM_000455.4	223	Gag/Aag	5/10	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.21	2		926	1081	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987135	36987135	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	80	840	0	ENST00000354822.5:c.554del	p.Pro185ArgfsTer43	p.P185Rfs*43	ENST00000354822	NM_001079668.2	185	cCg/cg	3/3	1	2	FACETS	0.892	0.784	1	0.892	0.784	1	CLONAL	1	TRUE	1	0.21	2		840	854	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306605	41306605	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	56	758	0	ENST00000373198.4:c.1054C>A	p.Pro352Thr	p.P352T	ENST00000373198	NM_133170.3	352	Ccc/Acc	7/32	1	2	FACETS	0.658	0.563	0.764	0.658	0.563	0.764	SUBCLONAL	1	TRUE	1	0.21	2		758	810	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544093	18544093	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	35	273	0	ENST00000266497.5:c.1910C>A	p.Pro637His	p.P637H	ENST00000266497		637	cCt/cAt	13/31	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.21	2		273	276	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093389	30093389	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs746086535	NA	P-0046180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	48	436	1	ENST00000331968.5:c.1874G>T	p.Ser625Ile	p.S625I	ENST00000331968	NM_002742.2	625	aGc/aTc	13/18	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.21	2		437	455	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968239	2968239	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	90	901	0	ENST00000396946.4:c.1747C>A	p.His583Asn	p.H583N	ENST00000396946	NM_032415.4	583	Cat/Aat	13/25	1	2	FACETS	0.763	0.675	0.858	0.763	0.675	0.858	SUBCLONAL	1	TRUE	1	0.21	2		901	1123	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829747	76829747	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046180-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	62	276	0	ENST00000373344.5:c.6294G>T	p.Trp2098Cys	p.W2098C	ENST00000373344	NM_000489.3	2098	tgG/tgT	28/35	1	1	FACETS	0.826	0.718	0.941	1	0.975	1	CLONAL	2	TRUE	0	0.21	1		276	320	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	78	241	0	ENST00000288602.6:c.1742A>T	p.Asn581Ile	p.N581I	ENST00000288602	NM_004333.4	581	aAt/aTt	15/18	1	2	FACETS	0.917	0.816	1	0.917	0.816	1	CLONAL	1	TRUE	1	0.629797232475618	2		241	270	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610330	10610330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	308	994	0	ENST00000171111.5:c.380G>A	p.Gly127Asp	p.G127D	ENST00000171111	NM_203500.1	127	gGt/gAt	2/6	0.629797232475618	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.629797232475618	1		994	668	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038828	47038828	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	288	934	0	ENST00000377604.3:c.835C>T	p.Gln279Ter	p.Q279*	ENST00000377604	NM_001204468.1	279	Cag/Tag	9/24	0.629797232475618	1	FACETS	0.993	0.942	1	0.993	0.942	1	CLONAL	1	TRUE	0	0.629797232475618	1		934	631	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871632	35871632	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	83	298	1	ENST00000216797.5:c.874del	p.Glu292SerfsTer24	p.E292Sfs*24	ENST00000216797	NM_020529.2	292	Gag/ag	5/6	1	2	FACETS	0.751	0.668	0.838	0.751	0.668	0.838	SUBCLONAL	1	TRUE	1	0.629797232475618	2		299	351	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992625	72992625	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	166	512	0	ENST00000268489.5:c.1420G>T	p.Glu474Ter	p.E474*	ENST00000268489	NM_006885.3	474	Gag/Tag	2/10	1	2	FACETS	0.948	0.876	1	0.948	0.876	1	CLONAL	1	TRUE	1	0.629797232475618	2		512	556	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207118	1207119	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	291	875	0	ENST00000326873.7:c.208dup	p.Glu70GlyfsTer93	p.E70Gfs*93	ENST00000326873	NM_000455.4	69	tcg/tcGg	1/10	0.629797232475618	1	FACETS	0.908	0.86	0.957	0.908	0.86	0.957	CLONAL	1	TRUE	0	0.629797232475618	1		875	697	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867553	35867553	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1435501978	NA	P-0046186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	56	216	0	ENST00000303115.3:c.367C>A	p.Leu123Ile	p.L123I	ENST00000303115	NM_002185.3	123	Cta/Ata	3/8	0.629797232475618	3	FACETS	0.702	0.605	0.807	0.351	0.302	0.404	SUBCLONAL	1	TRUE	1	0.629797232475618	3		216	333	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286533	33286533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	159	423	0	ENST00000374542.5:c.2210C>T	p.Ser737Leu	p.S737L	ENST00000374542	NM_001141970.1	737	tCa/tTa	8/8	1	2	FACETS	0.98	0.905	1	0.98	0.905	1	CLONAL	1	TRUE	1	0.629797232475618	2		423	515	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375970	8375970	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046186-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	91	332	0	ENST00000356435.5:c.4627C>G	p.Pro1543Ala	p.P1543A	ENST00000356435		1543	Cct/Gct	28/35	0.629797232475618	1	FACETS	0.733	0.66	0.809	0.733	0.66	0.809	SUBCLONAL	1	TRUE	0	0.629797232475618	1		332	270	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	77	427	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.838	0.742	0.94			1	INDETERMINATE	1	TRUE	NA	0.54505384299333	2		427	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0046233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	118	670	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.493	0.444	0.545	0.493	0.444	0.545	SUBCLONAL	1	TRUE	1	0.54505384299333	2		670	878	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0046233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	269	561	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.54505384299333	2		561	709	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0046233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	3063	799	0	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.54505384299333	15	FACETS	1	0.998	1			1	CLONAL	13	TRUE	NA	0.54505384299333	15		799	3785	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112176	115112176	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	132	563	1	ENST00000257566.3:c.1564C>A	p.Pro522Thr	p.P522T	ENST00000257566	NM_016569.3	522	Ccc/Acc	7/8	1	2	FACETS	0.892	0.814	0.974	0.892	0.814	0.974	CLONAL	1	TRUE	1	0.54505384299333	2		564	543	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822461	72822464	+	frameshift_variant	Frame_Shift_Del	DEL	CTCA	CTCA	-	novel	NA	P-0046233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	208	844	1	ENST00000268489.5:c.9711_9714del	p.Ser3237ArgfsTer3	p.S3237Rfs*3	ENST00000268489	NM_006885.3	3237	agTGAG/ag	10/10	1	2	FACETS	0.946	0.88	1	0.946	0.88	1	CLONAL	1	TRUE	1	0.54505384299333	2		845	807	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0046301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	11	292	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		292	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0046302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	770	590	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.793533863248181	4	FACETS	0.987	0.971	1	0.987	0.971	1	CLONAL	4	TRUE	0	0.796101467945788	4		590	880	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676236	29676236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	210	219	0	ENST00000356175.3:c.7225G>A	p.Glu2409Lys	p.E2409K	ENST00000356175	NM_000267.3	2409	Gaa/Aaa	48/57	0.777286429625816	2	FACETS	0.865	0.824	0.904	0.865	0.824	0.904	CLONAL	2	TRUE	0	0.796101467945788	2		219	305	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577166	64577166	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	448	641	0	ENST00000312049.6:c.416A>C	p.His139Pro	p.H139P	ENST00000312049	NM_130799.2	139	cAc/cCc	2/10	0.778141560868779	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.796101467945788	2		641	546	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431895	49431895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs988895659	NA	P-0046302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	374	729	0	ENST00000301067.7:c.9244C>T	p.Arg3082Trp	p.R3082W	ENST00000301067	NM_003482.3	3082	Cgg/Tgg	34/54	0.796101467945788	3	FACETS	0.952	0.912	0.991	0.952	0.912	0.991	CLONAL	2	TRUE	1	0.796101467945788	3		729	690	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719215	190719215	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046302-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	390	219	0	ENST00000441310.2:c.1217G>C	p.Cys406Ser	p.C406S	ENST00000441310	NM_000534.4	406	tGt/tCt	9/13	0.796101467945788	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.796101467945788	3		219	453	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0046303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	360	363	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.862696547709992	3	FACETS	0.944	0.92	0.966	0.944	0.92	0.966	CLONAL	3	FALSE	0	0.862696547709992	3		363	422	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781157	135781157	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751247705	NA	P-0046303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	470	608	0	ENST00000298552.3:c.1808C>T	p.Pro603Leu	p.P603L	ENST00000298552	NM_001162426.1	603	cCg/cTg	15/23	0.821926701821338	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	FALSE	0	0.862696547709992	2		608	542	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467885	66467885	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	92	271	0	ENST00000273854.3:c.384A>G	p.Ile128Met	p.I128M	ENST00000273854	NM_004439.5	128	atA/atG	3/18	1	2	FACETS	0.919	0.832	1	0.919	0.832	1	CLONAL	1	FALSE	1	0.862696547709992	2		271	232	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0046303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	395	363	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.601180908196872	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	0	0.601180908196872	3		363	553	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781157	135781157	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751247705	NA	P-0046303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	371	608	0	ENST00000298552.3:c.1808C>T	p.Pro603Leu	p.P603L	ENST00000298552	NM_001162426.1	603	cCg/cTg	15/23	0.597759271770165	2	FACETS	0.994	0.954	1	0.994	0.954	1	CLONAL	2	TRUE	0	0.601180908196872	2		608	621	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467885	66467885	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046303-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	109	271	0	ENST00000273854.3:c.384A>G	p.Ile128Met	p.I128M	ENST00000273854	NM_004439.5	128	atA/atG	3/18	0.24663696495444	3	FACETS	1	0.971	1	0.594	0.538	0.653	INDETERMINATE	1	TRUE	1	0.601180908196872	3		271	397	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0046304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	765	448	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.817613827789938	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.817613827789938	2		448	907	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420108	49420108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs398123729	NA	P-0046304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	439	491	0	ENST00000301067.7:c.15641G>T	p.Arg5214Leu	p.R5214L	ENST00000301067	NM_003482.3	5214	cGc/cTc	48/54	0.817613827789938	3	FACETS	1	0.974	1	0.517	0.492	0.542	CLONAL	1	TRUE	1	0.817613827789938	3		491	1464	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263871	133263871	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	912	287	0	ENST00000320574.5:c.31G>T	p.Ala11Ser	p.A11S	ENST00000320574	NM_006231.2	11	Gcg/Tcg	1/49	0.817613827789938	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	1	0.817613827789938	3		287	1409	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827946	72827946	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	426	586	0	ENST00000268489.5:c.8635G>C	p.Ala2879Pro	p.A2879P	ENST00000268489	NM_006885.3	2879	Gcc/Ccc	9/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.817613827789938	2		586	1001	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89383373	89383373	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	638	665	0	ENST00000301030.4:c.55A>T	p.Ser19Cys	p.S19C	ENST00000301030	NM_001256183.1	19	Agc/Tgc	3/13	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.817613827789938	2		665	1414	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63531788	63531788	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	374	491	0	ENST00000307078.5:c.2193G>T	p.Gln731His	p.Q731H	ENST00000307078	NM_004655.3	731	caG/caT	9/11	0.817613827789938	3	FACETS	0.917	0.87	0.966	0.459	0.435	0.483	CLONAL	1	TRUE	1	0.817613827789938	3		491	1405	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799216	42799216	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1309	852	745	0	ENST00000575354.2:c.4700G>T	p.Gly1567Val	p.G1567V	ENST00000575354	NM_015125.3	1567	gGc/gTc	20/20	0.267420938777085	6	FACETS	0.847	0.82	0.874	0.847	0.82	0.874	INDETERMINATE	3	TRUE	3	0.817613827789938	6		745	2161	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506471	148506471	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	99	232	0	ENST00000320356.2:c.2041G>T	p.Asp681Tyr	p.D681Y	ENST00000320356	NM_004456.4	681	Gat/Tat	18/20	0.723483569018453	3	FACETS	1	0.915	1	0.508	0.458	0.56	CLONAL	1	TRUE	1	0.817613827789938	3		232	336	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110251218	110251218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1435299107	NA	P-0046304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	1604	710	0	ENST00000374672.4:c.119C>T	p.Pro40Leu	p.P40L	ENST00000374672	NM_004235.4	40	cCg/cTg	2/5	0.817613827789938	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	1	0.817613827789938	3		710	2545	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411488	63411488	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1419	477	719	0	ENST00000330258.3:c.1679G>T	p.Arg560Leu	p.R560L	ENST00000330258	NM_152424.3	560	cGg/cTg	2/2	0.817613827789938	3	FACETS	0.867	0.826	0.908	0.433	0.413	0.454	CLONAL	1	TRUE	1	0.817613827789938	3		719	1896	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0046305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	99	325	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.29	2		325	530	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0046305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	37	308	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	0.733	0.606	0.875	0.733	0.606	0.875	SUBCLONAL	1	TRUE	1	0.29	2		308	348	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0046305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	61	510	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.29	2		510	418	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs371769427	NA	P-0046305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	49	235	1	ENST00000291552.4:c.101C>A	p.Ser34Tyr	p.S34Y	ENST00000291552	NM_006758.2	34	tCt/tAt	2/8	1	2	FACETS	0.997	0.848	1	0.997	0.848	1	CLONAL	1	TRUE	1	0.29	2		236	339	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107023	27107023	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	71	498	0	ENST00000324856.7:c.6634C>T	p.Gln2212Ter	p.Q2212*	ENST00000324856	NM_006015.4	2212	Cag/Tag	20/20	1	2	FACETS	0.728	0.635	0.828	0.728	0.635	0.828	SUBCLONAL	1	TRUE	1	0.29	2		498	673	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106539	27106539	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	122	668	0	ENST00000324856.7:c.6150G>A	p.Trp2050Ter	p.W2050*	ENST00000324856	NM_006015.4	2050	tgG/tgA	20/20	1	2	FACETS	0.804	0.725	0.887	0.804	0.725	0.887	CLONAL	1	TRUE	1	0.29	2		668	1047	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487930	56487930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370634710	NA	P-0046305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	42	582	0	ENST00000267101.3:c.1661C>T	p.Pro554Leu	p.P554L	ENST00000267101	NM_001982.3	554	cCg/cTg	14/28	1	2	FACETS	0.386	0.321	0.459	0.386	0.321	0.459	SUBCLONAL	1	TRUE	1	0.29	2		582	750	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466021	69466022	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCACCGACCAAG	novel	NA	P-0046305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	139	866	0	ENST00000227507.2:c.867_868insCAAGCCACCGAC	p.Asp289_Val290insGlnAlaThrAsp	p.D289_V290insQATD	ENST00000227507	NM_053056.2	287	ccc/cCCACCGACCAAGcc	5/5	1	2	FACETS	0.812	0.738	0.891	0.812	0.738	0.891	CLONAL	1	TRUE	1	0.29	2		866	1180	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0046307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	561	654	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.46554497286574	4	FACETS	0.908	0.878	0.938	0.908	0.878	0.938	CLONAL	4	TRUE	0	0.46554497286574	4		654	972	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0046307-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	65	215	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.46554497286574	3	FACETS	1	0.888	1	0.509	0.444	0.579	CLONAL	1	TRUE	1	0.46554497286574	3		215	338	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0046308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	28	181	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.765	0.61	0.942	0.765	0.61	0.942	CLONAL	1	TRUE	1	0.14	2		181	523	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443728	49443728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	52	670	0	ENST00000301067.7:c.3643G>A	p.Asp1215Asn	p.D1215N	ENST00000301067	NM_003482.3	1215	Gat/Aat	11/54	1	2	FACETS	0.802	0.681	0.936	0.802	0.681	0.936	CLONAL	1	TRUE	1	0.14	2		670	926	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270730	10270730	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	37	472	0	ENST00000340748.4:c.1005A>T	p.Lys335Asn	p.K335N	ENST00000340748		335	aaA/aaT	14/40	1	2	FACETS	0.784	0.645	0.941	0.784	0.645	0.941	CLONAL	1	TRUE	1	0.14	2		472	674	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878810	151878825	+	frameshift_variant	Frame_Shift_Del	DEL	AGTCTTAAAAGGTCCA	AGTCTTAAAAGGTCCA	-	novel	NA	P-0046308-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	31	337	0	ENST00000262189.6:c.6120_6135del	p.Gly2041GlnfsTer32	p.G2041Qfs*32	ENST00000262189	NM_170606.2	2040	ccTGGACCTTTTAAGACT/cc	36/59	1	2	FACETS	0.732	0.59	0.893	0.732	0.59	0.893	SUBCLONAL	1	TRUE	1	0.14	2		337	605	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	44	424	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.865	0.73	1	0.865	0.73	1	CLONAL	1	TRUE	1	0.378287587667094	2		424	269	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs967461896	NA	P-0046309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	79	681	0	ENST00000269305.4:c.526T>A	p.Cys176Ser	p.C176S	ENST00000269305	NM_001126112.2	176	Tgc/Agc	5/11	0.378287587667094	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.378287587667094	1		681	320	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335782	73335782	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs767632875	NA	P-0046309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	55	236	0	ENST00000377767.4:c.2511+2T>C		p.X837_splice	ENST00000377767	NM_014953.3	837			0.249176335578265	3	FACETS	1	0.966	1	0.717	0.62	0.821	CLONAL	1	TRUE	1	0.378287587667094	3		236	241	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	20	359	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.27	0.206	0.345	0.27	0.206	0.345	SUBCLONAL	1	TRUE	1	0.389678571630684	2		359	380	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	120	745	12	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	1	2	FACETS	0.848	0.767	0.934	0.848	0.767	0.934	CLONAL	1	TRUE	1	0.389678571630684	2		757	726	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	79	292	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.848	0.748	0.955	0.848	0.748	0.955	CLONAL	1	TRUE	1	0.389678571630684	2		292	478	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	138	267	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	1	0.935	1	1	0.992	1	CLONAL	2	TRUE	1	0.389678571630684	2		267	349	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	174	1071	8	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.896	0.824	0.97	0.896	0.824	0.97	CLONAL	1	TRUE	1	0.389678571630684	2		1079	997	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	184	985	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.389678571630684	2		991	874	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132875	64132875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746182941	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	228	953	0	ENST00000334205.4:c.1009C>T	p.Arg337Trp	p.R337W	ENST00000334205	NM_003942.2	337	Cgg/Tgg	9/17	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.389678571630684	2		953	1083	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437575	56437575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1459309530	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	170	623	0	ENST00000407977.2:c.887G>A	p.Arg296His	p.R296H	ENST00000407977		296	cGt/cAt	8/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.389678571630684	2		623	731	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561764	55561764	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913505	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	94	371	0	ENST00000288135.5:c.154G>A	p.Asp52Asn	p.D52N	ENST00000288135	NM_000222.2	52	Gac/Aac	2/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.389678571630684	2		371	433	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750945	128750945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	101	545	0	ENST00000377970.2:c.482C>T	p.Ser161Leu	p.S161L	ENST00000377970	NM_002467.4	161	tCa/tTa	2/3	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.389678571630684	2		545	518	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681119	117681120	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs748436511	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	87	440	0	ENST00000368508.3:c.3500dup	p.Leu1167PhefsTer26	p.L1167Ffs*26	ENST00000368508	NM_002944.2	1167	tta/ttTa	23/43	1	2	FACETS	0.879	0.781	0.984	0.879	0.781	0.984	CLONAL	1	TRUE	1	0.389678571630684	2		440	508	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341317	89341317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555523386	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	75	327	0	ENST00000301030.4:c.7618C>T	p.Arg2540Trp	p.R2540W	ENST00000301030	NM_001256183.1	2540	Cgg/Tgg	11/13	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.389678571630684	2		327	354	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15821896	15821896	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	66	255	0	ENST00000307771.7:c.294del	p.Lys98AsnfsTer10	p.K98Nfs*10	ENST00000307771	NM_005089.3	97	Aaa/aa	4/11	1	2	FACETS	0.803	0.699	0.914	0.803	0.699	0.914	CLONAL	1	TRUE	1	0.389678571630684	2		255	422	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825519	50825519	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	39	380	0	ENST00000398568.2:c.2156del	p.Asn719MetfsTer13	p.N719Mfs*13	ENST00000398568	NM_001042412.1	717	gAa/ga	14/18	1	2	FACETS	0.487	0.404	0.58	0.487	0.404	0.58	SUBCLONAL	1	TRUE	1	0.389678571630684	2		380	411	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877347	28877347	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	151	468	0	ENST00000282397.4:c.3974del	p.Pro1325GlnfsTer17	p.P1325Qfs*17	ENST00000282397	NM_002019.4	1325	cCa/ca	30/30	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.389678571630684	2		468	767	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	200	553	4	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.389678571630684	2		557	973	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048196	180048196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	214	949	0	ENST00000261937.6:c.2077G>A	p.Asp693Asn	p.D693N	ENST00000261937	NM_182925.4	693	Gac/Aac	14/30	1	2	FACETS	0.976	0.906	1	0.976	0.906	1	CLONAL	1	TRUE	1	0.389678571630684	2		949	1125	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216184	36216184	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	164	806	3	ENST00000222270.7:c.3596del	p.Gly1199AlafsTer156	p.G1199Afs*156	ENST00000222270	NM_014727.1	1198	Ggg/gg	11/37	1	2	FACETS	0.906	0.832	0.984	0.906	0.832	0.984	CLONAL	1	TRUE	1	0.389678571630684	2		809	929	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440951	56440951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777370273	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	154	677	2	ENST00000407977.2:c.386C>T	p.Ala129Val	p.A129V	ENST00000407977		129	gCg/gTg	4/10	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.389678571630684	2		679	753	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738482	145738482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373187237	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	104	941	0	ENST00000428558.2:c.2503G>A	p.Asp835Asn	p.D835N	ENST00000428558	NM_004260.3	835	Gac/Aac	16/22	1	2	FACETS	0.533	0.476	0.593	0.533	0.476	0.593	SUBCLONAL	1	TRUE	1	0.389678571630684	2		941	1002	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936058	71936058	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	10	33	0	ENST00000298229.2:c.35del	p.Gly12AlafsTer15	p.G12Afs*15	ENST00000298229	NM_001567.3	10	ccG/cc	1/28	1	2	FACETS	1	0.752	1	1	0.752	1	CLONAL	1	TRUE	1	0.389678571630684	2		33	47	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007741	45007744	+	frameshift_variant	Frame_Shift_Del	DEL	GAGA	GAGA	-	novel	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	159	348	0	ENST00000558401.1:c.192_195del	p.Arg65LeufsTer37	p.R65Lfs*37	ENST00000558401	NM_004048.2	63	gGAGAg/gg	2/4	0.389242877946015	2	FACETS	0.915	0.847	0.985	0.915	0.847	0.985	CLONAL	2	TRUE	0	0.389678571630684	2		348	446	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554218	63554218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555583417	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	149	594	0	ENST00000307078.5:c.521C>T	p.Ala174Val	p.A174V	ENST00000307078	NM_004655.3	174	gCg/gTg	2/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.389678571630684	2		594	701	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78933909	78933909	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1342049284	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	165	796	1	ENST00000306801.3:c.3509C>T	p.Thr1170Met	p.T1170M	ENST00000306801	NM_020761.2	1170	aCg/aTg	30/34	1	2	FACETS	0.965	0.886	1	0.965	0.886	1	CLONAL	1	TRUE	1	0.389678571630684	2		797	878	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939496	76939496	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057523785	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	124	558	0	ENST00000373344.5:c.1252C>T	p.Arg418Ter	p.R418*	ENST00000373344	NM_000489.3	418	Cga/Tga	9/35	1	2	FACETS	0.956	0.866	1	0.956	0.866	1	CLONAL	1	TRUE	1	0.389678571630684	2		558	666	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437530	56437531	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	196	662	0	ENST00000407977.2:c.931dup	p.Leu311ProfsTer132	p.L311Pfs*132	ENST00000407977		311	ctc/cCtc	8/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.389678571630684	2		662	896	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325173	39325178	+	inframe_deletion	In_Frame_Del	DEL	CCTGCC	CCTGCC	-	novel	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	70	745	0	ENST00000373001.3:c.141_146del	p.Ala48_Gly49del	p.A48_G49del	ENST00000373001	NM_022157.3	47	ggGGCAGGc/ggc	1/7	1	2	FACETS	0.44	0.382	0.502	0.44	0.382	0.502	SUBCLONAL	1	TRUE	1	0.389678571630684	2		745	817	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625284	69625284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782801923	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	205	984	2	ENST00000334134.2:c.509G>A	p.Arg170His	p.R170H	ENST00000334134	NM_005247.2	170	cGc/cAc	3/3	1	2	FACETS	0.991	0.918	1	0.991	0.918	1	CLONAL	1	TRUE	1	0.389678571630684	2		986	1062	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434903	49434903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1201197190	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	152	911	0	ENST00000301067.7:c.6650G>A	p.Arg2217His	p.R2217H	ENST00000301067	NM_003482.3	2217	cGt/cAt	31/54	1	2	FACETS	0.908	0.831	0.989	0.908	0.831	0.989	CLONAL	1	TRUE	1	0.389678571630684	2		911	859	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869504	102869504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	143	492	0	ENST00000307046.8:c.137C>T	p.Ala46Val	p.A46V	ENST00000307046	NM_001111285.1	46	gCc/gTc	2/4	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.389678571630684	2		492	630	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28901621	28901621	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	66	354	0	ENST00000282397.4:c.2774G>A	p.Arg925His	p.R925H	ENST00000282397	NM_002019.4	925	cGt/cAt	20/30	1	2	FACETS	0.807	0.703	0.918	0.807	0.703	0.918	CLONAL	1	TRUE	1	0.389678571630684	2		354	420	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483923	88483923	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	323	711	0	ENST00000360948.2:c.1647T>A	p.Phe549Leu	p.F549L	ENST00000360948	NM_001012338.2	549	ttT/ttA	14/19	0.389242877946015	2	FACETS	0.972	0.921	1	0.972	0.921	1	CLONAL	2	TRUE	0	0.389678571630684	2		711	853	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900825	3900825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200673670	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	137	623	0	ENST00000262367.5:c.271G>A	p.Ala91Thr	p.A91T	ENST00000262367	NM_004380.2	91	Gcc/Acc	2/31	1	2	FACETS	0.928	0.845	1	0.928	0.845	1	CLONAL	1	TRUE	1	0.389678571630684	2		623	758	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78820312	78820312	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	53	826	0	ENST00000306801.3:c.1252G>A	p.Val418Met	p.V418M	ENST00000306801	NM_020761.2	418	Gtg/Atg	11/34	1	2	FACETS	0.259	0.22	0.302	0.259	0.22	0.302	SUBCLONAL	1	TRUE	1	0.389678571630684	2		826	1051	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272291	15272291	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	232	929	0	ENST00000263388.2:c.6148C>A	p.Leu2050Ile	p.L2050I	ENST00000263388	NM_000435.2	2050	Ctc/Atc	33/33	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.389678571630684	2		929	1007	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945416	17945416	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	162	705	1	ENST00000458235.1:c.2314G>A	p.Ala772Thr	p.A772T	ENST00000458235	NM_000215.3	772	Gcc/Acc	17/24	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.389678571630684	2		706	779	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955088	17955088	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	244	938	1	ENST00000458235.1:c.139del	p.Asp47ThrfsTer100	p.D47Tfs*100	ENST00000458235	NM_000215.3	47	Gac/ac	2/24	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.389678571630684	2		939	1097	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794926	42794926	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	176	879	1	ENST00000575354.2:c.2006C>A	p.Ala669Asp	p.A669D	ENST00000575354	NM_015125.3	669	gCc/gAc	10/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.389678571630684	2		880	818	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803148	1803148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	186	1027	0	ENST00000260795.2:c.500C>T	p.Pro167Leu	p.P167L	ENST00000260795		167	cCg/cTg	4/17	1	2	FACETS	0.887	0.819	0.959	0.887	0.819	0.959	CLONAL	1	TRUE	1	0.389678571630684	2		1027	1076	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749467	41749467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	137	555	0	ENST00000226382.2:c.328C>T	p.Leu110Phe	p.L110F	ENST00000226382	NM_003924.3	110	Ctc/Ttc	2/3	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.389678571630684	2		555	672	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593691	55593691	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	103	414	0	ENST00000288135.5:c.1757G>T	p.Arg586Ile	p.R586I	ENST00000288135	NM_000222.2	586	aGa/aTa	11/21	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.389678571630684	2		414	512	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020958	26020973	+	frameshift_variant	Frame_Shift_Del	DEL	ACAGACCTGCGTTTCC	ACAGACCTGCGTTTCC	-	novel	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	91	504	0	ENST00000357647.3:c.242_257del	p.Thr81ArgfsTer5	p.T81Rfs*5	ENST00000357647	NM_003529.2	81	ACAGACCTGCGTTTCCag/ag	1/1	1	2	FACETS	0.852	0.759	0.952	0.852	0.759	0.952	CLONAL	1	TRUE	1	0.389678571630684	2		504	548	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450355	50450355	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	165	625	0	ENST00000331340.3:c.539A>G	p.Tyr180Cys	p.Y180C	ENST00000331340	NM_006060.4	180	tAc/tGc	5/8	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.389678571630684	2		625	731	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465542	8465542	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046311-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	128	512	0	ENST00000356435.5:c.3638G>T	p.Gly1213Val	p.G1213V	ENST00000356435		1213	gGa/gTa	21/35	1	2	FACETS	0.985	0.895	1	0.985	0.895	1	CLONAL	1	TRUE	1	0.389678571630684	2		512	667	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	364	427	0				ENST00000310581	NM_198253.2	-/1132			0.549447101471321	3	FACETS	0.887	0.85	0.923	1	0.995	1	CLONAL	3	TRUE	1	0.549447101471321	3		427	635	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934573	NA	P-0046313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	578	567	0	ENST00000269305.4:c.722C>A	p.Ser241Tyr	p.S241Y	ENST00000269305	NM_001126112.2	241	tCc/tAc	7/11	0.531690617846202	3	FACETS	0.92	0.89	0.949	0.92	0.89	0.949	CLONAL	3	TRUE	0	0.549447101471321	3		567	972	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974809	21974809	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	89	127	0	ENST00000304494.5:c.18del	p.Ser7AlafsTer19	p.S7Afs*19	ENST00000304494	NM_000077.4	6	ggG/gg	1/3	0.518851711077685	2	FACETS	0.81	0.735	0.886	0.81	0.735	0.886	CLONAL	2	TRUE	0	0.549447101471321	2		127	200	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910587	29910587	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	405	921	0	ENST00000376809.5:c.127G>T	p.Glu43Ter	p.E43*	ENST00000376809	NM_002116.7	43	Gag/Tag	2/8	0.549447101471321	3	FACETS	1	0.993	1	0.624	0.593	0.656	CLONAL	1	TRUE	1	0.549447101471321	3		921	1505	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106706	2106706	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139060277	NA	P-0046313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	427	747	1	ENST00000219476.3:c.710C>T	p.Pro237Leu	p.P237L	ENST00000219476	NM_000548.3	237	cCg/cTg	8/42	0.496789613319182	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.549447101471321	1		748	988	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129180	64129180	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	73	853	0	ENST00000334205.4:c.718C>G	p.Leu240Val	p.L240V	ENST00000334205	NM_003942.2	240	Ctg/Gtg	7/17	0.243845055779323	3	FACETS	0.281	0.245	0.321	0.141	0.122	0.161	INDETERMINATE	1	TRUE	1	0.549447101471321	3		853	1204	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999351	100999351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565374436	NA	P-0046313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	793	957	0	ENST00000325455.5:c.451C>T	p.Pro151Ser	p.P151S	ENST00000325455	NM_001202474.3	151	Cca/Tca	1/8	0.450252621485744	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	2	0.549447101471321	4		957	1927	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877502	28877502	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	44	272	0	ENST00000282397.4:c.3819G>C	p.Leu1273Phe	p.L1273F	ENST00000282397	NM_002019.4	1273	ttG/ttC	30/30	0.549447101471321	1	FACETS	0.394	0.332	0.462	0.394	0.332	0.462	SUBCLONAL	1	TRUE	0	0.549447101471321	1		272	295	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986892	36986892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1281277364	NA	P-0046313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	115	380	0	ENST00000354822.5:c.797G>A	p.Gly266Asp	p.G266D	ENST00000354822	NM_001079668.2	266	gGc/gAc	3/3	0.523182355698596	2	FACETS	0.754	0.682	0.83	0.377	0.341	0.415	SUBCLONAL	1	TRUE	0	0.549447101471321	2		380	555	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649237	23649237	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	64	240	0	ENST00000261584.4:c.145A>G	p.Lys49Glu	p.K49E	ENST00000261584	NM_024675.3	49	Aag/Gag	3/13	0.154338758366924	3	FACETS	0.623	0.54	0.712			1	INDETERMINATE	1	TRUE	NA	0.549447101471321	3		240	477	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215595217	215595217	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	30	133	0	ENST00000260947.4:c.1919T>C	p.Leu640Pro	p.L640P	ENST00000260947	NM_000465.2	640	cTa/cCa	10/11	0.255926441078599	3	FACETS	0.336	0.271	0.411	0.112	0.09	0.137	INDETERMINATE	1	TRUE	0	0.549447101471321	3		133	414	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663355	227663355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373040435	NA	P-0046313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	179	554	0	ENST00000305123.5:c.100G>A	p.Ala34Thr	p.A34T	ENST00000305123	NM_005544.2	34	Gcg/Acg	1/2	0.255926441078599	3	FACETS	1	0.963	1	0.356	0.329	0.385	INDETERMINATE	1	TRUE	0	0.549447101471321	3		554	777	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714447	40714447	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	44	444	0	ENST00000373198.4:c.3950C>A	p.Pro1317His	p.P1317H	ENST00000373198	NM_133170.3	1317	cCc/cAc	29/32	0.549447101471321	3	FACETS	0.267	0.223	0.315	0.089	0.074	0.105	SUBCLONAL	1	TRUE	0	0.549447101471321	3		444	766	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456513	89456513	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	111	207	0	ENST00000336596.2:c.1689G>T	p.Leu563Phe	p.L563F	ENST00000336596	NM_005233.5	563	ttG/ttT	8/17	0.243845055779323	3	FACETS	1	0.94	1	0.528	0.477	0.581	INDETERMINATE	1	TRUE	1	0.549447101471321	3		207	488	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539810	187539810	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	125	303	0	ENST00000441802.2:c.7930G>C	p.Glu2644Gln	p.E2644Q	ENST00000441802	NM_005245.3	2644	Gag/Cag	10/27	0.505859535648073	2	FACETS	0.942	0.858	1	0.471	0.429	0.515	CLONAL	1	TRUE	0	0.549447101471321	2		303	483	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876127	35876127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	144	353	0	ENST00000303115.3:c.919C>G	p.Gln307Glu	p.Q307E	ENST00000303115	NM_002185.3	307	Cag/Gag	8/8	0.150614899566238	3	FACETS	1	0.978	1	0.598	0.548	0.65	INDETERMINATE	1	TRUE	1	0.549447101471321	3		353	559	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851522	128851522	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	201	733	0	ENST00000249373.3:c.1847C>G	p.Ser616Cys	p.S616C	ENST00000249373	NM_005631.4	616	tCt/tGt	11/12	0.267444505310993	3	FACETS	0.861	0.797	0.927	0.287	0.265	0.309	INDETERMINATE	1	TRUE	0	0.549447101471321	3		733	1083	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873421	151873421	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	53	294	0	ENST00000262189.6:c.9117G>C	p.Gln3039His	p.Q3039H	ENST00000262189	NM_170606.2	3039	caG/caC	38/59	0.383261010282959	1	FACETS	0.339	0.289	0.393	0.339	0.289	0.393	SUBCLONAL	1	TRUE	0	0.549447101471321	1		294	413	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205099	123205099	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	231	232	0	ENST00000218089.9:c.2459C>T	p.Ser820Leu	p.S820L	ENST00000218089	NM_001042749.1	820	tCa/tTa	25/35	0.549447101471321	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.549447101471321	1		232	490	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373784	118373784	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	38	247	0	ENST00000534358.1:c.7177A>C	p.Asn2393His	p.N2393H	ENST00000534358	NM_005933.3	2393	Aac/Cac	27/36	0.182008214813905	4	FACETS	0.891	0.746	1	0.891	0.746	1	INDETERMINATE	2	FALSE	2	0.315222840570613	4		247	178	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73112851	73112851	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	22	220	0	ENST00000356692.5:c.448del	p.Met150Ter	p.M150*	ENST00000356692		149	cgA/cg	6/9	0.315222840570613	6	FACETS	1	0.916	1			1	CLONAL	1	FALSE	NA	0.315222840570613	6		220	160	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165668	108165671	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	novel	NA	P-0046336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	32	257	0	ENST00000278616.4:c.4793_4796del	p.Leu1598GlnfsTer2	p.L1598Qfs*2	ENST00000278616	NM_000051.3	1597	ttTCTC/tt	32/63	1	2	FACETS	0.973	0.793	1	0.973	0.793	1	CLONAL	1	TRUE	1	0.229104821270417	2		257	287	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198443	108198444	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	42	355	0	ENST00000278616.4:c.7049dup	p.Leu2350PhefsTer23	p.L2350Ffs*23	ENST00000278616	NM_000051.3	2349	-/T	48/63	0.229104821270417	3	FACETS	1	0.893	1	0.545	0.456	0.643	CLONAL	1	TRUE	1	0.229104821270417	3		355	375	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036037	180036037	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	422	497	0	ENST00000261937.6:c.3824G>T	p.Ser1275Ile	p.S1275I	ENST00000261937	NM_182925.4	1275	aGt/aTt	29/30	0.229104821270417	6	FACETS	1	0.972	1	1	0.972	1	CLONAL	6	TRUE	0	0.229104821270417	6		497	879	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043378	180043378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774554521	NA	P-0046336-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	380	522	0	ENST00000261937.6:c.3208C>T	p.Arg1070Cys	p.R1070C	ENST00000261937	NM_182925.4	1070	Cgc/Tgc	23/30	0.229104821270417	6	FACETS	1	0.967	1	1	0.967	1	CLONAL	6	TRUE	0	0.229104821270417	6		522	795	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0046337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	68	325	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.87	0.758	0.992	0.87	0.758	0.992	CLONAL	1	TRUE	1	0.28	2		325	558	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0046337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	1322	343	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.3	16	FACETS	1	0.995	1			1	CLONAL	14	TRUE	NA	0.28	16		343	1928	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356427	66356427	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1321339471	NA	P-0046337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	67	238	0	ENST00000273854.3:c.1070C>A	p.Pro357His	p.P357H	ENST00000273854	NM_004439.5	357	cCc/cAc	5/18	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.28	2		238	342	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040977	47040977	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046337-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	133	615	0	ENST00000377604.3:c.1507del	p.Ala503LeufsTer201	p.A503Lfs*201	ENST00000377604	NM_001204468.1	503	Gct/ct	14/24	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.28	2		615	718	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0046338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	446	519	1	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.326320169946253	4	FACETS	1	0.99	1	0.825	0.791	0.86	CLONAL	3	TRUE	0	0.367180064193868	4		520	1006	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127318	17127318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369906553	NA	P-0046338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	201	563	0	ENST00000285071.4:c.536G>A	p.Arg179Gln	p.R179Q	ENST00000285071	NM_144997.5	179	cGg/cAg	6/14	1	2	FACETS	0.812	0.756	0.87	1	0.992	1	CLONAL	2	TRUE	1	0.367180064193868	2		563	674	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178943818	178943818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	47	262	0	ENST00000263967.3:c.2485C>T	p.Leu829Phe	p.L829F	ENST00000263967	NM_006218.2	829	Ctt/Ttt	17/21	1	2	FACETS	0.928	0.788	1	0.928	0.788	1	CLONAL	1	TRUE	1	0.367180064193868	2		262	276	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398864	398864	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	75	461	0	ENST00000380956.4:c.674C>A	p.Pro225Gln	p.P225Q	ENST00000380956	NM_001195286.1	225	cCa/cAa	6/9	1	2	FACETS	0.812	0.713	0.918	0.812	0.713	0.918	CLONAL	1	TRUE	1	0.367180064193868	2		461	503	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855257	76855366	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAATTCATCCATACTGTCTTCATCAAAATAACCCTAGAGAAAAAAAAATGACCACTATTTTAATAGAATATCTCAACTTACACTGGAAATTATATTGATGTTCATTTAAG	AAATTCATCCATACTGTCTTCATCAAAATAACCCTAGAGAAAAAAAAATGACCACTATTTTAATAGAATATCTCAACTTACACTGGAAATTATATTGATGTTCATTTAAG	-	novel	NA	P-0046338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	44	165	0	ENST00000373344.5:c.5698-77_5730del		p.X1900_splice	ENST00000373344	NM_000489.3	1900		24/35	0.146649419292825	2	FACETS	1	0.945	1			1	INDETERMINATE	1	TRUE	NA	0.367180064193868	2		165	189	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577074	7577082	+	inframe_deletion	In_Frame_Del	DEL	ATTCTCTTC	ATTCTCTTC	-	novel	NA	P-0046339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	163	605	0	ENST00000269305.4:c.856_864del	p.Glu286_Asn288del	p.E286_N288del	ENST00000269305	NM_001126112.2	286	GAAGAGAAT/-	8/11	0.20135927741062	2	FACETS	1	0.987	1	0.713	0.655	0.775	CLONAL	1	TRUE	0	0.261989037013102	2		605	872	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	211	424	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.57254228808708	2	FACETS	0.887	0.836	0.938	0.887	0.836	0.938	CLONAL	2	TRUE	0	0.573151605240649	2		424	415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0046340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	482	812	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.573151605240649	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.573151605240649	2		812	805	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0046340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	100	389	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	0.573151605240649	2	FACETS	1	0.957	1	0.552	0.499	0.607	CLONAL	1	TRUE	0	0.573151605240649	2		389	316	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528647	89528647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536144760	NA	P-0046340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	115	149	1	ENST00000336596.2:c.2947G>A	p.Val983Met	p.V983M	ENST00000336596	NM_005233.5	983	Gtg/Atg	17/17	0.573151605240649	3	FACETS	0.906	0.829	0.984	0.906	0.829	0.984	CLONAL	2	TRUE	1	0.573151605240649	3		150	285	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199948	108199948	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs876658715	NA	P-0046340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	47	142	0	ENST00000278616.4:c.7290T>G	p.His2430Gln	p.H2430Q	ENST00000278616	NM_000051.3	2430	caT/caG	49/63	0.573151605240649	3	FACETS	0.812	0.69	0.943	0.406	0.345	0.472	CLONAL	1	TRUE	1	0.573151605240649	3		142	260	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862839	9862839	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	179	525	2	ENST00000330684.3:c.2464T>C	p.Tyr822His	p.Y822H	ENST00000330684	NM_001134407.1	822	Tac/Cac	12/13	0.491723425561257	4	FACETS	1	0.946	1	0.516	0.475	0.558	CLONAL	1	TRUE	2	0.573151605240649	4		527	952	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448374	56448375	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0046340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	424	544	2	ENST00000407977.2:c.272_273delinsTT	p.Cys91Phe	p.C91F	ENST00000407977		91	tGC/tTT	3/10	0.573151605240649	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.573151605240649	2		546	734	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158637111	158637163	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCTGCAAAGGAGAGAAAGGAAGGGGAAAAAAAAAAAAAAGAGGAATTACCGT	ATCTGCAAAGGAGAGAAAGGAAGGGGAAAAAAAAAAAAAAGAGGAATTACCGT	-	novel	NA	P-0046340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	260	324	0	ENST00000263640.3:c.68-51_69del		p.X23_splice	ENST00000263640	NM_001105.4	23		4/11	0.240180382458791	5	FACETS	0.838	0.79	0.887	0.838	0.79	0.887	INDETERMINATE	3	TRUE	2	0.573151605240649	5		324	671	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005874	69005874	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	122	347	1	ENST00000288368.4:c.2285A>G	p.Glu762Gly	p.E762G	ENST00000288368	NM_024870.2	762	gAg/gGg	21/40	0.531242541365248	5	FACETS	0.969	0.876	1	0.242	0.219	0.267	CLONAL	1	TRUE	1	0.573151605240649	5		348	817	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0046342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	247	767	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.598867437575577	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.598867437575577	1		767	485	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0046342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	246	409	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.598867437575577	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	1	0.598867437575577	3		410	529	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0046342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	243	362	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.598867437575577	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.598867437575577	2		362	394	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944279	81944279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747373917	NA	P-0046342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	320	582	2	ENST00000359376.3:c.1888C>T	p.Arg630Trp	p.R630W	ENST00000359376	NM_002661.3	630	Cgg/Tgg	18/33	0.598867437575577	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	1	0.598867437575577	3		584	694	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460527	149460527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139635308	NA	P-0046342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	183	578	1	ENST00000286301.3:c.110C>T	p.Thr37Met	p.T37M	ENST00000286301	NM_005211.3	37	aCg/aTg	3/22	0.598867437575577	3	FACETS	0.966	0.893	1	0.483	0.446	0.521	CLONAL	1	TRUE	1	0.598867437575577	3		579	822	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436533	110436533	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	178	627	0	ENST00000375856.3:c.1868T>C	p.Val623Ala	p.V623A	ENST00000375856	NM_003749.2	623	gTg/gCg	1/2	0.593955253112649	4	FACETS	0.954	0.879	1	0.318	0.293	0.345	CLONAL	1	TRUE	1	0.598867437575577	4		627	996	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593553	48593554	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	69	163	0	ENST00000342988.3:c.1307dup	p.Val437GlyfsTer3	p.V437Gfs*3	ENST00000342988	NM_005359.5	435	ata/atAa	10/12	0.598867437575577	1	FACETS	0.863	0.767	0.962	0.863	0.767	0.962	CLONAL	1	TRUE	0	0.598867437575577	1		163	187	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197358	26197358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	94	351	0	ENST00000356476.2:c.121C>T	p.Arg41Cys	p.R41C	ENST00000356476		41	Cgt/Tgt	1/1	1	2	FACETS	0.892	0.801	0.987	0.892	0.801	0.987	CLONAL	1	TRUE	1	0.598867437575577	2		351	352	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0046343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	95	391	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.948	0.846	1	0.948	0.846	1	CLONAL	1	TRUE	1	0.36119835085974	2		391	555	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0046343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	85	307	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.36119835085974	2		307	377	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0046343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	93	258	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.36119835085974	2		258	466	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100375	27100375	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	173	489	0	ENST00000324856.7:c.4087C>T	p.Gln1363Ter	p.Q1363*	ENST00000324856	NM_006015.4	1363	Caa/Taa	17/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.36119835085974	2		489	813	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0046343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	164	354	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.36119835085974	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.36119835085974	2		354	413	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939715	76939715	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149249195	NA	P-0046343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	87	508	0	ENST00000373344.5:c.1033G>A	p.Ala345Thr	p.A345T	ENST00000373344	NM_000489.3	345	Gca/Aca	9/35	1	2	FACETS	0.874	0.776	0.979	0.874	0.776	0.979	CLONAL	1	TRUE	1	0.36119835085974	2		508	551	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845597	63845598	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0046343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	55	210	0	ENST00000279873.7:c.1337_1338dup	p.Glu447MetfsTer33	p.E447Mfs*33	ENST00000279873	NM_032199.2	446	cat/cATat	9/10	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.36119835085974	2		210	255	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831330	72831330	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	104	384	0	ENST00000268489.5:c.5251C>T	p.Gln1751Ter	p.Q1751*	ENST00000268489	NM_006885.3	1751	Caa/Taa	9/10	1	2	FACETS	0.947	0.85	1	0.947	0.85	1	CLONAL	1	TRUE	1	0.36119835085974	2		384	608	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372439	55372440	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	156	702	0	ENST00000297316.4:c.1130dup	p.Tyr379LeufsTer5	p.Y379Lfs*5	ENST00000297316	NM_022454.3	377	ctc/cTtc	2/2	1	2	FACETS	0.826	0.755	0.9	0.826	0.755	0.9	CLONAL	1	TRUE	1	0.36119835085974	2		702	1046	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0046344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	218	494	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.474203925408655	3	FACETS	0.98	0.91	1	0.49	0.455	0.526	CLONAL	1	TRUE	1	0.474203925408655	3		494	1161	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0046344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	531	491	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.474203925408655	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.474203925408655	2		491	1071	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579406	7579406	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0046344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	278	569	0	ENST00000269305.4:c.281C>G	p.Ser94Ter	p.S94*	ENST00000269305	NM_001126112.2	94	tCa/tGa	4/11	0.474203925408655	1	FACETS	0.955	0.898	1	0.955	0.898	1	CLONAL	1	TRUE	0	0.474203925408655	1		569	937	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690814	89690814	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	73	230	0	ENST00000371953.3:c.221G>C	p.Arg74Thr	p.R74T	ENST00000371953	NM_000314.4	74	aGa/aCa	4/9	0.474203925408655	1	FACETS	0.983	0.872	1	0.983	0.872	1	CLONAL	1	TRUE	0	0.474203925408655	1		230	239	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925368	131925368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1561640018	NA	P-0046344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	64	124	0	ENST00000265335.6:c.1291G>A	p.Glu431Lys	p.E431K	ENST00000265335		431	Gag/Aag	9/25	1	2	FACETS	0.95	0.831	1	0.95	0.831	1	CLONAL	1	TRUE	1	0.474203925408655	2		124	284	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243708820	243708820	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	142	280	0	ENST00000263826.5:c.1243G>A	p.Asp415Asn	p.D415N	ENST00000263826	NM_005465.4	415	Gat/Aat	11/13	0.474203925408655	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.474203925408655	1		280	422	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118339506	118339506	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	194	289	0	ENST00000534358.1:c.449G>A	p.Gly150Asp	p.G150D	ENST00000534358	NM_005933.3	150	gGt/gAt	2/36	0.337041134916456	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.474203925408655	1		289	518	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033953	49033953	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	457	323	0	ENST00000267163.4:c.2090del	p.Asp697AlafsTer8	p.D697Afs*8	ENST00000267163	NM_000321.2	697	gAc/gc	20/27	0.474203925408655	3	FACETS	0.933	0.897	0.968	0.933	0.897	0.968	CLONAL	3	TRUE	0	0.474203925408655	3		323	852	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986829	36986829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	47	118	1	ENST00000354822.5:c.860G>A	p.Arg287His	p.R287H	ENST00000354822	NM_001079668.2	287	cGc/cAc	3/3	0.432218407035623	3	FACETS	0.689	0.583	0.804	0.23	0.194	0.268	SUBCLONAL	1	TRUE	0	0.474203925408655	3		119	356	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337228	89337228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	106	411	0	ENST00000301030.4:c.7803G>A	p.Met2601Ile	p.M2601I	ENST00000301030	NM_001256183.1	2601	atG/atA	12/13	0.474203925408655	1	FACETS	0.517	0.464	0.573	0.517	0.464	0.573	SUBCLONAL	1	TRUE	0	0.474203925408655	1		411	660	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260319	10260319	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	157	474	0	ENST00000340748.4:c.2348G>C	p.Trp783Ser	p.W783S	ENST00000340748		783	tGg/tCg	25/40	0.285669060845426	1	FACETS	0.6	0.55	0.652	0.6	0.55	0.652	SUBCLONAL	1	TRUE	0	0.474203925408655	1		474	842	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548288	41548288	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	146	255	0	ENST00000263253.7:c.3076G>T	p.Glu1026Ter	p.E1026*	ENST00000263253	NM_001429.3	1026	Gag/Tag	16/31	0.474203925408655	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.474203925408655	1		255	429	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188337	32188337	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs772628389	NA	P-0046344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	85	579	0	ENST00000375023.3:c.1004C>G	p.Ser335Cys	p.S335C	ENST00000375023	NM_004557.3	335	tCt/tGt	6/30	1	2	FACETS	0.327	0.288	0.37	0.327	0.288	0.37	SUBCLONAL	1	TRUE	1	0.474203925408655	2		579	1095	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0046358-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	404	415	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	0.545443772672535	3	FACETS	0.959	0.919	0.999	0.959	0.919	0.999	CLONAL	2	TRUE	1	0.702768849550524	3		415	810	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439671	51439684	+	frameshift_variant	Frame_Shift_Del	DEL	GAGCAGGTTTCCTG	GAGCAGGTTTCCTG	-	novel	NA	P-0046358-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	200	266	0	ENST00000262662.1:c.238_251del	p.Ala80HisfsTer11	p.A80Hfs*11	ENST00000262662		79	aGAGCAGGTTTCCTG/a	4/4	0.702768849550524	2	FACETS	0.988	0.941	1	0.988	0.941	1	CLONAL	2	TRUE	0	0.702768849550524	2		266	288	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707909	43707909	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046358-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	356	368	0	ENST00000382044.4:c.4972A>T	p.Ile1658Phe	p.I1658F	ENST00000382044	NM_001141980.1	1658	Atc/Ttc	23/28	0.236269150189979	3	FACETS	0.882	0.841	0.923	0.882	0.841	0.923	INDETERMINATE	2	TRUE	1	0.702768849550524	3		368	776	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183571	10183572	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0046358-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	142	233	0	ENST00000256474.2:c.44_45dup	p.Glu16ArgfsTer52	p.E16Rfs*52	ENST00000256474	NM_000551.3	14	ggc/gGCgc	1/3	1	2	FACETS	0.925	0.85	1	0.925	0.85	1	CLONAL	1	TRUE	1	0.702768849550524	2		233	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0046360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	840	736	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.66418345695535	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.753924581624906	4		736	1944	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129346	64129346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780738455	NA	P-0046360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	730	758	1	ENST00000334205.4:c.778C>T	p.Pro260Ser	p.P260S	ENST00000334205	NM_003942.2	260	Ccc/Tcc	8/17	0.753924581624906	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	1	0.753924581624906	3		759	1204	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037475	12037475	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	417	341	0	ENST00000396373.4:c.1106G>T	p.Arg369Leu	p.R369L	ENST00000396373	NM_001987.4	369	cGg/cTg	6/8	0.753924581624906	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.753924581624906	4		341	960	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860081	57860081	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	465	799	0	ENST00000228682.2:c.821G>T	p.Gly274Val	p.G274V	ENST00000228682	NM_005269.2	274	gGc/gTc	8/12	0.753924581624906	3	FACETS	1	0.989	1	0.557	0.531	0.583	CLONAL	1	TRUE	1	0.753924581624906	3		799	1526	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609461	81609461	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	191	409	0	ENST00000298171.2:c.1059C>A	p.Tyr353Ter	p.Y353*	ENST00000298171	NM_000369.2	353	taC/taA	10/10	0.609929760185944	3	FACETS	1	0.961	1	0.526	0.488	0.565	CLONAL	1	TRUE	1	0.753924581624906	3		409	663	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423549	88423549	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1361372348	NA	P-0046360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	580	611	0	ENST00000360948.2:c.2286G>T	p.Glu762Asp	p.E762D	ENST00000360948	NM_001012338.2	762	gaG/gaT	18/19	NA	2	FACETS	0.983	0.957	1			1	INDETERMINATE	2	TRUE	NA	0.753924581624906	2		611	783	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813728	50813729	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0046360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	343	651	1	ENST00000398568.2:c.1282_1283delinsTT	p.Gly428Leu	p.G428L	ENST00000398568	NM_001042412.1	428	GGa/TTa	8/18	0.666738091031372	1	FACETS	0.977	0.937	1	0.977	0.937	1	CLONAL	1	TRUE	0	0.753924581624906	1		652	580	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654636	67654636	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	507	485	0	ENST00000264010.4:c.1123G>T	p.Gly375Ter	p.G375*	ENST00000264010	NM_006565.3	375	Gga/Tga	6/12	0.734144174973856	4	FACETS	0.885	0.849	0.923			1	CLONAL	2	TRUE	NA	0.753924581624906	4		485	1332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0046360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	712	737	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	0.66418345695535	4	FACETS	0.908	0.876	0.94	0.908	0.876	0.94	CLONAL	2	TRUE	2	0.753924581624906	4		737	1825	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245032	41245032	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1050289746	NA	P-0046360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	324	700	0	ENST00000357654.3:c.2516A>G	p.His839Arg	p.H839R	ENST00000357654	NM_007294.3	839	cAc/cGc	10/23	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.753924581624906	2		700	799	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573658	48573658	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	143	347	0	ENST00000342988.3:c.242G>T	p.Arg81Met	p.R81M	ENST00000342988	NM_005359.5	81	aGg/aTg	2/12	0.736791097992963	2	FACETS	0.866	0.815	0.916	0.866	0.815	0.916	CLONAL	2	TRUE	0	0.753924581624906	2		347	219	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260638	10260638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	323	438	0	ENST00000340748.4:c.2224G>A	p.Gly742Arg	p.G742R	ENST00000340748		742	Ggg/Agg	24/40	0.747285995726977	2	FACETS	0.987	0.953	1	0.987	0.953	1	CLONAL	2	TRUE	0	0.753924581624906	2		438	434	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599929	10599929	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	716	611	0	ENST00000171111.5:c.1647del	p.Met550Ter	p.M550*	ENST00000171111	NM_203500.1	549	ccC/cc	5/6	0.747285995726977	2	FACETS	0.958	0.935	0.981	0.958	0.935	0.981	CLONAL	2	TRUE	0	0.753924581624906	2		611	991	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216128	36216128	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	269	550	0	ENST00000222270.7:c.3536G>C	p.Cys1179Ser	p.C1179S	ENST00000222270	NM_014727.1	1179	tGt/tCt	11/37	0.753098985455051	2	FACETS	1	0.949	1	0.503	0.475	0.532	CLONAL	1	TRUE	0	0.753924581624906	2		550	709	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57474028	57474028	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	196	287	0	ENST00000371085.3:c.245G>T	p.Ser82Ile	p.S82I	ENST00000371085	NM_000516.4	82	aGc/aTc	3/13	0.73120301644949	3	FACETS	0.91	0.844	0.978	0.455	0.422	0.489	CLONAL	1	TRUE	1	0.753924581624906	3		287	787	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231180	142231180	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	258	486	0	ENST00000350721.4:c.4774G>C	p.Ala1592Pro	p.A1592P	ENST00000350721	NM_001184.3	1592	Gca/Cca	27/47	0.753924581624906	3	FACETS	0.882	0.826	0.94	0.441	0.413	0.47	CLONAL	1	TRUE	1	0.753924581624906	3		486	1068	SUCCESS
APC	324	MSKCC	GRCh37	5	112174282	112174282	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0046360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	200	302	0	ENST00000257430.4:c.2991T>A	p.Tyr997Ter	p.Y997*	ENST00000257430	NM_000038.5	997	taT/taA	16/16	0.741539847876399	2	FACETS	0.918	0.874	0.96	0.918	0.874	0.96	CLONAL	2	TRUE	0	0.753924581624906	2		302	289	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518067	8518067	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	397	448	0	ENST00000356435.5:c.1324G>C	p.Glu442Gln	p.E442Q	ENST00000356435		442	Gaa/Caa	10/35	0.741539847876399	2	FACETS	0.932	0.901	0.962	0.932	0.901	0.962	CLONAL	2	TRUE	0	0.753924581624906	2		448	565	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317482	1317482	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	297	689	0	ENST00000400841.2:c.583G>C	p.Gly195Arg	p.G195R	ENST00000400841		195	Ggg/Cgg	5/6	1	1	FACETS	0.568	0.536	0.6	0.568	0.536	0.6	SUBCLONAL	1	TRUE	0	0.753924581624906	1		689	864	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409964	63409964	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	217	263	0	ENST00000330258.3:c.3203G>T	p.Ser1068Ile	p.S1068I	ENST00000330258	NM_152424.3	1068	aGc/aTc	2/2	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.753924581624906	1		263	305	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	95	427	0				ENST00000310581	NM_198253.2	-/1132			0.219895338233994	3	FACETS	1	0.907	1	1	0.907	1	CLONAL	2	TRUE	1	0.22	3		427	472	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0046361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	173	624	1	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.201698582449346	2	FACETS	0.982	0.905	1	0.982	0.905	1	CLONAL	2	TRUE	0	0.22	2		625	801	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717699	89717699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	87	381	1	ENST00000371953.3:c.724G>A	p.Glu242Lys	p.E242K	ENST00000371953	NM_000314.4	242	Gag/Aag	7/9	0.230567819476313	2	FACETS	1	0.977	1	0.718	0.637	0.804	CLONAL	1	TRUE	0	0.22	2		382	551	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632284	215632284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	63	501	0	ENST00000260947.4:c.1490C>T	p.Pro497Leu	p.P497L	ENST00000260947	NM_000465.2	497	cCa/cTa	6/11	1	2	FACETS	0.828	0.715	0.95	0.828	0.715	0.95	CLONAL	1	TRUE	1	0.22	2		501	692	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41560064	41560064	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	46	282	0	ENST00000263253.7:c.3736G>T	p.Glu1246Ter	p.E1246*	ENST00000263253	NM_001429.3	1246	Gaa/Taa	22/31	0.219895338233994	3	FACETS	1	0.864	1	0.513	0.433	0.603	CLONAL	1	TRUE	1	0.22	3		282	452	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778021	135778021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs118203685	NA	P-0046361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	125	498	0	ENST00000298552.3:c.2362G>T	p.Glu788Ter	p.E788*	ENST00000298552	NM_001162426.1	788	Gaa/Taa	18/23	0.201698582449346	2	FACETS	0.865	0.784	0.949	0.865	0.784	0.949	CLONAL	2	TRUE	0	0.22	2		498	657	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0046362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	8	404	0	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	0.161	0.103	0.236	0.161	0.103	0.236	SUBCLONAL	1	TRUE	1	0.35	2		404	284	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521285	187521285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200468783	NA	P-0046362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	36	542	1	ENST00000441802.2:c.11870G>A	p.Arg3957His	p.R3957H	ENST00000441802	NM_005245.3	3957	cGt/cAt	22/27	0.227309997490704	4	FACETS	0.66	0.542	0.791	0.33	0.271	0.396	SUBCLONAL	1	TRUE	2	0.35	4		543	421	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	110	427	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.987	0.89	1	0.987	0.89	1	CLONAL	1	TRUE	1	0.388263259750906	2		427	574	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	418	325	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.326370402490369	2	FACETS	0.933	0.89	0.977	0.933	0.89	0.977	CLONAL	2	TRUE	0	0.388263259750906	2		325	1154	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545870	41545870	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	308	374	0	ENST00000263253.7:c.2485C>T	p.Gln829Ter	p.Q829*	ENST00000263253	NM_001429.3	829	Cag/Tag	14/31	0.388263259750906	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.388263259750906	1		374	1081	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	132	181	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.388263259750906	2		181	644	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273836	18273836	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	144	355	0	ENST00000222254.8:c.1169C>G	p.Ser390Ter	p.S390*	ENST00000222254	NM_005027.3	390	tCa/tGa	10/16	1	2	FACETS	0.722	0.657	0.789	0.722	0.657	0.789	SUBCLONAL	1	TRUE	1	0.388263259750906	2		355	1028	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161310391	161310391	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	127	206	0	ENST00000367975.2:c.187C>T	p.Leu63Phe	p.L63F	ENST00000367975	NM_003001.3	63	Ctt/Ttt	4/6	0.313309905301205	3	FACETS	0.853	0.772	0.938	0.426	0.386	0.469	CLONAL	1	TRUE	1	0.388263259750906	3		206	916	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069267	30069267	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	46	282	0	ENST00000338641.4:c.1132G>T	p.Glu378Ter	p.E378*	ENST00000338641	NM_000268.3	378	Gag/Tag	12/16	0.388263259750906	1	FACETS	0.274	0.23	0.323	0.274	0.23	0.323	SUBCLONAL	1	TRUE	0	0.388263259750906	1		282	696	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169207	32169207	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	192	345	0	ENST00000375023.3:c.3826G>C	p.Glu1276Gln	p.E1276Q	ENST00000375023	NM_004557.3	1276	Gag/Cag	22/30	1	2	FACETS	0.873	0.806	0.942	0.873	0.806	0.942	CLONAL	1	TRUE	1	0.388263259750906	2		345	1133	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139648	202139648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	100	137	0	ENST00000358485.4:c.809C>T	p.Ser270Phe	p.S270F	ENST00000358485	NM_001080125.1	270	tCt/tTt	6/9	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.388263259750906	2		137	496	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319902	8319902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	87	202	0	ENST00000356435.5:c.5599G>A	p.Glu1867Lys	p.E1867K	ENST00000356435		1867	Gaa/Aaa	34/35	1	2	FACETS	0.796	0.706	0.892	0.796	0.706	0.892	SUBCLONAL	1	TRUE	1	0.388263259750906	2		202	563	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550913	150550913	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	50	210	0	ENST00000369026.2:c.743G>C	p.Arg248Pro	p.R248P	ENST00000369026	NM_021960.4	248	cGa/cCa	2/3	0.313309905301205	3	FACETS	0.325	0.275	0.381	0.163	0.137	0.191	SUBCLONAL	1	TRUE	1	0.388263259750906	3		210	946	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450591	70450591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	125	196	0	ENST00000373644.4:c.5431G>A	p.Glu1811Lys	p.E1811K	ENST00000373644	NM_030625.2	1811	Gaa/Aaa	12/12	1	2	FACETS	0.926	0.84	1	0.926	0.84	1	CLONAL	1	TRUE	1	0.388263259750906	2		196	695	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234309	39234309	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397517159	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	74	163	0	ENST00000402219.2:c.2536G>A	p.Glu846Lys	p.E846K	ENST00000402219	NM_005633.3	846	Gaa/Aaa	16/23	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.388263259750906	2		163	336	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928503	69928503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	205	334	1	ENST00000352241.4:c.323C>T	p.Ser108Phe	p.S108F	ENST00000352241	NM_198159.2	108	tCt/tTt	2/10	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.388263259750906	2		335	1052	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780677	56780677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502588	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	111	231	0	ENST00000337432.4:c.692C>T	p.Ser231Leu	p.S231L	ENST00000337432	NM_058216.2	231	tCa/tTa	4/9	0.208640606995611	3	FACETS	0.962	0.865	1	0.321	0.288	0.355	INDETERMINATE	1	TRUE	0	0.388263259750906	3		231	710	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79968621	79968621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs887040509	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	126	217	0	ENST00000265081.6:c.971C>T	p.Ser324Leu	p.S324L	ENST00000265081	NM_002439.4	324	tCa/tTa	6/24	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.388263259750906	2		217	635	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744512	41744512	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	170	320	0	ENST00000301178.4:c.1132G>C	p.Glu378Gln	p.E378Q	ENST00000301178	NM_021913.4	378	Gag/Cag	8/20	0.202111381547312	3	FACETS	0.894	0.82	0.971	0.298	0.273	0.324	INDETERMINATE	1	TRUE	0	0.388263259750906	3		320	1170	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166199	118166199	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	119	194	0	ENST00000369448.3:c.709G>C	p.Glu237Gln	p.E237Q	ENST00000369448	NM_017709.3	237	Gaa/Caa	2/2	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.388263259750906	2		194	577	SUCCESS
FH	2271	MSKCC	GRCh37	1	241671976	241671976	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745606057	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	105	248	0	ENST00000366560.3:c.665C>T	p.Ser222Phe	p.S222F	ENST00000366560	NM_000143.3	222	tCc/tTc	5/10	0.313309905301205	3	FACETS	0.831	0.745	0.923	0.416	0.372	0.462	CLONAL	1	TRUE	1	0.388263259750906	3		248	777	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258095	123258095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	120	203	0	ENST00000358487.5:c.1586C>T	p.Ser529Phe	p.S529F	ENST00000358487	NM_000141.4	529	tCt/tTt	12/18	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.388263259750906	2		203	580	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046497	30046497	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	135	266	0	ENST00000331968.5:c.2686G>A	p.Glu896Lys	p.E896K	ENST00000331968	NM_002742.2	896	Gag/Aag	18/18	1	2	FACETS	0.805	0.731	0.882	0.805	0.731	0.882	CLONAL	1	TRUE	1	0.388263259750906	2		266	864	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991303	41991303	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1322813353	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	29	216	0	ENST00000219905.7:c.2134G>C	p.Glu712Gln	p.E712Q	ENST00000219905	NM_001164273.1	712	Gaa/Caa	5/24	0.388263259750906	1	FACETS	0.237	0.189	0.291	0.237	0.189	0.291	SUBCLONAL	1	TRUE	0	0.388263259750906	1		216	509	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347475	91347475	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	145	207	0	ENST00000355112.3:c.3637G>C	p.Glu1213Gln	p.E1213Q	ENST00000355112	NM_000057.2	1213	Gag/Cag	19/22	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.388263259750906	2		207	698	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771320	68771320	+	start_lost	Translation_Start_Site	SNP	T	T	A	novel	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	89	174	0	ENST00000261769.5:c.2T>A	p.Met1?	p.M1?	ENST00000261769	NM_004360.3	1	aTg/aAg	1/16	0.388263259750906	1	FACETS	0.983	0.878	1	0.983	0.878	1	CLONAL	1	TRUE	0	0.388263259750906	1		174	376	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81914529	81914529	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	145	207	0	ENST00000359376.3:c.663C>G	p.Phe221Leu	p.F221L	ENST00000359376	NM_002661.3	221	ttC/ttG	8/33	0.388263259750906	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.388263259750906	1		207	584	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957093	81957093	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	140	171	0	ENST00000359376.3:c.2311C>T	p.Gln771Ter	p.Q771*	ENST00000359376	NM_002661.3	771	Cag/Tag	22/33	0.388263259750906	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.388263259750906	1		171	534	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47685250	47685250	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	183	185	0	ENST00000347630.2:c.700G>C	p.Glu234Gln	p.E234Q	ENST00000347630	NM_001007230.1	234	Gag/Cag	8/11	0.208640606995611	3	FACETS	1	0.94	1	0.675	0.627	0.724	INDETERMINATE	2	TRUE	0	0.388263259750906	3		185	556	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885865	59885865	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	103	216	0	ENST00000259008.2:c.881G>T	p.Arg294Ile	p.R294I	ENST00000259008	NM_032043.2	294	aGa/aTa	7/20	0.208640606995611	3	FACETS	0.873	0.781	0.97	0.291	0.26	0.324	INDETERMINATE	1	TRUE	0	0.388263259750906	3		216	726	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39573271	39573271	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	67	175	0	ENST00000262039.4:c.752A>T	p.Glu251Val	p.E251V	ENST00000262039	NM_002647.2	251	gAa/gTa	7/25	1	2	FACETS	0.869	0.759	0.988	0.869	0.759	0.988	CLONAL	1	TRUE	1	0.388263259750906	2		175	397	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026159	48026159	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs567785169	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	49	157	0	ENST00000234420.5:c.1037C>T	p.Ser346Phe	p.S346F	ENST00000234420	NM_000179.2	346	tCt/tTt	4/10	1	2	FACETS	0.491	0.416	0.574	0.491	0.416	0.574	SUBCLONAL	1	TRUE	1	0.388263259750906	2		157	514	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145589	61145589	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	75	203	2	ENST00000295025.8:c.701C>T	p.Ala234Val	p.A234V	ENST00000295025	NM_002908.2	234	gCt/gTt	7/11	1	2	FACETS	0.634	0.556	0.719	0.634	0.556	0.719	SUBCLONAL	1	TRUE	1	0.388263259750906	2		205	609	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439415	220439415	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	66	168	0	ENST00000243786.2:c.269-1G>C		p.X90_splice	ENST00000243786	NM_002191.3	90			1	2	FACETS	0.685	0.596	0.782	0.685	0.596	0.782	SUBCLONAL	1	TRUE	1	0.388263259750906	2		168	496	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750728	39750728	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	136	145	0	ENST00000361337.2:c.2128G>T	p.Glu710Ter	p.E710*	ENST00000361337	NM_003286.2	710	Gaa/Taa	20/21	0.236992623929392	3	FACETS	1	0.979	1	0.622	0.566	0.679	CLONAL	1	TRUE	1	0.388263259750906	3		145	673	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256765	46256765	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	63	170	0	ENST00000371998.3:c.821C>G	p.Ser274Ter	p.S274*	ENST00000371998		274	tCa/tGa	8/23	0.236992623929392	3	FACETS	0.668	0.578	0.766	0.334	0.289	0.383	SUBCLONAL	1	TRUE	1	0.388263259750906	3		170	580	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574896	41574896	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	152	297	0	ENST00000263253.7:c.7181G>C	p.Gly2394Ala	p.G2394A	ENST00000263253	NM_001429.3	2394	gGa/gCa	31/31	0.388263259750906	1	FACETS	0.735	0.672	0.8	0.735	0.672	0.8	SUBCLONAL	1	TRUE	0	0.388263259750906	1		297	859	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442595	52442595	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	98	173	0	ENST00000460680.1:c.150del	p.Phe50LeufsTer22	p.F50Lfs*22	ENST00000460680	NM_004656.3	50	ttC/tt	4/17	1	2	FACETS	0.79	0.706	0.88	0.79	0.706	0.88	SUBCLONAL	1	TRUE	1	0.388263259750906	2		173	639	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960067	134960067	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	54	332	0	ENST00000398015.3:c.2424G>A	p.Trp808Ter	p.W808*	ENST00000398015	NM_004441.4	808	tgG/tgA	13/16	1	2	FACETS	0.273	0.232	0.318	0.273	0.232	0.318	SUBCLONAL	1	TRUE	1	0.388263259750906	2		332	1019	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181348	185181348	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	73	127	0	ENST00000265026.3:c.1289G>C	p.Arg430Thr	p.R430T	ENST00000265026	NM_004721.4	430	aGa/aCa	8/14	1	2	FACETS	0.881	0.773	0.995	0.881	0.773	0.995	CLONAL	1	TRUE	1	0.388263259750906	2		127	427	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517807	187517807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	86	151	0	ENST00000441802.2:c.12887G>A	p.Arg4296Gln	p.R4296Q	ENST00000441802	NM_005245.3	4296	cGa/cAa	25/27	1	2	FACETS	0.881	0.782	0.986	0.881	0.782	0.986	CLONAL	1	TRUE	1	0.388263259750906	2		151	503	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021020	26021020	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs771277151	NA	P-0046363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	242	224	0	ENST00000357647.3:c.303G>C	p.Leu101Phe	p.L101F	ENST00000357647	NM_003529.2	101	ttG/ttC	1/1	0.344684461264617	2	FACETS	0.922	0.866	0.979	0.922	0.866	0.979	CLONAL	2	TRUE	0	0.388263259750906	2		224	676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579417	7579426	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGGGGGCT	GGAGGGGGCT	-	novel	NA	P-0046364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	642	702	0	ENST00000269305.4:c.261_270del	p.Ala88GlyfsTer32	p.A88Gfs*32	ENST00000269305	NM_001126112.2	87	ccAGCCCCCTCC/cc	4/11	0.618189266089868	2	FACETS	0.982	0.953	1	0.982	0.953	1	CLONAL	2	TRUE	0	0.618533417095746	2		702	1057	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0046365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	15	363	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.427	0.31	0.568	0.427	0.31	0.568	SUBCLONAL	1	TRUE	1	0.13	2		363	541	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0046365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	47	526	3	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.13	2		529	653	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939252	71939252	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	51	717	0	ENST00000298229.2:c.201C>G	p.His67Gln	p.H67Q	ENST00000298229	NM_001567.3	67	caC/caG	2/28	1	2	FACETS	0.943	0.799	1	0.943	0.799	1	CLONAL	1	TRUE	1	0.13	2		717	832	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	37	361	0				ENST00000310581	NM_198253.2	-/1132			0.193677705184577	1	FACETS	0.759	0.626	0.906	0.759	0.626	0.906	CLONAL	1	TRUE	0	0.221815439413559	1		361	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	88	816	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.221815439413559	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.221815439413559	1		816	591	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	67	630	3	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	0.979	0.851	1	0.979	0.851	1	CLONAL	1	TRUE	1	0.221815439413559	2		633	617	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696676	176696676	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	24	398	0	ENST00000439151.2:c.5377G>A	p.Glu1793Lys	p.E1793K	ENST00000439151	NM_022455.4	1793	Gag/Aag	16/23	1	2	FACETS	0.608	0.476	0.76	0.608	0.476	0.76	SUBCLONAL	1	TRUE	1	0.221815439413559	2		398	356	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577469	64577469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs794728616	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	70	657	0	ENST00000312049.6:c.113C>T	p.Ser38Phe	p.S38F	ENST00000312049	NM_130799.2	38	tCc/tTc	2/10	1	2	FACETS	0.945	0.823	1	0.945	0.823	1	CLONAL	1	TRUE	1	0.221815439413559	2		657	668	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001422	29001422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752383804	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	44	348	0	ENST00000282397.4:c.1310C>T	p.Ser437Leu	p.S437L	ENST00000282397	NM_002019.4	437	tCg/tTg	10/30	1	2	FACETS	0.936	0.786	1	0.936	0.786	1	CLONAL	1	TRUE	1	0.221815439413559	2		348	424	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448624	89448624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	75	447	0	ENST00000336596.2:c.1588C>T	p.Pro530Ser	p.P530S	ENST00000336596	NM_005233.5	530	Cca/Tca	7/17	0.221815439413559	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.221815439413559	1		447	569	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123826	46123826	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	24	297	0	ENST00000334344.6:c.93-1G>A		p.X31_splice	ENST00000334344	NM_152641.2	31			1	2	FACETS	0.613	0.48	0.766	0.613	0.48	0.766	SUBCLONAL	1	TRUE	1	0.221815439413559	2		297	353	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	43	345	0				ENST00000310581	NM_198253.2	-/1132			0.193677705184577	1	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	0	0.221815439413559	1		345	340	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793340	242793340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201540918	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	73	729	1	ENST00000334409.5:c.737C>T	p.Thr246Met	p.T246M	ENST00000334409	NM_005018.2	246	aCg/aTg	5/5	1	2	FACETS	0.768	0.67	0.874	0.768	0.67	0.874	SUBCLONAL	1	TRUE	1	0.221815439413559	2		730	857	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242646	16242646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	53	346	2	ENST00000375759.3:c.1267C>T	p.Arg423Cys	p.R423C	ENST00000375759	NM_015001.2	423	Cgc/Tgc	6/15	1	2	FACETS	0.933	0.796	1	0.933	0.796	1	CLONAL	1	TRUE	1	0.221815439413559	2		348	512	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864328	57864328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201538749	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	70	629	0	ENST00000228682.2:c.1805C>T	p.Ser602Leu	p.S602L	ENST00000228682	NM_005269.2	602	tCg/tTg	12/12	1	2	FACETS	0.873	0.76	0.995	0.873	0.76	0.995	CLONAL	1	TRUE	1	0.221815439413559	2		629	723	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012684	36012684	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	14	131	0	ENST00000358208.4:c.128C>T	p.Ser43Leu	p.S43L	ENST00000358208		43	tCg/tTg	2/12	1	2	FACETS	0.836	0.607	1	0.836	0.607	1	CLONAL	1	TRUE	1	0.221815439413559	2		131	151	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839778	27839778	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	76	524	0	ENST00000328488.2:c.316G>A	p.Glu106Lys	p.E106K	ENST00000328488	NM_003533.2	106	Gag/Aag	1/1	1	2	FACETS	0.99	0.868	1	0.99	0.868	1	CLONAL	1	TRUE	1	0.221815439413559	2		524	692	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954874	2954874	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	70	590	0	ENST00000396946.4:c.2836G>A	p.Glu946Lys	p.E946K	ENST00000396946	NM_032415.4	946	Gaa/Aaa	21/25	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.221815439413559	2		590	594	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426640	121426640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	60	524	0	ENST00000257555.6:c.331G>A	p.Asp111Asn	p.D111N	ENST00000257555		111	Gac/Aac	2/10	1	2	FACETS	0.949	0.818	1	0.949	0.818	1	CLONAL	1	TRUE	1	0.221815439413559	2		524	570	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911522	134911522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778136807	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	73	539	0	ENST00000398015.3:c.1987C>T	p.Arg663Trp	p.R663W	ENST00000398015	NM_004441.4	663	Cgg/Tgg	11/16	1	2	FACETS	0.99	0.865	1	0.99	0.865	1	CLONAL	1	TRUE	1	0.221815439413559	2		539	665	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696411	47696411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs968974699	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	58	526	0	ENST00000347630.2:c.412C>T	p.Arg138Cys	p.R138C	ENST00000347630	NM_001007230.1	138	Cgt/Tgt	6/11	1	2	FACETS	0.784	0.673	0.906	0.784	0.673	0.906	CLONAL	1	TRUE	1	0.221815439413559	2		526	667	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270165	66270165	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1416732153	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	37	284	0	ENST00000273854.3:c.1717C>T	p.Pro573Ser	p.P573S	ENST00000273854	NM_004439.5	573	Cct/Tct	8/18	1	2	FACETS	0.885	0.731	1	0.885	0.731	1	CLONAL	1	TRUE	1	0.221815439413559	2		284	377	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852174	63852174	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	65	493	0	ENST00000279873.7:c.2952G>C	p.Glu984Asp	p.E984D	ENST00000279873	NM_032199.2	984	gaG/gaC	10/10	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.221815439413559	2		493	570	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541511	29541511	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	28	279	0	ENST00000356175.3:c.1435G>A	p.Glu479Lys	p.E479K	ENST00000356175	NM_000267.3	479	Gaa/Aaa	13/57	1	2	FACETS	0.692	0.553	0.85	0.692	0.553	0.85	SUBCLONAL	1	TRUE	1	0.221815439413559	2		279	365	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073809	8073809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	40	330	1	ENST00000377482.5:c.850C>T	p.Pro284Ser	p.P284S	ENST00000377482	NM_018948.3	284	Ccc/Tcc	4/4	1	2	FACETS	0.92	0.766	1	0.92	0.766	1	CLONAL	1	TRUE	1	0.221815439413559	2		331	392	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258634	16258634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763007084	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	47	467	0	ENST00000375759.3:c.5899G>A	p.Glu1967Lys	p.E1967K	ENST00000375759	NM_015001.2	1967	Gag/Aag	11/15	1	2	FACETS	0.783	0.661	0.919	0.783	0.661	0.919	CLONAL	1	TRUE	1	0.221815439413559	2		467	541	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260102	16260102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	74	589	0	ENST00000375759.3:c.7367G>A	p.Ser2456Asn	p.S2456N	ENST00000375759	NM_015001.2	2456	aGt/aAt	11/15	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.221815439413559	2		589	659	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797363	45797363	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	76	606	0	ENST00000450313.1:c.1156C>T	p.Gln386Ter	p.Q386*	ENST00000450313	NM_012222.2	386	Caa/Taa	12/16	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.221815439413559	2		606	629	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310491	65310491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	61	533	0	ENST00000342505.4:c.2197C>T	p.Pro733Ser	p.P733S	ENST00000342505	NM_002227.2	733	Cca/Tca	16/25	1	2	FACETS	0.918	0.792	1	0.918	0.792	1	CLONAL	1	TRUE	1	0.221815439413559	2		533	599	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306540	163306540	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	37	333	0	ENST00000271452.3:c.338-1G>A		p.X113_splice	ENST00000271452	NM_145697.2	113			1	2	FACETS	0.714	0.589	0.855	0.714	0.589	0.855	SUBCLONAL	1	TRUE	1	0.221815439413559	2		333	467	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226568903	226568903	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	40	347	0	ENST00000366794.5:c.1166C>T	p.Pro389Leu	p.P389L	ENST00000366794	NM_001618.3	389	cCa/cTa	9/23	1	2	FACETS	0.823	0.685	0.978	0.823	0.685	0.978	CLONAL	1	TRUE	1	0.221815439413559	2		347	438	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333704	70333704	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	41	483	0	ENST00000373644.4:c.1609G>A	p.Gly537Ser	p.G537S	ENST00000373644	NM_030625.2	537	Ggt/Agt	2/12	1	2	FACETS	0.699	0.582	0.829	0.699	0.582	0.829	SUBCLONAL	1	TRUE	1	0.221815439413559	2		483	529	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659865	88659866	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	29	293	0	ENST00000372037.3:c.512_513delinsTT	p.Ser171Phe	p.S171F	ENST00000372037	NM_004329.2	171	tCC/tTT	7/13	1	2	FACETS	0.774	0.622	0.946	0.774	0.622	0.946	CLONAL	1	TRUE	1	0.221815439413559	2		293	338	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325061	123325062	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	57	609	1	ENST00000358487.5:c.266_267delinsAA	p.Gly89Glu	p.G89E	ENST00000358487	NM_000141.4	89	gGG/gAA	3/18	0.221815439413559	1	FACETS	0.711	0.609	0.822	0.711	0.609	0.822	SUBCLONAL	1	TRUE	0	0.221815439413559	1		610	643	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577346	64577347	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	85	718	0	ENST00000312049.6:c.235_236delinsTT	p.Pro79Phe	p.P79F	ENST00000312049	NM_130799.2	79	CCc/TTc	2/10	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.221815439413559	2		718	674	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200211	67200211	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371735596	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	83	708	0	ENST00000312629.5:c.519C>G	p.Phe173Leu	p.F173L	ENST00000312629	NM_003952.2	173	ttC/ttG	7/15	1	2	FACETS	0.921	0.811	1	0.921	0.811	1	CLONAL	1	TRUE	1	0.221815439413559	2		708	813	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373994	118373996	+	missense_variant	Missense_Mutation	TNP	TTG	TTG	ACT	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	26	366	0	ENST00000534358.1:c.7387_7389delinsACT	p.Leu2463Thr	p.L2463T	ENST00000534358	NM_005933.3	2463	TTG/ACT	27/36	1	2	FACETS	0.558	0.441	0.692	0.558	0.441	0.692	SUBCLONAL	1	TRUE	1	0.221815439413559	2		366	420	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398231	25398231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	35	350	0	ENST00000311936.3:c.88G>A	p.Asp30Asn	p.D30N	ENST00000311936	NM_004985.3	30	Gac/Aac	2/5	1	2	FACETS	0.666	0.545	0.801	0.666	0.545	0.801	SUBCLONAL	1	TRUE	1	0.221815439413559	2		350	474	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123826	46123827	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	24	304	0	ENST00000334344.6:c.93-1_93delinsAA		p.X31_splice	ENST00000334344	NM_152641.2	31		2/21	1	2	FACETS	0.585	0.458	0.731	0.585	0.458	0.731	SUBCLONAL	1	TRUE	1	0.221815439413559	2		304	370	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245201	46245202	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	57	469	0	ENST00000334344.6:c.3296_3297del	p.Tyr1099SerfsTer5	p.Y1099Sfs*5	ENST00000334344	NM_152641.2	1099	TAt/t	15/21	1	2	FACETS	0.883	0.758	1	0.883	0.758	1	CLONAL	1	TRUE	1	0.221815439413559	2		469	582	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438628	49438628	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	81	600	0	ENST00000301067.7:c.4862del	p.Pro1621GlnfsTer101	p.P1621Qfs*101	ENST00000301067	NM_003482.3	1621	cCa/ca	19/54	1	2	FACETS	0.979	0.862	1	0.979	0.862	1	CLONAL	1	TRUE	1	0.221815439413559	2		600	746	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865387	57865393	+	frameshift_variant	Frame_Shift_Del	DEL	ACTTGCC	ACTTGCC	-	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	86	847	0	ENST00000228682.2:c.2864_2870del	p.Asn955ThrfsTer19	p.N955Tfs*19	ENST00000228682	NM_005269.2	955	aACTTGCCc/ac	12/12	1	2	FACETS	0.855	0.755	0.962	0.855	0.755	0.962	CLONAL	1	TRUE	1	0.221815439413559	2		847	907	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856473	111856473	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1002118377	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	46	288	0	ENST00000341259.2:c.524G>A	p.Arg175Gln	p.R175Q	ENST00000341259	NM_005475.2	175	cGg/cAg	2/8	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.221815439413559	2		288	400	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911309	32911310	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	43	417	2	ENST00000380152.3:c.2817_2818delinsTT	p.Gln940Ter	p.Q940*	ENST00000380152		939	acCCaa/acTTaa	11/27	1	2	FACETS	0.694	0.58	0.82	0.694	0.58	0.82	SUBCLONAL	1	TRUE	1	0.221815439413559	2		419	559	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	338185	338185	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	101	755	0	ENST00000262320.3:c.2526G>C	p.Glu842Asp	p.E842D	ENST00000262320	NM_003502.3	842	gaG/gaC	11/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.221815439413559	2		755	748	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845600	72845600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772299356	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	75	755	0	ENST00000268489.5:c.3740C>T	p.Ser1247Leu	p.S1247L	ENST00000268489	NM_006885.3	1247	tCg/tTg	7/10	1	2	FACETS	0.902	0.789	1	0.902	0.789	1	CLONAL	1	TRUE	1	0.221815439413559	2		755	750	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341235	89341235	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	72	534	0	ENST00000301030.4:c.7700C>T	p.Pro2567Leu	p.P2567L	ENST00000301030	NM_001256183.1	2567	cCc/cTc	11/13	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.221815439413559	2		534	541	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347677	89347678	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	65	651	0	ENST00000301030.4:c.5272_5273delinsTT	p.Pro1758Phe	p.P1758F	ENST00000301030	NM_001256183.1	1758	CCc/TTc	9/13	1	2	FACETS	0.883	0.765	1	0.883	0.765	1	CLONAL	1	TRUE	1	0.221815439413559	2		651	664	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351134	89351134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	92	655	1	ENST00000301030.4:c.1816G>A	p.Glu606Lys	p.E606K	ENST00000301030	NM_001256183.1	606	Gag/Aag	9/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.221815439413559	2		656	720	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965209	15965209	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	32	291	0	ENST00000268712.3:c.5388-1G>A		p.X1796_splice	ENST00000268712	NM_006311.3	1796			0.221815439413559	1	FACETS	0.906	0.738	1	0.906	0.738	1	CLONAL	1	TRUE	0	0.221815439413559	1		291	283	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226362	41226362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	73	473	0	ENST00000357654.3:c.4661C>T	p.Pro1554Leu	p.P1554L	ENST00000357654	NM_007294.3	1554	cCa/cTa	14/23	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.221815439413559	2		473	603	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1206978	1206979	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	86	597	0	ENST00000326873.7:c.66_67delinsAA	p.Met22_Asp23delinsIleAsn	p.M22_D23delinsIN	ENST00000326873	NM_000455.4	22	atGGac/atAAac	1/10	0.221815439413559	1	FACETS	0.983	0.87	1	0.983	0.87	1	CLONAL	1	TRUE	0	0.221815439413559	1		597	701	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251547	10251547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762819722	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	74	610	0	ENST00000340748.4:c.3385G>A	p.Glu1129Lys	p.E1129K	ENST00000340748		1129	Gag/Aag	31/40	1	2	FACETS	0.984	0.861	1	0.984	0.861	1	CLONAL	1	TRUE	1	0.221815439413559	2		610	678	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254580	10254580	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	54	565	0	ENST00000340748.4:c.2930C>T	p.Ser977Phe	p.S977F	ENST00000340748		977	tCc/tTc	28/40	1	2	FACETS	0.789	0.673	0.916	0.789	0.673	0.916	CLONAL	1	TRUE	1	0.221815439413559	2		565	617	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271584	15271585	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	91	802	1	ENST00000263388.2:c.6854_6855delinsAA	p.Gly2285Glu	p.G2285E	ENST00000263388	NM_000435.2	2285	gGG/gAA	33/33	1	2	FACETS	0.914	0.81	1	0.914	0.81	1	CLONAL	1	TRUE	1	0.221815439413559	2		803	898	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276323	15276323	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	77	643	0	ENST00000263388.2:c.5671C>T	p.Leu1891Phe	p.L1891F	ENST00000263388	NM_000435.2	1891	Ctc/Ttc	31/33	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.221815439413559	2		643	674	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303214	15303214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760267181	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	98	801	0	ENST00000263388.2:c.314C>T	p.Ser105Leu	p.S105L	ENST00000263388	NM_000435.2	105	tCa/tTa	3/33	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.221815439413559	2		801	869	SUCCESS
ALK	238	MSKCC	GRCh37	2	29420411	29420411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	59	511	0	ENST00000389048.3:c.4070C>T	p.Pro1357Leu	p.P1357L	ENST00000389048	NM_004304.4	1357	cCt/cTt	27/29	1	2	FACETS	0.902	0.776	1	0.902	0.776	1	CLONAL	1	TRUE	1	0.221815439413559	2		511	590	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248675	212248675	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	45	424	1	ENST00000342788.4:c.3592G>A	p.Ala1198Thr	p.A1198T	ENST00000342788	NM_005235.2	1198	Gcc/Acc	28/28	1	2	FACETS	0.712	0.598	0.838	0.712	0.598	0.838	SUBCLONAL	1	TRUE	1	0.221815439413559	2		425	570	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251730	212251730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759088587	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	52	392	0	ENST00000342788.4:c.3329C>T	p.Thr1110Ile	p.T1110I	ENST00000342788	NM_005235.2	1110	aCc/aTc	27/28	1	2	FACETS	0.963	0.82	1	0.963	0.82	1	CLONAL	1	TRUE	1	0.221815439413559	2		392	487	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022460	31022460	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	39	312	0	ENST00000375687.4:c.1945G>T	p.Gly649Ter	p.G649*	ENST00000375687	NM_015338.5	649	Gga/Tga	13/13	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.221815439413559	2		312	336	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31025056	31025056	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	69	448	0	ENST00000375687.4:c.4541T>G	p.Ile1514Ser	p.I1514S	ENST00000375687	NM_015338.5	1514	aTc/aGc	13/13	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.221815439413559	2		448	562	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657032	45657032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	56	485	0	ENST00000407780.3:c.124G>A	p.Gly42Arg	p.G42R	ENST00000407780	NM_001283052.1	42	Gga/Aga	3/7	1	2	FACETS	0.94	0.806	1	0.94	0.806	1	CLONAL	1	TRUE	1	0.221815439413559	2		485	537	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960001	134960002	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	42	445	0	ENST00000398015.3:c.2358_2359delinsTT	p.Pro787Ser	p.P787S	ENST00000398015	NM_004441.4	786	atCCct/atTTct	13/16	1	2	FACETS	0.727	0.606	0.861	0.727	0.606	0.861	SUBCLONAL	1	TRUE	1	0.221815439413559	2		445	521	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520241	176520242	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	72	751	2	ENST00000292408.4:c.1160_1161delinsTT	p.Ala387Val	p.A387V	ENST00000292408	NM_213647.1	387	gCC/gTT	9/18	1	2	FACETS	0.899	0.785	1	0.899	0.785	1	CLONAL	1	TRUE	1	0.221815439413559	2		753	722	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225655	26225655	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	66	521	0	ENST00000360408.1:c.273G>T	p.Met91Ile	p.M91I	ENST00000360408	NM_003532.2	91	atG/atT	1/1	1	2	FACETS	0.985	0.855	1	0.985	0.855	1	CLONAL	1	TRUE	1	0.221815439413559	2		521	604	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183160	32183160	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	81	607	0	ENST00000375023.3:c.1864C>T	p.Gln622Ter	p.Q622*	ENST00000375023	NM_004557.3	622	Cag/Tag	12/30	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.221815439413559	2		607	711	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955130	93955130	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	55	377	1	ENST00000369303.4:c.2768C>A	p.Thr923Asn	p.T923N	ENST00000369303	NM_004440.3	923	aCt/aAt	16/17	1	2	FACETS	0.87	0.744	1	0.87	0.744	1	CLONAL	1	TRUE	1	0.221815439413559	2		378	570	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674294	117674294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	85	433	0	ENST00000368508.3:c.4180C>T	p.Leu1394Phe	p.L1394F	ENST00000368508	NM_002944.2	1394	Ctt/Ttt	26/43	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.221815439413559	2		433	638	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879415	151879415	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	61	454	0	ENST00000262189.6:c.5530G>A	p.Asp1844Asn	p.D1844N	ENST00000262189	NM_170606.2	1844	Gat/Aat	36/59	1	2	FACETS	0.903	0.779	1	0.903	0.779	1	CLONAL	1	TRUE	1	0.221815439413559	2		454	609	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407587	139407587	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0046366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	157	626	0	ENST00000277541.6:c.2354-1G>A		p.X785_splice	ENST00000277541	NM_017617.3	785			0.221815439413559	2	FACETS	0.975	0.895	1	0.975	0.895	1	CLONAL	2	TRUE	0	0.221815439413559	2		626	726	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637555	52637555	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	20	319	0	ENST00000394830.3:c.2761C>T	p.Arg921Ter	p.R921*	ENST00000394830	NM_018313.4	921	Cga/Tga	18/30	0.187239270926442	1	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	0	0.2	1		319	144	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0046367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	72	985	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.2	2		991	559	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0046367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	101	1018	4	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	0.132479333442454	3	FACETS	0.851	0.761	0.945	0.851	0.761	0.945	CLONAL	2	TRUE	1	0.2	3		1022	653	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346157	89346158	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs878855327	NA	P-0046367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	37	318	1	ENST00000301030.4:c.6792dup	p.Ala2265ArgfsTer8	p.A2265Rfs*8	ENST00000301030	NM_001256183.1	2264	-/C	9/13	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.2	2		319	307	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429977	78429978	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1200882279	NA	P-0046367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	26	271	0	ENST00000370768.2:c.901dup	p.Ile301AsnfsTer4	p.I301Nfs*4	ENST00000370768	NM_003902.3	301	ata/aAta	11/20	0.132479333442454	3	FACETS	0.786	0.627	0.964	0.786	0.627	0.964	CLONAL	2	TRUE	1	0.2	3		271	182	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0046367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	16	149	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	0.221330166633945	1	FACETS	0.889	0.661	1	0.889	0.661	1	CLONAL	1	TRUE	0	0.2	1		149	162	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0046367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	30	345	2	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.763	0.615	0.932	0.763	0.615	0.932	CLONAL	1	TRUE	1	0.2	2		347	393	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0046367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	61	424	2	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	0.221330166633945	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.2	1		426	488	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433847	78433848	+	splice_donor_variant	Splice_Site	DEL	AC	AC	-	rs1477051807	NA	P-0046367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	19	250	0	ENST00000370768.2:c.250+1_250+2del		p.X84_splice	ENST00000370768	NM_003902.3	84			0.132479333442454	3	FACETS	0.78	0.598	0.989	0.78	0.598	0.989	CLONAL	2	TRUE	1	0.2	3		250	134	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965666	90965666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	24	309	0	ENST00000265433.3:c.1651del	p.Arg551GlyfsTer8	p.R551Gfs*8	ENST00000265433	NM_002485.4	551	Agg/gg	11/16	1	2	FACETS	0.909	0.722	1	1	0.945	1	CLONAL	2	TRUE	1	0.2	2		309	132	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748509	43748509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371177206	NA	P-0046367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	38	328	0	ENST00000523873.1:c.463C>T	p.Arg155Cys	p.R155C	ENST00000523873		155	Cgc/Tgc	6/8	0.132479333442454	3	FACETS	1	0.89	1	0.551	0.456	0.657	CLONAL	1	TRUE	1	0.2	3		328	379	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723126	49723128	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs751306787	NA	P-0046367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	67	428	0	ENST00000449682.2:c.1288_1290del	p.Glu430del	p.E430del	ENST00000449682	NM_020998.3	430	GAG/-	11/18	0.260908009239104	2	FACETS	1	0.97	1	0.72	0.628	0.82	CLONAL	1	TRUE	0	0.2	2		428	465	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300040	137300040	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	80	610	1	ENST00000481739.1:c.331del	p.Leu111TrpfsTer57	p.L111Wfs*57	ENST00000481739	NM_002957.4	109	Ccc/cc	3/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.2	2		611	650	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436065	116436065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761522694	NA	P-0046367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	57	409	0	ENST00000397752.3:c.4060G>A	p.Ala1354Thr	p.A1354T	ENST00000397752	NM_000245.2	1354	Gct/Act	21/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.2	2		409	450	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471713	120471713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	53	408	1	ENST00000256646.2:c.3778C>T	p.Arg1260Cys	p.R1260C	ENST00000256646	NM_024408.3	1260	Cgt/Tgt	23/34	0.132479333442454	3	FACETS	1	0.925	1	0.569	0.486	0.661	CLONAL	1	TRUE	1	0.2	3		409	512	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783767	50783767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375455772	NA	P-0046367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	34	441	1	ENST00000398568.2:c.158G>A	p.Arg53His	p.R53H	ENST00000398568	NM_001042412.1	53	cGt/cAt	3/18	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.2	2		442	292	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431459	49431459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	76	611	0	ENST00000301067.7:c.9680C>T	p.Ala3227Val	p.A3227V	ENST00000301067	NM_003482.3	3227	gCa/gTa	34/54	0.132479333442454	3	FACETS	1	0.974	1	0.733	0.644	0.829	CLONAL	1	TRUE	1	0.2	3		611	570	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794779	120794779	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768324684	NA	P-0046367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	86	655	0	ENST00000257552.2:c.578C>T	p.Thr193Met	p.T193M	ENST00000257552	NM_002442.3	193	aCg/aTg	9/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.2	2		655	678	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348479	89348479	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1296165234	NA	P-0046367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	71	659	2	ENST00000301030.4:c.4471G>A	p.Glu1491Lys	p.E1491K	ENST00000301030	NM_001256183.1	1491	Gag/Aag	9/13	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.2	2		661	643	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021060	26021060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	52	351	1	ENST00000357647.3:c.343G>A	p.Ala115Thr	p.A115T	ENST00000357647	NM_003529.2	115	Gcc/Acc	1/1	0.3	4	FACETS	1	0.927	1			1	CLONAL	1	TRUE	NA	0.2	4		352	543	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965617	93965617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746058123	NA	P-0046367-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	21	348	0	ENST00000369303.4:c.2311G>A	p.Val771Ile	p.V771I	ENST00000369303	NM_004440.3	771	Gtt/Att	13/17	0.132479333442454	3	FACETS	0.951	0.734	1	0.475	0.367	0.601	CLONAL	1	TRUE	1	0.2	3		348	243	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0046386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	345	109	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.65275059732147	3	FACETS	0.992	0.946	1	0.992	0.946	1	CLONAL	2	TRUE	1	0.65275059732147	3		109	707	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441234	52441234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1440561167	NA	P-0046386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	192	395	0	ENST00000460680.1:c.536G>A	p.Arg179Gln	p.R179Q	ENST00000460680	NM_004656.3	179	cGg/cAg	7/17	0.65275059732147	1	FACETS	0.932	0.874	0.992	0.932	0.874	0.992	CLONAL	1	TRUE	0	0.65275059732147	1		395	425	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111501	8111512	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGAATGCCAA	GAGGAATGCCAA	T	novel	NA	P-0046386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	239	582	1	ENST00000346208.3:c.987_998delinsT	p.Arg329SerfsTer19	p.R329Sfs*19	ENST00000346208		329	agGAGGAATGCCAAt/agTt	5/6	1	2	FACETS	0.879	0.823	0.937	0.879	0.823	0.937	CLONAL	1	TRUE	1	0.65275059732147	2		583	833	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0046387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	122	363	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.23469505929337	5	FACETS	0.89	0.812	0.97	0.89	0.812	0.97	CLONAL	4	TRUE	1	0.23469505929337	5		363	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577507	7577507	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	121	561	0	ENST00000269305.4:c.774A>T	p.Glu258Asp	p.E258D	ENST00000269305	NM_001126112.2	258	gaA/gaT	7/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.23469505929337	2		561	963	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204938	128204938	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	112	723	0	ENST00000341105.2:c.503C>A	p.Ser168Tyr	p.S168Y	ENST00000341105	NM_032638.4	168	tCc/tAc	3/6	0.181726251610894	3	FACETS	0.846	0.758	0.939	0.423	0.379	0.47	CLONAL	1	TRUE	1	0.23469505929337	3		723	1261	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348446	89348446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	134	654	0	ENST00000301030.4:c.4504C>T	p.Pro1502Ser	p.P1502S	ENST00000301030	NM_001256183.1	1502	Ccc/Tcc	9/13	1	2	FACETS	0.951	0.862	1	0.951	0.862	1	CLONAL	1	TRUE	1	0.23469505929337	2		654	1201	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131392	202131392	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	35	439	0	ENST00000358485.4:c.360C>A	p.Phe120Leu	p.F120L	ENST00000358485	NM_001080125.1	120	ttC/ttA	2/9	1	2	FACETS	0.474	0.387	0.572	0.474	0.387	0.572	SUBCLONAL	1	TRUE	1	0.23469505929337	2		439	629	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334780	81334780	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046387-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	59	427	0	ENST00000222390.5:c.1936C>A	p.His646Asn	p.H646N	ENST00000222390	NM_000601.4	646	Cat/Aat	17/18	0.184806903349994	3	FACETS	1	0.965	1	0.699	0.603	0.802	CLONAL	1	TRUE	1	0.23469505929337	3		427	402	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469669	NA	P-0046389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	31	457	0	ENST00000374080.3:c.130G>A	p.Gly44Ser	p.G44S	ENST00000374080		44	Ggt/Agt	2/45	1	2	FACETS	0.492	0.396	0.601	0.492	0.396	0.601	SUBCLONAL	1	TRUE	1	0.13	2		457	970	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	16	440	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.314	0.23	0.414	0.314	0.23	0.414	SUBCLONAL	1	TRUE	1	0.13	2		440	785	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579349	7579349	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	34	540	0	ENST00000269305.4:c.338T>C	p.Phe113Ser	p.F113S	ENST00000269305	NM_001126112.2	113	tTc/tCc	4/11	1	2	FACETS	0.439	0.357	0.533	0.439	0.357	0.533	SUBCLONAL	1	TRUE	1	0.13	2		540	1191	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812335	212812335	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	27	203	0	ENST00000342788.4:c.241C>T	p.Arg81Ter	p.R81*	ENST00000342788	NM_005235.2	81	Cga/Tga	3/28	1	2	FACETS	1	0.818	1	1	0.818	1	CLONAL	1	TRUE	1	0.13	2		203	403	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	32	483	0	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	0.656	0.53	0.798	0.656	0.53	0.798	SUBCLONAL	1	TRUE	1	0.13	2		483	751	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025924	48025924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	41	258	0	ENST00000234420.5:c.802G>A	p.Asp268Asn	p.D268N	ENST00000234420	NM_000179.2	268	Gac/Aac	4/10	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.13	2		258	612	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0046390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	213	646	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.179775703026704	2	FACETS	1	0.972	1	0.544	0.505	0.584	INDETERMINATE	1	TRUE	0	0.39165674814797	2		646	1000	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0046390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	197	591	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.251156852399486	2	FACETS	1	0.99	1	0.709	0.659	0.761	CLONAL	1	TRUE	0	0.39165674814797	2		591	709	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032794	30032794	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434259	NA	P-0046390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	166	382	0	ENST00000338641.4:c.169C>T	p.Arg57Ter	p.R57*	ENST00000338641	NM_000268.3	57	Cga/Tga	2/16	0.251156852399486	2	FACETS	1	0.989	1	0.715	0.66	0.772	CLONAL	1	TRUE	0	0.39165674814797	2		382	593	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928881	49928881	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs551800134	NA	P-0046390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	200	747	0	ENST00000296474.3:c.3485C>A	p.Pro1162His	p.P1162H	ENST00000296474	NM_002447.2	1162	cCc/cAc	16/20	0.251156852399486	2	FACETS	1	0.986	1	0.624	0.579	0.671	CLONAL	1	TRUE	0	0.39165674814797	2		747	818	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041565	42041566	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	156	477	0	ENST00000219905.7:c.5764dup	p.Ile1922AsnfsTer4	p.I1922Nfs*4	ENST00000219905	NM_001164273.1	1920	-/A	17/24	0.244196211839588	2	FACETS	1	0.983	1	0.628	0.577	0.681	CLONAL	1	TRUE	0	0.39165674814797	2		477	634	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690817	89690818	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	70	258	0	ENST00000371953.3:c.226dup	p.Tyr76LeufsTer2	p.Y76Lfs*2	ENST00000371953	NM_000314.4	75	cat/caTt	4/9	0.298325330521058	2	FACETS	1	0.967	1	0.65	0.573	0.731	CLONAL	1	TRUE	0	0.39165674814797	2		258	275	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385230	4385230	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	109	430	0	ENST00000261254.3:c.255C>G	p.Asp85Glu	p.D85E	ENST00000261254	NM_001759.3	85	gaC/gaG	2/5	NA	2	FACETS	0.658	0.59	0.73			1	INDETERMINATE	1	TRUE	NA	0.39165674814797	2		430	846	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434595	110434595	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	128	447	0	ENST00000375856.3:c.3806A>G	p.Gln1269Arg	p.Q1269R	ENST00000375856	NM_003749.2	1269	cAg/cGg	1/2	0.378173919137079	1	FACETS	0.805	0.731	0.882	0.805	0.731	0.882	CLONAL	1	TRUE	0	0.39165674814797	1		447	653	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820717	3820717	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	290	786	0	ENST00000262367.5:c.2734del	p.Thr912ProfsTer15	p.T912Pfs*15	ENST00000262367	NM_004380.2	912	Acc/cc	14/31	0.251156852399486	2	FACETS	1	0.99	1	0.615	0.578	0.654	CLONAL	1	TRUE	0	0.39165674814797	2		786	1203	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97934332	97934332	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	44	246	0	ENST00000289081.3:c.443del	p.Gly148ValfsTer10	p.G148Vfs*10	ENST00000289081	NM_000136.2	148	gGt/gt	5/15	0.244196211839588	2	FACETS	1	0.949	1	0.646	0.55	0.748	CLONAL	1	TRUE	0	0.39165674814797	2		246	174	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250867	153250867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	15	391	1	ENST00000281708.4:c.1193C>T	p.Ser398Phe	p.S398F	ENST00000281708	NM_033632.3	398	tCt/tTt	8/12	1	2	FACETS	0.652	0.476	0.864	0.652	0.476	0.864	SUBCLONAL	1	TRUE	1	0.153804389922781	2		392	299	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17743024	17743024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	53	723	4	ENST00000250003.3:c.932C>T	p.Ala311Val	p.A311V	ENST00000250003	NM_002478.4	311	gCg/gTg	3/3	0.153804389922781	1	FACETS	0.818	0.696	0.952	0.818	0.696	0.952	CLONAL	1	TRUE	0	0.153804389922781	1		727	778	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037409	12037409	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	80	689	0	ENST00000396373.4:c.1040A>C	p.Gln347Pro	p.Q347P	ENST00000396373	NM_001987.4	347	cAg/cCg	6/8	0.153804389922781	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.153804389922781	1		689	848	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591110	67591110	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	23	306	0	ENST00000274335.5:c.1703C>G	p.Pro568Arg	p.P568R	ENST00000274335		568	cCa/cGa	12/15	1	2	FACETS	0.917	0.716	1	0.917	0.716	1	CLONAL	1	TRUE	1	0.153804389922781	2		306	326	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495441	149495441	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1444854414	NA	P-0046391-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	61	978	0	ENST00000261799.4:c.3206A>G	p.Glu1069Gly	p.E1069G	ENST00000261799	NM_002609.3	1069	gAa/gGa	23/23	1	2	FACETS	0.706	0.606	0.814	0.706	0.606	0.814	SUBCLONAL	1	TRUE	1	0.153804389922781	2		978	1124	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	27	424	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.641	0.51	0.791	0.641	0.51	0.791	SUBCLONAL	1	TRUE	1	0.22	2		424	383	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	58	473	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	0.0867960261038291	0	FACETS	1	0.91	1			1	INDETERMINATE	1	TRUE	0	0.22	0		474	383	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	103	407	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.892	0.801	0.987	1	0.986	1	CLONAL	2	TRUE	1	0.22	2		407	525	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	88	405	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.908	1	1	0.986	1	CLONAL	2	TRUE	1	0.22	2		408	392	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276860	15276861	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs753725730	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	69	601	3	ENST00000263388.2:c.5404dup	p.Ala1802GlyfsTer8	p.A1802Gfs*8	ENST00000263388	NM_000435.2	1802	gct/gGct	30/33	0.121364223884508	0	FACETS	0.925	0.807	1			1	INDETERMINATE	1	TRUE	0	0.22	0		604	529	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	70	510	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	0.964	0.84	1	0.964	0.84	1	CLONAL	1	TRUE	1	0.22	2		510	660	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212208	5212208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148739536	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	47	562	1	ENST00000357368.4:c.4823G>A	p.Arg1608Gln	p.R1608Q	ENST00000357368	NM_002850.3	1608	cGg/cAg	32/38	0.121364223884508	0	FACETS	0.805	0.68	0.942			1	INDETERMINATE	1	TRUE	0	0.22	0		563	414	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	30	255	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.812	0.655	0.989	0.812	0.655	0.989	CLONAL	1	TRUE	1	0.22	2		255	336	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042115	6042115	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881917	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	15	172	0	ENST00000265849.7:c.506G>A	p.Arg169His	p.R169H	ENST00000265849	NM_000535.5	169	cGc/cAc	5/15	1	2	FACETS	0.559	0.409	0.739	0.559	0.409	0.739	SUBCLONAL	1	TRUE	1	0.22	2		172	244	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056237	26056245	+	inframe_deletion	In_Frame_Del	DEL	CTTCTTGGG	CTTCTTGGG	-	rs749190253	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	41	425	0	ENST00000343677.2:c.412_420del	p.Pro138_Lys140del	p.P138_K140del	ENST00000343677	NM_005319.3	138	CCCAAGAAG/-	1/1	1	2	FACETS	0.717	0.597	0.851	0.717	0.597	0.851	SUBCLONAL	1	TRUE	1	0.22	2		425	520	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447774	187447774	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536118071	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	59	446	0	ENST00000232014.4:c.419G>A	p.Arg140His	p.R140H	ENST00000232014	NM_001130845.1	140	cGt/cAt	5/10	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.22	2		446	482	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741636	17741636	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1441843696	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	38	223	0	ENST00000250003.3:c.307C>T	p.Arg103Cys	p.R103C	ENST00000250003	NM_002478.4	103	Cgc/Tgc	1/3	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.22	2		223	231	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058747	180058748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755445139	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	52	653	1	ENST00000261937.6:c.89dup	p.Thr31AspfsTer15	p.T31Dfs*15	ENST00000261937	NM_182925.4	30	ccg/ccCg	2/30	0.0867960261038291	0	FACETS	0.683	0.581	0.794			1	INDETERMINATE	1	TRUE	0	0.22	0		654	540	SUCCESS
APC	324	MSKCC	GRCh37	5	112175952	112175952	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587783031	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	21	175	0	ENST00000257430.4:c.4666del	p.Thr1556LeufsTer9	p.T1556Lfs*9	ENST00000257430	NM_000038.5	1554	gAa/ga	16/16	1	2	FACETS	0.809	0.625	1	0.809	0.625	1	CLONAL	1	TRUE	1	0.22	2		175	236	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446845	187446845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201771435	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	72	521	0	ENST00000232014.4:c.1348G>A	p.Val450Ile	p.V450I	ENST00000232014	NM_001130845.1	450	Gtt/Att	5/10	1	2	FACETS	0.921	0.804	1	0.921	0.804	1	CLONAL	1	TRUE	1	0.22	2		521	711	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183297	56183297	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	54	412	0	ENST00000399503.3:c.4207G>T	p.Gly1403Ter	p.G1403*	ENST00000399503	NM_005921.1	1403	Gga/Tga	18/20	1	2	FACETS	0.957	0.818	1	0.957	0.818	1	CLONAL	1	TRUE	1	0.22	2		412	513	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609379	39609379	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749775725	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	50	292	0	ENST00000262039.4:c.1681C>T	p.Arg561Cys	p.R561C	ENST00000262039	NM_002647.2	561	Cgc/Tgc	15/25	1	2	FACETS	0.935	0.794	1	0.935	0.794	1	CLONAL	1	TRUE	1	0.22	2		292	486	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007331	143007332	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs772784869	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	42	275	0	ENST00000262992.4:c.2452dup	p.Arg818LysfsTer26	p.R818Kfs*26	ENST00000262992	NM_001101669.1	818	aga/aAga	22/24	1	2	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	1	0.22	2		275	374	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86637110	86637110	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	27	223	0	ENST00000274376.6:c.1021C>T	p.Arg341Trp	p.R341W	ENST00000274376	NM_002890.2	341	Cgg/Tgg	6/25	1	2	FACETS	0.72	0.573	0.887	0.72	0.573	0.887	SUBCLONAL	1	TRUE	1	0.22	2		223	341	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500802	8500802	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1413041664	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	54	372	0	ENST00000356435.5:c.2080G>A	p.Gly694Ser	p.G694S	ENST00000356435		694	Ggc/Agc	13/35	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.22	2		372	486	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480624	50480624	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	32	351	1	ENST00000394963.4:c.494G>A	p.Arg165Gln	p.R165Q	ENST00000394963	NM_003076.4	165	cGg/cAg	4/13	1	2	FACETS	0.843	0.685	1	0.843	0.685	1	CLONAL	1	TRUE	1	0.22	2		352	345	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048796	180048796	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	71	772	0	ENST00000261937.6:c.1766G>A	p.Arg589His	p.R589H	ENST00000261937	NM_182925.4	589	cGc/cAc	13/30	0.0867960261038291	0	FACETS	0.834	0.728	0.948			1	INDETERMINATE	1	TRUE	0	0.22	0		772	604	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943374	71943374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141305290	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	40	488	0	ENST00000298229.2:c.1706C>T	p.Thr569Met	p.T569M	ENST00000298229	NM_001567.3	569	aCg/aTg	14/28	1	2	FACETS	0.907	0.755	1	0.907	0.755	1	CLONAL	1	TRUE	1	0.22	2		488	401	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106004	8106004	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	57	400	0	ENST00000346208.3:c.824G>A	p.Arg275Gln	p.R275Q	ENST00000346208		275	cGg/cAg	4/6	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.22	2		400	511	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272519	11272519	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	42	341	0	ENST00000361445.4:c.3411G>T	p.Glu1137Asp	p.E1137D	ENST00000361445	NM_004958.3	1137	gaG/gaT	23/58	0.0867960261038291	0	FACETS	0.796	0.666	0.94			1	INDETERMINATE	1	TRUE	0	0.22	0		341	374	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173703	108173703	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	29	368	0	ENST00000278616.4:c.5443G>T	p.Asp1815Tyr	p.D1815Y	ENST00000278616	NM_000051.3	1815	Gac/Tac	36/63	1	2	FACETS	0.703	0.564	0.861	0.703	0.564	0.861	SUBCLONAL	1	TRUE	1	0.22	2		368	375	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438733	49438733	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1170765431	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	60	595	0	ENST00000301067.7:c.4757G>A	p.Arg1586His	p.R1586H	ENST00000301067	NM_003482.3	1586	cGc/cAc	19/54	1	2	FACETS	0.874	0.753	1	0.874	0.753	1	CLONAL	1	TRUE	1	0.22	2		595	624	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562580	21562580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1344470683	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	11	154	0	ENST00000382592.4:c.1339G>A	p.Val447Met	p.V447M	ENST00000382592	NM_014572.2	447	Gtg/Atg	4/8	1	2	FACETS	0.775	0.538	1	0.775	0.538	1	CLONAL	1	TRUE	1	0.22	2		154	129	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950837	32950837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80359124	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	41	338	0	ENST00000380152.3:c.8663G>A	p.Arg2888His	p.R2888H	ENST00000380152		2888	cGt/cAt	21/27	1	2	FACETS	0.944	0.787	1	0.944	0.787	1	CLONAL	1	TRUE	1	0.22	2		338	395	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56867238	56867238	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	37	391	0	ENST00000308159.5:c.1457G>T	p.Arg486Leu	p.R486L	ENST00000308159	NM_014669.4	486	cGc/cTc	13/22	0.121364223884508	0	FACETS	0.569	0.469	0.681			1	INDETERMINATE	1	TRUE	0	0.22	0		391	461	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993779	72993779	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	64	495	2	ENST00000268489.5:c.266C>T	p.Ala89Val	p.A89V	ENST00000268489	NM_006885.3	89	gCc/gTc	2/10	0.3	3	FACETS	0.801	0.697	0.914			1	CLONAL	2	TRUE	NA	0.22	3		497	403	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227091	2227091	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	72	595	4	ENST00000398665.3:c.4571G>A	p.Gly1524Asp	p.G1524D	ENST00000398665	NM_032482.2	1524	gGc/gAc	27/28	0.121364223884508	0	FACETS	1	0.917	1			1	INDETERMINATE	1	TRUE	0	0.22	0		599	481	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247835	10247835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780170131	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	49	749	0	ENST00000340748.4:c.4367G>A	p.Arg1456Gln	p.R1456Q	ENST00000340748		1456	cGg/cAg	36/40	0.121364223884508	0	FACETS	0.635	0.538	0.743			1	INDETERMINATE	1	TRUE	0	0.22	0		749	547	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610630	10610631	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	53	526	0	ENST00000171111.5:c.79dup	p.Ala27GlyfsTer11	p.A27Gfs*11	ENST00000171111	NM_203500.1	27	gca/gGca	2/6	0.121364223884508	0	FACETS	0.822	0.702	0.953			1	INDETERMINATE	1	TRUE	0	0.22	0		526	457	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672723	47672725	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs587779082	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	60	438	0	ENST00000233146.2:c.1316_1318del	p.Pro439del	p.P439del	ENST00000233146	NM_000251.2	438	aCTCct/act	8/16	1	2	FACETS	0.983	0.847	1	0.983	0.847	1	CLONAL	1	TRUE	1	0.22	2		438	555	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172172	99172172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372688727	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	32	479	1	ENST00000074304.5:c.1738G>A	p.Ala580Thr	p.A580T	ENST00000074304	NM_001134224.1	580	Gcc/Acc	17/26	1	2	FACETS	0.654	0.53	0.793	0.654	0.53	0.793	SUBCLONAL	1	TRUE	1	0.22	2		480	445	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108241	209108241	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs762089749	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	49	452	0	ENST00000345146.2:c.608A>G	p.Lys203Arg	p.K203R	ENST00000345146	NM_005896.2	203	aAg/aGg	6/10	1	2	FACETS	0.928	0.787	1	0.928	0.787	1	CLONAL	1	TRUE	1	0.22	2		452	480	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342936	225342936	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs763087632	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	45	354	0	ENST00000264414.4:c.2156A>G	p.His719Arg	p.H719R	ENST00000264414	NM_003590.4	719	cAc/cGc	15/16	1	2	FACETS	0.923	0.777	1	0.923	0.777	1	CLONAL	1	TRUE	1	0.22	2		354	443	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660126	227660126	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1244353274	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	53	576	0	ENST00000305123.5:c.3329C>T	p.Ala1110Val	p.A1110V	ENST00000305123	NM_005544.2	1110	gCc/gTc	1/2	1	2	FACETS	0.867	0.739	1	0.867	0.739	1	CLONAL	1	TRUE	1	0.22	2		576	556	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588742	52588742	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs145488469	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	41	477	0	ENST00000394830.3:c.4286C>T	p.Pro1429Leu	p.P1429L	ENST00000394830	NM_018313.4	1429	cCg/cTg	27/30	1	2	FACETS	0.8	0.666	0.948	0.8	0.666	0.948	CLONAL	1	TRUE	1	0.22	2		477	466	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247265	153247266	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCTG	novel	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	36	284	0	ENST00000281708.4:c.1533_1536dup	p.Arg513GlnfsTer5	p.R513Qfs*5	ENST00000281708	NM_033632.3	512	-/CAGG	10/12	1	2	FACETS	0.892	0.734	1	0.892	0.734	1	CLONAL	1	TRUE	1	0.22	2		284	367	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637260	176637260	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	45	493	0	ENST00000439151.2:c.1860G>T	p.Lys620Asn	p.K620N	ENST00000439151	NM_022455.4	620	aaG/aaT	5/23	0.0867960261038291	0	FACETS	0.712	0.599	0.837			1	INDETERMINATE	1	TRUE	0	0.22	0		493	448	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912288	29912288	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	69	890	0	ENST00000376809.5:c.907C>T	p.Gln303Ter	p.Q303*	ENST00000376809	NM_002116.7	303	Cag/Tag	5/8	1	2	FACETS	0.723	0.628	0.826	0.723	0.628	0.826	SUBCLONAL	1	TRUE	1	0.22	2		890	868	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959067	2959067	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376539147	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	58	618	0	ENST00000396946.4:c.2449G>A	p.Ala817Thr	p.A817T	ENST00000396946	NM_032415.4	817	Gcg/Acg	18/25	1	2	FACETS	0.997	0.857	1	0.997	0.857	1	CLONAL	1	TRUE	1	0.22	2		618	529	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522629	106522629	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	25	338	0	ENST00000359195.3:c.2606G>A	p.Cys869Tyr	p.C869Y	ENST00000359195	NM_002649.2	869	tGc/tAc	7/11	1	2	FACETS	0.63	0.496	0.783	0.63	0.496	0.783	SUBCLONAL	1	TRUE	1	0.22	2		338	361	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347939	128347939	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	80	561	0	ENST00000265960.3:c.566G>C	p.Arg189Thr	p.R189T	ENST00000265960	NM_001006617.1	189	aGa/aCa	5/12	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.22	2		561	676	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397732	139397734	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0046394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	51	643	0	ENST00000277541.6:c.5067_5069del	p.Ser1690del	p.S1690del	ENST00000277541	NM_017617.3	1689	tcCTCg/tcg	27/34	1	2	FACETS	0.944	0.803	1	0.944	0.803	1	CLONAL	1	TRUE	1	0.22	2		643	491	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0046395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	415	325	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.793785808754991	2	FACETS	0.887	0.864	0.909	0.887	0.864	0.909	CLONAL	2	TRUE	0	0.91691626474351	2		325	510	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0046395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	499	109	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.817317386400343	3	FACETS	0.988	0.956	1	0.988	0.956	1	CLONAL	2	TRUE	1	0.91691626474351	3		109	803	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0046395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	268	175	5	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.881770299621229	3	FACETS	0.929	0.903	0.952	0.929	0.903	0.952	CLONAL	3	TRUE	0	0.91691626474351	3		180	306	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347209	347209	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373454022	NA	P-0046395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	440	502	2	ENST00000262320.3:c.1802C>T	p.Ala601Val	p.A601V	ENST00000262320	NM_003502.3	601	gCg/gTg	7/11	0.817317386400343	3	FACETS	0.99	0.955	1	0.99	0.955	1	CLONAL	2	TRUE	1	0.91691626474351	3		504	707	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591826	48591826	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	402	332	6	ENST00000342988.3:c.989A>T	p.Glu330Val	p.E330V	ENST00000342988	NM_005359.5	330	gAa/gTa	9/12	0.813376238537601	2	FACETS	0.868	0.844	0.891	0.868	0.844	0.891	CLONAL	2	TRUE	0	0.91691626474351	2		338	505	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434369	121434369	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	271	624	0	ENST00000257555.6:c.1133C>A	p.Pro378His	p.P378H	ENST00000257555		378	cCc/cAc	6/10	0.813376238537601	2	FACETS	0.972	0.92	1	0.486	0.46	0.513	CLONAL	1	TRUE	0	0.91691626474351	2		624	608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578518	7578519	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGTTGG	novel	NA	P-0046395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	588	742	11	ENST00000269305.4:c.405_411dup	p.Ala138ProfsTer13	p.A138Pfs*13	ENST00000269305	NM_001126112.2	137	-/CCAACTG	5/11	0.814550408484271	2	FACETS	0.756	0.735	0.777	0.756	0.735	0.777	SUBCLONAL	2	TRUE	0	0.91691626474351	2		753	848	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259150	89259150	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	124	291	0	ENST00000336596.2:c.294del	p.Glu98AspfsTer16	p.E98Dfs*16	ENST00000336596	NM_005233.5	98	gaG/ga	3/17	0.817317386400343	3	FACETS	0.81	0.737	0.886	0.405	0.368	0.443	CLONAL	1	TRUE	1	0.91691626474351	3		291	487	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030201	180030201	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	511	493	9	ENST00000261937.6:c.4083C>A	p.Asn1361Lys	p.N1361K	ENST00000261937	NM_182925.4	1361	aaC/aaA	30/30	NA	2	FACETS	0.935	0.916	0.953			1	INDETERMINATE	2	TRUE	NA	0.91691626474351	2		502	596	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109315788	109315788	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	566	452	10	ENST00000436639.2:c.997G>A	p.Glu333Lys	p.E333K	ENST00000436639	NM_014454.2	333	Gaa/Aaa	6/10	0.849006439793982	3	FACETS	0.922	0.892	0.952	0.922	0.892	0.952	CLONAL	2	TRUE	1	0.91691626474351	3		462	976	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0046396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	175	289	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.765192700843643	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.765192700843643	1		289	277	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0046396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	148	292	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.10494378722262	3	FACETS	1	0.989	1	0.727	0.672	0.782	INDETERMINATE	1	TRUE	1	0.765192700843643	3		292	368	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0046396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	212	361	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.765192700843643	2		361	480	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993900	72993900	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	320	584	0	ENST00000268489.5:c.145C>T	p.Pro49Ser	p.P49S	ENST00000268489	NM_006885.3	49	Ccc/Tcc	2/10	0.765192700843643	1	FACETS	0.993	0.952	1	0.993	0.952	1	CLONAL	1	TRUE	0	0.765192700843643	1		584	520	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143448	108143448	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1555085973	NA	P-0046396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	471	356	0	ENST00000278616.4:c.3154-1G>A		p.X1052_splice	ENST00000278616	NM_000051.3	1052			0.765192700843643	3	FACETS	0.962	0.937	0.985	0.962	0.937	0.985	CLONAL	3	TRUE	0	0.765192700843643	3		356	590	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435658	18435658	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	42	243	0	ENST00000266497.5:c.643G>C	p.Gly215Arg	p.G215R	ENST00000266497		215	Gga/Cga	1/31	0.765192700843643	1	FACETS	0.506	0.431	0.584	0.506	0.431	0.584	SUBCLONAL	1	TRUE	0	0.765192700843643	1		243	134	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541715	120541716	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0046396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	331	605	1	ENST00000229340.5:c.141_142delinsTT	p.Arg48Trp	p.R48W	ENST00000229340	NM_006861.6	47	atCCgg/atTTgg	3/6	0.10494378722262	3	FACETS	1	0.993	1	0.648	0.614	0.682	INDETERMINATE	1	TRUE	1	0.765192700843643	3		606	923	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472634	88472634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	31	353	0	ENST00000360948.2:c.1921G>A	p.Asp641Asn	p.D641N	ENST00000360948	NM_001012338.2	641	Gat/Aat	16/19	0.670882321519552	2	FACETS	0.149	0.12	0.183	0.075	0.06	0.092	SUBCLONAL	1	TRUE	0	0.765192700843643	2		353	542	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670030	29670030	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	173	311	0	ENST00000356175.3:c.7003C>T	p.Pro2335Ser	p.P2335S	ENST00000356175	NM_000267.3	2335	Cca/Tca	47/57	0.406584758315236	1	FACETS	0.735	0.686	0.784	0.735	0.686	0.784	INDETERMINATE	1	TRUE	0	0.765192700843643	1		311	380	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790092	40790092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	261	531	0	ENST00000373198.4:c.2639C>T	p.Pro880Leu	p.P880L	ENST00000373198	NM_133170.3	880	cCc/cTc	18/32	1	2	FACETS	0.827	0.777	0.878	0.827	0.777	0.878	CLONAL	1	TRUE	1	0.765192700843643	2		531	825	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501457	149501457	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	331	663	0	ENST00000261799.4:c.2330A>G	p.Asn777Ser	p.N777S	ENST00000261799	NM_002609.3	777	aAc/aGc	16/23	0.406891324553471	1	FACETS	0.712	0.677	0.747	0.712	0.677	0.747	INDETERMINATE	1	TRUE	0	0.765192700843643	1		663	750	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679780	30679780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046396-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	312	470	1	ENST00000376406.3:c.1939G>A	p.Asp647Asn	p.D647N	ENST00000376406	NM_014641.2	647	Gat/Aat	5/15	0.10494378722262	3	FACETS	1	0.994	1	0.689	0.653	0.726	INDETERMINATE	1	TRUE	1	0.765192700843643	3		471	818	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241964	72241965	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0046398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	136	279	0	ENST00000357731.5:c.425_426del	p.Tyr142Ter	p.Y142*	ENST00000357731	NM_173808.2	142	tAT/t	3/7	1	2	FACETS	0.805	0.739	0.873	0.805	0.739	0.873	CLONAL	1	TRUE	1	0.806471129920909	2		279	419	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	34	424	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.878	0.72	1	1	0.957	1	CLONAL	2	TRUE	1	0.13	2		424	298	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995500	68995500	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	32	573	0	ENST00000288368.4:c.1904A>T	p.Lys635Met	p.K635M	ENST00000288368	NM_024870.2	635	aAg/aTg	18/40	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.13	2		573	371	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366962	40366962	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200396403	NA	P-0046399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	40	669	0	ENST00000397332.2:c.235C>T	p.Pro79Ser	p.P79S	ENST00000397332	NM_001033082.2	79	Ccc/Tcc	2/3	1	2	FACETS	0.796	0.659	0.949	0.796	0.659	0.949	CLONAL	1	TRUE	1	0.13	2		669	773	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914894	32914898	+	frameshift_variant	Frame_Shift_Del	DEL	TAACT	TAACT	-	rs80359584	NA	P-0046399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	12	400	0	ENST00000380152.3:c.6405_6409del	p.Asn2135LysfsTer3	p.N2135Kfs*3	ENST00000380152		2134	aaTAACTta/aata	11/27	1	2	FACETS	1	0.725	1	1	0.725	1	CLONAL	1	TRUE	1	0.13	2		400	179	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531828	41531828	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	20	500	0	ENST00000263253.7:c.1540A>T	p.Met514Leu	p.M514L	ENST00000263253	NM_001429.3	514	Atg/Ttg	7/31	1	2	FACETS	0.791	0.604	1	0.791	0.604	1	CLONAL	1	TRUE	1	0.13	2		500	389	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	67	427	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.979	0.858	1	0.979	0.858	1	CLONAL	1	TRUE	1	0.434454179970963	2		427	315	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0046400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	114	292	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.949	0.858	1	0.949	0.858	1	CLONAL	1	TRUE	1	0.434454179970963	2		292	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0046401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	552	701	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.733041367442647	1	FACETS	0.989	0.956	1	0.989	0.956	1	CLONAL	1	TRUE	0	0.733041367442647	1		701	965	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783196	9783196	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757531779	NA	P-0046401-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	379	580	0	ENST00000377346.4:c.2440G>A	p.Gly814Ser	p.G814S	ENST00000377346	NM_005026.3	814	Ggc/Agc	20/24	0.733041367442647	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.733041367442647	1		580	630	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	111	424	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.20182804630829	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.881054315924125	0		424	317	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0046402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	900	803	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.881054315924125	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.881054315924125	1		803	1073	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274911	41274911	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs868651538	NA	P-0046402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	492	421	0	ENST00000349496.5:c.1161T>A	p.Asn387Lys	p.N387K	ENST00000349496	NM_001904.3	387	aaT/aaA	8/15	0.881054315924125	3	FACETS	0.935	0.902	0.968	0.935	0.902	0.968	CLONAL	2	TRUE	1	0.881054315924125	3		421	860	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640719	3640719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1448955515	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	279	893	0	ENST00000294008.3:c.2920C>T	p.Leu974Phe	p.L974F	ENST00000294008	NM_032444.2	974	Ctt/Ttt	12/15	1	2	FACETS	0.968	0.908	1	0.968	0.908	1	CLONAL	1	TRUE	1	0.484953439147703	2		893	1189	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	316	752	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.484953439147703	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.484953439147703	1		752	907	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	163	361	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.484953439147703	2		361	555	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504401	8504401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757922864	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	169	494	0	ENST00000356435.5:c.1682G>A	p.Arg561Gln	p.R561Q	ENST00000356435		561	cGa/cAa	12/35	0.369913627704663	1	FACETS	0.876	0.809	0.944	0.876	0.809	0.944	CLONAL	1	TRUE	0	0.484953439147703	1		494	603	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858517	9858517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765370528	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	197	375	1	ENST00000330684.3:c.2884G>A	p.Glu962Lys	p.E962K	ENST00000330684	NM_001134407.1	962	Gaa/Aaa	13/13	1	2	FACETS	0.945	0.876	1	0.945	0.876	1	CLONAL	1	TRUE	1	0.484953439147703	2		376	860	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589323	28589323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	153	450	1	ENST00000241453.7:c.2724G>A	p.Met908Ile	p.M908I	ENST00000241453	NM_004119.2	908	atG/atA	22/24	0.409004593157727	4	FACETS	1	0.968	1	0.372	0.34	0.406	CLONAL	1	TRUE	1	0.484953439147703	4		451	839	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230641	46230641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	148	545	0	ENST00000334344.6:c.890C>T	p.Ser297Phe	p.S297F	ENST00000334344	NM_152641.2	297	tCc/tTc	8/21	0.484953439147703	1	FACETS	0.953	0.877	1	0.953	0.877	1	CLONAL	1	TRUE	0	0.484953439147703	1		545	485	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085647	16085647	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1238492356	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	253	690	1	ENST00000281043.3:c.823G>A	p.Glu275Lys	p.E275K	ENST00000281043	NM_005378.4	275	Gaa/Aaa	3/3	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.484953439147703	2		691	1026	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467675	50467675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759124417	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	215	692	0	ENST00000331340.3:c.910G>A	p.Glu304Lys	p.E304K	ENST00000331340	NM_006060.4	304	Gaa/Aaa	8/8	0.369832119303742	3	FACETS	1	0.931	1	0.501	0.465	0.538	CLONAL	1	TRUE	1	0.484953439147703	3		692	1099	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031895	26031895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1332600888	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	117	354	0	ENST00000244661.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000244661	NM_003537.3	132	Cgc/Tgc	1/1	0.467112229065649	3	FACETS	1	0.931	1	0.518	0.468	0.57	CLONAL	1	TRUE	1	0.484953439147703	3		354	579	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439303	149439303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778336583	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	135	751	0	ENST00000286301.3:c.2092G>A	p.Asp698Asn	p.D698N	ENST00000286301	NM_005211.3	698	Gac/Aac	15/22	0.369913627704663	1	FACETS	0.422	0.383	0.463	0.422	0.383	0.463	SUBCLONAL	1	TRUE	0	0.484953439147703	1		751	1000	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32182001	32182001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1311	292	924	0	ENST00000375023.3:c.2053G>A	p.Gly685Arg	p.G685R	ENST00000375023	NM_004557.3	685	Ggg/Agg	13/30	0.467112229065649	3	FACETS	0.933	0.876	0.993	0.467	0.438	0.497	CLONAL	1	TRUE	1	0.484953439147703	3		924	1603	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415040	116415040	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	201	712	0	ENST00000397752.3:c.3134C>T	p.Pro1045Leu	p.P1045L	ENST00000397752	NM_000245.2	1045	cCa/cTa	15/21	0.484953439147703	1	FACETS	0.944	0.879	1	0.944	0.879	1	CLONAL	1	TRUE	0	0.484953439147703	1		712	665	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041266	29041267	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	146	463	1	ENST00000282397.4:c.162-1_162delinsAA		p.X54_splice	ENST00000282397	NM_002019.4	54		3/30	0.409004593157727	4	FACETS	0.977	0.892	1	0.326	0.297	0.356	CLONAL	1	TRUE	1	0.484953439147703	4		464	915	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486026	29486026	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	52	287	0	ENST00000356175.3:c.205-2A>G		p.X69_splice	ENST00000356175	NM_000267.3	69			0.484953439147703	1	FACETS	0.923	0.8	1	0.923	0.8	1	CLONAL	1	TRUE	0	0.484953439147703	1		287	176	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915464	112915464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	154	601	0	ENST00000351677.2:c.863C>T	p.Thr288Ile	p.T288I	ENST00000351677	NM_002834.3	288	aCc/aTc	8/16	0.484953439147703	1	FACETS	0.92	0.847	0.995	0.92	0.847	0.995	CLONAL	1	TRUE	0	0.484953439147703	1		601	523	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795109	42795109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752503838	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	373	1118	2	ENST00000575354.2:c.2189C>T	p.Ser730Leu	p.S730L	ENST00000575354	NM_015125.3	730	tCg/tTg	10/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.484953439147703	2		1120	1345	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675049	40675049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764271025	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	237	810	0	ENST00000249776.8:c.13G>A	p.Glu5Lys	p.E5K	ENST00000249776	NM_033286.3	5	Gaa/Aaa	1/9	1	2	FACETS	0.881	0.822	0.943	0.881	0.822	0.943	CLONAL	1	TRUE	1	0.484953439147703	2		810	1109	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937178	36937178	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	351	925	2	ENST00000361632.4:c.1141G>A	p.Ala381Thr	p.A381T	ENST00000361632		381	Gct/Act	9/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.484953439147703	2		927	1360	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552648	18552648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	132	425	0	ENST00000266497.5:c.2059G>A	p.Glu687Lys	p.E687K	ENST00000266497		687	Gaa/Aaa	14/31	1	2	FACETS	0.888	0.809	0.971	0.888	0.809	0.971	CLONAL	1	TRUE	1	0.484953439147703	2		425	613	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340420	8340420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	119	645	0	ENST00000356435.5:c.5176G>A	p.Glu1726Lys	p.E1726K	ENST00000356435		1726	Gaa/Aaa	31/35	0.369913627704663	1	FACETS	0.423	0.381	0.467	0.423	0.381	0.467	SUBCLONAL	1	TRUE	0	0.484953439147703	1		645	879	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980753	70980753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	154	639	0	ENST00000276594.2:c.715C>T	p.Pro239Ser	p.P239S	ENST00000276594	NM_024504.3	239	Cct/Tct	3/8	1	2	FACETS	0.804	0.736	0.874	0.804	0.736	0.874	CLONAL	1	TRUE	1	0.484953439147703	2		639	790	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449821	8449821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754699635	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	209	557	0	ENST00000356435.5:c.3892G>A	p.Asp1298Asn	p.D1298N	ENST00000356435		1298	Gac/Aac	23/35	0.369913627704663	1	FACETS	0.864	0.804	0.925	0.864	0.804	0.925	CLONAL	1	TRUE	0	0.484953439147703	1		557	756	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101547	27101547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	347	945	0	ENST00000324856.7:c.4829G>A	p.Gly1610Glu	p.G1610E	ENST00000324856	NM_006015.4	1610	gGg/gAg	18/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.484953439147703	2		945	1314	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519809	29519809	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	285	716	1	ENST00000389048.3:c.1762G>A	p.Glu588Lys	p.E588K	ENST00000389048	NM_004304.4	588	Gaa/Aaa	9/29	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.484953439147703	2		717	1126	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47604193	47604193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	116	427	0	ENST00000263735.4:c.532C>T	p.Pro178Ser	p.P178S	ENST00000263735	NM_002354.2	178	Cca/Tca	5/9	1	2	FACETS	0.968	0.877	1	0.968	0.877	1	CLONAL	1	TRUE	1	0.484953439147703	2		427	494	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38504616	38504616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	288	851	1	ENST00000254066.5:c.227C>T	p.Pro76Leu	p.P76L	ENST00000254066	NM_000964.3	76	cCc/cTc	3/9	NA	2	FACETS	0.938	0.881	0.997			1	INDETERMINATE	1	TRUE	NA	0.484953439147703	2		852	1266	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803565	43803565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs541014818	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	266	813	0	ENST00000372470.3:c.46G>A	p.Ala16Thr	p.A16T	ENST00000372470	NM_005373.2	16	Gcc/Acc	1/12	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.484953439147703	2		813	1082	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601914	43601914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	268	1027	0	ENST00000355710.3:c.958C>T	p.Pro320Ser	p.P320S	ENST00000355710	NM_020975.4	320	Ccc/Tcc	5/20	0.369913627704663	1	FACETS	0.733	0.687	0.78	0.733	0.687	0.78	SUBCLONAL	1	TRUE	0	0.484953439147703	1		1027	1142	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572060	64572061	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	288	818	0	ENST00000312049.6:c.1578_1579delinsTT	p.Arg527Ter	p.R527*	ENST00000312049	NM_130799.2	526	gcCCga/gcTTga	10/10	1	2	FACETS	0.932	0.876	0.991	0.932	0.876	0.991	CLONAL	1	TRUE	1	0.484953439147703	2		818	1274	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342391	118342391	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555035511	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	59	263	0	ENST00000534358.1:c.517C>T	p.Arg173Ter	p.R173*	ENST00000534358	NM_005933.3	173	Cga/Tga	3/36	0.484953439147703	1	FACETS	0.823	0.717	0.935	0.823	0.717	0.935	CLONAL	1	TRUE	0	0.484953439147703	1		263	224	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536852	120536852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	336	872	0	ENST00000229340.5:c.334G>A	p.Asp112Asn	p.D112N	ENST00000229340	NM_006861.6	112	Gat/Aat	4/6	0.484953439147703	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.484953439147703	1		872	893	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959431	26959431	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs765207700	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	153	503	0	ENST00000381527.3:c.598C>T	p.Arg200Ter	p.R200*	ENST00000381527	NM_001260.1	200	Cga/Tga	6/13	0.409004593157727	4	FACETS	1	0.958	1	0.358	0.327	0.39	CLONAL	1	TRUE	1	0.484953439147703	4		503	872	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915319	32915319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748541466	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	170	782	0	ENST00000380152.3:c.6827C>T	p.Pro2276Leu	p.P2276L	ENST00000380152		2276	cCc/cTc	11/27	0.409004593157727	4	FACETS	1	0.972	1	0.375	0.345	0.407	CLONAL	1	TRUE	1	0.484953439147703	4		782	925	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961126	41961126	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	95	345	0	ENST00000219905.7:c.34C>T	p.Gln12Ter	p.Q12*	ENST00000219905	NM_001164273.1	12	Caa/Taa	2/24	1	2	FACETS	0.915	0.82	1	0.915	0.82	1	CLONAL	1	TRUE	1	0.484953439147703	2		345	428	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748812	43748812	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	312	1024	0	ENST00000382044.4:c.1994C>T	p.Ser665Leu	p.S665L	ENST00000382044	NM_001141980.1	665	tCa/tTa	12/28	1	2	FACETS	0.967	0.911	1	0.967	0.911	1	CLONAL	1	TRUE	1	0.484953439147703	2		1024	1330	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789594	3789594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	160	491	0	ENST00000262367.5:c.4265C>T	p.Pro1422Leu	p.P1422L	ENST00000262367	NM_004380.2	1422	cCc/cTc	25/31	1	2	FACETS	0.847	0.778	0.919	0.847	0.778	0.919	CLONAL	1	TRUE	1	0.484953439147703	2		491	779	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916149	9916149	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1555491625	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	203	639	0	ENST00000330684.3:c.2140G>T	p.Glu714Ter	p.E714*	ENST00000330684	NM_001134407.1	714	Gag/Tag	10/13	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.484953439147703	2		639	810	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992523	72992523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	353	959	0	ENST00000268489.5:c.1522C>T	p.His508Tyr	p.H508Y	ENST00000268489	NM_006885.3	508	Cat/Tat	2/10	0.484953439147703	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.484953439147703	1		959	1036	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897372	78897372	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	791	950	0	ENST00000306801.3:c.2707T>G	p.Ser903Ala	p.S903A	ENST00000306801	NM_020761.2	903	Tct/Gct	23/34	0.409004593157727	4	FACETS	0.915	0.886	0.944	0.915	0.886	0.944	CLONAL	3	TRUE	1	0.484953439147703	4		950	1765	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134300	11134300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	238	634	0	ENST00000358026.2:c.2966C>T	p.Pro989Leu	p.P989L	ENST00000358026	NM_001128849.1	989	cCc/cTc	20/36	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.484953439147703	2		634	952	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212404	36212404	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	388	1009	0	ENST00000222270.7:c.2155G>T	p.Val719Leu	p.V719L	ENST00000222270	NM_014727.1	719	Gtg/Ttg	3/37	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.484953439147703	2		1009	1365	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469614	25469615	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	324	918	3	ENST00000264709.3:c.1153_1154delinsTT	p.Pro385Leu	p.P385L	ENST00000264709	NM_175629.2	385	CCg/TTg	10/23	1	2	FACETS	0.997	0.941	1	0.997	0.941	1	CLONAL	1	TRUE	1	0.484953439147703	2		921	1340	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405926	49405927	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	228	711	1	ENST00000418115.1:c.211_212delinsTT	p.Pro71Phe	p.P71F	ENST00000418115	NM_001664.2	71	CCc/TTc	3/5	1	2	FACETS	0.906	0.844	0.97	0.906	0.844	0.97	CLONAL	1	TRUE	1	0.484953439147703	2		712	1038	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876368	35876368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	213	767	0	ENST00000303115.3:c.1160C>T	p.Ser387Phe	p.S387F	ENST00000303115	NM_002185.3	387	tCc/tTc	8/8	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.484953439147703	2		767	865	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589591	67589591	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	22	238	0	ENST00000274335.5:c.1354T>G	p.Tyr452Asp	p.Y452D	ENST00000274335		452	Tat/Gat	10/15	0.369913627704663	1	FACETS	0.323	0.251	0.405	0.323	0.251	0.405	SUBCLONAL	1	TRUE	0	0.484953439147703	1		238	213	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502764	149502764	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1176688330	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	198	540	1	ENST00000261799.4:c.2024G>A	p.Gly675Glu	p.G675E	ENST00000261799	NM_002609.3	675	gGa/gAa	15/23	0.369913627704663	1	FACETS	0.844	0.784	0.906	0.844	0.784	0.906	CLONAL	1	TRUE	0	0.484953439147703	1		541	733	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515168	149515168	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	317	808	0	ENST00000261799.4:c.314C>A	p.Ser105Tyr	p.S105Y	ENST00000261799	NM_002609.3	105	tCc/tAc	3/23	0.369913627704663	1	FACETS	0.92	0.869	0.972	0.92	0.869	0.972	CLONAL	1	TRUE	0	0.484953439147703	1		808	1077	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180614	32180614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	272	713	1	ENST00000375023.3:c.2513G>A	p.Gly838Glu	p.G838E	ENST00000375023	NM_004557.3	838	gGa/gAa	16/30	0.467112229065649	3	FACETS	1	0.981	1	0.556	0.521	0.592	CLONAL	1	TRUE	1	0.484953439147703	3		714	1253	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129121	152129121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	151	860	0	ENST00000206249.3:c.74C>T	p.Pro25Leu	p.P25L	ENST00000206249	NM_000125.3	25	cCc/cTc	1/8	0.316911196575224	1	FACETS	0.435	0.397	0.475	0.435	0.397	0.475	SUBCLONAL	1	TRUE	0	0.484953439147703	1		860	1085	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375955	8375955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	69	399	0	ENST00000356435.5:c.4642C>T	p.Pro1548Ser	p.P1548S	ENST00000356435		1548	Ccg/Tcg	28/35	0.369913627704663	1	FACETS	0.396	0.345	0.451	0.396	0.345	0.451	SUBCLONAL	1	TRUE	0	0.484953439147703	1		399	544	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485941	8485941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	105	522	0	ENST00000356435.5:c.2876G>A	p.Arg959Lys	p.R959K	ENST00000356435		959	aGg/aAg	17/35	0.369913627704663	1	FACETS	0.559	0.502	0.619	0.559	0.502	0.619	SUBCLONAL	1	TRUE	0	0.484953439147703	1		522	587	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223251	5223251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199604489	NA	P-0046406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	224	833	1	ENST00000357368.4:c.2552G>A	p.Arg851His	p.R851H	ENST00000357368	NM_002850.3	851	cGc/cAc	18/38	0.340818503291477	1	FACETS	0.934	0.869	1	0.934	0.869	1	CLONAL	1	TRUE	0	0.340818503291477	1		834	1167	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0046406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	284	887	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.215567136494446	2	FACETS	1	0.993	1	0.742	0.697	0.788	CLONAL	1	TRUE	0	0.340818503291477	2		887	1123	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24129420	24129420	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1417899723	NA	P-0046406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	239	444	0	ENST00000263121.7:c.64G>A	p.Asp22Asn	p.D22N	ENST00000263121	NM_003073.3	22	Gac/Aac	1/9	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.340818503291477	2		444	1096	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231410	46231410	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0046406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	115	386	0	ENST00000334344.6:c.1250C>G	p.Ser417Ter	p.S417*	ENST00000334344	NM_152641.2	417	tCa/tGa	10/21	0.340818503291477	1	FACETS	0.757	0.688	0.827	1	0.986	1	SUBCLONAL	2	TRUE	0	0.340818503291477	1		386	370	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665790	241665790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224007	NA	P-0046406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	36	500	1	ENST00000366560.3:c.1189G>A	p.Gly397Arg	p.G397R	ENST00000366560	NM_000143.3	397	Gga/Aga	8/10	NA	2	FACETS	0.318	0.26	0.382			1	INDETERMINATE	1	TRUE	NA	0.340818503291477	2		501	665	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120942	115120942	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	229	626	0	ENST00000257566.3:c.64C>A	p.Pro22Thr	p.P22T	ENST00000257566	NM_016569.3	22	Cct/Act	1/8	0.340818503291477	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.340818503291477	1		626	882	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050360	128050360	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	38	580	0	ENST00000285398.2:c.297C>G	p.Phe99Leu	p.F99L	ENST00000285398	NM_000122.1	99	ttC/ttG	3/15	0.314101328852606	1	FACETS	0.266	0.219	0.319	0.266	0.219	0.319	SUBCLONAL	1	TRUE	0	0.340818503291477	1		580	696	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067889	30067889	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs770949972	NA	P-0046406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	191	659	2	ENST00000338641.4:c.1074G>C	p.Arg358Ser	p.R358S	ENST00000338641	NM_000268.3	358	agG/agC	11/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.340818503291477	2		661	960	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748164	41748164	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	90	548	0	ENST00000226382.2:c.605C>A	p.Pro202His	p.P202H	ENST00000226382	NM_003924.3	202	cCc/cAc	3/3	1	2	FACETS	0.681	0.603	0.763	0.681	0.603	0.763	SUBCLONAL	1	TRUE	1	0.340818503291477	2		548	776	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777942	27777942	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200796448	NA	P-0046406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	111	429	0	ENST00000369163.2:c.91C>T	p.Pro31Ser	p.P31S	ENST00000369163	NM_003536.2	31	Ccg/Tcg	1/1	0.340818503291477	4	FACETS	0.752	0.674	0.835			1	SUBCLONAL	1	TRUE	NA	0.340818503291477	4		429	1162	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335737	81335737	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	42	409	0	ENST00000222390.5:c.1623G>C	p.Leu541Phe	p.L541F	ENST00000222390	NM_000601.4	541	ttG/ttC	15/18	1	2	FACETS	0.655	0.548	0.774	0.655	0.548	0.774	SUBCLONAL	1	TRUE	1	0.340818503291477	2		409	376	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845454	128845454	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	170	821	0	ENST00000249373.3:c.751A>G	p.Thr251Ala	p.T251A	ENST00000249373	NM_005631.4	251	Aca/Gca	4/12	1	2	FACETS	0.903	0.829	0.98	0.903	0.829	0.98	CLONAL	1	TRUE	1	0.340818503291477	2		821	1105	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	115	617	0	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.210825785077008	2		617	1061	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1250	84	931	3	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.597	0.525	0.675	0.597	0.525	0.675	SUBCLONAL	1	TRUE	1	0.210825785077008	2		934	1334	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1296	148	1262	4	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.972	0.885	1	0.972	0.885	1	CLONAL	1	TRUE	1	0.210825785077008	2		1266	1444	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	134	826	5	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.986	0.893	1	0.986	0.893	1	CLONAL	1	TRUE	1	0.210825785077008	2		831	1289	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	48	343	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.769	0.65	0.901	0.769	0.65	0.901	CLONAL	1	TRUE	1	0.210825785077008	2		343	592	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	119	578	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.210825785077008	2		578	1117	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878061	48878062	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1131690852	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	31	183	0	ENST00000267163.4:c.19dup	p.Arg7ProfsTer24	p.R7Pfs*24	ENST00000267163	NM_000321.2	5	acc/aCcc	1/27	0.210825785077008	1	FACETS	0.978	0.794	1	0.978	0.794	1	CLONAL	1	TRUE	0	0.210825785077008	1		183	269	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424178	49424178	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs886040960	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	88	386	2	ENST00000301067.7:c.13884del	p.Thr4629ProfsTer11	p.T4629Pfs*11	ENST00000301067	NM_003482.3	4628	ccC/cc	42/54	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.210825785077008	2		388	666	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1232964733	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	25	111	0	ENST00000324856.7:c.1015del	p.Ala339LeufsTer24	p.A339Lfs*24	ENST00000324856	NM_006015.4	337	tGg/tg	1/20	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.210825785077008	2		111	190	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	112	606	1	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.997	0.895	1	0.997	0.895	1	CLONAL	1	TRUE	1	0.210825785077008	2		607	1066	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509085	66509085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	20	158	0	ENST00000273854.3:c.242del	p.Asn81MetfsTer24	p.N81Mfs*24	ENST00000273854	NM_004439.5	81	aAt/at	2/18	1	2	FACETS	0.887	0.681	1	0.887	0.681	1	CLONAL	1	TRUE	1	0.210825785077008	2		158	214	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138729528	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	113	657	0	ENST00000269305.4:c.523C>T	p.Arg175Cys	p.R175C	ENST00000269305	NM_001126112.2	175	Cgc/Tgc	5/11	1	2	FACETS	0.973	0.873	1	0.973	0.873	1	CLONAL	1	TRUE	1	0.210825785077008	2		657	1102	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	82	473	0	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.210825785077008	2		473	697	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203493	108203493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140263969	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	24	115	0	ENST00000278616.4:c.7793G>A	p.Arg2598Gln	p.R2598Q	ENST00000278616	NM_000051.3	2598	cGa/cAa	53/63	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.210825785077008	2		115	198	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043349	6043349	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781716	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	29	193	1	ENST00000265849.7:c.325del	p.Glu109LysfsTer3	p.E109Kfs*3	ENST00000265849	NM_000535.5	109	Gaa/aa	4/15	1	2	FACETS	0.826	0.664	1	0.826	0.664	1	CLONAL	1	TRUE	1	0.210825785077008	2		194	333	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564680	86564680	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	102	636	0	ENST00000274376.6:c.416del	p.Pro139LeufsTer35	p.P139Lfs*35	ENST00000274376	NM_002890.2	138	Ccc/cc	1/25	1	2	FACETS	0.893	0.796	0.995	0.893	0.796	0.995	CLONAL	1	TRUE	1	0.210825785077008	2		636	1084	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349914	89349916	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs761762028	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	105	706	0	ENST00000301030.4:c.3034_3036del	p.Lys1012del	p.K1012del	ENST00000301030	NM_001256183.1	1012	AAG/-	9/13	1	2	FACETS	0.775	0.692	0.864	0.775	0.692	0.864	SUBCLONAL	1	TRUE	1	0.210825785077008	2		706	1285	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442566	52442566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553646022	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	60	298	0	ENST00000460680.1:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000460680	NM_004656.3	60	cGa/cAa	4/17	1	2	FACETS	0.923	0.795	1	0.923	0.795	1	CLONAL	1	TRUE	1	0.210825785077008	2		298	617	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023768	27023769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	55	402	1	ENST00000324856.7:c.879dup	p.Thr294HisfsTer106	p.T294Hfs*106	ENST00000324856	NM_006015.4	292	acc/aCcc	1/20	1	2	FACETS	0.84	0.718	0.974	0.84	0.718	0.974	CLONAL	1	TRUE	1	0.210825785077008	2		403	621	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088723	27088723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs990194975	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	89	522	0	ENST00000324856.7:c.2332G>A	p.Gly778Arg	p.G778R	ENST00000324856	NM_006015.4	778	Gga/Aga	7/20	1	2	FACETS	0.905	0.801	1	0.905	0.801	1	CLONAL	1	TRUE	1	0.210825785077008	2		522	933	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776310	76776310	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs122445099	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	62	380	0	ENST00000373344.5:c.7156C>T	p.Arg2386Ter	p.R2386*	ENST00000373344	NM_000489.3	2386	Cga/Tga	34/35	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.210825785077008	2		380	573	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856434	111856434	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs776317487	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	42	218	0	ENST00000341259.2:c.489del	p.Thr165ProfsTer32	p.T165Pfs*32	ENST00000341259	NM_005475.2	162	gCc/gc	2/8	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.210825785077008	2		218	365	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349688	70349688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	97	436	0	ENST00000374080.3:c.3850C>T	p.Arg1284Cys	p.R1284C	ENST00000374080		1284	Cgc/Tgc	27/45	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.210825785077008	2		436	786	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586144	29586144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555618691	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	40	258	0	ENST00000356175.3:c.4364G>A	p.Arg1455His	p.R1455H	ENST00000356175	NM_000267.3	1455	cGc/cAc	32/57	1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	1	0.210825785077008	2		258	373	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170487	11170489	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs1375203306	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	112	638	0	ENST00000358026.2:c.4792_4794del	p.Lys1598del	p.K1598del	ENST00000358026	NM_001128849.1	1597	gAGAag/gag	34/36	1	2	FACETS	0.925	0.83	1	0.925	0.83	1	CLONAL	1	TRUE	1	0.210825785077008	2		638	1149	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256811	133256811	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	rs1555230255	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	48	247	0	ENST00000320574.5:c.286-3C>T		p.X96_splice	ENST00000320574	NM_006231.2	96			1	2	FACETS	0.937	0.793	1	0.937	0.793	1	CLONAL	1	TRUE	1	0.210825785077008	2		247	486	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352586	118352586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782683534	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	64	348	0	ENST00000534358.1:c.3791G>A	p.Arg1264Gln	p.R1264Q	ENST00000534358	NM_005933.3	1264	cGa/cAa	7/36	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.210825785077008	2		348	603	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633171	3633171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218491919	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	143	792	2	ENST00000294008.3:c.5080G>A	p.Ala1694Thr	p.A1694T	ENST00000294008	NM_032444.2	1694	Gcc/Acc	14/15	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.210825785077008	2		794	1350	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801128	1801128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1333699127	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1289	176	876	3	ENST00000260795.2:c.257G>A	p.Arg86His	p.R86H	ENST00000260795		86	cGt/cAt	2/17	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.210825785077008	2		879	1465	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828113	3828113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	85	430	0	ENST00000262367.5:c.2012C>T	p.Ser671Leu	p.S671L	ENST00000262367	NM_004380.2	671	tCg/tTg	10/31	1	2	FACETS	0.96	0.847	1	0.96	0.847	1	CLONAL	1	TRUE	1	0.210825785077008	2		430	840	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649649	206649649	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781992974	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	119	550	0	ENST00000367120.3:c.484C>T	p.Arg162Trp	p.R162W	ENST00000367120	NM_014002.3	162	Cgg/Tgg	6/22	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.210825785077008	2		550	971	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856533	111856533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	55	293	0	ENST00000341259.2:c.584C>T	p.Ala195Val	p.A195V	ENST00000341259	NM_005475.2	195	gCg/gTg	2/8	1	2	FACETS	0.988	0.846	1	0.988	0.846	1	CLONAL	1	TRUE	1	0.210825785077008	2		293	528	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727424	66727424	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567009054	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	60	311	0	ENST00000307102.5:c.140G>A	p.Arg47Gln	p.R47Q	ENST00000307102	NM_002755.3	47	cGa/cAa	2/11	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.210825785077008	2		311	551	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38506076	38506076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1031458847	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	79	471	0	ENST00000254066.5:c.368C>T	p.Thr123Met	p.T123M	ENST00000254066	NM_000964.3	123	aCg/aTg	4/9	1	2	FACETS	0.874	0.768	0.99	0.874	0.768	0.99	CLONAL	1	TRUE	1	0.210825785077008	2		471	857	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210450	2210450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239394183	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	147	801	1	ENST00000398665.3:c.1057G>A	p.Ala353Thr	p.A353T	ENST00000398665	NM_032482.2	353	Gcg/Acg	13/28	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.210825785077008	2		802	1302	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965824	25965824	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	84	446	0	ENST00000435504.4:c.3382A>G	p.Ile1128Val	p.I1128V	ENST00000435504		1128	Att/Gtt	13/13	1	2	FACETS	0.935	0.825	1	0.935	0.825	1	CLONAL	1	TRUE	1	0.210825785077008	2		446	852	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698126	47698126	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167816	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	33	178	0	ENST00000233146.2:c.1684G>T	p.Glu562Ter	p.E562*	ENST00000233146	NM_000251.2	562	Gag/Tag	11/16	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.210825785077008	2		178	262	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705487	47705492	+	inframe_deletion	In_Frame_Del	DEL	GCATGG	GCATGG	-	novel	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	31	238	0	ENST00000233146.2:c.2289_2294del	p.Trp764_Ala765del	p.W764_A765del	ENST00000233146	NM_000251.2	763	GCATGG/-	14/16	1	2	FACETS	0.758	0.613	0.922	0.758	0.613	0.922	CLONAL	1	TRUE	1	0.210825785077008	2		238	388	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921785	111921785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758817904	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	42	268	0	ENST00000393256.3:c.574C>T	p.Arg192Cys	p.R192C	ENST00000393256	NM_006538.4	192	Cgc/Tgc	4/4	1	2	FACETS	0.777	0.648	0.92	0.777	0.648	0.92	CLONAL	1	TRUE	1	0.210825785077008	2		268	513	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225362471	225362471	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	33	179	0	ENST00000264414.4:c.1706del	p.Lys569ArgfsTer14	p.K569Rfs*14	ENST00000264414	NM_003590.4	569	aAg/ag	12/16	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.210825785077008	2		179	291	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380568	31380568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763492333	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	50	406	0	ENST00000328111.2:c.1058C>T	p.Thr353Met	p.T353M	ENST00000328111	NM_006892.3	353	aCg/aTg	9/23	1	2	FACETS	0.714	0.605	0.835	0.714	0.605	0.835	SUBCLONAL	1	TRUE	1	0.210825785077008	2		406	664	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568525	41568525	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	53	273	0	ENST00000263253.7:c.4475A>C	p.Glu1492Ala	p.E1492A	ENST00000263253	NM_001429.3	1492	gAa/gCa	28/31	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.210825785077008	2		273	476	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940238	49940238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145173827	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	123	649	0	ENST00000296474.3:c.805G>A	p.Val269Met	p.V269M	ENST00000296474	NM_002447.2	269	Gtg/Atg	1/20	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.210825785077008	2		649	1166	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799556	72799557	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	90	369	0	ENST00000325599.8:c.1612_1613del	p.Leu538AspfsTer16	p.L538Dfs*16	ENST00000325599	NM_018130.2	538	CTg/g	11/11	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.210825785077008	2		369	650	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1962784	1962784	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	65	274	0	ENST00000382891.5:c.3278T>C	p.Val1093Ala	p.V1093A	ENST00000382891	NM_133335.3	1093	gTt/gCt	18/22	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.210825785077008	2		274	599	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196477	106196477	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	41	265	0	ENST00000380013.4:c.4810G>T	p.Ala1604Ser	p.A1604S	ENST00000380013	NM_001127208.2	1604	Gct/Tct	11/11	1	2	FACETS	0.831	0.692	0.985	0.831	0.692	0.985	CLONAL	1	TRUE	1	0.210825785077008	2		265	468	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288606	33288606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	46	399	0	ENST00000374542.5:c.946G>A	p.Ala316Thr	p.A316T	ENST00000374542	NM_001141970.1	316	Gcc/Acc	3/8	1	2	FACETS	0.672	0.565	0.791	0.672	0.565	0.791	SUBCLONAL	1	TRUE	1	0.210825785077008	2		399	649	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985502	2985502	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	53	380	0	ENST00000396946.4:c.309C>A	p.Tyr103Ter	p.Y103*	ENST00000396946	NM_032415.4	103	taC/taA	4/25	1	2	FACETS	0.796	0.678	0.925	0.796	0.678	0.925	CLONAL	1	TRUE	1	0.210825785077008	2		380	632	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400269	139400269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	108	804	0	ENST00000277541.6:c.4079G>A	p.Gly1360Asp	p.G1360D	ENST00000277541	NM_017617.3	1360	gGc/gAc	25/34	1	2	FACETS	0.812	0.727	0.904	0.812	0.727	0.904	CLONAL	1	TRUE	1	0.210825785077008	2		804	1261	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223547	53223547	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	112	595	0	ENST00000375401.3:c.3812G>A	p.Arg1271Gln	p.R1271Q	ENST00000375401	NM_004187.3	1271	cGg/cAg	23/26	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.210825785077008	2		595	929	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786201059	NA	P-0046433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	637	705	0	ENST00000269305.4:c.856G>C	p.Glu286Gln	p.E286Q	ENST00000269305	NM_001126112.2	286	Gaa/Caa	8/11	0.713298307913094	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.713298307913094	1		705	1003	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086117	16086117	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	33	481	0	ENST00000281043.3:c.1293C>A	p.His431Gln	p.H431Q	ENST00000281043	NM_005378.4	431	caC/caA	3/3	0.713298307913094	1	FACETS	0.102	0.083	0.124	0.102	0.083	0.124	SUBCLONAL	1	TRUE	0	0.713298307913094	1		481	582	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064420	30064420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	236	371	0	ENST00000338641.4:c.984del	p.Lys329ArgfsTer17	p.K329Rfs*17	ENST00000338641	NM_000268.3	328	gaG/ga	10/16	0.713298307913094	2	FACETS	1	0.963	1	0.518	0.486	0.55	CLONAL	1	TRUE	0	0.713298307913094	2		371	639	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715408	117715408	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	20	291	1	ENST00000368508.3:c.1081A>G	p.Ile361Val	p.I361V	ENST00000368508	NM_002944.2	361	Att/Gtt	10/43	0.713298307913094	1	FACETS	0.096	0.073	0.124	0.096	0.073	0.124	SUBCLONAL	1	TRUE	0	0.713298307913094	1		292	374	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923159	39923162	+	protein_altering_variant	In_Frame_Del	DEL	TAAG	TAAG	C	novel	NA	P-0046433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	280	523	0	ENST00000378444.4:c.3546_3549delinsG	p.His1182_Leu1183delinsGln	p.H1182_L1183delinsQ	ENST00000378444	NM_001123385.1	1182	caCTTA/caG	8/15	0.713298307913094	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.713298307913094	1		523	497	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	41	424	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.884	0.741	1	0.884	0.741	1	CLONAL	1	TRUE	1	0.33	2		424	281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578537	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs879254214	NA	P-0046434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	157	727	0	ENST00000269305.4:c.393_395del	p.Asn131del	p.N131del	ENST00000269305	NM_001126112.2	131	aaCAAg/aag	5/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.33	NA		727	922	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041244	47041244	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	115	345	0	ENST00000377604.3:c.1672C>T	p.Gln558Ter	p.Q558*	ENST00000377604	NM_001204468.1	558	Cag/Tag	15/24	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.33	1		345	421	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660493	67660493	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	63	266	0	ENST00000264010.4:c.1393C>T	p.Gln465Ter	p.Q465*	ENST00000264010	NM_006565.3	465	Caa/Taa	8/12	1	2	FACETS	0.882	0.765	1	0.882	0.765	1	CLONAL	1	TRUE	1	0.33	2		266	433	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78704465	78704465	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	67	356	0	ENST00000306801.3:c.613T>A	p.Ser205Thr	p.S205T	ENST00000306801	NM_020761.2	205	Tcc/Acc	5/34	1	2	FACETS	0.763	0.664	0.87	0.763	0.664	0.87	SUBCLONAL	1	TRUE	1	0.33	2		356	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579355	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519997	NA	P-0046435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	490	201	2	ENST00000269305.4:c.332T>C	p.Leu111Pro	p.L111P	ENST00000269305	NM_001126112.2	111	cTg/cCg	4/11	0.76875855437659	1	FACETS	0.957	0.925	0.989	0.957	0.925	0.989	CLONAL	1	TRUE	0	0.785205588347721	1		203	792	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418394	49418394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1565756106	NA	P-0046435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	381	144	3	ENST00000301067.7:c.16019G>A	p.Arg5340Gln	p.R5340Q	ENST00000301067	NM_003482.3	5340	cGa/cAa	50/54	NA	2	FACETS	0.988	0.941	1			1	INDETERMINATE	1	TRUE	NA	0.785205588347721	2		147	982	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955526	48955526	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0046435-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	127	64	0	ENST00000267163.4:c.1642A>T	p.Lys548Ter	p.K548*	ENST00000267163	NM_000321.2	548	Aaa/Taa	17/27	0.76875855437659	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.785205588347721	1		64	196	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600447	10600447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	505	756	0	ENST00000171111.5:c.1408C>T	p.Arg470Cys	p.R470C	ENST00000171111	NM_203500.1	470	Cgt/Tgt	4/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		756	1084	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0046436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	217	468	0	ENST00000269305.4:c.96+1G>A		p.X32_splice	ENST00000269305	NM_001126112.2	32			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		468	525	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109668	115109668	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	555	811	0	ENST00000257566.3:c.2210G>T	p.Arg737Met	p.R737M	ENST00000257566	NM_016569.3	737	aGg/aTg	8/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		811	1674	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876458	35876458	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	112	555	0	ENST00000303115.3:c.1250C>A	p.Pro417His	p.P417H	ENST00000303115	NM_002185.3	417	cCt/cAt	8/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		555	1112	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41020916	41020916	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1210342872	NA	P-0046436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	112	448	0	ENST00000267868.3:c.538C>G	p.Leu180Val	p.L180V	ENST00000267868	NM_002875.4	180	Ctc/Gtc	7/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		448	506	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40876429	40876429	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	218	440	0	ENST00000428826.2:c.260G>T	p.Ser87Ile	p.S87I	ENST00000428826		87	aGc/aTc	5/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		440	405	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145667	11145667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	424	882	0	ENST00000358026.2:c.4032del	p.Ser1345ArgfsTer13	p.S1345Rfs*13	ENST00000358026	NM_001128849.1	1343	ctC/ct	29/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		882	976	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210704	36210704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746908334	NA	P-0046436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	63	813	2	ENST00000222270.7:c.455G>A	p.Arg152Gln	p.R152Q	ENST00000222270	NM_014727.1	152	cGg/cAg	3/37	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		815	1011	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206764	36206764	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	178	575	0	ENST00000300305.3:c.748C>G	p.Arg250Gly	p.R250G	ENST00000300305		250	Cgt/Ggt	6/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		575	928	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056989	180056989	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	220	962	1	ENST00000261937.6:c.630G>T	p.Trp210Cys	p.W210C	ENST00000261937	NM_182925.4	210	tgG/tgT	5/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		963	1330	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553158	106553158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748639953	NA	P-0046436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	136	588	1	ENST00000369096.4:c.1123G>A	p.Ala375Thr	p.A375T	ENST00000369096	NM_001198.3	375	Gct/Act	5/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		589	625	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117645539	117645539	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	85	403	0	ENST00000368508.3:c.5597T>C	p.Ile1866Thr	p.I1866T	ENST00000368508	NM_002944.2	1866	aTt/aCt	34/43	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		403	189	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760723	133760723	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1423362935	NA	P-0046436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	240	862	0	ENST00000318560.5:c.3046C>T	p.Arg1016Cys	p.R1016C	ENST00000318560	NM_005157.4	1016	Cgc/Tgc	11/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		862	1084	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037865	49037865	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0046437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	81	167	0	ENST00000267163.4:c.2107-2A>G		p.X703_splice	ENST00000267163	NM_000321.2	703			0.282507737870484	3	FACETS	1	0.932	1	0.704	0.629	0.781	CLONAL	2	TRUE	0	0.371355227436165	3		167	245	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	360	688	0	ENST00000269305.4:c.329del	p.Arg110LeufsTer13	p.R110Lfs*13	ENST00000269305	NM_001126112.2	110	cGt/ct	4/11	0.273914204262293	3	FACETS	1	0.991	1	0.791	0.752	0.83	CLONAL	2	TRUE	0	0.371355227436165	3		688	969	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004729	16004729	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1289168244	NA	P-0046437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	73	505	0	ENST00000268712.3:c.2525A>C	p.Lys842Thr	p.K842T	ENST00000268712	NM_006311.3	842	aAa/aCa	20/46	0.273914204262293	3	FACETS	0.72	0.63	0.818	0.24	0.21	0.273	SUBCLONAL	1	TRUE	0	0.371355227436165	3		505	647	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151871270	151871270	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	135	317	0	ENST00000262189.6:c.9320T>C	p.Ile3107Thr	p.I3107T	ENST00000262189	NM_170606.2	3107	aTa/aCa	39/59	0.240202573008071	3	FACETS	0.837	0.765	0.912	0.837	0.765	0.912	CLONAL	2	TRUE	1	0.371355227436165	3		317	515	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	125	427	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.807	0.735	0.881	0.807	0.735	0.881	CLONAL	1	TRUE	1	0.653820358580047	2		427	474	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0046438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	42	292	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.718	0.608	0.836	0.718	0.608	0.836	SUBCLONAL	1	TRUE	1	0.653820358580047	2		292	179	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272443	11272443	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	241	395	0	ENST00000361445.4:c.3487C>G	p.Leu1163Val	p.L1163V	ENST00000361445	NM_004958.3	1163	Ctg/Gtg	23/58	1	2	FACETS	0.969	0.908	1	0.969	0.908	1	CLONAL	1	TRUE	1	0.653820358580047	2		395	761	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382152	152382154	+	inframe_deletion	In_Frame_Del	DEL	TGG	TGG	-	novel	NA	P-0046439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	126	237	0	ENST00000206249.3:c.1265_1267del	p.Val422del	p.V422del	ENST00000206249	NM_000125.3	421	aTGGtg/atg	6/8	0.584181766204736	4	FACETS	1	0.971	1	0.58	0.527	0.635	CLONAL	1	TRUE	2	0.679434815496135	4		237	537	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111475	8111476	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	231	503	1	ENST00000346208.3:c.962dup	p.Thr322AspfsTer30	p.T322Dfs*30	ENST00000346208		321	cag/cAag	5/6	0.679434815496135	3	FACETS	1	0.981	1	0.563	0.526	0.601	CLONAL	1	TRUE	1	0.679434815496135	3		504	809	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645075	67645075	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	158	536	3	ENST00000264010.4:c.340C>T	p.Gln114Ter	p.Q114*	ENST00000264010	NM_006565.3	114	Cag/Tag	3/12	0.149431943241403	6	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.679434815496135	6		539	740	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645084	67645084	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	166	553	3	ENST00000264010.4:c.349C>T	p.Gln117Ter	p.Q117*	ENST00000264010	NM_006565.3	117	Caa/Taa	3/12	0.149431943241403	6	FACETS	0.767	0.706	0.831			1	INDETERMINATE	2	TRUE	NA	0.679434815496135	6		556	751	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382251	152382251	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046439-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	225	279	3	ENST00000206249.3:c.1361T>G	p.Leu454Arg	p.L454R	ENST00000206249	NM_000125.3	454	cTt/cGt	6/8	0.584181766204736	4	FACETS	0.962	0.903	1	0.962	0.903	1	CLONAL	2	TRUE	2	0.679434815496135	4		282	578	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599333	55599333	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913682	NA	P-0046440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	61	301	0	ENST00000288135.5:c.2459A>G	p.Asp820Gly	p.D820G	ENST00000288135	NM_000222.2	820	gAt/gGt	17/21	1	2	FACETS	0.674	0.587	0.767	0.674	0.587	0.767	SUBCLONAL	1	TRUE	1	0.672735975708459	2		301	269	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927650	131927650	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	58	202	0	ENST00000265335.6:c.1722del	p.Lys574AsnfsTer24	p.K574Nfs*24	ENST00000265335		573	Aaa/aa	11/25	0.672735975708459	4	FACETS	0.949	0.821	1	0.316	0.273	0.362	CLONAL	1	TRUE	1	0.672735975708459	4		202	304	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593587	55593646	+	inframe_deletion	In_Frame_Del	DEL	CATGTATGAAGTACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACAT	CATGTATGAAGTACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACAT	-	novel	NA	P-0046440-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	91	253	0	ENST00000288135.5:c.1653_1712del	p.Met552_Ile571del	p.M552_I571del	ENST00000288135	NM_000222.2	551	ccCATGTATGAAGTACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATa/cca	11/21	1	2	FACETS	0.977	0.879	1	0.977	0.879	1	CLONAL	1	TRUE	1	0.672735975708459	2		253	277	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs878854073	NA	P-0046443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	200	370	0	ENST00000269305.4:c.673-1G>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.657994917889194	2	FACETS	0.956	0.913	0.998	0.956	0.913	0.998	CLONAL	2	TRUE	0	0.752364012611547	2		370	278	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105258975	105258975	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	97	658	0	ENST00000349310.3:c.6C>A	p.Ser2Arg	p.S2R	ENST00000349310	NM_001014432.1	2	agC/agA	3/15	0.652194623051907	3	FACETS	0.634	0.566	0.705	0.317	0.283	0.353	SUBCLONAL	1	TRUE	1	0.752364012611547	3		658	560	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046444-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	10	427	0				ENST00000310581	NM_198253.2	-/1132			0.252099802185887	1	FACETS	0.573	0.39	0.8	0.573	0.39	0.8	SUBCLONAL	1	TRUE	0	0.252099802185887	1		427	121	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952006	178952006	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046444-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	23	435	0	ENST00000263967.3:c.3061T>C	p.Tyr1021His	p.Y1021H	ENST00000263967	NM_006218.2	1021	Tac/Cac	21/21	1	2	FACETS	0.616	0.481	0.773	0.616	0.481	0.773	SUBCLONAL	1	TRUE	1	0.252099802185887	2		435	296	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0046444-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	49	633	1	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	0.212280828934251	3	FACETS	1	0.89	1	0.53	0.45	0.618	CLONAL	1	TRUE	1	0.252099802185887	3		634	413	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115865	8115866	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0046444-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	33	659	0	ENST00000346208.3:c.1213dup	p.His405ProfsTer102	p.H405Pfs*102	ENST00000346208		404	agc/agCc	6/6	0.252099802185887	1	FACETS	0.394	0.32	0.478	0.394	0.32	0.478	SUBCLONAL	1	TRUE	0	0.252099802185887	1		659	581	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981088	201981089	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTCT	novel	NA	P-0046444-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	52	785	0	ENST00000359651.3:c.167_168insTTCT	p.Lys56AsnfsTer37	p.K56Nfs*37	ENST00000359651		56	aag/aaTTCTg	2/8	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.252099802185887	2		785	387	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024024	27024024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046444-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	18	56	0	ENST00000324856.7:c.1133del	p.Pro378LeufsTer13	p.P378Lfs*13	ENST00000324856	NM_006015.4	377	aCc/ac	1/20	0.212280828934251	3	FACETS	0.874	0.67	1	0.874	0.67	1	CLONAL	2	TRUE	1	0.252099802185887	3		56	92	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96931053	96931053	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs749807415	NA	P-0046444-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	47	183	0	ENST00000258439.3:c.67C>A	p.Leu23Met	p.L23M	ENST00000258439	NM_001193304.2	23	Ctg/Atg	2/4	0.252099802185887	3	FACETS	1	0.854	1	1	0.854	1	CLONAL	2	TRUE	1	0.252099802185887	3		183	210	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265455	198265455	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046444-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	70	388	0	ENST00000335508.6:c.2702A>G	p.Gln901Arg	p.Q901R	ENST00000335508	NM_012433.2	901	cAa/cGa	18/25	0.252099802185887	3	FACETS	0.953	0.837	1	0.953	0.837	1	CLONAL	2	TRUE	1	0.252099802185887	3		388	328	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938494	44938515	+	frameshift_variant	Frame_Shift_Del	DEL	CACTGGAACAAAGAAAATCTGG	CACTGGAACAAAGAAAATCTGG	-	novel	NA	P-0046444-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	33	226	0	ENST00000377967.4:c.3044_3065del	p.Thr1015IlefsTer26	p.T1015Ifs*26	ENST00000377967	NM_021140.2	1014	ccCACTGGAACAAAGAAAATCTGG/cc	20/29	1	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.252099802185887	1		226	196	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907705	76907705	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046444-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	14	252	0	ENST00000373344.5:c.4456G>C	p.Asp1486His	p.D1486H	ENST00000373344	NM_000489.3	1486	Gat/Cat	15/35	1	1	FACETS	0.408	0.295	0.545	0.408	0.295	0.545	SUBCLONAL	1	TRUE	0	0.252099802185887	1		252	238	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0046445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	118	494	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.551081128584301	4	FACETS	0.902	0.827	0.979			1	CLONAL	2	TRUE	NA	0.806243581222396	4		494	293	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936096	178936096	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519940	NA	P-0046445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	68	614	0	ENST00000263967.3:c.1638G>T	p.Gln546His	p.Q546H	ENST00000263967	NM_006218.2	546	caG/caT	10/21	0.806243581222396	2	FACETS	1	0.914	1	0.514	0.458	0.571	CLONAL	1	TRUE	0	0.806243581222396	2		614	164	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813504	32813504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	60	555	1	ENST00000354258.4:c.2279C>T	p.Thr760Ile	p.T760I	ENST00000354258	NM_000593.5	760	aCc/aTc	11/11	0.790830422215163	3	FACETS	0.779	0.678	0.887	0.39	0.339	0.444	SUBCLONAL	1	TRUE	1	0.806243581222396	3		556	268	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904986	101904986	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0046445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	61	279	0	ENST00000374994.4:c.973+1G>T		p.X325_splice	ENST00000374994	NM_004612.2	325			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.806243581222396	2		279	108	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460335	149460335	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	28	418	1	ENST00000286301.3:c.302T>C	p.Val101Ala	p.V101A	ENST00000286301	NM_005211.3	101	gTc/gCc	3/22	0.588768587630635	6	FACETS	0.803	0.645	0.98	0.268	0.215	0.327	CLONAL	1	TRUE	3	0.806243581222396	6		419	226	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578205	7578205	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782177	NA	P-0046446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	523	692	0	ENST00000269305.4:c.644G>T	p.Ser215Ile	p.S215I	ENST00000269305	NM_001126112.2	215	aGt/aTt	6/11	0.964363941363755	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.964363941363755	1		692	540	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878166	48878166	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	278	186	0	ENST00000267163.4:c.118G>T	p.Glu40Ter	p.E40*	ENST00000267163	NM_000321.2	40	Gag/Tag	1/27	0.964363941363755	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.964363941363755	2		186	283	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811755	102811755	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	436	636	0	ENST00000307046.8:c.429C>A	p.Asn143Lys	p.N143K	ENST00000307046	NM_001111285.1	143	aaC/aaA	4/4	1	2	FACETS	0.97	0.93	1	0.97	0.93	1	CLONAL	1	TRUE	1	0.964363941363755	2		636	932	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101776	71101776	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	149	153	0	ENST00000318789.4:c.422A>T	p.Gln141Leu	p.Q141L	ENST00000318789	NM_032682.5	141	cAg/cTg	9/21	0.964363941363755	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.964363941363755	1		153	156	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412656	63412656	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	406	680	0	ENST00000330258.3:c.511G>T	p.Gly171Cys	p.G171C	ENST00000330258	NM_152424.3	171	Ggc/Tgc	2/2	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.964363941363755	2		680	842	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49423014	49423014	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	566	654	0	ENST00000301067.7:c.14081A>T	p.Glu4694Val	p.E4694V	ENST00000301067	NM_003482.3	4694	gAg/gTg	44/54	0.964363941363755	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.964363941363755	1		654	573	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239848	41239848	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	842	531	0	ENST00000379561.5:c.502C>T	p.Leu168Phe	p.L168F	ENST00000379561	NM_002015.3	168	Ctc/Ttc	1/3	0.964363941363755	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.964363941363755	2		531	855	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063380	67063380	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	325	410	0	ENST00000412916.2:c.70G>T	p.Glu24Ter	p.E24*	ENST00000412916		24	Gag/Tag	1/6	1	2	FACETS	0.996	0.948	1	0.996	0.948	1	CLONAL	1	TRUE	1	0.964363941363755	2		410	677	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81892736	81892736	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1316325819	NA	P-0046446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	177	270	0	ENST00000359376.3:c.447G>T	p.Gln149His	p.Q149H	ENST00000359376	NM_002661.3	149	caG/caT	5/33	1	2	FACETS	0.984	0.921	1	0.984	0.921	1	CLONAL	1	TRUE	1	0.964363941363755	2		270	373	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937719	17937720	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	AA	novel	NA	P-0046446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	296	599	1	ENST00000458235.1:c.3208-1_3208delinsTT		p.X1070_splice	ENST00000458235	NM_000215.3	1070		24/24	1	2	FACETS	0.871	0.825	0.917	0.871	0.825	0.917	CLONAL	1	TRUE	1	0.964363941363755	2		600	705	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273196	198273197	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0046446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	241	554	0	ENST00000335508.6:c.1013_1014delinsTT	p.Trp338Phe	p.W338F	ENST00000335508	NM_012433.2	338	tGG/tTT	8/25	0.490011447191289	1	FACETS	0.351	0.329	0.374	0.351	0.329	0.374	INDETERMINATE	1	TRUE	0	0.964363941363755	1		554	737	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281517	198281517	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	236	537	0	ENST00000335508.6:c.614A>T	p.Asp205Val	p.D205V	ENST00000335508	NM_012433.2	205	gAt/gTt	6/25	0.490011447191289	1	FACETS	0.348	0.326	0.371	0.348	0.326	0.371	INDETERMINATE	1	TRUE	0	0.964363941363755	1		537	728	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945291	54945291	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1442832751	NA	P-0046446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	270	328	0	ENST00000312783.6:c.1135G>C	p.Glu379Gln	p.E379Q	ENST00000312783	NM_198436.1	379	Gaa/Caa	10/10	0.517551493373088	1	FACETS	0.74	0.709	0.769	0.74	0.709	0.769	INDETERMINATE	1	TRUE	0	0.964363941363755	1		328	392	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259270	89259270	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	309	348	0	ENST00000336596.2:c.414T>A	p.His138Gln	p.H138Q	ENST00000336596	NM_005233.5	138	caT/caA	3/17	0.964363941363755	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.964363941363755	1		348	317	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528579	89528579	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	213	279	0	ENST00000336596.2:c.2879G>T	p.Gly960Val	p.G960V	ENST00000336596	NM_005233.5	960	gGg/gTg	17/17	0.964363941363755	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.964363941363755	1		279	219	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861041	35861041	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	466	356	0	ENST00000303115.3:c.170G>T	p.Cys57Phe	p.C57F	ENST00000303115	NM_002185.3	57	tGt/tTt	2/8	0.858074366275353	3	FACETS	0.91	0.878	0.942			1	CLONAL	2	TRUE	NA	0.964363941363755	3		356	787	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951832	2951832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	248	789	0	ENST00000396946.4:c.3118G>A	p.Ala1040Thr	p.A1040T	ENST00000396946	NM_032415.4	1040	Gcc/Acc	23/25	1	2	FACETS	0.439	0.41	0.469	0.439	0.41	0.469	SUBCLONAL	1	TRUE	1	0.964363941363755	2		789	1172	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335670	81335670	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	342	441	0	ENST00000222390.5:c.1690G>C	p.Val564Leu	p.V564L	ENST00000222390	NM_000601.4	564	Gtt/Ctt	15/18	1	2	FACETS	0.993	0.947	1	0.993	0.947	1	CLONAL	1	TRUE	1	0.964363941363755	2		441	714	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386621	81386621	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0046446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	224	347	0	ENST00000222390.5:c.368-2A>C		p.X123_splice	ENST00000222390	NM_000601.4	123			1	2	FACETS	0.933	0.878	0.988	0.933	0.878	0.988	CLONAL	1	TRUE	1	0.964363941363755	2		347	498	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509861	106509861	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	422	564	0	ENST00000359195.3:c.1855C>A	p.Gln619Lys	p.Q619K	ENST00000359195	NM_002649.2	619	Caa/Aaa	2/11	1	2	FACETS	0.946	0.906	0.987	0.946	0.906	0.987	CLONAL	1	TRUE	1	0.964363941363755	2		564	925	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964424	70964424	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	394	626	0	ENST00000276594.2:c.1604A>T	p.His535Leu	p.H535L	ENST00000276594	NM_024504.3	535	cAt/cTt	8/8	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.964363941363755	2		626	817	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606473	93606473	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	818	989	0	ENST00000375746.1:c.293G>C	p.Gly98Ala	p.G98A	ENST00000375746	NM_001174167.1	98	gGc/gCc	2/14	0.964363941363755	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.964363941363755	1		989	834	SUCCESS
AR	367	MSKCC	GRCh37	X	66766390	66766390	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1479622768	NA	P-0046446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	56	66	0	ENST00000374690.3:c.1402G>T	p.Gly468Cys	p.G468C	ENST00000374690	NM_000044.3	468	Ggc/Tgc	1/8	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.964363941363755	2		66	108	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195157	123195157	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	155	483	0	ENST00000218089.9:c.1500C>A	p.Ser500Arg	p.S500R	ENST00000218089	NM_001042749.1	500	agC/agA	16/35	1	2	FACETS	0.448	0.411	0.487	0.448	0.411	0.487	SUBCLONAL	1	TRUE	1	0.964363941363755	2		483	717	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	74	427	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	1	0.905	1	1	0.988	1	CLONAL	3	TRUE	0	0.24	1		427	179	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0046447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	128	667	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.931	0.852	1	1	0.992	1	CLONAL	3	TRUE	1	0.24	2		667	382	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0046447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	138	109	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.966	1	1	0.993	1	CLONAL	3	TRUE	1	0.24	2		109	353	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467924	50467924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	73	584	0	ENST00000331340.3:c.1159G>A	p.Glu387Lys	p.E387K	ENST00000331340	NM_006060.4	387	Gag/Aag	8/8	1	2	FACETS	0.994	0.877	1	1	0.983	1	CLONAL	2	TRUE	1	0.24	2		584	306	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499393	89499393	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	138	439	0	ENST00000336596.2:c.2563C>T	p.Gln855Ter	p.Q855*	ENST00000336596	NM_005233.5	855	Cag/Tag	15/17	0.0660198849223168	3	FACETS	0.874	0.801	0.95	1	0.983	1	INDETERMINATE	3	TRUE	1	0.24	3		439	491	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287229	46287229	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0046447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	99	353	0	ENST00000334344.6:c.5174C>G	p.Ser1725Ter	p.S1725*	ENST00000334344	NM_152641.2	1725	tCa/tGa	19/21	0.0732573643704051	4	FACETS	1	0.971	1	1	0.971	1	INDETERMINATE	2	TRUE	2	0.24	4		353	417	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263992	104263992	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758001170	NA	P-0046447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	135	372	1	ENST00000369902.3:c.83C>T	p.Ser28Leu	p.S28L	ENST00000369902	NM_016169.3	28	tCg/tTg	1/12	1	2	FACETS	0.959	0.881	1	1	0.993	1	CLONAL	3	TRUE	1	0.24	2		373	391	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726954	46726954	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs186059216	NA	P-0046447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	156	496	1	ENST00000371975.4:c.788G>A	p.Gly263Glu	p.G263E	ENST00000371975	NM_003579.3	263	gGa/gAa	8/18	1	2	FACETS	1	0.961	1	1	0.994	1	CLONAL	3	TRUE	1	0.24	2		497	409	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959350	26959350	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	118	237	0	ENST00000381527.3:c.517G>T	p.Asp173Tyr	p.D173Y	ENST00000381527	NM_001260.1	173	Gac/Tac	6/13	0.244515220672864	0	FACETS	0.88	0.808	0.954			1	CLONAL	3	TRUE	0	0.24	0		237	283	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412986	49412986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	173	581	0	ENST00000418115.1:c.37G>A	p.Asp13Asn	p.D13N	ENST00000418115	NM_001664.2	13	Gat/Aat	2/5	0.0660198849223168	3	FACETS	0.977	0.905	1	1	0.99	1	INDETERMINATE	3	TRUE	1	0.24	3		581	551	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339633	116339633	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	105	321	0	ENST00000397752.3:c.495G>T	p.Gln165His	p.Q165H	ENST00000397752	NM_000245.2	165	caG/caT	2/21	1	2	FACETS	1	0.96	1	1	0.989	1	CLONAL	2	TRUE	1	0.24	2		321	390	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227933	123227933	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0046447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	147	172	0	ENST00000218089.9:c.3644C>G	p.Ser1215Ter	p.S1215*	ENST00000218089	NM_001042749.1	1215	tCa/tGa	33/35	1	1	FACETS	1	0.964	1	1	0.994	1	CLONAL	5	TRUE	0	0.24	1		172	210	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922986	44922994	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTACCTC	CTCTACCTC	G	novel	NA	P-0046447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	206	273	0	ENST00000377967.4:c.1847_1855delinsG	p.Thr616ArgfsTer2	p.T616Rfs*2	ENST00000377967	NM_021140.2	616	aCTCTACCTCat/aGat	16/29	1	1	FACETS	0.933	0.885	0.979	1	0.996	1	CLONAL	5	TRUE	0	0.24	1		273	324	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	49	267	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.849	0.723	0.984	0.849	0.723	0.984	CLONAL	1	TRUE	1	0.395504831543113	2		267	292	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	206	1071	8	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.93	0.862	1	0.93	0.862	1	CLONAL	1	TRUE	1	0.395504831543113	2		1079	1120	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	169	985	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.91	0.837	0.987	0.91	0.837	0.987	CLONAL	1	TRUE	1	0.395504831543113	2		991	939	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	65	1018	4	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.27	0.233	0.31	0.27	0.233	0.31	SUBCLONAL	1	TRUE	1	0.395504831543113	2		1022	1219	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	149	671	0	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	1	2	FACETS	0.982	0.899	1	0.982	0.899	1	CLONAL	1	TRUE	1	0.395504831543113	2		671	767	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	201	485	2	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.395504831543113	2		487	923	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	236	1262	4	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.908	0.846	0.973	0.908	0.846	0.973	CLONAL	1	TRUE	1	0.395504831543113	2		1266	1314	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1232964733	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	30	111	0	ENST00000324856.7:c.1015del	p.Ala339LeufsTer24	p.A339Lfs*24	ENST00000324856	NM_006015.4	337	tGg/tg	1/20	1	2	FACETS	0.903	0.736	1	0.903	0.736	1	CLONAL	1	TRUE	1	0.395504831543113	2		111	168	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261878	16261878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763414538	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	119	589	2	ENST00000375759.3:c.9143C>T	p.Thr3048Met	p.T3048M	ENST00000375759	NM_015001.2	3048	aCg/aTg	11/15	1	2	FACETS	0.889	0.804	0.979	0.889	0.804	0.979	CLONAL	1	TRUE	1	0.395504831543113	2		591	677	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264364	16264364	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	182	849	0	ENST00000375759.3:c.10567C>T	p.Gln3523Ter	p.Q3523*	ENST00000375759	NM_015001.2	3523	Cag/Tag	13/15	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.395504831543113	2		849	908	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057937	27057937	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	168	750	0	ENST00000324856.7:c.1650del	p.Tyr551ThrfsTer68	p.Y551Tfs*68	ENST00000324856	NM_006015.4	549	Ccc/cc	3/20	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.395504831543113	2		750	837	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307211	65307211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199886153	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	95	489	0	ENST00000342505.4:c.2477G>A	p.Arg826His	p.R826H	ENST00000342505	NM_002227.2	826	cGc/cAc	18/25	1	2	FACETS	0.766	0.683	0.855	0.766	0.683	0.855	SUBCLONAL	1	TRUE	1	0.395504831543113	2		489	627	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458005	120458005	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	121	724	1	ENST00000256646.2:c.7340del	p.Gly2447ValfsTer43	p.G2447Vfs*43	ENST00000256646	NM_024408.3	2447	gGt/gt	34/34	1	2	FACETS	0.826	0.747	0.909	0.826	0.747	0.909	CLONAL	1	TRUE	1	0.395504831543113	2		725	741	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	80	482	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.787	0.695	0.886	0.787	0.695	0.886	SUBCLONAL	1	TRUE	1	0.395504831543113	2		482	514	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903697	114903697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465566182	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	121	626	0	ENST00000543371.1:c.701C>T	p.Pro234Leu	p.P234L	ENST00000543371	NM_001198531.1	234	cCg/cTg	7/14	1	2	FACETS	0.807	0.73	0.889	0.807	0.73	0.889	CLONAL	1	TRUE	1	0.395504831543113	2		626	758	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948483	71948484	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	251	1289	3	ENST00000298229.2:c.3201dup	p.Ser1068GlnfsTer17	p.S1068Qfs*17	ENST00000298229	NM_001567.3	1065	-/C	26/28	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.395504831543113	2		1292	1195	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076639	102076642	+	frameshift_variant	Frame_Shift_Del	DEL	TCAG	TCAG	-	novel	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	29	382	0	ENST00000282441.5:c.822_825del	p.Ser274ArgfsTer5	p.S274Rfs*5	ENST00000282441	NM_001130145.2	273	aTCAGt/at	5/9	1	2	FACETS	0.286	0.229	0.352	0.286	0.229	0.352	SUBCLONAL	1	TRUE	1	0.395504831543113	2		382	512	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493621	56493621	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs1343971705	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	63	376	0	ENST00000267101.3:c.2938-1G>T		p.X980_splice	ENST00000267101	NM_001982.3	980			1	2	FACETS	0.69	0.598	0.789	0.69	0.598	0.789	SUBCLONAL	1	TRUE	1	0.395504831543113	2		376	462	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210862	133210862	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774726229	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	144	823	0	ENST00000320574.5:c.5914G>A	p.Val1972Met	p.V1972M	ENST00000320574	NM_006231.2	1972	Gtg/Atg	43/49	1	2	FACETS	0.761	0.693	0.832	0.761	0.693	0.832	SUBCLONAL	1	TRUE	1	0.395504831543113	2		823	957	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028601	42028601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376715603	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	139	699	0	ENST00000219905.7:c.4139G>A	p.Arg1380Gln	p.R1380Q	ENST00000219905	NM_001164273.1	1380	cGa/cAa	13/24	1	2	FACETS	0.997	0.909	1	0.997	0.909	1	CLONAL	1	TRUE	1	0.395504831543113	2		699	705	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729104	66729104	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	139	608	0	ENST00000307102.5:c.312A>C	p.Lys104Asn	p.K104N	ENST00000307102	NM_002755.3	104	aaA/aaC	3/11	1	2	FACETS	0.945	0.861	1	0.945	0.861	1	CLONAL	1	TRUE	1	0.395504831543113	2		608	744	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098651	2098653	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs778509364	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	159	589	0	ENST00000219476.3:c.37_39del	p.Glu13del	p.E13del	ENST00000219476	NM_000548.3	12	aAGGag/aag	2/42	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.395504831543113	2		589	708	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131664	2131664	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	197	1114	0	ENST00000219476.3:c.3679C>A	p.Pro1227Thr	p.P1227T	ENST00000219476	NM_000548.3	1227	Ccc/Acc	31/42	1	2	FACETS	0.961	0.889	1	0.961	0.889	1	CLONAL	1	TRUE	1	0.395504831543113	2		1114	1037	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348674	89348674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs963622923	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	168	784	0	ENST00000301030.4:c.4276G>A	p.Glu1426Lys	p.E1426K	ENST00000301030	NM_001256183.1	1426	Gaa/Aaa	9/13	1	2	FACETS	0.911	0.837	0.988	0.911	0.837	0.988	CLONAL	1	TRUE	1	0.395504831543113	2		784	933	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983995	7983995	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1388130253	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	64	385	0	ENST00000319144.4:c.631T>C	p.Phe211Leu	p.F211L	ENST00000319144	NM_001139.2	211	Ttc/Ctc	5/15	1	2	FACETS	0.838	0.729	0.956	0.838	0.729	0.956	CLONAL	1	TRUE	1	0.395504831543113	2		385	386	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973674	15973674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	128	505	1	ENST00000268712.3:c.4318G>A	p.Ala1440Thr	p.A1440T	ENST00000268712	NM_006311.3	1440	Gca/Aca	31/46	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.395504831543113	2		506	627	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486063	29486064	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs771115661	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	45	262	0	ENST00000356175.3:c.246_247del	p.Gln83ValfsTer23	p.Q83Vfs*23	ENST00000356175	NM_000267.3	80	taTCtc/tatc	3/57	1	2	FACETS	0.859	0.727	1	0.859	0.727	1	CLONAL	1	TRUE	1	0.395504831543113	2		262	265	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553478	29553478	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781807	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	246	720	3	ENST00000356175.3:c.2033del	p.Pro678ArgfsTer10	p.P678Rfs*10	ENST00000356175	NM_000267.3	676	aCc/ac	18/57	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.395504831543113	2		723	1132	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40460264	40460264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1331759850	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	153	672	0	ENST00000345506.4:c.1975C>T	p.Arg659Trp	p.R659W	ENST00000345506	NM_003152.3	659	Cgg/Tgg	17/20	1	2	FACETS	0.9	0.823	0.98	0.9	0.823	0.98	CLONAL	1	TRUE	1	0.395504831543113	2		672	860	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462635	40462635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762056710	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	137	658	2	ENST00000345506.4:c.2333G>A	p.Arg778His	p.R778H	ENST00000345506	NM_003152.3	778	cGc/cAc	20/20	1	2	FACETS	0.782	0.711	0.857	0.782	0.711	0.857	SUBCLONAL	1	TRUE	1	0.395504831543113	2		660	886	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210790	36210790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	215	1187	1	ENST00000222270.7:c.541C>T	p.Arg181Trp	p.R181W	ENST00000222270	NM_014727.1	181	Cgg/Tgg	3/37	1	2	FACETS	0.918	0.852	0.987	0.918	0.852	0.987	CLONAL	1	TRUE	1	0.395504831543113	2		1188	1184	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214720	36214720	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772989623	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	107	819	0	ENST00000222270.7:c.3146C>T	p.Ala1049Val	p.A1049V	ENST00000222270	NM_014727.1	1049	gCg/gTg	8/37	1	2	FACETS	0.763	0.685	0.846	0.763	0.685	0.846	SUBCLONAL	1	TRUE	1	0.395504831543113	2		819	709	SUCCESS
AXL	558	MSKCC	GRCh37	19	41759567	41759567	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	170	775	1	ENST00000301178.4:c.1990A>G	p.Ser664Gly	p.S664G	ENST00000301178	NM_021913.4	664	Agt/Ggt	17/20	1	2	FACETS	0.957	0.881	1	0.957	0.881	1	CLONAL	1	TRUE	1	0.395504831543113	2		776	898	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906379	50906379	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	211	1173	1	ENST00000440232.2:c.1040C>A	p.Pro347Gln	p.P347Q	ENST00000440232	NM_002691.3	347	cCg/cAg	9/27	1	2	FACETS	0.938	0.871	1	0.938	0.871	1	CLONAL	1	TRUE	1	0.395504831543113	2		1174	1137	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52722956	52722956	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	136	672	3	ENST00000322088.6:c.1141C>T	p.Arg381Trp	p.R381W	ENST00000322088	NM_014225.5	381	Cgg/Tgg	10/15	1	2	FACETS	0.835	0.759	0.914	0.835	0.759	0.914	CLONAL	1	TRUE	1	0.395504831543113	2		675	824	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52725442	52725442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767299944	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	143	799	0	ENST00000322088.6:c.1609C>T	p.Arg537Cys	p.R537C	ENST00000322088	NM_014225.5	537	Cgc/Tgc	13/15	1	2	FACETS	0.755	0.688	0.826	0.755	0.688	0.826	SUBCLONAL	1	TRUE	1	0.395504831543113	2		799	958	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703511	47703511	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs63751232	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	167	456	0	ENST00000233146.2:c.2011A>T	p.Asn671Tyr	p.N671Y	ENST00000233146	NM_000251.2	671	Aat/Tat	13/16	0.384838196494947	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.395504831543113	2		456	407	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	52	377	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	0.384838196494947	2	FACETS	0.442	0.376	0.515	0.221	0.188	0.258	SUBCLONAL	1	TRUE	0	0.395504831543113	2		379	595	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096319	178096321	+	inframe_deletion	In_Frame_Del	DEL	CTG	CTG	-	novel	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	121	474	0	ENST00000397062.3:c.1010_1012del	p.Ala337del	p.A337del	ENST00000397062	NM_006164.4	337	gCAGaa/gaa	5/5	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.395504831543113	2		474	591	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371604	225371606	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	61	386	0	ENST00000264414.4:c.998_1000del	p.Gly333del	p.G333del	ENST00000264414	NM_003590.4	333	gGAGaa/gaa	7/16	1	2	FACETS	0.935	0.812	1	0.935	0.812	1	CLONAL	1	TRUE	1	0.395504831543113	2		386	330	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795103	242795104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768249210	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	123	1124	3	ENST00000334409.5:c.105dup	p.Thr36HisfsTer70	p.T36Hfs*70	ENST00000334409	NM_005018.2	35	-/C	2/5	1	2	FACETS	0.527	0.475	0.582	0.527	0.475	0.582	SUBCLONAL	1	TRUE	1	0.395504831543113	2		1127	1180	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71064767	71064767	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	67	427	0	ENST00000318789.4:c.907T>G	p.Tyr303Asp	p.Y303D	ENST00000318789	NM_032682.5	303	Tat/Gat	12/21	1	2	FACETS	0.633	0.551	0.722	0.633	0.551	0.722	SUBCLONAL	1	TRUE	1	0.395504831543113	2		427	535	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448552	89448552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	91	494	0	ENST00000336596.2:c.1516G>A	p.Val506Ile	p.V506I	ENST00000336596	NM_005233.5	506	Gta/Ata	7/17	1	2	FACETS	0.716	0.636	0.801	0.716	0.636	0.801	SUBCLONAL	1	TRUE	1	0.395504831543113	2		494	643	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430873	181430873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	271	1125	0	ENST00000325404.1:c.725C>T	p.Ser242Leu	p.S242L	ENST00000325404	NM_003106.3	242	tCg/tTg	1/1	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.395504831543113	2		1125	1272	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957837	1957837	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	179	618	0	ENST00000382891.5:c.2803C>T	p.Arg935Ter	p.R935*	ENST00000382891	NM_133335.3	935	Cga/Tga	15/22	1	2	FACETS	0.943	0.869	1	0.943	0.869	1	CLONAL	1	TRUE	1	0.395504831543113	2		618	960	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279449	1279449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756152343	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	216	1124	0	ENST00000310581.5:c.2087G>A	p.Arg696His	p.R696H	ENST00000310581	NM_198253.2	696	cGt/cAt	5/16	1	2	FACETS	0.912	0.846	0.98	0.912	0.846	0.98	CLONAL	1	TRUE	1	0.395504831543113	2		1124	1198	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109321872	109321872	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745757510	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	60	383	1	ENST00000436639.2:c.551C>T	p.Ala184Val	p.A184V	ENST00000436639	NM_014454.2	184	gCg/gTg	4/10	1	2	FACETS	0.867	0.751	0.992	0.867	0.751	0.992	CLONAL	1	TRUE	1	0.395504831543113	2		384	350	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622179	162622179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781608005	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	106	346	0	ENST00000366898.1:c.518C>T	p.Thr173Met	p.T173M	ENST00000366898	NM_004562.2	173	aCg/aTg	4/12	1	2	FACETS	0.932	0.838	1	0.932	0.838	1	CLONAL	1	TRUE	1	0.395504831543113	2		346	575	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194706	29194706	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs974286158	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	202	1120	4	ENST00000240100.2:c.1022C>T	p.Ala341Val	p.A341V	ENST00000240100	NM_001394.6	341	gCg/gTg	4/4	0.35210725746287	3	FACETS	1	0.937	1	0.507	0.469	0.546	CLONAL	1	TRUE	1	0.395504831543113	3		1124	1207	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089744	5089745	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	40	193	0	ENST00000381652.3:c.2648dup	p.Leu884AlafsTer4	p.L884Afs*4	ENST00000381652	NM_004972.3	881	gta/gtAa	20/25	1	2	FACETS	0.787	0.658	0.928	0.787	0.658	0.928	CLONAL	1	TRUE	1	0.395504831543113	2		193	257	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202997	27202997	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	44	515	0	ENST00000380036.4:c.2089T>C	p.Tyr697His	p.Y697H	ENST00000380036	NM_000459.3	697	Tat/Cat	13/23	1	2	FACETS	0.373	0.312	0.441	0.373	0.312	0.441	SUBCLONAL	1	TRUE	1	0.395504831543113	2		515	596	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039668	47039668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	179	1017	0	ENST00000377604.3:c.1120G>A	p.Gly374Ser	p.G374S	ENST00000377604	NM_001204468.1	374	Ggc/Agc	11/24	1	2	FACETS	0.9	0.829	0.974	0.9	0.829	0.974	CLONAL	1	TRUE	1	0.395504831543113	2		1017	1006	SUCCESS
AR	367	MSKCC	GRCh37	X	66765149	66765151	+	inframe_deletion	In_Frame_Del	DEL	TGC	TGC	-	rs752055010	NA	P-0046448-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	20	361	1	ENST00000374690.3:c.170_172del	p.Leu57del	p.L57del	ENST00000374690	NM_000044.3	54	tTGCtg/ttg	1/8	1	2	FACETS	0.306	0.233	0.39	0.306	0.233	0.39	SUBCLONAL	1	TRUE	1	0.395504831543113	2		362	331	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692791	89692791	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1114167623	NA	P-0046451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	57	323	0	ENST00000371953.3:c.275A>G	p.Asp92Gly	p.D92G	ENST00000371953	NM_000314.4	92	gAc/gGc	5/9	0.423736658765677	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.423736658765677	1		323	179	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933307	100933307	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	173	511	1	ENST00000325455.5:c.2083G>A	p.Glu695Lys	p.E695K	ENST00000325455	NM_001202474.3	695	Gaa/Aaa	4/8	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.423736658765677	2		512	572	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197838	66197838	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	63	195	0	ENST00000273854.3:c.2861A>C	p.Asn954Thr	p.N954T	ENST00000273854	NM_004439.5	954	aAt/aCt	17/18	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.423736658765677	2		195	204	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285867	46285867	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	90	299	0	ENST00000334344.6:c.5135A>T	p.Lys1712Met	p.K1712M	ENST00000334344	NM_152641.2	1712	aAg/aTg	18/21	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.423736658765677	2		299	335	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788669	3788669	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	25	302	0	ENST00000262367.5:c.4285G>T	p.Val1429Leu	p.V1429L	ENST00000262367	NM_004380.2	1429	Gtg/Ttg	26/31	1	2	FACETS	0.266	0.209	0.332	0.266	0.209	0.332	SUBCLONAL	1	TRUE	1	0.423736658765677	2		302	443	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650717	67650717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1486997074	NA	P-0046451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	263	580	1	ENST00000264010.4:c.1022G>A	p.Arg341His	p.R341H	ENST00000264010	NM_006565.3	341	cGt/cAt	5/12	0.260288260538113	4	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.423736658765677	4		581	1193	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439110	56439916	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTGTTCCTCAGATACACTAGACACATTTCTGCCTTAAGGCCTTTGCATTTACTGTTCTCTCTGCCTAGATCCCTTTCTCCTCAGATACCTGCACAGATCACTCCCTCTCCCATTTAGGGTCTTTGCTGCAATGCCATCTTCTCAATGTGGCCTTCTCTGGACTTGCTTTTAAAAATTAACCCTGTTAATTTTTACTAAAAATACAAAAATTAGTAGCTCCCAGCTACTCGCGAGACTGAGGCAGGAGAATTGCTTGAACCCAGGAGGCAGAGATTGCAGTGAGCCGAGATCACGCCACTGCATTCCACCCTGGGCGACAGAGCAAGACTCTGTCTCAAAACAAACAAACAAACAAACAAACAAAAAAAAACCTTGTTCCCTTGCATTCCCTCCCTCCCCACTTTGCTATCAGCATTATCATTTTTTCTCCGTAGTACATATCACCATCTAAAACATTATAGATTTTACTTATTTAGTCTGTTTATTGTCTGTTTTTTCCCTCTAGAATAAAAAAGCTCTTTGAGGGTAGGAGTTTTTTGTCATCTTGTTCACTGTACTACCCTCAGCACCTGGAACAGTGCCTGACACATAATAGAGCTTGGTGTATTTGTTGAATGGATGAGTAATATGAGGAGAGGCTGCTGGAAATCAACAAAGACAGACGCTGGGGTATTTTGATGTAAATGGTTCCATAGGTATAAAGGTGCCTTCTTCACGTACTCCTTCCTTCTCCCTAACCACCCACCCACACACACGCACACGTTCACCGCCGCCAAAGACCCCACACTGCTCACCGGCCTGCTGTG	GCTGTTCCTCAGATACACTAGACACATTTCTGCCTTAAGGCCTTTGCATTTACTGTTCTCTCTGCCTAGATCCCTTTCTCCTCAGATACCTGCACAGATCACTCCCTCTCCCATTTAGGGTCTTTGCTGCAATGCCATCTTCTCAATGTGGCCTTCTCTGGACTTGCTTTTAAAAATTAACCCTGTTAATTTTTACTAAAAATACAAAAATTAGTAGCTCCCAGCTACTCGCGAGACTGAGGCAGGAGAATTGCTTGAACCCAGGAGGCAGAGATTGCAGTGAGCCGAGATCACGCCACTGCATTCCACCCTGGGCGACAGAGCAAGACTCTGTCTCAAAACAAACAAACAAACAAACAAACAAAAAAAAACCTTGTTCCCTTGCATTCCCTCCCTCCCCACTTTGCTATCAGCATTATCATTTTTTCTCCGTAGTACATATCACCATCTAAAACATTATAGATTTTACTTATTTAGTCTGTTTATTGTCTGTTTTTTCCCTCTAGAATAAAAAAGCTCTTTGAGGGTAGGAGTTTTTTGTCATCTTGTTCACTGTACTACCCTCAGCACCTGGAACAGTGCCTGACACATAATAGAGCTTGGTGTATTTGTTGAATGGATGAGTAATATGAGGAGAGGCTGCTGGAAATCAACAAAGACAGACGCTGGGGTATTTTGATGTAAATGGTTCCATAGGTATAAAGGTGCCTTCTTCACGTACTCCTTCCTTCTCCCTAACCACCCACCCACACACACGCACACGTTCACCGCCGCCAAAGACCCCACACTGCTCACCGGCCTGCTGTG	-	novel	NA	P-0046451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1	40	0	0	ENST00000407977.2:c.676_687+795del		p.X226_splice	ENST00000407977		226		6/10	0.423736658765677	0	FACETS		NA	1			1	NA	4	TRUE	0	0.423736658765677	0		0	41	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627850	14627850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	53	737	0	ENST00000254322.2:c.220G>A	p.Gly74Arg	p.G74R	ENST00000254322	NM_006145.1	74	Ggg/Agg	2/3	1	2	FACETS	0.245	0.208	0.286	0.245	0.208	0.286	SUBCLONAL	1	TRUE	1	0.423736658765677	2		737	1022	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655180	45655180	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	40	454	0	ENST00000407780.3:c.672G>T	p.Gln224His	p.Q224H	ENST00000407780	NM_001283052.1	224	caG/caT	4/7	NA	2	FACETS	0.278	0.23	0.332			1	INDETERMINATE	1	TRUE	NA	0.423736658765677	2		454	679	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275311	41275311	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	152	334	1	ENST00000349496.5:c.1477G>A	p.Val493Ile	p.V493I	ENST00000349496	NM_001904.3	493	Gtt/Att	9/15	1	2	FACETS	0.762	0.702	0.823	1	0.989	1	SUBCLONAL	2	TRUE	1	0.423736658765677	2		335	471	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980385	55980385	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	21	352	0	ENST00000263923.4:c.706C>A	p.Leu236Ile	p.L236I	ENST00000263923	NM_002253.2	236	Cta/Ata	6/30	1	2	FACETS	0.313	0.24	0.397	0.313	0.24	0.397	SUBCLONAL	1	TRUE	1	0.423736658765677	2		352	317	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524181	187524181	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	146	385	0	ENST00000441802.2:c.11358G>T	p.Arg3786Ser	p.R3786S	ENST00000441802	NM_005245.3	3786	agG/agT	20/27	0.423736658765677	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.423736658765677	1		385	392	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873375	151873375	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	106	313	0	ENST00000262189.6:c.9163C>G	p.Leu3055Val	p.L3055V	ENST00000262189	NM_170606.2	3055	Cta/Gta	38/59	1	2	FACETS	0.767	0.696	0.841	1	0.985	1	SUBCLONAL	2	TRUE	1	0.423736658765677	2		313	326	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527439	29527439	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs587781517	NA	P-0046452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	49	300	0	ENST00000356175.3:c.889-1G>A		p.X297_splice	ENST00000356175	NM_000267.3	297			0.190299235777776	1	FACETS	0.914	0.776	1	0.914	0.776	1	CLONAL	1	FALSE	0	0.218451663710422	1		300	437	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100329	27100377	+	frameshift_variant	Frame_Shift_Del	DEL	CACCCCTTCTGGCAGCCCCTTCCCCAGCCAGCAGACTACAATGTATCAA	CACCCCTTCTGGCAGCCCCTTCCCCAGCCAGCAGACTACAATGTATCAA	-	novel	NA	P-0046452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	121	764	0	ENST00000324856.7:c.4043_4091del	p.Thr1348SerfsTer117	p.T1348Sfs*117	ENST00000324856	NM_006015.4	1347	ggCACCCCTTCTGGCAGCCCCTTCCCCAGCCAGCAGACTACAATGTATCAA/gg	17/20	0.170895740978581	2	FACETS	1	0.958	1	0.557	0.502	0.615	CLONAL	1	FALSE	0	0.218451663710422	2		764	994	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578490	7578490	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046452-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1307	136	1080	0	ENST00000269305.4:c.440T>C	p.Val147Ala	p.V147A	ENST00000269305	NM_001126112.2	147	gTt/gCt	5/11	0.190299235777776	1	FACETS	0.769	0.696	0.845	0.769	0.696	0.845	SUBCLONAL	1	FALSE	0	0.218451663710422	1		1080	1443	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	471	938	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.720185005919806	2	FACETS	0.992	0.963	1	0.992	0.963	1	CLONAL	2	TRUE	0	0.723430243549999	2		938	656	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954198	48954198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123331	NA	P-0046453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	135	154	0	ENST00000267163.4:c.1399C>T	p.Arg467Ter	p.R467*	ENST00000267163	NM_000321.2	467	Cga/Tga	15/27	0.723430243549999	2	FACETS	0.889	0.834	0.942	0.889	0.834	0.942	CLONAL	2	TRUE	0	0.723430243549999	2		154	210	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413214	139413214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	294	902	0	ENST00000277541.6:c.928G>A	p.Gly310Arg	p.G310R	ENST00000277541	NM_017617.3	310	Ggg/Agg	6/34	0.173932740946628	2	FACETS	0.757	0.713	0.802	0.378	0.356	0.401	INDETERMINATE	1	TRUE	0	0.723430243549999	2		902	1074	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710750	117710750	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	56	272	0	ENST00000368508.3:c.1522G>T	p.Asp508Tyr	p.D508Y	ENST00000368508	NM_002944.2	508	Gac/Tac	12/43	0.245933874441025	3	FACETS	0.663	0.571	0.762	0.331	0.285	0.381	INDETERMINATE	1	TRUE	1	0.723430243549999	3		272	318	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400054	139400064	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTGTAGTCC	AGCTGTAGTCC	-	novel	NA	P-0046453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	365	862	0	ENST00000277541.6:c.4284_4294del	p.Asp1429ArgfsTer46	p.D1429Rfs*46	ENST00000277541	NM_017617.3	1428	ctGGACTACAGCTtc/cttc	25/34	0.173932740946628	2	FACETS	1	0.992	1	0.591	0.563	0.619	INDETERMINATE	1	TRUE	0	0.723430243549999	2		862	854	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	19	424	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.137532249390393	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		424	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0046455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	36	556	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		556	795	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	68	424	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.211069448775733	3	FACETS	0.819	0.715	0.93	0.819	0.715	0.93	CLONAL	2	TRUE	1	0.211069448775733	3		424	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0046456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	189	622	1	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	0.211069448775733	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.211069448775733	3		623	830	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	105	427	0				ENST00000310581	NM_198253.2	-/1132			0.103350660340869	4	FACETS	1	0.981	1	0.699	0.631	0.771	INDETERMINATE	1	TRUE	2	0.554262235752017	4		427	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0046457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	142	670	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.543	0.494	0.594	0.543	0.494	0.594	SUBCLONAL	1	TRUE	1	0.554262235752017	2		670	944	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0046457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	151	359	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.485612553464988	3	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.554262235752017	3		359	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0046457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	221	606	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	0.854	0.795	0.914	0.854	0.795	0.914	CLONAL	1	TRUE	1	0.554262235752017	2		606	934	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0046457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	100	388	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.554262235752017	1	FACETS	0.65	0.585	0.719	0.65	0.585	0.719	SUBCLONAL	1	TRUE	0	0.554262235752017	1		388	401	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579361	7579361	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1064796722	NA	P-0046457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	85	675	0	ENST00000269305.4:c.326T>C	p.Phe109Ser	p.F109S	ENST00000269305	NM_001126112.2	109	tTc/tCc	4/11	1	2	FACETS	0.323	0.284	0.364	0.323	0.284	0.364	SUBCLONAL	1	TRUE	1	0.554262235752017	2		675	950	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	267	427	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.878	0.828	0.928	1	0.996	1	CLONAL	4	TRUE	1	0.219785700214631	2		427	692	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	70	412	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	0.164308488115708	4	FACETS	0.855	0.752	0.964	1	0.965	1	CLONAL	3	TRUE	2	0.219785700214631	4		412	303	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752897	42752897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376964824	NA	P-0046459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1363	183	1106	0	ENST00000222329.4:c.1367C>T	p.Thr456Met	p.T456M	ENST00000222329	NM_006494.2	456	aCg/aTg	4/4	0.219785700214631	4	FACETS	1	0.985	1	0.657	0.604	0.712	CLONAL	1	TRUE	2	0.219785700214631	4		1106	1546	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424217	49424220	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GTTA	GTTA	-	novel	NA	P-0046459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	25	206	0	ENST00000301067.7:c.13842_13845del	p.Asn4615Ter	p.N4615*	ENST00000301067	NM_003482.3	4614	aaTAAC/aa	42/54	0.209713840976088	3	FACETS	0.644	0.507	0.802	0.322	0.253	0.401	SUBCLONAL	1	TRUE	1	0.219785700214631	3		206	392	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443558	49443559	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAAGGCCCCCTCC	novel	NA	P-0046459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	41	691	0	ENST00000301067.7:c.3812_3813insGGAGGGGGCCTTC	p.Leu1272GlufsTer18	p.L1272Efs*18	ENST00000301067	NM_003482.3	1271	cta/ctGGAGGGGGCCTTCa	11/54	0.209713840976088	3	FACETS	0.601	0.499	0.715	0.301	0.249	0.358	SUBCLONAL	1	TRUE	1	0.219785700214631	3		691	689	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917021	50917021	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1239	126	1007	0	ENST00000440232.2:c.2273C>A	p.Ser758Tyr	p.S758Y	ENST00000440232	NM_002691.3	758	tCc/tAc	19/27	0.219785700214631	4	FACETS	1	0.922	1	0.512	0.462	0.566	CLONAL	1	TRUE	2	0.219785700214631	4		1007	1365	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582221	52582222	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTCC	novel	NA	P-0046459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	34	275	0	ENST00000394830.3:c.4606_4607insGGAC	p.Glu1536GlyfsTer61	p.E1536Gfs*61	ENST00000394830	NM_018313.4	1536	gaa/gGGACaa	30/30	0.209713840976088	3	FACETS	0.707	0.577	0.853	0.353	0.288	0.427	SUBCLONAL	1	TRUE	1	0.219785700214631	3		275	486	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595975	52595975	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0046459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	85	348	1	ENST00000394830.3:c.3940A>T	p.Lys1314Ter	p.K1314*	ENST00000394830	NM_018313.4	1314	Aag/Tag	26/30	0.209713840976088	3	FACETS	1	0.959	1	1	0.984	1	CLONAL	3	TRUE	1	0.219785700214631	3		349	251	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288365	33288365	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1200333484	NA	P-0046459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	220	353	0	ENST00000374542.5:c.1043T>C	p.Val348Ala	p.V348A	ENST00000374542	NM_001141970.1	348	gTt/gCt	4/8	0.219785700214631	3	FACETS	1	0.98	1	1	0.993	1	CLONAL	3	TRUE	1	0.219785700214631	3		353	665	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240335	98240336	+	splice_donor_variant	Splice_Site	INS	-	-	C	novel	NA	P-0046459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	33	281	0	ENST00000331920.6:c.1347+1dup		p.X449_splice	ENST00000331920	NM_000264.3	449			0.219785700214631	3	FACETS	0.65	0.528	0.787	0.217	0.176	0.263	SUBCLONAL	1	TRUE	0	0.219785700214631	3		281	513	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221970	98221977	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGACGG	CGCGACGG	AGAAAA	novel	NA	P-0046459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	121	473	1	ENST00000331920.6:c.2792_2799delinsTTTTCT	p.Pro931LeufsTer27	p.P931Lfs*27	ENST00000331920	NM_000264.3	931	cCCGTCGCG/cTTTTCT	17/24	0.219785700214631	3	FACETS	0.867	0.784	0.954	0.578	0.522	0.636	CLONAL	2	TRUE	0	0.219785700214631	3		474	705	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952019	178952019	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1553826166	NA	P-0046460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	10	294	0	ENST00000263967.3:c.3074C>G	p.Thr1025Ser	p.T1025S	ENST00000263967	NM_006218.2	1025	aCc/aGc	21/21	1	2	FACETS	0.327	0.22	0.462	0.327	0.22	0.462	SUBCLONAL	1	TRUE	1	0.13	2		294	471	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	215	427	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		427	549	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453137	140453138	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGT	novel	NA	P-0046462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	93	318	0	ENST00000288602.6:c.1795_1797dup	p.Thr599dup	p.T599dup	ENST00000288602	NM_004333.4	599	-/ACA	15/18	0.296978541319265	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.2	3		318	423	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0046463-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	33	237	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	0.543479592511077	1	FACETS	0.34	0.278	0.409	0.34	0.278	0.409	SUBCLONAL	1	TRUE	0	0.560628422164863	1		237	249	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157834	106157834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs4145756	NA	P-0046464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	67	244	0	ENST00000380013.4:c.2735C>T	p.Ala912Val	p.A912V	ENST00000380013	NM_001127208.2	912	gCg/gTg	3/11	1	2	FACETS	0.852	0.746	0.965	0.852	0.746	0.965	CLONAL	1	TRUE	1	0.499222856246887	2		244	315	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383253	4383253	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	164	594	0	ENST00000261254.3:c.47G>A	p.Arg16Gln	p.R16Q	ENST00000261254	NM_001759.3	16	cGg/cAg	1/5	0.221385076629854	4	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.499222856246887	4		594	814	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108093	30108093	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	143	454	0	ENST00000331968.5:c.714G>T	p.Glu238Asp	p.E238D	ENST00000331968	NM_002742.2	238	gaG/gaT	5/18	0.499222856246887	3	FACETS	0.975	0.891	1	0.325	0.297	0.355	CLONAL	1	TRUE	0	0.499222856246887	3		454	734	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577529	7577530	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGGCC	novel	NA	P-0046464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	400	674	0	ENST00000269305.4:c.746_751dup	p.Arg249_Pro250dup	p.R249_P250dup	ENST00000269305	NM_001126112.2	249	atc/aGGCCCAtc	7/11	0.494139724157913	2	FACETS	0.833	0.795	0.871	0.833	0.795	0.871	CLONAL	2	TRUE	0	0.499222856246887	2		674	962	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967921	93967921	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	114	457	0	ENST00000369303.4:c.2006T>G	p.Val669Gly	p.V669G	ENST00000369303	NM_004440.3	669	gTt/gGt	11/17	0.48774041343044	3	FACETS	0.849	0.766	0.937	0.425	0.383	0.469	CLONAL	1	TRUE	1	0.499222856246887	3		457	672	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120464	94120464	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	98	332	0	ENST00000369303.4:c.587T>G	p.Val196Gly	p.V196G	ENST00000369303	NM_004440.3	196	gTt/gGt	3/17	0.48774041343044	3	FACETS	1	0.906	1	0.506	0.453	0.561	CLONAL	1	TRUE	1	0.499222856246887	3		332	485	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864626	56864626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046464-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	166	551	0	ENST00000519728.1:c.589C>T	p.Pro197Ser	p.P197S	ENST00000519728	NM_002350.3	197	Cca/Tca	7/13	0.459908626041973	3	FACETS	0.881	0.809	0.956	0.441	0.404	0.478	CLONAL	1	TRUE	1	0.499222856246887	3		551	943	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0046466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	370	609	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.501195350949178	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.522353739568306	2		609	693	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604712	55604712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs72549297	NA	P-0046466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	228	392	1	ENST00000288135.5:c.2920G>A	p.Asp974Asn	p.D974N	ENST00000288135	NM_000222.2	974	Gac/Aac	21/21	0.46416314130495	4	FACETS	0.953	0.893	1	0.953	0.893	1	CLONAL	2	TRUE	2	0.522353739568306	4		393	697	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591139	67591154	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	GACCAATACTTGATGT	GACCAATACTTGATGT	-	novel	NA	P-0046466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	64	216	0	ENST00000274335.5:c.1732_1745+2del		p.X578_splice	ENST00000274335		578		12/15	0.522353739568306	3	FACETS	0.776	0.684	0.873	0.776	0.684	0.873	SUBCLONAL	2	TRUE	1	0.522353739568306	3		216	199	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0046468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	769	574	0	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	0.653251000336623	3	FACETS	0.995	0.973	1	0.995	0.973	1	CLONAL	3	TRUE	0	0.667383635331614	3		574	1030	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243668570	243668570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	80	283	0	ENST00000263826.5:c.1421C>T	p.Ser474Phe	p.S474F	ENST00000263826	NM_005465.4	474	tCt/tTt	13/13	0.288257933999492	5	FACETS	0.693	0.61	0.783	0.139	0.122	0.157	INDETERMINATE	1	TRUE	0	0.667383635331614	5		283	692	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACT	novel	NA	P-0046468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	4166	539	0	ENST00000275493.2:c.2310_2311insTAC	p.Asp770_Asn771insTyr	p.D770_N771insY	ENST00000275493	NM_005228.3	770	gac/gACTac	20/28	0.667383635331614	18	FACETS	0.989	0.98	0.998	0.927	0.919	0.936	CLONAL	15	TRUE	2	0.667383635331614	18		539	5334	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570311	87570311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285612169	NA	P-0046468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	279	590	0	ENST00000277120.3:c.2051C>T	p.Ala684Val	p.A684V	ENST00000277120		684	gCg/gTg	17/19	1	2	FACETS	0.969	0.913	1	0.969	0.913	1	CLONAL	1	TRUE	1	0.667383635331614	2		590	863	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799333	88799333	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	185	411	0	ENST00000360948.2:c.52C>G	p.Leu18Val	p.L18V	ENST00000360948	NM_001012338.2	18	Ctg/Gtg	2/19	0.667383635331614	2	FACETS	0.98	0.91	1	0.49	0.455	0.525	CLONAL	1	TRUE	0	0.667383635331614	2		411	566	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190717439	190717439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	93	254	1	ENST00000441310.2:c.758C>T	p.Ser253Leu	p.S253L	ENST00000441310	NM_000534.4	253	tCa/tTa	7/13	0.637842426671131	4	FACETS	0.711	0.632	0.794	0.237	0.21	0.265	SUBCLONAL	1	TRUE	1	0.667383635331614	4		255	654	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608654	189608654	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	182	370	0	ENST00000264731.3:c.1729G>C	p.Glu577Gln	p.E577Q	ENST00000264731	NM_003722.4	577	Gag/Cag	13/14	0.667383635331614	2	FACETS	0.964	0.895	1	0.482	0.447	0.517	CLONAL	1	TRUE	0	0.667383635331614	2		370	566	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839894	27839894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747792724	NA	P-0046468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	276	626	0	ENST00000328488.2:c.200C>T	p.Pro67Leu	p.P67L	ENST00000328488	NM_003533.2	67	cCt/cTt	1/1	0.604364330480437	3	FACETS	0.997	0.937	1	0.499	0.468	0.53	CLONAL	1	TRUE	1	0.667383635331614	3		626	1106	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55269023	55269023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4647	454	523	0	ENST00000275493.2:c.3089C>T	p.Ser1030Leu	p.S1030L	ENST00000275493	NM_005228.3	1030	tCa/tTa	25/28	0.667383635331614	18	FACETS	0.845	0.801	0.891	0.106	0.1	0.112	CLONAL	2	TRUE	2	0.667383635331614	18		523	5101	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	387	486	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.914	0.872	0.955	1	0.997	1	CLONAL	2	TRUE	1	0.487483972031445	2		489	869	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	92	267	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	0.364175002101368	3	FACETS	0.79	0.711	0.873	0.79	0.711	0.873	SUBCLONAL	2	TRUE	1	0.487483972031445	3		267	297	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	196	473	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.487483972031445	2		474	781	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	92	275	1	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.487483972031445	2		276	374	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	59	312	2	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.838	0.727	0.956	0.838	0.727	0.956	CLONAL	1	TRUE	1	0.487483972031445	2		314	289	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	203	483	2	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.487483972031445	2		485	735	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	236	652	0	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	1	2	FACETS	0.948	0.885	1	0.948	0.885	1	CLONAL	1	TRUE	1	0.487483972031445	2		652	1021	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523009	25523009	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	295	923	1	ENST00000264709.3:c.176del	p.Pro59ArgfsTer13	p.P59Rfs*13	ENST00000264709	NM_175629.2	59	cCg/cg	3/23	1	2	FACETS	0.987	0.929	1	0.987	0.929	1	CLONAL	1	TRUE	1	0.487483972031445	2		924	1226	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154242	2154242	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755455183	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	237	945	4	ENST00000434045.2:c.686del	p.Pro229GlnfsTer27	p.P229Qfs*27	ENST00000434045	NM_001127598.1	229	cCa/ca	5/5	1	2	FACETS	0.968	0.903	1	0.968	0.903	1	CLONAL	1	TRUE	1	0.487483972031445	2		949	1005	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	508	836	1	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	0.487483972031445	2	FACETS	0.862	0.827	0.897	0.862	0.827	0.897	CLONAL	2	TRUE	0	0.487483972031445	2		837	1209	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045688	26045688	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1350355423	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	73	304	0	ENST00000540144.1:c.50C>T	p.Pro17Leu	p.P17L	ENST00000540144	NM_003531.2	17	cCg/cTg	1/1	1	2	FACETS	0.922	0.813	1	0.922	0.813	1	CLONAL	1	TRUE	1	0.487483972031445	2		304	325	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	342	749	0	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.487483972031445	2		749	1172	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563167	21563167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371775408	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	292	1012	1	ENST00000382592.4:c.752C>T	p.Ala251Val	p.A251V	ENST00000382592	NM_014572.2	251	gCg/gTg	4/8	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.487483972031445	2		1013	1106	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255346	16255346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151043425	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	172	464	0	ENST00000375759.3:c.2611C>T	p.Arg871Cys	p.R871C	ENST00000375759	NM_015001.2	871	Cgc/Tgc	11/15	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.487483972031445	2		464	695	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519505	137519506	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs780346130	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	101	304	0	ENST00000367739.4:c.1132_1133del	p.Ser378PhefsTer6	p.S378Ffs*6	ENST00000367739	NM_000416.2	378	AGt/t	7/7	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.487483972031445	2		304	354	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027087	71027087	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	179	517	1	ENST00000318789.4:c.1240del	p.Leu414Ter	p.L414*	ENST00000318789	NM_032682.5	414	Ctg/tg	15/21	1	2	FACETS	0.864	0.797	0.933	0.864	0.797	0.933	CLONAL	1	TRUE	1	0.487483972031445	2		518	850	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354007	15354008	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	46	236	2	ENST00000263377.2:c.2872dup	p.Leu958ProfsTer135	p.L958Pfs*135	ENST00000263377	NM_058243.2	958	ctg/cCtg	14/20	1	2	FACETS	0.689	0.584	0.803	0.689	0.584	0.803	SUBCLONAL	1	TRUE	1	0.487483972031445	2		238	274	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131704	2131704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567510707	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	311	913	2	ENST00000219476.3:c.3719G>A	p.Arg1240His	p.R1240H	ENST00000219476	NM_000548.3	1240	cGc/cAc	31/42	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.487483972031445	2		915	1219	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156703	106156703	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	105	353	0	ENST00000380013.4:c.1604A>G	p.Asn535Ser	p.N535S	ENST00000380013	NM_001127208.2	535	aAc/aGc	3/11	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.487483972031445	2		353	420	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933617	39933617	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	206	648	0	ENST00000378444.4:c.982del	p.Asp328ThrfsTer50	p.D328Tfs*50	ENST00000378444	NM_001123385.1	328	Gac/ac	4/15	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.487483972031445	2		648	840	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	264	920	5	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.86	0.805	0.916	0.86	0.805	0.916	CLONAL	1	TRUE	1	0.487483972031445	2		925	1260	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	250	1071	8	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.908	0.849	0.97	0.908	0.849	0.97	CLONAL	1	TRUE	1	0.487483972031445	2		1079	1129	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	164	431	0	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.487483972031445	2		431	558	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	199	590	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.487483972031445	2		590	763	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	330	687	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.487483972031445	2		687	1208	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	268	778	1	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	1	2	FACETS	0.874	0.819	0.931	0.874	0.819	0.931	CLONAL	1	TRUE	1	0.487483972031445	2		779	1258	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577103	7577103	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	237	748	1	ENST00000269305.4:c.835G>T	p.Gly279Trp	p.G279W	ENST00000269305	NM_001126112.2	279	Ggg/Tgg	8/11	1	2	FACETS	0.856	0.798	0.916	0.856	0.798	0.916	CLONAL	1	TRUE	1	0.487483972031445	2		749	1136	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874149	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	136	494	1	ENST00000262189.6:c.8389_8390del	p.Lys2797GlyfsTer11	p.K2797Gfs*11	ENST00000262189	NM_170606.2	2797	AAg/g	38/59	1	2	FACETS	0.984	0.899	1	0.984	0.899	1	CLONAL	1	TRUE	1	0.487483972031445	2		495	567	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455179	29455179	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148001139	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	187	601	1	ENST00000389048.3:c.2623G>A	p.Gly875Arg	p.G875R	ENST00000389048	NM_004304.4	875	Gga/Aga	15/29	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.487483972031445	2		602	722	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258894	16258894	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	214	658	0	ENST00000375759.3:c.6164del	p.Pro2055LeufsTer9	p.P2055Lfs*9	ENST00000375759	NM_015001.2	2053	aaC/aa	11/15	1	2	FACETS	0.958	0.892	1	0.958	0.892	1	CLONAL	1	TRUE	1	0.487483972031445	2		658	916	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420207	49420207	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	253	715	0	ENST00000301067.7:c.15542G>T	p.Gly5181Val	p.G5181V	ENST00000301067	NM_003482.3	5181	gGg/gTg	48/54	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.487483972031445	2		715	996	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142447	119142447	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs199739868	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	91	315	0	ENST00000264033.4:c.446G>A	p.Arg149Gln	p.R149Q	ENST00000264033	NM_005188.3	149	cGa/cAa	3/16	1	2	FACETS	0.911	0.814	1	0.911	0.814	1	CLONAL	1	TRUE	1	0.487483972031445	2		315	410	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562876	176562876	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1268581071	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	161	422	1	ENST00000439151.2:c.772T>C	p.Phe258Leu	p.F258L	ENST00000439151	NM_022455.4	258	Ttt/Ctt	2/23	1	2	FACETS	0.916	0.842	0.993	0.916	0.842	0.993	CLONAL	1	TRUE	1	0.487483972031445	2		423	721	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105967	27105967	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781684543	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	179	527	0	ENST00000324856.7:c.5578G>A	p.Glu1860Lys	p.E1860K	ENST00000324856	NM_006015.4	1860	Gag/Aag	20/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.487483972031445	2		527	693	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104533	193104533	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	117	288	0	ENST00000367435.3:c.320G>T	p.Ser107Ile	p.S107I	ENST00000367435	NM_024529.4	107	aGt/aTt	4/17	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.487483972031445	2		288	468	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343503	118343504	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	129	375	0	ENST00000534358.1:c.1635dup	p.Leu546IlefsTer35	p.L546Ifs*35	ENST00000534358	NM_005933.3	543	-/A	3/36	1	2	FACETS	0.969	0.883	1	0.969	0.883	1	CLONAL	1	TRUE	1	0.487483972031445	2		375	546	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046461	30046461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763048984	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	128	473	1	ENST00000331968.5:c.2722C>T	p.Arg908Cys	p.R908C	ENST00000331968	NM_002742.2	908	Cgt/Tgt	18/18	1	2	FACETS	0.81	0.736	0.888	0.81	0.736	0.888	CLONAL	1	TRUE	1	0.487483972031445	2		474	648	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73995409	73995409	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	140	535	0	ENST00000318443.5:c.718del	p.Gln240ArgfsTer20	p.Q240Rfs*20	ENST00000318443	NM_001024736.1	239	Ccc/cc	4/10	1	2	FACETS	0.899	0.821	0.98	0.899	0.821	0.98	CLONAL	1	TRUE	1	0.487483972031445	2		535	639	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063643	67063643	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	147	468	0	ENST00000412916.2:c.92G>A	p.Gly31Asp	p.G31D	ENST00000412916		31	gGc/gAc	2/6	1	2	FACETS	0.879	0.805	0.957	0.879	0.805	0.957	CLONAL	1	TRUE	1	0.487483972031445	2		468	686	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245968	41245968	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	164	526	0	ENST00000357654.3:c.1580del	p.Lys527ArgfsTer5	p.K527Rfs*5	ENST00000357654	NM_007294.3	527	aAg/ag	10/23	0.487483972031445	2	FACETS	0.859	0.79	0.931	0.43	0.395	0.466	CLONAL	1	TRUE	0	0.487483972031445	2		526	783	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024683	11024683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	125	535	0	ENST00000327064.4:c.800G>A	p.Arg267His	p.R267H	ENST00000327064	NM_199141.1	267	cGc/cAc	6/16	1	2	FACETS	0.908	0.825	0.994	0.908	0.825	0.994	CLONAL	1	TRUE	1	0.487483972031445	2		535	565	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902667	50902667	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755461109	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	308	892	0	ENST00000440232.2:c.242G>A	p.Arg81Gln	p.R81Q	ENST00000440232	NM_002691.3	81	cGg/cAg	3/27	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.487483972031445	2		892	1169	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578358	212578358	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	101	299	0	ENST00000342788.4:c.899A>G	p.Asp300Gly	p.D300G	ENST00000342788	NM_005235.2	300	gAt/gGt	8/28	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.487483972031445	2		299	414	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1941438	1941438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1213997018	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	180	547	0	ENST00000382891.5:c.1814C>T	p.Thr605Met	p.T605M	ENST00000382891	NM_133335.3	605	aCg/aTg	9/22	1	2	FACETS	0.811	0.748	0.876	0.811	0.748	0.876	CLONAL	1	TRUE	1	0.487483972031445	2		547	911	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945792	38945793	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	54	173	0	ENST00000357387.3:c.4433dup	p.Asn1478LysfsTer41	p.N1478Kfs*41	ENST00000357387	NM_152756.3	1478	aat/aaAt	34/38	1	2	FACETS	0.89	0.768	1	0.89	0.768	1	CLONAL	1	TRUE	1	0.487483972031445	2		173	249	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672769	30672770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	254	710	0	ENST00000376406.3:c.4190dup	p.Asn1397LysfsTer2	p.N1397Kfs*2	ENST00000376406	NM_014641.2	1397	aat/aaAt	10/15	1	2	FACETS	0.966	0.904	1	0.966	0.904	1	CLONAL	1	TRUE	1	0.487483972031445	2		710	1079	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021819	69021819	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	165	481	1	ENST00000288368.4:c.3107C>T	p.Ala1036Val	p.A1036V	ENST00000288368	NM_024870.2	1036	gCa/gTa	25/40	0.487483972031445	2	FACETS	0.862	0.793	0.934	0.431	0.396	0.467	CLONAL	1	TRUE	0	0.487483972031445	2		482	785	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285869	87285869	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	137	491	0	ENST00000277120.3:c.206C>T	p.Thr69Ile	p.T69I	ENST00000277120		69	aCc/aTc	2/19	1	2	FACETS	0.978	0.893	1	0.978	0.893	1	CLONAL	1	TRUE	1	0.487483972031445	2		491	575	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325488	1325488	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	185	456	0	ENST00000400841.2:c.187A>G	p.Asn63Asp	p.N63D	ENST00000400841		63	Aac/Gac	3/6	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.487483972031445	2		456	663	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952089	76952089	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	100	214	0	ENST00000373344.5:c.346A>T	p.Ile116Phe	p.I116F	ENST00000373344	NM_000489.3	116	Att/Ttt	5/35	1	2	FACETS	0.888	0.797	0.983	0.888	0.797	0.983	CLONAL	1	TRUE	1	0.487483972031445	2		214	462	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419049	419049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	15	315	0	ENST00000399788.2:c.3298G>A	p.Glu1100Lys	p.E1100K	ENST00000399788	NM_001042603.1	1100	Gaa/Aaa	22/28	0.173028109675306	3	FACETS	0.847	0.62	1	0.424	0.31	0.56	CLONAL	1	TRUE	1	0.17	3		315	226	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16097825	16097825	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs73281920	NA	P-0046470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	10	559	0	ENST00000268712.3:c.59A>C	p.Tyr20Ser	p.Y20S	ENST00000268712	NM_006311.3	20	tAt/tCt	2/46	0.173028109675306	3	FACETS	0.769	0.522	1	0.384	0.261	0.539	CLONAL	1	TRUE	1	0.17	3		559	166	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554312	81554313	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTA	novel	NA	P-0046470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	10	314	0	ENST00000298171.2:c.332_333insTTA	p.Thr111_Arg112insTyr	p.T111_R112insY	ENST00000298171	NM_000369.2	111	acc/acTTAc	4/10	1	2	FACETS	0.964	0.666	1	1	0.882	1	CLONAL	2	TRUE	1	0.17	2		314	61	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0046471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	248	882	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.527786503224993	1	FACETS	0.884	0.829	0.939	0.884	0.829	0.939	CLONAL	1	TRUE	0	0.532242446418549	1		882	774	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869486	102869486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755265524	NA	P-0046471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	150	426	0	ENST00000307046.8:c.155C>T	p.Thr52Met	p.T52M	ENST00000307046	NM_001111285.1	52	aCg/aTg	2/4	0.519154044284605	2	FACETS	0.991	0.91	1	0.495	0.455	0.537	CLONAL	1	TRUE	0	0.532242446418549	2		426	569	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163298020	163298020	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	154	310	0	ENST00000271452.3:c.201G>A	p.Met67Ile	p.M67I	ENST00000271452	NM_145697.2	67	atG/atA	4/14	1	2	FACETS	0.933	0.858	1	0.933	0.858	1	CLONAL	1	TRUE	1	0.532242446418549	2		310	620	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957914	1957914	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	64	295	0	ENST00000382891.5:c.2880C>A	p.Asn960Lys	p.N960K	ENST00000382891	NM_133335.3	960	aaC/aaA	15/22	0.150431443573334	4	FACETS	0.662	0.573	0.757			1	INDETERMINATE	1	TRUE	NA	0.532242446418549	4		295	557	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0046474-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	45	357	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.431748728415142	5	FACETS	0.901	0.772	1	0.6	0.514	0.692	CLONAL	2	TRUE	2	0.648328576051571	5		357	152	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604819	48604826	+	frameshift_variant	Frame_Shift_Del	DEL	CCCACAAC	CCCACAAC	-	novel	NA	P-0046474-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	35	297	0	ENST00000342988.3:c.1642_1649del	p.Pro548PhefsTer26	p.P548Ffs*26	ENST00000342988	NM_005359.5	547	gaCCCACAACct/gact	12/12	0.634133440308653	1	FACETS	0.657	0.552	0.769	0.657	0.552	0.769	SUBCLONAL	1	TRUE	0	0.648328576051571	1		297	111	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573980	7573980	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046474-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	67	675	0	ENST00000269305.4:c.1047del	p.Glu349AspfsTer21	p.E349Dfs*21	ENST00000269305	NM_001126112.2	349	gaA/ga	10/11	0.634133440308653	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.648328576051571	1		675	128	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075368	8075368	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046474-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	32	209	0	ENST00000377482.5:c.202G>C	p.Gly68Arg	p.G68R	ENST00000377482	NM_018948.3	68	Ggg/Cgg	3/4	0.41042323337611	5	FACETS	0.885	0.735	1	0.59	0.49	0.697	CLONAL	2	TRUE	2	0.648328576051571	5		209	110	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556463	29556463	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1567849208	NA	P-0046478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	373	452	0	ENST00000356175.3:c.2835del	p.Phe945LeufsTer9	p.F945Lfs*9	ENST00000356175	NM_000267.3	944	Ttt/tt	21/57	0.551350261240845	5	FACETS	0.953	0.921	0.983			1	CLONAL	5	TRUE	NA	0.555237761798666	5		452	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577083	7577084	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0046478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	857	1042	0	ENST00000269305.4:c.854_855del	p.Glu285GlyfsTer20	p.E285Gfs*20	ENST00000269305	NM_001126112.2	285	gAG/g	8/11	0.555237761798666	6	FACETS	1	0.994	1			1	CLONAL	6	TRUE	NA	0.555237761798666	6		1042	1055	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184150	56184150	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	94	371	0	ENST00000399503.3:c.4355A>G	p.Glu1452Gly	p.E1452G	ENST00000399503	NM_005921.1	1452	gAa/gGa	19/20	0.167909192442075	5	FACETS	1	0.962	1	0.758	0.684	0.834	INDETERMINATE	2	TRUE	2	0.555237761798666	5		371	273	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123022529	123022529	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	180	668	0	ENST00000355640.3:c.938G>T	p.Ser313Ile	p.S313I	ENST00000355640		313	aGt/aTt	3/7	NA	2	FACETS	0.937	0.879	0.994			1	INDETERMINATE	2	TRUE	NA	0.555237761798666	2		668	346	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	40	424	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.285473144969755	1	FACETS	0.584	0.486	0.693	0.584	0.486	0.693	SUBCLONAL	1	TRUE	0	0.29	1		424	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs863224451	NA	P-0046479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	116	751	2	ENST00000269305.4:c.824G>T	p.Cys275Phe	p.C275F	ENST00000269305	NM_001126112.2	275	tGt/tTt	8/11	0.229902742462804	1	FACETS	0.893	0.805	0.986	0.893	0.805	0.986	CLONAL	1	TRUE	0	0.29	1		753	766	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916851	48916851	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0046479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	64	295	0	ENST00000267163.4:c.380+1G>T		p.X127_splice	ENST00000267163	NM_000321.2	127			0.3	4	FACETS	0.863	0.758	0.973	0.863	0.758	0.973	CLONAL	3	TRUE	1	0.29	4		295	220	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0046480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	375	757	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.663084183121279	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.663084183121279	1		757	613	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533730	63533730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs950007141	NA	P-0046480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	101	635	1	ENST00000307078.5:c.1424C>T	p.Ser475Leu	p.S475L	ENST00000307078	NM_004655.3	475	tCg/tTg	6/11	0.663084183121279	2	FACETS	0.513	0.459	0.57	0.256	0.229	0.285	SUBCLONAL	1	TRUE	0	0.663084183121279	2		636	594	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72891512	72891512	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	185	475	0	ENST00000325599.8:c.250C>T	p.His84Tyr	p.H84Y	ENST00000325599	NM_018130.2	84	Cat/Tat	3/11	0.408649168390685	5	FACETS	1	0.939	1			1	CLONAL	1	TRUE	NA	0.663084183121279	5		475	1090	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015709	112015709	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	97	481	0	ENST00000368678.4:c.1133T>A	p.Ile378Asn	p.I378N	ENST00000368678		378	aTc/aAc	11/13	1	2	FACETS	0.51	0.455	0.567	0.51	0.455	0.567	SUBCLONAL	1	TRUE	1	0.663084183121279	2		481	574	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971183	21971183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046480-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	57	406	1	ENST00000304494.5:c.175G>A	p.Val59Met	p.V59M	ENST00000304494	NM_000077.4	59	Gtg/Atg	2/3	0.285056576141842	0	FACETS	0.167	0.144	0.193			1	INDETERMINATE	1	TRUE	0	0.663084183121279	0		407	346	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0046481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	55	359	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.718965576806251	2		359	116	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922695	44922695	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	87	188	0	ENST00000377967.4:c.1556del	p.Arg519HisfsTer29	p.R519Hfs*29	ENST00000377967	NM_021140.2	519	cGa/ca	16/29	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.718965576806251	1		188	123	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860713	3860713	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	313	687	0	ENST00000262367.5:c.866del	p.Gly289GlufsTer5	p.G289Efs*5	ENST00000262367	NM_004380.2	289	gGa/ga	3/31	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.718965576806251	2		687	787	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485809	57485809	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	287	518	1	ENST00000371085.3:c.1110G>T	p.Glu370Asp	p.E370D	ENST00000371085	NM_000516.4	370	gaG/gaT	13/13	1	2	FACETS	0.988	0.933	1	0.988	0.933	1	CLONAL	1	TRUE	1	0.718965576806251	2		519	808	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568635	41568635	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	72	497	0	ENST00000263253.7:c.4585del	p.Arg1529GlufsTer12	p.R1529Efs*12	ENST00000263253	NM_001429.3	1529	Cga/ga	28/31	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.718965576806251	2		497	198	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760443	133760443	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	359	812	0	ENST00000318560.5:c.2767del	p.Ala923ProfsTer19	p.A923Pfs*19	ENST00000318560	NM_005157.4	922	gcG/gc	11/11	1	2	FACETS	0.907	0.861	0.954	0.907	0.861	0.954	CLONAL	1	TRUE	1	0.718965576806251	2		812	1101	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390905	139390908	+	frameshift_variant	Frame_Shift_Del	DEL	AGGT	AGGT	CTG	novel	NA	P-0046481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	565	1063	1	ENST00000277541.6:c.7283_7286delinsCAG	p.His2428ProfsTer7	p.H2428Pfs*7	ENST00000277541	NM_017617.3	2428	cACCTg/cCAGg	34/34	1	2	FACETS	0.927	0.89	0.966	0.927	0.89	0.966	CLONAL	1	TRUE	1	0.718965576806251	2		1064	1695	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0046482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	178	803	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.266755976349026	1	FACETS	0.782	0.724	0.842	0.782	0.724	0.842	INDETERMINATE	1	TRUE	0	0.530118487425704	1		803	631	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591118	67591132	+	inframe_deletion	In_Frame_Del	DEL	ATCCAGCTGAGAAAG	ATCCAGCTGAGAAAG	-	novel	NA	P-0046482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	88	334	0	ENST00000274335.5:c.1712_1726del	p.Ile571_Lys575del	p.I571_K575del	ENST00000274335		571	ATCCAGCTGAGAAAG/-	12/15	0.174293936260987	3	FACETS	1	0.98	1	0.478	0.428	0.529	INDETERMINATE	1	TRUE	0	0.530118487425704	3		334	293	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964493	70964493	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	54	779	1	ENST00000276594.2:c.1535C>A	p.Ser512Tyr	p.S512Y	ENST00000276594	NM_024504.3	512	tCc/tAc	8/8	0.173929331072948	2	FACETS	0.277	0.236	0.322	0.138	0.118	0.161	INDETERMINATE	1	TRUE	0	0.530118487425704	2		780	736	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738156	145738156	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0046482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	82	1034	0	ENST00000428558.2:c.2756-2A>G		p.X919_splice	ENST00000428558	NM_004260.3	919			0.530118487425704	3	FACETS	0.495	0.436	0.559	0.248	0.218	0.28	SUBCLONAL	1	TRUE	1	0.530118487425704	3		1034	790	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913517	NA	P-0046483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	202	420	0	ENST00000288135.5:c.1676T>C	p.Val559Ala	p.V559A	ENST00000288135	NM_000222.2	559	gTt/gCt	11/21	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.726461061500498	2		420	520	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0046485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	245	435	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		435	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0046485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	512	812	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		812	715	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0046485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	557	633	1	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		634	908	SUCCESS
APC	324	MSKCC	GRCh37	5	112175426	112175426	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913326	NA	P-0046485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	91	342	0	ENST00000257430.4:c.4135G>T	p.Glu1379Ter	p.E1379*	ENST00000257430	NM_000038.5	1379	Gag/Tag	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		342	304	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281904	39281904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886041241	NA	P-0046485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	315	515	0	ENST00000402219.2:c.571G>A	p.Glu191Lys	p.E191K	ENST00000402219	NM_005633.3	191	Gaa/Aaa	5/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		515	890	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213588	36213588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	265	1103	1	ENST00000222270.7:c.2690C>T	p.Pro897Leu	p.P897L	ENST00000222270	NM_014727.1	897	cCt/cTt	5/37	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1104	1064	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266523	115266523	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	179	576	0	ENST00000438362.2:c.1992G>T	p.Met664Ile	p.M664I	ENST00000438362	NM_001242891.1	664	atG/atT	16/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		576	761	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982427	201982427	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0046485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	286	820	0	ENST00000359651.3:c.805+1G>A		p.X269_splice	ENST00000359651		269			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		820	1026	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945715	54945715	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1212	122	609	0	ENST00000312783.6:c.855G>C	p.Arg285Ser	p.R285S	ENST00000312783	NM_198436.1	285	agG/agC	9/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		609	1334	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390161	89390161	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	126	391	0	ENST00000336596.2:c.910T>G	p.Cys304Gly	p.C304G	ENST00000336596	NM_005233.5	304	Tgc/Ggc	4/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		391	432	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921346	178921346	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0046485-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	146	527	0	ENST00000263967.3:c.828T>A	p.Cys276Ter	p.C276*	ENST00000263967	NM_006218.2	276	tgT/tgA	5/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		527	630	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249393	153249393	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	49	608	0	ENST00000281708.4:c.1385C>T	p.Ser462Phe	p.S462F	ENST00000281708	NM_033632.3	462	tCc/tTc	9/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		608	558	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671528	30671528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368708770	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	73	954	1	ENST00000376406.3:c.5432G>A	p.Arg1811His	p.R1811H	ENST00000376406	NM_014641.2	1811	cGc/cAc	10/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		955	828	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	47	772	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		772	593	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	74	931	1	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		932	717	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467848	66467848	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1217481114	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	21	381	0	ENST00000273854.3:c.421C>T	p.Pro141Ser	p.P141S	ENST00000273854	NM_004439.5	141	Cct/Tct	3/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		381	373	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	18	246	1				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		247	198	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2957001	2957001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	74	606	1	ENST00000396946.4:c.2626G>A	p.Glu876Lys	p.E876K	ENST00000396946	NM_032415.4	876	Gaa/Aaa	20/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		607	546	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381514	81381514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	76	422	0	ENST00000222390.5:c.547G>A	p.Glu183Lys	p.E183K	ENST00000222390	NM_000601.4	183	Gaa/Aaa	5/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		422	493	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	66	965	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		965	789	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372442	55372442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	75	1042	0	ENST00000297316.4:c.1132C>T	p.Pro378Ser	p.P378S	ENST00000297316	NM_022454.3	378	Ccc/Tcc	2/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1042	586	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425644	49425644	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057517992	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	50	948	0	ENST00000301067.7:c.12844C>T	p.Arg4282Ter	p.R4282*	ENST00000301067	NM_003482.3	4282	Cga/Tga	39/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		948	519	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828186	72828186	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	57	739	0	ENST00000268489.5:c.8395C>T	p.Leu2799Phe	p.L2799F	ENST00000268489	NM_006885.3	2799	Ctt/Ttt	9/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		739	451	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864641	56864641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	62	631	0	ENST00000519728.1:c.604C>T	p.Pro202Ser	p.P202S	ENST00000519728	NM_002350.3	202	Ccc/Tcc	7/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		631	752	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2114342	2114342	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45517179	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	56	906	1	ENST00000219476.3:c.1513C>T	p.Arg505Ter	p.R505*	ENST00000219476	NM_000548.3	505	Cga/Tga	15/42	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		907	615	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248362	212248362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	29	298	0	ENST00000342788.4:c.3905G>A	p.Arg1302Lys	p.R1302K	ENST00000342788	NM_005235.2	1302	aGa/aAa	28/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		298	236	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981941	70981941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	64	975	1	ENST00000276594.2:c.155C>T	p.Pro52Leu	p.P52L	ENST00000276594	NM_024504.3	52	cCt/cTt	2/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		976	547	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539563	187539563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748950954	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	38	411	0	ENST00000441802.2:c.8177G>A	p.Arg2726Gln	p.R2726Q	ENST00000441802	NM_005245.3	2726	cGa/cAa	10/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		411	288	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542414	187542414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	39	470	0	ENST00000441802.2:c.5326G>A	p.Glu1776Lys	p.E1776K	ENST00000441802	NM_005245.3	1776	Gaa/Aaa	10/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		470	313	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807505	36807505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200986219	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	61	916	0	ENST00000373129.3:c.1159G>A	p.Glu387Lys	p.E387K	ENST00000373129	NM_032017.1	387	Gag/Aag	12/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		916	525	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344357	118344357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	17	316	0	ENST00000534358.1:c.2483C>T	p.Ser828Leu	p.S828L	ENST00000534358	NM_005933.3	828	tCa/tTa	3/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		316	227	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974679	21974680	+	stop_gained,splice_region_variant	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	140	619	0	ENST00000304494.5:c.147_148delinsTT	p.Gln50Ter	p.Q50*	ENST00000304494	NM_000077.4	49	atCCag/atTTag	1/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		619	472	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187854	11187854	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	30	554	1	ENST00000361445.4:c.6043G>A	p.Glu2015Lys	p.E2015K	ENST00000361445	NM_004958.3	2015	Gag/Aag	44/58	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		555	308	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120460290	120460303	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TGTTGTCCTGCATG	TGTTGTCCTGCATG	-	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	36	537	0	ENST00000256646.2:c.6012_6025del	p.Asp2004GlufsTer16	p.D2004Efs*16	ENST00000256646	NM_024408.3	2004	gaCATGCAGGACAACAag/gaag	33/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		537	504	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468055	120468056	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	31	876	3	ENST00000256646.2:c.4383_4384delinsTT	p.Pro1462Ser	p.P1462S	ENST00000256646	NM_024408.3	1461	aaCCcc/aaTTcc	25/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		879	500	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097680	8097680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867903546	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	26	480	0	ENST00000346208.3:c.62G>A	p.Gly21Glu	p.G21E	ENST00000346208		21	gGg/gAg	2/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		480	268	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431228	49431228	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1379753637	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	58	736	0	ENST00000301067.7:c.9911C>T	p.Pro3304Leu	p.P3304L	ENST00000301067	NM_003482.3	3304	cCc/cTc	34/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		736	484	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112893855	112893855	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	40	544	0	ENST00000351677.2:c.744G>A	p.Trp248Ter	p.W248*	ENST00000351677	NM_002834.3	248	tgG/tgA	6/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		544	432	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416689	121416689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	46	1027	0	ENST00000257555.6:c.118G>A	p.Gly40Arg	p.G40R	ENST00000257555		40	Gga/Aga	1/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1027	458	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023079	33023079	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	33	511	0	ENST00000300177.4:c.188G>A	p.Gly63Glu	p.G63E	ENST00000300177	NM_001191322.1	63	gGg/gAg	2/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		511	238	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358361	91358361	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	33	538	0	ENST00000355112.3:c.4106C>T	p.Ser1369Phe	p.S1369F	ENST00000355112	NM_000057.2	1369	tCc/tTc	22/22	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		538	549	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633417	3633418	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	48	1118	2	ENST00000294008.3:c.4833_4834delinsAA	p.Asp1612Asn	p.D1612N	ENST00000294008	NM_032444.2	1611	gaGGac/gaAAac	14/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1120	615	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640247	3640247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	75	1192	0	ENST00000294008.3:c.3392C>T	p.Pro1131Leu	p.P1131L	ENST00000294008	NM_032444.2	1131	cCt/cTt	12/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1192	743	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347635	89347635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776119333	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	45	836	1	ENST00000301030.4:c.5315C>T	p.Ser1772Leu	p.S1772L	ENST00000301030	NM_001256183.1	1772	tCg/tTg	9/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		837	451	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347984	89347984	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	72	1114	0	ENST00000301030.4:c.4966G>C	p.Glu1656Gln	p.E1656Q	ENST00000301030	NM_001256183.1	1656	Gag/Cag	9/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1114	682	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40491346	40491347	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	59	673	0	ENST00000264657.5:c.453_454delinsTT	p.Arg152Trp	p.R152W	ENST00000264657	NM_139276.2	151	gtCCgg/gtTTgg	5/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		673	685	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436162	56436163	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	37	722	3	ENST00000407977.2:c.974_975delinsTT	p.Ser325Phe	p.S325F	ENST00000407977		325	tCC/tTT	9/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		725	450	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760709	59760709	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	84	695	0	ENST00000259008.2:c.3698A>C	p.Asn1233Thr	p.N1233T	ENST00000259008	NM_032043.2	1233	aAc/aCc	20/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		695	676	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4102440	4102441	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	63	911	1	ENST00000262948.5:c.461_462delinsTT	p.Ser154Phe	p.S154F	ENST00000262948	NM_030662.3	154	tCC/tTT	4/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		912	586	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743936	41743936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	71	1090	0	ENST00000301178.4:c.871C>T	p.Pro291Ser	p.P291S	ENST00000301178	NM_021913.4	291	Ccc/Tcc	7/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1090	642	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868382	45868382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	73	909	0	ENST00000391945.4:c.395G>A	p.Gly132Glu	p.G132E	ENST00000391945	NM_000400.3	132	gGg/gAg	6/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		909	665	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99204020	99204020	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	25	382	0	ENST00000074304.5:c.2883C>A	p.Phe961Leu	p.F961L	ENST00000074304	NM_001134224.1	961	ttC/ttA	26/26	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		382	334	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374380	31374380	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs538400808	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	38	754	0	ENST00000328111.2:c.379C>T	p.Arg127Trp	p.R127W	ENST00000328111	NM_006892.3	127	Cgg/Tgg	5/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		754	446	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39658070	39658070	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	42	540	0	ENST00000361337.2:c.34-1G>A		p.X12_splice	ENST00000361337	NM_003286.2	12			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		540	489	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757432	40757432	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	40	826	0	ENST00000373198.4:c.2866G>A	p.Asp956Asn	p.D956N	ENST00000373198	NM_133170.3	956	Gac/Aac	20/32	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		826	437	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42879900	42879900	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1406664235	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	17	296	0	ENST00000398585.3:c.32G>T	p.Gly11Val	p.G11V	ENST00000398585	NM_001135099.1	11	gGg/gTg	1/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		296	229	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077492	30077492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199669486	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	23	420	0	ENST00000338641.4:c.1639G>A	p.Glu547Lys	p.E547K	ENST00000338641	NM_000268.3	547	Gag/Aag	15/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		420	339	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537064	41537064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	26	318	0	ENST00000263253.7:c.1891C>T	p.His631Tyr	p.H631Y	ENST00000263253	NM_001429.3	631	Cac/Tac	10/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		318	317	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205025	128205025	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	48	869	0	ENST00000341105.2:c.416C>T	p.Ser139Phe	p.S139F	ENST00000341105	NM_032638.4	139	tCt/tTt	3/6	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		869	427	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177889	142177889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	36	474	0	ENST00000350721.4:c.7414G>A	p.Gly2472Arg	p.G2472R	ENST00000350721	NM_001184.3	2472	Ggg/Agg	44/47	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		474	463	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215207	142215207	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376314540	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	22	227	0	ENST00000350721.4:c.5894C>T	p.Ser1965Phe	p.S1965F	ENST00000350721	NM_001184.3	1965	tCc/tTc	34/47	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		227	265	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748164	41748165	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	30	552	1	ENST00000226382.2:c.604_605delinsTT	p.Pro202Phe	p.P202F	ENST00000226382	NM_003924.3	202	CCc/TTc	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		553	298	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84390293	84390293	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1394165754	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	38	527	0	ENST00000321945.7:c.488G>C	p.Arg163Thr	p.R163T	ENST00000321945	NM_139076.2	163	aGg/aCg	6/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		527	530	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258961	153258962	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	32	286	0	ENST00000281708.4:c.853_854delinsTT	p.Pro285Phe	p.P285F	ENST00000281708	NM_033632.3	285	CCt/TTt	5/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		286	314	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538943	187538943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs35931295	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	34	557	0	ENST00000441802.2:c.8797C>T	p.Gln2933Ter	p.Q2933*	ENST00000441802	NM_005245.3	2933	Caa/Taa	10/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		557	425	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287215	33287215	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs550192421	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	63	744	1	ENST00000374542.5:c.1882C>T	p.Pro628Ser	p.P628S	ENST00000374542	NM_001141970.1	628	Ccc/Tcc	6/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		745	763	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982084	93982084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	45	559	0	ENST00000369303.4:c.1381C>T	p.Leu461Phe	p.L461F	ENST00000369303	NM_004440.3	461	Ctt/Ttt	6/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		559	534	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94129044	94129044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	34	404	1	ENST00000369303.4:c.16C>T	p.Arg6Trp	p.R6W	ENST00000369303	NM_004440.3	6	Cgg/Tgg	1/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		405	359	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552813	106552814	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	43	735	0	ENST00000369096.4:c.778_779delinsTT	p.Pro260Phe	p.P260F	ENST00000369096	NM_001198.3	260	CCc/TTc	5/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		735	818	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677888	117677888	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	40	458	0	ENST00000368508.3:c.4045A>C	p.Lys1349Gln	p.K1349Q	ENST00000368508	NM_002944.2	1349	Aaa/Caa	25/43	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		458	390	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704530	117704530	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	47	481	0	ENST00000368508.3:c.2446G>T	p.Gly816Trp	p.G816W	ENST00000368508	NM_002944.2	816	Ggg/Tgg	16/43	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		481	540	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527717	157527717	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	60	662	0	ENST00000346085.5:c.5442T>G	p.Ser1814Arg	p.S1814R	ENST00000346085	NM_020732.3	1814	agT/agG	20/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		662	572	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987359	2987360	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AT	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	45	694	1	ENST00000396946.4:c.69_70delinsAT	p.Trp23_Glu24delinsTer	p.W23_E24delins*	ENST00000396946	NM_032415.4	23	tgGGag/tgATag	3/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		695	705	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426861	6426861	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	48	537	0	ENST00000356142.4:c.54C>G	p.Cys18Trp	p.C18W	ENST00000356142	NM_018890.3	18	tgC/tgG	2/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		537	772	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836311	151836311	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	106	597	0	ENST00000262189.6:c.14494G>A	p.Asp4832Asn	p.D4832N	ENST00000262189	NM_170606.2	4832	Gac/Aac	57/59	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		597	596	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860626	151860626	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	72	707	0	ENST00000262189.6:c.10036C>A	p.Leu3346Ile	p.L3346I	ENST00000262189	NM_170606.2	3346	Ctc/Atc	43/59	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		707	487	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207363	29207363	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	31	530	0	ENST00000240100.2:c.433G>A	p.Gly145Ser	p.G145S	ENST00000240100	NM_001394.6	145	Ggc/Agc	1/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		530	343	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317148	87317149	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TG	TG	-	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	43	468	0	ENST00000277120.3:c.287+2_287+3del		p.X96_splice	ENST00000277120		96		3/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		468	334	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412705	139412705	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	124	982	0	ENST00000277541.6:c.1139C>G	p.Pro380Arg	p.P380R	ENST00000277541	NM_017617.3	380	cCc/cGc	7/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		982	655	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568590	41568592	+	missense_variant	Missense_Mutation	TNP	GAA	GAA	AAG	novel	NA	P-0046486-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	129	603	0	ENST00000263253.7:c.4540_4542delinsAAG	p.Glu1514Lys	p.E1514K	ENST00000263253	NM_001429.3	1514	GAA/AAG	28/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		603	667	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0046487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	80	409	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.993	0.88	1	0.993	0.88	1	CLONAL	1	TRUE	1	0.418316213104332	2		410	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0046487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	310	838	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.418316213104332	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.418316213104332	1		838	912	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63699963	63699963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1423129750	NA	P-0046487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	99	279	0	ENST00000279873.7:c.298G>A	p.Glu100Lys	p.E100K	ENST00000279873	NM_032199.2	100	Gaa/Aaa	3/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.418316213104332	2		279	388	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595943	43595943	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	259	837	1	ENST00000355710.3:c.110G>T	p.Trp37Leu	p.W37L	ENST00000355710	NM_020975.4	37	tGg/tTg	2/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.418316213104332	2		838	1072	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795072	45795072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369410616	NA	P-0046487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	245	591	0	ENST00000450313.1:c.1556G>A	p.Arg519Gln	p.R519Q	ENST00000450313	NM_012222.2	519	cGg/cAg	16/16	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.418316213104332	2		591	820	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827166	72827166	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	109	486	0	ENST00000268489.5:c.9415C>A	p.Pro3139Thr	p.P3139T	ENST00000268489	NM_006885.3	3139	Cca/Aca	9/10	1	2	FACETS	0.718	0.645	0.795	0.718	0.645	0.795	SUBCLONAL	1	TRUE	1	0.418316213104332	2		486	726	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176516663	176516663	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	60	758	1	ENST00000292408.4:c.60G>T	p.Leu20Phe	p.L20F	ENST00000292408	NM_213647.1	20	ttG/ttT	2/18	1	2	FACETS	0.334	0.286	0.385	0.334	0.286	0.385	SUBCLONAL	1	TRUE	1	0.418316213104332	2		759	860	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089788	5089788	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046487-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	34	237	0	ENST00000381652.3:c.2686G>T	p.Glu896Ter	p.E896*	ENST00000381652	NM_004972.3	896	Gaa/Taa	20/25	0.384400408088652	1	FACETS	0.471	0.386	0.565	0.471	0.386	0.565	SUBCLONAL	1	TRUE	0	0.418316213104332	1		237	273	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0046488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	48	336	1	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	1	2	FACETS	0.971	0.826	1	0.971	0.826	1	CLONAL	1	TRUE	1	0.332988194502331	2		337	297	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249002	55249003	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGTGGA	rs397517109	NA	P-0046488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	257	578	0	ENST00000275493.2:c.2303_2311dup	p.Ser768_Asp770dup	p.S768_D770dup	ENST00000275493	NM_005228.3	768	gcc/gcCAGCGTGGAc	20/28	0.245251705777477	4	FACETS	1	0.989	1	0.824	0.774	0.876	CLONAL	2	TRUE	1	0.332988194502331	4		578	832	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858020	152858020	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	201	374	0	ENST00000406277.2:c.595C>T	p.Gln199Ter	p.Q199*	ENST00000406277	NM_152274.4	199	Cag/Tag	6/7	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.332988194502331	2		374	504	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	93	424	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.173837082864987	4	FACETS	1	0.923	1	1	0.983	1	CLONAL	3	FALSE	2	0.251205545770595	4		424	300	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	46	931	3	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	FALSE	1	0.251205545770595	2		934	305	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	14	1071	8	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.498	0.36	0.664	0.498	0.36	0.664	SUBCLONAL	1	FALSE	1	0.251205545770595	2		1079	224	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874149	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	37	494	1	ENST00000262189.6:c.8389_8390del	p.Lys2797GlyfsTer11	p.K2797Gfs*11	ENST00000262189	NM_170606.2	2797	AAg/g	38/59	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.251205545770595	2		495	205	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733513	85733513	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs387906350	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	19	438	1	ENST00000370580.1:c.499del	p.Ser167LeufsTer6	p.S167Lfs*6	ENST00000370580	NM_003921.4	167	Tct/ct	3/3	1	2	FACETS	0.788	0.601	1	0.788	0.601	1	CLONAL	1	FALSE	1	0.251205545770595	2		439	192	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	40	405	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.937	0.79	1	1	0.968	1	CLONAL	2	FALSE	1	0.251205545770595	2		408	170	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	80	375	1	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	0.109903618851806	0	FACETS	0.921	0.822	1			1	INDETERMINATE	2	FALSE	0	0.251205545770595	0		376	259	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534325	63534325	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765865516	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	20	791	0	ENST00000307078.5:c.1196G>A	p.Arg399Gln	p.R399Q	ENST00000307078	NM_004655.3	399	cGa/cAa	5/11	1	2	FACETS	0.409	0.312	0.523	0.409	0.312	0.523	SUBCLONAL	1	FALSE	1	0.251205545770595	2		791	389	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116263	209116263	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	12	257	0	ENST00000345146.2:c.13del	p.Ile5SerfsTer7	p.I5Sfs*7	ENST00000345146	NM_005896.2	5	Atc/tc	3/10	1	2	FACETS	0.687	0.485	0.933	0.687	0.485	0.933	SUBCLONAL	1	FALSE	1	0.251205545770595	2		257	139	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822563	72822564	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	rs376311468	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	33	607	0	ENST00000268489.5:c.9609_9611dup	p.Gln3204dup	p.Q3204dup	ENST00000268489	NM_006885.3	3204	caa/caGCAa	10/10	0.109903618851806	0	FACETS	0.915	0.751	1			1	INDETERMINATE	1	FALSE	0	0.251205545770595	0		607	215	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026105	71026105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	28	333	0	ENST00000318789.4:c.1517C>T	p.Ala506Val	p.A506V	ENST00000318789	NM_032682.5	506	gCg/gTg	17/21	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.251205545770595	NA		333	329	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912188	114912188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	96	643	0	ENST00000543371.1:c.1258C>T	p.Arg420Trp	p.R420W	ENST00000543371	NM_001198531.1	420	Cgg/Tgg	11/14	1	2	FACETS	1	0.964	1	1	0.988	1	CLONAL	2	FALSE	1	0.251205545770595	2		643	331	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265522	152265522	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1467954450	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	66	564	0	ENST00000206249.3:c.975del	p.Ile326TyrfsTer17	p.I326Yfs*17	ENST00000206249	NM_000125.3	325	ccG/cc	4/8	0.204338664591032	3	FACETS	0.942	0.824	1	0.942	0.824	1	CLONAL	2	FALSE	1	0.251205545770595	3		564	314	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722761	49722761	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs62262682	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	10	61	1	ENST00000449682.2:c.1478G>T	p.Arg493Leu	p.R493L	ENST00000449682	NM_020998.3	493	cGt/cTt	13/18	1	2	FACETS	1	0.736	1	1	0.915	1	CLONAL	3	FALSE	1	0.251205545770595	2		62	26	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101259	27101259	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	18	625	0	ENST00000324856.7:c.4541del	p.Thr1514ArgfsTer13	p.T1514Rfs*13	ENST00000324856	NM_006015.4	1514	aCg/ag	18/20	1	2	FACETS	0.58	0.437	0.748	0.58	0.437	0.748	SUBCLONAL	1	FALSE	1	0.251205545770595	2		625	247	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967452	38967452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	38	347	0	ENST00000357387.3:c.1138C>T	p.Arg380Cys	p.R380C	ENST00000357387	NM_152756.3	380	Cgt/Tgt	13/38	1	2	FACETS	0.911	0.764	1	1	0.965	1	CLONAL	2	FALSE	1	0.251205545770595	2		347	166	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003784	+	frameshift_variant	Frame_Shift_Del	DEL	CTCT	CTCT	-	novel	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	81	547	0	ENST00000558401.1:c.41_44del	p.Ser14PhefsTer29	p.S14Ffs*29	ENST00000558401	NM_004048.2	13	CTCTct/ct	1/4	0.109903618851806	0	FACETS	0.93	0.822	1			1	INDETERMINATE	1	FALSE	0	0.251205545770595	0		547	519	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671654	67671655	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	13	529	0	ENST00000264010.4:c.2070dup	p.Glu691ArgfsTer5	p.E691Rfs*5	ENST00000264010	NM_006565.3	688	gta/gtAa	12/12	0.109903618851806	0	FACETS	0.351	0.25	0.473			1	INDETERMINATE	1	FALSE	0	0.251205545770595	0		529	221	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434595	110434595	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs555841746	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	154	662	0	ENST00000375856.3:c.3806A>C	p.Gln1269Pro	p.Q1269P	ENST00000375856	NM_003749.2	1269	cAg/cCg	1/2	0.204338664591032	3	FACETS	1	0.946	1	1	0.99	1	CLONAL	3	FALSE	1	0.251205545770595	3		662	447	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741839	17741840	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	17	207	0	ENST00000250003.3:c.515dup	p.Gly173TrpfsTer105	p.G173Wfs*105	ENST00000250003	NM_002478.4	170	-/C	1/3	1	2	FACETS	0.89	0.68	1	1	0.924	1	CLONAL	2	FALSE	1	0.251205545770595	2		207	76	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819743	81819743	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370242901	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	22	650	0	ENST00000359376.3:c.149G>A	p.Arg50Gln	p.R50Q	ENST00000359376	NM_002661.3	50	cGg/cAg	2/33	0.109903618851806	0	FACETS	0.364	0.282	0.46			1	INDETERMINATE	1	FALSE	0	0.251205545770595	0		650	360	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007794	45007797	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	43	445	0	ENST00000558401.1:c.244_247del	p.Phe82IlefsTer20	p.F82Ifs*20	ENST00000558401	NM_004048.2	81	TCTTtc/tc	2/4	0.109903618851806	0	FACETS	0.986	0.831	1			1	INDETERMINATE	1	FALSE	0	0.251205545770595	0		445	260	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931858	68931858	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	36	610	0	ENST00000288368.4:c.291del	p.Glu98AsnfsTer42	p.E98Nfs*42	ENST00000288368	NM_024870.2	96	caC/ca	3/40	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	FALSE	1	0.251205545770595	2		610	200	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244967	46244967	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	67	579	1	ENST00000334344.6:c.3065del	p.Pro1022HisfsTer38	p.P1022Hfs*38	ENST00000334344	NM_152641.2	1021	Ccc/cc	15/21	0.173837082864987	4	FACETS	1	0.909	1	1	0.977	1	CLONAL	3	FALSE	2	0.251205545770595	4		580	215	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36026125	36026125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367543241	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	87	936	1	ENST00000358208.4:c.727C>T	p.Arg243Cys	p.R243C	ENST00000358208		243	Cgc/Tgc	7/12	0.109903618851806	0	FACETS	0.793	0.709	0.881			1	INDETERMINATE	2	FALSE	0	0.251205545770595	0		937	327	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103666	47103666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	10	364	2	ENST00000409792.3:c.6280del	p.Arg2094GlyfsTer53	p.R2094Gfs*53	ENST00000409792	NM_014159.6	2094	Agg/gg	14/21	1	2	FACETS	0.442	0.3	0.621	0.442	0.3	0.621	SUBCLONAL	1	FALSE	1	0.251205545770595	2		366	180	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864377	162864377	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs75860381	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	75	470	0	ENST00000366898.1:c.136G>A	p.Ala46Thr	p.A46T	ENST00000366898	NM_004562.2	46	Gca/Aca	2/12	0.204338664591032	3	FACETS	0.855	0.759	0.956	1	0.969	1	CLONAL	3	FALSE	1	0.251205545770595	3		470	262	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436060	49436060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777415982	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	51	622	1	ENST00000301067.7:c.5921C>T	p.Thr1974Met	p.T1974M	ENST00000301067	NM_003482.3	1974	aCg/aTg	28/54	0.173837082864987	4	FACETS	1	0.864	1	1	0.864	1	CLONAL	2	FALSE	2	0.251205545770595	4		623	252	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955043	55955043	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	14	449	0	ENST00000263923.4:c.3502G>A	p.Ala1168Thr	p.A1168T	ENST00000263923	NM_002253.2	1168	Gct/Act	26/30	0.109903618851806	0	FACETS	0.348	0.251	0.465			1	INDETERMINATE	1	FALSE	0	0.251205545770595	0		449	240	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217225	11217225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	16	541	2	ENST00000361445.4:c.4453G>A	p.Glu1485Lys	p.E1485K	ENST00000361445	NM_004958.3	1485	Gag/Aag	30/58	1	2	FACETS	0.406	0.299	0.533	0.406	0.299	0.533	SUBCLONAL	1	FALSE	1	0.251205545770595	2		543	314	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346113	89346114	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs1555525296	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	12	251	1	ENST00000301030.4:c.6836_6837del	p.Val2279GlyfsTer16	p.V2279Gfs*16	ENST00000301030	NM_001256183.1	2279	gTG/g	9/13	0.109903618851806	0	FACETS	1	0.769	1			1	INDETERMINATE	1	FALSE	0	0.251205545770595	0		252	66	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10277309	10277309	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368960099	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	88	811	2	ENST00000340748.4:c.808G>A	p.Val270Met	p.V270M	ENST00000340748		270	Gtg/Atg	10/40	1	2	FACETS	0.968	0.864	1	1	0.985	1	CLONAL	2	FALSE	1	0.251205545770595	2		813	362	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038133	128038133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369244363	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	63	421	0	ENST00000285398.2:c.1417G>A	p.Glu473Lys	p.E473K	ENST00000285398	NM_000122.1	473	Gaa/Aaa	9/15	1	2	FACETS	1	0.905	1	1	0.981	1	CLONAL	2	FALSE	1	0.251205545770595	2		421	241	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805755	32805755	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	37	831	0	ENST00000374899.4:c.256del	p.Ala86ProfsTer34	p.A86Pfs*34	ENST00000374899	NM_018833.2	86	Gcc/cc	2/12	0.204338664591032	3	FACETS	0.921	0.761	1	0.461	0.38	0.55	CLONAL	1	FALSE	1	0.251205545770595	3		831	360	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332177	70332177	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1564947700	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	20	259	0	ENST00000373644.4:c.82C>T	p.Arg28Ter	p.R28*	ENST00000373644	NM_030625.2	28	Cga/Tga	2/12	1	2	FACETS	1	0.79	1	1	0.942	1	CLONAL	2	FALSE	1	0.251205545770595	2		259	79	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114905837	114905837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1290267513	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	92	572	0	ENST00000543371.1:c.856G>A	p.Val286Ile	p.V286I	ENST00000543371	NM_001198531.1	286	Gtc/Atc	8/14	1	2	FACETS	0.99	0.887	1	1	0.986	1	CLONAL	2	FALSE	1	0.251205545770595	2		572	370	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279509	123279509	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519040	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	25	663	0	ENST00000358487.5:c.923A>G	p.Tyr308Cys	p.Y308C	ENST00000358487	NM_000141.4	308	tAc/tGc	7/18	1	2	FACETS	0.628	0.495	0.78	0.628	0.495	0.78	SUBCLONAL	1	FALSE	1	0.251205545770595	2		663	317	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201496	67201496	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	52	875	1	ENST00000312629.5:c.941del	p.Gly314ValfsTer18	p.G314Vfs*18	ENST00000312629	NM_003952.2	313	Ggg/gg	11/15	1	2	FACETS	0.937	0.799	1	0.937	0.799	1	CLONAL	1	FALSE	1	0.251205545770595	2		876	442	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77043842	77043842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751082909	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	93	738	2	ENST00000356341.3:c.1484G>A	p.Arg495Gln	p.R495Q	ENST00000356341	NM_002576.4	495	cGg/cAg	14/15	1	2	FACETS	1	0.951	1	1	0.988	1	CLONAL	2	FALSE	1	0.251205545770595	2		740	337	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18478033	18478033	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	24	439	0	ENST00000266497.5:c.1272+1G>A		p.X424_splice	ENST00000266497		424			0.251205545770595	1	FACETS	0.777	0.612	0.965	0.777	0.612	0.965	CLONAL	1	FALSE	0	0.251205545770595	1		439	215	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552656	18552656	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	14	588	0	ENST00000266497.5:c.2067C>A	p.Cys689Ter	p.C689*	ENST00000266497		689	tgC/tgA	14/31	0.251205545770595	1	FACETS	0.513	0.371	0.683	0.513	0.371	0.683	SUBCLONAL	1	FALSE	0	0.251205545770595	1		588	190	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244605	46244605	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	11	486	2	ENST00000334344.6:c.2699C>A	p.Pro900His	p.P900H	ENST00000334344	NM_152641.2	900	cCt/cAt	15/21	0.173837082864987	4	FACETS	0.562	0.388	0.777	0.281	0.194	0.389	SUBCLONAL	1	FALSE	2	0.251205545770595	4		488	195	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748905	43748905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs917720125	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	24	864	0	ENST00000382044.4:c.1901C>T	p.Pro634Leu	p.P634L	ENST00000382044	NM_001141980.1	634	cCg/cTg	12/28	0.109903618851806	0	FACETS	0.579	0.455	0.721			1	INDETERMINATE	1	FALSE	0	0.251205545770595	0		864	247	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120491	2120491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751147419	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	22	822	1	ENST00000219476.3:c.1751C>T	p.Thr584Met	p.T584M	ENST00000219476	NM_000548.3	584	aCg/aTg	17/42	0.109903618851806	0	FACETS	0.437	0.339	0.551			1	INDETERMINATE	1	FALSE	0	0.251205545770595	0		823	300	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641240	23641240	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	48	750	0	ENST00000261584.4:c.2235del	p.Ala746HisfsTer18	p.A746Hfs*18	ENST00000261584	NM_024675.3	745	aaA/aa	5/13	0.109903618851806	0	FACETS	0.681	0.583	0.787			1	INDETERMINATE	2	FALSE	0	0.251205545770595	0		750	210	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832034	72832034	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	14	616	0	ENST00000268489.5:c.4547A>T	p.Asp1516Val	p.D1516V	ENST00000268489	NM_006885.3	1516	gAc/gTc	9/10	0.109903618851806	0	FACETS	0.437	0.316	0.582			1	INDETERMINATE	1	FALSE	0	0.251205545770595	0		616	191	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871559	37871559	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778264	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	113	843	1	ENST00000269571.5:c.1169C>T	p.Ala390Val	p.A390V	ENST00000269571		390	gCc/gTc	10/27	1	2	FACETS	1	0.968	1	1	0.99	1	CLONAL	2	FALSE	1	0.251205545770595	2		844	390	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868403	45868403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746621981	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	64	874	0	ENST00000391945.4:c.374G>A	p.Arg125His	p.R125H	ENST00000391945	NM_000400.3	125	cGc/cAc	6/23	1	2	FACETS	0.961	0.841	1	1	0.98	1	CLONAL	2	FALSE	1	0.251205545770595	2		874	265	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50138892	50138892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548040971	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	47	1180	2	ENST00000246792.3:c.598C>T	p.Pro200Ser	p.P200S	ENST00000246792	NM_006270.3	200	Ccg/Tcg	6/6	1	2	FACETS	0.756	0.638	0.886	0.756	0.638	0.886	SUBCLONAL	1	FALSE	1	0.251205545770595	2		1182	495	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469534	25469534	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	62	781	0	ENST00000264709.3:c.1234G>T	p.Gly412Trp	p.G412W	ENST00000264709	NM_175629.2	412	Ggg/Tgg	10/23	0.135844651423364	0	FACETS	0.884	0.776	0.998			1	INDETERMINATE	2	FALSE	0	0.251205545770595	0		781	209	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703581	47703581	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1114167857	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	69	598	0	ENST00000233146.2:c.2081T>C	p.Phe694Ser	p.F694S	ENST00000233146	NM_000251.2	694	tTt/tCt	13/16	0.251205545770595	0	FACETS	0.797	0.71	0.886			1	SUBCLONAL	3	FALSE	0	0.251205545770595	0		598	172	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017730	31017730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376793343	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	62	675	0	ENST00000375687.4:c.592G>A	p.Glu198Lys	p.E198K	ENST00000375687	NM_015338.5	198	Gag/Aag	8/13	0.109903618851806	0	FACETS	0.665	0.579	0.756			1	INDETERMINATE	2	FALSE	0	0.251205545770595	0		675	278	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960003	134960003	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	31	427	0	ENST00000398015.3:c.2360C>A	p.Pro787His	p.P787H	ENST00000398015	NM_004441.4	787	cCt/cAt	13/16	1	2	FACETS	0.762	0.624	0.914	1	0.947	1	CLONAL	2	FALSE	1	0.251205545770595	2		427	162	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535424	66535424	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	30	329	0	ENST00000273854.3:c.37C>T	p.Arg13Trp	p.R13W	ENST00000273854	NM_004439.5	13	Cgg/Tgg	1/18	0.109903618851806	0	FACETS	0.784	0.645	0.935			1	INDETERMINATE	2	FALSE	0	0.251205545770595	0		329	114	SUCCESS
APC	324	MSKCC	GRCh37	5	112128156	112128156	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	47	349	0	ENST00000257430.4:c.659del	p.Arg220LysfsTer73	p.R220Kfs*73	ENST00000257430	NM_000038.5	220	aGa/aa	7/16	1	2	FACETS	0.872	0.752	0.998	1	0.979	1	CLONAL	3	FALSE	1	0.251205545770595	2		349	143	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048638	180048638	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	51	766	0	ENST00000261937.6:c.1924del	p.Arg642AlafsTer43	p.R642Afs*43	ENST00000261937	NM_182925.4	642	Cgc/gc	13/30	0.251205545770595	0	FACETS	0.685	0.589	0.788			1	SUBCLONAL	2	FALSE	0	0.251205545770595	0		766	222	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31946713	31946713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145128680	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	55	603	1	ENST00000375333.2:c.601G>A	p.Val201Ile	p.V201I	ENST00000375333	NM_032454.1	201	Gtc/Atc	4/8	0.204338664591032	3	FACETS	0.761	0.654	0.875	0.761	0.654	0.875	SUBCLONAL	2	FALSE	1	0.251205545770595	3		604	324	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505472	157505473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	85	447	0	ENST00000346085.5:c.3456dup	p.Glu1153Ter	p.E1153*	ENST00000346085	NM_020732.3	1151	-/T	13/20	0.204338664591032	3	FACETS	0.934	0.836	1	1	0.978	1	CLONAL	3	FALSE	1	0.251205545770595	3		447	272	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211145	55211145	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	12	407	0	ENST00000275493.2:c.388A>C	p.Thr130Pro	p.T130P	ENST00000275493	NM_005228.3	130	Acc/Ccc	3/28	0.109903618851806	0	FACETS	0.356	0.25	0.486			1	INDETERMINATE	1	FALSE	0	0.251205545770595	0		407	201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0046493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	29	803	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.515	0.411	0.633	0.515	0.411	0.633	SUBCLONAL	1	TRUE	1	0.13	2		803	867	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0046493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	26	707	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	0.606	0.478	0.754	0.606	0.478	0.754	SUBCLONAL	1	TRUE	1	0.13	2		707	660	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440757	56440757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774211426	NA	P-0046493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	32	726	0	ENST00000407977.2:c.461C>T	p.Pro154Leu	p.P154L	ENST00000407977		154	cCg/cTg	5/10	1	2	FACETS	0.887	0.719	1	0.887	0.719	1	CLONAL	1	TRUE	1	0.13	2		726	555	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0046494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	7	292	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		292	347	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	66	424	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.721	0.627	0.823	0.721	0.627	0.823	SUBCLONAL	1	TRUE	1	0.352830338712317	2		424	519	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356133	66356133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1349813115	NA	P-0046495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	92	571	0	ENST00000273854.3:c.1364G>A	p.Arg455Gln	p.R455Q	ENST00000273854	NM_004439.5	455	cGg/cAg	5/18	1	2	FACETS	0.901	0.802	1	0.901	0.802	1	CLONAL	1	TRUE	1	0.352830338712317	2		571	579	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691947	30691947	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0046495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	64	379	0	ENST00000295754.5:c.449C>G	p.Ser150Ter	p.S150*	ENST00000295754	NM_003242.5	150	tCa/tGa	3/7	0.352830338712317	1	FACETS	0.756	0.658	0.862	0.756	0.658	0.862	SUBCLONAL	1	TRUE	0	0.352830338712317	1		379	395	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041022	47041022	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	157	826	0	ENST00000377604.3:c.1552C>T	p.Gln518Ter	p.Q518*	ENST00000377604	NM_001204468.1	518	Cag/Tag	14/24	0.352830338712317	1	FACETS	0.899	0.825	0.977	0.899	0.825	0.977	CLONAL	1	TRUE	0	0.352830338712317	1		826	815	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779676	3779676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1214172132	NA	P-0046495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	185	855	0	ENST00000262367.5:c.5372C>T	p.Ser1791Leu	p.S1791L	ENST00000262367	NM_004380.2	1791	tCg/tTg	31/31	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.352830338712317	2		855	1044	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154356	2154356	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	197	1071	1	ENST00000434045.2:c.572G>T	p.Arg191Leu	p.R191L	ENST00000434045	NM_001127598.1	191	cGt/cTt	5/5	1	2	FACETS	0.976	0.903	1	0.976	0.903	1	CLONAL	1	TRUE	1	0.352830338712317	2		1072	1144	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262458	10262458	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	160	786	0	ENST00000340748.4:c.2037T>A	p.Ser679Arg	p.S679R	ENST00000340748		679	agT/agA	22/40	1	2	FACETS	0.984	0.902	1	0.984	0.902	1	CLONAL	1	TRUE	1	0.352830338712317	2		786	922	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24135874	24135874	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	85	495	0	ENST00000263121.7:c.361A>T	p.Arg121Trp	p.R121W	ENST00000263121	NM_003073.3	121	Agg/Tgg	3/9	1	2	FACETS	0.901	0.798	1	0.901	0.798	1	CLONAL	1	TRUE	1	0.352830338712317	2		495	535	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665483	138665483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	132	619	0	ENST00000330315.3:c.82G>A	p.Glu28Lys	p.E28K	ENST00000330315	NM_023067.3	28	Gaa/Aaa	1/1	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.352830338712317	2		619	742	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356223	66356223	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	140	672	0	ENST00000273854.3:c.1274C>G	p.Ser425Cys	p.S425C	ENST00000273854	NM_004439.5	425	tCt/tGt	5/18	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.352830338712317	2		672	780	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874395	151874395	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	162	477	0	ENST00000262189.6:c.8143G>T	p.Glu2715Ter	p.E2715*	ENST00000262189	NM_170606.2	2715	Gaa/Taa	38/59	0.322662609188763	3	FACETS	0.894	0.824	0.967	0.894	0.824	0.967	CLONAL	2	TRUE	1	0.352830338712317	3		477	604	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528636	8528636	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	66	460	0	ENST00000356435.5:c.496G>C	p.Val166Leu	p.V166L	ENST00000356435		166	Gtg/Ctg	4/35	1	2	FACETS	0.701	0.609	0.8	0.701	0.609	0.8	SUBCLONAL	1	TRUE	1	0.352830338712317	2		460	534	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0046496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1274	446	767	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.516269494593358	7	FACETS	1	0.991	1	0.46	0.438	0.483	CLONAL	2	TRUE	2	0.516269494593358	7		767	1720	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480538	123480538	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	128	638	0	ENST00000371139.4:c.46G>A	p.Gly16Ser	p.G16S	ENST00000371139	NM_001114937.2	16	Ggc/Agc	1/4	NA	2	FACETS	0.932	0.849	1			1	INDETERMINATE	1	TRUE	NA	0.516269494593358	2		638	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578458	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	1053	957	0	ENST00000269305.4:c.472dup	p.Arg158ProfsTer23	p.R158Pfs*23	ENST00000269305	NM_001126112.2	158	cgc/cCgc	5/11	0.516269494593358	7	FACETS	1	0.996	1	0.884	0.86	0.907	CLONAL	4	TRUE	2	0.516269494593358	7		957	2115	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249417	110249436	+	frameshift_variant	Frame_Shift_Del	DEL	GTCTTCCCCTCTTTGGCTTG	GTCTTCCCCTCTTTGGCTTG	-	novel	NA	P-0046496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	386	1153	0	ENST00000374672.4:c.1137_1156del	p.Lys380IlefsTer13	p.K380Ifs*13	ENST00000374672	NM_004235.4	379	ccCAAGCCAAAGAGGGGAAGACga/ccga	4/5	0.492393205217092	4	FACETS	0.988	0.94	1	0.988	0.94	1	CLONAL	2	TRUE	2	0.516269494593358	4		1153	1147	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934155	48934155	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	178	312	0	ENST00000267163.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000267163	NM_000321.2	204	Gaa/Taa	7/27	0.896867394482155	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.896867394482155	1		312	209	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649626	48649626	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	147	1004	0	ENST00000376670.3:c.110G>C	p.Gly37Ala	p.G37A	ENST00000376670	NM_002049.3	37	gGg/gCg	2/6	1	2	FACETS	0.297	0.271	0.325	0.297	0.271	0.325	SUBCLONAL	1	TRUE	1	0.896867394482155	2		1004	1103	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0046498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	149	599	0	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		599	549	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211786	123211806	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TTTGTACAAATTTCTTTATAG	TTTGTACAAATTTCTTTATAG	-	novel	NA	P-0046498-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	99	251	0	ENST00000218089.9:c.2674-20_2674del		p.X892_splice	ENST00000218089	NM_001042749.1	892			1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		251	319	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0046513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	55	353	1	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.18	2		354	533	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222006	1222006	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0046513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	49	451	0	ENST00000326873.7:c.920+1G>T		p.X307_splice	ENST00000326873	NM_000455.4	307			0.234859255304117	1	FACETS	0.973	0.825	1	0.973	0.825	1	CLONAL	1	TRUE	0	0.18	1		451	509	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813300	102813300	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1436683139	NA	P-0046513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	47	426	0	ENST00000307046.8:c.389C>A	p.Pro130His	p.P130H	ENST00000307046	NM_001111285.1	130	cCc/cAc	3/4	1	2	FACETS	0.89	0.75	1	0.89	0.75	1	CLONAL	1	TRUE	1	0.18	2		426	587	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436014	110436014	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	62	662	0	ENST00000375856.3:c.2387G>T	p.Arg796Met	p.R796M	ENST00000375856	NM_003749.2	796	aGg/aTg	1/2	1	2	FACETS	0.786	0.677	0.904	0.786	0.677	0.904	CLONAL	1	TRUE	1	0.18	2		662	877	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059251	42059251	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	32	315	0	ENST00000219905.7:c.8971C>T	p.Pro2991Ser	p.P2991S	ENST00000219905	NM_001164273.1	2991	Cct/Tct	24/24	1	2	FACETS	0.833	0.676	1	0.833	0.676	1	CLONAL	1	TRUE	1	0.18	2		315	427	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56792488	56792488	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	55	438	0	ENST00000308159.5:c.218A>G	p.His73Arg	p.H73R	ENST00000308159	NM_014669.4	73	cAc/cGc	3/22	1	2	FACETS	0.997	0.852	1	0.997	0.852	1	CLONAL	1	TRUE	1	0.18	2		438	613	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474042	29474042	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	59	707	0	ENST00000389048.3:c.2133C>A	p.Ser711Arg	p.S711R	ENST00000389048	NM_004304.4	711	agC/agA	12/29	1	2	FACETS	0.825	0.708	0.952	0.825	0.708	0.952	CLONAL	1	TRUE	1	0.18	2		707	795	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306656	41306656	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	56	590	0	ENST00000373198.4:c.1003del	p.Ala335GlnfsTer5	p.A335Qfs*5	ENST00000373198	NM_133170.3	335	Gca/ca	7/32	1	2	FACETS	0.907	0.776	1	0.907	0.776	1	CLONAL	1	TRUE	1	0.18	2		590	686	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755688	57755688	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	74	643	0	ENST00000274289.3:c.99G>T	p.Lys33Asn	p.K33N	ENST00000274289	NM_006622.3	33	aaG/aaT	1/14	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.18	2		643	731	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729729	41729729	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	57	484	0	ENST00000242208.4:c.800G>T	p.Gly267Val	p.G267V	ENST00000242208	NM_002192.2	267	gGg/gTg	3/3	1	2	FACETS	0.991	0.85	1	0.991	0.85	1	CLONAL	1	TRUE	1	0.18	2		484	639	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846320	128846320	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	51	546	1	ENST00000249373.3:c.1156G>T	p.Val386Leu	p.V386L	ENST00000249373	NM_005631.4	386	Gtg/Ttg	6/12	1	2	FACETS	0.924	0.785	1	0.924	0.785	1	CLONAL	1	TRUE	1	0.18	2		547	613	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212789	27212789	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	63	683	0	ENST00000380036.4:c.2771C>A	p.Pro924Gln	p.P924Q	ENST00000380036	NM_000459.3	924	cCa/cAa	17/23	1	2	FACETS	0.836	0.722	0.961	0.836	0.722	0.961	CLONAL	1	TRUE	1	0.18	2		683	837	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044477	47044477	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	49	578	0	ENST00000377604.3:c.1974G>T	p.Trp658Cys	p.W658C	ENST00000377604	NM_001204468.1	658	tgG/tgT	18/24	1	2	FACETS	0.752	0.635	0.881	0.752	0.635	0.881	SUBCLONAL	1	TRUE	1	0.18	2		578	724	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630257	100630257	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1320514510	NA	P-0046513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	45	303	1	ENST00000308731.7:c.16C>A	p.Leu6Met	p.L6M	ENST00000308731	NM_000061.2	6	Ctg/Atg	2/19	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.18	2		304	472	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0046513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	23	409	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.152685850857204	1	FACETS	1	0.823	1	1	0.823	1	CLONAL	1	TRUE	0	0.208586784080531	1		410	187	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858014	9858014	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	33	532	0	ENST00000330684.3:c.3387C>A	p.His1129Gln	p.H1129Q	ENST00000330684	NM_001134407.1	1129	caC/caA	13/13	NA	2	FACETS	1	0.857	1			1	INDETERMINATE	1	TRUE	NA	0.208586784080531	2		532	299	SUCCESS
AR	367	MSKCC	GRCh37	X	66941763	66941763	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	17	487	1	ENST00000374690.3:c.2407C>A	p.Gln803Lys	p.Q803K	ENST00000374690	NM_000044.3	803	Cag/Aag	6/8	0.208586784080531	1	FACETS	0.471	0.351	0.614	0.471	0.351	0.614	SUBCLONAL	1	TRUE	0	0.208586784080531	1		488	310	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186830	108186830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866290641	NA	P-0046513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	30	325	1	ENST00000278616.4:c.6188G>A	p.Gly2063Glu	p.G2063E	ENST00000278616	NM_000051.3	2063	gGa/gAa	42/63	0.152685850857204	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.208586784080531	1		326	203	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112530	115112530	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1200233232	NA	P-0046513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	34	685	0	ENST00000257566.3:c.1210T>A	p.Cys404Ser	p.C404S	ENST00000257566	NM_016569.3	404	Tgc/Agc	7/8	0.152685850857204	1	FACETS	0.954	0.782	1	0.954	0.782	1	CLONAL	1	TRUE	0	0.208586784080531	1		685	306	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029424	16029424	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	32	339	0	ENST00000268712.3:c.1606G>T	p.Glu536Ter	p.E536*	ENST00000268712	NM_006311.3	536	Gag/Tag	15/46	1	2	FACETS	0.848	0.689	1	0.848	0.689	1	CLONAL	1	TRUE	1	0.208586784080531	2		339	362	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119875	70119875	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	18	530	0	ENST00000245479.2:c.877G>A	p.Glu293Lys	p.E293K	ENST00000245479	NM_000346.3	293	Gag/Aag	3/3	1	2	FACETS	0.529	0.398	0.685	0.529	0.398	0.685	SUBCLONAL	1	TRUE	1	0.208586784080531	2		530	326	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1953898	1953898	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	39	793	1	ENST00000382891.5:c.2077G>T	p.Ala693Ser	p.A693S	ENST00000382891	NM_133335.3	693	Gcc/Tcc	11/22	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.208586784080531	2		794	358	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350077	81350077	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	30	341	0	ENST00000222390.5:c.1255A>G	p.Met419Val	p.M419V	ENST00000222390	NM_000601.4	419	Atg/Gtg	10/18	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.208586784080531	2		341	218	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509991	106509991	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046513-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	22	500	0	ENST00000359195.3:c.1985A>T	p.Gln662Leu	p.Q662L	ENST00000359195	NM_002649.2	662	cAa/cTa	2/11	1	2	FACETS	0.659	0.511	0.831	0.659	0.511	0.831	SUBCLONAL	1	TRUE	1	0.208586784080531	2		500	320	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	66	424	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.220492149055884	2		424	546	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332868	152332868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745723014	NA	P-0046515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	69	163	0	ENST00000206249.3:c.1174G>A	p.Val392Ile	p.V392I	ENST00000206249	NM_000125.3	392	Gtc/Atc	5/8	0.221475403293781	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.220492149055884	1		163	512	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404305	139404305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777658333	NA	P-0046515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	83	270	0	ENST00000277541.6:c.2849C>T	p.Ala950Val	p.A950V	ENST00000277541	NM_017617.3	950	gCc/gTc	18/34	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.220492149055884	2		270	746	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431049	49431049	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1210590639	NA	P-0046515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	69	243	0	ENST00000301067.7:c.10090C>T	p.Gln3364Ter	p.Q3364*	ENST00000301067	NM_003482.3	3364	Cag/Tag	34/54	1	2	FACETS	0.927	0.807	1	0.927	0.807	1	CLONAL	1	TRUE	1	0.220492149055884	2		243	675	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930748	32930748	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0046515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	89	152	0	ENST00000380152.3:c.7617+2T>A		p.X2539_splice	ENST00000380152		2539			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.220492149055884	2		152	629	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0046525-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	14	435	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	0.159	0.114	0.214	0.159	0.114	0.214	SUBCLONAL	1	TRUE	1	0.35	2		435	503	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0046526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	166	429	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.336233477758913	2	FACETS	0.886	0.819	0.955	0.886	0.819	0.955	CLONAL	2	TRUE	0	0.34	2		429	551	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0046526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	37	527	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	1	2	FACETS	0.245	0.201	0.295	0.245	0.201	0.295	SUBCLONAL	1	TRUE	1	0.34	2		527	888	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56855497	56855497	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777022774	NA	P-0046526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	77	313	1	ENST00000308159.5:c.646G>A	p.Asp216Asn	p.D216N	ENST00000308159	NM_014669.4	216	Gat/Aat	7/22	1	2	FACETS	0.911	0.802	1	0.911	0.802	1	CLONAL	1	TRUE	1	0.34	2		314	497	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125789	47125789	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	92	287	1	ENST00000409792.3:c.5481G>A	p.Trp1827Ter	p.W1827*	ENST00000409792	NM_014159.6	1827	tgG/tgA	12/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.34	2		288	407	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1978223	1978223	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	156	542	0	ENST00000382891.5:c.3643G>C	p.Glu1215Gln	p.E1215Q	ENST00000382891	NM_133335.3	1215	Gag/Cag	21/22	1	2	FACETS	0.973	0.891	1	0.973	0.891	1	CLONAL	1	TRUE	1	0.34	2		542	943	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151654	55151654	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0046526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	101	406	0	ENST00000257290.5:c.2439+1G>C		p.X813_splice	ENST00000257290	NM_006206.4	813			1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.34	2		406	556	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155923	106155923	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1042729299	NA	P-0046526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	74	320	0	ENST00000380013.4:c.824A>G	p.Asn275Ser	p.N275S	ENST00000380013	NM_001127208.2	275	aAt/aGt	3/11	1	2	FACETS	0.942	0.828	1	0.942	0.828	1	CLONAL	1	TRUE	1	0.34	2		320	462	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903701	41903701	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	138	637	0	ENST00000372991.4:c.856G>T	p.Asp286Tyr	p.D286Y	ENST00000372991	NM_001760.3	286	Gat/Tat	5/5	1	2	FACETS	0.834	0.758	0.914	0.834	0.758	0.914	CLONAL	1	TRUE	1	0.34	2		637	973	SUCCESS
BTK	695	MSKCC	GRCh37	X	100612528	100612528	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	105	439	0	ENST00000308731.7:c.1146G>C	p.Lys382Asn	p.K382N	ENST00000308731	NM_000061.2	382	aaG/aaC	13/19	1	2	FACETS	0.982	0.881	1	0.982	0.881	1	CLONAL	1	TRUE	1	0.34	2		439	629	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0046527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	157	494	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	0.967	0.888	1	0.967	0.888	1	CLONAL	1	TRUE	1	0.431691576479014	2		494	752	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0046527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	306	350	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.431691576479014	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.431691576479014	1		350	798	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	273	421	1	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	0.135655544314241	5	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.431691576479014	5		422	909	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265256	16265256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768794824	NA	P-0046527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	230	428	0	ENST00000375759.3:c.10748G>A	p.Arg3583His	p.R3583H	ENST00000375759	NM_015001.2	3583	cGt/cAt	14/15	0.317427819356513	3	FACETS	0.818	0.765	0.873	0.818	0.765	0.873	CLONAL	2	TRUE	1	0.431691576479014	3		428	792	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864994	57864994	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046527-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1946	312	579	0	ENST00000228682.2:c.2471C>T	p.Ser824Phe	p.S824F	ENST00000228682	NM_005269.2	824	tCt/tTt	12/12	0.431691576479014	12	FACETS	1	0.948	1			1	CLONAL	2	TRUE	NA	0.431691576479014	12		579	2258	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0046529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	144	649	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.326911056862548	1	FACETS	0.407	0.371	0.444	0.407	0.371	0.444	INDETERMINATE	1	TRUE	0	0.617904988310436	1		649	792	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0046529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	42	199	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.617904988310436	1	FACETS	0.516	0.437	0.602	0.516	0.437	0.602	SUBCLONAL	1	TRUE	0	0.617904988310436	1		199	182	SUCCESS
APC	324	MSKCC	GRCh37	5	112154723	112154723	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775126020	NA	P-0046529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	77	392	1	ENST00000257430.4:c.994C>T	p.Arg332Ter	p.R332*	ENST00000257430	NM_000038.5	332	Cga/Tga	10/16	0.617904988310436	1	FACETS	0.622	0.552	0.695	0.622	0.552	0.695	SUBCLONAL	1	TRUE	0	0.617904988310436	1		393	277	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579373	7579373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781504	NA	P-0046529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	357	707	0	ENST00000269305.4:c.314G>A	p.Gly105Asp	p.G105D	ENST00000269305	NM_001126112.2	105	gGc/gAc	4/11	0.326911056862548	1	FACETS	0.959	0.913	1	0.959	0.913	1	INDETERMINATE	1	TRUE	0	0.617904988310436	1		707	833	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400932	72400932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	141	310	0	ENST00000357731.5:c.239C>T	p.Ala80Val	p.A80V	ENST00000357731	NM_173808.2	80	gCg/gTg	2/7	0.219210678522469	3	FACETS	1	0.982	1	0.629	0.577	0.682	INDETERMINATE	1	TRUE	1	0.617904988310436	3		310	475	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118950	70118950	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs373719106	NA	P-0046529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	364	679	0	ENST00000245479.2:c.522C>A	p.Tyr174Ter	p.Y174*	ENST00000245479	NM_000346.3	174	taC/taA	2/3	0.326911056862548	1	FACETS	0.968	0.923	1	0.968	0.923	1	INDETERMINATE	1	TRUE	0	0.617904988310436	1		679	841	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646155	215646155	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	252	388	0	ENST00000260947.4:c.443G>T	p.Ser148Ile	p.S148I	ENST00000260947	NM_000465.2	148	aGc/aTc	4/11	0.326419578125251	2	FACETS	1	0.994	1	0.732	0.692	0.773	INDETERMINATE	1	TRUE	0	0.617904988310436	2		388	557	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795030	242795030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779874434	NA	P-0046529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	268	805	1	ENST00000334409.5:c.179C>T	p.Ser60Leu	p.S60L	ENST00000334409	NM_005018.2	60	tCg/tTg	2/5	NA	2	FACETS	0.896	0.842	0.952			1	INDETERMINATE	1	TRUE	NA	0.617904988310436	2		806	968	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163603	32163603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	127	498	0	ENST00000375023.3:c.5623G>A	p.Ala1875Thr	p.A1875T	ENST00000375023	NM_004557.3	1875	Gct/Act	30/30	0.565666853183262	3	FACETS	0.541	0.489	0.595	0.27	0.244	0.298	SUBCLONAL	1	TRUE	1	0.617904988310436	3		498	995	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0046530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	172	594	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.431474127420754	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.431474127420754	1		594	602	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591104	67591115	+	inframe_deletion	In_Frame_Del	DEL	TTAAACCAGACC	TTAAACCAGACC	-	novel	NA	P-0046530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	201	262	0	ENST00000274335.5:c.1700_1711del	p.Lys567_Leu570del	p.K567_L570del	ENST00000274335		566	aTTAAACCAGACCtt/att	12/15	0.26191436839449	6	FACETS	1	0.978	1			1	CLONAL	3	TRUE	NA	0.431474127420754	6		262	523	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456266	32456266	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs771024882	NA	P-0046530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1530	158	691	0	ENST00000332351.3:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000332351	NM_024426.4	209	cAg/cCg	1/10	0.431474127420754	7	FACETS	0.902	0.823	0.985			1	CLONAL	1	TRUE	NA	0.431474127420754	7		691	1688	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054326	42054326	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0046532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	94	250	0	ENST00000219905.7:c.7511-1G>A		p.X2504_splice	ENST00000219905	NM_001164273.1	2504			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.51568518738608	2		250	315	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820602	44820602	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	213	336	0	ENST00000377967.4:c.299G>T	p.Gly100Val	p.G100V	ENST00000377967	NM_021140.2	100	gGt/gTt	3/29	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.51568518738608	2		336	650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203436	NA	P-0046533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	196	451	0	ENST00000269305.4:c.487T>C	p.Tyr163His	p.Y163H	ENST00000269305	NM_001126112.2	163	Tac/Cac	5/11	0.260826666406258	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	FALSE	0	0.3	2		451	620	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0046534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	493	512	0	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.531162728520243	2		512	852	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834552	156834552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540521894	NA	P-0046534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	268	478	0	ENST00000524377.1:c.320C>T	p.Ala107Val	p.A107V	ENST00000524377	NM_002529.3	107	gCg/gTg	3/17	0.188742646757875	3	FACETS	1	0.992	1	0.677	0.636	0.719	INDETERMINATE	1	TRUE	1	0.531162728520243	3		478	943	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561861	55561861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201872586	NA	P-0046534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	146	204	0	ENST00000288135.5:c.251C>T	p.Thr84Met	p.T84M	ENST00000288135	NM_000222.2	84	aCg/aTg	2/21	0.531162728520243	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.531162728520243	1		204	315	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114903718	114903718	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241370314	NA	P-0046534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	213	355	1	ENST00000543371.1:c.722C>T	p.Pro241Leu	p.P241L	ENST00000543371	NM_001198531.1	241	cCg/cTg	7/14	0.531162728520243	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.531162728520243	1		356	520	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944545	40944545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200852571	NA	P-0046534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	184	290	0	ENST00000373198.4:c.1957C>T	p.Arg653Trp	p.R653W	ENST00000373198	NM_133170.3	653	Cgg/Tgg	12/32	0.142179919893144	4	FACETS	1	0.989	1	0.358	0.331	0.386	INDETERMINATE	1	TRUE	0	0.531162728520243	4		290	741	SUCCESS
APC	324	MSKCC	GRCh37	5	112128209	112128212	+	frameshift_variant	Frame_Shift_Del	DEL	CAAG	CAAG	-	novel	NA	P-0046534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	90	227	0	ENST00000257430.4:c.715_718del	p.Ala239GlnfsTer53	p.A239Qfs*53	ENST00000257430	NM_000038.5	238	CAAGca/ca	7/16	0.531162728520243	1	FACETS	0.961	0.866	1	0.961	0.866	1	CLONAL	1	TRUE	0	0.531162728520243	1		227	259	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342066	70342066	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	156	191	0	ENST00000374080.3:c.1118G>T	p.Cys373Phe	p.C373F	ENST00000374080		373	tGt/tTt	8/45	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.531162728520243	1		191	291	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0046535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	76	385	0	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.206428184126814	2		385	548	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643566	38643578	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAATGTTAGGG	GAAAATGTTAGGG	-	novel	NA	P-0046535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	49	323	0	ENST00000299084.4:c.1044_1056del	p.Gly350MetfsTer52	p.G350Mfs*52	ENST00000299084	NM_152594.2	346	GAAAATGTTAGGGga/ga	7/7	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.206428184126814	2		323	454	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102033258	102033265	+	frameshift_variant	Frame_Shift_Del	DEL	CCACCAGT	CCACCAGT	-	novel	NA	P-0046535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	42	365	0	ENST00000282441.5:c.652_659del	p.Pro218AlafsTer14	p.P218Afs*14	ENST00000282441	NM_001130145.2	215	cCCACCAGT/c	3/9	1	2	FACETS	0.669	0.558	0.793	0.669	0.558	0.793	SUBCLONAL	1	TRUE	1	0.206428184126814	2		365	608	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808295	99808295	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	29	214	1	ENST00000280892.6:c.394C>T	p.Arg132Ter	p.R132*	ENST00000280892	NM_001130678.1	132	Cga/Tga	5/7	1	2	FACETS	0.717	0.575	0.878	0.717	0.575	0.878	SUBCLONAL	1	TRUE	1	0.206428184126814	2		215	392	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720720	89720721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs786204905	NA	P-0046536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	45	133	0	ENST00000371953.3:c.875dup	p.Asn292LysfsTer6	p.N292Kfs*6	ENST00000371953	NM_000314.4	291	gaa/gAaa	8/9	0.71435104525967	1	FACETS	0.794	0.691	0.899	0.794	0.691	0.899	SUBCLONAL	1	TRUE	0	0.71435104525967	1		133	102	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	234	328	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.578682026802224	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.71435104525967	1		328	421	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436394	110436394	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	89	361	0	ENST00000375856.3:c.2007C>G	p.Ser669Arg	p.S669R	ENST00000375856	NM_003749.2	669	agC/agG	1/2	0.554636577827286	1	FACETS	0.374	0.333	0.417	0.374	0.333	0.417	SUBCLONAL	1	TRUE	0	0.71435104525967	1		361	428	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339522	116339526	+	frameshift_variant	Frame_Shift_Del	DEL	TCAAC	TCAAC	-	novel	NA	P-0046536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	118	189	0	ENST00000397752.3:c.387_391del	p.Gln129HisfsTer2	p.Q129Hfs*2	ENST00000397752	NM_000245.2	128	gaTCAACtc/gatc	2/21	0.71435104525967	3	FACETS	1	0.94	1	0.523	0.475	0.572	CLONAL	1	TRUE	1	0.71435104525967	3		189	429	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360567	70360567	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1187648751	NA	P-0046536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	175	346	0	ENST00000374080.3:c.6127C>T	p.Arg2043Cys	p.R2043C	ENST00000374080		2043	Cgt/Tgt	42/45	0.285462806490744	1	FACETS	0.56	0.519	0.603	0.56	0.519	0.603	INDETERMINATE	1	TRUE	0	0.71435104525967	1		346	562	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	13	427	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.46	0.329	0.617	0.46	0.329	0.617	SUBCLONAL	1	TRUE	1	0.390048594555972	2		427	145	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0046537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	12	195	0	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	1	2	FACETS	0.419	0.295	0.569	0.419	0.295	0.569	SUBCLONAL	1	TRUE	1	0.390048594555972	2		195	147	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753045	57753045	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	42	281	0	ENST00000274289.3:c.971G>T	p.Ser324Ile	p.S324I	ENST00000274289	NM_006622.3	324	aGt/aTt	7/14	1	2	FACETS	0.775	0.651	0.911	0.775	0.651	0.911	CLONAL	1	TRUE	1	0.390048594555972	2		281	278	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841892	151841892	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	35	266	0	ENST00000262189.6:c.14249A>G	p.Tyr4750Cys	p.Y4750C	ENST00000262189	NM_170606.2	4750	tAt/tGt	55/59	1	2	FACETS	0.559	0.459	0.67	0.559	0.459	0.67	SUBCLONAL	1	TRUE	1	0.390048594555972	2		266	321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572932	7572933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	169	298	0	ENST00000269305.4:c.1176dup	p.Asp393ArgfsTer78	p.D393Rfs*78	ENST00000269305	NM_001126112.2	392	-/A	11/11	0.377552470244774	2	FACETS	0.94	0.874	1	0.94	0.874	1	CLONAL	2	TRUE	0	0.414271288995644	2		298	434	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496911	29496911	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0046538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	90	132	0	ENST00000356175.3:c.482T>G	p.Leu161Ter	p.L161*	ENST00000356175	NM_000267.3	161	tTa/tGa	5/57	0.377552470244774	2	FACETS	0.796	0.716	0.878	0.796	0.716	0.878	SUBCLONAL	2	TRUE	0	0.414271288995644	2		132	273	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576511	67576512	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0046538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	119	208	0	ENST00000274335.5:c.794_795del	p.Ser265Ter	p.S265*	ENST00000274335		264	CTc/c	5/15	0.377552470244774	2	FACETS	0.847	0.774	0.922	0.847	0.774	0.922	CLONAL	2	TRUE	0	0.414271288995644	2		208	339	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0046538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	9	220	3	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.377552470244774	2	FACETS	0.124	0.082	0.179	0.062	0.041	0.09	SUBCLONAL	1	TRUE	0	0.414271288995644	2		223	349	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600527	10600527	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046538-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	29	335	0	ENST00000171111.5:c.1328A>G	p.Tyr443Cys	p.Y443C	ENST00000171111	NM_203500.1	443	tAt/tGt	4/6	0.377552470244774	2	FACETS	0.325	0.26	0.398	0.162	0.13	0.199	SUBCLONAL	1	TRUE	0	0.414271288995644	2		335	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572932	7572933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046538-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	257	298	0	ENST00000269305.4:c.1176dup	p.Asp393ArgfsTer78	p.D393Rfs*78	ENST00000269305	NM_001126112.2	392	-/A	11/11	0.469981985149764	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.469981985149764	2		298	524	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496911	29496911	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0046538-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	82	132	0	ENST00000356175.3:c.482T>G	p.Leu161Ter	p.L161*	ENST00000356175	NM_000267.3	161	tTa/tGa	5/57	0.346432806815704	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	2	TRUE	0	0.469981985149764	2		132	171	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576511	67576512	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0046538-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	125	208	0	ENST00000274335.5:c.794_795del	p.Ser265Ter	p.S265*	ENST00000274335		264	CTc/c	5/15	0.469981985149764	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.469981985149764	2		208	242	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830877	3830877	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	74	308	0	ENST00000262367.5:c.1679C>T	p.Pro560Leu	p.P560L	ENST00000262367	NM_004380.2	560	cCa/cTa	8/31	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.447002651066663	2		308	301	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994388	25994388	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	49	217	0	ENST00000435504.4:c.425C>A	p.Ser142Ter	p.S142*	ENST00000435504		142	tCa/tAa	6/13	1	2	FACETS	0.974	0.834	1	0.974	0.834	1	CLONAL	1	TRUE	1	0.447002651066663	2		217	225	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067841	30067841	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046539-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	66	285	0	ENST00000338641.4:c.1026del	p.Lys343SerfsTer3	p.K343Sfs*3	ENST00000338641	NM_000268.3	342	gaG/ga	11/16	0.447002651066663	1	FACETS	0.984	0.866	1	0.984	0.866	1	CLONAL	1	TRUE	0	0.447002651066663	1		285	233	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	80	427	0				ENST00000310581	NM_198253.2	-/1132			0.593796188334009	4	FACETS	1	0.918	1	1	0.918	1	CLONAL	2	TRUE	2	0.668998806932086	4		427	195	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0046540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	416	757	1	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.365616316965772	6	FACETS	0.974	0.931	1	0.974	0.931	1	INDETERMINATE	3	TRUE	3	0.668998806932086	6		758	995	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455097	50455097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	177	270	0	ENST00000331340.3:c.644C>T	p.Ser215Phe	p.S215F	ENST00000331340	NM_006060.4	215	tCt/tTt	6/8	0.668998806932086	5	FACETS	0.856	0.793	0.922	0.571	0.528	0.615	CLONAL	2	TRUE	2	0.668998806932086	5		270	619	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194902	29194902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750523072	NA	P-0046540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	216	556	0	ENST00000240100.2:c.826G>A	p.Val276Met	p.V276M	ENST00000240100	NM_001394.6	276	Gtg/Atg	4/4	0.668998806932086	3	FACETS	1	0.972	1	0.541	0.504	0.579	CLONAL	1	TRUE	1	0.668998806932086	3		556	797	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809863	36809863	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046540-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	171	350	0	ENST00000373129.3:c.742del	p.Arg248GlyfsTer94	p.R248Gfs*94	ENST00000373129	NM_032017.1	248	Cgg/gg	9/12	0.668998806932086	3	FACETS	1	0.962	1	0.534	0.493	0.576	CLONAL	1	TRUE	1	0.668998806932086	3		350	639	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs760043106	NA	P-0046541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	410	397	0	ENST00000269305.4:c.584T>A	p.Ile195Asn	p.I195N	ENST00000269305	NM_001126112.2	195	aTc/aAc	6/11	0.3758787969122	4	FACETS	0.951	0.927	0.974			1	INDETERMINATE	4	TRUE	NA	0.76283078049093	4		397	498	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	324	438	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.639471016824716	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.76283078049093	4		438	667	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249393	153249393	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	1247	608	0	ENST00000281708.4:c.1385C>T	p.Ser462Phe	p.S462F	ENST00000281708	NM_033632.3	462	tCc/tTc	9/12	0.76283078049093	10	FACETS	0.983	0.969	0.997			1	CLONAL	9	TRUE	NA	0.76283078049093	10		608	1497	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203626	108203626	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs863224440	NA	P-0046541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	147	143	0	ENST00000278616.4:c.7926A>C	p.Arg2642Ser	p.R2642S	ENST00000278616	NM_000051.3	2642	agA/agC	53/63	0.76283078049093	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.76283078049093	2		143	187	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110897	8110897	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs752882057	NA	P-0046541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	432	422	0	ENST00000585124.1:c.198C>A	p.Asp66Glu	p.D66E	ENST00000585124	NM_004217.3	66	gaC/gaA	4/9	0.3758787969122	4	FACETS	0.916	0.891	0.939			1	INDETERMINATE	4	TRUE	NA	0.76283078049093	4		422	545	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443405	187443418	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	TAGGGTTTCTCACC	TAGGGTTTCTCACC	-	novel	NA	P-0046541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	162	215	0	ENST00000232014.4:c.1709-1_1721del		p.X570_splice	ENST00000232014	NM_001130845.1	570		8/10	0.69121774249936	3	FACETS	0.934	0.874	0.995	0.934	0.874	0.995	CLONAL	2	TRUE	1	0.76283078049093	3		215	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0046542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	74	812	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.19	2		812	731	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486845	56486845	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	68	240	0	ENST00000267101.3:c.1259G>C	p.Gly420Ala	p.G420A	ENST00000267101	NM_001982.3	420	gGc/gCc	11/28	0.132524178389411	3	FACETS	1	0.97	1	0.71	0.618	0.809	CLONAL	1	TRUE	1	0.19	3		240	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0046543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	148	561	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.284120433637362	2	FACETS	0.763	0.701	0.827	0.763	0.701	0.827	SUBCLONAL	2	TRUE	0	0.370681157159792	2		561	523	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497756	120497756	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	73	348	0	ENST00000256646.2:c.2126C>G	p.Pro709Arg	p.P709R	ENST00000256646	NM_024408.3	709	cCc/cGc	13/34	0.353142467882813	3	FACETS	0.813	0.712	0.922	0.407	0.356	0.461	CLONAL	1	TRUE	1	0.370681157159792	3		348	574	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40871220	40871220	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0046543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	60	250	0	ENST00000428826.2:c.670A>T	p.Lys224Ter	p.K224*	ENST00000428826		224	Aaa/Taa	8/21	0.330836401511684	3	FACETS	0.911	0.788	1	0.304	0.262	0.349	CLONAL	1	TRUE	0	0.370681157159792	3		250	421	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120773	94120773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241267544	NA	P-0046543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	62	320	0	ENST00000369303.4:c.278G>A	p.Gly93Asp	p.G93D	ENST00000369303	NM_004440.3	93	gGc/gAc	3/17	0.363912610235725	4	FACETS	0.784	0.677	0.9	0.261	0.225	0.3	SUBCLONAL	1	TRUE	1	0.370681157159792	4		320	585	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185502	27185502	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	69	280	0	ENST00000380036.4:c.1202C>A	p.Thr401Lys	p.T401K	ENST00000380036	NM_000459.3	401	aCg/aAg	9/23	0.370681157159792	5	FACETS	0.862	0.75	0.983	0.287	0.25	0.328	CLONAL	1	TRUE	2	0.370681157159792	5		280	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0046544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	242	803	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.591028741243712	1	FACETS	0.97	0.913	1	0.97	0.913	1	CLONAL	1	TRUE	0	0.591028741243712	1		803	595	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0046544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	156	451	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.407706111080728	1	FACETS	0.849	0.785	0.914	0.849	0.785	0.914	CLONAL	1	TRUE	0	0.591028741243712	1		451	438	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089721	27089721	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0046544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	129	413	1	ENST00000324856.7:c.2677A>T	p.Lys893Ter	p.K893*	ENST00000324856	NM_006015.4	893	Aaa/Taa	8/20	0.407706111080728	1	FACETS	0.436	0.395	0.478	0.436	0.395	0.478	SUBCLONAL	1	TRUE	0	0.591028741243712	1		414	706	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243777011	243777011	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	33	250	0	ENST00000263826.5:c.658C>T	p.Arg220Cys	p.R220C	ENST00000263826	NM_005465.4	220	Cgt/Tgt	7/13	0.407706111080728	1	FACETS	0.279	0.228	0.336	0.279	0.228	0.336	SUBCLONAL	1	TRUE	0	0.591028741243712	1		250	282	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912200	114912200	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0046544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	172	313	0	ENST00000543371.1:c.1269+1G>T		p.X423_splice	ENST00000543371	NM_001198531.1	423			1	2	FACETS	0.997	0.922	1	0.997	0.922	1	CLONAL	1	TRUE	1	0.591028741243712	2		313	584	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528080	103528080	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	37	258	1	ENST00000355739.4:c.3388C>T	p.Gln1130Ter	p.Q1130*	ENST00000355739	NM_000123.3	1130	Cag/Tag	15/15	0.156240125020176	2	FACETS	0.244	0.2	0.292	0.122	0.1	0.146	INDETERMINATE	1	TRUE	0	0.591028741243712	2		259	514	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181782	56181782	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	80	172	0	ENST00000399503.3:c.4006A>C	p.Ser1336Arg	p.S1336R	ENST00000399503	NM_005921.1	1336	Agt/Cgt	17/20	0.341110612259052	1	FACETS	0.736	0.657	0.819	0.736	0.657	0.819	INDETERMINATE	1	TRUE	0	0.591028741243712	1		172	259	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436653	8436653	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	38	304	0	ENST00000356435.5:c.4025T>A	p.Leu1342His	p.L1342H	ENST00000356435		1342	cTt/cAt	24/35	0.539698794686688	1	FACETS	0.253	0.209	0.302	0.253	0.209	0.302	SUBCLONAL	1	TRUE	0	0.591028741243712	1		304	358	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0046545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	132	220	3	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.3	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.37	2		223	314	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0046545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	67	321	1	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	0.877	0.765	0.997	0.877	0.765	0.997	CLONAL	1	TRUE	1	0.37	2		322	413	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032093	10032093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367543123	NA	P-0046545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	106	386	0	ENST00000330684.3:c.730C>T	p.Arg244Cys	p.R244C	ENST00000330684	NM_001134407.1	244	Cgc/Tgc	3/13	1	2	FACETS	0.912	0.819	1	0.912	0.819	1	CLONAL	1	TRUE	1	0.37	2		386	628	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655479	67655479	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs769948988	NA	P-0046545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	69	302	0	ENST00000264010.4:c.1342C>T	p.Arg448Ter	p.R448*	ENST00000264010	NM_006565.3	448	Cga/Tga	7/12	1	2	FACETS	0.982	0.859	1	0.982	0.859	1	CLONAL	1	TRUE	1	0.37	2		302	380	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105913	27105913	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	109	325	0	ENST00000324856.7:c.5524del	p.Leu1842CysfsTer41	p.L1842Cfs*41	ENST00000324856	NM_006015.4	1842	Ctg/tg	20/20	1	2	FACETS	0.894	0.804	0.989	0.894	0.804	0.989	CLONAL	1	TRUE	1	0.37	2		325	659	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107098	27107098	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	127	387	0	ENST00000324856.7:c.6709del	p.Ala2237ArgfsTer30	p.A2237Rfs*30	ENST00000324856	NM_006015.4	2237	Gcg/cg	20/20	1	2	FACETS	0.964	0.875	1	0.964	0.875	1	CLONAL	1	TRUE	1	0.37	2		387	712	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469814	157469818	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGG	CCAGG	-	novel	NA	P-0046545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	119	531	0	ENST00000346085.5:c.2608_2612del	p.Pro870AlafsTer70	p.P870Afs*70	ENST00000346085	NM_020732.3	870	CCAGGg/g	9/20	1	2	FACETS	0.832	0.751	0.917	0.832	0.751	0.917	CLONAL	1	TRUE	1	0.37	2		531	773	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0046546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	38	239	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.319161904828808	2		239	226	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0046546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	180	672	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.314310700443516	3	FACETS	0.896	0.828	0.966	0.597	0.552	0.644	CLONAL	2	TRUE	0	0.319161904828808	3		672	730	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0046546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	59	494	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.319161904828808	3	FACETS	0.893	0.777	1	0.893	0.777	1	CLONAL	2	TRUE	1	0.319161904828808	3		494	240	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0046546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	15	388	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.271155651725491	0	FACETS	0.37	0.271	0.487			1	SUBCLONAL	1	TRUE	0	0.319161904828808	0		388	173	SUCCESS
APC	324	MSKCC	GRCh37	5	112175621	112175621	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	32	345	0	ENST00000257430.4:c.4330C>T	p.Gln1444Ter	p.Q1444*	ENST00000257430	NM_000038.5	1444	Caa/Taa	16/16	1	2	FACETS	0.891	0.728	1	0.891	0.728	1	CLONAL	1	TRUE	1	0.319161904828808	2		345	225	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95598962	95598962	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	41	383	0	ENST00000393063.1:c.197C>A	p.Thr66Asn	p.T66N	ENST00000393063	NM_030621.3	66	aCt/aAt	4/28	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.319161904828808	2		383	214	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799222	88799222	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	43	530	0	ENST00000360948.2:c.163C>G	p.Pro55Ala	p.P55A	ENST00000360948	NM_001012338.2	55	Ccc/Gcc	2/19	1	2	FACETS	0.654	0.548	0.771	0.654	0.548	0.771	SUBCLONAL	1	TRUE	1	0.319161904828808	2		530	412	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27228211	27228211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs752902883	NA	P-0046546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	62	516	0	ENST00000380036.4:c.3208C>A	p.Leu1070Ile	p.L1070I	ENST00000380036	NM_000459.3	1070	Cta/Ata	22/23	0.319161904828808	3	FACETS	0.984	0.861	1	0.984	0.861	1	CLONAL	2	TRUE	1	0.319161904828808	3		516	229	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0046547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	381	803	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.494956560198908	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.494956560198908	2		803	759	SUCCESS
APC	324	MSKCC	GRCh37	5	112175411	112175411	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	88	276	0	ENST00000257430.4:c.4120G>T	p.Glu1374Ter	p.E1374*	ENST00000257430	NM_000038.5	1374	Gaa/Taa	16/16	0.494956560198908	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.494956560198908	1		276	231	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105238778	105238778	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	71	652	0	ENST00000349310.3:c.1184G>T	p.Gly395Val	p.G395V	ENST00000349310	NM_001014432.1	395	gGc/gTc	13/15	0.392234984360889	1	FACETS	0.311	0.271	0.354	0.311	0.271	0.354	SUBCLONAL	1	TRUE	0	0.494956560198908	1		652	695	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220269	5220269	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0046547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	225	679	0	ENST00000357368.4:c.3549+2T>A		p.X1183_splice	ENST00000357368	NM_002850.3	1183			0.254465320344409	2	FACETS	0.758	0.711	0.806	0.758	0.711	0.806	INDETERMINATE	2	TRUE	0	0.494956560198908	2		679	600	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950688	79950688	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	146	218	0	ENST00000265081.6:c.142G>T	p.Asp48Tyr	p.D48Y	ENST00000265081	NM_002439.4	48	Gac/Tac	1/24	1	2	FACETS	0.928	0.861	0.995	1	0.992	1	CLONAL	2	TRUE	1	0.494956560198908	2		218	318	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0046548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	187	699	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.295588855485944	2	FACETS	0.936	0.868	1	0.936	0.868	1	CLONAL	2	FALSE	0	0.3	2		699	666	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18439791	18439791	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	47	341	0	ENST00000266497.5:c.689G>T	p.Cys230Phe	p.C230F	ENST00000266497		230	tGt/tTt	2/31	0.3	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	FALSE	0	0.3	1		341	240	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016655	12016655	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	96	380	0	ENST00000353533.5:c.791C>G	p.Ala264Gly	p.A264G	ENST00000353533	NM_003010.3	264	gCt/gGt	7/11	0.295588855485944	2	FACETS	0.991	0.892	1	0.991	0.892	1	CLONAL	2	FALSE	0	0.3	2		380	323	SUCCESS
APC	324	MSKCC	GRCh37	5	112175365	112175366	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0046548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	63	282	0	ENST00000257430.4:c.4074_4075del	p.Lys1359IlefsTer15	p.K1359Ifs*15	ENST00000257430	NM_000038.5	1358	gcGAaa/gcaa	16/16	0.295588855485944	2	FACETS	0.875	0.766	0.99	0.875	0.766	0.99	CLONAL	2	FALSE	0	0.3	2		282	240	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577563	64577563	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	338	320	0	ENST00000312049.6:c.19C>T	p.Gln7Ter	p.Q7*	ENST00000312049	NM_130799.2	7	Cag/Tag	2/10	0.892205804272211	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.892205804272211	1		320	415	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47129614	47129614	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	229	349	0	ENST00000409792.3:c.5266G>T	p.Glu1756Ter	p.E1756*	ENST00000409792	NM_014159.6	1756	Gaa/Taa	10/21	0.884486051892024	1	FACETS	0.932	0.895	0.968	0.932	0.895	0.968	CLONAL	1	TRUE	0	0.892205804272211	1		349	305	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968975	15968975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	151	402	0	ENST00000268712.3:c.4775C>T	p.Ser1592Leu	p.S1592L	ENST00000268712	NM_006311.3	1592	tCa/tTa	33/46	1	2	FACETS	0.473	0.433	0.514	0.473	0.433	0.514	SUBCLONAL	1	TRUE	1	0.892205804272211	2		402	716	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891196	101891196	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	232	345	0	ENST00000374994.4:c.157C>A	p.Leu53Ile	p.L53I	ENST00000374994	NM_004612.2	53	Ctc/Atc	2/9	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.892205804272211	2		345	501	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	protein_altering_variant	In_Frame_Ins	INS	G	G	TGTGGGC	novel	NA	P-0046549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	519	603	0	ENST00000269305.4:c.535delinsGCCCACA	p.His179delinsAlaHisAsn	p.H179delinsAHN	ENST00000269305	NM_001126112.2	179	Cat/GCCCACAat	5/11	1	2	FACETS	0.914	0.877	0.951	0.914	0.877	0.951	CLONAL	1	TRUE	1	0.892205804272211	2		603	1273	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	108	427	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.973	1	1	0.99	1	CLONAL	2	FALSE	1	0.372850751353186	2		427	249	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205217	46205217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	32	346	0	ENST00000334344.6:c.301G>A	p.Glu101Lys	p.E101K	ENST00000334344	NM_152641.2	101	Gag/Aag	4/21	1	2	FACETS	1	0.882	1	1	0.967	1	CLONAL	2	FALSE	1	0.372850751353186	2		346	81	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059213	27059213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	90	520	1	ENST00000324856.7:c.1850C>T	p.Ser617Leu	p.S617L	ENST00000324856	NM_006015.4	617	tCa/tTa	4/20	1	2	FACETS	1	0.94	1	1	0.988	1	CLONAL	2	FALSE	1	0.372850751353186	2		521	229	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247875	59247875	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	248	670	2	ENST00000371222.2:c.868C>T	p.Gln290Ter	p.Q290*	ENST00000371222	NM_002228.3	290	Cag/Tag	1/1	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	FALSE	1	0.372850751353186	2		672	581	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984398	201984398	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	261	661	0	ENST00000359651.3:c.1063G>C	p.Gly355Arg	p.G355R	ENST00000359651		355	Ggc/Cgc	8/8	1	2	FACETS	1	0.985	1	1	0.996	1	CLONAL	2	FALSE	1	0.372850751353186	2		661	622	SUCCESS
EED	8726	MSKCC	GRCh37	11	85956278	85956278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	77	212	0	ENST00000263360.6:c.7G>A	p.Glu3Lys	p.E3K	ENST00000263360	NM_003797.3	3	Gag/Aag	1/12	1	2	FACETS	1	0.968	1	1	0.987	1	CLONAL	2	FALSE	1	0.372850751353186	2		212	172	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999618	100999618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762965993	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	199	811	1	ENST00000325455.5:c.184C>T	p.Arg62Trp	p.R62W	ENST00000325455	NM_001202474.3	62	Cgg/Tgg	1/8	1	2	FACETS	1	0.983	1	1	0.994	1	CLONAL	2	FALSE	1	0.372850751353186	2		812	465	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111957681	111957681	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	152	544	0	ENST00000375549.3:c.50G>A	p.Arg17Gln	p.R17Q	ENST00000375549	NM_003002.3	17	cGa/cAa	1/4	1	2	FACETS	0.877	0.808	0.947	1	0.991	1	CLONAL	2	FALSE	1	0.372850751353186	2		544	465	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383225	4383225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	90	476	0	ENST00000261254.3:c.19G>A	p.Glu7Lys	p.E7K	ENST00000261254	NM_001759.3	7	Gag/Aag	1/5	0.32131834211294	1	FACETS	0.755	0.68	0.833	1	0.982	1	SUBCLONAL	2	FALSE	0	0.372850751353186	1		476	260	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871780	12871780	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500189	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	53	222	0	ENST00000228872.4:c.497G>A	p.Arg166Lys	p.R166K	ENST00000228872	NM_004064.3	166	aGa/aAa	2/3	1	2	FACETS	0.994	0.869	1	1	0.978	1	CLONAL	2	FALSE	1	0.372850751353186	2		222	143	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243430	46243430	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	25	367	0	ENST00000334344.6:c.1783C>T	p.His595Tyr	p.H595Y	ENST00000334344	NM_152641.2	595	Cat/Tat	14/21	1	2	FACETS	1	0.874	1	1	0.959	1	CLONAL	2	FALSE	1	0.372850751353186	2		367	62	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431598	49431598	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	200	758	0	ENST00000301067.7:c.9541G>A	p.Glu3181Lys	p.E3181K	ENST00000301067	NM_003482.3	3181	Gag/Aag	34/54	0.372850751353186	4	FACETS	0.994	0.93	1	1	0.992	1	CLONAL	3	FALSE	2	0.372850751353186	4		758	494	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26927925	26927925	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	32	289	0	ENST00000381527.3:c.364C>T	p.Gln122Ter	p.Q122*	ENST00000381527	NM_001260.1	122	Cag/Tag	4/13	1	2	FACETS	1	0.922	1	1	0.969	1	CLONAL	2	FALSE	1	0.372850751353186	2		289	74	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061621	38061621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	88	167	0	ENST00000250448.2:c.368C>T	p.Ser123Phe	p.S123F	ENST00000250448	NM_004496.3	123	tCc/tTc	2/2	1	2	FACETS	1	0.906	1	1	0.987	1	CLONAL	2	FALSE	1	0.372850751353186	2		167	235	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023121	33023121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	85	593	2	ENST00000300177.4:c.230G>A	p.Ser77Asn	p.S77N	ENST00000300177	NM_001191322.1	77	aGc/aAc	2/2	1	2	FACETS	0.974	0.876	1	1	0.986	1	CLONAL	2	FALSE	1	0.372850751353186	2		595	234	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66779604	66779604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	85	433	0	ENST00000307102.5:c.934G>A	p.Glu312Lys	p.E312K	ENST00000307102	NM_002755.3	312	Gag/Aag	8/11	1	2	FACETS	1	0.963	1	1	0.988	1	CLONAL	2	FALSE	1	0.372850751353186	2		433	200	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293213	91293213	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200756519	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	39	424	0	ENST00000355112.3:c.715G>A	p.Asp239Asn	p.D239N	ENST00000355112	NM_000057.2	239	Gat/Aat	3/22	1	2	FACETS	1	0.894	1	1	0.973	1	CLONAL	2	FALSE	1	0.372850751353186	2		424	99	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639551	3639551	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	219	837	0	ENST00000294008.3:c.4088C>T	p.Ser1363Leu	p.S1363L	ENST00000294008	NM_032444.2	1363	tCa/tTa	12/15	1	2	FACETS	0.952	0.891	1	1	0.994	1	CLONAL	2	FALSE	1	0.372850751353186	2		837	617	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641214	3641214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs546657275	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	240	788	1	ENST00000294008.3:c.2425G>A	p.Glu809Lys	p.E809K	ENST00000294008	NM_032444.2	809	Gaa/Aaa	12/15	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	FALSE	1	0.372850751353186	2		789	564	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3794916	3794916	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	71	398	1	ENST00000262367.5:c.3961G>T	p.Glu1321Ter	p.E1321*	ENST00000262367	NM_004380.2	1321	Gaa/Taa	23/31	1	2	FACETS	1	0.967	1	1	0.986	1	CLONAL	2	FALSE	1	0.372850751353186	2		399	157	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348891	11348891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760173376	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	106	254	0	ENST00000332029.2:c.445G>A	p.Glu149Lys	p.E149K	ENST00000332029	NM_003745.1	149	Gag/Aag	2/2	1	2	FACETS	1	0.957	1	1	0.99	1	CLONAL	2	FALSE	1	0.372850751353186	2		254	263	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14016015	14016015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	25	244	0	ENST00000311895.7:c.335G>A	p.Arg112Lys	p.R112K	ENST00000311895	NM_005236.2	112	aGg/aAg	2/11	1	2	FACETS	0.931	0.76	1	1	0.953	1	CLONAL	2	FALSE	1	0.372850751353186	2		244	72	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351253	89351253	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	150	714	0	ENST00000301030.4:c.1697C>T	p.Ser566Leu	p.S566L	ENST00000301030	NM_001256183.1	566	tCa/tTa	9/13	1	2	FACETS	1	0.976	1	1	0.993	1	CLONAL	2	FALSE	1	0.372850751353186	2		714	358	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	200	667	0	ENST00000269571.5:c.829G>T	p.Asp277Tyr	p.D277Y	ENST00000269571		277	Gac/Tac	7/27	1	2	FACETS	1	0.957	1	1	0.994	1	CLONAL	2	FALSE	1	0.372850751353186	2		667	520	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	246	552	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	FALSE	1	0.372850751353186	2		552	572	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883728	37883728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	238	955	0	ENST00000269571.5:c.3340G>A	p.Glu1114Lys	p.E1114K	ENST00000269571		1114	Gag/Aag	26/27	1	2	FACETS	0.9	0.844	0.957	1	0.994	1	CLONAL	2	FALSE	1	0.372850751353186	2		955	709	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244157	41244157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555587816	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	45	491	0	ENST00000357654.3:c.3391G>A	p.Asp1131Asn	p.D1131N	ENST00000357654	NM_007294.3	1131	Gat/Aat	10/23	1	2	FACETS	0.838	0.731	0.946	1	0.979	1	CLONAL	3	FALSE	1	0.372850751353186	2		491	96	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246539	41246539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	74	583	0	ENST00000357654.3:c.1009G>A	p.Glu337Lys	p.E337K	ENST00000357654	NM_007294.3	337	Gaa/Aaa	10/23	1	2	FACETS	1	0.97	1	1	0.987	1	CLONAL	2	FALSE	1	0.372850751353186	2		583	162	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774771	73774771	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	124	455	2	ENST00000254810.4:c.316G>A	p.Glu106Lys	p.E106K	ENST00000254810	NM_005324.3	106	Gaa/Aaa	4/4	1	2	FACETS	0.921	0.843	1	1	0.99	1	CLONAL	2	FALSE	1	0.372850751353186	2		457	361	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56339023	56339023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	70	105	1	ENST00000348428.3:c.148G>A	p.Glu50Lys	p.E50K	ENST00000348428	NM_006785.3	50	Gag/Aag	1/17	1	2	FACETS	0.834	0.739	0.934	1	0.98	1	CLONAL	2	FALSE	1	0.372850751353186	2		106	225	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054560	13054560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167230978	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	84	471	0	ENST00000316448.5:c.1087G>A	p.Glu363Lys	p.E363K	ENST00000316448	NM_004343.3	363	Gag/Aag	9/9	1	2	FACETS	0.905	0.811	1	1	0.985	1	CLONAL	2	FALSE	1	0.372850751353186	2		471	249	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303666	30303666	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	191	476	0	ENST00000262643.3:c.94A>T	p.Lys32Ter	p.K32*	ENST00000262643	NM_001238.2	32	Aag/Tag	3/12	1	2	FACETS	1	0.976	1	1	0.994	1	CLONAL	2	FALSE	1	0.372850751353186	2		476	469	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860557	45860557	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	256	788	0	ENST00000391945.4:c.1450A>G	p.Thr484Ala	p.T484A	ENST00000391945	NM_000400.3	484	Acg/Gcg	15/23	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	FALSE	1	0.372850751353186	2		788	591	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445244	29445244	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145194836	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	102	1051	1	ENST00000389048.3:c.3481G>A	p.Glu1161Lys	p.E1161K	ENST00000389048	NM_004304.4	1161	Gaa/Aaa	22/29	1	2	FACETS	0.943	0.856	1	1	0.988	1	CLONAL	2	FALSE	1	0.372850751353186	2		1052	290	SUCCESS
ALK	238	MSKCC	GRCh37	2	29448386	29448386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	254	791	0	ENST00000389048.3:c.3113C>T	p.Ser1038Phe	p.S1038F	ENST00000389048	NM_004304.4	1038	tCt/tTt	19/29	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	FALSE	1	0.372850751353186	2		791	565	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605065	46605065	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	281	854	0	ENST00000263734.3:c.1282G>T	p.Gly428Cys	p.G428C	ENST00000263734	NM_001430.4	428	Ggc/Tgc	10/16	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	FALSE	1	0.372850751353186	2		854	631	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96931044	96931049	+	inframe_deletion	In_Frame_Del	DEL	GCTTGG	GCTTGG	-	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	77	233	0	ENST00000258439.3:c.71_76del	p.Pro24_Lys25del	p.P24_K25del	ENST00000258439	NM_001193304.2	24	cCCAAGCag/cag	2/4	1	2	FACETS	0.956	0.854	1	1	0.984	1	CLONAL	2	FALSE	1	0.372850751353186	2		233	216	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149715	202149715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	102	552	0	ENST00000358485.4:c.1156G>A	p.Asp386Asn	p.D386N	ENST00000358485	NM_001080125.1	386	Gat/Aat	8/9	1	2	FACETS	1	0.959	1	1	0.989	1	CLONAL	2	FALSE	1	0.372850751353186	2		552	250	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989521	212989521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	64	402	0	ENST00000342788.4:c.190G>A	p.Glu64Lys	p.E64K	ENST00000342788	NM_005235.2	64	Gag/Aag	2/28	1	2	FACETS	1	0.929	1	1	0.983	1	CLONAL	2	FALSE	1	0.372850751353186	2		402	161	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989592	212989592	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	32	336	1	ENST00000342788.4:c.119C>T	p.Ser40Phe	p.S40F	ENST00000342788	NM_005235.2	40	tCt/tTt	2/28	1	2	FACETS	0.876	0.731	1	1	0.96	1	CLONAL	2	FALSE	1	0.372850751353186	2		337	98	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400262	225400262	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	24	208	0	ENST00000264414.4:c.361G>A	p.Asp121Asn	p.D121N	ENST00000264414	NM_003590.4	121	Gac/Aac	3/16	1	2	FACETS	0.825	0.666	0.996	1	0.944	1	CLONAL	2	FALSE	1	0.372850751353186	2		208	78	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660831	227660831	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs555150176	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	116	639	1	ENST00000305123.5:c.2624G>A	p.Arg875Gln	p.R875Q	ENST00000305123	NM_005544.2	875	cGa/cAa	1/2	1	2	FACETS	1	0.955	1	1	0.99	1	CLONAL	2	FALSE	1	0.372850751353186	2		640	292	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663157	227663157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs570775459	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	204	732	0	ENST00000305123.5:c.298G>A	p.Glu100Lys	p.E100K	ENST00000305123	NM_005544.2	100	Gag/Aag	1/2	1	2	FACETS	1	0.975	1	1	0.994	1	CLONAL	2	FALSE	1	0.372850751353186	2		732	507	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022824	31022824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	110	591	0	ENST00000375687.4:c.2309C>T	p.Ser770Leu	p.S770L	ENST00000375687	NM_015338.5	770	tCa/tTa	13/13	1	2	FACETS	1	0.926	1	1	0.99	1	CLONAL	2	FALSE	1	0.372850751353186	2		591	290	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968335	134968335	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	85	565	0	ENST00000398015.3:c.2846+2T>A		p.X949_splice	ENST00000398015	NM_004441.4	949			1	2	FACETS	0.927	0.832	1	1	0.985	1	CLONAL	2	FALSE	1	0.372850751353186	2		565	246	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430868	181430868	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	184	863	0	ENST00000325404.1:c.720G>A	p.Met240Ile	p.M240I	ENST00000325404	NM_003106.3	240	atG/atA	1/1	1	2	FACETS	1	0.954	1	1	0.994	1	CLONAL	2	FALSE	1	0.372850751353186	2		863	479	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245402	153245402	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	59	559	1	ENST00000281708.4:c.1789G>A	p.Gly597Arg	p.G597R	ENST00000281708	NM_033632.3	597	Ggg/Agg	11/12	1	2	FACETS	0.837	0.744	0.931	1	0.984	1	CLONAL	3	FALSE	1	0.372850751353186	2		560	126	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250850	153250850	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	16	374	0	ENST00000281708.4:c.1210A>T	p.Lys404Ter	p.K404*	ENST00000281708	NM_033632.3	404	Aaa/Taa	8/12	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	FALSE	1	0.372850751353186	2		374	70	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958879	38958879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	22	234	0	ENST00000357387.3:c.2233G>A	p.Glu745Lys	p.E745K	ENST00000357387	NM_152756.3	745	Gaa/Aaa	23/38	1	2	FACETS	0.855	0.702	1	1	0.959	1	CLONAL	3	FALSE	1	0.372850751353186	2		234	46	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505133	149505133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1375143929	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	140	500	0	ENST00000261799.4:c.1682G>A	p.Arg561His	p.R561H	ENST00000261799	NM_002609.3	561	cGt/cAt	12/23	1	2	FACETS	1	0.96	1	1	0.992	1	CLONAL	2	FALSE	1	0.372850751353186	2		500	353	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021009	26021009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	142	502	0	ENST00000357647.3:c.292G>A	p.Glu98Lys	p.E98K	ENST00000357647	NM_003529.2	98	Gag/Aag	1/1	1	2	FACETS	1	0.957	1	1	0.992	1	CLONAL	2	FALSE	1	0.372850751353186	2		502	361	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197259	26197259	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	128	587	0	ENST00000356476.2:c.220G>A	p.Glu74Lys	p.E74K	ENST00000356476		74	Gag/Aag	1/1	1	2	FACETS	0.975	0.895	1	1	0.991	1	CLONAL	2	FALSE	1	0.372850751353186	2		587	352	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983870	2983870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	193	679	0	ENST00000396946.4:c.660G>A	p.Met220Ile	p.M220I	ENST00000396946	NM_032415.4	220	atG/atA	5/25	1	2	FACETS	1	0.982	1	1	0.994	1	CLONAL	2	FALSE	1	0.372850751353186	2		679	457	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380970	116380970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	153	577	0	ENST00000397752.3:c.1592C>T	p.Ser531Phe	p.S531F	ENST00000397752	NM_000245.2	531	tCt/tTt	5/21	1	2	FACETS	1	0.975	1	1	0.993	1	CLONAL	2	FALSE	1	0.372850751353186	2		577	367	SUCCESS
MET	4233	MSKCC	GRCh37	7	116409717	116409717	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	18	187	0	ENST00000397752.3:c.2602G>A	p.Glu868Lys	p.E868K	ENST00000397752	NM_000245.2	868	Gaa/Aaa	12/21	1	2	FACETS	1	0.898	1	1	0.949	1	CLONAL	2	FALSE	1	0.372850751353186	2		187	39	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879508	151879508	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	51	452	0	ENST00000262189.6:c.5437C>T	p.Gln1813Ter	p.Q1813*	ENST00000262189	NM_170606.2	1813	Cag/Tag	36/59	1	2	FACETS	0.937	0.815	1	1	0.976	1	CLONAL	2	FALSE	1	0.372850751353186	2		452	146	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287398	38287398	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778531708	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	173	774	0	ENST00000425967.3:c.259C>T	p.Arg87Cys	p.R87C	ENST00000425967	NM_001174067.1	87	Cgc/Tgc	4/19	0.134030821459823	0	FACETS	0.711	0.663	0.761			1	INDETERMINATE	2	FALSE	0	0.372850751353186	0		774	409	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104597	69104597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776501034	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	97	717	0	ENST00000288368.4:c.4441G>A	p.Glu1481Lys	p.E1481K	ENST00000288368	NM_024870.2	1481	Gaa/Aaa	37/40	0.372850751353186	6	FACETS	1	0.959	1	0.453	0.407	0.502	CLONAL	2	FALSE	1	0.372850751353186	6		717	401	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225896	53225896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	218	364	0	ENST00000375401.3:c.2953G>A	p.Glu985Lys	p.E985K	ENST00000375401	NM_004187.3	985	Gag/Aag	19/26	0.268940200804074	2	FACETS	1	0.985	1			1	CLONAL	4	FALSE	NA	0.372850751353186	2		364	278	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347265	70347265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	155	288	1	ENST00000374080.3:c.2929G>A	p.Asp977Asn	p.D977N	ENST00000374080		977	Gat/Aat	21/45	0.268940200804074	2	FACETS	1	0.988	1			1	CLONAL	4	FALSE	NA	0.372850751353186	2		289	189	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220440	123220440	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1569520709	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	54	297	0	ENST00000218089.9:c.3097C>T	p.Arg1033Ter	p.R1033*	ENST00000218089	NM_001042749.1	1033	Cga/Tga	30/35	0.268940200804074	2	FACETS	1	0.951	1			1	CLONAL	4	FALSE	NA	0.372850751353186	2		297	69	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224449	123224449	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747270306	NA	P-0046551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	46	240	0	ENST00000218089.9:c.3302G>A	p.Ser1101Asn	p.S1101N	ENST00000218089	NM_001042749.1	1101	aGt/aAt	31/35	0.268940200804074	2	FACETS	0.995	0.902	1			1	CLONAL	4	FALSE	NA	0.372850751353186	2		240	62	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573478	48573479	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0046552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	67	227	0	ENST00000342988.3:c.63_64del	p.His21GlnfsTer6	p.H21Qfs*6	ENST00000342988	NM_005359.5	21	cAT/c	2/12	0.673083852267628	1	FACETS	0.978	0.878	1	0.978	0.878	1	CLONAL	1	TRUE	0	0.673083852267628	1		227	135	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134251	11134251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218643327	NA	P-0046552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	490	575	1	ENST00000358026.2:c.2917C>T	p.Arg973Trp	p.R973W	ENST00000358026	NM_001128849.1	973	Cgg/Tgg	20/36	0.673083852267628	3	FACETS	0.978	0.94	1	0.978	0.94	1	CLONAL	2	TRUE	1	0.673083852267628	3		576	995	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81528563	81528563	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	49	229	0	ENST00000298171.2:c.242T>G	p.Ile81Ser	p.I81S	ENST00000298171	NM_000369.2	81	aTc/aGc	2/10	1	2	FACETS	0.964	0.834	1	0.964	0.834	1	CLONAL	1	TRUE	1	0.673083852267628	2		229	151	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577112	7577113	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0046552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	273	623	0	ENST00000269305.4:c.825_826del	p.Ala276LeufsTer29	p.A276Lfs*29	ENST00000269305	NM_001126112.2	275	tgTGcc/tgcc	8/11	0.673083852267628	1	FACETS	0.993	0.943	1	0.993	0.943	1	CLONAL	1	TRUE	0	0.673083852267628	1		623	542	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562935	29562935	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0046552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	212	359	0	ENST00000356175.3:c.3871-1G>T		p.X1291_splice	ENST00000356175	NM_000267.3	1291			0.669918197099999	2	FACETS	0.987	0.94	1	0.987	0.94	1	CLONAL	2	TRUE	0	0.673083852267628	2		359	319	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492731	56492731	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	450	500	0	ENST00000407977.2:c.208G>C	p.Ala70Pro	p.A70P	ENST00000407977		70	Gct/Cct	2/10	0.655992544454023	3	FACETS	0.949	0.92	0.977	0.949	0.92	0.977	CLONAL	3	TRUE	0	0.673083852267628	3		500	628	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031656	36031656	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2079	273	744	0	ENST00000358208.4:c.1485C>G	p.His495Gln	p.H495Q	ENST00000358208		495	caC/caG	12/12	0.673083852267628	7	FACETS	0.925	0.864	0.989			1	CLONAL	1	TRUE	NA	0.673083852267628	7		744	2352	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323207	31323207	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	44	605	0	ENST00000412585.2:c.782G>C	p.Gly261Ala	p.G261A	ENST00000412585	NM_005514.6	261	gGa/gCa	4/8	1	2	FACETS	0.158	0.132	0.187	0.158	0.132	0.187	SUBCLONAL	1	TRUE	1	0.673083852267628	2		605	828	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393591	139393591	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs3812597	NA	P-0046552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	367	748	2	ENST00000277541.6:c.6055G>T	p.Ala2019Ser	p.A2019S	ENST00000277541	NM_017617.3	2019	Gcc/Tcc	32/34	0.26697488452407	3	FACETS	1	0.995	1	0.738	0.702	0.775	INDETERMINATE	1	TRUE	1	0.673083852267628	3		750	987	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982099	201982107	+	frameshift_variant	Frame_Shift_Del	DEL	ACTCCTCAG	ACTCCTCAG	C	novel	NA	P-0046552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	208	625	0	ENST00000359651.3:c.623_631delinsC	p.His208ProfsTer6	p.H208Pfs*6	ENST00000359651		208	cACTCCTCAGac/cCac	5/8	1	2	FACETS	0.854	0.795	0.914	0.854	0.795	0.914	CLONAL	1	TRUE	1	0.673083852267628	2		625	724	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0046560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	339	572	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.742975066845521	6	FACETS	1	0.972	1			1	CLONAL	5	TRUE	NA	0.742975066845521	6		572	451	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106074	8106075	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0046560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	175	535	0	ENST00000346208.3:c.898dup	p.Leu300ProfsTer3	p.L300Pfs*3	ENST00000346208		298	-/C	4/6	1	2	FACETS	0.996	0.926	1	0.996	0.926	1	CLONAL	1	TRUE	1	0.742975066845521	2		535	473	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125513705	125513705	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	80	399	0	ENST00000428830.2:c.833T>A	p.Val278Asp	p.V278D	ENST00000428830	NM_001114121.2	278	gTc/gAc	9/14	NA	2	FACETS	0.992	0.89	1			1	INDETERMINATE	1	TRUE	NA	0.742975066845521	2		399	217	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849269	89849269	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	136	577	0	ENST00000389301.3:c.1624G>C	p.Glu542Gln	p.E542Q	ENST00000389301	NM_000135.2	542	Gag/Cag	17/43	0.701576770781833	2	FACETS	0.88	0.808	0.954	0.44	0.404	0.477	CLONAL	1	TRUE	0	0.742975066845521	2		577	416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0046560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	231	814	0	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	0.742975066845521	1	FACETS	0.958	0.908	1	0.958	0.908	1	CLONAL	1	TRUE	0	0.742975066845521	1		814	408	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214646	5214646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	234	981	0	ENST00000357368.4:c.4420G>A	p.Asp1474Asn	p.D1474N	ENST00000357368	NM_002850.3	1474	Gac/Aac	29/38	0.742975066845521	3	FACETS	0.996	0.931	1	0.498	0.465	0.532	CLONAL	1	TRUE	1	0.742975066845521	3		981	867	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222841	5222841	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	126	307	0	ENST00000357368.4:c.2962G>A	p.Glu988Lys	p.E988K	ENST00000357368	NM_002850.3	988	Gag/Aag	18/38	NA	2	FACETS	1	0.961	1			1	INDETERMINATE	1	TRUE	NA	0.742975066845521	2		307	315	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223186	5223186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	184	705	0	ENST00000357368.4:c.2617G>A	p.Glu873Lys	p.E873K	ENST00000357368	NM_002850.3	873	Gag/Aag	18/38	NA	2	FACETS	0.954	0.888	1			1	INDETERMINATE	1	TRUE	NA	0.742975066845521	2		705	519	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5225855	5225856	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TA	novel	NA	P-0046560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	213	746	0	ENST00000357368.4:c.2377-1_2377delinsTA		p.X793_splice	ENST00000357368	NM_002850.3	793		17/38	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.742975066845521	2		746	542	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229552	5229552	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	57	121	0	ENST00000357368.4:c.2299G>T	p.Glu767Ter	p.E767*	ENST00000357368	NM_002850.3	767	Gag/Tag	15/38	NA	2	FACETS	0.76	0.68	0.837			1	INDETERMINATE	2	TRUE	NA	0.742975066845521	2		121	101	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671263	30671263	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	353	647	0	ENST00000376406.3:c.5614G>C	p.Glu1872Gln	p.E1872Q	ENST00000376406	NM_014641.2	1872	Gag/Cag	11/15	0.742975066845521	3	FACETS	0.958	0.916	1	0.958	0.916	1	CLONAL	2	TRUE	1	0.742975066845521	3		647	680	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864788	117864788	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	122	343	0	ENST00000297338.2:c.1321G>A	p.Asp441Asn	p.D441N	ENST00000297338	NM_006265.2	441	Gat/Aat	10/14	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.742975066845521	2		343	268	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403423	139403423	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046560-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	226	995	0	ENST00000277541.6:c.3070G>A	p.Glu1024Lys	p.E1024K	ENST00000277541	NM_017617.3	1024	Gag/Aag	19/34	0.742975066845521	3	FACETS	0.9	0.839	0.963	0.45	0.419	0.482	CLONAL	1	TRUE	1	0.742975066845521	3		995	927	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0046561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	31	594	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	0.449	0.363	0.547	0.449	0.363	0.547	SUBCLONAL	1	FALSE	1	0.28699203667236	2		594	481	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604717	48604717	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	58	441	0	ENST00000342988.3:c.1541del	p.Pro514GlnfsTer23	p.P514Qfs*23	ENST00000342988	NM_005359.5	513	taC/ta	12/12	0.28699203667236	3	FACETS	0.805	0.697	0.921	0.805	0.697	0.921	CLONAL	2	FALSE	1	0.28699203667236	3		441	287	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034984	42034984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	23	617	0	ENST00000219905.7:c.4826C>T	p.Thr1609Ile	p.T1609I	ENST00000219905	NM_001164273.1	1609	aCt/aTt	15/24	1	2	FACETS	0.529	0.413	0.663	0.529	0.413	0.663	SUBCLONAL	1	FALSE	1	0.28699203667236	2		617	303	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46596966	46596966	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	17	406	0	ENST00000263734.3:c.781del	p.Ile261SerfsTer4	p.I261Sfs*4	ENST00000263734	NM_001430.4	260	agA/ag	7/16	0.28699203667236	3	FACETS	0.529	0.395	0.688	0.265	0.197	0.344	SUBCLONAL	1	FALSE	1	0.28699203667236	3		406	256	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	24	593	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.185	0.144	0.233	0.185	0.144	0.233	SUBCLONAL	1	TRUE	1	0.36383058098684	2		593	713	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188397	142188397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1169255490	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	31	301	0	ENST00000350721.4:c.6334C>T	p.Arg2112Cys	p.R2112C	ENST00000350721	NM_001184.3	2112	Cgt/Tgt	38/47	1	2	FACETS	0.775	0.631	0.935	0.775	0.631	0.935	CLONAL	1	TRUE	1	0.36383058098684	2		301	220	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164951	47164951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769535379	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	38	235	0	ENST00000409792.3:c.1175C>T	p.Ser392Phe	p.S392F	ENST00000409792	NM_014159.6	392	tCc/tTc	3/21	1	2	FACETS	0.985	0.822	1	0.985	0.822	1	CLONAL	1	TRUE	1	0.36383058098684	2		235	212	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	41	289	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	1	2	FACETS	0.86	0.721	1	0.86	0.721	1	CLONAL	1	TRUE	1	0.36383058098684	2		289	262	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270180	66270180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763063348	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	16	224	1	ENST00000273854.3:c.1702G>A	p.Asp568Asn	p.D568N	ENST00000273854	NM_004439.5	568	Gat/Aat	8/18	1	2	FACETS	0.35	0.259	0.46	0.35	0.259	0.46	SUBCLONAL	1	TRUE	1	0.36383058098684	2		225	251	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116179	209116179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555882127	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	71	327	0	ENST00000345146.2:c.97C>T	p.Pro33Ser	p.P33S	ENST00000345146	NM_005896.2	33	Ccc/Tcc	3/10	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.36383058098684	2		327	339	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983275	149983275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	137	967	4	ENST00000253339.5:c.2983C>T	p.Arg995Cys	p.R995C	ENST00000253339		995	Cgc/Tgc	7/7	0.0882598201227975	3	FACETS	1	0.954	1	1	0.954	1	INDETERMINATE	2	TRUE	1	0.36383058098684	3		971	421	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407527	407527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs908661692	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	22	330	0	ENST00000380956.4:c.1285G>A	p.Asp429Asn	p.D429N	ENST00000380956	NM_001195286.1	429	Gat/Aat	9/9	1	2	FACETS	0.386	0.299	0.487	0.386	0.299	0.487	SUBCLONAL	1	TRUE	1	0.36383058098684	2		330	313	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149683	202149683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762734568	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	50	502	0	ENST00000358485.4:c.1124C>T	p.Ser375Phe	p.S375F	ENST00000358485	NM_001080125.1	375	tCc/tTc	8/9	1	2	FACETS	0.558	0.473	0.65	0.558	0.473	0.65	SUBCLONAL	1	TRUE	1	0.36383058098684	2		502	493	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467824	66467824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	43	291	0	ENST00000273854.3:c.445G>A	p.Glu149Lys	p.E149K	ENST00000273854	NM_004439.5	149	Gaa/Aaa	3/18	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.36383058098684	2		291	190	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562951	21562951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761920534	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	106	442	0	ENST00000382592.4:c.968C>T	p.Pro323Leu	p.P323L	ENST00000382592	NM_014572.2	323	cCc/cTc	4/8	NA	2	FACETS	0.998	0.897	1			1	INDETERMINATE	1	TRUE	NA	0.36383058098684	2		442	584	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161330	55161330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	26	434	0	ENST00000257290.5:c.3161C>T	p.Ser1054Phe	p.S1054F	ENST00000257290	NM_006206.4	1054	tCc/tTc	23/23	1	2	FACETS	0.335	0.265	0.415	0.335	0.265	0.415	SUBCLONAL	1	TRUE	1	0.36383058098684	2		434	427	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346574	81346574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	45	249	0	ENST00000222390.5:c.1379C>T	p.Pro460Leu	p.P460L	ENST00000222390	NM_000601.4	460	cCt/cTt	11/18	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.36383058098684	2		249	232	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742814	17742814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	135	662	0	ENST00000250003.3:c.722G>A	p.Gly241Glu	p.G241E	ENST00000250003	NM_002478.4	241	gGg/gAg	3/3	0.36383058098684	0	FACETS	1	0.943	1			1	CLONAL	1	TRUE	0	0.36383058098684	0		662	455	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259197	89259197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	60	363	0	ENST00000336596.2:c.341G>A	p.Gly114Glu	p.G114E	ENST00000336596	NM_005233.5	114	gGa/gAa	3/17	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.36383058098684	2		363	305	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955863	55955863	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868047715	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	34	307	0	ENST00000263923.4:c.3299C>T	p.Ser1100Phe	p.S1100F	ENST00000263923	NM_002253.2	1100	tCc/tTc	24/30	1	2	FACETS	0.834	0.687	0.998	0.834	0.687	0.998	CLONAL	1	TRUE	1	0.36383058098684	2		307	224	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73334683	73334683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	43	230	0	ENST00000377767.4:c.2777C>T	p.Ser926Phe	p.S926F	ENST00000377767	NM_014953.3	926	tCc/tTc	20/21	1	2	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	1	0.36383058098684	2		230	234	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460582	149460582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	89	599	0	ENST00000286301.3:c.55G>A	p.Gly19Arg	p.G19R	ENST00000286301	NM_005211.3	19	Gga/Aga	3/22	1	2	FACETS	0.88	0.782	0.984	0.88	0.782	0.984	CLONAL	1	TRUE	1	0.36383058098684	2		599	556	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421355	12421355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777334819	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	29	577	0	ENST00000287820.6:c.235G>A	p.Glu79Lys	p.E79K	ENST00000287820	NM_015869.4	79	Gaa/Aaa	2/7	1	2	FACETS	0.302	0.242	0.372	0.302	0.242	0.372	SUBCLONAL	1	TRUE	1	0.36383058098684	2		577	527	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956771	68956771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774302685	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	98	568	0	ENST00000288368.4:c.889C>T	p.Arg297Cys	p.R297C	ENST00000288368	NM_024870.2	297	Cgt/Tgt	8/40	1	2	FACETS	0.8	0.715	0.892	0.8	0.715	0.892	SUBCLONAL	1	TRUE	1	0.36383058098684	2		568	673	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029456	14029456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1229724657	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	24	383	0	ENST00000311895.7:c.1667C>T	p.Pro556Leu	p.P556L	ENST00000311895	NM_005236.2	556	cCg/cTg	8/11	1	2	FACETS	0.319	0.249	0.399	0.319	0.249	0.399	SUBCLONAL	1	TRUE	1	0.36383058098684	2		383	414	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410883	31410883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	141	647	0	ENST00000344624.3:c.3637C>T	p.Arg1213Cys	p.R1213C	ENST00000344624		1213	Cgc/Tgc	28/33	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.36383058098684	2		647	715	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392143	81392143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	22	299	0	ENST00000222390.5:c.134C>T	p.Ser45Leu	p.S45L	ENST00000222390	NM_000601.4	45	tCa/tTa	2/18	1	2	FACETS	0.733	0.573	0.916	0.733	0.573	0.916	CLONAL	1	TRUE	1	0.36383058098684	2		299	165	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031678	69031678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	45	307	0	ENST00000288368.4:c.3433C>T	p.Pro1145Ser	p.P1145S	ENST00000288368	NM_024870.2	1145	Ccc/Tcc	28/40	1	2	FACETS	0.926	0.784	1	0.926	0.784	1	CLONAL	1	TRUE	1	0.36383058098684	2		307	267	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272321	15272321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	131	755	0	ENST00000263388.2:c.6118G>A	p.Gly2040Arg	p.G2040R	ENST00000263388	NM_000435.2	2040	Ggg/Agg	33/33	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.36383058098684	2		755	694	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564503	55564503	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1044091916	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	86	504	0	ENST00000288135.5:c.391G>A	p.Asp131Asn	p.D131N	ENST00000288135	NM_000222.2	131	Gac/Aac	3/21	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.36383058098684	2		504	459	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640719	3640719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1448955515	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	125	893	0	ENST00000294008.3:c.2920C>T	p.Leu974Phe	p.L974F	ENST00000294008	NM_032444.2	974	Ctt/Ttt	12/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.36383058098684	2		893	608	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961812	55961812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	42	355	0	ENST00000263923.4:c.2749G>A	p.Glu917Lys	p.E917K	ENST00000263923	NM_002253.2	917	Gaa/Aaa	20/30	1	2	FACETS	0.83	0.697	0.976	0.83	0.697	0.976	CLONAL	1	TRUE	1	0.36383058098684	2		355	278	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129983	55129983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763718380	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	86	536	0	ENST00000257290.5:c.517G>A	p.Asp173Asn	p.D173N	ENST00000257290	NM_006206.4	173	Gac/Aac	4/23	1	2	FACETS	0.849	0.752	0.951	0.849	0.752	0.951	CLONAL	1	TRUE	1	0.36383058098684	2		536	557	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400015	49400015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	40	530	0	ENST00000418115.1:c.322C>T	p.Pro108Ser	p.P108S	ENST00000418115	NM_001664.2	108	Ccc/Tcc	4/5	1	2	FACETS	0.371	0.307	0.442	0.371	0.307	0.442	SUBCLONAL	1	TRUE	1	0.36383058098684	2		530	593	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625656	1625656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	143	840	1	ENST00000344749.5:c.418C>T	p.Pro140Ser	p.P140S	ENST00000344749	NM_001136139.2	140	Cct/Tct	7/19	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.36383058098684	2		841	728	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98241337	98241337	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	147	565	1	ENST00000331920.6:c.1160G>A	p.Trp387Ter	p.W387*	ENST00000331920	NM_000264.3	387	tGg/tAg	8/24	0.36383058098684	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.36383058098684	1		566	581	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935268	36935268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	151	798	0	ENST00000361632.4:c.1459G>A	p.Gly487Arg	p.G487R	ENST00000361632		487	Ggg/Agg	10/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.36383058098684	2		798	789	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849483	89849483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776371246	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	106	550	0	ENST00000389301.3:c.1498C>T	p.Pro500Ser	p.P500S	ENST00000389301	NM_000135.2	500	Ccc/Tcc	16/43	1	2	FACETS	0.949	0.853	1	0.949	0.853	1	CLONAL	1	TRUE	1	0.36383058098684	2		550	614	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984930	55984930	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	72	413	0	ENST00000263923.4:c.199C>T	p.Gln67Ter	p.Q67*	ENST00000263923	NM_002253.2	67	Cag/Tag	3/30	1	2	FACETS	0.982	0.862	1	0.982	0.862	1	CLONAL	1	TRUE	1	0.36383058098684	2		413	403	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356137	66356137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290982378	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	87	444	0	ENST00000273854.3:c.1360G>A	p.Ala454Thr	p.A454T	ENST00000273854	NM_004439.5	454	Gcc/Acc	5/18	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.36383058098684	2		444	470	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805016	43805016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1464244274	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	105	587	0	ENST00000372470.3:c.466G>A	p.Glu156Lys	p.E156K	ENST00000372470	NM_005373.2	156	Gag/Aag	4/12	1	2	FACETS	0.97	0.871	1	0.97	0.871	1	CLONAL	1	TRUE	1	0.36383058098684	2		587	595	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023561	27023561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	78	251	0	ENST00000324856.7:c.667C>T	p.Pro223Ser	p.P223S	ENST00000324856	NM_006015.4	223	Ccc/Tcc	1/20	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.36383058098684	2		251	423	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512190	120512190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	40	467	0	ENST00000256646.2:c.1052C>T	p.Ser351Phe	p.S351F	ENST00000256646	NM_024408.3	351	tCc/tTc	6/34	1	2	FACETS	0.397	0.329	0.472	0.397	0.329	0.472	SUBCLONAL	1	TRUE	1	0.36383058098684	2		467	554	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724413	162724413	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1235183322	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	64	342	0	ENST00000367921.3:c.186-1G>A		p.X62_splice	ENST00000367921	NM_006182.2	62			1	2	FACETS	0.988	0.861	1	0.988	0.861	1	CLONAL	1	TRUE	1	0.36383058098684	2		342	356	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652465	206652466	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	33	533	1	ENST00000367120.3:c.1172_1173delinsTT	p.Ala391Val	p.A391V	ENST00000367120	NM_014002.3	391	gCC/gTT	10/22	1	2	FACETS	0.319	0.259	0.387	0.319	0.259	0.387	SUBCLONAL	1	TRUE	1	0.36383058098684	2		534	569	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809273	243809273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780868494	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	23	372	0	ENST00000263826.5:c.351G>A	p.Met117Ile	p.M117I	ENST00000263826	NM_005465.4	117	atG/atA	4/13	1	2	FACETS	0.504	0.394	0.63	0.504	0.394	0.63	SUBCLONAL	1	TRUE	1	0.36383058098684	2		372	251	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344230	118344230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	88	502	0	ENST00000534358.1:c.2356C>T	p.Pro786Ser	p.P786S	ENST00000534358	NM_005933.3	786	Cct/Tct	3/36	1	2	FACETS	0.868	0.771	0.972	0.868	0.771	0.972	CLONAL	1	TRUE	1	0.36383058098684	2		502	557	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416855	416855	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	91	418	0	ENST00000399788.2:c.3695C>T	p.Ser1232Phe	p.S1232F	ENST00000399788	NM_001042603.1	1232	tCc/tTc	23/28	0.0882598201227975	3	FACETS	1	0.966	1	0.607	0.541	0.677	INDETERMINATE	1	TRUE	1	0.36383058098684	3		418	487	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431630	49431630	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	50	764	0	ENST00000301067.7:c.9509C>A	p.Thr3170Lys	p.T3170K	ENST00000301067	NM_003482.3	3170	aCa/aAa	34/54	0.0882598201227975	3	FACETS	0.436	0.369	0.51	0.218	0.184	0.255	INDETERMINATE	1	TRUE	1	0.36383058098684	3		764	745	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438604	49438604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	52	678	0	ENST00000301067.7:c.4886C>T	p.Ser1629Phe	p.S1629F	ENST00000301067	NM_003482.3	1629	tCt/tTt	19/54	0.0882598201227975	3	FACETS	0.472	0.401	0.55	0.236	0.2	0.275	INDETERMINATE	1	TRUE	1	0.36383058098684	3		678	716	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145383	58145383	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761965434	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	102	561	0	ENST00000257904.6:c.118C>T	p.Pro40Ser	p.P40S	ENST00000257904	NM_000075.3	40	Ccc/Tcc	2/8	0.0882598201227975	3	FACETS	1	0.917	1	0.514	0.46	0.571	INDETERMINATE	1	TRUE	1	0.36383058098684	3		561	645	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967601	26967602	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	42	336	0	ENST00000381527.3:c.744_745delinsTT	p.His249Tyr	p.H249Y	ENST00000381527	NM_001260.1	248	caCCat/caTTat	7/13	NA	2	FACETS	0.888	0.746	1			1	INDETERMINATE	1	TRUE	NA	0.36383058098684	2		336	260	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623637	28623637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1317803354	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	48	422	0	ENST00000241453.7:c.920G>A	p.Arg307Lys	p.R307K	ENST00000241453	NM_004119.2	307	aGa/aAa	8/24	0.36383058098684	1	FACETS	0.712	0.606	0.829	0.712	0.606	0.829	SUBCLONAL	1	TRUE	0	0.36383058098684	1		422	303	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623870	28623870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778370	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	38	414	0	ENST00000241453.7:c.784C>T	p.Leu262Phe	p.L262F	ENST00000241453	NM_004119.2	262	Ctt/Ttt	7/24	0.36383058098684	1	FACETS	0.624	0.518	0.74	0.624	0.518	0.74	SUBCLONAL	1	TRUE	0	0.36383058098684	1		414	274	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913987	32913987	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	46	395	0	ENST00000380152.3:c.5495C>T	p.Ser1832Phe	p.S1832F	ENST00000380152		1832	tCt/tTt	11/27	1	2	FACETS	0.884	0.749	1	0.884	0.749	1	CLONAL	1	TRUE	1	0.36383058098684	2		395	286	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528213	103528213	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569686280	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	17	283	0	ENST00000355739.4:c.3521G>A	p.Arg1174Lys	p.R1174K	ENST00000355739	NM_000123.3	1174	aGg/aAg	15/15	1	2	FACETS	0.351	0.262	0.457	0.351	0.262	0.457	SUBCLONAL	1	TRUE	1	0.36383058098684	2		283	266	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988476	36988476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	34	440	1	ENST00000354822.5:c.177G>A	p.Met59Ile	p.M59I	ENST00000354822	NM_001079668.2	59	atG/atA	2/3	1	2	FACETS	0.405	0.331	0.489	0.405	0.331	0.489	SUBCLONAL	1	TRUE	1	0.36383058098684	2		441	461	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748951	43748951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	131	687	1	ENST00000382044.4:c.1855G>A	p.Asp619Asn	p.D619N	ENST00000382044	NM_001141980.1	619	Gat/Aat	12/28	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.36383058098684	2		688	697	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923392	9923392	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057520116	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	24	526	0	ENST00000330684.3:c.1895C>T	p.Ser632Phe	p.S632F	ENST00000330684	NM_001134407.1	632	tCt/tTt	9/13	1	2	FACETS	0.301	0.235	0.376	0.301	0.235	0.376	SUBCLONAL	1	TRUE	1	0.36383058098684	2		526	439	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9927982	9927982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768958947	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	49	324	0	ENST00000330684.3:c.1757G>A	p.Arg586Lys	p.R586K	ENST00000330684	NM_001134407.1	586	aGa/aAa	8/13	1	2	FACETS	0.965	0.824	1	0.965	0.824	1	CLONAL	1	TRUE	1	0.36383058098684	2		324	279	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041969	14041969	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	78	372	0	ENST00000311895.7:c.2516C>T	p.Pro839Leu	p.P839L	ENST00000311895	NM_005236.2	839	cCc/cTc	11/11	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.36383058098684	2		372	388	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627230	37627230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	28	435	0	ENST00000447079.4:c.1145C>T	p.Ser382Phe	p.S382F	ENST00000447079	NM_015083.1	382	tCc/tTc	2/14	1	2	FACETS	0.333	0.266	0.41	0.333	0.266	0.41	SUBCLONAL	1	TRUE	1	0.36383058098684	2		435	462	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865408	40865408	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	97	572	0	ENST00000428826.2:c.1024-1G>A		p.X342_splice	ENST00000428826		342			1	2	FACETS	0.91	0.813	1	0.91	0.813	1	CLONAL	1	TRUE	1	0.36383058098684	2		572	586	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804214	46804214	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	35	678	1	ENST00000290295.7:c.793C>T	p.Gln265Ter	p.Q265*	ENST00000290295	NM_006361.5	265	Cag/Tag	2/2	1	2	FACETS	0.279	0.228	0.337	0.279	0.228	0.337	SUBCLONAL	1	TRUE	1	0.36383058098684	2		679	690	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435395	56435395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	214	816	0	ENST00000407977.2:c.1742C>T	p.Pro581Leu	p.P581L	ENST00000407977		581	cCt/cTt	9/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.36383058098684	2		816	796	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435713	56435713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	71	662	0	ENST00000407977.2:c.1424C>T	p.Ser475Phe	p.S475F	ENST00000407977		475	tCc/tTc	9/10	1	2	FACETS	0.653	0.57	0.742	0.653	0.57	0.742	SUBCLONAL	1	TRUE	1	0.36383058098684	2		662	598	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240340	5240341	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	109	686	1	ENST00000357368.4:c.1573_1574delinsTT	p.Pro525Leu	p.P525L	ENST00000357368	NM_002850.3	525	CCg/TTg	12/38	1	2	FACETS	0.954	0.858	1	0.954	0.858	1	CLONAL	1	TRUE	1	0.36383058098684	2		687	628	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281193	15281193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	144	799	0	ENST00000263388.2:c.5063C>T	p.Ser1688Phe	p.S1688F	ENST00000263388	NM_000435.2	1688	tCt/tTt	27/33	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.36383058098684	2		799	722	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967818	18967818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs897698788	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	60	885	1	ENST00000262803.5:c.1957G>A	p.Gly653Arg	p.G653R	ENST00000262803	NM_002911.3	653	Ggg/Agg	14/24	1	2	FACETS	0.426	0.366	0.492	0.426	0.366	0.492	SUBCLONAL	1	TRUE	1	0.36383058098684	2		886	774	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605873	46605873	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	97	597	0	ENST00000263734.3:c.1521G>A	p.Met507Ile	p.M507I	ENST00000263734	NM_001430.4	507	atG/atA	11/16	1	2	FACETS	0.874	0.781	0.973	0.874	0.781	0.973	CLONAL	1	TRUE	1	0.36383058098684	2		597	610	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149749	202149749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	96	569	0	ENST00000358485.4:c.1190C>T	p.Ser397Phe	p.S397F	ENST00000358485	NM_001080125.1	397	tCt/tTt	8/9	1	2	FACETS	0.894	0.799	0.996	0.894	0.799	0.996	CLONAL	1	TRUE	1	0.36383058098684	2		569	590	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660339	227660339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	91	616	0	ENST00000305123.5:c.3116C>T	p.Ala1039Val	p.A1039V	ENST00000305123	NM_005544.2	1039	gCa/gTa	1/2	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.36383058098684	2		616	477	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54956553	54956553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	20	372	0	ENST00000312783.6:c.641C>T	p.Pro214Leu	p.P214L	ENST00000312783	NM_198436.1	214	cCa/cTa	7/10	1	2	FACETS	0.336	0.257	0.429	0.336	0.257	0.429	SUBCLONAL	1	TRUE	1	0.36383058098684	2		372	327	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627266	12627266	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	23	369	0	ENST00000251849.4:c.1450A>G	p.Ile484Val	p.I484V	ENST00000251849	NM_002880.3	484	Att/Gtt	14/17	1	2	FACETS	0.28	0.218	0.353	0.28	0.218	0.353	SUBCLONAL	1	TRUE	1	0.36383058098684	2		369	451	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927469	49927469	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	43	675	0	ENST00000296474.3:c.3835G>A	p.Glu1279Lys	p.E1279K	ENST00000296474	NM_002447.2	1279	Gaa/Aaa	19/20	1	2	FACETS	0.336	0.28	0.398	0.336	0.28	0.398	SUBCLONAL	1	TRUE	1	0.36383058098684	2		675	703	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936094	49936094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	113	746	1	ENST00000296474.3:c.1576G>A	p.Gly526Ser	p.G526S	ENST00000296474	NM_002447.2	526	Ggc/Agc	4/20	1	2	FACETS	0.988	0.891	1	0.988	0.891	1	CLONAL	1	TRUE	1	0.36383058098684	2		747	629	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89478287	89478287	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	33	308	0	ENST00000336596.2:c.2106G>A	p.Met702Ile	p.M702I	ENST00000336596	NM_005233.5	702	atG/atA	12/17	1	2	FACETS	0.852	0.699	1	0.852	0.699	1	CLONAL	1	TRUE	1	0.36383058098684	2		308	213	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521660	89521660	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	29	427	0	ENST00000336596.2:c.2737T>A	p.Phe913Ile	p.F913I	ENST00000336596	NM_005233.5	913	Ttc/Atc	16/17	1	2	FACETS	0.329	0.263	0.404	0.329	0.263	0.404	SUBCLONAL	1	TRUE	1	0.36383058098684	2		427	485	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957029	1957029	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747861024	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	86	618	0	ENST00000382891.5:c.2480C>T	p.Ala827Val	p.A827V	ENST00000382891	NM_133335.3	827	gCc/gTc	13/22	1	2	FACETS	0.622	0.55	0.699	0.622	0.55	0.699	SUBCLONAL	1	TRUE	1	0.36383058098684	2		618	760	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749551	41749551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs551983206	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	75	503	0	ENST00000226382.2:c.244C>T	p.Pro82Ser	p.P82S	ENST00000226382	NM_003924.3	82	Cct/Tct	2/3	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.36383058098684	2		503	383	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409368	31409368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	40	371	0	ENST00000344624.3:c.3739C>T	p.Pro1247Ser	p.P1247S	ENST00000344624		1247	Cca/Tca	29/33	1	2	FACETS	0.8	0.668	0.944	0.8	0.668	0.944	CLONAL	1	TRUE	1	0.36383058098684	2		371	275	SUCCESS
APC	324	MSKCC	GRCh37	5	112179329	112179329	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780553	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	54	314	0	ENST00000257430.4:c.8038C>T	p.Pro2680Ser	p.P2680S	ENST00000257430	NM_000038.5	2680	Ccc/Tcc	16/16	1	2	FACETS	0.964	0.828	1	0.964	0.828	1	CLONAL	1	TRUE	1	0.36383058098684	2		314	308	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915073	131915073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	66	420	0	ENST00000265335.6:c.430C>T	p.Leu144Phe	p.L144F	ENST00000265335		144	Ctt/Ttt	4/25	1	2	FACETS	0.978	0.853	1	0.978	0.853	1	CLONAL	1	TRUE	1	0.36383058098684	2		420	371	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514430	149514430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	40	634	0	ENST00000261799.4:c.514C>T	p.Pro172Ser	p.P172S	ENST00000261799	NM_002609.3	172	Ccc/Tcc	4/23	1	2	FACETS	0.34	0.281	0.405	0.34	0.281	0.405	SUBCLONAL	1	TRUE	1	0.36383058098684	2		634	647	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176678848	176678848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764613088	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	40	311	0	ENST00000439151.2:c.4759C>T	p.Arg1587Cys	p.R1587C	ENST00000439151	NM_022455.4	1587	Cgc/Tgc	12/23	1	2	FACETS	0.726	0.606	0.858	0.726	0.606	0.858	SUBCLONAL	1	TRUE	1	0.36383058098684	2		311	303	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046089	180046089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	43	143	0	ENST00000261937.6:c.2782G>A	p.Glu928Lys	p.E928K	ENST00000261937	NM_182925.4	928	Gag/Aag	20/30	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.36383058098684	2		143	212	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553434	106553434	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs555991112	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	62	455	1	ENST00000369096.4:c.1399C>T	p.Pro467Ser	p.P467S	ENST00000369096	NM_001198.3	467	Ccg/Tcg	5/7	1	2	FACETS	0.722	0.625	0.827	0.722	0.625	0.827	SUBCLONAL	1	TRUE	1	0.36383058098684	2		456	472	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715389	117715389	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	44	224	0	ENST00000368508.3:c.1100G>A	p.Gly367Glu	p.G367E	ENST00000368508	NM_002944.2	367	gGa/gAa	10/43	0.36383058098684	1	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	0	0.36383058098684	1		224	185	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355334	81355334	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	26	201	1	ENST00000222390.5:c.1041-1G>T		p.X347_splice	ENST00000222390	NM_000601.4	347			1	2	FACETS	0.711	0.567	0.874	0.711	0.567	0.874	SUBCLONAL	1	TRUE	1	0.36383058098684	2		202	201	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523594	106523594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	25	235	0	ENST00000359195.3:c.2746C>T	p.Pro916Ser	p.P916S	ENST00000359195	NM_002649.2	916	Cct/Tct	8/11	1	2	FACETS	0.611	0.484	0.756	0.611	0.484	0.756	SUBCLONAL	1	TRUE	1	0.36383058098684	2		235	225	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739343	145739343	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	202	781	0	ENST00000428558.2:c.2027T>C	p.Leu676Pro	p.L676P	ENST00000428558	NM_004260.3	676	cTt/cCt	12/22	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.36383058098684	2		781	787	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27192580	27192580	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	100	497	0	ENST00000380036.4:c.1583G>A	p.Gly528Glu	p.G528E	ENST00000380036	NM_000459.3	528	gGg/gAg	11/23	1	2	FACETS	0.949	0.85	1	0.949	0.85	1	CLONAL	1	TRUE	1	0.36383058098684	2		497	579	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482221	87482221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	103	568	0	ENST00000277120.3:c.1508G>A	p.Gly503Glu	p.G503E	ENST00000277120		503	gGg/gAg	14/19	0.36383058098684	1	FACETS	0.947	0.852	1	0.947	0.852	1	CLONAL	1	TRUE	0	0.36383058098684	1		568	489	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650560	48650560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046562-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	126	381	0	ENST00000376670.3:c.530G>A	p.Gly177Glu	p.G177E	ENST00000376670	NM_002049.3	177	gGg/gAg	3/6	1	1	FACETS	0.856	0.786	0.928	1	0.989	1	CLONAL	2	TRUE	0	0.36383058098684	1		381	331	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116179	209116179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555882127	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	172	327	0	ENST00000345146.2:c.97C>T	p.Pro33Ser	p.P33S	ENST00000345146	NM_005896.2	33	Ccc/Tcc	3/10	0.594123496512885	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.594123496512885	1		327	305	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	143	361	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.767	0.711	0.823	1	0.99	1	SUBCLONAL	2	TRUE	1	0.594123496512885	2		361	314	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257451	19257451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1918	258	975	0	ENST00000162023.5:c.682C>T	p.Leu228Phe	p.L228F	ENST00000162023		228	Ctc/Ttc	11/13	0.594123496512885	6	FACETS	0.873	0.814	0.935	0.218	0.203	0.234	CLONAL	1	TRUE	2	0.594123496512885	6		975	2176	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294235	11294235	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs951016084	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	178	520	3	ENST00000361445.4:c.2296C>T	p.Arg766Ter	p.R766*	ENST00000361445	NM_004958.3	766	Cga/Tga	14/58	0.594123496512885	3	FACETS	1	0.957	1	0.526	0.486	0.567	CLONAL	1	TRUE	1	0.594123496512885	3		523	739	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255835	16255835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	106	351	0	ENST00000375759.3:c.3100G>A	p.Glu1034Lys	p.E1034K	ENST00000375759	NM_015001.2	1034	Gag/Aag	11/15	0.594123496512885	3	FACETS	1	0.919	1	0.511	0.46	0.564	CLONAL	1	TRUE	1	0.594123496512885	3		351	453	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257158	16257158	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	136	416	0	ENST00000375759.3:c.4423C>T	p.Arg1475Ter	p.R1475*	ENST00000375759	NM_015001.2	1475	Cga/Tga	11/15	0.594123496512885	3	FACETS	1	0.961	1	0.545	0.498	0.594	CLONAL	1	TRUE	1	0.594123496512885	3		416	545	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258758	16258758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	124	502	0	ENST00000375759.3:c.6023C>T	p.Ala2008Val	p.A2008V	ENST00000375759	NM_015001.2	2008	gCt/gTt	11/15	0.594123496512885	3	FACETS	0.933	0.847	1	0.467	0.423	0.512	CLONAL	1	TRUE	1	0.594123496512885	3		502	580	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259576	16259576	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs779299660	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	143	518	0	ENST00000375759.3:c.6841T>G	p.Ser2281Ala	p.S2281A	ENST00000375759	NM_015001.2	2281	Tct/Gct	11/15	0.594123496512885	3	FACETS	1	0.942	1	0.519	0.474	0.565	CLONAL	1	TRUE	1	0.594123496512885	3		518	602	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259967	16259967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	158	610	3	ENST00000375759.3:c.7232C>T	p.Ser2411Leu	p.S2411L	ENST00000375759	NM_015001.2	2411	tCg/tTg	11/15	0.594123496512885	3	FACETS	0.924	0.848	1	0.462	0.424	0.501	CLONAL	1	TRUE	1	0.594123496512885	3		613	747	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105853	27105853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768785041	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	158	496	0	ENST00000324856.7:c.5464C>T	p.Pro1822Ser	p.P1822S	ENST00000324856	NM_006015.4	1822	Cca/Tca	20/20	0.594123496512885	3	FACETS	0.965	0.886	1	0.482	0.443	0.524	CLONAL	1	TRUE	1	0.594123496512885	3		496	715	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933244	36933245	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AT	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	290	655	2	ENST00000361632.4:c.1872_1873delinsAT	p.Glu625Ter	p.E625*	ENST00000361632		624	tcGGag/tcATag	14/16	0.594123496512885	3	FACETS	0.897	0.849	0.945	0.897	0.849	0.945	CLONAL	2	TRUE	1	0.594123496512885	3		657	706	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805753	43805753	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1361284210	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	245	767	0	ENST00000372470.3:c.809G>A	p.Gly270Glu	p.G270E	ENST00000372470	NM_005373.2	270	gGa/gAa	5/12	0.594123496512885	3	FACETS	1	0.975	1	0.541	0.506	0.577	CLONAL	1	TRUE	1	0.594123496512885	3		767	989	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733631	85733637	+	frameshift_variant	Frame_Shift_Del	DEL	ATCTGGA	ATCTGGA	-	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	179	382	0	ENST00000370580.1:c.375_381del	p.Phe125LeufsTer21	p.F125Lfs*21	ENST00000370580	NM_003921.4	125	ttTCCAGAT/tt	3/3	0.594123496512885	3	FACETS	0.861	0.802	0.921	0.861	0.802	0.921	CLONAL	2	TRUE	1	0.594123496512885	3		382	454	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551732	150551732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	64	157	0	ENST00000369026.2:c.275C>T	p.Thr92Ile	p.T92I	ENST00000369026	NM_021960.4	92	aCc/aTc	1/3	0.594123496512885	5	FACETS	1	0.973	1	0.499	0.437	0.566	CLONAL	1	TRUE	2	0.594123496512885	5		157	272	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844404	156844404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199826686	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	234	811	1	ENST00000524377.1:c.1237G>A	p.Glu413Lys	p.E413K	ENST00000524377	NM_002529.3	413	Gaa/Aaa	10/17	0.594123496512885	5	FACETS	1	0.984	1	0.396	0.368	0.424	CLONAL	1	TRUE	2	0.594123496512885	5		812	1255	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846343	156846343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	350	749	0	ENST00000524377.1:c.1784G>A	p.Gly595Glu	p.G595E	ENST00000524377	NM_002529.3	595	gGg/gAg	14/17	0.594123496512885	5	FACETS	0.909	0.86	0.958	0.606	0.573	0.639	CLONAL	2	TRUE	2	0.594123496512885	5		749	1226	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981532	201981532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777508355	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	120	806	0	ENST00000359651.3:c.446C>T	p.Ala149Val	p.A149V	ENST00000359651		149	gCc/gTc	3/8	0.393708764183751	2	FACETS	0.53	0.479	0.584	0.265	0.239	0.292	SUBCLONAL	1	TRUE	0	0.594123496512885	2		806	762	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100730	8100730	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	218	726	0	ENST00000346208.3:c.704C>T	p.Pro235Leu	p.P235L	ENST00000346208		235	cCc/cTc	3/6	NA	2	FACETS	0.827	0.77	0.886			1	INDETERMINATE	1	TRUE	NA	0.594123496512885	2		726	887	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606829	43606829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs537874538	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	263	861	2	ENST00000355710.3:c.1438G>A	p.Glu480Lys	p.E480K	ENST00000355710	NM_020975.4	480	Gaa/Aaa	7/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.594123496512885	2		863	809	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851318	63851318	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	194	612	0	ENST00000279873.7:c.2096T>G	p.Val699Gly	p.V699G	ENST00000279873	NM_032199.2	699	gTg/gGg	10/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.594123496512885	2		612	603	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851767	63851767	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	160	561	0	ENST00000279873.7:c.2545C>T	p.His849Tyr	p.H849Y	ENST00000279873	NM_032199.2	849	Cat/Tat	10/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.594123496512885	2		561	525	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925409	114925409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202133956	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	147	555	0	ENST00000543371.1:c.1487C>T	p.Ser496Phe	p.S496F	ENST00000543371	NM_001198531.1	496	tCc/tTc	14/14	1	2	FACETS	0.927	0.851	1	0.927	0.851	1	CLONAL	1	TRUE	1	0.594123496512885	2		555	534	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263314	123263314	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	95	341	0	ENST00000358487.5:c.1429C>T	p.Pro477Ser	p.P477S	ENST00000358487	NM_000141.4	477	Cca/Tca	10/18	1	2	FACETS	0.909	0.816	1	0.909	0.816	1	CLONAL	1	TRUE	1	0.594123496512885	2		341	352	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298222	123298222	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	81	305	0	ENST00000358487.5:c.632A>T	p.Asn211Ile	p.N211I	ENST00000358487	NM_000141.4	211	aAc/aTc	6/18	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.594123496512885	2		305	266	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325197	123325197	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	125	481	0	ENST00000358487.5:c.131T>C	p.Ile44Thr	p.I44T	ENST00000358487	NM_000141.4	44	aTc/aCc	3/18	1	2	FACETS	0.961	0.876	1	0.961	0.876	1	CLONAL	1	TRUE	1	0.594123496512885	2		481	438	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742960	17742960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1241501765	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	86	567	0	ENST00000250003.3:c.868G>A	p.Glu290Lys	p.E290K	ENST00000250003	NM_002478.4	290	Gag/Aag	3/3	0.594123496512885	1	FACETS	0.507	0.451	0.567	0.507	0.451	0.567	SUBCLONAL	1	TRUE	0	0.594123496512885	1		567	401	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128998	64128998	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141880979	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	199	774	0	ENST00000334205.4:c.628C>T	p.Arg210Cys	p.R210C	ENST00000334205	NM_003942.2	210	Cgt/Tgt	6/17	0.455265188883072	4	FACETS	0.971	0.898	1	0.485	0.449	0.523	CLONAL	1	TRUE	2	0.594123496512885	4		774	1100	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625177	69625177	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs535882027	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	202	848	1	ENST00000334134.2:c.616G>A	p.Val206Ile	p.V206I	ENST00000334134	NM_005247.2	206	Gtc/Atc	3/3	0.455265188883072	4	FACETS	1	0.948	1	0.515	0.477	0.554	CLONAL	1	TRUE	2	0.594123496512885	4		849	1053	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939825	71939825	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	208	861	1	ENST00000298229.2:c.452C>T	p.Ser151Phe	p.S151F	ENST00000298229	NM_001567.3	151	tCt/tTt	4/28	0.455265188883072	4	FACETS	0.852	0.789	0.918	0.426	0.394	0.459	CLONAL	1	TRUE	2	0.594123496512885	4		862	1310	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948506	71948506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	250	965	1	ENST00000298229.2:c.3218C>T	p.Pro1073Leu	p.P1073L	ENST00000298229	NM_001567.3	1073	cCa/cTa	26/28	0.455265188883072	4	FACETS	0.981	0.916	1	0.491	0.458	0.525	CLONAL	1	TRUE	2	0.594123496512885	4		966	1367	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090994	77090994	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144273203	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	100	399	1	ENST00000356341.3:c.236C>T	p.Ser79Leu	p.S79L	ENST00000356341	NM_002576.4	79	tCa/tTa	3/15	0.455265188883072	4	FACETS	0.853	0.763	0.948	0.427	0.381	0.474	CLONAL	1	TRUE	2	0.594123496512885	4		400	629	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165741	108165741	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	68	314	0	ENST00000278616.4:c.4864G>A	p.Glu1622Lys	p.E1622K	ENST00000278616	NM_000051.3	1622	Gaa/Aaa	32/63	0.594123496512885	3	FACETS	0.861	0.754	0.975	0.43	0.377	0.488	CLONAL	1	TRUE	1	0.594123496512885	3		314	345	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118361991	118361991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1472952558	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	99	283	0	ENST00000534358.1:c.4777C>T	p.Arg1593Cys	p.R1593C	ENST00000534358	NM_005933.3	1593	Cgc/Tgc	14/36	0.594123496512885	3	FACETS	1	0.965	1	0.581	0.523	0.642	CLONAL	1	TRUE	1	0.594123496512885	3		283	372	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376157	118376158	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	110	453	1	ENST00000534358.1:c.9550_9551delinsTT	p.Pro3184Phe	p.P3184F	ENST00000534358	NM_005933.3	3184	CCt/TTt	27/36	0.594123496512885	3	FACETS	0.813	0.732	0.898	0.406	0.366	0.449	CLONAL	1	TRUE	1	0.594123496512885	3		454	591	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435359	18435359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775821948	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	121	318	0	ENST00000266497.5:c.344C>T	p.Pro115Leu	p.P115L	ENST00000266497		115	cCa/cTa	1/31	0.594123496512885	3	FACETS	1	0.985	1	0.712	0.65	0.776	CLONAL	1	TRUE	1	0.594123496512885	3		318	371	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443931	18443931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	48	229	0	ENST00000266497.5:c.904C>T	p.His302Tyr	p.H302Y	ENST00000266497		302	Cat/Tat	3/31	0.594123496512885	3	FACETS	0.674	0.573	0.784	0.337	0.286	0.392	SUBCLONAL	1	TRUE	1	0.594123496512885	3		229	311	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466919	18466919	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	61	390	0	ENST00000266497.5:c.1058A>T	p.Lys353Ile	p.K353I	ENST00000266497		353	aAa/aTa	5/31	0.594123496512885	3	FACETS	0.569	0.492	0.653	0.285	0.246	0.327	SUBCLONAL	1	TRUE	1	0.594123496512885	3		390	468	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716366	18716366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs935135637	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	84	349	0	ENST00000266497.5:c.3713C>T	p.Ser1238Leu	p.S1238L	ENST00000266497		1238	tCa/tTa	26/31	0.594123496512885	3	FACETS	0.75	0.665	0.841	0.375	0.332	0.421	SUBCLONAL	1	TRUE	1	0.594123496512885	3		349	489	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793483	18793483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603405	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	50	269	0	ENST00000266497.5:c.4180G>A	p.Glu1394Lys	p.E1394K	ENST00000266497		1394	Gaa/Aaa	30/31	0.594123496512885	3	FACETS	0.654	0.557	0.759	0.327	0.278	0.38	SUBCLONAL	1	TRUE	1	0.594123496512885	3		269	334	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420471	49420471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	250	733	0	ENST00000301067.7:c.15278C>T	p.Ser5093Phe	p.S5093F	ENST00000301067	NM_003482.3	5093	tCc/tTc	48/54	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.594123496512885	2		733	702	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428663	49428663	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1449021357	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	203	652	2	ENST00000301067.7:c.10287G>A	p.Met3429Ile	p.M3429I	ENST00000301067	NM_003482.3	3429	atG/atA	35/54	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.594123496512885	2		654	682	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444816	49444816	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1316716261	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	247	874	1	ENST00000301067.7:c.2650C>T	p.Pro884Ser	p.P884S	ENST00000301067	NM_003482.3	884	Cct/Tct	10/54	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.594123496512885	2		875	828	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416704	121416704	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	226	810	1	ENST00000257555.6:c.133G>A	p.Asp45Asn	p.D45N	ENST00000257555		45	Gac/Aac	1/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.594123496512885	2		811	705	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601274	28601275	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	190	438	0	ENST00000241453.7:c.2157_2158delinsAA	p.Glu720Lys	p.E720K	ENST00000241453	NM_004119.2	719	aaGGaa/aaAAaa	17/24	0.455265188883072	4	FACETS	0.885	0.823	0.948	0.885	0.823	0.948	CLONAL	2	TRUE	2	0.594123496512885	4		438	576	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931718	28931718	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1363301507	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	130	424	0	ENST00000282397.4:c.2221G>C	p.Glu741Gln	p.E741Q	ENST00000282397	NM_002019.4	741	Gaa/Caa	15/30	0.455265188883072	4	FACETS	1	0.923	1	0.508	0.462	0.557	CLONAL	1	TRUE	2	0.594123496512885	4		424	686	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005419	29005419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55687105	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	68	328	0	ENST00000282397.4:c.842G>A	p.Arg281Gln	p.R281Q	ENST00000282397	NM_002019.4	281	cGa/cAa	7/30	0.455265188883072	4	FACETS	0.827	0.722	0.94	0.414	0.361	0.47	CLONAL	1	TRUE	2	0.594123496512885	4		328	441	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910654	32910654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	86	363	0	ENST00000380152.3:c.2162C>T	p.Pro721Leu	p.P721L	ENST00000380152		721	cCa/cTa	11/27	0.455265188883072	4	FACETS	0.97	0.861	1	0.485	0.43	0.543	CLONAL	1	TRUE	2	0.594123496512885	4		363	476	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281236	49281236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201100531	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	160	632	0	ENST00000282018.3:c.283G>A	p.Ala95Thr	p.A95T	ENST00000282018	NM_020377.2	95	Gct/Act	1/1	1	2	FACETS	0.988	0.912	1	0.988	0.912	1	CLONAL	1	TRUE	1	0.594123496512885	2		632	545	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73351584	73351584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	54	196	0	ENST00000377767.4:c.628C>T	p.Arg210Cys	p.R210C	ENST00000377767	NM_014953.3	210	Cgt/Tgt	4/21	1	2	FACETS	0.812	0.701	0.929	0.812	0.701	0.929	CLONAL	1	TRUE	1	0.594123496512885	2		196	224	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504536	103504536	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	82	302	0	ENST00000355739.4:c.157C>T	p.Pro53Ser	p.P53S	ENST00000355739	NM_000123.3	53	Cct/Tct	2/15	1	2	FACETS	0.905	0.806	1	0.905	0.806	1	CLONAL	1	TRUE	1	0.594123496512885	2		302	305	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434553	110434553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	143	324	0	ENST00000375856.3:c.3848C>T	p.Ser1283Phe	p.S1283F	ENST00000375856	NM_003749.2	1283	tCc/tTc	1/2	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.594123496512885	2		324	419	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023067	33023067	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	87	500	0	ENST00000300177.4:c.176G>A	p.Gly59Glu	p.G59E	ENST00000300177	NM_001191322.1	59	gGg/gAg	2/2	0.176387971008739	3	FACETS	0.844	0.751	0.943	0.281	0.25	0.315	INDETERMINATE	1	TRUE	0	0.594123496512885	3		500	450	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042574	42042574	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	99	432	0	ENST00000219905.7:c.6769C>T	p.Pro2257Ser	p.P2257S	ENST00000219905	NM_001164273.1	2257	Cct/Tct	17/24	0.176387971008739	3	FACETS	1	0.952	1	0.367	0.329	0.405	INDETERMINATE	1	TRUE	0	0.594123496512885	3		432	393	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476403	88476403	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	106	459	1	ENST00000360948.2:c.1729C>T	p.Pro577Ser	p.P577S	ENST00000360948	NM_001012338.2	577	Ccc/Tcc	15/19	0.314815735712366	1	FACETS	0.579	0.523	0.639	0.579	0.523	0.639	INDETERMINATE	1	TRUE	0	0.594123496512885	1		460	433	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295133	91295133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	64	319	0	ENST00000355112.3:c.916G>A	p.Glu306Lys	p.E306K	ENST00000355112	NM_000057.2	306	Gaa/Aaa	4/22	0.572389844653159	4	FACETS	0.959	0.835	1	0.32	0.278	0.364	CLONAL	1	TRUE	1	0.594123496512885	4		319	358	SUCCESS
BLM	641	MSKCC	GRCh37	15	91306215	91306215	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	269	306	0	ENST00000355112.3:c.1902A>T	p.Leu634Phe	p.L634F	ENST00000355112	NM_000057.2	634	ttA/ttT	8/22	0.572389844653159	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	1	0.594123496512885	4		306	441	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777996	3777996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	271	928	1	ENST00000262367.5:c.7052C>T	p.Ser2351Phe	p.S2351F	ENST00000262367	NM_004380.2	2351	tCt/tTt	31/31	0.489019158893683	4	FACETS	1	0.982	1	0.374	0.35	0.399	CLONAL	1	TRUE	1	0.594123496512885	4		929	1296	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820627	3820627	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	364	809	0	ENST00000262367.5:c.2824C>A	p.Pro942Thr	p.P942T	ENST00000262367	NM_004380.2	942	Cct/Act	14/31	0.489019158893683	4	FACETS	0.889	0.845	0.935	0.593	0.563	0.624	CLONAL	2	TRUE	1	0.594123496512885	4		809	1098	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858267	9858267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	158	463	0	ENST00000330684.3:c.3134C>T	p.Ser1045Phe	p.S1045F	ENST00000330684	NM_001134407.1	1045	tCc/tTc	13/13	0.489019158893683	4	FACETS	0.787	0.725	0.85	0.524	0.483	0.567	SUBCLONAL	2	TRUE	1	0.594123496512885	4		463	539	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858547	9858547	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1555482852	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	118	527	0	ENST00000330684.3:c.2854A>T	p.Lys952Ter	p.K952*	ENST00000330684	NM_001134407.1	952	Aaa/Taa	13/13	0.489019158893683	4	FACETS	1	0.947	1	0.356	0.322	0.392	CLONAL	1	TRUE	1	0.594123496512885	4		527	593	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923407	9923407	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	118	534	0	ENST00000330684.3:c.1880G>A	p.Ser627Asn	p.S627N	ENST00000330684	NM_001134407.1	627	aGc/aAc	9/13	0.489019158893683	4	FACETS	0.902	0.815	0.994	0.301	0.271	0.332	CLONAL	1	TRUE	1	0.594123496512885	4		534	702	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032197	10032197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774932381	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	409	632	0	ENST00000330684.3:c.626C>T	p.Ser209Phe	p.S209F	ENST00000330684	NM_001134407.1	209	tCc/tTc	3/13	0.489019158893683	4	FACETS	0.949	0.911	0.987	0.949	0.911	0.987	CLONAL	3	TRUE	1	0.594123496512885	4		632	771	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041840	14041840	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	98	396	0	ENST00000311895.7:c.2387C>T	p.Pro796Leu	p.P796L	ENST00000311895	NM_005236.2	796	cCc/cTc	11/11	0.489019158893683	4	FACETS	0.901	0.805	1	0.3	0.268	0.334	CLONAL	1	TRUE	1	0.594123496512885	4		396	584	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831515	72831515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	335	603	0	ENST00000268489.5:c.5066G>A	p.Gly1689Glu	p.G1689E	ENST00000268489	NM_006885.3	1689	gGg/gAg	9/10	0.58672988982354	3	FACETS	0.954	0.907	1	0.954	0.907	1	CLONAL	2	TRUE	1	0.594123496512885	3		603	767	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863224683	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	512	791	0	ENST00000269305.4:c.388C>T	p.Leu130Phe	p.L130F	ENST00000269305	NM_001126112.2	130	Ctc/Ttc	5/11	0.594123496512885	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.594123496512885	2		791	754	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990712	7990712	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	172	652	2	ENST00000319144.4:c.49G>A	p.Gly17Arg	p.G17R	ENST00000319144	NM_001139.2	17	Gga/Aga	1/15	0.594123496512885	2	FACETS	0.862	0.796	0.93	0.431	0.398	0.465	CLONAL	1	TRUE	0	0.594123496512885	2		654	672	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562641	29562641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854562	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	91	391	0	ENST00000356175.3:c.3721C>T	p.Arg1241Ter	p.R1241*	ENST00000356175	NM_000267.3	1241	Cga/Tga	28/57	0.594123496512885	1	FACETS	0.924	0.836	1	0.924	0.836	1	CLONAL	1	TRUE	0	0.594123496512885	1		391	233	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866081	37866081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113619125	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	190	740	1	ENST00000269571.5:c.590C>T	p.Pro197Leu	p.P197L	ENST00000269571		197	cCg/cTg	5/27	1	2	FACETS	0.739	0.683	0.796	0.739	0.683	0.796	SUBCLONAL	1	TRUE	1	0.594123496512885	2		741	866	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243037	41243037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	137	428	0	ENST00000357654.3:c.4109C>T	p.Ser1370Phe	p.S1370F	ENST00000357654	NM_007294.3	1370	tCt/tTt	11/23	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.594123496512885	2		428	449	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56432308	56432308	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs371814059	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	171	507	0	ENST00000407977.2:c.2348T>C	p.Val783Ala	p.V783A	ENST00000407977		783	gTg/gCg	10/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.594123496512885	2		507	539	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435416	56435416	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	220	809	0	ENST00000407977.2:c.1721G>A	p.Gly574Glu	p.G574E	ENST00000407977		574	gGa/gAa	9/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.594123496512885	2		809	697	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132235	7132235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs911929963	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	215	738	0	ENST00000302850.5:c.2776C>T	p.Arg926Trp	p.R926W	ENST00000302850	NM_000208.2	926	Cgg/Tgg	14/22	0.594123496512885	2	FACETS	0.923	0.86	0.988	0.462	0.43	0.494	CLONAL	1	TRUE	0	0.594123496512885	2		738	784	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246513	10246513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1241	214	827	0	ENST00000340748.4:c.4624C>T	p.Pro1542Ser	p.P1542S	ENST00000340748		1542	Cca/Tca	38/40	0.594123496512885	5	FACETS	0.936	0.868	1	0.312	0.289	0.336	CLONAL	1	TRUE	2	0.594123496512885	5		827	1455	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024650	11024650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	179	578	0	ENST00000327064.4:c.767C>T	p.Ser256Leu	p.S256L	ENST00000327064	NM_199141.1	256	tCg/tTg	6/16	0.594123496512885	5	FACETS	1	0.976	1	0.383	0.352	0.414	CLONAL	1	TRUE	2	0.594123496512885	5		578	993	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094995	11094996	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	582	937	1	ENST00000358026.2:c.168_169delinsTA	p.Pro57Thr	p.P57T	ENST00000358026	NM_001128849.1	56	atCCcc/atTAcc	2/36	0.594123496512885	5	FACETS	0.861	0.829	0.894	0.861	0.829	0.894	CLONAL	3	TRUE	2	0.594123496512885	5		938	1434	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097134	11097134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	229	772	1	ENST00000358026.2:c.625C>T	p.Pro209Ser	p.P209S	ENST00000358026	NM_001128849.1	209	Ccg/Tcg	4/36	0.594123496512885	5	FACETS	1	0.971	1	0.361	0.335	0.387	CLONAL	1	TRUE	2	0.594123496512885	5		773	1348	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629110	14629110	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768130288	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	275	387	0	ENST00000254322.2:c.52G>A	p.Glu18Lys	p.E18K	ENST00000254322	NM_006145.1	18	Gag/Aag	1/3	0.594123496512885	5	FACETS	0.964	0.92	1	1	0.994	1	CLONAL	4	TRUE	2	0.594123496512885	5		387	454	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272086	15272086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1233226731	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	159	693	0	ENST00000263388.2:c.6353C>T	p.Pro2118Leu	p.P2118L	ENST00000263388	NM_000435.2	2118	cCt/cTt	33/33	0.594123496512885	5	FACETS	1	0.966	1	0.368	0.337	0.4	CLONAL	1	TRUE	2	0.594123496512885	5		693	918	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349630	15349630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	203	822	0	ENST00000263377.2:c.3944C>T	p.Ser1315Phe	p.S1315F	ENST00000263377	NM_058243.2	1315	tCc/tTc	19/20	0.594123496512885	5	FACETS	1	0.976	1	0.375	0.347	0.404	CLONAL	1	TRUE	2	0.594123496512885	5		822	1149	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355317	15355317	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	96	273	0	ENST00000263377.2:c.2306C>A	p.Pro769His	p.P769H	ENST00000263377	NM_058243.2	769	cCt/cAt	13/20	0.594123496512885	5	FACETS	1	0.978	1	0.458	0.41	0.508	CLONAL	1	TRUE	2	0.594123496512885	5		273	445	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937688	17937688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	376	615	0	ENST00000458235.1:c.3239C>T	p.Pro1080Leu	p.P1080L	ENST00000458235	NM_000215.3	1080	cCt/cTt	24/24	0.594123496512885	6	FACETS	1	0.96	1	0.507	0.481	0.534	CLONAL	2	TRUE	2	0.594123496512885	6		615	1365	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950318	17950318	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1469	268	761	1	ENST00000458235.1:c.1409C>T	p.Thr470Ile	p.T470I	ENST00000458235	NM_000215.3	470	aCc/aTc	10/24	0.594123496512885	6	FACETS	1	0.982	1	0.284	0.265	0.304	CLONAL	1	TRUE	2	0.594123496512885	6		762	1737	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953135	17953135	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778420	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	291	485	0	ENST00000458235.1:c.851G>A	p.Gly284Glu	p.G284E	ENST00000458235	NM_000215.3	284	gGa/gAa	6/24	0.594123496512885	6	FACETS	0.908	0.853	0.963	0.454	0.426	0.482	CLONAL	2	TRUE	2	0.594123496512885	6		485	1181	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965826	18965827	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	186	517	0	ENST00000262803.5:c.1404_1405delinsTT	p.Pro469Ser	p.P469S	ENST00000262803	NM_002911.3	468	ctCCcc/ctTTcc	10/24	0.594123496512885	6	FACETS	1	0.967	1	0.273	0.251	0.295	CLONAL	1	TRUE	2	0.594123496512885	6		517	1256	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211012	36211012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	264	798	0	ENST00000222270.7:c.763C>T	p.Pro255Ser	p.P255S	ENST00000222270	NM_014727.1	255	Cct/Tct	3/37	0.455265188883072	4	FACETS	1	0.971	1	0.533	0.498	0.568	CLONAL	1	TRUE	2	0.594123496512885	4		798	1330	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211793	36211793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	222	832	0	ENST00000222270.7:c.1544C>T	p.Pro515Leu	p.P515L	ENST00000222270	NM_014727.1	515	cCc/cTc	3/37	0.455265188883072	4	FACETS	0.907	0.842	0.974	0.453	0.421	0.487	CLONAL	1	TRUE	2	0.594123496512885	4		832	1314	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223203	36223203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	305	1037	0	ENST00000222270.7:c.5753C>T	p.Pro1918Leu	p.P1918L	ENST00000222270	NM_014727.1	1918	cCt/cTt	28/37	0.455265188883072	4	FACETS	1	0.974	1	0.532	0.5	0.566	CLONAL	1	TRUE	2	0.594123496512885	4		1037	1537	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727151	41727151	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	347	524	0	ENST00000301178.4:c.409G>A	p.Gly137Ser	p.G137S	ENST00000301178	NM_021913.4	137	Ggc/Agc	3/20	0.455265188883072	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.594123496512885	4		524	881	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744456	41744456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	232	834	1	ENST00000301178.4:c.1076C>T	p.Pro359Leu	p.P359L	ENST00000301178	NM_021913.4	359	cCc/cTc	8/20	0.455265188883072	4	FACETS	1	0.971	1	0.538	0.501	0.576	CLONAL	1	TRUE	2	0.594123496512885	4		835	1158	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758807	41758807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	223	713	0	ENST00000301178.4:c.1861C>T	p.Pro621Ser	p.P621S	ENST00000301178	NM_021913.4	621	Cct/Tct	16/20	0.455265188883072	4	FACETS	1	0.934	1	0.502	0.467	0.539	CLONAL	1	TRUE	2	0.594123496512885	4		713	1191	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791248	42791248	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	215	801	0	ENST00000575354.2:c.308C>T	p.Pro103Leu	p.P103L	ENST00000575354	NM_015125.3	103	cCt/cTt	3/20	0.455265188883072	4	FACETS	0.939	0.871	1	0.469	0.435	0.505	CLONAL	1	TRUE	2	0.594123496512885	4		801	1229	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723098	52723098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	162	549	0	ENST00000322088.6:c.1283C>T	p.Pro428Leu	p.P428L	ENST00000322088	NM_014225.5	428	cCc/cTc	10/15	0.455265188883072	4	FACETS	1	0.95	1	0.524	0.481	0.569	CLONAL	1	TRUE	2	0.594123496512885	4		549	830	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498327	29498327	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766821017	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	164	570	0	ENST00000389048.3:c.1853G>A	p.Gly618Glu	p.G618E	ENST00000389048	NM_004304.4	618	gGa/gAa	10/29	0.594123496512885	5	FACETS	1	0.964	1	0.218	0.199	0.237	CLONAL	1	TRUE	0	0.594123496512885	5		570	959	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234211	39234211	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	129	477	0	ENST00000402219.2:c.2634G>A	p.Met878Ile	p.M878I	ENST00000402219	NM_005633.3	878	atG/atA	16/23	0.137369326944475	3	FACETS	0.966	0.879	1			1	INDETERMINATE	1	TRUE	NA	0.594123496512885	3		477	583	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47607029	47607029	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	203	446	0	ENST00000263735.4:c.779C>A	p.Ser260Ter	p.S260*	ENST00000263735	NM_002354.2	260	tCa/tAa	7/9	0.594123496512885	3	FACETS	0.883	0.826	0.94	0.883	0.826	0.94	CLONAL	2	TRUE	1	0.594123496512885	3		446	502	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61708342	61708342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	121	282	0	ENST00000401558.2:c.3047G>A	p.Arg1016Lys	p.R1016K	ENST00000401558	NM_003400.3	1016	aGa/aAa	24/25	0.364988314744917	2	FACETS	1	0.986	1	0.702	0.645	0.761	CLONAL	1	TRUE	0	0.594123496512885	2		282	290	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156105	99156108	+	frameshift_variant	Frame_Shift_Del	DEL	TCGT	TCGT	ATG	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	139	604	1	ENST00000074304.5:c.785_788delinsATG	p.Phe262TyrfsTer6	p.F262Yfs*6	ENST00000074304	NM_001134224.1	262	tTCGTg/tATGg	10/26	0.176387971008739	3	FACETS	0.834	0.76	0.911	0.278	0.253	0.304	INDETERMINATE	1	TRUE	0	0.594123496512885	3		605	728	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728659	190728659	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	46	321	0	ENST00000441310.2:c.2047C>T	p.Gln683Ter	p.Q683*	ENST00000441310	NM_000534.4	683	Cag/Tag	10/13	0.176387971008739	3	FACETS	0.676	0.573	0.789	0.225	0.191	0.263	INDETERMINATE	1	TRUE	0	0.594123496512885	3		321	297	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149790	202149791	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	77	576	0	ENST00000358485.4:c.1231_1232delinsTT	p.Pro411Phe	p.P411F	ENST00000358485	NM_001080125.1	411	CCc/TTc	8/9	0.176387971008739	3	FACETS	0.612	0.538	0.692	0.204	0.179	0.231	INDETERMINATE	1	TRUE	0	0.594123496512885	3		576	549	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248401	212248401	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1365124530	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	77	285	0	ENST00000342788.4:c.3866C>T	p.Ser1289Phe	p.S1289F	ENST00000342788	NM_005235.2	1289	tCc/tTc	28/28	0.594123496512885	1	FACETS	0.876	0.784	0.971	0.876	0.784	0.971	CLONAL	1	TRUE	0	0.594123496512885	1		285	208	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248774	212248774	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	59	221	0	ENST00000342788.4:c.3493C>T	p.Pro1165Ser	p.P1165S	ENST00000342788	NM_005235.2	1165	Cca/Tca	28/28	0.594123496512885	1	FACETS	0.918	0.81	1	0.918	0.81	1	CLONAL	1	TRUE	0	0.594123496512885	1		221	152	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812293	212812293	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569995088	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	36	629	2	ENST00000342788.4:c.283C>T	p.Arg95Cys	p.R95C	ENST00000342788	NM_005235.2	95	Cgt/Tgt	3/28	0.594123496512885	1	FACETS	0.38	0.315	0.452	0.38	0.315	0.452	SUBCLONAL	1	TRUE	0	0.594123496512885	1		631	224	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215617193	215617193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	69	281	0	ENST00000260947.4:c.1655C>T	p.Ser552Phe	p.S552F	ENST00000260947	NM_000465.2	552	tCc/tTc	7/11	0.594123496512885	1	FACETS	0.883	0.785	0.983	0.883	0.785	0.983	CLONAL	1	TRUE	0	0.594123496512885	1		281	185	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440058	220440059	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	329	857	1	ENST00000243786.2:c.911_912delinsTA	p.Ser304Leu	p.S304L	ENST00000243786	NM_002191.3	304	tCC/tTA	2/2	0.594123496512885	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.594123496512885	1		858	629	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520219	9520219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867360779	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	267	451	0	ENST00000353224.5:c.2050G>A	p.Glu684Lys	p.E684K	ENST00000353224	NM_177990.2	684	Gag/Aag	10/10	0.411966345621221	4	FACETS	0.914	0.86	0.968	0.914	0.86	0.968	CLONAL	2	TRUE	2	0.594123496512885	4		451	784	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546620	9546620	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764351685	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	257	484	0	ENST00000353224.5:c.1402G>A	p.Glu468Lys	p.E468K	ENST00000353224	NM_177990.2	468	Gag/Aag	5/10	0.411966345621221	4	FACETS	0.994	0.936	1	0.994	0.936	1	CLONAL	2	TRUE	2	0.594123496512885	4		484	694	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019434	31019434	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	123	471	0	ENST00000375687.4:c.931G>A	p.Glu311Lys	p.E311K	ENST00000375687	NM_015338.5	311	Gag/Aag	10/13	0.411966345621221	4	FACETS	0.788	0.712	0.867	0.394	0.356	0.434	SUBCLONAL	1	TRUE	2	0.594123496512885	4		471	838	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386360	31386360	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761304747	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	193	774	0	ENST00000328111.2:c.1585C>T	p.Pro529Ser	p.P529S	ENST00000328111	NM_006892.3	529	Ccg/Tcg	15/23	0.411966345621221	4	FACETS	0.978	0.904	1	0.489	0.452	0.528	CLONAL	1	TRUE	2	0.594123496512885	4		774	1059	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387050	31387050	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	179	608	0	ENST00000328111.2:c.1675G>A	p.Glu559Lys	p.E559K	ENST00000328111	NM_006892.3	559	Gaa/Aaa	16/23	0.411966345621221	4	FACETS	0.984	0.907	1	0.492	0.453	0.533	CLONAL	1	TRUE	2	0.594123496512885	4		608	976	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733295	40733295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	133	470	0	ENST00000373198.4:c.3511C>T	p.Pro1171Ser	p.P1171S	ENST00000373198	NM_133170.3	1171	Cct/Tct	26/32	0.411966345621221	4	FACETS	0.917	0.834	1	0.459	0.417	0.503	CLONAL	1	TRUE	2	0.594123496512885	4		470	778	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739001	40739001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	301	544	0	ENST00000373198.4:c.3283G>A	p.Glu1095Lys	p.E1095K	ENST00000373198	NM_133170.3	1095	Gaa/Aaa	24/32	0.411966345621221	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.594123496512885	4		544	787	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877449	40877449	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs201441123	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	115	457	0	ENST00000373198.4:c.2247G>T	p.Gln749His	p.Q749H	ENST00000373198	NM_133170.3	749	caG/caT	15/32	0.411966345621221	4	FACETS	0.987	0.892	1	0.494	0.446	0.544	CLONAL	1	TRUE	2	0.594123496512885	4		457	625	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306677	41306677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs724159835	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	181	742	0	ENST00000373198.4:c.982C>T	p.Arg328Cys	p.R328C	ENST00000373198	NM_133170.3	328	Cgc/Tgc	7/32	0.411966345621221	4	FACETS	0.955	0.88	1	0.478	0.44	0.517	CLONAL	1	TRUE	2	0.594123496512885	4		742	1017	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268774	46268774	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	196	513	1	ENST00000371998.3:c.3059T>A	p.Val1020Asp	p.V1020D	ENST00000371998		1020	gTt/gAt	16/23	0.411966345621221	4	FACETS	1	0.973	1	0.552	0.511	0.594	CLONAL	1	TRUE	2	0.594123496512885	4		514	953	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164712	36164712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	240	621	1	ENST00000300305.3:c.1163C>T	p.Ser388Leu	p.S388L	ENST00000300305		388	tCg/tTg	8/8	0.393708764183751	2	FACETS	0.902	0.843	0.962	0.451	0.421	0.481	CLONAL	1	TRUE	0	0.594123496512885	2		622	896	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067904	30067904	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	342	643	0	ENST00000338641.4:c.1089G>C	p.Met363Ile	p.M363I	ENST00000338641	NM_000268.3	363	atG/atC	11/16	0.455265188883072	4	FACETS	0.934	0.885	0.982	0.934	0.885	0.982	CLONAL	2	TRUE	2	0.594123496512885	4		643	983	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564760	41564760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	164	562	1	ENST00000263253.7:c.4061C>T	p.Pro1354Leu	p.P1354L	ENST00000263253	NM_001429.3	1354	cCa/cTa	25/31	0.455265188883072	4	FACETS	1	0.934	1	0.51	0.468	0.553	CLONAL	1	TRUE	2	0.594123496512885	4		563	863	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713843	30713843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	176	615	1	ENST00000295754.5:c.1168G>A	p.Asp390Asn	p.D390N	ENST00000295754	NM_003242.5	390	Gac/Aac	4/7	0.573356619715237	3	FACETS	0.917	0.846	0.991	0.459	0.423	0.496	CLONAL	1	TRUE	1	0.594123496512885	3		616	838	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053562	37053562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs4986984	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	100	452	0	ENST00000231790.2:c.649C>T	p.Arg217Cys	p.R217C	ENST00000231790	NM_000249.3	217	Cgc/Tgc	8/19	0.573356619715237	3	FACETS	0.749	0.67	0.832	0.374	0.335	0.416	SUBCLONAL	1	TRUE	1	0.594123496512885	3		452	583	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37061932	37061932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	122	441	0	ENST00000231790.2:c.1016C>T	p.Ser339Phe	p.S339F	ENST00000231790	NM_000249.3	339	tCc/tTc	11/19	0.573356619715237	3	FACETS	1	0.942	1	0.524	0.476	0.575	CLONAL	1	TRUE	1	0.594123496512885	3		441	508	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275290	41275290	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113411271	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	138	435	0	ENST00000349496.5:c.1456C>T	p.Arg486Cys	p.R486C	ENST00000349496	NM_001904.3	486	Cgc/Tgc	9/15	0.573356619715237	3	FACETS	0.977	0.892	1	0.488	0.446	0.533	CLONAL	1	TRUE	1	0.594123496512885	3		435	617	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412938	49412938	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	429	665	1	ENST00000418115.1:c.85C>T	p.Gln29Ter	p.Q29*	ENST00000418115	NM_001664.2	29	Cag/Tag	2/5	0.573356619715237	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.594123496512885	3		666	911	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935108	49935108	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760946033	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	160	611	1	ENST00000296474.3:c.1891C>T	p.Arg631Trp	p.R631W	ENST00000296474	NM_002447.2	631	Cgg/Tgg	6/20	0.573356619715237	3	FACETS	0.99	0.91	1	0.495	0.455	0.537	CLONAL	1	TRUE	1	0.594123496512885	3		612	706	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259118	89259118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771292552	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	110	344	0	ENST00000336596.2:c.262C>T	p.Pro88Ser	p.P88S	ENST00000336596	NM_005233.5	88	Ccc/Tcc	3/17	0.231483078161367	6	FACETS	0.764	0.689	0.843			1	INDETERMINATE	2	TRUE	NA	0.594123496512885	6		344	530	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188303	142188303	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	80	363	0	ENST00000350721.4:c.6428C>T	p.Ser2143Leu	p.S2143L	ENST00000350721	NM_001184.3	2143	tCa/tTa	38/47	0.594123496512885	2	FACETS	0.997	0.889	1	0.499	0.444	0.555	CLONAL	1	TRUE	0	0.594123496512885	2		363	270	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188402	142188402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751140070	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	52	272	0	ENST00000350721.4:c.6329C>T	p.Ser2110Phe	p.S2110F	ENST00000350721	NM_001184.3	2110	tCc/tTc	38/47	0.594123496512885	2	FACETS	0.796	0.686	0.913	0.398	0.343	0.457	CLONAL	1	TRUE	0	0.594123496512885	2		272	220	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612203	189612203	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	151	549	0	ENST00000264731.3:c.1955T>A	p.Phe652Tyr	p.F652Y	ENST00000264731	NM_003722.4	652	tTc/tAc	14/14	0.594123496512885	2	FACETS	0.989	0.91	1	0.494	0.455	0.535	CLONAL	1	TRUE	0	0.594123496512885	2		549	514	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1932473	1932473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	370	641	0	ENST00000382891.5:c.1531C>T	p.Pro511Ser	p.P511S	ENST00000382891	NM_133335.3	511	Cct/Tct	6/22	NA	2	FACETS	0.782	0.747	0.818			1	INDETERMINATE	2	TRUE	NA	0.594123496512885	2		641	796	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747919	41747919	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	131	331	1	ENST00000226382.2:c.850C>T	p.Pro284Ser	p.P284S	ENST00000226382	NM_003924.3	284	Ccg/Tcg	3/3	NA	2	FACETS	1	0.932	1			1	INDETERMINATE	1	TRUE	NA	0.594123496512885	2		332	432	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131211	55131211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772605262	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	72	344	0	ENST00000257290.5:c.754G>A	p.Glu252Lys	p.E252K	ENST00000257290	NM_006206.4	252	Gaa/Aaa	5/23	0.411966345621221	4	FACETS	0.844	0.739	0.955	0.422	0.369	0.478	CLONAL	1	TRUE	2	0.594123496512885	4		344	458	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138563	55138563	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	127	432	0	ENST00000257290.5:c.1240C>T	p.Pro414Ser	p.P414S	ENST00000257290	NM_006206.4	414	Cct/Tct	9/23	0.411966345621221	4	FACETS	1	0.91	1	0.501	0.455	0.55	CLONAL	1	TRUE	2	0.594123496512885	4		432	680	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152054	55152054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	157	573	0	ENST00000257290.5:c.2486G>A	p.Gly829Glu	p.G829E	ENST00000257290	NM_006206.4	829	gGa/gAa	18/23	0.411966345621221	4	FACETS	0.979	0.897	1	0.489	0.448	0.532	CLONAL	1	TRUE	2	0.594123496512885	4		573	861	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161362	55161362	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369389595	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	138	481	0	ENST00000257290.5:c.3193G>A	p.Glu1065Lys	p.E1065K	ENST00000257290	NM_006206.4	1065	Gag/Aag	23/23	0.411966345621221	4	FACETS	1	0.951	1	0.532	0.485	0.581	CLONAL	1	TRUE	2	0.594123496512885	4		481	696	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55597559	55597559	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	77	361	0	ENST00000288135.5:c.2207C>T	p.Ala736Val	p.A736V	ENST00000288135	NM_000222.2	736	gCc/gTc	15/21	0.411966345621221	4	FACETS	0.771	0.678	0.87	0.385	0.339	0.435	SUBCLONAL	1	TRUE	2	0.594123496512885	4		361	536	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948779	55948779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776015468	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	98	340	0	ENST00000263923.4:c.3686G>A	p.Arg1229Gln	p.R1229Q	ENST00000263923	NM_002253.2	1229	cGa/cAa	28/30	0.411966345621221	4	FACETS	1	0.938	1	0.533	0.478	0.592	CLONAL	1	TRUE	2	0.594123496512885	4		340	493	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955109	55955109	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	265	426	0	ENST00000263923.4:c.3436G>A	p.Glu1146Lys	p.E1146K	ENST00000263923	NM_002253.2	1146	Gag/Aag	26/30	0.411966345621221	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.594123496512885	4		426	659	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968163	55968163	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	106	471	0	ENST00000263923.4:c.2167A>C	p.Thr723Pro	p.T723P	ENST00000263923	NM_002253.2	723	Act/Cct	15/30	0.411966345621221	4	FACETS	0.751	0.674	0.834	0.376	0.337	0.417	SUBCLONAL	1	TRUE	2	0.594123496512885	4		471	757	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972013	55972013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	138	415	0	ENST00000263923.4:c.1631C>T	p.Ser544Phe	p.S544F	ENST00000263923	NM_002253.2	544	tCc/tTc	12/30	0.411966345621221	4	FACETS	1	0.958	1	0.541	0.493	0.591	CLONAL	1	TRUE	2	0.594123496512885	4		415	684	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984888	55984888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201719457	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	119	437	0	ENST00000263923.4:c.241G>A	p.Asp81Asn	p.D81N	ENST00000263923	NM_002253.2	81	Gat/Aat	3/30	0.594123496512885	3	FACETS	0.701	0.633	0.773			1	SUBCLONAL	1	TRUE	NA	0.594123496512885	3		437	741	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356101	66356101	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	61	393	0	ENST00000273854.3:c.1396C>T	p.Gln466Ter	p.Q466*	ENST00000273854	NM_004439.5	466	Caa/Taa	5/18	0.594123496512885	3	FACETS	0.402	0.346	0.462			1	SUBCLONAL	1	TRUE	NA	0.594123496512885	3		393	663	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155740	106155740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	84	359	0	ENST00000380013.4:c.641C>T	p.Ser214Phe	p.S214F	ENST00000380013	NM_001127208.2	214	tCt/tTt	3/11	0.314815735712366	1	FACETS	0.658	0.588	0.732	0.658	0.588	0.732	INDETERMINATE	1	TRUE	0	0.594123496512885	1		359	302	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193847	106193847	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1183128059	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	90	376	0	ENST00000380013.4:c.4309G>A	p.Glu1437Lys	p.E1437K	ENST00000380013	NM_001127208.2	1437	Gag/Aag	10/11	0.314815735712366	1	FACETS	0.712	0.639	0.788	0.712	0.639	0.788	INDETERMINATE	1	TRUE	0	0.594123496512885	1		376	299	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627767	187627767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	147	474	1	ENST00000441802.2:c.3215C>T	p.Ser1072Phe	p.S1072F	ENST00000441802	NM_005245.3	1072	tCc/tTc	2/27	0.58672988982354	3	FACETS	1	0.976	1	0.586	0.537	0.636	CLONAL	1	TRUE	1	0.594123496512885	3		475	548	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295204	1295205	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	181	106	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.85	0.812	0.886	1	0.995	1	CLONAL	3	TRUE	1	0.594123496512885	2		106	239	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295253	1295253	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1232074117	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	123	158	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.594123496512885	2		158	318	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31423012	31423012	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	125	510	0	ENST00000344624.3:c.3301T>C	p.Ser1101Pro	p.S1101P	ENST00000344624		1101	Tct/Cct	26/33	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.594123496512885	2		510	416	SUCCESS
APC	324	MSKCC	GRCh37	5	112173885	112173885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	92	339	0	ENST00000257430.4:c.2594C>T	p.Pro865Leu	p.P865L	ENST00000257430	NM_000038.5	865	cCa/cTa	16/16	0.542736360422088	3	FACETS	1	0.966	1	0.396	0.355	0.439	CLONAL	1	TRUE	0	0.594123496512885	3		339	338	SUCCESS
APC	324	MSKCC	GRCh37	5	112175589	112175589	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	99	329	0	ENST00000257430.4:c.4298C>T	p.Pro1433Leu	p.P1433L	ENST00000257430	NM_000038.5	1433	cCa/cTa	16/16	0.542736360422088	3	FACETS	1	0.982	1	0.482	0.436	0.53	CLONAL	1	TRUE	0	0.594123496512885	3		329	299	SUCCESS
APC	324	MSKCC	GRCh37	5	112176824	112176824	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060503338	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	79	298	0	ENST00000257430.4:c.5533C>T	p.His1845Tyr	p.H1845Y	ENST00000257430	NM_000038.5	1845	Cat/Tat	16/16	0.542736360422088	3	FACETS	1	0.968	1	0.417	0.371	0.465	CLONAL	1	TRUE	0	0.594123496512885	3		298	276	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562860	176562861	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	286	535	0	ENST00000439151.2:c.756_757delinsTT	p.Leu253Phe	p.L253F	ENST00000439151	NM_022455.4	252	gcCCtt/gcTTtt	2/23	0.594123496512885	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.594123496512885	2		535	463	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680359	30680359	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	144	625	0	ENST00000376406.3:c.1360G>A	p.Asp454Asn	p.D454N	ENST00000376406	NM_014641.2	454	Gac/Aac	5/15	0.455265188883072	4	FACETS	0.902	0.822	0.985	0.451	0.411	0.493	CLONAL	1	TRUE	2	0.594123496512885	4		625	857	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	218	677	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	0.455265188883072	4	FACETS	0.993	0.922	1	0.497	0.461	0.533	CLONAL	1	TRUE	2	0.594123496512885	4		677	1178	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189064	32189064	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	161	654	0	ENST00000375023.3:c.490C>G	p.Pro164Ala	p.P164A	ENST00000375023	NM_004557.3	164	Cca/Gca	4/30	0.455265188883072	4	FACETS	0.947	0.869	1	0.474	0.434	0.515	CLONAL	1	TRUE	2	0.594123496512885	4		654	912	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068107	94068107	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	58	182	0	ENST00000369303.4:c.855G>T	p.Lys285Asn	p.K285N	ENST00000369303	NM_004440.3	285	aaG/aaT	4/17	0.594123496512885	1	FACETS	0.572	0.497	0.652	0.572	0.497	0.652	SUBCLONAL	1	TRUE	0	0.594123496512885	1		182	240	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552739	106552739	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	86	401	0	ENST00000369096.4:c.704A>T	p.Lys235Ile	p.K235I	ENST00000369096	NM_001198.3	235	aAa/aTa	5/7	0.594123496512885	1	FACETS	0.697	0.624	0.773	0.697	0.624	0.773	SUBCLONAL	1	TRUE	0	0.594123496512885	1		401	292	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554975	106554975	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	188	516	0	ENST00000369096.4:c.2092C>T	p.His698Tyr	p.H698Y	ENST00000369096	NM_001198.3	698	Cat/Tat	7/7	0.594123496512885	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.594123496512885	1		516	369	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631392	117631392	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	56	359	0	ENST00000368508.3:c.6286C>G	p.Arg2096Gly	p.R2096G	ENST00000368508	NM_002944.2	2096	Cgg/Ggg	40/43	0.594123496512885	1	FACETS	0.482	0.416	0.552	0.482	0.416	0.552	SUBCLONAL	1	TRUE	0	0.594123496512885	1		359	275	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678025	117678025	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	62	387	0	ENST00000368508.3:c.3908G>T	p.Ser1303Ile	p.S1303I	ENST00000368508	NM_002944.2	1303	aGt/aTt	25/43	0.594123496512885	1	FACETS	0.622	0.544	0.704	0.622	0.544	0.704	SUBCLONAL	1	TRUE	0	0.594123496512885	1		387	236	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706929	117706929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777867372	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	98	453	0	ENST00000368508.3:c.2221C>T	p.His741Tyr	p.H741Y	ENST00000368508	NM_002944.2	741	Cac/Tac	15/43	0.594123496512885	1	FACETS	0.59	0.53	0.653	0.59	0.53	0.653	SUBCLONAL	1	TRUE	0	0.594123496512885	1		453	393	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724401	117724401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	105	559	0	ENST00000368508.3:c.478C>T	p.Pro160Ser	p.P160S	ENST00000368508	NM_002944.2	160	Ccc/Tcc	6/43	0.594123496512885	1	FACETS	0.55	0.495	0.607	0.55	0.495	0.607	SUBCLONAL	1	TRUE	0	0.594123496512885	1		559	452	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201811	152201811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	73	318	0	ENST00000206249.3:c.665C>T	p.Pro222Leu	p.P222L	ENST00000206249	NM_000125.3	222	cCa/cTa	3/8	0.594123496512885	1	FACETS	0.68	0.602	0.761	0.68	0.602	0.761	SUBCLONAL	1	TRUE	0	0.594123496512885	1		318	254	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683649	162683649	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	144	546	0	ENST00000366898.1:c.320T>G	p.Leu107Arg	p.L107R	ENST00000366898	NM_004562.2	107	cTc/cGc	3/12	0.594123496512885	1	FACETS	0.754	0.693	0.816	0.754	0.693	0.816	SUBCLONAL	1	TRUE	0	0.594123496512885	1		546	452	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683767	162683767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	92	486	0	ENST00000366898.1:c.202C>T	p.His68Tyr	p.H68Y	ENST00000366898	NM_004562.2	68	Cac/Tac	3/12	0.594123496512885	1	FACETS	0.637	0.571	0.705	0.637	0.571	0.705	SUBCLONAL	1	TRUE	0	0.594123496512885	1		486	342	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976862	2976862	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	104	553	0	ENST00000396946.4:c.1150C>T	p.His384Tyr	p.H384Y	ENST00000396946	NM_032415.4	384	Cac/Tac	9/25	NA	2	FACETS	0.489	0.438	0.543			1	INDETERMINATE	1	TRUE	NA	0.594123496512885	2		553	716	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441505	6441505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	72	248	0	ENST00000356142.4:c.352C>T	p.Pro118Ser	p.P118S	ENST00000356142	NM_018890.3	118	Cct/Tct	6/7	0.562752263345643	4	FACETS	1	0.954	1	0.589	0.518	0.664	CLONAL	1	TRUE	2	0.594123496512885	4		248	328	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6442026	6442027	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	46	111	0	ENST00000356142.4:c.585_586delinsTT	p.Leu196Phe	p.L196F	ENST00000356142	NM_018890.3	195	gtCCtc/gtTTtc	7/7	0.562752263345643	4	FACETS	1	0.926	1	0.574	0.489	0.666	CLONAL	1	TRUE	2	0.594123496512885	4		111	215	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210029	55210029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	128	442	0	ENST00000275493.2:c.139C>T	p.His47Tyr	p.H47Y	ENST00000275493	NM_005228.3	47	Cat/Tat	2/28	0.562752263345643	4	FACETS	1	0.919	1	0.507	0.46	0.556	CLONAL	1	TRUE	2	0.594123496512885	4		442	678	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381541	81381541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	73	309	0	ENST00000222390.5:c.520G>A	p.Glu174Lys	p.E174K	ENST00000222390	NM_000601.4	174	Gaa/Aaa	5/18	0.562752263345643	4	FACETS	0.896	0.787	1	0.448	0.393	0.507	CLONAL	1	TRUE	2	0.594123496512885	4		309	437	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509658	106509668	+	frameshift_variant	Frame_Shift_Del	DEL	TTCGCAAGCAA	TTCGCAAGCAA	-	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	133	552	0	ENST00000359195.3:c.1654_1664del	p.Arg552GlyfsTer7	p.R552Gfs*7	ENST00000359195	NM_002649.2	551	cTTCGCAAGCAA/c	2/11	0.562752263345643	4	FACETS	0.824	0.748	0.904	0.412	0.374	0.452	CLONAL	1	TRUE	2	0.594123496512885	4		552	866	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380017	116380017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752842662	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	299	399	0	ENST00000397752.3:c.1406G>A	p.Arg469Gln	p.R469Q	ENST00000397752	NM_000245.2	469	cGa/cAa	4/21	0.562752263345643	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.594123496512885	4		399	702	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411923	116411923	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs34589476	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	197	610	0	ENST00000397752.3:c.2908C>T	p.Arg970Cys	p.R970C	ENST00000397752	NM_000245.2	970	Cgc/Tgc	14/21	0.562752263345643	4	FACETS	0.929	0.859	1	0.464	0.429	0.501	CLONAL	1	TRUE	2	0.594123496512885	4		610	1138	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435945	116435945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395763398	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	256	484	0	ENST00000397752.3:c.3940G>A	p.Glu1314Lys	p.E1314K	ENST00000397752	NM_000245.2	1314	Gaa/Aaa	21/21	0.562752263345643	4	FACETS	0.834	0.783	0.886	0.834	0.783	0.886	CLONAL	2	TRUE	2	0.594123496512885	4		484	824	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850945	128850945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762491039	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	376	594	0	ENST00000249373.3:c.1792G>A	p.Gly598Arg	p.G598R	ENST00000249373	NM_005631.4	598	Ggg/Agg	10/12	0.562752263345643	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.594123496512885	4		594	941	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972963	68972963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142510968	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	101	422	0	ENST00000288368.4:c.1288G>A	p.Glu430Lys	p.E430K	ENST00000288368	NM_024870.2	430	Gaa/Aaa	11/40	0.58672988982354	3	FACETS	0.88	0.79	0.975	0.44	0.395	0.488	CLONAL	1	TRUE	1	0.594123496512885	3		422	501	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981327	68981328	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	66	328	0	ENST00000288368.4:c.1399_1400delinsAA	p.Gly467Lys	p.G467K	ENST00000288368	NM_024870.2	467	GGa/AAa	12/40	0.58672988982354	3	FACETS	0.853	0.745	0.967	0.426	0.372	0.484	CLONAL	1	TRUE	1	0.594123496512885	3		328	338	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5077454	5077454	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	55	278	0	ENST00000381652.3:c.1866T>G	p.Asn622Lys	p.N622K	ENST00000381652	NM_004972.3	622	aaT/aaG	15/25	0.594123496512885	1	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	0	0.594123496512885	1		278	130	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340386	8340386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	154	524	0	ENST00000356435.5:c.5210C>T	p.Ser1737Phe	p.S1737F	ENST00000356435		1737	tCc/tTc	31/35	0.594123496512885	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.594123496512885	1		524	334	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499838	8499838	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	126	393	0	ENST00000356435.5:c.2131C>T	p.Pro711Ser	p.P711S	ENST00000356435		711	Cct/Tct	14/35	0.594123496512885	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.594123496512885	1		393	275	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521454	8521454	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	145	574	0	ENST00000356435.5:c.784T>G	p.Ser262Ala	p.S262A	ENST00000356435		262	Tca/Gca	9/35	0.594123496512885	1	FACETS	0.983	0.91	1	0.983	0.91	1	CLONAL	1	TRUE	0	0.594123496512885	1		574	349	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971000	21971000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	198	359	0	ENST00000304494.5:c.358G>T	p.Glu120Ter	p.E120*	ENST00000304494	NM_000077.4	120	Gag/Tag	2/3	0.594123496512885	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.594123496512885	1		359	382	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209585	98209585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536440590	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	180	770	0	ENST00000331920.6:c.3953C>T	p.Pro1318Leu	p.P1318L	ENST00000331920	NM_000264.3	1318	cCg/cTg	23/24	NA	2	FACETS	0.932	0.863	1			1	INDETERMINATE	1	TRUE	NA	0.594123496512885	2		770	650	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760378	133760378	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761427686	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	78	660	0	ENST00000318560.5:c.2701C>T	p.Pro901Ser	p.P901S	ENST00000318560	NM_005157.4	901	Ccc/Tcc	11/11	0.489178235900477	1	FACETS	0.399	0.351	0.449	0.399	0.351	0.449	SUBCLONAL	1	TRUE	0	0.594123496512885	1		660	463	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781361	135781361	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1164741723	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	90	717	0	ENST00000298552.3:c.1604C>T	p.Pro535Leu	p.P535L	ENST00000298552	NM_001162426.1	535	cCt/cTt	15/23	0.489178235900477	1	FACETS	0.368	0.327	0.412	0.368	0.327	0.412	SUBCLONAL	1	TRUE	0	0.594123496512885	1		717	579	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814253	76814253	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	78	191	0	ENST00000373344.5:c.6391C>T	p.Arg2131Ter	p.R2131*	ENST00000373344	NM_000489.3	2131	Cga/Tga	29/35	0.594123496512885	2	FACETS	1	0.974	1			1	CLONAL	1	TRUE	NA	0.594123496512885	2		191	202	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854907	76854907	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	123	239	0	ENST00000373344.5:c.5929C>T	p.Pro1977Ser	p.P1977S	ENST00000373344	NM_000489.3	1977	Cct/Tct	25/35	0.594123496512885	2	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.594123496512885	2		239	309	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888843	76888843	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046563-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	207	206	0	ENST00000373344.5:c.4986del	p.Gln1663ArgfsTer17	p.Q1663Rfs*17	ENST00000373344	NM_000489.3	1662	ccT/cc	19/35	0.594123496512885	2	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.594123496512885	2		206	286	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625652	1625652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533848977	NA	P-0046564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	114	851	1	ENST00000344749.5:c.422C>T	p.Ser141Leu	p.S141L	ENST00000344749	NM_001136139.2	141	tCg/tTg	7/19	0.305284236921703	1	FACETS	0.75	0.679	0.825	0.75	0.679	0.825	SUBCLONAL	1	TRUE	0	0.464807268253378	1		852	502	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260325	10260325	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757300501	NA	P-0046564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	87	562	1	ENST00000340748.4:c.2342C>T	p.Ala781Val	p.A781V	ENST00000340748		781	gCg/gTg	25/40	0.305284236921703	1	FACETS	0.748	0.667	0.834	0.748	0.667	0.834	SUBCLONAL	1	TRUE	0	0.464807268253378	1		563	384	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18963795	18963795	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0046564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	39	333	0	ENST00000262803.5:c.973-1G>C		p.X325_splice	ENST00000262803	NM_002911.3	325			1	2	FACETS	0.746	0.623	0.88	0.746	0.623	0.88	SUBCLONAL	1	TRUE	1	0.464807268253378	2		333	225	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438656	49438656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	55	767	0	ENST00000301067.7:c.4834C>T	p.Arg1612Cys	p.R1612C	ENST00000301067	NM_003482.3	1612	Cgc/Tgc	19/54	0.164644193530993	3	FACETS	0.877	0.749	1	0.438	0.374	0.508	CLONAL	1	TRUE	1	0.22	3		767	633	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440856	52440856	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	67	709	0	ENST00000460680.1:c.648del	p.Ala217ProfsTer14	p.A217Pfs*14	ENST00000460680	NM_004656.3	216	ctC/ct	8/17	1	2	FACETS	0.971	0.844	1	0.971	0.844	1	CLONAL	1	TRUE	1	0.22	2		709	627	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702588	52702588	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	34	433	0	ENST00000394830.3:c.310del	p.Glu104LysfsTer9	p.E104Kfs*9	ENST00000394830	NM_018313.4	104	Gaa/aa	4/30	1	2	FACETS	0.719	0.587	0.867	0.719	0.587	0.867	SUBCLONAL	1	TRUE	1	0.22	2		433	430	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438656	49438656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	319	767	0	ENST00000301067.7:c.4834C>T	p.Arg1612Cys	p.R1612C	ENST00000301067	NM_003482.3	1612	Cgc/Tgc	19/54	1	2	FACETS	0.944	0.89	0.998	0.944	0.89	0.998	CLONAL	1	TRUE	1	0.563934291832968	2		767	1199	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440856	52440856	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	325	709	0	ENST00000460680.1:c.648del	p.Ala217ProfsTer14	p.A217Pfs*14	ENST00000460680	NM_004656.3	216	ctC/ct	8/17	0.563934291832968	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.563934291832968	1		709	802	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702588	52702588	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046566-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	213	433	0	ENST00000394830.3:c.310del	p.Glu104LysfsTer9	p.E104Kfs*9	ENST00000394830	NM_018313.4	104	Gaa/aa	4/30	0.563934291832968	1	FACETS	0.932	0.872	0.993	0.932	0.872	0.993	CLONAL	1	TRUE	0	0.563934291832968	1		433	582	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622502	28622502	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	30	454	0	ENST00000241453.7:c.1115G>C	p.Arg372Thr	p.R372T	ENST00000241453	NM_004119.2	372	aGg/aCg	9/24	0.291585153890856	0	FACETS	0.324	0.261	0.396			1	SUBCLONAL	1	TRUE	0	0.32	0		454	393	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857531	68857532	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	AA	novel	NA	P-0046567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	25	466	0	ENST00000261769.5:c.2164+3_2164+4dup		p.X722_splice	ENST00000261769	NM_004360.3	722			1	2	FACETS	0.435	0.343	0.542	0.435	0.343	0.542	SUBCLONAL	1	TRUE	1	0.32	2		466	359	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117862	70117862	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	72	564	0	ENST00000245479.2:c.330C>G	p.Asn110Lys	p.N110K	ENST00000245479	NM_000346.3	110	aaC/aaG	1/3	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.32	2		564	411	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279669	18279669	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748340519	NA	P-0046567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	51	706	0	ENST00000222254.8:c.1942G>A	p.Glu648Lys	p.E648K	ENST00000222254	NM_005027.3	648	Gag/Aag	15/16	1	2	FACETS	0.47	0.399	0.549	0.47	0.399	0.549	SUBCLONAL	1	TRUE	1	0.32	2		706	678	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0046568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	77	454	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	0.838	0.74	0.942	0.838	0.74	0.942	CLONAL	1	TRUE	1	0.470075604381867	2		454	391	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021785	71021785	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs112795301	NA	P-0046568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	71	320	0	ENST00000318789.4:c.1573C>T	p.Arg525Ter	p.R525*	ENST00000318789	NM_032682.5	525	Cga/Tga	18/21	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.470075604381867	2		320	266	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416659	29416659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	105	595	1	ENST00000389048.3:c.4294C>T	p.Arg1432Trp	p.R1432W	ENST00000389048	NM_004304.4	1432	Cgg/Tgg	29/29	1	2	FACETS	0.841	0.757	0.931	0.841	0.757	0.931	CLONAL	1	TRUE	1	0.470075604381867	2		596	531	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480460	89480460	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	70	331	0	ENST00000336596.2:c.2297G>A	p.Gly766Glu	p.G766E	ENST00000336596	NM_005233.5	766	gGa/gAa	13/17	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.470075604381867	2		331	284	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014154	70014154	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	122	571	0	ENST00000394351.3:c.1015A>G	p.Thr339Ala	p.T339A	ENST00000394351	NM_000248.3	339	Aca/Gca	9/9	1	2	FACETS	0.959	0.871	1	0.959	0.871	1	CLONAL	1	TRUE	1	0.470075604381867	2		571	541	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591014	67591015	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	35	204	0	ENST00000274335.5:c.1608dup	p.Glu537Ter	p.E537*	ENST00000274335		536	agt/agTt	12/15	0.123368399927629	4	FACETS	0.799	0.667	0.941	0.799	0.667	0.941	INDETERMINATE	2	TRUE	2	0.470075604381867	4		204	137	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591134	67591135	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0046568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	35	280	0	ENST00000274335.5:c.1732_1733dup	p.Asp578GlufsTer5	p.D578Efs*5	ENST00000274335		576	acg/acGAg	12/15	0.123368399927629	4	FACETS	0.995	0.822	1	0.498	0.411	0.593	INDETERMINATE	1	TRUE	2	0.470075604381867	4		280	220	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046317	69046317	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	21	541	0	ENST00000288368.4:c.3790G>T	p.Asp1264Tyr	p.D1264Y	ENST00000288368	NM_024870.2	1264	Gac/Tac	32/40	1	2	FACETS	0.221	0.169	0.281	0.221	0.169	0.281	SUBCLONAL	1	TRUE	1	0.470075604381867	2		541	405	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542213	141542213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046568-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	144	643	0	ENST00000220592.5:c.2510G>A	p.Arg837Gln	p.R837Q	ENST00000220592	NM_012154.3	837	cGa/cAa	19/19	1	2	FACETS	0.898	0.821	0.979	0.898	0.821	0.979	CLONAL	1	TRUE	1	0.470075604381867	2		643	682	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0046569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	29	286	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.207282407570839	1	FACETS	0.192	0.154	0.236	0.192	0.154	0.236	INDETERMINATE	1	TRUE	0	0.524634218156452	1		286	425	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500882	8500882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs191877533	NA	P-0046569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	132	458	0	ENST00000356435.5:c.2000C>T	p.Ser667Leu	p.S667L	ENST00000356435		667	tCg/tTg	13/35	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.524634218156452	2		458	441	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921522	178921523	+	inframe_insertion	In_Frame_Ins	INS	-	-	AATAAAAATTCTTTGTGCAACCTACGTGAATGT	novel	NA	P-0046569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	13	290	0	ENST00000263967.3:c.1007_1039dup	p.Ile336_Val346dup	p.I336_V346dup	ENST00000263967	NM_006218.2	336	aga/agAATAAAAATTCTTTGTGCAACCTACGTGAATGTa	5/21	0.207282407570839	1	FACETS	0.247	0.177	0.332	0.247	0.177	0.332	INDETERMINATE	1	TRUE	0	0.524634218156452	1		290	148	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0046570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	165	363	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.341955932976546	2	FACETS	1	0.988	1	0.692	0.639	0.746	CLONAL	1	TRUE	0	0.444021127683141	2		363	537	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971177	21971177	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913382	NA	P-0046570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	183	382	0	ENST00000304494.5:c.181G>T	p.Glu61Ter	p.E61*	ENST00000304494	NM_000077.4	61	Gag/Tag	2/3	0.444021127683141	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.444021127683141	1		382	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs530941076	NA	P-0046570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	173	697	0	ENST00000269305.4:c.658T>C	p.Tyr220His	p.Y220H	ENST00000269305	NM_001126112.2	220	Tat/Cat	6/11	0.444021127683141	1	FACETS	0.986	0.912	1	0.986	0.912	1	CLONAL	1	TRUE	0	0.444021127683141	1		697	615	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281320	49281320	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs776274176	NA	P-0046570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	188	747	0	ENST00000282018.3:c.367T>C	p.Tyr123His	p.Y123H	ENST00000282018	NM_020377.2	123	Tac/Cac	1/1	0.444021127683141	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.444021127683141	1		747	650	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652209	36652210	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	175	804	0	ENST00000244741.5:c.332dup	p.Asp112GlyfsTer17	p.D112Gfs*17	ENST00000244741	NM_000389.4	111	gtg/gTtg	2/3	1	2	FACETS	0.979	0.903	1	0.979	0.903	1	CLONAL	1	TRUE	1	0.444021127683141	2		804	805	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933622	39933622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200141801	NA	P-0046570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	118	688	0	ENST00000378444.4:c.977C>T	p.Pro326Leu	p.P326L	ENST00000378444	NM_001123385.1	326	cCg/cTg	4/15	1	2	FACETS	0.802	0.724	0.883	0.802	0.724	0.883	CLONAL	1	TRUE	1	0.444021127683141	2		688	663	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0046571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	105	363	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.211387665874044	3	FACETS	0.809	0.73	0.892	0.809	0.73	0.892	INDETERMINATE	2	TRUE	1	0.356474115639859	3		363	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0046571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	271	868	4	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	0.229555369799063	2	FACETS	0.849	0.799	0.901	0.849	0.799	0.901	CLONAL	2	TRUE	0	0.356474115639859	2		872	895	SUCCESS
APC	324	MSKCC	GRCh37	5	112175246	112175246	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1057517558	NA	P-0046571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	66	259	0	ENST00000257430.4:c.3956del	p.Pro1319LeufsTer2	p.P1319Lfs*2	ENST00000257430	NM_000038.5	1319	Cct/ct	16/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.356474115639859	2		259	268	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174399	11174400	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGG	novel	NA	P-0046571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	124	624	0	ENST00000361445.4:c.7273_7275dup	p.Pro2425dup	p.P2425dup	ENST00000361445	NM_004958.3	2425	-/CCC	53/58	0.356474115639859	1	FACETS	0.993	0.901	1	0.993	0.901	1	CLONAL	1	TRUE	0	0.356474115639859	1		624	576	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913517	NA	P-0046572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	177	349	0	ENST00000288135.5:c.1676T>A	p.Val559Asp	p.V559D	ENST00000288135	NM_000222.2	559	gTt/gAt	11/21	1	2	FACETS	0.969	0.904	1	0.969	0.904	1	CLONAL	1	TRUE	1	0.891308312238342	2		349	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579345	7579353	+	inframe_deletion	In_Frame_Del	DEL	CAAGAAGCC	CAAGAAGCC	-	novel	NA	P-0046573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	232	662	0	ENST00000269305.4:c.334_342del	p.Gly112_Leu114del	p.G112_L114del	ENST00000269305	NM_001126112.2	112	GGCTTCTTG/-	4/11	0.588755922351005	1	FACETS	0.969	0.911	1	0.969	0.911	1	CLONAL	1	TRUE	0	0.588755922351005	1		662	574	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945444	151945444	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	237	678	0	ENST00000262189.6:c.2075T>C	p.Val692Ala	p.V692A	ENST00000262189	NM_170606.2	692	gTc/gCc	14/59	1	2	FACETS	0.976	0.913	1	0.976	0.913	1	CLONAL	1	TRUE	1	0.588755922351005	2		678	825	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	79	424	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.916	0.812	1	0.916	0.812	1	CLONAL	1	TRUE	1	0.485769125095687	2		424	355	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0046574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	195	716	1	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.485769125095687	1	FACETS	0.939	0.874	1	0.939	0.874	1	CLONAL	1	TRUE	0	0.485769125095687	1		717	647	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245521	153245521	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	71	347	0	ENST00000281708.4:c.1670G>T	p.Gly557Val	p.G557V	ENST00000281708	NM_033632.3	557	gGa/gTa	11/12	1	2	FACETS	0.878	0.772	0.99	0.878	0.772	0.99	CLONAL	1	TRUE	1	0.485769125095687	2		347	333	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654616	67654616	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1259610303	NA	P-0046574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	101	427	0	ENST00000264010.4:c.1103G>A	p.Arg368His	p.R368H	ENST00000264010	NM_006565.3	368	cGt/cAt	6/12	1	2	FACETS	0.896	0.805	0.992	0.896	0.805	0.992	CLONAL	1	TRUE	1	0.485769125095687	2		427	464	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681139	37681139	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0046574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	112	429	0	ENST00000447079.4:c.3307+1G>A		p.X1103_splice	ENST00000447079	NM_015083.1	1103			1	2	FACETS	0.892	0.806	0.982	0.892	0.806	0.982	CLONAL	1	TRUE	1	0.485769125095687	2		429	517	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419867	41419867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1569159161	NA	P-0046574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	345	538	0	ENST00000373198.4:c.454G>A	p.Ala152Thr	p.A152T	ENST00000373198	NM_133170.3	152	Gcc/Acc	3/32	0.485769125095687	4	FACETS	0.973	0.928	1	0.973	0.928	1	CLONAL	3	TRUE	1	0.485769125095687	4		538	723	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936096	178936096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	47	469	0	ENST00000263967.3:c.1638G>C	p.Gln546His	p.Q546H	ENST00000263967	NM_006218.2	546	caG/caC	10/21	1	2	FACETS	0.62	0.526	0.723	0.62	0.526	0.723	SUBCLONAL	1	TRUE	1	0.485769125095687	2		469	312	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0046574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	77	215	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.485769125095687	2		215	270	SUCCESS
APC	324	MSKCC	GRCh37	5	112155002	112155002	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	108	510	1	ENST00000257430.4:c.1273G>T	p.Glu425Ter	p.E425*	ENST00000257430	NM_000038.5	425	Gaa/Taa	10/16	1	2	FACETS	0.844	0.76	0.932	0.844	0.76	0.932	CLONAL	1	TRUE	1	0.485769125095687	2		511	527	SUCCESS
APC	324	MSKCC	GRCh37	5	112175587	112175794	+	frameshift_variant	Frame_Shift_Del	DEL	ACCAAGCAGAAGTAAAACACCTCCACCACCTCCTCAAACAGCTCAAACCAAGCGAGAAGTACCTAAAAATAAAGCACCTACTGCTGAAAAGAGAGAGAGTGGACCTAAGCAAGCTGCAGTAAATGCTGCAGTTCAGAGGGTCCAGGTTCTTCCAGATGCTGATACTTTATTACATTTTGCCACGGAAAGTACTCCAGATGGATTTTCT	ACCAAGCAGAAGTAAAACACCTCCACCACCTCCTCAAACAGCTCAAACCAAGCGAGAAGTACCTAAAAATAAAGCACCTACTGCTGAAAAGAGAGAGAGTGGACCTAAGCAAGCTGCAGTAAATGCTGCAGTTCAGAGGGTCCAGGTTCTTCCAGATGCTGATACTTTATTACATTTTGCCACGGAAAGTACTCCAGATGGATTTTCT	-	novel	NA	P-0046574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	51	309	0	ENST00000257430.4:c.4296_4503del	p.Pro1433ValfsTer5	p.P1433Vfs*5	ENST00000257430	NM_000038.5	1432	ccACCAAGCAGAAGTAAAACACCTCCACCACCTCCTCAAACAGCTCAAACCAAGCGAGAAGTACCTAAAAATAAAGCACCTACTGCTGAAAAGAGAGAGAGTGGACCTAAGCAAGCTGCAGTAAATGCTGCAGTTCAGAGGGTCCAGGTTCTTCCAGATGCTGATACTTTATTACATTTTGCCACGGAAAGTACTCCAGATGGATTTTCT/cc	16/16	1	2	FACETS	0.593	0.506	0.688	0.593	0.506	0.688	SUBCLONAL	1	TRUE	1	0.485769125095687	2		309	354	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952063	76952063	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0046574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	16	296	0	ENST00000373344.5:c.370+2T>C		p.X124_splice	ENST00000373344	NM_000489.3	124			1	2	FACETS	0.262	0.194	0.344	0.262	0.194	0.344	SUBCLONAL	1	TRUE	1	0.485769125095687	2		296	251	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0046575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	31	359	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.994	0.804	1	0.994	0.804	1	CLONAL	1	TRUE	1	0.16	2		359	390	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0046575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	40	363	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.998	0.829	1	0.998	0.829	1	CLONAL	1	TRUE	1	0.16	2		363	501	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	52	473	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.954	0.811	1	0.954	0.811	1	CLONAL	1	TRUE	1	0.16	2		474	681	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	51	382	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.16	2		382	515	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0046575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	65	620	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.16	2		620	710	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597402	10597402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770453522	NA	P-0046575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	91	801	1	ENST00000171111.5:c.1801C>T	p.Arg601Trp	p.R601W	ENST00000171111	NM_203500.1	601	Cgg/Tgg	6/6	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.16	2		802	1025	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0046575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	15	353	0	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	0.609	0.444	0.807	0.609	0.444	0.807	SUBCLONAL	1	TRUE	1	0.16	2		353	308	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637649	176637650	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0046575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	47	495	0	ENST00000439151.2:c.2256_2257del	p.Pro753LysfsTer11	p.P753Kfs*11	ENST00000439151	NM_022455.4	750	gCT/g	5/23	1	2	FACETS	0.945	0.796	1	0.945	0.796	1	CLONAL	1	TRUE	1	0.16	2		495	622	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7120689	7120689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568426700	NA	P-0046575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	87	678	0	ENST00000302850.5:c.3601C>T	p.Arg1201Trp	p.R1201W	ENST00000302850	NM_000208.2	1201	Cgg/Tgg	20/22	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.16	2		678	950	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0046575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	41	625	5	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.719	0.597	0.855	0.719	0.597	0.855	SUBCLONAL	1	TRUE	1	0.16	2		630	713	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214893	36214894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0046575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	66	746	0	ENST00000222270.7:c.3325dup	p.Arg1109ProfsTer4	p.R1109Pfs*4	ENST00000222270	NM_014727.1	1107	acc/aCcc	8/37	1	2	FACETS	0.823	0.712	0.943	0.823	0.712	0.943	CLONAL	1	TRUE	1	0.16	2		746	1003	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226345	2226345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	101	949	1	ENST00000326181.6:c.1958G>A	p.Arg653Gln	p.R653Q	ENST00000326181	NM_032271.2	653	cGg/cAg	20/21	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.16	2		950	1074	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973793	131973793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782577	NA	P-0046575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	24	284	0	ENST00000265335.6:c.3496C>T	p.Arg1166Trp	p.R1166W	ENST00000265335		1166	Cgg/Tgg	23/25	1	2	FACETS	0.917	0.72	1	0.917	0.72	1	CLONAL	1	TRUE	1	0.16	2		284	327	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023460	27023461	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGGGGGC	novel	NA	P-0046575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	39	451	0	ENST00000324856.7:c.568_574dup	p.Leu192ArgfsTer210	p.L192Rfs*210	ENST00000324856	NM_006015.4	189	ggc/ggCGGGGGCc	1/20	1	2	FACETS	0.869	0.719	1	0.869	0.719	1	CLONAL	1	TRUE	1	0.16	2		451	561	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342848	118342848	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	23	265	1	ENST00000534358.1:c.977del	p.Lys326SerfsTer74	p.K326Sfs*74	ENST00000534358	NM_005933.3	325	gAa/ga	3/36	1	2	FACETS	0.943	0.736	1	0.943	0.736	1	CLONAL	1	TRUE	1	0.16	2		266	305	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924286	112924286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918467	NA	P-0046575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	47	681	1	ENST00000351677.2:c.1232C>T	p.Thr411Met	p.T411M	ENST00000351677	NM_002834.3	411	aCg/aTg	11/16	1	2	FACETS	0.811	0.683	0.954	0.811	0.683	0.954	CLONAL	1	TRUE	1	0.16	2		682	724	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129015	30129015	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	57	618	0	ENST00000263025.4:c.751C>G	p.Leu251Val	p.L251V	ENST00000263025	NM_002746.2	251	Ctg/Gtg	5/9	1	2	FACETS	0.969	0.83	1	0.969	0.83	1	CLONAL	1	TRUE	1	0.16	2		618	735	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602854	10602854	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	108	833	0	ENST00000171111.5:c.724G>A	p.Glu242Lys	p.E242K	ENST00000171111	NM_203500.1	242	Gag/Aag	3/6	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.16	2		833	1105	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638066	176638066	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	59	604	0	ENST00000439151.2:c.2669del	p.Phe890SerfsTer22	p.F890Sfs*22	ENST00000439151	NM_022455.4	889	cTt/ct	5/23	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.16	2		604	631	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120288	94120290	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0046575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	30	363	0	ENST00000369303.4:c.761_763del	p.Gly254del	p.G254del	ENST00000369303	NM_004440.3	254	gGAGaa/gaa	3/17	1	2	FACETS	0.904	0.728	1	0.904	0.728	1	CLONAL	1	TRUE	1	0.16	2		363	415	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0046576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	94	928	1	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	1	2	FACETS	0.407	0.361	0.457	0.407	0.361	0.457	SUBCLONAL	1	TRUE	1	0.363716710587813	2		929	1269	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0046577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	63	354	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.598	0.519	0.684	0.598	0.519	0.684	SUBCLONAL	1	TRUE	1	0.4909813453955	2		354	429	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0046577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	72	451	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	0.544	0.476	0.617	0.544	0.476	0.617	SUBCLONAL	1	TRUE	1	0.4909813453955	2		451	539	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0046577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	13	362	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.126	0.089	0.172	0.126	0.089	0.172	SUBCLONAL	1	TRUE	1	0.4909813453955	2		362	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578513	7578513	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	236	917	0	ENST00000269305.4:c.417G>C	p.Lys139Asn	p.K139N	ENST00000269305	NM_001126112.2	139	aaG/aaC	5/11	1	2	FACETS	0.909	0.848	0.971	0.909	0.848	0.971	CLONAL	1	TRUE	1	0.4909813453955	2		917	1058	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0046577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	49	325	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.4909813453955	5	FACETS	0.777	0.665	0.897	0.518	0.443	0.598	SUBCLONAL	2	TRUE	2	0.4909813453955	5		325	223	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0046577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	18	353	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	1	2	FACETS	0.461	0.349	0.591	0.461	0.349	0.591	SUBCLONAL	1	TRUE	1	0.4909813453955	2		353	159	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711933	89711933	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	44	494	0	ENST00000371953.3:c.551A>G	p.Asn184Ser	p.N184S	ENST00000371953	NM_000314.4	184	aAt/aGt	6/9	0.4909813453955	5	FACETS	1	0.884	1	0.353	0.297	0.414	CLONAL	1	TRUE	2	0.4909813453955	5		494	294	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720837	89720838	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs1249338494	NA	P-0046577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	50	326	0	ENST00000371953.3:c.989_990del	p.Lys330ArgfsTer12	p.K330Rfs*12	ENST00000371953	NM_000314.4	330	AAa/a	8/9	0.4909813453955	5	FACETS	1	0.96	1	0.462	0.395	0.534	CLONAL	1	TRUE	2	0.4909813453955	5		326	255	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161472	2161472	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	112	689	1	ENST00000434045.2:c.55T>C	p.Ser19Pro	p.S19P	ENST00000434045	NM_001127598.1	19	Tct/Cct	2/5	1	2	FACETS	0.554	0.498	0.614	0.554	0.498	0.614	SUBCLONAL	1	TRUE	1	0.4909813453955	2		690	823	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142443	119142443	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0046577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	62	364	0	ENST00000264033.4:c.444-2A>C		p.X148_splice	ENST00000264033	NM_005188.3	148			1	2	FACETS	0.957	0.835	1	0.957	0.835	1	CLONAL	1	TRUE	1	0.4909813453955	2		364	264	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577544	7577544	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587780074	NA	P-0046578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	325	726	1	ENST00000269305.4:c.737T>C	p.Met246Thr	p.M246T	ENST00000269305	NM_001126112.2	246	aTg/aCg	7/11	0.382872629409577	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.382872629409577	2		727	773	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436296	110436297	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGG	rs34412495	NA	P-0046578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	22	124	3	ENST00000375856.3:c.2102_2104dup	p.Ala701dup	p.A701dup	ENST00000375856	NM_003749.2	701	gtg/gCCGtg	1/2	0.20032940822768	3	FACETS	0.796	0.622	0.995	0.265	0.207	0.332	INDETERMINATE	1	TRUE	0	0.382872629409577	3		127	172	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035075	42035075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	246	694	0	ENST00000219905.7:c.4918del	p.Val1640SerfsTer10	p.V1640Sfs*10	ENST00000219905	NM_001164273.1	1639	gaG/ga	15/24	0.257383413541373	3	FACETS	1	0.98	1			1	CLONAL	2	TRUE	NA	0.382872629409577	3		694	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0046579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	24	593	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.36006820829147	3	FACETS	0.247	0.193	0.31	0.082	0.064	0.104	SUBCLONAL	1	TRUE	0	0.36006820829147	3		593	637	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	130	427	0				ENST00000310581	NM_198253.2	-/1132			0.36006820829147	6	FACETS	1	0.97	1	1	0.97	1	CLONAL	4	TRUE	2	0.36006820829147	6		427	282	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881392	37881392	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	183	674	0	ENST00000269571.5:c.2584A>G	p.Thr862Ala	p.T862A	ENST00000269571		862	Aca/Gca	21/27	0.36006820829147	9	FACETS	0.882	0.812	0.955			1	CLONAL	2	TRUE	NA	0.36006820829147	9		674	1303	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0046579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	37	757	1	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.36006820829147	3	FACETS	0.301	0.247	0.361	0.1	0.082	0.121	SUBCLONAL	1	TRUE	0	0.36006820829147	3		758	807	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576870	7576870	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs876659384	NA	P-0046579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	370	620	0	ENST00000269305.4:c.976G>T	p.Glu326Ter	p.E326*	ENST00000269305	NM_001126112.2	326	Gaa/Taa	9/11	0.36006820829147	3	FACETS	0.972	0.933	1	1	0.995	1	CLONAL	4	TRUE	0	0.36006820829147	3		620	624	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878061	48878062	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1131690852	NA	P-0046579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	52	183	0	ENST00000267163.4:c.19dup	p.Arg7ProfsTer24	p.R7Pfs*24	ENST00000267163	NM_000321.2	5	acc/aCcc	1/27	0.293291705775905	1	FACETS	1	0.936	1	1	0.981	1	CLONAL	2	TRUE	0	0.36006820829147	1		183	108	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270108	66270108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756653935	NA	P-0046579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	35	371	0	ENST00000273854.3:c.1774G>A	p.Val592Ile	p.V592I	ENST00000273854	NM_004439.5	592	Gtc/Atc	8/18	0.218407318692908	3	FACETS	0.811	0.667	0.97	0.27	0.222	0.324	CLONAL	1	TRUE	0	0.36006820829147	3		371	283	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78704435	78704435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	48	474	0	ENST00000306801.3:c.583G>A	p.Asp195Asn	p.D195N	ENST00000306801	NM_020761.2	195	Gac/Aac	5/34	0.36006820829147	4	FACETS	0.633	0.534	0.741	0.316	0.267	0.371	SUBCLONAL	1	TRUE	2	0.36006820829147	4		474	573	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449636	187449636	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	57	437	0	ENST00000232014.4:c.244G>A	p.Gly82Arg	p.G82R	ENST00000232014	NM_001130845.1	82	Gga/Aga	4/10	0.195066022568164	5	FACETS	1	0.89	1	0.347	0.298	0.401	INDETERMINATE	1	TRUE	2	0.36006820829147	5		437	468	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105721	27105721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	37	393	0	ENST00000324856.7:c.5332G>A	p.Glu1778Lys	p.E1778K	ENST00000324856	NM_006015.4	1778	Gaa/Aaa	20/20	0.195066022568164	5	FACETS	0.829	0.684	0.99	0.276	0.228	0.33	INDETERMINATE	1	TRUE	2	0.36006820829147	5		393	382	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105731	27105731	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	44	406	0	ENST00000324856.7:c.5342T>C	p.Val1781Ala	p.V1781A	ENST00000324856	NM_006015.4	1781	gTa/gCa	20/20	0.195066022568164	5	FACETS	0.909	0.764	1	0.303	0.254	0.357	INDETERMINATE	1	TRUE	2	0.36006820829147	5		406	414	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445455	49445464	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGAGATTC	AGGGAGATTC	-	novel	NA	P-0046579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	332	792	0	ENST00000301067.7:c.2002_2011del	p.Glu668CysfsTer259	p.E668Cfs*259	ENST00000301067	NM_003482.3	668	GAATCTCCCTtg/tg	10/54	0.36006820829147	3	FACETS	0.942	0.896	0.989	1	0.995	1	CLONAL	3	TRUE	1	0.36006820829147	3		792	770	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626826	14626826	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1437276279	NA	P-0046579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	58	624	0	ENST00000254322.2:c.949G>C	p.Glu317Gln	p.E317Q	ENST00000254322	NM_006145.1	317	Gag/Cag	3/3	0.195066022568164	5	FACETS	0.743	0.637	0.858	0.248	0.212	0.286	INDETERMINATE	1	TRUE	2	0.36006820829147	5		624	668	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147770	61147770	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	18	193	0	ENST00000295025.8:c.1080C>G	p.Phe360Leu	p.F360L	ENST00000295025	NM_002908.2	360	ttC/ttG	10/11	0.213834234067018	4	FACETS	0.525	0.396	0.678	0.263	0.197	0.339	INDETERMINATE	1	TRUE	2	0.36006820829147	4		193	259	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478028	138478028	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	36	369	0	ENST00000289153.2:c.158C>G	p.Ser53Cys	p.S53C	ENST00000289153	NM_006219.2	53	tCt/tGt	1/22	0.195066022568164	5	FACETS	0.88	0.725	1	0.293	0.241	0.351	INDETERMINATE	1	TRUE	2	0.36006820829147	5		369	350	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542231	141542231	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046579-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	27	481	0	ENST00000220592.5:c.2492C>G	p.Ser831Cys	p.S831C	ENST00000220592	NM_012154.3	831	tCt/tGt	19/19	0.150885859510447	4	FACETS	0.41	0.326	0.508	0.205	0.163	0.254	INDETERMINATE	1	TRUE	2	0.36006820829147	4		481	497	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0046580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	38	361	0				ENST00000310581	NM_198253.2	-/1132			0.173306380694038	0	FACETS	0.561	0.466	0.667			1	INDETERMINATE	1	TRUE	0	0.314576648204866	0		361	295	SUCCESS
ATM	472	MSKCC	GRCh37	11	108183151	108183151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	18	256	0	ENST00000278616.4:c.5932G>A	p.Glu1978Lys	p.E1978K	ENST00000278616	NM_000051.3	1978	Gaa/Aaa	40/63	0.314576648204866	3	FACETS	0.61	0.461	0.786			1	SUBCLONAL	1	TRUE	NA	0.314576648204866	3		256	217	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369231	118369231	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	26	316	0	ENST00000534358.1:c.5949G>C	p.Leu1983Phe	p.L1983F	ENST00000534358	NM_005933.3	1983	ttG/ttC	22/36	0.314576648204866	3	FACETS	0.492	0.389	0.61			1	SUBCLONAL	1	TRUE	NA	0.314576648204866	3		316	389	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145488	58145488	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	33	442	0	ENST00000257904.6:c.13C>G	p.Arg5Gly	p.R5G	ENST00000257904	NM_000075.3	5	Cga/Gga	2/8	0.314576648204866	3	FACETS	0.434	0.353	0.527	0.217	0.176	0.264	SUBCLONAL	1	TRUE	1	0.314576648204866	3		442	559	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513232	44513232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	32	370	0	ENST00000291552.4:c.703G>A	p.Glu235Lys	p.E235K	ENST00000291552	NM_006758.2	235	Gaa/Aaa	8/8	1	2	FACETS	0.365	0.296	0.444	0.365	0.296	0.444	SUBCLONAL	1	TRUE	1	0.314576648204866	2		370	557	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778822	76778822	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	20	237	0	ENST00000373344.5:c.6757G>A	p.Glu2253Lys	p.E2253K	ENST00000373344	NM_000489.3	2253	Gaa/Aaa	31/35	0.0890516890220487	2	FACETS	0.662	0.509	0.84			1	INDETERMINATE	1	TRUE	NA	0.314576648204866	2		237	192	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0046581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	67	333	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.392151416708839	2		333	281	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0046581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	91	509	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.392151416708839	2		509	449	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182641	38182641	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs387907272	NA	P-0046581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	13	406	0	ENST00000396334.3:c.794T>C	p.Leu265Pro	p.L265P	ENST00000396334	NM_002468.4	265	cTg/cCg	5/5	1	2	FACETS	0.17	0.121	0.231	0.17	0.121	0.231	SUBCLONAL	1	TRUE	1	0.392151416708839	2		406	389	SUCCESS
APC	324	MSKCC	GRCh37	5	112174998	112174999	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs1554085246	NA	P-0046581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	46	197	0	ENST00000257430.4:c.3709_3710del	p.Gln1237GlufsTer2	p.Q1237Efs*2	ENST00000257430	NM_000038.5	1236	gCA/g	16/16	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.392151416708839	2		197	221	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117435	115117435	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	80	361	0	ENST00000257566.3:c.739A>G	p.Lys247Glu	p.K247E	ENST00000257566	NM_016569.3	247	Aaa/Gaa	4/8	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.392151416708839	2		361	378	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500630	99500630	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	202	679	1	ENST00000268035.6:c.4063A>G	p.Asn1355Asp	p.N1355D	ENST00000268035	NM_000875.3	1355	Aac/Gac	21/21	0.392151416708839	2	FACETS	0.985	0.921	1	0.985	0.921	1	CLONAL	2	TRUE	0	0.392151416708839	2		680	523	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395659	45395659	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1064793873	NA	P-0046581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	72	422	0	ENST00000262160.6:c.475G>T	p.Glu159Ter	p.E159*	ENST00000262160	NM_005901.5	159	Gaa/Taa	4/11	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.392151416708839	2		422	288	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133761003	133761003	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1021481710	NA	P-0046581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	144	856	0	ENST00000318560.5:c.3326C>T	p.Ala1109Val	p.A1109V	ENST00000318560	NM_005157.4	1109	gCg/gTg	11/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.392151416708839	2		856	688	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0046582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	110	326	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.805035699436488	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.805035699436488	1		326	141	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685307	89685307	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123317	NA	P-0046582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	142	251	0	ENST00000371953.3:c.202T>C	p.Tyr68His	p.Y68H	ENST00000371953	NM_000314.4	68	Tac/Cac	3/9	0.805035699436488	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.805035699436488	2		251	176	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748895	41748895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138883984	NA	P-0046582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	553	695	0	ENST00000301178.4:c.1420C>T	p.Arg474Trp	p.R474W	ENST00000301178	NM_021913.4	474	Cgg/Tgg	11/20	0.805035699436488	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.805035699436488	3		695	621	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412647	63412648	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	356	711	0	ENST00000330258.3:c.519dup	p.Ser174Ter	p.S174*	ENST00000330258	NM_152424.3	173	-/T	2/2	0.663294892229016	4	FACETS	0.947	0.902	0.992			1	CLONAL	2	TRUE	NA	0.805035699436488	4		711	843	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830878	3830878	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	299	519	1	ENST00000262367.5:c.1678C>T	p.Pro560Ser	p.P560S	ENST00000262367	NM_004380.2	560	Cca/Tca	8/31	0.805035699436488	3	FACETS	0.974	0.929	1	0.974	0.929	1	CLONAL	2	TRUE	1	0.805035699436488	3		520	535	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830189	72830189	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	181	513	0	ENST00000268489.5:c.6392T>G	p.Leu2131Arg	p.L2131R	ENST00000268489	NM_006885.3	2131	cTc/cGc	9/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.805035699436488	2		513	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577107	7577115	+	inframe_deletion	In_Frame_Del	DEL	ACAGGCACA	ACAGGCACA	-	novel	NA	P-0046582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	362	721	0	ENST00000269305.4:c.823_831del	p.Cys275_Cys277del	p.C275_C277del	ENST00000269305	NM_001126112.2	275	TGTGCCTGT/-	8/11	0.805035699436488	2	FACETS	0.98	0.951	1	0.98	0.951	1	CLONAL	2	TRUE	0	0.805035699436488	2		721	459	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0046584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	25	175	0	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	1	2	FACETS	1	0.809	1	1	0.809	1	CLONAL	1	TRUE	1	0.2	2		175	244	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0046584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	81	633	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	1	2	FACETS	0.945	0.831	1	0.945	0.831	1	CLONAL	1	TRUE	1	0.2	2		633	857	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254727	46254728	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	27	292	0	ENST00000334344.6:c.4922dup	p.Trp1642ValfsTer15	p.W1642Vfs*15	ENST00000334344	NM_152641.2	1639	-/A	16/21	1	2	FACETS	0.696	0.553	0.859	0.696	0.553	0.859	SUBCLONAL	1	TRUE	1	0.2	2		292	388	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537964	212537964	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs761145883	NA	P-0046584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	40	367	0	ENST00000342788.4:c.1641G>T	p.Glu547Asp	p.E547D	ENST00000342788	NM_005235.2	547	gaG/gaT	14/28	1	2	FACETS	0.911	0.758	1	0.911	0.758	1	CLONAL	1	TRUE	1	0.2	2		367	439	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955043	55955043	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	39	401	0	ENST00000263923.4:c.3502G>T	p.Ala1168Ser	p.A1168S	ENST00000263923	NM_002253.2	1168	Gct/Tct	26/30	1	2	FACETS	0.728	0.602	0.868	0.728	0.602	0.868	SUBCLONAL	1	TRUE	1	0.2	2		401	536	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911648	39911648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752359195	NA	P-0046584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	30	212	0	ENST00000378444.4:c.4982G>A	p.Arg1661Gln	p.R1661Q	ENST00000378444	NM_001123385.1	1661	cGa/cAa	15/15	1	1	FACETS	0.857	0.692	1	0.857	0.692	1	CLONAL	1	TRUE	0	0.2	1		212	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0046586-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	22	572	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.419337349962514	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		572	77	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188177	11188177	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	129	446	0	ENST00000361445.4:c.5917A>T	p.Ile1973Phe	p.I1973F	ENST00000361445	NM_004958.3	1973	Atc/Ttc	43/58	0.903944854357413	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.903944854357413	1		446	138	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923059	39923059	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5	139	274	0	ENST00000378444.4:c.3649C>T	p.Arg1217Ter	p.R1217*	ENST00000378444	NM_001123385.1	1217	Cga/Tga	8/15	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.903944854357413	1		274	144	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123784	11123784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	140	489	0	ENST00000358026.2:c.2434C>T	p.Leu812Phe	p.L812F	ENST00000358026	NM_001128849.1	812	Ctc/Ttc	16/36	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.903944854357413	2		489	298	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112940038	112940038	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	176	626	0	ENST00000351677.2:c.1690A>C	p.Thr564Pro	p.T564P	ENST00000351677	NM_002834.3	564	Act/Cct	14/16	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.903944854357413	2		626	327	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	122	483	0	ENST00000397752.3:c.3028G>C	p.Asp1010His	p.D1010H	ENST00000397752	NM_000245.2	1010	Gat/Cat	14/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.21	2		483	849	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699363	47699363	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	36	303	0	ENST00000347630.2:c.145G>A	p.Gly49Ser	p.G49S	ENST00000347630	NM_001007230.1	49	Ggt/Agt	4/11	1	2	FACETS	0.631	0.518	0.759	0.631	0.518	0.759	SUBCLONAL	1	TRUE	1	0.21	2		303	543	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061191	38061191	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	23	348	0	ENST00000250448.2:c.798C>G	p.Phe266Leu	p.F266L	ENST00000250448	NM_004496.3	266	ttC/ttG	2/2	1	2	FACETS	0.497	0.387	0.625	0.497	0.387	0.625	SUBCLONAL	1	FALSE	1	0.230232289346544	2		348	402	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696450	47696450	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	67	454	0	ENST00000347630.2:c.373T>A	p.Phe125Ile	p.F125I	ENST00000347630	NM_001007230.1	125	Ttt/Att	6/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	FALSE	1	0.230232289346544	2		454	520	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426553	49426553	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	118	762	0	ENST00000301067.7:c.11935A>C	p.Asn3979His	p.N3979H	ENST00000301067	NM_003482.3	3979	Aac/Cac	39/54	0.103547311837212	3	FACETS	1	0.981	1	0.689	0.622	0.761	INDETERMINATE	1	FALSE	1	0.230232289346544	3		762	829	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0046592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	179	359	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.842710070086408	3	FACETS	0.935	0.879	0.99	0.935	0.879	0.99	CLONAL	2	TRUE	1	0.842710070086408	3		359	323	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039385	49039385	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs794727372	NA	P-0046592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	301	637	0	ENST00000267163.4:c.2370C>A	p.Tyr790Ter	p.Y790*	ENST00000267163	NM_000321.2	790	taC/taA	23/27	0.80833211987621	2	FACETS	0.897	0.866	0.927	0.897	0.866	0.927	CLONAL	2	TRUE	0	0.842710070086408	2		637	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579310	7579310	+	splice_donor_variant	Splice_Site	SNP	A	A	C	rs1555526469	NA	P-0046592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	719	514	0	ENST00000269305.4:c.375+2T>G		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.830437730601115	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.842710070086408	3		514	781	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293686	1293686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	389	907	0	ENST00000310581.5:c.1315G>A	p.Glu439Lys	p.E439K	ENST00000310581	NM_198253.2	439	Gag/Aag	2/16	0.83161308706631	3	FACETS	1	0.984	1	0.539	0.512	0.566	CLONAL	1	TRUE	1	0.842710070086408	3		907	1218	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438499	52438499	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046592-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	460	585	0	ENST00000460680.1:c.1220del	p.Asp407ValfsTer23	p.D407Vfs*23	ENST00000460680	NM_004656.3	407	gAt/gt	12/17	0.80833211987621	2	FACETS	0.992	0.969	1	0.992	0.969	1	CLONAL	2	TRUE	0	0.842710070086408	2		585	550	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	25	427	0				ENST00000310581	NM_198253.2	-/1132			0.48453902591334	0	FACETS	0.641	0.528	0.758			1	SUBCLONAL	1	FALSE	0	0.565348795311012	0		427	60	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	266	673	0	ENST00000269571.5:c.829G>C	p.Asp277His	p.D277H	ENST00000269571		277	Gac/Cac	7/27	0.565348795311012	6	FACETS	1	0.978	1			1	CLONAL	2	FALSE	NA	0.565348795311012	6		673	922	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0046593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	34	364	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	0.570764159775337	3	FACETS	0.476	0.39	0.573	0.238	0.195	0.287	SUBCLONAL	1	FALSE	1	0.565348795311012	3		364	324	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265579	198265579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	137	434	0	ENST00000335508.6:c.2578G>A	p.Glu860Lys	p.E860K	ENST00000335508	NM_012433.2	860	Gaa/Aaa	18/25	0.570764159775337	3	FACETS	0.906	0.836	0.978	0.906	0.836	0.978	CLONAL	2	FALSE	1	0.565348795311012	3		434	343	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923060	44923060	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	67	236	0	ENST00000377967.4:c.1921C>T	p.Gln641Ter	p.Q641*	ENST00000377967	NM_021140.2	641	Cag/Tag	16/29	0.350074622319743	2	FACETS	0.767	0.672	0.868			1	SUBCLONAL	1	FALSE	NA	0.565348795311012	2		236	309	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89880961	89880961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	55	419	0	ENST00000389301.3:c.250G>A	p.Glu84Lys	p.E84K	ENST00000389301	NM_000135.2	84	Gag/Aag	3/43	0.434659191208019	3	FACETS	0.678	0.582	0.782			1	SUBCLONAL	1	FALSE	NA	0.565348795311012	3		419	368	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976481	25976481	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs774776226	NA	P-0046593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	127	325	0	ENST00000435504.4:c.1064G>C	p.Arg355Thr	p.R355T	ENST00000435504		355	aGa/aCa	11/13	0.570764159775337	5	FACETS	1	0.959	1	0.431	0.394	0.469	CLONAL	2	FALSE	0	0.565348795311012	5		325	385	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133887	41133887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755827604	NA	P-0046593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	220	443	3	ENST00000379561.5:c.1741G>A	p.Val581Met	p.V581M	ENST00000379561	NM_002015.3	581	Gtg/Atg	2/3	0.547704913761457	4	FACETS	0.898	0.847	0.95	1	0.992	1	CLONAL	3	FALSE	2	0.565348795311012	4		446	452	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966722	44966722	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	163	209	0	ENST00000377967.4:c.3946G>T	p.Glu1316Ter	p.E1316*	ENST00000377967	NM_021140.2	1316	Gag/Tag	27/29	0.350074622319743	2	FACETS	0.929	0.887	0.967			1	CLONAL	3	FALSE	NA	0.565348795311012	2		209	207	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922994	44922994	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	89	292	0	ENST00000377967.4:c.1855C>T	p.His619Tyr	p.H619Y	ENST00000377967	NM_021140.2	619	Cat/Tat	16/29	0.350074622319743	2	FACETS	0.963	0.862	1			1	CLONAL	1	FALSE	NA	0.565348795311012	2		292	327	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436825	110436825	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	29	561	0	ENST00000375856.3:c.1576G>C	p.Glu526Gln	p.E526Q	ENST00000375856	NM_003749.2	526	Gag/Cag	1/2	0.00308330799816003	3	FACETS	0.516	0.416	0.629			1	INDETERMINATE	1	FALSE	NA	0.565348795311012	3		561	255	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073301	8073301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781338553	NA	P-0046593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	81	407	0	ENST00000377482.5:c.1358G>A	p.Arg453His	p.R453H	ENST00000377482	NM_018948.3	453	cGt/cAt	4/4	0.565348795311012	7	FACETS	1	0.961	1			1	CLONAL	1	FALSE	NA	0.565348795311012	7		407	570	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261989	16261989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	99	497	0	ENST00000375759.3:c.9254C>T	p.Thr3085Ile	p.T3085I	ENST00000375759	NM_015001.2	3085	aCc/aTc	11/15	0.570764159775337	4	FACETS	1	0.974	1			1	CLONAL	1	FALSE	NA	0.565348795311012	4		497	432	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105748	27105749	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	221	394	0	ENST00000324856.7:c.5360dup	p.Ile1788AspfsTer14	p.I1788Dfs*14	ENST00000324856	NM_006015.4	1787	gag/gAag	20/20	0.570764159775337	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	FALSE	0	0.565348795311012	3		394	326	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104386995	104386995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	151	329	0	ENST00000369902.3:c.1360G>A	p.Glu454Lys	p.E454K	ENST00000369902	NM_016169.3	454	Gag/Aag	11/12	0.565348795311012	6	FACETS	0.93	0.854	1	0.465	0.427	0.505	CLONAL	2	FALSE	2	0.565348795311012	6		329	612	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21643251	21643251	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	108	532	0	ENST00000421138.2:c.276C>G	p.Phe92Leu	p.F92L	ENST00000421138		92	ttC/ttG	5/16	1	2	FACETS	0.823	0.743	0.907	0.823	0.743	0.907	CLONAL	1	FALSE	1	0.565348795311012	2		532	464	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427306	49427306	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1426418887	NA	P-0046593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	100	649	1	ENST00000301067.7:c.11182A>G	p.Met3728Val	p.M3728V	ENST00000301067	NM_003482.3	3728	Atg/Gtg	39/54	0.350074622319743	5	FACETS	0.809	0.728	0.894			1	CLONAL	2	FALSE	NA	0.565348795311012	5		650	404	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856191	111856191	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs746394261	NA	P-0046593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	65	177	0	ENST00000341259.2:c.242A>G	p.Asp81Gly	p.D81G	ENST00000341259	NM_005475.2	81	gAc/gGc	2/8	NA	2	FACETS	1	0.943	1			1	INDETERMINATE	1	FALSE	NA	0.565348795311012	2		177	205	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936788	32936788	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	99	398	0	ENST00000380152.3:c.7934G>C	p.Arg2645Thr	p.R2645T	ENST00000380152		2645	aGa/aCa	17/27	0.547704913761457	4	FACETS	0.818	0.738	0.902	0.818	0.738	0.902	CLONAL	2	FALSE	2	0.565348795311012	4		398	335	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714322	43714322	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	72	428	0	ENST00000382044.4:c.3831G>C	p.Glu1277Asp	p.E1277D	ENST00000382044	NM_001141980.1	1277	gaG/gaC	19/28	0.570764159775337	3	FACETS	1	0.949	1	0.381	0.336	0.428	CLONAL	1	FALSE	0	0.565348795311012	3		428	286	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042133	14042133	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	91	319	2	ENST00000311895.7:c.2680G>T	p.Ala894Ser	p.A894S	ENST00000311895	NM_005236.2	894	Gcc/Tcc	11/11	0.570764159775337	3	FACETS	0.813	0.733	0.895			1	CLONAL	2	FALSE	NA	0.565348795311012	3		321	254	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37882872	37882872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	72	751	0	ENST00000269571.5:c.2930C>T	p.Ser977Phe	p.S977F	ENST00000269571		977	tCc/tTc	24/27	0.565348795311012	6	FACETS	0.661	0.576	0.753			1	SUBCLONAL	1	FALSE	NA	0.565348795311012	6		751	821	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40451825	40451825	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	26	404	2	ENST00000345506.4:c.607G>A	p.Ala203Thr	p.A203T	ENST00000345506	NM_003152.3	203	Gcc/Acc	7/20	0.411866009077059	4	FACETS	0.55	0.436	0.678			1	SUBCLONAL	1	FALSE	NA	0.565348795311012	4		406	262	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256173	41256173	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	59	533	0	ENST00000357654.3:c.407G>C	p.Arg136Thr	p.R136T	ENST00000357654	NM_007294.3	136	aGa/aCa	6/23	0.314204912887117	5	FACETS	0.71	0.611	0.818			1	INDETERMINATE	1	FALSE	NA	0.565348795311012	5		533	543	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256222	41256222	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	54	424	0	ENST00000357654.3:c.358G>C	p.Asp120His	p.D120H	ENST00000357654	NM_007294.3	120	Gat/Cat	6/23	0.314204912887117	5	FACETS	0.819	0.701	0.948			1	INDETERMINATE	1	FALSE	NA	0.565348795311012	5		424	431	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256276	41256276	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1555596491	NA	P-0046593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	28	266	1	ENST00000357654.3:c.304G>A	p.Ala102Thr	p.A102T	ENST00000357654	NM_007294.3	102	Gca/Aca	6/23	0.314204912887117	5	FACETS	0.712	0.571	0.871			1	INDETERMINATE	1	FALSE	NA	0.565348795311012	5		267	257	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120003	70120003	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	14	64	0	ENST00000245479.2:c.1005G>C	p.Trp335Cys	p.W335C	ENST00000245479	NM_000346.3	335	tgG/tgC	3/3	0.570764159775337	2	FACETS	0.812	0.603	1	0.406	0.301	0.525	CLONAL	1	FALSE	0	0.565348795311012	2		64	61	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1206976	1206976	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1174992777	NA	P-0046593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	327	573	0	ENST00000326873.7:c.64A>G	p.Met22Val	p.M22V	ENST00000326873	NM_000455.4	22	Atg/Gtg	1/10	0.570764159775337	4	FACETS	0.924	0.881	0.967			1	CLONAL	3	FALSE	NA	0.565348795311012	4		573	653	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091175	29091175	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs778989252	NA	P-0046593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	140	312	0	ENST00000328354.6:c.1315C>T	p.Gln439Ter	p.Q439*	ENST00000328354	NM_007194.3	439	Cag/Tag	12/15	0.570764159775337	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	FALSE	0	0.565348795311012	2		312	212	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402554	20402554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	30	255	0	ENST00000346618.3:c.91G>A	p.Ala31Thr	p.A31T	ENST00000346618	NM_001949.4	31	Gcc/Acc	1/7	NA	2	FACETS	0.577	0.469	0.697			1	INDETERMINATE	1	FALSE	NA	0.565348795311012	2		255	184	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918680	44918680	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	45	242	0	ENST00000377967.4:c.1163C>G	p.Ser388Cys	p.S388C	ENST00000377967	NM_021140.2	388	tCt/tGt	12/29	0.350074622319743	2	FACETS	0.619	0.524	0.723			1	SUBCLONAL	1	FALSE	NA	0.565348795311012	2		242	257	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44920612	44920612	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	47	193	0	ENST00000377967.4:c.1373C>G	p.Pro458Arg	p.P458R	ENST00000377967	NM_021140.2	458	cCt/cGt	14/29	0.350074622319743	2	FACETS	0.616	0.523	0.716			1	SUBCLONAL	1	FALSE	NA	0.565348795311012	2		193	270	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240816	53240816	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	100	269	0	ENST00000375401.3:c.1264G>T	p.Glu422Ter	p.E422*	ENST00000375401	NM_004187.3	422	Gag/Tag	10/26	1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	0	0.565348795311012	1		269	200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0046595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	176	593	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.257273898022567	2		593	1092	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967215	134967215	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	55	540	0	ENST00000398015.3:c.2554G>T	p.Ala852Ser	p.A852S	ENST00000398015	NM_004441.4	852	Gct/Tct	14/16	1	2	FACETS	0.502	0.428	0.583	0.502	0.428	0.583	SUBCLONAL	1	TRUE	1	0.257273898022567	2		540	852	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564590	55564590	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	51	604	0	ENST00000288135.5:c.478T>G	p.Leu160Val	p.L160V	ENST00000288135	NM_000222.2	160	Ttg/Gtg	3/21	1	2	FACETS	0.458	0.388	0.535	0.458	0.388	0.535	SUBCLONAL	1	TRUE	1	0.257273898022567	2		604	866	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993623	72993623	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750671779	NA	P-0046595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	76	640	1	ENST00000268489.5:c.422C>T	p.Ala141Val	p.A141V	ENST00000268489	NM_006885.3	141	gCg/gTg	2/10	1	2	FACETS	0.688	0.602	0.78	0.688	0.602	0.78	SUBCLONAL	1	TRUE	1	0.257273898022567	2		641	859	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645967	215645967	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1559425484	NA	P-0046595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	35	540	0	ENST00000260947.4:c.631T>G	p.Leu211Val	p.L211V	ENST00000260947	NM_000465.2	211	Tta/Gta	4/11	1	2	FACETS	0.67	0.549	0.805	0.67	0.549	0.805	SUBCLONAL	1	TRUE	1	0.257273898022567	2		540	406	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696644	47696644	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519964	NA	P-0046596-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	86	536	0	ENST00000347630.2:c.304T>G	p.Phe102Val	p.F102V	ENST00000347630	NM_001007230.1	102	Ttc/Gtc	5/11	1	2	FACETS	0.861	0.764	0.964	0.861	0.764	0.964	CLONAL	1	TRUE	1	0.401162507269031	2		536	498	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	76	424	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.201910625104072	4	FACETS	1	0.972	1	0.704	0.617	0.797	CLONAL	1	TRUE	2	0.18	4		424	708	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0046597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	50	589	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.98	0.831	1	0.98	0.831	1	CLONAL	1	TRUE	1	0.18	2		589	567	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0046597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	26	269	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	1	2	FACETS	0.722	0.572	0.895	0.722	0.572	0.895	SUBCLONAL	1	TRUE	1	0.18	2		269	400	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0046597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	38	343	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.658	0.542	0.787	0.658	0.542	0.787	SUBCLONAL	1	TRUE	1	0.18	2		343	642	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0046599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	21	292	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.608	0.467	0.772	0.608	0.467	0.772	SUBCLONAL	1	TRUE	1	0.18	2		292	384	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11181367	11181367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	31	675	0	ENST00000361445.4:c.6869C>T	p.Ala2290Val	p.A2290V	ENST00000361445	NM_004958.3	2290	gCc/gTc	49/58	0.293290640282957	0	FACETS	0.536	0.432	0.653			1	SUBCLONAL	1	TRUE	0	0.18	0		675	527	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484575	57484576	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GC	GC	TT	novel	NA	P-0046599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	58	558	1	ENST00000371085.3:c.660-1_660delinsTT		p.X220_splice	ENST00000371085	NM_000516.4	220		9/13	0.190207342752438	3	FACETS	1	0.945	1	0.603	0.518	0.696	CLONAL	1	TRUE	1	0.18	3		559	582	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115952	8115953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0046600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	188	440	0	ENST00000346208.3:c.1300dup	p.His434ProfsTer73	p.H434Pfs*73	ENST00000346208		433	cac/caCc	6/6	1	2	FACETS	0.957	0.89	1	0.957	0.89	1	CLONAL	1	TRUE	1	0.69545237868651	2		440	565	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845707	151845707	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	200	572	1	ENST00000262189.6:c.13305G>A	p.Trp4435Ter	p.W4435*	ENST00000262189	NM_170606.2	4435	tgG/tgA	52/59	0.69545237868651	1	FACETS	0.845	0.793	0.898	0.845	0.793	0.898	CLONAL	1	TRUE	0	0.69545237868651	1		573	444	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	125	427	0				ENST00000310581	NM_198253.2	-/1132			0.768221702304581	3	FACETS	0.986	0.898	1	0.493	0.449	0.538	CLONAL	1	TRUE	1	0.768221702304581	3		427	457	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519922	NA	P-0046601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	295	657	0	ENST00000397062.3:c.235G>A	p.Glu79Lys	p.E79K	ENST00000397062	NM_006164.4	79	Gag/Aag	2/5	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.768221702304581	2		657	764	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913255	NA	P-0046601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	252	647	0	ENST00000369535.4:c.183A>T	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caT	3/7	1	2	FACETS	0.858	0.806	0.911	0.858	0.806	0.911	CLONAL	1	TRUE	1	0.768221702304581	2		647	765	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266107	41266107	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	201	407	0	ENST00000349496.5:c.104T>G	p.Ile35Ser	p.I35S	ENST00000349496	NM_001904.3	35	aTc/aGc	3/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.768221702304581	2		407	476	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070880	30070880	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315504	NA	P-0046601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	247	674	1	ENST00000338641.4:c.1396C>T	p.Arg466Ter	p.R466*	ENST00000338641	NM_000268.3	466	Cga/Tga	13/16	1	2	FACETS	0.955	0.899	1	0.955	0.899	1	CLONAL	1	TRUE	1	0.768221702304581	2		675	673	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465604	99465604	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	261	564	0	ENST00000268035.6:c.2429C>G	p.Ala810Gly	p.A810G	ENST00000268035	NM_000875.3	810	gCt/gGt	11/21	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.768221702304581	2		564	598	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961912	15961916	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TACTT	TACTT	-	novel	NA	P-0046601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	137	328	0	ENST00000268712.3:c.5882-3_5883del		p.X1961_splice	ENST00000268712	NM_006311.3	1961		38/46	1	2	FACETS	0.941	0.866	1	0.941	0.866	1	CLONAL	1	TRUE	1	0.768221702304581	2		328	379	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367252	50367252	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	167	457	0	ENST00000331340.3:c.59T>C	p.Val20Ala	p.V20A	ENST00000331340	NM_006060.4	20	gTa/gCa	3/8	1	2	FACETS	0.947	0.879	1	0.947	0.879	1	CLONAL	1	TRUE	1	0.768221702304581	2		457	459	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650157	93650157	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs757495524	NA	P-0046601-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	232	546	0	ENST00000375746.1:c.1708C>A	p.Gln570Lys	p.Q570K	ENST00000375746	NM_001174167.1	570	Cag/Aag	12/14	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.768221702304581	2		546	589	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069356	30069356	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046602-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	399	575	1	ENST00000338641.4:c.1222del	p.Glu408LysfsTer18	p.E408Kfs*18	ENST00000338641	NM_000268.3	407	caG/ca	12/16	0.789475075832899	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.789475075832899	1		576	577	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	73	427	0				ENST00000310581	NM_198253.2	-/1132			0.198303133379708	3	FACETS	1	0.966	1	0.641	0.564	0.723	INDETERMINATE	1	TRUE	1	0.382080431799887	3		427	355	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579410	7579410	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567556123	NA	P-0046604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	238	537	0	ENST00000269305.4:c.277del	p.Leu93CysfsTer30	p.L93Cfs*30	ENST00000269305	NM_001126112.2	93	Ctg/tg	4/11	0.187190583690024	3	FACETS	1	0.969	1	0.703	0.659	0.747	INDETERMINATE	2	TRUE	0	0.382080431799887	3		537	704	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608277	100608277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	139	534	0	ENST00000308731.7:c.1813G>A	p.Glu605Lys	p.E605K	ENST00000308731	NM_000061.2	605	Gag/Aag	18/19	0.366231738993953	2	FACETS	0.944	0.86	1	0.472	0.43	0.516	CLONAL	1	TRUE	0	0.382080431799887	2		534	771	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207606	2207606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754413497	NA	P-0046604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	125	493	0	ENST00000398665.3:c.890C>T	p.Ser297Leu	p.S297L	ENST00000398665	NM_032482.2	297	tCg/tTg	11/28	0.304794074142333	2	FACETS	1	0.973	1	0.592	0.538	0.648	CLONAL	1	TRUE	0	0.382080431799887	2		493	553	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965476	68965476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751712561	NA	P-0046604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	84	419	0	ENST00000288368.4:c.1088G>A	p.Arg363Gln	p.R363Q	ENST00000288368	NM_024870.2	363	cGg/cAg	9/40	0.362518097256914	1	FACETS	0.621	0.549	0.697	0.621	0.549	0.697	SUBCLONAL	1	TRUE	0	0.382080431799887	1		419	573	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992171	72992171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	109	502	0	ENST00000268489.5:c.1874C>T	p.Ser625Phe	p.S625F	ENST00000268489	NM_006885.3	625	tCc/tTc	2/10	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.382080431799887	2		502	530	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482585	56482585	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	124	474	0	ENST00000267101.3:c.1042A>G	p.Ile348Val	p.I348V	ENST00000267101	NM_001982.3	348	Att/Gtt	9/28	1	2	FACETS	0.962	0.872	1	0.962	0.872	1	CLONAL	1	TRUE	1	0.382080431799887	2		474	675	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916780	48916784	+	frameshift_variant	Frame_Shift_Del	DEL	TTTAT	TTTAT	-	novel	NA	P-0046604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	71	353	0	ENST00000267163.4:c.311_315del	p.Phe104CysfsTer4	p.F104Cfs*4	ENST00000267163	NM_000321.2	104	TTTATt/t	3/27	1	2	FACETS	0.929	0.815	1	0.929	0.815	1	CLONAL	1	TRUE	1	0.382080431799887	2		353	400	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884160	37884160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1453	135	609	0	ENST00000269571.5:c.3631C>T	p.Pro1211Ser	p.P1211S	ENST00000269571		1211	Cct/Tct	27/27	0.382080431799887	11	FACETS	1	0.974	1			1	CLONAL	1	TRUE	NA	0.382080431799887	11		609	1588	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546084	41546084	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	198	452	0	ENST00000263253.7:c.2699C>T	p.Ser900Leu	p.S900L	ENST00000263253	NM_001429.3	900	tCa/tTa	14/31	0.198303133379708	3	FACETS	0.879	0.817	0.943	0.879	0.817	0.943	INDETERMINATE	2	TRUE	1	0.382080431799887	3		452	702	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274961	142274961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	82	300	1	ENST00000350721.4:c.2099C>T	p.Ser700Phe	p.S700F	ENST00000350721	NM_001184.3	700	tCt/tTt	10/47	0.187190583690024	3	FACETS	1	0.944	1	0.37	0.328	0.416	INDETERMINATE	1	TRUE	0	0.382080431799887	3		301	460	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55143573	55143573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	67	265	0	ENST00000257290.5:c.1805G>A	p.Gly602Glu	p.G602E	ENST00000257290	NM_006206.4	602	gGa/gAa	13/23	0.169304235609667	3	FACETS	0.876	0.763	0.997	0.438	0.381	0.499	INDETERMINATE	1	TRUE	1	0.382080431799887	3		265	477	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637612	176637612	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	131	432	0	ENST00000439151.2:c.2212C>G	p.Leu738Val	p.L738V	ENST00000439151	NM_022455.4	738	Ctt/Gtt	5/23	0.372582859175859	2	FACETS	1	0.969	1	0.57	0.519	0.624	CLONAL	1	TRUE	0	0.382080431799887	2		432	601	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500904	8500904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046604-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	162	398	0	ENST00000356435.5:c.1978C>T	p.His660Tyr	p.H660Y	ENST00000356435		660	Cac/Tac	13/35	0.187190583690024	3	FACETS	0.846	0.78	0.914	0.564	0.52	0.61	INDETERMINATE	2	TRUE	0	0.382080431799887	3		398	597	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	125	427	0				ENST00000310581	NM_198253.2	-/1132			0.30220717081078	4	FACETS	1	0.978	1	0.814	0.745	0.886	CLONAL	2	TRUE	1	0.365845114328554	4		427	382	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893318	32893318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507603	NA	P-0046605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	55	352	1	ENST00000380152.3:c.172G>A	p.Glu58Lys	p.E58K	ENST00000380152		58	Gaa/Aaa	3/27	0.365845114328554	4	FACETS	0.668	0.571	0.774	0.223	0.19	0.258	SUBCLONAL	1	TRUE	1	0.365845114328554	4		353	615	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24133968	24133968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	55	337	0	ENST00000263121.7:c.119G>A	p.Arg40Gln	p.R40Q	ENST00000263121	NM_003073.3	40	cGa/cAa	2/9	1	2	FACETS	0.754	0.647	0.87	0.754	0.647	0.87	SUBCLONAL	1	TRUE	1	0.365845114328554	2		337	399	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111012	193111012	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	106	247	0	ENST00000367435.3:c.545T>A	p.Ile182Asn	p.I182N	ENST00000367435	NM_024529.4	182	aTt/aAt	7/17	0.365845114328554	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.365845114328554	2		247	273	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36821013	36821013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	65	572	0	ENST00000373129.3:c.364G>A	p.Glu122Lys	p.E122K	ENST00000373129	NM_032017.1	122	Gag/Aag	6/12	0.282335285302608	4	FACETS	0.587	0.508	0.673			1	SUBCLONAL	1	TRUE	NA	0.365845114328554	4		572	827	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26970472	26970472	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	130	245	0	ENST00000381527.3:c.841A>G	p.Lys281Glu	p.K281E	ENST00000381527	NM_001260.1	281	Aaa/Gaa	8/13	0.365845114328554	4	FACETS	0.917	0.842	0.993	0.917	0.842	0.993	CLONAL	3	TRUE	1	0.365845114328554	4		245	353	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951110	48951110	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0046605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	233	361	0	ENST00000267163.4:c.1272C>G	p.Tyr424Ter	p.Y424*	ENST00000267163	NM_000321.2	424	taC/taG	13/27	0.365845114328554	3	FACETS	1	0.951	1			1	CLONAL	3	TRUE	NA	0.365845114328554	3		361	498	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105238728	105238728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1444891733	NA	P-0046605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	123	666	1	ENST00000349310.3:c.1234G>A	p.Val412Met	p.V412M	ENST00000349310	NM_001014432.1	412	Gtg/Atg	13/15	0.138024895939772	4	FACETS	1	0.98	1	0.654	0.592	0.719	INDETERMINATE	1	TRUE	2	0.365845114328554	4		667	702	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130419	29130419	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	108	584	0	ENST00000328354.6:c.291G>A	p.Trp97Ter	p.W97*	ENST00000328354	NM_007194.3	97	tgG/tgA	2/15	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.365845114328554	2		584	582	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710596	117710596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	93	308	0	ENST00000368508.3:c.1676G>A	p.Gly559Asp	p.G559D	ENST00000368508	NM_002944.2	559	gGc/gAc	12/43	0.138024895939772	4	FACETS	0.943	0.846	1	0.943	0.846	1	INDETERMINATE	2	TRUE	2	0.365845114328554	4		308	368	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6045547	6045547	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs766203500	NA	P-0046605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	47	253	0	ENST00000265849.7:c.139C>G	p.Leu47Val	p.L47V	ENST00000265849	NM_000535.5	47	Ctg/Gtg	2/15	0.227100585878851	4	FACETS	0.959	0.812	1	0.479	0.406	0.56	CLONAL	1	TRUE	2	0.365845114328554	4		253	366	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338689	70338914	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCAAACAGAAGGAGGTGCGTTCGAAAATCGGGGCTCTGGAGGGGCCGGGGGCACGCGGTCAGCCTAGGAGGAGGCACTGACGGCTGGGAATGGGGGGCGGGGCGGTTCGGTGAGAGCAAAAGTCCCGAAAGGGGGAAGAGTAAAGTGGGCTGGCGTGGGAGGGCAGGACGGGGGGCGGTGGGGGGTTCCAAGGTATGAATAGGGGGTGGTGTAGGGGCCGCACCA	CCCAAACAGAAGGAGGTGCGTTCGAAAATCGGGGCTCTGGAGGGGCCGGGGGCACGCGGTCAGCCTAGGAGGAGGCACTGACGGCTGGGAATGGGGGGCGGGGCGGTTCGGTGAGAGCAAAAGTCCCGAAAGGGGGAAGAGTAAAGTGGGCTGGCGTGGGAGGGCAGGACGGGGGGCGGTGGGGGGTTCCAAGGTATGAATAGGGGGTGGTGTAGGGGCCGCACCA	-	novel	NA	P-0046605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	114	240	0	ENST00000374080.3:c.85_99+211del		p.X29_splice	ENST00000374080		29		1/45	0.282335285302608	2	FACETS	1	0.948	1			1	CLONAL	2	TRUE	NA	0.365845114328554	2		240	296	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0046606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	522	572	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.760868897100024	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.760868897100024	2		572	678	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056648	26056648	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs755438887	NA	P-0046606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	126	189	0	ENST00000343677.2:c.9G>C	p.Glu3Asp	p.E3D	ENST00000343677	NM_005319.3	3	gaG/gaC	1/1	0.760868897100024	4	FACETS	0.99	0.9	1	0.33	0.3	0.362	CLONAL	1	TRUE	1	0.760868897100024	4		189	589	SUCCESS
FH	2271	MSKCC	GRCh37	1	241683007	241683007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	277	482	2	ENST00000366560.3:c.16C>T	p.Arg6Trp	p.R6W	ENST00000366560	NM_000143.3	6	Cgg/Tgg	1/10	0.760868897100024	5	FACETS	1	0.981	1	0.278	0.261	0.297	CLONAL	1	TRUE	1	0.760868897100024	5		484	1400	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168988	32168988	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	820	632	1	ENST00000375023.3:c.4045G>A	p.Glu1349Lys	p.E1349K	ENST00000375023	NM_004557.3	1349	Gaa/Aaa	22/30	0.760868897100024	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.760868897100024	3		633	1451	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099966	27099966	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	333	531	0	ENST00000324856.7:c.3845G>A	p.Gly1282Glu	p.G1282E	ENST00000324856	NM_006015.4	1282	gGa/gAa	15/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.760868897100024	2		531	859	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609077	43609077	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	309	630	2	ENST00000355710.3:c.1833C>A	p.Cys611Ter	p.C611*	ENST00000355710	NM_020975.4	611	tgC/tgA	10/20	1	2	FACETS	0.994	0.942	1	0.994	0.942	1	CLONAL	1	TRUE	1	0.760868897100024	2		632	817	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650617	18650627	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTGCAGGAA	GGCTGCAGGAA	-	novel	NA	P-0046606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	228	400	1	ENST00000266497.5:c.2832_2842del	p.Gln945GlyfsTer8	p.Q945Gfs*8	ENST00000266497		943	tGGCTGCAGGAA/t	20/31	0.760868897100024	1	FACETS	0.88	0.833	0.927	0.88	0.833	0.927	CLONAL	1	TRUE	0	0.760868897100024	1		401	422	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257669	19257669	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	387	678	0	ENST00000162023.5:c.557T>C	p.Leu186Pro	p.L186P	ENST00000162023		186	cTc/cCc	10/13	1	2	FACETS	0.977	0.931	1	0.977	0.931	1	CLONAL	1	TRUE	1	0.760868897100024	2		678	1041	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218134	36218134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1357583062	NA	P-0046606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	214	385	0	ENST00000222270.7:c.4081G>A	p.Asp1361Asn	p.D1361N	ENST00000222270	NM_014727.1	1361	Gat/Aat	15/37	0.760868897100024	3	FACETS	0.966	0.9	1	0.483	0.45	0.517	CLONAL	1	TRUE	1	0.760868897100024	3		385	804	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023609	31023609	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	363	498	2	ENST00000375687.4:c.3094G>C	p.Asp1032His	p.D1032H	ENST00000375687	NM_015338.5	1032	Gat/Cat	13/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.760868897100024	2		500	920	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31405819	31405906	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTTGCTGAATACTATTAAATAAAATAAAGTAAGACATACTTTAATTTCAAGATTCTTTTTTTTTTTTTTTTTTTTTTTTCAAAAAAT	GCTTGCTGAATACTATTAAATAAAATAAAGTAAGACATACTTTAATTTCAAGATTCTTTTTTTTTTTTTTTTTTTTTTTTCAAAAAAT	-	novel	NA	P-0046606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	138	213	0	ENST00000344624.3:c.3948-76_3959del		p.X1316_splice	ENST00000344624		1316		32/33	1	2	FACETS	0.874	0.803	0.947	0.874	0.803	0.947	CLONAL	1	TRUE	1	0.760868897100024	2		213	415	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665718	86665718	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0046606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	148	286	0	ENST00000274376.6:c.1698+1G>A		p.X566_splice	ENST00000274376	NM_002890.2	566			0.760868897100024	1	FACETS	0.938	0.878	0.997	0.938	0.878	0.997	CLONAL	1	TRUE	0	0.760868897100024	1		286	257	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682691	86682691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	123	222	0	ENST00000274376.6:c.2896C>T	p.Arg966Cys	p.R966C	ENST00000274376	NM_002890.2	966	Cgt/Tgt	23/25	0.760868897100024	1	FACETS	0.923	0.858	0.988	0.923	0.858	0.988	CLONAL	1	TRUE	0	0.760868897100024	1		222	217	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206783	27206783	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	239	371	0	ENST00000380036.4:c.2568A>T	p.Arg856Ser	p.R856S	ENST00000380036	NM_000459.3	856	agA/agT	15/23	0.760868897100024	1	FACETS	0.961	0.913	1	0.961	0.913	1	CLONAL	1	TRUE	0	0.760868897100024	1		371	405	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112269	115112269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446220330	NA	P-0046607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	113	110	0	ENST00000257566.3:c.1471G>A	p.Ala491Thr	p.A491T	ENST00000257566	NM_016569.3	491	Gcg/Acg	7/8	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.814462036730966	2		110	222	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216901	7216901	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	101	590	0	ENST00000380728.2:c.620G>T	p.Ser207Ile	p.S207I	ENST00000380728		207	aGt/aTt	7/11	1	2	FACETS	0.333	0.298	0.371	0.333	0.298	0.371	SUBCLONAL	1	TRUE	1	0.814462036730966	2		590	744	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605123	46605123	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	80	588	0	ENST00000263734.3:c.1340C>T	p.Thr447Ile	p.T447I	ENST00000263734	NM_001430.4	447	aCc/aTc	10/16	1	2	FACETS	0.202	0.177	0.229	0.202	0.177	0.229	SUBCLONAL	1	TRUE	1	0.814462036730966	2		588	972	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31424571	31424571	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	379	677	0	ENST00000344624.3:c.3224G>C	p.Arg1075Pro	p.R1075P	ENST00000344624		1075	cGc/cCc	25/33	1	2	FACETS	0.979	0.932	1	0.979	0.932	1	CLONAL	1	TRUE	1	0.814462036730966	2		677	951	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005317	150005317	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	361	594	0	ENST00000253339.5:c.908C>T	p.Pro303Leu	p.P303L	ENST00000253339		303	cCa/cTa	3/7	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.814462036730966	2		594	871	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0046608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	276	409	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.284953984819494	6	FACETS	0.961	0.906	1	0.769	0.725	0.814	CLONAL	4	TRUE	1	0.284953984819494	6		410	791	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043372	180043372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	96	557	0	ENST00000261937.6:c.3214G>A	p.Gly1072Ser	p.G1072S	ENST00000261937	NM_182925.4	1072	Ggc/Agc	23/30	1	2	FACETS	0.92	0.82	1	0.92	0.82	1	CLONAL	1	TRUE	1	0.284953984819494	2		557	732	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593580	55593580	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0046608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	68	346	0	ENST00000288135.5:c.1648-2A>T		p.X550_splice	ENST00000288135	NM_000222.2	550			1	2	FACETS	0.76	0.666	0.859	1	0.975	1	SUBCLONAL	2	TRUE	1	0.284953984819494	2		346	314	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325210	39325210	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	69	483	0	ENST00000373001.3:c.109G>A	p.Ala37Thr	p.A37T	ENST00000373001	NM_022157.3	37	Gcg/Acg	1/7	0.183433074593743	3	FACETS	0.712	0.619	0.813	0.356	0.309	0.407	SUBCLONAL	1	TRUE	1	0.284953984819494	3		483	777	SUCCESS
ATM	472	MSKCC	GRCh37	11	108213980	108213980	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	28	325	0	ENST00000278616.4:c.8300T>A	p.Leu2767His	p.L2767H	ENST00000278616	NM_000051.3	2767	cTt/cAt	57/63	0.284953984819494	3	FACETS	0.467	0.372	0.575	0.233	0.186	0.288	SUBCLONAL	1	TRUE	1	0.284953984819494	3		325	481	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041633	47041633	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046608-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	148	649	1	ENST00000377604.3:c.1858G>T	p.Glu620Ter	p.E620*	ENST00000377604	NM_001204468.1	620	Gag/Tag	17/24	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.284953984819494	2		650	697	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0046609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	220	620	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	0.191828949112858	1	FACETS	1	0.965	1	1	0.995	1	CLONAL	3	FALSE	0	0.213264661706906	1		620	589	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0046609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	78	330	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.865	0.768	0.965	1	0.987	1	CLONAL	3	FALSE	1	0.213264661706906	2		330	282	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0046609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	80	441	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	1	2	FACETS	0.923	0.823	1	1	0.987	1	CLONAL	3	FALSE	1	0.213264661706906	2		441	271	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023855	27023855	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	107	191	0	ENST00000324856.7:c.961C>T	p.Gln321Ter	p.Q321*	ENST00000324856	NM_006015.4	321	Cag/Tag	1/20	1	2	FACETS	0.924	0.837	1	1	0.991	1	CLONAL	3	FALSE	1	0.213264661706906	2		191	362	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087907	27087907	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	247	584	0	ENST00000324856.7:c.2194C>T	p.Gln732Ter	p.Q732*	ENST00000324856	NM_006015.4	732	Cag/Tag	6/20	1	2	FACETS	0.986	0.925	1	1	0.996	1	CLONAL	3	FALSE	1	0.213264661706906	2		584	783	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272853	18272853	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148193042	NA	P-0046609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	248	574	2	ENST00000222254.8:c.893C>T	p.Ala298Val	p.A298V	ENST00000222254	NM_005027.3	298	gCg/gTg	7/16	1	2	FACETS	1	0.974	1	1	0.996	1	CLONAL	3	FALSE	1	0.213264661706906	2		576	726	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921080	50921099	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCCTGCCCCCACCCGCAGC	CCCCTGCCCCCACCCGCAGC	-	novel	NA	P-0046609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	134	415	0	ENST00000440232.2:c.3219-18_3220del		p.X1073_splice	ENST00000440232	NM_002691.3	1073		27/27	1	2	FACETS	1	0.961	1	1	0.993	1	CLONAL	3	FALSE	1	0.213264661706906	2		415	388	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589632	67589634	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	novel	NA	P-0046609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	38	232	0	ENST00000274335.5:c.1397_1399del	p.Leu466del	p.L466del	ENST00000274335		465	agATTa/aga	10/15	1	2	FACETS	1	0.904	1	1	0.971	1	CLONAL	2	FALSE	1	0.213264661706906	2		232	160	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0046610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	487	672	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.283043611743121	4	FACETS	1	0.989	1	1	0.996	1	CLONAL	5	TRUE	0	0.283043611743121	4		672	833	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562787	21562787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381086646	NA	P-0046610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	221	447	0	ENST00000382592.4:c.1132C>T	p.Arg378Trp	p.R378W	ENST00000382592	NM_014572.2	378	Cgg/Tgg	4/8	0.283043611743121	6	FACETS	0.911	0.852	0.971	0.911	0.852	0.971	CLONAL	4	TRUE	2	0.283043611743121	6		447	671	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250455	26250455	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs750167375	NA	P-0046610-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	171	675	0	ENST00000446824.2:c.379C>G	p.Leu127Val	p.L127V	ENST00000446824	NM_021018.2	127	Ctc/Gtc	1/1	0.208281688511192	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.283043611743121	4		675	642	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	123	427	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.800896886728731	2		427	304	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0046611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	124	232	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.882	0.808	0.959	0.882	0.808	0.959	CLONAL	1	TRUE	1	0.800896886728731	2		233	351	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144113	11144113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	17	604	1	ENST00000358026.2:c.3694G>A	p.Gly1232Ser	p.G1232S	ENST00000358026	NM_001128849.1	1232	Ggc/Agc	26/36	1	2	FACETS	0.066	0.049	0.087	0.066	0.049	0.087	SUBCLONAL	1	TRUE	1	0.800896886728731	2		605	643	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs770248150	NA	P-0046611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	14	447	0	ENST00000311936.3:c.351A>T	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaT	4/5	1	2	FACETS	0.051	0.036	0.069	0.051	0.036	0.069	SUBCLONAL	1	TRUE	1	0.800896886728731	2		447	684	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55270273	55270273	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764780987	NA	P-0046611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	59	698	0	ENST00000275493.2:c.3226G>A	p.Ala1076Thr	p.A1076T	ENST00000275493	NM_005228.3	1076	Gcc/Acc	27/28	1	2	FACETS	0.202	0.173	0.234	0.202	0.173	0.234	SUBCLONAL	1	TRUE	1	0.800896886728731	2		698	728	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793331	42793331	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0046611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	35	576	0	ENST00000575354.2:c.1135-2A>T		p.X379_splice	ENST00000575354	NM_015125.3	379			0.800896886728731	1	FACETS	0.15	0.123	0.181	0.15	0.123	0.181	SUBCLONAL	1	TRUE	0	0.800896886728731	1		576	349	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0046612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	45	548	0	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	1	2	FACETS	0.751	0.631	0.882	0.751	0.631	0.882	SUBCLONAL	1	TRUE	1	0.27	2		548	444	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610185	81610185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142632518	NA	P-0046612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	39	370	0	ENST00000298171.2:c.1783G>A	p.Val595Ile	p.V595I	ENST00000298171	NM_000369.2	595	Gtc/Atc	10/10	0.24976916333051	3	FACETS	1	0.844	1	0.508	0.422	0.602	CLONAL	1	TRUE	1	0.27	3		370	323	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951053	48951053	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0046612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	18	197	0	ENST00000267163.4:c.1216-1G>C		p.X406_splice	ENST00000267163	NM_000321.2	406			1	2	FACETS	0.913	0.693	1	0.913	0.693	1	CLONAL	1	TRUE	1	0.27	2		197	146	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163297321	163297321	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	19	384	0	ENST00000271452.3:c.167T>C	p.Val56Ala	p.V56A	ENST00000271452	NM_145697.2	56	gTa/gCa	3/14	1	2	FACETS	0.543	0.413	0.696	0.543	0.413	0.696	SUBCLONAL	1	TRUE	1	0.27	2		384	259	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440125	99440125	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	51	380	0	ENST00000268035.6:c.1093C>G	p.Arg365Gly	p.R365G	ENST00000268035	NM_000875.3	365	Cga/Gga	4/21	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.27	2		380	332	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587385	29587386	+	splice_acceptor_variant	Splice_Site	DNP	AG	AG	TT	novel	NA	P-0046612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	28	258	1	ENST00000356175.3:c.4368-2_4368-1delinsTT		p.X1456_splice	ENST00000356175	NM_000267.3	1456			1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.27	2		259	194	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481604	40481604	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	25	565	0	ENST00000264657.5:c.1201A>C	p.Asn401His	p.N401H	ENST00000264657	NM_139276.2	401	Aac/Cac	13/24	1	2	FACETS	0.442	0.348	0.551	0.442	0.348	0.551	SUBCLONAL	1	TRUE	1	0.27	2		565	419	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799138	42799138	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	36	602	0	ENST00000575354.2:c.4622C>G	p.Thr1541Ser	p.T1541S	ENST00000575354	NM_015125.3	1541	aCt/aGt	20/20	1	2	FACETS	0.672	0.553	0.805	0.672	0.553	0.805	SUBCLONAL	1	TRUE	1	0.27	2		602	397	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681165	86681165	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	19	245	0	ENST00000274376.6:c.2806del	p.Ser936LeufsTer5	p.S936Lfs*5	ENST00000274376	NM_002890.2	936	Tct/ct	22/25	0.240362845728445	3	FACETS	0.787	0.6	1	0.393	0.3	0.503	CLONAL	1	TRUE	1	0.27	3		245	203	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287521	33287521	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	27	572	0	ENST00000374542.5:c.1576C>G	p.Arg526Gly	p.R526G	ENST00000374542	NM_001141970.1	526	Cgc/Ggc	6/8	1	2	FACETS	0.416	0.33	0.514	0.416	0.33	0.514	SUBCLONAL	1	TRUE	1	0.27	2		572	481	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633457	8633457	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	25	288	0	ENST00000356435.5:c.212T>C	p.Val71Ala	p.V71A	ENST00000356435		71	gTa/gCa	3/35	0.271305769817851	4	FACETS	0.769	0.606	0.954	0.384	0.303	0.477	CLONAL	1	TRUE	2	0.27	4		288	306	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0046613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	11	363	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.0825243372251718	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		363	454	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0046613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	18	390	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		390	293	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0046613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	18	486	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.0825243372251718	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		486	605	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891192	101891198	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGCTC	TGGGCTC	-	novel	NA	P-0046613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	23	363	0	ENST00000374994.4:c.155_161del	p.Gly52AlafsTer19	p.G52Afs*19	ENST00000374994	NM_004612.2	51	gaTGGGCTC/ga	2/9	0.134566361577443	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		363	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0046614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	198	672	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.23352266495921	2	FACETS	0.826	0.766	0.888	0.826	0.766	0.888	CLONAL	2	TRUE	0	0.28	2		672	856	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs1057519842	NA	P-0046614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	61	300	0	ENST00000274335.5:c.1727_1729del	p.Thr576del	p.T576del	ENST00000274335		575	aaGACg/aag	12/15	0.298620009365105	1	FACETS	0.932	0.807	1	0.932	0.807	1	CLONAL	1	TRUE	0	0.28	1		300	402	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445046	49445046	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs757089451	NA	P-0046614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	39	550	0	ENST00000301067.7:c.2420C>A	p.Ser807Tyr	p.S807Y	ENST00000301067	NM_003482.3	807	tCc/tAc	10/54	1	2	FACETS	0.39	0.322	0.466	0.39	0.322	0.466	SUBCLONAL	1	TRUE	1	0.28	2		550	714	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937644	76937644	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	26	444	0	ENST00000373344.5:c.3104T>C	p.Ile1035Thr	p.I1035T	ENST00000373344	NM_000489.3	1035	aTt/aCt	9/35	0.298620009365105	1	FACETS	0.343	0.271	0.426	0.343	0.271	0.426	SUBCLONAL	1	TRUE	0	0.28	1		444	465	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	108	427	0				ENST00000310581	NM_198253.2	-/1132			0.195139133721142	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	3	TRUE	0	0.211458948090234	3		427	338	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944961	31944961	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1441610501	NA	P-0046615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	48	474	0	ENST00000340398.3:c.140C>T	p.Ala47Val	p.A47V	ENST00000340398	NM_001013699.2	47	gCg/gTg	1/1	0.211458948090234	3	FACETS	0.858	0.725	1	0.429	0.362	0.503	CLONAL	1	TRUE	1	0.211458948090234	3		474	585	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069466	30069466	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0046615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	104	517	0	ENST00000338641.4:c.1331C>G	p.Ser444Ter	p.S444*	ENST00000338641	NM_000268.3	444	tCa/tGa	12/16	0.211458948090234	2	FACETS	0.931	0.837	1	0.931	0.837	1	CLONAL	2	TRUE	0	0.211458948090234	2		517	528	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650592	48650592	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	76	687	0	ENST00000376670.3:c.562C>T	p.Pro188Ser	p.P188S	ENST00000376670	NM_002049.3	188	Ccc/Tcc	3/6	0.0884972348524549	4	FACETS	1	0.941	1	0.563	0.493	0.638	INDETERMINATE	1	TRUE	2	0.211458948090234	4		687	774	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0046616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	157	589	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.88	0.812	0.949	0.88	0.812	0.949	CLONAL	1	TRUE	1	0.748270276251011	2		589	477	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0046616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	88	348	0	ENST00000311936.3:c.34_35delinsTT	p.Gly12Phe	p.G12F	ENST00000311936	NM_004985.3	12	GGt/TTt	2/5	1	2	FACETS	0.73	0.654	0.811	0.73	0.654	0.811	SUBCLONAL	1	TRUE	1	0.748270276251011	2		348	322	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0046616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	191	512	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	0.602265423920976	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.748270276251011	1		512	290	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216737	2216737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	431	640	0	ENST00000398665.3:c.2381G>A	p.Arg794Lys	p.R794K	ENST00000398665	NM_032482.2	794	aGg/aAg	20/28	0.738654233955581	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.748270276251011	2		640	565	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602390	10602391	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0046616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	542	662	0	ENST00000171111.5:c.1187dup	p.Tyr396Ter	p.Y396*	ENST00000171111	NM_203500.1	396	tac/taAc	3/6	0.738654233955581	2	FACETS	0.967	0.941	0.993	0.967	0.941	0.993	CLONAL	2	TRUE	0	0.748270276251011	2		662	749	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427251	49427268	+	inframe_deletion	In_Frame_Del	DEL	TGCTGCTGCTGCTGTTGC	TGCTGCTGCTGCTGTTGC	-	rs1328650739	NA	P-0046616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	135	553	0	ENST00000301067.7:c.11220_11237del	p.Gln3740_Gln3745del	p.Q3740_Q3745del	ENST00000301067	NM_003482.3	3740	caGCAACAGCAGCAGCAGCAc/cac	39/54	1	2	FACETS	0.607	0.554	0.663	0.607	0.554	0.663	SUBCLONAL	1	TRUE	1	0.748270276251011	2		553	594	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992062	72992062	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	386	554	0	ENST00000268489.5:c.1983G>A	p.Met661Ile	p.M661I	ENST00000268489	NM_006885.3	661	atG/atA	2/10	0.178134090655446	3	FACETS	0.949	0.909	0.989			1	INDETERMINATE	2	TRUE	NA	0.748270276251011	3		554	747	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207051	1207051	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	562	769	0	ENST00000326873.7:c.140del	p.Gly47AlafsTer4	p.G47Afs*4	ENST00000326873	NM_000455.4	47	Ggc/gc	1/10	0.738654233955581	2	FACETS	0.964	0.938	0.99	0.964	0.938	0.99	CLONAL	2	TRUE	0	0.748270276251011	2		769	779	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70971078	70971078	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0046617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	100	557	0	ENST00000276594.2:c.1184-1G>A		p.X395_splice	ENST00000276594	NM_024504.3	395			0.269353003577369	4	FACETS	1	0.952	1	0.559	0.499	0.623	CLONAL	1	TRUE	2	0.277358531545159	4		557	824	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067225	37067225	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs143009528	NA	P-0046617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	84	417	0	ENST00000231790.2:c.1136A>G	p.Tyr379Cys	p.Y379C	ENST00000231790	NM_000249.3	379	tAt/tGt	12/19	0.141217616546812	4	FACETS	1	0.971	1	0.66	0.584	0.742	INDETERMINATE	1	TRUE	2	0.277358531545159	4		417	586	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216627	36216627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	62	705	0	ENST00000222270.7:c.3793C>T	p.Leu1265Phe	p.L1265F	ENST00000222270	NM_014727.1	1265	Ctc/Ttc	13/37	0.269353003577369	4	FACETS	0.629	0.542	0.724	0.314	0.271	0.362	SUBCLONAL	1	TRUE	2	0.277358531545159	4		705	908	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425674	49425677	+	frameshift_variant	Frame_Shift_Del	DEL	CTGT	CTGT	-	novel	NA	P-0046617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	148	681	0	ENST00000301067.7:c.12811_12814del	p.Thr4271AlafsTer6	p.T4271Afs*6	ENST00000301067	NM_003482.3	4271	ACAGgc/gc	39/54	0.216304127692172	2	FACETS	0.822	0.753	0.894	0.822	0.753	0.894	CLONAL	2	TRUE	0	0.277358531545159	2		681	649	SUCCESS
BLM	641	MSKCC	GRCh37	15	91337417	91337417	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	54	308	0	ENST00000355112.3:c.3040C>A	p.His1014Asn	p.H1014N	ENST00000355112	NM_000057.2	1014	Cat/Aat	16/22	1	2	FACETS	0.856	0.732	0.991	0.856	0.732	0.991	CLONAL	1	TRUE	1	0.277358531545159	2		308	455	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891593	151891593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	206	434	0	ENST00000262189.6:c.4439C>T	p.Ser1480Leu	p.S1480L	ENST00000262189	NM_170606.2	1480	tCa/tTa	29/59	0.277358531545159	3	FACETS	0.873	0.814	0.933	1	0.989	1	CLONAL	3	TRUE	1	0.277358531545159	3		434	646	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891615	151891615	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	190	392	1	ENST00000262189.6:c.4417C>T	p.Gln1473Ter	p.Q1473*	ENST00000262189	NM_170606.2	1473	Cag/Tag	29/59	0.277358531545159	3	FACETS	0.86	0.799	0.922	1	0.988	1	CLONAL	3	TRUE	1	0.277358531545159	3		393	605	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0046621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	63	359	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.813	0.706	0.93	0.813	0.706	0.93	CLONAL	1	TRUE	1	0.361901266099285	2		359	428	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0046622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	69	594	1	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.250118215731126	2		595	513	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0046622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	56	572	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.250118215731126	2		572	429	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485816	57485816	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759578554	NA	P-0046622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	77	523	0	ENST00000371085.3:c.1117C>T	p.Arg373Cys	p.R373C	ENST00000371085	NM_000516.4	373	Cgc/Tgc	13/13	0.133317514285221	3	FACETS	0.792	0.694	0.898	0.396	0.347	0.449	INDETERMINATE	1	TRUE	1	0.250118215731126	3		523	875	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591903	48591903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	59	564	0	ENST00000342988.3:c.1066C>T	p.Pro356Ser	p.P356S	ENST00000342988	NM_005359.5	356	Cct/Tct	9/12	0.235623136891402	1	FACETS	0.681	0.586	0.785	0.681	0.586	0.785	SUBCLONAL	1	TRUE	0	0.250118215731126	1		564	606	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84390203	84390203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138594808	NA	P-0046622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	72	439	0	ENST00000321945.7:c.578G>A	p.Arg193Gln	p.R193Q	ENST00000321945	NM_139076.2	193	cGa/cAa	6/9	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.250118215731126	2		439	562	SUCCESS
APC	324	MSKCC	GRCh37	5	112175397	112175404	+	frameshift_variant	Frame_Shift_Del	DEL	CCAAAAGT	CCAAAAGT	-	novel	NA	P-0046622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	109	352	0	ENST00000257430.4:c.4109_4116del	p.Lys1370ThrfsTer2	p.K1370Tfs*2	ENST00000257430	NM_000038.5	1369	cCCAAAAGT/c	16/16	0.250118215731126	3	FACETS	1	0.953	1	0.728	0.658	0.801	CLONAL	2	TRUE	0	0.250118215731126	3		352	449	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0046623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	273	363	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.775664695325257	2		363	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0046623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	438	816	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.775664695325257	1	FACETS	0.981	0.946	1	0.981	0.946	1	CLONAL	1	TRUE	0	0.775664695325257	1		816	705	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900209	101900209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	274	468	0	ENST00000374994.4:c.643C>T	p.Arg215Ter	p.R215*	ENST00000374994	NM_004612.2	215	Cga/Tga	4/9	0.775664695325257	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.775664695325257	1		468	430	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099439	157099439	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs911746269	NA	P-0046623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	19	338	0	ENST00000346085.5:c.376C>T	p.Gln126Ter	p.Q126*	ENST00000346085	NM_020732.3	126	Cag/Tag	1/20	0.775664695325257	1	FACETS	0.085	0.064	0.11	0.085	0.064	0.11	SUBCLONAL	1	TRUE	0	0.775664695325257	1		338	353	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428450	49428450	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0046623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	463	867	0	ENST00000301067.7:c.10356-1G>A		p.X3452_splice	ENST00000301067	NM_003482.3	3452			1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.775664695325257	2		867	1116	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52621446	52621446	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	354	521	0	ENST00000394830.3:c.2971G>T	p.Glu991Ter	p.E991*	ENST00000394830	NM_018313.4	991	Gaa/Taa	20/30	0.775664695325257	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.775664695325257	1		521	513	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0046624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	122	325	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.439773370195168	3	FACETS	1	0.982	1	0.668	0.609	0.73	CLONAL	1	TRUE	1	0.551894361547426	3		325	422	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0046624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	116	109	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.111075007365669	4	FACETS	0.841	0.765	0.919	0.841	0.765	0.919	INDETERMINATE	2	TRUE	2	0.551894361547426	4		109	388	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0046624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	38	199	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.111075007365669	4	FACETS	1	0.863	1	0.519	0.433	0.613	INDETERMINATE	1	TRUE	2	0.551894361547426	4		199	206	SUCCESS
APC	324	MSKCC	GRCh37	5	112154723	112154723	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775126020	NA	P-0046624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	96	392	1	ENST00000257430.4:c.994C>T	p.Arg332Ter	p.R332*	ENST00000257430	NM_000038.5	332	Cga/Tga	10/16	0.111075007365669	4	FACETS	1	0.968	1	0.604	0.541	0.67	INDETERMINATE	1	TRUE	2	0.551894361547426	4		393	447	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666657	206666657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782804652	NA	P-0046624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	162	654	0	ENST00000367120.3:c.1991C>T	p.Ser664Leu	p.S664L	ENST00000367120	NM_014002.3	664	tCg/tTg	20/22	0.123851238743766	5	FACETS	1	0.983	1	0.319	0.293	0.347	INDETERMINATE	1	TRUE	1	0.551894361547426	5		654	840	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888210	112888210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121918464	NA	P-0046624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	86	560	0	ENST00000351677.2:c.226G>A	p.Glu76Lys	p.E76K	ENST00000351677	NM_002834.3	76	Gag/Aag	3/16	1	2	FACETS	0.885	0.79	0.986	0.885	0.79	0.986	CLONAL	1	TRUE	1	0.551894361547426	2		560	352	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0046624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	431	578	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	0.551894361547426	3	FACETS	0.938	0.897	0.98	0.938	0.897	0.98	CLONAL	2	TRUE	1	0.551894361547426	3		578	1062	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727943	41727943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770407415	NA	P-0046624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	127	712	0	ENST00000301178.4:c.568C>T	p.Arg190Cys	p.R190C	ENST00000301178	NM_021913.4	190	Cgc/Tgc	4/20	0.439773370195168	3	FACETS	0.775	0.702	0.851	0.387	0.351	0.426	SUBCLONAL	1	TRUE	1	0.551894361547426	3		712	758	SUCCESS
APC	324	MSKCC	GRCh37	5	112173657	112173658	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0046624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	75	425	0	ENST00000257430.4:c.2369_2370del	p.Arg790ThrfsTer8	p.R790Tfs*8	ENST00000257430	NM_000038.5	789	cAG/c	16/16	0.111075007365669	4	FACETS	1	0.965	1	0.63	0.556	0.708	INDETERMINATE	1	TRUE	2	0.551894361547426	4		425	335	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813333	102813333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs539899150	NA	P-0046624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	113	613	0	ENST00000307046.8:c.356G>A	p.Arg119His	p.R119H	ENST00000307046	NM_001111285.1	119	cGc/cAc	3/4	1	2	FACETS	0.686	0.619	0.757	0.686	0.619	0.757	SUBCLONAL	1	TRUE	1	0.551894361547426	2		613	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0046624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	293	699	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.551894361547426	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.551894361547426	1		699	694	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31493329	31493329	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	69	380	0	ENST00000344624.3:c.1827T>G	p.His609Gln	p.H609Q	ENST00000344624		609	caT/caG	10/33	0.111075007365669	4	FACETS	1	0.932	1	0.548	0.48	0.62	INDETERMINATE	1	TRUE	2	0.551894361547426	4		380	354	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0046625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	251	325	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.382410932170696	3	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.645128264473844	3		325	745	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0046625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	241	654	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.618259570468191	1	FACETS	0.87	0.819	0.921	0.87	0.819	0.921	CLONAL	1	TRUE	0	0.645128264473844	1		654	582	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0046625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	26	812	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.618259570468191	1	FACETS	0.088	0.069	0.109	0.088	0.069	0.109	SUBCLONAL	1	TRUE	0	0.645128264473844	1		812	624	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519893	NA	P-0046625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	40	779	0	ENST00000267101.3:c.310G>T	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ttg	3/28	0.356359627104236	3	FACETS	0.153	0.126	0.183	0.076	0.063	0.092	INDETERMINATE	1	TRUE	1	0.645128264473844	3		779	1074	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764146326	NA	P-0046625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	49	765	0	ENST00000269305.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000269305	NM_001126112.2	281	Gac/Aac	8/11	0.618259570468191	1	FACETS	0.161	0.136	0.189	0.161	0.136	0.189	SUBCLONAL	1	TRUE	0	0.645128264473844	1		765	640	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881329	37881329	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	4639	719	1	ENST00000269571.5:c.2521C>G	p.Leu841Val	p.L841V	ENST00000269571		841	Ctc/Gtc	21/27	0.645128264473844	19	FACETS	0.995	0.989	1			1	CLONAL	18	TRUE	NA	0.645128264473844	19		720	5205	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	359972	359972	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0046625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	167	627	1	ENST00000262320.3:c.1116+1G>A		p.X372_splice	ENST00000262320	NM_003502.3	372			0.645128264473844	1	FACETS	0.743	0.689	0.799	0.743	0.689	0.799	SUBCLONAL	1	TRUE	0	0.645128264473844	1		628	472	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591825	48591825	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	194	508	0	ENST00000342988.3:c.988G>T	p.Glu330Ter	p.E330*	ENST00000342988	NM_005359.5	330	Gaa/Taa	9/12	0.631780225419139	1	FACETS	0.937	0.877	0.996	0.937	0.877	0.996	CLONAL	1	TRUE	0	0.645128264473844	1		508	435	SUCCESS
APC	324	MSKCC	GRCh37	5	112176372	112176372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	66	307	0	ENST00000257430.4:c.5081G>A	p.Gly1694Asp	p.G1694D	ENST00000257430	NM_000038.5	1694	gGc/gAc	16/16	0.302498960056971	1	FACETS	0.409	0.357	0.464	0.409	0.357	0.464	INDETERMINATE	1	TRUE	0	0.645128264473844	1		307	339	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	249	427	0				ENST00000310581	NM_198253.2	-/1132			0.499970335816404	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.499970335816404	3		427	388	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696676	176696676	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	53	398	0	ENST00000439151.2:c.5377G>A	p.Glu1793Lys	p.E1793K	ENST00000439151	NM_022455.4	1793	Gag/Aag	16/23	0.499970335816404	3	FACETS	0.516	0.44	0.599	0.258	0.22	0.3	SUBCLONAL	1	TRUE	1	0.499970335816404	3		398	514	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023909	27023923	+	inframe_deletion	In_Frame_Del	DEL	GCTGCGGCGGCGGCA	GCTGCGGCGGCGGCA	-	rs751352361	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	15	53	0	ENST00000324856.7:c.1029_1043del	p.Ala345_Ala349del	p.A345_A349del	ENST00000324856	NM_006015.4	339	GCTGCGGCGGCGGCA/-	1/20	0.382104561095971	4	FACETS	0.857	0.635	1			1	CLONAL	1	TRUE	NA	0.499970335816404	4		53	105	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846065	68846065	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	169	653	0	ENST00000261769.5:c.1036C>T	p.Gln346Ter	p.Q346*	ENST00000261769	NM_004360.3	346	Caa/Taa	8/16	0.499970335816404	3	FACETS	0.838	0.77	0.91	0.419	0.385	0.455	CLONAL	1	TRUE	1	0.499970335816404	3		653	1008	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750924	128750924	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	151	614	0	ENST00000377970.2:c.461C>T	p.Ser154Leu	p.S154L	ENST00000377970	NM_002467.4	154	tCg/tTg	2/3	0.499970335816404	5	FACETS	1	0.976	1	0.295	0.269	0.322	CLONAL	1	TRUE	1	0.499970335816404	5		614	896	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856356	45856356	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	342	725	0	ENST00000391945.4:c.1816G>C	p.Glu606Gln	p.E606Q	ENST00000391945	NM_000400.3	606	Gag/Cag	19/23	0.499970335816404	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.499970335816404	3		725	849	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125036	46125036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	230	339	1	ENST00000334344.6:c.223G>A	p.Glu75Lys	p.E75K	ENST00000334344	NM_152641.2	75	Gag/Aag	3/21	0.499970335816404	4	FACETS	1	0.981	1			1	CLONAL	2	TRUE	NA	0.499970335816404	4		340	620	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495659	72495659	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	158	388	0	ENST00000477973.2:c.413G>A	p.Gly138Asp	p.G138D	ENST00000477973	NM_012234.5	138	gGc/gAc	1/4	0.499970335816404	5	FACETS	0.917	0.844	0.993	0.611	0.563	0.662	CLONAL	2	TRUE	2	0.499970335816404	5		388	603	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753175	57753175	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	50	332	0	ENST00000274289.3:c.841G>A	p.Glu281Lys	p.E281K	ENST00000274289	NM_006622.3	281	Gaa/Aaa	7/14	1	2	FACETS	0.548	0.466	0.637	0.548	0.466	0.637	SUBCLONAL	1	TRUE	1	0.499970335816404	2		332	365	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423497	116423497	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	174	398	0	ENST00000397752.3:c.3772C>T	p.Gln1258Ter	p.Q1258*	ENST00000397752	NM_000245.2	1258	Caa/Taa	19/21	0.0894181361055167	5	FACETS	0.873	0.812	0.936			1	INDETERMINATE	3	TRUE	NA	0.499970335816404	5		398	465	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	495088	495088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	211	472	0	ENST00000399788.2:c.218G>A	p.Arg73Lys	p.R73K	ENST00000399788	NM_001042603.1	73	aGa/aAa	2/28	0.395042360989974	5	FACETS	0.839	0.78	0.9	0.559	0.52	0.6	CLONAL	2	TRUE	2	0.499970335816404	5		472	880	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245521	153245521	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	138	347	0	ENST00000281708.4:c.1670G>T	p.Gly557Val	p.G557V	ENST00000281708	NM_033632.3	557	gGa/gTa	11/12	0.292823895769258	2	FACETS	1	0.985	1	0.667	0.612	0.722	INDETERMINATE	1	TRUE	0	0.499970335816404	2		347	414	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213953	36213953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	184	804	0	ENST00000222270.7:c.2779G>A	p.Val927Met	p.V927M	ENST00000222270	NM_014727.1	927	Gtg/Atg	6/37	0.499970335816404	3	FACETS	1	0.949	1	0.517	0.478	0.559	CLONAL	1	TRUE	1	0.499970335816404	3		804	889	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517414	176517414	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1217937501	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	68	533	0	ENST00000292408.4:c.115G>C	p.Glu39Gln	p.E39Q	ENST00000292408	NM_213647.1	39	Gag/Cag	3/18	0.499970335816404	3	FACETS	0.587	0.511	0.67	0.294	0.255	0.335	SUBCLONAL	1	TRUE	1	0.499970335816404	3		533	579	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139438540	139438540	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1217905346	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	223	700	0	ENST00000277541.6:c.76C>T	p.Gln26Ter	p.Q26*	ENST00000277541	NM_017617.3	26	Cag/Tag	2/34	0.388397901254686	3	FACETS	1	0.985	1	0.601	0.56	0.644	CLONAL	1	TRUE	1	0.499970335816404	3		700	927	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545870	41545870	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	203	374	0	ENST00000263253.7:c.2485C>T	p.Gln829Ter	p.Q829*	ENST00000263253	NM_001429.3	829	Cag/Tag	14/31	0.155638250791595	6	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.499970335816404	6		374	1088	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092818	27092836	+	frameshift_variant	Frame_Shift_Del	DEL	CCATATTCCATGGGTGGAA	CCATATTCCATGGGTGGAA	-	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	395	553	0	ENST00000324856.7:c.2843_2861del	p.Tyr948TrpfsTer14	p.Y948Wfs*14	ENST00000324856	NM_006015.4	947	CCATATTCCATGGGTGGAAcc/cc	9/20	0.382104561095971	4	FACETS	0.873	0.834	0.912			1	CLONAL	3	TRUE	NA	0.499970335816404	4		553	905	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28586398	28586398	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1185683806	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	133	553	0	ENST00000253063.3:c.40G>A	p.Asp14Asn	p.D14N	ENST00000253063	NM_031459.4	14	Gac/Aac	1/10	0.124354057995594	5	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.499970335816404	5		553	668	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325147	39325147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	278	498	0	ENST00000373001.3:c.172G>A	p.Asp58Asn	p.D58N	ENST00000373001	NM_022157.3	58	Gac/Aac	1/7	0.124354057995594	5	FACETS	0.978	0.926	1			1	INDETERMINATE	3	TRUE	NA	0.499970335816404	5		498	663	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375933	118375933	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	61	592	0	ENST00000534358.1:c.9326C>G	p.Ser3109Cys	p.S3109C	ENST00000534358	NM_005933.3	3109	tCt/tGt	27/36	NA	2	FACETS	0.449	0.387	0.515			1	INDETERMINATE	1	TRUE	NA	0.499970335816404	2		592	544	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484363	50484363	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	315	462	0	ENST00000394963.4:c.1123C>T	p.His375Tyr	p.H375Y	ENST00000394963	NM_003076.4	375	Cat/Tat	9/13	0.499970335816404	4	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.499970335816404	4		462	812	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864933	57864933	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264071704	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	536	718	0	ENST00000228682.2:c.2410C>T	p.Pro804Ser	p.P804S	ENST00000228682	NM_005269.2	804	Cct/Tct	12/12	0.499970335816404	5	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	TRUE	2	0.499970335816404	5		718	1238	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913809	32913809	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1566232201	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	127	480	0	ENST00000380152.3:c.5317G>A	p.Glu1773Lys	p.E1773K	ENST00000380152		1773	Gag/Aag	11/27	0.499970335816404	3	FACETS	1	0.946	1	0.528	0.48	0.579	CLONAL	1	TRUE	1	0.499970335816404	3		480	601	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005472	42005472	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	309	664	0	ENST00000219905.7:c.3208C>T	p.His1070Tyr	p.H1070Y	ENST00000219905	NM_001164273.1	1070	Cac/Tac	9/24	0.311099619446782	4	FACETS	0.914	0.863	0.966	0.914	0.863	0.966	CLONAL	2	TRUE	2	0.499970335816404	4		664	1014	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126100	2126100	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	189	741	0	ENST00000219476.3:c.2671C>T	p.His891Tyr	p.H891Y	ENST00000219476	NM_000548.3	891	Cac/Tac	24/42	0.499970335816404	3	FACETS	0.922	0.852	0.995	0.461	0.426	0.498	CLONAL	1	TRUE	1	0.499970335816404	3		741	1025	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772221	68772221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	393	682	0	ENST00000261769.5:c.70G>A	p.Glu24Lys	p.E24K	ENST00000261769	NM_004360.3	24	Gag/Aag	2/16	0.499970335816404	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.499970335816404	3		682	872	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827183	72827183	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	280	556	0	ENST00000268489.5:c.9398C>T	p.Ser3133Phe	p.S3133F	ENST00000268489	NM_006885.3	3133	tCc/tTc	9/10	0.499970335816404	3	FACETS	0.962	0.908	1	0.962	0.908	1	CLONAL	2	TRUE	1	0.499970335816404	3		556	728	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81971417	81971417	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	126	575	0	ENST00000359376.3:c.3107del	p.Tyr1036SerfsTer8	p.Y1036Sfs*8	ENST00000359376	NM_002661.3	1036	tAc/tc	28/33	0.499970335816404	3	FACETS	0.819	0.742	0.9	0.41	0.371	0.45	CLONAL	1	TRUE	1	0.499970335816404	3		575	769	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012186	16012186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	249	602	0	ENST00000268712.3:c.2096G>A	p.Cys699Tyr	p.C699Y	ENST00000268712	NM_006311.3	699	tGt/tAt	19/46	0.238496587250445	4	FACETS	0.968	0.908	1	0.968	0.908	1	INDETERMINATE	2	TRUE	2	0.499970335816404	4		602	772	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30302621	30302621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	21	106	0	ENST00000322652.5:c.712G>A	p.Glu238Lys	p.E238K	ENST00000322652	NM_015355.2	238	Gaa/Aaa	7/16	0.238496587250445	4	FACETS	0.846	0.657	1	0.423	0.328	0.531	INDETERMINATE	1	TRUE	2	0.499970335816404	4		106	149	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41197736	41197736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	336	693	1	ENST00000357654.3:c.5551G>A	p.Asp1851Asn	p.D1851N	ENST00000357654	NM_007294.3	1851	Gac/Aac	23/23	0.499970335816404	3	FACETS	0.96	0.911	1	0.96	0.911	1	CLONAL	2	TRUE	1	0.499970335816404	3		694	875	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492863	56492863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	215	473	0	ENST00000407977.2:c.76G>A	p.Gly26Arg	p.G26R	ENST00000407977		26	Gga/Aga	2/10	0.194745284392082	5	FACETS	1	0.988	1	0.829	0.776	0.884	INDETERMINATE	2	TRUE	2	0.499970335816404	5		473	605	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733105	74733118	+	frameshift_variant	Frame_Shift_Del	DEL	CGGGATGTACACGT	CGGGATGTACACGT	-	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	183	535	0	ENST00000359995.5:c.125_138del	p.Asp42AlafsTer23	p.D42Afs*23	ENST00000359995	NM_001195427.1	42	gACGTGTACATCCCG/g	1/3	0.238496587250445	4	FACETS	1	0.99	1	0.74	0.684	0.797	INDETERMINATE	1	TRUE	2	0.499970335816404	4		535	742	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121134	11121134	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	301	767	0	ENST00000358026.2:c.2201T>C	p.Val734Ala	p.V734A	ENST00000358026	NM_001128849.1	734	gTg/gCg	15/36	0.499970335816404	3	FACETS	0.918	0.868	0.968	0.918	0.868	0.968	CLONAL	2	TRUE	1	0.499970335816404	3		767	820	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281578	15281578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	345	694	0	ENST00000263388.2:c.4795C>T	p.His1599Tyr	p.H1599Y	ENST00000263388	NM_000435.2	1599	Cac/Tac	26/33	0.499970335816404	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.499970335816404	3		694	830	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937608	17937608	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	172	770	0	ENST00000458235.1:c.3319A>G	p.Thr1107Ala	p.T1107A	ENST00000458235	NM_000215.3	1107	Act/Gct	24/24	0.499970335816404	3	FACETS	0.919	0.845	0.995	0.459	0.422	0.498	CLONAL	1	TRUE	1	0.499970335816404	3		770	936	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61725840	61725840	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	296	363	0	ENST00000401558.2:c.727G>A	p.Glu243Lys	p.E243K	ENST00000401558	NM_003400.3	243	Gag/Aag	9/25	0.444732124616134	4	FACETS	0.908	0.862	0.955	0.908	0.862	0.955	CLONAL	3	TRUE	1	0.499970335816404	4		363	652	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99163051	99163051	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	75	373	0	ENST00000074304.5:c.1057C>G	p.Gln353Glu	p.Q353E	ENST00000074304	NM_001134224.1	353	Cag/Gag	13/26	0.499970335816404	3	FACETS	0.795	0.698	0.897	0.397	0.349	0.449	SUBCLONAL	1	TRUE	1	0.499970335816404	3		373	472	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151236	202151236	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	183	344	0	ENST00000358485.4:c.1536G>C	p.Lys512Asn	p.K512N	ENST00000358485	NM_001080125.1	512	aaG/aaC	9/9	0.499970335816404	3	FACETS	0.926	0.862	0.991	0.926	0.862	0.991	CLONAL	2	TRUE	1	0.499970335816404	3		344	494	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812338	212812338	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	56	308	0	ENST00000342788.4:c.238G>C	p.Val80Leu	p.V80L	ENST00000342788	NM_005235.2	80	Gtt/Ctt	3/28	0.499970335816404	3	FACETS	0.824	0.709	0.947	0.412	0.354	0.474	CLONAL	1	TRUE	1	0.499970335816404	3		308	340	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57470673	57470673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	290	335	0	ENST00000371085.3:c.146G>A	p.Gly49Glu	p.G49E	ENST00000371085	NM_000516.4	49	gGa/gAa	2/13	0.494581031682715	5	FACETS	0.958	0.912	1	0.958	0.912	1	CLONAL	4	TRUE	1	0.499970335816404	5		335	530	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183775	10183775	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1214305423	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	340	600	0	ENST00000256474.2:c.244C>T	p.Arg82Cys	p.R82C	ENST00000256474	NM_000551.3	82	Cgc/Tgc	1/3	0.499970335816404	5	FACETS	0.937	0.89	0.984	0.937	0.89	0.984	CLONAL	3	TRUE	2	0.499970335816404	5		600	847	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12393108	12393108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	287	605	0	ENST00000287820.6:c.17G>A	p.Gly6Glu	p.G6E	ENST00000287820	NM_015869.4	6	gGa/gAa	1/7	0.499970335816404	5	FACETS	0.941	0.885	0.998	0.627	0.59	0.665	CLONAL	2	TRUE	2	0.499970335816404	5		605	1068	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47079190	47079190	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	273	568	0	ENST00000409792.3:c.7316T>G	p.Leu2439Arg	p.L2439R	ENST00000409792	NM_014159.6	2439	cTg/cGg	18/21	0.499970335816404	5	FACETS	0.883	0.829	0.939	0.589	0.552	0.626	CLONAL	2	TRUE	2	0.499970335816404	5		568	1082	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723546	49723546	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766691780	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	31	65	0	ENST00000449682.2:c.1096G>A	p.Ala366Thr	p.A366T	ENST00000449682	NM_020998.3	366	Gcg/Acg	9/18	0.499970335816404	5	FACETS	1	0.883	1	0.723	0.6	0.855	CLONAL	2	TRUE	2	0.499970335816404	5		65	100	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143350335	143350335	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	25	309	0	ENST00000262992.4:c.127T>A	p.Phe43Ile	p.F43I	ENST00000262992	NM_001101669.1	43	Ttc/Atc	3/24	0.292823895769258	2	FACETS	0.375	0.296	0.465	0.187	0.148	0.233	INDETERMINATE	1	TRUE	0	0.499970335816404	2		309	267	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245405	153245405	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	74	630	0	ENST00000281708.4:c.1786T>G	p.Ser596Ala	p.S596A	ENST00000281708	NM_033632.3	596	Tct/Gct	11/12	0.292823895769258	2	FACETS	0.458	0.4	0.519	0.229	0.2	0.26	INDETERMINATE	1	TRUE	0	0.499970335816404	2		630	647	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488347	20488347	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	231	496	0	ENST00000346618.3:c.1003C>A	p.Leu335Ile	p.L335I	ENST00000346618	NM_001949.4	335	Cta/Ata	6/7	0.311099619446782	4	FACETS	0.938	0.878	0.999	0.938	0.878	0.999	CLONAL	2	TRUE	2	0.499970335816404	4		496	739	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903744	41903751	+	frameshift_variant	Frame_Shift_Del	DEL	CCGGGGGG	CCGGGGGG	-	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	161	702	0	ENST00000372991.4:c.806_813del	p.Ala269GlyfsTer52	p.A269Gfs*52	ENST00000372991	NM_001760.3	269	gCCCCCCGG/g	5/5	0.311099619446782	4	FACETS	0.988	0.905	1	0.494	0.452	0.537	CLONAL	1	TRUE	2	0.499970335816404	4		702	978	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423422	116423422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	100	367	0	ENST00000397752.3:c.3697G>A	p.Glu1233Lys	p.E1233K	ENST00000397752	NM_000245.2	1233	Gaa/Aaa	19/21	0.0894181361055167	5	FACETS	0.803	0.721	0.888			1	INDETERMINATE	2	TRUE	NA	0.499970335816404	5		367	436	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151181852	151181852	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	253	397	0	ENST00000262187.5:c.163C>T	p.His55Tyr	p.H55Y	ENST00000262187	NM_005614.3	55	Cat/Tat	3/8	0.444732124616134	4	FACETS	1	0.99	1	0.823	0.776	0.87	CLONAL	2	TRUE	1	0.499970335816404	4		397	615	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846072	151846072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	117	535	0	ENST00000262189.6:c.12940G>A	p.Glu4314Lys	p.E4314K	ENST00000262189	NM_170606.2	4314	Gaa/Aaa	52/59	0.444732124616134	4	FACETS	1	0.904	1	0.334	0.301	0.368	CLONAL	1	TRUE	1	0.499970335816404	4		535	701	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98222050	98222050	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	174	380	0	ENST00000331920.6:c.2719C>G	p.Leu907Val	p.L907V	ENST00000331920	NM_000264.3	907	Ctg/Gtg	17/24	0.388397901254686	3	FACETS	0.824	0.764	0.885	0.824	0.764	0.885	CLONAL	2	TRUE	1	0.499970335816404	3		380	528	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894923	101894923	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	31	394	0	ENST00000374994.4:c.476C>G	p.Pro159Arg	p.P159R	ENST00000374994	NM_004612.2	159	cCa/cGa	3/9	0.388397901254686	3	FACETS	0.291	0.235	0.356	0.146	0.117	0.178	SUBCLONAL	1	TRUE	1	0.499970335816404	3		394	532	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759631	133759631	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	287	675	0	ENST00000318560.5:c.1954G>A	p.Asp652Asn	p.D652N	ENST00000318560	NM_005157.4	652	Gac/Aac	11/11	0.388397901254686	3	FACETS	0.916	0.866	0.968	0.916	0.866	0.968	CLONAL	2	TRUE	1	0.499970335816404	3		675	783	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123499615	123499615	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	85	287	0	ENST00000371139.4:c.142C>G	p.His48Asp	p.H48D	ENST00000371139	NM_001114937.2	48	Cac/Gac	2/4	0.340090984226009	2	FACETS	0.815	0.725	0.911			1	CLONAL	1	TRUE	NA	0.499970335816404	2		287	417	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0046628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	359	494	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.348424806529898	6	FACETS	1	0.99	1	0.869	0.825	0.913	CLONAL	3	FALSE	2	0.348424806529898	6		494	1006	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691022	NA	P-0046628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	375	781	0	ENST00000269305.4:c.1024del	p.Arg342GlufsTer3	p.R342Efs*3	ENST00000269305	NM_001126112.2	342	Cga/ga	10/11	0.348424806529898	3	FACETS	0.962	0.917	1	0.962	0.917	1	CLONAL	3	FALSE	0	0.348424806529898	3		781	876	SUCCESS
APC	324	MSKCC	GRCh37	5	112178410	112178410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	38	442	0	ENST00000257430.4:c.7119G>A	p.Met2373Ile	p.M2373I	ENST00000257430	NM_000038.5	2373	atG/atA	16/16	0.348424806529898	1	FACETS	0.554	0.459	0.659	0.554	0.459	0.659	SUBCLONAL	1	FALSE	0	0.348424806529898	1		442	325	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223188	2223188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373051088	NA	P-0046628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	158	687	2	ENST00000326181.6:c.800C>T	p.Thr267Met	p.T267M	ENST00000326181	NM_032271.2	267	aCg/aTg	10/21	0.291930402135112	4	FACETS	0.92	0.845	0.997	0.46	0.422	0.499	CLONAL	2	FALSE	0	0.348424806529898	4		689	665	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41001254	41001254	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	31	529	0	ENST00000267868.3:c.375G>C	p.Met125Ile	p.M125I	ENST00000267868	NM_002875.4	125	atG/atC	5/10	0.329359542384423	3	FACETS	0.351	0.283	0.428	0.117	0.094	0.143	SUBCLONAL	1	FALSE	0	0.348424806529898	3		529	596	SUCCESS
APC	324	MSKCC	GRCh37	5	112178500	112178500	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	30	364	0	ENST00000257430.4:c.7209G>C	p.Gln2403His	p.Q2403H	ENST00000257430	NM_000038.5	2403	caG/caC	16/16	0.348424806529898	1	FACETS	0.497	0.402	0.605	0.497	0.402	0.605	SUBCLONAL	1	FALSE	0	0.348424806529898	1		364	286	SUCCESS
APC	324	MSKCC	GRCh37	5	112178870	112178870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	35	409	0	ENST00000257430.4:c.7579G>A	p.Asp2527Asn	p.D2527N	ENST00000257430	NM_000038.5	2527	Gat/Aat	16/16	0.348424806529898	1	FACETS	0.586	0.482	0.702	0.586	0.482	0.702	SUBCLONAL	1	FALSE	0	0.348424806529898	1		409	283	SUCCESS
APC	324	MSKCC	GRCh37	5	112179081	112179081	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	26	323	0	ENST00000257430.4:c.7790G>C	p.Gly2597Ala	p.G2597A	ENST00000257430	NM_000038.5	2597	gGa/gCa	16/16	0.348424806529898	1	FACETS	0.501	0.398	0.618	0.501	0.398	0.618	SUBCLONAL	1	FALSE	0	0.348424806529898	1		323	246	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259454	55259454	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs864621996	NA	P-0046628-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	302	551	0	ENST00000275493.2:c.2512C>G	p.Leu838Val	p.L838V	ENST00000275493	NM_005228.3	838	Ctg/Gtg	21/28	0.348424806529898	6	FACETS	1	0.982	1	0.82	0.775	0.866	CLONAL	3	FALSE	2	0.348424806529898	6		551	897	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	48	267	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.848	0.717	0.991	0.848	0.717	0.991	CLONAL	1	TRUE	1	0.25	2		267	453	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	79	1071	8	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.942	0.828	1	0.942	0.828	1	CLONAL	1	TRUE	1	0.25	2		1079	671	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	75	589	2	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.897	0.786	1	0.897	0.786	1	CLONAL	1	TRUE	1	0.25	2		591	669	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151289	202151290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	47	461	1	ENST00000358485.4:c.1596dup	p.Leu533ThrfsTer6	p.L533Tfs*6	ENST00000358485	NM_001080125.1	530	aga/agAa	9/9	1	2	FACETS	0.67	0.565	0.786	0.67	0.565	0.786	SUBCLONAL	1	TRUE	1	0.25	2		462	561	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	59	473	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	1	2	FACETS	0.821	0.706	0.946	0.821	0.706	0.946	CLONAL	1	TRUE	1	0.25	2		473	575	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777792	3777792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200566758	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	105	780	0	ENST00000262367.5:c.7256C>T	p.Ala2419Val	p.A2419V	ENST00000262367	NM_004380.2	2419	gCg/gTg	31/31	1	2	FACETS	0.903	0.808	1	0.903	0.808	1	CLONAL	1	TRUE	1	0.25	2		780	930	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944982	31944982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	83	630	0	ENST00000340398.3:c.119G>A	p.Arg40His	p.R40H	ENST00000340398	NM_001013699.2	40	cGc/cAc	1/1	1	2	FACETS	0.843	0.743	0.95	0.843	0.743	0.95	CLONAL	1	TRUE	1	0.25	2		630	788	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645983	215645984	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1559425604	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	53	476	1	ENST00000260947.4:c.614dup	p.Gln206AlafsTer8	p.Q206Afs*8	ENST00000260947	NM_000465.2	205	aag/aaAg	4/11	1	2	FACETS	0.719	0.612	0.835	0.719	0.612	0.835	SUBCLONAL	1	TRUE	1	0.25	2		477	590	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528825	157528825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	53	513	1	ENST00000346085.5:c.6554del	p.Pro2185ArgfsTer8	p.P2185Rfs*8	ENST00000346085	NM_020732.3	2184	Ccc/cc	20/20	1	2	FACETS	0.715	0.609	0.831	0.715	0.609	0.831	SUBCLONAL	1	TRUE	1	0.25	2		514	593	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141631	202141631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs17860424	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	85	372	0	ENST00000358485.4:c.919C>T	p.Arg307Trp	p.R307W	ENST00000358485	NM_001080125.1	307	Cgg/Tgg	7/9	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.25	2		372	563	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24135858	24135859	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1555876140	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	71	412	0	ENST00000263121.7:c.351dup	p.Thr118HisfsTer52	p.T118Hfs*52	ENST00000263121	NM_003073.3	115	-/C	3/9	1	2	FACETS	0.913	0.797	1	0.913	0.797	1	CLONAL	1	TRUE	1	0.25	2		412	622	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	41	345	2	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.708	0.59	0.84	0.708	0.59	0.84	SUBCLONAL	1	TRUE	1	0.25	2		347	463	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720712	89720712	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	14	116	0	ENST00000371953.3:c.867del	p.Val290Ter	p.V290*	ENST00000371953	NM_000314.4	288	gAa/ga	8/9	1	2	FACETS	0.629	0.456	0.837	0.629	0.456	0.837	SUBCLONAL	1	TRUE	1	0.25	2		116	178	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119781	70119781	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1274036689	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	34	549	0	ENST00000245479.2:c.788del	p.Gly263AlafsTer16	p.G263Afs*16	ENST00000245479	NM_000346.3	261	gaG/ga	3/3	1	2	FACETS	0.461	0.376	0.557	0.461	0.376	0.557	SUBCLONAL	1	TRUE	1	0.25	2		549	590	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347484	91347484	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	102	545	1	ENST00000355112.3:c.3651del	p.Lys1217AsnfsTer62	p.K1217Nfs*62	ENST00000355112	NM_000057.2	1216	Aaa/aa	19/22	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.25	2		546	742	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	53	424	2	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.25	2		426	386	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	90	461	2	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.25	2		463	685	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884864	134884864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257672576	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	86	522	0	ENST00000398015.3:c.1640C>T	p.Ala547Val	p.A547V	ENST00000398015	NM_004441.4	547	gCg/gTg	8/16	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.25	2		522	647	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396925	139396925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766358616	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	45	361	2	ENST00000277541.6:c.5183C>T	p.Pro1728Leu	p.P1728L	ENST00000277541	NM_017617.3	1728	cCg/cTg	28/34	1	2	FACETS	0.93	0.784	1	0.93	0.784	1	CLONAL	1	TRUE	1	0.25	2		363	387	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827892	40827892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573377632	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	76	475	0	ENST00000373198.4:c.2536G>A	p.Val846Ile	p.V846I	ENST00000373198	NM_133170.3	846	Gtc/Atc	17/32	0.3	1	FACETS	0.758	0.664	0.859	0.758	0.664	0.859	SUBCLONAL	1	TRUE	0	0.25	1		475	702	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037427	12037427	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777974779	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	83	600	1	ENST00000396373.4:c.1058G>A	p.Arg353Gln	p.R353Q	ENST00000396373	NM_001987.4	353	cGg/cAg	6/8	1	2	FACETS	0.841	0.741	0.947	0.841	0.741	0.947	CLONAL	1	TRUE	1	0.25	2		601	790	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910307	50910307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143076166	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	116	637	0	ENST00000440232.2:c.1562G>A	p.Arg521Gln	p.R521Q	ENST00000440232	NM_002691.3	521	cGg/cAg	13/27	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.25	2		637	754	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360946	118360946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1388016179	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	63	452	0	ENST00000534358.1:c.4678G>A	p.Ala1560Thr	p.A1560T	ENST00000534358	NM_005933.3	1560	Gcc/Acc	13/36	1	2	FACETS	0.753	0.651	0.865	0.753	0.651	0.865	SUBCLONAL	1	TRUE	1	0.25	2		452	669	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	74	558	4	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	0.953	0.835	1	0.953	0.835	1	CLONAL	1	TRUE	1	0.25	2		562	621	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468397	89468398	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1467832547	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	39	247	0	ENST00000336596.2:c.1938dup	p.Glu647ArgfsTer7	p.E647Rfs*7	ENST00000336596	NM_005233.5	644	tca/tcAa	11/17	1	2	FACETS	0.802	0.666	0.954	0.802	0.666	0.954	CLONAL	1	TRUE	1	0.25	2		247	389	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210893	36210893	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	63	678	4	ENST00000222270.7:c.649del	p.Arg217GlyfsTer22	p.R217Gfs*22	ENST00000222270	NM_014727.1	215	aCc/ac	3/37	1	2	FACETS	0.715	0.618	0.821	0.715	0.618	0.821	SUBCLONAL	1	TRUE	1	0.25	2		682	705	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429367	78429367	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	61	505	0	ENST00000370768.2:c.1075C>T	p.Arg359Ter	p.R359*	ENST00000370768	NM_003902.3	359	Cga/Tga	13/20	1	2	FACETS	0.684	0.59	0.788	0.684	0.59	0.788	SUBCLONAL	1	TRUE	1	0.25	2		505	713	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214713	36214714	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	69	495	0	ENST00000222270.7:c.3145dup	p.Ala1049GlyfsTer39	p.A1049Gfs*39	ENST00000222270	NM_014727.1	1047	cgg/cGgg	8/37	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.25	2		495	535	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520202	176520202	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763979974	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	76	658	0	ENST00000292408.4:c.1121C>T	p.Ala374Val	p.A374V	ENST00000292408	NM_213647.1	374	gCg/gTg	9/18	1	2	FACETS	0.918	0.806	1	0.918	0.806	1	CLONAL	1	TRUE	1	0.25	2		658	662	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941843	71941843	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514511	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	75	495	2	ENST00000298229.2:c.1201C>T	p.Arg401Trp	p.R401W	ENST00000298229	NM_001567.3	401	Cgg/Tgg	11/28	1	2	FACETS	0.997	0.874	1	0.997	0.874	1	CLONAL	1	TRUE	1	0.25	2		497	602	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804366	46804366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1466480316	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	89	535	0	ENST00000290295.7:c.641G>A	p.Arg214His	p.R214H	ENST00000290295	NM_006361.5	214	cGt/cAt	2/2	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.25	2		535	604	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190344	32190344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146490163	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	64	560	0	ENST00000375023.3:c.395G>A	p.Arg132His	p.R132H	ENST00000375023	NM_004557.3	132	cGc/cAc	3/30	1	2	FACETS	0.837	0.724	0.958	0.837	0.724	0.958	CLONAL	1	TRUE	1	0.25	2		560	612	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224340	36224340	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1568382485	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	45	614	1	ENST00000222270.7:c.6895del	p.Arg2299GlyfsTer26	p.R2299Gfs*26	ENST00000222270	NM_014727.1	2297	gCc/gc	28/37	1	2	FACETS	0.483	0.405	0.57	0.483	0.405	0.57	SUBCLONAL	1	TRUE	1	0.25	2		615	745	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561430	141561430	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	54	427	1	ENST00000220592.5:c.1375del	p.Gln459SerfsTer9	p.Q459Sfs*9	ENST00000220592	NM_012154.3	459	Cag/ag	11/19	1	2	FACETS	0.738	0.63	0.857	0.738	0.63	0.857	SUBCLONAL	1	TRUE	1	0.25	2		428	585	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36808981	36808981	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs534849916	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	76	556	2	ENST00000373129.3:c.1073C>T	p.Ala358Val	p.A358V	ENST00000373129	NM_032017.1	358	gCg/gTg	11/12	1	2	FACETS	0.901	0.79	1	0.901	0.79	1	CLONAL	1	TRUE	1	0.25	2		558	675	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637354	47637354	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs63750214	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	95	656	1	ENST00000233146.2:c.488T>A	p.Val163Asp	p.V163D	ENST00000233146	NM_000251.2	163	gTt/gAt	3/16	1	2	FACETS	0.897	0.798	1	0.897	0.798	1	CLONAL	1	TRUE	1	0.25	2		657	847	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395479	116395479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775965879	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	59	402	0	ENST00000397752.3:c.1772G>A	p.Arg591Gln	p.R591Q	ENST00000397752	NM_000245.2	591	cGg/cAg	6/21	1	2	FACETS	0.821	0.706	0.946	0.821	0.706	0.946	CLONAL	1	TRUE	1	0.25	2		402	575	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514056	69514056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138132534	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	82	627	2	ENST00000294312.3:c.625G>A	p.Val209Met	p.V209M	ENST00000294312	NM_005117.2	209	Gtg/Atg	3/3	1	2	FACETS	0.927	0.817	1	0.927	0.817	1	CLONAL	1	TRUE	1	0.25	2		629	708	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515170	148515170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1427041861	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	70	355	0	ENST00000320356.2:c.1039C>T	p.Arg347Trp	p.R347W	ENST00000320356	NM_004456.4	347	Cgg/Tgg	10/20	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.25	2		355	551	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981492	70981492	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	77	720	0	ENST00000276594.2:c.604C>A	p.Leu202Met	p.L202M	ENST00000276594	NM_024504.3	202	Ctg/Atg	2/8	1	2	FACETS	0.724	0.634	0.821	0.724	0.634	0.821	SUBCLONAL	1	TRUE	1	0.25	2		720	851	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517553	176517553	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149419025	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	95	708	2	ENST00000292408.4:c.254G>A	p.Arg85His	p.R85H	ENST00000292408	NM_213647.1	85	cGc/cAc	3/18	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.25	2		710	741	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918969	76918969	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	84	502	0	ENST00000373344.5:c.4022del	p.Leu1341CysfsTer5	p.L1341Cfs*5	ENST00000373344	NM_000489.3	1341	tTg/tg	12/35	1	2	FACETS	0.845	0.746	0.952	0.845	0.746	0.952	CLONAL	1	TRUE	1	0.25	2		502	795	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260647	1260647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	58	608	1	ENST00000310581.5:c.2912G>A	p.Arg971His	p.R971H	ENST00000310581	NM_198253.2	971	cGt/cAt	12/16	1	2	FACETS	0.636	0.546	0.736	0.636	0.546	0.736	SUBCLONAL	1	TRUE	1	0.25	2		609	729	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435313	56435313	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	58	583	0	ENST00000407977.2:c.1824del	p.Arg609GlyfsTer91	p.R609Gfs*91	ENST00000407977		608	ggG/gg	9/10	1	2	FACETS	0.704	0.604	0.813	0.704	0.604	0.813	SUBCLONAL	1	TRUE	1	0.25	2		583	659	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671528	30671528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368708770	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	109	954	1	ENST00000376406.3:c.5432G>A	p.Arg1811His	p.R1811H	ENST00000376406	NM_014641.2	1811	cGc/cAc	10/15	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.25	2		955	840	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261862	16261862	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	69	551	0	ENST00000375759.3:c.9127A>G	p.Ser3043Gly	p.S3043G	ENST00000375759	NM_015001.2	3043	Agc/Ggc	11/15	1	2	FACETS	0.937	0.817	1	0.937	0.817	1	CLONAL	1	TRUE	1	0.25	2		551	589	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807372	36807372	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372595502	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	78	618	0	ENST00000373129.3:c.1292G>A	p.Arg431His	p.R431H	ENST00000373129	NM_032017.1	431	cGc/cAc	12/12	1	2	FACETS	0.947	0.832	1	0.947	0.832	1	CLONAL	1	TRUE	1	0.25	2		618	659	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690317	117690317	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	60	412	0	ENST00000369458.3:c.812C>T	p.Ala271Val	p.A271V	ENST00000369458	NM_024626.3	271	gCa/gTa	5/6	1	2	FACETS	0.85	0.732	0.977	0.85	0.732	0.977	CLONAL	1	TRUE	1	0.25	2		412	565	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425301	49425301	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	120	665	0	ENST00000301067.7:c.13187C>A	p.Pro4396His	p.P4396H	ENST00000301067	NM_003482.3	4396	cCt/cAt	39/54	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.25	2		665	861	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112272	115112272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544562535	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	16	88	0	ENST00000257566.3:c.1468G>A	p.Ala490Thr	p.A490T	ENST00000257566	NM_016569.3	490	Gcc/Acc	7/8	1	2	FACETS	1	0.758	1	1	0.758	1	CLONAL	1	TRUE	1	0.25	2		88	126	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43699705	43699706	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	53	541	0	ENST00000382044.4:c.5809_5810del	p.Lys1937ValfsTer3	p.K1937Vfs*3	ENST00000382044	NM_001141980.1	1937	AAg/g	28/28	1	2	FACETS	0.596	0.507	0.694	0.596	0.507	0.694	SUBCLONAL	1	TRUE	1	0.25	2		541	711	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968210	15968210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372063300	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	27	289	0	ENST00000268712.3:c.5075C>T	p.Pro1692Leu	p.P1692L	ENST00000268712	NM_006311.3	1692	cCg/cTg	34/46	1	2	FACETS	0.5	0.397	0.618	0.5	0.397	0.618	SUBCLONAL	1	TRUE	1	0.25	2		289	432	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699374	47699374	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	67	451	0	ENST00000347630.2:c.134G>A	p.Arg45Gln	p.R45Q	ENST00000347630	NM_001007230.1	45	cGg/cAg	4/11	1	2	FACETS	0.949	0.825	1	0.949	0.825	1	CLONAL	1	TRUE	1	0.25	2		451	565	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492776	56492776	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	83	540	1	ENST00000407977.2:c.163del	p.Met55TrpfsTer7	p.M55Wfs*7	ENST00000407977		55	Atg/tg	2/10	1	2	FACETS	0.913	0.806	1	0.913	0.806	1	CLONAL	1	TRUE	1	0.25	2		541	727	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867516	78867516	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140597469	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	82	541	1	ENST00000306801.3:c.2252C>T	p.Ala751Val	p.A751V	ENST00000306801	NM_020761.2	751	gCg/gTg	20/34	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.25	2		542	654	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292598	15292598	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	83	664	0	ENST00000263388.2:c.2581G>A	p.Gly861Ser	p.G861S	ENST00000263388	NM_000435.2	861	Ggt/Agt	17/33	1	2	FACETS	0.884	0.78	0.996	0.884	0.78	0.996	CLONAL	1	TRUE	1	0.25	2		664	751	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702261	47702261	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	rs63750312	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	73	495	0	ENST00000233146.2:c.1857T>G	p.Tyr619Ter	p.Y619*	ENST00000233146	NM_000251.2	619	taT/taG	12/16	1	2	FACETS	0.817	0.714	0.928	0.817	0.714	0.928	CLONAL	1	TRUE	1	0.25	2		495	715	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031193	36031193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	91	673	0	ENST00000358208.4:c.1312C>T	p.Leu438Phe	p.L438F	ENST00000358208		438	Ctc/Ttc	11/12	1	2	FACETS	0.958	0.85	1	0.958	0.85	1	CLONAL	1	TRUE	1	0.25	2		673	760	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440364	187440364	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1426858162	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	92	515	0	ENST00000232014.4:c.2003G>A	p.Arg668His	p.R668H	ENST00000232014	NM_001130845.1	668	cGt/cAt	10/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.25	2		515	645	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607200	189607200	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	82	678	0	ENST00000264731.3:c.1583del	p.Pro528HisfsTer26	p.P528Hfs*26	ENST00000264731	NM_003722.4	527	Ccc/cc	12/14	1	2	FACETS	0.876	0.772	0.988	0.876	0.772	0.988	CLONAL	1	TRUE	1	0.25	2		678	749	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161352	55161352	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	57	447	0	ENST00000257290.5:c.3183G>T	p.Lys1061Asn	p.K1061N	ENST00000257290	NM_006206.4	1061	aaG/aaT	23/23	1	2	FACETS	0.817	0.701	0.944	0.817	0.701	0.944	CLONAL	1	TRUE	1	0.25	2		447	558	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221710	55221710	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	54	372	0	ENST00000275493.2:c.754C>A	p.Arg252Ser	p.R252S	ENST00000275493	NM_005228.3	252	Cgc/Agc	7/28	1	2	FACETS	0.887	0.758	1	0.887	0.758	1	CLONAL	1	TRUE	1	0.25	2		372	487	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874739	151874739	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs960435496	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	56	440	0	ENST00000262189.6:c.7799C>T	p.Pro2600Leu	p.P2600L	ENST00000262189	NM_170606.2	2600	cCg/cTg	38/59	1	2	FACETS	0.857	0.734	0.99	0.857	0.734	0.99	CLONAL	1	TRUE	1	0.25	2		440	523	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372123	55372123	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	40	334	0	ENST00000297316.4:c.817del	p.Arg273AspfsTer114	p.R273Dfs*114	ENST00000297316	NM_022454.3	271	caC/ca	2/2	1	2	FACETS	0.685	0.569	0.814	0.685	0.569	0.814	SUBCLONAL	1	TRUE	1	0.25	2		334	467	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247573	53247573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	56	403	1	ENST00000375401.3:c.236C>T	p.Thr79Met	p.T79M	ENST00000375401	NM_004187.3	79	aCg/aTg	3/26	1	2	FACETS	0.853	0.731	0.986	0.853	0.731	0.986	CLONAL	1	TRUE	1	0.25	2		404	525	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	23	427	0				ENST00000310581	NM_198253.2	-/1132			0.22494668356394	1	FACETS	0.753	0.589	0.942	0.753	0.589	0.942	CLONAL	1	TRUE	0	0.22494668356394	1		427	241	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133236053	133236053	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	58	492	0	ENST00000320574.5:c.3103G>A	p.Glu1035Lys	p.E1035K	ENST00000320574	NM_006231.2	1035	Gag/Aag	26/49	0.22494668356394	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.22494668356394	1		492	341	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866707	37866707	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	107	612	0	ENST00000269571.5:c.874G>C	p.Gly292Arg	p.G292R	ENST00000269571		292	Ggc/Cgc	7/27	0.22494668356394	5	FACETS	1	0.982	1	0.493	0.442	0.548	CLONAL	1	TRUE	2	0.22494668356394	5		612	860	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230707	46230707	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	53	288	0	ENST00000334344.6:c.956C>T	p.Ser319Phe	p.S319F	ENST00000334344	NM_152641.2	319	tCt/tTt	8/21	0.163481593615864	3	FACETS	1	0.957	1	0.672	0.575	0.778	CLONAL	1	TRUE	1	0.22494668356394	3		288	390	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098465	11098465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370097699	NA	P-0046646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	47	537	0	ENST00000358026.2:c.983C>T	p.Pro328Leu	p.P328L	ENST00000358026	NM_001128849.1	328	cCg/cTg	6/36	0.22494668356394	3	FACETS	1	0.884	1	0.528	0.446	0.619	CLONAL	1	TRUE	1	0.22494668356394	3		537	440	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910545	32910545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	82	256	0	ENST00000380152.3:c.2053G>A	p.Asp685Asn	p.D685N	ENST00000380152		685	Gat/Aat	11/27	0.22494668356394	5	FACETS	1	0.964	1			1	CLONAL	2	TRUE	NA	0.22494668356394	5		256	400	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265477	198265477	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	109	390	0	ENST00000335508.6:c.2680G>C	p.Asp894His	p.D894H	ENST00000335508	NM_012433.2	894	Gat/Cat	18/25	0.185174722289952	3	FACETS	1	0.913	1	0.676	0.609	0.746	CLONAL	2	TRUE	0	0.22494668356394	3		390	532	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379718	17379718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1193352612	NA	P-0046646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	69	745	0	ENST00000359435.4:c.103G>A	p.Glu35Lys	p.E35K	ENST00000359435	NM_001033549.1	35	Gag/Aag	2/9	0.22494668356394	3	FACETS	0.912	0.794	1	0.456	0.397	0.521	CLONAL	1	TRUE	1	0.22494668356394	3		745	748	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266609	115266609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	104	481	0	ENST00000438362.2:c.1906G>A	p.Glu636Lys	p.E636K	ENST00000438362	NM_001242891.1	636	Gag/Aag	16/20	0.173783080992041	5	FACETS	0.829	0.742	0.921	0.553	0.495	0.614	CLONAL	2	TRUE	2	0.22494668356394	5		481	746	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906718	32906718	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs80358407	NA	P-0046646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	40	437	0	ENST00000380152.3:c.1103C>G	p.Ser368Ter	p.S368*	ENST00000380152		368	tCa/tGa	10/27	0.22494668356394	5	FACETS	0.741	0.614	0.882			1	SUBCLONAL	1	TRUE	NA	0.22494668356394	5		437	642	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525912	41525912	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	82	333	0	ENST00000263253.7:c.1187C>G	p.Ser396Cys	p.S396C	ENST00000263253	NM_001429.3	396	tCt/tGt	5/31	0.163481593615864	3	FACETS	0.84	0.743	0.943	0.84	0.743	0.943	CLONAL	2	TRUE	1	0.22494668356394	3		333	483	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599246	55599246	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	37	294	0	ENST00000288135.5:c.2372G>A	p.Arg791Lys	p.R791K	ENST00000288135	NM_000222.2	791	aGa/aAa	17/21	1	2	FACETS	0.932	0.77	1	0.932	0.77	1	CLONAL	1	TRUE	1	0.22494668356394	2		294	353	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970829	79970829	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	29	320	0	ENST00000265081.6:c.1055A>T	p.Asp352Val	p.D352V	ENST00000265081	NM_002439.4	352	gAt/gTt	7/24	0.173783080992041	5	FACETS	0.854	0.685	1	0.285	0.228	0.349	CLONAL	1	TRUE	2	0.22494668356394	5		320	404	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858539	27858539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	31	281	0	ENST00000359303.2:c.32C>T	p.Ser11Phe	p.S11F	ENST00000359303	NM_003535.2	11	tCt/tTt	1/1	0.22494668356394	5	FACETS	1	0.834	1	0.344	0.278	0.418	CLONAL	1	TRUE	2	0.22494668356394	5		281	357	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913149	44913151	+	frameshift_variant	Frame_Shift_Del	DEL	AGT	AGT	GG	novel	NA	P-0046646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	167	234	0	ENST00000377967.4:c.824_826delinsGG	p.Lys275ArgfsTer50	p.K275Rfs*50	ENST00000377967	NM_021140.2	275	aAGTcc/aGGcc	10/29	0.22494668356394	4	FACETS	1	0.959	1			1	CLONAL	4	TRUE	NA	0.22494668356394	4		234	434	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587386	29587386	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0046647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	45	279	0	ENST00000356175.3:c.4368-1G>A		p.X1456_splice	ENST00000356175	NM_000267.3	1456			0.113169224176996	0	FACETS	1	0.868	1			1	INDETERMINATE	2	TRUE	0	0.271614189997995	0		279	120	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589570	67589593	+	protein_altering_variant	In_Frame_Del	DEL	GTAGGGAAAAAATTACATGAATAT	GTAGGGAAAAAATTACATGAATAT	AGCTTC	novel	NA	P-0046647-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	34	168	0	ENST00000274335.5:c.1333_1356delinsAGCTTC	p.Val445_Tyr452delinsSerPhe	p.V445_Y452delinsSF	ENST00000274335		445	GTAGGGAAAAAATTACATGAATAT/AGCTTC	10/15	0.178217626449338	4	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	2	0.271614189997995	4		168	130	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0046648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	128	109	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.328056518221114	3	FACETS	1	0.98	1	0.418	0.382	0.455	INDETERMINATE	1	TRUE	0	0.622877832712273	3		109	430	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0046648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	54	202	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.344787425343562	1	FACETS	0.812	0.71	0.918	0.812	0.71	0.918	INDETERMINATE	1	TRUE	0	0.622877832712273	1		202	147	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0046648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	312	654	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.622877832712273	1	FACETS	0.958	0.91	1	0.958	0.91	1	CLONAL	1	TRUE	0	0.622877832712273	1		654	720	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0046648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	64	318	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	0.404466774461398	1	FACETS	0.621	0.545	0.7	0.621	0.545	0.7	SUBCLONAL	1	TRUE	0	0.622877832712273	1		318	228	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0046648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	50	435	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.344787425343562	1	FACETS	0.416	0.355	0.481	0.416	0.355	0.481	INDETERMINATE	1	TRUE	0	0.622877832712273	1		435	266	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107258	193107258	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	27	274	0	ENST00000367435.3:c.467G>A	p.Arg156His	p.R156H	ENST00000367435	NM_024529.4	156	cGt/cAt	6/17	0.622877832712273	2	FACETS	0.292	0.232	0.36	0.146	0.116	0.18	SUBCLONAL	1	TRUE	0	0.622877832712273	2		274	297	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982309	201982309	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0046648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	132	705	0	ENST00000359651.3:c.689-1G>A		p.X230_splice	ENST00000359651		230			0.622877832712273	2	FACETS	0.421	0.381	0.463	0.21	0.19	0.232	SUBCLONAL	1	TRUE	0	0.622877832712273	2		705	1007	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873690	37873690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1246	168	717	0	ENST00000269571.5:c.1855G>A	p.Glu619Lys	p.E619K	ENST00000269571		619	Gag/Aag	15/27	0.622877832712273	3	FACETS	0.5	0.458	0.545	0.25	0.229	0.273	SUBCLONAL	1	TRUE	1	0.622877832712273	3		717	1414	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982113	201982113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751933012	NA	P-0046648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	163	729	0	ENST00000359651.3:c.637G>A	p.Gly213Ser	p.G213S	ENST00000359651		213	Ggt/Agt	5/8	0.622877832712273	2	FACETS	0.484	0.443	0.527	0.242	0.221	0.264	SUBCLONAL	1	TRUE	0	0.622877832712273	2		729	1081	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983150	201983150	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	77	507	1	ENST00000359651.3:c.999G>T	p.Met333Ile	p.M333I	ENST00000359651		333	atG/atT	7/8	0.622877832712273	2	FACETS	0.341	0.299	0.387	0.171	0.149	0.194	SUBCLONAL	1	TRUE	0	0.622877832712273	2		508	724	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727092	243727092	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	242	409	0	ENST00000263826.5:c.878G>T	p.Cys293Phe	p.C293F	ENST00000263826	NM_005465.4	293	tGc/tTc	9/13	0.622877832712273	2	FACETS	0.981	0.934	1	0.981	0.934	1	CLONAL	2	TRUE	0	0.622877832712273	2		409	396	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813469	102813469	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0046648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	114	492	0	ENST00000307046.8:c.221-1G>C		p.X74_splice	ENST00000307046	NM_001111285.1	74			0.322235163604577	1	FACETS	0.395	0.356	0.436	0.395	0.356	0.436	INDETERMINATE	1	TRUE	0	0.622877832712273	1		492	638	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882283	89882283	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0046648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	92	387	0	ENST00000389301.3:c.189+2T>A		p.X63_splice	ENST00000389301	NM_000135.2	63			0.404466774461398	1	FACETS	0.434	0.387	0.483	0.434	0.387	0.483	SUBCLONAL	1	TRUE	0	0.622877832712273	1		387	469	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594066	158594066	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	43	273	0	ENST00000263640.3:c.1507G>T	p.Asp503Tyr	p.D503Y	ENST00000263640	NM_001105.4	503	Gac/Tac	11/11	1	2	FACETS	0.424	0.356	0.498	0.424	0.356	0.498	SUBCLONAL	1	TRUE	1	0.622877832712273	2		273	326	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741644	145741644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1383587887	NA	P-0046648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	156	771	0	ENST00000428558.2:c.859G>A	p.Glu287Lys	p.E287K	ENST00000428558	NM_004260.3	287	Gag/Aag	5/22	1	2	FACETS	0.521	0.477	0.568	0.521	0.477	0.568	SUBCLONAL	1	TRUE	1	0.622877832712273	2		771	961	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341925	8341925	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	48	395	0	ENST00000356435.5:c.4715G>C	p.Arg1572Thr	p.R1572T	ENST00000356435		1572	aGa/aCa	29/35	0.622877832712273	3	FACETS	0.565	0.479	0.658	0.282	0.239	0.329	SUBCLONAL	1	TRUE	1	0.622877832712273	3		395	358	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	154	427	0				ENST00000310581	NM_198253.2	-/1132			0.130318842758452	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.714114829130735	0		427	452	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0046649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	209	667	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.156303028757496	1	FACETS	0.58	0.541	0.62	0.58	0.541	0.62	INDETERMINATE	1	TRUE	0	0.714114829130735	1		667	649	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191804	123191805	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1392503050	NA	P-0046649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	81	156	0	ENST00000218089.9:c.1400dup	p.Phe468LeufsTer5	p.F468Lfs*5	ENST00000218089	NM_001042749.1	465	gtt/gTtt	15/35	1	1	FACETS	0.947	0.861	1	0.947	0.861	1	CLONAL	1	TRUE	0	0.714114829130735	1		156	154	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725146	47725146	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs755473445	NA	P-0046649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	255	989	0	ENST00000449228.1:c.598C>G	p.Leu200Val	p.L200V	ENST00000449228	NM_001127240.2	200	Ctc/Gtc	4/4	0.1812004605702	5	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.714114829130735	5		989	1126	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564872	41564872	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0046649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	176	513	1	ENST00000263253.7:c.4172+1G>T		p.X1391_splice	ENST00000263253	NM_001429.3	1391			1	2	FACETS	0.918	0.851	0.986	0.918	0.851	0.986	CLONAL	1	TRUE	1	0.714114829130735	2		514	537	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660106	12660106	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	169	437	0	ENST00000251849.4:c.115C>T	p.Gln39Ter	p.Q39*	ENST00000251849	NM_002880.3	39	Cag/Tag	2/17	0.678374414097606	3	FACETS	0.935	0.862	1	0.467	0.431	0.505	CLONAL	1	TRUE	1	0.714114829130735	3		437	687	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797252	135797252	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	79	222	1	ENST00000298552.3:c.617A>C	p.His206Pro	p.H206P	ENST00000298552	NM_001162426.1	206	cAt/cCt	7/23	0.651539475322305	1	FACETS	0.837	0.756	0.919	0.837	0.756	0.919	CLONAL	1	TRUE	0	0.714114829130735	1		223	170	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870218	44870219	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0046649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	110	199	0	ENST00000377967.4:c.401_402dup	p.Gly135MetfsTer46	p.G135Mfs*46	ENST00000377967	NM_021140.2	133	tta/tTAta	5/29	1	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.714114829130735	1		199	187	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098957	178098957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	72	273	0	ENST00000397062.3:c.88C>T	p.Leu30Phe	p.L30F	ENST00000397062	NM_006164.4	30	Ctt/Ttt	2/5	1	2	FACETS	0.832	0.741	0.927	0.832	0.741	0.927	CLONAL	1	TRUE	1	0.856677059916486	2		273	202	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354342	354342	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	377	811	0	ENST00000262320.3:c.1216G>T	p.Glu406Ter	p.E406*	ENST00000262320	NM_003502.3	406	Gag/Tag	5/11	0.856677059916486	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.856677059916486	1		811	452	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981536	201981536	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1494	93	843	0	ENST00000359651.3:c.450C>G	p.Phe150Leu	p.F150L	ENST00000359651		150	ttC/ttG	3/8	0.672858066334839	4	FACETS	0.254	0.225	0.286	0.127	0.112	0.143	SUBCLONAL	1	TRUE	2	0.856677059916486	4		843	1587	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376713	8376713	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	192	396	0	ENST00000356435.5:c.4400A>T	p.Gln1467Leu	p.Q1467L	ENST00000356435		1467	cAg/cTg	27/35	1	2	FACETS	0.962	0.899	1	0.962	0.899	1	CLONAL	1	TRUE	1	0.856677059916486	2		396	466	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0046651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	80	318	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	0.497787795339227	6	FACETS	1	0.958	1	1	0.958	1	CLONAL	3	FALSE	3	0.638523499448734	6		318	171	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182196	99182196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751224706	NA	P-0046651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	11	538	0	ENST00000074304.5:c.2261C>T	p.Ser754Phe	p.S754F	ENST00000074304	NM_001134224.1	754	tCc/tTc	21/26	0.619872444419482	3	FACETS	0.382	0.265	0.525	0.191	0.132	0.263	SUBCLONAL	1	FALSE	1	0.638523499448734	3		538	119	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974770	21974770	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	88	324	0	ENST00000304494.5:c.57del	p.Ala20ArgfsTer6	p.A20Rfs*6	ENST00000304494	NM_000077.4	19	gcC/gc	1/3	0.644124471702678	5	FACETS	1	0.951	1			1	CLONAL	5	FALSE	NA	0.638523499448734	5		324	107	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902221	151902221	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1378676586	NA	P-0046651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	18	523	0	ENST00000262189.6:c.3931A>G	p.Ile1311Val	p.I1311V	ENST00000262189	NM_170606.2	1311	Att/Gtt	25/59	0.638523499448734	5	FACETS	1	0.811	1	0.357	0.273	0.454	CLONAL	1	FALSE	2	0.638523499448734	5		523	103	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579360	7579368	+	inframe_deletion	In_Frame_Del	DEL	GAAACCGTA	GAAACCGTA	-	novel	NA	P-0046651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	172	710	0	ENST00000269305.4:c.319_327del	p.Tyr107_Phe109del	p.Y107_F109del	ENST00000269305	NM_001126112.2	107	TACGGTTTC/-	4/11	0.447764642356083	5	FACETS	0.959	0.917	0.998			1	CLONAL	5	FALSE	NA	0.638523499448734	5		710	220	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400629	56400629	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	63	173	1	ENST00000348428.3:c.1223G>T	p.Gly408Val	p.G408V	ENST00000348428	NM_006785.3	408	gGg/gTg	11/17	0.590048110871512	3	FACETS	1	0.945	1	1	0.945	1	CLONAL	3	FALSE	0	0.638523499448734	3		174	84	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42759146	42759146	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	132	375	0	ENST00000222329.4:c.6G>C	p.Lys2Asn	p.K2N	ENST00000222329	NM_006494.2	2	aaG/aaC	1/4	0.638523499448734	8	FACETS	0.939	0.865	1			1	CLONAL	4	FALSE	NA	0.638523499448734	8		375	321	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443626	52443626	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0046651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	198	475	0	ENST00000460680.1:c.68-2A>T		p.X23_splice	ENST00000460680	NM_004656.3	23			0.580687439823989	5	FACETS	0.983	0.945	1	0.983	0.945	1	CLONAL	5	FALSE	0	0.638523499448734	5		475	247	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609722	117609722	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	25	415	0	ENST00000368508.3:c.6977C>G	p.Ser2326Cys	p.S2326C	ENST00000368508	NM_002944.2	2326	tCt/tGt	43/43	0.162935807479177	2	FACETS	1	0.826	1	0.508	0.413	0.61	INDETERMINATE	1	FALSE	0	0.638523499448734	2		415	77	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402819	139402820	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CA	CA	-	novel	NA	P-0046651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	138	783	0	ENST00000277541.6:c.3189_3190del	p.Cys1063Ter	p.C1063*	ENST00000277541	NM_017617.3	1063	tgTGac/tgac	20/34	0.644124471702678	3	FACETS	0.99	0.936	1	0.99	0.936	1	CLONAL	3	FALSE	0	0.638523499448734	3		783	192	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	435	427	0				ENST00000310581	NM_198253.2	-/1132			0.357968501912714	6	FACETS	0.922	0.884	0.96	0.922	0.884	0.96	CLONAL	5	TRUE	1	0.357968501912714	6		427	905	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs786201057	NA	P-0046652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	353	489	0	ENST00000269305.4:c.374C>G	p.Thr125Arg	p.T125R	ENST00000269305	NM_001126112.2	125	aCg/aGg	4/11	0.321391065339039	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	3	TRUE	0	0.357968501912714	3		489	767	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119325	3119325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	132	648	0	ENST00000078429.4:c.857C>T	p.Ser286Leu	p.S286L	ENST00000078429	NM_002067.2	286	tCg/tTg	6/7	0.342022789519677	3	FACETS	0.897	0.814	0.986	0.449	0.407	0.493	CLONAL	1	TRUE	1	0.357968501912714	3		648	969	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143985	11143985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	131	540	0	ENST00000358026.2:c.3566G>A	p.Arg1189Gln	p.R1189Q	ENST00000358026	NM_001128849.1	1189	cGa/cAa	26/36	0.342022789519677	3	FACETS	1	0.956	1	0.543	0.493	0.596	CLONAL	1	TRUE	1	0.357968501912714	3		540	794	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255772	16255772	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776153327	NA	P-0046652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	77	367	0	ENST00000375759.3:c.3037C>T	p.Arg1013Cys	p.R1013C	ENST00000375759	NM_015001.2	1013	Cgc/Tgc	11/15	0.342022789519677	3	FACETS	0.974	0.857	1	0.487	0.428	0.55	CLONAL	1	TRUE	1	0.357968501912714	3		367	521	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023303	27023303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	76	225	0	ENST00000324856.7:c.409C>T	p.His137Tyr	p.H137Y	ENST00000324856	NM_006015.4	137	Cac/Tac	1/20	0.342022789519677	3	FACETS	1	0.962	1	0.615	0.542	0.693	CLONAL	1	TRUE	1	0.357968501912714	3		225	407	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115889	8115889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	150	533	0	ENST00000346208.3:c.1235C>T	p.Ser412Phe	p.S412F	ENST00000346208		412	tCc/tTc	6/6	0.357968501912714	5	FACETS	1	0.939	1	0.346	0.315	0.378	CLONAL	1	TRUE	2	0.357968501912714	5		533	1242	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033906	49033906	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	183	356	0	ENST00000267163.4:c.2043G>A	p.Trp681Ter	p.W681*	ENST00000267163	NM_000321.2	681	tgG/tgA	20/27	NA	2	FACETS	0.94	0.873	1			1	INDETERMINATE	2	TRUE	NA	0.357968501912714	2		356	544	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250440	26250440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	105	426	0	ENST00000446824.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000446824	NM_021018.2	132	Cgc/Tgc	1/1	0.342022789519677	3	FACETS	1	0.911	1	0.509	0.456	0.564	CLONAL	1	TRUE	1	0.357968501912714	3		426	680	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28601351	28601351	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	115	510	0	ENST00000253063.3:c.1036G>C	p.Asp346His	p.D346H	ENST00000253063	NM_031459.4	346	Gac/Cac	8/10	0.342022789519677	3	FACETS	0.919	0.828	1	0.46	0.414	0.508	CLONAL	1	TRUE	1	0.357968501912714	3		510	824	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985510	2985510	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	99	475	0	ENST00000396946.4:c.301G>C	p.Glu101Gln	p.E101Q	ENST00000396946	NM_032415.4	101	Gaa/Caa	4/25	0.357968501912714	5	FACETS	0.93	0.829	1	0.31	0.276	0.346	CLONAL	1	TRUE	2	0.357968501912714	5		475	914	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526141	63526141	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	319	590	0	ENST00000307078.5:c.2485C>T	p.Pro829Ser	p.P829S	ENST00000307078	NM_004655.3	829	Ccg/Tcg	11/11	0.342022789519677	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.357968501912714	3		590	978	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682952	241682952	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	75	528	0	ENST00000366560.3:c.71C>A	p.Ser24Ter	p.S24*	ENST00000366560	NM_000143.3	24	tCg/tAg	1/10	0.357968501912714	3	FACETS	0.735	0.644	0.833	0.368	0.322	0.417	SUBCLONAL	1	TRUE	1	0.357968501912714	3		528	672	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104352338	104352338	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0046652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	93	388	0	ENST00000369902.3:c.455-1G>A		p.X152_splice	ENST00000369902	NM_016169.3	152			1	2	FACETS	0.995	0.888	1	0.995	0.888	1	CLONAL	1	TRUE	1	0.357968501912714	2		388	522	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202753	108202753	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	65	275	0	ENST00000278616.4:c.7777C>G	p.Gln2593Glu	p.Q2593E	ENST00000278616	NM_000051.3	2593	Cag/Gag	52/63	1	2	FACETS	0.938	0.817	1	0.938	0.817	1	CLONAL	1	TRUE	1	0.357968501912714	2		275	387	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003086	42003086	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	116	515	0	ENST00000219905.7:c.2623C>T	p.Gln875Ter	p.Q875*	ENST00000219905	NM_001164273.1	875	Caa/Taa	8/24	0.357968501912714	3	FACETS	0.884	0.797	0.977	0.442	0.398	0.489	CLONAL	1	TRUE	1	0.357968501912714	3		515	864	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286779	212286779	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	37	357	0	ENST00000342788.4:c.2917G>C	p.Glu973Gln	p.E973Q	ENST00000342788	NM_005235.2	973	Gag/Cag	24/28	0.342022789519677	3	FACETS	0.426	0.35	0.511	0.213	0.175	0.256	SUBCLONAL	1	TRUE	1	0.357968501912714	3		357	572	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612200	189612200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	121	519	0	ENST00000264731.3:c.1952C>T	p.Ser651Phe	p.S651F	ENST00000264731	NM_003722.4	651	tCt/tTt	14/14	0.319125670918585	4	FACETS	1	0.959	1	0.558	0.504	0.615	CLONAL	1	TRUE	2	0.357968501912714	4		519	823	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465621	8465621	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	118	361	0	ENST00000356435.5:c.3559G>A	p.Glu1187Lys	p.E1187K	ENST00000356435		1187	Gaa/Aaa	21/35	0.274970522897313	4	FACETS	1	0.969	1	0.59	0.532	0.651	CLONAL	1	TRUE	2	0.357968501912714	4		361	759	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133710875	133710875	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	90	558	0	ENST00000318560.5:c.42G>C	p.Lys14Asn	p.K14N	ENST00000318560	NM_005157.4	14	aaG/aaC	1/11	0.357968501912714	3	FACETS	0.794	0.704	0.89	0.397	0.352	0.445	SUBCLONAL	1	TRUE	1	0.357968501912714	3		558	747	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982440	25982440	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	18	321	0	ENST00000435504.4:c.850C>T	p.Arg284Ter	p.R284*	ENST00000435504		284	Cga/Tga	9/13	1	2	FACETS	0.678	0.51	0.878	0.678	0.51	0.878	SUBCLONAL	1	TRUE	1	0.15	2		321	354	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106228	27106228	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	28	641	0	ENST00000324856.7:c.5839C>T	p.Gln1947Ter	p.Q1947*	ENST00000324856	NM_006015.4	1947	Cag/Tag	20/20	1	2	FACETS	0.822	0.656	1	0.822	0.656	1	CLONAL	1	TRUE	1	0.15	2		641	454	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928872	44928872	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs755440519	NA	P-0046653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	18	209	0	ENST00000377967.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000377967	NM_021140.2	658	Cga/Tga	17/29	1	1	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	0	0.15	1		209	169	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863319	57863319	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	24	693	1	ENST00000228682.2:c.1418del	p.Gly473AlafsTer40	p.G473Afs*40	ENST00000228682	NM_005269.2	472	Ggg/gg	11/12	1	2	FACETS	0.681	0.533	0.853	0.681	0.533	0.853	SUBCLONAL	1	TRUE	1	0.15	2		694	470	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436224	110436224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755027066	NA	P-0046653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	18	540	1	ENST00000375856.3:c.2177G>A	p.Gly726Asp	p.G726D	ENST00000375856	NM_003749.2	726	gGc/gAc	1/2	0.124834363520498	3	FACETS	0.75	0.564	0.97	0.375	0.282	0.485	CLONAL	1	TRUE	1	0.15	3		541	344	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670340	134670340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415689583	NA	P-0046653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	18	433	1	ENST00000398015.3:c.251G>A	p.Arg84His	p.R84H	ENST00000398015	NM_004441.4	84	cGc/cAc	3/16	1	2	FACETS	0.803	0.604	1	0.803	0.604	1	CLONAL	1	TRUE	1	0.15	2		434	299	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998598	100998598	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1279278874	NA	P-0046653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	24	662	0	ENST00000325455.5:c.1204C>T	p.Arg402Cys	p.R402C	ENST00000325455	NM_001202474.3	402	Cgt/Tgt	1/8	1	2	FACETS	0.786	0.616	0.983	0.786	0.616	0.983	CLONAL	1	TRUE	1	0.15	2		662	407	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285748	87285748	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1440777069	NA	P-0046653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	30	576	0	ENST00000277120.3:c.85G>A	p.Ala29Thr	p.A29T	ENST00000277120		29	Gct/Act	2/19	1	2	FACETS	0.866	0.697	1	0.866	0.697	1	CLONAL	1	TRUE	1	0.15	2		576	462	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437677	52437677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	28	684	0	ENST00000460680.1:c.1484C>T	p.Thr495Met	p.T495M	ENST00000460680	NM_004656.3	495	aCg/aTg	13/17	1	2	FACETS	0.872	0.697	1	0.872	0.697	1	CLONAL	1	TRUE	1	0.15	2		684	428	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844190	68844190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567505715	NA	P-0046653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	26	677	0	ENST00000261769.5:c.778C>T	p.Pro260Ser	p.P260S	ENST00000261769	NM_004360.3	260	Ccc/Tcc	6/16	1	2	FACETS	0.741	0.586	0.919	0.741	0.586	0.919	CLONAL	1	TRUE	1	0.15	2		677	468	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828029	72828029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	33	833	0	ENST00000268489.5:c.8552G>A	p.Gly2851Asp	p.G2851D	ENST00000268489	NM_006885.3	2851	gGc/gAc	9/10	1	2	FACETS	0.715	0.581	0.868	0.715	0.581	0.868	SUBCLONAL	1	TRUE	1	0.15	2		833	615	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193458	99193458	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777173666	NA	P-0046653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	25	668	0	ENST00000074304.5:c.2653C>T	p.Arg885Cys	p.R885C	ENST00000074304	NM_001134224.1	885	Cgc/Tgc	25/26	1	2	FACETS	0.805	0.634	1	0.805	0.634	1	CLONAL	1	TRUE	1	0.15	2		668	414	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651261	45651261	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	24	684	0	ENST00000407780.3:c.764C>A	p.Ala255Asp	p.A255D	ENST00000407780	NM_001283052.1	255	gCc/gAc	5/7	1	2	FACETS	0.716	0.56	0.896	0.716	0.56	0.896	SUBCLONAL	1	TRUE	1	0.15	2		684	447	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664528	138664528	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	18	412	0	ENST00000330315.3:c.1037C>T	p.Ala346Val	p.A346V	ENST00000330315	NM_023067.3	346	gCt/gTt	1/1	1	2	FACETS	1	0.801	1	1	0.801	1	CLONAL	1	TRUE	1	0.15	2		412	224	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457796	149457796	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	20	526	0	ENST00000286301.3:c.608del	p.Pro203GlnfsTer3	p.P203Qfs*3	ENST00000286301	NM_005211.3	203	cCa/ca	5/22	0.237261288528992	0	FACETS	0.804	0.615	1			1	CLONAL	1	TRUE	0	0.15	0		526	282	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55269455	55269455	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	38	800	0	ENST00000275493.2:c.3142G>T	p.Ala1048Ser	p.A1048S	ENST00000275493	NM_005228.3	1048	Gct/Tct	26/28	1	2	FACETS	0.911	0.752	1	0.911	0.752	1	CLONAL	1	TRUE	1	0.15	2		800	556	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0046654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	98	435	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.52643518275337	2		435	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578547	7578547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	586	767	2	ENST00000269305.4:c.383del	p.Pro128LeufsTer42	p.P128Lfs*42	ENST00000269305	NM_001126112.2	128	cCt/ct	5/11	0.518484113215945	3	FACETS	0.936	0.907	0.966	0.936	0.907	0.966	CLONAL	3	TRUE	0	0.52643518275337	3		769	1001	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114900949	114900949	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	120	447	0	ENST00000543371.1:c.561del	p.Val188CysfsTer37	p.V188Cfs*37	ENST00000543371	NM_001198531.1	187	Aaa/aa	6/14	1	2	FACETS	0.887	0.805	0.973	0.887	0.805	0.973	CLONAL	1	TRUE	1	0.52643518275337	2		447	514	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408894	41408894	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	47	372	0	ENST00000373198.4:c.532G>T	p.Ala178Ser	p.A178S	ENST00000373198	NM_133170.3	178	Gcc/Tcc	4/32	0.295147534682815	4	FACETS	0.387	0.326	0.455			1	INDETERMINATE	1	TRUE	NA	0.52643518275337	4		372	704	SUCCESS
APC	324	MSKCC	GRCh37	5	112175277	112175278	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0046654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	43	180	0	ENST00000257430.4:c.3989dup	p.Arg1331Ter	p.R1331*	ENST00000257430	NM_000038.5	1329	cac/caCc	16/16	1	2	FACETS	0.817	0.692	0.952	0.817	0.692	0.952	CLONAL	1	TRUE	1	0.52643518275337	2		180	200	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866707	37866707	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	528	612	0	ENST00000269571.5:c.874G>C	p.Gly292Arg	p.G292R	ENST00000269571		292	Ggc/Cgc	7/27	0.0812843074771448	4	FACETS	0.937	0.903	0.972	1	0.998	1	INDETERMINATE	5	TRUE	2	0.27	4		612	1060	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0046655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	33	333	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.3	1	FACETS	0.745	0.609	0.896	0.745	0.609	0.896	SUBCLONAL	1	TRUE	0	0.27	1		333	284	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350291	15350291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1233820799	NA	P-0046655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	66	632	1	ENST00000263377.2:c.3488G>A	p.Arg1163Gln	p.R1163Q	ENST00000263377	NM_058243.2	1163	cGg/cAg	17/20	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.27	2		633	438	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504392	149504392	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs541926152	NA	P-0046655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	51	482	0	ENST00000261799.4:c.1810C>T	p.Arg604Cys	p.R604C	ENST00000261799	NM_002609.3	604	Cgc/Tgc	13/23	0.3	1	FACETS	0.86	0.733	0.998	0.86	0.733	0.998	CLONAL	1	TRUE	0	0.27	1		482	380	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604725	48604726	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs377767373	NA	P-0046655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	39	380	0	ENST00000342988.3:c.1549_1550del	p.Ser517HisfsTer9	p.S517Hfs*9	ENST00000342988	NM_005359.5	516	cAG/c	12/12	0.3	1	FACETS	0.853	0.71	1	0.853	0.71	1	CLONAL	1	TRUE	0	0.27	1		380	293	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023348	27023348	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	39	262	0	ENST00000324856.7:c.454C>T	p.Gln152Ter	p.Q152*	ENST00000324856	NM_006015.4	152	Caa/Taa	1/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.27	2		262	212	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471712	120471712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs75423398	NA	P-0046656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	33	396	1	ENST00000256646.2:c.3779G>A	p.Arg1260His	p.R1260H	ENST00000256646	NM_024408.3	1260	cGt/cAt	23/34	0.0746310440323632	4	FACETS	0.7	0.571	0.846			1	INDETERMINATE	1	FALSE	NA	0.333310062755964	4		397	377	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615569	100615569	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs128621193	NA	P-0046656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	59	366	0	ENST00000308731.7:c.763C>T	p.Arg255Ter	p.R255*	ENST00000308731	NM_000061.2	255	Cga/Tga	8/19	0.333310062755964	2	FACETS	1	0.93	1	0.558	0.483	0.639	CLONAL	1	FALSE	0	0.333310062755964	2		366	317	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729848	41729848	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	25	364	0	ENST00000242208.4:c.681C>G	p.Ile227Met	p.I227M	ENST00000242208	NM_002192.2	227	atC/atG	3/3	0.333310062755964	4	FACETS	0.662	0.523	0.822	0.221	0.174	0.274	SUBCLONAL	1	FALSE	1	0.333310062755964	4		364	302	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194831	30194831	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368595371	NA	P-0046656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	31	409	0	ENST00000331968.5:c.314G>A	p.Arg105His	p.R105H	ENST00000331968	NM_002742.2	105	cGc/cAc	2/18	0.30620727157662	4	FACETS	0.524	0.423	0.639	0.131	0.105	0.16	SUBCLONAL	1	FALSE	0	0.333310062755964	4		409	473	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456486	29456486	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	65	590	0	ENST00000389048.3:c.2432T>A	p.Val811Glu	p.V811E	ENST00000389048	NM_004304.4	811	gTg/gAg	14/29	0.213806434709013	3	FACETS	0.626	0.542	0.717	0.313	0.271	0.359	SUBCLONAL	1	FALSE	1	0.333310062755964	3		590	727	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578446	7578447	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCCATGG	novel	NA	P-0046656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	234	646	0	ENST00000269305.4:c.476_483dup	p.Ile162ProfsTer11	p.I162Pfs*11	ENST00000269305	NM_001126112.2	161	-/CCATGGCC	5/11	0.268612904644115	3	FACETS	0.863	0.81	0.916	0.863	0.81	0.916	CLONAL	3	FALSE	0	0.333310062755964	3		646	633	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0046658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	27	232	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.16665024309575	3	FACETS	0.894	0.727	1	0.447	0.363	0.537	INDETERMINATE	1	TRUE	1	0.841944815835505	3		233	102	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0046658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	44	361	0				ENST00000310581	NM_198253.2	-/1132			0.16665024309575	3	FACETS	1	0.936	1	0.585	0.502	0.671	INDETERMINATE	1	TRUE	1	0.841944815835505	3		361	127	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791981	42791985	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCC	AGGCC	-	novel	NA	P-0046658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	128	764	0	ENST00000575354.2:c.785_789del	p.Lys262ThrfsTer51	p.K262Tfs*51	ENST00000575354	NM_015125.3	262	aAGGCC/a	6/20	0.835211942810935	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.841944815835505	1		764	176	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589541	67589591	+	inframe_deletion	In_Frame_Del	DEL	AAGTTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATTACATGAAT	AAGTTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATTACATGAAT	-	novel	NA	P-0046658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	52	170	0	ENST00000274335.5:c.1305_1355del	p.Gln435_Tyr452delinsHis	p.Q435_Y452delinsH	ENST00000274335		435	cAAGTTGTCAAAGAAGATAATATTGAAGCTGTAGGGAAAAAATTACATGAATat/cat	10/15	0.16665024309575	3	FACETS	0.75	0.659	0.842	0.75	0.659	0.842	INDETERMINATE	2	TRUE	1	0.841944815835505	3		170	117	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0046660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	71	606	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	0.869	0.758	0.99	0.869	0.758	0.99	CLONAL	1	TRUE	1	0.22169683923114	2		606	737	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1255443	1255443	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763381198	NA	P-0046660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	34	548	0	ENST00000310581.5:c.3116C>T	p.Thr1039Met	p.T1039M	ENST00000310581	NM_198253.2	1039	aCg/aTg	14/16	1	2	FACETS	0.489	0.399	0.592	0.489	0.399	0.592	SUBCLONAL	1	TRUE	1	0.22169683923114	2		548	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0046661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	635	528	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.736559196400957	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	4	TRUE	0	0.736559196400957	4		528	740	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974769	21974770	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCCGT	rs1563892769	NA	P-0046661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	59	266	0	ENST00000304494.5:c.52_57dup	p.Thr18_Ala19dup	p.T18_A19dup	ENST00000304494	NM_000077.4	18	-/ACGGCC	1/3	0.736559196400957	3	FACETS	0.758	0.658	0.866	0.379	0.329	0.433	SUBCLONAL	1	TRUE	1	0.736559196400957	3		266	289	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812269	212812269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201152419	NA	P-0046661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	48	271	1	ENST00000342788.4:c.307C>T	p.Arg103Cys	p.R103C	ENST00000342788	NM_005235.2	103	Cgc/Tgc	3/28	0.736559196400957	3	FACETS	0.915	0.784	1	0.457	0.392	0.527	CLONAL	1	TRUE	1	0.736559196400957	3		272	195	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913385	NA	P-0046661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	288	548	0	ENST00000304494.5:c.247C>G	p.His83Asp	p.H83D	ENST00000304494	NM_000077.4	83	Cac/Gac	2/3	0.736559196400957	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.736559196400957	3		548	524	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440040	220440040	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	333	820	0	ENST00000243786.2:c.893A>G	p.His298Arg	p.H298R	ENST00000243786	NM_002191.3	298	cAc/cGc	2/2	0.736559196400957	3	FACETS	0.965	0.921	1	0.965	0.921	1	CLONAL	2	TRUE	1	0.736559196400957	3		820	641	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0046662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	330	649	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.799987803815732	2	FACETS	0.978	0.951	1	0.978	0.951	1	CLONAL	2	TRUE	0	0.854389240050151	2		649	395	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462609	92462609	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1230241694	NA	P-0046662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	75	396	0	ENST00000265734.4:c.29A>G	p.Asp10Gly	p.D10G	ENST00000265734	NM_001259.6	10	gAc/gGc	2/8	0.38409385591713	3	FACETS	1	0.943	1	0.547	0.487	0.61	INDETERMINATE	1	TRUE	1	0.854389240050151	3		396	229	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	189	427	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.86986318273498	NA		427	396	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0046663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	316	572	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	1	0.86986318273498	2		572	608	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0046663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	230	667	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.923	0.867	0.979	0.923	0.867	0.979	CLONAL	1	FALSE	1	0.86986318273498	2		667	573	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949124	44949124	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	289	509	0	ENST00000377967.4:c.3685C>T	p.Gln1229Ter	p.Q1229*	ENST00000377967	NM_021140.2	1229	Cag/Tag	25/29	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.86986318273498	2		509	608	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969382	44969383	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	240	449	0	ENST00000377967.4:c.4065dup	p.Val1356SerfsTer33	p.V1356Sfs*33	ENST00000377967	NM_021140.2	1355	ata/atAa	28/29	1	2	FACETS	0.906	0.852	0.961	0.906	0.852	0.961	CLONAL	1	FALSE	1	0.86986318273498	2		449	609	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220452	123220452	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046663-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	316	573	0	ENST00000218089.9:c.3109del	p.Val1037CysfsTer5	p.V1037Cfs*5	ENST00000218089	NM_001042749.1	1037	Gtg/tg	30/35	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.86986318273498	2		573	694	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	111	424	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.284351950127035	4	FACETS	0.964	0.871	1			1	CLONAL	2	TRUE	NA	0.292327261356078	4		424	509	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572189	64572189	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	119	661	2	ENST00000312049.6:c.1450C>T	p.Arg484Trp	p.R484W	ENST00000312049	NM_130799.2	484	Cgg/Tgg	10/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.292327261356078	2		663	683	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974783	21974786	+	frameshift_variant	Frame_Shift_Del	DEL	CAGT	CAGT	-	novel	NA	P-0046664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	55	260	0	ENST00000304494.5:c.41_44del	p.Asp14GlyfsTer11	p.D14Gfs*11	ENST00000304494	NM_000077.4	14	gACTGg/gg	1/3	0.292327261356078	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.292327261356078	1		260	258	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907037	101907037	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	40	261	0	ENST00000374994.4:c.997G>C	p.Asp333His	p.D333H	ENST00000374994	NM_004612.2	333	Gat/Cat	6/9	0.292327261356078	1	FACETS	0.872	0.729	1	0.872	0.729	1	CLONAL	1	TRUE	0	0.292327261356078	1		261	268	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940720	71940720	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs758146582	NA	P-0046664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	109	659	0	ENST00000298229.2:c.767C>G	p.Thr256Arg	p.T256R	ENST00000298229	NM_001567.3	256	aCa/aGa	7/28	1	2	FACETS	0.971	0.872	1	0.971	0.872	1	CLONAL	1	TRUE	1	0.292327261356078	2		659	768	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434414	110434414	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	129	807	0	ENST00000375856.3:c.3987C>G	p.His1329Gln	p.H1329Q	ENST00000375856	NM_003749.2	1329	caC/caG	1/2	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.292327261356078	2		807	861	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135378	30135378	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	33	322	0	ENST00000331968.5:c.440del	p.His147ProfsTer36	p.H147Pfs*36	ENST00000331968	NM_002742.2	147	cAc/cc	3/18	0.292327261356078	1	FACETS	0.557	0.454	0.673	0.557	0.454	0.673	SUBCLONAL	1	TRUE	0	0.292327261356078	1		322	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578443	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	162	804	2	ENST00000269305.4:c.487del	p.Tyr163ThrfsTer7	p.Y163Tfs*7	ENST00000269305	NM_001126112.2	163	Tac/ac	5/11	0.292327261356078	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.292327261356078	1		806	797	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981594	70981594	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	104	957	0	ENST00000276594.2:c.502C>G	p.Gln168Glu	p.Q168E	ENST00000276594	NM_024504.3	168	Cag/Gag	2/8	0.292327261356078	1	FACETS	0.658	0.588	0.732	0.658	0.588	0.732	SUBCLONAL	1	TRUE	0	0.292327261356078	1		957	924	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772013	135772013	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	85	473	0	ENST00000298552.3:c.3104G>T	p.Gly1035Val	p.G1035V	ENST00000298552	NM_001162426.1	1035	gGt/gTt	23/23	0.292327261356078	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.292327261356078	1		473	410	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267491	198267491	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763149798	NA	P-0046665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	52	309	0	ENST00000335508.6:c.1866G>T	p.Glu622Asp	p.E622D	ENST00000335508	NM_012433.2	622	gaG/gaT	14/25	0.257351966578881	1	FACETS	0.467	0.399	0.54	0.467	0.399	0.54	INDETERMINATE	1	TRUE	0	0.500194864024826	1		309	334	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939550	68939550	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	38	246	0	ENST00000288368.4:c.535A>T	p.Ile179Phe	p.I179F	ENST00000288368	NM_024870.2	179	Att/Ttt	5/40	0.500194864024826	6	FACETS	0.483	0.398	0.578	0.161	0.132	0.193	SUBCLONAL	1	TRUE	3	0.500194864024826	6		246	629	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	167	427	0				ENST00000310581	NM_198253.2	-/1132			0.3	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	3	TRUE	1	0.3	4		427	453	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0046666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	126	325	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.3	3	FACETS	0.931	0.847	1	0.931	0.847	1	CLONAL	2	TRUE	1	0.3	3		325	519	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0046666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	132	572	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.3	2		572	759	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609311	81609311	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs780949533	NA	P-0046666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	25	194	0	ENST00000298171.2:c.909G>C	p.Glu303Asp	p.E303D	ENST00000298171	NM_000369.2	303	gaG/gaC	10/10	1	2	FACETS	0.731	0.579	0.904	0.731	0.579	0.904	CLONAL	1	TRUE	1	0.3	2		194	228	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148507497	148507497	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	51	253	0	ENST00000320356.2:c.1957C>G	p.Gln653Glu	p.Q653E	ENST00000320356	NM_004456.4	653	Caa/Gaa	17/20	1	2	FACETS	0.912	0.777	1	0.912	0.777	1	CLONAL	1	TRUE	1	0.3	2		253	373	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551461	150551461	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs752398877	NA	P-0046666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	137	703	0	ENST00000369026.2:c.546C>G	p.Ile182Met	p.I182M	ENST00000369026	NM_021960.4	182	atC/atG	1/3	1	2	FACETS	0.872	0.792	0.957	0.872	0.792	0.957	CLONAL	1	TRUE	1	0.3	2		703	1047	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274827	38274827	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	46	299	0	ENST00000425967.3:c.1753G>C	p.Asp585His	p.D585H	ENST00000425967	NM_001174067.1	585	Gat/Cat	13/19	1	2	FACETS	0.816	0.689	0.955	0.816	0.689	0.955	CLONAL	1	TRUE	1	0.3	2		299	376	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790830	89790830	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	91	599	0	ENST00000336032.3:c.217C>G	p.Arg73Gly	p.R73G	ENST00000336032	NM_006813.2	73	Cgc/Ggc	1/2	1	2	FACETS	0.733	0.65	0.821	0.733	0.65	0.821	SUBCLONAL	1	TRUE	1	0.3	2		599	828	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551448	150551448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	127	697	0	ENST00000369026.2:c.559C>T	p.Arg187Trp	p.R187W	ENST00000369026	NM_021960.4	187	Cgg/Tgg	1/3	1	2	FACETS	0.828	0.749	0.912	0.828	0.749	0.912	CLONAL	1	TRUE	1	0.3	2		697	1022	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519920	NA	P-0046666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	53	280	2	ENST00000397062.3:c.85G>A	p.Asp29Asn	p.D29N	ENST00000397062	NM_006164.4	29	Gat/Aat	2/5	1	2	FACETS	0.805	0.688	0.933	0.805	0.688	0.933	CLONAL	1	TRUE	1	0.3	2		282	439	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373293	118373293	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	62	335	0	ENST00000534358.1:c.6686C>A	p.Ser2229Ter	p.S2229*	ENST00000534358	NM_005933.3	2229	tCa/tAa	27/36	NA	2	FACETS	0.908	0.787	1			1	INDETERMINATE	1	TRUE	NA	0.3	2		335	455	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22161984	22161984	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	71	383	0	ENST00000215832.6:c.271C>G	p.Arg91Gly	p.R91G	ENST00000215832	NM_002745.4	91	Cga/Gga	2/9	1	2	FACETS	0.905	0.791	1	0.905	0.791	1	CLONAL	1	TRUE	1	0.3	2		383	523	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285876	39285876	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1558493384	NA	P-0046666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	89	421	1	ENST00000402219.2:c.283G>A	p.Glu95Lys	p.E95K	ENST00000402219	NM_005633.3	95	Gaa/Aaa	3/23	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.3	2		422	587	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551538	150551538	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	131	606	0	ENST00000369026.2:c.469G>T	p.Asp157Tyr	p.D157Y	ENST00000369026	NM_021960.4	157	Gac/Tac	1/3	1	2	FACETS	0.86	0.779	0.945	0.86	0.779	0.945	CLONAL	1	TRUE	1	0.3	2		606	1016	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064428	30064428	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	61	346	0	ENST00000338641.4:c.992G>C	p.Arg331Thr	p.R331T	ENST00000338641	NM_000268.3	331	aGa/aCa	10/16	1	2	FACETS	0.994	0.861	1	0.994	0.861	1	CLONAL	1	TRUE	1	0.3	2		346	409	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067908	30067908	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	81	499	0	ENST00000338641.4:c.1093G>T	p.Glu365Ter	p.E365*	ENST00000338641	NM_000268.3	365	Gaa/Taa	11/16	1	2	FACETS	0.933	0.823	1	0.933	0.823	1	CLONAL	1	TRUE	1	0.3	2		499	579	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067911	30067911	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046666-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	83	494	0	ENST00000338641.4:c.1096G>T	p.Glu366Ter	p.E366*	ENST00000338641	NM_000268.3	366	Gaa/Taa	11/16	1	2	FACETS	0.966	0.854	1	0.966	0.854	1	CLONAL	1	TRUE	1	0.3	2		494	573	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604665	48604665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660045	NA	P-0046670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	89	317	0	ENST00000342988.3:c.1487G>A	p.Arg496His	p.R496H	ENST00000342988	NM_005359.5	496	cGt/cAt	12/12	0.580989410098376	1	FACETS	0.734	0.659	0.813	0.734	0.659	0.813	SUBCLONAL	1	TRUE	0	0.580989410098376	1		317	296	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0046670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	208	865	2	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	1	2	FACETS	0.889	0.827	0.953	0.889	0.827	0.953	CLONAL	1	TRUE	1	0.580989410098376	2		867	805	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0046670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	318	743	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.580989410098376	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.580989410098376	1		743	777	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275751	41275751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	177	539	0	ENST00000349496.5:c.1646G>A	p.Arg549His	p.R549H	ENST00000349496	NM_001904.3	549	cGc/cAc	10/15	1	2	FACETS	0.839	0.775	0.905	0.839	0.775	0.905	CLONAL	1	TRUE	1	0.580989410098376	2		539	726	SUCCESS
APC	324	MSKCC	GRCh37	5	112162946	112162946	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1057517561	NA	P-0046670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	107	277	0	ENST00000257430.4:c.1548+2T>C		p.X516_splice	ENST00000257430	NM_000038.5	516			0.580989410098376	1	FACETS	0.773	0.719	0.826	1	0.989	1	SUBCLONAL	2	TRUE	0	0.580989410098376	1		277	169	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861171	57861171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	129	587	0	ENST00000228682.2:c.968G>A	p.Arg323Gln	p.R323Q	ENST00000228682	NM_005269.2	323	cGg/cAg	9/12	1	2	FACETS	0.639	0.58	0.701	0.639	0.58	0.701	SUBCLONAL	1	TRUE	1	0.580989410098376	2		587	695	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303452	91303452	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	39	320	0	ENST00000355112.3:c.1163A>T	p.Asp388Val	p.D388V	ENST00000355112	NM_000057.2	388	gAt/gTt	6/22	0.43252122026464	1	FACETS	0.299	0.248	0.354	0.299	0.248	0.354	SUBCLONAL	1	TRUE	0	0.580989410098376	1		320	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0046671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	56	682	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	1	2	FACETS	0.965	0.825	1	0.965	0.825	1	CLONAL	1	TRUE	1	0.14	2		682	829	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057087	180057087	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	59	714	1	ENST00000261937.6:c.532C>A	p.Pro178Thr	p.P178T	ENST00000261937	NM_182925.4	178	Cca/Aca	5/30	0.260491549950462	0	FACETS	1	0.868	1			1	CLONAL	1	TRUE	0	0.14	0		715	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579336	7579336	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	207	620	0	ENST00000269305.4:c.351del	p.Thr118GlnfsTer5	p.T118Qfs*5	ENST00000269305	NM_001126112.2	117	ggG/gg	4/11	0.560195105887301	1	FACETS	0.948	0.889	1	0.948	0.889	1	CLONAL	1	TRUE	0	0.610389775534584	1		620	497	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604748	48604748	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	187	334	0	ENST00000342988.3:c.1570T>C	p.Trp524Arg	p.W524R	ENST00000342988	NM_005359.5	524	Tgg/Cgg	12/12	0.548636946836161	2	FACETS	0.813	0.763	0.863	0.813	0.763	0.863	CLONAL	2	TRUE	0	0.610389775534584	2		334	377	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412766	63412766	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	29	607	0	ENST00000330258.3:c.401A>G	p.His134Arg	p.H134R	ENST00000330258	NM_152424.3	134	cAt/cGt	2/2	0.293656300653953	1	FACETS	0.121	0.096	0.149	0.121	0.096	0.149	INDETERMINATE	1	TRUE	0	0.610389775534584	1		607	547	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435460	18435460	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	58	227	0	ENST00000266497.5:c.445A>G	p.Thr149Ala	p.T149A	ENST00000266497		149	Aca/Gca	1/31	NA	2	FACETS	0.845	0.735	0.961			1	INDETERMINATE	1	TRUE	NA	0.610389775534584	2		227	225	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432515	49432515	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	151	685	0	ENST00000301067.7:c.8624C>T	p.Ala2875Val	p.A2875V	ENST00000301067	NM_003482.3	2875	gCc/gTc	34/54	1	2	FACETS	0.7	0.641	0.761	0.7	0.641	0.761	SUBCLONAL	1	TRUE	1	0.610389775534584	2		685	707	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225648	26225648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770438126	NA	P-0046671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	110	474	0	ENST00000360408.1:c.266C>T	p.Ala89Val	p.A89V	ENST00000360408	NM_003532.2	89	gCg/gTg	1/1	0.170823777438277	4	FACETS	0.974	0.877	1	0.487	0.438	0.538	INDETERMINATE	1	TRUE	2	0.610389775534584	4		474	596	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779828	135779828	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046671-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	97	366	0	ENST00000298552.3:c.2011A>T	p.Ser671Cys	p.S671C	ENST00000298552	NM_001162426.1	671	Agc/Tgc	16/23	1	2	FACETS	0.809	0.726	0.895	0.809	0.726	0.895	CLONAL	1	TRUE	1	0.610389775534584	2		366	393	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0046673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	146	572	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.904	0.827	0.985	0.904	0.827	0.985	CLONAL	1	TRUE	1	0.436384272578723	2		572	740	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0046675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	170	575	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.366464939312503	2	FACETS	0.87	0.805	0.936	0.87	0.805	0.936	CLONAL	2	TRUE	0	0.371651314504073	2		575	526	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039133	49039133	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs587776786	NA	P-0046675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	199	160	2	ENST00000267163.4:c.2212-1G>A		p.X738_splice	ENST00000267163	NM_000321.2	738			0.371651314504073	6	FACETS	0.952	0.901	1			1	CLONAL	6	TRUE	NA	0.371651314504073	6		162	327	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865389	57865389	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	91	833	0	ENST00000228682.2:c.2866T>G	p.Leu956Val	p.L956V	ENST00000228682	NM_005269.2	956	Ttg/Gtg	12/12	0.371651314504073	3	FACETS	0.728	0.646	0.816	0.364	0.323	0.408	SUBCLONAL	1	TRUE	1	0.371651314504073	3		833	798	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991082	41991082	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	60	343	1	ENST00000219905.7:c.2035G>T	p.Val679Phe	p.V679F	ENST00000219905	NM_001164273.1	679	Gtt/Ttt	4/24	0.112960028457727	3	FACETS	0.801	0.691	0.92	0.267	0.23	0.307	INDETERMINATE	1	TRUE	0	0.371651314504073	3		344	478	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248469	212248469	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0046675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	63	365	0	ENST00000342788.4:c.3798T>G	p.Tyr1266Ter	p.Y1266*	ENST00000342788	NM_005235.2	1266	taT/taG	28/28	0.173790851493674	2	FACETS	0.792	0.687	0.905	0.396	0.343	0.453	INDETERMINATE	1	TRUE	0	0.371651314504073	2		365	428	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579354	7579355	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGA	novel	NA	P-0046676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	287	773	0	ENST00000269305.4:c.330_332dup	p.Leu111dup	p.L111dup	ENST00000269305	NM_001126112.2	111	ctg/ctTCTg	4/11	0.85407306263034	1	FACETS	0.992	0.956	1	0.992	0.956	1	CLONAL	1	TRUE	0	0.85407306263034	1		773	388	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050212	128050212	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	165	425	0	ENST00000285398.2:c.445C>G	p.Pro149Ala	p.P149A	ENST00000285398	NM_000122.1	149	Cct/Gct	3/15	1	2	FACETS	0.964	0.896	1	0.964	0.896	1	CLONAL	1	TRUE	1	0.85407306263034	2		425	401	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	154	427	0				ENST00000310581	NM_198253.2	-/1132			0.336961729336205	3	FACETS	0.987	0.919	1	0.987	0.919	1	INDETERMINATE	2	TRUE	1	0.664369693706455	3		427	313	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0046677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	171	667	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.664369693706455	2		667	481	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106255	27106255	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	178	527	0	ENST00000324856.7:c.5866G>C	p.Glu1956Gln	p.E1956Q	ENST00000324856	NM_006015.4	1956	Gag/Cag	20/20	0.407549736286161	3	FACETS	1	0.956	1	0.523	0.484	0.564	CLONAL	1	TRUE	1	0.664369693706455	3		527	682	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0046677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	196	646	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.664369693706455	1	FACETS	0.925	0.868	0.983	0.925	0.868	0.983	CLONAL	1	TRUE	0	0.664369693706455	1		646	426	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357577	89357577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	101	626	0	ENST00000301030.4:c.241G>A	p.Glu81Lys	p.E81K	ENST00000301030	NM_001256183.1	81	Gag/Aag	5/13	NA	2	FACETS	0.431	0.385	0.48			1	INDETERMINATE	1	TRUE	NA	0.664369693706455	2		626	705	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106279	27106279	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	208	568	0	ENST00000324856.7:c.5890G>T	p.Glu1964Ter	p.E1964*	ENST00000324856	NM_006015.4	1964	Gag/Tag	20/20	0.407549736286161	3	FACETS	1	0.982	1	0.577	0.537	0.618	CLONAL	1	TRUE	1	0.664369693706455	3		568	723	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319853	8319853	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	55	285	0	ENST00000356435.5:c.5648G>A	p.Arg1883Gln	p.R1883Q	ENST00000356435		1883	cGa/cAa	34/35	0.664369693706455	1	FACETS	0.539	0.468	0.615	0.539	0.468	0.615	SUBCLONAL	1	TRUE	0	0.664369693706455	1		285	205	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351980	89351980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	292	908	1	ENST00000301030.4:c.970G>A	p.Glu324Lys	p.E324K	ENST00000301030	NM_001256183.1	324	Gaa/Aaa	9/13	NA	2	FACETS	0.882	0.831	0.934			1	INDETERMINATE	1	TRUE	NA	0.664369693706455	2		909	997	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120720	115120720	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	264	747	0	ENST00000257566.3:c.286G>A	p.Glu96Lys	p.E96K	ENST00000257566	NM_016569.3	96	Gaa/Aaa	1/8	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.664369693706455	2		747	761	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023006	27023006	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	14	27	0	ENST00000324856.7:c.112G>T	p.Glu38Ter	p.E38*	ENST00000324856	NM_006015.4	38	Gag/Tag	1/20	0.407549736286161	3	FACETS	0.851	0.653	1	0.851	0.653	1	CLONAL	2	TRUE	1	0.664369693706455	3		27	33	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954222	32954222	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs80359180	NA	P-0046677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	249	454	0	ENST00000380152.3:c.9196C>T	p.Gln3066Ter	p.Q3066*	ENST00000380152		3066	Cag/Tag	24/27	0.531471761267361	3	FACETS	0.871	0.822	0.921	0.871	0.822	0.921	CLONAL	2	TRUE	1	0.664369693706455	3		454	573	SUCCESS
APC	324	MSKCC	GRCh37	5	112176324	112176324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1561597208	NA	P-0046677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	44	270	0	ENST00000257430.4:c.5033G>A	p.Gly1678Glu	p.G1678E	ENST00000257430	NM_000038.5	1678	gGg/gAg	16/16	0.336961729336205	3	FACETS	0.497	0.418	0.584	0.249	0.209	0.292	INDETERMINATE	1	TRUE	1	0.664369693706455	3		270	355	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655374	67655374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	68	413	0	ENST00000264010.4:c.1237C>A	p.His413Asn	p.H413N	ENST00000264010	NM_006565.3	413	Cat/Aat	7/12	0.407549736286161	3	FACETS	0.492	0.428	0.561	0.246	0.214	0.281	SUBCLONAL	1	TRUE	1	0.664369693706455	3		413	554	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	532722	532722	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	116	761	0	ENST00000451590.1:c.484G>C	p.Glu162Gln	p.E162Q	ENST00000451590	NM_001130442.1	162	Gag/Cag	5/5	NA	2	FACETS	0.505	0.455	0.557			1	INDETERMINATE	1	TRUE	NA	0.664369693706455	2		761	692	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120991	115120991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	166	490	0	ENST00000257566.3:c.15G>A	p.Met5Ile	p.M5I	ENST00000257566	NM_016569.3	5	atG/atA	1/8	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.664369693706455	2		490	487	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43739612	43739612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	152	397	0	ENST00000382044.4:c.2788C>T	p.Leu930Phe	p.L930F	ENST00000382044	NM_001141980.1	930	Ctt/Ttt	13/28	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.664369693706455	2		397	426	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89851368	89851368	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1429369721	NA	P-0046677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	81	398	0	ENST00000389301.3:c.1364C>A	p.Ser455Tyr	p.S455Y	ENST00000389301	NM_000135.2	455	tCc/tAc	15/43	NA	2	FACETS	0.46	0.406	0.518			1	INDETERMINATE	1	TRUE	NA	0.664369693706455	2		398	530	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440698	56440698	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	108	611	0	ENST00000407977.2:c.520G>C	p.Glu174Gln	p.E174Q	ENST00000407977		174	Gag/Cag	5/10	NA	2	FACETS	0.553	0.497	0.611			1	INDETERMINATE	1	TRUE	NA	0.664369693706455	2		611	588	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250151	39250151	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0046677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	217	568	0	ENST00000402219.2:c.1418C>G	p.Ser473Ter	p.S473*	ENST00000402219	NM_005633.3	473	tCa/tGa	10/23	0.343775371236105	1	FACETS	0.809	0.759	0.86	0.809	0.759	0.86	INDETERMINATE	1	TRUE	0	0.664369693706455	1		568	539	SUCCESS
APC	324	MSKCC	GRCh37	5	112176695	112176695	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	40	176	0	ENST00000257430.4:c.5404G>T	p.Glu1802Ter	p.E1802*	ENST00000257430	NM_000038.5	1802	Gag/Tag	16/16	0.336961729336205	3	FACETS	0.647	0.541	0.763	0.323	0.27	0.382	INDETERMINATE	1	TRUE	1	0.664369693706455	3		176	248	SUCCESS
APC	324	MSKCC	GRCh37	5	112179275	112179275	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1170745005	NA	P-0046677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	47	255	0	ENST00000257430.4:c.7984G>C	p.Glu2662Gln	p.E2662Q	ENST00000257430	NM_000038.5	2662	Gag/Cag	16/16	0.336961729336205	3	FACETS	0.531	0.449	0.62	0.265	0.224	0.31	INDETERMINATE	1	TRUE	1	0.664369693706455	3		255	355	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942882	68942882	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	89	473	0	ENST00000288368.4:c.694G>C	p.Glu232Gln	p.E232Q	ENST00000288368	NM_024870.2	232	Gaa/Caa	6/40	0.664369693706455	5	FACETS	0.482	0.426	0.542			1	SUBCLONAL	1	TRUE	NA	0.664369693706455	5		473	1110	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978484	70978484	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	56	340	0	ENST00000276594.2:c.1169C>G	p.Ser390Cys	p.S390C	ENST00000276594	NM_024504.3	390	tCt/tGt	5/8	NA	2	FACETS	0.648	0.561	0.742			1	INDETERMINATE	1	TRUE	NA	0.664369693706455	2		340	260	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434827	128434827	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	83	541	0	ENST00000265960.3:c.27C>G	p.Ile9Met	p.I9M	ENST00000265960	NM_001006617.1	9	atC/atG	2/12	0.664369693706455	1	FACETS	0.484	0.43	0.54	0.484	0.43	0.54	SUBCLONAL	1	TRUE	0	0.664369693706455	1		541	345	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802598	135802598	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	119	257	0	ENST00000298552.3:c.200C>T	p.Pro67Leu	p.P67L	ENST00000298552	NM_001162426.1	67	cCa/cTa	4/23	0.664369693706455	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.664369693706455	1		257	221	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176476	123176476	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	15	211	0	ENST00000218089.9:c.443T>C	p.Met148Thr	p.M148T	ENST00000218089	NM_001042749.1	148	aTg/aCg	7/35	0.343775371236105	1	FACETS	0.123	0.089	0.163	0.123	0.089	0.163	INDETERMINATE	1	TRUE	0	0.664369693706455	1		211	246	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577077	7577085	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTTCCTC	CTCTTCCTC	TTTTCCTT	novel	NA	P-0046677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	213	735	1	ENST00000269305.4:c.853_861delinsAAGGAAAA	p.Glu285LysfsTer60	p.E285Kfs*60	ENST00000269305	NM_001126112.2	285	GAGGAAGAG/AAGGAAAA	8/11	0.664369693706455	1	FACETS	0.958	0.902	1	0.958	0.902	1	CLONAL	1	TRUE	0	0.664369693706455	1		736	447	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0046678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	166	405	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.347075592964316	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.376790654937977	3		408	483	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0046678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	36	206	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	1	2	FACETS	0.827	0.685	0.984	0.827	0.685	0.984	CLONAL	1	TRUE	1	0.376790654937977	2		206	231	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577068	7577068	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	343	819	0	ENST00000269305.4:c.870del	p.Lys291ArgfsTer54	p.K291Rfs*54	ENST00000269305	NM_001126112.2	290	cgC/cg	8/11	0.314546085013091	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.376790654937977	2		819	835	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041137	180041137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1376446971	NA	P-0046678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	176	974	0	ENST00000261937.6:c.3262G>A	p.Asp1088Asn	p.D1088N	ENST00000261937	NM_182925.4	1088	Gac/Aac	24/30	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.376790654937977	2		974	760	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38184274	38184274	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	29	432	1	ENST00000317025.8:c.1682C>T	p.Ser561Phe	p.S561F	ENST00000317025	NM_023034.1	561	tCt/tTt	7/24	0.340894415703056	1	FACETS	0.227	0.182	0.279	0.227	0.182	0.279	SUBCLONAL	1	TRUE	0	0.376790654937977	1		433	550	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480320	56480320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	148	301	0	ENST00000267101.3:c.427C>A	p.Leu143Met	p.L143M	ENST00000267101	NM_001982.3	143	Ctg/Atg	4/28	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.72	2		301	354	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0046679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	262	572	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.992	0.934	1	0.992	0.934	1	CLONAL	1	TRUE	1	0.72	2		572	734	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	192	588	0	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	0.993	0.926	1	0.993	0.926	1	CLONAL	1	TRUE	1	0.72	2		588	537	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0046679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	129	454	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	0.907	0.831	0.986	0.907	0.831	0.986	CLONAL	1	TRUE	1	0.72	2		454	395	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699369	47699369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	154	344	0	ENST00000347630.2:c.139G>A	p.Glu47Lys	p.E47K	ENST00000347630	NM_001007230.1	47	Gaa/Aaa	4/11	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.72	2		344	427	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692830	89692830	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	69	145	0	ENST00000371953.3:c.314G>T	p.Cys105Phe	p.C105F	ENST00000371953	NM_000314.4	105	tGt/tTt	5/9	1	2	FACETS	0.913	0.808	1	0.913	0.808	1	CLONAL	1	TRUE	1	0.72	2		145	210	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692940	89692940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746152219	NA	P-0046679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	258	408	0	ENST00000371953.3:c.424C>T	p.Arg142Trp	p.R142W	ENST00000371953	NM_000314.4	142	Cgg/Tgg	5/9	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.72	2		408	630	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089763	27089766	+	frameshift_variant	Frame_Shift_Del	DEL	TCTA	TCTA	-	novel	NA	P-0046679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	174	444	0	ENST00000324856.7:c.2721_2724del	p.Ile908LysfsTer10	p.I908Kfs*10	ENST00000324856	NM_006015.4	907	TCTAtc/tc	8/20	1	2	FACETS	0.948	0.879	1	0.948	0.879	1	CLONAL	1	TRUE	1	0.72	2		444	510	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428688	49428688	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs377548063	NA	P-0046679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	209	522	0	ENST00000301067.7:c.10262T>C	p.Ile3421Thr	p.I3421T	ENST00000301067	NM_003482.3	3421	aTt/aCt	35/54	1	2	FACETS	0.958	0.895	1	0.958	0.895	1	CLONAL	1	TRUE	1	0.72	2		522	606	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417887	32417887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1564972874	NA	P-0046680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	186	524	0	ENST00000332351.3:c.1165C>T	p.Arg389Cys	p.R389C	ENST00000332351	NM_024426.4	389	Cgc/Tgc	7/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.512825335975448	2		524	659	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540206	23540207	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTCCTCCCTCTGGCTCTGGCTCTGGCTCCGGCTCCGG	novel	NA	P-0046680-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	94	425	0	ENST00000380871.4:c.160_196dup	p.Arg66ProfsTer54	p.R66Pfs*54	ENST00000380871	NM_006167.3	66	cgc/cCCGGAGCCGGAGCCAGAGCCAGAGCCAGAGGGAGGACgc	1/2	1	2	FACETS	0.644	0.574	0.718	0.644	0.574	0.718	SUBCLONAL	1	TRUE	1	0.512825335975448	2		425	569	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0046688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	69	325	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.773	0.678	0.872	1	0.976	1	SUBCLONAL	2	TRUE	1	0.29	2		325	308	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173673	108173677	+	frameshift_variant	Frame_Shift_Del	DEL	TGGAT	TGGAT	C	novel	NA	P-0046688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	18	311	1	ENST00000278616.4:c.5413_5417delinsC	p.Trp1805GlnfsTer4	p.W1805Qfs*4	ENST00000278616	NM_000051.3	1805	TGGATa/Ca	36/63	0.304163468615578	1	FACETS	0.863	0.657	1	0.863	0.657	1	CLONAL	1	TRUE	0	0.29	1		312	123	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054205	30054210	+	frameshift_variant	Frame_Shift_Del	DEL	GATAGC	GATAGC	T	novel	NA	P-0046689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	64	298	0	ENST00000338641.4:c.627_632delinsT	p.Lys209AsnfsTer17	p.K209Nfs*17	ENST00000338641	NM_000268.3	209	aaGATAGCt/aaTt	7/16	0.358400098510329	1	FACETS	0.792	0.69	0.902	0.792	0.69	0.902	CLONAL	1	TRUE	0	0.358400098510329	1		298	370	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	30	427	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.806	0.654	0.977	0.806	0.654	0.977	CLONAL	1	TRUE	1	0.330718286082066	2		427	225	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0046690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	241	803	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.186509970235535	3	FACETS	0.846	0.795	0.899	0.846	0.795	0.899	INDETERMINATE	3	TRUE	0	0.330718286082066	3		803	669	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879881	37879881	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	52	866	0	ENST00000269571.5:c.2176C>G	p.Leu726Val	p.L726V	ENST00000269571		726	Ctt/Gtt	18/27	0.216546163870966	2	FACETS	0.463	0.393	0.54	0.232	0.196	0.27	SUBCLONAL	1	TRUE	0	0.330718286082066	2		866	679	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853065	151853065	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	58	345	0	ENST00000262189.6:c.11890C>T	p.Gln3964Ter	p.Q3964*	ENST00000262189	NM_170606.2	3964	Cag/Tag	46/59	0.153007226472535	3	FACETS	0.931	0.802	1	0.466	0.401	0.536	INDETERMINATE	1	TRUE	1	0.330718286082066	3		345	439	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004226	150004226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	48	178	0	ENST00000253339.5:c.1999G>A	p.Glu667Lys	p.E667K	ENST00000253339		667	Gaa/Aaa	3/7	0.216546163870966	2	FACETS	1	0.916	1	0.556	0.474	0.645	CLONAL	1	TRUE	0	0.330718286082066	2		178	261	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257893	16257893	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	57	505	0	ENST00000375759.3:c.5158G>C	p.Glu1720Gln	p.E1720Q	ENST00000375759	NM_015001.2	1720	Gag/Cag	11/15	1	2	FACETS	0.684	0.587	0.789	0.684	0.587	0.789	SUBCLONAL	1	TRUE	1	0.330718286082066	2		505	504	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431975	49431975	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	88	695	1	ENST00000301067.7:c.9164del	p.Pro3055LeufsTer16	p.P3055Lfs*16	ENST00000301067	NM_003482.3	3055	cCt/ct	34/54	1	2	FACETS	0.978	0.869	1	0.978	0.869	1	CLONAL	1	TRUE	1	0.330718286082066	2		696	544	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004295	150004295	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	56	236	0	ENST00000253339.5:c.1930G>C	p.Glu644Gln	p.E644Q	ENST00000253339		644	Gag/Cag	3/7	0.216546163870966	2	FACETS	1	0.947	1	0.603	0.52	0.691	CLONAL	1	TRUE	0	0.330718286082066	2		236	281	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004355	150004355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	77	319	0	ENST00000253339.5:c.1870G>A	p.Glu624Lys	p.E624K	ENST00000253339		624	Gaa/Aaa	3/7	0.216546163870966	2	FACETS	1	0.97	1	0.658	0.581	0.738	CLONAL	1	TRUE	0	0.330718286082066	2		319	354	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265438	152265438	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	35	435	0	ENST00000206249.3:c.891G>A	p.Met297Ile	p.M297I	ENST00000206249	NM_000125.3	297	atG/atA	4/8	0.216546163870966	2	FACETS	0.492	0.403	0.592	0.246	0.201	0.296	SUBCLONAL	1	TRUE	0	0.330718286082066	2		435	430	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099784	157099785	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	64	338	0	ENST00000346085.5:c.722dup	p.Ser241ArgfsTer13	p.S241Rfs*13	ENST00000346085	NM_020732.3	241	agc/aGgc	1/20	0.216546163870966	2	FACETS	1	0.962	1	0.641	0.559	0.728	CLONAL	1	TRUE	0	0.330718286082066	2		338	302	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845440	151845440	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	42	558	0	ENST00000262189.6:c.13572G>T	p.Arg4524Ser	p.R4524S	ENST00000262189	NM_170606.2	4524	agG/agT	52/59	0.153007226472535	3	FACETS	0.474	0.395	0.563	0.237	0.197	0.282	INDETERMINATE	1	TRUE	1	0.330718286082066	3		558	624	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874686	151874686	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	91	392	1	ENST00000262189.6:c.7852C>T	p.Gln2618Ter	p.Q2618*	ENST00000262189	NM_170606.2	2618	Cag/Tag	38/59	0.153007226472535	3	FACETS	1	0.978	1	0.711	0.634	0.792	INDETERMINATE	1	TRUE	1	0.330718286082066	3		393	451	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359917	87359918	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	37	286	0	ENST00000277120.3:c.1226dup	p.Asp409GlufsTer7	p.D409Efs*7	ENST00000277120		409	gac/gAac	11/19	0.174386559638354	3	FACETS	0.647	0.534	0.773	0.324	0.267	0.387	INDETERMINATE	1	TRUE	1	0.330718286082066	3		286	403	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195119	123195126	+	frameshift_variant	Frame_Shift_Del	DEL	GCTACTGA	GCTACTGA	-	novel	NA	P-0046690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	91	430	0	ENST00000218089.9:c.1465_1472del	p.Thr489AlafsTer9	p.T489Afs*9	ENST00000218089	NM_001042749.1	488	GCTACTGAg/g	16/35	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.330718286082066	2		430	409	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	31	424	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.546	0.441	0.664	0.546	0.441	0.664	SUBCLONAL	1	TRUE	1	0.253647927520259	2		424	448	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0046692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	27	307	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.601	0.479	0.742	0.601	0.479	0.742	SUBCLONAL	1	TRUE	1	0.253647927520259	2		307	354	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0046692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	39	572	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.624	0.517	0.743	0.624	0.517	0.743	SUBCLONAL	1	TRUE	1	0.253647927520259	2		572	493	SUCCESS
APC	324	MSKCC	GRCh37	5	112162890	112162891	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTAT	novel	NA	P-0046692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	29	368	0	ENST00000257430.4:c.1495_1496insTATC	p.Arg499LeufsTer39	p.R499Lfs*39	ENST00000257430	NM_000038.5	498	-/CTAT	12/16	1	2	FACETS	0.608	0.488	0.745	0.608	0.488	0.745	SUBCLONAL	1	TRUE	1	0.253647927520259	2		368	376	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199903	128199903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777726701	NA	P-0046693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	353	484	0	ENST00000341105.2:c.1402G>A	p.Gly468Ser	p.G468S	ENST00000341105	NM_032638.4	468	Ggc/Agc	6/6	1	2	FACETS	0.991	0.945	1	0.991	0.945	1	CLONAL	1	TRUE	1	0.922664736702589	2		484	772	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	150	582	0	ENST00000269305.4:c.166G>T	p.Glu56Ter	p.E56*	ENST00000269305	NM_001126112.2	56	Gaa/Taa	4/11	0.545275938348151	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	0	0.545275938348151	1		582	279	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637555	52637555	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	70	319	0	ENST00000394830.3:c.2761C>T	p.Arg921Ter	p.R921*	ENST00000394830	NM_018313.4	921	Cga/Tga	18/30	0.545275938348151	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	0	0.545275938348151	1		319	167	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258970	153258970	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	51	172	0	ENST00000281708.4:c.845C>A	p.Ser282Ter	p.S282*	ENST00000281708	NM_033632.3	282	tCa/tAa	5/12	1	2	FACETS	0.99	0.854	1	0.99	0.854	1	CLONAL	1	FALSE	1	0.545275938348151	2		172	189	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149973	202149973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1272714323	NA	P-0046694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	139	449	0	ENST00000358485.4:c.1414C>T	p.Arg472Ter	p.R472*	ENST00000358485	NM_001080125.1	472	Cga/Tga	8/9	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.545275938348151	2		449	418	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564671	86564671	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	101	702	0	ENST00000274376.6:c.407del	p.Pro136LeufsTer38	p.P136Lfs*38	ENST00000274376	NM_002890.2	135	Ccc/cc	1/25	0.545275938348151	1	FACETS	0.976	0.886	1	0.976	0.886	1	CLONAL	1	FALSE	0	0.545275938348151	1		702	276	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391458	139391458	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201613894	NA	P-0046694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	121	803	1	ENST00000277541.6:c.6733G>A	p.Gly2245Arg	p.G2245R	ENST00000277541	NM_017617.3	2245	Ggg/Agg	34/34	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.545275938348151	2		804	410	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426700	49426700	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	76	272	0	ENST00000301067.7:c.11788C>T	p.Gln3930Ter	p.Q3930*	ENST00000301067	NM_003482.3	3930	Cag/Tag	39/54	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.545275938348151	2		272	205	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673717	176673717	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784117	NA	P-0046694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	78	231	0	ENST00000439151.2:c.4417C>T	p.Arg1473Ter	p.R1473*	ENST00000439151	NM_022455.4	1473	Cga/Tga	10/23	0.545275938348151	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	FALSE	0	0.545275938348151	1		231	177	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433632	49433633	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0046694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	140	821	0	ENST00000301067.7:c.7920_7921del	p.Pro2641CysfsTer13	p.P2641Cfs*13	ENST00000301067	NM_003482.3	2640	tcTCct/tcct	31/54	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.545275938348151	2		821	483	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024706	11024706	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139789571	NA	P-0046694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	57	304	0	ENST00000327064.4:c.823G>A	p.Ala275Thr	p.A275T	ENST00000327064	NM_199141.1	275	Gcc/Acc	6/16	1	2	FACETS	0.977	0.85	1	0.977	0.85	1	CLONAL	1	FALSE	1	0.545275938348151	2		304	214	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213908	36213909	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0046694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	93	618	0	ENST00000222270.7:c.2735_2736del	p.Ala912ValfsTer4	p.A912Vfs*4	ENST00000222270	NM_014727.1	912	GCg/g	6/37	0.208185056038785	1	FACETS	0.738	0.663	0.817	0.738	0.663	0.817	INDETERMINATE	1	FALSE	0	0.545275938348151	1		618	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0046695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	116	767	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.163193758562645	2	FACETS	0.852	0.769	0.938	0.852	0.769	0.938	CLONAL	2	TRUE	0	0.216189841280157	2		767	630	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275378	142275379	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0046695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	39	257	0	ENST00000350721.4:c.1924_1925del	p.Leu642ValfsTer8	p.L642Vfs*8	ENST00000350721	NM_001184.3	642	CTg/g	9/47	0.216189841280157	3	FACETS	1	0.909	1	0.574	0.477	0.682	CLONAL	1	TRUE	1	0.216189841280157	3		257	348	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	20	424	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.606	0.463	0.773	0.606	0.463	0.773	SUBCLONAL	1	FALSE	1	0.223007712352093	2		424	296	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0046697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	37	701	2	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.193729540023494	1	FACETS	0.59	0.486	0.706	0.59	0.486	0.706	SUBCLONAL	1	FALSE	0	0.223007712352093	1		703	500	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662320	67662320	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	46	467	0	ENST00000264010.4:c.1567del	p.Tyr523ThrfsTer61	p.Y523Tfs*61	ENST00000264010	NM_006565.3	522	ccT/cc	9/12	0.223007712352093	5	FACETS	0.858	0.721	1	0.286	0.24	0.337	CLONAL	1	FALSE	2	0.223007712352093	5		467	642	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843514	156843514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137994522	NA	P-0046697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	38	809	0	ENST00000524377.1:c.940C>T	p.Arg314Cys	p.R314C	ENST00000524377	NM_002529.3	314	Cgc/Tgc	8/17	1	2	FACETS	0.453	0.373	0.543	0.453	0.373	0.543	SUBCLONAL	1	FALSE	1	0.223007712352093	2		809	752	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348165	348253	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GAAGTGGTGCCAAGCGGGGGCGGGAGGCAGCTTGTGACACGGCCCTGGGGGCCCTGACGATGGATCGCCGTCCTCACCTTCCTCCTCCT	GAAGTGGTGCCAAGCGGGGGCGGGAGGCAGCTTGTGACACGGCCCTGGGGGCCCTGACGATGGATCGCCGTCCTCACCTTCCTCCTCCT	-	novel	NA	P-0046697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	42	1064	0	ENST00000262320.3:c.1255-2_1341del		p.X419_splice	ENST00000262320	NM_003502.3	419		6/11	0.193729540023494	1	FACETS	0.402	0.334	0.477	0.402	0.334	0.477	SUBCLONAL	1	FALSE	0	0.223007712352093	1		1064	833	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440963	56440963	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0046697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	75	578	0	ENST00000407977.2:c.376-2A>G		p.X126_splice	ENST00000407977		126			0.193729540023494	1	FACETS	0.956	0.838	1	0.956	0.838	1	CLONAL	1	FALSE	0	0.223007712352093	1		578	625	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967818	18967818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs897698788	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	204	885	1	ENST00000262803.5:c.1957G>A	p.Gly653Arg	p.G653R	ENST00000262803	NM_002911.3	653	Ggg/Agg	14/24	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.45	2		886	895	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	75	424	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.782	0.689	0.883	0.782	0.689	0.883	SUBCLONAL	1	TRUE	1	0.45	2		424	426	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	238	931	3	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.45	2		934	830	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	19	109	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.155	0.117	0.2	0.155	0.117	0.2	SUBCLONAL	1	TRUE	1	0.45	2		109	545	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	153	836	1	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.815	0.746	0.888	0.815	0.746	0.888	CLONAL	1	TRUE	1	0.45	2		837	834	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	204	687	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.45	2		687	748	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	50	382	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.496	0.421	0.578	0.496	0.421	0.578	SUBCLONAL	1	TRUE	1	0.45	2		382	448	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	289	985	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.944	0.895	0.995	1	0.996	1	CLONAL	2	TRUE	1	0.45	2		991	680	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	54	1018	4	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.276	0.234	0.321	0.276	0.234	0.321	SUBCLONAL	1	TRUE	1	0.45	2		1022	871	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	102	852	2	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	0.586	0.524	0.652	0.586	0.524	0.652	SUBCLONAL	1	TRUE	1	0.45	2		854	774	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934243	49934243	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1407832113	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	141	737	5	ENST00000296474.3:c.2264del	p.Gly755ValfsTer19	p.G755Vfs*19	ENST00000296474	NM_002447.2	755	gGt/gt	8/20	1	2	FACETS	0.916	0.837	0.999	0.916	0.837	0.999	CLONAL	1	TRUE	1	0.45	2		742	684	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36823859	36823859	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs767843123	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	24	363	0	ENST00000373129.3:c.323A>G	p.His108Arg	p.H108R	ENST00000373129	NM_032017.1	108	cAc/cGc	5/12	1	2	FACETS	0.289	0.226	0.362	0.289	0.226	0.362	SUBCLONAL	1	TRUE	1	0.45	2		363	369	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	26	272	2	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	0.228	0.18	0.284	0.228	0.18	0.284	SUBCLONAL	1	TRUE	1	0.45	2		274	506	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	114	405	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.45	2		408	401	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703631	47703631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750636	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	119	434	1	ENST00000233146.2:c.2131C>T	p.Arg711Ter	p.R711*	ENST00000233146	NM_000251.2	711	Cga/Tga	13/16	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.45	2		435	520	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366162	15366162	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1005077274	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	140	576	2	ENST00000263377.2:c.1993C>T	p.Arg665Cys	p.R665C	ENST00000263377	NM_058243.2	665	Cgt/Tgt	10/20	1	2	FACETS	0.937	0.856	1	0.937	0.856	1	CLONAL	1	TRUE	1	0.45	2		578	664	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979987	7979987	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746723399	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	159	684	4	ENST00000319144.4:c.1350del	p.Leu451SerfsTer16	p.L451Sfs*16	ENST00000319144	NM_001139.2	450	ggG/gg	10/15	1	2	FACETS	0.947	0.87	1	0.947	0.87	1	CLONAL	1	TRUE	1	0.45	2		688	746	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256768	19256769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1202792889	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	64	714	1	ENST00000162023.5:c.944dup	p.Val316SerfsTer6	p.V316Sfs*6	ENST00000162023		315	cca/ccCa	13/13	1	2	FACETS	0.504	0.437	0.578	0.504	0.437	0.578	SUBCLONAL	1	TRUE	1	0.45	2		715	564	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	81	490	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.781	0.691	0.877	0.781	0.691	0.877	SUBCLONAL	1	TRUE	1	0.45	2		490	461	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	71	701	2	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	1	2	FACETS	0.575	0.502	0.653	0.575	0.502	0.653	SUBCLONAL	1	TRUE	1	0.45	2		703	549	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	127	820	6	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.797	0.723	0.875	0.797	0.723	0.875	SUBCLONAL	1	TRUE	1	0.45	2		826	708	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429977	78429978	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1200882279	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	71	271	0	ENST00000370768.2:c.901dup	p.Ile301AsnfsTer4	p.I301Nfs*4	ENST00000370768	NM_003902.3	301	ata/aAta	11/20	1	2	FACETS	0.793	0.695	0.897	0.793	0.695	0.897	SUBCLONAL	1	TRUE	1	0.45	2		271	398	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417886	32417886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	35	478	3	ENST00000332351.3:c.1166G>A	p.Arg389His	p.R389H	ENST00000332351	NM_024426.4	389	cGc/cAc	7/10	1	2	FACETS	0.297	0.243	0.359	0.297	0.243	0.359	SUBCLONAL	1	TRUE	1	0.45	2		481	523	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	58	261	0	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	1	2	FACETS	0.608	0.524	0.699	0.608	0.524	0.699	SUBCLONAL	1	TRUE	1	0.45	2		261	424	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663267	227663267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1234435076	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	105	613	0	ENST00000305123.5:c.188C>T	p.Ser63Leu	p.S63L	ENST00000305123	NM_005544.2	63	tCg/tTg	1/2	1	2	FACETS	0.853	0.767	0.944	0.853	0.767	0.944	CLONAL	1	TRUE	1	0.45	2		613	547	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533905	63533905	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	106	534	0	ENST00000307078.5:c.1249del	p.Ala417ArgfsTer41	p.A417Rfs*41	ENST00000307078	NM_004655.3	417	Gcg/cg	6/11	1	2	FACETS	0.909	0.819	1	0.909	0.819	1	CLONAL	1	TRUE	1	0.45	2		534	518	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	27	375	1	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	1	2	FACETS	0.335	0.267	0.414	0.335	0.267	0.414	SUBCLONAL	1	TRUE	1	0.45	2		376	358	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	28	149	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	0.168715733290035	1	FACETS	0.516	0.415	0.628	0.516	0.415	0.628	INDETERMINATE	1	TRUE	0	0.45	1		149	187	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	49	790	2	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	1	2	FACETS	0.245	0.206	0.288	0.245	0.206	0.288	SUBCLONAL	1	TRUE	1	0.45	2		792	889	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	148	485	2	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.986	0.903	1	0.986	0.903	1	CLONAL	1	TRUE	1	0.45	2		487	667	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100728	8100728	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs771019738	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	50	585	0	ENST00000346208.3:c.708del	p.Ser237AlafsTer28	p.S237Afs*28	ENST00000346208		234	ttC/tt	3/6	1	2	FACETS	0.354	0.3	0.414	0.354	0.3	0.414	SUBCLONAL	1	TRUE	1	0.45	2		585	627	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724120	61724120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781425578	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	76	264	0	ENST00000401558.2:c.782G>A	p.Arg261Gln	p.R261Q	ENST00000401558	NM_003400.3	261	cGa/cAa	10/25	1	2	FACETS	0.915	0.808	1	0.915	0.808	1	CLONAL	1	TRUE	1	0.45	2		264	369	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204842	128204842	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs768767517	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	47	823	4	ENST00000341105.2:c.599del	p.Gly200ValfsTer18	p.G200Vfs*18	ENST00000341105	NM_032638.4	200	gGt/gt	3/6	1	2	FACETS	0.303	0.255	0.356	0.303	0.255	0.356	SUBCLONAL	1	TRUE	1	0.45	2		827	690	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629339	187629339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202126944	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	159	650	3	ENST00000441802.2:c.1643G>A	p.Arg548His	p.R548H	ENST00000441802	NM_005245.3	548	cGc/cAc	2/27	1	2	FACETS	0.976	0.897	1	0.976	0.897	1	CLONAL	1	TRUE	1	0.45	2		653	724	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	29	328	0	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.418	0.336	0.511	0.418	0.336	0.511	SUBCLONAL	1	TRUE	1	0.45	2		328	308	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	152	768	6	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	0.88	0.806	0.957	0.88	0.806	0.957	CLONAL	1	TRUE	1	0.45	2		774	768	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687471	37687472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs760014508	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	57	351	1	ENST00000447079.4:c.4382dup	p.Thr1463AsnfsTer50	p.T1463Nfs*50	ENST00000447079	NM_015083.1	1459	tgg/tGgg	14/14	1	2	FACETS	0.789	0.681	0.905	0.789	0.681	0.905	CLONAL	1	TRUE	1	0.45	2		352	321	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	130	264	2	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	1	2	FACETS	0.783	0.718	0.849	1	0.988	1	SUBCLONAL	2	TRUE	1	0.45	2		266	369	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771163	161771163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755627153	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	156	699	0	ENST00000366898.1:c.1366G>A	p.Val456Ile	p.V456I	ENST00000366898	NM_004562.2	456	Gtc/Atc	12/12	1	2	FACETS	0.998	0.916	1	0.998	0.916	1	CLONAL	1	TRUE	1	0.45	2		699	695	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166770	32166770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs947409717	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	78	854	0	ENST00000375023.3:c.4468C>T	p.Arg1490Trp	p.R1490W	ENST00000375023	NM_004557.3	1490	Cgg/Tgg	24/30	1	2	FACETS	0.449	0.394	0.508	0.449	0.394	0.508	SUBCLONAL	1	TRUE	1	0.45	2		854	772	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519545	137519545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56403507	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	82	340	0	ENST00000367739.4:c.1093G>A	p.Val365Met	p.V365M	ENST00000367739	NM_000416.2	365	Gtg/Atg	7/7	1	2	FACETS	0.985	0.875	1	0.985	0.875	1	CLONAL	1	TRUE	1	0.45	2		340	370	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736334	243736334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771134997	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	99	288	0	ENST00000263826.5:c.713C>T	p.Ser238Leu	p.S238L	ENST00000263826	NM_005465.4	238	tCg/tTg	8/13	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.45	2		288	434	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	120	475	0	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	1	2	FACETS	0.827	0.748	0.91	0.827	0.748	0.91	CLONAL	1	TRUE	1	0.45	2		475	645	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703538	47703538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63749932	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	92	469	1	ENST00000233146.2:c.2038C>T	p.Arg680Ter	p.R680*	ENST00000233146	NM_000251.2	680	Cga/Tga	13/16	1	2	FACETS	0.77	0.686	0.859	0.77	0.686	0.859	SUBCLONAL	1	TRUE	1	0.45	2		470	531	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39629562	39629562	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	25	238	0	ENST00000262039.4:c.2260del	p.Thr754GlnfsTer7	p.T754Qfs*7	ENST00000262039	NM_002647.2	752	acA/ac	21/25	1	2	FACETS	0.338	0.266	0.42	0.338	0.266	0.42	SUBCLONAL	1	TRUE	1	0.45	2		238	329	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276860	15276861	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs753725730	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	134	601	3	ENST00000263388.2:c.5404dup	p.Ala1802GlyfsTer8	p.A1802Gfs*8	ENST00000263388	NM_000435.2	1802	gct/gGct	30/33	1	2	FACETS	0.876	0.797	0.958	0.876	0.797	0.958	CLONAL	1	TRUE	1	0.45	2		604	680	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161939	47161939	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	66	260	0	ENST00000409792.3:c.4187del	p.Asn1396MetfsTer16	p.N1396Mfs*16	ENST00000409792	NM_014159.6	1396	aAt/at	3/21	1	2	FACETS	0.86	0.752	0.976	0.86	0.752	0.976	CLONAL	1	TRUE	1	0.45	2		260	341	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996146	73996146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	52	1016	0	ENST00000318443.5:c.880G>A	p.Val294Met	p.V294M	ENST00000318443	NM_001024736.1	294	Gtg/Atg	5/10	1	2	FACETS	0.255	0.216	0.298	0.255	0.216	0.298	SUBCLONAL	1	TRUE	1	0.45	2		1016	907	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084145	47084146	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	103	432	0	ENST00000409792.3:c.7143dup	p.Ser2382LeufsTer47	p.S2382Lfs*47	ENST00000409792	NM_014159.6	2381	-/C	17/21	1	2	FACETS	0.758	0.68	0.841	0.758	0.68	0.841	SUBCLONAL	1	TRUE	1	0.45	2		432	604	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291860	15291860	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146214060	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	191	1089	2	ENST00000263388.2:c.2906G>A	p.Arg969Gln	p.R969Q	ENST00000263388	NM_000435.2	969	cGg/cAg	18/33	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.45	2		1091	798	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066648	94066648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371089003	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	50	455	1	ENST00000369303.4:c.1111C>T	p.Arg371Trp	p.R371W	ENST00000369303	NM_004440.3	371	Cgg/Tgg	5/17	1	2	FACETS	0.425	0.36	0.496	0.425	0.36	0.496	SUBCLONAL	1	TRUE	1	0.45	2		456	523	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981721	101981721	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555075353	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	52	240	2	ENST00000282441.5:c.147del	p.Ala50ProfsTer24	p.A50Pfs*24	ENST00000282441	NM_001130145.2	48	Ccc/cc	1/9	1	2	FACETS	0.959	0.825	1	0.959	0.825	1	CLONAL	1	TRUE	1	0.45	2		242	241	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498235	498235	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	59	289	0	ENST00000399788.2:c.23del	p.Gly8AlafsTer58	p.G8Afs*58	ENST00000399788	NM_001042603.1	8	gGc/gc	1/28	1	2	FACETS	0.93	0.807	1	0.93	0.807	1	CLONAL	1	TRUE	1	0.45	2		289	282	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656840	45656840	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	46	619	7	ENST00000407780.3:c.316del	p.Gln106ArgfsTer11	p.Q106Rfs*11	ENST00000407780	NM_001283052.1	106	Cag/ag	3/7	1	2	FACETS	0.347	0.292	0.408	0.347	0.292	0.408	SUBCLONAL	1	TRUE	1	0.45	2		626	589	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211580	98211580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762040036	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	117	654	0	ENST00000331920.6:c.3575G>A	p.Arg1192His	p.R1192H	ENST00000331920	NM_000264.3	1192	cGc/cAc	22/24	1	2	FACETS	0.881	0.797	0.97	0.881	0.797	0.97	CLONAL	1	TRUE	1	0.45	2		654	590	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40497641	40497641	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1417279405	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	186	500	0	ENST00000264657.5:c.308G>A	p.Arg103Gln	p.R103Q	ENST00000264657	NM_139276.2	103	cGg/cAg	4/24	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.45	2		500	770	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795066	42795066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537583557	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	219	996	0	ENST00000575354.2:c.2146C>T	p.Arg716Trp	p.R716W	ENST00000575354	NM_015125.3	716	Cgg/Tgg	10/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.45	2		996	857	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282214	38282214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121909645	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	112	651	0	ENST00000425967.3:c.842G>A	p.Arg281Gln	p.R281Q	ENST00000425967	NM_001174067.1	281	cGg/cAg	8/19	1	2	FACETS	0.873	0.788	0.963	0.873	0.788	0.963	CLONAL	1	TRUE	1	0.45	2		651	570	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	176	1262	4	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.907	0.837	0.981	0.907	0.837	0.981	CLONAL	1	TRUE	1	0.45	2		1266	862	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444986	49444987	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	57	641	0	ENST00000301067.7:c.2479dup	p.Gln827ProfsTer3	p.Q827Pfs*3	ENST00000301067	NM_003482.3	827	caa/cCaa	10/54	1	2	FACETS	0.478	0.41	0.552	0.478	0.41	0.552	SUBCLONAL	1	TRUE	1	0.45	2		641	530	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798105	32798105	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1562326716	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	90	779	0	ENST00000374899.4:c.1574del	p.Gly525AspfsTer36	p.G525Dfs*36	ENST00000374899	NM_018833.2	525	gGa/ga	9/12	1	2	FACETS	0.536	0.475	0.601	0.536	0.475	0.601	SUBCLONAL	1	TRUE	1	0.45	2		779	746	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303222	11303222	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747412972	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	128	545	1	ENST00000361445.4:c.1361G>A	p.Arg454His	p.R454H	ENST00000361445	NM_004958.3	454	cGc/cAc	9/58	1	2	FACETS	0.991	0.902	1	0.991	0.902	1	CLONAL	1	TRUE	1	0.45	2		546	574	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639204	3639204	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs758409623	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	158	817	0	ENST00000294008.3:c.4435C>T	p.Arg1479Ter	p.R1479*	ENST00000294008	NM_032444.2	1479	Cga/Tga	12/15	1	2	FACETS	0.969	0.889	1	0.969	0.889	1	CLONAL	1	TRUE	1	0.45	2		817	725	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415639	49415639	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	33	356	0	ENST00000301067.7:c.16538A>G	p.Gln5513Arg	p.Q5513R	ENST00000301067	NM_003482.3	5513	cAg/cGg	54/54	1	2	FACETS	0.42	0.343	0.507	0.42	0.343	0.507	SUBCLONAL	1	TRUE	1	0.45	2		356	349	SUCCESS
APC	324	MSKCC	GRCh37	5	112174604	112174604	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768454793	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	74	322	0	ENST00000257430.4:c.3313C>T	p.Arg1105Trp	p.R1105W	ENST00000257430	NM_000038.5	1105	Cgg/Tgg	16/16	1	2	FACETS	0.891	0.785	1	0.891	0.785	1	CLONAL	1	TRUE	1	0.45	2		322	369	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434990	49434990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs541122919	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	125	631	0	ENST00000301067.7:c.6563G>A	p.Arg2188His	p.R2188H	ENST00000301067	NM_003482.3	2188	cGc/cAc	31/54	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.45	2		631	513	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862737	9862737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201072838	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	124	515	0	ENST00000330684.3:c.2566C>T	p.Arg856Trp	p.R856W	ENST00000330684	NM_001134407.1	856	Cgg/Tgg	12/13	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.45	2		515	533	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281668	49281668	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201815757	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	139	685	1	ENST00000282018.3:c.715C>T	p.Arg239Trp	p.R239W	ENST00000282018	NM_020377.2	239	Cgg/Tgg	1/1	1	2	FACETS	0.918	0.838	1	0.918	0.838	1	CLONAL	1	TRUE	1	0.45	2		686	673	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256789	133256789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770323795	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	92	350	0	ENST00000320574.5:c.305C>T	p.Pro102Leu	p.P102L	ENST00000320574	NM_006231.2	102	cCg/cTg	4/49	1	2	FACETS	0.934	0.834	1	0.934	0.834	1	CLONAL	1	TRUE	1	0.45	2		350	438	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741528	17741528	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	88	432	1	ENST00000250003.3:c.199G>A	p.Ala67Thr	p.A67T	ENST00000250003	NM_002478.4	67	Gcg/Acg	1/3	1	2	FACETS	0.837	0.745	0.935	0.837	0.745	0.935	CLONAL	1	TRUE	1	0.45	2		433	467	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098009	178098009	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749353894	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	81	287	0	ENST00000397062.3:c.371C>T	p.Ala124Val	p.A124V	ENST00000397062	NM_006164.4	124	gCg/gTg	3/5	1	2	FACETS	0.896	0.793	1	0.896	0.793	1	CLONAL	1	TRUE	1	0.45	2		287	402	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36823877	36823877	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373166224	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	59	413	0	ENST00000373129.3:c.305C>T	p.Thr102Met	p.T102M	ENST00000373129	NM_032017.1	102	aCg/aTg	5/12	1	2	FACETS	0.53	0.456	0.61	0.53	0.456	0.61	SUBCLONAL	1	TRUE	1	0.45	2		413	495	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919865	50919866	+	splice_acceptor_variant	Splice_Site	INS	-	-	G	rs756872503	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	89	948	4	ENST00000440232.2:c.2959dup		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	0.518	0.459	0.581	0.518	0.459	0.581	SUBCLONAL	1	TRUE	1	0.45	2		952	764	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163784	47163784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1313153861	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	79	330	0	ENST00000409792.3:c.2342C>T	p.Thr781Met	p.T781M	ENST00000409792	NM_014159.6	781	aCg/aTg	3/21	1	2	FACETS	0.863	0.763	0.969	0.863	0.763	0.969	CLONAL	1	TRUE	1	0.45	2		330	407	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105236688	105236688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	169	715	0	ENST00000349310.3:c.1433G>A	p.Gly478Asp	p.G478D	ENST00000349310	NM_001014432.1	478	gGc/gAc	15/15	1	2	FACETS	0.991	0.913	1	0.991	0.913	1	CLONAL	1	TRUE	1	0.45	2		715	758	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255248	16255248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752574502	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	21	341	0	ENST00000375759.3:c.2513C>T	p.Thr838Met	p.T838M	ENST00000375759	NM_015001.2	838	aCg/aTg	11/15	1	2	FACETS	0.241	0.185	0.307	0.241	0.185	0.307	SUBCLONAL	1	TRUE	1	0.45	2		341	387	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376554	118376554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201447376	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	79	306	0	ENST00000534358.1:c.9947C>T	p.Ala3316Val	p.A3316V	ENST00000534358	NM_005933.3	3316	gCg/gTg	27/36	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.45	2		306	327	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738112	145738112	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1554897277	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	50	954	0	ENST00000428558.2:c.2798A>G	p.His933Arg	p.H933R	ENST00000428558	NM_004260.3	933	cAc/cGc	17/22	1	2	FACETS	0.273	0.231	0.32	0.273	0.231	0.32	SUBCLONAL	1	TRUE	1	0.45	2		954	813	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219145	94219145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758112386	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	96	332	0	ENST00000323929.3:c.259C>T	p.Arg87Trp	p.R87W	ENST00000323929	NM_005591.3	87	Cgg/Tgg	4/20	1	2	FACETS	0.904	0.809	1	0.904	0.809	1	CLONAL	1	TRUE	1	0.45	2		332	472	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662085	227662085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755583840	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	141	737	0	ENST00000305123.5:c.1370G>A	p.Arg457His	p.R457H	ENST00000305123	NM_005544.2	457	cGc/cAc	1/2	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.45	2		737	565	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225998	53225998	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	193	541	1	ENST00000375401.3:c.2851C>T	p.Arg951Ter	p.R951*	ENST00000375401	NM_004187.3	951	Cga/Tga	19/26	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.45	1		542	446	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981407	70981407	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs751042462	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	85	817	1	ENST00000276594.2:c.689del	p.Pro230GlnfsTer64	p.P230Qfs*64	ENST00000276594	NM_024504.3	230	cCa/ca	2/8	1	2	FACETS	0.458	0.405	0.516	0.458	0.405	0.516	SUBCLONAL	1	TRUE	1	0.45	2		818	824	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525018	157525018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs544895806	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	27	283	0	ENST00000346085.5:c.4913G>A	p.Arg1638His	p.R1638H	ENST00000346085	NM_020732.3	1638	cGt/cAt	19/20	1	2	FACETS	0.308	0.245	0.381	0.308	0.245	0.381	SUBCLONAL	1	TRUE	1	0.45	2		283	389	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878808	151878808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	24	436	0	ENST00000262189.6:c.6137C>T	p.Pro2046Leu	p.P2046L	ENST00000262189	NM_170606.2	2046	cCa/cTa	36/59	1	2	FACETS	0.226	0.176	0.283	0.226	0.176	0.283	SUBCLONAL	1	TRUE	1	0.45	2		436	473	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43766907	43766907	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765177854	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	35	207	0	ENST00000382044.4:c.1144G>A	p.Val382Ile	p.V382I	ENST00000382044	NM_001141980.1	382	Gtt/Att	10/28	1	2	FACETS	0.568	0.467	0.679	0.568	0.467	0.679	SUBCLONAL	1	TRUE	1	0.45	2		207	274	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138201244	138201244	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543704449	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	89	411	0	ENST00000237289.4:c.1943C>T	p.Ala648Val	p.A648V	ENST00000237289	NM_001270507.1	648	gCg/gTg	8/9	1	2	FACETS	0.752	0.669	0.841	0.752	0.669	0.841	SUBCLONAL	1	TRUE	1	0.45	2		411	526	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439518	220439518	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540215120	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	91	790	0	ENST00000243786.2:c.371G>A	p.Arg124His	p.R124H	ENST00000243786	NM_002191.3	124	cGc/cAc	2/2	1	2	FACETS	0.64	0.569	0.716	0.64	0.569	0.716	SUBCLONAL	1	TRUE	1	0.45	2		790	632	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143080	30143080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374276783	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	52	821	0	ENST00000389048.3:c.446C>T	p.Ala149Val	p.A149V	ENST00000389048	NM_004304.4	149	gCg/gTg	1/29	1	2	FACETS	0.338	0.287	0.394	0.338	0.287	0.394	SUBCLONAL	1	TRUE	1	0.45	2		821	684	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26046027	26046027	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	64	284	3	ENST00000540144.1:c.389G>A	p.Arg130His	p.R130H	ENST00000540144	NM_003531.2	130	cGc/cAc	1/1	1	2	FACETS	0.9	0.785	1	0.9	0.785	1	CLONAL	1	TRUE	1	0.45	2		287	316	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306941	65306941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	104	363	0	ENST00000342505.4:c.2636G>A	p.Arg879His	p.R879H	ENST00000342505	NM_002227.2	879	cGt/cAt	19/25	1	2	FACETS	0.983	0.885	1	0.983	0.885	1	CLONAL	1	TRUE	1	0.45	2		363	470	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414976	78414976	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	86	337	0	ENST00000370768.2:c.1790T>C	p.Val597Ala	p.V597A	ENST00000370768	NM_003902.3	597	gTt/gCt	19/20	1	2	FACETS	0.885	0.787	0.989	0.885	0.787	0.989	CLONAL	1	TRUE	1	0.45	2		337	432	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716166	243716166	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	53	468	0	ENST00000263826.5:c.1028G>T	p.Arg343Met	p.R343M	ENST00000263826	NM_005465.4	343	aGg/aTg	10/13	1	2	FACETS	0.404	0.344	0.47	0.404	0.344	0.47	SUBCLONAL	1	TRUE	1	0.45	2		468	583	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63819032	63819032	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	51	169	1	ENST00000279873.7:c.1083del	p.Lys361AsnfsTer8	p.K361Nfs*8	ENST00000279873	NM_032199.2	360	cAa/ca	7/10	1	2	FACETS	0.81	0.693	0.935	0.81	0.693	0.935	CLONAL	1	TRUE	1	0.45	2		170	280	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154862	2154862	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369844466	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	125	824	1	ENST00000434045.2:c.359G>A	p.Arg120His	p.R120H	ENST00000434045	NM_001127598.1	120	cGt/cAt	4/5	1	2	FACETS	0.824	0.747	0.905	0.824	0.747	0.905	CLONAL	1	TRUE	1	0.45	2		825	674	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200097	67200097	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs753125285	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	51	611	0	ENST00000312629.5:c.484C>T	p.Arg162Ter	p.R162*	ENST00000312629	NM_003952.2	162	Cga/Tga	6/15	1	2	FACETS	0.391	0.332	0.457	0.391	0.332	0.457	SUBCLONAL	1	TRUE	1	0.45	2		611	579	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518577	69518577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	109	438	0	ENST00000294312.3:c.68G>A	p.Arg23His	p.R23H	ENST00000294312	NM_005117.2	23	cGc/cAc	1/3	1	2	FACETS	0.979	0.883	1	0.979	0.883	1	CLONAL	1	TRUE	1	0.45	2		438	495	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948686	71948686	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	40	959	0	ENST00000298229.2:c.3398T>C	p.Val1133Ala	p.V1133A	ENST00000298229	NM_001567.3	1133	gTg/gCg	26/28	1	2	FACETS	0.26	0.215	0.31	0.26	0.215	0.31	SUBCLONAL	1	TRUE	1	0.45	2		959	683	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77051749	77051749	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	35	465	0	ENST00000356341.3:c.1058C>T	p.Thr353Ile	p.T353I	ENST00000356341	NM_002576.4	353	aCa/aTa	11/15	1	2	FACETS	0.261	0.213	0.315	0.261	0.213	0.315	SUBCLONAL	1	TRUE	1	0.45	2		465	595	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984927	101984927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	25	343	0	ENST00000282441.5:c.374C>T	p.Ala125Val	p.A125V	ENST00000282441	NM_001130145.2	125	gCt/gTt	2/9	1	2	FACETS	0.249	0.195	0.31	0.249	0.195	0.31	SUBCLONAL	1	TRUE	1	0.45	2		343	447	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363776	118363776	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	25	273	0	ENST00000534358.1:c.5009C>T	p.Ala1670Val	p.A1670V	ENST00000534358	NM_005933.3	1670	gCc/gTc	16/36	1	2	FACETS	0.306	0.241	0.381	0.306	0.241	0.381	SUBCLONAL	1	TRUE	1	0.45	2		273	363	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800882	18800882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226573033	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	25	305	0	ENST00000266497.5:c.4258G>A	p.Val1420Met	p.V1420M	ENST00000266497		1420	Gtg/Atg	31/31	1	2	FACETS	0.247	0.194	0.309	0.247	0.194	0.309	SUBCLONAL	1	TRUE	1	0.45	2		305	449	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433770	49433770	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	44	1085	0	ENST00000301067.7:c.7783G>T	p.Gly2595Trp	p.G2595W	ENST00000301067	NM_003482.3	2595	Ggg/Tgg	31/54	1	2	FACETS	0.228	0.19	0.27	0.228	0.19	0.27	SUBCLONAL	1	TRUE	1	0.45	2		1085	859	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794719	120794719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	153	724	0	ENST00000257552.2:c.638G>A	p.Gly213Asp	p.G213D	ENST00000257552	NM_002442.3	213	gGc/gAc	9/15	1	2	FACETS	0.988	0.907	1	0.988	0.907	1	CLONAL	1	TRUE	1	0.45	2		724	688	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437125	121437125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	54	870	0	ENST00000257555.6:c.1556C>T	p.Pro519Leu	p.P519L	ENST00000257555		519	cCg/cTg	8/10	1	2	FACETS	0.304	0.259	0.354	0.304	0.259	0.354	SUBCLONAL	1	TRUE	1	0.45	2		870	789	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253975	133253975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777638541	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	106	474	0	ENST00000320574.5:c.775C>T	p.Arg259Cys	p.R259C	ENST00000320574	NM_006231.2	259	Cgc/Tgc	8/49	1	2	FACETS	0.869	0.782	0.961	0.869	0.782	0.961	CLONAL	1	TRUE	1	0.45	2		474	542	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562400	21562400	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764619975	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	142	717	1	ENST00000382592.4:c.1519G>A	p.Gly507Arg	p.G507R	ENST00000382592	NM_014572.2	507	Gga/Aga	4/8	1	2	FACETS	0.916	0.837	0.999	0.916	0.837	0.999	CLONAL	1	TRUE	1	0.45	2		718	689	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21565452	21565452	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1212679729	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	44	734	0	ENST00000382592.4:c.434G>T	p.Arg145Met	p.R145M	ENST00000382592	NM_014572.2	145	aGg/aTg	3/8	1	2	FACETS	0.255	0.213	0.301	0.255	0.213	0.301	SUBCLONAL	1	TRUE	1	0.45	2		734	768	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872007	35872008	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	33	479	0	ENST00000216797.5:c.605dup	p.Leu202PhefsTer7	p.L202Ffs*7	ENST00000216797	NM_020529.2	202	ttg/ttTg	4/6	1	2	FACETS	0.28	0.228	0.34	0.28	0.228	0.34	SUBCLONAL	1	TRUE	1	0.45	2		479	523	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570340	95570341	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	76	271	0	ENST00000393063.1:c.3392dup	p.Asn1131LysfsTer8	p.N1131Kfs*8	ENST00000393063	NM_030621.3	1131	aat/aaAt	22/28	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.45	2		271	325	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222372	2222372	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs914029813	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	133	853	1	ENST00000326181.6:c.656G>A	p.Arg219Gln	p.R219Q	ENST00000326181	NM_032271.2	219	cGg/cAg	8/21	1	2	FACETS	0.931	0.848	1	0.931	0.848	1	CLONAL	1	TRUE	1	0.45	2		854	635	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993380	72993380	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373712806	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	204	843	1	ENST00000268489.5:c.665C>T	p.Ala222Val	p.A222V	ENST00000268489	NM_006885.3	222	gCg/gTg	2/10	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.45	2		844	885	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873588	37873588	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	140	794	0	ENST00000269571.5:c.1753G>A	p.Val585Met	p.V585M	ENST00000269571		585	Gtg/Atg	15/27	1	2	FACETS	0.797	0.726	0.871	0.797	0.726	0.871	SUBCLONAL	1	TRUE	1	0.45	2		794	781	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858898	78858898	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1448287393	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	156	815	0	ENST00000306801.3:c.1933G>A	p.Ala645Thr	p.A645T	ENST00000306801	NM_020761.2	645	Gcc/Acc	17/34	1	2	FACETS	0.96	0.881	1	0.96	0.881	1	CLONAL	1	TRUE	1	0.45	2		815	722	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220342	5220342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	133	575	0	ENST00000357368.4:c.3478C>T	p.Pro1160Ser	p.P1160S	ENST00000357368	NM_002850.3	1160	Cca/Tca	21/38	0.168715733290035	1	FACETS	0.89	0.812	0.97	0.89	0.812	0.97	INDETERMINATE	1	TRUE	0	0.45	1		575	515	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291542	15291542	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	99	851	0	ENST00000263388.2:c.3092G>A	p.Arg1031His	p.R1031H	ENST00000263388	NM_000435.2	1031	cGc/cAc	19/33	1	2	FACETS	0.616	0.55	0.686	0.616	0.55	0.686	SUBCLONAL	1	TRUE	1	0.45	2		851	714	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279573	18279573	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	39	633	1	ENST00000222254.8:c.1846C>T	p.His616Tyr	p.H616Y	ENST00000222254	NM_005027.3	616	Cac/Tac	15/16	1	2	FACETS	0.29	0.239	0.346	0.29	0.239	0.346	SUBCLONAL	1	TRUE	1	0.45	2		634	598	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965716	18965716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753380786	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	44	822	2	ENST00000262803.5:c.1294G>A	p.Val432Met	p.V432M	ENST00000262803	NM_002911.3	432	Gtg/Atg	10/24	1	2	FACETS	0.27	0.226	0.32	0.27	0.226	0.32	SUBCLONAL	1	TRUE	1	0.45	2		824	723	SUCCESS
AXL	558	MSKCC	GRCh37	19	41736952	41736952	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	139	741	0	ENST00000301178.4:c.667G>T	p.Val223Leu	p.V223L	ENST00000301178	NM_021913.4	223	Gtg/Ttg	5/20	1	2	FACETS	0.915	0.835	0.999	0.915	0.835	0.999	CLONAL	1	TRUE	1	0.45	2		741	675	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860596	45860596	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	175	896	2	ENST00000391945.4:c.1411C>A	p.Leu471Met	p.L471M	ENST00000391945	NM_000400.3	471	Ctg/Atg	15/23	1	2	FACETS	0.897	0.827	0.97	0.897	0.827	0.97	CLONAL	1	TRUE	1	0.45	2		898	867	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213254	39213254	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	51	651	0	ENST00000402219.2:c.3713T>G	p.Leu1238Trp	p.L1238W	ENST00000402219	NM_005633.3	1238	tTg/tGg	23/23	1	2	FACETS	0.333	0.282	0.389	0.333	0.282	0.389	SUBCLONAL	1	TRUE	1	0.45	2		651	681	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257170	198257170	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	46	273	0	ENST00000335508.6:c.3772G>T	p.Ala1258Ser	p.A1258S	ENST00000335508	NM_012433.2	1258	Gcc/Tcc	25/25	1	2	FACETS	0.539	0.455	0.632	0.539	0.455	0.632	SUBCLONAL	1	TRUE	1	0.45	2		273	379	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394066	31394066	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	22	373	0	ENST00000328111.2:c.2353A>G	p.Lys785Glu	p.K785E	ENST00000328111	NM_006892.3	785	Aaa/Gaa	22/23	0.168715733290035	1	FACETS	0.178	0.138	0.226	0.178	0.138	0.226	INDETERMINATE	1	TRUE	0	0.45	1		373	425	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012608	36012608	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	39	406	2	ENST00000358208.4:c.52C>A	p.Leu18Met	p.L18M	ENST00000358208		18	Ctg/Atg	2/12	0.168715733290035	1	FACETS	0.295	0.244	0.352	0.295	0.244	0.352	INDETERMINATE	1	TRUE	0	0.45	1		408	455	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171690	36171690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	35	397	0	ENST00000300305.3:c.875C>T	p.Ala292Val	p.A292V	ENST00000300305		292	gCc/gTc	7/8	1	2	FACETS	0.341	0.279	0.411	0.341	0.279	0.411	SUBCLONAL	1	TRUE	1	0.45	2		397	456	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72873612	72873613	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	106	307	0	ENST00000325599.8:c.689dup	p.Leu230PhefsTer18	p.L230Ffs*18	ENST00000325599	NM_018130.2	230	ttg/ttTg	6/11	1	2	FACETS	0.85	0.765	0.941	0.85	0.765	0.941	CLONAL	1	TRUE	1	0.45	2		307	554	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664793	138664793	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	15	252	0	ENST00000330315.3:c.772T>C	p.Tyr258His	p.Y258H	ENST00000330315	NM_023067.3	258	Tac/Cac	1/1	1	2	FACETS	0.236	0.172	0.312	0.236	0.172	0.312	SUBCLONAL	1	TRUE	1	0.45	2		252	283	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808312	1808312	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	171	1098	0	ENST00000260795.2:c.2075del	p.Gly692AlafsTer16	p.G692Afs*16	ENST00000260795		690	ctG/ct	15/17	1	2	FACETS	0.957	0.882	1	0.957	0.882	1	CLONAL	1	TRUE	1	0.45	2		1098	794	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1956917	1956917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761204359	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	64	648	0	ENST00000382891.5:c.2368G>A	p.Val790Ile	p.V790I	ENST00000382891	NM_133335.3	790	Gtt/Att	13/22	1	2	FACETS	0.35	0.302	0.402	0.35	0.302	0.402	SUBCLONAL	1	TRUE	1	0.45	2		648	813	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230822	66230822	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	63	274	0	ENST00000273854.3:c.2149C>A	p.Gln717Lys	p.Q717K	ENST00000273854	NM_004439.5	717	Caa/Aaa	12/18	0.168715733290035	1	FACETS	0.599	0.521	0.684	0.599	0.521	0.684	INDETERMINATE	1	TRUE	0	0.45	1		274	362	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155661	106155661	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	67	299	0	ENST00000380013.4:c.565del	p.Ser189ValfsTer18	p.S189Vfs*18	ENST00000380013	NM_001127208.2	188	Aaa/aa	3/11	1	2	FACETS	0.844	0.738	0.957	0.844	0.738	0.957	CLONAL	1	TRUE	1	0.45	2		299	353	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168708	56168708	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	93	304	0	ENST00000399503.3:c.1562A>G	p.Gln521Arg	p.Q521R	ENST00000399503	NM_005921.1	521	cAa/cGa	9/20	1	2	FACETS	0.914	0.817	1	0.914	0.817	1	CLONAL	1	TRUE	1	0.45	2		304	452	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158431	26158433	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs1176218644	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	96	759	0	ENST00000289316.2:c.37_39del	p.Lys13del	p.K13del	ENST00000289316	NM_138720.2	12	AAG/-	1/2	1	2	FACETS	0.463	0.412	0.518	0.463	0.412	0.518	SUBCLONAL	1	TRUE	1	0.45	2		759	921	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671990	30671990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	158	702	0	ENST00000376406.3:c.4970C>T	p.Ala1657Val	p.A1657V	ENST00000376406	NM_014641.2	1657	gCc/gTc	10/15	1	2	FACETS	0.995	0.914	1	0.995	0.914	1	CLONAL	1	TRUE	1	0.45	2		702	706	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673764	30673764	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	35	471	0	ENST00000376406.3:c.3196del	p.Leu1066PhefsTer50	p.L1066Ffs*50	ENST00000376406	NM_014641.2	1066	Ctt/tt	10/15	1	2	FACETS	0.306	0.25	0.369	0.306	0.25	0.369	SUBCLONAL	1	TRUE	1	0.45	2		471	508	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324067	31324068	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	23	220	0	ENST00000412585.2:c.495_496del	p.Gln165HisfsTer11	p.Q165Hfs*11	ENST00000412585	NM_005514.6	165	caGAtc/catc	3/8	1	2	FACETS	0.433	0.339	0.542	0.433	0.339	0.542	SUBCLONAL	1	TRUE	1	0.45	2		220	236	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170022	32170022	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	191	978	1	ENST00000375023.3:c.3586G>T	p.Gly1196Ter	p.G1196*	ENST00000375023	NM_004557.3	1196	Gga/Tga	21/30	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.45	2		979	832	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797253	32797253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1373006520	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	72	866	0	ENST00000374899.4:c.1856G>A	p.Arg619Gln	p.R619Q	ENST00000374899	NM_018833.2	619	cGg/cAg	11/12	1	2	FACETS	0.328	0.286	0.374	0.328	0.286	0.374	SUBCLONAL	1	TRUE	1	0.45	2		866	975	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805362	32805363	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	57	477	0	ENST00000374899.4:c.559dup	p.His187ProfsTer59	p.H187Pfs*59	ENST00000374899	NM_018833.2	187	cat/cCat	3/12	1	2	FACETS	0.429	0.367	0.495	0.429	0.367	0.495	SUBCLONAL	1	TRUE	1	0.45	2		477	591	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631434	117631434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	24	247	0	ENST00000368508.3:c.6244G>A	p.Ala2082Thr	p.A2082T	ENST00000368508	NM_002944.2	2082	Gct/Act	40/43	1	2	FACETS	0.323	0.253	0.404	0.323	0.253	0.404	SUBCLONAL	1	TRUE	1	0.45	2		247	330	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709118	117709118	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	99	398	0	ENST00000368508.3:c.1839A>C	p.Lys613Asn	p.K613N	ENST00000368508	NM_002944.2	613	aaA/aaC	13/43	1	2	FACETS	0.98	0.88	1	0.98	0.88	1	CLONAL	1	TRUE	1	0.45	2		398	449	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527832	157527832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs183921218	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	74	373	0	ENST00000346085.5:c.5557G>A	p.Ala1853Thr	p.A1853T	ENST00000346085	NM_020732.3	1853	Gca/Aca	20/20	1	2	FACETS	0.894	0.787	1	0.894	0.787	1	CLONAL	1	TRUE	1	0.45	2		373	368	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468188	50468188	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	52	690	0	ENST00000331340.3:c.1423G>A	p.Val475Ile	p.V475I	ENST00000331340	NM_006060.4	475	Gtc/Atc	8/8	1	2	FACETS	0.372	0.316	0.434	0.372	0.316	0.434	SUBCLONAL	1	TRUE	1	0.45	2		690	621	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194648	29194648	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	169	921	2	ENST00000240100.2:c.1080del	p.Thr361ProfsTer62	p.T361Pfs*62	ENST00000240100	NM_001394.6	360	ccC/cc	4/4	1	2	FACETS	0.974	0.897	1	0.974	0.897	1	CLONAL	1	TRUE	1	0.45	2		923	771	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371944	55371944	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769494100	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	119	352	1	ENST00000297316.4:c.634C>T	p.Pro212Ser	p.P212S	ENST00000297316	NM_022454.3	212	Cct/Tct	2/2	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.45	2		353	438	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27190607	27190607	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	128	536	0	ENST00000380036.4:c.1408T>C	p.Tyr470His	p.Y470H	ENST00000380036	NM_000459.3	470	Tac/Cac	10/23	1	2	FACETS	0.921	0.837	1	0.921	0.837	1	CLONAL	1	TRUE	1	0.45	2		536	618	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570376	87570376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	128	879	0	ENST00000277120.3:c.2116G>A	p.Val706Met	p.V706M	ENST00000277120		706	Gtg/Atg	17/19	1	2	FACETS	0.76	0.689	0.834	0.76	0.689	0.834	SUBCLONAL	1	TRUE	1	0.45	2		879	749	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231256	98231256	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1274998781	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	60	711	0	ENST00000331920.6:c.2027A>G	p.Tyr676Cys	p.Y676C	ENST00000331920	NM_000264.3	676	tAc/tGc	14/24	1	2	FACETS	0.344	0.296	0.397	0.344	0.296	0.397	SUBCLONAL	1	TRUE	1	0.45	2		711	775	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931873	39931873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	155	358	0	ENST00000378444.4:c.2726G>A	p.Gly909Asp	p.G909D	ENST00000378444	NM_001123385.1	909	gGc/gAc	4/15	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.45	1		358	363	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931963	39931964	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	162	397	0	ENST00000378444.4:c.2635dup	p.Ser879LysfsTer38	p.S879Kfs*38	ENST00000378444	NM_001123385.1	879	agc/aAgc	4/15	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.45	1		397	404	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225904	53225904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	164	488	0	ENST00000375401.3:c.2945G>A	p.Arg982His	p.R982H	ENST00000375401	NM_004187.3	982	cGc/cAc	19/26	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.45	1		488	411	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360637	70360637	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	11	159	0	ENST00000374080.3:c.6197A>G	p.Gln2066Arg	p.Q2066R	ENST00000374080		2066	cAg/cGg	42/45	1	1	FACETS	0.177	0.122	0.246	0.177	0.122	0.246	SUBCLONAL	1	TRUE	0	0.45	1		159	214	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855036	76855036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557085912	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	18	183	0	ENST00000373344.5:c.5800G>A	p.Gly1934Arg	p.G1934R	ENST00000373344	NM_000489.3	1934	Ggg/Agg	25/35	1	1	FACETS	0.305	0.23	0.393	0.305	0.23	0.393	SUBCLONAL	1	TRUE	0	0.45	1		183	203	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61710094	61710094	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	22	182	2	ENST00000401558.2:c.2810C>A	p.Ala937Asp	p.A937D	ENST00000401558	NM_003400.3	937	gCt/gAt	22/25	1	2	FACETS	0.34	0.263	0.428	0.34	0.263	0.428	SUBCLONAL	1	TRUE	1	0.45	2		184	288	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0046699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	506	649	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.603923777613865	2	FACETS	0.933	0.901	0.965	0.933	0.901	0.965	CLONAL	2	TRUE	0	0.622061051342747	2		649	872	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0046699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	220	353	1	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.622061051342747	3	FACETS	0.824	0.772	0.875	0.824	0.772	0.875	CLONAL	2	TRUE	1	0.622061051342747	3		354	563	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508499	106508499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752602335	NA	P-0046699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	117	302	0	ENST00000359195.3:c.493G>A	p.Val165Ile	p.V165I	ENST00000359195	NM_002649.2	165	Gtc/Atc	2/11	0.609088391371225	3	FACETS	0.984	0.892	1	0.492	0.446	0.541	CLONAL	1	TRUE	1	0.622061051342747	3		302	501	SUCCESS
APC	324	MSKCC	GRCh37	5	112174438	112174438	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs863225340	NA	P-0046699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	46	167	0	ENST00000257430.4:c.3147G>A	p.Trp1049Ter	p.W1049*	ENST00000257430	NM_000038.5	1049	tgG/tgA	16/16	1	2	FACETS	0.672	0.572	0.78	0.672	0.572	0.78	SUBCLONAL	1	TRUE	1	0.622061051342747	2		167	220	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270144	66270144	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs901722071	NA	P-0046699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	126	255	0	ENST00000273854.3:c.1738A>G	p.Thr580Ala	p.T580A	ENST00000273854	NM_004439.5	580	Aca/Gca	8/18	0.213199773510611	1	FACETS	0.767	0.702	0.833	0.767	0.702	0.833	INDETERMINATE	1	TRUE	0	0.622061051342747	1		255	364	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604797	48604797	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	143	281	0	ENST00000342988.3:c.1619T>G	p.Leu540Arg	p.L540R	ENST00000342988	NM_005359.5	540	cTt/cGt	12/12	0.622061051342747	1	FACETS	0.951	0.88	1	0.951	0.88	1	CLONAL	1	TRUE	0	0.622061051342747	1		281	333	SUCCESS
APC	324	MSKCC	GRCh37	5	112175244	112175245	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0046699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	76	204	0	ENST00000257430.4:c.3954_3955dup	p.Pro1319LeufsTer3	p.P1319Lfs*3	ENST00000257430	NM_000038.5	1318	gat/gaTCt	16/16	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.622061051342747	2		204	243	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	124	427	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.739048944620854	2		427	282	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0046709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	180	292	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.739048944620854	2		292	449	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0046711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	60	409	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.801	0.698	0.911	0.801	0.698	0.911	CLONAL	1	TRUE	1	0.591979888632201	2		410	253	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0046711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	59	413	1	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	0.555039119031819	1	FACETS	0.821	0.721	0.925	0.821	0.721	0.925	CLONAL	1	TRUE	0	0.591979888632201	1		414	171	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604785	48604785	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	74	312	0	ENST00000342988.3:c.1607T>C	p.Leu536Pro	p.L536P	ENST00000342988	NM_005359.5	536	cTa/cCa	12/12	0.591979888632201	1	FACETS	0.884	0.79	0.982	0.884	0.79	0.982	CLONAL	1	TRUE	0	0.591979888632201	1		312	199	SUCCESS
APC	324	MSKCC	GRCh37	5	112174559	112174559	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	58	326	0	ENST00000257430.4:c.3268C>T	p.Gln1090Ter	p.Q1090*	ENST00000257430	NM_000038.5	1090	Caa/Taa	16/16	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.591979888632201	2		326	190	SUCCESS
APC	324	MSKCC	GRCh37	5	112175416	112175417	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	36	244	0	ENST00000257430.4:c.4126dup	p.Tyr1376LeufsTer10	p.Y1376Lfs*10	ENST00000257430	NM_000038.5	1375	-/T	16/16	1	2	FACETS	0.881	0.738	1	0.881	0.738	1	CLONAL	1	TRUE	1	0.591979888632201	2		244	138	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0046712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	26	878	1	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.425239529111659	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.425239529111659	1		879	79	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0046712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	43	279	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	0.308275068272239	4	FACETS	0.991	0.859	1	0.991	0.859	1	CLONAL	3	TRUE	1	0.425239529111659	4		279	97	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724439	162724439	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	31	401	0	ENST00000367921.3:c.211G>T	p.Ala71Ser	p.A71S	ENST00000367921	NM_006182.2	71	Gcc/Tcc	5/18	0.425239529111659	3	FACETS	0.931	0.774	1	0.931	0.774	1	CLONAL	2	TRUE	1	0.425239529111659	3		401	95	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229612	5229612	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	33	59	0	ENST00000357368.4:c.2239G>C	p.Gly747Arg	p.G747R	ENST00000357368	NM_002850.3	747	Ggc/Cgc	15/38	0.390296854914715	5	FACETS	1	0.921	1	0.792	0.661	0.931	CLONAL	2	TRUE	2	0.425239529111659	5		59	107	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945792	17945792	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	50	712	0	ENST00000458235.1:c.2068T>A	p.Trp690Arg	p.W690R	ENST00000458235	NM_000215.3	690	Tgg/Agg	16/24	NA	2	FACETS	0.84	0.73	0.954			1	INDETERMINATE	2	TRUE	NA	0.425239529111659	2		712	140	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645717	215645717	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	11	436	0	ENST00000260947.4:c.881G>T	p.Arg294Met	p.R294M	ENST00000260947	NM_000465.2	294	aGg/aTg	4/11	1	2	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	TRUE	1	0.425239529111659	2		436	39	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937825	76937825	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	10	456	0	ENST00000373344.5:c.2923G>T	p.Asp975Tyr	p.D975Y	ENST00000373344	NM_000489.3	975	Gat/Tat	9/35	0.425239529111659	1	FACETS	0.712	0.495	0.97	0.712	0.495	0.97	CLONAL	1	TRUE	0	0.425239529111659	1		456	52	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931682	39931682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	74	330	0	ENST00000378444.4:c.2917G>A	p.Val973Met	p.V973M	ENST00000378444	NM_001123385.1	973	Gtg/Atg	4/15	0.256129106676259	2	FACETS	0.866	0.77	0.967			1	CLONAL	2	TRUE	NA	0.36194233162189	2		330	236	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0046714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	70	390	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.12	2		390	801	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0046719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	204	654	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.397296280761265	1	FACETS	0.838	0.778	0.899	0.838	0.778	0.899	CLONAL	1	TRUE	0	0.4554306497496	1		654	826	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973028	25973028	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	132	364	0	ENST00000435504.4:c.1397C>T	p.Ser466Phe	p.S466F	ENST00000435504		466	tCc/tTc	12/13	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.4554306497496	2		364	557	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433060	49433060	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1251778848	NA	P-0046719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	289	795	0	ENST00000301067.7:c.8311C>T	p.Arg2771Ter	p.R2771*	ENST00000301067	NM_003482.3	2771	Cga/Tga	33/54	1	2	FACETS	0.964	0.905	1	0.964	0.905	1	CLONAL	1	TRUE	1	0.4554306497496	2		795	1317	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750615	41750615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	103	378	2	ENST00000226382.2:c.13G>A	p.Glu5Lys	p.E5K	ENST00000226382	NM_003924.3	5	Gaa/Aaa	1/3	1	2	FACETS	0.712	0.638	0.791	0.712	0.638	0.791	SUBCLONAL	1	TRUE	1	0.4554306497496	2		380	635	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425794	49425794	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	215	759	1	ENST00000301067.7:c.12694C>T	p.Gln4232Ter	p.Q4232*	ENST00000301067	NM_003482.3	4232	Cag/Tag	39/54	1	2	FACETS	0.81	0.752	0.871	0.81	0.752	0.871	CLONAL	1	TRUE	1	0.4554306497496	2		760	1165	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2099555	2100455	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTGGCTCACGCCTGTCATCCCAGCACTTTGGGAGGCCGAGGCGGGTGGATCACCTGAGGTCAGGAGTTTGAGACCAGCCTGGCCAACATGGCGAAACCCCGTCTCTACTAAAAATACCAAAAATTAGCCGGTCATAGTGGTGGGCGCCTGTAATTCCAGCTACTCGGGGGGCTGAGACGAGAATTGCTTGAACCCGGGAGGCGGAGGTTTCAGTGAGCCGTGATCGCGCCACTGCACTCCATCCTGGGGAAGAAGAGCAAAACTCCGTCTAAAAAAAAATTGTGCAGTTTGAAATTGTATTTCATGTTATGTTTTATCTCAATACAACATTTGCAGTTGTGAAAAAAAATTGCACATTCTCAACTCCTCGGGATGGAGCAGTAAAGCCCCTCAGTAAATCTTTTTTTTTTTTTTTTTTTGAGACCGAGTTTCGCTCTTGTCACCCAGGCTGGAGCGCAGGGGCGCGATCTCGGCTCACTGCAATCTCCGCCTCCTGGGTTCAAGGGATTCTCCTGCCTCACTCTCCCGAGTAGCTGGGATTATAGACGCCCACCACCACGCCCAGCAAATTTTTTGTATTTTTAGTAGAGACAGGGTTTCATCATGTTGGGCAGGCTGGTCTCAAACTCCTGACCTCTGGTGATCCACCTGCCTTGGCCCCCCAAAGTGCAGGGATTACAGGCCTGAGCCACCGCGGCTCGTCAAGTGAATCTTGATTCCAGAAAGATCTGTTTTAAGTCTCTAGTCTGGAAAATGCAGTGGGAGTCTTTAGGTGGTTTGTGACTTGCAGTTAAGGAGACCGTGGCCTGAGCACTGGCCCCTTTTTCTTCTTTCATCTCTCTCCAGGAACTGAGCATGGAATGTGGCCTCAACAATCGCATCCGGATGATAGGGCAGATTT	GTGGCTCACGCCTGTCATCCCAGCACTTTGGGAGGCCGAGGCGGGTGGATCACCTGAGGTCAGGAGTTTGAGACCAGCCTGGCCAACATGGCGAAACCCCGTCTCTACTAAAAATACCAAAAATTAGCCGGTCATAGTGGTGGGCGCCTGTAATTCCAGCTACTCGGGGGGCTGAGACGAGAATTGCTTGAACCCGGGAGGCGGAGGTTTCAGTGAGCCGTGATCGCGCCACTGCACTCCATCCTGGGGAAGAAGAGCAAAACTCCGTCTAAAAAAAAATTGTGCAGTTTGAAATTGTATTTCATGTTATGTTTTATCTCAATACAACATTTGCAGTTGTGAAAAAAAATTGCACATTCTCAACTCCTCGGGATGGAGCAGTAAAGCCCCTCAGTAAATCTTTTTTTTTTTTTTTTTTTGAGACCGAGTTTCGCTCTTGTCACCCAGGCTGGAGCGCAGGGGCGCGATCTCGGCTCACTGCAATCTCCGCCTCCTGGGTTCAAGGGATTCTCCTGCCTCACTCTCCCGAGTAGCTGGGATTATAGACGCCCACCACCACGCCCAGCAAATTTTTTGTATTTTTAGTAGAGACAGGGTTTCATCATGTTGGGCAGGCTGGTCTCAAACTCCTGACCTCTGGTGATCCACCTGCCTTGGCCCCCCAAAGTGCAGGGATTACAGGCCTGAGCCACCGCGGCTCGTCAAGTGAATCTTGATTCCAGAAAGATCTGTTTTAAGTCTCTAGTCTGGAAAATGCAGTGGGAGTCTTTAGGTGGTTTGTGACTTGCAGTTAAGGAGACCGTGGCCTGAGCACTGGCCCCTTTTTCTTCTTTCATCTCTCTCCAGGAACTGAGCATGGAATGTGGCCTCAACAATCGCATCCGGATGATAGGGCAGATTT	-	novel	NA	P-0046719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	0	37	0	0	ENST00000219476.3:c.138+804_196del		p.X46_splice	ENST00000219476	NM_000548.3	46		3/42	0.4554306497496	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	0	0.4554306497496	1		0	37	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222074	2222074	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	294	986	0	ENST00000398665.3:c.2906C>G	p.Ser969Cys	p.S969C	ENST00000398665	NM_032482.2	969	tCc/tGc	24/28	1	2	FACETS	0.929	0.873	0.987	0.929	0.873	0.987	CLONAL	1	TRUE	1	0.4554306497496	2		986	1390	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309622	30309623	+	missense_variant	Missense_Mutation	DNP	CA	CA	TC	novel	NA	P-0046719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	200	575	2	ENST00000307677.4:c.399_400delinsGA	p.Asp133_Gly134delinsGluArg	p.D133_G134delinsER	ENST00000307677	NM_138578.1	133	gaTGgg/gaGAgg	2/3	0.4554306497496	3	FACETS	0.865	0.8	0.933	0.432	0.4	0.467	CLONAL	1	TRUE	1	0.4554306497496	3		577	1247	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560493	65560493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	26	438	0	ENST00000358664.4:c.104G>A	p.Arg35His	p.R35H	ENST00000358664	NM_002382.4	35	cGt/cAt	3/5	1	2	FACETS	0.391	0.309	0.485	0.391	0.309	0.485	SUBCLONAL	1	TRUE	1	0.360361573551448	2		438	369	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655425	45655425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767656796	NA	P-0046720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	67	747	2	ENST00000407780.3:c.427G>A	p.Val143Ile	p.V143I	ENST00000407780	NM_001283052.1	143	Gtc/Atc	4/7	0.239083518048204	4	FACETS	1	0.967	1	0.678	0.592	0.77	CLONAL	1	TRUE	2	0.360361573551448	4		749	373	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091347	193091347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775940851	NA	P-0046720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	35	327	0	ENST00000367435.3:c.17G>A	p.Ser6Asn	p.S6N	ENST00000367435	NM_024529.4	6	aGc/aAc	1/17	1	2	FACETS	0.816	0.673	0.974	0.816	0.673	0.974	CLONAL	1	TRUE	1	0.360361573551448	2		327	238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs11575997	NA	P-0046720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	54	597	0	ENST00000269305.4:c.993+1G>T		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.300723298074646	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.360361573551448	1		597	210	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799686	3799686	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0046721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	122	203	0	ENST00000262367.5:c.3780-2A>G		p.X1260_splice	ENST00000262367	NM_004380.2	1260			1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.546953700299546	2		203	429	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688752	47688770	+	frameshift_variant	Frame_Shift_Del	DEL	TCAGGAACCTTTACCATGT	TCAGGAACCTTTACCATGT	-	novel	NA	P-0046721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	46	315	0	ENST00000347630.2:c.530_548del	p.Asn177SerfsTer8	p.N177Sfs*8	ENST00000347630	NM_001007230.1	177	aACATGGTAAAGGTTCCTGAg/ag	7/11	1	2	FACETS	0.381	0.321	0.448	0.381	0.321	0.448	SUBCLONAL	1	TRUE	1	0.546953700299546	2		315	441	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	60	271	0	ENST00000397062.3:c.101G>C	p.Arg34Pro	p.R34P	ENST00000397062	NM_006164.4	34	cGa/cCa	2/5	1	2	FACETS	0.9	0.777	1	0.9	0.777	1	CLONAL	1	TRUE	1	0.283776321466734	2		271	470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0046724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	120	551	2	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.236609085984349	1	FACETS	0.873	0.788	0.963	0.873	0.788	0.963	CLONAL	1	TRUE	0	0.283776321466734	1		553	831	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637121	176637122	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1299932363	NA	P-0046724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	74	436	1	ENST00000439151.2:c.1727dup	p.Asn576LysfsTer8	p.N576Kfs*8	ENST00000439151	NM_022455.4	574	gga/ggAa	5/23	0.236609085984349	1	FACETS	0.641	0.561	0.728	0.641	0.561	0.728	SUBCLONAL	1	TRUE	0	0.283776321466734	1		437	698	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970979	21970979	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	160	642	0	ENST00000304494.5:c.379del	p.Ala127HisfsTer19	p.A127Hfs*19	ENST00000304494	NM_000077.4	127	Gca/ca	2/3	0.283776321466734	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.283776321466734	1		642	937	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253850	30253850	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751979681	NA	P-0046724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	93	525	0	ENST00000307677.4:c.604G>A	p.Glu202Lys	p.E202K	ENST00000307677	NM_138578.1	202	Gag/Aag	3/3	0.283776321466734	5	FACETS	0.788	0.698	0.884			1	SUBCLONAL	1	TRUE	NA	0.283776321466734	5		525	1186	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600402	43600402	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	93	468	1	ENST00000355710.3:c.628G>T	p.Glu210Ter	p.E210*	ENST00000355710	NM_020975.4	210	Gag/Tag	4/20	0.149360444580234	1	FACETS	0.806	0.717	0.901	0.806	0.717	0.901	INDETERMINATE	1	TRUE	0	0.283776321466734	1		469	698	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30095705	30095705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	67	288	0	ENST00000331968.5:c.1783G>A	p.Gly595Arg	p.G595R	ENST00000331968	NM_002742.2	595	Gga/Aga	12/18	0.236609085984349	1	FACETS	0.923	0.805	1	0.923	0.805	1	CLONAL	1	TRUE	0	0.283776321466734	1		288	439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0046725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	478	701	2	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.663815430136575	2	FACETS	0.928	0.898	0.958	0.928	0.898	0.958	CLONAL	2	TRUE	0	0.703676014817356	2		703	732	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220428	1220428	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	722	706	0	ENST00000326873.7:c.521A>T	p.His174Leu	p.H174L	ENST00000326873	NM_000455.4	174	cAc/cTc	4/10	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	2	TRUE	NA	0.703676014817356	2		706	1025	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503222	125503222	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	97	200	0	ENST00000428830.2:c.589G>C	p.Val197Leu	p.V197L	ENST00000428830	NM_001114121.2	197	Gta/Cta	6/14	0.596009043070803	3	FACETS	0.929	0.835	1			1	CLONAL	1	TRUE	NA	0.703676014817356	3		200	401	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136811	2136811	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs45517380	NA	P-0046725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	335	769	0	ENST00000219476.3:c.4928A>G	p.Asn1643Ser	p.N1643S	ENST00000219476	NM_000548.3	1643	aAc/aGc	38/42	1	2	FACETS	0.971	0.92	1	0.971	0.92	1	CLONAL	1	TRUE	1	0.703676014817356	2		769	981	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226098	2226098	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	372	868	1	ENST00000326181.6:c.1795G>T	p.Val599Leu	p.V599L	ENST00000326181	NM_032271.2	599	Gtg/Ttg	19/21	1	2	FACETS	0.919	0.873	0.966	0.919	0.873	0.966	CLONAL	1	TRUE	1	0.703676014817356	2		869	1150	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458259	12458259	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	333	347	0	ENST00000287820.6:c.876C>A	p.Phe292Leu	p.F292L	ENST00000287820	NM_015869.4	292	ttC/ttA	6/7	0.676597338617123	2	FACETS	0.921	0.885	0.956	0.921	0.885	0.956	CLONAL	2	TRUE	0	0.703676014817356	2		347	514	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752343	57752344	+	missense_variant	Missense_Mutation	DNP	TT	TT	AG	novel	NA	P-0046725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	77	252	1	ENST00000274289.3:c.1229_1230delinsCT	p.Gln410Pro	p.Q410P	ENST00000274289	NM_006622.3	410	cAA/cCT	9/14	1	2	FACETS	0.655	0.58	0.735	0.655	0.58	0.735	SUBCLONAL	1	TRUE	1	0.703676014817356	2		253	334	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526718	106526718	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	131	294	0	ENST00000359195.3:c.3011C>A	p.Pro1004Gln	p.P1004Q	ENST00000359195	NM_002649.2	1004	cCa/cAa	10/11	1	2	FACETS	0.878	0.804	0.955	0.878	0.804	0.955	CLONAL	1	TRUE	1	0.703676014817356	2		294	424	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141568609	141568609	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	334	622	0	ENST00000220592.5:c.853A>C	p.Thr285Pro	p.T285P	ENST00000220592	NM_012154.3	285	Acc/Ccc	7/19	0.703676014817356	3	FACETS	0.886	0.836	0.937			1	CLONAL	1	TRUE	NA	0.703676014817356	3		622	1449	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300935	137300935	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	306	736	0	ENST00000481739.1:c.580A>C	p.Lys194Gln	p.K194Q	ENST00000481739	NM_002957.4	194	Aag/Cag	4/10	0.703676014817356	3	FACETS	0.879	0.828	0.933	0.44	0.414	0.467	CLONAL	1	TRUE	1	0.703676014817356	3		736	1337	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204494722	204494722	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	75	349	0	ENST00000367182.3:c.76C>A	p.Gln26Lys	p.Q26K	ENST00000367182	NM_001278516.1	26	Cag/Aag	2/11	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.429665932296756	2		349	310	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	351	424	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.797498641764758	2	FACETS	0.936	0.906	0.966	0.936	0.906	0.966	CLONAL	2	TRUE	0	0.797498641764758	2		424	470	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0046727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	152	359	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.797498641764758	2		359	377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578467	7578467	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	1172	842	2	ENST00000269305.4:c.463A>C	p.Thr155Pro	p.T155P	ENST00000269305	NM_001126112.2	155	Acc/Ccc	5/11	0.470906439532762	4	FACETS	0.993	0.976	1			1	CLONAL	4	TRUE	NA	0.615108945721251	4		844	1549	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600005	10600005	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	527	834	5	ENST00000171111.5:c.1571del	p.Gly524AlafsTer8	p.G524Afs*8	ENST00000171111	NM_203500.1	524	gGc/gc	5/6	0.615108945721251	2	FACETS	0.933	0.901	0.965	0.933	0.901	0.965	CLONAL	2	TRUE	0	0.615108945721251	2		839	918	SUCCESS
AR	367	MSKCC	GRCh37	X	66765159	66765206	+	inframe_deletion	In_Frame_Del	DEL	GCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA	GCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA	-	rs3032358	NA	P-0046728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	61	136	0	ENST00000374690.3:c.192_239del	p.Gln65_Gln80del	p.Q65_Q80del	ENST00000374690	NM_000044.3	57	ctGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAg/ctg	1/8	0.615108945721251	2	FACETS	0.963	0.844	1			1	CLONAL	1	TRUE	NA	0.615108945721251	2		136	206	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933195	100933195	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	332	319	2	ENST00000325455.5:c.2195G>A	p.Trp732Ter	p.W732*	ENST00000325455	NM_001202474.3	732	tGg/tAg	4/8	0.604273817578844	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	4	TRUE	0	0.615108945721251	4		321	408	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980278	201980278	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	154	534	1	ENST00000359651.3:c.14G>T	p.Cys5Phe	p.C5F	ENST00000359651		5	tGt/tTt	1/8	0.574045646899361	5	FACETS	0.796	0.726	0.868	0.199	0.181	0.217	SUBCLONAL	1	TRUE	1	0.615108945721251	5		535	1210	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859675	57859676	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0046728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	308	465	1	ENST00000228682.2:c.729_730delinsAA	p.Ser243_Gln244delinsArgLys	p.S243_Q244delinsRK	ENST00000228682	NM_005269.2	243	agCCag/agAAag	7/12	0.615108945721251	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.615108945721251	4		466	776	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753078	42753078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs567417863	NA	P-0046728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	80	885	1	ENST00000222329.4:c.1186G>A	p.Val396Ile	p.V396I	ENST00000222329	NM_006494.2	396	Gta/Ata	4/4	0.486582297675397	4	FACETS	0.312	0.273	0.354	0.156	0.136	0.177	SUBCLONAL	1	TRUE	2	0.615108945721251	4		886	1347	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281505	198281505	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	388	439	0	ENST00000335508.6:c.626G>T	p.Gly209Val	p.G209V	ENST00000335508	NM_012433.2	209	gGt/gTt	6/25	0.57130894981089	3	FACETS	0.887	0.854	0.92	0.887	0.854	0.92	CLONAL	3	TRUE	0	0.615108945721251	3		439	620	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632293	215632293	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587781334	NA	P-0046728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	31	409	0	ENST00000260947.4:c.1481A>G	p.Asn494Ser	p.N494S	ENST00000260947	NM_000465.2	494	aAt/aGt	6/11	0.426167981619364	3	FACETS	0.245	0.197	0.298	0.082	0.065	0.1	SUBCLONAL	1	TRUE	0	0.615108945721251	3		409	539	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543900	41543900	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	213	550	0	ENST00000263253.7:c.2191C>G	p.Pro731Ala	p.P731A	ENST00000263253	NM_001429.3	731	Cct/Gct	12/31	0.615108945721251	2	FACETS	1	0.97	1	0.533	0.497	0.569	CLONAL	1	TRUE	0	0.615108945721251	2		550	650	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390937	89390937	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	162	273	0	ENST00000336596.2:c.1003A>G	p.Asn335Asp	p.N335D	ENST00000336596	NM_005233.5	335	Aat/Gat	5/17	0.615108945721251	3	FACETS	0.888	0.825	0.951			1	CLONAL	2	TRUE	NA	0.615108945721251	3		273	388	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456719	138456719	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs773791563	NA	P-0046728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	78	312	0	ENST00000289153.2:c.631A>G	p.Ser211Gly	p.S211G	ENST00000289153	NM_006219.2	211	Agc/Ggc	4/22	0.594557695164972	3	FACETS	0.939	0.832	1	0.47	0.416	0.527	CLONAL	1	TRUE	1	0.615108945721251	3		312	353	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146586	185146586	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	294	484	0	ENST00000265026.3:c.217A>T	p.Ser73Cys	p.S73C	ENST00000265026	NM_004721.4	73	Agt/Tgt	2/14	0.474274980336014	5	FACETS	1	0.954	1	0.675	0.637	0.714	CLONAL	2	TRUE	2	0.615108945721251	5		484	908	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152473	56152473	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	179	201	0	ENST00000399503.3:c.529G>T	p.Asp177Tyr	p.D177Y	ENST00000399503	NM_005921.1	177	Gat/Tat	2/20	0.53431744875885	4	FACETS	0.922	0.865	0.978	0.922	0.865	0.978	CLONAL	3	TRUE	1	0.615108945721251	4		201	340	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637174	176637174	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	140	463	1	ENST00000439151.2:c.1774G>T	p.Gly592Cys	p.G592C	ENST00000439151	NM_022455.4	592	Ggc/Tgc	5/23	0.508583591226207	5	FACETS	1	0.972	1			1	CLONAL	1	TRUE	NA	0.615108945721251	5		464	757	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982134	93982134	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	68	325	0	ENST00000369303.4:c.1331C>G	p.Ser444Trp	p.S444W	ENST00000369303	NM_004440.3	444	tCg/tGg	6/17	0.615108945721251	4	FACETS	0.623	0.542	0.71	0.312	0.271	0.355	SUBCLONAL	1	TRUE	2	0.615108945721251	4		325	573	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984159	2984159	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	244	379	2	ENST00000396946.4:c.371A>G	p.His124Arg	p.H124R	ENST00000396946	NM_032415.4	124	cAc/cGc	5/25	0.375805712511478	4	FACETS	0.938	0.881	0.996	0.938	0.881	0.996	CLONAL	2	TRUE	2	0.615108945721251	4		381	683	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222974	53222974	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	520	398	0	ENST00000375401.3:c.4098G>T	p.Glu1366Asp	p.E1366D	ENST00000375401	NM_004187.3	1366	gaG/gaT	24/26	0.615108945721251	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.615108945721251	2		398	697	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411872	63411872	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	577	488	1	ENST00000330258.3:c.1295del	p.Gly432AlafsTer17	p.G432Afs*17	ENST00000330258	NM_152424.3	432	gGc/gc	2/2	0.615108945721251	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.615108945721251	2		489	790	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0046729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	198	767	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.333556322393607	1	FACETS	0.837	0.78	0.895	1	0.993	1	CLONAL	2	TRUE	0	0.333556322393607	1		767	591	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0046729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	53	232	0	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.333556322393607	2		232	270	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0046729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	72	354	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.333556322393607	2		354	339	SUCCESS
ALK	238	MSKCC	GRCh37	2	29473981	29473981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768366852	NA	P-0046729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	45	685	1	ENST00000389048.3:c.2194G>A	p.Asp732Asn	p.D732N	ENST00000389048	NM_004304.4	732	Gac/Aac	12/29	0.182710804033889	3	FACETS	0.453	0.38	0.534	0.151	0.126	0.178	INDETERMINATE	1	TRUE	0	0.333556322393607	3		686	695	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626680	12626680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751232720	NA	P-0046729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	38	439	0	ENST00000251849.4:c.1609G>A	p.Val537Ile	p.V537I	ENST00000251849	NM_002880.3	537	Gta/Ata	15/17	0.185130462521038	3	FACETS	0.529	0.436	0.632	0.264	0.218	0.316	INDETERMINATE	1	TRUE	1	0.333556322393607	3		439	503	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028615	12028615	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	66	236	0	ENST00000353533.5:c.818A>T	p.Glu273Val	p.E273V	ENST00000353533	NM_003010.3	273	gAa/gTa	8/11	0.333556322393607	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.333556322393607	1		236	293	SUCCESS
APC	324	MSKCC	GRCh37	5	112116559	112116559	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	24	249	0	ENST00000257430.4:c.604G>T	p.Glu202Ter	p.E202*	ENST00000257430	NM_000038.5	202	Gaa/Taa	6/16	1	2	FACETS	0.558	0.438	0.695	0.558	0.438	0.695	SUBCLONAL	1	TRUE	1	0.333556322393607	2		249	258	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0046731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	64	291	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.781	0.678	0.893	0.781	0.678	0.893	SUBCLONAL	1	TRUE	1	0.35	2		291	468	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589599	67589604	+	inframe_deletion	In_Frame_Del	DEL	TCAGTT	TCAGTT	-	novel	NA	P-0046731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	27	189	0	ENST00000274335.5:c.1365_1370del	p.Phe456_Gln457del	p.F456_Q457del	ENST00000274335		454	acTCAGTTt/act	10/15	1	2	FACETS	0.508	0.404	0.625	0.508	0.404	0.625	SUBCLONAL	1	TRUE	1	0.35	2		189	304	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844776	156844776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1292790967	NA	P-0046731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	121	706	1	ENST00000524377.1:c.1330C>T	p.Arg444Trp	p.R444W	ENST00000524377	NM_002529.3	444	Cgg/Tgg	11/17	1	2	FACETS	0.822	0.742	0.906	0.822	0.742	0.906	CLONAL	1	TRUE	1	0.35	2		707	841	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830585	72830586	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0046731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	96	562	1	ENST00000268489.5:c.5995_5996del	p.Lys1999GlufsTer29	p.K1999Efs*29	ENST00000268489	NM_006885.3	1999	AAg/g	9/10	1	2	FACETS	0.922	0.823	1	0.922	0.823	1	CLONAL	1	TRUE	1	0.35	2		563	595	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0046732-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	19	569	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		569	624	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	107	427	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.849	0.772	0.927	0.849	0.772	0.927	CLONAL	1	TRUE	1	0.857835831959513	2		427	294	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0046734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	190	591	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.98	0.916	1	0.98	0.916	1	CLONAL	1	TRUE	1	0.857835831959513	2		591	452	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577330	64577333	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	rs587776841	NA	P-0046734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	87	583	0	ENST00000312049.6:c.249_252del	p.Ile85SerfsTer33	p.I85Sfs*33	ENST00000312049	NM_130799.2	83	ctGTCT/ct	2/10	0.857835831959513	1	FACETS	0.417	0.373	0.462	0.417	0.373	0.462	SUBCLONAL	1	TRUE	0	0.857835831959513	1		583	278	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259469	55259469	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	149	550	0	ENST00000275493.2:c.2527del	p.Val843TyrfsTer3	p.V843Yfs*3	ENST00000275493	NM_005228.3	843	Gta/ta	21/28	1	2	FACETS	0.51	0.467	0.555	0.51	0.467	0.555	SUBCLONAL	1	TRUE	1	0.857835831959513	2		550	681	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035913	47035913	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	355	333	0	ENST00000377604.3:c.592del	p.Leu198TrpfsTer68	p.L198Wfs*68	ENST00000377604	NM_001204468.1	197	atC/at	7/24	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.857835831959513	1		333	416	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678515	88678516	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0046736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	21	519	1	ENST00000360948.2:c.1020_1021delinsTT	p.Gln340_Pro341delinsHisSer	p.Q340_P341delinsHS	ENST00000360948	NM_001012338.2	340	caGCct/caTTct	9/19	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		520	274	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170360	32170360	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046736-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	31	757	0	ENST00000375023.3:c.3248C>G	p.Thr1083Ser	p.T1083S	ENST00000375023	NM_004557.3	1083	aCc/aGc	21/30	0.154186091432613	4	FACETS		NA	1			1	NA	NA	FALSE	2	NA	4		757	514	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	178	427	0				ENST00000310581	NM_198253.2	-/1132			0.261248205229335	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.261248205229335	3		427	629	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0046737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	125	409	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.180885876622185	3	FACETS	0.926	0.841	1	0.926	0.841	1	CLONAL	2	TRUE	1	0.261248205229335	3		410	584	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205124	128205124	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	77	741	0	ENST00000341105.2:c.317C>G	p.Ser106Cys	p.S106C	ENST00000341105	NM_032638.4	106	tCt/tGt	3/6	1	2	FACETS	0.508	0.444	0.577	0.508	0.444	0.577	SUBCLONAL	1	TRUE	1	0.261248205229335	2		741	1161	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799243	45799243	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	99	423	0	ENST00000450313.1:c.190G>A	p.Ala64Thr	p.A64T	ENST00000450313	NM_012222.2	64	Gcc/Acc	3/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.261248205229335	2		423	665	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166824	32166824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs544666247	NA	P-0046737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1201	136	726	0	ENST00000375023.3:c.4414C>T	p.Arg1472Trp	p.R1472W	ENST00000375023	NM_004557.3	1472	Cgg/Tgg	24/30	1	2	FACETS	0.779	0.706	0.856	0.779	0.706	0.856	SUBCLONAL	1	TRUE	1	0.261248205229335	2		726	1337	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11193215	11193215	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	127	502	0	ENST00000361445.4:c.5286G>T	p.Gln1762His	p.Q1762H	ENST00000361445	NM_004958.3	1762	caG/caT	38/58	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.261248205229335	2		502	872	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733512	85733512	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	33	345	0	ENST00000370580.1:c.500C>G	p.Ser167Cys	p.S167C	ENST00000370580	NM_003921.4	167	tCt/tGt	3/3	1	2	FACETS	0.454	0.369	0.551	0.454	0.369	0.551	SUBCLONAL	1	TRUE	1	0.261248205229335	2		345	556	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17384925	17384925	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs369396136	NA	P-0046737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	68	711	0	ENST00000359435.4:c.475C>G	p.Leu159Val	p.L159V	ENST00000359435	NM_001033549.1	159	Ctg/Gtg	5/9	1	2	FACETS	0.424	0.367	0.486	0.424	0.367	0.486	SUBCLONAL	1	TRUE	1	0.261248205229335	2		711	1228	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210947	36210948	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0046737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1218	165	877	3	ENST00000222270.7:c.698_699delinsTT	p.Arg233Ile	p.R233I	ENST00000222270	NM_014727.1	233	aGG/aTT	3/37	1	2	FACETS	0.913	0.836	0.994	0.913	0.836	0.994	CLONAL	1	TRUE	1	0.261248205229335	2		880	1383	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965393	25965393	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	111	527	0	ENST00000435504.4:c.3813G>T	p.Lys1271Asn	p.K1271N	ENST00000435504		1271	aaG/aaT	13/13	1	2	FACETS	0.892	0.8	0.989	0.892	0.8	0.989	CLONAL	1	TRUE	1	0.261248205229335	2		527	953	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518255	187518255	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	70	295	0	ENST00000441802.2:c.12439G>C	p.Gly4147Arg	p.G4147R	ENST00000441802	NM_005245.3	4147	Ggc/Cgc	25/27	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.261248205229335	2		295	459	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1268654	1268654	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1326	169	775	0	ENST00000310581.5:c.2563G>T	p.Ala855Ser	p.A855S	ENST00000310581	NM_198253.2	855	Gcg/Tcg	9/16	0.261248205229335	3	FACETS	0.978	0.897	1	0.489	0.448	0.532	CLONAL	1	TRUE	1	0.261248205229335	3		775	1495	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047907	180047907	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	217	938	0	ENST00000261937.6:c.2268C>G	p.Cys756Trp	p.C756W	ENST00000261937	NM_182925.4	756	tgC/tgG	15/30	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.261248205229335	2		938	1267	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	319	649	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.580919353550802	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.580919353550802	1		649	707	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	220	473	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.580919353550802	2		474	692	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	67	275	1	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.693	0.606	0.785	0.693	0.606	0.785	SUBCLONAL	1	TRUE	1	0.580919353550802	2		276	333	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	59	202	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.580919353550802	1	FACETS	0.819	0.718	0.924	0.819	0.718	0.924	CLONAL	1	TRUE	0	0.580919353550802	1		202	176	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	351	405	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.984	1	1	0.997	1	CLONAL	2	TRUE	1	0.580919353550802	2		408	576	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872007	35872008	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	37	479	0	ENST00000216797.5:c.605dup	p.Leu202PhefsTer7	p.L202Ffs*7	ENST00000216797	NM_020529.2	202	ttg/ttTg	4/6	1	2	FACETS	0.175	0.144	0.211	0.175	0.144	0.211	SUBCLONAL	1	TRUE	1	0.580919353550802	2		479	726	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429346	47429346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755229896	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	322	841	0	ENST00000377045.4:c.1474G>A	p.Val492Ile	p.V492I	ENST00000377045	NM_001654.4	492	Gtc/Atc	14/16	0.380644907275283	1	FACETS	0.758	0.716	0.8	0.758	0.716	0.8	SUBCLONAL	1	TRUE	0	0.580919353550802	1		841	1038	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287520	33287520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141395832	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	73	639	1	ENST00000374542.5:c.1577G>A	p.Arg526His	p.R526H	ENST00000374542	NM_001141970.1	526	cGc/cAc	6/8	1	2	FACETS	0.272	0.237	0.31	0.272	0.237	0.31	SUBCLONAL	1	TRUE	1	0.580919353550802	2		640	925	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739003	40739003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1568940954	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	150	565	2	ENST00000373198.4:c.3281del	p.Pro1094ArgfsTer6	p.P1094Rfs*6	ENST00000373198	NM_133170.3	1094	cCg/cg	24/32	0.580919353550802	4	FACETS	0.645	0.588	0.705	0.215	0.196	0.235	SUBCLONAL	1	TRUE	1	0.580919353550802	4		567	1266	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133573	55133573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762106764	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	30	491	0	ENST00000257290.5:c.877C>T	p.Arg293Cys	p.R293C	ENST00000257290	NM_006206.4	293	Cgc/Tgc	6/23	1	2	FACETS	0.185	0.148	0.226	0.185	0.148	0.226	SUBCLONAL	1	TRUE	1	0.580919353550802	2		491	559	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312660	30312660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146187350	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	44	459	1	ENST00000262643.3:c.641C>T	p.Ala214Val	p.A214V	ENST00000262643	NM_001238.2	214	gCg/gTg	8/12	1	2	FACETS	0.237	0.198	0.28	0.237	0.198	0.28	SUBCLONAL	1	TRUE	1	0.580919353550802	2		460	640	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849801	156849801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754452975	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	67	526	0	ENST00000524377.1:c.2057G>A	p.Arg686His	p.R686H	ENST00000524377	NM_002529.3	686	cGc/cAc	16/17	1	2	FACETS	0.313	0.272	0.359	0.313	0.272	0.359	SUBCLONAL	1	TRUE	1	0.580919353550802	2		526	736	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592099	67592099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	24	251	0	ENST00000274335.5:c.1915C>T	p.Arg639Ter	p.R639*	ENST00000274335		639	Cga/Tga	14/15	1	2	FACETS	0.208	0.162	0.26	0.208	0.162	0.26	SUBCLONAL	1	TRUE	1	0.580919353550802	2		251	398	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726544	41726544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs891614619	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	206	659	0	ENST00000301178.4:c.89C>T	p.Thr30Met	p.T30M	ENST00000301178	NM_021913.4	30	aCg/aTg	2/20	1	2	FACETS	0.868	0.807	0.931	0.868	0.807	0.931	CLONAL	1	TRUE	1	0.580919353550802	2		659	817	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278073	18278073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	87	815	0	ENST00000222254.8:c.1693C>T	p.Pro565Ser	p.P565S	ENST00000222254	NM_005027.3	565	Ccg/Tcg	13/16	1	2	FACETS	0.273	0.24	0.307	0.273	0.24	0.307	SUBCLONAL	1	TRUE	1	0.580919353550802	2		815	1099	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233090	69233090	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746910913	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	114	281	0	ENST00000462284.1:c.961del	p.Leu321PhefsTer52	p.L321Ffs*52	ENST00000462284	NM_002392.5	319	Ccc/cc	11/11	1	2	FACETS	0.996	0.905	1	0.996	0.905	1	CLONAL	1	TRUE	1	0.580919353550802	2		281	394	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020764	37020764	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	56	500	2	ENST00000358127.4:c.81del	p.Phe27LeufsTer2	p.F27Lfs*2	ENST00000358127	NM_001280556.1	27	ttT/tt	2/10	1	2	FACETS	0.266	0.227	0.308	0.266	0.227	0.308	SUBCLONAL	1	TRUE	1	0.580919353550802	2		502	725	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384651	31384651	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1512	86	705	0	ENST00000328111.2:c.1359del	p.Leu454SerfsTer136	p.L454Sfs*136	ENST00000328111	NM_006892.3	451	gaG/ga	13/23	0.580919353550802	4	FACETS	0.293	0.258	0.331	0.098	0.086	0.111	SUBCLONAL	1	TRUE	1	0.580919353550802	4		705	1598	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972820	25972820	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	131	464	0	ENST00000435504.4:c.1605del	p.Lys535AsnfsTer3	p.K535Nfs*3	ENST00000435504		535	aaA/aa	12/13	1	2	FACETS	0.82	0.747	0.896	0.82	0.747	0.896	CLONAL	1	TRUE	1	0.580919353550802	2		464	550	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936277	78936277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1476697249	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	246	693	1	ENST00000306801.3:c.3709C>T	p.Arg1237Cys	p.R1237C	ENST00000306801	NM_020761.2	1237	Cgc/Tgc	32/34	1	2	FACETS	0.826	0.773	0.882	0.826	0.773	0.882	CLONAL	1	TRUE	1	0.580919353550802	2		694	1025	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016565	12016565	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	89	283	0	ENST00000353533.5:c.701A>G	p.Asn234Ser	p.N234S	ENST00000353533	NM_003010.3	234	aAt/aGt	7/11	0.580919353550802	1	FACETS	0.921	0.831	1	0.921	0.831	1	CLONAL	1	TRUE	0	0.580919353550802	1		283	236	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217236	7217236	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs775804583	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	291	608	0	ENST00000380728.2:c.469del	p.Gln157LysfsTer188	p.Q157Kfs*188	ENST00000380728		157	Caa/aa	6/11	0.580919353550802	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.580919353550802	1		608	655	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272513	15272513	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	281	709	0	ENST00000263388.2:c.5926del	p.Leu1976TyrfsTer36	p.L1976Yfs*36	ENST00000263388	NM_000435.2	1976	Cta/ta	33/33	1	2	FACETS	0.951	0.895	1	0.951	0.895	1	CLONAL	1	TRUE	1	0.580919353550802	2		709	1017	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404237	139404237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200699541	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	65	955	2	ENST00000277541.6:c.2917G>A	p.Ala973Thr	p.A973T	ENST00000277541	NM_017617.3	973	Gca/Aca	18/34	1	2	FACETS	0.18	0.155	0.208	0.18	0.155	0.208	SUBCLONAL	1	TRUE	1	0.580919353550802	2		957	1240	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210689	36210689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754616271	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	298	686	0	ENST00000222270.7:c.440G>A	p.Arg147Gln	p.R147Q	ENST00000222270	NM_014727.1	147	cGa/cAa	3/37	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.580919353550802	2		686	994	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845550	151845550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753793539	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	224	609	0	ENST00000262189.6:c.13462G>A	p.Ala4488Thr	p.A4488T	ENST00000262189	NM_170606.2	4488	Gcc/Acc	52/59	1	2	FACETS	0.971	0.907	1	0.971	0.907	1	CLONAL	1	TRUE	1	0.580919353550802	2		609	794	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17359617	17359617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	131	321	1	ENST00000375499.3:c.224C>T	p.Ala75Val	p.A75V	ENST00000375499	NM_003000.2	75	gCt/gTt	3/8	1	2	FACETS	0.924	0.844	1	0.924	0.844	1	CLONAL	1	TRUE	1	0.580919353550802	2		322	488	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549043	21549043	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	134	296	0	ENST00000382592.4:c.3233A>G	p.Asp1078Gly	p.D1078G	ENST00000382592	NM_014572.2	1078	gAt/gGt	8/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.580919353550802	2		296	364	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779193	3779193	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	45	562	0	ENST00000262367.5:c.5855del	p.Pro1952LeufsTer24	p.P1952Lfs*24	ENST00000262367	NM_004380.2	1952	cCt/ct	31/31	1	2	FACETS	0.226	0.189	0.267	0.226	0.189	0.267	SUBCLONAL	1	TRUE	1	0.580919353550802	2		562	686	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811554	56811554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780253	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	122	383	0	ENST00000337432.4:c.1102C>T	p.Arg368Trp	p.R368W	ENST00000337432	NM_058216.2	368	Cgg/Tgg	9/9	1	2	FACETS	0.882	0.802	0.966	0.882	0.802	0.966	CLONAL	1	TRUE	1	0.580919353550802	2		383	476	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209117	36209117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	39	71	0	ENST00000222270.7:c.197C>T	p.Ala66Val	p.A66V	ENST00000222270	NM_014727.1	66	gCc/gTc	1/37	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.580919353550802	2		71	132	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637247	47637248	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs63750924	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	159	446	0	ENST00000233146.2:c.387_388del	p.Gln130ValfsTer2	p.Q130Vfs*2	ENST00000233146	NM_000251.2	127	aaTCtc/aatc	3/16	0.580919353550802	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.580919353550802	1		446	377	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098651	47098651	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	79	656	0	ENST00000409792.3:c.6623C>A	p.Pro2208His	p.P2208H	ENST00000409792	NM_014159.6	2208	cCc/cAc	15/21	1	2	FACETS	0.315	0.276	0.357	0.315	0.276	0.357	SUBCLONAL	1	TRUE	1	0.580919353550802	2		656	864	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014137	70014137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	179	493	0	ENST00000394351.3:c.998C>T	p.Ala333Val	p.A333V	ENST00000394351	NM_000248.3	333	gCa/gTa	9/9	1	2	FACETS	0.855	0.79	0.922	0.855	0.79	0.922	CLONAL	1	TRUE	1	0.580919353550802	2		493	721	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928292	178928292	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	157	464	0	ENST00000263967.3:c.1478A>G	p.Glu493Gly	p.E493G	ENST00000263967	NM_006218.2	493	gAa/gGa	9/21	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.580919353550802	2		464	508	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589600	67589600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	44	187	0	ENST00000274335.5:c.1363C>T	p.Gln455Ter	p.Q455*	ENST00000274335		455	Cag/Tag	10/15	1	2	FACETS	0.929	0.793	1	0.929	0.793	1	CLONAL	1	TRUE	1	0.580919353550802	2		187	163	SUCCESS
APC	324	MSKCC	GRCh37	5	112174845	112174845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780595	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	67	185	0	ENST00000257430.4:c.3554C>T	p.Thr1185Ile	p.T1185I	ENST00000257430	NM_000038.5	1185	aCa/aTa	16/16	0.580919353550802	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.580919353550802	1		185	156	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32819925	32819925	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	361	706	2	ENST00000354258.4:c.985C>A	p.Leu329Met	p.L329M	ENST00000354258	NM_000593.5	329	Ctg/Atg	3/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.580919353550802	2		708	1126	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	80	617	0	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	1	FACETS	0.956	0.847	1	0.956	0.847	1	CLONAL	1	TRUE	0	0.346644303074163	1		617	399	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	166	486	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.346644303074163	2		489	738	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	72	292	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.994	0.872	1	0.994	0.872	1	CLONAL	1	TRUE	1	0.346644303074163	2		292	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	30	654	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.19	0.152	0.234	0.19	0.152	0.234	SUBCLONAL	1	TRUE	1	0.346644303074163	2		654	909	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	350	985	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	1	0.346644303074163	2		991	827	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	185	857	12	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.346644303074163	2		869	906	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	78	1018	4	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.405	0.355	0.46	0.405	0.355	0.46	SUBCLONAL	1	TRUE	1	0.346644303074163	2		1022	1111	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	162	852	2	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	0.983	0.901	1	0.983	0.901	1	CLONAL	1	TRUE	1	0.346644303074163	2		854	951	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	85	264	2	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	0.097278145829474	3	FACETS	0.773	0.688	0.863	0.773	0.688	0.863	INDETERMINATE	2	TRUE	1	0.346644303074163	3		266	372	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084145	47084146	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	89	432	0	ENST00000409792.3:c.7143dup	p.Ser2382LeufsTer47	p.S2382Lfs*47	ENST00000409792	NM_014159.6	2381	-/C	17/21	1	2	FACETS	0.805	0.714	0.902	0.805	0.714	0.902	CLONAL	1	TRUE	1	0.346644303074163	2		432	638	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798105	32798105	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1562326716	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	97	779	0	ENST00000374899.4:c.1574del	p.Gly525AspfsTer36	p.G525Dfs*36	ENST00000374899	NM_018833.2	525	gGa/ga	9/12	1	2	FACETS	0.597	0.531	0.668	0.597	0.531	0.668	SUBCLONAL	1	TRUE	1	0.346644303074163	2		779	937	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986893	36986893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1310962672	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	170	442	0	ENST00000354822.5:c.796G>A	p.Gly266Ser	p.G266S	ENST00000354822	NM_001079668.2	266	Ggc/Agc	3/3	1	2	FACETS	0.903	0.836	0.972	1	0.992	1	CLONAL	2	TRUE	1	0.346644303074163	2		442	543	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866439	42866439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61735791	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	211	900	1	ENST00000398585.3:c.193G>A	p.Ala65Thr	p.A65T	ENST00000398585	NM_001135099.1	65	Gca/Aca	3/14	0.0465731849680351	3	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.346644303074163	3		901	1078	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370903	55370903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	174	723	0	ENST00000297316.4:c.205C>T	p.Arg69Trp	p.R69W	ENST00000297316	NM_022454.3	69	Cgg/Tgg	1/2	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.346644303074163	2		723	803	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103755	47103756	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	111	427	2	ENST00000409792.3:c.6190_6191del	p.Asp2064ProfsTer8	p.D2064Pfs*8	ENST00000409792	NM_014159.6	2064	GAc/c	14/21	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.346644303074163	2		429	635	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789591	3789591	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	29	377	0	ENST00000262367.5:c.4268del	p.Pro1423LeufsTer36	p.P1423Lfs*36	ENST00000262367	NM_004380.2	1423	cCt/ct	25/31	1	2	FACETS	0.322	0.257	0.395	0.322	0.257	0.395	SUBCLONAL	1	TRUE	1	0.346644303074163	2		377	520	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952084	178952084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913281	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	64	336	1	ENST00000263967.3:c.3139C>T	p.His1047Tyr	p.H1047Y	ENST00000263967	NM_006218.2	1047	Cat/Tat	21/21	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.346644303074163	2		337	341	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	225	826	5	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.346644303074163	2		831	961	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	175	810	1	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.346644303074163	2		811	786	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	79	422	3	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.346644303074163	2		425	411	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	136	454	0	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.346644303074163	2		454	561	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412648	63412648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	163	333	2	ENST00000330258.3:c.519del	p.Phe173LeufsTer36	p.F173Lfs*36	ENST00000330258	NM_152424.3	173	ttT/tt	2/2	1	1	FACETS	1	0.936	1	1	0.993	1	CLONAL	2	TRUE	0	0.346644303074163	1		335	386	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933593	39933594	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	138	336	0	ENST00000378444.4:c.1005dup	p.Ser336LeufsTer45	p.S336Lfs*45	ENST00000378444	NM_001123385.1	335	-/C	4/15	1	1	FACETS	0.922	0.85	0.995	1	0.991	1	CLONAL	2	TRUE	0	0.346644303074163	1		336	357	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166916	32166916	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	142	863	1	ENST00000375023.3:c.4322del	p.Pro1441LeufsTer17	p.P1441Lfs*17	ENST00000375023	NM_004557.3	1441	cCt/ct	24/30	1	2	FACETS	0.684	0.622	0.75	0.684	0.622	0.75	SUBCLONAL	1	TRUE	1	0.346644303074163	2		864	1197	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	77	307	0	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	0.992	0.874	1	0.992	0.874	1	CLONAL	1	TRUE	1	0.346644303074163	2		307	448	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835781	68835781	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1060501215	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	107	463	3	ENST00000261769.5:c.377del	p.Pro126ArgfsTer89	p.P126Rfs*89	ENST00000261769	NM_004360.3	124	cgC/cg	3/16	1	2	FACETS	0.825	0.74	0.915	0.825	0.74	0.915	CLONAL	1	TRUE	1	0.346644303074163	2		466	748	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428247	47428247	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	176	382	0	ENST00000377045.4:c.1207A>G	p.Met403Val	p.M403V	ENST00000377045	NM_001654.4	403	Atg/Gtg	11/16	1	1	FACETS	0.918	0.855	0.983	1	0.993	1	CLONAL	2	TRUE	0	0.346644303074163	1		382	457	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511172	148511172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554486390	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	46	577	1	ENST00000320356.2:c.1730C>T	p.Pro577Leu	p.P577L	ENST00000320356	NM_004456.4	577	cCg/cTg	15/20	1	2	FACETS	0.348	0.292	0.41	0.348	0.292	0.41	SUBCLONAL	1	TRUE	1	0.346644303074163	2		578	762	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998756	100998756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749674024	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	206	749	0	ENST00000325455.5:c.1046C>T	p.Ser349Leu	p.S349L	ENST00000325455	NM_001202474.3	349	tCg/tTg	1/8	1	2	FACETS	0.816	0.76	0.874	1	0.992	1	CLONAL	2	TRUE	1	0.346644303074163	2		749	728	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100999	41100999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1371429276	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	117	652	4	ENST00000373198.4:c.1357C>T	p.Arg453Cys	p.R453C	ENST00000373198	NM_133170.3	453	Cgc/Tgc	8/32	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.346644303074163	2		656	585	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998627	100998629	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	rs751489196	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	124	675	1	ENST00000325455.5:c.1173_1175del	p.Glu392del	p.E392del	ENST00000325455	NM_001202474.3	391	gaGGAa/gaa	1/8	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.346644303074163	2		676	688	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17350503	17350503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201517260	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	120	574	1	ENST00000375499.3:c.607G>A	p.Gly203Arg	p.G203R	ENST00000375499	NM_003000.2	203	Gga/Aga	6/8	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.346644303074163	2		575	683	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340450	8340450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200354236	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	83	427	0	ENST00000356435.5:c.5146G>A	p.Ala1716Thr	p.A1716T	ENST00000356435		1716	Gct/Act	31/35	1	2	FACETS	0.919	0.813	1	0.919	0.813	1	CLONAL	1	TRUE	1	0.346644303074163	2		427	521	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025596	1025596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770234586	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	172	784	0	ENST00000358495.3:c.779G>A	p.Arg260Gln	p.R260Q	ENST00000358495	NM_134424.2	260	cGg/cAg	9/12	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.346644303074163	2		784	895	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152104	11152104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377573682	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	136	519	0	ENST00000358026.2:c.4388G>A	p.Arg1463His	p.R1463H	ENST00000358026	NM_001128849.1	1463	cGc/cAc	31/36	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.346644303074163	2		519	646	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209457	98209457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753535745	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	148	868	0	ENST00000331920.6:c.4081G>A	p.Val1361Met	p.V1361M	ENST00000331920	NM_000264.3	1361	Gtg/Atg	23/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.346644303074163	2		868	712	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231585	5231585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779378586	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	100	397	1	ENST00000357368.4:c.1891C>T	p.Arg631Cys	p.R631C	ENST00000357368	NM_002850.3	631	Cgc/Tgc	14/38	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.346644303074163	2		398	419	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	180	922	1	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.346644303074163	2		923	938	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906370	50906370	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs749601227	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	87	925	9	ENST00000440232.2:c.1036del	p.Glu346SerfsTer47	p.E346Sfs*47	ENST00000440232	NM_002691.3	344	tGg/tg	9/27	1	2	FACETS	0.595	0.526	0.67	0.595	0.526	0.67	SUBCLONAL	1	TRUE	1	0.346644303074163	2		934	843	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	rs267608078	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	29	383	0	ENST00000234420.5:c.3260_3261dup	p.Phe1088ProfsTer3	p.F1088Pfs*3	ENST00000234420	NM_000179.2	1085	acc/aCCcc	5/10	1	2	FACETS	0.304	0.243	0.373	0.304	0.243	0.373	SUBCLONAL	1	TRUE	1	0.346644303074163	2		383	551	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798511	32798511	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs765335850	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	62	680	0	ENST00000374899.4:c.1345C>T	p.Arg449Ter	p.R449*	ENST00000374899	NM_018833.2	449	Cga/Tga	8/12	1	2	FACETS	0.381	0.328	0.439	0.381	0.328	0.439	SUBCLONAL	1	TRUE	1	0.346644303074163	2		680	940	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56878487	56878487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752264053	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	117	381	0	ENST00000308159.5:c.2426C>T	p.Ala809Val	p.A809V	ENST00000308159	NM_014669.4	809	gCg/gTg	22/22	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.346644303074163	2		381	612	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998256	100998256	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	89	362	0	ENST00000325455.5:c.1546G>A	p.Gly516Ser	p.G516S	ENST00000325455	NM_001202474.3	516	Ggc/Agc	1/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.346644303074163	2		362	399	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149465987	149465987	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	224	922	1	ENST00000286301.3:c.4G>A	p.Gly2Ser	p.G2S	ENST00000286301	NM_005211.3	2	Ggc/Agc	2/22	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.346644303074163	2		923	1030	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376248	15376248	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	56	396	2	ENST00000263377.2:c.766del	p.Gln256SerfsTer27	p.Q256Sfs*27	ENST00000263377	NM_058243.2	256	Cag/ag	5/20	1	2	FACETS	0.839	0.722	0.967	0.839	0.722	0.967	CLONAL	1	TRUE	1	0.346644303074163	2		398	385	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756628	756628	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	133	439	0	ENST00000314574.4:c.200G>T	p.Gly67Val	p.G67V	ENST00000314574	NM_005433.3	67	gGg/gTg	2/12	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.346644303074163	2		439	563	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817720	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	81	335	2	ENST00000262367.5:c.3250dup	p.Ile1084AsnfsTer3	p.I1084Nfs*3	ENST00000262367	NM_004380.2	1084	atc/aAtc		1	2	FACETS	0.933	0.824	1	0.933	0.824	1	CLONAL	1	TRUE	1	0.346644303074163	2		337	501	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372202	55372202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764648837	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	144	539	3	ENST00000297316.4:c.892G>A	p.Gly298Ser	p.G298S	ENST00000297316	NM_022454.3	298	Ggc/Agc	2/2	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.346644303074163	2		542	579	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25462047	25462047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1202038704	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	41	541	1	ENST00000264709.3:c.2360C>T	p.Ala787Val	p.A787V	ENST00000264709	NM_175629.2	787	gCt/gTt	20/23	1	2	FACETS	0.329	0.273	0.391	0.329	0.273	0.391	SUBCLONAL	1	TRUE	1	0.346644303074163	2		542	720	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741678	17741678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	181	500	0	ENST00000250003.3:c.349C>T	p.Arg117Cys	p.R117C	ENST00000250003	NM_002478.4	117	Cgc/Tgc	1/3	1	2	FACETS	0.842	0.781	0.906	1	0.992	1	CLONAL	2	TRUE	1	0.346644303074163	2		500	620	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117191	7117191	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	176	712	4	ENST00000302850.5:c.4025del	p.Gly1342AlafsTer23	p.G1342Afs*23	ENST00000302850	NM_000208.2	1342	gGc/gc	22/22	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.346644303074163	2		716	737	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214710	36214710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	37	708	0	ENST00000222270.7:c.3136C>T	p.Arg1046Cys	p.R1046C	ENST00000222270	NM_014727.1	1046	Cgc/Tgc	8/37	1	2	FACETS	0.361	0.296	0.433	0.361	0.296	0.433	SUBCLONAL	1	TRUE	1	0.346644303074163	2		708	592	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294907	1294907	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	29	105	0	ENST00000310581.5:c.198del	p.Ala67ProfsTer11	p.A67Pfs*11	ENST00000310581	NM_198253.2	66	ccC/cc	1/16	0.346644303074163	1	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	0	0.346644303074163	1		105	131	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150042	202150042	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs768000891	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	223	487	0	ENST00000358485.4:c.1481+2T>C		p.X494_splice	ENST00000358485	NM_001080125.1	494			0.346644303074163	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.346644303074163	2		487	619	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941110	36941110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	112	684	0	ENST00000361632.4:c.229C>T	p.Arg77Cys	p.R77C	ENST00000361632		77	Cgt/Tgt	3/16	1	2	FACETS	0.876	0.788	0.968	0.876	0.788	0.968	CLONAL	1	TRUE	1	0.346644303074163	2		684	738	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830746	156830746	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1286464365	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	36	156	0	ENST00000524377.1:c.20G>A	p.Arg7His	p.R7H	ENST00000524377	NM_002529.3	7	cGc/cAc	1/17	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.346644303074163	2		156	189	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64126849	64126849	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	104	783	1	ENST00000334205.4:c.56-1G>A		p.X19_splice	ENST00000334205	NM_003942.2	19			1	2	FACETS	0.772	0.691	0.858	0.772	0.691	0.858	SUBCLONAL	1	TRUE	1	0.346644303074163	2		784	777	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946922	71946922	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773078981	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	175	797	0	ENST00000298229.2:c.2771C>T	p.Ala924Val	p.A924V	ENST00000298229	NM_001567.3	924	gCc/gTc	25/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.346644303074163	2		797	849	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195818	102195818	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	38	337	0	ENST00000263464.3:c.578G>A	p.Gly193Asp	p.G193D	ENST00000263464	NM_001165.4	193	gGc/gAc	2/9	1	2	FACETS	0.483	0.399	0.577	0.483	0.399	0.577	SUBCLONAL	1	TRUE	1	0.346644303074163	2		337	454	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432290	432290	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769805545	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	120	526	0	ENST00000399788.2:c.2233C>T	p.Arg745Cys	p.R745C	ENST00000399788	NM_001042603.1	745	Cgt/Tgt	16/28	1	2	FACETS	0.982	0.888	1	0.982	0.888	1	CLONAL	1	TRUE	1	0.346644303074163	2		526	705	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988412	36988412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1049229039	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	140	427	1	ENST00000354822.5:c.241G>A	p.Ala81Thr	p.A81T	ENST00000354822	NM_001079668.2	81	Gcg/Acg	2/3	1	2	FACETS	0.854	0.783	0.927	1	0.99	1	CLONAL	2	TRUE	1	0.346644303074163	2		428	473	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36989269	36989269	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	169	727	0	ENST00000354822.5:c.66del	p.Gly23AlafsTer11	p.G23Afs*11	ENST00000354822	NM_001079668.2	22	ccC/cc	1/3	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.346644303074163	2		727	720	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714236	43714237	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	186	764	0	ENST00000382044.4:c.3916dup	p.Asp1306GlyfsTer64	p.D1306Gfs*64	ENST00000382044	NM_001141980.1	1306	gat/gGat	19/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.346644303074163	2		764	893	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639594	3639594	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555450055	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	181	955	0	ENST00000294008.3:c.4045G>A	p.Gly1349Arg	p.G1349R	ENST00000294008	NM_032444.2	1349	Ggg/Agg	12/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.346644303074163	2		955	912	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644494	3644494	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555450869	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	180	785	0	ENST00000294008.3:c.2120A>G	p.Lys707Arg	p.K707R	ENST00000294008	NM_032444.2	707	aAg/aGg	10/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.346644303074163	2		785	908	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734125	58734125	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	75	535	0	ENST00000305921.3:c.1183C>A	p.Leu395Met	p.L395M	ENST00000305921	NM_003620.3	395	Ctg/Atg	5/6	1	2	FACETS	0.599	0.524	0.679	0.599	0.524	0.679	SUBCLONAL	1	TRUE	1	0.346644303074163	2		535	723	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244460	5244460	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	88	877	1	ENST00000357368.4:c.1022C>T	p.Thr341Ile	p.T341I	ENST00000357368	NM_002850.3	341	aCt/aTt	11/38	1	2	FACETS	0.61	0.54	0.686	0.61	0.54	0.686	SUBCLONAL	1	TRUE	1	0.346644303074163	2		878	832	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290999	15290999	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760205888	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	208	973	2	ENST00000263388.2:c.3211G>A	p.Val1071Met	p.V1071M	ENST00000263388	NM_000435.2	1071	Gtg/Atg	20/33	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.346644303074163	2		975	928	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919715	50919715	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	154	1022	0	ENST00000440232.2:c.2883G>C	p.Gln961His	p.Q961H	ENST00000440232	NM_002691.3	961	caG/caC	23/27	1	2	FACETS	0.965	0.883	1	0.965	0.883	1	CLONAL	1	TRUE	1	0.346644303074163	2		1022	921	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018202	48018202	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	60	530	1	ENST00000234420.5:c.402del	p.Phe134LeufsTer15	p.F134Lfs*15	ENST00000234420	NM_000179.2	133	Ttt/tt	2/10	1	2	FACETS	0.47	0.404	0.542	0.47	0.404	0.542	SUBCLONAL	1	TRUE	1	0.346644303074163	2		531	736	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663058	227663058	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs758241055	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	264	562	0	ENST00000305123.5:c.397G>T	p.Gly133Trp	p.G133W	ENST00000305123	NM_005544.2	133	Ggg/Tgg	1/2	0.346644303074163	2	FACETS	0.883	0.836	0.931	1	0.993	1	CLONAL	3	TRUE	0	0.346644303074163	2		562	575	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181359	185181359	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	18	252	0	ENST00000265026.3:c.1305del	p.Lys435AsnfsTer16	p.K435Nfs*16	ENST00000265026	NM_004721.4	434	Aaa/aa	8/14	1	2	FACETS	0.292	0.219	0.378	0.292	0.219	0.378	SUBCLONAL	1	TRUE	1	0.346644303074163	2		252	356	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582135	189582135	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1560274255	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	131	441	1	ENST00000264731.3:c.699del	p.Ala234LeufsTer8	p.A234Lfs*8	ENST00000264731	NM_003722.4	232	Aaa/aa	5/14	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.346644303074163	2		442	670	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803235	1803235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866735516	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	175	836	1	ENST00000260795.2:c.587G>A	p.Arg196His	p.R196H	ENST00000260795		196	cGc/cAc	4/17	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.346644303074163	2		837	839	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554941	187554941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	56	368	0	ENST00000441802.2:c.4220G>A	p.Gly1407Glu	p.G1407E	ENST00000441802	NM_005245.3	1407	gGa/gAa	7/27	1	2	FACETS	0.625	0.536	0.722	0.625	0.536	0.722	SUBCLONAL	1	TRUE	1	0.346644303074163	2		368	517	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797842	32797842	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	67	412	0	ENST00000374899.4:c.1660del	p.Val554CysfsTer7	p.V554Cfs*7	ENST00000374899	NM_018833.2	554	Gtg/tg	10/12	1	2	FACETS	0.839	0.731	0.955	0.839	0.731	0.955	CLONAL	1	TRUE	1	0.346644303074163	2		412	461	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677854	117677854	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	55	258	0	ENST00000368508.3:c.4079T>C	p.Ile1360Thr	p.I1360T	ENST00000368508	NM_002944.2	1360	aTc/aCc	25/43	1	2	FACETS	0.904	0.777	1	0.904	0.777	1	CLONAL	1	TRUE	1	0.346644303074163	2		258	351	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860788	151860788	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	94	406	0	ENST00000262189.6:c.9874C>T	p.Pro3292Ser	p.P3292S	ENST00000262189	NM_170606.2	3292	Cca/Tca	43/59	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.346644303074163	2		406	431	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938436	76938436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376906761	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	102	235	0	ENST00000373344.5:c.2312C>T	p.Ala771Val	p.A771V	ENST00000373344	NM_000489.3	771	gCg/gTg	9/35	1	1	FACETS	0.822	0.745	0.901	1	0.986	1	CLONAL	2	TRUE	0	0.346644303074163	1		235	296	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152864474	152864474	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs1557027764	NA	P-0046739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	17	44	0	ENST00000406277.2:c.52C>A	p.Pro18Thr	p.P18T	ENST00000406277	NM_152274.4	18	Ccg/Acg	3/7	NA		FACETS		NA	1				INDETERMINATE	NA	TRUE	NA	0.346644303074163	NA		44	56	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0046740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	368	744	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.693009037748003	1	FACETS	0.924	0.883	0.965	0.924	0.883	0.965	CLONAL	1	TRUE	0	0.693009037748003	1		744	751	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123722	11123722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263140481	NA	P-0046740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	354	723	0	ENST00000358026.2:c.2372C>T	p.Ala791Val	p.A791V	ENST00000358026	NM_001128849.1	791	gCg/gTg	16/36	0.693009037748003	1	FACETS	0.921	0.879	0.963	0.921	0.879	0.963	CLONAL	1	TRUE	0	0.693009037748003	1		723	725	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995569	68995569	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	444	557	0	ENST00000288368.4:c.1973C>A	p.Ser658Ter	p.S658*	ENST00000288368	NM_024870.2	658	tCg/tAg	18/40	0.638252059392733	2	FACETS	0.921	0.889	0.952	0.921	0.889	0.952	CLONAL	2	TRUE	0	0.693009037748003	2		557	696	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934152	48934152	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0046740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	131	234	0	ENST00000267163.4:c.610del		p.X204_splice	ENST00000267163	NM_000321.2	204			0.693009037748003	1	FACETS	0.977	0.906	1	0.977	0.906	1	CLONAL	1	TRUE	0	0.693009037748003	1		234	253	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241906	72241906	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	378	336	0	ENST00000357731.5:c.484G>T	p.Ala162Ser	p.A162S	ENST00000357731	NM_173808.2	162	Gcc/Tcc	3/7	0.693009037748003	2	FACETS	0.937	0.903	0.971	0.937	0.903	0.971	CLONAL	2	TRUE	0	0.693009037748003	2		336	582	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682999	241683028	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	GAGGAGCCGAAGTGCTCGGTACATGGTGCT	GAGGAGCCGAAGTGCTCGGTACATGGTGCT	-	novel	NA	P-0046740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	104	633	0	ENST00000366560.3:c.-6_24del		p.*2*	ENST00000366560	NM_000143.3	?-8/510		1/10	0.515861277553304	1	FACETS	0.182	0.162	0.203	0.182	0.162	0.203	SUBCLONAL	1	TRUE	0	0.693009037748003	1		633	1076	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604677	43604677	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	400	636	0	ENST00000355710.3:c.1262A>T	p.Gln421Leu	p.Q421L	ENST00000355710	NM_020975.4	421	cAg/cTg	6/20	0.693009037748003	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.693009037748003	1		636	711	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663186	227663186	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs748457020	NA	P-0046740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	707	913	0	ENST00000305123.5:c.269A>G	p.Asp90Gly	p.D90G	ENST00000305123	NM_005544.2	90	gAc/gGc	1/2	0.652125763513431	2	FACETS	0.895	0.87	0.92	0.895	0.87	0.92	CLONAL	2	TRUE	0	0.693009037748003	2		913	1140	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0046742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	184	325	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.524913241568776	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	0	0.61080115599768	3		325	254	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0046742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	15	279	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.28048884465276	2	FACETS	0.259	0.189	0.341	0.129	0.094	0.171	INDETERMINATE	1	TRUE	0	0.61080115599768	2		279	190	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0046742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	90	239	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.28048884465276	2	FACETS	1	0.983	1	0.726	0.659	0.794	INDETERMINATE	1	TRUE	0	0.61080115599768	2		239	203	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0046742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	463	812	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.598006101726034	2	FACETS	0.951	0.917	0.985	0.951	0.917	0.985	CLONAL	2	TRUE	0	0.61080115599768	2		812	797	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937904	36937904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1386293956	NA	P-0046742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	217	1005	0	ENST00000361632.4:c.932G>A	p.Arg311His	p.R311H	ENST00000361632		311	cGc/cAc	7/16	1	2	FACETS	0.814	0.758	0.872	0.814	0.758	0.872	CLONAL	1	TRUE	1	0.61080115599768	2		1005	873	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625219	69625219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	380	960	0	ENST00000334134.2:c.574C>T	p.Arg192Trp	p.R192W	ENST00000334134	NM_005247.2	192	Cgg/Tgg	3/3	0.28048884465276	2	FACETS	0.751	0.718	0.785	0.751	0.718	0.785	INDETERMINATE	2	TRUE	0	0.61080115599768	2		960	828	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683654	162684449	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CACCCGAGTCAAGCTCTGGGGCTCCCGCTCACAGCCTCCCGCCGCGTTTCTGGGGTCGTCGCCTCCAGTTGCATTCATTTCTTGACCTTTTCTCCACGGTCTCTGCACAATGTGAACAATGCTCTGCTGATCCAGGTCACAATTCTGTTTGGGAGCAAGGTAAAAAAAAAAAAAAAAAAAAAGGAAATGTCAAACATGAAATGCGAGATAGAGTTTAACTTGCCCTCCGTGGTAGAAGGGAAGCAAAAGTGACATGTAACTGACCAACTTAGGTGCTCCTTTGCCCACAGCAGTTACACACTACACACGGTAGACAAACAACACTGAACTGGGGCCAGAAACAGAAATTTGGGAATACGTGAAACACAATAGAATGCTGACGTCATATTCAAAAGGACATAAAATCTAGCAGGAAAAAATAATTACCAAACTGGATCTATAAGCACAGTGAAAACAATAATTCCTTTTTTCCCCCCAAGACAGAGTCTCACTCTGTCATCCAGGCTGGAGTGCAGTGGTGTGATTTCCGCTCATTGCAACCTCTGCCTGCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTATAGGCGGGCACCACCACACCTGGCTACGAAAAATATTCTTAAATAGTAAAACTGATTGACATCAGAATTGATATGTCATTCATCTCTGTTTTACAAAAGTACAGAAAGTGAGTTATTATCAATGAGAGGGCATTTCTTTAAAGCATCGGAAATGAATGCGTTTGAGTAGGCTCCACACACACCGCTCCACGGGCACCA	CACCCGAGTCAAGCTCTGGGGCTCCCGCTCACAGCCTCCCGCCGCGTTTCTGGGGTCGTCGCCTCCAGTTGCATTCATTTCTTGACCTTTTCTCCACGGTCTCTGCACAATGTGAACAATGCTCTGCTGATCCAGGTCACAATTCTGTTTGGGAGCAAGGTAAAAAAAAAAAAAAAAAAAAAGGAAATGTCAAACATGAAATGCGAGATAGAGTTTAACTTGCCCTCCGTGGTAGAAGGGAAGCAAAAGTGACATGTAACTGACCAACTTAGGTGCTCCTTTGCCCACAGCAGTTACACACTACACACGGTAGACAAACAACACTGAACTGGGGCCAGAAACAGAAATTTGGGAATACGTGAAACACAATAGAATGCTGACGTCATATTCAAAAGGACATAAAATCTAGCAGGAAAAAATAATTACCAAACTGGATCTATAAGCACAGTGAAAACAATAATTCCTTTTTTCCCCCCAAGACAGAGTCTCACTCTGTCATCCAGGCTGGAGTGCAGTGGTGTGATTTCCGCTCATTGCAACCTCTGCCTGCCGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTATAGGCGGGCACCACCACACCTGGCTACGAAAAATATTCTTAAATAGTAAAACTGATTGACATCAGAATTGATATGTCATTCATCTCTGTTTTACAAAAGTACAGAAAGTGAGTTATTATCAATGAGAGGGCATTTCTTTAAAGCATCGGAAATGAATGCGTTTGAGTAGGCTCCACACACACCGCTCCACGGGCACCA	-	novel	NA	P-0046742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	35	577	0	ENST00000366898.1:c.172-652_315del		p.X58_splice	ENST00000366898	NM_004562.2	58		3/12	0.576054154000237	2	FACETS	0.238	0.195	0.287	0.119	0.097	0.144	SUBCLONAL	1	TRUE	0	0.61080115599768	2		577	481	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	109	427	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.936	0.848	1	0.936	0.848	1	CLONAL	1	TRUE	1	0.613008833205739	2		427	380	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023696	27023696	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	175	656	0	ENST00000324856.7:c.802C>T	p.Gln268Ter	p.Q268*	ENST00000324856	NM_006015.4	268	Cag/Tag	1/20	0.564124585496628	1	FACETS	0.713	0.661	0.767	0.713	0.661	0.767	SUBCLONAL	1	TRUE	0	0.613008833205739	1		656	555	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983114	201983114	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	375	662	1	ENST00000359651.3:c.963del	p.Asn321LysfsTer4	p.N321Kfs*4	ENST00000359651		321	aaC/aa	7/8	0.522440620351911	2	FACETS	0.971	0.933	1	0.971	0.933	1	CLONAL	2	TRUE	0	0.613008833205739	2		663	630	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390691	118390691	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	91	339	0	ENST00000534358.1:c.11343del	p.Phe3781LeufsTer26	p.F3781Lfs*26	ENST00000534358	NM_005933.3	3781	Ttt/tt	33/36	1	2	FACETS	0.839	0.751	0.93	0.839	0.751	0.93	CLONAL	1	TRUE	1	0.613008833205739	2		339	354	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060821	38060822	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	417	999	0	ENST00000250448.2:c.1167dup	p.Gly390ArgfsTer25	p.G390Rfs*25	ENST00000250448	NM_004496.3	389	-/A	2/2	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.613008833205739	2		999	1257	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89842150	89842150	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1222254954	NA	P-0046752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	83	559	0	ENST00000389301.3:c.1900G>A	p.Asp634Asn	p.D634N	ENST00000389301	NM_000135.2	634	Gat/Aat	21/43	0.613008833205739	3	FACETS	0.489	0.431	0.551	0.244	0.215	0.276	SUBCLONAL	1	TRUE	1	0.613008833205739	3		559	724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578538	7578538	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	254	863	1	ENST00000269305.4:c.392A>C	p.Asn131Thr	p.N131T	ENST00000269305	NM_001126112.2	131	aAc/aCc	5/11	0.59358458931446	1	FACETS	0.902	0.85	0.955	0.902	0.85	0.955	CLONAL	1	TRUE	0	0.613008833205739	1		864	637	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412947	49412947	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	217	678	0	ENST00000418115.1:c.76A>C	p.Ser26Arg	p.S26R	ENST00000418115	NM_001664.2	26	Agc/Cgc	2/5	1	2	FACETS	0.969	0.904	1	0.969	0.904	1	CLONAL	1	TRUE	1	0.613008833205739	2		678	731	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908892	101908892	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0046752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	121	497	0	ENST00000374994.4:c.1255+1G>T		p.X419_splice	ENST00000374994	NM_004612.2	419			0.613008833205739	1	FACETS	0.789	0.721	0.858	0.789	0.721	0.858	SUBCLONAL	1	TRUE	0	0.613008833205739	1		497	347	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942708	44942708	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	118	412	0	ENST00000377967.4:c.3288G>A	p.Trp1096Ter	p.W1096*	ENST00000377967	NM_021140.2	1096	tgG/tgA	23/29	0.613008833205739	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.613008833205739	1		412	252	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	99	424	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.522083058461784	2		424	369	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993860	72993860	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs62639999	NA	P-0046753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	60	607	0	ENST00000268489.5:c.185C>T	p.Ala62Val	p.A62V	ENST00000268489	NM_006885.3	62	gCg/gTg	2/10	1	2	FACETS	0.354	0.304	0.408	0.354	0.304	0.408	SUBCLONAL	1	TRUE	1	0.522083058461784	2		607	650	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203492	108203492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs138941496	NA	P-0046753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	43	149	0	ENST00000278616.4:c.7792C>T	p.Arg2598Ter	p.R2598*	ENST00000278616	NM_000051.3	2598	Cga/Tga	53/63	0.522083058461784	3	FACETS	0.936	0.791	1	0.468	0.395	0.547	CLONAL	1	TRUE	1	0.522083058461784	3		149	222	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205774	108205774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555127177	NA	P-0046753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	169	289	0	ENST00000278616.4:c.8089A>G	p.Asn2697Asp	p.N2697D	ENST00000278616	NM_000051.3	2697	Aat/Gat	55/63	0.522083058461784	3	FACETS	0.947	0.88	1	0.947	0.88	1	CLONAL	2	TRUE	1	0.522083058461784	3		289	431	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207089	1207090	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0046753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	394	876	0	ENST00000326873.7:c.178_179dup	p.Gly61ThrfsTer4	p.G61Tfs*4	ENST00000326873	NM_000455.4	59	-/TA	1/10	0.522083058461784	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.522083058461784	1		876	987	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326437	62326437	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765060195	NA	P-0046753-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	341	1013	0	ENST00000360203.5:c.3362G>A	p.Arg1121His	p.R1121H	ENST00000360203	NM_001283009.1	1121	cGt/cAt	33/35	1	2	FACETS	0.984	0.93	1	0.984	0.93	1	CLONAL	1	TRUE	1	0.522083058461784	2		1013	1328	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	168	381	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.534625835516183	2		381	447	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	172	745	12	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.534625835516183	2		757	625	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	181	1071	8	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.709	0.654	0.766	0.709	0.654	0.766	SUBCLONAL	1	TRUE	1	0.534625835516183	2		1079	955	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	110	355	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.534625835516183	2		355	367	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913837	32913837	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359507	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	144	309	1	ENST00000380152.3:c.5351del	p.Asn1784ThrfsTer7	p.N1784Tfs*7	ENST00000380152		1782	cAa/ca	11/27	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.534625835516183	2		310	443	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	28	382	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.301	0.24	0.37	0.301	0.24	0.37	SUBCLONAL	1	TRUE	1	0.534625835516183	2		382	348	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	246	985	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.534625835516183	2		991	718	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	45	303	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	1	2	FACETS	0.523	0.441	0.612	0.523	0.441	0.612	SUBCLONAL	1	TRUE	1	0.534625835516183	2		303	322	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024001	27024002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	34	98	0	ENST00000324856.7:c.1113dup	p.Gln372AlafsTer28	p.Q372Afs*28	ENST00000324856	NM_006015.4	369	-/G	1/20	1	2	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	1	0.534625835516183	2		98	123	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438316	110438317	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTT	rs532810290	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	39	217	0	ENST00000375856.3:c.82_84dup	p.Asn28dup	p.N28dup	ENST00000375856	NM_003749.2	28	-/AAC	1/2	1	2	FACETS	0.6	0.501	0.709	0.6	0.501	0.709	SUBCLONAL	1	TRUE	1	0.534625835516183	2		217	243	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968322	2968323	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs762770988	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	161	569	0	ENST00000396946.4:c.1663dup	p.Arg555ProfsTer38	p.R555Pfs*38	ENST00000396946	NM_032415.4	555	cgg/cCgg	13/25	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.534625835516183	2		569	552	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541541	187541541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs980333559	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	41	306	0	ENST00000441802.2:c.6199G>A	p.Val2067Met	p.V2067M	ENST00000441802	NM_005245.3	2067	Gtg/Atg	10/27	1	2	FACETS	0.443	0.37	0.524	0.443	0.37	0.524	SUBCLONAL	1	TRUE	1	0.534625835516183	2		306	346	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	271	857	12	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.534625835516183	2		869	807	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	217	1018	4	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.971	0.905	1	0.971	0.905	1	CLONAL	1	TRUE	1	0.534625835516183	2		1022	836	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288710	15288710	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	13	97	0	ENST00000263388.2:c.4029del	p.Cys1344ValfsTer76	p.C1344Vfs*76	ENST00000263388	NM_000435.2	1343	ccC/cc	24/33	1	2	FACETS	0.593	0.43	0.785	0.593	0.43	0.785	SUBCLONAL	1	TRUE	1	0.534625835516183	2		97	82	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646085	215646085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	170	446	1	ENST00000260947.4:c.513del	p.Asp172MetfsTer40	p.D172Mfs*40	ENST00000260947	NM_000465.2	171	aaA/aa	4/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.534625835516183	2		447	579	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444659	78444659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs908264837	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	30	348	0	ENST00000370768.2:c.30del	p.Ser11LeufsTer43	p.S11Lfs*43	ENST00000370768	NM_003902.3	10	ccC/cc	1/20	1	2	FACETS	0.263	0.211	0.321	0.263	0.211	0.321	SUBCLONAL	1	TRUE	1	0.534625835516183	2		348	427	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211795	2211795	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	251	847	3	ENST00000398665.3:c.1516del	p.Gln506SerfsTer51	p.Q506Sfs*51	ENST00000398665	NM_032482.2	504	aCc/ac	16/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.534625835516183	2		850	837	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163553	32163554	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs777647776	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	63	736	1	ENST00000375023.3:c.5672dup	p.Gly1892ArgfsTer24	p.G1892Rfs*24	ENST00000375023	NM_004557.3	1891	ggc/ggGc	30/30	1	2	FACETS	0.403	0.348	0.462	0.403	0.348	0.462	SUBCLONAL	1	TRUE	1	0.534625835516183	2		737	585	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760024	133760024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	97	891	1	ENST00000318560.5:c.2352del	p.Arg785GlyfsTer3	p.R785Gfs*3	ENST00000318560	NM_005157.4	783	Ccc/cc	11/11	1	2	FACETS	0.455	0.405	0.508	0.455	0.405	0.508	SUBCLONAL	1	TRUE	1	0.534625835516183	2		892	797	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	103	903	4	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	1	2	FACETS	0.465	0.416	0.518	0.465	0.416	0.518	SUBCLONAL	1	TRUE	1	0.534625835516183	2		907	828	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466039	69466041	+	inframe_deletion	In_Frame_Del	DEL	GTG	GTG	-	novel	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	229	955	0	ENST00000227507.2:c.878_880del	p.Val293del	p.V293del	ENST00000227507	NM_053056.2	293	GTG/-	5/5	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.534625835516183	2		955	751	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346157	89346158	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs878855327	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	32	318	1	ENST00000301030.4:c.6792dup	p.Ala2265ArgfsTer8	p.A2265Rfs*8	ENST00000301030	NM_001256183.1	2264	-/C	9/13	1	2	FACETS	0.335	0.272	0.406	0.335	0.272	0.406	SUBCLONAL	1	TRUE	1	0.534625835516183	2		319	357	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088681	27088682	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	209	706	0	ENST00000324856.7:c.2296dup	p.Gln766ProfsTer51	p.Q766Pfs*51	ENST00000324856	NM_006015.4	764	tcc/tCcc	7/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.534625835516183	2		706	702	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70005612	70005614	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs1553704814	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	82	242	0	ENST00000394351.3:c.649_651del	p.Arg217del	p.R217del	ENST00000394351	NM_000248.3	214	cGAAga/cga	7/9	1	2	FACETS	0.845	0.751	0.945	0.845	0.751	0.945	CLONAL	1	TRUE	1	0.534625835516183	2		242	363	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112884083	112884083	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs79203122	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	171	442	1	ENST00000351677.2:c.18G>T	p.Trp6Cys	p.W6C	ENST00000351677	NM_002834.3	6	tgG/tgT	2/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.534625835516183	2		443	540	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041262	29041262	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	47	361	0	ENST00000282397.4:c.166del	p.Glu56LysfsTer12	p.E56Kfs*12	ENST00000282397	NM_002019.4	56	Gaa/aa	3/30	1	2	FACETS	0.473	0.4	0.552	0.473	0.4	0.552	SUBCLONAL	1	TRUE	1	0.534625835516183	2		361	372	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118943	70118943	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555629158	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	57	844	0	ENST00000245479.2:c.515A>G	p.Tyr172Cys	p.Y172C	ENST00000245479	NM_000346.3	172	tAc/tGc	2/3	1	2	FACETS	0.255	0.218	0.296	0.255	0.218	0.296	SUBCLONAL	1	TRUE	1	0.534625835516183	2		844	835	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30326004	30326005	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs769517721	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	67	197	0	ENST00000322652.5:c.2208dup	p.Gln737ThrfsTer20	p.Q737Tfs*20	ENST00000322652	NM_015355.2	734	-/A	16/16	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.534625835516183	2		197	227	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942195	71942195	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	92	749	0	ENST00000298229.2:c.1463del	p.Gly488AlafsTer43	p.G488Afs*43	ENST00000298229	NM_001567.3	487	Ggg/gg	12/28	1	2	FACETS	0.49	0.435	0.549	0.49	0.435	0.549	SUBCLONAL	1	TRUE	1	0.534625835516183	2		749	702	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088709	27088709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373690941	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	222	664	0	ENST00000324856.7:c.2318C>T	p.Pro773Leu	p.P773L	ENST00000324856	NM_006015.4	773	cCg/cTg	7/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.534625835516183	2		664	649	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821875	72821875	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	166	445	1	ENST00000268489.5:c.10300del	p.Leu3434SerfsTer51	p.L3434Sfs*51	ENST00000268489	NM_006885.3	3434	Ctc/tc	10/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.534625835516183	2		446	515	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528284	157528284	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs749055122	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	91	597	0	ENST00000346085.5:c.6013del	p.Val2005TrpfsTer16	p.V2005Wfs*16	ENST00000346085	NM_020732.3	2003	aaG/aa	20/20	1	2	FACETS	0.473	0.42	0.53	0.473	0.42	0.53	SUBCLONAL	1	TRUE	1	0.534625835516183	2		597	720	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518740	176518740	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1369223288	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	275	873	0	ENST00000292408.4:c.658G>A	p.Gly220Ser	p.G220S	ENST00000292408	NM_213647.1	220	Ggc/Agc	6/18	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.534625835516183	2		873	792	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180049806	180049806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs557205062	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	228	825	2	ENST00000261937.6:c.1582G>A	p.Val528Met	p.V528M	ENST00000261937	NM_182925.4	528	Gtg/Atg	12/30	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.534625835516183	2		827	681	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820901	36820901	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	67	647	0	ENST00000373129.3:c.476T>C	p.Leu159Pro	p.L159P	ENST00000373129	NM_032017.1	159	cTg/cCg	6/12	1	2	FACETS	0.403	0.35	0.46	0.403	0.35	0.46	SUBCLONAL	1	TRUE	1	0.534625835516183	2		647	622	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843662	156843662	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	260	967	0	ENST00000524377.1:c.1088C>T	p.Ala363Val	p.A363V	ENST00000524377	NM_002529.3	363	gCt/gTt	8/17	0.45560555485441	5	FACETS	1	0.988	1	0.307	0.287	0.328	CLONAL	1	TRUE	1	0.534625835516183	5		967	1427	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711908	89711913	+	inframe_deletion	In_Frame_Del	DEL	TATTAT	TATTAT	-	novel	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	92	423	0	ENST00000371953.3:c.529_534del	p.Tyr177_Tyr178del	p.Y177_Y178del	ENST00000371953	NM_000314.4	176	TATTAT/-	6/9	1	2	FACETS	0.86	0.77	0.956	0.86	0.77	0.956	CLONAL	1	TRUE	1	0.534625835516183	2		423	400	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325056	123325056	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	131	589	0	ENST00000358487.5:c.272A>G	p.Tyr91Cys	p.Y91C	ENST00000358487	NM_000141.4	91	tAc/tGc	3/18	1	2	FACETS	0.771	0.701	0.843	0.771	0.701	0.843	SUBCLONAL	1	TRUE	1	0.534625835516183	2		589	636	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129217	64129217	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs757236334	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	221	830	0	ENST00000334205.4:c.755G>A	p.Arg252Gln	p.R252Q	ENST00000334205	NM_003942.2	252	cGa/cAa	7/17	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.534625835516183	2		830	730	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344797	118344797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782295708	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	39	282	0	ENST00000534358.1:c.2923G>A	p.Asp975Asn	p.D975N	ENST00000534358	NM_005933.3	975	Gac/Aac	3/36	1	2	FACETS	0.482	0.401	0.571	0.482	0.401	0.571	SUBCLONAL	1	TRUE	1	0.534625835516183	2		282	303	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256158	133256158	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	179	520	1	ENST00000320574.5:c.503A>G	p.Lys168Arg	p.K168R	ENST00000320574	NM_006231.2	168	aAg/aGg	6/49	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.534625835516183	2		521	469	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222314	2222314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1285744402	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	251	920	0	ENST00000326181.6:c.603del	p.Ile202SerfsTer44	p.I202Sfs*44	ENST00000326181	NM_032271.2	200	Ccc/cc	8/21	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.534625835516183	2		920	851	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660457	67660457	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	47	298	0	ENST00000264010.4:c.1358-1G>A		p.X453_splice	ENST00000264010	NM_006565.3	453			1	2	FACETS	0.446	0.377	0.522	0.446	0.377	0.522	SUBCLONAL	1	TRUE	1	0.534625835516183	2		298	394	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832376	72832376	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	54	418	2	ENST00000268489.5:c.4205G>A	p.Arg1402His	p.R1402H	ENST00000268489	NM_006885.3	1402	cGc/cAc	9/10	1	2	FACETS	0.442	0.378	0.512	0.442	0.378	0.512	SUBCLONAL	1	TRUE	1	0.534625835516183	2		420	457	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676183	29676183	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	33	238	0	ENST00000356175.3:c.7175del	p.Leu2392TyrfsTer5	p.L2392Yfs*5	ENST00000356175	NM_000267.3	2391	aTt/at	48/57	1	2	FACETS	0.364	0.297	0.44	0.364	0.297	0.44	SUBCLONAL	1	TRUE	1	0.534625835516183	2		238	339	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676212	29676212	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	51	269	0	ENST00000356175.3:c.7203del	p.Lys2401AsnfsTer10	p.K2401Nfs*10	ENST00000356175	NM_000267.3	2401	Aaa/aa	48/57	1	2	FACETS	0.547	0.466	0.634	0.547	0.466	0.634	SUBCLONAL	1	TRUE	1	0.534625835516183	2		269	349	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244251	5244251	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	99	944	0	ENST00000357368.4:c.1231G>T	p.Gly411Trp	p.G411W	ENST00000357368	NM_002850.3	411	Ggg/Tgg	11/38	1	2	FACETS	0.41	0.365	0.458	0.41	0.365	0.458	SUBCLONAL	1	TRUE	1	0.534625835516183	2		944	903	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948775	17948775	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	258	783	0	ENST00000458235.1:c.1667A>C	p.Lys556Thr	p.K556T	ENST00000458235	NM_000215.3	556	aAg/aCg	12/24	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.534625835516183	2		783	735	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229458	36229458	+	stop_lost	Nonstop_Mutation	SNP	A	A	C	novel	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	88	438	0	ENST00000222270.7:c.8148A>C	p.Ter2716CysextTer47	p.*2716Cext*47	ENST00000222270	NM_014727.1	2716	tgA/tgC	37/37	1	2	FACETS	0.791	0.705	0.882	0.791	0.705	0.882	SUBCLONAL	1	TRUE	1	0.534625835516183	2		438	416	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765609	41765609	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	166	703	0	ENST00000301178.4:c.2485G>T	p.Gly829Cys	p.G829C	ENST00000301178	NM_021913.4	829	Ggt/Tgt	20/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.534625835516183	2		703	603	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919891	50919891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762280958	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	251	1055	0	ENST00000440232.2:c.2978C>T	p.Thr993Met	p.T993M	ENST00000440232	NM_002691.3	993	aCg/aTg	24/27	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.534625835516183	2		1055	810	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686277	30686277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	40	326	0	ENST00000295754.5:c.133G>A	p.Val45Ile	p.V45I	ENST00000295754	NM_003242.5	45	Gtc/Atc	2/7	1	2	FACETS	0.399	0.332	0.473	0.399	0.332	0.473	SUBCLONAL	1	TRUE	1	0.534625835516183	2		326	375	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952137	178952137	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	27	215	0	ENST00000263967.3:c.3192G>T	p.Gln1064His	p.Q1064H	ENST00000263967	NM_006218.2	1064	caG/caT	21/21	1	2	FACETS	0.395	0.315	0.485	0.395	0.315	0.485	SUBCLONAL	1	TRUE	1	0.534625835516183	2		215	256	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158519	26158519	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	73	479	0	ENST00000289316.2:c.122A>T	p.Tyr41Phe	p.Y41F	ENST00000289316	NM_138720.2	41	tAt/tTt	1/2	1	2	FACETS	0.525	0.46	0.595	0.525	0.46	0.595	SUBCLONAL	1	TRUE	1	0.534625835516183	2		479	520	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166715	32166715	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	155	919	0	ENST00000375023.3:c.4523G>A	p.Ser1508Asn	p.S1508N	ENST00000375023	NM_004557.3	1508	aGc/aAc	24/30	1	2	FACETS	0.654	0.598	0.712	0.654	0.598	0.712	SUBCLONAL	1	TRUE	1	0.534625835516183	2		919	887	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268082	55268082	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	233	696	0	ENST00000275493.2:c.2926del	p.Gln976SerfsTer26	p.Q976Sfs*26	ENST00000275493	NM_005228.3	974	gaC/ga	24/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.534625835516183	2		696	773	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739027	145739027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750126506	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	182	747	0	ENST00000428558.2:c.2128C>T	p.Arg710Cys	p.R710C	ENST00000428558	NM_004260.3	710	Cgc/Tgc	13/22	1	2	FACETS	0.991	0.918	1	0.991	0.918	1	CLONAL	1	TRUE	1	0.534625835516183	2		747	687	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223698	53223698	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	338	952	0	ENST00000375401.3:c.3661A>G	p.Ser1221Gly	p.S1221G	ENST00000375401	NM_004187.3	1221	Agc/Ggc	23/26	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.534625835516183	2		952	931	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409939	63409940	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0046754-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	148	566	0	ENST00000330258.3:c.3226_3227dup	p.Pro1077SerfsTer54	p.P1077Sfs*54	ENST00000330258	NM_152424.3	1076	aag/aaAAg	2/2	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.534625835516183	2		566	506	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521660	89521660	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	221	427	0	ENST00000336596.2:c.2737T>A	p.Phe913Ile	p.F913I	ENST00000336596	NM_005233.5	913	Ttc/Atc	16/17	0.628512798952696	2	FACETS	0.905	0.859	0.95	0.905	0.859	0.95	CLONAL	2	TRUE	0	0.663689657770577	2		427	368	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0046755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	395	409	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.459500074153804	6	FACETS	0.966	0.941	0.99			1	CLONAL	6	TRUE	NA	0.663689657770577	6		410	478	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211757	2211757	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	175	827	1	ENST00000398665.3:c.1473C>G	p.Phe491Leu	p.F491L	ENST00000398665	NM_032482.2	491	ttC/ttG	16/28	0.112115162092363	6	FACETS	0.953	0.881	1			1	INDETERMINATE	2	TRUE	NA	0.663689657770577	6		828	644	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	436	1050	0	ENST00000269305.4:c.461del	p.Gly154AlafsTer16	p.G154Afs*16	ENST00000269305	NM_001126112.2	154	gGc/gc	5/11	0.649696452117965	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.663689657770577	2		1050	657	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602872	10602872	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	613	1020	0	ENST00000171111.5:c.706G>T	p.Asp236Tyr	p.D236Y	ENST00000171111	NM_203500.1	236	Gac/Tac	3/6	0.663689657770577	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.663689657770577	2		1020	809	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340937	70340937	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	258	654	0	ENST00000374080.3:c.670C>A	p.His224Asn	p.H224N	ENST00000374080		224	Cat/Aat	5/45	0.24083101158224	5	FACETS	1	0.981	1	0.73	0.688	0.774	INDETERMINATE	2	TRUE	2	0.663689657770577	5		654	708	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30099962	30099962	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	92	421	0	ENST00000331968.5:c.1658G>T	p.Gly553Val	p.G553V	ENST00000331968	NM_002742.2	553	gGa/gTa	10/18	0.575747192500534	4	FACETS	0.815	0.726	0.91	0.407	0.363	0.455	CLONAL	1	TRUE	2	0.663689657770577	4		421	566	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222372	2222372	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	271	902	0	ENST00000326181.6:c.656G>C	p.Arg219Pro	p.R219P	ENST00000326181	NM_032271.2	219	cGg/cCg	8/21	0.535093019133133	3	FACETS	0.923	0.874	0.972	0.923	0.874	0.972	CLONAL	2	TRUE	1	0.663689657770577	3		902	589	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684320	29684320	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	29	410	1	ENST00000356175.3:c.7840G>T	p.Asp2614Tyr	p.D2614Y	ENST00000356175	NM_000267.3	2614	Gat/Tat	53/57	0.461460257710709	2	FACETS	0.301	0.242	0.368	0.151	0.121	0.184	SUBCLONAL	1	TRUE	0	0.663689657770577	2		411	290	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210818	2210818	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	104	525	0	ENST00000398665.3:c.1315C>G	p.Gln439Glu	p.Q439E	ENST00000398665	NM_032482.2	439	Cag/Gag	14/28	0.112115162092363	6	FACETS	0.905	0.816	0.997			1	INDETERMINATE	2	TRUE	NA	0.663689657770577	6		525	403	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462411	89462411	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	190	469	0	ENST00000336596.2:c.1883G>T	p.Gly628Val	p.G628V	ENST00000336596	NM_005233.5	628	gGa/gTa	10/17	0.628512798952696	2	FACETS	0.862	0.813	0.911	0.862	0.813	0.911	CLONAL	2	TRUE	0	0.663689657770577	2		469	332	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866618	117866618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	82	353	0	ENST00000297338.2:c.1027G>A	p.Asp343Asn	p.D343N	ENST00000297338	NM_006265.2	343	Gat/Aat	9/14	0.663689657770577	4	FACETS	0.76	0.671	0.854	0.253	0.223	0.285	SUBCLONAL	1	TRUE	1	0.663689657770577	4		353	541	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737642	145737642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	586	1035	1	ENST00000428558.2:c.3121G>A	p.Gly1041Arg	p.G1041R	ENST00000428558	NM_004260.3	1041	Ggg/Agg	19/22	0.663689657770577	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	1	0.663689657770577	4		1036	914	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376063	8376063	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	19	223	0	ENST00000356435.5:c.4534A>G	p.Arg1512Gly	p.R1512G	ENST00000356435		1512	Aga/Gga	28/35	0.663689657770577	2	FACETS	0.259	0.197	0.332	0.13	0.098	0.166	SUBCLONAL	1	TRUE	0	0.663689657770577	2		223	221	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123040972	123040972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046755-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	25	178	0	ENST00000355640.3:c.1435G>A	p.Asp479Asn	p.D479N	ENST00000355640		479	Gac/Aac	7/7	0.24083101158224	5	FACETS	1	0.924	1	0.456	0.366	0.555	INDETERMINATE	1	TRUE	2	0.663689657770577	5		178	110	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956676	93956676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465960814	NA	P-0046756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	100	211	0	ENST00000369303.4:c.2560C>T	p.Arg854Cys	p.R854C	ENST00000369303	NM_004440.3	854	Cgt/Tgt	15/17	0.572918437753443	1	FACETS	0.791	0.715	0.869	0.791	0.715	0.869	SUBCLONAL	1	TRUE	0	0.572918437753443	1		211	315	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562649	21562649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	295	414	0	ENST00000382592.4:c.1270C>T	p.Pro424Ser	p.P424S	ENST00000382592	NM_014572.2	424	Ccc/Tcc	4/8	0.572918437753443	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.572918437753443	1		414	695	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658857	3658857	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	239	364	0	ENST00000294008.3:c.109A>C	p.Ser37Arg	p.S37R	ENST00000294008	NM_032444.2	37	Agc/Cgc	2/15	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.572918437753443	2		364	828	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832052	72832052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	227	357	0	ENST00000268489.5:c.4529C>T	p.Ser1510Phe	p.S1510F	ENST00000268489	NM_006885.3	1510	tCt/tTt	9/10	1	2	FACETS	0.944	0.882	1	0.944	0.882	1	CLONAL	1	TRUE	1	0.572918437753443	2		357	839	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258991	153258992	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0046756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	50	155	1	ENST00000281708.4:c.823_824del	p.Gln275ValfsTer11	p.Q275Vfs*11	ENST00000281708	NM_033632.3	275	CAg/g	5/12	0.572918437753443	1	FACETS	0.809	0.7	0.922	0.809	0.7	0.922	CLONAL	1	TRUE	0	0.572918437753443	1		156	154	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0046757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	65	357	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.430209143736359	4	FACETS	1	0.956	1	0.615	0.536	0.699	CLONAL	1	TRUE	2	0.459083273432381	4		357	336	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0046757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	89	239	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.408446871918748	2	FACETS	0.941	0.853	1	0.941	0.853	1	CLONAL	2	TRUE	0	0.459083273432381	2		239	206	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052713	42052716	+	frameshift_variant	Frame_Shift_Del	DEL	CTCA	CTCA	-	novel	NA	P-0046757-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	118	344	0	ENST00000219905.7:c.7384_7387del	p.Leu2462PhefsTer12	p.L2462Ffs*12	ENST00000219905	NM_001164273.1	2462	CTCAtt/tt	20/24	0.369773952130882	4	FACETS	0.904	0.822	0.989	0.904	0.822	0.989	CLONAL	2	TRUE	2	0.459083273432381	4		344	415	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	186	427	0				ENST00000310581	NM_198253.2	-/1132			0.305181194440931	5	FACETS	1	0.984	1	0.798	0.743	0.854	INDETERMINATE	2	TRUE	2	0.569383059051066	5		427	506	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400019	49400019	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	194	519	0	ENST00000418115.1:c.318C>G	p.Phe106Leu	p.F106L	ENST00000418115	NM_001664.2	106	ttC/ttG	4/5	0.41717200636006	4	FACETS	1	0.985	1	0.416	0.385	0.448	CLONAL	1	TRUE	1	0.569383059051066	4		519	857	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1555525367	NA	P-0046758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	417	537	0	ENST00000269305.4:c.783-1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.569383059051066	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.569383059051066	3		537	610	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741363	17741363	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	517	894	0	ENST00000250003.3:c.34G>C	p.Asp12His	p.D12H	ENST00000250003	NM_002478.4	12	Gac/Cac	1/3	0.569383059051066	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.569383059051066	2		894	823	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378607	25378607	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	175	374	0	ENST00000311936.3:c.391C>A	p.Gln131Lys	p.Q131K	ENST00000311936	NM_004985.3	131	Cag/Aag	4/5	0.569383059051066	2	FACETS	0.888	0.832	0.944	0.888	0.832	0.944	CLONAL	2	TRUE	0	0.569383059051066	2		374	346	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416137	49416137	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0046758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	212	312	0	ENST00000301067.7:c.16339-1G>C		p.X5447_splice	ENST00000301067	NM_003482.3	5447			0.569383059051066	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.569383059051066	2		312	357	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42050023	42050023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	55	239	0	ENST00000219905.7:c.7177G>A	p.Glu2393Lys	p.E2393K	ENST00000219905	NM_001164273.1	2393	Gaa/Aaa	19/24	1	2	FACETS	0.74	0.639	0.849	0.74	0.639	0.849	SUBCLONAL	1	TRUE	1	0.569383059051066	2		239	261	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020368	69020368	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs769267089	NA	P-0046758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	81	380	0	ENST00000288368.4:c.2740G>T	p.Ala914Ser	p.A914S	ENST00000288368	NM_024870.2	914	Gcc/Tcc	24/40	0.367282922510656	6	FACETS	0.818	0.72	0.923	0.273	0.24	0.308	CLONAL	1	TRUE	3	0.569383059051066	6		380	744	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413014	63413014	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	89	440	0	ENST00000330258.3:c.153G>C	p.Arg51Ser	p.R51S	ENST00000330258	NM_152424.3	51	agG/agC	2/2	0.397092619276397	2	FACETS	0.555	0.493	0.621			1	SUBCLONAL	1	TRUE	NA	0.569383059051066	2		440	563	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197821	123197822	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0046758-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	180	166	0	ENST00000218089.9:c.1947_1948del	p.Arg649SerfsTer11	p.R649Sfs*11	ENST00000218089	NM_001042749.1	649	AGa/a	20/35	0.397092619276397	2	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.569383059051066	2		166	268	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	231	486	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.972	1	1	0.996	1	CLONAL	5	TRUE	1	0.154632935339693	2		489	565	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	77	292	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.893	1	1	0.987	1	CLONAL	3	TRUE	1	0.154632935339693	2		292	329	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	345	985	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.981	1	1	0.997	1	CLONAL	6	TRUE	1	0.154632935339693	2		991	707	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738411	145738416	+	inframe_deletion	In_Frame_Del	DEL	GGTGCA	GGTGCA	-	rs548804317	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	144	870	0	ENST00000428558.2:c.2569_2574del	p.Cys857_Thr858del	p.C857_T858del	ENST00000428558	NM_004260.3	857	TGCACC/-	16/22	0.154632935339693	7	FACETS	1	0.962	1	0.553	0.503	0.605	CLONAL	2	TRUE	3	0.154632935339693	7		870	1168	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	60	927	6	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.154632935339693	2		933	755	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030323	180030323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745546499	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	209	841	3	ENST00000261937.6:c.3961C>T	p.Arg1321Trp	p.R1321W	ENST00000261937	NM_182925.4	1321	Cgg/Tgg	30/30	1	2	FACETS	0.96	0.891	1	1	0.995	1	CLONAL	3	TRUE	1	0.154632935339693	2		844	939	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661664	227661664	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs761880048	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	136	612	8	ENST00000305123.5:c.1791del	p.His598ThrfsTer38	p.H598Tfs*38	ENST00000305123	NM_005544.2	597	ggG/gg	1/2	1	2	FACETS	1	0.946	1	1	0.993	1	CLONAL	3	TRUE	1	0.154632935339693	2		620	559	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593507	48593507	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1367209662	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	102	207	1	ENST00000342988.3:c.1258C>T	p.Arg420Cys	p.R420C	ENST00000342988	NM_005359.5	420	Cgt/Tgt	10/12	0.154632935339693	0	FACETS	0.996	0.904	1			1	CLONAL	4	TRUE	0	0.154632935339693	0		208	280	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176330	24176330	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1057517825	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	135	740	0	ENST00000263121.7:c.1121G>A	p.Arg374Gln	p.R374Q	ENST00000263121	NM_003073.3	374	cGg/cAg	9/9	1	2	FACETS	1	0.953	1	1	0.991	1	CLONAL	2	TRUE	1	0.154632935339693	2		740	813	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781901	3781903	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs751071525	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	177	533	0	ENST00000262367.5:c.4764_4766del	p.Lys1588del	p.K1588del	ENST00000262367	NM_004380.2	1588	aaGAAc/aac	29/31	1	2	FACETS	1	0.965	1	1	0.994	1	CLONAL	3	TRUE	1	0.154632935339693	2		533	710	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998169	100998169	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1252920750	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	62	413	1	ENST00000325455.5:c.1633C>A	p.Leu545Met	p.L545M	ENST00000325455	NM_001202474.3	545	Ctg/Atg	1/8	1	2	FACETS	0.946	0.82	1	1	0.978	1	CLONAL	2	TRUE	1	0.154632935339693	2		414	424	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870205	155870205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs563231684	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	126	422	0	ENST00000368323.3:c.634C>T	p.Arg212Trp	p.R212W	ENST00000368323	NM_006912.5	212	Cgg/Tgg	6/6	1	2	FACETS	1	0.96	1	1	0.992	1	CLONAL	3	TRUE	1	0.154632935339693	2		422	496	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713386	40713386	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	173	652	1	ENST00000373198.4:c.4129C>T	p.Arg1377Ter	p.R1377*	ENST00000373198	NM_133170.3	1377	Cga/Tga	30/32	1	2	FACETS	1	0.954	1	1	0.994	1	CLONAL	3	TRUE	1	0.154632935339693	2		653	713	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936307	49936307	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	158	476	0	ENST00000296474.3:c.1541G>T	p.Gly514Val	p.G514V	ENST00000296474	NM_002447.2	514	gGg/gTg	3/20	1	2	FACETS	0.907	0.836	0.981	1	0.994	1	CLONAL	4	TRUE	1	0.154632935339693	2		476	563	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188297	32188297	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs753855314	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	153	719	0	ENST00000375023.3:c.1044del	p.Gly349AlafsTer49	p.G349Afs*49	ENST00000375023	NM_004557.3	348	ggC/gg	6/30	1	2	FACETS	1	0.974	1	1	0.992	1	CLONAL	2	TRUE	1	0.154632935339693	2		719	853	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346220	152346220	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	111	440	7	ENST00000359321.1:c.350del	p.Leu117TrpfsTer17	p.L117Wfs*17	ENST00000359321	NM_005431.1	117	tTg/tg	3/3	1	2	FACETS	1	0.944	1	1	0.991	1	CLONAL	3	TRUE	1	0.154632935339693	2		447	451	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289272	33289272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751031043	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	132	409	0	ENST00000374542.5:c.280C>T	p.Arg94Cys	p.R94C	ENST00000374542	NM_001141970.1	94	Cgt/Tgt	3/8	1	2	FACETS	0.942	0.862	1	1	0.993	1	CLONAL	4	TRUE	1	0.154632935339693	2		409	453	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016675	12016675	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	74	198	1	ENST00000353533.5:c.811G>A	p.Ala271Thr	p.A271T	ENST00000353533	NM_003010.3	271	Gca/Aca	7/11	1	2	FACETS	1	0.936	1	1	0.987	1	CLONAL	3	TRUE	1	0.154632935339693	2		199	293	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	191	852	2	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	0.935	0.865	1	1	0.994	1	CLONAL	3	TRUE	1	0.154632935339693	2		854	881	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29106023	29106023	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587782152	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	75	228	1	ENST00000328354.6:c.817G>T	p.Glu273Ter	p.E273*	ENST00000328354	NM_007194.3	273	Gaa/Taa	7/15	1	2	FACETS	0.846	0.746	0.953	1	0.986	1	CLONAL	3	TRUE	1	0.154632935339693	2		229	382	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128246746	128246746	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	116	460	0	ENST00000265960.3:c.1183C>T	p.Arg395Ter	p.R395*	ENST00000265960	NM_001006617.1	395	Cga/Tga	9/12	0.154632935339693	3	FACETS	1	0.957	1	0.741	0.668	0.818	CLONAL	2	TRUE	0	0.154632935339693	3		460	727	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43730536	43730536	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	131	372	0	ENST00000382044.4:c.3177del	p.Thr1060ProfsTer36	p.T1060Pfs*36	ENST00000382044	NM_001141980.1	1059	ccC/cc	16/28	1	2	FACETS	0.993	0.904	1	1	0.992	1	CLONAL	3	TRUE	1	0.154632935339693	2		372	569	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858929	57858929	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	222	581	1	ENST00000228682.2:c.429del	p.Ser146ArgfsTer19	p.S146Rfs*19	ENST00000228682	NM_005269.2	142	cAa/ca	5/12	1	2	FACETS	0.967	0.904	1	1	0.996	1	CLONAL	4	TRUE	1	0.154632935339693	2		582	742	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138097	2138097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45517392	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	239	829	0	ENST00000219476.3:c.5117G>A	p.Arg1706His	p.R1706H	ENST00000219476	NM_000548.3	1706	cGc/cAc	40/42	1	2	FACETS	1	0.984	1	1	0.996	1	CLONAL	3	TRUE	1	0.154632935339693	2		829	886	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272238	15272238	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs760917811	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	316	757	1	ENST00000263388.2:c.6201del	p.Lys2069ArgfsTer16	p.K2069Rfs*16	ENST00000263388	NM_000435.2	2067	ccC/cc	33/33	0.154632935339693	5	FACETS	1	0.976	1	1	0.992	1	CLONAL	6	TRUE	0	0.154632935339693	5		758	801	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158637067	158637068	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	rs141073095	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	130	494	3	ENST00000263640.3:c.111_112dup	p.Glu38ValfsTer21	p.E38Vfs*21	ENST00000263640	NM_001105.4	38	gaa/gTGaa	4/11	1	2	FACETS	0.843	0.766	0.923	1	0.991	1	CLONAL	3	TRUE	1	0.154632935339693	2		497	665	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461564	138461564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202220571	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	93	366	0	ENST00000289153.2:c.457C>T	p.Arg153Cys	p.R153C	ENST00000289153	NM_006219.2	153	Cgc/Tgc	3/22	1	2	FACETS	1	0.902	1	1	0.989	1	CLONAL	3	TRUE	1	0.154632935339693	2		366	398	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182662919	182662919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451035070	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	43	351	0	ENST00000292782.4:c.743G>A	p.Arg248His	p.R248H	ENST00000292782	NM_020640.2	248	cGc/cAc	7/7	0.154632935339693	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.154632935339693	1		351	394	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653405	206653405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782442134	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	227	738	0	ENST00000367120.3:c.1289G>A	p.Arg430Gln	p.R430Q	ENST00000367120	NM_014002.3	430	cGg/cAg	12/22	1	2	FACETS	1	0.983	1	1	0.996	1	CLONAL	3	TRUE	1	0.154632935339693	2		738	848	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085894	16085894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398902296	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	22	373	0	ENST00000281043.3:c.1070G>A	p.Arg357His	p.R357H	ENST00000281043	NM_005378.4	357	cGt/cAt	3/3	0.154632935339693	1	FACETS	0.713	0.552	0.901	0.713	0.552	0.901	CLONAL	1	TRUE	0	0.154632935339693	1		373	368	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258520	19258520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376625415	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	376	798	1	ENST00000162023.5:c.380G>A	p.Arg127Gln	p.R127Q	ENST00000162023		127	cGa/cAa	8/13	0.154632935339693	5	FACETS	0.939	0.893	0.986	1	0.989	1	CLONAL	6	TRUE	0	0.154632935339693	5		799	1063	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186598	108186598	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	63	234	0	ENST00000278616.4:c.6055T>C	p.Tyr2019His	p.Y2019H	ENST00000278616	NM_000051.3	2019	Tat/Cat	41/63	1	2	FACETS	1	0.896	1	1	0.985	1	CLONAL	3	TRUE	1	0.154632935339693	2		234	264	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225519	133225519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143229302	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	155	558	2	ENST00000320574.5:c.4145G>A	p.Arg1382His	p.R1382H	ENST00000320574	NM_006231.2	1382	cGc/cAc	32/49	1	2	FACETS	1	0.976	1	1	0.994	1	CLONAL	3	TRUE	1	0.154632935339693	2		560	577	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176618907	176618907	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs967342981	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	91	290	0	ENST00000439151.2:c.950C>T	p.Thr317Met	p.T317M	ENST00000439151	NM_022455.4	317	aCg/aTg	3/23	1	2	FACETS	0.878	0.783	0.977	1	0.988	1	CLONAL	3	TRUE	1	0.154632935339693	2		290	447	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639236	3639236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs574214196	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	225	747	2	ENST00000294008.3:c.4403G>A	p.Arg1468His	p.R1468H	ENST00000294008	NM_032444.2	1468	cGc/cAc	12/15	1	2	FACETS	1	0.982	1	1	0.996	1	CLONAL	3	TRUE	1	0.154632935339693	2		749	847	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969982	161969983	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs745647746	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	150	501	1	ENST00000366898.1:c.986dup	p.Val330ArgfsTer17	p.V330Rfs*17	ENST00000366898	NM_004562.2	329	ggc/ggGc	9/12	0.135556214347996	3	FACETS	0.879	0.804	0.957	1	0.984	1	CLONAL	3	TRUE	1	0.154632935339693	3		502	793	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982082	70982082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	157	610	0	ENST00000276594.2:c.14G>A	p.Arg5Gln	p.R5Q	ENST00000276594	NM_024504.3	5	cGg/cAg	2/8	0.154632935339693	3	FACETS	0.918	0.842	0.998	1	0.986	1	CLONAL	3	TRUE	1	0.154632935339693	3		610	794	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357101	89357101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	231	664	1	ENST00000301030.4:c.533G>A	p.Arg178His	p.R178H	ENST00000301030	NM_001256183.1	178	cGc/cAc	6/13	1	2	FACETS	0.901	0.842	0.962	1	0.996	1	CLONAL	4	TRUE	1	0.154632935339693	2		665	829	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22417991	22417991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756680625	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	17	34	0	ENST00000344548.3:c.557G>A	p.Arg186His	p.R186H	ENST00000344548	NM_001039802.1	186	cGc/cAc	7/7	1	2	FACETS	0.936	0.73	1	1	0.953	1	CLONAL	5	TRUE	1	0.154632935339693	2		34	47	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46736427	46736427	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	126	411	1	ENST00000371975.4:c.1139G>T	p.Arg380Leu	p.R380L	ENST00000371975	NM_003579.3	380	cGg/cTg	10/18	1	2	FACETS	1	0.966	1	1	0.992	1	CLONAL	3	TRUE	1	0.154632935339693	2		412	484	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098420	108098420	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	61	217	0	ENST00000278616.4:c.71del	p.Lys24ArgfsTer10	p.K24Rfs*10	ENST00000278616	NM_000051.3	23	cgA/cg	2/63	1	2	FACETS	0.929	0.809	1	1	0.983	1	CLONAL	3	TRUE	1	0.154632935339693	2		217	283	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499733	18499733	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	74	263	0	ENST00000266497.5:c.1588T>C	p.Tyr530His	p.Y530H	ENST00000266497		530	Tat/Cat	10/31	1	2	FACETS	0.941	0.83	1	1	0.986	1	CLONAL	3	TRUE	1	0.154632935339693	2		263	339	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443653	49443653	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs773215579	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	179	599	0	ENST00000301067.7:c.3718A>G	p.Met1240Val	p.M1240V	ENST00000301067	NM_003482.3	1240	Atg/Gtg	11/54	1	2	FACETS	1	0.976	1	1	0.994	1	CLONAL	3	TRUE	1	0.154632935339693	2		599	682	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28963972	28963972	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	169	269	0	ENST00000282397.4:c.1930G>C	p.Gly644Arg	p.G644R	ENST00000282397	NM_002019.4	644	Ggg/Cgg	13/30	0.154632935339693	6	FACETS	1	0.953	1	1	0.99	1	CLONAL	7	TRUE	1	0.154632935339693	6		269	397	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396682	396682	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	154	584	0	ENST00000262320.3:c.344T>C	p.Leu115Pro	p.L115P	ENST00000262320	NM_003502.3	115	cTg/cCg	2/11	1	2	FACETS	1	0.97	1	1	0.994	1	CLONAL	3	TRUE	1	0.154632935339693	2		584	597	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821665	72821665	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781747615	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	58	181	0	ENST00000268489.5:c.10510G>A	p.Val3504Ile	p.V3504I	ENST00000268489	NM_006885.3	3504	Gtc/Atc	10/10	1	2	FACETS	0.897	0.782	1	1	0.984	1	CLONAL	4	TRUE	1	0.154632935339693	2		181	209	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214128	36214128	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	258	866	0	ENST00000222270.7:c.2954T>C	p.Leu985Pro	p.L985P	ENST00000222270	NM_014727.1	985	cTa/cCa	6/37	1	2	FACETS	0.916	0.859	0.974	1	0.996	1	CLONAL	4	TRUE	1	0.154632935339693	2		866	911	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50916686	50916686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1042614681	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	62	449	0	ENST00000440232.2:c.2158G>A	p.Val720Ile	p.V720I	ENST00000440232	NM_002691.3	720	Gtc/Atc	18/27	1	2	FACETS	0.875	0.758	1	1	0.976	1	CLONAL	2	TRUE	1	0.154632935339693	2		449	458	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435880	149435880	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	134	570	0	ENST00000286301.3:c.2344C>T	p.Arg782Cys	p.R782C	ENST00000286301	NM_005211.3	782	Cgt/Tgt	18/22	1	2	FACETS	1	0.977	1	1	0.992	1	CLONAL	2	TRUE	1	0.154632935339693	2		570	704	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509335	149509335	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	113	470	0	ENST00000261799.4:c.1564A>G	p.Ile522Val	p.I522V	ENST00000261799	NM_002609.3	522	Atc/Gtc	10/23	1	2	FACETS	0.924	0.835	1	1	0.991	1	CLONAL	3	TRUE	1	0.154632935339693	2		470	527	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515127	149515127	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	154	458	0	ENST00000261799.4:c.355T>G	p.Phe119Val	p.F119V	ENST00000261799	NM_002609.3	119	Ttt/Gtt	3/23	1	2	FACETS	1	0.927	1	1	0.993	1	CLONAL	3	TRUE	1	0.154632935339693	2		458	657	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286773	33286773	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	136	462	1	ENST00000374542.5:c.2163+1G>A		p.X721_splice	ENST00000374542	NM_001141970.1	721			1	2	FACETS	1	0.953	1	1	0.993	1	CLONAL	3	TRUE	1	0.154632935339693	2		463	551	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647446	117647448	+	inframe_deletion	In_Frame_Del	DEL	GCA	GCA	-	novel	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	69	368	0	ENST00000368508.3:c.5496_5498del	p.Ala1833del	p.A1833del	ENST00000368508	NM_002944.2	1832	gcTGCa/gca	33/43	0.135556214347996	3	FACETS	0.862	0.754	0.976	1	0.964	1	CLONAL	3	TRUE	1	0.154632935339693	3		368	372	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163730	152163730	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	59	192	0	ENST00000206249.3:c.453-2A>G		p.X151_splice	ENST00000206249	NM_000125.3	151			0.135556214347996	3	FACETS	0.938	0.814	1	1	0.967	1	CLONAL	3	TRUE	1	0.154632935339693	3		192	292	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300133	137300133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	386	743	0	ENST00000481739.1:c.418G>A	p.Asp140Asn	p.D140N	ENST00000481739	NM_002957.4	140	Gac/Aac	3/10	0.154632935339693	3	FACETS	1	0.987	1	1	0.996	1	CLONAL	5	TRUE	0	0.154632935339693	3		743	983	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370236	40370236	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	98	726	1	ENST00000293328.3:c.1102C>G	p.Gln368Glu	p.Q368E	ENST00000293328	NM_012448.3	368	Cag/Gag	9/19	1	2	FACETS	0.803	0.716	0.896	1	0.983	1	CLONAL	2	TRUE	1	0.154632935339693	2		727	789	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370235	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	101	681	1	ENST00000293328.3:c.1103del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000293328	NM_012448.3	368	cAg/cg	9/19	1	2	FACETS	0.889	0.794	0.989	1	0.985	1	CLONAL	2	TRUE	1	0.154632935339693	2		682	735	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910742	29910743	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	rs764090294	NA	P-0046759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	173	797	0	ENST00000376809.5:c.282_283del	p.Gln94HisfsTer4	p.Q94Hfs*4	ENST00000376809	NM_002116.7	94	caGTca/caca	2/8	1	2	FACETS	0.904	0.833	0.978	1	0.994	1	CLONAL	3	TRUE	1	0.154632935339693	2		797	825	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0046760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	326	803	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.360586742668566	2	FACETS	0.78	0.74	0.821	0.78	0.74	0.821	SUBCLONAL	2	TRUE	0	0.473725700148869	2		803	882	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241979	39241979	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs727505093	NA	P-0046760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	33	209	0	ENST00000402219.2:c.1867T>G	p.Phe623Val	p.F623V	ENST00000402219	NM_005633.3	623	Ttt/Gtt	11/23	0.361800638441603	3	FACETS	0.513	0.418	0.619	0.256	0.209	0.31	SUBCLONAL	1	TRUE	1	0.473725700148869	3		209	336	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097701	8097701	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	40	501	1	ENST00000346208.3:c.83A>T	p.His28Leu	p.H28L	ENST00000346208		28	cAc/cTc	2/6	0.356382988857072	3	FACETS	0.304	0.252	0.363	0.101	0.084	0.121	SUBCLONAL	1	TRUE	0	0.473725700148869	3		502	686	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313380	30313380	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	76	560	0	ENST00000262643.3:c.980G>C	p.Cys327Ser	p.C327S	ENST00000262643	NM_001238.2	327	tGt/tCt	11/12	0.341582814824465	3	FACETS	0.524	0.459	0.594	0.262	0.229	0.297	SUBCLONAL	1	TRUE	1	0.473725700148869	3		560	757	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543847	212543847	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	84	346	0	ENST00000342788.4:c.1552G>C	p.Asp518His	p.D518H	ENST00000342788	NM_005235.2	518	Gac/Cac	13/28	0.361800638441603	3	FACETS	0.837	0.741	0.939	0.419	0.37	0.47	CLONAL	1	TRUE	1	0.473725700148869	3		346	524	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947841	178947841	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	119	259	0	ENST00000263967.3:c.2716G>C	p.Val906Leu	p.V906L	ENST00000263967	NM_006218.2	906	Gta/Cta	19/21	0.350716499009907	3	FACETS	0.898	0.82	0.978	0.898	0.82	0.978	CLONAL	2	TRUE	1	0.473725700148869	3		259	346	SUCCESS
APC	324	MSKCC	GRCh37	5	112173659	112173659	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0046760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	174	223	1	ENST00000257430.4:c.2368A>T	p.Arg790Ter	p.R790*	ENST00000257430	NM_000038.5	790	Aga/Tga	16/16	0.297659240795546	3	FACETS	0.863	0.808	0.918			1	CLONAL	3	TRUE	NA	0.473725700148869	3		224	351	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965852	90965852	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs143948240	NA	P-0046760-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	49	237	0	ENST00000265433.3:c.1465C>G	p.Leu489Val	p.L489V	ENST00000265433	NM_002485.4	489	Ctt/Gtt	11/16	0.218890045407883	4	FACETS	0.722	0.613	0.842	0.361	0.306	0.421	INDETERMINATE	1	TRUE	2	0.473725700148869	4		237	422	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911698	26911712	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTACAGGAAGGATGA	TTACAGGAAGGATGA	-	novel	NA	P-0046773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	16	130	0	ENST00000381527.3:c.129-5_138del		p.X43_splice	ENST00000381527	NM_001260.1	43		2/13	1	2	FACETS	0.765	0.575	0.984	0.765	0.575	0.984	CLONAL	1	TRUE	1	0.454572401732949	2		130	92	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975698	26975698	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	46	285	0	ENST00000381527.3:c.1206G>T	p.Lys402Asn	p.K402N	ENST00000381527	NM_001260.1	402	aaG/aaT	12/13	1	2	FACETS	0.684	0.579	0.798	0.684	0.579	0.798	SUBCLONAL	1	TRUE	1	0.454572401732949	2		285	296	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828800	72828800	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	22	406	0	ENST00000268489.5:c.7781C>T	p.Pro2594Leu	p.P2594L	ENST00000268489	NM_006885.3	2594	cCt/cTt	9/10	0.454572401732949	1	FACETS	0.499	0.39	0.622	0.499	0.39	0.622	SUBCLONAL	1	TRUE	0	0.454572401732949	1		406	150	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579529	7579529	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658483	NA	P-0046773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	84	587	0	ENST00000269305.4:c.158G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tGg/tAg	4/11	0.454572401732949	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.454572401732949	1		587	247	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546686	9546686	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	43	280	0	ENST00000353224.5:c.1336A>G	p.Arg446Gly	p.R446G	ENST00000353224	NM_177990.2	446	Agg/Ggg	5/10	1	2	FACETS	0.98	0.831	1	0.98	0.831	1	CLONAL	1	TRUE	1	0.454572401732949	2		280	193	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0046774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	388	659	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	NA	2	FACETS	1	0.997	1			1	INDETERMINATE	2	FALSE	NA	0.766512562768472	2		659	419	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469672	NA	P-0046774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	299	367	0	ENST00000374080.3:c.131G>A	p.Gly44Asp	p.G44D	ENST00000374080		44	gGt/gAt	2/45	0.759080322858572	4	FACETS	0.919	0.878	0.959	0.919	0.878	0.959	CLONAL	3	FALSE	1	0.766512562768472	4		367	500	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937602	76937603	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	21	192	0	ENST00000373344.5:c.3145dup	p.Ile1049AsnfsTer4	p.I1049Nfs*4	ENST00000373344	NM_000489.3	1049	ata/aAta	9/35	0.293528971379284	2	FACETS	1	0.913	1	0.623	0.508	0.739	INDETERMINATE	1	FALSE	0	0.766512562768472	2		192	44	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574815	41574815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748953233	NA	P-0046774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	178	467	1	ENST00000263253.7:c.7100C>T	p.Pro2367Leu	p.P2367L	ENST00000263253	NM_001429.3	2367	cCg/cTg	31/31	NA	2	FACETS	1	0.952	1			1	INDETERMINATE	1	FALSE	NA	0.766512562768472	2		468	452	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217299	7217316	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGGGCTCCCTAGAAAGG	CAGGGCTCCCTAGAAAGG	-	novel	NA	P-0046776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	124	475	0	ENST00000380728.2:c.398-9_406del		p.X133_splice	ENST00000380728		133		6/11	0.408699802354744	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.408699802354744	1		475	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573959	7573995	+	frameshift_variant	Frame_Shift_Del	DEL	CCCAGCCTGGGCATCCTTGAGTTCCAAGGCCTCATTC	CCCAGCCTGGGCATCCTTGAGTTCCAAGGCCTCATTC	-	novel	NA	P-0046776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	76	615	0	ENST00000269305.4:c.1032_1068del	p.Asn345ArgfsTer13	p.N345Rfs*13	ENST00000269305	NM_001126112.2	344	ctGAATGAGGCCTTGGAACTCAAGGATGCCCAGGCTGGG/ct	10/11	0.408699802354744	1	FACETS	0.603	0.53	0.68	0.603	0.53	0.68	SUBCLONAL	1	TRUE	0	0.408699802354744	1		615	491	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394051	31394051	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	29	231	0	ENST00000328111.2:c.2338T>C	p.Ser780Pro	p.S780P	ENST00000328111	NM_006892.3	780	Tcg/Ccg	22/23	1	2	FACETS	0.486	0.391	0.594	0.486	0.391	0.594	SUBCLONAL	1	TRUE	1	0.408699802354744	2		231	292	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143044517	143044517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	63	260	0	ENST00000262992.4:c.1945G>A	p.Asp649Asn	p.D649N	ENST00000262992	NM_001101669.1	649	Gac/Aac	18/24	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.408699802354744	2		260	300	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980850	40980850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752620539	NA	P-0046777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	171	467	1	ENST00000373198.4:c.1636C>T	p.Arg546Trp	p.R546W	ENST00000373198	NM_133170.3	546	Cgg/Tgg	10/32	0.353687539237745	3	FACETS	1	0.982	1	0.596	0.553	0.641	INDETERMINATE	1	TRUE	1	0.793042405118207	3		468	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577557	7577557	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519982	NA	P-0046777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	250	474	0	ENST00000269305.4:c.724T>C	p.Cys242Arg	p.C242R	ENST00000269305	NM_001126112.2	242	Tgc/Cgc	7/11	0.759983840095111	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.793042405118207	1		474	329	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41199660	41199660	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs80357212	NA	P-0046777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	134	462	1	ENST00000357654.3:c.5467G>A	p.Ala1823Thr	p.A1823T	ENST00000357654	NM_007294.3	1823	Gca/Aca	22/23	0.752828086250665	1	FACETS	0.822	0.765	0.879	0.822	0.765	0.879	CLONAL	1	TRUE	0	0.793042405118207	1		463	248	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909896	100909896	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	44	214	0	ENST00000325455.5:c.2753C>A	p.Pro918His	p.P918H	ENST00000325455	NM_001202474.3	918	cCc/cAc	8/8	0.353687539237745	3	FACETS	1	0.942	1	0.601	0.516	0.689	INDETERMINATE	1	TRUE	1	0.793042405118207	3		214	129	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027518	48027518	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	29	220	0	ENST00000234420.5:c.2396T>C	p.Met799Thr	p.M799T	ENST00000234420	NM_000179.2	799	aTg/aCg	4/10	0.215503405685268	4	FACETS	0.771	0.638	0.912	0.771	0.638	0.912	INDETERMINATE	2	TRUE	2	0.793042405118207	4		220	85	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715595	30715634	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGGTGGGAACTGCAAGATACATGGCTCCAGAAGTCCTAGA	AGGTGGGAACTGCAAGATACATGGCTCCAGAAGTCCTAGA	-	novel	NA	P-0046777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	29	110	0	ENST00000295754.5:c.1255-1_1293del		p.X419_splice	ENST00000295754	NM_003242.5	419		5/7	0.768998928839651	1	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	0	0.793042405118207	1		110	44	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526471	31526471	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046777-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	192	632	0	ENST00000344624.3:c.569G>A	p.Ser190Asn	p.S190N	ENST00000344624		190	aGt/aAt	2/33	0.257172560540373	3	FACETS	1	0.988	1	0.649	0.605	0.694	INDETERMINATE	1	TRUE	1	0.793042405118207	3		632	521	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0046778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	264	670	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.391986807220264	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.391986807220264	2		670	658	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0046778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	29	182	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.391986807220264	2		182	140	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119886	70119887	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046778-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	339	516	0	ENST00000245479.2:c.889dup	p.Tyr297LeufsTer281	p.Y297Lfs*281	ENST00000245479	NM_000346.3	296	-/T	3/3	0.347153878833341	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	3	TRUE	1	0.391986807220264	4		516	794	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145743003	145743003	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	499	183	0	ENST00000428558.2:c.101C>T	p.Ala34Val	p.A34V	ENST00000428558	NM_004260.3	34	gCg/gTg	2/22	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.780613689659951	2		183	1080	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748035	72748035	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1315221405	NA	P-0046780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	615	504	0	ENST00000357731.5:c.143T>A	p.Met48Lys	p.M48K	ENST00000357731	NM_173808.2	48	aTg/aAg	1/7	0.780613689659951	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.780613689659951	1		504	796	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647455	3647456	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1254	414	673	1	ENST00000294008.3:c.1607dup	p.Thr537AspfsTer39	p.T537Dfs*39	ENST00000294008	NM_032444.2	536	ctg/ctTg	7/15	0.409056018057938	1	FACETS	0.388	0.368	0.408	0.388	0.368	0.408	INDETERMINATE	1	TRUE	0	0.780613689659951	1		674	1668	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578405	7578427	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCCTCACAACCTCCGTCATGT	GCGCCTCACAACCTCCGTCATGT	-	novel	NA	P-0046780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	782	629	0	ENST00000269305.4:c.503_525del	p.His168LeufsTer5	p.H168Lfs*5	ENST00000269305	NM_001126112.2	168	cACATGACGGAGGTTGTGAGGCGC/c	5/11	0.780613689659951	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.780613689659951	1		629	1113	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300122	15300122	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1227	883	654	1	ENST00000263388.2:c.1154G>T	p.Gly385Val	p.G385V	ENST00000263388	NM_000435.2	385	gGt/gTt	7/33	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.780613689659951	2		655	2110	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928292	69928292	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	379	348	1	ENST00000352241.4:c.112G>T	p.Ala38Ser	p.A38S	ENST00000352241	NM_198159.2	38	Gcc/Tcc	2/10	0.780613689659951	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.780613689659951	1		349	538	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593491	55593491	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0046780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	73	229	0	ENST00000288135.5:c.1647+1G>T		p.X549_splice	ENST00000288135	NM_000222.2	549			0.366086650650771	1	FACETS	0.546	0.486	0.608	0.546	0.486	0.608	INDETERMINATE	1	TRUE	0	0.780613689659951	1		229	209	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38186998	38187000	+	inframe_deletion	In_Frame_Del	DEL	CTG	CTG	-	rs775301845	NA	P-0046780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	332	469	0	ENST00000317025.8:c.1477_1479del	p.Gln493del	p.Q493del	ENST00000317025	NM_023034.1	493	CAG/-	6/24	1	2	FACETS	0.882	0.836	0.929	0.882	0.836	0.929	CLONAL	1	TRUE	1	0.780613689659951	2		469	964	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599338	55599338	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	118	302	0	ENST00000288135.5:c.2464A>T	p.Asn822Tyr	p.N822Y	ENST00000288135	NM_000222.2	822	Aat/Tat	17/21	0.253744266341495	4	FACETS	0.947	0.86	1	0.631	0.573	0.691	CLONAL	2	TRUE	1	0.40433532500184	4		302	433	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528596	8528596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	49	247	0	ENST00000356435.5:c.536G>A	p.Arg179Gln	p.R179Q	ENST00000356435		179	cGa/cAa	4/35	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.40433532500184	NA		247	401	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599266	55599266	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	109	273	0	ENST00000288135.5:c.2392A>G	p.Ile798Val	p.I798V	ENST00000288135	NM_000222.2	798	Atc/Gtc	17/21	0.253744266341495	4	FACETS	0.926	0.838	1	0.617	0.558	0.678	CLONAL	2	TRUE	1	0.40433532500184	4		273	409	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913906	32913906	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs80358765	NA	P-0046781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	123	308	0	ENST00000380152.3:c.5414A>G	p.Asn1805Ser	p.N1805S	ENST00000380152		1805	aAt/aGt	11/27	0.372917212512335	4	FACETS	0.931	0.847	1	0.931	0.847	1	CLONAL	2	TRUE	2	0.40433532500184	4		308	459	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29579964	29579964	+	intron_variant	Intron	SNP	C	C	A	novel	NA	P-0046781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	129	243	0	ENST00000356175.3:c.4110+3827C>A		p.*1370*	ENST00000356175	NM_000267.3	1373/2839			0.323665271065692	3	FACETS	1	0.982	1	0.825	0.76	0.891	CLONAL	2	TRUE	0	0.40433532500184	3		243	310	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533093	63533094	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	84	592	0	ENST00000307078.5:c.1800dup	p.Gly601ArgfsTer27	p.G601Rfs*27	ENST00000307078	NM_004655.3	600	-/C	7/11	0.40433532500184	3	FACETS	0.918	0.813	1	0.459	0.406	0.516	CLONAL	1	TRUE	1	0.40433532500184	3		592	544	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267385	198267385	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	121	330	0	ENST00000335508.6:c.1972T>C	p.Trp658Arg	p.W658R	ENST00000335508	NM_012433.2	658	Tgg/Cgg	14/25	0.40433532500184	3	FACETS	0.759	0.69	0.831	0.759	0.69	0.831	SUBCLONAL	2	TRUE	1	0.40433532500184	3		330	474	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729355	41729355	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	64	456	1	ENST00000242208.4:c.1174G>T	p.Val392Leu	p.V392L	ENST00000242208	NM_002192.2	392	Gtg/Ttg	3/3	0.253744266341495	4	FACETS	0.84	0.729	0.961	0.28	0.243	0.321	CLONAL	1	TRUE	1	0.40433532500184	4		457	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0046783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	8	816	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.900557569512435	2	FACETS	0.048	0.03	0.071	0.024	0.015	0.036	SUBCLONAL	1	TRUE	0	0.900557569512435	2		816	372	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs1202793339	NA	P-0046783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	292	364	1	ENST00000269305.4:c.560-1G>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.900557569512435	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.900557569512435	2		365	312	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828134	243828134	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	56	201	0	ENST00000263826.5:c.224G>T	p.Arg75Ile	p.R75I	ENST00000263826	NM_005465.4	75	aGa/aTa	3/13	1	2	FACETS	0.404	0.348	0.464	0.404	0.348	0.464	SUBCLONAL	1	TRUE	1	0.900557569512435	2		201	308	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497792	120497792	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	142	313	0	ENST00000256646.2:c.2090G>C	p.Cys697Ser	p.C697S	ENST00000256646	NM_024408.3	697	tGt/tCt	13/34	1	2	FACETS	0.869	0.802	0.937	0.869	0.802	0.937	CLONAL	1	TRUE	1	0.900557569512435	2		313	363	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332781	70332781	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	137	240	0	ENST00000373644.4:c.686C>G	p.Ser229Cys	p.S229C	ENST00000373644	NM_030625.2	229	tCt/tGt	2/12	0.383628910914043	2	FACETS	1	0.972	1	0.547	0.508	0.587	INDETERMINATE	1	TRUE	0	0.900557569512435	2		240	278	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77051717	77051717	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	150	286	0	ENST00000356341.3:c.1090G>C	p.Gly364Arg	p.G364R	ENST00000356341	NM_002576.4	364	Ggc/Cgc	11/15	0.284813225255194	4	FACETS	0.945	0.866	1	0.236	0.216	0.257	INDETERMINATE	1	TRUE	0	0.900557569512435	4		286	670	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435398	49435813	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCACTAGAGGACTGCTACACCCCAGCCCAGCCCCACTCACCTTCTGCACCTTGTTGATGCGGTGAGCTGCCCGGTTATCTTTGGCCTTTTGCTGAGGGATATGGGACACAGCCTTAGGGCCTAGTGCTTGGTCTCATGCCCCGCCCCCATACTGTAGTGTTTTCACACTCCCTACCCAGAAGCAGATCCCTTCTGGCCCAGCTGCTTTAGGAGTGGGGAGCGGAAAGAACTGAGGTAAATTACCCAAAGATCCCTCCCTCCCTCTCAGTTCCCACGCTAATCCATGCTCCTTTCTGCCTCACCAGGTAGGGGGCTTTGTCAGCTGCTGGAACCTTTCTCCAGAGCTTCATGATTTGTTTGCAACGGCTTGACCAGTCTGGAGGGCAGAGAGAGTGAGTCAGAGAAGACTTGGCAGG	CCACTAGAGGACTGCTACACCCCAGCCCAGCCCCACTCACCTTCTGCACCTTGTTGATGCGGTGAGCTGCCCGGTTATCTTTGGCCTTTTGCTGAGGGATATGGGACACAGCCTTAGGGCCTAGTGCTTGGTCTCATGCCCCGCCCCCATACTGTAGTGTTTTCACACTCCCTACCCAGAAGCAGATCCCTTCTGGCCCAGCTGCTTTAGGAGTGGGGAGCGGAAAGAACTGAGGTAAATTACCCAAAGATCCCTCCCTCCCTCTCAGTTCCCACGCTAATCCATGCTCCTTTCTGCCTCACCAGGTAGGGGGCTTTGTCAGCTGCTGGAACCTTTCTCCAGAGCTTCATGATTTGTTTGCAACGGCTTGACCAGTCTGGAGGGCAGAGAGAGTGAGTCAGAGAAGACTTGGCAGG	-	novel	NA	P-0046783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	103	413	0	ENST00000301067.7:c.6110-40_6234+40del		p.X2037_splice	ENST00000301067	NM_003482.3	2037		29-30/54	0.802102027568594	3	FACETS	0.685	0.616	0.758	0.343	0.308	0.379	SUBCLONAL	1	TRUE	1	0.900557569512435	3		413	484	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941710	48941710	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	61	139	0	ENST00000267163.4:c.1020T>A	p.Asp340Glu	p.D340E	ENST00000267163	NM_000321.2	340	gaT/gaA	10/27	0.900557569512435	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.900557569512435	1		139	71	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937622	17937622	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	253	469	0	ENST00000458235.1:c.3305G>C	p.Ser1102Thr	p.S1102T	ENST00000458235	NM_000215.3	1102	aGc/aCc	24/24	0.301799092182119	1	FACETS	0.558	0.527	0.589	0.558	0.527	0.589	INDETERMINATE	1	TRUE	0	0.900557569512435	1		469	554	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313204	30313204	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	123	312	0	ENST00000262643.3:c.898G>C	p.Ala300Pro	p.A300P	ENST00000262643	NM_001238.2	300	Gct/Cct	10/12	0.900557569512435	3	FACETS	0.451	0.408	0.497			1	SUBCLONAL	1	TRUE	NA	0.900557569512435	3		312	878	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056385	180056385	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	186	513	0	ENST00000261937.6:c.859A>C	p.Thr287Pro	p.T287P	ENST00000261937	NM_182925.4	287	Acc/Ccc	7/30	0.873382083179136	4	FACETS	1	0.948	1	0.343	0.318	0.37	CLONAL	1	TRUE	1	0.900557569512435	4		513	762	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124389	94124448	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAAGTGATATTTTATGATGAAAAAAACTTACCCCATTGGGTGGAGAGGAAATCCACTCC	AAAAGTGATATTTTATGATGAAAAAAACTTACCCCATTGGGTGGAGAGGAAATCCACTCC	-	novel	NA	P-0046783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	86	110	0	ENST00000369303.4:c.135_162+32del		p.X45_splice	ENST00000369303	NM_004440.3	45		2/17	0.900557569512435	3	FACETS	0.933	0.886	0.972	0.933	0.886	0.972	CLONAL	3	TRUE	0	0.900557569512435	3		110	99	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977586	2977586	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	173	432	1	ENST00000396946.4:c.1098C>A	p.Asn366Lys	p.N366K	ENST00000396946	NM_032415.4	366	aaC/aaA	8/25	0.266242201208409	6	FACETS	1	0.983	1	0.206	0.19	0.224	INDETERMINATE	1	TRUE	0	0.900557569512435	6		433	869	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44919302	44919302	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	78	236	1	ENST00000377967.4:c.1230G>T	p.Gln410His	p.Q410H	ENST00000377967	NM_021140.2	410	caG/caT	13/29	NA	2	FACETS	0.36	0.317	0.406			1	INDETERMINATE	1	TRUE	NA	0.900557569512435	2		237	481	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	125	424	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.223546524989205	5	FACETS	1	0.976	1	1	0.976	1	INDETERMINATE	3	TRUE	2	0.455835224461533	5		424	268	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0046784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	233	812	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.445392743610967	2	FACETS	0.903	0.85	0.957	0.903	0.85	0.957	CLONAL	2	TRUE	0	0.455835224461533	2		812	566	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440943	56440943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786205215	NA	P-0046784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	165	800	0	ENST00000407977.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000407977		132	Cga/Tga	4/10	0.455979171774471	3	FACETS	0.936	0.867	1	0.936	0.867	1	CLONAL	2	TRUE	1	0.455835224461533	3		800	475	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448310	56448310	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567880628	NA	P-0046784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	62	562	2	ENST00000407977.2:c.337C>T	p.Arg113Ter	p.R113*	ENST00000407977		113	Cga/Tga	3/10	0.455979171774471	3	FACETS	0.538	0.464	0.618	0.269	0.232	0.309	SUBCLONAL	1	TRUE	1	0.455835224461533	3		564	621	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692918	89692918	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1114167676	NA	P-0046784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	72	368	0	ENST00000371953.3:c.402G>T	p.Met134Ile	p.M134I	ENST00000371953	NM_000314.4	134	atG/atT	5/9	0.112869366566069	5	FACETS	0.957	0.845	1	0.638	0.563	0.716	INDETERMINATE	2	TRUE	2	0.455835224461533	5		368	278	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798741	135798741	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0046784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	13	144	0	ENST00000298552.3:c.502A>T	p.Lys168Ter	p.K168*	ENST00000298552	NM_001162426.1	168	Aaa/Taa	6/23	1	2	FACETS	0.554	0.399	0.738	0.554	0.399	0.738	SUBCLONAL	1	TRUE	1	0.455835224461533	2		144	103	SUCCESS
ATM	472	MSKCC	GRCh37	11	108159726	108159726	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046784-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	56	350	0	ENST00000278616.4:c.4132C>G	p.Pro1378Ala	p.P1378A	ENST00000278616	NM_000051.3	1378	Cca/Gca	28/63	0.112869366566069	5	FACETS	0.919	0.797	1	0.613	0.531	0.699	INDETERMINATE	2	TRUE	2	0.455835224461533	5		350	225	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0046786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	238	398	0	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	0.282871137951745	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	FALSE	0	0.282871137951745	3		398	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0046786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	155	368	1	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.264013815797741	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	FALSE	0	0.282871137951745	2		369	539	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021697	31021697	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	101	279	0	ENST00000375687.4:c.1696G>T	p.Glu566Ter	p.E566*	ENST00000375687	NM_015338.5	566	Gag/Tag	12/13	0.168244623638979	4	FACETS	0.987	0.887	1	0.987	0.887	1	INDETERMINATE	2	FALSE	2	0.282871137951745	4		279	464	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870616	40870617	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0046786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	58	332	0	ENST00000428826.2:c.786_787del	p.Glu262AspfsTer42	p.E262Dfs*42	ENST00000428826		262	gaGAtg/gatg	9/21	0.243630984456452	3	FACETS	0.888	0.764	1	0.444	0.382	0.512	CLONAL	1	FALSE	1	0.282871137951745	3		332	527	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754421	41754421	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	51	384	0	ENST00000301178.4:c.1540A>T	p.Asn514Tyr	p.N514Y	ENST00000301178	NM_021913.4	514	Aac/Tac	13/20	0.264013815797741	2	FACETS	0.724	0.616	0.843	0.362	0.308	0.422	SUBCLONAL	1	FALSE	0	0.282871137951745	2		384	498	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143423	30143423	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	135	310	0	ENST00000389048.3:c.103G>A	p.Gly35Arg	p.G35R	ENST00000389048	NM_004304.4	35	Ggg/Agg	1/29	0.168244623638979	4	FACETS	1	0.971	1	1	0.971	1	INDETERMINATE	2	FALSE	2	0.282871137951745	4		310	534	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131972891	131973770	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTGAGTACCATGGTGTATCACAAATGCTCTTTCCAAAGCCCTCTCCGCAGCTCTTCCCCTTATGACCTCTCATCATGCCAGCATTACCTCCCTGGACCCCTTTCTAAGCATGTCTTTGAGATTTTCTAAGAATTCTTATCTTGGCAACATCTTGTAGCAAGAAAATGTAAAGTTTTCTGTTCCAGAGCCTAACAGGACTTACATATTTGACTGCAGTAGGCATTATATTTAGCTGATGACATAATAGGTTCTGTCATAGTGTAGATAGGGATAAGCCAAAATGCAATAAGAAAAACCATCCAGAGGAAACTCTTTTTTTTTTCTTTTTCTTTTTTTTTTTTCCAGATGGAGTCTCGCACTTCTCTGTCACCCGGGCTGGAGCGCAGTGGTGCAATCTTGGCTCACTGCAACCTCCACCTCCTGGGTTCAGGTGATTCTCCCACCTCAGCCTCCCGAGTAGTAGCTGGAATTACAGGTGCGCGCTCCCACACCTGGCTAATTTTTTGTATTCTTAGTAGAGATGGGGTTTCACCATGTTGGCCAGGCTGGTCTCAAACTCCTGCCCTCAGGTGATCTGCCCACCTTGGCCTCCCAGTGTTGGGTTTACAGGCGTGAGCCACCGCGCCTGGCCTGGAGGAAACTCTTAACAGGGAAACTAAGAAAGAGTTGAGGCTGAGGAACTGGGGCATCTGGGTTGCTTCTGGCCAGACCACCAGGCTCTTGAATCCTCCCAGCCAGAGAAAGAGTTTCCACACCAGCCATTGTTTTCCTCTGGTAATGTCAGCCTCATCTGTTGTTCCTAGGCTTACTTGATATGTTTGTAAATGACAAAAGGCTACAGAGCATAGGTTCCTCTAAAATATTCTTCTTCCTGTGTC	AGGTGAGTACCATGGTGTATCACAAATGCTCTTTCCAAAGCCCTCTCCGCAGCTCTTCCCCTTATGACCTCTCATCATGCCAGCATTACCTCCCTGGACCCCTTTCTAAGCATGTCTTTGAGATTTTCTAAGAATTCTTATCTTGGCAACATCTTGTAGCAAGAAAATGTAAAGTTTTCTGTTCCAGAGCCTAACAGGACTTACATATTTGACTGCAGTAGGCATTATATTTAGCTGATGACATAATAGGTTCTGTCATAGTGTAGATAGGGATAAGCCAAAATGCAATAAGAAAAACCATCCAGAGGAAACTCTTTTTTTTTTCTTTTTCTTTTTTTTTTTTCCAGATGGAGTCTCGCACTTCTCTGTCACCCGGGCTGGAGCGCAGTGGTGCAATCTTGGCTCACTGCAACCTCCACCTCCTGGGTTCAGGTGATTCTCCCACCTCAGCCTCCCGAGTAGTAGCTGGAATTACAGGTGCGCGCTCCCACACCTGGCTAATTTTTTGTATTCTTAGTAGAGATGGGGTTTCACCATGTTGGCCAGGCTGGTCTCAAACTCCTGCCCTCAGGTGATCTGCCCACCTTGGCCTCCCAGTGTTGGGTTTACAGGCGTGAGCCACCGCGCCTGGCCTGGAGGAAACTCTTAACAGGGAAACTAAGAAAGAGTTGAGGCTGAGGAACTGGGGCATCTGGGTTGCTTCTGGCCAGACCACCAGGCTCTTGAATCCTCCCAGCCAGAGAAAGAGTTTCCACACCAGCCATTGTTTTCCTCTGGTAATGTCAGCCTCATCTGTTGTTCCTAGGCTTACTTGATATGTTTGTAAATGACAAAAGGCTACAGAGCATAGGTTCCTCTAAAATATTCTTCTTCCTGTGTC	-	novel	NA	P-0046786-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	38	154	0	ENST00000265335.6:c.3475+1_3476-1del		p.X1159_splice	ENST00000265335		1159		22/25	0.282871137951745	3	FACETS	1	0.926	1	0.608	0.506	0.721	CLONAL	1	FALSE	1	0.282871137951745	3		154	252	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940877	49940877	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	170	719	0	ENST00000296474.3:c.166C>T	p.Gln56Ter	p.Q56*	ENST00000296474	NM_002447.2	56	Cag/Tag	1/20	1	2	FACETS	0.832	0.768	0.898	0.832	0.768	0.898	CLONAL	1	TRUE	1	0.635717981403871	2		719	643	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979286	93979286	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	65	306	0	ENST00000369303.4:c.1542G>T	p.Gln514His	p.Q514H	ENST00000369303	NM_004440.3	514	caG/caT	7/17	1	2	FACETS	0.881	0.775	0.994	0.881	0.775	0.994	CLONAL	1	TRUE	1	0.635717981403871	2		306	232	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220691	1220691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	230	733	0	ENST00000326873.7:c.709G>A	p.Asp237Asn	p.D237N	ENST00000326873	NM_000455.4	237	Gac/Aac	5/10	0.635717981403871	1	FACETS	0.942	0.887	0.997	0.942	0.887	0.997	CLONAL	1	TRUE	0	0.635717981403871	1		733	524	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176104217	176104217	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	141	175	1	ENST00000367669.3:c.897G>T	p.Met299Ile	p.M299I	ENST00000367669	NM_022457.5	299	atG/atT	8/20	0.635534712885395	4	FACETS	0.945	0.881	1	0.945	0.881	1	CLONAL	3	TRUE	1	0.635717981403871	4		176	256	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479315	50479315	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	98	378	0	ENST00000394963.4:c.163G>T	p.Gly55Ter	p.G55*	ENST00000394963	NM_003076.4	55	Gga/Tga	1/13	0.635717981403871	3	FACETS	0.986	0.886	1	0.493	0.443	0.546	CLONAL	1	TRUE	1	0.635717981403871	3		378	412	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007734	45007734	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0046787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	20	255	0	ENST00000558401.1:c.181A>T	p.Lys61Ter	p.K61*	ENST00000558401	NM_004048.2	61	Aag/Tag	2/4	0.635717981403871	1	FACETS	0.25	0.192	0.316	0.25	0.192	0.316	SUBCLONAL	1	TRUE	0	0.635717981403871	1		255	172	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600004	10600005	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0046787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	176	693	0	ENST00000171111.5:c.1571dup	p.Tyr525LeufsTer2	p.Y525Lfs*2	ENST00000171111	NM_203500.1	524	ggc/ggGc	5/6	0.635717981403871	1	FACETS	0.897	0.836	0.959	0.897	0.836	0.959	CLONAL	1	TRUE	0	0.635717981403871	1		693	421	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797354	42797354	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	206	790	0	ENST00000575354.2:c.3716G>A	p.Trp1239Ter	p.W1239*	ENST00000575354	NM_015125.3	1239	tGg/tAg	15/20	0.635717981403871	1	FACETS	0.998	0.938	1	0.998	0.938	1	CLONAL	1	TRUE	0	0.635717981403871	1		790	443	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912383	50912383	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	58	649	0	ENST00000440232.2:c.1897A>C	p.Thr633Pro	p.T633P	ENST00000440232	NM_002691.3	633	Act/Cct	16/27	0.635717981403871	1	FACETS	0.318	0.274	0.366	0.318	0.274	0.366	SUBCLONAL	1	TRUE	0	0.635717981403871	1		649	391	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275204	41275205	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0046787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	98	286	1	ENST00000349496.5:c.1370_1371delinsTT	p.Arg457Ile	p.R457I	ENST00000349496	NM_001904.3	457	aGG/aTT	9/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.635717981403871	2		287	269	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933410	39933410	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	159	589	1	ENST00000378444.4:c.1189C>A	p.Pro397Thr	p.P397T	ENST00000378444	NM_001123385.1	397	Ccg/Acg	4/15	1	2	FACETS	0.901	0.831	0.974	0.901	0.831	0.974	CLONAL	1	TRUE	1	0.635717981403871	2		590	555	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220533	123220533	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046787-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	130	365	0	ENST00000218089.9:c.3190A>T	p.Ser1064Cys	p.S1064C	ENST00000218089	NM_001042749.1	1064	Agc/Tgc	30/35	1	2	FACETS	0.923	0.844	1	0.923	0.844	1	CLONAL	1	TRUE	1	0.635717981403871	2		365	443	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950531	38950531	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	82	193	0	ENST00000357387.3:c.3419A>G	p.Asp1140Gly	p.D1140G	ENST00000357387	NM_152756.3	1140	gAt/gGt	31/38	0.367085620574034	3	FACETS	0.808	0.72	0.9	0.808	0.72	0.9	CLONAL	2	TRUE	1	0.402184367321458	3		193	303	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0046789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	356	363	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.618860657161806	6	FACETS	0.958	0.916	0.999			1	CLONAL	4	TRUE	NA	0.618860657161806	6		363	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0046789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	507	882	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.618860657161806	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.618860657161806	2		882	802	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574014	7574014	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	34	581	0	ENST00000269305.4:c.1013del	p.Phe338SerfsTer7	p.F338Sfs*7	ENST00000269305	NM_001126112.2	338	tTc/tc	10/11	1	2	FACETS	0.444	0.362	0.537	0.444	0.362	0.537	SUBCLONAL	1	FALSE	1	0.3	2		581	510	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249472	153249472	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	28	333	0	ENST00000281708.4:c.1306A>G	p.Ser436Gly	p.S436G	ENST00000281708	NM_033632.3	436	Agt/Ggt	9/12	1	2	FACETS	0.566	0.452	0.694	0.566	0.452	0.694	SUBCLONAL	1	FALSE	1	0.3	2		333	330	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0046791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	106	594	1	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.248914914820442	3	FACETS	1	0.972	1			1	CLONAL	2	TRUE	NA	0.248914914820442	3		595	397	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974695	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691187	NA	P-0046791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	47	264	1	ENST00000304494.5:c.132del	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	taC/ta	1/3	0.248914914820442	1	FACETS	0.975	0.826	1	0.975	0.826	1	CLONAL	1	TRUE	0	0.248914914820442	1		265	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578436	7578439	+	frameshift_variant	Frame_Shift_Del	DEL	TGCT	TGCT	-	novel	NA	P-0046791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	79	586	0	ENST00000269305.4:c.491_494del	p.Lys164SerfsTer5	p.K164Sfs*5	ENST00000269305	NM_001126112.2	164	aAGCAg/ag	5/11	0.230896587733965	1	FACETS	0.952	0.838	1	0.952	0.838	1	CLONAL	1	TRUE	0	0.248914914820442	1		586	584	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586236	48586236	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs1555686071	NA	P-0046791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	38	195	0	ENST00000342988.3:c.905G>A	p.Trp302Ter	p.W302*	ENST00000342988	NM_005359.5	302	tGg/tAg	8/12	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.248914914820442	2		195	237	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89176402	89176402	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	61	129	0	ENST00000336596.2:c.132G>T	p.Trp44Cys	p.W44C	ENST00000336596	NM_005233.5	44	tgG/tgT	2/17	0.248914914820442	15	FACETS	0.934	0.808	1			1	CLONAL	3	TRUE	NA	0.248914914820442	15		129	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0046792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	13	672	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.432662099575868	2	FACETS	0.093	0.065	0.126	0.046	0.032	0.063	SUBCLONAL	1	TRUE	0	0.432662099575868	2		672	649	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579495	7579495	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	263	590	0	ENST00000269305.4:c.192del	p.Arg65GlufsTer58	p.R65Efs*58	ENST00000269305	NM_001126112.2	64	ccC/cc	4/11	0.432662099575868	2	FACETS	0.945	0.892	0.999	0.945	0.892	0.999	CLONAL	2	TRUE	0	0.432662099575868	2		590	643	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926518	59926518	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1330277587	NA	P-0046792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	95	300	0	ENST00000259008.2:c.479G>T	p.Arg160Ile	p.R160I	ENST00000259008	NM_032043.2	160	aGa/aTa	5/20	1	2	FACETS	0.972	0.87	1	0.972	0.87	1	CLONAL	1	TRUE	1	0.432662099575868	2		300	452	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399286	139399286	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	352	719	0	ENST00000277541.6:c.4857C>A	p.Tyr1619Ter	p.Y1619*	ENST00000277541	NM_017617.3	1619	taC/taA	26/34	0.421967739337558	3	FACETS	1	0.992	1	0.791	0.753	0.829	CLONAL	2	TRUE	0	0.432662099575868	3		719	834	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741620	145741620	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755963144	NA	P-0046792-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	179	681	0	ENST00000428558.2:c.883G>A	p.Glu295Lys	p.E295K	ENST00000428558	NM_004260.3	295	Gag/Aag	5/22	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.432662099575868	2		681	803	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	56	424	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.172214584702613	3	FACETS	0.758	0.651	0.874	0.379	0.325	0.437	INDETERMINATE	1	TRUE	1	0.439533513055214	3		424	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578476	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTGCCGGGCGG	GGGTGCCGGGCGG	-	rs876659215	NA	P-0046793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	387	593	0	ENST00000269305.4:c.454_466del	p.Pro152AlafsTer14	p.P152Afs*14	ENST00000269305	NM_001126112.2	152	CCGCCCGGCACCCgc/gc	5/11	0.410234678848577	2	FACETS	0.816	0.777	0.856	0.816	0.777	0.856	CLONAL	2	TRUE	0	0.439533513055214	2		593	1079	SUCCESS
APC	324	MSKCC	GRCh37	5	112154723	112154723	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775126020	NA	P-0046793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	29	392	1	ENST00000257430.4:c.994C>T	p.Arg332Ter	p.R332*	ENST00000257430	NM_000038.5	332	Cga/Tga	10/16	0.413346198725207	1	FACETS	0.317	0.254	0.388	0.317	0.254	0.388	SUBCLONAL	1	TRUE	0	0.439533513055214	1		393	325	SUCCESS
APC	324	MSKCC	GRCh37	5	112175921	112175921	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	14	144	1	ENST00000257430.4:c.4630G>T	p.Glu1544Ter	p.E1544*	ENST00000257430	NM_000038.5	1544	Gaa/Taa	16/16	0.413346198725207	1	FACETS	0.353	0.256	0.468	0.353	0.256	0.468	SUBCLONAL	1	TRUE	0	0.439533513055214	1		145	141	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654820	29654820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786203416	NA	P-0046793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	73	154	0	ENST00000356175.3:c.5509G>A	p.Ala1837Thr	p.A1837T	ENST00000356175	NM_000267.3	1837	Gca/Aca	37/57	1	2	FACETS	0.944	0.831	1	0.944	0.831	1	CLONAL	1	TRUE	1	0.439533513055214	2		154	352	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115111972	115111972	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	172	404	0	ENST00000257566.3:c.1768C>T	p.Gln590Ter	p.Q590*	ENST00000257566	NM_016569.3	590	Cag/Tag	7/8	1	2	FACETS	0.997	0.919	1	0.997	0.919	1	CLONAL	1	TRUE	1	0.439533513055214	2		404	785	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881392	37881392	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	109	674	0	ENST00000269571.5:c.2584A>G	p.Thr862Ala	p.T862A	ENST00000269571		862	Aca/Gca	21/27	1	2	FACETS	0.605	0.543	0.671	0.605	0.543	0.671	SUBCLONAL	1	TRUE	1	0.439533513055214	2		674	820	SUCCESS
APC	324	MSKCC	GRCh37	5	112174357	112174358	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs876658724	NA	P-0046793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	41	152	0	ENST00000257430.4:c.3067dup	p.Thr1023AsnfsTer6	p.T1023Nfs*6	ENST00000257430	NM_000038.5	1022	-/A	16/16	0.413346198725207	1	FACETS	0.846	0.715	0.987	0.846	0.715	0.987	CLONAL	1	TRUE	0	0.439533513055214	1		152	172	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88676898	88676898	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747371306	NA	P-0046793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	155	319	0	ENST00000372037.3:c.683G>A	p.Arg228Gln	p.R228Q	ENST00000372037	NM_004329.2	228	cGa/cAa	9/13	0.413346198725207	1	FACETS	0.916	0.842	0.992	0.916	0.842	0.992	CLONAL	1	TRUE	0	0.439533513055214	1		319	601	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196093	138196093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1405321250	NA	P-0046793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	89	154	0	ENST00000237289.4:c.407G>A	p.Arg136His	p.R136H	ENST00000237289	NM_001270507.1	136	cGc/cAc	3/9	NA	2	FACETS	1	0.926	1			1	INDETERMINATE	1	TRUE	NA	0.439533513055214	2		154	387	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464398	464398	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	95	241	0	ENST00000399788.2:c.796C>T	p.Arg266Ter	p.R266*	ENST00000399788	NM_001042603.1	266	Cga/Tga	7/28	0.320151980999379	1	FACETS	0.679	0.606	0.755	0.679	0.606	0.755	SUBCLONAL	1	TRUE	0	0.439533513055214	1		241	497	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965191	81965191	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	183	353	0	ENST00000359376.3:c.2671G>C	p.Asp891His	p.D891H	ENST00000359376	NM_002661.3	891	Gac/Cac	25/33	0.229649760312124	2	FACETS	1	0.989	1	0.7	0.649	0.752	INDETERMINATE	1	TRUE	0	0.439533513055214	2		353	595	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954976	2954976	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772829458	NA	P-0046793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	235	462	0	ENST00000396946.4:c.2734C>T	p.Arg912Trp	p.R912W	ENST00000396946	NM_032415.4	912	Cgg/Tgg	21/25	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.439533513055214	2		462	896	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057874	27057874	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	443	448	2	ENST00000324856.7:c.1582C>T	p.Gln528Ter	p.Q528*	ENST00000324856	NM_006015.4	528	Cag/Tag	3/20	NA	2	FACETS	0.961	0.925	0.996			1	INDETERMINATE	2	TRUE	NA	0.603459251766037	2		450	764	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541295	187541295	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	22	195	1	ENST00000441802.2:c.6445G>T	p.Glu2149Ter	p.E2149*	ENST00000441802	NM_005245.3	2149	Gaa/Taa	10/27	0.603459251766037	1	FACETS	0.209	0.162	0.263	0.209	0.162	0.263	SUBCLONAL	1	TRUE	0	0.603459251766037	1		196	244	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604634	43604634	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	251	458	0	ENST00000355710.3:c.1219A>C	p.Thr407Pro	p.T407P	ENST00000355710	NM_020975.4	407	Acc/Ccc	6/20	0.603459251766037	1	FACETS	0.991	0.935	1	0.991	0.935	1	CLONAL	1	TRUE	0	0.603459251766037	1		458	586	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604641	43604641	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	247	468	0	ENST00000355710.3:c.1226C>A	p.Ser409Tyr	p.S409Y	ENST00000355710	NM_020975.4	409	tCc/tAc	6/20	0.603459251766037	1	FACETS	0.986	0.929	1	0.986	0.929	1	CLONAL	1	TRUE	0	0.603459251766037	1		468	580	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236215	108236215	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	153	286	0	ENST00000278616.4:c.9151G>A	p.Gly3051Arg	p.G3051R	ENST00000278616	NM_000051.3	3051	Gga/Aga	63/63	1	2	FACETS	0.876	0.805	0.949	0.876	0.805	0.949	CLONAL	1	TRUE	1	0.603459251766037	2		286	579	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555263	106555263	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	126	287	2	ENST00000369096.4:c.2380T>C	p.Ser794Pro	p.S794P	ENST00000369096	NM_001198.3	794	Tca/Cca	7/7	0.603459251766037	1	FACETS	0.932	0.856	1	0.932	0.856	1	CLONAL	1	TRUE	0	0.603459251766037	1		289	313	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98009732	98009732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	17	175	1	ENST00000289081.3:c.232C>T	p.Pro78Ser	p.P78S	ENST00000289081	NM_000136.2	78	Cct/Tct	3/15	0.603459251766037	1	FACETS	0.14	0.104	0.182	0.14	0.104	0.182	SUBCLONAL	1	TRUE	0	0.603459251766037	1		176	282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0046795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	476	469	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	0.83034751153292	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	0	0.83034751153292	3		469	536	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950051	38950051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398517192	NA	P-0046795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	91	235	0	ENST00000357387.3:c.3899C>T	p.Ala1300Val	p.A1300V	ENST00000357387	NM_152756.3	1300	gCa/gTa	31/38	0.83034751153292	8	FACETS	0.951	0.843	1	0.158	0.14	0.178	CLONAL	1	TRUE	2	0.83034751153292	8		235	805	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953733	48953734	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0046795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	154	112	0	ENST00000267163.4:c.1337dup	p.Tyr446Ter	p.Y446*	ENST00000267163	NM_000321.2	446	tac/tAac	14/27	0.83034751153292	3	FACETS	0.994	0.958	1	0.994	0.958	1	CLONAL	3	TRUE	0	0.83034751153292	3		112	176	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336089	73336089	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	144	124	0	ENST00000377767.4:c.2314T>G	p.Tyr772Asp	p.Y772D	ENST00000377767	NM_014953.3	772	Tac/Gac	17/21	0.83034751153292	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.83034751153292	3		124	156	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762485	41762485	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	103	332	0	ENST00000301178.4:c.2165C>A	p.Ala722Asp	p.A722D	ENST00000301178	NM_021913.4	722	gCt/gAt	18/20	0.683742568309081	4	FACETS	0.798	0.716	0.885	0.399	0.358	0.443	SUBCLONAL	1	TRUE	2	0.83034751153292	4		332	569	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458296	12458296	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	248	333	0	ENST00000287820.6:c.913G>A	p.Val305Met	p.V305M	ENST00000287820	NM_015869.4	305	Gtg/Atg	6/7	0.83034751153292	2	FACETS	0.986	0.953	1	0.986	0.953	1	CLONAL	2	TRUE	0	0.83034751153292	2		333	303	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033164	69033164	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	90	242	0	ENST00000288368.4:c.3604C>T	p.Gln1202Ter	p.Q1202*	ENST00000288368	NM_024870.2	1202	Cag/Tag	30/40	0.50066496954971	4	FACETS	1	0.976	1	0.657	0.59	0.727	CLONAL	1	TRUE	2	0.83034751153292	4		242	302	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015067	37015067	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	170	396	0	ENST00000358127.4:c.337G>C	p.Glu113Gln	p.E113Q	ENST00000358127	NM_001280556.1	113	Gag/Cag	3/10	1	2	FACETS	0.941	0.875	1	0.941	0.875	1	CLONAL	1	TRUE	1	0.83034751153292	2		396	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578464	7578476	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTGCCGGGCGG	GGGTGCCGGGCGG	-	rs876659215	NA	P-0046796-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	138	593	0	ENST00000269305.4:c.454_466del	p.Pro152AlafsTer14	p.P152Afs*14	ENST00000269305	NM_001126112.2	152	CCGCCCGGCACCCgc/gc	5/11	0.307754224846652	1	FACETS	0.943	0.858	1	0.943	0.858	1	CLONAL	1	TRUE	0	0.307754224846652	1		593	805	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121016	29121016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137853010	NA	P-0046797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	29	288	0	ENST00000328354.6:c.541C>T	p.Arg181Cys	p.R181C	ENST00000328354	NM_007194.3	181	Cgt/Tgt	4/15	1	2	FACETS	0.221	0.177	0.271	0.221	0.177	0.271	SUBCLONAL	1	TRUE	1	0.728266157896351	2		288	360	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821566	72821581	+	frameshift_variant	Frame_Shift_Del	DEL	CGCTCTCGCACGCCAG	CGCTCTCGCACGCCAG	TGCGA	novel	NA	P-0046797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	75	133	0	ENST00000268489.5:c.10594_10609delinsTCGCA	p.Leu3532SerfsTer35	p.L3532Sfs*35	ENST00000268489	NM_006885.3	3532	CTGGCGTGCGAGAGCGcg/TCGCAcg	10/10	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.728266157896351	2		133	199	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	126	455	1	ENST00000418115.1:c.50G>T	p.Gly17Val	p.G17V	ENST00000418115	NM_001664.2	17	gGa/gTa	2/5	1	2	FACETS	1	0.972	1	1	0.991	1	CLONAL	2	TRUE	1	0.227352141254695	2		456	476	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284990	15284990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	106	764	2	ENST00000263388.2:c.4625C>T	p.Ser1542Leu	p.S1542L	ENST00000263388	NM_000435.2	1542	tCg/tTg	25/33	0.227352141254695	11	FACETS	0.911	0.815	1			1	CLONAL	2	TRUE	NA	0.227352141254695	11		766	1035	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061195	38061195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	114	365	0	ENST00000250448.2:c.794G>A	p.Arg265His	p.R265H	ENST00000250448	NM_004496.3	265	cGc/cAc	2/2	0.204666673075281	4	FACETS	1	0.913	1	1	0.985	1	CLONAL	3	TRUE	2	0.227352141254695	4		365	408	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846082	68846083	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	109	488	0	ENST00000261769.5:c.1055dup	p.Glu353Ter	p.E353*	ENST00000261769	NM_004360.3	351	-/G	8/16	0.227352141254695	0	FACETS	0.767	0.697	0.839			1	SUBCLONAL	3	TRUE	0	0.227352141254695	0		488	322	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0046801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	66	361	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.885	0.773	1	0.885	0.773	1	CLONAL	1	TRUE	1	0.398609536292216	2		361	374	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0046801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	129	391	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.313329836112989	3	FACETS	1	0.986	1	0.732	0.667	0.8	CLONAL	1	TRUE	1	0.398609536292216	3		392	530	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560902	9560902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756198440	NA	P-0046801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	145	659	1	ENST00000353224.5:c.880G>A	p.Glu294Lys	p.E294K	ENST00000353224	NM_177990.2	294	Gaa/Aaa	4/10	0.276997480165243	4	FACETS	1	0.933	1	1	0.933	1	CLONAL	2	TRUE	2	0.398609536292216	4		660	500	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974715	21974732	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCCCCCGCCTCCA	GCAGCGCCCCCGCCTCCA	-	novel	NA	P-0046801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	107	349	0	ENST00000304494.5:c.95_112del	p.Leu32_Leu37del	p.L32_L37del	ENST00000304494	NM_000077.4	32	cTGGAGGCGGGGGCGCTGCcc/ccc	1/3	0.334292870281977	2	FACETS	1	0.971	1	0.603	0.544	0.665	CLONAL	1	TRUE	0	0.398609536292216	2		349	445	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658469	117658469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	85	386	0	ENST00000368508.3:c.5114C>T	p.Ser1705Leu	p.S1705L	ENST00000368508	NM_002944.2	1705	tCa/tTa	31/43	0.276997480165243	4	FACETS	0.791	0.704	0.883	0.791	0.704	0.883	SUBCLONAL	2	TRUE	2	0.398609536292216	4		386	377	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858947	57858947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	233	625	0	ENST00000228682.2:c.443C>T	p.Ser148Phe	p.S148F	ENST00000228682	NM_005269.2	148	tCc/tTc	5/12	0.332404382642139	4	FACETS	0.819	0.764	0.876	0.819	0.764	0.876	CLONAL	2	TRUE	2	0.398609536292216	4		625	998	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770569	40770569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	97	342	0	ENST00000373198.4:c.2813G>A	p.Gly938Glu	p.G938E	ENST00000373198	NM_133170.3	938	gGg/gAg	19/32	0.276997480165243	4	FACETS	1	0.98	1	0.718	0.643	0.797	CLONAL	1	TRUE	2	0.398609536292216	4		342	474	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347270	89347270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	251	658	0	ENST00000301030.4:c.5680C>T	p.Pro1894Ser	p.P1894S	ENST00000301030	NM_001256183.1	1894	Ccc/Tcc	9/13	0.276997480165243	4	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	2	0.398609536292216	4		658	881	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215582	5215582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	242	679	0	ENST00000357368.4:c.4121C>T	p.Pro1374Leu	p.P1374L	ENST00000357368	NM_002850.3	1374	cCc/cTc	27/38	0.276997480165243	4	FACETS	0.772	0.721	0.825	0.772	0.721	0.825	SUBCLONAL	2	TRUE	2	0.398609536292216	4		679	1100	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394761	394761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	123	353	1	ENST00000399788.2:c.4934C>T	p.Pro1645Leu	p.P1645L	ENST00000399788	NM_001042603.1	1645	cCa/cTa	28/28	0.276997480165243	4	FACETS	0.853	0.775	0.934	0.853	0.775	0.934	CLONAL	2	TRUE	2	0.398609536292216	4		354	506	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624913	9624913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	108	375	0	ENST00000353224.5:c.64C>T	p.His22Tyr	p.H22Y	ENST00000353224	NM_177990.2	22	Cat/Tat	3/10	0.276997480165243	4	FACETS	0.855	0.773	0.942	0.855	0.773	0.942	CLONAL	2	TRUE	2	0.398609536292216	4		375	443	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775164	73775164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867543814	NA	P-0046801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	252	603	0	ENST00000254810.4:c.92C>T	p.Pro31Leu	p.P31L	ENST00000254810	NM_005324.3	31	cCc/cTc	2/4	0.332404382642139	4	FACETS	0.924	0.865	0.984	0.924	0.865	0.984	CLONAL	2	TRUE	2	0.398609536292216	4		603	957	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118339541	118339541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	118	393	0	ENST00000534358.1:c.484C>T	p.Pro162Ser	p.P162S	ENST00000534358	NM_005933.3	162	Ccc/Tcc	2/36	0.389011849288311	3	FACETS	1	0.983	1	0.709	0.642	0.778	CLONAL	1	TRUE	1	0.398609536292216	3		393	501	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937693	36937693	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	236	716	0	ENST00000361632.4:c.1045C>T	p.Pro349Ser	p.P349S	ENST00000361632		349	Ccc/Tcc	8/16	0.313329836112989	3	FACETS	1	0.992	1	0.746	0.697	0.797	CLONAL	1	TRUE	1	0.398609536292216	3		716	952	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025808	1025808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	130	378	0	ENST00000358495.3:c.722C>T	p.Ser241Phe	p.S241F	ENST00000358495	NM_134424.2	241	tCc/tTc	8/12	0.276997480165243	4	FACETS	0.859	0.783	0.938	0.859	0.783	0.938	CLONAL	2	TRUE	2	0.398609536292216	4		378	531	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602401	28602401	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	107	364	1	ENST00000241453.7:c.1967A>G	p.Glu656Gly	p.E656G	ENST00000241453	NM_004119.2	656	gAg/gGg	16/24	0.276997480165243	4	FACETS	0.859	0.776	0.946	0.859	0.776	0.946	CLONAL	2	TRUE	2	0.398609536292216	4		365	437	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2115545	2115546	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	269	608	0	ENST00000219476.3:c.1625_1626delinsTT	p.Pro542Leu	p.P542L	ENST00000219476	NM_000548.3	542	cCC/cTT	16/42	0.326115281643742	5	FACETS	1	0.986	1	0.77	0.723	0.817	CLONAL	2	TRUE	2	0.398609536292216	5		608	934	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228581	36228581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	290	732	0	ENST00000222270.7:c.7595G>A	p.Arg2532Gln	p.R2532Q	ENST00000222270	NM_014727.1	2532	cGg/cAg	34/37	0.276997480165243	4	FACETS	0.908	0.854	0.963	0.908	0.854	0.963	CLONAL	2	TRUE	2	0.398609536292216	4		732	1121	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881588	111881588	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1347714808	NA	P-0046801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	197	484	0	ENST00000393256.3:c.266T>G	p.Leu89Arg	p.L89R	ENST00000393256	NM_006538.4	89	cTg/cGg	2/4	0.276997480165243	4	FACETS	0.848	0.787	0.912	0.848	0.787	0.912	CLONAL	2	TRUE	2	0.398609536292216	4		484	815	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484621	57484622	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	129	462	0	ENST00000371085.3:c.705_706delinsTT	p.Gln236Ter	p.Q236*	ENST00000371085	NM_000516.4	235	atCCag/atTTag	9/13	0.276997480165243	4	FACETS	1	0.985	1	0.718	0.653	0.787	CLONAL	1	TRUE	2	0.398609536292216	4		462	630	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29115417	29115417	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0046801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	110	331	1	ENST00000328354.6:c.649A>T	p.Arg217Ter	p.R217*	ENST00000328354	NM_007194.3	217	Aga/Tga	5/15	0.332404382642139	4	FACETS	0.811	0.732	0.893	0.811	0.732	0.893	CLONAL	2	TRUE	2	0.398609536292216	4		332	476	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89176402	89176402	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	41	202	0	ENST00000336596.2:c.132G>A	p.Trp44Ter	p.W44*	ENST00000336596	NM_005233.5	44	tgG/tgA	2/17	0.280374447787124	3	FACETS	1	0.893	1	1	0.893	1	CLONAL	2	TRUE	1	0.398609536292216	3		202	117	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549745	187549745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	83	274	0	ENST00000441802.2:c.4496C>T	p.Pro1499Leu	p.P1499L	ENST00000441802	NM_005245.3	1499	cCa/cTa	8/27	0.276997480165243	4	FACETS	1	0.975	1	0.693	0.615	0.776	CLONAL	1	TRUE	2	0.398609536292216	4		274	420	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637867	176637867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	80	409	0	ENST00000439151.2:c.2467C>T	p.Pro823Ser	p.P823S	ENST00000439151	NM_022455.4	823	Cct/Tct	5/23	1	2	FACETS	0.865	0.764	0.972	0.865	0.764	0.972	CLONAL	1	TRUE	1	0.398609536292216	2		409	464	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979272	93979272	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	56	264	0	ENST00000369303.4:c.1556C>T	p.Thr519Ile	p.T519I	ENST00000369303	NM_004440.3	519	aCt/aTt	7/17	0.276997480165243	4	FACETS	0.862	0.747	0.984	0.862	0.747	0.984	CLONAL	2	TRUE	2	0.398609536292216	4		264	228	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249680	110249681	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0046801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	208	796	0	ENST00000374672.4:c.994_995delinsTT	p.Pro332Phe	p.P332F	ENST00000374672	NM_004235.4	332	CCt/TTt	3/5	0.389011849288311	3	FACETS	1	0.972	1	0.548	0.507	0.589	CLONAL	1	TRUE	1	0.398609536292216	3		796	1143	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619031	37619032	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0046802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	296	419	0	ENST00000447079.4:c.711dup	p.Ser238LeufsTer10	p.S238Lfs*10	ENST00000447079	NM_015083.1	236	agc/agCc	1/14	0.453408940885897	3	FACETS	0.883	0.837	0.929	0.589	0.558	0.62	CLONAL	2	TRUE	0	0.63324637005391	3		419	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579328	7579328	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	363	528	0	ENST00000269305.4:c.359del	p.Lys120SerfsTer3	p.K120Sfs*3	ENST00000269305	NM_001126112.2	120	aAg/ag	4/11	0.453408940885897	3	FACETS	1	0.993	1	0.779	0.746	0.811	CLONAL	2	TRUE	0	0.63324637005391	3		528	646	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451179	70451179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	126	435	0	ENST00000373644.4:c.6019G>A	p.Gly2007Ser	p.G2007S	ENST00000373644	NM_030625.2	2007	Ggt/Agt	12/12	0.15410315334623	6	FACETS	0.871	0.792	0.952			1	INDETERMINATE	2	TRUE	NA	0.63324637005391	6		435	518	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244474	41244474	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046802-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	127	374	0	ENST00000357654.3:c.3074C>A	p.Thr1025Lys	p.T1025K	ENST00000357654	NM_007294.3	1025	aCa/aAa	10/23	0.453408940885897	3	FACETS	1	0.97	1	0.382	0.348	0.417	CLONAL	1	TRUE	0	0.63324637005391	3		374	461	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551568	150551568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748263149	NA	P-0046803-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	190	519	0	ENST00000369026.2:c.439G>A	p.Val147Ile	p.V147I	ENST00000369026	NM_021960.4	147	Gtc/Atc	1/3	1	2	FACETS	0.658	0.609	0.709	0.658	0.609	0.709	SUBCLONAL	1	TRUE	1	0.72	2		519	802	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0046808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	55	363	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.85	0.73	0.981	0.85	0.73	0.981	CLONAL	1	TRUE	1	0.338683217271935	2		363	382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs530941076	NA	P-0046808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	138	488	0	ENST00000269305.4:c.658T>A	p.Tyr220Asn	p.Y220N	ENST00000269305	NM_001126112.2	220	Tat/Aat	6/11	0.338683217271935	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.338683217271935	1		488	667	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052632	42052632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779811318	NA	P-0046808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	98	317	1	ENST00000219905.7:c.7303C>T	p.Arg2435Trp	p.R2435W	ENST00000219905	NM_001164273.1	2435	Cgg/Tgg	20/24	0.338683217271935	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.338683217271935	1		318	463	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856217	111856217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879321203	NA	P-0046808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	71	251	0	ENST00000341259.2:c.268C>T	p.Arg90Trp	p.R90W	ENST00000341259	NM_005475.2	90	Cgg/Tgg	2/8	1	2	FACETS	0.875	0.766	0.993	0.875	0.766	0.993	CLONAL	1	TRUE	1	0.338683217271935	2		251	479	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584720	48584721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	75	286	0	ENST00000342988.3:c.799dup	p.Thr267AsnfsTer6	p.T267Nfs*6	ENST00000342988	NM_005359.5	266	-/A	7/12	0.338683217271935	1	FACETS	0.992	0.874	1	0.992	0.874	1	CLONAL	1	TRUE	0	0.338683217271935	1		286	371	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781515	135781515	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046808-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	75	274	0	ENST00000298552.3:c.1450A>G	p.Arg484Gly	p.R484G	ENST00000298552	NM_001162426.1	484	Aga/Gga	15/23	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.338683217271935	2		274	422	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0046809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	45	363	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.709	0.597	0.832	0.709	0.597	0.832	SUBCLONAL	1	FALSE	1	0.32815577485203	2		363	387	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138112	64138112	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	47	639	2	ENST00000334205.4:c.2035G>A	p.Ala679Thr	p.A679T	ENST00000334205	NM_003942.2	679	Gcg/Acg	16/17	1	2	FACETS	0.583	0.492	0.684	0.583	0.492	0.684	SUBCLONAL	1	FALSE	1	0.32815577485203	2		641	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579323	7579329	+	frameshift_variant	Frame_Shift_Del	DEL	CAGACTT	CAGACTT	-	novel	NA	P-0046809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	59	474	0	ENST00000269305.4:c.358_364del	p.Lys120Ter	p.K120*	ENST00000269305	NM_001126112.2	120	AAGTCTGtg/tg	4/11	0.32815577485203	1	FACETS	0.711	0.613	0.816	0.711	0.613	0.816	SUBCLONAL	1	FALSE	0	0.32815577485203	1		474	423	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955457	48955458	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0046809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	68	209	0	ENST00000267163.4:c.1575dup	p.Phe526LeufsTer2	p.F526Lfs*2	ENST00000267163	NM_000321.2	525	gcc/gCcc	17/27	0.217718361072409	3	FACETS	0.858	0.754	0.969	0.572	0.503	0.646	CLONAL	2	FALSE	0	0.32815577485203	3		209	281	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176700745	176700745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745582394	NA	P-0046810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	81	269	0	ENST00000439151.2:c.5582G>A	p.Arg1861Gln	p.R1861Q	ENST00000439151	NM_022455.4	1861	cGa/cAa	17/23	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.444582655021199	2		269	352	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556985	29556985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	29	125	0	ENST00000356175.3:c.2983C>G	p.Leu995Val	p.L995V	ENST00000356175	NM_000267.3	995	Ctg/Gtg	22/57	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.444582655021199	2		125	106	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158433	106158606	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTAGATACTCCTATAAAAAATTTATTGGATACACCTGTCAAGACTCAATATGATTTCCCATCTTGCAGATGTGTAGGTAAGTGCCAGAAATGTACTGAGACACATGGCGTTTATCCAGAATTAGCAAATTTATCTTCAGATATGGGATTTTCCTTCTTTTTTTAAATCTTGAGT	CTAGATACTCCTATAAAAAATTTATTGGATACACCTGTCAAGACTCAATATGATTTCCCATCTTGCAGATGTGTAGGTAAGTGCCAGAAATGTACTGAGACACATGGCGTTTATCCAGAATTAGCAAATTTATCTTCAGATATGGGATTTTCCTTCTTTTTTTAAATCTTGAGT	-	novel	NA	P-0046810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	19	156	0	ENST00000380013.4:c.3336_3409+100del		p.X1112_splice	ENST00000380013	NM_001127208.2	1112		3/11	0.444582655021199	1	FACETS	0.523	0.402	0.663	0.523	0.402	0.663	SUBCLONAL	1	TRUE	0	0.444582655021199	1		156	127	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279560	123279587	+	protein_altering_variant	In_Frame_Del	DEL	ATCCACTGGATGTGGGGCTGGGCATCAC	ATCCACTGGATGTGGGGCTGGGCATCAC	T	novel	NA	P-0046810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	293	560	0	ENST00000358487.5:c.845_872delinsA	p.Ser282_Ile291delinsAsn	p.S282_I291delinsN	ENST00000358487	NM_000141.4	282	aGTGATGCCCAGCCCCACATCCAGTGGATc/aAc	7/18	0.437600055723343	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.444582655021199	2		560	597	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0046811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	84	363	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.999	0.887	1	0.999	0.887	1	CLONAL	1	TRUE	1	0.415430465047384	2		363	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577115	7577115	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519983	NA	P-0046811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	153	603	0	ENST00000269305.4:c.823T>C	p.Cys275Arg	p.C275R	ENST00000269305	NM_001126112.2	275	Tgt/Cgt	8/11	0.415430465047384	1	FACETS	0.989	0.909	1	0.989	0.909	1	CLONAL	1	TRUE	0	0.415430465047384	1		603	590	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216631	2216631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769937964	NA	P-0046811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	206	921	1	ENST00000398665.3:c.2275C>T	p.Arg759Cys	p.R759C	ENST00000398665	NM_032482.2	759	Cgc/Tgc	20/28	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.415430465047384	2		922	870	SUCCESS
APC	324	MSKCC	GRCh37	5	112176027	112176030	+	frameshift_variant	Frame_Shift_Del	DEL	TTAT	TTAT	-	novel	NA	P-0046811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	41	256	0	ENST00000257430.4:c.4738_4741del	p.Ile1580LeufsTer69	p.I1580Lfs*69	ENST00000257430	NM_000038.5	1579	aTTATt/at	16/16	1	2	FACETS	0.949	0.799	1	0.949	0.799	1	CLONAL	1	TRUE	1	0.415430465047384	2		256	208	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549404	21549404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753026198	NA	P-0046811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	114	532	0	ENST00000382592.4:c.2872C>T	p.Arg958Cys	p.R958C	ENST00000382592	NM_014572.2	958	Cgc/Tgc	8/8	0.415430465047384	6	FACETS	1	0.958	1	0.225	0.202	0.249	CLONAL	1	TRUE	1	0.415430465047384	6		532	895	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248416	59248417	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0046811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	101	508	0	ENST00000371222.2:c.326dup	p.Phe110LeufsTer200	p.F110Lfs*200	ENST00000371222	NM_002228.3	109	ggc/ggGc	1/1	1	2	FACETS	0.865	0.775	0.96	0.865	0.775	0.96	CLONAL	1	TRUE	1	0.415430465047384	2		508	562	SUCCESS
APC	324	MSKCC	GRCh37	5	112174270	112174271	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	37	264	0	ENST00000257430.4:c.2983dup	p.Cys995LeufsTer13	p.C995Lfs*13	ENST00000257430	NM_000038.5	993	-/T	16/16	1	2	FACETS	0.727	0.603	0.863	0.727	0.603	0.863	SUBCLONAL	1	TRUE	1	0.415430465047384	2		264	245	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028168	69028168	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0046811-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	60	392	0	ENST00000288368.4:c.3326+1G>A		p.X1109_splice	ENST00000288368	NM_024870.2	1109			1	2	FACETS	0.979	0.85	1	0.979	0.85	1	CLONAL	1	TRUE	1	0.415430465047384	2		392	295	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0046812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	67	589	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.267924609553617	2		589	405	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0046812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	99	757	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.267924609553617	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.267924609553617	1		757	518	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037187	71037209	+	frameshift_variant	Frame_Shift_Del	DEL	GTGGGTCATCATGGCTTGCAGGC	GTGGGTCATCATGGCTTGCAGGC	-	novel	NA	P-0046812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	31	421	0	ENST00000318789.4:c.1082_1104del	p.Arg361ProfsTer92	p.R361Pfs*92	ENST00000318789	NM_032682.5	361	cGCCTGCAAGCCATGATGACCCAC/c	14/21	1	2	FACETS	0.595	0.481	0.724	0.595	0.481	0.724	SUBCLONAL	1	TRUE	1	0.267924609553617	2		421	389	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0046814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	238	137	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.474619073248536	11	FACETS	0.95	0.905	0.993			1	CLONAL	9	TRUE	NA	0.474619073248536	11		137	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578191	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs530941076	NA	P-0046814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	335	425	0	ENST00000269305.4:c.658T>G	p.Tyr220Asp	p.Y220D	ENST00000269305	NM_001126112.2	220	Tat/Gat	6/11	0.460391870057965	3	FACETS	0.945	0.904	0.987	0.945	0.904	0.987	CLONAL	3	TRUE	0	0.474619073248536	3		425	616	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125635	47125635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	146	229	0	ENST00000409792.3:c.5635C>T	p.Arg1879Cys	p.R1879C	ENST00000409792	NM_014159.6	1879	Cgc/Tgc	12/21	0.474619073248536	4	FACETS	1	0.969	1			1	CLONAL	2	TRUE	NA	0.474619073248536	4		229	412	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429349	78429349	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	328	330	0	ENST00000370768.2:c.1093C>T	p.Gln365Ter	p.Q365*	ENST00000370768	NM_003902.3	365	Caa/Taa	13/20	0.474619073248536	7	FACETS	0.952	0.904	1	0.952	0.904	1	CLONAL	4	TRUE	3	0.474619073248536	7		330	794	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678472	88678472	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	218	459	0	ENST00000360948.2:c.1064A>T	p.Glu355Val	p.E355V	ENST00000360948	NM_001012338.2	355	gAg/gTg	9/19	0.260997315968115	5	FACETS	1	0.982	1	0.758	0.708	0.809	INDETERMINATE	2	TRUE	2	0.474619073248536	5		459	692	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	112	427	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.847	0.769	0.929	0.847	0.769	0.929	CLONAL	1	TRUE	1	0.681341247457174	2		427	388	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0046815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	110	292	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.67797311043297	3	FACETS	0.919	0.83	1	0.46	0.415	0.506	CLONAL	1	TRUE	1	0.681341247457174	3		292	471	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412262	63412262	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1235049855	NA	P-0046815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	359	395	0	ENST00000330258.3:c.905A>G	p.Asn302Ser	p.N302S	ENST00000330258	NM_152424.3	302	aAt/aGt	2/2	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.681341247457174	1		395	513	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	66	427	0				ENST00000310581	NM_198253.2	-/1132			0.322112829750718	2	FACETS	1	0.942	1	0.562	0.494	0.634	CLONAL	1	TRUE	0	0.477431409835567	2		427	246	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913492	NA	P-0046816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	33	438	0	ENST00000286548.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000286548	NM_002072.3	209	cAa/cTa	5/7	1	2	FACETS	0.596	0.488	0.715	0.596	0.488	0.715	SUBCLONAL	1	TRUE	1	0.477431409835567	2		438	232	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980394	7980394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs562084711	NA	P-0046816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	200	806	0	ENST00000319144.4:c.1189G>A	p.Ala397Thr	p.A397T	ENST00000319144	NM_001139.2	397	Gcc/Acc	9/15	0.265940124835439	3	FACETS	1	0.988	1	0.655	0.608	0.704	INDETERMINATE	1	TRUE	1	0.477431409835567	3		806	792	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0046817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	10	572	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.11868388760138	4	FACETS	0.302	0.203	0.426	0.151	0.101	0.213	INDETERMINATE	1	FALSE	2	0.247606373809726	4		572	334	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0046817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	38	258	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.11868388760138	4	FACETS	1	0.942	1	0.672	0.558	0.798	INDETERMINATE	1	FALSE	2	0.247606373809726	4		258	285	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061272	38061942	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCCCGGCTTGTCCGGGGAGCGTGCCACCTTGACGAAGCAGTCATTGAAGGACAGCGAGTGGCGGATGGAGTTCTGCCAGCGCTGCTGGTTCTGCCGGTAATAGGGGAAGAGGTCCATGATCCACTGGTAGATCTCGCTCAGCGTGAGCATCTTGCTGGGCGCCTGCTGGATGGCCATGGTGATGAGCGAGATGTACGAGTAGGGCGGCTTGGCGTGCGGGTAGCTGCGCTTGAACGTCTTGGCGTCGCCGCCGCCGCCCGCGCGGCTGCGGCCCAGGTTGGACGGCGCGTACGCCATGGGGCTCATGCACGGGTTCATGGCGGCCGCGTAGGGGCCCAGGCCATTCATGGAGGCCGCCTGCTGCGCACCCATGGCGCCCATGCCGCTCGGGCTCAGCGCCGTACCCATGGCCGTCACGCCGGCCGCAGTCATGCTGTTCATGGCGCCCGCCGAGCCCCCCGGCATGCCGGCTACTGCGCCGGGACTCAGGCCGGCCCCTAGGCCCGGGTTGGCATAGGACATGTTGAAGGACGCCGGGGTCATGTTGCCGCTCGTAGTCATGGTGTTCATGGTCATGTAGGTGTTCATGGAGTTCATGGAGCCCAGGCCTGAGTTCATGTTGCTGACCGGGACGGAGGAGTAGGCCTGGAGTGGAGACAGCGAGTGAAGAA	GCCCGGCTTGTCCGGGGAGCGTGCCACCTTGACGAAGCAGTCATTGAAGGACAGCGAGTGGCGGATGGAGTTCTGCCAGCGCTGCTGGTTCTGCCGGTAATAGGGGAAGAGGTCCATGATCCACTGGTAGATCTCGCTCAGCGTGAGCATCTTGCTGGGCGCCTGCTGGATGGCCATGGTGATGAGCGAGATGTACGAGTAGGGCGGCTTGGCGTGCGGGTAGCTGCGCTTGAACGTCTTGGCGTCGCCGCCGCCGCCCGCGCGGCTGCGGCCCAGGTTGGACGGCGCGTACGCCATGGGGCTCATGCACGGGTTCATGGCGGCCGCGTAGGGGCCCAGGCCATTCATGGAGGCCGCCTGCTGCGCACCCATGGCGCCCATGCCGCTCGGGCTCAGCGCCGTACCCATGGCCGTCACGCCGGCCGCAGTCATGCTGTTCATGGCGCCCGCCGAGCCCCCCGGCATGCCGGCTACTGCGCCGGGACTCAGGCCGGCCCCTAGGCCCGGGTTGGCATAGGACATGTTGAAGGACGCCGGGGTCATGTTGCCGCTCGTAGTCATGGTGTTCATGGTCATGTAGGTGTTCATGGAGTTCATGGAGCCCAGGCCTGAGTTCATGTTGCTGACCGGGACGGAGGAGTAGGCCTGGAGTGGAGACAGCGAGTGAAGAA	-	novel	NA	P-0046817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	16	557	0	ENST00000250448.2:c.73-26_717del		p.X25_splice	ENST00000250448	NM_004496.3	25		2/2	0.102813053356634	3	FACETS	0.492	0.363	0.647	0.246	0.181	0.324	INDETERMINATE	1	FALSE	1	0.247606373809726	3		557	295	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642710	3642710	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs752675370	NA	P-0046817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	45	449	0	ENST00000294008.3:c.2317C>G	p.Leu773Val	p.L773V	ENST00000294008	NM_032444.2	773	Ctg/Gtg	11/15	0.238428193986794	1	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	FALSE	0	0.247606373809726	1		449	288	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145705	61145705	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	36	230	0	ENST00000295025.8:c.817G>A	p.Glu273Lys	p.E273K	ENST00000295025	NM_002908.2	273	Gaa/Aaa	7/11	0.247606373809726	5	FACETS	1	0.931	1			1	CLONAL	1	FALSE	NA	0.247606373809726	5		230	310	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	112	427	0				ENST00000310581	NM_198253.2	-/1132			0.263098407171691	4	FACETS	1	0.983	1	0.715	0.648	0.786	INDETERMINATE	1	FALSE	2	0.548491385972588	4		427	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0046818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	236	736	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.308358520916449	2	FACETS	1	0.986	1	0.592	0.554	0.63	INDETERMINATE	1	FALSE	0	0.548491385972588	2		736	727	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5465595	5465595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148141792	NA	P-0046818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	23	121	0	ENST00000381577.3:c.779G>A	p.Arg260His	p.R260H	ENST00000381577	NM_014143.3	260	cGt/cAt	5/7	0.263098407171691	4	FACETS	0.501	0.392	0.628	0.251	0.196	0.314	INDETERMINATE	1	FALSE	2	0.548491385972588	4		121	259	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416343	29416343	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1046265972	NA	P-0046818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	237	593	0	ENST00000389048.3:c.4610G>A	p.Gly1537Glu	p.G1537E	ENST00000389048	NM_004304.4	1537	gGa/gAa	29/29	0.306985014497567	5	FACETS	0.759	0.708	0.811	0.506	0.472	0.541	INDETERMINATE	2	FALSE	2	0.548491385972588	5		593	1038	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15821859	15821859	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	52	169	0	ENST00000307771.7:c.252A>C	p.Glu84Asp	p.E84D	ENST00000307771	NM_005089.3	84	gaA/gaC	4/11	0.160167252757134	3	FACETS	1	0.919	1	0.366	0.315	0.42	INDETERMINATE	1	FALSE	0	0.548491385972588	3		169	220	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0046834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	22	409	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.140726942353537	4	FACETS	1	0.877	1	0.599	0.467	0.75	INDETERMINATE	1	TRUE	2	0.254437750305564	4		410	181	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	66	483	2	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	0.254437750305564	3	FACETS	0.809	0.701	0.926	0.404	0.35	0.463	CLONAL	1	TRUE	1	0.254437750305564	3		485	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0046834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	78	672	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.933	0.82	1	0.933	0.82	1	CLONAL	1	TRUE	1	0.254437750305564	2		672	657	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0046834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	56	286	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.254437750305564	2		286	413	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0046834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	39	214	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	0.254437750305564	1	FACETS	0.778	0.646	0.923	0.778	0.646	0.923	CLONAL	1	TRUE	0	0.254437750305564	1		214	344	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	45	427	0				ENST00000310581	NM_198253.2	-/1132			0.339715244445483	5	FACETS	1	0.943	1	0.811	0.695	0.933	CLONAL	2	TRUE	2	0.404379791370019	5		427	147	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0046835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	114	606	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.404379791370019	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	2	TRUE	0	0.404379791370019	2		606	280	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416773	121416773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779442858	NA	P-0046835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	40	674	0	ENST00000257555.6:c.202C>T	p.Arg68Trp	p.R68W	ENST00000257555		68	Cgg/Tgg	1/10	0.367191807064815	3	FACETS	0.835	0.697	0.986	0.417	0.348	0.493	CLONAL	1	TRUE	1	0.404379791370019	3		674	285	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602848	10602848	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	129	729	0	ENST00000171111.5:c.730G>A	p.Glu244Lys	p.E244K	ENST00000171111	NM_203500.1	244	Gag/Aag	3/6	0.406291044782586	1	FACETS	0.751	0.69	0.813	1	0.988	1	SUBCLONAL	2	TRUE	0	0.404379791370019	1		729	339	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385386	4385386	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	39	217	0	ENST00000261254.3:c.411+1del		p.L137fs	ENST00000261254	NM_001759.3	137	ctG/ct	2/5	0.406291044782586	4	FACETS	1	0.941	1	0.651	0.545	0.767	CLONAL	1	TRUE	2	0.404379791370019	4		217	208	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394410	162394410	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	26	275	0	ENST00000366898.1:c.658A>G	p.Lys220Glu	p.K220E	ENST00000366898	NM_004562.2	220	Aag/Gag	6/12	0.367191807064815	3	FACETS	0.818	0.653	1	0.409	0.326	0.502	CLONAL	1	TRUE	1	0.404379791370019	3		275	189	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561495	141561495	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	119	548	2	ENST00000220592.5:c.1310T>G	p.Met437Arg	p.M437R	ENST00000220592	NM_012154.3	437	aTg/aGg	11/19	0.367191807064815	3	FACETS	0.938	0.856	1	0.938	0.856	1	CLONAL	2	TRUE	1	0.404379791370019	3		550	377	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939223	76939223	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	56	485	0	ENST00000373344.5:c.1525A>G	p.Thr509Ala	p.T509A	ENST00000373344	NM_000489.3	509	Act/Gct	9/35	0.367191807064815	3	FACETS	1	0.918	1	0.546	0.471	0.627	CLONAL	1	TRUE	1	0.404379791370019	3		485	305	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412252	139412252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057523819	NA	P-0046836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	43	856	0	ENST00000277541.6:c.1393G>A	p.Ala465Thr	p.A465T	ENST00000277541	NM_017617.3	465	Gcc/Acc	8/34	1	2	FACETS	0.614	0.512	0.726	0.614	0.512	0.726	SUBCLONAL	1	TRUE	1	0.222831654097098	2		856	629	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0046836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	20	237	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	0.816	0.626	1	0.816	0.626	1	CLONAL	1	TRUE	1	0.222831654097098	2		237	220	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164884	106164884	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1339287432	NA	P-0046836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	38	410	0	ENST00000380013.4:c.3752C>T	p.Thr1251Met	p.T1251M	ENST00000380013	NM_001127208.2	1251	aCg/aTg	6/11	1	2	FACETS	0.82	0.678	0.978	0.82	0.678	0.978	CLONAL	1	TRUE	1	0.222831654097098	2		410	416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579699	7579699	+	splice_donor_variant	Splice_Site	SNP	C	C	G	rs1131691003	NA	P-0046836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	72	441	0	ENST00000269305.4:c.96+1G>C		p.X32_splice	ENST00000269305	NM_001126112.2	32			0.222831654097098	2	FACETS	0.915	0.805	1	0.915	0.805	1	CLONAL	2	TRUE	0	0.222831654097098	2		441	353	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573133	64573133	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	66	432	0	ENST00000312049.6:c.1159G>T	p.Glu387Ter	p.E387*	ENST00000312049	NM_130799.2	387	Gag/Tag	8/10	0.0873083703049071	4	FACETS	0.852	0.742	0.97	0.852	0.742	0.97	INDETERMINATE	2	TRUE	2	0.222831654097098	4		432	425	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575555	64575570	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GCTGTCCAATTTGGTG	GCTGTCCAATTTGGTG	-	novel	NA	P-0046836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	84	542	0	ENST00000312049.6:c.447_462del	p.Thr150ProfsTer30	p.T150Pfs*30	ENST00000312049	NM_130799.2	149	ggCACCAAATTGGACAGC/gg	3/10	0.0873083703049071	4	FACETS	0.854	0.756	0.958	0.854	0.756	0.958	INDETERMINATE	2	TRUE	2	0.222831654097098	4		542	540	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629127	86629127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	27	262	0	ENST00000274376.6:c.872C>G	p.Thr291Arg	p.T291R	ENST00000274376	NM_002890.2	291	aCa/aGa	4/25	1	2	FACETS	0.962	0.768	1	0.962	0.768	1	CLONAL	1	TRUE	1	0.222831654097098	2		262	252	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0046837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	36	572	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.6	0.493	0.721	0.6	0.493	0.721	SUBCLONAL	1	TRUE	1	0.223390734108901	2		572	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0046837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	134	511	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	1	2	FACETS	0.877	0.798	0.959	1	0.989	1	CLONAL	2	TRUE	1	0.223390734108901	2		511	684	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0046837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	14	220	3	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.431	0.311	0.576	0.431	0.311	0.576	SUBCLONAL	1	TRUE	1	0.223390734108901	2		223	291	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249511	153249511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	96	368	0	ENST00000281708.4:c.1267G>A	p.Gly423Arg	p.G423R	ENST00000281708	NM_033632.3	423	Gga/Aga	9/12	1	2	FACETS	0.934	0.837	1	1	0.986	1	CLONAL	2	TRUE	1	0.223390734108901	2		368	460	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705326	43705326	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	47	550	1	ENST00000382044.4:c.5296G>A	p.Glu1766Lys	p.E1766K	ENST00000382044	NM_001141980.1	1766	Gaa/Aaa	24/28	0.223390734108901	1	FACETS	0.407	0.342	0.479	0.407	0.342	0.479	SUBCLONAL	1	TRUE	0	0.223390734108901	1		551	918	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481448	40481449	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	129	388	0	ENST00000264657.5:c.1260dup	p.Gly421TrpfsTer7	p.G421Wfs*7	ENST00000264657	NM_139276.2	420	-/T	14/24	1	2	FACETS	0.79	0.717	0.867	1	0.987	1	SUBCLONAL	2	TRUE	1	0.223390734108901	2		388	731	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994338	25994338	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	78	278	0	ENST00000435504.4:c.475C>T	p.Gln159Ter	p.Q159*	ENST00000435504		159	Cag/Tag	6/13	0.222769735214564	1	FACETS	0.719	0.635	0.809	0.719	0.635	0.809	INDETERMINATE	1	TRUE	0	0.4175081031563	1		278	411	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196460	106196460	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1441761527	NA	P-0046838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	61	336	0	ENST00000380013.4:c.4793A>G	p.Tyr1598Cys	p.Y1598C	ENST00000380013	NM_001127208.2	1598	tAt/tGt	11/11	1	2	FACETS	0.544	0.47	0.625	0.544	0.47	0.625	SUBCLONAL	1	TRUE	1	0.4175081031563	2		336	537	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	189	610	3	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.5	2		613	653	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	54	473	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.261	0.222	0.304	0.261	0.222	0.304	SUBCLONAL	1	TRUE	1	0.5	2		474	828	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	84	275	1	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.875	0.778	0.977	0.875	0.778	0.977	CLONAL	1	TRUE	1	0.5	2		276	384	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797376	42797376	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	314	749	0	ENST00000575354.2:c.3743del	p.Pro1248HisfsTer54	p.P1248Hfs*54	ENST00000575354	NM_015125.3	1246	agC/ag	15/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.5	2		749	1140	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	134	382	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.5	2		382	530	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	353	1018	4	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.5	2		1022	1230	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589575	67589576	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	30	137	0	ENST00000274335.5:c.1344dup	p.Leu449IlefsTer3	p.L449Ifs*3	ENST00000274335		446	-/A	10/15	1	2	FACETS	0.472	0.382	0.574	0.472	0.382	0.574	SUBCLONAL	1	TRUE	1	0.5	2		137	254	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952006	178952006	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	40	435	0	ENST00000263967.3:c.3061T>C	p.Tyr1021His	p.Y1021H	ENST00000263967	NM_006218.2	1021	Tac/Cac	21/21	1	2	FACETS	0.356	0.296	0.424	0.356	0.296	0.424	SUBCLONAL	1	TRUE	1	0.5	2		435	449	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807525	36807525	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778434947	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	191	657	1	ENST00000373129.3:c.1139G>A	p.Arg380His	p.R380H	ENST00000373129	NM_032017.1	380	cGt/cAt	12/12	1	2	FACETS	0.685	0.633	0.74	0.685	0.633	0.74	SUBCLONAL	1	TRUE	1	0.5	2		658	1115	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850705	63850705	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs201178069	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	105	229	1	ENST00000279873.7:c.1489del	p.Ile497Ter	p.I497*	ENST00000279873	NM_032199.2	495	Aaa/aa	10/10	1	2	FACETS	0.917	0.826	1	0.917	0.826	1	CLONAL	1	TRUE	1	0.5	2		230	458	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	87	294	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	0.613	0.543	0.687	0.613	0.543	0.687	SUBCLONAL	1	TRUE	1	0.5	2		294	568	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	194	671	0	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	1	2	FACETS	0.984	0.912	1	0.984	0.912	1	CLONAL	1	TRUE	1	0.5	2		671	789	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610099	43610099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760088950	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	150	593	1	ENST00000355710.3:c.2051C>T	p.Pro684Leu	p.P684L	ENST00000355710	NM_020975.4	684	cCg/cTg	11/20	1	2	FACETS	0.586	0.535	0.64	0.586	0.535	0.64	SUBCLONAL	1	TRUE	1	0.5	2		594	1024	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719640	190719640	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	17	149	0	ENST00000441310.2:c.1647del	p.Lys549AsnfsTer4	p.K549Nfs*4	ENST00000441310	NM_000534.4	548	Aaa/aa	9/13	1	2	FACETS	0.368	0.275	0.476	0.368	0.275	0.476	SUBCLONAL	1	TRUE	1	0.5	2		149	185	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	32	255	2	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.224	0.181	0.273	0.224	0.181	0.273	SUBCLONAL	1	TRUE	1	0.5	2		257	571	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934243	49934243	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1407832113	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	280	737	5	ENST00000296474.3:c.2264del	p.Gly755ValfsTer19	p.G755Vfs*19	ENST00000296474	NM_002447.2	755	gGt/gt	8/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.5	2		742	969	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885145	111885145	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs892433462	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	48	487	0	ENST00000341259.2:c.1038del	p.Leu347CysfsTer26	p.L347Cfs*26	ENST00000341259	NM_005475.2	345	Ggg/gg	6/8	1	2	FACETS	0.231	0.194	0.272	0.231	0.194	0.272	SUBCLONAL	1	TRUE	1	0.5	2		487	831	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687472	37687472	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	35	314	1	ENST00000447079.4:c.4382del	p.Gly1461AlafsTer38	p.G1461Afs*38	ENST00000447079	NM_015083.1	1459	tGg/tg	14/14	1	2	FACETS	0.255	0.209	0.308	0.255	0.209	0.308	SUBCLONAL	1	TRUE	1	0.5	2		315	548	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793362	242793362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137861407	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	343	724	0	ENST00000334409.5:c.715G>A	p.Val239Met	p.V239M	ENST00000334409	NM_005018.2	239	Gtg/Atg	5/5	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.5	2		724	1135	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733513	85733513	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs387906350	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	127	438	1	ENST00000370580.1:c.499del	p.Ser167LeufsTer6	p.S167Lfs*6	ENST00000370580	NM_003921.4	167	Tct/ct	3/3	1	2	FACETS	0.841	0.764	0.921	0.841	0.764	0.921	CLONAL	1	TRUE	1	0.5	2		439	604	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187558039	187558039	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	21	239	0	ENST00000441802.2:c.3672del	p.Lys1225AsnfsTer9	p.K1225Nfs*9	ENST00000441802	NM_005245.3	1224	ccC/cc	5/27	1	2	FACETS	0.223	0.171	0.283	0.223	0.171	0.283	SUBCLONAL	1	TRUE	1	0.5	2		239	377	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50481153	50481153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	114	287	0	ENST00000394963.4:c.539G>A	p.Arg180Gln	p.R180Q	ENST00000394963	NM_003076.4	180	cGg/cAg	5/13	1	2	FACETS	0.789	0.712	0.869	0.789	0.712	0.869	SUBCLONAL	1	TRUE	1	0.5	2		287	578	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538269	187538269	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs748652484	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	99	427	0	ENST00000441802.2:c.8965del	p.Arg2989GlyfsTer20	p.R2989Gfs*20	ENST00000441802	NM_005245.3	2989	Agg/gg	11/27	1	2	FACETS	0.619	0.553	0.689	0.619	0.553	0.689	SUBCLONAL	1	TRUE	1	0.5	2		427	640	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541040	187541040	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	149	349	0	ENST00000441802.2:c.6700G>A	p.Gly2234Arg	p.G2234R	ENST00000441802	NM_005245.3	2234	Gga/Aga	10/27	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.5	2		349	527	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913558	32913559	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359479	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	84	269	0	ENST00000380152.3:c.5073dup	p.Trp1692MetfsTer3	p.W1692Mfs*3	ENST00000380152		1689	gca/gcAa	11/27	1	2	FACETS	0.789	0.7	0.883	0.789	0.7	0.883	SUBCLONAL	1	TRUE	1	0.5	2		269	426	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582169	189582169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908836	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	248	421	1	ENST00000264731.3:c.728G>A	p.Arg243Gln	p.R243Q	ENST00000264731	NM_003722.4	243	cGg/cAg	5/14	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.5	2		422	886	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211461	46211461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	17	159	0	ENST00000334344.6:c.427C>T	p.Arg143Cys	p.R143C	ENST00000334344	NM_152641.2	143	Cgt/Tgt	5/21	1	2	FACETS	0.302	0.226	0.393	0.302	0.226	0.393	SUBCLONAL	1	TRUE	1	0.5	2		159	225	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850275	128850275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	231	637	1	ENST00000249373.3:c.1538C>T	p.Pro513Leu	p.P513L	ENST00000249373	NM_005631.4	513	cCg/cTg	9/12	1	2	FACETS	0.97	0.905	1	0.97	0.905	1	CLONAL	1	TRUE	1	0.5	2		638	953	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435111	110435111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	258	572	0	ENST00000375856.3:c.3290G>A	p.Arg1097His	p.R1097H	ENST00000375856	NM_003749.2	1097	cGc/cAc	1/2	1	2	FACETS	0.96	0.899	1	0.96	0.899	1	CLONAL	1	TRUE	1	0.5	2		572	1075	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841231	15841236	+	inframe_deletion	In_Frame_Del	DEL	AGCCGG	AGCCGG	-	rs752736259	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	118	299	0	ENST00000307771.7:c.1338_1343del	p.Ser447_Arg448del	p.S447_R448del	ENST00000307771	NM_005089.3	439	AGCCGG/-	11/11	1	2	FACETS	0.891	0.807	0.978	0.891	0.807	0.978	CLONAL	1	TRUE	1	0.5	2		299	530	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970914	79970915	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587776701	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	100	386	2	ENST00000265081.6:c.1148dup	p.Asn385GlnfsTer19	p.N385Qfs*19	ENST00000265081	NM_002439.4	380	-/A	7/24	1	2	FACETS	0.537	0.479	0.598	0.537	0.479	0.598	SUBCLONAL	1	TRUE	1	0.5	2		388	745	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518103	176518103	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs866476239	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	72	498	0	ENST00000292408.4:c.601C>T	p.Arg201Trp	p.R201W	ENST00000292408	NM_213647.1	201	Cgg/Tgg	5/18	1	2	FACETS	0.346	0.301	0.394	0.346	0.301	0.394	SUBCLONAL	1	TRUE	1	0.5	2		498	833	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266730	18266730	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756943808	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	54	636	1	ENST00000222254.8:c.41C>T	p.Pro14Leu	p.P14L	ENST00000222254	NM_005027.3	14	cCg/cTg	2/16	1	2	FACETS	0.204	0.173	0.238	0.204	0.173	0.238	SUBCLONAL	1	TRUE	1	0.5	2		637	1060	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653867	89653867	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	85	250	1	ENST00000371953.3:c.164+1G>A		p.X55_splice	ENST00000371953	NM_000314.4	55			1	2	FACETS	0.994	0.886	1	0.994	0.886	1	CLONAL	1	TRUE	1	0.5	2		251	342	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438211	49438211	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	250	505	1	ENST00000301067.7:c.5058del	p.Lys1686AsnfsTer36	p.K1686Nfs*36	ENST00000301067	NM_003482.3	1686	aaA/aa	20/54	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.5	2		506	852	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434005	49434005	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	60	797	0	ENST00000301067.7:c.7548del	p.Asn2517IlefsTer26	p.N2517Ifs*26	ENST00000301067	NM_003482.3	2516	ccC/cc	31/54	1	2	FACETS	0.227	0.194	0.262	0.227	0.194	0.262	SUBCLONAL	1	TRUE	1	0.5	2		797	1058	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939086	36939086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372288734	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	262	689	0	ENST00000361632.4:c.623C>T	p.Ala208Val	p.A208V	ENST00000361632		208	gCg/gTg	5/16	1	2	FACETS	0.943	0.884	1	0.943	0.884	1	CLONAL	1	TRUE	1	0.5	2		689	1111	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214714	36214714	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	178	596	2	ENST00000222270.7:c.3145del	p.Ala1049ArgfsTer133	p.A1049Rfs*133	ENST00000222270	NM_014727.1	1047	cGg/cg	8/37	1	2	FACETS	0.884	0.816	0.955	0.884	0.816	0.955	CLONAL	1	TRUE	1	0.5	2		598	805	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948755	71948755	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1565399032	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	72	787	1	ENST00000298229.2:c.3470del	p.Gly1157AspfsTer45	p.G1157Dfs*45	ENST00000298229	NM_001567.3	1156	cGg/cg	26/28	1	2	FACETS	0.247	0.215	0.283	0.247	0.215	0.283	SUBCLONAL	1	TRUE	1	0.5	2		788	1164	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098654	2098656	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	245	423	0	ENST00000219476.3:c.40_42del	p.Lys14del	p.K14del	ENST00000219476	NM_000548.3	13	gAGAag/gag	2/42	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.5	2		423	839	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738608	145738608	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1467362119	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	312	508	0	ENST00000428558.2:c.2456A>G	p.Gln819Arg	p.Q819R	ENST00000428558	NM_004260.3	819	cAg/cGg	15/22	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.5	2		508	882	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800903	120800903	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748469666	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	198	533	1	ENST00000257552.2:c.345del	p.Leu116CysfsTer3	p.L116Cfs*3	ENST00000257552	NM_002442.3	115	ggG/gg	6/15	1	2	FACETS	0.698	0.646	0.753	0.698	0.646	0.753	SUBCLONAL	1	TRUE	1	0.5	2		534	1134	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948102	178948102	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	57	193	0	ENST00000263967.3:c.2874G>T	p.Gln958His	p.Q958H	ENST00000263967	NM_006218.2	958	caG/caT	20/21	1	2	FACETS	0.661	0.57	0.759	0.661	0.57	0.759	SUBCLONAL	1	TRUE	1	0.5	2		193	345	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781836	3781836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	62	643	0	ENST00000262367.5:c.4831C>T	p.Pro1611Ser	p.P1611S	ENST00000262367	NM_004380.2	1611	Ccc/Tcc	29/31	1	2	FACETS	0.218	0.187	0.252	0.218	0.187	0.252	SUBCLONAL	1	TRUE	1	0.5	2		643	1137	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752897	42752897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376964824	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	206	1106	0	ENST00000222329.4:c.1367C>T	p.Thr456Met	p.T456M	ENST00000222329	NM_006494.2	456	aCg/aTg	4/4	1	2	FACETS	0.699	0.647	0.752	0.699	0.647	0.752	SUBCLONAL	1	TRUE	1	0.5	2		1106	1179	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36823859	36823859	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs767843123	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	36	363	0	ENST00000373129.3:c.323A>G	p.His108Arg	p.H108R	ENST00000373129	NM_032017.1	108	cAc/cGc	5/12	1	2	FACETS	0.222	0.182	0.268	0.222	0.182	0.268	SUBCLONAL	1	TRUE	1	0.5	2		363	648	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256718	16256719	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	29	367	0	ENST00000375759.3:c.3984_3985del	p.Ser1329CysfsTer5	p.S1329Cfs*5	ENST00000375759	NM_015001.2	1328	cTA/c	11/15	1	2	FACETS	0.213	0.17	0.262	0.213	0.17	0.262	SUBCLONAL	1	TRUE	1	0.5	2		367	544	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257692	16257692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1294074119	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	39	434	0	ENST00000375759.3:c.4957G>A	p.Ala1653Thr	p.A1653T	ENST00000375759	NM_015001.2	1653	Gca/Aca	11/15	1	2	FACETS	0.204	0.168	0.244	0.204	0.168	0.244	SUBCLONAL	1	TRUE	1	0.5	2		434	766	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333353	70333353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1220116067	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	52	622	1	ENST00000373644.4:c.1258G>A	p.Gly420Ser	p.G420S	ENST00000373644	NM_030625.2	420	Ggt/Agt	2/12	1	2	FACETS	0.206	0.174	0.241	0.206	0.174	0.241	SUBCLONAL	1	TRUE	1	0.5	2		623	1011	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090940	77090940	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs956235500	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	30	303	1	ENST00000356341.3:c.290C>T	p.Thr97Met	p.T97M	ENST00000356341	NM_002576.4	97	aCg/aTg	3/15	1	2	FACETS	0.203	0.163	0.249	0.203	0.163	0.249	SUBCLONAL	1	TRUE	1	0.5	2		304	590	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504498	103504498	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	34	208	0	ENST00000355739.4:c.119A>G	p.Lys40Arg	p.K40R	ENST00000355739	NM_000123.3	40	aAa/aGa	2/15	1	2	FACETS	0.337	0.275	0.406	0.337	0.275	0.406	SUBCLONAL	1	TRUE	1	0.5	2		208	404	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061346	38061346	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	235	610	0	ENST00000250448.2:c.643C>T	p.Gln215Ter	p.Q215*	ENST00000250448	NM_004496.3	215	Cag/Tag	2/2	1	2	FACETS	0.96	0.896	1	0.96	0.896	1	CLONAL	1	TRUE	1	0.5	2		610	979	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2093625	2093625	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1243	68	833	0	ENST00000219066.1:c.652G>T	p.Gly218Trp	p.G218W	ENST00000219066	NM_002528.5	218	Ggg/Tgg	4/6	1	2	FACETS	0.207	0.179	0.238	0.207	0.179	0.238	SUBCLONAL	1	TRUE	1	0.5	2		833	1311	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127723	2127723	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	173	437	0	ENST00000219476.3:c.2962C>A	p.Arg988Ser	p.R988S	ENST00000219476	NM_000548.3	988	Cgc/Agc	26/42	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.5	2		437	691	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489597	40489597	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	162	494	0	ENST00000264657.5:c.653T>C	p.Val218Ala	p.V218A	ENST00000264657	NM_139276.2	218	gTg/gCg	8/24	1	2	FACETS	0.761	0.699	0.827	0.761	0.699	0.827	SUBCLONAL	1	TRUE	1	0.5	2		494	851	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349921	15349921	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	278	586	0	ENST00000263377.2:c.3731A>G	p.Gln1244Arg	p.Q1244R	ENST00000263377	NM_058243.2	1244	cAg/cGg	18/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.5	2		586	1019	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029116	26029117	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	27	244	0	ENST00000435504.4:c.233dup	p.Met78IlefsTer26	p.M78Ifs*26	ENST00000435504		78	atg/atTg	4/13	1	2	FACETS	0.281	0.223	0.347	0.281	0.223	0.347	SUBCLONAL	1	TRUE	1	0.5	2		244	384	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702262	47702262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	158	396	0	ENST00000233146.2:c.1858G>A	p.Val620Ile	p.V620I	ENST00000233146	NM_000251.2	620	Gta/Ata	12/16	1	2	FACETS	0.916	0.842	0.993	0.916	0.842	0.993	CLONAL	1	TRUE	1	0.5	2		396	690	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561192	9561192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375668103	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	29	337	0	ENST00000353224.5:c.590C>T	p.Ala197Val	p.A197V	ENST00000353224	NM_177990.2	197	gCc/gTc	4/10	1	2	FACETS	0.207	0.165	0.255	0.207	0.165	0.255	SUBCLONAL	1	TRUE	1	0.5	2		337	560	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39704846	39704848	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs1477385476	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	14	105	0	ENST00000361337.2:c.193_195del	p.Glu65del	p.E65del	ENST00000361337	NM_003286.2	64	aAGGag/aag	4/21	1	2	FACETS	0.281	0.203	0.375	0.281	0.203	0.375	SUBCLONAL	1	TRUE	1	0.5	2		105	199	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46270994	46270994	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	176	393	0	ENST00000371998.3:c.3118C>T	p.Pro1040Ser	p.P1040S	ENST00000371998		1040	Cca/Tca	17/23	1	2	FACETS	0.939	0.867	1	0.939	0.867	1	CLONAL	1	TRUE	1	0.5	2		393	750	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656963	45656963	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	183	634	0	ENST00000407780.3:c.193T>C	p.Tyr65His	p.Y65H	ENST00000407780	NM_001283052.1	65	Tac/Cac	3/7	1	2	FACETS	0.647	0.596	0.7	0.647	0.596	0.7	SUBCLONAL	1	TRUE	1	0.5	2		634	1131	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089174	37089174	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	127	257	0	ENST00000231790.2:c.1896G>C	p.Glu632Asp	p.E632D	ENST00000231790	NM_000249.3	632	gaG/gaC	16/19	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.5	2		257	501	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37092143	37092143	+	stop_lost	Nonstop_Mutation	SNP	A	A	C	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	115	243	0	ENST00000231790.2:c.2270A>C	p.Ter757SerextTer36	p.*757Sext*36	ENST00000231790	NM_000249.3	757	tAa/tCa	19/19	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.5	2		243	369	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928451	69928451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	298	600	0	ENST00000352241.4:c.271C>T	p.Pro91Ser	p.P91S	ENST00000352241	NM_198159.2	91	Ccc/Tcc	2/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.5	2		600	1012	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73047249	73047251	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	92	290	0	ENST00000356692.5:c.57_59del	p.Glu20del	p.E20del	ENST00000356692		19	aAGGaa/aaa	2/9	1	2	FACETS	0.793	0.708	0.883	0.793	0.708	0.883	SUBCLONAL	1	TRUE	1	0.5	2		290	464	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540475	187540475	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs757470084	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	136	381	0	ENST00000441802.2:c.7265T>C	p.Ile2422Thr	p.I2422T	ENST00000441802	NM_005245.3	2422	aTa/aCa	10/27	1	2	FACETS	0.927	0.846	1	0.927	0.846	1	CLONAL	1	TRUE	1	0.5	2		381	587	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279474	1279474	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	61	751	0	ENST00000310581.5:c.2062A>G	p.Arg688Gly	p.R688G	ENST00000310581	NM_198253.2	688	Agg/Ggg	5/16	1	2	FACETS	0.217	0.186	0.251	0.217	0.186	0.251	SUBCLONAL	1	TRUE	1	0.5	2		751	1124	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176666865	176666865	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	18	234	0	ENST00000439151.2:c.4301A>G	p.Lys1434Arg	p.K1434R	ENST00000439151	NM_022455.4	1434	aAg/aGg	8/23	1	2	FACETS	0.21	0.157	0.272	0.21	0.157	0.272	SUBCLONAL	1	TRUE	1	0.5	2		234	343	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402602	20402602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	101	259	0	ENST00000346618.3:c.139G>A	p.Ala47Thr	p.A47T	ENST00000346618	NM_001949.4	47	Gcc/Acc	1/7	1	2	FACETS	0.871	0.782	0.964	0.871	0.782	0.964	CLONAL	1	TRUE	1	0.5	2		259	464	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323187	31323187	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	231	551	0	ENST00000412585.2:c.802T>C	p.Trp268Arg	p.W268R	ENST00000412585	NM_005514.6	268	Tgg/Cgg	4/8	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.5	2		551	909	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536079	106536079	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	21	227	0	ENST00000369096.4:c.46G>A	p.Ala16Thr	p.A16T	ENST00000369096	NM_001198.3	16	Gcc/Acc	2/7	1	2	FACETS	0.208	0.16	0.265	0.208	0.16	0.265	SUBCLONAL	1	TRUE	1	0.5	2		227	403	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987271	2987271	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	43	436	0	ENST00000396946.4:c.158A>G	p.Asp53Gly	p.D53G	ENST00000396946	NM_032415.4	53	gAt/gGt	3/25	1	2	FACETS	0.213	0.178	0.253	0.213	0.178	0.253	SUBCLONAL	1	TRUE	1	0.5	2		436	806	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56882312	56882312	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	276	458	0	ENST00000519728.1:c.1010G>A	p.Gly337Asp	p.G337D	ENST00000519728	NM_002350.3	337	gGc/gAc	10/13	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.5	2		458	878	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606475	93606475	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	266	809	0	ENST00000375746.1:c.295C>A	p.Leu99Met	p.L99M	ENST00000375746	NM_001174167.1	99	Ctg/Atg	2/14	1	2	FACETS	0.903	0.846	0.962	0.903	0.846	0.962	CLONAL	1	TRUE	1	0.5	2		809	1178	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98241392	98241392	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	130	388	0	ENST00000331920.6:c.1105C>A	p.Pro369Thr	p.P369T	ENST00000331920	NM_000264.3	369	Ccc/Acc	8/24	1	2	FACETS	0.609	0.552	0.669	0.609	0.552	0.669	SUBCLONAL	1	TRUE	1	0.5	2		388	854	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796819	135796819	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	25	262	0	ENST00000298552.3:c.668T>C	p.Met223Thr	p.M223T	ENST00000298552	NM_001162426.1	223	aTg/aCg	8/23	1	2	FACETS	0.234	0.184	0.292	0.234	0.184	0.292	SUBCLONAL	1	TRUE	1	0.5	2		262	427	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820597	44820597	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	29	376	0	ENST00000377967.4:c.294A>T	p.Gln98His	p.Q98H	ENST00000377967	NM_021140.2	98	caA/caT	3/29	1	2	FACETS	0.219	0.175	0.269	0.219	0.175	0.269	SUBCLONAL	1	TRUE	1	0.5	2		376	530	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936036	44936036	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	32	425	0	ENST00000377967.4:c.2797A>G	p.Lys933Glu	p.K933E	ENST00000377967	NM_021140.2	933	Aag/Gag	18/29	1	2	FACETS	0.217	0.175	0.264	0.217	0.175	0.264	SUBCLONAL	1	TRUE	1	0.5	2		425	591	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763983	76763983	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	144	486	0	ENST00000373344.5:c.7325C>T	p.Pro2442Leu	p.P2442L	ENST00000373344	NM_000489.3	2442	cCa/cTa	35/35	1	2	FACETS	0.678	0.619	0.741	0.678	0.619	0.741	SUBCLONAL	1	TRUE	1	0.5	2		486	849	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0046840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	67	812	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.724	0.628	0.829	0.724	0.628	0.829	SUBCLONAL	1	TRUE	1	0.2	2		812	925	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338671	70338671	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	44	576	0	ENST00000374080.3:c.67G>T	p.Asp23Tyr	p.D23Y	ENST00000374080		23	Gat/Tat	1/45	1	2	FACETS	0.674	0.564	0.796	0.674	0.564	0.796	SUBCLONAL	1	TRUE	1	0.2	2		576	653	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0046840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	58	470	0	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			1	2	FACETS	0.842	0.722	0.972	0.842	0.722	0.972	CLONAL	1	TRUE	1	0.2	2		470	689	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094488	27094488	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	86	350	0	ENST00000324856.7:c.3196C>T	p.Gln1066Ter	p.Q1066*	ENST00000324856	NM_006015.4	1066	Cag/Tag	11/20	1	2	FACETS	0.76	0.673	0.852	1	0.979	1	SUBCLONAL	2	TRUE	1	0.2	2		350	566	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589581	67589598	+	protein_altering_variant	In_Frame_Del	DEL	ATTACATGAATATAACAC	ATTACATGAATATAACAC	TAT	novel	NA	P-0046840-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	21	193	2	ENST00000274335.5:c.1344_1361delinsTAT	p.Lys448_Thr454delinsAsnIle	p.K448_T454delinsNI	ENST00000274335		448	aaATTACATGAATATAACACt/aaTATt	10/15	1	2	FACETS	0.837	0.646	1	0.837	0.646	1	CLONAL	1	TRUE	1	0.2	2		195	251	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	198	427	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.984	0.922	1	0.984	0.922	1	CLONAL	1	TRUE	1	0.854063224672849	2		427	471	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953837	55953837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	257	377	0	ENST00000263923.4:c.3599C>T	p.Ser1200Phe	p.S1200F	ENST00000263923	NM_002253.2	1200	tCc/tTc	27/30	0.358356308281113	1	FACETS	0.568	0.536	0.6	0.568	0.536	0.6	INDETERMINATE	1	TRUE	0	0.854063224672849	1		377	607	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230571	46230571	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	224	314	1	ENST00000334344.6:c.820C>T	p.Arg274Ter	p.R274*	ENST00000334344	NM_152641.2	274	Cga/Tga	8/21	1	2	FACETS	0.906	0.85	0.963	0.906	0.85	0.963	CLONAL	1	TRUE	1	0.854063224672849	2		315	579	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0046842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	294	452	0	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	1	2	FACETS	0.901	0.852	0.95	0.901	0.852	0.95	CLONAL	1	TRUE	1	0.854063224672849	2		452	764	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133979	41133979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149675484	NA	P-0046842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	168	511	0	ENST00000379561.5:c.1649C>T	p.Ser550Leu	p.S550L	ENST00000379561	NM_002015.3	550	tCg/tTg	2/3	0.600112978124152	1	FACETS	0.295	0.272	0.32	0.295	0.272	0.32	SUBCLONAL	1	TRUE	0	0.854063224672849	1		511	763	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381466	81381466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	214	252	1	ENST00000222390.5:c.595G>A	p.Glu199Lys	p.E199K	ENST00000222390	NM_000601.4	199	Gaa/Aaa	5/18	1	2	FACETS	0.966	0.906	1	0.966	0.906	1	CLONAL	1	TRUE	1	0.854063224672849	2		253	519	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715756	18715756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs950782237	NA	P-0046842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	204	253	0	ENST00000266497.5:c.3587C>T	p.Ser1196Phe	p.S1196F	ENST00000266497		1196	tCc/tTc	25/31	0.414083783594114	1	FACETS	0.664	0.625	0.704	0.664	0.625	0.704	INDETERMINATE	1	TRUE	0	0.854063224672849	1		253	412	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612101	189612101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778606951	NA	P-0046842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	335	495	0	ENST00000264731.3:c.1853G>A	p.Arg618Gln	p.R618Q	ENST00000264731	NM_003722.4	618	cGg/cAg	14/14	1	2	FACETS	0.961	0.914	1	0.961	0.914	1	CLONAL	1	TRUE	1	0.854063224672849	2		495	816	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135385	30135385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	233	289	0	ENST00000331968.5:c.433C>T	p.Arg145Cys	p.R145C	ENST00000331968	NM_002742.2	145	Cgt/Tgt	3/18	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.854063224672849	2		289	528	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866466	42866466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	490	604	0	ENST00000398585.3:c.166G>A	p.Gly56Arg	p.G56R	ENST00000398585	NM_001135099.1	56	Gga/Aga	3/14	0.600112978124152	1	FACETS	0.693	0.667	0.719	0.693	0.667	0.719	SUBCLONAL	1	TRUE	0	0.854063224672849	1		604	949	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851604	134851604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	314	488	0	ENST00000398015.3:c.1010C>T	p.Ser337Phe	p.S337F	ENST00000398015	NM_004441.4	337	tCc/tTc	5/16	1	2	FACETS	0.959	0.91	1	0.959	0.91	1	CLONAL	1	TRUE	1	0.854063224672849	2		488	767	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661898	29661898	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567615766	NA	P-0046842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	257	336	0	ENST00000356175.3:c.5792G>A	p.Trp1931Ter	p.W1931*	ENST00000356175	NM_000267.3	1931	tGg/tAg	39/57	1	2	FACETS	0.898	0.846	0.951	0.898	0.846	0.951	CLONAL	1	TRUE	1	0.854063224672849	2		336	670	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612286	189612286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	235	281	0	ENST00000264731.3:c.2038G>A	p.Glu680Lys	p.E680K	ENST00000264731	NM_003722.4	680	Gag/Aag	14/14	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.854063224672849	2		281	539	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857686	59857686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781321	NA	P-0046842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	199	270	0	ENST00000259008.2:c.1871C>T	p.Ser624Leu	p.S624L	ENST00000259008	NM_032043.2	624	tCg/tTg	13/20	1	2	FACETS	0.901	0.842	0.961	0.901	0.842	0.961	CLONAL	1	TRUE	1	0.854063224672849	2		270	517	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517785	176517785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	204	541	0	ENST00000292408.4:c.395C>T	p.Ser132Phe	p.S132F	ENST00000292408	NM_213647.1	132	tCc/tTc	4/18	0.501448867497505	1	FACETS	0.347	0.322	0.372	0.347	0.322	0.372	INDETERMINATE	1	TRUE	0	0.854063224672849	1		541	789	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551311	29551311	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	346	555	0	ENST00000389048.3:c.1319C>T	p.Ser440Phe	p.S440F	ENST00000389048	NM_004304.4	440	tCc/tTc	6/29	1	2	FACETS	0.845	0.802	0.888	0.845	0.802	0.888	CLONAL	1	TRUE	1	0.854063224672849	2		555	959	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092764	27092764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	162	386	0	ENST00000324856.7:c.2785C>T	p.Pro929Ser	p.P929S	ENST00000324856	NM_006015.4	929	Cct/Tct	9/20	0.532611385406	1	FACETS	0.349	0.321	0.378	0.349	0.321	0.378	SUBCLONAL	1	TRUE	0	0.854063224672849	1		386	623	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495442	56495442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	246	559	0	ENST00000267101.3:c.3632C>T	p.Pro1211Leu	p.P1211L	ENST00000267101	NM_001982.3	1211	cCc/cTc	28/28	1	2	FACETS	0.537	0.502	0.573	0.537	0.502	0.573	SUBCLONAL	1	TRUE	1	0.854063224672849	2		559	1073	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156120	119156121	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	353	513	0	ENST00000264033.4:c.1785_1786delinsTT	p.Pro596Ser	p.P596S	ENST00000264033	NM_005188.3	595	atCCcc/atTTcc	11/16	0.168437885650633	3	FACETS	0.981	0.929	1	0.327	0.309	0.345	INDETERMINATE	1	TRUE	0	0.854063224672849	3		513	1203	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888192	112888222	+	frameshift_variant	Frame_Shift_Del	DEL	AAATTTGCCACTTTGGCTGAGTTGGTCCAGT	AAATTTGCCACTTTGGCTGAGTTGGTCCAGT	-	novel	NA	P-0046842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	206	433	0	ENST00000351677.2:c.209_239del	p.Lys70IlefsTer9	p.K70Ifs*9	ENST00000351677	NM_002834.3	70	AAATTTGCCACTTTGGCTGAGTTGGTCCAGTat/at	3/16	0.358356308281113	1	FACETS	0.402	0.375	0.431	0.402	0.375	0.431	INDETERMINATE	1	TRUE	0	0.854063224672849	1		433	687	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915776	112915777	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	238	288	0	ENST00000351677.2:c.1049_1050delinsTT	p.Ser350Phe	p.S350F	ENST00000351677	NM_002834.3	350	tCC/tTT	9/16	0.358356308281113	1	FACETS	0.579	0.545	0.612	0.579	0.545	0.612	INDETERMINATE	1	TRUE	0	0.854063224672849	1		288	552	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004204	29004205	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0046842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	82	292	0	ENST00000282397.4:c.1088_1089delinsTT	p.Pro363Leu	p.P363L	ENST00000282397	NM_002019.4	363	cCC/cTT	8/30	0.600112978124152	1	FACETS	0.276	0.244	0.309	0.276	0.244	0.309	SUBCLONAL	1	TRUE	0	0.854063224672849	1		292	399	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40857116	40857116	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	252	345	0	ENST00000428826.2:c.1925A>T	p.Tyr642Phe	p.Y642F	ENST00000428826		642	tAc/tTc	17/21	1	2	FACETS	0.856	0.806	0.908	0.856	0.806	0.908	CLONAL	1	TRUE	1	0.854063224672849	2		345	689	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733286	40733286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	135	408	0	ENST00000373198.4:c.3520G>A	p.Glu1174Lys	p.E1174K	ENST00000373198	NM_133170.3	1174	Gag/Aag	26/32	0.711706751287622	1	FACETS	0.257	0.234	0.281	0.257	0.234	0.281	SUBCLONAL	1	TRUE	0	0.854063224672849	1		408	705	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548233	41548234	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0046842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	113	233	1	ENST00000263253.7:c.3021_3022delinsAA	p.Met1007_Glu1008delinsIleLys	p.M1007_E1008delinsIK	ENST00000263253	NM_001429.3	1007	atGGaa/atAAaa	16/31	1	2	FACETS	0.739	0.672	0.808	0.739	0.672	0.808	SUBCLONAL	1	TRUE	1	0.854063224672849	2		234	358	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127499	55127499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	277	349	1	ENST00000257290.5:c.287G>A	p.Gly96Glu	p.G96E	ENST00000257290	NM_006206.4	96	gGg/gAg	3/23	0.358356308281113	1	FACETS	0.56	0.529	0.591	0.56	0.529	0.591	INDETERMINATE	1	TRUE	0	0.854063224672849	1		350	664	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675973	30675973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	448	522	0	ENST00000376406.3:c.2383G>A	p.Val795Ile	p.V795I	ENST00000376406	NM_014641.2	795	Gtt/Att	8/15	0.462919462747613	4	FACETS	1	0.993	1	0.41	0.39	0.43	INDETERMINATE	1	TRUE	1	0.854063224672849	4		522	1581	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348978	70348978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046842-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	446	241	0	ENST00000374080.3:c.3490G>A	p.Asp1164Asn	p.D1164N	ENST00000374080		1164	Gac/Aac	25/45	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.854063224672849	1		241	557	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	28	150	0	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	1	FACETS	0.938	0.78	1	0.938	0.78	1	CLONAL	1	TRUE	0	0.603922787244293	1		150	69	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	121	312	2	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	0.603922787244293	3	FACETS	1	0.985	1	0.707	0.645	0.77	CLONAL	1	TRUE	1	0.603922787244293	3		314	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	221	672	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.603922787244293	2		672	718	SUCCESS
APC	324	MSKCC	GRCh37	5	112154723	112154723	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775126020	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	111	392	1	ENST00000257430.4:c.994C>T	p.Arg332Ter	p.R332*	ENST00000257430	NM_000038.5	332	Cga/Tga	10/16	1	2	FACETS	0.882	0.798	0.968	0.882	0.798	0.968	CLONAL	1	TRUE	1	0.603922787244293	2		393	417	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241895	133241895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483635586	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	154	439	0	ENST00000320574.5:c.2461C>T	p.Arg821Cys	p.R821C	ENST00000320574	NM_006231.2	821	Cgc/Tgc	21/49	1	2	FACETS	0.927	0.853	1	0.927	0.853	1	CLONAL	1	TRUE	1	0.603922787244293	2		439	550	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029446	16029446	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	142	272	2	ENST00000268712.3:c.1584del	p.Glu529LysfsTer26	p.E529Kfs*26	ENST00000268712	NM_006311.3	528	aaA/aa	15/46	1	2	FACETS	0.988	0.907	1	0.988	0.907	1	CLONAL	1	TRUE	1	0.603922787244293	2		274	476	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	103	239	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	0.997	0.902	1	0.997	0.902	1	CLONAL	1	TRUE	1	0.603922787244293	2		239	342	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	160	407	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.869	0.8	0.94	0.869	0.8	0.94	CLONAL	1	TRUE	1	0.603922787244293	2		407	610	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578388	7578388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514495	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	226	604	2	ENST00000269305.4:c.542G>A	p.Arg181His	p.R181H	ENST00000269305	NM_001126112.2	181	cGc/cAc	5/11	1	2	FACETS	0.995	0.93	1	0.995	0.93	1	CLONAL	1	TRUE	1	0.603922787244293	2		606	752	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	51	220	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	0.764	0.657	0.879	0.764	0.657	0.879	SUBCLONAL	1	TRUE	1	0.603922787244293	2		220	221	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376675	8376675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs571411218	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	158	399	1	ENST00000356435.5:c.4438G>A	p.Val1480Ile	p.V1480I	ENST00000356435		1480	Gtt/Att	27/35	1	2	FACETS	0.891	0.821	0.964	0.891	0.821	0.964	CLONAL	1	TRUE	1	0.603922787244293	2		400	587	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738073	145738073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773154902	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	701	818	0	ENST00000428558.2:c.2837G>A	p.Arg946His	p.R946H	ENST00000428558	NM_004260.3	946	cGt/cAt	17/22	0.555661362482169	4	FACETS	0.944	0.915	0.973	0.944	0.915	0.973	CLONAL	3	TRUE	1	0.603922787244293	4		818	1315	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	121	405	3	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.858	0.78	0.939	0.858	0.78	0.939	CLONAL	1	TRUE	1	0.603922787244293	2		408	467	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223251	5223251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199604489	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	482	833	1	ENST00000357368.4:c.2552G>A	p.Arg851His	p.R851H	ENST00000357368	NM_002850.3	851	cGc/cAc	18/38	0.582449467335745	2	FACETS	0.963	0.929	0.996	0.963	0.929	0.996	CLONAL	2	TRUE	0	0.603922787244293	2		834	829	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064376	30064376	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1365006505	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	122	304	0	ENST00000338641.4:c.940G>A	p.Asp314Asn	p.D314N	ENST00000338641	NM_000268.3	314	Gat/Aat	10/16	1	2	FACETS	0.92	0.838	1	0.92	0.838	1	CLONAL	1	TRUE	1	0.603922787244293	2		304	439	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620541	52620541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141958485	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	201	439	0	ENST00000394830.3:c.3212G>A	p.Arg1071His	p.R1071H	ENST00000394830	NM_018313.4	1071	cGc/cAc	21/30	1	2	FACETS	0.923	0.859	0.99	0.923	0.859	0.99	CLONAL	1	TRUE	1	0.603922787244293	2		439	721	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104359285	104359285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746448939	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	169	469	0	ENST00000369902.3:c.1006G>A	p.Ala336Thr	p.A336T	ENST00000369902	NM_016169.3	336	Gcc/Acc	8/12	1	2	FACETS	0.9	0.831	0.971	0.9	0.831	0.971	CLONAL	1	TRUE	1	0.603922787244293	2		469	622	SUCCESS
APC	324	MSKCC	GRCh37	5	112175902	112175903	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906236	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	52	170	0	ENST00000257430.4:c.4612_4613del	p.Glu1538IlefsTer5	p.E1538Ifs*5	ENST00000257430	NM_000038.5	1537	acAGaa/acaa	16/16	1	2	FACETS	0.82	0.707	0.94	0.82	0.707	0.94	CLONAL	1	TRUE	1	0.603922787244293	2		170	210	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215674196	215674196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	62	707	0	ENST00000260947.4:c.98C>T	p.Ala33Val	p.A33V	ENST00000260947	NM_000465.2	33	gCc/gTc	1/11	1	2	FACETS	0.282	0.243	0.325	0.282	0.243	0.325	SUBCLONAL	1	TRUE	1	0.603922787244293	2		707	728	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46603871	46603871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs539540390	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	166	519	1	ENST00000263734.3:c.1228G>A	p.Ala410Thr	p.A410T	ENST00000263734	NM_001430.4	410	Gcc/Acc	9/16	1	2	FACETS	0.888	0.819	0.959	0.888	0.819	0.959	CLONAL	1	TRUE	1	0.603922787244293	2		520	619	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068315	30068315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141649026	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	95	241	0	ENST00000331968.5:c.2084G>A	p.Arg695Gln	p.R695Q	ENST00000331968	NM_002742.2	695	cGg/cAg	15/18	1	2	FACETS	0.884	0.794	0.978	0.884	0.794	0.978	CLONAL	1	TRUE	1	0.603922787244293	2		241	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578184	7578184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146340390	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	248	500	1	ENST00000269305.4:c.665C>T	p.Pro222Leu	p.P222L	ENST00000269305	NM_001126112.2	222	cCg/cTg	6/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.603922787244293	2		501	754	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100181	27100182	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCA	rs374564889	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	77	447	0	ENST00000324856.7:c.3999_4001dup	p.Gln1334dup	p.Q1334dup	ENST00000324856	NM_006015.4	1334	ccg/ccGCAg	16/20	1	2	FACETS	0.495	0.435	0.559	0.495	0.435	0.559	SUBCLONAL	1	TRUE	1	0.603922787244293	2		447	515	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884875	134884875	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368240835	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	195	534	1	ENST00000398015.3:c.1651G>A	p.Val551Met	p.V551M	ENST00000398015	NM_004441.4	551	Gtg/Atg	8/16	1	2	FACETS	0.973	0.904	1	0.973	0.904	1	CLONAL	1	TRUE	1	0.603922787244293	2		535	664	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276929	123276929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200204947	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	112	255	0	ENST00000358487.5:c.988C>T	p.Arg330Trp	p.R330W	ENST00000358487	NM_000141.4	330	Cgg/Tgg	8/18	1	2	FACETS	0.953	0.865	1	0.953	0.865	1	CLONAL	1	TRUE	1	0.603922787244293	2		255	389	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946495	71946495	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs747360226	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	147	411	0	ENST00000298229.2:c.2659G>A	p.Glu887Lys	p.E887K	ENST00000298229	NM_001567.3	887	Gag/Aag	23/28	1	2	FACETS	0.876	0.803	0.95	0.876	0.803	0.95	CLONAL	1	TRUE	1	0.603922787244293	2		411	556	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509579	29509579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754343223	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	154	422	0	ENST00000356175.3:c.784C>T	p.Arg262Cys	p.R262C	ENST00000356175	NM_000267.3	262	Cgt/Tgt	8/57	1	2	FACETS	0.951	0.876	1	0.951	0.876	1	CLONAL	1	TRUE	1	0.603922787244293	2		422	536	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30293209	30293209	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	123	333	0	ENST00000322652.5:c.503del	p.Asn168MetfsTer22	p.N168Mfs*22	ENST00000322652	NM_015355.2	167	Aaa/aa	5/16	1	2	FACETS	0.788	0.716	0.863	0.788	0.716	0.863	SUBCLONAL	1	TRUE	1	0.603922787244293	2		333	517	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631620	90631620	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745751309	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	242	608	1	ENST00000330062.3:c.649G>A	p.Val217Met	p.V217M	ENST00000330062	NM_002168.2	217	Gtg/Atg	5/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.603922787244293	2		609	787	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720287	43720287	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151132652	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	185	460	1	ENST00000382044.4:c.3755G>A	p.Arg1252His	p.R1252H	ENST00000382044	NM_001141980.1	1252	cGc/cAc	18/28	1	2	FACETS	0.888	0.823	0.955	0.888	0.823	0.955	CLONAL	1	TRUE	1	0.603922787244293	2		461	690	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627233	12627233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs941573221	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	147	408	0	ENST00000251849.4:c.1483C>T	p.Arg495Cys	p.R495C	ENST00000251849	NM_002880.3	495	Cgc/Tgc	14/17	1	2	FACETS	0.913	0.839	0.991	0.913	0.839	0.991	CLONAL	1	TRUE	1	0.603922787244293	2		408	533	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858095	40858095	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	242	522	0	ENST00000428826.2:c.1769G>T	p.Gly590Val	p.G590V	ENST00000428826		590	gGg/gTg	16/21	1	2	FACETS	0.981	0.919	1	0.981	0.919	1	CLONAL	1	TRUE	1	0.603922787244293	2		522	817	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003773	45003773	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	168	514	0	ENST00000558401.1:c.29T>C	p.Leu10Pro	p.L10P	ENST00000558401	NM_004048.2	10	cTc/cCc	1/4	1	2	FACETS	0.918	0.848	0.991	0.918	0.848	0.991	CLONAL	1	TRUE	1	0.603922787244293	2		514	606	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656908	45656908	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	220	559	1	ENST00000407780.3:c.248G>A	p.Arg83Gln	p.R83Q	ENST00000407780	NM_001283052.1	83	cGa/cAa	3/7	1	2	FACETS	0.913	0.852	0.976	0.913	0.852	0.976	CLONAL	1	TRUE	1	0.603922787244293	2		560	798	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508460	106508460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	93	340	0	ENST00000359195.3:c.454C>T	p.Arg152Trp	p.R152W	ENST00000359195	NM_002649.2	152	Cgg/Tgg	2/11	1	2	FACETS	0.895	0.804	0.991	0.895	0.804	0.991	CLONAL	1	TRUE	1	0.603922787244293	2		340	344	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172373	108172373	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	79	254	0	ENST00000278616.4:c.5178-2A>G		p.X1726_splice	ENST00000278616	NM_000051.3	1726			1	2	FACETS	0.798	0.708	0.893	0.798	0.708	0.893	SUBCLONAL	1	TRUE	1	0.603922787244293	2		254	328	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931970	39931970	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	220	344	0	ENST00000378444.4:c.2629A>G	p.Thr877Ala	p.T877A	ENST00000378444	NM_001123385.1	877	Acc/Gcc	4/15	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.603922787244293	1		344	382	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295788	212295788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1412193732	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	115	448	0	ENST00000342788.4:c.2525G>A	p.Arg842Gln	p.R842Q	ENST00000342788	NM_005235.2	842	cGg/cAg	21/28	1	2	FACETS	0.787	0.713	0.864	0.787	0.713	0.864	SUBCLONAL	1	TRUE	1	0.603922787244293	2		448	484	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162117	38162117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs115403388	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	115	309	0	ENST00000317025.8:c.2599G>A	p.Val867Ile	p.V867I	ENST00000317025	NM_023034.1	867	Gtt/Att	14/24	1	2	FACETS	0.878	0.796	0.962	0.878	0.796	0.962	CLONAL	1	TRUE	1	0.603922787244293	2		309	434	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420526	49420526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764161037	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	207	625	0	ENST00000301067.7:c.15223G>A	p.Gly5075Arg	p.G5075R	ENST00000301067	NM_003482.3	5075	Ggg/Agg	48/54	1	2	FACETS	0.88	0.819	0.943	0.88	0.819	0.943	CLONAL	1	TRUE	1	0.603922787244293	2		625	779	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613085	52613085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1318993618	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	136	317	0	ENST00000394830.3:c.3443G>A	p.Arg1148His	p.R1148H	ENST00000394830	NM_018313.4	1148	cGt/cAt	22/30	1	2	FACETS	0.962	0.881	1	0.962	0.881	1	CLONAL	1	TRUE	1	0.603922787244293	2		317	468	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056208	27056208	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	113	535	0	ENST00000324856.7:c.1204T>G	p.Ser402Ala	p.S402A	ENST00000324856	NM_006015.4	402	Tcg/Gcg	2/20	1	2	FACETS	0.636	0.574	0.702	0.636	0.574	0.702	SUBCLONAL	1	TRUE	1	0.603922787244293	2		535	588	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175956092	175956092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	100	292	0	ENST00000367669.3:c.2120C>T	p.Ala707Val	p.A707V	ENST00000367669	NM_022457.5	707	gCa/gTa	18/20	1	2	FACETS	0.93	0.839	1	0.93	0.839	1	CLONAL	1	TRUE	1	0.603922787244293	2		292	356	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420852	49420852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	166	511	1	ENST00000301067.7:c.14897G>A	p.Arg4966Gln	p.R4966Q	ENST00000301067	NM_003482.3	4966	cGg/cAg	48/54	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.603922787244293	2		512	550	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431843	49431843	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778257510	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	177	605	3	ENST00000301067.7:c.9296G>A	p.Arg3099His	p.R3099H	ENST00000301067	NM_003482.3	3099	cGc/cAc	34/54	1	2	FACETS	0.922	0.853	0.992	0.922	0.853	0.992	CLONAL	1	TRUE	1	0.603922787244293	2		608	636	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118901	115118901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1312105333	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	77	283	1	ENST00000257566.3:c.440C>T	p.Ala147Val	p.A147V	ENST00000257566	NM_016569.3	147	gCc/gTc	2/8	1	2	FACETS	0.775	0.686	0.869	0.775	0.686	0.869	SUBCLONAL	1	TRUE	1	0.603922787244293	2		284	329	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630780	90630780	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	130	383	0	ENST00000330062.3:c.706T>G	p.Phe236Val	p.F236V	ENST00000330062	NM_002168.2	236	Ttc/Gtc	6/11	1	2	FACETS	0.864	0.789	0.943	0.864	0.789	0.943	CLONAL	1	TRUE	1	0.603922787244293	2		383	498	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343713	343713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377025983	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	218	658	0	ENST00000262320.3:c.1961C>T	p.Ser654Leu	p.S654L	ENST00000262320	NM_003502.3	654	tCg/tTg	8/11	1	2	FACETS	0.916	0.854	0.98	0.916	0.854	0.98	CLONAL	1	TRUE	1	0.603922787244293	2		658	788	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216569	7216569	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753866859	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	46	489	0	ENST00000380728.2:c.766A>G	p.Met256Val	p.M256V	ENST00000380728		256	Atg/Gtg	9/11	1	2	FACETS	0.254	0.214	0.299	0.254	0.214	0.299	SUBCLONAL	1	TRUE	1	0.603922787244293	2		489	599	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440942	56440942	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758854182	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	214	557	0	ENST00000407977.2:c.395G>A	p.Arg132Gln	p.R132Q	ENST00000407977		132	cGa/cAa	4/10	1	2	FACETS	0.978	0.912	1	0.978	0.912	1	CLONAL	1	TRUE	1	0.603922787244293	2		557	725	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58725439	58725439	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	136	372	0	ENST00000305921.3:c.1013T>C	p.Leu338Pro	p.L338P	ENST00000305921	NM_003620.3	338	cTg/cCg	4/6	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.603922787244293	2		372	445	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936747	78936747	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	193	684	0	ENST00000306801.3:c.3829A>G	p.Thr1277Ala	p.T1277A	ENST00000306801	NM_020761.2	1277	Acc/Gcc	33/34	1	2	FACETS	0.835	0.775	0.898	0.835	0.775	0.898	CLONAL	1	TRUE	1	0.603922787244293	2		684	765	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229543	5229543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	58	115	0	ENST00000357368.4:c.2308G>T	p.Gly770Trp	p.G770W	ENST00000357368	NM_002850.3	770	Ggg/Tgg	15/38	0.582449467335745	2	FACETS	0.889	0.775	1	0.445	0.387	0.505	CLONAL	1	TRUE	0	0.603922787244293	2		115	216	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246888	10246888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	521	712	1	ENST00000340748.4:c.4517G>A	p.Arg1506Gln	p.R1506Q	ENST00000340748		1506	cGg/cAg	37/40	0.582449467335745	2	FACETS	0.969	0.936	1	0.969	0.936	1	CLONAL	2	TRUE	0	0.603922787244293	2		713	890	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303094	15303094	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	211	773	0	ENST00000263388.2:c.356T>C	p.Leu119Pro	p.L119P	ENST00000263388	NM_000435.2	119	cTg/cCg	4/33	0.582449467335745	2	FACETS	0.757	0.704	0.812	0.379	0.352	0.406	SUBCLONAL	1	TRUE	0	0.603922787244293	2		773	923	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950304	17950304	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	214	617	0	ENST00000458235.1:c.1423T>G	p.Cys475Gly	p.C475G	ENST00000458235	NM_000215.3	475	Tgt/Ggt	10/24	0.582449467335745	2	FACETS	0.928	0.865	0.992	0.464	0.432	0.496	CLONAL	1	TRUE	0	0.603922787244293	2		617	764	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211108	36211108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150247325	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	89	740	0	ENST00000222270.7:c.859C>T	p.Arg287Cys	p.R287C	ENST00000222270	NM_014727.1	287	Cgt/Tgt	3/37	0.582449467335745	2	FACETS	0.312	0.276	0.351	0.156	0.138	0.176	SUBCLONAL	1	TRUE	0	0.603922787244293	2		740	944	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505421	25505421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758151481	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	138	656	0	ENST00000264709.3:c.337G>A	p.Gly113Arg	p.G113R	ENST00000264709	NM_175629.2	113	Ggg/Agg	4/23	1	2	FACETS	0.843	0.771	0.918	0.843	0.771	0.918	CLONAL	1	TRUE	1	0.603922787244293	2		656	542	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025889	48025890	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	99	254	0	ENST00000234420.5:c.768dup	p.Asp257Ter	p.D257*	ENST00000234420	NM_000179.2	256	agt/agTt	4/10	1	2	FACETS	0.832	0.748	0.92	0.832	0.748	0.92	CLONAL	1	TRUE	1	0.603922787244293	2		254	394	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198260936	198260936	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	166	490	0	ENST00000335508.6:c.3383T>C	p.Val1128Ala	p.V1128A	ENST00000335508	NM_012433.2	1128	gTa/gCa	23/25	1	2	FACETS	0.935	0.863	1	0.935	0.863	1	CLONAL	1	TRUE	1	0.603922787244293	2		490	588	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149814	202149814	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	42	488	0	ENST00000358485.4:c.1255T>C	p.Cys419Arg	p.C419R	ENST00000358485	NM_001080125.1	419	Tgt/Cgt	8/9	1	2	FACETS	0.275	0.23	0.326	0.275	0.23	0.326	SUBCLONAL	1	TRUE	1	0.603922787244293	2		488	505	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101089	41101089	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	172	590	0	ENST00000373198.4:c.1267A>G	p.Thr423Ala	p.T423A	ENST00000373198	NM_133170.3	423	Acc/Gcc	8/32	0.603922787244293	3	FACETS	0.918	0.846	0.993	0.459	0.423	0.497	CLONAL	1	TRUE	1	0.603922787244293	3		590	808	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44515847	44515847	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	37	385	0	ENST00000291552.4:c.206T>C	p.Val69Ala	p.V69A	ENST00000291552	NM_006758.2	69	gTg/gCg	4/8	1	2	FACETS	0.199	0.163	0.239	0.199	0.163	0.239	SUBCLONAL	1	TRUE	1	0.603922787244293	2		385	616	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29106001	29106001	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1490781911	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	112	254	0	ENST00000328354.6:c.839T>C	p.Leu280Pro	p.L280P	ENST00000328354	NM_007194.3	280	cTa/cCa	7/15	1	2	FACETS	0.832	0.753	0.914	0.832	0.753	0.914	CLONAL	1	TRUE	1	0.603922787244293	2		254	446	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533737	41533737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs953144031	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	145	406	1	ENST00000263253.7:c.1703G>A	p.Arg568Gln	p.R568Q	ENST00000263253	NM_001429.3	568	cGg/cAg	8/31	1	2	FACETS	0.841	0.771	0.914	0.841	0.771	0.914	CLONAL	1	TRUE	1	0.603922787244293	2		407	571	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713673	30713673	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	149	512	0	ENST00000295754.5:c.998T>G	p.Leu333Arg	p.L333R	ENST00000295754	NM_003242.5	333	cTa/cGa	4/7	1	2	FACETS	0.834	0.765	0.905	0.834	0.765	0.905	CLONAL	1	TRUE	1	0.603922787244293	2		512	592	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436335	52436335	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776746400	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	187	696	2	ENST00000460680.1:c.2159G>A	p.Arg720His	p.R720H	ENST00000460680	NM_004656.3	720	cGc/cAc	17/17	1	2	FACETS	0.844	0.782	0.908	0.844	0.782	0.908	CLONAL	1	TRUE	1	0.603922787244293	2		698	734	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430666	181430666	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	175	646	0	ENST00000325404.1:c.518T>C	p.Met173Thr	p.M173T	ENST00000325404	NM_003106.3	173	aTg/aCg	1/1	1	2	FACETS	0.92	0.851	0.991	0.92	0.851	0.991	CLONAL	1	TRUE	1	0.603922787244293	2		646	630	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808020	1808020	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	300	743	0	ENST00000260795.2:c.1996T>G	p.Leu666Val	p.L666V	ENST00000260795		666	Ttg/Gtg	14/17	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.603922787244293	2		743	918	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867491	35867491	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	67	218	0	ENST00000303115.3:c.305T>C	p.Ile102Thr	p.I102T	ENST00000303115	NM_002185.3	102	aTt/aCt	3/8	1	2	FACETS	0.757	0.664	0.856	0.757	0.664	0.856	SUBCLONAL	1	TRUE	1	0.603922787244293	2		218	293	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176683958	176683958	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	90	363	0	ENST00000439151.2:c.4772A>G	p.His1591Arg	p.H1591R	ENST00000439151	NM_022455.4	1591	cAt/cGt	13/23	NA	2	FACETS	0.6	0.534	0.669			1	INDETERMINATE	1	TRUE	NA	0.603922787244293	2		363	497	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910669	29910669	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs199474401	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	277	885	0	ENST00000376809.5:c.209A>C	p.Glu70Ala	p.E70A	ENST00000376809	NM_002116.7	70	gAg/gCg	2/8	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.603922787244293	2		885	913	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672867	30672867	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1277124877	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	187	524	0	ENST00000376406.3:c.4093T>C	p.Ser1365Pro	p.S1365P	ENST00000376406	NM_014641.2	1365	Tca/Cca	10/15	1	2	FACETS	0.953	0.884	1	0.953	0.884	1	CLONAL	1	TRUE	1	0.603922787244293	2		524	650	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935655	13935655	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	117	408	0	ENST00000405192.2:c.1201A>G	p.Met401Val	p.M401V	ENST00000405192	NM_001163147.1	401	Atg/Gtg	12/12	1	2	FACETS	0.778	0.705	0.854	0.778	0.705	0.854	SUBCLONAL	1	TRUE	1	0.603922787244293	2		408	498	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730011	41730011	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	206	506	0	ENST00000242208.4:c.518T>C	p.Ile173Thr	p.I173T	ENST00000242208	NM_002192.2	173	aTc/aCc	3/3	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.603922787244293	2		506	671	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133825	38133825	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs544880722	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	210	568	0	ENST00000317025.8:c.4061A>G	p.Gln1354Arg	p.Q1354R	ENST00000317025	NM_023034.1	1354	cAg/cGg	23/24	1	2	FACETS	0.874	0.813	0.936	0.874	0.813	0.936	CLONAL	1	TRUE	1	0.603922787244293	2		568	796	SUCCESS
AR	367	MSKCC	GRCh37	X	66765402	66765403	+	missense_variant	Missense_Mutation	DNP	CG	CG	GC	novel	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	146	345	0	ENST00000374690.3:c.414_415delinsGC	p.Val139Leu	p.V139L	ENST00000374690	NM_000044.3	138	gcCGtg/gcGCtg	1/8	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.603922787244293	1		345	273	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356449	70356449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1224410841	NA	P-0046843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	197	239	0	ENST00000374080.3:c.5344C>T	p.Arg1782Cys	p.R1782C	ENST00000374080		1782	Cgc/Tgc	37/45	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.603922787244293	1		239	343	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0046845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	141	354	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.867	0.796	0.941	1	0.99	1	CLONAL	2	FALSE	1	0.345837513104915	2		354	470	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522551	176522551	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774571806	NA	P-0046845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	318	757	2	ENST00000292408.4:c.1648G>A	p.Val550Met	p.V550M	ENST00000292408	NM_213647.1	550	Gtg/Atg	13/18	0.285161602409132	4	FACETS	0.937	0.883	0.992	0.625	0.589	0.661	CLONAL	2	FALSE	1	0.345837513104915	4		759	1321	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523143	176523143	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	302	699	1	ENST00000292408.4:c.1907G>T	p.Gly636Val	p.G636V	ENST00000292408	NM_213647.1	636	gGc/gTc	14/18	0.285161602409132	4	FACETS	0.917	0.863	0.973	0.612	0.575	0.649	CLONAL	2	FALSE	1	0.345837513104915	4		700	1281	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888163	112888163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397507509	NA	P-0046845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	149	499	0	ENST00000351677.2:c.179G>C	p.Gly60Ala	p.G60A	ENST00000351677	NM_002834.3	60	gGt/gCt	3/16	0.24781957705878	4	FACETS	1	0.986	1	0.48	0.438	0.523	CLONAL	1	FALSE	1	0.345837513104915	4		499	806	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0046847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	201	589	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.988	0.917	1	1	0.993	1	CLONAL	2	TRUE	1	0.236105615363635	2		589	862	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951053	48951053	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs587778831	NA	P-0046847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	12	191	0	ENST00000267163.4:c.1216-1G>A		p.X406_splice	ENST00000267163	NM_000321.2	406			0.236105615363635	1	FACETS	0.427	0.3	0.583	0.427	0.3	0.583	SUBCLONAL	1	TRUE	0	0.236105615363635	1		191	210	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720221	43720221	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	57	381	0	ENST00000382044.4:c.3821T>G	p.Val1274Gly	p.V1274G	ENST00000382044	NM_001141980.1	1274	gTa/gGa	18/28	1	2	FACETS	0.781	0.67	0.903	0.781	0.67	0.903	CLONAL	1	TRUE	1	0.236105615363635	2		381	618	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105744	27105760	+	frameshift_variant	Frame_Shift_Del	DEL	TGAGGAGATAGCCTTTT	TGAGGAGATAGCCTTTT	CAA	novel	NA	P-0046848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	155	363	1	ENST00000324856.7:c.5355_5371delinsCAA	p.Glu1786AsnfsTer11	p.E1786Nfs*11	ENST00000324856	NM_006015.4	1785	gaTGAGGAGATAGCCTTTTca/gaCAAca	20/20	0.616541295307236	3	FACETS	0.899	0.834	0.964	0.899	0.834	0.964	CLONAL	2	TRUE	1	0.616541295307236	3		364	366	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220123	5220123	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	162	644	0	ENST00000357368.4:c.3592C>T	p.His1198Tyr	p.H1198Y	ENST00000357368	NM_002850.3	1198	Cac/Tac	22/38	0.616541295307236	3	FACETS	1	0.974	1	0.564	0.52	0.61	CLONAL	1	TRUE	1	0.616541295307236	3		644	609	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297916	15297916	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	177	702	0	ENST00000263388.2:c.1840G>A	p.Gly614Ser	p.G614S	ENST00000263388	NM_000435.2	614	Ggt/Agt	11/33	0.616541295307236	3	FACETS	1	0.968	1	0.543	0.502	0.585	CLONAL	1	TRUE	1	0.616541295307236	3		702	692	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138376614	138376614	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	77	401	0	ENST00000289153.2:c.2860G>T	p.Glu954Ter	p.E954*	ENST00000289153	NM_006219.2	954	Gag/Tag	20/22	0.611643821097131	2	FACETS	0.987	0.879	1	0.494	0.439	0.55	CLONAL	1	TRUE	0	0.616541295307236	2		401	253	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0046848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	109	202	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.616541295307236	3	FACETS	0.847	0.786	0.907	1	0.984	1	CLONAL	3	TRUE	1	0.616541295307236	3		202	182	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450321	50450321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	126	601	0	ENST00000331340.3:c.505G>A	p.Gly169Arg	p.G169R	ENST00000331340	NM_006060.4	169	Ggg/Agg	5/8	0.616541295307236	4	FACETS	0.966	0.876	1	0.322	0.292	0.354	CLONAL	1	TRUE	1	0.616541295307236	4		601	684	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945117	151945117	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	16	286	0	ENST00000262189.6:c.2402C>G	p.Pro801Arg	p.P801R	ENST00000262189	NM_170606.2	801	cCt/cGt	14/59	0.616541295307236	4	FACETS	0.329	0.243	0.432	0.11	0.081	0.144	SUBCLONAL	1	TRUE	1	0.616541295307236	4		286	255	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	38	427	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.977	0.815	1	0.977	0.815	1	CLONAL	1	TRUE	1	0.358331460039598	2		427	217	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556079	29556079	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886041347	NA	P-0046849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	49	174	0	ENST00000356175.3:c.2446C>T	p.Arg816Ter	p.R816*	ENST00000356175	NM_000267.3	816	Cga/Tga	21/57	0.314317430321843	1	FACETS	0.931	0.797	1	0.931	0.797	1	CLONAL	1	TRUE	0	0.358331460039598	1		174	241	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0046849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	165	699	0	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.202355841055497	1	FACETS	0.896	0.823	0.971	0.896	0.823	0.971	INDETERMINATE	1	TRUE	0	0.358331460039598	1		699	844	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176476	123176479	+	frameshift_variant	Frame_Shift_Del	DEL	TGAC	TGAC	-	novel	NA	P-0046849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	32	248	0	ENST00000218089.9:c.446_449del	p.Thr149LysfsTer33	p.T149Kfs*33	ENST00000218089	NM_001042749.1	148	aTGACt/at	7/35	1	2	FACETS	0.618	0.503	0.747	0.618	0.503	0.747	SUBCLONAL	1	TRUE	1	0.358331460039598	2		248	289	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346350	73346350	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	45	255	0	ENST00000377767.4:c.1450A>G	p.Thr484Ala	p.T484A	ENST00000377767	NM_014953.3	484	Act/Gct	10/21	0.315128949102075	1	FACETS	0.991	0.843	1	0.991	0.843	1	CLONAL	1	TRUE	0	0.358331460039598	1		255	208	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243448	46243448	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	64	328	0	ENST00000334344.6:c.1801C>T	p.Arg601Trp	p.R601W	ENST00000334344	NM_152641.2	601	Cgg/Tgg	14/21	0.942692522473443	3	FACETS	0.36	0.312	0.412	0.18	0.156	0.206	SUBCLONAL	1	TRUE	1	0.942692522473443	3		328	555	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579435	7579438	+	frameshift_variant	Frame_Shift_Del	DEL	GGCC	GGCC	-	novel	NA	P-0046852-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	875	632	1	ENST00000269305.4:c.249_252del	p.Ala84LeufsTer38	p.A84Lfs*38	ENST00000269305	NM_001126112.2	83	gcGGCC/gc	4/11	0.942692522473443	2	FACETS	0.999	0.989	1	0.999	0.989	1	CLONAL	2	TRUE	0	0.942692522473443	2		633	929	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0046853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	46	199	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.243253674322513	3	FACETS	0.803	0.682	0.936	0.803	0.682	0.936	CLONAL	2	TRUE	1	0.243253674322513	3		199	264	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0046853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	179	594	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.243253674322513	3	FACETS	0.976	0.9	1	0.976	0.9	1	CLONAL	2	TRUE	1	0.243253674322513	3		594	846	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301887	65301888	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTGGA	novel	NA	P-0046853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	16	155	0	ENST00000342505.4:c.3147_3151dup	p.Glu1051ValfsTer5	p.E1051Vfs*5	ENST00000342505	NM_002227.2	1051	gaa/gTCCAGaa	23/25	1	2	FACETS	0.518	0.383	0.679	0.518	0.383	0.679	SUBCLONAL	1	TRUE	1	0.243253674322513	2		155	254	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563335	21563335	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	70	786	0	ENST00000382592.4:c.584G>T	p.Ser195Ile	p.S195I	ENST00000382592	NM_014572.2	195	aGc/aTc	4/8	0.226918026408056	4	FACETS	0.604	0.525	0.691	0.201	0.175	0.231	SUBCLONAL	1	TRUE	1	0.243253674322513	4		786	1184	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098749	2098749	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	62	302	0	ENST00000219476.3:c.133C>G	p.Leu45Val	p.L45V	ENST00000219476	NM_000548.3	45	Ctg/Gtg	2/42	0.146635229260819	5	FACETS	0.95	0.82	1	0.317	0.273	0.365	CLONAL	1	TRUE	2	0.243253674322513	5		302	732	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79968094	79968094	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1228477054	NA	P-0046853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	131	381	0	ENST00000265081.6:c.824A>G	p.His275Arg	p.H275R	ENST00000265081	NM_002439.4	275	cAt/cGt	5/24	0.243253674322513	3	FACETS	0.874	0.795	0.957	0.874	0.795	0.957	CLONAL	2	TRUE	1	0.243253674322513	3		381	691	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012275	152012275	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	49	342	0	ENST00000262189.6:c.538A>T	p.Thr180Ser	p.T180S	ENST00000262189	NM_170606.2	180	Acc/Tcc	4/59	0.213526121479229	4	FACETS	0.775	0.656	0.907	0.388	0.328	0.454	CLONAL	1	TRUE	2	0.243253674322513	4		342	646	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412551	63412551	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	55	538	0	ENST00000330258.3:c.616G>T	p.Glu206Ter	p.E206*	ENST00000330258	NM_152424.3	206	Gag/Tag	2/2	1	2	FACETS	0.698	0.596	0.809	0.698	0.596	0.809	SUBCLONAL	1	TRUE	1	0.243253674322513	2		538	648	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0046855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	28	526	3	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.509	0.405	0.629	0.509	0.405	0.629	SUBCLONAL	1	TRUE	1	0.15	2		529	733	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0046855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	39	707	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	0.731	0.604	0.874	0.731	0.604	0.874	SUBCLONAL	1	TRUE	1	0.15	2		707	711	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374943	45374943	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	33	335	0	ENST00000262160.6:c.900T>A	p.Asp300Glu	p.D300E	ENST00000262160	NM_005901.5	300	gaT/gaA	8/11	1	2	FACETS	0.676	0.549	0.82	0.676	0.549	0.82	SUBCLONAL	1	TRUE	1	0.15	2		335	651	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0046856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	112	363	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.936	0.844	1	1	0.988	1	CLONAL	2	TRUE	1	0.206407414589468	2		363	580	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0046856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	59	175	5	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.206407414589468	2	FACETS	0.979	0.849	1	0.979	0.849	1	CLONAL	2	TRUE	0	0.206407414589468	2		180	292	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428239	47428239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764255925	NA	P-0046856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	30	467	0	ENST00000377045.4:c.1199G>A	p.Arg400His	p.R400H	ENST00000377045	NM_001654.4	400	cGc/cAc	11/16	1	1	FACETS	0.491	0.395	0.601	0.491	0.395	0.601	SUBCLONAL	1	TRUE	0	0.206407414589468	1		467	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0046856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	146	716	1	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	1	2	FACETS	0.814	0.743	0.889	1	0.989	1	CLONAL	2	TRUE	1	0.206407414589468	2		717	869	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43771655	43771655	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	92	507	0	ENST00000382044.4:c.728del	p.Val243GlyfsTer12	p.V243Gfs*12	ENST00000382044	NM_001141980.1	243	gTg/gg	7/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.206407414589468	2		507	667	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120501	70120502	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0046856-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	53	740	0	ENST00000245479.2:c.1504_1505dup	p.Tyr503SerfsTer21	p.Y503Sfs*21	ENST00000245479	NM_000346.3	501	-/GT	3/3	1	2	FACETS	0.523	0.444	0.61	0.523	0.444	0.61	SUBCLONAL	1	TRUE	1	0.206407414589468	2		740	982	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0046857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	301	767	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.427860409993942	2	FACETS	0.996	0.945	1	0.996	0.945	1	CLONAL	2	TRUE	0	0.427860409993942	2		767	706	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0046857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	272	572	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.427860409993942	5	FACETS	0.974	0.914	1	0.649	0.609	0.69	CLONAL	2	TRUE	2	0.427860409993942	5		572	1072	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975399	13975399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs186330943	NA	P-0046857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	107	329	1	ENST00000405192.2:c.488G>A	p.Arg163Gln	p.R163Q	ENST00000405192	NM_001163147.1	163	cGg/cAg	7/12	0.427860409993942	4	FACETS	0.91	0.816	1	0.455	0.408	0.505	CLONAL	1	TRUE	2	0.427860409993942	4		330	785	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912786	50912786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61751955	NA	P-0046857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	360	757	0	ENST00000440232.2:c.2017G>A	p.Glu673Lys	p.E673K	ENST00000440232	NM_002691.3	673	Gag/Aag	17/27	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	1	TRUE	NA	0.427860409993942	2		757	1147	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943466	17943466	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	244	577	0	ENST00000458235.1:c.2542A>G	p.Thr848Ala	p.T848A	ENST00000458235	NM_000215.3	848	Aca/Gca	19/24	0.182564225617552	5	FACETS	0.903	0.844	0.964	0.602	0.562	0.643	INDETERMINATE	2	TRUE	2	0.427860409993942	5		577	1037	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251753	212251753	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	32	341	0	ENST00000342788.4:c.3306T>G	p.Phe1102Leu	p.F1102L	ENST00000342788	NM_005235.2	1102	ttT/ttG	27/28	0.749161861446559	1	FACETS	0.172	0.14	0.209	0.172	0.14	0.209	SUBCLONAL	1	TRUE	0	0.749161861446559	1		341	310	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	99	424	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.154136921004137	3	FACETS	1	0.98	1	0.736	0.658	0.819	CLONAL	1	FALSE	1	0.233203479749381	3		424	644	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0046859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	104	337	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.15933536932335	2	FACETS	0.885	0.796	0.979	0.885	0.796	0.979	CLONAL	2	FALSE	0	0.233203479749381	2		337	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579406	7579406	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	119	615	0	ENST00000269305.4:c.281C>A	p.Ser94Ter	p.S94*	ENST00000269305	NM_001126112.2	94	tCa/tAa	4/11	0.233203479749381	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	0	0.233203479749381	1		615	743	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106598	27106599	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0046859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	138	593	0	ENST00000324856.7:c.6209_6210del	p.Gln2070LeufsTer28	p.Q2070Lfs*28	ENST00000324856	NM_006015.4	2070	cAG/c	20/20	0.154136921004137	3	FACETS	0.871	0.793	0.952	0.871	0.793	0.952	CLONAL	2	FALSE	1	0.233203479749381	3		593	759	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215861	133215861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500803	NA	P-0046859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	27	350	1	ENST00000320574.5:c.5402G>A	p.Gly1801Asp	p.G1801D	ENST00000320574	NM_006231.2	1801	gGc/gAc	40/49	1	2	FACETS	0.583	0.464	0.72	0.583	0.464	0.72	SUBCLONAL	1	FALSE	1	0.233203479749381	2		351	397	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458407	12458407	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	136	481	0	ENST00000287820.6:c.1024C>A	p.Gln342Lys	p.Q342K	ENST00000287820	NM_015869.4	342	Caa/Aaa	6/7	1	2	FACETS	0.796	0.724	0.87	1	0.988	1	SUBCLONAL	2	FALSE	1	0.233203479749381	2		481	733	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0046860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	293	803	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.539509023926682	2		803	1006	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138642	55138642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143344944	NA	P-0046860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	96	350	0	ENST00000257290.5:c.1319C>T	p.Thr440Met	p.T440M	ENST00000257290	NM_006206.4	440	aCg/aTg	9/23	0.295692767244639	1	FACETS	0.413	0.368	0.461	0.413	0.368	0.461	INDETERMINATE	1	TRUE	0	0.539509023926682	1		350	629	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0046860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	109	182	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.478493501649625	1	FACETS	0.925	0.841	1	0.925	0.841	1	CLONAL	1	TRUE	0	0.539509023926682	1		182	319	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189003	32189003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751063545	NA	P-0046860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	229	561	1	ENST00000375023.3:c.551C>T	p.Pro184Leu	p.P184L	ENST00000375023	NM_004557.3	184	cCg/cTg	4/30	1	2	FACETS	0.905	0.844	0.968	0.905	0.844	0.968	CLONAL	1	TRUE	1	0.539509023926682	2		562	938	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042300	42042301	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs866465268	NA	P-0046860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	159	320	0	ENST00000219905.7:c.6499_6500del	p.Leu2167GlyfsTer27	p.L2167Gfs*27	ENST00000219905	NM_001164273.1	2165	gaCTct/gact	17/24	0.539509023926682	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.539509023926682	1		320	377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	334	517	0	ENST00000269305.4:c.406del	p.Gln136AsnfsTer34	p.Q136Nfs*34	ENST00000269305	NM_001126112.2	136	Caa/aa	5/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.539509023926682	2		517	1157	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271192	153271192	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0046860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	35	153	0	ENST00000281708.4:c.584+2T>C		p.X195_splice	ENST00000281708	NM_033632.3	195			0.295692767244639	1	FACETS	0.403	0.332	0.481	0.403	0.332	0.481	INDETERMINATE	1	TRUE	0	0.539509023926682	1		153	235	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780039	9780039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	279	495	1	ENST00000377346.4:c.1303G>A	p.Gly435Arg	p.G435R	ENST00000377346	NM_005026.3	435	Ggg/Agg	10/24	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.539509023926682	2		496	940	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805360	89805361	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0046860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	155	394	0	ENST00000389301.3:c.4188_4189dup	p.Thr1397LysfsTer11	p.T1397Kfs*11	ENST00000389301	NM_000135.2	1397	aca/aAAca	42/43	1	2	FACETS	0.86	0.79	0.933	0.86	0.79	0.933	CLONAL	1	TRUE	1	0.539509023926682	2		394	668	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589858	212589858	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	196	384	0	ENST00000342788.4:c.684C>A	p.Asp228Glu	p.D228E	ENST00000342788	NM_005235.2	228	gaC/gaA	6/28	0.235732777158002	3	FACETS	1	0.929	1	0.501	0.464	0.54	INDETERMINATE	1	TRUE	1	0.539509023926682	3		384	920	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314905	1314905	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	83	267	0	ENST00000400841.2:c.756G>T	p.Trp252Cys	p.W252C	ENST00000400841		252	tgG/tgT	6/6	0.539509023926682	2	FACETS	0.498	0.44	0.56			1	SUBCLONAL	1	TRUE	NA	0.539509023926682	2		267	618	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	344	424	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.262925555817448	5	FACETS	1	0.989	1			1	INDETERMINATE	3	TRUE	NA	0.477964966179488	5		424	732	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196879	108196880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs773570504	NA	P-0046861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	139	265	0	ENST00000278616.4:c.6908dup	p.Glu2304GlyfsTer69	p.E2304Gfs*69	ENST00000278616	NM_000051.3	2301	gca/gcAa	47/63	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.477964966179488	2		265	523	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038858	12038858	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0046861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	214	200	0	ENST00000396373.4:c.1153-2A>G		p.X385_splice	ENST00000396373	NM_001987.4	385			0.423500714467162	5	FACETS	1	0.986	1	0.868	0.817	0.918	CLONAL	3	TRUE	1	0.477964966179488	5		200	443	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291016	15291016	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	195	671	0	ENST00000263388.2:c.3194A>G	p.Asp1065Gly	p.D1065G	ENST00000263388	NM_000435.2	1065	gAc/gGc	20/33	1	2	FACETS	0.966	0.895	1	0.966	0.895	1	CLONAL	1	TRUE	1	0.477964966179488	2		671	845	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218660	36218660	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776889319	NA	P-0046861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	199	623	0	ENST00000222270.7:c.4364G>A	p.Arg1455His	p.R1455H	ENST00000222270	NM_014727.1	1455	cGc/cAc	17/37	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.477964966179488	2		623	772	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167792	185167792	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	136	347	0	ENST00000265026.3:c.1115T>A	p.Leu372His	p.L372H	ENST00000265026	NM_004721.4	372	cTt/cAt	6/14	0.228943382399551	1	FACETS	0.854	0.781	0.93	0.854	0.781	0.93	INDETERMINATE	1	TRUE	0	0.477964966179488	1		347	507	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401585	401585	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	119	392	0	ENST00000380956.4:c.907A>C	p.Asn303His	p.N303H	ENST00000380956	NM_001195286.1	303	Aac/Cac	7/9	0.416080501542546	1	FACETS	0.837	0.76	0.916	0.837	0.76	0.916	CLONAL	1	TRUE	0	0.477964966179488	1		392	453	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798478	32798478	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	154	538	0	ENST00000374899.4:c.1378G>C	p.Ala460Pro	p.A460P	ENST00000374899	NM_018833.2	460	Gcc/Ccc	8/12	1	2	FACETS	0.888	0.814	0.964	0.888	0.814	0.964	CLONAL	1	TRUE	1	0.477964966179488	2		538	726	SUCCESS
ATM	472	MSKCC	GRCh37	11	108128263	108128264	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	C	novel	NA	P-0046861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	111	259	0	ENST00000278616.4:c.2306_2307delinsC	p.Glu769AlafsTer8	p.E769Afs*8	ENST00000278616	NM_000051.3	769	gAG/gC	15/63	1	2	FACETS	0.944	0.853	1	0.944	0.853	1	CLONAL	1	TRUE	1	0.477964966179488	2		259	492	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933052	39933057	+	frameshift_variant	Frame_Shift_Del	DEL	GGACTT	GGACTT	A	novel	NA	P-0046861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	182	585	0	ENST00000378444.4:c.1542_1547delinsT	p.Ser515Ter	p.S515*	ENST00000378444	NM_001123385.1	514	ccAAGTCCt/ccTt	4/15	0.477964966179488	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.477964966179488	1		585	558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0046862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	260	670	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.455370693547021	1	FACETS	0.983	0.923	1	0.983	0.923	1	CLONAL	1	TRUE	0	0.455370693547021	1		670	897	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988970	85988970	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	63	216	3	ENST00000263360.6:c.1136T>C	p.Leu379Ser	p.L379S	ENST00000263360	NM_003797.3	379	tTg/tCg	11/12	0.455370693547021	3	FACETS	0.931	0.809	1	0.465	0.404	0.531	CLONAL	1	TRUE	1	0.455370693547021	3		219	365	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	125	593	0	ENST00000397752.3:c.3028G>A	p.Asp1010Asn	p.D1010N	ENST00000397752	NM_000245.2	1010	Gat/Aat	14/21	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.26	2		593	702	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041596	47041596	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	165	340	0	ENST00000377604.3:c.1821C>A	p.Tyr607Ter	p.Y607*	ENST00000377604	NM_001204468.1	607	taC/taA	17/24	0.261154326381505	2	FACETS	1	0.976	1			1	CLONAL	2	TRUE	NA	0.26	2		340	556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0046863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	48	752	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.209083102283307	1	FACETS	0.516	0.435	0.605	0.516	0.435	0.605	SUBCLONAL	1	TRUE	0	0.26	1		752	623	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377229	118377229	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	44	438	0	ENST00000534358.1:c.10622C>G	p.Pro3541Arg	p.P3541R	ENST00000534358	NM_005933.3	3541	cCa/cGa	27/36	1	2	FACETS	0.546	0.457	0.645	0.546	0.457	0.645	SUBCLONAL	1	TRUE	1	0.26	2		438	620	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533261	29533261	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786202145	NA	P-0046863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	27	285	0	ENST00000356175.3:c.1264G>A	p.Ala422Thr	p.A422T	ENST00000356175	NM_000267.3	422	Gca/Aca	12/57	1	2	FACETS	0.483	0.384	0.597	0.483	0.384	0.597	SUBCLONAL	1	TRUE	1	0.26	2		285	430	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186805	142186805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	14	316	0	ENST00000350721.4:c.6658G>A	p.Asp2220Asn	p.D2220N	ENST00000350721	NM_001184.3	2220	Gat/Aat	39/47	1	2	FACETS	0.429	0.31	0.573	0.429	0.31	0.573	SUBCLONAL	1	TRUE	1	0.26	2		316	251	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240755	53240755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	176	298	1	ENST00000375401.3:c.1325C>T	p.Ala442Val	p.A442V	ENST00000375401	NM_004187.3	442	gCt/gTt	10/26	0.261154326381505	2	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.26	2		299	568	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471665	120471665	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs141385984	NA	P-0046864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	142	378	0	ENST00000256646.2:c.3826G>C	p.Glu1276Gln	p.E1276Q	ENST00000256646	NM_024408.3	1276	Gag/Cag	23/34	1	2	FACETS	0.948	0.865	1	0.948	0.865	1	CLONAL	1	TRUE	1	0.378704646581077	2		378	791	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333593	70333593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	68	347	0	ENST00000373644.4:c.1498G>A	p.Glu500Lys	p.E500K	ENST00000373644	NM_030625.2	500	Gag/Aag	2/12	1	2	FACETS	0.796	0.695	0.905	0.796	0.695	0.905	CLONAL	1	TRUE	1	0.378704646581077	2		347	451	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405991	70405991	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	24	418	0	ENST00000373644.4:c.3505C>T	p.Gln1169Ter	p.Q1169*	ENST00000373644	NM_030625.2	1169	Caa/Taa	4/12	1	2	FACETS	0.279	0.218	0.35	0.279	0.218	0.35	SUBCLONAL	1	TRUE	1	0.378704646581077	2		418	454	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165711	108165711	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	14	273	0	ENST00000278616.4:c.4834G>C	p.Glu1612Gln	p.E1612Q	ENST00000278616	NM_000051.3	1612	Gaa/Caa	32/63	1	2	FACETS	0.289	0.208	0.386	0.289	0.208	0.386	SUBCLONAL	1	TRUE	1	0.378704646581077	2		273	256	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	495101	495101	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	22	359	0	ENST00000399788.2:c.205C>A	p.Arg69Ser	p.R69S	ENST00000399788	NM_001042603.1	69	Cgt/Agt	2/28	1	2	FACETS	0.294	0.227	0.372	0.294	0.227	0.372	SUBCLONAL	1	TRUE	1	0.378704646581077	2		359	395	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426751	49426751	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	74	264	0	ENST00000301067.7:c.11737C>T	p.Gln3913Ter	p.Q3913*	ENST00000301067	NM_003482.3	3913	Cag/Tag	39/54	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.378704646581077	2		264	346	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039501	49039501	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0046864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	29	311	0	ENST00000267163.4:c.2486C>G	p.Ser829Ter	p.S829*	ENST00000267163	NM_000321.2	829	tCa/tGa	23/27	0.378704646581077	1	FACETS	0.489	0.394	0.596	0.489	0.394	0.596	SUBCLONAL	1	TRUE	0	0.378704646581077	1		311	254	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988454	36988454	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	86	458	0	ENST00000354822.5:c.199C>G	p.Pro67Ala	p.P67A	ENST00000354822	NM_001079668.2	67	Ccg/Gcg	2/3	1	2	FACETS	0.491	0.433	0.553	0.491	0.433	0.553	SUBCLONAL	1	TRUE	1	0.378704646581077	2		458	925	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991473	72991473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1205716595	NA	P-0046864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	290	511	0	ENST00000268489.5:c.2572G>A	p.Glu858Lys	p.E858K	ENST00000268489	NM_006885.3	858	Gag/Aag	2/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.378704646581077	2		511	1186	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872559	37872559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293998208	NA	P-0046864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	56	424	0	ENST00000269571.5:c.1519G>A	p.Glu507Lys	p.E507K	ENST00000269571		507	Gag/Aag	13/27	1	2	FACETS	0.399	0.341	0.462	0.399	0.341	0.462	SUBCLONAL	1	TRUE	1	0.378704646581077	2		424	742	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591975	48591975	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	rs1568208291	NA	P-0046864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	52	254	0	ENST00000342988.3:c.1138A>T	p.Arg380Trp	p.R380W	ENST00000342988	NM_005359.5	380	Agg/Tgg	9/12	0.327600318102458	1	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	0	0.378704646581077	1		254	212	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265697	10265697	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	129	426	1	ENST00000340748.4:c.1480G>A	p.Glu494Lys	p.E494K	ENST00000340748		494	Gag/Aag	19/40	0.18322317937716	3	FACETS	0.983	0.892	1	0.492	0.446	0.54	INDETERMINATE	1	TRUE	1	0.378704646581077	3		427	824	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130268	11130268	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	108	470	0	ENST00000358026.2:c.2507G>T	p.Gly836Val	p.G836V	ENST00000358026	NM_001128849.1	836	gGa/gTa	18/36	0.18322317937716	3	FACETS	0.665	0.596	0.739	0.333	0.298	0.37	INDETERMINATE	1	TRUE	1	0.378704646581077	3		470	1020	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132409	11132409	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	140	621	1	ENST00000358026.2:c.2625G>A	p.Trp875Ter	p.W875*	ENST00000358026	NM_001128849.1	875	tgG/tgA	19/36	0.18322317937716	3	FACETS	0.705	0.64	0.774	0.353	0.32	0.387	INDETERMINATE	1	TRUE	1	0.378704646581077	3		622	1247	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264758	46264758	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779479555	NA	P-0046864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	56	355	0	ENST00000371998.3:c.1628C>T	p.Ser543Leu	p.S543L	ENST00000371998		543	tCa/tTa	12/23	1	2	FACETS	0.49	0.42	0.568	0.49	0.42	0.568	SUBCLONAL	1	TRUE	1	0.378704646581077	2		355	603	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264841	46264841	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	38	296	0	ENST00000371998.3:c.1711C>G	p.Leu571Val	p.L571V	ENST00000371998		571	Ctg/Gtg	12/23	1	2	FACETS	0.517	0.428	0.617	0.517	0.428	0.617	SUBCLONAL	1	TRUE	1	0.378704646581077	2		296	388	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252906	36252909	+	frameshift_variant	Frame_Shift_Del	DEL	CTTC	CTTC	TTA	novel	NA	P-0046864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	80	365	1	ENST00000300305.3:c.453_456delinsTAA	p.Met151IlefsTer25	p.M151Ifs*25	ENST00000300305		151	atGAAG/atTAA	4/8	1	2	FACETS	0.697	0.614	0.786	0.697	0.614	0.786	SUBCLONAL	1	TRUE	1	0.378704646581077	2		366	606	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272374	21272374	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	146	723	0	ENST00000354336.3:c.152C>T	p.Ser51Leu	p.S51L	ENST00000354336	NM_005207.3	51	tCg/tTg	1/3	1	2	FACETS	0.631	0.575	0.691	0.631	0.575	0.691	SUBCLONAL	1	TRUE	1	0.378704646581077	2		723	1221	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181964	38181967	+	frameshift_variant	Frame_Shift_Del	DEL	ACAG	ACAG	-	rs1275635349	NA	P-0046864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	337	468	0	ENST00000396334.3:c.591_594del	p.Asn199IlefsTer3	p.N199Ifs*3	ENST00000396334	NM_002468.4	196	gaACAG/ga	3/5	0.378704646581077	2	FACETS	0.949	0.9	0.998	0.949	0.9	0.998	CLONAL	2	TRUE	0	0.378704646581077	2		468	938	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0046864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	81	572	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.335843858958292	3	FACETS	1	0.912	1	0.519	0.459	0.584	CLONAL	1	TRUE	1	0.378704646581077	3		572	490	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0046864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	206	667	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.378704646581077	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.378704646581077	1		667	714	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554840	187554840	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	78	275	0	ENST00000441802.2:c.4321C>T	p.Gln1441Ter	p.Q1441*	ENST00000441802	NM_005245.3	1441	Cag/Tag	7/27	0.378704646581077	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.378704646581077	1		275	322	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449523	149449523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	135	561	1	ENST00000286301.3:c.1423G>A	p.Glu475Lys	p.E475K	ENST00000286301	NM_005211.3	475	Gag/Aag	10/22	1	2	FACETS	0.668	0.606	0.734	0.668	0.606	0.734	SUBCLONAL	1	TRUE	1	0.378704646581077	2		562	1067	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518104	176518104	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs147846257	NA	P-0046864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	151	467	0	ENST00000292408.4:c.602G>A	p.Arg201Gln	p.R201Q	ENST00000292408	NM_213647.1	201	cGg/cAg	5/18	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.378704646581077	2		467	750	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271384	26271384	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	171	480	0	ENST00000305910.3:c.229C>G	p.Gln77Glu	p.Q77E	ENST00000305910	NM_003534.2	77	Cag/Gag	1/1	0.378704646581077	2	FACETS	1	0.975	1	0.569	0.524	0.616	CLONAL	1	TRUE	0	0.378704646581077	2		480	793	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004769	150004769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	33	344	0	ENST00000253339.5:c.1456G>A	p.Val486Ile	p.V486I	ENST00000253339		486	Gtc/Atc	3/7	1	2	FACETS	0.358	0.291	0.434	0.358	0.291	0.434	SUBCLONAL	1	TRUE	1	0.378704646581077	2		344	487	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98003019	98003019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	15	235	0	ENST00000289081.3:c.257G>A	p.Ser86Asn	p.S86N	ENST00000289081	NM_000136.2	86	aGc/aAc	4/15	1	2	FACETS	0.419	0.307	0.553	0.419	0.307	0.553	SUBCLONAL	1	TRUE	1	0.378704646581077	2		235	189	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248044	110248044	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	58	358	0	ENST00000374672.4:c.1428G>C	p.Lys476Asn	p.K476N	ENST00000374672	NM_004235.4	476	aaG/aaC	5/5	1	2	FACETS	0.439	0.377	0.508	0.439	0.377	0.508	SUBCLONAL	1	TRUE	1	0.378704646581077	2		358	697	SUCCESS
AR	367	MSKCC	GRCh37	X	66766450	66766450	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	54	301	1	ENST00000374690.3:c.1462C>T	p.Gln488Ter	p.Q488*	ENST00000374690	NM_000044.3	488	Cag/Tag	1/8	1	2	FACETS	0.456	0.389	0.529	0.456	0.389	0.529	SUBCLONAL	1	TRUE	1	0.378704646581077	2		302	626	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692803	89692803	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554898074	NA	P-0046865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	36	169	0	ENST00000371953.3:c.287C>T	p.Pro96Leu	p.P96L	ENST00000371953	NM_000314.4	96	cCa/cTa	5/9	0.376289506855447	1	FACETS	0.805	0.669	0.954	0.805	0.669	0.954	CLONAL	1	TRUE	0	0.376289506855447	1		169	193	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675207	40675207	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1444208558	NA	P-0046865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	83	438	0	ENST00000249776.8:c.171G>C	p.Glu57Asp	p.E57D	ENST00000249776	NM_033286.3	57	gaG/gaC	1/9	0.23616246831474	1	FACETS	0.36	0.317	0.407	0.36	0.317	0.407	SUBCLONAL	1	TRUE	0	0.376289506855447	1		438	995	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906525	32906525	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	31	215	0	ENST00000380152.3:c.910G>T	p.Glu304Ter	p.E304*	ENST00000380152		304	Gaa/Taa	10/27	0.376289506855447	1	FACETS	0.679	0.554	0.818	0.679	0.554	0.818	SUBCLONAL	1	TRUE	0	0.376289506855447	1		215	197	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027127	49027127	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0046865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	19	192	0	ENST00000267163.4:c.1696-2A>G		p.X566_splice	ENST00000267163	NM_000321.2	566			0.376289506855447	1	FACETS	0.59	0.452	0.749	0.59	0.452	0.749	SUBCLONAL	1	TRUE	0	0.376289506855447	1		192	139	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637417	176637417	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	43	298	0	ENST00000439151.2:c.2017G>C	p.Glu673Gln	p.E673Q	ENST00000439151	NM_022455.4	673	Gag/Cag	5/23	1	2	FACETS	0.456	0.381	0.539	0.456	0.381	0.539	SUBCLONAL	1	TRUE	1	0.376289506855447	2		298	501	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722273	176722273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	214	380	0	ENST00000439151.2:c.7904G>A	p.Gly2635Glu	p.G2635E	ENST00000439151	NM_022455.4	2635	gGg/gAg	23/23	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.376289506855447	2		380	908	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056105	26057016	+	coding_sequence_variant,5_prime_UTR_variant	In_Frame_Del	DEL	TTTCTTGGGCTTCGCAACCTTGGCCTTCTTTGGGCTCTTAGCCACTTTCTTGGTTACAGTGGCCGCGGCCGGCTTCTTCGCTTTCTTCGGTGTTTTCTTAGCGCTCTTCTTCGGAGTTGCGCCGCCAGCCGCCTTCTTGGGCTTCTTGGCTGCCCCAACTGGCTTCTTAGGTTTGGTTCCGCCCGCCTTTTTAACCTTGGGCTTGGCTTCCCCGGAGGCTGCCTTCTTGTTGAGTTTAAAGGAGCCAGAAGCACCGGTGCCTTTCGTTTGCACCAGAGTGCCCTTGCTCACCAGGCTCTTGAGACCAAGTTTGATACGGCTGTTGTTTTTCTCCACATCATAGCCGGCGGCAGCCAACGCTTTTTTCAGAGCAGCCAGAGAAACTCCGCTACGCTCTTTAGAGGCGGCCACAGCCTTGGTGATGAGCTCTGACACCGGGGGACCAGACGCCTTACGAGGCGTACCCCCAGCCTTTTTGGCCGCCTTCTTCTTTACAGGGGCCTTCTCCGCAGGAGGCGCGGCAGCGGGAGCGGCAGGAGCAGTCTCGGACATGTTGAGAATCAAAAACTCGGGTACAAGTGGCAAAGCGCCGATGAAGCAGCGCCTGGGCAGGGCCGCTGTATATATAGAGCGCAGGCGCGCTCTGATTGGTGCTCTGGTCGCCCGCCTGGCTGGCAGGCTCTGAGCCGCTGCGCTGCTCCCAAGTTGTGTTTGTTCCACCTCACAAAAGGGGAAAAATATTAAAATTCCCCGCACCAAATCACTTGGGTTTGGTCAGGAAAGGATCTCAGAAGCCTCGGGCTTCATGCTCTTCATTTATTTTTTCCACAAACACAAAAACAACGCGTCCAGGCGTCCCCAATTCCCCCAACTCCGAAGGAAGTCTGGGGCAGTCAGAGACCACTTTCTGTT	TTTCTTGGGCTTCGCAACCTTGGCCTTCTTTGGGCTCTTAGCCACTTTCTTGGTTACAGTGGCCGCGGCCGGCTTCTTCGCTTTCTTCGGTGTTTTCTTAGCGCTCTTCTTCGGAGTTGCGCCGCCAGCCGCCTTCTTGGGCTTCTTGGCTGCCCCAACTGGCTTCTTAGGTTTGGTTCCGCCCGCCTTTTTAACCTTGGGCTTGGCTTCCCCGGAGGCTGCCTTCTTGTTGAGTTTAAAGGAGCCAGAAGCACCGGTGCCTTTCGTTTGCACCAGAGTGCCCTTGCTCACCAGGCTCTTGAGACCAAGTTTGATACGGCTGTTGTTTTTCTCCACATCATAGCCGGCGGCAGCCAACGCTTTTTTCAGAGCAGCCAGAGAAACTCCGCTACGCTCTTTAGAGGCGGCCACAGCCTTGGTGATGAGCTCTGACACCGGGGGACCAGACGCCTTACGAGGCGTACCCCCAGCCTTTTTGGCCGCCTTCTTCTTTACAGGGGCCTTCTCCGCAGGAGGCGCGGCAGCGGGAGCGGCAGGAGCAGTCTCGGACATGTTGAGAATCAAAAACTCGGGTACAAGTGGCAAAGCGCCGATGAAGCAGCGCCTGGGCAGGGCCGCTGTATATATAGAGCGCAGGCGCGCTCTGATTGGTGCTCTGGTCGCCCGCCTGGCTGGCAGGCTCTGAGCCGCTGCGCTGCTCCCAAGTTGTGTTTGTTCCACCTCACAAAAGGGGAAAAATATTAAAATTCCCCGCACCAAATCACTTGGGTTTGGTCAGGAAAGGATCTCAGAAGCCTCGGGCTTCATGCTCTTCATTTATTTTTTCCACAAACACAAAAACAACGCGTCCAGGCGTCCCCAATTCCCCCAACTCCGAAGGAAGTCTGGGGCAGTCAGAGACCACTTTCTGTT	-	novel	NA	P-0046865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	346	44	0				ENST00000343677	NM_005319.3	?-184/213		1/1	0.112789979988429	3	FACETS	0.948	0.897	0.999	0.948	0.897	0.999	INDETERMINATE	2	TRUE	1	0.376289506855447	3		44	1153	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878449	151878465	+	frameshift_variant	Frame_Shift_Del	DEL	GAGTTCCAGGAGGTTGA	GAGTTCCAGGAGGTTGA	-	novel	NA	P-0046865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	106	470	0	ENST00000262189.6:c.6480_6496del	p.Gln2161ProfsTer6	p.Q2161Pfs*6	ENST00000262189	NM_170606.2	2160	tcTCAACCTCCTGGAACTCcc/tccc	36/59	1	2	FACETS	0.627	0.562	0.697	0.627	0.562	0.697	SUBCLONAL	1	TRUE	1	0.376289506855447	2		470	898	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929062	44929062	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	C	C	AACCAAAG	novel	NA	P-0046865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	38	381	0	ENST00000377967.4:c.2162delinsAACCAAAG	p.Ser721Ter	p.S721*	ENST00000377967	NM_021140.2	721	tCa/tAACCAAAGa	17/29	0.376289506855447	1	FACETS	0.32	0.264	0.382	0.32	0.264	0.382	SUBCLONAL	1	TRUE	0	0.376289506855447	1		381	513	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0046866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	36	109	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.41	0.336	0.492	0.41	0.336	0.492	SUBCLONAL	1	TRUE	1	0.37	2		109	475	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	52	350	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	0.48	0.409	0.559	0.48	0.409	0.559	SUBCLONAL	1	TRUE	1	0.37	2		350	585	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237595	16237595	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0046866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	27	190	0	ENST00000375759.3:c.1043-1G>C		p.X348_splice	ENST00000375759	NM_015001.2	348			1	2	FACETS	0.389	0.309	0.48	0.389	0.309	0.48	SUBCLONAL	1	TRUE	1	0.37	2		190	375	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265823	16265851	+	frameshift_variant	Frame_Shift_Del	DEL	TGAGTTCTCTGAGAGTCACCTGTCCCGCC	TGAGTTCTCTGAGAGTCACCTGTCCCGCC	-	novel	NA	P-0046866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	52	492	0	ENST00000375759.3:c.10898_10926del	p.Glu3633GlyfsTer3	p.E3633Gfs*3	ENST00000375759	NM_015001.2	3632	tgTGAGTTCTCTGAGAGTCACCTGTCCCGCCtg/tgtg	15/15	1	2	FACETS	0.445	0.378	0.518	0.445	0.378	0.518	SUBCLONAL	1	TRUE	1	0.37	2		492	632	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712712	43712712	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	69	462	0	ENST00000382044.4:c.4472T>A	p.Phe1491Tyr	p.F1491Y	ENST00000382044	NM_001141980.1	1491	tTt/tAt	21/28	1	2	FACETS	0.56	0.487	0.639	0.56	0.487	0.639	SUBCLONAL	1	TRUE	1	0.37	2		462	666	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584587	48584587	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	42	336	0	ENST00000342988.3:c.760del	p.Thr254LeufsTer82	p.T254Lfs*82	ENST00000342988	NM_005359.5	254	Act/ct	6/12	1	2	FACETS	0.488	0.408	0.578	0.488	0.408	0.578	SUBCLONAL	1	TRUE	1	0.37	2		336	465	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201753	66201753	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	38	329	0	ENST00000273854.3:c.2749A>C	p.Lys917Gln	p.K917Q	ENST00000273854	NM_004439.5	917	Aaa/Caa	16/18	1	2	FACETS	0.41	0.338	0.49	0.41	0.338	0.49	SUBCLONAL	1	TRUE	1	0.37	2		329	501	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165339	32165349	+	frameshift_variant	Frame_Shift_Del	DEL	AGCAAACTGCT	AGCAAACTGCT	-	novel	NA	P-0046866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	68	550	0	ENST00000375023.3:c.4779_4789del	p.Ala1594TrpfsTer17	p.A1594Wfs*17	ENST00000375023	NM_004557.3	1593	tcAGCAGTTTGCTgt/tcgt	27/30	1	2	FACETS	0.489	0.425	0.559	0.489	0.425	0.559	SUBCLONAL	1	TRUE	1	0.37	2		550	751	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945702	151945702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1189672992	NA	P-0046866-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	37	338	0	ENST00000262189.6:c.1817C>T	p.Ser606Leu	p.S606L	ENST00000262189	NM_170606.2	606	tCa/tTa	14/59	1	2	FACETS	0.342	0.281	0.41	0.342	0.281	0.41	SUBCLONAL	1	TRUE	1	0.37	2		338	585	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195760	102195760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	61	291	0	ENST00000263464.3:c.520C>T	p.Leu174Phe	p.L174F	ENST00000263464	NM_001165.4	174	Ctt/Ttt	2/9	0.210732317824828	2	FACETS	1	0.97	1	0.741	0.643	0.847	CLONAL	1	TRUE	0	0.229909461983573	2		291	358	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220578	1220578	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0046868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	191	761	0	ENST00000326873.7:c.598-2A>C		p.X200_splice	ENST00000326873	NM_000455.4	200			0.229909461983573	2	FACETS	0.875	0.81	0.944	0.875	0.81	0.944	CLONAL	2	TRUE	0	0.229909461983573	2		761	949	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591588	38591588	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs757726772	NA	P-0046868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	52	389	0	ENST00000299084.4:c.47G>T	p.Arg16Leu	p.R16L	ENST00000299084	NM_152594.2	16	cGa/cTa	2/7	0.107988361606882	5	FACETS	0.969	0.824	1	0.323	0.274	0.376	INDETERMINATE	1	TRUE	2	0.229909461983573	5		389	628	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610359	10610360	+	missense_variant	Missense_Mutation	DNP	CT	CT	AA	novel	NA	P-0046868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	218	819	0	ENST00000171111.5:c.350_351delinsTT	p.Glu117Val	p.E117V	ENST00000171111	NM_203500.1	117	gAG/gTT	2/6	0.229909461983573	2	FACETS	0.897	0.834	0.962	0.897	0.834	0.962	CLONAL	2	TRUE	0	0.229909461983573	2		819	1057	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961237	1961237	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	62	413	0	ENST00000382891.5:c.3025G>T	p.Asp1009Tyr	p.D1009Y	ENST00000382891	NM_133335.3	1009	Gat/Tat	17/22	0.229909461983573	5	FACETS	1	0.913	1	0.359	0.31	0.413	CLONAL	1	TRUE	2	0.229909461983573	5		413	673	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0046870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	84	409	1	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.215999241792443	2	FACETS	0.888	0.791	0.989	0.888	0.791	0.989	CLONAL	2	TRUE	0	0.2791934390733	2		410	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0046870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	72	495	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.2791934390733	2		495	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs879253911	NA	P-0046870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	21	608	0	ENST00000269305.4:c.538G>T	p.Glu180Ter	p.E180*	ENST00000269305	NM_001126112.2	180	Gag/Tag	5/11	1	2	FACETS	0.297	0.227	0.378	0.297	0.227	0.378	SUBCLONAL	1	TRUE	1	0.2791934390733	2		608	507	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864117	57864117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749783306	NA	P-0046870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	139	521	0	ENST00000228682.2:c.1594C>T	p.Arg532Cys	p.R532C	ENST00000228682	NM_005269.2	532	Cgc/Tgc	12/12	0.215999241792443	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	2	TRUE	0	0.2791934390733	2		521	496	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243668602	243668602	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	66	301	0	ENST00000263826.5:c.1389G>C	p.Glu463Asp	p.E463D	ENST00000263826	NM_005465.4	463	gaG/gaC	13/13	0.2791934390733	3	FACETS	1	0.971	1	0.724	0.632	0.823	CLONAL	1	TRUE	1	0.2791934390733	3		301	372	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434839	110434839	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	78	595	0	ENST00000375856.3:c.3562G>T	p.Gly1188Cys	p.G1188C	ENST00000375856	NM_003749.2	1188	Ggc/Tgc	1/2	0.263714874499937	1	FACETS	0.874	0.769	0.986	0.874	0.769	0.986	CLONAL	1	TRUE	0	0.2791934390733	1		595	550	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042054	14042054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	41	297	0	ENST00000311895.7:c.2601G>A	p.Met867Ile	p.M867I	ENST00000311895	NM_005236.2	867	atG/atA	11/11	1	2	FACETS	0.859	0.718	1	0.859	0.718	1	CLONAL	1	TRUE	1	0.2791934390733	2		297	342	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224160	36224160	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	52	583	0	ENST00000222270.7:c.6710G>T	p.Gly2237Val	p.G2237V	ENST00000222270	NM_014727.1	2237	gGc/gTc	28/37	1	2	FACETS	0.679	0.577	0.789	0.679	0.577	0.789	SUBCLONAL	1	TRUE	1	0.2791934390733	2		583	549	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715679	30715679	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	27	254	0	ENST00000295754.5:c.1337A>C	p.Asp446Ala	p.D446A	ENST00000295754	NM_003242.5	446	gAt/gCt	5/7	0.2791934390733	1	FACETS	0.66	0.527	0.811	0.66	0.527	0.811	SUBCLONAL	1	TRUE	0	0.2791934390733	1		254	252	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467942	66467942	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	23	239	0	ENST00000273854.3:c.327G>C	p.Gln109His	p.Q109H	ENST00000273854	NM_004439.5	109	caG/caC	3/18	1	2	FACETS	0.586	0.458	0.735	0.586	0.458	0.735	SUBCLONAL	1	TRUE	1	0.2791934390733	2		239	281	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344962	70344962	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	74	235	0	ENST00000374080.3:c.2192A>C	p.His731Pro	p.H731P	ENST00000374080		731	cAc/cCc	15/45	1	1	FACETS	0.82	0.726	0.919	1	0.98	1	CLONAL	2	TRUE	0	0.2791934390733	1		235	278	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504042	123504042	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	17	114	0	ENST00000371139.4:c.218A>C	p.His73Pro	p.H73P	ENST00000371139	NM_001114937.2	73	cAt/cCt	3/4	0.2791934390733	2	FACETS	0.982	0.741	1			1	CLONAL	1	TRUE	NA	0.2791934390733	2		114	124	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450802	70450802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	174	365	0	ENST00000373644.4:c.5642G>A	p.Cys1881Tyr	p.C1881Y	ENST00000373644	NM_030625.2	1881	tGt/tAt	12/12	0.364854451969128	1	FACETS	0.397	0.366	0.429	0.397	0.366	0.429	INDETERMINATE	1	TRUE	0	0.751333992515556	1		365	729	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149539	61149539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	231	249	0	ENST00000295025.8:c.1729G>A	p.Glu577Lys	p.E577K	ENST00000295025	NM_002908.2	577	Gag/Aag	11/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.751333992515556	2		249	588	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386515	81386515	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	189	255	2	ENST00000222390.5:c.472C>T	p.His158Tyr	p.H158Y	ENST00000222390	NM_000601.4	158	Cac/Tac	4/18	1	2	FACETS	0.921	0.858	0.986	0.921	0.858	0.986	CLONAL	1	TRUE	1	0.751333992515556	2		257	546	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855050	76855050	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0046871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	167	206	0	ENST00000373344.5:c.5787-1G>C		p.X1929_splice	ENST00000373344	NM_000489.3	1929			0.751333992515556	1	FACETS	0.957	0.899	1	0.957	0.899	1	CLONAL	1	TRUE	0	0.751333992515556	1		206	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0046875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	369	803	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.0893547546110813	3	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.267085132742723	3		803	1302	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0046875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	886	494	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.267085132742723	9	FACETS	0.937	0.909	0.965	0.937	0.909	0.965	CLONAL	7	TRUE	2	0.267085132742723	9		494	1957	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514650	103514650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	75	386	0	ENST00000355739.4:c.1151C>T	p.Ser384Leu	p.S384L	ENST00000355739	NM_000123.3	384	tCa/tTa	8/15	1	2	FACETS	0.95	0.833	1	0.95	0.833	1	CLONAL	1	TRUE	1	0.267085132742723	2		386	591	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	228	427	0				ENST00000310581	NM_198253.2	-/1132			0.376299743945209	3	FACETS	0.882	0.836	0.928	1	0.989	1	CLONAL	4	TRUE	0	0.378461528505738	3		427	406	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022913	27022938	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGCCGCCGCCAGCAGCCTGGGCAA	CCCGCCGCCGCCAGCAGCCTGGGCAA	-	rs797045262	NA	P-0046876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	12	51	0	ENST00000324856.7:c.31_56del	p.Ser11AlafsTer91	p.S11Afs*91	ENST00000324856	NM_006015.4	7	CCCGCCGCCGCCAGCAGCCTGGGCAAc/c	1/20	1	2	FACETS	0.893	0.639	1	0.893	0.639	1	CLONAL	1	TRUE	1	0.378461528505738	2		51	71	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333143	70333143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767493807	NA	P-0046876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	72	674	0	ENST00000373644.4:c.1048G>A	p.Glu350Lys	p.E350K	ENST00000373644	NM_030625.2	350	Gaa/Aaa	2/12	1	2	FACETS	0.643	0.562	0.73	0.643	0.562	0.73	SUBCLONAL	1	TRUE	1	0.378461528505738	2		674	592	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0046876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	22	370	0	ENST00000288602.6:c.1397G>T	p.Gly466Val	p.G466V	ENST00000288602	NM_004333.4	466	gGa/gTa	11/18	1	2	FACETS	0.335	0.259	0.423	0.335	0.259	0.423	SUBCLONAL	1	TRUE	1	0.378461528505738	2		370	347	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380338	14380339	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCCCACGCC	novel	NA	P-0046876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	77	365	0	ENST00000256196.4:c.70_78dup	p.Gly24_Gly26dup	p.G24_G26dup	ENST00000256196		24	-/GGCGTGGGC	1/6	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.378461528505738	2		365	397	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715672	30715672	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	32	361	0	ENST00000295754.5:c.1330C>A	p.Gln444Lys	p.Q444K	ENST00000295754	NM_003242.5	444	Cag/Aag	5/7	1	2	FACETS	0.53	0.431	0.641	0.53	0.431	0.641	SUBCLONAL	1	TRUE	1	0.378461528505738	2		361	319	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885331	111885331	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	56	386	0	ENST00000341259.2:c.1219T>G	p.Phe407Val	p.F407V	ENST00000341259	NM_005475.2	407	Ttt/Gtt	6/8	1	2	FACETS	0.858	0.739	0.987	0.858	0.739	0.987	CLONAL	1	TRUE	1	0.378461528505738	2		386	345	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136281	202136282	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0046876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	180	465	0	ENST00000358485.4:c.526_527dup	p.Leu176PhefsTer2	p.L176Ffs*2	ENST00000358485	NM_001080125.1	175	-/TT	3/9	0.366854115434139	2	FACETS	0.857	0.795	0.92	0.857	0.795	0.92	CLONAL	2	TRUE	0	0.378461528505738	2		465	555	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412917	49412917	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	116	666	0	ENST00000418115.1:c.106C>T	p.Pro36Ser	p.P36S	ENST00000418115	NM_001664.2	36	Ccc/Tcc	2/5	1	2	FACETS	0.727	0.655	0.804	0.727	0.655	0.804	SUBCLONAL	1	TRUE	1	0.378461528505738	2		666	843	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170009682	170009682	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	87	303	0	ENST00000295797.4:c.1244G>A	p.Gly415Asp	p.G415D	ENST00000295797	NM_002740.5	415	gGt/gAt	13/18	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.378461528505738	2		303	442	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630063	187630063	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	111	579	0	ENST00000441802.2:c.919del	p.Arg307GlyfsTer49	p.R307Gfs*49	ENST00000441802	NM_005245.3	307	Agg/gg	2/27	1	2	FACETS	0.998	0.899	1	0.998	0.899	1	CLONAL	1	TRUE	1	0.378461528505738	2		579	588	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29195909	29195909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs918810034	NA	P-0046876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	139	800	0	ENST00000240100.2:c.689C>T	p.Ser230Leu	p.S230L	ENST00000240100	NM_001394.6	230	tCg/tTg	3/4	1	2	FACETS	0.942	0.858	1	0.942	0.858	1	CLONAL	1	TRUE	1	0.378461528505738	2		800	780	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445005	89445005	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112239794	NA	P-0046878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	56	352	2	ENST00000336596.2:c.1325C>T	p.Thr442Met	p.T442M	ENST00000336596	NM_005233.5	442	aCg/aTg	6/17	0.323484995486642	1	FACETS	0.832	0.716	0.957	0.832	0.716	0.957	CLONAL	1	TRUE	0	0.323484995486642	1		354	349	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716327	52716327	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	200	587	0	ENST00000322088.6:c.771G>T	p.Trp257Cys	p.W257C	ENST00000322088	NM_014225.5	257	tgG/tgT	6/15	0.0748945341212064	4	FACETS	1	0.99	1	0.729	0.674	0.785	INDETERMINATE	1	TRUE	2	0.323484995486642	4		587	1123	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465600	8465600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1427192894	NA	P-0046878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	20	411	0	ENST00000356435.5:c.3580G>A	p.Ala1194Thr	p.A1194T	ENST00000356435		1194	Gct/Act	21/35	1	2	FACETS	0.501	0.383	0.637	0.501	0.383	0.637	SUBCLONAL	1	TRUE	1	0.323484995486642	2		411	247	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620336	43620336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368550200	NA	P-0046878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	70	422	1	ENST00000355710.3:c.2945G>A	p.Arg982His	p.R982H	ENST00000355710	NM_020975.4	982	cGc/cAc	18/20	0.152196648085431	4	FACETS	0.798	0.695	0.909	0.266	0.231	0.303	INDETERMINATE	1	TRUE	1	0.323484995486642	4		423	718	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162771	47162771	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	19	384	0	ENST00000409792.3:c.3355A>C	p.Ser1119Arg	p.S1119R	ENST00000409792	NM_014159.6	1119	Agt/Cgt	3/21	1	2	FACETS	0.541	0.412	0.692	0.541	0.412	0.692	SUBCLONAL	1	TRUE	1	0.323484995486642	2		384	217	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591190	67591246	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	GGTGATTGCTACAATTCAGGATGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCA	GGTGATTGCTACAATTCAGGATGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCA	-	novel	NA	P-0046878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	15	313	0	ENST00000274335.5:c.1745+42_1748del		p.X582_splice	ENST00000274335		582			1	2	FACETS	0.713	0.526	0.935	0.713	0.526	0.935	CLONAL	1	TRUE	1	0.323484995486642	2		313	130	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	116	424	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.524645582520699	3	FACETS	0.949	0.869	1	0.949	0.869	1	CLONAL	2	TRUE	1	0.524645582520699	3		424	294	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0046879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	73	341	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.407224595650063	3	FACETS	1	0.976	1	0.729	0.646	0.815	CLONAL	1	TRUE	1	0.524645582520699	3		341	241	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0046879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	125	526	3	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.316747377597223	4	FACETS	0.931	0.851	1	0.931	0.851	1	CLONAL	2	TRUE	2	0.524645582520699	4		529	390	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47088069	47088069	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs769263465	NA	P-0046879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	103	403	0	ENST00000409792.3:c.7006A>G	p.Ile2336Val	p.I2336V	ENST00000409792	NM_014159.6	2336	Att/Gtt	16/21	0.524645582520699	3	FACETS	1	0.961	1	0.568	0.512	0.628	CLONAL	1	TRUE	1	0.524645582520699	3		403	436	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647685	2647685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	40	581	1	ENST00000342085.4:c.1588G>A	p.Gly530Arg	p.G530R	ENST00000342085	NM_002613.4	530	Ggg/Agg	14/14	0.524645582520699	3	FACETS	0.313	0.259	0.373	0.156	0.129	0.187	SUBCLONAL	1	TRUE	1	0.524645582520699	3		582	615	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	261	516	1	ENST00000269305.4:c.548C>A	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tAa	5/11	0.518351861486514	3	FACETS	0.9	0.856	0.944	0.9	0.856	0.944	CLONAL	3	TRUE	0	0.524645582520699	3		517	465	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563168	21563168	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766080720	NA	P-0046879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	137	792	0	ENST00000382592.4:c.751G>A	p.Ala251Thr	p.A251T	ENST00000382592	NM_014572.2	251	Gcg/Acg	4/8	NA	2	FACETS	1	0.938	1			1	INDETERMINATE	1	TRUE	NA	0.524645582520699	2		792	507	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350627	89350627	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1433932089	NA	P-0046879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	71	578	0	ENST00000301030.4:c.2323A>G	p.Lys775Glu	p.K775E	ENST00000301030	NM_001256183.1	775	Aaa/Gaa	9/13	0.491477007124583	2	FACETS	0.712	0.625	0.805	0.356	0.312	0.403	SUBCLONAL	1	TRUE	0	0.524645582520699	2		578	380	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924983	49924983	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	54	521	0	ENST00000296474.3:c.3960G>A	p.Met1320Ile	p.M1320I	ENST00000296474	NM_002447.2	1320	atG/atA	20/20	0.524645582520699	3	FACETS	0.637	0.545	0.736	0.318	0.272	0.368	SUBCLONAL	1	TRUE	1	0.524645582520699	3		521	408	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510154	149510154	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1013933182	NA	P-0046879-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	75	586	1	ENST00000261799.4:c.1315C>T	p.Arg439Trp	p.R439W	ENST00000261799	NM_002609.3	439	Cgg/Tgg	9/23	1	2	FACETS	0.529	0.465	0.599	0.529	0.465	0.599	SUBCLONAL	1	TRUE	1	0.524645582520699	2		587	540	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0046880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	242	675	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.334199178629494	3	FACETS	0.854	0.805	0.903	0.854	0.805	0.903	CLONAL	3	TRUE	0	0.405866832126821	3		675	560	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951129	48951132	+	frameshift_variant	Frame_Shift_Del	DEL	GCTA	GCTA	-	novel	NA	P-0046880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	79	331	0	ENST00000267163.4:c.1291_1294del	p.Ala431LysfsTer25	p.A431Kfs*25	ENST00000267163	NM_000321.2	431	GCTAaa/aa	13/27	0.280053106103285	2	FACETS	1	0.97	1	0.647	0.574	0.722	CLONAL	1	TRUE	0	0.405866832126821	2		331	301	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590540	95590540	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	20	203	0	ENST00000393063.1:c.1369T>G	p.Leu457Val	p.L457V	ENST00000393063	NM_030621.3	457	Tta/Gta	9/28	1	2	FACETS	0.481	0.369	0.61	0.481	0.369	0.61	SUBCLONAL	1	TRUE	1	0.405866832126821	2		203	205	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141665	202141665	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	29	333	0	ENST00000358485.4:c.953A>T	p.Asp318Val	p.D318V	ENST00000358485	NM_001080125.1	318	gAc/gTc	7/9	0.113624731541927	4	FACETS	0.537	0.431	0.658	0.269	0.215	0.329	INDETERMINATE	1	TRUE	2	0.405866832126821	4		333	374	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0046881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	533	415	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.841575360904865	2		415	1174	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579533	7579533	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	506	725	2	ENST00000269305.4:c.154C>T	p.Gln52Ter	p.Q52*	ENST00000269305	NM_001126112.2	52	Caa/Taa	4/11	0.841575360904865	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.841575360904865	1		727	668	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243897	41243901	+	frameshift_variant	Frame_Shift_Del	DEL	AGATA	AGATA	-	novel	NA	P-0046881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	345	487	0	ENST00000357654.3:c.3647_3651del	p.Leu1216Ter	p.L1216*	ENST00000357654	NM_007294.3	1216	tTATCT/t	10/23	0.841575360904865	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.841575360904865	1		487	451	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	372	424	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.710007560429315	3	FACETS	0.965	0.925	1	0.965	0.925	1	CLONAL	2	TRUE	1	0.825255784943208	3		424	660	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0046882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	518	803	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.690950517972244	2	FACETS	0.855	0.83	0.879	0.855	0.83	0.879	CLONAL	2	TRUE	0	0.825255784943208	2		803	734	SUCCESS
APC	324	MSKCC	GRCh37	5	112174379	112174379	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs587779786	NA	P-0046882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	78	215	0	ENST00000257430.4:c.3088A>T	p.Lys1030Ter	p.K1030*	ENST00000257430	NM_000038.5	1030	Aaa/Taa	16/16	1	2	FACETS	0.892	0.798	0.988	0.892	0.798	0.988	CLONAL	1	TRUE	1	0.825255784943208	2		215	212	SUCCESS
APC	324	MSKCC	GRCh37	5	112175530	112175530	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	113	298	0	ENST00000257430.4:c.4240del	p.Val1414Ter	p.V1414*	ENST00000257430	NM_000038.5	1413	atG/at	16/16	1	2	FACETS	0.91	0.831	0.991	0.91	0.831	0.991	CLONAL	1	TRUE	1	0.825255784943208	2		298	301	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740417	58740417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770633028	NA	P-0046882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	159	470	0	ENST00000305921.3:c.1322G>A	p.Arg441His	p.R441H	ENST00000305921	NM_003620.3	441	cGt/cAt	6/6	0.690950517972244	2	FACETS	0.774	0.715	0.835	0.387	0.357	0.418	SUBCLONAL	1	TRUE	0	0.825255784943208	2		470	498	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653847	89653893	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AATATTGATGATGTAGTAAGGTAAGAATGCTTTGATTTTCTATTTCA	AATATTGATGATGTAGTAAGGTAAGAATGCTTTGATTTTCTATTTCA	-	novel	NA	P-0046882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	56	337	0	ENST00000371953.3:c.155_164+37del		p.X52_splice	ENST00000371953	NM_000314.4	52		2/9	0.681776215227127	1	FACETS	0.395	0.343	0.449	0.395	0.343	0.449	SUBCLONAL	1	TRUE	0	0.825255784943208	1		337	202	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243983	41244069	+	inframe_deletion	In_Frame_Del	DEL	TCCTGCTAAGCTCTCCTTTCTGGACGCTTTTGCTAAAAACAGCAGAACTTTCCTTAATGTCATTTTCAGCAAAACTAGTATCTTCCT	TCCTGCTAAGCTCTCCTTTCTGGACGCTTTTGCTAAAAACAGCAGAACTTTCCTTAATGTCATTTTCAGCAAAACTAGTATCTTCCT	-	novel	NA	P-0046882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	212	561	0	ENST00000357654.3:c.3479_3565del	p.Lys1160_Arg1188del	p.K1160_R1188del	ENST00000357654	NM_007294.3	1160	aAGGAAGATACTAGTTTTGCTGAAAATGACATTAAGGAAAGTTCTGCTGTTTTTAGCAAAAGCGTCCAGAAAGGAGAGCTTAGCAGGAgt/agt	10/23	0.690950517972244	2	FACETS	0.765	0.714	0.817	0.382	0.357	0.409	SUBCLONAL	1	TRUE	0	0.825255784943208	2		561	672	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761461	59761461	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	134	370	0	ENST00000259008.2:c.2946A>T	p.Lys982Asn	p.K982N	ENST00000259008	NM_032043.2	982	aaA/aaT	20/20	0.690950517972244	2	FACETS	0.745	0.682	0.809	0.372	0.341	0.405	SUBCLONAL	1	TRUE	0	0.825255784943208	2		370	436	SUCCESS
APC	324	MSKCC	GRCh37	5	112174369	112174369	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046882-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	79	218	1	ENST00000257430.4:c.3078T>G	p.Asn1026Lys	p.N1026K	ENST00000257430	NM_000038.5	1026	aaT/aaG	16/16	1	2	FACETS	0.912	0.817	1	0.912	0.817	1	CLONAL	1	TRUE	1	0.825255784943208	2		219	210	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	56	424	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.871	0.75	1	0.871	0.75	1	CLONAL	1	TRUE	1	0.371533607795781	2		424	346	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0046883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	59	572	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.763	0.659	0.877	0.763	0.659	0.877	SUBCLONAL	1	TRUE	1	0.371533607795781	2		572	416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0046883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	198	751	2	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.371533607795781	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.371533607795781	1		753	763	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028657	12028657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	87	351	0	ENST00000353533.5:c.860G>A	p.Arg287His	p.R287H	ENST00000353533	NM_003010.3	287	cGc/cAc	8/11	0.371533607795781	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	0	0.371533607795781	1		351	376	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0046883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	55	279	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.809	0.695	0.933	0.809	0.695	0.933	CLONAL	1	TRUE	1	0.371533607795781	2		279	366	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0046883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	63	286	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.371533607795781	2		286	294	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524567	103524568	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs759551120	NA	P-0046883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	68	179	0	ENST00000355739.4:c.2705dup	p.Asn902LysfsTer7	p.N902Kfs*7	ENST00000355739	NM_000123.3	900	caa/cAaa	13/15	0.371533607795781	6	FACETS	0.967	0.847	1			1	CLONAL	2	TRUE	NA	0.371533607795781	6		179	330	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456461	32456461	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	87	413	0	ENST00000332351.3:c.431C>T	p.Pro144Leu	p.P144L	ENST00000332351	NM_024426.4	144	cCg/cTg	1/10	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.371533607795781	2		413	466	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376332	15376332	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200899247	NA	P-0046883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	138	682	0	ENST00000263377.2:c.682G>A	p.Val228Ile	p.V228I	ENST00000263377	NM_058243.2	228	Gtc/Atc	5/20	1	2	FACETS	0.944	0.86	1	0.944	0.86	1	CLONAL	1	TRUE	1	0.371533607795781	2		682	787	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346337	152346337	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	92	431	0	ENST00000359321.1:c.233T>A	p.Val78Asp	p.V78D	ENST00000359321	NM_005431.1	78	gTc/gAc	3/3	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.371533607795781	2		431	445	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790038	40790038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757402269	NA	P-0046884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	111	637	0	ENST00000373198.4:c.2693C>T	p.Thr898Met	p.T898M	ENST00000373198	NM_133170.3	898	aCg/aTg	18/32	1	2	FACETS	0.52	0.468	0.575	0.52	0.468	0.575	SUBCLONAL	1	TRUE	1	0.662319218753474	2		637	644	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678548	88678548	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	171	531	0	ENST00000360948.2:c.988C>A	p.Pro330Thr	p.P330T	ENST00000360948	NM_001012338.2	330	Cca/Aca	9/19	0.374646134666074	1	FACETS	0.923	0.862	0.985	0.923	0.862	0.985	INDETERMINATE	1	TRUE	0	0.662319218753474	1		531	374	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851316	156851316	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	138	878	0	ENST00000524377.1:c.2273C>A	p.Ala758Asp	p.A758D	ENST00000524377	NM_002529.3	758	gCc/gAc	17/17	0.464100463562352	4	FACETS	0.518	0.47	0.569	0.259	0.235	0.285	SUBCLONAL	1	TRUE	2	0.662319218753474	4		878	1337	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88651934	88651934	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	100	359	0	ENST00000372037.3:c.281C>G	p.Thr94Ser	p.T94S	ENST00000372037	NM_004329.2	94	aCc/aGc	5/13	0.198232880074657	2	FACETS	0.749	0.674	0.828	0.375	0.337	0.414	INDETERMINATE	1	TRUE	0	0.662319218753474	2		359	403	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708614	43708614	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	70	418	0	ENST00000382044.4:c.4682G>C	p.Gly1561Ala	p.G1561A	ENST00000382044	NM_001141980.1	1561	gGa/gCa	22/28	0.662319218753474	1	FACETS	0.434	0.381	0.49	0.434	0.381	0.49	SUBCLONAL	1	TRUE	0	0.662319218753474	1		418	326	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647161	23647161	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1196649458	NA	P-0046884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	121	621	1	ENST00000261584.4:c.706T>G	p.Phe236Val	p.F236V	ENST00000261584	NM_024675.3	236	Ttc/Gtc	4/13	1	2	FACETS	0.48	0.433	0.528	0.48	0.433	0.528	SUBCLONAL	1	TRUE	1	0.662319218753474	2		622	762	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41219633	41219633	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs80357061	NA	P-0046884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	293	358	0	ENST00000357654.3:c.5066T>G	p.Met1689Arg	p.M1689R	ENST00000357654	NM_007294.3	1689	aTg/aGg	16/23	0.662319218753474	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.662319218753474	2		358	437	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11022948	11022948	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	492	618	0	ENST00000327064.4:c.647G>T	p.Ser216Ile	p.S216I	ENST00000327064	NM_199141.1	216	aGc/aTc	5/16	0.637148742227326	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.662319218753474	4		618	1193	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224503	36224503	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	167	814	0	ENST00000222270.7:c.6965G>C	p.Ser2322Thr	p.S2322T	ENST00000222270	NM_014727.1	2322	aGc/aCc	29/37	0.50574573521672	4	FACETS	0.649	0.595	0.706			1	SUBCLONAL	1	TRUE	NA	0.662319218753474	4		814	1291	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164099	47164099	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	49	243	0	ENST00000409792.3:c.2027C>G	p.Ser676Cys	p.S676C	ENST00000409792	NM_014159.6	676	tCt/tGt	3/21	0.662319218753474	3	FACETS	0.473	0.402	0.552	0.237	0.201	0.276	SUBCLONAL	1	TRUE	1	0.662319218753474	3		243	416	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201680	66201680	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	147	414	0	ENST00000273854.3:c.2822G>C	p.Ser941Thr	p.S941T	ENST00000273854	NM_004439.5	941	aGt/aCt	16/18	1	2	FACETS	0.94	0.865	1	0.94	0.865	1	CLONAL	1	TRUE	1	0.662319218753474	2		414	472	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630184	100630198	+	inframe_deletion	In_Frame_Del	DEL	AACAGGCGCTTCTTG	AACAGGCGCTTCTTG	-	novel	NA	P-0046884-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	72	463	0	ENST00000308731.7:c.75_89del	p.Lys26_Phe30del	p.K26_F30del	ENST00000308731	NM_000061.2	25	ttCAAGAAGCGCCTGTTt/ttt	2/19	0.374646134666074	1	FACETS	0.322	0.282	0.365	0.322	0.282	0.365	INDETERMINATE	1	TRUE	0	0.662319218753474	1		463	452	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288774	33288774	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	65	591	0	ENST00000374542.5:c.778C>T	p.Arg260Cys	p.R260C	ENST00000374542	NM_001141970.1	260	Cgt/Tgt	3/8	1	2	FACETS	0.959	0.832	1	0.959	0.832	1	CLONAL	1	TRUE	1	0.239486275744516	2		591	566	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183788	10183788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882034	NA	P-0046886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	141	929	0	ENST00000256474.2:c.257C>T	p.Pro86Leu	p.P86L	ENST00000256474	NM_000551.3	86	cCc/cTc	1/3	0.239486275744516	2	FACETS	0.846	0.772	0.923	0.846	0.772	0.923	CLONAL	2	TRUE	0	0.239486275744516	2		929	696	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820786	3820786	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	83	997	0	ENST00000262367.5:c.2665T>G	p.Ser889Ala	p.S889A	ENST00000262367	NM_004380.2	889	Tca/Gca	14/31	0.239486275744516	3	FACETS	0.952	0.839	1	0.476	0.419	0.537	CLONAL	1	TRUE	1	0.239486275744516	3		997	815	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089875	16089875	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	35	339	0	ENST00000268712.3:c.235T>A	p.Ser79Thr	p.S79T	ENST00000268712	NM_006311.3	79	Tct/Act	3/46	1	2	FACETS	0.916	0.753	1	0.916	0.753	1	CLONAL	1	TRUE	1	0.239486275744516	2		339	319	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433482	138433482	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	39	483	0	ENST00000289153.2:c.1130A>G	p.Asn377Ser	p.N377S	ENST00000289153	NM_006219.2	377	aAt/aGt	7/22	0.239486275744516	5	FACETS	1	0.904	1	0.378	0.314	0.45	CLONAL	1	TRUE	2	0.239486275744516	5		483	390	SUCCESS
ATR	545	MSKCC	GRCh37	3	142185368	142185368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046886-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	65	308	0	ENST00000350721.4:c.6695G>A	p.Gly2232Glu	p.G2232E	ENST00000350721	NM_001184.3	2232	gGa/gAa	40/47	0.239486275744516	5	FACETS	1	0.938	1	1	0.938	1	CLONAL	3	TRUE	2	0.239486275744516	5		308	222	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0046887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	1168	325	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.913774222127205	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.913774222127205	2		325	1231	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969405	44969405	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	250	503	1	ENST00000377967.4:c.4087C>T	p.Arg1363Ter	p.R1363*	ENST00000377967	NM_021140.2	1363	Cga/Tga	28/29	0.192224513380662	2	FACETS	0.79	0.743	0.837	0.395	0.371	0.419	INDETERMINATE	1	TRUE	0	0.913774222127205	2		504	693	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957528	175957528	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	139	421	0	ENST00000367669.3:c.1868A>C	p.Lys623Thr	p.K623T	ENST00000367669	NM_022457.5	623	aAa/aCa	17/20	0.127133032328648	5	FACETS	1	0.961	1	0.364	0.332	0.398	INDETERMINATE	1	TRUE	2	0.913774222127205	5		421	660	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562847	21562847	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	110	749	0	ENST00000382592.4:c.1072G>C	p.Asp358His	p.D358H	ENST00000382592	NM_014572.2	358	Gac/Cac	4/8	0.484917655477939	1	FACETS	0.136	0.121	0.151	0.136	0.121	0.151	INDETERMINATE	1	TRUE	0	0.913774222127205	1		749	963	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456493	189456493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750962649	NA	P-0046887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	552	491	0	ENST00000264731.3:c.254C>T	p.Ala85Val	p.A85V	ENST00000264731	NM_003722.4	85	gCg/gTg	3/14	0.744449210625495	3	FACETS	0.85	0.82	0.879	0.85	0.82	0.879	CLONAL	2	TRUE	1	0.913774222127205	3		491	1036	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202880	27202880	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	302	484	0	ENST00000380036.4:c.1972T>G	p.Ser658Ala	p.S658A	ENST00000380036	NM_000459.3	658	Tct/Gct	13/23	0.302423650975311	2	FACETS	1	0.991	1	0.589	0.561	0.617	INDETERMINATE	1	TRUE	0	0.913774222127205	2		484	561	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888693	76888694	+	splice_donor_variant	Splice_Site	INS	-	-	CCTGGATCAACCAAAGCTTTGTTAAATATTT	novel	NA	P-0046887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	104	391	0	ENST00000373344.5:c.5105_5134+1dup		p.X1702_splice	ENST00000373344	NM_000489.3	1702			0.312206578987026	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.913774222127205	0		391	401	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0046890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	40	594	1	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.665277105575503	4	FACETS	0.482	0.4	0.572	0.241	0.2	0.286	SUBCLONAL	1	FALSE	2	0.653950456961832	4		595	420	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980311	55980311	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	12	406	0	ENST00000263923.4:c.780G>A	p.Trp260Ter	p.W260*	ENST00000263923	NM_002253.2	260	tgG/tgA	6/30	1	2	FACETS	0.171	0.12	0.235	0.171	0.12	0.235	SUBCLONAL	1	FALSE	1	0.653950456961832	2		406	214	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930723	32930724	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0046890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	13	481	0	ENST00000380152.3:c.7595_7596del	p.Pro2532LeufsTer6	p.P2532Lfs*6	ENST00000380152		2532	CCc/c	15/27	0.665475813973385	4	FACETS	0.322	0.23	0.435	0.161	0.115	0.218	SUBCLONAL	1	FALSE	2	0.653950456961832	4		481	204	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593541	48593565	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAAGTGCATATATAAAGGTTAGTTA	CAAGTGCATATATAAAGGTTAGTTA	-	novel	NA	P-0046890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	11	223	0	ENST00000342988.3:c.1295_1308+11del		p.X432_splice	ENST00000342988	NM_005359.5	432		10/12	0.188884512176664	3	FACETS	0.382	0.265	0.524	0.191	0.132	0.262	INDETERMINATE	1	FALSE	1	0.653950456961832	3		223	117	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579355	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519997	NA	P-0046891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	68	201	2	ENST00000269305.4:c.332T>C	p.Leu111Pro	p.L111P	ENST00000269305	NM_001126112.2	111	cTg/cCg	4/11	0.169663369296047	0	FACETS	0.394	0.341	0.451			1	SUBCLONAL	1	FALSE	0	0.255016458555725	0		203	1009	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164934	106164934	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	42	261	0	ENST00000380013.4:c.3802G>C	p.Glu1268Gln	p.E1268Q	ENST00000380013	NM_001127208.2	1268	Gag/Cag	6/11	1	2	FACETS	0.674	0.562	0.797	0.674	0.562	0.797	SUBCLONAL	1	FALSE	1	0.255016458555725	2		261	489	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242478	+	protein_altering_variant	In_Frame_Del	DEL	GAATTAAGAGAAG	GAATTAAGAGAAG	AATT	novel	NA	P-0046891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	51	348	2	ENST00000275493.2:c.2236_2248delinsAATT	p.Glu746_Ala750delinsAsnSer	p.E746_A750delinsNS	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGca/AATTca	19/28	1	2	FACETS	0.668	0.567	0.779	0.668	0.567	0.779	SUBCLONAL	1	FALSE	1	0.255016458555725	2		350	599	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0046892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	88	670	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.192287447946004	2		670	659	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589875	212589875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758827443	NA	P-0046892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	56	384	2	ENST00000342788.4:c.667G>A	p.Gly223Arg	p.G223R	ENST00000342788	NM_005235.2	223	Gga/Aga	6/28	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.192287447946004	2		386	553	SUCCESS
APC	324	MSKCC	GRCh37	5	112116558	112116558	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	32	250	0	ENST00000257430.4:c.603A>T	p.Glu201Asp	p.E201D	ENST00000257430	NM_000038.5	201	gaA/gaT	6/16	0.179649180876082	1	FACETS	0.974	0.792	1	0.974	0.792	1	CLONAL	1	TRUE	0	0.192287447946004	1		250	309	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	36	427	0				ENST00000310581	NM_198253.2	-/1132			0.179986911196315	2	FACETS	1	0.904	1	0.569	0.472	0.675	INDETERMINATE	1	FALSE	0	0.314768982235104	2		427	201	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059260	27059260	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	78	533	0	ENST00000324856.7:c.1897C>T	p.Gln633Ter	p.Q633*	ENST00000324856	NM_006015.4	633	Cag/Tag	4/20	0.255075573571022	4	FACETS	0.9	0.796	1	0.9	0.796	1	CLONAL	2	FALSE	2	0.314768982235104	4		533	362	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939417	36939417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	37	820	0	ENST00000361632.4:c.433G>A	p.Glu145Lys	p.E145K	ENST00000361632		145	Gag/Aag	4/16	0.196549187934897	3	FACETS	0.657	0.542	0.786	0.219	0.18	0.262	SUBCLONAL	1	FALSE	0	0.314768982235104	3		820	414	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480320	56480320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	38	301	0	ENST00000267101.3:c.427C>A	p.Leu143Met	p.L143M	ENST00000267101	NM_001982.3	143	Ctg/Atg	4/28	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	FALSE	1	0.314768982235104	2		301	216	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481402	56481402	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	54	623	1	ENST00000267101.3:c.589C>T	p.Pro197Ser	p.P197S	ENST00000267101	NM_001982.3	197	Cct/Tct	5/28	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	FALSE	1	0.314768982235104	2		624	338	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572986	7572986	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555524156	NA	P-0046894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	35	465	2	ENST00000269305.4:c.1123C>T	p.Gln375Ter	p.Q375*	ENST00000269305	NM_001126112.2	375	Cag/Tag	11/11	0.18573614277427	3	FACETS	0.83	0.683	0.995	0.415	0.341	0.498	INDETERMINATE	1	FALSE	1	0.314768982235104	3		467	310	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0046894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	43	767	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.18573614277427	3	FACETS	0.837	0.702	0.985	0.418	0.351	0.493	INDETERMINATE	1	FALSE	1	0.314768982235104	3		767	378	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281157	15281157	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	53	923	0	ENST00000263388.2:c.5099A>G	p.Asp1700Gly	p.D1700G	ENST00000263388	NM_000435.2	1700	gAc/gGc	27/33	0.314768982235104	1	FACETS	0.832	0.713	0.961	0.832	0.713	0.961	CLONAL	1	FALSE	0	0.314768982235104	1		923	341	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798842	42798842	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	74	777	1	ENST00000575354.2:c.4414G>A	p.Ala1472Thr	p.A1472T	ENST00000575354	NM_015125.3	1472	Gcc/Acc	19/20	1	2	FACETS	0.963	0.846	1	0.963	0.846	1	CLONAL	1	FALSE	1	0.314768982235104	2		778	488	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39240640	39240640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	16	323	0	ENST00000402219.2:c.2128C>T	p.Leu710Phe	p.L710F	ENST00000402219	NM_005633.3	710	Ctt/Ttt	13/23	0.314768982235104	1	FACETS	0.591	0.44	0.768	0.591	0.44	0.768	SUBCLONAL	1	FALSE	0	0.314768982235104	1		323	145	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	20	424	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.189	0.144	0.242	0.189	0.144	0.242	SUBCLONAL	1	TRUE	1	0.475440234468522	2		424	446	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0046895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	111	767	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.475440234468522	1	FACETS	0.868	0.787	0.953	0.868	0.787	0.953	CLONAL	1	TRUE	0	0.475440234468522	1		767	410	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665213	138665213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	71	668	0	ENST00000330315.3:c.352G>A	p.Glu118Lys	p.E118K	ENST00000330315	NM_023067.3	118	Gag/Aag	1/1	1	2	FACETS	0.471	0.411	0.536	0.471	0.411	0.536	SUBCLONAL	1	TRUE	1	0.475440234468522	2		668	634	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0046895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	83	359	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.954	0.848	1	0.954	0.848	1	CLONAL	1	TRUE	1	0.475440234468522	2		359	366	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	146	697	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.465265044196555	1	FACETS	0.934	0.859	1	0.934	0.859	1	CLONAL	1	TRUE	0	0.475440234468522	1		697	501	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12043942	12043942	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	51	282	0	ENST00000396373.4:c.1321G>A	p.Glu441Lys	p.E441K	ENST00000396373	NM_001987.4	441	Gag/Aag	8/8	1	2	FACETS	0.574	0.489	0.666	0.574	0.489	0.666	SUBCLONAL	1	TRUE	1	0.475440234468522	2		282	374	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149982897	149982897	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	25	321	0	ENST00000253339.5:c.3361G>C	p.Glu1121Gln	p.E1121Q	ENST00000253339		1121	Gag/Cag	7/7	0.465265044196555	1	FACETS	0.261	0.206	0.325	0.261	0.206	0.325	SUBCLONAL	1	TRUE	0	0.475440234468522	1		321	307	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205217	46205217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	46	346	0	ENST00000334344.6:c.301G>A	p.Glu101Lys	p.E101K	ENST00000334344	NM_152641.2	101	Gag/Aag	4/21	1	2	FACETS	0.49	0.413	0.574	0.49	0.413	0.574	SUBCLONAL	1	TRUE	1	0.475440234468522	2		346	395	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696716	47696716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	98	366	0	ENST00000347630.2:c.232G>A	p.Glu78Lys	p.E78K	ENST00000347630	NM_001007230.1	78	Gaa/Aaa	5/11	0.475440234468522	1	FACETS	0.991	0.895	1	0.991	0.895	1	CLONAL	1	TRUE	0	0.475440234468522	1		366	317	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458150	120458150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752104735	NA	P-0046895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	149	562	0	ENST00000256646.2:c.7195G>A	p.Glu2399Lys	p.E2399K	ENST00000256646	NM_024408.3	2399	Gag/Aag	34/34	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.475440234468522	2		562	591	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24129414	24129414	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	48	434	0	ENST00000263121.7:c.58G>C	p.Glu20Gln	p.E20Q	ENST00000263121	NM_003073.3	20	Gag/Cag	1/9	0.475440234468522	1	FACETS	0.529	0.45	0.615	0.529	0.45	0.615	SUBCLONAL	1	TRUE	0	0.475440234468522	1		434	291	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332684	70332684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	45	438	1	ENST00000373644.4:c.589G>A	p.Glu197Lys	p.E197K	ENST00000373644	NM_030625.2	197	Gag/Aag	2/12	1	2	FACETS	0.379	0.318	0.446	0.379	0.318	0.446	SUBCLONAL	1	TRUE	1	0.475440234468522	2		439	500	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344374	118344374	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	23	254	1	ENST00000534358.1:c.2500C>T	p.Pro834Ser	p.P834S	ENST00000534358	NM_005933.3	834	Cct/Tct	3/36	0.265234668300004	3	FACETS	0.307	0.239	0.386	0.154	0.119	0.193	INDETERMINATE	1	TRUE	1	0.475440234468522	3		255	390	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992130	11992130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	110	405	0	ENST00000396373.4:c.220G>A	p.Glu74Lys	p.E74K	ENST00000396373	NM_001987.4	74	Gaa/Aaa	3/8	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.475440234468522	2		405	454	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215731	133215731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	91	423	0	ENST00000320574.5:c.5532G>A	p.Met1844Ile	p.M1844I	ENST00000320574	NM_006231.2	1844	atG/atA	40/49	1	2	FACETS	0.864	0.771	0.962	0.864	0.771	0.962	CLONAL	1	TRUE	1	0.475440234468522	2		423	443	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3094725	3094725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	55	665	0	ENST00000078429.4:c.76G>A	p.Glu26Lys	p.E26K	ENST00000078429	NM_002067.2	26	Gag/Aag	1/7	1	2	FACETS	0.422	0.361	0.489	0.422	0.361	0.489	SUBCLONAL	1	TRUE	1	0.475440234468522	2		665	548	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11022931	11022931	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	129	574	0	ENST00000327064.4:c.630C>G	p.Ile210Met	p.I210M	ENST00000327064	NM_199141.1	210	atC/atG	5/16	1	2	FACETS	0.957	0.871	1	0.957	0.871	1	CLONAL	1	TRUE	1	0.475440234468522	2		574	567	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215609878	215609878	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1559386300	NA	P-0046895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	21	269	1	ENST00000260947.4:c.1816C>T	p.His606Tyr	p.H606Y	ENST00000260947	NM_000465.2	606	Cat/Tat	9/11	1	2	FACETS	0.304	0.234	0.385	0.304	0.234	0.385	SUBCLONAL	1	TRUE	1	0.475440234468522	2		270	291	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147508	47147508	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	28	364	0	ENST00000409792.3:c.4818C>G	p.Phe1606Leu	p.F1606L	ENST00000409792	NM_014159.6	1606	ttC/ttG	6/21	1	2	FACETS	0.298	0.238	0.367	0.298	0.238	0.367	SUBCLONAL	1	TRUE	1	0.475440234468522	2		364	395	SUCCESS
APC	324	MSKCC	GRCh37	5	112162840	112162840	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	83	316	0	ENST00000257430.4:c.1444G>C	p.Asp482His	p.D482H	ENST00000257430	NM_000038.5	482	Gac/Cac	12/16	0.265234668300004	3	FACETS	0.925	0.82	1	0.463	0.41	0.519	INDETERMINATE	1	TRUE	1	0.475440234468522	3		316	467	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973797	131973797	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	57	253	0	ENST00000265335.6:c.3500C>G	p.Ser1167Cys	p.S1167C	ENST00000265335		1167	tCt/tGt	23/25	0.265234668300004	3	FACETS	0.759	0.654	0.873	0.38	0.327	0.437	INDETERMINATE	1	TRUE	1	0.475440234468522	3		253	391	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271321	26271321	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	83	614	0	ENST00000305910.3:c.292G>C	p.Glu98Gln	p.E98Q	ENST00000305910	NM_003534.2	98	Gag/Cag	1/1	0.475440234468522	3	FACETS	0.569	0.502	0.642	0.285	0.251	0.321	SUBCLONAL	1	TRUE	1	0.475440234468522	3		614	759	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672323	30672323	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	63	511	1	ENST00000376406.3:c.4637C>T	p.Pro1546Leu	p.P1546L	ENST00000376406	NM_014641.2	1546	cCt/cTt	10/15	1	2	FACETS	0.464	0.401	0.532	0.464	0.401	0.532	SUBCLONAL	1	TRUE	1	0.475440234468522	2		512	571	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672515	30672515	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	73	503	0	ENST00000376406.3:c.4445C>T	p.Ser1482Phe	p.S1482F	ENST00000376406	NM_014641.2	1482	tCt/tTt	10/15	1	2	FACETS	0.528	0.462	0.599	0.528	0.462	0.599	SUBCLONAL	1	TRUE	1	0.475440234468522	2		503	582	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525952	148525952	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	83	277	0	ENST00000320356.2:c.505G>T	p.Glu169Ter	p.E169*	ENST00000320356	NM_004456.4	169	Gaa/Taa	6/20	1	2	FACETS	0.962	0.855	1	0.962	0.855	1	CLONAL	1	TRUE	1	0.475440234468522	2		277	363	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845410	151845410	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	57	526	0	ENST00000262189.6:c.13602G>C	p.Gln4534His	p.Q4534H	ENST00000262189	NM_170606.2	4534	caG/caC	52/59	1	2	FACETS	0.372	0.318	0.43	0.372	0.318	0.43	SUBCLONAL	1	TRUE	1	0.475440234468522	2		526	645	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97869420	97869420	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046895-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	104	601	0	ENST00000289081.3:c.1461C>G	p.Ile487Met	p.I487M	ENST00000289081	NM_000136.2	487	atC/atG	14/15	0.465265044196555	1	FACETS	0.646	0.581	0.715	0.646	0.581	0.715	SUBCLONAL	1	TRUE	0	0.475440234468522	1		601	516	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152093	55152093	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121908585	NA	P-0046896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	126	578	0	ENST00000257290.5:c.2525A>T	p.Asp842Val	p.D842V	ENST00000257290	NM_006206.4	842	gAc/gTc	18/23	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.544189882766112	2		578	436	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98241328	98241328	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	95	590	0	ENST00000331920.6:c.1169A>G	p.Asp390Gly	p.D390G	ENST00000331920	NM_000264.3	390	gAc/gGc	8/24	1	2	FACETS	0.843	0.756	0.935	0.843	0.756	0.935	CLONAL	1	TRUE	1	0.544189882766112	2		590	414	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0046904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	173	361	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		361	470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0046906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	464	774	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.727840998442451	2	FACETS	0.981	0.953	1	0.981	0.953	1	CLONAL	2	TRUE	0	0.758986769942075	2		774	623	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212518	36212518	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	616	968	0	ENST00000222270.7:c.2269C>T	p.Gln757Ter	p.Q757*	ENST00000222270	NM_014727.1	757	Cag/Tag	3/37	0.732718857747816	2	FACETS	0.986	0.962	1	0.986	0.962	1	CLONAL	2	TRUE	0	0.758986769942075	2		968	823	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279668	123279668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	145	407	0	ENST00000358487.5:c.764G>A	p.Arg255Gln	p.R255Q	ENST00000358487	NM_000141.4	255	cGg/cAg	7/18	0.758986769942075	3	FACETS	0.998	0.916	1	0.499	0.458	0.542	CLONAL	1	TRUE	1	0.758986769942075	3		407	528	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692800	89692800	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046906-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	131	349	0	ENST00000371953.3:c.284C>A	p.Pro95Gln	p.P95Q	ENST00000371953	NM_000314.4	95	cCa/cAa	5/9	0.757873513426527	1	FACETS	0.871	0.809	0.932	0.871	0.809	0.932	CLONAL	1	TRUE	0	0.758986769942075	1		349	246	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0046907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	111	381	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.42	2		381	458	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0046907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	102	610	3	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.42	2		613	483	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0046907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	105	391	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.42	2		391	394	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057988	27057988	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	182	690	0	ENST00000324856.7:c.1696C>T	p.Gln566Ter	p.Q566*	ENST00000324856	NM_006015.4	566	Cag/Tag	3/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.42	2		690	679	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0046907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	159	628	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.42	2		628	634	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591135	67591137	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0046907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	51	294	0	ENST00000274335.5:c.1728_1730del	p.Arg577del	p.R577del	ENST00000274335		576	acGAGa/aca	12/15	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.42	2		294	241	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720726	89720726	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	14	138	0	ENST00000371953.3:c.878del	p.Gly293GlufsTer14	p.G293Efs*14	ENST00000371953	NM_000314.4	293	Gga/ga	8/9	1	2	FACETS	0.538	0.392	0.711	0.538	0.392	0.711	SUBCLONAL	1	TRUE	1	0.42	2		138	124	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052633	42052633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	155	571	1	ENST00000219905.7:c.7304G>A	p.Arg2435Gln	p.R2435Q	ENST00000219905	NM_001164273.1	2435	cGg/cAg	20/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.42	2		572	656	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845564	63845564	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	68	251	0	ENST00000279873.7:c.1306del	p.Thr436GlnfsTer43	p.T436Qfs*43	ENST00000279873	NM_032199.2	435	Aaa/aa	9/10	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.42	2		251	321	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793175	42793175	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	250	961	1	ENST00000575354.2:c.1067C>T	p.Ser356Phe	p.S356F	ENST00000575354	NM_015125.3	356	tCc/tTc	7/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.42	2		962	974	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206593	108206593	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587782049	NA	P-0046908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	50	278	0	ENST00000278616.4:c.8173G>C	p.Asp2725His	p.D2725H	ENST00000278616	NM_000051.3	2725	Gat/Cat	56/63	0.255765604525017	1	FACETS	0.83	0.706	0.965	0.83	0.706	0.965	CLONAL	1	TRUE	0	0.255765604525017	1		278	411	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771326	68771338	+	frameshift_variant	Frame_Shift_Del	DEL	CTTGGAGCCGCAG	CTTGGAGCCGCAG	-	novel	NA	P-0046908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	63	362	0	ENST00000261769.5:c.9_21del	p.Trp4SerfsTer48	p.W4Sfs*48	ENST00000261769	NM_004360.3	3	cCTTGGAGCCGCAGc/cc	1/16	0.255765604525017	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.255765604525017	1		362	397	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241937	133241937	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	55	701	0	ENST00000320574.5:c.2419G>T	p.Ala807Ser	p.A807S	ENST00000320574	NM_006231.2	807	Gcc/Tcc	21/49	0.17424104538938	3	FACETS	0.988	0.85	1	0.988	0.85	1	CLONAL	2	TRUE	1	0.18	3		701	337	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0046910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	177	589	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.328232519289453	2	FACETS	0.802	0.743	0.862	0.802	0.743	0.862	CLONAL	2	FALSE	0	0.393482575322648	2		589	561	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0046910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	216	606	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	0.204582413715431	1	FACETS	1	0.988	1	1	0.988	1	INDETERMINATE	1	FALSE	0	0.393482575322648	1		606	693	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278106	41278106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	145	422	0	ENST00000349496.5:c.1982G>A	p.Arg661Gln	p.R661Q	ENST00000349496	NM_001904.3	661	cGa/cAa	13/15	0.104289583259497	4	FACETS	1	0.958	1	1	0.958	1	INDETERMINATE	2	FALSE	2	0.393482575322648	4		422	482	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	94	594	0	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	0.370944635778096	0	FACETS	0.771	0.691	0.854			1	SUBCLONAL	1	FALSE	0	0.393482575322648	0		594	376	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120258	70120259	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	228	947	0	ENST00000245479.2:c.1261dup	p.Ser421LysfsTer157	p.S421Kfs*157	ENST00000245479	NM_000346.3	420	-/A	3/3	0.104289583259497	4	FACETS	0.783	0.73	0.838	0.783	0.73	0.838	INDETERMINATE	2	FALSE	2	0.393482575322648	4		947	1031	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604665	48604665	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660045	NA	P-0046910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	64	317	0	ENST00000342988.3:c.1487G>A	p.Arg496His	p.R496H	ENST00000342988	NM_005359.5	496	cGt/cAt	12/12	0.370944635778096	0	FACETS	0.812	0.712	0.918			1	CLONAL	1	FALSE	0	0.393482575322648	0		317	243	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174458	11174458	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	112	750	1	ENST00000361445.4:c.7217T>A	p.Val2406Glu	p.V2406E	ENST00000361445	NM_004958.3	2406	gTg/gAg	53/58	0.393482575322648	0	FACETS	0.698	0.63	0.768			1	SUBCLONAL	1	FALSE	0	0.393482575322648	0		751	495	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17349143	17349143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs74315368	NA	P-0046910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	94	708	0	ENST00000375499.3:c.725G>A	p.Arg242His	p.R242H	ENST00000375499	NM_003000.2	242	cGc/cAc	7/8	0.393482575322648	1	FACETS	0.838	0.749	0.932	0.838	0.749	0.932	CLONAL	1	FALSE	0	0.393482575322648	1		708	458	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31511186	31511186	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746412985	NA	P-0046910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	121	830	0	ENST00000344624.3:c.1388G>A	p.Arg463Gln	p.R463Q	ENST00000344624		463	cGg/cAg	6/33	0.393482575322648	1	FACETS	0.594	0.536	0.655	0.594	0.536	0.655	SUBCLONAL	1	FALSE	0	0.393482575322648	1		830	832	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161298256	161298256	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778661	NA	P-0046910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	79	481	0	ENST00000367975.2:c.148C>T	p.Arg50Cys	p.R50C	ENST00000367975	NM_003001.3	50	Cgt/Tgt	3/6	1	2	FACETS	0.744	0.655	0.838	0.744	0.655	0.838	SUBCLONAL	1	FALSE	1	0.393482575322648	2		481	540	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56857706	56857706	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762899574	NA	P-0046910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	85	580	0	ENST00000308159.5:c.742G>A	p.Val248Met	p.V248M	ENST00000308159	NM_014669.4	248	Gtg/Atg	8/22	1	2	FACETS	0.681	0.603	0.766	0.681	0.603	0.766	SUBCLONAL	1	FALSE	1	0.393482575322648	2		580	634	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120418	70120437	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCCCATGTACACCCCCAT	CGCCCCATGTACACCCCCAT	-	novel	NA	P-0046910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	411	1073	0	ENST00000245479.2:c.1424_1443del	p.Pro475ArgfsTer96	p.P475Rfs*96	ENST00000245479	NM_000346.3	474	CGCCCCATGTACACCCCCATc/c	3/3	0.104289583259497	4	FACETS	0.866	0.825	0.906	1	0.994	1	INDETERMINATE	3	FALSE	2	0.393482575322648	4		1073	1121	SUCCESS
APC	324	MSKCC	GRCh37	5	112175153	112175153	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	14	197	0	ENST00000257430.4:c.3862G>T	p.Gly1288Ter	p.G1288*	ENST00000257430	NM_000038.5	1288	Gga/Tga	16/16	0.388741433343407	1	FACETS	0.372	0.27	0.494	0.372	0.27	0.494	SUBCLONAL	1	TRUE	0	0.388741433343407	1		197	156	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275239	41275239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046912-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	125	371	1	ENST00000349496.5:c.1405C>T	p.Arg469Cys	p.R469C	ENST00000349496	NM_001904.3	469	Cgt/Tgt	9/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.388741433343407	2		372	556	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352517	118352517	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs142658261	NA	P-0046913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	142	512	0	ENST00000534358.1:c.3722G>C	p.Ser1241Thr	p.S1241T	ENST00000534358	NM_005933.3	1241	aGt/aCt	7/36	0.463871937495464	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.476734369256528	1		512	444	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118712	115118715	+	frameshift_variant	Frame_Shift_Del	DEL	GTGA	GTGA	-	novel	NA	P-0046913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	137	534	0	ENST00000257566.3:c.626_629del	p.Leu209ProfsTer33	p.L209Pfs*33	ENST00000257566	NM_016569.3	209	cTCACc/cc	2/8	1	2	FACETS	0.939	0.857	1	0.939	0.857	1	CLONAL	1	TRUE	1	0.476734369256528	2		534	612	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842653	68842654	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0046913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	154	620	0	ENST00000261769.5:c.590dup	p.Asp198Ter	p.D198*	ENST00000261769	NM_004360.3	197	gct/gCct	5/16	0.476734369256528	1	FACETS	0.847	0.779	0.917	0.847	0.779	0.917	CLONAL	1	TRUE	0	0.476734369256528	1		620	581	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348898	89348898	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	137	1068	2	ENST00000301030.4:c.4052G>T	p.Arg1351Ile	p.R1351I	ENST00000301030	NM_001256183.1	1351	aGa/aTa	9/13	0.476734369256528	1	FACETS	0.596	0.542	0.651	0.596	0.542	0.651	SUBCLONAL	1	TRUE	0	0.476734369256528	1		1070	735	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351104	89351104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	111	809	0	ENST00000301030.4:c.1846G>A	p.Glu616Lys	p.E616K	ENST00000301030	NM_001256183.1	616	Gag/Aag	9/13	0.476734369256528	1	FACETS	0.598	0.539	0.66	0.598	0.539	0.66	SUBCLONAL	1	TRUE	0	0.476734369256528	1		809	593	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040659	16040659	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	78	283	0	ENST00000268712.3:c.1475G>A	p.Arg492Lys	p.R492K	ENST00000268712	NM_006311.3	492	aGa/aAa	14/46	1	2	FACETS	0.854	0.755	0.959	0.854	0.755	0.959	CLONAL	1	TRUE	1	0.476734369256528	2		283	383	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559113	29559113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781567020	NA	P-0046913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	52	131	0	ENST00000356175.3:c.3220G>A	p.Glu1074Lys	p.E1074K	ENST00000356175	NM_000267.3	1074	Gaa/Aaa	25/57	1	2	FACETS	0.905	0.779	1	0.905	0.779	1	CLONAL	1	TRUE	1	0.476734369256528	2		131	241	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880257	37880257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	136	561	0	ENST00000269571.5:c.2301C>G	p.Ile767Met	p.I767M	ENST00000269571		767	atC/atG	19/27	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.476734369256528	2		561	531	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884046	37884046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1455904690	NA	P-0046913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	222	1182	1	ENST00000269571.5:c.3517C>T	p.Leu1173Phe	p.L1173F	ENST00000269571		1173	Ctc/Ttc	27/27	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.476734369256528	2		1183	904	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246128	41246128	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	73	527	0	ENST00000357654.3:c.1420T>G	p.Leu474Val	p.L474V	ENST00000357654	NM_007294.3	474	Tta/Gta	10/23	1	2	FACETS	0.463	0.405	0.526	0.463	0.405	0.526	SUBCLONAL	1	TRUE	1	0.476734369256528	2		527	661	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804258	46804258	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751610575	NA	P-0046913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	199	1084	0	ENST00000290295.7:c.749C>T	p.Ser250Leu	p.S250L	ENST00000290295	NM_006361.5	250	tCg/tTg	2/2	1	2	FACETS	0.996	0.924	1	0.996	0.924	1	CLONAL	1	TRUE	1	0.476734369256528	2		1084	838	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591825	48591825	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	79	362	0	ENST00000342988.3:c.988G>C	p.Glu330Gln	p.E330Q	ENST00000342988	NM_005359.5	330	Gaa/Caa	9/12	0.463871937495464	1	FACETS	0.656	0.58	0.736	0.656	0.58	0.736	SUBCLONAL	1	TRUE	0	0.476734369256528	1		362	385	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0046913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	10	337	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.463871937495464	1	FACETS	0.08	0.054	0.114	0.08	0.054	0.114	SUBCLONAL	1	TRUE	0	0.476734369256528	1		337	397	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543871	212543871	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1361402584	NA	P-0046913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	125	459	0	ENST00000342788.4:c.1528G>A	p.Asp510Asn	p.D510N	ENST00000342788	NM_005235.2	510	Gat/Aat	13/28	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.476734369256528	2		459	453	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793425	242793425	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	156	1025	0	ENST00000334409.5:c.652G>A	p.Val218Met	p.V218M	ENST00000334409	NM_005018.2	218	Gtg/Atg	5/5	1	2	FACETS	0.821	0.753	0.893	0.821	0.753	0.893	CLONAL	1	TRUE	1	0.476734369256528	2		1025	797	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0046913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	132	137	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.463844248052088	2	FACETS	0.923	0.852	0.995	0.923	0.852	0.995	CLONAL	2	TRUE	0	0.476734369256528	2		137	300	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66468016	66468016	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	54	152	0	ENST00000273854.3:c.253G>C	p.Glu85Gln	p.E85Q	ENST00000273854	NM_004439.5	85	Gag/Cag	3/18	1	2	FACETS	0.858	0.739	0.985	0.858	0.739	0.985	CLONAL	1	TRUE	1	0.476734369256528	2		152	264	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178130	56178130	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	107	315	0	ENST00000399503.3:c.3103G>C	p.Glu1035Gln	p.E1035Q	ENST00000399503	NM_005921.1	1035	Gaa/Caa	14/20	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.476734369256528	2		315	435	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397138	397138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1461930692	NA	P-0046913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	109	517	0	ENST00000380956.4:c.523G>A	p.Asp175Asn	p.D175N	ENST00000380956	NM_001195286.1	175	Gac/Aac	5/9	1	2	FACETS	0.953	0.86	1	0.953	0.86	1	CLONAL	1	TRUE	1	0.476734369256528	2		517	480	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839802	27839802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	162	901	0	ENST00000328488.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000328488	NM_003533.2	98	Gag/Aag	1/1	1	2	FACETS	0.917	0.843	0.994	0.917	0.843	0.994	CLONAL	1	TRUE	1	0.476734369256528	2		901	741	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286913	33286913	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	160	772	0	ENST00000374542.5:c.2024C>A	p.Ser675Tyr	p.S675Y	ENST00000374542	NM_001141970.1	675	tCc/tAc	7/8	1	2	FACETS	0.895	0.822	0.971	0.895	0.822	0.971	CLONAL	1	TRUE	1	0.476734369256528	2		772	750	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266423	55266423	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	138	577	0	ENST00000275493.2:c.2715G>A	p.Trp905Ter	p.W905*	ENST00000275493	NM_005228.3	905	tgG/tgA	23/28	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.476734369256528	2		577	561	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	325	617	0	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	2	FACETS	0.935	0.888	0.983	0.935	0.888	0.983	CLONAL	1	TRUE	1	0.86	2		617	808	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	198	363	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.208033079106881	4	FACETS	0.896	0.838	0.954	0.896	0.838	0.954	INDETERMINATE	2	TRUE	2	0.86	4		363	478	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424409	47424409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779648831	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	319	869	2	ENST00000377045.4:c.329C>T	p.Ala110Val	p.A110V	ENST00000377045	NM_001654.4	110	gCg/gTg	5/16	1	2	FACETS	0.882	0.836	0.929	0.882	0.836	0.929	CLONAL	1	TRUE	1	0.86	2		871	841	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	62	150	0	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	2	FACETS	0.565	0.494	0.642	0.565	0.494	0.642	SUBCLONAL	1	TRUE	1	0.86	2		150	255	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717769	89717770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	103	198	0	ENST00000371953.3:c.800dup	p.Asp268GlyfsTer30	p.D268Gfs*30	ENST00000371953	NM_000314.4	265	cta/ctAa	7/9	1	2	FACETS	0.785	0.712	0.861	0.785	0.712	0.861	SUBCLONAL	1	TRUE	1	0.86	2		198	305	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	162	307	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.88	0.816	0.945	0.88	0.816	0.945	CLONAL	1	TRUE	1	0.86	2		307	428	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138642	55138642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143344944	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	300	350	0	ENST00000257290.5:c.1319C>T	p.Thr440Met	p.T440M	ENST00000257290	NM_006206.4	440	aCg/aTg	9/23	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.86	2		350	685	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053022	180053023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750808726	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	274	1044	2	ENST00000261937.6:c.1267dup	p.Gln423ProfsTer4	p.Q423Pfs*4	ENST00000261937	NM_182925.4	423	cag/cCag	10/30	1	2	FACETS	0.82	0.773	0.868	0.82	0.773	0.868	CLONAL	1	TRUE	1	0.86	2		1046	777	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	328	808	2	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.997	0.948	1	0.997	0.948	1	CLONAL	1	TRUE	1	0.86	2		810	765	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097084	11097084	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	352	974	0	ENST00000358026.2:c.579del	p.Gln194SerfsTer109	p.Q194Sfs*109	ENST00000358026	NM_001128849.1	192	aGg/ag	4/36	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.86	2		974	804	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	224	745	12	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	1	2	FACETS	0.81	0.759	0.863	0.81	0.759	0.863	CLONAL	1	TRUE	1	0.86	2		757	643	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084146	47084146	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	172	693	1	ENST00000409792.3:c.7143del	p.Ser2382LeufsTer29	p.S2382Lfs*29	ENST00000409792	NM_014159.6	2381	ccC/cc	17/21	1	2	FACETS	0.653	0.603	0.703	0.653	0.603	0.703	SUBCLONAL	1	TRUE	1	0.86	2		694	613	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274897	41274897	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	194	563	0	ENST00000349496.5:c.1147T>C	p.Trp383Arg	p.W383R	ENST00000349496	NM_001904.3	383	Tgg/Cgg	8/15	1	2	FACETS	0.962	0.9	1	0.962	0.9	1	CLONAL	1	TRUE	1	0.86	2		563	469	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466018	69466018	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	404	996	2	ENST00000227507.2:c.856A>G	p.Thr286Ala	p.T286A	ENST00000227507	NM_053056.2	286	Aca/Gca	5/5	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.86	2		998	940	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	239	486	3	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.892	0.839	0.946	0.892	0.839	0.946	CLONAL	1	TRUE	1	0.86	2		489	623	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193850	106193850	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	208	413	0	ENST00000380013.4:c.4317del	p.Lys1439AsnfsTer9	p.K1439Nfs*9	ENST00000380013	NM_001127208.2	1438	Aaa/aa	10/11	1	2	FACETS	0.947	0.887	1	0.947	0.887	1	CLONAL	1	TRUE	1	0.86	2		413	511	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	355	931	3	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.878	0.835	0.922	0.878	0.835	0.922	CLONAL	1	TRUE	1	0.86	2		934	940	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720666	89720666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	90	250	0	ENST00000371953.3:c.820del	p.Trp274GlyfsTer2	p.W274Gfs*2	ENST00000371953	NM_000314.4	273	Ttt/tt	8/9	1	2	FACETS	0.781	0.703	0.862	0.781	0.703	0.862	SUBCLONAL	1	TRUE	1	0.86	2		250	268	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981515	70981515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745606576	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	439	1206	0	ENST00000276594.2:c.581G>A	p.Arg194Gln	p.R194Q	ENST00000276594	NM_024504.3	194	cGg/cAg	2/8	0.188854116475277	3	FACETS	1	0.995	1	0.68	0.651	0.71	INDETERMINATE	1	TRUE	1	0.86	3		1206	1073	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087346	27087346	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	206	443	1	ENST00000324856.7:c.1921-1G>A		p.X641_splice	ENST00000324856	NM_006015.4	641			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.86	2		444	469	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168977	11168977	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs758517117	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	346	758	0	ENST00000358026.2:c.4567C>T	p.Arg1523Ter	p.R1523*	ENST00000358026	NM_001128849.1	1523	Cga/Tga	32/36	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.86	2		758	760	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794787	42794787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747706524	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	337	841	2	ENST00000575354.2:c.1867G>A	p.Gly623Arg	p.G623R	ENST00000575354	NM_015125.3	623	Gga/Aga	10/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.86	2		843	709	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230818	66230818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs910705978	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	111	446	2	ENST00000273854.3:c.2153G>A	p.Arg718His	p.R718H	ENST00000273854	NM_004439.5	718	cGc/cAc	12/18	1	2	FACETS	0.817	0.744	0.892	0.817	0.744	0.892	CLONAL	1	TRUE	1	0.86	2		448	316	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007140	152007140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	227	550	0	ENST00000262189.6:c.760C>T	p.Arg254Cys	p.R254C	ENST00000262189	NM_170606.2	254	Cgt/Tgt	6/59	1	2	FACETS	0.972	0.914	1	0.972	0.914	1	CLONAL	1	TRUE	1	0.86	2		550	543	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170474	11170474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749700321	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	370	895	5	ENST00000358026.2:c.4777C>T	p.Arg1593Trp	p.R1593W	ENST00000358026	NM_001128849.1	1593	Cgg/Tgg	34/36	1	2	FACETS	0.962	0.917	1	0.962	0.917	1	CLONAL	1	TRUE	1	0.86	2		900	894	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716059	52716059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	385	1011	1	ENST00000322088.6:c.624G>A	p.Met208Ile	p.M208I	ENST00000322088	NM_014225.5	208	atG/atA	5/15	1	2	FACETS	0.936	0.892	0.98	0.936	0.892	0.98	CLONAL	1	TRUE	1	0.86	2		1012	957	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222214	2222214	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768756000	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	325	1035	1	ENST00000398665.3:c.3046G>A	p.Ala1016Thr	p.A1016T	ENST00000398665	NM_032482.2	1016	Gcc/Acc	24/28	1	2	FACETS	0.934	0.887	0.982	0.934	0.887	0.982	CLONAL	1	TRUE	1	0.86	2		1036	809	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745566	162745566	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	275	582	0	ENST00000367921.3:c.1981G>T	p.Asp661Tyr	p.D661Y	ENST00000367921	NM_006182.2	661	Gat/Tat	15/18	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.86	2		582	579	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123245017	123245017	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	192	603	0	ENST00000358487.5:c.2087T>A	p.Ile696Asn	p.I696N	ENST00000358487	NM_000141.4	696	aTc/aAc	16/18	1	2	FACETS	0.816	0.761	0.873	0.816	0.761	0.873	CLONAL	1	TRUE	1	0.86	2		603	547	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943699	71943699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766706961	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	351	826	1	ENST00000298229.2:c.1742G>A	p.Arg581Gln	p.R581Q	ENST00000298229	NM_001567.3	581	cGg/cAg	15/28	1	2	FACETS	0.955	0.908	1	0.955	0.908	1	CLONAL	1	TRUE	1	0.86	2		827	855	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920693	100920693	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	130	513	1	ENST00000325455.5:c.2455del	p.Leu819SerfsTer3	p.L819Sfs*3	ENST00000325455	NM_001202474.3	819	Ctc/tc	6/8	1	2	FACETS	0.922	0.848	0.997	0.922	0.848	0.997	CLONAL	1	TRUE	1	0.86	2		514	328	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374197	118374197	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	128	434	0	ENST00000534358.1:c.7594del	p.Met2532TrpfsTer11	p.M2532Wfs*11	ENST00000534358	NM_005933.3	2530	ctA/ct	27/36	0.3	3	FACETS	1	0.958	1			1	INDETERMINATE	1	TRUE	NA	0.86	3		434	395	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257101	19257102	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	231	825	0	ENST00000162023.5:c.861dup	p.Ala288ArgfsTer34	p.A288Rfs*34	ENST00000162023		287	-/C	12/13	1	2	FACETS	0.821	0.77	0.874	0.821	0.77	0.874	CLONAL	1	TRUE	1	0.86	2		825	654	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527352	187527352	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	210	497	1	ENST00000441802.2:c.10222C>T	p.Leu3408Phe	p.L3408F	ENST00000441802	NM_005245.3	3408	Ctc/Ttc	17/27	1	2	FACETS	0.939	0.88	0.999	0.939	0.88	0.999	CLONAL	1	TRUE	1	0.86	2		498	520	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592163	67592164	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	103	239	0	ENST00000274335.5:c.1981_1982dup	p.Val662Ter	p.V662*	ENST00000274335		660	tct/tcTGt	14/15	1	2	FACETS	0.928	0.845	1	0.928	0.845	1	CLONAL	1	TRUE	1	0.86	2		239	258	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80169063	80169063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	176	646	0	ENST00000265081.6:c.3259G>A	p.Ala1087Thr	p.A1087T	ENST00000265081	NM_002439.4	1087	Gct/Act	23/24	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.86	2		646	403	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149498309	149498309	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	47	742	0	ENST00000261799.4:c.2904+1G>A		p.X968_splice	ENST00000261799	NM_002609.3	968			1	2	FACETS	0.172	0.144	0.202	0.172	0.144	0.202	SUBCLONAL	1	TRUE	1	0.86	2		742	636	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522693	176522693	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370892831	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	354	1098	3	ENST00000292408.4:c.1790C>T	p.Ala597Val	p.A597V	ENST00000292408	NM_213647.1	597	gCc/gTc	13/18	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.86	2		1101	823	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638998	176638998	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367995675	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	322	807	1	ENST00000439151.2:c.3598C>T	p.Arg1200Trp	p.R1200W	ENST00000439151	NM_022455.4	1200	Cgg/Tgg	5/23	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.86	2		808	732	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671248	30671248	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	110	901	1	ENST00000376406.3:c.5629C>T	p.Pro1877Ser	p.P1877S	ENST00000376406	NM_014641.2	1877	Cca/Tca	11/15	1	2	FACETS	0.266	0.238	0.296	0.266	0.238	0.296	SUBCLONAL	1	TRUE	1	0.86	2		902	961	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606281	93606281	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	317	884	0	ENST00000375746.1:c.101T>C	p.Met34Thr	p.M34T	ENST00000375746	NM_001174167.1	34	aTg/aCg	2/14	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.86	2		884	708	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921390	39921390	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	19	432	0	ENST00000378444.4:c.4428+2T>C		p.X1476_splice	ENST00000378444	NM_001123385.1	1476			1	2	FACETS	0.117	0.088	0.151	0.117	0.088	0.151	SUBCLONAL	1	TRUE	1	0.86	2		432	377	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350023	70350023	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	201	645	0	ENST00000374080.3:c.4009del	p.Glu1337LysfsTer8	p.E1337Kfs*8	ENST00000374080		1336	Ggg/gg	28/45	1	2	FACETS	0.71	0.661	0.761	0.71	0.661	0.761	SUBCLONAL	1	TRUE	1	0.86	2		645	658	SUCCESS
BTK	695	MSKCC	GRCh37	X	100604896	100604896	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	214	481	0	ENST00000308731.7:c.1957G>C	p.Asp653His	p.D653H	ENST00000308731	NM_000061.2	653	Gat/Cat	19/19	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.86	2		481	461	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	40	424	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.311088618277103	1	FACETS	0.522	0.435	0.619	0.522	0.435	0.619	SUBCLONAL	1	TRUE	0	0.358352956245395	1		424	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577555	7577555	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs375874539	NA	P-0046916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	119	629	0	ENST00000269305.4:c.726C>G	p.Cys242Trp	p.C242W	ENST00000269305	NM_001126112.2	242	tgC/tgG	7/11	0.311088618277103	1	FACETS	0.718	0.648	0.792	0.718	0.648	0.792	SUBCLONAL	1	TRUE	0	0.358352956245395	1		629	759	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349058	89349058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555528234	NA	P-0046916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1260	91	833	0	ENST00000301030.4:c.3892G>A	p.Asp1298Asn	p.D1298N	ENST00000301030	NM_001256183.1	1298	Gat/Aat	9/13	0.358352956245395	3	FACETS	0.443	0.392	0.499			1	SUBCLONAL	1	TRUE	NA	0.358352956245395	3		833	1351	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601830	43601830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34682185	NA	P-0046916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	104	506	0	ENST00000355710.3:c.874G>A	p.Val292Met	p.V292M	ENST00000355710	NM_020975.4	292	Gtg/Atg	5/20	1	2	FACETS	0.833	0.746	0.925	0.833	0.746	0.925	CLONAL	1	TRUE	1	0.358352956245395	2		506	697	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612745	228612745	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	132	674	0	ENST00000366696.1:c.282G>C	p.Gln94His	p.Q94H	ENST00000366696	NM_003493.2	94	caG/caC	1/1	1	2	FACETS	0.796	0.722	0.874	0.796	0.722	0.874	SUBCLONAL	1	TRUE	1	0.358352956245395	2		674	925	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31466378	31466379	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	103	566	0	ENST00000344624.3:c.2376dup	p.Leu793ThrfsTer15	p.L793Tfs*15	ENST00000344624		792	-/A	16/33	0.202633263208858	1	FACETS	0.77	0.69	0.854	0.77	0.69	0.854	INDETERMINATE	1	TRUE	0	0.358352956245395	1		566	613	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950661	38950661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1344643266	NA	P-0046916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	34	317	0	ENST00000357387.3:c.3289C>T	p.Arg1097Cys	p.R1097C	ENST00000357387	NM_152756.3	1097	Cgt/Tgt	31/38	1	2	FACETS	0.624	0.512	0.75	0.624	0.512	0.75	SUBCLONAL	1	TRUE	1	0.358352956245395	2		317	304	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0121611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	107	427	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.832	0.757	0.909	1	0.987	1	CLONAL	2	NA	1	0.441806074152309	2		427	291	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664937	138664937	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0121611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	91	371	0	ENST00000330315.3:c.628C>G	p.Pro210Ala	p.P210A	ENST00000330315	NM_023067.3	210	Ccc/Gcc	1/1	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	NA	1	0.441806074152309	2		371	275	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0046918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	83	232	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.613728099930702	2		233	264	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0046918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	240	804	0	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	1	2	FACETS	0.993	0.93	1	0.993	0.93	1	CLONAL	1	TRUE	1	0.613728099930702	2		804	788	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519999	NA	P-0046918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	187	538	2	ENST00000269305.4:c.716A>G	p.Asn239Ser	p.N239S	ENST00000269305	NM_001126112.2	239	aAc/aGc	7/11	1	2	FACETS	0.97	0.901	1	0.97	0.901	1	CLONAL	1	TRUE	1	0.613728099930702	2		540	628	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938089	76938092	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	novel	NA	P-0046918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	167	551	0	ENST00000373344.5:c.2656_2659del	p.Glu886LeufsTer18	p.E886Lfs*18	ENST00000373344	NM_000489.3	886	GAGAct/ct	9/35	0.208466337318212	1	FACETS	0.657	0.607	0.709	0.657	0.607	0.709	INDETERMINATE	1	TRUE	0	0.613728099930702	1		551	574	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157495214	157495216	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0046918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	25	394	0	ENST00000346085.5:c.3104_3106del	p.Glu1035del	p.E1035del	ENST00000346085	NM_020732.3	1033	aAAGaa/aaa	11/20	1	2	FACETS	0.172	0.135	0.215	0.172	0.135	0.215	SUBCLONAL	1	TRUE	1	0.613728099930702	2		394	474	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	40	427	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.512	0.424	0.609	0.512	0.424	0.609	SUBCLONAL	1	TRUE	1	0.261879076846348	2		427	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0046919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	133	736	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	1	2	FACETS	0.918	0.832	1	0.918	0.832	1	CLONAL	1	TRUE	1	0.261879076846348	2		736	1106	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0046919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	142	659	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	1	2	FACETS	0.97	0.882	1	0.97	0.882	1	CLONAL	1	TRUE	1	0.261879076846348	2		659	1118	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519865	66519865	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0046919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	42	291	0	ENST00000358598.2:c.349-1G>T		p.X117_splice	ENST00000358598	NM_212471.2	117			1	2	FACETS	0.794	0.664	0.938	0.794	0.664	0.938	CLONAL	1	TRUE	1	0.261879076846348	2		291	404	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955580	48955580	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587778857	NA	P-0046919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	25	228	0	ENST00000267163.4:c.1695+1G>A		p.X565_splice	ENST00000267163	NM_000321.2	565			0.261879076846348	1	FACETS	0.651	0.514	0.806	0.651	0.514	0.806	SUBCLONAL	1	TRUE	0	0.261879076846348	1		228	255	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056356	27056356	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0046919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	68	293	0	ENST00000324856.7:c.1350+2T>C		p.X450_splice	ENST00000324856	NM_006015.4	450			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.261879076846348	2		293	420	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727168	40727168	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	113	563	1	ENST00000373198.4:c.3796G>T	p.Val1266Leu	p.V1266L	ENST00000373198	NM_133170.3	1266	Gtg/Ttg	28/32	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.261879076846348	2		564	770	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829779	76829779	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	115	270	0	ENST00000373344.5:c.6262G>A	p.Gly2088Ser	p.G2088S	ENST00000373344	NM_000489.3	2088	Ggt/Agt	28/35	0.261879076846348	2	FACETS	0.836	0.762	0.913			1	CLONAL	3	TRUE	NA	0.261879076846348	2		270	350	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0046920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	34	325	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.37521027236474	1	FACETS	0.629	0.517	0.753	0.629	0.517	0.753	SUBCLONAL	1	TRUE	0	0.37521027236474	1		325	234	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588190	67588190	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0046920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	33	205	0	ENST00000274335.5:c.1019+1G>T		p.X340_splice	ENST00000274335		340			1	2	FACETS	0.999	0.823	1	0.999	0.823	1	CLONAL	1	TRUE	1	0.37521027236474	2		205	176	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914383	32914383	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs80358821	NA	P-0046920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	42	471	0	ENST00000380152.3:c.5891A>T	p.Lys1964Met	p.K1964M	ENST00000380152		1964	aAg/aTg	11/27	1	2	FACETS	0.591	0.494	0.697	0.591	0.494	0.697	SUBCLONAL	1	TRUE	1	0.37521027236474	2		471	379	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559891	29559898	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	ACTCCATA	ACTCCATA	-	novel	NA	P-0046920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	33	233	0	ENST00000356175.3:c.3488_3495del	p.His1163ArgfsTer29	p.H1163Rfs*29	ENST00000356175	NM_000267.3	1163	cACTCCATA/c	26/57	1	2	FACETS	0.811	0.665	0.972	0.811	0.665	0.972	CLONAL	1	TRUE	1	0.37521027236474	2		233	217	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937648	76937648	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	50	359	0	ENST00000373344.5:c.3100C>A	p.Gln1034Lys	p.Q1034K	ENST00000373344	NM_000489.3	1034	Caa/Aaa	9/35	1	2	FACETS	0.91	0.777	1	0.91	0.777	1	CLONAL	1	TRUE	1	0.37521027236474	2		359	293	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0046921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	22	325	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.998	0.774	1	0.998	0.774	1	CLONAL	1	TRUE	1	0.14	2		325	315	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101054	27101054	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	47	790	3	ENST00000324856.7:c.4336C>T	p.Arg1446Ter	p.R1446*	ENST00000324856	NM_006015.4	1446	Cga/Tga	18/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.14	2		793	504	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0046921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	24	387	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.794	0.621	0.993	0.794	0.621	0.993	CLONAL	1	TRUE	1	0.14	2		387	432	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121909229	NA	P-0046921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	17	380	0	ENST00000371953.3:c.389G>T	p.Arg130Leu	p.R130L	ENST00000371953	NM_000314.4	130	cGa/cTa	5/9	1	2	FACETS	0.858	0.64	1	0.858	0.64	1	CLONAL	1	TRUE	1	0.14	2		380	283	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692946	89692946	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1114167657	NA	P-0046921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	23	378	0	ENST00000371953.3:c.432del	p.Lys144AsnfsTer3	p.K144Nfs*3	ENST00000371953	NM_000314.4	144	Aaa/aa	5/9	1	2	FACETS	0.987	0.769	1	0.987	0.769	1	CLONAL	1	TRUE	1	0.14	2		378	333	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952074	178952075	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0046921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	14	277	0	ENST00000263967.3:c.3129_3130delinsTT	p.Met1043_Asn1044delinsIleTyr	p.M1043_N1044delinsIY	ENST00000263967	NM_006218.2	1043	atGAat/atTTat	21/21	1	2	FACETS	0.82	0.592	1	0.82	0.592	1	CLONAL	1	TRUE	1	0.14	2		277	244	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28644675	28644675	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	90	319	0	ENST00000241453.7:c.118C>A	p.His40Asn	p.H40N	ENST00000241453	NM_004119.2	40	Cat/Aat	2/24	1	2	FACETS	0.862	0.77	0.959	0.862	0.77	0.959	CLONAL	1	TRUE	1	0.524910353666155	2		319	398	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023072	33023072	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	114	508	0	ENST00000300177.4:c.181G>A	p.Gly61Ser	p.G61S	ENST00000300177	NM_001191322.1	61	Ggc/Agc	2/2	1	2	FACETS	0.737	0.666	0.813	0.737	0.666	0.813	SUBCLONAL	1	TRUE	1	0.524910353666155	2		508	589	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483068	29483068	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555604899	NA	P-0046922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	64	276	0	ENST00000356175.3:c.128T>C	p.Leu43Pro	p.L43P	ENST00000356175	NM_000267.3	43	cTa/cCa	2/57	NA	2	FACETS	0.945	0.828	1			1	INDETERMINATE	1	TRUE	NA	0.524910353666155	2		276	258	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654571	29654571	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	68	238	0	ENST00000356175.3:c.5260C>T	p.Gln1754Ter	p.Q1754*	ENST00000356175	NM_000267.3	1754	Caa/Taa	37/57	0.132484055874682	5	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.524910353666155	5		238	358	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0046922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	69	488	1	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	0.524910353666155	3	FACETS	0.798	0.698	0.905	0.399	0.349	0.453	CLONAL	1	TRUE	1	0.524910353666155	3		489	416	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447464	12447464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	182	588	0	ENST00000287820.6:c.703G>A	p.Glu235Lys	p.E235K	ENST00000287820	NM_015869.4	235	Gag/Aag	5/7	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.524910353666155	2		588	672	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515188	149515188	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0046922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	209	696	0	ENST00000261799.4:c.294C>G	p.Tyr98Ter	p.Y98*	ENST00000261799	NM_002609.3	98	taC/taG	3/23	1	2	FACETS	0.904	0.84	0.97	0.904	0.84	0.97	CLONAL	1	TRUE	1	0.524910353666155	2		696	881	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0046923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	85	320	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.261115225665617	2		320	507	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219341	1219341	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs760399253	NA	P-0046923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	121	835	0	ENST00000326873.7:c.393C>G	p.Tyr131Ter	p.Y131*	ENST00000326873	NM_000455.4	131	taC/taG	3/10	0.258599004589479	1	FACETS	0.912	0.823	1	0.912	0.823	1	CLONAL	1	FALSE	0	0.261115225665617	1		835	884	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341523	89341523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1349086238	NA	P-0046924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	15	539	0	ENST00000301030.4:c.7547G>A	p.Arg2516His	p.R2516H	ENST00000301030	NM_001256183.1	2516	cGt/cAt	10/13	0.95047245776137	1	FACETS	0.058	0.042	0.077	0.058	0.042	0.077	SUBCLONAL	1	TRUE	0	0.95047245776137	1		539	285	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699439	117699439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368878065	NA	P-0046924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	10	369	1	ENST00000369458.3:c.202G>A	p.Val68Met	p.V68M	ENST00000369458	NM_024626.3	68	Gtg/Atg	3/6	1	2	FACETS	0.105	0.071	0.148	0.105	0.071	0.148	SUBCLONAL	1	TRUE	1	0.95047245776137	2		370	200	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	90	427	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.925	0.831	1	0.925	0.831	1	CLONAL	1	TRUE	1	0.680683702403891	2		427	286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0046925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	174	767	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.747	0.69	0.807	0.747	0.69	0.807	SUBCLONAL	1	TRUE	1	0.680683702403891	2		767	684	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0046925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	120	292	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.680683702403891	3	FACETS	1	0.927	1	0.511	0.465	0.56	CLONAL	1	TRUE	1	0.680683702403891	3		292	462	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692979	89692979	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123325	NA	P-0046925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	164	352	0	ENST00000371953.3:c.463T>C	p.Tyr155His	p.Y155H	ENST00000371953	NM_000314.4	155	Tat/Cat	5/9	0.680683702403891	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.680683702403891	1		352	267	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417860	138417860	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	159	370	0	ENST00000289153.2:c.1659T>A	p.Asn553Lys	p.N553K	ENST00000289153	NM_006219.2	553	aaT/aaA	11/22	1	2	FACETS	0.998	0.923	1	0.998	0.923	1	CLONAL	1	TRUE	1	0.680683702403891	2		370	468	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0046926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	214	121	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.68256435509496	3	FACETS	1	0.94	1	0.505	0.47	0.541	CLONAL	1	TRUE	1	0.68256435509496	3		121	833	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0046926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	216	494	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.68256435509496	3	FACETS	0.94	0.875	1	0.47	0.437	0.504	CLONAL	1	TRUE	1	0.68256435509496	3		494	903	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0046926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	126	226	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.68256435509496	2		226	318	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245357	53245357	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	191	535	0	ENST00000375401.3:c.680T>C	p.Ile227Thr	p.I227T	ENST00000375401	NM_004187.3	227	aTt/aCt	6/26	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.68256435509496	2		535	557	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444663	78444663	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	148	401	0	ENST00000370768.2:c.26C>G	p.Pro9Arg	p.P9R	ENST00000370768	NM_003902.3	9	cCc/cGc	1/20	1	2	FACETS	0.997	0.919	1	0.997	0.919	1	CLONAL	1	TRUE	1	0.68256435509496	2		401	435	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0046927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	33	292	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.895	0.729	1	0.895	0.729	1	CLONAL	1	TRUE	1	0.169178030964842	2		292	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	56	582	0	ENST00000269305.4:c.166G>T	p.Glu56Ter	p.E56*	ENST00000269305	NM_001126112.2	56	Gaa/Taa	4/11	0.169178030964842	1	FACETS	0.722	0.617	0.838	0.722	0.617	0.838	SUBCLONAL	1	TRUE	0	0.169178030964842	1		582	839	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220382	1220382	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	75	592	0	ENST00000326873.7:c.475C>T	p.Gln159Ter	p.Q159*	ENST00000326873	NM_000455.4	159	Cag/Tag	4/10	0.169178030964842	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.169178030964842	1		592	747	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341269	8341269	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0046927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	19	209	0	ENST00000356435.5:c.4948-1G>A		p.X1650_splice	ENST00000356435		1650			1	2	FACETS	0.917	0.697	1	0.917	0.697	1	CLONAL	1	TRUE	1	0.169178030964842	2		209	245	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794763	120794763	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	76	758	1	ENST00000257552.2:c.594del	p.Arg199GlyfsTer50	p.R199Gfs*50	ENST00000257552	NM_002442.3	198	ggG/gg	9/15	1	2	FACETS	0.883	0.772	1	0.883	0.772	1	CLONAL	1	TRUE	1	0.169178030964842	2		759	1018	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21643285	21643285	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	51	402	0	ENST00000421138.2:c.242A>G	p.Asp81Gly	p.D81G	ENST00000421138		81	gAt/gGt	5/16	1	2	FACETS	0.92	0.781	1	0.92	0.781	1	CLONAL	1	TRUE	1	0.169178030964842	2		402	655	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748405	162748406	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	33	330	0	ENST00000367921.3:c.2323dup	p.Val775GlyfsTer21	p.V775Gfs*21	ENST00000367921	NM_006182.2	773	-/G	17/18	0.169178030964842	1	FACETS	0.787	0.64	0.952	0.787	0.64	0.952	CLONAL	1	TRUE	0	0.169178030964842	1		330	454	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591957	48591957	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	29	286	0	ENST00000342988.3:c.1120G>T	p.Glu374Ter	p.E374*	ENST00000342988	NM_005359.5	374	Gaa/Taa	9/12	0.169178030964842	1	FACETS	0.86	0.69	1	0.86	0.69	1	CLONAL	1	TRUE	0	0.169178030964842	1		286	365	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276675	15276675	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	82	635	1	ENST00000263388.2:c.5590G>T	p.Asp1864Tyr	p.D1864Y	ENST00000263388	NM_000435.2	1864	Gac/Tac	30/33	0.169178030964842	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.169178030964842	1		636	832	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549352	187549352	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	64	567	0	ENST00000441802.2:c.4766A>G	p.Lys1589Arg	p.K1589R	ENST00000441802	NM_005245.3	1589	aAg/aGg	9/27	1	2	FACETS	0.984	0.851	1	0.984	0.851	1	CLONAL	1	TRUE	1	0.169178030964842	2		567	769	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853080	151853080	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	31	343	0	ENST00000262189.6:c.11875G>C	p.Ala3959Pro	p.A3959P	ENST00000262189	NM_170606.2	3959	Gcc/Ccc	46/59	1	2	FACETS	0.743	0.6	0.906	0.743	0.6	0.906	CLONAL	1	TRUE	1	0.169178030964842	2		343	493	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971157	21971157	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	30	418	0	ENST00000304494.5:c.201del	p.Ala68ArgfsTer78	p.A68Rfs*78	ENST00000304494	NM_000077.4	67	ggC/gg	2/3	0.169178030964842	1	FACETS	0.624	0.502	0.764	0.624	0.502	0.764	SUBCLONAL	1	TRUE	0	0.169178030964842	1		418	520	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606582	93606582	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	52	451	0	ENST00000375746.1:c.402G>T	p.Gln134His	p.Q134H	ENST00000375746	NM_001174167.1	134	caG/caT	2/14	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.169178030964842	2		451	602	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209393	98209393	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	65	561	0	ENST00000331920.6:c.4145A>G	p.His1382Arg	p.H1382R	ENST00000331920	NM_000264.3	1382	cAc/cGc	23/24	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.169178030964842	2		561	714	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20152095	20152095	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	40	267	0	ENST00000379607.5:c.235del	p.Val79LeufsTer13	p.V79Lfs*13	ENST00000379607	NM_001412.3	79	Gtt/tt	4/7	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.169178030964842	2		267	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0046928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	107	767	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.288960951877937	2		767	650	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717769	89717770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	73	198	0	ENST00000371953.3:c.800dup	p.Asp268GlyfsTer30	p.D268Gfs*30	ENST00000371953	NM_000314.4	265	cta/ctAa	7/9	0.125404236594775	3	FACETS	1	0.953	1	1	0.953	1	INDETERMINATE	2	TRUE	1	0.347403828756294	3		198	217	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0046929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	73	356	1	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	0.289955345509182	2	FACETS	1	0.933	1	0.546	0.48	0.616	CLONAL	1	TRUE	0	0.347403828756294	2		357	385	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675571	86675571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1561325048	NA	P-0046929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	38	157	0	ENST00000274376.6:c.2513del	p.Asn838MetfsTer4	p.N838Mfs*4	ENST00000274376	NM_002890.2	836	gAa/ga	19/25	0.248866747688311	4	FACETS	1	0.921	1	1	0.967	1	CLONAL	3	TRUE	2	0.347403828756294	4		157	88	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936768	78936768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs987417975	NA	P-0046929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	378	632	0	ENST00000306801.3:c.3850G>A	p.Gly1284Arg	p.G1284R	ENST00000306801	NM_020761.2	1284	Gga/Aga	33/34	0.171895067597019	4	FACETS	1	0.991	1	1	0.996	1	INDETERMINATE	3	TRUE	2	0.347403828756294	4		632	847	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249360	153249361	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	187	294	0	ENST00000281708.4:c.1417dup	p.Arg473LysfsTer4	p.R473Kfs*4	ENST00000281708	NM_033632.3	473	aga/aAga	9/12	0.334190299150381	0	FACETS		NA	1			1	NA	4	TRUE	0	0.347403828756294	0		294	221	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691872	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs79375991	NA	P-0046929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	157	250	13	ENST00000295754.5:c.383del	p.Lys128SerfsTer35	p.K128Sfs*35	ENST00000295754	NM_003242.5	125	gAa/ga	3/7	0.323920646505249	0	FACETS	0.866	0.82	0.911			1	CLONAL	3	TRUE	0	0.347403828756294	0		263	227	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685269	89685269	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0046929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	14	148	0	ENST00000371953.3:c.165-1G>T		p.X55_splice	ENST00000371953	NM_000314.4	55			0.125404236594775	3	FACETS	0.852	0.649	1	1	0.874	1	INDETERMINATE	3	TRUE	1	0.347403828756294	3		148	37	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878749	151878749	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1211949081	NA	P-0046929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	188	301	2	ENST00000262189.6:c.6196C>T	p.Arg2066Ter	p.R2066*	ENST00000262189	NM_170606.2	2066	Cga/Tga	36/59	0.171895067597019	4	FACETS	1	0.982	1	1	0.993	1	INDETERMINATE	3	TRUE	2	0.347403828756294	4		303	427	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214367	55214367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778252	NA	P-0046929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	41	526	0	ENST00000275493.2:c.493C>T	p.Arg165Trp	p.R165W	ENST00000275493	NM_005228.3	165	Cgg/Tgg	4/28	0.171895067597019	4	FACETS	0.391	0.325	0.466	0.196	0.162	0.233	INDETERMINATE	1	TRUE	2	0.347403828756294	4		526	813	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964206	28964206	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	88	228	0	ENST00000282397.4:c.1696del	p.Met566CysfsTer8	p.M566Cfs*8	ENST00000282397	NM_002019.4	566	Atg/tg	13/30	0.347403828756294	1	FACETS	0.9	0.825	0.974	1	0.99	1	CLONAL	3	TRUE	0	0.347403828756294	1		228	155	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012245	152012245	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	119	342	3	ENST00000262189.6:c.568C>T	p.Arg190Ter	p.R190*	ENST00000262189	NM_170606.2	190	Cga/Tga	4/59	0.171895067597019	4	FACETS	1	0.952	1	1	0.988	1	INDETERMINATE	3	TRUE	2	0.347403828756294	4		345	292	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435670	149435670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	331	490	0	ENST00000286301.3:c.2473G>A	p.Glu825Lys	p.E825K	ENST00000286301	NM_005211.3	825	Gag/Aag	19/22	1	2	FACETS	1	0.991	1	1	0.997	1	CLONAL	2	TRUE	1	0.347403828756294	2		490	798	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350513	15350513	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	379	578	1	ENST00000263377.2:c.3402del	p.Lys1135SerfsTer18	p.K1135Sfs*18	ENST00000263377	NM_058243.2	1134	ccC/cc	16/20	0.117349042205517	4	FACETS	1	0.987	1	1	0.996	1	INDETERMINATE	3	TRUE	2	0.347403828756294	4		579	896	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830776	156830776	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	153	216	3	ENST00000524377.1:c.50C>T	p.Ala17Val	p.A17V	ENST00000524377	NM_002529.3	17	gCg/gTg	1/17	0.171895067597019	4	FACETS	1	0.976	1	1	0.991	1	INDETERMINATE	3	TRUE	2	0.347403828756294	4		219	354	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445980	49445981	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0046929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	497	788	1	ENST00000301067.7:c.1485_1486del	p.Pro496AlafsTer3	p.P496Afs*3	ENST00000301067	NM_003482.3	495	tcTCcg/tccg	10/54	0.171895067597019	4	FACETS	1	0.987	1	1	0.997	1	INDETERMINATE	3	TRUE	2	0.347403828756294	4		789	1201	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50816361	50816361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	109	241	0	ENST00000398568.2:c.1801G>A	p.Asp601Asn	p.D601N	ENST00000398568	NM_001042412.1	601	Gac/Aac	10/18	0.117349042205517	4	FACETS	0.907	0.832	0.982	1	0.989	1	INDETERMINATE	4	TRUE	2	0.347403828756294	4		241	233	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117594	70117594	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	351	562	0	ENST00000245479.2:c.62C>G	p.Ala21Gly	p.A21G	ENST00000245479	NM_000346.3	21	gCc/gGc	1/3	0.171895067597019	4	FACETS	0.879	0.838	0.921	1	0.996	1	INDETERMINATE	4	TRUE	2	0.347403828756294	4		562	774	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417859	138417859	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	160	338	0	ENST00000289153.2:c.1660G>A	p.Glu554Lys	p.E554K	ENST00000289153	NM_006219.2	554	Gaa/Aaa	11/22	0.347403828756294	7	FACETS	0.986	0.908	1	0.591	0.545	0.64	CLONAL	3	TRUE	2	0.347403828756294	7		338	582	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249711	110249711	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1190671294	NA	P-0046929-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	623	735	0	ENST00000374672.4:c.964G>C	p.Glu322Gln	p.E322Q	ENST00000374672	NM_004235.4	322	Gag/Cag	3/5	0.347403828756294	5	FACETS	0.945	0.914	0.975	1	0.997	1	CLONAL	5	TRUE	2	0.347403828756294	5		735	1155	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411884	116411893	+	intron_variant	Intron	DEL	TCTTTCTCTC	TCTTTCTCTC	-	novel	NA	P-0046949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	349	787	0	ENST00000397752.3:c.2888-18_2888-9del		p.*963*	ENST00000397752	NM_000245.2	-/1390			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		787	1475	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0000906-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	82	248	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.999	0.897	1	0.999	0.897	1	CLONAL	1	FALSE	1	0.739612257710768	2		249	222	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0000906-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	521	744	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.706350997983675	2	FACETS	0.922	0.894	0.949	0.922	0.894	0.949	CLONAL	2	FALSE	0	0.739612257710768	2		745	764	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911760	26911760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000906-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	111	274	0	ENST00000381527.3:c.185C>T	p.Ser62Leu	p.S62L	ENST00000381527	NM_001260.1	62	tCg/tTg	2/13	0.739612257710768	1	FACETS	0.96	0.888	1	0.96	0.888	1	CLONAL	1	FALSE	0	0.739612257710768	1		274	197	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223543	55223543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000906-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	531	640	0	ENST00000275493.2:c.910C>T	p.His304Tyr	p.H304Y	ENST00000275493	NM_005228.3	304	Cac/Tac	8/28	0.29502522252611	5	FACETS	0.896	0.862	0.93	0.538	0.517	0.558	INDETERMINATE	3	FALSE	0	0.739612257710768	5		640	1127	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717608	89717608	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1564566706	NA	P-0000906-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	161	349	0	ENST00000371953.3:c.635-2A>G		p.X212_splice	ENST00000371953	NM_000314.4	212			0.739612257710768	1	FACETS	0.973	0.913	1	0.973	0.913	1	CLONAL	1	FALSE	0	0.739612257710768	1		349	282	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40761099	40761099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393896368	NA	P-0000906-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	169	690	1	ENST00000392038.2:c.253G>A	p.Glu85Lys	p.E85K	ENST00000392038	NM_001626.4	85	Gag/Aag	4/14	0.272325930463007	1	FACETS	0.425	0.392	0.459	0.425	0.392	0.459	INDETERMINATE	1	FALSE	0	0.739612257710768	1		691	678	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161843	47161846	+	frameshift_variant	Frame_Shift_Del	DEL	CTAA	CTAA	-	novel	NA	P-0000906-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	172	340	0	ENST00000409792.3:c.4280_4283del	p.Val1427GlufsTer4	p.V1427Efs*4	ENST00000409792	NM_014159.6	1427	gTTAGa/ga	3/21	1	2	FACETS	0.959	0.89	1	0.959	0.89	1	CLONAL	1	FALSE	1	0.739612257710768	2		340	485	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268766	41268766	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000968-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	69	387	0	ENST00000349496.5:c.1004A>T	p.Lys335Ile	p.K335I	ENST00000349496	NM_001904.3	335	aAa/aTa	7/15	0.92452777768218	1	FACETS	0.302	0.265	0.34	0.302	0.265	0.34	SUBCLONAL	1	TRUE	0	0.92452777768218	1		387	266	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158451	106158451	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000968-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	131	204	0	ENST00000380013.4:c.3352A>G	p.Asn1118Asp	p.N1118D	ENST00000380013	NM_001127208.2	1118	Aat/Gat	3/11	0.45138957367435	3	FACETS	1	0.979	1	0.601	0.552	0.65	INDETERMINATE	1	TRUE	1	0.92452777768218	3		204	345	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412493	80412493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397514698	NA	P-0000968-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	169	336	0	ENST00000286548.4:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000286548	NM_002072.3	183	cGa/cAa	4/7	0.510307147541942	1	FACETS	0.692	0.652	0.732	0.692	0.652	0.732	INDETERMINATE	1	TRUE	0	0.92452777768218	1		336	284	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396497	396497	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000968-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	362	810	0	ENST00000262320.3:c.529A>T	p.Ile177Phe	p.I177F	ENST00000262320	NM_003502.3	177	Atc/Ttc	2/11	0.425249403161869	3	FACETS	1	0.988	1	0.562	0.534	0.591	INDETERMINATE	1	TRUE	1	0.92452777768218	3		810	1018	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0002380-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	409	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.942	0.896	0.988	0.942	0.896	0.988	CLONAL	1	FALSE	1	0.65743306295586	2		288	1321	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002380-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	12	151	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.676	0.488	0.892			1	INDETERMINATE	1	FALSE	NA	0.65743306295586	2		151	54	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508904	106508904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002380-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	213	236	1	ENST00000359195.3:c.898G>A	p.Gly300Arg	p.G300R	ENST00000359195	NM_002649.2	300	Gga/Aga	2/11	1	2	FACETS	0.97	0.906	1	0.97	0.906	1	CLONAL	1	FALSE	1	0.65743306295586	2		237	668	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375426	118375426	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782476723	NA	P-0002380-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	130	379	3	ENST00000534358.1:c.8819G>A	p.Arg2940Gln	p.R2940Q	ENST00000534358	NM_005933.3	2940	cGg/cAg	27/36	0.223510169604762	0	FACETS	0.175	0.158	0.192			1	INDETERMINATE	1	FALSE	0	0.65743306295586	0		382	776	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499752	18499752	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752594515	NA	P-0002380-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	281	221	0	ENST00000266497.5:c.1607C>T	p.Pro536Leu	p.P536L	ENST00000266497		536	cCa/cTa	10/31	0.358181538697784	1	FACETS	0.801	0.757	0.846	0.801	0.757	0.846	INDETERMINATE	1	FALSE	0	0.65743306295586	1		221	716	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436356	110436356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002380-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	37	115	0	ENST00000375856.3:c.2045G>A	p.Ser682Asn	p.S682N	ENST00000375856	NM_003749.2	682	aGc/aAc	1/2	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	FALSE	1	0.65743306295586	2		115	112	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857865	9857865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002380-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	283	381	0	ENST00000330684.3:c.3536C>T	p.Ser1179Phe	p.S1179F	ENST00000330684	NM_001134407.1	1179	tCc/tTc	13/13	0.155699527670766	0	FACETS	0.33	0.311	0.35			1	INDETERMINATE	1	FALSE	0	0.65743306295586	0		381	894	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260205	19260205	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002380-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	116	336	0	ENST00000162023.5:c.88A>G	p.Lys30Glu	p.K30E	ENST00000162023		30	Aag/Gag	7/13	0.65743306295586	1	FACETS	0.75	0.685	0.816	0.75	0.685	0.816	SUBCLONAL	1	FALSE	0	0.65743306295586	1		336	316	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156720	20156720	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002380-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	402	529	0	ENST00000379607.5:c.37C>G	p.Arg13Gly	p.R13G	ENST00000379607	NM_001412.3	13	Cgc/Ggc	2/7	NA	2	FACETS	1	0.956	1			1	INDETERMINATE	1	FALSE	NA	0.65743306295586	2		529	1217	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428164	47428164	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002380-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	221	519	0	ENST00000377045.4:c.1124G>C	p.Arg375Pro	p.R375P	ENST00000377045	NM_001654.4	375	cGg/cCg	11/16	NA	2	FACETS	0.815	0.76	0.871			1	INDETERMINATE	1	FALSE	NA	0.65743306295586	2		519	825	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0002392-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	270	510	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.602139438126258	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.637292950773363	1		510	550	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881415	48881415	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002392-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	31	122	0	ENST00000267163.4:c.138-1G>A		p.X46_splice	ENST00000267163	NM_000321.2	46			0.637292950773363	1	FACETS	0.861	0.723	1	0.861	0.723	1	CLONAL	1	TRUE	0	0.637292950773363	1		122	77	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187135	38187135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356401338	NA	P-0002392-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	281	678	1	ENST00000317025.8:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000317025	NM_023034.1	448	Cgg/Tgg	6/24	1	2	FACETS	0.934	0.879	0.99	0.934	0.879	0.99	CLONAL	1	TRUE	1	0.637292950773363	2		679	944	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649523	206649523	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0002392-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	205	435	0	ENST00000367120.3:c.359-1G>C		p.X120_splice	ENST00000367120	NM_014002.3	120			0.540788191154997	3	FACETS	1	0.975	1	0.55	0.511	0.59	CLONAL	1	TRUE	1	0.637292950773363	3		435	771	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536733	120536733	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002392-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	267	494	0	ENST00000229340.5:c.359A>G	p.Asn120Ser	p.N120S	ENST00000229340	NM_006861.6	120	aAt/aGt	5/6	1	2	FACETS	0.969	0.911	1	0.969	0.911	1	CLONAL	1	TRUE	1	0.637292950773363	2		494	865	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748184	43748184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002392-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	205	488	1	ENST00000382044.4:c.2622G>A	p.Met874Ile	p.M874I	ENST00000382044	NM_001141980.1	874	atG/atA	12/28	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.637292950773363	2		489	614	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39573253	39573253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002392-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	70	345	0	ENST00000262039.4:c.734C>T	p.Pro245Leu	p.P245L	ENST00000262039	NM_002647.2	245	cCa/cTa	7/25	1	2	FACETS	0.845	0.745	0.95	0.845	0.745	0.95	CLONAL	1	TRUE	1	0.637292950773363	2		345	260	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607634	46607635	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0002392-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	273	758	1	ENST00000263734.3:c.1823_1824delinsAT	p.Phe608Tyr	p.F608Y	ENST00000263734	NM_001430.4	608	tTC/tAT	12/16	1	2	FACETS	0.872	0.82	0.926	0.872	0.82	0.926	CLONAL	1	TRUE	1	0.637292950773363	2		759	982	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682358	52682358	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0002392-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	61	188	0	ENST00000394830.3:c.813+2T>C		p.X271_splice	ENST00000394830	NM_018313.4	271			0.635447050435282	1	FACETS	0.906	0.803	1	0.906	0.803	1	CLONAL	1	TRUE	0	0.637292950773363	1		188	144	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630849	187630849	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002392-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	187	504	1	ENST00000441802.2:c.133G>A	p.Glu45Lys	p.E45K	ENST00000441802	NM_005245.3	45	Gag/Aag	2/27	1	2	FACETS	0.934	0.868	1	0.934	0.868	1	CLONAL	1	TRUE	1	0.637292950773363	2		505	628	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031970	26031971	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0002392-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	143	324	2	ENST00000244661.2:c.318_319delinsAA	p.Asp107Asn	p.D107N	ENST00000244661	NM_003537.3	106	gaGGac/gaAAac	1/1	1	2	FACETS	0.88	0.807	0.955	0.88	0.807	0.955	CLONAL	1	TRUE	1	0.637292950773363	2		326	510	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271435	26271435	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002392-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	238	539	0	ENST00000305910.3:c.178G>A	p.Glu60Lys	p.E60K	ENST00000305910	NM_003534.2	60	Gag/Aag	1/1	1	2	FACETS	0.909	0.85	0.968	0.909	0.85	0.968	CLONAL	1	TRUE	1	0.637292950773363	2		539	822	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969956	161969956	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002392-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	271	590	0	ENST00000366898.1:c.1013G>A	p.Gly338Glu	p.G338E	ENST00000366898	NM_004562.2	338	gGa/gAa	9/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.637292950773363	2		590	791	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137325963	137325963	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002392-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	320	702	0	ENST00000481739.1:c.1151C>G	p.Ser384Trp	p.S384W	ENST00000481739	NM_002957.4	384	tCg/tGg	9/10	1	2	FACETS	0.993	0.939	1	0.993	0.939	1	CLONAL	1	TRUE	1	0.637292950773363	2		702	1011	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687400	117687400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146570171	NA	P-0002418-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	181	567	0	ENST00000368508.3:c.2651C>T	p.Ser884Phe	p.S884F	ENST00000368508	NM_002944.2	884	tCc/tTc	18/43	1	2	FACETS	1	0.961	1	1	0.993	1	CLONAL	2	TRUE	1	0.29	2		567	592	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0002418-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	134	525	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	0.295674497461994	1	FACETS	0.832	0.761	0.905	1	0.989	1	CLONAL	2	TRUE	0	0.29	1		525	475	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913492	NA	P-0002418-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	106	656	0	ENST00000286548.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000286548	NM_002072.3	209	cAa/cTa	5/7	0.295674497461994	4	FACETS	1	0.923	1	0.685	0.617	0.756	CLONAL	2	TRUE	1	0.29	4		656	459	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0002437-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	183	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.266739725516587	9	FACETS	0.974	0.912	1	1	0.982	1	CLONAL	7	FALSE	3	0.266739725516587	9		288	389	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002437-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	16	151	0				ENST00000310581	NM_198253.2	-/1132			0.127133806962744	1	FACETS	1	0.897	1	1	0.897	1	INDETERMINATE	1	FALSE	0	0.266739725516587	1		151	72	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230613	46230613	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002437-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	47	419	0	ENST00000334344.6:c.862C>T	p.Gln288Ter	p.Q288*	ENST00000334344	NM_152641.2	288	Cag/Tag	8/21	0.266739725516587	4	FACETS	0.922	0.785	1			1	CLONAL	2	FALSE	NA	0.266739725516587	4		419	242	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913407	NA	P-0002437-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	84	359	0	ENST00000349496.5:c.133T>G	p.Ser45Ala	p.S45A	ENST00000349496	NM_001904.3	45	Tct/Gct	3/15	0.266739725516587	6	FACETS	0.898	0.803	0.995	1	0.966	1	CLONAL	4	FALSE	3	0.266739725516587	6		359	269	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984939	55984939	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002437-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	82	416	0	ENST00000263923.4:c.190C>T	p.Pro64Ser	p.P64S	ENST00000263923	NM_002253.2	64	Ccc/Tcc	3/30	0.189229512763867	4	FACETS	1	0.918	1	1	0.981	1	CLONAL	3	FALSE	2	0.266739725516587	4		416	252	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557939	187557939	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002437-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	58	386	0	ENST00000441802.2:c.3772G>C	p.Glu1258Gln	p.E1258Q	ENST00000441802	NM_005245.3	1258	Gaa/Caa	5/27	0.12992309048231	4	FACETS	1	0.944	1	1	0.944	1	INDETERMINATE	2	FALSE	2	0.266739725516587	4		386	236	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131951729	131951729	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002437-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	54	309	0	ENST00000265335.6:c.3071T>C	p.Leu1024Ser	p.L1024S	ENST00000265335		1024	tTa/tCa	20/25	0.266739725516587	5	FACETS	1	0.927	1	0.747	0.644	0.857	CLONAL	2	FALSE	2	0.266739725516587	5		309	253	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143096	58143096	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002437-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	87	208	0	ENST00000257904.6:c.688A>C	p.Ile230Leu	p.I230L	ENST00000257904	NM_000075.3	230	Att/Ctt	7/8	0.266739725516587	9	FACETS	1	0.957	1	0.862	0.769	0.959	CLONAL	3	FALSE	5	0.266739725516587	9		208	366	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476301	88476301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002437-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	23	376	0	ENST00000360948.2:c.1831G>A	p.Asp611Asn	p.D611N	ENST00000360948	NM_001012338.2	611	Gac/Aac	15/19	0.116568830820417	3	FACETS	1	0.82	1			1	INDETERMINATE	1	FALSE	NA	0.266739725516587	3		376	186	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89881015	89881015	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs753727231	NA	P-0002437-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	71	388	0	ENST00000389301.3:c.196G>T	p.Gly66Cys	p.G66C	ENST00000389301	NM_000135.2	66	Ggt/Tgt	3/43	0.266739725516587	5	FACETS	0.845	0.745	0.951	0.845	0.745	0.951	CLONAL	3	FALSE	2	0.266739725516587	5		388	294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577552	7577552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002437-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	42	262	0	ENST00000269305.4:c.729G>A	p.Met243Ile	p.M243I	ENST00000269305	NM_001126112.2	243	atG/atA	7/11	0.266739725516587	5	FACETS	1	0.898	1	0.724	0.611	0.846	CLONAL	2	FALSE	2	0.266739725516587	5		262	203	SUCCESS
AXL	558	MSKCC	GRCh37	19	41759577	41759577	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367869435	NA	P-0002437-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	27	332	0	ENST00000301178.4:c.2000G>A	p.Arg667Lys	p.R667K	ENST00000301178	NM_021913.4	667	aGa/aAa	17/20	0.266739725516587	4	FACETS	0.878	0.708	1	0.878	0.708	1	CLONAL	2	FALSE	2	0.266739725516587	4		332	146	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579470	7579471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882018	NA	P-0004871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	87	335	0	ENST00000269305.4:c.216dup	p.Val73ArgfsTer76	p.V73Rfs*76	ENST00000269305	NM_001126112.2	72	-/C	4/11	0.151250681159479	4	FACETS	0.806	0.714	0.903	0.806	0.714	0.903	CLONAL	2	TRUE	2	0.22170465231802	4		335	595	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814930	139814930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371121908	NA	P-0004871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	116	661	1	ENST00000247668.2:c.923G>A	p.Arg308Gln	p.R308Q	ENST00000247668	NM_021138.3	308	cGg/cAg	8/11	0.22170465231802	1	FACETS	0.769	0.691	0.852	0.769	0.691	0.852	SUBCLONAL	1	TRUE	0	0.22170465231802	1		662	1210	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120535161	120535161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	187	548	0	ENST00000229340.5:c.494C>T	p.Thr165Met	p.T165M	ENST00000229340	NM_006861.6	165	aCg/aTg	6/6	0.146716759380335	3	FACETS	0.764	0.704	0.827	0.764	0.704	0.827	SUBCLONAL	2	TRUE	1	0.22170465231802	3		548	1226	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73334782	73334782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746804740	NA	P-0004871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	54	240	0	ENST00000377767.4:c.2678C>T	p.Ser893Leu	p.S893L	ENST00000377767	NM_014953.3	893	tCa/tTa	20/21	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.22170465231802	2		240	467	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335933	73335933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	79	313	0	ENST00000377767.4:c.2362C>T	p.His788Tyr	p.H788Y	ENST00000377767	NM_014953.3	788	Cat/Tat	18/21	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.22170465231802	2		313	689	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336116	73336116	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	101	415	0	ENST00000377767.4:c.2287C>T	p.His763Tyr	p.H763Y	ENST00000377767	NM_014953.3	763	Cat/Tat	17/21	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.22170465231802	2		415	855	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336224	73336224	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	83	306	0	ENST00000377767.4:c.2179C>T	p.Gln727Ter	p.Q727*	ENST00000377767	NM_014953.3	727	Cag/Tag	17/21	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.22170465231802	2		306	713	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938407	76938407	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	144	479	0	ENST00000373344.5:c.2341C>T	p.Arg781Ter	p.R781*	ENST00000373344	NM_000489.3	781	Cga/Tga	9/35	0.200400337412154	2	FACETS	0.818	0.747	0.893	0.818	0.747	0.893	CLONAL	2	TRUE	0	0.22170465231802	2		479	794	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0004933-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	268	267	0				ENST00000310581	NM_198253.2	-/1132			0.693925113292422	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.693925113292422	3		267	514	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453145	140453146	+	missense_variant	Missense_Mutation	DNP	AG	AG	GA	rs121913368	NA	P-0004933-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	326	445	1	ENST00000288602.6:c.1789_1790delinsTC	p.Leu597Ser	p.L597S	ENST00000288602	NM_004333.4	597	CTa/TCa	15/18	0.693925113292422	4	FACETS	0.973	0.943	1	0.973	0.943	1	CLONAL	4	TRUE	0	0.693925113292422	4		446	409	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0004933-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	344	297	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.660851320145573	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.693925113292422	2		297	460	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777894	NA	P-0004933-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	153	594	0	ENST00000361445.4:c.6644C>T	p.Ser2215Phe	p.S2215F	ENST00000361445	NM_004958.3	2215	tCt/tTt	47/58	NA	2	FACETS	0.926	0.854	1			1	INDETERMINATE	1	TRUE	NA	0.693925113292422	2		594	476	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972013	55972013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004933-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	130	497	0	ENST00000263923.4:c.1631C>T	p.Ser544Phe	p.S544F	ENST00000263923	NM_002253.2	544	tCc/tTc	12/30	1	2	FACETS	0.925	0.847	1	0.925	0.847	1	CLONAL	1	TRUE	1	0.693925113292422	2		497	405	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609907	117609907	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761470868	NA	P-0004933-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	128	574	0	ENST00000368508.3:c.6792G>A	p.Met2264Ile	p.M2264I	ENST00000368508	NM_002944.2	2264	atG/atA	43/43	NA	2	FACETS	0.941	0.861	1			1	INDETERMINATE	1	TRUE	NA	0.693925113292422	2		574	392	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911604	114911604	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004933-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	397	622	0	ENST00000543371.1:c.1122G>T	p.Leu374Phe	p.L374F	ENST00000543371	NM_001198531.1	374	ttG/ttT	10/14	0.680685665873946	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.693925113292422	2		622	568	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202531	67202531	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004933-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	454	646	0	ENST00000312629.5:c.1340T>C	p.Leu447Pro	p.L447P	ENST00000312629	NM_003952.2	447	cTa/cCa	15/15	0.693925113292422	3	FACETS	0.975	0.936	1	0.975	0.936	1	CLONAL	2	TRUE	1	0.693925113292422	3		646	904	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110618	8110618	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004933-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	167	623	0	ENST00000585124.1:c.274T>G	p.Tyr92Asp	p.Y92D	ENST00000585124	NM_004217.3	92	Tac/Gac	5/9	0.693925113292422	3	FACETS	0.866	0.797	0.937	0.433	0.398	0.469	CLONAL	1	TRUE	1	0.693925113292422	3		623	749	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439993	56439993	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004933-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	341	717	0	ENST00000407977.2:c.599G>A	p.Trp200Ter	p.W200*	ENST00000407977		200	tGg/tAg	6/10	0.693925113292422	3	FACETS	0.931	0.888	0.974	0.931	0.888	0.974	CLONAL	2	TRUE	1	0.693925113292422	3		717	711	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653807	89653807	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004933-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	215	500	1	ENST00000371953.3:c.107del	p.Gly36AspfsTer18	p.G36Dfs*18	ENST00000371953	NM_000314.4	35	atG/at	2/9	0.680685665873946	2	FACETS	0.953	0.908	0.998	0.953	0.908	0.998	CLONAL	2	TRUE	0	0.693925113292422	2		501	325	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826577	50826577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004933-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	92	504	0	ENST00000398568.2:c.2302C>T	p.Pro768Ser	p.P768S	ENST00000398568	NM_001042412.1	768	Cct/Tct	15/18	0.693925113292422	3	FACETS	0.968	0.867	1	0.484	0.433	0.537	CLONAL	1	TRUE	1	0.693925113292422	3		504	369	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38178604	38178606	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0004933-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	104	496	0	ENST00000317025.8:c.1793_1795del	p.Lys598del	p.K598del	ENST00000317025	NM_023034.1	598	aAGAtc/atc	8/24	0.685073178860086	4	FACETS	0.841	0.754	0.932	0.42	0.377	0.466	CLONAL	1	TRUE	2	0.693925113292422	4		496	604	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003747	45003747	+	start_lost	Translation_Start_Site	SNP	G	G	C	novel	NA	P-0004933-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	228	387	0	ENST00000558401.1:c.3G>C	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	atG/atC	1/4	0.693925113292422	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.693925113292422	1		387	404	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501361	140501361	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004933-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	251	315	0	ENST00000288602.6:c.712-1G>A		p.X238_splice	ENST00000288602	NM_004333.4	238			0.693925113292422	4	FACETS	0.931	0.896	0.964	0.931	0.896	0.964	CLONAL	4	TRUE	0	0.693925113292422	4		315	329	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005956	69005956	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004933-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	223	510	0	ENST00000288368.4:c.2367A>T	p.Glu789Asp	p.E789D	ENST00000288368	NM_024870.2	789	gaA/gaT	21/40	0.685073178860086	4	FACETS	0.889	0.834	0.946	0.889	0.834	0.946	CLONAL	2	TRUE	2	0.693925113292422	4		510	612	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009090	27009092	+	missense_variant	Missense_Mutation	TNP	AGC	AGC	TGT	novel	NA	P-0004933-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	273	137	0	ENST00000335756.4:c.26_28delinsTGT	p.Lys9_Pro10delinsMetSer	p.K9_P10delinsMS	ENST00000335756	NM_001809.3	9	aAGCcc/aTGTcc	1/5	0.693925113292422	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.693925113292422	3		137	334	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0005201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	306	430	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.58302037972823	4	FACETS	0.928	0.884	0.972	0.928	0.884	0.972	CLONAL	3	TRUE	1	0.58302037972823	4		430	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0005201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	578	613	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.58302037972823	3	FACETS	1	0.99	1	1	0.998	1	CLONAL	3	TRUE	1	0.58302037972823	3		613	824	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888172	112888172	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121918459	NA	P-0005201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	159	831	0	ENST00000351677.2:c.188A>G	p.Tyr63Cys	p.Y63C	ENST00000351677	NM_002834.3	63	tAt/tGt	3/16	0.511698754655617	4	FACETS	0.885	0.81	0.962	0.442	0.405	0.481	CLONAL	1	TRUE	2	0.58302037972823	4		831	976	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198272831	198272843	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CTCATTATGTGAC	CTCATTATGTGAC	-	novel	NA	P-0005201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	101	707	0	ENST00000335508.6:c.1118_1130del	p.Gly373ValfsTer2	p.G373Vfs*2	ENST00000335508	NM_012433.2	373	gGTCACATAATGAGt/gt	9/25	0.58302037972823	3	FACETS	0.726	0.65	0.807	0.363	0.325	0.404	SUBCLONAL	1	TRUE	1	0.58302037972823	3		707	616	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076902	41076902	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	333	803	1	ENST00000373198.4:c.1518G>A	p.Trp506Ter	p.W506*	ENST00000373198	NM_133170.3	506	tgG/tgA	9/32	0.511698754655617	4	FACETS	0.969	0.919	1	0.969	0.919	1	CLONAL	2	TRUE	2	0.58302037972823	4		804	933	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534341	187534341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	400	831	0	ENST00000441802.2:c.9385C>T	p.Pro3129Ser	p.P3129S	ENST00000441802	NM_005245.3	3129	Cct/Tct	13/27	0.528448955324505	3	FACETS	0.966	0.923	1	0.966	0.923	1	CLONAL	2	TRUE	1	0.58302037972823	3		831	917	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495442	149495442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576668629	NA	P-0005201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	263	1194	2	ENST00000261799.4:c.3205G>A	p.Glu1069Lys	p.E1069K	ENST00000261799	NM_002609.3	1069	Gaa/Aaa	23/23	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.58302037972823	2		1196	848	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710963	117710963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	209	439	0	ENST00000368508.3:c.1309C>T	p.Pro437Ser	p.P437S	ENST00000368508	NM_002944.2	437	Cct/Tct	12/43	0.58302037972823	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	1	0.58302037972823	3		439	456	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851369	151851369	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1261796800	NA	P-0005201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	731	785	0	ENST00000262189.6:c.12122C>T	p.Pro4041Leu	p.P4041L	ENST00000262189	NM_170606.2	4041	cCt/cTt	47/59	0.558341140712078	5	FACETS	0.993	0.965	1	0.993	0.965	1	CLONAL	4	TRUE	1	0.58302037972823	5		785	1184	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021821	69021821	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	714	755	0	ENST00000288368.4:c.3109C>A	p.Leu1037Met	p.L1037M	ENST00000288368	NM_024870.2	1037	Ctg/Atg	25/40	0.58302037972823	6	FACETS	1	0.98	1	1	0.98	1	CLONAL	4	TRUE	2	0.58302037972823	6		755	1309	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27209212	27209212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1332	181	785	0	ENST00000380036.4:c.2669G>A	p.Gly890Glu	p.G890E	ENST00000380036	NM_000459.3	890	gGa/gAa	16/23	0.58302037972823	7	FACETS	1	0.927	1			1	CLONAL	1	TRUE	NA	0.58302037972823	7		785	1513	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915952	127915952	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs865855853	NA	P-0005201-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	346	697	1	ENST00000373547.4:c.529C>T	p.Arg177Ter	p.R177*	ENST00000373547	NM_002721.4	177	Cga/Tga	6/7	0.58302037972823	3	FACETS	0.965	0.919	1	0.965	0.919	1	CLONAL	2	TRUE	1	0.58302037972823	3		698	794	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934578	NA	P-0005655-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	240	282	0	ENST00000269305.4:c.524G>T	p.Arg175Leu	p.R175L	ENST00000269305	NM_001126112.2	175	cGc/cTc	5/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.668053653431275	2		282	656	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574030	7574030	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005655-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	308	478	0	ENST00000269305.4:c.997del	p.Arg333ValfsTer12	p.R333Vfs*12	ENST00000269305	NM_001126112.2	333	Cgt/gt	10/11	1	2	FACETS	0.878	0.829	0.929	0.878	0.829	0.929	CLONAL	1	TRUE	1	0.668053653431275	2		478	1050	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300570	11300570	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764486955	NA	P-0005655-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	514	521	1	ENST00000361445.4:c.1576C>T	p.Arg526Cys	p.R526C	ENST00000361445	NM_004958.3	526	Cgt/Tgt	11/58	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	1	TRUE	NA	0.668053653431275	2		522	1245	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937383	76937383	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005655-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	151	582	0	ENST00000373344.5:c.3365del	p.Cys1122LeufsTer8	p.C1122Lfs*8	ENST00000373344	NM_000489.3	1122	tGt/tt	9/35	0.668102271976367	1	FACETS	0.647	0.597	0.7	0.647	0.597	0.7	SUBCLONAL	1	TRUE	0	0.668053653431275	1		582	465	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0006467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	183	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.23175321092198	1	FACETS	1	0.984	1	1	0.994	1	CLONAL	2	FALSE	0	0.23175321092198	1		288	580	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131301	202131301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748087575	NA	P-0006467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	130	239	0	ENST00000358485.4:c.269C>T	p.Pro90Leu	p.P90L	ENST00000358485	NM_001080125.1	90	cCg/cTg	2/9	0.23175321092198	0	FACETS	0.722	0.657	0.79			1	SUBCLONAL	2	FALSE	0	0.23175321092198	0		239	597	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893668	28893668	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs374452662	NA	P-0006467-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	243	238	2	ENST00000282397.4:c.3178C>T	p.Arg1060Ter	p.R1060*	ENST00000282397	NM_002019.4	1060	Cga/Tga	24/30	0.23175321092198	3	FACETS	1	0.983	1	1	0.994	1	CLONAL	3	FALSE	1	0.23175321092198	3		240	695	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574002	7574002	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs375338359	NA	P-0006532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	322	586	0	ENST00000269305.4:c.1025G>C	p.Arg342Pro	p.R342P	ENST00000269305	NM_001126112.2	342	cGa/cCa	10/11	0.826292568320081	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.826292568320081	1		586	445	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947568	48947580	+	frameshift_variant	Frame_Shift_Del	DEL	AATGATGATTTTA	AATGATGATTTTA	-	novel	NA	P-0006532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	217	332	0	ENST00000267163.4:c.1158_1170del	p.Met386IlefsTer11	p.M386Ifs*11	ENST00000267163	NM_000321.2	385	ttAATGATGATTTTA/tt	12/27	0.826292568320081	1	FACETS	0.859	0.815	0.902	0.859	0.815	0.902	CLONAL	1	TRUE	0	0.826292568320081	1		332	359	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692891	89692891	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	252	260	0	ENST00000371953.3:c.375A>T	p.Lys125Asn	p.K125N	ENST00000371953	NM_000314.4	125	aaA/aaT	5/9	0.826292568320081	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.826292568320081	1		260	324	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431694	49431703	+	frameshift_variant	Frame_Shift_Del	DEL	AATTGGCAGC	AATTGGCAGC	-	novel	NA	P-0006532-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	254	624	0	ENST00000301067.7:c.9436_9445del	p.Ala3146ProfsTer6	p.A3146Pfs*6	ENST00000301067	NM_003482.3	3146	GCTGCCAATTcc/cc	34/54	0.826292568320081	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.826292568320081	1		624	345	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0007232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	913	1058	3	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.173590477356026	6	FACETS	1	0.994	1			1	INDETERMINATE	5	TRUE	NA	0.750172077009041	6		1061	1175	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692886	89692886	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	184	395	0	ENST00000371953.3:c.370T>A	p.Cys124Ser	p.C124S	ENST00000371953	NM_000314.4	124	Tgt/Agt	5/9	0.714528954072894	1	FACETS	0.943	0.889	0.997	0.943	0.889	0.997	CLONAL	1	TRUE	0	0.750172077009041	1		395	325	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244907	46244907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	40	575	0	ENST00000334344.6:c.3001C>T	p.Pro1001Ser	p.P1001S	ENST00000334344	NM_152641.2	1001	Cct/Tct	15/21	0.502395356423242	1	FACETS	0.136	0.113	0.162	0.136	0.113	0.162	SUBCLONAL	1	TRUE	0	0.750172077009041	1		575	490	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608306	100608306	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	25	382	0	ENST00000308731.7:c.1784A>C	p.Lys595Thr	p.K595T	ENST00000308731	NM_000061.2	595	aAg/aCg	18/19	1	1	FACETS	0.086	0.067	0.107	0.086	0.067	0.107	SUBCLONAL	1	TRUE	0	0.750172077009041	1		382	486	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610556	215610556	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	44	468	0	ENST00000260947.4:c.1700A>C	p.Asp567Ala	p.D567A	ENST00000260947	NM_000465.2	567	gAt/gCt	8/11	1	2	FACETS	0.157	0.131	0.186	0.157	0.131	0.186	SUBCLONAL	1	TRUE	1	0.697311364395091	2		468	804	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747889	41747889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772358257	NA	P-0007293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1264	295	504	2	ENST00000226382.2:c.880G>A	p.Val294Ile	p.V294I	ENST00000226382	NM_003924.3	294	Gtc/Atc	3/3	0.380826914520154	5	FACETS	1	0.982	1	0.37	0.347	0.394	INDETERMINATE	1	TRUE	2	0.697311364395091	5		506	1559	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117717385	117717385	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	344	496	0	ENST00000368508.3:c.822A>C	p.Glu274Asp	p.E274D	ENST00000368508	NM_002944.2	274	gaA/gaC	8/43	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.697311364395091	2		496	811	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235809	108235809	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	419	384	0	ENST00000278616.4:c.8851G>T	p.Val2951Phe	p.V2951F	ENST00000278616	NM_000051.3	2951	Gtc/Ttc	62/63	0.63339880521246	3	FACETS	0.994	0.954	1	0.994	0.954	1	CLONAL	2	TRUE	1	0.697311364395091	3		384	815	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233201	46233201	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1927	375	542	0	ENST00000334344.6:c.1420A>T	p.Ser474Cys	p.S474C	ENST00000334344	NM_152641.2	474	Agt/Tgt	11/21	0.652921614219553	5	FACETS	0.956	0.903	1			1	CLONAL	1	TRUE	NA	0.697311364395091	5		542	2302	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874315	76874316	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0007293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	878	767	0	ENST00000373344.5:c.5406dup	p.Arg1803ThrfsTer7	p.R1803Tfs*7	ENST00000373344	NM_000489.3	1802	-/A	21/35	0.703752783073632	3	FACETS	0.863	0.837	0.889			1	CLONAL	2	TRUE	NA	0.697311364395091	3		767	1968	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0007690-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	664	578	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	0.606549338253318	1	FACETS	0.78	0.759	0.8	0.78	0.759	0.8	SUBCLONAL	1	TRUE	0	0.933532624888847	1		578	973	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437503	52437522	+	frameshift_variant	Frame_Shift_Del	DEL	AGATCACGGACAGCACGGTT	AGATCACGGACAGCACGGTT	-	novel	NA	P-0007690-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	630	612	0	ENST00000460680.1:c.1639_1658del	p.Asn547GlyfsTer13	p.N547Gfs*13	ENST00000460680	NM_004656.3	547	AACCGTGCTGTCCGTGATCTg/g	13/17	NA	2	FACETS	0.974	0.959	0.988			1	INDETERMINATE	2	TRUE	NA	0.933532624888847	2		612	693	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0008106-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	366	1058	3	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.560474279218491	2	FACETS	0.99	0.95	1	0.99	0.95	1	CLONAL	2	TRUE	0	0.583217093188689	2		1061	634	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0008106-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	51	248	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.916	0.79	1	0.916	0.79	1	CLONAL	1	TRUE	1	0.583217093188689	2		249	191	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961292	15961292	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008106-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	154	423	1	ENST00000268712.3:c.6097T>A	p.Ser2033Thr	p.S2033T	ENST00000268712	NM_006311.3	2033	Tct/Act	39/46	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.583217093188689	2		424	499	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492797	56492797	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1318096583	NA	P-0008106-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	205	484	0	ENST00000407977.2:c.142A>G	p.Ile48Val	p.I48V	ENST00000407977		48	Atc/Gtc	2/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.583217093188689	2		484	676	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372049	45372049	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008106-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	139	397	0	ENST00000262160.6:c.1120T>C	p.Cys374Arg	p.C374R	ENST00000262160	NM_005901.5	374	Tgt/Cgt	9/11	1	2	FACETS	0.961	0.881	1	0.961	0.881	1	CLONAL	1	TRUE	1	0.583217093188689	2		397	496	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244262	5244262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008106-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	173	524	0	ENST00000357368.4:c.1220C>T	p.Ser407Phe	p.S407F	ENST00000357368	NM_002850.3	407	tCc/tTc	11/38	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.583217093188689	2		524	572	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244184	153244184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759610249	NA	P-0008106-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	165	446	0	ENST00000281708.4:c.1973G>A	p.Arg658Gln	p.R658Q	ENST00000281708	NM_033632.3	658	cGa/cAa	12/12	1	2	FACETS	0.979	0.904	1	0.979	0.904	1	CLONAL	1	TRUE	1	0.583217093188689	2		446	578	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722230	176722230	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008106-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	124	373	0	ENST00000439151.2:c.7861G>T	p.Glu2621Ter	p.E2621*	ENST00000439151	NM_022455.4	2621	Gag/Tag	23/23	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.583217093188689	2		373	401	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026532	6026532	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008106-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	109	749	0	ENST00000265849.7:c.1864A>C	p.Met622Leu	p.M622L	ENST00000265849	NM_000535.5	622	Atg/Ctg	11/15	1	2	FACETS	0.604	0.543	0.668	0.604	0.543	0.668	SUBCLONAL	1	TRUE	1	0.583217093188689	2		749	619	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729922	41729922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008106-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	152	568	1	ENST00000242208.4:c.607G>A	p.Glu203Lys	p.E203K	ENST00000242208	NM_002192.2	203	Gaa/Aaa	3/3	1	2	FACETS	0.905	0.832	0.981	0.905	0.832	0.981	CLONAL	1	TRUE	1	0.583217093188689	2		569	576	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411537	63411537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772837332	NA	P-0008106-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	155	332	0	ENST00000330258.3:c.1630C>T	p.Pro544Ser	p.P544S	ENST00000330258	NM_152424.3	544	Ccc/Tcc	2/2	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.583217093188689	1		332	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0009432-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	247	744	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.62095423975443	1	FACETS	0.921	0.868	0.974	0.921	0.868	0.974	CLONAL	1	TRUE	0	0.623582099417425	1		745	592	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17355104	17355104	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009432-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	149	321	0	ENST00000375499.3:c.414T>A	p.Asp138Glu	p.D138E	ENST00000375499	NM_003000.2	138	gaT/gaA	4/8	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.623582099417425	2		321	471	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115975	8115975	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009432-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	153	340	0	ENST00000346208.3:c.1321del	p.Ala441ProfsTer34	p.A441Pfs*34	ENST00000346208		441	Gcc/cc	6/6	0.588475420100921	3	FACETS	1	0.962	1			1	CLONAL	1	TRUE	NA	0.623582099417425	3		340	596	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934245	48934279	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTGCTCAAAGAACCATATAGTAAGTATTTAATTTA	TTGCTCAAAGAACCATATAGTAAGTATTTAATTTA	-	novel	NA	P-0009432-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	66	222	0	ENST00000267163.4:c.701_718+17del		p.X234_splice	ENST00000267163	NM_000321.2	234		7/27	0.62095423975443	1	FACETS	0.65	0.573	0.732	0.65	0.573	0.732	SUBCLONAL	1	TRUE	0	0.623582099417425	1		222	224	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398286	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0009789-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	227	308	0	ENST00000311936.3:c.33_34delinsCT	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	11	gcTGgt/gcCTgt	2/5	0.624838622414027	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.624838622414027	3		308	437	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019560	42019560	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009789-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	170	356	0	ENST00000219905.7:c.3613G>T	p.Gly1205Ter	p.G1205*	ENST00000219905	NM_001164273.1	1205	Gga/Tga	10/24	0.60691726582433	2	FACETS	0.904	0.849	0.958	0.904	0.849	0.958	CLONAL	2	TRUE	0	0.624838622414027	2		356	301	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578509	7578509	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519978	NA	P-0009789-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	352	805	0	ENST00000269305.4:c.421T>C	p.Cys141Arg	p.C141R	ENST00000269305	NM_001126112.2	141	Tgc/Cgc	5/11	0.553684504551844	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.624838622414027	1		805	572	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952519	17952520	+	missense_variant	Missense_Mutation	DNP	TG	TG	AC	novel	NA	P-0009789-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	182	610	3	ENST00000458235.1:c.913_914delinsGT	p.Gln305Val	p.Q305V	ENST00000458235	NM_000215.3	305	CAg/GTg	7/24	0.202658216636794	3	FACETS	0.766	0.713	0.82	0.766	0.713	0.82	INDETERMINATE	2	TRUE	1	0.624838622414027	3		613	499	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15938117	15938117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769360451	NA	P-0009789-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	22	243	0	ENST00000268712.3:c.7097C>T	p.Thr2366Met	p.T2366M	ENST00000268712	NM_006311.3	2366	aCg/aTg	45/46	0.553684504551844	1	FACETS	0.253	0.197	0.318	0.253	0.197	0.318	SUBCLONAL	1	TRUE	0	0.624838622414027	1		243	191	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426489	49426489	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009789-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	408	797	1	ENST00000301067.7:c.11999G>T	p.Gly4000Val	p.G4000V	ENST00000301067	NM_003482.3	4000	gGc/gTc	39/54	0.624838622414027	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.624838622414027	3		798	819	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238115	133238115	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009789-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	35	273	0	ENST00000320574.5:c.2862G>C	p.Lys954Asn	p.K954N	ENST00000320574	NM_006231.2	954	aaG/aaC	24/49	0.624838622414027	3	FACETS	0.447	0.367	0.536	0.223	0.183	0.268	SUBCLONAL	1	TRUE	1	0.624838622414027	3		273	329	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061637	38061637	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009789-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	129	143	0	ENST00000250448.2:c.352G>A	p.Ala118Thr	p.A118T	ENST00000250448	NM_004496.3	118	Gcg/Acg	2/2	0.624838622414027	6	FACETS	0.913	0.839	0.989			1	CLONAL	3	TRUE	NA	0.624838622414027	6		143	339	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658546	3658546	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs753015235	NA	P-0009789-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	103	628	0	ENST00000294008.3:c.420G>C	p.Glu140Asp	p.E140D	ENST00000294008	NM_032444.2	140	gaG/gaC	2/15	0.4285642607053	2	FACETS	0.55	0.493	0.611	0.275	0.246	0.306	SUBCLONAL	1	TRUE	0	0.624838622414027	2		628	599	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831770	72831770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009789-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	75	631	0	ENST00000268489.5:c.4811C>T	p.Ala1604Val	p.A1604V	ENST00000268489	NM_006885.3	1604	gCc/gTc	9/10	0.299770291900273	0	FACETS	0.263	0.232	0.296			1	INDETERMINATE	1	TRUE	0	0.624838622414027	0		631	342	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607721	46607721	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009789-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	131	723	0	ENST00000263734.3:c.1910C>G	p.Thr637Ser	p.T637S	ENST00000263734	NM_001430.4	637	aCc/aGc	12/16	1	2	FACETS	0.79	0.72	0.862	0.79	0.72	0.862	SUBCLONAL	1	TRUE	1	0.624838622414027	2		723	531	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374354	138374354	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009789-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	71	250	0	ENST00000289153.2:c.3090A>C	p.Leu1030Phe	p.L1030F	ENST00000289153	NM_006219.2	1030	ttA/ttC	22/22	0.624838622414027	4	FACETS	0.886	0.776	1	0.295	0.258	0.334	CLONAL	1	TRUE	1	0.624838622414027	4		250	417	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969071	93969071	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0009789-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	141	143	0	ENST00000369303.4:c.1924+1G>C		p.X642_splice	ENST00000369303	NM_004440.3	642			0.610265457331224	2	FACETS	0.998	0.937	1	0.998	0.937	1	CLONAL	2	TRUE	0	0.624838622414027	2		143	226	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956753	68956753	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009789-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	258	502	1	ENST00000288368.4:c.871G>T	p.Gly291Ter	p.G291*	ENST00000288368	NM_024870.2	291	Gga/Tga	8/40	0.549678684190073	6	FACETS	0.939	0.88	1	0.47	0.44	0.5	CLONAL	2	TRUE	2	0.624838622414027	6		503	989	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0010596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	967	430	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.786826394548046	10	FACETS	0.979	0.96	0.998	0.979	0.96	0.998	CLONAL	8	TRUE	2	0.786826394548046	10		430	1301	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0010596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	148	248	1				ENST00000310581	NM_198253.2	-/1132			0.650133164284803	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.786826394548046	4		249	303	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120501	94120501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760168204	NA	P-0010596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	246	404	0	ENST00000369303.4:c.550C>T	p.Leu184Phe	p.L184F	ENST00000369303	NM_004440.3	184	Ctt/Ttt	3/17	0.370228079895371	5	FACETS	0.874	0.826	0.922	0.874	0.826	0.922	INDETERMINATE	3	TRUE	2	0.786826394548046	5		404	520	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211536	46211536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	205	352	0	ENST00000334344.6:c.502G>A	p.Gly168Arg	p.G168R	ENST00000334344	NM_152641.2	168	Gga/Aga	5/21	0.460833855694617	5	FACETS	1	0.98	1			1	INDETERMINATE	2	TRUE	NA	0.786826394548046	5		352	510	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309776	104309776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202247756	NA	P-0010596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	394	685	0	ENST00000369902.3:c.367C>T	p.Arg123Cys	p.R123C	ENST00000369902	NM_016169.3	123	Cgt/Tgt	3/12	0.650133164284803	4	FACETS	0.986	0.942	1	0.986	0.942	1	CLONAL	2	TRUE	2	0.786826394548046	4		685	907	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36421162	36421162	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750755857	NA	P-0010596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	211	345	0	ENST00000300305.3:c.35C>T	p.Ser12Leu	p.S12L	ENST00000300305		12	tCg/tTg	1/8	0.650133164284803	4	FACETS	0.994	0.934	1	0.994	0.934	1	CLONAL	2	TRUE	2	0.786826394548046	4		345	482	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729175	66729175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908596	NA	P-0010596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	170	716	1	ENST00000307102.5:c.383G>A	p.Gly128Asp	p.G128D	ENST00000307102	NM_002755.3	128	gGc/gAc	3/11	0.786826394548046	3	FACETS	0.892	0.823	0.963	0.446	0.411	0.482	CLONAL	1	TRUE	1	0.786826394548046	3		717	675	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852319	63852319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1340574832	NA	P-0010596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	254	502	0	ENST00000279873.7:c.3097C>T	p.Pro1033Ser	p.P1033S	ENST00000279873	NM_032199.2	1033	Ccc/Tcc	10/10	0.650133164284803	4	FACETS	0.93	0.877	0.984	0.93	0.877	0.984	CLONAL	2	TRUE	2	0.786826394548046	4		502	620	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666615	206666615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	506	544	0	ENST00000367120.3:c.1949C>T	p.Ser650Phe	p.S650F	ENST00000367120	NM_014002.3	650	tCt/tTt	20/22	0.777862232708001	5	FACETS	0.953	0.924	0.981	0.953	0.924	0.981	CLONAL	4	TRUE	1	0.786826394548046	5		544	736	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967173	134967173	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370164002	NA	P-0010596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	86	349	0	ENST00000398015.3:c.2512G>A	p.Glu838Lys	p.E838K	ENST00000398015	NM_004441.4	838	Gag/Aag	14/16	0.786826394548046	3	FACETS	0.961	0.859	1	0.48	0.429	0.534	CLONAL	1	TRUE	1	0.786826394548046	3		349	317	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196241	106196241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	150	308	0	ENST00000380013.4:c.4574C>T	p.Ser1525Phe	p.S1525F	ENST00000380013	NM_001127208.2	1525	tCc/tTc	11/11	0.687580067805509	4	FACETS	0.976	0.905	1	0.976	0.905	1	CLONAL	2	TRUE	2	0.786826394548046	4		308	349	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861010	35861010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	228	438	0	ENST00000303115.3:c.139G>A	p.Glu47Lys	p.E47K	ENST00000303115	NM_002185.3	47	Gaa/Aaa	2/8	0.650133164284803	4	FACETS	0.899	0.844	0.954	0.899	0.844	0.954	CLONAL	2	TRUE	2	0.786826394548046	4		438	576	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319853	8319853	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	274	464	0	ENST00000356435.5:c.5648G>A	p.Arg1883Gln	p.R1883Q	ENST00000356435		1883	cGa/cAa	34/35	0.370228079895371	5	FACETS	1	0.982	1	0.728	0.688	0.769	INDETERMINATE	2	TRUE	2	0.786826394548046	5		464	695	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250139	110250139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs965501282	NA	P-0010596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	251	545	0	ENST00000374672.4:c.536C>T	p.Pro179Leu	p.P179L	ENST00000374672	NM_004235.4	179	cCc/cTc	3/5	0.77589966129148	2	FACETS	0.994	0.958	1	0.994	0.958	1	CLONAL	2	TRUE	0	0.786826394548046	2		545	321	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160419	108160419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555097538	NA	P-0010596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	581	563	1	ENST00000278616.4:c.4327C>T	p.His1443Tyr	p.H1443Y	ENST00000278616	NM_000051.3	1443	Cac/Tac	29/63	0.766682597217824	3	FACETS	0.987	0.966	1	0.987	0.966	1	CLONAL	3	TRUE	0	0.786826394548046	3		564	695	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244380	46244380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	305	528	0	ENST00000334344.6:c.2474C>T	p.Ser825Leu	p.S825L	ENST00000334344	NM_152641.2	825	tCa/tTa	15/21	0.460833855694617	5	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.786826394548046	5		528	693	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73340179	73340179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	184	310	1	ENST00000377767.4:c.1901C>T	p.Ser634Phe	p.S634F	ENST00000377767	NM_014953.3	634	tCt/tTt	15/21	0.687580067805509	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	2	0.786826394548046	4		311	405	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028709	42028709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	170	640	0	ENST00000219905.7:c.4247C>T	p.Thr1416Ile	p.T1416I	ENST00000219905	NM_001164273.1	1416	aCt/aTt	13/24	0.786826394548046	3	FACETS	1	0.965	1	0.537	0.496	0.578	CLONAL	1	TRUE	1	0.786826394548046	3		640	561	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782214	56782214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	248	435	0	ENST00000308159.5:c.55G>A	p.Glu19Lys	p.E19K	ENST00000308159	NM_014669.4	19	Gag/Aag	2/22	0.598087821844679	3	FACETS	0.97	0.92	1	0.97	0.92	1	CLONAL	2	TRUE	1	0.786826394548046	3		435	453	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81916938	81916938	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	169	546	0	ENST00000359376.3:c.757G>A	p.Glu253Lys	p.E253K	ENST00000359376	NM_002661.3	253	Gaa/Aaa	9/33	0.20711206577593	2	FACETS	0.809	0.749	0.871	0.404	0.374	0.436	INDETERMINATE	1	TRUE	0	0.786826394548046	2		546	531	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7218299	7218299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	245	447	0	ENST00000380728.2:c.73G>A	p.Glu25Lys	p.E25K	ENST00000380728		25	Gag/Aag	2/11	0.786826394548046	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.786826394548046	3		447	418	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243954	5243954	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	153	470	0	ENST00000357368.4:c.1528G>T	p.Gly510Trp	p.G510W	ENST00000357368	NM_002850.3	510	Ggg/Tgg	11/38	0.768151286632897	3	FACETS	1	0.969	1	0.55	0.506	0.594	CLONAL	1	TRUE	1	0.786826394548046	3		470	493	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793099	42793099	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	337	665	0	ENST00000575354.2:c.991C>T	p.Pro331Ser	p.P331S	ENST00000575354	NM_015125.3	331	Ccg/Tcg	7/20	0.763843358388315	2	FACETS	0.948	0.916	0.978	0.948	0.916	0.978	CLONAL	2	TRUE	0	0.786826394548046	2		665	452	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023135	27023135	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	11	25	0	ENST00000324856.7:c.245del	p.Gly82ValfsTer19	p.G82Vfs*19	ENST00000324856	NM_006015.4	81	Ggg/gg	1/20	0.786826394548046	3	FACETS	0.999	0.718	1	0.499	0.359	0.658	CLONAL	1	TRUE	1	0.786826394548046	3		25	39	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056265	26056266	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0010596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	364	572	0	ENST00000343677.2:c.391_392delinsTT	p.Pro131Leu	p.P131L	ENST00000343677	NM_005319.3	131	CCa/TTa	1/1	0.528626958529065	6	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	3	0.786826394548046	6		572	757	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309968	30309969	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0010596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	293	546	1	ENST00000307677.4:c.53_54delinsTT	p.Ser18Phe	p.S18F	ENST00000307677	NM_138578.1	18	tCC/tTT	2/3	0.687580067805509	4	FACETS	0.937	0.888	0.987	0.937	0.888	0.987	CLONAL	2	TRUE	2	0.786826394548046	4		547	710	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945102	151945102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	95	626	0	ENST00000262189.6:c.2417C>T	p.Ser806Phe	p.S806F	ENST00000262189	NM_170606.2	806	tCc/tTc	14/59	0.786826394548046	10	FACETS	1	0.952	1	0.141	0.125	0.159	CLONAL	1	TRUE	2	0.786826394548046	10		626	885	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347548	118347548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	378	436	0	ENST00000534358.1:c.3185C>T	p.Ser1062Phe	p.S1062F	ENST00000534358	NM_005933.3	1062	tCt/tTt	4/36	0.766682597217824	3	FACETS	0.938	0.911	0.963	0.938	0.911	0.963	CLONAL	3	TRUE	0	0.786826394548046	3		436	476	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607459	46607459	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771840848	NA	P-0010596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	223	720	2	ENST00000263734.3:c.1648C>T	p.Arg550Trp	p.R550W	ENST00000263734	NM_001430.4	550	Cgg/Tgg	12/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.786826394548046	2		722	535	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878038	151878038	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	214	422	0	ENST00000262189.6:c.6907C>T	p.Pro2303Ser	p.P2303S	ENST00000262189	NM_170606.2	2303	Cca/Tca	36/59	0.786826394548046	10	FACETS	0.953	0.885	1	0.238	0.221	0.257	CLONAL	2	TRUE	2	0.786826394548046	10		422	1183	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884925	151884926	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	C	novel	NA	P-0010596-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	624	295	1	ENST00000262189.6:c.4667_4668delinsG	p.Phe1556CysfsTer7	p.F1556Cfs*7	ENST00000262189	NM_170606.2	1556	tTT/tG	32/59	0.786826394548046	10	FACETS	1	0.992	1	0.921	0.896	0.945	CLONAL	7	TRUE	2	0.786826394548046	10		296	893	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0011104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	47	265	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.903	0.764	1	0.903	0.764	1	CLONAL	1	TRUE	1	0.267581978810985	2		265	389	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453134	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913364	NA	P-0011104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	48	399	0	ENST00000288602.6:c.1801A>G	p.Lys601Glu	p.K601E	ENST00000288602	NM_004333.4	601	Aaa/Gaa	15/18	1	2	FACETS	0.959	0.813	1	0.959	0.813	1	CLONAL	1	TRUE	1	0.267581978810985	2		399	374	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088788	27088788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	77	565	0	ENST00000324856.7:c.2402del	p.Gly801ValfsTer32	p.G801Vfs*32	ENST00000324856	NM_006015.4	799	caG/ca	7/20	0.267581978810985	1	FACETS	0.652	0.571	0.738	0.652	0.571	0.738	SUBCLONAL	1	TRUE	0	0.267581978810985	1		565	765	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163910	47163910	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs539008365	NA	P-0011104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	62	469	0	ENST00000409792.3:c.2216A>G	p.His739Arg	p.H739R	ENST00000409792	NM_014159.6	739	cAt/cGt	3/21	1	2	FACETS	0.927	0.802	1	0.927	0.802	1	CLONAL	1	TRUE	1	0.267581978810985	2		469	500	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109908	115109908	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011104-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	86	429	0	ENST00000257566.3:c.1970C>G	p.Thr657Ser	p.T657S	ENST00000257566	NM_016569.3	657	aCc/aGc	8/8	1	2	FACETS	0.775	0.685	0.872	0.775	0.685	0.872	SUBCLONAL	1	TRUE	1	0.267581978810985	2		429	829	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0012428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	96	1058	3	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.801	0.713	0.895	0.801	0.713	0.895	CLONAL	1	TRUE	1	0.277754161941182	2		1061	863	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177636	56177636	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	85	323	0	ENST00000399503.3:c.2609A>T	p.Gln870Leu	p.Q870L	ENST00000399503	NM_005921.1	870	cAg/cTg	14/20	0.207685459526089	2	FACETS	1	0.965	1	0.615	0.545	0.689	CLONAL	1	TRUE	0	0.277754161941182	2		323	498	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032254	26032254	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012428-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	39	190	0	ENST00000244661.2:c.35C>T	p.Thr12Ile	p.T12I	ENST00000244661	NM_003537.3	12	aCc/aTc	1/1	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.277754161941182	2		190	269	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453145	140453146	+	missense_variant	Missense_Mutation	DNP	AG	AG	GA	rs121913368	NA	P-0013389-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	740	445	1	ENST00000288602.6:c.1789_1790delinsTC	p.Leu597Ser	p.L597S	ENST00000288602	NM_004333.4	597	CTa/TCa	15/18	0.595115965922856	5	FACETS	0.923	0.896	0.949	0.923	0.896	0.949	CLONAL	4	TRUE	1	0.595115965922856	5		446	1275	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189585683	189585683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013389-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	255	509	0	ENST00000264731.3:c.944G>A	p.Gly315Glu	p.G315E	ENST00000264731	NM_003722.4	315	gGg/gAg	7/14	0.186071986373271	4	FACETS	1	0.992	1	0.718	0.673	0.764	INDETERMINATE	1	TRUE	2	0.595115965922856	4		509	952	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501306	140501306	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013389-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	780	385	0	ENST00000288602.6:c.766T>C	p.Phe256Leu	p.F256L	ENST00000288602	NM_004333.4	256	Ttc/Ctc	6/18	0.595115965922856	5	FACETS	0.977	0.95	1	0.977	0.95	1	CLONAL	4	TRUE	1	0.595115965922856	5		385	1270	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310916	123310916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013389-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	265	617	4	ENST00000358487.5:c.512C>T	p.Ala171Val	p.A171V	ENST00000358487	NM_000141.4	171	gCg/gTg	5/18	0.239003645269071	1	FACETS	0.739	0.695	0.785	0.739	0.695	0.785	INDETERMINATE	1	TRUE	0	0.595115965922856	1		621	846	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922006	39922006	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs775698427	NA	P-0013389-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	389	476	0	ENST00000378444.4:c.4166A>G	p.Asp1389Gly	p.D1389G	ENST00000378444	NM_001123385.1	1389	gAt/gGt	9/15	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.595115965922856	1		476	695	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792120	42792121	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0013389-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	118	212	0	ENST00000575354.2:c.924_925delinsTT	p.Pro309Ser	p.P309S	ENST00000575354	NM_015125.3	308	gcCCct/gcTTct	6/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.595115965922856	2		212	353	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0013845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	284	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.351650507512681	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.420955460791274	4		288	838	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637948	39637948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013845-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	152	535	0	ENST00000262039.4:c.2365G>A	p.Gly789Ser	p.G789S	ENST00000262039	NM_002647.2	789	Ggc/Agc	22/25	1	2	FACETS	0.934	0.856	1	0.934	0.856	1	CLONAL	1	TRUE	1	0.420955460791274	2		535	773	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0014242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	262	306	0				ENST00000310581	NM_198253.2	-/1132			0.544518767414669	5	FACETS	1	0.988	1	1	0.988	1	CLONAL	4	TRUE	1	0.544518767414669	5		306	398	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0014242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	485	226	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.544518767414669	6	FACETS	0.932	0.9	0.963	1	0.995	1	CLONAL	5	TRUE	2	0.544518767414669	6		226	799	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0014242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	108	552	0	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.544518767414669	2		552	380	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561520	9561520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	138	748	0	ENST00000353224.5:c.262G>A	p.Asp88Asn	p.D88N	ENST00000353224	NM_177990.2	88	Gat/Aat	4/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.544518767414669	2		748	453	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258580	16258580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749892338	NA	P-0014242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	110	584	0	ENST00000375759.3:c.5845C>T	p.Arg1949Trp	p.R1949W	ENST00000375759	NM_015001.2	1949	Cgg/Tgg	11/15	0.199007565992584	1	FACETS	0.905	0.823	0.989	0.905	0.823	0.989	INDETERMINATE	1	TRUE	0	0.544518767414669	1		584	325	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873660	35873660	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs201559094	NA	P-0014242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	55	484	0	ENST00000303115.3:c.616C>T	p.Arg206Ter	p.R206*	ENST00000303115	NM_002185.3	206	Cga/Tga	5/8	0.544518767414669	5	FACETS	0.717	0.614	0.83	0.179	0.153	0.208	SUBCLONAL	1	TRUE	1	0.544518767414669	5		484	512	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55575658	55575658	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	120	770	1	ENST00000288135.5:c.1184C>T	p.Ser395Phe	p.S395F	ENST00000288135	NM_000222.2	395	tCc/tTc	7/21	0.199007565992584	1	FACETS	0.731	0.665	0.799	0.731	0.665	0.799	INDETERMINATE	1	TRUE	0	0.544518767414669	1		771	439	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496924	29496927	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs786201874	NA	P-0014242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	71	532	0	ENST00000356175.3:c.499_502del	p.Cys167GlnfsTer10	p.C167Qfs*10	ENST00000356175	NM_000267.3	165	acTGTT/ac	5/57	0.544518767414669	1	FACETS	0.666	0.587	0.749	0.666	0.587	0.749	SUBCLONAL	1	TRUE	0	0.544518767414669	1		532	285	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381514	81381514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	91	539	0	ENST00000222390.5:c.547G>A	p.Glu183Lys	p.E183K	ENST00000222390	NM_000601.4	183	Gaa/Aaa	5/18	1	2	FACETS	0.923	0.827	1	0.923	0.827	1	CLONAL	1	TRUE	1	0.544518767414669	2		539	362	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599234	28599234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763645640	NA	P-0014242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	142	907	2	ENST00000253063.3:c.680C>T	p.Ala227Val	p.A227V	ENST00000253063	NM_031459.4	227	gCc/gTc	5/10	0.199007565992584	1	FACETS	0.933	0.859	1	0.933	0.859	1	INDETERMINATE	1	TRUE	0	0.544518767414669	1		909	407	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458800	120458800	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	141	778	0	ENST00000256646.2:c.6545C>T	p.Pro2182Leu	p.P2182L	ENST00000256646	NM_024408.3	2182	cCt/cTt	34/34	0.544518767414669	6	FACETS	1	0.98	1	0.316	0.288	0.346	CLONAL	1	TRUE	2	0.544518767414669	6		778	856	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601977	43601977	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	156	890	0	ENST00000355710.3:c.1021C>T	p.Gln341Ter	p.Q341*	ENST00000355710	NM_020975.4	341	Cag/Tag	5/20	0.481877039625683	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.544518767414669	1		890	374	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405212	70405212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	145	731	0	ENST00000373644.4:c.2726C>T	p.Ser909Phe	p.S909F	ENST00000373644	NM_030625.2	909	tCc/tTc	4/12	0.481877039625683	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.544518767414669	1		731	343	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027169	49027169	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751560923	NA	P-0014242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	161	790	0	ENST00000267163.4:c.1736G>A	p.Arg579Gln	p.R579Q	ENST00000267163	NM_000321.2	579	cGa/cAa	18/27	0.392573743639736	3	FACETS	0.772	0.714	0.832	0.772	0.714	0.832	SUBCLONAL	2	TRUE	1	0.544518767414669	3		790	487	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527940	103527940	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	114	563	0	ENST00000355739.4:c.3248C>A	p.Thr1083Lys	p.T1083K	ENST00000355739	NM_000123.3	1083	aCa/aAa	15/15	1	2	FACETS	0.949	0.861	1	0.949	0.861	1	CLONAL	1	TRUE	1	0.544518767414669	2		563	441	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290228	15290228	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	118	1024	0	ENST00000263388.2:c.3407C>T	p.Ser1136Leu	p.S1136L	ENST00000263388	NM_000435.2	1136	tCa/tTa	21/33	1	2	FACETS	0.924	0.839	1	0.924	0.839	1	CLONAL	1	TRUE	1	0.544518767414669	2		1024	469	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637479	47637479	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	95	574	0	ENST00000233146.2:c.613G>A	p.Glu205Lys	p.E205K	ENST00000233146	NM_000251.2	205	Gag/Aag	3/16	1	2	FACETS	0.938	0.842	1	0.938	0.842	1	CLONAL	1	TRUE	1	0.544518767414669	2		574	372	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273135	198273135	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	152	864	0	ENST00000335508.6:c.1075C>T	p.Pro359Ser	p.P359S	ENST00000335508	NM_012433.2	359	Cca/Tca	8/25	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.544518767414669	2		864	506	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113155	209113155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371567806	NA	P-0014242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	84	573	0	ENST00000345146.2:c.352C>T	p.Pro118Ser	p.P118S	ENST00000345146	NM_005896.2	118	Ccc/Tcc	4/10	1	2	FACETS	0.924	0.823	1	0.924	0.823	1	CLONAL	1	TRUE	1	0.544518767414669	2		573	334	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385068	31385068	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	111	737	1	ENST00000328111.2:c.1453C>T	p.Arg485Ter	p.R485*	ENST00000328111	NM_006892.3	485	Cga/Tga	14/23	1	2	FACETS	0.978	0.886	1	0.978	0.886	1	CLONAL	1	TRUE	1	0.544518767414669	2		738	417	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485864	57485864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	74	489	1	ENST00000371085.3:c.1165C>T	p.Arg389Cys	p.R389C	ENST00000371085	NM_000516.4	389	Cgt/Tgt	13/13	1	2	FACETS	0.836	0.738	0.94	0.836	0.738	0.94	CLONAL	1	TRUE	1	0.544518767414669	2		490	325	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032752	30032752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	221	507	0	ENST00000338641.4:c.127G>A	p.Gly43Arg	p.G43R	ENST00000338641	NM_000268.3	43	Ggg/Agg	2/16	0.495026909425511	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.544518767414669	3		507	464	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702657	52702657	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	76	531	2	ENST00000394830.3:c.241C>T	p.Gln81Ter	p.Q81*	ENST00000394830	NM_018313.4	81	Caa/Taa	4/30	0.544518767414669	1	FACETS	0.797	0.708	0.889	0.797	0.708	0.889	SUBCLONAL	1	TRUE	0	0.544518767414669	1		533	255	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259571	89259571	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	76	479	0	ENST00000336596.2:c.715C>T	p.Pro239Ser	p.P239S	ENST00000336596	NM_005233.5	239	Cct/Tct	3/17	1	2	FACETS	0.99	0.878	1	0.99	0.878	1	CLONAL	1	TRUE	1	0.544518767414669	2		479	282	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851633	134851633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	98	604	0	ENST00000398015.3:c.1039G>A	p.Glu347Lys	p.E347K	ENST00000398015	NM_004441.4	347	Gag/Aag	5/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.544518767414669	2		604	303	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280395	1280395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747940807	NA	P-0014242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	114	797	5	ENST00000310581.5:c.1828C>T	p.Arg610Trp	p.R610W	ENST00000310581	NM_198253.2	610	Cgg/Tgg	4/16	0.544518767414669	5	FACETS	0.998	0.899	1	0.25	0.224	0.276	CLONAL	1	TRUE	1	0.544518767414669	5		802	762	SUCCESS
APC	324	MSKCC	GRCh37	5	112177943	112177943	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	127	639	0	ENST00000257430.4:c.6652C>T	p.Gln2218Ter	p.Q2218*	ENST00000257430	NM_000038.5	2218	Caa/Taa	16/16	0.544518767414669	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.544518767414669	1		639	294	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120359	94120359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778087526	NA	P-0014242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	86	393	0	ENST00000369303.4:c.692G>A	p.Arg231Gln	p.R231Q	ENST00000369303	NM_004440.3	231	cGa/cAa	3/17	0.544518767414669	1	FACETS	0.999	0.9	1	0.999	0.9	1	CLONAL	1	TRUE	0	0.544518767414669	1		393	230	SUCCESS
REL	5966	MSKCC	GRCh37	2	61121604	61121604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	29	646	0	ENST00000295025.8:c.226C>T	p.Pro76Ser	p.P76S	ENST00000295025	NM_002908.2	76	Cct/Tct	3/11	1	2	FACETS	0.27	0.216	0.331	0.27	0.216	0.331	SUBCLONAL	1	TRUE	1	0.544518767414669	2		646	395	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228433	228433	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223320182	NA	P-0014242-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	105	548	0	ENST00000264932.6:c.755C>T	p.Thr252Ile	p.T252I	ENST00000264932	NM_004168.2	252	aCt/aTt	6/15	0.544518767414669	5	FACETS	0.979	0.877	1	0.245	0.219	0.272	CLONAL	1	TRUE	1	0.544518767414669	5		548	716	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0014666-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	182	306	0				ENST00000310581	NM_198253.2	-/1132			0.791093949955955	3	FACETS	1	0.978	1			1	CLONAL	2	TRUE	NA	0.791093949955955	3		306	299	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578476	7578476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767328513	NA	P-0014666-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	200	550	2	ENST00000269305.4:c.454C>T	p.Pro152Ser	p.P152S	ENST00000269305	NM_001126112.2	152	Ccg/Tcg	5/11	0.765644111059073	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.791093949955955	1		552	294	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000018	42000018	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014666-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	177	692	0	ENST00000219905.7:c.2281C>T	p.Pro761Ser	p.P761S	ENST00000219905	NM_001164273.1	761	Cct/Tct	6/24	1	2	FACETS	0.988	0.92	1	0.988	0.92	1	CLONAL	1	TRUE	1	0.791093949955955	2		692	453	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852503	42852503	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014666-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	169	474	0	ENST00000398585.3:c.583C>T	p.Leu195Phe	p.L195F	ENST00000398585	NM_001135099.1	195	Ctt/Ttt	6/14	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.791093949955955	2		474	388	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678806	52678806	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0014666-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	172	177	0	ENST00000394830.3:c.814-1G>A		p.X272_splice	ENST00000394830	NM_018313.4	272			0.783804594616121	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.791093949955955	2		177	199	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196870	106196870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014666-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	80	258	0	ENST00000380013.4:c.5203G>A	p.Gly1735Arg	p.G1735R	ENST00000380013	NM_001127208.2	1735	Gga/Aga	11/11	1	2	FACETS	0.968	0.869	1	0.968	0.869	1	CLONAL	1	TRUE	1	0.791093949955955	2		258	209	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515361	149515361	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1021692167	NA	P-0014666-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	133	375	0	ENST00000261799.4:c.121G>A	p.Glu41Lys	p.E41K	ENST00000261799	NM_002609.3	41	Gag/Aag	3/23	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.791093949955955	2		375	322	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416680	121416680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014808-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	77	770	0	ENST00000257555.6:c.109C>T	p.Leu37Phe	p.L37F	ENST00000257555		37	Ctc/Ttc	1/10	0.681819601133459	4	FACETS	0.942	0.833	1	0.471	0.416	0.529	CLONAL	1	TRUE	2	0.791380534467976	4		770	370	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520126	9520126	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014808-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	55	335	0	ENST00000353224.5:c.2143C>A	p.Gln715Lys	p.Q715K	ENST00000353224	NM_177990.2	715	Caa/Aaa	10/10	0.791380534467976	3	FACETS	0.819	0.708	0.936	0.409	0.354	0.468	CLONAL	1	TRUE	1	0.791380534467976	3		335	237	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927018	131927018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753680691	NA	P-0014808-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	46	169	0	ENST00000265335.6:c.1555C>T	p.Arg519Cys	p.R519C	ENST00000265335		519	Cgt/Tgt	10/25	0.791380534467976	4	FACETS	1	0.909	1	0.363	0.31	0.421	CLONAL	1	TRUE	1	0.791380534467976	4		169	191	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321008	30321008	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014808-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	67	262	0	ENST00000322652.5:c.1418G>C	p.Arg473Thr	p.R473T	ENST00000322652	NM_015355.2	473	aGa/aCa	12/16	0.700882583559698	6	FACETS	0.934	0.823	1	0.623	0.549	0.701	CLONAL	2	TRUE	3	0.791380534467976	6		262	234	SUCCESS
AR	367	MSKCC	GRCh37	X	66765949	66765949	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014808-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	98	736	0	ENST00000374690.3:c.961G>A	p.Glu321Lys	p.E321K	ENST00000374690	NM_000044.3	321	Gaa/Aaa	1/8	0.335122502895183	5	FACETS	0.865	0.781	0.953	0.577	0.521	0.635	INDETERMINATE	2	TRUE	2	0.791380534467976	5		736	313	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217372	123217372	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014808-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	30	312	0	ENST00000218089.9:c.3026A>C	p.Lys1009Thr	p.K1009T	ENST00000218089	NM_001042749.1	1009	aAa/aCa	29/35	0.335122502895183	5	FACETS	0.754	0.611	0.913	0.251	0.203	0.305	INDETERMINATE	1	TRUE	2	0.791380534467976	5		312	220	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0015007-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	312	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.886675091202313	4	FACETS	0.901	0.855	0.947	0.901	0.855	0.947	CLONAL	2	TRUE	2	0.886675091202313	4		288	737	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015007-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	224	151	0				ENST00000310581	NM_198253.2	-/1132			0.738257075719463	2	FACETS	0.964	0.933	0.992	0.964	0.933	0.992	CLONAL	2	TRUE	0	0.886675091202313	2		151	262	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851426	156851426	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015007-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	435	520	0	ENST00000524377.1:c.2383C>A	p.Leu795Met	p.L795M	ENST00000524377	NM_002529.3	795	Ctg/Atg	17/17	0.571789090759869	4	FACETS	0.981	0.939	1			1	CLONAL	2	TRUE	NA	0.886675091202313	4		520	944	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624273	89624274	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015007-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	362	374	0	ENST00000371953.3:c.48dup	p.Gln17SerfsTer27	p.Q17Sfs*27	ENST00000371953	NM_000314.4	16	tat/taTt	1/9	0.886675091202313	2	FACETS	0.972	0.948	0.994	0.972	0.948	0.994	CLONAL	2	TRUE	0	0.886675091202313	2		374	420	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416895	416895	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015007-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	435	467	0	ENST00000399788.2:c.3655C>T	p.Arg1219Ter	p.R1219*	ENST00000399788	NM_001042603.1	1219	Cga/Tga	23/28	0.886675091202313	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.886675091202313	4		467	868	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184333	7184333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015007-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	403	520	0	ENST00000302850.5:c.968C>T	p.Ser323Phe	p.S323F	ENST00000302850	NM_000208.2	323	tCc/tTc	3/22	0.886675091202313	4	FACETS	0.937	0.896	0.979	0.937	0.896	0.979	CLONAL	2	TRUE	2	0.886675091202313	4		520	915	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434057	49434057	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015007-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	342	431	1	ENST00000301067.7:c.7496C>T	p.Pro2499Leu	p.P2499L	ENST00000301067	NM_003482.3	2499	cCc/cTc	31/54	0.886675091202313	4	FACETS	0.953	0.907	0.998	0.953	0.907	0.998	CLONAL	2	TRUE	2	0.886675091202313	4		432	764	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0015679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	352	430	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.832745316661187	6	FACETS	0.98	0.941	1	0.784	0.752	0.815	CLONAL	4	TRUE	1	0.832745316661187	6		430	575	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913492	NA	P-0015679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	178	656	0	ENST00000286548.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000286548	NM_002072.3	209	cAa/cTa	5/7	0.832745316661187	3	FACETS	0.884	0.817	0.953	0.442	0.408	0.477	CLONAL	1	TRUE	1	0.832745316661187	3		656	685	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717769	89717770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	159	235	0	ENST00000371953.3:c.800dup	p.Asp268GlyfsTer30	p.D268Gfs*30	ENST00000371953	NM_000314.4	265	cta/ctAa	7/9	0.820269345702063	2	FACETS	0.868	0.824	0.91	0.868	0.824	0.91	CLONAL	2	TRUE	0	0.832745316661187	2		235	220	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662691	117662691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368206665	NA	P-0015679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	292	413	0	ENST00000368508.3:c.4774C>T	p.Arg1592Cys	p.R1592C	ENST00000368508	NM_002944.2	1592	Cgt/Tgt	29/43	0.811149958347048	2	FACETS	0.958	0.927	0.987	0.958	0.927	0.987	CLONAL	2	TRUE	0	0.832745316661187	2		413	366	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562798	95562799	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1131691197	NA	P-0015679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	108	375	1	ENST00000393063.1:c.4458dup	p.Ser1487IlefsTer5	p.S1487Ifs*5	ENST00000393063	NM_030621.3	1486	-/A	24/28	1	2	FACETS	0.99	0.904	1	0.99	0.904	1	CLONAL	1	TRUE	1	0.832745316661187	2		376	262	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168513	56168513	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	94	230	0	ENST00000399503.3:c.1469T>A	p.Leu490His	p.L490H	ENST00000399503	NM_005921.1	490	cTt/cAt	8/20	0.702781112240469	3	FACETS	1	0.917	1	0.511	0.459	0.564	CLONAL	1	TRUE	1	0.832745316661187	3		230	313	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956729	68956729	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	196	544	0	ENST00000288368.4:c.847A>G	p.Lys283Glu	p.K283E	ENST00000288368	NM_024870.2	283	Aag/Gag	8/40	0.832745316661187	3	FACETS	0.921	0.855	0.989	0.46	0.427	0.495	CLONAL	1	TRUE	1	0.832745316661187	3		544	724	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94163081	94163081	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	23	418	0	ENST00000323929.3:c.2066G>C	p.Ser689Thr	p.S689T	ENST00000323929	NM_005591.3	689	aGt/aCt	19/20	NA	2	FACETS	0.19	0.148	0.239			1	INDETERMINATE	1	TRUE	NA	0.832745316661187	2		418	290	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437193	220437193	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	77	1362	0	ENST00000243786.2:c.97G>T	p.Val33Leu	p.V33L	ENST00000243786	NM_002191.3	33	Gtg/Ttg	1/2	1	2	FACETS	0.184	0.161	0.209	0.184	0.161	0.209	SUBCLONAL	1	TRUE	1	0.832745316661187	2		1362	1006	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920262	1920262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	39	667	0	ENST00000382891.5:c.1322G>A	p.Arg441Lys	p.R441K	ENST00000382891	NM_133335.3	441	aGg/aAg	5/22	0.480815866545005	4	FACETS	0.233	0.192	0.279	0.078	0.064	0.093	INDETERMINATE	1	TRUE	1	0.832745316661187	4		667	737	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118353185	118353185	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	111	465	0	ENST00000534358.1:c.4061C>G	p.Pro1354Arg	p.P1354R	ENST00000534358	NM_005933.3	1354	cCt/cGt	8/36	1	2	FACETS	0.673	0.604	0.747	0.673	0.604	0.747	SUBCLONAL	1	FALSE	1	0.3	2		465	1099	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944593	38944593	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1719	261	498	0	ENST00000357387.3:c.4868del	p.Leu1623Ter	p.L1623*	ENST00000357387	NM_152756.3	1623	tTg/tg	36/38	0.3	6	FACETS	1	0.991	1			1	CLONAL	1	FALSE	NA	0.3	6		498	1980	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118353185	118353185	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015717-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	97	465	0	ENST00000534358.1:c.4061C>G	p.Pro1354Arg	p.P1354R	ENST00000534358	NM_005933.3	1354	cCt/cGt	8/36	1	2	FACETS	0.774	0.688	0.865	0.774	0.688	0.865	SUBCLONAL	1	TRUE	1	0.24	2		465	1045	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944593	38944593	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015717-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2112	290	498	0	ENST00000357387.3:c.4868del	p.Leu1623Ter	p.L1623*	ENST00000357387	NM_152756.3	1623	tTg/tg	36/38	0.3	9	FACETS	0.926	0.866	0.987	0.264	0.247	0.282	CLONAL	2	TRUE	2	0.24	9		498	2402	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0015855-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	573	528	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.805505758850039	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.812135875136941	2		528	690	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0015855-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	181	248	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.984	0.917	1	0.984	0.917	1	CLONAL	1	TRUE	1	0.812135875136941	2		249	453	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074439	39074439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1298143494	NA	P-0015855-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	201	444	0	ENST00000357387.3:c.41G>A	p.Arg14Gln	p.R14Q	ENST00000357387	NM_152756.3	14	cGa/cAa	1/38	1	2	FACETS	0.945	0.883	1	0.945	0.883	1	CLONAL	1	TRUE	1	0.812135875136941	2		444	524	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227888	55227888	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1226827460	NA	P-0015855-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	154	262	0	ENST00000275493.2:c.1355C>T	p.Ser452Phe	p.S452F	ENST00000275493	NM_005228.3	452	tCc/tTc	12/28	1	2	FACETS	0.909	0.841	0.979	0.909	0.841	0.979	CLONAL	1	TRUE	1	0.812135875136941	2		262	417	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692914	89692915	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AATG	novel	NA	P-0015855-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	169	344	0	ENST00000371953.3:c.400_403dup	p.Ile135AsnfsTer46	p.I135Nfs*46	ENST00000371953	NM_000314.4	133	gta/gtAATGa	5/9	0.795779425854319	1	FACETS	0.997	0.944	1	0.997	0.944	1	CLONAL	1	TRUE	0	0.812135875136941	1		344	248	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218970	133218970	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015855-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	349	615	0	ENST00000320574.5:c.4966C>T	p.Pro1656Ser	p.P1656S	ENST00000320574	NM_006231.2	1656	Ccc/Tcc	38/49	1	2	FACETS	0.998	0.949	1	0.998	0.949	1	CLONAL	1	TRUE	1	0.812135875136941	2		615	861	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273289	18273289	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015855-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	212	383	0	ENST00000222254.8:c.1082T>A	p.Ile361Asn	p.I361N	ENST00000222254	NM_005027.3	361	aTc/aAc	9/16	1	2	FACETS	0.934	0.874	0.994	0.934	0.874	0.994	CLONAL	1	TRUE	1	0.812135875136941	2		383	559	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274712	198274712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015855-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	206	343	0	ENST00000335508.6:c.686C>T	p.Ser229Phe	p.S229F	ENST00000335508	NM_012433.2	229	tCc/tTc	7/25	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.812135875136941	2		343	479	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652797	212652798	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015855-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	67	323	1	ENST00000342788.4:c.508_509delinsTT	p.Pro170Leu	p.P170L	ENST00000342788	NM_005235.2	170	CCa/TTa	4/28	1	2	FACETS	0.833	0.737	0.933	0.833	0.737	0.933	CLONAL	1	TRUE	1	0.812135875136941	2		324	198	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543904	41543905	+	missense_variant	Missense_Mutation	DNP	CT	CT	TA	novel	NA	P-0015855-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	273	496	0	ENST00000263253.7:c.2195_2196delinsTA	p.Pro732Leu	p.P732L	ENST00000263253	NM_001429.3	732	cCT/cTA	12/31	0.577077544271258	3	FACETS	1	0.962	1			1	CLONAL	1	TRUE	NA	0.812135875136941	3		496	917	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39002707	39002707	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015855-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	189	307	0	ENST00000357387.3:c.322C>T	p.Arg108Ter	p.R108*	ENST00000357387	NM_152756.3	108	Cga/Tga	5/38	1	2	FACETS	0.997	0.931	1	0.997	0.931	1	CLONAL	1	TRUE	1	0.812135875136941	2		307	467	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528050	157528051	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015855-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	222	414	1	ENST00000346085.5:c.5775_5776delinsTT	p.Arg1926Ter	p.R1926*	ENST00000346085	NM_020732.3	1925	agCCga/agTTga	20/20	1	2	FACETS	0.938	0.879	0.997	0.938	0.879	0.997	CLONAL	1	TRUE	1	0.812135875136941	2		415	583	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534542	140534542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015855-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	201	313	0	ENST00000288602.6:c.371C>T	p.Ser124Phe	p.S124F	ENST00000288602	NM_004333.4	124	tCc/tTc	3/18	1	2	FACETS	0.925	0.865	0.987	0.925	0.865	0.987	CLONAL	1	TRUE	1	0.812135875136941	2		313	535	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638755	176638755	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015855-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	148	479	0	ENST00000439151.2:c.3356del	p.Pro1119LeufsTer22	p.P1119Lfs*22	ENST00000439151	NM_022455.4	1119	Cct/ct	5/23	0.795779425854319	1	FACETS	0.555	0.513	0.598	0.555	0.513	0.598	SUBCLONAL	1	TRUE	0	0.812135875136941	1		479	390	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0016533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	930	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.712392095780528	4	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	1	0.712392095780528	4		288	1352	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858585	9858585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	188	396	0	ENST00000330684.3:c.2816G>A	p.Gly939Glu	p.G939E	ENST00000330684	NM_001134407.1	939	gGg/gAg	13/13	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.712392095780528	2		396	438	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851675	63851676	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0016533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	323	583	0	ENST00000279873.7:c.2453_2454delinsTT	p.Ala818Val	p.A818V	ENST00000279873	NM_032199.2	818	gCC/gTT	10/10	0.166657627935036	6	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.712392095780528	6		583	933	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858558	57858558	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	412	589	0	ENST00000228682.2:c.296T>G	p.Ile99Ser	p.I99S	ENST00000228682	NM_005269.2	99	aTc/aGc	4/12	0.180706835807286	3	FACETS	0.775	0.74	0.81	0.775	0.74	0.81	INDETERMINATE	2	TRUE	1	0.712392095780528	3		589	1012	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134909	41134909	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	238	340	0	ENST00000379561.5:c.719A>G	p.Asn240Ser	p.N240S	ENST00000379561	NM_002015.3	240	aAt/aGt	2/3	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.712392095780528	2		340	577	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81962190	81962190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs114618894	NA	P-0016533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	255	577	2	ENST00000359376.3:c.2542C>T	p.Leu848Phe	p.L848F	ENST00000359376	NM_002661.3	848	Ctt/Ttt	24/33	0.482984585554104	1	FACETS	0.663	0.624	0.703	0.663	0.624	0.703	SUBCLONAL	1	TRUE	0	0.712392095780528	1		579	695	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754790	29754790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217100351	NA	P-0016533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	164	253	0	ENST00000389048.3:c.1145G>A	p.Gly382Glu	p.G382E	ENST00000389048	NM_004304.4	382	gGg/gAg	4/29	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.712392095780528	2		253	426	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0016799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	30	306	0				ENST00000310581	NM_198253.2	-/1132			0.22353295452004	1	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	0	0.22353295452004	1		306	197	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0016799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	87	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.22353295452004	2		288	558	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445451	49445451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	157	658	0	ENST00000301067.7:c.2015C>T	p.Ser672Phe	p.S672F	ENST00000301067	NM_003482.3	672	tCc/tTc	10/54	0.126403235114789	4	FACETS	0.936	0.861	1	1	0.987	1	INDETERMINATE	3	TRUE	2	0.22353295452004	4		658	612	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0016799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	71	308	1	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	0.22353295452004	5	FACETS	0.848	0.742	0.962	0.424	0.371	0.481	CLONAL	2	TRUE	1	0.22353295452004	5		309	500	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033905	49033906	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0016799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	158	444	0	ENST00000267163.4:c.2042_2043delinsAA	p.Trp681Ter	p.W681*	ENST00000267163	NM_000321.2	681	tGG/tAA	20/27	0.22353295452004	5	FACETS	0.89	0.817	0.965	0.667	0.613	0.724	CLONAL	3	TRUE	1	0.22353295452004	5		444	707	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578400	7578400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751477326	NA	P-0016799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	83	383	2	ENST00000269305.4:c.530C>T	p.Pro177Leu	p.P177L	ENST00000269305	NM_001126112.2	177	cCc/cTc	5/11	0.191290435417934	3	FACETS	1	0.895	1	1	0.895	1	CLONAL	2	TRUE	1	0.22353295452004	3		385	409	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0016853-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	166	528	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.349051432517953	2		528	789	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016853-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	31	151	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.875	0.713	1	0.875	0.713	1	CLONAL	1	FALSE	1	0.349051432517953	2		151	203	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0016853-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	48	355	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.349051432517953	1	FACETS	0.543	0.46	0.634	0.543	0.46	0.634	SUBCLONAL	1	FALSE	0	0.349051432517953	1		355	418	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419900	41419900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772557274	NA	P-0016853-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	66	318	0	ENST00000373198.4:c.421G>A	p.Val141Ile	p.V141I	ENST00000373198	NM_133170.3	141	Gtc/Atc	3/32	0.284048435580535	0	FACETS	0.575	0.501	0.655			1	SUBCLONAL	1	FALSE	0	0.349051432517953	0		318	428	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426121	47426121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519786	NA	P-0016853-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	125	530	0	ENST00000377045.4:c.641C>T	p.Ser214Phe	p.S214F	ENST00000377045	NM_001654.4	214	tCc/tTc	7/16	0.117493476041546	0	FACETS	0.61	0.553	0.671			1	INDETERMINATE	1	FALSE	0	0.349051432517953	0		530	764	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904872	101904872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863223832	NA	P-0016853-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	61	246	0	ENST00000374994.4:c.860C>T	p.Ser287Phe	p.S287F	ENST00000374994	NM_004612.2	287	tCc/tTc	5/9	0.349051432517953	1	FACETS	0.659	0.57	0.755	0.659	0.57	0.755	SUBCLONAL	1	FALSE	0	0.349051432517953	1		246	438	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435918	110435918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774519000	NA	P-0016853-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	142	321	0	ENST00000375856.3:c.2483C>T	p.Ser828Phe	p.S828F	ENST00000375856	NM_003749.2	828	tCc/tTc	1/2	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	1	FALSE	NA	0.349051432517953	2		321	698	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950469	68950469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016853-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	150	283	1	ENST00000288368.4:c.781C>T	p.Gln261Ter	p.Q261*	ENST00000288368	NM_024870.2	261	Caa/Taa	7/40	0.187109780286261	2	FACETS	0.794	0.73	0.861	0.794	0.73	0.861	INDETERMINATE	2	FALSE	0	0.349051432517953	2		284	541	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28971120	28971120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016853-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	58	261	0	ENST00000282397.4:c.1637G>A	p.Arg546Lys	p.R546K	ENST00000282397	NM_002019.4	546	aGa/aAa	12/30	0.167006270410732	1	FACETS	0.732	0.631	0.84	0.732	0.631	0.84	INDETERMINATE	1	FALSE	0	0.349051432517953	1		261	375	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39595478	39595478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016853-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	65	277	0	ENST00000262039.4:c.1364C>T	p.Ser455Leu	p.S455L	ENST00000262039	NM_002647.2	455	tCa/tTa	12/25	1	2	FACETS	0.765	0.664	0.873	0.765	0.664	0.873	SUBCLONAL	1	FALSE	1	0.349051432517953	2		277	487	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967804	18967804	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016853-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	80	437	0	ENST00000262803.5:c.1943T>C	p.Val648Ala	p.V648A	ENST00000262803	NM_002911.3	648	gTt/gCt	14/24	NA	2	FACETS	0.588	0.517	0.665			1	INDETERMINATE	1	FALSE	NA	0.349051432517953	2		437	779	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518174	187518174	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016853-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	45	270	0	ENST00000441802.2:c.12520C>T	p.Pro4174Ser	p.P4174S	ENST00000441802	NM_005245.3	4174	Ccg/Tcg	25/27	0.217231558286678	0	FACETS	0.466	0.393	0.547			1	SUBCLONAL	1	FALSE	0	0.349051432517953	0		270	360	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518061	176518061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016853-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	36	358	1	ENST00000292408.4:c.559G>A	p.Asp187Asn	p.D187N	ENST00000292408	NM_213647.1	187	Gat/Aat	5/18	1	2	FACETS	0.314	0.257	0.378	0.314	0.257	0.378	SUBCLONAL	1	FALSE	1	0.349051432517953	2		359	657	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913259	39913259	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016853-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	62	321	0	ENST00000378444.4:c.4856A>G	p.Asn1619Ser	p.N1619S	ENST00000378444	NM_001123385.1	1619	aAc/aGc	14/15	0.117493476041546	0	FACETS	0.436	0.377	0.501			1	INDETERMINATE	1	FALSE	0	0.349051432517953	0		321	530	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44910999	44910999	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016853-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	33	278	0	ENST00000377967.4:c.700A>G	p.Thr234Ala	p.T234A	ENST00000377967	NM_021140.2	234	Aca/Gca	9/29	0.117493476041546	0	FACETS	0.294	0.239	0.356			1	INDETERMINATE	1	FALSE	0	0.349051432517953	0		278	419	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410879	63410879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016853-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	52	368	0	ENST00000330258.3:c.2288G>A	p.Gly763Glu	p.G763E	ENST00000330258	NM_152424.3	763	gGg/gAg	2/2	0.117493476041546	0	FACETS	0.429	0.366	0.498			1	INDETERMINATE	1	FALSE	0	0.349051432517953	0		368	452	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856147	151856149	+	frameshift_variant	Frame_Shift_Del	DEL	CCC	CCC	T	novel	NA	P-0016853-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	48	237	0	ENST00000262189.6:c.11469_11471delinsA	p.Ala3825SerfsTer20	p.A3825Sfs*20	ENST00000262189	NM_170606.2	3823	ttGGGg/ttAg	44/59	1	2	FACETS	0.595	0.504	0.696	0.595	0.504	0.696	SUBCLONAL	1	FALSE	1	0.349051432517953	2		237	462	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0017539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	407	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.922330207403908	4	FACETS	0.952	0.911	0.994	0.952	0.911	0.994	CLONAL	2	TRUE	2	0.93422540659245	4		288	885	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0017539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	411	284	0				ENST00000310581	NM_198253.2	-/1132			0.93422540659245	4	FACETS	0.985	0.953	1	0.985	0.953	1	CLONAL	3	TRUE	1	0.93422540659245	4		284	576	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945213	32945213	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782010	NA	P-0017539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	449	358	0	ENST00000380152.3:c.8608C>T	p.Gln2870Ter	p.Q2870*	ENST00000380152		2870	Cag/Tag	20/27	0.516351992986689	4	FACETS	1	0.995	1	0.81	0.781	0.839	INDETERMINATE	2	TRUE	1	0.93422540659245	4		358	765	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717617	89717618	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0017539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	444	308	0	ENST00000371953.3:c.645dup	p.Val216CysfsTer27	p.V216Cfs*27	ENST00000371953	NM_000314.4	214	-/T	7/9	0.92613779767167	2	FACETS	0.986	0.969	1	0.986	0.969	1	CLONAL	2	TRUE	0	0.93422540659245	2		308	482	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060820	38060820	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	780	980	0	ENST00000250448.2:c.1169G>A	p.Gly390Glu	p.G390E	ENST00000250448	NM_004496.3	390	gGg/gAg	2/2	0.92613779767167	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.93422540659245	2		980	828	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229327	5229327	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0017539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	562	610	0	ENST00000357368.4:c.2376T>A	p.Tyr792Ter	p.Y792*	ENST00000357368	NM_002850.3	792	taT/taA	16/38	0.883570746040165	3	FACETS	0.941	0.911	0.971	0.941	0.911	0.971	CLONAL	2	TRUE	1	0.93422540659245	3		610	938	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449778	8449778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533663469	NA	P-0017539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	461	437	0	ENST00000356435.5:c.3935C>T	p.Ser1312Leu	p.S1312L	ENST00000356435		1312	tCa/tTa	23/35	0.92327219909971	2	FACETS	0.969	0.952	0.986	0.969	0.952	0.986	CLONAL	2	TRUE	0	0.93422540659245	2		437	509	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665053	29665053	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691093	NA	P-0017939-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	62	574	0	ENST00000356175.3:c.6652C>T	p.Gln2218Ter	p.Q2218*	ENST00000356175	NM_000267.3	2218	Caa/Taa	44/57	0.201347865779157	1	FACETS	0.912	0.789	1	0.912	0.789	1	CLONAL	1	TRUE	0	0.254682128450758	1		574	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	G	rs11575997	NA	P-0017939-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	87	628	0	ENST00000269305.4:c.993+1G>C		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.201347865779157	1	FACETS	0.919	0.814	1	0.919	0.814	1	CLONAL	1	TRUE	0	0.254682128450758	1		628	649	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631445	117631445	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs190667369	NA	P-0017939-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	38	338	0	ENST00000368508.3:c.6234-1G>A		p.X2078_splice	ENST00000368508	NM_002944.2	2078			0.254682128450758	1	FACETS	0.819	0.679	0.974	0.819	0.679	0.974	CLONAL	1	TRUE	0	0.254682128450758	1		338	318	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148914	119148914	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs749897878	NA	P-0017939-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	205	537	0	ENST00000264033.4:c.1134C>A	p.Phe378Leu	p.F378L	ENST00000264033	NM_005188.3	378	ttC/ttA	8/16	0.254682128450758	4	FACETS	1	0.975	1			1	CLONAL	3	TRUE	NA	0.254682128450758	4		537	618	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221759	36221759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017939-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	129	918	1	ENST00000222270.7:c.5428C>T	p.Pro1810Ser	p.P1810S	ENST00000222270	NM_014727.1	1810	Cct/Tct	26/37	0.201347865779157	1	FACETS	0.882	0.799	0.97	0.882	0.799	0.97	CLONAL	1	TRUE	0	0.254682128450758	1		919	1002	SUCCESS
APC	324	MSKCC	GRCh37	5	112176891	112176891	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017939-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	65	520	0	ENST00000257430.4:c.5600T>G	p.Phe1867Cys	p.F1867C	ENST00000257430	NM_000038.5	1867	tTt/tGt	16/16	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.254682128450758	2		520	428	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508811	106508811	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017939-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	86	462	0	ENST00000359195.3:c.805G>A	p.Asp269Asn	p.D269N	ENST00000359195	NM_002649.2	269	Gat/Aat	2/11	0.254682128450758	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.254682128450758	1		462	552	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846366	128846366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765478037	NA	P-0017939-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	62	687	2	ENST00000249373.3:c.1202C>T	p.Ala401Val	p.A401V	ENST00000249373	NM_005631.4	401	gCg/gTg	6/12	0.254682128450758	1	FACETS	0.636	0.549	0.731	0.636	0.549	0.731	SUBCLONAL	1	TRUE	0	0.254682128450758	1		689	668	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485828	8485828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017939-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	22	380	0	ENST00000356435.5:c.2989C>T	p.His997Tyr	p.H997Y	ENST00000356435		997	Cat/Tat	17/35	0.254682128450758	1	FACETS	0.464	0.359	0.585	0.464	0.359	0.585	SUBCLONAL	1	TRUE	0	0.254682128450758	1		380	325	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0018569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	74	528	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		528	1006	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431198	49431198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258642596	NA	P-0018679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	39	380	0	ENST00000301067.7:c.9941C>T	p.Ser3314Phe	p.S3314F	ENST00000301067	NM_003482.3	3314	tCc/tTc	34/54	1	2	FACETS	0.566	0.468	0.675	0.566	0.468	0.675	SUBCLONAL	1	TRUE	1	0.22972899718325	2		380	600	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0018679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	91	267	0				ENST00000310581	NM_198253.2	-/1132			0.22972899718325	1	FACETS	0.762	0.68	0.849	1	0.981	1	SUBCLONAL	2	TRUE	0	0.22972899718325	1		267	460	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0018679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	169	615	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.140802380355733	3	FACETS	0.874	0.804	0.948			1	CLONAL	2	TRUE	NA	0.22972899718325	3		615	938	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678055	117678055	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	80	342	1	ENST00000368508.3:c.3878C>T	p.Ser1293Phe	p.S1293F	ENST00000368508	NM_002944.2	1293	tCc/tTc	25/43	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.22972899718325	2		343	640	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577142	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0018679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	233	446	1	ENST00000269305.4:c.796_797delinsAA	p.Gly266Lys	p.G266K	ENST00000269305	NM_001126112.2	266	GGa/AAa	8/11	0.201401811028295	3	FACETS	1	0.982	1	0.763	0.712	0.816	CLONAL	2	TRUE	0	0.22972899718325	3		447	988	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266707	142266707	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	72	411	0	ENST00000350721.4:c.3217C>T	p.Gln1073Ter	p.Q1073*	ENST00000350721	NM_001184.3	1073	Caa/Taa	16/47	0.22972899718325	1	FACETS	0.724	0.632	0.824	0.724	0.632	0.824	SUBCLONAL	1	TRUE	0	0.22972899718325	1		411	766	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727179	40727179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	91	317	0	ENST00000373198.4:c.3785C>T	p.Pro1262Leu	p.P1262L	ENST00000373198	NM_133170.3	1262	cCt/cTt	28/32	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.22972899718325	2		317	591	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057287	30057287	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777059212	NA	P-0018679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	150	419	0	ENST00000338641.4:c.769C>T	p.Pro257Ser	p.P257S	ENST00000338641	NM_000268.3	257	Ccg/Tcg	8/16	0.22972899718325	3	FACETS	0.803	0.733	0.875	0.803	0.733	0.875	CLONAL	2	TRUE	1	0.22972899718325	3		419	907	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444938	49444938	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	39	280	0	ENST00000301067.7:c.2528C>T	p.Ser843Phe	p.S843F	ENST00000301067	NM_003482.3	843	tCc/tTc	10/54	1	2	FACETS	0.715	0.592	0.851	0.715	0.592	0.851	SUBCLONAL	1	TRUE	1	0.22972899718325	2		280	475	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258908	16258908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199635467	NA	P-0018679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	336	667	0	ENST00000375759.3:c.6173C>T	p.Ala2058Val	p.A2058V	ENST00000375759	NM_015001.2	2058	gCc/gTc	11/15	0.22972899718325	3	FACETS	0.876	0.828	0.925	1	0.993	1	CLONAL	3	TRUE	1	0.22972899718325	3		667	1241	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087401	27087401	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	49	437	0	ENST00000324856.7:c.1975C>T	p.Pro659Ser	p.P659S	ENST00000324856	NM_006015.4	659	Cct/Tct	5/20	0.22972899718325	3	FACETS	0.486	0.41	0.57	0.243	0.205	0.285	SUBCLONAL	1	TRUE	1	0.22972899718325	3		437	979	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699214	117699215	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0018679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	35	277	0	ENST00000369458.3:c.426_427delinsTT	p.Leu143Phe	p.L143F	ENST00000369458	NM_024626.3	142	aaCCtt/aaTTtt	3/6	0.140802380355733	3	FACETS	0.6	0.491	0.723			1	SUBCLONAL	1	TRUE	NA	0.22972899718325	3		277	566	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606776	43606776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1313331250	NA	P-0018679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	83	1052	2	ENST00000355710.3:c.1385C>T	p.Ser462Leu	p.S462L	ENST00000355710	NM_020975.4	462	tCg/tTg	7/20	1	2	FACETS	0.851	0.75	0.96	0.851	0.75	0.96	CLONAL	1	TRUE	1	0.22972899718325	2		1054	849	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434985	49434985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	73	225	1	ENST00000301067.7:c.6568C>T	p.Pro2190Ser	p.P2190S	ENST00000301067	NM_003482.3	2190	Ccc/Tcc	31/54	1	2	FACETS	0.792	0.696	0.895	1	0.977	1	SUBCLONAL	2	TRUE	1	0.22972899718325	2		226	401	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588594	28588594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	86	313	0	ENST00000241453.7:c.2854G>A	p.Glu952Lys	p.E952K	ENST00000241453	NM_004119.2	952	Gaa/Aaa	23/24	0.22972899718325	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.22972899718325	1		313	573	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73350188	73350188	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	50	292	0	ENST00000377767.4:c.697C>T	p.Pro233Ser	p.P233S	ENST00000377767	NM_014953.3	233	Ccc/Tcc	5/21	0.22972899718325	1	FACETS	0.87	0.739	1	0.87	0.739	1	CLONAL	1	TRUE	0	0.22972899718325	1		292	443	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788603	3788603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	48	392	0	ENST00000262367.5:c.4351C>T	p.His1451Tyr	p.H1451Y	ENST00000262367	NM_004380.2	1451	Cat/Tat	26/31	1	2	FACETS	0.479	0.403	0.562	0.479	0.403	0.562	SUBCLONAL	1	TRUE	1	0.22972899718325	2		392	873	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562664	29562665	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0018679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	124	374	0	ENST00000356175.3:c.3744_3745del	p.Arg1250AlafsTer13	p.R1250Afs*13	ENST00000356175	NM_000267.3	1248	gaTTct/gact	28/57	0.208288979055603	2	FACETS	0.793	0.718	0.871	0.793	0.718	0.871	SUBCLONAL	2	TRUE	0	0.22972899718325	2		374	681	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40457635	40457635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751813910	NA	P-0018679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	131	412	0	ENST00000345506.4:c.1388C>T	p.Ser463Phe	p.S463F	ENST00000345506	NM_003152.3	463	tCc/tTc	13/20	0.208288979055603	2	FACETS	1	0.986	1	0.747	0.679	0.82	CLONAL	1	TRUE	0	0.22972899718325	2		412	763	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212015	36212015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1475021403	NA	P-0018679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1320	136	756	0	ENST00000222270.7:c.1766C>T	p.Pro589Leu	p.P589L	ENST00000222270	NM_014727.1	589	cCt/cTt	3/37	0.205099137779423	3	FACETS	0.907	0.821	0.997			1	CLONAL	1	TRUE	NA	0.22972899718325	3		756	1456	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752886	42752886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	69	651	0	ENST00000222329.4:c.1378C>T	p.Pro460Ser	p.P460S	ENST00000222329	NM_006494.2	460	Cca/Tca	4/4	1	2	FACETS	0.6	0.52	0.685	0.6	0.52	0.685	SUBCLONAL	1	TRUE	1	0.22972899718325	2		651	1002	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36014517	36014517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	101	444	1	ENST00000358208.4:c.290C>T	p.Ser97Phe	p.S97F	ENST00000358208		97	tCt/tTt	3/12	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.22972899718325	2		445	870	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735455	40735455	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	46	460	0	ENST00000373198.4:c.3418G>C	p.Ala1140Pro	p.A1140P	ENST00000373198	NM_133170.3	1140	Gcc/Ccc	25/32	1	2	FACETS	0.508	0.427	0.599	0.508	0.427	0.599	SUBCLONAL	1	TRUE	1	0.22972899718325	2		460	788	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1953895	1953895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	124	524	0	ENST00000382891.5:c.2074C>T	p.Leu692Phe	p.L692F	ENST00000382891	NM_133335.3	692	Ctc/Ttc	11/22	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.22972899718325	2		524	944	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151628	55151628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	72	500	0	ENST00000257290.5:c.2414G>A	p.Gly805Glu	p.G805E	ENST00000257290	NM_006206.4	805	gGa/gAa	17/23	1	2	FACETS	0.723	0.63	0.823	0.723	0.63	0.823	SUBCLONAL	1	TRUE	1	0.22972899718325	2		500	867	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968153	55968153	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	39	393	0	ENST00000263923.4:c.2177G>A	p.Arg726Lys	p.R726K	ENST00000263923	NM_002253.2	726	aGa/aAa	15/30	1	2	FACETS	0.478	0.395	0.571	0.478	0.395	0.571	SUBCLONAL	1	TRUE	1	0.22972899718325	2		393	710	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199931	138199931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763387455	NA	P-0018679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	57	217	0	ENST00000237289.4:c.1349C>T	p.Pro450Leu	p.P450L	ENST00000237289	NM_001270507.1	450	cCt/cTt	7/9	1	2	FACETS	0.996	0.856	1	0.996	0.856	1	CLONAL	1	TRUE	1	0.22972899718325	2		217	498	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335688	81335688	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370757602	NA	P-0018679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	107	386	0	ENST00000222390.5:c.1672G>A	p.Asp558Asn	p.D558N	ENST00000222390	NM_000601.4	558	Gat/Aat	15/18	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.22972899718325	2		386	777	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372783	81372783	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs865828369	NA	P-0018679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	74	312	0	ENST00000222390.5:c.751C>T	p.Pro251Ser	p.P251S	ENST00000222390	NM_000601.4	251	Ccc/Tcc	7/18	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.22972899718325	2		312	627	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965791	90965791	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	64	179	0	ENST00000265433.3:c.1526C>T	p.Ser509Phe	p.S509F	ENST00000265433	NM_002485.4	509	tCt/tTt	11/16	0.208288979055603	2	FACETS	1	0.97	1	0.729	0.634	0.831	CLONAL	1	TRUE	0	0.22972899718325	2		179	382	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974683	21974693	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCCTCCGAC	CGGCCTCCGAC	-	novel	NA	P-0018679-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	97	347	0	ENST00000304494.5:c.134_144del	p.Gly45AspfsTer71	p.G45Dfs*71	ENST00000304494	NM_000077.4	45	gGTCGGAGGCCG/g	1/3	0.22972899718325	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.22972899718325	1		347	545	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	142	306	0				ENST00000310581	NM_198253.2	-/1132			0.71222996839326	1	FACETS	0.895	0.834	0.957	0.895	0.834	0.957	CLONAL	1	TRUE	0	0.738305616426091	1		306	271	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	208	695	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	0.738305616426091	4	FACETS	0.96	0.91	1	0.96	0.91	1	CLONAL	3	TRUE	1	0.738305616426091	4		695	340	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374251	138374251	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	256	760	0	ENST00000289153.2:c.3193C>T	p.Arg1065Trp	p.R1065W	ENST00000289153	NM_006219.2	1065	Cgg/Tgg	22/22	0.738305616426091	3	FACETS	0.857	0.81	0.904	0.857	0.81	0.904	CLONAL	2	TRUE	1	0.738305616426091	3		760	554	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	105	455	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.12106328194232	4	FACETS	1	0.984	1	0.749	0.679	0.822	INDETERMINATE	1	TRUE	2	0.738305616426091	4		455	330	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645366	215645366	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	129	762	0	ENST00000260947.4:c.1232C>T	p.Pro411Leu	p.P411L	ENST00000260947	NM_000465.2	411	cCc/cTc	4/11	0.581697353812102	3	FACETS	1	0.976	1	0.394	0.36	0.428	CLONAL	1	TRUE	0	0.738305616426091	3		762	405	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562641	29562641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854562	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	71	534	0	ENST00000356175.3:c.3721C>T	p.Arg1241Ter	p.R1241*	ENST00000356175	NM_000267.3	1241	Cga/Tga	28/57	0.12106328194232	4	FACETS	1	0.966	1	0.638	0.563	0.716	INDETERMINATE	1	TRUE	2	0.738305616426091	4		534	262	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584548	189584548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	171	816	0	ENST00000264731.3:c.844G>A	p.Gly282Arg	p.G282R	ENST00000264731	NM_003722.4	282	Gga/Aga	6/14	0.738305616426091	3	FACETS	1	0.973	1	0.553	0.512	0.596	CLONAL	1	TRUE	1	0.738305616426091	3		816	573	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076934	41076934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759824186	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	509	714	1	ENST00000373198.4:c.1486G>A	p.Gly496Arg	p.G496R	ENST00000373198	NM_133170.3	496	Ggg/Agg	9/32	0.738305616426091	6	FACETS	1	0.984	1	0.625	0.601	0.649	CLONAL	3	TRUE	1	0.738305616426091	6		715	1093	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560043	29560043	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs868450405	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	68	437	0	ENST00000356175.3:c.3520C>T	p.Gln1174Ter	p.Q1174*	ENST00000356175	NM_000267.3	1174	Cag/Tag	27/57	0.12106328194232	4	FACETS	1	0.97	1	0.678	0.598	0.762	INDETERMINATE	1	TRUE	2	0.738305616426091	4		437	236	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972936	68972936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	222	539	2	ENST00000288368.4:c.1261G>A	p.Glu421Lys	p.E421K	ENST00000288368	NM_024870.2	421	Gaa/Aaa	11/40	0.738305616426091	3	FACETS	1	0.991	1	0.796	0.757	0.833	CLONAL	2	TRUE	0	0.738305616426091	3		541	345	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209253	133209253	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	205	934	0	ENST00000320574.5:c.6133C>T	p.Pro2045Ser	p.P2045S	ENST00000320574	NM_006231.2	2045	Ccc/Tcc	44/49	0.12106328194232	4	FACETS	1	0.991	1	0.711	0.662	0.761	INDETERMINATE	1	TRUE	2	0.738305616426091	4		934	679	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981887	70981887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs887981235	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	478	853	1	ENST00000276594.2:c.209C>T	p.Pro70Leu	p.P70L	ENST00000276594	NM_024504.3	70	cCc/cTc	2/8	0.738305616426091	3	FACETS	0.885	0.858	0.91	0.885	0.858	0.91	CLONAL	3	TRUE	0	0.738305616426091	3		854	668	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780863	9780863	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs915886106	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	208	897	0	ENST00000377346.4:c.1585G>A	p.Asp529Asn	p.D529N	ENST00000377346	NM_005026.3	529	Gac/Aac	13/24	0.12106328194232	4	FACETS	0.8	0.747	0.854	0.8	0.747	0.854	INDETERMINATE	2	TRUE	2	0.738305616426091	4		897	612	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619163	43619163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	155	792	2	ENST00000355710.3:c.2846G>A	p.Gly949Glu	p.G949E	ENST00000355710	NM_020975.4	949	gGa/gAa	17/20	1	2	FACETS	0.954	0.882	1	0.954	0.882	1	CLONAL	1	TRUE	1	0.738305616426091	2		794	440	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343846	118343847	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	123	771	1	ENST00000534358.1:c.1972_1973delinsTT	p.Pro658Phe	p.P658F	ENST00000534358	NM_005933.3	658	CCc/TTc	3/36	0.12106328194232	4	FACETS	1	0.977	1	0.615	0.559	0.673	INDETERMINATE	1	TRUE	2	0.738305616426091	4		772	471	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431559	49431559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878976690	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	167	782	1	ENST00000301067.7:c.9580C>T	p.His3194Tyr	p.H3194Y	ENST00000301067	NM_003482.3	3194	Cac/Tac	34/54	0.12106328194232	4	FACETS	0.817	0.758	0.879	0.817	0.758	0.879	INDETERMINATE	2	TRUE	2	0.738305616426091	4		783	481	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438639	49438640	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	143	841	1	ENST00000301067.7:c.4850_4851delinsAA	p.Arg1617Gln	p.R1617Q	ENST00000301067	NM_003482.3	1617	cGG/cAA	19/54	0.12106328194232	4	FACETS	1	0.984	1	0.655	0.601	0.711	INDETERMINATE	1	TRUE	2	0.738305616426091	4		842	514	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487608	56487608	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1198371951	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	183	790	1	ENST00000267101.3:c.1541C>T	p.Pro514Leu	p.P514L	ENST00000267101	NM_001982.3	514	cCt/cTt	13/28	0.12106328194232	4	FACETS	1	0.99	1	0.735	0.682	0.79	INDETERMINATE	1	TRUE	2	0.738305616426091	4		791	586	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915464	112915464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	102	623	0	ENST00000351677.2:c.863C>T	p.Thr288Ile	p.T288I	ENST00000351677	NM_002834.3	288	aCc/aTc	8/16	0.12106328194232	4	FACETS	0.87	0.79	0.952	0.87	0.79	0.952	INDETERMINATE	2	TRUE	2	0.738305616426091	4		623	276	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121886	2121886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	202	991	0	ENST00000219476.3:c.2048C>T	p.Ser683Phe	p.S683F	ENST00000219476	NM_000548.3	683	tCc/tTc	19/42	0.12106328194232	4	FACETS	1	0.99	1	0.703	0.654	0.752	INDETERMINATE	1	TRUE	2	0.738305616426091	4		991	677	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857709	9857709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	103	370	0	ENST00000330684.3:c.3692G>A	p.Arg1231Lys	p.R1231K	ENST00000330684	NM_001134407.1	1231	aGg/aAg	13/13	0.12106328194232	4	FACETS	0.933	0.849	1	0.933	0.849	1	INDETERMINATE	2	TRUE	2	0.738305616426091	4		370	260	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761105	59761105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	60	687	0	ENST00000259008.2:c.3302C>T	p.Pro1101Leu	p.P1101L	ENST00000259008	NM_032043.2	1101	cCa/cTa	20/20	0.12106328194232	4	FACETS	1	0.939	1	0.567	0.494	0.645	INDETERMINATE	1	TRUE	2	0.738305616426091	4		687	249	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166326	7166326	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	539	916	1	ENST00000302850.5:c.1700C>T	p.Ser567Phe	p.S567F	ENST00000302850	NM_000208.2	567	tCc/tTc	8/22	0.716443781549476	4	FACETS	0.88	0.85	0.91	0.88	0.85	0.91	CLONAL	3	TRUE	1	0.738305616426091	4		917	961	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277062	18277063	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	443	758	6	ENST00000222254.8:c.1509_1510delinsAA	p.Glu504Lys	p.E504K	ENST00000222254	NM_005027.3	503	aaGGaa/aaAAaa	12/16	0.716443781549476	4	FACETS	0.902	0.868	0.935	0.902	0.868	0.935	CLONAL	3	TRUE	1	0.738305616426091	4		764	771	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763527	41763527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	191	422	0	ENST00000301178.4:c.2326G>A	p.Asp776Asn	p.D776N	ENST00000301178	NM_021913.4	776	Gat/Aat	19/20	0.738305616426091	3	FACETS	0.86	0.806	0.914	0.86	0.806	0.914	CLONAL	2	TRUE	1	0.738305616426091	3		422	412	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795486	42795486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	352	908	0	ENST00000575354.2:c.2566C>T	p.Pro856Ser	p.P856S	ENST00000575354	NM_015125.3	856	Cct/Tct	10/20	0.738305616426091	3	FACETS	0.982	0.939	1	0.982	0.939	1	CLONAL	2	TRUE	1	0.738305616426091	3		908	665	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551298	29551298	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	419	843	0	ENST00000389048.3:c.1332G>A	p.Trp444Ter	p.W444*	ENST00000389048	NM_004304.4	444	tgG/tgA	6/29	0.581697353812102	3	FACETS	1	0.995	1	0.814	0.786	0.842	CLONAL	2	TRUE	0	0.738305616426091	3		843	636	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142991	30142991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs62129830	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	310	1173	3	ENST00000389048.3:c.535C>T	p.Arg179Cys	p.R179C	ENST00000389048	NM_004304.4	179	Cgc/Tgc	1/29	0.581697353812102	3	FACETS	0.758	0.719	0.798	0.506	0.479	0.532	SUBCLONAL	2	TRUE	0	0.738305616426091	3		1176	758	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661309	227661309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746777476	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	379	808	1	ENST00000305123.5:c.2146C>T	p.Pro716Ser	p.P716S	ENST00000305123	NM_005544.2	716	Ccc/Tcc	1/2	0.581697353812102	3	FACETS	1	0.995	1	0.828	0.798	0.857	CLONAL	2	TRUE	0	0.738305616426091	3		809	566	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164551	36164551	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1227184605	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	119	472	0	ENST00000300305.3:c.1324C>T	p.Leu442Phe	p.L442F	ENST00000300305		442	Ctc/Ttc	8/8	0.12106328194232	4	FACETS	1	0.985	1	0.72	0.656	0.787	INDETERMINATE	1	TRUE	2	0.738305616426091	4		472	389	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987040	69987040	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	59	1062	0	ENST00000394351.3:c.101A>G	p.Gln34Arg	p.Q34R	ENST00000394351	NM_000248.3	34	cAg/cGg	2/9	0.738305616426091	3	FACETS	0.249	0.213	0.288	0.124	0.106	0.144	SUBCLONAL	1	TRUE	1	0.738305616426091	3		1062	880	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131100	55131100	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	87	623	0	ENST00000257290.5:c.643G>A	p.Asp215Asn	p.D215N	ENST00000257290	NM_006206.4	215	Gat/Aat	5/23	0.179509706378562	4	FACETS	1	0.98	1	0.721	0.646	0.799	INDETERMINATE	1	TRUE	2	0.738305616426091	4		623	284	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057108	180057108	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	rs753782192	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	571	827	0	ENST00000261937.6:c.514-3C>T		p.X172_splice	ENST00000261937	NM_182925.4	172			0.738305616426091	4	FACETS	0.911	0.881	0.94	0.911	0.881	0.94	CLONAL	3	TRUE	1	0.738305616426091	4		827	984	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952994	2952995	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	171	865	1	ENST00000396946.4:c.2945_2946delinsAT	p.Thr982Asn	p.T982N	ENST00000396946	NM_032415.4	982	aCC/aAT	22/25	0.738305616426091	4	FACETS	0.811	0.745	0.879	0.27	0.248	0.293	CLONAL	1	TRUE	1	0.738305616426091	4		866	993	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962939	2962939	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	199	986	0	ENST00000396946.4:c.1969G>A	p.Gly657Arg	p.G657R	ENST00000396946	NM_032415.4	657	Ggg/Agg	16/25	0.738305616426091	4	FACETS	0.824	0.762	0.888	0.275	0.254	0.296	CLONAL	1	TRUE	1	0.738305616426091	4		986	1137	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509213	106509213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	203	867	1	ENST00000359195.3:c.1207C>T	p.Pro403Ser	p.P403S	ENST00000359195	NM_002649.2	403	Ccc/Tcc	2/11	0.738305616426091	4	FACETS	1	0.958	1	0.349	0.324	0.375	CLONAL	1	TRUE	1	0.738305616426091	4		868	913	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875085	151875085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	26	163	1	ENST00000262189.6:c.7453C>T	p.Pro2485Ser	p.P2485S	ENST00000262189	NM_170606.2	2485	Cca/Tca	38/59	0.738305616426091	4	FACETS	0.716	0.572	0.877	0.239	0.19	0.293	SUBCLONAL	1	TRUE	1	0.738305616426091	4		164	171	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633355	8633355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	91	737	0	ENST00000356435.5:c.314G>A	p.Gly105Glu	p.G105E	ENST00000356435		105	gGa/gAa	3/35	0.12106328194232	4	FACETS	1	0.977	1	0.672	0.603	0.744	INDETERMINATE	1	TRUE	2	0.738305616426091	4		737	319	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882055	36882055	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773593708	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	212	1039	1	ENST00000358127.4:c.958C>T	p.Pro320Ser	p.P320S	ENST00000358127	NM_001280556.1	320	Ccc/Tcc	8/10	0.12106328194232	4	FACETS	0.759	0.708	0.81	0.759	0.708	0.81	INDETERMINATE	2	TRUE	2	0.738305616426091	4		1040	658	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779160	135779160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	145	627	1	ENST00000298552.3:c.2086C>T	p.Leu696Phe	p.L696F	ENST00000298552	NM_001162426.1	696	Ctt/Ttt	17/23	0.12106328194232	4	FACETS	1	0.988	1	0.736	0.677	0.797	INDETERMINATE	1	TRUE	2	0.738305616426091	4		628	464	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483033	29483034	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	64	723	0	ENST00000356175.3:c.94dup	p.Thr32AsnfsTer6	p.T32Nfs*6	ENST00000356175	NM_000267.3	31	-/A	2/57	1	2	FACETS	0.458	0.396	0.526	0.458	0.396	0.526	SUBCLONAL	1	TRUE	1	0.378214331571772	2		723	739	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71161724	71161724	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	82	469	0	ENST00000318789.4:c.245A>T	p.Lys82Ile	p.K82I	ENST00000318789	NM_032682.5	82	aAa/aTa	7/21	1	2	FACETS	0.925	0.818	1	0.925	0.818	1	CLONAL	1	TRUE	1	0.378214331571772	2		469	469	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0019066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	16	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.3	1	FACETS	0.614	0.453	0.808	0.614	0.453	0.808	SUBCLONAL	1	TRUE	0	0.14	1		288	346	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0019066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	29	719	5	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	1	2	FACETS	0.795	0.637	0.976	0.795	0.637	0.976	CLONAL	1	TRUE	1	0.14	2		724	521	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435136	110435136	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs780127725	NA	P-0019247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	130	587	0	ENST00000375856.3:c.3265G>C	p.Ala1089Pro	p.A1089P	ENST00000375856	NM_003749.2	1089	Gcc/Ccc	1/2	0.424487940530962	3	FACETS	1	0.961	1	0.552	0.502	0.605	CLONAL	1	TRUE	1	0.424487940530962	3		587	672	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724243	52724243	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	127	393	1	ENST00000322088.6:c.1375C>T	p.Arg459Cys	p.R459C	ENST00000322088	NM_014225.5	459	Cgc/Tgc	12/15	0.424487940530962	5	FACETS	0.865	0.787	0.947	0.577	0.524	0.631	CLONAL	2	TRUE	2	0.424487940530962	5		394	566	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066775	77066775	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1048522	NA	P-0019247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	138	474	0	ENST00000356341.3:c.710G>A	p.Arg237Gln	p.R237Q	ENST00000356341	NM_002576.4	237	cGg/cAg	7/15	0.249060214120523	2	FACETS	0.807	0.742	0.874	0.807	0.742	0.874	INDETERMINATE	2	TRUE	0	0.424487940530962	2		474	403	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246278	46246278	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	48	357	0	ENST00000334344.6:c.4372T>G	p.Ser1458Ala	p.S1458A	ENST00000334344	NM_152641.2	1458	Tca/Gca	15/21	0.382978704872311	3	FACETS	0.865	0.735	1	0.432	0.367	0.503	CLONAL	1	TRUE	1	0.424487940530962	3		357	317	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007833	45007834	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	72	444	0	ENST00000558401.1:c.285dup	p.Asp96ArgfsTer2	p.D96Rfs*2	ENST00000558401	NM_004048.2	94	gaa/gAaa	2/4	0.424487940530962	1	FACETS	0.786	0.692	0.886	0.786	0.692	0.886	SUBCLONAL	1	TRUE	0	0.424487940530962	1		444	340	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89845237	89845237	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	102	991	0	ENST00000389301.3:c.1798C>G	p.Arg600Gly	p.R600G	ENST00000389301	NM_000135.2	600	Cgt/Ggt	20/43	0.0973471839616632	5	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.424487940530962	5		991	605	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047923	180047923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	98	716	0	ENST00000261937.6:c.2252G>A	p.Cys751Tyr	p.C751Y	ENST00000261937	NM_182925.4	751	tGc/tAc	15/30	0.424487940530962	3	FACETS	1	0.9	1	0.503	0.45	0.56	CLONAL	1	TRUE	1	0.424487940530962	3		716	556	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435136	110435136	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs780127725	NA	P-0019247-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	56	587	0	ENST00000375856.3:c.3265G>C	p.Ala1089Pro	p.A1089P	ENST00000375856	NM_003749.2	1089	Gcc/Ccc	1/2	1	2	FACETS	0.542	0.463	0.627	0.542	0.463	0.627	SUBCLONAL	1	TRUE	1	0.309591739828781	2		587	668	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724243	52724243	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019247-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	56	393	1	ENST00000322088.6:c.1375C>T	p.Arg459Cys	p.R459C	ENST00000322088	NM_014225.5	459	Cgc/Tgc	12/15	0.309591739828781	3	FACETS	0.924	0.793	1	0.462	0.396	0.534	CLONAL	1	TRUE	1	0.309591739828781	3		394	452	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066775	77066775	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1048522	NA	P-0019247-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	84	474	0	ENST00000356341.3:c.710G>A	p.Arg237Gln	p.R237Q	ENST00000356341	NM_002576.4	237	cGg/cAg	7/15	1	2	FACETS	0.955	0.845	1	0.955	0.845	1	CLONAL	1	TRUE	1	0.309591739828781	2		474	568	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246278	46246278	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019247-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	42	357	0	ENST00000334344.6:c.4372T>G	p.Ser1458Ala	p.S1458A	ENST00000334344	NM_152641.2	1458	Tca/Gca	15/21	1	2	FACETS	0.643	0.537	0.76	0.643	0.537	0.76	SUBCLONAL	1	TRUE	1	0.309591739828781	2		357	422	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007833	45007834	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019247-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	39	444	0	ENST00000558401.1:c.285dup	p.Asp96ArgfsTer2	p.D96Rfs*2	ENST00000558401	NM_004048.2	94	gaa/gAaa	2/4	0.270686521630167	1	FACETS	0.612	0.508	0.727	0.612	0.508	0.727	SUBCLONAL	1	TRUE	0	0.309591739828781	1		444	348	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047923	180047923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019247-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	65	716	0	ENST00000261937.6:c.2252G>A	p.Cys751Tyr	p.C751Y	ENST00000261937	NM_182925.4	751	tGc/tAc	15/30	1	2	FACETS	0.483	0.417	0.554	0.483	0.417	0.554	SUBCLONAL	1	TRUE	1	0.309591739828781	2		716	870	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857956	9857956	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019247-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	55	583	1	ENST00000330684.3:c.3445G>T	p.Asp1149Tyr	p.D1149Y	ENST00000330684	NM_001134407.1	1149	Gac/Tac	13/13	0.309591739828781	3	FACETS	0.595	0.508	0.69	0.297	0.254	0.345	SUBCLONAL	1	TRUE	1	0.309591739828781	3		584	690	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435136	110435136	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs780127725	NA	P-0019247-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	54	587	0	ENST00000375856.3:c.3265G>C	p.Ala1089Pro	p.A1089P	ENST00000375856	NM_003749.2	1089	Gcc/Ccc	1/2	1	2	FACETS	0.599	0.511	0.697	0.599	0.511	0.697	SUBCLONAL	1	TRUE	1	0.240251572011452	2		587	750	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724243	52724243	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019247-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	63	393	1	ENST00000322088.6:c.1375C>T	p.Arg459Cys	p.R459C	ENST00000322088	NM_014225.5	459	Cgc/Tgc	12/15	0.126702422752503	3	FACETS	1	0.892	1	0.518	0.448	0.594	INDETERMINATE	1	TRUE	1	0.240251572011452	3		394	567	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066775	77066775	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1048522	NA	P-0019247-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	58	474	0	ENST00000356341.3:c.710G>A	p.Arg237Gln	p.R237Q	ENST00000356341	NM_002576.4	237	cGg/cAg	7/15	0.126702422752503	3	FACETS	0.966	0.83	1	0.483	0.415	0.557	INDETERMINATE	1	TRUE	1	0.240251572011452	3		474	560	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007833	45007834	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0019247-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	30	444	0	ENST00000558401.1:c.285dup	p.Asp96ArgfsTer2	p.D96Rfs*2	ENST00000558401	NM_004048.2	94	gaa/gAaa	2/4	1	2	FACETS	0.557	0.449	0.681	0.557	0.449	0.681	SUBCLONAL	1	TRUE	1	0.240251572011452	2		444	448	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047923	180047923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019247-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	47	716	0	ENST00000261937.6:c.2252G>A	p.Cys751Tyr	p.C751Y	ENST00000261937	NM_182925.4	751	tGc/tAc	15/30	1	2	FACETS	0.427	0.359	0.502	0.427	0.359	0.502	SUBCLONAL	1	TRUE	1	0.240251572011452	2		716	917	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857956	9857956	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019247-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	41	583	1	ENST00000330684.3:c.3445G>T	p.Asp1149Tyr	p.D1149Y	ENST00000330684	NM_001134407.1	1149	Gac/Tac	13/13	0.240251572011452	3	FACETS	0.519	0.431	0.618	0.26	0.215	0.309	SUBCLONAL	1	TRUE	1	0.240251572011452	3		584	736	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	238	306	0				ENST00000310581	NM_198253.2	-/1132			0.43453671855234	4	FACETS	0.871	0.82	0.923	1	0.991	1	CLONAL	3	TRUE	2	0.455731177964194	4		306	582	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346551	81346551	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444026216	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	57	448	0	ENST00000222390.5:c.1402C>T	p.Arg468Cys	p.R468C	ENST00000222390	NM_000601.4	468	Cgt/Tgt	11/18	0.455731177964194	5	FACETS	0.67	0.574	0.774	0.223	0.191	0.258	SUBCLONAL	1	TRUE	2	0.455731177964194	5		448	629	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670708	134670708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	187	697	2	ENST00000398015.3:c.619C>T	p.Pro207Ser	p.P207S	ENST00000398015	NM_004441.4	207	Cca/Tca	3/16	0.332956616831758	4	FACETS	0.933	0.866	1	0.933	0.866	1	CLONAL	2	TRUE	2	0.455731177964194	4		699	640	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716366	18716366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs935135637	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	230	757	0	ENST00000266497.5:c.3713C>T	p.Ser1238Leu	p.S1238L	ENST00000266497		1238	tCa/tTa	26/31	0.259101369143009	4	FACETS	0.913	0.853	0.974			1	INDETERMINATE	2	TRUE	NA	0.455731177964194	4		757	805	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210733	5210733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779302415	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	106	915	0	ENST00000357368.4:c.5318C>T	p.Ser1773Leu	p.S1773L	ENST00000357368	NM_002850.3	1773	tCg/tTg	34/38	0.260863090346868	4	FACETS	0.83	0.744	0.922	0.415	0.372	0.461	INDETERMINATE	1	TRUE	2	0.455731177964194	4		915	816	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	202	939	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	0.455731177964194	3	FACETS	0.955	0.884	1	0.318	0.294	0.343	CLONAL	1	TRUE	0	0.455731177964194	3		939	1140	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892263	9892263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	245	669	0	ENST00000330684.3:c.2227G>A	p.Glu743Lys	p.E743K	ENST00000330684	NM_001134407.1	743	Gaa/Aaa	11/13	0.455731177964194	3	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	1	0.455731177964194	3		669	644	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	16	372	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.43453671855234	4	FACETS	0.178	0.131	0.235	0.089	0.065	0.118	SUBCLONAL	1	TRUE	2	0.455731177964194	4		372	574	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593613	55593613	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913521	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	290	685	0	ENST00000288135.5:c.1679T>G	p.Val560Gly	p.V560G	ENST00000288135	NM_000222.2	560	gTt/gGt	11/21	0.449034452960785	4	FACETS	0.94	0.891	0.989	0.94	0.891	0.989	CLONAL	3	TRUE	1	0.455731177964194	4		685	657	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100906	41100906	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs560503250	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	77	611	0	ENST00000373198.4:c.1450G>A	p.Val484Ile	p.V484I	ENST00000373198	NM_133170.3	484	Gtt/Att	8/32	0.455731177964194	5	FACETS	0.825	0.724	0.933	0.275	0.241	0.311	CLONAL	1	TRUE	2	0.455731177964194	5		611	690	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195717	123195717	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	130	876	0	ENST00000218089.9:c.1631G>A	p.Gly544Glu	p.G544E	ENST00000218089	NM_001042749.1	544	gGa/gAa	17/35	0.446882460050278	3	FACETS	0.935	0.849	1	0.468	0.424	0.513	CLONAL	1	TRUE	1	0.455731177964194	3		876	749	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	337	845	2	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	0.321206765491682	3	FACETS	0.947	0.905	0.989	0.947	0.905	0.989	CLONAL	3	TRUE	0	0.455731177964194	3		847	639	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455091	50455091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1422790468	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	84	514	0	ENST00000331340.3:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000331340	NM_006060.4	213	cGa/cAa	6/8	0.455731177964194	5	FACETS	0.79	0.697	0.889	0.263	0.232	0.297	SUBCLONAL	1	TRUE	2	0.455731177964194	5		514	786	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143551	108143551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201780199	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	258	664	0	ENST00000278616.4:c.3256C>T	p.Arg1086Cys	p.R1086C	ENST00000278616	NM_000051.3	1086	Cgc/Tgc	22/63	0.410745485824205	3	FACETS	0.961	0.913	1	0.961	0.913	1	CLONAL	3	TRUE	0	0.455731177964194	3		664	482	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143018	7143018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753688285	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	130	747	1	ENST00000302850.5:c.2351C>T	p.Ser784Phe	p.S784F	ENST00000302850	NM_000208.2	784	tCc/tTc	12/22	0.260863090346868	4	FACETS	1	0.938	1	0.522	0.473	0.573	INDETERMINATE	1	TRUE	2	0.455731177964194	4		748	796	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	66	355	0	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	0.43453671855234	4	FACETS	0.735	0.638	0.839	0.367	0.319	0.42	SUBCLONAL	1	TRUE	2	0.455731177964194	4		355	574	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719178	61719178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	68	549	0	ENST00000401558.2:c.1879C>T	p.Pro627Ser	p.P627S	ENST00000401558	NM_003400.3	627	Cct/Tct	16/25	0.332956616831758	4	FACETS	0.754	0.657	0.86	0.377	0.328	0.43	SUBCLONAL	1	TRUE	2	0.455731177964194	4		549	576	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076862	41076862	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs750249800	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	186	526	0	ENST00000373198.4:c.1558G>A	p.Glu520Lys	p.E520K	ENST00000373198	NM_133170.3	520	Gag/Aag	9/32	0.455731177964194	5	FACETS	0.964	0.893	1	0.642	0.595	0.691	CLONAL	2	TRUE	2	0.455731177964194	5		526	713	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259262	89259262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770780950	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	157	464	0	ENST00000336596.2:c.406C>T	p.Arg136Ter	p.R136*	ENST00000336596	NM_005233.5	136	Cga/Tga	3/17	0.332956616831758	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.455731177964194	4		464	461	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729949	41729949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1165688714	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	158	860	0	ENST00000242208.4:c.580G>A	p.Glu194Lys	p.E194K	ENST00000242208	NM_002192.2	194	Gaa/Aaa	3/3	0.332956616831758	4	FACETS	1	0.973	1	0.574	0.526	0.624	CLONAL	1	TRUE	2	0.455731177964194	4		860	879	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101007	41101007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375946335	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	95	582	1	ENST00000373198.4:c.1349G>A	p.Arg450Gln	p.R450Q	ENST00000373198	NM_133170.3	450	cGa/cAa	8/32	0.455731177964194	5	FACETS	1	0.936	1	0.357	0.318	0.399	CLONAL	1	TRUE	2	0.455731177964194	5		583	655	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509768	187509768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766893768	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	52	249	0	ENST00000441802.2:c.13745C>T	p.Ser4582Phe	p.S4582F	ENST00000441802	NM_005245.3	4582	tCc/tTc	27/27	0.449034452960785	4	FACETS	1	0.871	1	0.34	0.29	0.393	CLONAL	1	TRUE	1	0.455731177964194	4		249	326	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020582	14020582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	89	523	0	ENST00000311895.7:c.553C>T	p.Leu185Phe	p.L185F	ENST00000311895	NM_005236.2	185	Ctt/Ttt	3/11	0.455731177964194	3	FACETS	0.901	0.801	1	0.451	0.4	0.504	CLONAL	1	TRUE	1	0.455731177964194	3		523	532	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611252	100611252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	55	562	0	ENST00000308731.7:c.1354C>T	p.Leu452Phe	p.L452F	ENST00000308731	NM_000061.2	452	Ctt/Ttt	15/19	0.446882460050278	3	FACETS	0.541	0.463	0.626	0.27	0.231	0.313	SUBCLONAL	1	TRUE	1	0.455731177964194	3		562	548	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161380	55161380	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376544204	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	115	585	1	ENST00000257290.5:c.3211G>A	p.Asp1071Asn	p.D1071N	ENST00000257290	NM_006206.4	1071	Gac/Aac	23/23	0.449034452960785	4	FACETS	1	0.942	1	0.354	0.319	0.391	CLONAL	1	TRUE	1	0.455731177964194	4		586	692	SUCCESS
AR	367	MSKCC	GRCh37	X	66905852	66905852	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	35	465	0	ENST00000374690.3:c.1769G>A	p.Gly590Glu	p.G590E	ENST00000374690	NM_000044.3	590	gGg/gAg	3/8	0.446882460050278	3	FACETS	0.503	0.413	0.604	0.251	0.206	0.302	SUBCLONAL	1	TRUE	1	0.455731177964194	3		465	375	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467663	50467663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	92	666	0	ENST00000331340.3:c.898G>A	p.Glu300Lys	p.E300K	ENST00000331340	NM_006060.4	300	Gag/Aag	8/8	0.455731177964194	5	FACETS	0.829	0.736	0.929	0.276	0.245	0.31	CLONAL	1	TRUE	2	0.455731177964194	5		666	820	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527607	41527607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	91	649	0	ENST00000263253.7:c.1498C>T	p.Pro500Ser	p.P500S	ENST00000263253	NM_001429.3	500	Ccc/Tcc	6/31	0.455731177964194	5	FACETS	0.785	0.696	0.881	0.262	0.232	0.294	SUBCLONAL	1	TRUE	2	0.455731177964194	5		649	856	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405216	139405216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	204	773	3	ENST00000277541.6:c.2629C>T	p.Pro877Ser	p.P877S	ENST00000277541	NM_017617.3	877	Ccg/Tcg	17/34	0.455731177964194	3	FACETS	0.915	0.853	0.977	0.915	0.853	0.977	CLONAL	2	TRUE	1	0.455731177964194	3		776	601	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538311	9538311	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	126	629	0	ENST00000353224.5:c.1687G>A	p.Gly563Arg	p.G563R	ENST00000353224	NM_177990.2	563	Gga/Aga	7/10	0.455731177964194	5	FACETS	1	0.912	1	0.336	0.304	0.37	CLONAL	1	TRUE	2	0.455731177964194	5		629	923	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683747	162683747	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	121	701	0	ENST00000366898.1:c.222G>A	p.Trp74Ter	p.W74*	ENST00000366898	NM_004562.2	74	tgG/tgA	3/12	0.455731177964194	2	FACETS	1	0.958	1	0.546	0.496	0.599	CLONAL	1	TRUE	0	0.455731177964194	2		701	486	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748120	41748120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759792321	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	95	199	0	ENST00000226382.2:c.649G>A	p.Gly217Arg	p.G217R	ENST00000226382	NM_003924.3	217	Ggg/Agg	3/3	0.352590324028835	5	FACETS	0.9	0.822	0.978			1	CLONAL	4	TRUE	NA	0.455731177964194	5		199	195	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523617	41523617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	291	791	1	ENST00000263253.7:c.1033C>T	p.Leu345Phe	p.L345F	ENST00000263253	NM_001429.3	345	Ctt/Ttt	4/31	0.455731177964194	5	FACETS	0.967	0.91	1	0.645	0.606	0.684	CLONAL	2	TRUE	2	0.455731177964194	5		792	1112	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873648	35873648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867618621	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	90	478	0	ENST00000303115.3:c.604G>A	p.Glu202Lys	p.E202K	ENST00000303115	NM_002185.3	202	Gag/Aag	5/8	0.43453671855234	4	FACETS	0.988	0.878	1	0.494	0.439	0.553	CLONAL	1	TRUE	2	0.455731177964194	4		478	582	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617551	100617551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	95	719	0	ENST00000308731.7:c.518G>A	p.Gly173Glu	p.G173E	ENST00000308731	NM_000061.2	173	gGa/gAa	6/19	0.446882460050278	3	FACETS	0.869	0.775	0.969	0.435	0.387	0.485	CLONAL	1	TRUE	1	0.455731177964194	3		719	589	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482607	56482607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs993665271	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	142	854	1	ENST00000267101.3:c.1064C>T	p.Thr355Ile	p.T355I	ENST00000267101	NM_001982.3	355	aCc/aTc	9/28	0.455731177964194	2	FACETS	0.925	0.845	1	0.462	0.422	0.504	CLONAL	1	TRUE	0	0.455731177964194	2		855	674	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169006	32169006	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1489506589	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	137	1038	2	ENST00000375023.3:c.4027C>T	p.Pro1343Ser	p.P1343S	ENST00000375023	NM_004557.3	1343	Cct/Tct	22/30	0.455731177964194	3	FACETS	0.937	0.853	1	0.312	0.284	0.342	CLONAL	1	TRUE	0	0.455731177964194	3		1040	788	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295830	15295830	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	257	897	0	ENST00000263388.2:c.2297G>A	p.Gly766Glu	p.G766E	ENST00000263388	NM_000435.2	766	gGa/gAa	15/33	0.260863090346868	4	FACETS	0.904	0.848	0.962	0.904	0.848	0.962	INDETERMINATE	2	TRUE	2	0.455731177964194	4		897	908	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755506	39755506	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	78	452	0	ENST00000288319.7:c.1259C>T	p.Ser420Phe	p.S420F	ENST00000288319	NM_182918.3	420	tCc/tTc	10/10	0.455731177964194	3	FACETS	0.977	0.863	1	0.489	0.431	0.55	CLONAL	1	TRUE	1	0.455731177964194	3		452	430	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52649421	52649421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1169377404	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	138	924	0	ENST00000394830.3:c.1870G>A	p.Glu624Lys	p.E624K	ENST00000394830	NM_018313.4	624	Gag/Aag	16/30	0.43453671855234	4	FACETS	0.983	0.894	1	0.491	0.447	0.538	CLONAL	1	TRUE	2	0.455731177964194	4		924	897	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181543	32181543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	412	741	0	ENST00000375023.3:c.2242C>T	p.Pro748Ser	p.P748S	ENST00000375023	NM_004557.3	748	Cct/Tct	14/30	0.455731177964194	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.455731177964194	3		741	679	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508967	106508967	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1361906308	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	62	465	0	ENST00000359195.3:c.961G>A	p.Glu321Lys	p.E321K	ENST00000359195	NM_002649.2	321	Gaa/Aaa	2/11	0.455731177964194	6	FACETS	0.733	0.632	0.842	0.183	0.158	0.211	SUBCLONAL	1	TRUE	2	0.455731177964194	6		465	710	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115751	8115751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	142	906	1	ENST00000346208.3:c.1097G>A	p.Arg366Gln	p.R366Q	ENST00000346208		366	cGa/cAa	6/6	0.455731177964194	2	FACETS	0.899	0.821	0.981	0.45	0.41	0.491	CLONAL	1	TRUE	0	0.455731177964194	2		907	693	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650845	37650845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	296	1005	2	ENST00000447079.4:c.2317C>T	p.Arg773Cys	p.R773C	ENST00000447079	NM_015083.1	773	Cgt/Tgt	5/14	0.455731177964194	3	FACETS	0.806	0.76	0.854	0.806	0.76	0.854	CLONAL	2	TRUE	1	0.455731177964194	3		1007	989	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506444	148506444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	93	585	1	ENST00000320356.2:c.2068C>T	p.Arg690Cys	p.R690C	ENST00000320356	NM_004456.4	690	Cgt/Tgt	18/20	0.455731177964194	6	FACETS	0.858	0.762	0.961	0.215	0.19	0.241	CLONAL	1	TRUE	2	0.455731177964194	6		586	909	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381523	81381523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	177	471	2	ENST00000222390.5:c.538C>T	p.Pro180Ser	p.P180S	ENST00000222390	NM_000601.4	180	Cct/Tct	5/18	0.455731177964194	5	FACETS	0.886	0.818	0.956	0.591	0.545	0.638	CLONAL	2	TRUE	2	0.455731177964194	5		473	738	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022570	12022570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	117	736	0	ENST00000396373.4:c.676G>A	p.Glu226Lys	p.E226K	ENST00000396373	NM_001987.4	226	Gag/Aag	5/8	0.43453671855234	4	FACETS	0.854	0.77	0.944	0.427	0.385	0.472	CLONAL	1	TRUE	2	0.455731177964194	4		736	875	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874197	155874197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375724784	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	150	761	1	ENST00000368323.3:c.334C>T	p.Arg112Cys	p.R112C	ENST00000368323	NM_006912.5	112	Cgt/Tgt	5/6	0.332956616831758	4	FACETS	0.91	0.831	0.994	0.455	0.415	0.497	CLONAL	1	TRUE	2	0.455731177964194	4		762	1053	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294409	1294409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758442518	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	118	767	0	ENST00000310581.5:c.592G>A	p.Gly198Arg	p.G198R	ENST00000310581	NM_198253.2	198	Gga/Aga	2/16	0.43453671855234	4	FACETS	0.952	0.859	1	0.476	0.429	0.525	CLONAL	1	TRUE	2	0.455731177964194	4		767	792	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964488	70964488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	162	770	0	ENST00000276594.2:c.1540G>A	p.Glu514Lys	p.E514K	ENST00000276594	NM_024504.3	514	Gag/Aag	8/8	0.332956616831758	4	FACETS	1	0.979	1	0.601	0.552	0.653	CLONAL	1	TRUE	2	0.455731177964194	4		770	861	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650562	18650562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	68	576	0	ENST00000266497.5:c.2773G>A	p.Asp925Asn	p.D925N	ENST00000266497		925	Gat/Aat	20/31	0.259101369143009	4	FACETS	0.824	0.718	0.939			1	INDETERMINATE	1	TRUE	NA	0.455731177964194	4		576	527	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050656	69050656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752015034	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	53	562	0	ENST00000288368.4:c.3991G>A	p.Glu1331Lys	p.E1331K	ENST00000288368	NM_024870.2	1331	Gaa/Aaa	33/40	0.332956616831758	4	FACETS	0.716	0.611	0.83	0.358	0.305	0.415	SUBCLONAL	1	TRUE	2	0.455731177964194	4		562	473	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865536	57865536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	141	822	0	ENST00000228682.2:c.3013G>A	p.Gly1005Arg	p.G1005R	ENST00000228682	NM_005269.2	1005	Gga/Aga	12/12	0.455731177964194	2	FACETS	1	0.962	1	0.545	0.498	0.593	CLONAL	1	TRUE	0	0.455731177964194	2		822	568	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714679	52714679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	250	715	1	ENST00000322088.6:c.437C>T	p.Ser146Leu	p.S146L	ENST00000322088	NM_014225.5	146	tCg/tTg	4/15	0.455731177964194	5	FACETS	0.984	0.921	1	0.656	0.614	0.699	CLONAL	2	TRUE	2	0.455731177964194	5		716	939	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39575945	39575945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	115	583	0	ENST00000262039.4:c.878G>A	p.Arg293Lys	p.R293K	ENST00000262039	NM_002647.2	293	aGa/aAa	8/25	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.455731177964194	2		583	471	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177414	56177414	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290999800	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	51	469	0	ENST00000399503.3:c.2387C>T	p.Ser796Phe	p.S796F	ENST00000399503	NM_005921.1	796	tCc/tTc	14/20	0.43453671855234	4	FACETS	0.585	0.497	0.682	0.292	0.248	0.341	SUBCLONAL	1	TRUE	2	0.455731177964194	4		469	557	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317623	163317623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747173543	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	103	741	0	ENST00000271452.3:c.1019C>T	p.Ser340Leu	p.S340L	ENST00000271452	NM_145697.2	340	tCg/tTg	12/14	0.332956616831758	4	FACETS	0.945	0.847	1	0.473	0.423	0.525	CLONAL	1	TRUE	2	0.455731177964194	4		741	696	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257207	16257207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	112	821	0	ENST00000375759.3:c.4472C>T	p.Pro1491Leu	p.P1491L	ENST00000375759	NM_015001.2	1491	cCa/cTa	11/15	0.446882460050278	3	FACETS	0.964	0.869	1	0.482	0.434	0.532	CLONAL	1	TRUE	1	0.455731177964194	3		821	626	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36934816	36934816	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	129	646	0	ENST00000361632.4:c.1517C>T	p.Pro506Leu	p.P506L	ENST00000361632		506	cCc/cTc	11/16	0.446882460050278	3	FACETS	1	0.974	1	0.595	0.541	0.651	CLONAL	1	TRUE	1	0.455731177964194	3		646	584	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076775	72076775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	126	741	0	ENST00000357731.5:c.722G>A	p.Gly241Asp	p.G241D	ENST00000357731	NM_173808.2	241	gGc/gAc	5/7	0.446882460050278	3	FACETS	0.916	0.83	1	0.458	0.415	0.504	CLONAL	1	TRUE	1	0.455731177964194	3		741	741	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175831	176175831	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	144	434	0	ENST00000367669.3:c.284C>T	p.Pro95Leu	p.P95L	ENST00000367669	NM_022457.5	95	cCc/cTc	1/20	0.332956616831758	4	FACETS	0.977	0.898	1	0.977	0.898	1	CLONAL	2	TRUE	2	0.455731177964194	4		434	471	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981105	201981105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1281932149	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	89	663	0	ENST00000359651.3:c.184G>A	p.Glu62Lys	p.E62K	ENST00000359651		62	Gaa/Aaa	2/8	0.332956616831758	4	FACETS	0.943	0.837	1	0.471	0.418	0.528	CLONAL	1	TRUE	2	0.455731177964194	4		663	603	SUCCESS
FH	2271	MSKCC	GRCh37	1	241672031	241672031	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	99	607	0	ENST00000366560.3:c.610C>T	p.His204Tyr	p.H204Y	ENST00000366560	NM_000143.3	204	Cat/Tat	5/10	0.332956616831758	4	FACETS	1	0.928	1	0.524	0.468	0.582	CLONAL	1	TRUE	2	0.455731177964194	4		607	604	SUCCESS
RET	5979	MSKCC	GRCh37	10	43613889	43613889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	133	924	0	ENST00000355710.3:c.2353C>T	p.Pro785Ser	p.P785S	ENST00000355710	NM_020975.4	785	Cca/Tca	13/20	0.446882460050278	3	FACETS	0.979	0.89	1	0.49	0.445	0.536	CLONAL	1	TRUE	1	0.455731177964194	3		924	732	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852076	63852076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1249802128	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	176	835	2	ENST00000279873.7:c.2854C>T	p.Pro952Ser	p.P952S	ENST00000279873	NM_032199.2	952	Ccc/Tcc	10/10	0.446882460050278	3	FACETS	1	0.981	1	0.595	0.549	0.643	CLONAL	1	TRUE	1	0.455731177964194	3		837	797	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852448	63852448	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	106	656	0	ENST00000279873.7:c.3226C>T	p.Pro1076Ser	p.P1076S	ENST00000279873	NM_032199.2	1076	Cct/Tct	10/10	0.446882460050278	3	FACETS	0.978	0.879	1	0.489	0.439	0.541	CLONAL	1	TRUE	1	0.455731177964194	3		656	584	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70442596	70442596	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	100	524	0	ENST00000373644.4:c.4918G>A	p.Glu1640Lys	p.E1640K	ENST00000373644	NM_030625.2	1640	Gaa/Aaa	10/12	0.446882460050278	3	FACETS	1	0.951	1	0.55	0.493	0.61	CLONAL	1	TRUE	1	0.455731177964194	3		524	490	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276929	123276929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200204947	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	115	615	0	ENST00000358487.5:c.988C>T	p.Arg330Trp	p.R330W	ENST00000358487	NM_000141.4	330	Cgg/Tgg	8/18	0.204495245801456	4	FACETS	1	0.938	1			1	INDETERMINATE	1	TRUE	NA	0.455731177964194	4		615	697	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574482	64574483	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	272	662	1	ENST00000312049.6:c.912_912+1delinsAA		p.X304_splice	ENST00000312049	NM_130799.2	304		6/10	0.455731177964194	3	FACETS	0.89	0.844	0.936	0.89	0.844	0.936	CLONAL	3	TRUE	0	0.455731177964194	3		663	549	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939807	71939807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	162	966	1	ENST00000298229.2:c.434C>T	p.Ser145Phe	p.S145F	ENST00000298229	NM_001567.3	145	tCt/tTt	4/28	0.455731177964194	3	FACETS	1	0.975	1	0.384	0.353	0.417	CLONAL	1	TRUE	0	0.455731177964194	3		967	757	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998475	100998475	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	285	527	1	ENST00000325455.5:c.1327C>A	p.Pro443Thr	p.P443T	ENST00000325455	NM_001202474.3	443	Ccc/Acc	1/8	0.410745485824205	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	3	TRUE	0	0.455731177964194	3		528	504	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359392	118359392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	98	541	1	ENST00000534358.1:c.4396C>T	p.Pro1466Ser	p.P1466S	ENST00000534358	NM_005933.3	1466	Cct/Tct	11/36	0.410745485824205	3	FACETS	1	0.94	1	0.357	0.32	0.397	CLONAL	1	TRUE	0	0.455731177964194	3		542	493	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371707	118371707	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	66	298	0	ENST00000534358.1:c.6164C>T	p.Ser2055Phe	p.S2055F	ENST00000534358	NM_005933.3	2055	tCc/tTc	25/36	0.410745485824205	3	FACETS	1	0.942	1	0.379	0.331	0.43	CLONAL	1	TRUE	0	0.455731177964194	3		298	313	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	459851	459851	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	133	1121	1	ENST00000399788.2:c.1244C>T	p.Ser415Leu	p.S415L	ENST00000399788	NM_001042603.1	415	tCa/tTa	10/28	0.238853242052409	5	FACETS	0.966	0.876	1			1	INDETERMINATE	1	TRUE	NA	0.455731177964194	5		1122	1017	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380243	25380243	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	152	925	1	ENST00000311936.3:c.215T>A	p.Met72Lys	p.M72K	ENST00000311936	NM_004985.3	72	aTg/aAg	3/5	0.259101369143009	4	FACETS	0.95	0.868	1			1	INDETERMINATE	1	TRUE	NA	0.455731177964194	4		926	1022	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431838	49431838	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	228	741	0	ENST00000301067.7:c.9301C>T	p.Pro3101Ser	p.P3101S	ENST00000301067	NM_003482.3	3101	Ccc/Tcc	34/54	0.455731177964194	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.455731177964194	2		741	434	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444013	49444013	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	103	784	0	ENST00000301067.7:c.3358G>T	p.Glu1120Ter	p.E1120*	ENST00000301067	NM_003482.3	1120	Gaa/Taa	11/54	0.455731177964194	2	FACETS	0.917	0.824	1	0.458	0.412	0.507	CLONAL	1	TRUE	0	0.455731177964194	2		784	493	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865774	57865774	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	141	895	0	ENST00000228682.2:c.3251C>T	p.Ala1084Val	p.A1084V	ENST00000228682	NM_005269.2	1084	gCt/gTt	12/12	0.455731177964194	2	FACETS	0.873	0.797	0.952	0.436	0.398	0.476	CLONAL	1	TRUE	0	0.455731177964194	2		895	709	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856638	111856639	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	261	411	3	ENST00000341259.2:c.689_690delinsAA	p.Pro230Gln	p.P230Q	ENST00000341259	NM_005475.2	230	cCC/cAA	2/8	0.455731177964194	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.455731177964194	3		414	422	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557751	21557752	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	135	785	2	ENST00000382592.4:c.2093_2094delinsTT	p.Thr698Ile	p.T698I	ENST00000382592	NM_014572.2	698	aCC/aTT	5/8	0.455731177964194	3	FACETS	1	0.929	1	0.512	0.466	0.56	CLONAL	1	TRUE	1	0.455731177964194	3		787	711	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28631561	28631561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	173	686	0	ENST00000241453.7:c.407C>T	p.Thr136Ile	p.T136I	ENST00000241453	NM_004119.2	136	aCc/aTc	4/24	0.455731177964194	3	FACETS	0.813	0.753	0.876	0.813	0.753	0.876	CLONAL	2	TRUE	1	0.455731177964194	3		686	573	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28886200	28886200	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	80	795	0	ENST00000282397.4:c.3422C>T	p.Pro1141Leu	p.P1141L	ENST00000282397	NM_002019.4	1141	cCa/cTa	26/30	0.455731177964194	3	FACETS	0.734	0.647	0.828	0.367	0.323	0.414	SUBCLONAL	1	TRUE	1	0.455731177964194	3		795	587	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906817	32906817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	110	999	1	ENST00000380152.3:c.1202C>T	p.Ser401Leu	p.S401L	ENST00000380152		401	tCa/tTa	10/27	0.455731177964194	3	FACETS	0.774	0.695	0.857	0.387	0.347	0.429	SUBCLONAL	1	TRUE	1	0.455731177964194	3		1000	766	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915300	32915300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	72	898	1	ENST00000380152.3:c.6808G>A	p.Gly2270Arg	p.G2270R	ENST00000380152		2270	Gga/Aga	11/27	0.455731177964194	3	FACETS	0.598	0.522	0.679	0.299	0.261	0.34	SUBCLONAL	1	TRUE	1	0.455731177964194	3		899	649	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435681	110435681	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	112	768	0	ENST00000375856.3:c.2720A>C	p.Tyr907Ser	p.Y907S	ENST00000375856	NM_003749.2	907	tAc/tCc	1/2	0.455731177964194	3	FACETS	0.944	0.851	1	0.472	0.425	0.522	CLONAL	1	TRUE	1	0.455731177964194	3		768	639	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987194	36987194	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	133	893	0	ENST00000354822.5:c.495G>A	p.Met165Ile	p.M165I	ENST00000354822	NM_001079668.2	165	atG/atA	3/3	0.332956616831758	4	FACETS	1	0.957	1	0.544	0.494	0.596	CLONAL	1	TRUE	2	0.455731177964194	4		893	781	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606081	81606081	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746685925	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	318	857	1	ENST00000298171.2:c.751G>A	p.Glu251Lys	p.E251K	ENST00000298171	NM_000369.2	251	Gaa/Aaa	9/10	0.332956616831758	4	FACETS	0.99	0.936	1	0.99	0.936	1	CLONAL	2	TRUE	2	0.455731177964194	4		858	1026	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023123	33023123	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	85	566	1	ENST00000300177.4:c.232C>T	p.Gln78Ter	p.Q78*	ENST00000300177	NM_001191322.1	78	Caa/Taa	2/2	NA	2	FACETS	0.886	0.787	0.99			1	INDETERMINATE	1	TRUE	NA	0.455731177964194	2		567	421	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041917	42041917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	92	687	1	ENST00000219905.7:c.6112C>T	p.Pro2038Ser	p.P2038S	ENST00000219905	NM_001164273.1	2038	Cca/Tca	17/24	NA	2	FACETS	0.809	0.722	0.902			1	INDETERMINATE	1	TRUE	NA	0.455731177964194	2		688	499	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483966	88483966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	74	665	0	ENST00000360948.2:c.1604G>A	p.Arg535Lys	p.R535K	ENST00000360948	NM_001012338.2	535	aGg/aAg	14/19	0.332956616831758	4	FACETS	0.655	0.573	0.743	0.327	0.286	0.372	SUBCLONAL	1	TRUE	2	0.455731177964194	4		665	722	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096205	2096205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	128	985	0	ENST00000219066.1:c.302C>T	p.Ala101Val	p.A101V	ENST00000219066	NM_002528.5	101	gCc/gTc	2/6	0.455731177964194	3	FACETS	0.812	0.736	0.893	0.406	0.368	0.447	CLONAL	1	TRUE	1	0.455731177964194	3		985	849	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100422	2100422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1394176023	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	142	850	0	ENST00000219476.3:c.160C>T	p.Leu54Phe	p.L54F	ENST00000219476	NM_000548.3	54	Ctc/Ttc	3/42	0.455731177964194	3	FACETS	1	0.913	1	0.5	0.456	0.546	CLONAL	1	TRUE	1	0.455731177964194	3		850	765	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134554	2134554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550084361	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	318	888	0	ENST00000219476.3:c.4331C>T	p.Pro1444Leu	p.P1444L	ENST00000219476	NM_000548.3	1444	cCc/cTc	34/42	0.455731177964194	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.455731177964194	3		888	721	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633174	3633174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	329	1081	0	ENST00000294008.3:c.5077G>A	p.Asp1693Asn	p.D1693N	ENST00000294008	NM_032444.2	1693	Gac/Aac	14/15	0.455731177964194	3	FACETS	0.993	0.941	1	0.993	0.941	1	CLONAL	2	TRUE	1	0.455731177964194	3		1081	893	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808023	3808024	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	179	543	3	ENST00000262367.5:c.3395_3396delinsTT	p.Pro1132Leu	p.P1132L	ENST00000262367	NM_004380.2	1132	cCC/cTT	18/31	0.455731177964194	3	FACETS	0.874	0.811	0.938	0.874	0.811	0.938	CLONAL	2	TRUE	1	0.455731177964194	3		546	552	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934597	9934597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	134	744	0	ENST00000330684.3:c.1558G>A	p.Glu520Lys	p.E520K	ENST00000330684	NM_001134407.1	520	Gaa/Aaa	7/13	0.455731177964194	3	FACETS	0.984	0.895	1	0.492	0.447	0.539	CLONAL	1	TRUE	1	0.455731177964194	3		744	734	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992447	72992447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772706179	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	165	1058	1	ENST00000268489.5:c.1598C>T	p.Ser533Phe	p.S533F	ENST00000268489	NM_006885.3	533	tCc/tTc	2/10	0.449034452960785	4	FACETS	1	0.935	1	0.34	0.312	0.37	CLONAL	1	TRUE	1	0.455731177964194	4		1059	1032	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993020	72993020	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	166	956	3	ENST00000268489.5:c.1025C>T	p.Pro342Leu	p.P342L	ENST00000268489	NM_006885.3	342	cCa/cTa	2/10	0.449034452960785	4	FACETS	1	0.931	1	0.339	0.31	0.368	CLONAL	1	TRUE	1	0.455731177964194	4		959	1044	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346759	89346759	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs926985506	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	44	463	0	ENST00000301030.4:c.6191C>T	p.Ser2064Phe	p.S2064F	ENST00000301030	NM_001256183.1	2064	tCc/tTc	9/13	0.449034452960785	4	FACETS	0.805	0.678	0.946	0.268	0.226	0.316	CLONAL	1	TRUE	1	0.455731177964194	4		463	349	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351351	89351351	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	133	857	0	ENST00000301030.4:c.1599del	p.Lys533AsnfsTer41	p.K533Nfs*41	ENST00000301030	NM_001256183.1	533	aaG/aa	9/13	0.449034452960785	4	FACETS	0.991	0.9	1	0.33	0.3	0.363	CLONAL	1	TRUE	1	0.455731177964194	4		857	857	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976569	7976569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	260	731	1	ENST00000319144.4:c.1823G>A	p.Gly608Glu	p.G608E	ENST00000319144	NM_001139.2	608	gGg/gAg	14/15	0.321206765491682	3	FACETS	0.863	0.817	0.909	0.863	0.817	0.909	CLONAL	3	TRUE	0	0.455731177964194	3		732	541	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40872452	40872452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	321	839	0	ENST00000428826.2:c.503C>T	p.Ser168Phe	p.S168F	ENST00000428826		168	tCc/tTc	7/21	0.455731177964194	3	FACETS	0.861	0.814	0.908	0.861	0.814	0.908	CLONAL	2	TRUE	1	0.455731177964194	3		839	1005	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435159	56435159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	154	664	0	ENST00000407977.2:c.1978C>T	p.Pro660Ser	p.P660S	ENST00000407977		660	Ccc/Tcc	9/10	0.455731177964194	3	FACETS	1	0.986	1	0.681	0.626	0.739	CLONAL	1	TRUE	1	0.455731177964194	3		664	609	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422892	45422892	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	67	328	0	ENST00000262160.6:c.236G>A	p.Ser79Asn	p.S79N	ENST00000262160	NM_005901.5	79	aGc/aAc	2/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.455731177964194	2		328	268	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222744	5222744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	125	721	0	ENST00000357368.4:c.3059C>T	p.Pro1020Leu	p.P1020L	ENST00000357368	NM_002850.3	1020	cCc/cTc	18/38	0.260863090346868	4	FACETS	1	0.964	1	0.563	0.51	0.619	INDETERMINATE	1	TRUE	2	0.455731177964194	4		721	709	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245939	5245939	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	155	944	1	ENST00000357368.4:c.836T>G	p.Met279Arg	p.M279R	ENST00000357368	NM_002850.3	279	aTg/aGg	10/38	0.260863090346868	4	FACETS	1	0.958	1	0.538	0.492	0.586	INDETERMINATE	1	TRUE	2	0.455731177964194	4		945	921	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270742	10270742	+	splice_region_variant,intron_variant	Splice_Region	DEL	G	G	-	rs780538171	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	48	379	3	ENST00000340748.4:c.996-3del		p.X332_splice	ENST00000340748		332			0.260863090346868	4	FACETS	0.647	0.547	0.757	0.323	0.273	0.379	INDETERMINATE	1	TRUE	2	0.455731177964194	4		382	474	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281506	15281506	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	209	781	0	ENST00000263388.2:c.4867C>T	p.Pro1623Ser	p.P1623S	ENST00000263388	NM_000435.2	1623	Ccg/Tcg	26/33	0.260863090346868	4	FACETS	0.918	0.856	0.983	0.918	0.856	0.983	INDETERMINATE	2	TRUE	2	0.455731177964194	4		781	727	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376284	15376284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	108	645	0	ENST00000263377.2:c.730C>T	p.Pro244Ser	p.P244S	ENST00000263377	NM_058243.2	244	Ccc/Tcc	5/20	0.260863090346868	4	FACETS	1	0.95	1	0.546	0.491	0.604	INDETERMINATE	1	TRUE	2	0.455731177964194	4		645	632	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216515	36216515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372953726	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	126	875	0	ENST00000222270.7:c.3778C>T	p.Arg1260Cys	p.R1260C	ENST00000222270	NM_014727.1	1260	Cgt/Tgt	12/37	0.455731177964194	5	FACETS	0.924	0.836	1	0.308	0.278	0.34	CLONAL	1	TRUE	2	0.455731177964194	5		875	1007	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794418	42794418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267605512	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1225	150	1246	1	ENST00000575354.2:c.1498C>T	p.Arg500Cys	p.R500C	ENST00000575354	NM_015125.3	500	Cgt/Tgt	10/20	0.455731177964194	5	FACETS	0.806	0.734	0.882	0.269	0.244	0.294	CLONAL	1	TRUE	2	0.455731177964194	5		1247	1375	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905125	50905125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	135	1029	0	ENST00000440232.2:c.407C>T	p.Ser136Phe	p.S136F	ENST00000440232	NM_002691.3	136	tCt/tTt	4/27	0.455731177964194	5	FACETS	0.981	0.89	1	0.327	0.296	0.359	CLONAL	1	TRUE	2	0.455731177964194	5		1029	1017	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905566	50905566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774789534	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	153	871	2	ENST00000440232.2:c.694C>T	p.Arg232Cys	p.R232C	ENST00000440232	NM_002691.3	232	Cgt/Tgt	6/27	0.455731177964194	5	FACETS	1	0.976	1	0.395	0.36	0.43	CLONAL	1	TRUE	2	0.455731177964194	5		873	955	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285848	39285848	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752017140	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	96	769	0	ENST00000402219.2:c.311C>T	p.Ser104Phe	p.S104F	ENST00000402219	NM_005633.3	104	tCt/tTt	3/23	0.332956616831758	4	FACETS	0.823	0.733	0.919	0.412	0.366	0.46	CLONAL	1	TRUE	2	0.455731177964194	4		769	745	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99136609	99136609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	194	554	0	ENST00000074304.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000074304	NM_001134224.1	33	tCt/tTt	3/26	0.446882460050278	3	FACETS	0.997	0.931	1	0.997	0.931	1	CLONAL	2	TRUE	1	0.455731177964194	3		554	524	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046353	128046353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	102	663	0	ENST00000285398.2:c.910C>T	p.Pro304Ser	p.P304S	ENST00000285398	NM_000122.1	304	Cct/Tct	7/15	0.446882460050278	3	FACETS	0.903	0.809	1	0.451	0.404	0.501	CLONAL	1	TRUE	1	0.455731177964194	3		663	609	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634848	158634848	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	132	359	1	ENST00000263640.3:c.338C>T	p.Ser113Phe	p.S113F	ENST00000263640	NM_001105.4	113	tCc/tTc	5/11	0.446882460050278	3	FACETS	0.931	0.854	1	0.931	0.854	1	CLONAL	2	TRUE	1	0.455731177964194	3		360	382	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198260816	198260816	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	87	926	0	ENST00000335508.6:c.3503C>T	p.Ala1168Val	p.A1168V	ENST00000335508	NM_012433.2	1168	gCc/gTc	23/25	0.446882460050278	3	FACETS	0.75	0.665	0.841	0.375	0.332	0.421	SUBCLONAL	1	TRUE	1	0.455731177964194	3		926	625	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426678	212426678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	145	703	0	ENST00000342788.4:c.2437G>A	p.Asp813Asn	p.D813N	ENST00000342788	NM_005235.2	813	Gat/Aat	20/28	0.446882460050278	3	FACETS	1	0.966	1	0.556	0.508	0.606	CLONAL	1	TRUE	1	0.455731177964194	3		703	703	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030002	36030002	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	102	654	0	ENST00000358208.4:c.1040-3C>T		p.X347_splice	ENST00000358208		347			0.455731177964194	5	FACETS	0.939	0.839	1	0.313	0.279	0.348	CLONAL	1	TRUE	2	0.455731177964194	5		654	803	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757468	40757468	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	128	693	1	ENST00000373198.4:c.2830G>A	p.Asp944Asn	p.D944N	ENST00000373198	NM_133170.3	944	Gac/Aac	20/32	0.455731177964194	5	FACETS	1	0.95	1	0.358	0.324	0.394	CLONAL	1	TRUE	2	0.455731177964194	5		694	881	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101088	41101088	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	186	658	1	ENST00000373198.4:c.1268C>T	p.Thr423Ile	p.T423I	ENST00000373198	NM_133170.3	423	aCc/aTc	8/32	0.455731177964194	5	FACETS	0.996	0.923	1	0.664	0.615	0.714	CLONAL	2	TRUE	2	0.455731177964194	5		659	690	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101131	41101131	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	89	691	1	ENST00000373198.4:c.1225C>T	p.Pro409Ser	p.P409S	ENST00000373198	NM_133170.3	409	Ccc/Tcc	8/32	0.455731177964194	5	FACETS	0.945	0.838	1	0.315	0.279	0.353	CLONAL	1	TRUE	2	0.455731177964194	5		692	696	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755752	39755752	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	151	502	0	ENST00000288319.7:c.1013A>C	p.Glu338Ala	p.E338A	ENST00000288319	NM_182918.3	338	gAg/gCg	10/10	0.455731177964194	3	FACETS	0.894	0.825	0.966	0.894	0.825	0.966	CLONAL	2	TRUE	1	0.455731177964194	3		502	455	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475621	12475621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	112	612	0	ENST00000287820.6:c.1495G>A	p.Glu499Lys	p.E499K	ENST00000287820	NM_015869.4	499	Gag/Aag	7/7	0.332956616831758	4	FACETS	0.926	0.833	1	0.463	0.416	0.512	CLONAL	1	TRUE	2	0.455731177964194	4		612	773	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713315	30713315	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	150	500	0	ENST00000295754.5:c.640G>C	p.Glu214Gln	p.E214Q	ENST00000295754	NM_003242.5	214	Gag/Cag	4/7	0.332956616831758	4	FACETS	0.801	0.735	0.87	0.801	0.735	0.87	CLONAL	2	TRUE	2	0.455731177964194	4		500	598	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180354	38180354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1489688140	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	103	857	0	ENST00000396334.3:c.202G>A	p.Asp68Asn	p.D68N	ENST00000396334	NM_002468.4	68	Gac/Aac	1/5	0.43453671855234	4	FACETS	0.725	0.648	0.807	0.362	0.324	0.404	SUBCLONAL	1	TRUE	2	0.455731177964194	4		857	908	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181442	38181442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	78	525	0	ENST00000396334.3:c.455C>T	p.Pro152Leu	p.P152L	ENST00000396334	NM_002468.4	152	cCa/cTa	2/5	0.43453671855234	4	FACETS	0.8	0.703	0.904	0.4	0.351	0.452	CLONAL	1	TRUE	2	0.455731177964194	4		525	623	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967251	134967251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1480515100	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	110	686	1	ENST00000398015.3:c.2590G>A	p.Asp864Asn	p.D864N	ENST00000398015	NM_004441.4	864	Gac/Aac	14/16	0.332956616831758	4	FACETS	0.957	0.861	1	0.479	0.43	0.53	CLONAL	1	TRUE	2	0.455731177964194	4		687	734	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279193	142279193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1351809006	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	89	735	0	ENST00000350721.4:c.1453C>T	p.Pro485Ser	p.P485S	ENST00000350721	NM_001184.3	485	Cct/Tct	6/47	0.332956616831758	4	FACETS	0.782	0.693	0.877	0.391	0.346	0.439	SUBCLONAL	1	TRUE	2	0.455731177964194	4		735	727	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279219	142279219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	86	724	1	ENST00000350721.4:c.1427C>T	p.Ser476Phe	p.S476F	ENST00000350721	NM_001184.3	476	tCc/tTc	6/47	0.332956616831758	4	FACETS	0.772	0.682	0.867	0.386	0.341	0.434	SUBCLONAL	1	TRUE	2	0.455731177964194	4		725	712	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146488	185146488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	54	591	0	ENST00000265026.3:c.119C>T	p.Pro40Leu	p.P40L	ENST00000265026	NM_004721.4	40	cCc/cTc	2/14	0.332956616831758	4	FACETS	0.494	0.421	0.574	0.247	0.21	0.287	SUBCLONAL	1	TRUE	2	0.455731177964194	4		591	699	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440362	187440362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	196	599	0	ENST00000232014.4:c.2005C>T	p.His669Tyr	p.H669Y	ENST00000232014	NM_001130845.1	669	Cac/Tac	10/10	0.332956616831758	4	FACETS	0.86	0.799	0.923	0.86	0.799	0.923	CLONAL	2	TRUE	2	0.455731177964194	4		599	728	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957879	1957879	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	323	589	0	ENST00000382891.5:c.2845C>T	p.Gln949Ter	p.Q949*	ENST00000382891	NM_133335.3	949	Cag/Tag	15/22	0.352590324028835	5	FACETS	1	0.981	1			1	CLONAL	3	TRUE	NA	0.455731177964194	5		589	747	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747912	41747912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	110	704	1	ENST00000226382.2:c.857C>T	p.Ser286Leu	p.S286L	ENST00000226382	NM_003924.3	286	tCg/tTg	3/3	0.352590324028835	5	FACETS	1	0.932	1			1	CLONAL	1	TRUE	NA	0.455731177964194	5		705	776	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146605	55146605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	328	785	4	ENST00000257290.5:c.2279C>T	p.Ser760Leu	p.S760L	ENST00000257290	NM_006206.4	760	tCa/tTa	16/23	0.449034452960785	4	FACETS	0.93	0.884	0.976	0.93	0.884	0.976	CLONAL	3	TRUE	1	0.455731177964194	4		789	751	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595563	55595563	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	197	498	0	ENST00000288135.5:c.2053A>C	p.Lys685Gln	p.K685Q	ENST00000288135	NM_000222.2	685	Aaa/Caa	14/21	0.449034452960785	4	FACETS	0.867	0.811	0.924	0.867	0.811	0.924	CLONAL	3	TRUE	1	0.455731177964194	4		498	484	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984968	55984968	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	94	486	0	ENST00000263923.4:c.162-1G>A		p.X54_splice	ENST00000263923	NM_002253.2	54			0.449034452960785	4	FACETS	1	0.898	1	0.336	0.299	0.375	CLONAL	1	TRUE	1	0.455731177964194	4		486	596	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356154	66356154	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	301	646	0	ENST00000273854.3:c.1343C>A	p.Ser448Tyr	p.S448Y	ENST00000273854	NM_004439.5	448	tCc/tAc	5/18	0.449034452960785	4	FACETS	0.883	0.837	0.929	0.883	0.837	0.929	CLONAL	3	TRUE	1	0.455731177964194	4		646	726	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361181	66361181	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764677767	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	32	518	0	ENST00000273854.3:c.991G>A	p.Glu331Lys	p.E331K	ENST00000273854	NM_004439.5	331	Gaa/Aaa	4/18	0.449034452960785	4	FACETS	0.334	0.27	0.407	0.111	0.09	0.136	SUBCLONAL	1	TRUE	1	0.455731177964194	4		518	612	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467497	66467497	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	210	369	0	ENST00000273854.3:c.772G>A	p.Val258Met	p.V258M	ENST00000273854	NM_004439.5	258	Gtg/Atg	3/18	0.449034452960785	4	FACETS	0.934	0.877	0.991	0.934	0.877	0.991	CLONAL	3	TRUE	1	0.455731177964194	4		369	479	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467499	66467499	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	205	370	0	ENST00000273854.3:c.770A>G	p.Glu257Gly	p.E257G	ENST00000273854	NM_004439.5	257	gAa/gGa	3/18	0.449034452960785	4	FACETS	0.919	0.862	0.977	0.919	0.862	0.977	CLONAL	3	TRUE	1	0.455731177964194	4		370	475	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541486	187541486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	289	513	0	ENST00000441802.2:c.6254C>T	p.Pro2085Leu	p.P2085L	ENST00000441802	NM_005245.3	2085	cCc/cTc	10/27	0.449034452960785	4	FACETS	0.962	0.912	1	0.962	0.912	1	CLONAL	3	TRUE	1	0.455731177964194	4		513	640	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554882	187554882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	106	480	0	ENST00000441802.2:c.4279C>T	p.Leu1427Phe	p.L1427F	ENST00000441802	NM_005245.3	1427	Ctc/Ttc	7/27	0.449034452960785	4	FACETS	1	0.943	1	0.358	0.321	0.397	CLONAL	1	TRUE	1	0.455731177964194	4		480	630	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628376	187628376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	428	799	1	ENST00000441802.2:c.2606C>T	p.Ser869Leu	p.S869L	ENST00000441802	NM_005245.3	869	tCa/tTa	2/27	0.449034452960785	4	FACETS	0.949	0.909	0.99	0.949	0.909	0.99	CLONAL	3	TRUE	1	0.455731177964194	4		800	960	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295216	1295216	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs35733142	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	68	426	0				ENST00000310581	NM_198253.2	-/1132			0.43453671855234	4	FACETS	0.936	0.817	1	0.468	0.408	0.533	CLONAL	1	TRUE	2	0.455731177964194	4		426	464	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31424551	31424551	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1427406017	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	155	943	0	ENST00000344624.3:c.3244C>T	p.Pro1082Ser	p.P1082S	ENST00000344624		1082	Cct/Tct	25/33	0.43453671855234	4	FACETS	0.85	0.777	0.927	0.425	0.388	0.464	CLONAL	1	TRUE	2	0.455731177964194	4		943	1165	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876381	35876382	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	163	712	2	ENST00000303115.3:c.1173_1174delinsAA	p.Glu392Lys	p.E392K	ENST00000303115	NM_002185.3	391	agGGag/agAAag	8/8	0.43453671855234	4	FACETS	1	0.981	1	0.614	0.564	0.666	CLONAL	1	TRUE	2	0.455731177964194	4		714	848	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876533	35876533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1329173277	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	207	788	0	ENST00000303115.3:c.1325G>A	p.Gly442Glu	p.G442E	ENST00000303115	NM_002185.3	442	gGa/gAa	8/8	0.43453671855234	4	FACETS	1	0.99	1	0.695	0.645	0.747	CLONAL	1	TRUE	2	0.455731177964194	4		788	951	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950392	38950393	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	70	530	2	ENST00000357387.3:c.3557_3558delinsTT	p.Thr1186Ile	p.T1186I	ENST00000357387	NM_152756.3	1186	aCC/aTT	31/38	0.43453671855234	4	FACETS	0.745	0.65	0.848	0.373	0.325	0.424	SUBCLONAL	1	TRUE	2	0.455731177964194	4		532	600	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80071535	80071535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	70	481	1	ENST00000265081.6:c.2276C>T	p.Ser759Phe	p.S759F	ENST00000265081	NM_002439.4	759	tCt/tTt	16/24	0.43453671855234	4	FACETS	0.775	0.676	0.882	0.388	0.338	0.441	SUBCLONAL	1	TRUE	2	0.455731177964194	4		482	577	SUCCESS
APC	324	MSKCC	GRCh37	5	112177569	112177569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879254172	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	124	553	0	ENST00000257430.4:c.6278C>T	p.Ser2093Phe	p.S2093F	ENST00000257430	NM_000038.5	2093	tCc/tTc	16/16	0.414011260258453	4	FACETS	0.762	0.692	0.834			1	SUBCLONAL	2	TRUE	NA	0.455731177964194	4		553	520	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149447873	149447873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	158	763	2	ENST00000286301.3:c.1531G>A	p.Asp511Asn	p.D511N	ENST00000286301	NM_005211.3	511	Gat/Aat	11/22	0.455731177964194	3	FACETS	0.995	0.912	1	0.497	0.456	0.541	CLONAL	1	TRUE	1	0.455731177964194	3		765	856	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497247	149497247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375922340	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	227	831	1	ENST00000261799.4:c.3071C>T	p.Pro1024Leu	p.P1024L	ENST00000261799	NM_002609.3	1024	cCc/cTc	22/23	0.455731177964194	3	FACETS	0.802	0.749	0.855	0.802	0.749	0.855	CLONAL	2	TRUE	1	0.455731177964194	3		832	763	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562973	176562973	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	122	802	2	ENST00000439151.2:c.869G>A	p.Gly290Glu	p.G290E	ENST00000439151	NM_022455.4	290	gGa/gAa	2/23	0.37759593664745	4	FACETS	0.86	0.777	0.948	0.43	0.388	0.474	CLONAL	1	TRUE	2	0.455731177964194	4		804	906	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057603	180057603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	273	828	0	ENST00000261937.6:c.352G>A	p.Ala118Thr	p.A118T	ENST00000261937	NM_182925.4	118	Gca/Aca	3/30	0.37759593664745	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.455731177964194	4		828	762	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910687	29910687	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	51	1012	0	ENST00000376809.5:c.227T>G	p.Ile76Arg	p.I76R	ENST00000376809	NM_002116.7	76	aTa/aGa	2/8	0.455731177964194	3	FACETS	0.291	0.246	0.34	0.097	0.082	0.114	SUBCLONAL	1	TRUE	0	0.455731177964194	3		1012	946	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30682885	30682885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762279433	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	162	847	3	ENST00000376406.3:c.68C>T	p.Ser23Phe	p.S23F	ENST00000376406	NM_014641.2	23	tCc/tTc	2/15	0.455731177964194	3	FACETS	1	0.962	1	0.36	0.33	0.391	CLONAL	1	TRUE	0	0.455731177964194	3		850	808	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89791019	89791019	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226649883	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	37	142	0	ENST00000336032.3:c.406G>A	p.Gly136Arg	p.G136R	ENST00000336032	NM_006813.2	136	Gga/Aga	1/2	NA	2	FACETS	1	0.949	1			1	INDETERMINATE	1	TRUE	NA	0.455731177964194	2		142	120	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553260	106553260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368878266	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	230	776	1	ENST00000369096.4:c.1225C>T	p.His409Tyr	p.H409Y	ENST00000369096	NM_001198.3	409	Cac/Tac	5/7	NA	2	FACETS	0.867	0.815	0.92			1	INDETERMINATE	2	TRUE	NA	0.455731177964194	2		777	582	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638338	117638338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	114	653	2	ENST00000368508.3:c.6103C>T	p.Leu2035Phe	p.L2035F	ENST00000368508	NM_002944.2	2035	Ctt/Ttt	38/43	0.305001933219328	1	FACETS	0.822	0.744	0.903	0.822	0.744	0.903	CLONAL	1	TRUE	0	0.455731177964194	1		655	470	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678977	117678977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1052987141	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	62	546	0	ENST00000368508.3:c.3844C>T	p.Pro1282Ser	p.P1282S	ENST00000368508	NM_002944.2	1282	Cct/Tct	24/43	0.305001933219328	1	FACETS	0.592	0.514	0.676	0.592	0.514	0.676	SUBCLONAL	1	TRUE	0	0.455731177964194	1		546	355	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683963	117683963	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761293495	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	76	818	0	ENST00000368508.3:c.3184G>A	p.Glu1062Lys	p.E1062K	ENST00000368508	NM_002944.2	1062	Gaa/Aaa	21/43	0.305001933219328	1	FACETS	0.546	0.48	0.616	0.546	0.48	0.616	SUBCLONAL	1	TRUE	0	0.455731177964194	1		818	472	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706872	117706872	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141715386	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	212	643	0	ENST00000368508.3:c.2278C>T	p.Leu760Phe	p.L760F	ENST00000368508	NM_002944.2	760	Ctc/Ttc	15/43	0.305001933219328	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.455731177964194	1		643	485	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710542	117710542	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	44	288	0	ENST00000368508.3:c.1730G>A	p.Trp577Ter	p.W577*	ENST00000368508	NM_002944.2	577	tGg/tAg	12/43	0.305001933219328	1	FACETS	0.847	0.721	0.982	0.847	0.721	0.982	CLONAL	1	TRUE	0	0.455731177964194	1		288	176	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710638	117710638	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	76	508	0	ENST00000368508.3:c.1634T>A	p.Leu545Ter	p.L545*	ENST00000368508	NM_002944.2	545	tTg/tAg	12/43	0.305001933219328	1	FACETS	0.627	0.552	0.706	0.627	0.552	0.706	SUBCLONAL	1	TRUE	0	0.455731177964194	1		508	411	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710693	117710693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	81	485	0	ENST00000368508.3:c.1579G>A	p.Glu527Lys	p.E527K	ENST00000368508	NM_002944.2	527	Gaa/Aaa	12/43	0.305001933219328	1	FACETS	0.668	0.591	0.749	0.668	0.591	0.749	SUBCLONAL	1	TRUE	0	0.455731177964194	1		485	411	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724380	117724380	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs769105985	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	146	809	0	ENST00000368508.3:c.499C>T	p.Arg167Ter	p.R167*	ENST00000368508	NM_002944.2	167	Cga/Tga	6/43	NA	2	FACETS	1	0.948	1			1	INDETERMINATE	1	TRUE	NA	0.455731177964194	2		809	612	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004321	150004321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	79	596	1	ENST00000253339.5:c.1904C>T	p.Ser635Phe	p.S635F	ENST00000253339		635	tCt/tTt	3/7	0.455731177964194	2	FACETS	0.927	0.821	1	0.463	0.41	0.52	CLONAL	1	TRUE	0	0.455731177964194	2		597	374	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468282	50468282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	132	689	1	ENST00000331340.3:c.1517C>T	p.Ser506Leu	p.S506L	ENST00000331340	NM_006060.4	506	tCg/tTg	8/8	0.455731177964194	5	FACETS	1	0.907	1	0.333	0.302	0.367	CLONAL	1	TRUE	2	0.455731177964194	5		690	975	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508918	106508918	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	71	466	0	ENST00000359195.3:c.912C>G	p.His304Gln	p.H304Q	ENST00000359195	NM_002649.2	304	caC/caG	2/11	0.455731177964194	6	FACETS	0.787	0.686	0.896	0.197	0.171	0.224	SUBCLONAL	1	TRUE	2	0.455731177964194	6		466	757	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509810	106509810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	134	723	1	ENST00000359195.3:c.1804G>A	p.Glu602Lys	p.E602K	ENST00000359195	NM_002649.2	602	Gaa/Aaa	2/11	0.455731177964194	6	FACETS	0.866	0.784	0.952	0.216	0.196	0.238	CLONAL	1	TRUE	2	0.455731177964194	6		724	1298	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526648	106526648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	126	701	1	ENST00000359195.3:c.2941G>A	p.Glu981Lys	p.E981K	ENST00000359195	NM_002649.2	981	Gag/Aag	10/11	0.455731177964194	6	FACETS	0.978	0.884	1	0.244	0.221	0.27	CLONAL	1	TRUE	2	0.455731177964194	6		702	1081	SUCCESS
MET	4233	MSKCC	GRCh37	7	116414965	116414965	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	428	975	1	ENST00000397752.3:c.3059C>T	p.Ser1020Leu	p.S1020L	ENST00000397752	NM_000245.2	1020	tCa/tTa	15/21	0.455731177964194	6	FACETS	1	0.992	1	0.59	0.561	0.619	CLONAL	2	TRUE	2	0.455731177964194	6		976	1521	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477831	140477831	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	82	784	0	ENST00000288602.6:c.1477C>T	p.Gln493Ter	p.Q493*	ENST00000288602	NM_004333.4	493	Cag/Tag	12/18	0.455731177964194	6	FACETS	0.7	0.616	0.791	0.175	0.154	0.198	SUBCLONAL	1	TRUE	2	0.455731177964194	6		784	982	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346137	152346138	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	216	752	1	ENST00000359321.1:c.432_433delinsTT	p.Leu145Phe	p.L145F	ENST00000359321	NM_005431.1	144	tgCCtt/tgTTtt	3/3	0.455731177964194	6	FACETS	0.789	0.733	0.848	0.395	0.366	0.424	SUBCLONAL	2	TRUE	2	0.455731177964194	6		753	1148	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346368	152346368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	175	728	0	ENST00000359321.1:c.202C>T	p.Pro68Ser	p.P68S	ENST00000359321	NM_005431.1	68	Ccc/Tcc	3/3	0.455731177964194	6	FACETS	0.849	0.782	0.918	0.424	0.391	0.459	CLONAL	2	TRUE	2	0.455731177964194	6		728	865	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370816	55370816	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	70	509	0	ENST00000297316.4:c.121del	p.Asp41ThrfsTer2	p.D41Tfs*2	ENST00000297316	NM_022454.3	40	Ggg/gg	1/2	0.332956616831758	4	FACETS	0.913	0.798	1	0.456	0.399	0.518	CLONAL	1	TRUE	2	0.455731177964194	4		509	490	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863046	56863046	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	181	883	2	ENST00000519728.1:c.313C>T	p.Leu105Phe	p.L105F	ENST00000519728	NM_002350.3	105	Ctt/Ttt	5/13	0.332956616831758	4	FACETS	1	0.989	1	0.723	0.668	0.78	CLONAL	1	TRUE	2	0.455731177964194	4		885	800	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005857	69005857	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	123	679	0	ENST00000288368.4:c.2268G>A	p.Trp756Ter	p.W756*	ENST00000288368	NM_024870.2	756	tgG/tgA	21/40	0.332956616831758	4	FACETS	1	0.976	1	0.621	0.562	0.682	CLONAL	1	TRUE	2	0.455731177964194	4		679	633	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020555	69020555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	170	706	1	ENST00000288368.4:c.2927C>T	p.Ser976Phe	p.S976F	ENST00000288368	NM_024870.2	976	tCt/tTt	24/40	0.332956616831758	4	FACETS	0.908	0.839	0.979	0.908	0.839	0.979	CLONAL	2	TRUE	2	0.455731177964194	4		707	598	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129904	69129904	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	157	431	0	ENST00000288368.4:c.4658G>A	p.Gly1553Glu	p.G1553E	ENST00000288368	NM_024870.2	1553	gGa/gAa	38/40	0.332956616831758	4	FACETS	0.904	0.832	0.977	0.904	0.832	0.977	CLONAL	2	TRUE	2	0.455731177964194	4		431	555	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69143593	69143593	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	249	583	0	ENST00000288368.4:c.4801C>T	p.Pro1601Ser	p.P1601S	ENST00000288368	NM_024870.2	1601	Ccc/Tcc	40/40	0.332956616831758	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.455731177964194	4		583	744	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980731	70980731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	190	907	0	ENST00000276594.2:c.737C>T	p.Ser246Phe	p.S246F	ENST00000276594	NM_024504.3	246	tCc/tTc	3/8	0.332956616831758	4	FACETS	0.867	0.804	0.932	0.867	0.804	0.932	CLONAL	2	TRUE	2	0.455731177964194	4		907	700	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141572694	141572694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756399814	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	102	638	0	ENST00000220592.5:c.376C>T	p.Arg126Cys	p.R126C	ENST00000220592	NM_012154.3	126	Cgc/Tgc	4/19	0.332956616831758	4	FACETS	1	0.901	1	0.503	0.45	0.559	CLONAL	1	TRUE	2	0.455731177964194	4		638	648	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460499	8460499	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764587066	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	173	774	0	ENST00000356435.5:c.3787G>A	p.Glu1263Lys	p.E1263K	ENST00000356435		1263	Gaa/Aaa	22/35	0.455731177964194	2	FACETS	1	0.971	1	0.553	0.51	0.597	CLONAL	1	TRUE	0	0.455731177964194	2		774	687	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27172652	27172652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	113	734	0	ENST00000380036.4:c.667C>T	p.Leu223Phe	p.L223F	ENST00000380036	NM_000459.3	223	Ctc/Ttc	5/23	0.455731177964194	2	FACETS	0.936	0.845	1	0.468	0.422	0.515	CLONAL	1	TRUE	0	0.455731177964194	2		734	530	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202829	27202829	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	86	683	0	ENST00000380036.4:c.1921C>T	p.Gln641Ter	p.Q641*	ENST00000380036	NM_000459.3	641	Caa/Taa	13/23	0.455731177964194	2	FACETS	0.852	0.757	0.952	0.426	0.378	0.476	CLONAL	1	TRUE	0	0.455731177964194	2		683	443	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285785	87285785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760689213	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	104	664	0	ENST00000277120.3:c.122C>T	p.Ser41Phe	p.S41F	ENST00000277120		41	tCt/tTt	2/19	0.455731177964194	3	FACETS	1	0.902	1	0.502	0.451	0.556	CLONAL	1	TRUE	1	0.455731177964194	3		664	558	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248088	98248088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369105527	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	123	780	0	ENST00000331920.6:c.463C>T	p.Pro155Ser	p.P155S	ENST00000331920	NM_000264.3	155	Cct/Tct	3/24	0.455731177964194	3	FACETS	1	0.976	1	0.616	0.559	0.675	CLONAL	1	TRUE	1	0.455731177964194	3		780	538	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390653	139390653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	160	862	1	ENST00000277541.6:c.7538C>T	p.Ser2513Phe	p.S2513F	ENST00000277541	NM_017617.3	2513	tCc/tTc	34/34	0.455731177964194	3	FACETS	1	0.982	1	0.62	0.57	0.672	CLONAL	1	TRUE	1	0.455731177964194	3		863	695	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393590	139393590	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	126	799	0	ENST00000277541.6:c.6056C>T	p.Ala2019Val	p.A2019V	ENST00000277541	NM_017617.3	2019	gCc/gTc	32/34	0.455731177964194	3	FACETS	1	0.957	1	0.547	0.496	0.6	CLONAL	1	TRUE	1	0.455731177964194	3		799	621	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139804390	139804390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750248731	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	119	973	1	ENST00000247668.2:c.547C>T	p.Pro183Ser	p.P183S	ENST00000247668	NM_021138.3	183	Ccc/Tcc	6/11	0.455731177964194	3	FACETS	0.943	0.852	1	0.471	0.426	0.519	CLONAL	1	TRUE	1	0.455731177964194	3		974	680	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932974	39932974	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	223	591	1	ENST00000378444.4:c.1625C>T	p.Ser542Leu	p.S542L	ENST00000378444	NM_001123385.1	542	tCa/tTa	4/15	0.455731177964194	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.455731177964194	2		592	485	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411992	63411992	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	64	713	0	ENST00000330258.3:c.1175A>T	p.Glu392Val	p.E392V	ENST00000330258	NM_152424.3	392	gAg/gTg	2/2	0.446882460050278	3	FACETS	0.581	0.503	0.665	0.29	0.251	0.333	SUBCLONAL	1	TRUE	1	0.455731177964194	3		713	594	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412088	63412088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs943717871	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	283	1043	0	ENST00000330258.3:c.1079C>T	p.Ser360Phe	p.S360F	ENST00000330258	NM_152424.3	360	tCc/tTc	2/2	0.446882460050278	3	FACETS	0.915	0.863	0.968	0.915	0.863	0.968	CLONAL	2	TRUE	1	0.455731177964194	3		1043	833	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412448	63412448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	130	965	1	ENST00000330258.3:c.719C>T	p.Ser240Phe	p.S240F	ENST00000330258	NM_152424.3	240	tCt/tTt	2/2	0.446882460050278	3	FACETS	0.904	0.82	0.992	0.452	0.41	0.496	CLONAL	1	TRUE	1	0.455731177964194	3		966	775	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349186	70349186	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1304464082	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	92	640	1	ENST00000374080.3:c.3598C>T	p.Arg1200Cys	p.R1200C	ENST00000374080		1200	Cgc/Tgc	26/45	0.446882460050278	3	FACETS	0.788	0.701	0.881	0.394	0.35	0.441	SUBCLONAL	1	TRUE	1	0.455731177964194	3		641	629	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349538	70349538	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	217	575	0	ENST00000374080.3:c.3700G>A	p.Glu1234Lys	p.E1234K	ENST00000374080		1234	Gaa/Aaa	27/45	0.446882460050278	3	FACETS	0.935	0.875	0.997	0.935	0.875	0.997	CLONAL	2	TRUE	1	0.455731177964194	3		575	625	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352994	70352994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	64	808	0	ENST00000374080.3:c.4549G>A	p.Asp1517Asn	p.D1517N	ENST00000374080		1517	Gac/Aac	33/45	0.446882460050278	3	FACETS	0.451	0.39	0.518	0.226	0.195	0.259	SUBCLONAL	1	TRUE	1	0.455731177964194	3		808	764	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123156381	123156381	+	splice_region_variant,5_prime_UTR_variant	Splice_Region	SNP	G	G	A	rs751957300	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	14	168	0	ENST00000218089.9:c.-97G>A		p.X33_splice	ENST00000218089	NM_001042749.1	33		3/35	0.446882460050278	3	FACETS	0.604	0.44	0.798	0.302	0.22	0.399	SUBCLONAL	1	TRUE	1	0.455731177964194	3		168	125	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227896	123227896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	61	471	0	ENST00000218089.9:c.3607G>A	p.Asp1203Asn	p.D1203N	ENST00000218089	NM_001042749.1	1203	Gat/Aat	33/35	0.446882460050278	3	FACETS	0.828	0.717	0.948	0.414	0.358	0.474	CLONAL	1	TRUE	1	0.455731177964194	3		471	397	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227785	53227786	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	A	novel	NA	P-0019263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	281	894	0	ENST00000375401.3:c.2402_2403delinsT	p.Ala801ValfsTer15	p.A801Vfs*15	ENST00000375401	NM_004187.3	801	gCC/gT	17/26	0.455731177964194	2	FACETS	0.995	0.943	1	0.995	0.943	1	CLONAL	2	TRUE	0	0.455731177964194	2		894	620	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295195	1295195	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0019305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	236	359	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		359	435	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0019909-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	80	1058	3	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.288933200584743	3	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	1	0.288933200584743	3		1061	300	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0019909-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	39	151	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.288933200584743	2		151	224	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238161	133238161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772307459	NA	P-0019909-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	36	1063	1	ENST00000320574.5:c.2816C>T	p.Ala939Val	p.A939V	ENST00000320574	NM_006231.2	939	gCc/gTc	24/49	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.288933200584743	2		1064	238	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425470	49425470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019909-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	21	1225	0	ENST00000301067.7:c.13018C>T	p.His4340Tyr	p.H4340Y	ENST00000301067	NM_003482.3	4340	Cat/Tat	39/54	1	2	FACETS	0.598	0.462	0.756	0.598	0.462	0.756	SUBCLONAL	1	TRUE	1	0.288933200584743	2		1225	243	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437442	110437442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1464082904	NA	P-0019909-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	25	1084	2	ENST00000375856.3:c.959C>T	p.Pro320Leu	p.P320L	ENST00000375856	NM_003749.2	320	cCc/cTc	1/2	1	2	FACETS	0.611	0.483	0.759	0.611	0.483	0.759	SUBCLONAL	1	TRUE	1	0.288933200584743	2		1086	283	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857304	9857304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019909-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	46	856	0	ENST00000330684.3:c.4097C>T	p.Pro1366Leu	p.P1366L	ENST00000330684	NM_001134407.1	1366	cCt/cTt	13/13	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.288933200584743	2		856	258	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514519	41514519	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019909-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	30	1197	0	ENST00000373198.4:c.142G>T	p.Gly48Trp	p.G48W	ENST00000373198	NM_133170.3	48	Ggg/Tgg	2/32	1	2	FACETS	0.752	0.608	0.915	0.752	0.608	0.915	CLONAL	1	TRUE	1	0.288933200584743	2		1197	276	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526178	189526178	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019909-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	37	1052	1	ENST00000264731.3:c.442C>T	p.Pro148Ser	p.P148S	ENST00000264731	NM_003722.4	148	Ccc/Tcc	4/14	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.288933200584743	2		1053	245	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1953914	1953914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019909-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	41	1312	0	ENST00000382891.5:c.2093C>T	p.Ser698Phe	p.S698F	ENST00000382891	NM_133335.3	698	tCc/tTc	11/22	1	2	FACETS	0.904	0.756	1	0.904	0.756	1	CLONAL	1	TRUE	1	0.288933200584743	2		1312	314	SUCCESS
APC	324	MSKCC	GRCh37	5	112175547	112175547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019909-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	37	581	1	ENST00000257430.4:c.4256G>A	p.Ser1419Asn	p.S1419N	ENST00000257430	NM_000038.5	1419	aGc/aAc	16/16	0.288933200584743	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	0	0.288933200584743	1		582	191	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709102	117709102	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1470291308	NA	P-0019909-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	30	1093	0	ENST00000368508.3:c.1855C>T	p.Pro619Ser	p.P619S	ENST00000368508	NM_002944.2	619	Cct/Tct	13/43	1	2	FACETS	0.821	0.664	0.996	0.821	0.664	0.996	CLONAL	1	TRUE	1	0.288933200584743	2		1093	253	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157971	27157971	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746368893	NA	P-0019909-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	34	1047	1	ENST00000380036.4:c.195G>A	p.Met65Ile	p.M65I	ENST00000380036	NM_000459.3	65	atG/atA	2/23	0.288933200584743	1	FACETS	0.911	0.75	1	0.911	0.75	1	CLONAL	1	TRUE	0	0.288933200584743	1		1048	221	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753852	133753852	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019909-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	39	1094	1	ENST00000318560.5:c.1321C>T	p.Pro441Ser	p.P441S	ENST00000318560	NM_005157.4	441	Ccg/Tcg	8/11	1	2	FACETS	0.934	0.778	1	0.934	0.778	1	CLONAL	1	TRUE	1	0.288933200584743	2		1095	289	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0020110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	289	528	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.684586859533005	1	FACETS	0.995	0.947	1	0.995	0.947	1	CLONAL	1	TRUE	0	0.684586859533005	1		528	558	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244361	41244361	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	63	1070	0	ENST00000357654.3:c.3187T>A	p.Ser1063Thr	p.S1063T	ENST00000357654	NM_007294.3	1063	Tcc/Acc	10/23	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.13	2		1070	788	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485921	8485921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	32	624	0	ENST00000356435.5:c.2896C>T	p.Leu966Phe	p.L966F	ENST00000356435		966	Ctc/Ttc	17/35	1	2	FACETS	0.84	0.68	1	0.84	0.68	1	CLONAL	1	TRUE	1	0.13	2		624	586	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971029	21971029	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519852	NA	P-0020191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	44	474	0	ENST00000304494.5:c.329G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tGg/tAg	2/3	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.13	2		474	631	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	356	284	0				ENST00000310581	NM_198253.2	-/1132			0.880066752915391	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.880066752915391	1		284	424	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	317	451	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.880066752915391	2		451	697	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	438	409	1	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.880066752915391	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.880066752915391	1		410	547	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	385	615	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.492703044456326	1	FACETS	0.719	0.69	0.748	0.719	0.69	0.748	INDETERMINATE	1	TRUE	0	0.880066752915391	1		615	681	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455576	189455576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754361670	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	250	711	1	ENST00000264731.3:c.110G>A	p.Arg37Gln	p.R37Q	ENST00000264731	NM_003722.4	37	cGa/cAa	2/14	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.880066752915391	2		712	548	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149260	119149260	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs868103494	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	340	759	0	ENST00000264033.4:c.1268T>A	p.Ile423Asn	p.I423N	ENST00000264033	NM_005188.3	423	aTt/aAt	9/16	0.880066752915391	1	FACETS	0.979	0.948	1	0.979	0.948	1	CLONAL	1	TRUE	0	0.880066752915391	1		759	442	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	302	845	3	ENST00000394830.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000394830	NM_018313.4	710	Cga/Tga	17/30	1	2	FACETS	0.975	0.925	1	0.975	0.925	1	CLONAL	1	TRUE	1	0.880066752915391	2		848	704	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865159	57865159	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	586	1178	0	ENST00000228682.2:c.2636C>A	p.Pro879His	p.P879H	ENST00000228682	NM_005269.2	879	cCt/cAt	12/12	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.880066752915391	2		1178	1244	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030213	180030213	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	353	789	2	ENST00000261937.6:c.4071C>A	p.Phe1357Leu	p.F1357L	ENST00000261937	NM_182925.4	1357	ttC/ttA	30/30	1	2	FACETS	0.886	0.843	0.931	0.886	0.843	0.931	CLONAL	1	TRUE	1	0.880066752915391	2		791	905	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850704	63850704	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	18	502	0	ENST00000279873.7:c.1482del	p.Ile497Ter	p.I497*	ENST00000279873	NM_032199.2	494	aaG/aa	10/10	0.880066752915391	1	FACETS	0.08	0.06	0.104	0.08	0.06	0.104	SUBCLONAL	1	TRUE	0	0.880066752915391	1		502	286	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811694	102811694	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	543	1009	0	ENST00000307046.8:c.490G>A	p.Gly164Arg	p.G164R	ENST00000307046	NM_001111285.1	164	Ggg/Agg	4/4	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.880066752915391	2		1009	1174	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858006	9858006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	369	678	0	ENST00000330684.3:c.3395C>T	p.Pro1132Leu	p.P1132L	ENST00000330684	NM_001134407.1	1132	cCa/cTa	13/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.880066752915391	2		678	813	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16055304	16055304	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	249	578	0	ENST00000268712.3:c.798T>A	p.Tyr266Ter	p.Y266*	ENST00000268712	NM_006311.3	266	taT/taA	8/46	0.880066752915391	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.880066752915391	1		578	305	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677742	47677742	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	novel	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	474	482	0	ENST00000347630.2:c.1123T>C	p.Ter375GlnextTer25	p.*375Qext*25	ENST00000347630	NM_001007230.1	375	Taa/Caa	11/11	0.880066752915391	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.880066752915391	3		482	763	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350738	15350738	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs567489459	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	491	1208	1	ENST00000263377.2:c.3265G>A	p.Val1089Ile	p.V1089I	ENST00000263377	NM_058243.2	1089	Gtc/Atc	15/20	1	2	FACETS	0.975	0.936	1	0.975	0.936	1	CLONAL	1	TRUE	1	0.880066752915391	2		1209	1144	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224222	36224222	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1281441914	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	451	999	1	ENST00000222270.7:c.6772C>T	p.Pro2258Ser	p.P2258S	ENST00000222270	NM_014727.1	2258	Cct/Tct	28/37	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.880066752915391	2		1000	941	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794866	42794866	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758817184	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	378	784	0	ENST00000575354.2:c.1946C>T	p.Ser649Phe	p.S649F	ENST00000575354	NM_015125.3	649	tCc/tTc	10/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.880066752915391	2		784	819	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794869	42794870	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	321	810	1	ENST00000575354.2:c.1949_1950delinsTT	p.Ala650Val	p.A650V	ENST00000575354	NM_015125.3	650	gCC/gTT	10/20	1	2	FACETS	0.93	0.883	0.978	0.93	0.883	0.978	CLONAL	1	TRUE	1	0.880066752915391	2		811	784	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716207	52716208	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	300	711	1	ENST00000322088.6:c.652-1_652delinsAA		p.X218_splice	ENST00000322088	NM_014225.5	218		6/15	1	2	FACETS	0.91	0.862	0.959	0.91	0.862	0.959	CLONAL	1	TRUE	1	0.880066752915391	2		712	749	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215617226	215617226	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777937955	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	193	474	0	ENST00000260947.4:c.1622C>T	p.Ser541Leu	p.S541L	ENST00000260947	NM_000465.2	541	tCg/tTg	7/11	1	2	FACETS	0.995	0.931	1	0.995	0.931	1	CLONAL	1	TRUE	1	0.880066752915391	2		474	441	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935592	49935592	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	434	948	0	ENST00000296474.3:c.1772G>A	p.Gly591Asp	p.G591D	ENST00000296474	NM_002447.2	591	gGc/gAc	5/20	1	2	FACETS	0.915	0.875	0.956	0.915	0.875	0.956	CLONAL	1	TRUE	1	0.880066752915391	2		948	1078	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682412	52682412	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	250	675	0	ENST00000394830.3:c.761T>C	p.Leu254Pro	p.L254P	ENST00000394830	NM_018313.4	254	cTc/cCc	8/30	1	2	FACETS	0.956	0.902	1	0.956	0.902	1	CLONAL	1	TRUE	1	0.880066752915391	2		675	594	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139832	55139832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	316	616	0	ENST00000257290.5:c.1493C>T	p.Ala498Val	p.A498V	ENST00000257290	NM_006206.4	498	gCc/gTc	10/23	0.194973226792396	1	FACETS	0.657	0.626	0.688	0.657	0.626	0.688	INDETERMINATE	1	TRUE	0	0.880066752915391	1		616	612	SUCCESS
APC	324	MSKCC	GRCh37	5	112116523	112116523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	153	407	0	ENST00000257430.4:c.568G>A	p.Glu190Lys	p.E190K	ENST00000257430	NM_000038.5	190	Gaa/Aaa	6/16	0.880066752915391	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.880066752915391	1		407	178	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323328	31323328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	204	446	0	ENST00000412585.2:c.661C>T	p.His221Tyr	p.H221Y	ENST00000412585	NM_005514.6	221	Cat/Tat	4/8	0.880066752915391	3	FACETS	0.869	0.808	0.932	0.435	0.404	0.466	CLONAL	1	TRUE	1	0.880066752915391	3		446	768	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288581	33288581	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	292	541	0	ENST00000374542.5:c.971T>C	p.Leu324Ser	p.L324S	ENST00000374542	NM_001141970.1	324	tTa/tCa	3/8	0.880066752915391	3	FACETS	0.987	0.93	1	0.494	0.465	0.523	CLONAL	1	TRUE	1	0.880066752915391	3		541	968	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117639379	117639379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	266	741	0	ENST00000368508.3:c.5977G>A	p.Glu1993Lys	p.E1993K	ENST00000368508	NM_002944.2	1993	Gaa/Aaa	37/43	1	2	FACETS	0.993	0.939	1	0.993	0.939	1	CLONAL	1	TRUE	1	0.880066752915391	2		741	609	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969942	161969942	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	435	695	0	ENST00000366898.1:c.1027C>T	p.Pro343Ser	p.P343S	ENST00000366898	NM_004562.2	343	Ccg/Tcg	9/12	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.880066752915391	2		695	919	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185543	27185543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1417765647	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	417	891	2	ENST00000380036.4:c.1243C>T	p.Leu415Phe	p.L415F	ENST00000380036	NM_000459.3	415	Ctc/Ttc	9/23	0.880066752915391	3	FACETS	0.96	0.913	1			1	CLONAL	1	TRUE	NA	0.880066752915391	3		893	1422	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27217705	27217705	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	309	758	1	ENST00000380036.4:c.3011G>A	p.Trp1004Ter	p.W1004*	ENST00000380036	NM_000459.3	1004	tGg/tAg	19/23	0.880066752915391	3	FACETS	0.886	0.836	0.938			1	CLONAL	1	TRUE	NA	0.880066752915391	3		759	1141	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637126	93637126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	303	584	0	ENST00000375746.1:c.1176G>A	p.Met392Ile	p.M392I	ENST00000375746	NM_001174167.1	392	atG/atA	9/14	1	2	FACETS	0.946	0.897	0.995	0.946	0.897	0.995	CLONAL	1	TRUE	1	0.880066752915391	2		584	728	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028832	47028832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781848934	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	478	997	3	ENST00000377604.3:c.136C>T	p.Arg46Cys	p.R46C	ENST00000377604	NM_001204468.1	46	Cgc/Tgc	3/24	1	2	FACETS	0.989	0.949	1	0.989	0.949	1	CLONAL	1	TRUE	1	0.880066752915391	2		1000	1098	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829826	76829826	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	novel	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	205	599	1	ENST00000373344.5:c.6218-3C>T		p.X2073_splice	ENST00000373344	NM_000489.3	2073			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.880066752915391	2		600	410	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855238	76855238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	254	751	0	ENST00000373344.5:c.5749G>A	p.Glu1917Lys	p.E1917K	ENST00000373344	NM_000489.3	1917	Gaa/Aaa	24/35	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.880066752915391	2		751	563	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850701	63850702	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020288-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	18	490	0	ENST00000279873.7:c.1481dup	p.Lys495GlufsTer33	p.K495Efs*33	ENST00000279873	NM_032199.2	493	-/A	10/10	0.880066752915391	1	FACETS	0.08	0.06	0.104	0.08	0.06	0.104	SUBCLONAL	1	TRUE	0	0.880066752915391	1		490	285	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0020319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	292	528	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.264077172813234	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	2	0.264077172813234	4		528	1372	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0020319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	285	1049	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.264077172813234	2	FACETS	0.992	0.933	1	0.992	0.933	1	CLONAL	2	TRUE	0	0.264077172813234	2		1049	1088	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382214	152382214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	200	881	0	ENST00000206249.3:c.1324G>A	p.Gly442Arg	p.G442R	ENST00000206249	NM_000125.3	442	Gga/Aga	6/8	0.264077172813234	2	FACETS	0.857	0.795	0.921	0.857	0.795	0.921	CLONAL	2	TRUE	0	0.264077172813234	2		881	884	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849054	156849054	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786205449	NA	P-0020319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1509	253	1039	1	ENST00000524377.1:c.1946G>A	p.Arg649Gln	p.R649Q	ENST00000524377	NM_002529.3	649	cGg/cAg	15/17	0.264077172813234	7	FACETS	0.903	0.842	0.966			1	CLONAL	2	TRUE	NA	0.264077172813234	7		1040	1762	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372314	55372314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	280	922	0	ENST00000297316.4:c.1004C>T	p.Pro335Leu	p.P335L	ENST00000297316	NM_022454.3	335	cCc/cTc	2/2	0.264077172813234	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.264077172813234	3		922	1100	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793457	18793457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202064696	NA	P-0020319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	182	637	0	ENST00000266497.5:c.4154C>T	p.Pro1385Leu	p.P1385L	ENST00000266497		1385	cCa/cTa	30/31	0.264077172813234	3	FACETS	0.99	0.915	1	0.99	0.915	1	CLONAL	2	TRUE	1	0.264077172813234	3		637	788	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031979	10031979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	140	934	4	ENST00000330684.3:c.844G>A	p.Asp282Asn	p.D282N	ENST00000330684	NM_001134407.1	282	Gat/Aat	3/13	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.264077172813234	2		938	1059	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163309256	163309256	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	162	627	0	ENST00000271452.3:c.595C>T	p.His199Tyr	p.H199Y	ENST00000271452	NM_145697.2	199	Cat/Tat	8/14	0.264077172813234	5	FACETS	0.924	0.847	1	0.616	0.565	0.669	CLONAL	2	TRUE	2	0.264077172813234	5		627	927	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406568	70406568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	147	945	0	ENST00000373644.4:c.4082C>T	p.Ser1361Leu	p.S1361L	ENST00000373644	NM_030625.2	1361	tCa/tTa	4/12	1	2	FACETS	0.993	0.905	1	0.993	0.905	1	CLONAL	1	TRUE	1	0.264077172813234	2		945	1121	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643536	38643536	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	238	722	1	ENST00000299084.4:c.1006G>T	p.Val336Leu	p.V336L	ENST00000299084	NM_152594.2	336	Gta/Tta	7/7	0.264077172813234	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.264077172813234	3		723	964	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250890	99250890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	207	655	0	ENST00000268035.6:c.194C>T	p.Ser65Phe	p.S65F	ENST00000268035	NM_000875.3	65	tCc/tTc	2/21	0.264077172813234	3	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	1	0.264077172813234	3		655	878	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942027	81942028	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	74	528	0	ENST00000359376.3:c.1564_1565delinsTT	p.Pro522Phe	p.P522F	ENST00000359376	NM_002661.3	522	CCc/TTc	17/33	1	2	FACETS	0.865	0.757	0.981	0.865	0.757	0.981	CLONAL	1	TRUE	1	0.264077172813234	2		528	648	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687061	37687061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	92	671	1	ENST00000447079.4:c.3965C>T	p.Ala1322Val	p.A1322V	ENST00000447079	NM_015083.1	1322	gCc/gTc	14/14	0.264077172813234	3	FACETS	0.858	0.761	0.962	0.429	0.38	0.481	CLONAL	1	TRUE	1	0.264077172813234	3		672	919	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538320	9538320	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	320	756	1	ENST00000353224.5:c.1678C>T	p.His560Tyr	p.H560Y	ENST00000353224	NM_177990.2	560	Cat/Tat	7/10	0.264077172813234	4	FACETS	0.957	0.904	1	0.957	0.904	1	CLONAL	3	TRUE	1	0.264077172813234	4		757	1067	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256765	46256765	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs757864008	NA	P-0020319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	87	539	0	ENST00000371998.3:c.821C>T	p.Ser274Leu	p.S274L	ENST00000371998		274	tCa/tTa	8/23	0.264077172813234	4	FACETS	0.885	0.782	0.996	0.295	0.26	0.332	CLONAL	1	TRUE	1	0.264077172813234	4		539	941	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588814	52588814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	141	818	0	ENST00000394830.3:c.4214C>T	p.Pro1405Leu	p.P1405L	ENST00000394830	NM_018313.4	1405	cCa/cTa	27/30	0.264077172813234	3	FACETS	1	0.97	1			1	CLONAL	1	TRUE	NA	0.264077172813234	3		818	1050	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928495	69928496	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	380	957	3	ENST00000352241.4:c.315_316delinsTT	p.Leu106Phe	p.L106F	ENST00000352241	NM_198159.2	105	acCCtt/acTTtt	2/10	0.264077172813234	4	FACETS	0.933	0.885	0.981			1	CLONAL	3	TRUE	NA	0.264077172813234	4		960	1300	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803604	1803604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	134	903	0	ENST00000260795.2:c.782C>T	p.Ala261Val	p.A261V	ENST00000260795		261	gCc/gTc	6/17	0.264077172813234	3	FACETS	1	0.95	1	0.535	0.485	0.588	CLONAL	1	TRUE	1	0.264077172813234	3		903	1073	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509943	187509943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	155	506	0	ENST00000441802.2:c.13570C>T	p.Gln4524Ter	p.Q4524*	ENST00000441802	NM_005245.3	4524	Caa/Taa	27/27	0.264077172813234	3	FACETS	0.951	0.872	1	0.951	0.872	1	CLONAL	2	TRUE	1	0.264077172813234	3		506	699	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120290	94120290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	125	506	0	ENST00000369303.4:c.761G>A	p.Gly254Glu	p.G254E	ENST00000369303	NM_004440.3	254	gGa/gAa	3/17	0.264077172813234	2	FACETS	0.9	0.818	0.985	0.9	0.818	0.985	CLONAL	2	TRUE	0	0.264077172813234	2		506	526	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223598	55223598	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	181	622	0	ENST00000275493.2:c.965G>A	p.Gly322Asp	p.G322D	ENST00000275493	NM_005228.3	322	gGc/gAc	8/28	0.264077172813234	3	FACETS	0.991	0.916	1	0.991	0.916	1	CLONAL	2	TRUE	1	0.264077172813234	3		622	783	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282199	38282199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	240	825	0	ENST00000425967.3:c.857C>T	p.Pro286Leu	p.P286L	ENST00000425967	NM_001174067.1	286	cCc/cTc	8/19	0.264077172813234	3	FACETS	0.985	0.92	1	0.985	0.92	1	CLONAL	2	TRUE	1	0.264077172813234	3		825	1044	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295253	+	upstream_gene_variant	5'Flank	ONP	GAGG	GAGG	AAGA	novel	NA	P-0020319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	152	733	0				ENST00000310581	NM_198253.2	-/1132			0.264077172813234	3	FACETS	0.957	0.877	1	0.957	0.877	1	CLONAL	2	TRUE	1	0.264077172813234	3		733	681	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	110	151	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.831	0.75	0.914	0.831	0.75	0.914	CLONAL	1	TRUE	1	0.564741185637157	2		151	469	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0020382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	885	1175	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	0.564741185637157	3	FACETS	0.995	0.971	1	0.995	0.971	1	CLONAL	3	TRUE	0	0.564741185637157	3		1175	1347	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750437	41750437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	170	801	0	ENST00000226382.2:c.191C>T	p.Ser64Phe	p.S64F	ENST00000226382	NM_003924.3	64	tCc/tTc	1/3	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.564741185637157	2		801	584	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515151	149515151	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558122968	NA	P-0020382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	257	1024	2	ENST00000261799.4:c.331G>A	p.Asp111Asn	p.D111N	ENST00000261799	NM_002609.3	111	Gat/Aat	3/23	1	2	FACETS	0.963	0.903	1	0.963	0.903	1	CLONAL	1	TRUE	1	0.564741185637157	2		1026	945	SUCCESS
BLM	641	MSKCC	GRCh37	15	91308637	91308637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866243946	NA	P-0020382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	143	587	0	ENST00000355112.3:c.2186C>T	p.Ser729Phe	p.S729F	ENST00000355112	NM_000057.2	729	tCc/tTc	9/22	0.564741185637157	3	FACETS	1	0.964	1	0.549	0.502	0.597	CLONAL	1	TRUE	1	0.564741185637157	3		587	592	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510880	157510880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	193	815	0	ENST00000346085.5:c.3655C>T	p.Pro1219Ser	p.P1219S	ENST00000346085	NM_020732.3	1219	Cct/Tct	14/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.564741185637157	2		815	662	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222346	53222346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	310	674	0	ENST00000375401.3:c.4486G>A	p.Glu1496Lys	p.E1496K	ENST00000375401	NM_004187.3	1496	Gaa/Aaa	26/26	1	1	FACETS	0.824	0.791	0.857	1	0.996	1	CLONAL	2	TRUE	0	0.564741185637157	1		674	478	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390106	89390106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	109	486	0	ENST00000336596.2:c.855G>A	p.Met285Ile	p.M285I	ENST00000336596	NM_005233.5	285	atG/atA	4/17	1	2	FACETS	0.93	0.842	1	0.93	0.842	1	CLONAL	1	TRUE	1	0.564741185637157	2		486	415	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248717	212248717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	109	559	0	ENST00000342788.4:c.3550G>A	p.Asp1184Asn	p.D1184N	ENST00000342788	NM_005235.2	1184	Gat/Aat	28/28	1	2	FACETS	0.923	0.835	1	0.923	0.835	1	CLONAL	1	TRUE	1	0.564741185637157	2		559	418	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612807	228612807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	249	971	1	ENST00000366696.1:c.220G>A	p.Glu74Lys	p.E74K	ENST00000366696	NM_003493.2	74	Gag/Aag	1/1	0.564741185637157	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.564741185637157	1		972	591	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374353	81374353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	124	563	1	ENST00000222390.5:c.709C>T	p.His237Tyr	p.H237Y	ENST00000222390	NM_000601.4	237	Cat/Tat	6/18	1	2	FACETS	0.911	0.829	0.996	0.911	0.829	0.996	CLONAL	1	TRUE	1	0.564741185637157	2		564	482	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056165	27056165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	164	739	0	ENST00000324856.7:c.1161G>A	p.Met387Ile	p.M387I	ENST00000324856	NM_006015.4	387	atG/atA	2/20	1	2	FACETS	0.974	0.899	1	0.974	0.899	1	CLONAL	1	TRUE	1	0.564741185637157	2		739	596	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644448	18644448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751457593	NA	P-0020382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	178	851	2	ENST00000266497.5:c.2626C>T	p.Leu876Phe	p.L876F	ENST00000266497		876	Ctt/Ttt	18/31	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.564741185637157	2		853	569	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955470	48955470	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	155	683	0	ENST00000267163.4:c.1586A>T	p.Tyr529Phe	p.Y529F	ENST00000267163	NM_000321.2	529	tAc/tTc	17/27	1	2	FACETS	0.961	0.885	1	0.961	0.885	1	CLONAL	1	TRUE	1	0.564741185637157	2		683	571	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032128	10032128	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747198986	NA	P-0020382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	195	880	0	ENST00000330684.3:c.695C>T	p.Ser232Phe	p.S232F	ENST00000330684	NM_001134407.1	232	tCc/tTc	3/13	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.564741185637157	2		880	639	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213209	39213209	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772527384	NA	P-0020382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	213	1014	0	ENST00000402219.2:c.3758C>T	p.Pro1253Leu	p.P1253L	ENST00000402219	NM_005633.3	1253	cCt/cTt	23/23	1	2	FACETS	0.897	0.835	0.961	0.897	0.835	0.961	CLONAL	1	TRUE	1	0.564741185637157	2		1014	841	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45658370	45658370	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	183	825	1	ENST00000407780.3:c.16C>T	p.Pro6Ser	p.P6S	ENST00000407780	NM_001283052.1	6	Cct/Tct	2/7	1	2	FACETS	0.935	0.866	1	0.935	0.866	1	CLONAL	1	TRUE	1	0.564741185637157	2		826	693	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181977	38181977	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs755841635	NA	P-0020382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	202	785	1	ENST00000396334.3:c.601C>T	p.Arg201Ter	p.R201*	ENST00000396334	NM_002468.4	201	Cga/Tga	3/5	1	2	FACETS	0.995	0.926	1	0.995	0.926	1	CLONAL	1	TRUE	1	0.564741185637157	2		786	719	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610631	52610631	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	162	840	1	ENST00000394830.3:c.3542C>T	p.Pro1181Leu	p.P1181L	ENST00000394830	NM_018313.4	1181	cCc/cTc	23/30	1	2	FACETS	0.921	0.848	0.996	0.921	0.848	0.996	CLONAL	1	TRUE	1	0.564741185637157	2		841	623	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457263	89457263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	122	778	0	ENST00000336596.2:c.1744C>T	p.His582Tyr	p.H582Y	ENST00000336596	NM_005233.5	582	Cat/Tat	9/17	1	2	FACETS	0.856	0.777	0.937	0.856	0.777	0.937	CLONAL	1	TRUE	1	0.564741185637157	2		778	505	SUCCESS
APC	324	MSKCC	GRCh37	5	112176390	112176390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660893	NA	P-0020382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	46	346	0	ENST00000257430.4:c.5099C>T	p.Ala1700Val	p.A1700V	ENST00000257430	NM_000038.5	1700	gCt/gTt	16/16	1	2	FACETS	0.654	0.555	0.761	0.654	0.555	0.761	SUBCLONAL	1	TRUE	1	0.564741185637157	2		346	249	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149465987	149465987	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	251	659	0	ENST00000286301.3:c.4G>A	p.Gly2Ser	p.G2S	ENST00000286301	NM_005211.3	2	Ggc/Agc	2/22	1	2	FACETS	0.953	0.893	1	0.953	0.893	1	CLONAL	1	TRUE	1	0.564741185637157	2		659	933	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038476	180038476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1327663265	NA	P-0020382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	239	1078	0	ENST00000261937.6:c.3541G>A	p.Glu1181Lys	p.E1181K	ENST00000261937	NM_182925.4	1181	Gaa/Aaa	27/30	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.564741185637157	2		1078	835	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172018	32172018	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	162	842	0	ENST00000375023.3:c.3014G>A	p.Gly1005Glu	p.G1005E	ENST00000375023	NM_004557.3	1005	gGa/gAa	19/30	1	2	FACETS	0.916	0.844	0.991	0.916	0.844	0.991	CLONAL	1	TRUE	1	0.564741185637157	2		842	626	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964400	93964400	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1051471746	NA	P-0020382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	121	794	1	ENST00000369303.4:c.2497G>A	p.Gly833Arg	p.G833R	ENST00000369303	NM_004440.3	833	Gga/Aga	14/17	1	2	FACETS	0.906	0.824	0.992	0.906	0.824	0.992	CLONAL	1	TRUE	1	0.564741185637157	2		795	473	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150381	157150381	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	195	810	1	ENST00000346085.5:c.1563G>A	p.Met521Ile	p.M521I	ENST00000346085	NM_020732.3	521	atG/atA	2/20	1	2	FACETS	0.963	0.894	1	0.963	0.894	1	CLONAL	1	TRUE	1	0.564741185637157	2		811	717	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467778	50467778	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	184	762	0	ENST00000331340.3:c.1013C>T	p.Ser338Phe	p.S338F	ENST00000331340	NM_006060.4	338	tCc/tTc	8/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.564741185637157	2		762	583	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371738	116371738	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	128	442	1	ENST00000397752.3:c.1217C>T	p.Ser406Leu	p.S406L	ENST00000397752	NM_000245.2	406	tCa/tTa	3/21	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.564741185637157	2		443	422	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238348	98238348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	149	715	0	ENST00000331920.6:c.1696C>T	p.Pro566Ser	p.P566S	ENST00000331920	NM_000264.3	566	Cca/Tca	12/24	1	2	FACETS	0.885	0.812	0.961	0.885	0.812	0.961	CLONAL	1	TRUE	1	0.564741185637157	2		715	596	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0020388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	209	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.196090049013501	6	FACETS	0.933	0.868	1	0.933	0.868	1	CLONAL	4	TRUE	2	0.196090049013501	6		288	795	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0020388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	121	284	0				ENST00000310581	NM_198253.2	-/1132			0.0702739360837403	4	FACETS	0.987	0.892	1	0.987	0.892	1	INDETERMINATE	2	TRUE	2	0.196090049013501	4		284	748	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248617	212248617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765120252	NA	P-0020388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	120	708	1	ENST00000342788.4:c.3650G>A	p.Gly1217Glu	p.G1217E	ENST00000342788	NM_005235.2	1217	gGa/gAa	28/28	0.0702739360837403	4	FACETS	0.92	0.83	1	0.92	0.83	1	INDETERMINATE	2	TRUE	2	0.196090049013501	4		709	796	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0020388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	273	631	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.196090049013501	3	FACETS	0.952	0.894	1	1	0.993	1	CLONAL	3	TRUE	1	0.196090049013501	3		631	1070	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216983	2216983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329819181	NA	P-0020388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	259	1070	0	ENST00000398665.3:c.2438C>T	p.Pro813Leu	p.P813L	ENST00000398665	NM_032482.2	813	cCc/cTc	21/28	0.0702739360837403	4	FACETS	1	0.982	1	1	0.982	1	INDETERMINATE	2	TRUE	2	0.196090049013501	4		1070	1386	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954933	2954933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755425231	NA	P-0020388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	436	1014	0	ENST00000396946.4:c.2777C>T	p.Pro926Leu	p.P926L	ENST00000396946	NM_032415.4	926	cCg/cTg	21/25	0.196090049013501	6	FACETS	1	0.989	1	1	0.989	1	CLONAL	4	TRUE	2	0.196090049013501	6		1014	1386	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670754	134670754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752494038	NA	P-0020388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	113	625	1	ENST00000398015.3:c.665G>A	p.Arg222Gln	p.R222Q	ENST00000398015	NM_004441.4	222	cGg/cAg	3/16	0.0702739360837403	4	FACETS	1	0.915	1	1	0.915	1	INDETERMINATE	2	TRUE	2	0.196090049013501	4		626	678	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797706	45797706	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	276	930	0	ENST00000450313.1:c.986T>G	p.Val329Gly	p.V329G	ENST00000450313	NM_012222.2	329	gTg/gGg	11/16	0.196090049013501	5	FACETS	0.91	0.853	0.969	0.91	0.853	0.969	CLONAL	3	TRUE	2	0.196090049013501	5		930	1334	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247571	123247571	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	86	896	0	ENST00000358487.5:c.1920G>A	p.Met640Ile	p.M640I	ENST00000358487	NM_000141.4	640	atG/atA	14/18	0.183689100663255	3	FACETS	1	0.935	1	0.544	0.48	0.613	CLONAL	1	TRUE	1	0.196090049013501	3		896	885	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911055	94911055	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	76	849	0	ENST00000536441.1:c.1075C>T	p.His359Tyr	p.H359Y	ENST00000536441	NM_144665.3	359	Cat/Tat	8/10	0.196090049013501	3	FACETS	1	0.965	1	0.644	0.565	0.729	CLONAL	1	TRUE	1	0.196090049013501	3		849	661	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445937	49445937	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1269	117	1310	1	ENST00000301067.7:c.1529C>T	p.Ser510Leu	p.S510L	ENST00000301067	NM_003482.3	510	tCa/tTa	10/54	0.196090049013501	3	FACETS	0.945	0.85	1	0.473	0.425	0.524	CLONAL	1	TRUE	1	0.196090049013501	3		1311	1386	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641338	23641338	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555460475	NA	P-0020388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	143	945	1	ENST00000261584.4:c.2137C>T	p.Pro713Ser	p.P713S	ENST00000261584	NM_024675.3	713	Cct/Tct	5/13	0.196090049013501	3	FACETS	0.885	0.806	0.967	0.885	0.806	0.967	CLONAL	2	TRUE	1	0.196090049013501	3		946	905	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783766	50783766	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1196482079	NA	P-0020388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	97	767	1	ENST00000398568.2:c.157C>T	p.Arg53Cys	p.R53C	ENST00000398568	NM_001042412.1	53	Cgt/Tgt	3/18	0.196090049013501	3	FACETS	0.828	0.739	0.923	0.828	0.739	0.923	CLONAL	2	TRUE	1	0.196090049013501	3		768	656	SUCCESS
YES1	7525	MSKCC	GRCh37	18	732954	732954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	44	695	1	ENST00000314574.4:c.1303C>T	p.Pro435Ser	p.P435S	ENST00000314574	NM_005433.3	435	Cca/Tca	11/12	0.183689100663255	3	FACETS	0.747	0.625	0.882	0.373	0.312	0.441	SUBCLONAL	1	TRUE	1	0.196090049013501	3		696	660	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208293	5208293	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	169	1049	2	ENST00000357368.4:c.5597C>T	p.Thr1866Ile	p.T1866I	ENST00000357368	NM_002850.3	1866	aCt/aTt	36/38	0.0702739360837403	4	FACETS	0.818	0.75	0.889	0.818	0.75	0.889	INDETERMINATE	2	TRUE	2	0.196090049013501	4		1051	1260	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097135	11097135	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778071122	NA	P-0020388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	201	946	1	ENST00000358026.2:c.626C>T	p.Pro209Leu	p.P209L	ENST00000358026	NM_001128849.1	209	cCg/cTg	4/36	0.0702739360837403	4	FACETS	1	0.975	1	1	0.975	1	INDETERMINATE	2	TRUE	2	0.196090049013501	4		947	1096	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670529	134670530	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0020388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	84	913	1	ENST00000398015.3:c.440_441delinsTT	p.Ser147Phe	p.S147F	ENST00000398015	NM_004441.4	147	tCC/tTT	3/16	0.0702739360837403	4	FACETS	1	0.895	1	0.508	0.448	0.574	INDETERMINATE	1	TRUE	2	0.196090049013501	4		914	1008	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806183	1806183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	99	1042	2	ENST00000260795.2:c.1202C>T	p.Pro401Leu	p.P401L	ENST00000260795		401	cCc/cTc	8/17	0.196090049013501	3	FACETS	0.974	0.867	1	0.487	0.433	0.545	CLONAL	1	TRUE	1	0.196090049013501	3		1044	1138	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843318	128843318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1496	112	1148	0	ENST00000249373.3:c.425C>T	p.Pro142Leu	p.P142L	ENST00000249373	NM_005631.4	142	cCc/cTc	2/12	0.196090049013501	6	FACETS	0.989	0.886	1	0.247	0.221	0.275	CLONAL	1	TRUE	2	0.196090049013501	6		1148	1608	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992980	68992980	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0020388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	114	523	0	ENST00000288368.4:c.1786-1G>A		p.X596_splice	ENST00000288368	NM_024870.2	596			0.196090049013501	6	FACETS	0.904	0.816	0.996	0.904	0.816	0.996	CLONAL	3	TRUE	3	0.196090049013501	6		523	597	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485939	8485939	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1381492310	NA	P-0020388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	42	508	0	ENST00000356435.5:c.2878G>A	p.Asp960Asn	p.D960N	ENST00000356435		960	Gat/Aat	17/35	0.188215159342703	3	FACETS	1	0.932	1	0.412	0.344	0.486	CLONAL	1	TRUE	0	0.196090049013501	3		508	381	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971066	21971066	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0020388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	242	703	0	ENST00000304494.5:c.292del	p.His98ThrfsTer48	p.H98Tfs*48	ENST00000304494	NM_000077.4	98	Cac/ac	2/3	0.188215159342703	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	TRUE	0	0.196090049013501	3		703	833	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576033	29576033	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	148	717	0	ENST00000356175.3:c.4006C>T	p.Gln1336Ter	p.Q1336*	ENST00000356175	NM_000267.3	1336	Cag/Tag	30/57	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.455102878684032	2		717	595	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0020451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	107	525	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.455102878684032	2		525	437	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0020451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	164	734	1	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	0.91	0.837	0.986	0.91	0.837	0.986	CLONAL	1	TRUE	1	0.455102878684032	2		735	792	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141790	108141790	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs995271490	NA	P-0020451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	29	444	0	ENST00000278616.4:c.2839-1G>C		p.X947_splice	ENST00000278616	NM_000051.3	947			0.455102878684032	1	FACETS	0.273	0.219	0.335	0.273	0.219	0.335	SUBCLONAL	1	TRUE	0	0.455102878684032	1		444	360	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880221	+	missense_variant	Missense_Mutation	DNP	TG	TG	GT	novel	NA	P-0020451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	125	695	2	ENST00000269571.5:c.2264_2265delinsGT	p.Leu755Cys	p.L755C	ENST00000269571		755	tTG/tGT	19/27	1	2	FACETS	0.796	0.722	0.874	0.796	0.722	0.874	SUBCLONAL	1	TRUE	1	0.455102878684032	2		697	690	SUCCESS
APC	324	MSKCC	GRCh37	5	112163650	112163650	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1458155204	NA	P-0020451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	93	422	0	ENST00000257430.4:c.1573T>G	p.Cys525Gly	p.C525G	ENST00000257430	NM_000038.5	525	Tgc/Ggc	13/16	1	2	FACETS	0.971	0.868	1	0.971	0.868	1	CLONAL	1	TRUE	1	0.455102878684032	2		422	421	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967915	93967915	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	124	621	0	ENST00000369303.4:c.2012A>G	p.Tyr671Cys	p.Y671C	ENST00000369303	NM_004440.3	671	tAc/tGc	11/17	0.455102878684032	1	FACETS	0.925	0.843	1	0.925	0.843	1	CLONAL	1	TRUE	0	0.455102878684032	1		621	455	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	264	151	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.919	0.863	0.977	0.919	0.863	0.977	CLONAL	1	TRUE	1	0.621488612221861	2		151	924	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244982	123244982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	319	864	1	ENST00000358487.5:c.2122C>T	p.Pro708Ser	p.P708S	ENST00000358487	NM_000141.4	708	Ccc/Tcc	16/18	0.621488612221861	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.621488612221861	1		865	676	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453138	140453139	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTA	rs727502902	NA	P-0020641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	638	635	0	ENST00000288602.6:c.1794_1796dup	p.Thr599dup	p.T599dup	ENST00000288602	NM_004333.4	599	aca/acTACa	15/18	0.618976016836598	4	FACETS	0.909	0.879	0.939	0.909	0.879	0.939	CLONAL	3	TRUE	1	0.621488612221861	4		635	1221	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356850483	NA	P-0020641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	235	635	3	ENST00000342505.4:c.1289C>T	p.Pro430Leu	p.P430L	ENST00000342505	NM_002227.2	430	cCg/cTg	9/25	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.621488612221861	2		638	742	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692986	89693051	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGTAAGGACCAGAGACAAAAAGGTAAGTTATTTTTTGATGTTTTTCCTTTCCTCTTCCTGGATCT	AAGTAAGGACCAGAGACAAAAAGGTAAGTTATTTTTTGATGTTTTTCCTTTCCTCTTCCTGGATCT	-	novel	NA	P-0020641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	145	609	0	ENST00000371953.3:c.470_492+43del		p.X157_splice	ENST00000371953	NM_000314.4	157		5/9	0.621488612221861	1	FACETS	0.71	0.653	0.768	0.71	0.653	0.768	SUBCLONAL	1	TRUE	0	0.621488612221861	1		609	453	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857149	9857149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	204	505	1	ENST00000330684.3:c.4252G>A	p.Gly1418Ser	p.G1418S	ENST00000330684	NM_001134407.1	1418	Ggc/Agc	13/13	1	2	FACETS	0.971	0.905	1	0.971	0.905	1	CLONAL	1	TRUE	1	0.621488612221861	2		506	676	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995216	15995216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	299	887	2	ENST00000268712.3:c.2977C>T	p.Pro993Ser	p.P993S	ENST00000268712	NM_006311.3	993	Cca/Tca	22/46	1	2	FACETS	0.964	0.909	1	0.964	0.909	1	CLONAL	1	TRUE	1	0.621488612221861	2		889	998	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897322	78897322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	364	1048	1	ENST00000306801.3:c.2657C>T	p.Ser886Phe	p.S886F	ENST00000306801	NM_020761.2	886	tCc/tTc	23/34	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.621488612221861	2		1049	1155	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1623990	1623991	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	257	1011	0	ENST00000344749.5:c.508_509delinsTT	p.Pro170Phe	p.P170F	ENST00000344749	NM_001136139.2	170	CCc/TTc	8/19	1	2	FACETS	0.847	0.793	0.901	0.847	0.793	0.901	CLONAL	1	TRUE	1	0.621488612221861	2		1011	977	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260139	10260140	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0020641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	289	928	0	ENST00000340748.4:c.2527_2528del	p.Trp843GlyfsTer27	p.W843Gfs*27	ENST00000340748		843	TGg/g	25/40	1	2	FACETS	0.957	0.901	1	0.957	0.901	1	CLONAL	1	TRUE	1	0.621488612221861	2		928	972	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278102	15278102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143939165	NA	P-0020641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	407	1323	3	ENST00000263388.2:c.5320G>A	p.Asp1774Asn	p.D1774N	ENST00000263388	NM_000435.2	1774	Gac/Aac	29/33	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.621488612221861	2		1326	1308	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52723473	52723473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	283	795	1	ENST00000322088.6:c.1334C>T	p.Ser445Phe	p.S445F	ENST00000322088	NM_014225.5	445	tCc/tTc	11/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.621488612221861	2		796	895	SUCCESS
ALK	238	MSKCC	GRCh37	2	29473983	29473983	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	358	958	0	ENST00000389048.3:c.2192C>T	p.Thr731Ile	p.T731I	ENST00000389048	NM_004304.4	731	aCc/aTc	12/29	1	2	FACETS	0.996	0.944	1	0.996	0.944	1	CLONAL	1	TRUE	1	0.621488612221861	2		958	1157	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566814	212566814	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	209	419	0	ENST00000342788.4:c.1367G>A	p.Gly456Glu	p.G456E	ENST00000342788	NM_005235.2	456	gGa/gAa	12/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.621488612221861	2		419	613	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561340	9561340	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	232	672	1	ENST00000353224.5:c.442G>A	p.Glu148Lys	p.E148K	ENST00000353224	NM_177990.2	148	Gag/Aag	4/10	1	2	FACETS	0.922	0.862	0.983	0.922	0.862	0.983	CLONAL	1	TRUE	1	0.621488612221861	2		673	810	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180624	32180624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1340588950	NA	P-0020641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	343	780	4	ENST00000375023.3:c.2503G>A	p.Gly835Ser	p.G835S	ENST00000375023	NM_004557.3	835	Ggc/Agc	16/30	0.621488612221861	3	FACETS	1	0.992	1	0.62	0.587	0.654	CLONAL	1	TRUE	1	0.621488612221861	3		784	1167	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395430	116395430	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	230	697	2	ENST00000397752.3:c.1723C>T	p.Leu575Phe	p.L575F	ENST00000397752	NM_000245.2	575	Ctt/Ttt	6/21	0.618976016836598	4	FACETS	0.866	0.805	0.929	0.289	0.268	0.31	CLONAL	1	TRUE	1	0.621488612221861	4		699	1386	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399273	139399273	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	500	1369	1	ENST00000277541.6:c.4870G>A	p.Glu1624Lys	p.E1624K	ENST00000277541	NM_017617.3	1624	Gag/Aag	26/34	0.610106762647361	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.621488612221861	1		1370	1060	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0020691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	365	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.416258788805641	6	FACETS	1	0.99	1	0.771	0.732	0.811	CLONAL	2	TRUE	3	0.625861645956394	6		288	1135	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	147	151	0				ENST00000310581	NM_198253.2	-/1132			0.237923830441526	2	FACETS	1	0.987	1	0.671	0.621	0.721	INDETERMINATE	1	TRUE	0	0.625861645956394	2		151	350	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717715	89717715	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1057519368	NA	P-0020691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	98	737	0	ENST00000371953.3:c.740T>A	p.Leu247Ter	p.L247*	ENST00000371953	NM_000314.4	247	tTa/tAa	7/9	0.446800625518082	0	FACETS	0.321	0.289	0.355			1	SUBCLONAL	1	TRUE	0	0.625861645956394	0		737	365	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517559	176517571	+	frameshift_variant	Frame_Shift_Del	DEL	AGATTGCCAGCTT	AGATTGCCAGCTT	-	novel	NA	P-0020691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	131	1030	0	ENST00000292408.4:c.260_272del	p.Glu87AlafsTer17	p.E87Afs*17	ENST00000292408	NM_213647.1	87	gAGATTGCCAGCTTc/gc	3/18	0.237923830441526	2	FACETS	0.592	0.538	0.649	0.296	0.269	0.325	INDETERMINATE	1	TRUE	0	0.625861645956394	2		1030	707	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0020768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	171	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.291575859235132	2		288	1166	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584482	189584482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	132	474	3	ENST00000264731.3:c.778C>T	p.Pro260Ser	p.P260S	ENST00000264731	NM_003722.4	260	Cct/Tct	6/14	1	2	FACETS	0.986	0.895	1	0.986	0.895	1	CLONAL	1	TRUE	1	0.291575859235132	2		477	918	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052983	180052983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1221447329	NA	P-0020768-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1489	301	1198	0	ENST00000261937.6:c.1307C>T	p.Ser436Leu	p.S436L	ENST00000261937	NM_182925.4	436	tCg/tTg	10/30	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.291575859235132	2		1198	1790	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0020913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	145	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		288	483	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	167	151	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		151	614	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0020913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	157	355	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		355	391	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812293	212812293	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569995088	NA	P-0020913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	57	518	0	ENST00000342788.4:c.283C>T	p.Arg95Cys	p.R95C	ENST00000342788	NM_005235.2	95	Cgt/Tgt	3/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		518	437	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923318	9923318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867335598	NA	P-0020913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	190	871	1	ENST00000330684.3:c.1969G>A	p.Glu657Lys	p.E657K	ENST00000330684	NM_001134407.1	657	Gaa/Aaa	9/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		872	708	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748479	43748479	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45533131	NA	P-0020913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	163	478	3	ENST00000523873.1:c.433C>T	p.Arg145Ter	p.R145*	ENST00000523873		145	Cga/Tga	6/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		481	500	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024491	31024491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	288	833	0	ENST00000375687.4:c.3976C>T	p.Pro1326Ser	p.P1326S	ENST00000375687	NM_015338.5	1326	Cct/Tct	13/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		833	871	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039893	47039893	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	346	468	0	ENST00000377604.3:c.1236G>A	p.Trp412Ter	p.W412*	ENST00000377604	NM_001204468.1	412	tgG/tgA	12/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		468	553	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354255	70354255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	355	506	0	ENST00000374080.3:c.4666G>A	p.Glu1556Lys	p.E1556K	ENST00000374080		1556	Gag/Aag	34/45	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		506	577	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553441	106553441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746535819	NA	P-0020913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	136	479	1	ENST00000369096.4:c.1406C>T	p.Ser469Leu	p.S469L	ENST00000369096	NM_001198.3	469	tCg/tTg	5/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		480	355	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820903	36820903	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	143	835	0	ENST00000373129.3:c.474C>A	p.Asn158Lys	p.N158K	ENST00000373129	NM_032017.1	158	aaC/aaA	6/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		835	845	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163742	72163742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	136	995	0	ENST00000357731.5:c.616G>A	p.Glu206Lys	p.E206K	ENST00000357731	NM_173808.2	206	Gaa/Aaa	4/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		995	616	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612783	228612783	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1202634115	NA	P-0020913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	257	826	1	ENST00000366696.1:c.244G>A	p.Asp82Asn	p.D82N	ENST00000366696	NM_003493.2	82	Gac/Aac	1/1	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		827	1039	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129815	30129815	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	293	798	0	ENST00000263025.4:c.398T>A	p.Leu133Gln	p.L133Q	ENST00000263025	NM_002746.2	133	cTg/cAg	3/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		798	886	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646830	37646830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	254	745	0	ENST00000447079.4:c.1952C>T	p.Ser651Leu	p.S651L	ENST00000447079	NM_015083.1	651	tCa/tTa	3/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		745	681	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918212	50918213	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0020913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	281	972	2	ENST00000440232.2:c.2529_2530delinsAA	p.Val844Ile	p.V844I	ENST00000440232	NM_002691.3	843	ctGGtc/ctAAtc	20/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		974	932	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085666	16085666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	121	890	1	ENST00000281043.3:c.842C>T	p.Thr281Ile	p.T281I	ENST00000281043	NM_005378.4	281	aCt/aTt	3/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		891	822	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266487	41266487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1158895192	NA	P-0020913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	95	627	0	ENST00000349496.5:c.284G>A	p.Arg95Gln	p.R95Q	ENST00000349496	NM_001904.3	95	cGa/cAa	4/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		627	446	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589606	67589606	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	91	546	2	ENST00000274335.5:c.1369C>T	p.Gln457Ter	p.Q457*	ENST00000274335		457	Caa/Taa	10/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		548	345	SUCCESS
APC	324	MSKCC	GRCh37	5	112178961	112178961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	134	534	0	ENST00000257430.4:c.7670C>T	p.Ser2557Phe	p.S2557F	ENST00000257430	NM_000038.5	2557	tCc/tTc	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		534	448	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971197	21971197	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0020913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	281	680	0	ENST00000304494.5:c.161del	p.Met54ArgfsTer92	p.M54Rfs*92	ENST00000304494	NM_000077.4	54	aTg/ag	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		680	529	SUCCESS
AR	367	MSKCC	GRCh37	X	66765014	66765014	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	318	458	2	ENST00000374690.3:c.26G>T	p.Arg9Met	p.R9M	ENST00000374690	NM_000044.3	9	aGg/aTg	1/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		460	535	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	136	151	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.671720438937884	2		151	339	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	583	939	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	0.671720438937884	4	FACETS	0.969	0.931	1	0.646	0.621	0.671	CLONAL	2	TRUE	1	0.671720438937884	4		939	1498	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871202	35871202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200772681	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	142	685	0	ENST00000303115.3:c.424G>A	p.Gly142Arg	p.G142R	ENST00000303115	NM_002185.3	142	Gga/Aga	4/8	1	2	FACETS	0.892	0.819	0.967	0.892	0.819	0.967	CLONAL	1	TRUE	1	0.671720438937884	2		685	474	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247617	123247617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	184	813	0	ENST00000358487.5:c.1874G>A	p.Arg625Gln	p.R625Q	ENST00000358487	NM_000141.4	625	cGa/cAa	14/18	1	2	FACETS	0.956	0.888	1	0.956	0.888	1	CLONAL	1	TRUE	1	0.671720438937884	2		813	573	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606776	43606776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1313331250	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	232	1052	2	ENST00000355710.3:c.1385C>T	p.Ser462Leu	p.S462L	ENST00000355710	NM_020975.4	462	tCg/tTg	7/20	1	2	FACETS	0.899	0.842	0.959	0.899	0.842	0.959	CLONAL	1	TRUE	1	0.671720438937884	2		1054	768	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354044	15354044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	165	649	0	ENST00000263377.2:c.2836C>T	p.Pro946Ser	p.P946S	ENST00000263377	NM_058243.2	946	Cct/Tct	14/20	1	2	FACETS	0.985	0.911	1	0.985	0.911	1	CLONAL	1	TRUE	1	0.671720438937884	2		649	499	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813334	102813334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1430553116	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	206	849	1	ENST00000307046.8:c.355C>T	p.Arg119Cys	p.R119C	ENST00000307046	NM_001111285.1	119	Cgc/Tgc	3/4	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.671720438937884	2		850	589	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256562	115256562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267606921	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	209	883	1	ENST00000369535.4:c.149C>T	p.Thr50Ile	p.T50I	ENST00000369535	NM_002524.4	50	aCc/aTc	3/7	NA	2	FACETS	0.929	0.866	0.993			1	INDETERMINATE	1	TRUE	NA	0.671720438937884	2		884	670	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164307	47164307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	140	525	0	ENST00000409792.3:c.1819C>T	p.Pro607Ser	p.P607S	ENST00000409792	NM_014159.6	607	Cct/Tct	3/21	1	2	FACETS	0.852	0.782	0.926	0.852	0.782	0.926	CLONAL	1	TRUE	1	0.671720438937884	2		525	489	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244981	123244981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	231	932	0	ENST00000358487.5:c.2123C>T	p.Pro708Leu	p.P708L	ENST00000358487	NM_000141.4	708	cCc/cTc	16/18	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.671720438937884	2		932	659	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469964	25469964	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	274	968	0	ENST00000264709.3:c.1078A>G	p.Asn360Asp	p.N360D	ENST00000264709	NM_175629.2	360	Aac/Gac	9/23	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.671720438937884	2		968	769	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40477071	40477072	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	176	621	0	ENST00000264657.5:c.1373_1374delinsTT	p.Ser458Phe	p.S458F	ENST00000264657	NM_139276.2	458	tCC/tTT	16/24	1	2	FACETS	0.907	0.84	0.975	0.907	0.84	0.975	CLONAL	1	TRUE	1	0.671720438937884	2		621	578	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920067	1920067	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1472983214	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	230	928	2	ENST00000382891.5:c.1127C>T	p.Ser376Phe	p.S376F	ENST00000382891	NM_133335.3	376	tCc/tTc	5/22	1	2	FACETS	0.951	0.89	1	0.951	0.89	1	CLONAL	1	TRUE	1	0.671720438937884	2		930	720	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69103983	69103983	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	211	1071	3	ENST00000288368.4:c.4373C>T	p.Ser1458Leu	p.S1458L	ENST00000288368	NM_024870.2	1458	tCa/tTa	36/40	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.671720438937884	2		1074	618	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287286	38287286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	249	1129	2	ENST00000425967.3:c.371C>T	p.Ser124Phe	p.S124F	ENST00000425967	NM_001174067.1	124	tCc/tTc	4/19	1	2	FACETS	0.933	0.875	0.991	0.933	0.875	0.991	CLONAL	1	TRUE	1	0.671720438937884	2		1131	795	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680659	30680659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	558	754	2	ENST00000376406.3:c.1060C>T	p.His354Tyr	p.H354Y	ENST00000376406	NM_014641.2	354	Cat/Tat	5/15	0.671720438937884	4	FACETS	0.985	0.953	1	0.985	0.953	1	CLONAL	3	TRUE	1	0.671720438937884	4		756	940	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100906	41100906	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs560503250	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	167	611	0	ENST00000373198.4:c.1450G>A	p.Val484Ile	p.V484I	ENST00000373198	NM_133170.3	484	Gtt/Att	8/32	1	2	FACETS	0.88	0.813	0.949	0.88	0.813	0.949	CLONAL	1	TRUE	1	0.671720438937884	2		611	565	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2493236	2493236	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	192	738	0	ENST00000355716.4:c.676A>T	p.Lys226Ter	p.K226*	ENST00000355716	NM_003820.2	226	Aaa/Taa	6/8	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.671720438937884	2		738	557	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259321	16259321	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	111	419	0	ENST00000375759.3:c.6586G>T	p.Glu2196Ter	p.E2196*	ENST00000375759	NM_015001.2	2196	Gag/Tag	11/15	1	2	FACETS	0.921	0.836	1	0.921	0.836	1	CLONAL	1	TRUE	1	0.671720438937884	2		419	359	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099107	27099107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	202	767	0	ENST00000324856.7:c.3523C>T	p.Pro1175Ser	p.P1175S	ENST00000324856	NM_006015.4	1175	Cca/Tca	13/20	1	2	FACETS	0.857	0.797	0.918	0.857	0.797	0.918	CLONAL	1	TRUE	1	0.671720438937884	2		767	702	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099332	27099332	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	257	904	0	ENST00000324856.7:c.3570del	p.Phe1191LeufsTer15	p.F1191Lfs*15	ENST00000324856	NM_006015.4	1190	gCc/gc	14/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.671720438937884	2		904	678	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933436	100933436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	129	542	0	ENST00000325455.5:c.1954G>A	p.Asp652Asn	p.D652N	ENST00000325455	NM_001202474.3	652	Gat/Aat	4/8	1	2	FACETS	0.908	0.83	0.988	0.908	0.83	0.988	CLONAL	1	TRUE	1	0.671720438937884	2		542	423	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427078	49427078	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	169	684	0	ENST00000301067.7:c.11410C>T	p.Pro3804Ser	p.P3804S	ENST00000301067	NM_003482.3	3804	Cct/Tct	39/54	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.671720438937884	2		684	481	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865614	57865614	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	268	1094	1	ENST00000228682.2:c.3091G>A	p.Gly1031Arg	p.G1031R	ENST00000228682	NM_005269.2	1031	Gga/Aga	12/12	1	2	FACETS	0.958	0.901	1	0.958	0.901	1	CLONAL	1	TRUE	1	0.671720438937884	2		1095	833	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220093	133220093	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	272	1096	0	ENST00000320574.5:c.4344T>G	p.Asn1448Lys	p.N1448K	ENST00000320574	NM_006231.2	1448	aaT/aaG	34/49	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.671720438937884	2		1096	793	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001940	29001940	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	243	833	0	ENST00000282397.4:c.1225A>T	p.Ile409Leu	p.I409L	ENST00000282397	NM_002019.4	409	Ata/Tta	9/30	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.671720438937884	2		833	662	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30095707	30095707	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	221	828	0	ENST00000331968.5:c.1781T>C	p.Phe594Ser	p.F594S	ENST00000331968	NM_002742.2	594	tTt/tCt	12/18	NA	2	FACETS	0.971	0.908	1			1	INDETERMINATE	1	TRUE	NA	0.671720438937884	2		828	678	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457421	67457421	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	206	900	0	ENST00000327367.4:c.395C>T	p.Thr132Ile	p.T132I	ENST00000327367	NM_005902.3	132	aCa/aTa	2/9	0.671720438937884	3	FACETS	0.923	0.857	0.991	0.308	0.285	0.331	CLONAL	1	TRUE	0	0.671720438937884	3		900	888	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858025	9858025	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	189	848	1	ENST00000330684.3:c.3376C>T	p.Pro1126Ser	p.P1126S	ENST00000330684	NM_001134407.1	1126	Cct/Tct	13/13	1	2	FACETS	0.957	0.89	1	0.957	0.89	1	CLONAL	1	TRUE	1	0.671720438937884	2		849	588	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041995	14041995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	139	540	0	ENST00000311895.7:c.2542C>T	p.Pro848Ser	p.P848S	ENST00000311895	NM_005236.2	848	Ccc/Tcc	11/11	1	2	FACETS	0.972	0.893	1	0.972	0.893	1	CLONAL	1	TRUE	1	0.671720438937884	2		540	426	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654800	29654800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555533638	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	177	632	0	ENST00000356175.3:c.5489C>T	p.Pro1830Leu	p.P1830L	ENST00000356175	NM_000267.3	1830	cCt/cTt	37/57	0.650834077812444	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.671720438937884	1		632	340	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41242979	41242979	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	187	799	0	ENST00000357654.3:c.4167T>G	p.Ser1389Arg	p.S1389R	ENST00000357654	NM_007294.3	1389	agT/agG	11/23	1	2	FACETS	0.941	0.874	1	0.941	0.874	1	CLONAL	1	TRUE	1	0.671720438937884	2		799	592	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435668	56435668	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	219	819	0	ENST00000407977.2:c.1469T>G	p.Val490Gly	p.V490G	ENST00000407977		490	gTc/gGc	9/10	1	2	FACETS	0.983	0.92	1	0.983	0.92	1	CLONAL	1	TRUE	1	0.671720438937884	2		819	663	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858940	78858940	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1171400798	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	159	646	0	ENST00000306801.3:c.1975G>A	p.Val659Ile	p.V659I	ENST00000306801	NM_020761.2	659	Gtc/Atc	17/34	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.671720438937884	2		646	461	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39575890	39575890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	170	738	2	ENST00000262039.4:c.823C>T	p.Arg275Trp	p.R275W	ENST00000262039	NM_002647.2	275	Cgg/Tgg	8/25	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.671720438937884	2		740	500	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265618	10265618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	208	870	0	ENST00000340748.4:c.1559C>T	p.Ser520Phe	p.S520F	ENST00000340748		520	tCc/tTc	19/40	1	2	FACETS	0.88	0.82	0.941	0.88	0.82	0.941	CLONAL	1	TRUE	1	0.671720438937884	2		870	704	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905489	50905489	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	304	1093	0	ENST00000440232.2:c.617C>T	p.Pro206Leu	p.P206L	ENST00000440232	NM_002691.3	206	cCc/cTc	6/27	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.671720438937884	2		1093	864	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498007	29498007	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	215	839	0	ENST00000389048.3:c.1999G>T	p.Gly667Trp	p.G667W	ENST00000389048	NM_004304.4	667	Ggg/Tgg	11/29	1	2	FACETS	0.955	0.892	1	0.955	0.892	1	CLONAL	1	TRUE	1	0.671720438937884	2		839	670	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738359	190738359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143554211	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	135	597	0	ENST00000441310.2:c.2611C>T	p.Arg871Cys	p.R871C	ENST00000441310	NM_000534.4	871	Cgc/Tgc	12/13	1	2	FACETS	0.876	0.802	0.952	0.876	0.802	0.952	CLONAL	1	TRUE	1	0.671720438937884	2		597	459	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537966	212537966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	143	676	0	ENST00000342788.4:c.1639G>A	p.Glu547Lys	p.E547K	ENST00000342788	NM_005235.2	547	Gag/Aag	14/28	1	2	FACETS	0.944	0.868	1	0.944	0.868	1	CLONAL	1	TRUE	1	0.671720438937884	2		676	451	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215595166	215595166	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	207	813	0	ENST00000260947.4:c.1970C>A	p.Pro657Gln	p.P657Q	ENST00000260947	NM_000465.2	657	cCa/cAa	10/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.671720438937884	2		813	559	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439544	220439544	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	255	949	2	ENST00000243786.2:c.397T>C	p.Phe133Leu	p.F133L	ENST00000243786	NM_002191.3	133	Ttc/Ctc	2/2	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.671720438937884	2		951	730	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371577	225371578	+	stop_gained,splice_region_variant	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	116	734	2	ENST00000264414.4:c.1026_1027delinsTT	p.Gln343Ter	p.Q343*	ENST00000264414	NM_003590.4	342	atCCag/atTTag	7/16	1	2	FACETS	0.859	0.781	0.94	0.859	0.781	0.94	CLONAL	1	TRUE	1	0.671720438937884	2		736	402	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546651	9546651	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	177	677	0	ENST00000353224.5:c.1371A>C	p.Glu457Asp	p.E457D	ENST00000353224	NM_177990.2	457	gaA/gaC	5/10	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.671720438937884	2		677	519	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877444	40877444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	132	479	0	ENST00000373198.4:c.2252C>T	p.Ser751Phe	p.S751F	ENST00000373198	NM_133170.3	751	tCt/tTt	15/32	1	2	FACETS	0.822	0.751	0.896	0.822	0.751	0.896	CLONAL	1	TRUE	1	0.671720438937884	2		479	478	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513297	44513298	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	88	1025	2	ENST00000291552.4:c.637_638delinsAA	p.Gly213Asn	p.G213N	ENST00000291552	NM_006758.2	213	GGt/AAt	8/8	0.416594212941956	1	FACETS	0.302	0.268	0.339	0.302	0.268	0.339	SUBCLONAL	1	TRUE	0	0.671720438937884	1		1027	576	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288071	21288071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	95	470	1	ENST00000354336.3:c.316C>T	p.Pro106Ser	p.P106S	ENST00000354336	NM_005207.3	106	Cca/Tca	2/3	1	2	FACETS	0.839	0.755	0.927	0.839	0.755	0.927	CLONAL	1	TRUE	1	0.671720438937884	2		471	337	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37059018	37059018	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	183	864	0	ENST00000231790.2:c.812C>T	p.Ser271Phe	p.S271F	ENST00000231790	NM_000249.3	271	tCc/tTc	10/19	1	2	FACETS	0.877	0.814	0.943	0.877	0.814	0.943	CLONAL	1	TRUE	1	0.671720438937884	2		864	621	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670364	134670364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	172	611	2	ENST00000398015.3:c.275C>T	p.Thr92Ile	p.T92I	ENST00000398015	NM_004441.4	92	aCt/aTt	3/16	1	2	FACETS	0.994	0.922	1	0.994	0.922	1	CLONAL	1	TRUE	1	0.671720438937884	2		613	515	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55974003	55974003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	220	859	2	ENST00000263923.4:c.1313G>A	p.Gly438Asp	p.G438D	ENST00000263923	NM_002253.2	438	gGc/gAc	10/30	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.671720438937884	2		861	626	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873742	35873742	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	106	581	0	ENST00000303115.3:c.698A>T	p.Asn233Ile	p.N233I	ENST00000303115	NM_002185.3	233	aAt/aTt	5/8	1	2	FACETS	0.846	0.765	0.93	0.846	0.765	0.93	CLONAL	1	TRUE	1	0.671720438937884	2		581	373	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672539	30672539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	187	789	4	ENST00000376406.3:c.4421C>T	p.Thr1474Ile	p.T1474I	ENST00000376406	NM_014641.2	1474	aCt/aTt	10/15	0.671720438937884	4	FACETS	0.921	0.85	0.994	0.307	0.283	0.332	CLONAL	1	TRUE	1	0.671720438937884	4		793	1011	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673676	30673676	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	213	845	1	ENST00000376406.3:c.3284C>T	p.Ser1095Phe	p.S1095F	ENST00000376406	NM_014641.2	1095	tCc/tTc	10/15	0.671720438937884	4	FACETS	0.912	0.847	0.981	0.304	0.282	0.327	CLONAL	1	TRUE	1	0.671720438937884	4		846	1162	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165258	32165258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764456869	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	287	1057	0	ENST00000375023.3:c.4870G>A	p.Ala1624Thr	p.A1624T	ENST00000375023	NM_004557.3	1624	Gcc/Acc	27/30	0.671720438937884	4	FACETS	1	0.974	1	0.356	0.334	0.379	CLONAL	1	TRUE	1	0.671720438937884	4		1057	1338	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797241	32797241	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778896765	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	254	1048	0	ENST00000374899.4:c.1868G>A	p.Arg623Gln	p.R623Q	ENST00000374899	NM_018833.2	623	cGa/cAa	11/12	0.671720438937884	4	FACETS	0.9	0.84	0.962	0.3	0.28	0.321	CLONAL	1	TRUE	1	0.671720438937884	4		1048	1405	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663701	117663701	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	113	431	1	ENST00000368508.3:c.4531C>T	p.Gln1511Ter	p.Q1511*	ENST00000368508	NM_002944.2	1511	Cag/Tag	28/43	NA	2	FACETS	1	0.942	1			1	INDETERMINATE	1	TRUE	NA	0.671720438937884	2		432	322	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718189	117718189	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1240410063	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	153	779	0	ENST00000368508.3:c.668G>A	p.Gly223Glu	p.G223E	ENST00000368508	NM_002944.2	223	gGa/gAa	7/43	NA	2	FACETS	0.821	0.755	0.889			1	INDETERMINATE	1	TRUE	NA	0.671720438937884	2		779	555	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528697	157528697	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	199	812	0	ENST00000346085.5:c.6422G>C	p.Gly2141Ala	p.G2141A	ENST00000346085	NM_020732.3	2141	gGg/gCg	20/20	1	2	FACETS	0.988	0.92	1	0.988	0.92	1	CLONAL	1	TRUE	1	0.671720438937884	2		812	600	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426893	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	156	848	2	ENST00000356142.4:c.85_86delinsAT	p.Pro29Ile	p.P29I	ENST00000356142	NM_018890.3	29	CCt/ATt	2/7	0.671720438937884	3	FACETS	0.718	0.658	0.781	0.359	0.329	0.391	SUBCLONAL	1	TRUE	1	0.671720438937884	3		850	864	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759373	133759373	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	462	947	0	ENST00000318560.5:c.1697del	p.Pro566LeufsTer19	p.P566Lfs*19	ENST00000318560	NM_005157.4	566	Cct/ct	11/11	0.667699650123046	2	FACETS	0.995	0.963	1	0.995	0.963	1	CLONAL	2	TRUE	0	0.671720438937884	2		947	691	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779103	135779104	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	321	693	3	ENST00000298552.3:c.2142_2143delinsTT	p.Arg715Trp	p.R715W	ENST00000298552	NM_001162426.1	714	ctCCgg/ctTTgg	17/23	0.667699650123046	2	FACETS	0.928	0.89	0.965	0.928	0.89	0.965	CLONAL	2	TRUE	0	0.671720438937884	2		696	515	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139392000	139392000	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	363	756	0	ENST00000277541.6:c.6191C>T	p.Pro2064Leu	p.P2064L	ENST00000277541	NM_017617.3	2064	cCc/cTc	34/34	0.667699650123046	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.671720438937884	2		756	515	SUCCESS
AR	367	MSKCC	GRCh37	X	66765319	66765319	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	301	495	0	ENST00000374690.3:c.331G>A	p.Asp111Asn	p.D111N	ENST00000374690	NM_000044.3	111	Gat/Aat	1/8	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.671720438937884	1		495	432	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0021121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	191	1058	3	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.327588423790064	2		1061	871	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	39	151	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.589	0.489	0.701	0.589	0.489	0.701	SUBCLONAL	1	TRUE	1	0.327588423790064	2		151	404	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663222	227663222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	110	912	0	ENST00000305123.5:c.233C>T	p.Ser78Phe	p.S78F	ENST00000305123	NM_005544.2	78	tCc/tTc	1/2	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.327588423790064	2		912	665	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245404	153245404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	110	1024	2	ENST00000281708.4:c.1787C>T	p.Ser596Phe	p.S596F	ENST00000281708	NM_033632.3	596	tCt/tTt	11/12	0.24345091546725	1	FACETS	0.72	0.647	0.798	0.72	0.647	0.798	SUBCLONAL	1	TRUE	0	0.327588423790064	1		1026	780	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0021121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	90	692	0	ENST00000304494.5:c.151-1G>A		p.X51_splice	ENST00000304494	NM_000077.4	51			0.327588423790064	1	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	0	0.327588423790064	1		692	452	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459136	120459136	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	103	1004	0	ENST00000256646.2:c.6209G>A	p.Ser2070Asn	p.S2070N	ENST00000256646	NM_024408.3	2070	aGc/aAc	34/34	1	2	FACETS	0.81	0.725	0.901	0.81	0.725	0.901	CLONAL	1	TRUE	1	0.327588423790064	2		1004	776	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218866	193218867	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	36	371	1	ENST00000367435.3:c.1424_1425delinsTT	p.Ala475Val	p.A475V	ENST00000367435	NM_024529.4	475	gCC/gTT	16/17	1	2	FACETS	0.829	0.685	0.989	0.829	0.685	0.989	CLONAL	1	TRUE	1	0.327588423790064	2		372	265	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274651	123274651	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1207716999	NA	P-0021121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	81	633	0	ENST00000358487.5:c.1267C>T	p.Pro423Ser	p.P423S	ENST00000358487	NM_000141.4	423	Ccc/Tcc	9/18	1	2	FACETS	0.97	0.857	1	0.97	0.857	1	CLONAL	1	TRUE	1	0.327588423790064	2		633	510	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443651	49443651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745355045	NA	P-0021121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	93	977	0	ENST00000301067.7:c.3720G>A	p.Met1240Ile	p.M1240I	ENST00000301067	NM_003482.3	1240	atG/atA	11/54	1	2	FACETS	0.726	0.645	0.813	0.726	0.645	0.813	SUBCLONAL	1	TRUE	1	0.327588423790064	2		977	782	SUCCESS
B2M	567	MSKCC	GRCh37	15	45008525	45008525	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs111795848	NA	P-0021121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	83	599	0	ENST00000558401.1:c.347-2A>T		p.X116_splice	ENST00000558401	NM_004048.2	116			0.327588423790064	1	FACETS	0.867	0.767	0.972	0.867	0.767	0.972	CLONAL	1	TRUE	0	0.327588423790064	1		599	489	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670728	67670728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	102	926	0	ENST00000264010.4:c.1973G>A	p.Arg658Lys	p.R658K	ENST00000264010	NM_006565.3	658	aGa/aAa	11/12	0.24345091546725	1	FACETS	0.832	0.745	0.924	0.832	0.745	0.924	CLONAL	1	TRUE	0	0.327588423790064	1		926	626	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250753	10250753	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	131	1174	0	ENST00000340748.4:c.3727T>C	p.Phe1243Leu	p.F1243L	ENST00000340748		1243	Ttc/Ctc	32/40	1	2	FACETS	0.956	0.867	1	0.956	0.867	1	CLONAL	1	TRUE	1	0.327588423790064	2		1174	837	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281179	15281179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1172987380	NA	P-0021121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	176	1371	1	ENST00000263388.2:c.5077C>T	p.Arg1693Trp	p.R1693W	ENST00000263388	NM_000435.2	1693	Cgg/Tgg	27/33	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.327588423790064	2		1372	994	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18972832	18972832	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	80	775	0	ENST00000262803.5:c.2471C>G	p.Ala824Gly	p.A824G	ENST00000262803	NM_002911.3	824	gCc/gGc	18/24	1	2	FACETS	0.883	0.779	0.995	0.883	0.779	0.995	CLONAL	1	TRUE	1	0.327588423790064	2		775	553	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719270	61719270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	123	754	2	ENST00000401558.2:c.1787G>A	p.Arg596His	p.R596H	ENST00000401558	NM_003400.3	596	cGc/cAc	16/25	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.327588423790064	2		756	602	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054193	30054193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	91	639	0	ENST00000338641.4:c.615G>A	p.Met205Ile	p.M205I	ENST00000338641	NM_000268.3	205	atG/atA	7/16	0.199763928531173	3	FACETS	1	0.96	1	0.585	0.52	0.653	CLONAL	1	TRUE	1	0.327588423790064	3		639	553	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164811	47164811	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	73	565	0	ENST00000409792.3:c.1315C>T	p.Pro439Ser	p.P439S	ENST00000409792	NM_014159.6	439	Cct/Tct	3/21	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.327588423790064	2		565	429	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564514	55564515	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	62	627	1	ENST00000288135.5:c.402_403delinsTT	p.Arg135Cys	p.R135C	ENST00000288135	NM_000222.2	134	gtCCgc/gtTTgc	3/21	0.24345091546725	1	FACETS	0.681	0.589	0.78	0.681	0.589	0.78	SUBCLONAL	1	TRUE	0	0.327588423790064	1		628	465	SUCCESS
APC	324	MSKCC	GRCh37	5	112176915	112176915	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	73	627	0	ENST00000257430.4:c.5624C>T	p.Ser1875Phe	p.S1875F	ENST00000257430	NM_000038.5	1875	tCc/tTc	16/16	1	2	FACETS	0.956	0.839	1	0.956	0.839	1	CLONAL	1	TRUE	1	0.327588423790064	2		627	466	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820818	32820819	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0021121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	60	980	0	ENST00000354258.4:c.775_776del	p.Leu259TrpfsTer14	p.L259Wfs*14	ENST00000354258	NM_000593.5	259	CTt/t	1/11	0.327588423790064	1	FACETS	0.493	0.425	0.568	0.493	0.425	0.568	SUBCLONAL	1	TRUE	0	0.327588423790064	1		980	621	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710591	117710591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	91	520	0	ENST00000368508.3:c.1681C>T	p.Pro561Ser	p.P561S	ENST00000368508	NM_002944.2	561	Ccg/Tcg	12/43	0.327588423790064	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.327588423790064	1		520	347	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860094	151860094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143821095	NA	P-0021121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	66	571	0	ENST00000262189.6:c.10568C>T	p.Pro3523Leu	p.P3523L	ENST00000262189	NM_170606.2	3523	cCt/cTt	43/59	1	2	FACETS	0.935	0.814	1	0.935	0.814	1	CLONAL	1	TRUE	1	0.327588423790064	2		571	431	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	229	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.972	0.914	1	0.972	0.914	1	CLONAL	1	TRUE	1	0.869702956222115	2		306	542	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	343	615	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	0.958	0.912	1	0.958	0.912	1	CLONAL	1	TRUE	1	0.869702956222115	2		615	823	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956220	55956220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190050670	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	313	727	2	ENST00000263923.4:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000263923	NM_002253.2	1032	cGa/cAa	23/30	1	2	FACETS	0.979	0.93	1	0.979	0.93	1	CLONAL	1	TRUE	1	0.869702956222115	2		729	735	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169174	32169174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	944	908	1	ENST00000375023.3:c.3859G>A	p.Glu1287Lys	p.E1287K	ENST00000375023	NM_004557.3	1287	Gaa/Aaa	22/30	0.775692037597651	4	FACETS	0.993	0.971	1	0.993	0.971	1	CLONAL	3	TRUE	1	0.869702956222115	4		909	1363	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976476	25976476	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	300	653	0	ENST00000435504.4:c.1069C>T	p.Arg357Ter	p.R357*	ENST00000435504		357	Cga/Tga	11/13	1	2	FACETS	0.866	0.819	0.913	0.866	0.819	0.913	CLONAL	1	TRUE	1	0.869702956222115	2		653	797	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331660	8331660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	273	666	0	ENST00000356435.5:c.5456G>A	p.Gly1819Glu	p.G1819E	ENST00000356435		1819	gGa/gAa	33/35	0.869702956222115	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.869702956222115	1		666	349	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453399	40453399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	405	963	0	ENST00000345506.4:c.1096C>T	p.Pro366Ser	p.P366S	ENST00000345506	NM_003152.3	366	Ccc/Tcc	10/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.869702956222115	2		963	931	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156719	20156719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	354	346	0	ENST00000379607.5:c.38G>A	p.Arg13His	p.R13H	ENST00000379607	NM_001412.3	13	cGc/cAc	2/7	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.869702956222115	1		346	418	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553539	29553539	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1131691099	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	214	489	2	ENST00000356175.3:c.2088G>A	p.Trp696Ter	p.W696*	ENST00000356175	NM_000267.3	696	tgG/tgA	18/57	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.869702956222115	2		491	490	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811603	102811603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	307	774	0	ENST00000307046.8:c.581G>A	p.Gly194Glu	p.G194E	ENST00000307046	NM_001111285.1	194	gGa/gAa	4/4	1	2	FACETS	0.987	0.937	1	0.987	0.937	1	CLONAL	1	TRUE	1	0.869702956222115	2		774	715	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633256	12633256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	763	795	0	ENST00000251849.4:c.1144C>T	p.Pro382Ser	p.P382S	ENST00000251849	NM_002880.3	382	Cca/Tca	11/17	0.864553251115169	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.869702956222115	2		795	863	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120497	94120497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	188	461	0	ENST00000369303.4:c.554C>T	p.Ala185Val	p.A185V	ENST00000369303	NM_004440.3	185	gCc/gTc	3/17	1	2	FACETS	0.992	0.927	1	0.992	0.927	1	CLONAL	1	TRUE	1	0.869702956222115	2		461	436	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514495	149514495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760987130	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	337	799	0	ENST00000261799.4:c.449G>A	p.Arg150Gln	p.R150Q	ENST00000261799	NM_002609.3	150	cGa/cAa	4/23	0.201259815668221	1	FACETS	0.575	0.547	0.603	0.575	0.547	0.603	INDETERMINATE	1	TRUE	0	0.869702956222115	1		799	762	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691123	18691123	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	265	571	0	ENST00000266497.5:c.3234G>A	p.Met1078Ile	p.M1078I	ENST00000266497		1078	atG/atA	23/31	1	2	FACETS	0.958	0.905	1	0.958	0.905	1	CLONAL	1	TRUE	1	0.869702956222115	2		571	636	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652390	206652390	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	668	894	1	ENST00000367120.3:c.1097C>T	p.Ser366Leu	p.S366L	ENST00000367120	NM_014002.3	366	tCa/tTa	10/22	0.863496203211124	3	FACETS	0.949	0.92	0.978	0.949	0.92	0.978	CLONAL	2	TRUE	1	0.869702956222115	3		895	1161	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570833	226570833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753458085	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	331	744	0	ENST00000366794.5:c.1063C>T	p.Arg355Cys	p.R355C	ENST00000366794	NM_001618.3	355	Cgt/Tgt	8/23	0.863496203211124	3	FACETS	0.903	0.853	0.953	0.451	0.426	0.477	CLONAL	1	TRUE	1	0.869702956222115	3		744	1210	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180519	94180519	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	260	573	0	ENST00000323929.3:c.1649T>A	p.Leu550Ter	p.L550*	ENST00000323929	NM_005591.3	550	tTa/tAa	15/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.869702956222115	2		573	578	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343036	118343036	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	155	321	0	ENST00000534358.1:c.1162G>T	p.Glu388Ter	p.E388*	ENST00000534358	NM_005933.3	388	Gaa/Taa	3/36	1	2	FACETS	0.987	0.917	1	0.987	0.917	1	CLONAL	1	TRUE	1	0.869702956222115	2		321	361	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218164	69218164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	290	578	0	ENST00000462284.1:c.380C>T	p.Ser127Phe	p.S127F	ENST00000462284	NM_002392.5	127	tCt/tTt	6/11	1	2	FACETS	0.978	0.926	1	0.978	0.926	1	CLONAL	1	TRUE	1	0.869702956222115	2		578	682	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107713	30107713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1160777726	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	307	717	1	ENST00000331968.5:c.967G>A	p.Glu323Lys	p.E323K	ENST00000331968	NM_002742.2	323	Gaa/Aaa	6/18	1	2	FACETS	0.992	0.941	1	0.992	0.941	1	CLONAL	1	TRUE	1	0.869702956222115	2		718	712	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422085	81422085	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1006500286	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	227	660	0	ENST00000298171.2:c.61G>A	p.Gly21Arg	p.G21R	ENST00000298171	NM_000369.2	21	Gga/Aga	1/10	1	2	FACETS	0.917	0.862	0.974	0.917	0.862	0.974	CLONAL	1	TRUE	1	0.869702956222115	2		660	569	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347422	91347422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	201	448	0	ENST00000355112.3:c.3584C>T	p.Ser1195Phe	p.S1195F	ENST00000355112	NM_000057.2	1195	tCc/tTc	19/22	1	2	FACETS	0.949	0.889	1	0.949	0.889	1	CLONAL	1	TRUE	1	0.869702956222115	2		448	487	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041834	14041835	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	208	591	1	ENST00000311895.7:c.2381_2382delinsTT	p.His794Leu	p.H794L	ENST00000311895	NM_005236.2	794	cAC/cTT	11/11	1	2	FACETS	0.836	0.782	0.892	0.836	0.782	0.892	CLONAL	1	TRUE	1	0.869702956222115	2		592	572	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063634	67063634	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	263	693	0	ENST00000412916.2:c.83A>G	p.Lys28Arg	p.K28R	ENST00000412916		28	aAg/aGg	2/6	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.869702956222115	2		693	584	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81891945	81891945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	247	684	0	ENST00000359376.3:c.415C>T	p.Pro139Ser	p.P139S	ENST00000359376	NM_002661.3	139	Ccc/Tcc	4/33	1	2	FACETS	0.878	0.826	0.93	0.878	0.826	0.93	CLONAL	1	TRUE	1	0.869702956222115	2		684	647	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679316	29679316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	243	527	0	ENST00000356175.3:c.7436C>T	p.Ser2479Phe	p.S2479F	ENST00000356175	NM_000267.3	2479	tCt/tTt	50/57	1	2	FACETS	0.98	0.924	1	0.98	0.924	1	CLONAL	1	TRUE	1	0.869702956222115	2		527	570	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965292	25965292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61744557	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	294	638	1	ENST00000435504.4:c.3914C>T	p.Pro1305Leu	p.P1305L	ENST00000435504		1305	cCc/cTc	13/13	1	2	FACETS	0.991	0.94	1	0.991	0.94	1	CLONAL	1	TRUE	1	0.869702956222115	2		639	682	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455261	29455262	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	278	732	0	ENST00000389048.3:c.2540_2541delinsAA	p.Arg847Lys	p.R847K	ENST00000389048	NM_004304.4	847	aGG/aAA	15/29	1	2	FACETS	0.988	0.935	1	0.988	0.935	1	CLONAL	1	TRUE	1	0.869702956222115	2		732	647	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131357	202131357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	195	589	1	ENST00000358485.4:c.325G>A	p.Glu109Lys	p.E109K	ENST00000358485	NM_001080125.1	109	Gaa/Aaa	2/9	1	2	FACETS	0.818	0.763	0.875	0.818	0.763	0.875	CLONAL	1	TRUE	1	0.869702956222115	2		590	548	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031630	36031630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	331	966	0	ENST00000358208.4:c.1459C>T	p.Pro487Ser	p.P487S	ENST00000358208		487	Ccg/Tcg	12/12	1	2	FACETS	0.983	0.935	1	0.983	0.935	1	CLONAL	1	TRUE	1	0.869702956222115	2		966	774	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613068	52613068	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	408	401	0	ENST00000394830.3:c.3458+2T>G		p.X1153_splice	ENST00000394830	NM_018313.4	1153			0.864553251115169	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.869702956222115	2		401	451	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200708	128200708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	361	1015	1	ENST00000341105.2:c.1097G>A	p.Gly366Glu	p.G366E	ENST00000341105	NM_032638.4	366	gGg/gAg	5/6	0.863496203211124	3	FACETS	1	0.954	1	0.503	0.477	0.53	CLONAL	1	TRUE	1	0.869702956222115	3		1016	1183	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238554	142238554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	220	411	0	ENST00000350721.4:c.4339C>T	p.Pro1447Ser	p.P1447S	ENST00000350721	NM_001184.3	1447	Cct/Tct	24/47	0.863496203211124	3	FACETS	0.922	0.861	0.986	0.461	0.43	0.493	CLONAL	1	TRUE	1	0.869702956222115	3		411	787	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245429	153245430	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	293	804	1	ENST00000281708.4:c.1761_1762delinsAA	p.Met587_Glu588delinsIleLys	p.M587_E588delinsIK	ENST00000281708	NM_033632.3	587	atGGaa/atAAaa	11/12	1	2	FACETS	0.845	0.799	0.892	0.845	0.799	0.892	CLONAL	1	TRUE	1	0.869702956222115	2		805	797	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226049	226049	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	93	124	0	ENST00000264932.6:c.508C>T	p.Gln170Ter	p.Q170*	ENST00000264932	NM_004168.2	170	Cag/Tag	5/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.869702956222115	2		124	165	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526700	31526700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	387	1038	0	ENST00000344624.3:c.340C>T	p.Pro114Ser	p.P114S	ENST00000344624		114	Cct/Tct	2/33	1	2	FACETS	0.963	0.919	1	0.963	0.919	1	CLONAL	1	TRUE	1	0.869702956222115	2		1038	924	SUCCESS
APC	324	MSKCC	GRCh37	5	112174119	112174119	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	193	458	0	ENST00000257430.4:c.2828C>T	p.Ser943Leu	p.S943L	ENST00000257430	NM_000038.5	943	tCa/tTa	16/16	1	2	FACETS	0.971	0.909	1	0.971	0.909	1	CLONAL	1	TRUE	1	0.869702956222115	2		458	457	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178548	32178548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	252	778	0	ENST00000375023.3:c.2846C>T	p.Pro949Leu	p.P949L	ENST00000375023	NM_004557.3	949	cCc/cTc	18/30	0.775692037597651	4	FACETS	0.948	0.886	1	0.316	0.295	0.337	CLONAL	1	TRUE	1	0.869702956222115	4		778	1143	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120465	94120465	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	171	430	0	ENST00000369303.4:c.586G>T	p.Val196Phe	p.V196F	ENST00000369303	NM_004440.3	196	Gtt/Ttt	3/17	1	2	FACETS	0.923	0.859	0.988	0.923	0.859	0.988	CLONAL	1	TRUE	1	0.869702956222115	2		430	426	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508433	106508433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	82	259	0	ENST00000359195.3:c.427C>T	p.Pro143Ser	p.P143S	ENST00000359195	NM_002649.2	143	Ccc/Tcc	2/11	1	2	FACETS	0.865	0.777	0.955	0.865	0.777	0.955	CLONAL	1	TRUE	1	0.869702956222115	2		259	218	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863263	56863264	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	273	820	2	ENST00000519728.1:c.407_408delinsAT	p.Arg136Asn	p.R136N	ENST00000519728	NM_002350.3	136	aGG/aAT	6/13	1	2	FACETS	0.888	0.838	0.938	0.888	0.838	0.938	CLONAL	1	TRUE	1	0.869702956222115	2		822	707	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930141	68930141	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	214	484	1	ENST00000288368.4:c.202G>A	p.Glu68Lys	p.E68K	ENST00000288368	NM_024870.2	68	Gaa/Aaa	2/40	1	2	FACETS	0.903	0.846	0.96	0.903	0.846	0.96	CLONAL	1	TRUE	1	0.869702956222115	2		485	545	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69050653	69050653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	217	541	0	ENST00000288368.4:c.3988G>A	p.Asp1330Asn	p.D1330N	ENST00000288368	NM_024870.2	1330	Gat/Aat	33/40	1	2	FACETS	0.877	0.822	0.933	0.877	0.822	0.933	CLONAL	1	TRUE	1	0.869702956222115	2		541	569	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389287	8389287	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	381	870	0	ENST00000356435.5:c.4331G>A	p.Trp1444Ter	p.W1444*	ENST00000356435		1444	tGg/tAg	26/35	0.869702956222115	1	FACETS	0.912	0.881	0.942	0.912	0.881	0.942	CLONAL	1	TRUE	0	0.869702956222115	1		870	543	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913492	NA	P-0021172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	106	656	0	ENST00000286548.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000286548	NM_002072.3	209	cAa/cTa	5/7	0.229737729006774	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.229737729006774	1		656	663	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390693	118390729	+	frameshift_variant	Frame_Shift_Del	DEL	TAACTTCCTGGCTTCTAAACATCGTCAGCCTCCTGAA	TAACTTCCTGGCTTCTAAACATCGTCAGCCTCCTGAA	-	novel	NA	P-0021172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	53	680	0	ENST00000534358.1:c.11345_11381del	p.Asn3782ThrfsTer13	p.N3782Tfs*13	ENST00000534358	NM_005933.3	3781	ttTAACTTCCTGGCTTCTAAACATCGTCAGCCTCCTGAA/tt	33/36	1	2	FACETS	0.853	0.727	0.99	0.853	0.727	0.99	CLONAL	1	TRUE	1	0.229737729006774	2		680	541	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437673	52437710	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCGTGTCTGTACTCTCATTGCTGGGGGTGGGTGAGG	GGCCGTGTCTGTACTCTCATTGCTGGGGGTGGGTGAGG	-	novel	NA	P-0021172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	79	1059	0	ENST00000460680.1:c.1451_1488del	p.Pro484LeufsTer2	p.P484Lfs*2	ENST00000460680	NM_004656.3	484	cCCTCACCCACCCCCAGCAATGAGAGTACAGACACGGCC/c	13/17	0.229737729006774	1	FACETS	0.968	0.852	1	0.968	0.852	1	CLONAL	1	TRUE	0	0.229737729006774	1		1059	629	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0021198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	129	525	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	0.624009133200861	3	FACETS	1	0.955	1	0.537	0.49	0.587	CLONAL	1	TRUE	1	0.623943100844828	3		525	505	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913492	NA	P-0021198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	55	656	0	ENST00000286548.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000286548	NM_002072.3	209	cAa/cTa	5/7	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.623943100844828	2		656	167	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275642	41275642	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	118	702	0	ENST00000349496.5:c.1537T>G	p.Leu513Val	p.L513V	ENST00000349496	NM_001904.3	513	Ttg/Gtg	10/15	1	2	FACETS	0.82	0.745	0.899	0.82	0.745	0.899	CLONAL	1	TRUE	1	0.623943100844828	2		702	461	SUCCESS
ATR	545	MSKCC	GRCh37	3	142243007	142243007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	34	716	0	ENST00000350721.4:c.3980C>T	p.Thr1327Ile	p.T1327I	ENST00000350721	NM_001184.3	1327	aCa/aTa	22/47	1	2	FACETS	0.295	0.241	0.356	0.295	0.241	0.356	SUBCLONAL	1	TRUE	1	0.623943100844828	2		716	369	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336393	80336393	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	163	805	0	ENST00000286548.4:c.926T>G	p.Ile309Ser	p.I309S	ENST00000286548	NM_002072.3	309	aTt/aGt	7/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.623943100844828	2		805	459	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332681	153332684	+	stop_gained	Nonsense_Mutation	DEL	GAGG	GAGG	C	novel	NA	P-0021198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	82	879	1	ENST00000281708.4:c.272_275delinsG	p.Ser91_Ser92delinsTer	p.S91_S92delins*	ENST00000281708	NM_033632.3	91	tCCTCa/tGa	2/12	0.623934343548779	1	FACETS	0.567	0.504	0.632	0.567	0.504	0.632	SUBCLONAL	1	TRUE	0	0.623943100844828	1		880	319	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	158	284	0				ENST00000310581	NM_198253.2	-/1132			0.604432087947914	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.604432087947914	1		284	359	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	212	932	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.604432087947914	1	FACETS	0.967	0.908	1	0.967	0.908	1	CLONAL	1	TRUE	0	0.604432087947914	1		933	506	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	190	782	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.604432087947914	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.604432087947914	1		782	421	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455653	189455653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	140	709	0	ENST00000264731.3:c.187G>A	p.Glu63Lys	p.E63K	ENST00000264731	NM_003722.4	63	Gaa/Aaa	2/14	1	2	FACETS	0.877	0.803	0.954	0.877	0.803	0.954	CLONAL	1	TRUE	1	0.604432087947914	2		709	528	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911760	26911760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	216	274	0	ENST00000381527.3:c.185C>T	p.Ser62Leu	p.S62L	ENST00000381527	NM_001260.1	62	tCg/tTg	2/13	0.604432087947914	1	FACETS	0.982	0.922	1	0.982	0.922	1	CLONAL	1	TRUE	0	0.604432087947914	1		274	508	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984848	9984848	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	201	960	0	ENST00000330684.3:c.1117G>A	p.Glu373Lys	p.E373K	ENST00000330684	NM_001134407.1	373	Gaa/Aaa	4/13	1	2	FACETS	0.931	0.866	0.998	0.931	0.866	0.998	CLONAL	1	TRUE	1	0.604432087947914	2		960	714	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	719	1537	1	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	0.604432087947914	2	FACETS	0.995	0.967	1	0.995	0.967	1	CLONAL	2	TRUE	0	0.604432087947914	2		1538	1195	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587161	189587161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173679499	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	206	932	2	ENST00000264731.3:c.1178G>A	p.Arg393Gln	p.R393Q	ENST00000264731	NM_003722.4	393	cGa/cAa	9/14	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.604432087947914	2		934	631	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482295	87482295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	254	1060	1	ENST00000277120.3:c.1582G>A	p.Glu528Lys	p.E528K	ENST00000277120		528	Gaa/Aaa	14/19	0.604432087947914	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.604432087947914	1		1061	532	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912075	56912075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	264	1108	4	ENST00000519728.1:c.1303G>A	p.Glu435Lys	p.E435K	ENST00000519728	NM_002350.3	435	Gaa/Aaa	12/13	0.604432087947914	1	FACETS	0.966	0.912	1	0.966	0.912	1	CLONAL	1	TRUE	0	0.604432087947914	1		1112	631	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612284	189612284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	122	564	1	ENST00000264731.3:c.2036G>A	p.Gly679Glu	p.G679E	ENST00000264731	NM_003722.4	679	gGg/gAg	14/14	1	2	FACETS	0.878	0.798	0.96	0.878	0.798	0.96	CLONAL	1	TRUE	1	0.604432087947914	2		565	460	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36823857	36823857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	173	603	0	ENST00000373129.3:c.325C>T	p.His109Tyr	p.H109Y	ENST00000373129	NM_032017.1	109	Cac/Tac	5/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.604432087947914	2		603	521	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958589	175958589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	337	826	1	ENST00000367669.3:c.1756C>T	p.Arg586Cys	p.R586C	ENST00000367669	NM_022457.5	586	Cgt/Tgt	16/20	0.604432087947914	3	FACETS	0.968	0.922	1	0.968	0.922	1	CLONAL	2	TRUE	1	0.604432087947914	3		827	750	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123245033	123245033	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	207	757	0	ENST00000358487.5:c.2071G>A	p.Val691Met	p.V691M	ENST00000358487	NM_000141.4	691	Gtg/Atg	16/18	0.604432087947914	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.604432087947914	1		757	421	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14317361	14317361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	294	982	0	ENST00000256196.4:c.149C>T	p.Ser50Phe	p.S50F	ENST00000256196		50	tCt/tTt	2/6	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.604432087947914	2		982	908	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442965	49442965	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770095362	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	291	959	0	ENST00000301067.7:c.3943C>T	p.Arg1315Cys	p.R1315C	ENST00000301067	NM_003482.3	1315	Cgt/Tgt	12/54	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.604432087947914	2		959	875	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444081	49444082	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	190	886	2	ENST00000301067.7:c.3289_3290delinsTT	p.Pro1097Leu	p.P1097L	ENST00000301067	NM_003482.3	1097	CCa/TTa	11/54	1	2	FACETS	0.894	0.83	0.961	0.894	0.83	0.961	CLONAL	1	TRUE	1	0.604432087947914	2		888	703	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121438916	121438916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1455363200	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	307	1287	0	ENST00000257555.6:c.1817G>A	p.Gly606Asp	p.G606D	ENST00000257555		606	gGc/gAc	10/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.604432087947914	2		1287	949	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133236043	133236043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	231	966	1	ENST00000320574.5:c.3113C>T	p.Ser1038Phe	p.S1038F	ENST00000320574	NM_006231.2	1038	tCc/tTc	26/49	1	2	FACETS	0.995	0.931	1	0.995	0.931	1	CLONAL	1	TRUE	1	0.604432087947914	2		967	768	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30095735	30095735	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	469	1010	0	ENST00000331968.5:c.1753C>T	p.Pro585Ser	p.P585S	ENST00000331968	NM_002742.2	585	Cct/Tct	12/18	0.604432087947914	3	FACETS	0.944	0.905	0.983	0.944	0.905	0.983	CLONAL	2	TRUE	1	0.604432087947914	3		1010	1070	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610068	81610068	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	139	707	0	ENST00000298171.2:c.1666C>T	p.Pro556Ser	p.P556S	ENST00000298171	NM_000369.2	556	Cct/Tct	10/10	1	2	FACETS	0.814	0.744	0.886	0.814	0.744	0.886	CLONAL	1	TRUE	1	0.604432087947914	2		707	565	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670058	29670058	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	191	877	0	ENST00000356175.3:c.7031A>T	p.Asn2344Ile	p.N2344I	ENST00000356175	NM_000267.3	2344	aAt/aTt	47/57	1	2	FACETS	0.885	0.821	0.951	0.885	0.821	0.951	CLONAL	1	TRUE	1	0.604432087947914	2		877	714	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29686029	29686029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	167	653	0	ENST00000356175.3:c.8093C>T	p.Ser2698Leu	p.S2698L	ENST00000356175	NM_000267.3	2698	tCa/tTa	55/57	1	2	FACETS	0.958	0.885	1	0.958	0.885	1	CLONAL	1	TRUE	1	0.604432087947914	2		653	577	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5206820	5206820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750035643	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	242	1204	0	ENST00000357368.4:c.5812G>A	p.Glu1938Lys	p.E1938K	ENST00000357368	NM_002850.3	1938	Gag/Aag	38/38	1	2	FACETS	0.969	0.908	1	0.969	0.908	1	CLONAL	1	TRUE	1	0.604432087947914	2		1204	826	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791269	42791269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769858953	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	215	933	0	ENST00000575354.2:c.329C>T	p.Pro110Leu	p.P110L	ENST00000575354	NM_015125.3	110	cCc/cTc	3/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.604432087947914	2		933	684	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855907	45855907	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	222	961	0	ENST00000391945.4:c.1903G>A	p.Ala635Thr	p.A635T	ENST00000391945	NM_000400.3	635	Gcg/Acg	21/23	1	2	FACETS	0.991	0.926	1	0.991	0.926	1	CLONAL	1	TRUE	1	0.604432087947914	2		961	741	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912408	50912408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	262	1078	1	ENST00000440232.2:c.1922C>T	p.Pro641Leu	p.P641L	ENST00000440232	NM_002691.3	641	cCc/cTc	16/27	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.604432087947914	2		1079	849	SUCCESS
ALK	238	MSKCC	GRCh37	2	29420520	29420520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	160	734	0	ENST00000389048.3:c.3961G>A	p.Glu1321Lys	p.E1321K	ENST00000389048	NM_004304.4	1321	Gaa/Aaa	27/29	1	2	FACETS	0.918	0.846	0.992	0.918	0.846	0.992	CLONAL	1	TRUE	1	0.604432087947914	2		734	577	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143140	30143141	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	195	954	1	ENST00000389048.3:c.385_386delinsAA	p.Gly129Asn	p.G129N	ENST00000389048	NM_004304.4	129	GGc/AAc	1/29	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.604432087947914	2		955	586	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023718	31023718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752058283	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	449	1051	3	ENST00000375687.4:c.3203G>A	p.Arg1068Gln	p.R1068Q	ENST00000375687	NM_015338.5	1068	cGa/cAa	13/13	0.439938601865948	3	FACETS	0.93	0.891	0.97	0.93	0.891	0.97	CLONAL	2	TRUE	1	0.604432087947914	3		1054	1040	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419977	41419977	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	186	780	1	ENST00000373198.4:c.344C>T	p.Ser115Phe	p.S115F	ENST00000373198	NM_133170.3	115	tCc/tTc	3/32	0.439938601865948	3	FACETS	0.924	0.855	0.997	0.462	0.427	0.499	CLONAL	1	TRUE	1	0.604432087947914	3		781	867	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977871	134977871	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	148	708	0	ENST00000398015.3:c.2864G>A	p.Gly955Asp	p.G955D	ENST00000398015	NM_004441.4	955	gGc/gAc	16/16	1	2	FACETS	0.914	0.839	0.991	0.914	0.839	0.991	CLONAL	1	TRUE	1	0.604432087947914	2		708	536	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155491	106155491	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	188	692	0	ENST00000380013.4:c.392G>A	p.Arg131Lys	p.R131K	ENST00000380013	NM_001127208.2	131	aGa/aAa	3/11	0.604432087947914	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.604432087947914	1		692	420	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672626	30672626	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	230	987	2	ENST00000376406.3:c.4334C>A	p.Pro1445His	p.P1445H	ENST00000376406	NM_014641.2	1445	cCt/cAt	10/15	1	2	FACETS	0.903	0.843	0.964	0.903	0.843	0.964	CLONAL	1	TRUE	1	0.604432087947914	2		989	843	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967993	93967993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	165	739	0	ENST00000369303.4:c.1934G>A	p.Gly645Asp	p.G645D	ENST00000369303	NM_004440.3	645	gGt/gAt	11/17	0.604432087947914	1	FACETS	0.952	0.886	1	0.952	0.886	1	CLONAL	1	TRUE	0	0.604432087947914	1		739	400	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268983	55268983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1345851089	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	278	1113	0	ENST00000275493.2:c.3049C>T	p.Leu1017Phe	p.L1017F	ENST00000275493	NM_005228.3	1017	Ctc/Ttc	25/28	1	2	FACETS	0.989	0.931	1	0.989	0.931	1	CLONAL	1	TRUE	1	0.604432087947914	2		1113	930	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845580	151845580	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1287135873	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	274	1113	2	ENST00000262189.6:c.13432C>T	p.Arg4478Ter	p.R4478*	ENST00000262189	NM_170606.2	4478	Cga/Tga	52/59	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.604432087947914	2		1115	856	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38194888	38194888	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	269	1085	1	ENST00000317025.8:c.845C>T	p.Pro282Leu	p.P282L	ENST00000317025	NM_023034.1	282	cCt/cTt	4/24	1	2	FACETS	0.826	0.775	0.879	0.826	0.775	0.879	CLONAL	1	TRUE	1	0.604432087947914	2		1086	1077	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486022	8486022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	210	841	0	ENST00000356435.5:c.2795C>T	p.Ser932Leu	p.S932L	ENST00000356435		932	tCa/tTa	17/35	0.604432087947914	1	FACETS	0.954	0.895	1	0.954	0.895	1	CLONAL	1	TRUE	0	0.604432087947914	1		841	508	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250277	110250277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	276	1084	0	ENST00000374672.4:c.398C>T	p.Ser133Leu	p.S133L	ENST00000374672	NM_004235.4	133	tCg/tTg	3/5	0.604432087947914	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.604432087947914	1		1084	581	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44970643	44970643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	188	964	1	ENST00000377967.4:c.4193C>T	p.Ser1398Phe	p.S1398F	ENST00000377967	NM_021140.2	1398	tCc/tTc	29/29	NA	2	FACETS	0.811	0.751	0.873			1	INDETERMINATE	1	TRUE	NA	0.604432087947914	2		965	767	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222475	53222475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782302305	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	300	1068	2	ENST00000375401.3:c.4357C>T	p.Arg1453Trp	p.R1453W	ENST00000375401	NM_004187.3	1453	Cgg/Tgg	26/26	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.604432087947914	2		1070	887	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349664	70349664	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	262	1074	0	ENST00000374080.3:c.3826G>A	p.Asp1276Asn	p.D1276N	ENST00000374080		1276	Gat/Aat	27/45	NA	2	FACETS	0.964	0.906	1			1	INDETERMINATE	1	TRUE	NA	0.604432087947914	2		1074	899	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972621	76972621	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	262	1063	2	ENST00000373344.5:c.120G>A	p.Met40Ile	p.M40I	ENST00000373344	NM_000489.3	40	atG/atA	2/35	1	2	FACETS	0.919	0.863	0.977	0.919	0.863	0.977	CLONAL	1	TRUE	1	0.604432087947914	2		1065	943	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020122	123020122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	231	1190	1	ENST00000355640.3:c.610G>A	p.Gly204Ser	p.G204S	ENST00000355640		204	Ggt/Agt	2/7	1	2	FACETS	0.797	0.744	0.852	0.797	0.744	0.852	SUBCLONAL	1	TRUE	1	0.604432087947914	2		1191	959	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0021504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	74	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.882	0.772	1	0.882	0.772	1	CLONAL	1	TRUE	1	0.264717734883477	2		306	634	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0021504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	211	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.250941799222571	3	FACETS	1	0.98	1			1	CLONAL	2	TRUE	NA	0.264717734883477	3		288	797	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332694	153332694	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	42	780	0	ENST00000281708.4:c.262G>A	p.Asp88Asn	p.D88N	ENST00000281708	NM_033632.3	88	Gat/Aat	2/12	0.264717734883477	1	FACETS	0.405	0.338	0.481	0.405	0.338	0.481	SUBCLONAL	1	TRUE	0	0.264717734883477	1		780	679	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865407	57865407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1449397447	NA	P-0021504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	121	1161	1	ENST00000228682.2:c.2884G>A	p.Gly962Ser	p.G962S	ENST00000228682	NM_005269.2	962	Ggt/Agt	12/12	1	2	FACETS	0.876	0.79	0.968	0.876	0.79	0.968	CLONAL	1	TRUE	1	0.264717734883477	2		1162	1043	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332691	153332691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	37	788	0	ENST00000281708.4:c.265G>A	p.Glu89Lys	p.E89K	ENST00000281708	NM_033632.3	89	Gag/Aag	2/12	0.264717734883477	1	FACETS	0.353	0.29	0.424	0.353	0.29	0.424	SUBCLONAL	1	TRUE	0	0.264717734883477	1		788	687	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332819	153332819	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	117	858	1	ENST00000281708.4:c.137G>A	p.Arg46Lys	p.R46K	ENST00000281708	NM_033632.3	46	aGa/aAa	2/12	0.264717734883477	1	FACETS	0.926	0.835	1	0.926	0.835	1	CLONAL	1	TRUE	0	0.264717734883477	1		859	828	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069124	5069124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	98	732	0	ENST00000381652.3:c.1429C>T	p.Leu477Phe	p.L477F	ENST00000381652	NM_004972.3	477	Ctt/Ttt	11/25	0.264717734883477	1	FACETS	0.932	0.832	1	0.932	0.832	1	CLONAL	1	TRUE	0	0.264717734883477	1		732	689	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410769	63410770	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021504-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	101	850	0	ENST00000330258.3:c.2397_2398delinsTT	p.Leu800Phe	p.L800F	ENST00000330258	NM_152424.3	799	aaCCtc/aaTTtc	2/2	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.264717734883477	2		850	724	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0021526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	1580	528	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.81759217161816	6	FACETS	1	0.998	1			1	CLONAL	5	TRUE	NA	0.81759217161816	6		528	1935	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359404	118359404	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	232	524	0	ENST00000534358.1:c.4408C>T	p.Gln1470Ter	p.Q1470*	ENST00000534358	NM_005933.3	1470	Cag/Tag	11/36	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.81759217161816	2		524	557	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	127	151	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.922	0.846	0.999	0.922	0.846	0.999	CLONAL	1	TRUE	1	0.81759217161816	2		151	337	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708999	117708999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34203286	NA	P-0021526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	212	577	0	ENST00000368508.3:c.1958C>T	p.Ser653Phe	p.S653F	ENST00000368508	NM_002944.2	653	tCt/tTt	13/43	1	2	FACETS	0.986	0.924	1	0.986	0.924	1	CLONAL	1	TRUE	1	0.81759217161816	2		577	526	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0021526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	179	517	1	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.676010842986084	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.81759217161816	1		518	239	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538897	23538897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1200957711	NA	P-0021526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	239	523	1	ENST00000380871.4:c.542G>A	p.Arg181Gln	p.R181Q	ENST00000380871	NM_006167.3	181	cGa/cAa	2/2	0.81759217161816	3	FACETS	1	0.957	1	0.514	0.481	0.548	CLONAL	1	TRUE	1	0.81759217161816	3		524	801	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134255	11134255	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	265	573	0	ENST00000358026.2:c.2921C>T	p.Pro974Leu	p.P974L	ENST00000358026	NM_001128849.1	974	cCc/cTc	20/36	0.81759217161816	3	FACETS	1	0.961	1	0.515	0.483	0.547	CLONAL	1	TRUE	1	0.81759217161816	3		573	887	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169552	27169552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	335	761	0	ENST00000380036.4:c.553G>A	p.Asp185Asn	p.D185N	ENST00000380036	NM_000459.3	185	Gat/Aat	4/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.81759217161816	2		761	797	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980355	201980355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764832150	NA	P-0021526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	316	721	1	ENST00000359651.3:c.91C>T	p.Pro31Ser	p.P31S	ENST00000359651		31	Cct/Tct	1/8	0.81759217161816	4	FACETS	1	0.977	1	0.356	0.335	0.377	CLONAL	1	TRUE	1	0.81759217161816	4		722	1316	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699332	18699332	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	212	515	0	ENST00000266497.5:c.3433G>T	p.Asp1145Tyr	p.D1145Y	ENST00000266497		1145	Gac/Tac	24/31	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.81759217161816	2		515	457	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49054143	49054143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1432581053	NA	P-0021526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	213	429	0	ENST00000267163.4:c.2723G>A	p.Arg908Gln	p.R908Q	ENST00000267163	NM_000321.2	908	cGa/cAa	27/27	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.81759217161816	2		429	491	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5258075	5258075	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	222	563	0	ENST00000357368.4:c.659A>G	p.Asn220Ser	p.N220S	ENST00000357368	NM_002850.3	220	aAc/aGc	8/38	0.786314224781669	5	FACETS	0.974	0.905	1	0.244	0.226	0.262	CLONAL	1	TRUE	1	0.81759217161816	5		563	1241	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223418	36223418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	572	807	0	ENST00000222270.7:c.5968G>A	p.Asp1990Asn	p.D1990N	ENST00000222270	NM_014727.1	1990	Gac/Aac	28/37	0.45668412747371	6	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.81759217161816	6		807	1609	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224559	36224559	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	540	812	0	ENST00000222270.7:c.7021G>T	p.Gly2341Trp	p.G2341W	ENST00000222270	NM_014727.1	2341	Ggg/Tgg	29/37	0.45668412747371	6	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.81759217161816	6		812	1524	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858010	45858010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	921	618	1	ENST00000391945.4:c.1643C>T	p.Thr548Ile	p.T548I	ENST00000391945	NM_000400.3	548	aCc/aTc	17/23	0.81494526717901	5	FACETS	0.996	0.975	1	0.996	0.975	1	CLONAL	4	TRUE	1	0.81759217161816	5		619	1259	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881389	111881389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	216	508	0	ENST00000393256.3:c.67G>A	p.Glu23Lys	p.E23K	ENST00000393256	NM_006538.4	23	Gag/Aag	2/4	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.81759217161816	2		508	516	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309925	30309925	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	261	574	0	ENST00000307677.4:c.97A>T	p.Asn33Tyr	p.N33Y	ENST00000307677	NM_138578.1	33	Aac/Tac	2/3	1	2	FACETS	0.966	0.911	1	0.966	0.911	1	CLONAL	1	TRUE	1	0.81759217161816	2		574	661	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932690	49932690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	278	736	1	ENST00000296474.3:c.3181G>A	p.Asp1061Asn	p.D1061N	ENST00000296474	NM_002447.2	1061	Gac/Aac	14/20	1	2	FACETS	0.935	0.883	0.988	0.935	0.883	0.988	CLONAL	1	TRUE	1	0.81759217161816	2		737	727	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498473	89498473	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	203	467	0	ENST00000336596.2:c.2445G>A	p.Trp815Ter	p.W815*	ENST00000336596	NM_005233.5	815	tgG/tgA	14/17	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.81759217161816	2		467	447	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446330	187446330	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	159	390	0	ENST00000232014.4:c.1358C>T	p.Ser453Phe	p.S453F	ENST00000232014	NM_001130845.1	453	tCc/tTc	6/10	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.81759217161816	2		390	388	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541690	187541690	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	201	416	0	ENST00000441802.2:c.6050T>A	p.Leu2017His	p.L2017H	ENST00000441802	NM_005245.3	2017	cTc/cAc	10/27	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.81759217161816	2		416	431	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876497	35876497	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	205	546	0	ENST00000303115.3:c.1289C>T	p.Pro430Leu	p.P430L	ENST00000303115	NM_002185.3	430	cCa/cTa	8/8	1	2	FACETS	0.92	0.86	0.981	0.92	0.86	0.981	CLONAL	1	TRUE	1	0.81759217161816	2		546	545	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048898	180048898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	220	715	1	ENST00000261937.6:c.1664C>T	p.Pro555Leu	p.P555L	ENST00000261937	NM_182925.4	555	cCc/cTc	13/30	1	2	FACETS	0.978	0.918	1	0.978	0.918	1	CLONAL	1	TRUE	1	0.81759217161816	2		716	550	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671853	30671853	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	311	732	0	ENST00000376406.3:c.5107C>T	p.Pro1703Ser	p.P1703S	ENST00000376406	NM_014641.2	1703	Cct/Tct	10/15	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.81759217161816	2		732	674	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372151	55372151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	210	610	0	ENST00000297316.4:c.841C>T	p.Pro281Ser	p.P281S	ENST00000297316	NM_022454.3	281	Ccc/Tcc	2/2	0.81759217161816	3	FACETS	1	0.971	1	0.537	0.501	0.574	CLONAL	1	TRUE	1	0.81759217161816	3		610	674	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022040	5022040	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	230	598	1	ENST00000381652.3:c.53C>T	p.Ser18Phe	p.S18F	ENST00000381652	NM_004972.3	18	tCt/tTt	3/25	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.81759217161816	2		599	545	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430405	47430406	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	213	598	1	ENST00000377045.4:c.1680_1681delinsTT	p.Pro561Ser	p.P561S	ENST00000377045	NM_001654.4	560	ttCCcc/ttTTcc	15/16	0.81759217161816	3	FACETS	0.967	0.901	1	0.484	0.45	0.518	CLONAL	1	TRUE	1	0.81759217161816	3		599	759	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0021584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	45	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.804	0.679	0.941	1	0.964	1	CLONAL	2	TRUE	1	0.18	2		288	311	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	55	151	0				ENST00000310581	NM_198253.2	-/1132			0.153202058895368	1	FACETS	0.604	0.515	0.703	0.604	0.515	0.703	SUBCLONAL	1	TRUE	0	0.18	1		151	920	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244400	5244400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs79388082	NA	P-0021584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	92	685	0	ENST00000357368.4:c.1082C>T	p.Ser361Phe	p.S361F	ENST00000357368	NM_002850.3	361	tCc/tTc	11/38	0.153202058895368	3	FACETS	0.916	0.812	1	0.458	0.406	0.515	CLONAL	1	TRUE	1	0.18	3		685	1216	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819206	3819206	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139896431	NA	P-0021584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	98	566	0	ENST00000262367.5:c.3029C>T	p.Pro1010Leu	p.P1010L	ENST00000262367	NM_004380.2	1010	cCt/cTt	15/31	0.153202058895368	3	FACETS	1	0.926	1	0.527	0.468	0.589	CLONAL	1	TRUE	1	0.18	3		566	1127	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579408	7579430	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGGGCCAGGAGGGGGCTGGTG	CAGGGGCCAGGAGGGGGCTGGTG	-	rs886041861	NA	P-0021584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1292	93	713	0	ENST00000269305.4:c.257_279del	p.Ala86ValfsTer55	p.A86Vfs*55	ENST00000269305	NM_001126112.2	86	gCACCAGCCCCCTCCTGGCCCCTG/g	4/11	1	2	FACETS	0.746	0.661	0.838	0.746	0.661	0.838	SUBCLONAL	1	TRUE	1	0.18	2		713	1385	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968326	2968326	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	62	595	0	ENST00000396946.4:c.1660C>T	p.Pro554Ser	p.P554S	ENST00000396946	NM_032415.4	554	Ccc/Tcc	13/25	1	2	FACETS	0.609	0.524	0.702	0.609	0.524	0.702	SUBCLONAL	1	TRUE	1	0.18	2		595	1132	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317926	8317926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	18	560	0	ENST00000356435.5:c.5687C>T	p.Ser1896Phe	p.S1896F	ENST00000356435		1896	tCc/tTc	35/35	1	2	FACETS	0.606	0.456	0.784	0.606	0.456	0.784	SUBCLONAL	1	TRUE	1	0.18	2		560	330	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343694	118343694	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	47	464	0	ENST00000534358.1:c.1820A>G	p.Lys607Arg	p.K607R	ENST00000534358	NM_005933.3	607	aAg/aGg	3/36	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.18	2		464	432	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022816	12022816	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1269640792	NA	P-0021584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	50	459	0	ENST00000396373.4:c.922C>T	p.His308Tyr	p.H308Y	ENST00000396373	NM_001987.4	308	Cat/Tat	5/8	0.153202058895368	3	FACETS	0.736	0.622	0.861	0.368	0.311	0.431	SUBCLONAL	1	TRUE	1	0.18	3		459	823	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15938123	15938123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1401344163	NA	P-0021584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	34	328	0	ENST00000268712.3:c.7091G>A	p.Arg2364Lys	p.R2364K	ENST00000268712	NM_006311.3	2364	aGg/aAg	45/46	1	2	FACETS	0.979	0.8	1	0.979	0.8	1	CLONAL	1	TRUE	1	0.18	2		328	386	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207648	2207649	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1404	109	635	1	ENST00000398665.3:c.932_933delinsTT	p.Ser311Phe	p.S311F	ENST00000398665	NM_032482.2	311	tCC/tTT	11/28	0.153202058895368	3	FACETS	0.873	0.78	0.971	0.436	0.39	0.486	CLONAL	1	TRUE	1	0.18	3		636	1513	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349589	15349589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1547	102	756	0	ENST00000263377.2:c.3985C>T	p.Arg1329Trp	p.R1329W	ENST00000263377	NM_058243.2	1329	Cgg/Tgg	19/20	0.153202058895368	3	FACETS	0.749	0.667	0.837	0.375	0.333	0.419	SUBCLONAL	1	TRUE	1	0.18	3		756	1649	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954260	17954261	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	61	535	2	ENST00000458235.1:c.348_349delinsTT	p.Arg117Cys	p.R117C	ENST00000458235	NM_000215.3	116	caCCgc/caTTgc	4/24	0.153202058895368	3	FACETS	0.679	0.584	0.784	0.34	0.292	0.392	SUBCLONAL	1	TRUE	1	0.18	3		537	1088	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451801	29451801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745317944	NA	P-0021584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	56	715	0	ENST00000389048.3:c.2764G>A	p.Gly922Arg	p.G922R	ENST00000389048	NM_004304.4	922	Gga/Aga	16/29	1	2	FACETS	0.585	0.499	0.679	0.585	0.499	0.679	SUBCLONAL	1	TRUE	1	0.18	2		715	1064	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488763	212488763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	22	457	0	ENST00000342788.4:c.2086G>A	p.Glu696Lys	p.E696K	ENST00000342788	NM_005235.2	696	Gaa/Aaa	18/28	1	2	FACETS	0.739	0.572	0.932	0.739	0.572	0.932	CLONAL	1	TRUE	1	0.18	2		457	331	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770621	40770621	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	28	450	0	ENST00000373198.4:c.2761G>A	p.Ala921Thr	p.A921T	ENST00000373198	NM_133170.3	921	Gct/Act	19/32	0.153202058895368	3	FACETS	0.626	0.499	0.771	0.313	0.249	0.386	SUBCLONAL	1	TRUE	1	0.18	3		450	542	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345944	152345944	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	48	501	0	ENST00000359321.1:c.626C>T	p.Pro209Leu	p.P209L	ENST00000359321	NM_005431.1	209	cCt/cTt	3/3	1	2	FACETS	0.895	0.756	1	0.895	0.756	1	CLONAL	1	TRUE	1	0.18	2		501	596	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194601	29194601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1489348650	NA	P-0021584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1619	108	805	3	ENST00000240100.2:c.1127C>T	p.Ser376Leu	p.S376L	ENST00000240100	NM_001394.6	376	tCg/tTg	4/4	1	2	FACETS	0.695	0.621	0.774	0.695	0.621	0.774	SUBCLONAL	1	TRUE	1	0.18	2		808	1727	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207522	29207522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	68	425	0	ENST00000240100.2:c.274G>A	p.Glu92Lys	p.E92K	ENST00000240100	NM_001394.6	92	Gag/Aag	1/4	1	2	FACETS	0.835	0.725	0.955	0.835	0.725	0.955	CLONAL	1	TRUE	1	0.18	2		425	905	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117870624	117870624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	18	489	1	ENST00000297338.2:c.448G>A	p.Gly150Arg	p.G150R	ENST00000297338	NM_006265.2	150	Ggg/Agg	5/14	1	2	FACETS	0.641	0.482	0.829	0.641	0.482	0.829	SUBCLONAL	1	TRUE	1	0.18	2		490	312	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923058	39923058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758185915	NA	P-0021584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	63	621	2	ENST00000378444.4:c.3650G>A	p.Arg1217Gln	p.R1217Q	ENST00000378444	NM_001123385.1	1217	cGa/cAa	8/15	1	2	FACETS	0.623	0.537	0.717	0.623	0.537	0.717	SUBCLONAL	1	TRUE	1	0.18	2		623	1124	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	74	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.863	0.755	0.979	0.863	0.755	0.979	CLONAL	1	TRUE	1	0.24127446313292	2		306	711	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066711	94066711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	60	697	0	ENST00000369303.4:c.1048G>A	p.Glu350Lys	p.E350K	ENST00000369303	NM_004440.3	350	Gaa/Aaa	5/17	1	2	FACETS	0.647	0.556	0.746	0.647	0.556	0.746	SUBCLONAL	1	TRUE	1	0.24127446313292	2		697	769	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	63	552	0	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	1	2	FACETS	0.598	0.515	0.687	0.598	0.515	0.687	SUBCLONAL	1	TRUE	1	0.24127446313292	2		552	874	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674156	117674156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867084033	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	68	688	0	ENST00000368508.3:c.4318C>T	p.Pro1440Ser	p.P1440S	ENST00000368508	NM_002944.2	1440	Cca/Tca	26/43	1	2	FACETS	0.787	0.684	0.899	0.787	0.684	0.899	SUBCLONAL	1	TRUE	1	0.24127446313292	2		688	716	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	122	454	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	1	2	FACETS	0.889	0.802	0.982	0.889	0.802	0.982	CLONAL	1	TRUE	1	0.24127446313292	2		454	1137	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041073	29041073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	48	695	1	ENST00000282397.4:c.355G>A	p.Glu119Lys	p.E119K	ENST00000282397	NM_002019.4	119	Gaa/Aaa	3/30	1	2	FACETS	0.555	0.468	0.651	0.555	0.468	0.651	SUBCLONAL	1	TRUE	1	0.24127446313292	2		696	717	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518175	8518175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1354824749	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	98	555	0	ENST00000356435.5:c.1216G>A	p.Glu406Lys	p.E406K	ENST00000356435		406	Gaa/Aaa	10/35	0.172165478168603	2	FACETS	1	0.975	1	0.664	0.593	0.739	CLONAL	1	TRUE	0	0.24127446313292	2		555	612	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971029	21971029	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519852	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	128	474	0	ENST00000304494.5:c.329G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tGg/tAg	2/3	0.172165478168603	2	FACETS	1	0.985	1	0.741	0.672	0.813	CLONAL	1	TRUE	0	0.24127446313292	2		474	716	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317926	8317926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	111	560	0	ENST00000356435.5:c.5687C>T	p.Ser1896Phe	p.S1896F	ENST00000356435		1896	tCc/tTc	35/35	0.172165478168603	2	FACETS	0.833	0.752	0.919	0.833	0.752	0.919	CLONAL	2	TRUE	0	0.24127446313292	2		560	552	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892299	9892299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs796052549	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	49	439	0	ENST00000330684.3:c.2191G>A	p.Asp731Asn	p.D731N	ENST00000330684	NM_001134407.1	731	Gat/Aat	11/13	1	2	FACETS	0.63	0.532	0.737	0.63	0.532	0.737	SUBCLONAL	1	TRUE	1	0.24127446313292	2		439	645	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730850	40730850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	86	1001	0	ENST00000373198.4:c.3685G>A	p.Asp1229Asn	p.D1229N	ENST00000373198	NM_133170.3	1229	Gac/Aac	27/32	1	2	FACETS	0.74	0.653	0.833	0.74	0.653	0.833	SUBCLONAL	1	TRUE	1	0.24127446313292	2		1001	964	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032045	26032045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	49	558	1	ENST00000244661.2:c.244G>A	p.Asp82Asn	p.D82N	ENST00000244661	NM_003537.3	82	Gat/Aat	1/1	0.241299104862665	3	FACETS	0.662	0.559	0.775	0.331	0.279	0.388	SUBCLONAL	1	TRUE	1	0.24127446313292	3		559	688	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572483	95572483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	47	597	0	ENST00000393063.1:c.2882C>T	p.Pro961Leu	p.P961L	ENST00000393063	NM_030621.3	961	cCt/cTt	19/28	1	2	FACETS	0.643	0.542	0.755	0.643	0.542	0.755	SUBCLONAL	1	TRUE	1	0.24127446313292	2		597	606	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858390	9858390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	43	613	1	ENST00000330684.3:c.3011C>T	p.Ser1004Phe	p.S1004F	ENST00000330684	NM_001134407.1	1004	tCc/tTc	13/13	1	2	FACETS	0.566	0.472	0.67	0.566	0.472	0.67	SUBCLONAL	1	TRUE	1	0.24127446313292	2		614	630	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994833	73994833	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	40	313	0	ENST00000318443.5:c.317C>T	p.Ser106Phe	p.S106F	ENST00000318443	NM_001024736.1	106	tCc/tTc	3/10	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.24127446313292	2		313	269	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520257	9520257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	45	425	0	ENST00000353224.5:c.2012C>T	p.Ser671Leu	p.S671L	ENST00000353224	NM_177990.2	671	tCa/tTa	10/10	1	2	FACETS	0.657	0.551	0.774	0.657	0.551	0.774	SUBCLONAL	1	TRUE	1	0.24127446313292	2		425	568	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164451	36164451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	28	392	2	ENST00000300305.3:c.1424C>T	p.Ala475Val	p.A475V	ENST00000300305		475	gCc/gTc	8/8	1	2	FACETS	0.645	0.515	0.792	0.645	0.515	0.792	SUBCLONAL	1	TRUE	1	0.24127446313292	2		394	360	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956149	55956149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	68	759	3	ENST00000263923.4:c.3166G>A	p.Asp1056Asn	p.D1056N	ENST00000263923	NM_002253.2	1056	Gat/Aat	23/30	1	2	FACETS	0.643	0.558	0.736	0.643	0.558	0.736	SUBCLONAL	1	TRUE	1	0.24127446313292	2		762	876	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509849	106509849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426277818	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	83	773	1	ENST00000359195.3:c.1843G>A	p.Glu615Lys	p.E615K	ENST00000359195	NM_002649.2	615	Gaa/Aaa	2/11	1	2	FACETS	0.755	0.665	0.852	0.755	0.665	0.852	SUBCLONAL	1	TRUE	1	0.24127446313292	2		774	911	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684323	29684323	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs567988442	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	77	709	2	ENST00000356175.3:c.7843C>T	p.Gln2615Ter	p.Q2615*	ENST00000356175	NM_000267.3	2615	Caa/Taa	53/57	1	2	FACETS	0.837	0.734	0.947	0.837	0.734	0.947	CLONAL	1	TRUE	1	0.24127446313292	2		711	763	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260485	16260486	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	38	538	2	ENST00000375759.3:c.7756dup	p.Thr2586AsnfsTer10	p.T2586Nfs*10	ENST00000375759	NM_015001.2	2584	gaa/gAaa	11/15	1	2	FACETS	0.491	0.404	0.587	0.491	0.404	0.587	SUBCLONAL	1	TRUE	1	0.24127446313292	2		540	642	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713479	40713479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	53	667	0	ENST00000373198.4:c.4036G>A	p.Asp1346Asn	p.D1346N	ENST00000373198	NM_133170.3	1346	Gat/Aat	30/32	1	2	FACETS	0.577	0.491	0.672	0.577	0.491	0.672	SUBCLONAL	1	TRUE	1	0.24127446313292	2		667	761	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339799	116339799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	60	603	0	ENST00000397752.3:c.661G>A	p.Glu221Lys	p.E221K	ENST00000397752	NM_000245.2	221	Gaa/Aaa	2/21	1	2	FACETS	0.717	0.617	0.826	0.717	0.617	0.826	SUBCLONAL	1	TRUE	1	0.24127446313292	2		603	694	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422104	81422104	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532920088	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	70	727	1	ENST00000298171.2:c.80C>T	p.Pro27Leu	p.P27L	ENST00000298171	NM_000369.2	27	cCa/cTa	1/10	1	2	FACETS	0.696	0.605	0.794	0.696	0.605	0.794	SUBCLONAL	1	TRUE	1	0.24127446313292	2		728	834	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673718	176673718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754590923	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	70	582	1	ENST00000439151.2:c.4418G>A	p.Arg1473Gln	p.R1473Q	ENST00000439151	NM_022455.4	1473	cGa/cAa	10/23	1	2	FACETS	0.857	0.747	0.976	0.857	0.747	0.976	CLONAL	1	TRUE	1	0.24127446313292	2		583	677	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524576	103524576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	27	365	0	ENST00000355739.4:c.2707C>T	p.Pro903Ser	p.P903S	ENST00000355739	NM_000123.3	903	Cca/Tca	13/15	1	2	FACETS	0.534	0.424	0.66	0.534	0.424	0.66	SUBCLONAL	1	TRUE	1	0.24127446313292	2		365	419	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043464	180043464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	61	869	2	ENST00000261937.6:c.3122G>A	p.Arg1041Gln	p.R1041Q	ENST00000261937	NM_182925.4	1041	cGg/cAg	23/30	1	2	FACETS	0.575	0.494	0.662	0.575	0.494	0.662	SUBCLONAL	1	TRUE	1	0.24127446313292	2		871	880	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295253	1295253	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1232074117	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	70	700	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.789	0.688	0.9	0.789	0.688	0.9	SUBCLONAL	1	TRUE	1	0.24127446313292	2		700	735	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375890	118375890	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	55	715	0	ENST00000534358.1:c.9283C>T	p.Gln3095Ter	p.Q3095*	ENST00000534358	NM_005933.3	3095	Caa/Taa	27/36	0.21345980618249	1	FACETS	0.597	0.51	0.693	0.597	0.51	0.693	SUBCLONAL	1	TRUE	0	0.24127446313292	1		715	671	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173622	108173622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881373	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	46	575	0	ENST00000278616.4:c.5362G>A	p.Gly1788Ser	p.G1788S	ENST00000278616	NM_000051.3	1788	Ggc/Agc	36/63	0.21345980618249	1	FACETS	0.742	0.625	0.87	0.742	0.625	0.87	SUBCLONAL	1	TRUE	0	0.24127446313292	1		575	452	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371984	55371984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	67	792	1	ENST00000297316.4:c.674C>T	p.Ser225Phe	p.S225F	ENST00000297316	NM_022454.3	225	tCc/tTc	2/2	1	2	FACETS	0.721	0.626	0.825	0.721	0.626	0.825	SUBCLONAL	1	TRUE	1	0.24127446313292	2		793	770	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695875	117695875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768482698	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	83	891	1	ENST00000369458.3:c.562G>A	p.Gly188Arg	p.G188R	ENST00000369458	NM_024626.3	188	Gga/Aga	4/6	1	2	FACETS	0.73	0.642	0.823	0.73	0.642	0.823	SUBCLONAL	1	TRUE	1	0.24127446313292	2		892	943	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552761	226552761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	79	715	0	ENST00000366794.5:c.2600C>T	p.Thr867Ile	p.T867I	ENST00000366794	NM_001618.3	867	aCc/aTc	19/23	0.241299104862665	3	FACETS	0.798	0.7	0.903	0.399	0.35	0.452	CLONAL	1	TRUE	1	0.24127446313292	3		715	920	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596101	43596101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	66	842	0	ENST00000355710.3:c.268G>A	p.Glu90Lys	p.E90K	ENST00000355710	NM_020975.4	90	Gag/Aag	2/20	1	2	FACETS	0.634	0.549	0.727	0.634	0.549	0.727	SUBCLONAL	1	TRUE	1	0.24127446313292	2		842	863	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725041	89725062	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAGGTGAAGCTGTACTTCACAA	TAGGTGAAGCTGTACTTCACAA	-	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	20	328	0	ENST00000371953.3:c.1027-3_1045del		p.X343_splice	ENST00000371953	NM_000314.4	343		9/9	0.24127446313292	1	FACETS	0.542	0.415	0.69	0.542	0.415	0.69	SUBCLONAL	1	TRUE	0	0.24127446313292	1		328	269	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588130	69588130	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	73	832	0	ENST00000168712.1:c.568G>C	p.Gly190Arg	p.G190R	ENST00000168712	NM_002007.2	190	Ggg/Cgg	3/3	1	2	FACETS	0.733	0.64	0.833	0.733	0.64	0.833	SUBCLONAL	1	TRUE	1	0.24127446313292	2		832	826	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94224082	94224082	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	66	641	0	ENST00000323929.3:c.70G>T	p.Gly24Ter	p.G24*	ENST00000323929	NM_005591.3	24	Gga/Tga	3/20	1	2	FACETS	0.85	0.737	0.971	0.85	0.737	0.971	CLONAL	1	TRUE	1	0.24127446313292	2		641	644	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148584	119149573	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CACTGGACACAAGCTTTAGTATATTCTTTATAGAACTGACAGCATAATTGAATTCATTGGAACCCATTGACTAGATTAGTGAATTTGTGTGTATGTGGTTTCACTTTAAACCCTGGAGCTTAAAATAGGACCCAGACTAGATGCTTTCTGGTTTAATAAAAAATAAACCACTGTTGTGACATTTTTATATAAGCAAAATTTGTATAGGAAACAAGTCTTCACTTTTTCTGTTAACATTTATAATTGCAGTTATTTATTCAACTAATAGTCTTTTAATTTTTTTTAATCAAAGGAACAATATGAATTATACTGTGAGATGGGCTCCACATTCCAACTATGTAAAATATGTGCTGAAAATGATAAGGATGTAAAGATTGAGCCCTGTGGACACCTCATGTGCACATCCTGTCTTACATCCTGGCAGGTACGGATCTAAACAGCGACTTTTTTCAGCTATGTAATAACCTTGGAAAATTCGGTATTATATAGCCTTTACTGATACAAGGGGTGGCCTGGCTTTTGGGGTTAGGTTTAAACTTTTACTTTTTTTTGATCTCTAGGAAATGTATTTTCTAGTAGATTAATATTTTAAGTATTTTCAGATGCATCTGTTACTATCTTTTGCTTCTTCTGCAGGAATCAGAAGGTCAGGGCTGTCCTTTCTGCCGATGTGAAATTAAAGGTACTGAACCCATCGTGGTAGATCCGTTTGATCCTAGAGGGAGTGGCAGCCTGTTGAGGCAAGGAGCAGAGGGAGCTCCCTCCCCAAATTATGATGATGATGATGATGAACGAGCTGATGATACTCTCTTCATGATGAAGGAATTGGCTGGTGCCAAGGTAAGATGGCAGTTTAGGAGACTGGCAAAATCCATTGTGAGTTGTCTTCTAAAGCCGTAAAACACTTAACGATATCCAAACTACAATGATAGGTAGTATTAATAGCTAATATTTATTGAGCATTTACTATATGACAGATATTGTGTTAAG	CACTGGACACAAGCTTTAGTATATTCTTTATAGAACTGACAGCATAATTGAATTCATTGGAACCCATTGACTAGATTAGTGAATTTGTGTGTATGTGGTTTCACTTTAAACCCTGGAGCTTAAAATAGGACCCAGACTAGATGCTTTCTGGTTTAATAAAAAATAAACCACTGTTGTGACATTTTTATATAAGCAAAATTTGTATAGGAAACAAGTCTTCACTTTTTCTGTTAACATTTATAATTGCAGTTATTTATTCAACTAATAGTCTTTTAATTTTTTTTAATCAAAGGAACAATATGAATTATACTGTGAGATGGGCTCCACATTCCAACTATGTAAAATATGTGCTGAAAATGATAAGGATGTAAAGATTGAGCCCTGTGGACACCTCATGTGCACATCCTGTCTTACATCCTGGCAGGTACGGATCTAAACAGCGACTTTTTTCAGCTATGTAATAACCTTGGAAAATTCGGTATTATATAGCCTTTACTGATACAAGGGGTGGCCTGGCTTTTGGGGTTAGGTTTAAACTTTTACTTTTTTTTGATCTCTAGGAAATGTATTTTCTAGTAGATTAATATTTTAAGTATTTTCAGATGCATCTGTTACTATCTTTTGCTTCTTCTGCAGGAATCAGAAGGTCAGGGCTGTCCTTTCTGCCGATGTGAAATTAAAGGTACTGAACCCATCGTGGTAGATCCGTTTGATCCTAGAGGGAGTGGCAGCCTGTTGAGGCAAGGAGCAGAGGGAGCTCCCTCCCCAAATTATGATGATGATGATGATGAACGAGCTGATGATACTCTCTTCATGATGAAGGAATTGGCTGGTGCCAAGGTAAGATGGCAGTTTAGGAGACTGGCAAAATCCATTGTGAGTTGTCTTCTAAAGCCGTAAAACACTTAACGATATCCAAACTACAATGATAGGTAGTATTAATAGCTAATATTTATTGAGCATTTACTATATGACAGATATTGTGTTAAG	-	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	19	306	0	ENST00000264033.4:c.1095+34_1431+154del		p.X365_splice	ENST00000264033	NM_005188.3	365		8-9/16	0.21345980618249	1	FACETS	0.438	0.332	0.563	0.438	0.332	0.563	SUBCLONAL	1	TRUE	0	0.24127446313292	1		306	316	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524124	18524124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1161481962	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	51	474	0	ENST00000266497.5:c.1636C>T	p.Pro546Ser	p.P546S	ENST00000266497		546	Ccc/Tcc	11/31	1	2	FACETS	0.963	0.82	1	0.963	0.82	1	CLONAL	1	TRUE	1	0.24127446313292	2		474	439	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432471	49432471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	85	842	0	ENST00000301067.7:c.8668C>T	p.Pro2890Ser	p.P2890S	ENST00000301067	NM_003482.3	2890	Cct/Tct	34/54	1	2	FACETS	0.779	0.688	0.878	0.779	0.688	0.878	SUBCLONAL	1	TRUE	1	0.24127446313292	2		842	904	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434291	49434291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	120	1148	0	ENST00000301067.7:c.7262C>T	p.Ser2421Phe	p.S2421F	ENST00000301067	NM_003482.3	2421	tCc/tTc	31/54	1	2	FACETS	0.839	0.755	0.927	0.839	0.755	0.927	CLONAL	1	TRUE	1	0.24127446313292	2		1148	1186	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445719	49445719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1251	141	1299	0	ENST00000301067.7:c.1747C>T	p.Pro583Ser	p.P583S	ENST00000301067	NM_003482.3	583	Cct/Tct	10/54	1	2	FACETS	0.84	0.762	0.921	0.84	0.762	0.921	CLONAL	1	TRUE	1	0.24127446313292	2		1299	1392	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225957	133225958	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	74	921	2	ENST00000320574.5:c.3939_3940delinsAA	p.Gly1314Arg	p.G1314R	ENST00000320574	NM_006231.2	1313	acGGgg/acAAgg	31/49	1	2	FACETS	0.646	0.564	0.734	0.646	0.564	0.734	SUBCLONAL	1	TRUE	1	0.24127446313292	2		923	950	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589298	28589298	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	51	583	0	ENST00000241453.7:c.2749G>A	p.Glu917Lys	p.E917K	ENST00000241453	NM_004119.2	917	Gaa/Aaa	22/24	1	2	FACETS	0.663	0.562	0.773	0.663	0.562	0.773	SUBCLONAL	1	TRUE	1	0.24127446313292	2		583	638	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012476	29012476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140749618	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	33	532	0	ENST00000282397.4:c.395G>A	p.Gly132Asp	p.G132D	ENST00000282397	NM_002019.4	132	gGt/gAt	4/30	1	2	FACETS	0.522	0.424	0.633	0.522	0.424	0.633	SUBCLONAL	1	TRUE	1	0.24127446313292	2		532	524	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779500	3779500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	124	1171	0	ENST00000262367.5:c.5548C>T	p.Leu1850Phe	p.L1850F	ENST00000262367	NM_004380.2	1850	Ctc/Ttc	31/31	1	2	FACETS	0.87	0.785	0.96	0.87	0.785	0.96	CLONAL	1	TRUE	1	0.24127446313292	2		1171	1182	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129737	30129737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	72	877	1	ENST00000263025.4:c.476C>T	p.Ser159Phe	p.S159F	ENST00000263025	NM_002746.2	159	tCc/tTc	3/9	1	2	FACETS	0.652	0.568	0.742	0.652	0.568	0.742	SUBCLONAL	1	TRUE	1	0.24127446313292	2		878	916	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821080	72821081	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	48	757	1	ENST00000268489.5:c.11094_11095delinsAA	p.Asp3699Asn	p.D3699N	ENST00000268489	NM_006885.3	3698	acGGac/acAAac	10/10	1	2	FACETS	0.445	0.374	0.522	0.445	0.374	0.522	SUBCLONAL	1	TRUE	1	0.24127446313292	2		758	895	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81902851	81902852	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	52	785	0	ENST00000359376.3:c.512_513delinsTT	p.Pro171Leu	p.P171L	ENST00000359376	NM_002661.3	171	cCC/cTT	6/33	1	2	FACETS	0.544	0.461	0.634	0.544	0.461	0.634	SUBCLONAL	1	TRUE	1	0.24127446313292	2		785	793	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652904	29652904	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	37	554	0	ENST00000356175.3:c.4839T>A	p.Tyr1613Ter	p.Y1613*	ENST00000356175	NM_000267.3	1613	taT/taA	36/57	1	2	FACETS	0.56	0.461	0.671	0.56	0.461	0.671	SUBCLONAL	1	TRUE	1	0.24127446313292	2		554	548	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40864381	40864381	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	86	954	2	ENST00000428826.2:c.1327C>T	p.Arg443Ter	p.R443*	ENST00000428826		443	Cga/Tga	12/21	1	2	FACETS	0.665	0.587	0.749	0.665	0.587	0.749	SUBCLONAL	1	TRUE	1	0.24127446313292	2		956	1072	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2185873	2185873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	97	909	0	ENST00000398665.3:c.145C>T	p.Pro49Ser	p.P49S	ENST00000398665	NM_032482.2	49	Ccg/Tcg	3/28	0.24127446313292	1	FACETS	0.78	0.694	0.871	0.78	0.694	0.871	SUBCLONAL	1	TRUE	0	0.24127446313292	1		909	907	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39214723	39214723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749989638	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	50	500	0	ENST00000402219.2:c.3401C>T	p.Ser1134Phe	p.S1134F	ENST00000402219	NM_005633.3	1134	tCt/tTt	22/23	1	2	FACETS	0.805	0.683	0.939	0.805	0.683	0.939	CLONAL	1	TRUE	1	0.24127446313292	2		500	515	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262578	39262578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867539471	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	59	782	1	ENST00000402219.2:c.928C>T	p.Arg310Cys	p.R310C	ENST00000402219	NM_005633.3	310	Cgt/Tgt	7/23	1	2	FACETS	0.644	0.553	0.744	0.644	0.553	0.744	SUBCLONAL	1	TRUE	1	0.24127446313292	2		783	759	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285854	39285854	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1553362937	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	57	789	0	ENST00000402219.2:c.305C>G	p.Pro102Arg	p.P102R	ENST00000402219	NM_005633.3	102	cCt/cGt	3/23	1	2	FACETS	0.776	0.665	0.897	0.776	0.665	0.897	SUBCLONAL	1	TRUE	1	0.24127446313292	2		789	609	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99162485	99162485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	52	598	0	ENST00000074304.5:c.1003C>T	p.Pro335Ser	p.P335S	ENST00000074304	NM_001134224.1	335	Ccc/Tcc	12/26	1	2	FACETS	0.647	0.55	0.754	0.647	0.55	0.754	SUBCLONAL	1	TRUE	1	0.24127446313292	2		598	666	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212289013	212289013	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	51	742	0	ENST00000342788.4:c.2733G>A	p.Trp911Ter	p.W911*	ENST00000342788	NM_005235.2	911	tgG/tgA	23/28	1	2	FACETS	0.773	0.657	0.9	0.773	0.657	0.9	SUBCLONAL	1	TRUE	1	0.24127446313292	2		742	547	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989553	212989553	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	63	542	1	ENST00000342788.4:c.158A>T	p.Tyr53Phe	p.Y53F	ENST00000342788	NM_005235.2	53	tAt/tTt	2/28	1	2	FACETS	0.778	0.673	0.893	0.778	0.673	0.893	SUBCLONAL	1	TRUE	1	0.24127446313292	2		543	671	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36014544	36014544	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	69	734	0	ENST00000358208.4:c.317A>C	p.Lys106Thr	p.K106T	ENST00000358208		106	aAg/aCg	3/12	1	2	FACETS	0.689	0.599	0.787	0.689	0.599	0.787	SUBCLONAL	1	TRUE	1	0.24127446313292	2		734	830	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727143	40727143	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	81	795	0	ENST00000373198.4:c.3821A>G	p.Asn1274Ser	p.N1274S	ENST00000373198	NM_133170.3	1274	aAc/aGc	28/32	1	2	FACETS	0.806	0.709	0.91	0.806	0.709	0.91	CLONAL	1	TRUE	1	0.24127446313292	2		795	833	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306605	41306605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	71	903	0	ENST00000373198.4:c.1054C>T	p.Pro352Ser	p.P352S	ENST00000373198	NM_133170.3	352	Ccc/Tcc	7/32	1	2	FACETS	0.657	0.572	0.749	0.657	0.572	0.749	SUBCLONAL	1	TRUE	1	0.24127446313292	2		903	896	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866385	42866386	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	72	907	3	ENST00000398585.3:c.246_247delinsTT	p.Pro83Ser	p.P83S	ENST00000398585	NM_001135099.1	82	taCCcg/taTTcg	3/14	1	2	FACETS	0.648	0.565	0.738	0.648	0.565	0.738	SUBCLONAL	1	TRUE	1	0.24127446313292	2		910	921	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421272	12421272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372494308	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	85	976	1	ENST00000287820.6:c.152C>T	p.Ser51Phe	p.S51F	ENST00000287820	NM_015869.4	51	tCc/tTc	2/7	1	2	FACETS	0.703	0.62	0.793	0.703	0.62	0.793	SUBCLONAL	1	TRUE	1	0.24127446313292	2		977	1002	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799950	72799950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	41	529	0	ENST00000325599.8:c.1219G>A	p.Glu407Lys	p.E407K	ENST00000325599	NM_018130.2	407	Gaa/Aaa	11/11	1	2	FACETS	0.638	0.531	0.757	0.638	0.531	0.757	SUBCLONAL	1	TRUE	1	0.24127446313292	2		529	533	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204578	128204578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768892880	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	78	773	1	ENST00000341105.2:c.863C>T	p.Ser288Phe	p.S288F	ENST00000341105	NM_032638.4	288	tCc/tTc	3/6	1	2	FACETS	0.793	0.696	0.898	0.793	0.696	0.898	SUBCLONAL	1	TRUE	1	0.24127446313292	2		774	815	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670600	134670600	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	88	964	0	ENST00000398015.3:c.511A>T	p.Asn171Tyr	p.N171Y	ENST00000398015	NM_004441.4	171	Aat/Tat	3/16	1	2	FACETS	0.715	0.632	0.805	0.715	0.632	0.805	SUBCLONAL	1	TRUE	1	0.24127446313292	2		964	1020	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272191	142272191	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	67	636	0	ENST00000350721.4:c.2683T>C	p.Cys895Arg	p.C895R	ENST00000350721	NM_001184.3	895	Tgt/Cgt	13/47	1	2	FACETS	0.805	0.699	0.92	0.805	0.699	0.92	CLONAL	1	TRUE	1	0.24127446313292	2		636	690	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281508	142281508	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	74	925	0	ENST00000350721.4:c.736del	p.Ser246ProfsTer2	p.S246Pfs*2	ENST00000350721	NM_001184.3	246	Tcc/cc	4/47	1	2	FACETS	0.653	0.57	0.743	0.653	0.57	0.743	SUBCLONAL	1	TRUE	1	0.24127446313292	2		925	939	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502443	186502444	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	40	597	0	ENST00000323963.5:c.166_167delinsTT	p.Pro56Phe	p.P56F	ENST00000323963		56	CCt/TTt	3/11	1	2	FACETS	0.516	0.428	0.615	0.516	0.428	0.615	SUBCLONAL	1	TRUE	1	0.24127446313292	2		597	642	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446271	187446271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	83	824	0	ENST00000232014.4:c.1417C>T	p.Pro473Ser	p.P473S	ENST00000232014	NM_001130845.1	473	Ccg/Tcg	6/10	1	2	FACETS	0.753	0.663	0.849	0.753	0.663	0.849	SUBCLONAL	1	TRUE	1	0.24127446313292	2		824	914	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961761	55961761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	55	762	0	ENST00000263923.4:c.2800G>A	p.Glu934Lys	p.E934K	ENST00000263923	NM_002253.2	934	Gaa/Aaa	20/30	1	2	FACETS	0.63	0.538	0.731	0.63	0.538	0.731	SUBCLONAL	1	TRUE	1	0.24127446313292	2		762	724	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99823118	99823118	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	35	421	0	ENST00000280892.6:c.94C>T	p.Pro32Ser	p.P32S	ENST00000280892	NM_001130678.1	32	Cct/Tct	2/7	1	2	FACETS	0.583	0.477	0.702	0.583	0.477	0.702	SUBCLONAL	1	TRUE	1	0.24127446313292	2		421	498	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155721	106155721	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	51	530	0	ENST00000380013.4:c.622C>T	p.Pro208Ser	p.P208S	ENST00000380013	NM_001127208.2	208	Cct/Tct	3/11	1	2	FACETS	0.648	0.55	0.756	0.648	0.55	0.756	SUBCLONAL	1	TRUE	1	0.24127446313292	2		530	652	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294364	1294364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	88	792	0	ENST00000310581.5:c.637C>T	p.Pro213Ser	p.P213S	ENST00000310581	NM_198253.2	213	Ccc/Tcc	2/16	1	2	FACETS	0.878	0.777	0.986	0.878	0.777	0.986	CLONAL	1	TRUE	1	0.24127446313292	2		792	831	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80021355	80021355	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	67	823	0	ENST00000265081.6:c.1424T>C	p.Phe475Ser	p.F475S	ENST00000265081	NM_002439.4	475	tTt/tCt	9/24	1	2	FACETS	0.649	0.562	0.743	0.649	0.562	0.743	SUBCLONAL	1	TRUE	1	0.24127446313292	2		823	856	SUCCESS
APC	324	MSKCC	GRCh37	5	112178340	112178341	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	63	618	0	ENST00000257430.4:c.7049_7050delinsTT	p.Ser2350Phe	p.S2350F	ENST00000257430	NM_000038.5	2350	tCC/tTT	16/16	1	2	FACETS	0.749	0.647	0.86	0.749	0.647	0.86	SUBCLONAL	1	TRUE	1	0.24127446313292	2		618	697	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672591	30672591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	79	752	1	ENST00000376406.3:c.4369C>T	p.Pro1457Ser	p.P1457S	ENST00000376406	NM_014641.2	1457	Cct/Tct	10/15	0.241299104862665	3	FACETS	0.853	0.749	0.966	0.427	0.374	0.483	CLONAL	1	TRUE	1	0.24127446313292	3		753	860	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171983	32171983	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	88	670	0	ENST00000375023.3:c.3049C>T	p.Pro1017Ser	p.P1017S	ENST00000375023	NM_004557.3	1017	Ccc/Tcc	19/30	0.241299104862665	3	FACETS	1	0.894	1	0.505	0.447	0.568	CLONAL	1	TRUE	1	0.24127446313292	3		670	809	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704499	117704499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	61	610	0	ENST00000368508.3:c.2477C>T	p.Pro826Leu	p.P826L	ENST00000368508	NM_002944.2	826	cCt/cTt	16/43	1	2	FACETS	0.926	0.799	1	0.926	0.799	1	CLONAL	1	TRUE	1	0.24127446313292	2		610	546	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201844	152201844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	56	676	0	ENST00000206249.3:c.698G>A	p.Arg233Lys	p.R233K	ENST00000206249	NM_000125.3	233	aGg/aAg	3/8	1	2	FACETS	0.63	0.538	0.73	0.63	0.538	0.73	SUBCLONAL	1	TRUE	1	0.24127446313292	2		676	737	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382134	152382134	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	54	529	0	ENST00000206249.3:c.1244G>A	p.Gly415Glu	p.G415E	ENST00000206249	NM_000125.3	415	gGa/gAa	6/8	1	2	FACETS	0.892	0.762	1	0.892	0.762	1	CLONAL	1	TRUE	1	0.24127446313292	2		529	502	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968206	68968206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	81	785	0	ENST00000288368.4:c.1235G>A	p.Gly412Glu	p.G412E	ENST00000288368	NM_024870.2	412	gGa/gAa	10/40	1	2	FACETS	0.781	0.687	0.882	0.781	0.687	0.882	SUBCLONAL	1	TRUE	1	0.24127446313292	2		785	860	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534822	5534822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	128	784	0	ENST00000397747.3:c.133G>A	p.Asp45Asn	p.D45N	ENST00000397747	NM_025239.3	45	Gac/Aac	3/7	0.172165478168603	2	FACETS	1	0.979	1	0.638	0.578	0.702	CLONAL	1	TRUE	0	0.24127446313292	2		784	831	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518411	8518411	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	59	326	0	ENST00000356435.5:c.980G>A	p.Gly327Glu	p.G327E	ENST00000356435		327	gGa/gAa	10/35	0.172165478168603	2	FACETS	1	0.965	1	0.695	0.601	0.796	CLONAL	1	TRUE	0	0.24127446313292	2		326	352	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966641	36966641	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	85	788	0	ENST00000358127.4:c.685T>C	p.Phe229Leu	p.F229L	ENST00000358127	NM_001280556.1	229	Ttc/Ctc	6/10	1	2	FACETS	0.941	0.831	1	0.941	0.831	1	CLONAL	1	TRUE	1	0.24127446313292	2		788	749	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342592	87342592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1456574135	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	55	686	1	ENST00000277120.3:c.877G>A	p.Glu293Lys	p.E293K	ENST00000277120		293	Gaa/Aaa	9/19	1	2	FACETS	0.665	0.568	0.771	0.665	0.568	0.771	SUBCLONAL	1	TRUE	1	0.24127446313292	2		687	686	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93636995	93636995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	45	609	0	ENST00000375746.1:c.1045G>A	p.Glu349Lys	p.E349K	ENST00000375746	NM_001174167.1	349	Gag/Aag	9/14	1	2	FACETS	0.623	0.523	0.734	0.623	0.523	0.734	SUBCLONAL	1	TRUE	1	0.24127446313292	2		609	599	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409009	139409009	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	111	1163	0	ENST00000277541.6:c.2160C>A	p.Cys720Ter	p.C720*	ENST00000277541	NM_017617.3	720	tgC/tgA	13/34	1	2	FACETS	0.843	0.756	0.935	0.843	0.756	0.935	CLONAL	1	TRUE	1	0.24127446313292	2		1163	1092	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317541	1317541	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	57	798	0	ENST00000400841.2:c.524T>G	p.Leu175Trp	p.L175W	ENST00000400841		175	tTg/tGg	5/6	1	1	FACETS	0.517	0.443	0.599	0.517	0.443	0.599	SUBCLONAL	1	TRUE	0	0.24127446313292	1		798	803	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0021737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	244	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.369776074376604	3	FACETS	0.983	0.932	1	0.983	0.932	1	CLONAL	3	FALSE	0	0.432711088434515	3		288	465	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	34	151	0				ENST00000310581	NM_198253.2	-/1132			0.105666543874637	0	FACETS	0.474	0.391	0.565			1	INDETERMINATE	1	FALSE	0	0.432711088434515	0		151	188	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030485	49030485	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs483352690	NA	P-0021737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	62	498	0	ENST00000267163.4:c.1960G>A	p.Val654Met	p.V654M	ENST00000267163	NM_000321.2	654	Gtg/Atg	19/27	NA	2	FACETS	0.838	0.728	0.956			1	INDETERMINATE	1	FALSE	NA	0.432711088434515	2		498	342	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047494	49047494	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0021737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	74	581	0	ENST00000267163.4:c.2490-2A>G		p.X830_splice	ENST00000267163	NM_000321.2	830			NA	2	FACETS	0.927	0.817	1			1	INDETERMINATE	1	FALSE	NA	0.432711088434515	2		581	369	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050953	49050953	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	72	545	0	ENST00000267163.4:c.2637T>G	p.Ile879Met	p.I879M	ENST00000267163	NM_000321.2	879	atT/atG	25/27	NA	2	FACETS	0.935	0.822	1			1	INDETERMINATE	1	FALSE	NA	0.432711088434515	2		545	356	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40685704	40685704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1566924358	NA	P-0021737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	73	691	0	ENST00000249776.8:c.857G>A	p.Arg286Lys	p.R286K	ENST00000249776	NM_033286.3	286	aGa/aAa	9/9	0.296173582470193	1	FACETS	0.627	0.55	0.708	0.627	0.55	0.708	SUBCLONAL	1	FALSE	0	0.432711088434515	1		691	422	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	73	151	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.72	0.631	0.816	0.72	0.631	0.816	SUBCLONAL	1	TRUE	1	0.403728262091955	2		151	502	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	289	552	0	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.403728262091955	2		552	1047	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517879	187517879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	81	520	0	ENST00000441802.2:c.12815C>T	p.Ser4272Phe	p.S4272F	ENST00000441802	NM_005245.3	4272	tCc/tTc	25/27	1	2	FACETS	0.612	0.539	0.69	0.612	0.539	0.69	SUBCLONAL	1	TRUE	1	0.403728262091955	2		520	656	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246629	46246629	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	62	226	0	ENST00000334344.6:c.4723C>T	p.Gln1575Ter	p.Q1575*	ENST00000334344	NM_152641.2	1575	Cag/Tag	15/21	1	2	FACETS	0.776	0.673	0.887	0.776	0.673	0.887	SUBCLONAL	1	TRUE	1	0.403728262091955	2		226	396	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221981	1221981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	326	654	0	ENST00000326873.7:c.896C>T	p.Ser299Phe	p.S299F	ENST00000326873	NM_000455.4	299	tCc/tTc	7/10	0.218974998647676	2	FACETS	0.779	0.737	0.822	0.779	0.737	0.822	INDETERMINATE	2	TRUE	0	0.403728262091955	2		654	1036	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954916	2954916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368431453	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	178	559	2	ENST00000396946.4:c.2794C>T	p.Arg932Trp	p.R932W	ENST00000396946	NM_032415.4	932	Cgg/Tgg	21/25	1	2	FACETS	0.938	0.865	1	0.938	0.865	1	CLONAL	1	TRUE	1	0.403728262091955	2		561	940	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976769	2976769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1402987893	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	156	697	0	ENST00000396946.4:c.1243G>A	p.Asp415Asn	p.D415N	ENST00000396946	NM_032415.4	415	Gac/Aac	9/25	1	2	FACETS	0.731	0.669	0.797	0.731	0.669	0.797	SUBCLONAL	1	TRUE	1	0.403728262091955	2		697	1057	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858164	152858164	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	178	339	0	ENST00000406277.2:c.451C>T	p.Gln151Ter	p.Q151*	ENST00000406277	NM_152274.4	151	Cag/Tag	6/7	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.403728262091955	1		339	526	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11293456	11293456	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	164	584	1	ENST00000361445.4:c.2420A>G	p.Gln807Arg	p.Q807R	ENST00000361445	NM_004958.3	807	cAg/cGg	15/58	1	2	FACETS	0.932	0.856	1	0.932	0.856	1	CLONAL	1	TRUE	1	0.403728262091955	2		585	872	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36814402	36814402	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	186	590	0	ENST00000373129.3:c.638C>G	p.Thr213Ser	p.T213S	ENST00000373129	NM_032017.1	213	aCc/aGc	8/12	1	2	FACETS	0.901	0.831	0.973	0.901	0.831	0.973	CLONAL	1	TRUE	1	0.403728262091955	2		590	1023	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658603	206658603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	110	546	0	ENST00000367120.3:c.1576G>A	p.Glu526Lys	p.E526K	ENST00000367120	NM_014002.3	526	Gag/Aag	15/22	1	2	FACETS	0.651	0.584	0.722	0.651	0.584	0.722	SUBCLONAL	1	TRUE	1	0.403728262091955	2		546	837	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404737	70404737	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	125	544	0	ENST00000373644.4:c.2251T>A	p.Leu751Met	p.L751M	ENST00000373644	NM_030625.2	751	Ttg/Atg	4/12	1	2	FACETS	0.771	0.698	0.848	0.771	0.698	0.848	SUBCLONAL	1	TRUE	1	0.403728262091955	2		544	803	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149260	119149260	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	179	589	0	ENST00000264033.4:c.1268T>C	p.Ile423Thr	p.I423T	ENST00000264033	NM_005188.3	423	aTt/aCt	9/16	0.378584812733966	1	FACETS	0.919	0.849	0.992	0.919	0.849	0.992	CLONAL	1	TRUE	0	0.403728262091955	1		589	770	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435583	18435583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746276290	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	97	321	0	ENST00000266497.5:c.568G>A	p.Glu190Lys	p.E190K	ENST00000266497		190	Gaa/Aaa	1/31	1	2	FACETS	0.95	0.85	1	0.95	0.85	1	CLONAL	1	TRUE	1	0.403728262091955	2		321	506	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624511	21624512	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	158	594	1	ENST00000421138.2:c.1517_1518delinsCT	p.Leu506Pro	p.L506P	ENST00000421138		506	cTG/cCT	14/16	1	2	FACETS	0.707	0.647	0.77	0.707	0.647	0.77	SUBCLONAL	1	TRUE	1	0.403728262091955	2		595	1107	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211635	46211639	+	frameshift_variant	Frame_Shift_Del	DEL	ACTTT	ACTTT	-	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	81	365	0	ENST00000334344.6:c.604_608del	p.Leu202ThrfsTer3	p.L202Tfs*3	ENST00000334344	NM_152641.2	201	ACTTTa/a	5/21	1	2	FACETS	0.727	0.642	0.818	0.727	0.642	0.818	SUBCLONAL	1	TRUE	1	0.403728262091955	2		365	552	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425823	49425824	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs754290613	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	95	483	0	ENST00000301067.7:c.12662_12664dup	p.Gln4221dup	p.Q4221dup	ENST00000301067	NM_003482.3	4221	cta/cAGCta	39/54	1	2	FACETS	0.582	0.517	0.65	0.582	0.517	0.65	SUBCLONAL	1	TRUE	1	0.403728262091955	2		483	809	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528243	103528243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199925057	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	90	285	0	ENST00000355739.4:c.3551G>A	p.Arg1184Lys	p.R1184K	ENST00000355739	NM_000123.3	1184	aGg/aAg	15/15	1	2	FACETS	0.849	0.756	0.948	0.849	0.756	0.948	CLONAL	1	TRUE	1	0.403728262091955	2		285	525	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222318	2222318	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	183	580	0	ENST00000326181.6:c.602C>A	p.Pro201His	p.P201H	ENST00000326181	NM_032271.2	201	cCc/cAc	8/21	1	2	FACETS	0.961	0.887	1	0.961	0.887	1	CLONAL	1	TRUE	1	0.403728262091955	2		580	943	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639612	3639612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	168	751	1	ENST00000294008.3:c.4027C>T	p.Pro1343Ser	p.P1343S	ENST00000294008	NM_032444.2	1343	Cct/Tct	12/15	1	2	FACETS	0.773	0.709	0.839	0.773	0.709	0.839	SUBCLONAL	1	TRUE	1	0.403728262091955	2		752	1077	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639874	3639874	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	175	548	0	ENST00000294008.3:c.3765G>A	p.Trp1255Ter	p.W1255*	ENST00000294008	NM_032444.2	1255	tgG/tgA	12/15	1	2	FACETS	0.935	0.861	1	0.935	0.861	1	CLONAL	1	TRUE	1	0.403728262091955	2		548	927	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647657	3647657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	195	775	0	ENST00000294008.3:c.1406C>T	p.Pro469Leu	p.P469L	ENST00000294008	NM_032444.2	469	cCa/cTa	7/15	1	2	FACETS	0.824	0.762	0.889	0.824	0.762	0.889	CLONAL	1	TRUE	1	0.403728262091955	2		775	1172	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857146	9857146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	88	388	1	ENST00000330684.3:c.4255C>T	p.His1419Tyr	p.H1419Y	ENST00000330684	NM_001134407.1	1419	Cac/Tac	13/13	1	2	FACETS	0.748	0.664	0.837	0.748	0.664	0.837	SUBCLONAL	1	TRUE	1	0.403728262091955	2		389	583	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984937	9984937	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1231057100	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	113	524	0	ENST00000330684.3:c.1028G>A	p.Trp343Ter	p.W343*	ENST00000330684	NM_001134407.1	343	tGg/tAg	4/13	1	2	FACETS	0.634	0.57	0.702	0.634	0.57	0.702	SUBCLONAL	1	TRUE	1	0.403728262091955	2		524	883	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655398	67655398	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	164	635	0	ENST00000264010.4:c.1261A>G	p.Thr421Ala	p.T421A	ENST00000264010	NM_006565.3	421	Acc/Gcc	7/12	1	2	FACETS	0.8	0.734	0.87	0.8	0.734	0.87	SUBCLONAL	1	TRUE	1	0.403728262091955	2		635	1015	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346770	89346771	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	73	373	3	ENST00000301030.4:c.6179_6180delinsTT	p.Ser2060Phe	p.S2060F	ENST00000301030	NM_001256183.1	2060	tCC/tTT	9/13	1	2	FACETS	0.652	0.57	0.739	0.652	0.57	0.739	SUBCLONAL	1	TRUE	1	0.403728262091955	2		376	555	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428351	33428351	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	177	583	0	ENST00000345365.6:c.772G>T	p.Gly258Trp	p.G258W	ENST00000345365	NM_002878.3	258	Ggg/Tgg	9/10	0.349719658443416	3	FACETS	0.92	0.846	0.997	0.46	0.423	0.499	CLONAL	1	TRUE	1	0.403728262091955	3		583	1146	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33446625	33446625	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	162	497	0	ENST00000345365.6:c.8T>G	p.Val3Gly	p.V3G	ENST00000345365	NM_002878.3	3	gTg/gGg	1/10	0.349719658443416	3	FACETS	0.914	0.838	0.994	0.457	0.419	0.497	CLONAL	1	TRUE	1	0.403728262091955	3		497	1055	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370313	40370313	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	373	721	0	ENST00000293328.3:c.1025T>G	p.Leu342Arg	p.L342R	ENST00000293328	NM_012448.3	342	cTg/cGg	9/19	0.349719658443416	3	FACETS	0.808	0.766	0.851	0.808	0.766	0.851	CLONAL	2	TRUE	1	0.403728262091955	3		721	1374	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211776	2211776	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	305	759	2	ENST00000398665.3:c.1492T>C	p.Phe498Leu	p.F498L	ENST00000398665	NM_032482.2	498	Ttc/Ctc	16/28	0.218974998647676	2	FACETS	1	0.994	1	0.736	0.694	0.778	INDETERMINATE	1	TRUE	0	0.403728262091955	2		761	1027	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7168101	7168101	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	97	415	0	ENST00000302850.5:c.1488A>T	p.Glu496Asp	p.E496D	ENST00000302850	NM_000208.2	496	gaA/gaT	7/22	1	2	FACETS	0.712	0.635	0.794	0.712	0.635	0.794	SUBCLONAL	1	TRUE	1	0.403728262091955	2		415	675	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265051	10265051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	194	562	1	ENST00000340748.4:c.1889C>T	p.Thr630Ile	p.T630I	ENST00000340748		630	aCt/aTt	21/40	1	2	FACETS	0.921	0.851	0.993	0.921	0.851	0.993	CLONAL	1	TRUE	1	0.403728262091955	2		563	1044	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17389727	17389727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754624710	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	183	701	0	ENST00000359435.4:c.860C>T	p.Pro287Leu	p.P287L	ENST00000359435	NM_001033549.1	287	cCa/cTa	9/9	1	2	FACETS	0.756	0.696	0.818	0.756	0.696	0.818	SUBCLONAL	1	TRUE	1	0.403728262091955	2		701	1199	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224710	36224710	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	194	713	0	ENST00000222270.7:c.7097del	p.Pro2366LeufsTer73	p.P2366Lfs*73	ENST00000222270	NM_014727.1	2366	Cct/ct	30/37	1	2	FACETS	0.793	0.732	0.856	0.793	0.732	0.856	SUBCLONAL	1	TRUE	1	0.403728262091955	2		713	1212	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445433	29445433	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	332	606	2	ENST00000389048.3:c.3400C>T	p.Gln1134Ter	p.Q1134*	ENST00000389048	NM_004304.4	1134	Cag/Tag	21/29	0.350565263015804	2	FACETS	0.964	0.915	1	0.964	0.915	1	CLONAL	2	TRUE	0	0.403728262091955	2		608	853	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033489	48033490	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	219	567	2	ENST00000234420.5:c.3793_3794delinsAA	p.Gly1265Lys	p.G1265K	ENST00000234420	NM_000179.2	1265	GGa/AAa	8/10	0.350565263015804	2	FACETS	1	0.991	1	0.726	0.678	0.776	CLONAL	1	TRUE	0	0.403728262091955	2		569	747	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024024	31024024	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	163	545	0	ENST00000375687.4:c.3509T>C	p.Leu1170Ser	p.L1170S	ENST00000375687	NM_015338.5	1170	tTa/tCa	13/13	1	2	FACETS	0.848	0.778	0.921	0.848	0.778	0.921	CLONAL	1	TRUE	1	0.403728262091955	2		545	952	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183667	10183667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	177	572	2	ENST00000256474.2:c.136G>A	p.Glu46Lys	p.E46K	ENST00000256474	NM_000551.3	46	Gag/Aag	1/3	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.403728262091955	2		574	829	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713138	30713138	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	70	304	0	ENST00000295754.5:c.463A>G	p.Thr155Ala	p.T155A	ENST00000295754	NM_003242.5	155	Acc/Gcc	4/7	1	2	FACETS	0.59	0.514	0.671	0.59	0.514	0.671	SUBCLONAL	1	TRUE	1	0.403728262091955	2		304	588	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185169101	185169101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	157	531	0	ENST00000265026.3:c.1196C>T	p.Ser399Phe	p.S399F	ENST00000265026	NM_004721.4	399	tCt/tTt	7/14	1	2	FACETS	0.943	0.864	1	0.943	0.864	1	CLONAL	1	TRUE	1	0.403728262091955	2		531	825	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191506	185191506	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	189	649	0	ENST00000265026.3:c.2387G>A	p.Gly796Asp	p.G796D	ENST00000265026	NM_004721.4	796	gGc/gAc	11/14	1	2	FACETS	0.99	0.915	1	0.99	0.915	1	CLONAL	1	TRUE	1	0.403728262091955	2		649	946	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526106	189526106	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	146	548	0	ENST00000264731.3:c.370A>T	p.Ile124Phe	p.I124F	ENST00000264731	NM_003722.4	124	Att/Ttt	4/14	1	2	FACETS	0.79	0.72	0.862	0.79	0.72	0.862	SUBCLONAL	1	TRUE	1	0.403728262091955	2		548	916	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803678	1803678	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	184	716	1	ENST00000260795.2:c.856C>T	p.Gln286Ter	p.Q286*	ENST00000260795		286	Cag/Tag	6/17	1	2	FACETS	0.886	0.817	0.957	0.886	0.817	0.957	CLONAL	1	TRUE	1	0.403728262091955	2		717	1029	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902481	1902481	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	136	551	0	ENST00000382891.5:c.100A>T	p.Lys34Ter	p.K34*	ENST00000382891	NM_133335.3	34	Aag/Tag	2/22	1	2	FACETS	0.75	0.682	0.822	0.75	0.682	0.822	SUBCLONAL	1	TRUE	1	0.403728262091955	2		551	898	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748279	41748279	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	136	596	0	ENST00000226382.2:c.490G>T	p.Ala164Ser	p.A164S	ENST00000226382	NM_003924.3	164	Gcg/Tcg	3/3	1	2	FACETS	0.771	0.701	0.845	0.771	0.701	0.845	SUBCLONAL	1	TRUE	1	0.403728262091955	2		596	874	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968619	55968619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775179342	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	154	592	0	ENST00000263923.4:c.2044G>A	p.Glu682Lys	p.E682K	ENST00000263923	NM_002253.2	682	Gaa/Aaa	14/30	1	2	FACETS	0.827	0.756	0.9	0.827	0.756	0.9	CLONAL	1	TRUE	1	0.403728262091955	2		592	923	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156535	106156535	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	103	393	0	ENST00000380013.4:c.1436G>A	p.Arg479Lys	p.R479K	ENST00000380013	NM_001127208.2	479	aGg/aAg	3/11	1	2	FACETS	0.787	0.706	0.874	0.787	0.706	0.874	SUBCLONAL	1	TRUE	1	0.403728262091955	2		393	648	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517878	187517879	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	81	517	3	ENST00000441802.2:c.12815_12816delinsTT	p.Ser4272Phe	p.S4272F	ENST00000441802	NM_005245.3	4272	tCC/tTT	25/27	1	2	FACETS	0.612	0.539	0.69	0.612	0.539	0.69	SUBCLONAL	1	TRUE	1	0.403728262091955	2		520	656	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754325	57754325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	148	465	0	ENST00000274289.3:c.526G>A	p.Val176Met	p.V176M	ENST00000274289	NM_006622.3	176	Gtg/Atg	4/14	1	2	FACETS	0.876	0.8	0.955	0.876	0.8	0.955	CLONAL	1	TRUE	1	0.403728262091955	2		465	837	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678001	117678001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs62430836	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	128	468	0	ENST00000368508.3:c.3932G>A	p.Arg1311Gln	p.R1311Q	ENST00000368508	NM_002944.2	1311	cGa/cAa	25/43	NA	2	FACETS	0.767	0.695	0.842			1	INDETERMINATE	1	TRUE	NA	0.403728262091955	2		468	827	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683766	162683766	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	112	444	0	ENST00000366898.1:c.203A>G	p.His68Arg	p.H68R	ENST00000366898	NM_004562.2	68	cAc/cGc	3/12	1	2	FACETS	0.81	0.729	0.895	0.81	0.729	0.895	CLONAL	1	TRUE	1	0.403728262091955	2		444	685	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468170	50468170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750786723	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	173	448	0	ENST00000331340.3:c.1405G>A	p.Val469Met	p.V469M	ENST00000331340	NM_006060.4	469	Gtg/Atg	8/8	1	2	FACETS	0.928	0.854	1	0.928	0.854	1	CLONAL	1	TRUE	1	0.403728262091955	2		448	924	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371770	55371770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763824540	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	80	238	0	ENST00000297316.4:c.460G>A	p.Gly154Ser	p.G154S	ENST00000297316	NM_022454.3	154	Ggc/Agc	2/2	1	2	FACETS	0.913	0.807	1	0.913	0.807	1	CLONAL	1	TRUE	1	0.403728262091955	2		238	434	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981302	68981302	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	108	405	0	ENST00000288368.4:c.1374G>C	p.Met458Ile	p.M458I	ENST00000288368	NM_024870.2	458	atG/atC	12/40	1	2	FACETS	0.907	0.816	1	0.907	0.816	1	CLONAL	1	TRUE	1	0.403728262091955	2		405	590	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009279	69009279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	137	479	0	ENST00000288368.4:c.2396C>T	p.Ala799Val	p.A799V	ENST00000288368	NM_024870.2	799	gCc/gTc	22/40	1	2	FACETS	0.936	0.853	1	0.936	0.853	1	CLONAL	1	TRUE	1	0.403728262091955	2		479	725	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981782	70981782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141129543	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	188	699	0	ENST00000276594.2:c.314C>T	p.Pro105Leu	p.P105L	ENST00000276594	NM_024504.3	105	cCc/cTc	2/8	1	2	FACETS	0.907	0.837	0.979	0.907	0.837	0.979	CLONAL	1	TRUE	1	0.403728262091955	2		699	1027	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27173262	27173262	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	165	684	0	ENST00000380036.4:c.803G>C	p.Cys268Ser	p.C268S	ENST00000380036	NM_000459.3	268	tGc/tCc	6/23	0.403728262091955	1	FACETS	0.786	0.722	0.852	0.786	0.722	0.852	SUBCLONAL	1	TRUE	0	0.403728262091955	1		684	830	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938418	44938418	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	128	276	0	ENST00000377967.4:c.2966T>G	p.Leu989Trp	p.L989W	ENST00000377967	NM_021140.2	989	tTg/tGg	20/29	1	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.403728262091955	1		276	477	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223539	53223539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	122	189	1	ENST00000375401.3:c.3820G>A	p.Glu1274Lys	p.E1274K	ENST00000375401	NM_004187.3	1274	Gag/Aag	23/26	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.403728262091955	1		190	328	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21624512	21624512	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	158	582	0	ENST00000421138.2:c.1517T>C	p.Leu506Pro	p.L506P	ENST00000421138		506	cTg/cCg	14/16	1	2	FACETS	0.711	0.65	0.775	0.711	0.65	0.775	SUBCLONAL	1	TRUE	1	0.403728262091955	2		582	1101	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	494	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.78	2		306	974	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716366	18716366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs935135637	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	128	757	0	ENST00000266497.5:c.3713C>T	p.Ser1238Leu	p.S1238L	ENST00000266497		1238	tCa/tTa	26/31	0.272227284141825	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.78	0		757	339	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	105	430	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.78	2		430	242	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120405	94120405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	127	437	0	ENST00000369303.4:c.646C>T	p.Pro216Ser	p.P216S	ENST00000369303	NM_004440.3	216	Cca/Tca	3/17	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.78	2		437	322	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450300	50450300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	387	845	1	ENST00000331340.3:c.484C>T	p.Arg162Trp	p.R162W	ENST00000331340	NM_006060.4	162	Cgg/Tgg	5/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.78	2		846	968	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244913	123244913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1224606327	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	480	931	0	ENST00000358487.5:c.2191G>A	p.Glu731Lys	p.E731K	ENST00000358487	NM_000141.4	731	Gaa/Aaa	16/18	1	2	FACETS	0.995	0.953	1	0.995	0.953	1	CLONAL	1	TRUE	1	0.78	2		931	1237	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560859	9560859	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	318	737	0	ENST00000353224.5:c.923C>T	p.Pro308Leu	p.P308L	ENST00000353224	NM_177990.2	308	cCc/cTc	4/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.78	2		737	767	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970901	21970901	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	618	1101	0	ENST00000304494.5:c.457G>C	p.Asp153His	p.D153H	ENST00000304494	NM_000077.4	153	Gac/Cac	2/3	1	2	FACETS	1	0.991	1	1	0.998	1	CLONAL	2	TRUE	1	0.78	2		1101	771	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564491	41564491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555911073	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	219	555	0	ENST00000263253.7:c.3913C>T	p.Arg1305Cys	p.R1305C	ENST00000263253	NM_001429.3	1305	Cgt/Tgt	24/31	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.78	2		555	557	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106612	27106612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	477	828	0	ENST00000324856.7:c.6223C>T	p.Pro2075Ser	p.P2075S	ENST00000324856	NM_006015.4	2075	Cca/Tca	20/20	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.78	2		828	1023	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46738376	46738376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	324	738	0	ENST00000371975.4:c.1277G>A	p.Arg426Lys	p.R426K	ENST00000371975	NM_003579.3	426	aGg/aAg	12/18	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.78	2		738	759	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375593	118375593	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	183	453	1	ENST00000534358.1:c.8986C>T	p.His2996Tyr	p.H2996Y	ENST00000534358	NM_005933.3	2996	Cat/Tat	27/36	0.27591146391693	3	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.78	3		454	441	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231185	46231186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TAAA	novel	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	56	529	0	ENST00000334344.6:c.1106_1107insAAAT	p.Phe369LeufsTer20	p.F369Lfs*20	ENST00000334344	NM_152641.2	369	ttt/tTAAAtt	9/21	NA	2	FACETS	0.662	0.574	0.754			1	INDETERMINATE	1	TRUE	NA	0.78	2		529	217	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678341	88678341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	294	843	2	ENST00000360948.2:c.1195C>T	p.Pro399Ser	p.P399S	ENST00000360948	NM_001012338.2	399	Ccc/Tcc	9/19	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.78	2		845	752	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225923	2225923	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1421625187	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	449	986	0	ENST00000326181.6:c.1715T>C	p.Ile572Thr	p.I572T	ENST00000326181	NM_032271.2	572	aTt/aCt	18/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.78	2		986	1091	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828989	72828989	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	409	938	0	ENST00000268489.5:c.7592A>G	p.Gln2531Arg	p.Q2531R	ENST00000268489	NM_006885.3	2531	cAg/cGg	9/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.78	2		938	983	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805378	46805378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	511	1042	1	ENST00000290295.7:c.578C>T	p.Pro193Leu	p.P193L	ENST00000290295	NM_006361.5	193	cCc/cTc	1/2	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.78	2		1043	1216	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285171	15285171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202085803	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	624	1112	2	ENST00000263388.2:c.4444G>A	p.Gly1482Ser	p.G1482S	ENST00000263388	NM_000435.2	1482	Ggc/Agc	25/33	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.78	2		1114	1414	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350292	15350292	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	366	869	0	ENST00000263377.2:c.3487C>G	p.Arg1163Gly	p.R1163G	ENST00000263377	NM_058243.2	1163	Cgg/Ggg	17/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.78	2		869	935	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353921	15353921	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs867317090	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	336	585	2	ENST00000263377.2:c.2959C>T	p.Gln987Ter	p.Q987*	ENST00000263377	NM_058243.2	987	Cag/Tag	14/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.78	2		587	801	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945747	17945747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	500	926	0	ENST00000458235.1:c.2113G>A	p.Glu705Lys	p.E705K	ENST00000458235	NM_000215.3	705	Gaa/Aaa	16/24	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.78	2		926	1145	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52725407	52725407	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	424	872	0	ENST00000322088.6:c.1574T>C	p.Val525Ala	p.V525A	ENST00000322088	NM_014225.5	525	gTt/gCt	13/15	1	2	FACETS	0.972	0.928	1	0.972	0.928	1	CLONAL	1	TRUE	1	0.78	2		872	1119	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286734	212286734	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	70	504	0	ENST00000342788.4:c.2962C>T	p.Gln988Ter	p.Q988*	ENST00000342788	NM_005235.2	988	Cag/Tag	24/28	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.78	2		504	163	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560860	9560860	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771654927	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	314	740	0	ENST00000353224.5:c.922C>T	p.Pro308Ser	p.P308S	ENST00000353224	NM_177990.2	308	Ccc/Tcc	4/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.78	2		740	772	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134885818	134885818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145366861	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	327	679	2	ENST00000398015.3:c.1729G>A	p.Asp577Asn	p.D577N	ENST00000398015	NM_004441.4	577	Gat/Aat	9/16	1	2	FACETS	0.975	0.925	1	0.975	0.925	1	CLONAL	1	TRUE	1	0.78	2		681	860	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946319	55946319	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	179	385	0	ENST00000263923.4:c.3860C>T	p.Pro1287Leu	p.P1287L	ENST00000263923	NM_002253.2	1287	cCc/cTc	30/30	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.78	2		385	383	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149452948	149452948	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	408	825	0	ENST00000286301.3:c.998G>C	p.Gly333Ala	p.G333A	ENST00000286301	NM_005211.3	333	gGt/gCt	7/22	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.78	2		825	955	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969129	93969129	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	128	621	0	ENST00000369303.4:c.1867C>T	p.Gln623Ter	p.Q623*	ENST00000369303	NM_004440.3	623	Caa/Taa	10/17	1	2	FACETS	0.919	0.843	0.997	0.919	0.843	0.997	CLONAL	1	TRUE	1	0.78	2		621	357	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459426	50459426	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	79	352	1	ENST00000331340.3:c.716-1G>T		p.X239_splice	ENST00000331340	NM_006060.4	239			1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.78	2		353	198	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355325	81355325	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750575553	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	122	439	0	ENST00000222390.5:c.1049G>A	p.Arg350Gln	p.R350Q	ENST00000222390	NM_000601.4	350	cGa/cAa	9/18	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.78	2		439	300	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477800	140477800	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	91	794	1	ENST00000288602.6:c.1508G>A	p.Gly503Glu	p.G503E	ENST00000288602	NM_004333.4	503	gGa/gAa	12/18	1	2	FACETS	0.904	0.816	0.996	0.904	0.816	0.996	CLONAL	1	TRUE	1	0.78	2		795	258	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044431	5044431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	127	786	1	ENST00000381652.3:c.379G>A	p.Gly127Ser	p.G127S	ENST00000381652	NM_004972.3	127	Ggc/Agc	5/25	1	2	FACETS	0.978	0.898	1	0.978	0.898	1	CLONAL	1	TRUE	1	0.78	2		787	333	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404535	8404535	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	76	339	0	ENST00000356435.5:c.4210+2T>G		p.X1404_splice	ENST00000356435		1404			1	2	FACETS	0.937	0.837	1	0.937	0.837	1	CLONAL	1	TRUE	1	0.78	2		339	208	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504363	8504363	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	246	788	0	ENST00000356435.5:c.1720G>A	p.Gly574Arg	p.G574R	ENST00000356435		574	Gga/Aga	12/35	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.78	2		788	601	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169504	27169504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866968099	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	377	843	0	ENST00000380036.4:c.505G>A	p.Glu169Lys	p.E169K	ENST00000380036	NM_000459.3	169	Gaa/Aaa	4/23	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.78	2		843	849	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760006	133760006	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021783-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	448	1077	2	ENST00000318560.5:c.2329C>T	p.Arg777Ter	p.R777*	ENST00000318560	NM_005157.4	777	Cga/Tga	11/11	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.78	2		1079	1085	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0021844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	376	578	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.625642536334831	2		578	1163	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176469	123176469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	243	224	0	ENST00000218089.9:c.436C>T	p.Arg146Ter	p.R146*	ENST00000218089	NM_001042749.1	146	Cga/Tga	7/35	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.625642536334831	1		224	401	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159746	20159746	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0021844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	308	293	0	ENST00000379607.5:c.13A>G	p.Lys5Glu	p.K5E	ENST00000379607	NM_001412.3	5	Aaa/Gaa	1/7	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.625642536334831	1		293	461	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165788	108165788	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0021844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	226	453	0	ENST00000278616.4:c.4909+2T>C		p.X1637_splice	ENST00000278616	NM_000051.3	1637			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.625642536334831	2		453	702	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438512	52438537	+	stop_gained	Nonsense_Mutation	DEL	CCTCATAGTCATCCTCATCATCTGAG	CCTCATAGTCATCCTCATCATCTGAG	AC	novel	NA	P-0021844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	272	726	3	ENST00000460680.1:c.1182_1207delinsGT	p.Tyr394_Asp403delinsTer	p.Y394_D403delins*	ENST00000460680	NM_004656.3	394	taCTCAGATGATGAGGATGACTATGAGGat/taGTat	12/17	0.625642536334831	1	FACETS	0.779	0.734	0.825	0.779	0.734	0.825	SUBCLONAL	1	TRUE	0	0.625642536334831	1		729	767	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	121	151	0				ENST00000310581	NM_198253.2	-/1132			0.240308483883889	5	FACETS	1	0.977	1	0.803	0.735	0.874	INDETERMINATE	2	FALSE	2	0.524820949801523	5		151	342	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	196	516	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	0.240308483883889	5	FACETS	1	0.985	1	0.799	0.745	0.854	INDETERMINATE	2	FALSE	2	0.524820949801523	5		516	557	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204920	128204920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253079679	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	168	1027	1	ENST00000341105.2:c.521C>T	p.Pro174Leu	p.P174L	ENST00000341105	NM_032638.4	174	cCa/cTa	3/6	0.240308483883889	5	FACETS	1	0.983	1	0.422	0.388	0.458	INDETERMINATE	1	FALSE	2	0.524820949801523	5		1028	903	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556852	29556852	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	191	505	0	ENST00000356175.3:c.2851-1G>A		p.X951_splice	ENST00000356175	NM_000267.3	951			0.240308483883889	5	FACETS	1	0.971	1	0.72	0.67	0.772	INDETERMINATE	2	FALSE	2	0.524820949801523	5		505	602	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858517	9858517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765370528	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	76	561	1	ENST00000330684.3:c.2884G>A	p.Glu962Lys	p.E962K	ENST00000330684	NM_001134407.1	962	Gaa/Aaa	13/13	0.508822458856235	3	FACETS	0.495	0.433	0.561	0.247	0.216	0.281	SUBCLONAL	1	FALSE	1	0.524820949801523	3		562	739	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562804	176562804	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771968592	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	78	748	0	ENST00000439151.2:c.700G>A	p.Glu234Lys	p.E234K	ENST00000439151	NM_022455.4	234	Gaa/Aaa	2/23	0.509612479232118	3	FACETS	0.484	0.425	0.548	0.242	0.212	0.274	SUBCLONAL	1	FALSE	1	0.524820949801523	3		748	775	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267710	198267710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	95	675	0	ENST00000335508.6:c.1769G>A	p.Arg590Lys	p.R590K	ENST00000335508	NM_012433.2	590	aGa/aAa	13/25	0.524820949801523	3	FACETS	0.522	0.464	0.584	0.261	0.232	0.292	SUBCLONAL	1	FALSE	1	0.524820949801523	3		675	876	SUCCESS
AR	367	MSKCC	GRCh37	X	66941766	66941766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	71	460	0	ENST00000374690.3:c.2410G>A	p.Glu804Lys	p.E804K	ENST00000374690	NM_000044.3	804	Gaa/Aaa	6/8	0.408718993140116	2	FACETS	0.601	0.526	0.682			1	SUBCLONAL	1	FALSE	NA	0.524820949801523	2		460	450	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341925	8341925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	62	665	0	ENST00000356435.5:c.4715G>A	p.Arg1572Lys	p.R1572K	ENST00000356435		1572	aGa/aAa	29/35	0.11880104903415	4	FACETS	0.65	0.562	0.746	0.325	0.281	0.373	INDETERMINATE	1	FALSE	2	0.524820949801523	4		665	554	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560970	9560970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781706438	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	45	647	1	ENST00000353224.5:c.812C>T	p.Ser271Leu	p.S271L	ENST00000353224	NM_177990.2	271	tCg/tTg	4/10	0.524820949801523	3	FACETS	0.295	0.247	0.348	0.147	0.123	0.174	SUBCLONAL	1	FALSE	1	0.524820949801523	3		648	735	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420082	41420082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	104	452	0	ENST00000373198.4:c.239C>T	p.Ser80Phe	p.S80F	ENST00000373198	NM_133170.3	80	tCt/tTt	3/32	0.524820949801523	3	FACETS	1	0.961	1	0.567	0.511	0.626	CLONAL	1	FALSE	1	0.524820949801523	3		452	441	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926872	112926872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397507541	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	65	846	1	ENST00000351677.2:c.1492C>T	p.Arg498Trp	p.R498W	ENST00000351677	NM_002834.3	498	Cgg/Tgg	13/16	0.508822458856235	3	FACETS	0.437	0.378	0.501	0.219	0.189	0.251	SUBCLONAL	1	FALSE	1	0.524820949801523	3		847	715	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376715	31376715	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs964977606	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	51	699	1	ENST00000328111.2:c.710C>T	p.Ser237Phe	p.S237F	ENST00000328111	NM_006892.3	237	tCc/tTc	7/23	0.524820949801523	3	FACETS	0.351	0.297	0.41	0.176	0.148	0.205	SUBCLONAL	1	FALSE	1	0.524820949801523	3		700	699	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923328	9923328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	122	801	1	ENST00000330684.3:c.1959G>A	p.Met653Ile	p.M653I	ENST00000330684	NM_001134407.1	653	atG/atA	9/13	0.508822458856235	3	FACETS	0.9	0.815	0.989	0.45	0.407	0.495	CLONAL	1	FALSE	1	0.524820949801523	3		802	652	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858394	9858394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	103	598	0	ENST00000330684.3:c.3007G>A	p.Glu1003Lys	p.E1003K	ENST00000330684	NM_001134407.1	1003	Gaa/Aaa	13/13	0.508822458856235	3	FACETS	0.903	0.81	1	0.451	0.405	0.5	CLONAL	1	FALSE	1	0.524820949801523	3		598	549	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631183	69631183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	124	741	0	ENST00000334134.2:c.229G>A	p.Glu77Lys	p.E77K	ENST00000334134	NM_005247.2	77	Gag/Aag	2/3	0.481250396654637	4	FACETS	1	0.961	1	0.555	0.503	0.61	CLONAL	1	FALSE	2	0.524820949801523	4		741	649	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658393	206658393	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	52	727	0	ENST00000367120.3:c.1487G>A	p.Arg496Lys	p.R496K	ENST00000367120	NM_014002.3	496	aGg/aAg	14/22	0.524820949801523	5	FACETS	0.383	0.325	0.448	0.128	0.108	0.15	SUBCLONAL	1	FALSE	2	0.524820949801523	5		727	924	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244973	123244973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	142	864	0	ENST00000358487.5:c.2131G>A	p.Glu711Lys	p.E711K	ENST00000358487	NM_000141.4	711	Gaa/Aaa	16/18	0.197558230194376	3	FACETS	0.953	0.87	1	0.318	0.29	0.347	INDETERMINATE	1	FALSE	0	0.524820949801523	3		864	717	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435313	18435313	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	211	593	0	ENST00000266497.5:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000266497		100	Caa/Taa	1/31	0.508822458856235	3	FACETS	0.838	0.783	0.893	0.838	0.783	0.893	CLONAL	2	FALSE	1	0.524820949801523	3		593	606	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691122	18691122	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	37	613	0	ENST00000266497.5:c.3233T>G	p.Met1078Arg	p.M1078R	ENST00000266497		1078	aTg/aGg	23/31	0.508822458856235	3	FACETS	0.286	0.235	0.343	0.143	0.117	0.172	SUBCLONAL	1	FALSE	1	0.524820949801523	3		613	623	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476319	88476319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	69	1005	2	ENST00000360948.2:c.1813G>A	p.Gly605Arg	p.G605R	ENST00000360948	NM_001012338.2	605	Gga/Aga	15/19	0.509612479232118	3	FACETS	0.392	0.341	0.448	0.196	0.17	0.224	SUBCLONAL	1	FALSE	1	0.524820949801523	3		1007	846	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556190	29556190	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	59	167	0	ENST00000356175.3:c.2557C>T	p.Gln853Ter	p.Q853*	ENST00000356175	NM_000267.3	853	Cag/Tag	21/57	0.240308483883889	5	FACETS	1	0.917	1	0.709	0.62	0.801	INDETERMINATE	2	FALSE	2	0.524820949801523	5		167	189	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533887	63533887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376630432	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	49	644	0	ENST00000307078.5:c.1267C>T	p.Leu423Phe	p.L423F	ENST00000307078	NM_004655.3	423	Ctc/Ttc	6/11	0.240308483883889	5	FACETS	0.533	0.451	0.624	0.178	0.15	0.208	INDETERMINATE	1	FALSE	2	0.524820949801523	5		644	626	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743053	743053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	1051	862	0	ENST00000314574.4:c.925C>T	p.Pro309Ser	p.P309S	ENST00000314574	NM_005433.3	309	Cca/Tca	8/12	0.524820949801523	5	FACETS	0.967	0.947	0.986	0.967	0.947	0.986	CLONAL	5	FALSE	0	0.524820949801523	5		862	1481	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756559	756559	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	550	510	0	ENST00000314574.4:c.269C>T	p.Thr90Ile	p.T90I	ENST00000314574	NM_005433.3	90	aCa/aTa	2/12	0.524820949801523	5	FACETS	0.951	0.924	0.977	0.951	0.924	0.977	CLONAL	5	FALSE	0	0.524820949801523	5		510	788	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223009	5223009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	236	679	0	ENST00000357368.4:c.2794C>T	p.Pro932Ser	p.P932S	ENST00000357368	NM_002850.3	932	Ccg/Tcg	18/38	0.298676860009976	4	FACETS	1	0.962	1	1	0.962	1	INDETERMINATE	2	FALSE	2	0.524820949801523	4		679	663	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138513	11138513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	51	1000	0	ENST00000358026.2:c.3269C>T	p.Pro1090Leu	p.P1090L	ENST00000358026	NM_001128849.1	1090	cCc/cTc	24/36	0.298676860009976	4	FACETS	0.331	0.28	0.387	0.165	0.14	0.194	INDETERMINATE	1	FALSE	2	0.524820949801523	4		1000	896	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257451	19257451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	153	934	0	ENST00000162023.5:c.682C>T	p.Leu228Phe	p.L228F	ENST00000162023		228	Ctc/Ttc	11/13	0.298676860009976	4	FACETS	0.951	0.87	1	0.475	0.435	0.518	INDETERMINATE	1	FALSE	2	0.524820949801523	4		934	935	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213971	36213971	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	59	1015	2	ENST00000222270.7:c.2797G>T	p.Gly933Trp	p.G933W	ENST00000222270	NM_014727.1	933	Ggg/Tgg	6/37	0.298676860009976	4	FACETS	0.339	0.29	0.392	0.169	0.145	0.196	INDETERMINATE	1	FALSE	2	0.524820949801523	4		1017	1012	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743906	41743906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	58	953	1	ENST00000301178.4:c.841G>A	p.Glu281Lys	p.E281K	ENST00000301178	NM_021913.4	281	Gag/Aag	7/20	0.298676860009976	4	FACETS	0.37	0.317	0.429	0.185	0.158	0.215	INDETERMINATE	1	FALSE	2	0.524820949801523	4		954	910	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793162	42793162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	56	975	0	ENST00000575354.2:c.1054C>T	p.Pro352Ser	p.P352S	ENST00000575354	NM_015125.3	352	Ccc/Tcc	7/20	0.298676860009976	4	FACETS	0.361	0.308	0.419	0.18	0.154	0.21	INDETERMINATE	1	FALSE	2	0.524820949801523	4		975	902	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989494	212989494	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	52	533	0	ENST00000342788.4:c.217G>A	p.Asp73Asn	p.D73N	ENST00000342788	NM_005235.2	73	Gac/Aac	2/28	0.524820949801523	3	FACETS	0.434	0.369	0.505	0.217	0.184	0.253	SUBCLONAL	1	FALSE	1	0.524820949801523	3		533	577	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561022	9561022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	44	568	1	ENST00000353224.5:c.760G>A	p.Glu254Lys	p.E254K	ENST00000353224	NM_177990.2	254	Gaa/Aaa	4/10	0.524820949801523	3	FACETS	0.331	0.277	0.392	0.166	0.138	0.196	SUBCLONAL	1	FALSE	1	0.524820949801523	3		569	639	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62293895	62293895	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	rs1163226089	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	60	958	1	ENST00000360203.5:c.396-4C>T		p.X132_splice	ENST00000360203	NM_001283009.1	132			0.524820949801523	3	FACETS	0.292	0.251	0.338	0.146	0.125	0.169	SUBCLONAL	1	FALSE	1	0.524820949801523	3		959	987	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462393	89462394	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	76	798	1	ENST00000336596.2:c.1865_1866delinsTT	p.Ser622Phe	p.S622F	ENST00000336596	NM_005233.5	622	tCC/tTT	10/17	0.240308483883889	5	FACETS	0.538	0.471	0.611	0.179	0.157	0.204	INDETERMINATE	1	FALSE	2	0.524820949801523	5		799	962	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851570	134851570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	113	668	4	ENST00000398015.3:c.976C>T	p.Pro326Ser	p.P326S	ENST00000398015	NM_004441.4	326	Ccc/Tcc	5/16	0.240308483883889	5	FACETS	1	0.977	1	0.43	0.387	0.474	INDETERMINATE	1	FALSE	2	0.524820949801523	5		672	597	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964367	55964367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	81	855	1	ENST00000263923.4:c.2446C>T	p.His816Tyr	p.H816Y	ENST00000263923	NM_002253.2	816	Cat/Tat	17/30	0.524820949801523	4	FACETS	0.488	0.429	0.552	0.244	0.214	0.276	SUBCLONAL	1	FALSE	2	0.524820949801523	4		856	964	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80057394	80057394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757559761	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	46	651	0	ENST00000265081.6:c.1793C>T	p.Ser598Leu	p.S598L	ENST00000265081	NM_002439.4	598	tCg/tTg	13/24	0.240308483883889	5	FACETS	0.419	0.352	0.494	0.14	0.117	0.165	INDETERMINATE	1	FALSE	2	0.524820949801523	5		651	747	SUCCESS
APC	324	MSKCC	GRCh37	5	112176363	112176363	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060503346	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	32	438	0	ENST00000257430.4:c.5072C>T	p.Pro1691Leu	p.P1691L	ENST00000257430	NM_000038.5	1691	cCt/cTt	16/16	0.509612479232118	3	FACETS	0.416	0.338	0.504	0.208	0.169	0.252	SUBCLONAL	1	FALSE	1	0.524820949801523	3		438	370	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460345	149460345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	148	579	0	ENST00000286301.3:c.292C>T	p.His98Tyr	p.H98Y	ENST00000286301	NM_005211.3	98	Cac/Tac	3/22	0.509612479232118	3	FACETS	0.908	0.839	0.979	0.908	0.839	0.979	CLONAL	2	FALSE	1	0.524820949801523	3		579	392	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642486	117642486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	364	903	0	ENST00000368508.3:c.5713G>A	p.Glu1905Lys	p.E1905K	ENST00000368508	NM_002944.2	1905	Gag/Aag	35/43	0.524820949801523	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	FALSE	0	0.524820949801523	2		903	666	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371771	116371771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	67	641	0	ENST00000397752.3:c.1250G>A	p.Arg417Gln	p.R417Q	ENST00000397752	NM_000245.2	417	cGa/cAa	3/21	0.481250396654637	4	FACETS	0.499	0.433	0.571	0.25	0.216	0.286	SUBCLONAL	1	FALSE	2	0.524820949801523	4		641	780	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345809	152345809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	164	716	0	ENST00000359321.1:c.761C>T	p.Ser254Leu	p.S254L	ENST00000359321	NM_005431.1	254	tCa/tTa	3/3	0.481250396654637	4	FACETS	1	0.962	1	0.54	0.496	0.586	CLONAL	1	FALSE	2	0.524820949801523	4		716	882	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934273	68934273	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	122	647	0	ENST00000288368.4:c.339A>C	p.Lys113Asn	p.K113N	ENST00000288368	NM_024870.2	113	aaA/aaC	4/40	0.197566201982024	5	FACETS	1	0.974	1	0.407	0.368	0.447	INDETERMINATE	1	FALSE	2	0.524820949801523	5		647	681	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486155	8486155	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	157	653	0	ENST00000356435.5:c.2662G>A	p.Gly888Arg	p.G888R	ENST00000356435		888	Gga/Aga	17/35	0.11880104903415	4	FACETS	0.903	0.833	0.975	0.903	0.833	0.975	INDETERMINATE	2	FALSE	2	0.524820949801523	4		653	505	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636826	8636826	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1353675904	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	66	665	0	ENST00000356435.5:c.83G>A	p.Arg28Gln	p.R28Q	ENST00000356435		28	cGa/cAa	2/35	0.11880104903415	4	FACETS	0.578	0.501	0.661	0.289	0.25	0.331	INDETERMINATE	1	FALSE	2	0.524820949801523	4		665	664	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93640015	93640015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	36	528	1	ENST00000375746.1:c.1344G>A	p.Met448Ile	p.M448I	ENST00000375746	NM_001174167.1	448	atG/atA	10/14	0.11880104903415	4	FACETS	0.418	0.343	0.502	0.209	0.171	0.251	INDETERMINATE	1	FALSE	2	0.524820949801523	4		529	501	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626629	100626629	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	241	407	0	ENST00000308731.7:c.301C>T	p.Pro101Ser	p.P101S	ENST00000308731	NM_000061.2	101	Ccc/Tcc	4/19	0.408718993140116	2	FACETS	1	0.992	1			1	CLONAL	2	FALSE	NA	0.524820949801523	2		407	376	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117874083	117874094	+	frameshift_variant	Frame_Shift_Del	DEL	AAGTCAGGCAGT	AAGTCAGGCAGT	G	novel	NA	P-0021847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	163	589	0	ENST00000297338.2:c.360_371delinsC	p.Leu121ArgfsTer2	p.L121Rfs*2	ENST00000297338	NM_006265.2	120	ccACTGCCTGACTTa/ccCa	4/14	0.197566201982024	5	FACETS	1	0.964	1	0.714	0.66	0.77	INDETERMINATE	2	FALSE	2	0.524820949801523	5		589	518	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0021883-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	347	578	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	0.766	0.727	0.805	1	0.995	1	SUBCLONAL	2	FALSE	1	0.478340823792779	2		578	947	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0021934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	72	284	0				ENST00000310581	NM_198253.2	-/1132			0.159189569754749	0	FACETS	0.603	0.534	0.676			1	INDETERMINATE	1	TRUE	0	0.482505344739119	0		284	256	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0021934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	335	451	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.23522399901786	3	FACETS	0.828	0.784	0.873	0.828	0.784	0.873	INDETERMINATE	2	TRUE	1	0.482505344739119	3		451	1041	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0021934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	120	358	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	0.947	0.86	1	0.947	0.86	1	CLONAL	1	TRUE	1	0.482505344739119	2		358	525	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356251	66356251	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	110	787	0	ENST00000273854.3:c.1246C>T	p.Pro416Ser	p.P416S	ENST00000273854	NM_004439.5	416	Ccc/Tcc	5/18	0.464681151781249	1	FACETS	0.526	0.473	0.582	0.526	0.473	0.582	SUBCLONAL	1	TRUE	0	0.482505344739119	1		787	658	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186812	108186812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	158	677	1	ENST00000278616.4:c.6170C>T	p.Ser2057Leu	p.S2057L	ENST00000278616	NM_000051.3	2057	tCa/tTa	42/63	1	2	FACETS	0.896	0.823	0.972	0.896	0.823	0.972	CLONAL	1	TRUE	1	0.482505344739119	2		678	731	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727403	66727441	+	inframe_deletion	In_Frame_Del	DEL	TAGAGCTTGATGAGCAGCAGCGAAAGCGCCTTGAGGCCT	TAGAGCTTGATGAGCAGCAGCGAAAGCGCCTTGAGGCCT	-	novel	NA	P-0021934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	101	481	0	ENST00000307102.5:c.120_158del	p.Glu41_Phe53del	p.E41_F53del	ENST00000307102	NM_002755.3	40	cTAGAGCTTGATGAGCAGCAGCGAAAGCGCCTTGAGGCCTtt/ctt	2/11	1	2	FACETS	0.885	0.795	0.98	0.885	0.795	0.98	CLONAL	1	TRUE	1	0.482505344739119	2		481	473	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024434	16024434	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	139	466	0	ENST00000268712.3:c.1784C>T	p.Ala595Val	p.A595V	ENST00000268712	NM_006311.3	595	gCt/gTt	16/46	0.130231671204262	3	FACETS	1	0.984	1	0.668	0.612	0.727	INDETERMINATE	1	TRUE	1	0.482505344739119	3		466	535	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845704	151845705	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	139	715	2	ENST00000262189.6:c.13307_13308delinsTT	p.Ser4436Phe	p.S4436F	ENST00000262189	NM_170606.2	4436	tCC/tTT	52/59	0.23522399901786	3	FACETS	0.997	0.91	1	0.499	0.455	0.545	INDETERMINATE	1	TRUE	1	0.482505344739119	3		717	717	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	33	151	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.98	0.798	1	0.98	0.798	1	CLONAL	1	TRUE	1	0.16	2		151	421	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576033	29576033	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	29	717	0	ENST00000356175.3:c.4006C>T	p.Gln1336Ter	p.Q1336*	ENST00000356175	NM_000267.3	1336	Cag/Tag	30/57	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.16	2		717	318	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	126	480	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.16	2		480	1133	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518111	8518111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	35	621	0	ENST00000356435.5:c.1280G>A	p.Arg427Gln	p.R427Q	ENST00000356435		427	cGa/cAa	10/35	1	2	FACETS	0.73	0.597	0.88	0.73	0.597	0.88	SUBCLONAL	1	TRUE	1	0.16	2		621	599	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826577	50826577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	20	504	0	ENST00000398568.2:c.2302C>T	p.Pro768Ser	p.P768S	ENST00000398568	NM_001042412.1	768	Cct/Tct	15/18	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.16	2		504	185	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858517	9858517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765370528	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	24	561	1	ENST00000330684.3:c.2884G>A	p.Glu962Lys	p.E962K	ENST00000330684	NM_001134407.1	962	Gaa/Aaa	13/13	1	2	FACETS	0.767	0.601	0.959	0.767	0.601	0.959	CLONAL	1	TRUE	1	0.16	2		562	391	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381541	81381541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	21	397	1	ENST00000222390.5:c.520G>A	p.Glu174Lys	p.E174K	ENST00000222390	NM_000601.4	174	Gaa/Aaa	5/18	1	2	FACETS	0.721	0.555	0.916	0.721	0.555	0.916	CLONAL	1	TRUE	1	0.16	2		398	364	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561450	9561450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	99	738	0	ENST00000353224.5:c.332G>A	p.Gly111Glu	p.G111E	ENST00000353224	NM_177990.2	111	gGa/gAa	4/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.16	2		738	1099	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313189	30313189	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139792204	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	33	870	1	ENST00000262643.3:c.883C>T	p.Pro295Ser	p.P295S	ENST00000262643	NM_001238.2	295	Cct/Tct	10/12	0.156594750279665	3	FACETS	0.685	0.557	0.831	0.343	0.278	0.416	SUBCLONAL	1	TRUE	1	0.16	3		871	650	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400190	41400190	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	31	613	0	ENST00000373198.4:c.569G>A	p.Arg190Lys	p.R190K	ENST00000373198	NM_133170.3	190	aGa/aAa	5/32	1	2	FACETS	0.755	0.61	0.921	0.755	0.61	0.921	CLONAL	1	TRUE	1	0.16	2		613	513	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917782	29917782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56077855	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1223	106	1030	2	ENST00000389048.3:c.886G>A	p.Glu296Lys	p.E296K	ENST00000389048	NM_004304.4	296	Gag/Aag	3/29	1	2	FACETS	0.997	0.891	1	0.997	0.891	1	CLONAL	1	TRUE	1	0.16	2		1032	1329	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215915	142215915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746443122	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	19	631	0	ENST00000350721.4:c.5678C>T	p.Ser1893Phe	p.S1893F	ENST00000350721	NM_001184.3	1893	tCc/tTc	33/47	1	2	FACETS	0.745	0.565	0.956	0.745	0.565	0.956	CLONAL	1	TRUE	1	0.16	2		631	319	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195717	123195717	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	28	876	0	ENST00000218089.9:c.1631G>A	p.Gly544Glu	p.G544E	ENST00000218089	NM_001042749.1	544	gGa/gAa	17/35	1	2	FACETS	0.911	0.728	1	0.911	0.728	1	CLONAL	1	TRUE	1	0.16	2		876	384	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809725	36809725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	51	694	0	ENST00000373129.3:c.880C>T	p.Pro294Ser	p.P294S	ENST00000373129	NM_032017.1	294	Cct/Tct	9/12	1	2	FACETS	0.788	0.668	0.921	0.788	0.668	0.921	CLONAL	1	TRUE	1	0.16	2		694	809	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8252010	8252010	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	64	885	0	ENST00000335790.3:c.67G>A	p.Gly23Ser	p.G23S	ENST00000335790	NM_002315.2	23	Ggc/Agc	2/4	1	2	FACETS	0.695	0.6	0.799	0.695	0.6	0.799	SUBCLONAL	1	TRUE	1	0.16	2		885	1151	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348727	118348727	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	22	427	0	ENST00000534358.1:c.3380C>T	p.Pro1127Leu	p.P1127L	ENST00000534358	NM_005933.3	1127	cCa/cTa	5/36	1	2	FACETS	0.689	0.533	0.871	0.689	0.533	0.871	SUBCLONAL	1	TRUE	1	0.16	2		427	399	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608236	28608236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	20	813	1	ENST00000241453.7:c.1820G>A	p.Arg607Lys	p.R607K	ENST00000241453	NM_004119.2	607	aGa/aAa	14/24	1	2	FACETS	0.769	0.588	0.982	0.769	0.588	0.982	CLONAL	1	TRUE	1	0.16	2		814	325	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913316	28913316	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	49	904	0	ENST00000282397.4:c.2477G>C	p.Arg826Thr	p.R826T	ENST00000282397	NM_002019.4	826	aGa/aCa	17/30	1	2	FACETS	0.909	0.768	1	0.909	0.768	1	CLONAL	1	TRUE	1	0.16	2		904	674	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738764	43738764	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	18	679	1	ENST00000382044.4:c.2861C>T	p.Thr954Ile	p.T954I	ENST00000382044	NM_001141980.1	954	aCc/aTc	14/28	0.156594750279665	1	FACETS	0.685	0.516	0.886	0.685	0.516	0.886	SUBCLONAL	1	TRUE	0	0.16	1		680	302	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372061	45372061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1416015925	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	27	724	0	ENST00000262160.6:c.1108C>T	p.Pro370Ser	p.P370S	ENST00000262160	NM_005901.5	370	Cct/Tct	9/11	1	2	FACETS	1	0.812	1	1	0.812	1	CLONAL	1	TRUE	1	0.16	2		724	331	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955113	17955114	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	70	1034	1	ENST00000458235.1:c.113_114delinsTT	p.Pro38Leu	p.P38L	ENST00000458235	NM_000215.3	38	cCC/cTT	2/24	0.156594750279665	3	FACETS	0.726	0.63	0.83	0.363	0.315	0.415	SUBCLONAL	1	TRUE	1	0.16	3		1035	1302	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25536841	25536841	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1364437125	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	81	504	0	ENST00000264709.3:c.13C>T	p.Pro5Ser	p.P5S	ENST00000264709	NM_175629.2	5	Ccc/Tcc	2/23	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.16	2		504	868	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274635	198274635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	101	782	0	ENST00000335508.6:c.763G>A	p.Asp255Asn	p.D255N	ENST00000335508	NM_012433.2	255	Gat/Aat	7/25	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.16	2		782	1107	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961514	54961514	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	42	702	0	ENST00000312783.6:c.118A>T	p.Asn40Tyr	p.N40Y	ENST00000312783	NM_198436.1	40	Aat/Tat	4/10	1	2	FACETS	0.829	0.691	0.983	0.829	0.691	0.983	CLONAL	1	TRUE	1	0.16	2		702	633	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171753	36171759	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CTTGTAT	CTTGTAT	-	novel	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	25	469	0	ENST00000300305.3:c.806_812del	p.Asp269GlyfsTer40	p.D269Gfs*40	ENST00000300305		269	gATACAAGg/gg	7/8	1	2	FACETS	0.698	0.549	0.869	0.698	0.549	0.869	SUBCLONAL	1	TRUE	1	0.16	2		469	448	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421364	12421364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	34	1042	2	ENST00000287820.6:c.244C>T	p.Pro82Ser	p.P82S	ENST00000287820	NM_015869.4	82	Cca/Tca	2/7	1	2	FACETS	0.758	0.618	0.915	0.758	0.618	0.915	CLONAL	1	TRUE	1	0.16	2		1044	561	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215312	142215312	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	64	685	0	ENST00000350721.4:c.5789T>G	p.Val1930Gly	p.V1930G	ENST00000350721	NM_001184.3	1930	gTa/gGa	34/47	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.16	2		685	662	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677962	117677962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	30	802	0	ENST00000368508.3:c.3971G>A	p.Arg1324Lys	p.R1324K	ENST00000368508	NM_002944.2	1324	aGg/aAg	25/43	0.156594750279665	3	FACETS	1	0.903	1	0.603	0.486	0.734	CLONAL	1	TRUE	1	0.16	3		802	336	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528493	157528494	+	missense_variant	Missense_Mutation	DNP	AC	AC	CA	novel	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	44	830	0	ENST00000346085.5:c.6218_6219delinsCA	p.Asn2073Thr	p.N2073T	ENST00000346085	NM_020732.3	2073	aAC/aCA	20/20	0.156594750279665	3	FACETS	0.716	0.598	0.847	0.358	0.299	0.424	SUBCLONAL	1	TRUE	1	0.16	3		830	830	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958220	2958220	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	68	737	0	ENST00000396946.4:c.2512G>C	p.Ala838Pro	p.A838P	ENST00000396946	NM_032415.4	838	Gcc/Ccc	19/25	1	2	FACETS	0.976	0.847	1	0.976	0.847	1	CLONAL	1	TRUE	1	0.16	2		737	871	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962806	2962806	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	94	861	0	ENST00000396946.4:c.2102C>T	p.Ala701Val	p.A701V	ENST00000396946	NM_032415.4	701	gCc/gTc	16/25	1	2	FACETS	0.933	0.828	1	0.933	0.828	1	CLONAL	1	TRUE	1	0.16	2		861	1259	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984157	2984157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	42	425	0	ENST00000396946.4:c.373G>A	p.Glu125Lys	p.E125K	ENST00000396946	NM_032415.4	125	Gag/Aag	5/25	1	2	FACETS	0.878	0.732	1	0.878	0.732	1	CLONAL	1	TRUE	1	0.16	2		425	598	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985549	2985549	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	47	813	2	ENST00000396946.4:c.262T>C	p.Tyr88His	p.Y88H	ENST00000396946	NM_032415.4	88	Tat/Cat	4/25	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.16	2		815	577	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339863	116339863	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	13	720	0	ENST00000397752.3:c.725G>A	p.Arg242Lys	p.R242K	ENST00000397752	NM_000245.2	242	aGa/aAa	2/21	1	2	FACETS	0.635	0.452	0.858	0.635	0.452	0.858	SUBCLONAL	1	TRUE	1	0.16	2		720	256	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212866	27212866	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1201741867	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	98	858	1	ENST00000380036.4:c.2848C>T	p.Arg950Trp	p.R950W	ENST00000380036	NM_000459.3	950	Cgg/Tgg	17/23	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.16	2		859	1189	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211496	98211496	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1375226181	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	78	655	0	ENST00000331920.6:c.3659C>T	p.Ser1220Phe	p.S1220F	ENST00000331920	NM_000264.3	1220	tCc/tTc	22/24	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.16	2		655	767	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870260	44870260	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0021948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	25	769	0	ENST00000377967.4:c.439C>T	p.Gln147Ter	p.Q147*	ENST00000377967	NM_021140.2	147	Cag/Tag	5/29	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.16	2		769	258	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	77	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.395750559288221	2		306	357	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	278	528	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.395750559288221	3	FACETS	0.956	0.906	1	0.956	0.906	1	CLONAL	3	TRUE	0	0.395750559288221	3		528	587	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115012	3115012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555702147	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	177	924	3	ENST00000078429.4:c.547C>T	p.Arg183Cys	p.R183C	ENST00000078429	NM_002067.2	183	Cgc/Tgc	4/7	0.376670610519831	3	FACETS	1	0.963	1	0.538	0.495	0.582	CLONAL	1	TRUE	1	0.395750559288221	3		927	996	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892299	9892299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs796052549	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	71	439	0	ENST00000330684.3:c.2191G>A	p.Asp731Asn	p.D731N	ENST00000330684	NM_001134407.1	731	Gat/Aat	11/13	0.376670610519831	3	FACETS	0.823	0.72	0.935	0.412	0.36	0.468	CLONAL	1	TRUE	1	0.395750559288221	3		439	522	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125764	47125764	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775677070	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	66	446	0	ENST00000409792.3:c.5506C>T	p.Pro1836Ser	p.P1836S	ENST00000409792	NM_014159.6	1836	Ccg/Tcg	12/21	0.331591682452999	3	FACETS	0.925	0.806	1	0.462	0.403	0.527	CLONAL	1	TRUE	1	0.395750559288221	3		446	432	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211536	46211536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	60	352	0	ENST00000334344.6:c.502G>A	p.Gly168Arg	p.G168R	ENST00000334344	NM_152641.2	168	Gga/Aga	5/21	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.395750559288221	2		352	258	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956676	93956676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465960814	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	109	413	0	ENST00000369303.4:c.2560C>T	p.Arg854Cys	p.R854C	ENST00000369303	NM_004440.3	854	Cgt/Tgt	15/17	0.331591682452999	3	FACETS	0.835	0.756	0.917	0.835	0.756	0.917	CLONAL	2	TRUE	1	0.395750559288221	3		413	395	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244778	46244778	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057524391	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	103	655	3	ENST00000334344.6:c.2872C>T	p.Gln958Ter	p.Q958*	ENST00000334344	NM_152641.2	958	Cag/Tag	15/21	1	2	FACETS	0.891	0.8	0.988	0.891	0.8	0.988	CLONAL	1	TRUE	1	0.395750559288221	2		658	584	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561430	9561430	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	107	643	1	ENST00000353224.5:c.352G>A	p.Gly118Ser	p.G118S	ENST00000353224	NM_177990.2	118	Ggc/Agc	4/10	0.331591682452999	3	FACETS	0.836	0.75	0.927	0.418	0.375	0.464	CLONAL	1	TRUE	1	0.395750559288221	3		644	775	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472433	88472433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	101	545	0	ENST00000360948.2:c.2122G>A	p.Asp708Asn	p.D708N	ENST00000360948	NM_001012338.2	708	Gat/Aat	16/19	0.331591682452999	3	FACETS	0.954	0.854	1	0.477	0.427	0.53	CLONAL	1	TRUE	1	0.395750559288221	3		545	641	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946418	2946418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	315	712	0	ENST00000396946.4:c.3319G>A	p.Glu1107Lys	p.E1107K	ENST00000396946	NM_032415.4	1107	Gag/Aag	25/25	0.336450267221709	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	2	0.395750559288221	4		712	1098	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675119	40675119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766760890	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	111	705	2	ENST00000249776.8:c.83C>T	p.Pro28Leu	p.P28L	ENST00000249776	NM_033286.3	28	cCg/cTg	1/9	0.331591682452999	3	FACETS	0.936	0.842	1	0.468	0.421	0.518	CLONAL	1	TRUE	1	0.395750559288221	3		707	718	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725021	162725021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542584476	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	154	616	0	ENST00000367921.3:c.493C>T	p.Arg165Trp	p.R165W	ENST00000367921	NM_006182.2	165	Cgg/Tgg	6/18	0.379619322425634	3	FACETS	0.871	0.802	0.943	0.871	0.802	0.943	CLONAL	2	TRUE	1	0.395750559288221	3		616	535	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256051	123256051	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	133	575	1	ENST00000358487.5:c.1858C>T	p.Gln620Ter	p.Q620*	ENST00000358487	NM_000141.4	620	Caa/Taa	13/18	0.331591682452999	3	FACETS	0.844	0.772	0.919	0.844	0.772	0.919	CLONAL	2	TRUE	1	0.395750559288221	3		576	477	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406233	406233	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	39	500	0	ENST00000399788.2:c.4208C>T	p.Ser1403Phe	p.S1403F	ENST00000399788	NM_001042603.1	1403	tCt/tTt	25/28	0.33707817649126	4	FACETS	0.734	0.609	0.872	0.245	0.203	0.291	SUBCLONAL	1	TRUE	1	0.395750559288221	4		500	375	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	495088	495088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	128	489	0	ENST00000399788.2:c.218G>A	p.Arg73Lys	p.R73K	ENST00000399788	NM_001042603.1	73	aGa/aAa	2/28	0.33707817649126	4	FACETS	1	0.978	1	0.805	0.737	0.874	CLONAL	2	TRUE	1	0.395750559288221	4		489	374	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888221	112888221	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	105	606	1	ENST00000351677.2:c.237G>T	p.Gln79His	p.Q79H	ENST00000351677	NM_002834.3	79	caG/caT	3/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.395750559288221	2		607	398	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610250	81610251	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	137	487	2	ENST00000298171.2:c.1848_1849delinsAT	p.Asp617Tyr	p.D617Y	ENST00000298171	NM_000369.2	616	ggGGac/ggATac	10/10	0.331591682452999	3	FACETS	0.823	0.753	0.895	0.823	0.753	0.895	CLONAL	2	TRUE	1	0.395750559288221	3		489	504	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858298	9858298	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs540445580	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	89	440	0	ENST00000330684.3:c.3103G>A	p.Asp1035Asn	p.D1035N	ENST00000330684	NM_001134407.1	1035	Gat/Aat	13/13	0.376670610519831	3	FACETS	1	0.969	1	0.624	0.556	0.695	CLONAL	1	TRUE	1	0.395750559288221	3		440	432	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984908	9984908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373239575	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	168	628	0	ENST00000330684.3:c.1057G>A	p.Glu353Lys	p.E353K	ENST00000330684	NM_001134407.1	353	Gaa/Aaa	4/13	0.376670610519831	3	FACETS	0.814	0.751	0.878	0.814	0.751	0.878	CLONAL	2	TRUE	1	0.395750559288221	3		628	625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578409	+	inframe_deletion	In_Frame_Del	DEL	CATGGTGGGGGCAGCGCC	CATGGTGGGGGCAGCGCC	-	novel	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	214	602	2	ENST00000269305.4:c.521_538del	p.Arg174_Glu180delinsLys	p.R174_E180delinsK	ENST00000269305	NM_001126112.2	174	aGGCGCTGCCCCCACCATGag/aag	5/11	0.367285419420656	2	FACETS	0.976	0.915	1	0.976	0.915	1	CLONAL	2	TRUE	0	0.395750559288221	2		604	554	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541553	29541553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	106	492	0	ENST00000356175.3:c.1477C>T	p.Leu493Phe	p.L493F	ENST00000356175	NM_000267.3	493	Ctc/Ttc	13/57	0.367285419420656	2	FACETS	0.834	0.757	0.914	0.834	0.757	0.914	CLONAL	2	TRUE	0	0.395750559288221	2		492	321	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1646376	1646377	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	235	695	3	ENST00000344749.5:c.122_123delinsTT	p.Ala41Val	p.A41V	ENST00000344749	NM_001136139.2	41	gCC/gTT	3/19	0.376670610519831	3	FACETS	0.93	0.871	0.99	0.93	0.871	0.99	CLONAL	2	TRUE	1	0.395750559288221	3		698	765	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918082	50918082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	105	729	0	ENST00000440232.2:c.2399C>T	p.Pro800Leu	p.P800L	ENST00000440232	NM_002691.3	800	cCa/cTa	20/27	0.376670610519831	3	FACETS	0.895	0.803	0.993	0.448	0.401	0.497	CLONAL	1	TRUE	1	0.395750559288221	3		729	710	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965104	25965104	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	213	561	1	ENST00000435504.4:c.4102C>T	p.Pro1368Ser	p.P1368S	ENST00000435504		1368	Cct/Tct	13/13	0.336450267221709	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.395750559288221	4		562	703	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551240	29551240	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55706535	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	218	659	0	ENST00000389048.3:c.1390G>A	p.Gly464Arg	p.G464R	ENST00000389048	NM_004304.4	464	Gga/Aga	6/29	0.336450267221709	4	FACETS	0.961	0.896	1	0.961	0.896	1	CLONAL	2	TRUE	2	0.395750559288221	4		659	800	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710637	40710637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1161104430	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	231	586	0	ENST00000373198.4:c.4214G>A	p.Gly1405Glu	p.G1405E	ENST00000373198	NM_133170.3	1405	gGa/gAa	31/32	0.331591682452999	3	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	1	0.395750559288221	3		586	696	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449457	149449457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746152726	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	110	524	1	ENST00000286301.3:c.1489G>A	p.Ala497Thr	p.A497T	ENST00000286301	NM_005211.3	497	Gcc/Acc	10/22	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.395750559288221	2		525	433	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517766	176517766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370322847	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	99	549	0	ENST00000292408.4:c.376G>A	p.Asp126Asn	p.D126N	ENST00000292408	NM_213647.1	126	Gat/Aat	4/18	1	2	FACETS	0.804	0.719	0.895	0.804	0.719	0.895	CLONAL	1	TRUE	1	0.395750559288221	2		549	622	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188202	32188202	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	177	604	0	ENST00000375023.3:c.1139T>C	p.Leu380Pro	p.L380P	ENST00000375023	NM_004557.3	380	cTc/cCc	6/30	0.331591682452999	3	FACETS	0.829	0.767	0.893	0.829	0.767	0.893	CLONAL	2	TRUE	1	0.395750559288221	3		604	646	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525064	157525065	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	45	460	2	ENST00000346085.5:c.4959_4960delinsAA	p.Trp1653_Ala1654delinsTer	p.W1653_A1654delins*	ENST00000346085	NM_020732.3	1653	tgGGct/tgAAct	19/20	0.331591682452999	3	FACETS	0.632	0.532	0.743	0.316	0.266	0.372	SUBCLONAL	1	TRUE	1	0.395750559288221	3		462	431	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509569	106509569	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	154	557	0	ENST00000359195.3:c.1563C>G	p.Asp521Glu	p.D521E	ENST00000359195	NM_002649.2	521	gaC/gaG	2/11	0.336450267221709	4	FACETS	0.811	0.744	0.88	0.811	0.744	0.88	CLONAL	2	TRUE	2	0.395750559288221	4		557	670	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878089	151878089	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	169	493	0	ENST00000262189.6:c.6856A>T	p.Thr2286Ser	p.T2286S	ENST00000262189	NM_170606.2	2286	Aca/Tca	36/59	0.336450267221709	4	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	2	0.395750559288221	4		493	580	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002812	69002812	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	85	271	1	ENST00000288368.4:c.2114-2A>G		p.X705_splice	ENST00000288368	NM_024870.2	705			0.336450267221709	4	FACETS	1	0.915	1	1	0.915	1	CLONAL	2	TRUE	2	0.395750559288221	4		272	292	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019961	123019961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	136	320	0	ENST00000355640.3:c.449C>T	p.Ser150Leu	p.S150L	ENST00000355640		150	tCa/tTa	2/7	0.22137100710514	2	FACETS	1	0.978	1			1	INDETERMINATE	2	TRUE	NA	0.395750559288221	2		320	298	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	110	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.513614338631273	2		306	380	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552663	18552663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	159	958	1	ENST00000266497.5:c.2074C>T	p.Pro692Ser	p.P692S	ENST00000266497		692	Cct/Tct	14/31	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.513614338631273	2		959	596	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670708	134670708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	156	697	2	ENST00000398015.3:c.619C>T	p.Pro207Ser	p.P207S	ENST00000398015	NM_004441.4	207	Cca/Tca	3/16	0.513614338631273	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.513614338631273	1		699	436	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644451	18644451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	154	750	1	ENST00000266497.5:c.2629C>T	p.Pro877Ser	p.P877S	ENST00000266497		877	Cct/Tct	18/31	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.513614338631273	2		751	554	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812196	212812196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	80	580	0	ENST00000342788.4:c.380G>A	p.Gly127Glu	p.G127E	ENST00000342788	NM_005235.2	127	gGa/gAa	3/28	1	2	FACETS	0.764	0.676	0.857	0.764	0.676	0.857	SUBCLONAL	1	TRUE	1	0.513614338631273	2		580	408	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292591	15292591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758913191	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	199	945	1	ENST00000263388.2:c.2588C>T	p.Ser863Leu	p.S863L	ENST00000263388	NM_000435.2	863	tCg/tTg	17/33	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.513614338631273	2		946	672	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528596	8528596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	116	621	1	ENST00000356435.5:c.536G>A	p.Arg179Gln	p.R179Q	ENST00000356435		179	cGa/cAa	4/35	0.513614338631273	1	FACETS	0.99	0.903	1	0.99	0.903	1	CLONAL	1	TRUE	0	0.513614338631273	1		622	339	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	164	771	2	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.513614338631273	2		773	627	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743975	41743975	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	205	1063	0	ENST00000301178.4:c.910C>T	p.Pro304Ser	p.P304S	ENST00000301178	NM_021913.4	304	Cct/Tct	7/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.513614338631273	2		1063	788	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971116	21971116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552823	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	102	499	0	ENST00000304494.5:c.242C>T	p.Pro81Leu	p.P81L	ENST00000304494	NM_000077.4	81	cCc/cTc	2/3	0.513614338631273	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.513614338631273	1		499	272	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857368	9857368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	112	637	0	ENST00000330684.3:c.4033C>T	p.Pro1345Ser	p.P1345S	ENST00000330684	NM_001134407.1	1345	Ccc/Tcc	13/13	1	2	FACETS	0.918	0.83	1	0.918	0.83	1	CLONAL	1	TRUE	1	0.513614338631273	2		637	475	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237622	16237622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	131	643	0	ENST00000375759.3:c.1069C>T	p.His357Tyr	p.H357Y	ENST00000375759	NM_015001.2	357	Cat/Tat	5/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.513614338631273	2		643	460	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257447	16257447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	153	764	0	ENST00000375759.3:c.4712G>A	p.Ser1571Asn	p.S1571N	ENST00000375759	NM_015001.2	1571	aGc/aAc	11/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.513614338631273	2		764	542	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259635	16259636	+	missense_variant	Missense_Mutation	DNP	AG	AG	GA	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	113	744	1	ENST00000375759.3:c.6900_6901delinsGA	p.Ala2301Thr	p.A2301T	ENST00000375759	NM_015001.2	2300	gaAGcc/gaGAcc	11/15	1	2	FACETS	0.787	0.711	0.867	0.787	0.711	0.867	SUBCLONAL	1	TRUE	1	0.513614338631273	2		745	559	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101168	27101168	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	202	873	1	ENST00000324856.7:c.4450C>T	p.Pro1484Ser	p.P1484S	ENST00000324856	NM_006015.4	1484	Ccc/Tcc	18/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.513614338631273	2		874	643	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804956	43804956	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	101	486	2	ENST00000372470.3:c.406C>T	p.Pro136Ser	p.P136S	ENST00000372470	NM_005373.2	136	Ccc/Tcc	4/12	1	2	FACETS	0.996	0.897	1	0.996	0.897	1	CLONAL	1	TRUE	1	0.513614338631273	2		488	395	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873232	71873232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	96	611	0	ENST00000357731.5:c.962G>A	p.Gly321Glu	p.G321E	ENST00000357731	NM_173808.2	321	gGa/gAa	7/7	1	2	FACETS	0.852	0.763	0.945	0.852	0.763	0.945	CLONAL	1	TRUE	1	0.513614338631273	2		611	439	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241933	72241933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	103	615	0	ENST00000357731.5:c.457G>A	p.Gly153Arg	p.G153R	ENST00000357731	NM_173808.2	153	Gga/Aga	3/7	1	2	FACETS	0.907	0.817	1	0.907	0.817	1	CLONAL	1	TRUE	1	0.513614338631273	2		615	442	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280145	115280145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754450380	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	144	571	0	ENST00000438362.2:c.487C>T	p.Pro163Ser	p.P163S	ENST00000438362	NM_001242891.1	163	Cca/Tca	5/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.513614338631273	2		571	512	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458225	120458225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	181	911	0	ENST00000256646.2:c.7120C>T	p.His2374Tyr	p.H2374Y	ENST00000256646	NM_024408.3	2374	Cat/Tat	34/34	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.513614338631273	2		911	681	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120478110	120478110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553195622	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	170	676	0	ENST00000256646.2:c.3640C>T	p.Pro1214Ser	p.P1214S	ENST00000256646	NM_024408.3	1214	Cca/Tca	22/34	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.513614338631273	2		676	590	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246493797	246493797	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	121	686	1	ENST00000388985.4:c.379del	p.Tyr127MetfsTer10	p.Y127Mfs*10	ENST00000388985		127	Tat/at	4/12	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.513614338631273	2		687	451	SUCCESS
RET	5979	MSKCC	GRCh37	10	43613845	43613845	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767414	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	174	947	0	ENST00000355710.3:c.2309G>A	p.Arg770Gln	p.R770Q	ENST00000355710	NM_020975.4	770	cGa/cAa	13/20	1	2	FACETS	0.917	0.846	0.99	0.917	0.846	0.99	CLONAL	1	TRUE	1	0.513614338631273	2		947	739	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852035	63852035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	156	799	1	ENST00000279873.7:c.2813C>T	p.Ser938Phe	p.S938F	ENST00000279873	NM_032199.2	938	tCc/tTc	10/10	1	2	FACETS	0.988	0.908	1	0.988	0.908	1	CLONAL	1	TRUE	1	0.513614338631273	2		800	615	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852712	63852712	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	164	832	0	ENST00000279873.7:c.3490C>T	p.Pro1164Ser	p.P1164S	ENST00000279873	NM_032199.2	1164	Cct/Tct	10/10	1	2	FACETS	0.998	0.92	1	0.998	0.92	1	CLONAL	1	TRUE	1	0.513614338631273	2		832	640	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70442609	70442609	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	175	746	0	ENST00000373644.4:c.4931T>C	p.Val1644Ala	p.V1644A	ENST00000373644	NM_030625.2	1644	gTt/gCt	10/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.513614338631273	2		746	594	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446447	70446447	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	155	701	0	ENST00000373644.4:c.5387C>T	p.Ser1796Leu	p.S1796L	ENST00000373644	NM_030625.2	1796	tCg/tTg	11/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.513614338631273	2		701	496	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944138	71944139	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	145	826	1	ENST00000298229.2:c.1971_1972delinsTT	p.Pro658Ser	p.P658S	ENST00000298229	NM_001567.3	657	ttCCca/ttTTca	17/28	1	2	FACETS	0.893	0.818	0.972	0.893	0.818	0.972	CLONAL	1	TRUE	1	0.513614338631273	2		827	632	SUCCESS
CBL	867	MSKCC	GRCh37	11	119146792	119146792	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	137	766	1	ENST00000264033.4:c.955C>A	p.Pro319Thr	p.P319T	ENST00000264033	NM_005188.3	319	Cct/Act	6/16	1	2	FACETS	0.986	0.902	1	0.986	0.902	1	CLONAL	1	TRUE	1	0.513614338631273	2		767	541	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409108	4409108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	139	653	1	ENST00000261254.3:c.803G>A	p.Gly268Glu	p.G268E	ENST00000261254	NM_001759.3	268	gGa/gAa	5/5	1	2	FACETS	0.986	0.902	1	0.986	0.902	1	CLONAL	1	TRUE	1	0.513614338631273	2		654	549	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435227	18435227	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1368182752	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	83	477	0	ENST00000266497.5:c.212G>A	p.Trp71Ter	p.W71*	ENST00000266497		71	tGg/tAg	1/31	1	2	FACETS	0.9	0.801	1	0.9	0.801	1	CLONAL	1	TRUE	1	0.513614338631273	2		477	359	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380196	25380196	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	132	632	0	ENST00000311936.3:c.262A>T	p.Lys88Ter	p.K88*	ENST00000311936	NM_004985.3	88	Aaa/Taa	3/5	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.513614338631273	2		632	514	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433806	49433806	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	225	1044	1	ENST00000301067.7:c.7747G>A	p.Ala2583Thr	p.A2583T	ENST00000301067	NM_003482.3	2583	Gcc/Acc	31/54	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.513614338631273	2		1045	832	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443489	49443490	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	126	654	2	ENST00000301067.7:c.3881_3882delinsTT	p.Ser1294Phe	p.S1294F	ENST00000301067	NM_003482.3	1294	tCC/tTT	11/54	1	2	FACETS	0.909	0.826	0.994	0.909	0.826	0.994	CLONAL	1	TRUE	1	0.513614338631273	2		656	540	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445532	49445532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757784071	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	248	926	0	ENST00000301067.7:c.1934C>T	p.Ser645Phe	p.S645F	ENST00000301067	NM_003482.3	645	tCc/tTc	10/54	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.513614338631273	2		926	781	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008060	29008060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143703839	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	81	592	1	ENST00000282397.4:c.709C>T	p.Pro237Ser	p.P237S	ENST00000282397	NM_002019.4	237	Cca/Tca	6/30	1	2	FACETS	0.876	0.778	0.98	0.876	0.778	0.98	CLONAL	1	TRUE	1	0.513614338631273	2		593	360	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893241	32893241	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	113	504	0	ENST00000380152.3:c.95T>C	p.Phe32Ser	p.F32S	ENST00000380152		32	tTt/tCt	3/27	1	2	FACETS	0.989	0.896	1	0.989	0.896	1	CLONAL	1	TRUE	1	0.513614338631273	2		504	445	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954186	32954186	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204070	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	128	848	3	ENST00000380152.3:c.9160C>T	p.Pro3054Ser	p.P3054S	ENST00000380152		3054	Ccc/Tcc	24/27	1	2	FACETS	0.94	0.856	1	0.94	0.856	1	CLONAL	1	TRUE	1	0.513614338631273	2		851	530	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881415	48881415	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	76	264	0	ENST00000267163.4:c.138del		p.X46_splice	ENST00000267163	NM_000321.2	46			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.513614338631273	2		264	233	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281980	49281980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777806801	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	186	935	2	ENST00000282018.3:c.1027G>A	p.Glu343Lys	p.E343K	ENST00000282018	NM_020377.2	343	Gaa/Aaa	1/1	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.513614338631273	2		937	684	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643705	38643705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1345810751	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	265	922	0	ENST00000299084.4:c.1175C>T	p.Ser392Leu	p.S392L	ENST00000299084	NM_152594.2	392	tCg/tTg	7/7	0.304690052872054	3	FACETS	0.852	0.802	0.903	0.852	0.802	0.903	INDETERMINATE	2	TRUE	1	0.513614338631273	3		922	761	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420180	88420180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	202	662	1	ENST00000360948.2:c.2506G>A	p.Asp836Asn	p.D836N	ENST00000360948	NM_001012338.2	836	Gac/Aac	19/19	0.304690052872054	3	FACETS	0.842	0.786	0.9	0.842	0.786	0.9	INDETERMINATE	2	TRUE	1	0.513614338631273	3		663	587	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476307	88476307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772244244	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	252	991	0	ENST00000360948.2:c.1825G>A	p.Asp609Asn	p.D609N	ENST00000360948	NM_001012338.2	609	Gat/Aat	15/19	0.304690052872054	3	FACETS	0.801	0.752	0.851	0.801	0.752	0.851	INDETERMINATE	2	TRUE	1	0.513614338631273	3		991	770	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669510	88669510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	195	199	1	ENST00000360948.2:c.1388G>A	p.Gly463Glu	p.G463E	ENST00000360948	NM_001012338.2	463	gGa/gAa	12/19	0.304690052872054	3	FACETS	0.773	0.72	0.828	0.773	0.72	0.828	INDETERMINATE	2	TRUE	1	0.513614338631273	3		200	617	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442836	99442836	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	226	748	0	ENST00000268035.6:c.1233G>C	p.Glu411Asp	p.E411D	ENST00000268035	NM_000875.3	411	gaG/gaC	5/21	0.304690052872054	3	FACETS	0.835	0.782	0.889	0.835	0.782	0.889	INDETERMINATE	2	TRUE	1	0.513614338631273	3		748	662	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500435	99500436	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	248	786	1	ENST00000268035.6:c.3868_3869delinsTT	p.Pro1290Leu	p.P1290L	ENST00000268035	NM_000875.3	1290	CCg/TTg	21/21	0.304690052872054	3	FACETS	0.828	0.778	0.879	0.828	0.778	0.879	INDETERMINATE	2	TRUE	1	0.513614338631273	3		787	733	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222201	2222202	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	127	802	4	ENST00000326181.6:c.485_486delinsTT	p.Pro162Leu	p.P162L	ENST00000326181	NM_032271.2	162	cCC/cTT	8/21	1	2	FACETS	0.866	0.788	0.948	0.866	0.788	0.948	CLONAL	1	TRUE	1	0.513614338631273	2		806	571	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223352	2223352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	137	831	1	ENST00000326181.6:c.964C>T	p.Leu322Phe	p.L322F	ENST00000326181	NM_032271.2	322	Ctc/Ttc	10/21	1	2	FACETS	0.865	0.789	0.943	0.865	0.789	0.943	CLONAL	1	TRUE	1	0.513614338631273	2		832	617	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777879	3777879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	205	1201	2	ENST00000262367.5:c.7169C>T	p.Thr2390Ile	p.T2390I	ENST00000262367	NM_004380.2	2390	aCc/aTc	31/31	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.513614338631273	2		1203	792	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779076	3779076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776500881	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	153	723	1	ENST00000262367.5:c.5972C>T	p.Pro1991Leu	p.P1991L	ENST00000262367	NM_004380.2	1991	cCg/cTg	31/31	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.513614338631273	2		724	568	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786787	3786788	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	110	611	3	ENST00000262367.5:c.4423_4424delinsTT	p.Pro1475Phe	p.P1475F	ENST00000262367	NM_004380.2	1475	CCt/TTt	27/31	1	2	FACETS	0.929	0.84	1	0.929	0.84	1	CLONAL	1	TRUE	1	0.513614338631273	2		614	461	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830809	3830809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	144	820	0	ENST00000262367.5:c.1747C>T	p.Pro583Ser	p.P583S	ENST00000262367	NM_004380.2	583	Cct/Tct	8/31	1	2	FACETS	0.884	0.809	0.963	0.884	0.809	0.963	CLONAL	1	TRUE	1	0.513614338631273	2		820	634	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857452	9857452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	107	676	0	ENST00000330684.3:c.3949G>A	p.Glu1317Lys	p.E1317K	ENST00000330684	NM_001134407.1	1317	Gaa/Aaa	13/13	1	2	FACETS	0.809	0.729	0.894	0.809	0.729	0.894	CLONAL	1	TRUE	1	0.513614338631273	2		676	515	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828723	72828723	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764788469	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	123	748	2	ENST00000268489.5:c.7858G>A	p.Glu2620Lys	p.E2620K	ENST00000268489	NM_006885.3	2620	Gaa/Aaa	9/10	1	2	FACETS	0.88	0.8	0.965	0.88	0.8	0.965	CLONAL	1	TRUE	1	0.513614338631273	2		750	544	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829202	72829202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1468327978	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	189	900	0	ENST00000268489.5:c.7379C>T	p.Pro2460Leu	p.P2460L	ENST00000268489	NM_006885.3	2460	cCc/cTc	9/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.513614338631273	2		900	713	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830907	72830907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	159	665	0	ENST00000268489.5:c.5674G>A	p.Glu1892Lys	p.E1892K	ENST00000268489	NM_006885.3	1892	Gag/Aag	9/10	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.513614338631273	2		665	594	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993830	72993830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	109	568	0	ENST00000268489.5:c.215C>T	p.Ser72Phe	p.S72F	ENST00000268489	NM_006885.3	72	tCc/tTc	2/10	1	2	FACETS	0.923	0.833	1	0.923	0.833	1	CLONAL	1	TRUE	1	0.513614338631273	2		568	460	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346532	89346533	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AT	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	151	787	2	ENST00000301030.4:c.6417_6418delinsAT	p.Glu2140Ter	p.E2140*	ENST00000301030	NM_001256183.1	2139	ccGGag/ccATag	9/13	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.513614338631273	2		789	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	167	631	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.513614338631273	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.513614338631273	1		631	423	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965476	15965476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	174	605	0	ENST00000268712.3:c.5330G>A	p.Gly1777Glu	p.G1777E	ENST00000268712	NM_006311.3	1777	gGa/gAa	36/46	0.513614338631273	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.513614338631273	1		605	392	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556313	29556318	+	inframe_deletion	In_Frame_Del	DEL	TTTATG	TTTATG	-	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	127	706	0	ENST00000356175.3:c.2680_2685del	p.Phe894_Met895del	p.F894_M895del	ENST00000356175	NM_000267.3	894	TTTATG/-	21/57	1	2	FACETS	0.912	0.83	0.998	0.912	0.83	0.998	CLONAL	1	TRUE	1	0.513614338631273	2		706	542	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246278	41246278	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763051683	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	186	873	0	ENST00000357654.3:c.1270G>A	p.Gly424Ser	p.G424S	ENST00000357654	NM_007294.3	424	Ggt/Agt	10/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.513614338631273	2		873	626	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805745	46805745	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs762197066	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	159	814	1	ENST00000290295.7:c.211C>T	p.Gln71Ter	p.Q71*	ENST00000290295	NM_006361.5	71	Cag/Tag	1/2	1	2	FACETS	0.975	0.897	1	0.975	0.897	1	CLONAL	1	TRUE	1	0.513614338631273	2		815	635	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752420	55752420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	220	947	1	ENST00000284073.2:c.878C>T	p.Ser293Phe	p.S293F	ENST00000284073	NM_138962.2	293	tCc/tTc	12/14	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.513614338631273	2		948	796	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58700953	58700953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	183	900	1	ENST00000305921.3:c.544G>A	p.Gly182Ser	p.G182S	ENST00000305921	NM_003620.3	182	Ggc/Agc	2/6	1	2	FACETS	0.997	0.923	1	0.997	0.923	1	CLONAL	1	TRUE	1	0.513614338631273	2		901	715	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732897	74732897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs976254083	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	56	169	0	ENST00000359995.5:c.346G>A	p.Gly116Arg	p.G116R	ENST00000359995	NM_001195427.1	116	Gga/Aga	1/3	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.513614338631273	2		169	173	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796041	78796041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	174	827	1	ENST00000306801.3:c.931G>A	p.Glu311Lys	p.E311K	ENST00000306801	NM_020761.2	311	Gaa/Aaa	8/34	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.513614338631273	2		828	676	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39537635	39537635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs950456446	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	104	591	0	ENST00000262039.4:c.169C>T	p.Leu57Phe	p.L57F	ENST00000262039	NM_002647.2	57	Ctt/Ttt	2/25	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.513614338631273	2		591	355	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45423051	45423051	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	121	514	0	ENST00000262160.6:c.77G>A	p.Gly26Glu	p.G26E	ENST00000262160	NM_005901.5	26	gGa/gAa	2/11	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.513614338631273	2		514	460	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591796	48591796	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	88	622	0	ENST00000342988.3:c.959C>T	p.Pro320Leu	p.P320L	ENST00000342988	NM_005359.5	320	cCt/cTt	9/12	1	2	FACETS	0.883	0.788	0.984	0.883	0.788	0.984	CLONAL	1	TRUE	1	0.513614338631273	2		622	388	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56409144	56409144	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	90	564	2	ENST00000348428.3:c.1651C>T	p.Arg551Ter	p.R551*	ENST00000348428	NM_006785.3	551	Cga/Tga	14/17	1	2	FACETS	0.757	0.675	0.844	0.757	0.675	0.844	SUBCLONAL	1	TRUE	1	0.513614338631273	2		566	463	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220433	1220433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881979	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	192	875	0	ENST00000326873.7:c.526G>A	p.Asp176Asn	p.D176N	ENST00000326873	NM_000455.4	176	Gac/Aac	4/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.513614338631273	2		875	715	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520017	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	178	801	2	ENST00000326873.7:c.647C>T	p.Ser216Phe	p.S216F	ENST00000326873	NM_000455.4	216	tCc/tTc	5/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.513614338631273	2		803	644	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094928	11094928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	156	820	0	ENST00000358026.2:c.101C>T	p.Pro34Leu	p.P34L	ENST00000358026	NM_001128849.1	34	cCc/cTc	2/36	1	2	FACETS	0.943	0.867	1	0.943	0.867	1	CLONAL	1	TRUE	1	0.513614338631273	2		820	644	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258583	19258583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	224	928	1	ENST00000162023.5:c.317C>T	p.Pro106Leu	p.P106L	ENST00000162023		106	cCt/cTt	8/13	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.513614338631273	2		929	733	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727958	41727958	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	124	722	0	ENST00000301178.4:c.583C>T	p.Pro195Ser	p.P195S	ENST00000301178	NM_021913.4	195	Cca/Tca	4/20	1	2	FACETS	0.952	0.866	1	0.952	0.866	1	CLONAL	1	TRUE	1	0.513614338631273	2		722	507	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743962	41743963	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	193	1078	3	ENST00000301178.4:c.897_898delinsTT	p.His300Tyr	p.H300Y	ENST00000301178	NM_021913.4	299	ctCCat/ctTTat	7/20	1	2	FACETS	0.947	0.877	1	0.947	0.877	1	CLONAL	1	TRUE	1	0.513614338631273	2		1081	794	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872382	45872383	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	180	939	2	ENST00000391945.4:c.128_129delinsTT	p.Pro43Leu	p.P43L	ENST00000391945	NM_000400.3	43	cCC/cTT	3/23	1	2	FACETS	0.967	0.894	1	0.967	0.894	1	CLONAL	1	TRUE	1	0.513614338631273	2		941	725	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085915	16085915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766312745	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	120	666	2	ENST00000281043.3:c.1091C>T	p.Pro364Leu	p.P364L	ENST00000281043	NM_005378.4	364	cCc/cTc	3/3	1	2	FACETS	0.944	0.857	1	0.944	0.857	1	CLONAL	1	TRUE	1	0.513614338631273	2		668	495	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966166	25966166	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	168	851	0	ENST00000435504.4:c.3040C>T	p.Pro1014Ser	p.P1014S	ENST00000435504		1014	Cca/Tca	13/13	1	2	FACETS	0.999	0.921	1	0.999	0.921	1	CLONAL	1	TRUE	1	0.513614338631273	2		851	655	SUCCESS
ALK	238	MSKCC	GRCh37	2	29497997	29497997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	139	736	0	ENST00000389048.3:c.2009C>T	p.Ser670Leu	p.S670L	ENST00000389048	NM_004304.4	670	tCa/tTa	11/29	1	2	FACETS	0.972	0.889	1	0.972	0.889	1	CLONAL	1	TRUE	1	0.513614338631273	2		736	557	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222510	39222510	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167317994	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	161	797	1	ENST00000402219.2:c.3100C>T	p.Pro1034Ser	p.P1034S	ENST00000402219	NM_005633.3	1034	Ccc/Tcc	20/23	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.513614338631273	2		798	551	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583396	46583396	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	141	784	1	ENST00000263734.3:c.324G>A	p.Met108Ile	p.M108I	ENST00000263734	NM_001430.4	108	atG/atA	3/16	1	2	FACETS	0.955	0.874	1	0.955	0.874	1	CLONAL	1	TRUE	1	0.513614338631273	2		785	575	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607529	46607529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	199	926	0	ENST00000263734.3:c.1718C>T	p.Pro573Leu	p.P573L	ENST00000263734	NM_001430.4	573	cCa/cTa	12/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.513614338631273	2		926	726	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116179	209116179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555882127	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	131	647	0	ENST00000345146.2:c.97C>T	p.Pro33Ser	p.P33S	ENST00000345146	NM_005896.2	33	Ccc/Tcc	3/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.513614338631273	2		647	478	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812278	212812278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	117	628	1	ENST00000342788.4:c.298G>A	p.Glu100Lys	p.E100K	ENST00000342788	NM_005235.2	100	Gag/Aag	3/28	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.513614338631273	2		629	412	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439806	220439806	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142337821	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	189	847	0	ENST00000243786.2:c.659G>A	p.Arg220Gln	p.R220Q	ENST00000243786	NM_002191.3	220	cGg/cAg	2/2	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.513614338631273	2		847	685	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546847	9546847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	139	607	0	ENST00000353224.5:c.1175C>T	p.Ser392Leu	p.S392L	ENST00000353224	NM_177990.2	392	tCg/tTg	5/10	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.513614338631273	2		607	515	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39713144	39713144	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1446671210	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	85	521	0	ENST00000361337.2:c.550A>G	p.Lys184Glu	p.K184E	ENST00000361337	NM_003286.2	184	Aaa/Gaa	8/21	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.513614338631273	2		521	309	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739100	40739101	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	133	830	2	ENST00000373198.4:c.3183_3184delinsTT	p.Arg1062Cys	p.R1062C	ENST00000373198	NM_133170.3	1061	ctCCgc/ctTTgc	24/32	1	2	FACETS	0.838	0.763	0.916	0.838	0.763	0.916	CLONAL	1	TRUE	1	0.513614338631273	2		832	618	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22123572	22123572	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	186	774	0	ENST00000215832.6:c.1004T>C	p.Leu335Ser	p.L335S	ENST00000215832	NM_002745.4	335	tTg/tCg	8/9	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.513614338631273	2		774	604	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513367	41513367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138538553	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	182	803	1	ENST00000263253.7:c.271C>T	p.Pro91Ser	p.P91S	ENST00000263253	NM_001429.3	91	Cct/Tct	2/31	1	2	FACETS	0.951	0.88	1	0.951	0.88	1	CLONAL	1	TRUE	1	0.513614338631273	2		804	745	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165321	47165321	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	110	641	0	ENST00000409792.3:c.805C>T	p.Gln269Ter	p.Q269*	ENST00000409792	NM_014159.6	269	Caa/Taa	3/21	1	2	FACETS	0.883	0.798	0.973	0.883	0.798	0.973	CLONAL	1	TRUE	1	0.513614338631273	2		641	485	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932925	49932926	+	missense_variant	Missense_Mutation	DNP	GT	GT	AA	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	218	1109	3	ENST00000296474.3:c.3018_3019delinsTT	p.Pro1007Ser	p.P1007S	ENST00000296474	NM_002447.2	1006	acACcc/acTTcc	13/20	1	2	FACETS	0.979	0.912	1	0.979	0.912	1	CLONAL	1	TRUE	1	0.513614338631273	2		1112	867	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247484	71247484	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	162	813	1	ENST00000318789.4:c.49C>T	p.Gln17Ter	p.Q17*	ENST00000318789	NM_032682.5	17	Cag/Tag	6/21	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.513614338631273	2		814	584	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498489	89498489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758657242	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	93	485	2	ENST00000336596.2:c.2461G>A	p.Gly821Arg	p.G821R	ENST00000336596	NM_005233.5	821	Gga/Aga	14/17	1	2	FACETS	0.917	0.821	1	0.917	0.821	1	CLONAL	1	TRUE	1	0.513614338631273	2		487	395	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499483	89499483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1426641543	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	120	652	0	ENST00000336596.2:c.2653C>T	p.Pro885Ser	p.P885S	ENST00000336596	NM_005233.5	885	Ccc/Tcc	15/17	1	2	FACETS	0.902	0.818	0.989	0.902	0.818	0.989	CLONAL	1	TRUE	1	0.513614338631273	2		652	518	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911651	134911651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	103	584	0	ENST00000398015.3:c.2116G>A	p.Asp706Asn	p.D706N	ENST00000398015	NM_004441.4	706	Gat/Aat	11/16	0.513614338631273	1	FACETS	0.987	0.895	1	0.987	0.895	1	CLONAL	1	TRUE	0	0.513614338631273	1		584	302	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590694	189590694	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	126	743	0	ENST00000264731.3:c.1259C>T	p.Ser420Phe	p.S420F	ENST00000264731	NM_003722.4	420	tCc/tTc	10/14	1	2	FACETS	0.875	0.795	0.958	0.875	0.795	0.958	CLONAL	1	TRUE	1	0.513614338631273	2		743	561	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957750	1957750	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	187	1004	0	ENST00000382891.5:c.2716C>T	p.Pro906Ser	p.P906S	ENST00000382891	NM_133335.3	906	Cca/Tca	15/22	0.513614338631273	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.513614338631273	1		1004	532	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332805	153332805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	164	801	0	ENST00000281708.4:c.151G>A	p.Glu51Lys	p.E51K	ENST00000281708	NM_033632.3	51	Gag/Aag	2/12	0.513614338631273	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.513614338631273	1		801	436	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293570	1293570	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	175	965	1	ENST00000310581.5:c.1431del	p.Trp478GlyfsTer31	p.W478Gfs*31	ENST00000310581	NM_198253.2	477	ctC/ct	2/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.513614338631273	2		966	632	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294367	1294368	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	107	500	3	ENST00000310581.5:c.633_634delinsAA	p.Val212Ile	p.V212I	ENST00000310581	NM_198253.2	211	ggGGtc/ggAAtc	2/16	1	2	FACETS	0.951	0.859	1	0.951	0.859	1	CLONAL	1	TRUE	1	0.513614338631273	2		503	438	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31504673	31504673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	170	911	0	ENST00000344624.3:c.1657C>T	p.Pro553Ser	p.P553S	ENST00000344624		553	Cct/Tct	8/33	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.513614338631273	2		911	622	SUCCESS
APC	324	MSKCC	GRCh37	5	112102981	112102981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554069763	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	107	729	2	ENST00000257430.4:c.316C>T	p.Arg106Cys	p.R106C	ENST00000257430	NM_000038.5	106	Cgt/Tgt	4/16	1	2	FACETS	0.859	0.774	0.948	0.859	0.774	0.948	CLONAL	1	TRUE	1	0.513614338631273	2		731	485	SUCCESS
APC	324	MSKCC	GRCh37	5	112178202	112178202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	117	545	0	ENST00000257430.4:c.6911C>T	p.Ser2304Phe	p.S2304F	ENST00000257430	NM_000038.5	2304	tCt/tTt	16/16	1	2	FACETS	0.951	0.863	1	0.951	0.863	1	CLONAL	1	TRUE	1	0.513614338631273	2		545	479	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505122	149505122	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1460983846	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	191	880	2	ENST00000261799.4:c.1693C>T	p.Arg565Ter	p.R565*	ENST00000261799	NM_002609.3	565	Cga/Tga	12/23	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.513614338631273	2		882	649	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524635	176524636	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	153	964	2	ENST00000292408.4:c.2367_2368delinsAA	p.Gly790Arg	p.G790R	ENST00000292408	NM_213647.1	789	ttGGga/ttAAga	18/18	1	2	FACETS	0.872	0.8	0.947	0.872	0.8	0.947	CLONAL	1	TRUE	1	0.513614338631273	2		966	683	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047996	180047996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	160	814	0	ENST00000261937.6:c.2179G>A	p.Ala727Thr	p.A727T	ENST00000261937	NM_182925.4	727	Gcg/Acg	15/30	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.513614338631273	2		814	526	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185029	32185029	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs767357300	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	163	882	0	ENST00000375023.3:c.1639C>T	p.Arg547Ter	p.R547*	ENST00000375023	NM_004557.3	547	Cga/Tga	10/30	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.513614338631273	2		882	596	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821503	32821503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775610295	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	192	747	0	ENST00000354258.4:c.91G>A	p.Gly31Arg	p.G31R	ENST00000354258	NM_000593.5	31	Gga/Aga	1/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.513614338631273	2		747	659	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288707	33288707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	128	636	0	ENST00000374542.5:c.845C>T	p.Thr282Ile	p.T282I	ENST00000374542	NM_001141970.1	282	aCc/aTc	3/8	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.513614338631273	2		636	496	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967841	93967841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	147	825	0	ENST00000369303.4:c.2086C>T	p.His696Tyr	p.H696Y	ENST00000369303	NM_004440.3	696	Cat/Tat	11/17	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.513614338631273	2		825	525	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120729	94120729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	104	702	0	ENST00000369303.4:c.322G>A	p.Asp108Asn	p.D108N	ENST00000369303	NM_004440.3	108	Gat/Aat	3/17	1	2	FACETS	0.856	0.771	0.946	0.856	0.771	0.946	CLONAL	1	TRUE	1	0.513614338631273	2		702	473	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117645507	117645507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147114498	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	136	876	1	ENST00000368508.3:c.5629C>T	p.Pro1877Ser	p.P1877S	ENST00000368508	NM_002944.2	1877	Cca/Tca	34/43	0.166148070766615	1	FACETS	0.755	0.691	0.823	0.755	0.691	0.823	INDETERMINATE	1	TRUE	0	0.513614338631273	1		877	521	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199705	138199705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	160	760	0	ENST00000237289.4:c.1123C>T	p.Pro375Ser	p.P375S	ENST00000237289	NM_001270507.1	375	Cct/Tct	7/9	NA	2	FACETS	0.987	0.909	1			1	INDETERMINATE	1	TRUE	NA	0.513614338631273	2		760	631	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527454	157527454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771781497	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	140	596	1	ENST00000346085.5:c.5179G>A	p.Asp1727Asn	p.D1727N	ENST00000346085	NM_020732.3	1727	Gat/Aat	20/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.513614338631273	2		597	484	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468222	50468222	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	185	873	0	ENST00000331340.3:c.1457T>C	p.Phe486Ser	p.F486S	ENST00000331340	NM_006060.4	486	tTc/tCc	8/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.513614338631273	2		873	663	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508381	106508381	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	218	457	0	ENST00000359195.3:c.375G>A	p.Trp125Ter	p.W125*	ENST00000359195	NM_002649.2	125	tgG/tgA	2/11	0.513614338631273	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.513614338631273	3		457	521	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508575	106508575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	104	473	0	ENST00000359195.3:c.569G>A	p.Ser190Asn	p.S190N	ENST00000359195	NM_002649.2	190	aGc/aAc	2/11	0.513614338631273	3	FACETS	1	0.938	1	0.529	0.476	0.585	CLONAL	1	TRUE	1	0.513614338631273	3		473	481	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508642	106508642	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1417633134	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	170	673	0	ENST00000359195.3:c.636G>A	p.Trp212Ter	p.W212*	ENST00000359195	NM_002649.2	212	tgG/tgA	2/11	0.513614338631273	3	FACETS	1	0.979	1	0.585	0.539	0.632	CLONAL	1	TRUE	1	0.513614338631273	3		673	711	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508905	106508905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755134917	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	93	574	0	ENST00000359195.3:c.899G>A	p.Gly300Glu	p.G300E	ENST00000359195	NM_002649.2	300	gGa/gAa	2/11	0.513614338631273	3	FACETS	0.747	0.665	0.834	0.374	0.332	0.417	SUBCLONAL	1	TRUE	1	0.513614338631273	3		574	609	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523522	106523522	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	112	551	1	ENST00000359195.3:c.2674C>T	p.Gln892Ter	p.Q892*	ENST00000359195	NM_002649.2	892	Cag/Tag	8/11	0.513614338631273	3	FACETS	0.988	0.891	1	0.494	0.445	0.545	CLONAL	1	TRUE	1	0.513614338631273	3		552	555	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523601	106523601	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	105	501	0	ENST00000359195.3:c.2753A>G	p.Glu918Gly	p.E918G	ENST00000359195	NM_002649.2	918	gAa/gGa	8/11	0.513614338631273	3	FACETS	1	0.908	1	0.505	0.454	0.558	CLONAL	1	TRUE	1	0.513614338631273	3		501	509	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403175	116403175	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	112	837	0	ENST00000397752.3:c.2436A>T	p.Gln812His	p.Q812H	ENST00000397752	NM_000245.2	812	caA/caT	11/21	0.513614338631273	3	FACETS	0.773	0.696	0.855	0.387	0.348	0.428	SUBCLONAL	1	TRUE	1	0.513614338631273	3		837	709	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453149	140453149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913361	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	109	661	0	ENST00000288602.6:c.1786G>A	p.Gly596Ser	p.G596S	ENST00000288602	NM_004333.4	596	Ggt/Agt	15/18	0.513614338631273	3	FACETS	0.979	0.882	1	0.489	0.441	0.54	CLONAL	1	TRUE	1	0.513614338631273	3		661	545	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140487360	140487360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507472	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	155	958	2	ENST00000288602.6:c.1165C>T	p.Arg389Cys	p.R389C	ENST00000288602	NM_004333.4	389	Cgt/Tgt	9/18	0.513614338631273	3	FACETS	0.923	0.845	1	0.461	0.422	0.502	CLONAL	1	TRUE	1	0.513614338631273	3		960	822	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859965	151859965	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	96	553	0	ENST00000262189.6:c.10697G>A	p.Ser3566Asn	p.S3566N	ENST00000262189	NM_170606.2	3566	aGc/aAc	43/59	0.513614338631273	3	FACETS	0.865	0.773	0.963	0.433	0.386	0.482	CLONAL	1	TRUE	1	0.513614338631273	3		553	543	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879256	151879256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761429170	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	161	684	1	ENST00000262189.6:c.5689C>T	p.Pro1897Ser	p.P1897S	ENST00000262189	NM_170606.2	1897	Cca/Tca	36/59	0.513614338631273	3	FACETS	1	0.936	1	0.511	0.469	0.554	CLONAL	1	TRUE	1	0.513614338631273	3		685	771	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968102	68968102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	108	780	1	ENST00000288368.4:c.1131G>A	p.Met377Ile	p.M377I	ENST00000288368	NM_024870.2	377	atG/atA	10/40	1	2	FACETS	0.773	0.696	0.854	0.773	0.696	0.854	SUBCLONAL	1	TRUE	1	0.513614338631273	2		781	544	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981273	68981273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	75	464	0	ENST00000288368.4:c.1345G>A	p.Asp449Asn	p.D449N	ENST00000288368	NM_024870.2	449	Gat/Aat	12/40	1	2	FACETS	0.854	0.754	0.96	0.854	0.754	0.96	CLONAL	1	TRUE	1	0.513614338631273	2		464	342	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69000044	69000044	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	142	681	1	ENST00000288368.4:c.2113G>A	p.Gly705Arg	p.G705R	ENST00000288368	NM_024870.2	705	Gga/Aga	19/40	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.513614338631273	2		682	493	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009388	69009389	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	143	841	0	ENST00000288368.4:c.2505_2506delinsAA	p.Val836Met	p.V836M	ENST00000288368	NM_024870.2	835	gtGGtg/gtAAtg	22/40	NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.513614338631273	2		841	510	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74858933	74858933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	158	938	0	ENST00000284811.8:c.271C>T	p.Pro91Ser	p.P91S	ENST00000284811		91	Cct/Tct	4/4	NA	2	FACETS	0.945	0.869	1			1	INDETERMINATE	1	TRUE	NA	0.513614338631273	2		938	651	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484186	8484186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	141	799	1	ENST00000356435.5:c.3346G>A	p.Gly1116Arg	p.G1116R	ENST00000356435		1116	Ggg/Agg	19/35	0.513614338631273	1	FACETS	0.99	0.911	1	0.99	0.911	1	CLONAL	1	TRUE	0	0.513614338631273	1		800	412	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486196	8486196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	123	555	0	ENST00000356435.5:c.2621C>T	p.Ser874Phe	p.S874F	ENST00000356435		874	tCt/tTt	17/35	0.513614338631273	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.513614338631273	1		555	336	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636706	8636706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	64	361	0	ENST00000356435.5:c.203G>A	p.Arg68Lys	p.R68K	ENST00000356435		68	aGa/aAa	2/35	0.513614338631273	1	FACETS	0.935	0.824	1	0.935	0.824	1	CLONAL	1	TRUE	0	0.513614338631273	1		361	198	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93636979	93636979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	70	601	1	ENST00000375746.1:c.1029G>A	p.Met343Ile	p.M343I	ENST00000375746	NM_001174167.1	343	atG/atA	9/14	0.166148070766615	1	FACETS	0.513	0.449	0.581	0.513	0.449	0.581	INDETERMINATE	1	TRUE	0	0.513614338631273	1		602	395	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293556	137293556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766062086	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	147	1054	0	ENST00000481739.1:c.107C>T	p.Ser36Phe	p.S36F	ENST00000481739	NM_002957.4	36	tCc/tTc	2/10	0.166148070766615	1	FACETS	0.63	0.577	0.686	0.63	0.577	0.686	INDETERMINATE	1	TRUE	0	0.513614338631273	1		1054	675	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139408990	139408990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	136	1037	2	ENST00000277541.6:c.2179C>T	p.His727Tyr	p.H727Y	ENST00000277541	NM_017617.3	727	Cac/Tac	13/34	0.166148070766615	1	FACETS	0.631	0.575	0.689	0.631	0.575	0.689	INDETERMINATE	1	TRUE	0	0.513614338631273	1		1039	624	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412659	139412659	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	170	1012	0	ENST00000277541.6:c.1185G>T	p.Lys395Asn	p.K395N	ENST00000277541	NM_017617.3	395	aaG/aaT	7/34	0.166148070766615	1	FACETS	0.708	0.653	0.765	0.708	0.653	0.765	INDETERMINATE	1	TRUE	0	0.513614338631273	1		1012	695	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417607	139417607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	214	988	0	ENST00000277541.6:c.437C>T	p.Ser146Phe	p.S146F	ENST00000277541	NM_017617.3	146	tCc/tTc	4/34	0.166148070766615	1	FACETS	0.822	0.767	0.88	0.822	0.767	0.88	INDETERMINATE	1	TRUE	0	0.513614338631273	1		988	753	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314895	1314895	+	incomplete_terminal_codon_variant,coding_sequence_variant	Silent	SNP	T	T	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	101	500	0	ENST00000400841.2:c.766A>T	p.Ter256=	p.*256=	ENST00000400841		256	Ag/Tg	6/6	1	1	FACETS	0.796	0.718	0.878	0.796	0.718	0.878	SUBCLONAL	1	TRUE	0	0.513614338631273	1		500	367	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1331502	1331502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	126	807	0	ENST00000400841.2:c.26G>A	p.Gly9Glu	p.G9E	ENST00000400841		9	gGa/gAa	1/6	1	1	FACETS	0.665	0.605	0.728	0.665	0.605	0.728	SUBCLONAL	1	TRUE	0	0.513614338631273	1		807	548	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224117	53224117	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	161	484	0	ENST00000375401.3:c.3434C>A	p.Ser1145Tyr	p.S1145Y	ENST00000375401	NM_004187.3	1145	tCt/tAt	22/26	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.513614338631273	1		484	320	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225222	53225222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	145	384	0	ENST00000375401.3:c.2996C>T	p.Pro999Leu	p.P999L	ENST00000375401	NM_004187.3	999	cCa/cTa	20/26	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.513614338631273	1		384	289	SUCCESS
AR	367	MSKCC	GRCh37	X	66766538	66766538	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	174	476	2	ENST00000374690.3:c.1550C>T	p.Pro517Leu	p.P517L	ENST00000374690	NM_000044.3	517	cCc/cTc	1/8	1	1	FACETS	0.782	0.734	0.83	1	0.992	1	SUBCLONAL	2	TRUE	0	0.513614338631273	1		478	322	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340967	70340967	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	196	407	0	ENST00000374080.3:c.700G>T	p.Asp234Tyr	p.D234Y	ENST00000374080		234	Gat/Tat	5/45	1	1	FACETS	0.859	0.813	0.906	1	0.994	1	CLONAL	2	TRUE	0	0.513614338631273	1		407	330	SUCCESS
BTK	695	MSKCC	GRCh37	X	100612496	100612496	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	112	377	0	ENST00000308731.7:c.1177+1G>A		p.X393_splice	ENST00000308731	NM_000061.2	393			1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.513614338631273	1		377	247	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500436	99500436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760362276	NA	P-0022019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	246	786	1	ENST00000268035.6:c.3869C>T	p.Pro1290Leu	p.P1290L	ENST00000268035	NM_000875.3	1290	cCg/cTg	21/21	0.304690052872054	3	FACETS	0.821	0.771	0.872	0.821	0.771	0.872	INDETERMINATE	2	TRUE	1	0.513614338631273	3		787	733	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0022042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	216	306	0				ENST00000310581	NM_198253.2	-/1132			0.764872944389442	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.813561384414223	3		306	347	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0022042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	250	528	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.813561384414223	2		528	608	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725567	117725567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767519397	NA	P-0022042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	242	553	0	ENST00000368508.3:c.314C>T	p.Pro105Leu	p.P105L	ENST00000368508	NM_002944.2	105	cCc/cTc	5/43	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.813561384414223	2		553	524	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069613	69069613	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	226	539	1	ENST00000288368.4:c.4288C>T	p.Gln1430Ter	p.Q1430*	ENST00000288368	NM_024870.2	1430	Caa/Taa	35/40	0.813561384414223	3	FACETS	0.984	0.92	1	0.492	0.46	0.526	CLONAL	1	TRUE	1	0.813561384414223	3		540	794	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143994	11143994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	206	503	0	ENST00000358026.2:c.3575G>A	p.Arg1192His	p.R1192H	ENST00000358026	NM_001128849.1	1192	cGc/cAc	26/36	1	2	FACETS	0.989	0.926	1	0.989	0.926	1	CLONAL	1	TRUE	1	0.813561384414223	2		503	512	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341734	8341734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	194	652	1	ENST00000356435.5:c.4906G>A	p.Glu1636Lys	p.E1636K	ENST00000356435		1636	Gaa/Aaa	29/35	0.808667756995495	1	FACETS	0.847	0.8	0.894	0.847	0.8	0.894	CLONAL	1	TRUE	0	0.813561384414223	1		653	334	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332853	153332853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751626529	NA	P-0022042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	260	566	0	ENST00000281708.4:c.103C>T	p.Arg35Cys	p.R35C	ENST00000281708	NM_033632.3	35	Cgt/Tgt	2/12	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.813561384414223	2		566	619	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750677	128750678	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0022042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	383	567	1	ENST00000377970.2:c.214_215delinsTT	p.Pro72Phe	p.P72F	ENST00000377970	NM_002467.4	72	CCc/TTc	2/3	0.813561384414223	3	FACETS	0.958	0.919	0.997	0.958	0.919	0.997	CLONAL	2	TRUE	1	0.813561384414223	3		568	691	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851734	63851734	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377304813	NA	P-0022042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	280	700	0	ENST00000279873.7:c.2512C>T	p.His838Tyr	p.H838Y	ENST00000279873	NM_032199.2	838	Cat/Tat	10/10	1	2	FACETS	0.99	0.936	1	0.99	0.936	1	CLONAL	1	TRUE	1	0.813561384414223	2		700	695	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99482482	99482482	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	236	628	2	ENST00000268035.6:c.3350G>T	p.Gly1117Val	p.G1117V	ENST00000268035	NM_000875.3	1117	gGa/gTa	18/21	1	2	FACETS	0.978	0.92	1	0.978	0.92	1	CLONAL	1	TRUE	1	0.813561384414223	2		630	593	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639161	3639161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs565491187	NA	P-0022042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	218	672	1	ENST00000294008.3:c.4478C>T	p.Ser1493Leu	p.S1493L	ENST00000294008	NM_032444.2	1493	tCg/tTg	12/15	1	2	FACETS	0.966	0.906	1	0.966	0.906	1	CLONAL	1	TRUE	1	0.813561384414223	2		673	555	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349937	89349937	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	312	881	0	ENST00000301030.4:c.3013C>T	p.Pro1005Ser	p.P1005S	ENST00000301030	NM_001256183.1	1005	Cca/Tca	9/13	1	2	FACETS	0.938	0.888	0.988	0.938	0.888	0.988	CLONAL	1	TRUE	1	0.813561384414223	2		881	818	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579421	7579421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881994	NA	P-0022042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	262	651	1	ENST00000269305.4:c.266C>T	p.Pro89Leu	p.P89L	ENST00000269305	NM_001126112.2	89	cCc/cTc	4/11	1	2	FACETS	0.983	0.928	1	0.983	0.928	1	CLONAL	1	TRUE	1	0.813561384414223	2		652	655	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37863384	37863384	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	242	603	0	ENST00000269571.5:c.215C>T	p.Ser72Phe	p.S72F	ENST00000269571		72	tCc/tTc	2/27	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.813561384414223	2		603	573	SUCCESS
AR	367	MSKCC	GRCh37	X	66905909	66905909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137852576	NA	P-0022042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	203	510	0	ENST00000374690.3:c.1826G>A	p.Arg609Lys	p.R609K	ENST00000374690	NM_000044.3	609	aGg/aAg	3/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.813561384414223	2		510	468	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875980	76875980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	188	436	0	ENST00000373344.5:c.5155G>A	p.Asp1719Asn	p.D1719N	ENST00000373344	NM_000489.3	1719	Gat/Aat	20/35	1	2	FACETS	0.985	0.92	1	0.985	0.92	1	CLONAL	1	TRUE	1	0.813561384414223	2		436	469	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907783	76907783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	188	390	1	ENST00000373344.5:c.4378G>A	p.Glu1460Lys	p.E1460K	ENST00000373344	NM_000489.3	1460	Gaa/Aaa	15/35	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.813561384414223	2		391	453	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0022057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	439	528	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.617792992380122	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.617792992380122	2		528	658	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561263	9561263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769939031	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	320	485	0	ENST00000353224.5:c.519G>A	p.Met173Ile	p.M173I	ENST00000353224	NM_177990.2	173	atG/atA	4/10	0.211853346667648	4	FACETS	0.893	0.849	0.939	1	0.996	1	CLONAL	4	TRUE	2	0.316436079745705	4		485	745	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421528	32421528	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	205	638	0	ENST00000332351.3:c.1064G>A	p.Arg355Lys	p.R355K	ENST00000332351	NM_024426.4	355	aGa/aAa	6/10	0.255961656384795	4	FACETS	0.947	0.879	1	0.947	0.879	1	CLONAL	2	TRUE	2	0.316436079745705	4		638	901	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444311	50444311	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778251001	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	201	364	2	ENST00000331340.3:c.241G>A	p.Asp81Asn	p.D81N	ENST00000331340	NM_006060.4	81	Gat/Aat	4/8	0.316436079745705	7	FACETS	1	0.938	1	0.505	0.469	0.542	CLONAL	3	TRUE	1	0.316436079745705	7		366	751	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579717	7579717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs922736614	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	134	669	0	ENST00000269305.4:c.79C>T	p.Pro27Ser	p.P27S	ENST00000269305	NM_001126112.2	27	Cct/Tct	3/11	0.316436079745705	3	FACETS	1	0.959	1	0.55	0.499	0.603	CLONAL	1	TRUE	1	0.316436079745705	3		669	892	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	242	409	1	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.316436079745705	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.316436079745705	2		410	642	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	256	151	0				ENST00000310581	NM_198253.2	-/1132			0.298430461549645	3	FACETS	0.908	0.855	0.962	1	0.992	1	CLONAL	3	TRUE	1	0.316436079745705	3		151	688	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468158	50468158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	538	566	1	ENST00000331340.3:c.1393G>A	p.Glu465Lys	p.E465K	ENST00000331340	NM_006060.4	465	Gaa/Aaa	8/8	0.316436079745705	7	FACETS	0.944	0.91	0.979	0.944	0.91	0.979	CLONAL	6	TRUE	1	0.316436079745705	7		567	1075	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1227	234	939	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	0.299039696044504	3	FACETS	1	0.983	1	0.391	0.363	0.419	CLONAL	1	TRUE	0	0.316436079745705	3		939	1461	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857436	9857436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	95	529	0	ENST00000330684.3:c.3965G>A	p.Gly1322Glu	p.G1322E	ENST00000330684	NM_001134407.1	1322	gGa/gAa	13/13	0.316436079745705	3	FACETS	1	0.963	1	0.592	0.528	0.66	CLONAL	1	TRUE	1	0.316436079745705	3		529	587	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658501	117658501	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	143	532	0	ENST00000368508.3:c.5082G>A	p.Trp1694Ter	p.W1694*	ENST00000368508	NM_002944.2	1694	tgG/tgA	31/43	0.211853346667648	4	FACETS	0.893	0.816	0.973	0.893	0.816	0.973	CLONAL	2	TRUE	2	0.316436079745705	4		532	666	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	308	747	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.316436079745705	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.316436079745705	3		747	1007	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877444	40877444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	163	479	0	ENST00000373198.4:c.2252C>T	p.Ser751Phe	p.S751F	ENST00000373198	NM_133170.3	751	tCt/tTt	15/32	0.211853346667648	4	FACETS	0.947	0.871	1	0.947	0.871	1	CLONAL	2	TRUE	2	0.316436079745705	4		479	716	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244913	123244913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1224606327	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	294	931	0	ENST00000358487.5:c.2191G>A	p.Glu731Lys	p.E731K	ENST00000358487	NM_000141.4	731	Gaa/Aaa	16/18	0.125808510408456	3	FACETS	1	0.947	1			1	INDETERMINATE	2	TRUE	NA	0.316436079745705	3		931	1070	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858517	9858517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765370528	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	94	561	1	ENST00000330684.3:c.2884G>A	p.Glu962Lys	p.E962K	ENST00000330684	NM_001134407.1	962	Gaa/Aaa	13/13	0.316436079745705	3	FACETS	0.975	0.868	1	0.487	0.434	0.545	CLONAL	1	TRUE	1	0.316436079745705	3		562	706	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197342	94197342	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375223186	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	180	609	0	ENST00000323929.3:c.1162C>T	p.Arg388Trp	p.R388W	ENST00000323929	NM_005591.3	388	Cgg/Tgg	11/20	0.316436079745705	5	FACETS	0.917	0.846	0.991	0.611	0.564	0.661	CLONAL	2	TRUE	2	0.316436079745705	5		609	915	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609673	28609673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	123	676	0	ENST00000241453.7:c.1556C>T	p.Ser519Phe	p.S519F	ENST00000241453	NM_004119.2	519	tCc/tTc	12/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.316436079745705	2		676	674	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206911	162206911	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	140	375	0	ENST00000366898.1:c.764C>T	p.Ser255Phe	p.S255F	ENST00000366898	NM_004562.2	255	tCc/tTc	7/12	0.211853346667648	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.316436079745705	4		375	506	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500876	149500876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	235	699	0	ENST00000261799.4:c.2354G>A	p.Arg785Lys	p.R785K	ENST00000261799	NM_002609.3	785	aGg/aAg	17/23	1	2	FACETS	0.976	0.914	1	1	0.994	1	CLONAL	2	TRUE	1	0.316436079745705	2		699	761	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220715	1220715	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	328	543	0	ENST00000326873.7:c.733C>T	p.Leu245Phe	p.L245F	ENST00000326873	NM_000455.4	245	Ctc/Ttc	5/10	0.316436079745705	2	FACETS	0.894	0.85	0.939	1	0.994	1	CLONAL	3	TRUE	0	0.316436079745705	2		543	773	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852608	63852608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	115	542	0	ENST00000279873.7:c.3386G>A	p.Gly1129Glu	p.G1129E	ENST00000279873	NM_032199.2	1129	gGa/gAa	10/10	0.316436079745705	3	FACETS	1	0.974	1	0.615	0.555	0.679	CLONAL	1	TRUE	1	0.316436079745705	3		542	684	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424958105	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	147	487	0	ENST00000334344.6:c.940C>T	p.Arg314Cys	p.R314C	ENST00000334344	NM_152641.2	314	Cgt/Tgt	8/21	0.292664238505699	4	FACETS	0.874	0.799	0.951	0.874	0.799	0.951	CLONAL	2	TRUE	2	0.316436079745705	4		487	700	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289974	15289974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265439284	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	356	861	0	ENST00000263388.2:c.3580C>T	p.Pro1194Ser	p.P1194S	ENST00000263388	NM_000435.2	1194	Ccc/Tcc	22/33	0.257642227341294	5	FACETS	0.939	0.89	0.989	0.939	0.89	0.989	CLONAL	3	TRUE	2	0.316436079745705	5		861	1178	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589808	28589808	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568745490	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	84	537	0	ENST00000241453.7:c.2572G>A	p.Glu858Lys	p.E858K	ENST00000241453	NM_004119.2	858	Gaa/Aaa	21/24	1	2	FACETS	0.868	0.767	0.975	0.868	0.767	0.975	CLONAL	1	TRUE	1	0.316436079745705	2		537	612	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457642	67457642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	122	765	0	ENST00000327367.4:c.452C>T	p.Pro151Leu	p.P151L	ENST00000327367	NM_005902.3	151	cCc/cTc	3/9	0.298430461549645	3	FACETS	0.94	0.849	1	0.47	0.424	0.519	CLONAL	1	TRUE	1	0.316436079745705	3		765	950	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699293	18699293	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	212	467	0	ENST00000266497.5:c.3394C>T	p.Gln1132Ter	p.Q1132*	ENST00000266497		1132	Caa/Taa	24/31	0.30532238783832	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	0	0.316436079745705	3		467	466	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561124	9561124	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	121	389	1	ENST00000353224.5:c.658C>T	p.Gln220Ter	p.Q220*	ENST00000353224	NM_177990.2	220	Cag/Tag	4/10	0.211853346667648	4	FACETS	0.946	0.859	1	0.946	0.859	1	CLONAL	2	TRUE	2	0.316436079745705	4		390	532	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831220	3831220	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1168098333	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	187	445	1	ENST00000262367.5:c.1661C>T	p.Ser554Phe	p.S554F	ENST00000262367	NM_004380.2	554	tCc/tTc	7/31	0.316436079745705	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.316436079745705	3		446	624	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408912	41408912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	122	444	1	ENST00000373198.4:c.514G>A	p.Gly172Ser	p.G172S	ENST00000373198	NM_133170.3	172	Ggt/Agt	4/32	0.211853346667648	4	FACETS	0.911	0.827	0.999	0.911	0.827	0.999	CLONAL	2	TRUE	2	0.316436079745705	4		445	557	SUCCESS
AR	367	MSKCC	GRCh37	X	66765647	66765647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	336	454	0	ENST00000374690.3:c.659C>T	p.Ser220Phe	p.S220F	ENST00000374690	NM_000044.3	220	tCc/tTc	1/8	0.264328027797468	2	FACETS	1	0.991	1			1	CLONAL	3	TRUE	NA	0.316436079745705	2		454	625	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129652	2129652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373939435	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	116	867	2	ENST00000219476.3:c.3379C>T	p.Arg1127Trp	p.R1127W	ENST00000219476	NM_000548.3	1127	Cgg/Tgg	29/42	0.316436079745705	3	FACETS	0.899	0.809	0.994	0.449	0.404	0.497	CLONAL	1	TRUE	1	0.316436079745705	3		869	945	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804359	43804359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749391587	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	298	552	1	ENST00000372470.3:c.359G>A	p.Arg120Gln	p.R120Q	ENST00000372470	NM_005373.2	120	cGg/cAg	3/12	0.306899516182267	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	1	0.316436079745705	4		553	764	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964477	93964477	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	123	618	0	ENST00000369303.4:c.2420C>T	p.Ala807Val	p.A807V	ENST00000369303	NM_004440.3	807	gCc/gTc	14/17	0.211853346667648	4	FACETS	1	0.982	1	0.683	0.618	0.752	CLONAL	1	TRUE	2	0.316436079745705	4		618	749	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588733	29588733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	97	304	0	ENST00000356175.3:c.4519C>T	p.His1507Tyr	p.H1507Y	ENST00000356175	NM_000267.3	1507	Cat/Tat	34/57	0.316436079745705	3	FACETS	0.879	0.789	0.973	0.879	0.789	0.973	CLONAL	2	TRUE	1	0.316436079745705	3		304	404	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265314	152265314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781741770	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	106	325	0	ENST00000206249.3:c.767G>A	p.Arg256Gln	p.R256Q	ENST00000206249	NM_000125.3	256	cGa/cAa	4/8	0.211853346667648	4	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	2	0.316436079745705	4		325	406	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39595510	39595510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	215	410	0	ENST00000262039.4:c.1396C>T	p.Pro466Ser	p.P466S	ENST00000262039	NM_002647.2	466	Cca/Tca	12/25	0.30532238783832	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	0	0.316436079745705	3		410	471	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905494	50905494	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	411	948	1	ENST00000440232.2:c.622C>T	p.Pro208Ser	p.P208S	ENST00000440232	NM_002691.3	208	Ccg/Tcg	6/27	0.257642227341294	5	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	2	0.316436079745705	5		949	1185	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	252	240	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.316436079745705	NA		240	633	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992737	68992737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200411060	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	296	806	0	ENST00000288368.4:c.1702G>A	p.Glu568Lys	p.E568K	ENST00000288368	NM_024870.2	568	Gaa/Aaa	16/40	0.316436079745705	5	FACETS	0.927	0.874	0.981	0.927	0.874	0.981	CLONAL	3	TRUE	2	0.316436079745705	5		806	992	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108091	30108091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80271647	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	176	608	1	ENST00000331968.5:c.716C>T	p.Ser239Leu	p.S239L	ENST00000331968	NM_002742.2	239	tCg/tTg	5/18	0.211853346667648	4	FACETS	0.979	0.904	1	0.979	0.904	1	CLONAL	2	TRUE	2	0.316436079745705	4		609	748	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965985	18965985	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	330	710	0	ENST00000262803.5:c.1478C>T	p.Pro493Leu	p.P493L	ENST00000262803	NM_002911.3	493	cCg/cTg	11/24	0.257642227341294	5	FACETS	0.938	0.887	0.99	0.938	0.887	0.99	CLONAL	3	TRUE	2	0.316436079745705	5		710	1093	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645919	67645919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	114	612	2	ENST00000264010.4:c.847C>T	p.Arg283Cys	p.R283C	ENST00000264010	NM_006565.3	283	Cgt/Tgt	4/12	0.316436079745705	3	FACETS	1	0.944	1			1	CLONAL	1	TRUE	NA	0.316436079745705	3		614	780	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458273	12458273	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	129	650	0	ENST00000287820.6:c.890C>T	p.Pro297Leu	p.P297L	ENST00000287820	NM_015869.4	297	cCc/cTc	6/7	0.316436079745705	3	FACETS	1	0.972	1	0.592	0.537	0.651	CLONAL	1	TRUE	1	0.316436079745705	3		650	797	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628185	187628185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767176687	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	218	733	0	ENST00000441802.2:c.2797C>T	p.Arg933Cys	p.R933C	ENST00000441802	NM_005245.3	933	Cgt/Tgt	2/27	0.316436079745705	2	FACETS	0.954	0.891	1	0.954	0.891	1	CLONAL	2	TRUE	0	0.316436079745705	2		733	722	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174907	11174907	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	323	697	0	ENST00000361445.4:c.7127C>T	p.Pro2376Leu	p.P2376L	ENST00000361445	NM_004958.3	2376	cCa/cTa	52/58	0.298805555152404	4	FACETS	0.935	0.885	0.986			1	CLONAL	3	TRUE	NA	0.316436079745705	4		697	958	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199421	16199421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749477752	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	77	407	1	ENST00000375759.3:c.194C>T	p.Ser65Leu	p.S65L	ENST00000375759	NM_015001.2	65	tCg/tTg	2/15	0.298805555152404	4	FACETS	1	0.881	1			1	CLONAL	1	TRUE	NA	0.316436079745705	4		408	639	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057758	27057758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	186	926	1	ENST00000324856.7:c.1466C>T	p.Pro489Leu	p.P489L	ENST00000324856	NM_006015.4	489	cCa/cTa	3/20	0.306899516182267	4	FACETS	1	0.959	1	0.355	0.327	0.385	CLONAL	1	TRUE	1	0.316436079745705	4		927	1453	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27093034	27093034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775307425	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	65	449	0	ENST00000324856.7:c.2965C>T	p.Pro989Ser	p.P989S	ENST00000324856	NM_006015.4	989	Ccc/Tcc	10/20	0.306899516182267	4	FACETS	0.837	0.726	0.958	0.279	0.242	0.32	CLONAL	1	TRUE	1	0.316436079745705	4		449	646	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599203	28599203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	146	853	0	ENST00000253063.3:c.649C>T	p.Leu217Phe	p.L217F	ENST00000253063	NM_031459.4	217	Ctc/Ttc	5/10	0.306899516182267	4	FACETS	1	0.957	1	0.361	0.329	0.395	CLONAL	1	TRUE	1	0.316436079745705	4		853	1121	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363484	40363484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	124	660	1	ENST00000397332.2:c.745C>T	p.Pro249Ser	p.P249S	ENST00000397332	NM_001033082.2	249	Cct/Tct	3/3	0.306899516182267	4	FACETS	1	0.958	1	0.37	0.334	0.408	CLONAL	1	TRUE	1	0.316436079745705	4		661	930	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803559	43803559	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557462648	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	96	715	0	ENST00000372470.3:c.40C>T	p.Leu14Phe	p.L14F	ENST00000372470	NM_005373.2	14	Ctc/Ttc	1/12	0.306899516182267	4	FACETS	0.859	0.764	0.96	0.286	0.254	0.32	CLONAL	1	TRUE	1	0.316436079745705	4		715	930	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263162	115263162	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	113	499	0	ENST00000438362.2:c.2188C>T	p.Gln730Ter	p.Q730*	ENST00000438362	NM_001242891.1	730	Cag/Tag	17/20	0.306899516182267	4	FACETS	1	0.973	1	0.412	0.371	0.456	CLONAL	1	TRUE	1	0.316436079745705	4		499	760	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458512	120458512	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	347	608	1	ENST00000256646.2:c.6833C>T	p.Thr2278Ile	p.T2278I	ENST00000256646	NM_024408.3	2278	aCc/aTc	34/34	0.306899516182267	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	1	0.316436079745705	4		609	899	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458650	120458650	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	104	526	1	ENST00000256646.2:c.6695C>T	p.Ser2232Phe	p.S2232F	ENST00000256646	NM_024408.3	2232	tCt/tTt	34/34	0.306899516182267	4	FACETS	1	0.946	1	0.364	0.325	0.405	CLONAL	1	TRUE	1	0.316436079745705	4		527	793	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471794	120471794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	88	475	0	ENST00000256646.2:c.3697C>T	p.Pro1233Ser	p.P1233S	ENST00000256646	NM_024408.3	1233	Ccc/Tcc	23/34	0.306899516182267	4	FACETS	0.989	0.876	1	0.33	0.292	0.37	CLONAL	1	TRUE	1	0.316436079745705	4		475	740	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844178	156844178	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	181	843	2	ENST00000524377.1:c.1181C>T	p.Ser394Phe	p.S394F	ENST00000524377	NM_002529.3	394	tCc/tTc	9/17	0.281298822213628	5	FACETS	1	0.982	1	0.307	0.282	0.333	CLONAL	1	TRUE	1	0.316436079745705	5		845	1375	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318826	163318826	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	123	513	2	ENST00000271452.3:c.1216C>T	p.Gln406Ter	p.Q406*	ENST00000271452	NM_145697.2	406	Caa/Taa	13/14	0.281298822213628	5	FACETS	0.889	0.805	0.976	0.444	0.402	0.488	CLONAL	2	TRUE	1	0.316436079745705	5		515	645	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666617	206666617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	101	663	0	ENST00000367120.3:c.1951C>T	p.His651Tyr	p.H651Y	ENST00000367120	NM_014002.3	651	Cac/Tac	20/22	0.316436079745705	3	FACETS	0.912	0.814	1	0.456	0.407	0.508	CLONAL	1	TRUE	1	0.316436079745705	3		663	811	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944311	206944311	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	109	600	1	ENST00000423557.1:c.319G>A	p.Ala107Thr	p.A107T	ENST00000423557	NM_000572.2	107	Gcg/Acg	3/5	0.316436079745705	3	FACETS	0.844	0.757	0.937	0.422	0.378	0.469	CLONAL	1	TRUE	1	0.316436079745705	3		601	945	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097751	8097751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	134	701	0	ENST00000346208.3:c.133G>A	p.Glu45Lys	p.E45K	ENST00000346208		45	Gag/Aag	2/6	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.316436079745705	2		701	798	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623649	43623649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	219	662	0	ENST00000355710.3:c.3277G>A	p.Asp1093Asn	p.D1093N	ENST00000355710	NM_020975.4	1093	Gat/Aat	20/20	1	2	FACETS	0.869	0.811	0.93	1	0.993	1	CLONAL	2	TRUE	1	0.316436079745705	2		662	796	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104264001	104264001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	289	590	0	ENST00000369902.3:c.92C>T	p.Pro31Leu	p.P31L	ENST00000369902	NM_016169.3	31	cCc/cTc	1/12	0.316436079745705	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.316436079745705	3		590	937	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123245042	123245042	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	66	409	1	ENST00000358487.5:c.2062T>A	p.Ser688Thr	p.S688T	ENST00000358487	NM_000141.4	688	Tcc/Acc	16/18	0.125808510408456	3	FACETS	1	0.879	1			1	INDETERMINATE	1	TRUE	NA	0.316436079745705	3		410	478	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123260373	123260373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	111	690	0	ENST00000358487.5:c.1528G>A	p.Glu510Lys	p.E510K	ENST00000358487	NM_000141.4	510	Gag/Aag	11/18	0.125808510408456	3	FACETS	0.86	0.772	0.953			1	INDETERMINATE	1	TRUE	NA	0.316436079745705	3		690	945	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263314	123263314	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	153	494	0	ENST00000358487.5:c.1429C>T	p.Pro477Ser	p.P477S	ENST00000358487	NM_000141.4	477	Cca/Tca	10/18	0.125808510408456	3	FACETS	1	0.951	1			1	INDETERMINATE	2	TRUE	NA	0.316436079745705	3		494	536	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200282	67200282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	242	658	3	ENST00000312629.5:c.590C>T	p.Pro197Leu	p.P197L	ENST00000312629	NM_003952.2	197	cCc/cTc	7/15	0.255961656384795	4	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	2	0.316436079745705	4		661	994	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589816	69589816	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	51	112	0	ENST00000168712.1:c.37C>T	p.Pro13Ser	p.P13S	ENST00000168712	NM_002007.2	13	Ccg/Tcg	1/3	0.255961656384795	4	FACETS	0.907	0.787	1	1	0.963	1	CLONAL	3	TRUE	2	0.316436079745705	4		112	156	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625447	69625447	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs79472069	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	248	756	0	ENST00000334134.2:c.346G>A	p.Glu116Lys	p.E116K	ENST00000334134	NM_005247.2	116	Gag/Aag	3/3	0.255961656384795	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.316436079745705	4		756	986	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933211	100933211	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	270	598	0	ENST00000325455.5:c.2179C>T	p.Leu727Phe	p.L727F	ENST00000325455	NM_001202474.3	727	Ctt/Ttt	4/8	0.316436079745705	5	FACETS	1	0.947	1	1	0.947	1	CLONAL	3	TRUE	2	0.316436079745705	5		598	833	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173613	108173613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	116	475	0	ENST00000278616.4:c.5353C>T	p.Pro1785Ser	p.P1785S	ENST00000278616	NM_000051.3	1785	Cct/Tct	36/63	0.316436079745705	2	FACETS	0.871	0.791	0.954	0.871	0.791	0.954	CLONAL	2	TRUE	0	0.316436079745705	2		475	421	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149245	119149245	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	214	644	0	ENST00000264033.4:c.1253T>G	p.Phe418Cys	p.F418C	ENST00000264033	NM_005188.3	418	tTc/tGc	9/16	0.316436079745705	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	0	0.316436079745705	2		644	673	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006405	12006405	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	343	543	0	ENST00000396373.4:c.375del	p.Lys125AsnfsTer84	p.K125Nfs*84	ENST00000396373	NM_001987.4	125	Aaa/aa	4/8	0.316436079745705	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.316436079745705	3		543	739	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125015	46125015	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	80	299	1	ENST00000334344.6:c.202C>T	p.Gln68Ter	p.Q68*	ENST00000334344	NM_152641.2	68	Cag/Tag	3/21	0.292664238505699	4	FACETS	1	0.977	1	0.748	0.661	0.84	CLONAL	1	TRUE	2	0.316436079745705	4		300	445	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444558	49444558	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	220	717	0	ENST00000301067.7:c.2813C>T	p.Pro938Leu	p.P938L	ENST00000301067	NM_003482.3	938	cCa/cTa	11/54	0.292664238505699	4	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	2	0.316436079745705	4		717	907	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445686	49445686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565819376	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	402	1097	0	ENST00000301067.7:c.1780C>T	p.Pro594Ser	p.P594S	ENST00000301067	NM_003482.3	594	Ccg/Tcg	10/54	0.292664238505699	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.316436079745705	4		1097	1541	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446731	49446731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	244	528	0	ENST00000301067.7:c.1079C>T	p.Ser360Phe	p.S360F	ENST00000301067	NM_003482.3	360	tCc/tTc	8/54	0.292664238505699	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.316436079745705	4		528	860	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858615	57858615	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	214	694	0	ENST00000228682.2:c.353G>A	p.Gly118Glu	p.G118E	ENST00000228682	NM_005269.2	118	gGa/gAa	4/12	0.292664238505699	4	FACETS	0.857	0.796	0.92	0.857	0.796	0.92	CLONAL	2	TRUE	2	0.316436079745705	4		694	1039	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858996	57858996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	285	723	0	ENST00000228682.2:c.492G>A	p.Met164Ile	p.M164I	ENST00000228682	NM_005269.2	164	atG/atA	5/12	0.292664238505699	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.316436079745705	4		723	1150	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110031	115110031	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	299	857	0	ENST00000257566.3:c.1847C>T	p.Ser616Phe	p.S616F	ENST00000257566	NM_016569.3	616	tCt/tTt	8/8	0.292664238505699	4	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	2	0.316436079745705	4		857	1234	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435363	121435386	+	inframe_deletion	In_Frame_Del	DEL	CAGCCGCTGCACCCCTCCTACCAG	CAGCCGCTGCACCCCTCCTACCAG	-	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	201	728	0	ENST00000257555.6:c.1404_1427del	p.His469_Leu476del	p.H469_L476del	ENST00000257555		466	CAGCCGCTGCACCCCTCCTACCAG/-	7/10	0.292664238505699	4	FACETS	0.822	0.762	0.885	0.822	0.762	0.885	CLONAL	2	TRUE	2	0.316436079745705	4		728	1017	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893575	28893575	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	82	481	2	ENST00000282397.4:c.3271del	p.Glu1091LysfsTer5	p.E1091Kfs*5	ENST00000282397	NM_002019.4	1091	Gaa/aa	24/30	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.316436079745705	2		483	511	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004306	29004306	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	51	357	0	ENST00000282397.4:c.989-2A>T		p.X330_splice	ENST00000282397	NM_002019.4	330			1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.316436079745705	2		357	321	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968947	32968947	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	61	514	0	ENST00000380152.3:c.9378G>C	p.Gln3126His	p.Q3126H	ENST00000380152		3126	caG/caC	25/27	1	2	FACETS	0.73	0.63	0.838	0.73	0.63	0.838	SUBCLONAL	1	TRUE	1	0.316436079745705	2		514	528	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762084	43762084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772476521	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	117	631	0	ENST00000382044.4:c.1361C>T	p.Pro454Leu	p.P454L	ENST00000382044	NM_001141980.1	454	cCt/cTt	11/28	0.298430461549645	3	FACETS	1	0.938	1	0.527	0.475	0.582	CLONAL	1	TRUE	1	0.316436079745705	3		631	812	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996237	73996237	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	106	295	0	ENST00000318443.5:c.971C>T	p.Ser324Phe	p.S324F	ENST00000318443	NM_001024736.1	324	tCc/tTc	5/10	0.298430461549645	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.316436079745705	3		295	332	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3929883	3929883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	133	668	0	ENST00000262367.5:c.35C>T	p.Pro12Leu	p.P12L	ENST00000262367	NM_004380.2	12	cCc/cTc	1/31	0.316436079745705	3	FACETS	1	0.958	1	0.549	0.498	0.602	CLONAL	1	TRUE	1	0.316436079745705	3		668	887	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858037	9858037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	83	628	0	ENST00000330684.3:c.3364G>A	p.Gly1122Ser	p.G1122S	ENST00000330684	NM_001134407.1	1122	Ggt/Agt	13/13	0.316436079745705	3	FACETS	0.869	0.767	0.979	0.435	0.383	0.49	CLONAL	1	TRUE	1	0.316436079745705	3		628	699	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831620	72831620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	228	666	0	ENST00000268489.5:c.4961C>T	p.Pro1654Leu	p.P1654L	ENST00000268489	NM_006885.3	1654	cCt/cTt	9/10	0.316436079745705	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.316436079745705	3		666	756	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965117	81965117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11548655	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	116	618	0	ENST00000359376.3:c.2597G>A	p.Gly866Glu	p.G866E	ENST00000359376	NM_002661.3	866	gGa/gAa	25/33	0.316436079745705	3	FACETS	1	0.955	1	0.552	0.498	0.61	CLONAL	1	TRUE	1	0.316436079745705	3		618	769	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81973526	81973526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372606303	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	188	569	0	ENST00000359376.3:c.3343C>T	p.Pro1115Ser	p.P1115S	ENST00000359376	NM_002661.3	1115	Cca/Tca	30/33	0.316436079745705	3	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	1	0.316436079745705	3		569	683	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032471	12032471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	153	373	0	ENST00000353533.5:c.907G>A	p.Gly303Ser	p.G303S	ENST00000353533	NM_003010.3	303	Ggc/Agc	9/11	0.316436079745705	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.316436079745705	3		373	496	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562976	29562976	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	106	632	0	ENST00000356175.3:c.3911T>G	p.Leu1304Ter	p.L1304*	ENST00000356175	NM_000267.3	1304	tTa/tGa	29/57	0.316436079745705	3	FACETS	1	0.938	1	0.532	0.477	0.591	CLONAL	1	TRUE	1	0.316436079745705	3		632	729	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588778	29588778	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	133	413	0	ENST00000356175.3:c.4564C>T	p.Leu1522Phe	p.L1522F	ENST00000356175	NM_000267.3	1522	Ctt/Ttt	34/57	0.316436079745705	3	FACETS	0.89	0.812	0.971	0.89	0.812	0.971	CLONAL	2	TRUE	1	0.316436079745705	3		413	547	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663385	29663385	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	149	558	0	ENST00000356175.3:c.5978T>A	p.Phe1993Tyr	p.F1993Y	ENST00000356175	NM_000267.3	1993	tTc/tAc	40/57	0.316436079745705	3	FACETS	0.795	0.728	0.865	0.795	0.728	0.865	SUBCLONAL	2	TRUE	1	0.316436079745705	3		558	686	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872643	37872643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746476368	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	313	923	0	ENST00000269571.5:c.1603C>T	p.Leu535Phe	p.L535F	ENST00000269571		535	Ctt/Ttt	13/27	0.316436079745705	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.316436079745705	3		923	1075	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359693	40359693	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	126	609	0	ENST00000293328.3:c.1960C>T	p.Arg654Trp	p.R654W	ENST00000293328	NM_012448.3	654	Cgg/Tgg	16/19	0.316436079745705	3	FACETS	1	0.973	1	0.601	0.545	0.661	CLONAL	1	TRUE	1	0.316436079745705	3		609	767	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359735	40359735	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	94	470	0	ENST00000293328.3:c.1918T>G	p.Phe640Val	p.F640V	ENST00000293328	NM_012448.3	640	Ttt/Gtt	16/19	0.316436079745705	3	FACETS	1	0.949	1	0.557	0.496	0.621	CLONAL	1	TRUE	1	0.316436079745705	3		470	618	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435024	56435024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	208	667	0	ENST00000407977.2:c.2113G>A	p.Gly705Ser	p.G705S	ENST00000407977		705	Ggc/Agc	9/10	0.316436079745705	7	FACETS	0.932	0.864	1	0.311	0.288	0.335	CLONAL	2	TRUE	1	0.316436079745705	7		667	1263	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436148	56436148	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760556127	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	242	640	1	ENST00000407977.2:c.989G>A	p.Arg330Gln	p.R330Q	ENST00000407977		330	cGa/cAa	9/10	0.316436079745705	7	FACETS	1	0.963	1	0.35	0.326	0.375	CLONAL	2	TRUE	1	0.316436079745705	7		641	1305	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56811539	56811539	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	194	592	0	ENST00000337432.4:c.1087T>A	p.Leu363Met	p.L363M	ENST00000337432	NM_058216.2	363	Ttg/Atg	9/9	0.316436079745705	7	FACETS	1	0.943	1	0.341	0.315	0.368	CLONAL	2	TRUE	1	0.316436079745705	7		592	1073	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63531750	63531750	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1228679390	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	153	674	0	ENST00000307078.5:c.2231C>T	p.Pro744Leu	p.P744L	ENST00000307078	NM_004655.3	744	cCa/cTa	9/11	0.316436079745705	7	FACETS	0.755	0.689	0.824	0.252	0.229	0.275	SUBCLONAL	2	TRUE	1	0.316436079745705	7		674	1147	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936846	78936846	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	161	537	0	ENST00000306801.3:c.3928C>T	p.His1310Tyr	p.H1310Y	ENST00000306801	NM_020761.2	1310	Cac/Tac	33/34	0.316436079745705	7	FACETS	0.973	0.892	1	0.324	0.297	0.353	CLONAL	2	TRUE	1	0.316436079745705	7		537	937	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7120734	7120734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	238	758	0	ENST00000302850.5:c.3556G>A	p.Glu1186Lys	p.E1186K	ENST00000302850	NM_000208.2	1186	Gaa/Aaa	20/22	0.257642227341294	5	FACETS	0.948	0.884	1	0.632	0.589	0.676	CLONAL	2	TRUE	2	0.316436079745705	5		758	1170	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166339	7166339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	326	725	0	ENST00000302850.5:c.1687C>T	p.Pro563Ser	p.P563S	ENST00000302850	NM_000208.2	563	Cca/Tca	8/22	0.257642227341294	5	FACETS	0.952	0.9	1	0.952	0.9	1	CLONAL	3	TRUE	2	0.316436079745705	5		725	1064	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7174720	7174720	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	203	559	0	ENST00000302850.5:c.997G>A	p.Gly333Ser	p.G333S	ENST00000302850	NM_000208.2	333	Ggt/Agt	4/22	0.257642227341294	5	FACETS	1	0.966	1	0.713	0.661	0.766	CLONAL	2	TRUE	2	0.316436079745705	5		559	885	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267835	7267835	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	163	561	0	ENST00000302850.5:c.173G>A	p.Gly58Glu	p.G58E	ENST00000302850	NM_000208.2	58	gGa/gAa	2/22	0.257642227341294	5	FACETS	0.87	0.799	0.945	0.58	0.532	0.63	CLONAL	2	TRUE	2	0.316436079745705	5		561	873	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291043	10291043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	182	569	0	ENST00000340748.4:c.428C>T	p.Ser143Phe	p.S143F	ENST00000340748		143	tCc/tTc	4/40	0.257642227341294	5	FACETS	1	0.96	1	0.706	0.652	0.762	CLONAL	2	TRUE	2	0.316436079745705	5		569	801	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17389744	17389744	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	382	890	1	ENST00000359435.4:c.877A>T	p.Asn293Tyr	p.N293Y	ENST00000359435	NM_001033549.1	293	Aac/Tac	9/9	0.257642227341294	5	FACETS	0.927	0.88	0.975	0.927	0.88	0.975	CLONAL	3	TRUE	2	0.316436079745705	5		891	1280	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212114	36212114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	444	644	0	ENST00000222270.7:c.1865C>T	p.Pro622Leu	p.P622L	ENST00000222270	NM_014727.1	622	cCc/cTc	3/37	0.237532676110463	3	FACETS	0.977	0.939	1			1	CLONAL	4	TRUE	NA	0.316436079745705	3		644	832	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082808	16082808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	52	145	0	ENST00000281043.3:c.622G>A	p.Ala208Thr	p.A208T	ENST00000281043	NM_005378.4	208	Gcc/Acc	2/3	0.255961656384795	4	FACETS	1	0.875	1	1	0.875	1	CLONAL	2	TRUE	2	0.316436079745705	4		145	213	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661594	227661594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	246	621	0	ENST00000305123.5:c.1861C>T	p.Pro621Ser	p.P621S	ENST00000305123	NM_005544.2	621	Cca/Tca	1/2	0.255961656384795	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.316436079745705	4		621	909	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944544	40944544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159842	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	140	587	0	ENST00000373198.4:c.1958G>A	p.Arg653Gln	p.R653Q	ENST00000373198	NM_133170.3	653	cGg/cAg	12/32	0.211853346667648	4	FACETS	1	0.987	1	0.748	0.681	0.817	CLONAL	1	TRUE	2	0.316436079745705	4		587	779	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41818364	41818364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	17	34	0	ENST00000373198.4:c.10C>T	p.Leu4Phe	p.L4F	ENST00000373198	NM_133170.3	4	Ctc/Ttc	1/32	0.211853346667648	4	FACETS	0.931	0.737	1	1	0.936	1	CLONAL	4	TRUE	2	0.316436079745705	4		34	38	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551049	41551049	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	130	713	0	ENST00000263253.7:c.3193C>G	p.Leu1065Val	p.L1065V	ENST00000263253	NM_001429.3	1065	Ctt/Gtt	17/31	0.264328027797468	4	FACETS	1	0.956	1			1	CLONAL	1	TRUE	NA	0.316436079745705	4		713	990	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421406	12421406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs181976291	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	112	659	1	ENST00000287820.6:c.286G>A	p.Asp96Asn	p.D96N	ENST00000287820	NM_015869.4	96	Gac/Aac	2/7	0.316436079745705	3	FACETS	1	0.901	1	0.501	0.45	0.555	CLONAL	1	TRUE	1	0.316436079745705	3		660	818	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928055	49928055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	195	750	0	ENST00000296474.3:c.3673G>A	p.Ala1225Thr	p.A1225T	ENST00000296474	NM_002447.2	1225	Gct/Act	18/20	0.316436079745705	3	FACETS	0.908	0.842	0.976	0.908	0.842	0.976	CLONAL	2	TRUE	1	0.316436079745705	3		750	786	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940441	49940441	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1338633573	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	260	770	0	ENST00000296474.3:c.602C>T	p.Ser201Phe	p.S201F	ENST00000296474	NM_002447.2	201	tCc/tTc	1/20	0.316436079745705	3	FACETS	0.978	0.917	1	0.978	0.917	1	CLONAL	2	TRUE	1	0.316436079745705	3		770	973	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52685815	52685815	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	156	539	0	ENST00000394830.3:c.657T>A	p.Asp219Glu	p.D219E	ENST00000394830	NM_018313.4	219	gaT/gaA	7/30	0.316436079745705	3	FACETS	0.945	0.869	1	0.945	0.869	1	CLONAL	2	TRUE	1	0.316436079745705	3		539	604	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968556	55968556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	219	580	0	ENST00000263923.4:c.2107G>A	p.Asp703Asn	p.D703N	ENST00000263923	NM_002253.2	703	Gat/Aat	14/30	0.298430461549645	3	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	1	0.316436079745705	3		580	798	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976722	55976722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	95	541	0	ENST00000263923.4:c.1103G>A	p.Gly368Glu	p.G368E	ENST00000263923	NM_002253.2	368	gGa/gAa	9/30	0.298430461549645	3	FACETS	1	0.934	1	0.533	0.475	0.595	CLONAL	1	TRUE	1	0.316436079745705	3		541	652	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157568	106157568	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	100	387	0	ENST00000380013.4:c.2469G>A	p.Met823Ile	p.M823I	ENST00000380013	NM_001127208.2	823	atG/atA	3/11	0.298430461549645	3	FACETS	0.859	0.772	0.95	0.859	0.772	0.95	CLONAL	2	TRUE	1	0.316436079745705	3		387	426	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541735	187541735	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	150	420	0	ENST00000441802.2:c.6005C>T	p.Thr2002Ile	p.T2002I	ENST00000441802	NM_005245.3	2002	aCt/aTt	10/27	0.316436079745705	2	FACETS	0.975	0.898	1	0.975	0.898	1	CLONAL	2	TRUE	0	0.316436079745705	2		420	486	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294085	1294085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543818650	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	152	921	0	ENST00000310581.5:c.916G>A	p.Gly306Ser	p.G306S	ENST00000310581	NM_198253.2	306	Ggc/Agc	2/16	0.316436079745705	3	FACETS	0.963	0.879	1	0.482	0.439	0.526	CLONAL	1	TRUE	1	0.316436079745705	3		921	1155	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871312	35871312	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	45	330	0	ENST00000303115.3:c.534G>C	p.Trp178Cys	p.W178C	ENST00000303115	NM_002185.3	178	tgG/tgC	4/8	0.298430461549645	3	FACETS	0.773	0.651	0.908	0.387	0.325	0.454	CLONAL	1	TRUE	1	0.316436079745705	3		330	426	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945126	38945126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	136	400	1	ENST00000357387.3:c.4678C>T	p.His1560Tyr	p.H1560Y	ENST00000357387	NM_152756.3	1560	Cat/Tat	35/38	0.298430461549645	3	FACETS	0.945	0.864	1	0.945	0.864	1	CLONAL	2	TRUE	1	0.316436079745705	3		401	527	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947524	38947524	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	135	305	0	ENST00000357387.3:c.4156T>C	p.Tyr1386His	p.Y1386H	ENST00000357387	NM_152756.3	1386	Tat/Cat	32/38	0.298430461549645	3	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	1	0.316436079745705	3		305	469	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959971	38959971	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	121	342	1	ENST00000357387.3:c.1961C>A	p.Thr654Asn	p.T654N	ENST00000357387	NM_152756.3	654	aCc/aAc	21/38	0.298430461549645	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.316436079745705	3		343	403	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590460	67590460	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	39	253	1	ENST00000274335.5:c.1522T>A	p.Tyr508Asn	p.Y508N	ENST00000274335		508	Tac/Aac	11/15	0.298430461549645	3	FACETS	0.842	0.7	1	0.421	0.35	0.5	CLONAL	1	TRUE	1	0.316436079745705	3		254	339	SUCCESS
APC	324	MSKCC	GRCh37	5	112173909	112173909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	135	372	0	ENST00000257430.4:c.2618C>T	p.Ser873Phe	p.S873F	ENST00000257430	NM_000038.5	873	tCt/tTt	16/16	0.298430461549645	3	FACETS	0.996	0.911	1	0.996	0.911	1	CLONAL	2	TRUE	1	0.316436079745705	3		372	496	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497181	149497181	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1262809438	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	69	480	1	ENST00000261799.4:c.3137G>A	p.Ser1046Asn	p.S1046N	ENST00000261799	NM_002609.3	1046	aGc/aAc	22/23	1	2	FACETS	0.738	0.643	0.84	0.738	0.643	0.84	SUBCLONAL	1	TRUE	1	0.316436079745705	2		481	591	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149503816	149503816	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779431081	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	178	512	0	ENST00000261799.4:c.2020G>A	p.Gly674Arg	p.G674R	ENST00000261799	NM_002609.3	674	Gga/Aga	14/23	1	2	FACETS	0.836	0.773	0.901	1	0.991	1	CLONAL	2	TRUE	1	0.316436079745705	2		512	673	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515443	149515443	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	63	453	1	ENST00000261799.4:c.41-2A>T		p.X14_splice	ENST00000261799	NM_002609.3	14			1	2	FACETS	0.823	0.713	0.941	0.823	0.713	0.941	CLONAL	1	TRUE	1	0.316436079745705	2		454	484	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818741	170818741	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	89	440	0	ENST00000296930.5:c.290C>T	p.Pro97Leu	p.P97L	ENST00000296930	NM_002520.6	97	cCa/cTa	4/11	1	2	FACETS	0.939	0.834	1	0.939	0.834	1	CLONAL	1	TRUE	1	0.316436079745705	2		440	599	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176516688	176516688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	161	540	0	ENST00000292408.4:c.85G>A	p.Glu29Lys	p.E29K	ENST00000292408	NM_213647.1	29	Gag/Aag	2/18	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.316436079745705	2		540	689	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520267	176520267	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761576473	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	247	699	0	ENST00000292408.4:c.1186C>T	p.His396Tyr	p.H396Y	ENST00000292408	NM_213647.1	396	Cac/Tac	9/18	1	2	FACETS	0.93	0.872	0.99	1	0.994	1	CLONAL	2	TRUE	1	0.316436079745705	2		699	839	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176563026	176563026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	74	487	0	ENST00000439151.2:c.922C>T	p.Pro308Ser	p.P308S	ENST00000439151	NM_022455.4	308	Cca/Tca	2/23	1	2	FACETS	0.823	0.722	0.933	0.823	0.722	0.933	CLONAL	1	TRUE	1	0.316436079745705	2		487	568	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056747	180056747	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	277	788	1	ENST00000261937.6:c.765G>A	p.Trp255Ter	p.W255*	ENST00000261937	NM_182925.4	255	tgG/tgA	6/30	1	2	FACETS	0.918	0.863	0.973	1	0.995	1	CLONAL	2	TRUE	1	0.316436079745705	2		789	954	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058724	180058724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	140	891	0	ENST00000261937.6:c.113C>T	p.Ser38Leu	p.S38L	ENST00000261937	NM_182925.4	38	tCa/tTa	2/30	1	2	FACETS	0.908	0.826	0.994	0.908	0.826	0.994	CLONAL	1	TRUE	1	0.316436079745705	2		891	975	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490545	20490545	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	205	551	0	ENST00000346618.3:c.1282C>T	p.Pro428Ser	p.P428S	ENST00000346618	NM_001949.4	428	Ccc/Tcc	7/7	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.316436079745705	NA		551	1250	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271580	26271581	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	51	372	0	ENST00000305910.3:c.32_33delinsTT	p.Ser11Phe	p.S11F	ENST00000305910	NM_003534.2	11	tCC/tTT	1/1	0.316436079745705	3	FACETS	0.837	0.713	0.973	0.279	0.237	0.325	CLONAL	1	TRUE	0	0.316436079745705	3		372	446	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673545	30673545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1166716221	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	261	710	0	ENST00000376406.3:c.3415C>T	p.Pro1139Ser	p.P1139S	ENST00000376406	NM_014641.2	1139	Ccc/Tcc	10/15	0.299039696044504	3	FACETS	0.966	0.906	1	0.644	0.604	0.685	CLONAL	2	TRUE	0	0.316436079745705	3		710	989	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163452	32163452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	515	712	0	ENST00000375023.3:c.5774C>T	p.Pro1925Leu	p.P1925L	ENST00000375023	NM_004557.3	1925	cCc/cTc	30/30	0.299039696044504	3	FACETS	0.895	0.858	0.933	0.895	0.858	0.933	CLONAL	3	TRUE	0	0.316436079745705	3		712	1404	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188626	32188626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	113	717	1	ENST00000375023.3:c.829C>T	p.Pro277Ser	p.P277S	ENST00000375023	NM_004557.3	277	Cca/Tca	5/30	0.299039696044504	3	FACETS	1	0.911	1	0.338	0.304	0.374	CLONAL	1	TRUE	0	0.316436079745705	3		718	816	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106543578	106543578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	72	323	0	ENST00000369096.4:c.380C>T	p.Pro127Leu	p.P127L	ENST00000369096	NM_001198.3	127	cCt/cTt	3/7	0.211853346667648	4	FACETS	0.788	0.692	0.89	0.788	0.692	0.89	SUBCLONAL	2	TRUE	2	0.316436079745705	4		323	380	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630038	117630038	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	103	503	0	ENST00000368508.3:c.6488C>T	p.Pro2163Leu	p.P2163L	ENST00000368508	NM_002944.2	2163	cCa/cTa	41/43	0.211853346667648	4	FACETS	1	0.98	1	0.708	0.635	0.786	CLONAL	1	TRUE	2	0.316436079745705	4		503	605	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519277	137519277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	121	507	0	ENST00000367739.4:c.1361C>T	p.Ser454Phe	p.S454F	ENST00000367739	NM_000416.2	454	tCc/tTc	7/7	0.211853346667648	4	FACETS	1	0.985	1	0.746	0.675	0.82	CLONAL	1	TRUE	2	0.316436079745705	4		507	675	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005533	150005533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	130	398	0	ENST00000253339.5:c.692G>A	p.Gly231Glu	p.G231E	ENST00000253339		231	gGa/gAa	3/7	0.211853346667648	4	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	2	0.316436079745705	4		398	514	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510868	157510869	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	186	674	1	ENST00000346085.5:c.3643_3644delinsTT	p.Pro1215Leu	p.P1215L	ENST00000346085	NM_020732.3	1215	CCa/TTa	14/20	0.211853346667648	4	FACETS	0.854	0.789	0.922	0.854	0.789	0.922	CLONAL	2	TRUE	2	0.316436079745705	4		675	906	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975376	13975376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	104	537	0	ENST00000405192.2:c.511C>T	p.Pro171Ser	p.P171S	ENST00000405192	NM_001163147.1	171	Cca/Tca	7/12	0.316436079745705	7	FACETS	1	0.957	1	0.189	0.169	0.211	CLONAL	1	TRUE	1	0.316436079745705	7		537	1036	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508071	106508071	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293906030	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	98	184	0	ENST00000359195.3:c.65G>A	p.Arg22Lys	p.R22K	ENST00000359195	NM_002649.2	22	aGg/aAg	2/11	0.316436079745705	7	FACETS	0.902	0.81	0.998	0.451	0.405	0.499	CLONAL	3	TRUE	1	0.316436079745705	7		184	410	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513224	106513224	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	235	260	0	ENST00000359195.3:c.2128C>T	p.Gln710Ter	p.Q710*	ENST00000359195	NM_002649.2	710	Cag/Tag	4/11	0.316436079745705	7	FACETS	1	0.98	1	0.556	0.52	0.593	CLONAL	3	TRUE	1	0.316436079745705	7		260	797	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860260	151860260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	223	539	1	ENST00000262189.6:c.10402C>T	p.Pro3468Ser	p.P3468S	ENST00000262189	NM_170606.2	3468	Ccc/Tcc	43/59	0.316436079745705	7	FACETS	0.899	0.838	0.962	0.45	0.419	0.481	CLONAL	3	TRUE	1	0.316436079745705	7		540	936	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860476	151860476	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1174	104	655	0	ENST00000262189.6:c.10186C>T	p.Gln3396Ter	p.Q3396*	ENST00000262189	NM_170606.2	3396	Caa/Taa	43/59	0.316436079745705	7	FACETS	0.921	0.822	1	0.154	0.137	0.172	CLONAL	1	TRUE	1	0.316436079745705	7		655	1278	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29197676	29197677	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	263	719	2	ENST00000240100.2:c.517_518delinsTT	p.Pro173Phe	p.P173F	ENST00000240100	NM_001394.6	173	CCc/TTc	2/4	0.316436079745705	5	FACETS	0.946	0.886	1	0.631	0.59	0.673	CLONAL	2	TRUE	2	0.316436079745705	5		721	1295	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279326	38279326	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	384	755	0	ENST00000425967.3:c.1163C>T	p.Thr388Ile	p.T388I	ENST00000425967	NM_001174067.1	388	aCc/aTc	9/19	0.316436079745705	5	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	2	0.316436079745705	5		755	1154	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956789	68956789	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	320	651	0	ENST00000288368.4:c.907G>A	p.Glu303Lys	p.E303K	ENST00000288368	NM_024870.2	303	Gag/Aag	8/40	0.316436079745705	5	FACETS	0.95	0.898	1	0.95	0.898	1	CLONAL	3	TRUE	2	0.316436079745705	5		651	1046	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995539	68995539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	261	730	0	ENST00000288368.4:c.1943C>T	p.Pro648Leu	p.P648L	ENST00000288368	NM_024870.2	648	cCt/cTt	18/40	0.316436079745705	5	FACETS	1	0.986	1	0.785	0.736	0.836	CLONAL	2	TRUE	2	0.316436079745705	5		730	1033	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976638	90976638	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1437392838	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	205	469	0	ENST00000265433.3:c.994G>A	p.Gly332Arg	p.G332R	ENST00000265433	NM_002485.4	332	Gga/Aga	8/16	0.316436079745705	5	FACETS	0.897	0.835	0.961	0.897	0.835	0.961	CLONAL	3	TRUE	2	0.316436079745705	5		469	710	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993013	90993013	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	173	541	0	ENST00000265433.3:c.429G>A	p.Trp143Ter	p.W143*	ENST00000265433	NM_002485.4	143	tgG/tgA	4/16	0.316436079745705	5	FACETS	0.898	0.827	0.972	0.599	0.551	0.648	CLONAL	2	TRUE	2	0.316436079745705	5		541	898	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751191	128751191	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1489420810	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	219	439	0	ENST00000377970.2:c.728A>T	p.Glu243Val	p.E243V	ENST00000377970	NM_002467.4	243	gAg/gTg	2/3	0.298805555152404	4	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.316436079745705	4		439	756	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126726	5126726	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	130	556	0	ENST00000381652.3:c.3334C>T	p.Gln1112Ter	p.Q1112*	ENST00000381652	NM_004972.3	1112	Caa/Taa	25/25	0.316436079745705	2	FACETS	0.929	0.85	1	0.929	0.85	1	CLONAL	2	TRUE	0	0.316436079745705	2		556	442	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524996	8524996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	159	401	1	ENST00000356435.5:c.608G>A	p.Gly203Glu	p.G203E	ENST00000356435		203	gGa/gAa	7/35	0.316436079745705	2	FACETS	0.978	0.902	1	0.978	0.902	1	CLONAL	2	TRUE	0	0.316436079745705	2		402	514	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637012	93637013	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	76	499	1	ENST00000375746.1:c.1062_1063delinsTT	p.Pro355Ser	p.P355S	ENST00000375746	NM_001174167.1	354	gaCCcc/gaTTcc	9/14	0.237532676110463	3	FACETS	0.951	0.835	1			1	CLONAL	1	TRUE	NA	0.316436079745705	3		500	585	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637050	93637050	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199772052	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	81	505	0	ENST00000375746.1:c.1100G>A	p.Arg367Gln	p.R367Q	ENST00000375746	NM_001174167.1	367	cGa/cAa	9/14	0.237532676110463	3	FACETS	0.941	0.83	1			1	CLONAL	1	TRUE	NA	0.316436079745705	3		505	630	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209372	98209372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	219	523	1	ENST00000331920.6:c.4166C>T	p.Pro1389Leu	p.P1389L	ENST00000331920	NM_000264.3	1389	cCt/cTt	23/24	0.237532676110463	3	FACETS	1	0.98	1			1	CLONAL	2	TRUE	NA	0.316436079745705	3		524	717	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128420073	128420073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	171	627	0	ENST00000265960.3:c.355G>A	p.Glu119Lys	p.E119K	ENST00000265960	NM_001006617.1	119	Gag/Aag	4/12	0.292664238505699	4	FACETS	0.864	0.796	0.936	0.864	0.796	0.936	CLONAL	2	TRUE	2	0.316436079745705	4		627	823	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759830	133759830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	197	536	0	ENST00000318560.5:c.2153C>T	p.Ser718Phe	p.S718F	ENST00000318560	NM_005157.4	718	tCc/tTc	11/11	0.292664238505699	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.316436079745705	4		536	733	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0022123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	154	306	0				ENST00000310581	NM_198253.2	-/1132			0.242534171343143	3	FACETS	0.937	0.868	1	1	0.985	1	CLONAL	4	TRUE	0	0.242534171343143	3		306	380	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857429	9857429	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	61	692	0	ENST00000330684.3:c.3972T>A	p.Phe1324Leu	p.F1324L	ENST00000330684	NM_001134407.1	1324	ttT/ttA	13/13	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.242534171343143	2		692	414	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88428945	88428945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	11	173	0	ENST00000360948.2:c.2155G>A	p.Asp719Asn	p.D719N	ENST00000360948	NM_001012338.2	719	Gat/Aat	17/19	0.199345779083595	1	FACETS	0.469	0.324	0.648	0.469	0.324	0.648	SUBCLONAL	1	TRUE	0	0.242534171343143	1		173	170	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0022123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	107	240	0				ENST00000310581	NM_198253.2	-/1132			0.242534171343143	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	3	TRUE	0	0.242534171343143	3		240	290	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654712	29654712	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	98	503	0	ENST00000356175.3:c.5401C>T	p.Gln1801Ter	p.Q1801*	ENST00000356175	NM_000267.3	1801	Cag/Tag	37/57	0.194097048627539	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	0	0.242534171343143	2		503	388	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293194	212293194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	22	512	0	ENST00000342788.4:c.2658G>A	p.Trp886Ter	p.W886*	ENST00000342788	NM_005235.2	886	tgG/tgA	22/28	1	2	FACETS	0.907	0.707	1	0.907	0.707	1	CLONAL	1	TRUE	1	0.242534171343143	2		512	200	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866579	78866579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	153	915	1	ENST00000306801.3:c.2152C>T	p.Arg718Cys	p.R718C	ENST00000306801	NM_020761.2	718	Cgt/Tgt	19/34	0.194097048627539	2	FACETS	0.995	0.914	1	0.995	0.914	1	CLONAL	2	TRUE	0	0.242534171343143	2		916	634	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650671	18650671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	13	523	0	ENST00000266497.5:c.2882G>A	p.Gly961Glu	p.G961E	ENST00000266497		961	gGa/gAa	20/31	0.201180719591674	3	FACETS	0.829	0.594	1	0.414	0.297	0.556	CLONAL	1	TRUE	1	0.242534171343143	3		523	145	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363122	40363122	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	47	726	0	ENST00000397332.2:c.1107G>T	p.Arg369Ser	p.R369S	ENST00000397332	NM_001033082.2	369	agG/agT	3/3	1	2	FACETS	0.843	0.712	0.987	0.843	0.712	0.987	CLONAL	1	TRUE	1	0.242534171343143	2		726	460	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100478	8100478	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0022123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	91	1002	0	ENST00000346208.3:c.452T>C	p.Phe151Ser	p.F151S	ENST00000346208		151	tTc/tCc	3/6	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.242534171343143	2		1002	625	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104352344	104352346	+	missense_variant	Missense_Mutation	TNP	ACC	ACC	TTT	novel	NA	P-0022123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	35	634	0	ENST00000369902.3:c.460_462delinsTTT	p.Thr154Phe	p.T154F	ENST00000369902	NM_016169.3	154	ACC/TTT	4/12	1	2	FACETS	0.834	0.685	1	0.834	0.685	1	CLONAL	1	TRUE	1	0.242534171343143	2		634	346	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487188	56487188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	47	788	0	ENST00000267101.3:c.1334C>T	p.Ser445Phe	p.S445F	ENST00000267101	NM_001982.3	445	tCc/tTc	12/28	0.242534171343143	14	FACETS	0.847	0.714	0.993			1	CLONAL	2	TRUE	NA	0.242534171343143	14		788	562	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138580	2138580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	106	853	0	ENST00000219476.3:c.5393C>T	p.Ser1798Phe	p.S1798F	ENST00000219476	NM_000548.3	1798	tCc/tTc	42/42	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.242534171343143	2		853	652	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640719	3640719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1448955515	NA	P-0022123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	96	884	3	ENST00000294008.3:c.2920C>T	p.Leu974Phe	p.L974F	ENST00000294008	NM_032444.2	974	Ctt/Ttt	12/15	1	2	FACETS	0.776	0.694	0.863	1	0.982	1	SUBCLONAL	2	TRUE	1	0.242534171343143	2		887	510	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458482	12458482	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	56	931	1	ENST00000287820.6:c.1099G>A	p.Val367Ile	p.V367I	ENST00000287820	NM_015869.4	367	Gtt/Att	6/7	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.242534171343143	2		932	449	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455652	189455653	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0022123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	20	602	1	ENST00000264731.3:c.186_187delinsAA	p.Glu63Lys	p.E63K	ENST00000264731	NM_003722.4	62	ctGGaa/ctAAaa	2/14	1	2	FACETS	0.988	0.761	1	0.988	0.761	1	CLONAL	1	TRUE	1	0.242534171343143	2		603	167	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964342	55964342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	21	691	0	ENST00000263923.4:c.2471C>T	p.Ala824Val	p.A824V	ENST00000263923	NM_002253.2	824	gCc/gTc	17/30	1	2	FACETS	0.538	0.414	0.682	0.538	0.414	0.682	SUBCLONAL	1	TRUE	1	0.242534171343143	2		691	322	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31511181	31511181	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	46	1041	1	ENST00000344624.3:c.1393C>T	p.Pro465Ser	p.P465S	ENST00000344624		465	Ccg/Tcg	6/33	0.242534171343143	3	FACETS	0.477	0.4	0.562	0.159	0.133	0.188	SUBCLONAL	1	TRUE	0	0.242534171343143	3		1042	892	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31939778	31939778	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	106	836	0	ENST00000375333.2:c.5A>T	p.Gln2Leu	p.Q2L	ENST00000375333	NM_032454.1	2	cAa/cTa	1/8	0.224049172607031	4	FACETS	0.813	0.73	0.901	0.813	0.73	0.901	CLONAL	2	TRUE	2	0.242534171343143	4		836	668	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170087	32170087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	174	998	0	ENST00000375023.3:c.3521G>A	p.Gly1174Glu	p.G1174E	ENST00000375023	NM_004557.3	1174	gGa/gAa	21/30	0.224049172607031	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	2	0.242534171343143	4		998	834	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631300	117631301	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0022123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	31	666	1	ENST00000368508.3:c.6377_6378delinsAA	p.Arg2126Gln	p.R2126Q	ENST00000368508	NM_002944.2	2126	cGG/cAA	40/43	0.188513150961305	2	FACETS	0.987	0.802	1	0.494	0.401	0.597	CLONAL	1	TRUE	0	0.242534171343143	2		667	259	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679006	117679006	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	27	615	0	ENST00000368508.3:c.3815A>T	p.Asn1272Ile	p.N1272I	ENST00000368508	NM_002944.2	1272	aAt/aTt	24/43	0.188513150961305	2	FACETS	1	0.836	1	0.525	0.42	0.643	CLONAL	1	TRUE	0	0.242534171343143	2		615	212	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69039639	69039639	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	28	720	0	ENST00000288368.4:c.3751C>A	p.Leu1251Ile	p.L1251I	ENST00000288368	NM_024870.2	1251	Ctt/Att	31/40	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.242534171343143	2		720	212	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0022140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	25	284	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.14	2		284	329	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455576	189455576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754361670	NA	P-0022140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	41	711	1	ENST00000264731.3:c.110G>A	p.Arg37Gln	p.R37Q	ENST00000264731	NM_003722.4	37	cGa/cAa	2/14	1	2	FACETS	0.749	0.622	0.891	0.749	0.622	0.891	SUBCLONAL	1	TRUE	1	0.14	2		712	782	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913255	NA	P-0022140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	45	822	0	ENST00000369535.4:c.183A>T	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caT	3/7	1	2	FACETS	0.733	0.614	0.866	0.733	0.614	0.866	SUBCLONAL	1	TRUE	1	0.14	2		822	877	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936310	49936310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	30	579	0	ENST00000296474.3:c.1538C>T	p.Ser513Phe	p.S513F	ENST00000296474	NM_002447.2	513	tCt/tTt	3/20	1	2	FACETS	0.84	0.676	1	0.84	0.676	1	CLONAL	1	TRUE	1	0.14	2		579	510	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940141	71940141	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0022140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	62	866	0	ENST00000298229.2:c.526A>C	p.Asn176His	p.N176H	ENST00000298229	NM_001567.3	176	Aat/Cat	5/28	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.14	2		866	836	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94209566	94209566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	37	451	0	ENST00000323929.3:c.548C>T	p.Ser183Phe	p.S183F	ENST00000323929	NM_005591.3	183	tCc/tTc	7/20	1	2	FACETS	0.994	0.818	1	0.994	0.818	1	CLONAL	1	TRUE	1	0.14	2		451	532	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424971	49424971	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1166177671	NA	P-0022140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	45	816	0	ENST00000301067.7:c.13517C>T	p.Pro4506Leu	p.P4506L	ENST00000301067	NM_003482.3	4506	cCc/cTc	39/54	1	2	FACETS	0.76	0.637	0.897	0.76	0.637	0.897	SUBCLONAL	1	TRUE	1	0.14	2		816	846	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578480	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	50	1049	0	ENST00000269305.4:c.450_451insT	p.Pro151SerfsTer30	p.P151Sfs*30	ENST00000269305	NM_001126112.2	150	-/T	5/11	1	2	FACETS	0.749	0.633	0.877	0.749	0.633	0.877	SUBCLONAL	1	TRUE	1	0.14	2		1049	954	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795512	42795512	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	48	956	10	ENST00000575354.2:c.2592C>G	p.Phe864Leu	p.F864L	ENST00000575354	NM_015125.3	864	ttC/ttG	10/20	1	2	FACETS	0.803	0.677	0.943	0.803	0.677	0.943	CLONAL	1	TRUE	1	0.14	2		966	854	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051208	128051208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	54	861	2	ENST00000285398.2:c.115C>T	p.Pro39Ser	p.P39S	ENST00000285398	NM_000122.1	39	Ccc/Tcc	2/15	1	2	FACETS	0.94	0.801	1	0.94	0.801	1	CLONAL	1	TRUE	1	0.14	2		863	821	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253762	30253762	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	35	574	0	ENST00000307677.4:c.692G>T	p.Ser231Ile	p.S231I	ENST00000307677	NM_138578.1	231	aGt/aTt	3/3	1	2	FACETS	0.907	0.743	1	0.907	0.743	1	CLONAL	1	TRUE	1	0.14	2		574	551	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176719091	176719091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	20	353	0	ENST00000439151.2:c.6395C>T	p.Ser2132Phe	p.S2132F	ENST00000439151	NM_022455.4	2132	tCc/tTc	22/23	1	2	FACETS	0.723	0.552	0.925	0.723	0.552	0.925	CLONAL	1	TRUE	1	0.14	2		353	395	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730107	41730107	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	31	532	0	ENST00000242208.4:c.422C>T	p.Ser141Phe	p.S141F	ENST00000242208	NM_002192.2	141	tCc/tTc	3/3	1	2	FACETS	0.811	0.655	0.989	0.811	0.655	0.989	CLONAL	1	TRUE	1	0.14	2		532	546	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978497	70978497	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	25	524	0	ENST00000276594.2:c.1156G>A	p.Gly386Arg	p.G386R	ENST00000276594	NM_024504.3	386	Ggg/Agg	5/8	1	2	FACETS	0.717	0.564	0.894	0.717	0.564	0.894	SUBCLONAL	1	TRUE	1	0.14	2		524	498	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0022146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	320	306	0				ENST00000310581	NM_198253.2	-/1132			0.82008092816259	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	2	0.870870855012374	4		306	575	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0022146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	375	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.82008092816259	4	FACETS	0.94	0.897	0.984	0.94	0.897	0.984	CLONAL	2	TRUE	2	0.870870855012374	4		288	857	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0022146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	703	454	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	0.82008092816259	4	FACETS	0.986	0.953	1	0.986	0.953	1	CLONAL	2	TRUE	2	0.870870855012374	4		454	1532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0022146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	528	808	2	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.870870855012374	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.870870855012374	2		810	588	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518437	204518437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201947927	NA	P-0022146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	200	531	0	ENST00000367182.3:c.1100C>T	p.Ser367Leu	p.S367L	ENST00000367182	NM_001278516.1	367	tCg/tTg	11/11	0.803812916033855	3	FACETS	1	0.953	1	0.515	0.479	0.552	CLONAL	1	TRUE	1	0.870870855012374	3		531	640	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434062	49434063	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0022146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	453	857	2	ENST00000301067.7:c.7490_7491delinsAT	p.Ala2497Asp	p.A2497D	ENST00000301067	NM_003482.3	2497	gCC/gAT	31/54	0.870870855012374	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.870870855012374	2		859	503	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866553	78866553	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145440027	NA	P-0022146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	628	863	0	ENST00000306801.3:c.2126G>A	p.Arg709Gln	p.R709Q	ENST00000306801	NM_020761.2	709	cGa/cAa	19/34	0.870870855012374	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.870870855012374	2		863	700	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262932	46262932	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs6094756	NA	P-0022146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	465	689	0	ENST00000371998.3:c.1105C>T	p.Leu369Phe	p.L369F	ENST00000371998		369	Ctt/Ttt	10/23	0.82008092816259	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.870870855012374	4		689	940	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158175	106158175	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	346	525	0	ENST00000380013.4:c.3076G>A	p.Glu1026Lys	p.E1026K	ENST00000380013	NM_001127208.2	1026	Gag/Aag	3/11	0.870870855012374	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.870870855012374	2		525	394	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93973581	93973581	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1179394255	NA	P-0022146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	322	554	0	ENST00000369303.4:c.1795C>T	p.His599Tyr	p.H599Y	ENST00000369303	NM_004440.3	599	Cat/Tat	9/17	0.870870855012374	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.870870855012374	3		554	492	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686904	117686904	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	134	371	1	ENST00000368508.3:c.2813G>A	p.Gly938Glu	p.G938E	ENST00000368508	NM_002944.2	938	gGg/gAg	19/43	0.870870855012374	3	FACETS	1	0.962	1	0.541	0.496	0.588	CLONAL	1	TRUE	1	0.870870855012374	3		372	408	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500990	8500990	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0022146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	194	547	0	ENST00000356435.5:c.1892A>C	p.Gln631Pro	p.Q631P	ENST00000356435		631	cAa/cCa	13/35	0.870870855012374	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.870870855012374	1		547	238	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971170	21971170	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	16	570	0	ENST00000304494.5:c.188T>C	p.Leu63Pro	p.L63P	ENST00000304494	NM_000077.4	63	cTg/cCg	2/3	0.843960804633462	0	FACETS		NA	1			1	NA	1	TRUE	0	0.870870855012374	0		570	65	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0022168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	3295	430	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.605817497444846	16	FACETS	1	0.998	1	1	0.998	1	CLONAL	15	TRUE	1	0.605817497444846	16		430	3746	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0022168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	149	355	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.605817497444846	2		355	462	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62294212	62294212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866785110	NA	P-0022168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4458	318	665	0	ENST00000360203.5:c.508C>T	p.Arg170Cys	p.R170C	ENST00000360203	NM_001283009.1	170	Cgc/Tgc	6/35	0.605817497444846	18	FACETS	1	0.99	1			1	CLONAL	1	TRUE	NA	0.605817497444846	18		665	4776	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11168338	11168338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	140	403	0	ENST00000361445.4:c.7534G>A	p.Asp2512Asn	p.D2512N	ENST00000361445	NM_004958.3	2512	Gac/Aac	57/58	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.605817497444846	2		403	419	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114135	115114135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	167	594	0	ENST00000257566.3:c.1082G>A	p.Gly361Glu	p.G361E	ENST00000257566	NM_016569.3	361	gGg/gAg	6/8	1	2	FACETS	0.955	0.883	1	0.955	0.883	1	CLONAL	1	TRUE	1	0.605817497444846	2		594	577	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525068	9525068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	125	536	1	ENST00000353224.5:c.1817C>T	p.Thr606Ile	p.T606I	ENST00000353224	NM_177990.2	606	aCt/aTt	8/10	1	2	FACETS	0.761	0.692	0.834	0.761	0.692	0.834	SUBCLONAL	1	TRUE	1	0.605817497444846	2		537	542	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224562	123224562	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	268	734	0	ENST00000218089.9:c.3415del	p.Met1139Ter	p.M1139*	ENST00000218089	NM_001042749.1	1139	Atg/tg	31/35	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		734	769	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0022907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	280	151	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.891	0.84	0.942	0.891	0.84	0.942	CLONAL	1	TRUE	1	0.768766222089137	2		151	818	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0022907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1693	36	553	1	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.477784407406837	4	FACETS	0.096	0.078	0.116			1	SUBCLONAL	1	TRUE	NA	0.768766222089137	4		554	1729	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913514	NA	P-0022907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	125	701	0	ENST00000288135.5:c.2466T>G	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaG	17/21	1	2	FACETS	0.676	0.616	0.739	0.676	0.616	0.739	SUBCLONAL	1	TRUE	1	0.768766222089137	2		701	481	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989402	7989402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150641093	NA	P-0022907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	444	1103	0	ENST00000319144.4:c.284G>A	p.Arg95His	p.R95H	ENST00000319144	NM_001139.2	95	cGt/cAt	2/15	1	2	FACETS	0.973	0.93	1	0.973	0.93	1	CLONAL	1	TRUE	1	0.768766222089137	2		1103	1187	SUCCESS
APC	324	MSKCC	GRCh37	5	112137020	112137020	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	51	587	0	ENST00000257430.4:c.774G>C	p.Glu258Asp	p.E258D	ENST00000257430	NM_000038.5	258	gaG/gaC	8/16	1	2	FACETS	0.173	0.146	0.202	0.173	0.146	0.202	SUBCLONAL	1	TRUE	1	0.768766222089137	2		587	768	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513181	106513181	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1478913019	NA	P-0022907-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	315	388	0	ENST00000359195.3:c.2085G>T	p.Leu695Phe	p.L695F	ENST00000359195	NM_002649.2	695	ttG/ttT	4/11	0.76506336259042	3	FACETS	0.928	0.885	0.972	0.928	0.885	0.972	CLONAL	2	TRUE	1	0.768766222089137	3		388	611	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0023323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	286	242	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	0.941	0.891	0.991	0.941	0.891	0.991	CLONAL	1	TRUE	1	0.90902367592476	2		242	669	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0023323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	738	500	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	0.70910012465989	4	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.90902367592476	4		500	1426	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0023323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	139	326	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.455072169649754	1	FACETS	0.374	0.343	0.406	0.374	0.343	0.406	INDETERMINATE	1	TRUE	0	0.90902367592476	1		326	446	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121913370	NA	P-0023323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	245	265	0	ENST00000288602.6:c.1742A>G	p.Asn581Ser	p.N581S	ENST00000288602	NM_004333.4	581	aAt/aGt	15/18	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.90902367592476	2		265	513	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557416	95557416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	148	714	0	ENST00000393063.1:c.5558C>T	p.Pro1853Leu	p.P1853L	ENST00000393063	NM_030621.3	1853	cCt/cTt	27/28	0.455072169649754	1	FACETS	0.296	0.271	0.322	0.296	0.271	0.322	INDETERMINATE	1	TRUE	0	0.90902367592476	1		714	600	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651335	52651335	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0023323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	201	947	1	ENST00000394830.3:c.1761A>G	p.Ile587Met	p.I587M	ENST00000394830	NM_018313.4	587	atA/atG	15/30	0.455072169649754	1	FACETS	0.315	0.292	0.338	0.315	0.292	0.338	INDETERMINATE	1	TRUE	0	0.90902367592476	1		948	766	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224260	55224260	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	167	808	0	ENST00000275493.2:c.1041C>G	p.Asp347Glu	p.D347E	ENST00000275493	NM_005228.3	347	gaC/gaG	9/28	1	2	FACETS	0.443	0.407	0.481	0.443	0.407	0.481	SUBCLONAL	1	TRUE	1	0.90902367592476	2		808	829	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123499629	123499629	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0023323-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	592	1003	0	ENST00000371139.4:c.156T>A	p.Tyr52Ter	p.Y52*	ENST00000371139	NM_001114937.2	52	taT/taA	2/4	0.56508318708027	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.90902367592476	1		1003	672	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0023775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	61	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.145178798385779	3	FACETS	0.999	0.871	1	0.666	0.58	0.758	INDETERMINATE	2	TRUE	0	0.253801198808231	3		288	271	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0023775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	29	151	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.816	0.665	0.983	1	0.949	1	CLONAL	2	TRUE	1	0.253801198808231	2		151	140	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202890	16202890	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	33	393	0	ENST00000375759.3:c.598C>T	p.Arg200Ter	p.R200*	ENST00000375759	NM_015001.2	200	Cga/Tga	3/15	1	2	FACETS	0.897	0.733	1	0.897	0.733	1	CLONAL	1	TRUE	1	0.253801198808231	2		393	290	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699447	117699447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	29	378	0	ENST00000369458.3:c.194C>T	p.Ser65Phe	p.S65F	ENST00000369458	NM_024626.3	65	tCt/tTt	3/6	1	2	FACETS	0.856	0.689	1	0.856	0.689	1	CLONAL	1	TRUE	1	0.253801198808231	2		378	267	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862826	9862826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	45	388	1	ENST00000330684.3:c.2477C>T	p.Ala826Val	p.A826V	ENST00000330684	NM_001134407.1	826	gCc/gTc	12/13	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.253801198808231	2		389	258	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244004	41244004	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs80357296	NA	P-0023775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	37	446	0	ENST00000357654.3:c.3544C>T	p.Gln1182Ter	p.Q1182*	ENST00000357654	NM_007294.3	1182	Cag/Tag	10/23	1	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	TRUE	1	0.253801198808231	2		446	287	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827928	40827928	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773152433	NA	P-0023775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	60	395	0	ENST00000373198.4:c.2500C>T	p.Arg834Cys	p.R834C	ENST00000373198	NM_133170.3	834	Cgc/Tgc	17/32	1	2	FACETS	0.832	0.723	0.949	1	0.975	1	CLONAL	2	TRUE	1	0.253801198808231	2		395	284	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0023794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	21	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.606	0.468	0.764	0.606	0.468	0.764	SUBCLONAL	1	TRUE	1	0.328737641201257	2		306	211	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0023794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	119	484	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	NA	2	FACETS	0.905	0.824	0.989			1	INDETERMINATE	2	TRUE	NA	0.328737641201257	2		484	400	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577557	7577557	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519982	NA	P-0023794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	83	432	0	ENST00000269305.4:c.724T>G	p.Cys242Gly	p.C242G	ENST00000269305	NM_001126112.2	242	Tgc/Ggc	7/11	0.328737641201257	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.328737641201257	1		432	356	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151625	55151625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571523023	NA	P-0023794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	60	398	0	ENST00000257290.5:c.2411G>A	p.Arg804Gln	p.R804Q	ENST00000257290	NM_006206.4	804	cGa/cAa	17/23	0.237218161644736	1	FACETS	0.739	0.638	0.847	0.739	0.638	0.847	SUBCLONAL	1	TRUE	0	0.328737641201257	1		398	413	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857197	9857197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866121846	NA	P-0023794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	23	320	0	ENST00000330684.3:c.4204C>T	p.Arg1402Trp	p.R1402W	ENST00000330684	NM_001134407.1	1402	Cgg/Tgg	13/13	0.328737641201257	1	FACETS	0.427	0.333	0.535	0.427	0.333	0.535	SUBCLONAL	1	TRUE	0	0.328737641201257	1		320	274	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912865	50912865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	26	485	0	ENST00000440232.2:c.2096C>T	p.Ser699Phe	p.S699F	ENST00000440232	NM_002691.3	699	tCc/tTc	17/27	0.328737641201257	1	FACETS	0.364	0.288	0.451	0.364	0.288	0.451	SUBCLONAL	1	TRUE	0	0.328737641201257	1		485	363	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222978	5222978	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1293966082	NA	P-0023794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	52	416	0	ENST00000357368.4:c.2825C>T	p.Ser942Leu	p.S942L	ENST00000357368	NM_002850.3	942	tCg/tTg	18/38	0.328737641201257	1	FACETS	0.994	0.853	1	0.994	0.853	1	CLONAL	1	TRUE	0	0.328737641201257	1		416	266	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045030	47045030	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0023794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	71	557	0	ENST00000377604.3:c.2355+1G>A		p.X785_splice	ENST00000377604	NM_001204468.1	785			1	2	FACETS	0.954	0.835	1	0.954	0.835	1	CLONAL	1	TRUE	1	0.328737641201257	2		557	453	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849479	68849479	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876659268	NA	P-0023794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	75	464	0	ENST00000261769.5:c.1382C>T	p.Pro461Leu	p.P461L	ENST00000261769	NM_004360.3	461	cCt/cTt	10/16	0.328737641201257	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.328737641201257	1		464	365	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178155	56178155	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	40	275	0	ENST00000399503.3:c.3128C>T	p.Ser1043Phe	p.S1043F	ENST00000399503	NM_005921.1	1043	tCc/tTc	14/20	1	2	FACETS	0.958	0.802	1	0.958	0.802	1	CLONAL	1	TRUE	1	0.328737641201257	2		275	254	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374365	81374365	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0023794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	50	308	0	ENST00000222390.5:c.697C>T	p.Gln233Ter	p.Q233*	ENST00000222390	NM_000601.4	233	Cag/Tag	6/18	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.328737641201257	2		308	283	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260838	16260895	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGCCAGTGAATGTTCTCACCACTCCAGTGAACGCCACGGTGGGCACAGTGAATGCC	GGGGCCAGTGAATGTTCTCACCACTCCAGTGAACGCCACGGTGGGCACAGTGAATGCC	TGT	novel	NA	P-0023794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	42	364	2	ENST00000375759.3:c.8103_8160delinsTGT	p.Gly2702ValfsTer13	p.G2702Vfs*13	ENST00000375759	NM_015001.2	2701	acGGGGCCAGTGAATGTTCTCACCACTCCAGTGAACGCCACGGTGGGCACAGTGAATGCC/acTGT	11/15	0.128325146439026	3	FACETS	1	0.89	1	0.539	0.453	0.634	INDETERMINATE	1	TRUE	1	0.328737641201257	3		366	276	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226279	133226279	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	38	411	0	ENST00000320574.5:c.3779C>T	p.Ala1260Val	p.A1260V	ENST00000320574	NM_006231.2	1260	gCc/gTc	30/49	1	2	FACETS	0.718	0.595	0.854	0.718	0.595	0.854	SUBCLONAL	1	TRUE	1	0.328737641201257	2		411	322	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028502	42028502	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	49	325	1	ENST00000219905.7:c.4040A>T	p.Asp1347Val	p.D1347V	ENST00000219905	NM_001164273.1	1347	gAt/gTt	13/24	1	2	FACETS	0.893	0.759	1	0.893	0.759	1	CLONAL	1	TRUE	1	0.328737641201257	2		326	334	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640979	3640979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	76	504	0	ENST00000294008.3:c.2660C>T	p.Ser887Phe	p.S887F	ENST00000294008	NM_032444.2	887	tCt/tTt	12/15	0.328737641201257	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.328737641201257	1		504	368	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589833	212589833	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0023794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	57	431	0	ENST00000342788.4:c.709G>A	p.Gly237Ser	p.G237S	ENST00000342788	NM_005235.2	237	Ggc/Agc	6/28	1	2	FACETS	0.974	0.84	1	0.974	0.84	1	CLONAL	1	TRUE	1	0.328737641201257	2		431	356	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55130094	55130094	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	27	351	0	ENST00000257290.5:c.628G>A	p.Ala210Thr	p.A210T	ENST00000257290	NM_006206.4	210	Gca/Aca	4/23	0.237218161644736	1	FACETS	0.51	0.407	0.627	0.51	0.407	0.627	SUBCLONAL	1	TRUE	0	0.328737641201257	1		351	269	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55270265	55270266	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0023794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	33	488	1	ENST00000275493.2:c.3218_3219delinsAT	p.Pro1073His	p.P1073H	ENST00000275493	NM_005228.3	1073	cCC/cAT	27/28	1	2	FACETS	0.558	0.455	0.673	0.558	0.455	0.673	SUBCLONAL	1	TRUE	1	0.328737641201257	2		489	360	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0024025-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	40	256	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	0.37660385649195	3	FACETS	0.858	0.718	1	0.286	0.239	0.338	CLONAL	1	FALSE	0	0.436953165665225	3		256	260	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0024025-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	62	605	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.428245780986881	5	FACETS	0.811	0.701	0.931			1	CLONAL	1	FALSE	NA	0.436953165665225	5		605	579	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0024025-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	266	696	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.386973632272015	4	FACETS	1	0.973	1	0.781	0.74	0.822	CLONAL	3	FALSE	0	0.436953165665225	4		696	560	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528711	8528711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774617096	NA	P-0024025-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	31	271	1	ENST00000356435.5:c.421C>T	p.Arg141Cys	p.R141C	ENST00000356435		141	Cgc/Tgc	4/35	0.436953165665225	3	FACETS	0.547	0.443	0.664	0.182	0.147	0.222	SUBCLONAL	1	FALSE	0	0.436953165665225	3		272	316	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242486	+	inframe_deletion	In_Frame_Del	DEL	TTAAGAGAAGCAACATCT	TTAAGAGAAGCAACATCT	-	rs121913440	NA	P-0024025-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	76	300	0	ENST00000275493.2:c.2239_2256del	p.Leu747_Ser752del	p.L747_S752del	ENST00000275493	NM_005228.3	747	TTAAGAGAAGCAACATCT/-	19/28	0.428245780986881	5	FACETS	0.838	0.747	0.933			1	CLONAL	3	FALSE	NA	0.436953165665225	5		300	229	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242713	16242713	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024025-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	59	407	0	ENST00000375759.3:c.1334T>A	p.Leu445His	p.L445H	ENST00000375759	NM_015001.2	445	cTt/cAt	6/15	0.37660385649195	3	FACETS	0.829	0.716	0.951	0.276	0.238	0.317	CLONAL	1	FALSE	0	0.436953165665225	3		407	397	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743346	162743346	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024025-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	56	284	0	ENST00000367921.3:c.1816G>T	p.Ala606Ser	p.A606S	ENST00000367921	NM_006182.2	606	Gct/Tct	14/18	0.436953165665225	5	FACETS	1	0.943	1	0.299	0.257	0.344	CLONAL	1	FALSE	1	0.436953165665225	5		284	355	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827161	170827161	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024025-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	93	194	0	ENST00000296930.5:c.529G>T	p.Asp177Tyr	p.D177Y	ENST00000296930	NM_002520.6	177	Gat/Tat	7/11	0.436953165665225	4	FACETS	1	0.967	1	0.586	0.529	0.645	CLONAL	2	FALSE	0	0.436953165665225	4		194	261	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209600	98209600	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024025-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	58	701	0	ENST00000331920.6:c.3938C>G	p.Pro1313Arg	p.P1313R	ENST00000331920	NM_000264.3	1313	cCa/cGa	23/24	0.37660385649195	3	FACETS	0.711	0.612	0.818	0.237	0.204	0.273	SUBCLONAL	1	FALSE	0	0.436953165665225	3		701	455	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188218	32188218	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024025-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	61	642	1	ENST00000375023.3:c.1123G>A	p.Gly375Ser	p.G375S	ENST00000375023	NM_004557.3	375	Ggc/Agc	6/30	0.436953165665225	4	FACETS	0.723	0.624	0.83	0.181	0.156	0.208	SUBCLONAL	1	FALSE	0	0.436953165665225	4		643	555	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140487374	140487374	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024025-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	66	426	0	ENST00000288602.6:c.1151G>C	p.Arg384Thr	p.R384T	ENST00000288602	NM_004333.4	384	aGa/aCa	9/18	0.386973632272015	4	FACETS	0.743	0.645	0.849	0.186	0.161	0.213	SUBCLONAL	1	FALSE	0	0.436953165665225	4		426	584	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197161	26197161	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024025-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	39	394	0	ENST00000356476.2:c.318G>T	p.Glu106Asp	p.E106D	ENST00000356476		106	gaG/gaT	1/1	0.436953165665225	0	FACETS	0.204	0.169	0.244			1	SUBCLONAL	1	FALSE	0	0.436953165665225	0		394	492	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190740	108190740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024025-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	39	270	0	ENST00000278616.4:c.6407G>A	p.Arg2136Lys	p.R2136K	ENST00000278616	NM_000051.3	2136	aGa/aAa	44/63	0.386973632272015	4	FACETS	0.699	0.58	0.83	0.175	0.145	0.208	SUBCLONAL	1	FALSE	0	0.436953165665225	4		270	367	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200940	108200940	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0024025-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	25	193	0	ENST00000278616.4:c.7308-1G>A		p.X2436_splice	ENST00000278616	NM_000051.3	2436			0.386973632272015	4	FACETS	0.642	0.508	0.796	0.161	0.127	0.199	SUBCLONAL	1	FALSE	0	0.436953165665225	4		193	256	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244970	46244970	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1160219479	NA	P-0024025-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	52	404	0	ENST00000334344.6:c.3064C>G	p.Pro1022Ala	p.P1022A	ENST00000334344	NM_152641.2	1022	Cca/Gca	15/21	0.386973632272015	4	FACETS	0.676	0.576	0.786	0.169	0.144	0.197	SUBCLONAL	1	FALSE	0	0.436953165665225	4		404	506	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643738	38643738	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs772476060	NA	P-0024154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	125	951	1	ENST00000299084.4:c.1208G>T	p.Arg403Leu	p.R403L	ENST00000299084	NM_152594.2	403	cGa/cTa	7/7	1	2	FACETS	0.859	0.779	0.942	0.859	0.779	0.942	CLONAL	1	FALSE	1	0.462703161362525	2		952	629	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27172734	27172734	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774928388	NA	P-0024154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	154	694	0	ENST00000380036.4:c.749C>T	p.Thr250Met	p.T250M	ENST00000380036	NM_000459.3	250	aCg/aTg	5/23	0.354726215258623	4	FACETS	0.949	0.874	1	0.949	0.874	1	CLONAL	2	FALSE	2	0.462703161362525	4		694	513	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0024221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	424	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.59150062100739	4	FACETS	0.938	0.903	0.973	0.938	0.903	0.973	CLONAL	3	TRUE	1	0.709550962461937	4		288	726	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	95	151	0				ENST00000310581	NM_198253.2	-/1132			0.505284700563526	3	FACETS	0.935	0.854	1	0.935	0.854	1	CLONAL	2	TRUE	1	0.709550962461937	3		151	194	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341914	8341914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	150	704	0	ENST00000356435.5:c.4726G>A	p.Glu1576Lys	p.E1576K	ENST00000356435		1576	Gaa/Aaa	29/35	0.709550962461937	1	FACETS	0.985	0.92	1	0.985	0.92	1	CLONAL	1	TRUE	0	0.709550962461937	1		704	277	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408885	41408885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868295248	NA	P-0024221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	137	592	1	ENST00000373198.4:c.541G>A	p.Glu181Lys	p.E181K	ENST00000373198	NM_133170.3	181	Gag/Aag	4/32	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.709550962461937	2		593	380	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812242	212812242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1226469223	NA	P-0024221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	349	503	0	ENST00000342788.4:c.334G>A	p.Glu112Lys	p.E112K	ENST00000342788	NM_005235.2	112	Gag/Aag	3/28	0.688443815363975	3	FACETS	0.89	0.859	0.921	0.89	0.859	0.921	CLONAL	3	TRUE	0	0.709550962461937	3		503	499	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021614	31021614	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	156	628	0	ENST00000375687.4:c.1613A>G	p.Lys538Arg	p.K538R	ENST00000375687	NM_015338.5	538	aAg/aGg	12/13	1	2	FACETS	0.926	0.855	0.999	0.926	0.855	0.999	CLONAL	1	TRUE	1	0.709550962461937	2		628	475	SUCCESS
ATR	545	MSKCC	GRCh37	3	142241623	142241623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	170	798	0	ENST00000350721.4:c.4213C>T	p.Leu1405Phe	p.L1405F	ENST00000350721	NM_001184.3	1405	Ctt/Ttt	23/47	0.41904002698156	3	FACETS	1	0.967	1	0.541	0.5	0.583	INDETERMINATE	1	TRUE	1	0.709550962461937	3		798	600	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455559	189455559	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	275	806	1	ENST00000264731.3:c.93G>A	p.Trp31Ter	p.W31*	ENST00000264731	NM_003722.4	31	tgG/tgA	2/14	0.41904002698156	3	FACETS	0.815	0.771	0.86	0.815	0.771	0.86	INDETERMINATE	2	TRUE	1	0.709550962461937	3		807	644	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0024536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	264	306	0				ENST00000310581	NM_198253.2	-/1132			0.496700549250672	4	FACETS	0.956	0.901	1	0.956	0.901	1	CLONAL	2	TRUE	2	0.640762220068152	4		306	707	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0024536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	397	500	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	0.640762220068152	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	1	0.640762220068152	4		500	663	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120377	94120377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	206	316	0	ENST00000369303.4:c.674C>T	p.Ser225Phe	p.S225F	ENST00000369303	NM_004440.3	225	tCc/tTc	3/17	0.497576767689526	5	FACETS	0.924	0.867	0.981			1	CLONAL	3	TRUE	NA	0.640762220068152	5		316	455	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13949269	13949269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	134	285	0	ENST00000405192.2:c.859G>A	p.Glu287Lys	p.E287K	ENST00000405192	NM_001163147.1	287	Gaa/Aaa	9/12	0.568510962182953	4	FACETS	0.831	0.762	0.902	0.831	0.762	0.902	CLONAL	2	TRUE	2	0.640762220068152	4		285	413	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358483	91358483	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	333	540	0	ENST00000355112.3:c.4228C>A	p.Leu1410Ile	p.L1410I	ENST00000355112	NM_000057.2	1410	Ctt/Att	22/22	0.487333966565428	5	FACETS	0.874	0.832	0.918	0.874	0.832	0.918	CLONAL	3	TRUE	2	0.640762220068152	5		540	777	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098753	2098753	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	308	528	0	ENST00000219476.3:c.137G>A	p.Arg46Lys	p.R46K	ENST00000219476	NM_000548.3	46	aGa/aAa	2/42	0.640762220068152	3	FACETS	0.918	0.872	0.965	0.918	0.872	0.965	CLONAL	2	TRUE	1	0.640762220068152	3		528	691	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606709	29606709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	327	524	0	ENST00000389048.3:c.1171G>A	p.Gly391Arg	p.G391R	ENST00000389048	NM_004304.4	391	Gga/Aga	5/29	0.640673227248668	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.640762220068152	3		524	646	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117079	193117079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	220	449	0	ENST00000367435.3:c.812C>T	p.Pro271Leu	p.P271L	ENST00000367435	NM_024529.4	271	cCa/cTa	8/17	0.640673227248668	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.640762220068152	3		449	450	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243416	46243416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	171	407	1	ENST00000334344.6:c.1769G>A	p.Gly590Glu	p.G590E	ENST00000334344	NM_152641.2	590	gGg/gAg	14/21	NA	2	FACETS	0.927	0.873	0.98			1	INDETERMINATE	2	TRUE	NA	0.640762220068152	2		408	288	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426640	121426640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	246	523	0	ENST00000257555.6:c.331G>A	p.Asp111Asn	p.D111N	ENST00000257555		111	Gac/Aac	2/10	0.640762220068152	2	FACETS	0.912	0.867	0.956	0.912	0.867	0.956	CLONAL	2	TRUE	0	0.640762220068152	2		523	421	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134445	2134445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	421	814	1	ENST00000219476.3:c.4222G>A	p.Gly1408Ser	p.G1408S	ENST00000219476	NM_000548.3	1408	Ggc/Agc	34/42	0.640762220068152	3	FACETS	0.965	0.924	1	0.965	0.924	1	CLONAL	2	TRUE	1	0.640762220068152	3		815	899	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778338	3778339	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0024536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	291	713	2	ENST00000262367.5:c.6709_6710delinsTT	p.Pro2237Phe	p.P2237F	ENST00000262367	NM_004380.2	2237	CCc/TTc	31/31	0.640762220068152	3	FACETS	0.826	0.782	0.871	0.826	0.782	0.871	CLONAL	2	TRUE	1	0.640762220068152	3		715	726	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576920	7576920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	343	640	1	ENST00000269305.4:c.926C>T	p.Pro309Leu	p.P309L	ENST00000269305	NM_001126112.2	309	cCc/cTc	9/11	0.640673227248668	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.640762220068152	3		641	702	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29563041	29563041	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1555615567	NA	P-0024536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	188	356	0	ENST00000356175.3:c.3974+2T>C		p.X1325_splice	ENST00000356175	NM_000267.3	1325			0.640762220068152	2	FACETS	0.943	0.892	0.994	0.943	0.892	0.994	CLONAL	2	TRUE	0	0.640762220068152	2		356	311	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007619	62007620	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0024536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	678	715	0	ENST00000392795.3:c.246_247dup	p.Met83ArgfsTer9	p.M83Rfs*9	ENST00000392795	NM_001039933.1	83	atg/aGAtg	3/6	0.640762220068152	6	FACETS	0.969	0.939	0.999	0.969	0.939	0.999	CLONAL	4	TRUE	2	0.640762220068152	6		715	1246	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303293	15303293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	292	1108	0	ENST00000263388.2:c.235G>A	p.Glu79Lys	p.E79K	ENST00000263388	NM_000435.2	79	Gag/Aag	3/33	0.640673227248668	3	FACETS	1	0.976	1	0.534	0.502	0.566	CLONAL	1	TRUE	1	0.640762220068152	3		1108	1127	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221279	36221279	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555731976	NA	P-0024536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	415	831	4	ENST00000222270.7:c.5113C>T	p.Arg1705Ter	p.R1705*	ENST00000222270	NM_014727.1	1705	Cga/Tga	24/37	0.640673227248668	3	FACETS	0.994	0.953	1	0.994	0.953	1	CLONAL	2	TRUE	1	0.640762220068152	3		835	860	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027757	48027757	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	224	456	0	ENST00000234420.5:c.2635G>C	p.Ala879Pro	p.A879P	ENST00000234420	NM_000179.2	879	Gct/Cct	4/10	0.640673227248668	3	FACETS	0.978	0.922	1	0.978	0.922	1	CLONAL	2	TRUE	1	0.640762220068152	3		456	472	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074200	30074200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	269	560	1	ENST00000338641.4:c.1462C>T	p.Pro488Ser	p.P488S	ENST00000338641	NM_000268.3	488	Cca/Tca	14/16	0.640673227248668	3	FACETS	0.956	0.905	1	0.956	0.905	1	CLONAL	2	TRUE	1	0.640762220068152	3		561	580	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522726	67522726	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	124	264	0	ENST00000274335.5:c.223G>A	p.Glu75Lys	p.E75K	ENST00000274335		75	Gaa/Aaa	1/15	0.496700549250672	4	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	2	0.640762220068152	4		264	314	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681004	117681004	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761671299	NA	P-0024536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	371	459	0	ENST00000368508.3:c.3616C>T	p.Leu1206Phe	p.L1206F	ENST00000368508	NM_002944.2	1206	Ctt/Ttt	23/43	0.608943555792018	5	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	2	0.640762220068152	5		459	704	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875095	151875095	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	rs748029485	NA	P-0024536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	42	72	1	ENST00000262189.6:c.7443A>T	p.Arg2481Ser	p.R2481S	ENST00000262189	NM_170606.2	2481	agA/agT	38/59	0.640673227248668	3	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	TRUE	1	0.640762220068152	3		73	80	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863343	56863343	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	185	330	0	ENST00000519728.1:c.487G>A	p.Gly163Arg	p.G163R	ENST00000519728	NM_002350.3	163	Gga/Aga	6/13	0.568510962182953	4	FACETS	0.983	0.916	1	0.983	0.916	1	CLONAL	2	TRUE	2	0.640762220068152	4		330	482	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141583012	141583013	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0024536-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	321	725	1	ENST00000220592.5:c.234_235delinsAA	p.Met78_Val79delinsIleIle	p.M78_V79delinsII	ENST00000220592	NM_012154.3	78	atGGtc/atAAtc	3/19	0.568510962182953	4	FACETS	0.896	0.849	0.945	0.896	0.849	0.945	CLONAL	2	TRUE	2	0.640762220068152	4		726	917	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0025166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	198	578	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	0.953	0.89	1	0.953	0.89	1	CLONAL	1	TRUE	1	0.788165048062863	2		578	527	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0025166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	166	525	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	0.998	0.927	1	0.998	0.927	1	CLONAL	1	TRUE	1	0.788165048062863	2		525	422	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913332	NA	P-0025166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	146	302	0	ENST00000257430.4:c.4348C>G	p.Arg1450Gly	p.R1450G	ENST00000257430	NM_000038.5	1450	Cga/Gga	16/16	1	2	FACETS	0.962	0.889	1	0.962	0.889	1	CLONAL	1	TRUE	1	0.788165048062863	2		302	385	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0025271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	67	242	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	0.982	0.853	1	0.982	0.853	1	CLONAL	1	TRUE	1	0.213289385713876	2		242	640	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593662	55593664	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0025271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	207	562	0	ENST00000288135.5:c.1729_1731del	p.Pro577del	p.P577del	ENST00000288135	NM_000222.2	576	ctTCCt/ctt	11/21	1	2	FACETS	1	0.979	1	1	0.994	1	CLONAL	2	TRUE	1	0.213289385713876	2		562	857	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245912910	245912910	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	131	475	0	ENST00000388985.4:c.1242G>C	p.Leu414Phe	p.L414F	ENST00000388985		414	ttG/ttC	12/12	0.213289385713876	3	FACETS	0.93	0.845	1	0.93	0.845	1	CLONAL	2	TRUE	1	0.213289385713876	3		475	731	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813411	102813411	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	69	504	0	ENST00000307046.8:c.278A>T	p.Asp93Val	p.D93V	ENST00000307046	NM_001111285.1	93	gAt/gTt	3/4	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.213289385713876	2		504	550	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867565	45867565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	92	617	0	ENST00000391945.4:c.743G>A	p.Ser248Asn	p.S248N	ENST00000391945	NM_000400.3	248	aGc/aAc	9/23	NA	3	FACETS	1	0.952	1			1	INDETERMINATE	1	TRUE	NA	0.213289385713876	3		617	842	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347969	89347969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	285	658	0	ENST00000301030.4:c.4981C>T	p.Pro1661Ser	p.P1661S	ENST00000301030	NM_001256183.1	1661	Cca/Tca	9/13	0.945612300641449	3	FACETS	0.969	0.913	1	0.485	0.456	0.513	CLONAL	1	TRUE	1	0.945612300641449	3		658	916	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007811	45007811	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0025325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	241	450	0	ENST00000558401.1:c.258C>G	p.Tyr86Ter	p.Y86*	ENST00000558401	NM_004048.2	86	taC/taG	2/4	0.945612300641449	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.945612300641449	1		450	248	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414398	6414398	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	274	241	0	ENST00000356142.4:c.32A>T	p.Asp11Val	p.D11V	ENST00000356142	NM_018890.3	11	gAc/gTc	1/7	0.464803199801989	6	FACETS	1	0.966	1	1	0.966	1	INDETERMINATE	3	TRUE	3	0.945612300641449	6		241	546	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0025327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	296	578	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	0.342841946837374	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.512883511451268	4		578	826	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267484	198267484	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775623976	NA	P-0025327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	102	525	0	ENST00000335508.6:c.1873C>T	p.Arg625Cys	p.R625C	ENST00000335508	NM_012433.2	625	Cgt/Tgt	14/25	1	2	FACETS	0.894	0.804	0.988	0.894	0.804	0.988	CLONAL	1	TRUE	1	0.512883511451268	2		525	445	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843495	3843495	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1384496494	NA	P-0025327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	144	638	0	ENST00000262367.5:c.1108C>G	p.Arg370Gly	p.R370G	ENST00000262367	NM_004380.2	370	Cga/Gga	4/31	0.485920430251948	3	FACETS	0.88	0.803	0.96	0.44	0.401	0.48	CLONAL	1	TRUE	1	0.512883511451268	3		638	802	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0025347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	142	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.993	0.907	1	0.993	0.907	1	CLONAL	1	TRUE	1	0.415826213448318	2		306	688	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561263	9561263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769939031	NA	P-0025347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	135	485	0	ENST00000353224.5:c.519G>A	p.Met173Ile	p.M173I	ENST00000353224	NM_177990.2	173	atG/atA	4/10	1	2	FACETS	0.791	0.719	0.866	0.791	0.719	0.866	SUBCLONAL	1	TRUE	1	0.415826213448318	2		485	821	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673130	30673130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	69	508	1	ENST00000376406.3:c.3830C>T	p.Ser1277Phe	p.S1277F	ENST00000376406	NM_014641.2	1277	tCt/tTt	10/15	0.217964390581659	3	FACETS	0.478	0.415	0.546	0.239	0.207	0.273	INDETERMINATE	1	TRUE	1	0.415826213448318	3		509	839	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453132	140453132	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913365	NA	P-0025347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	144	561	0	ENST00000288602.6:c.1803A>C	p.Lys601Asn	p.K601N	ENST00000288602	NM_004333.4	601	aaA/aaC	15/18	1	2	FACETS	0.962	0.879	1	0.962	0.879	1	CLONAL	1	TRUE	1	0.415826213448318	2		561	720	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210709	36210709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780868475	NA	P-0025347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	223	666	0	ENST00000222270.7:c.460C>T	p.Arg154Cys	p.R154C	ENST00000222270	NM_014727.1	154	Cgc/Tgc	3/37	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.415826213448318	2		666	967	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330547	65330547	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	218	598	0	ENST00000342505.4:c.1099T>G	p.Ser367Ala	p.S367A	ENST00000342505	NM_002227.2	367	Tct/Gct	8/25	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.415826213448318	2		598	990	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456797	32456797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	206	664	1	ENST00000332351.3:c.95G>A	p.Gly32Glu	p.G32E	ENST00000332351	NM_024426.4	32	gGa/gAa	1/10	0.415826213448318	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.415826213448318	1		665	731	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422712	49422712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777053146	NA	P-0025347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	211	585	0	ENST00000301067.7:c.14281C>T	p.Leu4761Phe	p.L4761F	ENST00000301067	NM_003482.3	4761	Ctt/Ttt	45/54	0.205973441536423	1	FACETS	1	0.939	1	1	0.939	1	INDETERMINATE	1	TRUE	0	0.415826213448318	1		585	797	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436084	49436084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	125	360	0	ENST00000301067.7:c.5897C>T	p.Pro1966Leu	p.P1966L	ENST00000301067	NM_003482.3	1966	cCc/cTc	28/54	0.205973441536423	1	FACETS	0.861	0.783	0.943	0.861	0.783	0.943	INDETERMINATE	1	TRUE	0	0.415826213448318	1		360	553	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560494	95560494	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0025347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	159	477	0	ENST00000393063.1:c.5096-1G>A		p.X1699_splice	ENST00000393063	NM_030621.3	1699			1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.415826213448318	2		477	741	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828381	72828381	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	162	631	2	ENST00000268489.5:c.8200C>T	p.His2734Tyr	p.H2734Y	ENST00000268489	NM_006885.3	2734	Cac/Tac	9/10	1	2	FACETS	0.95	0.873	1	0.95	0.873	1	CLONAL	1	TRUE	1	0.415826213448318	2		633	820	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545699	63545699	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	194	610	0	ENST00000307078.5:c.895G>C	p.Asp299His	p.D299H	ENST00000307078	NM_004655.3	299	Gac/Cac	3/11	0.408202930053082	3	FACETS	0.999	0.923	1	0.5	0.461	0.539	CLONAL	1	TRUE	1	0.415826213448318	3		610	1128	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119768	70119768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	179	606	0	ENST00000245479.2:c.770G>A	p.Arg257His	p.R257H	ENST00000245479	NM_000346.3	257	cGc/cAc	3/3	0.408202930053082	3	FACETS	0.96	0.884	1	0.48	0.442	0.52	CLONAL	1	TRUE	1	0.415826213448318	3		606	1083	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584367	39584409	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCAAACAGGCCTTGGAACTTCTGGGAAAATGGAAGCCGATG	GGCCAAACAGGCCTTGGAACTTCTGGGAAAATGGAAGCCGATG	-	novel	NA	P-0025347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	94	385	1	ENST00000262039.4:c.1033_1075del	p.Ala345MetfsTer2	p.A345Mfs*2	ENST00000262039	NM_002647.2	344	gaGGCCAAACAGGCCTTGGAACTTCTGGGAAAATGGAAGCCGATG/ga	10/25	1	2	FACETS	0.883	0.788	0.983	0.883	0.788	0.983	CLONAL	1	TRUE	1	0.415826213448318	2		386	512	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274344	5274345	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	novel	NA	P-0025347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	143	437	0	ENST00000357368.4:c.102_103delinsAA	p.Phe35Ile	p.F35I	ENST00000357368	NM_002850.3	34	agGTtt/agAAtt	3/38	1	2	FACETS	0.991	0.906	1	0.991	0.906	1	CLONAL	1	TRUE	1	0.415826213448318	2		437	694	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224343	36224344	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	267	735	2	ENST00000222270.7:c.6893_6894delinsTT	p.Pro2298Leu	p.P2298L	ENST00000222270	NM_014727.1	2298	cCC/cTT	28/37	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.415826213448318	2		737	1248	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224713	36224713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1280550594	NA	P-0025347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	301	828	1	ENST00000222270.7:c.7099C>T	p.Pro2367Ser	p.P2367S	ENST00000222270	NM_014727.1	2367	Ccc/Tcc	30/37	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.415826213448318	2		829	1292	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994410	25994410	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0025347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	110	341	1	ENST00000435504.4:c.404-1G>A		p.X135_splice	ENST00000435504		135			0.415826213448318	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.415826213448318	1		342	375	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447438	12447438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	189	623	1	ENST00000287820.6:c.677C>T	p.Ser226Phe	p.S226F	ENST00000287820	NM_015869.4	226	tCc/tTc	5/7	0.217964390581659	3	FACETS	1	0.976	1	0.567	0.523	0.611	INDETERMINATE	1	TRUE	1	0.415826213448318	3		624	969	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934849	49934849	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	328	623	0	ENST00000296474.3:c.2047G>A	p.Glu683Lys	p.E683K	ENST00000296474	NM_002447.2	683	Gag/Aag	7/20	0.217964390581659	3	FACETS	0.927	0.877	0.978	0.927	0.877	0.978	INDETERMINATE	2	TRUE	1	0.415826213448318	3		623	1028	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185169089	185169089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746110965	NA	P-0025347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	742	555	0	ENST00000265026.3:c.1184G>A	p.Arg395Gln	p.R395Q	ENST00000265026	NM_004721.4	395	cGa/cAa	7/14	0.415826213448318	6	FACETS	0.954	0.925	0.982			1	CLONAL	5	TRUE	NA	0.415826213448318	6		555	1371	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80074648	80074648	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	154	550	0	ENST00000265081.6:c.2428T>G	p.Phe810Val	p.F810V	ENST00000265081	NM_002439.4	810	Ttt/Gtt	17/24	1	2	FACETS	0.95	0.87	1	0.95	0.87	1	CLONAL	1	TRUE	1	0.415826213448318	2		550	780	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517785	176517785	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	248	705	0	ENST00000292408.4:c.395C>T	p.Ser132Phe	p.S132F	ENST00000292408	NM_213647.1	132	tCc/tTc	4/18	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.415826213448318	2		705	1121	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547265	106547265	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	125	379	0	ENST00000369096.4:c.502C>T	p.Pro168Ser	p.P168S	ENST00000369096	NM_001198.3	168	Ccc/Tcc	4/7	0.169632999816722	1	FACETS	0.895	0.814	0.98	0.895	0.814	0.98	INDETERMINATE	1	TRUE	0	0.415826213448318	1		379	532	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2952956	2952956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1338162870	NA	P-0025347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	241	705	2	ENST00000396946.4:c.2984C>T	p.Ser995Leu	p.S995L	ENST00000396946	NM_032415.4	995	tCg/tTg	22/25	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.415826213448318	2		707	1120	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266443	55266443	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	163	559	1	ENST00000275493.2:c.2735C>T	p.Ser912Phe	p.S912F	ENST00000275493	NM_005228.3	912	tCc/tTc	23/28	1	2	FACETS	0.992	0.912	1	0.992	0.912	1	CLONAL	1	TRUE	1	0.415826213448318	2		560	790	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231109	98231109	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	291	577	0	ENST00000331920.6:c.2174C>T	p.Pro725Leu	p.P725L	ENST00000331920	NM_000264.3	725	cCc/cTc	14/24	0.401781418869557	2	FACETS	0.92	0.87	0.97	0.92	0.87	0.97	CLONAL	2	TRUE	0	0.415826213448318	2		577	761	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391172	139391172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1254082910	NA	P-0025347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	333	752	0	ENST00000277541.6:c.7019C>T	p.Pro2340Leu	p.P2340L	ENST00000277541	NM_017617.3	2340	cCc/cTc	34/34	0.401781418869557	2	FACETS	0.863	0.818	0.908	0.863	0.818	0.908	CLONAL	2	TRUE	0	0.415826213448318	2		752	928	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	339	578	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	0.929	0.883	0.975	0.929	0.883	0.975	CLONAL	1	TRUE	1	0.89653998002776	2		578	814	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356269	66356269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200754741	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	72	613	0	ENST00000273854.3:c.1228G>A	p.Gly410Ser	p.G410S	ENST00000273854	NM_004439.5	410	Ggt/Agt	5/18	1	2	FACETS	0.284	0.248	0.322	0.284	0.248	0.322	SUBCLONAL	1	TRUE	1	0.89653998002776	2		613	566	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246447	46246447	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	17	372	0	ENST00000334344.6:c.4541C>T	p.Thr1514Ile	p.T1514I	ENST00000334344	NM_152641.2	1514	aCt/aTt	15/21	1	2	FACETS	0.133	0.099	0.173	0.133	0.099	0.173	SUBCLONAL	1	TRUE	1	0.89653998002776	2		372	286	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500886	8500886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	19	552	1	ENST00000356435.5:c.1996C>T	p.Pro666Ser	p.P666S	ENST00000356435		666	Cct/Tct	13/35	1	2	FACETS	0.118	0.089	0.153	0.118	0.089	0.153	SUBCLONAL	1	TRUE	1	0.89653998002776	2		553	358	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987144	36987144	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	48	616	0	ENST00000354822.5:c.545A>G	p.Asn182Ser	p.N182S	ENST00000354822	NM_001079668.2	182	aAc/aGc	3/3	1	2	FACETS	0.198	0.167	0.233	0.198	0.167	0.233	SUBCLONAL	1	TRUE	1	0.89653998002776	2		616	540	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358670	67358670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	76	521	0	ENST00000327367.4:c.178G>A	p.Val60Ile	p.V60I	ENST00000327367	NM_005902.3	60	Gtc/Atc	1/9	1	2	FACETS	0.286	0.251	0.324	0.286	0.251	0.324	SUBCLONAL	1	TRUE	1	0.89653998002776	2		521	592	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992292	72992292	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140602496	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	104	821	1	ENST00000268489.5:c.1753G>A	p.Gly585Ser	p.G585S	ENST00000268489	NM_006885.3	585	Ggc/Agc	2/10	1	2	FACETS	0.284	0.253	0.316	0.284	0.253	0.316	SUBCLONAL	1	TRUE	1	0.89653998002776	2		822	818	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356247	66356247	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199614818	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	85	698	0	ENST00000273854.3:c.1250G>A	p.Arg417Gln	p.R417Q	ENST00000273854	NM_004439.5	417	cGg/cAg	5/18	1	2	FACETS	0.32	0.283	0.359	0.32	0.283	0.359	SUBCLONAL	1	TRUE	1	0.89653998002776	2		698	593	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099858	157099858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	84	540	0	ENST00000346085.5:c.795G>A	p.Met265Ile	p.M265I	ENST00000346085	NM_020732.3	265	atG/atA	1/20	1	2	FACETS	0.189	0.166	0.213	0.189	0.166	0.213	SUBCLONAL	1	TRUE	1	0.89653998002776	2		540	992	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611845	100611845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782813365	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	32	357	1	ENST00000308731.7:c.1276G>A	p.Asp426Asn	p.D426N	ENST00000308731	NM_000061.2	426	Gac/Aac	14/19	1	1	FACETS	0.163	0.132	0.197	0.163	0.132	0.197	SUBCLONAL	1	TRUE	0	0.89653998002776	1		358	242	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993405	72993405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	75	752	0	ENST00000268489.5:c.640G>A	p.Ala214Thr	p.A214T	ENST00000268489	NM_006885.3	214	Gct/Act	2/10	1	2	FACETS	0.235	0.205	0.267	0.235	0.205	0.267	SUBCLONAL	1	TRUE	1	0.89653998002776	2		752	712	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807582	1807582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145183329	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	39	671	0	ENST00000260795.2:c.1751C>T	p.Pro584Leu	p.P584L	ENST00000260795		584	cCg/cTg	12/17	1	2	FACETS	0.113	0.093	0.135	0.113	0.093	0.135	SUBCLONAL	1	TRUE	1	0.89653998002776	2		671	770	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777863	3777863	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1300659854	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	77	819	0	ENST00000262367.5:c.7185A>G	p.Ile2395Met	p.I2395M	ENST00000262367	NM_004380.2	2395	atA/atG	31/31	1	2	FACETS	0.237	0.207	0.269	0.237	0.207	0.269	SUBCLONAL	1	TRUE	1	0.89653998002776	2		819	725	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046467	30046467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777521591	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	47	570	2	ENST00000331968.5:c.2716G>A	p.Gly906Ser	p.G906S	ENST00000331968	NM_002742.2	906	Ggt/Agt	18/18	1	2	FACETS	0.2	0.168	0.235	0.2	0.168	0.235	SUBCLONAL	1	TRUE	1	0.89653998002776	2		572	524	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300845	137300845	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	53	647	0	ENST00000481739.1:c.490C>A	p.Arg164Ser	p.R164S	ENST00000481739	NM_002957.4	164	Cgc/Agc	4/10	0.89653998002776	3	FACETS	0.165	0.14	0.193	0.083	0.07	0.097	SUBCLONAL	1	TRUE	1	0.89653998002776	3		647	1035	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792669	33792669	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1378898437	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	22	185	0	ENST00000498907.2:c.652A>G	p.Met218Val	p.M218V	ENST00000498907	NM_004364.3	218	Atg/Gtg	1/1	1	2	FACETS	0.132	0.102	0.167	0.132	0.102	0.167	SUBCLONAL	1	TRUE	1	0.89653998002776	2		185	372	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922811	44922811	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	32	249	0	ENST00000377967.4:c.1672G>A	p.Val558Ile	p.V558I	ENST00000377967	NM_021140.2	558	Gtc/Atc	16/29	1	1	FACETS	0.13	0.105	0.158	0.13	0.105	0.158	SUBCLONAL	1	TRUE	0	0.89653998002776	1		249	303	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799180	88799180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	36	671	2	ENST00000360948.2:c.205G>A	p.Ala69Thr	p.A69T	ENST00000360948	NM_001012338.2	69	Gcc/Acc	2/19	1	2	FACETS	0.157	0.129	0.19	0.157	0.129	0.19	SUBCLONAL	1	TRUE	1	0.89653998002776	2		673	510	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923175	39923175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375639152	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	42	307	0	ENST00000378444.4:c.3533G>A	p.Ser1178Asn	p.S1178N	ENST00000378444	NM_001123385.1	1178	aGt/aAt	8/15	1	1	FACETS	0.238	0.201	0.279	0.238	0.201	0.279	SUBCLONAL	1	TRUE	0	0.89653998002776	1		307	217	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11297908	11297908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	26	508	0	ENST00000361445.4:c.2200C>T	p.Leu734Phe	p.L734F	ENST00000361445	NM_004958.3	734	Ctc/Ttc	13/58	1	2	FACETS	0.112	0.088	0.139	0.112	0.088	0.139	SUBCLONAL	1	TRUE	1	0.89653998002776	2		508	520	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199569	16199570	+	missense_variant	Missense_Mutation	DNP	TG	TG	CA	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	58	535	2	ENST00000375759.3:c.342_343inv	p.Ala115Thr	p.A115T	ENST00000375759	NM_015001.2	114	ccTGct/ccCAct	2/15	1	2	FACETS	0.207	0.178	0.24	0.207	0.178	0.24	SUBCLONAL	1	TRUE	1	0.89653998002776	2		537	624	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202844	16202845	+	missense_variant	Missense_Mutation	DNP	CG	CG	TA	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	76	571	2	ENST00000375759.3:c.552_553delinsTA	p.Ala185Thr	p.A185T	ENST00000375759	NM_015001.2	184	taCGct/taTAct	3/15	1	2	FACETS	0.319	0.28	0.36	0.319	0.28	0.36	SUBCLONAL	1	TRUE	1	0.89653998002776	2		573	532	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46597588	46597588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771431827	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	34	670	0	ENST00000262741.5:c.37G>A	p.Ala13Thr	p.A13T	ENST00000262741	NM_003629.3	13	Gca/Aca	1/10	1	2	FACETS	0.114	0.093	0.138	0.114	0.093	0.138	SUBCLONAL	1	TRUE	1	0.89653998002776	2		670	665	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46597605	46597606	+	missense_variant	Missense_Mutation	DNP	CT	CT	TC	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	30	601	0	ENST00000262741.5:c.19_20delinsGA	p.Ser7Asp	p.S7D	ENST00000262741	NM_003629.3	7	AGt/GAt	1/10	1	2	FACETS	0.117	0.094	0.144	0.117	0.094	0.144	SUBCLONAL	1	TRUE	1	0.89653998002776	2		601	572	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436096	51436096	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	28	454	0	ENST00000262662.1:c.56A>T	p.Glu19Val	p.E19V	ENST00000262662		19	gAg/gTg	3/4	1	2	FACETS	0.139	0.111	0.172	0.139	0.111	0.172	SUBCLONAL	1	TRUE	1	0.89653998002776	2		454	449	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436108	51436108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	30	463	0	ENST00000262662.1:c.68G>A	p.Ser23Asn	p.S23N	ENST00000262662		23	aGt/aAt	3/4	1	2	FACETS	0.151	0.121	0.185	0.151	0.121	0.185	SUBCLONAL	1	TRUE	1	0.89653998002776	2		463	443	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436121	51436121	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	33	468	0	ENST00000262662.1:c.81T>G	p.Asn27Lys	p.N27K	ENST00000262662		27	aaT/aaG	3/4	1	2	FACETS	0.197	0.16	0.238	0.197	0.16	0.238	SUBCLONAL	1	TRUE	1	0.89653998002776	2		468	374	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282445	115282445	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	37	604	0	ENST00000438362.2:c.205G>A	p.Ala69Thr	p.A69T	ENST00000438362	NM_001242891.1	69	Gca/Aca	3/20	1	2	FACETS	0.225	0.185	0.269	0.225	0.185	0.269	SUBCLONAL	1	TRUE	1	0.89653998002776	2		604	367	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849872	156849872	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370593942	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	65	646	0	ENST00000524377.1:c.2128G>A	p.Val710Met	p.V710M	ENST00000524377	NM_002529.3	710	Gtg/Atg	16/17	1	2	FACETS	0.195	0.169	0.224	0.195	0.169	0.224	SUBCLONAL	1	TRUE	1	0.89653998002776	2		646	742	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115817	8115817	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs745424381	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	41	656	0	ENST00000346208.3:c.1163A>G	p.Asn388Ser	p.N388S	ENST00000346208		388	aAc/aGc	6/6	1	2	FACETS	0.131	0.108	0.156	0.131	0.108	0.156	SUBCLONAL	1	TRUE	1	0.89653998002776	2		656	699	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623584	43623585	+	missense_variant	Missense_Mutation	DNP	GA	GA	AG	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	35	453	0	ENST00000355710.3:c.3212_3213delinsAG	p.Gly1071Glu	p.G1071E	ENST00000355710	NM_020975.4	1071	gGA/gAG	20/20	1	2	FACETS	0.207	0.17	0.249	0.207	0.17	0.249	SUBCLONAL	1	TRUE	1	0.89653998002776	2		453	377	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623625	43623625	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	48	547	0	ENST00000355710.3:c.3253A>T	p.Thr1085Ser	p.T1085S	ENST00000355710	NM_020975.4	1085	Act/Tct	20/20	1	2	FACETS	0.253	0.214	0.296	0.253	0.214	0.296	SUBCLONAL	1	TRUE	1	0.89653998002776	2		547	423	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623629	43623629	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	54	545	1	ENST00000355710.3:c.3257G>T	p.Gly1086Val	p.G1086V	ENST00000355710	NM_020975.4	1086	gGg/gTg	20/20	1	2	FACETS	0.281	0.241	0.326	0.281	0.241	0.326	SUBCLONAL	1	TRUE	1	0.89653998002776	2		546	428	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623634	43623634	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	57	546	1	ENST00000355710.3:c.3262C>T	p.Pro1088Ser	p.P1088S	ENST00000355710	NM_020975.4	1088	Cca/Tca	20/20	1	2	FACETS	0.304	0.261	0.351	0.304	0.261	0.351	SUBCLONAL	1	TRUE	1	0.89653998002776	2		547	418	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623643	43623643	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	56	541	0	ENST00000355710.3:c.3271C>G	p.Pro1091Ala	p.P1091A	ENST00000355710	NM_020975.4	1091	Cca/Gca	20/20	1	2	FACETS	0.297	0.255	0.343	0.297	0.255	0.343	SUBCLONAL	1	TRUE	1	0.89653998002776	2		541	420	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623673	43623673	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	48	563	0	ENST00000355710.3:c.3301C>G	p.Leu1101Val	p.L1101V	ENST00000355710	NM_020975.4	1101	Ctt/Gtt	20/20	1	2	FACETS	0.243	0.206	0.285	0.243	0.206	0.285	SUBCLONAL	1	TRUE	1	0.89653998002776	2		563	440	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623680	43623680	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	47	566	0	ENST00000355710.3:c.3308C>A	p.Pro1103His	p.P1103H	ENST00000355710	NM_020975.4	1103	cCc/cAc	20/20	1	2	FACETS	0.24	0.202	0.281	0.24	0.202	0.281	SUBCLONAL	1	TRUE	1	0.89653998002776	2		566	437	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623696	43623697	+	missense_variant	Missense_Mutation	DNP	AA	AA	TG	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	32	564	1	ENST00000355710.3:c.3324_3325delinsTG	p.Leu1108_Met1109delinsPheVal	p.L1108_M1109delinsFV	ENST00000355710	NM_020975.4	1108	ttAAtg/ttTGtg	20/20	1	2	FACETS	0.174	0.141	0.211	0.174	0.141	0.211	SUBCLONAL	1	TRUE	1	0.89653998002776	2		565	411	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623704	43623704	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	31	540	0	ENST00000355710.3:c.3332C>A	p.Thr1111Lys	p.T1111K	ENST00000355710	NM_020975.4	1111	aCg/aAg	20/20	1	2	FACETS	0.178	0.144	0.217	0.178	0.144	0.217	SUBCLONAL	1	TRUE	1	0.89653998002776	2		540	388	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724437	112724438	+	missense_variant	Missense_Mutation	DNP	AT	AT	GG	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	21	612	0	ENST00000369452.4:c.321_322delinsGG	p.Ser108Ala	p.S108A	ENST00000369452	NM_007373.3	107	ttATcc/ttGGcc	2/9	1	2	FACETS	0.156	0.119	0.198	0.156	0.119	0.198	SUBCLONAL	1	TRUE	1	0.89653998002776	2		612	301	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724690	112724691	+	missense_variant	Missense_Mutation	DNP	GA	GA	AC	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	29	633	2	ENST00000369452.4:c.574_575delinsAC	p.Asp192Thr	p.D192T	ENST00000369452	NM_007373.3	192	GAt/ACt	2/9	1	2	FACETS	0.159	0.127	0.196	0.159	0.127	0.196	SUBCLONAL	1	TRUE	1	0.89653998002776	2		635	406	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724699	112724699	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	28	618	0	ENST00000369452.4:c.583A>G	p.Thr195Ala	p.T195A	ENST00000369452	NM_007373.3	195	Acc/Gcc	2/9	1	2	FACETS	0.152	0.121	0.188	0.152	0.121	0.188	SUBCLONAL	1	TRUE	1	0.89653998002776	2		618	410	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724769	112724769	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	19	416	0	ENST00000369452.4:c.653G>C	p.Ser218Thr	p.S218T	ENST00000369452	NM_007373.3	218	aGc/aCc	2/9	1	2	FACETS	0.14	0.106	0.18	0.14	0.106	0.18	SUBCLONAL	1	TRUE	1	0.89653998002776	2		416	303	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710607	114710607	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	29	473	0	ENST00000543371.1:c.92G>T	p.Ser31Ile	p.S31I	ENST00000543371	NM_001198531.1	31	aGc/aTc	1/14	1	2	FACETS	0.125	0.1	0.154	0.125	0.1	0.154	SUBCLONAL	1	TRUE	1	0.89653998002776	2		473	518	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920429	114920429	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1385296187	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	40	530	0	ENST00000543371.1:c.1370C>G	p.Thr457Ser	p.T457S	ENST00000543371	NM_001198531.1	457	aCt/aGt	13/14	1	2	FACETS	0.167	0.138	0.199	0.167	0.138	0.199	SUBCLONAL	1	TRUE	1	0.89653998002776	2		530	534	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925360	114925360	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	66	605	0	ENST00000543371.1:c.1438C>G	p.Leu480Val	p.L480V	ENST00000543371	NM_001198531.1	480	Ctc/Gtc	14/14	1	2	FACETS	0.237	0.205	0.271	0.237	0.205	0.271	SUBCLONAL	1	TRUE	1	0.89653998002776	2		605	621	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274741	123274741	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	50	678	0	ENST00000358487.5:c.1177G>C	p.Val393Leu	p.V393L	ENST00000358487	NM_000141.4	393	Gta/Cta	9/18	1	2	FACETS	0.196	0.166	0.229	0.196	0.166	0.229	SUBCLONAL	1	TRUE	1	0.89653998002776	2		678	570	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276857	123276857	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	25	484	0	ENST00000358487.5:c.1060T>A	p.Ser354Thr	p.S354T	ENST00000358487	NM_000141.4	354	Tct/Act	8/18	1	2	FACETS	0.215	0.169	0.266	0.215	0.169	0.266	SUBCLONAL	1	TRUE	1	0.89653998002776	2		484	260	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741804	17741804	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	35	423	0	ENST00000250003.3:c.475G>A	p.Gly159Ser	p.G159S	ENST00000250003	NM_002478.4	159	Ggc/Agc	1/3	1	2	FACETS	0.207	0.17	0.249	0.207	0.17	0.249	SUBCLONAL	1	TRUE	1	0.89653998002776	2		423	377	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741917	17741917	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	16	262	0	ENST00000250003.3:c.588C>G	p.Asp196Glu	p.D196E	ENST00000250003	NM_002478.4	196	gaC/gaG	1/3	1	2	FACETS	0.129	0.095	0.169	0.129	0.095	0.169	SUBCLONAL	1	TRUE	1	0.89653998002776	2		262	277	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589559	69589560	+	missense_variant	Missense_Mutation	DNP	CG	CG	GA	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	41	331	0	ENST00000168712.1:c.293_294delinsTC	p.Ala98Val	p.A98V	ENST00000168712	NM_002007.2	98	gCG/gTC	1/3	1	2	FACETS	0.221	0.184	0.262	0.221	0.184	0.262	SUBCLONAL	1	TRUE	1	0.89653998002776	2		331	414	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589567	69589567	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	46	344	0	ENST00000168712.1:c.286C>A	p.Leu96Ile	p.L96I	ENST00000168712	NM_002007.2	96	Ctc/Atc	1/3	1	2	FACETS	0.228	0.192	0.268	0.228	0.192	0.268	SUBCLONAL	1	TRUE	1	0.89653998002776	2		344	450	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94908761	94908761	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	35	605	0	ENST00000536441.1:c.1293A>C	p.Arg431Ser	p.R431S	ENST00000536441	NM_144665.3	431	agA/agC	9/10	1	2	FACETS	0.226	0.185	0.271	0.226	0.185	0.271	SUBCLONAL	1	TRUE	1	0.89653998002776	2		605	346	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924640	94924640	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	37	678	0	ENST00000536441.1:c.270G>C	p.Leu90Phe	p.L90F	ENST00000536441	NM_144665.3	90	ttG/ttC	3/10	1	2	FACETS	0.181	0.148	0.217	0.181	0.148	0.217	SUBCLONAL	1	TRUE	1	0.89653998002776	2		678	457	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924667	94924667	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	60	711	0	ENST00000536441.1:c.243A>C	p.Leu81Phe	p.L81F	ENST00000536441	NM_144665.3	81	ttA/ttC	3/10	1	2	FACETS	0.285	0.246	0.328	0.285	0.246	0.328	SUBCLONAL	1	TRUE	1	0.89653998002776	2		711	469	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924669	94924669	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	52	703	1	ENST00000536441.1:c.241T>A	p.Leu81Ile	p.L81I	ENST00000536441	NM_144665.3	81	Tta/Ata	3/10	1	2	FACETS	0.234	0.199	0.273	0.234	0.199	0.273	SUBCLONAL	1	TRUE	1	0.89653998002776	2		704	495	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924729	94924730	+	missense_variant	Missense_Mutation	DNP	AG	AG	GA	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	40	758	0	ENST00000536441.1:c.180_181delinsTC	p.Phe61Leu	p.F61L	ENST00000536441	NM_144665.3	60	aaCTtt/aaTCtt	3/10	1	2	FACETS	0.182	0.151	0.217	0.182	0.151	0.217	SUBCLONAL	1	TRUE	1	0.89653998002776	2		758	490	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981808	101981829	+	missense_variant	Missense_Mutation	ONP	ACGGCCAACGTGCCCCAGACCG	ACGGCCAACGTGCCCCAGACCG	GGCGCCAACGTGCCGCACACGC	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	73	673	1	ENST00000282441.5:c.229_250delinsGGCGCCAACGTGCCGCACACGC	p.Thr77_Val84delinsGlyAlaAsnValProHisThrLeu	p.T77_V84delinsGANVPHTL	ENST00000282441	NM_001130145.2	77	ACGGCCAACGTGCCCCAGACCGtg/GGCGCCAACGTGCCGCACACGCtg	1/9	1	2	FACETS	0.164	0.143	0.187	0.164	0.143	0.187	SUBCLONAL	1	TRUE	1	0.89653998002776	2		674	992	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076787	102076787	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	46	662	0	ENST00000282441.5:c.966G>T	p.Gln322His	p.Q322H	ENST00000282441	NM_001130145.2	322	caG/caT	5/9	1	2	FACETS	0.147	0.123	0.174	0.147	0.123	0.174	SUBCLONAL	1	TRUE	1	0.89653998002776	2		662	697	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383367	4383367	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	26	576	0	ENST00000261254.3:c.161A>T	p.Tyr54Phe	p.Y54F	ENST00000261254	NM_001759.3	54	tAc/tTc	1/5	1	2	FACETS	0.134	0.105	0.166	0.134	0.105	0.166	SUBCLONAL	1	TRUE	1	0.89653998002776	2		576	434	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383372	4383372	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	26	554	0	ENST00000261254.3:c.166C>A	p.Arg56Ser	p.R56S	ENST00000261254	NM_001759.3	56	Cgc/Agc	1/5	1	2	FACETS	0.124	0.098	0.155	0.124	0.098	0.155	SUBCLONAL	1	TRUE	1	0.89653998002776	2		554	466	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123880	46123880	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	29	425	0	ENST00000334344.6:c.146G>C	p.Gly49Ala	p.G49A	ENST00000334344	NM_152641.2	49	gGt/gCt	2/21	1	2	FACETS	0.114	0.091	0.14	0.114	0.091	0.14	SUBCLONAL	1	TRUE	1	0.89653998002776	2		425	569	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123916	46123916	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1358258248	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	22	326	0	ENST00000334344.6:c.182C>G	p.Ala61Gly	p.A61G	ENST00000334344	NM_152641.2	61	gCg/gGg	2/21	1	2	FACETS	0.123	0.095	0.156	0.123	0.095	0.156	SUBCLONAL	1	TRUE	1	0.89653998002776	2		326	399	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245408	46245408	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	28	493	0	ENST00000334344.6:c.3502T>A	p.Ser1168Thr	p.S1168T	ENST00000334344	NM_152641.2	1168	Tct/Act	15/21	1	2	FACETS	0.215	0.172	0.263	0.215	0.172	0.263	SUBCLONAL	1	TRUE	1	0.89653998002776	2		493	291	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245455	46245456	+	missense_variant	Missense_Mutation	DNP	AC	AC	TA	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	25	385	2	ENST00000334344.6:c.3549_3550delinsTA	p.Pro1184Thr	p.P1184T	ENST00000334344	NM_152641.2	1183	gcACct/gcTAct	15/21	1	2	FACETS	0.198	0.156	0.247	0.198	0.156	0.247	SUBCLONAL	1	TRUE	1	0.89653998002776	2		387	281	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245456	46245456	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	25	385	1	ENST00000334344.6:c.3550C>A	p.Pro1184Thr	p.P1184T	ENST00000334344	NM_152641.2	1184	Cct/Act	15/21	1	2	FACETS	0.2	0.158	0.248	0.2	0.158	0.248	SUBCLONAL	1	TRUE	1	0.89653998002776	2		386	279	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245606	46245606	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs769648999	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	13	347	0	ENST00000334344.6:c.3700A>G	p.Thr1234Ala	p.T1234A	ENST00000334344	NM_152641.2	1234	Act/Gct	15/21	1	2	FACETS	0.131	0.093	0.177	0.131	0.093	0.177	SUBCLONAL	1	TRUE	1	0.89653998002776	2		347	222	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245677	46245678	+	missense_variant	Missense_Mutation	DNP	TG	TG	CA	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	26	396	2	ENST00000334344.6:c.3771_3772inv	p.Val1258Ile	p.V1258I	ENST00000334344	NM_152641.2	1257	caTGtt/caCAtt	15/21	1	2	FACETS	0.182	0.144	0.226	0.182	0.144	0.226	SUBCLONAL	1	TRUE	1	0.89653998002776	2		398	318	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245731	46245732	+	missense_variant	Missense_Mutation	DNP	CA	CA	TG	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	19	457	2	ENST00000334344.6:c.3825_3826inv	p.Thr1276Ala	p.T1276A	ENST00000334344	NM_152641.2	1275	gcCAca/gcTGca	15/21	1	2	FACETS	0.135	0.102	0.174	0.135	0.102	0.174	SUBCLONAL	1	TRUE	1	0.89653998002776	2		459	314	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245753	46245753	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	26	454	0	ENST00000334344.6:c.3847A>G	p.Thr1283Ala	p.T1283A	ENST00000334344	NM_152641.2	1283	Aca/Gca	15/21	1	2	FACETS	0.204	0.161	0.252	0.204	0.161	0.252	SUBCLONAL	1	TRUE	1	0.89653998002776	2		454	285	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245773	46245773	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	22	455	0	ENST00000334344.6:c.3867T>G	p.His1289Gln	p.H1289Q	ENST00000334344	NM_152641.2	1289	caT/caG	15/21	1	2	FACETS	0.163	0.126	0.206	0.163	0.126	0.206	SUBCLONAL	1	TRUE	1	0.89653998002776	2		455	301	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246080	46246080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	11	342	1	ENST00000334344.6:c.4174C>T	p.Pro1392Ser	p.P1392S	ENST00000334344	NM_152641.2	1392	Cca/Tca	15/21	1	2	FACETS	0.117	0.081	0.163	0.117	0.081	0.163	SUBCLONAL	1	TRUE	1	0.89653998002776	2		343	209	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246140	46246142	+	missense_variant	Missense_Mutation	TNP	CTA	CTA	GGG	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	14	406	2	ENST00000334344.6:c.4234_4236delinsGGG	p.Leu1412Gly	p.L1412G	ENST00000334344	NM_152641.2	1412	CTA/GGG	15/21	1	2	FACETS	0.147	0.106	0.197	0.147	0.106	0.197	SUBCLONAL	1	TRUE	1	0.89653998002776	2		408	212	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246249	46246249	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	24	405	0	ENST00000334344.6:c.4343T>C	p.Leu1448Pro	p.L1448P	ENST00000334344	NM_152641.2	1448	cTt/cCt	15/21	1	2	FACETS	0.189	0.148	0.236	0.189	0.148	0.236	SUBCLONAL	1	TRUE	1	0.89653998002776	2		405	283	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246322	46246322	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	28	405	2	ENST00000334344.6:c.4416T>A	p.His1472Gln	p.H1472Q	ENST00000334344	NM_152641.2	1472	caT/caA	15/21	1	2	FACETS	0.214	0.171	0.263	0.214	0.171	0.263	SUBCLONAL	1	TRUE	1	0.89653998002776	2		407	292	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246329	46246329	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	26	410	0	ENST00000334344.6:c.4423A>G	p.Thr1475Ala	p.T1475A	ENST00000334344	NM_152641.2	1475	Acc/Gcc	15/21	1	2	FACETS	0.204	0.162	0.253	0.204	0.162	0.253	SUBCLONAL	1	TRUE	1	0.89653998002776	2		410	284	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246450	46246450	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	18	374	0	ENST00000334344.6:c.4544T>C	p.Val1515Ala	p.V1515A	ENST00000334344	NM_152641.2	1515	gTa/gCa	15/21	1	2	FACETS	0.159	0.12	0.206	0.159	0.12	0.206	SUBCLONAL	1	TRUE	1	0.89653998002776	2		374	252	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246471	46246471	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	24	340	0	ENST00000334344.6:c.4565C>A	p.Thr1522Asn	p.T1522N	ENST00000334344	NM_152641.2	1522	aCt/aAt	15/21	1	2	FACETS	0.195	0.153	0.244	0.195	0.153	0.244	SUBCLONAL	1	TRUE	1	0.89653998002776	2		340	274	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246487	46246488	+	missense_variant	Missense_Mutation	DNP	CG	CG	TC	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	23	328	3	ENST00000334344.6:c.4581_4582delinsTC	p.Ala1528Pro	p.A1528P	ENST00000334344	NM_152641.2	1527	gtCGca/gtTCca	15/21	1	2	FACETS	0.225	0.176	0.282	0.225	0.176	0.282	SUBCLONAL	1	TRUE	1	0.89653998002776	2		331	228	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215806	133215806	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	68	657	1	ENST00000320574.5:c.5457G>T	p.Met1819Ile	p.M1819I	ENST00000320574	NM_006231.2	1819	atG/atT	40/49	1	2	FACETS	0.204	0.177	0.234	0.204	0.177	0.234	SUBCLONAL	1	TRUE	1	0.89653998002776	2		658	743	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215862	133215862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	53	429	0	ENST00000320574.5:c.5401G>A	p.Gly1801Ser	p.G1801S	ENST00000320574	NM_006231.2	1801	Ggc/Agc	40/49	1	2	FACETS	0.288	0.246	0.334	0.288	0.246	0.334	SUBCLONAL	1	TRUE	1	0.89653998002776	2		429	410	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975670	26975670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	27	459	0	ENST00000381527.3:c.1178G>A	p.Ser393Asn	p.S393N	ENST00000381527	NM_001260.1	393	aGc/aAc	12/13	1	2	FACETS	0.148	0.118	0.184	0.148	0.118	0.184	SUBCLONAL	1	TRUE	1	0.89653998002776	2		459	406	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26978168	26978168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	52	634	0	ENST00000381527.3:c.1345G>A	p.Ala449Thr	p.A449T	ENST00000381527	NM_001260.1	449	Gct/Act	13/13	1	2	FACETS	0.218	0.185	0.254	0.218	0.185	0.254	SUBCLONAL	1	TRUE	1	0.89653998002776	2		634	532	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239821	41239822	+	missense_variant	Missense_Mutation	DNP	CC	CC	GG	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	81	608	2	ENST00000379561.5:c.528_529inv	p.Ala177Pro	p.A177P	ENST00000379561	NM_002015.3	176	tcGGcg/tcCCcg	1/3	1	2	FACETS	0.218	0.192	0.247	0.218	0.192	0.247	SUBCLONAL	1	TRUE	1	0.89653998002776	2		610	827	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437508	110437508	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	42	586	0	ENST00000375856.3:c.893T>C	p.Phe298Ser	p.F298S	ENST00000375856	NM_003749.2	298	tTc/tCc	1/2	1	2	FACETS	0.124	0.103	0.148	0.124	0.103	0.148	SUBCLONAL	1	TRUE	1	0.89653998002776	2		586	755	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437610	110437610	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1287695683	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	79	612	0	ENST00000375856.3:c.791T>C	p.Val264Ala	p.V264A	ENST00000375856	NM_003749.2	264	gTc/gCc	1/2	1	2	FACETS	0.203	0.177	0.23	0.203	0.177	0.23	SUBCLONAL	1	TRUE	1	0.89653998002776	2		612	870	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437697	110437697	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	46	653	0	ENST00000375856.3:c.704A>T	p.Gln235Leu	p.Q235L	ENST00000375856	NM_003749.2	235	cAg/cTg	1/2	1	2	FACETS	0.137	0.115	0.162	0.137	0.115	0.162	SUBCLONAL	1	TRUE	1	0.89653998002776	2		653	750	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437974	110437974	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	43	167	0	ENST00000375856.3:c.427G>C	p.Val143Leu	p.V143L	ENST00000375856	NM_003749.2	143	Gtc/Ctc	1/2	1	2	FACETS	0.266	0.223	0.314	0.266	0.223	0.314	SUBCLONAL	1	TRUE	1	0.89653998002776	2		167	360	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046435	30046447	+	stop_retained_variant,3_prime_UTR_variant	Silent	DEL	AGATGGAACTCAG	AGATGGAACTCAG	GATGCAACTTAA	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	40	536	2	ENST00000331968.5:c.2736_*9delinsTTAAGTTGCATC		p.*912*	ENST00000331968	NM_002742.2	912		18/18	1	2	FACETS	0.189	0.157	0.225	0.189	0.157	0.225	SUBCLONAL	1	TRUE	1	0.89653998002776	2		538	472	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987169	36987169	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	51	613	0	ENST00000354822.5:c.520G>A	p.Gly174Ser	p.G174S	ENST00000354822	NM_001079668.2	174	Ggc/Agc	3/3	1	2	FACETS	0.204	0.173	0.238	0.204	0.173	0.238	SUBCLONAL	1	TRUE	1	0.89653998002776	2		613	558	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987187	36987187	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	40	625	0	ENST00000354822.5:c.502A>G	p.Ser168Gly	p.S168G	ENST00000354822	NM_001079668.2	168	Agc/Ggc	3/3	1	2	FACETS	0.16	0.133	0.191	0.16	0.133	0.191	SUBCLONAL	1	TRUE	1	0.89653998002776	2		625	556	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061418	38061418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	49	542	1	ENST00000250448.2:c.571C>T	p.Leu191Phe	p.L191F	ENST00000250448	NM_004496.3	191	Ctc/Ttc	2/2	1	2	FACETS	0.262	0.222	0.305	0.262	0.222	0.305	SUBCLONAL	1	TRUE	1	0.89653998002776	2		543	418	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061506	38061507	+	missense_variant	Missense_Mutation	DNP	CG	CG	GC	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	54	411	1	ENST00000250448.2:c.482_483delinsGC	p.Thr161Ser	p.T161S	ENST00000250448	NM_004496.3	161	aCG/aGC	2/2	1	2	FACETS	0.274	0.235	0.318	0.274	0.235	0.318	SUBCLONAL	1	TRUE	1	0.89653998002776	2		412	439	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560260	95560261	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	17	444	1	ENST00000393063.1:c.5328_5329delinsAA	p.Leu1777Ile	p.L1777I	ENST00000393063	NM_030621.3	1776	caGCtt/caAAtt	25/28	1	2	FACETS	0.128	0.095	0.167	0.128	0.095	0.167	SUBCLONAL	1	TRUE	1	0.89653998002776	2		445	296	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562760	95562760	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	27	436	0	ENST00000393063.1:c.4497G>T	p.Glu1499Asp	p.E1499D	ENST00000393063	NM_030621.3	1499	gaG/gaT	24/28	1	2	FACETS	0.22	0.175	0.271	0.22	0.175	0.271	SUBCLONAL	1	TRUE	1	0.89653998002776	2		436	274	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570298	95570298	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	15	438	0	ENST00000393063.1:c.3435T>A	p.Asn1145Lys	p.N1145K	ENST00000393063	NM_030621.3	1145	aaT/aaA	22/28	1	2	FACETS	0.117	0.085	0.155	0.117	0.085	0.155	SUBCLONAL	1	TRUE	1	0.89653998002776	2		438	287	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570305	95570306	+	missense_variant	Missense_Mutation	DNP	AG	AG	GC	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	16	432	0	ENST00000393063.1:c.3427_3428delinsGC	p.Leu1143Ala	p.L1143A	ENST00000393063	NM_030621.3	1143	CTa/GCa	22/28	1	2	FACETS	0.127	0.093	0.167	0.127	0.093	0.167	SUBCLONAL	1	TRUE	1	0.89653998002776	2		432	282	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570349	95570350	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACT	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	16	360	0	ENST00000393063.1:c.3383_3384insAGT	p.Val1128dup	p.V1128dup	ENST00000393063	NM_030621.3	1128	gtc/gtAGTc	22/28	1	2	FACETS	0.147	0.109	0.194	0.147	0.109	0.194	SUBCLONAL	1	TRUE	1	0.89653998002776	2		360	242	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570376	95570376	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	14	338	0	ENST00000393063.1:c.3357T>A	p.Asp1119Glu	p.D1119E	ENST00000393063	NM_030621.3	1119	gaT/gaA	22/28	1	2	FACETS	0.151	0.109	0.202	0.151	0.109	0.202	SUBCLONAL	1	TRUE	1	0.89653998002776	2		338	207	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95599774	95599774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748788519	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	52	419	0	ENST00000393063.1:c.22C>T	p.Pro8Ser	p.P8S	ENST00000393063	NM_030621.3	8	Ccc/Tcc	3/28	1	2	FACETS	0.233	0.198	0.272	0.233	0.198	0.272	SUBCLONAL	1	TRUE	1	0.89653998002776	2		419	497	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95599790	95599791	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTCA	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	40	380	0	ENST00000393063.1:c.2_5dup	p.Lys2AsnfsTer39	p.K2Nfs*39	ENST00000393063	NM_030621.3	2	aaa/aaTGAAa	3/28	1	2	FACETS	0.202	0.168	0.241	0.202	0.168	0.241	SUBCLONAL	1	TRUE	1	0.89653998002776	2		380	441	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243063	105243063	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	40	672	0	ENST00000349310.3:c.220A>G	p.Ile74Val	p.I74V	ENST00000349310	NM_001014432.1	74	Atc/Gtc	5/15	1	2	FACETS	0.113	0.093	0.135	0.113	0.093	0.135	SUBCLONAL	1	TRUE	1	0.89653998002776	2		672	789	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591650	38591650	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	24	549	0	ENST00000299084.4:c.109A>G	p.Ser37Gly	p.S37G	ENST00000299084	NM_152594.2	37	Agt/Ggt	2/7	1	2	FACETS	0.127	0.099	0.16	0.127	0.099	0.16	SUBCLONAL	1	TRUE	1	0.89653998002776	2		549	421	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799194	88799194	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	38	685	0	ENST00000360948.2:c.191A>G	p.Asn64Ser	p.N64S	ENST00000360948	NM_001012338.2	64	aAc/aGc	2/19	1	2	FACETS	0.164	0.135	0.196	0.164	0.135	0.196	SUBCLONAL	1	TRUE	1	0.89653998002776	2		685	518	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631627	90631628	+	missense_variant	Missense_Mutation	DNP	TG	TG	GC	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	42	619	0	ENST00000330062.3:c.641_642delinsGC	p.Ala214Gly	p.A214G	ENST00000330062	NM_002168.2	214	gCA/gGC	5/11	1	2	FACETS	0.13	0.108	0.155	0.13	0.108	0.155	SUBCLONAL	1	TRUE	1	0.89653998002776	2		619	720	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631640	90631640	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	42	645	0	ENST00000330062.3:c.629A>T	p.Tyr210Phe	p.Y210F	ENST00000330062	NM_002168.2	210	tAc/tTc	5/11	1	2	FACETS	0.14	0.116	0.167	0.14	0.116	0.167	SUBCLONAL	1	TRUE	1	0.89653998002776	2		645	668	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781216	3781217	+	missense_variant	Missense_Mutation	DNP	GC	GC	TG	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	45	715	1	ENST00000262367.5:c.5148_5149delinsCA	p.Arg1717Ser	p.R1717S	ENST00000262367	NM_004380.2	1716	acGCgc/acCAgc	30/31	1	2	FACETS	0.112	0.093	0.132	0.112	0.093	0.132	SUBCLONAL	1	TRUE	1	0.89653998002776	2		716	898	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781357	3781357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	68	754	0	ENST00000262367.5:c.5008C>T	p.Leu1670Phe	p.L1670F	ENST00000262367	NM_004380.2	1670	Ctc/Ttc	30/31	1	2	FACETS	0.171	0.148	0.196	0.171	0.148	0.196	SUBCLONAL	1	TRUE	1	0.89653998002776	2		754	885	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063337	67063337	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	34	366	0	ENST00000412916.2:c.27A>C	p.Arg9Ser	p.R9S	ENST00000412916		9	agA/agC	1/6	1	2	FACETS	0.158	0.129	0.191	0.158	0.129	0.191	SUBCLONAL	1	TRUE	1	0.89653998002776	2		366	480	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063668	67063669	+	missense_variant	Missense_Mutation	DNP	AC	AC	GA	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	41	433	2	ENST00000412916.2:c.117_118delinsGA	p.Arg40Ser	p.R40S	ENST00000412916		39	gaACgc/gaGAgc	2/6	1	2	FACETS	0.127	0.105	0.151	0.127	0.105	0.151	SUBCLONAL	1	TRUE	1	0.89653998002776	2		435	723	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070621	67070621	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	21	287	0	ENST00000412916.2:c.245G>C	p.Ser82Thr	p.S82T	ENST00000412916		82	aGc/aCc	3/6	1	2	FACETS	0.124	0.095	0.157	0.124	0.095	0.157	SUBCLONAL	1	TRUE	1	0.89653998002776	2		287	379	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821082	72821082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458157669	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	63	630	1	ENST00000268489.5:c.11093C>T	p.Thr3698Met	p.T3698M	ENST00000268489	NM_006885.3	3698	aCg/aTg	10/10	1	2	FACETS	0.258	0.223	0.296	0.258	0.223	0.296	SUBCLONAL	1	TRUE	1	0.89653998002776	2		631	544	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821095	72821096	+	missense_variant	Missense_Mutation	DNP	TC	TC	CT	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	54	664	2	ENST00000268489.5:c.11079_11080delinsAG	p.Thr3694Ala	p.T3694A	ENST00000268489	NM_006885.3	3693	ctGAcc/ctAGcc	10/10	1	2	FACETS	0.207	0.177	0.241	0.207	0.177	0.241	SUBCLONAL	1	TRUE	1	0.89653998002776	2		666	581	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821139	72821139	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	76	585	0	ENST00000268489.5:c.11036T>C	p.Val3679Ala	p.V3679A	ENST00000268489	NM_006885.3	3679	gTg/gCg	10/10	1	2	FACETS	0.236	0.207	0.268	0.236	0.207	0.268	SUBCLONAL	1	TRUE	1	0.89653998002776	2		585	718	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821442	72821443	+	missense_variant	Missense_Mutation	DNP	AA	AA	GG	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	38	654	0	ENST00000268489.5:c.10732_10733delinsCC	p.Phe3578Pro	p.F3578P	ENST00000268489	NM_006885.3	3578	TTc/CCc	10/10	1	2	FACETS	0.12	0.099	0.144	0.12	0.099	0.144	SUBCLONAL	1	TRUE	1	0.89653998002776	2		654	705	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821520	72821521	+	missense_variant	Missense_Mutation	DNP	AA	AA	GG	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	51	505	0	ENST00000268489.5:c.10654_10655delinsCC	p.Leu3552Pro	p.L3552P	ENST00000268489	NM_006885.3	3552	TTg/CCg	10/10	1	2	FACETS	0.213	0.181	0.249	0.213	0.181	0.249	SUBCLONAL	1	TRUE	1	0.89653998002776	2		505	534	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821653	72821653	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760410635	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	23	104	0	ENST00000268489.5:c.10522G>A	p.Gly3508Ser	p.G3508S	ENST00000268489	NM_006885.3	3508	Ggc/Agc	10/10	1	2	FACETS	0.309	0.243	0.384	0.309	0.243	0.384	SUBCLONAL	1	TRUE	1	0.89653998002776	2		104	166	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821691	72821691	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	40	296	0	ENST00000268489.5:c.10484T>C	p.Val3495Ala	p.V3495A	ENST00000268489	NM_006885.3	3495	gTg/gCg	10/10	1	2	FACETS	0.208	0.173	0.247	0.208	0.173	0.247	SUBCLONAL	1	TRUE	1	0.89653998002776	2		296	429	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822026	72822029	+	missense_variant	Missense_Mutation	ONP	TAGT	TAGT	CGCC	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	15	298	0	ENST00000268489.5:c.10146_10149delinsGGCG	p.Leu3383Ala	p.L3383A	ENST00000268489	NM_006885.3	3382	caACTA/caGGCG	10/10	1	2	FACETS	0.118	0.086	0.157	0.118	0.086	0.157	SUBCLONAL	1	TRUE	1	0.89653998002776	2		298	283	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822048	72822052	+	protein_altering_variant	In_Frame_Del	DEL	TGAAT	TGAAT	AA	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	22	325	1	ENST00000268489.5:c.10123_10127delinsTT	p.Ile3375_Gln3376delinsLeu	p.I3375_Q3376delinsL	ENST00000268489	NM_006885.3	3375	ATTCAg/TTg	10/10	1	2	FACETS	0.182	0.141	0.229	0.182	0.141	0.229	SUBCLONAL	1	TRUE	1	0.89653998002776	2		326	270	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822118	72822118	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	42	442	0	ENST00000268489.5:c.10057A>C	p.Met3353Leu	p.M3353L	ENST00000268489	NM_006885.3	3353	Atg/Ctg	10/10	1	2	FACETS	0.231	0.193	0.273	0.231	0.193	0.273	SUBCLONAL	1	TRUE	1	0.89653998002776	2		442	406	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827419	72827419	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	53	642	0	ENST00000268489.5:c.9162C>A	p.Asp3054Glu	p.D3054E	ENST00000268489	NM_006885.3	3054	gaC/gaA	9/10	1	2	FACETS	0.247	0.21	0.287	0.247	0.21	0.287	SUBCLONAL	1	TRUE	1	0.89653998002776	2		642	479	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827563	72827563	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	59	657	0	ENST00000268489.5:c.9018A>C	p.Leu3006Phe	p.L3006F	ENST00000268489	NM_006885.3	3006	ttA/ttC	9/10	1	2	FACETS	0.264	0.227	0.304	0.264	0.227	0.304	SUBCLONAL	1	TRUE	1	0.89653998002776	2		657	498	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831451	72831452	+	missense_variant	Missense_Mutation	DNP	GG	GG	TA	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	23	504	1	ENST00000268489.5:c.5129_5130delinsTA	p.Ala1710Val	p.A1710V	ENST00000268489	NM_006885.3	1710	gCC/gTA	9/10	1	2	FACETS	0.133	0.103	0.168	0.133	0.103	0.168	SUBCLONAL	1	TRUE	1	0.89653998002776	2		505	385	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991527	72991527	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	76	739	0	ENST00000268489.5:c.2518A>T	p.Thr840Ser	p.T840S	ENST00000268489	NM_006885.3	840	Acc/Tcc	2/10	1	2	FACETS	0.215	0.188	0.244	0.215	0.188	0.244	SUBCLONAL	1	TRUE	1	0.89653998002776	2		739	790	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991534	72991547	+	missense_variant	Missense_Mutation	ONP	CTGTTGCAGTAACA	CTGTTGCAGTAACA	TTGCTGAAGCAGCG	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	81	739	3	ENST00000268489.5:c.2498_2511delinsCGCTGCTTCAGCAA	p.Met833Thr	p.M833T	ENST00000268489	NM_006885.3	833	aTGTTACTGCAACAG/aCGCTGCTTCAGCAA	2/10	1	2	FACETS	0.24	0.211	0.271	0.24	0.211	0.271	SUBCLONAL	1	TRUE	1	0.89653998002776	2		742	754	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991542	72991543	+	missense_variant	Missense_Mutation	DNP	GT	GT	AG	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	63	732	1	ENST00000268489.5:c.2502_2503delinsCT	p.Leu834Phe	p.L834F	ENST00000268489	NM_006885.3	834	ttACtg/ttCTtg	2/10	1	2	FACETS	0.196	0.169	0.226	0.196	0.169	0.226	SUBCLONAL	1	TRUE	1	0.89653998002776	2		733	716	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992153	72992153	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	69	569	0	ENST00000268489.5:c.1892T>G	p.Val631Gly	p.V631G	ENST00000268489	NM_006885.3	631	gTt/gGt	2/10	1	2	FACETS	0.267	0.232	0.304	0.267	0.232	0.304	SUBCLONAL	1	TRUE	1	0.89653998002776	2		569	577	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992172	72992172	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	67	622	0	ENST00000268489.5:c.1873T>C	p.Ser625Pro	p.S625P	ENST00000268489	NM_006885.3	625	Tcc/Ccc	2/10	1	2	FACETS	0.255	0.221	0.291	0.255	0.221	0.291	SUBCLONAL	1	TRUE	1	0.89653998002776	2		622	587	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992272	72992275	+	missense_variant	Missense_Mutation	ONP	AGCG	AGCG	GATA	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	65	798	5	ENST00000268489.5:c.1770_1773delinsTATC	p.Ala591Ile	p.A591I	ENST00000268489	NM_006885.3	590	ttCGCT/ttTATC	2/10	1	2	FACETS	0.192	0.166	0.22	0.192	0.166	0.22	SUBCLONAL	1	TRUE	1	0.89653998002776	2		803	756	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992324	72992324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	115	841	1	ENST00000268489.5:c.1721G>A	p.Ser574Asn	p.S574N	ENST00000268489	NM_006885.3	574	aGt/aAt	2/10	1	2	FACETS	0.319	0.287	0.352	0.319	0.287	0.352	SUBCLONAL	1	TRUE	1	0.89653998002776	2		842	805	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992338	72992339	+	missense_variant	Missense_Mutation	DNP	AC	AC	GT	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	121	836	1	ENST00000268489.5:c.1706_1707inv	p.Arg569His	p.R569H	ENST00000268489	NM_006885.3	569	cGT/cAC	2/10	1	2	FACETS	0.344	0.311	0.38	0.344	0.311	0.38	SUBCLONAL	1	TRUE	1	0.89653998002776	2		837	784	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992366	72992368	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	119	776	0	ENST00000268489.5:c.1677_1679del	p.Val560del	p.V560del	ENST00000268489	NM_006885.3	559	gtTGTc/gtc	2/10	1	2	FACETS	0.394	0.356	0.435	0.394	0.356	0.435	SUBCLONAL	1	TRUE	1	0.89653998002776	2		776	673	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992496	72992497	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCTGCTGCTGCC	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	60	769	0	ENST00000268489.5:c.1548_1549insGGCAGCAGCAGC	p.Gly516_Ser517insGlySerSerSer	p.G516_S517insGSSS	ENST00000268489	NM_006885.3	516	-/GGCAGCAGCAGC	2/10	1	2	FACETS	0.191	0.164	0.221	0.191	0.164	0.221	SUBCLONAL	1	TRUE	1	0.89653998002776	2		769	699	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992503	72992504	+	missense_variant	Missense_Mutation	DNP	TG	TG	CA	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	71	737	1	ENST00000268489.5:c.1541_1542inv	p.Ala514Val	p.A514V	ENST00000268489	NM_006885.3	514	gCA/gTG	2/10	1	2	FACETS	0.217	0.189	0.247	0.217	0.189	0.247	SUBCLONAL	1	TRUE	1	0.89653998002776	2		738	730	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992515	72992515	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	69	737	0	ENST00000268489.5:c.1530G>C	p.Glu510Asp	p.E510D	ENST00000268489	NM_006885.3	510	gaG/gaC	2/10	1	2	FACETS	0.208	0.18	0.237	0.208	0.18	0.237	SUBCLONAL	1	TRUE	1	0.89653998002776	2		737	741	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992521	72992521	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	67	743	0	ENST00000268489.5:c.1524T>G	p.His508Gln	p.H508Q	ENST00000268489	NM_006885.3	508	caT/caG	2/10	1	2	FACETS	0.203	0.176	0.233	0.203	0.176	0.233	SUBCLONAL	1	TRUE	1	0.89653998002776	2		743	736	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992542	72992542	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	43	704	1	ENST00000268489.5:c.1503G>T	p.Glu501Asp	p.E501D	ENST00000268489	NM_006885.3	501	gaG/gaT	2/10	1	2	FACETS	0.137	0.114	0.163	0.137	0.114	0.163	SUBCLONAL	1	TRUE	1	0.89653998002776	2		705	698	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992545	72992545	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	41	691	0	ENST00000268489.5:c.1500T>G	p.Asp500Glu	p.D500E	ENST00000268489	NM_006885.3	500	gaT/gaG	2/10	1	2	FACETS	0.133	0.11	0.158	0.133	0.11	0.158	SUBCLONAL	1	TRUE	1	0.89653998002776	2		691	689	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992992	72992992	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	71	856	0	ENST00000268489.5:c.1053A>T	p.Leu351Phe	p.L351F	ENST00000268489	NM_006885.3	351	ttA/ttT	2/10	1	2	FACETS	0.303	0.265	0.345	0.303	0.265	0.345	SUBCLONAL	1	TRUE	1	0.89653998002776	2		856	522	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993008	72993008	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	83	839	0	ENST00000268489.5:c.1037A>C	p.Asn346Thr	p.N346T	ENST00000268489	NM_006885.3	346	aAc/aCc	2/10	1	2	FACETS	0.325	0.287	0.366	0.325	0.287	0.366	SUBCLONAL	1	TRUE	1	0.89653998002776	2		839	569	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993109	72993109	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	82	732	0	ENST00000268489.5:c.936C>G	p.Asp312Glu	p.D312E	ENST00000268489	NM_006885.3	312	gaC/gaG	2/10	1	2	FACETS	0.252	0.221	0.284	0.252	0.221	0.284	SUBCLONAL	1	TRUE	1	0.89653998002776	2		732	727	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993375	72993376	+	missense_variant	Missense_Mutation	DNP	GC	GC	TG	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	80	719	3	ENST00000268489.5:c.669_670delinsCA	p.Leu224Ile	p.L224I	ENST00000268489	NM_006885.3	223	ggGCtc/ggCAtc	2/10	1	2	FACETS	0.243	0.214	0.275	0.243	0.214	0.275	SUBCLONAL	1	TRUE	1	0.89653998002776	2		722	734	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993414	72993414	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	74	744	1	ENST00000268489.5:c.631C>T	p.Pro211Ser	p.P211S	ENST00000268489	NM_006885.3	211	Cca/Tca	2/10	1	2	FACETS	0.243	0.212	0.276	0.243	0.212	0.276	SUBCLONAL	1	TRUE	1	0.89653998002776	2		745	679	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993962	72993962	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	36	690	0	ENST00000268489.5:c.83A>G	p.Asn28Ser	p.N28S	ENST00000268489	NM_006885.3	28	aAc/aGc	2/10	1	2	FACETS	0.123	0.1	0.148	0.123	0.1	0.148	SUBCLONAL	1	TRUE	1	0.89653998002776	2		690	654	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993967	72993967	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	41	687	2	ENST00000268489.5:c.78A>T	p.Glu26Asp	p.E26D	ENST00000268489	NM_006885.3	26	gaA/gaT	2/10	1	2	FACETS	0.138	0.114	0.164	0.138	0.114	0.164	SUBCLONAL	1	TRUE	1	0.89653998002776	2		689	665	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72994017	72994017	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	43	633	0	ENST00000268489.5:c.28T>C	p.Ser10Pro	p.S10P	ENST00000268489	NM_006885.3	10	Tcg/Ccg	2/10	1	2	FACETS	0.151	0.126	0.179	0.151	0.126	0.179	SUBCLONAL	1	TRUE	1	0.89653998002776	2		633	634	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72994020	72994020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200637584	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	44	651	1	ENST00000268489.5:c.25G>A	p.Val9Ile	p.V9I	ENST00000268489	NM_006885.3	9	Gtc/Atc	2/10	1	2	FACETS	0.152	0.127	0.18	0.152	0.127	0.18	SUBCLONAL	1	TRUE	1	0.89653998002776	2		652	644	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89345561	89345594	+	missense_variant	Missense_Mutation	ONP	GGGCGCCTGCGGCGTGATACAGCACAGGATCTTG	GGGCGCCTGCGGCGTGATACAGCACAGGATCTTG	TGGAGCCTGGGGAGTGATGTAGCAGAGGATTTTC	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	22	110	1	ENST00000301030.4:c.7356_7389delinsGAAAATCCTCTGCTACATCACTCCCCAGGCTCCA	p.Cys2457Tyr	p.C2457Y	ENST00000301030	NM_001256183.1	2452	cgCAAGATCCTGTGCTGTATCACGCCGCAGGCGCCC/cgGAAAATCCTCTGCTACATCACTCCCCAGGCTCCA	9/13	1	2	FACETS	0.409	0.321	0.507	0.409	0.321	0.507	SUBCLONAL	1	TRUE	1	0.89653998002776	2		111	120	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348964	89348964	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	303	710	0	ENST00000301030.4:c.3986del	p.Pro1329LeufsTer16	p.P1329Lfs*16	ENST00000301030	NM_001256183.1	1329	cCt/ct	9/13	1	2	FACETS	0.862	0.816	0.909	0.862	0.816	0.909	CLONAL	1	TRUE	1	0.89653998002776	2		710	784	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490272	29490287	+	missense_variant	Missense_Mutation	ONP	TTTTCTTCACACCTGT	TTTTCTTCACACCTGT	CTTCATCCACACTTAC	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	19	505	1	ENST00000356175.3:c.357_372delinsCTTCATCCACACTTAC	p.Leu121_Cys124delinsIleHisThrTyr	p.L121_C124delinsIHTY	ENST00000356175	NM_000267.3	119	caTTTTCTTCACACCTGT/caCTTCATCCACACTTAC	4/57	1	2	FACETS	0.113	0.085	0.146	0.113	0.085	0.146	SUBCLONAL	1	TRUE	1	0.89653998002776	2		506	374	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490341	29490341	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	20	558	0	ENST00000356175.3:c.426A>T	p.Leu142Phe	p.L142F	ENST00000356175	NM_000267.3	142	ttA/ttT	4/57	1	2	FACETS	0.122	0.093	0.157	0.122	0.093	0.157	SUBCLONAL	1	TRUE	1	0.89653998002776	2		558	365	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510556	38510556	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	30	426	0	ENST00000254066.5:c.810C>G	p.Ile270Met	p.I270M	ENST00000254066	NM_000964.3	270	atC/atG	7/9	1	2	FACETS	0.116	0.093	0.142	0.116	0.093	0.142	SUBCLONAL	1	TRUE	1	0.89653998002776	2		426	577	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511541	38511542	+	missense_variant	Missense_Mutation	DNP	CG	CG	AA	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	39	536	2	ENST00000254066.5:c.1039_1040delinsAA	p.Arg347Lys	p.R347K	ENST00000254066	NM_000964.3	347	CGg/AAg	8/9	1	2	FACETS	0.136	0.112	0.163	0.136	0.112	0.163	SUBCLONAL	1	TRUE	1	0.89653998002776	2		538	639	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511551	38511552	+	missense_variant	Missense_Mutation	DNP	TG	TG	AA	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	39	562	0	ENST00000254066.5:c.1049_1050delinsAA	p.Met350Lys	p.M350K	ENST00000254066	NM_000964.3	350	aTG/aAA	8/9	1	2	FACETS	0.127	0.105	0.153	0.127	0.105	0.153	SUBCLONAL	1	TRUE	1	0.89653998002776	2		562	683	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511583	38511583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	41	597	0	ENST00000254066.5:c.1081G>A	p.Val361Ile	p.V361I	ENST00000254066	NM_000964.3	361	Gtc/Atc	8/9	1	2	FACETS	0.112	0.093	0.134	0.112	0.093	0.134	SUBCLONAL	1	TRUE	1	0.89653998002776	2		597	814	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512347	38512347	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	32	529	0	ENST00000254066.5:c.1258C>A	p.Leu420Met	p.L420M	ENST00000254066	NM_000964.3	420	Ctg/Atg	9/9	1	2	FACETS	0.138	0.111	0.168	0.138	0.111	0.168	SUBCLONAL	1	TRUE	1	0.89653998002776	2		529	518	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554201	63554201	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	43	651	0	ENST00000307078.5:c.538T>A	p.Ser180Thr	p.S180T	ENST00000307078	NM_004655.3	180	Tcg/Acg	2/11	1	2	FACETS	0.21	0.176	0.249	0.21	0.176	0.249	SUBCLONAL	1	TRUE	1	0.89653998002776	2		651	456	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554261	63554261	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	49	681	0	ENST00000307078.5:c.478G>A	p.Gly160Ser	p.G160S	ENST00000307078	NM_004655.3	160	Ggc/Agc	2/11	1	2	FACETS	0.241	0.204	0.281	0.241	0.204	0.281	SUBCLONAL	1	TRUE	1	0.89653998002776	2		681	454	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554356	63554356	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	76	709	0	ENST00000307078.5:c.383T>C	p.Leu128Ser	p.L128S	ENST00000307078	NM_004655.3	128	tTa/tCa	2/11	1	2	FACETS	0.368	0.323	0.415	0.368	0.323	0.415	SUBCLONAL	1	TRUE	1	0.89653998002776	2		709	461	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554378	63554378	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	71	720	0	ENST00000307078.5:c.361A>G	p.Asn121Asp	p.N121D	ENST00000307078	NM_004655.3	121	Aac/Gac	2/11	1	2	FACETS	0.33	0.288	0.375	0.33	0.288	0.375	SUBCLONAL	1	TRUE	1	0.89653998002776	2		720	480	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118993	70119007	+	missense_variant	Missense_Mutation	ONP	GCAGAGGAGGCCACG	GCAGAGGAGGCCACG	CAGGAGGAGGGCTCC	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	42	645	2	ENST00000245479.2:c.565_579delinsCAGGAGGAGGGCTCC	p.Ala189_Thr193delinsGlnGluGluGlySer	p.A189_T193delinsQEEGS	ENST00000245479	NM_000346.3	189	GCAGAGGAGGCCACG/CAGGAGGAGGGCTCC	2/3	1	2	FACETS	0.126	0.105	0.15	0.126	0.105	0.15	SUBCLONAL	1	TRUE	1	0.89653998002776	2		647	743	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120330	70120330	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	83	911	0	ENST00000245479.2:c.1332C>G	p.Asp444Glu	p.D444E	ENST00000245479	NM_000346.3	444	gaC/gaG	3/3	1	2	FACETS	0.176	0.154	0.199	0.176	0.154	0.199	SUBCLONAL	1	TRUE	1	0.89653998002776	2		911	1052	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120343	70120343	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	102	931	0	ENST00000245479.2:c.1345A>G	p.Ser449Gly	p.S449G	ENST00000245479	NM_000346.3	449	Agc/Ggc	3/3	1	2	FACETS	0.207	0.184	0.231	0.207	0.184	0.231	SUBCLONAL	1	TRUE	1	0.89653998002776	2		931	1100	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120363	70120378	+	missense_variant	Missense_Mutation	ONP	GGCAGGCCAGGGCACC	GGCAGGCCAGGGCACC	CGCCGGGCAGAGCGGA	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	61	927	3	ENST00000245479.2:c.1365_1380delinsCGCCGGGCAGAGCGGA	p.Gly459_Thr460delinsSerGly	p.G459_T460delinsSG	ENST00000245479	NM_000346.3	455	gcGGCAGGCCAGGGCACC/gcCGCCGGGCAGAGCGGA	3/3	1	2	FACETS	0.127	0.109	0.147	0.127	0.109	0.147	SUBCLONAL	1	TRUE	1	0.89653998002776	2		930	1068	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120412	70120412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1336660139	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	105	846	3	ENST00000245479.2:c.1414G>A	p.Ala472Thr	p.A472T	ENST00000245479	NM_000346.3	472	Gct/Act	3/3	1	2	FACETS	0.248	0.221	0.276	0.248	0.221	0.276	SUBCLONAL	1	TRUE	1	0.89653998002776	2		849	946	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896608	78896608	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs547787723	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	54	540	0	ENST00000306801.3:c.2605G>A	p.Val869Met	p.V869M	ENST00000306801	NM_020761.2	869	Gtg/Atg	22/34	1	2	FACETS	0.157	0.133	0.183	0.157	0.133	0.183	SUBCLONAL	1	TRUE	1	0.89653998002776	2		540	768	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896624	78896624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1310325848	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	37	450	0	ENST00000306801.3:c.2621C>T	p.Ala874Val	p.A874V	ENST00000306801	NM_020761.2	874	gCg/gTg	22/34	1	2	FACETS	0.148	0.121	0.178	0.148	0.121	0.178	SUBCLONAL	1	TRUE	1	0.89653998002776	2		450	558	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246939	10246939	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	38	606	3	ENST00000340748.4:c.4466C>A	p.Ala1489Asp	p.A1489D	ENST00000340748		1489	gCc/gAc	37/40	1	2	FACETS	0.117	0.096	0.14	0.117	0.096	0.14	SUBCLONAL	1	TRUE	1	0.89653998002776	2		609	725	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250805	10250820	+	missense_variant	Missense_Mutation	ONP	GGGCGGCCCGCCGCAC	GGGCGGCCCGCCGCAC	CGGGCGTCCCCCGCAG	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	38	597	3	ENST00000340748.4:c.3660_3675delinsCTGCGGGGGACGCCCG	p.Pro1224Arg	p.P1224R	ENST00000340748		1220	ctGTGCGGCGGGCCGCCC/ctCTGCGGGGGACGCCCG	32/40	1	2	FACETS	0.123	0.101	0.148	0.123	0.101	0.148	SUBCLONAL	1	TRUE	1	0.89653998002776	2		600	688	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602373	10602373	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	87	786	0	ENST00000171111.5:c.1205A>G	p.Gln402Arg	p.Q402R	ENST00000171111	NM_203500.1	402	cAg/cGg	3/6	1	2	FACETS	0.191	0.168	0.215	0.191	0.168	0.215	SUBCLONAL	1	TRUE	1	0.89653998002776	2		786	1018	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602399	10602408	+	missense_variant	Missense_Mutation	ONP	CAGGGCGCTG	CAGGGCGCTG	GATGGCGGCC	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	67	740	5	ENST00000171111.5:c.1170_1179delinsGGCCGCCATC	p.Ser391_Leu393delinsAlaAlaIle	p.S391_L393delinsAAI	ENST00000171111	NM_203500.1	390	tcCAGCGCCCTG/tcGGCCGCCATC	3/6	1	2	FACETS	0.154	0.133	0.177	0.154	0.133	0.177	SUBCLONAL	1	TRUE	1	0.89653998002776	2		745	970	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602406	10602408	+	missense_variant	Missense_Mutation	TNP	CTG	CTG	GCC	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	65	699	1	ENST00000171111.5:c.1170_1172delinsGGC	p.Ser391Ala	p.S391A	ENST00000171111	NM_203500.1	390	tcCAGc/tcGGCc	3/6	1	2	FACETS	0.149	0.129	0.172	0.149	0.129	0.172	SUBCLONAL	1	TRUE	1	0.89653998002776	2		700	970	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602743	10602743	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	54	660	0	ENST00000171111.5:c.835A>C	p.Asn279His	p.N279H	ENST00000171111	NM_203500.1	279	Aac/Cac	3/6	1	2	FACETS	0.126	0.107	0.147	0.126	0.107	0.147	SUBCLONAL	1	TRUE	1	0.89653998002776	2		660	958	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602755	10602755	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	56	683	0	ENST00000171111.5:c.823T>G	p.Ser275Ala	p.S275A	ENST00000171111	NM_203500.1	275	Tcg/Gcg	3/6	1	2	FACETS	0.126	0.108	0.147	0.126	0.108	0.147	SUBCLONAL	1	TRUE	1	0.89653998002776	2		683	988	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602818	10602819	+	missense_variant	Missense_Mutation	DNP	TG	TG	GC	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	80	748	1	ENST00000171111.5:c.759_760delinsGC	p.Lys254Gln	p.K254Q	ENST00000171111	NM_203500.1	253	gtCAag/gtGCag	3/6	1	2	FACETS	0.17	0.149	0.193	0.17	0.149	0.193	SUBCLONAL	1	TRUE	1	0.89653998002776	2		749	1050	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602870	10602870	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	60	772	0	ENST00000171111.5:c.708C>G	p.Asp236Glu	p.D236E	ENST00000171111	NM_203500.1	236	gaC/gaG	3/6	1	2	FACETS	0.125	0.107	0.145	0.125	0.107	0.145	SUBCLONAL	1	TRUE	1	0.89653998002776	2		772	1069	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024640	11024640	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs984768015	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	47	601	0	ENST00000327064.4:c.757A>G	p.Ile253Val	p.I253V	ENST00000327064	NM_199141.1	253	Atc/Gtc	6/16	1	2	FACETS	0.149	0.125	0.175	0.149	0.125	0.175	SUBCLONAL	1	TRUE	1	0.89653998002776	2		601	705	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097085	11097085	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	54	624	0	ENST00000358026.2:c.576G>C	p.Arg192Ser	p.R192S	ENST00000358026	NM_001128849.1	192	agG/agC	4/36	1	2	FACETS	0.18	0.153	0.21	0.18	0.153	0.21	SUBCLONAL	1	TRUE	1	0.89653998002776	2		624	668	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098513	11098514	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	49	580	0	ENST00000358026.2:c.1031_1032delinsAG	p.Pro344Gln	p.P344Q	ENST00000358026	NM_001128849.1	344	cCA/cAG	6/36	1	2	FACETS	0.164	0.138	0.192	0.164	0.138	0.192	SUBCLONAL	1	TRUE	1	0.89653998002776	2		580	668	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098531	11098531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	61	638	0	ENST00000358026.2:c.1049G>A	p.Ser350Asn	p.S350N	ENST00000358026	NM_001128849.1	350	aGc/aAc	6/36	1	2	FACETS	0.167	0.143	0.192	0.167	0.143	0.192	SUBCLONAL	1	TRUE	1	0.89653998002776	2		638	817	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349595	15349595	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	49	743	2	ENST00000263377.2:c.3979T>A	p.Leu1327Met	p.L1327M	ENST00000263377	NM_058243.2	1327	Ttg/Atg	19/20	1	2	FACETS	0.148	0.124	0.173	0.148	0.124	0.173	SUBCLONAL	1	TRUE	1	0.89653998002776	2		745	741	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375346	15375346	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	41	603	2	ENST00000263377.2:c.1081C>A	p.Leu361Ile	p.L361I	ENST00000263377	NM_058243.2	361	Ctc/Atc	6/20	1	2	FACETS	0.13	0.107	0.154	0.13	0.107	0.154	SUBCLONAL	1	TRUE	1	0.89653998002776	2		605	706	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792355	33792355	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	35	745	0	ENST00000498907.2:c.966C>G	p.Asp322Glu	p.D322E	ENST00000498907	NM_004364.3	322	gaC/gaG	1/1	1	2	FACETS	0.115	0.094	0.14	0.115	0.094	0.14	SUBCLONAL	1	TRUE	1	0.89653998002776	2		745	677	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792364	33792365	+	missense_variant	Missense_Mutation	DNP	AC	AC	GG	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	37	719	2	ENST00000498907.2:c.956_957delinsCC	p.Ser319Thr	p.S319T	ENST00000498907	NM_004364.3	319	aGT/aCC	1/1	1	2	FACETS	0.122	0.1	0.147	0.122	0.1	0.147	SUBCLONAL	1	TRUE	1	0.89653998002776	2		721	677	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793064	33793065	+	missense_variant	Missense_Mutation	DNP	CG	CG	TT	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	43	373	2	ENST00000498907.2:c.256_257delinsAA	p.Arg86Lys	p.R86K	ENST00000498907	NM_004364.3	86	CGg/AAg	1/1	1	2	FACETS	0.19	0.159	0.225	0.19	0.159	0.225	SUBCLONAL	1	TRUE	1	0.89653998002776	2		375	504	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229247	36229248	+	missense_variant	Missense_Mutation	DNP	AT	AT	GC	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	45	702	0	ENST00000222270.7:c.7937_7938delinsGC	p.Asn2646Ser	p.N2646S	ENST00000222270	NM_014727.1	2646	aAT/aGC	37/37	1	2	FACETS	0.129	0.108	0.153	0.129	0.108	0.153	SUBCLONAL	1	TRUE	1	0.89653998002776	2		702	778	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229289	36229289	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	76	701	0	ENST00000222270.7:c.7979T>A	p.Phe2660Tyr	p.F2660Y	ENST00000222270	NM_014727.1	2660	tTc/tAc	37/37	1	2	FACETS	0.204	0.178	0.232	0.204	0.178	0.232	SUBCLONAL	1	TRUE	1	0.89653998002776	2		701	831	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229317	36229317	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	57	651	0	ENST00000222270.7:c.8007G>C	p.Gln2669His	p.Q2669H	ENST00000222270	NM_014727.1	2669	caG/caC	37/37	1	2	FACETS	0.169	0.144	0.196	0.169	0.144	0.196	SUBCLONAL	1	TRUE	1	0.89653998002776	2		651	754	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229322	36229322	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	53	665	0	ENST00000222270.7:c.8012A>G	p.His2671Arg	p.H2671R	ENST00000222270	NM_014727.1	2671	cAc/cGc	37/37	1	2	FACETS	0.16	0.136	0.186	0.16	0.136	0.186	SUBCLONAL	1	TRUE	1	0.89653998002776	2		665	740	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716032	52716033	+	missense_variant	Missense_Mutation	DNP	CA	CA	GC	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	40	620	2	ENST00000322088.6:c.597_598delinsGC	p.Asp199_Asn200delinsGluHis	p.D199_N200delinsEH	ENST00000322088	NM_014225.5	199	gaCAac/gaGCac	5/15	1	2	FACETS	0.15	0.124	0.18	0.15	0.124	0.18	SUBCLONAL	1	TRUE	1	0.89653998002776	2		622	593	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082313	16082313	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	65	691	0	ENST00000281043.3:c.127A>G	p.Thr43Ala	p.T43A	ENST00000281043	NM_005378.4	43	Acc/Gcc	2/3	1	2	FACETS	0.239	0.207	0.274	0.239	0.207	0.274	SUBCLONAL	1	TRUE	1	0.89653998002776	2		691	606	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082520	16082520	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	32	559	1	ENST00000281043.3:c.334C>A	p.Leu112Ile	p.L112I	ENST00000281043	NM_005378.4	112	Ctc/Atc	2/3	1	2	FACETS	0.131	0.105	0.159	0.131	0.105	0.159	SUBCLONAL	1	TRUE	1	0.89653998002776	2		560	547	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152264	99152264	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	37	562	0	ENST00000074304.5:c.343G>A	p.Val115Ile	p.V115I	ENST00000074304	NM_001134224.1	115	Gtc/Atc	6/26	1	2	FACETS	0.217	0.179	0.26	0.217	0.179	0.26	SUBCLONAL	1	TRUE	1	0.89653998002776	2		562	380	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182134	99182135	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	23	450	0	ENST00000074304.5:c.2199_2200delinsTT	p.Leu734Phe	p.L734F	ENST00000074304	NM_001134224.1	733	agCCtt/agTTtt	21/26	1	2	FACETS	0.14	0.109	0.176	0.14	0.109	0.176	SUBCLONAL	1	TRUE	1	0.89653998002776	2		450	367	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99203979	99203979	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	23	485	0	ENST00000074304.5:c.2842A>T	p.Ser948Cys	p.S948C	ENST00000074304	NM_001134224.1	948	Agt/Tgt	26/26	1	2	FACETS	0.209	0.163	0.262	0.209	0.163	0.262	SUBCLONAL	1	TRUE	1	0.89653998002776	2		485	245	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99204027	99204027	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	21	425	0	ENST00000074304.5:c.2890C>T	p.His964Tyr	p.H964Y	ENST00000074304	NM_001134224.1	964	Cat/Tat	26/26	1	2	FACETS	0.186	0.143	0.236	0.186	0.143	0.236	SUBCLONAL	1	TRUE	1	0.89653998002776	2		425	252	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281561	198281570	+	protein_altering_variant	In_Frame_Del	DEL	GGACGCTGCT	GGACGCTGCT	AGATGCG	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	41	561	2	ENST00000335508.6:c.561_570delinsCGCATCT	p.Ala189del	p.A189del	ENST00000335508	NM_012433.2	187	gcAGCAGCGTCC/gcCGCATCT	6/25	1	2	FACETS	0.174	0.144	0.206	0.174	0.144	0.206	SUBCLONAL	1	TRUE	1	0.89653998002776	2		563	527	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021670	31021670	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	23	535	0	ENST00000375687.4:c.1669A>T	p.Thr557Ser	p.T557S	ENST00000375687	NM_015338.5	557	Acc/Tcc	12/13	1	2	FACETS	0.112	0.087	0.141	0.112	0.087	0.141	SUBCLONAL	1	TRUE	1	0.89653998002776	2		535	459	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022282	31022283	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	36	457	1	ENST00000375687.4:c.1767_1768delinsAG	p.Thr590Ala	p.T590A	ENST00000375687	NM_015338.5	589	ccCAct/ccAGct	13/13	1	2	FACETS	0.183	0.15	0.22	0.183	0.15	0.22	SUBCLONAL	1	TRUE	1	0.89653998002776	2		458	439	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31025063	31025064	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	24	510	2	ENST00000375687.4:c.4548_4549delinsTA	p.Gln1517Lys	p.Q1517K	ENST00000375687	NM_015338.5	1516	tgCCaa/tgTAaa	13/13	1	2	FACETS	0.112	0.087	0.14	0.112	0.087	0.14	SUBCLONAL	1	TRUE	1	0.89653998002776	2		512	480	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36024682	36024682	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	96	721	0	ENST00000358208.4:c.671A>G	p.Asn224Ser	p.N224S	ENST00000358208		224	aAc/aGc	6/12	1	2	FACETS	0.289	0.257	0.323	0.289	0.257	0.323	SUBCLONAL	1	TRUE	1	0.89653998002776	2		721	742	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031686	36031686	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs771233913	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	100	618	0	ENST00000358208.4:c.1515G>C	p.Glu505Asp	p.E505D	ENST00000358208		505	gaG/gaC	12/12	1	2	FACETS	0.285	0.254	0.317	0.285	0.254	0.317	SUBCLONAL	1	TRUE	1	0.89653998002776	2		618	784	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466791	57466791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	41	235	1	ENST00000371085.3:c.10C>T	p.Leu4Phe	p.L4F	ENST00000371085	NM_000516.4	4	Ctc/Ttc	1/13	1	2	FACETS	0.246	0.205	0.291	0.246	0.205	0.291	SUBCLONAL	1	TRUE	1	0.89653998002776	2		236	372	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206711	36206711	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	48	624	0	ENST00000300305.3:c.801G>T	p.Met267Ile	p.M267I	ENST00000300305		267	atG/atT	6/8	1	2	FACETS	0.164	0.138	0.193	0.164	0.138	0.193	SUBCLONAL	1	TRUE	1	0.89653998002776	2		624	651	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206746	36206746	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	71	580	0	ENST00000300305.3:c.766T>A	p.Ser256Thr	p.S256T	ENST00000300305		256	Tcc/Acc	6/8	1	2	FACETS	0.24	0.209	0.274	0.24	0.209	0.274	SUBCLONAL	1	TRUE	1	0.89653998002776	2		580	659	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206876	36206876	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	42	428	0	ENST00000300305.3:c.636T>G	p.Asp212Glu	p.D212E	ENST00000300305		212	gaT/gaG	6/8	1	2	FACETS	0.192	0.16	0.228	0.192	0.16	0.228	SUBCLONAL	1	TRUE	1	0.89653998002776	2		428	488	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259328	36259328	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	30	436	0	ENST00000300305.3:c.163G>C	p.Ala55Pro	p.A55P	ENST00000300305		55	Gcg/Ccg	3/8	1	2	FACETS	0.133	0.107	0.163	0.133	0.107	0.163	SUBCLONAL	1	TRUE	1	0.89653998002776	2		436	502	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259391	36259391	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	69	541	1	ENST00000300305.3:c.100G>A	p.Ala34Thr	p.A34T	ENST00000300305		34	Gcc/Acc	3/8	1	2	FACETS	0.215	0.186	0.245	0.215	0.186	0.245	SUBCLONAL	1	TRUE	1	0.89653998002776	2		542	717	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755782	39755782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	24	408	0	ENST00000288319.7:c.983G>A	p.Ser328Asn	p.S328N	ENST00000288319	NM_182918.3	328	aGc/aAc	10/10	1	2	FACETS	0.113	0.088	0.142	0.113	0.088	0.142	SUBCLONAL	1	TRUE	1	0.89653998002776	2		408	474	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24129419	24129419	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	43	459	0	ENST00000263121.7:c.63C>G	p.Asp21Glu	p.D21E	ENST00000263121	NM_003073.3	21	gaC/gaG	1/9	1	2	FACETS	0.146	0.121	0.173	0.146	0.121	0.173	SUBCLONAL	1	TRUE	1	0.89653998002776	2		459	659	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000062	30000062	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	33	589	0	ENST00000338641.4:c.75G>C	p.Arg25Ser	p.R25S	ENST00000338641	NM_000268.3	25	agG/agC	1/16	1	2	FACETS	0.12	0.097	0.146	0.12	0.097	0.146	SUBCLONAL	1	TRUE	1	0.89653998002776	2		589	612	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572876	41572876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	83	621	1	ENST00000263253.7:c.5161G>A	p.Ala1721Thr	p.A1721T	ENST00000263253	NM_001429.3	1721	Gct/Act	31/31	1	2	FACETS	0.249	0.219	0.281	0.249	0.219	0.281	SUBCLONAL	1	TRUE	1	0.89653998002776	2		622	743	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572882	41572882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	69	627	1	ENST00000263253.7:c.5167G>A	p.Ala1723Thr	p.A1723T	ENST00000263253	NM_001429.3	1723	Gcc/Acc	31/31	1	2	FACETS	0.212	0.184	0.242	0.212	0.184	0.242	SUBCLONAL	1	TRUE	1	0.89653998002776	2		628	727	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574795	41574795	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	94	700	0	ENST00000263253.7:c.7080A>T	p.Glu2360Asp	p.E2360D	ENST00000263253	NM_001429.3	2360	gaA/gaT	31/31	1	2	FACETS	0.28	0.248	0.313	0.28	0.248	0.313	SUBCLONAL	1	TRUE	1	0.89653998002776	2		700	750	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574877	41574877	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	55	605	1	ENST00000263253.7:c.7162G>A	p.Ala2388Thr	p.A2388T	ENST00000263253	NM_001429.3	2388	Gca/Aca	31/31	1	2	FACETS	0.169	0.144	0.196	0.169	0.144	0.196	SUBCLONAL	1	TRUE	1	0.89653998002776	2		606	726	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574891	41574891	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	52	616	0	ENST00000263253.7:c.7176C>A	p.Asp2392Glu	p.D2392E	ENST00000263253	NM_001429.3	2392	gaC/gaA	31/31	1	2	FACETS	0.16	0.136	0.187	0.16	0.136	0.187	SUBCLONAL	1	TRUE	1	0.89653998002776	2		616	725	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574904	41574904	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	42	594	0	ENST00000263253.7:c.7189A>T	p.Thr2397Ser	p.T2397S	ENST00000263253	NM_001429.3	2397	Acc/Tcc	31/31	1	2	FACETS	0.136	0.113	0.162	0.136	0.113	0.162	SUBCLONAL	1	TRUE	1	0.89653998002776	2		594	690	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574909	41574909	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	43	583	0	ENST00000263253.7:c.7194T>G	p.Asp2398Glu	p.D2398E	ENST00000263253	NM_001429.3	2398	gaT/gaG	31/31	1	2	FACETS	0.149	0.124	0.177	0.149	0.124	0.177	SUBCLONAL	1	TRUE	1	0.89653998002776	2		583	644	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574959	41574960	+	frameshift_variant,stop_lost	Frame_Shift_Del	DEL	AG	AG	-	rs1385527956	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	21	459	0	ENST00000263253.7:c.*2_*3del		p.*2415fs	ENST00000263253	NM_001429.3	2415	tAG/t	31/31	1	2	FACETS	0.125	0.095	0.159	0.125	0.095	0.159	SUBCLONAL	1	TRUE	1	0.89653998002776	2		459	376	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436830	52436830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	46	745	0	ENST00000460680.1:c.1948C>T	p.Leu650Phe	p.L650F	ENST00000460680	NM_004656.3	650	Ctc/Ttc	15/17	1	2	FACETS	0.145	0.121	0.171	0.145	0.121	0.171	SUBCLONAL	1	TRUE	1	0.89653998002776	2		745	709	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588783	52588783	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1234047813	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	40	598	1	ENST00000394830.3:c.4245T>A	p.His1415Gln	p.H1415Q	ENST00000394830	NM_018313.4	1415	caT/caA	27/30	1	2	FACETS	0.124	0.103	0.149	0.124	0.103	0.149	SUBCLONAL	1	TRUE	1	0.89653998002776	2		599	718	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588799	52588799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	57	565	3	ENST00000394830.3:c.4229G>T	p.Gly1410Val	p.G1410V	ENST00000394830	NM_018313.4	1410	gGg/gTg	27/30	1	2	FACETS	0.181	0.155	0.21	0.181	0.155	0.21	SUBCLONAL	1	TRUE	1	0.89653998002776	2		568	703	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588839	52588839	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	59	581	0	ENST00000394830.3:c.4189C>A	p.Leu1397Ile	p.L1397I	ENST00000394830	NM_018313.4	1397	Ctt/Att	27/30	1	2	FACETS	0.209	0.179	0.241	0.209	0.179	0.241	SUBCLONAL	1	TRUE	1	0.89653998002776	2		581	631	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588887	52588888	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	26	519	2	ENST00000394830.3:c.4140_4141delinsAA	p.Met1380_Gly1381delinsIleSer	p.M1380_G1381delinsIS	ENST00000394830	NM_018313.4	1380	atGGgt/atAAgt	27/30	1	2	FACETS	0.115	0.091	0.143	0.115	0.091	0.143	SUBCLONAL	1	TRUE	1	0.89653998002776	2		521	504	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928419	69928419	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	39	505	0	ENST00000352241.4:c.239T>A	p.Leu80Gln	p.L80Q	ENST00000352241	NM_198159.2	80	cTg/cAg	2/10	1	2	FACETS	0.13	0.107	0.156	0.13	0.107	0.156	SUBCLONAL	1	TRUE	1	0.89653998002776	2		505	669	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987082	69987082	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	39	593	0	ENST00000394351.3:c.143T>C	p.Val48Ala	p.V48A	ENST00000394351	NM_000248.3	48	gTc/gCc	2/9	1	2	FACETS	0.132	0.108	0.158	0.132	0.108	0.158	SUBCLONAL	1	TRUE	1	0.89653998002776	2		593	661	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021742	71021743	+	missense_variant	Missense_Mutation	DNP	AC	AC	TG	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	44	544	1	ENST00000318789.4:c.1615_1616delinsCA	p.Val539Gln	p.V539Q	ENST00000318789	NM_032682.5	539	GTa/CAa	18/21	1	2	FACETS	0.26	0.219	0.306	0.26	0.219	0.306	SUBCLONAL	1	TRUE	1	0.89653998002776	2		545	377	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428273	72428273	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	17	475	0	ENST00000477973.2:c.619C>G	p.Leu207Val	p.L207V	ENST00000477973	NM_012234.5	207	Ctg/Gtg	3/4	1	2	FACETS	0.149	0.111	0.194	0.149	0.111	0.194	SUBCLONAL	1	TRUE	1	0.89653998002776	2		475	255	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665307	138665309	+	missense_variant	Missense_Mutation	TNP	CGC	CGC	GCT	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	66	734	2	ENST00000330315.3:c.256_258delinsAGC	p.Ala86Ser	p.A86S	ENST00000330315	NM_023067.3	86	GCG/AGC	1/1	1	2	FACETS	0.233	0.202	0.267	0.233	0.202	0.267	SUBCLONAL	1	TRUE	1	0.89653998002776	2		736	631	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665411	138665411	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	43	606	0	ENST00000330315.3:c.154G>T	p.Ala52Ser	p.A52S	ENST00000330315	NM_023067.3	52	Gcg/Tcg	1/1	1	2	FACETS	0.165	0.138	0.196	0.165	0.138	0.196	SUBCLONAL	1	TRUE	1	0.89653998002776	2		606	581	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430614	181430614	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	43	488	0	ENST00000325404.1:c.466C>A	p.Arg156Ser	p.R156S	ENST00000325404	NM_003106.3	156	Cgc/Agc	1/1	1	2	FACETS	0.196	0.163	0.232	0.196	0.163	0.232	SUBCLONAL	1	TRUE	1	0.89653998002776	2		488	490	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430648	181430648	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	68	497	0	ENST00000325404.1:c.500G>C	p.Ser167Thr	p.S167T	ENST00000325404	NM_003106.3	167	aGc/aCc	1/1	1	2	FACETS	0.281	0.244	0.32	0.281	0.244	0.32	SUBCLONAL	1	TRUE	1	0.89653998002776	2		497	540	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430704	181430704	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	72	519	1	ENST00000325404.1:c.556C>T	p.Leu186Phe	p.L186F	ENST00000325404	NM_003106.3	186	Ctc/Ttc	1/1	1	2	FACETS	0.286	0.25	0.325	0.286	0.25	0.325	SUBCLONAL	1	TRUE	1	0.89653998002776	2		520	561	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430716	181430717	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	72	538	1	ENST00000325404.1:c.568_569delinsAA	p.Gly190Asn	p.G190N	ENST00000325404	NM_003106.3	190	GGc/AAc	1/1	1	2	FACETS	0.299	0.261	0.339	0.299	0.261	0.339	SUBCLONAL	1	TRUE	1	0.89653998002776	2		539	538	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155356	185155356	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	22	517	0	ENST00000265026.3:c.597A>C	p.Glu199Asp	p.E199D	ENST00000265026	NM_004721.4	199	gaA/gaC	3/14	1	2	FACETS	0.113	0.087	0.143	0.113	0.087	0.143	SUBCLONAL	1	TRUE	1	0.89653998002776	2		517	436	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502836	186502837	+	missense_variant	Missense_Mutation	DNP	GT	GT	TC	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	44	567	0	ENST00000323963.5:c.294_295delinsTC	p.Glu98_Phe99delinsAspLeu	p.E98_F99delinsDL	ENST00000323963		98	gaGTtc/gaTCtc	4/11	1	2	FACETS	0.214	0.179	0.252	0.214	0.179	0.252	SUBCLONAL	1	TRUE	1	0.89653998002776	2		567	459	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444608	187444618	+	missense_variant	Missense_Mutation	ONP	GTCTGCAGCGT	GTCTGCAGCGT	ACTTGCAGAGA	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	32	569	2	ENST00000232014.4:c.1609_1619delinsTCTCTGCAAGT	p.Thr537_Thr540delinsSerLeuGlnVal	p.T537_T540delinsSLQV	ENST00000232014	NM_001130845.1	537	ACGCTGCAGACc/TCTCTGCAAGTc	7/10	1	2	FACETS	0.119	0.096	0.145	0.119	0.096	0.145	SUBCLONAL	1	TRUE	1	0.89653998002776	2		571	599	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526147	189526147	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1401203192	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	60	619	0	ENST00000264731.3:c.411C>G	p.Asp137Glu	p.D137E	ENST00000264731	NM_003722.4	137	gaC/gaG	4/14	1	2	FACETS	0.166	0.143	0.192	0.166	0.143	0.192	SUBCLONAL	1	TRUE	1	0.89653998002776	2		619	804	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608609	189608609	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	41	724	0	ENST00000264731.3:c.1684C>G	p.Leu562Val	p.L562V	ENST00000264731	NM_003722.4	562	Ctg/Gtg	13/14	1	2	FACETS	0.171	0.142	0.203	0.171	0.142	0.203	SUBCLONAL	1	TRUE	1	0.89653998002776	2		724	535	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807802	1807802	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	43	586	0	ENST00000260795.2:c.1861C>A	p.Arg621Ser	p.R621S	ENST00000260795		621	Cgc/Agc	13/17	1	2	FACETS	0.153	0.128	0.182	0.153	0.128	0.182	SUBCLONAL	1	TRUE	1	0.89653998002776	2		586	626	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280010	66280010	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	20	243	0	ENST00000273854.3:c.1679C>G	p.Thr560Ser	p.T560S	ENST00000273854	NM_004439.5	560	aCc/aGc	7/18	1	2	FACETS	0.259	0.199	0.329	0.259	0.199	0.329	SUBCLONAL	1	TRUE	1	0.89653998002776	2		243	172	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280040	66280040	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	18	297	0	ENST00000273854.3:c.1649T>G	p.Val550Gly	p.V550G	ENST00000273854	NM_004439.5	550	gTc/gGc	7/18	1	2	FACETS	0.173	0.13	0.223	0.173	0.13	0.223	SUBCLONAL	1	TRUE	1	0.89653998002776	2		297	232	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356127	66356127	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	29	584	1	ENST00000273854.3:c.1370A>T	p.Tyr457Phe	p.Y457F	ENST00000273854	NM_004439.5	457	tAt/tTt	5/18	1	2	FACETS	0.171	0.137	0.21	0.171	0.137	0.21	SUBCLONAL	1	TRUE	1	0.89653998002776	2		585	378	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356145	66356145	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1227900265	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	27	614	1	ENST00000273854.3:c.1352G>A	p.Ser451Asn	p.S451N	ENST00000273854	NM_004439.5	451	aGc/aAc	5/18	1	2	FACETS	0.15	0.119	0.186	0.15	0.119	0.186	SUBCLONAL	1	TRUE	1	0.89653998002776	2		615	401	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356148	66356149	+	missense_variant	Missense_Mutation	DNP	AA	AA	TG	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	26	636	1	ENST00000273854.3:c.1348_1349delinsCA	p.Leu450Gln	p.L450Q	ENST00000273854	NM_004439.5	450	TTg/CAg	5/18	1	2	FACETS	0.139	0.109	0.172	0.139	0.109	0.172	SUBCLONAL	1	TRUE	1	0.89653998002776	2		637	418	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356241	66356241	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	89	716	0	ENST00000273854.3:c.1256G>C	p.Ser419Thr	p.S419T	ENST00000273854	NM_004439.5	419	aGc/aCc	5/18	1	2	FACETS	0.325	0.288	0.364	0.325	0.288	0.364	SUBCLONAL	1	TRUE	1	0.89653998002776	2		716	611	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356276	66356297	+	missense_variant	Missense_Mutation	ONP	CTCCTCACACACACCTGCATGG	CTCCTCACACACACCTGCATGG	TGCCTCGCACAGACCTGAGTGT	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	43	596	2	ENST00000273854.3:c.1200_1221delinsACACTCAGGTCTGTGCGAGGCA	p.Ala402_Glu407delinsSerGlyLeuCysGluAla	p.A402_E407delinsSGLCEA	ENST00000273854	NM_004439.5	400	tcCCATGCAGGTGTGTGTGAGGAG/tcACACTCAGGTCTGTGCGAGGCA	5/18	1	2	FACETS	0.182	0.152	0.216	0.182	0.152	0.216	SUBCLONAL	1	TRUE	1	0.89653998002776	2		598	526	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356409	66356409	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	49	446	0	ENST00000273854.3:c.1088A>G	p.Asn363Ser	p.N363S	ENST00000273854	NM_004439.5	363	aAt/aGt	5/18	1	2	FACETS	0.4	0.341	0.464	0.4	0.341	0.464	SUBCLONAL	1	TRUE	1	0.89653998002776	2		446	273	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155716	106155716	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	16	389	0	ENST00000380013.4:c.617T>C	p.Leu206Pro	p.L206P	ENST00000380013	NM_001127208.2	206	cTa/cCa	3/11	1	2	FACETS	0.162	0.12	0.213	0.162	0.12	0.213	SUBCLONAL	1	TRUE	1	0.89653998002776	2		389	220	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142950033	142950033	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	17	593	0	ENST00000262992.4:c.2677A>G	p.Ile893Val	p.I893V	ENST00000262992	NM_001101669.1	893	Atc/Gtc	24/24	1	2	FACETS	0.114	0.084	0.148	0.114	0.084	0.148	SUBCLONAL	1	TRUE	1	0.89653998002776	2		593	334	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094867	143094867	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	23	513	0	ENST00000262992.4:c.1277C>G	p.Thr426Ser	p.T426S	ENST00000262992	NM_001101669.1	426	aCc/aGc	14/24	1	2	FACETS	0.13	0.1	0.163	0.13	0.1	0.163	SUBCLONAL	1	TRUE	1	0.89653998002776	2		513	396	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094871	143094871	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	24	498	1	ENST00000262992.4:c.1273G>T	p.Ala425Ser	p.A425S	ENST00000262992	NM_001101669.1	425	Gca/Tca	14/24	1	2	FACETS	0.133	0.103	0.166	0.133	0.103	0.166	SUBCLONAL	1	TRUE	1	0.89653998002776	2		499	404	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094887	143094887	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	21	544	1	ENST00000262992.4:c.1257A>T	p.Gln419His	p.Q419H	ENST00000262992	NM_001101669.1	419	caA/caT	14/24	1	2	FACETS	0.113	0.086	0.144	0.113	0.086	0.144	SUBCLONAL	1	TRUE	1	0.89653998002776	2		545	416	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31401568	31401569	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	29	744	0	ENST00000344624.3:c.4095_4096delinsAA	p.Pro1366Thr	p.P1366T	ENST00000344624		1365	gaGCca/gaAAca	33/33	1	2	FACETS	0.126	0.101	0.155	0.126	0.101	0.155	SUBCLONAL	1	TRUE	1	0.89653998002776	2		744	512	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111425	56111425	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1436258505	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	52	329	0	ENST00000399503.3:c.25G>A	p.Ala9Thr	p.A9T	ENST00000399503	NM_005921.1	9	Gcc/Acc	1/20	1	2	FACETS	0.195	0.165	0.227	0.195	0.165	0.227	SUBCLONAL	1	TRUE	1	0.89653998002776	2		329	595	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183236	56183236	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	32	481	0	ENST00000399503.3:c.4146G>T	p.Gln1382His	p.Q1382H	ENST00000399503	NM_005921.1	1382	caG/caT	18/20	1	2	FACETS	0.197	0.16	0.239	0.197	0.16	0.239	SUBCLONAL	1	TRUE	1	0.89653998002776	2		481	362	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80074576	80074577	+	missense_variant	Missense_Mutation	DNP	GT	GT	AC	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	20	606	4	ENST00000265081.6:c.2356_2357inv	p.Val786Thr	p.V786T	ENST00000265081	NM_002439.4	786	GTa/ACa	17/24	1	2	FACETS	0.125	0.095	0.16	0.125	0.095	0.16	SUBCLONAL	1	TRUE	1	0.89653998002776	2		610	358	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80074630	80074630	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1165114619	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	23	566	0	ENST00000265081.6:c.2410A>G	p.Ser804Gly	p.S804G	ENST00000265081	NM_002439.4	804	Agt/Ggt	17/24	1	2	FACETS	0.147	0.114	0.184	0.147	0.114	0.184	SUBCLONAL	1	TRUE	1	0.89653998002776	2		566	350	SUCCESS
APC	324	MSKCC	GRCh37	5	112154765	112154765	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	24	545	0	ENST00000257430.4:c.1036T>G	p.Ser346Ala	p.S346A	ENST00000257430	NM_000038.5	346	Tcc/Gcc	10/16	1	2	FACETS	0.171	0.134	0.214	0.171	0.134	0.214	SUBCLONAL	1	TRUE	1	0.89653998002776	2		545	313	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393287	393287	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	88	575	0	ENST00000380956.4:c.135G>C	p.Glu45Asp	p.E45D	ENST00000380956	NM_001195286.1	45	gaG/gaC	2/9	0.822299116756057	3	FACETS	0.238	0.209	0.268			1	SUBCLONAL	1	TRUE	NA	0.89653998002776	3		575	1197	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43749695	43749695	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs758505735	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	41	458	0	ENST00000523873.1:c.548C>A	p.Pro183His	p.P183H	ENST00000523873		183	cCc/cAc	7/8	1	2	FACETS	0.163	0.135	0.194	0.163	0.135	0.194	SUBCLONAL	1	TRUE	1	0.89653998002776	2		458	560	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43749701	43749701	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	42	501	0	ENST00000523873.1:c.554G>A	p.Gly185Glu	p.G185E	ENST00000523873		185	gGg/gAg	7/8	1	2	FACETS	0.157	0.13	0.186	0.157	0.13	0.186	SUBCLONAL	1	TRUE	1	0.89653998002776	2		501	597	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43749769	43749770	+	missense_variant	Missense_Mutation	DNP	AA	AA	TT	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	41	584	0	ENST00000523873.1:c.622_623inv	p.Asn208Phe	p.N208F	ENST00000523873		208	AAc/TTc	7/8	1	2	FACETS	0.118	0.097	0.141	0.118	0.097	0.141	SUBCLONAL	1	TRUE	1	0.89653998002776	2		584	776	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64286819	64286819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	27	533	0	ENST00000370651.3:c.34G>A	p.Val12Ile	p.V12I	ENST00000370651	NM_003463.4	12	Gtc/Atc	2/6	1	2	FACETS	0.167	0.132	0.206	0.167	0.132	0.206	SUBCLONAL	1	TRUE	1	0.89653998002776	2		533	361	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066571	94066572	+	missense_variant	Missense_Mutation	DNP	CT	CT	TA	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	24	526	0	ENST00000369303.4:c.1187_1188delinsTA	p.Glu396Val	p.E396V	ENST00000369303	NM_004440.3	396	gAG/gTA	5/17	1	2	FACETS	0.201	0.157	0.25	0.201	0.157	0.25	SUBCLONAL	1	TRUE	1	0.89653998002776	2		526	267	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066661	94066661	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	25	572	0	ENST00000369303.4:c.1098A>C	p.Arg366Ser	p.R366S	ENST00000369303	NM_004440.3	366	agA/agC	5/17	1	2	FACETS	0.127	0.1	0.159	0.127	0.1	0.159	SUBCLONAL	1	TRUE	1	0.89653998002776	2		572	439	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120774	94120774	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	20	549	0	ENST00000369303.4:c.277G>A	p.Gly93Ser	p.G93S	ENST00000369303	NM_004440.3	93	Ggc/Agc	3/17	1	2	FACETS	0.126	0.096	0.161	0.126	0.096	0.161	SUBCLONAL	1	TRUE	1	0.89653998002776	2		549	355	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120780	94120780	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	20	568	0	ENST00000369303.4:c.271T>G	p.Ser91Ala	p.S91A	ENST00000369303	NM_004440.3	91	Tcc/Gcc	3/17	1	2	FACETS	0.131	0.1	0.167	0.131	0.1	0.167	SUBCLONAL	1	TRUE	1	0.89653998002776	2		568	341	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554870	106554870	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	24	463	0	ENST00000369096.4:c.1987G>C	p.Val663Leu	p.V663L	ENST00000369096	NM_001198.3	663	Gtg/Ctg	7/7	1	2	FACETS	0.125	0.098	0.157	0.125	0.098	0.157	SUBCLONAL	1	TRUE	1	0.89653998002776	2		463	428	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109309760	109309761	+	missense_variant	Missense_Mutation	DNP	TG	TG	CA	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	20	621	0	ENST00000436639.2:c.1554_1555inv	p.Lys519Glu	p.K519E	ENST00000436639	NM_014454.2	518	ttCAag/ttTGag	9/10	1	2	FACETS	0.113	0.086	0.144	0.113	0.086	0.144	SUBCLONAL	1	TRUE	1	0.89653998002776	2		621	396	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001178	150001178	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	33	603	1	ENST00000253339.5:c.2426T>C	p.Ile809Thr	p.I809T	ENST00000253339		809	aTa/aCa	4/7	1	2	FACETS	0.22	0.18	0.266	0.22	0.18	0.266	SUBCLONAL	1	TRUE	1	0.89653998002776	2		604	334	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001196	150001196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	31	610	0	ENST00000253339.5:c.2408G>A	p.Ser803Asn	p.S803N	ENST00000253339		803	aGt/aAt	4/7	1	2	FACETS	0.196	0.158	0.238	0.196	0.158	0.238	SUBCLONAL	1	TRUE	1	0.89653998002776	2		610	353	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001209	150001210	+	missense_variant	Missense_Mutation	DNP	TG	TG	CA	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	27	621	1	ENST00000253339.5:c.2394_2395inv	p.Ile799Val	p.I799V	ENST00000253339		798	ggCAtc/ggTGtc	4/7	1	2	FACETS	0.179	0.142	0.221	0.179	0.142	0.221	SUBCLONAL	1	TRUE	1	0.89653998002776	2		622	337	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023180	150023180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747900347	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	18	616	0	ENST00000253339.5:c.83G>A	p.Arg28Gln	p.R28Q	ENST00000253339		28	cGg/cAg	1/7	1	2	FACETS	0.121	0.09	0.156	0.121	0.09	0.156	SUBCLONAL	1	TRUE	1	0.89653998002776	2		616	333	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099895	157099896	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	70	583	3	ENST00000346085.5:c.832_833delinsAA	p.Gly278Asn	p.G278N	ENST00000346085	NM_020732.3	278	GGc/AAc	1/20	1	2	FACETS	0.151	0.131	0.173	0.151	0.131	0.173	SUBCLONAL	1	TRUE	1	0.89653998002776	2		586	1033	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469876	157469886	+	missense_variant	Missense_Mutation	ONP	ATGTGGTGCTG	ATGTGGTGCTG	CTGCGGTACCA	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	39	598	2	ENST00000346085.5:c.2670_2680delinsCTGCGGTACCA	p.Ala893_Val894delinsThrMet	p.A893_V894delinsTM	ENST00000346085	NM_020732.3	890	ccATGTGGTGCTGtg/ccCTGCGGTACCAtg	9/20	1	2	FACETS	0.118	0.097	0.142	0.118	0.097	0.142	SUBCLONAL	1	TRUE	1	0.89653998002776	2		600	735	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469923	157469923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	59	608	0	ENST00000346085.5:c.2717A>G	p.Asn906Ser	p.N906S	ENST00000346085	NM_020732.3	906	aAc/aGc	9/20	1	2	FACETS	0.186	0.159	0.215	0.186	0.159	0.215	SUBCLONAL	1	TRUE	1	0.89653998002776	2		608	709	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469962	157469963	+	missense_variant	Missense_Mutation	DNP	GT	GT	AC	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	47	500	2	ENST00000346085.5:c.2756_2757inv	p.Ser919Asn	p.S919N	ENST00000346085	NM_020732.3	919	aGT/aAC	9/20	1	2	FACETS	0.18	0.151	0.212	0.18	0.151	0.212	SUBCLONAL	1	TRUE	1	0.89653998002776	2		502	582	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528161	157528162	+	missense_variant	Missense_Mutation	DNP	TG	TG	CA	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	56	541	1	ENST00000346085.5:c.5886_5887inv	p.Ala1963Thr	p.A1963T	ENST00000346085	NM_020732.3	1962	gaTGcc/gaCAcc	20/20	1	2	FACETS	0.26	0.223	0.301	0.26	0.223	0.301	SUBCLONAL	1	TRUE	1	0.89653998002776	2		542	480	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528248	157528275	+	missense_variant	Missense_Mutation	ONP	ACCGCAGACCTATGAGAAAGAGGAGGAT	ACCGCAGACCTATGAGAAAGAGGAGGAT	GCCTCAGACTTACGAGAAGGAGGAAGAG	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	95	506	2	ENST00000346085.5:c.5973_6000delinsGCCTCAGACTTACGAGAAGGAGGAAGAG	p.Asp2000Glu	p.D2000E	ENST00000346085	NM_020732.3	1991	gcACCGCAGACCTATGAGAAAGAGGAGGAT/gcGCCTCAGACTTACGAGAAGGAGGAAGAG	20/20	1	2	FACETS	0.294	0.262	0.329	0.294	0.262	0.329	SUBCLONAL	1	TRUE	1	0.89653998002776	2		508	720	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528606	157528606	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	65	645	0	ENST00000346085.5:c.6331T>C	p.Phe2111Leu	p.F2111L	ENST00000346085	NM_020732.3	2111	Ttc/Ctc	20/20	1	2	FACETS	0.28	0.243	0.321	0.28	0.243	0.321	SUBCLONAL	1	TRUE	1	0.89653998002776	2		645	517	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528702	157528702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530084903	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	56	494	3	ENST00000346085.5:c.6427G>A	p.Ala2143Thr	p.A2143T	ENST00000346085	NM_020732.3	2143	Gca/Aca	20/20	1	2	FACETS	0.276	0.237	0.319	0.276	0.237	0.319	SUBCLONAL	1	TRUE	1	0.89653998002776	2		497	452	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739956	41739957	+	missense_variant	Missense_Mutation	DNP	AG	AG	TT	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	24	461	1	ENST00000242208.4:c.16_17delinsAA	p.Leu6Lys	p.L6K	ENST00000242208	NM_002192.2	6	CTg/AAg	2/3	1	2	FACETS	0.118	0.092	0.148	0.118	0.092	0.148	SUBCLONAL	1	TRUE	1	0.89653998002776	2		462	454	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444232	50444233	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CA	CA	TG	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	18	311	0	ENST00000331340.3:c.162_163inv	p.Ser55Gly	p.S55G	ENST00000331340	NM_006060.4	54	gcCAgt/gcTGgt	4/8	1	2	FACETS	0.185	0.139	0.239	0.185	0.139	0.239	SUBCLONAL	1	TRUE	1	0.89653998002776	2		311	217	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444239	50444239	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	30	328	0	ENST00000331340.3:c.169G>A	p.Val57Ile	p.V57I	ENST00000331340	NM_006060.4	57	Gtt/Att	4/8	1	2	FACETS	0.272	0.22	0.33	0.272	0.22	0.33	SUBCLONAL	1	TRUE	1	0.89653998002776	2		328	246	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444245	50444245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	31	334	1	ENST00000331340.3:c.175G>A	p.Val59Ile	p.V59I	ENST00000331340	NM_006060.4	59	Gta/Ata	4/8	1	2	FACETS	0.26	0.211	0.315	0.26	0.211	0.315	SUBCLONAL	1	TRUE	1	0.89653998002776	2		335	266	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444340	50444340	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	42	345	0	ENST00000331340.3:c.270G>C	p.Glu90Asp	p.E90D	ENST00000331340	NM_006060.4	90	gaG/gaC	4/8	1	2	FACETS	0.271	0.226	0.32	0.271	0.226	0.32	SUBCLONAL	1	TRUE	1	0.89653998002776	2		345	346	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444360	50444380	+	missense_variant	Missense_Mutation	ONP	GGGACCAAGGCAGCTCGGCTT	GGGACCAAGGCAGCTCGGCTT	ATGGCCCAGGCAGCAAGGCTA	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	22	421	4	ENST00000331340.3:c.290_310delinsATGGCCCAGGCAGCAAGGCTA	p.Arg97_Leu104delinsAsnGlyProGlySerLysAlaMet	p.R97_L104delinsNGPGSKAM	ENST00000331340	NM_006060.4	97	aGGGACCAAGGCAGCTCGGCTTtg/aATGGCCCAGGCAGCAAGGCTAtg	4/8	1	2	FACETS	0.116	0.09	0.147	0.116	0.09	0.147	SUBCLONAL	1	TRUE	1	0.89653998002776	2		425	422	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459449	50459449	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	16	335	0	ENST00000331340.3:c.738C>G	p.His246Gln	p.H246Q	ENST00000331340	NM_006060.4	246	caC/caG	7/8	1	2	FACETS	0.174	0.129	0.228	0.174	0.129	0.228	SUBCLONAL	1	TRUE	1	0.89653998002776	2		335	205	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459558	50459558	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	37	309	0	ENST00000331340.3:c.847C>G	p.Leu283Val	p.L283V	ENST00000331340	NM_006060.4	283	Ctt/Gtt	7/8	1	2	FACETS	0.292	0.241	0.347	0.292	0.241	0.347	SUBCLONAL	1	TRUE	1	0.89653998002776	2		309	283	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381543	81381543	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	18	373	0	ENST00000222390.5:c.518A>G	p.Gln173Arg	p.Q173R	ENST00000222390	NM_000601.4	173	cAg/cGg	5/18	1	2	FACETS	0.145	0.109	0.188	0.145	0.109	0.188	SUBCLONAL	1	TRUE	1	0.89653998002776	2		373	276	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462490	92462490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1368516053	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	64	570	0	ENST00000265734.4:c.148G>A	p.Gly50Ser	p.G50S	ENST00000265734	NM_001259.6	50	Ggc/Agc	2/8	1	2	FACETS	0.196	0.169	0.226	0.196	0.169	0.226	SUBCLONAL	1	TRUE	1	0.89653998002776	2		570	727	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845088	128845106	+	missense_variant	Missense_Mutation	ONP	AGTGCCCTTGGTTCGGACA	AGTGCCCTTGGTTCGGACA	GGCGCCGTTGGTGCGCACG	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	40	723	6	ENST00000249373.3:c.582_600delinsGGCGCCGTTGGTGCGCACG	p.Val195Ala	p.V195A	ENST00000249373	NM_005631.4	194	gaAGTGCCCTTGGTTCGGACA/gaGGCGCCGTTGGTGCGCACG	3/12	1	2	FACETS	0.121	0.099	0.144	0.121	0.099	0.144	SUBCLONAL	1	TRUE	1	0.89653998002776	2		729	740	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850255	128850255	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	39	677	0	ENST00000249373.3:c.1518C>G	p.Asp506Glu	p.D506E	ENST00000249373	NM_005631.4	506	gaC/gaG	9/12	1	2	FACETS	0.126	0.104	0.151	0.126	0.104	0.151	SUBCLONAL	1	TRUE	1	0.89653998002776	2		677	690	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850328	128850328	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	71	611	1	ENST00000249373.3:c.1591G>T	p.Ala531Ser	p.A531S	ENST00000249373	NM_005631.4	531	Gcc/Tcc	9/12	1	2	FACETS	0.25	0.218	0.285	0.25	0.218	0.285	SUBCLONAL	1	TRUE	1	0.89653998002776	2		612	633	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850374	128850374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778073136	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	55	415	0	ENST00000249373.3:c.1637G>A	p.Arg546Lys	p.R546K	ENST00000249373	NM_005631.4	546	aGg/aAg	9/12	1	2	FACETS	0.228	0.195	0.264	0.228	0.195	0.264	SUBCLONAL	1	TRUE	1	0.89653998002776	2		415	538	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842263	151842263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760994115	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	18	418	2	ENST00000262189.6:c.14149G>A	p.Ala4717Thr	p.A4717T	ENST00000262189	NM_170606.2	4717	Gcc/Acc	54/59	1	2	FACETS	0.121	0.09	0.156	0.121	0.09	0.156	SUBCLONAL	1	TRUE	1	0.89653998002776	2		420	333	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845464	151845464	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	38	676	0	ENST00000262189.6:c.13548A>C	p.Leu4516Phe	p.L4516F	ENST00000262189	NM_170606.2	4516	ttA/ttC	52/59	1	2	FACETS	0.201	0.166	0.24	0.201	0.166	0.24	SUBCLONAL	1	TRUE	1	0.89653998002776	2		676	422	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845480	151845480	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	39	679	0	ENST00000262189.6:c.13532T>C	p.Ile4511Thr	p.I4511T	ENST00000262189	NM_170606.2	4511	aTt/aCt	52/59	1	2	FACETS	0.202	0.167	0.241	0.202	0.167	0.241	SUBCLONAL	1	TRUE	1	0.89653998002776	2		679	431	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194823	29194823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	66	791	0	ENST00000240100.2:c.905G>A	p.Arg302Lys	p.R302K	ENST00000240100	NM_001394.6	302	aGg/aAg	4/4	0.166235034008495	2	FACETS	0.178	0.154	0.204	0.089	0.077	0.102	INDETERMINATE	1	TRUE	0	0.89653998002776	2		791	828	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38156992	38156993	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGG	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	33	664	0	ENST00000317025.8:c.2727_2728insCCT	p.Ser909_Ser910insPro	p.S909_S910insP	ENST00000317025	NM_023034.1	909	-/CCT	15/24	0.166235034008495	2	FACETS	0.189	0.153	0.228	0.094	0.076	0.114	INDETERMINATE	1	TRUE	0	0.89653998002776	2		664	390	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38157079	38157079	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	45	662	0	ENST00000317025.8:c.2641A>C	p.Met881Leu	p.M881L	ENST00000317025	NM_023034.1	881	Atg/Ctg	15/24	0.166235034008495	2	FACETS	0.216	0.182	0.255	0.108	0.091	0.128	INDETERMINATE	1	TRUE	0	0.89653998002776	2		662	464	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38157103	38157103	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	40	523	0	ENST00000317025.8:c.2617A>G	p.Ile873Val	p.I873V	ENST00000317025	NM_023034.1	873	Ata/Gta	15/24	0.166235034008495	2	FACETS	0.216	0.179	0.257	0.108	0.089	0.129	INDETERMINATE	1	TRUE	0	0.89653998002776	2		523	413	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205536	38205536	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	26	686	0	ENST00000317025.8:c.154A>G	p.Thr52Ala	p.T52A	ENST00000317025	NM_023034.1	52	Act/Gct	2/24	0.166235034008495	2	FACETS	0.125	0.098	0.156	0.063	0.049	0.078	INDETERMINATE	1	TRUE	0	0.89653998002776	2		686	464	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205580	38205580	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	52	717	0	ENST00000317025.8:c.110A>G	p.Asn37Ser	p.N37S	ENST00000317025	NM_023034.1	37	aAc/aGc	2/24	0.166235034008495	2	FACETS	0.214	0.182	0.249	0.107	0.091	0.125	INDETERMINATE	1	TRUE	0	0.89653998002776	2		717	542	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205583	38205584	+	missense_variant	Missense_Mutation	DNP	TT	TT	GC	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	52	727	1	ENST00000317025.8:c.106_107delinsGC	p.Asn36Ala	p.N36A	ENST00000317025	NM_023034.1	36	AAc/GCc	2/24	0.166235034008495	2	FACETS	0.21	0.178	0.244	0.105	0.089	0.122	INDETERMINATE	1	TRUE	0	0.89653998002776	2		728	553	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277101	38277101	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	48	607	0	ENST00000425967.3:c.1327A>C	p.Met443Leu	p.M443L	ENST00000425967	NM_001174067.1	443	Atg/Ctg	10/19	0.166235034008495	2	FACETS	0.175	0.148	0.206	0.088	0.074	0.103	INDETERMINATE	1	TRUE	0	0.89653998002776	2		607	611	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277110	38277110	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	43	613	1	ENST00000425967.3:c.1318C>A	p.His440Asn	p.H440N	ENST00000425967	NM_001174067.1	440	Cac/Aac	10/19	0.166235034008495	2	FACETS	0.167	0.139	0.198	0.084	0.069	0.099	INDETERMINATE	1	TRUE	0	0.89653998002776	2		614	574	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277117	38277118	+	missense_variant	Missense_Mutation	DNP	AC	AC	TG	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	33	634	2	ENST00000425967.3:c.1310_1311delinsCA	p.Ser437Thr	p.S437T	ENST00000425967	NM_001174067.1	437	aGT/aCA	10/19	0.166235034008495	2	FACETS	0.135	0.109	0.164	0.067	0.054	0.082	INDETERMINATE	1	TRUE	0	0.89653998002776	2		636	546	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277149	38277149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752627281	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	45	656	2	ENST00000425967.3:c.1279G>A	p.Val427Ile	p.V427I	ENST00000425967	NM_001174067.1	427	Gtc/Atc	10/19	0.166235034008495	2	FACETS	0.187	0.156	0.22	0.093	0.078	0.11	INDETERMINATE	1	TRUE	0	0.89653998002776	2		658	538	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277158	38277158	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	32	659	1	ENST00000425967.3:c.1270T>A	p.Ser424Thr	p.S424T	ENST00000425967	NM_001174067.1	424	Tcg/Acg	10/19	0.166235034008495	2	FACETS	0.134	0.108	0.163	0.067	0.054	0.082	INDETERMINATE	1	TRUE	0	0.89653998002776	2		660	532	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277160	38277160	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	34	663	0	ENST00000425967.3:c.1268G>T	p.Gly423Val	p.G423V	ENST00000425967	NM_001174067.1	423	gGg/gTg	10/19	0.166235034008495	2	FACETS	0.143	0.116	0.173	0.072	0.058	0.087	INDETERMINATE	1	TRUE	0	0.89653998002776	2		663	530	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371638	55371638	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	103	567	0	ENST00000297316.4:c.328A>T	p.Thr110Ser	p.T110S	ENST00000297316	NM_022454.3	110	Acg/Tcg	2/2	0.166235034008495	2	FACETS	0.356	0.319	0.396	0.178	0.159	0.198	INDETERMINATE	1	TRUE	0	0.89653998002776	2		567	645	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371762	55371762	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	54	333	0	ENST00000297316.4:c.452T>C	p.Val151Ala	p.V151A	ENST00000297316	NM_022454.3	151	gTg/gCg	2/2	0.166235034008495	2	FACETS	0.258	0.22	0.299	0.129	0.11	0.15	INDETERMINATE	1	TRUE	0	0.89653998002776	2		333	467	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56854496	56854496	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	19	604	0	ENST00000519728.1:c.78T>A	p.Asn26Lys	p.N26K	ENST00000519728	NM_002350.3	26	aaT/aaA	2/13	0.166235034008495	2	FACETS	0.115	0.087	0.148	0.057	0.043	0.074	INDETERMINATE	1	TRUE	0	0.89653998002776	2		604	369	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879398	56879399	+	missense_variant	Missense_Mutation	DNP	CT	CT	GC	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	36	656	1	ENST00000519728.1:c.915_916delinsGC	p.Tyr306His	p.Y306H	ENST00000519728	NM_002350.3	305	ctCTac/ctGCac	9/13	0.166235034008495	2	FACETS	0.128	0.104	0.154	0.064	0.052	0.077	INDETERMINATE	1	TRUE	0	0.89653998002776	2		657	629	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864715	68864715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	47	435	1	ENST00000288368.4:c.86G>A	p.Ser29Asn	p.S29N	ENST00000288368	NM_024870.2	29	aGc/aAc	1/40	0.166235034008495	2	FACETS	0.178	0.15	0.209	0.089	0.075	0.105	INDETERMINATE	1	TRUE	0	0.89653998002776	2		436	589	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864724	68864725	+	missense_variant	Missense_Mutation	DNP	AG	AG	TC	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	42	457	0	ENST00000288368.4:c.95_96delinsTC	p.Gln32Leu	p.Q32L	ENST00000288368	NM_024870.2	32	cAG/cTC	1/40	0.166235034008495	2	FACETS	0.15	0.125	0.178	0.075	0.062	0.089	INDETERMINATE	1	TRUE	0	0.89653998002776	2		457	624	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942777	68942777	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	27	530	0	ENST00000288368.4:c.589G>T	p.Val197Leu	p.V197L	ENST00000288368	NM_024870.2	197	Gtg/Ttg	6/40	0.166235034008495	2	FACETS	0.121	0.096	0.15	0.06	0.048	0.075	INDETERMINATE	1	TRUE	0	0.89653998002776	2		530	498	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499790	8499791	+	missense_variant	Missense_Mutation	DNP	AT	AT	CA	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	48	588	0	ENST00000356435.5:c.2178_2179delinsTG	p.Ser727Ala	p.S727A	ENST00000356435		726	acATct/acTGct	14/35	1	2	FACETS	0.236	0.199	0.276	0.236	0.199	0.276	SUBCLONAL	1	TRUE	1	0.89653998002776	2		588	454	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500826	8500826	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	25	561	0	ENST00000356435.5:c.2056A>T	p.Thr686Ser	p.T686S	ENST00000356435		686	Act/Tct	13/35	1	2	FACETS	0.128	0.1	0.16	0.128	0.1	0.16	SUBCLONAL	1	TRUE	1	0.89653998002776	2		561	435	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500871	8500871	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	22	561	0	ENST00000356435.5:c.2011A>C	p.Lys671Gln	p.K671Q	ENST00000356435		671	Aaa/Caa	13/35	1	2	FACETS	0.14	0.108	0.177	0.14	0.108	0.177	SUBCLONAL	1	TRUE	1	0.89653998002776	2		561	351	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500876	8500876	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	23	546	0	ENST00000356435.5:c.2006C>G	p.Thr669Ser	p.T669S	ENST00000356435		669	aCt/aGt	13/35	1	2	FACETS	0.143	0.111	0.18	0.143	0.111	0.18	SUBCLONAL	1	TRUE	1	0.89653998002776	2		546	359	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500951	8500951	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	27	480	0	ENST00000356435.5:c.1931A>C	p.Glu644Ala	p.E644A	ENST00000356435		644	gAa/gCa	13/35	1	2	FACETS	0.201	0.16	0.247	0.201	0.16	0.247	SUBCLONAL	1	TRUE	1	0.89653998002776	2		480	300	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500971	8500971	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	26	430	0	ENST00000356435.5:c.1911A>C	p.Lys637Asn	p.K637N	ENST00000356435		637	aaA/aaC	13/35	1	2	FACETS	0.2	0.158	0.247	0.2	0.158	0.247	SUBCLONAL	1	TRUE	1	0.89653998002776	2		430	290	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500991	8500991	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	22	393	0	ENST00000356435.5:c.1891C>A	p.Gln631Lys	p.Q631K	ENST00000356435		631	Caa/Aaa	13/35	1	2	FACETS	0.191	0.148	0.241	0.191	0.148	0.241	SUBCLONAL	1	TRUE	1	0.89653998002776	2		393	257	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127916193	127916193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	23	509	3	ENST00000373547.4:c.451G>A	p.Val151Ile	p.V151I	ENST00000373547	NM_002721.4	151	Gta/Ata	5/7	0.89653998002776	3	FACETS	0.169	0.131	0.212	0.084	0.065	0.106	SUBCLONAL	1	TRUE	1	0.89653998002776	3		512	441	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412276	139412276	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1445	86	686	0	ENST00000277541.6:c.1369G>C	p.Val457Leu	p.V457L	ENST00000277541	NM_017617.3	457	Gtc/Ctc	8/34	0.89653998002776	3	FACETS	0.181	0.159	0.205	0.091	0.079	0.103	SUBCLONAL	1	TRUE	1	0.89653998002776	3		686	1531	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412312	139412312	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1319	75	632	0	ENST00000277541.6:c.1333A>T	p.Thr445Ser	p.T445S	ENST00000277541	NM_017617.3	445	Acg/Tcg	8/34	0.89653998002776	3	FACETS	0.174	0.151	0.198	0.087	0.075	0.099	SUBCLONAL	1	TRUE	1	0.89653998002776	3		632	1394	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412336	139412336	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	62	601	0	ENST00000277541.6:c.1309G>C	p.Glu437Gln	p.E437Q	ENST00000277541	NM_017617.3	437	Gag/Cag	8/34	0.89653998002776	3	FACETS	0.164	0.141	0.19	0.082	0.07	0.095	SUBCLONAL	1	TRUE	1	0.89653998002776	3		601	1218	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413104	139413104	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1281	70	629	0	ENST00000277541.6:c.1038C>G	p.His346Gln	p.H346Q	ENST00000277541	NM_017617.3	346	caC/caG	6/34	0.89653998002776	3	FACETS	0.167	0.145	0.192	0.084	0.072	0.096	SUBCLONAL	1	TRUE	1	0.89653998002776	3		629	1351	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413116	139413134	+	missense_variant	Missense_Mutation	ONP	GGCGCTGGCACAGTCATCA	GGCGCTGGCACAGTCATCA	AGCCATGGCGCAGTCGTCG	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1374	98	708	4	ENST00000277541.6:c.1008_1026delinsCGACGACTGCGCCATGGCT	p.Ser341Met	p.S341M	ENST00000277541	NM_017617.3	336	atTGATGACTGTGCCAGCGCC/atCGACGACTGCGCCATGGCT	6/34	0.89653998002776	3	FACETS	0.215	0.191	0.241	0.108	0.095	0.121	SUBCLONAL	1	TRUE	1	0.89653998002776	3		712	1472	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156734	20156734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	95	194	0	ENST00000379607.5:c.23G>A	p.Gly8Glu	p.G8E	ENST00000379607	NM_001412.3	8	gGa/gAa	2/7	1	1	FACETS	0.999	0.944	1	0.999	0.944	1	CLONAL	1	TRUE	0	0.89653998002776	1		194	117	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923137	39923137	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	40	341	0	ENST00000378444.4:c.3571C>G	p.Leu1191Val	p.L1191V	ENST00000378444	NM_001123385.1	1191	Ctg/Gtg	8/15	1	1	FACETS	0.194	0.162	0.229	0.194	0.162	0.229	SUBCLONAL	1	TRUE	0	0.89653998002776	1		341	254	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923142	39923142	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	39	342	0	ENST00000378444.4:c.3566G>A	p.Ser1189Asn	p.S1189N	ENST00000378444	NM_001123385.1	1189	aGt/aAt	8/15	1	1	FACETS	0.198	0.165	0.235	0.198	0.165	0.235	SUBCLONAL	1	TRUE	0	0.89653998002776	1		342	242	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923149	39923150	+	missense_variant	Missense_Mutation	DNP	GT	GT	TG	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	38	344	1	ENST00000378444.4:c.3558_3559delinsCA	p.His1187Asn	p.H1187N	ENST00000378444	NM_001123385.1	1186	ccACat/ccCAat	8/15	1	1	FACETS	0.189	0.157	0.224	0.189	0.157	0.224	SUBCLONAL	1	TRUE	0	0.89653998002776	1		345	248	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923153	39923153	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs772803832	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	37	348	0	ENST00000378444.4:c.3555C>G	p.Asp1185Glu	p.D1185E	ENST00000378444	NM_001123385.1	1185	gaC/gaG	8/15	1	1	FACETS	0.185	0.153	0.22	0.185	0.153	0.22	SUBCLONAL	1	TRUE	0	0.89653998002776	1		348	246	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732824	44732825	+	missense_variant	Missense_Mutation	DNP	TA	TA	CG	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	79	262	0	ENST00000377967.4:c.27_28delinsCG	p.Thr10Ala	p.T10A	ENST00000377967	NM_021140.2	9	gcTAcc/gcCGcc	1/29	1	1	FACETS	0.214	0.189	0.241	0.214	0.189	0.241	SUBCLONAL	1	TRUE	0	0.89653998002776	1		262	454	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732894	44732894	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	37	222	0	ENST00000377967.4:c.97G>C	p.Glu33Gln	p.E33Q	ENST00000377967	NM_021140.2	33	Gag/Cag	1/29	1	1	FACETS	0.106	0.087	0.127	0.106	0.087	0.127	SUBCLONAL	1	TRUE	0	0.89653998002776	1		222	429	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732907	44732908	+	missense_variant	Missense_Mutation	DNP	CG	CG	AC	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	24	255	0	ENST00000377967.4:c.110_111delinsAC	p.Ala37Asp	p.A37D	ENST00000377967	NM_021140.2	37	gCG/gAC	1/29	1	1	FACETS	0.068	0.053	0.086	0.068	0.053	0.086	SUBCLONAL	1	TRUE	0	0.89653998002776	1		255	434	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732910	44732910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	24	256	0	ENST00000377967.4:c.113C>T	p.Ser38Phe	p.S38F	ENST00000377967	NM_021140.2	38	tCc/tTc	1/29	1	1	FACETS	0.069	0.053	0.087	0.069	0.053	0.087	SUBCLONAL	1	TRUE	0	0.89653998002776	1		256	429	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732912	44732912	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	24	263	0	ENST00000377967.4:c.115C>G	p.Pro39Ala	p.P39A	ENST00000377967	NM_021140.2	39	Ccc/Gcc	1/29	1	1	FACETS	0.07	0.054	0.088	0.07	0.054	0.088	SUBCLONAL	1	TRUE	0	0.89653998002776	1		263	422	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879878	44879878	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	46	280	0	ENST00000377967.4:c.467T>C	p.Val156Ala	p.V156A	ENST00000377967	NM_021140.2	156	gTg/gCg	6/29	1	1	FACETS	0.278	0.236	0.322	0.278	0.236	0.322	SUBCLONAL	1	TRUE	0	0.89653998002776	1		280	204	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918665	44918665	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	55	292	0	ENST00000377967.4:c.1148G>A	p.Ser383Asn	p.S383N	ENST00000377967	NM_021140.2	383	aGt/aAt	12/29	1	1	FACETS	0.289	0.25	0.331	0.289	0.25	0.331	SUBCLONAL	1	TRUE	0	0.89653998002776	1		292	234	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922674	44922674	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	23	170	0	ENST00000377967.4:c.1535C>A	p.Pro512Gln	p.P512Q	ENST00000377967	NM_021140.2	512	cCa/cAa	16/29	1	1	FACETS	0.187	0.147	0.233	0.187	0.147	0.233	SUBCLONAL	1	TRUE	0	0.89653998002776	1		170	151	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922772	44922772	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	40	230	0	ENST00000377967.4:c.1633C>G	p.Leu545Val	p.L545V	ENST00000377967	NM_021140.2	545	Ctt/Gtt	16/29	1	1	FACETS	0.186	0.155	0.22	0.186	0.155	0.22	SUBCLONAL	1	TRUE	0	0.89653998002776	1		230	265	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922794	44922795	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	27	234	1	ENST00000377967.4:c.1655_1656delinsAT	p.Ser552Asn	p.S552N	ENST00000377967	NM_021140.2	552	aGC/aAT	16/29	1	1	FACETS	0.122	0.097	0.151	0.122	0.097	0.151	SUBCLONAL	1	TRUE	0	0.89653998002776	1		235	272	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922799	44922799	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	27	238	0	ENST00000377967.4:c.1660T>G	p.Ser554Ala	p.S554A	ENST00000377967	NM_021140.2	554	Tct/Gct	16/29	1	1	FACETS	0.124	0.099	0.153	0.124	0.099	0.153	SUBCLONAL	1	TRUE	0	0.89653998002776	1		238	268	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922806	44922806	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	31	251	0	ENST00000377967.4:c.1667C>G	p.Pro556Arg	p.P556R	ENST00000377967	NM_021140.2	556	cCt/cGt	16/29	1	1	FACETS	0.132	0.106	0.16	0.132	0.106	0.16	SUBCLONAL	1	TRUE	0	0.89653998002776	1		251	290	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922838	44922838	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	30	264	0	ENST00000377967.4:c.1699T>A	p.Leu567Met	p.L567M	ENST00000377967	NM_021140.2	567	Ttg/Atg	16/29	1	1	FACETS	0.129	0.104	0.157	0.129	0.104	0.157	SUBCLONAL	1	TRUE	0	0.89653998002776	1		264	286	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922856	44922868	+	missense_variant	Missense_Mutation	ONP	TCTGCAGGCCATG	TCTGCAGGCCATG	CCAGCAGGCCCCA	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	34	258	2	ENST00000377967.4:c.1717_1729delinsCCAGCAGGCCCCA	p.Ser573_Val577delinsProAlaGlyProIle	p.S573_V577delinsPAGPI	ENST00000377967	NM_021140.2	573	TCTGCAGGCCATGtt/CCAGCAGGCCCCAtt	16/29	1	1	FACETS	0.158	0.129	0.19	0.158	0.129	0.19	SUBCLONAL	1	TRUE	0	0.89653998002776	1		260	265	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922883	44922883	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	48	260	0	ENST00000377967.4:c.1744T>G	p.Ser582Ala	p.S582A	ENST00000377967	NM_021140.2	582	Tca/Gca	16/29	1	1	FACETS	0.244	0.208	0.283	0.244	0.208	0.283	SUBCLONAL	1	TRUE	0	0.89653998002776	1		260	242	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922895	44922895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	48	258	0	ENST00000377967.4:c.1756G>A	p.Gly586Arg	p.G586R	ENST00000377967	NM_021140.2	586	Gga/Aga	16/29	1	1	FACETS	0.251	0.214	0.291	0.251	0.214	0.291	SUBCLONAL	1	TRUE	0	0.89653998002776	1		258	235	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922938	44922938	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	70	281	0	ENST00000377967.4:c.1799G>A	p.Gly600Glu	p.G600E	ENST00000377967	NM_021140.2	600	gGa/gAa	16/29	1	1	FACETS	0.32	0.282	0.361	0.32	0.282	0.361	SUBCLONAL	1	TRUE	0	0.89653998002776	1		281	269	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922974	44922974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs973676174	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	83	413	0	ENST00000377967.4:c.1835G>A	p.Arg612Gln	p.R612Q	ENST00000377967	NM_021140.2	612	cGa/cAa	16/29	1	1	FACETS	0.311	0.277	0.348	0.311	0.277	0.348	SUBCLONAL	1	TRUE	0	0.89653998002776	1		413	328	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922985	44922985	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	85	332	0	ENST00000377967.4:c.1846A>T	p.Thr616Ser	p.T616S	ENST00000377967	NM_021140.2	616	Act/Tct	16/29	1	1	FACETS	0.304	0.271	0.339	0.304	0.271	0.339	SUBCLONAL	1	TRUE	0	0.89653998002776	1		332	344	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928852	44928852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750754452	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	54	234	0	ENST00000377967.4:c.1952C>T	p.Ser651Leu	p.S651L	ENST00000377967	NM_021140.2	651	tCg/tTg	17/29	1	1	FACETS	0.284	0.245	0.326	0.284	0.245	0.326	SUBCLONAL	1	TRUE	0	0.89653998002776	1		234	234	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928914	44928914	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	86	296	3	ENST00000377967.4:c.2014G>T	p.Ala672Ser	p.A672S	ENST00000377967	NM_021140.2	672	Gct/Tct	17/29	1	1	FACETS	0.341	0.305	0.38	0.341	0.305	0.38	SUBCLONAL	1	TRUE	0	0.89653998002776	1		299	310	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928920	44928920	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	93	303	0	ENST00000377967.4:c.2020T>A	p.Ser674Thr	p.S674T	ENST00000377967	NM_021140.2	674	Tct/Act	17/29	1	1	FACETS	0.369	0.332	0.408	0.369	0.332	0.408	SUBCLONAL	1	TRUE	0	0.89653998002776	1		303	310	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928949	44928950	+	missense_variant	Missense_Mutation	DNP	CA	CA	TG	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	76	298	1	ENST00000377967.4:c.2049_2050inv	p.Thr684Ala	p.T684A	ENST00000377967	NM_021140.2	683	ccCAcc/ccTGcc	17/29	1	1	FACETS	0.316	0.28	0.354	0.316	0.28	0.354	SUBCLONAL	1	TRUE	0	0.89653998002776	1		299	296	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928953	44928954	+	missense_variant	Missense_Mutation	DNP	CT	CT	AC	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	76	301	0	ENST00000377967.4:c.2053_2054delinsAC	p.Leu685Thr	p.L685T	ENST00000377967	NM_021140.2	685	CTg/ACg	17/29	1	1	FACETS	0.304	0.269	0.341	0.304	0.269	0.341	SUBCLONAL	1	TRUE	0	0.89653998002776	1		301	308	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929071	44929071	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs749563708	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	63	256	0	ENST00000377967.4:c.2171T>C	p.Ile724Thr	p.I724T	ENST00000377967	NM_021140.2	724	aTa/aCa	17/29	1	1	FACETS	0.38	0.334	0.428	0.38	0.334	0.428	SUBCLONAL	1	TRUE	0	0.89653998002776	1		256	204	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929074	44929076	+	missense_variant	Missense_Mutation	TNP	TGA	TGA	CAG	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	62	249	0	ENST00000377967.4:c.2174_2176delinsCAG	p.Leu725_Thr726delinsSerAla	p.L725_T726delinsSA	ENST00000377967	NM_021140.2	725	tTGAcg/tCAGcg	17/29	1	1	FACETS	0.362	0.317	0.409	0.362	0.317	0.409	SUBCLONAL	1	TRUE	0	0.89653998002776	1		249	211	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929099	44929100	+	missense_variant	Missense_Mutation	DNP	CA	CA	TT	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	77	252	0	ENST00000377967.4:c.2199_2200delinsTT	p.Thr734Ser	p.T734S	ENST00000377967	NM_021140.2	733	caCAct/caTTct	17/29	1	1	FACETS	0.4	0.356	0.445	0.4	0.356	0.445	SUBCLONAL	1	TRUE	0	0.89653998002776	1		252	237	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929100	44929100	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	77	250	0	ENST00000377967.4:c.2200A>T	p.Thr734Ser	p.T734S	ENST00000377967	NM_021140.2	734	Act/Tct	17/29	1	1	FACETS	0.405	0.361	0.451	0.405	0.361	0.451	SUBCLONAL	1	TRUE	0	0.89653998002776	1		250	234	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929127	44929127	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	90	275	0	ENST00000377967.4:c.2227A>G	p.Ser743Gly	p.S743G	ENST00000377967	NM_021140.2	743	Agt/Ggt	17/29	1	1	FACETS	0.443	0.399	0.488	0.443	0.399	0.488	SUBCLONAL	1	TRUE	0	0.89653998002776	1		275	250	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929160	44929160	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	99	292	0	ENST00000377967.4:c.2260A>G	p.Met754Val	p.M754V	ENST00000377967	NM_021140.2	754	Atg/Gtg	17/29	1	1	FACETS	0.435	0.394	0.478	0.435	0.394	0.478	SUBCLONAL	1	TRUE	0	0.89653998002776	1		292	280	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929179	44929180	+	missense_variant	Missense_Mutation	DNP	GC	GC	CT	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	96	333	1	ENST00000377967.4:c.2279_2280delinsCT	p.Cys760Ser	p.C760S	ENST00000377967	NM_021140.2	760	tGC/tCT	17/29	1	1	FACETS	0.406	0.366	0.447	0.406	0.366	0.447	SUBCLONAL	1	TRUE	0	0.89653998002776	1		334	291	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929336	44929336	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1385511724	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	28	317	0	ENST00000377967.4:c.2436T>G	p.Asp812Glu	p.D812E	ENST00000377967	NM_021140.2	812	gaT/gaG	17/29	1	1	FACETS	0.137	0.11	0.168	0.137	0.11	0.168	SUBCLONAL	1	TRUE	0	0.89653998002776	1		317	251	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929343	44929343	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376391350	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	27	320	0	ENST00000377967.4:c.2443G>A	p.Val815Ile	p.V815I	ENST00000377967	NM_021140.2	815	Gtt/Att	17/29	1	1	FACETS	0.121	0.096	0.149	0.121	0.096	0.149	SUBCLONAL	1	TRUE	0	0.89653998002776	1		320	275	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929404	44929404	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	45	292	0	ENST00000377967.4:c.2504A>C	p.Gln835Pro	p.Q835P	ENST00000377967	NM_021140.2	835	cAg/cCg	17/29	1	1	FACETS	0.175	0.147	0.205	0.175	0.147	0.205	SUBCLONAL	1	TRUE	0	0.89653998002776	1		292	317	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929450	44929465	+	protein_altering_variant	In_Frame_Del	DEL	GCTACACACAATTAAT	GCTACACACAATTAAT	ACATACAGTTAAC	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	41	301	1	ENST00000377967.4:c.2550_2565delinsACATACAGTTAAC	p.Leu851_Ile854delinsHisThrVal	p.L851_I854delinsHTV	ENST00000377967	NM_021140.2	850	ggGCTACACACAATTAAT/ggACATACAGTTAAC	17/29	1	1	FACETS	0.21	0.176	0.247	0.21	0.176	0.247	SUBCLONAL	1	TRUE	0	0.89653998002776	1		302	240	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936011	44936012	+	missense_variant	Missense_Mutation	DNP	AT	AT	GC	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	45	318	0	ENST00000377967.4:c.2772_2773delinsGC	p.Ser925Pro	p.S925P	ENST00000377967	NM_021140.2	924	ccATct/ccGCct	18/29	1	1	FACETS	0.192	0.162	0.224	0.192	0.162	0.224	SUBCLONAL	1	TRUE	0	0.89653998002776	1		318	289	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936015	44936015	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	47	319	0	ENST00000377967.4:c.2776T>C	p.Ser926Pro	p.S926P	ENST00000377967	NM_021140.2	926	Tca/Cca	18/29	1	1	FACETS	0.202	0.171	0.236	0.202	0.171	0.236	SUBCLONAL	1	TRUE	0	0.89653998002776	1		319	286	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966728	44966728	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	18	327	0	ENST00000377967.4:c.3952A>G	p.Ile1318Val	p.I1318V	ENST00000377967	NM_021140.2	1318	Ata/Gta	27/29	1	1	FACETS	0.133	0.101	0.172	0.133	0.101	0.172	SUBCLONAL	1	TRUE	0	0.89653998002776	1		327	166	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969355	44969355	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	14	235	0	ENST00000377967.4:c.4037A>G	p.Asn1346Ser	p.N1346S	ENST00000377967	NM_021140.2	1346	aAt/aGt	28/29	1	1	FACETS	0.115	0.083	0.153	0.115	0.083	0.153	SUBCLONAL	1	TRUE	0	0.89653998002776	1		235	150	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969380	44969381	+	missense_variant	Missense_Mutation	DNP	CA	CA	TG	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	12	254	1	ENST00000377967.4:c.4062_4063inv	p.Ile1355Val	p.I1355V	ENST00000377967	NM_021140.2	1354	taCAta/taTGta	28/29	1	1	FACETS	0.08	0.056	0.11	0.08	0.056	0.11	SUBCLONAL	1	TRUE	0	0.89653998002776	1		255	184	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969410	44969423	+	missense_variant	Missense_Mutation	ONP	AACAAGCGGAAACT	AACAAGCGGAAACT	GATAAGCACGAACC	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	12	305	2	ENST00000377967.4:c.4092_4105delinsGATAAGCACGAACC	p.Thr1365_Gly1367delinsIleSerThr	p.T1365_G1367delinsIST	ENST00000377967	NM_021140.2	1364	aaAACAAGCGGAAACTtg/aaGATAAGCACGAACCtg	28/29	1	1	FACETS	0.078	0.055	0.107	0.078	0.055	0.107	SUBCLONAL	1	TRUE	0	0.89653998002776	1		307	189	SUCCESS
AR	367	MSKCC	GRCh37	X	66943595	66943596	+	missense_variant	Missense_Mutation	DNP	TT	TT	AC	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	13	279	1	ENST00000374690.3:c.2675_2676delinsAC	p.Phe892Tyr	p.F892Y	ENST00000374690	NM_000044.3	892	tTT/tAC	8/8	1	1	FACETS	0.09	0.064	0.121	0.09	0.064	0.121	SUBCLONAL	1	TRUE	0	0.89653998002776	1		280	178	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346936	70346936	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	36	232	1	ENST00000374080.3:c.2803G>T	p.Ala935Ser	p.A935S	ENST00000374080		935	Gcc/Tcc	20/45	1	1	FACETS	0.174	0.143	0.207	0.174	0.143	0.207	SUBCLONAL	1	TRUE	0	0.89653998002776	1		233	255	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763858	76763858	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	43	333	0	ENST00000373344.5:c.7450C>G	p.Pro2484Ala	p.P2484A	ENST00000373344	NM_000489.3	2484	Cca/Gca	35/35	1	1	FACETS	0.237	0.2	0.278	0.237	0.2	0.278	SUBCLONAL	1	TRUE	0	0.89653998002776	1		333	223	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763867	76763867	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	48	335	0	ENST00000373344.5:c.7441A>G	p.Ser2481Gly	p.S2481G	ENST00000373344	NM_000489.3	2481	Agc/Ggc	35/35	1	1	FACETS	0.27	0.23	0.312	0.27	0.23	0.312	SUBCLONAL	1	TRUE	0	0.89653998002776	1		335	219	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763918	76763918	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	39	296	0	ENST00000373344.5:c.7390G>T	p.Ala2464Ser	p.A2464S	ENST00000373344	NM_000489.3	2464	Gct/Tct	35/35	1	1	FACETS	0.279	0.234	0.328	0.279	0.234	0.328	SUBCLONAL	1	TRUE	0	0.89653998002776	1		296	172	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763924	76763924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	37	295	0	ENST00000373344.5:c.7384C>T	p.Pro2462Ser	p.P2462S	ENST00000373344	NM_000489.3	2462	Cca/Tca	35/35	1	1	FACETS	0.262	0.218	0.309	0.262	0.218	0.309	SUBCLONAL	1	TRUE	0	0.89653998002776	1		295	174	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76764008	76764039	+	missense_variant	Missense_Mutation	ONP	CCAGTGTTGCTTGTTGATAAGTCATTTGTTGC	CCAGTGTTGCTTGTTGATAAGTCATTTGTTGC	TCATTGCTGTTTGCTGGTAAGACATGTGCTGT	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	11	366	2	ENST00000373344.5:c.7269_7300delinsACAGCACATGTCTTACCAGCAAACAGCAATGA	p.Gln2425_Gly2434delinsHisMetSerTyrGlnGlnThrAlaMetSer	p.Q2425_G2434delinsHMSYQQTAMS	ENST00000373344	NM_000489.3	2423	caGCAACAAATGACTTATCAACAAGCAACACTGGgt/caACAGCACATGTCTTACCAGCAAACAGCAATGAgt	35/35	1	1	FACETS	0.062	0.043	0.087	0.062	0.043	0.087	SUBCLONAL	1	TRUE	0	0.89653998002776	1		368	217	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76949418	76949418	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1569540319	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	14	190	0	ENST00000373344.5:c.379A>G	p.Ile127Val	p.I127V	ENST00000373344	NM_000489.3	127	Att/Gtt	6/35	1	1	FACETS	0.122	0.088	0.162	0.122	0.088	0.162	SUBCLONAL	1	TRUE	0	0.89653998002776	1		190	141	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611152	100611152	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	52	294	0	ENST00000308731.7:c.1454A>T	p.Tyr485Phe	p.Y485F	ENST00000308731	NM_000061.2	485	tAc/tTc	15/19	1	1	FACETS	0.229	0.196	0.265	0.229	0.196	0.265	SUBCLONAL	1	TRUE	0	0.89653998002776	1		294	279	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611226	100611226	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	20	262	0	ENST00000308731.7:c.1380G>C	p.Leu460Phe	p.L460F	ENST00000308731	NM_000061.2	460	ttG/ttC	15/19	1	1	FACETS	0.109	0.083	0.139	0.109	0.083	0.139	SUBCLONAL	1	TRUE	0	0.89653998002776	1		262	225	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205020	123205020	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	15	185	0	ENST00000218089.9:c.2380A>G	p.Ile794Val	p.I794V	ENST00000218089	NM_001042749.1	794	Att/Gtt	25/35	1	1	FACETS	0.188	0.139	0.245	0.188	0.139	0.245	SUBCLONAL	1	TRUE	0	0.89653998002776	1		185	98	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205022	123205022	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	15	236	0	ENST00000218089.9:c.2382T>G	p.Ile794Met	p.I794M	ENST00000218089	NM_001042749.1	794	atT/atG	25/35	1	1	FACETS	0.161	0.118	0.21	0.161	0.118	0.21	SUBCLONAL	1	TRUE	0	0.89653998002776	1		236	115	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205050	123205050	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	14	306	0	ENST00000218089.9:c.2410T>A	p.Ser804Thr	p.S804T	ENST00000218089	NM_001042749.1	804	Tca/Aca	25/35	1	1	FACETS	0.112	0.081	0.149	0.112	0.081	0.149	SUBCLONAL	1	TRUE	0	0.89653998002776	1		306	154	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38156995	38156995	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	34	667	0	ENST00000317025.8:c.2725T>C	p.Ser909Pro	p.S909P	ENST00000317025	NM_023034.1	909	Tct/Cct	15/24	0.166235034008495	2	FACETS	0.196	0.16	0.236	0.098	0.08	0.118	INDETERMINATE	1	TRUE	0	0.89653998002776	2		667	387	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429376	78429377	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCC	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	37	526	0	ENST00000370768.2:c.1063_1065dup	p.Gly355dup	p.G355dup	ENST00000370768	NM_003902.3	355	-/GGA	13/20	1	2	FACETS	0.178	0.146	0.213	0.178	0.146	0.213	SUBCLONAL	1	TRUE	1	0.89653998002776	2		526	465	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099887	157099888	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	66	566	0	ENST00000346085.5:c.824_825insC	p.Ala276GlyfsTer259	p.A276Gfs*259	ENST00000346085	NM_020732.3	275	ggg/ggCg	1/20	1	2	FACETS	0.143	0.123	0.164	0.143	0.123	0.164	SUBCLONAL	1	TRUE	1	0.89653998002776	2		566	1032	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611116	100611117	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	39	346	0	ENST00000308731.7:c.1489_1490insTG	p.Gln497LeufsTer4	p.Q497Lfs*4	ENST00000308731	NM_000061.2	497	cag/cTGag	15/19	1	1	FACETS	0.168	0.14	0.2	0.168	0.14	0.2	SUBCLONAL	1	TRUE	0	0.89653998002776	1		346	285	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611119	100611120	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	41	331	0	ENST00000308731.7:c.1486_1487del	p.Gln496AlafsTer11	p.Q496Afs*11	ENST00000308731	NM_000061.2	496	CAg/g	15/19	1	1	FACETS	0.182	0.152	0.214	0.182	0.152	0.214	SUBCLONAL	1	TRUE	0	0.89653998002776	1		331	278	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164874	123164876	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	11	161	0	ENST00000218089.9:c.190_192del	p.Pro64del	p.P64del	ENST00000218089	NM_001042749.1	63	CCT/-	5/35	1	1	FACETS	0.13	0.09	0.179	0.13	0.09	0.179	SUBCLONAL	1	TRUE	0	0.89653998002776	1		161	104	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822048	72822050	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	21	311	0	ENST00000268489.5:c.10125_10127del	p.Ile3375_Gln3376delinsMet	p.I3375_Q3376delinsM	ENST00000268489	NM_006885.3	3375	atTCAg/atg	10/10	1	2	FACETS	0.185	0.142	0.235	0.185	0.142	0.235	SUBCLONAL	1	TRUE	1	0.89653998002776	2		311	253	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099869	157099884	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCCGCCGCCGCCGC	CCTCCGCCGCCGCCGC	-	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	62	530	0	ENST00000346085.5:c.807_822del	p.Ser270GlyfsTer94	p.S270Gfs*94	ENST00000346085	NM_020732.3	269	gCCTCCGCCGCCGCCGCc/gc	1/20	1	2	FACETS	0.135	0.116	0.156	0.135	0.116	0.156	SUBCLONAL	1	TRUE	1	0.89653998002776	2		530	1022	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929450	44929452	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	41	299	0	ENST00000377967.4:c.2550_2552del	p.Leu851del	p.L851del	ENST00000377967	NM_021140.2	850	ggGCTa/gga	17/29	1	1	FACETS	0.211	0.177	0.249	0.211	0.177	0.249	SUBCLONAL	1	TRUE	0	0.89653998002776	1		299	239	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574824	41574826	+	missense_variant	Missense_Mutation	TNP	ATT	ATT	GTG	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	69	662	0	ENST00000263253.7:c.7109_7111delinsGTG	p.Asn2370_Ser2371delinsSerAla	p.N2370_S2371delinsSA	ENST00000263253	NM_001429.3	2370	aATTca/aGTGca	31/31	1	2	FACETS	0.23	0.2	0.262	0.23	0.2	0.262	SUBCLONAL	1	TRUE	1	0.89653998002776	2		662	670	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992313	72992313	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025368-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	99	831	0	ENST00000268489.5:c.1732A>G	p.Arg578Gly	p.R578G	ENST00000268489	NM_006885.3	578	Agg/Ggg	2/10	1	2	FACETS	0.271	0.241	0.302	0.271	0.241	0.302	SUBCLONAL	1	TRUE	1	0.89653998002776	2		831	815	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115013	3115013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	171	859	0	ENST00000078429.4:c.548G>A	p.Arg183His	p.R183H	ENST00000078429	NM_002067.2	183	cGc/cAc	4/7	0.36129089708744	5	FACETS	0.91	0.848	0.973	1	0.985	1	CLONAL	4	FALSE	2	0.36129089708744	5		859	401	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441415	52441415	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	97	565	0	ENST00000460680.1:c.437G>C	p.Arg146Thr	p.R146T	ENST00000460680	NM_004656.3	146	aGg/aCg	6/17	0.36129089708744	3	FACETS	1	0.938	1	1	0.985	1	CLONAL	4	FALSE	0	0.36129089708744	3		565	156	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0025541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	177	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.813473374240454	2		306	398	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0025541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	570	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.813473374240454	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.813473374240454	3		288	962	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000018	42000018	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	339	692	0	ENST00000219905.7:c.2281C>T	p.Pro761Ser	p.P761S	ENST00000219905	NM_001164273.1	761	Cct/Tct	6/24	1	2	FACETS	0.928	0.881	0.976	0.928	0.881	0.976	CLONAL	1	TRUE	1	0.813473374240454	2		692	898	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424958105	NA	P-0025541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	461	487	0	ENST00000334344.6:c.940C>T	p.Arg314Cys	p.R314C	ENST00000334344	NM_152641.2	314	Cgt/Tgt	8/21	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	2	TRUE	NA	0.813473374240454	2		487	562	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397762	116397762	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	637	599	1	ENST00000397752.3:c.2036G>A	p.Gly679Glu	p.G679E	ENST00000397752	NM_000245.2	679	gGa/gAa	8/21	0.813473374240454	3	FACETS	0.941	0.911	0.971	0.941	0.911	0.971	CLONAL	2	TRUE	1	0.813473374240454	3		600	1171	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65312344	65312344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	36	548	0	ENST00000342505.4:c.1975C>T	p.Arg659Cys	p.R659C	ENST00000342505	NM_002227.2	659	Cgc/Tgc	14/25	0.813473374240454	2	FACETS	0.129	0.105	0.156	0.065	0.052	0.078	SUBCLONAL	1	TRUE	0	0.813473374240454	2		548	686	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137253	64137253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	214	542	1	ENST00000334205.4:c.1685C>T	p.Pro562Leu	p.P562L	ENST00000334205	NM_003942.2	562	cCc/cTc	14/17	1	2	FACETS	0.918	0.86	0.978	0.918	0.86	0.978	CLONAL	1	TRUE	1	0.813473374240454	2		543	573	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346817	89346817	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526095	NA	P-0025541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	140	303	0	ENST00000301030.4:c.6133C>T	p.Pro2045Ser	p.P2045S	ENST00000301030	NM_001256183.1	2045	Ccc/Tcc	9/13	0.813473374240454	1	FACETS	0.92	0.863	0.975	0.92	0.863	0.975	CLONAL	1	TRUE	0	0.813473374240454	1		303	222	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980349	7980349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	260	447	0	ENST00000319144.4:c.1234G>A	p.Ala412Thr	p.A412T	ENST00000319144	NM_001139.2	412	Gcc/Acc	9/15	0.813473374240454	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.813473374240454	1		447	366	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209110138	209110138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1315254690	NA	P-0025541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	237	503	0	ENST00000345146.2:c.425C>T	p.Thr142Ile	p.T142I	ENST00000345146	NM_005896.2	142	aCt/aTt	5/10	1	2	FACETS	0.954	0.897	1	0.954	0.897	1	CLONAL	1	TRUE	1	0.813473374240454	2		503	611	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729981	30729981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746373651	NA	P-0025541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	199	387	0	ENST00000295754.5:c.1502C>T	p.Pro501Leu	p.P501L	ENST00000295754	NM_003242.5	501	cCc/cTc	6/7	1	2	FACETS	0.956	0.893	1	0.956	0.893	1	CLONAL	1	TRUE	1	0.813473374240454	2		387	512	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014113	70014113	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	272	488	2	ENST00000394351.3:c.974G>T	p.Ser325Ile	p.S325I	ENST00000394351	NM_000248.3	325	aGc/aTc	9/9	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.813473374240454	2		490	667	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004961	150004961	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs953489812	NA	P-0025541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	326	478	0	ENST00000253339.5:c.1264T>C	p.Tyr422His	p.Y422H	ENST00000253339		422	Tat/Cat	3/7	0.168457550355463	2	FACETS	1	0.993	1	0.626	0.597	0.655	INDETERMINATE	1	TRUE	0	0.813473374240454	2		478	640	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151935825	151935825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1297640475	NA	P-0025541-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4	16	6	0	ENST00000262189.6:c.2619del	p.Gln873HisfsTer40	p.Q873Hfs*40	ENST00000262189	NM_170606.2	873	caG/ca	15/59	0.813473374240454	3	FACETS	0.922	0.786	1	1	0.938	1	CLONAL	3	TRUE	1	0.813473374240454	3		6	20	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755531	39755531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	265	502	0	ENST00000288319.7:c.1234C>T	p.Pro412Ser	p.P412S	ENST00000288319	NM_182918.3	412	Ccc/Tcc	10/10	0.759911858504251	3	FACETS	0.994	0.945	1	0.994	0.945	1	CLONAL	2	TRUE	1	0.759911858504251	3		502	484	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588210	69588210	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	174	662	0	ENST00000168712.1:c.488C>T	p.Pro163Leu	p.P163L	ENST00000168712	NM_002007.2	163	cCc/cTc	3/3	0.102989374410332	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.759911858504251	0		662	468	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125523671	125523673	+	inframe_deletion	In_Frame_Del	DEL	AAT	AAT	-	novel	NA	P-0025561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	134	544	0	ENST00000428830.2:c.1266_1268del	p.Asn422del	p.N422del	ENST00000428830	NM_001114121.2	422	AAT/-	12/14	1	2	FACETS	0.923	0.848	1	0.923	0.848	1	CLONAL	1	TRUE	1	0.759911858504251	2		544	382	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233757	133233759	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs1555225139	NA	P-0025561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	417	625	0	ENST00000320574.5:c.3545_3547del	p.Lys1182del	p.K1182del	ENST00000320574	NM_006231.2	1182	aAGAtc/atc	29/49	0.759911858504251	2	FACETS	0.994	0.965	1	0.994	0.965	1	CLONAL	2	TRUE	0	0.759911858504251	2		625	552	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106162523	106162523	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	101	412	0	ENST00000380013.4:c.3437C>T	p.Pro1146Leu	p.P1146L	ENST00000380013	NM_001127208.2	1146	cCt/cTt	4/11	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.759911858504251	2		412	257	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148526831	148526831	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	214	497	0	ENST00000320356.2:c.473A>T	p.His158Leu	p.H158L	ENST00000320356	NM_004456.4	158	cAc/cTc	5/20	0.752343264940933	4	FACETS	0.923	0.865	0.981	0.923	0.865	0.981	CLONAL	2	TRUE	2	0.759911858504251	4		497	537	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0025565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	261	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.632919148982614	2		306	698	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0025565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	242	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.632919148982614	2		288	715	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0025565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	169	364	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.975	0.902	1	0.975	0.902	1	CLONAL	1	TRUE	1	0.632919148982614	2		364	548	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579584	7579585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	249	599	0	ENST00000269305.4:c.102dup	p.Pro36AlafsTer7	p.P36Afs*7	ENST00000269305	NM_001126112.2	34	-/C	4/11	0.632919148982614	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.632919148982614	1		599	520	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421528	32421528	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	316	638	0	ENST00000332351.3:c.1064G>A	p.Arg355Lys	p.R355K	ENST00000332351	NM_024426.4	355	aGa/aAa	6/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.632919148982614	2		638	887	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444311	50444311	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778251001	NA	P-0025565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	160	364	2	ENST00000331340.3:c.241G>A	p.Asp81Asn	p.D81N	ENST00000331340	NM_006060.4	81	Gat/Aat	4/8	1	2	FACETS	0.895	0.825	0.967	0.895	0.825	0.967	CLONAL	1	TRUE	1	0.632919148982614	2		366	565	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021804	246021804	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1279348499	NA	P-0025565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	248	629	0	ENST00000388985.4:c.1070C>T	p.Pro357Leu	p.P357L	ENST00000388985		357	cCa/cTa	10/12	1	2	FACETS	0.963	0.903	1	0.963	0.903	1	CLONAL	1	TRUE	1	0.632919148982614	2		629	814	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519956	66519956	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	150	471	0	ENST00000358598.2:c.439A>C	p.Ser147Arg	p.S147R	ENST00000358598	NM_212471.2	147	Agt/Cgt	4/11	1	2	FACETS	0.746	0.684	0.811	0.746	0.684	0.811	SUBCLONAL	1	TRUE	1	0.632919148982614	2		471	635	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276608	15276608	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	312	634	0	ENST00000263388.2:c.5657G>A	p.Gly1886Asp	p.G1886D	ENST00000263388	NM_000435.2	1886	gGt/gAt	30/33	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.632919148982614	2		634	932	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560959	9560959	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	225	514	0	ENST00000353224.5:c.823C>T	p.Gln275Ter	p.Q275*	ENST00000353224	NM_177990.2	275	Cag/Tag	4/10	1	2	FACETS	0.961	0.898	1	0.961	0.898	1	CLONAL	1	TRUE	1	0.632919148982614	2		514	740	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368151	31368151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	265	574	1	ENST00000328111.2:c.22C>T	p.Leu8Phe	p.L8F	ENST00000328111	NM_006892.3	8	Ctc/Ttc	2/23	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.632919148982614	2		575	804	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267868	46267868	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	303	626	2	ENST00000371998.3:c.2629C>T	p.Pro877Ser	p.P877S	ENST00000371998		877	Ccc/Tcc	14/23	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.632919148982614	2		628	950	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713518	30713518	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0025565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	260	488	0	ENST00000295754.5:c.843T>A	p.Tyr281Ter	p.Y281*	ENST00000295754	NM_003242.5	281	taT/taA	4/7	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.632919148982614	2		488	759	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147594	47147594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	199	375	0	ENST00000409792.3:c.4732G>A	p.Glu1578Lys	p.E1578K	ENST00000409792	NM_014159.6	1578	Gaa/Aaa	6/21	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.632919148982614	2		375	609	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185195134	185195134	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	189	361	0	ENST00000265026.3:c.2451A>C	p.Glu817Asp	p.E817D	ENST00000265026	NM_004721.4	817	gaA/gaC	12/14	1	2	FACETS	0.997	0.927	1	0.997	0.927	1	CLONAL	1	TRUE	1	0.632919148982614	2		361	599	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494265	140494265	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	316	811	0	ENST00000288602.6:c.983C>T	p.Pro328Leu	p.P328L	ENST00000288602	NM_004333.4	328	cCc/cTc	8/18	1	2	FACETS	0.962	0.909	1	0.962	0.909	1	CLONAL	1	TRUE	1	0.632919148982614	2		811	1038	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611920	100611920	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	260	308	0	ENST00000308731.7:c.1201G>A	p.Asp401Asn	p.D401N	ENST00000308731	NM_000061.2	401	Gac/Aac	14/19	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.632919148982614	1		308	416	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587251	212587251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868149408	NA	P-0025828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	82	359	0	ENST00000342788.4:c.750G>A	p.Met250Ile	p.M250I	ENST00000342788	NM_005235.2	250	atG/atA	7/28	1	2	FACETS	0.923	0.821	1	0.923	0.821	1	CLONAL	1	TRUE	1	0.545322271608571	2		359	326	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39595496	39595496	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025828-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	82	407	0	ENST00000262039.4:c.1382A>C	p.Lys461Thr	p.K461T	ENST00000262039	NM_002647.2	461	aAa/aCa	12/25	1	2	FACETS	0.857	0.761	0.957	0.857	0.761	0.957	CLONAL	1	TRUE	1	0.545322271608571	2		407	351	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0025831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	42	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.27928827074658	2		306	204	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0025831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	210	528	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.254003539420659	2	FACETS	0.992	0.924	1	0.992	0.924	1	CLONAL	2	TRUE	0	0.27928827074658	2		528	758	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156738	2156738	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	93	617	0	ENST00000434045.2:c.184G>A	p.Gly62Arg	p.G62R	ENST00000434045	NM_001127598.1	62	Ggg/Agg	3/5	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.27928827074658	2		617	657	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77085401	77085401	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349619138	NA	P-0025831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	88	541	0	ENST00000356341.3:c.449C>T	p.Ala150Val	p.A150V	ENST00000356341	NM_002576.4	150	gCt/gTt	5/15	1	2	FACETS	0.994	0.881	1	0.994	0.881	1	CLONAL	1	TRUE	1	0.27928827074658	2		541	634	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012441	29012441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55974987	NA	P-0025831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	102	578	0	ENST00000282397.4:c.430G>A	p.Glu144Lys	p.E144K	ENST00000282397	NM_002019.4	144	Gaa/Aaa	4/30	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.27928827074658	2		578	692	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777807	3777807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	138	845	1	ENST00000262367.5:c.7241C>T	p.Thr2414Ile	p.T2414I	ENST00000262367	NM_004380.2	2414	aCc/aTc	31/31	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.27928827074658	2		846	897	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872927	136872927	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	66	431	0	ENST00000241393.3:c.571C>T	p.Pro191Ser	p.P191S	ENST00000241393	NM_003467.2	191	Ccc/Tcc	2/2	1	2	FACETS	0.853	0.741	0.974	0.853	0.741	0.974	CLONAL	1	TRUE	1	0.27928827074658	2		431	554	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543799	212543799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	102	457	0	ENST00000342788.4:c.1600G>A	p.Glu534Lys	p.E534K	ENST00000342788	NM_005235.2	534	Gag/Aag	13/28	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.27928827074658	2		457	625	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566773	212566773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	60	426	0	ENST00000342788.4:c.1408C>T	p.His470Tyr	p.H470Y	ENST00000342788	NM_005235.2	470	Cat/Tat	12/28	1	2	FACETS	0.802	0.691	0.922	0.802	0.691	0.922	CLONAL	1	TRUE	1	0.27928827074658	2		426	536	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748126	41748126	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	25	133	0	ENST00000226382.2:c.643G>A	p.Gly215Ser	p.G215S	ENST00000226382	NM_003924.3	215	Ggc/Agc	3/3	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.27928827074658	2		133	137	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295230	1295230	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs796516131	NA	P-0025831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	30	341	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.27928827074658	2		341	160	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188214	32188214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	94	612	0	ENST00000375023.3:c.1127C>T	p.Ser376Phe	p.S376F	ENST00000375023	NM_004557.3	376	tCt/tTt	6/30	0.279328259972944	3	FACETS	1	0.92	1	0.52	0.463	0.582	CLONAL	1	TRUE	1	0.27928827074658	3		612	737	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513231	106513231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	57	339	0	ENST00000359195.3:c.2135G>A	p.Arg712Lys	p.R712K	ENST00000359195	NM_002649.2	712	aGg/aAg	4/11	1	2	FACETS	0.885	0.761	1	0.885	0.761	1	CLONAL	1	TRUE	1	0.27928827074658	2		339	461	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27168534	27168534	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	89	665	0	ENST00000380036.4:c.406G>A	p.Gly136Arg	p.G136R	ENST00000380036	NM_000459.3	136	Gga/Aga	3/23	1	2	FACETS	0.907	0.804	1	0.907	0.804	1	CLONAL	1	TRUE	1	0.27928827074658	2		665	703	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760907	133760907	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	110	790	0	ENST00000318560.5:c.3230T>G	p.Met1077Arg	p.M1077R	ENST00000318560	NM_005157.4	1077	aTg/aGg	11/11	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.27928827074658	2		790	766	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781449	135781449	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	87	453	1	ENST00000298552.3:c.1516C>T	p.Pro506Ser	p.P506S	ENST00000298552	NM_001162426.1	506	Ccc/Tcc	15/23	1	2	FACETS	0.961	0.852	1	0.961	0.852	1	CLONAL	1	TRUE	1	0.27928827074658	2		454	648	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0026030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	77	306	0				ENST00000310581	NM_198253.2	-/1132			0.243034883753097	3	FACETS	1	0.961	1	0.8	0.71	0.895	CLONAL	2	TRUE	0	0.243034883753097	3		306	296	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0026030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	16	695	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	NA	2	FACETS	0.855	0.636	1			1	INDETERMINATE	1	TRUE	NA	0.243034883753097	2		695	154	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230571	46230571	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	24	306	2	ENST00000334344.6:c.820C>T	p.Arg274Ter	p.R274*	ENST00000334344	NM_152641.2	274	Cga/Tga	8/21	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.243034883753097	2		308	157	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579717	7579717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs922736614	NA	P-0026030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	63	669	0	ENST00000269305.4:c.79C>T	p.Pro27Ser	p.P27S	ENST00000269305	NM_001126112.2	27	Cct/Tct	3/11	0.166008453860527	2	FACETS	0.858	0.748	0.976	0.858	0.748	0.976	CLONAL	2	TRUE	0	0.243034883753097	2		669	302	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005419	29005419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55687105	NA	P-0026030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	15	398	0	ENST00000282397.4:c.842G>A	p.Arg281Gln	p.R281Q	ENST00000282397	NM_002019.4	281	cGa/cAa	7/30	0.166008453860527	2	FACETS	1	0.786	1	0.537	0.396	0.701	CLONAL	1	TRUE	0	0.243034883753097	2		398	115	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533467	533467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894231	NA	P-0026030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	106	594	0	ENST00000451590.1:c.436G>A	p.Ala146Thr	p.A146T	ENST00000451590	NM_001130442.1	146	Gcc/Acc	4/5	0.243034883753097	3	FACETS	1	0.923	1	1	0.923	1	CLONAL	2	TRUE	1	0.243034883753097	3		594	476	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149242	119149242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779039234	NA	P-0026030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	34	603	0	ENST00000264033.4:c.1250C>T	p.Pro417Leu	p.P417L	ENST00000264033	NM_005188.3	417	cCt/cTt	9/16	0.243034883753097	3	FACETS	0.904	0.74	1	0.452	0.37	0.544	CLONAL	1	TRUE	1	0.243034883753097	3		603	347	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118878	61118878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	43	285	0	ENST00000295025.8:c.71G>A	p.Arg24Lys	p.R24K	ENST00000295025	NM_002908.2	24	aGa/aAa	2/11	0.152564323202096	2	FACETS	1	0.951	1	0.68	0.573	0.797	CLONAL	1	TRUE	0	0.243034883753097	2		285	260	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202123028	202123028	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs34210251	NA	P-0026030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	99	396	2	ENST00000358485.4:c.74C>T	p.Pro25Leu	p.P25L	ENST00000358485	NM_001080125.1	25	cCc/cTc	1/9	0.243034883753097	4	FACETS	1	0.968	1	0.794	0.713	0.879	CLONAL	2	TRUE	1	0.243034883753097	4		398	425	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359404	118359404	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	18	524	0	ENST00000534358.1:c.4408C>T	p.Gln1470Ter	p.Q1470*	ENST00000534358	NM_005933.3	1470	Cag/Tag	11/36	0.243034883753097	3	FACETS	0.491	0.369	0.636	0.246	0.184	0.318	SUBCLONAL	1	TRUE	1	0.243034883753097	3		524	338	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43818322	43818322	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	94	579	0	ENST00000372470.3:c.1787C>G	p.Pro596Arg	p.P596R	ENST00000372470	NM_005373.2	596	cCt/cGt	12/12	0.243034883753097	3	FACETS	0.929	0.83	1	0.929	0.83	1	CLONAL	2	TRUE	1	0.243034883753097	3		579	467	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120479960	120479960	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs782760871	NA	P-0026030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	45	432	0	ENST00000256646.2:c.3467A>G	p.Asn1156Ser	p.N1156S	ENST00000256646	NM_024408.3	1156	aAc/aGc	21/34	0.243034883753097	3	FACETS	1	0.879	1	0.526	0.443	0.617	CLONAL	1	TRUE	1	0.243034883753097	3		432	395	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377330	118377330	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	69	267	0	ENST00000534358.1:c.10723C>T	p.Gln3575Ter	p.Q3575*	ENST00000534358	NM_005933.3	3575	Caa/Taa	27/36	0.243034883753097	3	FACETS	1	0.92	1	1	0.92	1	CLONAL	2	TRUE	1	0.243034883753097	3		267	300	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148529	119148529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	13	383	0	ENST00000264033.4:c.1070C>T	p.Pro357Leu	p.P357L	ENST00000264033	NM_005188.3	357	cCc/cTc	7/16	0.243034883753097	3	FACETS	0.663	0.474	0.892	0.331	0.237	0.446	SUBCLONAL	1	TRUE	1	0.243034883753097	3		383	181	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420193	49420193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	51	497	1	ENST00000301067.7:c.15556C>T	p.His5186Tyr	p.H5186Y	ENST00000301067	NM_003482.3	5186	Cac/Tac	48/54	1	2	FACETS	0.997	0.849	1	0.997	0.849	1	CLONAL	1	TRUE	1	0.243034883753097	2		498	421	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434167	121434167	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867236572	NA	P-0026030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	79	634	0	ENST00000257555.6:c.1058C>T	p.Pro353Leu	p.P353L	ENST00000257555		353	cCc/cTc	5/10	1	2	FACETS	0.759	0.671	0.854	1	0.978	1	SUBCLONAL	2	TRUE	1	0.243034883753097	2		634	428	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644596	3644596	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	53	479	0	ENST00000294008.3:c.2018C>T	p.Ser673Phe	p.S673F	ENST00000294008	NM_032444.2	673	tCc/tTc	10/15	0.243034883753097	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.243034883753097	1		479	326	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533368	29533368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	22	213	0	ENST00000356175.3:c.1373del	p.Pro458GlnfsTer15	p.P458Qfs*15	ENST00000356175	NM_000267.3	457	caC/ca	12/57	0.166008453860527	2	FACETS	0.794	0.625	0.983	0.794	0.625	0.983	CLONAL	2	TRUE	0	0.243034883753097	2		213	114	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221438	36221438	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0026030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	69	641	2	ENST00000222270.7:c.5198-1G>T		p.X1733_splice	ENST00000222270	NM_014727.1	1733			0.166668185516937	3	FACETS	1	0.962	1	0.641	0.559	0.729	CLONAL	1	TRUE	1	0.243034883753097	3		643	497	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46608782	46608783	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0026030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	94	619	0	ENST00000263734.3:c.2093_2094delinsTT	p.Ala698Val	p.A698V	ENST00000263734	NM_001430.4	698	gCC/gTT	13/16	0.152564323202096	2	FACETS	0.965	0.864	1	0.965	0.864	1	CLONAL	2	TRUE	0	0.243034883753097	2		619	401	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525084	9525084	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0026030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	42	476	0	ENST00000353224.5:c.1801A>T	p.Lys601Ter	p.K601*	ENST00000353224	NM_177990.2	601	Aaa/Taa	8/10	0.243034883753097	3	FACETS	0.778	0.655	0.913	0.778	0.655	0.913	CLONAL	2	TRUE	1	0.243034883753097	3		476	249	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790078	40790078	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	33	386	0	ENST00000373198.4:c.2653C>T	p.Gln885Ter	p.Q885*	ENST00000373198	NM_133170.3	885	Caa/Taa	18/32	0.243034883753097	3	FACETS	0.765	0.623	0.925	0.383	0.311	0.463	CLONAL	1	TRUE	1	0.243034883753097	3		386	398	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62293892	62293892	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0026030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	107	696	0	ENST00000360203.5:c.396-7C>T		p.X132_splice	ENST00000360203	NM_001283009.1	132			0.243034883753097	3	FACETS	0.872	0.785	0.965	0.872	0.785	0.965	CLONAL	2	TRUE	1	0.243034883753097	3		696	566	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526781	31526781	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	141	528	1	ENST00000344624.3:c.259C>T	p.Pro87Ser	p.P87S	ENST00000344624		87	Ccg/Tcg	2/33	0.243034883753097	3	FACETS	0.981	0.902	1	0.981	0.902	1	CLONAL	3	TRUE	0	0.243034883753097	3		529	442	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161990389	161990389	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs137853055	NA	P-0026030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	27	359	0	ENST00000366898.1:c.931C>T	p.Gln311Ter	p.Q311*	ENST00000366898	NM_004562.2	311	Cag/Tag	8/12	0.243034883753097	3	FACETS	1	0.931	1	0.716	0.575	0.874	CLONAL	1	TRUE	1	0.243034883753097	3		359	174	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339869	116339869	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	22	351	0	ENST00000397752.3:c.731C>T	p.Ser244Phe	p.S244F	ENST00000397752	NM_000245.2	244	tCt/tTt	2/21	0.243034883753097	4	FACETS	1	0.909	1	0.682	0.533	0.852	CLONAL	1	TRUE	2	0.243034883753097	4		351	165	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069587	69069587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs901857351	NA	P-0026030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	27	452	0	ENST00000288368.4:c.4262G>A	p.Arg1421Lys	p.R1421K	ENST00000288368	NM_024870.2	1421	aGa/aAa	35/40	0.233299299816062	4	FACETS	0.973	0.784	1	0.973	0.784	1	CLONAL	2	TRUE	2	0.243034883753097	4		452	142	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141545646	141545646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	116	613	1	ENST00000220592.5:c.2192C>T	p.Pro731Leu	p.P731L	ENST00000220592	NM_012154.3	731	cCa/cTa	17/19	0.233299299816062	4	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	2	0.243034883753097	4		614	557	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041599	47041599	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0026030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	79	541	0	ENST00000377604.3:c.1824G>A	p.Trp608Ter	p.W608*	ENST00000377604	NM_001204468.1	608	tgG/tgA	17/24	1	2	FACETS	0.77	0.681	0.866	1	0.978	1	SUBCLONAL	2	TRUE	1	0.243034883753097	2		541	422	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727888	78727888	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026158-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	68	709	2	ENST00000306801.3:c.733G>A	p.Ala245Thr	p.A245T	ENST00000306801	NM_020761.2	245	Gcc/Acc	6/34	0.544262703662667	6	FACETS	1	0.954	1	0.404	0.352	0.459	CLONAL	1	TRUE	3	0.544262703662667	6		711	431	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595943	43595943	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026158-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	99	1046	0	ENST00000355710.3:c.110G>T	p.Trp37Leu	p.W37L	ENST00000355710	NM_020975.4	37	tGg/tTg	2/20	0.39784920296821	3	FACETS	0.939	0.842	1			1	CLONAL	1	TRUE	NA	0.544262703662667	3		1046	493	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131976435	131976435	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026158-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	124	599	0	ENST00000265335.6:c.3690G>C	p.Leu1230Phe	p.L1230F	ENST00000265335		1230	ttG/ttC	24/25	0.478527812123609	4	FACETS	0.836	0.762	0.912	0.836	0.762	0.912	CLONAL	2	TRUE	2	0.544262703662667	4		599	421	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249136	55249136	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026158-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	150	790	0	ENST00000275493.2:c.2434C>A	p.Gln812Lys	p.Q812K	ENST00000275493	NM_005228.3	812	Cag/Aag	20/28	0.295578177710736	5	FACETS	1	0.978	1	0.776	0.716	0.838	INDETERMINATE	2	TRUE	2	0.544262703662667	5		790	430	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0026314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	14	306	0				ENST00000310581	NM_198253.2	-/1132			0.279301969615136	0	FACETS	0.645	0.471	0.851			1	SUBCLONAL	1	FALSE	0	0.279301969615136	0		306	112	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0026314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	78	528	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.22763120082981	2	FACETS	0.916	0.813	1	0.916	0.813	1	CLONAL	2	FALSE	0	0.279301969615136	2		528	305	SUCCESS
AXL	558	MSKCC	GRCh37	19	41737181	41737181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	17	340	0	ENST00000301178.4:c.761C>T	p.Pro254Leu	p.P254L	ENST00000301178	NM_021913.4	254	cCc/cTc	6/20	1	2	FACETS	0.505	0.377	0.656	0.505	0.377	0.656	SUBCLONAL	1	FALSE	1	0.279301969615136	2		340	241	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964962	55964962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	20	249	0	ENST00000263923.4:c.2275G>A	p.Glu759Lys	p.E759K	ENST00000263923	NM_002253.2	759	Gaa/Aaa	16/30	0.127857836288122	0	FACETS	0.965	0.75	1			1	INDETERMINATE	1	FALSE	0	0.279301969615136	0		249	107	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805400	46805400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	26	483	0	ENST00000290295.7:c.556G>A	p.Gly186Arg	p.G186R	ENST00000290295	NM_006361.5	186	Gga/Aga	1/2	1	2	FACETS	0.926	0.739	1	0.926	0.739	1	CLONAL	1	FALSE	1	0.279301969615136	2		483	201	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227102	2227102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	27	373	1	ENST00000398665.3:c.4582G>A	p.Gly1528Arg	p.G1528R	ENST00000398665	NM_032482.2	1528	Ggg/Agg	27/28	0.202471123294612	1	FACETS	0.582	0.464	0.716	0.582	0.464	0.716	SUBCLONAL	1	FALSE	0	0.279301969615136	1		374	286	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628335	187628335	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	27	266	1	ENST00000441802.2:c.2647C>A	p.Leu883Met	p.L883M	ENST00000441802	NM_005245.3	883	Ctg/Atg	2/27	0.127857836288122	0	FACETS	0.642	0.514	0.787			1	INDETERMINATE	1	FALSE	0	0.279301969615136	0		267	217	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295217	1295217	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs796849347	NA	P-0026314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	12	200	0				ENST00000310581	NM_198253.2	-/1132			0.279301969615136	0	FACETS	0.794	0.567	1			1	CLONAL	1	FALSE	0	0.279301969615136	0		200	78	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038350	180038350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1425090483	NA	P-0026406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	124	506	0	ENST00000261937.6:c.3667C>T	p.Arg1223Cys	p.R1223C	ENST00000261937	NM_182925.4	1223	Cgc/Tgc	27/30	0.374906322999813	1	FACETS	0.45	0.408	0.495	0.45	0.408	0.495	SUBCLONAL	1	TRUE	0	0.59887655630719	1		506	644	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0026522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	121	242	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	0.73	0.664	0.798	0.73	0.664	0.798	SUBCLONAL	1	TRUE	1	0.727325084806004	2		242	456	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0026522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	377	578	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.727325084806004	2		578	961	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0026651-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	27	151	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.8	1	1	0.8	1	CLONAL	1	TRUE	1	0.15	2		151	358	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519893	NA	P-0026651-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	56	721	0	ENST00000267101.3:c.310G>T	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ttg	3/28	1	2	FACETS	0.819	0.699	0.95	0.819	0.699	0.95	CLONAL	1	TRUE	1	0.15	2		721	912	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968278	15968279	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0026651-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	23	353	0	ENST00000268712.3:c.5006dup	p.Thr1670AsnfsTer44	p.T1670Nfs*44	ENST00000268712	NM_006311.3	1669	gga/ggGa	34/46	1	2	FACETS	0.727	0.566	0.914	0.727	0.566	0.914	CLONAL	1	TRUE	1	0.15	2		353	422	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0026789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	29	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.959	0.775	1	0.959	0.775	1	CLONAL	1	TRUE	1	0.28528811261818	2		306	212	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0026789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	126	1058	3	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.177142284027758	3	FACETS	0.938	0.853	1			1	CLONAL	2	TRUE	NA	0.28528811261818	3		1061	538	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456447	189456447	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	25	336	0	ENST00000264731.3:c.208C>T	p.Gln70Ter	p.Q70*	ENST00000264731	NM_003722.4	70	Cag/Tag	3/14	1	2	FACETS	0.685	0.541	0.848	0.685	0.541	0.848	SUBCLONAL	1	TRUE	1	0.28528811261818	2		336	256	SUCCESS
APC	324	MSKCC	GRCh37	5	112177901	112177901	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs752654519	NA	P-0026789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	51	265	0	ENST00000257430.4:c.6610C>T	p.Arg2204Ter	p.R2204*	ENST00000257430	NM_000038.5	2204	Cga/Tga	16/16	0.28528811261818	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	0	0.28528811261818	1		265	282	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650419	12650419	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	34	294	0	ENST00000251849.4:c.427C>T	p.Arg143Trp	p.R143W	ENST00000251849	NM_002880.3	143	Cgg/Tgg	5/17	1	2	FACETS	0.787	0.645	0.945	0.787	0.645	0.945	CLONAL	1	TRUE	1	0.28528811261818	2		294	303	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156354	106156354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0026789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	36	264	0	ENST00000380013.4:c.1255C>T	p.Pro419Ser	p.P419S	ENST00000380013	NM_001127208.2	419	Cct/Tct	3/11	1	2	FACETS	0.873	0.721	1	0.873	0.721	1	CLONAL	1	TRUE	1	0.28528811261818	2		264	289	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279347	38279347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	57	673	0	ENST00000425967.3:c.1142C>T	p.Ser381Phe	p.S381F	ENST00000425967	NM_001174067.1	381	tCc/tTc	9/19	1	2	FACETS	0.755	0.648	0.872	0.755	0.648	0.872	SUBCLONAL	1	TRUE	1	0.28528811261818	2		673	529	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790000	40790000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159843	NA	P-0026789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	33	607	0	ENST00000373198.4:c.2731G>A	p.Glu911Lys	p.E911K	ENST00000373198	NM_133170.3	911	Gaa/Aaa	18/32	1	2	FACETS	0.922	0.755	1	0.922	0.755	1	CLONAL	1	TRUE	1	0.28528811261818	2		607	251	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231201	46231201	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0026789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	20	260	0	ENST00000334344.6:c.1120+1G>A		p.X374_splice	ENST00000334344	NM_152641.2	374			1	2	FACETS	0.701	0.538	0.89	0.701	0.538	0.89	SUBCLONAL	1	TRUE	1	0.28528811261818	2		260	200	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111470	8111470	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	46	477	0	ENST00000346208.3:c.956A>G	p.Asn319Ser	p.N319S	ENST00000346208		319	aAc/aGc	5/6	1	2	FACETS	0.825	0.696	0.966	0.825	0.696	0.966	CLONAL	1	TRUE	1	0.28528811261818	2		477	391	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244427	46244427	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555154946	NA	P-0026789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	45	389	0	ENST00000334344.6:c.2521C>T	p.Gln841Ter	p.Q841*	ENST00000334344	NM_152641.2	841	Cag/Tag	15/21	1	2	FACETS	0.891	0.751	1	0.891	0.751	1	CLONAL	1	TRUE	1	0.28528811261818	2		389	354	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005401	42005401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1265236875	NA	P-0026789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	39	489	0	ENST00000219905.7:c.3137C>T	p.Pro1046Leu	p.P1046L	ENST00000219905	NM_001164273.1	1046	cCc/cTc	9/24	1	2	FACETS	0.664	0.55	0.79	0.664	0.55	0.79	SUBCLONAL	1	TRUE	1	0.28528811261818	2		489	412	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198260808	198260808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	35	382	0	ENST00000335508.6:c.3511C>T	p.Pro1171Ser	p.P1171S	ENST00000335508	NM_012433.2	1171	Ccg/Tcg	23/25	1	2	FACETS	0.644	0.528	0.774	0.644	0.528	0.774	SUBCLONAL	1	TRUE	1	0.28528811261818	2		382	381	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518246	187518246	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	21	244	0	ENST00000441802.2:c.12448C>T	p.His4150Tyr	p.H4150Y	ENST00000441802	NM_005245.3	4150	Cac/Tac	25/27	1	2	FACETS	0.779	0.603	0.981	0.779	0.603	0.981	CLONAL	1	TRUE	1	0.28528811261818	2		244	189	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69011957	69011957	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	82	496	0	ENST00000288368.4:c.2594A>G	p.Gln865Arg	p.Q865R	ENST00000288368	NM_024870.2	865	cAa/cGa	23/40	1	2	FACETS	0.968	0.854	1	0.968	0.854	1	CLONAL	1	TRUE	1	0.28528811261818	2		496	594	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0026906-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	249	306	0	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.853206911143455	2		306	506	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115279467	115279467	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0026906-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	128	363	0	ENST00000438362.2:c.550del	p.Tyr184IlefsTer2	p.Y184Ifs*2	ENST00000438362	NM_001242891.1	184	Tat/at	6/20	0.828666880799327	1	FACETS	0.951	0.895	1	0.951	0.895	1	CLONAL	1	TRUE	0	0.853206911143455	1		363	181	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593598	55593645	+	inframe_deletion	In_Frame_Del	DEL	TACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACA	TACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACA	-	novel	NA	P-0026906-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	154	327	0	ENST00000288135.5:c.1666_1713del	p.Gln556_Ile571del	p.Q556_I571del	ENST00000288135	NM_000222.2	555	gTACAGTGGAAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACAta/gta	11/21	1	2	FACETS	0.994	0.923	1	0.994	0.923	1	CLONAL	1	TRUE	1	0.853206911143455	2		327	363	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0027076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	273	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.753545362295812	3	FACETS	0.806	0.763	0.849	0.806	0.763	0.849	CLONAL	2	TRUE	1	0.753545362295812	3		288	619	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467511	66467511	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	139	286	0	ENST00000273854.3:c.758C>T	p.Ser253Phe	p.S253F	ENST00000273854	NM_004439.5	253	tCc/tTc	3/18	1	2	FACETS	0.842	0.773	0.913	0.842	0.773	0.913	CLONAL	1	TRUE	1	0.753545362295812	2		286	438	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0027076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	67	284	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.999	0.887	1			1	INDETERMINATE	1	TRUE	NA	0.753545362295812	2		284	178	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223853	53223853	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	194	823	2	ENST00000375401.3:c.3506C>T	p.Ser1169Leu	p.S1169L	ENST00000375401	NM_004187.3	1169	tCg/tTg	23/26	1	2	FACETS	0.928	0.865	0.992	0.928	0.865	0.992	CLONAL	1	TRUE	1	0.753545362295812	2		825	555	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933202	36933202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	165	697	0	ENST00000361632.4:c.1915C>T	p.Leu639Phe	p.L639F	ENST00000361632		639	Ctc/Ttc	14/16	1	2	FACETS	0.984	0.913	1	0.984	0.913	1	CLONAL	1	TRUE	1	0.753545362295812	2		697	445	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690379	117690379	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	135	475	0	ENST00000369458.3:c.750C>G	p.His250Gln	p.H250Q	ENST00000369458	NM_024626.3	250	caC/caG	5/6	1	2	FACETS	0.803	0.736	0.873	0.803	0.736	0.873	CLONAL	1	TRUE	1	0.753545362295812	2		475	446	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650836	93650837	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0027076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	111	432	1	ENST00000375746.1:c.1762_1763delinsAA	p.Gly588Lys	p.G588K	ENST00000375746	NM_001174167.1	588	GGa/AAa	13/14	1	2	FACETS	0.801	0.727	0.877	0.801	0.727	0.877	CLONAL	1	TRUE	1	0.753545362295812	2		433	368	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355271	81355271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	112	317	0	ENST00000222390.5:c.1103C>T	p.Thr368Ile	p.T368I	ENST00000222390	NM_000601.4	368	aCt/aTt	9/18	0.771688537890434	5	FACETS	0.763	0.686	0.844	0.254	0.228	0.282	SUBCLONAL	1	TRUE	2	0.771688537890434	5		317	821	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625405	69625405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1442579536	NA	P-0027150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1729	238	628	2	ENST00000334134.2:c.388G>A	p.Ala130Thr	p.A130T	ENST00000334134	NM_005247.2	130	Gcc/Acc	3/3	0.633150600868941	5	FACETS	0.745	0.692	0.8	0.186	0.173	0.2	SUBCLONAL	1	TRUE	1	0.633150600868941	5		630	1967	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139459	47139459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	356	413	0	ENST00000409792.3:c.5128C>T	p.Arg1710Cys	p.R1710C	ENST00000409792	NM_014159.6	1710	Cgt/Tgt	9/21	0.633150600868941	3	FACETS	0.915	0.872	0.958	0.915	0.872	0.958	CLONAL	2	TRUE	1	0.633150600868941	3		413	809	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162402	47162402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	145	334	0	ENST00000409792.3:c.3724del	p.Glu1242ArgfsTer17	p.E1242Rfs*17	ENST00000409792	NM_014159.6	1242	Gag/ag	3/21	0.633150600868941	3	FACETS	1	0.96	1	0.538	0.493	0.585	CLONAL	1	TRUE	1	0.633150600868941	3		334	560	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0027588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	246	601	0	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	0.328802669466015	3	FACETS	0.876	0.821	0.933	0.876	0.821	0.933	CLONAL	2	TRUE	1	0.392862219162963	3		601	855	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80109515	80109515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	134	738	1	ENST00000265081.6:c.2768C>T	p.Pro923Leu	p.P923L	ENST00000265081	NM_002439.4	923	cCt/cTt	20/24	0.392862219162963	3	FACETS	0.856	0.776	0.939	0.428	0.388	0.47	CLONAL	1	TRUE	1	0.392862219162963	3		739	954	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0027603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	231	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.884	0.827	0.943	0.884	0.827	0.943	CLONAL	1	TRUE	1	0.670136161617084	2		306	780	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0027603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	567	1058	3	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.670136161617084	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.670136161617084	2		1061	834	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0027603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	167	451	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.670136161617084	2		451	465	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0027603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	233	119	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.670136161617084	2		119	650	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0027603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	456	409	1	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.670136161617084	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.670136161617084	1		410	735	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912815	100912815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1000609240	NA	P-0027603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	172	416	1	ENST00000325455.5:c.2507G>A	p.Arg836Gln	p.R836Q	ENST00000325455	NM_001202474.3	836	cGa/cAa	7/8	1	2	FACETS	0.947	0.877	1	0.947	0.877	1	CLONAL	1	TRUE	1	0.670136161617084	2		417	542	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641509	23641509	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	266	637	2	ENST00000261584.4:c.1966C>T	p.Pro656Ser	p.P656S	ENST00000261584	NM_024675.3	656	Cca/Tca	5/13	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.670136161617084	2		639	774	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512350	149512350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754790326	NA	P-0027603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	440	535	0	ENST00000261799.4:c.1090G>A	p.Glu364Lys	p.E364K	ENST00000261799	NM_002609.3	364	Gaa/Aaa	7/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.670136161617084	2		535	1249	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046410	69046410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868582467	NA	P-0027603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	349	317	0	ENST00000288368.4:c.3883G>A	p.Glu1295Lys	p.E1295K	ENST00000288368	NM_024870.2	1295	Gaa/Aaa	32/40	1	2	FACETS	0.972	0.921	1	0.972	0.921	1	CLONAL	1	TRUE	1	0.670136161617084	2		317	1072	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431198	49431198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258642596	NA	P-0027603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	419	380	0	ENST00000301067.7:c.9941C>T	p.Ser3314Phe	p.S3314F	ENST00000301067	NM_003482.3	3314	tCc/tTc	34/54	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.670136161617084	2		380	1132	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651144	206651144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs533634715	NA	P-0027603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1870	455	682	2	ENST00000367120.3:c.754C>T	p.Arg252Trp	p.R252W	ENST00000367120	NM_014002.3	252	Cgg/Tgg	8/22	0.668541323727904	4	FACETS	0.975	0.927	1	0.488	0.463	0.513	CLONAL	1	TRUE	2	0.670136161617084	4		684	2325	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434553	110434553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	833	500	0	ENST00000375856.3:c.3848C>T	p.Ser1283Phe	p.S1283F	ENST00000375856	NM_003749.2	1283	tCc/tTc	1/2	0.656114267953744	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.670136161617084	3		500	1624	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921533	178921533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	108	316	0	ENST00000263967.3:c.1015C>T	p.Leu339Phe	p.L339F	ENST00000263967	NM_006218.2	339	Ctt/Ttt	5/21	1	2	FACETS	0.929	0.843	1	0.929	0.843	1	CLONAL	1	TRUE	1	0.670136161617084	2		316	347	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106207	27106207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	750	546	0	ENST00000324856.7:c.5818C>T	p.Pro1940Ser	p.P1940S	ENST00000324856	NM_006015.4	1940	Cca/Tca	20/20	0.670136161617084	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.670136161617084	2		546	1087	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653803	89653803	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554893773	NA	P-0027603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	99	475	0	ENST00000371953.3:c.101C>T	p.Ala34Val	p.A34V	ENST00000371953	NM_000314.4	34	gCt/gTt	2/9	0.670136161617084	1	FACETS	0.922	0.842	1	0.922	0.842	1	CLONAL	1	TRUE	0	0.670136161617084	1		475	213	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104264016	104264016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566714720	NA	P-0027603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	633	506	1	ENST00000369902.3:c.107C>T	p.Ala36Val	p.A36V	ENST00000369902	NM_016169.3	36	gCc/gTc	1/12	0.670136161617084	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.670136161617084	1		507	1072	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420888	49420888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565761336	NA	P-0027603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	388	468	0	ENST00000301067.7:c.14861C>T	p.Ser4954Leu	p.S4954L	ENST00000301067	NM_003482.3	4954	tCa/tTa	48/54	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.670136161617084	2		468	1123	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438280	110438280	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0027603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	682	271	0	ENST00000375856.3:c.121A>T	p.Lys41Ter	p.K41*	ENST00000375856	NM_003749.2	41	Aag/Tag	1/2	0.656114267953744	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.670136161617084	3		271	1314	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379844	17379844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	532	788	0	ENST00000359435.4:c.229C>T	p.Pro77Ser	p.P77S	ENST00000359435	NM_001033549.1	77	Ccg/Tcg	2/9	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.670136161617084	2		788	1516	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622567	158622567	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	319	592	0	ENST00000263640.3:c.932C>T	p.Ser311Phe	p.S311F	ENST00000263640	NM_001105.4	311	tCc/tTc	8/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.670136161617084	2		592	883	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461476	138461476	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	215	533	0	ENST00000289153.2:c.545C>T	p.Pro182Leu	p.P182L	ENST00000289153	NM_006219.2	182	cCa/cTa	3/22	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.670136161617084	2		533	632	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539111	187539111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253875433	NA	P-0027603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	210	491	0	ENST00000441802.2:c.8629C>T	p.His2877Tyr	p.H2877Y	ENST00000441802	NM_005245.3	2877	Cat/Tat	10/27	1	2	FACETS	0.844	0.786	0.903	0.844	0.786	0.903	CLONAL	1	TRUE	1	0.670136161617084	2		491	743	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046431	69046431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	344	546	1	ENST00000288368.4:c.3904G>A	p.Glu1302Lys	p.E1302K	ENST00000288368	NM_024870.2	1302	Gaa/Aaa	32/40	1	2	FACETS	0.935	0.886	0.985	0.935	0.886	0.985	CLONAL	1	TRUE	1	0.670136161617084	2		547	1098	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028852	47028852	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	386	654	0	ENST00000377604.3:c.156G>C	p.Glu52Asp	p.E52D	ENST00000377604	NM_001204468.1	52	gaG/gaC	3/24	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.670136161617084	2		654	1134	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650258	48650258	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	360	608	0	ENST00000376670.3:c.228G>T	p.Gln76His	p.Q76H	ENST00000376670	NM_002049.3	76	caG/caT	3/6	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.670136161617084	2		608	1059	SUCCESS
AR	367	MSKCC	GRCh37	X	66863238	66863238	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	259	489	0	ENST00000374690.3:c.1757G>A	p.Arg586Lys	p.R586K	ENST00000374690	NM_000044.3	586	aGa/aAa	2/8	1	2	FACETS	0.974	0.915	1	0.974	0.915	1	CLONAL	1	TRUE	1	0.670136161617084	2		489	794	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874374	76874374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	138	564	1	ENST00000373344.5:c.5348C>T	p.Pro1783Leu	p.P1783L	ENST00000373344	NM_000489.3	1783	cCa/cTa	21/35	1	2	FACETS	0.951	0.873	1	0.951	0.873	1	CLONAL	1	TRUE	1	0.670136161617084	2		565	433	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907718	76907719	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0027603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	215	545	0	ENST00000373344.5:c.4442_4443delinsAA	p.Arg1481Gln	p.R1481Q	ENST00000373344	NM_000489.3	1481	cGG/cAA	15/35	1	2	FACETS	0.841	0.784	0.899	0.841	0.784	0.899	CLONAL	1	TRUE	1	0.670136161617084	2		545	763	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152857964	152857964	+	splice_region_variant,synonymous_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0027603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	84	132	0	ENST00000406277.2:c.651G>A		p.X217_splice	ENST00000406277	NM_152274.4	217	caG/caA	6/7	1	2	FACETS	0.979	0.878	1	0.979	0.878	1	CLONAL	1	TRUE	1	0.670136161617084	2		132	256	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0027707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	175	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.967	0.894	1	0.967	0.894	1	CLONAL	1	TRUE	1	0.537810942226932	2		306	673	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528489	29528489	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764079291	NA	P-0027707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	323	631	1	ENST00000356175.3:c.1246C>T	p.Arg416Ter	p.R416*	ENST00000356175	NM_000267.3	416	Cga/Tga	11/57	1	2	FACETS	0.873	0.831	0.915	1	0.996	1	CLONAL	2	TRUE	1	0.537810942226932	2		632	688	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966381	25966381	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1182809842	NA	P-0027707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	279	888	0	ENST00000435504.4:c.2825C>T	p.Pro942Leu	p.P942L	ENST00000435504		942	cCa/cTa	13/13	1	2	FACETS	0.876	0.822	0.931	0.876	0.822	0.931	CLONAL	1	TRUE	1	0.537810942226932	2		888	1185	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68999979	68999979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	203	697	1	ENST00000288368.4:c.2048C>T	p.Ser683Leu	p.S683L	ENST00000288368	NM_024870.2	683	tCa/tTa	19/40	1	2	FACETS	0.883	0.82	0.948	0.883	0.82	0.948	CLONAL	1	TRUE	1	0.537810942226932	2		698	855	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624284	89624284	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554890393	NA	P-0027707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	203	542	0	ENST00000371953.3:c.58G>T	p.Gly20Ter	p.G20*	ENST00000371953	NM_000314.4	20	Gga/Tga	1/9	1	2	FACETS	0.964	0.896	1	0.964	0.896	1	CLONAL	1	TRUE	1	0.537810942226932	2		542	783	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720822	89720823	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	111	413	0	ENST00000371953.3:c.975dup	p.Asp326Ter	p.D326*	ENST00000371953	NM_000314.4	325	ctt/cTtt	8/9	1	2	FACETS	0.759	0.685	0.837	0.759	0.685	0.837	SUBCLONAL	1	TRUE	1	0.537810942226932	2		413	544	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112590	115112590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750675454	NA	P-0027707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	323	919	1	ENST00000257566.3:c.1150G>A	p.Glu384Lys	p.E384K	ENST00000257566	NM_016569.3	384	Gag/Aag	7/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.537810942226932	2		920	1098	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727432	66727432	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	207	471	1	ENST00000307102.5:c.148C>T	p.Leu50Phe	p.L50F	ENST00000307102	NM_002755.3	50	Ctt/Ttt	2/11	1	2	FACETS	0.972	0.904	1	0.972	0.904	1	CLONAL	1	TRUE	1	0.537810942226932	2		472	792	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420327	88420327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548727485	NA	P-0027707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	157	533	1	ENST00000360948.2:c.2359C>T	p.Arg787Cys	p.R787C	ENST00000360948	NM_001012338.2	787	Cgt/Tgt	19/19	1	2	FACETS	0.8	0.734	0.868	0.8	0.734	0.868	SUBCLONAL	1	TRUE	1	0.537810942226932	2		534	730	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991478	72991478	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	316	882	0	ENST00000268489.5:c.2567C>T	p.Pro856Leu	p.P856L	ENST00000268489	NM_006885.3	856	cCc/cTc	2/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.537810942226932	2		882	1128	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212110	36212110	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	245	662	1	ENST00000222270.7:c.1861C>T	p.Pro621Ser	p.P621S	ENST00000222270	NM_014727.1	621	Cct/Tct	3/37	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.537810942226932	2		663	813	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216444	36216445	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0027707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	370	974	2	ENST00000222270.7:c.3707_3708delinsTT	p.Pro1236Leu	p.P1236L	ENST00000222270	NM_014727.1	1236	cCC/cTT	12/37	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.537810942226932	2		976	1229	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538941	23538942	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0027707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	196	638	1	ENST00000380871.4:c.497_498delinsTT	p.Thr166Ile	p.T166I	ENST00000380871	NM_006167.3	166	aCC/aTT	2/2	1	2	FACETS	0.84	0.778	0.903	0.84	0.778	0.903	CLONAL	1	TRUE	1	0.537810942226932	2		639	868	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486078	8486078	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	145	634	0	ENST00000356435.5:c.2739del	p.Pro914GlnfsTer66	p.P914Qfs*66	ENST00000356435		913	atT/at	17/35	1	2	FACETS	0.805	0.736	0.876	0.805	0.736	0.876	CLONAL	1	TRUE	1	0.537810942226932	2		634	670	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95596510	95596510	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs769827245	NA	P-0027735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	327	301	0	ENST00000393063.1:c.458A>G	p.Tyr153Cys	p.Y153C	ENST00000393063	NM_030621.3	153	tAt/tGt	6/28	0.63718699996147	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.663779242946969	3		301	624	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0027937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	211	578	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	0.875	0.815	0.937	0.875	0.815	0.937	CLONAL	1	TRUE	1	0.613687517766197	2		578	786	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0027937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	193	151	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.613687517766197	2		151	570	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156735	20156735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	193	389	0	ENST00000379607.5:c.22G>A	p.Gly8Arg	p.G8R	ENST00000379607	NM_001412.3	8	Gga/Aga	2/7	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.613687517766197	1		389	306	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0028078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	147	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.577904132143153	2		306	395	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0028078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	111	364	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.917	0.83	1	0.917	0.83	1	CLONAL	1	FALSE	1	0.577904132143153	2		364	419	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0028078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	429	1058	3	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.577904132143153	3	FACETS	1	0.984	1			1	CLONAL	2	FALSE	NA	0.577904132143153	3		1061	908	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935508	13935508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536563766	NA	P-0028078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	155	275	0	ENST00000405192.2:c.1348G>A	p.Glu450Lys	p.E450K	ENST00000405192	NM_001163147.1	450	Gaa/Aaa	12/12	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.577904132143153	2		275	409	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390157	89390157	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	117	384	0	ENST00000336596.2:c.906G>A	p.Met302Ile	p.M302I	ENST00000336596	NM_005233.5	302	atG/atA	4/17	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.577904132143153	2		384	380	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210688	36210688	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	158	544	2	ENST00000222270.7:c.439C>T	p.Arg147Ter	p.R147*	ENST00000222270	NM_014727.1	147	Cga/Tga	3/37	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.577904132143153	2		546	502	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405099	70405100	+	missense_variant	Missense_Mutation	DNP	TC	TC	GT	novel	NA	P-0028078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	198	574	1	ENST00000373644.4:c.2613_2614delinsGT	p.Pro872Ser	p.P872S	ENST00000373644	NM_030625.2	871	tcTCcc/tcGTcc	4/12	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.577904132143153	2		575	579	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226430	133226430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	148	534	0	ENST00000320574.5:c.3628C>T	p.Pro1210Ser	p.P1210S	ENST00000320574	NM_006231.2	1210	Cct/Tct	30/49	1	2	FACETS	0.97	0.891	1	0.97	0.891	1	CLONAL	1	FALSE	1	0.577904132143153	2		534	528	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880909	28880909	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	149	406	2	ENST00000282397.4:c.3721G>A	p.Asp1241Asn	p.D1241N	ENST00000282397	NM_002019.4	1241	Gac/Aac	29/30	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.577904132143153	2		408	416	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348784	89348784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758148858	NA	P-0028078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	244	889	1	ENST00000301030.4:c.4166C>T	p.Ser1389Phe	p.S1389F	ENST00000301030	NM_001256183.1	1389	tCc/tTc	9/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.577904132143153	2		890	784	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584576	187584576	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	178	502	1	ENST00000441802.2:c.3457C>T	p.Pro1153Ser	p.P1153S	ENST00000441802	NM_005245.3	1153	Cct/Tct	3/27	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.577904132143153	2		503	538	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295230	1295230	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs796516131	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	268	341	0				ENST00000310581	NM_198253.2	-/1132			0.513472490632054	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.540612137277116	3		341	580	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	267	151	0				ENST00000310581	NM_198253.2	-/1132			0.513472490632054	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.540612137277116	3		151	580	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213909	66213909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	132	319	1	ENST00000273854.3:c.2521C>T	p.Pro841Ser	p.P841S	ENST00000273854	NM_004439.5	841	Cca/Tca	15/18	1	2	FACETS	0.993	0.907	1	0.993	0.907	1	CLONAL	1	TRUE	1	0.540612137277116	2		320	492	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913355	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	260	365	0	ENST00000288602.6:c.1406G>T	p.Gly469Val	p.G469V	ENST00000288602	NM_004333.4	469	gGa/gTa	11/18	0.540612137277116	4	FACETS	0.992	0.933	1	0.992	0.933	1	CLONAL	2	TRUE	2	0.540612137277116	4		365	747	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496908	29496908	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	192	242	0	ENST00000356175.3:c.480-1G>A		p.X160_splice	ENST00000356175	NM_000267.3	160			0.540612137277116	4	FACETS	0.975	0.908	1	0.975	0.908	1	CLONAL	2	TRUE	2	0.540612137277116	4		242	561	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236203	108236203	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434219	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	223	493	1	ENST00000278616.4:c.9139C>T	p.Arg3047Ter	p.R3047*	ENST00000278616	NM_000051.3	3047	Cga/Tga	63/63	0.540612137277116	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.540612137277116	1		494	593	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348188	348188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1266269685	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	196	563	0	ENST00000262320.3:c.1318C>T	p.Pro440Ser	p.P440S	ENST00000262320	NM_003502.3	440	Ccc/Tcc	6/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.540612137277116	2		563	713	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793483	18793483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603405	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	257	282	0	ENST00000266497.5:c.4180G>A	p.Glu1394Lys	p.E1394K	ENST00000266497		1394	Gaa/Aaa	30/31	0.540612137277116	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.540612137277116	4		282	671	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714396	117714396	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	271	441	0	ENST00000368508.3:c.1253C>T	p.Ser418Leu	p.S418L	ENST00000368508	NM_002944.2	418	tCa/tTa	11/43	0.540612137277116	2	FACETS	0.918	0.871	0.965	0.918	0.871	0.965	CLONAL	2	TRUE	0	0.540612137277116	2		441	546	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857020	9857020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555481892	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	67	246	0	ENST00000330684.3:c.4381G>A	p.Glu1461Lys	p.E1461K	ENST00000330684	NM_001134407.1	1461	Gaa/Aaa	13/13	1	2	FACETS	0.805	0.705	0.911	0.805	0.705	0.911	CLONAL	1	TRUE	1	0.540612137277116	2		246	308	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456474	189456474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1484040098	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	144	436	0	ENST00000264731.3:c.235G>A	p.Glu79Lys	p.E79K	ENST00000264731	NM_003722.4	79	Gaa/Aaa	3/14	0.22552793196785	5	FACETS	1	0.983	1	0.436	0.398	0.475	INDETERMINATE	1	TRUE	2	0.540612137277116	5		436	738	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713470	40713470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318044562	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	171	572	2	ENST00000373198.4:c.4045C>T	p.Arg1349Cys	p.R1349C	ENST00000373198	NM_133170.3	1349	Cgt/Tgt	30/32	0.540612137277116	4	FACETS	0.912	0.838	0.989	0.456	0.419	0.495	CLONAL	1	TRUE	2	0.540612137277116	4		574	1069	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681030	37681030	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	164	372	0	ENST00000447079.4:c.3199C>T	p.Arg1067Ter	p.R1067*	ENST00000447079	NM_015083.1	1067	Cga/Tga	12/14	0.540612137277116	4	FACETS	0.843	0.773	0.917	0.421	0.386	0.459	CLONAL	1	TRUE	2	0.540612137277116	4		372	1109	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120794	94120794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs570778929	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	353	505	2	ENST00000369303.4:c.257G>A	p.Arg86Gln	p.R86Q	ENST00000369303	NM_004440.3	86	cGg/cAg	3/17	0.540612137277116	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.540612137277116	2		507	636	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961910	15961910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	185	263	0	ENST00000268712.3:c.5885C>T	p.Ser1962Phe	p.S1962F	ENST00000268712	NM_006311.3	1962	tCt/tTt	38/46	0.540612137277116	4	FACETS	0.993	0.924	1	0.993	0.924	1	CLONAL	2	TRUE	2	0.540612137277116	4		263	531	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933653	39933653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200052076	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	354	234	0	ENST00000378444.4:c.946C>T	p.Pro316Ser	p.P316S	ENST00000378444	NM_001123385.1	316	Ccc/Tcc	4/15	0.540612137277116	2	FACETS	0.866	0.836	0.896			1	CLONAL	3	TRUE	NA	0.540612137277116	2		234	504	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412196	63412196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	552	388	0	ENST00000330258.3:c.971C>T	p.Ser324Leu	p.S324L	ENST00000330258	NM_152424.3	324	tCa/tTa	2/2	0.540612137277116	2	FACETS	0.854	0.83	0.878			1	CLONAL	3	TRUE	NA	0.540612137277116	2		388	797	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346551	81346551	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444026216	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	240	448	0	ENST00000222390.5:c.1402C>T	p.Arg468Cys	p.R468C	ENST00000222390	NM_000601.4	468	Cgt/Tgt	11/18	0.540612137277116	4	FACETS	0.957	0.897	1	0.957	0.897	1	CLONAL	2	TRUE	2	0.540612137277116	4		448	715	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546098	29546098	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1567843917	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	437	492	0	ENST00000356175.3:c.1603C>T	p.Gln535Ter	p.Q535*	ENST00000356175	NM_000267.3	535	Cag/Tag	14/57	0.540612137277116	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.540612137277116	4		492	1137	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458579	120458579	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	197	550	0	ENST00000256646.2:c.6766C>G	p.Arg2256Gly	p.R2256G	ENST00000256646	NM_024408.3	2256	Cgc/Ggc	34/34	0.540612137277116	5	FACETS	1	0.95	1			1	CLONAL	1	TRUE	NA	0.540612137277116	5		550	1274	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846344	156846345	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	200	575	1	ENST00000524377.1:c.1785_1786delinsAA	p.Asp596Asn	p.D596N	ENST00000524377	NM_002529.3	595	ggGGac/ggAAac	14/17	0.540612137277116	3	FACETS	0.991	0.919	1	0.496	0.459	0.534	CLONAL	1	TRUE	1	0.540612137277116	3		576	948	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021816	246021816	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	412	567	2	ENST00000388985.4:c.1058G>T	p.Arg353Leu	p.R353L	ENST00000388985		353	cGg/cTg	10/12	0.540612137277116	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.540612137277116	3		569	921	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18473905	18473905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768312472	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	286	414	0	ENST00000266497.5:c.1147G>A	p.Asp383Asn	p.D383N	ENST00000266497		383	Gac/Aac	6/31	0.540612137277116	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	2	0.540612137277116	4		414	802	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691220	18691220	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	208	320	0	ENST00000266497.5:c.3331C>T	p.Gln1111Ter	p.Q1111*	ENST00000266497		1111	Caa/Taa	23/31	0.540612137277116	4	FACETS	0.919	0.857	0.982	0.919	0.857	0.982	CLONAL	2	TRUE	2	0.540612137277116	4		320	645	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112370	115112370	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371891930	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	607	284	1	ENST00000257566.3:c.1370C>T	p.Pro457Leu	p.P457L	ENST00000257566	NM_016569.3	457	cCg/cTg	7/8	0.540612137277116	7	FACETS	1	0.985	1			1	CLONAL	5	TRUE	NA	0.540612137277116	7		285	1029	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416857	121416857	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1319520178	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	1099	677	0	ENST00000257555.6:c.286G>A	p.Glu96Lys	p.E96K	ENST00000257555		96	Gag/Aag	1/10	0.540612137277116	7	FACETS	0.969	0.946	0.993			1	CLONAL	5	TRUE	NA	0.540612137277116	7		677	1973	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054441	42054441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	346	567	0	ENST00000219905.7:c.7625C>T	p.Pro2542Leu	p.P2542L	ENST00000219905	NM_001164273.1	2542	cCc/cTc	22/24	0.540612137277116	4	FACETS	0.973	0.923	1	0.973	0.923	1	CLONAL	2	TRUE	2	0.540612137277116	4		567	1013	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727460	88727460	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	357	487	0	ENST00000360948.2:c.319A>T	p.Lys107Ter	p.K107*	ENST00000360948	NM_001012338.2	107	Aag/Tag	3/19	0.540612137277116	4	FACETS	0.998	0.948	1	0.998	0.948	1	CLONAL	2	TRUE	2	0.540612137277116	4		487	1019	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59793321	59793321	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	334	420	0	ENST00000259008.2:c.2483C>G	p.Ala828Gly	p.A828G	ENST00000259008	NM_032043.2	828	gCc/gGc	17/20	0.540612137277116	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	2	0.540612137277116	4		420	792	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220091	36220102	+	inframe_deletion	In_Frame_Del	DEL	ACGAGTGGACAC	ACGAGTGGACAC	-	novel	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	241	637	0	ENST00000222270.7:c.4814_4825del	p.Glu1605_His1608del	p.E1605_H1608del	ENST00000222270	NM_014727.1	1604	aACGAGTGGACACac/aac	22/37	0.540612137277116	3	FACETS	1	0.943	1	0.506	0.472	0.541	CLONAL	1	TRUE	1	0.540612137277116	3		637	1120	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45864881	45864881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756071720	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	524	705	0	ENST00000391945.4:c.1138C>T	p.Arg380Trp	p.R380W	ENST00000391945	NM_000400.3	380	Cgg/Tgg	12/23	0.540612137277116	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.540612137277116	3		705	1197	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711149	61711149	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	411	625	1	ENST00000401558.2:c.2600C>T	p.Pro867Leu	p.P867L	ENST00000401558	NM_003400.3	867	cCa/cTa	21/25	0.540612137277116	3	FACETS	0.949	0.906	0.992	0.949	0.906	0.992	CLONAL	2	TRUE	1	0.540612137277116	3		626	1018	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561475	9561475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	332	472	0	ENST00000353224.5:c.307G>A	p.Glu103Lys	p.E103K	ENST00000353224	NM_177990.2	103	Gaa/Aaa	4/10	0.540612137277116	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	2	0.540612137277116	4		472	918	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713425	40713425	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	368	606	2	ENST00000373198.4:c.4090G>A	p.Asp1364Asn	p.D1364N	ENST00000373198	NM_133170.3	1364	Gac/Aac	30/32	0.540612137277116	4	FACETS	0.941	0.893	0.989	0.941	0.893	0.989	CLONAL	2	TRUE	2	0.540612137277116	4		608	1115	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434179	12434179	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1475289630	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	390	482	1	ENST00000287820.6:c.547C>T	p.His183Tyr	p.H183Y	ENST00000287820	NM_015869.4	183	Cac/Tac	4/7	0.435095770742375	4	FACETS	0.857	0.818	0.895	0.857	0.818	0.895	CLONAL	3	TRUE	1	0.540612137277116	4		483	865	SUCCESS
ATR	545	MSKCC	GRCh37	3	142185204	142185204	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	237	505	0	ENST00000350721.4:c.6859C>T	p.Pro2287Ser	p.P2287S	ENST00000350721	NM_001184.3	2287	Cct/Tct	40/47	0.22552793196785	5	FACETS	0.873	0.816	0.932	0.582	0.544	0.622	INDETERMINATE	2	TRUE	2	0.540612137277116	5		505	909	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506972	186506972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	153	310	0	ENST00000323963.5:c.1138G>A	p.Glu380Lys	p.E380K	ENST00000323963		380	Gaa/Aaa	11/11	0.22552793196785	5	FACETS	0.873	0.802	0.946	0.582	0.535	0.631	INDETERMINATE	2	TRUE	2	0.540612137277116	5		310	587	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55960972	55960972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs897282597	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	228	373	0	ENST00000263923.4:c.2968G>A	p.Glu990Lys	p.E990K	ENST00000263923	NM_002253.2	990	Gaa/Aaa	21/30	0.513472490632054	3	FACETS	0.935	0.878	0.992	0.935	0.878	0.992	CLONAL	2	TRUE	1	0.540612137277116	3		373	573	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534358	187534358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	202	533	0	ENST00000441802.2:c.9368C>T	p.Pro3123Leu	p.P3123L	ENST00000441802	NM_005245.3	3123	cCc/cTc	13/27	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.540612137277116	2		533	630	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158586	26158586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	535	428	1	ENST00000289316.2:c.189G>A	p.Met63Ile	p.M63I	ENST00000289316	NM_138720.2	63	atG/atA	1/2	0.540612137277116	6	FACETS	0.959	0.924	0.994	0.959	0.924	0.994	CLONAL	4	TRUE	2	0.540612137277116	6		429	1074	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169976	32169976	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1228	442	599	0	ENST00000375023.3:c.3632G>A	p.Trp1211Ter	p.W1211*	ENST00000375023	NM_004557.3	1211	tGg/tAg	21/30	0.540612137277116	6	FACETS	1	0.967	1	0.509	0.485	0.535	CLONAL	2	TRUE	2	0.540612137277116	6		599	1670	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798168	32798168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	446	597	0	ENST00000374899.4:c.1511C>T	p.Pro504Leu	p.P504L	ENST00000374899	NM_018833.2	504	cCc/cTc	9/12	0.540612137277116	6	FACETS	1	0.987	1	0.549	0.523	0.576	CLONAL	2	TRUE	2	0.540612137277116	6		597	1564	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444402	50444402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	89	416	0	ENST00000331340.3:c.332G>A	p.Arg111Gln	p.R111Q	ENST00000331340	NM_006060.4	111	cGa/cAa	4/8	0.22552793196785	5	FACETS	0.802	0.711	0.9	0.267	0.237	0.3	INDETERMINATE	1	TRUE	2	0.540612137277116	5		416	743	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444459	50444459	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	169	387	0	ENST00000331340.3:c.389A>C	p.Asn130Thr	p.N130T	ENST00000331340	NM_006060.4	130	aAt/aCt	4/8	0.22552793196785	5	FACETS	0.948	0.876	1	0.632	0.584	0.682	INDETERMINATE	2	TRUE	2	0.540612137277116	5		387	597	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355286	81355286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	260	319	0	ENST00000222390.5:c.1088C>T	p.Pro363Leu	p.P363L	ENST00000222390	NM_000601.4	363	cCc/cTc	9/18	0.540612137277116	4	FACETS	0.967	0.91	1	0.967	0.91	1	CLONAL	2	TRUE	2	0.540612137277116	4		319	766	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878941	151878941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	319	500	0	ENST00000262189.6:c.6004G>A	p.Gly2002Arg	p.G2002R	ENST00000262189	NM_170606.2	2002	Gga/Aga	36/59	0.540612137277116	4	FACETS	0.915	0.865	0.965	0.915	0.865	0.965	CLONAL	2	TRUE	2	0.540612137277116	4		500	994	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5081726	5081727	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	TT	TT	GA	novel	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	183	201	0	ENST00000381652.3:c.2436_2437delinsGA	p.Asp812_Tyr813delinsGluAsn	p.D812_Y813delinsEN	ENST00000381652	NM_004972.3	812	gaTTat/gaGAat	19/25	0.540612137277116	3	FACETS	0.896	0.844	0.947	0.896	0.844	0.947	CLONAL	3	TRUE	0	0.540612137277116	3		201	320	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126384	5126384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762830653	NA	P-0028101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	356	371	0	ENST00000381652.3:c.3229C>T	p.His1077Tyr	p.H1077Y	ENST00000381652	NM_004972.3	1077	Cat/Tat	24/25	0.540612137277116	3	FACETS	0.955	0.917	0.992	0.955	0.917	0.992	CLONAL	3	TRUE	0	0.540612137277116	3		371	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579369	7579369	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555526581	NA	P-0028270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	690	685	0	ENST00000269305.4:c.318C>G	p.Ser106Arg	p.S106R	ENST00000269305	NM_001126112.2	106	agC/agG	4/11	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	5	TRUE	NA	0.337248099397444	2		685	802	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246871	41246871	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1376262238	NA	P-0028270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	101	236	0	ENST00000357654.3:c.677G>A	p.Cys226Tyr	p.C226Y	ENST00000357654	NM_007294.3	226	tGt/tAt	10/23	1	2	FACETS	1	0.959	1	1	0.989	1	CLONAL	2	TRUE	1	0.337248099397444	2		236	272	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144756	58144756	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	217	435	0	ENST00000257904.6:c.472G>C	p.Asp158His	p.D158H	ENST00000257904	NM_000075.3	158	Gac/Cac	4/8	1	2	FACETS	0.853	0.801	0.905	1	0.995	1	CLONAL	3	TRUE	1	0.337248099397444	2		435	503	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888842	76888842	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	126	370	0	ENST00000373344.5:c.4987C>T	p.Gln1663Ter	p.Q1663*	ENST00000373344	NM_000489.3	1663	Cag/Tag	19/35	0.337248099397444	1	FACETS	0.98	0.9	1	1	0.991	1	CLONAL	2	TRUE	0	0.337248099397444	1		370	317	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0028379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	318	528	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.846712056263527	2		528	741	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369198	118369199	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0028379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	37	455	0	ENST00000534358.1:c.5921_5922dup	p.Val1975LysfsTer10	p.V1975Kfs*10	ENST00000534358	NM_005933.3	1972	-/AA	22/36	0.846712056263527	1	FACETS	0.112	0.092	0.135	0.112	0.092	0.135	SUBCLONAL	1	TRUE	0	0.846712056263527	1		455	448	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0028514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	289	578	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.684109374685761	2		578	830	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266711	198266711	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	213	612	0	ENST00000335508.6:c.2221A>G	p.Lys741Glu	p.K741E	ENST00000335508	NM_012433.2	741	Aag/Gag	15/25	1	2	FACETS	0.931	0.869	0.994	0.931	0.869	0.994	CLONAL	1	TRUE	1	0.684109374685761	2		612	669	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443587	52443605	+	frameshift_variant	Frame_Shift_Del	DEL	AAGGTCGTAGATCTCCTCC	AAGGTCGTAGATCTCCTCC	-	novel	NA	P-0028514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	170	587	0	ENST00000460680.1:c.87_105del	p.Glu30ArgfsTer36	p.E30Rfs*36	ENST00000460680	NM_004656.3	29	gtGGAGGAGATCTACGACCTT/gt	3/17	0.684109374685761	1	FACETS	0.861	0.803	0.919	0.861	0.803	0.919	CLONAL	1	TRUE	0	0.684109374685761	1		587	380	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584456	52584457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028514-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	22	519	0	ENST00000394830.3:c.4556dup	p.Trp1520ValfsTer76	p.W1520Vfs*76	ENST00000394830	NM_018313.4	1519	aag/aaAg	29/30	0.684109374685761	1	FACETS	0.103	0.079	0.13	0.103	0.079	0.13	SUBCLONAL	1	TRUE	0	0.684109374685761	1		519	412	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	29	151	0				ENST00000310581	NM_198253.2	-/1132			0.138094980814366	3	FACETS	0.892	0.715	1	0.446	0.357	0.547	CLONAL	1	FALSE	1	0.139374707557656	3		151	499	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885832	23885832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	62	433	0	ENST00000374561.5:c.86G>A	p.Gly29Glu	p.G29E	ENST00000374561	NM_002167.4	29	gGg/gAg	1/3	1	2	FACETS	0.953	0.825	1	1	0.978	1	CLONAL	2	FALSE	1	0.139374707557656	2		433	467	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572008	64572008	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	44	687	0	ENST00000312049.6:c.1631C>T	p.Pro544Leu	p.P544L	ENST00000312049	NM_130799.2	544	cCa/cTa	10/10	1	2	FACETS	0.761	0.636	0.9	0.761	0.636	0.9	SUBCLONAL	1	FALSE	1	0.139374707557656	2		687	830	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435100	18435100	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	40	456	0	ENST00000266497.5:c.85C>G	p.Gln29Glu	p.Q29E	ENST00000266497		29	Caa/Gaa	1/31	0.120289342966987	3	FACETS	1	0.935	1	0.638	0.53	0.759	CLONAL	1	FALSE	1	0.139374707557656	3		456	481	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628742	21628742	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	21	429	0	ENST00000421138.2:c.966T>A	p.Phe322Leu	p.F322L	ENST00000421138		322	ttT/ttA	10/16	0.120289342966987	3	FACETS	0.853	0.656	1	0.426	0.328	0.542	CLONAL	1	FALSE	1	0.139374707557656	3		429	378	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856100	111856100	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0028681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	105	653	0	ENST00000341259.2:c.151G>T	p.Glu51Ter	p.E51*	ENST00000341259	NM_005475.2	51	Gag/Tag	2/8	0.139374707557656	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	FALSE	0	0.139374707557656	2		653	701	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114153	115114153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	92	627	1	ENST00000257566.3:c.1064C>T	p.Pro355Leu	p.P355L	ENST00000257566	NM_016569.3	355	cCa/cTa	6/8	0.139374707557656	2	FACETS	0.938	0.833	1	0.938	0.833	1	CLONAL	2	FALSE	0	0.139374707557656	2		628	704	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120789198	120789198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1171645839	NA	P-0028681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	71	573	2	ENST00000257552.2:c.739C>T	p.Arg247Cys	p.R247C	ENST00000257552	NM_002442.3	247	Cgt/Tgt	11/15	0.139374707557656	2	FACETS	0.866	0.757	0.985	0.866	0.757	0.985	CLONAL	2	FALSE	0	0.139374707557656	2		575	588	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219908	133219908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs969429633	NA	P-0028681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	96	540	0	ENST00000320574.5:c.4453C>T	p.Arg1485Cys	p.R1485C	ENST00000320574	NM_006231.2	1485	Cgc/Tgc	35/49	0.139374707557656	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	FALSE	0	0.139374707557656	2		540	618	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058216	42058218	+	missense_variant	Missense_Mutation	TNP	TTT	TTT	ATC	novel	NA	P-0028681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	17	171	0	ENST00000219905.7:c.7936_7938delinsATC	p.Phe2646Ile	p.F2646I	ENST00000219905	NM_001164273.1	2646	TTT/ATC	24/24	1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	FALSE	1	0.139374707557656	2		171	203	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670427	88670427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	46	349	0	ENST00000360948.2:c.1259C>T	p.Thr420Ile	p.T420I	ENST00000360948	NM_001012338.2	420	aCt/aTt	11/19	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.139374707557656	2		349	464	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877435	89877435	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	48	703	0	ENST00000389301.3:c.328G>A	p.Gly110Ser	p.G110S	ENST00000389301	NM_000135.2	110	Ggt/Agt	4/43	1	2	FACETS	0.873	0.736	1	0.873	0.736	1	CLONAL	1	FALSE	1	0.139374707557656	2		703	789	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576033	29576033	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	27	717	0	ENST00000356175.3:c.4006C>T	p.Gln1336Ter	p.Q1336*	ENST00000356175	NM_000267.3	1336	Cag/Tag	30/57	1	2	FACETS	0.749	0.595	0.927	0.749	0.595	0.927	CLONAL	1	FALSE	1	0.139374707557656	2		717	517	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585361	29585361	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1555618492	NA	P-0028681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	35	455	0	ENST00000356175.3:c.4111-1G>A		p.X1371_splice	ENST00000356175	NM_000267.3	1371			1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	FALSE	1	0.139374707557656	2		455	482	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627241	37627241	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1245259027	NA	P-0028681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	26	535	0	ENST00000447079.4:c.1156C>T	p.Pro386Ser	p.P386S	ENST00000447079	NM_015083.1	386	Cct/Tct	2/14	1	2	FACETS	0.722	0.57	0.896	0.722	0.57	0.896	SUBCLONAL	1	FALSE	1	0.139374707557656	2		535	517	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61717908	61717908	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778783944	NA	P-0028681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	33	363	1	ENST00000401558.2:c.1891C>T	p.His631Tyr	p.H631Y	ENST00000401558	NM_003400.3	631	Cat/Tat	17/25	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	FALSE	1	0.139374707557656	2		364	448	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024905	31024905	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	58	571	0	ENST00000375687.4:c.4390C>A	p.Pro1464Thr	p.P1464T	ENST00000375687	NM_015338.5	1464	Ccc/Acc	13/13	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.139374707557656	2		571	620	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0028681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	26	320	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	FALSE	1	0.139374707557656	2		320	329	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147487	47147488	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CT	CT	TC	novel	NA	P-0028681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	35	432	1	ENST00000409792.3:c.4838_4839delinsGA	p.Glu1613Gly	p.E1613G	ENST00000409792	NM_014159.6	1613	gAG/gGA	6/21	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	FALSE	1	0.139374707557656	2		433	408	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156729	106156729	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1440692352	NA	P-0028681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	35	397	1	ENST00000380013.4:c.1630C>T	p.Arg544Ter	p.R544*	ENST00000380013	NM_001127208.2	544	Cga/Tga	3/11	1	2	FACETS	1	0.823	1	1	0.823	1	CLONAL	1	FALSE	1	0.139374707557656	2		398	500	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029290	143029290	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0028681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	34	325	0	ENST00000262992.4:c.2330T>C	p.Leu777Pro	p.L777P	ENST00000262992	NM_001101669.1	777	cTa/cCa	21/24	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	FALSE	1	0.139374707557656	2		325	421	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0028681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	55	426	0	ENST00000356142.4:c.85C>G	p.Pro29Ala	p.P29A	ENST00000356142	NM_018890.3	29	Cct/Gct	2/7	0.120289342966987	3	FACETS	0.831	0.711	0.961	0.831	0.711	0.961	CLONAL	2	FALSE	1	0.139374707557656	3		426	508	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	32	293	0	ENST00000288602.6:c.1742A>T	p.Asn581Ile	p.N581I	ENST00000288602	NM_004333.4	581	aAt/aTt	15/18	0.120289342966987	3	FACETS	0.841	0.685	1	0.841	0.685	1	CLONAL	2	FALSE	1	0.139374707557656	3		293	292	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742058	145742058	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766844431	NA	P-0028681-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	42	734	0	ENST00000428558.2:c.445C>T	p.Pro149Ser	p.P149S	ENST00000428558	NM_004260.3	149	Ccc/Tcc	5/22	1	2	FACETS	0.798	0.665	0.948	0.798	0.665	0.948	CLONAL	1	FALSE	1	0.139374707557656	2		734	755	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842075	3842075	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1302427305	NA	P-0028693-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	108	141	0	ENST00000262367.5:c.1237C>T	p.Arg413Ter	p.R413*	ENST00000262367	NM_004380.2	413	Cga/Tga	5/31	1	2	FACETS	0.829	0.755	0.905	0.829	0.755	0.905	CLONAL	1	FALSE	1	0.892181808125198	2		141	292	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801726	3801726	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs587783483	NA	P-0028693-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	166	211	0	ENST00000262367.5:c.3779+1G>A		p.X1260_splice	ENST00000262367	NM_004380.2	1260			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.892181808125198	2		211	354	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949128	44949129	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028693-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	179	236	0	ENST00000377967.4:c.3690dup	p.Ile1231TyrfsTer20	p.I1231Yfs*20	ENST00000377967	NM_021140.2	1230	gct/gcTt	25/29	1	2	FACETS	0.859	0.8	0.92	0.859	0.8	0.92	CLONAL	1	FALSE	1	0.892181808125198	2		236	467	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035295	42035301	+	frameshift_variant	Frame_Shift_Del	DEL	CCAACTT	CCAACTT	-	novel	NA	P-0028693-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	156	270	0	ENST00000219905.7:c.5138_5144del	p.Pro1713HisfsTer19	p.P1713Hfs*19	ENST00000219905	NM_001164273.1	1713	CCAACTTca/ca	15/24	1	2	FACETS	0.793	0.733	0.854	0.793	0.733	0.854	SUBCLONAL	1	FALSE	1	0.892181808125198	2		270	441	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523614	41523616	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0028693-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	478	367	0	ENST00000263253.7:c.1032_1034del	p.Leu346del	p.L346del	ENST00000263253	NM_001429.3	344	CTC/-	4/31	0.823183511605792	2	FACETS	0.921	0.899	0.941	0.921	0.899	0.941	CLONAL	2	FALSE	0	0.892181808125198	2		367	582	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266061	41266062	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0028693-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	128	187	0	ENST00000349496.5:c.59dup	p.Ala21GlyfsTer3	p.A21Gfs*3	ENST00000349496	NM_001904.3	20	gcg/gCcg	3/15	1	2	FACETS	0.888	0.817	0.961	0.888	0.817	0.961	CLONAL	1	FALSE	1	0.892181808125198	2		187	323	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900122	151900122	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028693-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	102	105	0	ENST00000262189.6:c.3989del	p.Leu1330Ter	p.L1330*	ENST00000262189	NM_170606.2	1330	tTa/ta	26/59	1	2	FACETS	0.831	0.755	0.91	0.831	0.755	0.91	CLONAL	1	FALSE	1	0.892181808125198	2		105	275	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0028707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	72	393	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	0.839	0.732	0.955	0.839	0.732	0.955	CLONAL	1	TRUE	1	0.229098804812512	2		393	749	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442069	52442081	+	frameshift_variant	Frame_Shift_Del	DEL	GAGTTGCACAAGA	GAGTTGCACAAGA	-	novel	NA	P-0028707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	66	570	0	ENST00000460680.1:c.268_280del	p.Ser90MetfsTer4	p.S90Mfs*4	ENST00000460680	NM_004656.3	90	TCTTGTGCAACTCat/at	5/17	0.229098804812512	1	FACETS	0.692	0.6	0.792	0.692	0.6	0.792	SUBCLONAL	1	TRUE	0	0.229098804812512	1		570	737	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0028849-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	333	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.344058473541062	3	FACETS	0.995	0.948	1	0.995	0.948	1	CLONAL	3	FALSE	0	0.373590489883336	3		288	709	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0028849-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	59	151	0				ENST00000310581	NM_198253.2	-/1132			0.177565155382108	0	FACETS	0.57	0.493	0.653			1	INDETERMINATE	1	FALSE	0	0.373590489883336	0		151	347	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729163	66729163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516792	NA	P-0028849-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	294	726	1	ENST00000307102.5:c.371C>T	p.Pro124Leu	p.P124L	ENST00000307102	NM_002755.3	124	cCg/cTg	3/11	0.244978243339966	5	FACETS	0.953	0.896	1	0.636	0.597	0.675	CLONAL	2	FALSE	2	0.373590489883336	5		727	1288	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112250	115112250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1345506334	NA	P-0028849-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	93	209	1	ENST00000257566.3:c.1490C>T	p.Pro497Leu	p.P497L	ENST00000257566	NM_016569.3	497	cCc/cTc	7/8	0.136237824207945	3	FACETS	0.998	0.899	1	0.998	0.899	1	INDETERMINATE	2	FALSE	1	0.373590489883336	3		210	296	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566827	212566827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202247795	NA	P-0028849-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	88	323	0	ENST00000342788.4:c.1354G>A	p.Glu452Lys	p.E452K	ENST00000342788	NM_005235.2	452	Gaa/Aaa	12/28	1	2	FACETS	0.882	0.784	0.987	0.882	0.784	0.987	CLONAL	1	FALSE	1	0.373590489883336	2		323	534	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100079	27100079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028849-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	128	617	0	ENST00000324856.7:c.3875C>T	p.Pro1292Leu	p.P1292L	ENST00000324856	NM_006015.4	1292	cCt/cTt	16/20	0.152313971347915	0	FACETS	0.548	0.497	0.602			1	INDETERMINATE	1	FALSE	0	0.373590489883336	0		617	783	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86686692	86686692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781719475	NA	P-0028849-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	73	470	1	ENST00000274376.6:c.3136G>A	p.Val1046Ile	p.V1046I	ENST00000274376	NM_002890.2	1046	Gtc/Atc	25/25	0.177565155382108	0	FACETS	0.413	0.361	0.469			1	INDETERMINATE	1	FALSE	0	0.373590489883336	0		471	593	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622481	28622481	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028849-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	224	628	0	ENST00000241453.7:c.1136T>G	p.Ile379Ser	p.I379S	ENST00000241453	NM_004119.2	379	aTc/aGc	9/24	0.205701448054305	4	FACETS	0.805	0.75	0.862	0.805	0.75	0.862	INDETERMINATE	2	FALSE	2	0.373590489883336	4		628	1023	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966430	25966430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028849-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	271	652	1	ENST00000435504.4:c.2776C>T	p.Leu926Phe	p.L926F	ENST00000435504		926	Ctt/Ttt	13/13	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.373590489883336	2		653	1157	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024379	31024380	+	missense_variant	Missense_Mutation	DNP	TC	TC	GT	novel	NA	P-0028849-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	170	647	3	ENST00000375687.4:c.3864_3865delinsGT	p.Arg1289Trp	p.R1289W	ENST00000375687	NM_015338.5	1288	ggTCgg/ggGTgg	13/13	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.373590489883336	2		650	883	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030005	36030005	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028849-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	77	710	0	ENST00000358208.4:c.1040G>A	p.Gly347Glu	p.G347E	ENST00000358208		347	gGg/gAg	9/12	1	2	FACETS	0.429	0.376	0.487	0.429	0.376	0.487	SUBCLONAL	1	FALSE	1	0.373590489883336	2		710	960	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71161764	71161764	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028849-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	139	401	0	ENST00000318789.4:c.205C>T	p.Leu69Phe	p.L69F	ENST00000318789	NM_032682.5	69	Ctt/Ttt	7/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.373590489883336	2		401	590	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1255482	1255482	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0028849-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	117	764	2	ENST00000310581.5:c.3077G>A	p.Trp1026Ter	p.W1026*	ENST00000310581	NM_198253.2	1026	tGg/tAg	14/16	0.177565155382108	0	FACETS	0.499	0.45	0.551			1	INDETERMINATE	1	FALSE	0	0.373590489883336	0		766	786	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140886	37140886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028849-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	74	536	0	ENST00000373509.5:c.722C>T	p.Pro241Leu	p.P241L	ENST00000373509	NM_002648.3	241	cCt/cTt	5/6	0.188394661258573	2	FACETS	0.475	0.415	0.54	0.238	0.207	0.27	INDETERMINATE	1	FALSE	0	0.373590489883336	2		536	834	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111995822	111995822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028849-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	43	412	0	ENST00000368678.4:c.1276C>T	p.Pro426Ser	p.P426S	ENST00000368678		426	Ccc/Tcc	12/13	0.188394661258573	2	FACETS	0.35	0.292	0.415	0.175	0.146	0.208	INDETERMINATE	1	FALSE	0	0.373590489883336	2		412	657	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058557	69058557	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028849-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	322	757	0	ENST00000288368.4:c.4201T>C	p.Phe1401Leu	p.F1401L	ENST00000288368	NM_024870.2	1401	Ttt/Ctt	34/40	0.276191934010236	4	FACETS	0.987	0.932	1	0.987	0.932	1	CLONAL	2	FALSE	2	0.373590489883336	4		757	1199	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0028941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	60	69	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.162635653194082	5	FACETS	0.804	0.701	0.914	0.536	0.467	0.609	INDETERMINATE	2	TRUE	2	0.569019545506006	5		69	243	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577599	7577600	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1567550002	NA	P-0028941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	176	450	0	ENST00000269305.4:c.681dup	p.Asp228Ter	p.D228*	ENST00000269305	NM_001126112.2	227	-/T	7/11	0.452607911014233	2	FACETS	1	0.989	1	0.687	0.64	0.736	CLONAL	1	TRUE	0	0.569019545506006	2		450	450	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89862427	89862427	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0028941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	26	498	0	ENST00000389301.3:c.894-1G>A		p.X298_splice	ENST00000389301	NM_000135.2	298			0.452607911014233	2	FACETS	0.197	0.156	0.245	0.099	0.078	0.123	SUBCLONAL	1	TRUE	0	0.569019545506006	2		498	463	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612236	189612236	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	27	410	0	ENST00000264731.3:c.1988T>G	p.Phe663Cys	p.F663C	ENST00000264731	NM_003722.4	663	tTt/tGt	14/14	0.394750654629585	3	FACETS	0.23	0.183	0.285	0.115	0.091	0.143	SUBCLONAL	1	TRUE	1	0.569019545506006	3		410	529	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717769	89717770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0029409-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	64	235	0	ENST00000371953.3:c.800dup	p.Asp268GlyfsTer30	p.D268Gfs*30	ENST00000371953	NM_000314.4	265	cta/ctAa	7/9	0.234888107206528	2	FACETS	0.804	0.706	0.908	0.804	0.706	0.908	CLONAL	2	TRUE	0	0.340071380479214	2		235	234	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118855	115118856	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0029409-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	69	360	0	ENST00000257566.3:c.485_486del	p.Arg162LeufsTer2	p.R162Lfs*2	ENST00000257566	NM_016569.3	162	cGT/c	2/8	0.270379139985292	4	FACETS	1	0.963	1	0.641	0.561	0.728	CLONAL	1	TRUE	2	0.340071380479214	4		360	424	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048735	180048735	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029409-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	157	627	0	ENST00000261937.6:c.1827C>G	p.Asp609Glu	p.D609E	ENST00000261937	NM_182925.4	609	gaC/gaG	13/30	0.340071380479214	3	FACETS	0.827	0.76	0.897	0.827	0.76	0.897	CLONAL	2	TRUE	1	0.340071380479214	3		627	653	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222513	2222513	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029409-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	50	666	0	ENST00000326181.6:c.707A>C	p.Asn236Thr	p.N236T	ENST00000326181	NM_032271.2	236	aAc/aCc	9/21	0.340071380479214	3	FACETS	0.436	0.368	0.51	0.218	0.184	0.255	SUBCLONAL	1	TRUE	1	0.340071380479214	3		666	790	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382185	152382185	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0029409-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	42	319	0	ENST00000206249.3:c.1295C>A	p.Ser432Ter	p.S432*	ENST00000206249	NM_000125.3	432	tCa/tAa	6/8	0.294087282611082	2	FACETS	0.782	0.655	0.921	0.391	0.327	0.461	CLONAL	1	TRUE	0	0.340071380479214	2		319	316	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	198	151	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.892730641429299	2		151	432	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	CT	rs121913227	NA	P-0029475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	337	377	0	ENST00000288602.6:c.1798_1799delinsAG	p.Val600Arg	p.V600R	ENST00000288602	NM_004333.4	600	GTg/AGg	15/18	0.284378677622275	3	FACETS	1	0.993	1	0.633	0.601	0.665	INDETERMINATE	1	TRUE	1	0.892730641429299	3		377	863	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346885	89346885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373218212	NA	P-0029475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	132	315	0	ENST00000301030.4:c.6065C>T	p.Pro2022Leu	p.P2022L	ENST00000301030	NM_001256183.1	2022	cCt/cTt	9/13	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.892730641429299	2		315	269	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692920	89692921	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs398123323	NA	P-0029475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	238	633	0	ENST00000371953.3:c.405dup	p.Cys136MetfsTer44	p.C136Mfs*44	ENST00000371953	NM_000314.4	135	ata/atAa	5/9	0.892730641429299	1	FACETS	0.9	0.863	0.936	0.9	0.863	0.936	CLONAL	1	TRUE	0	0.892730641429299	1		633	328	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515213	106515213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267601224	NA	P-0029475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	332	535	0	ENST00000359195.3:c.2356C>T	p.Pro786Ser	p.P786S	ENST00000359195	NM_002649.2	786	Cca/Tca	5/11	0.284378677622275	3	FACETS	1	0.991	1	0.602	0.571	0.633	INDETERMINATE	1	TRUE	1	0.892730641429299	3		535	894	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485307	8485307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	282	520	0	ENST00000356435.5:c.3073C>T	p.His1025Tyr	p.H1025Y	ENST00000356435		1025	Cat/Tat	18/35	1	2	FACETS	0.953	0.902	1	0.953	0.902	1	CLONAL	1	TRUE	1	0.892730641429299	2		520	663	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272152	15272152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745724101	NA	P-0029475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	341	641	0	ENST00000263388.2:c.6287C>T	p.Ser2096Leu	p.S2096L	ENST00000263388	NM_000435.2	2096	tCg/tTg	33/33	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.892730641429299	2		641	721	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940759	71940759	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0029475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	92	709	0	ENST00000298229.2:c.806C>G	p.Ser269Ter	p.S269*	ENST00000298229	NM_001567.3	269	tCa/tGa	7/28	0.892730641429299	1	FACETS	0.245	0.218	0.273	0.245	0.218	0.273	SUBCLONAL	1	TRUE	0	0.892730641429299	1		709	466	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942609	71942609	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	75	776	1	ENST00000298229.2:c.1565T>A	p.Ile522Asn	p.I522N	ENST00000298229	NM_001567.3	522	aTc/aAc	13/28	0.892730641429299	1	FACETS	0.2	0.175	0.226	0.2	0.175	0.226	SUBCLONAL	1	TRUE	0	0.892730641429299	1		777	465	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425456	49425457	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0029475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	332	722	1	ENST00000301067.7:c.13031_13032delinsTT	p.Pro4344Leu	p.P4344L	ENST00000301067	NM_003482.3	4344	cCC/cTT	39/54	1	2	FACETS	0.898	0.853	0.944	0.898	0.853	0.944	CLONAL	1	TRUE	1	0.892730641429299	2		723	828	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924302	112924303	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAA	novel	NA	P-0029475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	78	720	0	ENST00000351677.2:c.1249_1251dup	p.Gln417dup	p.Q417dup	ENST00000351677	NM_002834.3	417	-/CAA	11/16	1	2	FACETS	0.192	0.168	0.218	0.192	0.168	0.218	SUBCLONAL	1	TRUE	1	0.892730641429299	2		720	908	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041180	29041180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	360	682	0	ENST00000282397.4:c.248G>A	p.Arg83Lys	p.R83K	ENST00000282397	NM_002019.4	83	aGa/aAa	3/30	1	2	FACETS	0.895	0.852	0.939	0.895	0.852	0.939	CLONAL	1	TRUE	1	0.892730641429299	2		682	901	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832575	72832575	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	246	353	0	ENST00000268489.5:c.4006G>C	p.Ala1336Pro	p.A1336P	ENST00000268489	NM_006885.3	1336	Gca/Cca	9/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.892730641429299	2		353	527	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696372	47696372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	360	616	1	ENST00000347630.2:c.451C>T	p.Pro151Ser	p.P151S	ENST00000347630	NM_001007230.1	151	Cct/Tct	6/11	1	2	FACETS	0.987	0.941	1	0.987	0.941	1	CLONAL	1	TRUE	1	0.892730641429299	2		617	817	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293132	212293132	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0029475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	281	461	0	ENST00000342788.4:c.2719+1G>A		p.X907_splice	ENST00000342788	NM_005235.2	907			1	2	FACETS	0.982	0.93	1	0.982	0.93	1	CLONAL	1	TRUE	1	0.892730641429299	2		461	641	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568868	212568868	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	356	640	0	ENST00000342788.4:c.1250T>A	p.Phe417Tyr	p.F417Y	ENST00000342788	NM_005235.2	417	tTt/tAt	11/28	1	2	FACETS	0.967	0.921	1	0.967	0.921	1	CLONAL	1	TRUE	1	0.892730641429299	2		640	825	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968676	55968676	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0029475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	286	415	0	ENST00000263923.4:c.1988-1G>A		p.X663_splice	ENST00000263923	NM_002253.2	663			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.892730641429299	2		415	617	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143324209	143324209	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0029475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	187	392	0	ENST00000262992.4:c.256-2A>G		p.X86_splice	ENST00000262992	NM_001101669.1	86			1	2	FACETS	0.888	0.828	0.948	0.888	0.828	0.948	CLONAL	1	TRUE	1	0.892730641429299	2		392	472	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053120	180053120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	257	613	0	ENST00000261937.6:c.1249G>A	p.Val417Met	p.V417M	ENST00000261937	NM_182925.4	417	Gtg/Atg	9/30	1	2	FACETS	0.918	0.866	0.971	0.918	0.866	0.971	CLONAL	1	TRUE	1	0.892730641429299	2		613	627	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942626	71942626	+	frameshift_variant	Frame_Shift_Ins	INS	T	T	AC	novel	NA	P-0029475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	71	777	1	ENST00000298229.2:c.1582delinsAC	p.Ser528ThrfsTer24	p.S528Tfs*24	ENST00000298229	NM_001567.3	528	Tcc/ACcc	13/28	0.892730641429299	1	FACETS	0.187	0.163	0.212	0.187	0.163	0.212	SUBCLONAL	1	TRUE	0	0.892730641429299	1		778	472	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0029544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	95	243	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.315038631349774	2		243	474	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909625	76909625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781849044	NA	P-0029544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	121	206	0	ENST00000373344.5:c.4280G>A	p.Arg1427His	p.R1427H	ENST00000373344	NM_000489.3	1427	cGt/cAt	14/35	1	1	FACETS	0.778	0.709	0.85	1	0.987	1	SUBCLONAL	2	TRUE	0	0.315038631349774	1		206	416	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675571	86675571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1561325048	NA	P-0029544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	56	208	0	ENST00000274376.6:c.2513del	p.Asn838MetfsTer4	p.N838Mfs*4	ENST00000274376	NM_002890.2	836	gAa/ga	19/25	0.315038631349774	1	FACETS	0.846	0.728	0.973	0.846	0.728	0.973	CLONAL	1	TRUE	0	0.315038631349774	1		208	354	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203488	108203488	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0029544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	44	165	0	ENST00000278616.4:c.7789-1G>A		p.X2597_splice	ENST00000278616	NM_000051.3	2597			1	2	FACETS	0.824	0.694	0.967	0.824	0.694	0.967	CLONAL	1	TRUE	1	0.315038631349774	2		165	339	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162007	22162007	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	121	381	0	ENST00000215832.6:c.248T>C	p.Ile83Thr	p.I83T	ENST00000215832	NM_002745.4	83	aTc/aCc	2/9	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.315038631349774	2		381	687	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710858	117710858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	81	369	0	ENST00000368508.3:c.1414G>A	p.Asp472Asn	p.D472N	ENST00000368508	NM_002944.2	472	Gac/Aac	12/43	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.315038631349774	2		369	469	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673421	30673422	+	missense_variant	Missense_Mutation	DNP	GA	GA	TG	novel	NA	P-0029544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	75	489	0	ENST00000376406.3:c.3538_3539delinsCA	p.Ser1180His	p.S1180H	ENST00000376406	NM_014641.2	1180	TCt/CAt	10/15	1	2	FACETS	0.704	0.617	0.798	0.704	0.617	0.798	SUBCLONAL	1	TRUE	1	0.315038631349774	2		489	676	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0029950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	1490	528	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.817131368489607	5	FACETS	0.993	0.977	1			1	CLONAL	4	TRUE	NA	0.86	5		528	1998	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0029950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	211	119	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.953	0.893	1	0.953	0.893	1	CLONAL	1	TRUE	1	0.86	2		119	515	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0029950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	260	151	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.998	0.943	1	0.998	0.943	1	CLONAL	1	TRUE	1	0.86	2		151	606	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980811	40980811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	288	576	0	ENST00000373198.4:c.1675G>A	p.Gly559Arg	p.G559R	ENST00000373198	NM_133170.3	559	Ggg/Agg	10/32	1	2	FACETS	0.877	0.829	0.925	0.877	0.829	0.925	CLONAL	1	TRUE	1	0.86	2		576	764	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608264	28608264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1312380044	NA	P-0029950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	293	513	0	ENST00000241453.7:c.1792G>A	p.Glu598Lys	p.E598K	ENST00000241453	NM_004119.2	598	Gaa/Aaa	14/24	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.86	2		513	657	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039185	49039185	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0029950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	211	404	0	ENST00000267163.4:c.2263T>A	p.Phe755Ile	p.F755I	ENST00000267163	NM_000321.2	755	Ttc/Atc	22/27	1	2	FACETS	0.883	0.826	0.94	0.883	0.826	0.94	CLONAL	1	TRUE	1	0.86	2		404	556	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578284	212578284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	207	556	0	ENST00000342788.4:c.973C>T	p.Pro325Ser	p.P325S	ENST00000342788	NM_005235.2	325	Cct/Tct	8/28	1	2	FACETS	0.888	0.831	0.946	0.888	0.831	0.946	CLONAL	1	TRUE	1	0.86	2		556	542	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506379	120506379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553199314	NA	P-0029950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1634	356	487	0	ENST00000256646.2:c.1733C>T	p.Pro578Leu	p.P578L	ENST00000256646	NM_024408.3	578	cCt/cTt	11/34	0.817131368489607	5	FACETS	0.953	0.899	1			1	CLONAL	1	TRUE	NA	0.86	5		487	1990	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202346	138202346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780709741	NA	P-0029950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	326	481	0	ENST00000237289.4:c.2263G>A	p.Glu755Lys	p.E755K	ENST00000237289	NM_001270507.1	755	Gaa/Aaa	9/9	1	2	FACETS	0.956	0.908	1	0.956	0.908	1	CLONAL	1	TRUE	1	0.86	2		481	793	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392013	118392013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	240	397	0	ENST00000534358.1:c.11524C>T	p.His3842Tyr	p.H3842Y	ENST00000534358	NM_005933.3	3842	Cat/Tat	35/36	1	2	FACETS	0.924	0.869	0.979	0.924	0.869	0.979	CLONAL	1	TRUE	1	0.86	2		397	604	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782840	66782840	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	254	473	0	ENST00000307102.5:c.1069G>C	p.Val357Leu	p.V357L	ENST00000307102	NM_002755.3	357	Gtt/Ctt	11/11	1	2	FACETS	0.85	0.8	0.901	0.85	0.8	0.901	CLONAL	1	TRUE	1	0.86	2		473	695	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645915	67645916	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0029950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	289	493	2	ENST00000264010.4:c.843_844delinsAA	p.Asp282Asn	p.D282N	ENST00000264010	NM_006565.3	281	ttGGat/ttAAat	4/12	1	2	FACETS	0.897	0.848	0.947	0.897	0.848	0.947	CLONAL	1	TRUE	1	0.86	2		495	749	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164451	47164451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	180	274	0	ENST00000409792.3:c.1675C>T	p.Leu559Phe	p.L559F	ENST00000409792	NM_014159.6	559	Ctt/Ttt	3/21	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.86	2		274	407	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245518	153245518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	183	346	0	ENST00000281708.4:c.1673C>T	p.Ser558Phe	p.S558F	ENST00000281708	NM_033632.3	558	tCt/tTt	11/12	1	2	FACETS	0.929	0.867	0.993	0.929	0.867	0.993	CLONAL	1	TRUE	1	0.86	2		346	458	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997786	149997786	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	292	453	0	ENST00000253339.5:c.2681T>C	p.Leu894Ser	p.L894S	ENST00000253339		894	tTa/tCa	5/7	1	2	FACETS	0.943	0.893	0.994	0.943	0.893	0.994	CLONAL	1	TRUE	1	0.86	2		453	720	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141545667	141545667	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029950-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	397	568	1	ENST00000220592.5:c.2171T>C	p.Val724Ala	p.V724A	ENST00000220592	NM_012154.3	724	gTt/gCt	17/19	1	2	FACETS	0.925	0.882	0.968	0.925	0.882	0.968	CLONAL	1	TRUE	1	0.86	2		569	998	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0030112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	114	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.21227139028338	2	FACETS	0.885	0.799	0.975	0.885	0.799	0.975	CLONAL	2	TRUE	0	0.223262986781996	2		288	577	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	34	151	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.557	0.454	0.673	0.557	0.454	0.673	SUBCLONAL	1	TRUE	1	0.223262986781996	2		151	547	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519874	NA	P-0030112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	341	522	1	ENST00000356142.4:c.85C>A	p.Pro29Thr	p.P29T	ENST00000356142	NM_018890.3	29	Cct/Act	2/7	0.223262986781996	5	FACETS	0.984	0.935	1	0.984	0.935	1	CLONAL	5	TRUE	0	0.223262986781996	5		523	829	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971029	21971029	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519852	NA	P-0030112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	251	474	0	ENST00000304494.5:c.329G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tGg/tAg	2/3	0.223262986781996	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.223262986781996	3		474	722	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426738	212426738	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	53	533	1	ENST00000342788.4:c.2377C>T	p.Gln793Ter	p.Q793*	ENST00000342788	NM_005235.2	793	Cag/Tag	20/28	0.223262986781996	3	FACETS	0.732	0.623	0.852	0.366	0.311	0.426	SUBCLONAL	1	TRUE	1	0.223262986781996	3		534	721	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992729	68992729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779079528	NA	P-0030112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	155	636	2	ENST00000288368.4:c.1694C>T	p.Ser565Leu	p.S565L	ENST00000288368	NM_024870.2	565	tCg/tTg	16/40	0.223262986781996	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.223262986781996	3		638	624	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972864	55972864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866807777	NA	P-0030112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	75	407	0	ENST00000263923.4:c.1526G>A	p.Gly509Glu	p.G509E	ENST00000263923	NM_002253.2	509	gGa/gAa	11/30	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.223262986781996	2		407	549	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396785	396785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	112	617	0	ENST00000262320.3:c.241C>T	p.Pro81Ser	p.P81S	ENST00000262320	NM_003502.3	81	Cca/Tca	2/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.223262986781996	2		617	759	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845938	72845938	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0030112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	72	380	0	ENST00000268489.5:c.3530-1G>A		p.X1177_splice	ENST00000268489	NM_006885.3	1177			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.223262986781996	2		380	487	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562669	29562669	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199474765	NA	P-0030112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	70	501	0	ENST00000356175.3:c.3749G>A	p.Arg1250Gln	p.R1250Q	ENST00000356175	NM_000267.3	1250	cGg/cAg	28/57	1	2	FACETS	0.994	0.867	1	0.994	0.867	1	CLONAL	1	TRUE	1	0.223262986781996	2		501	631	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028052	48028052	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	105	352	0	ENST00000234420.5:c.2930A>G	p.Tyr977Cys	p.Y977C	ENST00000234420	NM_000179.2	977	tAc/tGc	4/10	0.223262986781996	3	FACETS	0.954	0.858	1	0.954	0.858	1	CLONAL	2	TRUE	1	0.223262986781996	3		352	548	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502450	186502450	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	37	333	0	ENST00000323963.5:c.173C>A	p.Ala58Asp	p.A58D	ENST00000323963		58	gCt/gAt	3/11	1	2	FACETS	0.762	0.628	0.911	0.762	0.628	0.911	CLONAL	1	TRUE	1	0.223262986781996	2		333	435	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1795668	1795668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	19	84	0	ENST00000260795.2:c.7G>A	p.Ala3Thr	p.A3T	ENST00000260795		3	Gcc/Acc	1/17	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.223262986781996	2		84	130	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30668348	30668348	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	72	650	0	ENST00000376406.3:c.6164T>C	p.Val2055Ala	p.V2055A	ENST00000376406	NM_014641.2	2055	gTt/gCt	15/15	1	2	FACETS	0.786	0.685	0.894	0.786	0.685	0.894	SUBCLONAL	1	TRUE	1	0.223262986781996	2		650	821	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528056	157528056	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs779936373	NA	P-0030112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	50	486	0	ENST00000346085.5:c.5781C>G	p.Asp1927Glu	p.D1927E	ENST00000346085	NM_020732.3	1927	gaC/gaG	20/20	1	2	FACETS	0.596	0.505	0.698	0.596	0.505	0.698	SUBCLONAL	1	TRUE	1	0.223262986781996	2		486	751	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912079	56912079	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030112-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	54	606	0	ENST00000519728.1:c.1307T>C	p.Ile436Thr	p.I436T	ENST00000519728	NM_002350.3	436	aTt/aCt	12/13	0.223262986781996	3	FACETS	0.601	0.512	0.699	0.3	0.255	0.35	SUBCLONAL	1	TRUE	1	0.223262986781996	3		606	895	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0030246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	324	578	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	0.982	0.931	1	0.982	0.931	1	CLONAL	1	TRUE	1	0.778162452016551	2		578	848	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441478	52441527	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TACGGGGAAGAAAATAAGGCCGTATCAGAATAATTTCTCCTCAGGTAGGA	TACGGGGAAGAAAATAAGGCCGTATCAGAATAATTTCTCCTCAGGTAGGA	-	novel	NA	P-0030246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	124	364	0	ENST00000460680.1:c.376-51_376-2del		p.X126_splice	ENST00000460680	NM_004656.3	126			0.778162452016551	1	FACETS	0.795	0.735	0.854	0.795	0.735	0.854	SUBCLONAL	1	TRUE	0	0.778162452016551	1		364	245	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643755	52643758	+	frameshift_variant	Frame_Shift_Del	DEL	ATCA	ATCA	-	novel	NA	P-0030246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	313	558	0	ENST00000394830.3:c.2138_2141del	p.Met713ArgfsTer17	p.M713Rfs*17	ENST00000394830	NM_018313.4	713	aTGATg/ag	17/30	0.778162452016551	1	FACETS	0.967	0.927	1	0.967	0.927	1	CLONAL	1	TRUE	0	0.778162452016551	1		558	508	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	84	151	0				ENST00000310581	NM_198253.2	-/1132			0.364682953329218	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.692477772167446	0		151	317	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074205	8074205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	108	512	0	ENST00000377482.5:c.454C>T	p.Pro152Ser	p.P152S	ENST00000377482	NM_018948.3	152	Cct/Tct	4/4	0.301444348880971	3	FACETS	0.476	0.427	0.529	0.238	0.213	0.265	INDETERMINATE	1	TRUE	1	0.692477772167446	3		512	882	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804214	43804214	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	318	413	0	ENST00000372470.3:c.214G>A	p.Glu72Lys	p.E72K	ENST00000372470	NM_005373.2	72	Gag/Aag	3/12	0.301444348880971	3	FACETS	0.859	0.816	0.902	0.859	0.816	0.902	INDETERMINATE	2	TRUE	1	0.692477772167446	3		413	720	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307172	65307172	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	402	492	0	ENST00000342505.4:c.2516G>A	p.Arg839Gln	p.R839Q	ENST00000342505	NM_002227.2	839	cGa/cAa	18/25	0.301444348880971	3	FACETS	0.871	0.833	0.91	0.871	0.833	0.91	INDETERMINATE	2	TRUE	1	0.692477772167446	3		492	897	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	213	226	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.301444348880971	3	FACETS	1	0.97	1	0.536	0.499	0.573	INDETERMINATE	1	TRUE	1	0.692477772167446	3		226	773	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458438	120458438	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	340	592	0	ENST00000256646.2:c.6907C>T	p.Pro2303Ser	p.P2303S	ENST00000256646	NM_024408.3	2303	Ccc/Tcc	34/34	0.301444348880971	3	FACETS	0.83	0.79	0.871	0.83	0.79	0.871	INDETERMINATE	2	TRUE	1	0.692477772167446	3		592	796	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567723	226567723	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	404	564	1	ENST00000366794.5:c.1443G>A	p.Trp481Ter	p.W481*	ENST00000366794	NM_001618.3	481	tgG/tgA	10/23	0.301444348880971	3	FACETS	0.866	0.828	0.904	0.866	0.828	0.904	INDETERMINATE	2	TRUE	1	0.692477772167446	3		565	907	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451473	70451473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	410	737	0	ENST00000373644.4:c.6313C>T	p.Pro2105Ser	p.P2105S	ENST00000373644	NM_030625.2	2105	Cct/Tct	12/12	0.692477772167446	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.692477772167446	1		737	719	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710619	114710619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	144	601	1	ENST00000543371.1:c.104C>T	p.Ser35Phe	p.S35F	ENST00000543371	NM_001198531.1	35	tCc/tTc	1/14	0.692477772167446	1	FACETS	0.493	0.451	0.535	0.493	0.451	0.535	SUBCLONAL	1	TRUE	0	0.692477772167446	1		602	552	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742452	17742452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	118	463	2	ENST00000250003.3:c.634G>A	p.Asp212Asn	p.D212N	ENST00000250003	NM_002478.4	212	Gac/Aac	2/3	0.692477772167446	1	FACETS	0.371	0.335	0.408	0.371	0.335	0.408	SUBCLONAL	1	TRUE	0	0.692477772167446	1		465	601	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999087	100999087	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1299240489	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	265	604	2	ENST00000325455.5:c.715G>A	p.Gly239Ser	p.G239S	ENST00000325455	NM_001202474.3	239	Ggc/Agc	1/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.692477772167446	2		606	706	SUCCESS
ATM	472	MSKCC	GRCh37	11	108154937	108154969	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AATTTTTCTATTTTTAGATCTTGTTATAAGGTT	AATTTTTCTATTTTTAGATCTTGTTATAAGGTT	-	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	95	257	0	ENST00000278616.4:c.3747-17_3762del		p.X1249_splice	ENST00000278616	NM_000051.3	1249		26/63	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.692477772167446	2		257	246	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373167	118373167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	109	477	0	ENST00000534358.1:c.6560C>T	p.Ser2187Phe	p.S2187F	ENST00000534358	NM_005933.3	2187	tCc/tTc	27/36	1	2	FACETS	0.42	0.377	0.466	0.42	0.377	0.466	SUBCLONAL	1	TRUE	1	0.692477772167446	2		477	749	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552663	18552663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	98	958	1	ENST00000266497.5:c.2074C>T	p.Pro692Ser	p.P692S	ENST00000266497		692	Cct/Tct	14/31	0.692477772167446	1	FACETS	0.353	0.316	0.393	0.353	0.316	0.393	SUBCLONAL	1	TRUE	0	0.692477772167446	1		959	524	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641487	18641487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	97	564	0	ENST00000266497.5:c.2486C>T	p.Ser829Phe	p.S829F	ENST00000266497		829	tCc/tTc	17/31	0.692477772167446	1	FACETS	0.442	0.397	0.49	0.442	0.397	0.49	SUBCLONAL	1	TRUE	0	0.692477772167446	1		564	414	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431618	49431618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374526821	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	275	660	0	ENST00000301067.7:c.9521C>T	p.Ser3174Phe	p.S3174F	ENST00000301067	NM_003482.3	3174	tCt/tTt	34/54	0.19320755869464	3	FACETS	1	0.991	1	0.649	0.611	0.687	INDETERMINATE	1	TRUE	1	0.692477772167446	3		660	824	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865156	57865156	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	205	774	0	ENST00000228682.2:c.2633G>A	p.Arg878Lys	p.R878K	ENST00000228682	NM_005269.2	878	aGg/aAg	12/12	0.19320755869464	3	FACETS	0.645	0.597	0.695	0.322	0.298	0.348	INDETERMINATE	1	TRUE	1	0.692477772167446	3		774	1236	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856277	111856277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	48	47	0	ENST00000341259.2:c.328C>T	p.Pro110Ser	p.P110S	ENST00000341259	NM_005475.2	110	Ccc/Tcc	2/8	1	2	FACETS	0.77	0.68	0.859	1	0.973	1	SUBCLONAL	2	TRUE	1	0.692477772167446	2		47	90	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432191	121432191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	171	544	0	ENST00000257555.6:c.938C>T	p.Ser313Phe	p.S313F	ENST00000257555		313	tCc/tTc	4/10	1	2	FACETS	0.533	0.49	0.578	0.533	0.49	0.578	SUBCLONAL	1	TRUE	1	0.692477772167446	2		544	926	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123888165	123888165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	134	396	0	ENST00000330479.4:c.643G>A	p.Glu215Lys	p.E215K	ENST00000330479	NM_020382.3	215	Gaa/Aaa	6/9	1	2	FACETS	0.612	0.558	0.669	0.612	0.558	0.669	SUBCLONAL	1	TRUE	1	0.692477772167446	2		396	632	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225647	133225648	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	306	611	0	ENST00000320574.5:c.4016_4017delinsTT	p.Thr1339Ile	p.T1339I	ENST00000320574	NM_006231.2	1339	aCC/aTT	32/49	1	2	FACETS	0.939	0.887	0.992	0.939	0.887	0.992	CLONAL	1	TRUE	1	0.692477772167446	2		611	941	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588668	28588668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	104	549	0	ENST00000241453.7:c.2780C>T	p.Ala927Val	p.A927V	ENST00000241453	NM_004119.2	927	gCt/gTt	23/24	1	2	FACETS	0.432	0.386	0.479	0.432	0.386	0.479	SUBCLONAL	1	TRUE	1	0.692477772167446	2		549	696	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626709	28626709	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	324	551	1	ENST00000241453.7:c.587G>A	p.Trp196Ter	p.W196*	ENST00000241453	NM_004119.2	196	tGg/tAg	5/24	1	2	FACETS	0.983	0.931	1	0.983	0.931	1	CLONAL	1	TRUE	1	0.692477772167446	2		552	952	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041751	29041751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	86	383	1	ENST00000282397.4:c.68C>T	p.Ser23Phe	p.S23F	ENST00000282397	NM_002019.4	23	tCt/tTt	2/30	1	2	FACETS	0.48	0.426	0.538	0.48	0.426	0.538	SUBCLONAL	1	TRUE	1	0.692477772167446	2		384	517	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32899288	32899288	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	217	515	0	ENST00000380152.3:c.392C>T	p.Ser131Phe	p.S131F	ENST00000380152		131	tCc/tTc	4/27	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.692477772167446	2		515	586	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914707	32914707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80358862	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	213	570	0	ENST00000380152.3:c.6215C>T	p.Ser2072Phe	p.S2072F	ENST00000380152		2072	tCc/tTc	11/27	1	2	FACETS	0.952	0.89	1	0.952	0.89	1	CLONAL	1	TRUE	1	0.692477772167446	2		570	646	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134688	41134688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1034299550	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	84	456	0	ENST00000379561.5:c.940C>T	p.Arg314Cys	p.R314C	ENST00000379561	NM_002015.3	314	Cgc/Tgc	2/3	1	2	FACETS	0.377	0.333	0.424	0.377	0.333	0.424	SUBCLONAL	1	TRUE	1	0.692477772167446	2		456	644	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560489	95560489	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	105	508	0	ENST00000393063.1:c.5100T>G	p.Cys1700Trp	p.C1700W	ENST00000393063	NM_030621.3	1700	tgT/tgG	25/28	1	2	FACETS	0.408	0.365	0.453	0.408	0.365	0.453	SUBCLONAL	1	TRUE	1	0.692477772167446	2		508	743	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40685731	40685731	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	313	692	0	ENST00000249776.8:c.884T>A	p.Leu295Ter	p.L295*	ENST00000249776	NM_033286.3	295	tTa/tAa	9/9	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.692477772167446	2		692	793	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058361	42058361	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	99	487	0	ENST00000219905.7:c.8081C>T	p.Ser2694Phe	p.S2694F	ENST00000219905	NM_001164273.1	2694	tCc/tTc	24/24	1	2	FACETS	0.58	0.52	0.643	0.58	0.52	0.643	SUBCLONAL	1	TRUE	1	0.692477772167446	2		487	493	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712784	43712784	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	417	681	0	ENST00000382044.4:c.4400C>T	p.Ser1467Phe	p.S1467F	ENST00000382044	NM_001141980.1	1467	tCt/tTt	21/28	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.692477772167446	2		681	1031	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472540	88472540	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	152	617	0	ENST00000360948.2:c.2015C>T	p.Ser672Phe	p.S672F	ENST00000360948	NM_001012338.2	672	tCc/tTc	16/19	1	2	FACETS	0.459	0.419	0.501	0.459	0.419	0.501	SUBCLONAL	1	TRUE	1	0.692477772167446	2		617	956	SUCCESS
BLM	641	MSKCC	GRCh37	15	91306278	91306278	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	108	511	0	ENST00000355112.3:c.1965G>T	p.Met655Ile	p.M655I	ENST00000355112	NM_000057.2	655	atG/atT	8/22	1	2	FACETS	0.431	0.387	0.478	0.431	0.387	0.478	SUBCLONAL	1	TRUE	1	0.692477772167446	2		511	723	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640325	3640325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	216	774	0	ENST00000294008.3:c.3314C>T	p.Ser1105Phe	p.S1105F	ENST00000294008	NM_032444.2	1105	tCc/tTc	12/15	1	2	FACETS	0.497	0.461	0.535	0.497	0.461	0.535	SUBCLONAL	1	TRUE	1	0.692477772167446	2		774	1254	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858585	9858585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	209	396	0	ENST00000330684.3:c.2816G>A	p.Gly939Glu	p.G939E	ENST00000330684	NM_001134407.1	939	gGg/gAg	13/13	1	2	FACETS	0.919	0.857	0.982	0.919	0.857	0.982	CLONAL	1	TRUE	1	0.692477772167446	2		396	657	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916195	9916195	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	137	540	0	ENST00000330684.3:c.2094T>A	p.Tyr698Ter	p.Y698*	ENST00000330684	NM_001134407.1	698	taT/taA	10/13	1	2	FACETS	0.535	0.487	0.585	0.535	0.487	0.585	SUBCLONAL	1	TRUE	1	0.692477772167446	2		540	740	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943770	9943770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	98	543	0	ENST00000330684.3:c.1171C>T	p.Pro391Ser	p.P391S	ENST00000330684	NM_001134407.1	391	Ccc/Tcc	5/13	1	2	FACETS	0.38	0.339	0.424	0.38	0.339	0.424	SUBCLONAL	1	TRUE	1	0.692477772167446	2		543	744	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132644	67132644	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	228	675	0	ENST00000412916.2:c.527C>T	p.Ser176Phe	p.S176F	ENST00000412916		176	tCc/tTc	6/6	1	2	FACETS	0.91	0.851	0.969	0.91	0.851	0.969	CLONAL	1	TRUE	1	0.692477772167446	2		675	724	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993063	72993063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	197	788	1	ENST00000268489.5:c.982G>A	p.Gly328Arg	p.G328R	ENST00000268489	NM_006885.3	328	Ggg/Agg	2/10	1	2	FACETS	0.499	0.461	0.538	0.499	0.461	0.538	SUBCLONAL	1	TRUE	1	0.692477772167446	2		789	1141	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942153	81942153	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	314	576	0	ENST00000359376.3:c.1690C>T	p.Arg564Trp	p.R564W	ENST00000359376	NM_002661.3	564	Cgg/Tgg	17/33	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.692477772167446	2		576	907	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984783	11984783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	97	515	0	ENST00000353533.5:c.329G>A	p.Arg110Gln	p.R110Q	ENST00000353533	NM_003010.3	110	cGa/cAa	3/11	0.692477772167446	1	FACETS	0.328	0.293	0.365	0.328	0.293	0.365	SUBCLONAL	1	TRUE	0	0.692477772167446	1		515	558	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559101	29559101	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202023	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	78	117	0	ENST00000356175.3:c.3208C>T	p.Gln1070Ter	p.Q1070*	ENST00000356175	NM_000267.3	1070	Cag/Tag	25/57	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.692477772167446	2		117	195	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661898	29661898	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567615766	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	114	595	0	ENST00000356175.3:c.5792G>A	p.Trp1931Ter	p.W1931*	ENST00000356175	NM_000267.3	1931	tGg/tAg	39/57	1	2	FACETS	0.524	0.473	0.578	0.524	0.473	0.578	SUBCLONAL	1	TRUE	1	0.692477772167446	2		595	628	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40376862	40376862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	221	671	0	ENST00000293328.3:c.310G>A	p.Glu104Lys	p.E104K	ENST00000293328	NM_012448.3	104	Gag/Aag	4/19	1	2	FACETS	0.48	0.445	0.516	0.48	0.445	0.516	SUBCLONAL	1	TRUE	1	0.692477772167446	2		671	1330	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435465	56435465	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	375	656	0	ENST00000407977.2:c.1672T>C	p.Tyr558His	p.Y558H	ENST00000407977		558	Tac/Cac	9/10	0.394798305144217	3	FACETS	1	0.993	1	0.635	0.603	0.667	INDETERMINATE	1	TRUE	1	0.692477772167446	3		656	1148	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763256	59763256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	266	673	0	ENST00000259008.2:c.2846C>T	p.Pro949Leu	p.P949L	ENST00000259008	NM_032043.2	949	cCt/cTt	19/20	0.394798305144217	3	FACETS	1	0.988	1	0.603	0.566	0.64	INDETERMINATE	1	TRUE	1	0.692477772167446	3		673	858	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007630	62007630	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	368	636	0	ENST00000392795.3:c.237G>A	p.Trp79Ter	p.W79*	ENST00000392795	NM_001039933.1	79	tgG/tgA	3/6	0.443840936870822	1	FACETS	0.867	0.828	0.907	0.867	0.828	0.907	CLONAL	1	TRUE	0	0.692477772167446	1		636	801	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223138	5223139	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	177	643	2	ENST00000357368.4:c.2664_2665delinsTT	p.Arg889Cys	p.R889C	ENST00000357368	NM_002850.3	888	gaCCgc/gaTTgc	18/38	1	2	FACETS	0.542	0.499	0.587	0.542	0.499	0.587	SUBCLONAL	1	TRUE	1	0.692477772167446	2		645	943	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117417	7117417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	117	519	0	ENST00000302850.5:c.3799G>A	p.Asp1267Asn	p.D1267N	ENST00000302850	NM_000208.2	1267	Gac/Aac	22/22	1	2	FACETS	0.48	0.433	0.529	0.48	0.433	0.529	SUBCLONAL	1	TRUE	1	0.692477772167446	2		519	704	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285120	15285120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	147	620	0	ENST00000263388.2:c.4495G>A	p.Asp1499Asn	p.D1499N	ENST00000263388	NM_000435.2	1499	Gat/Aat	25/33	1	2	FACETS	0.45	0.411	0.492	0.45	0.411	0.492	SUBCLONAL	1	TRUE	1	0.692477772167446	2		620	943	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379868	17379868	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765555081	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	411	772	0	ENST00000359435.4:c.253C>T	p.Arg85Trp	p.R85W	ENST00000359435	NM_001033549.1	85	Cgg/Tgg	2/9	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.692477772167446	2		772	1164	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260070	19260070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	188	596	1	ENST00000162023.5:c.223C>T	p.Pro75Ser	p.P75S	ENST00000162023		75	Ccc/Tcc	7/13	1	2	FACETS	0.476	0.439	0.515	0.476	0.439	0.515	SUBCLONAL	1	TRUE	1	0.692477772167446	2		597	1140	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228148	36228148	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	362	617	0	ENST00000222270.7:c.7534G>T	p.Ala2512Ser	p.A2512S	ENST00000222270	NM_014727.1	2512	Gca/Tca	33/37	1	2	FACETS	0.999	0.949	1	0.999	0.949	1	CLONAL	1	TRUE	1	0.692477772167446	2		617	1047	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727080	41727080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	373	631	0	ENST00000301178.4:c.338G>A	p.Gly113Glu	p.G113E	ENST00000301178	NM_021913.4	113	gGa/gAa	3/20	1	2	FACETS	0.963	0.915	1	0.963	0.915	1	CLONAL	1	TRUE	1	0.692477772167446	2		631	1119	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754689	41754689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349708742	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	366	665	0	ENST00000301178.4:c.1675G>A	p.Asp559Asn	p.D559N	ENST00000301178	NM_021913.4	559	Gac/Aac	14/20	1	2	FACETS	0.957	0.909	1	0.957	0.909	1	CLONAL	1	TRUE	1	0.692477772167446	2		665	1104	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796595	42796595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	139	558	0	ENST00000575354.2:c.3152C>T	p.Ala1051Val	p.A1051V	ENST00000575354	NM_015125.3	1051	gCc/gTc	13/20	1	2	FACETS	0.531	0.484	0.581	0.531	0.484	0.581	SUBCLONAL	1	TRUE	1	0.692477772167446	2		558	756	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856357	45856358	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	343	695	0	ENST00000391945.4:c.1814_1815delinsTT	p.Ser605Phe	p.S605F	ENST00000391945	NM_000400.3	605	tCC/tTT	19/23	1	2	FACETS	0.997	0.945	1	0.997	0.945	1	CLONAL	1	TRUE	1	0.692477772167446	2		695	994	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910249	50910249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777866589	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	139	562	0	ENST00000440232.2:c.1504G>A	p.Asp502Asn	p.D502N	ENST00000440232	NM_002691.3	502	Gac/Aac	13/27	1	2	FACETS	0.462	0.42	0.506	0.462	0.42	0.506	SUBCLONAL	1	TRUE	1	0.692477772167446	2		562	869	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910288	50910288	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1169141963	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	320	614	0	ENST00000440232.2:c.1543G>A	p.Asp515Asn	p.D515N	ENST00000440232	NM_002691.3	515	Gat/Aat	13/27	1	2	FACETS	0.923	0.873	0.974	0.923	0.873	0.974	CLONAL	1	TRUE	1	0.692477772167446	2		614	1001	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707861	47707861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	28	460	0	ENST00000233146.2:c.2485C>T	p.His829Tyr	p.H829Y	ENST00000233146	NM_000251.2	829	Cat/Tat	15/16	0.337191029691753	2	FACETS	0.149	0.118	0.184	0.074	0.059	0.092	INDETERMINATE	1	TRUE	0	0.692477772167446	2		460	544	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158637104	158637104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377197386	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	405	593	0	ENST00000263640.3:c.76C>T	p.Pro26Ser	p.P26S	ENST00000263640	NM_001105.4	26	Ccc/Tcc	4/11	0.337191029691753	2	FACETS	1	0.996	1	0.699	0.669	0.729	INDETERMINATE	1	TRUE	0	0.692477772167446	2		593	837	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131271	202131271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	132	571	0	ENST00000358485.4:c.239C>T	p.Ser80Phe	p.S80F	ENST00000358485	NM_001080125.1	80	tCc/tTc	2/9	0.337191029691753	2	FACETS	0.44	0.399	0.483	0.22	0.199	0.242	INDETERMINATE	1	TRUE	0	0.692477772167446	2		571	866	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	214	265	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.337191029691753	2	FACETS	1	0.993	1	0.729	0.687	0.771	INDETERMINATE	1	TRUE	0	0.692477772167446	2		265	424	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248617	212248617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765120252	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	107	708	1	ENST00000342788.4:c.3650G>A	p.Gly1217Glu	p.G1217E	ENST00000342788	NM_005235.2	1217	gGa/gAa	28/28	0.337191029691753	2	FACETS	0.394	0.353	0.438	0.197	0.176	0.219	INDETERMINATE	1	TRUE	0	0.692477772167446	2		709	784	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212522511	212522511	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879054297	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	83	505	0	ENST00000342788.4:c.1914G>A	p.Trp638Ter	p.W638*	ENST00000342788	NM_005235.2	638	tgG/tgA	16/28	0.337191029691753	2	FACETS	0.347	0.306	0.391	0.174	0.153	0.196	INDETERMINATE	1	TRUE	0	0.692477772167446	2		505	690	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439721	220439721	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	554	654	0	ENST00000243786.2:c.574C>T	p.Pro192Ser	p.P192S	ENST00000243786	NM_002191.3	192	Ccc/Tcc	2/2	0.337191029691753	2	FACETS	0.82	0.792	0.847	0.82	0.792	0.847	INDETERMINATE	2	TRUE	0	0.692477772167446	2		654	976	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242800938	242800938	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	184	666	1	ENST00000334409.5:c.53G>A	p.Gly18Asp	p.G18D	ENST00000334409	NM_005018.2	18	gGc/gAc	1/5	0.337191029691753	2	FACETS	0.602	0.556	0.65	0.301	0.278	0.325	INDETERMINATE	1	TRUE	0	0.692477772167446	2		667	883	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770629	40770629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	121	439	0	ENST00000373198.4:c.2753G>A	p.Gly918Glu	p.G918E	ENST00000373198	NM_133170.3	918	gGg/gAg	19/32	1	2	FACETS	0.515	0.466	0.567	0.515	0.466	0.567	SUBCLONAL	1	TRUE	1	0.692477772167446	2		439	678	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827958	40827958	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs200990749	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	140	572	1	ENST00000373198.4:c.2470G>T	p.Asp824Tyr	p.D824Y	ENST00000373198	NM_133170.3	824	Gac/Tac	17/32	1	2	FACETS	0.494	0.45	0.541	0.494	0.45	0.541	SUBCLONAL	1	TRUE	1	0.692477772167446	2		573	818	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656977	45656977	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	136	694	0	ENST00000407780.3:c.179A>C	p.Lys60Thr	p.K60T	ENST00000407780	NM_001283052.1	60	aAa/aCa	3/7	1	2	FACETS	0.377	0.342	0.414	0.377	0.342	0.414	SUBCLONAL	1	TRUE	1	0.692477772167446	2		694	1041	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715633	30715633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	83	393	0	ENST00000295754.5:c.1291G>A	p.Glu431Lys	p.E431K	ENST00000295754	NM_003242.5	431	Gaa/Aaa	5/7	1	2	FACETS	0.457	0.404	0.513	0.457	0.404	0.513	SUBCLONAL	1	TRUE	1	0.692477772167446	2		393	525	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468397	89468398	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1467832547	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	153	362	1	ENST00000336596.2:c.1938dup	p.Glu647ArgfsTer7	p.E647Rfs*7	ENST00000336596	NM_005233.5	644	tca/tcAa	11/17	1	2	FACETS	0.917	0.845	0.99	0.917	0.845	0.99	CLONAL	1	TRUE	1	0.692477772167446	2		363	482	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205104	128205104	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	311	665	0	ENST00000341105.2:c.337C>T	p.His113Tyr	p.H113Y	ENST00000341105	NM_032638.4	113	Cac/Tac	3/6	0.692477772167446	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.692477772167446	1		665	576	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277609	142277609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs983647070	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	193	492	1	ENST00000350721.4:c.1742C>T	p.Ser581Leu	p.S581L	ENST00000350721	NM_001184.3	581	tCa/tTa	8/47	0.692477772167446	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.692477772167446	1		493	336	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807180	1807180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1319246268	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	136	669	0	ENST00000260795.2:c.1511C>T	p.Thr504Ile	p.T504I	ENST00000260795		504	aCc/aTc	10/17	1	2	FACETS	0.401	0.364	0.44	0.401	0.364	0.44	SUBCLONAL	1	TRUE	1	0.692477772167446	2		669	980	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808928	1808928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	158	670	0	ENST00000260795.2:c.2360C>T	p.Ser787Phe	p.S787F	ENST00000260795		787	tCc/tTc	17/17	1	2	FACETS	0.474	0.434	0.516	0.474	0.434	0.516	SUBCLONAL	1	TRUE	1	0.692477772167446	2		670	962	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902511	1902511	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	452	621	0	ENST00000382891.5:c.130T>G	p.Cys44Gly	p.C44G	ENST00000382891	NM_133335.3	44	Tgt/Ggt	2/22	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.692477772167446	2		621	1091	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750615	41750615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	214	519	0	ENST00000226382.2:c.13G>A	p.Glu5Lys	p.E5K	ENST00000226382	NM_003924.3	5	Gaa/Aaa	1/3	1	2	FACETS	0.904	0.844	0.965	0.904	0.844	0.965	CLONAL	1	TRUE	1	0.692477772167446	2		519	684	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55960968	55960968	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	205	432	0	ENST00000263923.4:c.2971+1G>A		p.X991_splice	ENST00000263923	NM_002253.2	991			1	2	FACETS	0.937	0.874	1	0.937	0.874	1	CLONAL	1	TRUE	1	0.692477772167446	2		432	632	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979555	55979555	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	358	670	0	ENST00000263923.4:c.892A>G	p.Thr298Ala	p.T298A	ENST00000263923	NM_002253.2	298	Acc/Gcc	7/30	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.692477772167446	2		670	960	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156493	106156493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	266	530	0	ENST00000380013.4:c.1394C>T	p.Pro465Leu	p.P465L	ENST00000380013	NM_001127208.2	465	cCa/cTa	3/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.692477772167446	2		530	718	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157401	106157401	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1396808968	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	105	559	0	ENST00000380013.4:c.2302G>A	p.Asp768Asn	p.D768N	ENST00000380013	NM_001127208.2	768	Gat/Aat	3/11	1	2	FACETS	0.477	0.428	0.529	0.477	0.428	0.529	SUBCLONAL	1	TRUE	1	0.692477772167446	2		559	636	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525056	187525056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	285	648	0	ENST00000441802.2:c.10624C>T	p.Pro3542Ser	p.P3542S	ENST00000441802	NM_005245.3	3542	Ccg/Tcg	19/27	1	2	FACETS	0.994	0.938	1	0.994	0.938	1	CLONAL	1	TRUE	1	0.692477772167446	2		648	828	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542540	187542540	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	237	659	0	ENST00000441802.2:c.5200A>T	p.Thr1734Ser	p.T1734S	ENST00000441802	NM_005245.3	1734	Aca/Tca	10/27	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.692477772167446	2		659	660	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629247	187629247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	346	716	0	ENST00000441802.2:c.1735C>T	p.Pro579Ser	p.P579S	ENST00000441802	NM_005245.3	579	Ccc/Tcc	2/27	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.692477772167446	2		716	979	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875669	35875669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	112	471	2	ENST00000303115.3:c.856C>T	p.Leu286Phe	p.L286F	ENST00000303115	NM_002185.3	286	Ctt/Ttt	7/8	0.364682953329218	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.692477772167446	0		473	454	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174806	56174806	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	126	374	1	ENST00000399503.3:c.1966-1G>T		p.X656_splice	ENST00000399503	NM_005921.1	656			0.364682953329218	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.692477772167446	0		375	391	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750426	57750426	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	188	559	0	ENST00000274289.3:c.2042T>C	p.Leu681Ser	p.L681S	ENST00000274289	NM_006622.3	681	tTa/tCa	14/14	0.364682953329218	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.692477772167446	0		559	543	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80063759	80063759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769417932	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	74	476	0	ENST00000265081.6:c.1904C>T	p.Thr635Ile	p.T635I	ENST00000265081	NM_002439.4	635	aCc/aTc	14/24	0.364682953329218	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.692477772167446	0		476	363	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517792	176517793	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	129	695	0	ENST00000292408.4:c.402_403delinsAA	p.Asp135Asn	p.D135N	ENST00000292408	NM_213647.1	134	agGGac/agAAac	4/18	0.364682953329218	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.692477772167446	0		695	673	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181943	32181943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	442	615	0	ENST00000375023.3:c.2111G>A	p.Gly704Glu	p.G704E	ENST00000375023	NM_004557.3	704	gGg/gAg	13/30	0.19320755869464	3	FACETS	0.802	0.767	0.837	0.802	0.767	0.837	INDETERMINATE	2	TRUE	1	0.692477772167446	3		615	1072	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188871	32188871	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773548435	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	197	649	0	ENST00000375023.3:c.683G>A	p.Gly228Asp	p.G228D	ENST00000375023	NM_004557.3	228	gGt/gAt	4/30	0.19320755869464	3	FACETS	0.877	0.813	0.944	0.439	0.406	0.472	INDETERMINATE	1	TRUE	1	0.692477772167446	3		649	873	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140842	37140842	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	331	576	0	ENST00000373509.5:c.678G>A	p.Trp226Ter	p.W226*	ENST00000373509	NM_002648.3	226	tgG/tgA	5/6	0.19320755869464	3	FACETS	1	0.991	1	0.612	0.579	0.645	INDETERMINATE	1	TRUE	1	0.692477772167446	3		576	1052	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964510	93964510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1435219791	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	66	435	1	ENST00000369303.4:c.2387G>A	p.Gly796Glu	p.G796E	ENST00000369303	NM_004440.3	796	gGa/gAa	14/17	0.19320755869464	3	FACETS	0.532	0.463	0.607	0.266	0.231	0.304	INDETERMINATE	1	TRUE	1	0.692477772167446	3		436	482	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630083	117630083	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	74	410	0	ENST00000368508.3:c.6443G>A	p.Gly2148Glu	p.G2148E	ENST00000368508	NM_002944.2	2148	gGa/gAa	41/43	0.19320755869464	3	FACETS	0.566	0.497	0.641	0.283	0.248	0.321	INDETERMINATE	1	TRUE	1	0.692477772167446	3		410	508	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631404	117631404	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	255	467	1	ENST00000368508.3:c.6274T>A	p.Tyr2092Asn	p.Y2092N	ENST00000368508	NM_002944.2	2092	Tat/Aat	40/43	0.19320755869464	3	FACETS	0.772	0.728	0.817	0.772	0.728	0.817	INDETERMINATE	2	TRUE	1	0.692477772167446	3		468	642	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710875	117710875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140178288	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	147	546	1	ENST00000368508.3:c.1397G>A	p.Arg466Gln	p.R466Q	ENST00000368508	NM_002944.2	466	cGa/cAa	12/43	0.19320755869464	3	FACETS	0.662	0.605	0.723	0.331	0.302	0.362	INDETERMINATE	1	TRUE	1	0.692477772167446	3		547	863	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420006	152420006	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	388	597	0	ENST00000206249.3:c.1693C>T	p.Gln565Ter	p.Q565*	ENST00000206249	NM_000125.3	565	Caa/Taa	8/8	0.19320755869464	3	FACETS	0.769	0.733	0.805	0.769	0.733	0.805	INDETERMINATE	2	TRUE	1	0.692477772167446	3		597	981	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683648	162683666	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGTCCACCCGAGTCAAG	GAGGTCCACCCGAGTCAAG	-	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	292	530	0	ENST00000366898.1:c.303_321del	p.Ser101ArgfsTer70	p.S101Rfs*70	ENST00000366898	NM_004562.2	101	agCTTGACTCGGGTGGACCTC/ag	3/12	0.19320755869464	3	FACETS	0.758	0.717	0.799	0.758	0.717	0.799	INDETERMINATE	2	TRUE	1	0.692477772167446	3		530	749	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519874	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	192	522	1	ENST00000356142.4:c.85C>A	p.Pro29Thr	p.P29T	ENST00000356142	NM_018890.3	29	Cct/Act	2/7	0.19320755869464	3	FACETS	0.908	0.841	0.977	0.454	0.42	0.489	INDETERMINATE	1	TRUE	1	0.692477772167446	3		523	822	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935653	13935653	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	322	560	0	ENST00000405192.2:c.1203G>T	p.Met401Ile	p.M401I	ENST00000405192	NM_001163147.1	401	atG/atT	12/12	0.19320755869464	3	FACETS	1	0.994	1	0.696	0.66	0.734	INDETERMINATE	1	TRUE	1	0.692477772167446	3		560	899	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221771	55221771	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	316	635	0	ENST00000275493.2:c.815C>T	p.Pro272Leu	p.P272L	ENST00000275493	NM_005228.3	272	cCc/cTc	7/28	0.19320755869464	3	FACETS	1	0.985	1	0.561	0.529	0.593	INDETERMINATE	1	TRUE	1	0.692477772167446	3		635	1096	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873848	151873848	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199939847	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	117	584	0	ENST00000262189.6:c.8690C>T	p.Ser2897Phe	p.S2897F	ENST00000262189	NM_170606.2	2897	tCc/tTc	38/59	0.19320755869464	3	FACETS	0.56	0.504	0.618	0.28	0.252	0.309	INDETERMINATE	1	TRUE	1	0.692477772167446	3		584	813	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972963	68972963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142510968	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	115	516	0	ENST00000288368.4:c.1288G>A	p.Glu430Lys	p.E430K	ENST00000288368	NM_024870.2	430	Gaa/Aaa	11/40	0.692477772167446	1	FACETS	0.374	0.337	0.412	0.374	0.337	0.412	SUBCLONAL	1	TRUE	0	0.692477772167446	1		516	581	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031679	69031679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1294114324	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	225	527	1	ENST00000288368.4:c.3434C>T	p.Pro1145Leu	p.P1145L	ENST00000288368	NM_024870.2	1145	cCc/cTc	28/40	0.692477772167446	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.692477772167446	1		528	421	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123114	5123114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	95	484	0	ENST00000381652.3:c.3170C>T	p.Pro1057Leu	p.P1057L	ENST00000381652	NM_004972.3	1057	cCa/cTa	23/25	0.364682953329218	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.692477772167446	0		484	460	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436605	8436605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201031030	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	92	600	0	ENST00000356435.5:c.4073C>T	p.Ser1358Phe	p.S1358F	ENST00000356435		1358	tCc/tTc	24/35	0.364682953329218	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.692477772167446	0		600	369	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499707	8499707	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	213	628	0	ENST00000356435.5:c.2262G>A	p.Met754Ile	p.M754I	ENST00000356435		754	atG/atA	14/35	0.364682953329218	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.692477772167446	0		628	657	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507320	8507321	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	54	471	1	ENST00000356435.5:c.1657_1658delinsAT	p.Asp553Ile	p.D553I	ENST00000356435		553	GAt/ATt	11/35	0.364682953329218	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.692477772167446	0		472	375	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169486	27169486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	55	520	0	ENST00000380036.4:c.487C>T	p.His163Tyr	p.H163Y	ENST00000380036	NM_000459.3	163	Cat/Tat	4/23	0.364682953329218	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.692477772167446	0		520	507	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27206766	27206766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	206	609	1	ENST00000380036.4:c.2551G>A	p.Asp851Asn	p.D851N	ENST00000380036	NM_000459.3	851	Gat/Aat	15/23	0.364682953329218	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.692477772167446	0		610	604	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27209136	27209136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	106	629	0	ENST00000380036.4:c.2593G>A	p.Asp865Asn	p.D865N	ENST00000380036	NM_000459.3	865	Gat/Aat	16/23	0.364682953329218	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.692477772167446	0		629	583	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27217711	27217711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	153	617	1	ENST00000380036.4:c.3017C>T	p.Ala1006Val	p.A1006V	ENST00000380036	NM_000459.3	1006	gCc/gTc	19/23	0.364682953329218	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.692477772167446	0		618	724	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641056	93641056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	57	484	0	ENST00000375746.1:c.1402G>A	p.Asp468Asn	p.D468N	ENST00000375746	NM_001174167.1	468	Gat/Aat	11/14	0.364682953329218	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.692477772167446	0		484	456	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915935	127915935	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	198	570	0	ENST00000373547.4:c.546T>G	p.Asn182Lys	p.N182K	ENST00000373547	NM_002721.4	182	aaT/aaG	6/7	0.364682953329218	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.692477772167446	0		570	644	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738198	133738198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	253	525	0	ENST00000318560.5:c.598C>T	p.His200Tyr	p.H200Y	ENST00000318560	NM_005157.4	200	Cat/Tat	4/11	0.364682953329218	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.692477772167446	0		525	683	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566484	139566484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	90	684	0	ENST00000308874.7:c.743G>A	p.Gly248Asp	p.G248D	ENST00000308874		248	gGc/gAc	9/10	0.364682953329218	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.692477772167446	0		684	671	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933076	39933076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773646449	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	205	369	0	ENST00000378444.4:c.1523C>T	p.Ser508Phe	p.S508F	ENST00000378444	NM_001123385.1	508	tCc/tTc	4/15	1	1	FACETS	0.64	0.597	0.684	0.64	0.597	0.684	SUBCLONAL	1	TRUE	0	0.692477772167446	1		369	605	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224261	36224262	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	T	novel	NA	P-0030290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	285	607	0	ENST00000222270.7:c.6811_6812delinsT	p.Pro2271CysfsTer54	p.P2271Cfs*54	ENST00000222270	NM_014727.1	2271	CCg/Tg	28/37	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.692477772167446	2		607	803	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0030388-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	98	1058	3	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.903	0.814	0.995	0.903	0.814	0.995	CLONAL	1	TRUE	1	0.663928187568892	2		1061	327	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0030490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	307	578	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.55279578307608	2		578	1065	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156740	20156740	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	127	167	0	ENST00000379607.5:c.17G>A	p.Gly6Asp	p.G6D	ENST00000379607	NM_001412.3	6	gGt/gAt	2/7	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.55279578307608	1		167	228	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366991	118366991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377588214	NA	P-0030490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	173	552	0	ENST00000534358.1:c.5573G>A	p.Arg1858Gln	p.R1858Q	ENST00000534358	NM_005933.3	1858	cGa/cAa	20/36	1	2	FACETS	0.951	0.879	1	0.951	0.879	1	CLONAL	1	TRUE	1	0.55279578307608	2		552	658	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0030646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	125	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.411930232253011	2		306	515	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0030646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	180	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.17519560581713	3	FACETS	1	0.99	1	0.743	0.687	0.801	INDETERMINATE	1	TRUE	1	0.411930232253011	3		288	709	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435604	149435604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	66	379	0	ENST00000286301.3:c.2539G>A	p.Glu847Lys	p.E847K	ENST00000286301	NM_005211.3	847	Gag/Aag	19/22	0.304976032579332	1	FACETS	0.46	0.4	0.526	0.46	0.4	0.526	SUBCLONAL	1	TRUE	0	0.411930232253011	1		379	553	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670708	134670708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	64	697	2	ENST00000398015.3:c.619C>T	p.Pro207Ser	p.P207S	ENST00000398015	NM_004441.4	207	Cca/Tca	3/16	1	2	FACETS	0.464	0.402	0.533	0.464	0.402	0.533	SUBCLONAL	1	TRUE	1	0.411930232253011	2		699	669	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686238	117686238	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs772772410	NA	P-0030646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	39	267	0	ENST00000368508.3:c.3103C>T	p.Arg1035Ter	p.R1035*	ENST00000368508	NM_002944.2	1035	Cga/Tga	20/43	0.411930232253011	1	FACETS	0.427	0.355	0.507	0.427	0.355	0.507	SUBCLONAL	1	TRUE	0	0.411930232253011	1		267	352	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566453	41566453	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1225	105	319	0	ENST00000263253.7:c.4330G>A	p.Asp1444Asn	p.D1444N	ENST00000263253	NM_001429.3	1444	Gat/Aat	27/31	0.411930232253011	7	FACETS	0.778	0.695	0.867			1	SUBCLONAL	1	TRUE	NA	0.411930232253011	7		319	1330	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609111	43609111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767402	NA	P-0030646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	186	571	1	ENST00000355710.3:c.1867G>A	p.Glu623Lys	p.E623K	ENST00000355710	NM_020975.4	623	Gaa/Aaa	10/20	1	2	FACETS	0.963	0.889	1	0.963	0.889	1	CLONAL	1	TRUE	1	0.411930232253011	2		572	938	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716366	18716366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs935135637	NA	P-0030646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	102	757	0	ENST00000266497.5:c.3713C>T	p.Ser1238Leu	p.S1238L	ENST00000266497		1238	tCa/tTa	26/31	1	2	FACETS	0.819	0.734	0.908	0.819	0.734	0.908	CLONAL	1	TRUE	1	0.411930232253011	2		757	605	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644451	18644451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	48	750	1	ENST00000266497.5:c.2629C>T	p.Pro877Ser	p.P877S	ENST00000266497		877	Cct/Tct	18/31	1	2	FACETS	0.369	0.312	0.433	0.369	0.312	0.433	SUBCLONAL	1	TRUE	1	0.411930232253011	2		751	631	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31486624	31486624	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	106	378	0	ENST00000344624.3:c.1888C>T	p.His630Tyr	p.H630Y	ENST00000344624		630	Cat/Tat	11/33	1	2	FACETS	0.826	0.742	0.915	0.826	0.742	0.915	CLONAL	1	TRUE	1	0.411930232253011	2		378	623	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156703	55156703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	101	301	0	ENST00000257290.5:c.3104G>A	p.Gly1035Asp	p.G1035D	ENST00000257290	NM_006206.4	1035	gGc/gAc	22/23	1	2	FACETS	0.918	0.824	1	0.918	0.824	1	CLONAL	1	TRUE	1	0.411930232253011	2		301	534	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727072	40727072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	56	383	1	ENST00000373198.4:c.3892G>A	p.Asp1298Asn	p.D1298N	ENST00000373198	NM_133170.3	1298	Gac/Aac	28/32	1	2	FACETS	0.471	0.403	0.545	0.471	0.403	0.545	SUBCLONAL	1	TRUE	1	0.411930232253011	2		384	577	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771499	112771499	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1016085845	NA	P-0030646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	63	436	1	ENST00000369452.4:c.1672C>T	p.Pro558Ser	p.P558S	ENST00000369452	NM_007373.3	558	Cct/Tct	9/9	1	2	FACETS	0.454	0.393	0.522	0.454	0.393	0.522	SUBCLONAL	1	TRUE	1	0.411930232253011	2		437	673	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871789	35871789	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	105	386	0	ENST00000216797.5:c.717T>G	p.Cys239Trp	p.C239W	ENST00000216797	NM_020529.2	239	tgT/tgG	5/6	1	2	FACETS	0.72	0.645	0.799	0.72	0.645	0.799	SUBCLONAL	1	TRUE	1	0.411930232253011	2		386	708	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350794	15350794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	214	608	1	ENST00000263377.2:c.3209C>T	p.Ser1070Phe	p.S1070F	ENST00000263377	NM_058243.2	1070	tCc/tTc	15/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.411930232253011	2		609	925	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793424	42793424	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	51	357	0	ENST00000575354.2:c.1226C>T	p.Ala409Val	p.A409V	ENST00000575354	NM_015125.3	409	gCc/gTc	8/20	1	2	FACETS	0.396	0.336	0.462	0.396	0.336	0.462	SUBCLONAL	1	TRUE	1	0.411930232253011	2		357	625	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855574	45855574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201392911	NA	P-0030646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	103	504	0	ENST00000391945.4:c.2083C>T	p.Arg695Cys	p.R695C	ENST00000391945	NM_000400.3	695	Cgc/Tgc	22/23	1	2	FACETS	0.584	0.522	0.65	0.584	0.522	0.65	SUBCLONAL	1	TRUE	1	0.411930232253011	2		504	856	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249758	39249758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	44	355	0	ENST00000402219.2:c.1811G>A	p.Gly604Glu	p.G604E	ENST00000402219	NM_005633.3	604	gGa/gAa	10/23	1	2	FACETS	0.368	0.308	0.434	0.368	0.308	0.434	SUBCLONAL	1	TRUE	1	0.411930232253011	2		355	581	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285165	212285165	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0030646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	50	243	0	ENST00000342788.4:c.3135+1G>A		p.X1045_splice	ENST00000342788	NM_005235.2	1045			1	2	FACETS	0.557	0.473	0.648	0.557	0.473	0.648	SUBCLONAL	1	TRUE	1	0.411930232253011	2		243	436	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566445	41566445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1221	99	320	0	ENST00000263253.7:c.4322G>A	p.Ser1441Asn	p.S1441N	ENST00000263253	NM_001429.3	1441	aGt/aAt	27/31	0.411930232253011	7	FACETS	0.739	0.657	0.827			1	SUBCLONAL	1	TRUE	NA	0.411930232253011	7		320	1320	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566491	41566491	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1222	108	317	0	ENST00000263253.7:c.4368G>C	p.Lys1456Asn	p.K1456N	ENST00000263253	NM_001429.3	1456	aaG/aaC	27/31	0.411930232253011	7	FACETS	0.8	0.716	0.891			1	SUBCLONAL	1	TRUE	NA	0.411930232253011	7		317	1330	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650749	12650750	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0030646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	49	500	0	ENST00000251849.4:c.405_406delinsTT	p.Leu136Phe	p.L136F	ENST00000251849	NM_002880.3	135	ccCCtc/ccTTtc	4/17	1	2	FACETS	0.329	0.278	0.386	0.329	0.278	0.386	SUBCLONAL	1	TRUE	1	0.411930232253011	2		500	723	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508439	106508439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	79	138	0	ENST00000359195.3:c.433G>A	p.Glu145Lys	p.E145K	ENST00000359195	NM_002649.2	145	Gag/Aag	2/11	0.17519560581713	3	FACETS	1	0.978	1	0.744	0.66	0.831	INDETERMINATE	1	TRUE	1	0.411930232253011	3		138	311	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964419	70964419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1254551312	NA	P-0030646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	34	327	0	ENST00000276594.2:c.1609C>T	p.Arg537Trp	p.R537W	ENST00000276594	NM_024504.3	537	Cgg/Tgg	8/8	1	2	FACETS	0.286	0.233	0.345	0.286	0.233	0.345	SUBCLONAL	1	TRUE	1	0.411930232253011	2		327	578	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518429	8518429	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs995119754	NA	P-0030646-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	58	153	0	ENST00000356435.5:c.962C>T	p.Ala321Val	p.A321V	ENST00000356435		321	gCc/gTc	10/35	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.411930232253011	2		153	260	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0030729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	1244	527	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.6850179241302	6	FACETS	0.977	0.958	0.995			1	CLONAL	5	TRUE	NA	0.6850179241302	6		527	1763	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061208	38061208	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1292426539	NA	P-0030729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	199	490	0	ENST00000250448.2:c.781C>G	p.Arg261Gly	p.R261G	ENST00000250448	NM_004496.3	261	Cgc/Ggc	2/2	1	2	FACETS	0.945	0.88	1	0.945	0.88	1	CLONAL	1	TRUE	1	0.6850179241302	2		490	615	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139873	55139873	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs866988382	NA	P-0030729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	180	427	0	ENST00000257290.5:c.1534C>T	p.Arg512Ter	p.R512*	ENST00000257290	NM_006206.4	512	Cga/Tga	10/23	1	2	FACETS	0.966	0.897	1	0.966	0.897	1	CLONAL	1	TRUE	1	0.6850179241302	2		427	544	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176105675	176105675	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	171	384	0	ENST00000367669.3:c.840A>C	p.Glu280Asp	p.E280D	ENST00000367669	NM_022457.5	280	gaA/gaC	7/20	0.664309705509973	4	FACETS	1	0.934	1	0.339	0.312	0.367	CLONAL	1	TRUE	1	0.6850179241302	4		384	828	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853186	68853186	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0030729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	223	464	0	ENST00000261769.5:c.1569T>G	p.Tyr523Ter	p.Y523*	ENST00000261769	NM_004360.3	523	taT/taG	11/16	0.6850179241302	1	FACETS	0.909	0.857	0.961	0.909	0.857	0.961	CLONAL	1	TRUE	0	0.6850179241302	1		464	471	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120227	70120236	+	frameshift_variant	Frame_Shift_Del	DEL	AGCAGCAGCA	AGCAGCAGCA	-	novel	NA	P-0030729-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	266	602	0	ENST00000245479.2:c.1229_1238del	p.Gln410ProfsTer57	p.Q410Pfs*57	ENST00000245479	NM_000346.3	410	cAGCAGCAGCAc/cc	3/3	0.6850179241302	3	FACETS	0.915	0.857	0.974	0.457	0.428	0.487	CLONAL	1	TRUE	1	0.6850179241302	3		602	1140	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0030785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	275	393	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.624391518281408	2		393	864	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159749	20159749	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	249	291	0	ENST00000379607.5:c.10A>T	p.Asn4Tyr	p.N4Y	ENST00000379607	NM_001412.3	4	Aat/Tat	1/7	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.624391518281408	1		291	386	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441188	52441188	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0030785-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	111	268	0	ENST00000460680.1:c.580+2T>G		p.X194_splice	ENST00000460680	NM_004656.3	194			0.624391518281408	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.624391518281408	1		268	236	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0030804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	556	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.673044236116028	3	FACETS	0.957	0.922	0.992	0.957	0.922	0.992	CLONAL	2	TRUE	1	0.673044236116028	3		288	1154	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	437	151	0				ENST00000310581	NM_198253.2	-/1132			0.673044236116028	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.673044236116028	3		151	830	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242427	55242427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	139	518	0	ENST00000275493.2:c.2197C>T	p.Pro733Ser	p.P733S	ENST00000275493	NM_005228.3	733	Cca/Tca	19/28	0.673044236116028	3	FACETS	0.478	0.434	0.524	0.239	0.217	0.262	SUBCLONAL	1	TRUE	1	0.673044236116028	3		518	1155	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36945039	36945039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	527	749	1	ENST00000361632.4:c.59C>T	p.Pro20Leu	p.P20L	ENST00000361632		20	cCc/cTc	2/16	0.321471447760907	3	FACETS	0.833	0.8	0.866	0.833	0.8	0.866	INDETERMINATE	2	TRUE	1	0.673044236116028	3		750	1257	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	258	326	0	ENST00000304494.5:c.143C>T	p.Pro48Leu	p.P48L	ENST00000304494	NM_000077.4	48	cCg/cTg	1/3	0.673044236116028	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.673044236116028	1		326	464	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451027	70451027	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	233	517	0	ENST00000373644.4:c.5867C>T	p.Pro1956Leu	p.P1956L	ENST00000373644	NM_030625.2	1956	cCa/cTa	12/12	0.673044236116028	1	FACETS	0.982	0.927	1	0.982	0.927	1	CLONAL	1	TRUE	0	0.673044236116028	1		517	468	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537975	212537975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267599192	NA	P-0030804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	198	362	1	ENST00000342788.4:c.1630C>T	p.Arg544Trp	p.R544W	ENST00000342788	NM_005235.2	544	Cgg/Tgg	14/28	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.673044236116028	2		363	576	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509236	106509236	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	331	595	0	ENST00000359195.3:c.1230G>A	p.Trp410Ter	p.W410*	ENST00000359195	NM_002649.2	410	tgG/tgA	2/11	0.673044236116028	3	FACETS	0.936	0.884	0.99	0.468	0.442	0.495	CLONAL	1	TRUE	1	0.673044236116028	3		595	1404	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18649003	18649003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	189	370	0	ENST00000266497.5:c.2678C>T	p.Ser893Leu	p.S893L	ENST00000266497		893	tCa/tTa	19/31	1	2	FACETS	0.835	0.774	0.896	0.835	0.774	0.896	CLONAL	1	TRUE	1	0.673044236116028	2		370	673	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931790	28931791	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	novel	NA	P-0030804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	225	391	1	ENST00000282397.4:c.2148_2149delinsAA	p.Phe717Ile	p.F717I	ENST00000282397	NM_002019.4	716	ctGTtt/ctAAtt	15/30	1	2	FACETS	0.922	0.862	0.984	0.922	0.862	0.984	CLONAL	1	TRUE	1	0.673044236116028	2		392	725	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748864	43748864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs951927958	NA	P-0030804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	408	678	0	ENST00000382044.4:c.1942G>A	p.Asp648Asn	p.D648N	ENST00000382044	NM_001141980.1	648	Gat/Aat	12/28	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.673044236116028	2		678	1169	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222427	2222427	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463511212	NA	P-0030804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	242	468	1	ENST00000398665.3:c.3259G>A	p.Gly1087Ser	p.G1087S	ENST00000398665	NM_032482.2	1087	Ggc/Agc	24/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.673044236116028	2		469	666	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31464384	31464384	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	928	815	0	ENST00000344624.3:c.2533C>T	p.Gln845Ter	p.Q845*	ENST00000344624		845	Caa/Taa	17/33	0.673044236116028	3	FACETS	0.977	0.949	1	0.977	0.949	1	CLONAL	2	TRUE	1	0.673044236116028	3		815	1887	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547383	106547383	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	250	387	0	ENST00000369096.4:c.620G>A	p.Arg207Lys	p.R207K	ENST00000369096	NM_001198.3	207	aGg/aAg	4/7	1	2	FACETS	0.976	0.917	1	0.976	0.917	1	CLONAL	1	TRUE	1	0.673044236116028	2		387	761	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148529795	148529795	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030804-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	523	458	0	ENST00000320356.2:c.294A>T	p.Leu98Phe	p.L98F	ENST00000320356	NM_004456.4	98	ttA/ttT	4/20	0.673044236116028	3	FACETS	0.954	0.918	0.99	0.954	0.918	0.99	CLONAL	2	TRUE	1	0.673044236116028	3		458	1089	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0030810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	225	359	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	0.673587505293499	3	FACETS	0.958	0.904	1	0.639	0.602	0.675	CLONAL	2	TRUE	0	0.673587505293499	3		359	466	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433837	49433837	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs375926448	NA	P-0030810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	254	859	0	ENST00000301067.7:c.7716G>C	p.Leu2572Phe	p.L2572F	ENST00000301067	NM_003482.3	2572	ttG/ttC	31/54	0.673587505293499	3	FACETS	0.907	0.848	0.967	0.453	0.424	0.484	CLONAL	1	TRUE	1	0.673587505293499	3		859	1112	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913250	NA	P-0030830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	247	364	0	ENST00000369535.4:c.34G>T	p.Gly12Cys	p.G12C	ENST00000369535	NM_002524.4	12	Ggt/Tgt	2/7	0.692031222294065	3	FACETS	0.898	0.848	0.948	0.898	0.848	0.948	CLONAL	2	TRUE	1	0.692031222294065	3		364	535	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165644	118165644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs538766512	NA	P-0030830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	111	347	0	ENST00000369448.3:c.154G>A	p.Val52Ile	p.V52I	ENST00000369448	NM_017709.3	52	Gtc/Atc	2/2	0.692031222294065	3	FACETS	0.879	0.795	0.968	0.44	0.397	0.484	CLONAL	1	TRUE	1	0.692031222294065	3		347	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0030834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	283	690	1	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.348171896574755	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.352398632834665	2		691	801	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398303	25398304	+	missense_variant	Missense_Mutation	DNP	GT	GT	TA	novel	NA	P-0030834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	148	399	1	ENST00000311936.3:c.15_16delinsTA	p.Lys5_Leu6delinsAsnIle	p.K5_L6delinsNI	ENST00000311936	NM_004985.3	5	aaACtt/aaTAtt	2/5	0.348171896574755	2	FACETS	0.805	0.739	0.872	0.805	0.739	0.872	CLONAL	2	TRUE	0	0.352398632834665	2		400	522	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975728	26975733	+	inframe_deletion	In_Frame_Del	DEL	CTCAGG	CTCAGG	-	novel	NA	P-0030834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	69	444	0	ENST00000381527.3:c.1236_1241del	p.Ser413_Gly414del	p.S413_G414del	ENST00000381527	NM_001260.1	412	acCTCAGGt/act	12/13	1	2	FACETS	0.769	0.671	0.875	0.769	0.671	0.875	SUBCLONAL	1	TRUE	1	0.352398632834665	2		444	509	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643566	38643578	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAATGTTAGGG	GAAAATGTTAGGG	-	novel	NA	P-0030834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	116	551	1	ENST00000299084.4:c.1044_1056del	p.Gly350MetfsTer52	p.G350Mfs*52	ENST00000299084	NM_152594.2	346	GAAAATGTTAGGGga/ga	7/7	0.352398632834665	1	FACETS	0.799	0.721	0.881	0.799	0.721	0.881	SUBCLONAL	1	TRUE	0	0.352398632834665	1		552	679	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945641	38945641	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	21	293	0	ENST00000357387.3:c.4585C>A	p.Leu1529Met	p.L1529M	ENST00000357387	NM_152756.3	1529	Ctg/Atg	34/38	0.282220778806993	1	FACETS	0.259	0.199	0.329	0.259	0.199	0.329	SUBCLONAL	1	TRUE	0	0.352398632834665	1		293	379	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486076	8486076	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	108	499	2	ENST00000356435.5:c.2741C>A	p.Pro914Gln	p.P914Q	ENST00000356435		914	cCa/cAa	17/35	0.352398632834665	1	FACETS	0.933	0.841	1	0.933	0.841	1	CLONAL	1	TRUE	0	0.352398632834665	1		501	541	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658326	18658326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560894742	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	204	373	0	ENST00000266497.5:c.3131C>T	p.Ser1044Leu	p.S1044L	ENST00000266497		1044	tCg/tTg	22/31	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.764627436009112	2		373	467	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210733	5210733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779302415	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	64	915	0	ENST00000357368.4:c.5318C>T	p.Ser1773Leu	p.S1773L	ENST00000357368	NM_002850.3	1773	tCg/tTg	34/38	1	2	FACETS	0.24	0.207	0.275	0.24	0.207	0.275	SUBCLONAL	1	TRUE	1	0.764627436009112	2		915	698	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940657	131940657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	258	398	0	ENST00000265335.6:c.2684C>T	p.Ser895Phe	p.S895F	ENST00000265335		895	tCc/tTc	16/25	0.119591019250034	3	FACETS	1	0.993	1	0.714	0.673	0.756	INDETERMINATE	1	TRUE	1	0.764627436009112	3		398	653	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175874	24175874	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	185	373	0	ENST00000263121.7:c.1102C>T	p.Gln368Ter	p.Q368*	ENST00000263121	NM_003073.3	368	Cag/Tag	8/9	1	2	FACETS	0.864	0.803	0.927	0.864	0.803	0.927	CLONAL	1	TRUE	1	0.764627436009112	2		373	560	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	90	267	0				ENST00000310581	NM_198253.2	-/1132			0.363277504731079	1	FACETS	0.79	0.72	0.861	0.79	0.72	0.861	INDETERMINATE	1	TRUE	0	0.764627436009112	1		267	184	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877402	89877402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780035612	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	359	498	1	ENST00000389301.3:c.361G>A	p.Val121Met	p.V121M	ENST00000389301	NM_000135.2	121	Gtg/Atg	4/43	0.396341939990591	5	FACETS	1	0.971	1	0.687	0.653	0.722	INDETERMINATE	2	TRUE	2	0.764627436009112	5		499	978	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132542	11132542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	288	458	0	ENST00000358026.2:c.2758G>A	p.Glu920Lys	p.E920K	ENST00000358026	NM_001128849.1	920	Gag/Aag	19/36	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.764627436009112	2		458	748	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740467	58740467	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs773389405	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	175	433	2	ENST00000305921.3:c.1372C>T	p.Arg458Ter	p.R458*	ENST00000305921	NM_003620.3	458	Cga/Tga	6/6	1	2	FACETS	0.755	0.699	0.813	0.755	0.699	0.813	SUBCLONAL	1	TRUE	1	0.764627436009112	2		435	606	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739881	145739881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764297840	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	87	441	2	ENST00000428558.2:c.1649C>T	p.Ala550Val	p.A550V	ENST00000428558	NM_004260.3	550	gCg/gTg	10/22	0.107923078103984	6	FACETS	0.662	0.585	0.745	0.221	0.195	0.249	INDETERMINATE	1	TRUE	3	0.764627436009112	6		443	869	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201885	152201885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778449608	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	174	396	0	ENST00000206249.3:c.739G>A	p.Glu247Lys	p.E247K	ENST00000206249	NM_000125.3	247	Gaa/Aaa	3/8	0.764627436009112	1	FACETS	0.76	0.71	0.81	0.76	0.71	0.81	SUBCLONAL	1	TRUE	0	0.764627436009112	1		396	370	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201966	102201966	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	49	225	0	ENST00000263464.3:c.1318G>T	p.Glu440Ter	p.E440*	ENST00000263464	NM_001165.4	440	Gaa/Taa	6/9	0.291793894610052	2	FACETS	0.451	0.385	0.524	0.226	0.192	0.262	INDETERMINATE	1	TRUE	0	0.764627436009112	2		225	284	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253151	133253151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	248	396	0	ENST00000320574.5:c.890C>T	p.Ser297Phe	p.S297F	ENST00000320574	NM_006231.2	297	tCc/tTc	9/49	0.363277504731079	1	FACETS	0.814	0.771	0.858	0.814	0.771	0.858	INDETERMINATE	1	TRUE	0	0.764627436009112	1		396	492	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031678	69031678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	227	316	0	ENST00000288368.4:c.3433C>T	p.Pro1145Ser	p.P1145S	ENST00000288368	NM_024870.2	1145	Ccc/Tcc	28/40	0.107923078103984	6	FACETS	1	0.989	1	0.823	0.772	0.875	INDETERMINATE	2	TRUE	3	0.764627436009112	6		316	608	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066711	94066711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	248	697	0	ENST00000369303.4:c.1048G>A	p.Glu350Lys	p.E350K	ENST00000369303	NM_004440.3	350	Gaa/Aaa	5/17	0.764627436009112	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.764627436009112	1		697	378	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271283	1271283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1169312254	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	143	342	0	ENST00000310581.5:c.2419G>A	p.Asp807Asn	p.D807N	ENST00000310581	NM_198253.2	807	Gac/Aac	8/16	0.363277504731079	1	FACETS	0.465	0.426	0.505	0.465	0.426	0.505	INDETERMINATE	1	TRUE	0	0.764627436009112	1		342	497	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285182	212285182	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	111	358	0	ENST00000342788.4:c.3119G>T	p.Arg1040Ile	p.R1040I	ENST00000342788	NM_005235.2	1040	aGa/aTa	25/28	0.340909317477987	1	FACETS	0.485	0.44	0.531	0.485	0.44	0.531	INDETERMINATE	1	TRUE	0	0.764627436009112	1		358	370	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799087	45799087	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs373766973	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	159	440	0	ENST00000450313.1:c.346C>T	p.Arg116Trp	p.R116W	ENST00000450313	NM_012222.2	116	Cgg/Tgg	3/16	0.764627436009112	2	FACETS	0.654	0.602	0.708	0.327	0.301	0.354	SUBCLONAL	1	TRUE	0	0.764627436009112	2		440	636	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560813	9560813	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	128	335	0	ENST00000353224.5:c.969G>T	p.Glu323Asp	p.E323D	ENST00000353224	NM_177990.2	323	gaG/gaT	4/10	0.635791459883787	3	FACETS	0.815	0.741	0.892	0.407	0.37	0.446	CLONAL	1	TRUE	1	0.764627436009112	3		335	568	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948820	71948820	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	421	474	0	ENST00000298229.2:c.3532C>T	p.Gln1178Ter	p.Q1178*	ENST00000298229	NM_001567.3	1178	Cag/Tag	26/28	0.764627436009112	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.764627436009112	1		474	570	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434366	49434366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs894385834	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	195	501	0	ENST00000301067.7:c.7187G>A	p.Cys2396Tyr	p.C2396Y	ENST00000301067	NM_003482.3	2396	tGt/tAt	31/54	0.1524351075622	2	FACETS	0.854	0.795	0.915	0.427	0.397	0.458	INDETERMINATE	1	TRUE	0	0.764627436009112	2		501	597	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811716	102811716	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	175	499	0	ENST00000307046.8:c.468T>A	p.His156Gln	p.H156Q	ENST00000307046	NM_001111285.1	156	caT/caA	4/4	0.363277504731079	1	FACETS	0.46	0.425	0.495	0.46	0.425	0.495	INDETERMINATE	1	TRUE	0	0.764627436009112	1		499	615	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335654	73335654	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	19	247	0	ENST00000377767.4:c.2517C>A	p.Phe839Leu	p.F839L	ENST00000377767	NM_014953.3	839	ttC/ttA	19/21	0.119591019250034	3	FACETS	0.197	0.149	0.253	0.098	0.074	0.127	INDETERMINATE	1	TRUE	1	0.764627436009112	3		247	349	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093381	30093381	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1469866177	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	120	419	0	ENST00000331968.5:c.1882C>T	p.Arg628Cys	p.R628C	ENST00000331968	NM_002742.2	628	Cgt/Tgt	13/18	0.195054256476689	2	FACETS	0.511	0.463	0.562	0.256	0.231	0.281	INDETERMINATE	1	TRUE	0	0.764627436009112	2		419	614	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713239	43713239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771109427	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	192	508	0	ENST00000382044.4:c.4234C>T	p.Arg1412Trp	p.R1412W	ENST00000382044	NM_001141980.1	1412	Cgg/Tgg	20/28	0.363277504731079	1	FACETS	0.439	0.407	0.472	0.439	0.407	0.472	INDETERMINATE	1	TRUE	0	0.764627436009112	1		508	707	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3929909	3929909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	112	213	0	ENST00000262367.5:c.9G>T	p.Glu3Asp	p.E3D	ENST00000262367	NM_004380.2	3	gaG/gaT	1/31	1	2	FACETS	0.694	0.629	0.762	0.694	0.629	0.762	SUBCLONAL	1	TRUE	1	0.764627436009112	2		213	422	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646537	23646537	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	160	426	0	ENST00000261584.4:c.1330A>C	p.Asn444His	p.N444H	ENST00000261584	NM_024675.3	444	Aat/Cat	4/13	1	2	FACETS	0.615	0.565	0.666	0.615	0.565	0.666	SUBCLONAL	1	TRUE	1	0.764627436009112	2		426	681	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846060	68846060	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	489	451	0	ENST00000261769.5:c.1031T>G	p.Val344Gly	p.V344G	ENST00000261769	NM_004360.3	344	gTg/gGg	8/16	0.396341939990591	5	FACETS	1	0.995	1	0.825	0.792	0.859	INDETERMINATE	2	TRUE	2	0.764627436009112	5		451	1109	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991469	72991469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	400	472	0	ENST00000268489.5:c.2576C>T	p.Ala859Val	p.A859V	ENST00000268489	NM_006885.3	859	gCc/gTc	2/10	0.396341939990591	5	FACETS	1	0.957	1	0.67	0.638	0.702	INDETERMINATE	2	TRUE	2	0.764627436009112	5		472	1118	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120440	70120440	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	270	545	2	ENST00000245479.2:c.1442C>T	p.Ala481Val	p.A481V	ENST00000245479	NM_000346.3	481	gCc/gTc	3/3	1	2	FACETS	0.916	0.863	0.97	0.916	0.863	0.97	CLONAL	1	TRUE	1	0.764627436009112	2		547	771	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748880	41748880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	216	459	0	ENST00000301178.4:c.1405C>T	p.Leu469Phe	p.L469F	ENST00000301178	NM_021913.4	469	Ctc/Ttc	11/20	1	2	FACETS	0.926	0.867	0.987	0.926	0.867	0.987	CLONAL	1	TRUE	1	0.764627436009112	2		459	610	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39237764	39237764	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	167	383	0	ENST00000402219.2:c.2471T>G	p.Met824Arg	p.M824R	ENST00000402219	NM_005633.3	824	aTg/aGg	15/23	0.340909317477987	1	FACETS	0.496	0.458	0.535	0.496	0.458	0.535	INDETERMINATE	1	TRUE	0	0.764627436009112	1		383	544	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047339	128047339	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs138385061	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	223	390	0	ENST00000285398.2:c.583C>T	p.Arg195Ter	p.R195*	ENST00000285398	NM_000122.1	195	Cga/Tga	5/15	0.340909317477987	1	FACETS	0.725	0.682	0.768	0.725	0.682	0.768	INDETERMINATE	1	TRUE	0	0.764627436009112	1		390	497	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46255777	46255777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769864577	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	190	391	1	ENST00000371998.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371998		130	cGa/cAa	6/23	0.635791459883787	3	FACETS	1	0.958	1	0.523	0.485	0.561	CLONAL	1	TRUE	1	0.764627436009112	3		392	657	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940229	49940229	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	171	429	0	ENST00000296474.3:c.814G>T	p.Asp272Tyr	p.D272Y	ENST00000296474	NM_002447.2	272	Gat/Tat	1/20	0.291793894610052	2	FACETS	0.652	0.602	0.704	0.326	0.301	0.352	INDETERMINATE	1	TRUE	0	0.764627436009112	2		429	686	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807394	1807394	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	71	299	0	ENST00000260795.2:c.1643G>T	p.Gly548Val	p.G548V	ENST00000260795		548	gGc/gTc	11/17	0.299035201724539	3	FACETS	0.45	0.393	0.512	0.225	0.196	0.256	INDETERMINATE	1	TRUE	1	0.764627436009112	3		299	570	SUCCESS
APC	324	MSKCC	GRCh37	5	112177392	112177392	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	26	318	0	ENST00000257430.4:c.6101C>A	p.Ser2034Tyr	p.S2034Y	ENST00000257430	NM_000038.5	2034	tCt/tAt	16/16	0.119591019250034	3	FACETS	0.211	0.166	0.262	0.105	0.083	0.131	INDETERMINATE	1	TRUE	1	0.764627436009112	3		318	446	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339875	116339875	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	465	377	0	ENST00000397752.3:c.737C>T	p.Pro246Leu	p.P246L	ENST00000397752	NM_000245.2	246	cCc/cTc	2/21	0.47770094362172	6	FACETS	0.904	0.87	0.937	0.904	0.87	0.937	CLONAL	4	TRUE	2	0.764627436009112	6		377	851	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833957	44833957	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	186	401	0	ENST00000377967.4:c.381G>C	p.Trp127Cys	p.W127C	ENST00000377967	NM_021140.2	127	tgG/tgC	4/29	0.340909317477987	1	FACETS	0.611	0.569	0.653	0.611	0.569	0.653	INDETERMINATE	1	TRUE	0	0.764627436009112	1		401	492	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341421	70341421	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	33	455	0	ENST00000374080.3:c.856G>T	p.Glu286Ter	p.E286*	ENST00000374080		286	Gaa/Taa	7/45	0.340909317477987	1	FACETS	0.085	0.069	0.104	0.085	0.069	0.104	INDETERMINATE	1	TRUE	0	0.764627436009112	1		455	625	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938617	76938617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	176	450	0	ENST00000373344.5:c.2131C>T	p.Pro711Ser	p.P711S	ENST00000373344	NM_000489.3	711	Cct/Tct	9/35	0.340909317477987	1	FACETS	0.52	0.482	0.559	0.52	0.482	0.559	INDETERMINATE	1	TRUE	0	0.764627436009112	1		450	547	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256527	115256530	+	missense_variant	Missense_Mutation	ONP	CTTG	CTTG	TTTT	novel	NA	P-0030903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	426	422	0	ENST00000369535.4:c.181_184delinsAAAA	p.Gln61_Glu62delinsLysLys	p.Q61_E62delinsKK	ENST00000369535	NM_002524.4	61	CAAGaa/AAAAaa	3/7	0.764627436009112	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.764627436009112	2		422	554	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0030938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	194	242	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	0.861	0.799	0.925	0.861	0.799	0.925	CLONAL	1	TRUE	1	0.592312276325468	2		242	761	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593607	55593615	+	inframe_deletion	In_Frame_Del	DEL	AGGTTGTTG	AGGTTGTTG	-	novel	NA	P-0030938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	425	592	0	ENST00000288135.5:c.1676_1684del	p.Val559_Glu561del	p.V559_E561del	ENST00000288135	NM_000222.2	558	aAGGTTGTTGag/aag	11/21	0.301020948559045	3	FACETS	0.852	0.814	0.891			1	INDETERMINATE	2	TRUE	NA	0.592312276325468	3		592	1091	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453153	140453153	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913337	NA	P-0030938-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	451	525	0	ENST00000288602.6:c.1782T>A	p.Asp594Glu	p.D594E	ENST00000288602	NM_004333.4	594	gaT/gaA	15/18	0.550657763211765	3	FACETS	0.984	0.943	1	0.656	0.629	0.684	CLONAL	2	TRUE	0	0.592312276325468	3		525	1003	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89828360	89828360	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	149	459	0	ENST00000389301.3:c.2849A>G	p.Glu950Gly	p.E950G	ENST00000389301	NM_000135.2	950	gAa/gGa	29/43	1	2	FACETS	0.875	0.807	0.945	0.875	0.807	0.945	CLONAL	1	TRUE	1	0.791918249939194	2		459	430	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279543	1279543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6827	3599	845	0	ENST00000310581.5:c.1993C>T	p.Leu665Phe	p.L665F	ENST00000310581	NM_198253.2	665	Ctc/Ttc	5/16	0.791918249939194	26	FACETS	1	0.993	1			1	CLONAL	9	TRUE	NA	0.791918249939194	26		845	10426	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279550	1279550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6914	3593	818	1	ENST00000310581.5:c.1986C>A	p.Phe662Leu	p.F662L	ENST00000310581	NM_198253.2	662	ttC/ttA	5/16	0.791918249939194	26	FACETS	1	0.99	1			1	CLONAL	9	TRUE	NA	0.791918249939194	26		819	10507	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931486	131931486	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	186	425	0	ENST00000265335.6:c.2191G>T	p.Gly731Ter	p.G731*	ENST00000265335		731	Gga/Tga	13/25	1	2	FACETS	0.999	0.932	1	0.999	0.932	1	CLONAL	1	TRUE	1	0.791918249939194	2		425	470	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0031475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	153	615	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	0.669	0.614	0.726	0.669	0.614	0.726	SUBCLONAL	1	TRUE	1	0.741497970124567	2		615	617	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851558	134851558	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs770155473	NA	P-0031475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	144	365	0	ENST00000398015.3:c.964G>A	p.Val322Ile	p.V322I	ENST00000398015	NM_004441.4	322	Gtc/Atc	5/16	1	2	FACETS	0.879	0.808	0.951	0.879	0.808	0.951	CLONAL	1	TRUE	1	0.741497970124567	2		365	442	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594261	55594261	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	191	380	0	ENST00000288135.5:c.1964A>C	p.Asn655Thr	p.N655T	ENST00000288135	NM_000222.2	655	aAt/aCt	13/21	0.741497970124567	3	FACETS	0.974	0.903	1	0.487	0.451	0.524	CLONAL	1	TRUE	1	0.741497970124567	3		380	725	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981497	201981497	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	59	544	0	ENST00000359651.3:c.411T>A	p.Ser137Arg	p.S137R	ENST00000359651		137	agT/agA	3/8	0.195969146617173	3	FACETS	0.327	0.28	0.377	0.163	0.14	0.189	INDETERMINATE	1	TRUE	1	0.741497970124567	3		544	668	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21623960	21623967	+	frameshift_variant	Frame_Shift_Del	DEL	GTTCAGAA	GTTCAGAA	-	novel	NA	P-0031475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	50	132	1	ENST00000421138.2:c.1733_1740del	p.Leu578GlnfsTer2	p.L578Qfs*2	ENST00000421138		578	cTTCTGAAC/c	15/16	1	2	FACETS	0.97	0.843	1	0.97	0.843	1	CLONAL	1	TRUE	1	0.741497970124567	2		133	139	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38591636	38591636	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0031475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	285	453	0	ENST00000299084.4:c.95T>A	p.Leu32Ter	p.L32*	ENST00000299084	NM_152594.2	32	tTa/tAa	2/7	1	2	FACETS	0.862	0.825	0.898	1	0.996	1	CLONAL	2	TRUE	1	0.741497970124567	2		453	446	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040927	42040927	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0031475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	42	459	0	ENST00000219905.7:c.5305C>T	p.Gln1769Ter	p.Q1769*	ENST00000219905	NM_001164273.1	1769	Cag/Tag	16/24	0.732241096315358	1	FACETS	0.161	0.134	0.19	0.161	0.134	0.19	SUBCLONAL	1	TRUE	0	0.741497970124567	1		459	444	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594233	55594233	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	181	377	0	ENST00000288135.5:c.1936T>A	p.Tyr646Asn	p.Y646N	ENST00000288135	NM_000222.2	646	Tac/Aac	13/21	0.741497970124567	3	FACETS	0.937	0.867	1	0.469	0.433	0.505	CLONAL	1	TRUE	1	0.741497970124567	3		377	714	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181527	32181527	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0031475-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	51	543	0	ENST00000375023.3:c.2258G>T	p.Cys753Phe	p.C753F	ENST00000375023	NM_004557.3	753	tGc/tTc	14/30	0.741497970124567	3	FACETS	0.193	0.163	0.226	0.096	0.081	0.113	SUBCLONAL	1	TRUE	1	0.741497970124567	3		543	977	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0031703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	99	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.832	0.743	0.926	0.832	0.743	0.926	CLONAL	1	TRUE	1	0.352489248149345	2		288	675	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0031711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	122	578	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	0.975	0.883	1	0.975	0.883	1	CLONAL	1	TRUE	1	0.3723304013598	2		578	672	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443731	52443809	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAAATCTTCCACGAGCAGGGTGAAGAGGCCTGGGTGGGGCGACAAGAGGAGGGGGTGATGGTCAGGCAGGCGCGTCCCG	GAAATCTTCCACGAGCAGGGTGAAGAGGCCTGGGTGGGGCGACAAGAGGAGGGGGTGATGGTCAGGCAGGCGCGTCCCG	-	novel	NA	P-0031711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	89	572	0	ENST00000460680.1:c.37+49_66del		p.X13_splice	ENST00000460680	NM_004656.3	13		2/17	0.3723304013598	1	FACETS	0.669	0.594	0.748	0.669	0.594	0.748	SUBCLONAL	1	TRUE	0	0.3723304013598	1		572	582	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879885	37879885	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	126	675	0	ENST00000269571.5:c.2180G>C	p.Gly727Ala	p.G727A	ENST00000269571		727	gGa/gCa	18/27	0.682721912879379	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.682721912879379	1		675	211	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs121913468	NA	P-0031916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	78	318	0	ENST00000269571.5:c.2305G>C	p.Asp769His	p.D769H	ENST00000269571		769	Gac/Cac	19/27	0.682721912879379	1	FACETS	0.86	0.775	0.946	0.86	0.775	0.946	CLONAL	1	TRUE	0	0.682721912879379	1		318	175	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221846	55221846	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0031916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	182	673	1	ENST00000275493.2:c.889+1G>A		p.X297_splice	ENST00000275493	NM_005228.3	297			0.682721912879379	3	FACETS	1	0.977	1	0.564	0.523	0.607	CLONAL	1	TRUE	1	0.682721912879379	3		674	634	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964415	70964415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777306806	NA	P-0031916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	115	392	1	ENST00000276594.2:c.1613G>A	p.Arg538His	p.R538H	ENST00000276594	NM_024504.3	538	cGt/cAt	8/8	0.682721912879379	3	FACETS	1	0.94	1	0.524	0.475	0.575	CLONAL	1	TRUE	1	0.682721912879379	3		393	431	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426223	49426223	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0031916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	134	742	0	ENST00000301067.7:c.12265C>G	p.Leu4089Val	p.L4089V	ENST00000301067	NM_003482.3	4089	Ctg/Gtg	39/54	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.682721912879379	2		742	374	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032313-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	166	151	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.957	0.89	1	0.957	0.89	1	CLONAL	1	TRUE	1	0.869518086286007	2		151	399	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054440	42054440	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032313-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	249	367	0	ENST00000219905.7:c.7624C>G	p.Pro2542Ala	p.P2542A	ENST00000219905	NM_001164273.1	2542	Ccc/Gcc	22/24	1	2	FACETS	0.966	0.911	1	0.966	0.911	1	CLONAL	1	TRUE	1	0.869518086286007	2		367	593	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	98	451	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	1	2	FACETS	0.805	0.727	0.885	0.805	0.727	0.885	CLONAL	1	TRUE	1	0.809216136329013	2		451	301	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	228	409	1	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.80342617099148	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.809216136329013	1		410	324	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911514	131911514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143802516	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	75	519	0	ENST00000265335.6:c.259C>T	p.Arg87Cys	p.R87C	ENST00000265335		87	Cgt/Tgt	3/25	0.47012315555835	1	FACETS	0.367	0.324	0.411	0.367	0.324	0.411	INDETERMINATE	1	TRUE	0	0.809216136329013	1		519	301	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170021	32170021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	830	942	1	ENST00000375023.3:c.3587G>A	p.Gly1196Glu	p.G1196E	ENST00000375023	NM_004557.3	1196	gGa/gAa	21/30	0.808905554672359	3	FACETS	0.957	0.93	0.983	0.638	0.62	0.656	CLONAL	2	TRUE	0	0.809216136329013	3		943	1506	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259388	89259388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	194	540	0	ENST00000336596.2:c.532G>A	p.Gly178Arg	p.G178R	ENST00000336596	NM_005233.5	178	Gga/Aga	3/17	1	2	FACETS	0.822	0.766	0.88	0.822	0.766	0.88	CLONAL	1	TRUE	1	0.809216136329013	2		540	583	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528768	8528768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	168	404	0	ENST00000356435.5:c.364C>T	p.Pro122Ser	p.P122S	ENST00000356435		122	Ccc/Tcc	4/35	1	2	FACETS	0.972	0.904	1	0.972	0.904	1	CLONAL	1	TRUE	1	0.809216136329013	2		404	427	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	275	552	0	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	1	2	FACETS	0.909	0.857	0.961	0.909	0.857	0.961	CLONAL	1	TRUE	1	0.809216136329013	2		552	748	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468158	50468158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	285	566	1	ENST00000331340.3:c.1393G>A	p.Glu465Lys	p.E465K	ENST00000331340	NM_006060.4	465	Gaa/Aaa	8/8	1	2	FACETS	0.987	0.933	1	0.987	0.933	1	CLONAL	1	TRUE	1	0.809216136329013	2		567	714	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	164	430	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.809216136329013	3	FACETS	0.895	0.837	0.953	0.895	0.837	0.953	CLONAL	2	TRUE	1	0.809216136329013	3		430	318	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42842607	42842607	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	326	782	1	ENST00000398585.3:c.1250G>A	p.Trp417Ter	p.W417*	ENST00000398585	NM_001135099.1	417	tGg/tAg	11/14	1	2	FACETS	0.888	0.842	0.936	0.888	0.842	0.936	CLONAL	1	TRUE	1	0.809216136329013	2		783	907	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453185	140453185	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	57	319	0	ENST00000288602.6:c.1750C>T	p.Leu584Phe	p.L584F	ENST00000288602	NM_004333.4	584	Ctt/Ttt	15/18	0.809216136329013	3	FACETS	0.876	0.761	0.997	0.438	0.38	0.499	CLONAL	1	TRUE	1	0.809216136329013	3		319	226	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162475188	162475188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	190	509	0	ENST00000366898.1:c.553G>A	p.Asp185Asn	p.D185N	ENST00000366898	NM_004562.2	185	Gat/Aat	5/12	0.809216136329013	1	FACETS	0.92	0.871	0.968	0.92	0.871	0.968	CLONAL	1	TRUE	0	0.809216136329013	1		509	304	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488718	212488718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267599191	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	394	633	0	ENST00000342788.4:c.2131C>T	p.Arg711Cys	p.R711C	ENST00000342788	NM_005235.2	711	Cgt/Tgt	18/28	0.351647656322606	4	FACETS	0.889	0.848	0.931	0.889	0.848	0.931	INDETERMINATE	2	TRUE	2	0.809216136329013	4		633	991	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112623	115112623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	188	857	0	ENST00000257566.3:c.1117G>A	p.Gly373Ser	p.G373S	ENST00000257566	NM_016569.3	373	Ggt/Agt	7/8	0.407078889376261	2	FACETS	0.507	0.468	0.547	0.253	0.234	0.274	INDETERMINATE	1	TRUE	0	0.809216136329013	2		857	917	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022962	33022962	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	232	351	0	ENST00000300177.4:c.71G>A	p.Gly24Glu	p.G24E	ENST00000300177	NM_001191322.1	24	gGg/gAg	2/2	1	2	FACETS	0.999	0.939	1	0.999	0.939	1	CLONAL	1	TRUE	1	0.809216136329013	2		351	574	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394449	162394449	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	77	196	0	ENST00000366898.1:c.619G>A	p.Glu207Lys	p.E207K	ENST00000366898	NM_004562.2	207	Gaa/Aaa	6/12	0.809216136329013	1	FACETS	0.497	0.443	0.553	0.497	0.443	0.553	SUBCLONAL	1	TRUE	0	0.809216136329013	1		196	228	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	832	939	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	0.808905554672359	3	FACETS	1	0.975	1	0.668	0.65	0.686	CLONAL	2	TRUE	0	0.809216136329013	3		939	1441	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431915	49431915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	420	908	1	ENST00000301067.7:c.9224C>T	p.Ser3075Leu	p.S3075L	ENST00000301067	NM_003482.3	3075	tCg/tTg	34/54	1	2	FACETS	0.965	0.921	1	0.965	0.921	1	CLONAL	1	TRUE	1	0.809216136329013	2		909	1076	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485256	8485256	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159854	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	143	497	0	ENST00000356435.5:c.3124G>A	p.Glu1042Lys	p.E1042K	ENST00000356435		1042	Gag/Aag	18/35	1	2	FACETS	0.987	0.912	1	0.987	0.912	1	CLONAL	1	TRUE	1	0.809216136329013	2		497	358	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706859	117706859	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	206	423	1	ENST00000368508.3:c.2291G>A	p.Gly764Glu	p.G764E	ENST00000368508	NM_002944.2	764	gGa/gAa	15/43	0.809216136329013	1	FACETS	0.965	0.918	1	0.965	0.918	1	CLONAL	1	TRUE	0	0.809216136329013	1		424	314	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109319805	109319805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	46	627	1	ENST00000436639.2:c.883C>T	p.Pro295Ser	p.P295S	ENST00000436639	NM_014454.2	295	Cct/Tct	5/10	0.809216136329013	1	FACETS	0.157	0.132	0.184	0.157	0.132	0.184	SUBCLONAL	1	TRUE	0	0.809216136329013	1		628	432	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687106	176687106	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	175	668	1	ENST00000439151.2:c.5083C>T	p.Pro1695Ser	p.P1695S	ENST00000439151	NM_022455.4	1695	Cct/Tct	14/23	0.47012315555835	1	FACETS	0.389	0.359	0.42	0.389	0.359	0.42	INDETERMINATE	1	TRUE	0	0.809216136329013	1		669	662	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665110	138665110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1330762569	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	210	429	0	ENST00000330315.3:c.455C>T	p.Pro152Leu	p.P152L	ENST00000330315	NM_023067.3	152	cCc/cTc	1/1	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.809216136329013	2		429	483	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675097	40675097	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	404	823	1	ENST00000249776.8:c.61G>A	p.Glu21Lys	p.E21K	ENST00000249776	NM_033286.3	21	Gag/Aag	1/9	1	2	FACETS	0.98	0.935	1	0.98	0.935	1	CLONAL	1	TRUE	1	0.809216136329013	2		824	1019	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134857	41134857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	149	531	0	ENST00000379561.5:c.771G>A	p.Met257Ile	p.M257I	ENST00000379561	NM_002015.3	257	atG/atA	2/3	0.47012315555835	1	FACETS	0.411	0.377	0.445	0.411	0.377	0.445	INDETERMINATE	1	TRUE	0	0.809216136329013	1		531	534	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656292	18656292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867409592	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	167	505	0	ENST00000266497.5:c.2971G>A	p.Glu991Lys	p.E991K	ENST00000266497		991	Gaa/Aaa	21/31	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.809216136329013	2		505	375	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941007	71941007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1179011278	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	464	938	1	ENST00000298229.2:c.883C>T	p.Pro295Ser	p.P295S	ENST00000298229	NM_001567.3	295	Cca/Tca	8/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.809216136329013	2		939	1122	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484129	8484129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	188	560	0	ENST00000356435.5:c.3403G>A	p.Glu1135Lys	p.E1135K	ENST00000356435		1135	Gag/Aag	19/35	1	2	FACETS	0.918	0.856	0.982	0.918	0.856	0.982	CLONAL	1	TRUE	1	0.809216136329013	2		560	506	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	161	248	1				ENST00000310581	NM_198253.2	-/1132			0.47012315555835	1	FACETS	0.774	0.724	0.824	0.774	0.724	0.824	INDETERMINATE	1	TRUE	0	0.809216136329013	1		249	306	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466940	18466940	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	149	461	0	ENST00000266497.5:c.1079C>T	p.Ser360Phe	p.S360F	ENST00000266497		360	tCt/tTt	5/31	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.809216136329013	2		461	364	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656232	18656232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	138	495	0	ENST00000266497.5:c.2911C>T	p.Pro971Ser	p.P971S	ENST00000266497		971	Cct/Tct	21/31	1	2	FACETS	0.824	0.757	0.893	0.824	0.757	0.893	CLONAL	1	TRUE	1	0.809216136329013	2		495	414	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431483	49431483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	403	814	0	ENST00000301067.7:c.9656C>T	p.Ala3219Val	p.A3219V	ENST00000301067	NM_003482.3	3219	gCt/gTt	34/54	1	2	FACETS	0.965	0.921	1	0.965	0.921	1	CLONAL	1	TRUE	1	0.809216136329013	2		814	1032	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623551	28623551	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	82	567	0	ENST00000241453.7:c.1006C>T	p.Pro336Ser	p.P336S	ENST00000241453	NM_004119.2	336	Ccc/Tcc	8/24	0.398972857208273	1	FACETS	0.305	0.271	0.342	0.305	0.271	0.342	INDETERMINATE	1	TRUE	0	0.809216136329013	1		567	395	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994616	73994616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1022188310	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	439	1057	0	ENST00000318443.5:c.100C>T	p.Pro34Ser	p.P34S	ENST00000318443	NM_001024736.1	34	Cct/Tct	3/10	1	2	FACETS	0.972	0.929	1	0.972	0.929	1	CLONAL	1	TRUE	1	0.809216136329013	2		1057	1116	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81902892	81902892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	224	573	0	ENST00000359376.3:c.553G>A	p.Asp185Asn	p.D185N	ENST00000359376	NM_002661.3	185	Gat/Aat	6/33	1	2	FACETS	0.896	0.84	0.953	0.896	0.84	0.953	CLONAL	1	TRUE	1	0.809216136329013	2		573	618	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763497	59763497	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1060501766	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	149	652	1	ENST00000259008.2:c.2605C>T	p.Gln869Ter	p.Q869*	ENST00000259008	NM_032043.2	869	Cag/Tag	19/20	1	2	FACETS	0.885	0.817	0.955	0.885	0.817	0.955	CLONAL	1	TRUE	1	0.809216136329013	2		653	416	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66520171	66520171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	245	634	1	ENST00000358598.2:c.455C>T	p.Ala152Val	p.A152V	ENST00000358598	NM_212471.2	152	gCc/gTc	5/11	1	2	FACETS	0.943	0.887	1	0.943	0.887	1	CLONAL	1	TRUE	1	0.809216136329013	2		635	642	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414901	56414902	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	158	737	0	ENST00000348428.3:c.2302_2303delinsTT	p.Pro768Leu	p.P768L	ENST00000348428	NM_006785.3	768	CCa/TTa	17/17	0.398972857208273	1	FACETS	0.392	0.361	0.425	0.392	0.361	0.425	INDETERMINATE	1	TRUE	0	0.809216136329013	1		737	593	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302896	15302896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555729477	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	453	1028	0	ENST00000263388.2:c.554G>A	p.Cys185Tyr	p.C185Y	ENST00000263388	NM_000435.2	185	tGt/tAt	4/33	1	2	FACETS	0.975	0.933	1	0.975	0.933	1	CLONAL	1	TRUE	1	0.809216136329013	2		1028	1148	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095752	178095753	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	AG	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	177	534	0	ENST00000397062.3:c.1578_1579delinsCT	p.Glu526_Gln527delinsAspTer	p.E526_Q527delinsD*	ENST00000397062	NM_006164.4	526	gaGCaa/gaCTaa	5/5	0.351647656322606	4	FACETS	0.958	0.894	1	0.958	0.894	1	INDETERMINATE	2	TRUE	2	0.809216136329013	4		534	413	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288988	212288988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	145	602	0	ENST00000342788.4:c.2758C>T	p.Pro920Ser	p.P920S	ENST00000342788	NM_005235.2	920	Ccc/Tcc	23/28	0.351647656322606	4	FACETS	0.779	0.718	0.842	0.779	0.718	0.842	INDETERMINATE	2	TRUE	2	0.809216136329013	4		602	416	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755735	39755735	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	300	631	0	ENST00000288319.7:c.1030C>A	p.Pro344Thr	p.P344T	ENST00000288319	NM_182918.3	344	Ccc/Acc	10/10	1	2	FACETS	0.989	0.936	1	0.989	0.936	1	CLONAL	1	TRUE	1	0.809216136329013	2		631	750	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604320	189604320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	239	441	1	ENST00000264731.3:c.1487C>T	p.Pro496Leu	p.P496L	ENST00000264731	NM_003722.4	496	cCt/cTt	11/14	1	2	FACETS	0.991	0.933	1	0.991	0.933	1	CLONAL	1	TRUE	1	0.809216136329013	2		442	596	SUCCESS
APC	324	MSKCC	GRCh37	5	112102045	112102045	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772787939	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	35	398	0	ENST00000257430.4:c.158G>A	p.Gly53Glu	p.G53E	ENST00000257430	NM_000038.5	53	gGa/gAa	3/16	NA	2	FACETS	1	0.896	1			1	INDETERMINATE	1	TRUE	NA	0.809216136329013	2		398	81	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047257	180047257	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276261095	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	207	898	0	ENST00000261937.6:c.2458G>A	p.Gly820Arg	p.G820R	ENST00000261937	NM_182925.4	820	Ggg/Agg	17/30	0.47012315555835	1	FACETS	0.383	0.356	0.411	0.383	0.356	0.411	INDETERMINATE	1	TRUE	0	0.809216136329013	1		898	796	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052981	180052981	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	403	1133	0	ENST00000261937.6:c.1309C>G	p.Arg437Gly	p.R437G	ENST00000261937	NM_182925.4	437	Cgt/Ggt	10/30	0.47012315555835	1	FACETS	0.712	0.681	0.742	0.712	0.681	0.742	INDETERMINATE	1	TRUE	0	0.809216136329013	1		1133	833	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509918	106509918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1263614656	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	610	741	0	ENST00000359195.3:c.1912G>A	p.Glu638Lys	p.E638K	ENST00000359195	NM_002649.2	638	Gaa/Aaa	2/11	0.809216136329013	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.809216136329013	3		741	1047	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002843	69002843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	151	330	0	ENST00000288368.4:c.2143C>T	p.Pro715Ser	p.P715S	ENST00000288368	NM_024870.2	715	Cct/Tct	20/40	1	2	FACETS	0.895	0.827	0.965	0.895	0.827	0.965	CLONAL	1	TRUE	1	0.809216136329013	2		330	417	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739839	145739839	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	465	920	2	ENST00000428558.2:c.1691C>T	p.Ser564Phe	p.S564F	ENST00000428558	NM_004260.3	564	tCt/tTt	10/22	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.809216136329013	2		922	1023	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499777	8499777	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	331	720	0	ENST00000356435.5:c.2192C>T	p.Ser731Leu	p.S731L	ENST00000356435		731	tCa/tTa	14/35	1	2	FACETS	0.987	0.937	1	0.987	0.937	1	CLONAL	1	TRUE	1	0.809216136329013	2		720	829	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528711	8528711	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	236	451	0	ENST00000356435.5:c.421C>G	p.Arg141Gly	p.R141G	ENST00000356435		141	Cgc/Ggc	4/35	1	2	FACETS	0.999	0.94	1	0.999	0.94	1	CLONAL	1	TRUE	1	0.809216136329013	2		451	584	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200105	123200105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	86	350	0	ENST00000218089.9:c.2177C>T	p.Pro726Leu	p.P726L	ENST00000218089	NM_001042749.1	726	cCt/cTt	22/35	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.809216136329013	1		350	107	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0032591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	37	1049	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	1	2	FACETS	0.647	0.531	0.777	0.647	0.531	0.777	SUBCLONAL	1	TRUE	1	0.13	2		1049	880	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858017	152858017	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	11	170	0	ENST00000406277.2:c.598del	p.Val200SerfsTer144	p.V200Sfs*144	ENST00000406277	NM_152274.4	200	Gtc/tc	6/7	0.3	2	FACETS	0.806	0.562	1	0.806	0.562	1	CLONAL	2	TRUE	0	0.13	2		170	105	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0032812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	104	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.298723507051177	3	FACETS	0.929	0.838	1	0.929	0.838	1	CLONAL	2	TRUE	1	0.32	3		288	406	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0032812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	51	248	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.9	0.768	1	0.9	0.768	1	CLONAL	1	TRUE	1	0.32	2		249	354	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561564	9561564	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867333778	NA	P-0032812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	63	575	0	ENST00000353224.5:c.218G>A	p.Gly73Glu	p.G73E	ENST00000353224	NM_177990.2	73	gGa/gAa	4/10	1	2	FACETS	0.786	0.681	0.9	0.786	0.681	0.9	SUBCLONAL	1	TRUE	1	0.32	2		575	501	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857429	9857429	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	91	692	0	ENST00000330684.3:c.3972T>A	p.Phe1324Leu	p.F1324L	ENST00000330684	NM_001134407.1	1324	ttT/ttA	13/13	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.32	2		692	542	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521923	157521923	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554235546	NA	P-0032812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	125	352	0	ENST00000346085.5:c.4195C>T	p.Gln1399Ter	p.Q1399*	ENST00000346085	NM_020732.3	1399	Cag/Tag	18/20	0.260752635334141	2	FACETS	0.822	0.749	0.899	0.822	0.749	0.899	CLONAL	2	TRUE	0	0.32	2		352	475	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0032845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	256	528	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.721448876712107	2		528	638	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0032845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	86	265	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.977	0.878	1	0.977	0.878	1	CLONAL	1	TRUE	1	0.721448876712107	2		265	244	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0032845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	106	248	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.924	0.839	1	0.924	0.839	1	CLONAL	1	TRUE	1	0.721448876712107	2		249	318	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097809	27097809	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	118	248	0	ENST00000324856.7:c.3398C>T	p.Pro1133Leu	p.P1133L	ENST00000324856	NM_006015.4	1133	cCc/cTc	12/20	1	2	FACETS	0.985	0.9	1	0.985	0.9	1	CLONAL	1	TRUE	1	0.721448876712107	2		248	332	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830895	156830895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	210	429	0	ENST00000524377.1:c.169G>A	p.Asp57Asn	p.D57N	ENST00000524377	NM_002529.3	57	Gat/Aat	1/17	0.721448876712107	3	FACETS	1	0.964	1	0.526	0.49	0.563	CLONAL	1	TRUE	1	0.721448876712107	3		429	753	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619168	43619168	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	203	487	0	ENST00000355710.3:c.2851C>T	p.Pro951Ser	p.P951S	ENST00000355710	NM_020975.4	951	Ccc/Tcc	17/20	1	2	FACETS	0.986	0.92	1	0.986	0.92	1	CLONAL	1	TRUE	1	0.721448876712107	2		487	571	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112598	115112598	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	300	630	0	ENST00000257566.3:c.1142G>A	p.Ser381Asn	p.S381N	ENST00000257566	NM_016569.3	381	aGc/aAc	7/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.721448876712107	2		630	789	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432143	121432143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223268118	NA	P-0032845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	240	554	0	ENST00000257555.6:c.890C>T	p.Pro297Leu	p.P297L	ENST00000257555		297	cCt/cTt	4/10	1	2	FACETS	0.983	0.923	1	0.983	0.923	1	CLONAL	1	TRUE	1	0.721448876712107	2		554	677	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437073	110437073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	50	65	0	ENST00000375856.3:c.1328C>T	p.Thr443Ile	p.T443I	ENST00000375856	NM_003749.2	443	aCc/aTc	1/2	1	2	FACETS	0.83	0.717	0.949	0.83	0.717	0.949	CLONAL	1	TRUE	1	0.721448876712107	2		65	167	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476402	88476402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1456055401	NA	P-0032845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	154	383	0	ENST00000360948.2:c.1730C>T	p.Pro577Leu	p.P577L	ENST00000360948	NM_001012338.2	577	cCc/cTc	15/19	1	2	FACETS	0.959	0.886	1	0.959	0.886	1	CLONAL	1	TRUE	1	0.721448876712107	2		383	445	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56792538	56792538	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	251	414	0	ENST00000308159.5:c.268C>T	p.Leu90Phe	p.L90F	ENST00000308159	NM_014669.4	90	Ctt/Ttt	3/22	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.721448876712107	2		414	610	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546026	29546026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	125	256	1	ENST00000356175.3:c.1531C>T	p.Pro511Ser	p.P511S	ENST00000356175	NM_000267.3	511	Cca/Tca	14/57	1	2	FACETS	0.924	0.845	1	0.924	0.845	1	CLONAL	1	TRUE	1	0.721448876712107	2		257	375	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290048	15290049	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0032845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	187	633	2	ENST00000263388.2:c.3505_3506delinsTT	p.Pro1169Leu	p.P1169L	ENST00000263388	NM_000435.2	1169	CCg/TTg	22/33	1	2	FACETS	0.799	0.741	0.858	0.799	0.741	0.858	SUBCLONAL	1	TRUE	1	0.721448876712107	2		635	649	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222808	36222808	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0032845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	277	622	0	ENST00000222270.7:c.5438-1G>A		p.X1813_splice	ENST00000222270	NM_014727.1	1813			1	2	FACETS	0.986	0.93	1	0.986	0.93	1	CLONAL	1	TRUE	1	0.721448876712107	2		622	779	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495314	212495314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1337377088	NA	P-0032845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	83	307	0	ENST00000342788.4:c.1952C>T	p.Pro651Leu	p.P651L	ENST00000342788	NM_005235.2	651	cCc/cTc	17/28	1	2	FACETS	0.843	0.753	0.936	0.843	0.753	0.936	CLONAL	1	TRUE	1	0.721448876712107	2		307	273	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024207	31024207	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs74638057	NA	P-0032845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	187	401	0	ENST00000375687.4:c.3692C>T	p.Ser1231Phe	p.S1231F	ENST00000375687	NM_015338.5	1231	tCc/tTc	13/13	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.721448876712107	2		401	514	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196318	106196318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	112	273	0	ENST00000380013.4:c.4651C>T	p.His1551Tyr	p.H1551Y	ENST00000380013	NM_001127208.2	1551	Cac/Tac	11/11	1	2	FACETS	0.862	0.784	0.944	0.862	0.784	0.944	CLONAL	1	TRUE	1	0.721448876712107	2		273	360	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190843	32190843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	296	622	0	ENST00000375023.3:c.94C>T	p.Pro32Ser	p.P32S	ENST00000375023	NM_004557.3	32	Cca/Tca	2/30	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.721448876712107	2		622	750	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967924	93967924	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	190	438	0	ENST00000369303.4:c.2003A>C	p.Lys668Thr	p.K668T	ENST00000369303	NM_004440.3	668	aAa/aCa	11/17	1	2	FACETS	0.936	0.871	1	0.936	0.871	1	CLONAL	1	TRUE	1	0.721448876712107	2		438	563	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674156	117674156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867084033	NA	P-0032845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	151	688	0	ENST00000368508.3:c.4318C>T	p.Pro1440Ser	p.P1440S	ENST00000368508	NM_002944.2	1440	Cca/Tca	26/43	1	2	FACETS	0.912	0.841	0.985	0.912	0.841	0.985	CLONAL	1	TRUE	1	0.721448876712107	2		688	459	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938546	44938546	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	144	358	0	ENST00000377967.4:c.3094A>G	p.Ile1032Val	p.I1032V	ENST00000377967	NM_021140.2	1032	Att/Gtt	20/29	0.564610957365548	1	FACETS	0.773	0.716	0.831	0.773	0.716	0.831	SUBCLONAL	1	TRUE	0	0.721448876712107	1		358	330	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	90	151	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.537706916302091	2		151	293	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156735	20156735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	160	389	0	ENST00000379607.5:c.22G>A	p.Gly8Arg	p.G8R	ENST00000379607	NM_001412.3	8	Gga/Aga	2/7	1	2	FACETS	0.918	0.845	0.994	0.918	0.845	0.994	CLONAL	1	TRUE	1	0.537706916302091	2		389	648	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935508	13935508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536563766	NA	P-0032984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	109	275	0	ENST00000405192.2:c.1348G>A	p.Glu450Lys	p.E450K	ENST00000405192	NM_001163147.1	450	Gaa/Aaa	12/12	1	2	FACETS	0.911	0.823	1	0.911	0.823	1	CLONAL	1	TRUE	1	0.537706916302091	2		275	445	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0032984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	234	615	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.425250559718738	3	FACETS	1	0.952	1	0.513	0.478	0.549	CLONAL	1	TRUE	1	0.537706916302091	3		615	1076	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0032984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	159	355	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	0.537706916302091	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.537706916302091	1		355	377	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193857	106193857	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1157107314	NA	P-0032984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	106	258	1	ENST00000380013.4:c.4319G>A	p.Arg1440Gln	p.R1440Q	ENST00000380013	NM_001127208.2	1440	cGg/cAg	10/11	0.537706916302091	2	FACETS	0.825	0.743	0.91	0.412	0.371	0.455	CLONAL	1	TRUE	0	0.537706916302091	2		259	478	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481412	140481412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913353	NA	P-0032984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	151	389	0	ENST00000288602.6:c.1396G>A	p.Gly466Arg	p.G466R	ENST00000288602	NM_004333.4	466	Gga/Aga	11/18	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.537706916302091	2		389	545	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005901	69005901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	165	446	0	ENST00000288368.4:c.2312C>T	p.Ser771Phe	p.S771F	ENST00000288368	NM_024870.2	771	tCt/tTt	21/40	NA	2	FACETS	0.884	0.814	0.957			1	INDETERMINATE	1	TRUE	NA	0.537706916302091	2		446	694	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992708	68992708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	143	483	0	ENST00000288368.4:c.1673C>T	p.Pro558Leu	p.P558L	ENST00000288368	NM_024870.2	558	cCc/cTc	16/40	NA	2	FACETS	0.724	0.661	0.79			1	INDETERMINATE	1	TRUE	NA	0.537706916302091	2		483	735	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387372	17387372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	236	782	0	ENST00000359435.4:c.638C>T	p.Thr213Ile	p.T213I	ENST00000359435	NM_001033549.1	213	aCc/aTc	7/9	1	2	FACETS	0.916	0.856	0.979	0.916	0.856	0.979	CLONAL	1	TRUE	1	0.537706916302091	2		782	958	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971304	15971304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752564662	NA	P-0032984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	166	461	0	ENST00000268712.3:c.4645C>T	p.Pro1549Ser	p.P1549S	ENST00000268712	NM_006311.3	1549	Ccc/Tcc	32/46	1	2	FACETS	0.983	0.907	1	0.983	0.907	1	CLONAL	1	TRUE	1	0.537706916302091	2		461	628	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962562	100962562	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	170	443	0	ENST00000325455.5:c.1835A>C	p.Asp612Ala	p.D612A	ENST00000325455	NM_001202474.3	612	gAt/gCt	3/8	1	2	FACETS	0.964	0.89	1	0.964	0.89	1	CLONAL	1	TRUE	1	0.537706916302091	2		443	656	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143035	58143035	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	223	480	0	ENST00000257904.6:c.749C>T	p.Pro250Leu	p.P250L	ENST00000257904	NM_000075.3	250	cCc/cTc	7/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.537706916302091	2		480	725	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670721	67670721	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	137	406	0	ENST00000264010.4:c.1966C>T	p.Pro656Ser	p.P656S	ENST00000264010	NM_006565.3	656	Cct/Tct	11/12	1	2	FACETS	0.942	0.861	1	0.942	0.861	1	CLONAL	1	TRUE	1	0.537706916302091	2		406	541	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794727	42794727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1252708116	NA	P-0032984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	173	522	1	ENST00000575354.2:c.1807C>T	p.Pro603Ser	p.P603S	ENST00000575354	NM_015125.3	603	Ccc/Tcc	10/20	1	2	FACETS	0.981	0.906	1	0.981	0.906	1	CLONAL	1	TRUE	1	0.537706916302091	2		523	656	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825353	134825353	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	112	355	0	ENST00000398015.3:c.869A>G	p.Asn290Ser	p.N290S	ENST00000398015	NM_004441.4	290	aAc/aGc	4/16	1	2	FACETS	0.896	0.811	0.985	0.896	0.811	0.985	CLONAL	1	TRUE	1	0.537706916302091	2		355	465	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502410	186502410	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201474676	NA	P-0032984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	154	398	0	ENST00000323963.5:c.133C>T	p.Leu45Phe	p.L45F	ENST00000323963		45	Ctt/Ttt	3/11	1	2	FACETS	0.927	0.852	1	0.927	0.852	1	CLONAL	1	TRUE	1	0.537706916302091	2		398	618	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522425	187522425	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	283	447	0	ENST00000441802.2:c.11638G>A	p.Glu3880Lys	p.E3880K	ENST00000441802	NM_005245.3	3880	Gag/Aag	21/27	0.537706916302091	3	FACETS	0.914	0.863	0.964	0.914	0.863	0.964	CLONAL	2	TRUE	1	0.537706916302091	3		447	731	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468137	31468137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	150	439	0	ENST00000344624.3:c.2275C>T	p.Arg759Cys	p.R759C	ENST00000344624		759	Cgt/Tgt	15/33	1	2	FACETS	0.946	0.868	1	0.946	0.868	1	CLONAL	1	TRUE	1	0.537706916302091	2		439	590	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992708	68992709	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0032984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	143	488	0	ENST00000288368.4:c.1673_1674delinsTT	p.Pro558Leu	p.P558L	ENST00000288368	NM_024870.2	558	cCC/cTT	16/40	NA	2	FACETS	0.724	0.661	0.79			1	INDETERMINATE	1	TRUE	NA	0.537706916302091	2		488	735	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507374	8507374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	128	311	0	ENST00000356435.5:c.1604C>T	p.Ser535Phe	p.S535F	ENST00000356435		535	tCt/tTt	11/35	0.537706916302091	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.537706916302091	1		311	347	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0032996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	55	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.842	0.737	0.952	0.842	0.737	0.952	CLONAL	1	TRUE	1	0.847945295548327	2		288	154	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42026723	42026723	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	73	361	0	ENST00000219905.7:c.3848del	p.Pro1283LeufsTer8	p.P1283Lfs*8	ENST00000219905	NM_001164273.1	1283	Cct/ct	12/24	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.847945295548327	2		361	162	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245547	153245547	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0032996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	52	254	0	ENST00000281708.4:c.1645-1G>T		p.X549_splice	ENST00000281708	NM_033632.3	549			0.847945295548327	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.847945295548327	1		254	60	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964962	55964962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	84	249	0	ENST00000263923.4:c.2275G>A	p.Glu759Lys	p.E759K	ENST00000263923	NM_002253.2	759	Gaa/Aaa	16/30	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.80651343666214	2		249	195	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	116	151	0				ENST00000310581	NM_198253.2	-/1132			0.80651343666214	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.80651343666214	3		151	183	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793483	18793483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603405	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	123	282	0	ENST00000266497.5:c.4180G>A	p.Glu1394Lys	p.E1394K	ENST00000266497		1394	Gaa/Aaa	30/31	0.328654443723931	2	FACETS	1	0.988	1	0.706	0.656	0.755	INDETERMINATE	1	TRUE	0	0.80651343666214	2		282	216	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713470	40713470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318044562	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	188	572	2	ENST00000373198.4:c.4045C>T	p.Arg1349Cys	p.R1349C	ENST00000373198	NM_133170.3	1349	Cgt/Tgt	30/32	0.24947291349362	3	FACETS	1	0.99	1	0.693	0.647	0.74	INDETERMINATE	1	TRUE	1	0.80651343666214	3		574	472	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468397	89468397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	95	194	0	ENST00000336596.2:c.1931C>T	p.Ser644Leu	p.S644L	ENST00000336596	NM_005233.5	644	tCa/tTa	11/17	0.80651343666214	3	FACETS	0.913	0.837	0.989	0.913	0.837	0.989	CLONAL	2	TRUE	1	0.80651343666214	3		194	181	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518026	187518026	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	315	491	0	ENST00000441802.2:c.12668C>T	p.Pro4223Leu	p.P4223L	ENST00000441802	NM_005245.3	4223	cCc/cTc	25/27	0.696049083739273	3	FACETS	0.945	0.902	0.988	0.945	0.902	0.988	CLONAL	2	TRUE	1	0.80651343666214	3		491	580	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	409	516	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	0.699880664032585	4	FACETS	1	0.99	1			1	CLONAL	4	TRUE	NA	0.80651343666214	4		516	451	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421568	32421568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267602851	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	371	510	1	ENST00000332351.3:c.1024G>A	p.Asp342Asn	p.D342N	ENST00000332351	NM_024426.4	342	Gat/Aat	6/10	0.527984571516499	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	2	0.80651343666214	4		511	812	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662652	117662652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	149	465	0	ENST00000368508.3:c.4813G>A	p.Glu1605Lys	p.E1605K	ENST00000368508	NM_002944.2	1605	Gaa/Aaa	29/43	0.80651343666214	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.80651343666214	1		465	211	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747342068	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	525	735	1	ENST00000269305.4:c.394A>G	p.Lys132Glu	p.K132E	ENST00000269305	NM_001126112.2	132	Aag/Gag	5/11	0.80651343666214	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.80651343666214	2		736	619	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729727	41729727	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	273	449	0	ENST00000242208.4:c.802G>A	p.Glu268Lys	p.E268K	ENST00000242208	NM_002192.2	268	Gaa/Aaa	3/3	0.577306747040235	4	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	2	0.80651343666214	4		449	599	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134988	41134988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	20	241	0	ENST00000379561.5:c.640C>T	p.Arg214Cys	p.R214C	ENST00000379561	NM_002015.3	214	Cgt/Tgt	2/3	1	2	FACETS	0.249	0.191	0.317	0.249	0.191	0.317	SUBCLONAL	1	TRUE	1	0.80651343666214	2		241	199	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795006	42795006	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550975604	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	355	673	0	ENST00000575354.2:c.2086C>T	p.Arg696Trp	p.R696W	ENST00000575354	NM_015125.3	696	Cgg/Tgg	10/20	0.80651343666214	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.80651343666214	2		673	418	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024254	31024254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146747814	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	57	402	1	ENST00000375687.4:c.3739C>T	p.Arg1247Cys	p.R1247C	ENST00000375687	NM_015338.5	1247	Cgt/Tgt	13/13	0.24947291349362	3	FACETS	0.529	0.455	0.608	0.264	0.227	0.304	INDETERMINATE	1	TRUE	1	0.80651343666214	3		403	375	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857436	9857436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	379	529	0	ENST00000330684.3:c.3965G>A	p.Gly1322Glu	p.G1322E	ENST00000330684	NM_001134407.1	1322	gGa/gAa	13/13	0.80651343666214	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.80651343666214	3		529	423	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112440	115112440	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1033763029	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	315	437	3	ENST00000257566.3:c.1300G>A	p.Asp434Asn	p.D434N	ENST00000257566	NM_016569.3	434	Gac/Aac	7/8	0.80651343666214	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.80651343666214	2		440	362	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680388	30680388	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748459364	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	173	520	1	ENST00000376406.3:c.1331G>A	p.Arg444Gln	p.R444Q	ENST00000376406	NM_014641.2	444	cGa/cAa	5/15	0.80651343666214	3	FACETS	0.974	0.901	1	0.487	0.45	0.525	CLONAL	1	TRUE	1	0.80651343666214	3		521	618	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189427	56189427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	376	516	0	ENST00000399503.3:c.4459C>T	p.Arg1487Cys	p.R1487C	ENST00000399503	NM_005921.1	1487	Cgt/Tgt	20/20	0.80651343666214	3	FACETS	0.969	0.929	1	0.969	0.929	1	CLONAL	2	TRUE	1	0.80651343666214	3		516	675	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340072	116340072	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751572663	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	68	224	0	ENST00000397752.3:c.934G>A	p.Glu312Lys	p.E312K	ENST00000397752	NM_000245.2	312	Gaa/Aaa	2/21	0.662284700919384	6	FACETS	1	0.967	1	0.445	0.39	0.504	CLONAL	1	TRUE	3	0.80651343666214	6		224	330	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940120	31940120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	209	680	0	ENST00000375333.2:c.262G>A	p.Glu88Lys	p.E88K	ENST00000375333	NM_032454.1	88	Gaa/Aaa	2/8	0.80651343666214	3	FACETS	0.97	0.903	1	0.485	0.451	0.519	CLONAL	1	TRUE	1	0.80651343666214	3		680	750	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300200	15300200	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1487017745	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	212	577	0	ENST00000263388.2:c.1076C>T	p.Pro359Leu	p.P359L	ENST00000263388	NM_000435.2	359	cCc/cTc	7/33	0.80651343666214	3	FACETS	0.986	0.919	1	0.493	0.459	0.528	CLONAL	1	TRUE	1	0.80651343666214	3		577	748	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552876	106552876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1003783236	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	265	594	1	ENST00000369096.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000369096	NM_001198.3	281	Gat/Aat	5/7	0.80651343666214	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.80651343666214	1		595	326	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730858	40730858	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200227405	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	252	646	2	ENST00000373198.4:c.3677G>A	p.Arg1226Gln	p.R1226Q	ENST00000373198	NM_133170.3	1226	cGa/cAa	27/32	0.24947291349362	3	FACETS	0.815	0.771	0.86	0.815	0.771	0.86	INDETERMINATE	2	TRUE	1	0.80651343666214	3		648	538	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808247	99808247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	144	468	2	ENST00000280892.6:c.442C>T	p.Arg148Cys	p.R148C	ENST00000280892	NM_001130678.1	148	Cgc/Tgc	5/7	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.80651343666214	2		470	331	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521486	8521486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752937985	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	296	570	0	ENST00000356435.5:c.752G>A	p.Gly251Glu	p.G251E	ENST00000356435		251	gGa/gAa	9/35	0.801600941235531	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.80651343666214	2		570	364	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942079	71942079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139442327	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	204	641	3	ENST00000298229.2:c.1343C>T	p.Ser448Leu	p.S448L	ENST00000298229	NM_001567.3	448	tCg/tTg	12/28	0.80651343666214	3	FACETS	1	0.971	1	0.539	0.502	0.576	CLONAL	1	TRUE	1	0.80651343666214	3		644	659	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528192	103528192	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	79	281	0	ENST00000355739.4:c.3500C>T	p.Ser1167Phe	p.S1167F	ENST00000355739	NM_000123.3	1167	tCt/tTt	15/15	0.114385269132085	6	FACETS	0.845	0.75	0.944			1	INDETERMINATE	2	TRUE	NA	0.80651343666214	6		281	303	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092764	27092764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	114	437	0	ENST00000324856.7:c.2785C>T	p.Pro929Ser	p.P929S	ENST00000324856	NM_006015.4	929	Cct/Tct	9/20	0.80651343666214	3	FACETS	0.781	0.706	0.859	0.39	0.353	0.43	SUBCLONAL	1	TRUE	1	0.80651343666214	3		437	508	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100833	27100833	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	136	382	0	ENST00000324856.7:c.4115C>T	p.Pro1372Leu	p.P1372L	ENST00000324856	NM_006015.4	1372	cCa/cTa	18/20	0.80651343666214	3	FACETS	1	0.972	1	0.567	0.521	0.616	CLONAL	1	TRUE	1	0.80651343666214	3		382	417	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106561	27106561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	202	572	1	ENST00000324856.7:c.6172G>A	p.Glu2058Lys	p.E2058K	ENST00000324856	NM_006015.4	2058	Gaa/Aaa	20/20	0.80651343666214	3	FACETS	1	0.95	1	0.512	0.477	0.549	CLONAL	1	TRUE	1	0.80651343666214	3		573	686	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106071	8106072	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	106	387	1	ENST00000346208.3:c.891_892delinsTT	p.Arg298Trp	p.R298W	ENST00000346208		297	aaCCgg/aaTTgg	4/6	1	2	FACETS	0.932	0.849	1	0.932	0.849	1	CLONAL	1	TRUE	1	0.80651343666214	2		388	282	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499713	18499713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	203	403	1	ENST00000266497.5:c.1568C>T	p.Ser523Phe	p.S523F	ENST00000266497		523	tCc/tTc	10/31	0.328654443723931	2	FACETS	1	0.991	1	0.649	0.611	0.686	INDETERMINATE	1	TRUE	0	0.80651343666214	2		404	388	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444315	49444315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	460	629	0	ENST00000301067.7:c.3056C>T	p.Pro1019Leu	p.P1019L	ENST00000301067	NM_003482.3	1019	cCc/cTc	11/54	0.80651343666214	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.80651343666214	2		629	528	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924427	112924428	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	210	314	0	ENST00000351677.2:c.1373_1374delinsTT	p.His458Leu	p.H458L	ENST00000351677	NM_002834.3	458	cAC/cTT	11/16	0.80651343666214	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.80651343666214	2		314	240	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218930	133218930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	391	676	3	ENST00000320574.5:c.5006C>T	p.Ser1669Phe	p.S1669F	ENST00000320574	NM_006231.2	1669	tCc/tTc	38/49	0.80651343666214	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.80651343666214	2		679	481	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589783	28589783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	127	428	2	ENST00000241453.7:c.2597C>T	p.Thr866Ile	p.T866I	ENST00000241453	NM_004119.2	866	aCc/aTc	21/24	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.80651343666214	2		430	315	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931804	28931804	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	136	349	0	ENST00000282397.4:c.2135G>A	p.Gly712Glu	p.G712E	ENST00000282397	NM_002019.4	712	gGa/gAa	15/30	1	2	FACETS	0.947	0.872	1	0.947	0.872	1	CLONAL	1	TRUE	1	0.80651343666214	2		349	356	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012471	29012471	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	91	364	0	ENST00000282397.4:c.400C>G	p.Pro134Ala	p.P134A	ENST00000282397	NM_002019.4	134	Cct/Gct	4/30	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.80651343666214	2		364	219	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678598	88678598	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	175	267	1	ENST00000360948.2:c.938C>T	p.Pro313Leu	p.P313L	ENST00000360948	NM_001012338.2	313	cCt/cTt	9/19	0.80651343666214	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.80651343666214	2		268	216	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478095	99478095	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs569704719	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	321	399	0	ENST00000268035.6:c.2999C>T	p.Thr1000Ile	p.T1000I	ENST00000268035	NM_000875.3	1000	aCc/aTc	16/21	0.80651343666214	2	FACETS	0.971	0.94	1	0.971	0.94	1	CLONAL	2	TRUE	0	0.80651343666214	2		399	410	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857952	9857952	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	513	472	0	ENST00000330684.3:c.3449C>A	p.Pro1150His	p.P1150H	ENST00000330684	NM_001134407.1	1150	cCc/cAc	13/13	0.80651343666214	3	FACETS	0.971	0.949	0.991	0.971	0.949	0.991	CLONAL	3	TRUE	0	0.80651343666214	3		472	613	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436145	56436145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1342743047	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	659	458	0	ENST00000407977.2:c.992C>T	p.Ser331Phe	p.S331F	ENST00000407977		331	tCt/tTt	9/10	0.80651343666214	4	FACETS	1	0.996	1	1	0.996	1	CLONAL	4	TRUE	0	0.80651343666214	4		458	716	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59871088	59871088	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs775171520	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	253	289	0	ENST00000259008.2:c.1343G>A	p.Trp448Ter	p.W448*	ENST00000259008	NM_032043.2	448	tGg/tAg	10/20	0.80651343666214	4	FACETS	0.977	0.949	1	0.977	0.949	1	CLONAL	4	TRUE	0	0.80651343666214	4		289	290	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226928	2226928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1188300147	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	109	210	0	ENST00000398665.3:c.4408C>T	p.Pro1470Ser	p.P1470S	ENST00000398665	NM_032482.2	1470	Ccg/Tcg	27/28	0.80651343666214	3	FACETS	1	0.978	1	0.624	0.568	0.681	CLONAL	1	TRUE	1	0.80651343666214	3		210	304	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366209	15366209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	377	631	0	ENST00000263377.2:c.1946C>T	p.Pro649Leu	p.P649L	ENST00000263377	NM_058243.2	649	cCc/cTc	10/20	0.80651343666214	3	FACETS	0.947	0.907	0.986	0.947	0.907	0.986	CLONAL	2	TRUE	1	0.80651343666214	3		631	693	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967261	25967261	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	107	412	0	ENST00000435504.4:c.1945C>T	p.Pro649Ser	p.P649S	ENST00000435504		649	Cct/Tct	13/13	0.80651343666214	3	FACETS	0.902	0.815	0.992	0.451	0.407	0.496	CLONAL	1	TRUE	1	0.80651343666214	3		412	413	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530085	212530085	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561997094	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	90	339	0	ENST00000342788.4:c.1834C>T	p.Arg612Trp	p.R612W	ENST00000342788	NM_005235.2	612	Cgg/Tgg	15/28	0.80651343666214	3	FACETS	0.955	0.856	1	0.477	0.428	0.529	CLONAL	1	TRUE	1	0.80651343666214	3		339	328	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019175	31019175	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	182	435	3	ENST00000375687.4:c.770C>T	p.Ser257Phe	p.S257F	ENST00000375687	NM_015338.5	257	tCc/tTc	9/13	0.24947291349362	3	FACETS	1	0.987	1	0.638	0.594	0.684	INDETERMINATE	1	TRUE	1	0.80651343666214	3		438	496	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727073	40727073	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	199	421	0	ENST00000373198.4:c.3891G>T	p.Met1297Ile	p.M1297I	ENST00000373198	NM_133170.3	1297	atG/atT	28/32	0.24947291349362	3	FACETS	0.853	0.802	0.904	0.853	0.802	0.904	INDETERMINATE	2	TRUE	1	0.80651343666214	3		421	406	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72881599	72881599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	143	382	2	ENST00000325599.8:c.520C>T	p.Pro174Ser	p.P174S	ENST00000325599	NM_018130.2	174	Cca/Tca	5/11	0.80651343666214	3	FACETS	0.989	0.908	1	0.495	0.454	0.537	CLONAL	1	TRUE	1	0.80651343666214	3		384	503	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664504	138664504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1202654322	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	78	182	2	ENST00000330315.3:c.1061C>T	p.Ala354Val	p.A354V	ENST00000330315	NM_023067.3	354	gCc/gTc	1/1	0.80651343666214	3	FACETS	0.923	0.82	1	0.462	0.41	0.516	CLONAL	1	TRUE	1	0.80651343666214	3		184	294	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444542	187444542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	338	529	0	ENST00000232014.4:c.1685C>T	p.Ala562Val	p.A562V	ENST00000232014	NM_001130845.1	562	gCc/gTc	7/10	0.80651343666214	3	FACETS	0.928	0.886	0.969	0.928	0.886	0.969	CLONAL	2	TRUE	1	0.80651343666214	3		529	634	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446146	187446146	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	148	499	0	ENST00000232014.4:c.1540+2T>A		p.X514_splice	ENST00000232014	NM_001130845.1	514			0.80651343666214	3	FACETS	0.935	0.858	1	0.467	0.429	0.507	CLONAL	1	TRUE	1	0.80651343666214	3		499	551	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293456	1293457	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	149	591	2	ENST00000310581.5:c.1544_1545delinsAA	p.Arg515Gln	p.R515Q	ENST00000310581	NM_198253.2	515	cGG/cAA	2/16	0.80651343666214	3	FACETS	0.854	0.783	0.928	0.427	0.391	0.464	CLONAL	1	TRUE	1	0.80651343666214	3		593	607	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752341	57752341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	232	431	0	ENST00000274289.3:c.1232C>T	p.Pro411Leu	p.P411L	ENST00000274289	NM_006622.3	411	cCc/cTc	9/14	0.80651343666214	3	FACETS	0.963	0.913	1	0.963	0.913	1	CLONAL	2	TRUE	1	0.80651343666214	3		431	419	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504315	149504315	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	415	574	1	ENST00000261799.4:c.1887G>A	p.Met629Ile	p.M629I	ENST00000261799	NM_002609.3	629	atG/atA	13/23	0.80651343666214	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.80651343666214	3		575	678	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710534	117710534	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	34	164	0	ENST00000368508.3:c.1738C>T	p.Pro580Ser	p.P580S	ENST00000368508	NM_002944.2	580	Cct/Tct	12/43	0.80651343666214	1	FACETS	0.645	0.548	0.744	0.645	0.548	0.744	SUBCLONAL	1	TRUE	0	0.80651343666214	1		164	78	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372765	81372765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	138	316	0	ENST00000222390.5:c.769G>A	p.Asp257Asn	p.D257N	ENST00000222390	NM_000601.4	257	Gat/Aat	7/18	0.80651343666214	3	FACETS	0.904	0.827	0.984	0.452	0.413	0.492	CLONAL	1	TRUE	1	0.80651343666214	3		316	531	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397828	116397828	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	125	485	0	ENST00000397752.3:c.2102G>A	p.Ser701Asn	p.S701N	ENST00000397752	NM_000245.2	701	aGt/aAt	8/21	0.662284700919384	6	FACETS	1	0.975	1	0.405	0.367	0.445	CLONAL	1	TRUE	3	0.80651343666214	6		485	667	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514429	148514429	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	128	427	0	ENST00000320356.2:c.1295C>T	p.Pro432Leu	p.P432L	ENST00000320356	NM_004456.4	432	cCt/cTt	11/20	0.662284700919384	6	FACETS	1	0.969	1	0.385	0.349	0.422	CLONAL	1	TRUE	3	0.80651343666214	6		427	719	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538756	23538756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	74	278	0	ENST00000380871.4:c.683G>A	p.Ser228Asn	p.S228N	ENST00000380871	NM_006167.3	228	aGc/aAc	2/2	1	2	FACETS	0.9	0.802	1	0.9	0.802	1	CLONAL	1	TRUE	1	0.80651343666214	2		278	204	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058530	69058530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	253	605	1	ENST00000288368.4:c.4174C>T	p.Pro1392Ser	p.P1392S	ENST00000288368	NM_024870.2	1392	Cct/Tct	34/40	0.328654443723931	2	FACETS	1	0.994	1	0.719	0.684	0.754	INDETERMINATE	1	TRUE	0	0.80651343666214	2		606	436	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561478	141561478	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	103	432	0	ENST00000220592.5:c.1327C>T	p.His443Tyr	p.H443Y	ENST00000220592	NM_012154.3	443	Cac/Tac	11/19	0.314402323200944	3	FACETS	0.759	0.683	0.84	0.253	0.227	0.28	INDETERMINATE	1	TRUE	0	0.80651343666214	3		432	472	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471083	8471083	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	71	241	2	ENST00000356435.5:c.3416G>A	p.Gly1139Asp	p.G1139D	ENST00000356435		1139	gGt/gAt	20/35	0.801600941235531	2	FACETS	1	0.953	1	0.557	0.499	0.616	CLONAL	1	TRUE	0	0.80651343666214	2		243	158	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342874	87342874	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	205	368	0	ENST00000277120.3:c.1159G>A	p.Gly387Ser	p.G387S	ENST00000277120		387	Ggt/Agt	9/19	0.80651343666214	2	FACETS	1	0.992	1	0.691	0.652	0.729	CLONAL	1	TRUE	0	0.80651343666214	2		368	368	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97934380	97934380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	130	287	0	ENST00000289081.3:c.395C>T	p.Ala132Val	p.A132V	ENST00000289081	NM_000136.2	132	gCt/gTt	5/15	0.80651343666214	2	FACETS	1	0.985	1	0.635	0.588	0.681	CLONAL	1	TRUE	0	0.80651343666214	2		287	254	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356173	70356173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	523	366	1	ENST00000374080.3:c.5068C>T	p.Leu1690Phe	p.L1690F	ENST00000374080		1690	Ctt/Ttt	37/45	0.699880664032585	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.80651343666214	2		367	586	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924427	112924427	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	210	314	0	ENST00000351677.2:c.1373A>T	p.His458Leu	p.H458L	ENST00000351677	NM_002834.3	458	cAc/cTc	11/16	0.80651343666214	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.80651343666214	2		314	240	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812196	212812196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	32	580	0	ENST00000342788.4:c.380G>A	p.Gly127Glu	p.G127E	ENST00000342788	NM_005235.2	127	gGa/gAa	3/28	1	2	FACETS	0.973	0.788	1	0.973	0.788	1	CLONAL	1	TRUE	1	0.11	2		580	598	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0033199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	504	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.531132950075412	6	FACETS	0.977	0.941	1			1	CLONAL	4	TRUE	NA	0.531132950075412	6		288	1001	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0033199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	95	248	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.977	0.878	1	0.977	0.878	1	CLONAL	1	TRUE	1	0.531132950075412	2		249	366	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857436	9857436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	131	529	0	ENST00000330684.3:c.3965G>A	p.Gly1322Glu	p.G1322E	ENST00000330684	NM_001134407.1	1322	gGa/gAa	13/13	1	2	FACETS	0.895	0.816	0.978	0.895	0.816	0.978	CLONAL	1	TRUE	1	0.531132950075412	2		529	551	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145431	58145431	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11547328	NA	P-0033199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	144	338	0	ENST00000257904.6:c.70C>T	p.Arg24Cys	p.R24C	ENST00000257904	NM_000075.3	24	Cgt/Tgt	2/8	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.531132950075412	2		338	523	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579314	7579314	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs1057520003	NA	P-0033199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	128	441	0	ENST00000269305.4:c.373A>C	p.Thr125Pro	p.T125P	ENST00000269305	NM_001126112.2	125	Acg/Ccg	4/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.531132950075412	2		441	387	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718234	117718234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	191	435	0	ENST00000368508.3:c.623C>T	p.Pro208Leu	p.P208L	ENST00000368508	NM_002944.2	208	cCc/cTc	7/43	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.531132950075412	2		435	689	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622236	117622236	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866580908	NA	P-0033199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	195	478	0	ENST00000368508.3:c.6634C>T	p.Gln2212Ter	p.Q2212*	ENST00000368508	NM_002944.2	2212	Cag/Tag	42/43	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.531132950075412	2		478	732	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779798	3779798	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	239	701	0	ENST00000262367.5:c.5250T>G	p.Asp1750Glu	p.D1750E	ENST00000262367	NM_004380.2	1750	gaT/gaG	31/31	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.531132950075412	2		701	853	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110165	8110165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774454455	NA	P-0033199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	170	494	0	ENST00000585124.1:c.440G>A	p.Arg147Gln	p.R147Q	ENST00000585124	NM_004217.3	147	cGg/cAg	6/9	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.531132950075412	2		494	637	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37672024	37672024	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	217	547	1	ENST00000447079.4:c.2809C>T	p.Gln937Ter	p.Q937*	ENST00000447079	NM_015083.1	937	Caa/Taa	9/14	1	2	FACETS	0.99	0.923	1	0.99	0.923	1	CLONAL	1	TRUE	1	0.531132950075412	2		548	825	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447202	187447202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	171	578	1	ENST00000232014.4:c.991C>T	p.Pro331Ser	p.P331S	ENST00000232014	NM_001130845.1	331	Cca/Tca	5/10	1	2	FACETS	0.92	0.849	0.994	0.92	0.849	0.994	CLONAL	1	TRUE	1	0.531132950075412	2		579	700	SUCCESS
APC	324	MSKCC	GRCh37	5	112179204	112179204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	89	311	0	ENST00000257430.4:c.7913C>T	p.Ala2638Val	p.A2638V	ENST00000257430	NM_000038.5	2638	gCt/gTt	16/16	1	2	FACETS	0.823	0.735	0.917	0.823	0.735	0.917	CLONAL	1	TRUE	1	0.531132950075412	2		311	407	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197114	26197114	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748604014	NA	P-0033199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	167	460	0	ENST00000356476.2:c.365C>T	p.Pro122Leu	p.P122L	ENST00000356476		122	cCc/cTc	1/1	1	2	FACETS	0.998	0.921	1	0.998	0.921	1	CLONAL	1	TRUE	1	0.531132950075412	2		460	630	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971126	21971128	+	frameshift_variant	Frame_Shift_Del	DEL	GAG	GAG	AA	novel	NA	P-0033199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	152	319	1	ENST00000304494.5:c.230_232delinsTT	p.Thr77IlefsTer69	p.T77Ifs*69	ENST00000304494	NM_000077.4	77	aCTCtc/aTTtc	2/3	0.531132950075412	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.531132950075412	1		320	385	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855211	76855211	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	186	560	0	ENST00000373344.5:c.5776G>A	p.Asp1926Asn	p.D1926N	ENST00000373344	NM_000489.3	1926	Gat/Aat	24/35	1	2	FACETS	0.88	0.814	0.948	0.88	0.814	0.948	CLONAL	1	TRUE	1	0.531132950075412	2		560	796	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087568	27087570	+	stop_gained	Nonsense_Mutation	TNP	CTC	CTC	TTA	novel	NA	P-0033199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	204	578	0	ENST00000324856.7:c.2142_2144delinsTTA	p.Ser715Ter	p.S715*	ENST00000324856	NM_006015.4	714	ctCTCg/ctTTAg	5/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.531132950075412	2		578	724	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	172	267	0				ENST00000310581	NM_198253.2	-/1132			0.600719033393795	3	FACETS	0.996	0.93	1			1	CLONAL	2	TRUE	NA	0.600719033393795	3		267	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	203	787	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.474581584746512	4	FACETS	1	0.988	1	0.818	0.768	0.868	CLONAL	2	TRUE	1	0.600719033393795	4		787	441	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593613	55593613	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913521	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	793	365	0	ENST00000288135.5:c.1679T>A	p.Val560Asp	p.V560D	ENST00000288135	NM_000222.2	560	gTt/gAt	11/21	0.600719033393795	16	FACETS	1	0.986	1			1	CLONAL	13	TRUE	NA	0.600719033393795	16		365	1047	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359066	81359066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	122	572	0	ENST00000222390.5:c.895C>T	p.Pro299Ser	p.P299S	ENST00000222390	NM_000601.4	299	Cct/Tct	8/18	0.600719033393795	6	FACETS	1	0.918	1	0.505	0.459	0.552	CLONAL	2	TRUE	2	0.600719033393795	6		572	443	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727151	41727151	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	109	839	1	ENST00000301178.4:c.409G>A	p.Gly137Ser	p.G137S	ENST00000301178	NM_021913.4	137	Ggc/Agc	3/20	0.585316709653199	4	FACETS	1	0.916	1	0.51	0.459	0.563	CLONAL	1	TRUE	2	0.600719033393795	4		840	570	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205332	46205332	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	36	405	0	ENST00000334344.6:c.416C>T	p.Ser139Leu	p.S139L	ENST00000334344	NM_152641.2	139	tCg/tTg	4/21	0.600719033393795	6	FACETS	1	0.829	1	0.251	0.207	0.299	CLONAL	1	TRUE	2	0.600719033393795	6		405	263	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231742	66231742	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	32	559	0	ENST00000273854.3:c.1958C>T	p.Pro653Leu	p.P653L	ENST00000273854	NM_004439.5	653	cCa/cTa	11/18	NA	2	FACETS	0.692	0.569	0.826			1	INDETERMINATE	1	TRUE	NA	0.600719033393795	2		559	154	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100388	8100388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	98	1112	0	ENST00000346208.3:c.362C>T	p.Ser121Phe	p.S121F	ENST00000346208		121	tCc/tTc	3/6	0.600719033393795	2	FACETS	0.919	0.828	1	0.46	0.414	0.507	CLONAL	1	TRUE	0	0.600719033393795	2		1112	355	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561520	9561520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	130	748	0	ENST00000353224.5:c.262G>A	p.Asp88Asn	p.D88N	ENST00000353224	NM_177990.2	88	Gat/Aat	4/10	0.454313252937581	6	FACETS	1	0.972	1	0.765	0.7	0.832	CLONAL	2	TRUE	3	0.600719033393795	6		748	415	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971093	21971094	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	440	768	1	ENST00000304494.5:c.264_265delinsAA	p.Gly89Ser	p.G89S	ENST00000304494	NM_000077.4	88	gaGGgc/gaAAgc	2/3	0.600719033393795	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	4	TRUE	0	0.600719033393795	4		769	541	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256666	16256666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	76	523	0	ENST00000375759.3:c.3931C>T	p.Pro1311Ser	p.P1311S	ENST00000375759	NM_015001.2	1311	Cct/Tct	11/15	0.275348357822491	6	FACETS	0.876	0.775	0.982	0.438	0.387	0.491	INDETERMINATE	2	TRUE	2	0.600719033393795	6		523	318	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743942	40743942	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868489194	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	71	598	0	ENST00000373198.4:c.3053G>A	p.Arg1018Gln	p.R1018Q	ENST00000373198	NM_133170.3	1018	cGa/cAa	23/32	NA	2	FACETS	0.642	0.564	0.726			1	INDETERMINATE	1	TRUE	NA	0.600719033393795	2		598	368	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554099	63554099	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	137	842	0	ENST00000307078.5:c.640G>A	p.Gly214Arg	p.G214R	ENST00000307078	NM_004655.3	214	Gga/Aga	2/11	0.474581584746512	4	FACETS	1	0.978	1	0.405	0.369	0.442	CLONAL	1	TRUE	1	0.600719033393795	4		842	601	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157539	106157539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs192553789	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	40	286	0	ENST00000380013.4:c.2440C>T	p.Arg814Cys	p.R814C	ENST00000380013	NM_001127208.2	814	Cgt/Tgt	3/11	0.600719033393795	3	FACETS	1	0.936	1	0.61	0.516	0.709	CLONAL	1	TRUE	1	0.600719033393795	3		286	142	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527934	157527934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	47	586	0	ENST00000346085.5:c.5659G>A	p.Ala1887Thr	p.A1887T	ENST00000346085	NM_020732.3	1887	Gca/Aca	20/20	0.311553399657843	4	FACETS	0.686	0.581	0.802	0.172	0.145	0.201	INDETERMINATE	1	TRUE	0	0.600719033393795	4		586	365	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	183	454	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	0.172125500612299	3	FACETS	1	0.991	1	0.749	0.696	0.803	INDETERMINATE	1	TRUE	1	0.600719033393795	3		454	529	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508561	106508561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	114	330	0	ENST00000359195.3:c.555G>A	p.Met185Ile	p.M185I	ENST00000359195	NM_002649.2	185	atG/atA	2/11	0.600719033393795	6	FACETS	1	0.921	1	0.754	0.69	0.819	CLONAL	3	TRUE	2	0.600719033393795	6		330	277	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610228	81610228	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139352934	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	76	521	0	ENST00000298171.2:c.1826G>A	p.Arg609Gln	p.R609Q	ENST00000298171	NM_000369.2	609	cGa/cAa	10/10	NA	2	FACETS	0.816	0.723	0.915			1	INDETERMINATE	1	TRUE	NA	0.600719033393795	2		521	310	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166742	32166742	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369417177	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	168	1156	2	ENST00000375023.3:c.4496G>A	p.Arg1499Gln	p.R1499Q	ENST00000375023	NM_004557.3	1499	cGa/cAa	24/30	0.600719033393795	5	FACETS	1	0.98	1	0.602	0.553	0.653	CLONAL	1	TRUE	3	0.600719033393795	5		1158	883	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658501	117658501	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	56	532	0	ENST00000368508.3:c.5082G>A	p.Trp1694Ter	p.W1694*	ENST00000368508	NM_002944.2	1694	tgG/tgA	31/43	0.332256665855816	3	FACETS	0.97	0.839	1	0.485	0.419	0.555	INDETERMINATE	1	TRUE	1	0.600719033393795	3		532	250	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445635	49445635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1304802509	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	266	1614	1	ENST00000301067.7:c.1831C>T	p.Pro611Ser	p.P611S	ENST00000301067	NM_003482.3	611	Cca/Tca	10/54	0.600719033393795	6	FACETS	0.914	0.858	0.973	0.457	0.429	0.487	CLONAL	2	TRUE	2	0.600719033393795	6		1615	1066	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974723	21974723	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746834149	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	337	482	0	ENST00000304494.5:c.104G>A	p.Gly35Glu	p.G35E	ENST00000304494	NM_000077.4	35	gGg/gAg	1/3	0.600719033393795	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	4	TRUE	0	0.600719033393795	4		482	403	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268749	46268749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1410071299	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	49	702	1	ENST00000371998.3:c.3034G>A	p.Asp1012Asn	p.D1012N	ENST00000371998		1012	Gat/Aat	16/23	0.275348357822491	6	FACETS	0.706	0.598	0.824	0.176	0.149	0.206	INDETERMINATE	1	TRUE	2	0.600719033393795	6		703	509	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	441059	441059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	44	496	0	ENST00000399788.2:c.1699C>T	p.Pro567Ser	p.P567S	ENST00000399788	NM_001042603.1	567	Cct/Tct	13/28	0.572370385277004	3	FACETS	0.648	0.546	0.759	0.324	0.273	0.38	SUBCLONAL	1	TRUE	1	0.600719033393795	3		496	294	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417871	32417871	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	89	620	0	ENST00000332351.3:c.1181C>T	p.Ala394Val	p.A394V	ENST00000332351	NM_024426.4	394	gCt/gTt	7/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.600719033393795	2		620	274	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292498	15292498	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	257	1324	0	ENST00000263388.2:c.2681A>G	p.Asn894Ser	p.N894S	ENST00000263388	NM_000435.2	894	aAc/aGc	17/33	0.585316709653199	4	FACETS	0.925	0.871	0.981	0.925	0.871	0.981	CLONAL	2	TRUE	2	0.600719033393795	4		1324	740	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059165	42059165	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	74	404	0	ENST00000219905.7:c.8885C>T	p.Ser2962Phe	p.S2962F	ENST00000219905	NM_001164273.1	2962	tCc/tTc	24/24	0.172125500612299	3	FACETS	1	0.972	1	0.662	0.588	0.739	INDETERMINATE	1	TRUE	1	0.600719033393795	3		404	242	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780296	9780296	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	104	681	0	ENST00000377346.4:c.1466A>C	p.Glu489Ala	p.E489A	ENST00000377346	NM_005026.3	489	gAg/gCg	11/24	0.275348357822491	6	FACETS	0.927	0.836	1	0.464	0.418	0.511	INDETERMINATE	2	TRUE	2	0.600719033393795	6		681	411	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100729	8100729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	94	980	1	ENST00000346208.3:c.703C>T	p.Pro235Ser	p.P235S	ENST00000346208		235	Ccc/Tcc	3/6	0.600719033393795	2	FACETS	0.889	0.798	0.984	0.445	0.399	0.492	CLONAL	1	TRUE	0	0.600719033393795	2		981	352	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989488	85989488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	64	535	0	ENST00000263360.6:c.1247C>T	p.Thr416Ile	p.T416I	ENST00000263360	NM_003797.3	416	aCc/aTc	12/12	0.377461312503444	5	FACETS	1	0.931	1			1	CLONAL	1	TRUE	NA	0.600719033393795	5		535	365	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207765	102207765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	157	473	1	ENST00000263464.3:c.1747C>T	p.Pro583Ser	p.P583S	ENST00000263464	NM_001165.4	583	Cct/Tct	9/9	0.319041375315998	6	FACETS	0.953	0.89	1	0.953	0.89	1	INDETERMINATE	4	TRUE	2	0.600719033393795	6		474	302	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416192	416192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	47	481	0	ENST00000399788.2:c.3994C>T	p.Pro1332Ser	p.P1332S	ENST00000399788	NM_001042603.1	1332	Cct/Tct	24/28	0.572370385277004	3	FACETS	0.707	0.6	0.823	0.353	0.3	0.412	SUBCLONAL	1	TRUE	1	0.600719033393795	3		481	288	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21630868	21630868	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	85	661	1	ENST00000421138.2:c.736C>T	p.Pro246Ser	p.P246S	ENST00000421138		246	Cct/Tct	8/16	NA	2	FACETS	0.809	0.721	0.901			1	INDETERMINATE	1	TRUE	NA	0.600719033393795	2		662	350	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443529	49443529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	132	722	0	ENST00000301067.7:c.3842G>A	p.Gly1281Glu	p.G1281E	ENST00000301067	NM_003482.3	1281	gGa/gAa	11/54	0.600719033393795	6	FACETS	1	0.98	1	0.322	0.292	0.353	CLONAL	1	TRUE	2	0.600719033393795	6		722	751	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50481231	50481232	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	92	443	1	ENST00000394963.4:c.617_618delinsTT	p.Ser206Phe	p.S206F	ENST00000394963	NM_003076.4	206	tCC/tTT	5/13	0.600719033393795	6	FACETS	1	0.924	1	0.262	0.233	0.293	CLONAL	1	TRUE	2	0.600719033393795	6		444	643	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50488282	50488283	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	183	756	0	ENST00000394963.4:c.1196_1197delinsTT	p.Thr399Ile	p.T399I	ENST00000394963	NM_003076.4	399	aCC/aTT	10/13	0.600719033393795	6	FACETS	0.836	0.773	0.902	0.418	0.386	0.451	CLONAL	2	TRUE	2	0.600719033393795	6		756	802	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975717	26975718	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	130	423	1	ENST00000381527.3:c.1225_1226delinsTT	p.Pro409Phe	p.P409F	ENST00000381527	NM_001260.1	409	CCt/TTt	12/13	0.600719033393795	4	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	2	0.600719033393795	4		424	343	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589810	28589810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	85	540	1	ENST00000241453.7:c.2570C>T	p.Pro857Leu	p.P857L	ENST00000241453	NM_004119.2	857	cCc/cTc	21/24	0.600719033393795	4	FACETS	1	0.936	1	0.539	0.479	0.603	CLONAL	1	TRUE	2	0.600719033393795	4		541	420	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919588	28919588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	107	580	0	ENST00000282397.4:c.2349G>A	p.Met783Ile	p.M783I	ENST00000282397	NM_002019.4	783	atG/atA	16/30	0.600719033393795	4	FACETS	0.777	0.703	0.853	0.777	0.703	0.853	SUBCLONAL	2	TRUE	2	0.600719033393795	4		580	367	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931748	28931748	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	71	582	0	ENST00000282397.4:c.2191T>G	p.Cys731Gly	p.C731G	ENST00000282397	NM_002019.4	731	Tgc/Ggc	15/30	0.600719033393795	4	FACETS	0.843	0.738	0.955	0.421	0.369	0.478	CLONAL	1	TRUE	2	0.600719033393795	4		582	449	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005348	29005348	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	140	752	0	ENST00000282397.4:c.913G>C	p.Asp305His	p.D305H	ENST00000282397	NM_002019.4	305	Gac/Cac	7/30	0.600719033393795	4	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	2	0.600719033393795	4		752	367	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912142	32912143	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	78	856	1	ENST00000380152.3:c.3650_3651delinsAA	p.Arg1217Lys	p.R1217K	ENST00000380152		1217	aGG/aAA	11/27	0.600719033393795	4	FACETS	0.786	0.692	0.886	0.393	0.346	0.443	SUBCLONAL	1	TRUE	2	0.600719033393795	4		857	529	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944608	32944608	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	107	808	1	ENST00000380152.3:c.8401T>C	p.Phe2801Leu	p.F2801L	ENST00000380152		2801	Ttt/Ctt	19/27	0.600719033393795	4	FACETS	1	0.927	1	0.518	0.466	0.573	CLONAL	1	TRUE	2	0.600719033393795	4		809	550	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950806	32950806	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs398122711	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	125	299	0	ENST00000380152.3:c.8633-1G>A		p.X2878_splice	ENST00000380152		2878			0.600719033393795	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.600719033393795	4		299	287	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610647	81610647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	92	304	0	ENST00000298171.2:c.2245C>T	p.Pro749Ser	p.P749S	ENST00000298171	NM_000369.2	749	Cca/Tca	10/10	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.600719033393795	2		304	224	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643331	38643331	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	69	513	0	ENST00000299084.4:c.801G>A	p.Trp267Ter	p.W267*	ENST00000299084	NM_152594.2	267	tgG/tgA	7/7	0.172125500612299	3	FACETS	1	0.974	1	0.708	0.627	0.792	INDETERMINATE	1	TRUE	1	0.600719033393795	3		513	211	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2107121	2107121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	125	1241	0	ENST00000219476.3:c.790C>T	p.Leu264Phe	p.L264F	ENST00000219476	NM_000548.3	264	Ctt/Ttt	9/42	0.585316709653199	4	FACETS	0.968	0.878	1	0.484	0.439	0.532	CLONAL	1	TRUE	2	0.600719033393795	4		1241	688	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778968	3778968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	89	703	0	ENST00000262367.5:c.6080C>T	p.Pro2027Leu	p.P2027L	ENST00000262367	NM_004380.2	2027	cCc/cTc	31/31	0.585316709653199	4	FACETS	1	0.959	1	0.58	0.517	0.646	CLONAL	1	TRUE	2	0.600719033393795	4		703	409	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991942	72991942	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	91	717	0	ENST00000268489.5:c.2103T>A	p.Cys701Ter	p.C701*	ENST00000268489	NM_006885.3	701	tgT/tgA	2/10	0.600719033393795	4	FACETS	0.96	0.856	1	0.48	0.428	0.536	CLONAL	1	TRUE	2	0.600719033393795	4		717	505	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836615	89836615	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145334278	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	147	1024	1	ENST00000389301.3:c.2275C>T	p.Pro759Ser	p.P759S	ENST00000389301	NM_000135.2	759	Cct/Tct	25/43	0.600719033393795	4	FACETS	1	0.977	1	0.594	0.544	0.647	CLONAL	1	TRUE	2	0.600719033393795	4		1025	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573007	7573026	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCTGTAGGAGACAGAAGCA	GGCTGTAGGAGACAGAAGCA	-	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	71	475	0	ENST00000269305.4:c.1101-18_1102del		p.X367_splice	ENST00000269305	NM_001126112.2	367		11/11	0.474581584746512	4	FACETS	1	0.949	1	0.383	0.337	0.433	CLONAL	1	TRUE	1	0.600719033393795	4		475	329	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973592	15973592	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	184	473	0	ENST00000268712.3:c.4400C>T	p.Pro1467Leu	p.P1467L	ENST00000268712	NM_006311.3	1467	cCc/cTc	31/46	0.474581584746512	4	FACETS	0.851	0.798	0.905	0.851	0.798	0.905	CLONAL	3	TRUE	1	0.600719033393795	4		473	384	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7163064	7163064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263032915	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	198	785	3	ENST00000302850.5:c.2008G>A	p.Glu670Lys	p.E670K	ENST00000302850	NM_000208.2	670	Gag/Aag	9/22	0.585316709653199	4	FACETS	0.977	0.912	1	0.977	0.912	1	CLONAL	2	TRUE	2	0.600719033393795	4		788	540	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952568	17952568	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	90	650	0	ENST00000458235.1:c.865C>T	p.Leu289Phe	p.L289F	ENST00000458235	NM_000215.3	289	Ctc/Ttc	7/24	0.585316709653199	4	FACETS	0.959	0.854	1	0.48	0.427	0.536	CLONAL	1	TRUE	2	0.600719033393795	4		650	500	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953923	17953923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	132	1210	1	ENST00000458235.1:c.479G>A	p.Gly160Asp	p.G160D	ENST00000458235	NM_000215.3	160	gGt/gAt	5/24	0.585316709653199	4	FACETS	0.926	0.841	1	0.463	0.42	0.507	CLONAL	1	TRUE	2	0.600719033393795	4		1211	760	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273089	18273089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	132	856	1	ENST00000222254.8:c.979G>A	p.Asp327Asn	p.D327N	ENST00000222254	NM_005027.3	327	Gat/Aat	8/16	0.585316709653199	4	FACETS	1	0.91	1	0.5	0.455	0.548	CLONAL	1	TRUE	2	0.600719033393795	4		857	703	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212123	36212123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568369252	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	84	714	0	ENST00000222270.7:c.1874C>T	p.Pro625Leu	p.P625L	ENST00000222270	NM_014727.1	625	cCt/cTt	3/37	0.585316709653199	4	FACETS	0.895	0.793	1	0.448	0.396	0.502	CLONAL	1	TRUE	2	0.600719033393795	4		714	500	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42381375	42381375	+	start_lost	Translation_Start_Site	SNP	A	A	C	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	101	686	0	ENST00000221972.3:c.1A>C	p.Met1?	p.M1?	ENST00000221972	NM_021601.3	1	Atg/Ctg	1/5	0.585316709653199	4	FACETS	0.98	0.879	1	0.49	0.439	0.544	CLONAL	1	TRUE	2	0.600719033393795	4		686	549	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594129	158594129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	58	484	0	ENST00000263640.3:c.1444C>T	p.Pro482Ser	p.P482S	ENST00000263640	NM_001105.4	482	Cca/Tca	11/11	0.474581584746512	4	FACETS	0.957	0.827	1	0.319	0.275	0.366	CLONAL	1	TRUE	1	0.600719033393795	4		484	323	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225449666	225449667	+	missense_variant	Missense_Mutation	DNP	AG	AG	TA	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	150	443	2	ENST00000264414.4:c.60_61delinsTA	p.Phe21Ile	p.F21I	ENST00000264414	NM_003590.4	20	gcCTtt/gcTAtt	1/16	0.600719033393795	5	FACETS	0.944	0.868	1	0.629	0.579	0.681	CLONAL	2	TRUE	2	0.600719033393795	5		445	503	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624940	9624940	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1186099038	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	91	424	0	ENST00000353224.5:c.37G>T	p.Gly13Cys	p.G13C	ENST00000353224	NM_177990.2	13	Ggc/Tgc	3/10	0.454313252937581	6	FACETS	0.845	0.762	0.931	0.845	0.762	0.931	CLONAL	3	TRUE	3	0.600719033393795	6		424	263	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755647	39755647	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	234	935	1	ENST00000288319.7:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000288319	NM_182918.3	373	tAt/tGt	10/10	0.600719033393795	4	FACETS	1	0.988	1	0.793	0.748	0.839	CLONAL	2	TRUE	1	0.600719033393795	4		936	524	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21304081	21304081	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	315	620	0	ENST00000354336.3:c.860C>T	p.Pro287Leu	p.P287L	ENST00000354336	NM_005207.3	287	cCc/cTc	3/3	0.600719033393795	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	1	0.600719033393795	4		620	545	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574472	41574472	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1327511041	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	164	770	0	ENST00000263253.7:c.6757G>A	p.Ala2253Thr	p.A2253T	ENST00000263253	NM_001429.3	2253	Gca/Aca	31/31	0.600719033393795	3	FACETS	0.937	0.872	1			1	CLONAL	2	TRUE	NA	0.600719033393795	3		770	379	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722256	49722256	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	94	908	0	ENST00000449682.2:c.1684G>A	p.Gly562Arg	p.G562R	ENST00000449682	NM_020998.3	562	Gga/Aga	15/18	0.275348357822491	6	FACETS	0.844	0.756	0.937	0.422	0.378	0.469	INDETERMINATE	2	TRUE	2	0.600719033393795	6		908	408	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595875	52595875	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	117	813	0	ENST00000394830.3:c.4040C>T	p.Ala1347Val	p.A1347V	ENST00000394830	NM_018313.4	1347	gCc/gTc	26/30	0.275348357822491	6	FACETS	0.831	0.753	0.913	0.415	0.376	0.457	INDETERMINATE	2	TRUE	2	0.600719033393795	6		813	516	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119624639	119624639	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	68	530	0	ENST00000316626.5:c.776G>A	p.Gly259Glu	p.G259E	ENST00000316626		259	gGg/gAg	7/12	0.600719033393795	3	FACETS	0.995	0.873	1	0.497	0.436	0.562	CLONAL	1	TRUE	1	0.600719033393795	3		530	296	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205080	128205080	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	273	1143	0	ENST00000341105.2:c.361T>G	p.Phe121Val	p.F121V	ENST00000341105	NM_032638.4	121	Ttc/Gtc	3/6	0.600719033393795	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.600719033393795	3		1143	547	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169953063	169953064	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	183	698	1	ENST00000295797.4:c.147_148delinsTT	p.Leu50Phe	p.L50F	ENST00000295797	NM_002740.5	49	ggCCtt/ggTTtt	2/18	0.600719033393795	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.600719033393795	2		699	269	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917437	178917492	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATGTAATAGAATGTTATATTCTTTATGTAATTTTATTAAAGGTTTTGCTATCGGCA	ATGTAATAGAATGTTATATTCTTTATGTAATTTTATTAAAGGTTTTGCTATCGGCA	-	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	25	194	0	ENST00000263967.3:c.353-41_367del		p.X118_splice	ENST00000263967	NM_006218.2	118		3/21	0.600719033393795	2	FACETS	1	0.905	1	0.595	0.485	0.71	CLONAL	1	TRUE	0	0.600719033393795	2		194	70	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504006	186504006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	51	366	0	ENST00000323963.5:c.571C>T	p.Arg191Cys	p.R191C	ENST00000323963		191	Cgt/Tgt	6/11	0.600719033393795	2	FACETS	0.866	0.747	0.993	0.433	0.373	0.497	CLONAL	1	TRUE	0	0.600719033393795	2		366	196	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1918661	1918662	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	142	521	1	ENST00000382891.5:c.824_825delinsAA	p.Trp275Ter	p.W275*	ENST00000382891	NM_133335.3	275	tGG/tAA	4/22	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.600719033393795	2		522	330	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127439	55127439	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553902415	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	1174	717	0	ENST00000257290.5:c.227A>G	p.Asn76Ser	p.N76S	ENST00000257290	NM_006206.4	76	aAc/aGc	3/23	0.600719033393795	16	FACETS	0.984	0.97	0.998			1	CLONAL	15	TRUE	NA	0.600719033393795	16		717	1378	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152054	55152054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1397	107	805	0	ENST00000257290.5:c.2486G>A	p.Gly829Glu	p.G829E	ENST00000257290	NM_006206.4	829	gGa/gAa	18/23	0.600719033393795	16	FACETS	1	0.97	1			1	CLONAL	1	TRUE	NA	0.600719033393795	16		805	1504	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193772	106193772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	49	300	0	ENST00000380013.4:c.4234G>A	p.Asp1412Asn	p.D1412N	ENST00000380013	NM_001127208.2	1412	Gat/Aat	10/11	0.600719033393795	3	FACETS	1	0.873	1	0.51	0.437	0.588	CLONAL	1	TRUE	1	0.600719033393795	3		300	208	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197111	106197111	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	54	364	0	ENST00000380013.4:c.5444G>C	p.Gly1815Ala	p.G1815A	ENST00000380013	NM_001127208.2	1815	gGc/gCc	11/11	0.600719033393795	3	FACETS	1	0.867	1	0.502	0.433	0.575	CLONAL	1	TRUE	1	0.600719033393795	3		364	233	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524510	187524511	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AT	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	100	858	1	ENST00000441802.2:c.11169_11170delinsAT	p.Glu3724Ter	p.E3724*	ENST00000441802	NM_005245.3	3723	gaGGaa/gaATaa	19/27	0.600719033393795	3	FACETS	1	0.929	1	0.52	0.468	0.575	CLONAL	1	TRUE	1	0.600719033393795	3		859	416	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629714	187629714	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	208	784	2	ENST00000441802.2:c.1268del	p.Leu423Ter	p.L423*	ENST00000441802	NM_005245.3	423	tTa/ta	2/27	0.600719033393795	3	FACETS	0.946	0.888	1	0.946	0.888	1	CLONAL	2	TRUE	1	0.600719033393795	3		786	476	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947463	38947463	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	59	363	0	ENST00000357387.3:c.4217C>T	p.Ser1406Phe	p.S1406F	ENST00000357387	NM_152756.3	1406	tCt/tTt	32/38	0.484558152539862	5	FACETS	1	0.952	1	0.409	0.355	0.468	CLONAL	1	TRUE	2	0.600719033393795	5		363	304	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958579	38958580	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	51	229	0	ENST00000357387.3:c.2385_2386delinsTT	p.His796Tyr	p.H796Y	ENST00000357387	NM_152756.3	795	tcCCac/tcTTac	24/38	0.484558152539862	5	FACETS	0.928	0.802	1	0.618	0.535	0.707	CLONAL	2	TRUE	2	0.600719033393795	5		229	174	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501554	149501554	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	118	795	0	ENST00000261799.4:c.2233A>G	p.Lys745Glu	p.K745E	ENST00000261799	NM_002609.3	745	Aag/Gag	16/23	0.600719033393795	3	FACETS	1	0.946	1	0.531	0.482	0.583	CLONAL	1	TRUE	1	0.600719033393795	3		795	481	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513304	149513304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753192549	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	172	623	0	ENST00000261799.4:c.779C>T	p.Pro260Leu	p.P260L	ENST00000261799	NM_002609.3	260	cCg/cTg	6/23	0.600719033393795	3	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	1	0.600719033393795	3		623	368	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513463	149513463	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1338652552	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	106	717	0	ENST00000261799.4:c.740G>A	p.Trp247Ter	p.W247*	ENST00000261799	NM_002609.3	247	tGg/tAg	5/23	0.600719033393795	3	FACETS	1	0.916	1	0.509	0.459	0.561	CLONAL	1	TRUE	1	0.600719033393795	3		717	451	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672561	30672561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	124	1003	0	ENST00000376406.3:c.4399C>T	p.Pro1467Ser	p.P1467S	ENST00000376406	NM_014641.2	1467	Cct/Tct	10/15	0.600719033393795	5	FACETS	1	0.968	1	0.578	0.524	0.635	CLONAL	1	TRUE	3	0.600719033393795	5		1003	679	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948262	31948262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	295	1081	0	ENST00000375333.2:c.850G>A	p.Asp284Asn	p.D284N	ENST00000375333	NM_032454.1	284	Gat/Aat	6/8	0.600719033393795	5	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	3	0.600719033393795	5		1081	749	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190408	32190408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	132	1235	0	ENST00000375023.3:c.331G>A	p.Gly111Ser	p.G111S	ENST00000375023	NM_004557.3	111	Ggt/Agt	3/30	0.600719033393795	5	FACETS	1	0.969	1	0.575	0.523	0.63	CLONAL	1	TRUE	3	0.600719033393795	5		1235	726	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815329	32815330	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	148	1142	1	ENST00000354258.4:c.2043_2044delinsTT	p.His682Tyr	p.H682Y	ENST00000354258	NM_000593.5	681	gcCCat/gcTTat	9/11	0.600719033393795	5	FACETS	1	0.94	1	0.518	0.473	0.566	CLONAL	1	TRUE	3	0.600719033393795	5		1143	904	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790641	89790641	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	268	1485	1	ENST00000336032.3:c.28G>A	p.Glu10Lys	p.E10K	ENST00000336032	NM_006813.2	10	Gag/Aag	1/2	0.600719033393795	5	FACETS	0.91	0.855	0.966	0.91	0.855	0.966	CLONAL	2	TRUE	3	0.600719033393795	5		1486	932	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686842	117686842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	42	305	0	ENST00000368508.3:c.2875G>A	p.Glu959Lys	p.E959K	ENST00000368508	NM_002944.2	959	Gaa/Aaa	19/43	0.332256665855816	3	FACETS	0.838	0.707	0.981	0.419	0.353	0.491	INDETERMINATE	1	TRUE	1	0.600719033393795	3		305	217	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525573	137525573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765210093	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	156	675	0	ENST00000367739.4:c.442C>T	p.Pro148Ser	p.P148S	ENST00000367739	NM_000416.2	148	Cct/Tct	4/7	0.311553399657843	4	FACETS	1	0.963	1	0.778	0.73	0.826	INDETERMINATE	3	TRUE	0	0.600719033393795	4		675	267	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522611	157522611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	102	627	0	ENST00000346085.5:c.4883C>T	p.Ser1628Phe	p.S1628F	ENST00000346085	NM_020732.3	1628	tCc/tTc	18/20	0.311553399657843	4	FACETS	0.797	0.72	0.877	0.399	0.36	0.439	INDETERMINATE	2	TRUE	0	0.600719033393795	4		627	341	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206881	162206881	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs752922983	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	70	358	0	ENST00000366898.1:c.794A>G	p.His265Arg	p.H265R	ENST00000366898	NM_004562.2	265	cAc/cGc	7/12	0.311553399657843	4	FACETS	0.84	0.744	0.94	0.42	0.372	0.47	INDETERMINATE	2	TRUE	0	0.600719033393795	4		358	222	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963895	2963896	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	260	845	0	ENST00000396946.4:c.1911_1912delinsTT	p.Leu638Phe	p.L638F	ENST00000396946	NM_032415.4	637	aaCCtc/aaTTtc	15/25	0.275348357822491	6	FACETS	1	0.984	1	0.83	0.785	0.875	INDETERMINATE	3	TRUE	2	0.600719033393795	6		845	574	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468293	50468293	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	63	612	0	ENST00000331340.3:c.1528A>G	p.Thr510Ala	p.T510A	ENST00000331340	NM_006060.4	510	Acg/Gcg	8/8	0.481764425888179	6	FACETS	1	0.897	1	0.347	0.3	0.397	CLONAL	1	TRUE	3	0.600719033393795	6		612	444	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372729	81372729	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	79	456	1	ENST00000222390.5:c.805C>T	p.Pro269Ser	p.P269S	ENST00000222390	NM_000601.4	269	Cca/Tca	7/18	0.600719033393795	6	FACETS	1	0.952	1	0.29	0.255	0.326	CLONAL	1	TRUE	2	0.600719033393795	6		457	500	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606536	93606537	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	94	869	0	ENST00000375746.1:c.356_357delinsTT	p.Pro119Leu	p.P119L	ENST00000375746	NM_001174167.1	119	cCC/cTT	2/14	0.172125500612299	3	FACETS	0.988	0.885	1	0.494	0.442	0.548	INDETERMINATE	1	TRUE	1	0.600719033393795	3		869	412	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781263	135781263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	90	633	0	ENST00000298552.3:c.1702G>A	p.Gly568Arg	p.G568R	ENST00000298552	NM_001162426.1	568	Gga/Aga	15/23	0.600719033393795	3	FACETS	1	0.948	1	0.549	0.491	0.609	CLONAL	1	TRUE	1	0.600719033393795	3		633	355	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418357	139418357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	369	1553	0	ENST00000277541.6:c.215G>A	p.Gly72Glu	p.G72E	ENST00000277541	NM_017617.3	72	gGg/gAg	3/34	0.566009019662044	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.600719033393795	3		1553	754	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006821	47006821	+	5_prime_UTR_variant	5'UTR	SNP	G	G	A	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	304	450	0	ENST00000377604.3:c.-60G>A		p.*20*	ENST00000377604	NM_001204468.1	-/852		2/24	0.534966911814296	2	FACETS	0.929	0.903	0.954			1	CLONAL	3	TRUE	NA	0.600719033393795	2		450	363	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861461	152861462	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0033378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	48	170	0	ENST00000406277.2:c.290_290+1delinsAA		p.X97_splice	ENST00000406277	NM_152274.4	97		4/7	0.534966911814296		FACETS		0.964	1				CLONAL	1	TRUE	NA	0.600719033393795	2		170	117	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0033470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	180	528	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.921	0.849	0.996	0.921	0.849	0.996	CLONAL	1	TRUE	1	0.40085710543395	2		528	975	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0033470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	55	248	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.921	0.793	1	0.921	0.793	1	CLONAL	1	TRUE	1	0.40085710543395	2		249	298	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955550	48955550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913304	NA	P-0033470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	98	376	0	ENST00000267163.4:c.1666C>T	p.Arg556Ter	p.R556*	ENST00000267163	NM_000321.2	556	Cga/Tga	17/27	0.40085710543395	5	FACETS	1	0.956	1	0.378	0.337	0.422	CLONAL	1	TRUE	2	0.40085710543395	5		376	690	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316237	11316237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748631718	NA	P-0033470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	86	382	0	ENST00000361445.4:c.517C>T	p.Arg173Cys	p.R173C	ENST00000361445	NM_004958.3	173	Cgt/Tgt	5/58	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.40085710543395	2		382	387	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0033470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	159	355	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.360400936952724	2	FACETS	1	0.989	1	0.741	0.684	0.801	CLONAL	1	TRUE	0	0.40085710543395	2		355	535	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857635	9857635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866748846	NA	P-0033470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	82	523	0	ENST00000330684.3:c.3766G>A	p.Glu1256Lys	p.E1256K	ENST00000330684	NM_001134407.1	1256	Gag/Aag	13/13	1	2	FACETS	0.96	0.851	1	0.96	0.851	1	CLONAL	1	TRUE	1	0.40085710543395	2		523	426	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614583	38614583	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434312	NA	P-0033470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	215	554	0	ENST00000299084.4:c.349C>T	p.Arg117Ter	p.R117*	ENST00000299084	NM_152594.2	117	Cga/Tga	3/7	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.40085710543395	2		554	937	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421547	32421547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	138	607	0	ENST00000332351.3:c.1045C>T	p.Leu349Phe	p.L349F	ENST00000332351	NM_024426.4	349	Ctc/Ttc	6/10	1	2	FACETS	0.971	0.885	1	0.971	0.885	1	CLONAL	1	TRUE	1	0.40085710543395	2		607	709	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033967	49033967	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1131690865	NA	P-0033470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	192	408	0	ENST00000267163.4:c.2104C>T	p.Gln702Ter	p.Q702*	ENST00000267163	NM_000321.2	702	Caa/Taa	20/27	0.40085710543395	5	FACETS	1	0.93	1	0.668	0.62	0.719	CLONAL	2	TRUE	2	0.40085710543395	5		408	765	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972729	25972729	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	149	515	0	ENST00000435504.4:c.1696C>T	p.Leu566Phe	p.L566F	ENST00000435504		566	Ctc/Ttc	12/13	0.145448584659446	3	FACETS	1	0.986	1	0.693	0.635	0.753	INDETERMINATE	1	TRUE	1	0.40085710543395	3		515	644	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546862	9546862	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	117	525	0	ENST00000353224.5:c.1160C>T	p.Ser387Phe	p.S387F	ENST00000353224	NM_177990.2	387	tCc/tTc	5/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.40085710543395	2		525	518	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561532	9561532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755247878	NA	P-0033470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	101	547	1	ENST00000353224.5:c.250G>A	p.Gly84Ser	p.G84S	ENST00000353224	NM_177990.2	84	Ggc/Agc	4/10	1	2	FACETS	0.818	0.732	0.909	0.818	0.732	0.909	CLONAL	1	TRUE	1	0.40085710543395	2		548	616	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36028554	36028554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388365171	NA	P-0033470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	121	621	0	ENST00000358208.4:c.896C>T	p.Thr299Ile	p.T299I	ENST00000358208		299	aCc/aTc	8/12	1	2	FACETS	0.975	0.883	1	0.975	0.883	1	CLONAL	1	TRUE	1	0.40085710543395	2		621	619	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447183	187447183	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	164	711	0	ENST00000232014.4:c.1010C>T	p.Ser337Phe	p.S337F	ENST00000232014	NM_001130845.1	337	tCt/tTt	5/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.40085710543395	2		711	761	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542585	187542585	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs200903267	NA	P-0033470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	121	614	0	ENST00000441802.2:c.5155A>G	p.Ile1719Val	p.I1719V	ENST00000441802	NM_005245.3	1719	Atc/Gtc	10/27	1	2	FACETS	0.964	0.873	1	0.964	0.873	1	CLONAL	1	TRUE	1	0.40085710543395	2		614	626	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268856	98268856	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	63	341	0	ENST00000331920.6:c.227C>T	p.Pro76Leu	p.P76L	ENST00000331920	NM_000264.3	76	cCg/cTg	2/24	1	2	FACETS	0.97	0.845	1	0.97	0.845	1	CLONAL	1	TRUE	1	0.40085710543395	2		341	324	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922791	44922791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	113	478	1	ENST00000377967.4:c.1652C>T	p.Pro551Leu	p.P551L	ENST00000377967	NM_021140.2	551	cCt/cTt	16/29	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.40085710543395	2		479	523	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412056	63412056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	110	824	0	ENST00000330258.3:c.1111G>A	p.Glu371Lys	p.E371K	ENST00000330258	NM_152424.3	371	Gag/Aag	2/2	1	2	FACETS	0.741	0.666	0.82	0.741	0.666	0.82	SUBCLONAL	1	TRUE	1	0.40085710543395	2		824	741	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0033620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	128	289	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.533568053962833	2		289	395	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099397	27099397	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	164	309	0	ENST00000324856.7:c.3634C>T	p.Gln1212Ter	p.Q1212*	ENST00000324856	NM_006015.4	1212	Cag/Tag	14/20	NA	2	FACETS	0.891	0.82	0.964			1	INDETERMINATE	1	TRUE	NA	0.533568053962833	2		309	690	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252878	36252878	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	189	357	0	ENST00000300305.3:c.484A>T	p.Arg162Trp	p.R162W	ENST00000300305		162	Agg/Tgg	4/8	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.533568053962833	2		357	669	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112596	2112596	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs769147552	NA	P-0033620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	167	520	0	ENST00000219476.3:c.1356C>G	p.Phe452Leu	p.F452L	ENST00000219476	NM_000548.3	452	ttC/ttG	13/42	1	2	FACETS	0.903	0.832	0.977	0.903	0.832	0.977	CLONAL	1	TRUE	1	0.533568053962833	2		520	693	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586240	48586241	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGGC	novel	NA	P-0033620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	96	458	0	ENST00000342988.3:c.909_910insAGGC	p.Val304ArgfsTer5	p.V304Rfs*5	ENST00000342988	NM_005359.5	303	-/AGGC	8/12	0.533568053962833	1	FACETS	0.541	0.484	0.601	0.541	0.484	0.601	SUBCLONAL	1	TRUE	0	0.533568053962833	1		458	488	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324585	62324585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556575959	NA	P-0033620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	226	596	0	ENST00000360203.5:c.2941G>A	p.Glu981Lys	p.E981K	ENST00000360203	NM_001283009.1	981	Gag/Aag	30/35	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.533568053962833	2		596	810	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185169137	185169137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	156	407	0	ENST00000265026.3:c.1232C>T	p.Ser411Phe	p.S411F	ENST00000265026	NM_004721.4	411	tCt/tTt	7/14	1	2	FACETS	0.816	0.748	0.885	0.816	0.748	0.885	CLONAL	1	TRUE	1	0.533568053962833	2		407	717	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506980	186506980	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	94	253	0	ENST00000323963.5:c.1146G>C	p.Lys382Asn	p.K382N	ENST00000323963		382	aaG/aaC	11/11	1	2	FACETS	0.759	0.679	0.844	0.759	0.679	0.844	SUBCLONAL	1	TRUE	1	0.533568053962833	2		253	464	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875096	151875096	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0033620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	26	70	0	ENST00000262189.6:c.7443-1G>C		p.X2481_splice	ENST00000262189	NM_170606.2	2481			1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.533568053962833	2		70	82	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409414	80409414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	149	390	0	ENST00000286548.4:c.700G>A	p.Glu234Lys	p.E234K	ENST00000286548	NM_002072.3	234	Gaa/Aaa	5/7	1	2	FACETS	0.926	0.85	1	0.926	0.85	1	CLONAL	1	TRUE	1	0.533568053962833	2		390	603	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	110	151	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.613388792276843	2		151	322	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	263	454	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.613388792276843	2		454	801	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485860	8485860	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778486665	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	128	403	0	ENST00000356435.5:c.2957C>T	p.Pro986Leu	p.P986L	ENST00000356435		986	cCa/cTa	17/35	1	2	FACETS	0.896	0.817	0.977	0.896	0.817	0.977	CLONAL	1	TRUE	1	0.613388792276843	2		403	466	SUCCESS
APC	324	MSKCC	GRCh37	5	112177677	112177677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782301	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	114	313	0	ENST00000257430.4:c.6386C>T	p.Ser2129Leu	p.S2129L	ENST00000257430	NM_000038.5	2129	tCg/tTg	16/16	1	2	FACETS	0.92	0.835	1	0.92	0.835	1	CLONAL	1	TRUE	1	0.613388792276843	2		313	404	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611248	100611248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782457670	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	143	446	0	ENST00000308731.7:c.1358C>T	p.Ser453Phe	p.S453F	ENST00000308731	NM_000061.2	453	tCc/tTc	15/19	1	2	FACETS	0.998	0.917	1	0.998	0.917	1	CLONAL	1	TRUE	1	0.613388792276843	2		446	467	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687400	117687400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146570171	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	155	567	0	ENST00000368508.3:c.2651C>T	p.Ser884Phe	p.S884F	ENST00000368508	NM_002944.2	884	tCc/tTc	18/43	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.613388792276843	2		567	431	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552823	106552823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1042709746	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	198	502	0	ENST00000369096.4:c.788G>A	p.Gly263Glu	p.G263E	ENST00000369096	NM_001198.3	263	gGa/gAa	5/7	1	2	FACETS	0.934	0.869	1	0.934	0.869	1	CLONAL	1	TRUE	1	0.613388792276843	2		502	691	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803171	1803171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1161547820	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	238	649	0	ENST00000260795.2:c.523C>T	p.Arg175Cys	p.R175C	ENST00000260795		175	Cgc/Tgc	4/17	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.613388792276843	2		649	753	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976861	55976861	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	185	515	0	ENST00000263923.4:c.1051C>T	p.Pro351Ser	p.P351S	ENST00000263923	NM_002253.2	351	Cct/Tct	8/30	1	2	FACETS	0.941	0.873	1	0.941	0.873	1	CLONAL	1	TRUE	1	0.613388792276843	2		515	641	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866442	42866442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	585	794	0	ENST00000398585.3:c.190C>T	p.Pro64Ser	p.P64S	ENST00000398585	NM_001135099.1	64	Ccc/Tcc	3/14	0.589236026171473	3	FACETS	0.984	0.949	1	0.984	0.949	1	CLONAL	2	TRUE	1	0.613388792276843	3		794	1266	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622239	162622239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55654276	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	155	444	0	ENST00000366898.1:c.458C>T	p.Pro153Leu	p.P153L	ENST00000366898	NM_004562.2	153	cCc/cTc	4/12	1	2	FACETS	0.974	0.897	1	0.974	0.897	1	CLONAL	1	TRUE	1	0.613388792276843	2		444	519	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244982	123244982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	207	864	1	ENST00000358487.5:c.2122C>T	p.Pro708Ser	p.P708S	ENST00000358487	NM_000141.4	708	Ccc/Tcc	16/18	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.613388792276843	2		865	671	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683508	182683508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	125	517	1	ENST00000292782.4:c.37C>T	p.Arg13Cys	p.R13C	ENST00000292782	NM_020640.2	13	Cgt/Tgt	2/7	1	2	FACETS	0.756	0.687	0.828	0.756	0.687	0.828	SUBCLONAL	1	TRUE	1	0.613388792276843	2		518	539	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626628	100626628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	145	370	1	ENST00000308731.7:c.302C>T	p.Pro101Leu	p.P101L	ENST00000308731	NM_000061.2	101	cCc/cTc	4/19	1	2	FACETS	0.907	0.833	0.985	0.907	0.833	0.985	CLONAL	1	TRUE	1	0.613388792276843	2		371	521	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2492117	2492117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs944782838	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	199	556	0	ENST00000355716.4:c.515C>T	p.Pro172Leu	p.P172L	ENST00000355716	NM_003820.2	172	cCc/cTc	5/8	1	2	FACETS	0.953	0.886	1	0.953	0.886	1	CLONAL	1	TRUE	1	0.613388792276843	2		556	681	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176469	123176469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	109	224	0	ENST00000218089.9:c.436C>T	p.Arg146Ter	p.R146*	ENST00000218089	NM_001042749.1	146	Cga/Tga	7/35	1	2	FACETS	0.974	0.883	1	0.974	0.883	1	CLONAL	1	TRUE	1	0.613388792276843	2		224	365	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781403	135781403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759379027	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	156	428	0	ENST00000298552.3:c.1562C>T	p.Ser521Leu	p.S521L	ENST00000298552	NM_001162426.1	521	tCg/tTg	15/23	1	2	FACETS	0.883	0.813	0.956	0.883	0.813	0.956	CLONAL	1	TRUE	1	0.613388792276843	2		428	576	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045815	143045815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	166	470	0	ENST00000262992.4:c.1819C>T	p.Leu607Phe	p.L607F	ENST00000262992	NM_001101669.1	607	Ctt/Ttt	17/24	1	2	FACETS	0.889	0.82	0.96	0.889	0.82	0.96	CLONAL	1	TRUE	1	0.613388792276843	2		470	609	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17354360	17354360	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	133	367	0	ENST00000375499.3:c.424G>A	p.Asp142Asn	p.D142N	ENST00000375499	NM_003000.2	142	Gat/Aat	5/8	1	2	FACETS	0.992	0.909	1	0.992	0.909	1	CLONAL	1	TRUE	1	0.613388792276843	2		367	437	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852253	63852254	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	150	428	0	ENST00000279873.7:c.3031_3032delinsTT	p.Pro1011Leu	p.P1011L	ENST00000279873	NM_032199.2	1011	CCg/TTg	10/10	1	2	FACETS	0.939	0.863	1	0.939	0.863	1	CLONAL	1	TRUE	1	0.613388792276843	2		428	521	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298148	123298148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	137	519	0	ENST00000358487.5:c.706G>A	p.Glu236Lys	p.E236K	ENST00000358487	NM_000141.4	236	Gaa/Aaa	6/18	1	2	FACETS	0.778	0.711	0.848	0.778	0.711	0.848	SUBCLONAL	1	TRUE	1	0.613388792276843	2		519	574	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129352	64129352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369902429	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	166	519	0	ENST00000334205.4:c.784C>T	p.Pro262Ser	p.P262S	ENST00000334205	NM_003942.2	262	Ccc/Tcc	8/17	1	2	FACETS	0.896	0.827	0.967	0.896	0.827	0.967	CLONAL	1	TRUE	1	0.613388792276843	2		519	604	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202509	67202510	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	180	660	1	ENST00000312629.5:c.1318_1319delinsTT	p.Pro440Leu	p.P440L	ENST00000312629	NM_003952.2	440	CCg/TTg	15/15	1	2	FACETS	0.748	0.691	0.807	0.748	0.691	0.807	SUBCLONAL	1	TRUE	1	0.613388792276843	2		661	785	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863432	57863433	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	196	493	1	ENST00000228682.2:c.1527_1528delinsTT	p.Arg510Trp	p.R510W	ENST00000228682	NM_005269.2	509	ctCCgg/ctTTgg	11/12	0.613388792276843	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.613388792276843	1		494	430	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233142	69233142	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	111	299	0	ENST00000462284.1:c.1007T>A	p.Leu336His	p.L336H	ENST00000462284	NM_002392.5	336	cTt/cAt	11/11	0.613388792276843	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.613388792276843	1		299	230	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926248	112926248	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121918468	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	378	511	2	ENST00000351677.2:c.1381G>T	p.Ala461Ser	p.A461S	ENST00000351677	NM_002834.3	461	Gct/Tct	12/16	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	2	TRUE	NA	0.613388792276843	2		513	605	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434860	110434860	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	247	728	0	ENST00000375856.3:c.3541T>A	p.Ser1181Thr	p.S1181T	ENST00000375856	NM_003749.2	1181	Tct/Act	1/2	1	2	FACETS	0.91	0.852	0.969	0.91	0.852	0.969	CLONAL	1	TRUE	1	0.613388792276843	2		728	885	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352677	68352677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1342492018	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	129	389	1	ENST00000487270.1:c.544G>A	p.Glu182Lys	p.E182K	ENST00000487270	NM_133509.3	182	Gaa/Aaa	6/11	1	2	FACETS	0.893	0.815	0.974	0.893	0.815	0.974	CLONAL	1	TRUE	1	0.613388792276843	2		390	471	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251006	99251006	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	151	459	0	ENST00000268035.6:c.310A>G	p.Thr104Ala	p.T104A	ENST00000268035	NM_000875.3	104	Acg/Gcg	2/21	1	2	FACETS	0.864	0.794	0.936	0.864	0.794	0.936	CLONAL	1	TRUE	1	0.613388792276843	2		459	570	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396754	396754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	169	500	0	ENST00000262320.3:c.272C>T	p.Ser91Phe	p.S91F	ENST00000262320	NM_003502.3	91	tCc/tTc	2/11	1	2	FACETS	0.905	0.836	0.976	0.905	0.836	0.976	CLONAL	1	TRUE	1	0.613388792276843	2		500	609	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118583	17118583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	173	487	0	ENST00000285071.4:c.1348C>T	p.His450Tyr	p.H450Y	ENST00000285071	NM_144997.5	450	Cac/Tac	12/14	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.613388792276843	2		487	557	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557315	29557315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	119	321	0	ENST00000356175.3:c.3028C>T	p.Gln1010Ter	p.Q1010*	ENST00000356175	NM_000267.3	1010	Caa/Taa	23/57	1	2	FACETS	0.977	0.89	1	0.977	0.89	1	CLONAL	1	TRUE	1	0.613388792276843	2		321	397	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29563006	29563006	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs876658235	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	193	499	2	ENST00000356175.3:c.3941G>A	p.Trp1314Ter	p.W1314*	ENST00000356175	NM_000267.3	1314	tGg/tAg	29/57	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.613388792276843	2		501	621	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487506	38487507	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	116	427	0	ENST00000254066.5:c.36_37delinsAA	p.Gly13Ser	p.G13S	ENST00000254066	NM_000964.3	12	ggGGgc/ggAAgc	2/9	1	2	FACETS	0.839	0.761	0.92	0.839	0.761	0.92	CLONAL	1	TRUE	1	0.613388792276843	2		427	451	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59820487	59820487	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	130	336	0	ENST00000259008.2:c.2266C>T	p.Leu756Phe	p.L756F	ENST00000259008	NM_032043.2	756	Ctc/Ttc	16/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.613388792276843	2		336	398	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853910	59853910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	111	328	0	ENST00000259008.2:c.1949C>T	p.Thr650Ile	p.T650I	ENST00000259008	NM_032043.2	650	aCc/aTc	14/20	1	2	FACETS	0.878	0.796	0.964	0.878	0.796	0.964	CLONAL	1	TRUE	1	0.613388792276843	2		328	412	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212135	36212135	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs548700728	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	245	365	1	ENST00000222270.7:c.1886C>T	p.Pro629Leu	p.P629L	ENST00000222270	NM_014727.1	629	cCg/cTg	3/37	0.609979854523281	2	FACETS	0.96	0.913	1	0.96	0.913	1	CLONAL	2	TRUE	0	0.613388792276843	2		366	416	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262354	39262354	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	139	373	0	ENST00000402219.2:c.1073A>G	p.Lys358Arg	p.K358R	ENST00000402219	NM_005633.3	358	aAg/aGg	8/23	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.613388792276843	2		373	447	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630344	47630344	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs56170584	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	156	469	0	ENST00000233146.2:c.14C>G	p.Pro5Arg	p.P5R	ENST00000233146	NM_000251.2	5	cCg/cGg	1/16	1	2	FACETS	0.965	0.89	1	0.965	0.89	1	CLONAL	1	TRUE	1	0.613388792276843	2		469	527	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944545	40944545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200852571	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	663	367	1	ENST00000373198.4:c.1957C>T	p.Arg653Trp	p.R653W	ENST00000373198	NM_133170.3	653	Cgg/Tgg	12/32	0.532118817762454	6	FACETS	0.947	0.92	0.972	0.947	0.92	0.972	CLONAL	5	TRUE	1	0.613388792276843	6		368	1017	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799689	72799689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	215	526	0	ENST00000325599.8:c.1480C>T	p.Pro494Ser	p.P494S	ENST00000325599	NM_018130.2	494	Ccc/Tcc	11/11	1	2	FACETS	0.993	0.927	1	0.993	0.927	1	CLONAL	1	TRUE	1	0.613388792276843	2		526	706	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114170	73114170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	130	291	0	ENST00000356692.5:c.806C>T	p.Ser269Phe	p.S269F	ENST00000356692		269	tCt/tTt	8/9	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.613388792276843	2		291	396	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462299	89462299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	132	344	0	ENST00000336596.2:c.1771C>T	p.Pro591Ser	p.P591S	ENST00000336596	NM_005233.5	591	Cca/Tca	10/17	1	2	FACETS	0.999	0.914	1	0.999	0.914	1	CLONAL	1	TRUE	1	0.613388792276843	2		344	431	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917628	178917628	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	121	320	0	ENST00000263967.3:c.503C>T	p.Pro168Leu	p.P168L	ENST00000263967	NM_006218.2	168	cCt/cTt	3/21	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.613388792276843	2		320	372	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526531	31526532	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	258	721	2	ENST00000344624.3:c.508_509delinsTT	p.Pro170Leu	p.P170L	ENST00000344624		170	CCg/TTg	2/33	1	2	FACETS	0.938	0.88	0.997	0.938	0.88	0.997	CLONAL	1	TRUE	1	0.613388792276843	2		723	897	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86637108	86637108	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	52	239	0	ENST00000274376.6:c.1019G>A	p.Gly340Asp	p.G340D	ENST00000274376	NM_002890.2	340	gGc/gAc	6/25	1	2	FACETS	0.665	0.571	0.766	0.665	0.571	0.766	SUBCLONAL	1	TRUE	1	0.613388792276843	2		239	255	SUCCESS
APC	324	MSKCC	GRCh37	5	112175433	112175433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	97	236	0	ENST00000257430.4:c.4142C>T	p.Pro1381Leu	p.P1381L	ENST00000257430	NM_000038.5	1381	cCa/cTa	16/16	1	2	FACETS	0.904	0.813	0.998	0.904	0.813	0.998	CLONAL	1	TRUE	1	0.613388792276843	2		236	350	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497259	149497259	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	194	610	0	ENST00000261799.4:c.3059A>C	p.Asp1020Ala	p.D1020A	ENST00000261799	NM_002609.3	1020	gAc/gCc	22/23	1	2	FACETS	0.879	0.816	0.943	0.879	0.816	0.943	CLONAL	1	TRUE	1	0.613388792276843	2		610	720	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679668	30679668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	195	546	0	ENST00000376406.3:c.2051C>T	p.Ser684Phe	p.S684F	ENST00000376406	NM_014641.2	684	tCt/tTt	5/15	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.613388792276843	2		546	629	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974393	93974393	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	109	346	0	ENST00000369303.4:c.1661C>T	p.Pro554Leu	p.P554L	ENST00000369303	NM_004440.3	554	cCt/cTt	8/17	1	2	FACETS	0.95	0.861	1	0.95	0.861	1	CLONAL	1	TRUE	1	0.613388792276843	2		346	374	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700292	117700292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	135	361	0	ENST00000368508.3:c.2527G>A	p.Gly843Arg	p.G843R	ENST00000368508	NM_002944.2	843	Ggg/Agg	17/43	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.613388792276843	2		361	416	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958126	2958126	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs763435728	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	215	615	0	ENST00000396946.4:c.2606G>A	p.Arg869Gln	p.R869Q	ENST00000396946	NM_032415.4	869	cGg/cAg	19/25	0.613388792276843	1	FACETS	0.914	0.857	0.971	0.914	0.857	0.971	CLONAL	1	TRUE	0	0.613388792276843	1		615	532	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388118	81388118	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	121	358	0	ENST00000222390.5:c.257C>T	p.Ala86Val	p.A86V	ENST00000222390	NM_000601.4	86	gCt/gTt	3/18	0.589236026171473	3	FACETS	1	0.963	1	0.557	0.506	0.609	CLONAL	1	TRUE	1	0.613388792276843	3		358	463	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930115	68930115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	122	348	0	ENST00000288368.4:c.176C>T	p.Ser59Leu	p.S59L	ENST00000288368	NM_024870.2	59	tCa/tTa	2/40	1	2	FACETS	0.912	0.831	0.997	0.912	0.831	0.997	CLONAL	1	TRUE	1	0.613388792276843	2		348	436	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978647	70978647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	236	624	0	ENST00000276594.2:c.1006G>A	p.Glu336Lys	p.E336K	ENST00000276594	NM_024504.3	336	Gag/Aag	5/8	1	2	FACETS	0.997	0.933	1	0.997	0.933	1	CLONAL	1	TRUE	1	0.613388792276843	2		624	772	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981890	70981890	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	226	655	0	ENST00000276594.2:c.206T>A	p.Phe69Tyr	p.F69Y	ENST00000276594	NM_024504.3	69	tTc/tAc	2/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.613388792276843	2		655	719	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923369	36923369	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	206	505	0	ENST00000358127.4:c.893C>T	p.Ser298Phe	p.S298F	ENST00000358127	NM_001280556.1	298	tCc/tTc	7/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.613388792276843	2		505	630	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391433	139391433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1204397173	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	203	597	0	ENST00000277541.6:c.6758C>T	p.Pro2253Leu	p.P2253L	ENST00000277541	NM_017617.3	2253	cCc/cTc	34/34	1	2	FACETS	0.982	0.915	1	0.982	0.915	1	CLONAL	1	TRUE	1	0.613388792276843	2		597	674	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860009	152860010	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTGG	novel	NA	P-0033654-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	109	368	0	ENST00000406277.2:c.415_418dup	p.His140ProfsTer66	p.H140Pfs*66	ENST00000406277	NM_152274.4	140	cac/cCCACac	5/7	1		FACETS		0.767	0.933				CLONAL	1	TRUE	1	0.613388792276843	2		368	419	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0033795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	1108	528	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.80942807824019	4	FACETS	0.993	0.981	1	0.993	0.981	1	CLONAL	4	TRUE	0	0.80942807824019	4		528	1247	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0033795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	331	248	1				ENST00000310581	NM_198253.2	-/1132			0.80942807824019	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.80942807824019	3		249	552	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862896	9862896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1198247451	NA	P-0033795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	269	627	0	ENST00000330684.3:c.2407G>A	p.Glu803Lys	p.E803K	ENST00000330684	NM_001134407.1	803	Gag/Aag	12/13	1	2	FACETS	0.997	0.941	1	0.997	0.941	1	CLONAL	1	TRUE	1	0.80942807824019	2		627	667	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230613	46230613	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	180	419	0	ENST00000334344.6:c.862C>T	p.Gln288Ter	p.Q288*	ENST00000334344	NM_152641.2	288	Cag/Tag	8/21	1	2	FACETS	0.986	0.919	1	0.986	0.919	1	CLONAL	1	TRUE	1	0.80942807824019	2		419	451	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135079	11135079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770969438	NA	P-0034041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	223	626	0	ENST00000358026.2:c.3046G>A	p.Val1016Met	p.V1016M	ENST00000358026	NM_001128849.1	1016	Gtg/Atg	21/36	0.610093952005674	3	FACETS	1	0.96	1	0.521	0.486	0.558	CLONAL	1	TRUE	1	0.610093952005674	3		626	915	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650668	67650668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	347	431	4	ENST00000264010.4:c.973C>T	p.Pro325Ser	p.P325S	ENST00000264010	NM_006565.3	325	Cca/Tca	5/12	0.610093952005674	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.610093952005674	2		435	532	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007149	62007149	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1415561170	NA	P-0034041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	400	525	0	ENST00000392795.3:c.533T>C	p.Ile178Thr	p.I178T	ENST00000392795	NM_001039933.1	178	aTc/aCc	4/6	0.560239597033164	4	FACETS	0.978	0.932	1	0.978	0.932	1	CLONAL	2	TRUE	2	0.610093952005674	4		525	1079	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953237	17953254	+	inframe_deletion	In_Frame_Del	DEL	GCCCCGGCTGGATCCAGC	GCCCCGGCTGGATCCAGC	-	novel	NA	P-0034041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	214	696	0	ENST00000458235.1:c.732_749del	p.Leu245_Ala250del	p.L245_A250del	ENST00000458235	NM_000215.3	244	cgGCTGGATCCAGCCGGGGCc/cgc	6/24	0.610093952005674	3	FACETS	0.91	0.846	0.977	0.455	0.423	0.489	CLONAL	1	TRUE	1	0.610093952005674	3		696	1006	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871965	45871965	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	166	586	1	ENST00000391945.4:c.283G>A	p.Glu95Lys	p.E95K	ENST00000391945	NM_000400.3	95	Gag/Aag	5/23	0.610093952005674	2	FACETS	0.676	0.622	0.733	0.338	0.311	0.367	SUBCLONAL	1	TRUE	0	0.610093952005674	2		587	805	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661887	227661887	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	55	673	0	ENST00000305123.5:c.1568A>G	p.Lys523Arg	p.K523R	ENST00000305123	NM_005544.2	523	aAg/aGg	1/2	0.610093952005674	3	FACETS	0.238	0.202	0.277	0.119	0.101	0.139	SUBCLONAL	1	TRUE	1	0.610093952005674	3		673	989	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279799	46279799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	149	494	0	ENST00000371998.3:c.3725G>A	p.Arg1242Lys	p.R1242K	ENST00000371998		1242	aGg/aAg	20/23	0.610093952005674	4	FACETS	0.941	0.86	1	0.47	0.43	0.513	CLONAL	1	TRUE	2	0.610093952005674	4		494	836	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140810	37140810	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	333	488	1	ENST00000373509.5:c.646C>A	p.His216Asn	p.H216N	ENST00000373509	NM_002648.3	216	Cat/Aat	5/6	0.610093952005674	4	FACETS	0.966	0.916	1	0.966	0.916	1	CLONAL	2	TRUE	2	0.610093952005674	4		489	910	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0034168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	82	284	0				ENST00000310581	NM_198253.2	-/1132			0.333491291775479	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.333491291775479	1		284	339	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720677	89720678	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	39	194	0	ENST00000371953.3:c.829dup	p.Thr277AsnfsTer21	p.T277Nfs*21	ENST00000371953	NM_000314.4	276	-/A	8/9	0.333491291775479	1	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	0	0.333491291775479	1		194	189	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133235998	133235998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1359871633	NA	P-0034168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	147	679	0	ENST00000320574.5:c.3158C>T	p.Ser1053Phe	p.S1053F	ENST00000320574	NM_006231.2	1053	tCc/tTc	26/49	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.333491291775479	2		679	770	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049724	16049724	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	148	640	0	ENST00000268712.3:c.1048C>T	p.Arg350Ter	p.R350*	ENST00000268712	NM_006311.3	350	Cga/Tga	10/46	1	2	FACETS	0.956	0.873	1	0.956	0.873	1	CLONAL	1	TRUE	1	0.333491291775479	2		640	928	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538344	9538344	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	104	558	0	ENST00000353224.5:c.1654G>A	p.Val552Ile	p.V552I	ENST00000353224	NM_177990.2	552	Gtt/Att	7/10	1	2	FACETS	0.952	0.854	1	0.952	0.854	1	CLONAL	1	TRUE	1	0.333491291775479	2		558	655	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120405	94120405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	149	437	0	ENST00000369303.4:c.646C>T	p.Pro216Ser	p.P216S	ENST00000369303	NM_004440.3	216	Cca/Tca	3/17	0.333491291775479	1	FACETS	0.758	0.698	0.821	1	0.989	1	SUBCLONAL	2	TRUE	0	0.333491291775479	1		437	491	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0034178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	59	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.187147979015481	2	FACETS	0.978	0.844	1	0.489	0.422	0.562	CLONAL	1	TRUE	0	0.284480861292822	2		288	424	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468158	50468158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	175	566	1	ENST00000331340.3:c.1393G>A	p.Glu465Lys	p.E465K	ENST00000331340	NM_006060.4	465	Gaa/Aaa	8/8	0.187147979015481	2	FACETS	1	0.984	1	0.638	0.587	0.691	CLONAL	1	TRUE	0	0.284480861292822	2		567	964	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465483	99465483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1270131506	NA	P-0034178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	78	721	1	ENST00000268035.6:c.2308G>A	p.Glu770Lys	p.E770K	ENST00000268035	NM_000875.3	770	Gag/Aag	11/21	1	2	FACETS	0.694	0.609	0.786	0.694	0.609	0.786	SUBCLONAL	1	TRUE	1	0.284480861292822	2		722	790	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980007	7980007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147992320	NA	P-0034178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	62	866	0	ENST00000319144.4:c.1330G>A	p.Val444Ile	p.V444I	ENST00000319144	NM_001139.2	444	Gtt/Att	10/15	1	2	FACETS	0.393	0.338	0.453	0.393	0.338	0.453	SUBCLONAL	1	TRUE	1	0.284480861292822	2		866	1109	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292591	15292591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758913191	NA	P-0034178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	149	945	1	ENST00000263388.2:c.2588C>T	p.Ser863Leu	p.S863L	ENST00000263388	NM_000435.2	863	tCg/tTg	17/33	1	2	FACETS	0.95	0.866	1	0.95	0.866	1	CLONAL	1	TRUE	1	0.284480861292822	2		946	1103	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724637	43724637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	109	1156	1	ENST00000382044.4:c.3430C>T	p.Pro1144Ser	p.P1144S	ENST00000382044	NM_001141980.1	1144	Cct/Tct	17/28	1	2	FACETS	0.632	0.565	0.702	0.632	0.565	0.702	SUBCLONAL	1	TRUE	1	0.284480861292822	2		1157	1213	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874550	35874550	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1055222075	NA	P-0034178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	59	661	0	ENST00000303115.3:c.707-1G>A		p.X236_splice	ENST00000303115	NM_002185.3	236			1	2	FACETS	0.552	0.474	0.637	0.552	0.474	0.637	SUBCLONAL	1	TRUE	1	0.284480861292822	2		661	752	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675907	30675907	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	247	1008	0	ENST00000376406.3:c.2449C>T	p.Pro817Ser	p.P817S	ENST00000376406	NM_014641.2	817	Cca/Tca	8/15	0.19020094766911	3	FACETS	1	0.992	1	0.738	0.688	0.789	CLONAL	1	TRUE	1	0.284480861292822	3		1008	1344	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	97	151	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.885	0.799	0.975	0.885	0.799	0.975	CLONAL	1	TRUE	1	0.704643349662051	2		151	311	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950061	38950061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	147	456	0	ENST00000357387.3:c.3889C>T	p.Pro1297Ser	p.P1297S	ENST00000357387	NM_152756.3	1297	Cct/Tct	31/38	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.704643349662051	2		456	415	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913351	NA	P-0034282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	297	410	2	ENST00000288602.6:c.1397G>A	p.Gly466Glu	p.G466E	ENST00000288602	NM_004333.4	466	gGa/gAa	11/18	0.704643349662051	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.704643349662051	2		412	416	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs770248150	NA	P-0034282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	171	550	0	ENST00000311936.3:c.351A>T	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaT	4/5	1	2	FACETS	0.954	0.884	1	0.954	0.884	1	CLONAL	1	TRUE	1	0.704643349662051	2		550	509	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945093	31945093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	175	653	0	ENST00000340398.3:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000340398	NM_001013699.2	3	cGa/cAa	1/1	1	2	FACETS	0.776	0.718	0.836	0.776	0.718	0.836	SUBCLONAL	1	TRUE	1	0.704643349662051	2		653	640	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104619	69104619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753704	NA	P-0034282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	232	745	0	ENST00000288368.4:c.4463C>T	p.Ser1488Leu	p.S1488L	ENST00000288368	NM_024870.2	1488	tCg/tTg	37/40	1	2	FACETS	0.952	0.892	1	0.952	0.892	1	CLONAL	1	TRUE	1	0.704643349662051	2		745	692	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955960	55955960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs895270961	NA	P-0034282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	119	453	0	ENST00000263923.4:c.3202C>T	p.Pro1068Ser	p.P1068S	ENST00000263923	NM_002253.2	1068	Cct/Tct	24/30	1	2	FACETS	0.915	0.835	0.998	0.915	0.835	0.998	CLONAL	1	TRUE	1	0.704643349662051	2		453	369	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450763	70450763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755857428	NA	P-0034282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	133	478	0	ENST00000373644.4:c.5603C>T	p.Ala1868Val	p.A1868V	ENST00000373644	NM_030625.2	1868	gCc/gTc	12/12	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.704643349662051	2		478	371	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11554273	NA	P-0034282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	185	500	0	ENST00000371085.3:c.601C>G	p.Arg201Gly	p.R201G	ENST00000371085	NM_000516.4	201	Cgt/Ggt	8/13	1	2	FACETS	0.989	0.92	1	0.989	0.92	1	CLONAL	1	TRUE	1	0.704643349662051	2		500	531	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222961	36222961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	327	933	2	ENST00000222270.7:c.5590C>T	p.Arg1864Ter	p.R1864*	ENST00000222270	NM_014727.1	1864	Cga/Tga	27/37	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.704643349662051	2		935	850	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965586	93965586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372024057	NA	P-0034282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	172	487	1	ENST00000369303.4:c.2342G>A	p.Arg781Gln	p.R781Q	ENST00000369303	NM_004440.3	781	cGa/cAa	13/17	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.704643349662051	2		488	481	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118348885	118348885	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	128	259	0	ENST00000534358.1:c.3539del	p.Gly1180ValfsTer5	p.G1180Vfs*5	ENST00000534358	NM_005933.3	1180	Ggt/gt	5/36	0.704643349662051	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.704643349662051	1		259	211	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352579	118352579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	139	448	0	ENST00000534358.1:c.3784C>T	p.Pro1262Ser	p.P1262S	ENST00000534358	NM_005933.3	1262	Cct/Tct	7/36	0.704643349662051	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.704643349662051	1		448	239	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285807	46285807	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0034282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	131	404	1	ENST00000334344.6:c.5075C>A	p.Ser1692Ter	p.S1692*	ENST00000334344	NM_152641.2	1692	tCa/tAa	18/21	1	2	FACETS	0.961	0.881	1	0.961	0.881	1	CLONAL	1	TRUE	1	0.704643349662051	2		405	387	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287465	46287465	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0034282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	169	500	1	ENST00000334344.6:c.5324T>A	p.Ile1775Lys	p.I1775K	ENST00000334344	NM_152641.2	1775	aTa/aAa	20/21	1	2	FACETS	0.919	0.851	0.989	0.919	0.851	0.989	CLONAL	1	TRUE	1	0.704643349662051	2		501	522	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28631579	28631579	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	151	356	0	ENST00000241453.7:c.389T>A	p.Ile130Asn	p.I130N	ENST00000241453	NM_004119.2	130	aTt/aAt	4/24	1	2	FACETS	0.965	0.891	1	0.965	0.891	1	CLONAL	1	TRUE	1	0.704643349662051	2		356	444	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570399	95570399	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587778229	NA	P-0034282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	130	368	0	ENST00000393063.1:c.3334A>G	p.Asn1112Asp	p.N1112D	ENST00000393063	NM_030621.3	1112	Aac/Gac	22/28	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.704643349662051	2		368	362	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292626	91292626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	81	249	2	ENST00000355112.3:c.128C>T	p.Ser43Leu	p.S43L	ENST00000355112	NM_000057.2	43	tCa/tTa	3/22	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.704643349662051	2		251	225	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820642	3820642	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752062116	NA	P-0034282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	599	832	0	ENST00000262367.5:c.2809C>T	p.Pro937Ser	p.P937S	ENST00000262367	NM_004380.2	937	Ccg/Tcg	14/31	0.704643349662051	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.704643349662051	3		832	1099	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819628	81819628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	345	502	0	ENST00000359376.3:c.34G>A	p.Glu12Lys	p.E12K	ENST00000359376	NM_002661.3	12	Gaa/Aaa	2/33	0.704643349662051	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.704643349662051	3		502	656	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526519	66526519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	354	468	0	ENST00000358598.2:c.1075C>T	p.Leu359Phe	p.L359F	ENST00000358598	NM_212471.2	359	Ctt/Ttt	11/11	0.704643349662051	3	FACETS	0.992	0.948	1	0.992	0.948	1	CLONAL	2	TRUE	1	0.704643349662051	3		468	685	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302249	15302249	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	198	646	0	ENST00000263388.2:c.1022C>T	p.Pro341Leu	p.P341L	ENST00000263388	NM_000435.2	341	cCc/cTc	6/33	1	2	FACETS	0.934	0.87	0.999	0.934	0.87	0.999	CLONAL	1	TRUE	1	0.704643349662051	2		646	602	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366210	15366210	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	239	769	0	ENST00000263377.2:c.1945C>T	p.Pro649Ser	p.P649S	ENST00000263377	NM_058243.2	649	Ccc/Tcc	10/20	1	2	FACETS	0.922	0.864	0.98	0.922	0.864	0.98	CLONAL	1	TRUE	1	0.704643349662051	2		769	736	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266628	142266628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	138	439	0	ENST00000350721.4:c.3296C>T	p.Ser1099Leu	p.S1099L	ENST00000350721	NM_001184.3	1099	tCa/tTa	16/47	1	2	FACETS	0.999	0.919	1	0.999	0.919	1	CLONAL	1	TRUE	1	0.704643349662051	2		439	392	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38942435	38942435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	134	474	0	ENST00000357387.3:c.5098C>T	p.Pro1700Ser	p.P1700S	ENST00000357387	NM_152756.3	1700	Cct/Tct	38/38	1	2	FACETS	0.756	0.691	0.824	0.756	0.691	0.824	SUBCLONAL	1	TRUE	1	0.704643349662051	2		474	503	SUCCESS
APC	324	MSKCC	GRCh37	5	112179177	112179177	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	98	339	0	ENST00000257430.4:c.7886C>T	p.Thr2629Ile	p.T2629I	ENST00000257430	NM_000038.5	2629	aCc/aTc	16/16	1	2	FACETS	0.953	0.861	1	0.953	0.861	1	CLONAL	1	TRUE	1	0.704643349662051	2		339	292	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149440512	149440512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	155	564	0	ENST00000286301.3:c.1882G>A	p.Glu628Lys	p.E628K	ENST00000286301	NM_005211.3	628	Gag/Aag	14/22	0.396933332528251	1	FACETS	0.54	0.497	0.584	0.54	0.497	0.584	INDETERMINATE	1	TRUE	0	0.704643349662051	1		564	528	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185037	32185037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	136	532	1	ENST00000375023.3:c.1631C>T	p.Ser544Phe	p.S544F	ENST00000375023	NM_004557.3	544	tCc/tTc	10/30	1	2	FACETS	0.825	0.755	0.897	0.825	0.755	0.897	CLONAL	1	TRUE	1	0.704643349662051	2		533	468	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	64	151	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.633	0.552	0.72	0.633	0.552	0.72	SUBCLONAL	1	TRUE	1	0.609195784821601	2		151	332	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494148	140494148	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267601317	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	194	758	1	ENST00000288602.6:c.1100C>T	p.Pro367Leu	p.P367L	ENST00000288602	NM_004333.4	367	cCc/cTc	8/18	0.609195784821601	3	FACETS	0.711	0.657	0.767	0.355	0.328	0.384	SUBCLONAL	1	TRUE	1	0.609195784821601	3		759	1169	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501356	140501356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	73	185	0	ENST00000288602.6:c.716G>A	p.Arg239Gln	p.R239Q	ENST00000288602	NM_004333.4	239	cGa/cAa	6/18	0.609195784821601	3	FACETS	0.861	0.758	0.971	0.431	0.379	0.486	CLONAL	1	TRUE	1	0.609195784821601	3		185	363	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132428	11132428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	109	640	0	ENST00000358026.2:c.2644G>A	p.Glu882Lys	p.E882K	ENST00000358026	NM_001128849.1	882	Gaa/Aaa	19/36	1	2	FACETS	0.641	0.578	0.708	0.641	0.578	0.708	SUBCLONAL	1	TRUE	1	0.609195784821601	2		640	558	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032069	10032069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868215122	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	86	502	1	ENST00000330684.3:c.754G>A	p.Asp252Asn	p.D252N	ENST00000330684	NM_001134407.1	252	Gat/Aat	3/13	0.39350648788938	3	FACETS	0.676	0.599	0.758	0.338	0.299	0.379	SUBCLONAL	1	TRUE	1	0.609195784821601	3		503	545	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729679	41729679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1488698571	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	103	524	0	ENST00000242208.4:c.850G>A	p.Glu284Lys	p.E284K	ENST00000242208	NM_002192.2	284	Gaa/Aaa	3/3	1	2	FACETS	0.657	0.59	0.727	0.657	0.59	0.727	SUBCLONAL	1	TRUE	1	0.609195784821601	2		524	515	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998688	100998688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	118	683	0	ENST00000325455.5:c.1114G>A	p.Asp372Asn	p.D372N	ENST00000325455	NM_001202474.3	372	Gac/Aac	1/8	1	2	FACETS	0.62	0.56	0.682	0.62	0.56	0.682	SUBCLONAL	1	TRUE	1	0.609195784821601	2		683	625	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453145	140453146	+	missense_variant	Missense_Mutation	DNP	AG	AG	GA	rs121913368	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	158	445	1	ENST00000288602.6:c.1789_1790delinsTC	p.Leu597Ser	p.L597S	ENST00000288602	NM_004333.4	597	CTa/TCa	15/18	0.609195784821601	3	FACETS	0.783	0.725	0.843	0.783	0.725	0.843	SUBCLONAL	2	TRUE	1	0.609195784821601	3		446	432	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494160	140494160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	259	755	0	ENST00000288602.6:c.1088C>T	p.Ser363Phe	p.S363F	ENST00000288602	NM_004333.4	363	tCc/tTc	8/18	0.609195784821601	3	FACETS	0.968	0.906	1	0.484	0.453	0.516	CLONAL	1	TRUE	1	0.609195784821601	3		755	1146	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444346	50444346	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	73	334	1	ENST00000331340.3:c.276G>A	p.Met92Ile	p.M92I	ENST00000331340	NM_006060.4	92	atG/atA	4/8	1	2	FACETS	0.761	0.671	0.856	0.761	0.671	0.856	SUBCLONAL	1	TRUE	1	0.609195784821601	2		335	315	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332469	70332469	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866518744	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	108	515	0	ENST00000373644.4:c.374C>T	p.Ser125Phe	p.S125F	ENST00000373644	NM_030625.2	125	tCc/tTc	2/12	1	2	FACETS	0.683	0.616	0.754	0.683	0.616	0.754	SUBCLONAL	1	TRUE	1	0.609195784821601	2		515	519	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119634982	119634982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	46	185	0	ENST00000316626.5:c.517C>T	p.His173Tyr	p.H173Y	ENST00000316626		173	Cat/Tat	5/12	1	2	FACETS	0.659	0.561	0.766	0.659	0.561	0.766	SUBCLONAL	1	TRUE	1	0.609195784821601	2		185	229	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059183	27059183	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1010301017	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	74	384	0	ENST00000324856.7:c.1820C>T	p.Ser607Leu	p.S607L	ENST00000324856	NM_006015.4	607	tCa/tTa	4/20	1	2	FACETS	0.612	0.538	0.69	0.612	0.538	0.69	SUBCLONAL	1	TRUE	1	0.609195784821601	2		384	397	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101197	41101197	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568910629	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	86	539	0	ENST00000373198.4:c.1159G>A	p.Val387Ile	p.V387I	ENST00000373198	NM_133170.3	387	Gta/Ata	8/32	1	2	FACETS	0.66	0.586	0.737	0.66	0.586	0.737	SUBCLONAL	1	TRUE	1	0.609195784821601	2		539	428	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344269	118344269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	105	446	0	ENST00000534358.1:c.2395C>T	p.Pro799Ser	p.P799S	ENST00000534358	NM_005933.3	799	Cct/Tct	3/36	1	2	FACETS	0.654	0.588	0.724	0.654	0.588	0.724	SUBCLONAL	1	TRUE	1	0.609195784821601	2		446	527	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004816	150004816	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	104	462	0	ENST00000253339.5:c.1409G>A	p.Gly470Glu	p.G470E	ENST00000253339		470	gGa/gAa	3/7	1	2	FACETS	0.684	0.615	0.757	0.684	0.615	0.757	SUBCLONAL	1	TRUE	1	0.609195784821601	2		462	499	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056321	27056321	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	77	314	0	ENST00000324856.7:c.1317del	p.Ser440ValfsTer179	p.S440Vfs*179	ENST00000324856	NM_006015.4	439	caG/ca	2/20	1	2	FACETS	0.78	0.691	0.875	0.78	0.691	0.875	SUBCLONAL	1	TRUE	1	0.609195784821601	2		314	324	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932131	36932132	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	49	446	1	ENST00000361632.4:c.2337_2338delinsTT	p.Leu780Phe	p.L780F	ENST00000361632		779	ggCCtc/ggTTtc	16/16	1	2	FACETS	0.437	0.371	0.509	0.437	0.371	0.509	SUBCLONAL	1	TRUE	1	0.609195784821601	2		447	368	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246021805	246021805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	127	550	1	ENST00000388985.4:c.1069C>T	p.Pro357Ser	p.P357S	ENST00000388985		357	Cca/Tca	10/12	1	2	FACETS	0.741	0.673	0.811	0.741	0.673	0.811	SUBCLONAL	1	TRUE	1	0.609195784821601	2		551	563	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219145	94219145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758112386	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	75	428	0	ENST00000323929.3:c.259C>T	p.Arg87Trp	p.R87W	ENST00000323929	NM_005591.3	87	Cgg/Tgg	4/20	1	2	FACETS	0.463	0.406	0.524	0.463	0.406	0.524	SUBCLONAL	1	TRUE	1	0.609195784821601	2		428	532	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446936	18446936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	70	317	0	ENST00000266497.5:c.1021G>A	p.Glu341Lys	p.E341K	ENST00000266497		341	Gaa/Aaa	4/31	1	2	FACETS	0.566	0.496	0.641	0.566	0.496	0.641	SUBCLONAL	1	TRUE	1	0.609195784821601	2		317	406	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800940	18800940	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	72	354	0	ENST00000266497.5:c.4316C>T	p.Pro1439Leu	p.P1439L	ENST00000266497		1439	cCa/cTa	31/31	1	2	FACETS	0.598	0.525	0.676	0.598	0.525	0.676	SUBCLONAL	1	TRUE	1	0.609195784821601	2		354	395	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611397	28611397	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	111	490	0	ENST00000241453.7:c.1234C>T	p.Gln412Ter	p.Q412*	ENST00000241453	NM_004119.2	412	Cag/Tag	10/24	1	2	FACETS	0.595	0.536	0.658	0.595	0.536	0.658	SUBCLONAL	1	TRUE	1	0.609195784821601	2		490	612	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012402	29012402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	106	577	0	ENST00000282397.4:c.469C>T	p.Pro157Ser	p.P157S	ENST00000282397	NM_002019.4	157	Ccc/Tcc	4/30	1	2	FACETS	0.572	0.514	0.634	0.572	0.514	0.634	SUBCLONAL	1	TRUE	1	0.609195784821601	2		577	608	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43739672	43739672	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761309980	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	46	162	0	ENST00000382044.4:c.2728C>T	p.His910Tyr	p.H910Y	ENST00000382044	NM_001141980.1	910	Cat/Tat	13/28	1	2	FACETS	0.771	0.657	0.892	0.771	0.657	0.892	SUBCLONAL	1	TRUE	1	0.609195784821601	2		162	196	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3652201	3652201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	125	698	0	ENST00000294008.3:c.868G>A	p.Glu290Lys	p.E290K	ENST00000294008	NM_032444.2	290	Gaa/Aaa	4/15	0.39350648788938	3	FACETS	0.698	0.632	0.767	0.349	0.316	0.384	SUBCLONAL	1	TRUE	1	0.609195784821601	3		698	767	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819308	3819308	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	210	552	0	ENST00000262367.5:c.2927C>T	p.Ser976Phe	p.S976F	ENST00000262367	NM_004380.2	976	tCc/tTc	15/31	0.39350648788938	3	FACETS	1	0.989	1	0.652	0.608	0.697	CLONAL	1	TRUE	1	0.609195784821601	3		552	690	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831335	72831335	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	71	400	0	ENST00000268489.5:c.5246A>G	p.Gln1749Arg	p.Q1749R	ENST00000268489	NM_006885.3	1749	cAg/cGg	9/10	1	2	FACETS	0.678	0.595	0.765	0.678	0.595	0.765	SUBCLONAL	1	TRUE	1	0.609195784821601	2		400	344	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510602	38510602	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	104	497	1	ENST00000254066.5:c.856T>C	p.Phe286Leu	p.F286L	ENST00000254066	NM_000964.3	286	Ttc/Ctc	7/9	1	2	FACETS	0.638	0.573	0.707	0.638	0.573	0.707	SUBCLONAL	1	TRUE	1	0.609195784821601	2		498	535	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224139	36224139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	70	661	0	ENST00000222270.7:c.6689C>T	p.Thr2230Ile	p.T2230I	ENST00000222270	NM_014727.1	2230	aCc/aTc	28/37	1	2	FACETS	0.404	0.352	0.46	0.404	0.352	0.46	SUBCLONAL	1	TRUE	1	0.609195784821601	2		661	569	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227730	36227730	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	90	537	0	ENST00000222270.7:c.7297+2T>C		p.X2433_splice	ENST00000222270	NM_014727.1	2433			1	2	FACETS	0.63	0.561	0.703	0.63	0.561	0.703	SUBCLONAL	1	TRUE	1	0.609195784821601	2		537	469	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765592	41765592	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	90	609	1	ENST00000301178.4:c.2468A>G	p.Asn823Ser	p.N823S	ENST00000301178	NM_021913.4	823	aAc/aGc	20/20	1	2	FACETS	0.516	0.458	0.577	0.516	0.458	0.577	SUBCLONAL	1	TRUE	1	0.609195784821601	2		610	573	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910656	50910656	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1060501838	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	102	565	0	ENST00000440232.2:c.1759A>T	p.Ile587Phe	p.I587F	ENST00000440232	NM_002691.3	587	Atc/Ttc	14/27	1	2	FACETS	0.603	0.541	0.669	0.603	0.541	0.669	SUBCLONAL	1	TRUE	1	0.609195784821601	2		565	555	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607658	46607658	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	122	664	1	ENST00000263734.3:c.1847C>T	p.Ser616Phe	p.S616F	ENST00000263734	NM_001430.4	616	tCc/tTc	12/16	1	2	FACETS	0.652	0.591	0.717	0.652	0.591	0.717	SUBCLONAL	1	TRUE	1	0.609195784821601	2		665	614	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273224	198273224	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	134	607	0	ENST00000335508.6:c.986C>T	p.Pro329Leu	p.P329L	ENST00000335508	NM_012433.2	329	cCt/cTt	8/25	1	2	FACETS	0.662	0.602	0.724	0.662	0.602	0.724	SUBCLONAL	1	TRUE	1	0.609195784821601	2		607	665	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273270	198273270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	108	500	0	ENST00000335508.6:c.940C>T	p.Pro314Ser	p.P314S	ENST00000335508	NM_012433.2	314	Cct/Tct	8/25	1	2	FACETS	0.645	0.58	0.712	0.645	0.58	0.712	SUBCLONAL	1	TRUE	1	0.609195784821601	2		500	550	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523316	9523316	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	80	477	2	ENST00000353224.5:c.1921C>T	p.Pro641Ser	p.P641S	ENST00000353224	NM_177990.2	641	Ccc/Tcc	9/10	1	2	FACETS	0.573	0.507	0.645	0.573	0.507	0.645	SUBCLONAL	1	TRUE	1	0.609195784821601	2		479	458	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73096456	73096456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	36	117	0	ENST00000356692.5:c.236C>T	p.Pro79Leu	p.P79L	ENST00000356692		79	cCc/cTc	3/9	1	2	FACETS	0.579	0.481	0.688	0.579	0.481	0.688	SUBCLONAL	1	TRUE	1	0.609195784821601	2		117	204	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916869	178916869	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	124	578	0	ENST00000263967.3:c.256A>T	p.Thr86Ser	p.T86S	ENST00000263967	NM_006218.2	86	Aca/Tca	2/21	1	2	FACETS	0.588	0.533	0.647	0.588	0.533	0.647	SUBCLONAL	1	TRUE	1	0.609195784821601	2		578	692	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957008	1957008	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758343111	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	122	483	0	ENST00000382891.5:c.2459G>A	p.Arg820Gln	p.R820Q	ENST00000382891	NM_133335.3	820	cGg/cAg	13/22	1	2	FACETS	0.779	0.708	0.854	0.779	0.708	0.854	SUBCLONAL	1	TRUE	1	0.609195784821601	2		483	514	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628527	187628527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	133	699	1	ENST00000441802.2:c.2455C>T	p.Pro819Ser	p.P819S	ENST00000441802	NM_005245.3	819	Cca/Tca	2/27	1	2	FACETS	0.651	0.592	0.712	0.651	0.592	0.712	SUBCLONAL	1	TRUE	1	0.609195784821601	2		700	671	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295334	1295334	+	upstream_gene_variant	5'Flank	SNP	C	C	T	rs894008518	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	91	443	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.78	0.698	0.867	0.78	0.698	0.867	SUBCLONAL	1	TRUE	1	0.609195784821601	2		443	383	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527399	137527399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	69	321	0	ENST00000367739.4:c.247C>T	p.His83Tyr	p.H83Y	ENST00000367739	NM_000416.2	83	Cat/Tat	3/7	1	2	FACETS	0.521	0.455	0.591	0.521	0.455	0.591	SUBCLONAL	1	TRUE	1	0.609195784821601	2		321	435	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729597	41729597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	73	469	0	ENST00000242208.4:c.932G>A	p.Gly311Asp	p.G311D	ENST00000242208	NM_002192.2	311	gGc/gAc	3/3	1	2	FACETS	0.546	0.479	0.617	0.546	0.479	0.617	SUBCLONAL	1	TRUE	1	0.609195784821601	2		469	439	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046395	69046395	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	95	485	0	ENST00000288368.4:c.3868T>C	p.Phe1290Leu	p.F1290L	ENST00000288368	NM_024870.2	1290	Ttt/Ctt	32/40	1	2	FACETS	0.583	0.52	0.649	0.583	0.52	0.649	SUBCLONAL	1	TRUE	1	0.609195784821601	2		485	535	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965887	90965887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767123014	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	57	278	0	ENST00000265433.3:c.1430C>T	p.Ser477Leu	p.S477L	ENST00000265433	NM_002485.4	477	tCa/tTa	11/16	1	2	FACETS	0.517	0.445	0.594	0.517	0.445	0.594	SUBCLONAL	1	TRUE	1	0.609195784821601	2		278	362	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410754	63410754	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	83	296	0	ENST00000330258.3:c.2413C>A	p.Pro805Thr	p.P805T	ENST00000330258	NM_152424.3	805	Ccc/Acc	2/2	1	1	FACETS	0.687	0.613	0.763	0.687	0.613	0.763	SUBCLONAL	1	TRUE	0	0.609195784821601	1		296	276	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0034370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	119	528	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.143988460386637	2	FACETS	0.952	0.86	1	0.952	0.86	1	CLONAL	2	FALSE	0	0.162963510498566	2		528	767	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	24	326	0	ENST00000304494.5:c.143C>T	p.Pro48Leu	p.P48L	ENST00000304494	NM_000077.4	48	cCg/cTg	1/3	1	2	FACETS	0.682	0.534	0.853	0.682	0.534	0.853	SUBCLONAL	1	FALSE	1	0.162963510498566	2		326	432	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0034370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	33	248	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	FALSE	1	0.162963510498566	2		249	357	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636143	28636143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371663652	NA	P-0034370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	61	515	0	ENST00000241453.7:c.229G>A	p.Glu77Lys	p.E77K	ENST00000241453	NM_004119.2	77	Gaa/Aaa	3/24	0.162963510498566	1	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	FALSE	0	0.162963510498566	1		515	677	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42002918	42002918	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	39	307	1	ENST00000219905.7:c.2455C>T	p.Arg819Cys	p.R819C	ENST00000219905	NM_001164273.1	819	Cgt/Tgt	8/24	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	FALSE	1	0.162963510498566	2		308	446	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100324	27100324	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0034370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	132	431	0	ENST00000324856.7:c.4036C>T	p.Gln1346Ter	p.Q1346*	ENST00000324856	NM_006015.4	1346	Caa/Taa	17/20	0.143988460386637	2	FACETS	0.959	0.87	1	0.959	0.87	1	CLONAL	2	FALSE	0	0.162963510498566	2		431	845	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246498703	246498703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	133	429	0	ENST00000388985.4:c.302C>T	p.Ser101Phe	p.S101F	ENST00000388985		101	tCc/tTc	3/12	0.143988460386637	2	FACETS	0.988	0.898	1	0.988	0.898	1	CLONAL	2	FALSE	0	0.162963510498566	2		429	826	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410327	63410327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	88	535	0	ENST00000330258.3:c.2840C>T	p.Ser947Phe	p.S947F	ENST00000330258	NM_152424.3	947	tCc/tTc	2/2	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.162963510498566	2		535	870	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163772	72163772	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148707586	NA	P-0034370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	69	452	0	ENST00000357731.5:c.586G>A	p.Asp196Asn	p.D196N	ENST00000357731	NM_173808.2	196	Gac/Aac	4/7	0.143988460386637	2	FACETS	0.939	0.82	1	0.939	0.82	1	CLONAL	2	FALSE	0	0.162963510498566	2		452	451	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1036377	1036377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	77	478	0	ENST00000358495.3:c.401C>T	p.Ser134Phe	p.S134F	ENST00000358495	NM_134424.2	134	tCc/tTc	6/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.162963510498566	2		478	784	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526441	66526441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	71	386	0	ENST00000358598.2:c.997C>T	p.Arg333Cys	p.R333C	ENST00000358598	NM_212471.2	333	Cgt/Tgt	11/11	0.108884206522114	3	FACETS	1	0.961	1	0.635	0.553	0.723	CLONAL	1	FALSE	1	0.162963510498566	3		386	742	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916950	178916950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	42	312	0	ENST00000263967.3:c.337C>T	p.Leu113Phe	p.L113F	ENST00000263967	NM_006218.2	113	Ctc/Ttc	2/21	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	FALSE	1	0.162963510498566	2		312	432	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047255	180047256	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0034370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	94	485	2	ENST00000261937.6:c.2459_2460delinsAA	p.Gly820Glu	p.G820E	ENST00000261937	NM_182925.4	820	gGG/gAA	17/30	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.162963510498566	2		487	813	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980752	70980753	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0034370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	36	366	0	ENST00000276594.2:c.715_716delinsTT	p.Pro239Phe	p.P239F	ENST00000276594	NM_024504.3	239	CCt/TTt	3/8	0.162963510498566	1	FACETS	0.894	0.735	1	0.894	0.735	1	CLONAL	1	FALSE	0	0.162963510498566	1		366	454	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213481	27213481	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0034370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	36	338	0	ENST00000380036.4:c.2878-1G>A		p.X960_splice	ENST00000380036	NM_000459.3	960			1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	FALSE	1	0.162963510498566	2		338	405	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42381403	42381403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555843091	NA	P-0034514-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	229	792	0	ENST00000221972.3:c.29C>T	p.Ala10Val	p.A10V	ENST00000221972	NM_021601.3	10	gCt/gTt	1/5	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.491051059466067	2		792	797	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720800	89720809	+	frameshift_variant	Frame_Shift_Del	DEL	ACTTACTTTA	ACTTACTTTA	-	novel	NA	P-0034514-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	31	103	1	ENST00000371953.3:c.953_962del	p.Leu318GlnfsTer23	p.L318Qfs*23	ENST00000371953	NM_000314.4	317	gtACTTACTTTA/gt	8/9	0.284796778638682	1	FACETS	0.253	0.204	0.308	0.253	0.204	0.308	INDETERMINATE	1	TRUE	0	0.491051059466067	1		104	377	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0034984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	61	578	0	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	0.752	0.655	0.855	0.752	0.655	0.855	SUBCLONAL	1	TRUE	1	0.596448376187861	2		578	272	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437596	52437597	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0034984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	74	721	0	ENST00000460680.1:c.1564_1565del	p.Pro522CysfsTer14	p.P522Cfs*14	ENST00000460680	NM_004656.3	522	CCt/t	13/17	0.510135690813447	1	FACETS	0.893	0.798	0.991	0.893	0.798	0.991	CLONAL	1	TRUE	0	0.596448376187861	1		721	195	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18960968	18960968	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	82	723	0	ENST00000262803.5:c.546G>C	p.Glu182Asp	p.E182D	ENST00000262803	NM_002911.3	182	gaG/gaC	4/24	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.596448376187861	2		723	265	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662769	227662769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	81	810	0	ENST00000305123.5:c.686C>T	p.Ala229Val	p.A229V	ENST00000305123	NM_005544.2	229	gCc/gTc	1/2	1	2	FACETS	0.844	0.75	0.942	0.844	0.75	0.942	CLONAL	1	TRUE	1	0.596448376187861	2		810	322	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0035069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	249	528	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.93746363085492	2		528	523	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	154	151	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		151	390	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0035595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	258	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.539622483903837	3	FACETS	0.94	0.887	0.993	0.94	0.887	0.993	CLONAL	2	TRUE	1	0.570940703838731	3		288	618	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711975	89711975	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1554900635	NA	P-0035595-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	181	510	0	ENST00000371953.3:c.593T>A	p.Met198Lys	p.M198K	ENST00000371953	NM_000314.4	198	aTg/aAg	6/9	0.570940703838731	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.570940703838731	1		510	442	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0035813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	10	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		288	326	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046410	69046410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868582467	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	117	317	0	ENST00000288368.4:c.3883G>A	p.Glu1295Lys	p.E1295K	ENST00000288368	NM_024870.2	1295	Gaa/Aaa	32/40	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.361672407487744	2		317	588	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	158	939	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.361672407487744	2		939	778	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	413	248	1				ENST00000310581	NM_198253.2	-/1132			0.346188874192277	5	FACETS	1	0.979	1	1	0.979	1	CLONAL	4	TRUE	1	0.361672407487744	5		249	852	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074204	8074204	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	62	347	0	ENST00000377482.5:c.455C>T	p.Pro152Leu	p.P152L	ENST00000377482	NM_018948.3	152	cCt/cTt	4/4	0.361672407487744	3	FACETS	0.836	0.724	0.958			1	CLONAL	1	TRUE	NA	0.361672407487744	3		347	484	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075670	8075670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	57	417	0	ENST00000377482.5:c.10G>A	p.Ala4Thr	p.A4T	ENST00000377482	NM_018948.3	4	Gca/Aca	2/4	0.361672407487744	3	FACETS	0.957	0.824	1			1	CLONAL	1	TRUE	NA	0.361672407487744	3		417	389	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs984459719	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	184	683	0	ENST00000324856.7:c.2291C>T	p.Ser764Phe	p.S764F	ENST00000324856	NM_006015.4	764	tCc/tTc	7/20	0.275104443684742	4	FACETS	1	0.983	1	0.617	0.568	0.667	CLONAL	1	TRUE	2	0.361672407487744	4		683	1123	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932125	36932126	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	76	493	0	ENST00000361632.4:c.2343_2344delinsTT	p.Pro782Ser	p.P782S	ENST00000361632		781	acCCcc/acTTcc	16/16	0.275104443684742	4	FACETS	1	0.939	1	0.556	0.488	0.628	CLONAL	1	TRUE	2	0.361672407487744	4		493	515	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804269	43804269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766638870	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	130	532	0	ENST00000372470.3:c.269G>A	p.Arg90Gln	p.R90Q	ENST00000372470	NM_005373.2	90	cGa/cAa	3/12	0.275104443684742	4	FACETS	1	0.969	1	0.579	0.525	0.635	CLONAL	1	TRUE	2	0.361672407487744	4		532	846	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78426053	78426053	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	90	481	0	ENST00000370768.2:c.1472C>T	p.Pro491Leu	p.P491L	ENST00000370768	NM_003902.3	491	cCt/cTt	15/20	0.275104443684742	4	FACETS	1	0.955	1	0.573	0.509	0.641	CLONAL	1	TRUE	2	0.361672407487744	4		481	591	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459215	120459215	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1221302379	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	102	507	1	ENST00000256646.2:c.6130C>T	p.Arg2044Cys	p.R2044C	ENST00000256646	NM_024408.3	2044	Cgt/Tgt	34/34	0.275104443684742	4	FACETS	1	0.957	1	0.567	0.508	0.63	CLONAL	1	TRUE	2	0.361672407487744	4		508	677	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111538	8111538	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	180	502	0	ENST00000346208.3:c.1024G>A	p.Gly342Arg	p.G342R	ENST00000346208		342	Ggg/Agg	5/6	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.361672407487744	2		502	731	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276956	123276956	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	33	273	0	ENST00000358487.5:c.961G>A	p.Asp321Asn	p.D321N	ENST00000358487	NM_000141.4	321	Gac/Aac	8/18	1	2	FACETS	0.699	0.572	0.841	0.699	0.572	0.841	SUBCLONAL	1	TRUE	1	0.361672407487744	2		273	261	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310950	123310950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	95	452	0	ENST00000358487.5:c.478G>A	p.Glu160Lys	p.E160K	ENST00000358487	NM_000141.4	160	Gaa/Aaa	5/18	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.361672407487744	2		452	515	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310974	123310974	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	73	390	0	ENST00000358487.5:c.455-1G>A		p.X152_splice	ENST00000358487	NM_000141.4	152			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.361672407487744	2		390	358	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32439155	32439155	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	52	602	0	ENST00000332351.3:c.918G>A	p.Trp306Ter	p.W306*	ENST00000332351	NM_024426.4	306	tgG/tgA	4/10	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.361672407487744	2		602	249	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948777	71948778	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	156	836	1	ENST00000298229.2:c.3489_3490delinsTT	p.Arg1164Trp	p.R1164W	ENST00000298229	NM_001567.3	1163	ggCCgg/ggTTgg	26/28	1	2	FACETS	0.936	0.857	1	0.936	0.857	1	CLONAL	1	TRUE	1	0.361672407487744	2		837	922	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377121	118377121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	64	316	0	ENST00000534358.1:c.10514C>T	p.Ser3505Phe	p.S3505F	ENST00000534358	NM_005933.3	3505	tCc/tTc	27/36	1	2	FACETS	0.946	0.824	1	0.946	0.824	1	CLONAL	1	TRUE	1	0.361672407487744	2		316	374	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435382	18435382	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	18	268	0	ENST00000266497.5:c.367G>T	p.Glu123Ter	p.E123*	ENST00000266497		123	Gaa/Taa	1/31	1	2	FACETS	0.607	0.46	0.778	0.607	0.46	0.778	SUBCLONAL	1	TRUE	1	0.361672407487744	2		268	164	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552778	18552778	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	31	396	0	ENST00000266497.5:c.2189C>T	p.Ser730Phe	p.S730F	ENST00000266497		730	tCc/tTc	14/31	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.361672407487744	2		396	170	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944748	31944748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	26	153	0	ENST00000340398.3:c.353C>T	p.Thr118Ile	p.T118I	ENST00000340398	NM_001013699.2	118	aCc/aTc	1/1	1	2	FACETS	0.734	0.585	0.901	0.734	0.585	0.901	CLONAL	1	TRUE	1	0.361672407487744	2		153	196	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230679	46230679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	52	495	0	ENST00000334344.6:c.928C>T	p.Arg310Cys	p.R310C	ENST00000334344	NM_152641.2	310	Cgt/Tgt	8/21	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.361672407487744	2		495	274	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420841	49420841	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	135	498	0	ENST00000301067.7:c.14908G>A	p.Glu4970Lys	p.E4970K	ENST00000301067	NM_003482.3	4970	Gaa/Aaa	48/54	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.361672407487744	2		498	693	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443622	49443622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	135	654	0	ENST00000301067.7:c.3749C>T	p.Pro1250Leu	p.P1250L	ENST00000301067	NM_003482.3	1250	cCa/cTa	11/54	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.361672407487744	2		654	716	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445541	49445541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	146	790	0	ENST00000301067.7:c.1925C>T	p.Ser642Leu	p.S642L	ENST00000301067	NM_003482.3	642	tCa/tTa	10/54	1	2	FACETS	0.938	0.856	1	0.938	0.856	1	CLONAL	1	TRUE	1	0.361672407487744	2		790	861	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445613	49445613	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	233	972	2	ENST00000301067.7:c.1853C>T	p.Ser618Phe	p.S618F	ENST00000301067	NM_003482.3	618	tCc/tTc	10/54	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.361672407487744	2		974	1194	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448353	49448353	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	127	581	0	ENST00000301067.7:c.358T>C	p.Phe120Leu	p.F120L	ENST00000301067	NM_003482.3	120	Ttc/Ctc	3/54	1	2	FACETS	0.966	0.876	1	0.966	0.876	1	CLONAL	1	TRUE	1	0.361672407487744	2		581	727	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481403	56481403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	194	665	0	ENST00000267101.3:c.590C>T	p.Pro197Leu	p.P197L	ENST00000267101	NM_001982.3	197	cCt/cTt	5/28	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.361672407487744	2		665	952	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112910775	112910775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	60	397	0	ENST00000351677.2:c.784C>T	p.Leu262Phe	p.L262F	ENST00000351677	NM_002834.3	262	Ctc/Ttc	7/16	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.361672407487744	2		397	320	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608247	28608247	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	56	643	0	ENST00000241453.7:c.1809G>A	p.Trp603Ter	p.W603*	ENST00000241453	NM_004119.2	603	tgG/tgA	14/24	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.361672407487744	2		643	267	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893318	32893318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507603	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	29	365	0	ENST00000380152.3:c.172G>A	p.Glu58Lys	p.E58K	ENST00000380152		58	Gaa/Aaa	3/27	1	2	FACETS	0.891	0.722	1	0.891	0.722	1	CLONAL	1	TRUE	1	0.361672407487744	2		365	180	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915204	32915204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749590229	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	33	568	0	ENST00000380152.3:c.6712G>A	p.Asp2238Asn	p.D2238N	ENST00000380152		2238	Gat/Aat	11/27	1	2	FACETS	0.877	0.72	1	0.877	0.72	1	CLONAL	1	TRUE	1	0.361672407487744	2		568	208	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023301	33023301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	148	702	0	ENST00000300177.4:c.410C>T	p.Ser137Phe	p.S137F	ENST00000300177	NM_001191322.1	137	tCc/tTc	2/2	0.288616754241247	0	FACETS	0.786	0.719	0.854			1	SUBCLONAL	1	TRUE	0	0.361672407487744	0		702	665	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961408	41961408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	54	507	0	ENST00000219905.7:c.316C>T	p.Pro106Ser	p.P106S	ENST00000219905	NM_001164273.1	106	Cct/Tct	2/24	0.288616754241247	0	FACETS	0.843	0.729	0.965			1	CLONAL	1	TRUE	0	0.361672407487744	0		507	226	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028498	42028498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	57	471	0	ENST00000219905.7:c.4036G>A	p.Glu1346Lys	p.E1346K	ENST00000219905	NM_001164273.1	1346	Gaa/Aaa	13/24	0.288616754241247	0	FACETS	0.592	0.51	0.68			1	SUBCLONAL	1	TRUE	0	0.361672407487744	0		471	340	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66779586	66779586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761222249	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	66	478	0	ENST00000307102.5:c.916C>T	p.Pro306Ser	p.P306S	ENST00000307102	NM_002755.3	306	Cct/Tct	8/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.361672407487744	NA		478	464	SUCCESS
BLM	641	MSKCC	GRCh37	15	91308526	91308526	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	60	390	0	ENST00000355112.3:c.2075G>A	p.Gly692Glu	p.G692E	ENST00000355112	NM_000057.2	692	gGa/gAa	9/22	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.361672407487744	2		390	326	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343582	343582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	187	823	2	ENST00000262320.3:c.2092C>T	p.His698Tyr	p.H698Y	ENST00000262320	NM_003502.3	698	Cac/Tac	8/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.361672407487744	2		825	915	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857500	9857500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	84	468	0	ENST00000330684.3:c.3901G>A	p.Glu1301Lys	p.E1301K	ENST00000330684	NM_001134407.1	1301	Gag/Aag	13/13	1	2	FACETS	0.97	0.86	1	0.97	0.86	1	CLONAL	1	TRUE	1	0.361672407487744	2		468	479	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857692	9857692	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1389208302	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	80	471	0	ENST00000330684.3:c.3709G>A	p.Asp1237Asn	p.D1237N	ENST00000330684	NM_001134407.1	1237	Gat/Aat	13/13	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.361672407487744	2		471	436	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934842	9934842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	57	557	0	ENST00000330684.3:c.1448G>A	p.Gly483Glu	p.G483E	ENST00000330684	NM_001134407.1	483	gGg/gAg	6/13	1	2	FACETS	0.888	0.765	1	0.888	0.765	1	CLONAL	1	TRUE	1	0.361672407487744	2		557	355	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647529	23647529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374425261	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	68	723	0	ENST00000261584.4:c.338C>T	p.Pro113Leu	p.P113L	ENST00000261584	NM_024675.3	113	cCa/cTa	4/13	1	2	FACETS	0.777	0.677	0.884	0.777	0.677	0.884	SUBCLONAL	1	TRUE	1	0.361672407487744	2		723	484	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50788299	50788299	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	76	766	0	ENST00000398568.2:c.877A>C	p.Ser293Arg	p.S293R	ENST00000398568	NM_001042412.1	293	Agt/Cgt	5/18	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.361672407487744	2		766	409	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50815298	50815298	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	127	560	0	ENST00000398568.2:c.1651C>T	p.Gln551Ter	p.Q551*	ENST00000398568	NM_001042412.1	551	Cag/Tag	9/18	1	2	FACETS	0.986	0.895	1	0.986	0.895	1	CLONAL	1	TRUE	1	0.361672407487744	2		560	712	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821470	72821471	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	131	639	0	ENST00000268489.5:c.10704_10705delinsTT	p.Pro3569Ser	p.P3569S	ENST00000268489	NM_006885.3	3568	caCCct/caTTct	10/10	1	2	FACETS	0.841	0.763	0.924	0.841	0.763	0.924	CLONAL	1	TRUE	1	0.361672407487744	2		639	861	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577068	7577070	+	frameshift_variant	Frame_Shift_Del	DEL	GCG	GCG	CA	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	204	726	2	ENST00000269305.4:c.868_870delinsTG	p.Arg290Ter	p.R290*	ENST00000269305	NM_001126112.2	290	CGC/TG	8/11	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.361672407487744	2		728	1126	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	160	654	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.361672407487744	2		654	742	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131264	17131265	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	244	802	1	ENST00000285071.4:c.187_188delinsTT	p.Pro63Phe	p.P63F	ENST00000285071	NM_144997.5	63	CCc/TTc	4/14	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.361672407487744	2		803	1247	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858062	40858062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	164	674	1	ENST00000428826.2:c.1802C>T	p.Ser601Phe	p.S601F	ENST00000428826		601	tCc/tTc	16/21	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.361672407487744	2		675	850	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394723	45394723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	81	408	0	ENST00000262160.6:c.626G>A	p.Gly209Glu	p.G209E	ENST00000262160	NM_005901.5	209	gGa/gAa	5/11	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.361672407487744	2		408	396	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400713	56400713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	52	311	0	ENST00000348428.3:c.1307C>T	p.Ser436Phe	p.S436F	ENST00000348428	NM_006785.3	436	tCt/tTt	11/17	1	2	FACETS	0.781	0.676	0.893	1	0.97	1	SUBCLONAL	2	TRUE	1	0.361672407487744	2		311	184	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217785	2217788	+	frameshift_variant	Frame_Shift_Del	DEL	CGCC	CGCC	TCT	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	149	691	2	ENST00000398665.3:c.2559_2562delinsTCT	p.Ala854LeufsTer214	p.A854Lfs*214	ENST00000398665	NM_032482.2	853	cgCGCC/cgTCT	22/28	0.114769046689099	4	FACETS	1	0.947	1	0.526	0.48	0.575	INDETERMINATE	1	TRUE	2	0.361672407487744	4		693	1066	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7174603	7174603	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs387906540	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	119	535	0	ENST00000302850.5:c.1114C>T	p.Arg372Ter	p.R372*	ENST00000302850	NM_000208.2	372	Cga/Tga	4/22	0.114769046689099	4	FACETS	1	0.965	1	0.575	0.519	0.634	INDETERMINATE	1	TRUE	2	0.361672407487744	4		535	779	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302774	15302774	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	126	669	0	ENST00000263388.2:c.676C>T	p.Pro226Ser	p.P226S	ENST00000263388	NM_000435.2	226	Cct/Tct	4/33	0.114769046689099	4	FACETS	1	0.983	1	0.701	0.636	0.769	INDETERMINATE	1	TRUE	2	0.361672407487744	4		669	677	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976220	18976220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1482801009	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	140	725	1	ENST00000262803.5:c.2980C>T	p.Pro994Ser	p.P994S	ENST00000262803	NM_002911.3	994	Ccg/Tcg	21/24	0.114769046689099	4	FACETS	1	0.982	1	0.653	0.595	0.714	INDETERMINATE	1	TRUE	2	0.361672407487744	4		726	807	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794473	42794473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757042769	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	244	893	0	ENST00000575354.2:c.1553C>T	p.Pro518Leu	p.P518L	ENST00000575354	NM_015125.3	518	cCg/cTg	10/20	0.114769046689099	4	FACETS	0.797	0.744	0.851	0.797	0.744	0.851	INDETERMINATE	2	TRUE	2	0.361672407487744	4		893	1153	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797952	42797952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	200	802	1	ENST00000575354.2:c.4004C>T	p.Pro1335Leu	p.P1335L	ENST00000575354	NM_015125.3	1335	cCc/cTc	16/20	0.114769046689099	4	FACETS	1	0.99	1	0.741	0.686	0.798	INDETERMINATE	1	TRUE	2	0.361672407487744	4		803	1016	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716064	52716064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	205	864	0	ENST00000322088.6:c.629C>T	p.Ser210Phe	p.S210F	ENST00000322088	NM_014225.5	210	tCc/tTc	5/15	0.114769046689099	4	FACETS	1	0.99	1	0.704	0.652	0.758	INDETERMINATE	1	TRUE	2	0.361672407487744	4		864	1096	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716281	52716281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1177432332	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	166	613	0	ENST00000322088.6:c.725C>T	p.Ala242Val	p.A242V	ENST00000322088	NM_014225.5	242	gCc/gTc	6/15	0.114769046689099	4	FACETS	0.84	0.773	0.909	0.84	0.773	0.909	INDETERMINATE	2	TRUE	2	0.361672407487744	4		613	744	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464538	25464539	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	135	700	1	ENST00000264709.3:c.1974_1975delinsTT	p.Arg659Cys	p.R659C	ENST00000264709	NM_175629.2	658	gaCCgc/gaTTgc	17/23	0.11372892544758	0	FACETS	0.571	0.519	0.626			1	INDETERMINATE	1	TRUE	0	0.361672407487744	0		701	834	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497897	25497898	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	110	515	2	ENST00000264709.3:c.551_552delinsTT	p.Pro184Leu	p.P184L	ENST00000264709	NM_175629.2	184	cCC/cTT	6/23	0.11372892544758	0	FACETS	0.635	0.572	0.702			1	INDETERMINATE	1	TRUE	0	0.361672407487744	0		517	611	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965859	25965859	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	121	613	0	ENST00000435504.4:c.3347C>T	p.Ser1116Phe	p.S1116F	ENST00000435504		1116	tCc/tTc	13/13	0.11372892544758	0	FACETS	0.661	0.598	0.727			1	INDETERMINATE	1	TRUE	0	0.361672407487744	0		613	646	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029127	26029127	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	34	433	0	ENST00000435504.4:c.223C>T	p.Pro75Ser	p.P75S	ENST00000435504		75	Cca/Tca	4/13	0.11372892544758	0	FACETS	0.465	0.382	0.558			1	INDETERMINATE	1	TRUE	0	0.361672407487744	0		433	258	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872503	136872503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	56	299	0	ENST00000241393.3:c.995G>A	p.Gly332Glu	p.G332E	ENST00000241393	NM_003467.2	332	gGa/gAa	2/2	1	2	FACETS	0.944	0.814	1	0.944	0.814	1	CLONAL	1	TRUE	1	0.361672407487744	2		299	328	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568836	212568836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	44	456	0	ENST00000342788.4:c.1282C>T	p.Leu428Phe	p.L428F	ENST00000342788	NM_005235.2	428	Ctc/Ttc	11/28	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.361672407487744	2		456	231	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812293	212812293	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569995088	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	38	518	0	ENST00000342788.4:c.283C>T	p.Arg95Cys	p.R95C	ENST00000342788	NM_005235.2	95	Cgt/Tgt	3/28	1	2	FACETS	0.942	0.786	1	0.942	0.786	1	CLONAL	1	TRUE	1	0.361672407487744	2		518	223	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662506	227662506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	88	505	0	ENST00000305123.5:c.949G>A	p.Val317Met	p.V317M	ENST00000305123	NM_005544.2	317	Gtg/Atg	1/2	1	2	FACETS	0.832	0.738	0.932	0.832	0.738	0.932	CLONAL	1	TRUE	1	0.361672407487744	2		505	585	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031230	36031230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	173	612	0	ENST00000358208.4:c.1349C>T	p.Ser450Phe	p.S450F	ENST00000358208		450	tCc/tTc	11/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.361672407487744	2		612	800	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944523	40944523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	104	511	0	ENST00000373198.4:c.1979C>T	p.Ser660Phe	p.S660F	ENST00000373198	NM_133170.3	660	tCt/tTt	12/32	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.361672407487744	2		511	502	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306689	41306689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868376470	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	145	659	0	ENST00000373198.4:c.970G>A	p.Glu324Lys	p.E324K	ENST00000373198	NM_133170.3	324	Gaa/Aaa	7/32	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.361672407487744	2		659	704	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385212	41385212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	119	627	0	ENST00000373198.4:c.749C>T	p.Ala250Val	p.A250V	ENST00000373198	NM_133170.3	250	gCc/gTc	6/32	1	2	FACETS	0.824	0.743	0.908	0.824	0.743	0.908	CLONAL	1	TRUE	1	0.361672407487744	2		627	799	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42851168	42851168	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	45	597	0	ENST00000398585.3:c.725G>A	p.Gly242Glu	p.G242E	ENST00000398585	NM_001135099.1	242	gGa/gAa	7/14	1	2	FACETS	0.707	0.596	0.829	0.707	0.596	0.829	SUBCLONAL	1	TRUE	1	0.361672407487744	2		597	352	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860327	42860327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs989768620	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	149	493	0	ENST00000398585.3:c.550C>T	p.Arg184Trp	p.R184W	ENST00000398585	NM_001135099.1	184	Cgg/Tgg	5/14	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.361672407487744	2		493	765	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41521995	41521995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764980716	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	55	547	0	ENST00000263253.7:c.857C>T	p.Pro286Leu	p.P286L	ENST00000263253	NM_001429.3	286	cCa/cTa	3/31	1	2	FACETS	0.854	0.734	0.984	0.854	0.734	0.984	CLONAL	1	TRUE	1	0.361672407487744	2		547	356	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059133	47059133	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	104	510	0	ENST00000409792.3:c.7528C>T	p.Arg2510Cys	p.R2510C	ENST00000409792	NM_014159.6	2510	Cgc/Tgc	20/21	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.361672407487744	2		510	551	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165249	47165249	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	33	492	0	ENST00000409792.3:c.877C>T	p.Pro293Ser	p.P293S	ENST00000409792	NM_014159.6	293	Cca/Tca	3/21	1	2	FACETS	0.899	0.738	1	0.899	0.738	1	CLONAL	1	TRUE	1	0.361672407487744	2		492	203	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247492	71247492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	129	587	0	ENST00000318789.4:c.41C>T	p.Ser14Leu	p.S14L	ENST00000318789	NM_032682.5	14	tCa/tTa	6/21	1	2	FACETS	0.922	0.836	1	0.922	0.836	1	CLONAL	1	TRUE	1	0.361672407487744	2		587	774	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480306	89480306	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	19	261	0	ENST00000336596.2:c.2143G>A	p.Asp715Asn	p.D715N	ENST00000336596	NM_005233.5	715	Gat/Aat	13/17	1	2	FACETS	0.682	0.522	0.868	0.682	0.522	0.868	SUBCLONAL	1	TRUE	1	0.361672407487744	2		261	154	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498375	89498375	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	29	222	0	ENST00000336596.2:c.2347G>A	p.Gly783Arg	p.G783R	ENST00000336596	NM_005233.5	783	Gga/Aga	14/17	1	2	FACETS	0.96	0.779	1	0.96	0.779	1	CLONAL	1	TRUE	1	0.361672407487744	2		222	167	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374251	138374251	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	72	760	0	ENST00000289153.2:c.3193C>T	p.Arg1065Trp	p.R1065W	ENST00000289153	NM_006219.2	1065	Cgg/Tgg	22/22	1	2	FACETS	0.917	0.805	1	0.917	0.805	1	CLONAL	1	TRUE	1	0.361672407487744	2		760	434	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504403	186504403	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	30	534	0	ENST00000323963.5:c.740T>G	p.Ile247Ser	p.I247S	ENST00000323963		247	aTc/aGc	7/11	1	2	FACETS	0.734	0.595	0.89	0.734	0.595	0.89	SUBCLONAL	1	TRUE	1	0.361672407487744	2		534	226	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747900	41747900	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	49	520	2	ENST00000226382.2:c.869C>T	p.Pro290Leu	p.P290L	ENST00000226382	NM_003924.3	290	cCc/cTc	3/3	1	2	FACETS	0.371	0.313	0.434	0.371	0.313	0.434	SUBCLONAL	1	TRUE	1	0.361672407487744	2		522	731	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593586	55593586	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	35	387	0	ENST00000288135.5:c.1652C>T	p.Pro551Leu	p.P551L	ENST00000288135	NM_000222.2	551	cCc/cTc	11/21	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.361672407487744	2		387	153	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955863	55955863	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868047715	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	56	337	0	ENST00000263923.4:c.3299C>T	p.Ser1100Phe	p.S1100F	ENST00000263923	NM_002253.2	1100	tCc/tTc	24/30	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.361672407487744	2		337	276	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961796	55961796	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	55	436	0	ENST00000263923.4:c.2765G>A	p.Gly922Glu	p.G922E	ENST00000263923	NM_002253.2	922	gGa/gAa	20/30	1	2	FACETS	0.859	0.738	0.99	0.859	0.738	0.99	CLONAL	1	TRUE	1	0.361672407487744	2		436	354	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294121	1294121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886059906	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1621	182	997	0	ENST00000310581.5:c.880C>T	p.His294Tyr	p.H294Y	ENST00000310581	NM_198253.2	294	Cac/Tac	2/16	0.346188874192277	5	FACETS	0.861	0.791	0.935	0.215	0.197	0.234	CLONAL	1	TRUE	1	0.361672407487744	5		997	1803	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295196	1295196	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	276	339	0				ENST00000310581	NM_198253.2	-/1132			0.346188874192277	5	FACETS	1	0.984	1	1	0.984	1	CLONAL	4	TRUE	1	0.361672407487744	5		339	541	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861085	35861085	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	178	420	0	ENST00000303115.3:c.214G>A	p.Glu72Lys	p.E72K	ENST00000303115	NM_002185.3	72	Gaa/Aaa	2/8	0.346188874192277	5	FACETS	1	0.981	1	0.857	0.798	0.916	CLONAL	3	TRUE	1	0.361672407487744	5		420	443	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874636	35874636	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	61	449	0	ENST00000303115.3:c.792G>A	p.Trp264Ter	p.W264*	ENST00000303115	NM_002185.3	264	tgG/tgA	6/8	0.346188874192277	5	FACETS	1	0.914	1	0.27	0.233	0.31	CLONAL	1	TRUE	1	0.361672407487744	5		449	482	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520326	176520327	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	148	655	1	ENST00000292408.4:c.1245_1246delinsTT	p.Arg416Ter	p.R416*	ENST00000292408	NM_213647.1	415	gcCCga/gcTTga	9/18	0.361672407487744	1	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	0	0.361672407487744	1		656	638	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672029	30672029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	144	797	0	ENST00000376406.3:c.4931G>A	p.Arg1644Lys	p.R1644K	ENST00000376406	NM_014641.2	1644	aGg/aAg	10/15	1	2	FACETS	0.899	0.82	0.982	0.899	0.82	0.982	CLONAL	1	TRUE	1	0.361672407487744	2		797	886	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948254	31948255	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	140	688	1	ENST00000375333.2:c.842_843delinsTT	p.Thr281Ile	p.T281I	ENST00000375333	NM_032454.1	281	aCC/aTT	6/8	1	2	FACETS	0.851	0.774	0.931	0.851	0.774	0.931	CLONAL	1	TRUE	1	0.361672407487744	2		689	910	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956573	93956573	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	48	445	0	ENST00000369303.4:c.2663G>A	p.Gly888Glu	p.G888E	ENST00000369303	NM_004440.3	888	gGa/gAa	15/17	1	2	FACETS	0.822	0.698	0.957	0.822	0.698	0.957	CLONAL	1	TRUE	1	0.361672407487744	2		445	323	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979282	93979282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	45	425	0	ENST00000369303.4:c.1546C>T	p.Arg516Trp	p.R516W	ENST00000369303	NM_004440.3	516	Cgg/Tgg	7/17	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.361672407487744	2		425	208	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120360	94120360	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs749418654	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	59	296	0	ENST00000369303.4:c.691C>T	p.Arg231Ter	p.R231*	ENST00000369303	NM_004440.3	231	Cga/Tga	3/17	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.361672407487744	2		296	265	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521873	157521873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	97	386	0	ENST00000346085.5:c.4145C>T	p.Pro1382Leu	p.P1382L	ENST00000346085	NM_020732.3	1382	cCc/cTc	18/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.361672407487744	2		386	449	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987263	2987263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	103	640	0	ENST00000396946.4:c.166G>A	p.Asp56Asn	p.D56N	ENST00000396946	NM_032415.4	56	Gat/Aat	3/25	0.141926289201846	0	FACETS	0.666	0.598	0.738			1	INDETERMINATE	1	TRUE	0	0.361672407487744	0		640	546	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467750	50467750	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	123	480	0	ENST00000331340.3:c.985C>T	p.Pro329Ser	p.P329S	ENST00000331340	NM_006060.4	329	Ccg/Tcg	8/8	0.141926289201846	0	FACETS	0.787	0.714	0.862			1	INDETERMINATE	1	TRUE	0	0.361672407487744	0		480	552	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852129	128852130	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	299	866	1	ENST00000249373.3:c.2201_2202delinsTT	p.Ser734Phe	p.S734F	ENST00000249373	NM_005631.4	734	tCC/tTT	12/12	0.336599001277542	4	FACETS	0.856	0.805	0.909	0.571	0.537	0.606	CLONAL	2	TRUE	1	0.361672407487744	4		867	1315	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852146	128852146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	194	880	0	ENST00000249373.3:c.2218G>A	p.Glu740Lys	p.E740K	ENST00000249373	NM_005631.4	740	Gag/Aag	12/12	0.336599001277542	4	FACETS	1	0.965	1	0.36	0.332	0.389	CLONAL	1	TRUE	1	0.361672407487744	4		880	1353	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29197742	29197742	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	202	827	0	ENST00000240100.2:c.452C>T	p.Ser151Phe	p.S151F	ENST00000240100	NM_001394.6	151	tCc/tTc	2/4	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.361672407487744	2		827	974	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939506	68939506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1309816810	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	18	431	0	ENST00000288368.4:c.491G>A	p.Gly164Glu	p.G164E	ENST00000288368	NM_024870.2	164	gGa/gAa	5/40	1	2	FACETS	0.673	0.51	0.861	0.673	0.51	0.861	SUBCLONAL	1	TRUE	1	0.361672407487744	2		431	148	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992719	68992719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778128731	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	48	636	0	ENST00000288368.4:c.1684C>T	p.Arg562Cys	p.R562C	ENST00000288368	NM_024870.2	562	Cgt/Tgt	16/40	1	2	FACETS	0.87	0.74	1	0.87	0.74	1	CLONAL	1	TRUE	1	0.361672407487744	2		636	305	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058575	69058575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	80	702	0	ENST00000288368.4:c.4219C>T	p.Leu1407Phe	p.L1407F	ENST00000288368	NM_024870.2	1407	Ctt/Ttt	34/40	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.361672407487744	2		702	396	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742986	145742986	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	89	185	0	ENST00000428558.2:c.118G>A	p.Ala40Thr	p.A40T	ENST00000428558	NM_004260.3	40	Gcg/Acg	2/22	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.361672407487744	2		185	345	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317921	8317921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150063446	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	37	395	1	ENST00000356435.5:c.5692C>T	p.Arg1898Cys	p.R1898C	ENST00000356435		1898	Cgt/Tgt	35/35	0.337254800764453	0	FACETS	0.5	0.415	0.595			1	SUBCLONAL	1	TRUE	0	0.361672407487744	0		396	261	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528596	8528596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	30	621	1	ENST00000356435.5:c.536G>A	p.Arg179Gln	p.R179Q	ENST00000356435		179	cGa/cAa	4/35	0.337254800764453	0	FACETS	0.535	0.434	0.647			1	SUBCLONAL	1	TRUE	0	0.361672407487744	0		622	198	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528705	8528706	+	missense_variant	Missense_Mutation	DNP	CC	CC	GT	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	56	347	1	ENST00000356435.5:c.426_427delinsAC	p.Ala143Pro	p.A143P	ENST00000356435		142	acGGcc/acACcc	4/35	0.337254800764453	0	FACETS	0.534	0.459	0.615			1	SUBCLONAL	1	TRUE	0	0.361672407487744	0		348	370	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93629441	93629441	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	64	355	0	ENST00000375746.1:c.875G>T	p.Arg292Ile	p.R292I	ENST00000375746	NM_001174167.1	292	aGa/aTa	7/14	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.361672407487744	2		355	336	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771828	135771828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779599439	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	163	698	0	ENST00000298552.3:c.3289C>T	p.Arg1097Cys	p.R1097C	ENST00000298552	NM_001162426.1	1097	Cgt/Tgt	23/23	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.361672407487744	2		698	875	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391340	139391340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1341934554	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	294	834	2	ENST00000277541.6:c.6851C>T	p.Thr2284Ile	p.T2284I	ENST00000277541	NM_017617.3	2284	aCc/aTc	34/34	1	2	FACETS	0.776	0.731	0.822	1	0.994	1	SUBCLONAL	2	TRUE	1	0.361672407487744	2		836	1048	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938668	76938668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	46	365	0	ENST00000373344.5:c.2080C>T	p.Pro694Ser	p.P694S	ENST00000373344	NM_000489.3	694	Cca/Tca	9/35	1	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.361672407487744	1		365	154	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528705	8528705	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	54	348	0	ENST00000356435.5:c.427G>C	p.Ala143Pro	p.A143P	ENST00000356435		143	Gcc/Ccc	4/35	0.337254800764453	0	FACETS	0.521	0.446	0.601			1	SUBCLONAL	1	TRUE	0	0.361672407487744	0		348	366	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852129	128852129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1179087143	NA	P-0035910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	299	865	1	ENST00000249373.3:c.2201C>T	p.Ser734Phe	p.S734F	ENST00000249373	NM_005631.4	734	tCc/tTc	12/12	0.336599001277542	4	FACETS	0.856	0.805	0.909	0.571	0.537	0.606	CLONAL	2	TRUE	1	0.361672407487744	4		866	1315	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	37	248	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.966	0.8	1	0.966	0.8	1	CLONAL	1	TRUE	1	0.270700818184574	2		249	283	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709162	117709162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867987684	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	71	463	0	ENST00000368508.3:c.1795G>A	p.Glu599Lys	p.E599K	ENST00000368508	NM_002944.2	599	Gaa/Aaa	13/43	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.270700818184574	2		463	393	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40743950	40743950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781527200	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	85	623	0	ENST00000392038.2:c.757C>T	p.Arg253Trp	p.R253W	ENST00000392038	NM_001626.4	253	Cgg/Tgg	9/14	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.270700818184574	2		623	526	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453145	140453145	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913366	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	137	428	0	ENST00000288602.6:c.1790T>G	p.Leu597Arg	p.L597R	ENST00000288602	NM_004333.4	597	cTa/cGa	15/18	0.270700818184574	3	FACETS	0.996	0.91	1	0.996	0.91	1	CLONAL	2	TRUE	1	0.270700818184574	3		428	577	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs886039483	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	242	862	0	ENST00000269305.4:c.376T>G	p.Tyr126Asp	p.Y126D	ENST00000269305	NM_001126112.2	126	Tac/Gac	5/11	0.270700818184574	1	FACETS	0.947	0.887	1	1	0.994	1	CLONAL	2	TRUE	0	0.270700818184574	1		862	816	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923335	9923335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	115	631	2	ENST00000330684.3:c.1952C>T	p.Ala651Val	p.A651V	ENST00000330684	NM_001134407.1	651	gCc/gTc	9/13	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.270700818184574	2		633	600	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285682	46285682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	113	500	0	ENST00000334344.6:c.5042C>T	p.Ser1681Phe	p.S1681F	ENST00000334344	NM_152641.2	1681	tCt/tTt	17/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.270700818184574	2		500	709	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962858	2962858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	101	782	0	ENST00000396946.4:c.2050G>A	p.Gly684Arg	p.G684R	ENST00000396946	NM_032415.4	684	Ggg/Agg	16/25	0.270700818184574	3	FACETS	1	0.956	1	0.567	0.507	0.631	CLONAL	1	TRUE	1	0.270700818184574	3		782	747	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411267	63411267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866313799	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	139	878	0	ENST00000330258.3:c.1900C>T	p.Arg634Cys	p.R634C	ENST00000330258	NM_152424.3	634	Cgt/Tgt	2/2	0.270700818184574	1	FACETS	0.775	0.708	0.844	1	0.988	1	SUBCLONAL	2	TRUE	0	0.270700818184574	1		878	573	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312713	91312713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1279814185	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	81	405	0	ENST00000355112.3:c.2452C>T	p.Arg818Cys	p.R818C	ENST00000355112	NM_000057.2	818	Cgc/Tgc	12/22	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.270700818184574	2		405	510	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576880	212576880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	64	458	1	ENST00000342788.4:c.1019G>A	p.Gly340Glu	p.G340E	ENST00000342788	NM_005235.2	340	gGa/gAa	9/28	1	2	FACETS	0.961	0.834	1	0.961	0.834	1	CLONAL	1	TRUE	1	0.270700818184574	2		459	492	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284946	15284946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	228	844	1	ENST00000263388.2:c.4669C>T	p.Pro1557Ser	p.P1557S	ENST00000263388	NM_000435.2	1557	Cct/Tct	25/33	0.270700818184574	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.270700818184574	3		845	766	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509774	106509774	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	153	626	0	ENST00000359195.3:c.1768C>T	p.Pro590Ser	p.P590S	ENST00000359195	NM_002649.2	590	Cct/Tct	2/11	0.270700818184574	3	FACETS	0.895	0.82	0.973	0.895	0.82	0.973	CLONAL	2	TRUE	1	0.270700818184574	3		626	717	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93968002	93968002	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs766856886	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	87	431	0	ENST00000369303.4:c.1925G>A	p.Gly642Glu	p.G642E	ENST00000369303	NM_004440.3	642	gGa/gAa	11/17	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.270700818184574	2		431	519	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608604	189608604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	140	717	0	ENST00000264731.3:c.1679C>T	p.Ser560Leu	p.S560L	ENST00000264731	NM_003722.4	560	tCa/tTa	13/14	0.270700818184574	3	FACETS	1	0.979	1	0.628	0.571	0.688	CLONAL	1	TRUE	1	0.270700818184574	3		717	935	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139895	55139895	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	56	295	0	ENST00000257290.5:c.1556C>T	p.Pro519Leu	p.P519L	ENST00000257290	NM_006206.4	519	cCc/cTc	10/23	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.270700818184574	2		295	323	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135098	11135098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	118	860	0	ENST00000358026.2:c.3065C>T	p.Ser1022Phe	p.S1022F	ENST00000358026	NM_001128849.1	1022	tCc/tTc	21/36	0.270700818184574	3	FACETS	1	0.979	1	0.657	0.593	0.725	CLONAL	1	TRUE	1	0.270700818184574	3		860	753	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612211	189612211	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	165	530	1	ENST00000264731.3:c.1963C>T	p.Arg655Ter	p.R655*	ENST00000264731	NM_003722.4	655	Cga/Tga	14/14	0.270700818184574	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.270700818184574	3		531	604	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685305	89685305	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	60	381	0	ENST00000371953.3:c.200T>A	p.Ile67Lys	p.I67K	ENST00000371953	NM_000314.4	67	aTa/aAa	3/9	1	2	FACETS	0.953	0.823	1	0.953	0.823	1	CLONAL	1	TRUE	1	0.270700818184574	2		381	465	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237728	16237728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	116	607	1	ENST00000375759.3:c.1175C>T	p.Ala392Val	p.A392V	ENST00000375759	NM_015001.2	392	gCc/gTc	5/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.270700818184574	2		608	674	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163784	72163784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	66	641	0	ENST00000357731.5:c.574G>A	p.Gly192Arg	p.G192R	ENST00000357731	NM_173808.2	192	Gga/Aga	4/7	1	2	FACETS	0.835	0.725	0.954	0.835	0.725	0.954	CLONAL	1	TRUE	1	0.270700818184574	2		641	584	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615008	43615008	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1372786615	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	71	616	0	ENST00000355710.3:c.2422A>G	p.Lys808Glu	p.K808E	ENST00000355710	NM_020975.4	808	Aaa/Gaa	14/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.270700818184574	2		616	419	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925340	114925340	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	84	616	0	ENST00000543371.1:c.1418T>C	p.Ile473Thr	p.I473T	ENST00000543371	NM_001198531.1	473	aTa/aCa	14/14	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.270700818184574	2		616	585	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998444	100998444	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	53	345	0	ENST00000325455.5:c.1358C>A	p.Ser453Tyr	p.S453Y	ENST00000325455	NM_001202474.3	453	tCc/tAc	1/8	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.270700818184574	2		345	295	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998544	100998544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	65	577	0	ENST00000325455.5:c.1258G>A	p.Gly420Arg	p.G420R	ENST00000325455	NM_001202474.3	420	Ggg/Agg	1/8	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.270700818184574	2		577	367	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376188	118376188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	95	552	0	ENST00000534358.1:c.9581C>T	p.Pro3194Leu	p.P3194L	ENST00000534358	NM_005933.3	3194	cCt/cTt	27/36	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.270700818184574	2		552	535	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420092	420092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760930800	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	144	607	1	ENST00000399788.2:c.3175C>T	p.Arg1059Trp	p.R1059W	ENST00000399788	NM_001042603.1	1059	Cgg/Tgg	21/28	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.270700818184574	2		608	771	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446008	49446009	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	158	1097	1	ENST00000301067.7:c.1457_1458delinsTT	p.Ser486Phe	p.S486F	ENST00000301067	NM_003482.3	486	tCC/tTT	10/54	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.270700818184574	2		1098	1015	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437430	121437430	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1168108747	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	75	482	0	ENST00000257555.6:c.1768G>A	p.Val590Met	p.V590M	ENST00000257555		590	Gtg/Atg	9/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.270700818184574	2		482	443	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919626	28919626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	316	666	2	ENST00000282397.4:c.2311C>T	p.Leu771Phe	p.L771F	ENST00000282397	NM_002019.4	771	Ctc/Ttc	16/30	0.270700818184574	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	0	0.270700818184574	3		668	849	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562313	95562313	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	100	485	0	ENST00000393063.1:c.4944T>A	p.Cys1648Ter	p.C1648*	ENST00000393063	NM_030621.3	1648	tgT/tgA	24/28	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.270700818184574	2		485	556	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020438	14020438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	94	452	0	ENST00000311895.7:c.409C>T	p.His137Tyr	p.H137Y	ENST00000311895	NM_005236.2	137	Cac/Tac	3/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.270700818184574	2		452	600	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511694	66511695	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	AATA	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	112	423	0	ENST00000358598.2:c.155_158dup	p.Tyr53Ter	p.Y53*	ENST00000358598	NM_212471.2	52	gaa/gAATAaa	2/11	0.270700818184574	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.270700818184574	1		423	481	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101103	4101104	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	119	453	1	ENST00000262948.5:c.618_619delinsAA	p.Glu207Lys	p.E207K	ENST00000262948	NM_030662.3	206	ggGGag/ggAAag	6/11	0.270700818184574	3	FACETS	0.909	0.829	0.991	1	0.983	1	CLONAL	3	TRUE	1	0.270700818184574	3		454	366	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231498	5231498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	123	668	0	ENST00000357368.4:c.1978C>T	p.Pro660Ser	p.P660S	ENST00000357368	NM_002850.3	660	Ccg/Tcg	14/38	0.270700818184574	3	FACETS	1	0.983	1	0.702	0.635	0.772	CLONAL	1	TRUE	1	0.270700818184574	3		668	735	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288748	15288748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	10	59	0	ENST00000263388.2:c.3991C>T	p.Pro1331Ser	p.P1331S	ENST00000263388	NM_000435.2	1331	Ccg/Tcg	24/33	0.270700818184574	3	FACETS	0.902	0.617	1	0.451	0.308	0.626	CLONAL	1	TRUE	1	0.270700818184574	3		59	93	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366147	15366147	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	132	716	0	ENST00000263377.2:c.2008T>C	p.Tyr670His	p.Y670H	ENST00000263377	NM_058243.2	670	Tat/Cat	10/20	0.270700818184574	3	FACETS	1	0.984	1	0.698	0.634	0.766	CLONAL	1	TRUE	1	0.270700818184574	3		716	793	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366227	15366227	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868727577	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	236	875	2	ENST00000263377.2:c.1928C>T	p.Ser643Phe	p.S643F	ENST00000263377	NM_058243.2	643	tCc/tTc	10/20	0.270700818184574	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.270700818184574	3		877	931	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213599	36213599	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754201347	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	126	902	4	ENST00000222270.7:c.2701C>T	p.Arg901Trp	p.R901W	ENST00000222270	NM_014727.1	901	Cgg/Tgg	5/37	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.270700818184574	2		906	815	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100933	41100933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	98	596	0	ENST00000373198.4:c.1423G>A	p.Glu475Lys	p.E475K	ENST00000373198	NM_133170.3	475	Gag/Aag	8/32	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.270700818184574	2		596	600	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422928	12422928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765206131	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	146	769	1	ENST00000287820.6:c.418C>T	p.Arg140Cys	p.R140C	ENST00000287820	NM_015869.4	140	Cgt/Tgt	3/7	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.270700818184574	2		770	803	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165786	47165786	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	116	677	1	ENST00000409792.3:c.340C>T	p.Pro114Ser	p.P114S	ENST00000409792	NM_014159.6	114	Cct/Tct	3/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.270700818184574	2		678	747	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643668	52643668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	125	665	0	ENST00000394830.3:c.2228C>T	p.Ser743Phe	p.S743F	ENST00000394830	NM_018313.4	743	tCt/tTt	17/30	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.270700818184574	2		665	671	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916849	178916850	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	103	743	3	ENST00000263967.3:c.236_237delinsAA	p.Arg79Lys	p.R79K	ENST00000263967	NM_006218.2	79	aGG/aAA	2/21	1	2	FACETS	0.814	0.727	0.906	0.814	0.727	0.906	CLONAL	1	TRUE	1	0.270700818184574	2		746	935	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184640	185184640	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	59	328	0	ENST00000265026.3:c.1532A>G	p.Tyr511Cys	p.Y511C	ENST00000265026	NM_004721.4	511	tAt/tGt	10/14	0.270700818184574	3	FACETS	1	0.898	1	0.525	0.453	0.604	CLONAL	1	TRUE	1	0.270700818184574	3		328	471	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143181667	143181667	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	102	497	0	ENST00000262992.4:c.666T>A	p.Asp222Glu	p.D222E	ENST00000262992	NM_001101669.1	222	gaT/gaA	9/24	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.270700818184574	2		497	578	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947428	38947428	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	86	368	0	ENST00000357387.3:c.4252T>A	p.Tyr1418Asn	p.Y1418N	ENST00000357387	NM_152756.3	1418	Tat/Aat	32/38	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.270700818184574	2		368	466	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952447	38952447	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	79	415	0	ENST00000357387.3:c.2978T>G	p.Val993Gly	p.V993G	ENST00000357387	NM_152756.3	993	gTg/gGg	30/38	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.270700818184574	2		415	523	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564516	86564516	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	79	611	0	ENST00000274376.6:c.248G>T	p.Gly83Val	p.G83V	ENST00000274376	NM_002890.2	83	gGa/gTa	1/25	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.270700818184574	2		611	457	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497200	149497200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	105	624	0	ENST00000261799.4:c.3118G>A	p.Gly1040Ser	p.G1040S	ENST00000261799	NM_002609.3	1040	Ggt/Agt	22/23	1	2	FACETS	0.777	0.699	0.859	1	0.984	1	SUBCLONAL	2	TRUE	1	0.270700818184574	2		624	499	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057743	180057743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	87	701	0	ENST00000261937.6:c.212G>A	p.Gly71Glu	p.G71E	ENST00000261937	NM_182925.4	71	gGa/gAa	3/30	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.270700818184574	2		701	549	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140885	37140885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	127	612	0	ENST00000373509.5:c.721C>T	p.Pro241Ser	p.P241S	ENST00000373509	NM_002648.3	241	Cct/Tct	5/6	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.270700818184574	2		612	710	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93973593	93973593	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	51	443	0	ENST00000369303.4:c.1783G>A	p.Glu595Lys	p.E595K	ENST00000369303	NM_004440.3	595	Gag/Aag	9/17	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.270700818184574	2		443	347	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068007	94068008	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	39	320	1	ENST00000369303.4:c.954_955delinsAA	p.Ala319Thr	p.A319T	ENST00000369303	NM_004440.3	318	agGGct/agAAct	4/17	1	2	FACETS	0.792	0.657	0.94	0.792	0.657	0.94	CLONAL	1	TRUE	1	0.270700818184574	2		321	364	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658349	117658349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	128	1011	0	ENST00000368508.3:c.5234G>A	p.Ser1745Asn	p.S1745N	ENST00000368508	NM_002944.2	1745	aGc/aAc	31/43	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.270700818184574	2		1011	830	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715366	117715366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	66	424	1	ENST00000368508.3:c.1123G>A	p.Asp375Asn	p.D375N	ENST00000368508	NM_002944.2	375	Gat/Aat	10/43	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.270700818184574	2		425	388	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099340	157099340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1250963206	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	39	282	0	ENST00000346085.5:c.277C>T	p.His93Tyr	p.H93Y	ENST00000346085	NM_020732.3	93	Cac/Tac	1/20	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.270700818184574	2		282	238	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949069	151949069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776295921	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	102	630	1	ENST00000262189.6:c.1576C>T	p.Arg526Cys	p.R526C	ENST00000262189	NM_170606.2	526	Cgt/Tgt	11/59	0.270700818184574	3	FACETS	0.996	0.89	1	0.498	0.445	0.555	CLONAL	1	TRUE	1	0.270700818184574	3		631	859	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863311	56863311	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	92	567	0	ENST00000519728.1:c.455C>T	p.Ala152Val	p.A152V	ENST00000519728	NM_002350.3	152	gCt/gTt	6/13	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.270700818184574	2		567	657	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934289	68934289	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	78	596	0	ENST00000288368.4:c.355T>C	p.Tyr119His	p.Y119H	ENST00000288368	NM_024870.2	119	Tat/Cat	4/40	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.270700818184574	2		596	567	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626640	100626640	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	106	575	0	ENST00000308731.7:c.290G>T	p.Arg97Met	p.R97M	ENST00000308731	NM_000061.2	97	aGg/aTg	4/19	0.270700818184574	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.270700818184574	1		575	505	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970900	21970900	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	107	791	1	ENST00000304494.5:c.457+1G>A		p.X153_splice	ENST00000304494	NM_000077.4	153			0.270700818184574	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.270700818184574	1		792	647	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964427	55964429	+	missense_variant	Missense_Mutation	TNP	CCC	CCC	TCT	novel	NA	P-0035974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	69	472	2	ENST00000263923.4:c.2384_2386delinsAGA	p.Gly795_Glu796delinsGluLys	p.G795_E796delinsEK	ENST00000263923	NM_002253.2	795	gGGGaa/gAGAaa	17/30	1	2	FACETS	0.924	0.805	1	0.924	0.805	1	CLONAL	1	TRUE	1	0.270700818184574	2		474	552	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0036089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	43	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.345546669950516	4	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	FALSE	2	0.345546669950516	4		288	145	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0036089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	69	248	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.972	0.85	1	0.972	0.85	1	CLONAL	1	FALSE	1	0.345546669950516	2		249	411	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020291	123020291	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	32	371	3	ENST00000355640.3:c.779C>T	p.Pro260Leu	p.P260L	ENST00000355640		260	cCa/cTa	2/7	0.345546669950516	2	FACETS	1	0.867	1			1	CLONAL	2	FALSE	NA	0.345546669950516	2		374	89	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316164	11316164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1247403646	NA	P-0036089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	43	635	1	ENST00000361445.4:c.590C>T	p.Ala197Val	p.A197V	ENST00000361445	NM_004958.3	197	gCc/gTc	5/58	1	2	FACETS	0.563	0.471	0.664	0.563	0.471	0.664	SUBCLONAL	1	FALSE	1	0.345546669950516	2		636	442	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932883	36932883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	134	876	6	ENST00000361632.4:c.1988C>T	p.Pro663Leu	p.P663L	ENST00000361632		663	cCa/cTa	15/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.345546669950516	2		882	577	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989478	85989478	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	49	605	0	ENST00000263360.6:c.1237A>T	p.Ile413Phe	p.I413F	ENST00000263360	NM_003797.3	413	Att/Ttt	12/12	0.345546669950516	3	FACETS	0.909	0.782	1	0.909	0.782	1	CLONAL	2	FALSE	1	0.345546669950516	3		605	183	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884837	111884837	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	29	434	0	ENST00000341259.2:c.926G>A	p.Gly309Glu	p.G309E	ENST00000341259	NM_005475.2	309	gGg/gAg	4/8	0.286788251101717	3	FACETS	0.871	0.703	1	0.436	0.351	0.53	CLONAL	1	FALSE	1	0.345546669950516	3		434	226	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295717	15295717	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	56	735	0	ENST00000263388.2:c.2410G>A	p.Gly804Ser	p.G804S	ENST00000263388	NM_000435.2	804	Ggc/Agc	15/33	0.345546669950516	3	FACETS	0.715	0.612	0.826	0.357	0.306	0.413	SUBCLONAL	1	FALSE	1	0.345546669950516	3		735	532	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955170	93955170	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs947671764	NA	P-0036089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	18	499	0	ENST00000369303.4:c.2728C>T	p.Pro910Ser	p.P910S	ENST00000369303	NM_004440.3	910	Cca/Tca	16/17	0.163635856697811	2	FACETS	0.854	0.65	1	0.427	0.325	0.544	INDETERMINATE	1	FALSE	0	0.345546669950516	2		499	122	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543560	148543560	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0036089-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	48	474	0	ENST00000320356.2:c.246+2T>C		p.X82_splice	ENST00000320356	NM_004456.4	82			0.345546669950516	4	FACETS	1	0.95	1	0.647	0.55	0.752	CLONAL	1	FALSE	2	0.345546669950516	4		474	289	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	9	695	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	1	2	FACETS	1	0.739	1	1	0.739	1	CLONAL	1	TRUE	1	0.19	2		695	84	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	37	151	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.805	0.663	0.963	0.805	0.663	0.963	CLONAL	1	TRUE	1	0.19	2		151	484	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599275	28599275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	87	758	1	ENST00000253063.3:c.721C>T	p.Pro241Ser	p.P241S	ENST00000253063	NM_031459.4	241	Cca/Tca	5/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.19	2		759	777	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804298	43804298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760631916	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	39	549	0	ENST00000372470.3:c.298G>A	p.Glu100Lys	p.E100K	ENST00000372470	NM_005373.2	100	Gaa/Aaa	3/12	1	2	FACETS	0.604	0.499	0.721	0.604	0.499	0.721	SUBCLONAL	1	TRUE	1	0.19	2		549	680	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550733	150550733	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	23	371	0	ENST00000369026.2:c.923A>G	p.Lys308Arg	p.K308R	ENST00000369026	NM_021960.4	308	aAa/aGa	2/3	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.19	2		371	204	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850894	63850894	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	34	398	0	ENST00000279873.7:c.1672G>A	p.Gly558Arg	p.G558R	ENST00000279873	NM_032199.2	558	Ggg/Agg	10/10	1	2	FACETS	0.858	0.701	1	0.858	0.701	1	CLONAL	1	TRUE	1	0.19	2		398	417	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426846	70426847	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	39	400	0	ENST00000373644.4:c.4506_4507delinsTT	p.Arg1503Trp	p.R1503W	ENST00000373644	NM_030625.2	1502	gtCCgg/gtTTgg	7/12	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.19	2		400	400	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195467	102195467	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	11	359	0	ENST00000263464.3:c.227G>C	p.Trp76Ser	p.W76S	ENST00000263464	NM_001165.4	76	tGg/tCg	2/9	1	2	FACETS	0.845	0.587	1	0.845	0.587	1	CLONAL	1	TRUE	1	0.19	2		359	137	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434337	49434337	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	55	761	0	ENST00000301067.7:c.7216G>T	p.Asp2406Tyr	p.D2406Y	ENST00000301067	NM_003482.3	2406	Gac/Tac	31/54	1	2	FACETS	0.669	0.57	0.777	0.669	0.57	0.777	SUBCLONAL	1	TRUE	1	0.19	2		761	866	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437990	49437991	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	53	551	0	ENST00000301067.7:c.5180_5181delinsTT	p.Pro1727Leu	p.P1727L	ENST00000301067	NM_003482.3	1727	cCC/cTT	21/54	1	2	FACETS	0.772	0.657	0.898	0.772	0.657	0.898	SUBCLONAL	1	TRUE	1	0.19	2		551	723	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444704	49444705	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	58	734	1	ENST00000301067.7:c.2761_2762delinsAT	p.Gly921Met	p.G921M	ENST00000301067	NM_003482.3	921	GGg/ATg	10/54	1	2	FACETS	0.752	0.644	0.87	0.752	0.644	0.87	SUBCLONAL	1	TRUE	1	0.19	2		735	812	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865062	57865062	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	74	804	2	ENST00000228682.2:c.2539C>T	p.Leu847Phe	p.L847F	ENST00000228682	NM_005269.2	847	Ctc/Ttc	12/12	1	2	FACETS	0.965	0.844	1	0.965	0.844	1	CLONAL	1	TRUE	1	0.19	2		806	807	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257231	133257231	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1284171482	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	18	524	0	ENST00000320574.5:c.247G>A	p.Asp83Asn	p.D83N	ENST00000320574	NM_006231.2	83	Gat/Aat	3/49	1	2	FACETS	0.789	0.595	1	0.789	0.595	1	CLONAL	1	TRUE	1	0.19	2		524	240	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614451	38614451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	14	464	0	ENST00000299084.4:c.217G>A	p.Glu73Lys	p.E73K	ENST00000299084	NM_152594.2	73	Gaa/Aaa	3/7	0.137960724875688	1	FACETS	0.866	0.638	1	1	0.905	1	CLONAL	2	TRUE	0	0.19	1		464	77	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43767822	43767823	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	46	494	0	ENST00000382044.4:c.1025_1026delinsTT	p.Thr342Ile	p.T342I	ENST00000382044	NM_001141980.1	342	aCC/aTT	9/28	0.137960724875688	1	FACETS	0.942	0.794	1	0.942	0.794	1	CLONAL	1	TRUE	0	0.19	1		494	465	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782314	56782314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	47	471	0	ENST00000308159.5:c.155C>T	p.Ser52Phe	p.S52F	ENST00000308159	NM_014669.4	52	tCc/tTc	2/22	0.137960724875688	3	FACETS	0.868	0.732	1	0.434	0.366	0.51	CLONAL	1	TRUE	1	0.19	3		471	624	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350377	89350377	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	49	808	0	ENST00000301030.4:c.2573G>A	p.Trp858Ter	p.W858*	ENST00000301030	NM_001256183.1	858	tGg/tAg	9/13	0.137960724875688	3	FACETS	0.969	0.82	1	0.484	0.41	0.567	CLONAL	1	TRUE	1	0.19	3		808	583	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654857	29654857	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786202112	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	19	237	0	ENST00000356175.3:c.5546G>A	p.Arg1849Gln	p.R1849Q	ENST00000356175	NM_000267.3	1849	cGg/cAg	37/57	0.137960724875688	1	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	0	0.19	1		237	151	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884011	37884011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150680317	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	80	699	1	ENST00000269571.5:c.3482G>A	p.Arg1161Gln	p.R1161Q	ENST00000269571		1161	cGa/cAa	27/27	0.137960724875688	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.19	1		700	725	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867539	78867539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs910802262	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	77	515	0	ENST00000306801.3:c.2275C>T	p.Leu759Phe	p.L759F	ENST00000306801	NM_020761.2	759	Ctc/Ttc	20/34	0.137960724875688	1	FACETS	0.856	0.75	0.97	0.856	0.75	0.97	CLONAL	1	TRUE	0	0.19	1		515	857	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923306	78923306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	63	523	0	ENST00000306801.3:c.3329C>T	p.Thr1110Ile	p.T1110I	ENST00000306801	NM_020761.2	1110	aCc/aTc	28/34	0.137960724875688	1	FACETS	0.875	0.756	1	0.875	0.756	1	CLONAL	1	TRUE	0	0.19	1		523	686	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117183	7117183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	68	642	1	ENST00000302850.5:c.4033G>A	p.Gly1345Arg	p.G1345R	ENST00000302850	NM_000208.2	1345	Gga/Aga	22/22	0.201298665244494	4	FACETS	1	0.945	1	0.584	0.508	0.667	CLONAL	1	TRUE	2	0.19	4		643	729	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142994	7142994	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769165470	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	59	640	0	ENST00000302850.5:c.2375C>T	p.Pro792Leu	p.P792L	ENST00000302850	NM_000208.2	792	cCg/cTg	12/22	0.201298665244494	4	FACETS	0.985	0.846	1	0.493	0.423	0.569	CLONAL	1	TRUE	2	0.19	4		640	750	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955096	17955096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201650430	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	69	700	0	ENST00000458235.1:c.131C>T	p.Ser44Phe	p.S44F	ENST00000458235	NM_000215.3	44	tCc/tTc	2/24	0.201298665244494	4	FACETS	1	0.871	1	0.501	0.436	0.573	CLONAL	1	TRUE	2	0.19	4		700	862	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40743959	40743959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	65	466	0	ENST00000392038.2:c.748G>A	p.Glu250Lys	p.E250K	ENST00000392038	NM_001626.4	250	Gag/Aag	9/14	0.201298665244494	4	FACETS	1	0.913	1	0.536	0.464	0.615	CLONAL	1	TRUE	2	0.19	4		466	759	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140363	50140363	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1187025466	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	51	426	0	ENST00000246792.3:c.178C>T	p.Pro60Ser	p.P60S	ENST00000246792	NM_006270.3	60	Ccc/Tcc	2/6	0.201298665244494	4	FACETS	1	0.907	1	0.548	0.465	0.639	CLONAL	1	TRUE	2	0.19	4		426	583	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416745	29416745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1212504281	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	35	344	0	ENST00000389048.3:c.4208C>T	p.Pro1403Leu	p.P1403L	ENST00000389048	NM_004304.4	1403	cCa/cTa	29/29	0.137960724875688	0	FACETS	0.988	0.813	1			1	CLONAL	1	TRUE	0	0.19	0		344	302	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736158	204736158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs963824682	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	24	459	1	ENST00000302823.3:c.515C>T	p.Ser172Leu	p.S172L	ENST00000302823	NM_005214.4	172	tCg/tTg	3/4	0.137960724875688	1	FACETS	0.642	0.503	0.803	0.642	0.503	0.803	SUBCLONAL	1	TRUE	0	0.19	1		460	356	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376178	225376178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	22	695	0	ENST00000264414.4:c.776C>T	p.Pro259Leu	p.P259L	ENST00000264414	NM_003590.4	259	cCa/cTa	6/16	0.137960724875688	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	0	0.19	1		695	153	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727090	40727090	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	50	496	0	ENST00000373198.4:c.3874G>A	p.Val1292Met	p.V1292M	ENST00000373198	NM_133170.3	1292	Gtg/Atg	28/32	1	2	FACETS	0.791	0.67	0.925	0.791	0.67	0.925	CLONAL	1	TRUE	1	0.19	2		496	665	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770557	40770557	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	33	261	0	ENST00000373198.4:c.2825C>T	p.Ser942Phe	p.S942F	ENST00000373198	NM_133170.3	942	tCc/tTc	19/32	1	2	FACETS	1	0.821	1	1	0.821	1	CLONAL	1	TRUE	1	0.19	2		261	345	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877330	40877330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750253646	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	28	381	0	ENST00000373198.4:c.2366G>A	p.Arg789Lys	p.R789K	ENST00000373198	NM_133170.3	789	aGg/aAg	15/32	1	2	FACETS	0.801	0.64	0.984	0.801	0.64	0.984	CLONAL	1	TRUE	1	0.19	2		381	368	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181441	38181441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	62	397	0	ENST00000396334.3:c.454C>T	p.Pro152Ser	p.P152S	ENST00000396334	NM_002468.4	152	Cca/Tca	2/5	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.19	2		397	580	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584608	52584608	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	46	552	0	ENST00000394830.3:c.4405C>A	p.Pro1469Thr	p.P1469T	ENST00000394830	NM_018313.4	1469	Ccc/Acc	29/30	1	2	FACETS	0.668	0.561	0.786	0.668	0.561	0.786	SUBCLONAL	1	TRUE	1	0.19	2		552	725	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176561	142176561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	18	414	0	ENST00000350721.4:c.7540C>T	p.Arg2514Cys	p.R2514C	ENST00000350721	NM_001184.3	2514	Cgc/Tgc	45/47	1	2	FACETS	1	0.828	1	1	0.828	1	CLONAL	1	TRUE	1	0.19	2		414	169	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671754	30671754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	43	636	0	ENST00000376406.3:c.5206C>T	p.Pro1736Ser	p.P1736S	ENST00000376406	NM_014641.2	1736	Ccc/Tcc	10/15	0.137960724875688	3	FACETS	0.722	0.603	0.855	0.361	0.301	0.428	SUBCLONAL	1	TRUE	1	0.19	3		636	686	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663685	117663685	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	11	387	0	ENST00000368508.3:c.4547T>C	p.Leu1516Pro	p.L1516P	ENST00000368508	NM_002944.2	1516	cTt/cCt	28/43	0.137960724875688	3	FACETS	1	0.732	1	1	0.732	1	CLONAL	2	TRUE	1	0.19	3		387	61	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411592	116411592	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	12	472	0	ENST00000397752.3:c.2771T>C	p.Ile924Thr	p.I924T	ENST00000397752	NM_000245.2	924	aTa/aCa	13/21	1	2	FACETS	0.82	0.586	1	1	0.883	1	CLONAL	2	TRUE	1	0.19	2		472	77	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508776	148508776	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	16	408	0	ENST00000320356.2:c.1888G>A	p.Gly630Arg	p.G630R	ENST00000320356	NM_004456.4	630	Ggg/Agg	16/20	1	2	FACETS	0.985	0.732	1	0.985	0.732	1	CLONAL	1	TRUE	1	0.19	2		408	171	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38173538	38173539	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	12	479	1	ENST00000317025.8:c.1877_1878delinsTT	p.Ser626Phe	p.S626F	ENST00000317025	NM_023034.1	626	tCC/tTT	10/24	1	2	FACETS	0.686	0.483	0.936	0.686	0.483	0.936	SUBCLONAL	1	TRUE	1	0.19	2		480	184	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030808	69030808	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	41	340	0	ENST00000288368.4:c.3350C>T	p.Ser1117Phe	p.S1117F	ENST00000288368	NM_024870.2	1117	tCc/tTc	27/40	1	2	FACETS	0.894	0.744	1	0.894	0.744	1	CLONAL	1	TRUE	1	0.19	2		340	483	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033228	69033228	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	14	448	0	ENST00000288368.4:c.3668G>A	p.Trp1223Ter	p.W1223*	ENST00000288368	NM_024870.2	1223	tGg/tAg	30/40	1	2	FACETS	0.565	0.408	0.755	0.565	0.408	0.755	SUBCLONAL	1	TRUE	1	0.19	2		448	261	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471053	8471053	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	24	376	0	ENST00000356435.5:c.3446A>T	p.Lys1149Ile	p.K1149I	ENST00000356435		1149	aAa/aTa	20/35	0.137960724875688	1	FACETS	1	0.89	1	1	0.956	1	CLONAL	2	TRUE	0	0.19	1		376	97	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157900	27157900	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	74	587	0	ENST00000380036.4:c.124C>T	p.Leu42Phe	p.L42F	ENST00000380036	NM_000459.3	42	Ctc/Ttc	2/23	0.137960724875688	1	FACETS	0.753	0.661	0.851	1	0.975	1	SUBCLONAL	2	TRUE	0	0.19	1		587	468	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185489	27185489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1254840237	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	31	447	1	ENST00000380036.4:c.1189G>A	p.Asp397Asn	p.D397N	ENST00000380036	NM_000459.3	397	Gac/Aac	9/23	0.137960724875688	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.19	1		448	218	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779088	135779089	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	44	399	0	ENST00000298552.3:c.2157_2158delinsTT	p.Leu720Phe	p.L720F	ENST00000298552	NM_001162426.1	719	ctCCtc/ctTTtc	17/23	0.137960724875688	1	FACETS	0.702	0.588	0.829	0.702	0.588	0.829	SUBCLONAL	1	TRUE	0	0.19	1		399	597	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044763	47044764	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	53	370	1	ENST00000377604.3:c.2163_2164delinsTT	p.Pro722Ser	p.P722S	ENST00000377604	NM_001204468.1	721	cgCCca/cgTTca	19/24	0.3	2	FACETS	0.76	0.651	0.879	0.76	0.651	0.879	SUBCLONAL	2	TRUE	0	0.19	2		371	367	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860031	152860031	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	44	242	0	ENST00000406277.2:c.397C>T	p.Gln133Ter	p.Q133*	ENST00000406277	NM_152274.4	133	Cag/Tag	5/7	0.3		FACETS		0.813	1				CLONAL	2	TRUE	0	0.19	2		242	241	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0036159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	141	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.631183918274997	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.631183918274997	1		288	281	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0036159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	126	248	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.631183918274997	2		249	384	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0036159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	23	456	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.143	0.111	0.181	0.143	0.111	0.181	SUBCLONAL	1	TRUE	1	0.631183918274997	2		456	508	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520257	9520257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	167	425	0	ENST00000353224.5:c.2012C>T	p.Ser671Leu	p.S671L	ENST00000353224	NM_177990.2	671	tCa/tTa	10/10	0.631183918274997	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.631183918274997	1		425	354	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28601376	28601376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	252	618	0	ENST00000253063.3:c.1061G>A	p.Arg354Gln	p.R354Q	ENST00000253063	NM_031459.4	354	cGg/cAg	8/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.631183918274997	2		618	775	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405914	49405914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	251	604	0	ENST00000418115.1:c.224C>T	p.Pro75Leu	p.P75L	ENST00000418115	NM_001664.2	75	cCa/cTa	3/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.631183918274997	2		604	728	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144595	55144595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	155	498	0	ENST00000257290.5:c.2069G>A	p.Arg690Lys	p.R690K	ENST00000257290	NM_006206.4	690	aGg/aAg	15/23	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.631183918274997	2		498	483	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885897	111885897	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	284	720	0	ENST00000341259.2:c.1519C>T	p.Pro507Ser	p.P507S	ENST00000341259	NM_005475.2	507	Ccc/Tcc	8/8	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.631183918274997	2		720	889	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331730	68331730	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	59	211	0	ENST00000487270.1:c.326C>T	p.Pro109Leu	p.P109L	ENST00000487270	NM_133509.3	109	cCa/cTa	5/11	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.631183918274997	2		211	185	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533069	63533069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1389567952	NA	P-0036159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	225	646	1	ENST00000307078.5:c.1825C>T	p.Pro609Ser	p.P609S	ENST00000307078	NM_004655.3	609	Ccc/Tcc	7/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.631183918274997	2		647	698	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164481	36164481	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	150	385	0	ENST00000300305.3:c.1394A>G	p.Asn465Ser	p.N465S	ENST00000300305		465	aAc/aGc	8/8	1	2	FACETS	0.962	0.886	1	0.962	0.886	1	CLONAL	1	TRUE	1	0.631183918274997	2		385	494	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458429	12458429	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	287	764	2	ENST00000287820.6:c.1046G>A	p.Gly349Glu	p.G349E	ENST00000287820	NM_015869.4	349	gGa/gAa	6/7	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.631183918274997	2		766	862	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934273	49934273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	233	621	0	ENST00000296474.3:c.2234C>T	p.Ala745Val	p.A745V	ENST00000296474	NM_002447.2	745	gCc/gTc	8/20	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.631183918274997	2		621	734	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79966069	79966069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs558080525	NA	P-0036159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	185	586	0	ENST00000265081.6:c.733G>A	p.Asp245Asn	p.D245N	ENST00000265081	NM_002439.4	245	Gat/Aat	4/24	1	2	FACETS	0.953	0.885	1	0.953	0.885	1	CLONAL	1	TRUE	1	0.631183918274997	2		586	615	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0036240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	152	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.241422761959639	4	FACETS	1	0.98	1	0.808	0.743	0.875	CLONAL	2	TRUE	1	0.287990233112815	4		288	561	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	76	151	0				ENST00000310581	NM_198253.2	-/1132			0.287990233112815	3	FACETS	0.961	0.851	1	0.961	0.851	1	CLONAL	2	TRUE	1	0.287990233112815	3		151	314	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199514	16199514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	62	478	0	ENST00000375759.3:c.287C>T	p.Ser96Phe	p.S96F	ENST00000375759	NM_015001.2	96	tCc/tTc	2/15	1	2	FACETS	0.68	0.587	0.781	0.68	0.587	0.781	SUBCLONAL	1	TRUE	1	0.287990233112815	2		478	633	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352692	68352692	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	45	424	0	ENST00000487270.1:c.559G>A	p.Glu187Lys	p.E187K	ENST00000487270	NM_133509.3	187	Gaa/Aaa	6/11	0.287990233112815	1	FACETS	0.672	0.566	0.789	0.672	0.566	0.789	SUBCLONAL	1	TRUE	0	0.287990233112815	1		424	398	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831298	3831298	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	56	378	0	ENST00000262367.5:c.1583C>T	p.Pro528Leu	p.P528L	ENST00000262367	NM_004380.2	528	cCa/cTa	7/31	1	2	FACETS	0.9	0.773	1	0.9	0.773	1	CLONAL	1	TRUE	1	0.287990233112815	2		378	432	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347285	89347285	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs202034147	NA	P-0036240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	88	619	0	ENST00000301030.4:c.5665A>G	p.Lys1889Glu	p.K1889E	ENST00000301030	NM_001256183.1	1889	Aaa/Gaa	9/13	0.287990233112815	1	FACETS	0.812	0.72	0.911	0.812	0.72	0.911	CLONAL	1	TRUE	0	0.287990233112815	1		619	644	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40855800	40855800	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1458266017	NA	P-0036240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	75	550	0	ENST00000428826.2:c.2056C>T	p.Arg686Ter	p.R686*	ENST00000428826		686	Cga/Tga	19/21	1	2	FACETS	0.754	0.66	0.855	0.754	0.66	0.855	SUBCLONAL	1	TRUE	1	0.287990233112815	2		550	691	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732283	74732283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	55	263	0	ENST00000359995.5:c.626C>T	p.Pro209Leu	p.P209L	ENST00000359995	NM_001195427.1	209	cCc/cTc	2/3	1	2	FACETS	0.95	0.815	1	0.95	0.815	1	CLONAL	1	TRUE	1	0.287990233112815	2		263	402	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520177	9520177	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	81	452	0	ENST00000353224.5:c.2092C>T	p.Pro698Ser	p.P698S	ENST00000353224	NM_177990.2	698	Cca/Tca	10/10	1	2	FACETS	0.903	0.796	1	0.903	0.796	1	CLONAL	1	TRUE	1	0.287990233112815	2		452	623	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383227	31383227	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148132847	NA	P-0036240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	81	435	0	ENST00000328111.2:c.1139G>A	p.Arg380Gln	p.R380Q	ENST00000328111	NM_006892.3	380	cGa/cAa	11/23	1	2	FACETS	0.967	0.853	1	0.967	0.853	1	CLONAL	1	TRUE	1	0.287990233112815	2		435	582	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420106	41420106	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	37	281	0	ENST00000373198.4:c.215G>A	p.Gly72Glu	p.G72E	ENST00000373198	NM_133170.3	72	gGa/gAa	3/32	1	2	FACETS	0.883	0.731	1	0.883	0.731	1	CLONAL	1	TRUE	1	0.287990233112815	2		281	291	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55570044	55570044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	61	375	0	ENST00000288135.5:c.911C>T	p.Thr304Ile	p.T304I	ENST00000288135	NM_000222.2	304	aCc/aTc	5/21	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.287990233112815	2		375	381	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593308	67593308	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	55	373	0	ENST00000274335.5:c.2054A>G	p.Tyr685Cys	p.Y685C	ENST00000274335		685	tAt/tGt	15/15	0.287990233112815	1	FACETS	0.75	0.643	0.866	0.75	0.643	0.866	SUBCLONAL	1	TRUE	0	0.287990233112815	1		373	436	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166850	32166850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	100	634	2	ENST00000375023.3:c.4388G>A	p.Gly1463Glu	p.G1463E	ENST00000375023	NM_004557.3	1463	gGg/gAg	24/30	1	2	FACETS	0.775	0.691	0.864	0.775	0.691	0.864	SUBCLONAL	1	TRUE	1	0.287990233112815	2		636	896	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971121	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0036240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	78	297	1	ENST00000304494.5:c.237_238delinsTT	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	79	acCCga/acTTga	2/3	0.287990233112815	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.287990233112815	1		298	400	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0036241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	125	430	0	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.182909384219233	3	FACETS	1	0.971	1	0.777	0.705	0.851	CLONAL	2	TRUE	0	0.206606342335074	3		430	573	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0036241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	34	248	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.206606342335074	2		249	284	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0036241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	39	355	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.206606342335074	1	FACETS	0.666	0.552	0.794	0.666	0.552	0.794	SUBCLONAL	1	TRUE	0	0.206606342335074	1		355	508	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871202	35871202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200772681	NA	P-0036241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	41	685	0	ENST00000303115.3:c.424G>A	p.Gly142Arg	p.G142R	ENST00000303115	NM_002185.3	142	Gga/Aga	4/8	1	2	FACETS	0.658	0.547	0.782	0.658	0.547	0.782	SUBCLONAL	1	TRUE	1	0.206606342335074	2		685	603	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669525	88669525	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1361454724	NA	P-0036241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	64	384	1	ENST00000360948.2:c.1373G>A	p.Arg458Gln	p.R458Q	ENST00000360948	NM_001012338.2	458	cGa/cAa	12/19	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.206606342335074	2		385	618	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992052	72992052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	74	532	0	ENST00000268489.5:c.1993C>T	p.Arg665Cys	p.R665C	ENST00000268489	NM_006885.3	665	Cgt/Tgt	2/10	1	2	FACETS	0.908	0.794	1	0.908	0.794	1	CLONAL	1	TRUE	1	0.206606342335074	2		532	789	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964501	93964501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	55	489	0	ENST00000369303.4:c.2396C>T	p.Pro799Leu	p.P799L	ENST00000369303	NM_004440.3	799	cCa/cTa	14/17	1	2	FACETS	0.786	0.672	0.912	0.786	0.672	0.912	CLONAL	1	TRUE	1	0.206606342335074	2		489	677	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273019	115273019	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	56	566	2	ENST00000438362.2:c.1354C>T	p.His452Tyr	p.H452Y	ENST00000438362	NM_001242891.1	452	Cat/Tat	12/20	1	2	FACETS	0.683	0.583	0.792	0.683	0.583	0.792	SUBCLONAL	1	TRUE	1	0.206606342335074	2		568	794	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8252036	8252036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	42	546	0	ENST00000335790.3:c.41C>T	p.Ser14Phe	p.S14F	ENST00000335790	NM_002315.2	14	tCc/tTc	2/4	1	2	FACETS	0.521	0.434	0.619	0.521	0.434	0.619	SUBCLONAL	1	TRUE	1	0.206606342335074	2		546	780	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679747	88679747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	69	505	0	ENST00000360948.2:c.716C>T	p.Pro239Leu	p.P239L	ENST00000360948	NM_001012338.2	239	cCt/cTt	7/19	1	2	FACETS	0.881	0.766	1	0.881	0.766	1	CLONAL	1	TRUE	1	0.206606342335074	2		505	758	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149745	202149745	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	81	575	0	ENST00000358485.4:c.1186A>G	p.Thr396Ala	p.T396A	ENST00000358485	NM_001080125.1	396	Aca/Gca	8/9	1	2	FACETS	0.956	0.841	1	0.956	0.841	1	CLONAL	1	TRUE	1	0.206606342335074	2		575	820	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149767	202149767	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	83	589	0	ENST00000358485.4:c.1208A>G	p.Lys403Arg	p.K403R	ENST00000358485	NM_001080125.1	403	aAg/aGg	8/9	1	2	FACETS	0.953	0.84	1	0.953	0.84	1	CLONAL	1	TRUE	1	0.206606342335074	2		589	843	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385261	41385261	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	54	477	0	ENST00000373198.4:c.700G>A	p.Asp234Asn	p.D234N	ENST00000373198	NM_133170.3	234	Gac/Aac	6/32	1	2	FACETS	0.84	0.717	0.976	0.84	0.717	0.976	CLONAL	1	TRUE	1	0.206606342335074	2		477	622	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62325764	62325764	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766826026	NA	P-0036241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	62	493	0	ENST00000360203.5:c.3032C>T	p.Ala1011Val	p.A1011V	ENST00000360203	NM_001283009.1	1011	gCt/gTt	31/35	1	2	FACETS	0.86	0.742	0.988	0.86	0.742	0.988	CLONAL	1	TRUE	1	0.206606342335074	2		493	698	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573279	41573279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201644988	NA	P-0036241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	83	668	1	ENST00000263253.7:c.5564C>T	p.Pro1855Leu	p.P1855L	ENST00000263253	NM_001429.3	1855	cCa/cTa	31/31	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.206606342335074	2		669	772	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250921	153250922	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0036241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	22	268	0	ENST00000281708.4:c.1138dup	p.Asp380GlyfsTer2	p.D380Gfs*2	ENST00000281708	NM_033632.3	380	gat/gGat	8/12	1	2	FACETS	0.55	0.426	0.695	0.55	0.426	0.695	SUBCLONAL	1	TRUE	1	0.206606342335074	2		268	387	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176666778	176666778	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	36	284	0	ENST00000439151.2:c.4214A>T	p.Gln1405Leu	p.Q1405L	ENST00000439151	NM_022455.4	1405	cAa/cTa	8/23	1	2	FACETS	0.78	0.641	0.935	0.78	0.641	0.935	CLONAL	1	TRUE	1	0.206606342335074	2		284	447	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608315	100608315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	98	482	0	ENST00000308731.7:c.1775C>T	p.Ser592Phe	p.S592F	ENST00000308731	NM_000061.2	592	tCc/tTc	18/19	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.206606342335074	2		482	819	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608914	100608914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	77	529	0	ENST00000308731.7:c.1694C>T	p.Pro565Leu	p.P565L	ENST00000308731	NM_000061.2	565	cCa/cTa	17/19	1	2	FACETS	0.91	0.798	1	0.91	0.798	1	CLONAL	1	TRUE	1	0.206606342335074	2		529	819	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786696	3786696	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036424-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	123	777	0	ENST00000262367.5:c.4515G>C	p.Lys1505Asn	p.K1505N	ENST00000262367	NM_004380.2	1505	aaG/aaC	27/31	0.20063016684017	4	FACETS	0.823	0.746	0.903			1	INDETERMINATE	1	TRUE	NA	0.887383445147444	4		777	636	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0036712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	44	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.208154624506066	3	FACETS	1	0.96	1	0.749	0.633	0.875	CLONAL	1	TRUE	1	0.260407813792753	3		288	255	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0036712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	35	151	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.738	0.606	0.887	0.738	0.606	0.887	SUBCLONAL	1	TRUE	1	0.260407813792753	2		151	364	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259388	89259388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	55	540	0	ENST00000336596.2:c.532G>A	p.Gly178Arg	p.G178R	ENST00000336596	NM_005233.5	178	Gga/Aga	3/17	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.260407813792753	2		540	340	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423632	88423632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1478926904	NA	P-0036712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	46	406	0	ENST00000360948.2:c.2203C>T	p.Arg735Cys	p.R735C	ENST00000360948	NM_001012338.2	735	Cgc/Tgc	18/19	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.260407813792753	2		406	349	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916248	9916248	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397518472	NA	P-0036712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	35	386	0	ENST00000330684.3:c.2041C>T	p.Arg681Ter	p.R681*	ENST00000330684	NM_001134407.1	681	Cga/Tga	10/13	1	2	FACETS	0.947	0.779	1	0.947	0.779	1	CLONAL	1	TRUE	1	0.260407813792753	2		386	284	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032197	10032197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774932381	NA	P-0036712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	63	708	0	ENST00000330684.3:c.626C>T	p.Ser209Phe	p.S209F	ENST00000330684	NM_001134407.1	209	tCc/tTc	3/13	1	2	FACETS	0.793	0.686	0.91	0.793	0.686	0.91	CLONAL	1	TRUE	1	0.260407813792753	2		708	610	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164850	47164850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1184046423	NA	P-0036712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	42	327	1	ENST00000409792.3:c.1276C>T	p.His426Tyr	p.H426Y	ENST00000409792	NM_014159.6	426	Cat/Tat	3/21	1	2	FACETS	0.983	0.824	1	0.983	0.824	1	CLONAL	1	TRUE	1	0.260407813792753	2		328	328	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073970	8073970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	62	445	0	ENST00000377482.5:c.689G>A	p.Gly230Glu	p.G230E	ENST00000377482	NM_018948.3	230	gGa/gAa	4/4	1	2	FACETS	0.921	0.797	1	0.921	0.797	1	CLONAL	1	TRUE	1	0.260407813792753	2		445	517	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239733	41239733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	95	694	0	ENST00000379561.5:c.617C>T	p.Ser206Leu	p.S206L	ENST00000379561	NM_002015.3	206	tCg/tTg	1/3	1	2	FACETS	0.758	0.673	0.848	0.758	0.673	0.848	SUBCLONAL	1	TRUE	1	0.260407813792753	2		694	963	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422107	81422107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	68	511	0	ENST00000298171.2:c.83C>T	p.Pro28Leu	p.P28L	ENST00000298171	NM_000369.2	28	cCc/cTc	1/10	1	2	FACETS	0.834	0.726	0.952	0.834	0.726	0.952	CLONAL	1	TRUE	1	0.260407813792753	2		511	626	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289074	33289074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	87	650	0	ENST00000374542.5:c.478C>T	p.Pro160Ser	p.P160S	ENST00000374542	NM_001141970.1	160	Cct/Tct	3/8	1	2	FACETS	0.727	0.642	0.818	0.727	0.642	0.818	SUBCLONAL	1	TRUE	1	0.260407813792753	2		650	919	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679003	117679003	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	19	417	0	ENST00000368508.3:c.3818C>T	p.Ser1273Leu	p.S1273L	ENST00000368508	NM_002944.2	1273	tCa/tTa	24/43	1	2	FACETS	0.682	0.519	0.872	0.682	0.519	0.872	SUBCLONAL	1	TRUE	1	0.260407813792753	2		417	214	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022097	5022097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748500115	NA	P-0036712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	46	555	1	ENST00000381652.3:c.110C>T	p.Pro37Leu	p.P37L	ENST00000381652	NM_004972.3	37	cCa/cTa	3/25	0.260407813792753	1	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	TRUE	0	0.260407813792753	1		556	307	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295230	1295230	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs796516131	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	70	341	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.965	0.848	1	0.965	0.848	1	CLONAL	1	TRUE	1	0.451874142366961	2		341	321	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005419	29005419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55687105	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	87	398	0	ENST00000282397.4:c.842G>A	p.Arg281Gln	p.R281Q	ENST00000282397	NM_002019.4	281	cGa/cAa	7/30	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.451874142366961	2		398	377	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456447	189456447	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	157	336	0	ENST00000264731.3:c.208C>T	p.Gln70Ter	p.Q70*	ENST00000264731	NM_003722.4	70	Cag/Tag	3/14	0.424155926150417	2	FACETS	0.976	0.907	1	0.976	0.907	1	CLONAL	2	TRUE	0	0.451874142366961	2		336	356	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	63	248	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.84	0.731	0.956	0.84	0.731	0.956	CLONAL	1	TRUE	1	0.451874142366961	2		249	332	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262592	16262592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	78	390	0	ENST00000375759.3:c.9857C>A	p.Pro3286His	p.P3286H	ENST00000375759	NM_015001.2	3286	cCt/cAt	11/15	1	2	FACETS	0.794	0.7	0.893	0.794	0.7	0.893	SUBCLONAL	1	TRUE	1	0.451874142366961	2		390	435	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023748	27023748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	107	391	1	ENST00000324856.7:c.854G>A	p.Gly285Glu	p.G285E	ENST00000324856	NM_006015.4	285	gGa/gAa	1/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.451874142366961	2		392	392	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101423	27101423	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	98	525	0	ENST00000324856.7:c.4705C>T	p.Pro1569Ser	p.P1569S	ENST00000324856	NM_006015.4	1569	Cca/Tca	18/20	1	2	FACETS	0.96	0.861	1	0.96	0.861	1	CLONAL	1	TRUE	1	0.451874142366961	2		525	452	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935268	36935268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	162	807	0	ENST00000361632.4:c.1459G>A	p.Gly487Arg	p.G487R	ENST00000361632		487	Ggg/Agg	10/16	1	2	FACETS	0.956	0.879	1	0.956	0.879	1	CLONAL	1	TRUE	1	0.451874142366961	2		807	750	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166271	118166271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	54	288	0	ENST00000369448.3:c.781G>A	p.Glu261Lys	p.E261K	ENST00000369448	NM_017709.3	261	Gaa/Aaa	2/2	1	2	FACETS	0.845	0.727	0.971	0.845	0.727	0.971	CLONAL	1	TRUE	1	0.451874142366961	2		288	283	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849128	156849128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	176	888	0	ENST00000524377.1:c.2020G>A	p.Asp674Asn	p.D674N	ENST00000524377	NM_002529.3	674	Gat/Aat	15/17	0.39575805963509	3	FACETS	0.873	0.803	0.946	0.436	0.401	0.473	CLONAL	1	TRUE	1	0.451874142366961	3		888	1094	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104377181	104377182	+	missense_variant	Missense_Mutation	DNP	TA	TA	CT	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	142	817	0	ENST00000369902.3:c.1292_1293delinsCT	p.Leu431Ser	p.L431S	ENST00000369902	NM_016169.3	431	tTA/tCT	10/12	1	2	FACETS	0.794	0.724	0.867	0.794	0.724	0.867	SUBCLONAL	1	TRUE	1	0.451874142366961	2		817	792	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256135	123256135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141929882	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	146	587	1	ENST00000358487.5:c.1774C>T	p.Arg592Cys	p.R592C	ENST00000358487	NM_000141.4	592	Cgt/Tgt	13/18	0.39575805963509	3	FACETS	1	0.937	1	0.516	0.471	0.562	CLONAL	1	TRUE	1	0.451874142366961	3		588	768	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324081	123324081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	95	500	0	ENST00000358487.5:c.389C>T	p.Ser130Phe	p.S130F	ENST00000358487	NM_000141.4	130	tCc/tTc	4/18	0.39575805963509	3	FACETS	0.845	0.754	0.942	0.423	0.377	0.471	CLONAL	1	TRUE	1	0.451874142366961	3		500	610	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141997	108141997	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780619	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	95	437	0	ENST00000278616.4:c.2941C>T	p.Arg981Cys	p.R981C	ENST00000278616	NM_000051.3	981	Cgt/Tgt	20/63	0.451874142366961	1	FACETS	0.941	0.846	1	0.941	0.846	1	CLONAL	1	TRUE	0	0.451874142366961	1		437	346	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103398	119103398	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	56	290	0	ENST00000264033.4:c.436C>T	p.Gln146Ter	p.Q146*	ENST00000264033	NM_005188.3	146	Cag/Tag	2/16	0.451874142366961	1	FACETS	0.918	0.798	1	0.918	0.798	1	CLONAL	1	TRUE	0	0.451874142366961	1		290	209	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417041	417041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	97	414	0	ENST00000399788.2:c.3509C>T	p.Ala1170Val	p.A1170V	ENST00000399788	NM_001042603.1	1170	gCc/gTc	23/28	1	2	FACETS	0.906	0.811	1	0.906	0.811	1	CLONAL	1	TRUE	1	0.451874142366961	2		414	474	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431735	49431735	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	106	661	1	ENST00000301067.7:c.9404C>T	p.Thr3135Ile	p.T3135I	ENST00000301067	NM_003482.3	3135	aCc/aTc	34/54	1	2	FACETS	0.927	0.835	1	0.927	0.835	1	CLONAL	1	TRUE	1	0.451874142366961	2		662	506	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112892368	112892368	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	80	358	0	ENST00000351677.2:c.526G>A	p.Glu176Lys	p.E176K	ENST00000351677	NM_002834.3	176	Gaa/Aaa	5/16	1	2	FACETS	0.833	0.737	0.935	0.833	0.737	0.935	CLONAL	1	TRUE	1	0.451874142366961	2		358	425	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112910803	112910803	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	112	395	0	ENST00000351677.2:c.812A>T	p.Gln271Leu	p.Q271L	ENST00000351677	NM_002834.3	271	cAa/cTa	7/16	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.451874142366961	2		395	489	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601256	28601256	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	100	469	0	ENST00000241453.7:c.2176T>C	p.Tyr726His	p.Y726H	ENST00000241453	NM_004119.2	726	Tac/Cac	17/24	1	2	FACETS	0.934	0.838	1	0.934	0.838	1	CLONAL	1	TRUE	1	0.451874142366961	2		469	474	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964022	28964022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	97	471	0	ENST00000282397.4:c.1880C>T	p.Ser627Phe	p.S627F	ENST00000282397	NM_002019.4	627	tCc/tTc	13/30	1	2	FACETS	0.929	0.833	1	0.929	0.833	1	CLONAL	1	TRUE	1	0.451874142366961	2		471	462	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012452	29012452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	87	464	0	ENST00000282397.4:c.419G>A	p.Ser140Asn	p.S140N	ENST00000282397	NM_002019.4	140	aGt/aAt	4/30	1	2	FACETS	0.893	0.795	0.997	0.893	0.795	0.997	CLONAL	1	TRUE	1	0.451874142366961	2		464	431	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944632	32944632	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	132	565	0	ENST00000380152.3:c.8425T>C	p.Phe2809Leu	p.F2809L	ENST00000380152		2809	Ttc/Ctc	19/27	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.451874142366961	2		565	574	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336134	73336134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	39	221	0	ENST00000377767.4:c.2269G>A	p.Gly757Arg	p.G757R	ENST00000377767	NM_014953.3	757	Gga/Aga	17/21	1	2	FACETS	0.863	0.723	1	0.863	0.723	1	CLONAL	1	TRUE	1	0.451874142366961	2		221	200	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569948	95569948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	115	474	0	ENST00000393063.1:c.3785C>T	p.Pro1262Leu	p.P1262L	ENST00000393063	NM_030621.3	1262	cCt/cTt	22/28	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.451874142366961	2		474	467	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041734	42041734	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	93	440	0	ENST00000219905.7:c.5929C>T	p.Gln1977Ter	p.Q1977*	ENST00000219905	NM_001164273.1	1977	Cag/Tag	17/24	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.451874142366961	2		440	368	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052602	42052602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	129	375	1	ENST00000219905.7:c.7273C>T	p.Arg2425Cys	p.R2425C	ENST00000219905	NM_001164273.1	2425	Cgc/Tgc	20/24	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.451874142366961	2		376	546	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713311	43713311	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	195	864	0	ENST00000382044.4:c.4162C>G	p.Leu1388Val	p.L1388V	ENST00000382044	NM_001141980.1	1388	Ctt/Gtt	20/28	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.451874142366961	2		864	852	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472652	88472652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	76	299	0	ENST00000360948.2:c.1903G>A	p.Asp635Asn	p.D635N	ENST00000360948	NM_001012338.2	635	Gat/Aat	16/19	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.451874142366961	2		299	269	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476280	88476280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	140	608	0	ENST00000360948.2:c.1852G>A	p.Glu618Lys	p.E618K	ENST00000360948	NM_001012338.2	618	Gaa/Aaa	15/19	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.451874142366961	2		608	599	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478235	99478236	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTC	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	67	303	0	ENST00000268035.6:c.3141_3143dup	p.Leu1048dup	p.L1048dup	ENST00000268035	NM_000875.3	1048	ttt/tTTCtt	16/21	1	2	FACETS	0.888	0.777	1	0.888	0.777	1	CLONAL	1	TRUE	1	0.451874142366961	2		303	334	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396431	396431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	192	798	1	ENST00000262320.3:c.595C>T	p.Pro199Ser	p.P199S	ENST00000262320	NM_003502.3	199	Ccc/Tcc	2/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.451874142366961	2		799	796	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632744	23632744	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	73	485	0	ENST00000261584.4:c.3052G>T	p.Glu1018Ter	p.E1018*	ENST00000261584	NM_024675.3	1018	Gag/Tag	10/13	1	2	FACETS	0.8	0.703	0.903	0.8	0.703	0.903	CLONAL	1	TRUE	1	0.451874142366961	2		485	404	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671678	67671679	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	119	468	0	ENST00000264010.4:c.2087_2088delinsTT	p.Pro696Leu	p.P696L	ENST00000264010	NM_006565.3	696	cCC/cTT	12/12	1	2	FACETS	0.986	0.894	1	0.986	0.894	1	CLONAL	1	TRUE	1	0.451874142366961	2		468	534	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346081	89346081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	18	118	0	ENST00000301030.4:c.6869C>T	p.Pro2290Leu	p.P2290L	ENST00000301030	NM_001256183.1	2290	cCc/cTc	9/13	1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.451874142366961	2		118	71	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350869	89350869	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	222	858	0	ENST00000301030.4:c.2081T>G	p.Phe694Cys	p.F694C	ENST00000301030	NM_001256183.1	694	tTt/tGt	9/13	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.451874142366961	2		858	981	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958242	11958242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1261150954	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	73	302	0	ENST00000353533.5:c.152C>T	p.Pro51Leu	p.P51L	ENST00000353533	NM_003010.3	51	cCa/cTa	2/11	1	2	FACETS	0.926	0.815	1	0.926	0.815	1	CLONAL	1	TRUE	1	0.451874142366961	2		302	349	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554601	29554602	+	missense_variant	Missense_Mutation	DNP	AA	AA	GT	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	43	234	0	ENST00000356175.3:c.2386_2387delinsGT	p.Lys796Val	p.K796V	ENST00000356175	NM_000267.3	796	AAa/GTa	20/57	1	2	FACETS	0.774	0.652	0.906	0.774	0.652	0.906	CLONAL	1	TRUE	1	0.451874142366961	2		234	246	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576001	29576001	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	67	321	0	ENST00000356175.3:c.3975-1G>A		p.X1325_splice	ENST00000356175	NM_000267.3	1325			1	2	FACETS	0.888	0.777	1	0.888	0.777	1	CLONAL	1	TRUE	1	0.451874142366961	2		321	334	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653151	29653151	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	90	344	0	ENST00000356175.3:c.5086G>T	p.Glu1696Ter	p.E1696*	ENST00000356175	NM_000267.3	1696	Gag/Tag	36/57	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.451874142366961	2		344	362	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864574	37864574	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	81	386	0	ENST00000269571.5:c.226G>A	p.Asp76Asn	p.D76N	ENST00000269571		76	Gat/Aat	3/27	1	2	FACETS	0.996	0.884	1	0.996	0.884	1	CLONAL	1	TRUE	1	0.451874142366961	2		386	360	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857681	59857681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	85	343	1	ENST00000259008.2:c.1876G>A	p.Glu626Lys	p.E626K	ENST00000259008	NM_032043.2	626	Gaa/Aaa	13/20	1	2	FACETS	0.904	0.804	1	0.904	0.804	1	CLONAL	1	TRUE	1	0.451874142366961	2		344	416	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222899	36222899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	179	961	3	ENST00000222270.7:c.5528C>T	p.Pro1843Leu	p.P1843L	ENST00000222270	NM_014727.1	1843	cCt/cTt	27/37	1	2	FACETS	0.955	0.881	1	0.955	0.881	1	CLONAL	1	TRUE	1	0.451874142366961	2		964	830	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792107	42792107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1382074611	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	117	470	0	ENST00000575354.2:c.911G>A	p.Gly304Asp	p.G304D	ENST00000575354	NM_015125.3	304	gGc/gAc	6/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.451874142366961	2		470	406	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965017	25965017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	118	486	0	ENST00000435504.4:c.4189C>T	p.Pro1397Ser	p.P1397S	ENST00000435504		1397	Cct/Tct	13/13	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.451874142366961	2		486	508	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185035	99185035	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	78	337	0	ENST00000074304.5:c.2437T>C	p.Phe813Leu	p.F813L	ENST00000074304	NM_001134224.1	813	Ttt/Ctt	23/26	1	2	FACETS	0.951	0.841	1	0.951	0.841	1	CLONAL	1	TRUE	1	0.451874142366961	2		337	363	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538275	9538275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	258	547	1	ENST00000353224.5:c.1723C>T	p.Leu575Phe	p.L575F	ENST00000353224	NM_177990.2	575	Ctc/Ttc	7/10	0.21109224756531	3	FACETS	0.936	0.88	0.992	0.936	0.88	0.992	INDETERMINATE	2	TRUE	1	0.451874142366961	3		548	748	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31015959	31015959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	157	387	0	ENST00000375687.4:c.281C>T	p.Pro94Leu	p.P94L	ENST00000375687	NM_015338.5	94	cCa/cTa	5/13	0.21109224756531	3	FACETS	0.859	0.793	0.927	0.859	0.793	0.927	INDETERMINATE	2	TRUE	1	0.451874142366961	3		387	496	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739115	40739115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	101	424	0	ENST00000373198.4:c.3169G>A	p.Glu1057Lys	p.E1057K	ENST00000373198	NM_133170.3	1057	Gag/Aag	24/32	0.21109224756531	3	FACETS	0.943	0.845	1	0.472	0.422	0.524	INDETERMINATE	1	TRUE	1	0.451874142366961	3		424	581	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827900	40827900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767977370	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	221	531	0	ENST00000373198.4:c.2528C>T	p.Ser843Phe	p.S843F	ENST00000373198	NM_133170.3	843	tCt/tTt	17/32	0.21109224756531	3	FACETS	0.878	0.821	0.936	0.878	0.821	0.936	INDETERMINATE	2	TRUE	1	0.451874142366961	3		531	683	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817438	39817438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748243137	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	109	498	0	ENST00000288319.7:c.125G>A	p.Gly42Glu	p.G42E	ENST00000288319	NM_182918.3	42	gGa/gAa	2/10	1	2	FACETS	0.893	0.805	0.986	0.893	0.805	0.986	CLONAL	1	TRUE	1	0.451874142366961	2		498	540	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852517	42852517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	124	606	1	ENST00000398585.3:c.569G>A	p.Gly190Glu	p.G190E	ENST00000398585	NM_001135099.1	190	gGa/gAa	6/14	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.451874142366961	2		607	536	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655440	45655440	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	127	579	0	ENST00000407780.3:c.412T>G	p.Phe138Val	p.F138V	ENST00000407780	NM_001283052.1	138	Ttc/Gtc	4/7	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.451874142366961	2		579	543	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035181	30035181	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	101	450	0	ENST00000338641.4:c.343C>T	p.Gln115Ter	p.Q115*	ENST00000338641	NM_000268.3	115	Caa/Taa	3/16	0.451874142366961	3	FACETS	0.94	0.842	1	0.47	0.421	0.522	CLONAL	1	TRUE	1	0.451874142366961	3		450	583	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259116	89259117	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	84	271	0	ENST00000336596.2:c.260_261delinsAT	p.Val87Asp	p.V87D	ENST00000336596	NM_005233.5	87	gTC/gAT	3/17	0.451874142366961	3	FACETS	1	0.941	1	0.547	0.485	0.611	CLONAL	1	TRUE	1	0.451874142366961	3		271	417	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133586	55133586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501507	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	114	413	0	ENST00000257290.5:c.890G>A	p.Arg297Lys	p.R297K	ENST00000257290	NM_006206.4	297	aGg/aAg	6/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.451874142366961	2		413	443	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156489	55156489	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1290364180	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	97	355	0	ENST00000257290.5:c.2890A>G	p.Lys964Glu	p.K964E	ENST00000257290	NM_006206.4	964	Aaa/Gaa	22/23	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.451874142366961	2		355	363	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157485	106157485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747398674	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	62	259	0	ENST00000380013.4:c.2386G>A	p.Glu796Lys	p.E796K	ENST00000380013	NM_001127208.2	796	Gag/Aag	3/11	1	2	FACETS	0.959	0.836	1	0.959	0.836	1	CLONAL	1	TRUE	1	0.451874142366961	2		259	286	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541439	187541439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1246955615	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	111	408	1	ENST00000441802.2:c.6301C>T	p.Arg2101Cys	p.R2101C	ENST00000441802	NM_005245.3	2101	Cgc/Tgc	10/27	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.451874142366961	2		409	434	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435618	149435618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	94	478	0	ENST00000286301.3:c.2525G>A	p.Gly842Asp	p.G842D	ENST00000286301	NM_005211.3	842	gGc/gAc	19/22	0.175431504199483	0	FACETS	0.529	0.473	0.588			1	INDETERMINATE	1	TRUE	0	0.451874142366961	0		478	431	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500491	149500491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770930584	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	140	635	0	ENST00000261799.4:c.2546G>A	p.Arg849Gln	p.R849Q	ENST00000261799	NM_002609.3	849	cGa/cAa	18/23	0.175431504199483	0	FACETS	0.563	0.515	0.614			1	INDETERMINATE	1	TRUE	0	0.451874142366961	0		635	603	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250700	26250700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	110	419	0	ENST00000446824.2:c.134G>A	p.Gly45Asp	p.G45D	ENST00000446824	NM_021018.2	45	gGt/gAt	1/1	0.451874142366961	3	FACETS	1	0.912	1	0.507	0.456	0.56	CLONAL	1	TRUE	1	0.451874142366961	3		419	589	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323150	31323150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	138	626	0	ENST00000412585.2:c.839G>A	p.Arg280Lys	p.R280K	ENST00000412585	NM_005514.6	280	aGa/aAa	4/8	0.451874142366961	3	FACETS	0.892	0.812	0.977	0.446	0.406	0.489	CLONAL	1	TRUE	1	0.451874142366961	3		626	839	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797788	32797788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370090254	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	128	561	0	ENST00000374899.4:c.1714G>A	p.Glu572Lys	p.E572K	ENST00000374899	NM_018833.2	572	Gaa/Aaa	10/12	0.451874142366961	3	FACETS	0.95	0.862	1	0.475	0.431	0.522	CLONAL	1	TRUE	1	0.451874142366961	3		561	731	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956552	93956552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754119070	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	99	417	0	ENST00000369303.4:c.2684G>A	p.Arg895Gln	p.R895Q	ENST00000369303	NM_004440.3	895	cGa/cAa	15/17	0.451874142366961	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.451874142366961	1		417	318	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068097	94068097	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	63	259	0	ENST00000369303.4:c.865C>T	p.Gln289Ter	p.Q289*	ENST00000369303	NM_004440.3	289	Caa/Taa	4/17	0.451874142366961	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.451874142366961	1		259	201	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725567	117725567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767519397	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	104	553	0	ENST00000368508.3:c.314C>T	p.Pro105Leu	p.P105L	ENST00000368508	NM_002944.2	105	cCc/cTc	5/43	0.451874142366961	1	FACETS	0.995	0.9	1	0.995	0.9	1	CLONAL	1	TRUE	0	0.451874142366961	1		553	358	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6037030	6037030	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1562671039	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	93	260	0	ENST00000265849.7:c.730C>T	p.Gln244Ter	p.Q244*	ENST00000265849	NM_000535.5	244	Cag/Tag	7/15	0.223180964129396	3	FACETS	1	0.972	1	0.631	0.565	0.7	INDETERMINATE	1	TRUE	1	0.451874142366961	3		260	400	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220344	55220344	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	101	555	0	ENST00000275493.2:c.734A>G	p.Glu245Gly	p.E245G	ENST00000275493	NM_005228.3	245	gAg/gGg	6/28	0.223180964129396	3	FACETS	0.932	0.835	1	0.466	0.417	0.518	INDETERMINATE	1	TRUE	1	0.451874142366961	3		555	588	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55232974	55232974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1249099747	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	98	322	0	ENST00000275493.2:c.1724G>A	p.Gly575Glu	p.G575E	ENST00000275493	NM_005228.3	575	gGa/gAa	15/28	0.223180964129396	3	FACETS	0.755	0.68	0.834	0.755	0.68	0.834	INDETERMINATE	2	TRUE	1	0.451874142366961	3		322	352	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359032	81359032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	144	537	0	ENST00000222390.5:c.929G>A	p.Gly310Glu	p.G310E	ENST00000222390	NM_000601.4	310	gGa/gAa	8/18	0.223180964129396	3	FACETS	1	0.986	1	0.696	0.638	0.757	INDETERMINATE	1	TRUE	1	0.451874142366961	3		537	561	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945093	151945093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746147314	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	41	542	1	ENST00000262189.6:c.2426G>A	p.Gly809Glu	p.G809E	ENST00000262189	NM_170606.2	809	gGa/gAa	14/59	0.223180964129396	3	FACETS	0.499	0.415	0.591	0.249	0.207	0.296	INDETERMINATE	1	TRUE	1	0.451874142366961	3		543	446	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879289	56879289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	143	539	0	ENST00000519728.1:c.806G>A	p.Ser269Asn	p.S269N	ENST00000519728	NM_002350.3	269	aGt/aAt	9/13	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.451874142366961	2		539	621	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069575	69069575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	69	355	0	ENST00000288368.4:c.4250G>A	p.Gly1417Glu	p.G1417E	ENST00000288368	NM_024870.2	1417	gGa/gAa	35/40	1	2	FACETS	0.825	0.723	0.935	0.825	0.723	0.935	CLONAL	1	TRUE	1	0.451874142366961	2		355	370	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524946	8524946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567730036	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	158	361	0	ENST00000356435.5:c.658C>T	p.Pro220Ser	p.P220S	ENST00000356435		220	Cct/Tct	7/35	0.451874142366961	2	FACETS	0.879	0.815	0.943	0.879	0.815	0.943	CLONAL	2	TRUE	0	0.451874142366961	2		361	398	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27228284	27228284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	182	521	1	ENST00000380036.4:c.3281G>A	p.Arg1094Lys	p.R1094K	ENST00000380036	NM_000459.3	1094	aGa/aAa	22/23	0.451874142366961	2	FACETS	0.948	0.885	1	0.948	0.885	1	CLONAL	2	TRUE	0	0.451874142366961	2		522	425	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317533	1317533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199794164	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	139	563	1	ENST00000400841.2:c.532G>A	p.Glu178Lys	p.E178K	ENST00000400841		178	Gag/Aag	5/6	1	1	FACETS	0.79	0.722	0.861	0.79	0.722	0.861	SUBCLONAL	1	TRUE	0	0.451874142366961	1		564	603	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913538	39913538	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	107	264	0	ENST00000378444.4:c.4790C>T	p.Thr1597Ile	p.T1597I	ENST00000378444	NM_001123385.1	1597	aCt/aTt	13/15	1	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.451874142366961	1		264	261	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223368	53223368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	185	344	0	ENST00000375401.3:c.3991C>T	p.Pro1331Ser	p.P1331S	ENST00000375401	NM_004187.3	1331	Cct/Tct	23/26	1	1	FACETS	0.864	0.81	0.917	1	0.993	1	CLONAL	2	TRUE	0	0.451874142366961	1		344	367	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938304	76938304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	161	319	0	ENST00000373344.5:c.2444C>T	p.Ser815Phe	p.S815F	ENST00000373344	NM_000489.3	815	tCt/tTt	9/35	1	1	FACETS	0.777	0.723	0.831	1	0.991	1	SUBCLONAL	2	TRUE	0	0.451874142366961	1		319	355	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0036794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	170	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.966	0.9	1	0.966	0.9	1	CLONAL	1	TRUE	1	0.907227097247691	2		288	388	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0036794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	155	248	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.861	0.797	0.925	0.861	0.797	0.925	CLONAL	1	TRUE	1	0.907227097247691	2		249	397	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367257	50367257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1245618829	NA	P-0036794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	164	255	0	ENST00000331340.3:c.64G>A	p.Asp22Asn	p.D22N	ENST00000331340	NM_006060.4	22	Gat/Aat	3/8	1	2	FACETS	0.937	0.871	1	0.937	0.871	1	CLONAL	1	TRUE	1	0.907227097247691	2		255	386	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258683	16258683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs559309170	NA	P-0036794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	245	432	0	ENST00000375759.3:c.5948C>T	p.Ser1983Leu	p.S1983L	ENST00000375759	NM_015001.2	1983	tCg/tTg	11/15	0.879404329760197	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.907227097247691	1		432	287	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591116	67591116	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	127	262	0	ENST00000274335.5:c.1709T>C	p.Leu570Pro	p.L570P	ENST00000274335		570	cTt/cCt	12/15	0.907227097247691	1	FACETS	0.938	0.89	0.983	0.938	0.89	0.983	CLONAL	1	TRUE	0	0.907227097247691	1		262	163	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729162	66729162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519732	NA	P-0036794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	417	636	0	ENST00000307102.5:c.370C>T	p.Pro124Ser	p.P124S	ENST00000307102	NM_002755.3	124	Ccg/Tcg	3/11	1	2	FACETS	0.972	0.93	1	0.972	0.93	1	CLONAL	1	TRUE	1	0.907227097247691	2		636	946	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155180	55155180	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600187	NA	P-0036794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	281	516	1	ENST00000257290.5:c.2779G>A	p.Glu927Lys	p.E927K	ENST00000257290	NM_006206.4	927	Gag/Aag	21/23	1	2	FACETS	0.988	0.936	1	0.988	0.936	1	CLONAL	1	TRUE	1	0.907227097247691	2		517	627	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715746	18715746	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1191317818	NA	P-0036794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	205	322	0	ENST00000266497.5:c.3577C>T	p.Pro1193Ser	p.P1193S	ENST00000266497		1193	Cct/Tct	25/31	0.243701164732121	1	FACETS	0.585	0.55	0.62	0.585	0.55	0.62	INDETERMINATE	1	TRUE	0	0.907227097247691	1		322	422	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244838	46244838	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	400	640	2	ENST00000334344.6:c.2932C>G	p.Pro978Ala	p.P978A	ENST00000334344	NM_152641.2	978	Cca/Gca	15/21	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.907227097247691	2		642	864	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549227	21549227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	518	813	1	ENST00000382592.4:c.3049G>A	p.Gly1017Ser	p.G1017S	ENST00000382592	NM_014572.2	1017	Ggt/Agt	8/8	1	2	FACETS	0.96	0.923	0.998	0.96	0.923	0.998	CLONAL	1	TRUE	1	0.907227097247691	2		814	1189	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120236	70120236	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	417	732	0	ENST00000245479.2:c.1238A>C	p.His413Pro	p.H413P	ENST00000245479	NM_000346.3	413	cAc/cCc	3/3	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.907227097247691	2		732	894	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948764	55948764	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	284	620	0	ENST00000263923.4:c.3701T>G	p.Val1234Gly	p.V1234G	ENST00000263923	NM_002253.2	1234	gTg/gGg	28/30	1	2	FACETS	0.859	0.812	0.906	0.859	0.812	0.906	CLONAL	1	TRUE	1	0.907227097247691	2		620	729	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222269	53222269	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036794-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	195	864	0	ENST00000375401.3:c.4563G>C	p.Glu1521Asp	p.E1521D	ENST00000375401	NM_004187.3	1521	gaG/gaC	26/26	0.593066759475305	1	FACETS	0.287	0.266	0.309	0.287	0.266	0.309	SUBCLONAL	1	TRUE	0	0.907227097247691	1		864	817	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453138	140453139	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTA	rs727502902	NA	P-0036832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	92	635	0	ENST00000288602.6:c.1794_1796dup	p.Thr599dup	p.T599dup	ENST00000288602	NM_004333.4	599	aca/acTACa	15/18	0.130274939775903	4	FACETS	1	0.97	1	0.632	0.562	0.706	INDETERMINATE	1	TRUE	2	0.33	4		635	587	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0036844-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	307	243	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.525513459056125	5	FACETS	0.968	0.921	1	0.968	0.921	1	CLONAL	3	TRUE	2	0.644612107575374	5		243	645	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0036844-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	277	385	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.644612107575374	3	FACETS	1	0.992	1	0.672	0.633	0.711	CLONAL	1	TRUE	1	0.644612107575374	3		385	846	SUCCESS
ATR	545	MSKCC	GRCh37	3	142204007	142204007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369309229	NA	P-0036844-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	350	339	0	ENST00000350721.4:c.6196C>T	p.Arg2066Trp	p.R2066W	ENST00000350721	NM_001184.3	2066	Cgg/Tgg	36/47	0.525513459056125	5	FACETS	0.905	0.862	0.948	0.905	0.862	0.948	CLONAL	3	TRUE	2	0.644612107575374	5		339	787	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588611	28588611	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036844-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	77	372	0	ENST00000241453.7:c.2837A>G	p.Gln946Arg	p.Q946R	ENST00000241453	NM_004119.2	946	cAg/cGg	23/24	0.193121110421338	3	FACETS	0.617	0.543	0.696	0.206	0.181	0.232	INDETERMINATE	1	TRUE	0	0.644612107575374	3		372	512	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0036862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	129	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.259378810980963	4	FACETS	0.948	0.864	1	0.948	0.864	1	CLONAL	2	TRUE	2	0.347888684419196	4		288	527	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0036862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	96	248	1				ENST00000310581	NM_198253.2	-/1132			0.299409444092303	2	FACETS	0.758	0.681	0.838	0.758	0.681	0.838	SUBCLONAL	2	TRUE	0	0.347888684419196	2		249	364	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665053	29665053	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691093	NA	P-0036862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	156	574	0	ENST00000356175.3:c.6652C>T	p.Gln2218Ter	p.Q2218*	ENST00000356175	NM_000267.3	2218	Caa/Taa	44/57	0.192633027862926	2	FACETS	0.884	0.816	0.955	0.884	0.816	0.955	INDETERMINATE	2	TRUE	0	0.347888684419196	2		574	507	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279562	123279562	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	158	351	0	ENST00000358487.5:c.870G>A	p.Trp290Ter	p.W290*	ENST00000358487	NM_000141.4	290	tgG/tgA	7/18	0.283457989778784	2	FACETS	1	0.979	1	0.602	0.553	0.654	CLONAL	1	TRUE	0	0.347888684419196	2		351	754	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578480	7578482	+	frameshift_variant	Frame_Shift_Del	DEL	TGT	TGT	GG	novel	NA	P-0036862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	222	366	1	ENST00000269305.4:c.448_450delinsCC	p.Thr150ProfsTer20	p.T150Pfs*20	ENST00000269305	NM_001126112.2	150	ACA/CC	5/11	0.192633027862926	2	FACETS	1	0.99	1	0.673	0.627	0.721	INDETERMINATE	1	TRUE	0	0.347888684419196	2		367	948	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149726	202149732	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCCCC	GGCCCCC	-	novel	NA	P-0036862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	153	333	0	ENST00000358485.4:c.1167_1173del	p.Ala390SerfsTer4	p.A390Sfs*4	ENST00000358485	NM_001080125.1	389	gaGGCCCCC/ga	8/9	0.299409444092303	2	FACETS	1	0.986	1	0.685	0.629	0.744	CLONAL	1	TRUE	0	0.347888684419196	2		333	642	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488766	212488767	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	130	274	1	ENST00000342788.4:c.2082_2083delinsAA	p.Val695Met	p.V695M	ENST00000342788	NM_005235.2	694	ttGGtg/ttAAtg	18/28	0.299409444092303	2	FACETS	0.787	0.718	0.858	0.787	0.718	0.858	SUBCLONAL	2	TRUE	0	0.347888684419196	2		275	475	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651283	45651283	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	185	441	0	ENST00000407780.3:c.742A>T	p.Ser248Cys	p.S248C	ENST00000407780	NM_001283052.1	248	Agt/Tgt	5/7	0.199659843501114	4	FACETS	1	0.989	1	0.718	0.663	0.776	INDETERMINATE	1	TRUE	2	0.347888684419196	4		441	998	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155736	106155736	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1486874084	NA	P-0036862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	115	217	0	ENST00000380013.4:c.637G>A	p.Val213Ile	p.V213I	ENST00000380013	NM_001127208.2	213	Gtt/Att	3/11	0.287474524320988	4	FACETS	0.809	0.731	0.89	0.809	0.731	0.89	CLONAL	2	TRUE	2	0.347888684419196	4		217	551	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400027	139400027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754838691	NA	P-0036862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	210	335	0	ENST00000277541.6:c.4321C>T	p.Pro1441Ser	p.P1441S	ENST00000277541	NM_017617.3	1441	Ccc/Tcc	25/34	0.283457989778784	2	FACETS	1	0.991	1	0.741	0.689	0.794	CLONAL	1	TRUE	0	0.347888684419196	2		335	815	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727453	66727453	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397516790	NA	P-0036873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	115	578	0	ENST00000307102.5:c.169A>G	p.Lys57Glu	p.K57E	ENST00000307102	NM_002755.3	57	Aag/Gag	2/11	1	2	FACETS	0.975	0.881	1	0.975	0.881	1	CLONAL	1	TRUE	1	0.408855035207659	2		578	577	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982080	93982080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	238	500	0	ENST00000369303.4:c.1385C>T	p.Ser462Phe	p.S462F	ENST00000369303	NM_004440.3	462	tCc/tTc	6/17	0.408855035207659	2	FACETS	0.997	0.938	1	0.997	0.938	1	CLONAL	2	TRUE	0	0.408855035207659	2		500	584	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264412	46264412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746670862	NA	P-0036873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	123	497	0	ENST00000371998.3:c.1459C>T	p.Arg487Cys	p.R487C	ENST00000371998		487	Cgt/Tgt	11/23	0.350954702123652	4	FACETS	1	0.965	1	0.38	0.344	0.419	CLONAL	1	TRUE	1	0.408855035207659	4		497	743	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441974	6441974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	65	684	1	ENST00000356142.4:c.533C>T	p.Ala178Val	p.A178V	ENST00000356142	NM_018890.3	178	gCg/gTg	7/7	0.398159243716972	4	FACETS	0.474	0.409	0.544	0.237	0.204	0.272	SUBCLONAL	1	TRUE	2	0.408855035207659	4		685	946	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156120	106156120	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs751272814	NA	P-0036873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	80	332	0	ENST00000380013.4:c.1021C>T	p.Gln341Ter	p.Q341*	ENST00000380013	NM_001127208.2	341	Cag/Tag	3/11	1	2	FACETS	0.991	0.877	1	0.991	0.877	1	CLONAL	1	TRUE	1	0.408855035207659	2		332	395	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925427	114925427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	134	590	0	ENST00000543371.1:c.1505C>T	p.Ser502Phe	p.S502F	ENST00000543371	NM_001198531.1	502	tCc/tTc	14/14	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.408855035207659	2		590	646	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609739	28609739	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762585560	NA	P-0036873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	142	753	0	ENST00000241453.7:c.1490C>T	p.Ser497Leu	p.S497L	ENST00000241453	NM_004119.2	497	tCg/tTg	12/24	0.392562872271709	3	FACETS	0.834	0.759	0.913	0.417	0.379	0.457	CLONAL	1	TRUE	1	0.408855035207659	3		753	1003	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121892	2121893	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	378	820	1	ENST00000219476.3:c.2054_2055delinsTT	p.Pro685Leu	p.P685L	ENST00000219476	NM_000548.3	685	cCC/cTT	19/42	0.350584676566149	3	FACETS	1	0.974	1			1	CLONAL	2	TRUE	NA	0.408855035207659	3		821	1076	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110494	8110494	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	69	419	0	ENST00000585124.1:c.398A>C	p.His133Pro	p.H133P	ENST00000585124	NM_004217.3	133	cAc/cCc	5/9	0.398159243716972	4	FACETS	0.869	0.758	0.989	0.435	0.379	0.495	CLONAL	1	TRUE	2	0.408855035207659	4		419	547	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348448	56348449	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0036873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	70	315	1	ENST00000348428.3:c.256_257delinsAA	p.Gly86Lys	p.G86K	ENST00000348428	NM_006785.3	86	GGa/AAa	2/17	0.408855035207659	3	FACETS	1	0.894	1	0.512	0.448	0.58	CLONAL	1	TRUE	1	0.408855035207659	3		316	403	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286765	212286765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	165	440	1	ENST00000342788.4:c.2931G>A	p.Met977Ile	p.M977I	ENST00000342788	NM_005235.2	977	atG/atA	24/28	0.398159243716972	4	FACETS	0.89	0.82	0.962	0.89	0.82	0.962	CLONAL	2	TRUE	2	0.408855035207659	4		441	639	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0036888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	348	469	2	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		471	443	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0037144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	72	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.581271664974576	3	FACETS	1	0.973	1	0.686	0.608	0.767	CLONAL	1	TRUE	1	0.581271664974576	3		288	233	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	66	151	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.48854665247789	2		151	263	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210733	5210733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779302415	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	307	915	0	ENST00000357368.4:c.5318C>T	p.Ser1773Leu	p.S1773L	ENST00000357368	NM_002850.3	1773	tCg/tTg	34/38	0.476396734679105	3	FACETS	0.971	0.92	1	0.971	0.92	1	CLONAL	2	TRUE	1	0.48854665247789	3		915	805	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	126	747	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.863	0.784	0.945	0.863	0.784	0.945	CLONAL	1	TRUE	1	0.48854665247789	2		747	598	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	163	631	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.48854665247789	2		631	656	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435667	18435667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	38	216	0	ENST00000266497.5:c.652G>A	p.Glu218Lys	p.E218K	ENST00000266497		218	Gaa/Aaa	1/31	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.48854665247789	2		216	148	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344943	70344943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	120	530	0	ENST00000374080.3:c.2173C>T	p.Leu725Phe	p.L725F	ENST00000374080		725	Ctt/Ttt	15/45	1	2	FACETS	0.88	0.798	0.967	0.88	0.798	0.967	CLONAL	1	TRUE	1	0.48854665247789	2		530	558	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546620	9546620	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764351685	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	34	458	0	ENST00000353224.5:c.1402G>A	p.Glu468Lys	p.E468K	ENST00000353224	NM_177990.2	468	Gag/Aag	5/10	NA	2	FACETS	0.33	0.269	0.398			1	INDETERMINATE	1	TRUE	NA	0.48854665247789	2		458	422	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198453	108198453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	63	317	0	ENST00000278616.4:c.7057C>T	p.Pro2353Ser	p.P2353S	ENST00000278616	NM_000051.3	2353	Cct/Tct	48/63	1	2	FACETS	0.945	0.825	1	0.945	0.825	1	CLONAL	1	TRUE	1	0.48854665247789	2		317	273	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652303	48652303	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	171	666	0	ENST00000376670.3:c.974G>A	p.Gly325Glu	p.G325E	ENST00000376670	NM_002049.3	325	gGa/gAa	6/6	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.48854665247789	2		666	694	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245343	46245343	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	88	427	0	ENST00000334344.6:c.3437C>T	p.Ser1146Leu	p.S1146L	ENST00000334344	NM_152641.2	1146	tCg/tTg	15/21	1	2	FACETS	0.898	0.801	1	0.898	0.801	1	CLONAL	1	TRUE	1	0.48854665247789	2		427	401	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955873	55955873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	79	361	0	ENST00000263923.4:c.3289G>A	p.Glu1097Lys	p.E1097K	ENST00000263923	NM_002253.2	1097	Gaa/Aaa	24/30	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.48854665247789	2		361	278	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987272	2987272	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	141	507	0	ENST00000396946.4:c.157G>A	p.Asp53Asn	p.D53N	ENST00000396946	NM_032415.4	53	Gat/Aat	3/25	1	2	FACETS	0.973	0.89	1	0.973	0.89	1	CLONAL	1	TRUE	1	0.48854665247789	2		507	593	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101176	41101176	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370385649	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	176	529	0	ENST00000373198.4:c.1180G>A	p.Glu394Lys	p.E394K	ENST00000373198	NM_133170.3	394	Gaa/Aaa	8/32	0.476396734679105	3	FACETS	1	0.99	1	0.728	0.673	0.784	CLONAL	1	TRUE	1	0.48854665247789	3		529	616	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575116	48575116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	46	327	0	ENST00000342988.3:c.310C>T	p.Leu104Phe	p.L104F	ENST00000342988	NM_005359.5	104	Ctt/Ttt	3/12	0.236352997879497	3	FACETS	0.934	0.793	1	0.467	0.396	0.543	INDETERMINATE	1	TRUE	1	0.48854665247789	3		327	251	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139929	50139929	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374650566	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	353	715	1	ENST00000246792.3:c.400G>A	p.Asp134Asn	p.D134N	ENST00000246792	NM_006270.3	134	Gac/Aac	4/6	0.476396734679105	3	FACETS	0.961	0.913	1	0.961	0.913	1	CLONAL	2	TRUE	1	0.48854665247789	3		716	936	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031984	10031984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs185993125	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	118	603	0	ENST00000330684.3:c.839C>T	p.Ser280Phe	p.S280F	ENST00000330684	NM_001134407.1	280	tCc/tTc	3/13	1	2	FACETS	0.806	0.73	0.887	0.806	0.73	0.887	CLONAL	1	TRUE	1	0.48854665247789	2		603	599	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211154	36211154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	207	864	2	ENST00000222270.7:c.905C>T	p.Pro302Leu	p.P302L	ENST00000222270	NM_014727.1	302	cCc/cTc	3/37	0.476396734679105	3	FACETS	0.983	0.911	1	0.491	0.455	0.529	CLONAL	1	TRUE	1	0.48854665247789	3		866	1073	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247617	123247617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	159	813	0	ENST00000358487.5:c.1874G>A	p.Arg625Gln	p.R625Q	ENST00000358487	NM_000141.4	625	cGa/cAa	14/18	1	2	FACETS	0.882	0.82	0.945	1	0.992	1	CLONAL	2	TRUE	1	0.48854665247789	2		813	369	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492925	8492925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	115	514	0	ENST00000356435.5:c.2404G>A	p.Ala802Thr	p.A802T	ENST00000356435		802	Gcc/Acc	16/35	1	2	FACETS	0.943	0.854	1	0.943	0.854	1	CLONAL	1	TRUE	1	0.48854665247789	2		514	499	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522581	176522581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	167	709	0	ENST00000292408.4:c.1678G>A	p.Glu560Lys	p.E560K	ENST00000292408	NM_213647.1	560	Gag/Aag	13/18	0.236352997879497	3	FACETS	1	0.964	1	0.54	0.497	0.585	INDETERMINATE	1	TRUE	1	0.48854665247789	3		709	787	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754866	29754866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	130	368	1	ENST00000389048.3:c.1069C>T	p.Pro357Ser	p.P357S	ENST00000389048	NM_004304.4	357	Ccc/Tcc	4/29	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.48854665247789	2		369	460	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344458	118344458	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	66	171	0	ENST00000534358.1:c.2584C>T	p.Arg862Ter	p.R862*	ENST00000534358	NM_005933.3	862	Cga/Tga	3/36	1	2	FACETS	0.951	0.834	1	0.951	0.834	1	CLONAL	1	TRUE	1	0.48854665247789	2		171	284	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204920	128204920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253079679	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	148	1027	1	ENST00000341105.2:c.521C>T	p.Pro174Leu	p.P174L	ENST00000341105	NM_032638.4	174	cCa/cTa	3/6	0.48854665247789	1	FACETS	0.848	0.779	0.919	0.848	0.779	0.919	CLONAL	1	TRUE	0	0.48854665247789	1		1028	540	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651181	206651181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	148	685	0	ENST00000367120.3:c.791C>T	p.Pro264Leu	p.P264L	ENST00000367120	NM_014002.3	264	cCc/cTc	8/22	0.476396734679105	3	FACETS	0.891	0.814	0.972	0.446	0.407	0.486	CLONAL	1	TRUE	1	0.48854665247789	3		685	846	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665755	29665756	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs876657715	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	29	198	0	ENST00000356175.3:c.6791dup	p.Tyr2264Ter	p.Y2264*	ENST00000356175	NM_000267.3	2264	tac/tAac	45/57	0.48854665247789	1	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	0	0.48854665247789	1		198	83	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911165	40911165	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	44	318	0	ENST00000373198.4:c.2140G>A	p.Glu714Lys	p.E714K	ENST00000373198	NM_133170.3	714	Gag/Aag	13/32	0.476396734679105	3	FACETS	1	0.851	1	0.503	0.425	0.586	CLONAL	1	TRUE	1	0.48854665247789	3		318	223	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11210192	11210192	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	278	482	0	ENST00000361445.4:c.4561T>G	p.Trp1521Gly	p.W1521G	ENST00000361445	NM_004958.3	1521	Tgg/Ggg	31/58	0.43824158580102	4	FACETS	0.993	0.936	1	0.993	0.936	1	CLONAL	2	TRUE	2	0.48854665247789	4		482	853	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799099	45799099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	357	717	0	ENST00000450313.1:c.334C>T	p.Pro112Ser	p.P112S	ENST00000450313	NM_012222.2	112	Cca/Tca	3/16	0.43824158580102	4	FACETS	0.975	0.925	1	0.975	0.925	1	CLONAL	2	TRUE	2	0.48854665247789	4		717	1116	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874280	155874280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869025196	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	196	437	0	ENST00000368323.3:c.251C>T	p.Ala84Val	p.A84V	ENST00000368323	NM_006912.5	84	gCc/gTc	5/6	0.402994661606573	4	FACETS	0.912	0.848	0.977	0.912	0.848	0.977	CLONAL	2	TRUE	2	0.48854665247789	4		437	655	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204515983	204515983	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	56	290	0	ENST00000367182.3:c.881C>T	p.Thr294Ile	p.T294I	ENST00000367182	NM_001278516.1	294	aCc/aTc	10/11	0.476396734679105	3	FACETS	0.897	0.773	1	0.449	0.386	0.515	CLONAL	1	TRUE	1	0.48854665247789	3		290	318	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226568840	226568840	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	165	625	1	ENST00000366794.5:c.1229C>T	p.Ala410Val	p.A410V	ENST00000366794	NM_001618.3	410	gCc/gTc	9/23	0.476396734679105	3	FACETS	1	0.955	1	0.528	0.485	0.572	CLONAL	1	TRUE	1	0.48854665247789	3		626	796	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310839	123310839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1292300276	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	130	543	0	ENST00000358487.5:c.589G>A	p.Glu197Lys	p.E197K	ENST00000358487	NM_000141.4	197	Gag/Aag	5/18	1	2	FACETS	0.914	0.833	1	0.914	0.833	1	CLONAL	1	TRUE	1	0.48854665247789	2		543	582	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534705	18534705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	72	328	0	ENST00000266497.5:c.1763C>T	p.Ser588Phe	p.S588F	ENST00000266497		588	tCc/tTc	12/31	0.250353268467336	0	FACETS	0.467	0.411	0.526			1	INDETERMINATE	1	TRUE	0	0.48854665247789	0		328	323	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431049	49431049	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1210590639	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	140	649	0	ENST00000301067.7:c.10090C>T	p.Gln3364Ter	p.Q3364*	ENST00000301067	NM_003482.3	3364	Cag/Tag	34/54	1	2	FACETS	0.884	0.808	0.965	0.884	0.808	0.965	CLONAL	1	TRUE	1	0.48854665247789	2		649	648	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121438903	121438903	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	173	697	0	ENST00000257555.6:c.1804G>A	p.Asp602Asn	p.D602N	ENST00000257555		602	Gac/Aac	10/10	1	2	FACETS	0.993	0.917	1	0.993	0.917	1	CLONAL	1	TRUE	1	0.48854665247789	2		697	713	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041742	29041742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	60	354	0	ENST00000282397.4:c.77G>A	p.Gly26Asp	p.G26D	ENST00000282397	NM_002019.4	26	gGt/gAt	2/30	0.48854665247789	1	FACETS	0.745	0.649	0.848	0.745	0.649	0.848	SUBCLONAL	1	TRUE	0	0.48854665247789	1		354	249	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610246	81610246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	93	398	0	ENST00000298171.2:c.1844C>T	p.Pro615Leu	p.P615L	ENST00000298171	NM_000369.2	615	cCa/cTa	10/10	1	2	FACETS	0.917	0.821	1	0.917	0.821	1	CLONAL	1	TRUE	1	0.48854665247789	2		398	415	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42026784	42026784	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	58	284	0	ENST00000219905.7:c.3908A>G	p.Lys1303Arg	p.K1303R	ENST00000219905	NM_001164273.1	1303	aAa/aGa	12/24	1	2	FACETS	0.927	0.805	1	0.927	0.805	1	CLONAL	1	TRUE	1	0.48854665247789	2		284	256	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821890	72821890	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529936440	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	82	312	0	ENST00000268489.5:c.10285C>T	p.Arg3429Cys	p.R3429C	ENST00000268489	NM_006885.3	3429	Cgt/Tgt	10/10	1	2	FACETS	0.925	0.821	1	0.925	0.821	1	CLONAL	1	TRUE	1	0.48854665247789	2		312	363	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346570	89346570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	106	482	0	ENST00000301030.4:c.6380C>T	p.Pro2127Leu	p.P2127L	ENST00000301030	NM_001256183.1	2127	cCc/cTc	9/13	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.48854665247789	2		482	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579406	7579406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	125	610	0	ENST00000269305.4:c.281C>T	p.Ser94Leu	p.S94L	ENST00000269305	NM_001126112.2	94	tCa/tTa	4/11	1	2	FACETS	0.823	0.747	0.902	0.823	0.747	0.902	CLONAL	1	TRUE	1	0.48854665247789	2		610	622	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138431139	138431139	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	48	277	0	ENST00000289153.2:c.1310C>T	p.Pro437Leu	p.P437L	ENST00000289153	NM_006219.2	437	cCt/cTt	8/22	0.48854665247789	1	FACETS	0.811	0.696	0.934	0.811	0.696	0.934	CLONAL	1	TRUE	0	0.48854665247789	1		277	183	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133602	55133602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	90	355	0	ENST00000257290.5:c.906G>A	p.Met302Ile	p.M302I	ENST00000257290	NM_006206.4	302	atG/atA	6/23	1	2	FACETS	0.993	0.888	1	0.993	0.888	1	CLONAL	1	TRUE	1	0.48854665247789	2		355	371	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295201	1295201	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	62	202	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.48854665247789	2		204	251	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876205	35876205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	103	475	0	ENST00000303115.3:c.997G>A	p.Glu333Lys	p.E333K	ENST00000303115	NM_002185.3	333	Gaa/Aaa	8/8	1	2	FACETS	0.822	0.738	0.91	0.822	0.738	0.91	CLONAL	1	TRUE	1	0.48854665247789	2		475	513	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876469	35876469	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	127	544	0	ENST00000303115.3:c.1261C>T	p.Leu421Phe	p.L421F	ENST00000303115	NM_002185.3	421	Ctc/Ttc	8/8	1	2	FACETS	0.904	0.822	0.99	0.904	0.822	0.99	CLONAL	1	TRUE	1	0.48854665247789	2		544	575	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522623	176522623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773674820	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	220	726	0	ENST00000292408.4:c.1720C>T	p.Pro574Ser	p.P574S	ENST00000292408	NM_213647.1	574	Ccc/Tcc	13/18	0.236352997879497	3	FACETS	1	0.992	1	0.742	0.693	0.793	INDETERMINATE	1	TRUE	1	0.48854665247789	3		726	755	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641065	117641065	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	62	493	0	ENST00000368508.3:c.5906G>A	p.Gly1969Glu	p.G1969E	ENST00000368508	NM_002944.2	1969	gGa/gAa	36/43	1	2	FACETS	0.673	0.584	0.769	0.673	0.584	0.769	SUBCLONAL	1	TRUE	1	0.48854665247789	2		493	377	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117707019	117707019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745980825	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	115	453	0	ENST00000368508.3:c.2131G>A	p.Asp711Asn	p.D711N	ENST00000368508	NM_002944.2	711	Gat/Aat	15/43	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.48854665247789	2		453	427	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001386	150001386	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	72	517	0	ENST00000253339.5:c.2218G>A	p.Asp740Asn	p.D740N	ENST00000253339		740	Gat/Aat	4/7	1	2	FACETS	0.979	0.864	1	0.979	0.864	1	CLONAL	1	TRUE	1	0.48854665247789	2		517	301	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730045	41730045	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	121	471	0	ENST00000242208.4:c.484C>T	p.Pro162Ser	p.P162S	ENST00000242208	NM_002192.2	162	Ccc/Tcc	3/3	1	2	FACETS	0.866	0.785	0.951	0.866	0.785	0.951	CLONAL	1	TRUE	1	0.48854665247789	2		471	572	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55219011	55219011	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	76	308	0	ENST00000275493.2:c.584C>T	p.Pro195Leu	p.P195L	ENST00000275493	NM_005228.3	195	cCc/cTc	5/28	1	2	FACETS	0.784	0.691	0.882	0.784	0.691	0.882	SUBCLONAL	1	TRUE	1	0.48854665247789	2		308	397	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92247472	92247472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	75	258	0	ENST00000265734.4:c.748C>T	p.Pro250Ser	p.P250S	ENST00000265734	NM_001259.6	250	Ccc/Tcc	7/8	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.48854665247789	2		258	288	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545696	106545696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	90	496	0	ENST00000359195.3:c.3173G>A	p.Gly1058Glu	p.G1058E	ENST00000359195	NM_002649.2	1058	gGg/gAg	11/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.48854665247789	2		496	348	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891130	151891130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	98	378	0	ENST00000262189.6:c.4624C>T	p.Pro1542Ser	p.P1542S	ENST00000262189	NM_170606.2	1542	Ccc/Tcc	31/59	1	2	FACETS	0.908	0.814	1	0.908	0.814	1	CLONAL	1	TRUE	1	0.48854665247789	2		378	442	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371875	55371875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769172253	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	91	133	0	ENST00000297316.4:c.565C>T	p.Pro189Ser	p.P189S	ENST00000297316	NM_022454.3	189	Ccc/Tcc	2/2	0.476396734679105	3	FACETS	1	0.922	1	1	0.922	1	CLONAL	2	TRUE	1	0.48854665247789	3		133	227	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866531	56866531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	325	624	1	ENST00000519728.1:c.778G>A	p.Glu260Lys	p.E260K	ENST00000519728	NM_002350.3	260	Gaa/Aaa	8/13	0.476396734679105	3	FACETS	0.938	0.89	0.988	0.938	0.89	0.988	CLONAL	2	TRUE	1	0.48854665247789	3		625	882	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030835	69030835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	184	307	1	ENST00000288368.4:c.3377G>A	p.Ser1126Asn	p.S1126N	ENST00000288368	NM_024870.2	1126	aGc/aAc	27/40	0.476396734679105	3	FACETS	0.978	0.912	1	0.978	0.912	1	CLONAL	2	TRUE	1	0.48854665247789	3		308	479	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465564	8465564	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	78	510	0	ENST00000356435.5:c.3616G>A	p.Gly1206Arg	p.G1206R	ENST00000356435		1206	Ggg/Agg	21/35	1	2	FACETS	0.915	0.81	1	0.915	0.81	1	CLONAL	1	TRUE	1	0.48854665247789	2		510	349	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518346	8518346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	68	314	1	ENST00000356435.5:c.1045G>A	p.Glu349Lys	p.E349K	ENST00000356435		349	Gag/Aag	10/35	1	2	FACETS	0.901	0.79	1	0.901	0.79	1	CLONAL	1	TRUE	1	0.48854665247789	2		315	309	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410718	63410718	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	122	657	0	ENST00000330258.3:c.2449G>A	p.Asp817Asn	p.D817N	ENST00000330258	NM_152424.3	817	Gat/Aat	2/2	1	2	FACETS	0.925	0.84	1	0.925	0.84	1	CLONAL	1	TRUE	1	0.48854665247789	2		657	540	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938502	76938502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	64	529	0	ENST00000373344.5:c.2246C>T	p.Ser749Phe	p.S749F	ENST00000373344	NM_000489.3	749	tCt/tTt	9/35	1	2	FACETS	0.967	0.846	1	0.967	0.846	1	CLONAL	1	TRUE	1	0.48854665247789	2		529	271	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661764	227661764	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	149	630	0	ENST00000305123.5:c.1691G>C	p.Ser564Thr	p.S564T	ENST00000305123	NM_005544.2	564	aGt/aCt	1/2	0.608513381196103	3	FACETS	1	0.927	1	0.506	0.463	0.55	CLONAL	1	TRUE	1	0.609174122043303	3		630	631	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983138	111983138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037443-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	17	370	0	ENST00000368678.4:c.1409G>A	p.Arg470Gln	p.R470Q	ENST00000368678		470	cGg/cAg	13/13	0.609174122043303	1	FACETS	0.167	0.124	0.217	0.167	0.124	0.217	SUBCLONAL	1	TRUE	0	0.609174122043303	1		370	233	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0037493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	118	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.818	0.744	0.894	0.818	0.744	0.894	CLONAL	1	TRUE	1	0.730770021073487	2		288	395	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149242	119149242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779039234	NA	P-0037528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	28	603	0	ENST00000264033.4:c.1250C>T	p.Pro417Leu	p.P417L	ENST00000264033	NM_005188.3	417	cCt/cTt	9/16	1	2	FACETS	0.799	0.638	0.983	0.799	0.638	0.983	CLONAL	1	TRUE	1	0.16	2		603	438	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs79184941	NA	P-0037528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	11	346	0	ENST00000358487.5:c.755C>T	p.Ser252Leu	p.S252L	ENST00000358487	NM_000141.4	252	tCg/tTg	7/18	1	2	FACETS	0.59	0.407	0.818	0.59	0.407	0.818	SUBCLONAL	1	TRUE	1	0.16	2		346	233	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979257	93979257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	19	388	0	ENST00000369303.4:c.1571G>A	p.Gly524Glu	p.G524E	ENST00000369303	NM_004440.3	524	gGa/gAa	7/17	1	2	FACETS	0.794	0.603	1	0.794	0.603	1	CLONAL	1	TRUE	1	0.16	2		388	299	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961812	55961812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	52	508	1	ENST00000263923.4:c.2749G>A	p.Glu917Lys	p.E917K	ENST00000263923	NM_002253.2	917	Gaa/Aaa	20/30	1	2	FACETS	0.858	0.733	0.994	1	0.971	1	CLONAL	2	TRUE	1	0.16	2		509	379	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858064	9858064	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	33	680	0	ENST00000330684.3:c.3337C>T	p.Pro1113Ser	p.P1113S	ENST00000330684	NM_001134407.1	1113	Cct/Tct	13/13	1	2	FACETS	0.971	0.79	1	0.971	0.79	1	CLONAL	1	TRUE	1	0.16	2		680	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579519	7579520	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0037528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	68	727	0	ENST00000269305.4:c.167_168del	p.Glu56GlyfsTer6	p.E56Gfs*6	ENST00000269305	NM_001126112.2	56	gAA/g	4/11	1	2	FACETS	0.85	0.741	0.967	1	0.977	1	CLONAL	2	TRUE	1	0.16	2		727	500	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995359	15995359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	51	442	0	ENST00000268712.3:c.2834C>T	p.Pro945Leu	p.P945L	ENST00000268712	NM_006311.3	945	cCa/cTa	22/46	1	2	FACETS	0.932	0.796	1	1	0.973	1	CLONAL	2	TRUE	1	0.16	2		442	342	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321487	62321487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	29	743	0	ENST00000360203.5:c.2189C>T	p.Pro730Leu	p.P730L	ENST00000360203	NM_001283009.1	730	cCc/cTc	25/35	1	2	FACETS	0.729	0.584	0.895	0.729	0.584	0.895	SUBCLONAL	1	TRUE	1	0.16	2		743	497	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93953224	93953224	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	32	601	0	ENST00000369303.4:c.2917C>T	p.His973Tyr	p.H973Y	ENST00000369303	NM_004440.3	973	Cat/Tat	17/17	1	2	FACETS	0.875	0.71	1	0.875	0.71	1	CLONAL	1	TRUE	1	0.16	2		601	457	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938866	76938866	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	27	753	0	ENST00000373344.5:c.1882G>T	p.Gly628Ter	p.G628*	ENST00000373344	NM_000489.3	628	Gga/Tga	9/35	0.143797368332131	1	FACETS	0.61	0.484	0.754	0.61	0.484	0.754	SUBCLONAL	1	TRUE	0	0.16	1		753	509	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394449	162394449	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	267	196	0	ENST00000366898.1:c.619G>A	p.Glu207Lys	p.E207K	ENST00000366898	NM_004562.2	207	Gaa/Aaa	6/12	0.800718072007224	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.800718072007224	1		196	387	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	689	248	1				ENST00000310581	NM_198253.2	-/1132			0.583613754947374	6	FACETS	0.942	0.919	0.964	0.942	0.919	0.964	CLONAL	5	TRUE	1	0.800718072007224	6		249	951	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940120	31940120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	417	680	0	ENST00000375333.2:c.262G>A	p.Glu88Lys	p.E88K	ENST00000375333	NM_032454.1	88	Gaa/Aaa	2/8	0.781128697387995	3	FACETS	0.922	0.876	0.969	0.461	0.438	0.485	CLONAL	1	TRUE	1	0.800718072007224	3		680	1582	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149436936	149436936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	347	627	0	ENST00000286301.3:c.2233G>A	p.Glu745Lys	p.E745K	ENST00000286301	NM_005211.3	745	Gag/Aag	17/22	1	2	FACETS	0.913	0.867	0.96	0.913	0.867	0.96	CLONAL	1	TRUE	1	0.800718072007224	2		627	949	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059260	27059260	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	410	547	0	ENST00000324856.7:c.1897C>T	p.Gln633Ter	p.Q633*	ENST00000324856	NM_006015.4	633	Cag/Tag	4/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.800718072007224	2		547	942	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245858	46245858	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	218	443	0	ENST00000334344.6:c.3952C>T	p.Gln1318Ter	p.Q1318*	ENST00000334344	NM_152641.2	1318	Cag/Tag	15/21	1	2	FACETS	0.911	0.853	0.969	0.911	0.853	0.969	CLONAL	1	TRUE	1	0.800718072007224	2		443	598	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115012	3115012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555702147	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	793	924	3	ENST00000078429.4:c.547C>T	p.Arg183Cys	p.R183C	ENST00000078429	NM_002067.2	183	Cgc/Tgc	4/7	0.486517012352156	3	FACETS	0.917	0.89	0.944	0.917	0.89	0.944	CLONAL	2	TRUE	1	0.800718072007224	3		927	1512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578217	7578217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	437	762	0	ENST00000269305.4:c.632C>T	p.Thr211Ile	p.T211I	ENST00000269305	NM_001126112.2	211	aCt/aTt	6/11	1	2	FACETS	0.964	0.921	1	0.964	0.921	1	CLONAL	1	TRUE	1	0.800718072007224	2		762	1132	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547019	9547019	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	199	309	0	ENST00000353224.5:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000353224	NM_177990.2	335	Cga/Tga	5/10	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.800718072007224	2		309	401	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861245	57861245	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1460787785	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	335	562	0	ENST00000228682.2:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000228682	NM_005269.2	348	Cga/Tga	9/12	1	2	FACETS	0.973	0.924	1	0.973	0.924	1	CLONAL	1	TRUE	1	0.800718072007224	2		562	860	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953195	81953195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs187454354	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	292	391	1	ENST00000359376.3:c.2161G>A	p.Glu721Lys	p.E721K	ENST00000359376	NM_002661.3	721	Gag/Aag	20/33	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.800718072007224	2		392	725	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246058	41246058	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555591693	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	385	819	0	ENST00000357654.3:c.1490C>T	p.Pro497Leu	p.P497L	ENST00000357654	NM_007294.3	497	cCc/cTc	10/23	0.784194163984391	3	FACETS	0.98	0.93	1	0.49	0.465	0.516	CLONAL	1	TRUE	1	0.800718072007224	3		819	1374	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670153	29670153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1135402900	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	238	411	0	ENST00000356175.3:c.7126G>A	p.Gly2376Arg	p.G2376R	ENST00000356175	NM_000267.3	2376	Ggg/Agg	47/57	1	2	FACETS	0.978	0.919	1	0.978	0.919	1	CLONAL	1	TRUE	1	0.800718072007224	2		411	608	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273995	10273995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778499284	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	528	843	1	ENST00000330684.3:c.274G>A	p.Gly92Arg	p.G92R	ENST00000330684	NM_001134407.1	92	Ggg/Agg	2/13	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.800718072007224	2		844	1288	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471052	25471052	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	618	857	0	ENST00000264709.3:c.709C>T	p.Gln237Ter	p.Q237*	ENST00000264709	NM_175629.2	237	Cag/Tag	7/23	0.143252471604244	3	FACETS	0.788	0.76	0.817	0.788	0.76	0.817	INDETERMINATE	2	TRUE	1	0.800718072007224	3		857	1371	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3824672	3824672	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776898396	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	352	560	1	ENST00000262367.5:c.2181G>A	p.Met727Ile	p.M727I	ENST00000262367	NM_004380.2	727	atG/atA	12/31	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.800718072007224	2		561	874	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274824	123274824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	35	527	0	ENST00000358487.5:c.1094G>A	p.Arg365Lys	p.R365K	ENST00000358487	NM_000141.4	365	aGa/aAa	9/18	0.741633838744027	1	FACETS	0.104	0.085	0.126	0.104	0.085	0.126	SUBCLONAL	1	TRUE	0	0.800718072007224	1		527	502	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998952	100998952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	288	479	0	ENST00000325455.5:c.850G>A	p.Glu284Lys	p.E284K	ENST00000325455	NM_001202474.3	284	Gag/Aag	1/8	0.800718072007224	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.800718072007224	1		479	427	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344885	118344885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	254	337	0	ENST00000534358.1:c.3011C>T	p.Ser1004Phe	p.S1004F	ENST00000534358	NM_005933.3	1004	tCc/tTc	3/36	0.800718072007224	1	FACETS	0.993	0.95	1	0.993	0.95	1	CLONAL	1	TRUE	0	0.800718072007224	1		337	383	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376322	118376322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	363	591	0	ENST00000534358.1:c.9715C>T	p.Pro3239Ser	p.P3239S	ENST00000534358	NM_005933.3	3239	Ccc/Tcc	27/36	0.800718072007224	1	FACETS	0.969	0.933	1	0.969	0.933	1	CLONAL	1	TRUE	0	0.800718072007224	1		591	561	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245006	46245006	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	430	640	0	ENST00000334344.6:c.3100C>T	p.Gln1034Ter	p.Q1034*	ENST00000334344	NM_152641.2	1034	Caa/Taa	15/21	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.800718072007224	2		640	996	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446487	49446487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756036854	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	271	440	0	ENST00000301067.7:c.1118C>T	p.Ser373Leu	p.S373L	ENST00000301067	NM_003482.3	373	tCa/tTa	9/54	1	2	FACETS	0.926	0.873	0.979	0.926	0.873	0.979	CLONAL	1	TRUE	1	0.800718072007224	2		440	731	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622469	28622469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs750134667	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	301	645	0	ENST00000241453.7:c.1148G>A	p.Trp383Ter	p.W383*	ENST00000241453	NM_004119.2	383	tGg/tAg	9/24	1	2	FACETS	0.875	0.827	0.924	0.875	0.827	0.924	CLONAL	1	TRUE	1	0.800718072007224	2		645	859	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774125	66774125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759605592	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	606	1019	1	ENST00000307102.5:c.601C>T	p.Arg201Cys	p.R201C	ENST00000307102	NM_002755.3	201	Cgt/Tgt	6/11	1	2	FACETS	0.98	0.943	1	0.98	0.943	1	CLONAL	1	TRUE	1	0.800718072007224	2		1020	1545	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81973550	81973550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	378	665	0	ENST00000359376.3:c.3367G>A	p.Glu1123Lys	p.E1123K	ENST00000359376	NM_002661.3	1123	Gaa/Aaa	30/33	1	2	FACETS	0.914	0.87	0.959	0.914	0.87	0.959	CLONAL	1	TRUE	1	0.800718072007224	2		665	1033	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654616	29654616	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	186	350	0	ENST00000356175.3:c.5305G>T	p.Glu1769Ter	p.E1769*	ENST00000356175	NM_000267.3	1769	Gaa/Taa	37/57	1	2	FACETS	0.878	0.817	0.94	0.878	0.817	0.94	CLONAL	1	TRUE	1	0.800718072007224	2		350	529	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883218	37883218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	765	683	1	ENST00000269571.5:c.3121G>A	p.Gly1041Ser	p.G1041S	ENST00000269571		1041	Ggc/Agc	25/27	0.784194163984391	3	FACETS	0.891	0.864	0.918	0.891	0.864	0.918	CLONAL	2	TRUE	1	0.800718072007224	3		684	1502	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143096	7143096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	500	506	0	ENST00000302850.5:c.2273C>T	p.Ser758Phe	p.S758F	ENST00000302850	NM_000208.2	758	tCt/tTt	12/22	0.486517012352156	3	FACETS	0.86	0.827	0.893	0.86	0.827	0.893	CLONAL	2	TRUE	1	0.800718072007224	3		506	1017	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220973	36220973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	372	521	1	ENST00000222270.7:c.5023C>T	p.Gln1675Ter	p.Q1675*	ENST00000222270	NM_014727.1	1675	Cag/Tag	23/37	1	2	FACETS	0.972	0.925	1	0.972	0.925	1	CLONAL	1	TRUE	1	0.800718072007224	2		522	956	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919743	50919743	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs897259743	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	452	691	0	ENST00000440232.2:c.2911G>A	p.Glu971Lys	p.E971K	ENST00000440232	NM_002691.3	971	Gag/Aag	23/27	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.800718072007224	2		691	1104	SUCCESS
ALK	238	MSKCC	GRCh37	2	29497988	29497988	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	443	597	0	ENST00000389048.3:c.2018A>G	p.Gln673Arg	p.Q673R	ENST00000389048	NM_004304.4	673	cAg/cGg	11/29	0.143252471604244	3	FACETS	1	0.996	1	0.701	0.67	0.731	INDETERMINATE	1	TRUE	1	0.800718072007224	3		597	1106	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155815	106155815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	311	540	0	ENST00000380013.4:c.716C>T	p.Ser239Phe	p.S239F	ENST00000380013	NM_001127208.2	239	tCc/tTc	3/11	1	2	FACETS	0.967	0.917	1	0.967	0.917	1	CLONAL	1	TRUE	1	0.800718072007224	2		540	803	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539321	187539321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	357	586	0	ENST00000441802.2:c.8419C>T	p.Pro2807Ser	p.P2807S	ENST00000441802	NM_005245.3	2807	Ccg/Tcg	10/27	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.800718072007224	2		586	879	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294165	1294165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	1716	688	0	ENST00000310581.5:c.836C>T	p.Ala279Val	p.A279V	ENST00000310581	NM_198253.2	279	gCc/gTc	2/16	0.583613754947374	6	FACETS	0.953	0.938	0.967	0.953	0.938	0.967	CLONAL	5	TRUE	1	0.800718072007224	6		688	2341	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295200	1295200	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1271046482	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	99	184	0				ENST00000310581	NM_198253.2	-/1132			0.583613754947374	6	FACETS	1	0.894	1	0.2	0.178	0.223	CLONAL	1	TRUE	1	0.800718072007224	6		184	643	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286925	33286925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	885	784	0	ENST00000374542.5:c.2012C>T	p.Ser671Phe	p.S671F	ENST00000374542	NM_001141970.1	671	tCc/tTc	7/8	0.781128697387995	3	FACETS	0.987	0.961	1	0.987	0.961	1	CLONAL	2	TRUE	1	0.800718072007224	3		784	1568	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6045603	6045603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	262	341	1	ENST00000265849.7:c.83C>T	p.Ser28Phe	p.S28F	ENST00000265849	NM_000535.5	28	tCt/tTt	2/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.800718072007224	2		342	607	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729933	41729933	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111379520	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	450	791	0	ENST00000242208.4:c.596G>A	p.Gly199Glu	p.G199E	ENST00000242208	NM_002192.2	199	gGg/gAg	3/3	1	2	FACETS	0.981	0.938	1	0.981	0.938	1	CLONAL	1	TRUE	1	0.800718072007224	2		791	1146	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467645	50467645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773981346	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	250	397	0	ENST00000331340.3:c.880G>A	p.Asp294Asn	p.D294N	ENST00000331340	NM_006060.4	294	Gac/Aac	8/8	1	2	FACETS	0.977	0.92	1	0.977	0.92	1	CLONAL	1	TRUE	1	0.800718072007224	2		397	639	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341964	8341964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1287979283	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	247	457	0	ENST00000356435.5:c.4676G>A	p.Arg1559Gln	p.R1559Q	ENST00000356435		1559	cGg/cAg	29/35	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.800718072007224	2		457	605	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781158	135781158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	417	749	3	ENST00000298552.3:c.1807C>T	p.Pro603Ser	p.P603S	ENST00000298552	NM_001162426.1	603	Ccg/Tcg	15/23	0.800718072007224	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.800718072007224	1		752	619	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347294	70347295	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0037606-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	367	581	1	ENST00000374080.3:c.2958_2959delinsAT	p.Asn987Tyr	p.N987Y	ENST00000374080		986	aaGAac/aaATac	21/45	1	2	FACETS	0.967	0.92	1	0.967	0.92	1	CLONAL	1	TRUE	1	0.800718072007224	2		582	948	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0037685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	54	454	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	1	2	FACETS	0.772	0.657	0.898	0.772	0.657	0.898	SUBCLONAL	1	TRUE	1	0.15	2		454	933	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0037685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	32	480	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.518	0.419	0.632	0.518	0.419	0.632	SUBCLONAL	1	TRUE	1	0.15	2		480	823	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88428945	88428945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	15	173	0	ENST00000360948.2:c.2155G>A	p.Asp719Asn	p.D719N	ENST00000360948	NM_001012338.2	719	Gat/Aat	17/19	1	2	FACETS	0.685	0.5	0.907	0.685	0.5	0.907	SUBCLONAL	1	TRUE	1	0.15	2		173	292	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0037685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	45	411	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.761	0.638	0.899	0.761	0.638	0.899	SUBCLONAL	1	TRUE	1	0.15	2		411	788	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770824	59770824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45572934	NA	P-0037685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	36	276	0	ENST00000259008.2:c.2542C>T	p.Arg848Cys	p.R848C	ENST00000259008	NM_032043.2	848	Cgc/Tgc	18/20	1	2	FACETS	0.996	0.818	1	0.996	0.818	1	CLONAL	1	TRUE	1	0.15	2		276	482	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417634	139417634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749786734	NA	P-0037685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	49	499	1	ENST00000277541.6:c.410C>T	p.Ser137Leu	p.S137L	ENST00000277541	NM_017617.3	137	tCg/tTg	4/34	1	2	FACETS	0.829	0.7	0.972	0.829	0.7	0.972	CLONAL	1	TRUE	1	0.15	2		500	788	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933350	39933350	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	48	271	0	ENST00000378444.4:c.1249G>C	p.Asp417His	p.D417H	ENST00000378444	NM_001123385.1	417	Gac/Cac	4/15	1	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.15	1		271	440	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388640	31388640	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0037685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	30	338	0	ENST00000328111.2:c.1906-1G>T		p.X636_splice	ENST00000328111	NM_006892.3	636			1	2	FACETS	0.709	0.57	0.868	0.709	0.57	0.868	SUBCLONAL	1	TRUE	1	0.15	2		338	564	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045670	26045670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	14	143	0	ENST00000540144.1:c.32C>T	p.Ser11Phe	p.S11F	ENST00000540144	NM_003531.2	11	tCt/tTt	1/1	1	2	FACETS	0.721	0.521	0.963	0.721	0.521	0.963	CLONAL	1	TRUE	1	0.15	2		143	259	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561211	9561211	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	35	309	1	ENST00000353224.5:c.571G>A	p.Asp191Asn	p.D191N	ENST00000353224	NM_177990.2	191	Gat/Aat	4/10	1	2	FACETS	0.731	0.598	0.882	0.731	0.598	0.882	SUBCLONAL	1	TRUE	1	0.15	2		310	638	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478106	99478106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	32	279	0	ENST00000268035.6:c.3010G>A	p.Glu1004Lys	p.E1004K	ENST00000268035	NM_000875.3	1004	Gaa/Aaa	16/21	1	2	FACETS	0.847	0.686	1	0.847	0.686	1	CLONAL	1	TRUE	1	0.15	2		279	504	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798597	45798597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780087	NA	P-0037685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	43	448	0	ENST00000450313.1:c.497C>T	p.Ser166Phe	p.S166F	ENST00000450313	NM_012222.2	166	tCc/tTc	6/16	1	2	FACETS	0.705	0.588	0.836	0.705	0.588	0.836	SUBCLONAL	1	TRUE	1	0.15	2		448	813	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186825	11186825	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	31	262	0	ENST00000361445.4:c.6380C>T	p.Ser2127Phe	p.S2127F	ENST00000361445	NM_004958.3	2127	tCc/tTc	46/58	1	2	FACETS	0.749	0.604	0.913	0.749	0.604	0.913	CLONAL	1	TRUE	1	0.15	2		262	552	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980376	201980376	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752009282	NA	P-0037685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	58	534	1	ENST00000359651.3:c.112G>A	p.Asp38Asn	p.D38N	ENST00000359651		38	Gat/Aat	1/8	1	2	FACETS	0.881	0.755	1	0.881	0.755	1	CLONAL	1	TRUE	1	0.15	2		535	878	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287474	46287474	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	28	311	0	ENST00000334344.6:c.5333A>C	p.Asn1778Thr	p.N1778T	ENST00000334344	NM_152641.2	1778	aAt/aCt	20/21	1	2	FACETS	0.771	0.615	0.95	0.771	0.615	0.95	CLONAL	1	TRUE	1	0.15	2		311	484	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612228	1612251	+	inframe_deletion	In_Frame_Del	DEL	CAGGATGACCTGCACGGCCTGCTG	CAGGATGACCTGCACGGCCTGCTG	-	rs1250066379	NA	P-0037685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	30	358	0	ENST00000344749.5:c.1768_1791del	p.Gln590_Leu597del	p.Q590_L597del	ENST00000344749	NM_001136139.2	590	CAGCAGGCCGTGCAGGTCATCCTG/-	18/19	1	2	FACETS	0.693	0.557	0.848	0.693	0.557	0.848	SUBCLONAL	1	TRUE	1	0.15	2		358	577	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123705	11123705	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	41	442	0	ENST00000358026.2:c.2355G>T	p.Lys785Asn	p.K785N	ENST00000358026	NM_001128849.1	785	aaG/aaT	16/36	1	2	FACETS	0.715	0.593	0.85	0.715	0.593	0.85	SUBCLONAL	1	TRUE	1	0.15	2		442	765	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220898	36220898	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	16	172	0	ENST00000222270.7:c.4948A>C	p.Thr1650Pro	p.T1650P	ENST00000222270	NM_014727.1	1650	Acg/Ccg	23/37	1	2	FACETS	0.746	0.551	0.979	0.746	0.551	0.979	CLONAL	1	TRUE	1	0.15	2		172	286	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966463	25966463	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201545861	NA	P-0037685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	50	494	0	ENST00000435504.4:c.2743C>T	p.Pro915Ser	p.P915S	ENST00000435504		915	Cca/Tca	13/13	1	2	FACETS	0.701	0.593	0.821	0.701	0.593	0.821	SUBCLONAL	1	TRUE	1	0.15	2		494	951	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99179955	99179955	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	49	451	0	ENST00000074304.5:c.1898T>C	p.Leu633Pro	p.L633P	ENST00000074304	NM_001134224.1	633	cTg/cCg	19/26	1	2	FACETS	0.789	0.666	0.925	0.789	0.666	0.925	CLONAL	1	TRUE	1	0.15	2		451	828	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661386	227661386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	36	351	0	ENST00000305123.5:c.2069C>T	p.Pro690Leu	p.P690L	ENST00000305123	NM_005544.2	690	cCt/cTt	1/2	1	2	FACETS	0.725	0.594	0.872	0.725	0.594	0.872	SUBCLONAL	1	TRUE	1	0.15	2		351	662	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526169	189526169	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	93	385	0	ENST00000264731.3:c.433G>A	p.Ala145Thr	p.A145T	ENST00000264731	NM_003722.4	145	Gcg/Acg	4/14	1	2	FACETS	0.877	0.78	0.98	1	0.984	1	CLONAL	2	TRUE	1	0.15	2		385	707	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196976	106196976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs556077207	NA	P-0037685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	27	189	0	ENST00000380013.4:c.5309C>T	p.Pro1770Leu	p.P1770L	ENST00000380013	NM_001127208.2	1770	cCg/cTg	11/11	1	2	FACETS	0.989	0.787	1	0.989	0.787	1	CLONAL	1	TRUE	1	0.15	2		189	364	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249511	153249512	+	stop_gained	Nonsense_Mutation	DNP	CA	CA	AC	novel	NA	P-0037685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	29	374	0	ENST00000281708.4:c.1266_1267delinsGT	p.Gly423Ter	p.G423*	ENST00000281708	NM_033632.3	422	ggTGga/ggGTga	9/12	1	2	FACETS	0.569	0.455	0.7	0.569	0.455	0.7	SUBCLONAL	1	TRUE	1	0.15	2		374	679	SUCCESS
APC	324	MSKCC	GRCh37	5	112090591	112090591	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	20	161	0	ENST00000257430.4:c.4G>C	p.Ala2Pro	p.A2P	ENST00000257430	NM_000038.5	2	Gct/Cct	2/16	1	2	FACETS	0.907	0.694	1	0.907	0.694	1	CLONAL	1	TRUE	1	0.15	2		161	294	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706847	117706847	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	22	190	1	ENST00000368508.3:c.2303T>C	p.Val768Ala	p.V768A	ENST00000368508	NM_002944.2	768	gTg/gCg	15/43	1	2	FACETS	0.739	0.572	0.934	0.739	0.572	0.934	CLONAL	1	TRUE	1	0.15	2		191	397	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971194	21971194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561034503	NA	P-0037685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	23	203	0	ENST00000304494.5:c.164G>A	p.Gly55Asp	p.G55D	ENST00000304494	NM_000077.4	55	gGc/gAc	2/3	1	2	FACETS	0.921	0.718	1	0.921	0.718	1	CLONAL	1	TRUE	1	0.15	2		203	333	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152861508	152861508	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	54	140	0	ENST00000406277.2:c.244G>T	p.Glu82Ter	p.E82*	ENST00000406277	NM_152274.4	82	Gaa/Taa	4/7	1		FACETS		0.885	1				CLONAL	2	TRUE	0	0.15	1		140	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579360	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0037685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	30	425	0	ENST00000269305.4:c.327_328delinsAT	p.Phe109_Arg110delinsLeuCys	p.F109_R110delinsLC	ENST00000269305	NM_001126112.2	109	ttCCgt/ttATgt	4/11	1	2	FACETS	0.533	0.428	0.654	0.533	0.428	0.654	SUBCLONAL	1	TRUE	1	0.15	2		425	750	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0037749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	281	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.227161197293192	3	FACETS	0.969	0.915	1	0.646	0.61	0.683	INDETERMINATE	2	TRUE	0	0.482412989024069	3		288	746	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0037749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	123	248	1				ENST00000310581	NM_198253.2	-/1132			0.348118310859682	1	FACETS	0.718	0.652	0.787	0.718	0.652	0.787	SUBCLONAL	1	TRUE	0	0.482412989024069	1		249	539	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0037749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	312	454	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.482412989024069	2		454	1255	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543871	212543871	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1361402584	NA	P-0037749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	177	450	0	ENST00000342788.4:c.1528G>A	p.Asp510Asn	p.D510N	ENST00000342788	NM_005235.2	510	Gat/Aat	13/28	1	2	FACETS	0.946	0.873	1	0.946	0.873	1	CLONAL	1	TRUE	1	0.482412989024069	2		450	776	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940126	31940126	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	293	724	1	ENST00000375333.2:c.268C>T	p.Pro90Ser	p.P90S	ENST00000375333	NM_032454.1	90	Cct/Tct	2/8	1	2	FACETS	0.939	0.883	0.998	0.939	0.883	0.998	CLONAL	1	TRUE	1	0.482412989024069	2		725	1293	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037444	12037444	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs141938078	NA	P-0037749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	176	575	0	ENST00000396373.4:c.1075C>T	p.Arg359Ter	p.R359*	ENST00000396373	NM_001987.4	359	Cga/Tga	6/8	0.31330800085144	1	FACETS	0.679	0.626	0.734	0.679	0.626	0.734	SUBCLONAL	1	TRUE	0	0.482412989024069	1		575	815	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244613	41244613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80356970	NA	P-0037749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	149	663	0	ENST00000357654.3:c.2935C>T	p.Arg979Cys	p.R979C	ENST00000357654	NM_007294.3	979	Cgt/Tgt	10/23	1	2	FACETS	0.71	0.649	0.774	0.71	0.649	0.774	SUBCLONAL	1	TRUE	1	0.482412989024069	2		663	870	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911065	94911066	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0037749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	118	486	1	ENST00000536441.1:c.1064_1065delinsTT	p.Thr355Ile	p.T355I	ENST00000536441	NM_144665.3	355	aCC/aTT	8/10	1	2	FACETS	0.711	0.642	0.784	0.711	0.642	0.784	SUBCLONAL	1	TRUE	1	0.482412989024069	2		487	688	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920735	100920735	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	127	557	0	ENST00000325455.5:c.2413C>T	p.Pro805Ser	p.P805S	ENST00000325455	NM_001202474.3	805	Cca/Tca	6/8	1	2	FACETS	0.984	0.896	1	0.984	0.896	1	CLONAL	1	TRUE	1	0.482412989024069	2		557	535	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620118	21620118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	113	594	0	ENST00000382592.4:c.48del	p.Gln17SerfsTer10	p.Q17Sfs*10	ENST00000382592	NM_014572.2	16	cgG/cg	2/8	0.348118310859682	1	FACETS	0.412	0.371	0.457	0.412	0.371	0.457	SUBCLONAL	1	TRUE	0	0.482412989024069	1		594	862	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25459858	25459858	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879540431	NA	P-0037749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	254	678	1	ENST00000264709.3:c.2425G>A	p.Val809Met	p.V809M	ENST00000264709	NM_175629.2	809	Gtg/Atg	21/23	1	2	FACETS	0.984	0.921	1	0.984	0.921	1	CLONAL	1	TRUE	1	0.482412989024069	2		679	1070	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62318996	62318996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	218	632	0	ENST00000360203.5:c.1354G>A	p.Val452Met	p.V452M	ENST00000360203	NM_001283009.1	452	Gtg/Atg	17/35	1	2	FACETS	0.879	0.818	0.943	0.879	0.818	0.943	CLONAL	1	TRUE	1	0.482412989024069	2		632	1028	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176639138	176639138	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	109	544	1	ENST00000439151.2:c.3738C>A	p.Asp1246Glu	p.D1246E	ENST00000439151	NM_022455.4	1246	gaC/gaA	5/23	0.348118310859682	1	FACETS	0.454	0.408	0.503	0.454	0.408	0.503	SUBCLONAL	1	TRUE	0	0.482412989024069	1		545	755	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163834	32163834	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	192	567	0	ENST00000375023.3:c.5392C>T	p.Gln1798Ter	p.Q1798*	ENST00000375023	NM_004557.3	1798	Cag/Tag	30/30	1	2	FACETS	0.928	0.859	0.999	0.928	0.859	0.999	CLONAL	1	TRUE	1	0.482412989024069	2		567	858	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528349	157528349	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1554237887	NA	P-0037749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	298	727	0	ENST00000346085.5:c.6074T>A	p.Leu2025Ter	p.L2025*	ENST00000346085	NM_020732.3	2025	tTg/tAg	20/20	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.482412989024069	2		727	1199	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921533	178921533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	47	316	0	ENST00000263967.3:c.1015C>T	p.Leu339Phe	p.L339F	ENST00000263967	NM_006218.2	339	Ctt/Ttt	5/21	1	2	FACETS	0.901	0.763	1	0.901	0.763	1	CLONAL	1	TRUE	1	0.292308689298233	2		316	357	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	39	151	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.836	1	1	0.836	1	CLONAL	1	TRUE	1	0.292308689298233	2		151	266	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	88	480	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.292308689298233	1	FACETS	0.938	0.833	1	0.938	0.833	1	CLONAL	1	TRUE	0	0.292308689298233	1		480	548	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2214564	2214564	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200661860	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	92	837	0	ENST00000398665.3:c.1892C>T	p.Ser631Leu	p.S631L	ENST00000398665	NM_032482.2	631	tCg/tTg	19/28	1	2	FACETS	0.962	0.856	1	0.962	0.856	1	CLONAL	1	TRUE	1	0.292308689298233	2		837	654	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945092	38945092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769767383	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	49	359	0	ENST00000357387.3:c.4712C>T	p.Ser1571Leu	p.S1571L	ENST00000357387	NM_152756.3	1571	tCg/tTg	35/38	1	2	FACETS	0.78	0.661	0.909	0.78	0.661	0.909	CLONAL	1	TRUE	1	0.292308689298233	2		359	430	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918761	32918761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1239798218	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	22	198	0	ENST00000380152.3:c.6908C>T	p.Ser2303Phe	p.S2303F	ENST00000380152		2303	tCc/tTc	12/27	1	2	FACETS	0.509	0.394	0.641	0.509	0.394	0.641	SUBCLONAL	1	TRUE	1	0.292308689298233	2		198	296	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88428945	88428945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	33	173	0	ENST00000360948.2:c.2155G>A	p.Asp719Asn	p.D719N	ENST00000360948	NM_001012338.2	719	Gat/Aat	17/19	1	2	FACETS	0.586	0.478	0.709	0.586	0.478	0.709	SUBCLONAL	1	TRUE	1	0.292308689298233	2		173	385	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522569	106522569	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746783339	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	29	321	0	ENST00000359195.3:c.2546G>A	p.Arg849Gln	p.R849Q	ENST00000359195	NM_002649.2	849	cGa/cAa	7/11	1	2	FACETS	0.535	0.429	0.655	0.535	0.429	0.655	SUBCLONAL	1	TRUE	1	0.292308689298233	2		321	371	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412278	63412278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	96	911	1	ENST00000330258.3:c.889G>A	p.Glu297Lys	p.E297K	ENST00000330258	NM_152424.3	297	Gag/Aag	2/2	0.292308689298233	1	FACETS	0.915	0.816	1	0.915	0.816	1	CLONAL	1	TRUE	0	0.292308689298233	1		912	613	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497196	149497196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	28	536	2	ENST00000261799.4:c.3122C>T	p.Ser1041Phe	p.S1041F	ENST00000261799	NM_002609.3	1041	tCc/tTc	22/23	0.292308689298233	0	FACETS	0.292	0.232	0.359			1	SUBCLONAL	1	TRUE	0	0.292308689298233	0		538	465	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556852	29556852	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	58	505	0	ENST00000356175.3:c.2851-1G>A		p.X951_splice	ENST00000356175	NM_000267.3	951			0.292308689298233	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.292308689298233	1		505	315	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974679	21974679	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs864622636	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	69	468	2	ENST00000304494.5:c.148C>T	p.Gln50Ter	p.Q50*	ENST00000304494	NM_000077.4	50	Cag/Tag	1/3	0.292308689298233	1	FACETS	0.922	0.806	1	0.922	0.806	1	CLONAL	1	TRUE	0	0.292308689298233	1		470	437	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499711	8499711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	105	478	0	ENST00000356435.5:c.2258G>A	p.Arg753Lys	p.R753K	ENST00000356435		753	aGg/aAg	14/35	0.292308689298233	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.292308689298233	1		478	503	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2492096	2492097	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs772088410	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	89	790	0	ENST00000355716.4:c.500dup	p.Thr169AspfsTer65	p.T169Dfs*65	ENST00000355716	NM_003820.2	165	tgc/tgCc	5/8	1	2	FACETS	0.899	0.798	1	0.899	0.798	1	CLONAL	1	TRUE	1	0.292308689298233	2		790	677	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945795	17945795	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	38	706	1	ENST00000458235.1:c.2065C>T	p.Pro689Ser	p.P689S	ENST00000458235	NM_000215.3	689	Ccc/Tcc	16/24	1	2	FACETS	0.455	0.375	0.544	0.455	0.375	0.544	SUBCLONAL	1	TRUE	1	0.292308689298233	2		707	572	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481408	140481408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867748453	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	31	377	0	ENST00000288602.6:c.1400C>T	p.Ser467Leu	p.S467L	ENST00000288602	NM_004333.4	467	tCa/tTa	11/18	1	2	FACETS	0.485	0.392	0.591	0.485	0.392	0.591	SUBCLONAL	1	TRUE	1	0.292308689298233	2		377	437	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120501	94120501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760168204	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	54	404	0	ENST00000369303.4:c.550C>T	p.Leu184Phe	p.L184F	ENST00000369303	NM_004440.3	184	Ctt/Ttt	3/17	0.292308689298233	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.292308689298233	1		404	290	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892263	9892263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	20	669	0	ENST00000330684.3:c.2227G>A	p.Glu743Lys	p.E743K	ENST00000330684	NM_001134407.1	743	Gaa/Aaa	11/13	0.292308689298233	1	FACETS	0.339	0.258	0.433	0.339	0.258	0.433	SUBCLONAL	1	TRUE	0	0.292308689298233	1		669	345	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445451	49445451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	107	658	0	ENST00000301067.7:c.2015C>T	p.Ser672Phe	p.S672F	ENST00000301067	NM_003482.3	672	tCc/tTc	10/54	1	2	FACETS	0.922	0.827	1	0.922	0.827	1	CLONAL	1	TRUE	1	0.292308689298233	2		658	794	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819620	81819620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	54	502	0	ENST00000359376.3:c.26C>T	p.Ser9Phe	p.S9F	ENST00000359376	NM_002661.3	9	tCc/tTc	2/33	0.292308689298233	1	FACETS	0.693	0.593	0.803	0.693	0.593	0.803	SUBCLONAL	1	TRUE	0	0.292308689298233	1		502	455	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046482	69046482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	52	464	0	ENST00000288368.4:c.3955C>T	p.His1319Tyr	p.H1319Y	ENST00000288368	NM_024870.2	1319	Cac/Tac	32/40	1	2	FACETS	0.639	0.544	0.743	0.639	0.544	0.743	SUBCLONAL	1	TRUE	1	0.292308689298233	2		464	557	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88678962	88678962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	18	227	0	ENST00000372037.3:c.902C>T	p.Ser301Phe	p.S301F	ENST00000372037	NM_004329.2	301	tCc/tTc	10/13	1	2	FACETS	0.465	0.35	0.6	0.465	0.35	0.6	SUBCLONAL	1	TRUE	1	0.292308689298233	2		227	265	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972915	68972915	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs201372935	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	19	310	0	ENST00000288368.4:c.1240G>A	p.Glu414Lys	p.E414K	ENST00000288368	NM_024870.2	414	Gaa/Aaa	11/40	1	2	FACETS	0.372	0.282	0.479	0.372	0.282	0.479	SUBCLONAL	1	TRUE	1	0.292308689298233	2		310	349	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450987	70450987	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	43	613	0	ENST00000373644.4:c.5827C>T	p.Pro1943Ser	p.P1943S	ENST00000373644	NM_030625.2	1943	Ccc/Tcc	12/12	1	2	FACETS	0.673	0.564	0.794	0.673	0.564	0.794	SUBCLONAL	1	TRUE	1	0.292308689298233	2		613	437	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926252	112926252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	36	443	1	ENST00000351677.2:c.1385G>A	p.Gly462Glu	p.G462E	ENST00000351677	NM_002834.3	462	gGa/gAa	12/16	0.292308689298233	1	FACETS	0.435	0.357	0.523	0.435	0.357	0.523	SUBCLONAL	1	TRUE	0	0.292308689298233	1		444	483	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226355	133226355	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	44	902	0	ENST00000320574.5:c.3703C>T	p.Leu1235Phe	p.L1235F	ENST00000320574	NM_006231.2	1235	Ctt/Ttt	30/49	0.292308689298233	1	FACETS	0.397	0.332	0.469	0.397	0.332	0.469	SUBCLONAL	1	TRUE	0	0.292308689298233	1		902	648	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967560	26967560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	52	343	0	ENST00000381527.3:c.703C>T	p.His235Tyr	p.H235Y	ENST00000381527	NM_001260.1	235	Cac/Tac	7/13	1	2	FACETS	0.772	0.658	0.896	0.772	0.658	0.896	SUBCLONAL	1	TRUE	1	0.292308689298233	2		343	461	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28631584	28631584	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	50	286	0	ENST00000241453.7:c.384G>A	p.Met128Ile	p.M128I	ENST00000241453	NM_004119.2	128	atG/atA	4/24	1	2	FACETS	0.994	0.847	1	0.994	0.847	1	CLONAL	1	TRUE	1	0.292308689298233	2		286	344	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66735633	66735633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	36	310	0	ENST00000307102.5:c.454G>A	p.Asp152Asn	p.D152N	ENST00000307102	NM_002755.3	152	Gat/Aat	4/11	1	2	FACETS	0.547	0.45	0.657	0.547	0.45	0.657	SUBCLONAL	1	TRUE	1	0.292308689298233	2		310	450	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354594	91354594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	50	422	0	ENST00000355112.3:c.4034C>T	p.Ser1345Phe	p.S1345F	ENST00000355112	NM_000057.2	1345	tCt/tTt	21/22	1	2	FACETS	0.72	0.612	0.839	0.72	0.612	0.839	SUBCLONAL	1	TRUE	1	0.292308689298233	2		422	475	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857755	9857755	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	28	481	0	ENST00000330684.3:c.3646A>C	p.Ser1216Arg	p.S1216R	ENST00000330684	NM_001134407.1	1216	Agc/Cgc	13/13	0.292308689298233	1	FACETS	0.395	0.315	0.486	0.395	0.315	0.486	SUBCLONAL	1	TRUE	0	0.292308689298233	1		481	414	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819622	81819622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	38	502	0	ENST00000359376.3:c.28C>T	p.Leu10Phe	p.L10F	ENST00000359376	NM_002661.3	10	Ctt/Ttt	2/33	0.292308689298233	1	FACETS	0.478	0.395	0.571	0.478	0.395	0.571	SUBCLONAL	1	TRUE	0	0.292308689298233	1		502	464	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686919	37686919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	57	585	0	ENST00000447079.4:c.3823C>T	p.Pro1275Ser	p.P1275S	ENST00000447079	NM_015083.1	1275	Ccg/Tcg	14/14	0.292308689298233	1	FACETS	0.785	0.676	0.904	0.785	0.676	0.904	CLONAL	1	TRUE	0	0.292308689298233	1		585	424	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752455	55752455	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	94	905	2	ENST00000284073.2:c.913C>T	p.Gln305Ter	p.Q305*	ENST00000284073	NM_138962.2	305	Cag/Tag	12/14	1	2	FACETS	0.792	0.704	0.886	0.792	0.704	0.886	SUBCLONAL	1	TRUE	1	0.292308689298233	2		907	812	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853772	59853772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147755155	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	45	325	0	ENST00000259008.2:c.2087C>T	p.Pro696Leu	p.P696L	ENST00000259008	NM_032043.2	696	cCa/cTa	14/20	1	2	FACETS	0.768	0.646	0.901	0.768	0.646	0.901	CLONAL	1	TRUE	1	0.292308689298233	2		325	401	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976103	18976104	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	51	743	0	ENST00000262803.5:c.2863_2864delinsTT	p.Pro955Phe	p.P955F	ENST00000262803	NM_002911.3	955	CCt/TTt	21/24	1	2	FACETS	0.661	0.562	0.77	0.661	0.562	0.77	SUBCLONAL	1	TRUE	1	0.292308689298233	2		743	528	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216664	36216664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs558770050	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	76	800	1	ENST00000222270.7:c.3830C>T	p.Pro1277Leu	p.P1277L	ENST00000222270	NM_014727.1	1277	cCg/cTg	13/37	1	2	FACETS	0.772	0.677	0.874	0.772	0.677	0.874	SUBCLONAL	1	TRUE	1	0.292308689298233	2		801	674	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455218	29455218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1461504517	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	63	592	0	ENST00000389048.3:c.2584G>A	p.Glu862Lys	p.E862K	ENST00000389048	NM_004304.4	862	Gag/Aag	15/29	1	2	FACETS	0.845	0.732	0.968	0.845	0.732	0.968	CLONAL	1	TRUE	1	0.292308689298233	2		592	510	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560899	9560899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	59	456	0	ENST00000353224.5:c.883C>T	p.Pro295Ser	p.P295S	ENST00000353224	NM_177990.2	295	Ccg/Tcg	4/10	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.292308689298233	2		456	392	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735500	40735500	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	39	650	0	ENST00000373198.4:c.3373A>C	p.Asn1125His	p.N1125H	ENST00000373198	NM_133170.3	1125	Aat/Cat	25/32	1	2	FACETS	0.501	0.414	0.597	0.501	0.414	0.597	SUBCLONAL	1	TRUE	1	0.292308689298233	2		650	533	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47079248	47079248	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	64	480	0	ENST00000409792.3:c.7258C>T	p.Pro2420Ser	p.P2420S	ENST00000409792	NM_014159.6	2420	Cct/Tct	18/21	1	2	FACETS	0.948	0.823	1	0.948	0.823	1	CLONAL	1	TRUE	1	0.292308689298233	2		480	462	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143326468	143326468	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	37	263	0	ENST00000262992.4:c.146A>G	p.Asp49Gly	p.D49G	ENST00000262992	NM_001101669.1	49	gAt/gGt	4/24	1	2	FACETS	0.789	0.652	0.94	0.789	0.652	0.94	CLONAL	1	TRUE	1	0.292308689298233	2		263	321	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37141814	37141814	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	68	534	0	ENST00000373509.5:c.889C>T	p.Gln297Ter	p.Q297*	ENST00000373509	NM_002648.3	297	Cag/Tag	6/6	1	2	FACETS	0.883	0.769	1	0.883	0.769	1	CLONAL	1	TRUE	1	0.292308689298233	2		534	527	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104660	69104660	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	34	537	1	ENST00000288368.4:c.4504G>A	p.Ala1502Thr	p.A1502T	ENST00000288368	NM_024870.2	1502	Gct/Act	37/40	1	2	FACETS	0.375	0.306	0.454	0.375	0.306	0.454	SUBCLONAL	1	TRUE	1	0.292308689298233	2		538	620	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331706	8331706	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	56	420	0	ENST00000356435.5:c.5410C>T	p.Gln1804Ter	p.Q1804*	ENST00000356435		1804	Cag/Tag	33/35	0.292308689298233	1	FACETS	0.901	0.776	1	0.901	0.776	1	CLONAL	1	TRUE	0	0.292308689298233	1		420	363	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321391	1321391	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	29	423	0	ENST00000400841.2:c.364C>T	p.Pro122Ser	p.P122S	ENST00000400841		122	Ccg/Tcg	4/6	0.292308689298233	1	FACETS	0.517	0.415	0.632	0.517	0.415	0.632	SUBCLONAL	1	TRUE	0	0.292308689298233	1		423	328	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424501	47424501	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	60	593	0	ENST00000377045.4:c.421C>T	p.Pro141Ser	p.P141S	ENST00000377045	NM_001654.4	141	Ccc/Tcc	5/16	0.292308689298233	1	FACETS	0.833	0.72	0.955	0.833	0.72	0.955	CLONAL	1	TRUE	0	0.292308689298233	1		593	421	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412320	63412320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	83	833	0	ENST00000330258.3:c.847G>A	p.Glu283Lys	p.E283K	ENST00000330258	NM_152424.3	283	Gag/Aag	2/2	0.292308689298233	1	FACETS	0.846	0.748	0.951	0.846	0.748	0.951	CLONAL	1	TRUE	0	0.292308689298233	1		833	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579717	7579717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs922736614	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	267	669	0	ENST00000269305.4:c.79C>T	p.Pro27Ser	p.P27S	ENST00000269305	NM_001126112.2	27	Cct/Tct	3/11	0.67936946343437	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.739555583762964	1		669	452	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046410	69046410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868582467	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	168	317	0	ENST00000288368.4:c.3883G>A	p.Glu1295Lys	p.E1295K	ENST00000288368	NM_024870.2	1295	Gaa/Aaa	32/40	0.69150662865628	3	FACETS	0.833	0.767	0.901	0.417	0.383	0.451	CLONAL	1	TRUE	1	0.739555583762964	3		317	747	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	186	151	0				ENST00000310581	NM_198253.2	-/1132			0.69150662865628	3	FACETS	1	0.96	1	0.526	0.488	0.565	CLONAL	1	TRUE	1	0.739555583762964	3		151	655	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394449	162394449	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	102	196	0	ENST00000366898.1:c.619G>A	p.Glu207Lys	p.E207K	ENST00000366898	NM_004562.2	207	Gaa/Aaa	6/12	0.739555583762964	1	FACETS	0.977	0.901	1	0.977	0.901	1	CLONAL	1	TRUE	0	0.739555583762964	1		196	178	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561564	9561564	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867333778	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	136	575	0	ENST00000353224.5:c.218G>A	p.Gly73Glu	p.G73E	ENST00000353224	NM_177990.2	73	gGa/gAa	4/10	0.69150662865628	3	FACETS	0.876	0.8	0.955	0.438	0.4	0.478	CLONAL	1	TRUE	1	0.739555583762964	3		575	575	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770557	40770557	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	129	261	0	ENST00000373198.4:c.2825C>T	p.Ser942Phe	p.S942F	ENST00000373198	NM_133170.3	942	tCc/tTc	19/32	0.69150662865628	3	FACETS	0.859	0.783	0.94	0.43	0.391	0.47	CLONAL	1	TRUE	1	0.739555583762964	3		261	556	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344458	118344458	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	104	171	0	ENST00000534358.1:c.2584C>T	p.Arg862Ter	p.R862*	ENST00000534358	NM_005933.3	862	Cga/Tga	3/36	0.728668195158087	1	FACETS	0.969	0.894	1	0.969	0.894	1	CLONAL	1	TRUE	0	0.739555583762964	1		171	183	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	440	355	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	0.722709642996108	2	FACETS	0.995	0.965	1	0.995	0.965	1	CLONAL	2	TRUE	0	0.739555583762964	2		355	598	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956220	55956220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190050670	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	154	727	2	ENST00000263923.4:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000263923	NM_002253.2	1032	cGa/cAa	23/30	1	2	FACETS	0.903	0.834	0.975	0.903	0.834	0.975	CLONAL	1	TRUE	1	0.739555583762964	2		729	461	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530383	187530383	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	134	207	0	ENST00000441802.2:c.10160C>T	p.Pro3387Leu	p.P3387L	ENST00000441802	NM_005245.3	3387	cCc/cTc	16/27	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.739555583762964	2		207	356	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206941988	206941988	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376415487	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	162	141	0	ENST00000423557.1:c.530G>A	p.Arg177Gln	p.R177Q	ENST00000423557	NM_000572.2	177	cGa/cAa	5/5	0.722709642996108	2	FACETS	0.901	0.852	0.949	0.901	0.852	0.949	CLONAL	2	TRUE	0	0.739555583762964	2		141	243	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047156	77047156	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	189	318	0	ENST00000356341.3:c.1388C>T	p.Pro463Leu	p.P463L	ENST00000356341	NM_002576.4	463	cCa/cTa	13/15	1	2	FACETS	0.875	0.814	0.938	0.875	0.814	0.938	CLONAL	1	TRUE	1	0.739555583762964	2		318	584	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576097	29576098	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	191	260	0	ENST00000356175.3:c.4076dup	p.Gln1360SerfsTer14	p.Q1360Sfs*14	ENST00000356175	NM_000267.3	1357	ttc/ttCc	30/57	1	2	FACETS	0.894	0.832	0.957	0.894	0.832	0.957	CLONAL	1	TRUE	1	0.739555583762964	2		260	578	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	165	771	2	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	1	2	FACETS	0.875	0.809	0.942	0.875	0.809	0.942	CLONAL	1	TRUE	1	0.739555583762964	2		773	510	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097604	11097604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	281	540	1	ENST00000358026.2:c.784C>T	p.Pro262Ser	p.P262S	ENST00000358026	NM_001128849.1	262	Ccc/Tcc	5/36	1	2	FACETS	0.894	0.843	0.946	0.894	0.843	0.946	CLONAL	1	TRUE	1	0.739555583762964	2		541	850	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813768	50813768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	246	442	0	ENST00000398568.2:c.1322C>T	p.Ser441Phe	p.S441F	ENST00000398568	NM_001042412.1	441	tCt/tTt	8/18	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.739555583762964	2		442	657	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679186	88679186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	208	301	1	ENST00000360948.2:c.851G>A	p.Cys284Tyr	p.C284Y	ENST00000360948	NM_001012338.2	284	tGc/tAc	8/19	0.531665743109355	3	FACETS	1	0.98	1	0.563	0.525	0.603	CLONAL	1	TRUE	1	0.739555583762964	3		302	684	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961751	55961751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	122	234	0	ENST00000263923.4:c.2810C>T	p.Pro937Leu	p.P937L	ENST00000263923	NM_002253.2	937	cCc/cTc	20/30	1	2	FACETS	0.844	0.77	0.92	0.844	0.77	0.92	CLONAL	1	TRUE	1	0.739555583762964	2		234	391	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5465594	5465594	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568608390	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	162	126	0	ENST00000381577.3:c.778C>T	p.Arg260Cys	p.R260C	ENST00000381577	NM_014143.3	260	Cgt/Tgt	5/7	0.722709642996108	2	FACETS	0.928	0.879	0.976	0.928	0.879	0.976	CLONAL	2	TRUE	0	0.739555583762964	2		126	236	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248710	212248710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	127	264	0	ENST00000342788.4:c.3557C>T	p.Pro1186Leu	p.P1186L	ENST00000342788	NM_005235.2	1186	cCc/cTc	28/28	1	2	FACETS	0.949	0.869	1	0.949	0.869	1	CLONAL	1	TRUE	1	0.739555583762964	2		264	362	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681443	30681443	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	158	211	0	ENST00000376406.3:c.569C>T	p.Ser190Phe	p.S190F	ENST00000376406	NM_014641.2	190	tCt/tTt	4/15	1	2	FACETS	0.98	0.907	1	0.98	0.907	1	CLONAL	1	TRUE	1	0.739555583762964	2		211	436	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306942	65306942	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	138	277	0	ENST00000342505.4:c.2635del	p.Arg879ValfsTer32	p.R879Vfs*32	ENST00000342505	NM_002227.2	879	Cgt/gt	19/25	0.728668195158087	1	FACETS	0.956	0.892	1	0.956	0.892	1	CLONAL	1	TRUE	0	0.739555583762964	1		277	246	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724614	162724615	+	missense_variant	Missense_Mutation	DNP	GG	GG	AC	novel	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	507	296	0	ENST00000367921.3:c.386_387delinsAC	p.Trp129Tyr	p.W129Y	ENST00000367921	NM_006182.2	129	tGG/tAC	5/18	0.541095190118108	6	FACETS	0.888	0.856	0.92			1	CLONAL	4	TRUE	NA	0.739555583762964	6		296	957	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612921	228612921	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	355	296	0	ENST00000366696.1:c.106G>T	p.Val36Leu	p.V36L	ENST00000366696	NM_003493.2	36	Gtg/Ttg	1/1	0.722709642996108	2	FACETS	0.913	0.879	0.945	0.913	0.879	0.945	CLONAL	2	TRUE	0	0.739555583762964	2		296	526	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771427	112771427	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501926	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	236	401	0	ENST00000369452.4:c.1600C>T	p.Pro534Ser	p.P534S	ENST00000369452	NM_007373.3	534	Ccc/Tcc	9/9	1	2	FACETS	0.868	0.814	0.924	0.868	0.814	0.924	CLONAL	1	TRUE	1	0.739555583762964	2		401	735	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442737	442738	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	170	309	1	ENST00000399788.2:c.1568_1569delinsTT	p.Pro523Leu	p.P523L	ENST00000399788	NM_001042603.1	523	cCC/cTT	12/28	NA	2	FACETS	0.9	0.834	0.967			1	INDETERMINATE	1	TRUE	NA	0.739555583762964	2		310	511	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230569	46230569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769348347	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	158	255	1	ENST00000334344.6:c.818C>T	p.Pro273Leu	p.P273L	ENST00000334344	NM_152641.2	273	cCt/cTt	8/21	1	2	FACETS	0.937	0.866	1	0.937	0.866	1	CLONAL	1	TRUE	1	0.739555583762964	2		256	456	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910578	32910578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs431825291	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	178	227	0	ENST00000380152.3:c.2086G>A	p.Glu696Lys	p.E696K	ENST00000380152		696	Gaa/Aaa	11/27	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.739555583762964	2		227	409	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341316	89341316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567544257	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	110	171	0	ENST00000301030.4:c.7619G>A	p.Arg2540Gln	p.R2540Q	ENST00000301030	NM_001256183.1	2540	cGg/cAg	11/13	1	2	FACETS	0.985	0.898	1	0.985	0.898	1	CLONAL	1	TRUE	1	0.739555583762964	2		171	302	SUCCESS
ALK	238	MSKCC	GRCh37	2	29420540	29420540	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	138	190	0	ENST00000389048.3:c.3941C>T	p.Ser1314Phe	p.S1314F	ENST00000389048	NM_004304.4	1314	tCc/tTc	27/29	1	2	FACETS	0.974	0.897	1	0.974	0.897	1	CLONAL	1	TRUE	1	0.739555583762964	2		190	383	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713461	40713461	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	232	434	0	ENST00000373198.4:c.4054C>T	p.Gln1352Ter	p.Q1352*	ENST00000373198	NM_133170.3	1352	Cag/Tag	30/32	0.69150662865628	3	FACETS	0.967	0.903	1	0.483	0.451	0.516	CLONAL	1	TRUE	1	0.739555583762964	3		434	889	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169999716	169999716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	150	219	0	ENST00000295797.4:c.1027C>T	p.His343Tyr	p.H343Y	ENST00000295797	NM_002740.5	343	Cat/Tat	11/18	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.739555583762964	2		219	398	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55603375	55603376	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	97	185	0	ENST00000288135.5:c.2731_2732delinsTT	p.Pro911Phe	p.P911F	ENST00000288135	NM_000222.2	911	CCc/TTc	20/21	1	2	FACETS	0.852	0.769	0.938	0.852	0.769	0.938	CLONAL	1	TRUE	1	0.739555583762964	2		185	308	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672981	30672981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	212	507	0	ENST00000376406.3:c.3979C>T	p.Pro1327Ser	p.P1327S	ENST00000376406	NM_014641.2	1327	Ccc/Tcc	10/15	1	2	FACETS	0.89	0.831	0.95	0.89	0.831	0.95	CLONAL	1	TRUE	1	0.739555583762964	2		507	644	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681033	117681034	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	116	247	1	ENST00000368508.3:c.3586_3587delinsAA	p.Gly1196Lys	p.G1196K	ENST00000368508	NM_002944.2	1196	GGa/AAa	23/43	0.739555583762964	1	FACETS	0.856	0.789	0.922	0.856	0.789	0.922	CLONAL	1	TRUE	0	0.739555583762964	1		248	231	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864440	162864440	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1440010564	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	164	302	0	ENST00000366898.1:c.73C>T	p.Gln25Ter	p.Q25*	ENST00000366898	NM_004562.2	25	Cag/Tag	2/12	0.739555583762964	1	FACETS	0.919	0.861	0.977	0.919	0.861	0.977	CLONAL	1	TRUE	0	0.739555583762964	1		302	304	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962324	2962324	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	486	473	0	ENST00000396946.4:c.2213G>A	p.Trp738Ter	p.W738*	ENST00000396946	NM_032415.4	738	tGg/tAg	17/25	0.693201728394473	3	FACETS	0.964	0.928	1	0.964	0.928	1	CLONAL	2	TRUE	1	0.739555583762964	3		473	934	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279338	38279338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	311	484	2	ENST00000425967.3:c.1151C>T	p.Ser384Phe	p.S384F	ENST00000425967	NM_001174067.1	384	tCt/tTt	9/19	0.69150662865628	3	FACETS	0.95	0.895	1	0.475	0.447	0.503	CLONAL	1	TRUE	1	0.739555583762964	3		486	1213	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015067	37015067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	494	375	0	ENST00000358127.4:c.337G>A	p.Glu113Lys	p.E113K	ENST00000358127	NM_001280556.1	113	Gag/Aag	3/10	0.728769291106826	2	FACETS	0.975	0.947	1	0.975	0.947	1	CLONAL	2	TRUE	0	0.739555583762964	2		375	685	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409809	63409809	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754401246	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	171	300	1	ENST00000330258.3:c.3358C>T	p.Leu1120Phe	p.L1120F	ENST00000330258	NM_152424.3	1120	Ctt/Ttt	2/2	0.69150662865628	3	FACETS	0.944	0.871	1	0.472	0.435	0.51	CLONAL	1	TRUE	1	0.739555583762964	3		301	671	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920137	76920137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	309	252	0	ENST00000373344.5:c.3940G>A	p.Glu1314Lys	p.E1314K	ENST00000373344	NM_000489.3	1314	Gag/Aag	11/35	0.69150662865628	3	FACETS	0.862	0.819	0.905	0.862	0.819	0.905	CLONAL	2	TRUE	1	0.739555583762964	3		252	664	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179142	123179142	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	323	288	0	ENST00000218089.9:c.591G>A	p.Met197Ile	p.M197I	ENST00000218089	NM_001042749.1	197	atG/atA	8/35	0.69150662865628	3	FACETS	0.908	0.865	0.951	0.908	0.865	0.951	CLONAL	2	TRUE	1	0.739555583762964	3		288	659	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790000	40790000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159843	NA	P-0038393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	99	607	0	ENST00000373198.4:c.2731G>A	p.Glu911Lys	p.E911K	ENST00000373198	NM_133170.3	911	Gaa/Aaa	18/32	NA	2	FACETS	0.749	0.671	0.83			1	INDETERMINATE	1	TRUE	NA	0.536482569817696	2		607	493	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589771	55589773	+	inframe_deletion	In_Frame_Del	DEL	ACG	ACG	-	novel	NA	P-0038393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	202	492	0	ENST00000288135.5:c.1255_1257del	p.Asp419del	p.D419del	ENST00000288135	NM_000222.2	418	tACGac/tac	8/21	0.226305335617928	6	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.536482569817696	6		492	666	SUCCESS
CBL	867	MSKCC	GRCh37	11	119145581	119145581	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	129	460	0	ENST00000264033.4:c.787G>C	p.Val263Leu	p.V263L	ENST00000264033	NM_005188.3	263	Gta/Cta	5/16	0.503667038900987	1	FACETS	0.994	0.912	1	0.994	0.912	1	CLONAL	1	TRUE	0	0.536482569817696	1		460	354	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148948	119148959	+	inframe_deletion	In_Frame_Del	DEL	GATGTAAAGATT	GATGTAAAGATT	-	novel	NA	P-0038393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	155	560	0	ENST00000264033.4:c.1170_1181del	p.Asp390_Ile393del	p.D390_I393del	ENST00000264033	NM_005188.3	390	GATGTAAAGATT/-	8/16	0.503667038900987	1	FACETS	0.923	0.853	0.996	0.923	0.853	0.996	CLONAL	1	TRUE	0	0.536482569817696	1		560	458	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749106	43749106	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	176	818	0	ENST00000382044.4:c.1700C>A	p.Ala567Asp	p.A567D	ENST00000382044	NM_001141980.1	567	gCt/gAt	12/28	1	2	FACETS	0.852	0.786	0.92	0.852	0.786	0.92	CLONAL	1	TRUE	1	0.536482569817696	2		818	770	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856056	68856056	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	131	731	1	ENST00000261769.5:c.1864A>G	p.Asn622Asp	p.N622D	ENST00000261769	NM_004360.3	622	Aat/Gat	12/16	1	2	FACETS	0.789	0.718	0.863	0.789	0.718	0.863	SUBCLONAL	1	TRUE	1	0.536482569817696	2		732	619	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585399	29585399	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038393-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	119	607	0	ENST00000356175.3:c.4148C>A	p.Ala1383Glu	p.A1383E	ENST00000356175	NM_000267.3	1383	gCa/gAa	31/57	1	2	FACETS	0.711	0.643	0.782	0.711	0.643	0.782	SUBCLONAL	1	TRUE	1	0.536482569817696	2		607	624	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	132	248	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.983	0.894	1	0.983	0.894	1	CLONAL	1	TRUE	1	0.38	2		249	707	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636143	28636143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371663652	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	81	515	0	ENST00000241453.7:c.229G>A	p.Glu77Lys	p.E77K	ENST00000241453	NM_004119.2	77	Gaa/Aaa	3/24	0.3	2	FACETS	0.511	0.449	0.577			1	SUBCLONAL	1	TRUE	NA	0.38	2		515	835	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541097	187541097	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	39	333	0	ENST00000441802.2:c.6643T>C	p.Phe2215Leu	p.F2215L	ENST00000441802	NM_005245.3	2215	Ttc/Ctc	10/27	0.174150395568427	1	FACETS	0.369	0.306	0.44	0.369	0.306	0.44	INDETERMINATE	1	TRUE	0	0.38	1		333	450	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058631	72058631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	48	390	0	ENST00000357731.5:c.809G>A	p.Gly270Glu	p.G270E	ENST00000357731	NM_173808.2	270	gGa/gAa	6/7	0.174150395568427	1	FACETS	0.455	0.385	0.532	0.455	0.385	0.532	INDETERMINATE	1	TRUE	0	0.38	1		390	450	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544119	18544119	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	28	394	0	ENST00000266497.5:c.1936C>T	p.Leu646Phe	p.L646F	ENST00000266497		646	Ctt/Ttt	13/31	0.174150395568427	1	FACETS	0.363	0.29	0.446	0.363	0.29	0.446	INDETERMINATE	1	TRUE	0	0.38	1		394	329	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231092	53231092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	183	331	0	ENST00000375401.3:c.1810G>A	p.Gly604Ser	p.G604S	ENST00000375401	NM_004187.3	604	Ggc/Agc	13/26	1	1	FACETS	0.814	0.759	0.871	1	0.992	1	CLONAL	2	TRUE	0	0.38	1		331	479	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864423	57864423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1359000505	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	70	584	0	ENST00000228682.2:c.1900G>A	p.Gly634Arg	p.G634R	ENST00000228682	NM_005269.2	634	Ggg/Agg	12/12	0.174150395568427	1	FACETS	0.465	0.405	0.529	0.465	0.405	0.529	INDETERMINATE	1	TRUE	0	0.38	1		584	642	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408864	41408864	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	68	447	0	ENST00000373198.4:c.562C>T	p.Pro188Ser	p.P188S	ENST00000373198	NM_133170.3	188	Cca/Tca	4/32	1	2	FACETS	0.516	0.449	0.59	0.516	0.449	0.59	SUBCLONAL	1	TRUE	1	0.38	2		447	693	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955064	17955064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749334592	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	118	735	2	ENST00000458235.1:c.163G>A	p.Val55Met	p.V55M	ENST00000458235	NM_000215.3	55	Gtg/Atg	2/24	0.174150395568427	1	FACETS	0.518	0.466	0.572	0.518	0.466	0.572	INDETERMINATE	1	TRUE	0	0.38	1		737	972	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363517	40363517	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	74	574	0	ENST00000397332.2:c.712C>T	p.His238Tyr	p.H238Y	ENST00000397332	NM_001033082.2	238	Cat/Tat	3/3	0.174150395568427	1	FACETS	0.429	0.375	0.487	0.429	0.375	0.487	INDETERMINATE	1	TRUE	0	0.38	1		574	736	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443403	187443403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755666072	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	59	371	0	ENST00000232014.4:c.1723C>T	p.Arg575Cys	p.R575C	ENST00000232014	NM_001130845.1	575	Cgt/Tgt	8/10	0.174150395568427	1	FACETS	0.504	0.434	0.58	0.504	0.434	0.58	INDETERMINATE	1	TRUE	0	0.38	1		371	499	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182662947	182662947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	50	449	0	ENST00000292782.4:c.715C>T	p.Leu239Phe	p.L239F	ENST00000292782	NM_020640.2	239	Ctt/Ttt	7/7	0.174150395568427	1	FACETS	0.459	0.39	0.535	0.459	0.39	0.535	INDETERMINATE	1	TRUE	0	0.38	1		449	464	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43769857	43769857	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	68	545	1	ENST00000382044.4:c.889C>T	p.Gln297Ter	p.Q297*	ENST00000382044	NM_001141980.1	297	Cag/Tag	8/28	0.174150395568427	1	FACETS	0.479	0.417	0.547	0.479	0.417	0.547	INDETERMINATE	1	TRUE	0	0.38	1		546	605	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935354	36935354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	99	708	2	ENST00000361632.4:c.1373G>A	p.Gly458Asp	p.G458D	ENST00000361632		458	gGc/gAc	10/16	0.174150395568427	1	FACETS	0.552	0.492	0.615	0.552	0.492	0.615	INDETERMINATE	1	TRUE	0	0.38	1		710	765	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202705	108202705	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064795004	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	45	365	0	ENST00000278616.4:c.7729G>A	p.Val2577Ile	p.V2577I	ENST00000278616	NM_000051.3	2577	Gta/Ata	52/63	0.381116573378626	1	FACETS	0.568	0.479	0.665	0.568	0.479	0.665	SUBCLONAL	1	TRUE	0	0.38	1		365	338	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813297	102813297	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	52	451	0	ENST00000307046.8:c.392A>G	p.Lys131Arg	p.K131R	ENST00000307046	NM_001111285.1	131	aAg/aGg	3/4	0.174150395568427	1	FACETS	0.448	0.381	0.521	0.448	0.381	0.521	INDETERMINATE	1	TRUE	0	0.38	1		451	495	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906441	32906441	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1485423178	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	31	391	0	ENST00000380152.3:c.826G>A	p.Val276Ile	p.V276I	ENST00000380152		276	Gta/Ata	10/27	0.3	2	FACETS	0.425	0.344	0.517			1	SUBCLONAL	1	TRUE	NA	0.38	2		391	384	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524592	103524592	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	40	271	0	ENST00000355739.4:c.2723A>C	p.Asn908Thr	p.N908T	ENST00000355739	NM_000123.3	908	aAt/aCt	13/15	0.381116573378626	1	FACETS	0.491	0.409	0.582	0.491	0.409	0.582	SUBCLONAL	1	TRUE	0	0.38	1		271	347	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647653	2647653	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1423482494	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	58	556	1	ENST00000342085.4:c.1556C>T	p.Pro519Leu	p.P519L	ENST00000342085	NM_002613.4	519	cCt/cTt	14/14	0.174150395568427	1	FACETS	0.388	0.333	0.448	0.388	0.333	0.448	INDETERMINATE	1	TRUE	0	0.38	1		557	637	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944202	81944202	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs755757354	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	106	736	0	ENST00000359376.3:c.1811A>G	p.Asn604Ser	p.N604S	ENST00000359376	NM_002661.3	604	aAc/aGc	18/33	0.174150395568427	1	FACETS	0.593	0.531	0.658	0.593	0.531	0.658	INDETERMINATE	1	TRUE	0	0.38	1		736	762	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357482	89357483	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	70	636	1	ENST00000301030.4:c.335_336delinsTT	p.Ser112Phe	p.S112F	ENST00000301030	NM_001256183.1	112	tCC/tTT	5/13	0.174150395568427	1	FACETS	0.39	0.339	0.445	0.39	0.339	0.445	INDETERMINATE	1	TRUE	0	0.38	1		637	765	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55334894	55334896	+	frameshift_variant	Frame_Shift_Del	DEL	TAC	TAC	CA	novel	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	139	497	0	ENST00000284073.2:c.171_173delinsCA	p.Thr58ArgfsTer18	p.T58Rfs*18	ENST00000284073	NM_138962.2	57	acTACg/acCAg	3/14	1	2	FACETS	0.944	0.86	1	0.944	0.86	1	CLONAL	1	TRUE	1	0.38	2		497	775	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867528	78867528	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs759154872	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	90	580	0	ENST00000306801.3:c.2264C>A	p.Ser755Tyr	p.S755Y	ENST00000306801	NM_020761.2	755	tCc/tAc	20/34	1	2	FACETS	0.618	0.548	0.693	0.618	0.548	0.693	SUBCLONAL	1	TRUE	1	0.38	2		580	766	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39647353	39647353	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	46	285	0	ENST00000262039.4:c.2525T>C	p.Val842Ala	p.V842A	ENST00000262039	NM_002647.2	842	gTt/gCt	24/25	0.174150395568427	1	FACETS	0.526	0.444	0.616	0.526	0.444	0.616	INDETERMINATE	1	TRUE	0	0.38	1		285	373	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794793	42794793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	152	624	2	ENST00000575354.2:c.1873G>A	p.Gly625Arg	p.G625R	ENST00000575354	NM_015125.3	625	Gga/Aga	10/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.38	2		626	741	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023273	31023274	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	47	566	1	ENST00000375687.4:c.2758_2759delinsTT	p.Pro920Leu	p.P920L	ENST00000375687	NM_015338.5	920	CCa/TTa	13/13	1	2	FACETS	0.318	0.267	0.374	0.318	0.267	0.374	SUBCLONAL	1	TRUE	1	0.38	2		567	778	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710638	40710638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	192	505	0	ENST00000373198.4:c.4213G>A	p.Gly1405Arg	p.G1405R	ENST00000373198	NM_133170.3	1405	Gga/Aga	31/32	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.38	2		505	750	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980814	40980814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	67	592	0	ENST00000373198.4:c.1672C>T	p.Pro558Ser	p.P558S	ENST00000373198	NM_133170.3	558	Cca/Tca	10/32	1	2	FACETS	0.41	0.355	0.47	0.41	0.355	0.47	SUBCLONAL	1	TRUE	1	0.38	2		592	860	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277898	41277898	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	54	348	0	ENST00000349496.5:c.1862T>C	p.Leu621Pro	p.L621P	ENST00000349496	NM_001904.3	621	cTt/cCt	12/15	0.174150395568427	1	FACETS	0.515	0.441	0.596	0.515	0.441	0.596	INDETERMINATE	1	TRUE	0	0.38	1		348	447	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72873652	72873653	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	47	401	0	ENST00000325599.8:c.649_650delinsTT	p.Pro217Phe	p.P217F	ENST00000325599	NM_018130.2	217	CCt/TTt	6/11	0.174150395568427	1	FACETS	0.43	0.363	0.504	0.43	0.363	0.504	INDETERMINATE	1	TRUE	0	0.38	1		401	466	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191265	185191265	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1178055532	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	71	464	0	ENST00000265026.3:c.2146G>A	p.Gly716Ser	p.G716S	ENST00000265026	NM_004721.4	716	Ggc/Agc	11/14	0.174150395568427	1	FACETS	0.556	0.486	0.632	0.556	0.486	0.632	INDETERMINATE	1	TRUE	0	0.38	1		464	544	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594196	55594197	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	novel	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	424	321	0	ENST00000288135.5:c.1899_1900delinsTT	p.Glu633_Arg634delinsAspTrp	p.E633_R634delinsDW	ENST00000288135	NM_000222.2	633	gaACgg/gaTTgg	13/21	0.3	8	FACETS	1	0.977	1			1	CLONAL	6	TRUE	NA	0.38	8		321	777	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524912	187524912	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	84	640	0	ENST00000441802.2:c.10768T>C	p.Phe3590Leu	p.F3590L	ENST00000441802	NM_005245.3	3590	Ttc/Ctc	19/27	0.174150395568427	1	FACETS	0.476	0.42	0.536	0.476	0.42	0.536	INDETERMINATE	1	TRUE	0	0.38	1		640	752	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532929	187532930	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	67	255	0	ENST00000441802.2:c.9464-1_9464delinsAA		p.X3155_splice	ENST00000441802	NM_005245.3	3155		14/27	0.174150395568427	1	FACETS	0.975	0.855	1	0.975	0.855	1	INDETERMINATE	1	TRUE	0	0.38	1		255	293	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515220	31515220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	85	786	1	ENST00000344624.3:c.1165G>A	p.Glu389Lys	p.E389K	ENST00000344624		389	Gaa/Aaa	5/33	1	2	FACETS	0.443	0.391	0.5	0.443	0.391	0.5	SUBCLONAL	1	TRUE	1	0.38	2		787	1009	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721906	176721906	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	52	480	1	ENST00000439151.2:c.7537C>T	p.Leu2513Phe	p.L2513F	ENST00000439151	NM_022455.4	2513	Ctt/Ttt	23/23	0.174150395568427	1	FACETS	0.348	0.296	0.406	0.348	0.296	0.406	INDETERMINATE	1	TRUE	0	0.38	1		481	637	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673242	30673242	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	62	630	0	ENST00000376406.3:c.3718C>T	p.Pro1240Ser	p.P1240S	ENST00000376406	NM_014641.2	1240	Cct/Tct	10/15	1	2	FACETS	0.443	0.382	0.51	0.443	0.382	0.51	SUBCLONAL	1	TRUE	1	0.38	2		630	736	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31939922	31939922	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1199799566	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	102	642	0	ENST00000375333.2:c.149C>T	p.Pro50Leu	p.P50L	ENST00000375333	NM_032454.1	50	cCc/cTc	1/8	1	2	FACETS	0.586	0.523	0.653	0.586	0.523	0.653	SUBCLONAL	1	TRUE	1	0.38	2		642	916	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552808	106552808	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	77	670	0	ENST00000369096.4:c.773C>T	p.Ser258Phe	p.S258F	ENST00000369096	NM_001198.3	258	tCc/tTc	5/7	1	2	FACETS	0.422	0.369	0.479	0.422	0.369	0.479	SUBCLONAL	1	TRUE	1	0.38	2		670	961	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739770	41739770	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	87	674	0	ENST00000242208.4:c.203T>A	p.Leu68Ter	p.L68*	ENST00000242208	NM_002192.2	68	tTg/tAg	2/3	0.254768180685581	3	FACETS	0.545	0.482	0.614	0.273	0.241	0.307	SUBCLONAL	1	TRUE	1	0.38	3		674	999	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878137	151878137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038799-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	135	529	0	ENST00000262189.6:c.6808G>A	p.Asp2270Asn	p.D2270N	ENST00000262189	NM_170606.2	2270	Gat/Aat	36/59	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.38	2		529	648	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0039052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	87	528	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.210485455571694	2		528	746	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0039052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	40	248	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.210485455571694	2		249	296	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099329	193099329	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	57	344	0	ENST00000367435.3:c.263G>C	p.Arg88Thr	p.R88T	ENST00000367435	NM_024529.4	88	aGa/aCa	3/17	1	2	FACETS	0.981	0.842	1	0.981	0.842	1	CLONAL	1	TRUE	1	0.210485455571694	2		344	552	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560902	9560902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756198440	NA	P-0039052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	69	632	0	ENST00000353224.5:c.880G>A	p.Glu294Lys	p.E294K	ENST00000353224	NM_177990.2	294	Gaa/Aaa	4/10	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.210485455571694	2		632	552	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632230	215632230	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	36	320	0	ENST00000260947.4:c.1544C>T	p.Ser515Phe	p.S515F	ENST00000260947	NM_000465.2	515	tCc/tTc	6/11	1	2	FACETS	0.79	0.649	0.947	0.79	0.649	0.947	CLONAL	1	TRUE	1	0.210485455571694	2		320	433	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481403	140481403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913357	NA	P-0039052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	59	377	0	ENST00000288602.6:c.1405G>A	p.Gly469Arg	p.G469R	ENST00000288602	NM_004333.4	469	Gga/Aga	11/18	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.210485455571694	2		377	475	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56412976	56412976	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	39	381	0	ENST00000348428.3:c.1990C>T	p.Pro664Ser	p.P664S	ENST00000348428	NM_006785.3	664	Ccc/Tcc	16/17	1	2	FACETS	0.749	0.62	0.892	0.749	0.62	0.892	SUBCLONAL	1	TRUE	1	0.210485455571694	2		381	495	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543379	65543379	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs762084527	NA	P-0039052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	68	503	0	ENST00000358664.4:c.298C>T	p.Arg100Cys	p.R100C	ENST00000358664	NM_002382.4	100	Cgt/Tgt	5/5	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.210485455571694	2		503	585	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771139	161771139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	73	646	3	ENST00000366898.1:c.1390G>A	p.Asp464Asn	p.D464N	ENST00000366898	NM_004562.2	464	Gac/Aac	12/12	0.210485455571694	1	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	0	0.210485455571694	1		649	612	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874206	155874206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	92	676	0	ENST00000368323.3:c.325C>T	p.His109Tyr	p.H109Y	ENST00000368323	NM_006912.5	109	Cat/Tat	5/6	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.210485455571694	2		676	871	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812299	212812299	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	31	338	0	ENST00000342788.4:c.277C>T	p.Gln93Ter	p.Q93*	ENST00000342788	NM_005235.2	93	Cag/Tag	3/28	1	2	FACETS	0.647	0.523	0.788	0.647	0.523	0.788	SUBCLONAL	1	TRUE	1	0.210485455571694	2		338	455	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492939	8492939	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	64	523	0	ENST00000356435.5:c.2390C>T	p.Ser797Phe	p.S797F	ENST00000356435		797	tCc/tTc	16/35	0.210485455571694	1	FACETS	0.919	0.796	1	0.919	0.796	1	CLONAL	1	TRUE	0	0.210485455571694	1		523	592	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871203	35871203	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	53	301	0	ENST00000303115.3:c.425G>A	p.Gly142Glu	p.G142E	ENST00000303115	NM_002185.3	142	gGa/gAa	4/8	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.210485455571694	2		301	478	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123246892	123246892	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	73	512	0	ENST00000358487.5:c.2033G>T	p.Arg678Ile	p.R678I	ENST00000358487	NM_000141.4	678	aGa/aTa	15/18	0.210485455571694	1	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	0	0.210485455571694	1		512	612	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514326	69514326	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	146	499	0	ENST00000294312.3:c.355G>A	p.Asp119Asn	p.D119N	ENST00000294312	NM_005117.2	119	Gac/Aac	3/3	0.210485455571694	11	FACETS	1	0.941	1			1	CLONAL	2	TRUE	NA	0.210485455571694	11		499	1294	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421672	49421672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	93	761	0	ENST00000301067.7:c.14557G>A	p.Gly4853Ser	p.G4853S	ENST00000301067	NM_003482.3	4853	Ggc/Agc	47/54	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.210485455571694	2		761	813	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422966	49422966	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	88	764	0	ENST00000301067.7:c.14129C>T	p.Ser4710Phe	p.S4710F	ENST00000301067	NM_003482.3	4710	tCc/tTc	44/54	1	2	FACETS	0.922	0.815	1	0.922	0.815	1	CLONAL	1	TRUE	1	0.210485455571694	2		764	907	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828702	72828702	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761054206	NA	P-0039052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	75	610	1	ENST00000268489.5:c.7879G>A	p.Gly2627Ser	p.G2627S	ENST00000268489	NM_006885.3	2627	Ggc/Agc	9/10	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.210485455571694	2		611	708	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81939102	81939103	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0039052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	53	549	1	ENST00000359376.3:c.1457_1458delinsTT	p.Ser486Phe	p.S486F	ENST00000359376	NM_002661.3	486	tCC/tTT	15/33	1	2	FACETS	0.839	0.715	0.975	0.839	0.715	0.975	CLONAL	1	TRUE	1	0.210485455571694	2		550	600	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243479	41243479	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	88	576	0	ENST00000357654.3:c.4069G>A	p.Glu1357Lys	p.E1357K	ENST00000357654	NM_007294.3	1357	Gaa/Aaa	10/23	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.210485455571694	2		576	815	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213593	36213593	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1200877558	NA	P-0039052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	110	914	1	ENST00000222270.7:c.2695C>T	p.Arg899Trp	p.R899W	ENST00000222270	NM_014727.1	899	Cgg/Tgg	5/37	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.210485455571694	2		915	1020	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437253	220437253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754976939	NA	P-0039052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	127	943	1	ENST00000243786.2:c.157C>T	p.Pro53Ser	p.P53S	ENST00000243786	NM_002191.3	53	Cct/Tct	1/2	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.210485455571694	2		944	973	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256464	46256464	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	65	404	0	ENST00000371998.3:c.692A>C	p.Gln231Pro	p.Q231P	ENST00000371998		231	cAg/cCg	7/23	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.210485455571694	2		404	504	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55974045	55974045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775023030	NA	P-0039052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	76	517	0	ENST00000263923.4:c.1271G>A	p.Gly424Asp	p.G424D	ENST00000263923	NM_002253.2	424	gGt/gAt	10/30	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.210485455571694	2		517	580	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681580	30681580	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	60	501	0	ENST00000376406.3:c.517G>A	p.Asp173Asn	p.D173N	ENST00000376406	NM_014641.2	173	Gat/Aat	3/15	0.204072346871759	3	FACETS	0.929	0.8	1	0.465	0.4	0.536	CLONAL	1	TRUE	1	0.210485455571694	3		501	678	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500796	8500796	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	46	371	0	ENST00000356435.5:c.2086G>A	p.Gly696Ser	p.G696S	ENST00000356435		696	Ggc/Agc	13/35	0.210485455571694	1	FACETS	0.863	0.728	1	0.863	0.728	1	CLONAL	1	TRUE	0	0.210485455571694	1		371	453	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813116	76813116	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	51	251	0	ENST00000373344.5:c.6505G>A	p.Gly2169Arg	p.G2169R	ENST00000373344	NM_000489.3	2169	Gga/Aga	30/35	1	1	FACETS	0.831	0.712	0.958	1	0.97	1	CLONAL	2	TRUE	0	0.210485455571694	1		251	261	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0039162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	778	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.393903272862302	11	FACETS	0.977	0.953	1	0.977	0.953	1	CLONAL	10	TRUE	1	0.393903272862302	11		288	1121	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0039162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	133	248	1				ENST00000310581	NM_198253.2	-/1132			0.3401492461299	1	FACETS	0.991	0.905	1	0.991	0.905	1	CLONAL	1	TRUE	0	0.393903272862302	1		249	547	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885474	23885474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138633497	NA	P-0039162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	30	420	0	ENST00000374561.5:c.337G>A	p.Asp113Asn	p.D113N	ENST00000374561	NM_002167.4	113	Gac/Aac	2/3	0.383857603067801	1	FACETS	0.228	0.183	0.279	0.228	0.183	0.279	SUBCLONAL	1	TRUE	0	0.393903272862302	1		420	537	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885870	111885870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	115	750	2	ENST00000341259.2:c.1492C>T	p.Leu498Phe	p.L498F	ENST00000341259	NM_005475.2	498	Ctt/Ttt	8/8	1	2	FACETS	0.625	0.562	0.692	0.625	0.562	0.692	SUBCLONAL	1	TRUE	1	0.393903272862302	2		752	934	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	355	451	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.738052578776875	5	FACETS	0.895	0.854	0.936	0.895	0.854	0.936	CLONAL	3	TRUE	2	0.738052578776875	5		451	755	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	356	151	0				ENST00000310581	NM_198253.2	-/1132			0.712745845819454	4	FACETS	0.994	0.947	1	0.994	0.947	1	CLONAL	2	TRUE	2	0.738052578776875	4		151	843	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561564	9561564	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867333778	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	474	575	0	ENST00000353224.5:c.218G>A	p.Gly73Glu	p.G73E	ENST00000353224	NM_177990.2	73	gGa/gAa	4/10	0.738052578776875	5	FACETS	0.994	0.963	1	0.994	0.963	1	CLONAL	4	TRUE	1	0.738052578776875	5		575	681	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530085	212530085	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs561997094	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	328	339	0	ENST00000342788.4:c.1834C>T	p.Arg612Trp	p.R612W	ENST00000342788	NM_005235.2	612	Cgg/Tgg	15/28	0.738052578776875	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	1	0.738052578776875	4		339	485	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	441059	441059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	463	496	0	ENST00000399788.2:c.1699C>T	p.Pro567Ser	p.P567S	ENST00000399788	NM_001042603.1	567	Cct/Tct	13/28	0.265984561040918	5	FACETS	0.929	0.906	0.951			1	INDETERMINATE	5	TRUE	NA	0.738052578776875	5		496	569	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919626	28919626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	331	666	2	ENST00000282397.4:c.2311C>T	p.Leu771Phe	p.L771F	ENST00000282397	NM_002019.4	771	Ctc/Ttc	16/30	0.623593837312251	4	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	2	0.738052578776875	4		668	778	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956220	55956220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190050670	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	177	727	2	ENST00000263923.4:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000263923	NM_002253.2	1032	cGa/cAa	23/30	0.738052578776875	3	FACETS	0.983	0.909	1	0.491	0.454	0.53	CLONAL	1	TRUE	1	0.738052578776875	3		729	668	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560902	9560902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756198440	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	182	632	0	ENST00000353224.5:c.880G>A	p.Glu294Lys	p.E294K	ENST00000353224	NM_177990.2	294	Gaa/Aaa	4/10	0.738052578776875	5	FACETS	0.89	0.82	0.964	0.223	0.205	0.241	CLONAL	1	TRUE	1	0.738052578776875	5		632	1167	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11181312	11181313	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	451	598	1	ENST00000361445.4:c.6923_6924delinsTT	p.Pro2308Leu	p.P2308L	ENST00000361445	NM_004958.3	2308	cCC/cTT	49/58	0.738052578776875	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.738052578776875	3		599	816	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599253	28599254	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	360	988	0	ENST00000253063.3:c.699_700delinsTT	p.Pro234Ser	p.P234S	ENST00000253063	NM_031459.4	233	ccCCct/ccTTct	5/10	0.738052578776875	3	FACETS	1	0.952	1	0.503	0.476	0.53	CLONAL	1	TRUE	1	0.738052578776875	3		988	1328	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941221	36941221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754120929	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	298	883	0	ENST00000361632.4:c.118G>A	p.Asp40Asn	p.D40N	ENST00000361632		40	Gat/Aat	3/16	0.738052578776875	3	FACETS	1	0.95	1	0.504	0.475	0.535	CLONAL	1	TRUE	1	0.738052578776875	3		883	1096	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843739	156843739	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	1091	1174	0	ENST00000524377.1:c.1165G>A	p.Asp389Asn	p.D389N	ENST00000524377	NM_002529.3	389	Gac/Aac	8/17	0.738052578776875	5	FACETS	0.985	0.96	1	0.985	0.96	1	CLONAL	3	TRUE	2	0.738052578776875	5		1174	2108	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326475	161326475	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs942160050	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1409	280	896	0	ENST00000367975.2:c.250C>T	p.Leu84Phe	p.L84F	ENST00000367975	NM_003001.3	84	Ctt/Ttt	5/6	0.738052578776875	5	FACETS	0.947	0.886	1	0.316	0.295	0.337	CLONAL	1	TRUE	2	0.738052578776875	5		896	1689	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226558140	226558140	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1458089304	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	184	586	0	ENST00000366794.5:c.2149C>T	p.Gln717Ter	p.Q717*	ENST00000366794	NM_001618.3	717	Cag/Tag	15/23	0.738052578776875	5	FACETS	0.892	0.822	0.965	0.297	0.274	0.322	CLONAL	1	TRUE	2	0.738052578776875	5		586	1178	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615100	43615101	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	598	982	2	ENST00000355710.3:c.2514_2515delinsAA	p.Asp839Asn	p.D839N	ENST00000355710	NM_020975.4	838	ctGGac/ctAAac	14/20	0.712745845819454	4	FACETS	0.961	0.925	0.997	0.961	0.925	0.997	CLONAL	2	TRUE	2	0.738052578776875	4		984	1465	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239471	123239471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	445	808	0	ENST00000358487.5:c.2366C>T	p.Ser789Phe	p.S789F	ENST00000358487	NM_000141.4	789	tCt/tTt	18/18	0.712745845819454	4	FACETS	0.949	0.908	0.991	0.949	0.908	0.991	CLONAL	2	TRUE	2	0.738052578776875	4		808	1104	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195971	102195971	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765714914	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	268	334	0	ENST00000263464.3:c.731G>A	p.Arg244Lys	p.R244K	ENST00000263464	NM_001165.4	244	aGa/aAa	2/9	0.738052578776875	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	0	0.738052578776875	3		334	321	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343372	118343372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	136	434	0	ENST00000534358.1:c.1498C>T	p.Pro500Ser	p.P500S	ENST00000534358	NM_005933.3	500	Cct/Tct	3/36	0.738052578776875	3	FACETS	0.959	0.877	1	0.32	0.292	0.349	CLONAL	1	TRUE	0	0.738052578776875	3		434	526	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343804	118343804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868981857	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	564	541	0	ENST00000534358.1:c.1930C>T	p.Arg644Cys	p.R644C	ENST00000534358	NM_005933.3	644	Cgc/Tgc	3/36	0.738052578776875	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	0	0.738052578776875	3		541	670	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374712	118374712	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	414	477	0	ENST00000534358.1:c.8105C>T	p.Ser2702Phe	p.S2702F	ENST00000534358	NM_005933.3	2702	tCc/tTc	27/36	0.738052578776875	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.738052578776875	3		477	497	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149241	119149242	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	500	636	1	ENST00000264033.4:c.1249_1250delinsAT	p.Pro417Ile	p.P417I	ENST00000264033	NM_005188.3	417	CCt/ATt	9/16	0.738052578776875	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.738052578776875	3		637	600	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432401	49432401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	786	1038	0	ENST00000301067.7:c.8738C>T	p.Pro2913Leu	p.P2913L	ENST00000301067	NM_003482.3	2913	cCc/cTc	34/54	0.738052578776875	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	1	0.738052578776875	3		1038	1327	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445045	49445046	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	593	796	2	ENST00000301067.7:c.2420_2421delinsTT	p.Ser807Phe	p.S807F	ENST00000301067	NM_003482.3	807	tCC/tTT	10/54	0.738052578776875	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.738052578776875	3		798	1039	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864540	57864540	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	307	899	1	ENST00000228682.2:c.2017G>A	p.Gly673Arg	p.G673R	ENST00000228682	NM_005269.2	673	Gga/Aga	12/12	0.738052578776875	3	FACETS	0.974	0.918	1	0.487	0.459	0.516	CLONAL	1	TRUE	1	0.738052578776875	3		900	1169	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813409	102813409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	205	615	0	ENST00000307046.8:c.280G>A	p.Glu94Lys	p.E94K	ENST00000307046	NM_001111285.1	94	Gag/Aag	3/4	0.738052578776875	3	FACETS	0.941	0.875	1	0.471	0.437	0.505	CLONAL	1	TRUE	1	0.738052578776875	3		615	808	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112884091	112884091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	161	575	0	ENST00000351677.2:c.26C>T	p.Pro9Leu	p.P9L	ENST00000351677	NM_002834.3	9	cCa/cTa	2/16	0.738052578776875	3	FACETS	1	0.924	1	0.501	0.462	0.542	CLONAL	1	TRUE	1	0.738052578776875	3		575	596	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589742	28589742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	303	494	0	ENST00000241453.7:c.2638G>A	p.Glu880Lys	p.E880K	ENST00000241453	NM_004119.2	880	Gaa/Aaa	21/24	0.623593837312251	4	FACETS	0.997	0.945	1	0.997	0.945	1	CLONAL	2	TRUE	2	0.738052578776875	4		494	716	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602314	28602314	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	326	567	0	ENST00000241453.7:c.2053+1G>A		p.X685_splice	ENST00000241453	NM_004119.2	685			0.623593837312251	4	FACETS	0.918	0.871	0.966	0.918	0.871	0.966	CLONAL	2	TRUE	2	0.738052578776875	4		567	836	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001438	29001438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1473309404	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	231	326	0	ENST00000282397.4:c.1294G>A	p.Glu432Lys	p.E432K	ENST00000282397	NM_002019.4	432	Gaa/Aaa	10/30	0.623593837312251	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.738052578776875	4		326	526	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041073	29041073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	107	695	1	ENST00000282397.4:c.355G>A	p.Glu119Lys	p.E119K	ENST00000282397	NM_002019.4	119	Gaa/Aaa	3/30	0.623593837312251	4	FACETS	0.794	0.713	0.879	0.397	0.356	0.44	SUBCLONAL	1	TRUE	2	0.738052578776875	4		696	635	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609655	81609655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	493	764	0	ENST00000298171.2:c.1253G>A	p.Arg418Lys	p.R418K	ENST00000298171	NM_000369.2	418	aGa/aAa	10/10	0.712745845819454	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.738052578776875	4		764	1123	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610608	81610608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	273	520	0	ENST00000298171.2:c.2206G>A	p.Glu736Lys	p.E736K	ENST00000298171	NM_000369.2	736	Gaa/Aaa	10/10	0.712745845819454	4	FACETS	0.967	0.914	1	0.967	0.914	1	CLONAL	2	TRUE	2	0.738052578776875	4		520	665	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472609	88472609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	330	566	0	ENST00000360948.2:c.1946G>A	p.Gly649Asp	p.G649D	ENST00000360948	NM_001012338.2	649	gGt/gAt	16/19	0.738052578776875	4	FACETS	1	0.976	1	0.694	0.66	0.728	CLONAL	2	TRUE	1	0.738052578776875	4		566	747	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680747	88680748	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	250	760	1	ENST00000360948.2:c.509_510delinsAA	p.Trp170Ter	p.W170*	ENST00000360948	NM_001012338.2	170	tGG/tAA	6/19	0.738052578776875	4	FACETS	0.943	0.88	1	0.314	0.293	0.336	CLONAL	1	TRUE	1	0.738052578776875	4		761	1249	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99452036	99452036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	501	467	0	ENST00000268035.6:c.1370C>T	p.Ser457Phe	p.S457F	ENST00000268035	NM_000875.3	457	tCc/tTc	6/21	0.738052578776875	4	FACETS	0.994	0.962	1	0.994	0.962	1	CLONAL	3	TRUE	1	0.738052578776875	4		467	791	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2093621	2093621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	350	1040	1	ENST00000219066.1:c.656C>T	p.Pro219Leu	p.P219L	ENST00000219066	NM_002528.5	219	cCc/cTc	4/6	0.738052578776875	3	FACETS	1	0.98	1	0.535	0.506	0.564	CLONAL	1	TRUE	1	0.738052578776875	3		1041	1214	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900423	3900423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	626	940	1	ENST00000262367.5:c.673C>T	p.Pro225Ser	p.P225S	ENST00000262367	NM_004380.2	225	Ccg/Tcg	2/31	0.738052578776875	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.738052578776875	3		941	1097	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857944	9857944	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267604687	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	480	669	1	ENST00000330684.3:c.3457G>A	p.Asp1153Asn	p.D1153N	ENST00000330684	NM_001134407.1	1153	Gat/Aat	13/13	0.738052578776875	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.738052578776875	3		670	864	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041996	14041996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	127	418	0	ENST00000311895.7:c.2543C>T	p.Pro848Leu	p.P848L	ENST00000311895	NM_005236.2	848	cCc/cTc	11/11	0.738052578776875	3	FACETS	0.956	0.871	1	0.478	0.435	0.522	CLONAL	1	TRUE	1	0.738052578776875	3		418	493	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864569	56864569	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	159	478	0	ENST00000308159.5:c.1057C>T	p.Gln353Ter	p.Q353*	ENST00000308159	NM_014669.4	353	Cag/Tag	10/22	0.738052578776875	3	FACETS	0.882	0.811	0.955	0.441	0.405	0.478	CLONAL	1	TRUE	1	0.738052578776875	3		478	669	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867302	68867302	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	217	638	0	ENST00000261769.5:c.2549C>T	p.Ser850Phe	p.S850F	ENST00000261769	NM_004360.3	850	tCc/tTc	16/16	0.738052578776875	3	FACETS	0.949	0.884	1	0.475	0.442	0.508	CLONAL	1	TRUE	1	0.738052578776875	3		638	848	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993593	72993593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	253	787	0	ENST00000268489.5:c.452C>T	p.Thr151Ile	p.T151I	ENST00000268489	NM_006885.3	151	aCc/aTc	2/10	0.738052578776875	3	FACETS	1	0.962	1	0.517	0.485	0.551	CLONAL	1	TRUE	1	0.738052578776875	3		787	907	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81927337	81927338	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	572	897	1	ENST00000359376.3:c.1010_1011delinsAA	p.Arg337Gln	p.R337Q	ENST00000359376	NM_002661.3	337	cGG/cAA	12/33	0.738052578776875	3	FACETS	0.959	0.926	0.993	0.959	0.926	0.993	CLONAL	2	TRUE	1	0.738052578776875	3		898	1106	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780068	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	626	492	0	ENST00000269305.4:c.472C>T	p.Arg158Cys	p.R158C	ENST00000269305	NM_001126112.2	158	Cgc/Tgc	5/11	0.636726986556029	4	FACETS	0.967	0.931	1	0.967	0.931	1	CLONAL	2	TRUE	2	0.738052578776875	4		492	1525	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108232	8108232	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	531	833	1	ENST00000585124.1:c.992C>T	p.Ser331Phe	p.S331F	ENST00000585124	NM_004217.3	331	tCt/tTt	9/9	0.636726986556029	4	FACETS	0.913	0.877	0.951	0.913	0.877	0.951	CLONAL	2	TRUE	2	0.738052578776875	4		834	1369	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546086	29546086	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057518134	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	324	582	0	ENST00000356175.3:c.1591C>T	p.Gln531Ter	p.Q531*	ENST00000356175	NM_000267.3	531	Caa/Taa	14/57	0.636726986556029	4	FACETS	0.886	0.84	0.933	0.886	0.84	0.933	CLONAL	2	TRUE	2	0.738052578776875	4		582	861	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592305	29592305	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	218	440	0	ENST00000356175.3:c.4720C>T	p.Gln1574Ter	p.Q1574*	ENST00000356175	NM_000267.3	1574	Caa/Taa	35/57	0.636726986556029	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.738052578776875	4		440	484	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369270	40369270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781121963	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	385	651	1	ENST00000293328.3:c.1288C>T	p.Arg430Cys	p.R430C	ENST00000293328	NM_012448.3	430	Cgt/Tgt	11/19	0.636726986556029	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.738052578776875	4		652	875	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246713	41246713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1380919500	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	321	607	0	ENST00000357654.3:c.835C>T	p.His279Tyr	p.H279Y	ENST00000357654	NM_007294.3	279	Cat/Tat	10/23	0.636726986556029	4	FACETS	0.995	0.945	1	0.995	0.945	1	CLONAL	2	TRUE	2	0.738052578776875	4		607	760	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805706	46805706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	619	942	0	ENST00000290295.7:c.250G>A	p.Gly84Arg	p.G84R	ENST00000290295	NM_006361.5	84	Gga/Aga	1/2	0.636726986556029	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.738052578776875	4		942	1387	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621008	1621008	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	731	1054	2	ENST00000344749.5:c.1052C>T	p.Ser351Phe	p.S351F	ENST00000344749	NM_001136139.2	351	tCc/tTc	13/19	0.636726986556029	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.738052578776875	4		1056	1692	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221039	5221039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	426	705	0	ENST00000357368.4:c.3427C>T	p.Pro1143Ser	p.P1143S	ENST00000357368	NM_002850.3	1143	Cct/Tct	20/38	0.636726986556029	4	FACETS	0.965	0.922	1	0.965	0.922	1	CLONAL	2	TRUE	2	0.738052578776875	4		705	1040	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117138	7117138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	578	910	0	ENST00000302850.5:c.4078C>T	p.Pro1360Ser	p.P1360S	ENST00000302850	NM_000208.2	1360	Cct/Tct	22/22	0.636726986556029	4	FACETS	0.969	0.932	1	0.969	0.932	1	CLONAL	2	TRUE	2	0.738052578776875	4		910	1405	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11015752	11015752	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	349	484	2	ENST00000327064.4:c.346G>A	p.Asp116Asn	p.D116N	ENST00000327064	NM_199141.1	116	Gat/Aat	2/16	0.636726986556029	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.738052578776875	4		486	779	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350516	15350517	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	670	901	2	ENST00000263377.2:c.3398_3399delinsTT	p.Pro1133Leu	p.P1133L	ENST00000263377	NM_058243.2	1133	cCC/cTT	16/20	0.636726986556029	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	2	0.738052578776875	4		903	1455	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353723	15353723	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	650	965	0	ENST00000263377.2:c.3157C>T	p.Pro1053Ser	p.P1053S	ENST00000263377	NM_058243.2	1053	Ccc/Tcc	14/20	0.636726986556029	4	FACETS	0.985	0.95	1	0.985	0.95	1	CLONAL	2	TRUE	2	0.738052578776875	4		965	1554	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19261496	19261496	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763146191	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	491	651	0	ENST00000162023.5:c.49C>T	p.Arg17Trp	p.R17W	ENST00000162023		17	Cgg/Tgg	6/13	0.636726986556029	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.738052578776875	4		651	1124	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216626	36216627	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	530	869	3	ENST00000222270.7:c.3792_3793delinsTT	p.Leu1265Phe	p.L1265F	ENST00000222270	NM_014727.1	1264	caCCtc/caTTtc	13/37	0.636726986556029	4	FACETS	0.938	0.901	0.976	0.938	0.901	0.976	CLONAL	2	TRUE	2	0.738052578776875	4		872	1330	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743975	41743975	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	702	1063	0	ENST00000301178.4:c.910C>T	p.Pro304Ser	p.P304S	ENST00000301178	NM_021913.4	304	Cct/Tct	7/20	0.636726986556029	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.738052578776875	4		1063	1613	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758775	41758775	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374737642	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	674	1001	1	ENST00000301178.4:c.1829G>A	p.Arg610Gln	p.R610Q	ENST00000301178	NM_021913.4	610	cGa/cAa	16/20	0.636726986556029	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.738052578776875	4		1002	1504	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466778	25466778	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	714	682	0	ENST00000264709.3:c.1925G>A	p.Gly642Glu	p.G642E	ENST00000264709	NM_175629.2	642	gGa/gAa	16/23	0.738052578776875	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.738052578776875	3		682	825	SUCCESS
REL	5966	MSKCC	GRCh37	2	61128146	61128146	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	275	356	0	ENST00000295025.8:c.322C>T	p.Arg108Ter	p.R108*	ENST00000295025	NM_002908.2	108	Cga/Tga	4/11	0.738052578776875	4	FACETS	0.923	0.88	0.965	0.923	0.88	0.965	CLONAL	3	TRUE	1	0.738052578776875	4		356	468	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726900	61726900	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	124	454	0	ENST00000401558.2:c.538G>A	p.Asp180Asn	p.D180N	ENST00000401558	NM_003400.3	180	Gat/Aat	7/25	0.738052578776875	4	FACETS	0.878	0.796	0.964	0.293	0.265	0.322	CLONAL	1	TRUE	1	0.738052578776875	4		454	665	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251853	212251853	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	238	347	0	ENST00000342788.4:c.3206G>A	p.Gly1069Glu	p.G1069E	ENST00000342788	NM_005235.2	1069	gGa/gAa	27/28	0.738052578776875	4	FACETS	0.892	0.846	0.937	0.892	0.846	0.937	CLONAL	3	TRUE	1	0.738052578776875	4		347	419	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426665	212426665	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	166	629	1	ENST00000342788.4:c.2450C>T	p.Ser817Leu	p.S817L	ENST00000342788	NM_005235.2	817	tCa/tTa	20/28	0.738052578776875	4	FACETS	0.885	0.814	0.96	0.295	0.271	0.32	CLONAL	1	TRUE	1	0.738052578776875	4		630	883	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426789	212426789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	163	501	0	ENST00000342788.4:c.2326G>A	p.Asp776Asn	p.D776N	ENST00000342788	NM_005235.2	776	Gat/Aat	20/28	0.738052578776875	4	FACETS	0.928	0.853	1	0.309	0.284	0.336	CLONAL	1	TRUE	1	0.738052578776875	4		501	827	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632269	215632269	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	153	542	1	ENST00000260947.4:c.1505C>T	p.Ala502Val	p.A502V	ENST00000260947	NM_000465.2	502	gCc/gTc	6/11	0.738052578776875	4	FACETS	0.849	0.777	0.924	0.283	0.259	0.308	CLONAL	1	TRUE	1	0.738052578776875	4		543	849	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561543	9561543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	571	635	0	ENST00000353224.5:c.239C>T	p.Thr80Ile	p.T80I	ENST00000353224	NM_177990.2	80	aCc/aTc	4/10	0.738052578776875	5	FACETS	1	0.981	1	1	0.981	1	CLONAL	4	TRUE	1	0.738052578776875	5		635	806	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739037	40739037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	265	710	0	ENST00000373198.4:c.3247G>A	p.Gly1083Ser	p.G1083S	ENST00000373198	NM_133170.3	1083	Ggc/Agc	24/32	0.738052578776875	5	FACETS	1	0.957	1	0.258	0.241	0.275	CLONAL	1	TRUE	1	0.738052578776875	5		710	1468	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747103	40747103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	244	709	0	ENST00000373198.4:c.2979G>A	p.Met993Ile	p.M993I	ENST00000373198	NM_133170.3	993	atG/atA	22/32	0.738052578776875	5	FACETS	1	0.959	1	0.26	0.242	0.278	CLONAL	1	TRUE	1	0.738052578776875	5		709	1341	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877408	40877408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	843	668	0	ENST00000373198.4:c.2288C>T	p.Thr763Ile	p.T763I	ENST00000373198	NM_133170.3	763	aCc/aTc	15/32	0.738052578776875	5	FACETS	0.974	0.951	0.996	0.974	0.951	0.996	CLONAL	4	TRUE	1	0.738052578776875	5		668	1236	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944527	40944527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371433526	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	809	609	0	ENST00000373198.4:c.1975G>A	p.Asp659Asn	p.D659N	ENST00000373198	NM_133170.3	659	Gat/Aat	12/32	0.738052578776875	5	FACETS	1	0.989	1	1	0.989	1	CLONAL	4	TRUE	1	0.738052578776875	5		609	1132	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514563	41514563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	169	499	0	ENST00000373198.4:c.98C>T	p.Ser33Phe	p.S33F	ENST00000373198	NM_133170.3	33	tCc/tTc	2/32	0.738052578776875	5	FACETS	0.997	0.916	1	0.249	0.229	0.271	CLONAL	1	TRUE	1	0.738052578776875	5		499	968	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62298863	62298863	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1215252604	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1442	332	819	1	ENST00000360203.5:c.656C>T	p.Ala219Val	p.A219V	ENST00000360203	NM_001283009.1	219	gCc/gTc	8/35	0.738052578776875	5	FACETS	1	0.977	1	0.267	0.251	0.283	CLONAL	1	TRUE	1	0.738052578776875	5		820	1774	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775521	39775521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	384	733	0	ENST00000288319.7:c.499G>A	p.Glu167Lys	p.E167K	ENST00000288319	NM_182918.3	167	Gaa/Aaa	4/10	0.716693796065721	2	FACETS	0.982	0.95	1	0.982	0.95	1	CLONAL	2	TRUE	0	0.738052578776875	2		733	530	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164466	47164467	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	102	371	0	ENST00000409792.3:c.1659_1660delinsTT	p.Arg554Cys	p.R554C	ENST00000409792	NM_014159.6	553	tcCCgt/tcTTgt	3/21	0.738052578776875	3	FACETS	1	0.92	1	0.511	0.461	0.564	CLONAL	1	TRUE	1	0.738052578776875	3		371	370	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445106	89445106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301060598	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	92	372	0	ENST00000336596.2:c.1426G>A	p.Glu476Lys	p.E476K	ENST00000336596	NM_005233.5	476	Gaa/Aaa	6/17	0.738052578776875	3	FACETS	0.862	0.771	0.957	0.431	0.385	0.479	CLONAL	1	TRUE	1	0.738052578776875	3		372	396	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119634978	119634978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	222	314	1	ENST00000316626.5:c.521C>T	p.Ser174Phe	p.S174F	ENST00000316626		174	tCc/tTc	5/12	0.738052578776875	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.738052578776875	3		315	344	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960122	134960122	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528389234	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	224	672	0	ENST00000398015.3:c.2479G>A	p.Asp827Asn	p.D827N	ENST00000398015	NM_004441.4	827	Gat/Aat	13/16	0.738052578776875	3	FACETS	1	0.962	1	0.522	0.487	0.558	CLONAL	1	TRUE	1	0.738052578776875	3		672	796	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176527	142176527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	153	557	0	ENST00000350721.4:c.7574C>T	p.Pro2525Leu	p.P2525L	ENST00000350721	NM_001184.3	2525	cCt/cTt	45/47	0.738052578776875	3	FACETS	0.93	0.855	1	0.465	0.427	0.505	CLONAL	1	TRUE	1	0.738052578776875	3		557	610	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191527	185191527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754424536	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	236	608	1	ENST00000265026.3:c.2408G>A	p.Arg803Gln	p.R803Q	ENST00000265026	NM_004721.4	803	cGa/cAa	11/14	0.738052578776875	3	FACETS	1	0.948	1	0.508	0.475	0.542	CLONAL	1	TRUE	1	0.738052578776875	3		609	862	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455576	189455576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754361670	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	248	711	1	ENST00000264731.3:c.110G>A	p.Arg37Gln	p.R37Q	ENST00000264731	NM_003722.4	37	cGa/cAa	2/14	0.613788562932122	3	FACETS	0.933	0.883	0.983	0.933	0.883	0.983	CLONAL	2	TRUE	1	0.738052578776875	3		712	493	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584549	189584549	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	296	482	0	ENST00000264731.3:c.845G>A	p.Gly282Glu	p.G282E	ENST00000264731	NM_003722.4	282	gGa/gAa	6/14	0.613788562932122	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.738052578776875	3		482	529	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806164	1806164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	340	1004	1	ENST00000260795.2:c.1183C>T	p.Leu395Phe	p.L395F	ENST00000260795		395	Ctc/Ttc	8/17	0.738052578776875	3	FACETS	0.99	0.936	1	0.495	0.468	0.523	CLONAL	1	TRUE	1	0.738052578776875	3		1005	1274	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146616	55146616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs34392012	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	349	443	1	ENST00000257290.5:c.2290C>T	p.Arg764Cys	p.R764C	ENST00000257290	NM_006206.4	764	Cgt/Tgt	16/23	0.738052578776875	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.738052578776875	3		444	603	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948196	55948196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	137	616	1	ENST00000263923.4:c.3775G>A	p.Asp1259Asn	p.D1259N	ENST00000263923	NM_002253.2	1259	Gac/Aac	29/30	0.738052578776875	3	FACETS	0.983	0.899	1	0.492	0.449	0.535	CLONAL	1	TRUE	1	0.738052578776875	3		617	517	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968582	55968582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	206	709	0	ENST00000263923.4:c.2081C>T	p.Pro694Leu	p.P694L	ENST00000263923	NM_002253.2	694	cCc/cTc	14/30	0.738052578776875	3	FACETS	1	0.932	1	0.501	0.466	0.537	CLONAL	1	TRUE	1	0.738052578776875	3		709	763	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510336	187510336	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	109	300	0	ENST00000441802.2:c.13177C>T	p.Pro4393Ser	p.P4393S	ENST00000441802	NM_005245.3	4393	Cct/Tct	27/27	0.738052578776875	3	FACETS	1	0.947	1	0.533	0.483	0.586	CLONAL	1	TRUE	1	0.738052578776875	3		300	379	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530980	187530980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173149913	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	295	526	1	ENST00000441802.2:c.10043C>T	p.Ala3348Val	p.A3348V	ENST00000441802	NM_005245.3	3348	gCc/gTc	15/27	0.738052578776875	3	FACETS	0.96	0.914	1	0.96	0.914	1	CLONAL	2	TRUE	1	0.738052578776875	3		527	570	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539623	187539623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	242	432	0	ENST00000441802.2:c.8117C>T	p.Pro2706Leu	p.P2706L	ENST00000441802	NM_005245.3	2706	cCt/cTt	10/27	0.738052578776875	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.738052578776875	3		432	436	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1268746	1268746	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	550	856	5	ENST00000310581.5:c.2471C>T	p.Ser824Phe	p.S824F	ENST00000310581	NM_198253.2	824	tCc/tTc	9/16	0.712745845819454	4	FACETS	0.924	0.888	0.961	0.924	0.888	0.961	CLONAL	2	TRUE	2	0.738052578776875	4		861	1401	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875645	35875645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201449880	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	248	386	0	ENST00000303115.3:c.832G>A	p.Asp278Asn	p.D278N	ENST00000303115	NM_002185.3	278	Gat/Aat	7/8	0.712745845819454	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.738052578776875	4		386	532	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80064748	80064748	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs376667075	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	243	583	0	ENST00000265081.6:c.2179C>T	p.Arg727Ter	p.R727*	ENST00000265081	NM_002439.4	727	Cga/Tga	15/24	0.738052578776875	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.738052578776875	2		583	323	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047190	180047190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770500099	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	609	847	1	ENST00000261937.6:c.2525G>A	p.Arg842Gln	p.R842Q	ENST00000261937	NM_182925.4	842	cGa/cAa	17/30	0.738052578776875	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.738052578776875	2		848	773	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158577	26158578	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	352	644	1	ENST00000289316.2:c.180_181delinsAA	p.Met60_Gly61delinsIleArg	p.M60_G61delinsIR	ENST00000289316	NM_138720.2	60	atGGgg/atAAgg	1/2	0.738052578776875	3	FACETS	0.912	0.871	0.953	0.912	0.871	0.953	CLONAL	2	TRUE	1	0.738052578776875	3		645	716	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680751	30680751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	205	585	0	ENST00000376406.3:c.968C>T	p.Pro323Leu	p.P323L	ENST00000376406	NM_014641.2	323	cCt/cTt	5/15	0.738052578776875	3	FACETS	0.998	0.928	1	0.499	0.464	0.535	CLONAL	1	TRUE	1	0.738052578776875	3		585	762	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169252	32169252	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	536	782	0	ENST00000375023.3:c.3781G>A	p.Asp1261Asn	p.D1261N	ENST00000375023	NM_004557.3	1261	Gat/Aat	22/30	0.738052578776875	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.738052578776875	3		782	987	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170030	32170030	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	690	1073	0	ENST00000375023.3:c.3578G>A	p.Gly1193Asp	p.G1193D	ENST00000375023	NM_004557.3	1193	gGc/gAc	21/30	0.738052578776875	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.738052578776875	3		1073	1274	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188281	32188281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	701	964	0	ENST00000375023.3:c.1060G>A	p.Glu354Lys	p.E354K	ENST00000375023	NM_004557.3	354	Gag/Aag	6/30	0.738052578776875	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	1	0.738052578776875	3		964	1201	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066762	94066762	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	124	422	0	ENST00000369303.4:c.997T>A	p.Ser333Thr	p.S333T	ENST00000369303	NM_004440.3	333	Tct/Act	5/17	0.738052578776875	3	FACETS	1	0.969	1	0.567	0.517	0.618	CLONAL	1	TRUE	1	0.738052578776875	3		422	406	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553324	106553324	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	422	584	1	ENST00000369096.4:c.1289G>A	p.Ser430Asn	p.S430N	ENST00000369096	NM_001198.3	430	aGc/aAc	5/7	0.738052578776875	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.738052578776875	3		585	752	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112029135	112029135	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs778635709	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	122	408	0	ENST00000368678.4:c.433C>T	p.Gln145Ter	p.Q145*	ENST00000368678		145	Cag/Tag	5/13	0.738052578776875	3	FACETS	0.955	0.868	1	0.477	0.434	0.523	CLONAL	1	TRUE	1	0.738052578776875	3		408	474	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622137	117622137	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs142264513	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	82	355	0	ENST00000368508.3:c.6733G>A	p.Gly2245Ser	p.G2245S	ENST00000368508	NM_002944.2	2245	Ggt/Agt	42/43	0.738052578776875	3	FACETS	1	0.932	1	0.53	0.473	0.59	CLONAL	1	TRUE	1	0.738052578776875	3		355	287	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715330	117715330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	156	312	0	ENST00000368508.3:c.1159G>A	p.Glu387Lys	p.E387K	ENST00000368508	NM_002944.2	387	Gaa/Aaa	10/43	0.738052578776875	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.738052578776875	3		312	264	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332843	152332843	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	185	529	1	ENST00000206249.3:c.1149G>A	p.Trp383Ter	p.W383*	ENST00000206249	NM_000125.3	383	tgG/tgA	5/8	0.738052578776875	3	FACETS	0.975	0.903	1	0.487	0.451	0.525	CLONAL	1	TRUE	1	0.738052578776875	3		530	704	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522299	157522299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867707366	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	579	746	0	ENST00000346085.5:c.4571C>T	p.Ser1524Leu	p.S1524L	ENST00000346085	NM_020732.3	1524	tCg/tTg	18/20	0.738052578776875	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.738052578776875	3		746	1025	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984094	2984094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	350	584	0	ENST00000396946.4:c.436G>A	p.Asp146Asn	p.D146N	ENST00000396946	NM_032415.4	146	Gac/Aac	5/25	0.738052578776875	5	FACETS	0.969	0.92	1	0.646	0.613	0.68	CLONAL	2	TRUE	2	0.738052578776875	5		584	1031	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026826	6026827	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	434	636	1	ENST00000265849.7:c.1569_1570delinsTT	p.Pro524Ser	p.P524S	ENST00000265849	NM_000535.5	523	tcCCca/tcTTca	11/15	0.738052578776875	5	FACETS	0.985	0.94	1	0.657	0.626	0.687	CLONAL	2	TRUE	2	0.738052578776875	5		637	1258	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946203	13946203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	476	491	0	ENST00000405192.2:c.893G>A	p.Gly298Glu	p.G298E	ENST00000405192	NM_001163147.1	298	gGa/gAa	10/12	0.738052578776875	5	FACETS	0.994	0.957	1	0.994	0.957	1	CLONAL	3	TRUE	2	0.738052578776875	5		491	911	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729763	41729763	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	340	462	0	ENST00000242208.4:c.766C>T	p.Leu256Phe	p.L256F	ENST00000242208	NM_002192.2	256	Ctc/Ttc	3/3	0.738052578776875	5	FACETS	1	0.99	1	0.767	0.729	0.805	CLONAL	2	TRUE	2	0.738052578776875	5		462	844	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450363	50450363	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1441542459	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	229	600	0	ENST00000331340.3:c.547C>T	p.Arg183Cys	p.R183C	ENST00000331340	NM_006060.4	183	Cgc/Tgc	5/8	0.738052578776875	5	FACETS	1	0.972	1	0.361	0.335	0.387	CLONAL	1	TRUE	2	0.738052578776875	5		600	1209	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92252390	92252390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373488172	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	149	327	1	ENST00000265734.4:c.658C>T	p.Arg220Cys	p.R220C	ENST00000265734	NM_001259.6	220	Cgt/Tgt	6/8	0.738052578776875	5	FACETS	0.841	0.773	0.91	0.56	0.515	0.607	CLONAL	2	TRUE	2	0.738052578776875	5		328	506	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508910	106508910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	446	571	0	ENST00000359195.3:c.904G>A	p.Glu302Lys	p.E302K	ENST00000359195	NM_002649.2	302	Gag/Aag	2/11	0.738052578776875	5	FACETS	1	0.976	1	0.688	0.657	0.72	CLONAL	2	TRUE	2	0.738052578776875	5		571	1233	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38153446	38153446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780316096	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	622	523	0	ENST00000317025.8:c.2783C>T	p.Ser928Leu	p.S928L	ENST00000317025	NM_023034.1	928	tCg/tTg	16/24	0.738052578776875	6	FACETS	0.99	0.959	1	0.99	0.959	1	CLONAL	4	TRUE	2	0.738052578776875	6		523	1054	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277160	38277160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	1042	771	0	ENST00000425967.3:c.1268G>A	p.Gly423Glu	p.G423E	ENST00000425967	NM_001174067.1	423	gGg/gAg	10/19	0.738052578776875	6	FACETS	1	0.991	1	1	0.991	1	CLONAL	4	TRUE	2	0.738052578776875	6		771	1696	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989689	68989690	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	303	655	0	ENST00000288368.4:c.1627_1628delinsAA	p.Gly543Lys	p.G543K	ENST00000288368	NM_024870.2	543	GGa/AAa	15/40	0.738052578776875	6	FACETS	0.832	0.783	0.882	0.416	0.391	0.441	CLONAL	2	TRUE	2	0.738052578776875	6		655	1222	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005933	69005933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868574550	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	254	623	0	ENST00000288368.4:c.2344G>A	p.Asp782Asn	p.D782N	ENST00000288368	NM_024870.2	782	Gat/Aat	21/40	0.738052578776875	6	FACETS	0.907	0.85	0.965	0.453	0.425	0.483	CLONAL	2	TRUE	2	0.738052578776875	6		623	940	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970964	70970964	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868518861	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1344	493	924	0	ENST00000276594.2:c.1297C>T	p.Pro433Ser	p.P433S	ENST00000276594	NM_024504.3	433	Ccc/Tcc	6/8	0.738052578776875	6	FACETS	0.9	0.859	0.942	0.45	0.429	0.471	CLONAL	2	TRUE	2	0.738052578776875	6		924	1837	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044504	5044504	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs925878120	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	401	436	0	ENST00000381652.3:c.452C>T	p.Ser151Phe	p.S151F	ENST00000381652	NM_004972.3	151	tCt/tTt	5/25	0.738052578776875	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	1	0.738052578776875	4		436	605	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8339038	8339038	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	389	465	1	ENST00000356435.5:c.5263C>T	p.His1755Tyr	p.H1755Y	ENST00000356435		1755	Cac/Tac	32/35	0.738052578776875	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	1	0.738052578776875	4		466	591	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486041	8486041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	561	661	0	ENST00000356435.5:c.2776C>T	p.His926Tyr	p.H926Y	ENST00000356435		926	Cac/Tac	17/35	0.738052578776875	4	FACETS	0.995	0.965	1	0.995	0.965	1	CLONAL	3	TRUE	1	0.738052578776875	4		661	885	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517990	8517990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	143	486	0	ENST00000356435.5:c.1401G>A	p.Met467Ile	p.M467I	ENST00000356435		467	atG/atA	10/35	0.738052578776875	4	FACETS	1	0.959	1	0.36	0.329	0.393	CLONAL	1	TRUE	1	0.738052578776875	4		486	623	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518111	8518111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	199	621	0	ENST00000356435.5:c.1280G>A	p.Arg427Gln	p.R427Q	ENST00000356435		427	cGa/cAa	10/35	0.738052578776875	4	FACETS	1	0.981	1	0.387	0.359	0.416	CLONAL	1	TRUE	1	0.738052578776875	4		621	807	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27190619	27190619	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	581	731	0	ENST00000380036.4:c.1420G>A	p.Gly474Arg	p.G474R	ENST00000380036	NM_000459.3	474	Gga/Aga	10/23	0.738052578776875	4	FACETS	0.957	0.927	0.987	0.957	0.927	0.987	CLONAL	3	TRUE	1	0.738052578776875	4		731	953	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27204953	27204953	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45510599	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	205	615	0	ENST00000380036.4:c.2254C>T	p.Leu752Phe	p.L752F	ENST00000380036	NM_000459.3	752	Ctt/Ttt	14/23	0.738052578776875	4	FACETS	1	0.944	1	0.34	0.315	0.366	CLONAL	1	TRUE	1	0.738052578776875	4		615	947	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882004	36882004	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	973	789	1	ENST00000358127.4:c.1009C>T	p.Pro337Ser	p.P337S	ENST00000358127	NM_001280556.1	337	Cct/Tct	8/10	0.738052578776875	4	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	1	0.738052578776875	4		790	1384	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911463	101911463	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	221	232	0	ENST00000374994.4:c.1388C>T	p.Ala463Val	p.A463V	ENST00000374994	NM_004612.2	463	gCc/gTc	9/9	0.738052578776875	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	3	TRUE	1	0.738052578776875	4		232	341	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759395	133759395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1194832601	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	284	830	1	ENST00000318560.5:c.1718C>T	p.Pro573Leu	p.P573L	ENST00000318560	NM_005157.4	573	cCt/cTt	11/11	0.738052578776875	4	FACETS	0.984	0.924	1	0.328	0.308	0.349	CLONAL	1	TRUE	1	0.738052578776875	4		831	1359	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801003	135801003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554820276	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	138	478	0	ENST00000298552.3:c.334C>T	p.Leu112Phe	p.L112F	ENST00000298552	NM_001162426.1	112	Ctt/Ttt	5/23	0.738052578776875	4	FACETS	0.974	0.889	1	0.325	0.296	0.355	CLONAL	1	TRUE	1	0.738052578776875	4		478	667	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396736	139396736	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	853	929	0	ENST00000277541.6:c.5372C>T	p.Ser1791Phe	p.S1791F	ENST00000277541	NM_017617.3	1791	tCc/tTc	28/34	0.738052578776875	4	FACETS	0.959	0.934	0.983	0.959	0.934	0.983	CLONAL	3	TRUE	1	0.738052578776875	4		929	1397	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400119	139400119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	1069	1073	0	ENST00000277541.6:c.4229C>T	p.Pro1410Leu	p.P1410L	ENST00000277541	NM_017617.3	1410	cCc/cTc	25/34	0.738052578776875	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	1	0.738052578776875	4		1073	1641	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412337	139412337	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1237	302	931	0	ENST00000277541.6:c.1308C>G	p.Phe436Leu	p.F436L	ENST00000277541	NM_017617.3	436	ttC/ttG	8/34	0.738052578776875	4	FACETS	0.924	0.868	0.982	0.308	0.289	0.328	CLONAL	1	TRUE	1	0.738052578776875	4		931	1539	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923820	39923820	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	602	885	0	ENST00000378444.4:c.3271C>T	p.Pro1091Ser	p.P1091S	ENST00000378444	NM_001123385.1	1091	Ccc/Tcc	7/15	0.738052578776875	5	FACETS	1	0.977	1	0.681	0.655	0.708	CLONAL	2	TRUE	2	0.738052578776875	5		885	1682	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409829	63409829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	202	601	0	ENST00000330258.3:c.3338G>A	p.Arg1113Lys	p.R1113K	ENST00000330258	NM_152424.3	1113	aGg/aAg	2/2	0.738052578776875	5	FACETS	1	0.932	1	0.336	0.311	0.362	CLONAL	1	TRUE	2	0.738052578776875	5		601	1145	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411524	63411524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	629	933	1	ENST00000330258.3:c.1643C>T	p.Ser548Phe	p.S548F	ENST00000330258	NM_152424.3	548	tCc/tTc	2/2	0.738052578776875	5	FACETS	0.986	0.948	1	0.657	0.632	0.683	CLONAL	2	TRUE	2	0.738052578776875	5		934	1822	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412679	63412679	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	661	729	1	ENST00000330258.3:c.488C>T	p.Pro163Leu	p.P163L	ENST00000330258	NM_152424.3	163	cCc/cTc	2/2	0.738052578776875	5	FACETS	0.987	0.956	1	0.987	0.956	1	CLONAL	3	TRUE	2	0.738052578776875	5		730	1274	SUCCESS
AR	367	MSKCC	GRCh37	X	66765506	66765506	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	994	1036	1	ENST00000374690.3:c.518G>A	p.Gly173Asp	p.G173D	ENST00000374690	NM_000044.3	173	gGc/gAc	1/8	0.738052578776875	5	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	2	0.738052578776875	5		1037	1791	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344992	70344992	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	716	650	0	ENST00000374080.3:c.2222C>T	p.Pro741Leu	p.P741L	ENST00000374080		741	cCc/cTc	15/45	0.738052578776875	5	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	2	0.738052578776875	5		650	1306	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351928	70351928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	577	625	0	ENST00000374080.3:c.4125G>A	p.Met1375Ile	p.M1375I	ENST00000374080		1375	atG/atA	30/45	0.738052578776875	5	FACETS	0.939	0.906	0.973	0.939	0.906	0.973	CLONAL	3	TRUE	2	0.738052578776875	5		625	1169	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939496	76939496	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057523785	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	484	677	0	ENST00000373344.5:c.1252C>T	p.Arg418Ter	p.R418*	ENST00000373344	NM_000489.3	418	Cga/Tga	9/35	0.738052578776875	5	FACETS	0.957	0.92	0.993	0.957	0.92	0.993	CLONAL	3	TRUE	2	0.738052578776875	5		677	963	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76954116	76954116	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	288	364	0	ENST00000373344.5:c.135T>A	p.Asp45Glu	p.D45E	ENST00000373344	NM_000489.3	45	gaT/gaA	3/35	0.738052578776875	5	FACETS	0.955	0.908	1	0.955	0.908	1	CLONAL	3	TRUE	2	0.738052578776875	5		364	574	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630211	100630211	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	472	618	0	ENST00000308731.7:c.62C>T	p.Ser21Leu	p.S21L	ENST00000308731	NM_000061.2	21	tCa/tTa	2/19	0.738052578776875	5	FACETS	0.943	0.906	0.979	0.943	0.906	0.979	CLONAL	3	TRUE	2	0.738052578776875	5		618	953	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191747	123191747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	314	472	0	ENST00000218089.9:c.1336G>A	p.Gly446Arg	p.G446R	ENST00000218089	NM_001042749.1	446	Gga/Aga	15/35	0.738052578776875	5	FACETS	0.91	0.866	0.954	0.91	0.866	0.954	CLONAL	3	TRUE	2	0.738052578776875	5		472	657	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	184	151	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.927	0.863	0.992	0.927	0.863	0.992	CLONAL	1	TRUE	1	0.800364573031653	2		151	496	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508779	29508779	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	220	610	0	ENST00000356175.3:c.706C>T	p.Gln236Ter	p.Q236*	ENST00000356175	NM_000267.3	236	Cag/Tag	7/57	0.800364573031653	1	FACETS	0.964	0.917	1	0.964	0.917	1	CLONAL	1	TRUE	0	0.800364573031653	1		610	342	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40476813	40476813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	344	762	0	ENST00000264657.5:c.1516G>A	p.Glu506Lys	p.E506K	ENST00000264657	NM_139276.2	506	Gag/Aag	17/24	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.800364573031653	2		762	854	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987076	36987076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	334	719	1	ENST00000354822.5:c.613G>A	p.Glu205Lys	p.E205K	ENST00000354822	NM_001079668.2	205	Gag/Aag	3/3	1	2	FACETS	0.945	0.897	0.994	0.945	0.897	0.994	CLONAL	1	TRUE	1	0.800364573031653	2		720	883	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49439896	49439896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	399	770	0	ENST00000301067.7:c.4645G>A	p.Glu1549Lys	p.E1549K	ENST00000301067	NM_003482.3	1549	Gaa/Aaa	17/54	0.800364573031653	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.800364573031653	1		770	565	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148991	119148991	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	319	570	0	ENST00000264033.4:c.1211G>T	p.Cys404Phe	p.C404F	ENST00000264033	NM_005188.3	404	tGt/tTt	8/16	0.800364573031653	1	FACETS	0.966	0.927	1	0.966	0.927	1	CLONAL	1	TRUE	0	0.800364573031653	1		570	495	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724448	162724448	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	254	560	0	ENST00000367921.3:c.220C>T	p.Pro74Ser	p.P74S	ENST00000367921	NM_006182.2	74	Cct/Tct	5/18	1	2	FACETS	0.952	0.896	1	0.952	0.896	1	CLONAL	1	TRUE	1	0.800364573031653	2		560	667	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577469	64577469	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	285	624	0	ENST00000312049.6:c.113C>A	p.Ser38Tyr	p.S38Y	ENST00000312049	NM_130799.2	38	tCc/tAc	2/10	1	2	FACETS	0.91	0.859	0.961	0.91	0.859	0.961	CLONAL	1	TRUE	1	0.800364573031653	2		624	783	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619823	1619823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1481750909	NA	P-0039360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	755	773	0	ENST00000344749.5:c.1123C>T	p.Pro375Ser	p.P375S	ENST00000344749	NM_001136139.2	375	Ccc/Tcc	14/19	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.800364573031653	2		773	930	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128030488	128030488	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1272649511	NA	P-0039360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	327	647	0	ENST00000285398.2:c.1780C>T	p.Gln594Ter	p.Q594*	ENST00000285398	NM_000122.1	594	Cag/Tag	11/15	1	2	FACETS	0.969	0.92	1	0.969	0.92	1	CLONAL	1	TRUE	1	0.800364573031653	2		647	843	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755405	39755405	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	262	715	0	ENST00000288319.7:c.1360A>G	p.Asn454Asp	p.N454D	ENST00000288319	NM_182918.3	454	Aat/Gat	10/10	1	2	FACETS	0.904	0.852	0.958	0.904	0.852	0.958	CLONAL	1	TRUE	1	0.800364573031653	2		715	724	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927393	49927393	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs998378597	NA	P-0039360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	392	792	0	ENST00000296474.3:c.3911G>T	p.Arg1304Leu	p.R1304L	ENST00000296474	NM_002447.2	1304	cGg/cTg	19/20	0.800364573031653	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.800364573031653	1		792	559	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858062	152858062	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	278	318	0	ENST00000406277.2:c.553C>T	p.Gln185Ter	p.Q185*	ENST00000406277	NM_152274.4	185	Cag/Tag	6/7	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.800364573031653	1		318	351	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0039410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	98	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.226194604058298	3	FACETS	1	0.914	1	1	0.914	1	CLONAL	2	TRUE	1	0.226194604058298	3		288	472	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0039410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	31	248	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.727	0.588	0.884	0.727	0.588	0.884	SUBCLONAL	1	TRUE	1	0.226194604058298	2		249	377	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0039410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	16	326	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	0.366	0.269	0.481	0.366	0.269	0.481	SUBCLONAL	1	TRUE	1	0.226194604058298	2		326	387	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971187	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0039410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	71	332	0	ENST00000304494.5:c.171_172delinsTT	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	57	gcCCga/gcTTga	2/3	0.226194604058298	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.226194604058298	1		332	392	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222727	5222727	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746980740	NA	P-0039410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	46	486	1	ENST00000357368.4:c.3076C>T	p.Arg1026Cys	p.R1026C	ENST00000357368	NM_002850.3	1026	Cgc/Tgc	18/38	1	2	FACETS	0.794	0.669	0.933	0.794	0.669	0.933	CLONAL	1	TRUE	1	0.226194604058298	2		487	512	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477813	140477813	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs180177037	NA	P-0039410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	43	406	0	ENST00000288602.6:c.1495A>G	p.Lys499Glu	p.K499E	ENST00000288602	NM_004333.4	499	Aaa/Gaa	12/18	0.226194604058298	3	FACETS	0.694	0.58	0.821	0.347	0.29	0.411	SUBCLONAL	1	TRUE	1	0.226194604058298	3		406	610	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956771	68956771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774302685	NA	P-0039410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	170	642	1	ENST00000288368.4:c.889C>T	p.Arg297Cys	p.R297C	ENST00000288368	NM_024870.2	297	Cgt/Tgt	8/40	0.0848255058891156	3	FACETS	0.887	0.816	0.962	0.887	0.816	0.962	INDETERMINATE	2	TRUE	1	0.226194604058298	3		643	943	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149504382	149504382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	29	514	0	ENST00000261799.4:c.1820G>A	p.Gly607Asp	p.G607D	ENST00000261799	NM_002609.3	607	gGc/gAc	13/23	1	2	FACETS	0.496	0.397	0.609	0.496	0.397	0.609	SUBCLONAL	1	TRUE	1	0.226194604058298	2		514	517	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677912	117677912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765109582	NA	P-0039410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	25	364	0	ENST00000368508.3:c.4021G>A	p.Ala1341Thr	p.A1341T	ENST00000368508	NM_002944.2	1341	Gct/Act	25/43	0.226194604058298	1	FACETS	0.495	0.39	0.616	0.495	0.39	0.616	SUBCLONAL	1	TRUE	0	0.226194604058298	1		364	396	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870265	44870265	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0039410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	28	347	0	ENST00000377967.4:c.443+1G>C		p.X148_splice	ENST00000377967	NM_021140.2	148			1	2	FACETS	0.592	0.473	0.729	0.592	0.473	0.729	SUBCLONAL	1	TRUE	1	0.226194604058298	2		347	418	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	214	151	0				ENST00000310581	NM_198253.2	-/1132			0.437391773355329	3	FACETS	1	0.972	1			1	CLONAL	2	TRUE	NA	0.607600956415086	3		151	437	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0039415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	822	454	0	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	0.593174261508691	5	FACETS	1	0.972	1	1	0.972	1	CLONAL	3	TRUE	2	0.607600956415086	5		454	1720	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0039415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	252	297	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.607600956415086	2	FACETS	0.987	0.94	1	0.987	0.94	1	CLONAL	2	TRUE	0	0.607600956415086	2		297	420	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857524	9857524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778230379	NA	P-0039415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	559	446	0	ENST00000330684.3:c.3877G>A	p.Asp1293Asn	p.D1293N	ENST00000330684	NM_001134407.1	1293	Gat/Aat	13/13	0.607600956415086	5	FACETS	0.981	0.951	1	0.981	0.951	1	CLONAL	4	TRUE	1	0.607600956415086	5		446	896	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859016	57859016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765428970	NA	P-0039415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	202	725	0	ENST00000228682.2:c.512G>A	p.Arg171Gln	p.R171Q	ENST00000228682	NM_005269.2	171	cGg/cAg	5/12	0.607600956415086	3	FACETS	0.929	0.862	0.999	0.465	0.431	0.5	CLONAL	1	TRUE	1	0.607600956415086	3		725	933	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972913	55972913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	316	575	0	ENST00000263923.4:c.1477G>A	p.Gly493Arg	p.G493R	ENST00000263923	NM_002253.2	493	Gga/Aga	11/30	0.600909949473203	4	FACETS	0.921	0.871	0.971	0.921	0.871	0.971	CLONAL	2	TRUE	2	0.607600956415086	4		575	908	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9787030	9787030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397518423	NA	P-0039415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	810	534	1	ENST00000377346.4:c.3061G>A	p.Glu1021Lys	p.E1021K	ENST00000377346	NM_005026.3	1021	Gaa/Aaa	24/24	0.607600956415086	5	FACETS	1	0.989	1			1	CLONAL	4	TRUE	NA	0.607600956415086	5		535	1244	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266485	198266485	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	106	279	0	ENST00000335508.6:c.2351T>C	p.Met784Thr	p.M784T	ENST00000335508	NM_012433.2	784	aTg/aCg	16/25	0.607600956415086	3	FACETS	1	0.906	1	0.502	0.453	0.554	CLONAL	1	TRUE	1	0.607600956415086	3		279	453	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745609	162745609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	137	458	0	ENST00000367921.3:c.2024C>T	p.Ser675Phe	p.S675F	ENST00000367921	NM_006182.2	675	tCc/tTc	15/18	0.600909949473203	4	FACETS	0.876	0.797	0.958	0.438	0.398	0.479	CLONAL	1	TRUE	2	0.607600956415086	4		458	828	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476403	88476403	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	298	473	0	ENST00000360948.2:c.1729C>T	p.Pro577Ser	p.P577S	ENST00000360948	NM_001012338.2	577	Ccc/Tcc	15/19	0.593174261508691	5	FACETS	0.987	0.931	1	0.658	0.621	0.696	CLONAL	2	TRUE	2	0.607600956415086	5		473	950	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672800	86672800	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764802465	NA	P-0039415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	88	355	0	ENST00000274376.6:c.2287G>A	p.Glu763Lys	p.E763K	ENST00000274376	NM_002890.2	763	Gaa/Aaa	17/25	0.607600956415086	3	FACETS	0.817	0.727	0.913	0.409	0.363	0.457	CLONAL	1	TRUE	1	0.607600956415086	3		355	462	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521067	187521067	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	150	401	0	ENST00000441802.2:c.12088C>T	p.Pro4030Ser	p.P4030S	ENST00000441802	NM_005245.3	4030	Ccg/Tcg	22/27	0.607600956415086	3	FACETS	1	0.966	1	0.549	0.504	0.596	CLONAL	1	TRUE	1	0.607600956415086	3		401	586	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38173545	38173545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	303	364	1	ENST00000317025.8:c.1871C>T	p.Ser624Leu	p.S624L	ENST00000317025	NM_023034.1	624	tCa/tTa	10/24	0.607600956415086	3	FACETS	0.999	0.949	1	0.999	0.949	1	CLONAL	2	TRUE	1	0.607600956415086	3		365	651	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165783	118165783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	238	389	0	ENST00000369448.3:c.293C>T	p.Ala98Val	p.A98V	ENST00000369448	NM_017709.3	98	gCt/gTt	2/2	0.607600956415086	2	FACETS	0.997	0.948	1	0.997	0.948	1	CLONAL	2	TRUE	0	0.607600956415086	2		389	393	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510217	120510217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	131	373	0	ENST00000256646.2:c.1292G>A	p.Gly431Glu	p.G431E	ENST00000256646	NM_024408.3	431	gGa/gAa	8/34	0.607600956415086	6	FACETS	1	0.91	1			1	CLONAL	1	TRUE	NA	0.607600956415086	6		373	952	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589385	28589385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	235	421	0	ENST00000241453.7:c.2662C>T	p.Pro888Ser	p.P888S	ENST00000241453	NM_004119.2	888	Cct/Tct	22/24	0.600909949473203	4	FACETS	0.946	0.888	1	0.946	0.888	1	CLONAL	2	TRUE	2	0.607600956415086	4		421	657	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576180	88576180	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	197	650	0	ENST00000360948.2:c.1493C>T	p.Pro498Leu	p.P498L	ENST00000360948	NM_001012338.2	498	cCc/cTc	13/19	0.593174261508691	5	FACETS	1	0.934	1	0.337	0.311	0.364	CLONAL	1	TRUE	2	0.607600956415086	5		650	1226	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349103	11349103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	128	318	0	ENST00000332029.2:c.233G>A	p.Gly78Glu	p.G78E	ENST00000332029	NM_003745.1	78	gGa/gAa	2/2	0.607600956415086	5	FACETS	1	0.957	1	0.274	0.248	0.301	CLONAL	1	TRUE	1	0.607600956415086	5		318	736	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50818352	50818352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	179	277	0	ENST00000398568.2:c.1930C>T	p.Pro644Ser	p.P644S	ENST00000398568	NM_001042412.1	644	Cct/Tct	11/18	0.607600956415086	3	FACETS	0.863	0.804	0.923	0.863	0.804	0.923	CLONAL	2	TRUE	1	0.607600956415086	3		277	445	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448342	56448342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	248	797	0	ENST00000407977.2:c.305G>A	p.Gly102Glu	p.G102E	ENST00000407977		102	gGa/gAa	3/10	0.607600956415086	3	FACETS	0.958	0.895	1	0.479	0.447	0.512	CLONAL	1	TRUE	1	0.607600956415086	3		797	1111	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790090	40790090	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	366	621	0	ENST00000373198.4:c.2641C>G	p.Arg881Gly	p.R881G	ENST00000373198	NM_133170.3	881	Cgg/Ggg	18/32	0.593174261508691	5	FACETS	0.926	0.878	0.975	0.618	0.585	0.65	CLONAL	2	TRUE	2	0.607600956415086	5		621	1243	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196646	106196646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	278	503	0	ENST00000380013.4:c.4979G>A	p.Arg1660Lys	p.R1660K	ENST00000380013	NM_001127208.2	1660	aGg/aAg	11/11	0.600909949473203	4	FACETS	0.985	0.93	1	0.985	0.93	1	CLONAL	2	TRUE	2	0.607600956415086	4		503	747	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293790	1293790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	288	977	0	ENST00000310581.5:c.1211C>T	p.Pro404Leu	p.P404L	ENST00000310581	NM_198253.2	404	cCc/cTc	2/16	0.437391773355329	3	FACETS	0.968	0.909	1			1	CLONAL	1	TRUE	NA	0.607600956415086	3		977	1277	SUCCESS
APC	324	MSKCC	GRCh37	5	112173792	112173792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	108	320	0	ENST00000257430.4:c.2501C>T	p.Ser834Phe	p.S834F	ENST00000257430	NM_000038.5	834	tCc/tTc	16/16	0.607600956415086	3	FACETS	0.995	0.898	1	0.497	0.449	0.548	CLONAL	1	TRUE	1	0.607600956415086	3		320	466	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721607	176721607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	163	556	0	ENST00000439151.2:c.7238C>T	p.Ser2413Phe	p.S2413F	ENST00000439151	NM_022455.4	2413	tCt/tTt	23/23	0.607600956415086	3	FACETS	0.914	0.841	0.991	0.457	0.42	0.496	CLONAL	1	TRUE	1	0.607600956415086	3		556	765	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056973	180056973	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	256	836	1	ENST00000261937.6:c.646C>A	p.Leu216Ile	p.L216I	ENST00000261937	NM_182925.4	216	Ctt/Att	5/30	0.607600956415086	3	FACETS	0.971	0.908	1	0.485	0.454	0.518	CLONAL	1	TRUE	1	0.607600956415086	3		837	1132	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453131	140453136	+	protein_altering_variant	In_Frame_Del	DEL	ATTTCA	ATTTCA	TAT	novel	NA	P-0039415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	284	433	1	ENST00000288602.6:c.1799_1804delinsATA	p.Val600_Ser602delinsAspThr	p.V600_S602delinsDT	ENST00000288602	NM_004333.4	600	gTGAAATct/gATAct	15/18	0.607600956415086	4	FACETS	0.834	0.791	0.876	0.834	0.791	0.876	CLONAL	3	TRUE	1	0.607600956415086	4		434	601	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518308	8518308	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	151	223	0	ENST00000356435.5:c.1083A>T	p.Lys361Asn	p.K361N	ENST00000356435		361	aaA/aaT	10/35	0.607600956415086	2	FACETS	0.941	0.882	1	0.941	0.882	1	CLONAL	2	TRUE	0	0.607600956415086	2		223	264	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938305	76938305	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	164	263	0	ENST00000373344.5:c.2443T>G	p.Ser815Ala	p.S815A	ENST00000373344	NM_000489.3	815	Tct/Gct	9/35	0.60346306398307	2	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.607600956415086	2		263	434	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615576	100615576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	436	249	0	ENST00000308731.7:c.756G>A	p.Trp252Ter	p.W252*	ENST00000308731	NM_000061.2	252	tgG/tgA	8/19	0.607600956415086	3	FACETS	0.889	0.867	0.91			1	CLONAL	4	TRUE	NA	0.607600956415086	3		249	526	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0039629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	110	615	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.28818237553989	2		615	582	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0039629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	66	248	1				ENST00000310581	NM_198253.2	-/1132			0.115854739905391	0	FACETS	0.921	0.804	1			1	INDETERMINATE	1	FALSE	0	0.28818237553989	0		249	354	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713457	30713457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	92	698	1	ENST00000295754.5:c.782C>T	p.Ala261Val	p.A261V	ENST00000295754	NM_003242.5	261	gCc/gTc	4/7	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.28818237553989	2		699	536	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157470057	157470057	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554226145	NA	P-0039629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	77	530	0	ENST00000346085.5:c.2851C>T	p.Gln951Ter	p.Q951*	ENST00000346085	NM_020732.3	951	Cag/Tag	9/20	0.140724997445095	4	FACETS	0.92	0.813	1	0.92	0.813	1	INDETERMINATE	2	FALSE	2	0.28818237553989	4		530	374	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209262	133209262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147954675	NA	P-0039629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	146	941	1	ENST00000320574.5:c.6124G>A	p.Gly2042Arg	p.G2042R	ENST00000320574	NM_006231.2	2042	Gga/Aga	44/49	1	2	FACETS	0.761	0.696	0.828	1	0.988	1	SUBCLONAL	2	FALSE	1	0.28818237553989	2		942	666	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28631532	28631532	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	57	514	0	ENST00000241453.7:c.436C>T	p.Gln146Ter	p.Q146*	ENST00000241453	NM_004119.2	146	Cag/Tag	4/24	0.28818237553989	0	FACETS	1	0.94	1			1	CLONAL	1	FALSE	0	0.28818237553989	0		514	244	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0039687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	109	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.31129768049377	3	FACETS	0.833	0.751	0.918	0.833	0.751	0.918	CLONAL	2	TRUE	1	0.31129768049377	3		288	486	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0039687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	41	248	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.85	0.711	1	0.85	0.711	1	CLONAL	1	TRUE	1	0.31129768049377	2		249	310	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807365	3807365	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	39	380	0	ENST00000262367.5:c.3622C>T	p.Pro1208Ser	p.P1208S	ENST00000262367	NM_004380.2	1208	Cca/Tca	19/31	1	2	FACETS	0.525	0.435	0.626	0.525	0.435	0.626	SUBCLONAL	1	TRUE	1	0.31129768049377	2		380	477	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725524	117725524	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1388562198	NA	P-0039687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	61	471	0	ENST00000368508.3:c.357G>A	p.Trp119Ter	p.W119*	ENST00000368508	NM_002944.2	119	tgG/tgA	5/43	1	2	FACETS	0.692	0.597	0.796	0.692	0.597	0.796	SUBCLONAL	1	TRUE	1	0.31129768049377	2		471	566	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280034	18280034	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs202137312	NA	P-0039687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	20	328	0	ENST00000222254.8:c.2117A>G	p.Asp706Gly	p.D706G	ENST00000222254	NM_005027.3	706	gAc/gGc	16/16	1	2	FACETS	0.322	0.246	0.412	0.322	0.246	0.412	SUBCLONAL	1	TRUE	1	0.31129768049377	2		328	399	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879061	151879061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs965807663	NA	P-0039687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	37	512	0	ENST00000262189.6:c.5884C>T	p.Pro1962Ser	p.P1962S	ENST00000262189	NM_170606.2	1962	Ccc/Tcc	36/59	0.31129768049377	3	FACETS	0.377	0.309	0.453	0.188	0.154	0.227	SUBCLONAL	1	TRUE	1	0.31129768049377	3		512	729	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40678643	40678643	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	52	516	0	ENST00000249776.8:c.385G>A	p.Gly129Arg	p.G129R	ENST00000249776	NM_033286.3	129	Gga/Aga	3/9	1	2	FACETS	0.519	0.441	0.604	0.519	0.441	0.604	SUBCLONAL	1	TRUE	1	0.31129768049377	2		516	644	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81979789	81979789	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781497956	NA	P-0039687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	33	450	0	ENST00000359376.3:c.3491C>T	p.Ser1164Phe	p.S1164F	ENST00000359376	NM_002661.3	1164	tCc/tTc	31/33	1	2	FACETS	0.463	0.377	0.56	0.463	0.377	0.56	SUBCLONAL	1	TRUE	1	0.31129768049377	2		450	458	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696399	47696400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	131	578	0	ENST00000347630.2:c.423dup	p.Leu142SerfsTer4	p.L142Sfs*4	ENST00000347630	NM_001007230.1	141	-/T	6/11	0.138542157448139	4	FACETS	1	0.981	1	0.666	0.604	0.731	INDETERMINATE	1	TRUE	2	0.31129768049377	4		578	829	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705287	52705287	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	33	420	0	ENST00000322088.6:c.169G>A	p.Asp57Asn	p.D57N	ENST00000322088	NM_014225.5	57	Gat/Aat	2/15	1	2	FACETS	0.424	0.345	0.514	0.424	0.345	0.514	SUBCLONAL	1	TRUE	1	0.31129768049377	2		420	500	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306658	41306658	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	72	568	0	ENST00000373198.4:c.1001G>T	p.Trp334Leu	p.W334L	ENST00000373198	NM_133170.3	334	tGg/tTg	7/32	1	2	FACETS	0.629	0.548	0.715	0.629	0.548	0.715	SUBCLONAL	1	TRUE	1	0.31129768049377	2		568	736	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876232	35876232	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	38	480	0	ENST00000303115.3:c.1024G>A	p.Gly342Arg	p.G342R	ENST00000303115	NM_002185.3	342	Ggg/Agg	8/8	1	2	FACETS	0.414	0.342	0.496	0.414	0.342	0.496	SUBCLONAL	1	TRUE	1	0.31129768049377	2		480	589	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971133	21971147	+	inframe_deletion	In_Frame_Del	DEL	GGGGTCGGCGCAGTT	GGGGTCGGCGCAGTT	-	novel	NA	P-0039687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	27	472	0	ENST00000304494.5:c.211_225del	p.Asn71_Pro75del	p.N71_P75del	ENST00000304494	NM_000077.4	71	AACTGCGCCGACCCC/-	2/3	1	2	FACETS	0.398	0.316	0.492	0.398	0.316	0.492	SUBCLONAL	1	TRUE	1	0.31129768049377	2		472	436	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410667	63410667	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868452636	NA	P-0039687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	137	646	0	ENST00000330258.3:c.2500C>T	p.Leu834Phe	p.L834F	ENST00000330258	NM_152424.3	834	Ctt/Ttt	2/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.31129768049377	2		646	747	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0040090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	291	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.414232620651583	7	FACETS	0.979	0.931	1	0.979	0.931	1	CLONAL	5	TRUE	2	0.414232620651583	7		288	584	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	208	151	0				ENST00000310581	NM_198253.2	-/1132			0.414232620651583	5	FACETS	0.952	0.89	1	0.952	0.89	1	CLONAL	3	TRUE	2	0.414232620651583	5		151	570	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0040090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	282	297	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.414232620651583	3	FACETS	0.905	0.865	0.944	1	0.993	1	CLONAL	4	TRUE	0	0.414232620651583	3		297	454	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673725	30673725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs78556678	NA	P-0040090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	88	476	0	ENST00000376406.3:c.3235C>T	p.Arg1079Cys	p.R1079C	ENST00000376406	NM_014641.2	1079	Cgt/Tgt	10/15	0.414232620651583	5	FACETS	0.836	0.74	0.939	0.279	0.246	0.313	CLONAL	1	TRUE	2	0.414232620651583	5		476	824	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29083947	29083947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876658872	NA	P-0040090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	40	164	0	ENST00000328354.6:c.1570G>A	p.Glu524Lys	p.E524K	ENST00000328354	NM_007194.3	524	Gaa/Aaa	15/15	0.414232620651583	5	FACETS	1	0.93	1	0.408	0.341	0.481	CLONAL	1	TRUE	2	0.414232620651583	5		164	256	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435988	116435988	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755043272	NA	P-0040090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	492	510	0	ENST00000397752.3:c.3983C>T	p.Pro1328Leu	p.P1328L	ENST00000397752	NM_000245.2	1328	cCa/cTa	21/21	0.414232620651583	7	FACETS	0.936	0.9	0.973	0.936	0.9	0.973	CLONAL	5	TRUE	2	0.414232620651583	7		510	1033	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413114	63413114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	158	598	0	ENST00000330258.3:c.53G>A	p.Gly18Glu	p.G18E	ENST00000330258	NM_152424.3	18	gGg/gAg	2/2	0.414232620651583	2	FACETS	1	0.979	1	0.598	0.55	0.648	CLONAL	1	TRUE	0	0.414232620651583	2		598	638	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094322	27094322	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	105	350	0	ENST00000324856.7:c.3030G>T	p.Lys1010Asn	p.K1010N	ENST00000324856	NM_006015.4	1010	aaG/aaT	11/20	0.414232620651583	3	FACETS	1	0.932	1	0.524	0.47	0.58	CLONAL	1	TRUE	1	0.414232620651583	3		350	584	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436532	49436532	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	109	494	0	ENST00000301067.7:c.5774T>A	p.Phe1925Tyr	p.F1925Y	ENST00000301067	NM_003482.3	1925	tTt/tAt	26/54	0.414232620651583	5	FACETS	0.925	0.83	1	0.308	0.276	0.343	CLONAL	1	TRUE	2	0.414232620651583	5		494	922	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448350	49448351	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	107	532	0	ENST00000301067.7:c.360_361delinsTT	p.Pro121Ser	p.P121S	ENST00000301067	NM_003482.3	120	ttCCct/ttTTct	3/54	0.414232620651583	5	FACETS	0.961	0.861	1	0.32	0.287	0.356	CLONAL	1	TRUE	2	0.414232620651583	5		532	872	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95584063	95584063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	134	260	0	ENST00000393063.1:c.1405C>T	p.Pro469Ser	p.P469S	ENST00000393063	NM_030621.3	469	Cca/Tca	10/28	0.414232620651583	6	FACETS	0.846	0.774	0.921	0.846	0.774	0.921	CLONAL	3	TRUE	3	0.414232620651583	6		260	466	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537890	212537890	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	90	360	0	ENST00000342788.4:c.1715C>A	p.Pro572Gln	p.P572Q	ENST00000342788	NM_005235.2	572	cCg/cAg	14/28	0.406465630920206	4	FACETS	1	0.895	1	0.336	0.298	0.376	CLONAL	1	TRUE	1	0.414232620651583	4		360	610	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161999	47161999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747176449	NA	P-0040090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	108	299	0	ENST00000409792.3:c.4127C>T	p.Ser1376Phe	p.S1376F	ENST00000409792	NM_014159.6	1376	tCc/tTc	3/21	0.162473020292884	6	FACETS	1	0.975	1	0.823	0.745	0.905	INDETERMINATE	2	TRUE	3	0.414232620651583	6		299	386	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662386	117662386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	143	370	0	ENST00000368508.3:c.4991C>T	p.Ser1664Phe	p.S1664F	ENST00000368508	NM_002944.2	1664	tCc/tTc	30/43	0.414232620651583	3	FACETS	0.962	0.885	1	0.962	0.885	1	CLONAL	2	TRUE	1	0.414232620651583	3		370	433	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874418	151874418	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040090-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	120	249	0	ENST00000262189.6:c.8120T>C	p.Val2707Ala	p.V2707A	ENST00000262189	NM_170606.2	2707	gTt/gCt	38/59	0.414232620651583	7	FACETS	1	0.917	1	0.405	0.367	0.445	CLONAL	2	TRUE	2	0.414232620651583	7		249	582	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	78	248	1				ENST00000310581	NM_198253.2	-/1132			0.143967297578719	4	FACETS	0.94	0.83	1	0.94	0.83	1	CLONAL	2	TRUE	2	0.236962132328641	4		249	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	189	631	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.215190579674453	2	FACETS	0.833	0.774	0.895	1	0.986	1	CLONAL	3	TRUE	0	0.236962132328641	2		631	638	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161718	47161718	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	55	272	0	ENST00000409792.3:c.4408C>T	p.Pro1470Ser	p.P1470S	ENST00000409792	NM_014159.6	1470	Cca/Tca	3/21	0.143967297578719	4	FACETS	0.878	0.755	1	0.878	0.755	1	CLONAL	2	TRUE	2	0.236962132328641	4		272	327	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747137	40747137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752831315	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	77	496	0	ENST00000373198.4:c.2945C>T	p.Pro982Leu	p.P982L	ENST00000373198	NM_133170.3	982	cCg/cTg	22/32	0.204014800813528	3	FACETS	1	0.969	1	0.664	0.584	0.75	CLONAL	1	TRUE	1	0.236962132328641	3		496	547	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871777	37871777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147382623	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	158	730	2	ENST00000269571.5:c.1301G>A	p.Arg434Gln	p.R434Q	ENST00000269571		434	cGa/cAa	11/27	0.143967297578719	4	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	2	0.236962132328641	4		732	785	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812335	212812335	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	19	256	0	ENST00000342788.4:c.241C>T	p.Arg81Ter	p.R81*	ENST00000342788	NM_005235.2	81	Cga/Tga	3/28	1	2	FACETS	0.482	0.365	0.619	0.482	0.365	0.619	SUBCLONAL	1	TRUE	1	0.236962132328641	2		256	333	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149260	119149260	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs868103494	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	114	759	0	ENST00000264033.4:c.1268T>A	p.Ile423Asn	p.I423N	ENST00000264033	NM_005188.3	423	aTt/aAt	9/16	0.215190579674453	2	FACETS	0.841	0.76	0.927	0.841	0.76	0.927	CLONAL	2	TRUE	0	0.236962132328641	2		759	572	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414262	32414262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144788858	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	171	467	0	ENST00000332351.3:c.1289G>A	p.Arg430Gln	p.R430Q	ENST00000332351	NM_024426.4	430	cGa/cAa	8/10	0.164980598191001	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.236962132328641	3		467	683	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045755	143045755	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781219504	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	37	464	0	ENST00000262992.4:c.1879G>A	p.Val627Ile	p.V627I	ENST00000262992	NM_001101669.1	627	Gtc/Atc	17/24	1	2	FACETS	0.615	0.506	0.736	0.615	0.506	0.736	SUBCLONAL	1	TRUE	1	0.236962132328641	2		464	508	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100312	27100312	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	134	697	1	ENST00000324856.7:c.4024C>T	p.Gln1342Ter	p.Q1342*	ENST00000324856	NM_006015.4	1342	Cag/Tag	17/20	0.143967297578719	4	FACETS	0.908	0.826	0.995	0.908	0.826	0.995	CLONAL	2	TRUE	2	0.236962132328641	4		698	770	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022562	31022562	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1245899583	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	132	625	0	ENST00000375687.4:c.2047A>G	p.Thr683Ala	p.T683A	ENST00000375687	NM_015338.5	683	Acc/Gcc	13/13	0.204014800813528	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.236962132328641	3		625	537	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931901	68931901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	84	528	0	ENST00000288368.4:c.331C>T	p.His111Tyr	p.H111Y	ENST00000288368	NM_024870.2	111	Cac/Tac	3/40	0.164980598191001	3	FACETS	1	0.971	1	0.663	0.586	0.745	CLONAL	1	TRUE	1	0.236962132328641	3		528	598	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681033	117681033	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	81	494	0	ENST00000368508.3:c.3587G>A	p.Gly1196Glu	p.G1196E	ENST00000368508	NM_002944.2	1196	gGa/gAa	23/43	0.236962132328641	3	FACETS	1	0.974	1	0.698	0.616	0.785	CLONAL	1	TRUE	1	0.236962132328641	3		494	548	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196487	106196487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	48	391	0	ENST00000380013.4:c.4820C>T	p.Ser1607Leu	p.S1607L	ENST00000380013	NM_001127208.2	1607	tCa/tTa	11/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.236962132328641	2		391	305	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482840	140482840	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	128	650	0	ENST00000288602.6:c.1295C>T	p.Ser432Leu	p.S432L	ENST00000288602	NM_004333.4	432	tCa/tTa	10/18	0.236962132328641	6	FACETS	0.905	0.82	0.995	0.452	0.41	0.498	CLONAL	2	TRUE	2	0.236962132328641	6		650	880	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770576	40770576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	97	390	0	ENST00000373198.4:c.2806C>T	p.Arg936Ter	p.R936*	ENST00000373198	NM_133170.3	936	Cga/Tga	19/32	0.204014800813528	3	FACETS	0.914	0.818	1	0.914	0.818	1	CLONAL	2	TRUE	1	0.236962132328641	3		390	501	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709176	117709176	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	54	297	0	ENST00000368508.3:c.1781T>A	p.Ile594Asn	p.I594N	ENST00000368508	NM_002944.2	594	aTt/aAt	13/43	0.236962132328641	3	FACETS	1	0.965	1	0.728	0.625	0.84	CLONAL	1	TRUE	1	0.236962132328641	3		297	350	SUCCESS
AR	367	MSKCC	GRCh37	X	66765070	66765070	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	152	444	0	ENST00000374690.3:c.82C>T	p.Gln28Ter	p.Q28*	ENST00000374690	NM_000044.3	28	Cag/Tag	1/8	0.236962132328641	2	FACETS	1	0.962	1			1	CLONAL	3	TRUE	NA	0.236962132328641	2		444	402	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609672	117609672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	63	353	0	ENST00000368508.3:c.7027G>A	p.Gly2343Arg	p.G2343R	ENST00000368508	NM_002944.2	2343	Gga/Aga	43/43	0.215190579674453	2	FACETS	0.766	0.667	0.873	0.766	0.667	0.873	SUBCLONAL	2	TRUE	0	0.236962132328641	2		353	347	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272383	11272383	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	107	502	1	ENST00000361445.4:c.3547C>T	p.Gln1183Ter	p.Q1183*	ENST00000361445	NM_004958.3	1183	Cag/Tag	23/58	0.143967297578719	4	FACETS	0.888	0.798	0.983	0.888	0.798	0.983	CLONAL	2	TRUE	2	0.236962132328641	4		503	629	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999053	100999053	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1584	84	705	0	ENST00000325455.5:c.749del	p.Gly250GlufsTer51	p.G250Efs*51	ENST00000325455	NM_001202474.3	250	gGa/ga	1/8	0.236962132328641	21	FACETS	1	0.972	1			1	CLONAL	1	TRUE	NA	0.236962132328641	21		705	1668	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865183	57865183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	222	939	0	ENST00000228682.2:c.2660C>T	p.Thr887Ile	p.T887I	ENST00000228682	NM_005269.2	887	aCc/aTc	12/12	0.215190579674453	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.236962132328641	2		939	803	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219249	133219249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	139	748	0	ENST00000320574.5:c.4795G>A	p.Glu1599Lys	p.E1599K	ENST00000320574	NM_006231.2	1599	Gaa/Aaa	37/49	0.215190579674453	2	FACETS	0.919	0.839	1	0.919	0.839	1	CLONAL	2	TRUE	0	0.236962132328641	2		748	638	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95579538	95579538	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	57	363	0	ENST00000393063.1:c.1931A>G	p.Asp644Gly	p.D644G	ENST00000393063	NM_030621.3	644	gAt/gGt	13/28	0.164980598191001	3	FACETS	0.9	0.778	1	0.9	0.778	1	CLONAL	2	TRUE	1	0.236962132328641	3		363	299	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961580	41961580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	28	549	0	ENST00000219905.7:c.488C>T	p.Pro163Leu	p.P163L	ENST00000219905	NM_001164273.1	163	cCt/cTt	2/24	0.215190579674453	2	FACETS	0.481	0.384	0.593	0.241	0.192	0.297	SUBCLONAL	1	TRUE	0	0.236962132328641	2		549	491	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845592	72845592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762050236	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	172	728	0	ENST00000268489.5:c.3748C>T	p.Pro1250Ser	p.P1250S	ENST00000268489	NM_006885.3	1250	Ccc/Tcc	7/10	0.236962132328641	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.236962132328641	2		728	675	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562721	29562722	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	78	455	1	ENST00000356175.3:c.3801_3802delinsAA	p.Ala1268Thr	p.A1268T	ENST00000356175	NM_000267.3	1267	ttGGca/ttAAca	28/57	0.143967297578719	4	FACETS	0.767	0.675	0.865	0.767	0.675	0.865	SUBCLONAL	2	TRUE	2	0.236962132328641	4		456	531	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719250	61719250	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	41	377	0	ENST00000401558.2:c.1807C>T	p.Gln603Ter	p.Q603*	ENST00000401558	NM_003400.3	603	Cag/Tag	16/25	0.164980598191001	3	FACETS	1	0.893	1	0.547	0.456	0.646	CLONAL	1	TRUE	1	0.236962132328641	3		377	354	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663276	227663276	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	65	596	1	ENST00000305123.5:c.179C>T	p.Pro60Leu	p.P60L	ENST00000305123	NM_005544.2	60	cCc/cTc	1/2	1	2	FACETS	0.966	0.838	1	0.966	0.838	1	CLONAL	1	TRUE	1	0.236962132328641	2		597	568	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22142599	22142599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	106	512	0	ENST00000215832.6:c.803C>T	p.Pro268Leu	p.P268L	ENST00000215832	NM_002745.4	268	cCa/cTa	6/9	0.143967297578719	4	FACETS	0.938	0.843	1	0.938	0.843	1	CLONAL	2	TRUE	2	0.236962132328641	4		512	590	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799878	72799878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	167	458	0	ENST00000325599.8:c.1291G>A	p.Glu431Lys	p.E431K	ENST00000325599	NM_018130.2	431	Gag/Aag	11/11	0.236962132328641	5	FACETS	1	0.973	1			1	CLONAL	3	TRUE	NA	0.236962132328641	5		458	571	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457253	89457253	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1278755088	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	80	353	0	ENST00000336596.2:c.1734A>T	p.Glu578Asp	p.E578D	ENST00000336596	NM_005233.5	578	gaA/gaT	9/17	0.236962132328641	3	FACETS	0.919	0.813	1			1	CLONAL	2	TRUE	NA	0.236962132328641	3		353	411	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480399	89480399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	97	313	0	ENST00000336596.2:c.2236G>A	p.Asp746Asn	p.D746N	ENST00000336596	NM_005233.5	746	Gac/Aac	13/17	0.236962132328641	3	FACETS	0.989	0.886	1			1	CLONAL	2	TRUE	NA	0.236962132328641	3		313	463	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599339	55599339	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs993022333	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	77	422	0	ENST00000288135.5:c.2465A>T	p.Asn822Ile	p.N822I	ENST00000288135	NM_000222.2	822	aAt/aTt	17/21	1	2	FACETS	0.759	0.669	0.855	1	0.977	1	SUBCLONAL	2	TRUE	1	0.236962132328641	2		422	428	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976834	55976834	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	72	530	0	ENST00000263923.4:c.1078C>T	p.Pro360Ser	p.P360S	ENST00000263923	NM_002253.2	360	Cca/Tca	8/30	1	2	FACETS	0.939	0.821	1	0.939	0.821	1	CLONAL	1	TRUE	1	0.236962132328641	2		530	647	SUCCESS
APC	324	MSKCC	GRCh37	5	112179156	112179156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267600320	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	44	339	0	ENST00000257430.4:c.7865C>T	p.Pro2622Leu	p.P2622L	ENST00000257430	NM_000038.5	2622	cCc/cTc	16/16	0.143967297578719	4	FACETS	1	0.958	1	0.736	0.62	0.863	CLONAL	1	TRUE	2	0.236962132328641	4		339	312	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979375	93979375	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	41	332	0	ENST00000369303.4:c.1453C>T	p.Gln485Ter	p.Q485*	ENST00000369303	NM_004440.3	485	Caa/Taa	7/17	0.215190579674453	2	FACETS	1	0.953	1	0.715	0.6	0.84	CLONAL	1	TRUE	0	0.236962132328641	2		332	242	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663616	117663616	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	108	502	0	ENST00000368508.3:c.4616C>T	p.Pro1539Leu	p.P1539L	ENST00000368508	NM_002944.2	1539	cCt/cTt	28/43	0.236962132328641	3	FACETS	0.873	0.785	0.965	0.873	0.785	0.965	CLONAL	2	TRUE	1	0.236962132328641	3		502	584	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710657	117710657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	56	340	0	ENST00000368508.3:c.1615G>A	p.Glu539Lys	p.E539K	ENST00000368508	NM_002944.2	539	Gaa/Aaa	12/43	0.236962132328641	3	FACETS	1	0.961	1	0.681	0.586	0.785	CLONAL	1	TRUE	1	0.236962132328641	3		340	388	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714445	117714445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1307627482	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	74	385	0	ENST00000368508.3:c.1204G>A	p.Glu402Lys	p.E402K	ENST00000368508	NM_002944.2	402	Gaa/Aaa	11/43	0.236962132328641	3	FACETS	0.826	0.726	0.932	0.826	0.726	0.932	CLONAL	2	TRUE	1	0.236962132328641	3		385	423	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978791	13978791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	145	671	0	ENST00000405192.2:c.316G>A	p.Glu106Lys	p.E106K	ENST00000405192	NM_001163147.1	106	Gaa/Aaa	6/12	0.143967297578719	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.236962132328641	4		671	680	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151932999	151932999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1320275944	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	19	84	0	ENST00000262189.6:c.2672C>T	p.Pro891Leu	p.P891L	ENST00000262189	NM_170606.2	891	cCa/cTa	16/59	0.216072067443795	4	FACETS	1	0.88	1	0.636	0.486	0.809	CLONAL	1	TRUE	2	0.236962132328641	4		84	156	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132732	152132732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	108	369	0	ENST00000262189.6:c.140C>T	p.Pro47Leu	p.P47L	ENST00000262189	NM_170606.2	47	cCt/cTt	1/59	0.216072067443795	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.236962132328641	4		369	462	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90960083	90960083	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	46	300	0	ENST00000265433.3:c.1883A>G	p.Glu628Gly	p.E628G	ENST00000265433	NM_002485.4	628	gAa/gGa	12/16	0.215190579674453	2	FACETS	1	0.957	1	0.703	0.596	0.82	CLONAL	1	TRUE	0	0.236962132328641	2		300	276	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340429	8340429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	117	510	0	ENST00000356435.5:c.5167G>A	p.Glu1723Lys	p.E1723K	ENST00000356435		1723	Gag/Aag	31/35	0.236962132328641	2	FACETS	0.959	0.869	1	0.959	0.869	1	CLONAL	2	TRUE	0	0.236962132328641	2		510	515	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486341	8486342	+	stop_gained	Nonsense_Mutation	DNP	TC	TC	AT	novel	NA	P-0040246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	66	285	0	ENST00000356435.5:c.2475_2476delinsAT	p.Lys826Ter	p.K826*	ENST00000356435		825	ggGAaa/ggATaa	17/35	0.236962132328641	2	FACETS	0.913	0.799	1	0.913	0.799	1	CLONAL	2	TRUE	0	0.236962132328641	2		285	305	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0040944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	120	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.957	0.868	1	0.957	0.868	1	CLONAL	1	TRUE	1	0.49	2		288	512	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476367	88476367	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	143	537	0	ENST00000360948.2:c.1765G>T	p.Ala589Ser	p.A589S	ENST00000360948	NM_001012338.2	589	Gcc/Tcc	15/19	1	2	FACETS	0.733	0.669	0.801	0.733	0.669	0.801	SUBCLONAL	1	TRUE	1	0.49	2		537	796	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0041359-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	286	248	1				ENST00000310581	NM_198253.2	-/1132			0.496746517574992	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.821230852286531	3		249	482	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19261496	19261496	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763146191	NA	P-0041359-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	146	651	0	ENST00000162023.5:c.49C>T	p.Arg17Trp	p.R17W	ENST00000162023		17	Cgg/Tgg	6/13	0.525907934070639	1	FACETS	0.369	0.338	0.401	0.369	0.338	0.401	SUBCLONAL	1	TRUE	0	0.821230852286531	1		651	568	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0041359-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	13	456	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.430762469626694	3	FACETS	0.096	0.068	0.131	0.032	0.022	0.044	INDETERMINATE	1	TRUE	0	0.821230852286531	3		456	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578507	7578507	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519977	NA	P-0041359-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	761	998	1	ENST00000269305.4:c.423C>G	p.Cys141Trp	p.C141W	ENST00000269305	NM_001126112.2	141	tgC/tgG	5/11	0.813854030110524	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.821230852286531	2		999	895	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447419	49447419	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041359-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	582	633	0	ENST00000301067.7:c.679del	p.Ala227LeufsTer34	p.A227Lfs*34	ENST00000301067	NM_003482.3	227	Gct/ct	6/54	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	2	TRUE	NA	0.821230852286531	2		633	663	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371864	116371864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750256779	NA	P-0041359-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	306	279	0	ENST00000397752.3:c.1343G>A	p.Gly448Glu	p.G448E	ENST00000397752	NM_000245.2	448	gGa/gAa	3/21	0.496746517574992	3	FACETS	0.961	0.917	1	0.961	0.917	1	CLONAL	2	TRUE	1	0.821230852286531	3		279	547	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500790	8500790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041359-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	79	353	0	ENST00000356435.5:c.2092G>A	p.Glu698Lys	p.E698K	ENST00000356435		698	Gag/Aag	13/35	0.30349039982074	1	FACETS	0.301	0.266	0.338	0.301	0.266	0.338	INDETERMINATE	1	TRUE	0	0.821230852286531	1		353	377	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206803	162206803	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0041359-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	19	288	0	ENST00000366898.1:c.871+1G>C		p.X291_splice	ENST00000366898	NM_004562.2	291			1	2	FACETS	0.131	0.099	0.168	0.131	0.099	0.168	SUBCLONAL	1	TRUE	1	0.821230852286531	2		288	354	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796929	78796939	+	frameshift_variant	Frame_Shift_Del	DEL	CGAAATTTTTT	CGAAATTTTTT	A	novel	NA	P-0041359-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	59	410	2	ENST00000306801.3:c.1042_1052delinsA	p.Arg348AsnfsTer7	p.R348Nfs*7	ENST00000306801	NM_020761.2	348	CGAAATTTTTTa/Aa	9/34	0.068354296084538	4	FACETS	0.418	0.359	0.482	0.209	0.179	0.241	INDETERMINATE	1	TRUE	2	0.821230852286531	4		412	626	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0041581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	71	357	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.244478092657551	4	FACETS	0.977	0.864	1	0.651	0.576	0.73	INDETERMINATE	2	TRUE	1	0.424412367507907	4		357	244	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0041581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	31	473	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.244478092657551	4	FACETS	1	0.909	1	0.399	0.326	0.479	INDETERMINATE	1	TRUE	1	0.424412367507907	4		473	174	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842714	68842715	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	53	479	0	ENST00000261769.5:c.651dup	p.Glu218ArgfsTer5	p.E218Rfs*5	ENST00000261769	NM_004360.3	217	aca/acAa	5/16	0.424412367507907	1	FACETS	0.979	0.847	1	0.979	0.847	1	CLONAL	1	TRUE	0	0.424412367507907	1		479	201	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300417	11300417	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041581-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	29	555	0	ENST00000361445.4:c.1729A>C	p.Ser577Arg	p.S577R	ENST00000361445	NM_004958.3	577	Agc/Cgc	11/58	1	2	FACETS	0.67	0.541	0.814	0.67	0.541	0.814	SUBCLONAL	1	TRUE	1	0.424412367507907	2		555	204	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0042033-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	110	605	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.284422809736238	4	FACETS	0.971	0.872	1	0.486	0.436	0.539	CLONAL	1	TRUE	2	0.321508223337393	4		605	931	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0042033-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	73	321	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.284422809736238	4	FACETS	1	0.957	1	0.606	0.531	0.686	CLONAL	1	TRUE	2	0.321508223337393	4		321	495	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610337	10610337	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042033-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	196	875	0	ENST00000171111.5:c.373A>T	p.Ile125Phe	p.I125F	ENST00000171111	NM_203500.1	125	Att/Ttt	2/6	0.258895626287808	2	FACETS	1	0.99	1	0.736	0.683	0.792	CLONAL	1	TRUE	0	0.321508223337393	2		875	828	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907161	101907161	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042033-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	38	242	0	ENST00000374994.4:c.1121G>C	p.Gly374Ala	p.G374A	ENST00000374994	NM_004612.2	374	gGa/gCa	6/9	0.321508223337393	1	FACETS	0.79	0.658	0.937	0.79	0.658	0.937	CLONAL	1	TRUE	0	0.321508223337393	1		242	251	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123895	46123896	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0042033-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	29	176	0	ENST00000334344.6:c.161_162del	p.Val54AspfsTer11	p.V54Dfs*11	ENST00000334344	NM_152641.2	54	gTC/g	2/21	0.295876408972951	2	FACETS	0.569	0.457	0.696	0.285	0.228	0.348	SUBCLONAL	1	TRUE	0	0.321508223337393	2		176	317	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32438063	32438063	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762688982	NA	P-0042033-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	85	465	0	ENST00000332351.3:c.974C>T	p.Ser325Leu	p.S325L	ENST00000332351	NM_024426.4	325	tCa/tTa	5/10	1	2	FACETS	0.856	0.757	0.961	0.856	0.757	0.961	CLONAL	1	TRUE	1	0.321508223337393	2		465	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577604	7577616	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCAACCTAGGAGA	CCAACCTAGGAGA	-	novel	NA	P-0042033-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	123	432	0	ENST00000269305.4:c.673-8_677del		p.X225_splice	ENST00000269305	NM_001126112.2	225		7/11	0.295876408972951	2	FACETS	0.802	0.73	0.877	0.802	0.73	0.877	CLONAL	2	TRUE	0	0.321508223337393	2		432	477	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561423	9561423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201131316	NA	P-0042212-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	58	350	0	ENST00000353224.5:c.359C>T	p.Ala120Val	p.A120V	ENST00000353224	NM_177990.2	120	gCg/gTg	4/10	0.324160834253667	0	FACETS	0.59	0.511	0.675			1	SUBCLONAL	1	TRUE	0	0.402382917394592	0		350	292	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207168	1207168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520039	NA	P-0042212-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	115	648	0	ENST00000326873.7:c.256C>T	p.Arg86Ter	p.R86*	ENST00000326873	NM_000455.4	86	Cga/Tga	1/10	0.402382917394592	1	FACETS	0.961	0.871	1	0.961	0.871	1	CLONAL	1	TRUE	0	0.402382917394592	1		648	475	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485280	8485280	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042212-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	36	368	0	ENST00000356435.5:c.3100G>T	p.Val1034Leu	p.V1034L	ENST00000356435		1034	Gtg/Ttg	18/35	0.215710182688332	0	FACETS	0.604	0.503	0.715			1	INDETERMINATE	1	TRUE	0	0.402382917394592	0		368	177	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730099	41730099	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042212-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	41	353	0	ENST00000242208.4:c.430G>T	p.Gly144Cys	p.G144C	ENST00000242208	NM_002192.2	144	Ggc/Tgc	3/3	1	2	FACETS	0.822	0.689	0.966	0.822	0.689	0.966	CLONAL	1	TRUE	1	0.402382917394592	2		353	248	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528428	29528428	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs876660782	NA	P-0042212-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	43	231	0	ENST00000356175.3:c.1186-1G>T		p.X396_splice	ENST00000356175	NM_000267.3	396			1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.402382917394592	2		231	176	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553614	29553615	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0042212-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	57	279	0	ENST00000356175.3:c.2166_2167dup	p.Val723GlyfsTer26	p.V723Gfs*26	ENST00000356175	NM_000267.3	721	-/GG	18/57	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.402382917394592	2		279	266	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610498	10610498	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042212-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	91	580	0	ENST00000171111.5:c.212G>C	p.Arg71Pro	p.R71P	ENST00000171111	NM_203500.1	71	cGg/cCg	2/6	0.402382917394592	1	FACETS	0.908	0.811	1	0.908	0.811	1	CLONAL	1	TRUE	0	0.402382917394592	1		580	398	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280753	41280753	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042212-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	86	378	0	ENST00000349496.5:c.2266C>G	p.Leu756Val	p.L756V	ENST00000349496	NM_001904.3	756	Ctg/Gtg	15/15	0.148879502493569	4	FACETS	0.864	0.771	0.962	0.864	0.771	0.962	INDETERMINATE	2	TRUE	2	0.402382917394592	4		378	347	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680620	30680620	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042212-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	66	420	0	ENST00000376406.3:c.1099G>T	p.Ala367Ser	p.A367S	ENST00000376406	NM_014641.2	367	Gcc/Tcc	5/15	0.148879502493569	4	FACETS	1	0.964	1	0.652	0.569	0.74	INDETERMINATE	1	TRUE	2	0.402382917394592	4		420	353	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0042397-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	131	456	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.647657367470801	3	FACETS	0.786	0.714	0.86			1	SUBCLONAL	1	TRUE	NA	0.668054517193384	3		456	666	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983066	201983066	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042397-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	377	579	0	ENST00000359651.3:c.915C>A	p.Phe305Leu	p.F305L	ENST00000359651		305	ttC/ttA	7/8	0.427421234770752	4	FACETS	0.863	0.82	0.906	0.863	0.82	0.906	CLONAL	2	TRUE	2	0.668054517193384	4		579	1091	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76919014	76919014	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0042789-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	78	144	0	ENST00000373344.5:c.3977C>G	p.Ser1326Ter	p.S1326*	ENST00000373344	NM_000489.3	1326	tCa/tGa	12/35	1	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.625887373807194	1		144	147	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715881	117715881	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042789-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	66	324	0	ENST00000368508.3:c.877C>A	p.Leu293Ile	p.L293I	ENST00000368508	NM_002944.2	293	Ctc/Atc	9/43	0.44605861004812	4	FACETS	0.857	0.747	0.975			1	CLONAL	1	TRUE	NA	0.625887373807194	4		324	400	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778815	9778815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042789-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	158	812	0	ENST00000377346.4:c.1084G>A	p.Glu362Lys	p.E362K	ENST00000377346	NM_005026.3	362	Gag/Aag	9/24	0.625887373807194	5	FACETS	1	0.939	1	0.343	0.314	0.374	CLONAL	1	TRUE	2	0.625887373807194	5		812	950	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30194877	30194877	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45458201	NA	P-0042789-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	84	394	0	ENST00000331968.5:c.268C>T	p.Pro90Ser	p.P90S	ENST00000331968	NM_002742.2	90	Cct/Tct	2/18	0.625887373807194	3	FACETS	0.899	0.799	1	0.45	0.399	0.503	CLONAL	1	TRUE	1	0.625887373807194	3		394	392	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641271	12641271	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1372834568	NA	P-0042789-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	21	434	0	ENST00000251849.4:c.1027G>C	p.Glu343Gln	p.E343Q	ENST00000251849	NM_002880.3	343	Gaa/Caa	10/17	0.625143116309781	3	FACETS	0.213	0.164	0.271	0.071	0.054	0.091	SUBCLONAL	1	TRUE	0	0.625887373807194	3		434	413	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106543511	106543511	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042789-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	61	285	0	ENST00000369096.4:c.313G>C	p.Glu105Gln	p.E105Q	ENST00000369096	NM_001198.3	105	Gaa/Caa	3/7	0.250460494721273	3	FACETS	0.892	0.776	1			1	INDETERMINATE	1	TRUE	NA	0.625887373807194	3		285	287	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103804	47103804	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0043860-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	359	509	0	ENST00000409792.3:c.6142A>T	p.Arg2048Ter	p.R2048*	ENST00000409792	NM_014159.6	2048	Aga/Tga	14/21	0.364294610316948	3	FACETS	1	0.995	1	0.724	0.687	0.763	CLONAL	1	TRUE	1	0.521566846373474	3		509	1198	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142950	47142951	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0043860-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	172	341	0	ENST00000409792.3:c.5012_5013del	p.Tyr1671TrpfsTer40	p.Y1671Wfs*40	ENST00000409792	NM_014159.6	1671	tAT/t	8/21	0.364294610316948	3	FACETS	1	0.979	1	0.584	0.539	0.631	CLONAL	1	TRUE	1	0.521566846373474	3		341	712	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	79	151	0				ENST00000310581	NM_198253.2	-/1132			0.322066159022957	1	FACETS	0.836	0.748	0.926	0.836	0.748	0.926	INDETERMINATE	1	TRUE	0	0.605001201502743	1		151	218	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0043891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	30	456	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.605001201502743	3	FACETS	0.802	0.654	0.966	0.401	0.327	0.483	CLONAL	1	TRUE	1	0.605001201502743	3		456	161	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341555	89341555	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	113	569	0	ENST00000301030.4:c.7515C>G	p.Phe2505Leu	p.F2505L	ENST00000301030	NM_001256183.1	2505	ttC/ttG	10/13	1	2	FACETS	0.817	0.74	0.898	0.817	0.74	0.898	CLONAL	1	TRUE	1	0.605001201502743	2		569	457	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4387995	4387995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	117	425	0	ENST00000261254.3:c.481G>A	p.Glu161Lys	p.E161K	ENST00000261254	NM_001759.3	161	Gag/Aag	3/5	0.501266271804989	1	FACETS	0.84	0.768	0.915	0.84	0.768	0.915	CLONAL	1	TRUE	0	0.605001201502743	1		425	321	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647921	3647921	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146021821	NA	P-0043891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	212	762	0	ENST00000294008.3:c.1243G>A	p.Glu415Lys	p.E415K	ENST00000294008	NM_032444.2	415	Gag/Aag	6/15	0.605001201502743	1	FACETS	0.996	0.935	1	0.996	0.935	1	CLONAL	1	TRUE	0	0.605001201502743	1		762	491	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983111	201983111	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	160	462	0	ENST00000359651.3:c.960G>C	p.Lys320Asn	p.K320N	ENST00000359651		320	aaG/aaC	7/8	0.496557975413981	0	FACETS	0.582	0.541	0.623			1	SUBCLONAL	1	TRUE	0	0.605001201502743	0		462	359	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057318	180057318	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	137	635	0	ENST00000261937.6:c.420C>G	p.Ile140Met	p.I140M	ENST00000261937	NM_182925.4	140	atC/atG	4/30	NA	2	FACETS	0.949	0.87	1			1	INDETERMINATE	1	TRUE	NA	0.605001201502743	2		635	477	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983030	201983030	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	228	697	0	ENST00000359651.3:c.879G>C	p.Met293Ile	p.M293I	ENST00000359651		293	atG/atC	7/8	0.496557975413981	0	FACETS	0.624	0.589	0.66			1	SUBCLONAL	1	TRUE	0	0.605001201502743	0		697	477	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333291	70333291	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	25	493	0	ENST00000373644.4:c.1196C>G	p.Pro399Arg	p.P399R	ENST00000373644	NM_030625.2	399	cCt/cGt	2/12	NA	2	FACETS	0.179	0.141	0.224			1	INDETERMINATE	1	TRUE	NA	0.605001201502743	2		493	461	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394715	394715	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	116	376	0	ENST00000399788.2:c.4980G>T	p.Lys1660Asn	p.K1660N	ENST00000399788	NM_001042603.1	1660	aaG/aaT	28/28	0.605001201502743	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.605001201502743	1		376	264	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028627	12028627	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	54	264	0	ENST00000353533.5:c.830C>G	p.Pro277Arg	p.P277R	ENST00000353533	NM_003010.3	277	cCa/cGa	8/11	0.200564308358419	3	FACETS	1	0.88	1	0.51	0.44	0.584	INDETERMINATE	1	TRUE	1	0.605001201502743	3		264	228	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41267767	41267767	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs80356880	NA	P-0043891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	63	336	0	ENST00000357654.3:c.110C>G	p.Thr37Arg	p.T37R	ENST00000357654	NM_007294.3	37	aCa/aGa	3/23	1	2	FACETS	0.917	0.804	1	0.917	0.804	1	CLONAL	1	TRUE	1	0.605001201502743	2		336	227	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170732	7170732	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	129	493	0	ENST00000302850.5:c.1299G>C	p.Gln433His	p.Q433H	ENST00000302850	NM_000208.2	433	caG/caC	6/22	0.605001201502743	1	FACETS	0.893	0.821	0.967	0.893	0.821	0.967	CLONAL	1	TRUE	0	0.605001201502743	1		493	333	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256708	19256708	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1335518697	NA	P-0043891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	184	634	1	ENST00000162023.5:c.1005G>T	p.Lys335Asn	p.K335N	ENST00000162023		335	aaG/aaT	13/13	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.605001201502743	2		635	608	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564557	41564557	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	122	392	0	ENST00000263253.7:c.3979C>G	p.His1327Asp	p.H1327D	ENST00000263253	NM_001429.3	1327	Cat/Gat	24/31	0.580547801469666	3	FACETS	1	0.941	1	0.349	0.317	0.382	CLONAL	1	TRUE	0	0.605001201502743	3		392	502	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157758	106157758	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	15	166	0	ENST00000380013.4:c.2659G>C	p.Glu887Gln	p.E887Q	ENST00000380013	NM_001127208.2	887	Gag/Cag	3/11	1	2	FACETS	0.333	0.245	0.437	0.333	0.245	0.437	SUBCLONAL	1	TRUE	1	0.605001201502743	2		166	149	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436137	116436137	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	35	247	0	ENST00000397752.3:c.4132G>C	p.Glu1378Gln	p.E1378Q	ENST00000397752	NM_000245.2	1378	Gag/Cag	21/21	1	2	FACETS	0.432	0.355	0.516	0.432	0.355	0.516	SUBCLONAL	1	TRUE	1	0.605001201502743	2		247	268	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949731	151949731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	72	301	0	ENST00000262189.6:c.1369G>A	p.Asp457Asn	p.D457N	ENST00000262189	NM_170606.2	457	Gac/Aac	10/59	1	2	FACETS	0.964	0.853	1	0.964	0.853	1	CLONAL	1	TRUE	1	0.605001201502743	2		301	247	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041427	47041427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043891-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	135	287	2	ENST00000377604.3:c.1771G>A	p.Asp591Asn	p.D591N	ENST00000377604	NM_001204468.1	591	Gac/Aac	16/24	1	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.605001201502743	1		289	256	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0043949-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	57	469	2	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.32253470583709	2		471	344	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982977	201982978	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0043949-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	124	671	0	ENST00000359651.3:c.829dup	p.Glu277GlyfsTer24	p.E277Gfs*24	ENST00000359651		276	tgg/tGgg	7/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.32253470583709	2		671	640	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197793	123197794	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043949-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	112	221	0	ENST00000218089.9:c.1918dup	p.Cys640LeufsTer2	p.C640Lfs*2	ENST00000218089	NM_001042749.1	639	-/T	20/35	1	1	FACETS	0.949	0.865	1	1	0.989	1	CLONAL	2	TRUE	0	0.32253470583709	1		221	307	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0043972-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	126	429	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.273082661364842	4	FACETS	0.987	0.895	1	0.987	0.895	1	CLONAL	2	TRUE	2	0.23	4		429	683	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927429	178927429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1401795892	NA	P-0043972-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	52	374	0	ENST00000263967.3:c.1192C>T	p.Arg398Cys	p.R398C	ENST00000263967	NM_006218.2	398	Cgt/Tgt	7/21	0.3	5	FACETS	0.797	0.677	0.929	0.266	0.225	0.31	CLONAL	1	TRUE	2	0.23	5		374	763	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038841	47038844	+	frameshift_variant	Frame_Shift_Del	DEL	CCTC	CCTC	-	novel	NA	P-0043972-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	203	392	0	ENST00000377604.3:c.850_853del	p.Ser284LysfsTer23	p.S284Kfs*23	ENST00000377604	NM_001204468.1	283	gCCTCc/gc	9/24	0.3	2	FACETS	0.922	0.86	0.986			1	CLONAL	3	TRUE	NA	0.23	2		392	638	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0044344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	54	213	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.473435587253902	2		213	225	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0044344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	99	277	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.903	0.81	1	0.903	0.81	1	CLONAL	1	TRUE	1	0.473435587253902	2		277	463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540652	NA	P-0044344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	214	520	0	ENST00000269305.4:c.743G>T	p.Arg248Leu	p.R248L	ENST00000269305	NM_001126112.2	248	cGg/cTg	7/11	1	2	FACETS	0.918	0.853	0.985	0.918	0.853	0.985	CLONAL	1	TRUE	1	0.473435587253902	2		520	985	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099124	27099124	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0044344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	259	328	0	ENST00000324856.7:c.3539+1G>T		p.X1180_splice	ENST00000324856	NM_006015.4	1180			1	2	FACETS	0.993	0.94	1	1	0.995	1	CLONAL	2	TRUE	1	0.473435587253902	2		328	551	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196695	106196695	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	117	353	0	ENST00000380013.4:c.5028T>A	p.His1676Gln	p.H1676Q	ENST00000380013	NM_001127208.2	1676	caT/caA	11/11	0.30438719589825	1	FACETS	0.762	0.691	0.837	0.762	0.691	0.837	SUBCLONAL	1	TRUE	0	0.473435587253902	1		353	495	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	225	151	0				ENST00000310581	NM_198253.2	-/1132			0.27944707327717	5	FACETS	1	0.988	1	0.815	0.764	0.867	INDETERMINATE	2	TRUE	2	0.541018920540537	5		151	616	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	160	236	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.541018920540537	2		236	449	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517766	176517766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370322847	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	121	549	0	ENST00000292408.4:c.376G>A	p.Asp126Asn	p.D126N	ENST00000292408	NM_213647.1	126	Gat/Aat	4/18	0.450366986622472	3	FACETS	0.591	0.533	0.653	0.197	0.177	0.218	SUBCLONAL	1	TRUE	0	0.541018920540537	3		549	961	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409078	139409078	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	192	739	0	ENST00000277541.6:c.2091C>G	p.Ile697Met	p.I697M	ENST00000277541	NM_017617.3	697	atC/atG	13/34	0.450366986622472	3	FACETS	0.758	0.7	0.818	0.253	0.233	0.273	SUBCLONAL	1	TRUE	0	0.541018920540537	3		739	1190	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641161	23641161	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	164	493	0	ENST00000261584.4:c.2314G>A	p.Asp772Asn	p.D772N	ENST00000261584	NM_024675.3	772	Gat/Aat	5/13	1	2	FACETS	0.757	0.696	0.821	0.757	0.696	0.821	SUBCLONAL	1	TRUE	1	0.541018920540537	2		493	801	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041720	47041720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	114	415	0	ENST00000377604.3:c.1945C>T	p.Gln649Ter	p.Q649*	ENST00000377604	NM_001204468.1	649	Caa/Taa	17/24	0.469985585500292	3	FACETS	0.769	0.693	0.849	0.385	0.346	0.425	SUBCLONAL	1	TRUE	1	0.541018920540537	3		415	696	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054983	176054983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs991566021	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	56	377	0	ENST00000367669.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000367669	NM_022457.5	357	cGa/cAa	10/20	0.469985585500292	3	FACETS	0.36	0.307	0.417	0.18	0.153	0.209	SUBCLONAL	1	TRUE	1	0.541018920540537	3		377	731	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46270961	46270961	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	106	358	0	ENST00000371998.3:c.3085C>G	p.Leu1029Val	p.L1029V	ENST00000371998		1029	Ctt/Gtt	17/23	0.450145966367635	2	FACETS	0.764	0.688	0.844	0.382	0.344	0.422	SUBCLONAL	1	TRUE	0	0.541018920540537	2		358	513	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770065	56770065	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs752608224	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	156	394	0	ENST00000337432.4:c.61C>G	p.Pro21Ala	p.P21A	ENST00000337432	NM_058216.2	21	Cca/Gca	1/9	0.469985585500292	3	FACETS	0.854	0.782	0.929	0.427	0.391	0.465	CLONAL	1	TRUE	1	0.541018920540537	3		394	858	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950005	44950005	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	119	340	0	ENST00000377967.4:c.3774G>A	p.Trp1258Ter	p.W1258*	ENST00000377967	NM_021140.2	1258	tgG/tgA	26/29	0.469985585500292	3	FACETS	0.848	0.767	0.934	0.424	0.383	0.467	CLONAL	1	TRUE	1	0.541018920540537	3		340	659	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216714	7216714	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	122	382	0	ENST00000380728.2:c.709C>T	p.Gln237Ter	p.Q237*	ENST00000380728		237	Cag/Tag	8/11	0.4605271093848	1	FACETS	0.787	0.717	0.859	0.787	0.717	0.859	SUBCLONAL	1	TRUE	0	0.541018920540537	1		382	418	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607164	189607164	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	222	567	1	ENST00000264731.3:c.1543G>A	p.Asp515Asn	p.D515N	ENST00000264731	NM_003722.4	515	Gac/Aac	12/14	0.469985585500292	3	FACETS	1	0.959	1	0.521	0.485	0.559	CLONAL	1	TRUE	1	0.541018920540537	3		568	1000	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885835	23885835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs34462407	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	135	407	0	ENST00000374561.5:c.83G>A	p.Arg28Gln	p.R28Q	ENST00000374561	NM_002167.4	28	cGa/cAa	1/3	1	2	FACETS	0.844	0.77	0.922	0.844	0.77	0.922	CLONAL	1	TRUE	1	0.541018920540537	2		407	591	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2202742	2202742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	169	464	0	ENST00000398665.3:c.751C>T	p.His251Tyr	p.H251Y	ENST00000398665	NM_032482.2	251	Cac/Tac	9/28	0.231006460985138	3	FACETS	1	0.93	1	0.337	0.31	0.365	INDETERMINATE	1	TRUE	0	0.541018920540537	3		464	785	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28644733	28644733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	78	283	0	ENST00000241453.7:c.60G>A	p.Met20Ile	p.M20I	ENST00000241453	NM_004119.2	20	atG/atA	2/24	1	2	FACETS	0.773	0.684	0.868	0.773	0.684	0.868	SUBCLONAL	1	TRUE	1	0.541018920540537	2		283	373	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462171	120462171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1296823228	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	135	415	0	ENST00000256646.2:c.5545G>A	p.Glu1849Lys	p.E1849K	ENST00000256646	NM_024408.3	1849	Gaa/Aaa	31/34	1	2	FACETS	0.899	0.821	0.981	0.899	0.821	0.981	CLONAL	1	TRUE	1	0.541018920540537	2		415	555	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879331	151879331	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1563292120	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	103	373	1	ENST00000262189.6:c.5614C>T	p.Gln1872Ter	p.Q1872*	ENST00000262189	NM_170606.2	1872	Cag/Tag	36/59	0.541018920540537	3	FACETS	0.739	0.662	0.82	0.246	0.22	0.274	SUBCLONAL	1	TRUE	0	0.541018920540537	3		374	655	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657031	45657031	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	146	341	0	ENST00000407780.3:c.125G>A	p.Gly42Glu	p.G42E	ENST00000407780	NM_001283052.1	42	gGa/gAa	3/7	1	2	FACETS	0.901	0.826	0.979	0.901	0.826	0.979	CLONAL	1	TRUE	1	0.541018920540537	2		341	599	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494200	140494200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	111	621	0	ENST00000288602.6:c.1048G>A	p.Asp350Asn	p.D350N	ENST00000288602	NM_004333.4	350	Gat/Aat	8/18	0.541018920540537	3	FACETS	0.415	0.372	0.461	0.138	0.124	0.154	SUBCLONAL	1	TRUE	0	0.541018920540537	3		621	1256	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740204	162740204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749040833	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	143	357	0	ENST00000367921.3:c.1406C>T	p.Ser469Leu	p.S469L	ENST00000367921	NM_006182.2	469	tCg/tTg	12/18	0.469985585500292	3	FACETS	0.921	0.841	1	0.461	0.42	0.503	CLONAL	1	TRUE	1	0.541018920540537	3		357	729	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100219	157100219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	13	35	0	ENST00000346085.5:c.1156G>A	p.Gly386Arg	p.G386R	ENST00000346085	NM_020732.3	386	Ggg/Agg	1/20	0.450145966367635	2	FACETS	0.843	0.618	1	0.422	0.309	0.55	CLONAL	1	TRUE	0	0.541018920540537	2		35	57	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383225	4383225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	124	320	0	ENST00000261254.3:c.19G>A	p.Glu7Lys	p.E7K	ENST00000261254	NM_001759.3	7	Gag/Aag	1/5	NA	2	FACETS	0.939	0.855	1			1	INDETERMINATE	1	TRUE	NA	0.541018920540537	2		320	488	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475121	475121	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	110	368	0	ENST00000399788.2:c.516C>A	p.Phe172Leu	p.F172L	ENST00000399788	NM_001042603.1	172	ttC/ttA	4/28	NA	2	FACETS	0.805	0.727	0.888			1	INDETERMINATE	1	TRUE	NA	0.541018920540537	2		368	505	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106248	2106248	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	162	512	0	ENST00000219476.3:c.648+3C>T		p.X216_splice	ENST00000219476	NM_000548.3	216			1	2	FACETS	0.784	0.72	0.85	0.784	0.72	0.85	SUBCLONAL	1	TRUE	1	0.541018920540537	2		512	764	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922734	44922734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	101	320	0	ENST00000377967.4:c.1595C>T	p.Ser532Leu	p.S532L	ENST00000377967	NM_021140.2	532	tCa/tTa	16/29	0.469985585500292	3	FACETS	0.811	0.726	0.9	0.405	0.363	0.45	CLONAL	1	TRUE	1	0.541018920540537	3		320	585	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115801	8115801	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	160	474	0	ENST00000346208.3:c.1147G>A	p.Glu383Lys	p.E383K	ENST00000346208		383	Gag/Aag	6/6	0.450145966367635	2	FACETS	0.876	0.806	0.949	0.438	0.403	0.475	CLONAL	1	TRUE	0	0.541018920540537	2		474	675	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637723	176637723	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	91	472	0	ENST00000439151.2:c.2323C>A	p.Gln775Lys	p.Q775K	ENST00000439151	NM_022455.4	775	Caa/Aaa	5/23	0.450366986622472	3	FACETS	0.45	0.399	0.506	0.15	0.133	0.169	SUBCLONAL	1	TRUE	0	0.541018920540537	3		472	949	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881413	111881413	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	280	343	0	ENST00000393256.3:c.91G>T	p.Gly31Trp	p.G31W	ENST00000393256	NM_006538.4	31	Ggg/Tgg	2/4	0.469985585500292	3	FACETS	0.934	0.883	0.986	0.934	0.883	0.986	CLONAL	2	TRUE	1	0.541018920540537	3		343	704	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938646	76938646	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs797044563	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	112	396	0	ENST00000373344.5:c.2102G>A	p.Arg701His	p.R701H	ENST00000373344	NM_000489.3	701	cGt/cAt	9/35	0.469985585500292	3	FACETS	0.726	0.653	0.802	0.363	0.326	0.401	SUBCLONAL	1	TRUE	1	0.541018920540537	3		396	725	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112131	115112131	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772620679	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	201	531	0	ENST00000257566.3:c.1609G>A	p.Ala537Thr	p.A537T	ENST00000257566	NM_016569.3	537	Gct/Act	7/8	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.541018920540537	2		531	729	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931652	39931652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	171	513	0	ENST00000378444.4:c.2947G>A	p.Glu983Lys	p.E983K	ENST00000378444	NM_001123385.1	983	Gaa/Aaa	4/15	0.469985585500292	3	FACETS	0.864	0.794	0.936	0.432	0.397	0.468	CLONAL	1	TRUE	1	0.541018920540537	3		513	930	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032111	26032111	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753823527	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	104	320	1	ENST00000244661.2:c.178G>A	p.Glu60Lys	p.E60K	ENST00000244661	NM_003537.3	60	Gag/Aag	1/1	0.469985585500292	3	FACETS	0.817	0.733	0.905	0.408	0.366	0.453	CLONAL	1	TRUE	1	0.541018920540537	3		321	598	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254713	16254713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	136	467	2	ENST00000375759.3:c.1978G>A	p.Glu660Lys	p.E660K	ENST00000375759	NM_015001.2	660	Gaa/Aaa	11/15	1	2	FACETS	0.693	0.631	0.759	0.693	0.631	0.759	SUBCLONAL	1	TRUE	1	0.541018920540537	2		469	725	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935406	36935406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	227	656	0	ENST00000361632.4:c.1321G>A	p.Asp441Asn	p.D441N	ENST00000361632		441	Gac/Aac	10/16	1	2	FACETS	0.847	0.789	0.906	0.847	0.789	0.906	CLONAL	1	TRUE	1	0.541018920540537	2		656	991	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843677	156843677	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	235	732	1	ENST00000524377.1:c.1103G>T	p.Gly368Val	p.G368V	ENST00000524377	NM_002529.3	368	gGc/gTc	8/17	0.469985585500292	3	FACETS	0.912	0.85	0.977	0.456	0.425	0.489	CLONAL	1	TRUE	1	0.541018920540537	3		733	1210	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32439180	32439180	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	87	370	0	ENST00000332351.3:c.893C>A	p.Thr298Lys	p.T298K	ENST00000332351	NM_024426.4	298	aCa/aAa	4/10	1	2	FACETS	0.65	0.577	0.727	0.65	0.577	0.727	SUBCLONAL	1	TRUE	1	0.541018920540537	2		370	495	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212886	94212886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	66	296	0	ENST00000323929.3:c.356C>T	p.Ser119Leu	p.S119L	ENST00000323929	NM_005591.3	119	tCa/tTa	5/20	1	2	FACETS	0.687	0.6	0.781	0.687	0.6	0.781	SUBCLONAL	1	TRUE	1	0.541018920540537	2		296	355	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432609	49432609	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	206	664	0	ENST00000301067.7:c.8530G>C	p.Glu2844Gln	p.E2844Q	ENST00000301067	NM_003482.3	2844	Gaa/Caa	34/54	1	2	FACETS	0.829	0.769	0.89	0.829	0.769	0.89	CLONAL	1	TRUE	1	0.541018920540537	2		664	919	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554373	81554373	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs751583621	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	88	233	0	ENST00000298171.2:c.392+1G>A		p.X131_splice	ENST00000298171	NM_000369.2	131			1	2	FACETS	0.924	0.826	1	0.924	0.826	1	CLONAL	1	TRUE	1	0.541018920540537	2		233	352	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14028060	14028060	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	76	196	0	ENST00000311895.7:c.1114G>T	p.Glu372Ter	p.E372*	ENST00000311895	NM_005236.2	372	Gaa/Taa	7/11	1	2	FACETS	0.851	0.753	0.955	0.851	0.753	0.955	CLONAL	1	TRUE	1	0.541018920540537	2		196	330	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646895	37646895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	169	491	0	ENST00000447079.4:c.2017C>T	p.Pro673Ser	p.P673S	ENST00000447079	NM_015083.1	673	Cca/Tca	3/14	0.469985585500292	3	FACETS	0.868	0.798	0.941	0.434	0.399	0.471	CLONAL	1	TRUE	1	0.541018920540537	3		491	914	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244513	41244513	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	131	449	0	ENST00000357654.3:c.3035G>T	p.Arg1012Ile	p.R1012I	ENST00000357654	NM_007294.3	1012	aGa/aTa	10/23	0.469985585500292	3	FACETS	0.755	0.685	0.828	0.377	0.342	0.414	SUBCLONAL	1	TRUE	1	0.541018920540537	3		449	815	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435240	56435240	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	198	609	0	ENST00000407977.2:c.1897T>A	p.Cys633Ser	p.C633S	ENST00000407977		633	Tgc/Agc	9/10	0.469985585500292	3	FACETS	0.97	0.898	1	0.485	0.449	0.522	CLONAL	1	TRUE	1	0.541018920540537	3		609	959	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761169	59761169	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	144	437	0	ENST00000259008.2:c.3238G>C	p.Asp1080His	p.D1080H	ENST00000259008	NM_032043.2	1080	Gat/Cat	20/20	0.469985585500292	3	FACETS	0.816	0.744	0.891	0.408	0.372	0.446	CLONAL	1	TRUE	1	0.541018920540537	3		437	829	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775007	73775007	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	84	287	0	ENST00000254810.4:c.166C>T	p.Gln56Ter	p.Q56*	ENST00000254810	NM_005324.3	56	Cag/Tag	3/4	0.469985585500292	3	FACETS	0.817	0.724	0.916	0.408	0.362	0.458	CLONAL	1	TRUE	1	0.541018920540537	3		287	483	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57569878	57569878	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	65	197	0	ENST00000316660.6:c.59-1G>C		p.X20_splice	ENST00000316660	NM_021127.2	20			0.519481819604677	3	FACETS	0.848	0.739	0.964	0.424	0.369	0.482	CLONAL	1	TRUE	1	0.541018920540537	3		197	360	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244406	5244406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	191	657	0	ENST00000357368.4:c.1076C>T	p.Pro359Leu	p.P359L	ENST00000357368	NM_002850.3	359	cCt/cTt	11/38	0.231006460985138	3	FACETS	0.853	0.788	0.92	0.284	0.262	0.307	INDETERMINATE	1	TRUE	0	0.541018920540537	3		657	1052	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10259674	10259674	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	70	310	0	ENST00000340748.4:c.2558C>T	p.Ser853Phe	p.S853F	ENST00000340748		853	tCc/tTc	26/40	0.231006460985138	3	FACETS	0.587	0.512	0.668	0.196	0.17	0.223	INDETERMINATE	1	TRUE	0	0.541018920540537	3		310	560	SUCCESS
CALR	811	MSKCC	GRCh37	19	13049971	13049971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	67	422	0	ENST00000316448.5:c.115G>A	p.Glu39Lys	p.E39K	ENST00000316448	NM_004343.3	39	Gaa/Aaa	2/9	0.231006460985138	3	FACETS	0.451	0.391	0.515	0.15	0.13	0.172	INDETERMINATE	1	TRUE	0	0.541018920540537	3		422	698	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627326	14627326	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	351	643	0	ENST00000254322.2:c.744G>C	p.Lys248Asn	p.K248N	ENST00000254322	NM_006145.1	248	aaG/aaC	2/3	0.231006460985138	3	FACETS	1	0.994	1	0.465	0.44	0.49	INDETERMINATE	1	TRUE	0	0.541018920540537	3		643	1182	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50138873	50138873	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	262	819	0	ENST00000246792.3:c.617C>A	p.Pro206His	p.P206H	ENST00000246792	NM_006270.3	206	cCc/cAc	6/6	0.469985585500292	3	FACETS	0.86	0.804	0.918	0.43	0.402	0.459	CLONAL	1	TRUE	1	0.541018920540537	3		819	1431	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39222396	39222396	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	188	528	0	ENST00000402219.2:c.3214G>C	p.Glu1072Gln	p.E1072Q	ENST00000402219	NM_005633.3	1072	Gaa/Caa	20/23	0.469985585500292	3	FACETS	0.934	0.863	1	0.467	0.431	0.504	CLONAL	1	TRUE	1	0.541018920540537	3		528	945	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249822	39249822	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	119	313	0	ENST00000402219.2:c.1747G>A	p.Glu583Lys	p.E583K	ENST00000402219	NM_005633.3	583	Gaa/Aaa	10/23	0.469985585500292	3	FACETS	0.872	0.789	0.959	0.436	0.394	0.48	CLONAL	1	TRUE	1	0.541018920540537	3		313	641	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46597021	46597021	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	170	367	1	ENST00000263734.3:c.835G>A	p.Glu279Lys	p.E279K	ENST00000263734	NM_001430.4	279	Gaa/Aaa	7/16	0.469985585500292	3	FACETS	1	0.965	1	0.54	0.498	0.584	CLONAL	1	TRUE	1	0.541018920540537	3		368	739	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22123503	22123503	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	197	340	0	ENST00000215832.6:c.1073A>T	p.Tyr358Phe	p.Y358F	ENST00000215832	NM_002745.4	358	tAc/tTc	8/9	0.450145966367635	2	FACETS	0.752	0.704	0.802	0.752	0.704	0.802	SUBCLONAL	2	TRUE	0	0.541018920540537	2		340	484	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537076	41537076	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	85	222	0	ENST00000263253.7:c.1903G>T	p.Glu635Ter	p.E635*	ENST00000263253	NM_001429.3	635	Gag/Tag	10/31	0.450145966367635	2	FACETS	0.847	0.754	0.945	0.423	0.377	0.473	CLONAL	1	TRUE	0	0.541018920540537	2		222	371	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543888	41543888	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	173	469	0	ENST00000263253.7:c.2182del	p.Arg728GlyfsTer48	p.R728Gfs*48	ENST00000263253	NM_001429.3	727	Ccc/cc	12/31	0.450145966367635	2	FACETS	0.94	0.869	1	0.47	0.434	0.508	CLONAL	1	TRUE	0	0.541018920540537	2		469	680	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188218	10188218	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	134	443	0	ENST00000256474.2:c.361G>C	p.Asp121His	p.D121H	ENST00000256474	NM_000551.3	121	Gat/Cat	2/3	1	2	FACETS	0.726	0.661	0.795	0.726	0.661	0.795	SUBCLONAL	1	TRUE	1	0.541018920540537	2		443	682	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437813	52437813	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	160	530	0	ENST00000460680.1:c.1348G>C	p.Glu450Gln	p.E450Q	ENST00000460680	NM_004656.3	450	Gag/Cag	13/17	1	2	FACETS	0.729	0.669	0.792	0.729	0.669	0.792	SUBCLONAL	1	TRUE	1	0.541018920540537	2		530	811	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178943749	178943749	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	57	159	0	ENST00000263967.3:c.2417-1G>A		p.X806_splice	ENST00000263967	NM_006218.2	806			0.469985585500292	3	FACETS	0.79	0.681	0.907	0.395	0.34	0.454	CLONAL	1	TRUE	1	0.541018920540537	3		159	339	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178943761	178943761	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	59	176	0	ENST00000263967.3:c.2428G>C	p.Asp810His	p.D810H	ENST00000263967	NM_006218.2	810	Gat/Cat	17/21	0.469985585500292	3	FACETS	0.733	0.633	0.841	0.367	0.316	0.421	SUBCLONAL	1	TRUE	1	0.541018920540537	3		176	378	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55962419	55962419	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	93	343	0	ENST00000263923.4:c.2705T>C	p.Leu902Pro	p.L902P	ENST00000263923	NM_002253.2	902	cTa/cCa	19/30	0.469985585500292	3	FACETS	0.715	0.637	0.798	0.357	0.318	0.399	SUBCLONAL	1	TRUE	1	0.541018920540537	3		343	611	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55987277	55987277	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	96	231	0	ENST00000263923.4:c.148C>T	p.Gln50Ter	p.Q50*	ENST00000263923	NM_002253.2	50	Caa/Taa	2/30	0.469985585500292	3	FACETS	0.92	0.823	1	0.46	0.411	0.511	CLONAL	1	TRUE	1	0.541018920540537	3		231	490	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249498	153249498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	129	398	0	ENST00000281708.4:c.1280C>T	p.Ser427Leu	p.S427L	ENST00000281708	NM_033632.3	427	tCa/tTa	9/12	0.469985585500292	3	FACETS	0.853	0.775	0.936	0.427	0.387	0.468	CLONAL	1	TRUE	1	0.541018920540537	3		398	710	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521484	187521484	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	92	304	0	ENST00000441802.2:c.11671G>C	p.Asp3891His	p.D3891H	ENST00000441802	NM_005245.3	3891	Gac/Cac	22/27	0.469985585500292	3	FACETS	0.793	0.706	0.885	0.396	0.353	0.443	SUBCLONAL	1	TRUE	1	0.541018920540537	3		304	545	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592042	67592042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	89	185	0	ENST00000274335.5:c.1858G>A	p.Asp620Asn	p.D620N	ENST00000274335		620	Gat/Aat	14/15	0.450145966367635	2	FACETS	1	0.96	1	0.571	0.513	0.632	CLONAL	1	TRUE	0	0.541018920540537	2		185	288	SUCCESS
APC	324	MSKCC	GRCh37	5	112174337	112174337	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	20	186	0	ENST00000257430.4:c.3046G>A	p.Asp1016Asn	p.D1016N	ENST00000257430	NM_000038.5	1016	Gat/Aat	16/16	0.450145966367635	2	FACETS	0.225	0.171	0.287	0.112	0.085	0.144	SUBCLONAL	1	TRUE	0	0.541018920540537	2		186	329	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858334	27858334	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	223	413	0	ENST00000359303.2:c.237C>G	p.Phe79Leu	p.F79L	ENST00000359303	NM_003535.2	79	ttC/ttG	1/1	0.469985585500292	3	FACETS	1	0.989	1	0.653	0.609	0.698	CLONAL	1	TRUE	1	0.541018920540537	3		413	802	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675932	30675932	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	231	579	0	ENST00000376406.3:c.2424G>C	p.Gln808His	p.Q808H	ENST00000376406	NM_014641.2	808	caG/caC	8/15	0.469985585500292	3	FACETS	0.983	0.916	1	0.491	0.458	0.526	CLONAL	1	TRUE	1	0.541018920540537	3		579	1104	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188794	32188794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	208	571	0	ENST00000375023.3:c.760G>A	p.Glu254Lys	p.E254K	ENST00000375023	NM_004557.3	254	Gag/Aag	4/30	0.469985585500292	3	FACETS	0.891	0.827	0.959	0.446	0.413	0.48	CLONAL	1	TRUE	1	0.541018920540537	3		571	1096	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32820183	32820183	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	168	446	0	ENST00000354258.4:c.875C>G	p.Ser292Cys	p.S292C	ENST00000354258	NM_000593.5	292	tCc/tGc	2/11	0.469985585500292	3	FACETS	0.842	0.774	0.913	0.421	0.387	0.457	CLONAL	1	TRUE	1	0.541018920540537	3		446	937	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041209	112041209	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	224	377	1	ENST00000368678.4:c.46G>T	p.Glu16Ter	p.E16*	ENST00000368678		16	Gag/Tag	3/13	0.450145966367635	2	FACETS	0.761	0.715	0.808	0.761	0.715	0.808	SUBCLONAL	2	TRUE	0	0.541018920540537	2		378	544	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997712	149997712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	88	263	0	ENST00000253339.5:c.2755C>T	p.Pro919Ser	p.P919S	ENST00000253339		919	Cct/Tct	5/7	0.450145966367635	2	FACETS	0.795	0.709	0.887	0.398	0.354	0.444	SUBCLONAL	1	TRUE	0	0.541018920540537	2		263	409	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004316	150004316	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	101	212	0	ENST00000253339.5:c.1909C>T	p.Gln637Ter	p.Q637*	ENST00000253339		637	Caa/Taa	3/7	0.450145966367635	2	FACETS	0.833	0.749	0.922	0.417	0.374	0.461	CLONAL	1	TRUE	0	0.541018920540537	2		212	448	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419880	152419880	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	123	334	0	ENST00000206249.3:c.1567G>C	p.Glu523Gln	p.E523Q	ENST00000206249	NM_000125.3	523	Gag/Cag	8/8	0.450145966367635	2	FACETS	0.789	0.716	0.866	0.395	0.358	0.433	SUBCLONAL	1	TRUE	0	0.541018920540537	2		334	576	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951918	2951918	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	135	453	0	ENST00000396946.4:c.3032G>C	p.Arg1011Thr	p.R1011T	ENST00000396946	NM_032415.4	1011	aGa/aCa	23/25	0.541018920540537	3	FACETS	0.688	0.625	0.755			1	SUBCLONAL	1	TRUE	NA	0.541018920540537	3		453	921	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946060	13946060	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	100	244	0	ENST00000405192.2:c.1036G>T	p.Glu346Ter	p.E346*	ENST00000405192	NM_001163147.1	346	Gaa/Taa	10/12	0.459789379855106	4	FACETS	1	0.95	1	0.275	0.246	0.305	CLONAL	1	TRUE	0	0.541018920540537	4		244	518	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439630	140439630	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	118	386	0	ENST00000288602.6:c.2109G>C	p.Glu703Asp	p.E703D	ENST00000288602	NM_004333.4	703	gaG/gaC	17/18	0.541018920540537	3	FACETS	0.701	0.632	0.773	0.234	0.21	0.258	SUBCLONAL	1	TRUE	0	0.541018920540537	3		386	791	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860539	151860539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	71	436	0	ENST00000262189.6:c.10123C>A	p.Pro3375Thr	p.P3375T	ENST00000262189	NM_170606.2	3375	Cca/Aca	43/59	0.541018920540537	3	FACETS	0.366	0.318	0.418	0.122	0.106	0.14	SUBCLONAL	1	TRUE	0	0.541018920540537	3		436	911	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860608	151860608	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	55	447	0	ENST00000262189.6:c.10054C>T	p.Gln3352Ter	p.Q3352*	ENST00000262189	NM_170606.2	3352	Cag/Tag	43/59	0.541018920540537	3	FACETS	0.306	0.261	0.356	0.102	0.087	0.119	SUBCLONAL	1	TRUE	0	0.541018920540537	3		447	844	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879084	151879084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	169	381	0	ENST00000262189.6:c.5861C>T	p.Ser1954Phe	p.S1954F	ENST00000262189	NM_170606.2	1954	tCt/tTt	36/59	0.541018920540537	3	FACETS	0.91	0.837	0.986	0.303	0.279	0.329	CLONAL	1	TRUE	0	0.541018920540537	3		381	872	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945321	151945321	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	31	98	0	ENST00000262189.6:c.2198C>A	p.Ser733Tyr	p.S733Y	ENST00000262189	NM_170606.2	733	tCt/tAt	14/59	0.541018920540537	3	FACETS	0.804	0.657	0.967	0.268	0.219	0.323	CLONAL	1	TRUE	0	0.541018920540537	3		98	181	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129936	69129936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	77	259	0	ENST00000288368.4:c.4690G>A	p.Asp1564Asn	p.D1564N	ENST00000288368	NM_024870.2	1564	Gat/Aat	38/40	0.450366986622472	3	FACETS	0.816	0.72	0.92	0.272	0.24	0.307	CLONAL	1	TRUE	0	0.541018920540537	3		259	443	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891193	101891193	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	327	246	0	ENST00000374994.4:c.154G>T	p.Gly52Trp	p.G52W	ENST00000374994	NM_004612.2	52	Ggg/Tgg	2/9	0.450366986622472	3	FACETS	0.964	0.924	1	0.964	0.924	1	CLONAL	3	TRUE	0	0.541018920540537	3		246	531	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776220	135776220	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	112	264	0	ENST00000298552.3:c.2507C>T	p.Ser836Leu	p.S836L	ENST00000298552	NM_001162426.1	836	tCa/tTa	20/23	0.450366986622472	3	FACETS	0.886	0.799	0.977	0.295	0.266	0.326	CLONAL	1	TRUE	0	0.541018920540537	3		264	594	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403521	139403521	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	158	539	0	ENST00000277541.6:c.2972C>G	p.Ser991Cys	p.S991C	ENST00000277541	NM_017617.3	991	tCc/tGc	19/34	0.450366986622472	3	FACETS	0.817	0.749	0.889	0.272	0.249	0.297	CLONAL	1	TRUE	0	0.541018920540537	3		539	908	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922157	39922157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1322918571	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	168	540	0	ENST00000378444.4:c.4015G>A	p.Glu1339Lys	p.E1339K	ENST00000378444	NM_001123385.1	1339	Gag/Aag	9/15	0.469985585500292	3	FACETS	0.909	0.836	0.985	0.455	0.418	0.493	CLONAL	1	TRUE	1	0.541018920540537	3		540	868	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763958	76763958	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	289	507	0	ENST00000373344.5:c.7350C>A	p.Asn2450Lys	p.N2450K	ENST00000373344	NM_000489.3	2450	aaC/aaA	35/35	0.469985585500292	3	FACETS	0.848	0.801	0.896	0.848	0.801	0.896	CLONAL	2	TRUE	1	0.541018920540537	3		507	800	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813035	76813035	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044669-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	118	342	0	ENST00000373344.5:c.6586G>C	p.Glu2196Gln	p.E2196Q	ENST00000373344	NM_000489.3	2196	Gag/Cag	30/35	0.469985585500292	3	FACETS	0.81	0.732	0.893	0.405	0.366	0.447	CLONAL	1	TRUE	1	0.541018920540537	3		342	684	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0044706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	76	531	0	ENST00000311936.3:c.34_35delinsTT	p.Gly12Phe	p.G12F	ENST00000311936	NM_004985.3	12	GGt/TTt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		531	331	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180982	108180982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781963	NA	P-0044706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	70	236	0	ENST00000278616.4:c.5858C>T	p.Thr1953Ile	p.T1953I	ENST00000278616	NM_000051.3	1953	aCa/aTa	39/63	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		236	172	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266714	198266714	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	91	501	0	ENST00000335508.6:c.2218G>C	p.Gly740Arg	p.G740R	ENST00000335508	NM_012433.2	740	Gga/Cga	15/25	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		501	423	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982355	201982355	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	342	518	0	ENST00000359651.3:c.734G>T	p.Arg245Leu	p.R245L	ENST00000359651		245	cGg/cTg	6/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		518	1265	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456505	99456505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	40	261	0	ENST00000268035.6:c.1822G>A	p.Ala608Thr	p.A608T	ENST00000268035	NM_000875.3	608	Gct/Act	8/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		261	278	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641183	3641183	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	157	509	0	ENST00000294008.3:c.2456T>C	p.Leu819Ser	p.L819S	ENST00000294008	NM_032444.2	819	tTg/tCg	12/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		509	1018	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381551	81381551	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044706-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	62	327	0	ENST00000222390.5:c.510A>T	p.Lys170Asn	p.K170N	ENST00000222390	NM_000601.4	170	aaA/aaT	5/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		327	285	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0044938-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	388	716	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.746156983330637	2	FACETS	0.999	0.969	1	0.999	0.969	1	CLONAL	2	TRUE	0	0.772172267393715	2		716	503	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513224	106513224	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044938-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	91	260	0	ENST00000359195.3:c.2128C>T	p.Gln710Ter	p.Q710*	ENST00000359195	NM_002649.2	710	Cag/Tag	4/11	0.743947753134913	3	FACETS	0.92	0.824	1	0.46	0.412	0.511	CLONAL	1	TRUE	1	0.772172267393715	3		260	355	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114682	73114682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747658097	NA	P-0044938-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	358	321	0	ENST00000356692.5:c.1063G>A	p.Glu355Lys	p.E355K	ENST00000356692		355	Gag/Aag	9/9	0.624595566983631	6	FACETS	1	0.987	1			1	CLONAL	3	TRUE	NA	0.772172267393715	6		321	724	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972633	25972633	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1304291937	NA	P-0044938-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	129	316	0	ENST00000435504.4:c.1792C>G	p.Gln598Glu	p.Q598E	ENST00000435504		598	Cag/Gag	12/13	0.743947753134913	3	FACETS	1	0.937	1	0.516	0.471	0.562	CLONAL	1	TRUE	1	0.772172267393715	3		316	449	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984428	201984428	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044938-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	689	503	0	ENST00000359651.3:c.1093G>T	p.Glu365Ter	p.E365*	ENST00000359651		365	Gag/Tag	8/8	0.726693874459514	6	FACETS	0.922	0.894	0.95	0.738	0.715	0.76	CLONAL	4	TRUE	1	0.772172267393715	6		503	1231	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968832	32968832	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044938-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	60	161	0	ENST00000380152.3:c.9266del	p.Pro3089LeufsTer15	p.P3089Lfs*15	ENST00000380152		3088	gCc/gc	25/27	1	2	FACETS	0.809	0.709	0.914	0.809	0.709	0.914	CLONAL	1	TRUE	1	0.772172267393715	2		161	192	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027697	48027697	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044938-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	82	187	0	ENST00000234420.5:c.2575C>T	p.Leu859Phe	p.L859F	ENST00000234420	NM_000179.2	859	Ctt/Ttt	4/10	0.743947753134913	3	FACETS	1	0.915	1	0.515	0.459	0.573	CLONAL	1	TRUE	1	0.772172267393715	3		187	286	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799185	45799185	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs370124822	NA	P-0044938-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	221	516	0	ENST00000450313.1:c.248C>G	p.Ser83Ter	p.S83*	ENST00000450313	NM_012222.2	83	tCa/tGa	3/16	0.772172267393715	3	FACETS	1	0.956	1	0.515	0.481	0.551	CLONAL	1	TRUE	1	0.772172267393715	3		516	770	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233186	46233186	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044938-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	307	248	0	ENST00000334344.6:c.1405G>T	p.Glu469Ter	p.E469*	ENST00000334344	NM_152641.2	469	Gaa/Taa	11/21	0.718191183545666	3	FACETS	0.993	0.964	1	0.993	0.964	1	CLONAL	3	TRUE	0	0.772172267393715	3		248	370	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427871	49427871	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044938-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	250	503	0	ENST00000301067.7:c.10719G>C	p.Lys3573Asn	p.K3573N	ENST00000301067	NM_003482.3	3573	aaG/aaC	38/54	0.718191183545666	3	FACETS	1	0.99	1	0.419	0.394	0.445	CLONAL	1	TRUE	0	0.772172267393715	3		503	714	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514958	103514958	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044938-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	92	226	0	ENST00000355739.4:c.1459C>T	p.Pro487Ser	p.P487S	ENST00000355739	NM_000123.3	487	Ccg/Tcg	8/15	1	2	FACETS	0.924	0.834	1	0.924	0.834	1	CLONAL	1	TRUE	1	0.772172267393715	2		226	258	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249766	39249766	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044938-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	148	322	0	ENST00000402219.2:c.1803C>G	p.Ile601Met	p.I601M	ENST00000402219	NM_005633.3	601	atC/atG	10/23	0.743947753134913	3	FACETS	0.954	0.876	1	0.477	0.438	0.518	CLONAL	1	TRUE	1	0.772172267393715	3		322	557	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319885	62319885	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs115423936	NA	P-0044938-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1706	573	696	1	ENST00000360203.5:c.1727G>T	p.Arg576Leu	p.R576L	ENST00000360203	NM_001283009.1	576	cGc/cTc	21/35	0.772172267393715	8	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.772172267393715	8		697	2279	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123048	5123048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045132-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	174	46	0	ENST00000381652.3:c.3104C>T	p.Ser1035Leu	p.S1035L	ENST00000381652	NM_004972.3	1035	tCa/tTa	23/25	0.557088900174188	1	FACETS	0.968	0.91	1	0.968	0.91	1	CLONAL	1	TRUE	0	0.734034744809192	1		46	310	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792731	33792732	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCGGGT	rs762459325	NA	P-0045132-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	20	6	0	ENST00000498907.2:c.584_589dup	p.His195_Pro196dup	p.H195_P196dup	ENST00000498907	NM_004364.3	195	ccg/cACCCGCcg	1/1	1	2	FACETS	0.359	0.276	0.453	0.359	0.276	0.453	SUBCLONAL	1	TRUE	1	0.734034744809192	2		6	152	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574027	7574027	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882028	NA	P-0045132-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	420	72	0	ENST00000269305.4:c.1000G>T	p.Gly334Trp	p.G334W	ENST00000269305	NM_001126112.2	334	Ggg/Tgg	10/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.734034744809192	2		72	1110	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0045132-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	409	85	0	ENST00000269305.4:c.920-2A>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.734034744809192	2		85	1098	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063386	67063386	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045132-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	334	31	0	ENST00000412916.2:c.76G>T	p.Glu26Ter	p.E26*	ENST00000412916		26	Gag/Tag	1/6	0.4767285019307	1	FACETS	0.993	0.951	1	0.993	0.951	1	CLONAL	1	TRUE	0	0.734034744809192	1		31	580	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584506	189584506	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045132-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	191	36	0	ENST00000264731.3:c.802G>C	p.Glu268Gln	p.E268Q	ENST00000264731	NM_003722.4	268	Gag/Cag	6/14	0.734034744809192	3	FACETS	0.95	0.881	1			1	CLONAL	1	TRUE	NA	0.734034744809192	3		36	749	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187158	11187158	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045132-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	53	70	0	ENST00000361445.4:c.6260A>T	p.Lys2087Met	p.K2087M	ENST00000361445	NM_004958.3	2087	aAg/aTg	45/58	0.663090123137649	1	FACETS	0.132	0.112	0.153	0.132	0.112	0.153	SUBCLONAL	1	TRUE	0	0.734034744809192	1		70	695	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343608	118343608	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045132-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	312	50	0	ENST00000534358.1:c.1734C>G	p.Ile578Met	p.I578M	ENST00000534358	NM_005933.3	578	atC/atG	3/36	0.663090123137649	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.734034744809192	1		50	505	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416437	49416437	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045132-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	384	94	0	ENST00000301067.7:c.16274A>T	p.Glu5425Val	p.E5425V	ENST00000301067	NM_003482.3	5425	gAg/gTg	51/54	1	2	FACETS	0.963	0.916	1	0.963	0.916	1	CLONAL	1	TRUE	1	0.734034744809192	2		94	1087	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218928	133218928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500823	NA	P-0045132-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	611	120	0	ENST00000320574.5:c.5008G>A	p.Asp1670Asn	p.D1670N	ENST00000320574	NM_006231.2	1670	Gac/Aac	38/49	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.734034744809192	2		120	1609	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89865584	89865584	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045132-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	59	57	0	ENST00000389301.3:c.883G>C	p.Val295Leu	p.V295L	ENST00000389301	NM_000135.2	295	Gtg/Ctg	10/43	0.734034744809192	1	FACETS	0.149	0.128	0.172	0.149	0.128	0.172	SUBCLONAL	1	TRUE	0	0.734034744809192	1		57	683	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222006	1222006	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1131690920	NA	P-0045132-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	511	82	1	ENST00000326873.7:c.920+1G>A		p.X307_splice	ENST00000326873	NM_000455.4	307			0.734034744809192	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.734034744809192	1		83	810	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752739	42752739	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045132-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	593	114	0	ENST00000222329.4:c.1525G>A	p.Glu509Lys	p.E509K	ENST00000222329	NM_006494.2	509	Gag/Aag	4/4	1	2	FACETS	0.998	0.959	1	0.998	0.959	1	CLONAL	1	TRUE	1	0.734034744809192	2		114	1619	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158595023	158595023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045132-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	196	37	0	ENST00000263640.3:c.1324G>A	p.Glu442Lys	p.E442K	ENST00000263640	NM_001105.4	442	Gaa/Aaa	10/11	0.734034744809192	1	FACETS	0.96	0.906	1	0.96	0.906	1	CLONAL	1	TRUE	0	0.734034744809192	1		37	352	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719421	190719421	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045132-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	84	26	0	ENST00000441310.2:c.1423A>G	p.Ile475Val	p.I475V	ENST00000441310	NM_000534.4	475	Ata/Gta	9/13	0.734034744809192	1	FACETS	0.911	0.83	0.992	0.911	0.83	0.992	CLONAL	1	TRUE	0	0.734034744809192	1		26	159	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14017064	14017064	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045132-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	122	45	0	ENST00000405192.2:c.223C>T	p.Gln75Ter	p.Q75*	ENST00000405192	NM_001163147.1	75	Cag/Tag	5/12	1	2	FACETS	0.944	0.864	1	0.944	0.864	1	CLONAL	1	TRUE	1	0.734034744809192	2		45	352	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55086975	55086975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045132-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	315	38	0	ENST00000275493.2:c.5G>A	p.Arg2Gln	p.R2Q	ENST00000275493	NM_005228.3	2	cGa/cAa	1/28	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.734034744809192	2		38	737	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0045176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	91	260	0	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.588114165437952	2		260	251	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0045176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	249	418	0	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	1	0.959	1	1	0.996	1	CLONAL	2	TRUE	1	0.588114165437952	2		418	420	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443613	52443613	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	157	541	0	ENST00000460680.1:c.79del	p.Val27CysfsTer45	p.V27Cfs*45	ENST00000460680	NM_004656.3	27	Gtg/tg	3/17	0.588114165437952	3	FACETS	1	0.988	1	0.468	0.432	0.505	CLONAL	1	TRUE	0	0.588114165437952	3		541	492	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0045176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	67	362	17	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.588114165437952	2		379	168	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740216	162740216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775098890	NA	P-0045176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	138	459	1	ENST00000367921.3:c.1418G>A	p.Arg473His	p.R473H	ENST00000367921	NM_006182.2	473	cGc/cAc	12/18	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.588114165437952	2		460	383	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430901	181430901	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	194	1022	1	ENST00000325404.1:c.758del	p.Pro253LeufsTer21	p.P253Lfs*21	ENST00000325404	NM_003106.3	251	agC/ag	1/1	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.588114165437952	2		1023	527	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0045176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	18	219	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	0.11389645762699	3	FACETS	0.279	0.21	0.361	0.139	0.105	0.181	INDETERMINATE	1	TRUE	1	0.588114165437952	3		219	284	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265323	152265323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866869178	NA	P-0045176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	68	315	0	ENST00000206249.3:c.776G>A	p.Arg259Gln	p.R259Q	ENST00000206249	NM_000125.3	259	cGa/cAa	4/8	1	2	FACETS	0.972	0.857	1	0.972	0.857	1	CLONAL	1	TRUE	1	0.588114165437952	2		315	238	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098422	11098422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764188556	NA	P-0045176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	130	567	3	ENST00000358026.2:c.940G>A	p.Ala314Thr	p.A314T	ENST00000358026	NM_001128849.1	314	Gcg/Acg	6/36	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.588114165437952	2		570	348	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286254	66286254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	95	266	0	ENST00000273854.3:c.1432G>A	p.Gly478Arg	p.G478R	ENST00000273854	NM_004439.5	478	Ggg/Agg	6/18	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.588114165437952	2		266	289	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465049	120465049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	79	354	0	ENST00000256646.2:c.5023C>T	p.Arg1675Cys	p.R1675C	ENST00000256646	NM_024408.3	1675	Cgc/Tgc	28/34	1	2	FACETS	0.977	0.87	1	0.977	0.87	1	CLONAL	1	TRUE	1	0.588114165437952	2		354	275	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976703	2976703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	137	545	0	ENST00000396946.4:c.1309C>T	p.Arg437Cys	p.R437C	ENST00000396946	NM_032415.4	437	Cgc/Tgc	9/25	0.577285531313827	0	FACETS	0.541	0.498	0.584			1	SUBCLONAL	1	TRUE	0	0.588114165437952	0		545	355	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948653	71948653	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147991973	NA	P-0045176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	168	917	0	ENST00000298229.2:c.3365C>T	p.Ser1122Leu	p.S1122L	ENST00000298229	NM_001567.3	1122	tCg/tTg	26/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.588114165437952	2		917	502	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349640	89349641	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs772267579	NA	P-0045176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	200	663	11	ENST00000301030.4:c.3309dup	p.Asp1104ArgfsTer2	p.D1104Rfs*2	ENST00000301030	NM_001256183.1	1103	-/A	9/13	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.588114165437952	2		674	656	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998128	169998128	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs753143066	NA	P-0045176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	230	568	9	ENST00000295797.4:c.826del	p.Thr276GlnfsTer7	p.T276Qfs*7	ENST00000295797	NM_002740.5	273	ttA/tt	9/18	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.588114165437952	2		577	641	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862193	68862193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779648243	NA	P-0045176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	169	472	0	ENST00000261769.5:c.2281G>A	p.Gly761Arg	p.G761R	ENST00000261769	NM_004360.3	761	Gga/Aga	14/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.588114165437952	2		472	483	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193218952	193218952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	114	218	1	ENST00000367435.3:c.1510C>T	p.Arg504Cys	p.R504C	ENST00000367435	NM_024529.4	504	Cgt/Tgt	16/17	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.588114165437952	2		219	325	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665790	241665790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224007	NA	P-0045176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	64	391	0	ENST00000366560.3:c.1189G>A	p.Gly397Arg	p.G397R	ENST00000366560	NM_000143.3	397	Gga/Aga	8/10	1	2	FACETS	0.601	0.523	0.685	0.601	0.523	0.685	SUBCLONAL	1	TRUE	1	0.588114165437952	2		391	362	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068397	16068397	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs761125618	NA	P-0045176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	21	50	0	ENST00000268712.3:c.514T>C	p.Ser172Pro	p.S172P	ENST00000268712	NM_006311.3	172	Tca/Cca	5/46	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.588114165437952	2		50	55	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119052	70119052	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	177	648	0	ENST00000245479.2:c.624G>T	p.Gln208His	p.Q208H	ENST00000245479	NM_000346.3	208	caG/caT	2/3	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.588114165437952	2		648	418	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009098	27009098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	93	243	0	ENST00000335756.4:c.34G>A	p.Ala12Thr	p.A12T	ENST00000335756	NM_001809.3	12	Gcc/Acc	1/5	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.588114165437952	2		243	234	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272280	21272281	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0045176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	132	594	0	ENST00000354336.3:c.60_61del	p.Arg21ProfsTer51	p.R21Pfs*51	ENST00000354336	NM_005207.3	20	TCt/t	1/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.588114165437952	2		594	363	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013729	170013729	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1389006052	NA	P-0045176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	164	341	0	ENST00000295797.4:c.1448G>A	p.Arg483His	p.R483H	ENST00000295797	NM_002740.5	483	cGt/cAt	15/18	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.588114165437952	2		341	454	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294129	1294129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1416937312	NA	P-0045176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	236	1067	2	ENST00000310581.5:c.872G>A	p.Gly291Asp	p.G291D	ENST00000310581	NM_198253.2	291	gGc/gAc	2/16	0.558212184218883	1	FACETS	0.982	0.924	1	0.982	0.924	1	CLONAL	1	TRUE	0	0.588114165437952	1		1069	577	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56174820	56174820	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	91	251	0	ENST00000399503.3:c.1979C>T	p.Ala660Val	p.A660V	ENST00000399503	NM_005921.1	660	gCc/gTc	11/20	0.11389645762699	3	FACETS	0.831	0.751	0.913	0.831	0.751	0.913	INDETERMINATE	2	TRUE	1	0.588114165437952	3		251	241	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517624	176517624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548911521	NA	P-0045176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	185	848	1	ENST00000292408.4:c.325G>A	p.Val109Ile	p.V109I	ENST00000292408	NM_213647.1	109	Gtc/Atc	3/18	0.11389645762699	3	FACETS	0.797	0.742	0.853	0.797	0.742	0.853	INDETERMINATE	2	TRUE	1	0.588114165437952	3		849	511	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396247	139396248	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0045176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	227	915	0	ENST00000277541.6:c.5590dup	p.Gln1864ProfsTer3	p.Q1864Pfs*3	ENST00000277541	NM_017617.3	1864	cag/cCag	30/34	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.588114165437952	2		915	664	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412212	139412212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	245	795	0	ENST00000277541.6:c.1433G>A	p.Cys478Tyr	p.C478Y	ENST00000277541	NM_017617.3	478	tGc/tAc	8/34	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.588114165437952	2		795	625	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969470	44969471	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0045176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	162	343	0	ENST00000377967.4:c.4153dup	p.Gln1385ProfsTer4	p.Q1385Pfs*4	ENST00000377967	NM_021140.2	1384	-/C	28/29	0.421927051483782	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.588114165437952	1		343	341	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	185	566	2	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	0.14961625514861	3	FACETS	0.809	0.753	0.866	0.539	0.502	0.578	INDETERMINATE	2	TRUE	0	0.569139276226423	3		568	516	SUCCESS
APC	324	MSKCC	GRCh37	5	112175530	112175530	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	190	350	1	ENST00000257430.4:c.4240del	p.Val1414Ter	p.V1414*	ENST00000257430	NM_000038.5	1413	atG/at	16/16	0.474111374320133	2	FACETS	0.881	0.827	0.934	0.881	0.827	0.934	CLONAL	2	TRUE	0	0.569139276226423	2		351	379	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121913370	NA	P-0045220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	84	265	0	ENST00000288602.6:c.1742A>G	p.Asn581Ser	p.N581S	ENST00000288602	NM_004333.4	581	aAt/aGt	15/18	0.230374595602493	5	FACETS	1	0.963	1	0.773	0.694	0.854	INDETERMINATE	2	TRUE	2	0.569139276226423	5		265	236	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0045220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	25	341	1	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	0.474111374320133	2	FACETS	0.322	0.254	0.399	0.161	0.127	0.2	SUBCLONAL	1	TRUE	0	0.569139276226423	2		342	273	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498423	89498423	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1203973847	NA	P-0045220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	46	353	1	ENST00000336596.2:c.2395C>T	p.Arg799Cys	p.R799C	ENST00000336596	NM_005233.5	799	Cgc/Tgc	14/17	0.14961625514861	3	FACETS	0.532	0.449	0.624	0.177	0.149	0.208	INDETERMINATE	1	TRUE	0	0.569139276226423	3		354	390	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349365	73349365	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs760292076	NA	P-0045220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	49	379	0	ENST00000377767.4:c.971A>G	p.Glu324Gly	p.E324G	ENST00000377767	NM_014953.3	324	gAa/gGa	6/21	0.444592313740625	4	FACETS	0.633	0.537	0.738	0.316	0.268	0.369	SUBCLONAL	1	TRUE	2	0.569139276226423	4		379	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578404	+	inframe_deletion	In_Frame_Del	DEL	GCA	GCA	-	novel	NA	P-0045220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	391	891	0	ENST00000269305.4:c.526_528del	p.Cys176del	p.C176del	ENST00000269305	NM_001126112.2	176	TGC/-	5/11	0.558760662339524	2	FACETS	0.961	0.922	1	0.961	0.922	1	CLONAL	2	TRUE	0	0.569139276226423	2		891	715	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845229	151845229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	240	556	1	ENST00000262189.6:c.13783C>T	p.Arg4595Cys	p.R4595C	ENST00000262189	NM_170606.2	4595	Cgc/Tgc	52/59	0.230374595602493	5	FACETS	1	0.983	1	0.755	0.709	0.803	INDETERMINATE	2	TRUE	2	0.569139276226423	5		557	690	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745198	41745198	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1354928632	NA	P-0045220-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	162	824	0	ENST00000301178.4:c.1264C>T	p.Pro422Ser	p.P422S	ENST00000301178	NM_021913.4	422	Ccc/Tcc	9/20	0.14961625514861	3	FACETS	0.906	0.832	0.983	0.302	0.277	0.328	INDETERMINATE	1	TRUE	0	0.569139276226423	3		824	807	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0045226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	394	631	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.854267133663201	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.854267133663201	1		631	490	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0045226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	496	618	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	0.153014246221927	3	FACETS	0.869	0.837	0.902	0.58	0.558	0.601	INDETERMINATE	2	TRUE	0	0.854267133663201	3		618	953	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681074	117681077	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	rs779372215	NA	P-0045226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	138	554	0	ENST00000368508.3:c.3543_3546del	p.Arg1182LeufsTer60	p.R1182Lfs*60	ENST00000368508	NM_002944.2	1181	gaAAGA/ga	23/43	1	2	FACETS	0.479	0.436	0.523	0.479	0.436	0.523	SUBCLONAL	1	TRUE	1	0.854267133663201	2		554	675	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609006	43609006	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045226-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	171	718	0	ENST00000355710.3:c.1762G>A	p.Gly588Ser	p.G588S	ENST00000355710	NM_020975.4	588	Ggc/Agc	10/20	1	2	FACETS	0.494	0.454	0.534	0.494	0.454	0.534	SUBCLONAL	1	TRUE	1	0.854267133663201	2		718	811	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912660	NA	P-0045284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	536	792	0	ENST00000269305.4:c.839G>T	p.Arg280Ile	p.R280I	ENST00000269305	NM_001126112.2	280	aGa/aTa	8/11	0.565041192528211	1	FACETS	0.784	0.759	0.809	1	0.997	1	SUBCLONAL	2	TRUE	0	0.565041192528211	1		792	868	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0045284-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	80	451	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.747	0.662	0.837	0.747	0.662	0.837	SUBCLONAL	1	TRUE	1	0.565041192528211	2		451	379	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500479	149500490	+	inframe_deletion	In_Frame_Del	DEL	CGCATGATGTCT	CGCATGATGTCT	-	novel	NA	P-0045456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	604	660	0	ENST00000261799.4:c.2547_2558del	p.Ile851_Asp854del	p.I851_D854del	ENST00000261799	NM_002609.3	849	cgAGACATCATGCGg/cgg	18/23	0.7907074491005	3	FACETS	0.888	0.858	0.919	0.592	0.572	0.613	CLONAL	2	TRUE	0	0.7907074491005	3		660	1200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574035	7574035	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs867389695	NA	P-0045456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	632	543	0	ENST00000269305.4:c.994-2A>G		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.7907074491005	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.7907074491005	2		543	769	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288965	33288965	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774538403	NA	P-0045456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	83	491	0	ENST00000374542.5:c.587C>T	p.Ala196Val	p.A196V	ENST00000374542	NM_001141970.1	196	gCg/gTg	3/8	0.7907074491005	3	FACETS	0.369	0.325	0.417	0.185	0.162	0.209	SUBCLONAL	1	TRUE	1	0.7907074491005	3		491	793	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535425	187535425	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	109	362	0	ENST00000441802.2:c.9149C>G	p.Ala3050Gly	p.A3050G	ENST00000441802	NM_005245.3	3050	gCa/gGa	12/27	1	2	FACETS	0.931	0.849	1	0.931	0.849	1	CLONAL	1	TRUE	1	0.7907074491005	2		362	296	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339242	70339268	+	inframe_deletion	In_Frame_Del	DEL	ATGTAAAACAAGGTTTCAATAACCAGC	ATGTAAAACAAGGTTTCAATAACCAGC	-	novel	NA	P-0045456-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	178	528	0	ENST00000374080.3:c.119_145del	p.Asn40_Pro49delinsThr	p.N40_P49delinsT	ENST00000374080		40	aATGTAAAACAAGGTTTCAATAACCAGCct/act	2/45	0.7907074491005	1	FACETS	0.843	0.792	0.893	0.843	0.792	0.893	CLONAL	1	TRUE	0	0.7907074491005	1		528	323	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0045479-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	10	69	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		69	347	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0045479-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	10	356	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.126255129432465	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		358	370	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436149	56436149	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045479-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	42	751	0	ENST00000407977.2:c.988C>T	p.Arg330Ter	p.R330*	ENST00000407977		330	Cga/Tga	9/10	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		751	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0045528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	118	452	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.456501882516174	1	FACETS	0.879	0.798	0.963	0.879	0.798	0.963	CLONAL	1	TRUE	0	0.456501882516174	1		452	454	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054369	42054369	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	59	235	0	ENST00000219905.7:c.7553A>T	p.Tyr2518Phe	p.Y2518F	ENST00000219905	NM_001164273.1	2518	tAt/tTt	22/24	1	2	FACETS	0.891	0.773	1	0.891	0.773	1	CLONAL	1	TRUE	1	0.456501882516174	2		235	290	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550457	29550475	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGCAGCTCACAAATGCTTT	TGCAGCTCACAAATGCTTT	A	novel	NA	P-0045528-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	41	105	0	ENST00000356175.3:c.1722-5_1735delinsA		p.X574_splice	ENST00000356175	NM_000267.3	574		16/57	0.456501882516174	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.456501882516174	1		105	106	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	121	151	0				ENST00000310581	NM_198253.2	-/1132			0.481128643279605	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.481128643279605	3		151	300	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0045572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	124	256	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.481128643279605	2		256	479	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11177068	11177068	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	52	263	1	ENST00000361445.4:c.7009G>A	p.Gly2337Arg	p.G2337R	ENST00000361445	NM_004958.3	2337	Gga/Aga	50/58	1	2	FACETS	0.438	0.373	0.51	0.438	0.373	0.51	SUBCLONAL	1	TRUE	1	0.481128643279605	2		264	493	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023307	27023307	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0045572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	15	47	0	ENST00000324856.7:c.413C>G	p.Ser138Ter	p.S138*	ENST00000324856	NM_006015.4	138	tCa/tGa	1/20	1	2	FACETS	0.67	0.498	0.871	0.67	0.498	0.871	SUBCLONAL	1	TRUE	1	0.481128643279605	2		47	93	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959416	26959416	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	60	385	0	ENST00000381527.3:c.583G>T	p.Val195Phe	p.V195F	ENST00000381527	NM_001260.1	195	Gtt/Ttt	6/13	1	2	FACETS	0.4	0.344	0.461	0.4	0.344	0.461	SUBCLONAL	1	TRUE	1	0.481128643279605	2		385	623	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437493	110437493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749782460	NA	P-0045572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	83	433	0	ENST00000375856.3:c.908G>A	p.Arg303His	p.R303H	ENST00000375856	NM_003749.2	303	cGc/cAc	1/2	1	2	FACETS	0.483	0.426	0.544	0.483	0.426	0.544	SUBCLONAL	1	TRUE	1	0.481128643279605	2		433	714	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141406	11141406	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	162	459	0	ENST00000358026.2:c.3383G>A	p.Gly1128Glu	p.G1128E	ENST00000358026	NM_001128849.1	1128	gGa/gAa	25/36	1	2	FACETS	0.933	0.858	1	0.933	0.858	1	CLONAL	1	TRUE	1	0.481128643279605	2		459	722	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220059	36220068	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GGAGGCGGGG	GGAGGCGGGG	-	novel	NA	P-0045572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	79	619	0	ENST00000222270.7:c.4780-1_4788del		p.X1594_splice	ENST00000222270	NM_014727.1	1594		22/37	1	2	FACETS	0.382	0.335	0.432	0.382	0.335	0.432	SUBCLONAL	1	TRUE	1	0.481128643279605	2		619	860	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428962	47428962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	86	568	2	ENST00000377045.4:c.1325C>T	p.Thr442Met	p.T442M	ENST00000377045	NM_001654.4	442	aCg/aTg	13/16	0.270575856435884	1	FACETS	0.283	0.249	0.318	0.283	0.249	0.318	INDETERMINATE	1	TRUE	0	0.481128643279605	1		570	961	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974754	21974766	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGACCCCGGGC	CCCGACCCCGGGC	-	novel	NA	P-0045650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	40	174	0	ENST00000304494.5:c.61_73del	p.Ala21Ter	p.A21*	ENST00000304494	NM_000077.4	21	GCCCGGGGTCGGGta/ta	1/3	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	FALSE	1	0.25497403421602	2		174	286	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600429	10600429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	92	543	0	ENST00000171111.5:c.1426G>A	p.Gly476Arg	p.G476R	ENST00000171111	NM_203500.1	476	Ggg/Agg	4/6	1	2	FACETS	0.776	0.688	0.87	0.776	0.688	0.87	SUBCLONAL	1	FALSE	1	0.25497403421602	2		543	930	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225449660	225449660	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0045650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	20	186	0	ENST00000264414.4:c.66+1G>T		p.X22_splice	ENST00000264414	NM_003590.4	22			1	2	FACETS	0.393	0.3	0.503	0.393	0.3	0.503	SUBCLONAL	1	FALSE	1	0.25497403421602	2		186	399	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197724	66197724	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs773062561	NA	P-0045650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	20	249	0	ENST00000273854.3:c.2975G>T	p.Ser992Ile	p.S992I	ENST00000273854	NM_004439.5	992	aGt/aTt	17/18	1	2	FACETS	0.545	0.417	0.694	0.545	0.417	0.694	SUBCLONAL	1	FALSE	1	0.25497403421602	2		249	288	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576863	7576872	+	frameshift_variant	Frame_Shift_Del	DEL	AAATATTCTC	AAATATTCTC	-	novel	NA	P-0045650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	57	426	0	ENST00000269305.4:c.974_983del	p.Gly325AlafsTer17	p.G325Afs*17	ENST00000269305	NM_001126112.2	325	gGAGAATATTTc/gc	9/11	1	2	FACETS	0.693	0.594	0.802	0.693	0.594	0.802	SUBCLONAL	1	FALSE	1	0.25497403421602	2		426	645	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193219841	193219841	+	stop_lost	Nonstop_Mutation	SNP	G	G	T	novel	NA	P-0045650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	21	166	0	ENST00000367435.3:c.1595G>T	p.Ter532LeuextTer29	p.*532Lext*29	ENST00000367435	NM_024529.4	532	tGa/tTa	17/17	1	2	FACETS	0.886	0.686	1	0.886	0.686	1	CLONAL	1	FALSE	1	0.25497403421602	2		166	186	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926879	112926879	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	47	445	0	ENST00000351677.2:c.1499A>T	p.Gln500Leu	p.Q500L	ENST00000351677	NM_002834.3	500	cAg/cTg	13/16	1	2	FACETS	0.537	0.452	0.632	0.537	0.452	0.632	SUBCLONAL	1	FALSE	1	0.25497403421602	2		445	686	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096066	11096066	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	81	527	0	ENST00000358026.2:c.340G>C	p.Asp114His	p.D114H	ENST00000358026	NM_001128849.1	114	Gac/Cac	3/36	1	2	FACETS	0.868	0.764	0.979	0.868	0.764	0.979	CLONAL	1	FALSE	1	0.25497403421602	2		527	732	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134224	11134224	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	60	426	0	ENST00000358026.2:c.2890A>T	p.Ile964Phe	p.I964F	ENST00000358026	NM_001128849.1	964	Atc/Ttc	20/36	1	2	FACETS	0.725	0.624	0.835	0.725	0.624	0.835	SUBCLONAL	1	FALSE	1	0.25497403421602	2		426	649	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456456	89456456	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	28	243	0	ENST00000336596.2:c.1632G>A	p.Met544Ile	p.M544I	ENST00000336596	NM_005233.5	544	atG/atA	8/17	1	2	FACETS	0.735	0.588	0.9	0.735	0.588	0.9	SUBCLONAL	1	FALSE	1	0.25497403421602	2		243	299	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499355	89499355	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	43	264	0	ENST00000336596.2:c.2525G>T	p.Arg842Leu	p.R842L	ENST00000336596	NM_005233.5	842	cGa/cTa	15/17	1	2	FACETS	0.899	0.754	1	0.899	0.754	1	CLONAL	1	FALSE	1	0.25497403421602	2		264	375	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920337	134920337	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	46	275	0	ENST00000398015.3:c.2152G>T	p.Val718Leu	p.V718L	ENST00000398015	NM_004441.4	718	Gtg/Ttg	12/16	1	2	FACETS	0.82	0.691	0.962	0.82	0.691	0.962	CLONAL	1	FALSE	1	0.25497403421602	2		275	440	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55987320	55987320	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	18	221	0	ENST00000263923.4:c.105C>A	p.Ser35Arg	p.S35R	ENST00000263923	NM_002253.2	35	agC/agA	2/30	1	2	FACETS	0.513	0.387	0.663	0.513	0.387	0.663	SUBCLONAL	1	FALSE	1	0.25497403421602	2		221	275	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967197	93967197	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	17	206	0	ENST00000369303.4:c.2155C>A	p.Leu719Ile	p.L719I	ENST00000369303	NM_004440.3	719	Cta/Ata	12/17	1	2	FACETS	0.59	0.441	0.766	0.59	0.441	0.766	SUBCLONAL	1	FALSE	1	0.25497403421602	2		206	226	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161970037	161970037	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0045650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	80	422	0	ENST00000366898.1:c.934-2A>C		p.X312_splice	ENST00000366898	NM_004562.2	312			1	2	FACETS	0.916	0.806	1	0.916	0.806	1	CLONAL	1	FALSE	1	0.25497403421602	2		422	685	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394398	162394398	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	41	232	0	ENST00000366898.1:c.670G>T	p.Val224Leu	p.V224L	ENST00000366898	NM_004562.2	224	Gta/Tta	6/12	1	2	FACETS	0.86	0.718	1	0.86	0.718	1	CLONAL	1	FALSE	1	0.25497403421602	2		232	374	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245298	53245298	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	88	310	0	ENST00000375401.3:c.739G>T	p.Gly247Cys	p.G247C	ENST00000375401	NM_004187.3	247	Ggc/Tgc	6/26	0.0171504653078394	2	FACETS	1	0.974	1			1	INDETERMINATE	1	FALSE	NA	0.25497403421602	2		310	510	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	105	151	0				ENST00000310581	NM_198253.2	-/1132			0.814771640249607	4	FACETS	1	0.979	1	0.662	0.599	0.727	CLONAL	1	TRUE	2	0.833003284762915	4		151	349	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0045651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	524	553	1	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	NA	2	FACETS	0.855	0.83	0.878			1	INDETERMINATE	2	TRUE	NA	0.833003284762915	2		554	736	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0045651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	416	616	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.751422625371793	2	FACETS	0.921	0.895	0.947	0.921	0.895	0.947	CLONAL	2	TRUE	0	0.833003284762915	2		616	542	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788618	3788618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398124146	NA	P-0045651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	143	277	0	ENST00000262367.5:c.4336C>T	p.Arg1446Cys	p.R1446C	ENST00000262367	NM_004380.2	1446	Cgc/Tgc	26/31	0.232703682174919	1	FACETS	0.715	0.666	0.765	0.715	0.666	0.765	INDETERMINATE	1	TRUE	0	0.833003284762915	1		277	280	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138480	11138480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	111	464	0	ENST00000358026.2:c.3236C>T	p.Ser1079Leu	p.S1079L	ENST00000358026	NM_001128849.1	1079	tCg/tTg	24/36	0.331422299420918	2	FACETS	0.573	0.518	0.631	0.287	0.259	0.316	INDETERMINATE	1	TRUE	0	0.833003284762915	2		464	465	SUCCESS
AR	367	MSKCC	GRCh37	X	66863144	66863144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	103	249	0	ENST00000374690.3:c.1663C>T	p.Pro555Ser	p.P555S	ENST00000374690	NM_000044.3	555	Cca/Tca	2/8	1	1	FACETS	0.517	0.47	0.566	0.517	0.47	0.566	SUBCLONAL	1	TRUE	0	0.833003284762915	1		249	279	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045756	26045756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	73	406	0	ENST00000540144.1:c.118C>T	p.His40Tyr	p.H40Y	ENST00000540144	NM_003531.2	40	Cat/Tat	1/1	0.433774223525943	4	FACETS	0.682	0.598	0.772	0.171	0.149	0.193	INDETERMINATE	1	TRUE	0	0.833003284762915	4		406	471	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389278	8389278	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752508898	NA	P-0045651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	149	379	0	ENST00000356435.5:c.4340G>A	p.Arg1447Gln	p.R1447Q	ENST00000356435		1447	cGg/cAg	26/35	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.833003284762915	2		379	305	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027156	49027156	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778864	NA	P-0045651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	125	276	0	ENST00000267163.4:c.1723C>T	p.Gln575Ter	p.Q575*	ENST00000267163	NM_000321.2	575	Caa/Taa	18/27	NA	2	FACETS	0.872	0.823	0.919			1	INDETERMINATE	2	TRUE	NA	0.833003284762915	2		276	172	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128018835	128018835	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	156	416	0	ENST00000285398.2:c.2033G>T	p.Arg678Ile	p.R678I	ENST00000285398	NM_000122.1	678	aGa/aTa	13/15	1	2	FACETS	0.965	0.895	1	0.965	0.895	1	CLONAL	1	TRUE	1	0.833003284762915	2		416	388	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723037	49723037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767971831	NA	P-0045651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	35	333	0	ENST00000449682.2:c.1379G>A	p.Arg460Gln	p.R460Q	ENST00000449682	NM_020998.3	460	cGa/cAa	11/18	0.527697809557525	3	FACETS	0.284	0.233	0.342	0.142	0.116	0.171	SUBCLONAL	1	TRUE	1	0.833003284762915	3		333	419	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653271	29653271	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0045651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	111	200	0	ENST00000356175.3:c.5205+1G>C		p.X1735_splice	ENST00000356175	NM_000267.3	1735			0.441327228640039	2	FACETS	1	0.985	1	0.663	0.613	0.713	INDETERMINATE	1	TRUE	0	0.833003284762915	2		200	201	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224504	108224504	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	108	231	0	ENST00000278616.4:c.8683G>C	p.Glu2895Gln	p.E2895Q	ENST00000278616	NM_000051.3	2895	Gaa/Caa	60/63	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.833003284762915	2		231	210	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101583	27101583	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	238	644	0	ENST00000324856.7:c.4866del	p.Ser1623ArgfsTer3	p.S1623Rfs*3	ENST00000324856	NM_006015.4	1622	gCc/gc	18/20	0.486838199821267	3	FACETS	1	0.938	1	0.501	0.469	0.534	INDETERMINATE	1	TRUE	1	0.833003284762915	3		644	808	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427021	49427022	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCCTGGGGGCCAA	novel	NA	P-0045651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	323	589	0	ENST00000301067.7:c.11466_11467insTTGGCCCCCAGGGC	p.Pro3823LeufsTer12	p.P3823Lfs*12	ENST00000301067	NM_003482.3	3822	-/TTGGCCCCCAGGGC	39/54	0.62046410428283	3	FACETS	1	0.992	1			1	CLONAL	1	TRUE	NA	0.833003284762915	3		589	891	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505391	25505391	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	227	597	0	ENST00000264709.3:c.367G>C	p.Glu123Gln	p.E123Q	ENST00000264709	NM_175629.2	123	Gag/Cag	4/23	NA	2	FACETS	0.927	0.87	0.985			1	INDETERMINATE	1	TRUE	NA	0.833003284762915	2		597	588	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652028	36652029	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0045651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	656	762	0	ENST00000244741.5:c.152dup	p.Asp52ArgfsTer11	p.D52Rfs*11	ENST00000244741	NM_000389.4	50	-/T	2/3	0.724846370493502	2	FACETS	0.908	0.887	0.929	0.908	0.887	0.929	CLONAL	2	TRUE	0	0.833003284762915	2		762	867	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891214	151891214	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0045651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	76	364	0	ENST00000262189.6:c.4541-1G>C		p.X1514_splice	ENST00000262189	NM_170606.2	1514			1	2	FACETS	0.484	0.427	0.545	0.484	0.427	0.545	SUBCLONAL	1	TRUE	1	0.833003284762915	2		364	377	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922487	56922487	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	173	331	0	ENST00000519728.1:c.1357A>G	p.Met453Val	p.M453V	ENST00000519728	NM_002350.3	453	Atg/Gtg	13/13	0.231013171109822	5	FACETS	0.984	0.914	1	0.656	0.609	0.703	INDETERMINATE	2	TRUE	2	0.833003284762915	5		331	475	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776158	135776158	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	185	391	1	ENST00000298552.3:c.2569G>T	p.Glu857Ter	p.E857*	ENST00000298552	NM_001162426.1	857	Gag/Tag	20/23	0.231013171109822	5	FACETS	0.982	0.914	1	0.654	0.609	0.7	INDETERMINATE	2	TRUE	2	0.833003284762915	5		392	509	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608963	100608963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045651-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	16	224	0	ENST00000308731.7:c.1645G>A	p.Asp549Asn	p.D549N	ENST00000308731	NM_000061.2	549	Gat/Aat	17/19	1	1	FACETS	0.12	0.088	0.157	0.12	0.088	0.157	SUBCLONAL	1	TRUE	0	0.833003284762915	1		224	187	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	95	151	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.97	0.88	1	0.97	0.88	1	CLONAL	1	TRUE	1	0.826212398593118	2		151	237	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0045652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	111	201	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.826212398593118	2		201	254	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0045652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	14	192	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	NA	2	FACETS	0.12	0.086	0.161			1	INDETERMINATE	1	TRUE	NA	0.826212398593118	2		192	282	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952142	178952142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1253171657	NA	P-0045652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	25	172	0	ENST00000263967.3:c.3197C>T	p.Ala1066Val	p.A1066V	ENST00000263967	NM_006218.2	1066	gCa/gTa	21/21	NA	2	FACETS	0.255	0.202	0.316			1	INDETERMINATE	1	TRUE	NA	0.826212398593118	2		172	237	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791715	42791715	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157030312	NA	P-0045652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	57	579	1	ENST00000575354.2:c.601C>T	p.Arg201Trp	p.R201W	ENST00000575354	NM_015125.3	201	Cgg/Tgg	5/20	0.826212398593118	1	FACETS	0.209	0.179	0.24	0.209	0.179	0.24	SUBCLONAL	1	TRUE	0	0.826212398593118	1		580	388	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610644	81610644	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	35	234	0	ENST00000298171.2:c.2242A>G	p.Thr748Ala	p.T748A	ENST00000298171	NM_000369.2	748	Acc/Gcc	10/10	1	2	FACETS	0.247	0.203	0.297	0.247	0.203	0.297	SUBCLONAL	1	TRUE	1	0.826212398593118	2		234	343	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180824	106180826	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0045652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	61	241	0	ENST00000380013.4:c.3854_3856del	p.Phe1285del	p.F1285del	ENST00000380013	NM_001127208.2	1284	tcCTTc/tcc	7/11	0.233047201837897	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.826212398593118	0		241	224	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239439	123239439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	58	386	0	ENST00000358487.5:c.2398C>T	p.Pro800Ser	p.P800S	ENST00000358487	NM_000141.4	800	Cca/Tca	18/18	1	2	FACETS	0.266	0.229	0.307	0.266	0.229	0.307	SUBCLONAL	1	TRUE	1	0.826212398593118	2		386	527	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899177	78899177	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	43	370	0	ENST00000306801.3:c.2816A>G	p.Asp939Gly	p.D939G	ENST00000306801	NM_020761.2	939	gAc/gGc	24/34	0.826212398593118	3	FACETS	0.187	0.156	0.222	0.094	0.078	0.111	SUBCLONAL	1	TRUE	1	0.826212398593118	3		370	785	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109308818	109308818	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	23	152	0	ENST00000436639.2:c.1585C>T	p.Leu529Phe	p.L529F	ENST00000436639	NM_014454.2	529	Ctt/Ttt	10/10	1	2	FACETS	0.217	0.169	0.271	0.217	0.169	0.271	SUBCLONAL	1	TRUE	1	0.826212398593118	2		152	257	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413018	63413018	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045652-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	47	361	0	ENST00000330258.3:c.149G>A	p.Gly50Asp	p.G50D	ENST00000330258	NM_152424.3	50	gGt/gAt	2/2	1	1	FACETS	0.162	0.137	0.19	0.162	0.137	0.19	SUBCLONAL	1	TRUE	0	0.826212398593118	1		361	412	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0045653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	14	240	0	ENST00000349496.5:c.101G>A	p.Gly34Glu	p.G34E	ENST00000349496	NM_001904.3	34	gGa/gAa	3/15	1	2	FACETS	0.317	0.228	0.425	0.317	0.228	0.425	SUBCLONAL	1	TRUE	1	0.26	2		240	340	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0045653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	441	399	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.3	6	FACETS	1	0.989	1	1	0.989	1	CLONAL	5	TRUE	1	0.26	6		399	947	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0045655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	354	696	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.502714751002178	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	0	0.591641435277483	3		696	499	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554453	63554453	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045655-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	60	573	0	ENST00000307078.5:c.286del	p.Arg96GlufsTer13	p.R96Efs*13	ENST00000307078	NM_004655.3	96	Cga/ga	2/11	0.156030348394403	3	FACETS	0.705	0.61	0.807	0.235	0.203	0.269	INDETERMINATE	1	TRUE	0	0.591641435277483	3		573	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0045657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	525	804	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	0.865835565748692	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.865835565748692	2		804	593	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530456	187530456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1373676802	NA	P-0045657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	190	264	0	ENST00000441802.2:c.10087G>A	p.Asp3363Asn	p.D3363N	ENST00000441802	NM_005245.3	3363	Gat/Aat	16/27	0.865835565748692	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.865835565748692	2		264	211	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372530	118372530	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	332	407	0	ENST00000534358.1:c.6463C>G	p.Pro2155Ala	p.P2155A	ENST00000534358	NM_005933.3	2155	Cca/Gca	26/36	0.865835565748692	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.865835565748692	3		407	522	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937028	48937028	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	196	259	0	ENST00000267163.4:c.796del	p.Gln266AsnfsTer2	p.Q266Nfs*2	ENST00000267163	NM_000321.2	266	Caa/aa	8/27	0.865835565748692	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.865835565748692	2		259	222	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022983	33022983	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	131	394	0	ENST00000300177.4:c.92G>A	p.Gly31Asp	p.G31D	ENST00000300177	NM_001191322.1	31	gGt/gAt	2/2	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.865835565748692	2		394	262	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555122	106555122	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770948121	NA	P-0045657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	286	429	0	ENST00000369096.4:c.2239G>A	p.Asp747Asn	p.D747N	ENST00000369096	NM_001198.3	747	Gat/Aat	7/7	0.762561148274472	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.865835565748692	4		429	575	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38314960	38314960	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	404	626	0	ENST00000425967.3:c.104G>T	p.Trp35Leu	p.W35L	ENST00000425967	NM_001174067.1	35	tGg/tTg	3/19	0.826800512996181	4	FACETS	0.93	0.889	0.972	0.93	0.889	0.972	CLONAL	2	TRUE	2	0.865835565748692	4		626	936	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504389	8504389	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045657-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	112	343	0	ENST00000356435.5:c.1694A>T	p.Glu565Val	p.E565V	ENST00000356435		565	gAg/gTg	12/35	0.865835565748692	3	FACETS	0.872	0.79	0.958	0.436	0.395	0.479	CLONAL	1	TRUE	1	0.865835565748692	3		343	425	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0045659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	35	295	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.256614621620643	2		295	261	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940889	49940889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144338909	NA	P-0045659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	131	698	0	ENST00000296474.3:c.154G>A	p.Gly52Arg	p.G52R	ENST00000296474	NM_002447.2	52	Gga/Aga	1/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.256614621620643	2		698	846	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692892	89692892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554898129	NA	P-0045659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	49	295	0	ENST00000371953.3:c.376G>A	p.Ala126Thr	p.A126T	ENST00000371953	NM_000314.4	126	Gct/Act	5/9	0.208303752188728	3	FACETS	1	0.961	1	0.723	0.616	0.839	CLONAL	1	TRUE	1	0.256614621620643	3		295	298	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589629	67589630	+	inframe_insertion	In_Frame_Ins	INS	-	-	AGATTA	novel	NA	P-0045659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	12	146	0	ENST00000274335.5:c.1393_1398dup	p.Arg465_Leu466dup	p.R465_L466dup	ENST00000274335		465	-/AGATTA	10/15	1	2	FACETS	0.596	0.42	0.81	0.596	0.42	0.81	SUBCLONAL	1	TRUE	1	0.256614621620643	2		146	157	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692889	89692889	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	43	282	0	ENST00000371953.3:c.373A>G	p.Lys125Glu	p.K125E	ENST00000371953	NM_000314.4	125	Aaa/Gaa	5/9	0.208303752188728	3	FACETS	1	0.945	1	0.652	0.548	0.765	CLONAL	1	TRUE	1	0.256614621620643	3		282	290	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591287	67591288	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0045659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	15	250	0	ENST00000274335.5:c.1787_1788dup	p.Trp597SerfsTer66	p.W597Sfs*66	ENST00000274335		595	-/GA	13/15	1	2	FACETS	0.435	0.317	0.575	0.435	0.317	0.575	SUBCLONAL	1	TRUE	1	0.256614621620643	2		250	269	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148504777	148504778	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	58	317	0	ENST00000320356.2:c.2216dup	p.Lys740GlufsTer23	p.K740Efs*23	ENST00000320356	NM_004456.4	739	ctg/ctTg	20/20	1	2	FACETS	0.972	0.837	1	0.972	0.837	1	CLONAL	1	TRUE	1	0.256614621620643	2		317	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0045660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	201	509	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	0.635796740165824	1	FACETS	0.938	0.879	0.997	0.938	0.879	0.997	CLONAL	1	TRUE	0	0.635796740165824	1		509	460	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247373	153247373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	40	199	0	ENST00000281708.4:c.1429G>A	p.Gly477Ser	p.G477S	ENST00000281708	NM_033632.3	477	Ggt/Agt	10/12	0.476165876191637	1	FACETS	0.403	0.338	0.474	0.403	0.338	0.474	SUBCLONAL	1	TRUE	0	0.635796740165824	1		199	213	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120258	70120259	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	484	539	0	ENST00000245479.2:c.1261dup	p.Ser421LysfsTer157	p.S421Kfs*157	ENST00000245479	NM_000346.3	420	-/A	3/3	0.472836543258665	3	FACETS	0.935	0.898	0.973	0.935	0.898	0.973	CLONAL	2	TRUE	1	0.635796740165824	3		539	1073	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917730	29917730	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	132	579	0	ENST00000389048.3:c.938A>C	p.Lys313Thr	p.K313T	ENST00000389048	NM_004304.4	313	aAg/aCg	3/29	0.315276192010351	2	FACETS	0.58	0.527	0.635	0.29	0.263	0.318	INDETERMINATE	1	TRUE	0	0.635796740165824	2		579	716	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420432	49420432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778486	NA	P-0045660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	177	599	1	ENST00000301067.7:c.15317G>A	p.Arg5106His	p.R5106H	ENST00000301067	NM_003482.3	5106	cGc/cAc	48/54	0.476165876191637	1	FACETS	0.726	0.674	0.78	0.726	0.674	0.78	SUBCLONAL	1	TRUE	0	0.635796740165824	1		600	523	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008044	29008044	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0045660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	46	298	0	ENST00000282397.4:c.725T>A	p.Leu242Ter	p.L242*	ENST00000282397	NM_002019.4	242	tTa/tAa	6/30	0.33557028894091	3	FACETS	0.573	0.484	0.67	0.191	0.161	0.224	INDETERMINATE	1	TRUE	0	0.635796740165824	3		298	333	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72863717	72863717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	239	497	0	ENST00000268489.5:c.3490G>A	p.Ala1164Thr	p.A1164T	ENST00000268489	NM_006885.3	1164	Gct/Act	5/10	0.431260456904612	1	FACETS	0.892	0.84	0.945	0.892	0.84	0.945	CLONAL	1	TRUE	0	0.635796740165824	1		497	575	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119936	70119937	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0045660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	55	385	0	ENST00000245479.2:c.940_941dup	p.Tyr315ProfsTer69	p.Y315Pfs*69	ENST00000245479	NM_000346.3	313	gtc/gtCAc	3/3	0.472836543258665	3	FACETS	0.397	0.339	0.46	0.198	0.169	0.23	SUBCLONAL	1	TRUE	1	0.635796740165824	3		385	575	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249400	153249400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	84	362	0	ENST00000281708.4:c.1378C>T	p.His460Tyr	p.H460Y	ENST00000281708	NM_033632.3	460	Cat/Tat	9/12	0.476165876191637	1	FACETS	0.78	0.701	0.862	0.78	0.701	0.862	SUBCLONAL	1	TRUE	0	0.635796740165824	1		362	231	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0045661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	97	226	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.30164054953189	1	FACETS	0.875	0.787	0.966	0.875	0.787	0.966	CLONAL	1	TRUE	0	0.47920288481603	1		226	352	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0045661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	208	558	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.47920288481603	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.47920288481603	1		558	632	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295801	212295801	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1423325504	NA	P-0045661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	81	320	1	ENST00000342788.4:c.2512C>T	p.Arg838Ter	p.R838*	ENST00000342788	NM_005235.2	838	Cga/Tga	21/28	1	2	FACETS	0.729	0.644	0.818	0.729	0.644	0.818	SUBCLONAL	1	TRUE	1	0.47920288481603	2		321	464	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226617	1226617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754853898	NA	P-0045661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	143	418	0	ENST00000326873.7:c.1273C>T	p.Arg425Cys	p.R425C	ENST00000326873	NM_000455.4	425	Cgc/Tgc	9/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.47920288481603	2		418	543	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729709	41729709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768547360	NA	P-0045661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	123	497	0	ENST00000242208.4:c.820G>A	p.Gly274Arg	p.G274R	ENST00000242208	NM_002192.2	274	Gga/Aga	3/3	1	2	FACETS	0.866	0.785	0.95	0.866	0.785	0.95	CLONAL	1	TRUE	1	0.47920288481603	2		497	593	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930577	32930577	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	48	191	0	ENST00000380152.3:c.7448G>T	p.Ser2483Ile	p.S2483I	ENST00000380152		2483	aGt/aTt	15/27	0.47920288481603	3	FACETS	0.694	0.588	0.809	0.347	0.294	0.405	SUBCLONAL	1	TRUE	1	0.47920288481603	3		191	358	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201706	66201706	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045661-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	104	312	0	ENST00000273854.3:c.2796G>C	p.Leu932Phe	p.L932F	ENST00000273854	NM_004439.5	932	ttG/ttC	16/18	0.160107028716563	0	FACETS	0.534	0.482	0.59			1	INDETERMINATE	1	TRUE	0	0.47920288481603	0		312	423	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0045662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	47	357	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.166298636743915	4	FACETS	0.765	0.646	0.895	0.382	0.323	0.448	INDETERMINATE	1	TRUE	2	0.384002475793523	4		357	443	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2193700	2193700	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	184	551	0	ENST00000398665.3:c.506T>C	p.Val169Ala	p.V169A	ENST00000398665	NM_032482.2	169	gTc/gCc	6/28	0.384002475793523	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.384002475793523	1		551	597	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255892	16255892	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0045662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	32	295	0	ENST00000375759.3:c.3157A>T	p.Lys1053Ter	p.K1053*	ENST00000375759	NM_015001.2	1053	Aaa/Taa	11/15	0.275561040442473	3	FACETS	0.436	0.353	0.529	0.218	0.176	0.265	SUBCLONAL	1	TRUE	1	0.384002475793523	3		295	456	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604653	43604653	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	67	457	0	ENST00000355710.3:c.1238G>T	p.Ser413Ile	p.S413I	ENST00000355710	NM_020975.4	413	aGc/aTc	6/20	0.166298636743915	4	FACETS	0.715	0.621	0.818	0.358	0.31	0.409	INDETERMINATE	1	TRUE	2	0.384002475793523	4		457	675	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303483	91303483	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	26	262	0	ENST00000355112.3:c.1194C>A	p.Asn398Lys	p.N398K	ENST00000355112	NM_000057.2	398	aaC/aaA	6/22	0.134769360056473	3	FACETS	0.413	0.327	0.512	0.206	0.163	0.256	INDETERMINATE	1	TRUE	1	0.384002475793523	3		262	391	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164839	36164851	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGGTCGGAGAT	GGGGGTCGGAGAT	-	novel	NA	P-0045662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	236	762	0	ENST00000300305.3:c.1024_1036del	p.Ile342AlafsTer248	p.I342Afs*248	ENST00000300305		342	ATCTCCGACCCCCgc/gc	8/8	0.275561040442473	3	FACETS	0.757	0.707	0.808	0.757	0.707	0.808	SUBCLONAL	2	TRUE	1	0.384002475793523	3		762	968	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077444	30077444	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0045662-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	38	185	0	ENST00000338641.4:c.1591A>T	p.Lys531Ter	p.K531*	ENST00000338641	NM_000268.3	531	Aag/Tag	15/16	0.319864389531221	2	FACETS	0.98	0.818	1	0.49	0.409	0.578	CLONAL	1	TRUE	0	0.384002475793523	2		185	202	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522598	157522598	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554236040	NA	P-0045691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	70	410	0	ENST00000346085.5:c.4870C>T	p.Arg1624Ter	p.R1624*	ENST00000346085	NM_020732.3	1624	Cga/Tga	18/20	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.230847097939997	2		410	546	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0045691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	100	576	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.230847097939997	2		576	608	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44911036	44911037	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	20	91	0	ENST00000377967.4:c.738dup	p.Gln247ThrfsTer16	p.Q247Tfs*16	ENST00000377967	NM_021140.2	246	tta/ttAa	9/29	1	1	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	0	0.230847097939997	1		91	115	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104268936	104268936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	82	478	0	ENST00000369902.3:c.193C>T	p.Pro65Ser	p.P65S	ENST00000369902	NM_016169.3	65	Cca/Tca	2/12	0.194448327679725	3	FACETS	1	0.943	1	0.56	0.493	0.631	CLONAL	1	TRUE	1	0.230847097939997	3		478	708	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117593	70117594	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	A	novel	NA	P-0045691-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	51	736	0	ENST00000245479.2:c.61_62delinsA	p.Ala21ThrfsTer40	p.A21Tfs*40	ENST00000245479	NM_000346.3	21	GCc/Ac	1/3	0.196346186084928	1	FACETS	0.659	0.56	0.768	0.659	0.56	0.768	SUBCLONAL	1	TRUE	0	0.230847097939997	1		736	593	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107125	27107125	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	121	417	0	ENST00000324856.7:c.6736G>T	p.Glu2246Ter	p.E2246*	ENST00000324856	NM_006015.4	2246	Gag/Tag	20/20	0.360254237020025	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	0	0.360254237020025	1		417	462	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170013719	170013719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388201066	NA	P-0045706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	297	279	0	ENST00000295797.4:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000295797	NM_002740.5	480	Cgc/Tgc	15/18	0.228111060775178	5	FACETS	0.955	0.911	0.998	0.955	0.911	0.998	CLONAL	5	FALSE	0	0.360254237020025	5		279	532	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040707	47040707	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	124	468	0	ENST00000377604.3:c.1342C>T	p.Gln448Ter	p.Q448*	ENST00000377604	NM_001204468.1	448	Cag/Tag	13/24	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	FALSE	1	0.360254237020025	2		468	680	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322596	39322596	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	26	331	0	ENST00000373001.3:c.396G>T	p.Met132Ile	p.M132I	ENST00000373001	NM_022157.3	132	atG/atT	2/7	0.360254237020025	1	FACETS	0.521	0.415	0.642	0.521	0.415	0.642	SUBCLONAL	1	FALSE	0	0.360254237020025	1		331	227	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982134	201982135	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	86	560	0	ENST00000359651.3:c.659dup	p.Asp220GlufsTer4	p.D220Efs*4	ENST00000359651		220	gat/gAat	5/8	1	2	FACETS	0.745	0.659	0.836	0.745	0.659	0.836	SUBCLONAL	1	FALSE	1	0.360254237020025	2		560	641	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186767	108186767	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	68	297	0	ENST00000278616.4:c.6125G>A	p.Trp2042Ter	p.W2042*	ENST00000278616	NM_000051.3	2042	tGg/tAg	42/63	0.205322064376072	1	FACETS	1	0.954	1	1	0.954	1	INDETERMINATE	1	FALSE	0	0.360254237020025	1		297	262	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060648	38060648	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	101	618	0	ENST00000250448.2:c.1341G>T	p.Arg447Ser	p.R447S	ENST00000250448	NM_004496.3	447	agG/agT	2/2	0.360254237020025	3	FACETS	0.634	0.566	0.708	0.317	0.283	0.354	SUBCLONAL	1	FALSE	1	0.360254237020025	3		618	1043	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118864	70118864	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	89	405	0	ENST00000245479.2:c.436C>A	p.Leu146Met	p.L146M	ENST00000245479	NM_000346.3	146	Ctg/Atg	2/3	1	2	FACETS	0.982	0.874	1	0.982	0.874	1	CLONAL	1	FALSE	1	0.360254237020025	2		405	503	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802647	139802661	+	inframe_deletion	In_Frame_Del	DEL	GCATTGCCGGGCACC	GCATTGCCGGGCACC	-	novel	NA	P-0045706-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	66	423	0	ENST00000247668.2:c.492_506del	p.His165_Pro169del	p.H165_P169del	ENST00000247668	NM_021138.3	164	cgGCATTGCCGGGCACCc/cgc	5/11	1	2	FACETS	0.653	0.567	0.746	0.653	0.567	0.746	SUBCLONAL	1	FALSE	1	0.360254237020025	2		423	561	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610292	10610292	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201447398	NA	P-0045709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	130	605	1	ENST00000171111.5:c.418G>A	p.Ala140Thr	p.A140T	ENST00000171111	NM_203500.1	140	Gcc/Acc	2/6	1	2	FACETS	0.908	0.825	0.994	0.908	0.825	0.994	CLONAL	1	TRUE	1	0.417028956961826	2		606	687	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128246833	128246833	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	122	428	0	ENST00000265960.3:c.1096G>A	p.Asp366Asn	p.D366N	ENST00000265960	NM_001006617.1	366	Gat/Aat	9/12	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.417028956961826	2		428	553	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0045711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	119	248	1				ENST00000310581	NM_198253.2	-/1132			0.547489627706767	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.591759997885458	3		249	235	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246091283	246091283	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	83	270	0	ENST00000388985.4:c.652G>A	p.Gly218Arg	p.G218R	ENST00000388985		218	Ggg/Agg	7/12	0.470930522771116	4	FACETS	1	0.907	1	0.513	0.455	0.575	CLONAL	1	TRUE	2	0.591759997885458	4		270	435	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155036	108155036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	88	284	0	ENST00000278616.4:c.3829G>A	p.Glu1277Lys	p.E1277K	ENST00000278616	NM_000051.3	1277	Gag/Aag	26/63	0.547489627706767	3	FACETS	1	0.963	1	0.588	0.525	0.652	CLONAL	1	TRUE	1	0.591759997885458	3		284	328	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111957656	111957656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	201	399	0	ENST00000375549.3:c.25G>A	p.Ala9Thr	p.A9T	ENST00000375549	NM_003002.3	9	Gcc/Acc	1/4	0.547489627706767	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.591759997885458	3		399	401	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779532	3779532	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	307	686	0	ENST00000262367.5:c.5516C>T	p.Pro1839Leu	p.P1839L	ENST00000262367	NM_004380.2	1839	cCc/cTc	31/31	0.470930522771116	4	FACETS	0.889	0.84	0.939	0.889	0.84	0.939	CLONAL	2	TRUE	2	0.591759997885458	4		686	929	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831420	89831420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	186	411	0	ENST00000389301.3:c.2656G>A	p.Glu886Lys	p.E886K	ENST00000389301	NM_000135.2	886	Gag/Aag	28/43	0.470930522771116	4	FACETS	0.989	0.921	1	0.989	0.921	1	CLONAL	2	TRUE	2	0.591759997885458	4		411	506	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097264	11097264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316419985	NA	P-0045711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	214	511	0	ENST00000358026.2:c.755C>T	p.Pro252Leu	p.P252L	ENST00000358026	NM_001128849.1	252	cCt/cTt	4/36	0.470930522771116	4	FACETS	0.994	0.931	1	0.994	0.931	1	CLONAL	2	TRUE	2	0.591759997885458	4		511	579	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523319	9523319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1416163895	NA	P-0045711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	158	319	0	ENST00000353224.5:c.1918G>A	p.Glu640Lys	p.E640K	ENST00000353224	NM_177990.2	640	Gag/Aag	9/10	0.464142122956675	5	FACETS	0.873	0.804	0.945	0.582	0.536	0.63	CLONAL	2	TRUE	2	0.591759997885458	5		319	577	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212086	142212086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1317262144	NA	P-0045711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	285	366	0	ENST00000350721.4:c.5966C>T	p.Thr1989Ile	p.T1989I	ENST00000350721	NM_001184.3	1989	aCc/aTc	35/47	0.590856479382333	4	FACETS	0.891	0.854	0.928	0.891	0.854	0.928	CLONAL	4	TRUE	0	0.591759997885458	4		366	430	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439338	149439338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	246	418	0	ENST00000286301.3:c.2057G>A	p.Ser686Asn	p.S686N	ENST00000286301	NM_005211.3	686	aGc/aAc	15/22	0.547489627706767	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.591759997885458	3		418	524	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843351	128843351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	252	531	0	ENST00000249373.3:c.458C>T	p.Pro153Leu	p.P153L	ENST00000249373	NM_005631.4	153	cCc/cTc	2/12	0.534551303380169	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	2	0.591759997885458	4		531	649	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151880094	151880094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045711-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	148	312	0	ENST00000262189.6:c.5230G>A	p.Glu1744Lys	p.E1744K	ENST00000262189	NM_170606.2	1744	Gaa/Aaa	35/59	0.534551303380169	4	FACETS	0.901	0.83	0.973	0.901	0.83	0.973	CLONAL	2	TRUE	2	0.591759997885458	4		312	442	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0045712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	74	69	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.304184345090081	4	FACETS	1	0.892	1	1	0.892	1	CLONAL	2	TRUE	2	0.405703383832421	4		69	255	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858210	9858210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756930722	NA	P-0045712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	96	407	1	ENST00000330684.3:c.3191C>T	p.Thr1064Met	p.T1064M	ENST00000330684	NM_001134407.1	1064	aCg/aTg	13/13	0.309591655623139	4	FACETS	0.859	0.772	0.952	0.859	0.772	0.952	CLONAL	2	TRUE	2	0.405703383832421	4		408	387	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679823	88679823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777599584	NA	P-0045712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	47	367	0	ENST00000360948.2:c.640G>A	p.Val214Met	p.V214M	ENST00000360948	NM_001012338.2	214	Gtg/Atg	7/19	0.359766649000646	3	FACETS	0.929	0.788	1	0.464	0.394	0.541	CLONAL	1	TRUE	1	0.405703383832421	3		367	300	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342401	118342401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	64	188	0	ENST00000534358.1:c.527G>A	p.Arg176His	p.R176H	ENST00000534358	NM_005933.3	176	cGt/cAt	3/36	0.405703383832421	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.405703383832421	2		188	130	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873757	35873757	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1566591086	NA	P-0045712-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	161	434	0	ENST00000216797.5:c.94A>G	p.Ser32Gly	p.S32G	ENST00000216797	NM_020529.2	32	Agc/Ggc	1/6	0.355591709755519	3	FACETS	0.899	0.83	0.97	0.899	0.83	0.97	CLONAL	2	TRUE	1	0.405703383832421	3		434	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0045714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	175	369	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.565616315479034	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	FALSE	0	0.588725077097521	2		369	292	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0045714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	70	178	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	0.434469937852583	5	FACETS	0.982	0.881	1	0.737	0.66	0.813	CLONAL	3	FALSE	1	0.588725077097521	5		178	152	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396305	139396305	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	207	577	0	ENST00000277541.6:c.5533C>T	p.Gln1845Ter	p.Q1845*	ENST00000277541	NM_017617.3	1845	Cag/Tag	30/34	0.565616315479034	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	FALSE	0	0.588725077097521	2		577	321	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056560	26056560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766992808	NA	P-0045714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	88	201	0	ENST00000343677.2:c.97C>T	p.Arg33Cys	p.R33C	ENST00000343677	NM_005319.3	33	Cgt/Tgt	1/1	0.588725077097521	11	FACETS	0.858	0.764	0.957			1	CLONAL	3	FALSE	NA	0.588725077097521	11		201	424	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462237	120462237	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0045714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	30	258	0	ENST00000256646.2:c.5480-1G>T		p.X1827_splice	ENST00000256646	NM_024408.3	1827			0.564974784238029	4	FACETS	1	0.929	1	0.653	0.536	0.78	CLONAL	1	FALSE	2	0.588725077097521	4		258	124	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610339	81610339	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	25	245	0	ENST00000298171.2:c.1937C>T	p.Ser646Leu	p.S646L	ENST00000298171	NM_000369.2	646	tCa/tTa	10/10	0.564974784238029	4	FACETS	0.906	0.722	1	0.453	0.361	0.556	CLONAL	1	FALSE	2	0.588725077097521	4		245	149	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070832	30070832	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	68	310	0	ENST00000338641.4:c.1348G>A	p.Glu450Lys	p.E450K	ENST00000338641	NM_000268.3	450	Gag/Aag	13/16	0.588725077097521	3	FACETS	1	0.929	1	0.542	0.476	0.611	CLONAL	1	FALSE	1	0.588725077097521	3		310	276	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564814	41564814	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760707534	NA	P-0045714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	168	355	0	ENST00000263253.7:c.4115G>A	p.Cys1372Tyr	p.C1372Y	ENST00000263253	NM_001429.3	1372	tGc/tAc	25/31	0.588725077097521	3	FACETS	0.945	0.88	1	0.945	0.88	1	CLONAL	2	FALSE	1	0.588725077097521	3		355	391	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74859044	74859044	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045714-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	37	285	0	ENST00000284811.8:c.160G>C	p.Glu54Gln	p.E54Q	ENST00000284811		54	Gag/Cag	4/4	0.588725077097521	8	FACETS	1	0.868	1	0.177	0.146	0.211	CLONAL	1	FALSE	2	0.588725077097521	8		285	328	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643429	52643429	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	239	212	0	ENST00000394830.3:c.2467G>C	p.Asp823His	p.D823H	ENST00000394830	NM_018313.4	823	Gac/Cac	17/30	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.737480965370094	2		212	624	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0045727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	113	480	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.569631424247649	1	FACETS	0.852	0.777	0.93	0.852	0.777	0.93	CLONAL	1	TRUE	0	0.57696040490538	1		480	327	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0045727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	160	456	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.57696040490538	2		456	550	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249510	153249510	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1157879635	NA	P-0045727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	108	347	1	ENST00000281708.4:c.1268G>T	p.Gly423Val	p.G423V	ENST00000281708	NM_033632.3	423	gGa/gTa	9/12	1	2	FACETS	0.847	0.765	0.933	0.847	0.765	0.933	CLONAL	1	TRUE	1	0.57696040490538	2		348	442	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111855996	111855996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779622961	NA	P-0045727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	118	544	0	ENST00000341259.2:c.47C>T	p.Ser16Leu	p.S16L	ENST00000341259	NM_005475.2	16	tCa/tTa	2/8	1	2	FACETS	0.876	0.795	0.96	0.876	0.795	0.96	CLONAL	1	TRUE	1	0.57696040490538	2		544	467	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388662	31388662	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	103	453	0	ENST00000328111.2:c.1927G>C	p.Asp643His	p.D643H	ENST00000328111	NM_006892.3	643	Gac/Cac	18/23	0.526894922361297	4	FACETS	0.935	0.839	1	0.312	0.279	0.346	CLONAL	1	TRUE	1	0.57696040490538	4		453	602	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796508	42796508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770714432	NA	P-0045727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	172	825	2	ENST00000575354.2:c.3065C>T	p.Ala1022Val	p.A1022V	ENST00000575354	NM_015125.3	1022	gCg/gTg	13/20	0.562180693153972	3	FACETS	0.926	0.853	1	0.463	0.426	0.501	CLONAL	1	TRUE	1	0.57696040490538	3		827	830	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56415064	56415064	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	80	235	0	ENST00000348428.3:c.2465C>G	p.Ser822Cys	p.S822C	ENST00000348428	NM_006785.3	822	tCt/tGt	17/17	0.529720248880339	1	FACETS	0.815	0.729	0.905	0.815	0.729	0.905	CLONAL	1	TRUE	0	0.57696040490538	1		235	242	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424521	47424521	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	106	383	0	ENST00000377045.4:c.441G>C	p.Met147Ile	p.M147I	ENST00000377045	NM_001654.4	147	atG/atC	5/16	1	2	FACETS	0.998	0.904	1	0.998	0.904	1	CLONAL	1	TRUE	1	0.57696040490538	2		383	368	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0045741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	35	243	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.865	0.711	1	0.865	0.711	1	CLONAL	1	TRUE	1	0.24	2		243	337	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0045741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	30	304	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	0.3	2	FACETS	0.691	0.557	0.842			1	SUBCLONAL	1	TRUE	NA	0.24	2		304	362	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243482	41243482	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	52	530	0	ENST00000357654.3:c.4066C>G	p.Gln1356Glu	p.Q1356E	ENST00000357654	NM_007294.3	1356	Caa/Gaa	10/23	1	2	FACETS	0.73	0.621	0.849	0.73	0.621	0.849	SUBCLONAL	1	TRUE	1	0.24	2		530	594	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106412	27106412	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	63	464	0	ENST00000324856.7:c.6023del	p.Leu2008ArgfsTer7	p.L2008Rfs*7	ENST00000324856	NM_006015.4	2008	cTg/cg	20/20	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.24	2		464	492	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878847	117878847	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045741-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	71	270	0	ENST00000297338.2:c.122T>C	p.Val41Ala	p.V41A	ENST00000297338	NM_006265.2	41	gTg/gCg	2/14	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.24	2		270	435	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	242	151	0				ENST00000310581	NM_198253.2	-/1132			0.301663279579372	5	FACETS	0.879	0.827	0.932	0.879	0.827	0.932	INDETERMINATE	3	TRUE	2	0.50451028232715	5		151	639	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652198	36652199	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0045742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	158	550	0	ENST00000244741.5:c.322dup	p.Glu108GlyfsTer21	p.E108Gfs*21	ENST00000244741	NM_000389.4	107	gag/gaGg	2/3	0.454158980408078	3	FACETS	1	0.931	1	0.508	0.466	0.552	CLONAL	1	TRUE	1	0.50451028232715	3		550	772	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246473	46246473	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	176	199	0	ENST00000334344.6:c.4567G>A	p.Asp1523Asn	p.D1523N	ENST00000334344	NM_152641.2	1523	Gat/Aat	15/21	0.50451028232715	5	FACETS	0.941	0.877	1			1	CLONAL	3	TRUE	NA	0.50451028232715	5		199	434	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973826	131973826	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	76	322	0	ENST00000265335.6:c.3529G>C	p.Asp1177His	p.D1177H	ENST00000265335		1177	Gat/Cat	23/25	1	2	FACETS	0.744	0.656	0.838	0.744	0.656	0.838	SUBCLONAL	1	TRUE	1	0.50451028232715	2		322	405	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106648	27106648	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	118	539	0	ENST00000324856.7:c.6259G>T	p.Gly2087Ter	p.G2087*	ENST00000324856	NM_006015.4	2087	Gga/Tga	20/20	0.472588688145184	4	FACETS	0.729	0.657	0.806	0.243	0.219	0.269	SUBCLONAL	1	TRUE	1	0.50451028232715	4		539	965	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651978	36651979	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0045742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	318	616	0	ENST00000244741.5:c.102_103del	p.Cys34Ter	p.C34*	ENST00000244741	NM_000389.4	34	TGt/t	2/3	0.454158980408078	3	FACETS	0.895	0.848	0.943	0.895	0.848	0.943	CLONAL	2	TRUE	1	0.50451028232715	3		616	882	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665819	241665819	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	224	346	0	ENST00000366560.3:c.1160T>C	p.Val387Ala	p.V387A	ENST00000366560	NM_000143.3	387	gTc/gCc	8/10	0.330531131782032	5	FACETS	1	0.971	1			1	CLONAL	2	TRUE	NA	0.50451028232715	5		346	731	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942079	81942079	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	101	519	0	ENST00000359376.3:c.1616A>C	p.Lys539Thr	p.K539T	ENST00000359376	NM_002661.3	539	aAg/aCg	17/33	0.485404196738173	2	FACETS	0.652	0.584	0.724	0.326	0.292	0.362	SUBCLONAL	1	TRUE	0	0.50451028232715	2		519	614	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011105	12011105	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0045742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	25	249	0	ENST00000353533.5:c.514-2A>C		p.X172_splice	ENST00000353533	NM_003010.3	172			0.424661397185176	3	FACETS	0.489	0.386	0.606	0.244	0.193	0.303	SUBCLONAL	1	TRUE	1	0.50451028232715	3		249	254	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094866	11094902	+	frameshift_variant	Frame_Shift_Del	DEL	GCCAGGTCCTTCCCCGGGCCCTGGCCCTTCCCCTGGA	GCCAGGTCCTTCCCCGGGCCCTGGCCCTTCCCCTGGA	-	novel	NA	P-0045742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	114	770	0	ENST00000358026.2:c.43_79del	p.Gly15CysfsTer16	p.G15Cfs*16	ENST00000358026	NM_001128849.1	13	cgGCCAGGTCCTTCCCCGGGCCCTGGCCCTTCCCCTGGA/cg	2/36	0.50451028232715	3	FACETS	0.532	0.478	0.589	0.266	0.239	0.295	SUBCLONAL	1	TRUE	1	0.50451028232715	3		770	1064	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466791	25466793	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	novel	NA	P-0045742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	273	554	0	ENST00000264709.3:c.1910_1912del	p.Leu637_Ser638delinsPro	p.L637_S638delinsP	ENST00000264709	NM_175629.2	637	cTGTct/cct	16/23	0.454158980408078	3	FACETS	0.922	0.87	0.975	0.922	0.87	0.975	CLONAL	2	TRUE	1	0.50451028232715	3		554	735	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989511	212989511	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	80	270	0	ENST00000342788.4:c.200G>C	p.Ser67Thr	p.S67T	ENST00000342788	NM_005235.2	67	aGc/aCc	2/28	1	2	FACETS	0.97	0.861	1	0.97	0.861	1	CLONAL	1	TRUE	1	0.50451028232715	2		270	327	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628658	187628664	+	frameshift_variant	Frame_Shift_Del	DEL	TTCAGCA	TTCAGCA	-	novel	NA	P-0045742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	472	582	0	ENST00000441802.2:c.2318_2324del	p.Met773LysfsTer16	p.M773Kfs*16	ENST00000441802	NM_005245.3	773	aTGCTGAAa/aa	2/27	0.50451028232715	3	FACETS	0.984	0.949	1	0.984	0.949	1	CLONAL	3	TRUE	0	0.50451028232715	3		582	794	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64286858	64286858	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	67	339	0	ENST00000370651.3:c.73C>G	p.Pro25Ala	p.P25A	ENST00000370651	NM_003463.4	25	Cca/Gca	2/6	0.249722014902812	6	FACETS	0.997	0.868	1			1	INDETERMINATE	1	TRUE	NA	0.50451028232715	6		339	535	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611791	100611791	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045742-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	125	415	0	ENST00000308731.7:c.1330G>C	p.Glu444Gln	p.E444Q	ENST00000308731	NM_000061.2	444	Gaa/Caa	14/19	0.454158980408078	3	FACETS	0.95	0.862	1	0.475	0.431	0.522	CLONAL	1	TRUE	1	0.50451028232715	3		415	653	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0045743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	342	69	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.312306852452158	5	FACETS	0.985	0.937	1	0.985	0.937	1	CLONAL	4	TRUE	1	0.312306852452158	5		69	816	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882019	NA	P-0045743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	173	173	0	ENST00000269305.4:c.455dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	ccg/ccCg	5/11	0.17588192805392	1	FACETS	1	0.969	1	1	0.969	1	INDETERMINATE	1	TRUE	0	0.312306852452158	1		173	848	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974675	21974675	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1060501265	NA	P-0045743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	87	85	0	ENST00000304494.5:c.150+2T>C		p.X50_splice	ENST00000304494	NM_000077.4	50			0.264563552957847	2	FACETS	1	0.953	1	0.569	0.505	0.636	CLONAL	1	TRUE	0	0.312306852452158	2		85	490	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866987936	NA	P-0045747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	12	232	0	ENST00000281708.4:c.1436G>T	p.Arg479Leu	p.R479L	ENST00000281708	NM_033632.3	479	cGa/cTa	10/12	1	2	FACETS	0.268	0.187	0.367	0.268	0.187	0.367	SUBCLONAL	1	TRUE	1	0.251967069986826	2		232	356	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142901	30142901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1365924896	NA	P-0045747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	91	688	9	ENST00000389048.3:c.625C>T	p.Arg209Cys	p.R209C	ENST00000389048	NM_004304.4	209	Cgc/Tgc	1/29	1	2	FACETS	0.873	0.775	0.979	0.873	0.775	0.979	CLONAL	1	TRUE	1	0.251967069986826	2		697	827	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716081	52716081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	43	634	0	ENST00000322088.6:c.646G>A	p.Glu216Lys	p.E216K	ENST00000322088	NM_014225.5	216	Gag/Aag	5/15	0.251967069986826	1	FACETS	0.366	0.305	0.434	0.366	0.305	0.434	SUBCLONAL	1	TRUE	0	0.251967069986826	1		634	816	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480397	56480397	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	76	504	0	ENST00000267101.3:c.504G>C	p.Arg168Ser	p.R168S	ENST00000267101	NM_001982.3	168	agG/agC	4/28	1	2	FACETS	0.907	0.796	1	0.907	0.796	1	CLONAL	1	TRUE	1	0.251967069986826	2		504	665	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921807	111921807	+	stop_lost	Nonstop_Mutation	SNP	G	G	C	novel	NA	P-0045747-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	25	297	0	ENST00000393256.3:c.596G>C	p.Ter199SerextTer70	p.*199Sext*70	ENST00000393256	NM_006538.4	199	tGa/tCa	4/4	1	2	FACETS	0.438	0.344	0.546	0.438	0.344	0.546	SUBCLONAL	1	TRUE	1	0.251967069986826	2		297	453	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099315	157099332	+	inframe_deletion	In_Frame_Del	DEL	CCACCACCACCACCATGC	CCACCACCACCACCATGC	-	rs750515649	NA	P-0045748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	23	264	0	ENST00000346085.5:c.267_284del	p.Ala90_His95del	p.A90_H95del	ENST00000346085	NM_020732.3	84	caCCACCACCACCACCATGCc/cac	1/20	0.136599427983825	3	FACETS	0.753	0.589	0.94	0.753	0.589	0.94	CLONAL	2	TRUE	1	0.15	3		264	219	SUCCESS
APC	324	MSKCC	GRCh37	5	112175600	112175600	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0045748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	38	269	0	ENST00000257430.4:c.4309A>T	p.Lys1437Ter	p.K1437*	ENST00000257430	NM_000038.5	1437	Aaa/Taa	16/16	1	2	FACETS	0.857	0.716	1	1	0.972	1	CLONAL	3	TRUE	1	0.15	2		269	197	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206933	162206933	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777074432	NA	P-0045748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	13	207	0	ENST00000366898.1:c.742G>A	p.Val248Ile	p.V248I	ENST00000366898	NM_004562.2	248	Gtc/Atc	7/12	0.136599427983825	3	FACETS	1	0.833	1	0.63	0.451	0.845	CLONAL	1	TRUE	1	0.15	3		207	148	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574030	7574030	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	322	478	0	ENST00000269305.4:c.997del	p.Arg333ValfsTer12	p.R333Vfs*12	ENST00000269305	NM_001126112.2	333	Cgt/gt	10/11	0.768649558853429	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.768649558853429	1		478	493	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25462017	25462017	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs767588813	NA	P-0045749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	199	501	0	ENST00000264709.3:c.2390A>G	p.Asn797Ser	p.N797S	ENST00000264709	NM_175629.2	797	aAc/aGc	20/23	1	2	FACETS	0.782	0.728	0.838	0.782	0.728	0.838	SUBCLONAL	1	TRUE	1	0.768649558853429	2		501	662	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346346	73346346	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	148	276	0	ENST00000377767.4:c.1454A>T	p.Asp485Val	p.D485V	ENST00000377767	NM_014953.3	485	gAt/gTt	10/21	0.768649558853429	2	FACETS	1	0.983	1	0.604	0.561	0.647	CLONAL	1	TRUE	0	0.768649558853429	2		276	319	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562648	29562648	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs137854564	NA	P-0045749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	222	357	0	ENST00000356175.3:c.3728T>C	p.Leu1243Pro	p.L1243P	ENST00000356175	NM_000267.3	1243	cTg/cCg	28/57	0.768649558853429	1	FACETS	0.961	0.912	1	0.961	0.912	1	CLONAL	1	TRUE	0	0.768649558853429	1		357	370	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082820	16082820	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	48	36	0	ENST00000281043.3:c.634G>T	p.Ala212Ser	p.A212S	ENST00000281043	NM_005378.4	212	Gcc/Tcc	2/3	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.768649558853429	2		36	89	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039451	49039451	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	CG	novel	NA	P-0045749-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	225	359	0	ENST00000267163.4:c.2436delinsCG	p.Tyr813ValfsTer2	p.Y813Vfs*2	ENST00000267163	NM_000321.2	812	ccA/ccCG	23/27	0.768649558853429	1	FACETS	0.946	0.898	0.994	0.946	0.898	0.994	CLONAL	1	TRUE	0	0.768649558853429	1		359	381	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871249	12871249	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0045750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	55	137	0	ENST00000228872.4:c.475+1G>A		p.X159_splice	ENST00000228872	NM_004064.3	159			0.409051711694429	3	FACETS	1	0.962	1	0.675	0.583	0.772	CLONAL	1	TRUE	1	0.409051711694429	3		137	240	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161655	56161655	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0045750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	112	325	0	ENST00000399503.3:c.1153-1G>C		p.X385_splice	ENST00000399503	NM_005921.1	385			0.122534046681205	4	FACETS	0.779	0.704	0.858	0.779	0.704	0.858	INDETERMINATE	2	TRUE	2	0.409051711694429	4		325	495	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178673	56178674	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCATC	novel	NA	P-0045750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	53	154	0	ENST00000399503.3:c.3647_3651dup	p.Ile1218SerfsTer29	p.I1218Sfs*29	ENST00000399503	NM_005921.1	1216	atc/aTCATCtc	14/20	0.122534046681205	4	FACETS	0.819	0.706	0.938	0.819	0.706	0.938	INDETERMINATE	2	TRUE	2	0.409051711694429	4		154	223	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0045838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	77	424	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.733	0.645	0.829	0.733	0.645	0.829	SUBCLONAL	1	TRUE	1	0.365828046234534	2		424	574	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0045838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	127	626	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.711	0.643	0.783	0.711	0.643	0.783	SUBCLONAL	1	TRUE	1	0.365828046234534	2		626	976	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098803	178098803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	62	589	0	ENST00000397062.3:c.242G>A	p.Gly81Asp	p.G81D	ENST00000397062	NM_006164.4	81	gGt/gAt	2/5	1	2	FACETS	0.308	0.265	0.356	0.308	0.265	0.356	SUBCLONAL	1	TRUE	1	0.365828046234534	2		589	1099	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692811	89692811	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	42	270	0	ENST00000371953.3:c.295G>T	p.Glu99Ter	p.E99*	ENST00000371953	NM_000314.4	99	Gaa/Taa	5/9	1	2	FACETS	0.673	0.564	0.794	0.673	0.564	0.794	SUBCLONAL	1	TRUE	1	0.365828046234534	2		270	341	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591111	67591137	+	inframe_deletion	In_Frame_Del	DEL	AGACCTTATCCAGCTGAGAAAGACGAG	AGACCTTATCCAGCTGAGAAAGACGAG	-	novel	NA	P-0045838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	32	254	0	ENST00000274335.5:c.1709_1735del	p.Leu570_Asp578del	p.L570_D578del	ENST00000274335		568	ccAGACCTTATCCAGCTGAGAAAGACGAGa/cca	12/15	1	2	FACETS	0.422	0.342	0.511	0.422	0.342	0.511	SUBCLONAL	1	TRUE	1	0.365828046234534	2		254	415	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941880	71941880	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	65	785	0	ENST00000298229.2:c.1238A>G	p.Asn413Ser	p.N413S	ENST00000298229	NM_001567.3	413	aAc/aGc	11/28	1	2	FACETS	0.33	0.285	0.379	0.33	0.285	0.379	SUBCLONAL	1	TRUE	1	0.365828046234534	2		785	1078	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211893	36211893	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	96	819	0	ENST00000222270.7:c.1644T>G	p.Asp548Glu	p.D548E	ENST00000222270	NM_014727.1	548	gaT/gaG	3/37	1	2	FACETS	0.399	0.354	0.447	0.399	0.354	0.447	SUBCLONAL	1	TRUE	1	0.365828046234534	2		819	1316	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249887	39249904	+	inframe_deletion	In_Frame_Del	DEL	TCCTGTAGCATTGTTACA	TCCTGTAGCATTGTTACA	-	novel	NA	P-0045838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	114	552	0	ENST00000402219.2:c.1665_1682del	p.Asp555_Gln560del	p.D555_Q560del	ENST00000402219	NM_005633.3	555	gaTGTAACAATGCTACAGGAa/gaa	10/23	1	2	FACETS	0.74	0.666	0.819	0.74	0.666	0.819	SUBCLONAL	1	TRUE	1	0.365828046234534	2		552	842	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0045856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	14	372	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	0.880201277114207	3	FACETS	0.098	0.07	0.132	0.049	0.035	0.066	SUBCLONAL	1	TRUE	1	0.880201277114207	3		372	468	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0045856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	137	240	0	ENST00000349496.5:c.101G>A	p.Gly34Glu	p.G34E	ENST00000349496	NM_001904.3	34	gGa/gAa	3/15	0.880201277114207	3	FACETS	0.898	0.822	0.977	0.449	0.411	0.489	CLONAL	1	TRUE	1	0.880201277114207	3		240	499	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36821031	36821031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356391159	NA	P-0045856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	185	527	0	ENST00000373129.3:c.346C>T	p.Arg116Cys	p.R116C	ENST00000373129	NM_032017.1	116	Cgc/Tgc	6/12	0.880201277114207	3	FACETS	0.836	0.774	0.9	0.418	0.387	0.45	CLONAL	1	TRUE	1	0.880201277114207	3		527	724	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030394	49030394	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	242	275	0	ENST00000267163.4:c.1870del	p.Ser624LeufsTer19	p.S624Lfs*19	ENST00000267163	NM_000321.2	623	aaT/aa	19/27	0.863411758783649	2	FACETS	0.985	0.956	1	0.985	0.956	1	CLONAL	2	TRUE	0	0.880201277114207	2		275	279	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843698	151843698	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370620314	NA	P-0045856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	22	365	0	ENST00000262189.6:c.14017C>T	p.Arg4673Cys	p.R4673C	ENST00000262189	NM_170606.2	4673	Cgc/Tgc	53/59	0.394802719879825	4	FACETS	0.222	0.172	0.281	0.111	0.086	0.141	INDETERMINATE	1	TRUE	2	0.880201277114207	4		365	423	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874661	151874662	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0045856-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	278	384	0	ENST00000262189.6:c.7876_7877del	p.Glu2626ThrfsTer30	p.E2626Tfs*30	ENST00000262189	NM_170606.2	2626	GAa/a	38/59	0.394802719879825	4	FACETS	1	0.985	1	1	0.985	1	INDETERMINATE	2	TRUE	2	0.880201277114207	4		384	543	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0045911-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	66	302	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.15897748902128	2	FACETS	1	0.964	1	0.661	0.576	0.752	CLONAL	1	TRUE	0	0.246671897008221	2		302	405	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs730881677	NA	P-0045911-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	59	262	0	ENST00000304494.5:c.151-1G>T		p.X51_splice	ENST00000304494	NM_000077.4	51			0.159854638273348	2	FACETS	1	0.915	1	0.542	0.468	0.623	CLONAL	1	TRUE	0	0.246671897008221	2		262	441	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858119	152858119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370810560	NA	P-0045911-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	75	737	0	ENST00000406277.2:c.496G>A	p.Val166Ile	p.V166I	ENST00000406277	NM_152274.4	166	Gtc/Atc	6/7	1	2	FACETS	0.601	0.525	0.683	0.601	0.525	0.683	SUBCLONAL	1	TRUE	1	0.246671897008221	2		737	1012	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986595	36986596	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0045911-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	21	341	0	ENST00000354822.5:c.1093_1094del	p.Ala365GlnfsTer73	p.A365Qfs*73	ENST00000354822	NM_001079668.2	365	GCc/c	3/3	1	2	FACETS	0.425	0.326	0.54	0.425	0.326	0.54	SUBCLONAL	1	TRUE	1	0.246671897008221	2		341	401	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408924	41408924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778928297	NA	P-0045911-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	29	296	0	ENST00000373198.4:c.502G>A	p.Val168Ile	p.V168I	ENST00000373198	NM_133170.3	168	Gtc/Atc	4/32	1	2	FACETS	0.561	0.45	0.688	0.561	0.45	0.688	SUBCLONAL	1	TRUE	1	0.246671897008221	2		296	419	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965683	90965683	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045911-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	31	249	0	ENST00000265433.3:c.1634T>C	p.Leu545Pro	p.L545P	ENST00000265433	NM_002485.4	545	cTa/cCa	11/16	1	2	FACETS	0.665	0.538	0.808	0.665	0.538	0.808	SUBCLONAL	1	TRUE	1	0.246671897008221	2		249	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0045917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	51	680	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.275215128729769	1	FACETS	0.47	0.399	0.549	0.47	0.399	0.549	SUBCLONAL	1	TRUE	0	0.275215128729769	1		680	680	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0045917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	27	358	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	0.468	0.372	0.578	0.468	0.372	0.578	SUBCLONAL	1	TRUE	1	0.275215128729769	2		358	419	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149925	99149925	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	36	583	0	ENST00000074304.5:c.237C>G	p.Phe79Leu	p.F79L	ENST00000074304	NM_001134224.1	79	ttC/ttG	5/26	1	2	FACETS	0.381	0.312	0.459	0.381	0.312	0.459	SUBCLONAL	1	TRUE	1	0.275215128729769	2		583	686	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0045922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	48	69	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.114021355156806	0	FACETS	0.599	0.51	0.696			1	INDETERMINATE	1	TRUE	0	0.358241404486968	0		69	287	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0045922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	86	356	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.329297003620029	2	FACETS	0.953	0.856	1	0.953	0.856	1	CLONAL	2	TRUE	0	0.358241404486968	2		358	252	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0045922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	54	371	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.329297003620029	2	FACETS	0.884	0.759	1	0.442	0.379	0.51	CLONAL	1	TRUE	0	0.358241404486968	2		371	341	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807820	3807820	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	33	413	0	ENST00000262367.5:c.3599G>A	p.Cys1200Tyr	p.C1200Y	ENST00000262367	NM_004380.2	1200	tGt/tAt	18/31	1	2	FACETS	0.711	0.582	0.855	0.711	0.582	0.855	SUBCLONAL	1	TRUE	1	0.358241404486968	2		413	259	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176105664	176105664	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	43	355	0	ENST00000367669.3:c.851A>G	p.Lys284Arg	p.K284R	ENST00000367669	NM_022457.5	284	aAg/aGg	7/20	1	2	FACETS	0.953	0.803	1	0.953	0.803	1	CLONAL	1	TRUE	1	0.358241404486968	2		355	252	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244172	46244172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	40	377	0	ENST00000334344.6:c.2266G>A	p.Val756Ile	p.V756I	ENST00000334344	NM_152641.2	756	Gtt/Att	15/21	0.358241404486968	3	FACETS	0.947	0.791	1	0.474	0.395	0.559	CLONAL	1	TRUE	1	0.358241404486968	3		377	278	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14028114	14028114	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1243767638	NA	P-0045922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	43	360	1	ENST00000311895.7:c.1168G>T	p.Glu390Ter	p.E390*	ENST00000311895	NM_005236.2	390	Gaa/Taa	7/11	1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	1	0.358241404486968	2		361	239	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649267	23649267	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	43	372	0	ENST00000261584.4:c.115C>A	p.Gln39Lys	p.Q39K	ENST00000261584	NM_024675.3	39	Caa/Aaa	3/13	1	2	FACETS	0.886	0.746	1	0.886	0.746	1	CLONAL	1	TRUE	1	0.358241404486968	2		372	271	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860405	42860405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199865751	NA	P-0045922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	103	625	2	ENST00000398585.3:c.472G>A	p.Asp158Asn	p.D158N	ENST00000398585	NM_001135099.1	158	Gac/Aac	5/14	0.198162371292024	3	FACETS	1	0.982	1	0.742	0.667	0.82	INDETERMINATE	1	TRUE	1	0.358241404486968	3		627	457	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670328	134670328	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559321367	NA	P-0045922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	46	397	0	ENST00000398015.3:c.239G>A	p.Arg80Gln	p.R80Q	ENST00000398015	NM_004441.4	80	cGg/cAg	3/16	0.198162371292024	3	FACETS	0.926	0.783	1	0.463	0.391	0.541	INDETERMINATE	1	TRUE	1	0.358241404486968	3		397	327	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951911	178951911	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	66	409	0	ENST00000263967.3:c.2966T>G	p.Leu989Arg	p.L989R	ENST00000263967	NM_006218.2	989	cTa/cGa	21/21	0.198162371292024	3	FACETS	1	0.972	1	0.729	0.638	0.825	INDETERMINATE	1	TRUE	1	0.358241404486968	3		409	298	SUCCESS
APC	324	MSKCC	GRCh37	5	112175475	112175475	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045922-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	80	377	0	ENST00000257430.4:c.4184del	p.Ser1395IlefsTer20	p.S1395Ifs*20	ENST00000257430	NM_000038.5	1395	aGt/at	16/16	0.329297003620029	2	FACETS	0.9	0.804	1	0.9	0.804	1	CLONAL	2	TRUE	0	0.358241404486968	2		377	248	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0045944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	558	680	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.83269782114634	4	FACETS	0.994	0.977	1			1	CLONAL	4	TRUE	NA	0.83269782114634	4		680	618	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37680930	37680930	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	336	293	1	ENST00000447079.4:c.3103del	p.His1035ThrfsTer22	p.H1035Tfs*22	ENST00000447079	NM_015083.1	1033	ctC/ct	12/14	0.803466003458506	5	FACETS	0.953	0.93	0.973			1	CLONAL	5	TRUE	NA	0.83269782114634	5		294	381	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40469200	40469200	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1064794957	NA	P-0045944-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	33	196	0	ENST00000264657.5:c.2144C>T	p.Pro715Leu	p.P715L	ENST00000264657	NM_139276.2	715	cCa/cTa	22/24	0.831040369622473	2	FACETS	0.591	0.49	0.701	0.296	0.245	0.351	SUBCLONAL	1	TRUE	0	0.83269782114634	2		196	134	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0045945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	85	242	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	0.878	0.785	0.974	0.878	0.785	0.974	CLONAL	1	TRUE	1	0.672458250180276	2		242	288	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913492	NA	P-0045945-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	87	393	0	ENST00000286548.4:c.626A>C	p.Gln209Pro	p.Q209P	ENST00000286548	NM_002072.3	209	cAa/cCa	5/7	1	2	FACETS	0.804	0.718	0.893	0.804	0.718	0.893	CLONAL	1	TRUE	1	0.672458250180276	2		393	322	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411884	116411893	+	intron_variant	Intron	DEL	TCTTTCTCTC	TCTTTCTCTC	-	novel	NA	P-0045946-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	98	616	0	ENST00000397752.3:c.2888-18_2888-9del		p.*963*	ENST00000397752	NM_000245.2	-/1390			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		616	846	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0045947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	316	530	0	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	0.549948838240534	3	FACETS	1	0.989	1			1	CLONAL	3	TRUE	NA	0.549553827139652	3		530	455	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436052	110436052	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	35	830	0	ENST00000375856.3:c.2349C>G	p.Phe783Leu	p.F783L	ENST00000375856	NM_003749.2	783	ttC/ttG	1/2	0.549948838240534	3	FACETS	0.249	0.204	0.301			1	SUBCLONAL	1	TRUE	NA	0.549553827139652	3		830	651	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255496	16255496	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	85	407	0	ENST00000375759.3:c.2761C>G	p.Gln921Glu	p.Q921E	ENST00000375759	NM_015001.2	921	Cag/Gag	11/15	0.315917095659093	5	FACETS	1	0.951	1	0.378	0.335	0.424	INDETERMINATE	1	TRUE	2	0.549553827139652	5		407	498	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572671	64572671	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0045947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	233	519	0	ENST00000312049.6:c.1186-1G>C		p.X396_splice	ENST00000312049	NM_130799.2	396			0.549948838240534	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.549553827139652	3		519	462	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959435	26959435	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	39	395	0	ENST00000381527.3:c.602C>G	p.Ala201Gly	p.A201G	ENST00000381527	NM_001260.1	201	gCc/gGc	6/13	0.457903450609551	3	FACETS	0.514	0.427	0.611			1	SUBCLONAL	1	TRUE	NA	0.549553827139652	3		395	352	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396562	30396562	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	58	330	0	ENST00000331968.5:c.157C>G	p.Leu53Val	p.L53V	ENST00000331968	NM_002742.2	53	Ctg/Gtg	1/18	0.457903450609551	3	FACETS	0.747	0.645	0.858			1	SUBCLONAL	1	TRUE	NA	0.549553827139652	3		330	360	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39535296	39535296	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	11	151	0	ENST00000262039.4:c.40G>C	p.Asp14His	p.D14H	ENST00000262039	NM_002647.2	14	Gac/Cac	1/25	0.503381197777269	4	FACETS	0.323	0.223	0.447	0.108	0.074	0.149	SUBCLONAL	1	TRUE	1	0.549553827139652	4		151	192	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610084	10610084	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	95	518	0	ENST00000171111.5:c.626T>A	p.Met209Lys	p.M209K	ENST00000171111	NM_203500.1	209	aTg/aAg	2/6	0.549948838240534	3	FACETS	0.901	0.806	1	0.3	0.268	0.334	CLONAL	1	TRUE	0	0.549553827139652	3		518	489	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160401	99160401	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	149	474	0	ENST00000074304.5:c.880A>T	p.Ile294Phe	p.I294F	ENST00000074304	NM_001134224.1	294	Att/Ttt	11/26	0.549553827139652	9	FACETS	0.808	0.737	0.882	0.231	0.21	0.252	CLONAL	2	TRUE	2	0.549553827139652	9		474	981	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39751847	39751847	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	158	303	0	ENST00000361337.2:c.2208G>A	p.Trp736Ter	p.W736*	ENST00000361337	NM_003286.2	736	tgG/tgA	21/21	0.549553827139652	5	FACETS	0.837	0.775	0.899			1	CLONAL	3	TRUE	NA	0.549553827139652	5		303	418	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165142	32166164	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGGTTGGGGTTGGCTCCAGCCTCAAGGAGGCGGCGGGCAGCGGTTGGCCGGGAGAATCGGGCAGCCAGGTGCAGGGGGGTCTCCCCAGTGCCCACGGTGTGAGCCTGGGGACAGGCCCCTCCATCCAGCAGAGGTTCCCAGGGCTCAGGACATCCCAACCATGCCCCTTGGAAGGTCCCGGACTGTACTTCCCCACAGCAAACTGCTGACATCAGGGGTGTCACCCCATCTGTTGGTAAGACAGAGTAATGGGTCAATCTAAAGGACACAACAAGGGGGAAGGGACAACATGTAAGCTCAGAGAGAATCAAAACCTGAGGTGTTGGGAAGCTAAGTTCTGGCTCTGTGTGGCTTTAGCCAAGTGACTTTTCTGCTTTTCTCTGACTTCAGTTTCTTCCTCTGTAAAAGGAACCTGCAGCTTAATTCTCTGACATTCCAGGGCAGTGGTTTTCTCTTTTTTTTTTTTTTTTTTCTGAGACGGAGTCTCGCCCTGTCACCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCTCCTCCCAGGTTCACGCCATTCTCCTGCCTTAGCCTCCAGAGCAGCTGGGACTACAGGCTCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACTGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTTGTGATCCACCCGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCACGCCCGGCCTAGCAGTGGTTTTCTCAAACGAGTCTGGATCAGATTCACCTGAAGGGCTTGTTAAAACAGATTGCCTAACATTTTAAATTCCTGAGTCAGTAGCTCTGTAGTGGAGCCCAATAATTTGCATTTCTGACAAATTCCCAGGTGATGCTGATTTTGCTGTCTGAGGACCACACTTTGAGAATCATTGTTCTAAGGCACTCAGTCTAAAATTATTTCCTCTAGTTCTGATATTAAAGGACTCTCTGATTCTAATAGGGTCAAAGGACTTTT	CTGGTTGGGGTTGGCTCCAGCCTCAAGGAGGCGGCGGGCAGCGGTTGGCCGGGAGAATCGGGCAGCCAGGTGCAGGGGGGTCTCCCCAGTGCCCACGGTGTGAGCCTGGGGACAGGCCCCTCCATCCAGCAGAGGTTCCCAGGGCTCAGGACATCCCAACCATGCCCCTTGGAAGGTCCCGGACTGTACTTCCCCACAGCAAACTGCTGACATCAGGGGTGTCACCCCATCTGTTGGTAAGACAGAGTAATGGGTCAATCTAAAGGACACAACAAGGGGGAAGGGACAACATGTAAGCTCAGAGAGAATCAAAACCTGAGGTGTTGGGAAGCTAAGTTCTGGCTCTGTGTGGCTTTAGCCAAGTGACTTTTCTGCTTTTCTCTGACTTCAGTTTCTTCCTCTGTAAAAGGAACCTGCAGCTTAATTCTCTGACATTCCAGGGCAGTGGTTTTCTCTTTTTTTTTTTTTTTTTTCTGAGACGGAGTCTCGCCCTGTCACCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCTCCTCCCAGGTTCACGCCATTCTCCTGCCTTAGCCTCCAGAGCAGCTGGGACTACAGGCTCCCGCCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACTGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTTGTGATCCACCCGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCACGCCCGGCCTAGCAGTGGTTTTCTCAAACGAGTCTGGATCAGATTCACCTGAAGGGCTTGTTAAAACAGATTGCCTAACATTTTAAATTCCTGAGTCAGTAGCTCTGTAGTGGAGCCCAATAATTTGCATTTCTGACAAATTCCCAGGTGATGCTGATTTTGCTGTCTGAGGACCACACTTTGAGAATCATTGTTCTAAGGCACTCAGTCTAAAATTATTTCCTCTAGTTCTGATATTAAAGGACTCTCTGATTCTAATAGGGTCAAAGGACTTTT	-	novel	NA	P-0045947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	249	725	0	ENST00000375023.3:c.4756+34_4986del		p.X1586_splice	ENST00000375023	NM_004557.3	1586		27/30	0.549948838240534	5	FACETS	0.929	0.87	0.989	0.619	0.58	0.659	CLONAL	2	TRUE	2	0.549553827139652	5		725	890	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751169	128751169	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	253	483	0	ENST00000377970.2:c.706G>T	p.Asp236Tyr	p.D236Y	ENST00000377970	NM_002467.4	236	Gat/Tat	2/3	0.549948838240534	5	FACETS	1	0.945	1	0.75	0.708	0.792	CLONAL	3	TRUE	1	0.549553827139652	5		483	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0045948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	111	631	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.254347426185154	1	FACETS	0.777	0.697	0.86	0.777	0.697	0.86	SUBCLONAL	1	FALSE	0	0.283345164781547	1		631	866	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556722	41556722	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	21	233	0	ENST00000263253.7:c.3667C>T	p.Gln1223Ter	p.Q1223*	ENST00000263253	NM_001429.3	1223	Caa/Taa	20/31	0.193331171935613	1	FACETS	0.352	0.271	0.448	0.352	0.271	0.448	SUBCLONAL	1	FALSE	0	0.283345164781547	1		233	361	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89869669	89869669	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs1353992080	NA	P-0045948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	75	431	0	ENST00000389301.3:c.790C>T	p.Gln264Ter	p.Q264*	ENST00000389301	NM_000135.2	264	Cag/Tag	8/43	0.257958342427464	1	FACETS	0.66	0.578	0.749	0.66	0.578	0.749	SUBCLONAL	1	FALSE	0	0.283345164781547	1		431	688	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873387	136873387	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	39	291	0	ENST00000241393.3:c.111T>A	p.Asn37Lys	p.N37K	ENST00000241393	NM_003467.2	37	aaT/aaA	2/2	1	2	FACETS	0.598	0.496	0.713	0.598	0.496	0.713	SUBCLONAL	1	FALSE	1	0.283345164781547	2		291	460	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340177	116340177	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs200074800	NA	P-0045948-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	27	184	0	ENST00000397752.3:c.1039G>T	p.Ala347Ser	p.A347S	ENST00000397752	NM_000245.2	347	Gca/Tca	2/21	0.283345164781547	1	FACETS	0.61	0.487	0.75	0.61	0.487	0.75	SUBCLONAL	1	FALSE	0	0.283345164781547	1		184	268	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717777	89717777	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0045949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	21	262	0	ENST00000371953.3:c.801+1G>T		p.X267_splice	ENST00000371953	NM_000314.4	267			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		262	246	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0045951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	160	69	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.762655619433945	3	FACETS	0.836	0.779	0.894	0.836	0.779	0.894	CLONAL	2	TRUE	1	0.782895997655553	3		69	340	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098950	178098950	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	96	255	0	ENST00000397062.3:c.95T>A	p.Val32Glu	p.V32E	ENST00000397062	NM_006164.4	32	gTa/gAa	2/5	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.782895997655553	2		255	241	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659245	86659245	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045951-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	63	206	0	ENST00000274376.6:c.1534C>G	p.Arg512Gly	p.R512G	ENST00000274376	NM_002890.2	512	Cga/Gga	11/25	1	2	FACETS	0.941	0.832	1	0.941	0.832	1	CLONAL	1	TRUE	1	0.782895997655553	2		206	171	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0045952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	242	409	1	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.978	1	1	0.995	1	CLONAL	2	TRUE	1	0.368365739641829	2		410	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0045952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	151	376	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.188709004244062	1	FACETS	1	0.954	1	1	0.954	1	INDETERMINATE	1	TRUE	0	0.368365739641829	1		376	632	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410611	32410611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749266841	NA	P-0045952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	93	380	0	ENST00000332351.3:c.1547C>T	p.Ala516Val	p.A516V	ENST00000332351	NM_024426.4	516	gCg/gTg	10/10	0.368365739641829	1	FACETS	0.945	0.845	1	0.945	0.845	1	CLONAL	1	TRUE	0	0.368365739641829	1		380	436	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90971041	90971041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200297914	NA	P-0045952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	65	245	0	ENST00000265433.3:c.1036G>A	p.Val346Met	p.V346M	ENST00000265433	NM_002485.4	346	Gtg/Atg	9/16	1	2	FACETS	0.88	0.766	1	0.88	0.766	1	CLONAL	1	TRUE	1	0.368365739641829	2		245	401	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971178	21971178	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1286147184	NA	P-0045952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	118	336	0	ENST00000579755.1:c.223G>A	p.Gly75Arg	p.G75R	ENST00000579755		75	Gga/Aga	2/3	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.368365739641829	2		336	499	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131740	2131740	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	197	635	2	ENST00000219476.3:c.3755C>A	p.Ser1252Ter	p.S1252*	ENST00000219476	NM_000548.3	1252	tCa/tAa	31/42	0.368365739641829	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.368365739641829	1		637	785	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294420	1294420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	266	477	0	ENST00000310581.5:c.581G>A	p.Arg194Gln	p.R194Q	ENST00000310581	NM_198253.2	194	cGa/cAa	2/16	1	2	FACETS	0.889	0.837	0.943	1	0.995	1	CLONAL	2	TRUE	1	0.368365739641829	2		477	812	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0045953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	36	380	0	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.214587803695864	3	FACETS	1	0.827	1	0.5	0.413	0.598	CLONAL	1	TRUE	1	0.29	3		380	284	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956724	68956724	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs372931548	NA	P-0045953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	14	348	0	ENST00000288368.4:c.842G>A	p.Arg281Gln	p.R281Q	ENST00000288368	NM_024870.2	281	cGg/cAg	8/40	1	2	FACETS	0.352	0.254	0.471	0.352	0.254	0.471	SUBCLONAL	1	TRUE	1	0.29	2		348	274	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395184	139395185	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0045953-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	19	759	0	ENST00000277541.6:c.5752_5753dup	p.Ser1919ProfsTer63	p.S1919Pfs*63	ENST00000277541	NM_017617.3	1918	gcc/gcGCc	31/34	1	2	FACETS	0.518	0.394	0.664	0.518	0.394	0.664	SUBCLONAL	1	TRUE	1	0.29	2		759	253	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0045954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	242	613	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.337905378918584	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.338254016848483	2		613	704	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0045954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	130	356	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.295910336888949	4	FACETS	1	0.965	1			1	CLONAL	2	TRUE	NA	0.338254016848483	4		356	463	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0045954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	50	356	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.338254016848483	1	FACETS	0.756	0.644	0.877	0.756	0.644	0.877	SUBCLONAL	1	TRUE	0	0.338254016848483	1		358	325	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	21	387	0	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	0.338254016848483	1	FACETS	0.291	0.224	0.37	0.291	0.224	0.37	SUBCLONAL	1	TRUE	0	0.338254016848483	1		387	354	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982016	93982016	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	43	211	0	ENST00000369303.4:c.1449A>C	p.Lys483Asn	p.K483N	ENST00000369303	NM_004440.3	483	aaA/aaC	6/17	1	2	FACETS	0.898	0.756	1	0.898	0.756	1	CLONAL	1	TRUE	1	0.338254016848483	2		211	283	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652793	212652793	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	21	319	0	ENST00000342788.4:c.513G>A	p.Trp171Ter	p.W171*	ENST00000342788	NM_005235.2	171	tgG/tgA	4/28	0.307625988695419	3	FACETS	0.511	0.394	0.648	0.256	0.197	0.324	SUBCLONAL	1	TRUE	1	0.338254016848483	3		319	284	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931899	68931899	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	135	441	0	ENST00000288368.4:c.329T>G	p.Leu110Arg	p.L110R	ENST00000288368	NM_024870.2	110	cTt/cGt	3/40	0.223455640152782	2	FACETS	0.866	0.793	0.941	0.866	0.793	0.941	CLONAL	2	TRUE	0	0.338254016848483	2		441	461	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974676	21974676	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0045954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	177	414	0	ENST00000304494.5:c.150+1G>A		p.X50_splice	ENST00000304494	NM_000077.4	50			0.307625988695419	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.338254016848483	3		414	525	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11314006	11314006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	88	450	0	ENST00000361445.4:c.730G>A	p.Gly244Arg	p.G244R	ENST00000361445	NM_004958.3	244	Gga/Aga	6/58	0.3210498139094	3	FACETS	0.918	0.813	1	0.459	0.406	0.515	CLONAL	1	TRUE	1	0.338254016848483	3		450	663	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880873	28880873	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	26	476	0	ENST00000282397.4:c.3757C>A	p.Pro1253Thr	p.P1253T	ENST00000282397	NM_002019.4	1253	Ccc/Acc	29/30	0.337905378918584	2	FACETS	0.309	0.244	0.384	0.154	0.122	0.192	SUBCLONAL	1	TRUE	0	0.338254016848483	2		476	498	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218598	36218598	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0045954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	92	600	0	ENST00000222270.7:c.4303-1G>A		p.X1435_splice	ENST00000222270	NM_014727.1	1435			0.307625988695419	3	FACETS	0.888	0.789	0.994	0.444	0.394	0.497	CLONAL	1	TRUE	1	0.338254016848483	3		600	716	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652824	212652824	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	23	346	0	ENST00000342788.4:c.482T>C	p.Ile161Thr	p.I161T	ENST00000342788	NM_005235.2	161	aTt/aCt	4/28	0.307625988695419	3	FACETS	0.535	0.418	0.671	0.268	0.209	0.336	SUBCLONAL	1	TRUE	1	0.338254016848483	3		346	297	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400088	41400088	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	62	337	0	ENST00000373198.4:c.671A>C	p.Lys224Thr	p.K224T	ENST00000373198	NM_133170.3	224	aAg/aCg	5/32	0.210909850868882	5	FACETS	1	0.902	1	0.351	0.303	0.403	CLONAL	1	TRUE	2	0.338254016848483	5		337	525	SUCCESS
AR	367	MSKCC	GRCh37	X	66941796	66941796	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	112	204	0	ENST00000374690.3:c.2440T>C	p.Phe814Leu	p.F814L	ENST00000374690	NM_000044.3	814	Ttc/Ctc	6/8	0.295910336888949	2	FACETS	0.931	0.856	1			1	CLONAL	3	TRUE	NA	0.338254016848483	2		204	237	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541723	187541735	+	frameshift_variant	Frame_Shift_Del	DEL	TTCCCAATAGCAG	TTCCCAATAGCAG	CA	novel	NA	P-0045954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	46	310	1	ENST00000441802.2:c.6005_6017delinsTG	p.Thr2002MetfsTer5	p.T2002Mfs*5	ENST00000441802	NM_005245.3	2002	aCTGCTATTGGGAAt/aTGt	10/27	1	2	FACETS	0.784	0.662	0.917	0.784	0.662	0.917	CLONAL	1	TRUE	1	0.338254016848483	2		311	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	304	699	0	ENST00000269305.4:c.470T>G	p.Val157Gly	p.V157G	ENST00000269305	NM_001126112.2	157	gTc/gGc	5/11	0.723005829808829	1	FACETS	0.942	0.898	0.986	0.942	0.898	0.986	CLONAL	1	TRUE	0	0.723005829808829	1		699	570	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953760	48953760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913302	NA	P-0045956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	72	161	0	ENST00000267163.4:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000267163	NM_000321.2	455	Cga/Tga	14/27	0.723005829808829	1	FACETS	0.865	0.779	0.951	0.865	0.779	0.951	CLONAL	1	TRUE	0	0.723005829808829	1		161	147	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753719	42753719	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	295	694	0	ENST00000222329.4:c.545G>T	p.Gly182Val	p.G182V	ENST00000222329	NM_006494.2	182	gGc/gTc	4/4	1	2	FACETS	0.973	0.919	1	0.973	0.919	1	CLONAL	1	TRUE	1	0.723005829808829	2		694	839	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253968	133253968	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	184	448	0	ENST00000320574.5:c.782A>T	p.Asp261Val	p.D261V	ENST00000320574	NM_006231.2	261	gAt/gTt	8/49	0.723005829808829	3	FACETS	0.849	0.785	0.916	0.425	0.392	0.458	CLONAL	1	TRUE	1	0.723005829808829	3		448	816	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650720	67650720	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1002125753	NA	P-0045956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	301	512	0	ENST00000264010.4:c.1025G>T	p.Arg342Leu	p.R342L	ENST00000264010	NM_006565.3	342	cGt/cTt	5/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.723005829808829	2		512	806	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281300	15281351	+	frameshift_variant	Frame_Shift_Del	DEL	GACAGCGCCCGCCACTAGCAGTGGCAGCAGCGGGACGCTGGGTTCTGGAGGC	GACAGCGCCCGCCACTAGCAGTGGCAGCAGCGGGACGCTGGGTTCTGGAGGC	-	novel	NA	P-0045956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	219	678	0	ENST00000263388.2:c.4905_4956del	p.Glu1635AspfsTer53	p.E1635Dfs*53	ENST00000263388	NM_000435.2	1635	gaGCCTCCAGAACCCAGCGTCCCGCTGCTGCCACTGCTAGTGGCGGGCGCTGTC/ga	27/33	1	2	FACETS	0.825	0.771	0.882	0.825	0.771	0.882	CLONAL	1	TRUE	1	0.723005829808829	2		678	734	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64288912	64288912	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	245	400	0	ENST00000370651.3:c.308A>G	p.His103Arg	p.H103R	ENST00000370651	NM_003463.4	103	cAt/cGt	4/6	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.723005829808829	2		400	661	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146211	38146211	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	293	581	0	ENST00000317025.8:c.3295A>G	p.Asn1099Asp	p.N1099D	ENST00000317025	NM_023034.1	1099	Aac/Gac	19/24	1	2	FACETS	0.996	0.941	1	0.996	0.941	1	CLONAL	1	TRUE	1	0.723005829808829	2		581	814	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978521	70978521	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	155	414	0	ENST00000276594.2:c.1132G>C	p.Val378Leu	p.V378L	ENST00000276594	NM_024504.3	378	Gtg/Ctg	5/8	1	2	FACETS	0.988	0.913	1	0.988	0.913	1	CLONAL	1	TRUE	1	0.723005829808829	2		414	434	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944635	38944635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	172	299	1	ENST00000357387.3:c.4826G>A	p.Arg1609His	p.R1609H	ENST00000357387	NM_152756.3	1609	cGt/cAt	36/38	0.723005829808829	3	FACETS	1	0.974	1	0.559	0.517	0.603	CLONAL	1	TRUE	1	0.723005829808829	3		300	579	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045956-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	325	699	0	ENST00000269305.4:c.470T>G	p.Val157Gly	p.V157G	ENST00000269305	NM_001126112.2	157	gTc/gGc	5/11	0.725186030094649	3	FACETS	0.988	0.959	1	0.988	0.959	1	CLONAL	3	FALSE	0	0.749920938535508	3		699	402	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953760	48953760	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913302	NA	P-0045956-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	30	161	0	ENST00000267163.4:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000267163	NM_000321.2	455	Cga/Tga	14/27	0.731344511912056	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	FALSE	0	0.749920938535508	2		161	38	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753719	42753719	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045956-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	227	694	0	ENST00000222329.4:c.545G>T	p.Gly182Val	p.G182V	ENST00000222329	NM_006494.2	182	gGc/gTc	4/4	0.749920938535508	4	FACETS	0.936	0.879	0.993	0.936	0.879	0.993	CLONAL	2	FALSE	2	0.749920938535508	4		694	566	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253968	133253968	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045956-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	64	448	0	ENST00000320574.5:c.782A>T	p.Asp261Val	p.D261V	ENST00000320574	NM_006231.2	261	gAt/gTt	8/49	0.749920938535508	7	FACETS	0.87	0.76	0.986	0.348	0.304	0.395	CLONAL	2	FALSE	2	0.749920938535508	7		448	282	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650720	67650720	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1002125753	NA	P-0045956-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	175	512	0	ENST00000264010.4:c.1025G>T	p.Arg342Leu	p.R342L	ENST00000264010	NM_006565.3	342	cGt/cTt	5/12	0.749920938535508	4	FACETS	0.869	0.808	0.931	0.869	0.808	0.931	CLONAL	2	FALSE	2	0.749920938535508	4		512	470	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281300	15281351	+	frameshift_variant	Frame_Shift_Del	DEL	GACAGCGCCCGCCACTAGCAGTGGCAGCAGCGGGACGCTGGGTTCTGGAGGC	GACAGCGCCCGCCACTAGCAGTGGCAGCAGCGGGACGCTGGGTTCTGGAGGC	-	novel	NA	P-0045956-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	192	678	0	ENST00000263388.2:c.4905_4956del	p.Glu1635AspfsTer53	p.E1635Dfs*53	ENST00000263388	NM_000435.2	1635	gaGCCTCCAGAACCCAGCGTCCCGCTGCTGCCACTGCTAGTGGCGGGCGCTGTC/ga	27/33	0.749920938535508	4	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	FALSE	2	0.749920938535508	4		678	447	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64288912	64288912	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045956-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	61	400	0	ENST00000370651.3:c.308A>G	p.His103Arg	p.H103R	ENST00000370651	NM_003463.4	103	cAt/cGt	4/6	0.513308574380572	6	FACETS	0.929	0.823	1	0.929	0.823	1	CLONAL	3	FALSE	3	0.749920938535508	6		400	146	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146211	38146211	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045956-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	122	581	0	ENST00000317025.8:c.3295A>G	p.Asn1099Asp	p.N1099D	ENST00000317025	NM_023034.1	1099	Aac/Gac	19/24	0.343317998768965	5	FACETS	1	0.98	1	0.817	0.752	0.884	INDETERMINATE	2	FALSE	2	0.749920938535508	5		581	282	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978521	70978521	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045956-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	75	414	0	ENST00000276594.2:c.1132G>C	p.Val378Leu	p.V378L	ENST00000276594	NM_024504.3	378	Gtg/Ctg	5/8	0.343317998768965	5	FACETS	1	0.939	1	0.716	0.64	0.794	INDETERMINATE	2	FALSE	2	0.749920938535508	5		414	198	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638546	176638609	+	frameshift_variant	Frame_Shift_Del	DEL	AGACCGAGCGCAAAAGAAAACTGAATCAGCTTCCAAGTGTGACTCTTGATGCTGTACTGCAGGG	AGACCGAGCGCAAAAGAAAACTGAATCAGCTTCCAAGTGTGACTCTTGATGCTGTACTGCAGGG	-	novel	NA	P-0045956-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	10	481	0	ENST00000439151.2:c.3154_3217del	p.Arg1052AsnfsTer6	p.R1052Nfs*6	ENST00000439151	NM_022455.4	1049	aAGACCGAGCGCAAAAGAAAACTGAATCAGCTTCCAAGTGTGACTCTTGATGCTGTACTGCAGGGa/aa	5/23	0.749920938535508	4	FACETS	0.239	0.162	0.337	0.12	0.081	0.169	SUBCLONAL	1	FALSE	2	0.749920938535508	4		481	195	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881001	37881002	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGCTCCCC	rs397516981	NA	P-0045957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	276	649	0	ENST00000269571.5:c.2331_2339dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	gtg/gtGGGCTCCCCg	20/27	1	2	FACETS	0.821	0.772	0.872	0.821	0.772	0.872	CLONAL	1	TRUE	1	0.699376610167443	2		649	961	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372707	81372707	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	76	259	0	ENST00000222390.5:c.827C>A	p.Pro276His	p.P276H	ENST00000222390	NM_000601.4	276	cCt/cAt	7/18	0.3540622077516	1	FACETS	0.496	0.44	0.555	0.496	0.44	0.555	INDETERMINATE	1	TRUE	0	0.699376610167443	1		259	285	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577065	7577065	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	279	604	0	ENST00000269305.4:c.873del	p.Glu294SerfsTer51	p.E294Sfs*51	ENST00000269305	NM_001126112.2	291	aaG/aa	8/11	0.680362970521715	1	FACETS	0.928	0.881	0.975	0.928	0.881	0.975	CLONAL	1	TRUE	0	0.699376610167443	1		604	559	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610123	43610123	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	180	547	0	ENST00000355710.3:c.2075C>A	p.Ala692Asp	p.A692D	ENST00000355710	NM_020975.4	692	gCc/gAc	11/20	1	2	FACETS	0.927	0.861	0.996	0.927	0.861	0.996	CLONAL	1	TRUE	1	0.699376610167443	2		547	555	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515212	31515212	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	383	619	0	ENST00000344624.3:c.1173G>T	p.Glu391Asp	p.E391D	ENST00000344624		391	gaG/gaT	5/33	0.133386586125006	5	FACETS	0.852	0.813	0.891	0.639	0.61	0.668	INDETERMINATE	3	TRUE	1	0.699376610167443	5		619	878	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392049	81392049	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045957-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	37	215	0	ENST00000222390.5:c.228G>T	p.Arg76Ser	p.R76S	ENST00000222390	NM_000601.4	76	agG/agT	2/18	0.3540622077516	1	FACETS	0.593	0.501	0.691	0.593	0.501	0.691	INDETERMINATE	1	TRUE	0	0.699376610167443	1		215	116	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856424	111856424	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	23	124	0	ENST00000341259.2:c.475A>C	p.Thr159Pro	p.T159P	ENST00000341259	NM_005475.2	159	Acc/Ccc	2/8	1	2	FACETS	0.284	0.222	0.355	0.284	0.222	0.355	SUBCLONAL	1	TRUE	1	0.750067384929996	2		124	216	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148958	119148958	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	35	295	0	ENST00000264033.4:c.1178T>A	p.Ile393Asn	p.I393N	ENST00000264033	NM_005188.3	393	aTt/aAt	8/16	0.750067384929996	1	FACETS	0.192	0.158	0.231	0.192	0.158	0.231	SUBCLONAL	1	TRUE	0	0.750067384929996	1		295	303	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931648	39931648	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	233	356	0	ENST00000378444.4:c.2951T>A	p.Leu984Gln	p.L984Q	ENST00000378444	NM_001123385.1	984	cTg/cAg	4/15	0.177474139626911	3	FACETS	1	0.991	1	0.681	0.639	0.724	INDETERMINATE	1	TRUE	1	0.750067384929996	3		356	627	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0045959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	126	518	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.352351749318497	2		518	623	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0045959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	66	418	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.352351749318497	1	FACETS	0.7	0.609	0.797	0.7	0.609	0.797	SUBCLONAL	1	TRUE	0	0.352351749318497	1		418	441	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428299	33428299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368914740	NA	P-0045959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	98	482	0	ENST00000345365.6:c.824G>A	p.Arg275Gln	p.R275Q	ENST00000345365	NM_002878.3	275	cGg/cAg	9/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.352351749318497	2		482	447	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653807	89653807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554893782	NA	P-0045959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	71	244	0	ENST00000371953.3:c.105G>A	p.Met35Ile	p.M35I	ENST00000371953	NM_000314.4	35	atG/atA	2/9	0.352351749318497	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.352351749318497	1		244	288	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368258	45368258	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	76	343	0	ENST00000262160.6:c.1344G>A	p.Trp448Ter	p.W448*	ENST00000262160	NM_005901.5	448	tgG/tgA	11/11	0.352351749318497	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.352351749318497	1		343	322	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247168	153247168	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	55	200	0	ENST00000281708.4:c.1634A>T	p.Tyr545Phe	p.Y545F	ENST00000281708	NM_033632.3	545	tAt/tTt	10/12	0.104394659474409	3	FACETS	1	0.956	1	0.646	0.557	0.742	INDETERMINATE	1	TRUE	1	0.352351749318497	3		200	284	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191157	185191157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs903937665	NA	P-0045959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	71	462	1	ENST00000265026.3:c.2038C>T	p.Arg680Trp	p.R680W	ENST00000265026	NM_004721.4	680	Cgg/Tgg	11/14	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.352351749318497	2		463	357	SUCCESS
APC	324	MSKCC	GRCh37	5	112173817	112173820	+	frameshift_variant	Frame_Shift_Del	DEL	TAGT	TAGT	-	rs879254091	NA	P-0045959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	50	276	0	ENST00000257430.4:c.2527_2530del	p.Ser843LeufsTer17	p.S843Lfs*17	ENST00000257430	NM_000038.5	842	gaTAGT/ga	16/16	0.104394659474409	3	FACETS	1	0.909	1	0.545	0.465	0.632	INDETERMINATE	1	TRUE	1	0.352351749318497	3		276	306	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252110	226252110	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	15	59	0	ENST00000366813.1:c.58C>G	p.Gln20Glu	p.Q20E	ENST00000366813		20	Caa/Gaa	1/3	1	2	FACETS	1	0.822	1	1	0.822	1	CLONAL	1	TRUE	1	0.352351749318497	2		59	75	SUCCESS
APC	324	MSKCC	GRCh37	5	112175770	112175771	+	frameshift_variant	Frame_Shift_Ins	INS	GG	GG	AGA	novel	NA	P-0045959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	39	250	0	ENST00000257430.4:c.4479_4480delinsAGA	p.Ser1495LysfsTer19	p.S1495Kfs*19	ENST00000257430	NM_000038.5	1493	acGGaa/acAGAaa	16/16	0.104394659474409	3	FACETS	1	0.895	1	0.549	0.459	0.649	INDETERMINATE	1	TRUE	1	0.352351749318497	3		250	237	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477789	140477790	+	splice_donor_variant	Splice_Site	INS	-	-	CCTGAGTAC	novel	NA	P-0045959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	58	345	0	ENST00000288602.6:c.1510_1517+1dup		p.X504_splice	ENST00000288602	NM_004333.4	504			1	2	FACETS	0.769	0.663	0.885	0.769	0.663	0.885	SUBCLONAL	1	TRUE	1	0.352351749318497	2		345	428	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220715	1220715	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	58	543	0	ENST00000326873.7:c.733C>T	p.Leu245Phe	p.L245F	ENST00000326873	NM_000455.4	245	Ctc/Ttc	5/10	0.228982855102916	1	FACETS	0.685	0.588	0.791	0.685	0.588	0.791	SUBCLONAL	1	TRUE	0	0.228982855102916	1		543	655	SUCCESS
APC	324	MSKCC	GRCh37	5	112175621	112175621	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	36	320	0	ENST00000257430.4:c.4330C>T	p.Gln1444Ter	p.Q1444*	ENST00000257430	NM_000038.5	1444	Caa/Taa	16/16	1	2	FACETS	0.769	0.632	0.921	0.769	0.632	0.921	CLONAL	1	TRUE	1	0.228982855102916	2		320	409	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725522	162725522	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	36	428	0	ENST00000367921.3:c.634C>G	p.Leu212Val	p.L212V	ENST00000367921	NM_006182.2	212	Ctg/Gtg	7/18	1	2	FACETS	0.618	0.507	0.742	0.618	0.507	0.742	SUBCLONAL	1	TRUE	1	0.228982855102916	2		428	509	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575505	64575505	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	63	565	1	ENST00000312049.6:c.512G>T	p.Arg171Leu	p.R171L	ENST00000312049	NM_130799.2	171	cGg/cTg	3/10	1	2	FACETS	0.754	0.651	0.866	0.754	0.651	0.866	SUBCLONAL	1	TRUE	1	0.228982855102916	2		566	730	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221981	1221981	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	63	604	1	ENST00000326873.7:c.896C>G	p.Ser299Cys	p.S299C	ENST00000326873	NM_000455.4	299	tCc/tGc	7/10	0.228982855102916	1	FACETS	0.608	0.524	0.698	0.608	0.524	0.698	SUBCLONAL	1	TRUE	0	0.228982855102916	1		605	802	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138551	11138551	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	64	565	0	ENST00000358026.2:c.3307T>C	p.Cys1103Arg	p.C1103R	ENST00000358026	NM_001128849.1	1103	Tgc/Cgc	24/36	0.228982855102916	1	FACETS	0.68	0.588	0.78	0.68	0.588	0.78	SUBCLONAL	1	TRUE	0	0.228982855102916	1		565	728	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917722	29917722	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1254406721	NA	P-0045964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	56	554	0	ENST00000389048.3:c.946C>A	p.Pro316Thr	p.P316T	ENST00000389048	NM_004304.4	316	Ccc/Acc	3/29	1	2	FACETS	0.651	0.557	0.755	0.651	0.557	0.755	SUBCLONAL	1	TRUE	1	0.228982855102916	2		554	751	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437884	110437884	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045964-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	15	88	1	ENST00000375856.3:c.517G>T	p.Gly173Cys	p.G173C	ENST00000375856	NM_003749.2	173	Ggc/Tgc	1/2	0.228982855102916	1	FACETS	1	0.764	1	1	0.764	1	CLONAL	1	TRUE	0	0.228982855102916	1		89	112	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0045965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	109	404	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.372952782834299	1	FACETS	0.834	0.751	0.922	0.834	0.751	0.922	CLONAL	1	TRUE	0	0.372952782834299	1		404	570	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0045965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	92	429	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.239865690669136	3	FACETS	1	0.968	1	0.612	0.546	0.682	CLONAL	1	TRUE	1	0.372952782834299	3		429	478	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0045968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	35	69	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.209577482121112	3	FACETS	1	0.923	1	0.621	0.511	0.744	CLONAL	1	TRUE	1	0.209577482121112	3		69	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882019	NA	P-0045968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	102	173	0	ENST00000269305.4:c.455dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	ccg/ccCg	5/11	1	2	FACETS	0.848	0.76	0.94	1	0.985	1	CLONAL	2	TRUE	1	0.209577482121112	2		173	574	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163823	72163823	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0045968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	28	192	0	ENST00000357731.5:c.536-1G>A		p.X179_splice	ENST00000357731	NM_173808.2	179			0.18505381526915	2	FACETS	1	0.92	1	0.655	0.527	0.798	CLONAL	1	TRUE	0	0.209577482121112	2		192	204	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144096	55144096	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	61	335	0	ENST00000257290.5:c.1925T>C	p.Met642Thr	p.M642T	ENST00000257290	NM_006206.4	642	aTg/aCg	14/23	0.18505381526915	2	FACETS	0.818	0.709	0.934	0.818	0.709	0.934	CLONAL	2	TRUE	0	0.209577482121112	2		335	356	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936025	44936027	+	frameshift_variant	Frame_Shift_Del	DEL	CTC	CTC	GA	novel	NA	P-0045968-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	47	436	0	ENST00000377967.4:c.2786_2788delinsGA	p.Pro929ArgfsTer8	p.P929Rfs*8	ENST00000377967	NM_021140.2	929	cCTCcc/cGAcc	18/29	0.209577482121112	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.209577482121112	1		436	353	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593613	55593613	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913521	NA	P-0045969-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	93	365	0	ENST00000288135.5:c.1679T>A	p.Val560Asp	p.V560D	ENST00000288135	NM_000222.2	560	gTt/gAt	11/21	1	2	FACETS	0.986	0.883	1	0.986	0.883	1	CLONAL	1	TRUE	1	0.482468169130556	2		365	391	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0045970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	14	236	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.634	0.459	0.845	0.634	0.459	0.845	SUBCLONAL	1	TRUE	1	0.23	2		236	192	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11540654	NA	P-0045970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	8	575	0	ENST00000269305.4:c.329G>T	p.Arg110Leu	p.R110L	ENST00000269305	NM_001126112.2	110	cGt/cTt	4/11	1	2	FACETS	0.199	0.127	0.292	0.199	0.127	0.292	SUBCLONAL	1	TRUE	1	0.23	2		575	350	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225338994	225338994	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	10	349	0	ENST00000264414.4:c.2275G>T	p.Glu759Ter	p.E759*	ENST00000264414	NM_003590.4	759	Gag/Tag	16/16	1	2	FACETS	0.608	0.413	0.851	0.608	0.413	0.851	SUBCLONAL	1	TRUE	1	0.23	2		349	143	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007581	62007581	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1277301487	NA	P-0045970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	39	581	0	ENST00000392795.3:c.286C>T	p.Arg96Cys	p.R96C	ENST00000392795	NM_001039933.1	96	Cgc/Tgc	3/6	1	2	FACETS	0.759	0.629	0.903	0.759	0.629	0.903	CLONAL	1	TRUE	1	0.23	2		581	447	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254677	46254677	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	17	336	0	ENST00000334344.6:c.4867G>C	p.Asp1623His	p.D1623H	ENST00000334344	NM_152641.2	1623	Gat/Cat	16/21	1	2	FACETS	0.624	0.466	0.81	0.624	0.466	0.81	SUBCLONAL	1	TRUE	1	0.23	2		336	237	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29482999	29482999	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs1131691100	NA	P-0045970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	16	211	0	ENST00000356175.3:c.61-2A>T		p.X21_splice	ENST00000356175	NM_000267.3	21			1	2	FACETS	0.809	0.609	1	1	0.91	1	CLONAL	2	TRUE	1	0.23	2		211	86	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101982	11101982	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	49	589	0	ENST00000358026.2:c.1402C>A	p.Arg468Ser	p.R468S	ENST00000358026	NM_001128849.1	468	Cgc/Agc	8/36	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.23	2		589	371	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25458655	25458655	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	32	476	0	ENST00000264709.3:c.2518A>G	p.Ile840Val	p.I840V	ENST00000264709	NM_175629.2	840	Ata/Gta	22/23	1	2	FACETS	0.872	0.71	1	0.872	0.71	1	CLONAL	1	TRUE	1	0.23	2		476	319	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873633	35873633	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	14	228	0	ENST00000303115.3:c.589C>A	p.Pro197Thr	p.P197T	ENST00000303115	NM_002185.3	197	Ccg/Acg	5/8	1	2	FACETS	0.84	0.61	1	0.84	0.61	1	CLONAL	1	TRUE	1	0.23	2		228	145	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180638	32180638	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	43	499	0	ENST00000375023.3:c.2489G>C	p.Cys830Ser	p.C830S	ENST00000375023	NM_004557.3	830	tGc/tCc	16/30	0.132318700125523	3	FACETS	1	0.886	1	0.536	0.449	0.632	INDETERMINATE	1	TRUE	1	0.23	3		499	389	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0045971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	77	69	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.211230954698157	3	FACETS	1	0.947	1	0.564	0.499	0.634	INDETERMINATE	1	TRUE	1	0.472616484853571	3		69	357	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0045971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	91	525	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	0.211230954698157	3	FACETS	0.644	0.572	0.722	0.322	0.286	0.361	INDETERMINATE	1	TRUE	1	0.472616484853571	3		525	739	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575080	48575080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	37	214	0	ENST00000342988.3:c.274C>T	p.His92Tyr	p.H92Y	ENST00000342988	NM_005359.5	92	Cat/Tat	3/12	0.377907708057824	1	FACETS	0.432	0.357	0.514	0.432	0.357	0.514	SUBCLONAL	1	TRUE	0	0.472616484853571	1		214	277	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464983	120464983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1359123761	NA	P-0045971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	37	307	0	ENST00000256646.2:c.5089G>A	p.Val1697Ile	p.V1697I	ENST00000256646	NM_024408.3	1697	Gta/Ata	28/34	1	2	FACETS	0.405	0.334	0.484	0.405	0.334	0.484	SUBCLONAL	1	TRUE	1	0.472616484853571	2		307	387	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445824	49445825	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0045971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	228	594	0	ENST00000301067.7:c.1641dup	p.Pro548ThrfsTer3	p.P548Tfs*3	ENST00000301067	NM_003482.3	547	-/A	10/54	0.211230954698157	3	FACETS	1	0.99	1	0.681	0.635	0.728	INDETERMINATE	1	TRUE	1	0.472616484853571	3		594	876	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263883	133263883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771930571	NA	P-0045971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	44	228	0	ENST00000320574.5:c.19G>A	p.Gly7Arg	p.G7R	ENST00000320574	NM_006231.2	7	Ggg/Agg	1/49	0.211230954698157	3	FACETS	0.802	0.677	0.939	0.401	0.338	0.47	INDETERMINATE	1	TRUE	1	0.472616484853571	3		228	287	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45657020	45657020	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	59	361	0	ENST00000407780.3:c.136G>A	p.Asp46Asn	p.D46N	ENST00000407780	NM_001283052.1	46	Gat/Aat	3/7	0.285390911120537	3	FACETS	0.549	0.473	0.633	0.275	0.236	0.317	SUBCLONAL	1	TRUE	1	0.472616484853571	3		361	562	SUCCESS
APC	324	MSKCC	GRCh37	5	112175513	112175514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	149	258	0	ENST00000257430.4:c.4224dup	p.Pro1409ThrfsTer14	p.P1409Tfs*14	ENST00000257430	NM_000038.5	1408	gaa/gAaa	16/16	0.318962112065135	3	FACETS	0.984	0.91	1	0.656	0.606	0.707	CLONAL	2	TRUE	0	0.472616484853571	3		258	396	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928223	178928225	+	missense_variant	Missense_Mutation	TNP	CTC	CTC	TTT	novel	NA	P-0045971-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	90	287	0	ENST00000263967.3:c.1409_1411delinsTTT	p.Thr470_Pro471delinsIleSer	p.T470_P471delinsIS	ENST00000263967	NM_006218.2	470	aCTCca/aTTTca	9/21	0.140067036666853	4	FACETS	1	0.974	1	0.655	0.584	0.73	INDETERMINATE	1	TRUE	2	0.472616484853571	4		287	428	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0045972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	82	680	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.147059697771701	2	FACETS	1	0.957	1	1	0.957	1	INDETERMINATE	2	TRUE	0	0.264369304230476	2		680	271	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0045972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	95	459	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.264369304230476	5	FACETS	0.907	0.814	1	0.907	0.814	1	CLONAL	3	TRUE	2	0.264369304230476	5		459	369	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257747	133257747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	21	438	1	ENST00000320574.5:c.181G>A	p.Gly61Ser	p.G61S	ENST00000320574	NM_006231.2	61	Ggc/Agc	2/49	0.224922312930976	1	FACETS	0.532	0.41	0.674	0.532	0.41	0.674	SUBCLONAL	1	TRUE	0	0.264369304230476	1		439	259	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486220	99486220	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	22	558	0	ENST00000268035.6:c.3526G>T	p.Val1176Leu	p.V1176L	ENST00000268035	NM_000875.3	1176	Gtg/Ttg	19/21	0.224922312930976	1	FACETS	0.615	0.478	0.772	0.615	0.478	0.772	SUBCLONAL	1	TRUE	0	0.264369304230476	1		558	235	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210809	2210809	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	46	412	0	ENST00000398665.3:c.1306C>A	p.Leu436Met	p.L436M	ENST00000398665	NM_032482.2	436	Ctg/Atg	14/28	0.264369304230476	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.264369304230476	1		412	207	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140550012	140550012	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045972-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	39	230	0	ENST00000288602.6:c.139G>C	p.Val47Leu	p.V47L	ENST00000288602	NM_004333.4	47	Gtg/Ctg	2/18	0.230004802623696	4	FACETS	0.88	0.736	1	0.88	0.736	1	CLONAL	2	TRUE	2	0.264369304230476	4		230	212	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0045973-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	15	480	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.308	0.224	0.41	0.308	0.224	0.41	SUBCLONAL	1	TRUE	1	0.138393124306117	2		480	704	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157485	106157485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747398674	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	11	259	0	ENST00000380013.4:c.2386G>A	p.Glu796Lys	p.E796K	ENST00000380013	NM_001127208.2	796	Gag/Aag	3/11	0.117344580061674	4	FACETS	1	0.805	1	0.606	0.426	0.821	INDETERMINATE	1	FALSE	2	0.343415197702188	4		259	71	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	85	297	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.343415197702188	2	FACETS	0.945	0.847	1	0.945	0.847	1	CLONAL	2	FALSE	0	0.343415197702188	2		297	262	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	95	680	1	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.343415197702188	2		681	484	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149465987	149465987	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	132	659	0	ENST00000286301.3:c.4G>A	p.Gly2Ser	p.G2S	ENST00000286301	NM_005211.3	2	Ggc/Agc	2/22	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.343415197702188	2		659	630	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	86	696	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.343415197702188	2		696	395	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	67	423	1	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.343415197702188	2		424	342	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101268	27101268	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	56	568	2	ENST00000324856.7:c.4555del	p.Gln1519ArgfsTer8	p.Q1519Rfs*8	ENST00000324856	NM_006015.4	1517	gCc/gc	18/20	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	FALSE	1	0.343415197702188	2		570	293	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	192	549	3	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	1	0.961	1	1	0.994	1	CLONAL	2	FALSE	1	0.343415197702188	2		552	535	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794440	42794441	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	128	789	0	ENST00000575354.2:c.1526dup	p.Leu510ThrfsTer4	p.L510Tfs*4	ENST00000575354	NM_015125.3	507	cgc/cgCc	10/20	0.117344580061674	4	FACETS	0.809	0.735	0.886	0.809	0.735	0.886	INDETERMINATE	2	FALSE	2	0.343415197702188	4		789	619	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733279	40733279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201275244	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	44	447	0	ENST00000373198.4:c.3527G>A	p.Arg1176His	p.R1176H	ENST00000373198	NM_133170.3	1176	cGt/cAt	26/32	0.259002163848116	1	FACETS	0.852	0.721	0.996	0.852	0.721	0.996	CLONAL	1	FALSE	0	0.343415197702188	1		447	249	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755678	39755678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	81	544	0	ENST00000288319.7:c.1087G>A	p.Asp363Asn	p.D363N	ENST00000288319	NM_182918.3	363	Gat/Aat	10/10	0.29861196554021	0	FACETS	0.822	0.729	0.92			1	CLONAL	1	FALSE	0	0.343415197702188	0		544	377	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031750	36031750	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879255268	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	94	630	0	ENST00000358208.4:c.1579G>A	p.Glu527Lys	p.E527K	ENST00000358208		527	Gag/Aag	12/12	0.259002163848116	1	FACETS	0.981	0.878	1	0.981	0.878	1	CLONAL	1	FALSE	0	0.343415197702188	1		630	462	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152103	11152103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778681	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	78	428	0	ENST00000358026.2:c.4387C>T	p.Arg1463Cys	p.R1463C	ENST00000358026	NM_001128849.1	1463	Cgc/Tgc	31/36	0.117344580061674	4	FACETS	1	0.972	1	0.684	0.603	0.77	INDETERMINATE	1	FALSE	2	0.343415197702188	4		428	446	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5246048	5246048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781664688	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	52	350	0	ENST00000357368.4:c.727G>A	p.Val243Met	p.V243M	ENST00000357368	NM_002850.3	243	Gtg/Atg	10/38	0.117344580061674	4	FACETS	0.765	0.656	0.881	0.765	0.656	0.881	INDETERMINATE	2	FALSE	2	0.343415197702188	4		350	266	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220131	133220131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764904030	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	84	530	0	ENST00000320574.5:c.4306C>T	p.Arg1436Trp	p.R1436W	ENST00000320574	NM_006231.2	1436	Cgg/Tgg	34/49	0.117344580061674	4	FACETS	0.75	0.666	0.84	0.75	0.666	0.84	INDETERMINATE	2	FALSE	2	0.343415197702188	4		530	438	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564739	86564740	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs797044451	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	70	622	0	ENST00000274376.6:c.475_476del	p.Leu159GlyfsTer20	p.L159Gfs*20	ENST00000274376	NM_002890.2	157	gaCTct/gact	1/25	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.343415197702188	2		622	360	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526755	31526755	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	61	435	1	ENST00000344624.3:c.285del	p.Cys96AlafsTer12	p.C96Afs*12	ENST00000344624		95	ccC/cc	2/33	1	2	FACETS	0.955	0.828	1	0.955	0.828	1	CLONAL	1	FALSE	1	0.343415197702188	2		436	372	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815802	32815802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	77	640	0	ENST00000354258.4:c.1814G>A	p.Ser605Asn	p.S605N	ENST00000354258	NM_000593.5	605	aGc/aAc	8/11	0.343415197702188	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	FALSE	0	0.343415197702188	1		640	350	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863053	56863054	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	15	449	1	ENST00000519728.1:c.327dup	p.Glu110ArgfsTer40	p.E110Rfs*40	ENST00000519728	NM_002350.3	107	aca/acAa	5/13	1	2	FACETS	0.824	0.61	1	0.824	0.61	1	CLONAL	1	FALSE	1	0.343415197702188	2		450	106	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805537	32805539	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	117	761	0	ENST00000374899.4:c.472_474del	p.Phe158del	p.F158del	ENST00000374899	NM_018833.2	158	TTC/-	2/12	0.343415197702188	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	0	0.343415197702188	1		761	402	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55704619	55704619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567945640	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	79	585	0	ENST00000284073.2:c.682C>T	p.Arg228Cys	p.R228C	ENST00000284073	NM_138962.2	228	Cgt/Tgt	10/14	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	1	0.343415197702188	2		585	427	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638499	176638499	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	39	564	1	ENST00000439151.2:c.3103del	p.Ser1035GlnfsTer5	p.S1035Qfs*5	ENST00000439151	NM_022455.4	1033	gcT/gc	5/23	1	2	FACETS	0.958	0.8	1	0.958	0.8	1	CLONAL	1	FALSE	1	0.343415197702188	2		565	237	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705316	43705316	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	74	585	0	ENST00000382044.4:c.5305+1G>A		p.X1769_splice	ENST00000382044	NM_001141980.1	1769			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.343415197702188	2		585	331	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416542	49416542	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	66	465	0	ENST00000301067.7:c.16169G>A	p.Arg5390Gln	p.R5390Q	ENST00000301067	NM_003482.3	5390	cGg/cAg	51/54	0.117344580061674	4	FACETS	1	0.942	1	0.575	0.5	0.655	INDETERMINATE	1	FALSE	2	0.343415197702188	4		465	449	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11227542	11227542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763335354	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	38	377	1	ENST00000361445.4:c.4286C>T	p.Ala1429Val	p.A1429V	ENST00000361445	NM_004958.3	1429	gCg/gTg	29/58	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	FALSE	1	0.343415197702188	2		378	197	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101345	27101345	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	82	600	0	ENST00000324856.7:c.4627G>T	p.Gly1543Cys	p.G1543C	ENST00000324856	NM_006015.4	1543	Ggc/Tgc	18/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.343415197702188	2		600	420	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652339	206652339	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	126	702	0	ENST00000367120.3:c.1046A>C	p.His349Pro	p.H349P	ENST00000367120	NM_014002.3	349	cAc/cCc	10/22	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.343415197702188	2		702	636	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724381	112724381	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	25	406	0	ENST00000369452.4:c.265G>T	p.Glu89Ter	p.E89*	ENST00000369452	NM_007373.3	89	Gag/Tag	2/9	1	2	FACETS	0.783	0.621	0.965	0.783	0.621	0.965	CLONAL	1	FALSE	1	0.343415197702188	2		406	186	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201004	108201004	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	21	337	0	ENST00000278616.4:c.7371G>T	p.Glu2457Asp	p.E2457D	ENST00000278616	NM_000051.3	2457	gaG/gaT	50/63	1	2	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	FALSE	1	0.343415197702188	2		337	112	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447341	49447341	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775185224	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	99	573	0	ENST00000301067.7:c.757G>A	p.Gly253Arg	p.G253R	ENST00000301067	NM_003482.3	253	Ggg/Agg	6/54	0.117344580061674	4	FACETS	1	0.981	1	0.738	0.661	0.819	INDETERMINATE	1	FALSE	2	0.343415197702188	4		573	525	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350003	15350003	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	124	629	0	ENST00000263377.2:c.3649G>T	p.Ala1217Ser	p.A1217S	ENST00000263377	NM_058243.2	1217	Gcc/Tcc	18/20	0.117344580061674	4	FACETS	0.874	0.794	0.958	0.874	0.794	0.958	INDETERMINATE	2	FALSE	2	0.343415197702188	4		629	555	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176505	142176505	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	16	373	0	ENST00000350721.4:c.7596del	p.Arg2533GlufsTer8	p.R2533Efs*8	ENST00000350721	NM_001184.3	2532	ttT/tt	45/47	0.259002163848116	1	FACETS	1	0.811	1	1	0.811	1	CLONAL	1	FALSE	0	0.343415197702188	1		373	71	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694685	176694685	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	19	339	0	ENST00000439151.2:c.5269A>G	p.Arg1757Gly	p.R1757G	ENST00000439151	NM_022455.4	1757	Agg/Ggg	15/23	1	2	FACETS	0.728	0.557	0.925	0.728	0.557	0.925	CLONAL	1	FALSE	1	0.343415197702188	2		339	152	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045888	26045888	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1327625572	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	42	526	0	ENST00000540144.1:c.250C>A	p.Arg84Ser	p.R84S	ENST00000540144	NM_003531.2	84	Cgt/Agt	1/1	0.343415197702188	1	FACETS	0.947	0.799	1	0.947	0.799	1	CLONAL	1	FALSE	0	0.343415197702188	1		526	214	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527593	157527593	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	94	415	0	ENST00000346085.5:c.5318A>G	p.Asp1773Gly	p.D1773G	ENST00000346085	NM_020732.3	1773	gAc/gGc	20/20	0.117344580061674	4	FACETS	0.973	0.872	1	0.973	0.872	1	INDETERMINATE	2	FALSE	2	0.343415197702188	4		415	378	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964530	70964530	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773418455	NA	P-0045974-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	41	471	0	ENST00000276594.2:c.1498G>A	p.Ala500Thr	p.A500T	ENST00000276594	NM_024504.3	500	Gcc/Acc	8/8	1	2	FACETS	0.878	0.736	1	0.878	0.736	1	CLONAL	1	FALSE	1	0.343415197702188	2		471	272	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0045975-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	101	369	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.203109210724355	2	FACETS	1	0.978	1	0.683	0.613	0.758	CLONAL	1	TRUE	0	0.285293298156882	2		369	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0045981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	51	567	1	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.303959167398626	0	FACETS	0.366	0.314	0.422			1	INDETERMINATE	1	FALSE	0	0.552041471464547	0		568	226	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0045981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	25	301	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.592	0.472	0.727	0.592	0.472	0.727	SUBCLONAL	1	FALSE	1	0.552041471464547	2		301	153	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518267	8518267	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	39	270	0	ENST00000356435.5:c.1124C>A	p.Thr375Asn	p.T375N	ENST00000356435		375	aCc/aAc	10/35	0.552041471464547	1	FACETS	0.93	0.792	1	0.93	0.792	1	CLONAL	1	FALSE	0	0.552041471464547	1		270	110	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690819	89690820	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0045981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	33	259	0	ENST00000371953.3:c.227_228del	p.Tyr76Ter	p.Y76*	ENST00000371953	NM_000314.4	76	TAt/t	4/9	0.184977134894732	1	FACETS	0.521	0.43	0.622	0.521	0.43	0.622	INDETERMINATE	1	FALSE	0	0.552041471464547	1		259	166	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061163	38061175	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCGGCCCCCGG	CGCCGGCCCCCGG	-	novel	NA	P-0045981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	88	148	0	ENST00000250448.2:c.814_826del	p.Pro272AlafsTer45	p.P272Afs*45	ENST00000250448	NM_004496.3	272	CCGGGGGCCGGCGgc/gc	2/2	1	2	FACETS	1	0.923	1	1	0.988	1	CLONAL	2	FALSE	1	0.552041471464547	2		148	158	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058024	27058025	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0045981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	91	416	0	ENST00000324856.7:c.1733_1734del	p.Ala578ValfsTer44	p.A578Vfs*44	ENST00000324856	NM_006015.4	578	GCg/g	3/20	1	2	FACETS	0.903	0.809	1	0.903	0.809	1	CLONAL	1	FALSE	1	0.552041471464547	2		416	365	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279544	123279544	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	96	517	0	ENST00000358487.5:c.888G>C	p.Lys296Asn	p.K296N	ENST00000358487	NM_000141.4	296	aaG/aaC	7/18	0.184977134894732	1	FACETS	0.711	0.639	0.786	0.711	0.639	0.786	INDETERMINATE	1	FALSE	0	0.552041471464547	1		517	354	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871014	12871028	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	AAGGGCAGCTTGCCC	AAGGGCAGCTTGCCC	TAGAG	novel	NA	P-0045981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	39	337	0	ENST00000228872.4:c.241_255delinsTAGAG	p.Lys81Ter	p.K81*	ENST00000228872	NM_004064.3	81	AAGGGCAGCTTGCCC/TAGAG	1/3	0.278003254732106	3	FACETS	0.432	0.358	0.515	0.216	0.179	0.258	INDETERMINATE	1	FALSE	1	0.552041471464547	3		337	417	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425758	49425758	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555187899	NA	P-0045981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	15	688	0	ENST00000301067.7:c.12730C>T	p.Gln4244Ter	p.Q4244*	ENST00000301067	NM_003482.3	4244	Cag/Tag	39/54	0.278003254732106	3	FACETS	0.294	0.215	0.389	0.147	0.107	0.195	INDETERMINATE	1	FALSE	1	0.552041471464547	3		688	236	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151294	202151294	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0045981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	49	262	0	ENST00000358485.4:c.1594A>T	p.Lys532Ter	p.K532*	ENST00000358485	NM_001080125.1	532	Aaa/Taa	9/9	1	2	FACETS	0.862	0.739	0.993	0.862	0.739	0.993	CLONAL	1	FALSE	1	0.552041471464547	2		262	206	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5078355	5078355	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045981-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	12	266	0	ENST00000381652.3:c.2042T>G	p.Leu681Arg	p.L681R	ENST00000381652	NM_004972.3	681	cTt/cGt	16/25	0.552041471464547	1	FACETS	0.284	0.201	0.384	0.284	0.201	0.384	SUBCLONAL	1	FALSE	0	0.552041471464547	1		266	111	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608642	189608642	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs143884625	NA	P-0045982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	104	426	0	ENST00000264731.3:c.1717A>G	p.Ile573Val	p.I573V	ENST00000264731	NM_003722.4	573	Atc/Gtc	13/14	0.45114324688513	2	FACETS	1	0.91	1	0.506	0.455	0.559	CLONAL	1	TRUE	0	0.45114324688513	2		426	456	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938325	76938325	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	252	532	0	ENST00000373344.5:c.2423G>C	p.Arg808Pro	p.R808P	ENST00000373344	NM_000489.3	808	cGa/cCa	9/35	0.296661672236674	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.45114324688513	4		532	686	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0045983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	211	681	1	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.361833390058908	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.361833390058908	1		682	730	SUCCESS
APC	324	MSKCC	GRCh37	5	112175240	112175240	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	48	201	0	ENST00000257430.4:c.3949G>T	p.Glu1317Ter	p.E1317*	ENST00000257430	NM_000038.5	1317	Gaa/Taa	16/16	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.361833390058908	2		201	199	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527614	29527614	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0045983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	116	380	0	ENST00000356175.3:c.1062+1G>A		p.X354_splice	ENST00000356175	NM_000267.3	354			0.205404341850903	3	FACETS	1	0.98	1	0.665	0.602	0.732	INDETERMINATE	1	TRUE	1	0.361833390058908	3		380	569	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118370594	118370594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781848142	NA	P-0045983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	33	201	0	ENST00000534358.1:c.6124G>A	p.Asp2042Asn	p.D2042N	ENST00000534358	NM_005933.3	2042	Gac/Aac	24/36	1	2	FACETS	0.546	0.446	0.659	0.546	0.446	0.659	SUBCLONAL	1	TRUE	1	0.361833390058908	2		201	334	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968954	15968967	+	frameshift_variant	Frame_Shift_Del	DEL	CTTGGGTAACCTGG	CTTGGGTAACCTGG	-	novel	NA	P-0045983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	97	423	0	ENST00000268712.3:c.4783_4796del	p.Pro1595SerfsTer17	p.P1595Sfs*17	ENST00000268712	NM_006311.3	1595	CCAGGTTACCCAAGt/t	33/46	0.361833390058908	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.361833390058908	1		423	387	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449641	187449641	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	83	363	0	ENST00000232014.4:c.239del	p.Pro80LeufsTer26	p.P80Lfs*26	ENST00000232014	NM_001130845.1	80	cCt/ct	4/10	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.361833390058908	2		363	451	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	288	679	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.987	0.931	1	1	0.995	1	CLONAL	2	TRUE	1	0.316715858919694	2		683	921	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	142	374	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.784	0.717	0.853	1	0.988	1	SUBCLONAL	2	TRUE	1	0.316715858919694	2		374	572	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372025	55372025	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	162	318	2	ENST00000297316.4:c.715G>A	p.Ala239Thr	p.A239T	ENST00000297316	NM_022454.3	239	Gcc/Acc	2/2	1	2	FACETS	1	0.985	1	1	0.993	1	CLONAL	2	TRUE	1	0.316715858919694	2		320	413	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242758	16242758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1366443836	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	179	391	0	ENST00000375759.3:c.1379G>A	p.Arg460His	p.R460H	ENST00000375759	NM_015001.2	460	cGc/cAc	6/15	1	2	FACETS	0.947	0.877	1	1	0.993	1	CLONAL	2	TRUE	1	0.316715858919694	2		391	597	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17371320	17371320	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs74315370	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	201	435	0	ENST00000375499.3:c.136C>T	p.Arg46Ter	p.R46*	ENST00000375499	NM_003000.2	46	Cga/Tga	2/8	1	2	FACETS	0.99	0.922	1	1	0.994	1	CLONAL	2	TRUE	1	0.316715858919694	2		435	641	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	224	482	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.966	1	1	0.995	1	CLONAL	2	TRUE	1	0.316715858919694	2		483	674	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106803	27106804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	239	586	0	ENST00000324856.7:c.6420dup	p.Phe2141LeufsTer9	p.F2141Lfs*9	ENST00000324856	NM_006015.4	2138	-/C	20/20	1	2	FACETS	0.965	0.904	1	1	0.994	1	CLONAL	2	TRUE	1	0.316715858919694	2		586	782	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46725734	46725734	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	62	426	0	ENST00000371975.4:c.374del	p.Pro125ArgfsTer2	p.P125Rfs*2	ENST00000371975	NM_003579.3	124	Ccc/cc	5/18	1	2	FACETS	0.661	0.571	0.759	0.661	0.571	0.759	SUBCLONAL	1	TRUE	1	0.316715858919694	2		426	592	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737052	162737052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765973930	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	179	378	0	ENST00000367921.3:c.1196G>A	p.Arg399Gln	p.R399Q	ENST00000367921	NM_006182.2	399	cGg/cAg	11/18	1	2	FACETS	0.971	0.9	1	1	0.993	1	CLONAL	2	TRUE	1	0.316715858919694	2		378	582	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456756	32456756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	260	462	0	ENST00000332351.3:c.136G>A	p.Ala46Thr	p.A46T	ENST00000332351	NM_024426.4	46	Gcc/Acc	1/10	1	2	FACETS	1	0.98	1	1	0.995	1	CLONAL	2	TRUE	1	0.316715858919694	2		462	751	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	146	868	3	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.807	0.735	0.883	0.807	0.735	0.883	CLONAL	1	TRUE	1	0.316715858919694	2		871	1142	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912716	100912716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1450222910	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	163	363	0	ENST00000325455.5:c.2606G>A	p.Arg869His	p.R869H	ENST00000325455	NM_001202474.3	869	cGt/cAt	7/8	1	2	FACETS	1	0.96	1	1	0.993	1	CLONAL	2	TRUE	1	0.316715858919694	2		363	487	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102033297	102033297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266360089	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	221	424	0	ENST00000282441.5:c.683C>T	p.Ala228Val	p.A228V	ENST00000282441	NM_001130145.2	228	gCt/gTt	3/9	1	2	FACETS	1	0.976	1	1	0.995	1	CLONAL	2	TRUE	1	0.316715858919694	2		424	643	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498215	498215	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	64	272	1	ENST00000399788.2:c.43C>T	p.Pro15Ser	p.P15S	ENST00000399788	NM_001042603.1	15	Cca/Tca	1/28	1	2	FACETS	0.871	0.756	0.995	0.871	0.756	0.995	CLONAL	1	TRUE	1	0.316715858919694	2		273	464	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524207	18524207	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	34	450	0	ENST00000266497.5:c.1719T>G	p.Asn573Lys	p.N573K	ENST00000266497		573	aaT/aaG	11/31	1	2	FACETS	0.34	0.277	0.412	0.34	0.277	0.412	SUBCLONAL	1	TRUE	1	0.316715858919694	2		450	631	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444377	49444378	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	181	598	0	ENST00000301067.7:c.2993dup	p.Met999TyrfsTer69	p.M999Yfs*69	ENST00000301067	NM_003482.3	998	cct/ccCt	11/54	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.316715858919694	2		598	798	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112610	115112610	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	293	676	0	ENST00000257566.3:c.1130C>T	p.Ala377Val	p.A377V	ENST00000257566	NM_016569.3	377	gCc/gTc	7/8	1	2	FACETS	0.97	0.914	1	1	0.995	1	CLONAL	2	TRUE	1	0.316715858919694	2		676	954	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	287	654	1	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.899	0.846	0.953	1	0.995	1	CLONAL	2	TRUE	1	0.316715858919694	2		655	1008	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202834	133202834	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	255	584	0	ENST00000320574.5:c.6400G>A	p.Asp2134Asn	p.D2134N	ENST00000320574	NM_006231.2	2134	Gat/Aat	46/49	1	2	FACETS	1	0.946	1	1	0.995	1	CLONAL	2	TRUE	1	0.316715858919694	2		584	799	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975440	26975440	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	140	299	0	ENST00000381527.3:c.1066C>T	p.Arg356Ter	p.R356*	ENST00000381527	NM_001260.1	356	Cga/Tga	11/13	1	2	FACETS	0.925	0.848	1	1	0.991	1	CLONAL	2	TRUE	1	0.316715858919694	2		299	478	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911073	32911074	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359335	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	37	281	0	ENST00000380152.3:c.2588dup	p.Asn863LysfsTer18	p.N863Kfs*18	ENST00000380152		861	caa/cAaa	11/27	1	2	FACETS	0.531	0.438	0.635	0.531	0.438	0.635	SUBCLONAL	1	TRUE	1	0.316715858919694	2		281	440	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021395	42021395	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	54	265	0	ENST00000219905.7:c.3691T>C	p.Tyr1231His	p.Y1231H	ENST00000219905	NM_001164273.1	1231	Tac/Cac	11/24	1	2	FACETS	0.78	0.668	0.903	0.78	0.668	0.903	CLONAL	1	TRUE	1	0.316715858919694	2		265	437	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707894	43707894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767106305	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	325	610	0	ENST00000382044.4:c.4987C>T	p.Arg1663Cys	p.R1663C	ENST00000382044	NM_001141980.1	1663	Cgt/Tgt	23/28	1	2	FACETS	1	0.982	1	1	0.996	1	CLONAL	2	TRUE	1	0.316715858919694	2		610	949	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724657	43724657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752085386	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	249	596	0	ENST00000382044.4:c.3410G>A	p.Arg1137Gln	p.R1137Q	ENST00000382044	NM_001141980.1	1137	cGg/cAg	17/28	1	2	FACETS	0.948	0.889	1	1	0.995	1	CLONAL	2	TRUE	1	0.316715858919694	2		596	829	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748999	43748999	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	319	685	0	ENST00000382044.4:c.1807A>G	p.Ser603Gly	p.S603G	ENST00000382044	NM_001141980.1	603	Agt/Ggt	12/28	1	2	FACETS	1	0.954	1	1	0.996	1	CLONAL	2	TRUE	1	0.316715858919694	2		685	998	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2090156	2090156	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	341	803	0	ENST00000219066.1:c.793G>T	p.Ala265Ser	p.A265S	ENST00000219066	NM_002528.5	265	Gcc/Tcc	5/6	1	2	FACETS	0.992	0.94	1	1	0.996	1	CLONAL	2	TRUE	1	0.316715858919694	2		803	1085	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121536	2121536	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45517206	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	317	714	0	ENST00000219476.3:c.1865G>A	p.Arg622Gln	p.R622Q	ENST00000219476	NM_000548.3	622	cGg/cAg	18/42	1	2	FACETS	0.985	0.931	1	1	0.996	1	CLONAL	2	TRUE	1	0.316715858919694	2		714	1016	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646981	23646981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	278	534	0	ENST00000261584.4:c.886del	p.Met296Ter	p.M296*	ENST00000261584	NM_024675.3	296	Atg/tg	4/13	1	2	FACETS	1	0.961	1	1	0.995	1	CLONAL	2	TRUE	1	0.316715858919694	2		534	856	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	173	383	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.868	0.803	0.936	1	0.992	1	CLONAL	2	TRUE	1	0.316715858919694	2		384	629	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829700	72829700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	236	577	0	ENST00000268489.5:c.6881G>A	p.Arg2294Gln	p.R2294Q	ENST00000268489	NM_006885.3	2294	cGa/cAa	9/10	1	2	FACETS	0.957	0.896	1	1	0.994	1	CLONAL	2	TRUE	1	0.316715858919694	2		577	779	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347173	89347173	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	253	530	0	ENST00000301030.4:c.5777del	p.Pro1926ArgfsTer37	p.P1926Rfs*37	ENST00000301030	NM_001256183.1	1926	cCg/cg	9/13	1	2	FACETS	0.962	0.903	1	1	0.995	1	CLONAL	2	TRUE	1	0.316715858919694	2		530	830	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	122	680	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	1	2	FACETS	0.787	0.71	0.868	0.787	0.71	0.868	SUBCLONAL	1	TRUE	1	0.316715858919694	2		680	979	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618570	37618572	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	240	443	0	ENST00000447079.4:c.248_250del	p.Phe83del	p.F83del	ENST00000447079	NM_015083.1	82	acCTTc/acc	1/14	1	2	FACETS	1	0.978	1	1	0.995	1	CLONAL	2	TRUE	1	0.316715858919694	2		443	696	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533700	63533700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	148	591	0	ENST00000307078.5:c.1454G>A	p.Gly485Asp	p.G485D	ENST00000307078	NM_004655.3	485	gGc/gAc	6/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.316715858919694	2		591	694	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554738	63554738	+	start_lost	Translation_Start_Site	SNP	T	T	G	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	67	352	0	ENST00000307078.5:c.1A>C	p.Met1?	p.M1?	ENST00000307078	NM_004655.3	1	Atg/Ctg	2/11	1	2	FACETS	0.858	0.747	0.978	0.858	0.747	0.978	CLONAL	1	TRUE	1	0.316715858919694	2		352	493	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526447	66526447	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555815121	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	188	385	0	ENST00000358598.2:c.1003C>T	p.Arg335Cys	p.R335C	ENST00000358598	NM_212471.2	335	Cgt/Tgt	11/11	1	2	FACETS	1	0.976	1	1	0.994	1	CLONAL	2	TRUE	1	0.316715858919694	2		385	538	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39623715	39623715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	114	281	0	ENST00000262039.4:c.2122G>A	p.Ala708Thr	p.A708T	ENST00000262039	NM_002647.2	708	Gca/Aca	20/25	1	2	FACETS	0.923	0.838	1	1	0.988	1	CLONAL	2	TRUE	1	0.316715858919694	2		281	390	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637885	39637885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200000040	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	155	360	0	ENST00000262039.4:c.2302C>T	p.Arg768Trp	p.R768W	ENST00000262039	NM_002647.2	768	Cgg/Tgg	22/25	1	2	FACETS	1	0.957	1	1	0.992	1	CLONAL	2	TRUE	1	0.316715858919694	2		360	464	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217776	2217777	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	258	630	0	ENST00000398665.3:c.2555_2556del	p.Glu852AlafsTer57	p.E852Afs*57	ENST00000398665	NM_032482.2	850	ctGAga/ctga	22/28	1	2	FACETS	0.974	0.915	1	1	0.995	1	CLONAL	2	TRUE	1	0.316715858919694	2		630	836	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599976	10599976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774683169	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	298	781	0	ENST00000171111.5:c.1600G>A	p.Val534Met	p.V534M	ENST00000171111	NM_203500.1	534	Gtg/Atg	5/6	1	2	FACETS	0.934	0.881	0.989	1	0.995	1	CLONAL	2	TRUE	1	0.316715858919694	2		781	1007	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602358	10602358	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1371897807	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	361	726	0	ENST00000171111.5:c.1220C>T	p.Ala407Val	p.A407V	ENST00000171111	NM_203500.1	407	gCc/gTc	3/6	1	2	FACETS	1	0.978	1	1	0.996	1	CLONAL	2	TRUE	1	0.316715858919694	2		726	1082	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030342	11030344	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	225	492	0	ENST00000327064.4:c.1094_1096del	p.Gly365del	p.G365del	ENST00000327064	NM_199141.1	364	gaAGGa/gaa	9/16	1	2	FACETS	1	0.963	1	1	0.995	1	CLONAL	2	TRUE	1	0.316715858919694	2		492	682	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967792	18967792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	353	759	2	ENST00000262803.5:c.1931C>T	p.Pro644Leu	p.P644L	ENST00000262803	NM_002911.3	644	cCg/cTg	14/24	1	2	FACETS	1	0.954	1	1	0.996	1	CLONAL	2	TRUE	1	0.316715858919694	2		761	1108	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210420	36210420	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1299531345	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	91	581	0	ENST00000222270.7:c.413G>A	p.Arg138His	p.R138H	ENST00000222270	NM_014727.1	138	cGc/cAc	2/37	1	2	FACETS	0.732	0.649	0.82	0.732	0.649	0.82	SUBCLONAL	1	TRUE	1	0.316715858919694	2		581	785	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214082	36214082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	342	788	0	ENST00000222270.7:c.2908C>T	p.Arg970Trp	p.R970W	ENST00000222270	NM_014727.1	970	Cgg/Tgg	6/37	1	2	FACETS	1	0.963	1	1	0.996	1	CLONAL	2	TRUE	1	0.316715858919694	2		788	1058	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214749	36214749	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	261	557	0	ENST00000222270.7:c.3175G>A	p.Val1059Met	p.V1059M	ENST00000222270	NM_014727.1	1059	Gtg/Atg	8/37	1	2	FACETS	1	0.978	1	1	0.995	1	CLONAL	2	TRUE	1	0.316715858919694	2		557	762	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762855	40762855	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	84	576	0	ENST00000392038.2:c.153del	p.Leu52Ter	p.L52*	ENST00000392038	NM_001626.4	51	ccC/cc	3/14	1	2	FACETS	0.759	0.67	0.854	0.759	0.67	0.854	SUBCLONAL	1	TRUE	1	0.316715858919694	2		576	699	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765717	41765717	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1466592724	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	249	569	2	ENST00000301178.4:c.2593C>T	p.Arg865Cys	p.R865C	ENST00000301178	NM_021913.4	865	Cgc/Tgc	20/20	1	2	FACETS	1	0.948	1	1	0.995	1	CLONAL	2	TRUE	1	0.316715858919694	2		571	778	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752859	42752859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780261925	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	362	856	0	ENST00000222329.4:c.1405G>A	p.Gly469Ser	p.G469S	ENST00000222329	NM_006494.2	469	Ggc/Agc	4/4	1	2	FACETS	0.986	0.936	1	1	0.996	1	CLONAL	2	TRUE	1	0.316715858919694	2		856	1159	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796905	42796906	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	366	873	0	ENST00000575354.2:c.3365_3366del	p.Val1122GlyfsTer28	p.V1122Gfs*28	ENST00000575354	NM_015125.3	1121	acTGtg/actg	14/20	1	2	FACETS	0.934	0.886	0.983	1	0.996	1	CLONAL	2	TRUE	1	0.316715858919694	2		873	1237	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797778	42797778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778127638	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	124	709	1	ENST00000575354.2:c.3830G>A	p.Arg1277His	p.R1277H	ENST00000575354	NM_015125.3	1277	cGc/cAc	16/20	1	2	FACETS	0.775	0.7	0.855	0.775	0.7	0.855	SUBCLONAL	1	TRUE	1	0.316715858919694	2		710	1010	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724296	52724297	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	62	600	0	ENST00000322088.6:c.1429dup	p.Trp477LeufsTer34	p.W477Lfs*34	ENST00000322088	NM_014225.5	476	-/T	12/15	1	2	FACETS	0.591	0.51	0.679	0.591	0.51	0.679	SUBCLONAL	1	TRUE	1	0.316715858919694	2		600	663	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661664	227661664	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs761880048	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	262	572	9	ENST00000305123.5:c.1791del	p.His598ThrfsTer38	p.H598Tfs*38	ENST00000305123	NM_005544.2	597	ggG/gg	1/2	1	2	FACETS	1	0.975	1	1	0.995	1	CLONAL	2	TRUE	1	0.316715858919694	2		581	776	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31381402	31381402	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	126	291	0	ENST00000328111.2:c.1126+1G>A		p.X376_splice	ENST00000328111	NM_006892.3	376			1	2	FACETS	0.923	0.843	1	1	0.989	1	CLONAL	2	TRUE	1	0.316715858919694	2		291	431	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478739	57478739	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	133	353	0	ENST00000371085.3:c.325G>A	p.Ala109Thr	p.A109T	ENST00000371085	NM_000516.4	109	Gcc/Acc	5/13	1	2	FACETS	0.905	0.828	0.985	1	0.99	1	CLONAL	2	TRUE	1	0.316715858919694	2		353	464	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650824	12650824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773801570	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	48	294	1	ENST00000251849.4:c.331C>T	p.Arg111Cys	p.R111C	ENST00000251849	NM_002880.3	111	Cgc/Tgc	4/17	1	2	FACETS	0.687	0.582	0.803	0.687	0.582	0.803	SUBCLONAL	1	TRUE	1	0.316715858919694	2		295	441	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509085	66509085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	74	193	0	ENST00000273854.3:c.242del	p.Asn81MetfsTer24	p.N81Mfs*24	ENST00000273854	NM_004439.5	81	aAt/at	2/18	1	2	FACETS	0.865	0.766	0.969	1	0.981	1	CLONAL	2	TRUE	1	0.316715858919694	2		193	270	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	144	263	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.975	1	1	0.992	1	CLONAL	2	TRUE	1	0.316715858919694	2		263	400	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509927	187509927	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555931755	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	133	297	0	ENST00000441802.2:c.13586C>T	p.Ala4529Val	p.A4529V	ENST00000441802	NM_005245.3	4529	gCg/gTg	27/27	1	2	FACETS	0.95	0.87	1	1	0.99	1	CLONAL	2	TRUE	1	0.316715858919694	2		297	442	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540501	187540501	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	41	305	0	ENST00000441802.2:c.7239del	p.Ala2414ProfsTer9	p.A2414Pfs*9	ENST00000441802	NM_005245.3	2413	aaA/aa	10/27	1	2	FACETS	0.577	0.48	0.684	0.577	0.48	0.684	SUBCLONAL	1	TRUE	1	0.316715858919694	2		305	449	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1255459	1255459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777672180	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	105	813	1	ENST00000310581.5:c.3100C>T	p.Arg1034Cys	p.R1034C	ENST00000310581	NM_198253.2	1034	Cgc/Tgc	14/16	1	2	FACETS	0.535	0.477	0.596	0.535	0.477	0.596	SUBCLONAL	1	TRUE	1	0.316715858919694	2		814	1240	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278779	1278779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs576633619	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	262	866	1	ENST00000310581.5:c.2263G>A	p.Val755Ile	p.V755I	ENST00000310581	NM_198253.2	755	Gtc/Atc	6/16	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.316715858919694	2		867	1253	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468062	31468062	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	172	375	0	ENST00000344624.3:c.2350T>C	p.Tyr784His	p.Y784H	ENST00000344624		784	Tat/Cat	15/33	1	2	FACETS	0.914	0.846	0.985	1	0.992	1	CLONAL	2	TRUE	1	0.316715858919694	2		375	594	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963007	38963007	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	22	211	0	ENST00000357387.3:c.1537C>T	p.Arg513Ter	p.R513*	ENST00000357387	NM_152756.3	513	Cga/Tga	17/38	1	2	FACETS	0.473	0.366	0.596	0.473	0.366	0.596	SUBCLONAL	1	TRUE	1	0.316715858919694	2		211	294	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685331	86685331	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	62	110	0	ENST00000274376.6:c.3047G>A	p.Arg1016His	p.R1016H	ENST00000274376	NM_002890.2	1016	cGt/cAt	24/25	1	2	FACETS	1	0.955	1	1	0.983	1	CLONAL	2	TRUE	1	0.316715858919694	2		110	166	SUCCESS
APC	324	MSKCC	GRCh37	5	112116587	112116587	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	39	253	0	ENST00000257430.4:c.636del	p.Lys212AsnfsTer7	p.K212Nfs*7	ENST00000257430	NM_000038.5	211	gAa/ga	6/16	1	2	FACETS	0.69	0.573	0.819	0.69	0.573	0.819	SUBCLONAL	1	TRUE	1	0.316715858919694	2		253	357	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149436912	149436912	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372068592	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	262	610	0	ENST00000286301.3:c.2257C>T	p.Arg753Trp	p.R753W	ENST00000286301	NM_005211.3	753	Cgg/Tgg	17/22	1	2	FACETS	0.993	0.933	1	1	0.995	1	CLONAL	2	TRUE	1	0.316715858919694	2		610	833	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051013	180051013	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	289	712	0	ENST00000261937.6:c.1470G>T	p.Arg490Ser	p.R490S	ENST00000261937	NM_182925.4	490	agG/agT	11/30	NA	2	FACETS	0.967	0.911	1			1	INDETERMINATE	2	TRUE	NA	0.316715858919694	2		712	944	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168725	32168725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1311075766	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	281	649	0	ENST00000375023.3:c.4198C>T	p.Arg1400Cys	p.R1400C	ENST00000375023	NM_004557.3	1400	Cgc/Tgc	23/30	1	2	FACETS	0.958	0.902	1	1	0.995	1	CLONAL	2	TRUE	1	0.316715858919694	2		649	926	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288983	33288983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1026215586	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	89	453	0	ENST00000374542.5:c.569G>A	p.Arg190His	p.R190H	ENST00000374542	NM_001141970.1	190	cGt/cAt	3/8	1	2	FACETS	0.766	0.679	0.859	0.766	0.679	0.859	SUBCLONAL	1	TRUE	1	0.316715858919694	2		453	734	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955064	93955064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151105732	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	57	222	0	ENST00000369303.4:c.2834C>T	p.Thr945Met	p.T945M	ENST00000369303	NM_004440.3	945	aCg/aTg	16/17	1	2	FACETS	0.962	0.829	1	0.962	0.829	1	CLONAL	1	TRUE	1	0.316715858919694	2		222	374	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900081	151900081	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	155	265	0	ENST00000262189.6:c.4030del	p.Ile1344Ter	p.I1344*	ENST00000262189	NM_170606.2	1344	Ata/ta	26/59	1	2	FACETS	1	0.941	1	1	0.992	1	CLONAL	2	TRUE	1	0.316715858919694	2		265	478	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840621	36840621	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	240	542	0	ENST00000358127.4:c.1112A>G	p.Tyr371Cys	p.Y371C	ENST00000358127	NM_001280556.1	371	tAt/tGt	10/10	1	2	FACETS	1	0.982	1	1	0.995	1	CLONAL	2	TRUE	1	0.316715858919694	2		542	680	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760024	133760024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	289	675	0	ENST00000318560.5:c.2352del	p.Arg785GlyfsTer3	p.R785Gfs*3	ENST00000318560	NM_005157.4	783	Ccc/cc	11/11	1	2	FACETS	0.97	0.914	1	1	0.995	1	CLONAL	2	TRUE	1	0.316715858919694	2		675	941	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413100	139413100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201236538	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	328	699	0	ENST00000277541.6:c.1042G>A	p.Ala348Thr	p.A348T	ENST00000277541	NM_017617.3	348	Gcc/Acc	6/34	1	2	FACETS	1	0.97	1	1	0.996	1	CLONAL	2	TRUE	1	0.316715858919694	2		699	1000	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411822	63411822	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	147	760	0	ENST00000330258.3:c.1345G>A	p.Ala449Thr	p.A449T	ENST00000330258	NM_152424.3	449	Gcc/Acc	2/2	0.316715858919694	1	FACETS	0.921	0.841	1	0.921	0.841	1	CLONAL	1	TRUE	0	0.316715858919694	1		760	848	SUCCESS
AR	367	MSKCC	GRCh37	X	66766585	66766585	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	138	666	1	ENST00000374690.3:c.1597G>A	p.Gly533Arg	p.G533R	ENST00000374690	NM_000044.3	533	Gga/Aga	1/8	0.316715858919694	1	FACETS	0.994	0.906	1	0.994	0.906	1	CLONAL	1	TRUE	0	0.316715858919694	1		667	738	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361128	70361133	+	inframe_deletion	In_Frame_Del	DEL	CAGCAG	CAGCAG	-	novel	NA	P-0045984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	77	604	0	ENST00000374080.3:c.6324_6329del	p.Gln2114_Gln2115del	p.Q2114_Q2115del	ENST00000374080		2106	CAGCAG/-	43/45	0.316715858919694	1	FACETS	0.58	0.509	0.657	0.58	0.509	0.657	SUBCLONAL	1	TRUE	0	0.316715858919694	1		604	705	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041704	42041704	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	164	358	0	ENST00000219905.7:c.5899del	p.Gln1967ArgfsTer2	p.Q1967Rfs*2	ENST00000219905	NM_001164273.1	1967	Cag/ag	17/24	0.648970433889431	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.654125532143328	2		358	245	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683564	29683564	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0045985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	103	191	0	ENST00000356175.3:c.7639A>T	p.Lys2547Ter	p.K2547*	ENST00000356175	NM_000267.3	2547	Aaa/Taa	51/57	0.646452045578587	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.654125532143328	2		191	141	SUCCESS
APC	324	MSKCC	GRCh37	5	112176628	112176628	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs748063409	NA	P-0045985-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	125	182	0	ENST00000257430.4:c.5337A>G	p.Ile1779Met	p.I1779M	ENST00000257430	NM_000038.5	1779	atA/atG	16/16	0.654125532143328	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	2	0.654125532143328	4		182	292	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	49	151	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.667321357240731	2		151	133	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828584	72828584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763156400	NA	P-0045986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	263	654	0	ENST00000268489.5:c.7997C>T	p.Pro2666Leu	p.P2666L	ENST00000268489	NM_006885.3	2666	cCg/cTg	9/10	0.141009767474505	3	FACETS	1	0.99	1	0.629	0.591	0.667	INDETERMINATE	1	TRUE	1	0.667321357240731	3		654	836	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916734	48916734	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0045986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	146	276	0	ENST00000267163.4:c.266del		p.X89_splice	ENST00000267163	NM_000321.2	89			0.667321357240731	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.667321357240731	1		276	291	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715848	117715848	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	169	305	0	ENST00000368508.3:c.910A>G	p.Arg304Gly	p.R304G	ENST00000368508	NM_002944.2	304	Aga/Gga	9/43	0.667321357240731	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.667321357240731	1		305	309	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0045987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	188	696	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.751267769322699	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.751267769322699	1		696	303	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553422	29553451	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CAAATATATGTCTTCCACCCTTGACTCTCA	CAAATATATGTCTTCCACCCTTGACTCTCA	-	novel	NA	P-0045987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	180	292	0	ENST00000356175.3:c.2002-31_2002-2del		p.X668_splice	ENST00000356175	NM_000267.3	668			0.751267769322699	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.751267769322699	1		292	239	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630662	158630662	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045987-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	103	272	0	ENST00000263640.3:c.581C>G	p.Ser194Cys	p.S194C	ENST00000263640	NM_001105.4	194	tCt/tGt	6/11	1	2	FACETS	0.816	0.738	0.897	0.816	0.738	0.897	CLONAL	1	TRUE	1	0.751267769322699	2		272	336	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0045988-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	28	81	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	1	2	FACETS	0.747	0.603	0.908	0.747	0.603	0.908	CLONAL	1	TRUE	1	0.430811374316149	2		81	174	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577576	7577578	+	inframe_deletion	In_Frame_Del	DEL	GTT	GTT	-	novel	NA	P-0045988-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	524	495	0	ENST00000269305.4:c.703_705del	p.Asn235del	p.N235del	ENST00000269305	NM_001126112.2	235	AAC/-	7/11	NA	2	FACETS	0.982	0.944	1			1	INDETERMINATE	2	TRUE	NA	0.430811374316149	2		495	1238	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0045989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	67	310	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.905	0.79	1	0.905	0.79	1	CLONAL	1	TRUE	1	0.343415575261417	2		310	431	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272512	142272512	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	32	374	0	ENST00000350721.4:c.2603C>T	p.Thr868Ile	p.T868I	ENST00000350721	NM_001184.3	868	aCc/aTc	12/47	1	2	FACETS	0.467	0.379	0.566	0.467	0.379	0.566	SUBCLONAL	1	TRUE	1	0.343415575261417	2		374	399	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321349	1321349	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	45	448	0	ENST00000400841.2:c.406G>C	p.Val136Leu	p.V136L	ENST00000400841		136	Gtg/Ctg	4/6	1	2	FACETS	0.408	0.342	0.481	0.408	0.342	0.481	SUBCLONAL	1	TRUE	1	0.343415575261417	2		448	643	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0045990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	58	302	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.677862806921605	3	FACETS	0.756	0.654	0.865	0.378	0.327	0.433	SUBCLONAL	1	TRUE	1	0.677862806921605	3		302	303	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0045990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	207	528	2	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.66412019644964	2	FACETS	0.948	0.885	1	0.474	0.442	0.507	CLONAL	1	TRUE	0	0.677862806921605	2		530	644	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276250	15276250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747223569	NA	P-0045990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	402	605	2	ENST00000263388.2:c.5744G>A	p.Arg1915His	p.R1915H	ENST00000263388	NM_000435.2	1915	cGc/cAc	31/33	0.677862806921605	3	FACETS	0.909	0.869	0.948	0.909	0.869	0.948	CLONAL	2	TRUE	1	0.677862806921605	3		607	874	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911520	134911520	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756316035	NA	P-0045990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	179	385	0	ENST00000398015.3:c.1985G>A	p.Arg662His	p.R662H	ENST00000398015	NM_004441.4	662	cGt/cAt	11/16	0.66412019644964	2	FACETS	1	0.982	1	0.58	0.54	0.621	CLONAL	1	TRUE	0	0.677862806921605	2		385	455	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357070	70357070	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773713291	NA	P-0045990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	208	692	0	ENST00000374080.3:c.5585G>A	p.Arg1862His	p.R1862H	ENST00000374080		1862	cGc/cAc	39/45	0.168959785212231	3	FACETS	0.894	0.831	0.96	0.298	0.277	0.32	INDETERMINATE	1	TRUE	0	0.677862806921605	3		692	919	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938961	76938961	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	102	395	0	ENST00000373344.5:c.1787C>G	p.Ser596Cys	p.S596C	ENST00000373344	NM_000489.3	596	tCt/tGt	9/35	0.168959785212231	3	FACETS	0.787	0.716	0.859	0.525	0.477	0.573	INDETERMINATE	2	TRUE	0	0.677862806921605	3		395	256	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073621	8073621	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	274	321	0	ENST00000377482.5:c.1038G>A	p.Met346Ile	p.M346I	ENST00000377482	NM_018948.3	346	atG/atA	4/4	0.673822503244964	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.677862806921605	2		321	397	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604683	48604683	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	86	271	0	ENST00000342988.3:c.1506del	p.Met503Ter	p.M503*	ENST00000342988	NM_005359.5	502	aGg/ag	12/12	0.675582355881802	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.677862806921605	1		271	157	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275767	38275767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121909637	NA	P-0045990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	54	432	0	ENST00000425967.3:c.1502G>A	p.Arg501His	p.R501H	ENST00000425967	NM_001174067.1	501	cGc/cAc	11/19	0.675582355881802	1	FACETS	0.343	0.295	0.395	0.343	0.295	0.395	SUBCLONAL	1	TRUE	0	0.677862806921605	1		432	307	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776321	76776321	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	120	441	0	ENST00000373344.5:c.7145T>A	p.Leu2382His	p.L2382H	ENST00000373344	NM_000489.3	2382	cTt/cAt	34/35	0.168959785212231	3	FACETS	1	0.953	1	0.358	0.326	0.392	INDETERMINATE	1	TRUE	0	0.677862806921605	3		441	441	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0045991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	44	456	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.467	0.396	0.543	0.467	0.396	0.543	SUBCLONAL	1	TRUE	1	0.966873606663672	2		456	195	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0045991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	82	549	3	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	0.244	0.215	0.276	0.244	0.215	0.276	SUBCLONAL	1	TRUE	1	0.966873606663672	2		552	694	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	191	482	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.568	0.527	0.611	0.568	0.527	0.611	SUBCLONAL	1	TRUE	1	0.966873606663672	2		483	695	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	154	868	3	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.272	0.248	0.297	0.272	0.248	0.297	SUBCLONAL	1	TRUE	1	0.966873606663672	2		871	1172	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	54	283	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.26	0.223	0.302	0.26	0.223	0.302	SUBCLONAL	1	TRUE	1	0.966873606663672	2		283	429	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0045991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	13	405	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	1	2	FACETS	0.046	0.032	0.063	0.046	0.032	0.063	SUBCLONAL	1	TRUE	1	0.966873606663672	2		405	581	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0045991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	94	478	0	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.296	0.264	0.331	0.296	0.264	0.331	SUBCLONAL	1	TRUE	1	0.966873606663672	2		478	656	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560514	65560514	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	139	365	0	ENST00000358664.4:c.83A>G	p.His28Arg	p.H28R	ENST00000358664	NM_002382.4	28	cAt/cGt	3/5	1	2	FACETS	0.531	0.486	0.579	0.531	0.486	0.579	SUBCLONAL	1	TRUE	1	0.966873606663672	2		365	541	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0045991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	36	305	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.191	0.157	0.23	0.191	0.157	0.23	SUBCLONAL	1	TRUE	1	0.966873606663672	2		305	389	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372092	55372093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0045991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	75	332	0	ENST00000297316.4:c.788dup	p.Glu264GlyfsTer101	p.E264Gfs*101	ENST00000297316	NM_022454.3	261	ggc/ggCc	2/2	1	2	FACETS	0.248	0.217	0.281	0.248	0.217	0.281	SUBCLONAL	1	TRUE	1	0.966873606663672	2		332	626	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100043	157100043	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1455234951	NA	P-0045991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	14	14	0	ENST00000346085.5:c.980G>C	p.Gly327Ala	p.G327A	ENST00000346085	NM_020732.3	327	gGa/gCa	1/20	1	2	FACETS	0.591	0.443	0.756	0.591	0.443	0.756	SUBCLONAL	1	TRUE	1	0.966873606663672	2		14	49	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624294	89624295	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	85	303	0	ENST00000371953.3:c.69dup	p.Asp24ArgfsTer20	p.D24Rfs*20	ENST00000371953	NM_000314.4	23	tta/ttAa	1/9	1	2	FACETS	0.459	0.408	0.513	0.459	0.408	0.513	SUBCLONAL	1	TRUE	1	0.966873606663672	2		303	383	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67646013	67646014	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs1470210640	NA	P-0045991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	125	350	4	ENST00000264010.4:c.950_951del	p.Thr317ArgfsTer91	p.T317Rfs*91	ENST00000264010	NM_006565.3	314	aAC/a	4/12	1	2	FACETS	0.502	0.457	0.55	0.502	0.457	0.55	SUBCLONAL	1	TRUE	1	0.966873606663672	2		354	515	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047942	180047942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138368337	NA	P-0045991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	297	830	2	ENST00000261937.6:c.2233C>T	p.Arg745Cys	p.R745C	ENST00000261937	NM_182925.4	745	Cgc/Tgc	15/30	1	2	FACETS	0.552	0.52	0.585	0.552	0.52	0.585	SUBCLONAL	1	TRUE	1	0.966873606663672	2		832	1113	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	288	780	2	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	0.614	0.578	0.65	0.614	0.578	0.65	SUBCLONAL	1	TRUE	1	0.966873606663672	2		782	971	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624290	89624290	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660420	NA	P-0045991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	89	297	0	ENST00000371953.3:c.64G>T	p.Asp22Tyr	p.D22Y	ENST00000371953	NM_000314.4	22	Gac/Tac	1/9	1	2	FACETS	0.496	0.443	0.552	0.496	0.443	0.552	SUBCLONAL	1	TRUE	1	0.966873606663672	2		297	371	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361098	70361103	+	inframe_deletion	In_Frame_Del	DEL	CAGCAG	CAGCAG	-	rs766775649	NA	P-0045991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	102	471	1	ENST00000374080.3:c.6303_6308del	p.Gln2114_Gln2115del	p.Q2114_Q2115del	ENST00000374080		2096	CAGCAG/-	43/45	1	2	FACETS	0.365	0.327	0.405	0.365	0.327	0.405	SUBCLONAL	1	TRUE	1	0.966873606663672	2		472	578	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435296	18435296	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533181600	NA	P-0045991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	37	130	0	ENST00000266497.5:c.281G>A	p.Arg94His	p.R94H	ENST00000266497		94	cGt/cAt	1/31	1	2	FACETS	0.397	0.33	0.469	0.397	0.33	0.469	SUBCLONAL	1	TRUE	1	0.966873606663672	2		130	193	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653845	89653845	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	23	51	0	ENST00000371953.3:c.143A>G	p.Asn48Ser	p.N48S	ENST00000371953	NM_000314.4	48	aAc/aGc	2/9	1	2	FACETS	0.501	0.399	0.613	0.501	0.399	0.613	SUBCLONAL	1	TRUE	1	0.966873606663672	2		51	95	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434491	49434491	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	97	814	0	ENST00000301067.7:c.7062del	p.Ala2355ProfsTer29	p.A2355Pfs*29	ENST00000301067	NM_003482.3	2354	ccT/cc	31/54	1	2	FACETS	0.227	0.202	0.254	0.227	0.202	0.254	SUBCLONAL	1	TRUE	1	0.966873606663672	2		814	883	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120791128	120791128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	133	673	0	ENST00000257552.2:c.707C>T	p.Ala236Val	p.A236V	ENST00000257552	NM_002442.3	236	gCc/gTc	10/15	1	2	FACETS	0.284	0.257	0.312	0.284	0.257	0.312	SUBCLONAL	1	TRUE	1	0.966873606663672	2		673	970	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892212	9892212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555488119	NA	P-0045991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	154	525	2	ENST00000330684.3:c.2278G>A	p.Gly760Ser	p.G760S	ENST00000330684	NM_001134407.1	760	Ggt/Agt	11/13	1	2	FACETS	0.527	0.485	0.572	0.527	0.485	0.572	SUBCLONAL	1	TRUE	1	0.966873606663672	2		527	604	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50820822	50820822	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	23	84	0	ENST00000398568.2:c.1997T>C	p.Val666Ala	p.V666A	ENST00000398568	NM_001042412.1	666	gTg/gCg	12/18	1	2	FACETS	0.35	0.276	0.433	0.35	0.276	0.433	SUBCLONAL	1	TRUE	1	0.966873606663672	2		84	136	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828914	72828914	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	188	505	0	ENST00000268489.5:c.7667del	p.Ala2556GlyfsTer56	p.A2556Gfs*56	ENST00000268489	NM_006885.3	2556	gCg/gg	9/10	1	2	FACETS	0.617	0.573	0.663	0.617	0.573	0.663	SUBCLONAL	1	TRUE	1	0.966873606663672	2		505	630	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121037	3121037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772471502	NA	P-0045991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	202	760	1	ENST00000078429.4:c.940G>A	p.Val314Met	p.V314M	ENST00000078429	NM_002067.2	314	Gtg/Atg	7/7	1	2	FACETS	0.505	0.468	0.542	0.505	0.468	0.542	SUBCLONAL	1	TRUE	1	0.966873606663672	2		761	828	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128030455	128030455	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	167	367	0	ENST00000285398.2:c.1813A>G	p.Ile605Val	p.I605V	ENST00000285398	NM_000122.1	605	Atc/Gtc	11/15	1	2	FACETS	0.609	0.563	0.657	0.609	0.563	0.657	SUBCLONAL	1	TRUE	1	0.966873606663672	2		367	567	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685322	86685322	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	49	129	0	ENST00000274376.6:c.3038G>C	p.Ser1013Thr	p.S1013T	ENST00000274376	NM_002890.2	1013	aGt/aCt	24/25	1	2	FACETS	0.557	0.479	0.64	0.557	0.479	0.64	SUBCLONAL	1	TRUE	1	0.966873606663672	2		129	182	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864332	151864332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1251668458	NA	P-0045991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	104	308	0	ENST00000262189.6:c.9649C>T	p.Arg3217Cys	p.R3217C	ENST00000262189	NM_170606.2	3217	Cgt/Tgt	42/59	1	2	FACETS	0.431	0.387	0.477	0.431	0.387	0.477	SUBCLONAL	1	TRUE	1	0.966873606663672	2		308	499	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93657859	93657859	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	81	412	0	ENST00000375746.1:c.1885T>A	p.Tyr629Asn	p.Y629N	ENST00000375746	NM_001174167.1	629	Tac/Aac	14/14	1	2	FACETS	0.261	0.229	0.294	0.261	0.229	0.294	SUBCLONAL	1	TRUE	1	0.966873606663672	2		412	643	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250028	110250028	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	60	620	0	ENST00000374672.4:c.647A>C	p.Gln216Pro	p.Q216P	ENST00000374672	NM_004235.4	216	cAg/cCg	3/5	1	2	FACETS	0.166	0.142	0.192	0.166	0.142	0.192	SUBCLONAL	1	TRUE	1	0.966873606663672	2		620	747	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224226	53224226	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556835545	NA	P-0045991-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	141	746	1	ENST00000375401.3:c.3325G>A	p.Gly1109Ser	p.G1109S	ENST00000375401	NM_004187.3	1109	Ggc/Agc	22/26	1	2	FACETS	0.277	0.252	0.304	0.277	0.252	0.304	SUBCLONAL	1	TRUE	1	0.966873606663672	2		747	1052	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	97	151	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.767739306306576	2		151	250	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0045992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	47	310	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.68	0.583	0.784	0.68	0.583	0.784	SUBCLONAL	1	TRUE	1	0.767739306306576	2		310	180	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0045993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	504	744	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.717127168541125	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.717127168541125	1		745	874	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644715	134644715	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs556035012	NA	P-0045993-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	271	399	0	ENST00000398015.3:c.116C>T	p.Ala39Val	p.A39V	ENST00000398015	NM_004441.4	39	gCg/gTg	2/16	1	2	FACETS	0.939	0.884	0.995	0.939	0.884	0.995	CLONAL	1	TRUE	1	0.717127168541125	2		399	805	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587780070	NA	P-0045994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	209	656	0	ENST00000269305.4:c.535C>G	p.His179Asp	p.H179D	ENST00000269305	NM_001126112.2	179	Cat/Gat	5/11	0.570084477438371	1	FACETS	0.926	0.866	0.987	0.926	0.866	0.987	CLONAL	1	TRUE	0	0.570084477438371	1		656	566	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304151	65304160	+	frameshift_variant	Frame_Shift_Del	DEL	ACAAATCTGA	ACAAATCTGA	-	novel	NA	P-0045994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	98	134	0	ENST00000342505.4:c.2955_2964del	p.Gln986ArgfsTer29	p.Q986Rfs*29	ENST00000342505	NM_002227.2	985	gtTCAGATTTGT/gt	21/25	0.570084477438371	1	FACETS	0.866	0.783	0.95	0.866	0.783	0.95	CLONAL	1	TRUE	0	0.570084477438371	1		134	284	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344339	118344368	+	inframe_deletion	In_Frame_Del	DEL	CTCCGGCAGAGCCATTTTCATCAAGTAGTC	CTCCGGCAGAGCCATTTTCATCAAGTAGTC	-	novel	NA	P-0045994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	69	215	0	ENST00000534358.1:c.2467_2496del	p.Pro823_Pro832del	p.P823_P832del	ENST00000534358	NM_005933.3	822	gCTCCGGCAGAGCCATTTTCATCAAGTAGTCct/gct	3/36	NA	2	FACETS	0.725	0.636	0.82			1	INDETERMINATE	1	TRUE	NA	0.570084477438371	2		215	334	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41209099	41209100	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0045994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	161	428	0	ENST00000357654.3:c.5246_5247del	p.Pro1749GlnfsTer80	p.P1749Qfs*80	ENST00000357654	NM_007294.3	1749	cCA/c	19/23	0.570084477438371	1	FACETS	0.726	0.67	0.784	0.726	0.67	0.784	SUBCLONAL	1	TRUE	0	0.570084477438371	1		428	556	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371756	45371757	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	129	162	0	ENST00000262160.6:c.1234dup	p.Cys412LeufsTer28	p.C412Lfs*28	ENST00000262160	NM_005901.5	412	tgc/tTgc	10/11	0.570084477438371	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.570084477438371	1		162	309	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985647	60985647	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	10	71	0	ENST00000333681.4:c.253G>T	p.Ala85Ser	p.A85S	ENST00000333681		85	Gcg/Tcg	2/3	0.570084477438371	1	FACETS	0.322	0.22	0.445	0.322	0.22	0.445	SUBCLONAL	1	TRUE	0	0.570084477438371	1		71	78	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5463115	5463115	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	63	102	0	ENST00000381577.3:c.676A>C	p.Ile226Leu	p.I226L	ENST00000381577	NM_014143.3	226	Atc/Ctc	4/7	0.570084477438371	1	FACETS	0.873	0.77	0.98	0.873	0.77	0.98	CLONAL	1	TRUE	0	0.570084477438371	1		102	181	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0045995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	978	712	1	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	0.786883544129349	4	FACETS	1	0.992	1			1	CLONAL	4	TRUE	NA	0.868529995089494	4		713	1049	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1620984	1620984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772853413	NA	P-0045995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1433	269	870	1	ENST00000344749.5:c.1076C>T	p.Ser359Phe	p.S359F	ENST00000344749	NM_001136139.2	359	tCc/tTc	13/19	0.868529995089494	5	FACETS	0.838	0.783	0.895	0.21	0.195	0.224	CLONAL	1	TRUE	1	0.868529995089494	5		871	1702	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448319	56448319	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	278	646	0	ENST00000407977.2:c.328G>T	p.Glu110Ter	p.E110*	ENST00000407977		110	Gag/Tag	3/10	0.868529995089494	5	FACETS	0.984	0.922	1	0.246	0.23	0.262	CLONAL	1	TRUE	1	0.868529995089494	5		646	1498	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911010	32911010	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	109	112	0	ENST00000380152.3:c.2518A>G	p.Met840Val	p.M840V	ENST00000380152		840	Atg/Gtg	11/27	0.851236248158443	3	FACETS	0.976	0.935	1	0.976	0.935	1	CLONAL	3	TRUE	0	0.868529995089494	3		112	123	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076799	72076799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	266	348	0	ENST00000357731.5:c.698G>A	p.Gly233Asp	p.G233D	ENST00000357731	NM_173808.2	233	gGc/gAc	5/7	0.769611910295851	4	FACETS	0.978	0.926	1	0.978	0.926	1	CLONAL	2	TRUE	2	0.868529995089494	4		348	585	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111957641	111957641	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	222	469	0	ENST00000375549.3:c.10C>G	p.Leu4Val	p.L4V	ENST00000375549	NM_003002.3	4	Ctc/Gtc	1/4	0.868529995089494	5	FACETS	1	0.96	1	0.348	0.324	0.374	CLONAL	1	TRUE	2	0.868529995089494	5		469	1126	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218967	133218967	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1198380388	NA	P-0045995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	540	682	0	ENST00000320574.5:c.4969A>G	p.Ile1657Val	p.I1657V	ENST00000320574	NM_006231.2	1657	Att/Gtt	38/49	0.868529995089494	3	FACETS	0.966	0.934	0.998	0.966	0.934	0.998	CLONAL	2	TRUE	1	0.868529995089494	3		682	923	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041174	29041174	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	151	409	0	ENST00000282397.4:c.254G>C	p.Gly85Ala	p.G85A	ENST00000282397	NM_002019.4	85	gGc/gCc	3/30	0.851236248158443	3	FACETS	0.915	0.841	0.991	0.305	0.28	0.331	CLONAL	1	TRUE	0	0.868529995089494	3		409	545	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486062	29486062	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs4795581	NA	P-0045995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	16	73	0	ENST00000356175.3:c.239A>G	p.Tyr80Cys	p.Y80C	ENST00000356175	NM_000267.3	80	tAt/tGt	3/57	0.868529995089494	5	FACETS	0.84	0.63	1	0.21	0.157	0.271	CLONAL	1	TRUE	1	0.868529995089494	5		73	101	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152128	11152130	+	inframe_deletion	In_Frame_Del	DEL	AGC	AGC	-	rs754509103	NA	P-0045995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	594	474	0	ENST00000358026.2:c.4414_4416del	p.Gln1472del	p.Q1472del	ENST00000358026	NM_001128849.1	1471	aAGCag/aag	31/36	0.868529995089494	5	FACETS	0.969	0.943	0.993	0.969	0.943	0.993	CLONAL	4	TRUE	1	0.868529995089494	5		474	813	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45864787	45864787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	210	601	0	ENST00000391945.4:c.1232C>T	p.Ala411Val	p.A411V	ENST00000391945	NM_000400.3	411	gCc/gTc	12/23	0.868529995089494	5	FACETS	0.857	0.794	0.923	0.214	0.198	0.231	CLONAL	1	TRUE	1	0.868529995089494	5		601	1299	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519882	29519882	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs565743321	NA	P-0045995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	512	475	0	ENST00000389048.3:c.1689C>A	p.Asn563Lys	p.N563K	ENST00000389048	NM_004304.4	563	aaC/aaA	9/29	0.841348852568028	4	FACETS	0.935	0.906	0.964	0.935	0.906	0.964	CLONAL	3	TRUE	1	0.868529995089494	4		475	785	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225561	225561	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs933414586	NA	P-0045995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	37	135	0	ENST00000264932.6:c.340A>G	p.Met114Val	p.M114V	ENST00000264932	NM_004168.2	114	Atg/Gtg	4/15	0.714304576608432	5	FACETS	0.981	0.817	1	0.327	0.272	0.387	CLONAL	1	TRUE	2	0.868529995089494	5		135	200	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94128997	94128997	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	157	304	0	ENST00000369303.4:c.63T>G	p.Phe21Leu	p.F21L	ENST00000369303	NM_004440.3	21	ttT/ttG	1/17	0.74651699223287	4	FACETS	0.955	0.877	1	0.478	0.438	0.519	CLONAL	1	TRUE	2	0.868529995089494	4		304	707	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372025	55372025	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	497	288	0	ENST00000297316.4:c.715G>T	p.Ala239Ser	p.A239S	ENST00000297316	NM_022454.3	239	Gcc/Tcc	2/2	0.796562846535282	4	FACETS	0.953	0.923	0.982	0.953	0.923	0.982	CLONAL	3	TRUE	1	0.868529995089494	4		288	748	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608226	100608226	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045995-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	135	211	0	ENST00000308731.7:c.1864G>C	p.Ala622Pro	p.A622P	ENST00000308731	NM_000061.2	622	Gct/Cct	18/19	0.868529995089494	3	FACETS	0.814	0.743	0.887			1	CLONAL	1	TRUE	NA	0.868529995089494	3		211	548	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	39	236	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	FALSE	1	0.455528265370726	2		236	163	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	699	514	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	0.181456192156258	2	FACETS	1	0.996	1	1	0.996	1	INDETERMINATE	2	FALSE	0	0.455528265370726	2		514	1323	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100425	8100425	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1349	111	881	4	ENST00000346208.3:c.404del	p.Pro135ArgfsTer60	p.P135Rfs*60	ENST00000346208		133	taC/ta	3/6	0.455528265370726	4	FACETS	0.486	0.435	0.54	0.162	0.145	0.18	SUBCLONAL	1	FALSE	1	0.455528265370726	4		885	1460	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588875	29588875	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	30	186	0	ENST00000356175.3:c.4661G>T	p.Arg1554Met	p.R1554M	ENST00000356175	NM_000267.3	1554	aGg/aTg	34/57	1	2	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	FALSE	1	0.455528265370726	2		186	127	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866468	42866468	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs61735790	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	201	710	0	ENST00000398585.3:c.164A>G	p.His55Arg	p.H55R	ENST00000398585	NM_001135099.1	55	cAt/cGt	3/14	0.289414792506466	1	FACETS	0.921	0.856	0.988	0.921	0.856	0.988	CLONAL	1	FALSE	0	0.455528265370726	1		710	740	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	359996	359996	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324067997	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	115	709	0	ENST00000262320.3:c.1093C>T	p.Arg365Trp	p.R365W	ENST00000262320	NM_003502.3	365	Cgg/Tgg	4/11	0.289414792506466	1	FACETS	0.419	0.377	0.464	0.419	0.377	0.464	SUBCLONAL	1	FALSE	0	0.455528265370726	1		709	931	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304375	91304375	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	47	300	0	ENST00000355112.3:c.1772G>T	p.Arg591Leu	p.R591L	ENST00000355112	NM_000057.2	591	cGg/cTg	7/22	0.289414792506466	1	FACETS	0.731	0.624	0.847	0.731	0.624	0.847	SUBCLONAL	1	FALSE	0	0.455528265370726	1		300	218	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs878854073	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	105	415	0	ENST00000269305.4:c.673-1G>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.455528265370726	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	0	0.455528265370726	1		415	325	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803117	1803117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1330260382	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	156	713	0	ENST00000260795.2:c.469G>A	p.Glu157Lys	p.E157K	ENST00000260795		157	Gag/Aag	4/17	1	2	FACETS	0.616	0.563	0.672	0.616	0.563	0.672	SUBCLONAL	1	FALSE	1	0.455528265370726	2		713	1111	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878785	151878785	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	88	369	0	ENST00000262189.6:c.6160C>G	p.Gln2054Glu	p.Q2054E	ENST00000262189	NM_170606.2	2054	Cag/Gag	36/59	0.26605968458543	1	FACETS	1	0.982	1	1	0.982	1	INDETERMINATE	1	FALSE	0	0.455528265370726	1		369	208	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239382	123239382	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	30	326	0	ENST00000358487.5:c.2455G>T	p.Val819Phe	p.V819F	ENST00000358487	NM_000141.4	819	Gtt/Ttt	18/18	0.289414792506466	1	FACETS	0.737	0.603	0.884	0.737	0.603	0.884	SUBCLONAL	1	FALSE	0	0.455528265370726	1		326	138	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156655	2156655	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs553443857	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	202	648	0	ENST00000434045.2:c.267C>A	p.Cys89Ter	p.C89*	ENST00000434045	NM_001127598.1	89	tgC/tgA	3/5	0.455528265370726	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	0	0.455528265370726	1		648	645	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115514	108115514	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	22	175	1	ENST00000278616.4:c.663-1G>T		p.X221_splice	ENST00000278616	NM_000051.3	221			1	2	FACETS	0.956	0.755	1	0.956	0.755	1	CLONAL	1	FALSE	1	0.455528265370726	2		176	101	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534755	18534755	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	89	359	0	ENST00000266497.5:c.1813G>T	p.Val605Leu	p.V605L	ENST00000266497		605	Gta/Tta	12/31	0.455528265370726	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	0	0.455528265370726	1		359	263	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864309	57864309	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	153	621	1	ENST00000228682.2:c.1786G>T	p.Ala596Ser	p.A596S	ENST00000228682	NM_005269.2	596	Gcc/Tcc	12/12	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.455528265370726	2		622	592	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2097785	2097785	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	158	550	0	ENST00000219066.1:c.64A>C	p.Ser22Arg	p.S22R	ENST00000219066	NM_002528.5	22	Agc/Cgc	1/6	0.289414792506466	1	FACETS	0.569	0.521	0.62	0.569	0.521	0.62	SUBCLONAL	1	FALSE	0	0.455528265370726	1		550	941	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778938	3778938	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1481703137	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	125	541	0	ENST00000262367.5:c.6110G>A	p.Arg2037Lys	p.R2037K	ENST00000262367	NM_004380.2	2037	aGg/aAg	31/31	0.289414792506466	1	FACETS	0.894	0.814	0.977	0.894	0.814	0.977	CLONAL	1	FALSE	0	0.455528265370726	1		541	474	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821594	72821611	+	inframe_deletion	In_Frame_Del	DEL	GCCGCCGCCGCCGCCGCC	GCCGCCGCCGCCGCCGCC	-	rs374416547	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	19	81	0	ENST00000268489.5:c.10564_10581del	p.Gly3522_Gly3527del	p.G3522_G3527del	ENST00000268489	NM_006885.3	3522	GGCGGCGGCGGCGGCGGC/-	10/10	0.433985747822251	2	FACETS	0.787	0.607	0.992	0.393	0.303	0.496	CLONAL	1	FALSE	0	0.455528265370726	2		81	106	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487529	38487529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773378786	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	192	534	1	ENST00000254066.5:c.59C>T	p.Pro20Leu	p.P20L	ENST00000254066	NM_000964.3	20	cCg/cTg	2/9	1	2	FACETS	0.959	0.888	1	0.959	0.888	1	CLONAL	1	FALSE	1	0.455528265370726	2		535	879	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243882	41243882	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	73	440	0	ENST00000357654.3:c.3666G>T	p.Glu1222Asp	p.E1222D	ENST00000357654	NM_007294.3	1222	gaG/gaT	10/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.455528265370726	2		440	240	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435200	56435200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	167	515	0	ENST00000407977.2:c.1937G>T	p.Ser646Ile	p.S646I	ENST00000407977		646	aGc/aTc	9/10	1	2	FACETS	0.984	0.906	1	0.984	0.906	1	CLONAL	1	FALSE	1	0.455528265370726	2		515	745	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858356	59858356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	10	238	0	ENST00000259008.2:c.1639G>A	p.Asp547Asn	p.D547N	ENST00000259008	NM_032043.2	547	Gat/Aat	12/20	1	2	FACETS	0.426	0.291	0.593	0.426	0.291	0.593	SUBCLONAL	1	FALSE	1	0.455528265370726	2		238	103	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733240	74733240	+	start_lost	Translation_Start_Site	SNP	C	C	G	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	81	469	0	ENST00000359995.5:c.3G>C	p.Met1?	p.M1?	ENST00000359995	NM_001195427.1	1	atG/atC	1/3	1	2	FACETS	0.484	0.426	0.546	0.484	0.426	0.546	SUBCLONAL	1	FALSE	1	0.455528265370726	2		469	735	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245846	5245846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	277	830	0	ENST00000357368.4:c.929C>T	p.Thr310Ile	p.T310I	ENST00000357368	NM_002850.3	310	aCc/aTc	10/38	0.455528265370726	1	FACETS	0.845	0.793	0.898	0.845	0.793	0.898	CLONAL	1	FALSE	0	0.455528265370726	1		830	1112	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098551	11098551	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	397	540	0	ENST00000358026.2:c.1069A>T	p.Lys357Ter	p.K357*	ENST00000358026	NM_001128849.1	357	Aag/Tag	6/36	0.368018369509218	3	FACETS	0.853	0.811	0.895	0.853	0.811	0.895	CLONAL	2	FALSE	1	0.455528265370726	3		540	1255	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387354	17387354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs555163333	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	464	851	1	ENST00000359435.4:c.620C>T	p.Pro207Leu	p.P207L	ENST00000359435	NM_001033549.1	207	cCg/cTg	7/9	0.368018369509218	3	FACETS	0.922	0.881	0.963	0.922	0.881	0.963	CLONAL	2	FALSE	1	0.455528265370726	3		852	1357	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277036	18277036	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	137	404	0	ENST00000222254.8:c.1483G>T	p.Gly495Cys	p.G495C	ENST00000222254	NM_005027.3	495	Ggc/Tgc	12/16	0.368018369509218	3	FACETS	1	0.973	1	0.583	0.532	0.637	CLONAL	1	FALSE	1	0.455528265370726	3		404	633	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551215	29551215	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	149	466	0	ENST00000389048.3:c.1414+1G>T		p.X472_splice	ENST00000389048	NM_004304.4	472			1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	FALSE	1	0.455528265370726	2		466	637	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735467	204735467	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	42	381	0	ENST00000302823.3:c.268A>T	p.Met90Leu	p.M90L	ENST00000302823	NM_005214.4	90	Atg/Ttg	2/4	1	2	FACETS	0.505	0.423	0.596	0.505	0.423	0.596	SUBCLONAL	1	FALSE	1	0.455528265370726	2		381	365	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793415	242793415	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	162	660	0	ENST00000334409.5:c.662T>A	p.Val221Glu	p.V221E	ENST00000334409	NM_005018.2	221	gTg/gAg	5/5	1	2	FACETS	0.976	0.897	1	0.976	0.897	1	CLONAL	1	FALSE	1	0.455528265370726	2		660	729	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023803	31023803	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1305212991	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	236	545	0	ENST00000375687.4:c.3288G>T	p.Met1096Ile	p.M1096I	ENST00000375687	NM_015338.5	1096	atG/atT	13/13	0.287764643791246	2	FACETS	0.859	0.808	0.911	0.859	0.808	0.911	CLONAL	2	FALSE	0	0.455528265370726	2		545	603	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324294	62324294	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745711145	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	166	783	0	ENST00000360203.5:c.2789C>T	p.Ala930Val	p.A930V	ENST00000360203	NM_001283009.1	930	gCc/gTc	29/35	0.287764643791246	2	FACETS	0.583	0.534	0.634	0.291	0.267	0.317	SUBCLONAL	1	FALSE	0	0.455528265370726	2		783	1251	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421258	12421258	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	54	566	0	ENST00000287820.6:c.138C>G	p.Ser46Arg	p.S46R	ENST00000287820	NM_015869.4	46	agC/agG	2/7	0.181456192156258	2	FACETS	0.529	0.453	0.613	0.265	0.226	0.307	INDETERMINATE	1	FALSE	0	0.455528265370726	2		566	448	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947808	178947808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	18	204	0	ENST00000263967.3:c.2683G>A	p.Asp895Asn	p.D895N	ENST00000263967	NM_006218.2	895	Gac/Aac	19/21	0.181456192156258	2	FACETS	0.806	0.617	1	0.403	0.308	0.511	INDETERMINATE	1	FALSE	0	0.455528265370726	2		204	98	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607174	189607174	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	186	645	0	ENST00000264731.3:c.1553G>T	p.Gly518Val	p.G518V	ENST00000264731	NM_003722.4	518	gGa/gTa	12/14	0.181456192156258	2	FACETS	1	0.959	1	0.526	0.487	0.567	INDETERMINATE	1	FALSE	0	0.455528265370726	2		645	776	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808380	1808380	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	271	892	0	ENST00000260795.2:c.2138T>C	p.Met713Thr	p.M713T	ENST00000260795		713	aTg/aCg	15/17	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.455528265370726	2		892	1086	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247306	153247306	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	60	264	0	ENST00000281708.4:c.1496G>T	p.Gly499Val	p.G499V	ENST00000281708	NM_033632.3	499	gGt/gTt	10/12	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	FALSE	1	0.455528265370726	2		264	253	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522567	187522567	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	18	322	0	ENST00000441802.2:c.11496G>C	p.Met3832Ile	p.M3832I	ENST00000441802	NM_005245.3	3832	atG/atC	21/27	1	2	FACETS	0.523	0.397	0.67	0.523	0.397	0.67	SUBCLONAL	1	FALSE	1	0.455528265370726	2		322	151	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959992	38959992	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	40	162	0	ENST00000357387.3:c.1940A>G	p.Gln647Arg	p.Q647R	ENST00000357387	NM_152756.3	647	cAa/cGa	21/38	0.234083575683365	4	FACETS	1	0.916	1	0.741	0.632	0.855	INDETERMINATE	2	FALSE	1	0.455528265370726	4		162	115	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39074242	39074242	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	176	293	0	ENST00000357387.3:c.68A>T	p.Glu23Val	p.E23V	ENST00000357387	NM_152756.3	23	gAg/gTg	2/38	0.234083575683365	4	FACETS	1	0.983	1	0.416	0.383	0.45	INDETERMINATE	1	FALSE	1	0.455528265370726	4		293	901	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80040407	80040407	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	42	375	0	ENST00000265081.6:c.1736G>T	p.Trp579Leu	p.W579L	ENST00000265081	NM_002439.4	579	tGg/tTg	12/24	0.455528265370726	1	FACETS	0.896	0.76	1	0.896	0.76	1	CLONAL	1	FALSE	0	0.455528265370726	1		375	159	SUCCESS
APC	324	MSKCC	GRCh37	5	112173666	112173666	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	38	253	0	ENST00000257430.4:c.2375A>T	p.Lys792Met	p.K792M	ENST00000257430	NM_000038.5	792	aAg/aTg	16/16	0.455528265370726	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	0	0.455528265370726	1		253	93	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924477	131924477	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1316248605	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	36	258	0	ENST00000265335.6:c.1150G>C	p.Glu384Gln	p.E384Q	ENST00000265335		384	Gag/Cag	8/25	0.455528265370726	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	0	0.455528265370726	1		258	103	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513324	149513324	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	87	405	0	ENST00000261799.4:c.760-1G>T		p.X254_splice	ENST00000261799	NM_002609.3	254			0.455528265370726	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	0	0.455528265370726	1		405	268	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515222	149515222	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	167	665	0	ENST00000261799.4:c.260T>A	p.Leu87Gln	p.L87Q	ENST00000261799	NM_002609.3	87	cTg/cAg	3/23	0.455528265370726	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	0	0.455528265370726	1		665	555	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021009	26021009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	41	320	0	ENST00000357647.3:c.292G>A	p.Glu98Lys	p.E98K	ENST00000357647	NM_003529.2	98	Gag/Aag	1/1	0.441324047074008	2	FACETS	0.457	0.381	0.541	0.228	0.19	0.271	SUBCLONAL	1	FALSE	0	0.455528265370726	2		320	394	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997759	149997759	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	190	404	0	ENST00000253339.5:c.2708A>T	p.Gln903Leu	p.Q903L	ENST00000253339		903	cAg/cTg	5/7	0.441324047074008	2	FACETS	0.915	0.855	0.975	0.915	0.855	0.975	CLONAL	2	FALSE	0	0.455528265370726	2		404	456	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508328	106508328	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs769318398	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	74	315	0	ENST00000359195.3:c.322G>T	p.Glu108Ter	p.E108*	ENST00000359195	NM_002649.2	108	Gag/Tag	2/11	0.234083575683365	4	FACETS	1	0.971	1	0.453	0.399	0.51	INDETERMINATE	1	FALSE	1	0.455528265370726	4		315	348	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873453	151873453	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	115	356	0	ENST00000262189.6:c.9085C>T	p.Gln3029Ter	p.Q3029*	ENST00000262189	NM_170606.2	3029	Caa/Taa	38/59	0.26605968458543	1	FACETS	1	0.984	1	1	0.984	1	INDETERMINATE	1	FALSE	0	0.455528265370726	1		356	284	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340360	8340360	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	74	383	0	ENST00000356435.5:c.5236C>A	p.Leu1746Met	p.L1746M	ENST00000356435		1746	Ctg/Atg	31/35	0.455528265370726	1	FACETS	0.89	0.787	0.997	0.89	0.787	0.997	CLONAL	1	FALSE	0	0.455528265370726	1		383	282	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341867	8341867	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	29	366	0	ENST00000356435.5:c.4773G>T	p.Gln1591His	p.Q1591H	ENST00000356435		1591	caG/caT	29/35	0.455528265370726	1	FACETS	0.655	0.533	0.791	0.655	0.533	0.791	SUBCLONAL	1	FALSE	0	0.455528265370726	1		366	150	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76812945	76812945	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	37	146	0	ENST00000373344.5:c.6676A>T	p.Arg2226Trp	p.R2226W	ENST00000373344	NM_000489.3	2226	Agg/Tgg	30/35	0.201282047544594	2	FACETS	1	0.899	1			1	INDETERMINATE	2	FALSE	NA	0.455528265370726	2		146	77	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613313	100613313	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	68	226	0	ENST00000308731.7:c.1087C>A	p.Gln363Lys	p.Q363K	ENST00000308731	NM_000061.2	363	Cag/Aag	12/19	0.201282047544594	2	FACETS	0.834	0.741	0.929			1	INDETERMINATE	2	FALSE	NA	0.455528265370726	2		226	179	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496914	29496916	+	stop_gained	Nonsense_Mutation	TNP	AGG	AGG	TGT	novel	NA	P-0045996-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	11	98	0	ENST00000356175.3:c.485_487delinsTGT	p.Gln162_Glu163delinsLeuTer	p.Q162_E163delinsL*	ENST00000356175	NM_000267.3	162	cAGGaa/cTGTaa	5/57	1	2	FACETS	0.743	0.523	1	0.743	0.523	1	CLONAL	1	FALSE	1	0.455528265370726	2		98	65	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0045997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	66	301	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.439898172302286	2		301	296	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584497	48584497	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	69	259	0	ENST00000342988.3:c.670C>T	p.Gln224Ter	p.Q224*	ENST00000342988	NM_005359.5	224	Cag/Tag	6/12	0.439898172302286	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.439898172302286	1		259	204	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939086	36939086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372288734	NA	P-0045997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	121	685	1	ENST00000361632.4:c.623C>T	p.Ala208Val	p.A208V	ENST00000361632		208	gCg/gTg	5/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.439898172302286	2		686	509	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438161	56438161	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	139	607	0	ENST00000407977.2:c.832G>T	p.Glu278Ter	p.E278*	ENST00000407977		278	Gag/Tag	7/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.439898172302286	2		607	514	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0045998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	407	528	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.729657694467947	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	1	0.729657694467947	3		528	639	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127933377	127933377	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	118	410	0	ENST00000373547.4:c.158A>T	p.Asp53Val	p.D53V	ENST00000373547	NM_002721.4	53	gAt/gTt	2/7	1	2	FACETS	0.995	0.91	1	0.995	0.91	1	CLONAL	1	TRUE	1	0.729657694467947	2		410	325	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101022	4101022	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	156	500	0	ENST00000262948.5:c.700A>C	p.Met234Leu	p.M234L	ENST00000262948	NM_030662.3	234	Atg/Ctg	6/11	0.665923514588237	3	FACETS	0.889	0.816	0.965	0.444	0.408	0.483	CLONAL	1	TRUE	1	0.67058566797309	3		500	699	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556193	29556193	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555614261	NA	P-0046006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	58	150	1	ENST00000356175.3:c.2560C>T	p.Gln854Ter	p.Q854*	ENST00000356175	NM_000267.3	854	Cag/Tag	21/57	1	2	FACETS	0.856	0.75	0.967	0.856	0.75	0.967	CLONAL	1	TRUE	1	0.78313409056156	2		151	173	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0046017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	22	324	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.862	0.675	1	0.862	0.675	1	CLONAL	1	TRUE	1	0.347303497075241	2		324	147	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750600586	NA	P-0046017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	60	844	1	ENST00000269305.4:c.413C>T	p.Ala138Val	p.A138V	ENST00000269305	NM_001126112.2	138	gCc/gTc	5/11	0.347303497075241	1	FACETS	0.811	0.703	0.928	0.811	0.703	0.928	CLONAL	1	TRUE	0	0.347303497075241	1		845	352	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575209	48575209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767326	NA	P-0046017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	11	235	0	ENST00000342988.3:c.403C>T	p.Arg135Ter	p.R135*	ENST00000342988	NM_005359.5	135	Cga/Tga	3/12	0.253468150212196	1	FACETS	0.534	0.372	0.73	0.534	0.372	0.73	SUBCLONAL	1	TRUE	0	0.347303497075241	1		235	98	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487930	56487930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370634710	NA	P-0046017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	47	575	0	ENST00000267101.3:c.1661C>T	p.Pro554Leu	p.P554L	ENST00000267101	NM_001982.3	554	cCg/cTg	14/28	1	2	FACETS	0.884	0.75	1	0.884	0.75	1	CLONAL	1	TRUE	1	0.347303497075241	2		575	306	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222119	2222119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762523174	NA	P-0046017-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	41	969	0	ENST00000398665.3:c.2951C>T	p.Thr984Met	p.T984M	ENST00000398665	NM_032482.2	984	aCg/aTg	24/28	0.347303497075241	1	FACETS	0.717	0.601	0.845	0.717	0.601	0.845	SUBCLONAL	1	TRUE	0	0.347303497075241	1		969	272	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0046018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	171	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.962	0.892	1	0.962	0.892	1	CLONAL	1	TRUE	1	0.706920711699268	2		288	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0046018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	356	744	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.706920711699268	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.706920711699268	1		745	636	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953258	81953258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776768909	NA	P-0046018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	150	285	0	ENST00000359376.3:c.2224C>T	p.Arg742Cys	p.R742C	ENST00000359376	NM_002661.3	742	Cgc/Tgc	20/33	1	2	FACETS	0.923	0.85	0.997	0.923	0.85	0.997	CLONAL	1	TRUE	1	0.706920711699268	2		285	460	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604704	48604704	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	214	354	0	ENST00000342988.3:c.1526G>A	p.Trp509Ter	p.W509*	ENST00000342988	NM_005359.5	509	tGg/tAg	12/12	0.706920711699268	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.706920711699268	1		354	386	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610073	28610073	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046018-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	274	400	0	ENST00000241453.7:c.1417A>G	p.Asn473Asp	p.N473D	ENST00000241453	NM_004119.2	473	Aac/Gac	11/24	0.182614511611011	3	FACETS	1	0.993	1	0.723	0.682	0.764	INDETERMINATE	1	TRUE	1	0.706920711699268	3		400	726	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0046019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	98	236	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.806	0.723	0.893	0.806	0.723	0.893	CLONAL	1	TRUE	1	0.549148866622672	2		236	443	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143437	108143455	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTTTCCCGTAGGCTGATC	CTTTTCCCGTAGGCTGATC	-	novel	NA	P-0046019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	94	346	0	ENST00000278616.4:c.3154-9_3163del		p.X1052_splice	ENST00000278616	NM_000051.3	1052		22/63	1	2	FACETS	0.839	0.751	0.931	0.839	0.751	0.931	CLONAL	1	TRUE	1	0.549148866622672	2		346	408	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865345	57865345	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	262	832	0	ENST00000228682.2:c.2822C>A	p.Ala941Asp	p.A941D	ENST00000228682	NM_005269.2	941	gCt/gAt	12/12	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.549148866622672	2		832	938	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351648	89351648	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	112	727	0	ENST00000301030.4:c.1302G>T	p.Leu434Phe	p.L434F	ENST00000301030	NM_001256183.1	434	ttG/ttT	9/13	1	2	FACETS	0.418	0.375	0.463	0.418	0.375	0.463	SUBCLONAL	1	TRUE	1	0.549148866622672	2		727	977	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435927	56435927	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	130	550	0	ENST00000407977.2:c.1210C>G	p.Arg404Gly	p.R404G	ENST00000407977		404	Cgc/Ggc	9/10	1	2	FACETS	0.858	0.781	0.937	0.858	0.781	0.937	CLONAL	1	TRUE	1	0.549148866622672	2		550	552	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913315	NA	P-0046019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	139	695	0	ENST00000326873.7:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000326873	NM_000455.4	194	Gac/Tac	4/10	0.549148866622672	1	FACETS	0.823	0.756	0.893	0.823	0.756	0.893	CLONAL	1	TRUE	0	0.549148866622672	1		695	446	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597429	10597430	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCAGGTGTCTGTATCTGGGTCGTAA	novel	NA	P-0046019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	186	890	0	ENST00000171111.5:c.1749_1773dup	p.Ser592LeufsTer35	p.S592Lfs*35	ENST00000171111	NM_203500.1	591	-/TTACGACCCAGATACAGACACCTGG	6/6	0.549148866622672	1	FACETS	0.578	0.534	0.624	0.578	0.534	0.624	SUBCLONAL	1	TRUE	0	0.549148866622672	1		890	850	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652869	212652869	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	70	319	1	ENST00000342788.4:c.437G>T	p.Gly146Val	p.G146V	ENST00000342788	NM_005235.2	146	gGa/gTa	4/28	1	2	FACETS	0.782	0.687	0.883	0.782	0.687	0.883	SUBCLONAL	1	TRUE	1	0.549148866622672	2		320	326	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683466	182683466	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	134	441	0	ENST00000292782.4:c.79G>T	p.Val27Leu	p.V27L	ENST00000292782	NM_020640.2	27	Gta/Tta	2/7	1	2	FACETS	0.839	0.765	0.915	0.839	0.765	0.915	CLONAL	1	TRUE	1	0.549148866622672	2		441	582	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372137	55372137	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	97	315	0	ENST00000297316.4:c.827C>A	p.Pro276Gln	p.P276Q	ENST00000297316	NM_022454.3	276	cCa/cAa	2/2	1	2	FACETS	0.883	0.793	0.978	0.883	0.793	0.978	CLONAL	1	TRUE	1	0.549148866622672	2		315	400	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650325	48650325	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs184815507	NA	P-0046019-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	226	415	0	ENST00000376670.3:c.295G>A	p.Gly99Ser	p.G99S	ENST00000376670	NM_002049.3	99	Ggc/Agc	3/6	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.549148866622672	1		415	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0046020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	222	780	3	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.452747891646183	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.452747891646183	1		783	694	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94910901	94910901	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	86	366	0	ENST00000536441.1:c.1229A>G	p.His410Arg	p.H410R	ENST00000536441	NM_144665.3	410	cAc/cGc	8/10	1	2	FACETS	0.833	0.74	0.932	0.833	0.74	0.932	CLONAL	1	TRUE	1	0.452747891646183	2		366	456	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224519	53224519	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	165	792	0	ENST00000375401.3:c.3194T>G	p.Leu1065Arg	p.L1065R	ENST00000375401	NM_004187.3	1065	cTg/cGg	21/26	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.452747891646183	NA		792	795	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608872	100608872	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046020-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	144	416	0	ENST00000308731.7:c.1736A>T	p.Asp579Val	p.D579V	ENST00000308731	NM_000061.2	579	gAc/gTc	17/19	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.452747891646183	2		416	612	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0046021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	106	763	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.37130442284718	1	FACETS	0.67	0.603	0.741	0.67	0.603	0.741	SUBCLONAL	1	TRUE	0	0.449877284051365	1		763	545	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149922	202149922	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	123	612	0	ENST00000358485.4:c.1363G>T	p.Glu455Ter	p.E455*	ENST00000358485	NM_001080125.1	455	Gag/Tag	8/9	1	2	FACETS	0.889	0.806	0.976	0.889	0.806	0.976	CLONAL	1	TRUE	1	0.449877284051365	2		612	615	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735519	204735519	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	52	407	0	ENST00000302823.3:c.320C>A	p.Ser107Tyr	p.S107Y	ENST00000302823	NM_005214.4	107	tCc/tAc	2/4	0.449877284051365	1	FACETS	0.388	0.33	0.451	0.388	0.33	0.451	SUBCLONAL	1	TRUE	0	0.449877284051365	1		407	462	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827903	40827904	+	missense_variant	Missense_Mutation	DNP	CT	CT	AA	novel	NA	P-0046021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	34	475	0	ENST00000373198.4:c.2524_2525delinsTT	p.Ser842Phe	p.S842F	ENST00000373198	NM_133170.3	842	AGt/TTt	17/32	0.338263341659635	0	FACETS	0.16	0.13	0.194			1	SUBCLONAL	1	TRUE	0	0.449877284051365	0		475	519	SUCCESS
APC	324	MSKCC	GRCh37	5	112174410	112174410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1178716584	NA	P-0046021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	33	237	0	ENST00000257430.4:c.3119G>A	p.Arg1040Lys	p.R1040K	ENST00000257430	NM_000038.5	1040	aGg/aAg	16/16	0.435920483365768	1	FACETS	0.729	0.602	0.868	0.729	0.602	0.868	SUBCLONAL	1	TRUE	0	0.449877284051365	1		237	156	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158553	26158553	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs769513470	NA	P-0046021-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	59	569	0	ENST00000289316.2:c.156C>A	p.Asp52Glu	p.D52E	ENST00000289316	NM_138720.2	52	gaC/gaA	1/2	NA	2	FACETS	0.407	0.35	0.47			1	INDETERMINATE	1	TRUE	NA	0.449877284051365	2		569	644	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508458	106508458	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	19	333	0	ENST00000359195.3:c.452A>G	p.Gln151Arg	p.Q151R	ENST00000359195	NM_002649.2	151	cAg/cGg	2/11	1	2	FACETS	0.157	0.119	0.202	0.157	0.119	0.202	SUBCLONAL	1	TRUE	1	0.952044251978245	2		333	254	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239982	98239982	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	386	395	0	ENST00000331920.6:c.1350del	p.Ala451ProfsTer5	p.A451Pfs*5	ENST00000331920	NM_000264.3	450	ctC/ct	10/24	0.952044251978245	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.952044251978245	2		395	397	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0046023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	13	324	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.729	1	1	0.729	1	CLONAL	1	TRUE	1	0.15	2		324	170	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713789	30713789	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0046023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	35	616	0	ENST00000295754.5:c.1114A>T	p.Lys372Ter	p.K372*	ENST00000295754	NM_003242.5	372	Aag/Tag	4/7	1	2	FACETS	0.911	0.746	1	0.911	0.746	1	CLONAL	1	TRUE	1	0.15	2		616	512	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039612	47039612	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	24	270	1	ENST00000377604.3:c.1064A>T	p.Glu355Val	p.E355V	ENST00000377604	NM_001204468.1	355	gAg/gTg	11/24	0.3	2	FACETS	0.777	0.612	0.964	0.777	0.612	0.964	CLONAL	2	TRUE	0	0.15	2		271	206	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0046025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	90	765	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.911	0.81	1	0.911	0.81	1	CLONAL	1	TRUE	1	0.36	2		765	549	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72897473	72897473	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	86	348	0	ENST00000325599.8:c.19G>T	p.Asp7Tyr	p.D7Y	ENST00000325599	NM_018130.2	7	Gac/Tac	1/11	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.36	2		348	472	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928919	44928932	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTGGTATTCAGA	CTCTGGTATTCAGA	-	novel	NA	P-0046025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	109	384	0	ENST00000377967.4:c.2019_2032del	p.Gly675GlufsTer8	p.G675Efs*8	ENST00000377967	NM_021140.2	673	ggCTCTGGTATTCAGAat/ggat	17/29	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.36	2		384	541	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123199739	123199740	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	60	279	0	ENST00000218089.9:c.2040dup	p.Glu681Ter	p.E681*	ENST00000218089	NM_001042749.1	680	gat/gaTt	21/35	1	2	FACETS	0.831	0.719	0.953	0.831	0.719	0.953	CLONAL	1	TRUE	1	0.36	2		279	401	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41558769	41558790	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTGGATCCTGAACTGTAAGTA	ACTGGATCCTGAACTGTAAGTA	GC	novel	NA	P-0046025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	46	326	1	ENST00000263253.7:c.3714_3728+7delinsGC		p.X1238_splice	ENST00000263253	NM_001429.3	1238		21/31	1	2	FACETS	0.572	0.482	0.671	0.572	0.482	0.671	SUBCLONAL	1	TRUE	1	0.36	2		327	447	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0046026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	102	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.444674413781483	2		288	417	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0046026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	84	347	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.444674413781483	2		347	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519991	NA	P-0046026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	160	643	0	ENST00000269305.4:c.536A>T	p.His179Leu	p.H179L	ENST00000269305	NM_001126112.2	179	cAt/cTt	5/11	0.444674413781483	1	FACETS	0.963	0.888	1	0.963	0.888	1	CLONAL	1	TRUE	0	0.444674413781483	1		643	581	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0046026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	74	297	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.853	0.751	0.962	0.853	0.751	0.962	CLONAL	1	TRUE	1	0.444674413781483	2		297	390	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202801	128202801	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	168	702	1	ENST00000341105.2:c.919C>T	p.Arg307Trp	p.R307W	ENST00000341105	NM_032638.4	307	Cgg/Tgg	4/6	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.444674413781483	2		703	702	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732916	30732917	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCAGATGGTGTGTGAGACGTTGACTGAGTGCTGGGACCACGACCCAGAGGCCCGTCTCACA	novel	NA	P-0046026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	16	259	0	ENST00000295754.5:c.1530_1590dup	p.Ala531ProfsTer5	p.A531Pfs*5	ENST00000295754	NM_003242.5	510	atc/atCCAGATGGTGTGTGAGACGTTGACTGAGTGCTGGGACCACGACCCAGAGGCCCGTCTCACAc	7/7	1	2	FACETS	0.254	0.188	0.334	0.254	0.188	0.334	SUBCLONAL	1	TRUE	1	0.444674413781483	2		259	283	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	95	69	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.338159337392685	1	FACETS	0.871	0.787	0.958	0.871	0.787	0.958	INDETERMINATE	1	TRUE	0	0.572211439769715	1		69	272	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0046027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	681	1084	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.512362163694623	2	FACETS	0.924	0.895	0.953	0.924	0.895	0.953	CLONAL	2	TRUE	0	0.572211439769715	2		1084	1288	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0046027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	148	309	4	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.927	0.851	1	0.927	0.851	1	CLONAL	1	TRUE	1	0.572211439769715	2		313	558	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870301	155870301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764151643	NA	P-0046027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	156	655	0	ENST00000368323.3:c.538C>T	p.Arg180Trp	p.R180W	ENST00000368323	NM_006912.5	180	Cgg/Tgg	6/6	1	2	FACETS	0.94	0.865	1	0.94	0.865	1	CLONAL	1	TRUE	1	0.572211439769715	2		655	580	SUCCESS
APC	324	MSKCC	GRCh37	5	112175399	112175399	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	128	334	0	ENST00000257430.4:c.4111del	p.Ser1371ValfsTer44	p.S1371Vfs*44	ENST00000257430	NM_000038.5	1370	Aaa/aa	16/16	0.512362163694623	2	FACETS	0.771	0.711	0.832	0.771	0.711	0.832	SUBCLONAL	2	TRUE	0	0.572211439769715	2		334	290	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539727	187539727	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	70	470	0	ENST00000441802.2:c.8013C>G	p.Phe2671Leu	p.F2671L	ENST00000441802	NM_005245.3	2671	ttC/ttG	10/27	1	2	FACETS	0.737	0.647	0.832	0.737	0.647	0.832	SUBCLONAL	1	TRUE	1	0.572211439769715	2		470	332	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412643	139412643	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046027-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	300	1276	0	ENST00000277541.6:c.1201C>T	p.Pro401Ser	p.P401S	ENST00000277541	NM_017617.3	401	Ccc/Tcc	7/34	0.572211439769715	3	FACETS	0.88	0.827	0.935	0.44	0.413	0.468	CLONAL	1	TRUE	1	0.572211439769715	3		1276	1532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0046028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	243	376	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.194594508105264	3	FACETS	1	0.975	1	0.721	0.675	0.769	CLONAL	2	TRUE	0	0.291708496062681	3		376	882	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0046028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	77	347	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.291708496062681	2		347	437	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0046028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	84	652	0	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	1	2	FACETS	0.666	0.587	0.751	0.666	0.587	0.751	SUBCLONAL	1	TRUE	1	0.291708496062681	2		652	865	SUCCESS
APC	324	MSKCC	GRCh37	5	112173995	112173995	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	48	365	0	ENST00000257430.4:c.2704G>T	p.Glu902Ter	p.E902*	ENST00000257430	NM_000038.5	902	Gaa/Taa	16/16	1	2	FACETS	0.78	0.66	0.911	0.78	0.66	0.911	CLONAL	1	TRUE	1	0.291708496062681	2		365	422	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411411	63411411	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	278	430	4	ENST00000330258.3:c.1756C>T	p.Arg586Ter	p.R586*	ENST00000330258	NM_152424.3	586	Cga/Tga	2/2	0.291708496062681	2	FACETS	1	0.976	1			1	CLONAL	3	TRUE	NA	0.291708496062681	2		434	605	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653782	89653782	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs886041877	NA	P-0046028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	104	325	0	ENST00000371953.3:c.80A>C	p.Tyr27Ser	p.Y27S	ENST00000371953	NM_000314.4	27	tAt/tCt	2/9	0.291708496062681	2	FACETS	0.961	0.868	1	0.961	0.868	1	CLONAL	2	TRUE	0	0.291708496062681	2		325	371	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs199469669	NA	P-0046032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	209	240	0	ENST00000374080.3:c.130G>T	p.Gly44Cys	p.G44C	ENST00000374080		44	Ggt/Tgt	2/45	1	1	FACETS	0.947	0.897	0.996	1	0.996	1	CLONAL	6	TRUE	0	0.189679478583189	1		240	351	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198193	185198193	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544421900	NA	P-0046032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	204	554	1	ENST00000265026.3:c.2675C>T	p.Thr892Met	p.T892M	ENST00000265026	NM_004721.4	892	aCg/aTg	13/14	1	2	FACETS	1	0.977	1	1	0.995	1	CLONAL	3	TRUE	1	0.189679478583189	2		555	649	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672758	86672758	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1204340475	NA	P-0046032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	158	302	0	ENST00000274376.6:c.2245C>T	p.Arg749Ter	p.R749*	ENST00000274376	NM_002890.2	749	Cga/Tga	17/25	0.189679478583189	0	FACETS	0.928	0.868	0.987			1	CLONAL	5	TRUE	0	0.189679478583189	0		302	291	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094394	27094394	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	79	519	0	ENST00000324856.7:c.3103del	p.Ala1035ProfsTer4	p.A1035Pfs*4	ENST00000324856	NM_006015.4	1034	aaG/aa	11/20	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.189679478583189	2		519	723	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427240	49427240	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	249	679	1	ENST00000301067.7:c.11248C>T	p.Gln3750Ter	p.Q3750*	ENST00000301067	NM_003482.3	3750	Cag/Tag	39/54	1	2	FACETS	0.99	0.928	1	1	0.996	1	CLONAL	3	TRUE	1	0.189679478583189	2		680	884	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112379	115112386	+	frameshift_variant	Frame_Shift_Del	DEL	CGCTCCTC	CGCTCCTC	-	novel	NA	P-0046033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	40	308	0	ENST00000257566.3:c.1354_1361del	p.Glu452GlnfsTer237	p.E452Qfs*237	ENST00000257566	NM_016569.3	452	GAGGAGCGc/c	7/8	0.196154960903851	2	FACETS	0.971	0.808	1	0.486	0.404	0.577	CLONAL	1	TRUE	0	0.196154960903851	2		308	420	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0046034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	150	321	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.157800661257987	7	FACETS	0.959	0.881	1	0.959	0.881	1	CLONAL	5	FALSE	2	0.157800661257987	7		321	553	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	71	69	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.114986657560453	0	FACETS	0.422	0.37	0.478			1	INDETERMINATE	1	TRUE	0	0.46	0		69	395	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	72	527	2	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.855	0.752	0.965	0.855	0.752	0.965	CLONAL	1	TRUE	1	0.46	2		529	366	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	139	507	3	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.831	0.758	0.908	0.831	0.758	0.908	CLONAL	1	TRUE	1	0.46	2		510	727	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	101	295	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.982	0.883	1	0.982	0.883	1	CLONAL	1	TRUE	1	0.46	2		296	447	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	68	301	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.46	2		301	282	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	164	654	1	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.806	0.74	0.874	0.806	0.74	0.874	CLONAL	1	TRUE	1	0.46	2		655	885	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	111	309	4	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.975	0.881	1	0.975	0.881	1	CLONAL	1	TRUE	1	0.46	2		313	495	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	66	216	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.938	0.821	1	0.938	0.821	1	CLONAL	1	TRUE	1	0.46	2		216	306	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434070	121434070	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766770471	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	159	427	1	ENST00000257555.6:c.961C>T	p.Arg321Cys	p.R321C	ENST00000257555		321	Cgc/Tgc	5/10	1	2	FACETS	0.937	0.86	1	0.937	0.86	1	CLONAL	1	TRUE	1	0.46	2		428	738	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	52	330	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.46	2		330	217	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	31	263	0	ENST00000375687.4:c.1933_1934dup	p.Gly646ValfsTer58	p.G646Vfs*58	ENST00000375687	NM_015338.5	642	-/GG	13/13	1	2	FACETS	0.483	0.392	0.585	0.483	0.392	0.585	SUBCLONAL	1	TRUE	1	0.46	2		263	279	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522601	176522601	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	114	659	0	ENST00000292408.4:c.1703del	p.Pro568GlnfsTer53	p.P568Qfs*53	ENST00000292408	NM_213647.1	566	cgC/cg	13/18	1	2	FACETS	0.481	0.432	0.533	0.481	0.432	0.533	SUBCLONAL	1	TRUE	1	0.46	2		659	1031	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638456	176638456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750354456	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	157	523	1	ENST00000439151.2:c.3056G>A	p.Arg1019His	p.R1019H	ENST00000439151	NM_022455.4	1019	cGc/cAc	5/23	1	2	FACETS	0.863	0.791	0.938	0.863	0.791	0.938	CLONAL	1	TRUE	1	0.46	2		524	791	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298579	11298579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751242124	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	162	474	0	ENST00000361445.4:c.1882C>T	p.Arg628Cys	p.R628C	ENST00000361445	NM_004958.3	628	Cgc/Tgc	12/58	0.114986657560453	3	FACETS	1	0.952	1	0.526	0.483	0.571	INDETERMINATE	1	TRUE	1	0.46	3		474	824	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922048	39922048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375650828	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	226	326	1	ENST00000378444.4:c.4124G>A	p.Arg1375Gln	p.R1375Q	ENST00000378444	NM_001123385.1	1375	cGg/cAg	9/15	0.3	2	FACETS	0.903	0.849	0.958	0.903	0.849	0.958	CLONAL	2	TRUE	0	0.46	2		327	544	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117594	70117594	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	278	526	0	ENST00000245479.2:c.66del	p.Ser23AlafsTer38	p.S23Afs*38	ENST00000245479	NM_000346.3	21	gCc/gc	1/3	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.46	2		526	891	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139625	202139626	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	90	223	0	ENST00000358485.4:c.790dup	p.Val264GlyfsTer13	p.V264Gfs*13	ENST00000358485	NM_001080125.1	262	-/G	6/9	1	2	FACETS	0.875	0.781	0.976	0.875	0.781	0.976	CLONAL	1	TRUE	1	0.46	2		223	447	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713345	30713345	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748195637	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	153	336	0	ENST00000295754.5:c.670C>T	p.Arg224Cys	p.R224C	ENST00000295754	NM_003242.5	224	Cgc/Tgc	4/7	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.46	2		336	637	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214696	5214696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369756620	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	219	620	2	ENST00000357368.4:c.4370G>A	p.Cys1457Tyr	p.C1457Y	ENST00000357368	NM_002850.3	1457	tGt/tAt	29/38	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.46	2		622	905	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133236017	133236017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555225676	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	155	480	0	ENST00000320574.5:c.3139G>A	p.Gly1047Arg	p.G1047R	ENST00000320574	NM_006231.2	1047	Ggg/Agg	26/49	1	2	FACETS	0.97	0.89	1	0.97	0.89	1	CLONAL	1	TRUE	1	0.46	2		480	695	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023290	27023290	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	59	80	0	ENST00000324856.7:c.400del	p.Ala134ArgfsTer98	p.A134Rfs*98	ENST00000324856	NM_006015.4	132	gtG/gt	1/20	0.114986657560453	3	FACETS	1	0.878	1	0.507	0.439	0.58	INDETERMINATE	1	TRUE	1	0.46	3		80	311	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210697	36210697	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	181	538	0	ENST00000222270.7:c.448C>T	p.Arg150Ter	p.R150*	ENST00000222270	NM_014727.1	150	Cga/Tga	3/37	1	2	FACETS	0.743	0.685	0.804	0.743	0.685	0.804	SUBCLONAL	1	TRUE	1	0.46	2		538	1059	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355347	15355347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767979123	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	137	300	0	ENST00000263377.2:c.2276C>T	p.Pro759Leu	p.P759L	ENST00000263377	NM_058243.2	759	cCg/cTg	13/20	1	2	FACETS	0.98	0.894	1	0.98	0.894	1	CLONAL	1	TRUE	1	0.46	2		300	608	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	236	670	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	0.350497538818145	3	FACETS	1	0.986	1	0.599	0.559	0.641	CLONAL	1	TRUE	1	0.46	3		670	1053	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042041	42042041	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	72	352	0	ENST00000219905.7:c.6240del	p.Val2081TrpfsTer21	p.V2081Wfs*21	ENST00000219905	NM_001164273.1	2079	gAa/ga	17/24	1	2	FACETS	0.923	0.813	1	0.923	0.813	1	CLONAL	1	TRUE	1	0.46	2		352	339	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463271	25463271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770568549	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	182	427	1	ENST00000264709.3:c.2222C>T	p.Ala741Val	p.A741V	ENST00000264709	NM_175629.2	741	gCg/gTg	19/23	0.114986657560453	0	FACETS	0.626	0.579	0.674			1	INDETERMINATE	1	TRUE	0	0.46	0		428	683	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041312	42041312	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	108	362	0	ENST00000219905.7:c.5507C>A	p.Ser1836Tyr	p.S1836Y	ENST00000219905	NM_001164273.1	1836	tCt/tAt	17/24	1	2	FACETS	0.947	0.854	1	0.947	0.854	1	CLONAL	1	TRUE	1	0.46	2		362	496	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49399928	49399928	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	138	384	0	ENST00000418115.1:c.408+1G>A		p.X136_splice	ENST00000418115	NM_001664.2	136			1	2	FACETS	0.884	0.806	0.965	0.884	0.806	0.965	CLONAL	1	TRUE	1	0.46	2		384	679	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198252	138198252	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	52	201	0	ENST00000237289.4:c.845G>T	p.Arg282Ile	p.R282I	ENST00000237289	NM_001270507.1	282	aGa/aTa	6/9	0.114986657560453	3	FACETS	1	0.896	1	0.527	0.452	0.607	INDETERMINATE	1	TRUE	1	0.46	3		201	264	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301104	65301104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs543134894	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	100	206	0	ENST00000342505.4:c.3344C>T	p.Pro1115Leu	p.P1115L	ENST00000342505	NM_002227.2	1115	cCg/cTg	24/25	0.114986657560453	3	FACETS	1	0.981	1	0.709	0.639	0.783	INDETERMINATE	1	TRUE	1	0.46	3		206	377	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727455	88727455	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	121	423	1	ENST00000360948.2:c.323+1G>A		p.X108_splice	ENST00000360948	NM_001012338.2	108			0.3	0	FACETS	0.471	0.427	0.518			1	SUBCLONAL	1	TRUE	0	0.46	0		424	603	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782308	56782308	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34670294	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	81	403	0	ENST00000308159.5:c.149G>A	p.Arg50His	p.R50H	ENST00000308159	NM_014669.4	50	cGc/cAc	2/22	1	2	FACETS	0.406	0.357	0.459	0.406	0.357	0.459	SUBCLONAL	1	TRUE	1	0.46	2		403	867	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89383348	89383348	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	180	517	0	ENST00000301030.4:c.80G>T	p.Gly27Val	p.G27V	ENST00000301030	NM_001256183.1	27	gGg/gTg	3/13	1	2	FACETS	0.829	0.764	0.896	0.829	0.764	0.896	CLONAL	1	TRUE	1	0.46	2		517	944	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46275980	46275980	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	102	383	0	ENST00000371998.3:c.3416T>C	p.Met1139Thr	p.M1139T	ENST00000371998		1139	aTg/aCg	18/23	1	2	FACETS	0.829	0.744	0.919	0.829	0.744	0.919	CLONAL	1	TRUE	1	0.46	2		383	535	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288162	21288162	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	119	337	0	ENST00000354336.3:c.407G>T	p.Gly136Val	p.G136V	ENST00000354336	NM_005207.3	136	gGg/gTg	2/3	1	2	FACETS	0.903	0.818	0.992	0.903	0.818	0.992	CLONAL	1	TRUE	1	0.46	2		337	573	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31448657	31448657	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757002340	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	65	344	0	ENST00000344624.3:c.2879C>T	p.Ser960Leu	p.S960L	ENST00000344624		960	tCg/tTg	20/33	0.114986657560453	0	FACETS	0.437	0.381	0.497			1	INDETERMINATE	1	TRUE	0	0.46	0		344	349	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158453	26158453	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	230	567	0	ENST00000289316.2:c.56T>C	p.Val19Ala	p.V19A	ENST00000289316	NM_138720.2	19	gTg/gCg	1/2	0.199609196794221	4	FACETS	1	0.981	1	0.575	0.535	0.617	INDETERMINATE	1	TRUE	2	0.46	4		567	1269	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324681	31324681	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	343	584	0	ENST00000412585.2:c.127del	p.Glu43SerfsTer16	p.E43Sfs*16	ENST00000412585	NM_005514.6	43	Gag/ag	2/8	0.199609196794221	4	FACETS	0.937	0.887	0.988	0.937	0.887	0.988	INDETERMINATE	2	TRUE	2	0.46	4		584	1162	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382229	152382229	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	65	309	0	ENST00000206249.3:c.1339T>C	p.Cys447Arg	p.C447R	ENST00000206249	NM_000125.3	447	Tgc/Cgc	6/8	0.114986657560453	3	FACETS	0.85	0.74	0.968	0.425	0.37	0.484	INDETERMINATE	1	TRUE	1	0.46	3		309	409	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240002	53240002	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	160	319	0	ENST00000375401.3:c.1439C>A	p.Pro480Gln	p.P480Q	ENST00000375401	NM_004187.3	480	cCg/cAg	11/26	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.46	1		319	413	SUCCESS
AR	367	MSKCC	GRCh37	X	66941758	66941758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	129	237	1	ENST00000374690.3:c.2407del	p.Gln803ArgfsTer6	p.Q803Rfs*6	ENST00000374690	NM_000044.3	801	aCc/ac	6/8	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.46	1		238	300	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0046037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	103	236	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.378744722078921	3	FACETS	0.954	0.863	1	0.954	0.863	1	CLONAL	2	TRUE	1	0.378744722078921	3		236	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0046037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	126	369	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.332358843998307	2	FACETS	0.981	0.9	1	0.981	0.9	1	CLONAL	2	TRUE	0	0.378744722078921	2		369	339	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023678	27023678	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	47	276	0	ENST00000324856.7:c.784T>A	p.Ser262Thr	p.S262T	ENST00000324856	NM_006015.4	262	Tcg/Acg	1/20	0.378744722078921	3	FACETS	0.765	0.654	0.883	0.765	0.654	0.883	SUBCLONAL	2	TRUE	1	0.378744722078921	3		276	193	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001439	29001439	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	25	228	0	ENST00000282397.4:c.1293C>A	p.Tyr431Ter	p.Y431*	ENST00000282397	NM_002019.4	431	taC/taA	10/30	1	2	FACETS	0.691	0.548	0.853	0.691	0.548	0.853	SUBCLONAL	1	TRUE	1	0.378744722078921	2		228	191	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197741	66197741	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	45	360	0	ENST00000273854.3:c.2958C>A	p.Phe986Leu	p.F986L	ENST00000273854	NM_004439.5	986	ttC/ttA	17/18	1	2	FACETS	0.917	0.777	1	0.917	0.777	1	CLONAL	1	TRUE	1	0.378744722078921	2		360	259	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31521236	31521236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	169	368	0	ENST00000344624.3:c.941C>T	p.Ser314Phe	p.S314F	ENST00000344624		314	tCt/tTt	3/33	0.378744722078921	6	FACETS	0.9	0.832	0.97	0.675	0.624	0.728	CLONAL	3	TRUE	2	0.378744722078921	6		368	581	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31521282	31521282	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	209	457	0	ENST00000344624.3:c.895A>G	p.Arg299Gly	p.R299G	ENST00000344624		299	Aga/Gga	3/33	0.378744722078921	6	FACETS	0.941	0.878	1	0.706	0.658	0.755	CLONAL	3	TRUE	2	0.378744722078921	6		457	687	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339475	81339475	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	31	358	0	ENST00000222390.5:c.1529G>T	p.Ser510Ile	p.S510I	ENST00000222390	NM_000601.4	510	aGt/aTt	13/18	0.378744722078921	3	FACETS	0.732	0.594	0.886	0.366	0.297	0.443	SUBCLONAL	1	TRUE	1	0.378744722078921	3		358	266	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	10	151	0				ENST00000310581	NM_198253.2	-/1132			0.208796997033212	1	FACETS	0.512	0.349	0.714	0.512	0.349	0.714	SUBCLONAL	1	FALSE	0	0.288215941706178	1		151	116	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604479	43604479	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	40	746	0	ENST00000355710.3:c.1064G>T	p.Arg355Met	p.R355M	ENST00000355710	NM_020975.4	355	aGg/aTg	6/20	1	2	FACETS	0.907	0.757	1	0.907	0.757	1	CLONAL	1	FALSE	1	0.288215941706178	2		746	306	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602840	10602840	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	56	1176	0	ENST00000171111.5:c.738C>G	p.Phe246Leu	p.F246L	ENST00000171111	NM_203500.1	246	ttC/ttG	3/6	0.288215941706178	1	FACETS	0.794	0.682	0.915	0.794	0.682	0.915	CLONAL	1	FALSE	0	0.288215941706178	1		1176	419	SUCCESS
AR	367	MSKCC	GRCh37	X	66765955	66765955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1021234843	NA	P-0046049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	55	1050	2	ENST00000374690.3:c.967G>A	p.Glu323Lys	p.E323K	ENST00000374690	NM_000044.3	323	Gag/Aag	1/8	0.155170928544678	0	FACETS	0.77	0.661	0.887			1	INDETERMINATE	1	FALSE	0	0.288215941706178	0		1052	353	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683824	117683824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754292558	NA	P-0046049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	66	512	0	ENST00000368508.3:c.3323C>T	p.Pro1108Leu	p.P1108L	ENST00000368508	NM_002944.2	1108	cCc/cTc	21/43	0.288215941706178	3	FACETS	0.832	0.728	0.943	0.832	0.728	0.943	CLONAL	2	FALSE	1	0.288215941706178	3		512	315	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567716	226567716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781134011	NA	P-0046049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	32	738	0	ENST00000366794.5:c.1450G>A	p.Glu484Lys	p.E484K	ENST00000366794	NM_001618.3	484	Gag/Aag	10/23	1	2	FACETS	0.685	0.557	0.829	0.685	0.557	0.829	SUBCLONAL	1	FALSE	1	0.288215941706178	2		738	324	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366772	40366772	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	23	607	1	ENST00000397332.2:c.425G>T	p.Arg142Leu	p.R142L	ENST00000397332	NM_001033082.2	142	cGg/cTg	2/3	0.288215941706178	3	FACETS	0.628	0.49	0.786	0.314	0.245	0.393	SUBCLONAL	1	FALSE	1	0.288215941706178	3		608	291	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138106	64138106	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	48	1019	0	ENST00000334205.4:c.2029G>T	p.Gly677Cys	p.G677C	ENST00000334205	NM_003942.2	677	Ggc/Tgc	16/17	1	2	FACETS	0.952	0.808	1	0.952	0.808	1	CLONAL	1	FALSE	1	0.288215941706178	2		1019	350	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133930	41133931	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0046049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	25	557	1	ENST00000379561.5:c.1697_1698delinsCT	p.Leu566Pro	p.L566P	ENST00000379561	NM_002015.3	566	cTG/cCT	2/3	0.212595775574961	4	FACETS	0.633	0.499	0.787	0.317	0.249	0.394	SUBCLONAL	1	FALSE	2	0.288215941706178	4		558	353	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105543	30105543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	88	689	0	ENST00000331968.5:c.1143G>T	p.Glu381Asp	p.E381D	ENST00000331968	NM_002742.2	381	gaG/gaT	7/18	0.283877058658523	3	FACETS	1	0.96	1	0.59	0.523	0.661	CLONAL	1	FALSE	1	0.288215941706178	3		689	592	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554362	81554362	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	25	322	1	ENST00000298171.2:c.382C>A	p.Leu128Ile	p.L128I	ENST00000298171	NM_000369.2	128	Cta/Ata	4/10	0.283877058658523	3	FACETS	1	0.845	1	0.539	0.428	0.665	CLONAL	1	FALSE	1	0.288215941706178	3		323	184	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95578545	95578545	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	19	304	0	ENST00000393063.1:c.2080G>T	p.Val694Leu	p.V694L	ENST00000393063	NM_030621.3	694	Gta/Tta	14/28	0.283877058658523	3	FACETS	0.67	0.51	0.858	0.335	0.255	0.429	SUBCLONAL	1	FALSE	1	0.288215941706178	3		304	225	SUCCESS
BLM	641	MSKCC	GRCh37	15	91306374	91306374	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	26	328	1	ENST00000355112.3:c.2061C>G	p.Ile687Met	p.I687M	ENST00000355112	NM_000057.2	687	atC/atG	8/22	1	2	FACETS	0.764	0.608	0.942	0.764	0.608	0.942	CLONAL	1	FALSE	1	0.288215941706178	2		329	236	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639671	3639671	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0046049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	60	1117	0	ENST00000294008.3:c.3968C>G	p.Ser1323Ter	p.S1323*	ENST00000294008	NM_032444.2	1323	tCa/tGa	12/15	0.288215941706178	1	FACETS	0.846	0.732	0.971	0.846	0.732	0.971	CLONAL	1	FALSE	0	0.288215941706178	1		1117	421	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647443	3647444	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0046049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	33	985	0	ENST00000294008.3:c.1619_1620delinsCT	p.Trp540Ser	p.W540S	ENST00000294008	NM_032444.2	540	tGG/tCT	7/15	0.288215941706178	1	FACETS	0.69	0.564	0.831	0.69	0.564	0.831	SUBCLONAL	1	FALSE	0	0.288215941706178	1		985	284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577157	+	splice_acceptor_variant	Splice_Site	DNP	CT	CT	AA	novel	NA	P-0046049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	29	591	1	ENST00000269305.4:c.783-2_783-1delinsTT		p.X261_splice	ENST00000269305	NM_001126112.2	261			1	2	FACETS	0.828	0.668	1	0.828	0.668	1	CLONAL	1	FALSE	1	0.288215941706178	2		592	243	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980455	7980455	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	33	867	2	ENST00000319144.4:c.1128G>T	p.Trp376Cys	p.W376C	ENST00000319144	NM_001139.2	376	tgG/tgT	9/15	1	2	FACETS	0.709	0.579	0.855	0.709	0.579	0.855	SUBCLONAL	1	FALSE	1	0.288215941706178	2		869	323	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145602	11145602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	46	845	0	ENST00000358026.2:c.3964G>A	p.Asp1322Asn	p.D1322N	ENST00000358026	NM_001128849.1	1322	Gac/Aac	29/36	0.288215941706178	1	FACETS	0.936	0.793	1	0.936	0.793	1	CLONAL	1	FALSE	0	0.288215941706178	1		845	292	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349602	15349602	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	44	1199	0	ENST00000263377.2:c.3972G>T	p.Gln1324His	p.Q1324H	ENST00000263377	NM_058243.2	1324	caG/caT	19/20	0.288215941706178	1	FACETS	0.699	0.587	0.821	0.699	0.587	0.821	SUBCLONAL	1	FALSE	0	0.288215941706178	1		1199	374	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645753	215645753	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0046049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	35	513	0	ENST00000260947.4:c.845T>A	p.Leu282Ter	p.L282*	ENST00000260947	NM_000465.2	282	tTg/tAg	4/11	0.283877058658523	3	FACETS	0.996	0.82	1	0.498	0.41	0.596	CLONAL	1	FALSE	1	0.288215941706178	3		513	279	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202824	128202824	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	47	918	0	ENST00000341105.2:c.896G>T	p.Gly299Val	p.G299V	ENST00000341105	NM_032638.4	299	gGg/gTg	4/6	1	2	FACETS	0.832	0.704	0.973	0.832	0.704	0.973	CLONAL	1	FALSE	1	0.288215941706178	2		918	392	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138376575	138376575	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	39	567	0	ENST00000289153.2:c.2899G>T	p.Val967Phe	p.V967F	ENST00000289153	NM_006219.2	967	Gtc/Ttc	20/22	1	2	FACETS	0.867	0.722	1	0.867	0.722	1	CLONAL	1	FALSE	1	0.288215941706178	2		567	312	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970923	79970923	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	27	556	0	ENST00000265081.6:c.1149G>T	p.Lys383Asn	p.K383N	ENST00000265081	NM_002439.4	383	aaG/aaT	7/24	0.288215941706178	1	FACETS	0.429	0.341	0.529	0.429	0.341	0.529	SUBCLONAL	1	FALSE	0	0.288215941706178	1		556	374	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372695	81372695	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	30	349	0	ENST00000222390.5:c.839G>T	p.Trp280Leu	p.W280L	ENST00000222390	NM_000601.4	280	tGg/tTg	7/18	0.283877058658523	3	FACETS	0.964	0.781	1	0.482	0.39	0.585	CLONAL	1	FALSE	1	0.288215941706178	3		349	247	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843278	128843278	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs41303402	NA	P-0046049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	41	1101	2	ENST00000249373.3:c.385G>T	p.Val129Leu	p.V129L	ENST00000249373	NM_005631.4	129	Gta/Tta	2/12	0.283877058658523	3	FACETS	0.85	0.709	1	0.425	0.354	0.503	CLONAL	1	FALSE	1	0.288215941706178	3		1103	383	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009386	69009386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	28	571	0	ENST00000288368.4:c.2503G>A	p.Val835Met	p.V835M	ENST00000288368	NM_024870.2	835	Gtg/Atg	22/40	1	2	FACETS	0.554	0.443	0.68	0.554	0.443	0.68	SUBCLONAL	1	FALSE	1	0.288215941706178	2		571	351	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923442	36923442	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1483261647	NA	P-0046049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	36	915	0	ENST00000358127.4:c.820C>A	p.Leu274Met	p.L274M	ENST00000358127	NM_001280556.1	274	Ctg/Atg	7/10	0.208796997033212	1	FACETS	0.654	0.539	0.782	0.654	0.539	0.782	SUBCLONAL	1	FALSE	0	0.288215941706178	1		915	327	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0046050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	232	495	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.366518110516277	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.36055620954227	3		495	645	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0046050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	186	854	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.19975424346142	2	FACETS	1	0.969	1	0.546	0.505	0.59	INDETERMINATE	1	TRUE	0	0.36055620954227	2		854	944	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038526	47038526	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	128	882	1	ENST00000377604.3:c.688C>T	p.Arg230Ter	p.R230*	ENST00000377604	NM_001204468.1	230	Cga/Tga	8/24	0.366518110516277	1	FACETS	0.743	0.674	0.816	0.743	0.674	0.816	SUBCLONAL	1	TRUE	0	0.36055620954227	1		883	783	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115416	115115416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	157	659	0	ENST00000257566.3:c.910C>T	p.Arg304Trp	p.R304W	ENST00000257566	NM_016569.3	304	Cgg/Tgg	5/8	0.304230488899922	2	FACETS	0.839	0.774	0.906	0.839	0.774	0.906	CLONAL	2	TRUE	0	0.36055620954227	2		659	519	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442718	442718	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	258	542	0	ENST00000399788.2:c.1588C>G	p.Pro530Ala	p.P530A	ENST00000399788	NM_001042603.1	530	Cct/Gct	12/28	0.366518110516277	4	FACETS	0.845	0.795	0.897	0.845	0.795	0.897	CLONAL	3	TRUE	1	0.36055620954227	4		542	768	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832885	3832885	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	95	456	0	ENST00000262367.5:c.1373G>C	p.Gly458Ala	p.G458A	ENST00000262367	NM_004380.2	458	gGt/gCt	6/31	0.186837315173018	4	FACETS	1	0.963	1	0.593	0.528	0.661	INDETERMINATE	1	TRUE	2	0.36055620954227	4		456	605	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0046051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	319	528	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.985	0.934	1	0.985	0.934	1	CLONAL	1	TRUE	1	0.810980476694224	2		528	799	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0046051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	308	451	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.407895018524799	1	FACETS	0.673	0.639	0.707	0.673	0.639	0.707	INDETERMINATE	1	TRUE	0	0.810980476694224	1		451	671	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0046051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	403	248	1				ENST00000310581	NM_198253.2	-/1132			0.189556197326408	4	FACETS	0.893	0.859	0.926	0.893	0.859	0.926	INDETERMINATE	3	TRUE	1	0.810980476694224	4		249	672	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40855800	40855800	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1458266017	NA	P-0046051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	330	550	0	ENST00000428826.2:c.2056C>T	p.Arg686Ter	p.R686*	ENST00000428826		686	Cga/Tga	19/21	0.407895018524799	1	FACETS	0.744	0.71	0.779	0.744	0.71	0.779	INDETERMINATE	1	TRUE	0	0.810980476694224	1		550	650	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547022	9547022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs58486349	NA	P-0046051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	125	303	0	ENST00000353224.5:c.1000G>A	p.Asp334Asn	p.D334N	ENST00000353224	NM_177990.2	334	Gat/Aat	5/10	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.810980476694224	2		303	307	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	C	novel	NA	P-0046051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	302	631	2	ENST00000558401.1:c.1A>C	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Ctg	1/4	0.810980476694224	1	FACETS	0.956	0.917	0.995	0.956	0.917	0.995	CLONAL	1	TRUE	0	0.810980476694224	1		633	463	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661726	227661726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760281604	NA	P-0046051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	205	812	0	ENST00000305123.5:c.1729G>A	p.Val577Met	p.V577M	ENST00000305123	NM_005544.2	577	Gtg/Atg	1/2	0.459067096554804	3	FACETS	0.65	0.602	0.7	0.325	0.301	0.35	INDETERMINATE	1	TRUE	1	0.810980476694224	3		812	1093	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211459	46211469	+	frameshift_variant	Frame_Shift_Del	DEL	TGCGTCAAAGT	TGCGTCAAAGT	-	novel	NA	P-0046051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	75	155	0	ENST00000334344.6:c.426_436del	p.Arg143TrpfsTer7	p.R143Wfs*7	ENST00000334344	NM_152641.2	142	cTGCGTCAAAGT/c	5/21	0.248434413901424	2	FACETS	1	0.914	1	0.511	0.458	0.565	INDETERMINATE	1	TRUE	0	0.810980476694224	2		155	181	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494880	56494881	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	390	625	1	ENST00000267101.3:c.3237_3238delinsTT	p.Arg1080Cys	p.R1080C	ENST00000267101	NM_001982.3	1079	ccCCgt/ccTTgt	27/28	0.248434413901424	2	FACETS	1	0.993	1	0.589	0.563	0.615	INDETERMINATE	1	TRUE	0	0.810980476694224	2		626	817	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219497	133219497	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	228	907	3	ENST00000320574.5:c.4637T>C	p.Leu1546Pro	p.L1546P	ENST00000320574	NM_006231.2	1546	cTg/cCg	36/49	0.564722638048564	1	FACETS	0.379	0.353	0.405	0.379	0.353	0.405	SUBCLONAL	1	TRUE	0	0.810980476694224	1		910	882	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720294	43720295	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0046051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	306	611	0	ENST00000382044.4:c.3747_3748delinsTA	p.Glu1250Lys	p.E1250K	ENST00000382044	NM_001141980.1	1249	cgGGaa/cgTAaa	18/28	0.810980476694224	1	FACETS	0.999	0.96	1	0.999	0.96	1	CLONAL	1	TRUE	0	0.810980476694224	1		611	449	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575077	48575077	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	187	328	0	ENST00000342988.3:c.271C>T	p.Pro91Ser	p.P91S	ENST00000342988	NM_005359.5	91	Cct/Tct	3/12	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.810980476694224	2		328	459	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215520	5215520	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	389	1031	2	ENST00000357368.4:c.4183C>T	p.Gln1395Ter	p.Q1395*	ENST00000357368	NM_002850.3	1395	Cag/Tag	27/38	0.313210434464363	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.810980476694224	0		1033	985	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221256	36221257	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	425	845	3	ENST00000222270.7:c.5090_5091delinsTT	p.Pro1697Leu	p.P1697L	ENST00000222270	NM_014727.1	1697	cCC/cTT	24/37	1	2	FACETS	0.843	0.804	0.883	0.843	0.804	0.883	CLONAL	1	TRUE	1	0.810980476694224	2		848	1243	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147221	61147221	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	182	313	1	ENST00000295025.8:c.899T>G	p.Phe300Cys	p.F300C	ENST00000295025	NM_002908.2	300	tTc/tGc	8/11	0.41041625196757	1	FACETS	0.635	0.593	0.678	0.635	0.593	0.678	INDETERMINATE	1	TRUE	0	0.810980476694224	1		314	420	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622254	117622254	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	133	419	0	ENST00000368508.3:c.6616C>T	p.Pro2206Ser	p.P2206S	ENST00000368508	NM_002944.2	2206	Cct/Tct	42/43	0.743524528662777	1	FACETS	0.65	0.6	0.7	0.65	0.6	0.7	SUBCLONAL	1	TRUE	0	0.810980476694224	1		419	300	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982083	70982083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1355431485	NA	P-0046051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	335	764	0	ENST00000276594.2:c.13C>T	p.Arg5Trp	p.R5W	ENST00000276594	NM_024504.3	5	Cgg/Tgg	2/8	0.483696245998266	4	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.810980476694224	4		764	1423	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032159	26032160	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	T	novel	NA	P-0046051-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	793	532	4	ENST00000244661.2:c.129_130delinsA	p.Pro44ArgfsTer19	p.P44Rfs*19	ENST00000244661	NM_003537.3	43	cgCCcg/cgAcg	1/1	0.810980476694224	4	FACETS	0.949	0.924	0.973			1	CLONAL	3	TRUE	NA	0.810980476694224	4		536	1244	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0046052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	120	456	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.36	2		456	523	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0046052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	9	252	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	1	2	FACETS	0.284	0.188	0.406	0.284	0.188	0.406	SUBCLONAL	1	TRUE	1	0.36	2		252	176	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028651	12028651	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	87	401	0	ENST00000353533.5:c.854A>T	p.Asp285Val	p.D285V	ENST00000353533	NM_003010.3	285	gAt/gTt	8/11	0.299934999507837	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.36	1		401	272	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0046053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	22	744	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.3	2	FACETS	0.199	0.153	0.252			1	SUBCLONAL	1	TRUE	NA	0.31	2		745	715	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0046053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	166	406	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.3	2	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.31	2		406	718	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0046053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	39	201	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	1	0.31	2		201	245	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0046054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	261	715	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.615718581552355	2	FACETS	0.991	0.946	1	0.991	0.946	1	CLONAL	2	TRUE	0	0.625557523978264	2		715	421	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618952	37618953	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0046054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	124	544	0	ENST00000447079.4:c.629dup	p.Tyr210Ter	p.Y210*	ENST00000447079	NM_015083.1	210	tac/tAac	1/14	0.58718650794687	2	FACETS	1	0.968	1	0.56	0.512	0.609	CLONAL	1	TRUE	0	0.625557523978264	2		544	354	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031638	36031638	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	164	1034	0	ENST00000358208.4:c.1467G>C	p.Glu489Asp	p.E489D	ENST00000358208		489	gaG/gaC	12/12	0.405142827559014	4	FACETS	0.935	0.858	1	0.467	0.429	0.508	CLONAL	1	TRUE	2	0.625557523978264	4		1034	912	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0046063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	215	612	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.278639983327188	2	FACETS	0.792	0.739	0.848	0.792	0.739	0.848	SUBCLONAL	2	TRUE	0	0.356497331909807	2		612	761	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971116	21971116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552823	NA	P-0046063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	114	499	0	ENST00000304494.5:c.242C>T	p.Pro81Leu	p.P81L	ENST00000304494	NM_000077.4	81	cCc/cTc	2/3	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.356497331909807	2		499	596	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575152	48575152	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	76	360	0	ENST00000342988.3:c.346C>T	p.Gln116Ter	p.Q116*	ENST00000342988	NM_005359.5	116	Cag/Tag	3/12	0.356497331909807	1	FACETS	0.944	0.834	1	0.944	0.834	1	CLONAL	1	TRUE	0	0.356497331909807	1		360	371	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510563	38510563	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	59	679	0	ENST00000254066.5:c.817A>C	p.Ile273Leu	p.I273L	ENST00000254066	NM_000964.3	273	Atc/Ctc	7/9	1	2	FACETS	0.616	0.531	0.71	0.616	0.531	0.71	SUBCLONAL	1	TRUE	1	0.356497331909807	2		679	537	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271277	153271277	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs13146842	NA	P-0046063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	30	196	1	ENST00000281708.4:c.502-1G>T		p.X168_splice	ENST00000281708	NM_033632.3	168			1	2	FACETS	0.809	0.657	0.979	0.809	0.657	0.979	CLONAL	1	TRUE	1	0.356497331909807	2		197	208	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087886	27087898	+	frameshift_variant	Frame_Shift_Del	DEL	CCACCTCGGCCAC	CCACCTCGGCCAC	ACG	novel	NA	P-0046063-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	114	666	1	ENST00000324856.7:c.2173_2185delinsACG	p.Pro725ThrfsTer14	p.P725Tfs*14	ENST00000324856	NM_006015.4	725	CCACCTCGGCCACcc/ACGcc	6/20	0.356497331909807	1	FACETS	0.792	0.714	0.874	0.792	0.714	0.874	SUBCLONAL	1	TRUE	0	0.356497331909807	1		667	664	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0046064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	48	310	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.506	0.428	0.592	0.506	0.428	0.592	SUBCLONAL	1	TRUE	1	0.435904581922887	2		310	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578179	7578179	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	78	521	0	ENST00000269305.4:c.670G>T	p.Glu224Ter	p.E224*	ENST00000269305	NM_001126112.2	224	Gag/Tag	6/11	1	2	FACETS	0.546	0.48	0.618	0.546	0.48	0.618	SUBCLONAL	1	TRUE	1	0.435904581922887	2		521	655	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31493382	31493382	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	35	246	0	ENST00000344624.3:c.1774A>C	p.Ile592Leu	p.I592L	ENST00000344624		592	Ata/Cta	10/33	1	2	FACETS	0.371	0.304	0.446	0.371	0.304	0.446	SUBCLONAL	1	TRUE	1	0.435904581922887	2		246	433	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244269	5244269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568465790	NA	P-0046064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	98	802	1	ENST00000357368.4:c.1213G>A	p.Val405Ile	p.V405I	ENST00000357368	NM_002850.3	405	Gtc/Atc	11/38	1	2	FACETS	0.544	0.485	0.608	0.544	0.485	0.608	SUBCLONAL	1	TRUE	1	0.435904581922887	2		803	826	SUCCESS
APC	324	MSKCC	GRCh37	5	112175383	112175384	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046064-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	57	232	0	ENST00000257430.4:c.4094dup	p.Ala1366CysfsTer9	p.A1366Cfs*9	ENST00000257430	NM_000038.5	1364	-/G	16/16	1	2	FACETS	0.902	0.78	1	0.902	0.78	1	CLONAL	1	TRUE	1	0.435904581922887	2		232	290	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0046065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	105	527	2	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.246084644180921	2		529	690	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0046065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	158	679	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.246084644180921	2		683	1025	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300579	11300579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376836258	NA	P-0046065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	140	557	0	ENST00000361445.4:c.1567G>A	p.Asp523Asn	p.D523N	ENST00000361445	NM_004958.3	523	Gac/Aac	11/58	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.246084644180921	2		557	923	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097751	27097751	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	122	464	1	ENST00000324856.7:c.3344del	p.Pro1115GlnfsTer46	p.P1115Qfs*46	ENST00000324856	NM_006015.4	1114	Ccc/cc	12/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.246084644180921	2		465	752	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426123	138426123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217537873	NA	P-0046065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	40	268	0	ENST00000289153.2:c.1408G>A	p.Glu470Lys	p.E470K	ENST00000289153	NM_006219.2	470	Gaa/Aaa	9/22	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.246084644180921	2		268	304	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	116	378	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.246084644180921	2		378	657	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222731	5222731	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs756013055	NA	P-0046065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	170	666	0	ENST00000357368.4:c.3072del	p.Val1025SerfsTer18	p.V1025Sfs*18	ENST00000357368	NM_002850.3	1024	ccC/cc	18/38	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.246084644180921	2		666	1037	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0046065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	72	239	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.246084644180921	2		239	462	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0046065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	43	495	5	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.457	0.381	0.542	0.457	0.381	0.542	SUBCLONAL	1	TRUE	1	0.246084644180921	2		500	764	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100577	157100577	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1289149988	NA	P-0046065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	89	367	1	ENST00000346085.5:c.1518del	p.Gly507AspfsTer16	p.G507Dfs*16	ENST00000346085	NM_020732.3	505	aCc/ac	1/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.246084644180921	2		368	648	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023560	27023560	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1462224784	NA	P-0046065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	109	430	0	ENST00000324856.7:c.671del	p.Pro224ArgfsTer8	p.P224Rfs*8	ENST00000324856	NM_006015.4	222	taC/ta	1/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.246084644180921	2		430	753	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850704	63850705	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	48	269	0	ENST00000279873.7:c.1489dup	p.Ile497AsnfsTer31	p.I497Nfs*31	ENST00000279873	NM_032199.2	494	-/A	10/10	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.246084644180921	2		269	344	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220632	1220632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782146	NA	P-0046065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1157	224	878	1	ENST00000326873.7:c.650C>T	p.Pro217Leu	p.P217L	ENST00000326873	NM_000455.4	217	cCg/cTg	5/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.246084644180921	2		879	1381	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800902	120800903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs748469666	NA	P-0046065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	195	738	2	ENST00000257552.2:c.345dup	p.Leu116AlafsTer15	p.L116Afs*15	ENST00000257552	NM_002442.3	115	-/G	6/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.246084644180921	2		740	1211	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27217701	27217701	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772600804	NA	P-0046065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	129	541	0	ENST00000380036.4:c.3007C>T	p.Arg1003Cys	p.R1003C	ENST00000380036	NM_000459.3	1003	Cgc/Tgc	19/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.246084644180921	2		541	796	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868201	37868201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776515406	NA	P-0046065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	144	613	1	ENST00000269571.5:c.922G>A	p.Val308Met	p.V308M	ENST00000269571		308	Gtg/Atg	8/27	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.246084644180921	2		614	1036	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352601	118352602	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0046065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	98	464	0	ENST00000534358.1:c.3808_3809del	p.Lys1270GlufsTer2	p.K1270Efs*2	ENST00000534358	NM_005933.3	1269	gAA/g	7/36	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.246084644180921	2		464	688	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891205	151891205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776685589	NA	P-0046065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	86	415	0	ENST00000262189.6:c.4549G>A	p.Gly1517Arg	p.G1517R	ENST00000262189	NM_170606.2	1517	Gga/Aga	31/59	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.246084644180921	2		415	573	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843634	156843634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201035170	NA	P-0046065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	210	854	1	ENST00000524377.1:c.1060G>A	p.Val354Ile	p.V354I	ENST00000524377	NM_002529.3	354	Gtc/Atc	8/17	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.246084644180921	2		855	1257	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184460	7184460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	174	775	0	ENST00000302850.5:c.841G>A	p.Val281Met	p.V281M	ENST00000302850	NM_000208.2	281	Gtg/Atg	3/22	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.246084644180921	2		775	1149	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045760	26045760	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	77	408	1	ENST00000540144.1:c.122G>A	p.Arg41His	p.R41H	ENST00000540144	NM_003531.2	41	cGc/cAc	1/1	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.246084644180921	2		409	560	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624241	89624242	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913290	NA	P-0046065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	52	201	0	ENST00000371953.3:c.18dup	p.Glu7ArgfsTer4	p.E7Rfs*4	ENST00000371953	NM_000314.4	5	-/A	1/9	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.246084644180921	2		201	328	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206611	108206611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1215175886	NA	P-0046065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	62	290	0	ENST00000278616.4:c.8191G>A	p.Val2731Ile	p.V2731I	ENST00000278616	NM_000051.3	2731	Gtc/Atc	56/63	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.246084644180921	2		290	361	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434082	49434082	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	144	717	0	ENST00000301067.7:c.7471del	p.Ala2491LeufsTer52	p.A2491Lfs*52	ENST00000301067	NM_003482.3	2491	Gct/ct	31/54	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.246084644180921	2		717	932	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201562	133201562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766291093	NA	P-0046065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	174	807	0	ENST00000320574.5:c.6676G>A	p.Gly2226Arg	p.G2226R	ENST00000320574	NM_006231.2	2226	Ggg/Agg	48/49	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.246084644180921	2		807	1071	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822218	72822220	+	inframe_deletion	In_Frame_Del	DEL	ATA	ATA	-	rs766523677	NA	P-0046065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	163	761	0	ENST00000268489.5:c.9955_9957del	p.Tyr3319del	p.Y3319del	ENST00000268489	NM_006885.3	3319	TAT/-	10/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.246084644180921	2		761	1056	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677772	47677772	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	110	409	0	ENST00000347630.2:c.1093G>T	p.Gly365Ter	p.G365*	ENST00000347630	NM_001007230.1	365	Gga/Tga	11/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.246084644180921	2		409	677	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244164	5244164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1016675364	NA	P-0046065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	189	828	1	ENST00000357368.4:c.1318G>A	p.Ala440Thr	p.A440T	ENST00000357368	NM_002850.3	440	Gcg/Acg	11/38	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.246084644180921	2		829	1182	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015144	71015144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	72	296	0	ENST00000318789.4:c.1786G>A	p.Gly596Ser	p.G596S	ENST00000318789	NM_032682.5	596	Ggc/Agc	20/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.246084644180921	2		296	495	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942810	68942813	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	novel	NA	P-0046065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	107	545	0	ENST00000288368.4:c.622_625del	p.Cys208ProfsTer3	p.C208Pfs*3	ENST00000288368	NM_024870.2	208	TGTTcc/cc	6/40	0.246084644180921	3	FACETS	1	0.949	1	0.549	0.491	0.61	CLONAL	1	TRUE	1	0.246084644180921	3		545	890	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933962	39933962	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	80	649	0	ENST00000378444.4:c.637T>C	p.Tyr213His	p.Y213H	ENST00000378444	NM_001123385.1	213	Tat/Cat	4/15	1	2	FACETS	0.707	0.621	0.799	0.707	0.621	0.799	SUBCLONAL	1	TRUE	1	0.246084644180921	2		649	920	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339548	70339557	+	protein_altering_variant	In_Frame_Del	DEL	TTCAGCAGCA	TTCAGCAGCA	G	novel	NA	P-0046065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	72	450	0	ENST00000374080.3:c.217_226delinsG	p.Phe73_Ile76delinsVal	p.F73_I76delinsV	ENST00000374080		73	TTCAGCAGCAtt/Gtt	3/45	1	2	FACETS	0.862	0.753	0.98	0.862	0.753	0.98	CLONAL	1	TRUE	1	0.246084644180921	2		450	679	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0046066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	250	356	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.168786073831468	3	FACETS	0.865	0.815	0.915	0.865	0.815	0.915	INDETERMINATE	2	TRUE	1	0.625327820695489	3		356	607	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0046066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	263	716	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.625327820695489	1	FACETS	0.972	0.919	1	0.972	0.919	1	CLONAL	1	TRUE	0	0.625327820695489	1		716	595	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0046066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	47	201	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	1	2	FACETS	0.68	0.58	0.788	0.68	0.58	0.788	SUBCLONAL	1	TRUE	1	0.625327820695489	2		201	221	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119762	70119763	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	312	591	1	ENST00000245479.2:c.768dup	p.Arg257AlafsTer39	p.R257Afs*39	ENST00000245479	NM_000346.3	255	gag/gaGg	3/3	0.596578657116079	2	FACETS	0.871	0.831	0.91	0.871	0.831	0.91	CLONAL	2	TRUE	0	0.625327820695489	2		592	573	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591925	48591925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660556	NA	P-0046066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	161	434	0	ENST00000342988.3:c.1088G>A	p.Cys363Tyr	p.C363Y	ENST00000342988	NM_005359.5	363	tGt/tAt	9/12	0.625327820695489	1	FACETS	0.931	0.866	0.998	0.931	0.866	0.998	CLONAL	1	TRUE	0	0.625327820695489	1		434	380	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710564	114710564	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	194	478	0	ENST00000543371.1:c.49G>T	p.Glu17Ter	p.E17*	ENST00000543371	NM_001198531.1	17	Gaa/Taa	1/14	0.168786073831468	3	FACETS	1	0.985	1	0.607	0.564	0.651	INDETERMINATE	1	TRUE	1	0.625327820695489	3		478	671	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415897	49415897	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	32	512	0	ENST00000301067.7:c.16450G>A	p.Glu5484Lys	p.E5484K	ENST00000301067	NM_003482.3	5484	Gaa/Aaa	53/54	0.534006743965041	1	FACETS	0.152	0.123	0.185	0.152	0.123	0.185	SUBCLONAL	1	TRUE	0	0.625327820695489	1		512	462	SUCCESS
APC	324	MSKCC	GRCh37	5	112174828	112174828	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0046066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	66	190	0	ENST00000257430.4:c.3537T>G	p.Tyr1179Ter	p.Y1179*	ENST00000257430	NM_000038.5	1179	taT/taG	16/16	1	2	FACETS	0.91	0.801	1	0.91	0.801	1	CLONAL	1	TRUE	1	0.625327820695489	2		190	232	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	325	151	0				ENST00000310581	NM_198253.2	-/1132			0.609982571305545	7	FACETS	0.993	0.951	1	0.993	0.951	1	CLONAL	5	TRUE	2	0.609982571305545	7		151	542	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652126	36652139	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGAGGCCGGGAT	GGCGAGGCCGGGAT	-	novel	NA	P-0046069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	383	1009	1	ENST00000244741.5:c.249_262del	p.Arg84ValfsTer40	p.R84Vfs*40	ENST00000244741	NM_000389.4	83	cGGCGAGGCCGGGAT/c	2/3	0.334646675619765	5	FACETS	0.848	0.809	0.888	0.848	0.809	0.888	INDETERMINATE	3	TRUE	2	0.609982571305545	5		1010	945	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88671966	88671966	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0046069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	14	182	0	ENST00000360948.2:c.1205-1G>A		p.X402_splice	ENST00000360948	NM_001012338.2	402			0.163430436230702	5	FACETS	0.488	0.354	0.65	0.163	0.118	0.217	INDETERMINATE	1	TRUE	2	0.609982571305545	5		182	180	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976739	2976739	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	82	870	0	ENST00000396946.4:c.1273G>A	p.Glu425Lys	p.E425K	ENST00000396946	NM_032415.4	425	Gag/Aag	9/25	0.55301572804251	4	FACETS	0.45	0.396	0.509	0.225	0.198	0.255	SUBCLONAL	1	TRUE	2	0.609982571305545	4		870	962	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18964115	18964115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	92	661	2	ENST00000262803.5:c.1112C>T	p.Ala371Val	p.A371V	ENST00000262803	NM_002911.3	371	gCg/gTg	8/24	0.163430436230702	5	FACETS	1	0.896	1	0.335	0.298	0.375	INDETERMINATE	1	TRUE	2	0.609982571305545	5		663	574	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627173	37627173	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0046069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	52	376	0	ENST00000447079.4:c.1088C>G	p.Ser363Ter	p.S363*	ENST00000447079	NM_015083.1	363	tCa/tGa	2/14	0.609982571305545	4	FACETS	0.532	0.453	0.619	0.177	0.151	0.207	SUBCLONAL	1	TRUE	1	0.609982571305545	4		376	516	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983122	201983123	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	68	693	0	ENST00000359651.3:c.971_972insA	p.Met324IlefsTer147	p.M324Ifs*147	ENST00000359651		324	atg/atAg	7/8	0.382442381532832	6	FACETS	0.606	0.526	0.693	0.151	0.131	0.174	SUBCLONAL	1	TRUE	2	0.609982571305545	6		693	817	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163446	108163446	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	61	578	0	ENST00000278616.4:c.4537C>G	p.Leu1513Val	p.L1513V	ENST00000278616	NM_000051.3	1513	Cta/Gta	30/63	0.334646675619765	5	FACETS	0.72	0.622	0.827	0.24	0.207	0.276	INDETERMINATE	1	TRUE	2	0.609982571305545	5		578	532	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843609	3843610	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0046069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	44	518	0	ENST00000262367.5:c.993_994del	p.Val332GlyfsTer17	p.V332Gfs*17	ENST00000262367	NM_004380.2	331	tcAGtg/tctg	4/31	1	2	FACETS	0.353	0.296	0.415	0.353	0.296	0.415	SUBCLONAL	1	TRUE	1	0.609982571305545	2		518	409	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99152591	99152591	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0046069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	41	389	0	ENST00000074304.5:c.388-1G>C		p.X130_splice	ENST00000074304	NM_001134224.1	130			1	2	FACETS	0.478	0.4	0.564	0.478	0.4	0.564	SUBCLONAL	1	TRUE	1	0.609982571305545	2		389	281	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967238	134967238	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	78	732	1	ENST00000398015.3:c.2577C>A	p.Asp859Glu	p.D859E	ENST00000398015	NM_004441.4	859	gaC/gaA	14/16	0.136161721099167	6	FACETS	0.711	0.624	0.805			1	INDETERMINATE	1	TRUE	NA	0.609982571305545	6		733	798	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748123	41748123	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	17	229	1	ENST00000226382.2:c.646G>A	p.Gly216Ser	p.G216S	ENST00000226382	NM_003924.3	216	Ggc/Agc	3/3	0.330838346150149	4	FACETS	0.47	0.352	0.609	0.235	0.176	0.305	INDETERMINATE	1	TRUE	2	0.609982571305545	4		230	191	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554936	106554936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs966974441	NA	P-0046069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	33	466	2	ENST00000369096.4:c.2053C>T	p.Arg685Trp	p.R685W	ENST00000369096	NM_001198.3	685	Cgg/Tgg	7/7	1	2	FACETS	0.322	0.262	0.389	0.322	0.262	0.389	SUBCLONAL	1	TRUE	1	0.609982571305545	2		468	336	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0046070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	65	357	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.965	0.839	1	0.965	0.839	1	CLONAL	1	TRUE	1	0.306981562503942	2		357	439	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0046070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	140	574	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.306981562503942	2		574	780	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265175	5265175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147257283	NA	P-0046070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	152	983	0	ENST00000357368.4:c.412G>A	p.Asp138Asn	p.D138N	ENST00000357368	NM_002850.3	138	Gac/Aac	5/38	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.306981562503942	2		983	970	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409974	139409974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367873715	NA	P-0046070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	194	1176	0	ENST00000277541.6:c.1864G>A	p.Asp622Asn	p.D622N	ENST00000277541	NM_017617.3	622	Gac/Aac	11/34	0.306981562503942	3	FACETS	1	0.98	1	0.393	0.363	0.424	CLONAL	1	TRUE	0	0.306981562503942	3		1176	1237	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432030	49432030	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	225	846	1	ENST00000301067.7:c.9109del	p.His3037ThrfsTer34	p.H3037Tfs*34	ENST00000301067	NM_003482.3	3037	Cac/ac	34/54	1	2	FACETS	0.753	0.701	0.806	1	0.992	1	SUBCLONAL	2	TRUE	1	0.306981562503942	2		847	974	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022738	12022738	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772622167	NA	P-0046070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	115	549	3	ENST00000396373.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000396373	NM_001987.4	282	Cgg/Tgg	5/8	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.306981562503942	2		552	702	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099939	27099940	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGGAC	novel	NA	P-0046070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	127	824	0	ENST00000324856.7:c.3819_3823dup	p.Pro1275ArgfsTer16	p.P1275Rfs*16	ENST00000324856	NM_006015.4	1273	atg/atGGGACg	15/20	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.306981562503942	2		824	811	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363074	40363074	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	105	488	0	ENST00000397332.2:c.1155G>C	p.Gln385His	p.Q385H	ENST00000397332	NM_001033082.2	385	caG/caC	3/3	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.306981562503942	2		488	532	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224591	108224591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	78	295	0	ENST00000278616.4:c.8770G>A	p.Glu2924Lys	p.E2924K	ENST00000278616	NM_000051.3	2924	Gaa/Aaa	60/63	0.306981562503942	3	FACETS	0.775	0.686	0.871	0.775	0.686	0.871	SUBCLONAL	2	TRUE	1	0.306981562503942	3		295	378	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434269	49434269	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	171	1037	0	ENST00000301067.7:c.7284del	p.Pro2429LeufsTer56	p.P2429Lfs*56	ENST00000301067	NM_003482.3	2428	cgG/cg	31/54	1	2	FACETS	0.981	0.901	1	0.981	0.901	1	CLONAL	1	TRUE	1	0.306981562503942	2		1037	1136	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569978	95569978	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0046070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	128	395	0	ENST00000393063.1:c.3755C>G	p.Ser1252Ter	p.S1252*	ENST00000393063	NM_030621.3	1252	tCa/tGa	22/28	0.306981562503942	3	FACETS	0.86	0.783	0.941	0.86	0.783	0.941	CLONAL	2	TRUE	1	0.306981562503942	3		395	559	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39644795	39644795	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0046070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	35	205	0	ENST00000262039.4:c.2523+1G>A		p.X841_splice	ENST00000262039	NM_002647.2	841			1	2	FACETS	0.987	0.815	1	0.987	0.815	1	CLONAL	1	TRUE	1	0.306981562503942	2		205	231	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313373	30313373	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	120	597	1	ENST00000262643.3:c.973G>T	p.Glu325Ter	p.E325*	ENST00000262643	NM_001238.2	325	Gag/Tag	11/12	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.306981562503942	2		598	714	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400309	225400309	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	40	260	0	ENST00000264414.4:c.314T>G	p.Leu105Arg	p.L105R	ENST00000264414	NM_003590.4	105	cTa/cGa	3/16	1	2	FACETS	0.969	0.81	1	0.969	0.81	1	CLONAL	1	TRUE	1	0.306981562503942	2		260	269	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374837	149374837	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	116	370	0	ENST00000360632.3:c.257G>T	p.Arg86Leu	p.R86L	ENST00000360632	NM_015472.4	86	cGc/cTc	2/7	1	2	FACETS	0.827	0.75	0.907	1	0.987	1	CLONAL	2	TRUE	1	0.306981562503942	2		370	457	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253746	153253746	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0046070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	48	309	0	ENST00000281708.4:c.985+2T>A		p.X329_splice	ENST00000281708	NM_033632.3	329			1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.306981562503942	2		309	300	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197082	26197082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763703948	NA	P-0046070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	115	495	0	ENST00000356476.2:c.397G>A	p.Gly133Arg	p.G133R	ENST00000356476		133	Ggg/Agg	1/1	0.306981562503942	3	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.306981562503942	3		495	644	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151868428	151868428	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0046070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	41	429	0	ENST00000262189.6:c.9375-1G>A		p.X3125_splice	ENST00000262189	NM_170606.2	3125			0.184056615540785	2	FACETS	0.518	0.431	0.614	0.259	0.215	0.307	INDETERMINATE	1	TRUE	0	0.306981562503942	2		429	516	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271233	153271233	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	CAA	novel	NA	P-0046070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	36	236	0	ENST00000281708.4:c.545delinsTTG	p.Ser182PhefsTer58	p.S182Ffs*58	ENST00000281708	NM_033632.3	182	tCt/tTTGt	3/12	1	2	FACETS	0.998	0.826	1	0.998	0.826	1	CLONAL	1	TRUE	1	0.306981562503942	2		236	235	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992721	68992721	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs764112302	NA	P-0046071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	72	492	2	ENST00000288368.4:c.1693del	p.Ser565ArgfsTer10	p.S565Rfs*10	ENST00000288368	NM_024870.2	562	cgT/cg	16/40	1	2	FACETS	0.865	0.756	0.983	0.865	0.756	0.983	CLONAL	1	TRUE	1	0.26	2		494	640	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0046071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	190	528	2	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.26	2		530	981	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	52	476	1	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	1	2	FACETS	0.451	0.383	0.527	0.451	0.383	0.527	SUBCLONAL	1	TRUE	1	0.26	2		477	886	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0046071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	167	321	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.177471095150803	3	FACETS	0.932	0.857	1	0.932	0.857	1	CLONAL	2	TRUE	1	0.26	3		321	779	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660469	67660469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	97	266	1	ENST00000264010.4:c.1369C>T	p.Arg457Ter	p.R457*	ENST00000264010	NM_006565.3	457	Cga/Tga	8/12	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.26	2		267	540	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0046071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	18	464	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.247	0.185	0.321	0.247	0.185	0.321	SUBCLONAL	1	TRUE	1	0.26	2		464	560	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0046071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	103	397	0	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.26	2		397	691	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118885	70118885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	165	532	0	ENST00000245479.2:c.457C>T	p.Pro153Ser	p.P153S	ENST00000245479	NM_000346.3	153	Ccc/Tcc	2/3	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.26	2		532	1069	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233090	69233090	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs746910913	NA	P-0046071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	72	220	3	ENST00000462284.1:c.961del	p.Leu321PhefsTer52	p.L321Ffs*52	ENST00000462284	NM_002392.5	319	Ccc/cc	11/11	0.177471095150803	3	FACETS	1	0.972	1	0.706	0.619	0.8	CLONAL	1	TRUE	1	0.26	3		223	443	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134251	11134251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218643327	NA	P-0046071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	153	416	2	ENST00000358026.2:c.2917C>T	p.Arg973Trp	p.R973W	ENST00000358026	NM_001128849.1	973	Cgg/Tgg	20/36	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.26	2		418	954	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345226	73345226	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1162786323	NA	P-0046071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	47	229	0	ENST00000377767.4:c.1663G>A	p.Val555Met	p.V555M	ENST00000377767	NM_014953.3	555	Gtg/Atg	12/21	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.26	2		229	347	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117962	70117963	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	80	195	0	ENST00000245479.2:c.431+1dup		p.R144fs	ENST00000245479	NM_000346.3	144	aga/aGga	1/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.26	2		195	447	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225657	26225657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202067024	NA	P-0046071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	63	394	0	ENST00000360408.1:c.275C>T	p.Ala92Val	p.A92V	ENST00000360408	NM_003532.2	92	gCg/gTg	1/1	0.22281178220428	2	FACETS	0.447	0.385	0.515	0.224	0.192	0.258	SUBCLONAL	1	TRUE	0	0.26	2		394	1083	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087940	27087940	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	150	409	0	ENST00000324856.7:c.2227C>T	p.Gln743Ter	p.Q743*	ENST00000324856	NM_006015.4	743	Caa/Taa	6/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.26	2		409	868	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925621	114925621	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763934346	NA	P-0046071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	89	517	0	ENST00000543371.1:c.1699G>A	p.Ala567Thr	p.A567T	ENST00000543371	NM_001198531.1	567	Gcc/Acc	14/14	1	2	FACETS	0.66	0.583	0.742	0.66	0.583	0.742	SUBCLONAL	1	TRUE	1	0.26	2		517	1038	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879626	123879626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376869233	NA	P-0046071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	149	254	0	ENST00000330479.4:c.322G>A	p.Ala108Thr	p.A108T	ENST00000330479	NM_020382.3	108	Gcc/Acc	4/9	0.177471095150803	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.26	3		254	571	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359974	87359974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs958492686	NA	P-0046071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	33	201	0	ENST00000277120.3:c.1282C>T	p.Arg428Trp	p.R428W	ENST00000277120		428	Cgg/Tgg	11/19	1	2	FACETS	0.573	0.466	0.693	0.573	0.466	0.693	SUBCLONAL	1	TRUE	1	0.26	2		201	443	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73995362	73995362	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763918983	NA	P-0046071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	113	340	0	ENST00000318443.5:c.668G>A	p.Arg223His	p.R223H	ENST00000318443	NM_001024736.1	223	cGc/cAc	4/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.26	2		340	609	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197365	94197365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781646	NA	P-0046071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	96	370	2	ENST00000323929.3:c.1139G>A	p.Arg380His	p.R380H	ENST00000323929	NM_005591.3	380	cGc/cAc	11/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.26	2		372	565	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41020910	41020910	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	129	360	0	ENST00000267868.3:c.532T>C	p.Tyr178His	p.Y178H	ENST00000267868	NM_002875.4	178	Tat/Cat	7/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.26	2		360	728	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797378	42797378	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	192	708	0	ENST00000575354.2:c.3740C>A	p.Pro1247His	p.P1247H	ENST00000575354	NM_015125.3	1247	cCc/cAc	15/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.26	2		708	1214	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248700	212248700	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	78	379	0	ENST00000342788.4:c.3567C>G	p.His1189Gln	p.H1189Q	ENST00000342788	NM_005235.2	1189	caC/caG	28/28	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.26	2		379	546	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266031	41266617	+	splice_donor_variant,splice_acceptor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	TTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAAC	TTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAAC	-	novel	NA	P-0046071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	54	223	0	ENST00000349496.5:c.31_417del		p.X11_splice	ENST00000349496	NM_001904.3	11	TTGGACATGGCCATGGAACCAGACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAAC/-	3-4/15	1	2	FACETS	0.996	0.853	1	0.996	0.853	1	CLONAL	1	TRUE	1	0.26	2		223	417	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213900	66213900	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	55	267	0	ENST00000273854.3:c.2530T>C	p.Trp844Arg	p.W844R	ENST00000273854	NM_004439.5	844	Tgg/Cgg	15/18	1	2	FACETS	0.94	0.806	1	0.94	0.806	1	CLONAL	1	TRUE	1	0.26	2		267	450	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524456	187524456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	120	420	0	ENST00000441802.2:c.11224G>A	p.Asp3742Asn	p.D3742N	ENST00000441802	NM_005245.3	3742	Gac/Aac	19/27	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.26	2		420	825	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819948	170819953	+	inframe_deletion	In_Frame_Del	DEL	GATGAC	GATGAC	-	rs1561865841	NA	P-0046071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	23	267	0	ENST00000296930.5:c.495_500del	p.Asp167_Asp168del	p.D167_D168del	ENST00000296930	NM_002520.6	164	GATGAC/-	6/11	1	2	FACETS	0.397	0.308	0.499	0.397	0.308	0.499	SUBCLONAL	1	TRUE	1	0.26	2		267	446	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31322945	31322948	+	frameshift_variant	Frame_Shift_Del	DEL	GACA	GACA	-	novel	NA	P-0046071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	303	551	0	ENST00000412585.2:c.948_951del	p.Val317Ter	p.V317*	ENST00000412585	NM_005514.6	316	gcTGTC/gc	5/8	0.22281178220428	2	FACETS	0.963	0.907	1	0.963	0.907	1	CLONAL	2	TRUE	0	0.26	2		551	1210	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553306	106553306	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1484048958	NA	P-0046071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	76	390	0	ENST00000369096.4:c.1271G>A	p.Gly424Asp	p.G424D	ENST00000369096	NM_001198.3	424	gGc/gAc	5/7	1	2	FACETS	0.786	0.689	0.891	0.786	0.689	0.891	SUBCLONAL	1	TRUE	1	0.26	2		390	744	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553408	106553408	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	69	306	0	ENST00000369096.4:c.1373A>G	p.His458Arg	p.H458R	ENST00000369096	NM_001198.3	458	cAc/cGc	5/7	1	2	FACETS	0.949	0.828	1	0.949	0.828	1	CLONAL	1	TRUE	1	0.26	2		306	559	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843774	151843775	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	81	266	0	ENST00000262189.6:c.13940dup	p.Ser4648ValfsTer2	p.S4648Vfs*2	ENST00000262189	NM_170606.2	4647	aag/aaAg	53/59	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.26	2		266	555	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132765	152132765	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	160	341	0	ENST00000262189.6:c.107C>A	p.Pro36His	p.P36H	ENST00000262189	NM_170606.2	36	cCt/cAt	1/59	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.26	2		341	889	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0046075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	93	236	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.982	0.876	1	1	0.989	1	CLONAL	3	TRUE	1	0.12	2		236	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0046075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	93	680	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	1	0.95	1	1	0.987	1	CLONAL	2	TRUE	1	0.12	2		680	692	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600369	10600369	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	64	814	1	ENST00000171111.5:c.1486G>T	p.Glu496Ter	p.E496*	ENST00000171111	NM_203500.1	496	Gag/Tag	4/6	0.250063293390417	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.12	1		815	723	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693003	89693003	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1554898235	NA	P-0046075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	42	299	0	ENST00000371953.3:c.487A>T	p.Lys163Ter	p.K163*	ENST00000371953	NM_000314.4	163	Aaa/Taa	5/9	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.12	2		299	468	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374583	118374583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1390104203	NA	P-0046075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	38	308	1	ENST00000534358.1:c.7976G>A	p.Arg2659Gln	p.R2659Q	ENST00000534358	NM_005933.3	2659	cGa/cAa	27/36	1	2	FACETS	0.902	0.748	1	1	0.963	1	CLONAL	2	TRUE	1	0.12	2		309	351	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928307	69928307	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	41	429	0	ENST00000352241.4:c.127G>T	p.Ala43Ser	p.A43S	ENST00000352241	NM_198159.2	43	Gcc/Tcc	2/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.12	2		429	498	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965654	93965654	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	42	356	0	ENST00000369303.4:c.2274C>A	p.Asp758Glu	p.D758E	ENST00000369303	NM_004440.3	758	gaC/gaA	13/17	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.12	2		356	478	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850361	128850361	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	52	597	0	ENST00000249373.3:c.1624C>A	p.Leu542Met	p.L542M	ENST00000249373	NM_005631.4	542	Ctg/Atg	9/12	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.12	2		597	610	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0046076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	131	456	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.44917650571504	2		456	517	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913396	NA	P-0046076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	126	412	0	ENST00000349496.5:c.95A>G	p.Asp32Gly	p.D32G	ENST00000349496	NM_001904.3	32	gAc/gGc	3/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.44917650571504	2		412	501	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345240	70345240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	157	708	1	ENST00000374080.3:c.2266G>A	p.Val756Ile	p.V756I	ENST00000374080		756	Gta/Ata	16/45	0.109314052225732	5	FACETS	1	0.983	1	0.319	0.292	0.348	INDETERMINATE	1	TRUE	1	0.44917650571504	5		709	916	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356421	66356421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	114	342	0	ENST00000273854.3:c.1076C>T	p.Ser359Phe	p.S359F	ENST00000273854	NM_004439.5	359	tCt/tTt	5/18	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.44917650571504	2		342	368	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653827	89653848	+	frameshift_variant	Frame_Shift_Del	DEL	TTGAAGGCGTATACAGGAACAA	TTGAAGGCGTATACAGGAACAA	-	novel	NA	P-0046076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	87	388	0	ENST00000371953.3:c.126_147del	p.Glu43LeufsTer4	p.E43Lfs*4	ENST00000371953	NM_000314.4	42	cTTGAAGGCGTATACAGGAACAAt/ct	2/9	0.44917650571504	3	FACETS	0.81	0.725	0.897	0.54	0.483	0.598	CLONAL	2	TRUE	0	0.44917650571504	3		388	293	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249115	55249115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	219	897	1	ENST00000275493.2:c.2413C>T	p.His805Tyr	p.H805Y	ENST00000275493	NM_005228.3	805	Cac/Tac	20/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.44917650571504	2		898	831	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0046078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	512	715	1	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.847308588448702	2	FACETS	0.991	0.97	1	0.991	0.97	1	CLONAL	2	TRUE	0	0.864345913405687	2		716	598	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039339	49039339	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0046078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	284	619	2	ENST00000267163.4:c.2326-2A>T		p.X776_splice	ENST00000267163	NM_000321.2	776			0.864345913405687	1	FACETS	0.962	0.926	0.996	0.962	0.926	0.996	CLONAL	1	TRUE	0	0.864345913405687	1		621	388	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70360757	70360757	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	211	233	0	ENST00000373644.4:c.1934G>A	p.Arg645Lys	p.R645K	ENST00000373644	NM_030625.2	645	aGg/aAg	3/12	0.864345913405687	3	FACETS	0.857	0.808	0.906	0.857	0.808	0.906	CLONAL	2	TRUE	1	0.864345913405687	3		233	408	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280667	115280667	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	246	563	0	ENST00000438362.2:c.364G>T	p.Asp122Tyr	p.D122Y	ENST00000438362	NM_001242891.1	122	Gac/Tac	4/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.864345913405687	2		563	562	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115268967	115268967	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	206	514	0	ENST00000438362.2:c.1643A>T	p.Gln548Leu	p.Q548L	ENST00000438362	NM_001242891.1	548	cAg/cTg	14/20	1	2	FACETS	0.91	0.851	0.969	0.91	0.851	0.969	CLONAL	1	TRUE	1	0.864345913405687	2		514	524	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117426	4117426	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1179753041	NA	P-0046078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	239	930	1	ENST00000262948.5:c.294G>T	p.Met98Ile	p.M98I	ENST00000262948	NM_030662.3	98	atG/atT	2/11	0.21743005459194	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.864345913405687	0		931	586	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881563	111881563	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	282	703	0	ENST00000393256.3:c.241A>T	p.Ile81Phe	p.I81F	ENST00000393256	NM_006538.4	81	Atc/Ttc	2/4	NA	2	FACETS	0.992	0.939	1			1	INDETERMINATE	1	TRUE	NA	0.864345913405687	2		703	658	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46255796	46255796	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	220	485	0	ENST00000371998.3:c.408T>G	p.Phe136Leu	p.F136L	ENST00000371998		136	ttT/ttG	6/23	1	2	FACETS	0.955	0.897	1	0.955	0.897	1	CLONAL	1	TRUE	1	0.864345913405687	2		485	533	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374763	149374763	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	214	618	2	ENST00000360632.3:c.331G>T	p.Ala111Ser	p.A111S	ENST00000360632	NM_015472.4	111	Gcg/Tcg	2/7	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.864345913405687	2		620	475	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295243	1295243	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0046078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	137	378	0				ENST00000310581	NM_198253.2	-/1132			0.720995974089289	3	FACETS	1	0.976	1	0.581	0.534	0.629	CLONAL	1	TRUE	1	0.864345913405687	3		378	391	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513299	106513299	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	118	327	0	ENST00000359195.3:c.2203del	p.Gln735LysfsTer4	p.Q735Kfs*4	ENST00000359195	NM_002649.2	735	Caa/aa	4/11	NA	2	FACETS	0.904	0.828	0.982			1	INDETERMINATE	1	TRUE	NA	0.864345913405687	2		327	302	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931822	68931822	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	153	534	0	ENST00000288368.4:c.252T>A	p.His84Gln	p.H84Q	ENST00000288368	NM_024870.2	84	caT/caA	3/40	0.223414881428171	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.864345913405687	0		534	426	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046388	69046388	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	201	605	0	ENST00000288368.4:c.3861C>A	p.Asn1287Lys	p.N1287K	ENST00000288368	NM_024870.2	1287	aaC/aaA	32/40	0.223414881428171	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.864345913405687	0		605	425	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908765	101908765	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0046078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	125	270	0	ENST00000374994.4:c.1131-2A>G		p.X377_splice	ENST00000374994	NM_004612.2	377			1	2	FACETS	0.91	0.835	0.985	0.91	0.835	0.985	CLONAL	1	TRUE	1	0.864345913405687	2		270	318	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937135	39937135	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046078-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	243	1052	1	ENST00000378444.4:c.48C>A	p.Asn16Lys	p.N16K	ENST00000378444	NM_001123385.1	16	aaC/aaA	2/15	1	2	FACETS	0.801	0.752	0.851	0.801	0.752	0.851	CLONAL	1	TRUE	1	0.864345913405687	2		1053	702	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0046079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	149	236	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.161531273412748	5	FACETS	1	0.973	1			1	INDETERMINATE	2	TRUE	NA	0.522610711522952	5		236	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0046079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	367	369	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	0.508992502562302	1	FACETS	0.915	0.869	0.962	0.915	0.869	0.962	CLONAL	1	TRUE	0	0.522610711522952	1		369	1134	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438087	438087	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	404	488	0	ENST00000399788.2:c.1882G>C	p.Asp628His	p.D628H	ENST00000399788	NM_001042603.1	628	Gat/Cat	14/28	0.522610711522952	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.522610711522952	3		488	948	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641479	23641479	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	258	790	0	ENST00000261584.4:c.1996A>T	p.Thr666Ser	p.T666S	ENST00000261584	NM_024675.3	666	Aca/Tca	5/13	1	2	FACETS	0.974	0.912	1	0.974	0.912	1	CLONAL	1	TRUE	1	0.522610711522952	2		790	1014	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721175	61721175	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0046079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	125	496	0	ENST00000401558.2:c.1099A>T	p.Lys367Ter	p.K367*	ENST00000401558	NM_003400.3	367	Aaa/Taa	12/25	1	2	FACETS	0.978	0.891	1	0.978	0.891	1	CLONAL	1	TRUE	1	0.522610711522952	2		496	489	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860574	151860574	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs746127093	NA	P-0046079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	263	646	0	ENST00000262189.6:c.10088G>C	p.Cys3363Ser	p.C3363S	ENST00000262189	NM_170606.2	3363	tGt/tCt	43/59	0.280185773269864	3	FACETS	1	0.989	1	0.622	0.583	0.662	INDETERMINATE	1	TRUE	1	0.522610711522952	3		646	1020	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486236	8486236	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs780545572	NA	P-0046079-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	285	415	0	ENST00000356435.5:c.2581G>T	p.Gly861Cys	p.G861C	ENST00000356435		861	Ggc/Tgc	17/35	0.522610711522952	2	FACETS	0.948	0.901	0.996	0.948	0.901	0.996	CLONAL	2	TRUE	0	0.522610711522952	2		415	575	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99162467	99162467	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	51	514	0	ENST00000074304.5:c.985A>G	p.Lys329Glu	p.K329E	ENST00000074304	NM_001134224.1	329	Aaa/Gaa	12/26	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.249487125583677	2		514	358	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207119	1207132	+	frameshift_variant	Frame_Shift_Del	DEL	GGAGACGCTGTGCA	GGAGACGCTGTGCA	-	novel	NA	P-0046080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	230	1061	0	ENST00000326873.7:c.211_224del	p.Thr71GlyfsTer87	p.T71Gfs*87	ENST00000326873	NM_000455.4	69	tcGGAGACGCTGTGCAgg/tcgg	1/10	0.249487125583677	2	FACETS	0.951	0.887	1	0.951	0.887	1	CLONAL	2	TRUE	0	0.249487125583677	2		1061	969	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548343	41548343	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0046080-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	78	386	0	ENST00000263253.7:c.3131C>G	p.Ser1044Ter	p.S1044*	ENST00000263253	NM_001429.3	1044	tCa/tGa	16/31	NA	3	FACETS	0.886	0.783	0.995			1	INDETERMINATE	2	TRUE	NA	0.249487125583677	3		386	397	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	33	69	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.466	0.378	0.565	0.466	0.378	0.565	SUBCLONAL	1	TRUE	1	0.247243520054174	2		69	573	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0046081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	82	324	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.247243520054174	2		324	573	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628681	21628681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	84	638	2	ENST00000421138.2:c.1027G>A	p.Ala343Thr	p.A343T	ENST00000421138		343	Gct/Act	10/16	1	2	FACETS	0.996	0.88	1	0.996	0.88	1	CLONAL	1	TRUE	1	0.247243520054174	2		640	682	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577148	7577148	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1060501194	NA	P-0046081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	105	741	2	ENST00000269305.4:c.790del	p.Leu264TyrfsTer81	p.L264Yfs*81	ENST00000269305	NM_001126112.2	264	Cta/ta	8/11	0.247243520054174	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.247243520054174	1		743	697	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604835	48604835	+	stop_lost	Nonstop_Mutation	SNP	T	T	G	novel	NA	P-0046081-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	67	350	0	ENST00000342988.3:c.1657T>G	p.Ter553GlyextTer40	p.*553Gext*40	ENST00000342988	NM_005359.5	553	Tga/Gga	12/12	0.247243520054174	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.247243520054174	1		350	377	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0046082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	60	602	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.916	0.789	1	0.916	0.789	1	CLONAL	1	TRUE	1	0.2	2		602	655	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0046082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	87	887	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.2	2		887	805	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243045	105243045	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	98	1115	0	ENST00000349310.3:c.238T>C	p.Trp80Arg	p.W80R	ENST00000349310	NM_001014432.1	80	Tgg/Cgg	5/15	1	2	FACETS	0.912	0.812	1	0.912	0.812	1	CLONAL	1	TRUE	1	0.2	2		1115	1074	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341929	8341929	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	26	335	0	ENST00000356435.5:c.4711G>C	p.Glu1571Gln	p.E1571Q	ENST00000356435		1571	Gaa/Caa	29/35	1	2	FACETS	0.539	0.426	0.67	0.539	0.426	0.67	SUBCLONAL	1	TRUE	1	0.2	2		335	482	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797757	42797757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776048328	NA	P-0046082-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	89	1017	0	ENST00000575354.2:c.3809C>T	p.Pro1270Leu	p.P1270L	ENST00000575354	NM_015125.3	1270	cCc/cTc	16/20	1	2	FACETS	0.918	0.813	1	0.918	0.813	1	CLONAL	1	TRUE	1	0.2	2		1017	969	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028757	47028757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782165166	NA	P-0046083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1967	205	751	1	ENST00000377604.3:c.61C>T	p.Arg21Cys	p.R21C	ENST00000377604	NM_001204468.1	21	Cgc/Tgc	3/24	0.322919786654932	5	FACETS	0.868	0.801	0.938			1	CLONAL	1	TRUE	NA	0.322919786654932	5		752	2172	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055948	180055948	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1554	129	850	0	ENST00000261937.6:c.1037C>G	p.Thr346Arg	p.T346R	ENST00000261937	NM_182925.4	346	aCg/aGg	8/30	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.322919786654932	NA		850	1683	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593588	55593614	+	inframe_deletion	In_Frame_Del	DEL	ATGTATGAAGTACAGTGGAAGGTTGTT	ATGTATGAAGTACAGTGGAAGGTTGTT	-	novel	NA	P-0046084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	111	391	0	ENST00000288135.5:c.1654_1680del	p.Met552_Val560del	p.M552_V560del	ENST00000288135	NM_000222.2	552	ATGTATGAAGTACAGTGGAAGGTTGTT/-	11/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.391689456087447	2		391	468	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0046091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1350	142	553	1	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.404218288526571	4	FACETS	0.51	0.463	0.56	0.255	0.231	0.28	SUBCLONAL	1	TRUE	2	0.595727125824788	4		554	1492	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665213	138665213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	570	791	0	ENST00000330315.3:c.352G>A	p.Glu118Lys	p.E118K	ENST00000330315	NM_023067.3	118	Gag/Aag	1/1	0.185407459901017	4	FACETS	1	0.989	1	1	0.989	1	INDETERMINATE	2	TRUE	2	0.595727125824788	4		791	1421	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	601	499	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	0.310768726858245	5	FACETS	1	0.988	1			1	INDETERMINATE	3	TRUE	NA	0.595727125824788	5		499	1215	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65569036	65569036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	79	573	0	ENST00000358664.4:c.22G>A	p.Glu8Lys	p.E8K	ENST00000358664	NM_002382.4	8	Gag/Aag	1/5	1	2	FACETS	0.341	0.3	0.386	0.341	0.3	0.386	SUBCLONAL	1	TRUE	1	0.595727125824788	2		573	777	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1453	107	635	0	ENST00000267101.3:c.273G>T	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atT	3/28	0.310768726858245	5	FACETS	0.436	0.389	0.486			1	INDETERMINATE	1	TRUE	NA	0.595727125824788	5		635	1560	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271395	26271395	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	111	673	0	ENST00000305910.3:c.218G>A	p.Arg73Gln	p.R73Q	ENST00000305910	NM_003534.2	73	cGa/cAa	1/1	0.595727125824788	3	FACETS	0.435	0.39	0.483	0.145	0.13	0.161	SUBCLONAL	1	TRUE	0	0.595727125824788	3		673	1112	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032558	12032558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1355543573	NA	P-0046091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	167	407	0	ENST00000353533.5:c.994G>A	p.Glu332Lys	p.E332K	ENST00000353533	NM_003010.3	332	Gag/Aag	9/11	1	2	FACETS	0.877	0.809	0.948	0.877	0.809	0.948	CLONAL	1	TRUE	1	0.595727125824788	2		407	639	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908200	28908200	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	60	494	0	ENST00000282397.4:c.2555C>A	p.Ser852Ter	p.S852*	ENST00000282397	NM_002019.4	852	tCa/tAa	18/30	0.595727125824788	1	FACETS	0.231	0.198	0.266	0.231	0.198	0.266	SUBCLONAL	1	TRUE	0	0.595727125824788	1		494	613	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022572	12022572	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1049947201	NA	P-0046091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	112	682	0	ENST00000396373.4:c.678G>C	p.Glu226Asp	p.E226D	ENST00000396373	NM_001987.4	226	gaG/gaC	5/8	1	2	FACETS	0.344	0.308	0.382	0.344	0.308	0.382	SUBCLONAL	1	TRUE	1	0.595727125824788	2		682	1093	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428067	49428067	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772010347	NA	P-0046091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	318	652	0	ENST00000301067.7:c.10523G>A	p.Arg3508Gln	p.R3508Q	ENST00000301067	NM_003482.3	3508	cGg/cAg	38/54	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.595727125824788	2		652	1036	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202771	133202771	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	288	680	0	ENST00000320574.5:c.6463G>A	p.Glu2155Lys	p.E2155K	ENST00000320574	NM_006231.2	2155	Gag/Aag	46/49	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.595727125824788	2		680	935	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100085	30100085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	501	658	0	ENST00000331968.5:c.1535G>A	p.Ser512Asn	p.S512N	ENST00000331968	NM_002742.2	512	aGc/aAc	10/18	1	2	FACETS	0.762	0.732	0.792	1	0.997	1	SUBCLONAL	2	TRUE	1	0.595727125824788	2		658	1104	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020543	14020543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	66	408	0	ENST00000311895.7:c.514G>A	p.Asp172Asn	p.D172N	ENST00000311895	NM_005236.2	172	Gat/Aat	3/11	0.41411783684519	5	FACETS	0.39	0.337	0.448			1	SUBCLONAL	1	TRUE	NA	0.595727125824788	5		408	1076	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627158	37627158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	68	370	0	ENST00000447079.4:c.1073G>A	p.Arg358Lys	p.R358K	ENST00000447079	NM_015083.1	358	aGa/aAa	2/14	0.404218288526571	4	FACETS	0.472	0.41	0.54	0.236	0.205	0.27	SUBCLONAL	1	TRUE	2	0.595727125824788	4		370	771	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78899247	78899247	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	331	597	0	ENST00000306801.3:c.2886G>C	p.Trp962Cys	p.W962C	ENST00000306801	NM_020761.2	962	tgG/tgC	24/34	0.595727125824788	3	FACETS	1	0.989	1	0.586	0.554	0.62	CLONAL	1	TRUE	1	0.595727125824788	3		597	1230	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11022891	11022891	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	94	904	0	ENST00000327064.4:c.590T>C	p.Ile197Thr	p.I197T	ENST00000327064	NM_199141.1	197	aTc/aCc	5/16	1	2	FACETS	0.238	0.211	0.267	0.238	0.211	0.267	SUBCLONAL	1	TRUE	1	0.595727125824788	2		904	1326	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46266471	46266471	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0046091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	42	389	0	ENST00000371998.3:c.2456C>G	p.Ser819Ter	p.S819*	ENST00000371998		819	tCa/tGa	13/23	0.158148497724441	5	FACETS	0.376	0.312	0.446	0.125	0.104	0.149	INDETERMINATE	1	TRUE	2	0.595727125824788	5		389	711	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278198	41278198	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	45	340	0	ENST00000349496.5:c.2074G>A	p.Glu692Lys	p.E692K	ENST00000349496	NM_001904.3	692	Gag/Aag	13/15	0.185407459901017	4	FACETS	0.374	0.313	0.441	0.187	0.156	0.221	INDETERMINATE	1	TRUE	2	0.595727125824788	4		340	645	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643360	52643360	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	69	381	0	ENST00000394830.3:c.2536G>C	p.Glu846Gln	p.E846Q	ENST00000394830	NM_018313.4	846	Gaa/Caa	17/30	0.185407459901017	4	FACETS	0.504	0.438	0.575	0.252	0.219	0.288	INDETERMINATE	1	TRUE	2	0.595727125824788	4		381	734	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680487	30680487	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0046091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	101	610	0	ENST00000376406.3:c.1232C>G	p.Ser411Ter	p.S411*	ENST00000376406	NM_014641.2	411	tCa/tGa	5/15	0.595727125824788	3	FACETS	0.419	0.373	0.468	0.14	0.124	0.156	SUBCLONAL	1	TRUE	0	0.595727125824788	3		610	1050	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046418	69046418	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	93	546	0	ENST00000288368.4:c.3891G>C	p.Glu1297Asp	p.E1297D	ENST00000288368	NM_024870.2	1297	gaG/gaC	32/40	0.185407459901017	4	FACETS	0.479	0.424	0.537	0.239	0.212	0.269	INDETERMINATE	1	TRUE	2	0.595727125824788	4		546	1041	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072585	5072585	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1289792896	NA	P-0046091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	40	335	0	ENST00000381652.3:c.1735C>G	p.Leu579Val	p.L579V	ENST00000381652	NM_004972.3	579	Ctt/Gtt	13/25	1	2	FACETS	0.28	0.232	0.333	0.28	0.232	0.333	SUBCLONAL	1	TRUE	1	0.595727125824788	2		335	480	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024458	31024458	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	TT	novel	NA	P-0046091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	76	660	0	ENST00000375687.4:c.3943delinsTT	p.Gln1315LeufsTer14	p.Q1315Lfs*14	ENST00000375687	NM_015338.5	1315	Cag/TTag	13/13	0.158148497724441	5	FACETS	0.379	0.331	0.431	0.126	0.11	0.144	INDETERMINATE	1	TRUE	2	0.595727125824788	5		660	1275	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512314	38512319	+	missense_variant	Missense_Mutation	ONP	CTCATC	CTCATC	TTCATT	novel	NA	P-0046091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1278	303	746	0	ENST00000254066.5:c.1225_1230delinsTTCATT	p.Leu409Phe	p.L409F	ENST00000254066	NM_000964.3	409	CTCATC/TTCATT	9/9	0.404218288526571	4	FACETS	1	0.959	1	0.513	0.482	0.546	CLONAL	1	TRUE	2	0.595727125824788	4		746	1581	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0046092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	373	765	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.483144430985927	10	FACETS	0.999	0.979	1			1	CLONAL	11	FALSE	NA	0.483144430985927	10		765	412	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	46	416	0	ENST00000335508.6:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000335508	NM_012433.2	902	Gaa/Aaa	18/25	0.118845136440746	4	FACETS	0.899	0.772	1	0.899	0.772	1	INDETERMINATE	2	FALSE	2	0.483144430985927	4		416	157	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566442	41566442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	46	341	0	ENST00000263253.7:c.4319C>T	p.Pro1440Leu	p.P1440L	ENST00000263253	NM_001429.3	1440	cCa/cTa	27/31	0.484499377920372	3	FACETS	1	0.949	1	0.639	0.546	0.739	CLONAL	1	FALSE	1	0.483144430985927	3		341	185	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981167	201981168	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	725	996	0	ENST00000359651.3:c.248dup	p.Asn83LysfsTer9	p.N83Kfs*9	ENST00000359651		82	-/A	2/8	0.484499377920372	4	FACETS	1	0.995	1	1	0.998	1	CLONAL	4	FALSE	1	0.483144430985927	4		996	1040	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779192	135779192	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0046092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	81	369	0	ENST00000298552.3:c.2054C>G	p.Ser685Ter	p.S685*	ENST00000298552	NM_001162426.1	685	tCa/tGa	17/23	0.484499377920372	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	3	FALSE	0	0.483144430985927	3		369	126	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661952	29661952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	29	382	1	ENST00000356175.3:c.5846G>A	p.Arg1949Lys	p.R1949K	ENST00000356175	NM_000267.3	1949	aGa/aAa	39/57	0.466951165522191	4	FACETS	0.767	0.619	0.934	0.384	0.309	0.467	CLONAL	1	FALSE	2	0.483144430985927	4		383	232	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747098	40747098	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	11	621	0	ENST00000373198.4:c.2984G>C	p.Trp995Ser	p.W995S	ENST00000373198	NM_133170.3	995	tGg/tCg	22/32	0.277484913209185	4	FACETS	0.334	0.231	0.463	0.167	0.115	0.232	INDETERMINATE	1	FALSE	2	0.483144430985927	4		621	202	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12647715	12647715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	73	252	0	ENST00000251849.4:c.665C>T	p.Ser222Phe	p.S222F	ENST00000251849	NM_002880.3	222	tCc/tTc	6/17	0.483144430985927	8	FACETS	1	0.896	1	0.607	0.538	0.679	CLONAL	3	FALSE	3	0.483144430985927	8		252	244	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805482	1805482	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	583	868	1	ENST00000260795.2:c.994G>C	p.Glu332Gln	p.E332Q	ENST00000260795		332	Gag/Cag	7/17	0.483144430985927	10	FACETS	1	0.993	1			1	CLONAL	11	FALSE	NA	0.483144430985927	10		869	635	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522640	67522640	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	32	327	0	ENST00000274335.5:c.137A>G	p.Gln46Arg	p.Q46R	ENST00000274335		46	cAg/cGg	1/15	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.483144430985927	NA		327	189	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370865	55370865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	77	733	0	ENST00000297316.4:c.167C>T	p.Ala56Val	p.A56V	ENST00000297316	NM_022454.3	56	gCc/gTc	1/2	0.263796396423675	2	FACETS	1	0.911	1	1	0.911	1	INDETERMINATE	2	FALSE	0	0.483144430985927	2		733	158	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457279	67457284	+	missense_variant	Missense_Mutation	ONP	CATGTC	CATGTC	TATGTA	novel	NA	P-0046092-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	181	866	1	ENST00000327367.4:c.253_258delinsTATGTA	p.His85Tyr	p.H85Y	ENST00000327367	NM_005902.3	85	CATGTC/TATGTA	2/9	0.263796396423675	2	FACETS	1	0.969	1	1	0.969	1	INDETERMINATE	2	FALSE	0	0.483144430985927	2		867	356	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	418	69	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.384600329132035	4	FACETS	1	0.99	1			1	CLONAL	3	TRUE	NA	0.472182804730524	4		69	792	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971177	21971177	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913382	NA	P-0046093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	357	561	0	ENST00000304494.5:c.181G>T	p.Glu61Ter	p.E61*	ENST00000304494	NM_000077.4	61	Gag/Tag	2/3	0.459590539277038	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.472182804730524	2		561	675	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578224	7578224	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1429743956	NA	P-0046093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	433	767	0	ENST00000269305.4:c.625A>T	p.Arg209Ter	p.R209*	ENST00000269305	NM_001126112.2	209	Aga/Tga	6/11	0.395163607028841	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.472182804730524	2		767	894	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243906	41243906	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs398122675	NA	P-0046093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	206	551	0	ENST00000357654.3:c.3642G>T	p.Glu1214Asp	p.E1214D	ENST00000357654	NM_007294.3	1214	gaG/gaT	10/23	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.472182804730524	2		551	794	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259176	89259177	+	missense_variant	Missense_Mutation	DNP	AT	AT	TA	novel	NA	P-0046093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	35	356	0	ENST00000336596.2:c.320_321delinsTA	p.Asn107Ile	p.N107I	ENST00000336596	NM_005233.5	107	aAT/aTA	3/17	0.469663927167691	3	FACETS	0.305	0.249	0.368	0.153	0.124	0.184	SUBCLONAL	1	TRUE	1	0.472182804730524	3		356	600	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836325	151836326	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0046093-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	170	495	0	ENST00000262189.6:c.14478_14479dup	p.Phe4827CysfsTer9	p.F4827Cfs*9	ENST00000262189	NM_170606.2	4827	ttc/tGTtc	57/59	0.469663927167691	3	FACETS	0.978	0.9	1	0.489	0.45	0.53	CLONAL	1	TRUE	1	0.472182804730524	3		495	910	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578412	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCGCCTCA	CAGCGCCTCA	-	novel	NA	P-0046094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	288	863	0	ENST00000269305.4:c.518_527del	p.Val173AlafsTer71	p.V173Afs*71	ENST00000269305	NM_001126112.2	173	gTGAGGCGCTGc/gc	5/11	0.953348405074709	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.953348405074709	1		863	311	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939827	76939828	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TTAA	novel	NA	P-0046094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	130	584	0	ENST00000373344.5:c.920_921insTTAA	p.Lys307AsnfsTer2	p.K307Nfs*2	ENST00000373344	NM_000489.3	307	aaa/aaTTAAa	9/35	0.304141121741502	1	FACETS	0.562	0.521	0.603	0.562	0.521	0.603	INDETERMINATE	1	TRUE	0	0.953348405074709	1		584	254	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	70	69	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.789	0.691	0.893	0.789	0.691	0.893	SUBCLONAL	1	TRUE	1	0.461170925303785	2		69	385	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0046096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	147	357	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.461170925303785	2		357	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0046096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	206	763	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	1	2	FACETS	0.95	0.882	1	0.95	0.882	1	CLONAL	1	TRUE	1	0.461170925303785	2		763	940	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0046096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	270	780	3	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.461170925303785	2		783	1146	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247878	59247878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	304	885	0	ENST00000371222.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000371222	NM_002228.3	289	Gct/Act	1/1	1	2	FACETS	0.995	0.936	1	0.995	0.936	1	CLONAL	1	TRUE	1	0.461170925303785	2		885	1325	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202590	67202590	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	282	963	0	ENST00000312629.5:c.1399C>G	p.Pro467Ala	p.P467A	ENST00000312629	NM_003952.2	467	Ccc/Gcc	15/15	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.461170925303785	2		963	1205	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557426	95557426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	96	418	0	ENST00000393063.1:c.5548C>T	p.Pro1850Ser	p.P1850S	ENST00000393063	NM_030621.3	1850	Ccc/Tcc	27/28	1	2	FACETS	0.982	0.88	1	0.982	0.88	1	CLONAL	1	TRUE	1	0.461170925303785	2		418	424	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119945	70119946	+	stop_gained,inframe_insertion	Nonsense_Mutation	INS	-	-	GTA	novel	NA	P-0046096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	158	517	0	ENST00000245479.2:c.948_949insTAG	p.Thr316_Gly317insTer	p.T316_G317ins*	ENST00000245479	NM_000346.3	316	acg/acGTAg	3/3	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.461170925303785	2		517	660	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39618806	39618806	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	43	234	0	ENST00000262039.4:c.2030C>T	p.Thr677Ile	p.T677I	ENST00000262039	NM_002647.2	677	aCa/aTa	18/25	0.461170925303785	1	FACETS	0.776	0.658	0.902	0.776	0.658	0.902	CLONAL	1	TRUE	0	0.461170925303785	1		234	185	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228077	36228077	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	278	883	0	ENST00000222270.7:c.7463A>G	p.Tyr2488Cys	p.Y2488C	ENST00000222270	NM_014727.1	2488	tAt/tGt	33/37	0.420031718392739	3	FACETS	1	0.984	1	0.573	0.537	0.61	CLONAL	1	TRUE	1	0.461170925303785	3		883	1295	SUCCESS
APC	324	MSKCC	GRCh37	5	112151204	112151204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201856	NA	P-0046096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	85	327	0	ENST00000257430.4:c.847C>T	p.Arg283Ter	p.R283*	ENST00000257430	NM_000038.5	283	Cga/Tga	9/16	1	2	FACETS	0.901	0.801	1	0.901	0.801	1	CLONAL	1	TRUE	1	0.461170925303785	2		327	409	SUCCESS
APC	324	MSKCC	GRCh37	5	112175783	112175786	+	frameshift_variant	Frame_Shift_Del	DEL	GATG	GATG	-	novel	NA	P-0046096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	67	317	0	ENST00000257430.4:c.4495_4498del	p.Gly1499PhefsTer7	p.G1499Ffs*7	ENST00000257430	NM_000038.5	1498	GATGga/ga	16/16	1	2	FACETS	0.792	0.692	0.899	0.792	0.692	0.899	SUBCLONAL	1	TRUE	1	0.461170925303785	2		317	367	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508164	106508164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540366635	NA	P-0046096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	86	343	0	ENST00000359195.3:c.158G>A	p.Ser53Asn	p.S53N	ENST00000359195	NM_002649.2	53	aGc/aAc	2/11	0.45145583504742	3	FACETS	0.948	0.842	1	0.474	0.421	0.531	CLONAL	1	TRUE	1	0.461170925303785	3		343	484	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372193	55372193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753081636	NA	P-0046096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	168	457	0	ENST00000297316.4:c.883G>A	p.Val295Met	p.V295M	ENST00000297316	NM_022454.3	295	Gtg/Atg	2/2	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.461170925303785	2		457	715	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412367	63412367	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	268	955	1	ENST00000330258.3:c.800C>A	p.Ser267Ter	p.S267*	ENST00000330258	NM_152424.3	267	tCa/tAa	2/2	0.461170925303785	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.461170925303785	1		956	880	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0046097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	302	284	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.759522870621972	NA		284	621	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881329	37881329	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	751	942	0	ENST00000269571.5:c.2521C>G	p.Leu841Val	p.L841V	ENST00000269571		841	Ctc/Gtc	21/27	0.716530776261691	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.759522870621972	3		942	1339	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913471	NA	P-0046097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	756	1056	0	ENST00000269571.5:c.2329G>C	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ctg	20/27	0.716530776261691	3	FACETS	0.978	0.949	1	0.978	0.949	1	CLONAL	2	TRUE	1	0.759522870621972	3		1056	1404	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433896	49433896	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	478	1245	0	ENST00000301067.7:c.7657C>T	p.Gln2553Ter	p.Q2553*	ENST00000301067	NM_003482.3	2553	Cag/Tag	31/54	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.759522870621972	2		1245	1147	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257806	133257806	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148269473	NA	P-0046097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	262	589	1	ENST00000320574.5:c.122C>T	p.Thr41Met	p.T41M	ENST00000320574	NM_006231.2	41	aCg/aTg	2/49	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.759522870621972	2		590	675	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249511	153249511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	386	553	0	ENST00000281708.4:c.1267G>A	p.Gly423Arg	p.G423R	ENST00000281708	NM_033632.3	423	Gga/Aga	9/12	0.716530776261691	3	FACETS	0.983	0.943	1	0.983	0.943	1	CLONAL	2	TRUE	1	0.759522870621972	3		553	713	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820903	3820903	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	756	895	1	ENST00000262367.5:c.2548C>T	p.Gln850Ter	p.Q850*	ENST00000262367	NM_004380.2	850	Cag/Tag	14/31	0.759522870621972	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.759522870621972	2		896	977	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190691	108190691	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	230	364	0	ENST00000278616.4:c.6358G>T	p.Glu2120Ter	p.E2120*	ENST00000278616	NM_000051.3	2120	Gaa/Taa	44/63	0.759522870621972	2	FACETS	0.94	0.9	0.979	0.94	0.9	0.979	CLONAL	2	TRUE	0	0.759522870621972	2		364	322	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711991	89711991	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	135	378	0	ENST00000371953.3:c.609T>G	p.Ile203Met	p.I203M	ENST00000371953	NM_000314.4	203	atT/atG	6/9	1	2	FACETS	0.943	0.867	1	0.943	0.867	1	CLONAL	1	TRUE	1	0.759522870621972	2		378	377	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95596442	95596442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1177718322	NA	P-0046097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	95	331	0	ENST00000393063.1:c.526G>A	p.Glu176Lys	p.E176K	ENST00000393063	NM_030621.3	176	Gag/Aag	6/28	0.759522870621972	3	FACETS	0.824	0.738	0.914	0.412	0.369	0.457	CLONAL	1	TRUE	1	0.759522870621972	3		331	419	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37871714	37871714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	309	901	0	ENST00000269571.5:c.1238C>T	p.Ser413Leu	p.S413L	ENST00000269571		413	tCa/tTa	11/27	0.716530776261691	3	FACETS	0.863	0.813	0.915	0.431	0.406	0.458	CLONAL	1	TRUE	1	0.759522870621972	3		901	1301	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872207	45872207	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	567	841	0	ENST00000391945.4:c.227C>G	p.Thr76Ser	p.T76S	ENST00000391945	NM_000400.3	76	aCt/aGt	4/23	0.314235662056713	5	FACETS	1	0.995	1	0.796	0.766	0.827	INDETERMINATE	2	TRUE	2	0.759522870621972	5		841	1337	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641538	47641538	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1553352545	NA	P-0046097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	124	345	0	ENST00000233146.2:c.923G>C	p.Arg308Thr	p.R308T	ENST00000233146	NM_000251.2	308	aGa/aCa	5/16	1	2	FACETS	0.928	0.849	1	0.928	0.849	1	CLONAL	1	TRUE	1	0.759522870621972	2		345	352	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025783	48025783	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757817018	NA	P-0046097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	57	210	0	ENST00000234420.5:c.661G>A	p.Glu221Lys	p.E221K	ENST00000234420	NM_000179.2	221	Gaa/Aaa	4/10	1	2	FACETS	0.711	0.619	0.809	0.711	0.619	0.809	SUBCLONAL	1	TRUE	1	0.759522870621972	2		210	211	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321504	62321504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	371	1099	0	ENST00000360203.5:c.2206G>A	p.Asp736Asn	p.D736N	ENST00000360203	NM_001283009.1	736	Gac/Aac	25/35	0.716530776261691	3	FACETS	1	0.95	1	0.501	0.475	0.528	CLONAL	1	TRUE	1	0.759522870621972	3		1099	1345	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156625	106156625	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	167	455	0	ENST00000380013.4:c.1526C>T	p.Ser509Leu	p.S509L	ENST00000380013	NM_001127208.2	509	tCa/tTa	3/11	0.716530776261691	3	FACETS	0.991	0.915	1	0.496	0.457	0.535	CLONAL	1	TRUE	1	0.759522870621972	3		455	612	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637588	176637588	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	201	526	0	ENST00000439151.2:c.2188C>G	p.Leu730Val	p.L730V	ENST00000439151	NM_022455.4	730	Ctc/Gtc	5/23	0.716530776261691	3	FACETS	0.882	0.819	0.947	0.441	0.409	0.474	CLONAL	1	TRUE	1	0.759522870621972	3		526	828	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289340	33289340	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	502	451	0	ENST00000374542.5:c.212T>G	p.Leu71Arg	p.L71R	ENST00000374542	NM_001141970.1	71	cTt/cGt	3/8	0.759522870621972	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.759522870621972	3		451	603	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509861	106509861	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	230	686	0	ENST00000359195.3:c.1855C>G	p.Gln619Glu	p.Q619E	ENST00000359195	NM_002649.2	619	Caa/Gaa	2/11	0.759522870621972	3	FACETS	0.891	0.831	0.952	0.445	0.415	0.476	CLONAL	1	TRUE	1	0.759522870621972	3		686	938	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054709	5054709	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	252	327	0	ENST00000381652.3:c.761A>G	p.Tyr254Cys	p.Y254C	ENST00000381652	NM_004972.3	254	tAt/tGt	7/25	0.759522870621972	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.759522870621972	2		327	330	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922734	44922734	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0046097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	178	255	0	ENST00000377967.4:c.1595C>G	p.Ser532Ter	p.S532*	ENST00000377967	NM_021140.2	532	tCa/tGa	16/29	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.759522870621972	1		255	241	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205114	123205114	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0046097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	331	242	0	ENST00000218089.9:c.2474T>A	p.Leu825Ter	p.L825*	ENST00000218089	NM_001042749.1	825	tTg/tAg	25/35	0.759522870621972	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.759522870621972	2		242	382	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750639	128750639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775522201	NA	P-0046098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	222	739	0	ENST00000377970.2:c.176C>T	p.Ala59Val	p.A59V	ENST00000377970	NM_002467.4	59	gCg/gTg	2/3	0.722830257644411	4	FACETS	0.964	0.907	1	0.964	0.907	1	CLONAL	2	TRUE	2	0.897133476034942	4		739	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578537	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs879254214	NA	P-0046098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	774	1099	1	ENST00000269305.4:c.393_395del	p.Asn131del	p.N131del	ENST00000269305	NM_001126112.2	131	aaCAAg/aag	5/11	0.897133476034942	3	FACETS	0.978	0.964	0.99	0.978	0.964	0.99	CLONAL	3	TRUE	0	0.897133476034942	3		1100	852	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467829	66467829	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	27	337	0	ENST00000273854.3:c.440G>T	p.Cys147Phe	p.C147F	ENST00000273854	NM_004439.5	147	tGt/tTt	3/18	0.265908861513697	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.897133476034942	0		337	60	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500923	8500923	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	55	494	0	ENST00000356435.5:c.1959T>A	p.Asp653Glu	p.D653E	ENST00000356435		653	gaT/gaA	13/35	0.741016417985336	5	FACETS	0.89	0.766	1	0.297	0.255	0.342	CLONAL	1	TRUE	2	0.897133476034942	5		494	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576870	7576870	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs876659384	NA	P-0046101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	134	396	0	ENST00000269305.4:c.976G>T	p.Glu326Ter	p.E326*	ENST00000269305	NM_001126112.2	326	Gaa/Taa	9/11	0.270610656995208	2	FACETS	1	0.986	1	0.722	0.659	0.787	CLONAL	1	TRUE	0	0.35155847573569	2		396	528	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47600981	47600981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	98	330	1	ENST00000263735.4:c.219G>A	p.Met73Ile	p.M73I	ENST00000263735	NM_002354.2	73	atG/atA	3/9	0.186448313756934	4	FACETS	1	0.98	1	0.722	0.646	0.802	INDETERMINATE	1	TRUE	2	0.35155847573569	4		331	522	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845871	151845871	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	59	408	1	ENST00000262189.6:c.13141G>T	p.Glu4381Ter	p.E4381*	ENST00000262189	NM_170606.2	4381	Gaa/Taa	52/59	0.255612269090131	4	FACETS	0.784	0.674	0.903			1	CLONAL	1	TRUE	NA	0.35155847573569	4		409	579	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864399	57864399	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	122	514	0	ENST00000228682.2:c.1876T>A	p.Tyr626Asn	p.Y626N	ENST00000228682	NM_005269.2	626	Tat/Aat	12/12	0.35155847573569	3	FACETS	0.996	0.901	1	0.332	0.3	0.366	CLONAL	1	TRUE	0	0.35155847573569	3		514	819	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248492	212248492	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	55	310	0	ENST00000342788.4:c.3775C>G	p.Leu1259Val	p.L1259V	ENST00000342788	NM_005235.2	1259	Ctg/Gtg	28/28	0.347497096251027	3	FACETS	0.948	0.814	1	0.474	0.407	0.547	CLONAL	1	TRUE	1	0.35155847573569	3		310	388	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713418	40713418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	151	468	0	ENST00000373198.4:c.4097C>T	p.Pro1366Leu	p.P1366L	ENST00000373198	NM_133170.3	1366	cCc/cTc	30/32	0.30467487848875	4	FACETS	0.854	0.783	0.928	0.427	0.391	0.464	CLONAL	2	TRUE	0	0.35155847573569	4		468	680	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637708	52637708	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	123	235	0	ENST00000394830.3:c.2608C>T	p.Gln870Ter	p.Q870*	ENST00000394830	NM_018313.4	870	Cag/Tag	18/30	0.280819239738912	3	FACETS	0.899	0.826	0.974	0.899	0.826	0.974	CLONAL	3	TRUE	0	0.35155847573569	3		235	305	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665118	138665118	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	134	343	0	ENST00000330315.3:c.447G>A	p.Met149Ile	p.M149I	ENST00000330315	NM_023067.3	149	atG/atA	1/1	0.30467487848875	4	FACETS	1	0.953	1	0.531	0.485	0.578	CLONAL	2	TRUE	0	0.35155847573569	4		343	485	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374684	149374684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	135	464	0	ENST00000360632.3:c.410C>T	p.Thr137Ile	p.T137I	ENST00000360632	NM_015472.4	137	aCt/aTt	2/7	0.30467487848875	4	FACETS	1	0.979	1	0.314	0.285	0.345	CLONAL	1	TRUE	0	0.35155847573569	4		464	826	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420645	49420645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	286	386	0	ENST00000301067.7:c.15104G>A	p.Cys5035Tyr	p.C5035Y	ENST00000301067	NM_003482.3	5035	tGt/tAt	48/54	0.428818275519559	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.508541820857522	4		386	818	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543268	65543268	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs17852278	NA	P-0046102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	184	263	0	ENST00000358664.4:c.409G>T	p.Gly137Cys	p.G137C	ENST00000358664	NM_002382.4	137	Ggc/Tgc	5/5	0.505487003403286	2	FACETS	0.955	0.895	1	0.955	0.895	1	CLONAL	2	TRUE	0	0.508541820857522	2		263	379	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478113	99478113	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	216	274	0	ENST00000268035.6:c.3017G>T	p.Gly1006Val	p.G1006V	ENST00000268035	NM_000875.3	1006	gGg/gTg	16/21	0.455133355988649	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.508541820857522	3		274	481	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0046102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	342	275	0	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.496294913385744	3	FACETS	0.997	0.956	1	0.997	0.956	1	CLONAL	3	TRUE	0	0.508541820857522	3		275	564	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8111110	8111110	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1272390478	NA	P-0046102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	177	448	0	ENST00000585124.1:c.97C>A	p.Pro33Thr	p.P33T	ENST00000585124	NM_004217.3	33	Cct/Act	3/9	0.496294913385744	3	FACETS	1	0.978	1	0.384	0.355	0.415	CLONAL	1	TRUE	0	0.508541820857522	3		448	757	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004725	16004725	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	97	338	0	ENST00000268712.3:c.2529A>T	p.Glu843Asp	p.E843D	ENST00000268712	NM_006311.3	843	gaA/gaT	20/46	0.455133355988649	3	FACETS	0.876	0.784	0.974	0.438	0.392	0.487	CLONAL	1	TRUE	1	0.508541820857522	3		338	546	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068403	26068403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs868222609	NA	P-0046102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	98	203	0	ENST00000435504.4:c.87G>T	p.Met29Ile	p.M29I	ENST00000435504		29	atG/atT	2/13	0.384387553591407	5	FACETS	1	0.981	1	0.494	0.443	0.548	CLONAL	1	TRUE	2	0.508541820857522	5		203	458	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371721	225371721	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0046102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	45	205	0	ENST00000264414.4:c.884-1G>C		p.X295_splice	ENST00000264414	NM_003590.4	295			0.452359871851645	3	FACETS	0.841	0.712	0.981	0.42	0.356	0.491	CLONAL	1	TRUE	1	0.508541820857522	3		205	264	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560829	9560829	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	197	250	0	ENST00000353224.5:c.953A>G	p.Tyr318Cys	p.Y318C	ENST00000353224	NM_177990.2	318	tAc/tGc	4/10	0.428818275519559	4	FACETS	0.915	0.851	0.98	0.915	0.851	0.98	CLONAL	2	TRUE	2	0.508541820857522	4		250	639	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565575	41565575	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	134	158	0	ENST00000263253.7:c.4241A>G	p.Tyr1414Cys	p.Y1414C	ENST00000263253	NM_001429.3	1414	tAt/tGt	26/31	0.508541820857522	3	FACETS	0.939	0.864	1	0.939	0.864	1	CLONAL	2	TRUE	1	0.508541820857522	3		158	352	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540539	187540540	+	stop_gained	Nonsense_Mutation	DNP	CG	CG	AC	novel	NA	P-0046102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	118	230	1	ENST00000441802.2:c.7200_7201delinsGT	p.Ser2400_Glu2401delinsArgTer	p.S2400_E2401delinsR*	ENST00000441802	NM_005245.3	2400	agCGag/agGTag	10/27	0.505487003403286	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	0	0.508541820857522	2		231	232	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31431749	31431749	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	130	176	0	ENST00000344624.3:c.3079G>T	p.Gly1027Trp	p.G1027W	ENST00000344624		1027	Ggg/Tgg	23/33	0.428818275519559	4	FACETS	0.936	0.857	1	0.936	0.857	1	CLONAL	2	TRUE	2	0.508541820857522	4		176	412	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871251	35871251	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	46	183	0	ENST00000303115.3:c.473A>T	p.Lys158Met	p.K158M	ENST00000303115	NM_002185.3	158	aAg/aTg	4/8	0.428818275519559	4	FACETS	0.702	0.592	0.822	0.351	0.296	0.411	SUBCLONAL	1	TRUE	2	0.508541820857522	4		183	389	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839969	27839969	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	219	429	0	ENST00000328488.2:c.125A>T	p.Tyr42Phe	p.Y42F	ENST00000328488	NM_003533.2	42	tAc/tTc	1/1	0.428818275519559	4	FACETS	0.862	0.804	0.921	0.862	0.804	0.921	CLONAL	2	TRUE	2	0.508541820857522	4		429	754	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358920	81358920	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0046102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	135	193	0	ENST00000222390.5:c.1040+1G>A		p.X347_splice	ENST00000222390	NM_000601.4	347			0.428818275519559	4	FACETS	0.947	0.868	1	0.947	0.868	1	CLONAL	2	TRUE	2	0.508541820857522	4		193	423	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974676	21974676	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0046102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	224	266	0	ENST00000304494.5:c.150+1G>T		p.X50_splice	ENST00000304494	NM_000077.4	50			0.505487003403286	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.508541820857522	2		266	428	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099397	27099397	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	235	309	0	ENST00000324856.7:c.3634C>T	p.Gln1212Ter	p.Q1212*	ENST00000324856	NM_006015.4	1212	Cag/Tag	14/20	0.347112814327931	3	FACETS	1	0.979	1	0.713	0.675	0.751	INDETERMINATE	2	TRUE	0	0.645976946109123	3		309	450	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0046104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	237	236	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.645976946109123	3	FACETS	0.93	0.889	0.97	0.93	0.889	0.97	CLONAL	3	TRUE	0	0.645976946109123	3		236	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	rs786202799	NA	P-0046104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	392	450	0	ENST00000269305.4:c.376-2A>T		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.645976946109123	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.645976946109123	2		450	584	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692949	89692949	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167627	NA	P-0046104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	227	314	0	ENST00000371953.3:c.437del	p.Leu146Ter	p.L146*	ENST00000371953	NM_000314.4	145	Ttt/tt	5/9	0.645976946109123	2	FACETS	0.96	0.913	1	0.96	0.913	1	CLONAL	2	TRUE	0	0.645976946109123	2		314	366	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799086	45799086	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	330	533	1	ENST00000450313.1:c.347G>T	p.Arg116Leu	p.R116L	ENST00000450313	NM_012222.2	116	cGg/cTg	3/16	0.347112814327931	3	FACETS	1	0.991	1	0.766	0.733	0.8	INDETERMINATE	2	TRUE	0	0.645976946109123	3		534	588	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410704	32410704	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	77	251	0	ENST00000332351.3:c.1454G>T	p.Arg485Leu	p.R485L	ENST00000332351	NM_024426.4	485	cGg/cTg	10/10	1	2	FACETS	0.774	0.686	0.867	0.774	0.686	0.867	SUBCLONAL	1	TRUE	1	0.645976946109123	2		251	308	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231486	46231486	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	162	154	0	ENST00000334344.6:c.1326C>G	p.Ser442Arg	p.S442R	ENST00000334344	NM_152641.2	442	agC/agG	10/21	0.645976946109123	3	FACETS	0.983	0.933	1	0.983	0.933	1	CLONAL	3	TRUE	0	0.645976946109123	3		154	225	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003750	45003759	+	frameshift_variant	Frame_Shift_Del	DEL	TCGCTCCGTG	TCGCTCCGTG	-	novel	NA	P-0046104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	209	372	0	ENST00000558401.1:c.6_15del	p.Arg3ProfsTer2	p.R3Pfs*2	ENST00000558401	NM_004048.2	2	tcTCGCTCCGTG/tc	1/4	0.615296585698164	2	FACETS	0.865	0.818	0.912	0.865	0.818	0.912	CLONAL	2	TRUE	0	0.645976946109123	2		372	374	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25990544	25990544	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0046104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	112	281	0	ENST00000435504.4:c.683C>G	p.Ser228Ter	p.S228*	ENST00000435504		228	tCa/tGa	8/13	0.43273443123673	3	FACETS	1	0.965	1	0.566	0.513	0.621	CLONAL	1	TRUE	1	0.645976946109123	3		281	405	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466824	57466824	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	71	137	0	ENST00000371085.3:c.43G>C	p.Glu15Gln	p.E15Q	ENST00000371085	NM_000516.4	15	Gag/Cag	1/13	0.349421045199618	3	FACETS	1	0.97	1	0.658	0.583	0.736	INDETERMINATE	1	TRUE	1	0.645976946109123	3		137	221	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435622	149435622	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs895002138	NA	P-0046104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	239	428	0	ENST00000286301.3:c.2521T>C	p.Tyr841His	p.Y841H	ENST00000286301	NM_005211.3	841	Tat/Cat	19/22	0.186434972837746	3	FACETS	0.975	0.921	1	0.65	0.614	0.686	INDETERMINATE	2	TRUE	0	0.645976946109123	3		428	502	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374409	81374409	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	141	200	0	ENST00000222390.5:c.653G>T	p.Ser218Ile	p.S218I	ENST00000222390	NM_000601.4	218	aGt/aTt	6/18	0.3401154899072	5	FACETS	1	0.941	1	0.685	0.63	0.742	INDETERMINATE	2	TRUE	2	0.645976946109123	5		200	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0046106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	341	376	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.752472098304073	2	FACETS	0.981	0.95	1	0.981	0.95	1	CLONAL	2	TRUE	0	0.780892343551856	2		376	445	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661964	29661964	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	217	226	0	ENST00000356175.3:c.5859del	p.Asp1955ThrfsTer3	p.D1955Tfs*3	ENST00000356175	NM_000267.3	1953	aTt/at	39/57	0.752472098304073	2	FACETS	0.972	0.932	1	0.972	0.932	1	CLONAL	2	TRUE	0	0.780892343551856	2		226	286	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293668	1293668	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	182	633	0	ENST00000310581.5:c.1333C>G	p.Pro445Ala	p.P445A	ENST00000310581	NM_198253.2	445	Ccc/Gcc	2/16	0.453455603219049	4	FACETS	0.74	0.682	0.801	0.37	0.341	0.401	INDETERMINATE	1	TRUE	2	0.780892343551856	4		633	1122	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882025	NA	P-0046108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	208	349	0	ENST00000269305.4:c.646G>C	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ctg	6/11	0.419935713440329	2	FACETS	0.891	0.833	0.949	0.891	0.833	0.949	CLONAL	2	TRUE	0	0.419935713440329	2		349	556	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129671	11129671	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	287	385	0	ENST00000358026.2:c.2481del	p.Ser828ProfsTer3	p.S828Pfs*3	ENST00000358026	NM_001128849.1	826	gCc/gc	17/36	0.419935713440329	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.419935713440329	2		385	643	SUCCESS
APC	324	MSKCC	GRCh37	5	112111390	112111390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs863225362	NA	P-0046108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	55	120	0	ENST00000257430.4:c.487C>T	p.Gln163Ter	p.Q163*	ENST00000257430	NM_000038.5	163	Cag/Tag	5/16	0.419935713440329	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.419935713440329	2		120	115	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672767	30672767	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1300485516	NA	P-0046108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	111	347	1	ENST00000376406.3:c.4193G>T	p.Arg1398Ile	p.R1398I	ENST00000376406	NM_014641.2	1398	aGa/aTa	10/15	0.382433664155477	3	FACETS	0.87	0.783	0.963	0.435	0.391	0.482	CLONAL	1	TRUE	1	0.419935713440329	3		348	735	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111168	193111168	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	162	108	0	ENST00000367435.3:c.701G>C	p.Arg234Pro	p.R234P	ENST00000367435	NM_024529.4	234	cGa/cCa	7/17	0.419935713440329	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	1	0.419935713440329	4		108	322	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372403	118372403	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	112	241	1	ENST00000534358.1:c.6336G>C	p.Glu2112Asp	p.E2112D	ENST00000534358	NM_005933.3	2112	gaG/gaC	26/36	0.41006828195312	3	FACETS	0.823	0.747	0.903	0.823	0.747	0.903	CLONAL	2	TRUE	1	0.419935713440329	3		242	392	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641506	18641506	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	41	154	0	ENST00000266497.5:c.2505C>G	p.Ile835Met	p.I835M	ENST00000266497		835	atC/atG	17/31	1	2	FACETS	0.817	0.686	0.96	0.817	0.686	0.96	CLONAL	1	TRUE	1	0.419935713440329	2		154	239	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856026	111856026	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	233	351	0	ENST00000341259.2:c.77G>T	p.Trp26Leu	p.W26L	ENST00000341259	NM_005475.2	26	tGg/tTg	2/8	0.382433664155477	3	FACETS	0.874	0.818	0.932	0.874	0.818	0.932	CLONAL	2	TRUE	1	0.419935713440329	3		351	768	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562804	95562804	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs772462662	NA	P-0046108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	59	180	0	ENST00000393063.1:c.4453A>C	p.Lys1485Gln	p.K1485Q	ENST00000393063	NM_030621.3	1485	Aaa/Caa	24/28	0.419935713440329	2	FACETS	1	0.898	1	0.52	0.452	0.594	CLONAL	1	TRUE	0	0.419935713440329	2		180	270	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724623	43724623	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	246	430	0	ENST00000382044.4:c.3444G>C	p.Leu1148Phe	p.L1148F	ENST00000382044	NM_001141980.1	1148	ttG/ttC	17/28	0.41006828195312	3	FACETS	0.879	0.825	0.936	0.879	0.825	0.936	CLONAL	2	TRUE	1	0.419935713440329	3		430	806	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43733751	43733751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	108	190	0	ENST00000382044.4:c.3071C>T	p.Ser1024Phe	p.S1024F	ENST00000382044	NM_001141980.1	1024	tCt/tTt	15/28	0.41006828195312	3	FACETS	0.943	0.856	1	0.943	0.856	1	CLONAL	2	TRUE	1	0.419935713440329	3		190	330	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831674	72831674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	216	356	0	ENST00000268489.5:c.4907G>A	p.Ser1636Asn	p.S1636N	ENST00000268489	NM_006885.3	1636	aGc/aAc	9/10	0.419935713440329	2	FACETS	0.976	0.916	1	0.976	0.916	1	CLONAL	2	TRUE	0	0.419935713440329	2		356	527	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11999012	11999012	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0046108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	87	135	0	ENST00000353533.5:c.513+1G>T		p.X171_splice	ENST00000353533	NM_003010.3	171			0.419935713440329	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.419935713440329	2		135	174	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47679358	47679358	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	181	225	0	ENST00000347630.2:c.849G>C	p.Glu283Asp	p.E283D	ENST00000347630	NM_001007230.1	283	gaG/gaC	10/11	0.382433664155477	3	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	1	0.419935713440329	3		225	514	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622538	158622538	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	301	272	0	ENST00000263640.3:c.961A>G	p.Ile321Val	p.I321V	ENST00000263640	NM_001105.4	321	Ata/Gta	8/11	0.275782602304481	5	FACETS	1	0.987	1			1	CLONAL	3	TRUE	NA	0.419935713440329	5		272	692	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119595335	119595335	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	120	144	0	ENST00000316626.5:c.834G>T	p.Arg278Ser	p.R278S	ENST00000316626		278	agG/agT	8/12	0.419935713440329	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	0	0.419935713440329	3		144	201	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526299	189526299	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	91	284	0	ENST00000264731.3:c.563A>T	p.Lys188Met	p.K188M	ENST00000264731	NM_003722.4	188	aAg/aTg	4/14	0.388933401893147	4	FACETS	0.954	0.848	1	0.477	0.424	0.534	CLONAL	1	TRUE	2	0.419935713440329	4		284	645	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582116	189582117	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0046108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	65	262	0	ENST00000264731.3:c.675_676delinsAA	p.Arg226Ser	p.R226S	ENST00000264731	NM_003722.4	225	atCCgc/atAAgc	5/14	0.388933401893147	4	FACETS	0.754	0.654	0.862	0.377	0.327	0.431	SUBCLONAL	1	TRUE	2	0.419935713440329	4		262	583	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980496	1980496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151213547	NA	P-0046108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	215	530	0	ENST00000382891.5:c.3958C>T	p.Arg1320Trp	p.R1320W	ENST00000382891	NM_133335.3	1320	Cgg/Tgg	22/22	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.419935713440329	2		530	936	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133583	55133583	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	68	264	0	ENST00000257290.5:c.887C>A	p.Thr296Asn	p.T296N	ENST00000257290	NM_006206.4	296	aCc/aAc	6/23	1	2	FACETS	0.953	0.834	1	0.953	0.834	1	CLONAL	1	TRUE	1	0.419935713440329	2		264	340	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940638	131940638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	127	187	0	ENST00000265335.6:c.2665G>A	p.Glu889Lys	p.E889K	ENST00000265335		889	Gag/Aag	16/25	0.419935713440329	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.419935713440329	2		187	267	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397235	397235	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	112	216	0	ENST00000380956.4:c.620G>T	p.Gly207Val	p.G207V	ENST00000380956	NM_001195286.1	207	gGc/gTc	5/9	0.382433664155477	3	FACETS	0.752	0.681	0.826	0.752	0.681	0.826	SUBCLONAL	2	TRUE	1	0.419935713440329	3		216	429	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675492	30675492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	272	410	0	ENST00000376406.3:c.2864G>A	p.Ser955Asn	p.S955N	ENST00000376406	NM_014641.2	955	aGc/aAc	8/15	0.382433664155477	3	FACETS	0.95	0.895	1	0.95	0.895	1	CLONAL	2	TRUE	1	0.419935713440329	3		410	825	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181023	32181023	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	296	455	0	ENST00000375023.3:c.2327G>T	p.Cys776Phe	p.C776F	ENST00000375023	NM_004557.3	776	tGc/tTc	15/30	0.382433664155477	3	FACETS	0.978	0.924	1	0.978	0.924	1	CLONAL	2	TRUE	1	0.419935713440329	3		455	872	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222519	157222519	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	287	289	0	ENST00000346085.5:c.1786C>G	p.Gln596Glu	p.Q596E	ENST00000346085	NM_020732.3	596	Cag/Gag	4/20	0.208679727726043	5	FACETS	1	0.984	1	1	0.984	1	INDETERMINATE	3	TRUE	2	0.419935713440329	5		289	675	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864481	162864481	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	138	218	1	ENST00000366898.1:c.32A>T	p.His11Leu	p.H11L	ENST00000366898	NM_004562.2	11	cAt/cTt	2/12	0.208679727726043	5	FACETS	1	0.975	1	0.775	0.71	0.841	INDETERMINATE	2	TRUE	2	0.419935713440329	5		219	461	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949733	151949733	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	138	196	0	ENST00000262189.6:c.1367G>C	p.Cys456Ser	p.C456S	ENST00000262189	NM_170606.2	456	tGt/tCt	10/59	0.190513330743771	3	FACETS	1	0.978	1	0.777	0.717	0.838	INDETERMINATE	2	TRUE	0	0.419935713440329	3		196	341	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38315034	38315034	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	222	343	0	ENST00000425967.3:c.30G>C	p.Arg10Ser	p.R10S	ENST00000425967	NM_001174067.1	10	agG/agC	3/19	0.419935713440329	2	FACETS	0.988	0.928	1	0.988	0.928	1	CLONAL	2	TRUE	0	0.419935713440329	2		343	535	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70971032	70971032	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	147	323	0	ENST00000276594.2:c.1229C>A	p.Thr410Asn	p.T410N	ENST00000276594	NM_024504.3	410	aCc/aAc	6/8	0.347428870571032	3	FACETS	1	0.981	1	0.623	0.57	0.678	CLONAL	1	TRUE	1	0.419935713440329	3		323	680	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739643	145739643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1544	357	561	0	ENST00000428558.2:c.1808G>A	p.Cys603Tyr	p.C603Y	ENST00000428558	NM_004260.3	603	tGc/tAc	11/22	0.419935713440329	5	FACETS	1	0.994	1	0.486	0.459	0.514	CLONAL	1	TRUE	2	0.419935713440329	5		561	1901	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039873	47039873	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	314	480	0	ENST00000377604.3:c.1216G>A	p.Ala406Thr	p.A406T	ENST00000377604	NM_001204468.1	406	Gcc/Acc	12/24	0.242177276676014	1	FACETS	0.808	0.767	0.849	1	0.995	1	INDETERMINATE	2	TRUE	0	0.419935713440329	1		480	731	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044531	47044531	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	208	448	0	ENST00000377604.3:c.2028C>G	p.Ile676Met	p.I676M	ENST00000377604	NM_001204468.1	676	atC/atG	18/24	0.242177276676014	1	FACETS	1	0.991	1	1	0.991	1	INDETERMINATE	1	TRUE	0	0.419935713440329	1		448	551	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224163	98224163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138154222	NA	P-0046109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	26	201	0	ENST00000331920.6:c.2678G>A	p.Arg893His	p.R893H	ENST00000331920	NM_000264.3	893	cGc/cAc	16/24	0.527869742474663	3	FACETS	0.378	0.3	0.468	0.189	0.15	0.234	SUBCLONAL	1	TRUE	1	0.527869742474663	3		201	329	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408930	41408930	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	27	162	0	ENST00000373198.4:c.496G>A	p.Glu166Lys	p.E166K	ENST00000373198	NM_133170.3	166	Gaa/Aaa	4/32	0.356223964084335	4	FACETS	0.467	0.371	0.575	0.233	0.185	0.288	SUBCLONAL	1	TRUE	2	0.527869742474663	4		162	335	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828184	243828184	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	10	154	0	ENST00000263826.5:c.174A>T	p.Lys58Asn	p.K58N	ENST00000263826	NM_005465.4	58	aaA/aaT	3/13	0.527869742474663	3	FACETS	0.278	0.189	0.391	0.139	0.094	0.196	SUBCLONAL	1	TRUE	1	0.527869742474663	3		154	172	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467828	50467828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1040607869	NA	P-0046110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	483	382	0	ENST00000331340.3:c.1063G>A	p.Ala355Thr	p.A355T	ENST00000331340	NM_006060.4	355	Gcg/Acg	8/8	0.194909028065978	3	FACETS	1	0.965	1	0.667	0.643	0.689	INDETERMINATE	2	TRUE	0	0.866648091079681	3		382	799	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579317	7579317	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	679	367	0	ENST00000269305.4:c.370T>C	p.Cys124Arg	p.C124R	ENST00000269305	NM_001126112.2	124	Tgc/Cgc	4/11	0.866648091079681	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.866648091079681	2		367	778	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101423	27101423	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	352	283	0	ENST00000324856.7:c.4706del	p.Pro1569HisfsTer43	p.P1569Hfs*43	ENST00000324856	NM_006015.4	1569	Cca/ca	18/20	0.36724691899764	4	FACETS	0.889	0.846	0.932	0.889	0.846	0.932	INDETERMINATE	2	TRUE	2	0.866648091079681	4		283	853	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241952	72241952	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	177	166	0	ENST00000357731.5:c.438T>A	p.Asn146Lys	p.N146K	ENST00000357731	NM_173808.2	146	aaT/aaA	3/7	0.853427245128106	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.866648091079681	2		166	198	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858977	243858977	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0046110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	133	211	0	ENST00000263826.5:c.88A>T	p.Lys30Ter	p.K30*	ENST00000263826	NM_005465.4	30	Aag/Tag	2/13	0.404758477269389	4	FACETS	0.924	0.853	0.996	0.924	0.853	0.996	INDETERMINATE	2	TRUE	2	0.866648091079681	4		211	310	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302276	15302276	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs774985086	NA	P-0046110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	1141	552	0	ENST00000263388.2:c.995G>T	p.Arg332Leu	p.R332L	ENST00000263388	NM_000435.2	332	cGc/cTc	6/33	0.866648091079681	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.866648091079681	3		552	1250	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606137	47606137	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	59	191	0	ENST00000263735.4:c.601C>A	p.Gln201Lys	p.Q201K	ENST00000263735	NM_002354.2	201	Caa/Aaa	6/9	0.849052348792348	2	FACETS	0.63	0.55	0.715	0.315	0.275	0.358	SUBCLONAL	1	TRUE	0	0.866648091079681	2		191	216	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0046111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	30	119	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.204994032156938	2	FACETS	1	0.851	1	0.529	0.429	0.64	CLONAL	1	TRUE	0	0.269022143262146	2		119	211	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	93	69	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.269022143262146	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.269022143262146	3		69	361	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0046111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	140	804	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	0.269022143262146	2	FACETS	1	0.976	1	0.602	0.548	0.658	CLONAL	1	TRUE	0	0.269022143262146	2		804	865	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0046111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	143	613	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.269022143262146	2	FACETS	1	0.985	1	0.69	0.63	0.754	CLONAL	1	TRUE	0	0.269022143262146	2		613	770	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669510	88669510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	22	199	1	ENST00000360948.2:c.1388G>A	p.Gly463Glu	p.G463E	ENST00000360948	NM_001012338.2	463	gGa/gAa	12/19	0.255617535966067	1	FACETS	0.426	0.33	0.538	0.426	0.33	0.538	SUBCLONAL	1	TRUE	0	0.269022143262146	1		200	332	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242725	66242725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768535351	NA	P-0046111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	13	138	0	ENST00000273854.3:c.1847G>A	p.Ser616Asn	p.S616N	ENST00000273854	NM_004439.5	616	aGc/aAc	9/18	0.204994032156938	2	FACETS	0.417	0.297	0.562	0.208	0.148	0.281	SUBCLONAL	1	TRUE	0	0.269022143262146	2		138	232	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614584	38614584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749378713	NA	P-0046111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	51	258	1	ENST00000299084.4:c.350G>A	p.Arg117Gln	p.R117Q	ENST00000299084	NM_152594.2	117	cGa/cAa	3/7	0.255617535966067	1	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	0	0.269022143262146	1		259	309	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138561	11138561	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	37	331	0	ENST00000358026.2:c.3317C>A	p.Thr1106Asn	p.T1106N	ENST00000358026	NM_001128849.1	1106	aCc/aAc	24/36	1	2	FACETS	0.447	0.368	0.537	0.447	0.368	0.537	SUBCLONAL	1	TRUE	1	0.269022143262146	2		331	615	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022295	26022295	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs944105395	NA	P-0046111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	171	306	1	ENST00000435504.4:c.362G>A	p.Gly121Asp	p.G121D	ENST00000435504		121	gGc/gAc	5/13	0.204994032156938	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.269022143262146	2		307	563	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180049806	180049806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs557205062	NA	P-0046111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	108	417	0	ENST00000261937.6:c.1582G>A	p.Val528Met	p.V528M	ENST00000261937	NM_182925.4	528	Gtg/Atg	12/30	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.269022143262146	2		417	705	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577591	7577591	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	123	319	0	ENST00000269305.4:c.690del	p.Thr231ProfsTer16	p.T231Pfs*16	ENST00000269305	NM_001126112.2	230	acC/ac	7/11	0.589636761744199	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.589636761744199	1		319	277	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287446	46287446	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs774801990	NA	P-0046112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	50	193	1	ENST00000334344.6:c.5305C>T	p.Arg1769Ter	p.R1769*	ENST00000334344	NM_152641.2	1769	Cga/Tga	20/21	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.589636761744199	2		194	167	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385239	41385239	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377294483	NA	P-0046112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	131	430	0	ENST00000373198.4:c.722G>A	p.Arg241His	p.R241H	ENST00000373198	NM_133170.3	241	cGt/cAt	6/32	0.589636761744199	3	FACETS	0.948	0.863	1	0.474	0.431	0.519	CLONAL	1	TRUE	1	0.589636761744199	3		430	607	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939033	48939034	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	C	novel	NA	P-0046112-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	28	90	0	ENST00000267163.4:c.865_866delinsC	p.Lys289GlnfsTer12	p.K289Qfs*12	ENST00000267163	NM_000321.2	289	AAa/Ca	9/27	1	2	FACETS	0.848	0.691	1	0.848	0.691	1	CLONAL	1	TRUE	1	0.589636761744199	2		90	112	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47108598	47108598	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	99	126	0	ENST00000409792.3:c.6071G>A	p.Arg2024Gln	p.R2024Q	ENST00000409792	NM_014159.6	2024	cGa/cAa	13/21	0.679338678622562	1	FACETS	0.848	0.773	0.924	0.848	0.773	0.924	CLONAL	1	TRUE	0	0.679338678622562	1		126	227	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923159	48923159	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	34	42	0	ENST00000267163.4:c.607+1del		p.G203fs	ENST00000267163	NM_000321.2	203	Ggg/gg	6/27	0.679338678622562	1	FACETS	0.606	0.508	0.711	0.606	0.508	0.711	SUBCLONAL	1	TRUE	0	0.679338678622562	1		42	109	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435318	49435318	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	92	315	0	ENST00000301067.7:c.6235C>T	p.Gln2079Ter	p.Q2079*	ENST00000301067	NM_003482.3	2079	Cag/Tag	31/54	0.679338678622562	1	FACETS	0.335	0.298	0.374	0.335	0.298	0.374	SUBCLONAL	1	TRUE	0	0.679338678622562	1		315	534	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808865	3808881	+	frameshift_variant	Frame_Shift_Del	DEL	AGGAGCTGGGGATCTAC	AGGAGCTGGGGATCTAC	-	novel	NA	P-0046113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	138	164	0	ENST00000262367.5:c.3343_3359del	p.Val1115ArgfsTer7	p.V1115Rfs*7	ENST00000262367	NM_004380.2	1115	GTAGATCCCCAGCTCCTc/c	17/31	1	2	FACETS	0.795	0.728	0.865	0.795	0.728	0.865	SUBCLONAL	1	TRUE	1	0.679338678622562	2		164	511	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526622	31526622	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	126	201	0	ENST00000344624.3:c.418G>C	p.Gly140Arg	p.G140R	ENST00000344624		140	Ggc/Cgc	2/33	1	2	FACETS	0.63	0.572	0.69	0.63	0.572	0.69	SUBCLONAL	1	TRUE	1	0.679338678622562	2		201	589	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0046149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	175	324	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.162976665378585	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.244561554369403	2		324	663	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	121	673	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.244561554369403	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.244561554369403	1		673	708	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967794	18967794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	93	896	1	ENST00000262803.5:c.1933G>A	p.Glu645Lys	p.E645K	ENST00000262803	NM_002911.3	645	Gag/Aag	14/24	0.244561554369403	1	FACETS	0.666	0.59	0.746	0.666	0.59	0.746	SUBCLONAL	1	TRUE	0	0.244561554369403	1		897	1003	SUCCESS
ATR	545	MSKCC	GRCh37	3	142257436	142257436	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	44	254	0	ENST00000350721.4:c.3613C>T	p.His1205Tyr	p.H1205Y	ENST00000350721	NM_001184.3	1205	Cat/Tat	19/47	1	2	FACETS	0.777	0.652	0.915	0.777	0.652	0.915	CLONAL	1	TRUE	1	0.244561554369403	2		254	463	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864045	97864045	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	115	506	0	ENST00000289081.3:c.1621C>T	p.Pro541Ser	p.P541S	ENST00000289081	NM_000136.2	541	Cct/Tct	15/15	0.244561554369403	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.244561554369403	1		506	615	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39935747	39935747	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	52	205	0	ENST00000378444.4:c.125G>T	p.Arg42Ile	p.R42I	ENST00000378444	NM_001123385.1	42	aGa/aTa	3/15	1	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.244561554369403	1		205	251	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412975	63412975	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046149-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	103	445	3	ENST00000330258.3:c.192G>T	p.Lys64Asn	p.K64N	ENST00000330258	NM_152424.3	64	aaG/aaT	2/2	1	1	FACETS	0.827	0.744	0.914	1	0.985	1	CLONAL	2	TRUE	0	0.244561554369403	1		448	447	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922974	44922974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs973676174	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	78	413	0	ENST00000377967.4:c.1835G>A	p.Arg612Gln	p.R612Q	ENST00000377967	NM_021140.2	612	cGa/cAa	16/29	NA	2	FACETS	0.904	0.794	1			1	INDETERMINATE	1	TRUE	NA	0.23	2		413	750	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	196	679	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.848	0.785	0.914	1	0.992	1	CLONAL	2	TRUE	1	0.23	2		683	1005	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627688	37627688	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	76	367	0	ENST00000447079.4:c.1607del	p.Pro536HisfsTer74	p.P536Hfs*74	ENST00000447079	NM_015083.1	535	Ccc/cc	2/14	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.23	2		367	625	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	68	423	1	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.808	0.702	0.923	0.808	0.702	0.923	CLONAL	1	TRUE	1	0.23	2		424	732	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515036	103515036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775996769	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	35	219	0	ENST00000355739.4:c.1537G>A	p.Ala513Thr	p.A513T	ENST00000355739	NM_000123.3	513	Gca/Aca	8/15	1	2	FACETS	0.786	0.645	0.945	0.786	0.645	0.945	CLONAL	1	TRUE	1	0.23	2		219	387	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587460	29587460	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659607	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	33	337	0	ENST00000356175.3:c.4441G>A	p.Gly1481Ser	p.G1481S	ENST00000356175	NM_000267.3	1481	Ggc/Agc	33/57	1	2	FACETS	0.96	0.784	1	0.96	0.784	1	CLONAL	1	TRUE	1	0.23	2		337	299	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505378	125505378	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs757716680	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	25	218	0	ENST00000428830.2:c.676del	p.Thr226HisfsTer14	p.T226Hfs*14	ENST00000428830	NM_001114121.2	223	gAa/ga	7/14	1	2	FACETS	0.979	0.776	1	0.979	0.776	1	CLONAL	1	TRUE	1	0.23	2		218	222	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564642	55564642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	78	448	0	ENST00000288135.5:c.530G>A	p.Arg177His	p.R177H	ENST00000288135	NM_000222.2	177	cGc/cAc	3/21	1	2	FACETS	0.992	0.871	1	0.992	0.871	1	CLONAL	1	TRUE	1	0.23	2		448	684	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	116	611	6	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.944	0.849	1	0.944	0.849	1	CLONAL	1	TRUE	1	0.23	2		617	1069	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	15	248	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	0.795	0.584	1	0.795	0.584	1	CLONAL	1	TRUE	1	0.23	2		248	164	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843535	156843535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369367198	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	87	658	0	ENST00000524377.1:c.961G>A	p.Val321Met	p.V321M	ENST00000524377	NM_002529.3	321	Gtg/Atg	8/17	0.221683129368124	3	FACETS	0.764	0.674	0.861	0.382	0.337	0.431	SUBCLONAL	1	TRUE	1	0.23	3		658	1104	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	90	557	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.922	0.817	1	0.922	0.817	1	CLONAL	1	TRUE	1	0.23	2		557	849	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047906	180047906	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1274	138	882	0	ENST00000261937.6:c.2269G>A	p.Val757Ile	p.V757I	ENST00000261937	NM_182925.4	757	Gtc/Atc	15/30	1	2	FACETS	0.85	0.771	0.934	0.85	0.771	0.934	CLONAL	1	TRUE	1	0.23	2		882	1412	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928078	178928080	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs587776933	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	21	319	0	ENST00000263967.3:c.1359_1361del	p.Glu453del	p.E453del	ENST00000263967	NM_006218.2	452	ttAGAa/tta	8/21	1	2	FACETS	0.804	0.621	1	0.804	0.621	1	CLONAL	1	TRUE	1	0.23	2		319	227	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864656	37864656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs950730453	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	126	665	0	ENST00000269571.5:c.308G>A	p.Arg103Gln	p.R103Q	ENST00000269571		103	cGa/cAa	3/27	1	2	FACETS	0.925	0.835	1	0.925	0.835	1	CLONAL	1	TRUE	1	0.23	2		665	1185	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103409	2103409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372321790	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1198	161	902	0	ENST00000219476.3:c.292C>T	p.Arg98Trp	p.R98W	ENST00000219476	NM_000548.3	98	Cgg/Tgg	4/42	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.23	2		902	1359	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867533	78867533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs185118480	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	86	564	0	ENST00000306801.3:c.2269G>A	p.Gly757Arg	p.G757R	ENST00000306801	NM_020761.2	757	Gga/Aga	20/34	1	2	FACETS	0.789	0.696	0.888	0.789	0.696	0.888	SUBCLONAL	1	TRUE	1	0.23	2		564	948	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891277	101891277	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	41	334	1	ENST00000374994.4:c.238C>T	p.Arg80Ter	p.R80*	ENST00000374994	NM_004612.2	80	Cga/Tga	2/9	1	2	FACETS	0.891	0.744	1	0.891	0.744	1	CLONAL	1	TRUE	1	0.23	2		335	400	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630626	158630626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912678	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	19	201	0	ENST00000263640.3:c.617G>A	p.Arg206His	p.R206H	ENST00000263640	NM_001105.4	206	cGc/cAc	6/11	1	2	FACETS	0.638	0.485	0.818	0.638	0.485	0.818	SUBCLONAL	1	TRUE	1	0.23	2		201	259	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258889	16258889	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	78	510	7	ENST00000375759.3:c.6158del	p.Asn2053ThrfsTer11	p.N2053Tfs*11	ENST00000375759	NM_015001.2	2052	Aaa/aa	11/15	1	2	FACETS	0.811	0.712	0.919	0.811	0.712	0.919	CLONAL	1	TRUE	1	0.23	2		517	836	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212008	5212008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753640223	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	58	603	0	ENST00000357368.4:c.5023G>A	p.Glu1675Lys	p.E1675K	ENST00000357368	NM_002850.3	1675	Gaa/Aaa	32/38	1	2	FACETS	0.525	0.45	0.608	0.525	0.45	0.608	SUBCLONAL	1	TRUE	1	0.23	2		603	960	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151290	202151290	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	15	221	0	ENST00000358485.4:c.1596del	p.Lys532AsnfsTer73	p.K532Nfs*73	ENST00000358485	NM_001080125.1	530	agA/ag	9/9	1	2	FACETS	0.5	0.365	0.661	0.5	0.365	0.661	SUBCLONAL	1	TRUE	1	0.23	2		221	261	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485416	57485416	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1418870137	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	32	243	0	ENST00000371085.3:c.998G>A	p.Arg333His	p.R333H	ENST00000371085	NM_000516.4	333	cGc/cAc	12/13	1	2	FACETS	0.616	0.499	0.747	0.616	0.499	0.747	SUBCLONAL	1	TRUE	1	0.23	2		243	452	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229612	5229612	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1246891588	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	23	88	0	ENST00000357368.4:c.2239G>A	p.Gly747Ser	p.G747S	ENST00000357368	NM_002850.3	747	Ggc/Agc	15/38	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.23	2		88	135	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436342	52436342	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1186981831	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	62	669	0	ENST00000460680.1:c.2152C>T	p.Arg718Trp	p.R718W	ENST00000460680	NM_004656.3	718	Cgg/Tgg	17/17	1	2	FACETS	0.512	0.441	0.59	0.512	0.441	0.59	SUBCLONAL	1	TRUE	1	0.23	2		669	1053	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052633	42052633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	75	299	0	ENST00000219905.7:c.7304G>A	p.Arg2435Gln	p.R2435Q	ENST00000219905	NM_001164273.1	2435	cGg/cAg	20/24	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.23	2		299	629	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991949	72991949	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs753977275	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	95	467	0	ENST00000268489.5:c.2096del	p.Gly699AlafsTer125	p.G699Afs*125	ENST00000268489	NM_006885.3	699	gGc/gc	2/10	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.23	2		467	795	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859625	57859625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200097138	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	102	516	0	ENST00000228682.2:c.679C>T	p.Arg227Cys	p.R227C	ENST00000228682	NM_005269.2	227	Cgt/Tgt	7/12	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.23	2		516	835	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427369	49427369	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1565779294	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	120	584	1	ENST00000301067.7:c.11119C>T	p.Arg3707Ter	p.R3707*	ENST00000301067	NM_003482.3	3707	Cga/Tga	39/54	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.23	2		585	961	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438211	49438211	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	81	530	0	ENST00000301067.7:c.5058del	p.Lys1686AsnfsTer36	p.K1686Nfs*36	ENST00000301067	NM_003482.3	1686	aaA/aa	20/54	1	2	FACETS	0.879	0.774	0.993	0.879	0.774	0.993	CLONAL	1	TRUE	1	0.23	2		530	801	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005423	29005423	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	24	266	0	ENST00000282397.4:c.838C>T	p.Arg280Ter	p.R280*	ENST00000282397	NM_002019.4	280	Cga/Tga	7/30	1	2	FACETS	0.782	0.614	0.974	0.782	0.614	0.974	CLONAL	1	TRUE	1	0.23	2		266	267	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156541	55156541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368266633	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	88	421	0	ENST00000257290.5:c.2942G>A	p.Arg981His	p.R981H	ENST00000257290	NM_006206.4	981	cGt/cAt	22/23	1	2	FACETS	0.937	0.829	1	0.937	0.829	1	CLONAL	1	TRUE	1	0.23	2		421	817	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158026	27158026	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	74	463	0	ENST00000380036.4:c.255del	p.Val86LeufsTer31	p.V86Lfs*31	ENST00000380036	NM_000459.3	84	Aaa/aa	2/23	1	2	FACETS	0.857	0.749	0.973	0.857	0.749	0.973	CLONAL	1	TRUE	1	0.23	2		463	751	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759592	133759592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	94	704	1	ENST00000318560.5:c.1915C>T	p.Arg639Ter	p.R639*	ENST00000318560	NM_005157.4	639	Cga/Tga	11/11	1	2	FACETS	0.74	0.656	0.829	0.74	0.656	0.829	SUBCLONAL	1	TRUE	1	0.23	2		705	1105	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837937	156837937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141021604	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1197	292	811	0	ENST00000524377.1:c.470G>A	p.Arg157His	p.R157H	ENST00000524377	NM_002529.3	157	cGc/cAc	5/17	0.221683129368124	3	FACETS	0.951	0.892	1	0.951	0.892	1	CLONAL	2	TRUE	1	0.23	3		811	1489	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246446	53246446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201805773	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	72	492	0	ENST00000375401.3:c.536G>A	p.Arg179His	p.R179H	ENST00000375401	NM_004187.3	179	cGt/cAt	5/26	NA	2	FACETS	0.858	0.749	0.976			1	INDETERMINATE	1	TRUE	NA	0.23	2		492	730	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404305	139404305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777658333	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	132	799	1	ENST00000277541.6:c.2849C>T	p.Ala950Val	p.A950V	ENST00000277541	NM_017617.3	950	gCc/gTc	18/34	1	2	FACETS	0.912	0.826	1	0.912	0.826	1	CLONAL	1	TRUE	1	0.23	2		800	1258	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337289	89337289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	91	511	1	ENST00000301030.4:c.7742G>A	p.Arg2581His	p.R2581H	ENST00000301030	NM_001256183.1	2581	cGt/cAt	12/13	1	2	FACETS	0.858	0.761	0.963	0.858	0.761	0.963	CLONAL	1	TRUE	1	0.23	2		512	922	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294258	1294258	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	100	693	1	ENST00000310581.5:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000310581	NM_198253.2	248	cGg/cAg	2/16	1	2	FACETS	0.862	0.768	0.962	0.862	0.768	0.962	CLONAL	1	TRUE	1	0.23	2		694	1009	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217906	2217906	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769883924	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	127	748	1	ENST00000398665.3:c.2680G>A	p.Ala894Thr	p.A894T	ENST00000398665	NM_032482.2	894	Gcc/Acc	22/28	1	2	FACETS	0.956	0.864	1	0.956	0.864	1	CLONAL	1	TRUE	1	0.23	2		749	1155	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956759	68956759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777080876	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	173	554	0	ENST00000288368.4:c.877C>T	p.Arg293Trp	p.R293W	ENST00000288368	NM_024870.2	293	Cgg/Tgg	8/40	0.221683129368124	3	FACETS	0.93	0.856	1	0.93	0.856	1	CLONAL	2	TRUE	1	0.23	3		554	902	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932891	39932891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748813798	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	78	633	2	ENST00000378444.4:c.1708G>A	p.Ala570Thr	p.A570T	ENST00000378444	NM_001123385.1	570	Gca/Aca	4/15	NA	2	FACETS	0.689	0.603	0.781			1	INDETERMINATE	1	TRUE	NA	0.23	2		635	985	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346226	89346226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	60	348	0	ENST00000301030.4:c.6724G>A	p.Ala2242Thr	p.A2242T	ENST00000301030	NM_001256183.1	2242	Gcg/Acg	9/13	1	2	FACETS	0.959	0.827	1	0.959	0.827	1	CLONAL	1	TRUE	1	0.23	2		348	544	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849300	76849302	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs782391479	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	26	300	0	ENST00000373344.5:c.5974_5976del	p.Ser1992del	p.S1992del	ENST00000373344	NM_000489.3	1992	TCT/-	26/35	0.3	1	FACETS	0.676	0.536	0.835	0.676	0.536	0.835	SUBCLONAL	1	TRUE	0	0.23	1		300	296	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551408	141551408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1205353566	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	95	619	0	ENST00000220592.5:c.1889G>A	p.Arg630His	p.R630H	ENST00000220592	NM_012154.3	630	cGc/cAc	15/19	0.221683129368124	3	FACETS	0.783	0.695	0.877	0.391	0.347	0.439	SUBCLONAL	1	TRUE	1	0.23	3		619	1177	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396838	396838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759464398	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	126	677	1	ENST00000262320.3:c.188G>A	p.Arg63His	p.R63H	ENST00000262320	NM_003502.3	63	cGc/cAc	2/11	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.23	2		678	1069	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191804	123191805	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1392503050	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	16	225	0	ENST00000218089.9:c.1400dup	p.Phe468LeufsTer5	p.F468Lfs*5	ENST00000218089	NM_001042749.1	465	gtt/gTtt	15/35	0.3	1	FACETS	0.655	0.486	0.855	0.655	0.486	0.855	SUBCLONAL	1	TRUE	0	0.23	1		225	188	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436084	51436084	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	32	257	0	ENST00000262662.1:c.49del	p.Asp17ThrfsTer2	p.D17Tfs*2	ENST00000262662		15	aGg/ag	3/4	1	2	FACETS	0.541	0.439	0.658	0.541	0.439	0.658	SUBCLONAL	1	TRUE	1	0.23	2		257	514	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325825	65325825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375122732	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	65	413	0	ENST00000342505.4:c.1297G>A	p.Val433Ile	p.V433I	ENST00000342505	NM_002227.2	433	Gtc/Atc	9/25	1	2	FACETS	0.819	0.71	0.938	0.819	0.71	0.938	CLONAL	1	TRUE	1	0.23	2		413	690	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846253	156846253	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	140	749	0	ENST00000524377.1:c.1694C>A	p.Thr565Asn	p.T565N	ENST00000524377	NM_002529.3	565	aCc/aAc	14/17	0.221683129368124	3	FACETS	1	0.958	1	0.548	0.497	0.601	CLONAL	1	TRUE	1	0.23	3		749	1239	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749984	162749984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	71	367	0	ENST00000367921.3:c.2516G>A	p.Arg839His	p.R839H	ENST00000367921	NM_006182.2	839	cGt/cAt	18/18	0.221683129368124	3	FACETS	0.993	0.867	1	0.497	0.433	0.565	CLONAL	1	TRUE	1	0.23	3		367	693	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406322	70406322	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs778566641	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	60	435	0	ENST00000373644.4:c.3836A>G	p.Asp1279Gly	p.D1279G	ENST00000373644	NM_030625.2	1279	gAt/gGt	4/12	1	2	FACETS	0.893	0.77	1	0.893	0.77	1	CLONAL	1	TRUE	1	0.23	2		435	584	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416782	121416782	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	125	837	0	ENST00000257555.6:c.211G>C	p.Glu71Gln	p.E71Q	ENST00000257555		71	Gag/Cag	1/10	1	2	FACETS	0.871	0.786	0.961	0.871	0.786	0.961	CLONAL	1	TRUE	1	0.23	2		837	1248	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912987	32912987	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	53	344	0	ENST00000380152.3:c.4495A>G	p.Thr1499Ala	p.T1499A	ENST00000380152		1499	Act/Gct	11/27	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.23	2		344	357	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524557	103524557	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	21	106	0	ENST00000355739.4:c.2688G>A	p.Trp896Ter	p.W896*	ENST00000355739	NM_000123.3	896	tgG/tgA	13/15	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.23	2		106	149	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779076	3779076	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	102	644	0	ENST00000262367.5:c.5972del	p.Pro1991ArgfsTer8	p.P1991Rfs*8	ENST00000262367	NM_004380.2	1991	cCg/cg	31/31	1	2	FACETS	0.902	0.805	1	0.902	0.805	1	CLONAL	1	TRUE	1	0.23	2		644	983	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821565	72821565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1369608013	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	59	175	0	ENST00000268489.5:c.10610C>T	p.Ala3537Val	p.A3537V	ENST00000268489	NM_006885.3	3537	gCg/gTg	10/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.23	2		175	371	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984006	7984006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	59	289	0	ENST00000319144.4:c.620C>T	p.Thr207Met	p.T207M	ENST00000319144	NM_001139.2	207	aCg/aTg	5/15	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.23	2		289	480	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56401613	56401613	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs769025149	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	24	214	0	ENST00000348428.3:c.1475C>T	p.Thr492Met	p.T492M	ENST00000348428	NM_006785.3	492	aCg/aTg	12/17	1	2	FACETS	0.725	0.569	0.903	0.725	0.569	0.903	CLONAL	1	TRUE	1	0.23	2		214	288	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184489	7184489	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	70	577	0	ENST00000302850.5:c.812del	p.Pro271ArgfsTer11	p.P271Rfs*11	ENST00000302850	NM_000208.2	271	cCg/cg	3/22	1	2	FACETS	0.578	0.502	0.66	0.578	0.502	0.66	SUBCLONAL	1	TRUE	1	0.23	2		577	1053	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311679	30311679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372635299	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	20	341	0	ENST00000262643.3:c.533C>T	p.Ala178Val	p.A178V	ENST00000262643	NM_001238.2	178	gCg/gTg	7/12	1	2	FACETS	0.674	0.516	0.858	0.674	0.516	0.858	SUBCLONAL	1	TRUE	1	0.23	2		341	258	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966069	25966069	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	96	540	0	ENST00000435504.4:c.3137A>G	p.Asp1046Gly	p.D1046G	ENST00000435504		1046	gAc/gGc	13/13	0.22257065306377	2	FACETS	1	0.905	1	0.509	0.453	0.569	CLONAL	1	TRUE	0	0.23	2		540	820	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178136	56178139	+	frameshift_variant	Frame_Shift_Del	DEL	AAAG	AAAG	-	novel	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	25	216	0	ENST00000399503.3:c.3110_3113del	p.Lys1037ThrfsTer44	p.K1037Tfs*44	ENST00000399503	NM_005921.1	1037	AAAGac/ac	14/20	1	2	FACETS	0.739	0.584	0.918	0.739	0.584	0.918	CLONAL	1	TRUE	1	0.23	2		216	294	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163651	32163651	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774609136	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	74	424	2	ENST00000375023.3:c.5575C>T	p.Pro1859Ser	p.P1859S	ENST00000375023	NM_004557.3	1859	Ccg/Tcg	30/30	1	2	FACETS	0.972	0.851	1	0.972	0.851	1	CLONAL	1	TRUE	1	0.23	2		426	662	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798418	32798418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776413811	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	115	580	0	ENST00000374899.4:c.1438C>T	p.Arg480Cys	p.R480C	ENST00000374899	NM_018833.2	480	Cgc/Tgc	8/12	1	2	FACETS	0.957	0.86	1	0.957	0.86	1	CLONAL	1	TRUE	1	0.23	2		580	1045	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38147025	38147025	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	32	308	0	ENST00000317025.8:c.3119-2A>G		p.X1040_splice	ENST00000317025	NM_023034.1	1040			0.221683129368124	3	FACETS	0.961	0.781	1	0.48	0.39	0.581	CLONAL	1	TRUE	1	0.23	3		308	323	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187254	38187254	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	74	501	2	ENST00000317025.8:c.1223del	p.Lys408ArgfsTer19	p.K408Rfs*19	ENST00000317025	NM_023034.1	408	aAg/ag	6/24	0.221683129368124	3	FACETS	0.837	0.731	0.952	0.419	0.365	0.476	CLONAL	1	TRUE	1	0.23	3		503	857	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752911	128752911	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	60	255	0	ENST00000377970.2:c.1072A>G	p.Thr358Ala	p.T358A	ENST00000377970	NM_002467.4	358	Acc/Gcc	3/3	0.221683129368124	3	FACETS	1	0.911	1	0.538	0.463	0.618	CLONAL	1	TRUE	1	0.23	3		255	541	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737064	145737064	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs781543298	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	207	632	1	ENST00000428558.2:c.3502G>A	p.Gly1168Arg	p.G1168R	ENST00000428558	NM_004260.3	1168	Gga/Aga	21/22	0.221683129368124	3	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	1	0.23	3		633	1002	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759560	133759560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755654666	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	84	694	1	ENST00000318560.5:c.1883C>T	p.Pro628Leu	p.P628L	ENST00000318560	NM_005157.4	628	cCg/cTg	11/11	1	2	FACETS	0.692	0.61	0.781	0.692	0.61	0.781	SUBCLONAL	1	TRUE	1	0.23	2		695	1055	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391715	139391715	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502233	NA	P-0046150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	114	818	0	ENST00000277541.6:c.6476G>A	p.Arg2159His	p.R2159H	ENST00000277541	NM_017617.3	2159	cGc/cAc	34/34	1	2	FACETS	0.769	0.69	0.853	0.769	0.69	0.853	SUBCLONAL	1	TRUE	1	0.23	2		818	1289	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	213	378	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	0.570820926639568	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.570820926639568	1		378	454	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACAACCCCC	rs397517115	NA	P-0046151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	211	459	0	ENST00000275493.2:c.2311_2319dup	p.Asn771_His773dup	p.N771_H773dup	ENST00000275493	NM_005228.3	771	gac/gACAACCCCCac	20/28	0.561312425769713	4	FACETS	0.864	0.801	0.93	0.288	0.267	0.31	CLONAL	1	TRUE	1	0.570820926639568	4		459	1344	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207081	1207081	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs137854584	NA	P-0046151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	354	705	1	ENST00000326873.7:c.169G>T	p.Glu57Ter	p.E57*	ENST00000326873	NM_000455.4	57	Gaa/Taa	1/10	0.570820926639568	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.570820926639568	1		706	818	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829323	72829323	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	278	483	0	ENST00000268489.5:c.7258A>C	p.Asn2420His	p.N2420H	ENST00000268489	NM_006885.3	2420	Aat/Cat	9/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.570820926639568	2		483	906	SUCCESS
APC	324	MSKCC	GRCh37	5	112175533	112175533	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046151-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	101	213	0	ENST00000257430.4:c.4243del	p.Ser1415ValfsTer4	p.S1415Vfs*4	ENST00000257430	NM_000038.5	1414	gtA/gt	16/16	0.570820926639568	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	0	0.570820926639568	1		213	249	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307256	118307256	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	87	180	0	ENST00000534358.1:c.29C>T	p.Pro10Leu	p.P10L	ENST00000534358	NM_005933.3	10	cCc/cTc	1/36	1	2	FACETS	0.994	0.894	1	0.994	0.894	1	CLONAL	1	TRUE	1	0.7	2		180	250	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177002	56177017	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTGTCTTATAGATA	CTTTGTCTTATAGATA	-	novel	NA	P-0046152-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	74	226	0	ENST00000399503.3:c.2272_2287del	p.Leu758AspfsTer36	p.L758Dfs*36	ENST00000399503	NM_005921.1	758	CTTTGTCTTATAGATAga/ga	13/20	1	2	FACETS	0.795	0.704	0.89	0.795	0.704	0.89	SUBCLONAL	1	TRUE	1	0.7	2		226	266	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	53	238	0	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	1	2	FACETS	0.875	0.746	1	0.875	0.746	1	CLONAL	1	TRUE	1	0.24	2		238	505	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0046153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	41	302	0	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	0.81	0.675	0.959	0.81	0.675	0.959	CLONAL	1	TRUE	1	0.24	2		302	422	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097761	27097762	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0046153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	58	357	0	ENST00000324856.7:c.3351_3352del	p.Phe1118CysfsTer4	p.F1118Cfs*4	ENST00000324856	NM_006015.4	1117	aTC/a	12/20	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.24	2		357	464	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113304	209113304	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	49	258	0	ENST00000345146.2:c.203A>G	p.Asn68Ser	p.N68S	ENST00000345146	NM_005896.2	68	aAt/aGt	4/10	1	2	FACETS	0.965	0.819	1	0.965	0.819	1	CLONAL	1	TRUE	1	0.24	2		258	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0046154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	148	612	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.566199552125871	1	FACETS	0.797	0.737	0.858	0.797	0.737	0.858	SUBCLONAL	1	TRUE	0	0.662328461472974	1		612	375	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0046154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	74	343	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.624079819476064	2	FACETS	0.939	0.858	1	0.939	0.858	1	CLONAL	2	TRUE	0	0.662328461472974	2		343	119	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188164	11188164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777893	NA	P-0046154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	130	473	0	ENST00000361445.4:c.5930C>T	p.Thr1977Ile	p.T1977I	ENST00000361445	NM_004958.3	1977	aCa/aTa	43/58	0.631177426653122	1	FACETS	0.995	0.921	1	0.995	0.921	1	CLONAL	1	TRUE	0	0.662328461472974	1		473	264	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411246	63411246	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	278	376	0	ENST00000330258.3:c.1921C>T	p.Arg641Ter	p.R641*	ENST00000330258	NM_152424.3	641	Cga/Tga	2/2	0.543050829303762	2	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.662328461472974	2		376	387	SUCCESS
APC	324	MSKCC	GRCh37	5	112175101	112175101	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs587783033	NA	P-0046154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	19	139	0	ENST00000257430.4:c.3814del	p.Ser1272GlnfsTer16	p.S1272Qfs*16	ENST00000257430	NM_000038.5	1270	tgT/tg	16/16	1	2	FACETS	0.765	0.596	0.952	0.765	0.596	0.952	CLONAL	1	TRUE	1	0.662328461472974	2		139	75	SUCCESS
APC	324	MSKCC	GRCh37	5	112175908	112175908	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	29	175	0	ENST00000257430.4:c.4617del	p.Glu1540SerfsTer25	p.E1540Sfs*25	ENST00000257430	NM_000038.5	1539	tcA/tc	16/16	1	2	FACETS	1	0.85	1	1	0.85	1	CLONAL	1	TRUE	1	0.662328461472974	2		175	85	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104356987	104356987	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	192	652	1	ENST00000369902.3:c.847G>A	p.Glu283Lys	p.E283K	ENST00000369902	NM_016169.3	283	Gag/Aag	7/12	1	2	FACETS	0.925	0.86	0.991	0.925	0.86	0.991	CLONAL	1	TRUE	1	0.662328461472974	2		653	627	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246191	46246191	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs747198269	NA	P-0046154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	48	335	0	ENST00000334344.6:c.4285A>T	p.Ser1429Cys	p.S1429C	ENST00000334344	NM_152641.2	1429	Agc/Tgc	15/21	NA	2	FACETS	0.824	0.707	0.947			1	INDETERMINATE	1	TRUE	NA	0.662328461472974	2		335	176	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575096	48575096	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1555685159	NA	P-0046154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	41	306	0	ENST00000342988.3:c.290G>T	p.Arg97Leu	p.R97L	ENST00000342988	NM_005359.5	97	cGt/cTt	3/12	0.605493344483556	1	FACETS	0.69	0.589	0.796	0.69	0.589	0.796	SUBCLONAL	1	TRUE	0	0.662328461472974	1		306	120	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591136	67591137	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAG	novel	NA	P-0046154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	46	280	0	ENST00000274335.5:c.1730_1732dup	p.Arg577_Asp578insGly	p.R577_D578insG	ENST00000274335		577	aga/aGAGga	12/15	0.484228059403693	1	FACETS	0.876	0.763	0.992	0.876	0.763	0.992	CLONAL	1	TRUE	0	0.662328461472974	1		280	106	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6031609	6031609	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	25	189	0	ENST00000265849.7:c.983A>T	p.Asp328Val	p.D328V	ENST00000265849	NM_000535.5	328	gAt/gTt	9/15	0.624406795742177	3	FACETS	0.703	0.561	0.862	0.351	0.28	0.431	SUBCLONAL	1	TRUE	1	0.662328461472974	3		189	143	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0046155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	41	541	0	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	1	2	FACETS	0.632	0.524	0.751	0.632	0.524	0.751	SUBCLONAL	1	TRUE	1	0.172441898857327	2		541	753	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0046156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	113	248	1				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.962	1			1	INDETERMINATE	1	TRUE	NA	0.7484580881381	2		249	276	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158201	47158202	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CA	CA	-	novel	NA	P-0046156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	146	297	0	ENST00000409792.3:c.4497_4498del	p.Cys1499Ter	p.C1499*	ENST00000409792	NM_014159.6	1499	tgTGag/tgag	4/21	1	2	FACETS	0.835	0.768	0.904	0.835	0.768	0.904	CLONAL	1	TRUE	1	0.7484580881381	2		297	467	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683511	182683512	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	211	337	0	ENST00000292782.4:c.33dup	p.Val12SerfsTer11	p.V12Sfs*11	ENST00000292782	NM_020640.2	11	-/A	2/7	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.7484580881381	2		337	550	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0046157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	221	284	0				ENST00000310581	NM_198253.2	-/1132			0.484291866721544	5	FACETS	0.917	0.86	0.974			1	CLONAL	3	TRUE	NA	0.484291866721544	5		284	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0046157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	490	613	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.484291866721544	3	FACETS	0.936	0.902	0.97	0.936	0.902	0.97	CLONAL	3	TRUE	0	0.484291866721544	3		613	895	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0046157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	155	179	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	0.484291866721544	3	FACETS	0.889	0.831	0.948	0.889	0.831	0.948	CLONAL	3	TRUE	0	0.484291866721544	3		179	298	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881002	37881003	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCTCCCCA	rs397516982	NA	P-0046157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	492	624	0	ENST00000269571.5:c.2332_2340dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	-/GGCTCCCCA	20/27	0.484291866721544	4	FACETS	1	0.995	1	0.826	0.792	0.861	CLONAL	2	TRUE	1	0.484291866721544	4		624	1217	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752411	57752412	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0046157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	74	134	0	ENST00000274289.3:c.1161_1162del	p.Arg387SerfsTer3	p.R387Sfs*3	ENST00000274289	NM_006622.3	387	agAGtg/agtg	9/14	0.484291866721544	3	FACETS	0.84	0.747	0.936	0.56	0.498	0.624	CLONAL	2	TRUE	0	0.484291866721544	3		134	226	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870836	12870836	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	126	200	0	ENST00000228872.4:c.64del	p.Glu22SerfsTer20	p.E22Sfs*20	ENST00000228872	NM_004064.3	21	gcG/gc	1/3	0.457403532087339	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	0	0.484291866721544	2		200	258	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989503	85989516	+	frameshift_variant	Frame_Shift_Del	DEL	ATAGCAGCATTCTT	ATAGCAGCATTCTT	-	novel	NA	P-0046157-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	91	296	0	ENST00000263360.6:c.1267_1280del	p.Ser423CysfsTer3	p.S423Cfs*3	ENST00000263360	NM_003797.3	421	gATAGCAGCATTCTT/g	12/12	0.484291866721544	4	FACETS	0.991	0.882	1	0.33	0.294	0.369	CLONAL	1	TRUE	1	0.484291866721544	4		296	563	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0046158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	268	295	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.592539388285159	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.592539388285159	3		295	520	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912029	127912029	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	120	301	1	ENST00000373547.4:c.841G>T	p.Glu281Ter	p.E281*	ENST00000373547	NM_002721.4	281	Gaa/Taa	7/7	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.592539388285159	2		302	303	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248528	212248528	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	458	507	0	ENST00000342788.4:c.3739C>A	p.Leu1247Met	p.L1247M	ENST00000342788	NM_005235.2	1247	Ctg/Atg	28/28	0.592539388285159	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	4	TRUE	0	0.592539388285159	4		507	600	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143167	30143167	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	486	804	1	ENST00000389048.3:c.359C>A	p.Ala120Asp	p.A120D	ENST00000389048	NM_004304.4	120	gCc/gAc	1/29	0.450876210096006	5	FACETS	0.999	0.966	1	0.999	0.966	1	CLONAL	4	TRUE	1	0.592539388285159	5		805	775	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186757	108186757	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs864622251	NA	P-0046158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	245	289	0	ENST00000278616.4:c.6115G>T	p.Glu2039Ter	p.E2039*	ENST00000278616	NM_000051.3	2039	Gaa/Taa	42/63	0.592539388285159	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	0	0.592539388285159	3		289	345	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561327	9561327	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1369133982	NA	P-0046158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	72	375	0	ENST00000353224.5:c.455A>G	p.Tyr152Cys	p.Y152C	ENST00000353224	NM_177990.2	152	tAt/tGt	4/10	0.530329885060175	3	FACETS	0.988	0.87	1	0.494	0.435	0.556	CLONAL	1	TRUE	1	0.592539388285159	3		375	319	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589519	69589519	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs779390973	NA	P-0046158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	71	127	0	ENST00000168712.1:c.334C>G	p.Arg112Gly	p.R112G	ENST00000168712	NM_002007.2	112	Cgc/Ggc	1/3	0.592539388285159	5	FACETS	1	0.952	1	1	0.952	1	CLONAL	3	TRUE	2	0.592539388285159	5		127	138	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604578	43604578	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	172	805	2	ENST00000355710.3:c.1163T>A	p.Val388Asp	p.V388D	ENST00000355710	NM_020975.4	388	gTc/gAc	6/20	0.592539388285159	3	FACETS	0.95	0.876	1	0.475	0.438	0.514	CLONAL	1	TRUE	1	0.592539388285159	3		807	792	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896476	28896476	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	120	295	0	ENST00000282397.4:c.2974G>C	p.Glu992Gln	p.E992Q	ENST00000282397	NM_002019.4	992	Gag/Cag	22/30	0.530329885060175	3	FACETS	0.8	0.732	0.87	0.8	0.732	0.87	SUBCLONAL	2	TRUE	1	0.592539388285159	3		295	328	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647134	23647134	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	151	603	0	ENST00000261584.4:c.733del	p.Ala245ArgfsTer34	p.A245Rfs*34	ENST00000261584	NM_024675.3	245	Gcg/cg	4/13	0.12828209247998	4	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.592539388285159	4		603	676	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400683	56400683	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	70	248	0	ENST00000348428.3:c.1277T>A	p.Val426Asp	p.V426D	ENST00000348428	NM_006785.3	426	gTc/gAc	11/17	0.592539388285159	4	FACETS	1	0.919	1	0.354	0.311	0.401	CLONAL	1	TRUE	1	0.592539388285159	4		248	354	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46603838	46603838	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	490	603	0	ENST00000263734.3:c.1195G>T	p.Glu399Ter	p.E399*	ENST00000263734	NM_001430.4	399	Gag/Tag	9/16	0.592539388285159	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	1	0.592539388285159	4		603	854	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	114	151	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.573660403642086	2		151	313	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720857	89720857	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs786201816	NA	P-0046159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	200	274	0	ENST00000371953.3:c.1008C>G	p.Tyr336Ter	p.Y336*	ENST00000371953	NM_000314.4	336	taC/taG	8/9	0.573660403642086	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.573660403642086	1		274	425	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874647	151874647	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	143	295	0	ENST00000262189.6:c.7891T>C	p.Ser2631Pro	p.S2631P	ENST00000262189	NM_170606.2	2631	Tct/Cct	38/59	0.573660403642086	3	FACETS	0.99	0.905	1	0.495	0.452	0.539	CLONAL	1	TRUE	1	0.573660403642086	3		295	648	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	146	151	0				ENST00000310581	NM_198253.2	-/1132			0.238615496331828	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.2679906044239	4		151	634	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0046160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	197	780	3	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.2679906044239	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.2679906044239	2		783	722	SUCCESS
AR	367	MSKCC	GRCh37	X	66766441	66766441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	47	340	0	ENST00000374690.3:c.1453C>T	p.Arg485Trp	p.R485W	ENST00000374690	NM_000044.3	485	Cgg/Tgg	1/8	0.191689572784714	1	FACETS	0.56	0.473	0.657	0.56	0.473	0.657	SUBCLONAL	1	TRUE	0	0.2679906044239	1		340	542	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214792	36214792	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	177	770	0	ENST00000222270.7:c.3218G>A	p.Arg1073His	p.R1073H	ENST00000222270	NM_014727.1	1073	cGc/cAc	8/37	1	2	FACETS	0.979	0.9	1	0.979	0.9	1	CLONAL	1	TRUE	1	0.2679906044239	2		770	1349	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36824346	36824346	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	67	541	0	ENST00000373129.3:c.190C>G	p.Gln64Glu	p.Q64E	ENST00000373129	NM_032017.1	64	Cag/Gag	4/12	0.2679906044239	2	FACETS	0.979	0.852	1	0.489	0.426	0.558	CLONAL	1	TRUE	0	0.2679906044239	2		541	511	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367833	15367833	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1233	190	894	0	ENST00000263377.2:c.1493G>A	p.Ser498Asn	p.S498N	ENST00000263377	NM_058243.2	498	aGt/aAt	8/20	0.238615496331828	4	FACETS	1	0.984	1	0.632	0.582	0.684	CLONAL	1	TRUE	2	0.2679906044239	4		894	1423	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197518	106197519	+	missense_variant	Missense_Mutation	DNP	CG	CG	TT	novel	NA	P-0046160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	15	302	0	ENST00000380013.4:c.5851_5852delinsTT	p.Arg1951Leu	p.R1951L	ENST00000380013	NM_001127208.2	1951	CGg/TTg	11/11	0.2679906044239	3	FACETS	0.788	0.579	1	0.394	0.289	0.519	CLONAL	1	TRUE	1	0.2679906044239	3		302	161	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0046161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	25	710	2	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	1	2	FACETS	0.081	0.063	0.102	0.081	0.063	0.102	SUBCLONAL	1	TRUE	1	0.731675377726694	2		712	842	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64126708	64126708	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0046161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	119	291	0	ENST00000334205.4:c.1A>G	p.Met1?	p.M1?	ENST00000334205	NM_003942.2	1	Atg/Gtg	1/17	1	2	FACETS	0.962	0.879	1	0.962	0.879	1	CLONAL	1	TRUE	1	0.731675377726694	2		291	338	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175854	24175855	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGAG	novel	NA	P-0046161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	187	469	0	ENST00000263121.7:c.1083_1086dup	p.Lys363GlyfsTer83	p.K363Gfs*83	ENST00000263121	NM_003073.3	361	atg/atGGAGg	8/9	1	2	FACETS	0.961	0.894	1	0.961	0.894	1	CLONAL	1	TRUE	1	0.731675377726694	2		469	532	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47088082	47088082	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	AT	novel	NA	P-0046161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	182	325	0	ENST00000409792.3:c.6993delinsAT	p.Gln2332SerfsTer37	p.Q2332Sfs*37	ENST00000409792	NM_014159.6	2331	atC/atAT	16/21	0.731675377726694	2	FACETS	0.861	0.814	0.906	0.861	0.814	0.906	CLONAL	2	TRUE	0	0.731675377726694	2		325	289	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	14	69	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.234	0.169	0.312	0.234	0.169	0.312	SUBCLONAL	1	TRUE	1	0.567710974227965	2		69	211	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765621	41765621	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	225	809	0	ENST00000301178.4:c.2501del	p.Pro834LeufsTer122	p.P834Lfs*122	ENST00000301178	NM_021913.4	833	Ccc/cc	20/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.567710974227965	2		809	754	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117755	70117755	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	57	985	1	ENST00000245479.2:c.223G>T	p.Glu75Ter	p.E75*	ENST00000245479	NM_000346.3	75	Gag/Tag	1/3	1	2	FACETS	0.209	0.178	0.242	0.209	0.178	0.242	SUBCLONAL	1	TRUE	1	0.567710974227965	2		986	962	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121802	2121802	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	78	1096	0	ENST00000219476.3:c.1964C>A	p.Ser655Tyr	p.S655Y	ENST00000219476	NM_000548.3	655	tCt/tAt	19/42	1	2	FACETS	0.261	0.228	0.296	0.261	0.228	0.296	SUBCLONAL	1	TRUE	1	0.567710974227965	2		1096	1054	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410342	63410342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368031008	NA	P-0046162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	75	932	0	ENST00000330258.3:c.2825G>A	p.Arg942Gln	p.R942Q	ENST00000330258	NM_152424.3	942	cGa/cAa	2/2	1	2	FACETS	0.261	0.228	0.297	0.261	0.228	0.297	SUBCLONAL	1	TRUE	1	0.567710974227965	2		932	1013	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237768	16237768	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	28	289	1	ENST00000375759.3:c.1215G>T	p.Gln405His	p.Q405H	ENST00000375759	NM_015001.2	405	caG/caT	5/15	1	2	FACETS	0.286	0.228	0.351	0.286	0.228	0.351	SUBCLONAL	1	TRUE	1	0.567710974227965	2		290	345	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36824385	36824385	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	73	747	1	ENST00000373129.3:c.151C>T	p.Gln51Ter	p.Q51*	ENST00000373129	NM_032017.1	51	Cag/Tag	4/12	1	2	FACETS	0.311	0.272	0.354	0.311	0.272	0.354	SUBCLONAL	1	TRUE	1	0.567710974227965	2		748	826	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341239	341239	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	77	1126	0	ENST00000262320.3:c.2245G>C	p.Val749Leu	p.V749L	ENST00000262320	NM_003502.3	749	Gtg/Ctg	9/11	1	2	FACETS	0.25	0.219	0.285	0.25	0.219	0.285	SUBCLONAL	1	TRUE	1	0.567710974227965	2		1126	1083	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836974	89836974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	92	765	0	ENST00000389301.3:c.2220G>C	p.Glu740Asp	p.E740D	ENST00000389301	NM_000135.2	740	gaG/gaC	24/43	1	2	FACETS	0.346	0.306	0.388	0.346	0.306	0.388	SUBCLONAL	1	TRUE	1	0.567710974227965	2		765	938	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295734	15295734	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1325571065	NA	P-0046162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	277	1038	2	ENST00000263388.2:c.2393G>A	p.Cys798Tyr	p.C798Y	ENST00000263388	NM_000435.2	798	tGc/tAc	15/33	1	2	FACETS	0.895	0.841	0.951	0.895	0.841	0.951	CLONAL	1	TRUE	1	0.567710974227965	2		1040	1090	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209106733	209106733	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	169	491	0	ENST00000345146.2:c.835G>T	p.Asp279Tyr	p.D279Y	ENST00000345146	NM_005896.2	279	Gac/Tac	7/10	1	2	FACETS	0.954	0.881	1	0.954	0.881	1	CLONAL	1	TRUE	1	0.567710974227965	2		491	624	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646012	215646012	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs376259263	NA	P-0046162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	80	321	0	ENST00000260947.4:c.586A>G	p.Lys196Glu	p.K196E	ENST00000260947	NM_000465.2	196	Aaa/Gaa	4/11	1	2	FACETS	0.992	0.884	1	0.992	0.884	1	CLONAL	1	TRUE	1	0.567710974227965	2		321	284	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574301	41574302	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TA	novel	NA	P-0046162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	41	637	0	ENST00000263253.7:c.6586_6587delinsTA	p.Gly2196Ter	p.G2196*	ENST00000263253	NM_001429.3	2196	GGa/TAa	31/31	1	2	FACETS	0.256	0.212	0.304	0.256	0.212	0.304	SUBCLONAL	1	TRUE	1	0.567710974227965	2		637	565	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916918	178916926	+	inframe_deletion	In_Frame_Del	DEL	TTGAACCAG	TTGAACCAG	-	novel	NA	P-0046162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	76	276	0	ENST00000263967.3:c.306_314del	p.Glu103_Val105del	p.E103_V105del	ENST00000263967	NM_006218.2	102	aTTGAACCAGta/ata	2/21	0.541616278136424	3	FACETS	1	0.975	1	0.687	0.611	0.767	CLONAL	1	TRUE	1	0.567710974227965	3		276	250	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555068	106555068	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	21	470	0	ENST00000369096.4:c.2185G>C	p.Glu729Gln	p.E729Q	ENST00000369096	NM_001198.3	729	Gaa/Caa	7/7	0.567710974227965	1	FACETS	0.141	0.108	0.18	0.141	0.108	0.18	SUBCLONAL	1	TRUE	0	0.567710974227965	1		470	375	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527276	137527276	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	12	322	0	ENST00000367739.4:c.370G>C	p.Asp124His	p.D124H	ENST00000367739	NM_000416.2	124	Gat/Cat	3/7	0.567710974227965	1	FACETS	0.159	0.111	0.217	0.159	0.111	0.217	SUBCLONAL	1	TRUE	0	0.567710974227965	1		322	191	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502292	157502292	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	34	575	0	ENST00000346085.5:c.3325G>C	p.Glu1109Gln	p.E1109Q	ENST00000346085	NM_020732.3	1109	Gag/Cag	12/20	0.567710974227965	1	FACETS	0.195	0.159	0.236	0.195	0.159	0.236	SUBCLONAL	1	TRUE	0	0.567710974227965	1		575	439	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983981	2983981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866164446	NA	P-0046162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	47	764	0	ENST00000396946.4:c.549G>A	p.Met183Ile	p.M183I	ENST00000396946	NM_032415.4	183	atG/atA	5/25	1	2	FACETS	0.221	0.185	0.26	0.221	0.185	0.26	SUBCLONAL	1	TRUE	1	0.567710974227965	2		764	750	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0046163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	26	248	1				ENST00000310581	NM_198253.2	-/1132			0.321957814611539	0	FACETS	0.812	0.656	0.985			1	CLONAL	1	TRUE	0	0.363639627835609	0		249	112	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44896902	44896902	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	15	71	0	ENST00000377967.4:c.622C>T	p.Gln208Ter	p.Q208*	ENST00000377967	NM_021140.2	208	Caa/Taa	8/29	0.363639627835609	2	FACETS	0.878	0.668	1			1	CLONAL	2	TRUE	NA	0.363639627835609	2		71	47	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144114	11144114	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	99	828	0	ENST00000358026.2:c.3695G>A	p.Gly1232Asp	p.G1232D	ENST00000358026	NM_001128849.1	1232	gGc/gAc	26/36	1	2	FACETS	0.92	0.823	1	0.92	0.823	1	CLONAL	1	TRUE	1	0.363639627835609	2		828	592	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981819	201981820	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0046163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	278	939	0	ENST00000359651.3:c.534dup	p.Tyr179LeufsTer17	p.Y179Lfs*17	ENST00000359651		177	agc/agCc	4/8	0.363639627835609	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.363639627835609	2		939	617	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279586	18279586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776438063	NA	P-0046163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	97	735	0	ENST00000222254.8:c.1859G>A	p.Arg620His	p.R620H	ENST00000222254	NM_005027.3	620	cGc/cAc	15/16	1	2	FACETS	0.792	0.706	0.882	0.792	0.706	0.882	SUBCLONAL	1	TRUE	1	0.363639627835609	2		735	674	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551066	41551067	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAATCCC	novel	NA	P-0046163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	81	567	0	ENST00000263253.7:c.3211_3217dup	p.Leu1073ArgfsTer18	p.L1073Rfs*18	ENST00000263253	NM_001429.3	1070	-/GAATCCC	17/31	1	2	FACETS	0.911	0.805	1	0.911	0.805	1	CLONAL	1	TRUE	1	0.363639627835609	2		567	489	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55087035	55087035	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	103	420	0	ENST00000275493.2:c.65G>T	p.Ser22Ile	p.S22I	ENST00000275493	NM_005228.3	22	aGt/aTt	1/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.363639627835609	2		420	452	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781116	135781116	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1564481122	NA	P-0046163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	59	626	0	ENST00000298552.3:c.1849del	p.His617IlefsTer12	p.H617Ifs*12	ENST00000298552	NM_001162426.1	617	Cat/at	15/23	0.354958111090867	1	FACETS	0.948	0.823	1	0.948	0.823	1	CLONAL	1	TRUE	0	0.363639627835609	1		626	280	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0046165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	346	680	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.209575156894098	3	FACETS	0.917	0.875	0.96			1	INDETERMINATE	3	TRUE	NA	0.418151580504353	3		680	727	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023559	27023560	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0046165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	123	503	0	ENST00000324856.7:c.671dup	p.Pro225AlafsTer175	p.P225Afs*175	ENST00000324856	NM_006015.4	222	tac/taCc	1/20	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.418151580504353	2		503	463	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251644	212251644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368679346	NA	P-0046165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	85	457	0	ENST00000342788.4:c.3415C>T	p.Arg1139Trp	p.R1139W	ENST00000342788	NM_005235.2	1139	Cgg/Tgg	27/28	0.359281968382033	3	FACETS	0.945	0.838	1	0.315	0.279	0.354	CLONAL	1	TRUE	0	0.418151580504353	3		457	520	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833925	44833925	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	79	61	0	ENST00000377967.4:c.349C>T	p.Gln117Ter	p.Q117*	ENST00000377967	NM_021140.2	117	Cag/Tag	4/29	0.391210317125136	2	FACETS	0.857	0.779	0.934			1	CLONAL	3	TRUE	NA	0.418151580504353	2		61	147	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978662	70978662	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	512	516	0	ENST00000276594.2:c.991G>T	p.Ala331Ser	p.A331S	ENST00000276594	NM_024504.3	331	Gcc/Tcc	5/8	0.418151580504353	3	FACETS	0.911	0.876	0.946	1	0.996	1	CLONAL	3	TRUE	1	0.418151580504353	3		516	1083	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207092	1207092	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555735008	NA	P-0046167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	182	745	0	ENST00000326873.7:c.180del	p.Tyr60Ter	p.Y60*	ENST00000326873	NM_000455.4	60	taC/ta	1/10	0.578585771211534	1	FACETS	0.926	0.862	0.991	0.926	0.862	0.991	CLONAL	1	TRUE	0	0.578585771211534	1		745	483	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203487	108203487	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0046177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	185	130	0	ENST00000278616.4:c.7789-2A>T		p.X2597_splice	ENST00000278616	NM_000051.3	2597			0.649570419740788	3	FACETS	0.959	0.913	1	0.959	0.913	1	CLONAL	3	TRUE	0	0.657222702860316	3		130	260	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0046177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	453	236	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.63771663198568	4	FACETS	0.94	0.905	0.975	0.94	0.905	0.975	CLONAL	3	TRUE	1	0.657222702860316	4		236	810	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222987	1222987	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	517	618	0	ENST00000326873.7:c.924G>T	p.Trp308Cys	p.W308C	ENST00000326873	NM_000455.4	308	tgG/tgT	8/10	0.657222702860316	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.657222702860316	2		618	745	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222992	1222992	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	532	633	0	ENST00000326873.7:c.929G>T	p.Arg310Leu	p.R310L	ENST00000326873	NM_000455.4	310	cGg/cTg	8/10	0.657222702860316	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.657222702860316	2		633	773	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944448	40944448	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	199	592	0	ENST00000373198.4:c.2054A>G	p.Lys685Arg	p.K685R	ENST00000373198	NM_133170.3	685	aAg/aGg	12/32	0.128574236126196	3	FACETS	0.916	0.85	0.985			1	INDETERMINATE	1	TRUE	NA	0.657222702860316	3		592	878	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480428	89480428	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046177-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	148	385	0	ENST00000336596.2:c.2265C>G	p.Asn755Lys	p.N755K	ENST00000336596	NM_005233.5	755	aaC/aaG	13/17	0.657222702860316	2	FACETS	0.95	0.875	1	0.475	0.437	0.514	CLONAL	1	TRUE	0	0.657222702860316	2		385	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0046195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	336	813	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.461860371692585	2	FACETS	0.778	0.739	0.817	0.778	0.739	0.817	SUBCLONAL	2	TRUE	0	0.512502645433153	2		813	843	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480122	50480122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	72	327	1	ENST00000394963.4:c.356G>A	p.Arg119Gln	p.R119Q	ENST00000394963	NM_003076.4	119	cGa/cAa	2/13	0.479471967426056	3	FACETS	1	0.942	1	0.559	0.492	0.629	CLONAL	1	TRUE	1	0.512502645433153	3		328	316	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107195	27107195	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	272	456	0	ENST00000324856.7:c.6806C>A	p.Ser2269Ter	p.S2269*	ENST00000324856	NM_006015.4	2269	tCa/tAa	20/20	0.513375660626059	3	FACETS	0.905	0.861	0.949			1	CLONAL	3	TRUE	NA	0.512502645433153	3		456	491	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563278	21563278	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs750461080	NA	P-0046195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	192	1062	1	ENST00000382592.4:c.641A>G	p.Tyr214Cys	p.Y214C	ENST00000382592	NM_014572.2	214	tAc/tGc	4/8	0.147631515759889	4	FACETS	1	0.945	1			1	INDETERMINATE	1	TRUE	NA	0.512502645433153	4		1063	1103	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624303	89624309	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTGTAT	CCTGTAT	-	novel	NA	P-0046195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	22	525	0	ENST00000371953.3:c.79_79+6del		p.X27_splice	ENST00000371953	NM_000314.4	27		1/9	0.513375660626059	1	FACETS	0.456	0.357	0.568	0.456	0.357	0.568	SUBCLONAL	1	TRUE	0	0.512502645433153	1		525	140	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987222	36987222	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	151	820	0	ENST00000354822.5:c.467C>G	p.Ser156Cys	p.S156C	ENST00000354822	NM_001079668.2	156	tCc/tGc	3/3	0.513375660626059	3	FACETS	0.932	0.853	1	0.466	0.426	0.508	CLONAL	1	TRUE	1	0.512502645433153	3		820	794	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566248	95566248	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	18	347	0	ENST00000393063.1:c.4075C>G	p.Leu1359Val	p.L1359V	ENST00000393063	NM_030621.3	1359	Ctt/Gtt	23/28	1	2	FACETS	0.65	0.497	0.826	0.65	0.497	0.826	SUBCLONAL	1	TRUE	1	0.512502645433153	2		347	108	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511532	38511532	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	115	635	0	ENST00000254066.5:c.1030C>T	p.Gln344Ter	p.Q344*	ENST00000254066	NM_000964.3	344	Cag/Tag	8/9	0.359833728968877	3	FACETS	0.834	0.752	0.92	0.278	0.25	0.307	CLONAL	1	TRUE	0	0.512502645433153	3		635	676	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860343	151860343	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	30	403	0	ENST00000262189.6:c.10319A>C	p.Glu3440Ala	p.E3440A	ENST00000262189	NM_170606.2	3440	gAg/gCg	43/59	1	2	FACETS	0.937	0.768	1	0.937	0.768	1	CLONAL	1	TRUE	1	0.512502645433153	2		403	125	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022075	5022075	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	26	395	0	ENST00000381652.3:c.88A>C	p.Asn30His	p.N30H	ENST00000381652	NM_004972.3	30	Aat/Cat	3/25	0.388306304620218	3	FACETS	0.85	0.681	1	0.425	0.34	0.519	CLONAL	1	TRUE	1	0.512502645433153	3		395	150	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0046196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	159	558	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.551700829932884	1	FACETS	0.909	0.841	0.979	0.909	0.841	0.979	CLONAL	1	TRUE	0	0.551700829932884	1		558	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0046199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	38	744	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.209	0.172	0.251	0.209	0.172	0.251	SUBCLONAL	1	TRUE	1	0.543184460774609	2		745	669	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0046199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	33	626	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.203	0.164	0.246	0.203	0.164	0.246	SUBCLONAL	1	TRUE	1	0.543184460774609	2		626	599	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492776	50492776	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1289355349	NA	P-0046199-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	32	424	0	ENST00000394963.4:c.1541A>G	p.Asn514Ser	p.N514S	ENST00000394963	NM_003076.4	514	aAt/aGt	13/13	1	2	FACETS	0.273	0.221	0.331	0.273	0.221	0.331	SUBCLONAL	1	TRUE	1	0.543184460774609	2		424	432	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248998	55248999	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCCAGCG	rs727504263	NA	P-0046200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	156	485	0	ENST00000275493.2:c.2300_2308dup	p.Ala767_Val769dup	p.A767_V769dup	ENST00000275493	NM_005228.3	767	atg/aTGGCCAGCGtg	20/28	1	2	FACETS	0.807	0.741	0.877	0.807	0.741	0.877	CLONAL	1	TRUE	1	0.523728070416893	2		485	738	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627837	14627837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046200-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	341	658	0	ENST00000254322.2:c.233G>A	p.Ser78Asn	p.S78N	ENST00000254322	NM_006145.1	78	aGt/aAt	2/3	0.271400944074755	3	FACETS	0.765	0.725	0.806	0.765	0.725	0.806	INDETERMINATE	2	TRUE	1	0.523728070416893	3		658	1074	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0046201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	414	584	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.550777773587474	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.551249714216308	2		584	747	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012389	29012389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161996687	NA	P-0046201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	32	370	0	ENST00000282397.4:c.482C>T	p.Thr161Met	p.T161M	ENST00000282397	NM_002019.4	161	aCg/aTg	4/30	0.551249714216308	4	FACETS	0.657	0.536	0.794	0.219	0.178	0.265	SUBCLONAL	1	TRUE	1	0.551249714216308	4		370	274	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436026	56436026	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771831816	NA	P-0046201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	310	380	0	ENST00000407977.2:c.1111C>T	p.Arg371Ter	p.R371*	ENST00000407977		371	Cga/Tga	9/10	0.550003405279084	2	FACETS	0.973	0.928	1	0.973	0.928	1	CLONAL	2	TRUE	0	0.551249714216308	2		380	578	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870882	12870882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	134	170	0	ENST00000228872.4:c.109G>A	p.Asp37Asn	p.D37N	ENST00000228872	NM_004064.3	37	Gac/Aac	1/3	0.261406457763808	5	FACETS	0.914	0.836	0.995	0.609	0.557	0.663	INDETERMINATE	2	TRUE	2	0.551249714216308	5		170	486	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916120	9916120	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0046201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	45	300	0	ENST00000330684.3:c.2168+1G>A		p.X723_splice	ENST00000330684	NM_001134407.1	723			0.507288979584387	2	FACETS	0.8	0.696	0.906	0.8	0.696	0.906	CLONAL	2	TRUE	0	0.551249714216308	2		300	102	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64289166	64289166	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	25	251	0	ENST00000370651.3:c.334C>T	p.Pro112Ser	p.P112S	ENST00000370651	NM_003463.4	112	Cca/Tca	5/6	0.551249714216308	3	FACETS	1	0.917	1	0.643	0.519	0.777	CLONAL	1	TRUE	1	0.551249714216308	3		251	90	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	509	695	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	0.920204984831002	4	FACETS	0.974	0.96	0.987	0.974	0.96	0.987	CLONAL	4	TRUE	0	0.920204984831002	4		695	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	638	1049	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.920204984831002	2	FACETS	0.936	0.903	0.97	0.468	0.451	0.485	CLONAL	1	TRUE	0	0.920204984831002	2		1049	1481	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602493	10602493	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	671	820	0	ENST00000171111.5:c.1085G>C	p.Arg362Pro	p.R362P	ENST00000171111	NM_203500.1	362	cGg/cCg	3/6	0.920204984831002	2	FACETS	0.98	0.965	0.994	0.98	0.965	0.994	CLONAL	2	TRUE	0	0.920204984831002	2		820	744	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	202	370	0	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	0.503460701774342	4	FACETS	1	0.988	1	0.427	0.398	0.457	INDETERMINATE	1	TRUE	1	0.920204984831002	4		370	658	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481581	40481581	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	960	459	0	ENST00000264657.5:c.1224C>G	p.Phe408Leu	p.F408L	ENST00000264657	NM_139276.2	408	ttC/ttG	13/24	0.920204984831002	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	1	0.920204984831002	4		459	1280	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220415	1220415	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913323	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	771	720	0	ENST00000326873.7:c.508C>T	p.Gln170Ter	p.Q170*	ENST00000326873	NM_000455.4	170	Cag/Tag	4/10	0.920204984831002	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.920204984831002	2		720	824	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563465	87563465	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs202136187	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	298	500	0	ENST00000277120.3:c.1853A>G	p.Lys618Arg	p.K618R	ENST00000277120		618	aAg/aGg	16/19	0.868392903015112	4	FACETS	1	0.983	1	0.556	0.524	0.59	CLONAL	1	TRUE	2	0.920204984831002	4		500	1118	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76812962	76812962	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1557059602	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	450	169	1	ENST00000373344.5:c.6659C>T	p.Ser2220Leu	p.S2220L	ENST00000373344	NM_000489.3	2220	tCa/tTa	30/35	0.752544787972616	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.920204984831002	2		170	473	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156693	20156693	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	143	192	0	ENST00000379607.5:c.64G>C	p.Glu22Gln	p.E22Q	ENST00000379607	NM_001412.3	22	Gaa/Caa	2/7	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.920204984831002	1		192	159	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876425	35876425	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	389	586	0	ENST00000303115.3:c.1217T>G	p.Leu406Arg	p.L406R	ENST00000303115	NM_002185.3	406	cTt/cGt	8/8	0.868392903015112	4	FACETS	1	0.96	1	0.507	0.481	0.534	CLONAL	1	TRUE	2	0.920204984831002	4		586	1600	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858336	9858336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1349281989	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	507	365	1	ENST00000330684.3:c.3065G>A	p.Arg1022His	p.R1022H	ENST00000330684	NM_001134407.1	1022	cGc/cAc	13/13	0.503460701774342	4	FACETS	0.861	0.833	0.889	0.861	0.833	0.889	INDETERMINATE	3	TRUE	1	0.920204984831002	4		366	819	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523600	106523600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	506	203	0	ENST00000359195.3:c.2752G>A	p.Glu918Lys	p.E918K	ENST00000359195	NM_002649.2	918	Gaa/Aaa	8/11	0.920204984831002	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	4	TRUE	0	0.920204984831002	4		203	528	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953016	2953016	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	324	718	0	ENST00000396946.4:c.2924G>T	p.Arg975Leu	p.R975L	ENST00000396946	NM_032415.4	975	cGg/cTg	22/25	0.909066729287495	4	FACETS	1	0.972	1	0.524	0.494	0.554	CLONAL	1	TRUE	2	0.920204984831002	4		718	1291	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045491	47045491	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	650	276	0	ENST00000377604.3:c.2458G>T	p.Glu820Ter	p.E820*	ENST00000377604	NM_001204468.1	820	Gaa/Taa	22/24	0.752544787972616	2	FACETS	1	0.998	1			1	CLONAL	2	TRUE	NA	0.920204984831002	2		276	675	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629391	187629391	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	373	564	1	ENST00000441802.2:c.1591C>T	p.Pro531Ser	p.P531S	ENST00000441802	NM_005245.3	531	Cct/Tct	2/27	0.672321526912188	4	FACETS	1	0.982	1	0.538	0.509	0.567	CLONAL	1	TRUE	2	0.920204984831002	4		565	1447	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70442602	70442602	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	454	350	0	ENST00000373644.4:c.4924G>C	p.Glu1642Gln	p.E1642Q	ENST00000373644	NM_030625.2	1642	Gaa/Caa	10/12	0.920204984831002	3	FACETS	0.9	0.867	0.934	0.9	0.867	0.934	CLONAL	2	TRUE	1	0.920204984831002	3		350	800	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725089	89725089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	90	82	0	ENST00000371953.3:c.1072G>A	p.Glu358Lys	p.E358K	ENST00000371953	NM_000314.4	358	Gag/Aag	9/9	0.920204984831002	3	FACETS	0.845	0.773	0.917	0.845	0.773	0.917	CLONAL	2	TRUE	1	0.920204984831002	3		82	169	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996845	100996845	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	1053	411	0	ENST00000325455.5:c.1682C>A	p.Ser561Ter	p.S561*	ENST00000325455	NM_001202474.3	561	tCa/tAa	2/8	0.920190793187811	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.920204984831002	3		411	1096	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117762	108117762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	366	184	0	ENST00000278616.4:c.973C>T	p.His325Tyr	p.H325Y	ENST00000278616	NM_000051.3	325	Cat/Tat	8/63	0.920190793187811	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.920204984831002	3		184	379	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544088	18544088	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	259	209	0	ENST00000266497.5:c.1905G>C	p.Met635Ile	p.M635I	ENST00000266497		635	atG/atC	13/31	0.785068148313319	4	FACETS	0.869	0.82	0.918	0.869	0.82	0.918	CLONAL	2	TRUE	2	0.920204984831002	4		209	622	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445505	49445505	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747101567	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1529	386	603	0	ENST00000301067.7:c.1961C>T	p.Ser654Phe	p.S654F	ENST00000301067	NM_003482.3	654	tCc/tTc	10/54	0.920204984831002	6	FACETS	1	0.992	1	0.311	0.294	0.328	CLONAL	1	TRUE	2	0.920204984831002	6		603	1915	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95596463	95596463	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	116	242	0	ENST00000393063.1:c.505A>G	p.Ile169Val	p.I169V	ENST00000393063	NM_030621.3	169	Att/Gtt	6/28	0.920204984831002	3	FACETS	0.898	0.816	0.983	0.449	0.408	0.492	CLONAL	1	TRUE	1	0.920204984831002	3		242	410	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032002	10032002	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	397	580	0	ENST00000330684.3:c.821C>G	p.Ser274Trp	p.S274W	ENST00000330684	NM_001134407.1	274	tCg/tGg	3/13	0.503460701774342	4	FACETS	1	0.994	1	0.45	0.428	0.473	INDETERMINATE	1	TRUE	1	0.920204984831002	4		580	1227	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512384	38512384	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774473938	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	212	434	3	ENST00000254066.5:c.1295G>A	p.Arg432Gln	p.R432Q	ENST00000254066	NM_000964.3	432	cGg/cAg	9/9	0.920204984831002	4	FACETS	1	0.962	1	0.35	0.325	0.375	CLONAL	1	TRUE	1	0.920204984831002	4		437	843	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017155	31017155	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	105	219	0	ENST00000375687.4:c.486G>C	p.Lys162Asn	p.K162N	ENST00000375687	NM_015338.5	162	aaG/aaC	7/13	0.920204984831002	3	FACETS	0.868	0.784	0.955	0.434	0.392	0.478	CLONAL	1	TRUE	1	0.920204984831002	3		219	384	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180244	38180244	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	1116	680	0	ENST00000396334.3:c.92C>G	p.Ser31Cys	p.S31C	ENST00000396334	NM_002468.4	31	tCc/tGc	1/5	0.785068148313319	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.920204984831002	4		680	2289	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180445	38180445	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	1281	620	0	ENST00000396334.3:c.293C>G	p.Ser98Cys	p.S98C	ENST00000396334	NM_002468.4	98	tCt/tGt	1/5	0.785068148313319	4	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	2	0.920204984831002	4		620	2412	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155979	106155979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753147592	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	338	244	1	ENST00000380013.4:c.880G>A	p.Glu294Lys	p.E294K	ENST00000380013	NM_001127208.2	294	Gag/Aag	3/11	0.920204984831002	3	FACETS	0.966	0.927	1	0.966	0.927	1	CLONAL	2	TRUE	1	0.920204984831002	3		245	555	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106162579	106162579	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	149	182	0	ENST00000380013.4:c.3493G>T	p.Glu1165Ter	p.E1165*	ENST00000380013	NM_001127208.2	1165	Gaa/Taa	4/11	0.920204984831002	3	FACETS	0.869	0.812	0.926	0.869	0.812	0.926	CLONAL	2	TRUE	1	0.920204984831002	3		182	272	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196946	106196946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	131	166	0	ENST00000380013.4:c.5279C>T	p.Ser1760Phe	p.S1760F	ENST00000380013	NM_001127208.2	1760	tCt/tTt	11/11	0.920204984831002	3	FACETS	0.912	0.833	0.993	0.456	0.416	0.497	CLONAL	1	TRUE	1	0.920204984831002	3		166	456	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159120	143159120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	99	274	0	ENST00000262992.4:c.733G>A	p.Asp245Asn	p.D245N	ENST00000262992	NM_001101669.1	245	Gac/Aac	10/24	0.920204984831002	3	FACETS	0.818	0.736	0.904	0.409	0.368	0.452	CLONAL	1	TRUE	1	0.920204984831002	3		274	384	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176719030	176719030	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	158	242	0	ENST00000439151.2:c.6334G>A	p.Glu2112Lys	p.E2112K	ENST00000439151	NM_022455.4	2112	Gaa/Aaa	22/23	0.920204984831002	3	FACETS	0.853	0.785	0.923			1	CLONAL	1	TRUE	NA	0.920204984831002	3		242	588	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032008	26032008	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	354	375	0	ENST00000244661.2:c.281A>C	p.Gln94Pro	p.Q94P	ENST00000244661	NM_003537.3	94	cAg/cCg	1/1	0.920190793187811	3	FACETS	1	0.977	1	0.35	0.332	0.369	CLONAL	1	TRUE	0	0.920204984831002	3		375	1070	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392114	81392114	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1443711585	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	326	214	0	ENST00000222390.5:c.163C>G	p.Pro55Ala	p.P55A	ENST00000222390	NM_000601.4	55	Cca/Gca	2/18	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.920204984831002	2		214	353	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156740	20156740	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8	103	127	0	ENST00000379607.5:c.17G>C	p.Gly6Ala	p.G6A	ENST00000379607	NM_001412.3	6	gGt/gCt	2/7	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.920204984831002	1		127	111	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0046209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	164	399	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.34	2		399	955	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221743	55221743	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519829	NA	P-0046209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	167	496	0	ENST00000275493.2:c.787A>C	p.Thr263Pro	p.T263P	ENST00000275493	NM_005228.3	263	Acc/Ccc	7/28	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.34	2		496	934	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56477640	56477640	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	284	537	0	ENST00000267101.3:c.188T>C	p.Leu63Pro	p.L63P	ENST00000267101	NM_001982.3	63	cTt/cCt	2/28	0.276131410345271	3	FACETS	0.773	0.726	0.822			1	SUBCLONAL	2	TRUE	NA	0.34	3		537	1264	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	162	151	0				ENST00000310581	NM_198253.2	-/1132			0.459696956953193	4	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	2	0.662821686426296	4		151	404	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525048	9525048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	105	461	0	ENST00000353224.5:c.1837G>A	p.Glu613Lys	p.E613K	ENST00000353224	NM_177990.2	613	Gag/Aag	8/10	0.384984350816332	1	FACETS	0.501	0.452	0.552	0.501	0.452	0.552	INDETERMINATE	1	TRUE	0	0.662821686426296	1		461	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0046210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	144	826	2	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.662821686426296	1	FACETS	0.991	0.922	1	0.991	0.922	1	CLONAL	1	TRUE	0	0.662821686426296	1		828	293	SUCCESS
APC	324	MSKCC	GRCh37	5	112173354	112173354	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0046210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	135	251	0	ENST00000257430.4:c.2063C>G	p.Ser688Ter	p.S688*	ENST00000257430	NM_000038.5	688	tCa/tGa	16/16	0.60627645441416	2	FACETS	0.886	0.827	0.943	0.886	0.827	0.943	CLONAL	2	TRUE	0	0.662821686426296	2		251	230	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463300	25463300	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	76	447	0	ENST00000264709.3:c.2193C>G	p.Phe731Leu	p.F731L	ENST00000264709	NM_175629.2	731	ttC/ttG	19/23	1	2	FACETS	0.936	0.833	1	0.936	0.833	1	CLONAL	1	TRUE	1	0.662821686426296	2		447	245	SUCCESS
ATM	472	MSKCC	GRCh37	11	108159810	108159810	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	45	99	0	ENST00000278616.4:c.4216G>C	p.Glu1406Gln	p.E1406Q	ENST00000278616	NM_000051.3	1406	Gaa/Caa	28/63	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.662821686426296	2		99	115	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609830	81609830	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	125	371	0	ENST00000298171.2:c.1428C>A	p.Tyr476Ter	p.Y476*	ENST00000298171	NM_000369.2	476	taC/taA	10/10	0.201377952548973	3	FACETS	0.823	0.757	0.891	0.823	0.757	0.891	INDETERMINATE	2	TRUE	1	0.662821686426296	3		371	305	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43769955	43769955	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	91	278	0	ENST00000382044.4:c.791C>T	p.Ser264Leu	p.S264L	ENST00000382044	NM_001141980.1	264	tCa/tTa	8/28	0.436435082068608	1	FACETS	0.858	0.778	0.939	0.858	0.778	0.939	CLONAL	1	TRUE	0	0.662821686426296	1		278	214	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831456	72831456	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	83	555	0	ENST00000268489.5:c.5125G>C	p.Glu1709Gln	p.E1709Q	ENST00000268489	NM_006885.3	1709	Gag/Cag	9/10	0.384984350816332	1	FACETS	0.618	0.552	0.686	0.618	0.552	0.686	INDETERMINATE	1	TRUE	0	0.662821686426296	1		555	271	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149290781	149290781	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs764139095	NA	P-0046210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	216	359	0	ENST00000360632.3:c.438A>G	p.Ile146Met	p.I146M	ENST00000360632	NM_015472.4	146	atA/atG	3/7	0.582949261119781	4	FACETS	0.985	0.924	1	0.985	0.924	1	CLONAL	2	TRUE	2	0.662821686426296	4		359	550	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629037	187629037	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	133	525	0	ENST00000441802.2:c.1945G>C	p.Asp649His	p.D649H	ENST00000441802	NM_005245.3	649	Gat/Cat	2/27	NA	2	FACETS	1	0.935	1			1	INDETERMINATE	1	TRUE	NA	0.662821686426296	2		525	393	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132725	152132725	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	98	368	0	ENST00000262189.6:c.147G>C	p.Gln49His	p.Q49H	ENST00000262189	NM_170606.2	49	caG/caC	1/59	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.662821686426296	2		368	295	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38178595	38178595	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	61	360	0	ENST00000317025.8:c.1804G>C	p.Glu602Gln	p.E602Q	ENST00000317025	NM_023034.1	602	Gag/Cag	8/24	0.589413397258162	4	FACETS	0.351	0.301	0.404			1	SUBCLONAL	1	TRUE	NA	0.662821686426296	4		360	873	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275774	38275774	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	44	599	0	ENST00000425967.3:c.1495G>A	p.Asp499Asn	p.D499N	ENST00000425967	NM_001174067.1	499	Gac/Aac	11/19	0.589413397258162	4	FACETS	0.3	0.25	0.354			1	SUBCLONAL	1	TRUE	NA	0.662821686426296	4		599	737	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922016	39922016	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	123	321	1	ENST00000378444.4:c.4156G>A	p.Glu1386Lys	p.E1386K	ENST00000378444	NM_001123385.1	1386	Gag/Aag	9/15	0.589413397258162	2	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.662821686426296	2		322	323	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	321	151	0				ENST00000310581	NM_198253.2	-/1132			0.745400345775275	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.811687072504828	3		151	549	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652147	36652148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	233	720	0	ENST00000244741.5:c.270dup	p.Gly91ArgfsTer38	p.G91Rfs*38	ENST00000244741	NM_000389.4	90	gga/ggAa	2/3	1	2	FACETS	0.853	0.8	0.907	0.853	0.8	0.907	CLONAL	1	TRUE	1	0.811687072504828	2		720	673	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29107942	29107942	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs749366698	NA	P-0046211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	223	529	0	ENST00000328354.6:c.747G>T	p.Lys249Asn	p.K249N	ENST00000328354	NM_007194.3	249	aaG/aaT	6/15	1	2	FACETS	0.916	0.859	0.974	0.916	0.859	0.974	CLONAL	1	TRUE	1	0.811687072504828	2		529	600	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	250	622	0	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	0.504055009143682	1	FACETS	0.992	0.932	1	0.992	0.932	1	CLONAL	1	TRUE	0	0.504055009143682	1		622	748	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	142	354	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	0.504055009143682	1	FACETS	0.93	0.855	1	0.93	0.855	1	CLONAL	1	TRUE	0	0.504055009143682	1		354	453	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919336	48919336	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0046212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	37	154	0	ENST00000267163.4:c.500+1G>A		p.X167_splice	ENST00000267163	NM_000321.2	167			0.504055009143682	1	FACETS	0.796	0.668	0.932	0.796	0.668	0.932	CLONAL	1	TRUE	0	0.504055009143682	1		154	138	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0046214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	130	763	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.237535222574089	2		763	1023	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0046214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1305	208	824	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.237535222574089	2		824	1513	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791527	42791527	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	61	687	1	ENST00000575354.2:c.508C>T	p.Arg170Trp	p.R170W	ENST00000575354	NM_015125.3	170	Cgg/Tgg	4/20	0.237535222574089	1	FACETS	0.436	0.375	0.503	0.436	0.375	0.503	SUBCLONAL	1	TRUE	0	0.237535222574089	1		688	1038	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368424	225368424	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	66	306	0	ENST00000264414.4:c.1322T>C	p.Leu441Pro	p.L441P	ENST00000264414	NM_003590.4	441	cTc/cCc	9/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.237535222574089	2		306	444	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247384	153247384	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0046214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	50	167	0	ENST00000281708.4:c.1419-1G>A		p.X473_splice	ENST00000281708	NM_033632.3	473			0.237535222574089	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.237535222574089	1		167	297	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293592	1293592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1013341756	NA	P-0046217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	24	843	0	ENST00000310581.5:c.1409G>A	p.Arg470His	p.R470H	ENST00000310581	NM_198253.2	470	cGc/cAc	2/16	1	2	FACETS	0.395	0.31	0.494	0.395	0.31	0.494	SUBCLONAL	1	TRUE	1	0.36569852219667	2		843	332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574026	7574026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	46	680	0	ENST00000269305.4:c.1001G>T	p.Gly334Val	p.G334V	ENST00000269305	NM_001126112.2	334	gGg/gTg	10/11	0.36569852219667	1	FACETS	0.867	0.737	1	0.867	0.737	1	CLONAL	1	TRUE	0	0.36569852219667	1		680	237	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044464	5044464	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	22	445	1	ENST00000381652.3:c.412C>T	p.Arg138Ter	p.R138*	ENST00000381652	NM_004972.3	138	Cga/Tga	5/25	0.36569852219667	1	FACETS	0.793	0.623	0.984	0.793	0.623	0.984	CLONAL	1	TRUE	0	0.36569852219667	1		446	124	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224198	36224198	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1351767688	NA	P-0046217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	136	607	0	ENST00000222270.7:c.6748C>T	p.Arg2250Cys	p.R2250C	ENST00000222270	NM_014727.1	2250	Cgc/Tgc	28/37	1	2	FACETS	1	0.97	1	1	0.992	1	CLONAL	2	TRUE	1	0.36569852219667	2		607	337	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78426120	78426120	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	40	491	1	ENST00000370768.2:c.1405del	p.His469MetfsTer196	p.H469Mfs*196	ENST00000370768	NM_003902.3	469	Cat/at	15/20	1	2	FACETS	0.872	0.729	1	0.872	0.729	1	CLONAL	1	TRUE	1	0.36569852219667	2		492	251	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518439	204518439	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	14	374	0	ENST00000367182.3:c.1102G>T	p.Ala368Ser	p.A368S	ENST00000367182	NM_001278516.1	368	Gct/Tct	11/11	1	2	FACETS	0.781	0.572	1	0.781	0.572	1	CLONAL	1	TRUE	1	0.36569852219667	2		374	98	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70432693	70432693	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	16	391	0	ENST00000373644.4:c.4715G>T	p.Gly1572Val	p.G1572V	ENST00000373644	NM_030625.2	1572	gGa/gTa	8/12	1	2	FACETS	1	0.812	1	1	0.812	1	CLONAL	1	TRUE	1	0.36569852219667	2		391	80	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425773	49425773	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	46	757	0	ENST00000301067.7:c.12715C>T	p.Gln4239Ter	p.Q4239*	ENST00000301067	NM_003482.3	4239	Cag/Tag	39/54	1	2	FACETS	0.968	0.821	1	0.968	0.821	1	CLONAL	1	TRUE	1	0.36569852219667	2		757	260	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438279	49438279	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	61	640	0	ENST00000301067.7:c.4990del	p.Ile1664LeufsTer58	p.I1664Lfs*58	ENST00000301067	NM_003482.3	1664	Att/tt	20/54	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.36569852219667	2		640	291	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288487	15288487	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	17	219	0	ENST00000263388.2:c.4252T>C	p.Ser1418Pro	p.S1418P	ENST00000263388	NM_000435.2	1418	Tcg/Ccg	24/33	1	2	FACETS	0.567	0.425	0.733	0.567	0.425	0.733	SUBCLONAL	1	TRUE	1	0.36569852219667	2		219	164	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665553	138665553	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	40	311	0	ENST00000330315.3:c.12C>A	p.Ser4Arg	p.S4R	ENST00000330315	NM_023067.3	4	agC/agA	1/1	0.177819004435748	3	FACETS	1	0.918	1	0.58	0.486	0.683	INDETERMINATE	1	TRUE	1	0.36569852219667	3		311	223	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630068	187630068	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	35	592	0	ENST00000441802.2:c.914C>A	p.Thr305Lys	p.T305K	ENST00000441802	NM_005245.3	305	aCa/aAa	2/27	0.36569852219667	1	FACETS	0.884	0.733	1	0.884	0.733	1	CLONAL	1	TRUE	0	0.36569852219667	1		592	177	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396929	139396929	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	34	337	0	ENST00000277541.6:c.5179G>T	p.Glu1727Ter	p.E1727*	ENST00000277541	NM_017617.3	1727	Gag/Tag	28/34	0.36569852219667	1	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	0	0.36569852219667	1		337	145	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554978	187554979	+	splice_acceptor_variant	Splice_Site	DEL	CT	CT	A	novel	NA	P-0046217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	18	295	0	ENST00000441802.2:c.4184-2_4184-1delinsT		p.X1395_splice	ENST00000441802	NM_005245.3	1395			0.36569852219667	1	FACETS	0.789	0.603	1	0.789	0.603	1	CLONAL	1	TRUE	0	0.36569852219667	1		295	102	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578455	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882000	NA	P-0046218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	88	804	0	ENST00000269305.4:c.475G>C	p.Ala159Pro	p.A159P	ENST00000269305	NM_001126112.2	159	Gcc/Ccc	5/11	0.577046802261289	1	FACETS	0.953	0.863	1	0.953	0.863	1	CLONAL	1	TRUE	0	0.623193209718233	1		804	204	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037866	49037866	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs587778860	NA	P-0046218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	42	135	0	ENST00000267163.4:c.2107-1G>C		p.X703_splice	ENST00000267163	NM_000321.2	703			0.577046802261289	1	FACETS	0.851	0.732	0.975	0.851	0.732	0.975	CLONAL	1	TRUE	0	0.623193209718233	1		135	109	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934105	39934105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs538820529	NA	P-0046218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	35	267	0	ENST00000378444.4:c.494C>T	p.Ala165Val	p.A165V	ENST00000378444	NM_001123385.1	165	gCg/gTg	4/15	1	1	FACETS	0.569	0.474	0.67	0.569	0.474	0.67	SUBCLONAL	1	TRUE	0	0.623193209718233	1		267	136	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866609	37866609	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs769870618	NA	P-0046218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	74	608	0	ENST00000269571.5:c.776A>G	p.Asn259Ser	p.N259S	ENST00000269571		259	aAc/aGc	7/27	0.577046802261289	1	FACETS	0.865	0.773	0.959	0.865	0.773	0.959	CLONAL	1	TRUE	0	0.623193209718233	1		608	189	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218414	1218414	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0046218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	64	487	1	ENST00000326873.7:c.291-2A>T		p.X97_splice	ENST00000326873	NM_000455.4	97			0.577046802261289	1	FACETS	0.867	0.769	0.969	0.867	0.769	0.969	CLONAL	1	TRUE	0	0.623193209718233	1		488	163	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21627910	21627910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1176731657	NA	P-0046218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	29	336	0	ENST00000421138.2:c.1220G>A	p.Arg407Gln	p.R407Q	ENST00000421138		407	cGa/cAa	12/16	0.623193209718233	1	FACETS	0.439	0.357	0.529	0.439	0.357	0.529	SUBCLONAL	1	TRUE	0	0.623193209718233	1		336	146	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859627	151859627	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	13	411	0	ENST00000262189.6:c.11035G>T	p.Glu3679Ter	p.E3679*	ENST00000262189	NM_170606.2	3679	Gaa/Taa	43/59	1	2	FACETS	0.193	0.137	0.261	0.193	0.137	0.261	SUBCLONAL	1	TRUE	1	0.623193209718233	2		411	216	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264425	16264425	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	36	679	1	ENST00000375759.3:c.10628G>T	p.Gly3543Val	p.G3543V	ENST00000375759	NM_015001.2	3543	gGa/gTa	13/15	0.254343357612128	1	FACETS	0.386	0.32	0.459	0.386	0.32	0.459	INDETERMINATE	1	TRUE	0	0.623193209718233	1		680	206	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325150	39325150	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	62	555	0	ENST00000373001.3:c.169G>T	p.Ala57Ser	p.A57S	ENST00000373001	NM_022157.3	57	Gct/Tct	1/7	0.254343357612128	1	FACETS	0.628	0.55	0.71	0.628	0.55	0.71	INDETERMINATE	1	TRUE	0	0.623193209718233	1		555	218	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258030	123258030	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	13	442	0	ENST00000358487.5:c.1651C>T	p.Leu551Phe	p.L551F	ENST00000358487	NM_000141.4	551	Ctt/Ttt	12/18	1	2	FACETS	0.167	0.119	0.226	0.167	0.119	0.226	SUBCLONAL	1	TRUE	1	0.623193209718233	2		442	250	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230547	46230548	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	35	349	0	ENST00000334344.6:c.799dup	p.Glu267GlyfsTer13	p.E267Gfs*13	ENST00000334344	NM_152641.2	266	tgg/tGgg	8/21	0.416997285289258	3	FACETS	0.698	0.577	0.832			1	SUBCLONAL	1	TRUE	NA	0.623193209718233	3		349	211	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748855	43748856	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AT	novel	NA	P-0046218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	94	630	0	ENST00000382044.4:c.1950_1951delinsAT	p.Glu651Ter	p.E651*	ENST00000382044	NM_001141980.1	650	gaGGaa/gaATaa	12/28	0.623193209718233	1	FACETS	0.891	0.808	0.976	0.891	0.808	0.976	CLONAL	1	TRUE	0	0.623193209718233	1		630	233	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498525	89498526	+	splice_donor_variant	Splice_Site	INS	-	-	T	novel	NA	P-0046218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	50	227	0	ENST00000336596.2:c.2496+2dup		p.X832_splice	ENST00000336596	NM_005233.5	832			0.566331185239726	1	FACETS	0.856	0.746	0.97	0.856	0.746	0.97	CLONAL	1	TRUE	0	0.623193209718233	1		227	129	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430957	181430961	+	frameshift_variant	Frame_Shift_Del	DEL	TCCGG	TCCGG	-	novel	NA	P-0046218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	50	737	0	ENST00000325404.1:c.809_813del	p.Leu270ArgfsTer38	p.L270Rfs*38	ENST00000325404	NM_003106.3	270	cTCCGG/c	1/1	0.261936976401883	3	FACETS	0.723	0.618	0.838	0.362	0.309	0.419	INDETERMINATE	1	TRUE	1	0.623193209718233	3		737	291	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590496	67590496	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	31	167	0	ENST00000274335.5:c.1558G>C	p.Glu520Gln	p.E520Q	ENST00000274335		520	Gaa/Caa	11/15	0.560417002133727	1	FACETS	0.611	0.505	0.726	0.611	0.505	0.726	SUBCLONAL	1	TRUE	0	0.623193209718233	1		167	112	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161970008	161970008	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	14	630	0	ENST00000366898.1:c.961G>A	p.Glu321Lys	p.E321K	ENST00000366898	NM_004562.2	321	Gag/Aag	9/12	0.566331185239726	1	FACETS	0.141	0.102	0.189	0.141	0.102	0.189	SUBCLONAL	1	TRUE	0	0.623193209718233	1		630	219	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250103	110250103	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	70	681	0	ENST00000374672.4:c.572A>G	p.Asn191Ser	p.N191S	ENST00000374672	NM_004235.4	191	aAc/aGc	3/5	0.279781038862144	1	FACETS	0.647	0.572	0.726	0.647	0.572	0.726	INDETERMINATE	1	TRUE	0	0.623193209718233	1		681	239	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0046219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	58	236	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.277166504827756	1	FACETS	0.703	0.604	0.81	0.703	0.604	0.81	SUBCLONAL	1	TRUE	0	0.277166504827756	1		236	513	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437227	220437227	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	79	887	1	ENST00000243786.2:c.131C>A	p.Pro44His	p.P44H	ENST00000243786	NM_002191.3	44	cCc/cAc	1/2	1	2	FACETS	0.537	0.471	0.608	0.537	0.471	0.608	SUBCLONAL	1	TRUE	1	0.277166504827756	2		888	1062	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741539	17741539	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	50	359	0	ENST00000250003.3:c.210C>A	p.His70Gln	p.H70Q	ENST00000250003	NM_002478.4	70	caC/caA	1/3	1	2	FACETS	0.592	0.503	0.689	0.592	0.503	0.689	SUBCLONAL	1	TRUE	1	0.390245215165712	2		359	433	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112919968	112919968	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	55	516	0	ENST00000351677.2:c.1183G>T	p.Asp395Tyr	p.D395Y	ENST00000351677	NM_002834.3	395	Gac/Tac	10/16	1	2	FACETS	0.595	0.509	0.688	0.595	0.509	0.688	SUBCLONAL	1	TRUE	1	0.390245215165712	2		516	474	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201382	133201382	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	76	711	0	ENST00000320574.5:c.6762G>T	p.Gln2254His	p.Q2254H	ENST00000320574	NM_006231.2	2254	caG/caT	49/49	1	2	FACETS	0.556	0.487	0.63	0.556	0.487	0.63	SUBCLONAL	1	TRUE	1	0.390245215165712	2		711	701	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103510680	103510680	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	30	294	2	ENST00000355739.4:c.584G>T	p.Ser195Ile	p.S195I	ENST00000355739	NM_000123.3	195	aGc/aTc	6/15	1	2	FACETS	0.594	0.48	0.721	0.594	0.48	0.721	SUBCLONAL	1	TRUE	1	0.390245215165712	2		296	259	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588745	29588745	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	42	253	0	ENST00000356175.3:c.4532del	p.Gly1511GlufsTer42	p.G1511Efs*42	ENST00000356175	NM_000267.3	1511	Gga/ga	34/57	1	2	FACETS	0.809	0.68	0.951	0.809	0.68	0.951	CLONAL	1	TRUE	1	0.390245215165712	2		253	266	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679433	29679433	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1555536380	NA	P-0046220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	55	297	0	ENST00000356175.3:c.7552+1G>T		p.X2518_splice	ENST00000356175	NM_000267.3	2518			1	2	FACETS	0.673	0.577	0.777	0.673	0.577	0.777	SUBCLONAL	1	TRUE	1	0.390245215165712	2		297	419	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379489	225379489	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	28	302	0	ENST00000264414.4:c.379G>T	p.Asp127Tyr	p.D127Y	ENST00000264414	NM_003590.4	127	Gac/Tac	4/16	1	2	FACETS	0.593	0.476	0.725	0.593	0.476	0.725	SUBCLONAL	1	TRUE	1	0.390245215165712	2		302	242	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385147	41385147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	68	768	0	ENST00000373198.4:c.814G>A	p.Asp272Asn	p.D272N	ENST00000373198	NM_133170.3	272	Gat/Aat	6/32	1	2	FACETS	0.363	0.315	0.416	0.363	0.315	0.416	SUBCLONAL	1	TRUE	1	0.390245215165712	2		768	960	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225692	26225692	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	148	671	0	ENST00000360408.1:c.310C>A	p.Leu104Ile	p.L104I	ENST00000360408	NM_003532.2	104	Ctt/Att	1/1	0.165814855732452	3	FACETS	1	0.976	1	0.592	0.541	0.645	INDETERMINATE	1	TRUE	1	0.390245215165712	3		671	766	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339203	116339203	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587780739	NA	P-0046220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	68	331	1	ENST00000397752.3:c.65G>T	p.Ser22Ile	p.S22I	ENST00000397752	NM_000245.2	22	aGc/aTc	2/21	1	2	FACETS	0.905	0.791	1	0.905	0.791	1	CLONAL	1	TRUE	1	0.390245215165712	2		332	385	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465477	8465477	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	18	339	0	ENST00000356435.5:c.3703C>T	p.His1235Tyr	p.H1235Y	ENST00000356435		1235	Cat/Tat	21/35	1	2	FACETS	0.309	0.232	0.399	0.309	0.232	0.399	SUBCLONAL	1	TRUE	1	0.390245215165712	2		339	299	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218611	98218611	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	90	498	1	ENST00000331920.6:c.3253A>T	p.Ile1085Phe	p.I1085F	ENST00000331920	NM_000264.3	1085	Atc/Ttc	19/24	1	2	FACETS	0.733	0.651	0.821	0.733	0.651	0.821	SUBCLONAL	1	TRUE	1	0.390245215165712	2		499	629	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0046221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	184	343	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.157275808841355	5	FACETS	1	0.978	1			1	INDETERMINATE	2	TRUE	NA	0.501029960758896	5		343	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0046221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	215	510	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.501029960758896	2		510	820	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920398	114920398	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	212	390	0	ENST00000543371.1:c.1339T>G	p.Cys447Gly	p.C447G	ENST00000543371	NM_001198531.1	447	Tgt/Ggt	13/14	0.252221022643434	1	FACETS	0.989	0.924	1	0.989	0.924	1	INDETERMINATE	1	TRUE	0	0.501029960758896	1		390	641	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184573	11184573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587777894	NA	P-0046222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	118	594	0	ENST00000361445.4:c.6644C>T	p.Ser2215Phe	p.S2215F	ENST00000361445	NM_004958.3	2215	tCt/tTt	47/58	1	2	FACETS	0.86	0.778	0.946	0.86	0.778	0.946	CLONAL	1	TRUE	1	0.444829612011629	2		594	617	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443599	52443601	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0046222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	107	523	0	ENST00000460680.1:c.91_93del	p.Glu31del	p.E31del	ENST00000460680	NM_004656.3	31	GAG/-	3/17	0.419160879049603	1	FACETS	0.899	0.812	0.99	0.899	0.812	0.99	CLONAL	1	TRUE	0	0.444829612011629	1		523	416	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864309	57864309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777242040	NA	P-0046222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	109	629	0	ENST00000228682.2:c.1786G>A	p.Ala596Thr	p.A596T	ENST00000228682	NM_005269.2	596	Gcc/Acc	12/12	0.361940916947411	3	FACETS	0.895	0.805	0.991	0.448	0.402	0.496	CLONAL	1	TRUE	1	0.444829612011629	3		629	669	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183863	10183864	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTA	novel	NA	P-0046222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	91	527	0	ENST00000256474.2:c.334_336dup	p.Tyr112dup	p.Y112dup	ENST00000256474	NM_000551.3	112	agc/agCTAc	1/3	0.419160879049603	1	FACETS	0.865	0.774	0.96	0.865	0.774	0.96	CLONAL	1	TRUE	0	0.444829612011629	1		527	368	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184159	123184159	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	48	253	0	ENST00000218089.9:c.1017+1del		p.K339fs	ENST00000218089	NM_001042749.1	339	aaG/aa	11/35	0.444829612011629	1	FACETS	0.823	0.704	0.949	0.823	0.704	0.949	CLONAL	1	TRUE	0	0.444829612011629	1		253	204	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0046223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	393	644	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.585487622993652	2	FACETS	0.825	0.79	0.86	0.825	0.79	0.86	CLONAL	2	TRUE	0	0.615191372305281	2		644	774	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0046223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	117	260	0	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	0.615191372305281	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.615191372305281	1		260	240	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0046224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	50	243	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.741	0.632	0.859	0.741	0.632	0.859	SUBCLONAL	1	TRUE	1	0.429798939512771	2		243	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0046224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1270	108	959	0	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	0.354791721093398	1	FACETS	0.286	0.256	0.319	0.286	0.256	0.319	SUBCLONAL	1	TRUE	0	0.429798939512771	1		959	1378	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0046224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	343	518	1	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	0.427312151719796	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.429798939512771	2		519	751	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0046224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	32	81	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	1	2	FACETS	0.919	0.756	1	0.919	0.756	1	CLONAL	1	TRUE	1	0.429798939512771	2		81	162	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520008	NA	P-0046224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	276	725	0	ENST00000269305.4:c.613T>C	p.Tyr205His	p.Y205H	ENST00000269305	NM_001126112.2	205	Tat/Cat	6/11	0.354791721093398	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.429798939512771	1		725	936	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562687	29562687	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1555615457	NA	P-0046224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	110	537	0	ENST00000356175.3:c.3767T>G	p.Leu1256Arg	p.L1256R	ENST00000356175	NM_000267.3	1256	cTg/cGg	28/57	1	2	FACETS	0.887	0.799	0.979	0.887	0.799	0.979	CLONAL	1	TRUE	1	0.429798939512771	2		537	577	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918942	76918942	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	133	311	0	ENST00000373344.5:c.4049del	p.Gly1350GlufsTer25	p.G1350Efs*25	ENST00000373344	NM_000489.3	1350	gGa/ga	12/35	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.429798939512771	1		311	347	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133263850	133263850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	12	151	0	ENST00000320574.5:c.52G>A	p.Glu18Lys	p.E18K	ENST00000320574	NM_006231.2	18	Gag/Aag	1/49	1	2	FACETS	0.596	0.42	0.813	0.596	0.42	0.813	SUBCLONAL	1	TRUE	1	0.22	2		151	183	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578433	7578433	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555526101	NA	P-0046225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	60	1567	0	ENST00000269305.4:c.497C>G	p.Ser166Ter	p.S166*	ENST00000269305	NM_001126112.2	166	tCa/tGa	5/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.22	2		1567	397	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786758	3786758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	32	520	0	ENST00000262367.5:c.4453C>T	p.His1485Tyr	p.H1485Y	ENST00000262367	NM_004380.2	1485	Cat/Tat	27/31	0.3	1	FACETS	0.86	0.7	1	0.86	0.7	1	CLONAL	1	TRUE	0	0.22	1		520	301	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412006	63412006	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	20	745	0	ENST00000330258.3:c.1161G>C	p.Glu387Asp	p.E387D	ENST00000330258	NM_152424.3	387	gaG/gaC	2/2	1	1	FACETS	0.65	0.498	0.827	0.65	0.498	0.827	SUBCLONAL	1	TRUE	0	0.22	1		745	249	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	48	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.971	0.825	1	0.971	0.825	1	CLONAL	1	TRUE	1	0.32	2		288	309	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436026	56436026	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771831816	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	80	380	0	ENST00000407977.2:c.1111C>T	p.Arg371Ter	p.R371*	ENST00000407977		371	Cga/Tga	9/10	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.32	2		380	473	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027494	48027494	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755587950	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	56	255	0	ENST00000234420.5:c.2372G>A	p.Arg791His	p.R791H	ENST00000234420	NM_000179.2	791	cGt/cAt	4/10	1	2	FACETS	0.854	0.734	0.984	0.854	0.734	0.984	CLONAL	1	TRUE	1	0.32	2		255	410	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339111	65339111	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	91	385	2	ENST00000342505.4:c.425del	p.Lys142ArgfsTer26	p.K142Rfs*26	ENST00000342505	NM_002227.2	142	aAg/ag	5/25	1	2	FACETS	0.891	0.792	0.997	0.891	0.792	0.997	CLONAL	1	TRUE	1	0.32	2		387	638	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789591	3789591	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	30	350	2	ENST00000262367.5:c.4268del	p.Pro1423LeufsTer36	p.P1423Lfs*36	ENST00000262367	NM_004380.2	1423	cCt/ct	25/31	1	2	FACETS	0.338	0.272	0.414	0.338	0.272	0.414	SUBCLONAL	1	TRUE	1	0.32	2		352	554	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874637	35874637	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	65	287	0	ENST00000303115.3:c.799del	p.Arg267GlyfsTer28	p.R267Gfs*28	ENST00000303115	NM_002185.3	265	Aaa/aa	6/8	1	2	FACETS	0.897	0.78	1	0.897	0.78	1	CLONAL	1	TRUE	1	0.32	2		287	453	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007619	45007619	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs111482205	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	25	148	0	ENST00000558401.1:c.68-2A>G		p.X23_splice	ENST00000558401	NM_004048.2	23			1	2	FACETS	0.713	0.565	0.882	0.713	0.565	0.882	SUBCLONAL	1	TRUE	1	0.32	2		148	219	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063358	67063359	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	75	274	0	ENST00000412916.2:c.54dup	p.Arg19Ter	p.R19*	ENST00000412916		16	-/T	1/6	1	2	FACETS	0.936	0.822	1	0.936	0.822	1	CLONAL	1	TRUE	1	0.32	2		274	501	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495415	56495415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373454755	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	123	606	0	ENST00000267101.3:c.3605G>A	p.Arg1202Gln	p.R1202Q	ENST00000267101	NM_001982.3	1202	cGg/cAg	28/28	1	2	FACETS	0.934	0.845	1	0.934	0.845	1	CLONAL	1	TRUE	1	0.32	2		606	823	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007689	45007690	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	78	200	0	ENST00000558401.1:c.137_138del	p.Tyr46CysfsTer10	p.Y46Cfs*10	ENST00000558401	NM_004048.2	46	TAt/t	2/4	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.32	2		200	380	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264985	46264985	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	33	333	0	ENST00000371998.3:c.1860del	p.Lys620AsnfsTer18	p.K620Nfs*18	ENST00000371998		619	Aaa/aa	12/23	1	2	FACETS	0.427	0.347	0.517	0.427	0.347	0.517	SUBCLONAL	1	TRUE	1	0.32	2		333	483	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732969	30732969	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	76	340	0	ENST00000295754.5:c.1582C>A	p.Arg528Ser	p.R528S	ENST00000295754	NM_003242.5	528	Cgt/Agt	7/7	1	2	FACETS	0.988	0.869	1	0.988	0.869	1	CLONAL	1	TRUE	1	0.32	2		340	481	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439919	56439919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	122	519	2	ENST00000407977.2:c.673del	p.Arg225AlafsTer194	p.R225Afs*194	ENST00000407977		225	Cgc/gc	6/10	1	2	FACETS	0.962	0.869	1	0.962	0.869	1	CLONAL	1	TRUE	1	0.32	2		521	793	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788618	3788618	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	76	317	0	ENST00000262367.5:c.4336C>A	p.Arg1446Ser	p.R1446S	ENST00000262367	NM_004380.2	1446	Cgc/Agc	26/31	1	2	FACETS	0.942	0.829	1	0.942	0.829	1	CLONAL	1	TRUE	1	0.32	2		317	504	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119794	70119794	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	121	586	0	ENST00000245479.2:c.800del	p.Pro267LeufsTer12	p.P267Lfs*12	ENST00000245479	NM_000346.3	266	Ccc/cc	3/3	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.32	2		586	706	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188297	32188297	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs753855314	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	132	730	1	ENST00000375023.3:c.1044del	p.Gly349AlafsTer49	p.G349Afs*49	ENST00000375023	NM_004557.3	348	ggC/gg	6/30	1	2	FACETS	0.923	0.837	1	0.923	0.837	1	CLONAL	1	TRUE	1	0.32	2		731	894	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273944	10273944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	167	782	0	ENST00000330684.3:c.325G>A	p.Val109Ile	p.V109I	ENST00000330684	NM_001134407.1	109	Gta/Ata	2/13	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.32	2		782	930	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	103	527	2	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.849	0.766	0.936	1	0.986	1	CLONAL	2	TRUE	1	0.32	2		529	379	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647657	3647657	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs774532876	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	209	764	13	ENST00000294008.3:c.1406del	p.Pro469HisfsTer4	p.P469Hfs*4	ENST00000294008	NM_032444.2	469	cCa/ca	7/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.32	2		777	1106	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214398	36214398	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs868041281	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	49	630	2	ENST00000222270.7:c.3057del	p.Gly1020AlafsTer4	p.G1020Afs*4	ENST00000222270	NM_014727.1	1018	Aaa/aa	7/37	1	2	FACETS	0.406	0.342	0.475	0.406	0.342	0.475	SUBCLONAL	1	TRUE	1	0.32	2		632	755	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	123	507	3	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.904	0.818	0.996	0.904	0.818	0.996	CLONAL	1	TRUE	1	0.32	2		510	850	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323315	31323315	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	83	420	0	ENST00000412585.2:c.674T>G	p.Leu225Arg	p.L225R	ENST00000412585	NM_005514.6	225	cTg/cGg	4/8	1	2	FACETS	0.973	0.861	1	0.973	0.861	1	CLONAL	1	TRUE	1	0.32	2		420	533	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663295	227663295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753900721	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	40	478	3	ENST00000305123.5:c.160C>T	p.Arg54Trp	p.R54W	ENST00000305123	NM_005544.2	54	Cgg/Tgg	1/2	1	2	FACETS	0.416	0.345	0.495	0.416	0.345	0.495	SUBCLONAL	1	TRUE	1	0.32	2		481	601	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216188	36216188	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	52	617	1	ENST00000222270.7:c.3596G>C	p.Gly1199Ala	p.G1199A	ENST00000222270	NM_014727.1	1199	gGc/gCc	11/37	1	2	FACETS	0.399	0.338	0.465	0.399	0.338	0.465	SUBCLONAL	1	TRUE	1	0.32	2		618	815	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258894	16258894	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	47	543	3	ENST00000375759.3:c.6164del	p.Pro2055LeufsTer9	p.P2055Lfs*9	ENST00000375759	NM_015001.2	2053	aaC/aa	11/15	1	2	FACETS	0.322	0.27	0.379	0.322	0.27	0.379	SUBCLONAL	1	TRUE	1	0.32	2		546	913	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295278	1295278	+	upstream_gene_variant	5'Flank	SNP	C	C	T	rs914835735	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	111	455	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.32	2		457	575	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136269	2136269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777592623	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	147	666	0	ENST00000219476.3:c.4738C>T	p.Arg1580Trp	p.R1580W	ENST00000219476	NM_000548.3	1580	Cgg/Tgg	37/42	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.32	2		666	908	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8252034	8252034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536636517	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	106	559	0	ENST00000335790.3:c.43G>A	p.Val15Ile	p.V15I	ENST00000335790	NM_002315.2	15	Gtc/Atc	2/4	1	2	FACETS	0.882	0.791	0.979	0.882	0.791	0.979	CLONAL	1	TRUE	1	0.32	2		559	751	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677990	58677990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1375271471	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	56	213	0	ENST00000305921.3:c.215C>T	p.Ala72Val	p.A72V	ENST00000305921	NM_003620.3	72	gCc/gTc	1/6	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.32	2		213	274	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939697	76939697	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	71	409	0	ENST00000373344.5:c.1051G>T	p.Glu351Ter	p.E351*	ENST00000373344	NM_000489.3	351	Gag/Tag	9/35	1	2	FACETS	0.969	0.848	1	0.969	0.848	1	CLONAL	1	TRUE	1	0.32	2		409	458	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807448	36807448	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs777493861	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	55	645	0	ENST00000373129.3:c.1216A>G	p.Ser406Gly	p.S406G	ENST00000373129	NM_032017.1	406	Agc/Ggc	12/12	1	2	FACETS	0.397	0.338	0.461	0.397	0.338	0.461	SUBCLONAL	1	TRUE	1	0.32	2		645	866	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248325	59248325	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536167705	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	24	183	0	ENST00000371222.2:c.418G>A	p.Ala140Thr	p.A140T	ENST00000371222	NM_002228.3	140	Gca/Aca	1/1	1	2	FACETS	0.664	0.523	0.825	0.664	0.523	0.825	SUBCLONAL	1	TRUE	1	0.32	2		183	226	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138107	64138107	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	41	658	0	ENST00000334205.4:c.2030G>A	p.Gly677Asp	p.G677D	ENST00000334205	NM_003942.2	677	gGc/gAc	16/17	1	2	FACETS	0.341	0.283	0.406	0.341	0.283	0.406	SUBCLONAL	1	TRUE	1	0.32	2		658	752	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577292	64577292	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	125	668	0	ENST00000312049.6:c.290T>C	p.Ile97Thr	p.I97T	ENST00000312049	NM_130799.2	97	aTc/aCc	2/10	1	2	FACETS	0.993	0.899	1	0.993	0.899	1	CLONAL	1	TRUE	1	0.32	2		668	787	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941409	71941409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763945939	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	117	634	0	ENST00000298229.2:c.1094G>A	p.Arg365His	p.R365H	ENST00000298229	NM_001567.3	365	cGc/cAc	10/28	1	2	FACETS	0.887	0.8	0.98	0.887	0.8	0.98	CLONAL	1	TRUE	1	0.32	2		634	824	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377187	118377187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147844226	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	94	337	0	ENST00000534358.1:c.10580G>A	p.Arg3527Gln	p.R3527Q	ENST00000534358	NM_005933.3	3527	cGg/cAg	27/36	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.32	2		337	587	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392843	118392843	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	37	379	1	ENST00000534358.1:c.11875C>T	p.Pro3959Ser	p.P3959S	ENST00000534358	NM_005933.3	3959	Ccc/Tcc	36/36	1	2	FACETS	0.423	0.348	0.507	0.423	0.348	0.507	SUBCLONAL	1	TRUE	1	0.32	2		380	547	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955558	48955558	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	14	164	0	ENST00000267163.4:c.1674G>A	p.Met558Ile	p.M558I	ENST00000267163	NM_000321.2	558	atG/atA	17/27	1	2	FACETS	0.449	0.325	0.598	0.449	0.325	0.598	SUBCLONAL	1	TRUE	1	0.32	2		164	195	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828234	72828234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1454751620	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	115	546	0	ENST00000268489.5:c.8347G>A	p.Val2783Ile	p.V2783I	ENST00000268489	NM_006885.3	2783	Gtc/Atc	9/10	1	2	FACETS	0.916	0.825	1	0.916	0.825	1	CLONAL	1	TRUE	1	0.32	2		546	785	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214668	5214668	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	120	714	0	ENST00000357368.4:c.4398del	p.Pro1467ArgfsTer23	p.P1467Rfs*23	ENST00000357368	NM_002850.3	1466	ggG/gg	29/38	1	2	FACETS	0.776	0.699	0.856	0.776	0.699	0.856	SUBCLONAL	1	TRUE	1	0.32	2		714	967	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215543	36215543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	59	630	0	ENST00000222270.7:c.3340C>A	p.Pro1114Thr	p.P1114T	ENST00000222270	NM_014727.1	1114	Cca/Aca	9/37	1	2	FACETS	0.35	0.3	0.405	0.35	0.3	0.405	SUBCLONAL	1	TRUE	1	0.32	2		630	1054	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137387	202137387	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	55	231	0	ENST00000358485.4:c.616del	p.Glu206ArgfsTer14	p.E206Rfs*14	ENST00000358485	NM_001080125.1	205	atG/at	4/9	1	2	FACETS	0.924	0.794	1	0.924	0.794	1	CLONAL	1	TRUE	1	0.32	2		231	372	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62305301	62305301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1457145320	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	57	747	0	ENST00000360203.5:c.774G>A	p.Met258Ile	p.M258I	ENST00000360203	NM_001283009.1	258	atG/atA	10/35	1	2	FACETS	0.348	0.297	0.404	0.348	0.297	0.404	SUBCLONAL	1	TRUE	1	0.32	2		747	1023	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574852	41574852	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	114	511	0	ENST00000263253.7:c.7137T>A	p.Asn2379Lys	p.N2379K	ENST00000263253	NM_001429.3	2379	aaT/aaA	31/31	1	2	FACETS	0.927	0.834	1	0.927	0.834	1	CLONAL	1	TRUE	1	0.32	2		511	769	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626352	12626352	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	69	440	0	ENST00000251849.4:c.1797del	p.Gln601ArgfsTer39	p.Q601Rfs*39	ENST00000251849	NM_002880.3	599	ttT/tt	16/17	1	2	FACETS	0.697	0.607	0.794	0.697	0.607	0.794	SUBCLONAL	1	TRUE	1	0.32	2		440	619	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799655	72799655	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	108	518	0	ENST00000325599.8:c.1514T>C	p.Val505Ala	p.V505A	ENST00000325599	NM_018130.2	505	gTt/gCt	11/11	1	2	FACETS	0.847	0.76	0.939	0.847	0.76	0.939	CLONAL	1	TRUE	1	0.32	2		518	797	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946360	2946360	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	64	769	0	ENST00000396946.4:c.3377del	p.Gly1126AlafsTer3	p.G1126Afs*3	ENST00000396946	NM_032415.4	1126	gGc/gc	25/25	1	2	FACETS	0.395	0.341	0.454	0.395	0.341	0.454	SUBCLONAL	1	TRUE	1	0.32	2		769	1013	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739593	41739593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	22	303	0	ENST00000242208.4:c.380C>T	p.Ala127Val	p.A127V	ENST00000242208	NM_002192.2	127	gCc/gTc	2/3	1	2	FACETS	0.32	0.247	0.405	0.32	0.247	0.405	SUBCLONAL	1	TRUE	1	0.32	2		303	430	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089816	5089816	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	20	212	0	ENST00000381652.3:c.2714T>C	p.Leu905Pro	p.L905P	ENST00000381652	NM_004972.3	905	cTa/cCa	20/25	1	2	FACETS	0.463	0.354	0.59	0.463	0.354	0.59	SUBCLONAL	1	TRUE	1	0.32	2		212	270	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411771	63411772	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	154	713	0	ENST00000330258.3:c.1395dup	p.Asn466GlnfsTer2	p.N466Qfs*2	ENST00000330258	NM_152424.3	465	-/C	2/2	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.32	2		713	954	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576870	7576870	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs876659384	NA	P-0046230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	79	396	0	ENST00000269305.4:c.976G>T	p.Glu326Ter	p.E326*	ENST00000269305	NM_001126112.2	326	Gaa/Taa	9/11	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	FALSE	1	0.146596396473692	2		396	998	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0046230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	80	495	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	0.114396114393733	3	FACETS	1	0.969	1	0.666	0.585	0.753	CLONAL	1	FALSE	1	0.146596396473692	3		495	880	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214592	5214592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369295620	NA	P-0046230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	86	628	0	ENST00000357368.4:c.4474C>T	p.Arg1492Trp	p.R1492W	ENST00000357368	NM_002850.3	1492	Cgg/Tgg	29/38	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	FALSE	1	0.146596396473692	2		628	1083	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044723	47044723	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	110	410	0	ENST00000377604.3:c.2123del	p.His708ProfsTer94	p.H708Pfs*94	ENST00000377604	NM_001204468.1	708	cAc/cc	19/24	1	1	FACETS	0.988	0.888	1	1	0.988	1	CLONAL	2	FALSE	0	0.146596396473692	1		410	704	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913517	NA	P-0046231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	208	293	0	ENST00000288135.5:c.1676T>C	p.Val559Ala	p.V559A	ENST00000288135	NM_000222.2	559	gTt/gCt	11/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.778792759076784	2		293	486	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172433	108172433	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	195	281	0	ENST00000278616.4:c.5236G>T	p.Gly1746Ter	p.G1746*	ENST00000278616	NM_000051.3	1746	Gga/Tga	35/63	1	2	FACETS	0.956	0.892	1	0.956	0.892	1	CLONAL	1	TRUE	1	0.778792759076784	2		281	524	SUCCESS
APC	324	MSKCC	GRCh37	5	112151282	112151282	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs786204118	NA	P-0046232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	27	230	3	ENST00000257430.4:c.925G>T	p.Gly309Ter	p.G309*	ENST00000257430	NM_000038.5	309	Gga/Tga	9/16	1	2	FACETS	0.833	0.663	1	0.833	0.663	1	CLONAL	1	TRUE	1	0.18	2		233	360	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	144	151	0				ENST00000310581	NM_198253.2	-/1132			0.416847441152411	5	FACETS	1	0.969	1	0.729	0.674	0.785	INDETERMINATE	2	FALSE	2	0.835395372932425	5		151	355	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681030	37681030	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	277	372	0	ENST00000447079.4:c.3199C>T	p.Arg1067Ter	p.R1067*	ENST00000447079	NM_015083.1	1067	Cga/Tga	12/14	0.480119573148082	5	FACETS	1	0.961	1	0.681	0.643	0.72	INDETERMINATE	2	FALSE	2	0.835395372932425	5		372	731	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0046234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	301	456	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.416847441152411	5	FACETS	0.89	0.847	0.934	0.89	0.847	0.934	INDETERMINATE	3	FALSE	2	0.835395372932425	5		456	608	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0046234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	967	628	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.806541839024157	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	4	FALSE	0	0.835395372932425	4		628	1061	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118365476	118365476	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0046234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	289	160	0	ENST00000534358.1:c.5357C>G	p.Ser1786Ter	p.S1786*	ENST00000534358	NM_005933.3	1786	tCa/tGa	18/36	0.835395372932425	3	FACETS	0.988	0.962	1	0.988	0.962	1	CLONAL	3	FALSE	0	0.835395372932425	3		160	331	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039427	49039427	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	408	414	0	ENST00000267163.4:c.2412del	p.Tyr805IlefsTer5	p.Y805Ifs*5	ENST00000267163	NM_000321.2	804	atC/at	23/27	0.823504471859911	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	FALSE	0	0.835395372932425	2		414	480	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281987	49281987	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	425	391	0	ENST00000282018.3:c.1034G>C	p.Arg345Thr	p.R345T	ENST00000282018	NM_020377.2	345	aGa/aCa	1/1	0.823504471859911	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	FALSE	0	0.835395372932425	2		391	506	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822208	72822208	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	521	619	0	ENST00000268489.5:c.9967A>C	p.Ile3323Leu	p.I3323L	ENST00000268489	NM_006885.3	3323	Atc/Ctc	10/10	0.528152868790265	6	FACETS	1	0.978	1	1	0.978	1	CLONAL	3	FALSE	3	0.835395372932425	6		619	1085	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794653	42794653	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1349144815	NA	P-0046234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	407	742	0	ENST00000575354.2:c.1733C>T	p.Ala578Val	p.A578V	ENST00000575354	NM_015125.3	578	gCt/gTt	10/20	0.379023965364733	5	FACETS	0.971	0.932	1			1	INDETERMINATE	3	FALSE	NA	0.835395372932425	5		742	754	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741724	145741724	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1515	127	766	0	ENST00000428558.2:c.779A>G	p.Glu260Gly	p.E260G	ENST00000428558	NM_004260.3	260	gAg/gGg	5/22	0.835395372932425	6	FACETS	0.495	0.446	0.546	0.124	0.111	0.137	SUBCLONAL	1	FALSE	2	0.835395372932425	6		766	1642	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183797	10183797	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs5030807	NA	P-0046235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	132	658	0	ENST00000256474.2:c.266T>A	p.Leu89His	p.L89H	ENST00000256474	NM_000551.3	89	cTc/cAc	1/3	0.298722384467596	1	FACETS	0.747	0.678	0.82	0.747	0.678	0.82	SUBCLONAL	1	FALSE	0	0.356250407247663	1		658	815	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38631984	38631984	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	67	453	3	ENST00000299084.4:c.470T>C	p.Phe157Ser	p.F157S	ENST00000299084	NM_152594.2	157	tTt/tCt	5/7	0.187846109364487	1	FACETS	0.47	0.408	0.537	0.47	0.408	0.537	INDETERMINATE	1	FALSE	0	0.356250407247663	1		456	658	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839745	42839751	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGCTT	CCAGCTT	-	novel	NA	P-0046235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	146	529	0	ENST00000398585.3:c.1488_1494del	p.Ser497ValfsTer16	p.S497Vfs*16	ENST00000398585	NM_001135099.1	496	acAAGCTGG/ac	13/14	1	2	FACETS	0.912	0.832	0.995	0.912	0.832	0.995	CLONAL	1	FALSE	1	0.356250407247663	2		529	899	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164929	47164930	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0046235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	36	211	0	ENST00000409792.3:c.1196_1197del	p.Glu399AlafsTer9	p.E399Afs*9	ENST00000409792	NM_014159.6	399	gAG/g	3/21	0.298722384467596	1	FACETS	0.615	0.508	0.734	0.615	0.508	0.734	SUBCLONAL	1	FALSE	0	0.356250407247663	1		211	270	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398628	116398628	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	37	321	0	ENST00000397752.3:c.2218G>T	p.Glu740Ter	p.E740*	ENST00000397752	NM_000245.2	740	Gaa/Taa	9/21	0.167461888232487	3	FACETS	0.537	0.442	0.642	0.268	0.221	0.321	INDETERMINATE	1	FALSE	1	0.356250407247663	3		321	456	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151174422	151174422	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	89	254	0	ENST00000262187.5:c.272A>C	p.Lys91Thr	p.K91T	ENST00000262187	NM_005614.3	91	aAa/aCa	4/8	0.167461888232487	3	FACETS	1	0.968	1	0.621	0.553	0.693	INDETERMINATE	1	FALSE	1	0.356250407247663	3		254	474	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	522	528	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.512264652442867	5	FACETS	0.939	0.904	0.973			1	CLONAL	3	TRUE	NA	0.764733380394338	5		528	1041	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	124	284	0				ENST00000310581	NM_198253.2	-/1132			0.154244909605258	3	FACETS	1	0.985	1	0.679	0.623	0.737	INDETERMINATE	1	TRUE	1	0.764733380394338	3		284	330	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1326	334	939	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	0.764733380394338	6	FACETS	1	0.993	1	0.333	0.313	0.353	CLONAL	1	TRUE	2	0.764733380394338	6		939	1660	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641144	117641144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866970127	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	257	526	0	ENST00000368508.3:c.5827G>A	p.Glu1943Lys	p.E1943K	ENST00000368508	NM_002944.2	1943	Gaa/Aaa	36/43	0.764733380394338	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.764733380394338	1		526	354	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442819	99442819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1365982598	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	321	472	0	ENST00000268035.6:c.1216C>T	p.Arg406Cys	p.R406C	ENST00000268035	NM_000875.3	406	Cgc/Tgc	5/21	0.493691259525145	4	FACETS	0.946	0.898	0.995	0.946	0.898	0.995	CLONAL	2	TRUE	2	0.764733380394338	4		472	783	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971149	21971149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786202575	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	292	402	0	ENST00000304494.5:c.209C>T	p.Pro70Leu	p.P70L	ENST00000304494	NM_000077.4	70	cCc/cTc	2/3	0.764733380394338	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.764733380394338	1		402	364	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518175	8518175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1354824749	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	143	555	0	ENST00000356435.5:c.1216G>A	p.Glu406Lys	p.E406K	ENST00000356435		406	Gaa/Aaa	10/35	0.764733380394338	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.764733380394338	1		555	217	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271638	15271639	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	402	867	1	ENST00000263388.2:c.6800_6801delinsTT	p.Ser2267Phe	p.S2267F	ENST00000263388	NM_000435.2	2267	tCC/tTT	33/33	0.42401490491375	4	FACETS	1	0.961	1	1	0.961	1	INDETERMINATE	2	TRUE	2	0.764733380394338	4		868	922	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857368	9857368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	139	637	0	ENST00000330684.3:c.4033C>T	p.Pro1345Ser	p.P1345S	ENST00000330684	NM_001134407.1	1345	Ccc/Tcc	13/13	0.655553455548513	1	FACETS	0.864	0.804	0.923	0.864	0.804	0.923	CLONAL	1	TRUE	0	0.764733380394338	1		637	260	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528051	157528051	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554237658	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	275	423	0	ENST00000346085.5:c.5776C>T	p.Arg1926Ter	p.R1926*	ENST00000346085	NM_020732.3	1926	Cga/Tga	20/20	0.695266104889123	2	FACETS	0.904	0.867	0.939	0.904	0.867	0.939	CLONAL	2	TRUE	0	0.764733380394338	2		423	398	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002653	37002653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	105	529	0	ENST00000358127.4:c.596G>A	p.Arg199Lys	p.R199K	ENST00000358127	NM_001280556.1	199	aGa/aAa	5/10	0.764733380394338	1	FACETS	0.597	0.543	0.653	0.597	0.543	0.653	SUBCLONAL	1	TRUE	0	0.764733380394338	1		529	284	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069613	69069613	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	120	539	1	ENST00000288368.4:c.4288C>T	p.Gln1430Ter	p.Q1430*	ENST00000288368	NM_024870.2	1430	Caa/Taa	35/40	0.154244909605258	3	FACETS	1	0.978	1	0.614	0.561	0.669	INDETERMINATE	1	TRUE	1	0.764733380394338	3		540	353	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088709	27088709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373690941	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	204	600	0	ENST00000324856.7:c.2318C>T	p.Pro773Leu	p.P773L	ENST00000324856	NM_006015.4	773	cCg/cTg	7/20	0.537671211824402	3	FACETS	0.901	0.837	0.966	0.45	0.418	0.483	CLONAL	1	TRUE	1	0.764733380394338	3		600	819	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057098	180057098	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773696166	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	141	624	1	ENST00000261937.6:c.521C>T	p.Ser174Leu	p.S174L	ENST00000261937	NM_182925.4	174	tCg/tTg	5/30	1	2	FACETS	0.889	0.817	0.962	0.889	0.817	0.962	CLONAL	1	TRUE	1	0.764733380394338	2		625	415	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145758	11145758	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1447890611	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	89	660	0	ENST00000358026.2:c.4120C>T	p.Arg1374Cys	p.R1374C	ENST00000358026	NM_001128849.1	1374	Cgc/Tgc	29/36	0.42401490491375	4	FACETS	0.473	0.418	0.531	0.236	0.209	0.266	INDETERMINATE	1	TRUE	2	0.764733380394338	4		660	869	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258491	16258491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	64	490	0	ENST00000375759.3:c.5756C>T	p.Pro1919Leu	p.P1919L	ENST00000375759	NM_015001.2	1919	cCt/cTt	11/15	0.537671211824402	3	FACETS	0.431	0.373	0.493	0.215	0.186	0.247	SUBCLONAL	1	TRUE	1	0.764733380394338	3		490	537	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305347	39305348	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	230	438	0	ENST00000373001.3:c.1077_1078delinsTT	p.Arg360Ter	p.R360*	ENST00000373001	NM_022157.3	359	ttCCga/ttTTga	7/7	0.537671211824402	3	FACETS	0.892	0.842	0.942	0.892	0.842	0.942	CLONAL	2	TRUE	1	0.764733380394338	3		438	466	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430776	78430776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1434698050	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	244	432	0	ENST00000370768.2:c.613G>A	p.Gly205Arg	p.G205R	ENST00000370768	NM_003902.3	205	Gga/Aga	8/20	NA	2	FACETS	0.919	0.881	0.957			1	INDETERMINATE	2	TRUE	NA	0.764733380394338	2		432	347	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615027	43615027	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	89	631	1	ENST00000355710.3:c.2441G>A	p.Gly814Asp	p.G814D	ENST00000355710	NM_020975.4	814	gGc/gAc	14/20	0.395598915120931	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.764733380394338	0		632	264	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332450	70332450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568924164	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	25	522	0	ENST00000373644.4:c.355C>T	p.Pro119Ser	p.P119S	ENST00000373644	NM_030625.2	119	Cca/Tca	2/12	1	2	FACETS	0.131	0.103	0.164	0.131	0.103	0.164	SUBCLONAL	1	TRUE	1	0.764733380394338	2		522	499	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263961	104263961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	14	217	0	ENST00000369902.3:c.52C>T	p.Pro18Ser	p.P18S	ENST00000369902	NM_016169.3	18	Cct/Tct	1/12	1	2	FACETS	0.215	0.156	0.287	0.215	0.156	0.287	SUBCLONAL	1	TRUE	1	0.764733380394338	2		217	170	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912830	100912830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	28	282	0	ENST00000325455.5:c.2492C>T	p.Pro831Leu	p.P831L	ENST00000325455	NM_001202474.3	831	cCt/cTt	7/8	NA	2	FACETS	0.238	0.19	0.292			1	INDETERMINATE	1	TRUE	NA	0.764733380394338	2		282	308	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120714	115120714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	207	660	0	ENST00000257566.3:c.292G>A	p.Glu98Lys	p.E98K	ENST00000257566	NM_016569.3	98	Gag/Aag	1/8	0.167911459085887	3	FACETS	0.781	0.733	0.83	0.521	0.488	0.554	INDETERMINATE	2	TRUE	0	0.764733380394338	3		660	479	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891725	28891725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	29	463	1	ENST00000282397.4:c.3296C>T	p.Pro1099Leu	p.P1099L	ENST00000282397	NM_002019.4	1099	cCa/cTa	25/30	0.154244909605258	3	FACETS	0.223	0.178	0.273	0.111	0.089	0.137	INDETERMINATE	1	TRUE	1	0.764733380394338	3		464	471	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119810	17119810	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	29	580	0	ENST00000285071.4:c.1184T>C	p.Leu395Pro	p.L395P	ENST00000285071	NM_144997.5	395	cTt/cCt	11/14	0.682489998445002	2	FACETS	0.191	0.153	0.234	0.095	0.076	0.117	SUBCLONAL	1	TRUE	0	0.764733380394338	2		580	398	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627943	37627943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	304	465	0	ENST00000447079.4:c.1858C>T	p.Pro620Ser	p.P620S	ENST00000447079	NM_015083.1	620	Cca/Tca	2/14	0.530507821721704	4	FACETS	0.924	0.876	0.973	0.924	0.876	0.973	CLONAL	2	TRUE	2	0.764733380394338	4		465	759	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223526	36223526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	84	849	0	ENST00000222270.7:c.6076G>A	p.Glu2026Lys	p.E2026K	ENST00000222270	NM_014727.1	2026	Gag/Aag	28/37	0.42401490491375	4	FACETS	0.437	0.385	0.493	0.219	0.192	0.247	INDETERMINATE	1	TRUE	2	0.764733380394338	4		849	887	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731547	47731547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	45	21	0	ENST00000449228.1:c.245C>T	p.Pro82Leu	p.P82L	ENST00000449228	NM_001127240.2	82	cCc/cTc	2/4	0.42401490491375	4	FACETS	0.911	0.807	1	1	0.968	1	INDETERMINATE	3	TRUE	2	0.764733380394338	4		21	76	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576863	212576863	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	135	320	0	ENST00000342788.4:c.1036C>T	p.Gln346Ter	p.Q346*	ENST00000342788	NM_005235.2	346	Cag/Tag	9/28	NA	2	FACETS	1	0.956	1			1	INDETERMINATE	1	TRUE	NA	0.764733380394338	2		320	335	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281779	46281780	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	88	553	0	ENST00000371998.3:c.4226_4227delinsTT	p.Pro1409Leu	p.P1409L	ENST00000371998		1409	cCC/cTT	22/23	0.764733380394338	3	FACETS	0.71	0.632	0.793	0.355	0.316	0.397	SUBCLONAL	1	TRUE	1	0.764733380394338	3		553	448	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651527	52651527	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	114	380	0	ENST00000394830.3:c.1569G>A	p.Met523Ile	p.M523I	ENST00000394830	NM_018313.4	523	atG/atA	15/30	0.493691259525145	4	FACETS	0.861	0.777	0.949	0.431	0.388	0.475	CLONAL	1	TRUE	2	0.764733380394338	4		380	611	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670630	134670630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	28	641	0	ENST00000398015.3:c.541G>A	p.Gly181Arg	p.G181R	ENST00000398015	NM_004441.4	181	Gga/Aga	3/16	NA	2	FACETS	0.136	0.108	0.168			1	INDETERMINATE	1	TRUE	NA	0.764733380394338	2		641	539	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683483	182683483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	213	288	0	ENST00000292782.4:c.62C>T	p.Ser21Phe	p.S21F	ENST00000292782	NM_020640.2	21	tCt/tTt	2/7	0.415016192552772	4	FACETS	0.803	0.751	0.856	0.803	0.751	0.856	INDETERMINATE	2	TRUE	2	0.764733380394338	4		288	612	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806126	1806126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	333	681	0	ENST00000260795.2:c.1145G>A	p.Gly382Asp	p.G382D	ENST00000260795		382	gGc/gAc	8/17	0.322918982505329	4	FACETS	0.929	0.883	0.976	0.929	0.883	0.976	INDETERMINATE	2	TRUE	2	0.764733380394338	4		681	827	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293482	1293482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	207	712	0	ENST00000310581.5:c.1519G>A	p.Glu507Lys	p.E507K	ENST00000310581	NM_198253.2	507	Gag/Aag	2/16	0.154244909605258	3	FACETS	1	0.991	1	0.703	0.658	0.749	INDETERMINATE	1	TRUE	1	0.764733380394338	3		712	532	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519492	176519492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	336	701	0	ENST00000292408.4:c.898C>T	p.Pro300Ser	p.P300S	ENST00000292408	NM_213647.1	300	Ccc/Tcc	7/18	0.409574970237045	4	FACETS	0.986	0.938	1			1	INDETERMINATE	2	TRUE	NA	0.764733380394338	4		701	786	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056640	26056640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1440238210	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	81	148	0	ENST00000343677.2:c.17C>T	p.Pro6Leu	p.P6L	ENST00000343677	NM_005319.3	6	cCt/cTt	1/1	0.764733380394338	8	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.764733380394338	8		148	466	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138761	37138761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	221	506	0	ENST00000373509.5:c.194C>T	p.Ala65Val	p.A65V	ENST00000373509	NM_002648.3	65	gCc/gTc	3/6	0.764733380394338	6	FACETS	0.795	0.74	0.851	0.397	0.37	0.426	SUBCLONAL	2	TRUE	2	0.764733380394338	6		506	920	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455143	50455143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	23	249	0	ENST00000331340.3:c.690G>A	p.Met230Ile	p.M230I	ENST00000331340	NM_006060.4	230	atG/atA	6/8	1	2	FACETS	0.208	0.162	0.261	0.208	0.162	0.261	SUBCLONAL	1	TRUE	1	0.764733380394338	2		249	289	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031702	69031702	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	138	398	0	ENST00000288368.4:c.3457G>A	p.Asp1153Asn	p.D1153N	ENST00000288368	NM_024870.2	1153	Gat/Aat	28/40	0.154244909605258	3	FACETS	1	0.988	1	0.715	0.659	0.771	INDETERMINATE	1	TRUE	1	0.764733380394338	3		398	349	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93607852	93607852	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	126	324	1	ENST00000375746.1:c.554G>A	p.Gly185Glu	p.G185E	ENST00000375746	NM_001174167.1	185	gGa/gAa	3/14	0.764733380394338	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.764733380394338	1		325	195	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760126	133760126	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046236-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	76	632	0	ENST00000318560.5:c.2449C>T	p.Pro817Ser	p.P817S	ENST00000318560	NM_005157.4	817	Ccc/Tcc	11/11	0.682489998445002	2	FACETS	0.456	0.401	0.514	0.228	0.2	0.257	SUBCLONAL	1	TRUE	0	0.764733380394338	2		632	436	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	179	151	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.969	0.904	1	0.969	0.904	1	CLONAL	1	TRUE	1	0.867103437084472	2		151	426	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0046237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	10707	447	1	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.867103437084472	32	FACETS	0.989	0.986	0.992	0.989	0.986	0.992	CLONAL	31	TRUE	1	0.867103437084472	32		448	11281	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226662	2226662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046237-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	316	677	1	ENST00000398665.3:c.4142G>A	p.Gly1381Asp	p.G1381D	ENST00000398665	NM_032482.2	1381	gGc/gAc	27/28	0.867103437084472	3	FACETS	1	0.972	1	0.522	0.493	0.551	CLONAL	1	TRUE	1	0.867103437084472	3		678	1001	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0046238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	124	613	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.781	0.706	0.861	1	0.985	1	SUBCLONAL	2	TRUE	1	0.16	2		613	992	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604789	48604789	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	45	351	0	ENST00000342988.3:c.1611C>G	p.Asp537Glu	p.D537E	ENST00000342988	NM_005359.5	537	gaC/gaG	12/12	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.16	2		351	537	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0046238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	44	356	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.876	0.733	1	0.876	0.733	1	CLONAL	1	TRUE	1	0.16	2		356	628	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26974623	26974623	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	32	411	0	ENST00000381527.3:c.967C>T	p.Arg323Ter	p.R323*	ENST00000381527	NM_001260.1	323	Cga/Tga	10/13	1	2	FACETS	0.63	0.51	0.766	0.63	0.51	0.766	SUBCLONAL	1	TRUE	1	0.16	2		411	635	SUCCESS
APC	324	MSKCC	GRCh37	5	112175725	112175748	+	frameshift_variant	Frame_Shift_Del	DEL	GGTCCAGGTTCTTCCAGATGCTGA	GGTCCAGGTTCTTCCAGATGCTGA	CATT	novel	NA	P-0046238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	17	309	0	ENST00000257430.4:c.4434_4457delinsCATT	p.Arg1478SerfsTer29	p.R1478Sfs*29	ENST00000257430	NM_000038.5	1478	agGGTCCAGGTTCTTCCAGATGCTGAt/agCATTt	16/16	1	2	FACETS	0.625	0.466	0.815	0.625	0.466	0.815	SUBCLONAL	1	TRUE	1	0.16	2		309	340	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0046240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	83	301	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.198751979438768	4	FACETS	1	0.967	1	0.826	0.735	0.921	CLONAL	2	TRUE	1	0.252839594384952	4		301	332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0046240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	167	614	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.252839594384952	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.252839594384952	1		614	814	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971196	21971198	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	novel	NA	P-0046240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	95	358	0	ENST00000304494.5:c.160_162del	p.Met54del	p.M54del	ENST00000304494	NM_000077.4	54	ATG/-	2/3	0.252839594384952	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.252839594384952	1		358	442	SUCCESS
AXL	558	MSKCC	GRCh37	19	41725365	41725365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754135882	NA	P-0046241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1447	127	266	0	ENST00000301178.4:c.68C>T	p.Ala23Val	p.A23V	ENST00000301178	NM_021913.4	23	gCg/gTg	1/20	0.245522164477026	5	FACETS	0.899	0.811	0.993	0.3	0.27	0.331	CLONAL	1	TRUE	2	0.245522164477026	5		266	1574	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863677	68863677	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	175	188	0	ENST00000261769.5:c.2416G>T	p.Glu806Ter	p.E806*	ENST00000261769	NM_004360.3	806	Gaa/Taa	15/16	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	2	TRUE	NA	0.245522164477026	2		188	664	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574055	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTGCAGCAACAGAGGAGGGGGA	CTGCAGCAACAGAGGAGGGGGA	-	novel	NA	P-0046241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	148	270	0	ENST00000269305.4:c.994-22_994-1del		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.23075850647276	2	FACETS	1	0.985	1	0.683	0.623	0.745	CLONAL	1	TRUE	0	0.245522164477026	2		270	883	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0046242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	178	376	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.410584254526216	1	FACETS	0.969	0.896	1	0.969	0.896	1	CLONAL	1	TRUE	0	0.410584254526216	1		376	711	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0046242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	75	316	1	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	1	2	FACETS	0.796	0.7	0.899	0.796	0.7	0.899	SUBCLONAL	1	TRUE	1	0.410584254526216	2		317	459	SUCCESS
APC	324	MSKCC	GRCh37	5	112175788	112175788	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	78	275	1	ENST00000257430.4:c.4497del	p.Ser1501LeufsTer6	p.S1501Lfs*6	ENST00000257430	NM_000038.5	1499	ggA/gg	16/16	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.410584254526216	2		276	363	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245380	153245380	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	267	409	5	ENST00000281708.4:c.1811A>C	p.Lys604Thr	p.K604T	ENST00000281708	NM_033632.3	604	aAa/aCa	11/12	0.406258468771457	2	FACETS	0.973	0.919	1	0.973	0.919	1	CLONAL	2	TRUE	0	0.410584254526216	2		414	668	SUCCESS
APC	324	MSKCC	GRCh37	5	112173912	112173912	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	86	300	1	ENST00000257430.4:c.2621C>A	p.Ser874Ter	p.S874*	ENST00000257430	NM_000038.5	874	tCa/tAa	16/16	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.410584254526216	2		301	419	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828694	72828694	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs376175083	NA	P-0046242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	66	664	1	ENST00000268489.5:c.7887C>A	p.Asn2629Lys	p.N2629K	ENST00000268489	NM_006885.3	2629	aaC/aaA	9/10	1	2	FACETS	0.428	0.37	0.49	0.428	0.37	0.49	SUBCLONAL	1	TRUE	1	0.410584254526216	2		665	752	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390150	89390150	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	45	315	0	ENST00000336596.2:c.899G>T	p.Gly300Val	p.G300V	ENST00000336596	NM_005233.5	300	gGt/gTt	4/17	1	2	FACETS	0.43	0.361	0.506	0.43	0.361	0.506	SUBCLONAL	1	TRUE	1	0.410584254526216	2		315	510	SUCCESS
APC	324	MSKCC	GRCh37	5	112102108	112102108	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0046242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	52	122	1	ENST00000257430.4:c.220+1G>T		p.X74_splice	ENST00000257430	NM_000038.5	74			1	2	FACETS	0.928	0.796	1	0.928	0.796	1	CLONAL	1	TRUE	1	0.410584254526216	2		123	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567556006	NA	P-0046243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	584	824	0	ENST00000269305.4:c.298del	p.Gln100ArgfsTer23	p.Q100Rfs*23	ENST00000269305	NM_001126112.2	100	Cag/ag	4/11	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.700118523638978	2		824	817	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058004	27058004	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	405	601	0	ENST00000324856.7:c.1712C>A	p.Ser571Ter	p.S571*	ENST00000324856	NM_006015.4	571	tCg/tAg	3/20	0.698646504227826	4	FACETS	0.973	0.928	1	0.973	0.928	1	CLONAL	2	TRUE	2	0.700118523638978	4		601	1011	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612790	228612790	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	522	796	0	ENST00000366696.1:c.237T>A	p.Phe79Leu	p.F79L	ENST00000366696	NM_003493.2	79	ttT/ttA	1/1	0.698646504227826	5	FACETS	0.972	0.931	1	0.648	0.62	0.676	CLONAL	2	TRUE	2	0.700118523638978	5		796	1573	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437988	49437988	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	259	690	1	ENST00000301067.7:c.5183A>G	p.Asp1728Gly	p.D1728G	ENST00000301067	NM_003482.3	1728	gAc/gGc	21/54	0.698646504227826	3	FACETS	1	0.966	1			1	CLONAL	1	TRUE	NA	0.700118523638978	3		691	956	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991861	72991861	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	231	626	1	ENST00000268489.5:c.2184C>G	p.Cys728Trp	p.C728W	ENST00000268489	NM_006885.3	728	tgC/tgG	2/10	0.696098466711726	3	FACETS	1	0.944	1	0.506	0.473	0.541	CLONAL	1	TRUE	1	0.700118523638978	3		627	880	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78599536	78599536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	184	562	0	ENST00000306801.3:c.208G>A	p.Val70Met	p.V70M	ENST00000306801	NM_020761.2	70	Gtg/Atg	2/34	0.700118523638978	6	FACETS	0.954	0.879	1	0.239	0.219	0.259	CLONAL	1	TRUE	2	0.700118523638978	6		562	1322	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298723	15298723	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	339	899	0	ENST00000263388.2:c.1575G>C	p.Gln525His	p.Q525H	ENST00000263388	NM_000435.2	525	caG/caC	10/33	0.696098466711726	3	FACETS	1	0.979	1	0.533	0.504	0.563	CLONAL	1	TRUE	1	0.700118523638978	3		899	1226	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449717	187449717	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	174	318	0	ENST00000232014.4:c.163G>C	p.Gly55Arg	p.G55R	ENST00000232014	NM_001130845.1	55	Ggc/Cgc	4/10	0.589285297938311	4	FACETS	0.895	0.832	0.96	0.895	0.832	0.96	CLONAL	2	TRUE	2	0.700118523638978	4		318	472	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586386	189586386	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	123	323	0	ENST00000264731.3:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000264731	NM_003722.4	337	cGa/cTa	8/14	0.589285297938311	4	FACETS	1	0.961	1	0.554	0.503	0.607	CLONAL	1	TRUE	2	0.700118523638978	4		323	539	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280034	66280034	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	51	221	0	ENST00000273854.3:c.1655G>A	p.Ser552Asn	p.S552N	ENST00000273854	NM_004439.5	552	aGt/aAt	7/18	0.696098466711726	3	FACETS	0.906	0.78	1	0.453	0.39	0.521	CLONAL	1	TRUE	1	0.700118523638978	3		221	217	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609752	117609752	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs773542381	NA	P-0046243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	165	412	0	ENST00000368508.3:c.6947G>T	p.Cys2316Phe	p.C2316F	ENST00000368508	NM_002944.2	2316	tGc/tTc	43/43	0.698646504227826	3	FACETS	1	0.969	1	0.547	0.504	0.59	CLONAL	1	TRUE	1	0.700118523638978	3		412	582	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540131	23540131	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	88	261	0	ENST00000380871.4:c.272del	p.Ala91GlufsTer46	p.A91Efs*46	ENST00000380871	NM_006167.3	91	gCa/ga	1/2	0.698646504227826	3	FACETS	1	0.98	1	0.467	0.421	0.515	CLONAL	1	TRUE	0	0.700118523638978	3		261	242	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426451	47426451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1229309673	NA	P-0046243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	265	382	0	ENST00000377045.4:c.794C>T	p.Ser265Leu	p.S265L	ENST00000377045	NM_001654.4	265	tCg/tTg	9/16	0.622648336617595	2	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.700118523638978	2		382	647	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443617	49443618	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	A	novel	NA	P-0046243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	240	680	2	ENST00000301067.7:c.3753_3754delinsT	p.Arg1252GlufsTer78	p.R1252Efs*78	ENST00000301067	NM_003482.3	1251	gcCCga/gcTga	11/54	0.698646504227826	3	FACETS	1	0.937	1			1	CLONAL	1	TRUE	NA	0.700118523638978	3		682	924	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0046244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	84	236	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.145299431089847	3	FACETS	0.789	0.702	0.88	0.526	0.468	0.587	INDETERMINATE	2	TRUE	0	0.349338058668567	3		236	358	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0046244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	88	347	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.346511947045354	3	FACETS	0.967	0.866	1	0.967	0.866	1	CLONAL	2	TRUE	1	0.349338058668567	3		347	306	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745588	162745588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754868982	NA	P-0046244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	43	558	0	ENST00000367921.3:c.2003G>A	p.Arg668His	p.R668H	ENST00000367921	NM_006182.2	668	cGc/cAc	15/18	1	2	FACETS	0.476	0.398	0.563	0.476	0.398	0.563	SUBCLONAL	1	TRUE	1	0.349338058668567	2		558	517	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478103	99478103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	92	582	0	ENST00000268035.6:c.3007C>T	p.Arg1003Trp	p.R1003W	ENST00000268035	NM_000875.3	1003	Cgg/Tgg	16/21	1	2	FACETS	0.863	0.768	0.965	0.863	0.768	0.965	CLONAL	1	TRUE	1	0.349338058668567	2		582	610	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101054	26101054	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	191	1055	0	ENST00000435504.4:c.38G>T	p.Trp13Leu	p.W13L	ENST00000435504		13	tGg/tTg	1/13	0.190032362241157	2	FACETS	1	0.975	1	0.561	0.519	0.606	INDETERMINATE	1	TRUE	0	0.349338058668567	2		1055	974	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265508	152265508	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	172	681	0	ENST00000206249.3:c.961G>C	p.Asp321His	p.D321H	ENST00000206249	NM_000125.3	321	Gat/Cat	4/8	0.190032362241157	2	FACETS	0.803	0.743	0.866	0.803	0.743	0.866	INDETERMINATE	2	TRUE	0	0.349338058668567	2		681	613	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411185	63411185	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	163	486	0	ENST00000330258.3:c.1982del	p.Pro661HisfsTer3	p.P661Hfs*3	ENST00000330258	NM_152424.3	661	cCa/ca	2/2	0.310865171177544	2	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.349338058668567	2		486	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0046246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	736	823	0	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.58650114518394	3	FACETS	0.952	0.928	0.976	0.952	0.928	0.976	CLONAL	3	TRUE	0	0.625272832842306	3		823	1082	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464957	120464957	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	177	447	0	ENST00000256646.2:c.5115G>T	p.Lys1705Asn	p.K1705N	ENST00000256646	NM_024408.3	1705	aaG/aaT	28/34	0.524747802123174	4	FACETS	1	0.97	1	0.367	0.338	0.397	CLONAL	1	TRUE	1	0.625272832842306	4		447	836	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115843	8115844	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0046247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	237	557	0	ENST00000346208.3:c.1191dup	p.Arg398GlnfsTer109	p.R398Qfs*109	ENST00000346208		397	tcc/tCcc	6/6	0.214279457766277	3	FACETS	1	0.99	1	0.639	0.599	0.679	INDETERMINATE	1	TRUE	1	0.74252439258665	3		557	685	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	77	69	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.170672389757469	2	FACETS	0.933	0.823	1	0.933	0.823	1	CLONAL	2	TRUE	0	0.193666449465155	2		69	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	143	770	0	ENST00000269305.4:c.313G>T	p.Gly105Cys	p.G105C	ENST00000269305	NM_001126112.2	105	Ggc/Tgc	4/11	0.193666449465155	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.193666449465155	1		770	934	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229189	36229189	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	197	636	0	ENST00000222270.7:c.7879G>A	p.Gly2627Arg	p.G2627R	ENST00000222270	NM_014727.1	2627	Ggg/Agg	37/37	0.193666449465155	2	FACETS	0.891	0.827	0.957	1	0.988	1	CLONAL	3	TRUE	0	0.193666449465155	2		636	761	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099458	27099459	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	173	410	0	ENST00000324856.7:c.3697dup	p.Tyr1233LeufsTer11	p.Y1233Lfs*11	ENST00000324856	NM_006015.4	1232	cct/ccTt	14/20	0.276155682420373	3	FACETS	0.888	0.826	0.951	0.888	0.826	0.951	INDETERMINATE	2	TRUE	1	0.577035634463172	3		410	435	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672337	86672338	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0046249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	162	301	0	ENST00000274376.6:c.2140_2141del	p.Met714GlyfsTer11	p.M714Gfs*11	ENST00000274376	NM_002890.2	713	tcTAtg/tctg	16/25	0.19103563345108	3	FACETS	0.907	0.842	0.972	0.604	0.561	0.648	INDETERMINATE	2	TRUE	0	0.577035634463172	3		301	399	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674290	86674290	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1396225514	NA	P-0046249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	56	347	0	ENST00000274376.6:c.2422C>T	p.Gln808Ter	p.Q808*	ENST00000274376	NM_002890.2	808	Cag/Tag	18/25	0.19103563345108	3	FACETS	0.593	0.509	0.684	0.198	0.169	0.228	INDETERMINATE	1	TRUE	0	0.577035634463172	3		347	422	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593613	55593613	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913521	NA	P-0046251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	231	685	0	ENST00000288135.5:c.1679T>G	p.Val560Gly	p.V560G	ENST00000288135	NM_000222.2	560	gTt/gGt	11/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.894894670064914	2		685	502	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0046252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	38	343	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.418378204575493	0	FACETS	0.618	0.518	0.726			1	SUBCLONAL	1	FALSE	0	0.418378204575493	0		343	171	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0046252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	48	504	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.418378204575493	0	FACETS	0.607	0.518	0.701			1	SUBCLONAL	1	FALSE	0	0.418378204575493	0		504	220	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119884	70119884	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	105	664	0	ENST00000245479.2:c.886C>T	p.Gln296Ter	p.Q296*	ENST00000245479	NM_000346.3	296	Cag/Tag	3/3	0.418378204575493	0	FACETS	0.598	0.538	0.661			1	SUBCLONAL	1	FALSE	0	0.418378204575493	0		664	488	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589622	67589624	+	inframe_deletion	In_Frame_Del	DEL	AAT	AAT	-	novel	NA	P-0046252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	22	218	0	ENST00000274335.5:c.1386_1388del	p.Glu462_Tyr463delinsAsp	p.E462_Y463delinsD	ENST00000274335		462	gAATat/gat	10/15	0.418378204575493	0	FACETS	0.606	0.478	0.747			1	SUBCLONAL	1	FALSE	0	0.418378204575493	0		218	101	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629108	86629108	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853218	NA	P-0046252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	22	273	0	ENST00000274376.6:c.853C>T	p.Arg285Ter	p.R285*	ENST00000274376	NM_002890.2	285	Cga/Tga	4/25	0.418378204575493	0	FACETS	0.506	0.397	0.627			1	SUBCLONAL	1	FALSE	0	0.418378204575493	0		273	121	SUCCESS
APC	324	MSKCC	GRCh37	5	112175640	112175640	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	57	321	0	ENST00000257430.4:c.4349del	p.Arg1450GlnfsTer23	p.R1450Qfs*23	ENST00000257430	NM_000038.5	1450	cGa/ca	16/16	0.418378204575493	0	FACETS	0.631	0.547	0.721			1	SUBCLONAL	1	FALSE	0	0.418378204575493	0		321	251	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593557	48593557	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	33	167	0	ENST00000342988.3:c.1308G>C	p.Lys436Asn	p.K436N	ENST00000342988	NM_005359.5	436	aaG/aaC	10/12	0.418378204575493	1	FACETS	0.872	0.722	1	0.872	0.722	1	CLONAL	1	FALSE	0	0.418378204575493	1		167	143	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944877	31944877	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	83	440	0	ENST00000340398.3:c.224C>T	p.Ala75Val	p.A75V	ENST00000340398	NM_001013699.2	75	gCg/gTg	1/1	0.418378204575493	0	FACETS	0.58	0.515	0.649			1	SUBCLONAL	1	FALSE	0	0.418378204575493	0		440	398	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117687	70117688	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GTGTT	novel	NA	P-0046252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	134	923	0	ENST00000245479.2:c.157_158insGTTGT	p.Phe53CysfsTer10	p.F53Cfs*10	ENST00000245479	NM_000346.3	52	acg/acGTGTTg	1/3	0.418378204575493	0	FACETS	0.554	0.504	0.606			1	SUBCLONAL	1	FALSE	0	0.418378204575493	0		923	673	SUCCESS
APC	324	MSKCC	GRCh37	5	112162932	112162933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	40	318	0	ENST00000257430.4:c.1537dup	p.Val513GlyfsTer24	p.V513Gfs*24	ENST00000257430	NM_000038.5	512	-/G	12/16	0.418378204575493	0	FACETS	0.598	0.503	0.701			1	SUBCLONAL	1	FALSE	0	0.418378204575493	0		318	186	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0046253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	205	509	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	0.371911294559801	2	FACETS	0.854	0.799	0.91	0.854	0.799	0.91	CLONAL	2	TRUE	0	0.458140507568659	2		509	524	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568555	41568555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555911573	NA	P-0046253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	188	487	0	ENST00000263253.7:c.4505C>T	p.Pro1502Leu	p.P1502L	ENST00000263253	NM_001429.3	1502	cCt/cTt	28/31	0.102266311796043	4	FACETS	0.831	0.77	0.894	0.831	0.77	0.894	INDETERMINATE	2	TRUE	2	0.458140507568659	4		487	720	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845814	151845814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	215	645	0	ENST00000262189.6:c.13198C>T	p.Arg4400Trp	p.R4400W	ENST00000262189	NM_170606.2	4400	Cgg/Tgg	52/59	0.375866906623365	3	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	TRUE	1	0.458140507568659	3		645	574	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493468	56493468	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1234718257	NA	P-0046253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	358	481	0	ENST00000267101.3:c.2876A>C	p.Lys959Thr	p.K959T	ENST00000267101	NM_001982.3	959	aAa/aCa	24/28	0.458140507568659	5	FACETS	0.897	0.856	0.937			1	CLONAL	4	TRUE	NA	0.458140507568659	5		481	735	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0046259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	268	744	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.282646580198491	3	FACETS	1	0.99	1	0.826	0.779	0.874	CLONAL	2	TRUE	0	0.349574288647379	3		745	727	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0046259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	92	302	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.349574288647379	3	FACETS	0.789	0.706	0.876	0.789	0.706	0.876	SUBCLONAL	2	TRUE	1	0.349574288647379	3		302	392	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0046259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	94	222	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	0.349574288647379	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.349574288647379	2		222	252	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	52	233	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	0.282646580198491	3	FACETS	1	0.926	1	0.733	0.637	0.833	CLONAL	2	TRUE	0	0.349574288647379	3		233	159	SUCCESS
CBL	867	MSKCC	GRCh37	11	119168095	119168095	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs757126995	NA	P-0046259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	87	416	0	ENST00000264033.4:c.2155G>A	p.Ala719Thr	p.A719T	ENST00000264033	NM_005188.3	719	Gca/Aca	14/16	0.206772606770704	3	FACETS	0.81	0.723	0.902	0.81	0.723	0.902	INDETERMINATE	2	TRUE	1	0.349574288647379	3		416	361	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998890	11998890	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0046259-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	40	202	0	ENST00000353533.5:c.394-2A>T		p.X132_splice	ENST00000353533	NM_003010.3	132			0.282646580198491	3	FACETS	0.988	0.838	1	0.659	0.559	0.765	CLONAL	2	TRUE	0	0.349574288647379	3		202	136	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937657	32937657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046260-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	39	417	0	ENST00000380152.3:c.8318C>T	p.Ser2773Phe	p.S2773F	ENST00000380152		2773	tCt/tTt	18/27	0.19917829462506	5	FACETS	0.821	0.685	0.97	0.547	0.456	0.647	CLONAL	2	TRUE	2	0.26	5		417	254	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0046261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	364	459	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.403962035754983	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.477890515121345	4		459	1034	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915007	32915007	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0046261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	187	381	0	ENST00000380152.3:c.6515C>G	p.Ser2172Ter	p.S2172*	ENST00000380152		2172	tCa/tGa	11/27	0.453771901078135	2	FACETS	0.862	0.805	0.92	0.862	0.805	0.92	CLONAL	2	TRUE	0	0.477890515121345	2		381	454	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934864	9934864	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	114	450	0	ENST00000330684.3:c.1426G>T	p.Asp476Tyr	p.D476Y	ENST00000330684	NM_001134407.1	476	Gac/Tac	6/13	0.463774274543814	5	FACETS	0.83	0.746	0.919	0.207	0.186	0.23	CLONAL	1	TRUE	1	0.477890515121345	5		450	987	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577495	7577553	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGACCTGGAGTCTTCCAGTGTGATGATGGTGAGGATGGGCCTCCGGTTCATGCCGCCCA	TGACCTGGAGTCTTCCAGTGTGATGATGGTGAGGATGGGCCTCCGGTTCATGCCGCCCA	-	novel	NA	P-0046261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	104	766	0	ENST00000269305.4:c.728_782+4del		p.X243_splice	ENST00000269305	NM_001126112.2	243		7/11	0.477890515121345	1	FACETS	0.746	0.672	0.824	0.746	0.672	0.824	SUBCLONAL	1	TRUE	0	0.477890515121345	1		766	444	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78933877	78933877	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0046261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	159	661	0	ENST00000306801.3:c.3478-1G>A		p.X1160_splice	ENST00000306801	NM_020761.2	1160			0.191626923020999	3	FACETS	1	0.981	1	0.608	0.559	0.659	INDETERMINATE	1	TRUE	1	0.477890515121345	3		661	678	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547031	9547031	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	71	237	0	ENST00000353224.5:c.991G>T	p.Val331Leu	p.V331L	ENST00000353224	NM_177990.2	331	Gtg/Ttg	5/10	0.144349779679936	3	FACETS	1	0.96	1	0.408	0.359	0.459	INDETERMINATE	1	TRUE	0	0.477890515121345	3		237	301	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5055717	5055720	+	frameshift_variant	Frame_Shift_Del	DEL	AAGC	AAGC	-	novel	NA	P-0046261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	68	261	0	ENST00000381652.3:c.991_994del	p.Ala331ThrfsTer11	p.A331Tfs*11	ENST00000381652	NM_004972.3	329	AAGCaa/aa	8/25	0.477890515121345	1	FACETS	0.958	0.846	1	0.958	0.846	1	CLONAL	1	TRUE	0	0.477890515121345	1		261	226	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0046262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	503	747	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.824369880237062	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.824369880237062	1		747	681	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041439	47041439	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	447	351	0	ENST00000377604.3:c.1783C>T	p.Gln595Ter	p.Q595*	ENST00000377604	NM_001204468.1	595	Cag/Tag	16/24	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.824369880237062	1		351	539	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652250	36652251	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGC	novel	NA	P-0046262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	444	783	0	ENST00000244741.5:c.373_376dup	p.Gln126ArgfsTer4	p.Q126Rfs*4	ENST00000244741	NM_000389.4	124	-/GAGC	2/3	0.457552081322572	1	FACETS	0.669	0.642	0.697	0.669	0.642	0.697	INDETERMINATE	1	TRUE	0	0.824369880237062	1		783	946	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433527	49433527	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	797	1049	0	ENST00000301067.7:c.8026G>C	p.Glu2676Gln	p.E2676Q	ENST00000301067	NM_003482.3	2676	Gag/Cag	31/54	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.824369880237062	2		1049	1853	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69203049	69203049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	219	387	0	ENST00000462284.1:c.76C>T	p.Pro26Ser	p.P26S	ENST00000462284	NM_002392.5	26	Cca/Tca	2/11	1	2	FACETS	0.81	0.757	0.864	0.81	0.757	0.864	CLONAL	1	TRUE	1	0.824369880237062	2		387	656	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527680	103527680	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	70	237	0	ENST00000355739.4:c.2988C>G	p.Phe996Leu	p.F996L	ENST00000355739	NM_000123.3	996	ttC/ttG	15/15	1	2	FACETS	0.502	0.441	0.568	0.502	0.441	0.568	SUBCLONAL	1	TRUE	1	0.824369880237062	2		237	338	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708587	43708587	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	119	502	0	ENST00000382044.4:c.4709C>G	p.Ser1570Cys	p.S1570C	ENST00000382044	NM_001141980.1	1570	tCt/tGt	22/28	0.390028899589104	1	FACETS	0.245	0.221	0.27	0.245	0.221	0.27	INDETERMINATE	1	TRUE	0	0.824369880237062	1		502	693	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198272733	198272733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	276	449	0	ENST00000335508.6:c.1228G>A	p.Glu410Lys	p.E410K	ENST00000335508	NM_012433.2	410	Gaa/Aaa	9/25	0.454756944234416	1	FACETS	0.744	0.707	0.781	0.744	0.707	0.781	INDETERMINATE	1	TRUE	0	0.824369880237062	1		449	529	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295219	1295222	+	upstream_gene_variant	5'Flank	DEL	GGGC	GGGC	-	novel	NA	P-0046262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	92	283	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.44	0.392	0.491			1	INDETERMINATE	1	TRUE	NA	0.824369880237062	2		283	507	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120389	94120389	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1207755122	NA	P-0046262-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	27	324	0	ENST00000369303.4:c.662G>T	p.Gly221Val	p.G221V	ENST00000369303	NM_004440.3	221	gGt/gTt	3/17	0.519920735718188	1	FACETS	0.113	0.089	0.139	0.113	0.089	0.139	SUBCLONAL	1	TRUE	0	0.824369880237062	1		324	342	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0046263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	244	437	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	1	2	FACETS	0.935	0.881	0.99	0.935	0.881	0.99	CLONAL	1	TRUE	1	0.881283572897203	2		437	592	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597502	28597502	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	65	392	0	ENST00000241453.7:c.2403T>G	p.Phe801Leu	p.F801L	ENST00000241453	NM_004119.2	801	ttT/ttG	19/24	1	2	FACETS	0.314	0.272	0.359	0.314	0.272	0.359	SUBCLONAL	1	TRUE	1	0.881283572897203	2		392	470	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917764	151917764	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046263-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	113	70	1	ENST00000262189.6:c.3556C>T	p.Gln1186Ter	p.Q1186*	ENST00000262189	NM_170606.2	1186	Cag/Tag	23/59	0.852791983353227	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.881283572897203	3		71	149	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	106	355	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.18201920047467	4	FACETS	1	0.96	1	1	0.96	1	INDETERMINATE	2	TRUE	2	0.547100815754965	4		355	273	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	280	527	2	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.293384511666078	4	FACETS	1	0.988	1	1	0.996	1	INDETERMINATE	4	TRUE	2	0.547100815754965	4		529	372	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	177	356	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.18201920047467	4	FACETS	1	0.984	1	1	0.984	1	INDETERMINATE	2	TRUE	2	0.547100815754965	4		356	420	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	111	418	0	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.91	0.823	1	0.91	0.823	1	CLONAL	1	TRUE	1	0.547100815754965	2		418	446	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	34	308	1	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	0.232755845551061	4	FACETS	0.943	0.791	1	0.943	0.791	1	INDETERMINATE	2	TRUE	2	0.547100815754965	4		309	102	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	131	566	2	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	0.18201920047467	4	FACETS	0.988	0.907	1	0.988	0.907	1	INDETERMINATE	2	TRUE	2	0.547100815754965	4		568	375	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	101	679	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.242383209047512	4	FACETS	0.908	0.813	1	0.454	0.406	0.505	INDETERMINATE	1	TRUE	2	0.547100815754965	4		683	629	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	146	374	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.18201920047467	4	FACETS	1	0.946	1	1	0.946	1	INDETERMINATE	2	TRUE	2	0.547100815754965	4		374	400	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs767894241	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	145	577	0	ENST00000358127.4:c.76dup	p.Val26GlyfsTer49	p.V26Gfs*49	ENST00000358127	NM_001280556.1	26	gtt/gGtt	2/10	0.122600000986784	0	FACETS	0.544	0.501	0.589			1	INDETERMINATE	1	TRUE	0	0.547100815754965	0		577	441	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238941	5238941	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs913402227	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	115	596	1	ENST00000357368.4:c.1838C>T	p.Thr613Met	p.T613M	ENST00000357368	NM_002850.3	613	aCg/aTg	13/38	0.397148271392172	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.547100815754965	1		597	269	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030485	49030485	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs483352690	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	62	498	0	ENST00000267163.4:c.1960G>A	p.Val654Met	p.V654M	ENST00000267163	NM_000321.2	654	Gtg/Atg	19/27	0.232755845551061	4	FACETS	1	0.918	1	1	0.918	1	INDETERMINATE	2	TRUE	2	0.547100815754965	4		498	167	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508533	106508533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773456619	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	70	413	0	ENST00000359195.3:c.527C>T	p.Thr176Met	p.T176M	ENST00000359195	NM_002649.2	176	aCg/aTg	2/11	0.293384511666078	4	FACETS	0.872	0.772	0.977	0.872	0.772	0.977	INDETERMINATE	2	TRUE	2	0.547100815754965	4		413	227	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	209	418	2	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	0.18201920047467	4	FACETS	1	0.985	1	1	0.985	1	INDETERMINATE	2	TRUE	2	0.547100815754965	4		420	506	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245587	41245587	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs80357522	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	202	677	2	ENST00000357654.3:c.1961del	p.Lys654SerfsTer47	p.K654Sfs*47	ENST00000357654	NM_007294.3	654	aAg/ag	10/23	0.242383209047512	4	FACETS	1	0.981	1	1	0.981	1	INDETERMINATE	2	TRUE	2	0.547100815754965	4		679	509	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932085	39932085	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	282	787	0	ENST00000378444.4:c.2514del	p.Lys839SerfsTer17	p.K839Sfs*17	ENST00000378444	NM_001123385.1	838	ccC/cc	4/15	0.309004158428804	4	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.547100815754965	4		787	646	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298606	11298606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199712134	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	187	708	1	ENST00000361445.4:c.1855C>T	p.Arg619Cys	p.R619C	ENST00000361445	NM_004958.3	619	Cgc/Tgc	12/58	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.547100815754965	2		709	521	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057937	27057937	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	286	684	0	ENST00000324856.7:c.1650del	p.Tyr551ThrfsTer68	p.Y551Tfs*68	ENST00000324856	NM_006015.4	549	Ccc/cc	3/20	0.402336392035124	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.547100815754965	4		684	778	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149799	202149799	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	141	596	1	ENST00000358485.4:c.1245del	p.Phe415LeufsTer26	p.F415Lfs*26	ENST00000358485	NM_001080125.1	414	Ttt/tt	8/9	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.547100815754965	2		597	351	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691872	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs79375991	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	174	335	11	ENST00000295754.5:c.383del	p.Lys128SerfsTer35	p.K128Sfs*35	ENST00000295754	NM_003242.5	125	gAa/ga	3/7	0.293384511666078	4	FACETS	1	0.977	1	1	0.993	1	INDETERMINATE	3	TRUE	2	0.547100815754965	4		346	304	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422454	47422454	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	92	750	0	ENST00000377045.4:c.88C>T	p.Arg30Cys	p.R30C	ENST00000377045	NM_001654.4	30	Cgc/Tgc	2/16	0.488196687088298	1	FACETS	0.429	0.382	0.48	0.429	0.382	0.48	SUBCLONAL	1	TRUE	0	0.547100815754965	1		750	569	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346157	89346158	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs878855327	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	99	445	0	ENST00000301030.4:c.6792dup	p.Ala2265ArgfsTer8	p.A2265Rfs*8	ENST00000301030	NM_001256183.1	2264	-/C	9/13	0.448068271284297	4	FACETS	0.819	0.738	0.902			1	CLONAL	2	TRUE	NA	0.547100815754965	4		445	342	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275192	41275192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	155	398	0	ENST00000349496.5:c.1358G>A	p.Arg453Gln	p.R453Q	ENST00000349496	NM_001904.3	453	cGg/cAg	9/15	0.293384511666078	4	FACETS	1	0.98	1	1	0.98	1	INDETERMINATE	2	TRUE	2	0.547100815754965	4		398	376	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432117	121432118	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776825	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	256	872	29	ENST00000257555.6:c.872dup	p.Gly292ArgfsTer25	p.G292Rfs*25	ENST00000257555		288	-/C	4/10	0.18201920047467	4	FACETS	1	0.968	1	1	0.968	1	INDETERMINATE	2	TRUE	2	0.547100815754965	4		901	695	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413710	138413710	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	137	430	5	ENST00000289153.2:c.1810del	p.Arg604GlyfsTer4	p.R604Gfs*4	ENST00000289153	NM_006219.2	604	Cgg/gg	12/22	0.18201920047467	4	FACETS	0.899	0.825	0.975	0.899	0.825	0.975	INDETERMINATE	2	TRUE	2	0.547100815754965	4		435	431	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513298	44513298	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761520409	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	60	716	1	ENST00000291552.4:c.637G>A	p.Gly213Ser	p.G213S	ENST00000291552	NM_006758.2	213	Ggt/Agt	8/8	0.547100815754965	4	FACETS	0.433	0.372	0.5	0.217	0.186	0.25	SUBCLONAL	1	TRUE	2	0.547100815754965	4		717	783	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68862139	68862139	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	244	536	2	ENST00000261769.5:c.2231del	p.Pro744GlnfsTer26	p.P744Qfs*26	ENST00000261769	NM_004360.3	743	Ccc/cc	14/16	0.497227684096704	3	FACETS	0.904	0.851	0.959			1	CLONAL	2	TRUE	NA	0.547100815754965	3		538	628	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62311299	62311299	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs201938707	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	190	392	0	ENST00000360203.5:c.1135C>T	p.Arg379Cys	p.R379C	ENST00000360203	NM_001283009.1	379	Cgt/Tgt	13/35	0.18201920047467	4	FACETS	0.882	0.827	0.938	1	0.99	1	INDETERMINATE	3	TRUE	2	0.547100815754965	4		392	406	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604668	48604668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	148	377	0	ENST00000342988.3:c.1490G>A	p.Arg497His	p.R497H	ENST00000342988	NM_005359.5	497	cGc/cAc	12/12	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.547100815754965	2		377	369	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754574	42754574	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768322408	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	401	822	0	ENST00000222329.4:c.166G>A	p.Val56Ile	p.V56I	ENST00000222329	NM_006494.2	56	Gtc/Atc	2/4	0.232755845551061	4	FACETS	1	0.994	1	1	0.994	1	INDETERMINATE	2	TRUE	2	0.547100815754965	4		822	916	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928640	49928640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375490243	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	416	719	0	ENST00000296474.3:c.3634C>T	p.Arg1212Trp	p.R1212W	ENST00000296474	NM_002447.2	1212	Cgg/Tgg	17/20	0.547100815754965	4	FACETS	0.836	0.8	0.873			1	CLONAL	3	TRUE	NA	0.547100815754965	4		719	938	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968233	134968233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753895808	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	91	706	0	ENST00000398015.3:c.2746G>A	p.Val916Met	p.V916M	ENST00000398015	NM_004441.4	916	Gtg/Atg	15/16	0.547100815754965	1	FACETS	0.863	0.777	0.953	0.863	0.777	0.953	CLONAL	1	TRUE	0	0.547100815754965	1		706	280	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845391	151845391	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	226	664	0	ENST00000262189.6:c.13621C>T	p.Arg4541Ter	p.R4541*	ENST00000262189	NM_170606.2	4541	Cga/Tga	52/59	0.241950285604556	5	FACETS	0.894	0.84	0.949	0.894	0.84	0.949	INDETERMINATE	3	TRUE	2	0.547100815754965	5		664	561	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381559	81381559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777026877	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	71	256	0	ENST00000222390.5:c.502C>T	p.Arg168Trp	p.R168W	ENST00000222390	NM_000601.4	168	Cgg/Tgg	5/18	0.293384511666078	4	FACETS	0.851	0.753	0.953	0.851	0.753	0.953	INDETERMINATE	2	TRUE	2	0.547100815754965	4		256	236	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372259	55372264	+	inframe_deletion	In_Frame_Del	DEL	CACCAG	CACCAG	-	rs564144826	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	69	496	0	ENST00000297316.4:c.972_977del	p.Gln324_His325del	p.Q324_H325del	ENST00000297316	NM_022454.3	317	CACCAG/-	2/2	1	2	FACETS	0.891	0.784	1	0.891	0.784	1	CLONAL	1	TRUE	1	0.547100815754965	2		496	283	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182508	99182508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	204	760	1	ENST00000074304.5:c.2311C>T	p.Arg771Trp	p.R771W	ENST00000074304	NM_001134224.1	771	Cgg/Tgg	22/26	1	2	FACETS	0.764	0.716	0.813	1	0.992	1	SUBCLONAL	2	TRUE	1	0.547100815754965	2		761	488	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226098	2226098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	410	1080	2	ENST00000326181.6:c.1795G>A	p.Val599Met	p.V599M	ENST00000326181	NM_032271.2	599	Gtg/Atg	19/21	0.18201920047467	4	FACETS	0.866	0.828	0.903	1	0.995	1	INDETERMINATE	3	TRUE	2	0.547100815754965	4		1082	893	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434142	49434142	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057518571	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	292	914	0	ENST00000301067.7:c.7411C>T	p.Arg2471Ter	p.R2471*	ENST00000301067	NM_003482.3	2471	Cga/Tga	31/54	0.547100815754965	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	2	0.547100815754965	4		914	698	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928834	49928834	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs878910700	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	394	887	0	ENST00000296474.3:c.3532C>T	p.Arg1178Trp	p.R1178W	ENST00000296474	NM_002447.2	1178	Cgg/Tgg	16/20	0.547100815754965	4	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.547100815754965	4		887	920	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804163	46804163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752722523	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	178	681	0	ENST00000290295.7:c.844G>A	p.Ala282Thr	p.A282T	ENST00000290295	NM_006361.5	282	Gct/Act	2/2	0.242383209047512	4	FACETS	1	0.977	1	1	0.977	1	INDETERMINATE	2	TRUE	2	0.547100815754965	4		681	452	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489465	40489465	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	239	511	0	ENST00000264657.5:c.785G>T	p.Arg262Leu	p.R262L	ENST00000264657	NM_139276.2	262	cGg/cTg	8/24	0.242383209047512	4	FACETS	1	0.972	1	1	0.972	1	INDETERMINATE	2	TRUE	2	0.547100815754965	4		511	638	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354151	15354152	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	111	761	0	ENST00000263377.2:c.2728dup	p.Gln910ProfsTer7	p.Q910Pfs*7	ENST00000263377	NM_058243.2	910	caa/cCaa	14/20	0.232755845551061	4	FACETS	1	0.978	1	0.651	0.588	0.717	INDETERMINATE	1	TRUE	2	0.547100815754965	4		761	482	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510219	187510219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1276553545	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	175	515	2	ENST00000441802.2:c.13294G>A	p.Glu4432Lys	p.E4432K	ENST00000441802	NM_005245.3	4432	Gaa/Aaa	27/27	1	2	FACETS	0.753	0.701	0.805	1	0.991	1	SUBCLONAL	2	TRUE	1	0.547100815754965	2		517	425	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212236	36212236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301144035	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	85	778	0	ENST00000222270.7:c.1987G>A	p.Glu663Lys	p.E663K	ENST00000222270	NM_014727.1	663	Gaa/Aaa	3/37	0.232755845551061	4	FACETS	0.753	0.666	0.847	0.377	0.333	0.424	INDETERMINATE	1	TRUE	2	0.547100815754965	4		778	638	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858934	45858934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772572683	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	259	743	0	ENST00000391945.4:c.1532G>A	p.Arg511Gln	p.R511Q	ENST00000391945	NM_000400.3	511	cGg/cAg	16/23	0.232755845551061	4	FACETS	1	0.982	1	1	0.982	1	INDETERMINATE	2	TRUE	2	0.547100815754965	4		743	668	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636775	8636775	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	96	511	0	ENST00000356435.5:c.134G>T	p.Cys45Phe	p.C45F	ENST00000356435		45	tGc/tTc	2/35	0.122600000986784	0	FACETS	0.556	0.502	0.611			1	INDETERMINATE	1	TRUE	0	0.547100815754965	0		511	286	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445514	49445514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356632640	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	244	756	0	ENST00000301067.7:c.1952C>T	p.Ser651Leu	p.S651L	ENST00000301067	NM_003482.3	651	tCg/tTg	10/54	0.547100815754965	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	2	0.547100815754965	4		756	674	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1627405	1627405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199628190	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	356	965	1	ENST00000344749.5:c.319G>A	p.Ala107Thr	p.A107T	ENST00000344749	NM_001136139.2	107	Gcc/Acc	6/19	0.241950285604556	5	FACETS	0.982	0.936	1	0.982	0.936	1	INDETERMINATE	3	TRUE	2	0.547100815754965	5		966	804	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868981	117868981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs575505257	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	106	298	1	ENST00000297338.2:c.718G>A	p.Gly240Ser	p.G240S	ENST00000297338	NM_006265.2	240	Ggt/Agt	7/14	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.547100815754965	2		299	301	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274303	5274304	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs777078756	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	199	873	1	ENST00000357368.4:c.143dup	p.Val49CysfsTer11	p.V49Cfs*11	ENST00000357368	NM_002850.3	48	ggt/ggGt	3/38	0.397148271392172	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.547100815754965	1		874	500	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094797	2094797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1324289477	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	376	832	0	ENST00000219066.1:c.383G>A	p.Arg128His	p.R128H	ENST00000219066	NM_002528.5	128	cGc/cAc	3/6	0.18201920047467	4	FACETS	1	0.993	1	1	0.993	1	INDETERMINATE	2	TRUE	2	0.547100815754965	4		832	871	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254716	16254716	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	201	478	0	ENST00000375759.3:c.1981T>C	p.Trp661Arg	p.W661R	ENST00000375759	NM_015001.2	661	Tgg/Cgg	11/15	0.402336392035124	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.547100815754965	4		478	523	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944489	71944489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375770720	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	232	696	0	ENST00000298229.2:c.2045G>A	p.Arg682Gln	p.R682Q	ENST00000298229	NM_001567.3	682	cGg/cAg	18/28	0.232755845551061	4	FACETS	1	0.984	1	1	0.984	1	INDETERMINATE	2	TRUE	2	0.547100815754965	4		696	580	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478828	56478828	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	400	713	0	ENST00000267101.3:c.284C>A	p.Ser95Tyr	p.S95Y	ENST00000267101	NM_001982.3	95	tCt/tAt	3/28	0.547100815754965	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	2	0.547100815754965	4		713	1008	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112110	115112110	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	195	845	2	ENST00000257566.3:c.1630G>A	p.Ala544Thr	p.A544T	ENST00000257566	NM_016569.3	544	Gcc/Acc	7/8	0.18201920047467	4	FACETS	0.884	0.829	0.939	1	0.99	1	INDETERMINATE	3	TRUE	2	0.547100815754965	4		847	416	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112136	115112136	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866685357	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	146	832	0	ENST00000257566.3:c.1604C>T	p.Ala535Val	p.A535V	ENST00000257566	NM_016569.3	535	gCg/gTg	7/8	0.18201920047467	4	FACETS	1	0.967	1	1	0.967	1	INDETERMINATE	2	TRUE	2	0.547100815754965	4		832	380	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620120	21620120	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769538257	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	186	584	0	ENST00000382592.4:c.46C>T	p.Arg16Trp	p.R16W	ENST00000382592	NM_014572.2	16	Cgg/Tgg	2/8	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.547100815754965	2		584	533	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944538	32944538	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs397507979	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	131	389	0	ENST00000380152.3:c.8332-1G>A		p.X2778_splice	ENST00000380152		2778			0.232755845551061	4	FACETS	1	0.981	1	1	0.981	1	INDETERMINATE	2	TRUE	2	0.547100815754965	4		389	306	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923125	48923126	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	38	205	0	ENST00000267163.4:c.575_576del	p.Lys192SerfsTer10	p.K192Sfs*10	ENST00000267163	NM_000321.2	191	ctAAaa/ctaa	6/27	0.232755845551061	4	FACETS	0.853	0.721	0.993	0.853	0.721	0.993	INDETERMINATE	2	TRUE	2	0.547100815754965	4		205	126	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610171	81610171	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	82	411	0	ENST00000298171.2:c.1769A>G	p.Asn590Ser	p.N590S	ENST00000298171	NM_000369.2	590	aAc/aGc	10/10	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.547100815754965	2		411	216	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42002992	42002992	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	34	556	0	ENST00000219905.7:c.2533del	p.Ser845LeufsTer28	p.S845Lfs*28	ENST00000219905	NM_001164273.1	843	ggT/gg	8/24	0.293384511666078	4	FACETS	0.376	0.307	0.455	0.188	0.153	0.228	INDETERMINATE	1	TRUE	2	0.547100815754965	4		556	511	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533761	63533761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886041137	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	184	840	1	ENST00000307078.5:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000307078	NM_004655.3	465	Cgc/Tgc	6/11	0.242383209047512	4	FACETS	1	0.982	1	1	0.982	1	INDETERMINATE	2	TRUE	2	0.547100815754965	4		841	451	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296391	15296391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770737365	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	296	1022	0	ENST00000263388.2:c.2051C>T	p.Pro684Leu	p.P684L	ENST00000263388	NM_000435.2	684	cCg/cTg	13/33	0.232755845551061	4	FACETS	1	0.982	1	1	0.982	1	INDETERMINATE	2	TRUE	2	0.547100815754965	4		1022	770	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639697	47639697	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	97	151	0	ENST00000233146.2:c.790del	p.Gln264ArgfsTer10	p.Q264Rfs*10	ENST00000233146	NM_000251.2	264	Cag/ag	4/16	1	2	FACETS	0.969	0.913	1	1	0.992	1	CLONAL	3	TRUE	1	0.547100815754965	2		151	122	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660088	227660088	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	146	781	1	ENST00000305123.5:c.3367del	p.Ala1123GlnfsTer3	p.A1123Qfs*3	ENST00000305123	NM_005544.2	1123	Gca/ca	1/2	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.547100815754965	2		782	423	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523683	41523683	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	364	798	0	ENST00000263253.7:c.1102del	p.His368ThrfsTer5	p.H368Tfs*5	ENST00000263253	NM_001429.3	367	Ccc/cc	4/31	0.18201920047467	4	FACETS	0.836	0.797	0.875	1	0.993	1	INDETERMINATE	3	TRUE	2	0.547100815754965	4		798	821	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49724621	49724621	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	89	641	1	ENST00000449682.2:c.568G>A	p.Val190Met	p.V190M	ENST00000449682	NM_020998.3	190	Gtg/Atg	5/18	0.547100815754965	4	FACETS	0.838	0.744	0.938			1	CLONAL	1	TRUE	NA	0.547100815754965	4		642	601	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495717	72495717	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	169	453	0	ENST00000477973.2:c.355T>C	p.Cys119Arg	p.C119R	ENST00000477973	NM_012234.5	119	Tgc/Cgc	1/4	0.18201920047467	4	FACETS	1	0.954	1	1	0.954	1	INDETERMINATE	2	TRUE	2	0.547100815754965	4		453	461	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430600	181430601	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	14	578	0	ENST00000325404.1:c.455dup	p.Val153ArgfsTer157	p.V153Rfs*157	ENST00000325404	NM_003106.3	151	gcg/gcGg	1/1	0.18201920047467	4	FACETS	0.305	0.22	0.407	0.152	0.11	0.204	INDETERMINATE	1	TRUE	2	0.547100815754965	4		578	260	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536223	106536223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	167	474	0	ENST00000369096.4:c.190G>A	p.Asp64Asn	p.D64N	ENST00000369096	NM_001198.3	64	Gac/Aac	2/7	0.136867396613818	4	FACETS	0.994	0.922	1	0.994	0.922	1	INDETERMINATE	2	TRUE	2	0.547100815754965	4		474	475	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109314066	109314066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780468161	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	118	419	0	ENST00000436639.2:c.1157G>A	p.Arg386His	p.R386H	ENST00000436639	NM_014454.2	386	cGt/cAt	7/10	0.136867396613818	4	FACETS	1	0.937	1	1	0.937	1	INDETERMINATE	2	TRUE	2	0.547100815754965	4		419	324	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462597	92462597	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	145	519	0	ENST00000265734.4:c.41A>G	p.Glu14Gly	p.E14G	ENST00000265734	NM_001259.6	14	gAa/gGa	2/8	0.293384511666078	4	FACETS	1	0.984	1	1	0.984	1	INDETERMINATE	2	TRUE	2	0.547100815754965	4		519	332	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132834	152132834	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs866392536	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	191	604	0	ENST00000262189.6:c.38A>C	p.Gln13Pro	p.Q13P	ENST00000262189	NM_170606.2	13	cAg/cCg	1/59	0.241950285604556	5	FACETS	1	0.981	1	0.765	0.712	0.819	INDETERMINATE	2	TRUE	2	0.547100815754965	5		604	554	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207578	29207578	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	226	650	0	ENST00000240100.2:c.218T>C	p.Val73Ala	p.V73A	ENST00000240100	NM_001394.6	73	gTg/gCg	1/4	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.547100815754965	2		650	625	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249347	110249348	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	408	1049	0	ENST00000374672.4:c.1225_1226del	p.Lys409GlufsTer14	p.K409Efs*14	ENST00000374672	NM_004235.4	409	AAg/g	4/5	0.18201920047467	4	FACETS	0.849	0.812	0.886	1	0.994	1	INDETERMINATE	3	TRUE	2	0.547100815754965	4		1049	906	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395213	139395213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751228412	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	325	987	1	ENST00000277541.6:c.5725G>A	p.Val1909Ile	p.V1909I	ENST00000277541	NM_017617.3	1909	Gtc/Atc	31/34	0.18201920047467	4	FACETS	1	0.992	1	1	0.992	1	INDETERMINATE	2	TRUE	2	0.547100815754965	4		988	750	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55130079	55130079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775304724	NA	P-0046264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	104	459	0	ENST00000257290.5:c.613G>A	p.Val205Ile	p.V205I	ENST00000257290	NM_006206.4	205	Gtt/Att	4/23	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.547100815754965	2		459	275	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	83	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.899	0.798	1	0.899	0.798	1	CLONAL	1	TRUE	1	0.461385358590606	2		288	400	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	140	527	2	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.461385358590606	2		529	461	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214398	36214398	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs868041281	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	181	630	2	ENST00000222270.7:c.3057del	p.Gly1020AlafsTer4	p.G1020Afs*4	ENST00000222270	NM_014727.1	1018	Aaa/aa	7/37	1	2	FACETS	0.912	0.842	0.985	0.912	0.842	0.985	CLONAL	1	TRUE	1	0.461385358590606	2		632	860	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	462	679	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.999	0.959	1	1	0.997	1	CLONAL	2	TRUE	1	0.461385358590606	2		683	1002	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913559	32913559	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359479	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	101	396	0	ENST00000380152.3:c.5073del	p.Lys1691AsnfsTer15	p.K1691Nfs*15	ENST00000380152		1689	gcA/gc	11/27	0.461385358590606	3	FACETS	0.973	0.883	1	0.973	0.883	1	CLONAL	2	TRUE	1	0.461385358590606	3		396	277	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736166	204736166	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	125	372	2	ENST00000302823.3:c.529del	p.Tyr177IlefsTer10	p.Y177Ifs*10	ENST00000302823	NM_005214.4	175	Ttt/tt	3/4	0.309808087499382	3	FACETS	1	0.979	1	0.635	0.577	0.695	CLONAL	1	TRUE	1	0.461385358590606	3		374	525	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	86	295	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.78	0.692	0.873	0.78	0.692	0.873	SUBCLONAL	1	TRUE	1	0.461385358590606	2		296	478	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308382	15308383	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs749829137	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	192	943	2	ENST00000263388.2:c.125dup	p.Cys43LeufsTer32	p.C43Lfs*32	ENST00000263388	NM_000435.2	42	cct/ccCt	2/33	1	2	FACETS	0.78	0.721	0.842	0.78	0.721	0.842	SUBCLONAL	1	TRUE	1	0.461385358590606	2		945	1067	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	89	342	3	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.895	0.798	0.998	0.895	0.798	0.998	CLONAL	1	TRUE	1	0.461385358590606	2		345	431	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760264	133760264	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	47	741	1	ENST00000318560.5:c.2591del	p.Gly864AlafsTer12	p.G864Afs*12	ENST00000318560	NM_005157.4	863	Ggg/gg	11/11	1	2	FACETS	0.256	0.215	0.301	0.256	0.215	0.301	SUBCLONAL	1	TRUE	1	0.461385358590606	2		742	797	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	272	680	1	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.461385358590606	2		681	1160	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652386	206652386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781784265	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	260	863	0	ENST00000367120.3:c.1093G>A	p.Val365Ile	p.V365I	ENST00000367120	NM_014002.3	365	Gtc/Atc	10/22	1	2	FACETS	0.949	0.888	1	0.949	0.888	1	CLONAL	1	TRUE	1	0.461385358590606	2		863	1188	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736510	85736511	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs387906351	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	51	281	3	ENST00000370580.1:c.136dup	p.Ile46AsnfsTer4	p.I46Nfs*4	ENST00000370580	NM_003921.4	46	ata/aAta	2/3	1	2	FACETS	0.747	0.639	0.864	0.747	0.639	0.864	SUBCLONAL	1	TRUE	1	0.461385358590606	2		284	296	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216380	7216380	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	229	785	4	ENST00000380728.2:c.868del	p.Gln290SerfsTer55	p.Q290Sfs*55	ENST00000380728		290	Cag/ag	10/11	1	2	FACETS	0.968	0.903	1	0.968	0.903	1	CLONAL	1	TRUE	1	0.461385358590606	2		789	1025	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347080	89347080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs922813408	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	232	866	1	ENST00000301030.4:c.5870C>T	p.Ala1957Val	p.A1957V	ENST00000301030	NM_001256183.1	1957	gCg/gTg	9/13	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.461385358590606	2		867	935	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536939	120536939	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760171048	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	202	715	0	ENST00000229340.5:c.247G>A	p.Gly83Arg	p.G83R	ENST00000229340	NM_006861.6	83	Ggg/Agg	4/6	1	2	FACETS	0.945	0.876	1	0.945	0.876	1	CLONAL	1	TRUE	1	0.461385358590606	2		715	927	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992721	68992721	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs764112302	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	93	492	2	ENST00000288368.4:c.1693del	p.Ser565ArgfsTer10	p.S565Rfs*10	ENST00000288368	NM_024870.2	562	cgT/cg	16/40	0.461385358590606	3	FACETS	1	0.917	1	0.516	0.46	0.574	CLONAL	1	TRUE	1	0.461385358590606	3		494	481	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	147	486	1	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	0.461385358590606	2	FACETS	1	0.927	1	0.507	0.464	0.551	CLONAL	1	TRUE	0	0.461385358590606	2		487	629	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627688	37627688	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	190	367	0	ENST00000447079.4:c.1607del	p.Pro536HisfsTer74	p.P536Hfs*74	ENST00000447079	NM_015083.1	535	Ccc/cc	2/14	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.461385358590606	2		367	686	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46602913	46602913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766854881	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	237	843	1	ENST00000263734.3:c.971C>T	p.Thr324Met	p.T324M	ENST00000263734	NM_001430.4	324	aCg/aTg	8/16	1	2	FACETS	0.93	0.867	0.994	0.93	0.867	0.994	CLONAL	1	TRUE	1	0.461385358590606	2		844	1105	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589609	67589610	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	25	205	0	ENST00000274335.5:c.1378dup	p.Ser460LysfsTer5	p.S460Kfs*5	ENST00000274335		458	gaa/gAaa	10/15	1	2	FACETS	0.704	0.561	0.864	0.704	0.561	0.864	SUBCLONAL	1	TRUE	1	0.461385358590606	2		205	154	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32931923	32931924	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs878853303	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	52	322	0	ENST00000380152.3:c.7667dup	p.Asn2556LysfsTer10	p.N2556Kfs*10	ENST00000380152		2554	-/A	16/27	0.461385358590606	3	FACETS	0.98	0.841	1	0.49	0.42	0.566	CLONAL	1	TRUE	1	0.461385358590606	3		322	283	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519037	103519037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434571	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	175	619	0	ENST00000355739.4:c.2375C>T	p.Ala792Val	p.A792V	ENST00000355739	NM_000123.3	792	gCg/gTg	11/15	0.461385358590606	3	FACETS	0.912	0.839	0.988	0.456	0.419	0.494	CLONAL	1	TRUE	1	0.461385358590606	3		619	1024	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217662	7217662	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	127	474	1	ENST00000380728.2:c.265C>T	p.Gln89Ter	p.Q89*	ENST00000380728		89	Cag/Tag	4/11	1	2	FACETS	0.859	0.78	0.942	0.859	0.78	0.942	CLONAL	1	TRUE	1	0.461385358590606	2		475	641	SUCCESS
AR	367	MSKCC	GRCh37	X	66766196	66766196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772490323	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	190	276	0	ENST00000374690.3:c.1208C>T	p.Ala403Val	p.A403V	ENST00000374690	NM_000044.3	403	gCg/gTg	1/8	1	1	FACETS	0.91	0.857	0.963	1	0.994	1	CLONAL	2	TRUE	0	0.461385358590606	1		276	348	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214714	36214714	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	178	823	2	ENST00000222270.7:c.3145del	p.Ala1049ArgfsTer133	p.A1049Rfs*133	ENST00000222270	NM_014727.1	1047	cGg/cg	8/37	1	2	FACETS	0.938	0.865	1	0.938	0.865	1	CLONAL	1	TRUE	1	0.461385358590606	2		825	823	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730186	133730186	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	123	477	0	ENST00000318560.5:c.254-2A>G		p.X85_splice	ENST00000318560	NM_005157.4	85			1	2	FACETS	0.944	0.857	1	0.944	0.857	1	CLONAL	1	TRUE	1	0.461385358590606	2		477	565	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211545	98211545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370675945	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	229	765	0	ENST00000331920.6:c.3610G>A	p.Val1204Met	p.V1204M	ENST00000331920	NM_000264.3	1204	Gtg/Atg	22/24	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.461385358590606	2		765	988	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077585	30077585	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	35	351	0	ENST00000338641.4:c.1736del	p.Lys579SerfsTer20	p.K579Sfs*20	ENST00000338641	NM_000268.3	578	Aaa/aa	15/16	1	2	FACETS	0.296	0.242	0.356	0.296	0.242	0.356	SUBCLONAL	1	TRUE	1	0.461385358590606	2		351	513	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94910992	94910992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	151	608	2	ENST00000536441.1:c.1138C>T	p.Arg380Trp	p.R380W	ENST00000536441	NM_144665.3	380	Cgg/Tgg	8/10	1	2	FACETS	0.94	0.862	1	0.94	0.862	1	CLONAL	1	TRUE	1	0.461385358590606	2		610	696	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522596	176522596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754440305	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	333	1094	1	ENST00000292408.4:c.1693C>T	p.Arg565Trp	p.R565W	ENST00000292408	NM_213647.1	565	Cgg/Tgg	13/18	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.461385358590606	2		1095	1345	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167563	24167563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	217	668	0	ENST00000263121.7:c.947G>A	p.Arg316Gln	p.R316Q	ENST00000263121	NM_003073.3	316	cGg/cAg	7/9	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.461385358590606	2		668	894	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285086	15285086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	299	1065	2	ENST00000263388.2:c.4529G>A	p.Arg1510His	p.R1510H	ENST00000263388	NM_000435.2	1510	cGc/cAc	25/33	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.461385358590606	2		1067	1195	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291460	11291460	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1330725518	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	166	523	2	ENST00000361445.4:c.2546C>T	p.Ala849Val	p.A849V	ENST00000361445	NM_004958.3	849	gCc/gTc	17/58	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.461385358590606	2		525	667	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710650	114710650	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	145	471	0	ENST00000543371.1:c.135A>T	p.Lys45Asn	p.K45N	ENST00000543371	NM_001198531.1	45	aaA/aaT	1/14	1	2	FACETS	0.998	0.913	1	0.998	0.913	1	CLONAL	1	TRUE	1	0.461385358590606	2		471	630	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201787	102201787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	86	367	0	ENST00000263464.3:c.1139C>A	p.Pro380His	p.P380H	ENST00000263464	NM_001165.4	380	cCt/cAt	6/9	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.461385358590606	2		367	361	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390331	118390331	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1131691648	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	161	504	0	ENST00000534358.1:c.11147-2A>G		p.X3716_splice	ENST00000534358	NM_005933.3	3716			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.461385358590606	2		504	670	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861162	57861162	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	179	637	0	ENST00000228682.2:c.959C>A	p.Thr320Lys	p.T320K	ENST00000228682	NM_005269.2	320	aCg/aAg	9/12	1	2	FACETS	0.818	0.754	0.884	0.818	0.754	0.884	CLONAL	1	TRUE	1	0.461385358590606	2		637	949	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416854	121416856	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	312	1077	0	ENST00000257555.6:c.287_289del	p.Glu96del	p.E96del	ENST00000257555		95	GAG/-	1/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.461385358590606	2		1077	1221	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647863	3647863	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763337738	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	270	991	0	ENST00000294008.3:c.1301C>T	p.Pro434Leu	p.P434L	ENST00000294008	NM_032444.2	434	cCg/cTg	6/15	1	2	FACETS	0.967	0.907	1	0.967	0.907	1	CLONAL	1	TRUE	1	0.461385358590606	2		991	1210	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786817	3786817	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	123	412	0	ENST00000262367.5:c.4395-1G>T		p.X1465_splice	ENST00000262367	NM_004380.2	1465			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.461385358590606	2		412	473	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89354980	89354980	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	300	955	0	ENST00000301030.4:c.700G>A	p.Asp234Asn	p.D234N	ENST00000301030	NM_001256183.1	234	Gac/Aac	7/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.461385358590606	2		955	1254	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321657	30321657	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	37	536	0	ENST00000322652.5:c.1512G>T	p.Gln504His	p.Q504H	ENST00000322652	NM_015355.2	504	caG/caT	13/16	1	2	FACETS	0.242	0.198	0.29	0.242	0.198	0.29	SUBCLONAL	1	TRUE	1	0.461385358590606	2		536	664	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10257041	10257041	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	176	650	0	ENST00000340748.4:c.2832G>T	p.Glu944Asp	p.E944D	ENST00000340748		944	gaG/gaT	27/40	1	2	FACETS	0.974	0.899	1	0.974	0.899	1	CLONAL	1	TRUE	1	0.461385358590606	2		650	783	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270332	10270332	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1344636403	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	198	596	0	ENST00000340748.4:c.1232+2T>C		p.X411_splice	ENST00000340748		411			1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.461385358590606	2		596	817	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274095	18274095	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	190	681	0	ENST00000222254.8:c.1313G>T	p.Ser438Ile	p.S438I	ENST00000222254	NM_005027.3	438	aGc/aTc	11/16	1	2	FACETS	0.975	0.902	1	0.975	0.902	1	CLONAL	1	TRUE	1	0.461385358590606	2		681	845	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961041	18961041	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	237	600	0	ENST00000262803.5:c.619C>G	p.Leu207Val	p.L207V	ENST00000262803	NM_002911.3	207	Ctg/Gtg	4/24	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.461385358590606	2		600	863	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223931	36223931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779123379	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	338	1155	0	ENST00000222270.7:c.6481C>T	p.Arg2161Cys	p.R2161C	ENST00000222270	NM_014727.1	2161	Cgc/Tgc	28/37	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.461385358590606	2		1155	1387	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467481	25467481	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	248	809	1	ENST00000264709.3:c.1595G>T	p.Gly532Val	p.G532V	ENST00000264709	NM_175629.2	532	gGc/gTc	14/23	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.461385358590606	2		810	1072	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143125	30143125	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	232	823	0	ENST00000389048.3:c.401A>C	p.Lys134Thr	p.K134T	ENST00000389048	NM_004304.4	134	aAg/aCg	1/29	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.461385358590606	2		823	999	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224510	39224510	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	83	475	1	ENST00000402219.2:c.2848del	p.Arg950AspfsTer7	p.R950Dfs*7	ENST00000402219	NM_005633.3	950	Aga/ga	18/23	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.461385358590606	2		476	330	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023110	48023110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	111	357	0	ENST00000234420.5:c.535G>A	p.Ala179Thr	p.A179T	ENST00000234420	NM_000179.2	179	Gca/Aca	3/10	1	2	FACETS	0.972	0.878	1	0.972	0.878	1	CLONAL	1	TRUE	1	0.461385358590606	2		357	495	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268324	46268324	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	97	367	0	ENST00000371998.3:c.2711G>T	p.Gly904Val	p.G904V	ENST00000371998		904	gGg/gTg	15/23	1	2	FACETS	0.916	0.821	1	0.916	0.821	1	CLONAL	1	TRUE	1	0.461385358590606	2		367	459	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574451	41574451	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	199	748	0	ENST00000263253.7:c.6739del	p.Gln2247ArgfsTer32	p.Q2247Rfs*32	ENST00000263253	NM_001429.3	2246	Ccc/cc	31/31	1	2	FACETS	0.99	0.919	1	0.99	0.919	1	CLONAL	1	TRUE	1	0.461385358590606	2		748	871	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924904	49924904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	296	895	0	ENST00000296474.3:c.4039G>A	p.Ala1347Thr	p.A1347T	ENST00000296474	NM_002447.2	1347	Gca/Aca	20/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.461385358590606	2		895	1125	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953861	55953861	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	29	507	0	ENST00000263923.4:c.3575T>A	p.Leu1192His	p.L1192H	ENST00000263923	NM_002253.2	1192	cTc/cAc	27/30	1	2	FACETS	0.223	0.178	0.275	0.223	0.178	0.275	SUBCLONAL	1	TRUE	1	0.461385358590606	2		507	563	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630522	187630522	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs368811089	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	210	652	0	ENST00000441802.2:c.460T>C	p.Tyr154His	p.Y154H	ENST00000441802	NM_005245.3	154	Tac/Cac	2/27	1	2	FACETS	0.951	0.884	1	0.951	0.884	1	CLONAL	1	TRUE	1	0.461385358590606	2		652	957	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722372	176722372	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	39	483	0	ENST00000439151.2:c.8003G>T	p.Gly2668Val	p.G2668V	ENST00000439151	NM_022455.4	2668	gGg/gTg	23/23	1	2	FACETS	0.244	0.202	0.292	0.244	0.202	0.292	SUBCLONAL	1	TRUE	1	0.461385358590606	2		483	692	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323093	31323094	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CC	CC	-	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	184	830	0	ENST00000412585.2:c.895_895+1del		p.X299_splice	ENST00000412585	NM_005514.6	299		4/8	0.461385358590606	2	FACETS	0.894	0.826	0.965	0.447	0.413	0.483	CLONAL	1	TRUE	0	0.461385358590606	2		830	892	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324204	31324204	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs151341215	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	413	427	0	ENST00000412585.2:c.359A>G	p.Gln120Arg	p.Q120R	ENST00000412585	NM_005514.6	120	cAg/cGg	3/8	0.461385358590606	2	FACETS	0.917	0.884	0.949	1	0.996	1	CLONAL	3	TRUE	0	0.461385358590606	2		427	651	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821059	32821059	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs763585575	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	643	1146	0	ENST00000354258.4:c.535T>C	p.Trp179Arg	p.W179R	ENST00000354258	NM_000593.5	179	Tgg/Cgg	1/11	0.461385358590606	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.461385358590606	2		1146	1330	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891151	151891151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	159	537	1	ENST00000262189.6:c.4603C>T	p.Pro1535Ser	p.P1535S	ENST00000262189	NM_170606.2	1535	Cca/Tca	31/59	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.461385358590606	2		538	687	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841320	15841320	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	28	244	0	ENST00000307771.7:c.1404G>T	p.Arg468Ser	p.R468S	ENST00000307771	NM_005089.3	468	agG/agT	11/11	1	1	FACETS	0.23	0.183	0.283	0.23	0.183	0.283	SUBCLONAL	1	TRUE	0	0.461385358590606	1		244	406	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032593	47032593	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0046266-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	280	432	0	ENST00000377604.3:c.499T>G	p.Ser167Ala	p.S167A	ENST00000377604	NM_001204468.1	167	Tca/Gca	5/24	1	1	FACETS	0.795	0.754	0.836	1	0.995	1	SUBCLONAL	2	TRUE	0	0.461385358590606	1		432	587	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0046267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	91	324	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.25491864949704	2		324	545	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0046267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	98	716	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.22653007710574	1	FACETS	0.769	0.685	0.859	0.769	0.685	0.859	SUBCLONAL	1	TRUE	0	0.25491864949704	1		716	872	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138516	11138516	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555781772	NA	P-0046267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	93	748	0	ENST00000358026.2:c.3272A>G	p.Lys1091Arg	p.K1091R	ENST00000358026	NM_001128849.1	1091	aAa/aGa	24/36	0.25491864949704	1	FACETS	0.736	0.653	0.824	0.736	0.653	0.824	SUBCLONAL	1	TRUE	0	0.25491864949704	1		748	865	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505634	186505635	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0046267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	81	316	0	ENST00000323963.5:c.1043_1044del	p.Tyr348Ter	p.Y348*	ENST00000323963		348	TAt/t	10/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.25491864949704	2		316	447	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859205	151859206	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0046267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	23	356	0	ENST00000262189.6:c.11456_11457del	p.Gly3819AlafsTer26	p.G3819Afs*26	ENST00000262189	NM_170606.2	3819	gGA/g	43/59	1	2	FACETS	0.616	0.481	0.772	0.616	0.481	0.772	SUBCLONAL	1	TRUE	1	0.25491864949704	2		356	293	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873378	151873396	+	frameshift_variant	Frame_Shift_Del	DEL	GTAGAGGCTGTTCTTCTAG	GTAGAGGCTGTTCTTCTAG	-	novel	NA	P-0046267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	62	372	0	ENST00000262189.6:c.9142_9160del	p.Leu3048PhefsTer22	p.L3048Ffs*22	ENST00000262189	NM_170606.2	3048	CTAGAAGAACAGCCTCTACtt/tt	38/59	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.25491864949704	2		372	483	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	113	69	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.63783004841703	3	FACETS	0.95	0.872	1	0.95	0.872	1	CLONAL	2	TRUE	1	0.63783004841703	3		69	246	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479811	67479811	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500766	NA	P-0046268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	167	633	1	ENST00000327367.4:c.1118G>A	p.Arg373His	p.R373H	ENST00000327367	NM_005902.3	373	cGc/cAc	8/9	0.23850203160174	2	FACETS	0.595	0.547	0.645	0.298	0.273	0.323	INDETERMINATE	1	TRUE	0	0.63783004841703	2		634	880	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0046268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	484	631	0	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	0.63783004841703	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.63783004841703	2		631	738	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981303	201981303	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	535	766	0	ENST00000359651.3:c.382C>A	p.Leu128Ile	p.L128I	ENST00000359651		128	Ctc/Atc	2/8	0.598912817365193	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.63783004841703	3		766	1100	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573663	48573663	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	34	257	0	ENST00000342988.3:c.247C>T	p.Gln83Ter	p.Q83*	ENST00000342988	NM_005359.5	83	Cag/Tag	2/12	0.637276160236395	2	FACETS	1	0.957	1	0.72	0.614	0.828	CLONAL	1	TRUE	0	0.63783004841703	2		257	74	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528106	157528106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs917324402	NA	P-0046268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	172	605	1	ENST00000346085.5:c.5831G>A	p.Arg1944Gln	p.R1944Q	ENST00000346085	NM_020732.3	1944	cGa/cAa	20/20	0.595045217612808	2	FACETS	0.825	0.762	0.89	0.412	0.381	0.445	CLONAL	1	TRUE	0	0.63783004841703	2		606	654	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0046269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	17	248	1				ENST00000310581	NM_198253.2	-/1132			0.372676697200939	0	FACETS	0.39	0.303	0.485			1	INDETERMINATE	1	TRUE	0	0.62619815952244	0		249	52	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0046269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6475	1842	774	3	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.62619815952244	93	FACETS	0.993	0.969	1			1	CLONAL	21	TRUE	NA	0.62619815952244	93		777	8317	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15838367	15838367	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046269-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	36	330	0	ENST00000307771.7:c.865G>C	p.Gly289Arg	p.G289R	ENST00000307771	NM_005089.3	289	Gga/Cga	10/11	0.443429984289028	1	FACETS	0.534	0.446	0.629	0.534	0.446	0.629	SUBCLONAL	1	TRUE	0	0.62619815952244	1		330	148	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0046270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	57	301	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.2	2		301	563	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057835	27057835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	58	891	0	ENST00000324856.7:c.1543C>T	p.Gln515Ter	p.Q515*	ENST00000324856	NM_006015.4	515	Cag/Tag	3/20	1	2	FACETS	0.577	0.494	0.668	0.577	0.494	0.668	SUBCLONAL	1	TRUE	1	0.2	2		891	1005	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508535	106508535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	37	398	0	ENST00000359195.3:c.529C>T	p.Arg177Cys	p.R177C	ENST00000359195	NM_002649.2	177	Cgc/Tgc	2/11	1	2	FACETS	0.82	0.676	0.982	0.82	0.676	0.982	CLONAL	1	TRUE	1	0.2	2		398	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576851	7576851	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0046270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	83	625	0	ENST00000269305.4:c.993+2T>C		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.3	2	FACETS	1	0.936	1			1	CLONAL	1	TRUE	NA	0.2	2		625	758	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434488	110434488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	83	676	1	ENST00000375856.3:c.3913G>A	p.Gly1305Arg	p.G1305R	ENST00000375856	NM_003749.2	1305	Ggg/Agg	1/2	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.2	2		677	783	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929124	44929124	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046270-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	55	577	0	ENST00000377967.4:c.2224G>A	p.Ala742Thr	p.A742T	ENST00000377967	NM_021140.2	742	Gcc/Acc	17/29	0.194112915090677	1	FACETS	0.792	0.677	0.918	0.792	0.677	0.918	CLONAL	1	TRUE	0	0.2	1		577	625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579336	7579336	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	211	654	0	ENST00000269305.4:c.351del	p.Thr118GlnfsTer5	p.T118Qfs*5	ENST00000269305	NM_001126112.2	117	ggG/gg	4/11	0.287263106819178	3	FACETS	0.863	0.807	0.92	0.863	0.807	0.92	CLONAL	3	TRUE	0	0.324407517379465	3		654	584	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662735	117662735	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	66	316	0	ENST00000368508.3:c.4730C>A	p.Ser1577Tyr	p.S1577Y	ENST00000368508	NM_002944.2	1577	tCt/tAt	29/43	0.246608880785308	4	FACETS	1	0.971	1	0.72	0.629	0.819	CLONAL	1	TRUE	2	0.324407517379465	4		316	374	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967099	18967099	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	186	728	1	ENST00000262803.5:c.1814A>T	p.Glu605Val	p.E605V	ENST00000262803	NM_002911.3	605	gAg/gTg	13/24	0.144066193576364	4	FACETS	1	0.951	1	1	0.951	1	INDETERMINATE	2	TRUE	2	0.324407517379465	4		729	734	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1918623	1918623	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0046273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	123	348	0	ENST00000382891.5:c.786T>A	p.Tyr262Ter	p.Y262*	ENST00000382891	NM_133335.3	262	taT/taA	4/22	0.300106876526607	2	FACETS	0.97	0.885	1	0.97	0.885	1	CLONAL	2	TRUE	0	0.324407517379465	2		348	391	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554342	106554342	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	106	376	0	ENST00000369096.4:c.1870G>T	p.Val624Leu	p.V624L	ENST00000369096	NM_001198.3	624	Gta/Tta	6/7	0.246608880785308	4	FACETS	0.941	0.848	1	0.941	0.848	1	CLONAL	2	TRUE	2	0.324407517379465	4		376	460	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163819	152163819	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	118	401	0	ENST00000206249.3:c.540G>T	p.Lys180Asn	p.K180N	ENST00000206249	NM_000125.3	180	aaG/aaT	2/8	0.246608880785308	4	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	2	0.324407517379465	4		401	458	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0046274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	116	301	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.829	0.753	0.907	0.829	0.753	0.907	CLONAL	1	TRUE	1	0.682744405571813	2		301	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0046274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	249	820	1	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.656820174554482	1	FACETS	0.965	0.913	1	0.965	0.913	1	CLONAL	1	TRUE	0	0.682744405571813	1		821	498	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050980	49050980	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0046274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	68	184	0	ENST00000267163.4:c.2663+1G>A		p.X888_splice	ENST00000267163	NM_000321.2	888			0.682744405571813	1	FACETS	0.958	0.86	1	0.958	0.86	1	CLONAL	1	TRUE	0	0.682744405571813	1		184	137	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288681	33288681	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	151	420	0	ENST00000374542.5:c.871C>T	p.Arg291Trp	p.R291W	ENST00000374542	NM_001141970.1	291	Cgg/Tgg	3/8	0.347579006935779	5	FACETS	0.892	0.821	0.965	0.595	0.547	0.643	INDETERMINATE	2	TRUE	2	0.682744405571813	5		420	502	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249409	110249409	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	286	939	0	ENST00000374672.4:c.1164G>C	p.Trp388Cys	p.W388C	ENST00000374672	NM_004235.4	388	tgG/tgC	4/5	1	2	FACETS	0.902	0.85	0.955	0.902	0.85	0.955	CLONAL	1	TRUE	1	0.682744405571813	2		939	929	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061208	38061208	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1292426539	NA	P-0046276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	62	490	0	ENST00000250448.2:c.781C>G	p.Arg261Gly	p.R261G	ENST00000250448	NM_004496.3	261	Cgc/Ggc	2/2	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.219645135024715	2		490	464	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618596	37618606	+	frameshift_variant	Frame_Shift_Del	DEL	TAGACCGAAGG	TAGACCGAAGG	-	novel	NA	P-0046276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	133	491	0	ENST00000447079.4:c.272_282del	p.Leu91ArgfsTer32	p.L91Rfs*32	ENST00000447079	NM_015083.1	91	cTAGACCGAAGG/c	1/14	0.219645135024715	6	FACETS	1	0.91	1			1	CLONAL	2	FALSE	NA	0.219645135024715	6		491	870	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912245	97912247	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0046276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	35	498	0	ENST00000289081.3:c.644_646del	p.Leu215del	p.L215del	ENST00000289081	NM_000136.2	215	cTCCag/cag	7/15	1	2	FACETS	0.488	0.399	0.589	0.488	0.399	0.589	SUBCLONAL	1	FALSE	1	0.219645135024715	2		498	653	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0046277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	410	324	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.527463755507588	5	FACETS	0.998	0.967	1			1	CLONAL	5	TRUE	NA	0.527463755507588	5		324	558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0046277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	221	780	3	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.508498743983693	2	FACETS	0.931	0.878	0.984	0.931	0.878	0.984	CLONAL	2	TRUE	0	0.527463755507588	2		783	450	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097705	27097706	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0046277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	88	489	0	ENST00000324856.7:c.3296_3297del	p.Cys1099SerfsTer5	p.C1099Sfs*5	ENST00000324856	NM_006015.4	1098	caGTgt/cagt	12/20	0.465532017729835	3	FACETS	0.899	0.8	1	0.45	0.4	0.502	CLONAL	1	TRUE	1	0.527463755507588	3		489	469	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106566	27106566	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	227	768	0	ENST00000324856.7:c.6177del	p.Asn2059LysfsTer76	p.N2059Kfs*76	ENST00000324856	NM_006015.4	2059	aaC/aa	20/20	0.465532017729835	3	FACETS	0.954	0.896	1	0.954	0.896	1	CLONAL	2	TRUE	1	0.527463755507588	3		768	570	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0046278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	468	654	2	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	1	2	FACETS	0.984	0.943	1	0.984	0.943	1	CLONAL	1	TRUE	1	0.829778190653953	2		656	1146	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577095	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519984	NA	P-0046278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	874	629	1	ENST00000269305.4:c.843C>G	p.Asp281Glu	p.D281E	ENST00000269305	NM_001126112.2	281	gaC/gaG	8/11	0.810101948133005	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.829778190653953	2		630	1050	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974727	21974744	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAGCAGCGCCCGCA	CCTCCAGCAGCGCCCGCA	-	novel	NA	P-0046278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	434	311	0	ENST00000304494.5:c.83_100del	p.Val28_Glu33del	p.V28_E33del	ENST00000304494	NM_000077.4	28	gTGCGGGCGCTGCTGGAGGcg/gcg	1/3	0.829778190653953	2	FACETS	0.953	0.927	0.977	0.953	0.927	0.977	CLONAL	2	TRUE	0	0.829778190653953	2		311	549	SUCCESS
APC	324	MSKCC	GRCh37	5	112176520	112176521	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554086550	NA	P-0046278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	173	245	0	ENST00000257430.4:c.5234dup	p.Ile1746AspfsTer23	p.I1746Dfs*23	ENST00000257430	NM_000038.5	1743	-/A	16/16	0.829778190653953	1	FACETS	0.942	0.892	0.99	0.942	0.892	0.99	CLONAL	1	TRUE	0	0.829778190653953	1		245	259	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210689	36210689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754616271	NA	P-0046278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	344	568	0	ENST00000222270.7:c.440G>A	p.Arg147Gln	p.R147Q	ENST00000222270	NM_014727.1	147	cGa/cAa	3/37	1	2	FACETS	0.947	0.899	0.994	0.947	0.899	0.994	CLONAL	1	TRUE	1	0.829778190653953	2		568	876	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57567463	57567464	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	212	337	0	ENST00000316660.6:c.55dup	p.Ala19GlyfsTer69	p.A19Gfs*69	ENST00000316660	NM_021127.2	18	-/G	1/2	0.829778190653953	1	FACETS	0.946	0.901	0.99	0.946	0.901	0.99	CLONAL	1	TRUE	0	0.829778190653953	1		337	316	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045951	26045952	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0046278-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	319	458	0	ENST00000540144.1:c.313_314del	p.Phe105ArgfsTer11	p.F105Rfs*11	ENST00000540144	NM_003531.2	105	TTc/c	1/1	1	2	FACETS	0.995	0.944	1	0.995	0.944	1	CLONAL	1	TRUE	1	0.829778190653953	2		458	773	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0046279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	62	324	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.231673131265667	2		324	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577122	+	missense_variant	Missense_Mutation	DNP	GC	GC	CT	novel	NA	P-0046279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	67	591	0	ENST00000269305.4:c.816_817delinsAG	p.Arg273Gly	p.R273G	ENST00000269305	NM_001126112.2	272	gtGCgt/gtAGgt	8/11	0.231673131265667	1	FACETS	0.862	0.75	0.984	0.862	0.75	0.984	CLONAL	1	TRUE	0	0.231673131265667	1		591	593	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16001787	16001787	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	51	313	0	ENST00000268712.3:c.2714C>A	p.Pro905His	p.P905H	ENST00000268712	NM_006311.3	905	cCt/cAt	21/46	0.231673131265667	1	FACETS	0.828	0.705	0.964	0.828	0.705	0.964	CLONAL	1	TRUE	0	0.231673131265667	1		313	470	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603013	48603014	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0046279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	34	223	0	ENST00000342988.3:c.1315dup	p.Asp439GlyfsTer55	p.D439Gfs*55	ENST00000342988	NM_005359.5	438	-/G	11/12	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.231673131265667	2		223	257	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163924	47163931	+	frameshift_variant	Frame_Shift_Del	DEL	ATCATCCA	ATCATCCA	-	novel	NA	P-0046279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	33	284	0	ENST00000409792.3:c.2195_2202del	p.Leu732TyrfsTer6	p.L732Yfs*6	ENST00000409792	NM_014159.6	732	tTGGATGAT/t	3/21	1	2	FACETS	0.69	0.562	0.834	0.69	0.562	0.834	SUBCLONAL	1	TRUE	1	0.231673131265667	2		284	413	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0046280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	673	1049	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.841422554050837	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.855295386908444	2		1049	761	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224295	36224295	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1908	230	716	0	ENST00000222270.7:c.6845C>A	p.Ser2282Tyr	p.S2282Y	ENST00000222270	NM_014727.1	2282	tCc/tAc	28/37	0.855295386908444	8	FACETS	0.897	0.832	0.965			1	CLONAL	1	TRUE	NA	0.855295386908444	8		716	2138	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082406	16082406	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	151	776	0	ENST00000281043.3:c.224del	p.Pro75ArgfsTer56	p.P75Rfs*56	ENST00000281043	NM_005378.4	74	Ccc/cc	2/3	0.855295386908444	3	FACETS	0.576	0.527	0.628	0.288	0.263	0.314	SUBCLONAL	1	TRUE	1	0.855295386908444	3		776	875	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478594	57478594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	68	351	0	ENST00000371085.3:c.266C>T	p.Ala89Val	p.A89V	ENST00000371085	NM_000516.4	89	gCa/gTa	4/13	0.855295386908444	5	FACETS	0.448	0.388	0.512	0.149	0.129	0.171	SUBCLONAL	1	TRUE	2	0.855295386908444	5		351	811	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279546	1279546	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs797046042	NA	P-0046280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	134	891	2	ENST00000310581.5:c.1990G>A	p.Val664Met	p.V664M	ENST00000310581	NM_198253.2	664	Gtg/Atg	5/16	0.537960325624109	3	FACETS	0.568	0.516	0.622	0.284	0.258	0.311	SUBCLONAL	1	TRUE	1	0.855295386908444	3		893	788	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183868	10183868	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs5030810	NA	P-0046281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	110	538	0	ENST00000256474.2:c.337C>T	p.Arg113Ter	p.R113*	ENST00000256474	NM_000551.3	113	Cga/Tga	1/3	1	2	FACETS	0.956	0.858	1	0.956	0.858	1	CLONAL	1	TRUE	1	0.243508590308059	2		538	945	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131687	2131691	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCA	CCTCA	-	novel	NA	P-0046281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	157	803	0	ENST00000219476.3:c.3702_3706del	p.Leu1235GlyfsTer3	p.L1235Gfs*3	ENST00000219476	NM_000548.3	1234	gcCCTCAtg/gctg	31/42	1	2	FACETS	0.99	0.904	1	0.99	0.904	1	CLONAL	1	TRUE	1	0.243508590308059	2		803	1303	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940198	49940198	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1200160517	NA	P-0046281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	138	682	0	ENST00000296474.3:c.845G>A	p.Arg282Gln	p.R282Q	ENST00000296474	NM_002447.2	282	cGg/cAg	1/20	0.243508590308059	1	FACETS	0.914	0.83	1	0.914	0.83	1	CLONAL	1	TRUE	0	0.243508590308059	1		682	1089	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637706	52637706	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	65	279	0	ENST00000394830.3:c.2610del	p.Gln870HisfsTer45	p.Q870Hfs*45	ENST00000394830	NM_018313.4	870	caG/ca	18/30	0.243508590308059	1	FACETS	0.961	0.835	1	0.961	0.835	1	CLONAL	1	TRUE	0	0.243508590308059	1		279	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578226	7578226	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1464727668	NA	P-0046282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	343	767	0	ENST00000269305.4:c.623A>T	p.Asp208Val	p.D208V	ENST00000269305	NM_001126112.2	208	gAc/gTc	6/11	0.684664752032165	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.693015857177704	1		767	583	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215908	41215908	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658672	NA	P-0046282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	327	500	0	ENST00000357654.3:c.5135G>A	p.Trp1712Ter	p.W1712*	ENST00000357654	NM_007294.3	1712	tGg/tAg	17/23	0.668470262652014	2	FACETS	0.869	0.833	0.905	0.869	0.833	0.905	CLONAL	2	TRUE	0	0.693015857177704	2		500	543	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805797	43805797	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	270	672	0	ENST00000372470.3:c.853G>C	p.Val285Leu	p.V285L	ENST00000372470	NM_005373.2	285	Gtg/Ctg	5/12	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.693015857177704	2		672	719	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964421	93964421	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs766582260	NA	P-0046282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	110	491	0	ENST00000369303.4:c.2476A>G	p.Met826Val	p.M826V	ENST00000369303	NM_004440.3	826	Atg/Gtg	14/17	0.260690206305178	1	FACETS	0.348	0.313	0.385	0.348	0.313	0.385	INDETERMINATE	1	TRUE	0	0.693015857177704	1		491	596	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873671	151873671	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046282-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	210	588	0	ENST00000262189.6:c.8867del	p.Pro2956LeufsTer3	p.P2956Lfs*3	ENST00000262189	NM_170606.2	2956	cCt/ct	38/59	0.202704799246894	3	FACETS	1	0.988	1	0.627	0.585	0.67	INDETERMINATE	1	TRUE	1	0.693015857177704	3		588	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0046283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	31	834	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.307930942870715	1	FACETS	0.767	0.625	0.926	0.767	0.625	0.926	CLONAL	1	TRUE	0	0.307930942870715	1		834	222	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828998	72828998	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	21	699	0	ENST00000268489.5:c.7583T>A	p.Ile2528Asn	p.I2528N	ENST00000268489	NM_006885.3	2528	aTc/aAc	9/10	0.107177280202629	0	FACETS	0.497	0.384	0.626			1	INDETERMINATE	1	TRUE	0	0.307930942870715	0		699	190	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627812	37627812	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	59	657	0	ENST00000447079.4:c.1728del	p.Pro577LeufsTer33	p.P577Lfs*33	ENST00000447079	NM_015083.1	576	gTt/gt	2/14	0.307930942870715	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.307930942870715	1		657	260	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0046284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	176	243	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.847585077243737	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.841473880260281	3		243	278	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188188	32188188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370312303	NA	P-0046284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	138	710	0	ENST00000375023.3:c.1153C>T	p.Arg385Cys	p.R385C	ENST00000375023	NM_004557.3	385	Cgc/Tgc	6/30	0.150476145790692	3	FACETS	1	0.986	1	0.675	0.623	0.729	INDETERMINATE	1	TRUE	1	0.841473880260281	3		710	345	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0046284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	114	256	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	0.150476145790692	3	FACETS	1	0.983	1	0.671	0.613	0.729	INDETERMINATE	1	TRUE	1	0.841473880260281	3		256	287	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094442	27094442	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	461	700	0	ENST00000324856.7:c.3151del	p.Leu1051SerfsTer8	p.L1051Sfs*8	ENST00000324856	NM_006015.4	1050	gaC/ga	11/20	0.385781851790195	6	FACETS	0.92	0.886	0.953	1	0.995	1	INDETERMINATE	4	TRUE	3	0.841473880260281	6		700	799	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107084	27107087	+	frameshift_variant	Frame_Shift_Del	DEL	GGCG	GGCG	-	novel	NA	P-0046284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	212	566	0	ENST00000324856.7:c.6698_6701del	p.Arg2233LeufsTer33	p.R2233Lfs*33	ENST00000324856	NM_006015.4	2232	cGGCGg/cg	20/20	0.385781851790195	6	FACETS	0.8	0.744	0.857	0.533	0.496	0.572	INDETERMINATE	2	TRUE	3	0.841473880260281	6		566	845	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253239	133253239	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	18	564	0	ENST00000320574.5:c.802G>A	p.Asp268Asn	p.D268N	ENST00000320574	NM_006231.2	268	Gac/Aac	9/49	0.841473880260281	2	FACETS	0.128	0.096	0.166	0.064	0.048	0.083	SUBCLONAL	1	TRUE	0	0.841473880260281	2		564	335	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	69	69	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.245289575344175	3	FACETS	0.776	0.675	0.886	0.388	0.337	0.443	SUBCLONAL	1	TRUE	1	0.245289575344175	3		69	814	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900168	101900168	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	39	275	0	ENST00000374994.4:c.602T>C	p.Ile201Thr	p.I201T	ENST00000374994	NM_004612.2	201	aTt/aCt	4/9	0.195873460938687	0	FACETS	0.548	0.454	0.652			1	SUBCLONAL	1	TRUE	0	0.245289575344175	0		275	438	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753901	133753901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	109	511	1	ENST00000318560.5:c.1370G>A	p.Arg457His	p.R457H	ENST00000318560	NM_005157.4	457	cGc/cAc	8/11	0.195873460938687	0	FACETS	0.868	0.779	0.962			1	CLONAL	1	TRUE	0	0.245289575344175	0		512	773	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412045	116412045	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0046288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	320	526	0	ENST00000397752.3:c.3028+2T>C		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.260368767080567	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.272452167203376	2		526	1065	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579337	7579338	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGAATG	novel	NA	P-0046288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	162	722	0	ENST00000269305.4:c.343_349dup	p.Gly117AlafsTer34	p.G117Afs*34	ENST00000269305	NM_001126112.2	117	ggg/gCATTCTGgg	4/11	0.272452167203376	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.272452167203376	1		722	1026	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119634894	119634894	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	69	182	0	ENST00000316626.5:c.605G>A	p.Gly202Glu	p.G202E	ENST00000316626		202	gGa/gAa	5/12	0.179521483810921	3	FACETS	1	0.942	1	0.571	0.498	0.649	CLONAL	1	TRUE	1	0.272452167203376	3		182	504	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241659	55241659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1273890779	NA	P-0046288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	84	700	0	ENST00000275493.2:c.2107C>T	p.Leu703Phe	p.L703F	ENST00000275493	NM_005228.3	703	Ctc/Ttc	18/28	0.206219009059683	0	FACETS	0.426	0.375	0.481			1	SUBCLONAL	1	TRUE	0	0.272452167203376	0		700	1052	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0046289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	537	820	1	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.387561953970894	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.387561953970894	2		821	1194	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483366	120483366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	45	297	0	ENST00000256646.2:c.2995G>T	p.Gly999Cys	p.G999C	ENST00000256646	NM_024408.3	999	Ggt/Tgt	19/34	0.387561953970894	6	FACETS	0.494	0.413	0.583			1	SUBCLONAL	1	TRUE	NA	0.387561953970894	6		297	835	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503986	186503986	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0046289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	49	232	0	ENST00000323963.5:c.551A>G	p.Glu184Gly	p.E184G	ENST00000323963		184	gAa/gGa	6/11	0.344614820183178	4	FACETS	0.675	0.571	0.788	0.337	0.285	0.394	SUBCLONAL	1	TRUE	2	0.387561953970894	4		232	520	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456975	149456975	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	86	462	0	ENST00000286301.3:c.753C>A	p.Asp251Glu	p.D251E	ENST00000286301	NM_005211.3	251	gaC/gaA	6/22	0.387561953970894	1	FACETS	0.641	0.568	0.719	0.641	0.568	0.719	SUBCLONAL	1	TRUE	0	0.387561953970894	1		462	558	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47144882	47144882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768604404	NA	P-0046290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	13	500	0	ENST00000409792.3:c.4871C>T	p.Ser1624Phe	p.S1624F	ENST00000409792	NM_014159.6	1624	tCt/tTt	7/21	0.288704132600293	6	FACETS	0.794	0.567	1	0.198	0.141	0.267	CLONAL	1	FALSE	2	0.288704132600293	6		500	179	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161906	47161907	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	11	472	1	ENST00000409792.3:c.4219dup	p.Arg1407LysfsTer8	p.R1407Kfs*8	ENST00000409792	NM_014159.6	1407	agg/aAgg	3/21	0.288704132600293	6	FACETS	0.985	0.685	1	0.246	0.171	0.339	CLONAL	1	FALSE	2	0.288704132600293	6		473	122	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577477	64577576	+	frameshift_variant	Frame_Shift_Del	DEL	CACCAGGTCCGGCTCCTCTCGGCCCAGCTCGGCAGCAAACAGGCGCACCACGTCGTCGATGGAGCGCAGCGGGAACAGCGTCTTCTGGGCGGCCTTCAGC	CACCAGGTCCGGCTCCTCTCGGCCCAGCTCGGCAGCAAACAGGCGCACCACGTCGTCGATGGAGCGCAGCGGGAACAGCGTCTTCTGGGCGGCCTTCAGC	-	novel	NA	P-0046290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	58	766	0	ENST00000312049.6:c.6_105del	p.Leu3SerfsTer83	p.L3Sfs*83	ENST00000312049	NM_130799.2	2	ggGCTGAAGGCCGCCCAGAAGACGCTGTTCCCGCTGCGCTCCATCGACGACGTGGTGCGCCTGTTTGCTGCCGAGCTGGGCCGAGAGGAGCCGGACCTGGTG/gg	2/10	0.288704132600293	4	FACETS	0.766	0.662	0.878	0.511	0.441	0.586	SUBCLONAL	2	FALSE	1	0.288704132600293	4		766	338	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912095	76912095	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	47	239	0	ENST00000373344.5:c.4169del	p.Ser1390MetfsTer100	p.S1390Mfs*100	ENST00000373344	NM_000489.3	1390	aGt/at	13/35	0.288704132600293	2	FACETS	0.868	0.752	0.988			1	CLONAL	3	FALSE	NA	0.288704132600293	2		239	125	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	101	151	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.824	0.744	0.907			1	INDETERMINATE	1	TRUE	NA	0.704540032313656	2		151	348	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0046292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	118	357	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.704540032313656	2		357	322	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947865	178947865	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776932	NA	P-0046292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	21	314	0	ENST00000263967.3:c.2740G>A	p.Gly914Arg	p.G914R	ENST00000263967	NM_006218.2	914	Gga/Aga	19/21	1	2	FACETS	0.211	0.162	0.267	0.211	0.162	0.267	SUBCLONAL	1	TRUE	1	0.704540032313656	2		314	283	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0046292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	376	765	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.948	0.914	0.981	1	0.997	1	CLONAL	2	TRUE	1	0.704540032313656	2		765	563	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052726	42052726	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	26	394	0	ENST00000219905.7:c.7397G>C	p.Arg2466Pro	p.R2466P	ENST00000219905	NM_001164273.1	2466	cGa/cCa	20/24	1	2	FACETS	0.192	0.152	0.239	0.192	0.152	0.239	SUBCLONAL	1	TRUE	1	0.704540032313656	2		394	384	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430001	78430001	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	75	254	0	ENST00000370768.2:c.878G>T	p.Arg293Ile	p.R293I	ENST00000370768	NM_003902.3	293	aGa/aTa	11/20	1	2	FACETS	0.914	0.813	1	0.914	0.813	1	CLONAL	1	TRUE	1	0.704540032313656	2		254	233	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026871	71026871	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	15	277	0	ENST00000318789.4:c.1351G>A	p.Asp451Asn	p.D451N	ENST00000318789	NM_032682.5	451	Gat/Aat	16/21	1	2	FACETS	0.191	0.139	0.253	0.191	0.139	0.253	SUBCLONAL	1	TRUE	1	0.704540032313656	2		277	223	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945109	44945109	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0046292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	74	165	0	ENST00000377967.4:c.3434-1G>A		p.X1145_splice	ENST00000377967	NM_021140.2	1145			1	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.704540032313656	1		165	115	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706949	117706949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779006477	NA	P-0046292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	194	497	1	ENST00000368508.3:c.2201C>T	p.Thr734Met	p.T734M	ENST00000368508	NM_002944.2	734	aCg/aTg	15/43	1	2	FACETS	0.938	0.874	1	0.938	0.874	1	CLONAL	1	TRUE	1	0.704540032313656	2		498	587	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797314	135797314	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	15	286	0	ENST00000298552.3:c.555del	p.Tyr185Ter	p.Y185*	ENST00000298552	NM_001162426.1	185	taC/ta	7/23	0.704540032313656	1	FACETS	0.124	0.091	0.165	0.124	0.091	0.165	SUBCLONAL	1	TRUE	0	0.704540032313656	1		286	222	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023174	48023174	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs63751077	NA	P-0046292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	183	479	0	ENST00000234420.5:c.599C>G	p.Ser200Ter	p.S200*	ENST00000234420	NM_000179.2	200	tCa/tGa	3/10	1	2	FACETS	0.957	0.889	1	0.957	0.889	1	CLONAL	1	TRUE	1	0.704540032313656	2		479	543	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805533	1805533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532318669	NA	P-0046292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	545	847	1	ENST00000260795.2:c.1045C>T	p.His349Tyr	p.H349Y	ENST00000260795		349	Cat/Tat	7/17	1	2	FACETS	0.939	0.91	0.967	1	0.998	1	CLONAL	2	TRUE	1	0.704540032313656	2		848	824	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245515	46245515	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	98	345	0	ENST00000334344.6:c.3609G>A	p.Met1203Ile	p.M1203I	ENST00000334344	NM_152641.2	1203	atG/atA	15/21	1	2	FACETS	0.835	0.753	0.921	0.835	0.753	0.921	CLONAL	1	TRUE	1	0.704540032313656	2		345	333	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245765	46245765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	121	415	1	ENST00000334344.6:c.3859G>A	p.Glu1287Lys	p.E1287K	ENST00000334344	NM_152641.2	1287	Gaa/Aaa	15/21	1	2	FACETS	0.968	0.884	1	0.968	0.884	1	CLONAL	1	TRUE	1	0.704540032313656	2		416	355	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420758	49420758	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs774443846	NA	P-0046292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	268	755	0	ENST00000301067.7:c.14991G>C	p.Gln4997His	p.Q4997H	ENST00000301067	NM_003482.3	4997	caG/caC	48/54	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.704540032313656	2		755	722	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61717803	61717803	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	108	426	0	ENST00000401558.2:c.1996G>C	p.Asp666His	p.D666H	ENST00000401558	NM_003400.3	666	Gat/Cat	17/25	1	2	FACETS	0.761	0.688	0.836	0.761	0.688	0.836	SUBCLONAL	1	TRUE	1	0.704540032313656	2		426	403	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721108	61721108	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	35	413	0	ENST00000401558.2:c.1166C>G	p.Ser389Cys	p.S389C	ENST00000401558	NM_003400.3	389	tCt/tGt	12/25	1	2	FACETS	0.235	0.193	0.283	0.235	0.193	0.283	SUBCLONAL	1	TRUE	1	0.704540032313656	2		413	422	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651994	36651995	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	189	951	0	ENST00000244741.5:c.116_117insA	p.Cys41LeufsTer7	p.C41Lfs*7	ENST00000244741	NM_000389.4	39	gcg/gcAg	2/3	1	2	FACETS	0.509	0.469	0.549	0.509	0.469	0.549	SUBCLONAL	1	TRUE	1	0.704540032313656	2		951	1055	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652154	36652155	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	301	942	0	ENST00000244741.5:c.277dup	p.Arg93LysfsTer36	p.R93Kfs*36	ENST00000244741	NM_000389.4	92	-/A	2/3	1	2	FACETS	0.977	0.923	1	0.977	0.923	1	CLONAL	1	TRUE	1	0.704540032313656	2		942	875	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511344	157511344	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	24	408	0	ENST00000346085.5:c.3862G>A	p.Val1288Met	p.V1288M	ENST00000346085	NM_020732.3	1288	Gtg/Atg	15/20	1	2	FACETS	0.176	0.138	0.221	0.176	0.138	0.221	SUBCLONAL	1	TRUE	1	0.704540032313656	2		408	387	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133922	38133922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	267	765	0	ENST00000317025.8:c.3964G>A	p.Asp1322Asn	p.D1322N	ENST00000317025	NM_023034.1	1322	Gat/Aat	23/24	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.704540032313656	2		765	753	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0046293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	11	391	0	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	0.272121446192471	0	FACETS	0.082	0.056	0.114			1	INDETERMINATE	1	FALSE	0	0.463465124357646	0		391	311	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913338	NA	P-0046293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	113	231	0	ENST00000288602.6:c.1781A>C	p.Asp594Ala	p.D594A	ENST00000288602	NM_004333.4	594	gAt/gCt	15/18	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.463465124357646	2		231	382	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398255	25398255	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913236	NA	P-0046293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	137	369	1	ENST00000311936.3:c.64C>A	p.Gln22Lys	p.Q22K	ENST00000311936	NM_004985.3	22	Cag/Aag	2/5	0.170442141915532	4	FACETS	0.816	0.746	0.889	0.816	0.746	0.889	INDETERMINATE	2	FALSE	2	0.463465124357646	4		370	530	SUCCESS
APC	324	MSKCC	GRCh37	5	112175530	112175530	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	100	350	1	ENST00000257430.4:c.4240del	p.Val1414Ter	p.V1414*	ENST00000257430	NM_000038.5	1413	atG/at	16/16	0.137072462712029	4	FACETS	0.831	0.748	0.917	0.831	0.748	0.917	INDETERMINATE	2	FALSE	2	0.463465124357646	4		351	380	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158402	26158402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778040224	NA	P-0046293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	296	774	1	ENST00000289316.2:c.5C>T	p.Pro2Leu	p.P2L	ENST00000289316	NM_138720.2	2	cCt/cTt	1/2	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.463465124357646	2		775	1252	SUCCESS
APC	324	MSKCC	GRCh37	5	112173374	112173374	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	59	178	0	ENST00000257430.4:c.2083C>T	p.Gln695Ter	p.Q695*	ENST00000257430	NM_000038.5	695	Cag/Tag	16/16	0.137072462712029	4	FACETS	1	0.968	1	0.714	0.62	0.814	INDETERMINATE	1	FALSE	2	0.463465124357646	4		178	261	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125525140	125525140	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	91	306	0	ENST00000428830.2:c.1356G>C	p.Lys452Asn	p.K452N	ENST00000428830	NM_001114121.2	452	aaG/aaC	13/14	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.463465124357646	2		306	342	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748660	43748661	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	185	708	0	ENST00000382044.4:c.2145dup	p.Glu716ArgfsTer9	p.E716Rfs*9	ENST00000382044	NM_001141980.1	715	-/A	12/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.463465124357646	2		708	688	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371711	45371711	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	12	274	0	ENST00000262160.6:c.1280G>A	p.Arg427Gln	p.R427Q	ENST00000262160	NM_005901.5	427	cGa/cAa	10/11	0.463465124357646	1	FACETS	0.182	0.127	0.248	0.182	0.127	0.248	SUBCLONAL	1	FALSE	0	0.463465124357646	1		274	219	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395727	45395727	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	83	304	0	ENST00000262160.6:c.407A>T	p.Asp136Val	p.D136V	ENST00000262160	NM_005901.5	136	gAt/gTt	4/11	0.463465124357646	1	FACETS	0.936	0.835	1	0.936	0.835	1	CLONAL	1	FALSE	0	0.463465124357646	1		304	294	SUCCESS
CALR	811	MSKCC	GRCh37	19	13049548	13049548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	346	822	1	ENST00000316448.5:c.55C>T	p.Pro19Ser	p.P19S	ENST00000316448	NM_004343.3	19	Cct/Tct	1/9	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.463465124357646	2		823	1231	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028097	69028097	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	112	434	2	ENST00000288368.4:c.3256T>A	p.Cys1086Ser	p.C1086S	ENST00000288368	NM_024870.2	1086	Tgt/Agt	26/40	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.463465124357646	2		436	406	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0046294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	67	288	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.19	2		288	526	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0046294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	30	243	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.7	0.564	0.856	0.7	0.564	0.856	SUBCLONAL	1	TRUE	1	0.19	2		243	451	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0046294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	35	459	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	1	2	FACETS	0.684	0.559	0.823	0.684	0.559	0.823	SUBCLONAL	1	TRUE	1	0.19	2		459	539	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112919929	112919929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1214510641	NA	P-0046295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	19	202	0	ENST00000351677.2:c.1144G>A	p.Val382Ile	p.V382I	ENST00000351677	NM_002834.3	382	Gtc/Atc	10/16	1	2	FACETS	0.536	0.406	0.689	0.536	0.406	0.689	SUBCLONAL	1	FALSE	1	0.19021001102791	2		202	373	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0046295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	17	214	0	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			0.19021001102791	1	FACETS	0.59	0.44	0.768	0.59	0.44	0.768	SUBCLONAL	1	FALSE	0	0.19021001102791	1		214	274	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579345	7579346	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	126	801	0	ENST00000269305.4:c.341dup	p.Leu114PhefsTer35	p.L114Ffs*35	ENST00000269305	NM_001126112.2	114	ttg/ttTg	4/11	0.19021001102791	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	0	0.19021001102791	1		801	1089	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410611	32410611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749266841	NA	P-0046295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	79	380	0	ENST00000332351.3:c.1547C>T	p.Ala516Val	p.A516V	ENST00000332351	NM_024426.4	516	gCg/gTg	10/10	0.19021001102791	1	FACETS	0.949	0.834	1	0.949	0.834	1	CLONAL	1	FALSE	0	0.19021001102791	1		380	792	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070880	30070880	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74315504	NA	P-0046295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	90	596	0	ENST00000338641.4:c.1396C>T	p.Arg466Ter	p.R466*	ENST00000338641	NM_000268.3	466	Cga/Tga	13/16	0.19021001102791	1	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	FALSE	0	0.19021001102791	1		596	843	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243776999	243776999	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	108	456	0	ENST00000263826.5:c.670G>A	p.Val224Met	p.V224M	ENST00000263826	NM_005465.4	224	Gtg/Atg	7/13	0.153595119322976	2	FACETS	0.824	0.74	0.913	0.824	0.74	0.913	CLONAL	2	FALSE	0	0.19021001102791	2		456	689	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640577	3640577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200842643	NA	P-0046295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1215	66	949	1	ENST00000294008.3:c.3062G>A	p.Arg1021His	p.R1021H	ENST00000294008	NM_032444.2	1021	cGc/cAc	12/15	0.19021001102791	1	FACETS	0.49	0.424	0.563	0.49	0.424	0.563	SUBCLONAL	1	FALSE	0	0.19021001102791	1		950	1281	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551020	41551020	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	77	334	0	ENST00000263253.7:c.3164G>A	p.Arg1055Gln	p.R1055Q	ENST00000263253	NM_001429.3	1055	cGa/cAa	17/31	0.19021001102791	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	FALSE	0	0.19021001102791	1		334	681	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242478	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAG	AATTAAGAGAAG	CAC	rs727503015	NA	P-0046296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	121	309	0	ENST00000275493.2:c.2237_2248delinsCAC	p.Glu746_Ala750delinsAlaPro	p.E746_A750delinsAP	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGca/gCACca	19/28	1	2	FACETS	0.9	0.816	0.988	0.9	0.816	0.988	CLONAL	1	TRUE	1	0.471883354010763	2		309	570	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356394	70356412	+	frameshift_variant	Frame_Shift_Del	DEL	TCCAGAGCCCCCCAAAACT	TCCAGAGCCCCCCAAAACT	CGGCTCCAG	novel	NA	P-0046296-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	160	679	0	ENST00000374080.3:c.5289_5307delinsCGGCTCCAG	p.Pro1764GlyfsTer48	p.P1764Gfs*48	ENST00000374080		1763	gcTCCAGAGCCCCCCAAAACT/gcCGGCTCCAG	37/45	1	2	FACETS	0.859	0.789	0.933	0.859	0.789	0.933	CLONAL	1	TRUE	1	0.471883354010763	2		679	789	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687049	37687049	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs151051059	NA	P-0046297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	323	523	0	ENST00000447079.4:c.3953A>G	p.His1318Arg	p.H1318R	ENST00000447079	NM_015083.1	1318	cAt/cGt	14/14	1	2	FACETS	0.953	0.906	1	0.953	0.906	1	CLONAL	1	TRUE	1	0.936142076411449	2		523	724	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs1023835002	NA	P-0046298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	21	506	0	ENST00000558401.1:c.1A>G	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Gtg	1/4	0.384111961299834	2	FACETS	0.268	0.206	0.341	0.134	0.103	0.171	SUBCLONAL	1	TRUE	0	0.384111961299834	2		506	408	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	227	591	2	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.384111961299834	2	FACETS	0.97	0.91	1	0.97	0.91	1	CLONAL	2	TRUE	0	0.384111961299834	2		593	609	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446138	49446138	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0046298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	182	870	0	ENST00000301067.7:c.1328del	p.Pro443HisfsTer487	p.P443Hfs*487	ENST00000301067	NM_003482.3	443	cCa/ca	10/54	0.116211002953224	6	FACETS	0.812	0.748	0.878	0.541	0.499	0.585	INDETERMINATE	2	TRUE	3	0.384111961299834	6		870	1032	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416220	29416220	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	45	580	1	ENST00000389048.3:c.4733C>A	p.Pro1578His	p.P1578H	ENST00000389048	NM_004304.4	1578	cCt/cAt	29/29	0.116211002953224	6	FACETS	0.505	0.423	0.597	0.168	0.141	0.199	INDETERMINATE	1	TRUE	3	0.384111961299834	6		581	820	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129396	152129396	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	28	558	0	ENST00000206249.3:c.349C>G	p.Leu117Val	p.L117V	ENST00000206249	NM_000125.3	117	Ctg/Gtg	1/8	0.384111961299834	2	FACETS	0.275	0.219	0.339	0.137	0.109	0.17	SUBCLONAL	1	TRUE	0	0.384111961299834	2		558	531	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239915	53239934	+	frameshift_variant	Frame_Shift_Del	DEL	GAGAAGACCATGCCCACGTA	GAGAAGACCATGCCCACGTA	-	novel	NA	P-0046298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	147	615	0	ENST00000375401.3:c.1507_1526del	p.Tyr503SerfsTer7	p.Y503Sfs*7	ENST00000375401	NM_004187.3	503	TACGTGGGCATGGTCTTCTCa/a	11/26	0.384111961299834	2	FACETS	1	0.979	1	0.607	0.556	0.661	CLONAL	1	TRUE	0	0.384111961299834	2		615	630	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	8	69	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.167269797344826	2	FACETS	1	0.809	1	0.682	0.459	0.941	INDETERMINATE	1	TRUE	0	0.390941434907028	2		69	30	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0046299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	21	811	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	0.37434072613073	1	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	0	0.390941434907028	1		811	77	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971209	21971209	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1554654224	NA	P-0046299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	12	385	0	ENST00000304494.5:c.151-2A>G		p.X51_splice	ENST00000304494	NM_000077.4	51			0.108702570388441	0	FACETS	0.959	0.703	1			1	INDETERMINATE	1	TRUE	0	0.390941434907028	0		385	39	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0046300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	53	518	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.804	0.686	0.932	0.804	0.686	0.932	CLONAL	1	TRUE	1	0.288631223165179	2		518	457	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374828	149374828	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	66	325	0	ENST00000360632.3:c.266C>G	p.Ser89Trp	p.S89W	ENST00000360632	NM_015472.4	89	tCg/tGg	2/7	1	2	FACETS	0.967	0.841	1	0.967	0.841	1	CLONAL	1	TRUE	1	0.288631223165179	2		325	473	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248679	59248679	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	176	779	0	ENST00000371222.2:c.64G>T	p.Glu22Ter	p.E22*	ENST00000371222	NM_002228.3	22	Gag/Tag	1/1	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.288631223165179	2		779	1218	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056050	26056050	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	103	330	0	ENST00000343677.2:c.607G>C	p.Val203Leu	p.V203L	ENST00000343677	NM_005319.3	203	Gtc/Ctc	1/1	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.288631223165179	2		330	640	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502190	157502190	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	63	496	0	ENST00000346085.5:c.3223C>G	p.Arg1075Gly	p.R1075G	ENST00000346085	NM_020732.3	1075	Cga/Gga	12/20	1	2	FACETS	0.575	0.496	0.661	0.575	0.496	0.661	SUBCLONAL	1	TRUE	1	0.288631223165179	2		496	759	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829040	128829042	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	rs570242755	NA	P-0046314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	11	6	0	ENST00000249373.3:c.67_69del	p.Leu23del	p.L23del	ENST00000249373	NM_005631.4	16	ggGCTg/ggg	1/12	0.690680879478627	5	FACETS	0.302	0.208	0.418	0.101	0.069	0.14	SUBCLONAL	1	TRUE	2	0.690680879478627	5		6	215	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491332	2491333	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	396	351	0	ENST00000355716.4:c.377dup	p.Cys127LeufsTer107	p.C127Lfs*107	ENST00000355716	NM_003820.2	125	-/T	4/8	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.690680879478627	2		351	870	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058788	42058790	+	inframe_deletion	In_Frame_Del	DEL	ACT	ACT	-	novel	NA	P-0046314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	49	69	0	ENST00000219905.7:c.8509_8511del	p.Leu2837del	p.L2837del	ENST00000219905	NM_001164273.1	2836	caACTa/caa	24/24	0.244131759839065	1	FACETS	0.999	0.883	1	0.999	0.883	1	INDETERMINATE	1	TRUE	0	0.690680879478627	1		69	93	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948229	31948230	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0046314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	191	186	0	ENST00000375333.2:c.818dup	p.His273GlnfsTer32	p.H273Qfs*32	ENST00000375333	NM_032454.1	273	cat/cAat	6/8	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.690680879478627	2		186	410	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92355103	92355103	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0046314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	112	54	0	ENST00000265734.4:c.374T>G	p.Met125Arg	p.M125R	ENST00000265734	NM_001259.6	125	aTg/aGg	4/8	0.690680879478627	5	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	2	0.690680879478627	5		54	197	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859457	151859457	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	253	155	0	ENST00000262189.6:c.11205del	p.Lys3735AsnfsTer10	p.K3735Nfs*10	ENST00000262189	NM_170606.2	3735	aaA/aa	43/59	0.690680879478627	5	FACETS	0.951	0.9	1	0.951	0.9	1	CLONAL	3	TRUE	2	0.690680879478627	5		155	523	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244091	153244091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	10	387	1	ENST00000281708.4:c.2066G>A	p.Arg689Gln	p.R689Q	ENST00000281708	NM_033632.3	689	cGg/cAg	12/12	0.170601290928387	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		388	391	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109311998	109311998	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	21	355	0	ENST00000436639.2:c.1274G>A	p.Arg425His	p.R425H	ENST00000436639	NM_014454.2	425	cGc/cAc	8/10	0.220700700021848	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		355	190	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	112	151	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		151	283	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs121913468	NA	P-0046317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	17	414	1	ENST00000269571.5:c.2305G>T	p.Asp769Tyr	p.D769Y	ENST00000269571		769	Gac/Tac	19/27	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		415	413	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882019	NA	P-0046320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	58	173	0	ENST00000269305.4:c.455dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	ccg/ccCg	5/11	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.13	2		173	827	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637423	47637423	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	27	482	0	ENST00000233146.2:c.557A>T	p.Asn186Ile	p.N186I	ENST00000233146	NM_000251.2	186	aAt/aTt	3/16	1	2	FACETS	0.802	0.637	0.992	0.802	0.637	0.992	CLONAL	1	TRUE	1	0.13	2		482	518	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0046321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	76	69	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.243622923536881	3	FACETS	0.956	0.844	1	0.637	0.563	0.717	CLONAL	2	TRUE	0	0.243622923536881	3		69	366	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0046321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	143	480	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.186435971613989	3	FACETS	0.844	0.774	0.917	0.844	0.774	0.917	CLONAL	3	TRUE	0	0.243622923536881	3		480	520	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655318	45655318	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	60	932	1	ENST00000407780.3:c.534C>A	p.Ser178Arg	p.S178R	ENST00000407780	NM_001283052.1	178	agC/agA	4/7	0.237140692021873	2	FACETS	0.889	0.766	1	0.445	0.383	0.512	CLONAL	1	TRUE	0	0.243622923536881	2		933	554	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058568	69058568	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046321-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	36	502	0	ENST00000288368.4:c.4212T>A	p.His1404Gln	p.H1404Q	ENST00000288368	NM_024870.2	1404	caT/caA	34/40	1	2	FACETS	0.912	0.752	1	0.912	0.752	1	CLONAL	1	TRUE	1	0.243622923536881	2		502	324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579315	7579316	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1267047192	NA	P-0046322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	142	592	0	ENST00000269305.4:c.371dup	p.Cys124TrpfsTer25	p.C124Wfs*25	ENST00000269305	NM_001126112.2	124	tgc/tgGc	4/11	0.224879967504523	2	FACETS	0.961	0.878	1	0.961	0.878	1	CLONAL	2	TRUE	0	0.229121928945398	2		592	645	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678541	88678541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145157285	NA	P-0046322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	63	390	0	ENST00000360948.2:c.995C>T	p.Thr332Met	p.T332M	ENST00000360948	NM_001012338.2	332	aCg/aTg	9/19	0.171574518194026	4	FACETS	0.768	0.666	0.878	0.768	0.666	0.878	SUBCLONAL	2	TRUE	2	0.229121928945398	4		390	440	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0046326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	316	324	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.42562550112798	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.442551780351896	3		324	800	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518099	8518099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764400127	NA	P-0046326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	88	450	0	ENST00000356435.5:c.1292C>T	p.Ser431Leu	p.S431L	ENST00000356435		431	tCg/tTg	10/35	0.203547106996378	2	FACETS	0.644	0.571	0.721	0.322	0.285	0.361	INDETERMINATE	1	TRUE	0	0.442551780351896	2		450	618	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961104	55961104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371148535	NA	P-0046326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	400	599	0	ENST00000263923.4:c.2836C>T	p.Arg946Cys	p.R946C	ENST00000263923	NM_002253.2	946	Cgt/Tgt	21/30	0.442551780351896	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.442551780351896	2		599	896	SUCCESS
APC	324	MSKCC	GRCh37	5	112175548	112175548	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0046326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	121	290	0	ENST00000257430.4:c.4260del	p.Ser1421ValfsTer52	p.S1421Vfs*52	ENST00000257430	NM_000038.5	1419	agC/ag	16/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.442551780351896	2		290	439	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217842	2217842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046326-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	168	638	0	ENST00000398665.3:c.2616C>A	p.Ser872Arg	p.S872R	ENST00000398665	NM_032482.2	872	agC/agA	22/28	0.436917576981036	3	FACETS	0.925	0.85	1	0.463	0.425	0.502	CLONAL	1	TRUE	1	0.442551780351896	3		638	1002	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0046327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	243	549	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.343599958522302	2	FACETS	0.812	0.761	0.863	0.812	0.761	0.863	CLONAL	2	TRUE	0	0.406259406292851	2		549	737	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114905847	114905847	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	246	567	0	ENST00000543371.1:c.866C>G	p.Ser289Cys	p.S289C	ENST00000543371	NM_001198531.1	289	tCc/tGc	8/14	0.343599958522302	2	FACETS	0.898	0.845	0.953	0.898	0.845	0.953	CLONAL	2	TRUE	0	0.406259406292851	2		567	674	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354401	40354401	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	211	1036	0	ENST00000293328.3:c.2194C>G	p.Pro732Ala	p.P732A	ENST00000293328	NM_012448.3	732	Cca/Gca	18/19	0.343599958522302	2	FACETS	0.969	0.899	1	0.484	0.449	0.521	CLONAL	1	TRUE	0	0.406259406292851	2		1036	1072	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444589	187444589	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0046327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	147	680	0	ENST00000232014.4:c.1638C>G	p.Tyr546Ter	p.Y546*	ENST00000232014	NM_001130845.1	546	taC/taG	7/10	0.343159671904075	3	FACETS	0.846	0.771	0.925	0.423	0.385	0.463	CLONAL	1	TRUE	1	0.406259406292851	3		680	1029	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106182986	106182986	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	59	264	0	ENST00000380013.4:c.4025C>G	p.Pro1342Arg	p.P1342R	ENST00000380013	NM_001127208.2	1342	cCt/cGt	8/11	0.333172133225349	2	FACETS	0.764	0.66	0.877	0.382	0.33	0.439	SUBCLONAL	1	TRUE	0	0.406259406292851	2		264	380	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631339	117631339	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	86	396	0	ENST00000368508.3:c.6339T>A	p.Asp2113Glu	p.D2113E	ENST00000368508	NM_002944.2	2113	gaT/gaA	40/43	0.159715532862531	3	FACETS	0.865	0.766	0.97	0.288	0.255	0.324	INDETERMINATE	1	TRUE	0	0.406259406292851	3		396	589	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397668	139397668	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	98	688	0	ENST00000277541.6:c.5133C>A	p.Ser1711Arg	p.S1711R	ENST00000277541	NM_017617.3	1711	agC/agA	27/34	0.343599958522302	2	FACETS	0.688	0.614	0.767	0.344	0.307	0.384	SUBCLONAL	1	TRUE	0	0.406259406292851	2		688	701	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050819	49050876	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAATTCTGTAATTTGTAGACTTCTGAGAAGTTCCAGAAAATAAATCAGATGGTATGTA	GAATTCTGTAATTTGTAGACTTCTGAGAAGTTCCAGAAAATAAATCAGATGGTATGTA	TCATTTGAGC	novel	NA	P-0046327-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	41	335	1	ENST00000267163.4:c.2521-18_2560delinsTCATTTGAGC		p.X841_splice	ENST00000267163	NM_000321.2	841		25/27	0.315053129763463	1	FACETS	0.437	0.365	0.517	0.437	0.365	0.517	SUBCLONAL	1	TRUE	0	0.406259406292851	1		336	368	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71161705	71161705	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046328-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	44	315	0	ENST00000318789.4:c.264C>G	p.Asp88Glu	p.D88E	ENST00000318789	NM_032682.5	88	gaC/gaG	7/21	1	2	FACETS	0.316	0.265	0.373	0.316	0.265	0.373	SUBCLONAL	1	TRUE	1	0.587844184314722	2		315	473	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0046329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	17	213	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.929	0.699	1	0.929	0.699	1	CLONAL	1	FALSE	1	0.261529071283255	2		213	140	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937423	178937423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046329-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	64	189	0	ENST00000263967.3:c.1811G>A	p.Cys604Tyr	p.C604Y	ENST00000263967	NM_006218.2	604	tGt/tAt	12/21	1	2	FACETS	1	0.957	1	1	0.984	1	CLONAL	2	FALSE	1	0.261529071283255	2		189	204	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913255	NA	P-0003533-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	14	563	1	ENST00000369535.4:c.183A>T	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caT	3/7	1	2	FACETS	0.115	0.082	0.155	0.115	0.082	0.155	SUBCLONAL	1	TRUE	1	0.357661817835512	2		564	683	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775907	9775907	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003533-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	250	334	22	ENST00000377346.4:c.371G>A	p.Gly124Asp	p.G124D	ENST00000377346	NM_005026.3	124	gGc/gAc	5/24	0.357661817835512	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	0	0.357661817835512	2		356	695	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578499	7578499	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003533-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	316	486	16	ENST00000269305.4:c.431del	p.Gln144ArgfsTer26	p.Q144Rfs*26	ENST00000269305	NM_001126112.2	144	cAg/cg	5/11	1	2	FACETS	0.953	0.902	1	1	0.996	1	CLONAL	2	TRUE	1	0.357661817835512	2		502	927	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0005964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	303	374	0	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.847742235870428	2		374	683	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007475	62007475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1389559363	NA	P-0005964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	57	472	0	ENST00000392795.3:c.392C>T	p.Ser131Leu	p.S131L	ENST00000392795	NM_001039933.1	131	tCg/tTg	3/6	1	2	FACETS	0.189	0.162	0.219	0.189	0.162	0.219	SUBCLONAL	1	TRUE	1	0.847742235870428	2		472	711	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0006249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	189	278	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.355674976816216	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.355674976816216	2		278	433	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522416	176522416	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519792	NA	P-0006249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	300	884	0	ENST00000292408.4:c.1605C>G	p.Asn535Lys	p.N535K	ENST00000292408	NM_213647.1	535	aaC/aaG	12/18	0.355674976816216	3	FACETS	0.955	0.901	1	0.955	0.901	1	CLONAL	2	TRUE	1	0.355674976816216	3		884	1040	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188989	11188989	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	99	473	0	ENST00000361445.4:c.5734G>C	p.Asp1912His	p.D1912H	ENST00000361445	NM_004958.3	1912	Gat/Cat	41/58	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.355674976816216	2		473	552	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748169	72748169	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	78	342	0	ENST00000357731.5:c.9G>C	p.Met3Ile	p.M3I	ENST00000357731	NM_173808.2	3	atG/atC	1/7	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.355674976816216	2		342	423	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852540	63852540	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	100	489	0	ENST00000279873.7:c.3318G>C	p.Leu1106Phe	p.L1106F	ENST00000279873	NM_032199.2	1106	ttG/ttC	10/10	1	2	FACETS	0.917	0.821	1	0.917	0.821	1	CLONAL	1	TRUE	1	0.355674976816216	2		489	613	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1040472	1040472	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	116	724	0	ENST00000358495.3:c.100G>T	p.Glu34Ter	p.E34*	ENST00000358495	NM_134424.2	34	Gaa/Taa	3/12	0.12539779465409	3	FACETS	0.831	0.748	0.919			1	INDETERMINATE	1	TRUE	NA	0.355674976816216	3		724	924	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491373	18491373	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	176	334	0	ENST00000266497.5:c.1286A>G	p.Asn429Ser	p.N429S	ENST00000266497		429	aAt/aGt	8/31	0.355674976816216	3	FACETS	0.854	0.795	0.914	1	0.987	1	CLONAL	3	TRUE	1	0.355674976816216	3		334	455	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859039	57859039	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0006249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	163	779	0	ENST00000228682.2:c.534+1G>A		p.X178_splice	ENST00000228682	NM_005269.2	178			0.355674976816216	3	FACETS	0.998	0.914	1	0.499	0.457	0.543	CLONAL	1	TRUE	1	0.355674976816216	3		779	1082	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061240	38061240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	68	743	0	ENST00000250448.2:c.749C>T	p.Ser250Phe	p.S250F	ENST00000250448	NM_004496.3	250	tCc/tTc	2/2	0.354599985267196	3	FACETS	0.636	0.553	0.726	0.318	0.276	0.363	SUBCLONAL	1	TRUE	1	0.355674976816216	3		743	708	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019480	42019480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	95	670	0	ENST00000219905.7:c.3533C>T	p.Ser1178Phe	p.S1178F	ENST00000219905	NM_001164273.1	1178	tCt/tTt	10/24	1	2	FACETS	0.715	0.637	0.799	0.715	0.637	0.799	SUBCLONAL	1	TRUE	1	0.355674976816216	2		670	747	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830754	3830754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	70	440	0	ENST00000262367.5:c.1802G>A	p.Arg601Gln	p.R601Q	ENST00000262367	NM_004380.2	601	cGg/cAg	8/31	0.214417780933205	4	FACETS	0.768	0.669	0.875	0.384	0.334	0.438	SUBCLONAL	1	TRUE	2	0.355674976816216	4		440	695	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229569	5229569	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	52	172	0	ENST00000357368.4:c.2282T>A	p.Val761Glu	p.V761E	ENST00000357368	NM_002850.3	761	gTg/gAg	15/38	0.355674976816216	3	FACETS	1	0.919	1	0.555	0.476	0.642	CLONAL	1	TRUE	1	0.355674976816216	3		172	310	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233621	233621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	44	367	0	ENST00000264932.6:c.925G>A	p.Glu309Lys	p.E309K	ENST00000264932	NM_004168.2	309	Gaa/Aaa	8/15	0.355674976816216	3	FACETS	0.653	0.548	0.769	0.327	0.274	0.385	SUBCLONAL	1	TRUE	1	0.355674976816216	3		367	446	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177011	56177014	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	-	novel	NA	P-0006249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	124	329	0	ENST00000399503.3:c.2286_2289del	p.Arg763CysfsTer35	p.R763Cfs*35	ENST00000399503	NM_005921.1	761	ATAGat/at	13/20	0.355674976816216	3	FACETS	0.877	0.799	0.959	0.877	0.799	0.959	CLONAL	2	TRUE	1	0.355674976816216	3		329	468	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184093	56184094	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	AC	novel	NA	P-0006249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	68	405	0	ENST00000399503.3:c.4298_4299insAC	p.Trp1433Ter	p.W1433*	ENST00000399503	NM_005921.1	1433	tgg/tgACg	19/20	0.355674976816216	3	FACETS	0.927	0.808	1	0.463	0.404	0.527	CLONAL	1	TRUE	1	0.355674976816216	3		405	486	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524347	176524347	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	106	934	0	ENST00000292408.4:c.2208C>G	p.Phe736Leu	p.F736L	ENST00000292408	NM_213647.1	736	ttC/ttG	17/18	0.355674976816216	3	FACETS	0.648	0.58	0.721	0.324	0.29	0.361	SUBCLONAL	1	TRUE	1	0.355674976816216	3		934	1083	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983017	149983017	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757876116	NA	P-0006249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	189	580	0	ENST00000253339.5:c.3241C>T	p.Arg1081Ter	p.R1081*	ENST00000253339		1081	Cga/Tga	7/7	0.354599985267196	3	FACETS	0.963	0.894	1	0.963	0.894	1	CLONAL	2	TRUE	1	0.355674976816216	3		580	650	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505458	157505458	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554231838	NA	P-0006249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	80	507	0	ENST00000346085.5:c.3439C>T	p.Gln1147Ter	p.Q1147*	ENST00000346085	NM_020732.3	1147	Cag/Tag	13/20	0.354599985267196	3	FACETS	0.68	0.598	0.769	0.34	0.299	0.385	SUBCLONAL	1	TRUE	1	0.355674976816216	3		507	779	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499771	8499771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748340591	NA	P-0006249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	124	610	1	ENST00000356435.5:c.2198G>A	p.Arg733His	p.R733H	ENST00000356435		733	cGc/cAc	14/35	1	2	FACETS	0.99	0.897	1	0.99	0.897	1	CLONAL	1	TRUE	1	0.355674976816216	2		611	704	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637008	93637008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201479078	NA	P-0006249-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	59	539	0	ENST00000375746.1:c.1058C>T	p.Ala353Val	p.A353V	ENST00000375746	NM_001174167.1	353	gCg/gTg	9/14	1	2	FACETS	0.559	0.48	0.644	0.559	0.48	0.644	SUBCLONAL	1	TRUE	1	0.355674976816216	2		539	594	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746017	162746017	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008530-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	44	354	0	ENST00000367921.3:c.2140C>T	p.Arg714Ter	p.R714*	ENST00000367921	NM_006182.2	714	Cga/Tga	16/18	1	2	FACETS	0.65	0.543	0.769	0.65	0.543	0.769	SUBCLONAL	1	TRUE	1	0.16	2		354	846	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0009399-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	147	348	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	0.507288043144759	6	FACETS	0.809	0.743	0.878	0.54	0.495	0.586	INDETERMINATE	2	TRUE	3	0.951851433129038	6		348	554	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150022928	150022928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009399-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	153	384	0	ENST00000253339.5:c.335C>T	p.Ala112Val	p.A112V	ENST00000253339		112	gCt/gTt	1/7	0.951851433129038	3	FACETS	1	0.945	1	0.515	0.475	0.556	CLONAL	1	TRUE	1	0.951851433129038	3		384	461	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835662	68835662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009399-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	237	701	0	ENST00000261769.5:c.253G>T	p.Val85Phe	p.V85F	ENST00000261769	NM_004360.3	85	Gtc/Ttc	3/16	0.951851433129038	3	FACETS	1	0.981	1	0.555	0.521	0.59	CLONAL	1	TRUE	1	0.951851433129038	3		701	662	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579378	7579378	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0009399-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	538	945	0	ENST00000269305.4:c.309C>G	p.Tyr103Ter	p.Y103*	ENST00000269305	NM_001126112.2	103	taC/taG	4/11	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.951851433129038	2		945	560	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0009538-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	192	262	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.717202971574854	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	4	TRUE	0	0.717202971574854	4		262	227	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009538-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	33	425	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.717202971574854	2		425	85	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0009538-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	130	734	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	0.691902705967049	2	FACETS	0.996	0.939	1	0.996	0.939	1	CLONAL	2	TRUE	0	0.717202971574854	2		734	182	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729154	66729154	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519731	NA	P-0009538-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	44	548	0	ENST00000307102.5:c.362G>C	p.Cys121Ser	p.C121S	ENST00000307102	NM_002755.3	121	tGc/tCc	3/11	0.703549858048306	3	FACETS	0.556	0.468	0.651	0.278	0.234	0.326	SUBCLONAL	1	TRUE	1	0.717202971574854	3		548	300	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759841	133759841	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372281632	NA	P-0009538-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	97	830	0	ENST00000318560.5:c.2164G>A	p.Val722Ile	p.V722I	ENST00000318560	NM_005157.4	722	Gtt/Att	11/11	0.672560730506189	3	FACETS	1	0.922	1	0.515	0.463	0.569	CLONAL	1	TRUE	1	0.717202971574854	3		830	357	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858202	9858202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009538-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	82	463	0	ENST00000330684.3:c.3199C>T	p.Arg1067Trp	p.R1067W	ENST00000330684	NM_001134407.1	1067	Cgg/Tgg	13/13	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.717202971574854	2		463	192	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024497	16024497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009538-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	118	470	0	ENST00000268712.3:c.1721C>T	p.Thr574Ile	p.T574I	ENST00000268712	NM_006311.3	574	aCt/aTt	16/46	0.691902705967049	2	FACETS	0.979	0.919	1	0.979	0.919	1	CLONAL	2	TRUE	0	0.717202971574854	2		470	168	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302860	15302860	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009538-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	84	1069	1	ENST00000263388.2:c.590C>T	p.Pro197Leu	p.P197L	ENST00000263388	NM_000435.2	197	cCc/cTc	4/33	0.675117541143973	3	FACETS	0.902	0.803	1	0.451	0.401	0.503	CLONAL	1	TRUE	1	0.717202971574854	3		1070	353	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217305	123217305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009538-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	54	213	0	ENST00000218089.9:c.2959C>T	p.Pro987Ser	p.P987S	ENST00000218089	NM_001042749.1	987	Ccg/Tcg	29/35	1	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.717202971574854	1		213	79	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165509	47165509	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009538-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	11	486	0	ENST00000409792.3:c.617C>A	p.Ala206Glu	p.A206E	ENST00000409792	NM_014159.6	206	gCa/gAa	3/21	0.710621339292362	3	FACETS	0.235	0.163	0.326	0.078	0.054	0.109	SUBCLONAL	1	TRUE	0	0.717202971574854	3		486	177	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878538	151878538	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009538-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	168	558	2	ENST00000262189.6:c.6407G>A	p.Gly2136Glu	p.G2136E	ENST00000262189	NM_170606.2	2136	gGa/gAa	36/59	0.717202971574854	4	FACETS	0.925	0.869	0.979	0.694	0.652	0.735	CLONAL	3	TRUE	0	0.717202971574854	4		560	290	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293637	137293637	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009538-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	150	1026	0	ENST00000481739.1:c.188C>A	p.Pro63Gln	p.P63Q	ENST00000481739	NM_002957.4	63	cCg/cAg	2/10	0.672560730506189	3	FACETS	0.96	0.895	1	0.96	0.895	1	CLONAL	2	TRUE	1	0.717202971574854	3		1026	296	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	245	425	0				ENST00000310581	NM_198253.2	-/1132			0.294063430024758	3	FACETS	0.864	0.813	0.915	0.864	0.813	0.915	CLONAL	3	TRUE	0	0.35	3		425	635	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0012809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	385	714	0	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	0.218428422300908	3	FACETS	1	0.967	1	0.682	0.647	0.717	CLONAL	2	TRUE	0	0.35	3		714	1264	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0012809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	114	347	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.154557411694432	4	FACETS	0.88	0.802	0.961	0.88	0.802	0.961	INDETERMINATE	3	TRUE	1	0.35	4		347	333	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467548	66467548	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	56	328	1	ENST00000273854.3:c.721G>T	p.Ala241Ser	p.A241S	ENST00000273854	NM_004439.5	241	Gct/Tct	3/18	0.299346476915654	3	FACETS	0.752	0.645	0.869	0.376	0.322	0.435	SUBCLONAL	1	TRUE	1	0.35	3		329	500	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031883	26031884	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs758780418	NA	P-0012809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	60	261	0	ENST00000244661.2:c.405_406del	p.Arg135SerfsTer12	p.R135Sfs*12	ENST00000244661	NM_003537.3	135	agAGcg/agcg	1/1	0.301413904310783	3	FACETS	0.933	0.806	1	0.466	0.403	0.535	CLONAL	1	TRUE	1	0.35	3		261	432	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398290	25398290	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	64	326	0	ENST00000311936.3:c.29G>T	p.Gly10Val	p.G10V	ENST00000311936	NM_004985.3	10	gGa/gTa	2/5	0.154557411694432	4	FACETS	0.767	0.669	0.871	0.511	0.446	0.581	INDETERMINATE	2	TRUE	1	0.35	4		326	322	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873251	136873251	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	133	429	0	ENST00000241393.3:c.247G>T	p.Ala83Ser	p.A83S	ENST00000241393	NM_003467.2	83	Gcc/Tcc	2/2	0.289676162172502	3	FACETS	1	0.985	1	0.722	0.658	0.79	CLONAL	1	TRUE	1	0.35	3		429	618	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288768	11288768	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	115	552	1	ENST00000361445.4:c.2987C>A	p.Thr996Lys	p.T996K	ENST00000361445	NM_004958.3	996	aCg/aAg	19/58	0.301413904310783	3	FACETS	0.761	0.685	0.843	0.381	0.342	0.422	SUBCLONAL	1	TRUE	1	0.35	3		553	1014	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939042	36939043	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0012809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	165	816	0	ENST00000361632.4:c.666_667delinsTT	p.Met222_Asp223delinsIleTyr	p.M222_D223delinsIY	ENST00000361632		222	atGGat/atTTat	5/16	0.301413904310783	3	FACETS	0.85	0.779	0.925	0.425	0.389	0.463	CLONAL	1	TRUE	1	0.35	3		816	1303	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196257	108196257	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	88	336	0	ENST00000278616.4:c.6793T>C	p.Phe2265Leu	p.F2265L	ENST00000278616	NM_000051.3	2265	Ttc/Ctc	46/63	0.301413904310783	2	FACETS	0.971	0.873	1	0.971	0.873	1	CLONAL	2	TRUE	0	0.35	2		336	259	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425417	49425417	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	413	1004	0	ENST00000301067.7:c.13071G>T	p.Arg4357Ser	p.R4357S	ENST00000301067	NM_003482.3	4357	agG/agT	39/54	0.154557411694432	4	FACETS	1	0.967	1	0.682	0.648	0.716	INDETERMINATE	2	TRUE	1	0.35	4		1004	1558	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135327	30135327	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	79	383	0	ENST00000331968.5:c.491G>T	p.Gly164Val	p.G164V	ENST00000331968	NM_002742.2	164	gGa/gTa	3/18	0.299346476915654	3	FACETS	0.901	0.793	1	0.45	0.396	0.508	CLONAL	1	TRUE	1	0.35	3		383	589	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736106	204736106	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	140	287	0	ENST00000302823.3:c.463G>T	p.Glu155Ter	p.E155*	ENST00000302823	NM_005214.4	155	Gaa/Taa	3/4	0.289676162172502	3	FACETS	0.882	0.807	0.959	0.882	0.807	0.959	CLONAL	2	TRUE	1	0.35	3		287	533	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385002	31385002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	152	589	0	ENST00000328111.2:c.1387C>T	p.Leu463Phe	p.L463F	ENST00000328111	NM_006892.3	463	Ctt/Ttt	14/23	0.299346476915654	3	FACETS	0.944	0.862	1	0.472	0.431	0.515	CLONAL	1	TRUE	1	0.35	3		589	1081	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356193	66356193	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	243	546	0	ENST00000273854.3:c.1304C>A	p.Thr435Lys	p.T435K	ENST00000273854	NM_004439.5	435	aCa/aAa	5/18	0.299346476915654	3	FACETS	0.87	0.813	0.928	0.87	0.813	0.928	CLONAL	2	TRUE	1	0.35	3		546	938	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168957	32168957	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1346	460	1079	0	ENST00000375023.3:c.4076A>G	p.Tyr1359Cys	p.Y1359C	ENST00000375023	NM_004557.3	1359	tAt/tGt	22/30	0.301413904310783	3	FACETS	0.855	0.814	0.897	0.855	0.814	0.897	CLONAL	2	TRUE	1	0.35	3		1079	1806	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372226	55372228	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	novel	NA	P-0012809-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	419	574	0	ENST00000297316.4:c.921_923del	p.Gly308del	p.G308del	ENST00000297316	NM_022454.3	306	GGC/-	2/2	0.277941607297055	5	FACETS	0.834	0.793	0.875	0.834	0.793	0.875	CLONAL	3	TRUE	2	0.35	5		574	1460	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0013435-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	597	359	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.706027632525243	6	FACETS	0.985	0.959	1			1	CLONAL	5	TRUE	NA	0.706027632525243	6		359	828	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0013435-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	1010	609	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.706027632525243	6	FACETS	1	0.997	1			1	CLONAL	3	TRUE	NA	0.706027632525243	6		609	1980	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578443	7578444	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0013435-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	660	604	2	ENST00000269305.4:c.486_487del	p.Tyr163GlnfsTer17	p.Y163Qfs*17	ENST00000269305	NM_001126112.2	162	atCTac/atac	5/11	0.687191458798576	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.706027632525243	2		606	934	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354688	70354688	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013435-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	121	452	0	ENST00000374080.3:c.4853A>C	p.Lys1618Thr	p.K1618T	ENST00000374080		1618	aAg/aCg	35/45	NA	2	FACETS	0.447	0.404	0.492			1	INDETERMINATE	1	TRUE	NA	0.706027632525243	2		452	767	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28586215	28586388	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	GAGCGTTCTGGAGCCCCGAGAGACGCCCCGGGGTTCTAGAAGCTCCCCGGCGGCGCCCAGTCCCGGCTTCATTCGGGCGTCCCTCCGAAACCCACTCGGGTGCACGGGTCGTCGGCGAGCCGCGACCGGGTCCTGGCGCGCACCATGATCGTGGCGGACTCCGAGTGCCGCGCA	GAGCGTTCTGGAGCCCCGAGAGACGCCCCGGGGTTCTAGAAGCTCCCCGGCGGCGCCCAGTCCCGGCTTCATTCGGGCGTCCCTCCGAAACCCACTCGGGTGCACGGGTCGTCGGCGAGCCGCGACCGGGTCCTGGCGCGCACCATGATCGTGGCGGACTCCGAGTGCCGCGCA	-	novel	NA	P-0013435-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	93	57	0	ENST00000253063.3:c.-140_34del		p.*47*	ENST00000253063	NM_031459.4	?-10/480		1/10	0.687191458798576	2	FACETS	1	0.984	1	0.724	0.661	0.786	CLONAL	1	TRUE	0	0.706027632525243	2		57	182	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266106	41266147	+	inframe_deletion	In_Frame_Del	DEL	ATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGT	ATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGT	-	novel	NA	P-0013435-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	143	273	0	ENST00000349496.5:c.104_145del	p.Ile35_Gly48del	p.I35_G48del	ENST00000349496	NM_001904.3	35	ATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGT/-	3/15	0.24342992807817	4	FACETS	1	0.985	1	0.455	0.417	0.494	INDETERMINATE	1	TRUE	1	0.706027632525243	4		273	506	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11308130	11308130	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758906272	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	210	406	0	ENST00000361445.4:c.862G>A	p.Glu288Lys	p.E288K	ENST00000361445	NM_004958.3	288	Gaa/Aaa	7/58	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.857620734197704	2		406	467	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692986	89692989	+	frameshift_variant	Frame_Shift_Del	DEL	AAGT	AAGT	-	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	243	419	0	ENST00000371953.3:c.473_476del	p.Val158GlyfsTer8	p.V158Gfs*8	ENST00000371953	NM_000314.4	157	gAAGTa/ga	5/9	0.857620734197704	1	FACETS	0.927	0.888	0.966	0.927	0.888	0.966	CLONAL	1	TRUE	0	0.857620734197704	1		419	349	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367115	40367115	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	231	498	0	ENST00000397332.2:c.82G>A	p.Gly28Arg	p.G28R	ENST00000397332	NM_001033082.2	28	Gga/Aga	2/3	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.857620734197704	2		498	529	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456460	89456460	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1221318412	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	188	261	0	ENST00000336596.2:c.1636G>A	p.Ala546Thr	p.A546T	ENST00000336596	NM_005233.5	546	Gcc/Acc	8/17	1	2	FACETS	0.951	0.888	1	0.951	0.888	1	CLONAL	1	TRUE	1	0.857620734197704	2		261	461	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168761	32168761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	263	614	0	ENST00000375023.3:c.4162G>A	p.Asp1388Asn	p.D1388N	ENST00000375023	NM_004557.3	1388	Gat/Aat	23/30	1	2	FACETS	0.986	0.931	1	0.986	0.931	1	CLONAL	1	TRUE	1	0.857620734197704	2		614	622	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128432122	128432122	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	212	294	0	ENST00000265960.3:c.324G>A	p.Trp108Ter	p.W108*	ENST00000265960	NM_001006617.1	108	tgG/tgA	3/12	1	2	FACETS	0.891	0.834	0.948	0.891	0.834	0.948	CLONAL	1	TRUE	1	0.857620734197704	2		294	555	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350074	81350074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	199	233	0	ENST00000222390.5:c.1258G>A	p.Glu420Lys	p.E420K	ENST00000222390	NM_000601.4	420	Gaa/Aaa	10/18	0.851040725203571	3	FACETS	0.921	0.856	0.988	0.46	0.428	0.494	CLONAL	1	TRUE	1	0.857620734197704	3		233	720	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953403	17953403	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	266	740	1	ENST00000458235.1:c.583C>T	p.Pro195Ser	p.P195S	ENST00000458235	NM_000215.3	195	Ccc/Tcc	6/24	1	2	FACETS	0.975	0.921	1	0.975	0.921	1	CLONAL	1	TRUE	1	0.857620734197704	2		741	636	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89869722	89869722	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs555519520	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	195	373	0	ENST00000389301.3:c.737G>A	p.Gly246Glu	p.G246E	ENST00000389301	NM_000135.2	246	gGa/gAa	8/43	1	2	FACETS	0.932	0.871	0.994	0.932	0.871	0.994	CLONAL	1	TRUE	1	0.857620734197704	2		373	488	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435135	49435135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	193	520	1	ENST00000301067.7:c.6418G>A	p.Asp2140Asn	p.D2140N	ENST00000301067	NM_003482.3	2140	Gac/Aac	31/54	1	2	FACETS	0.909	0.849	0.97	0.909	0.849	0.97	CLONAL	1	TRUE	1	0.857620734197704	2		521	495	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026073	14026073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1181017510	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	198	233	0	ENST00000311895.7:c.1033C>T	p.His345Tyr	p.H345Y	ENST00000311895	NM_005236.2	345	Cat/Tat	6/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.857620734197704	2		233	428	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170882	99170882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	239	548	1	ENST00000074304.5:c.1511C>T	p.Thr504Ile	p.T504I	ENST00000074304	NM_001134224.1	504	aCc/aTc	16/26	1	2	FACETS	0.886	0.833	0.94	0.886	0.833	0.94	CLONAL	1	TRUE	1	0.857620734197704	2		549	629	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105895	27105895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1478098345	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	204	452	0	ENST00000324856.7:c.5506G>A	p.Glu1836Lys	p.E1836K	ENST00000324856	NM_006015.4	1836	Gag/Aag	20/20	1	2	FACETS	0.898	0.84	0.957	0.898	0.84	0.957	CLONAL	1	TRUE	1	0.857620734197704	2		452	530	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115273179	115273179	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	252	352	0	ENST00000438362.2:c.1279G>A	p.Asp427Asn	p.D427N	ENST00000438362	NM_001242891.1	427	Gat/Aat	11/20	1	2	FACETS	0.92	0.866	0.974	0.92	0.866	0.974	CLONAL	1	TRUE	1	0.857620734197704	2		352	639	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849015	156849015	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771421920	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	269	616	0	ENST00000524377.1:c.1907C>T	p.Ala636Val	p.A636V	ENST00000524377	NM_002529.3	636	gCg/gTg	15/17	1	2	FACETS	0.979	0.925	1	0.979	0.925	1	CLONAL	1	TRUE	1	0.857620734197704	2		616	641	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982146	201982146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	287	648	0	ENST00000359651.3:c.670G>A	p.Gly224Ser	p.G224S	ENST00000359651		224	Ggc/Agc	5/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.857620734197704	2		648	643	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252119	226252119	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	34	54	0	ENST00000366813.1:c.67A>G	p.Thr23Ala	p.T23A	ENST00000366813		23	Aca/Gca	1/3	1	2	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	1	0.857620734197704	2		54	79	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200604	67200604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	266	661	0	ENST00000312629.5:c.715G>A	p.Glu239Lys	p.E239K	ENST00000312629	NM_003952.2	239	Gag/Aag	9/15	1	2	FACETS	0.953	0.9	1	0.953	0.9	1	CLONAL	1	TRUE	1	0.857620734197704	2		661	651	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101984899	101984899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	188	376	0	ENST00000282441.5:c.346G>A	p.Gly116Arg	p.G116R	ENST00000282441	NM_001130145.2	116	Gga/Aga	2/9	1	2	FACETS	0.97	0.906	1	0.97	0.906	1	CLONAL	1	TRUE	1	0.857620734197704	2		376	452	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158406	108158406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	212	308	0	ENST00000278616.4:c.4073G>A	p.Ser1358Asn	p.S1358N	ENST00000278616	NM_000051.3	1358	aGt/aAt	27/63	1	2	FACETS	0.938	0.879	0.998	0.938	0.879	0.998	CLONAL	1	TRUE	1	0.857620734197704	2		308	527	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426943	49426943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	211	494	1	ENST00000301067.7:c.11545G>A	p.Gly3849Arg	p.G3849R	ENST00000301067	NM_003482.3	3849	Gga/Aga	39/54	1	2	FACETS	0.943	0.884	1	0.943	0.884	1	CLONAL	1	TRUE	1	0.857620734197704	2		495	522	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536948	120536948	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	234	513	0	ENST00000229340.5:c.238G>A	p.Gly80Arg	p.G80R	ENST00000229340	NM_006861.6	80	Ggg/Agg	4/6	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.857620734197704	2		513	539	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953602	32953602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	233	411	1	ENST00000380152.3:c.8903C>T	p.Thr2968Ile	p.T2968I	ENST00000380152		2968	aCc/aTc	22/27	0.123966423788667	3	FACETS	1	0.992	1	0.68	0.639	0.721	INDETERMINATE	1	TRUE	1	0.857620734197704	3		412	571	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939060	48939060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	153	199	0	ENST00000267163.4:c.892C>T	p.Pro298Ser	p.P298S	ENST00000267163	NM_000321.2	298	Cct/Tct	9/27	0.123966423788667	3	FACETS	1	0.985	1	0.633	0.585	0.681	INDETERMINATE	1	TRUE	1	0.857620734197704	3		199	403	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436410	110436410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	331	709	0	ENST00000375856.3:c.1991G>A	p.Gly664Asp	p.G664D	ENST00000375856	NM_003749.2	664	gGc/gAc	1/2	0.123966423788667	3	FACETS	1	0.994	1	0.694	0.659	0.729	INDETERMINATE	1	TRUE	1	0.857620734197704	3		709	795	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639209	3639209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	278	722	2	ENST00000294008.3:c.4430C>T	p.Pro1477Leu	p.P1477L	ENST00000294008	NM_032444.2	1477	cCc/cTc	12/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.857620734197704	2		724	635	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821800	72821800	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	248	429	0	ENST00000268489.5:c.10375C>T	p.Pro3459Ser	p.P3459S	ENST00000268489	NM_006885.3	3459	Cca/Tca	10/10	1	2	FACETS	0.99	0.934	1	0.99	0.934	1	CLONAL	1	TRUE	1	0.857620734197704	2		429	584	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215908	41215908	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658672	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	251	358	0	ENST00000357654.3:c.5135G>A	p.Trp1712Ter	p.W1712*	ENST00000357654	NM_007294.3	1712	tGg/tAg	17/23	1	2	FACETS	0.984	0.928	1	0.984	0.928	1	CLONAL	1	TRUE	1	0.857620734197704	2		358	595	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805426	46805426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	305	712	0	ENST00000290295.7:c.530G>A	p.Gly177Asp	p.G177D	ENST00000290295	NM_006361.5	177	gGc/gAc	1/2	1	2	FACETS	0.947	0.898	0.997	0.947	0.898	0.997	CLONAL	1	TRUE	1	0.857620734197704	2		712	751	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132610	11132610	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	285	728	0	ENST00000358026.2:c.2826G>A	p.Trp942Ter	p.W942*	ENST00000358026	NM_001128849.1	942	tgG/tgA	19/36	1	2	FACETS	0.924	0.874	0.975	0.924	0.874	0.975	CLONAL	1	TRUE	1	0.857620734197704	2		728	719	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221690	36221690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	290	740	1	ENST00000222270.7:c.5359G>A	p.Gly1787Arg	p.G1787R	ENST00000222270	NM_014727.1	1787	Ggg/Agg	26/37	1	2	FACETS	0.973	0.922	1	0.973	0.922	1	CLONAL	1	TRUE	1	0.857620734197704	2		741	695	SUCCESS
AXL	558	MSKCC	GRCh37	19	41725337	41725337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs112524750	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	261	840	1	ENST00000301178.4:c.40G>A	p.Ala14Thr	p.A14T	ENST00000301178	NM_021913.4	14	Gcc/Acc	1/20	1	2	FACETS	0.966	0.912	1	0.966	0.912	1	CLONAL	1	TRUE	1	0.857620734197704	2		841	630	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703527	47703527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520735	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	217	365	0	ENST00000233146.2:c.2027C>T	p.Ser676Leu	p.S676L	ENST00000233146	NM_000251.2	676	tCa/tTa	13/16	1	2	FACETS	0.91	0.853	0.968	0.91	0.853	0.968	CLONAL	1	TRUE	1	0.857620734197704	2		365	556	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47709982	47709982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	191	255	0	ENST00000233146.2:c.2699C>T	p.Ser900Leu	p.S900L	ENST00000233146	NM_000251.2	900	tCa/tTa	16/16	1	2	FACETS	0.988	0.924	1	0.988	0.924	1	CLONAL	1	TRUE	1	0.857620734197704	2		255	451	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610503	215610503	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	261	327	0	ENST00000260947.4:c.1753C>T	p.Leu585Phe	p.L585F	ENST00000260947	NM_000465.2	585	Ctc/Ttc	8/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.857620734197704	2		327	588	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272443	21272443	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	346	710	0	ENST00000354336.3:c.221G>A	p.Gly74Glu	p.G74E	ENST00000354336	NM_005207.3	74	gGg/gAg	1/3	1	2	FACETS	0.963	0.916	1	0.963	0.916	1	CLONAL	1	TRUE	1	0.857620734197704	2		710	838	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091795	29091795	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	267	384	0	ENST00000328354.6:c.1162C>T	p.Pro388Ser	p.P388S	ENST00000328354	NM_007194.3	388	Ccc/Tcc	11/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.857620734197704	2		384	604	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713784	30713784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs550421922	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	262	498	0	ENST00000295754.5:c.1109G>A	p.Arg370Lys	p.R370K	ENST00000295754	NM_003242.5	370	aGg/aAg	4/7	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.857620734197704	2		498	560	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936668	49936668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1471738292	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	245	529	0	ENST00000296474.3:c.1259C>T	p.Thr420Ile	p.T420I	ENST00000296474	NM_002447.2	420	aCc/aTc	2/20	1	2	FACETS	0.992	0.935	1	0.992	0.935	1	CLONAL	1	TRUE	1	0.857620734197704	2		529	576	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610575	52610575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	153	289	0	ENST00000394830.3:c.3598C>T	p.Pro1200Ser	p.P1200S	ENST00000394830	NM_018313.4	1200	Ccc/Tcc	23/30	1	2	FACETS	0.941	0.872	1	0.941	0.872	1	CLONAL	1	TRUE	1	0.857620734197704	2		289	379	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808340	99808340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1179083091	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	162	287	1	ENST00000280892.6:c.349G>A	p.Gly117Ser	p.G117S	ENST00000280892	NM_001130678.1	117	Ggt/Agt	5/7	1	2	FACETS	0.87	0.807	0.935	0.87	0.807	0.935	CLONAL	1	TRUE	1	0.857620734197704	2		288	434	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245528	153245528	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	162	254	0	ENST00000281708.4:c.1663G>A	p.Val555Met	p.V555M	ENST00000281708	NM_033632.3	555	Gtg/Atg	11/12	1	2	FACETS	0.915	0.849	0.982	0.915	0.849	0.982	CLONAL	1	TRUE	1	0.857620734197704	2		254	413	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532758	187532758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1157129991	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	246	379	0	ENST00000441802.2:c.9635C>T	p.Ala3212Val	p.A3212V	ENST00000441802	NM_005245.3	3212	gCc/gTc	14/27	NA	2	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.857620734197704	2		379	562	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751111	57751111	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	114	210	0	ENST00000274289.3:c.1755+1G>A		p.X585_splice	ENST00000274289	NM_006622.3	585			0.123966423788667	3	FACETS	1	0.985	1	0.706	0.647	0.766	INDETERMINATE	1	TRUE	1	0.857620734197704	3		210	269	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433772	149433772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	301	573	0	ENST00000286301.3:c.2779C>T	p.Pro927Ser	p.P927S	ENST00000286301	NM_005211.3	927	Ccg/Tcg	22/22	1	2	FACETS	0.996	0.944	1	0.996	0.944	1	CLONAL	1	TRUE	1	0.857620734197704	2		573	705	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722358	176722358	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	182	389	0	ENST00000439151.2:c.7989G>A	p.Trp2663Ter	p.W2663*	ENST00000439151	NM_022455.4	2663	tgG/tgA	23/23	1	2	FACETS	0.864	0.805	0.925	0.864	0.805	0.925	CLONAL	1	TRUE	1	0.857620734197704	2		389	491	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163267	32163267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	413	770	2	ENST00000375023.3:c.5959C>T	p.Pro1987Ser	p.P1987S	ENST00000375023	NM_004557.3	1987	Ccc/Tcc	30/30	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.857620734197704	2		772	956	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026700	6026700	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767724368	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	376	621	0	ENST00000265849.7:c.1696C>T	p.Pro566Ser	p.P566S	ENST00000265849	NM_000535.5	566	Cct/Tct	11/15	0.857620734197704	3	FACETS	1	0.988	1	0.557	0.529	0.586	CLONAL	1	TRUE	1	0.857620734197704	3		621	1124	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971267	13971267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1159395009	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	233	440	0	ENST00000405192.2:c.662C>T	p.Pro221Leu	p.P221L	ENST00000405192	NM_001163147.1	221	cCc/cTc	8/12	0.857620734197704	3	FACETS	0.95	0.889	1	0.475	0.444	0.507	CLONAL	1	TRUE	1	0.857620734197704	3		440	817	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740731	145740731	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750720279	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	296	650	0	ENST00000428558.2:c.1369G>A	p.Gly457Arg	p.G457R	ENST00000428558	NM_004260.3	457	Ggg/Agg	7/22	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.857620734197704	2		650	654	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247007	53247007	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	243	527	0	ENST00000375401.3:c.493G>A	p.Glu165Lys	p.E165K	ENST00000375401	NM_004187.3	165	Gaa/Aaa	4/26	1	2	FACETS	0.975	0.919	1	0.975	0.919	1	CLONAL	1	TRUE	1	0.857620734197704	2		527	581	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357208	70357208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013580-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	229	473	0	ENST00000374080.3:c.5723G>A	p.Gly1908Glu	p.G1908E	ENST00000374080		1908	gGa/gAa	39/45	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.857620734197704	2		473	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0016705-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	86	712	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.15	2		712	902	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245891	5245891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1045893958	NA	P-0016705-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	66	1109	0	ENST00000357368.4:c.884G>A	p.Arg295Gln	p.R295Q	ENST00000357368	NM_002850.3	295	cGg/cAg	10/38	1	2	FACETS	0.837	0.724	0.96	0.837	0.724	0.96	CLONAL	1	TRUE	1	0.15	2		1109	1052	SUCCESS
APC	324	MSKCC	GRCh37	5	112174214	112174214	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016705-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	22	302	0	ENST00000257430.4:c.2926del	p.Arg976GlufsTer4	p.R976Efs*4	ENST00000257430	NM_000038.5	975	Aaa/aa	16/16	0.149705362319829	1	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	0	0.15	1		302	239	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466773	25466773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1431156021	NA	P-0016705-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	35	598	0	ENST00000264709.3:c.1930G>A	p.Ala644Thr	p.A644T	ENST00000264709	NM_175629.2	644	Gct/Act	16/23	1	2	FACETS	0.691	0.565	0.834	0.691	0.565	0.834	SUBCLONAL	1	TRUE	1	0.15	2		598	675	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41021819	41021819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371150683	NA	P-0016705-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	37	480	0	ENST00000267868.3:c.761G>A	p.Arg254Gln	p.R254Q	ENST00000267868	NM_002875.4	254	cGa/cAa	8/10	1	2	FACETS	0.753	0.619	0.904	0.753	0.619	0.904	CLONAL	1	TRUE	1	0.15	2		480	655	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0017278-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	707	346	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.732890041693475	7	FACETS	0.97	0.936	1	0.582	0.561	0.603	CLONAL	3	TRUE	2	0.732890041693475	7		346	1877	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231281	46231281	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017536-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	14	180	0	ENST00000334344.6:c.1121G>T	p.Gly374Val	p.G374V	ENST00000334344	NM_152641.2	374	gGc/gTc	10/21	0.190285176339903	3	FACETS	0.428	0.309	0.572	0.214	0.154	0.286	SUBCLONAL	1	FALSE	1	0.3	3		180	251	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0017937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	58	454	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.30032546165673	4	FACETS	1	0.902	1	0.264	0.227	0.303	CLONAL	1	TRUE	0	0.464429139792782	4		454	347	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880998	37880998	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs144434331	NA	P-0017937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	78	730	1	ENST00000269571.5:c.2327G>T	p.Gly776Val	p.G776V	ENST00000269571		776	gGt/gTt	20/27	1	2	FACETS	0.952	0.842	1	0.952	0.842	1	CLONAL	1	TRUE	1	0.464429139792782	2		731	353	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606042	81606042	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	52	588	0	ENST00000298171.2:c.712G>C	p.Val238Leu	p.V238L	ENST00000298171	NM_000369.2	238	Gtc/Ctc	9/10	0.450174506936944	2	FACETS	0.808	0.694	0.932	0.404	0.347	0.466	CLONAL	1	TRUE	0	0.464429139792782	2		588	277	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592345	29592345	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	51	603	0	ENST00000356175.3:c.4760A>T	p.Tyr1587Phe	p.Y1587F	ENST00000356175	NM_000267.3	1587	tAt/tTt	35/57	1	2	FACETS	0.9	0.772	1	0.9	0.772	1	CLONAL	1	TRUE	1	0.464429139792782	2		603	244	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140151	50140151	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148755459	NA	P-0017937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	66	659	0	ENST00000246792.3:c.274G>A	p.Ala92Thr	p.A92T	ENST00000246792	NM_006270.3	92	Gcc/Acc	3/6	0.38694319860915	2	FACETS	0.854	0.746	0.968	0.427	0.373	0.484	CLONAL	1	TRUE	0	0.464429139792782	2		659	333	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980565	1980565	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs142054662	NA	P-0017937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	66	696	0	ENST00000382891.5:c.4027C>G	p.Pro1343Ala	p.P1343A	ENST00000382891	NM_133335.3	1343	Cca/Gca	22/22	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.464429139792782	2		696	261	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935522	13935522	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	15	314	1	ENST00000405192.2:c.1334C>A	p.Pro445His	p.P445H	ENST00000405192	NM_001163147.1	445	cCc/cAc	12/12	0.440449955507601	3	FACETS	0.328	0.239	0.433	0.164	0.119	0.217	SUBCLONAL	1	TRUE	1	0.464429139792782	3		315	243	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334773	81334773	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017937-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	18	680	0	ENST00000222390.5:c.1943G>A	p.Gly648Glu	p.G648E	ENST00000222390	NM_000601.4	648	gGg/gAg	17/18	0.440449955507601	3	FACETS	0.314	0.236	0.406	0.157	0.118	0.203	SUBCLONAL	1	TRUE	1	0.464429139792782	3		680	304	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	405	294	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.495313222245754	7	FACETS	1	0.989	1	0.673	0.642	0.705	CLONAL	3	TRUE	2	0.495313222245754	7		294	1087	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281129	49281129	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	18	937	0	ENST00000282018.3:c.176C>G	p.Ser59Cys	p.S59C	ENST00000282018	NM_020377.2	59	tCc/tGc	1/1	1	2	FACETS	0.204	0.153	0.264	0.204	0.153	0.264	SUBCLONAL	1	TRUE	1	0.495313222245754	2		937	357	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151946981	151946981	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018947-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	76	575	0	ENST00000262189.6:c.1793C>G	p.Thr598Arg	p.T598R	ENST00000262189	NM_170606.2	598	aCa/aGa	13/59	0.297675044043223	3	FACETS	1	0.929	1	0.536	0.473	0.603	CLONAL	1	TRUE	1	0.495313222245754	3		575	357	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954022	32954023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs397507419	NA	P-0019178-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	95	375	6	ENST00000380152.3:c.9097dup	p.Thr3033AsnfsTer11	p.T3033Nfs*11	ENST00000380152		3030	aca/acAa	23/27	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.584451731994595	2		381	265	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0019948-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	263	358	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.954064551183637	7	FACETS	1	0.986	1			1	CLONAL	3	TRUE	NA	0.954064551183637	7		358	557	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0019948-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	178	156	0	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	0.954064551183637	7	FACETS	0.897	0.829	0.967			1	CLONAL	2	TRUE	NA	0.954064551183637	7		156	704	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052601	42052601	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0019948-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	280	405	0	ENST00000219905.7:c.7272T>G	p.Tyr2424Ter	p.Y2424*	ENST00000219905	NM_001164273.1	2424	taT/taG	20/24	0.932366577495223	3	FACETS	0.963	0.944	0.98	0.963	0.944	0.98	CLONAL	3	TRUE	0	0.954064551183637	3		405	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0020970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	194	565	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.368344181640571	2	FACETS	0.905	0.846	0.964	0.905	0.846	0.964	CLONAL	2	TRUE	0	0.449576519253471	2		567	477	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557272	29557278	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATATAGG	ATATAGG	-	novel	NA	P-0020970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	43	150	0	ENST00000356175.3:c.2991-6_2991del		p.X997_splice	ENST00000356175	NM_000267.3	997		23/57	0.368344181640571	2	FACETS	0.862	0.743	0.985	0.862	0.743	0.985	CLONAL	2	TRUE	0	0.449576519253471	2		150	111	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837909	156837909	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	236	538	0	ENST00000524377.1:c.442A>T	p.Asn148Tyr	p.N148Y	ENST00000524377	NM_002529.3	148	Aac/Tac	5/17	0.323953517521225	4	FACETS	0.854	0.798	0.911	0.854	0.798	0.911	CLONAL	2	TRUE	2	0.449576519253471	4		538	891	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244798	41244845	+	inframe_deletion	In_Frame_Del	DEL	ATATTAGACTCATTCTTTCCTTGATTTTCTTCCTTTTGTTCACATTCA	ATATTAGACTCATTCTTTCCTTGATTTTCTTCCTTTTGTTCACATTCA	-	novel	NA	P-0020970-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	107	493	0	ENST00000357654.3:c.2703_2750del	p.Glu902_Ile917del	p.E902_I917del	ENST00000357654	NM_007294.3	901	ttTGAATGTGAACAAAAGGAAGAAAATCAAGGAAAGAATGAGTCTAATATc/ttc	10/23	0.368344181640571	2	FACETS	1	0.978	1	0.642	0.581	0.705	CLONAL	1	TRUE	0	0.449576519253471	2		493	371	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0021679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	160	879	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.681945354110799	3	FACETS	1	0.974	1	0.564	0.52	0.609	CLONAL	1	TRUE	1	0.681945354110799	3		879	558	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405899	70405899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	240	384	0	ENST00000373644.4:c.3413C>T	p.Ser1138Leu	p.S1138L	ENST00000373644	NM_030625.2	1138	tCa/tTa	4/12	0.681945354110799	3	FACETS	1	0.937	1	0.501	0.468	0.535	CLONAL	1	TRUE	1	0.681945354110799	3		384	942	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405524	70405524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369726331	NA	P-0021679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	459	366	0	ENST00000373644.4:c.3038C>T	p.Ser1013Phe	p.S1013F	ENST00000373644	NM_030625.2	1013	tCc/tTc	4/12	0.681945354110799	3	FACETS	0.773	0.74	0.807	0.773	0.74	0.807	SUBCLONAL	2	TRUE	1	0.681945354110799	3		366	1167	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405595	70405595	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	367	368	0	ENST00000373644.4:c.3109C>A	p.Gln1037Lys	p.Q1037K	ENST00000373644	NM_030625.2	1037	Cag/Aag	4/12	0.681945354110799	3	FACETS	1	0.994	1	0.678	0.644	0.712	CLONAL	1	TRUE	1	0.681945354110799	3		368	1065	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230526	46230526	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs750746147	NA	P-0021679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	77	284	0	ENST00000334344.6:c.775G>C	p.Gly259Arg	p.G259R	ENST00000334344	NM_152641.2	259	Ggt/Cgt	8/21	0.681945354110799	3	FACETS	0.909	0.805	1	0.455	0.402	0.51	CLONAL	1	TRUE	1	0.681945354110799	3		284	333	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457635	67457635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1429991069	NA	P-0021679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	375	709	3	ENST00000327367.4:c.445G>A	p.Glu149Lys	p.E149K	ENST00000327367	NM_005902.3	149	Gag/Aag	3/9	0.681945354110799	3	FACETS	0.977	0.934	1	0.977	0.934	1	CLONAL	2	TRUE	1	0.681945354110799	3		712	755	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679370	29679370	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1060500265	NA	P-0021679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	103	360	0	ENST00000356175.3:c.7490C>A	p.Ala2497Asp	p.A2497D	ENST00000356175	NM_000267.3	2497	gCc/gAc	50/57	0.681945354110799	3	FACETS	0.986	0.888	1	0.493	0.444	0.544	CLONAL	1	TRUE	1	0.681945354110799	3		360	411	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27205002	27205002	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	134	558	0	ENST00000380036.4:c.2303T>A	p.Ile768Asn	p.I768N	ENST00000380036	NM_000459.3	768	aTc/aAc	14/23	0.681945354110799	4	FACETS	0.902	0.82	0.987	0.451	0.41	0.494	CLONAL	1	TRUE	2	0.681945354110799	4		558	733	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515628	31515628	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1323090785	NA	P-0021679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	109	456	0	ENST00000344624.3:c.991C>T	p.Pro331Ser	p.P331S	ENST00000344624		331	Cca/Tca	4/33	0.681945354110799	4	FACETS	0.901	0.811	0.995	0.45	0.405	0.498	CLONAL	1	TRUE	2	0.681945354110799	4		456	597	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38157014	38157014	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2193	118	483	1	ENST00000317025.8:c.2706G>T	p.Met902Ile	p.M902I	ENST00000317025	NM_023034.1	902	atG/atT	15/24	0.681945354110799	17	FACETS	0.916	0.822	1			1	CLONAL	1	TRUE	NA	0.681945354110799	17		484	2311	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133753820	133753820	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	137	560	0	ENST00000318560.5:c.1289G>C	p.Trp430Ser	p.W430S	ENST00000318560	NM_005157.4	430	tGg/tCg	8/11	0.681945354110799	4	FACETS	1	0.933	1	0.514	0.468	0.561	CLONAL	1	TRUE	2	0.681945354110799	4		560	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0021747-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	73	740	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.291282307949042	3	FACETS	0.932	0.823	1	0.932	0.823	1	CLONAL	2	TRUE	1	0.291282307949042	3		740	308	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227991	55227991	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021747-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	31	306	0	ENST00000275493.2:c.1458G>C	p.Gln486His	p.Q486H	ENST00000275493	NM_005228.3	486	caG/caC	12/28	0.287663669273637	4	FACETS	0.929	0.762	1	0.929	0.762	1	CLONAL	2	TRUE	2	0.291282307949042	4		306	148	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786740	3786740	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021747-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	37	582	0	ENST00000262367.5:c.4471C>G	p.Gln1491Glu	p.Q1491E	ENST00000262367	NM_004380.2	1491	Caa/Gaa	27/31	0.201512145558497	4	FACETS	1	0.912	1	0.584	0.483	0.695	CLONAL	1	TRUE	2	0.291282307949042	4		582	281	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198240	185198240	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0021747-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	36	616	0	ENST00000265026.3:c.2722G>C	p.Asp908His	p.D908H	ENST00000265026	NM_004721.4	908	Gac/Cac	13/14	0.291282307949042	8	FACETS	0.892	0.733	1	0.223	0.183	0.268	CLONAL	1	TRUE	4	0.291282307949042	8		616	519	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961227	1961227	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021747-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	18	524	0	ENST00000382891.5:c.3015C>G	p.Ile1005Met	p.I1005M	ENST00000382891	NM_133335.3	1005	atC/atG	17/22	0.175444796079742	4	FACETS	0.572	0.431	0.739	0.286	0.215	0.37	SUBCLONAL	1	TRUE	2	0.291282307949042	4		524	279	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64289965	64289965	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022051-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	102	259	0	ENST00000370651.3:c.408G>C	p.Lys136Asn	p.K136N	ENST00000370651	NM_003463.4	136	aaG/aaC	6/6	0.680835128191946	3	FACETS	0.893	0.803	0.987	0.446	0.401	0.494	CLONAL	1	TRUE	1	0.680835128191946	3		259	450	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6442018	6442018	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0022051-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	71	126	0	ENST00000356142.4:c.577C>T	p.Arg193Ter	p.R193*	ENST00000356142	NM_018890.3	193	Cga/Tga	7/7	0.680835128191946	5	FACETS	1	0.974	1	0.362	0.319	0.408	CLONAL	1	TRUE	1	0.680835128191946	5		126	291	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206594	108206594	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0022582-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	120	244	0	ENST00000278616.4:c.8174A>T	p.Asp2725Val	p.D2725V	ENST00000278616	NM_000051.3	2725	gAt/gTt	56/63	0.713966360192909	1	FACETS	0.841	0.775	0.908	0.841	0.775	0.908	CLONAL	1	TRUE	0	0.713966360192909	1		244	257	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159754	20159754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022582-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	281	510	1	ENST00000379607.5:c.5C>T	p.Pro2Leu	p.P2L	ENST00000379607	NM_001412.3	2	cCc/cTc	1/7	0.713966360192909	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.713966360192909	1		511	506	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211666	36211666	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0022582-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	270	593	0	ENST00000222270.7:c.1417C>G	p.Pro473Ala	p.P473A	ENST00000222270	NM_014727.1	473	Ccc/Gcc	3/37	1	2	FACETS	0.933	0.878	0.988	0.933	0.878	0.988	CLONAL	1	TRUE	1	0.713966360192909	2		593	811	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412427	63412428	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0022903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	81	807	0	ENST00000330258.3:c.739_740delinsAG	p.Pro247Arg	p.P247R	ENST00000330258	NM_152424.3	247	CCa/AGa	2/2	0.351129502603964	2	FACETS	0.384	0.338	0.435			1	SUBCLONAL	1	TRUE	NA	0.438188263971107	2		807	962	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0023994-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	44	278	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.21	2		278	347	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971153	21971153	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913383	NA	P-0023994-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	63	463	0	ENST00000304494.5:c.205G>T	p.Glu69Ter	p.E69*	ENST00000304494	NM_000077.4	69	Gag/Tag	2/3	0.256008695411041	0	FACETS	1	0.916	1			1	CLONAL	1	TRUE	0	0.21	0		463	440	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115928	8115929	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023994-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	76	423	0	ENST00000346208.3:c.1275dup	p.Ser426IlefsTer81	p.S426Ifs*81	ENST00000346208		425	cca/ccAa	6/6	0.18180802983035	0	FACETS	0.9	0.79	1			1	CLONAL	1	TRUE	0	0.21	0		423	635	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846342	156846342	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746049437	NA	P-0023994-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	120	831	0	ENST00000524377.1:c.1783G>A	p.Gly595Arg	p.G595R	ENST00000524377	NM_002529.3	595	Ggg/Agg	14/17	0.3	3	FACETS	1	0.972	1	0.607	0.547	0.671	CLONAL	1	TRUE	1	0.21	3		831	1040	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405968	49405968	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023994-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	111	464	0	ENST00000418115.1:c.170T>C	p.Leu57Ser	p.L57S	ENST00000418115	NM_001664.2	57	tTg/tCg	3/5	1	2	FACETS	0.772	0.694	0.853	1	0.984	1	SUBCLONAL	2	TRUE	1	0.21	2		464	685	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873687	151873688	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATGA	novel	NA	P-0023994-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	154	468	0	ENST00000262189.6:c.8847_8850dup	p.Val2951SerfsTer18	p.V2951Sfs*18	ENST00000262189	NM_170606.2	2950	-/TCAT	38/59	0.245365511465363	4	FACETS	0.849	0.779	0.922			1	CLONAL	3	TRUE	NA	0.21	4		468	697	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878867	151878868	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0023994-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	80	506	1	ENST00000262189.6:c.6077dup	p.Tyr2026Ter	p.Y2026*	ENST00000262189	NM_170606.2	2026	tat/taAt	36/59	0.245365511465363	4	FACETS	1	0.97	1			1	CLONAL	1	TRUE	NA	0.21	4		507	687	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111462	8111463	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGT	novel	NA	P-0023994-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	121	558	0	ENST00000346208.3:c.949_951dup	p.Cys317dup	p.C317dup	ENST00000346208		317	-/TGT	5/6	0.18180802983035	0	FACETS	1	0.927	1			1	CLONAL	1	TRUE	0	0.21	0		558	882	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652819	29652842	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTTGTCATTTTCCTTAGGTTCA	TTTTTGTCATTTTCCTTAGGTTCA	-	novel	NA	P-0023994-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	24	181	0	ENST00000356175.3:c.4773-19_4777del		p.X1591_splice	ENST00000356175	NM_000267.3	1591		36/57	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.21	2		181	177	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0024340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	93	425	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.986	0.888	1	0.986	0.888	1	CLONAL	1	TRUE	1	0.650711966362107	2		425	290	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268483	46268483	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs778964948	NA	P-0024340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	176	338	0	ENST00000371998.3:c.2870C>G	p.Ser957Cys	p.S957C	ENST00000371998		957	tCt/tGt	15/23	0.650711966362107	3	FACETS	0.948	0.887	1	0.948	0.887	1	CLONAL	2	TRUE	1	0.650711966362107	3		338	378	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480320	56480320	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	23	362	0	ENST00000267101.3:c.427C>G	p.Leu143Val	p.L143V	ENST00000267101	NM_001982.3	143	Ctg/Gtg	4/28	1	2	FACETS	0.19	0.147	0.238	0.19	0.147	0.238	SUBCLONAL	1	TRUE	1	0.650711966362107	2		362	373	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981495	201981496	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0024340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	236	656	0	ENST00000359651.3:c.409_410insT	p.Ser137MetfsTer5	p.S137Mfs*5	ENST00000359651		137	agt/aTgt	3/8	0.400121976915583	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.650711966362107	1		656	409	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440530	49440530	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	41	675	1	ENST00000301067.7:c.4280G>T	p.Cys1427Phe	p.C1427F	ENST00000301067	NM_003482.3	1427	tGt/tTt	15/54	1	2	FACETS	0.178	0.147	0.212	0.178	0.147	0.212	SUBCLONAL	1	TRUE	1	0.650711966362107	2		676	708	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122524	17122524	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0024340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	126	519	0	ENST00000285071.4:c.872-1G>A		p.X291_splice	ENST00000285071	NM_144997.5	291			0.650711966362107	2	FACETS	1	0.922	1	0.504	0.461	0.549	CLONAL	1	TRUE	0	0.650711966362107	2		519	384	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798200	42798200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	216	737	0	ENST00000575354.2:c.4154C>A	p.Ala1385Asp	p.A1385D	ENST00000575354	NM_015125.3	1385	gCc/gAc	17/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.650711966362107	2		737	642	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967332	25967332	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	98	284	0	ENST00000435504.4:c.1874G>C	p.Arg625Thr	p.R625T	ENST00000435504		625	aGa/aCa	13/13	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.650711966362107	2		284	293	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624965	9624965	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	57	239	0	ENST00000353224.5:c.12G>C	p.Lys4Asn	p.K4N	ENST00000353224	NM_177990.2	4	aaG/aaC	3/10	0.650711966362107	3	FACETS	0.673	0.58	0.773	0.337	0.29	0.387	SUBCLONAL	1	TRUE	1	0.650711966362107	3		239	345	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021799	71021799	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	95	277	0	ENST00000318789.4:c.1559A>C	p.His520Pro	p.H520P	ENST00000318789	NM_032682.5	520	cAc/cCc	18/21	1	2	FACETS	0.888	0.798	0.98	0.888	0.798	0.98	CLONAL	1	TRUE	1	0.650711966362107	2		277	329	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523095	176523095	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024340-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	163	744	0	ENST00000292408.4:c.1859T>G	p.Val620Gly	p.V620G	ENST00000292408	NM_213647.1	620	gTg/gGg	14/18	1	2	FACETS	0.975	0.901	1	0.975	0.901	1	CLONAL	1	TRUE	1	0.650711966362107	2		744	514	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0024949-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	58	347	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.852	0.733	0.981	0.852	0.733	0.981	CLONAL	1	TRUE	1	0.289650191373036	2		347	470	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355283	81355283	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024949-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	26	288	0	ENST00000222390.5:c.1091G>T	p.Trp364Leu	p.W364L	ENST00000222390	NM_000601.4	364	tGg/tTg	9/18	1	2	FACETS	0.471	0.373	0.584	0.471	0.373	0.584	SUBCLONAL	1	TRUE	1	0.289650191373036	2		288	381	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274723	123274723	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1441011501	NA	P-0024949-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	32	531	0	ENST00000358487.5:c.1195C>T	p.Arg399Ter	p.R399*	ENST00000358487	NM_000141.4	399	Cga/Tga	9/18	0.289650191373036	1	FACETS	0.361	0.292	0.438	0.361	0.292	0.438	SUBCLONAL	1	TRUE	0	0.289650191373036	1		531	524	SUCCESS
ATM	472	MSKCC	GRCh37	11	108164163	108164164	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs864622164	NA	P-0024949-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	38	175	0	ENST00000278616.4:c.4741dup	p.Ile1581AsnfsTer5	p.I1581Nfs*5	ENST00000278616	NM_000051.3	1579	caa/cAaa	31/63	0.289650191373036	1	FACETS	0.721	0.599	0.858	0.721	0.599	0.858	SUBCLONAL	1	TRUE	0	0.289650191373036	1		175	311	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156848936	156848936	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024949-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	189	785	1	ENST00000524377.1:c.1828C>A	p.Leu610Met	p.L610M	ENST00000524377	NM_002529.3	610	Ctg/Atg	15/17	0.289650191373036	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.289650191373036	3		786	694	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70432717	70432717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024949-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	26	408	0	ENST00000373644.4:c.4739C>T	p.Ser1580Leu	p.S1580L	ENST00000373644	NM_030625.2	1580	tCa/tTa	8/12	1	2	FACETS	0.357	0.282	0.443	0.357	0.282	0.443	SUBCLONAL	1	TRUE	1	0.289650191373036	2		408	503	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066811	30066811	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024949-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	61	462	0	ENST00000331968.5:c.2320T>C	p.Tyr774His	p.Y774H	ENST00000331968	NM_002742.2	774	Tat/Cat	16/18	0.289650191373036	7	FACETS	0.883	0.76	1			1	CLONAL	1	TRUE	NA	0.289650191373036	7		462	822	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260251	10260251	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024949-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	48	712	0	ENST00000340748.4:c.2416G>T	p.Gly806Trp	p.G806W	ENST00000340748		806	Ggg/Tgg	25/40	1	2	FACETS	0.53	0.448	0.622	0.53	0.448	0.622	SUBCLONAL	1	TRUE	1	0.289650191373036	2		712	625	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463289	25463289	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024949-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	48	588	0	ENST00000264709.3:c.2204A>T	p.Tyr735Phe	p.Y735F	ENST00000264709	NM_175629.2	735	tAc/tTc	19/23	1	2	FACETS	0.647	0.547	0.758	0.647	0.547	0.758	SUBCLONAL	1	TRUE	1	0.289650191373036	2		588	512	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164090	47164090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750308104	NA	P-0024949-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	14	261	0	ENST00000409792.3:c.2036C>T	p.Ala679Val	p.A679V	ENST00000409792	NM_014159.6	679	gCa/gTa	3/21	1	2	FACETS	0.346	0.25	0.464	0.346	0.25	0.464	SUBCLONAL	1	TRUE	1	0.289650191373036	2		261	279	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90995076	90995087	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGTTCTCCTGA	TGGTTCTCCTGA	ATTTAT	novel	NA	P-0024949-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	105	319	1	ENST00000265433.3:c.38-4_45delinsATAAAT		p.X13_splice	ENST00000265433	NM_002485.4	13		2/16	0.289650191373036	4	FACETS	0.838	0.753	0.927	0.559	0.502	0.618	CLONAL	2	TRUE	1	0.289650191373036	4		320	558	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47004897	47004897	+	intron_variant	Intron	SNP	G	G	T	rs1251032975	NA	P-0024949-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	63	710	0	ENST00000377604.3:c.-126+13G>T		p.*42*	ENST00000377604	NM_001204468.1	-/163			1	2	FACETS	0.68	0.587	0.78	0.68	0.587	0.78	SUBCLONAL	1	TRUE	1	0.289650191373036	2		710	640	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040675	47040675	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024949-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	75	952	0	ENST00000377604.3:c.1310A>G	p.Tyr437Cys	p.Y437C	ENST00000377604	NM_001204468.1	437	tAc/tGc	13/24	1	2	FACETS	0.71	0.622	0.806	0.71	0.622	0.806	SUBCLONAL	1	TRUE	1	0.289650191373036	2		952	729	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893363	32893363	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398122741	NA	P-0026387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	144	342	0	ENST00000380152.3:c.217C>T	p.Gln73Ter	p.Q73*	ENST00000380152		73	Cag/Tag	3/27	0.291795799250892	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	0	0.291795799250892	2		342	483	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793244	242793244	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs773969430	NA	P-0026387-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	150	839	1	ENST00000334409.5:c.833G>T	p.Arg278Met	p.R278M	ENST00000334409	NM_005018.2	278	aGg/aTg	5/5	NA	2	FACETS	0.861	0.785	0.941			1	INDETERMINATE	1	TRUE	NA	0.291795799250892	2		840	1194	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0026774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	138	278	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.928	0.849	1	0.928	0.849	1	CLONAL	1	TRUE	1	0.574091378762797	2		278	518	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0026774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	285	698	1	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.574091378762797	2		699	973	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093455	30093455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776034417	NA	P-0026774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	134	402	0	ENST00000331968.5:c.1808G>A	p.Arg603His	p.R603H	ENST00000331968	NM_002742.2	603	cGt/cAt	13/18	1	2	FACETS	0.967	0.884	1	0.967	0.884	1	CLONAL	1	TRUE	1	0.574091378762797	2		402	483	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508629	106508629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751048583	NA	P-0026774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	222	545	0	ENST00000359195.3:c.623C>T	p.Pro208Leu	p.P208L	ENST00000359195	NM_002649.2	208	cCg/cTg	2/11	1	2	FACETS	0.921	0.859	0.984	0.921	0.859	0.984	CLONAL	1	TRUE	1	0.574091378762797	2		545	840	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266125	+	missense_variant	Missense_Mutation	DNP	AC	AC	CT	novel	NA	P-0026774-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	143	394	1	ENST00000349496.5:c.121_122delinsCT	p.Thr41Leu	p.T41L	ENST00000349496	NM_001904.3	41	ACc/CTc	3/15	1	2	FACETS	0.874	0.8	0.95	0.874	0.8	0.95	CLONAL	1	TRUE	1	0.574091378762797	2		395	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0027956-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	486	670	1	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	NA	2	FACETS	0.984	0.954	1			1	INDETERMINATE	2	TRUE	NA	0.713922996232763	2		671	692	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0027956-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	44	143	1	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	0.713922996232763	2	FACETS	0.52	0.44	0.607			1	SUBCLONAL	1	TRUE	NA	0.713922996232763	2		144	237	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899060	40899060	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027956-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	187	557	0	ENST00000373198.4:c.2210C>A	p.Thr737Asn	p.T737N	ENST00000373198	NM_133170.3	737	aCt/aAt	14/32	0.713922996232763	3	FACETS	1	0.942	1	0.509	0.472	0.548	CLONAL	1	TRUE	1	0.713922996232763	3		557	698	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192627	138192627	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0027956-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	53	376	0	ENST00000237289.4:c.263A>T	p.Glu88Val	p.E88V	ENST00000237289	NM_001270507.1	88	gAa/gTa	2/9	1	2	FACETS	0.304	0.259	0.353	0.304	0.259	0.353	SUBCLONAL	1	TRUE	1	0.713922996232763	2		376	488	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371939	55371939	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027956-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	129	388	0	ENST00000297316.4:c.629G>A	p.Gly210Asp	p.G210D	ENST00000297316	NM_022454.3	210	gGc/gAc	2/2	0.713922996232763	2	FACETS	1	0.937	1	0.512	0.47	0.555	CLONAL	1	TRUE	0	0.713922996232763	2		388	353	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579397	7579397	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs730881995	NA	P-0028245-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	24	932	0	ENST00000269305.4:c.290T>A	p.Val97Asp	p.V97D	ENST00000269305	NM_001126112.2	97	gTc/gAc	4/11	0.194973050024296	1	FACETS	0.922	0.725	1	0.922	0.725	1	CLONAL	1	FALSE	0	0.194973050024296	1		932	241	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221946	1221946	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0028245-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	52	989	0	ENST00000326873.7:c.863-2A>T		p.X288_splice	ENST00000326873	NM_000455.4	288			1	2	FACETS	0.984	0.845	1	1	0.976	1	CLONAL	2	FALSE	1	0.194973050024296	2		989	271	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597902	52598110	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTATGAAGTCTTTCCTTTAATCTTTAAGTGAATAAATATTTTCTATTTGAAATATTTACTACTCTAGTTTAAGATCTAATAAAAAATTAAAAACACTGGACTACACTATGTTGCTATCAGTTAATGGAAGTGCTCTTTTTTCCTTAAGTTTTTCAAGCTTTACCTGAAGTAGTAAATTTCATCATCTACCACTTTAGCAGAGAGTGAA	ATTATGAAGTCTTTCCTTTAATCTTTAAGTGAATAAATATTTTCTATTTGAAATATTTACTACTCTAGTTTAAGATCTAATAAAAAATTAAAAACACTGGACTACACTATGTTGCTATCAGTTAATGGAAGTGCTCTTTTTTCCTTAAGTTTTTCAAGCTTTACCTGAAGTAGTAAATTTCATCATCTACCACTTTAGCAGAGAGTGAA	-	novel	NA	P-0028245-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	11	75	0	ENST00000394830.3:c.3756_3800+164del		p.X1252_splice	ENST00000394830	NM_018313.4	1252		24/30	0.194973050024296	1	FACETS	1	0.804	1	1	0.924	1	CLONAL	3	FALSE	0	0.194973050024296	1		75	30	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597407	10597413	+	protein_altering_variant	In_Frame_Del	DEL	GATGTCA	GATGTCA	T	novel	NA	P-0028245-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	15	904	0	ENST00000171111.5:c.1790_1796delinsA	p.Met597_Ser599delinsLys	p.M597_S599delinsK	ENST00000171111	NM_203500.1	597	aTGACATCg/aAg	6/6	1	2	FACETS	0.57	0.416	0.754	0.57	0.416	0.754	SUBCLONAL	1	FALSE	1	0.194973050024296	2		904	270	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295186	1295187	+	upstream_gene_variant	5'Flank	INS	-	-	GGGGCCGCGGAAAGGAAGGGGA	novel	NA	P-0028277-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	18	207	0				ENST00000310581	NM_198253.2	-/1132			0.281452961898137	5	FACETS	0.546	0.411	0.707	0.182	0.137	0.236	SUBCLONAL	1	TRUE	2	0.281452961898137	5		207	333	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105536	30105536	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028277-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	101	568	0	ENST00000331968.5:c.1150G>T	p.Asp384Tyr	p.D384Y	ENST00000331968	NM_002742.2	384	Gat/Tat	7/18	0.170475547165855	4	FACETS	1	0.971	1	0.624	0.558	0.694	CLONAL	1	TRUE	2	0.281452961898137	4		568	737	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0028553-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	675	156	0	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	0.818924246369706	4	FACETS	1	0.976	1			1	CLONAL	2	TRUE	NA	0.902041593647379	4		156	1407	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593594	55593608	+	inframe_deletion	In_Frame_Del	DEL	GAAGTACAGTGGAAG	GAAGTACAGTGGAAG	-	novel	NA	P-0028553-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	627	150	0	ENST00000288135.5:c.1661_1675del	p.Glu554_Lys558del	p.E554_K558del	ENST00000288135	NM_000222.2	554	GAAGTACAGTGGAAG/-	11/21	0.818924246369706	4	FACETS	0.857	0.831	0.882			1	CLONAL	3	TRUE	NA	0.902041593647379	4		150	1029	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965154	15965155	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0028553-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	258	148	0	ENST00000268712.3:c.5441dup	p.Tyr1814Ter	p.Y1814*	ENST00000268712	NM_006311.3	1814	tac/taAc	37/46	1	2	FACETS	0.89	0.839	0.941	0.89	0.839	0.941	CLONAL	1	TRUE	1	0.902041593647379	2		148	643	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225603	2225603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	267	628	1	ENST00000326181.6:c.1606G>A	p.Gly536Ser	p.G536S	ENST00000326181	NM_032271.2	536	Ggc/Agc	17/21	1	2	FACETS	0.907	0.856	0.959	0.907	0.856	0.959	CLONAL	1	TRUE	1	0.855586993351932	2		629	688	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257565	19257565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	114	669	1	ENST00000162023.5:c.661G>A	p.Gly221Arg	p.G221R	ENST00000162023		221	Gga/Aga	10/13	0.855586993351932	2	FACETS	0.374	0.337	0.414	0.187	0.168	0.207	SUBCLONAL	1	TRUE	0	0.855586993351932	2		670	712	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534392	63534392	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1439	152	728	0	ENST00000307078.5:c.1129A>T	p.Arg377Trp	p.R377W	ENST00000307078	NM_004655.3	377	Agg/Tgg	5/11	0.855586993351932	4	FACETS	0.414	0.377	0.454	0.138	0.125	0.152	SUBCLONAL	1	TRUE	1	0.855586993351932	4		728	1591	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296133	15296133	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2139	129	762	0	ENST00000263388.2:c.2231G>T	p.Arg744Met	p.R744M	ENST00000263388	NM_000435.2	744	aGg/aTg	14/33	0.855586993351932	6	FACETS	0.36	0.325	0.398			1	SUBCLONAL	1	TRUE	NA	0.855586993351932	6		762	2268	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455542	189455542	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	52	521	1	ENST00000264731.3:c.76C>T	p.Pro26Ser	p.P26S	ENST00000264731	NM_003722.4	26	Cca/Tca	2/14	0.855586993351932	2	FACETS	0.181	0.154	0.212	0.091	0.077	0.106	SUBCLONAL	1	TRUE	0	0.855586993351932	2		522	670	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79968560	79968560	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	116	435	3	ENST00000265081.6:c.910G>T	p.Val304Leu	p.V304L	ENST00000265081	NM_002439.4	304	Gtg/Ttg	6/24	1	2	FACETS	0.435	0.393	0.48	0.435	0.393	0.48	SUBCLONAL	1	TRUE	1	0.855586993351932	2		438	623	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220314	55220314	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0028607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	41	687	0	ENST00000275493.2:c.704A>T	p.Gln235Leu	p.Q235L	ENST00000275493	NM_005228.3	235	cAg/cTg	6/28	1	2	FACETS	0.128	0.106	0.153	0.128	0.106	0.153	SUBCLONAL	1	TRUE	1	0.855586993351932	2		687	749	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391479	139391479	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	70	640	1	ENST00000277541.6:c.6712C>T	p.Pro2238Ser	p.P2238S	ENST00000277541	NM_017617.3	2238	Ccc/Tcc	34/34	0.730682407257395	3	FACETS	0.202	0.175	0.232	0.101	0.087	0.116	SUBCLONAL	1	TRUE	1	0.855586993351932	3		641	1155	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391679	139391679	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	88	729	0	ENST00000277541.6:c.6512A>T	p.Lys2171Met	p.K2171M	ENST00000277541	NM_017617.3	2171	aAg/aTg	34/34	0.730682407257395	3	FACETS	0.255	0.225	0.287	0.127	0.112	0.144	SUBCLONAL	1	TRUE	1	0.855586993351932	3		729	1152	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351935	70351935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028607-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	92	306	0	ENST00000374080.3:c.4132C>T	p.Leu1378Phe	p.L1378F	ENST00000374080		1378	Ctc/Ttc	30/45	0.778355731890204	2	FACETS	0.293	0.26	0.328			1	SUBCLONAL	1	TRUE	NA	0.855586993351932	2		306	735	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0029401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	69	359	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.179457760838859	5	FACETS	0.929	0.813	1	0.62	0.542	0.702	CLONAL	2	TRUE	2	0.261796145875477	5		359	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0029401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	139	435	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.243307479616916	2	FACETS	0.827	0.755	0.902	0.827	0.755	0.902	CLONAL	2	TRUE	0	0.261796145875477	2		435	642	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798968	45798968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781444	NA	P-0029401-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	133	459	0	ENST00000450313.1:c.377G>A	p.Arg126Gln	p.R126Q	ENST00000450313	NM_012222.2	126	cGg/cAg	4/16	0.261796145875477	3	FACETS	0.802	0.73	0.879	0.802	0.73	0.879	CLONAL	2	TRUE	1	0.261796145875477	3		459	716	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0030168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	87	545	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.946	0.84	1	0.946	0.84	1	CLONAL	1	TRUE	1	0.339194128953005	2		545	542	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112602	115112602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs865915137	NA	P-0030168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	148	902	1	ENST00000257566.3:c.1138G>A	p.Glu380Lys	p.E380K	ENST00000257566	NM_016569.3	380	Gag/Aag	7/8	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.339194128953005	2		903	826	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480410	56480410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	82	568	0	ENST00000267101.3:c.517G>A	p.Glu173Lys	p.E173K	ENST00000267101	NM_001982.3	173	Gag/Aag	4/28	1	2	FACETS	0.957	0.847	1	0.957	0.847	1	CLONAL	1	TRUE	1	0.339194128953005	2		568	505	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727571	66727571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	62	352	0	ENST00000307102.5:c.287G>A	p.Arg96Lys	p.R96K	ENST00000307102	NM_002755.3	96	aGa/aAa	2/11	1	2	FACETS	0.999	0.867	1	0.999	0.867	1	CLONAL	1	TRUE	1	0.339194128953005	2		352	366	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112745494	112745494	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	60	492	0	ENST00000369452.4:c.812A>G	p.Asn271Ser	p.N271S	ENST00000369452	NM_007373.3	271	aAt/aGt	3/9	1	2	FACETS	0.79	0.682	0.906	0.79	0.682	0.906	CLONAL	1	TRUE	1	0.339194128953005	2		492	448	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845698	68845698	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	96	659	0	ENST00000261769.5:c.944A>G	p.Asn315Ser	p.N315S	ENST00000261769	NM_004360.3	315	aAt/aGt	7/16	0.313579733306271	1	FACETS	0.953	0.853	1	0.953	0.853	1	CLONAL	1	TRUE	0	0.339194128953005	1		659	493	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777862	27777862	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1297719047	NA	P-0030168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	35	299	0	ENST00000369163.2:c.11C>T	p.Thr4Met	p.T4M	ENST00000369163	NM_003536.2	4	aCg/aTg	1/1	0.221141188307017	0	FACETS	0.472	0.388	0.565			1	SUBCLONAL	1	TRUE	0	0.339194128953005	0		299	289	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090669	71090669	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	45	265	0	ENST00000318789.4:c.679G>C	p.Glu227Gln	p.E227Q	ENST00000318789	NM_032682.5	227	Gaa/Caa	11/21	1	2	FACETS	0.948	0.801	1	0.948	0.801	1	CLONAL	1	TRUE	1	0.339194128953005	2		265	280	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171648	32171648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	97	673	1	ENST00000375023.3:c.3130G>A	p.Glu1044Lys	p.E1044K	ENST00000375023	NM_004557.3	1044	Gag/Aag	20/30	1	2	FACETS	0.884	0.789	0.985	0.884	0.789	0.985	CLONAL	1	TRUE	1	0.339194128953005	2		674	647	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210199	123210199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030168-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	58	483	0	ENST00000218089.9:c.2551G>A	p.Glu851Lys	p.E851K	ENST00000218089	NM_001042749.1	851	Gaa/Aaa	26/35	1	2	FACETS	0.675	0.58	0.777	0.675	0.58	0.777	SUBCLONAL	1	TRUE	1	0.339194128953005	2		483	507	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0030653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	270	346	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.175261166406625	3	FACETS	0.971	0.913	1	1	0.995	1	CLONAL	4	TRUE	1	0.175261166406625	3		346	863	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243048	105243048	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519804	NA	P-0030653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	119	922	0	ENST00000349310.3:c.235C>A	p.Gln79Lys	p.Q79K	ENST00000349310	NM_001014432.1	79	Cag/Aag	5/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.175261166406625	2		922	933	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782082	NA	P-0030653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	142	745	0	ENST00000269305.4:c.745A>T	p.Arg249Trp	p.R249W	ENST00000269305	NM_001126112.2	249	Agg/Tgg	7/11	1	2	FACETS	0.899	0.819	0.983	1	0.99	1	CLONAL	2	TRUE	1	0.175261166406625	2		745	901	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43699737	43699739	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	rs754334940	NA	P-0030653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	92	557	0	ENST00000382044.4:c.5776_5778del	p.Val1926del	p.V1926del	ENST00000382044	NM_001141980.1	1926	GTG/-	28/28	0.175261166406625	3	FACETS	1	0.964	1	0.607	0.538	0.68	CLONAL	1	TRUE	1	0.175261166406625	3		557	941	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0030653-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	111	346	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.183698677789577	3	FACETS	0.946	0.853	1	0.946	0.853	1	CLONAL	2	TRUE	1	0.22	3		346	592	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243048	105243048	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519804	NA	P-0030653-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	108	922	0	ENST00000349310.3:c.235C>A	p.Gln79Lys	p.Q79K	ENST00000349310	NM_001014432.1	79	Cag/Aag	5/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.22	2		922	758	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs587782082	NA	P-0030653-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	65	745	0	ENST00000269305.4:c.745A>T	p.Arg249Trp	p.R249W	ENST00000269305	NM_001126112.2	249	Agg/Tgg	7/11	1	2	FACETS	0.926	0.803	1	0.926	0.803	1	CLONAL	1	TRUE	1	0.22	2		745	638	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43699737	43699739	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	rs754334940	NA	P-0030653-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	26	557	0	ENST00000382044.4:c.5776_5778del	p.Val1926del	p.V1926del	ENST00000382044	NM_001141980.1	1926	GTG/-	28/28	1	2	FACETS	0.462	0.365	0.573	0.462	0.365	0.573	SUBCLONAL	1	TRUE	1	0.22	2		557	512	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0030893-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	51	737	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	1	2	FACETS	0.738	0.625	0.863	0.738	0.625	0.863	SUBCLONAL	1	TRUE	1	0.15	2		737	921	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120457996	120457996	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs756211019	NA	P-0030893-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	38	614	0	ENST00000256646.2:c.7349G>T	p.Gly2450Val	p.G2450V	ENST00000256646	NM_024408.3	2450	gGa/gTa	34/34	1	2	FACETS	0.761	0.627	0.911	0.761	0.627	0.911	CLONAL	1	TRUE	1	0.15	2		614	666	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94169065	94169065	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs876658165	NA	P-0030893-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	19	269	0	ENST00000323929.3:c.1927G>T	p.Val643Leu	p.V643L	ENST00000323929	NM_005591.3	643	Gtg/Ttg	18/20	1	2	FACETS	0.734	0.557	0.944	0.734	0.557	0.944	CLONAL	1	TRUE	1	0.15	2		269	345	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663772	29663773	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030893-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	53	534	0	ENST00000356175.3:c.6206dup	p.Asn2070GlnfsTer5	p.N2070Qfs*5	ENST00000356175	NM_000267.3	2068	-/T	41/57	1	2	FACETS	0.918	0.781	1	0.918	0.781	1	CLONAL	1	TRUE	1	0.15	2		534	770	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602289	10602289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1308006383	NA	P-0030893-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	61	808	1	ENST00000171111.5:c.1289G>A	p.Gly430Asp	p.G430D	ENST00000171111	NM_203500.1	430	gGc/gAc	3/6	1	2	FACETS	0.887	0.763	1	0.887	0.763	1	CLONAL	1	TRUE	1	0.15	2		809	917	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913471	NA	P-0031715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	38	688	0	ENST00000269571.5:c.2329G>A	p.Val777Met	p.V777M	ENST00000269571		777	Gtg/Atg	20/27	0.226631844611887	3	FACETS	0.411	0.339	0.493	0.206	0.169	0.247	SUBCLONAL	1	TRUE	1	0.261838686590161	3		688	798	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130637	29130637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142243299	NA	P-0031715-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	76	474	0	ENST00000328354.6:c.73G>A	p.Val25Ile	p.V25I	ENST00000328354	NM_007194.3	25	Gtt/Att	2/15	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.261838686590161	2		474	575	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0032166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	80	425	0				ENST00000310581	NM_198253.2	-/1132			0.183749336214665	4	FACETS	0.935	0.836	1	0.935	0.836	1	INDETERMINATE	2	TRUE	2	0.569171823005424	4		425	236	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916644	178916644	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0032166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	117	254	0	ENST00000263967.3:c.31T>G	p.Trp11Gly	p.W11G	ENST00000263967	NM_006218.2	11	Tgg/Ggg	2/21	0.105748935028642	4	FACETS	0.881	0.803	0.962	0.881	0.803	0.962	INDETERMINATE	2	TRUE	2	0.569171823005424	4		254	366	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18762522	18762522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	159	357	1	ENST00000266497.5:c.4018G>A	p.Asp1340Asn	p.D1340N	ENST00000266497		1340	Gat/Aat	29/31	0.105748935028642	4	FACETS	0.866	0.8	0.935	0.866	0.8	0.935	INDETERMINATE	2	TRUE	2	0.569171823005424	4		358	506	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5557669	5557669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	261	474	0	ENST00000397747.3:c.683C>T	p.Pro228Leu	p.P228L	ENST00000397747	NM_025239.3	228	cCc/cTc	5/7	0.569171823005424	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.569171823005424	1		474	498	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0032338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	154	556	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.854	0.78	0.932	1	0.99	1	CLONAL	2	TRUE	1	0.163437830892164	2		556	1103	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604788	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555687605	NA	P-0032338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	86	321	0	ENST00000342988.3:c.1610A>G	p.Asp537Gly	p.D537G	ENST00000342988	NM_005359.5	537	gAc/gGc	12/12	0.105076246009397	3	FACETS	0.973	0.862	1	0.649	0.575	0.728	CLONAL	2	TRUE	0	0.163437830892164	3		321	585	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610695	52610695	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	104	494	0	ENST00000394830.3:c.3478C>T	p.Arg1160Ter	p.R1160*	ENST00000394830	NM_018313.4	1160	Cga/Tga	23/30	0.105076246009397	3	FACETS	1	0.972	1	0.827	0.743	0.916	CLONAL	2	TRUE	0	0.163437830892164	3		494	555	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224792	123224792	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs777611309	NA	P-0032338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	49	235	0	ENST00000218089.9:c.3556C>T	p.Arg1186Ter	p.R1186*	ENST00000218089	NM_001042749.1	1186	Cga/Tga	32/35	1	1	FACETS	0.761	0.646	0.885	1	0.964	1	SUBCLONAL	2	TRUE	0	0.163437830892164	1		235	362	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524178	18524178	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	41	418	0	ENST00000266497.5:c.1690G>T	p.Gly564Trp	p.G564W	ENST00000266497		564	Ggg/Tgg	11/31	0.137912045688981	4	FACETS	0.823	0.684	0.979	0.206	0.171	0.245	CLONAL	1	TRUE	0	0.163437830892164	4		418	709	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524172	18524173	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0032338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	35	411	0	ENST00000266497.5:c.1685dup	p.Phe563ValfsTer40	p.F563Vfs*40	ENST00000266497		562	ctg/cTtg	11/31	0.137912045688981	4	FACETS	0.715	0.584	0.863	0.179	0.146	0.216	SUBCLONAL	1	TRUE	0	0.163437830892164	4		411	697	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0032641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	44	677	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	1	2	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	FALSE	1	0.469124158543208	2		677	187	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509579	29509579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754343223	NA	P-0032641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	28	630	0	ENST00000356175.3:c.784C>T	p.Arg262Cys	p.R262C	ENST00000356175	NM_000267.3	262	Cgt/Tgt	8/57	0.455454645447511	3	FACETS	0.715	0.576	0.872	0.358	0.288	0.436	SUBCLONAL	1	FALSE	1	0.469124158543208	3		630	206	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729445	41729445	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	23	651	1	ENST00000242208.4:c.1084T>C	p.Ser362Pro	p.S362P	ENST00000242208	NM_002192.2	362	Tcc/Ccc	3/3	0.469124158543208	6	FACETS	0.776	0.607	0.97	0.259	0.202	0.324	CLONAL	1	FALSE	3	0.469124158543208	6		652	245	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210075	55210075	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0033073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	22051	439	0	ENST00000275493.2:c.185T>G	p.Leu62Arg	p.L62R	ENST00000275493	NM_005228.3	62	cTt/cGt	2/28	0.710097342675571	56	FACETS	0.992	0.99	0.994	0.992	0.99	0.994	CLONAL	56	TRUE	0	0.710097342675571	56		439	22549	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720680	89720681	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0033073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	173	327	0	ENST00000371953.3:c.833dup	p.Phe279LeufsTer19	p.F279Lfs*19	ENST00000371953	NM_000314.4	277	-/T	8/9	0.710097342675571	1	FACETS	0.927	0.868	0.985	0.927	0.868	0.985	CLONAL	1	TRUE	0	0.710097342675571	1		327	339	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943950	71943950	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	249	807	0	ENST00000298229.2:c.1883T>C	p.Phe628Ser	p.F628S	ENST00000298229	NM_001567.3	628	tTt/tCt	16/28	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.710097342675571	2		807	695	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801737	3801737	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	143	358	0	ENST00000262367.5:c.3769C>T	p.Gln1257Ter	p.Q1257*	ENST00000262367	NM_004380.2	1257	Cag/Tag	20/31	1	2	FACETS	0.917	0.844	0.993	0.917	0.844	0.993	CLONAL	1	TRUE	1	0.710097342675571	2		358	439	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753279	42753279	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1307797425	NA	P-0033073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	344	1053	0	ENST00000222329.4:c.985C>T	p.Arg329Cys	p.R329C	ENST00000222329	NM_006494.2	329	Cgc/Tgc	4/4	1	2	FACETS	0.998	0.947	1	0.998	0.947	1	CLONAL	1	TRUE	1	0.710097342675571	2		1053	971	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535358	66535358	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	217	643	2	ENST00000273854.3:c.103C>A	p.Pro35Thr	p.P35T	ENST00000273854	NM_004439.5	35	Cct/Act	1/18	0.174659228036525	3	FACETS	1	0.988	1	0.631	0.59	0.673	INDETERMINATE	1	TRUE	1	0.710097342675571	3		645	656	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555126	106555126	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	143	446	1	ENST00000369096.4:c.2243A>G	p.Asp748Gly	p.D748G	ENST00000369096	NM_001198.3	748	gAc/gGc	7/7	1	2	FACETS	0.686	0.628	0.746	0.686	0.628	0.746	SUBCLONAL	1	TRUE	1	0.710097342675571	2		447	587	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0033823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	30	294	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.834	1	1	0.834	1	CLONAL	1	TRUE	1	0.13	2		294	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0033823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	45	565	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.13	2		567	678	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584513	48584514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs377767334	NA	P-0033823-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	12	323	0	ENST00000342988.3:c.692dup	p.Ser232GlnfsTer3	p.S232Qfs*3	ENST00000342988	NM_005359.5	229	ctg/ctGg	6/12	1	2	FACETS	0.419	0.293	0.575	0.419	0.293	0.575	SUBCLONAL	1	TRUE	1	0.13	2		323	441	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0034426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	70	403	0				ENST00000310581	NM_198253.2	-/1132			0.72456477123724	3	FACETS	1	0.93	1	0.537	0.474	0.602	CLONAL	1	TRUE	1	0.755067216471336	3		403	238	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99491921	99491921	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034426-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	137	440	0	ENST00000268035.6:c.3706A>T	p.Asn1236Tyr	p.N1236Y	ENST00000268035	NM_000875.3	1236	Aac/Tac	20/21	0.72456477123724	3	FACETS	0.95	0.869	1	0.475	0.434	0.518	CLONAL	1	TRUE	1	0.755067216471336	3		440	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782664	NA	P-0034994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	214	589	0	ENST00000269305.4:c.711G>C	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atC	7/11	0.733912429642781	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.733912429642781	2		589	288	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012731	36012731	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1260223338	NA	P-0034994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	10	150	1	ENST00000358208.4:c.175G>A	p.Ala59Thr	p.A59T	ENST00000358208		59	Gcc/Acc	2/12	0.486438482331022	5	FACETS	0.288	0.195	0.405	0.096	0.065	0.135	SUBCLONAL	1	TRUE	2	0.733912429642781	5		151	199	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606106	81606106	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1215944830	NA	P-0034994-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	17	621	0	ENST00000298171.2:c.776C>A	p.Thr259Asn	p.T259N	ENST00000298171	NM_000369.2	259	aCt/aAt	9/10	0.506604263438385	3	FACETS	0.2	0.149	0.261	0.067	0.049	0.087	SUBCLONAL	1	TRUE	0	0.733912429642781	3		621	317	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0035999-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	156	618	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	0.833	0.763	0.905	1	0.99	1	CLONAL	2	TRUE	1	0.234728762907064	2		619	798	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156719	20156719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035999-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	127	230	0	ENST00000379607.5:c.38G>A	p.Arg13His	p.R13H	ENST00000379607	NM_001412.3	13	cGc/cAc	2/7	0.234728762907064	2	FACETS	0.952	0.871	1			1	CLONAL	3	TRUE	NA	0.234728762907064	2		230	379	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171431	123171431	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035999-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	39	235	0	ENST00000218089.9:c.343C>G	p.Leu115Val	p.L115V	ENST00000218089	NM_001042749.1	115	Ctt/Gtt	6/35	1	1	FACETS	0.886	0.737	1	0.886	0.737	1	CLONAL	1	TRUE	0	0.234728762907064	1		235	331	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29107969	29107969	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035999-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	51	478	0	ENST00000328354.6:c.720G>T	p.Arg240Ser	p.R240S	ENST00000328354	NM_007194.3	240	agG/agT	6/15	0.181923593798665	4	FACETS	0.713	0.604	0.832	0.356	0.302	0.416	SUBCLONAL	1	TRUE	2	0.234728762907064	4		478	753	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231773	36231773	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1569061762	NA	P-0036731-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	160	661	0	ENST00000300305.3:c.611G>A	p.Arg204Gln	p.R204Q	ENST00000300305		204	cGa/cAa	5/8	1	2	FACETS	0.992	0.912	1	0.992	0.912	1	CLONAL	1	TRUE	1	0.462888335177093	2		661	697	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270607	98270607	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs779791579	NA	P-0036731-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	12	14	0	ENST00000331920.6:c.37C>G	p.Arg13Gly	p.R13G	ENST00000331920	NM_000264.3	13	Cgc/Ggc	1/24	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.462888335177093	2		14	36	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857311	68857312	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0036731-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	88	251	0	ENST00000261769.5:c.1947_1948insTT	p.Ile650LeufsTer4	p.I650Lfs*4	ENST00000261769	NM_004360.3	649	tct/tcTTt	13/16	0.462888335177093	1	FACETS	0.997	0.894	1	0.997	0.894	1	CLONAL	1	TRUE	0	0.462888335177093	1		251	293	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941851	71941853	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0036731-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	177	524	0	ENST00000298229.2:c.1211_1213del	p.Phe404del	p.F404del	ENST00000298229	NM_001567.3	403	gcCTTc/gcc	11/28	0.462888335177093	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.462888335177093	1		524	532	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510611	38510611	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036731-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	165	598	0	ENST00000254066.5:c.865G>T	p.Gly289Trp	p.G289W	ENST00000254066	NM_000964.3	289	Ggg/Tgg	7/9	1	2	FACETS	0.908	0.835	0.984	0.908	0.835	0.984	CLONAL	1	TRUE	1	0.462888335177093	2		598	785	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0037224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	43	331	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	1	2	FACETS	0.802	0.674	0.944	0.802	0.674	0.944	CLONAL	1	TRUE	1	0.313397449472265	2		331	342	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913250	NA	P-0037224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	20	382	0	ENST00000369535.4:c.34G>A	p.Gly12Ser	p.G12S	ENST00000369535	NM_002524.4	12	Ggt/Agt	2/7	1	2	FACETS	0.291	0.222	0.373	0.291	0.222	0.373	SUBCLONAL	1	TRUE	1	0.313397449472265	2		382	438	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251754	212251754	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	25	336	0	ENST00000342788.4:c.3305T>G	p.Phe1102Cys	p.F1102C	ENST00000342788	NM_005235.2	1102	tTt/tGt	27/28	1	2	FACETS	0.438	0.345	0.545	0.438	0.345	0.545	SUBCLONAL	1	TRUE	1	0.313397449472265	2		336	364	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579592	7579592	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0037224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	76	652	0	ENST00000269305.4:c.97-2A>T		p.X33_splice	ENST00000269305	NM_001126112.2	33			1	2	FACETS	0.73	0.641	0.827	0.73	0.641	0.827	SUBCLONAL	1	TRUE	1	0.313397449472265	2		652	664	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593505	48593505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	27	254	0	ENST00000342988.3:c.1256G>A	p.Gly419Glu	p.G419E	ENST00000342988	NM_005359.5	419	gGg/gAg	10/12	1	2	FACETS	0.633	0.505	0.779	0.633	0.505	0.779	SUBCLONAL	1	TRUE	1	0.313397449472265	2		254	272	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332865	152332865	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	75	353	0	ENST00000206249.3:c.1171C>A	p.Leu391Ile	p.L391I	ENST00000206249	NM_000125.3	391	Ctc/Atc	5/8	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.313397449472265	2		353	471	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783214	9783214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	59	664	0	ENST00000377346.4:c.2458G>A	p.Asp820Asn	p.D820N	ENST00000377346	NM_005026.3	820	Gac/Aac	20/24	1	2	FACETS	0.527	0.452	0.608	0.527	0.452	0.608	SUBCLONAL	1	TRUE	1	0.313397449472265	2		664	715	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436181	56436197	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCTCTGGAAAAAAGAA	CCCTCTGGAAAAAAGAA	-	novel	NA	P-0037224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	62	549	0	ENST00000407977.2:c.953-13_956del		p.X318_splice	ENST00000407977		318		9/10	1	2	FACETS	0.693	0.599	0.795	0.693	0.599	0.795	SUBCLONAL	1	TRUE	1	0.313397449472265	2		549	571	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467958	50467958	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1219777993	NA	P-0037224-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	80	677	2	ENST00000331340.3:c.1193C>T	p.Thr398Met	p.T398M	ENST00000331340	NM_006060.4	398	aCg/aTg	8/8	0.279075353980718	3	FACETS	0.773	0.68	0.873	0.386	0.34	0.437	SUBCLONAL	1	TRUE	1	0.313397449472265	3		679	764	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0037411-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	552	667	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.808547044911099	2	FACETS	0.98	0.957	1	0.98	0.957	1	CLONAL	2	TRUE	0	0.816024619587472	2		669	690	SUCCESS
APC	324	MSKCC	GRCh37	5	112175476	112175476	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037411-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	435	428	0	ENST00000257430.4:c.4188del	p.Phe1396LeufsTer19	p.F1396Lfs*19	ENST00000257430	NM_000038.5	1395	agT/ag	16/16	0.816024619587472	3	FACETS	0.979	0.957	1	0.979	0.957	1	CLONAL	3	TRUE	0	0.816024619587472	3		428	511	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775614	9775614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766440014	NA	P-0037411-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	484	1067	1	ENST00000377346.4:c.157G>A	p.Ala53Thr	p.A53T	ENST00000377346	NM_005026.3	53	Gcc/Acc	4/24	0.808547044911099	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.816024619587472	2		1068	582	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753149	42753151	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs199960550	NA	P-0037411-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	344	1286	14	ENST00000222329.4:c.1113_1115del	p.Ser373del	p.S373del	ENST00000222329	NM_006494.2	371	tcTTCc/tcc	4/4	0.532301990681304	3	FACETS	1	0.989	1	0.572	0.542	0.603	CLONAL	1	TRUE	1	0.816024619587472	3		1300	1037	SUCCESS
APC	324	MSKCC	GRCh37	5	112179566	112179566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755366812	NA	P-0037411-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	146	478	4	ENST00000257430.4:c.8275C>T	p.Arg2759Cys	p.R2759C	ENST00000257430	NM_000038.5	2759	Cgt/Tgt	16/16	0.816024619587472	3	FACETS	0.918	0.842	0.996	0.306	0.28	0.332	CLONAL	1	TRUE	0	0.816024619587472	3		482	549	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0038276-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	81	262	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.866	0.77	0.967	0.866	0.77	0.967	CLONAL	1	TRUE	1	0.59	2		262	317	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0038276-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	74	403	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.899	0.796	1	0.899	0.796	1	CLONAL	1	TRUE	1	0.59	2		403	279	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239419	105239419	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038276-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	138	766	0	ENST00000349310.3:c.968A>G	p.Asp323Gly	p.D323G	ENST00000349310	NM_001014432.1	323	gAc/gGc	12/15	1	2	FACETS	0.973	0.891	1	0.973	0.891	1	CLONAL	1	TRUE	1	0.59	2		766	481	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044541	47044541	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0038276-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	182	765	3	ENST00000377604.3:c.2038C>T	p.Arg680Ter	p.R680*	ENST00000377604	NM_001204468.1	680	Cga/Tga	18/24	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.59	2		768	601	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0038373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	263	425	0				ENST00000310581	NM_198253.2	-/1132			0.480521309207601	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	TRUE	0	0.517721386578335	3		425	418	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938948	76938948	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0038373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	139	714	0	ENST00000373344.5:c.1800T>G	p.Ile600Met	p.I600M	ENST00000373344	NM_000489.3	600	atT/atG	9/35	0.517721386578335	3	FACETS	0.901	0.821	0.985	0.451	0.41	0.493	CLONAL	1	TRUE	1	0.517721386578335	3		714	750	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	57	294	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.317343465008157	2		294	345	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627415	37627415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415916204	NA	P-0038685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	143	615	1	ENST00000249071.6:c.304C>T	p.Arg102Trp	p.R102W	ENST00000249071	NM_002872.4	102	Cgg/Tgg	5/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.317343465008157	2		616	749	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219343	1219344	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0038685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	108	475	0	ENST00000326873.7:c.396_397del	p.Cys134TrpfsTer28	p.C134Wfs*28	ENST00000326873	NM_000455.4	132	tGC/t	3/10	0.317343465008157	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.317343465008157	1		475	562	SUCCESS
APC	324	MSKCC	GRCh37	5	112174205	112174205	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	57	241	0	ENST00000257430.4:c.2915del	p.Gly972ValfsTer8	p.G972Vfs*8	ENST00000257430	NM_000038.5	972	Ggt/gt	16/16	0.317343465008157	1	FACETS	0.942	0.813	1	0.942	0.813	1	CLONAL	1	TRUE	0	0.317343465008157	1		241	321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519986	NA	P-0038838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	554	775	0	ENST00000269305.4:c.809T>C	p.Phe270Ser	p.F270S	ENST00000269305	NM_001126112.2	270	tTt/tCt	8/11	0.840226525825941	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.840226525825941	2		775	647	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944486	40944486	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1303359688	NA	P-0038838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	193	645	0	ENST00000373198.4:c.2016C>A	p.Asn672Lys	p.N672K	ENST00000373198	NM_133170.3	672	aaC/aaA	12/32	0.256568879664958	4	FACETS	1	0.952	1	0.259	0.24	0.279	INDETERMINATE	1	TRUE	0	0.840226525825941	4		645	816	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425038	49425038	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783690	NA	P-0038838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	324	945	1	ENST00000301067.7:c.13450C>T	p.Arg4484Ter	p.R4484*	ENST00000301067	NM_003482.3	4484	Cga/Tga	39/54	0.804090272805072	3	FACETS	1	0.958	1	0.508	0.48	0.537	CLONAL	1	TRUE	1	0.840226525825941	3		946	1078	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197182	106197182	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	173	405	0	ENST00000380013.4:c.5515G>T	p.Gly1839Cys	p.G1839C	ENST00000380013	NM_001127208.2	1839	Ggt/Tgt	11/11	0.840226525825941	2	FACETS	1	0.989	1	0.641	0.602	0.681	CLONAL	1	TRUE	0	0.840226525825941	2		405	321	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435035	18435035	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	91	277	0	ENST00000266497.5:c.20C>G	p.Thr7Arg	p.T7R	ENST00000266497		7	aCg/aGg	1/31	0.804090272805072	3	FACETS	0.779	0.696	0.866	0.389	0.348	0.433	SUBCLONAL	1	TRUE	1	0.840226525825941	3		277	395	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396300	139396300	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038838-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	290	976	0	ENST00000277541.6:c.5538G>T	p.Gln1846His	p.Q1846H	ENST00000277541	NM_017617.3	1846	caG/caT	30/34	0.2321986572635	3	FACETS	1	0.951	1	0.337	0.317	0.357	INDETERMINATE	1	TRUE	0	0.840226525825941	3		976	971	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0039161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	406	457	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.670322074806803	5	FACETS	0.95	0.91	0.99	0.95	0.91	0.99	CLONAL	3	TRUE	2	0.713430010771014	5		457	827	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1202793339	NA	P-0039161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	348	599	0	ENST00000269305.4:c.560-1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.708803855135459	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.713430010771014	2		599	477	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714573	52714575	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0039161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	378	631	0	ENST00000322088.6:c.332_334del	p.Ser111del	p.S111del	ENST00000322088	NM_014225.5	111	TCC/-	4/15	0.515754405005747	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	2	0.713430010771014	4		631	904	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683721	162683721	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	428	476	0	ENST00000366898.1:c.248C>G	p.Thr83Ser	p.T83S	ENST00000366898	NM_004562.2	83	aCt/aGt	3/12	0.713430010771014	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.713430010771014	2		476	566	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0039430-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	41	333	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.232520165162622	2		333	286	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288645	33288645	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039430-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	46	381	0	ENST00000374542.5:c.907G>T	p.Gly303Cys	p.G303C	ENST00000374542	NM_001141970.1	303	Ggc/Tgc	3/8	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.232520165162622	2		381	382	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610247	10610247	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039430-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	93	591	0	ENST00000171111.5:c.463G>T	p.Val155Phe	p.V155F	ENST00000171111	NM_203500.1	155	Gtc/Ttc	2/6	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.232520165162622	2		591	662	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562628	29562628	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1555615431	NA	P-0039430-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	64	282	0	ENST00000356175.3:c.3709-1G>A		p.X1237_splice	ENST00000356175	NM_000267.3	1237			0.232916785525004	3	FACETS	0.837	0.729	0.953	0.837	0.729	0.953	CLONAL	2	TRUE	1	0.232520165162622	3		282	367	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221976	1221976	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs730881984	NA	P-0039430-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	133	595	0	ENST00000326873.7:c.891G>T	p.Arg297Ser	p.R297S	ENST00000326873	NM_000455.4	297	agG/agT	7/10	1	2	FACETS	0.811	0.738	0.888	1	0.988	1	CLONAL	2	TRUE	1	0.232520165162622	2		595	705	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752723	42752724	+	missense_variant	Missense_Mutation	DNP	CG	CG	AT	novel	NA	P-0039430-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	66	565	1	ENST00000222329.4:c.1540_1541delinsAT	p.Arg514Ile	p.R514I	ENST00000222329	NM_006494.2	514	CGt/ATt	4/4	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.232520165162622	2		566	521	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665329	138665329	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039430-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	35	588	2	ENST00000330315.3:c.236G>T	p.Gly79Val	p.G79V	ENST00000330315	NM_023067.3	79	gGc/gTc	1/1	1	2	FACETS	0.432	0.353	0.521	0.432	0.353	0.521	SUBCLONAL	1	TRUE	1	0.232520165162622	2		590	697	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183205	56183205	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039430-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	26	248	0	ENST00000399503.3:c.4115G>T	p.Gly1372Val	p.G1372V	ENST00000399503	NM_005921.1	1372	gGt/gTt	18/20	1	2	FACETS	0.676	0.535	0.836	0.676	0.535	0.836	SUBCLONAL	1	TRUE	1	0.232520165162622	2		248	331	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753187	128753187	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs779123478	NA	P-0040451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	185	330	0	ENST00000377970.2:c.1348C>G	p.Arg450Gly	p.R450G	ENST00000377970	NM_002467.4	450	Cgg/Ggg	3/3	0.600778129227643	9	FACETS	1	0.963	1			1	CLONAL	2	TRUE	NA	0.600778129227643	9		330	894	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576893	7576893	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	488	796	0	ENST00000269305.4:c.953del	p.Pro318GlnfsTer27	p.P318Qfs*27	ENST00000269305	NM_001126112.2	318	cCa/ca	9/11	0.588795479469692	2	FACETS	0.929	0.896	0.963	0.929	0.896	0.963	CLONAL	2	TRUE	0	0.600778129227643	2		796	874	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020290	123020290	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040451-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	261	538	0	ENST00000355640.3:c.778C>G	p.Pro260Ala	p.P260A	ENST00000355640		260	Cca/Gca	2/7	0.600947340395456	4	FACETS	1	0.992	1			1	CLONAL	1	TRUE	NA	0.600778129227643	4		538	1013	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101612	27101612	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	60	883	3	ENST00000324856.7:c.4899del	p.Met1634Ter	p.M1634*	ENST00000324856	NM_006015.4	1632	Ccc/cc	18/20	1	2	FACETS	0.841	0.723	0.971	0.841	0.723	0.971	CLONAL	1	TRUE	1	0.15	2		886	951	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	113	654	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.0738356890379119	3	FACETS	1	0.924	1			1	INDETERMINATE	2	TRUE	NA	0.15	3		654	785	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033967	49033967	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1131690865	NA	P-0040843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	25	312	0	ENST00000267163.4:c.2104C>T	p.Gln702Ter	p.Q702*	ENST00000267163	NM_000321.2	702	Caa/Taa	20/27	1	2	FACETS	0.903	0.712	1	0.903	0.712	1	CLONAL	1	TRUE	1	0.15	2		312	369	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553117	106553117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750485966	NA	P-0040843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	35	642	1	ENST00000369096.4:c.1082C>T	p.Ser361Phe	p.S361F	ENST00000369096	NM_001198.3	361	tCc/tTc	5/7	1	2	FACETS	0.803	0.657	0.968	0.803	0.657	0.968	CLONAL	1	TRUE	1	0.15	2		643	581	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	57	425	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.821	0.714	0.935			1	INDETERMINATE	1	TRUE	NA	0.628015450467839	2		425	221	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220274	55220274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11519	1772	618	0	ENST00000275493.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000275493	NM_005228.3	222	Cgc/Tgc	6/28	0.628015450467839	56	FACETS	0.953	0.928	0.979			1	CLONAL	8	TRUE	NA	0.628015450467839	56		618	13291	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0041092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13850	663	488	0	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.628015450467839	56	FACETS	0.871	0.832	0.911			1	CLONAL	3	TRUE	NA	0.628015450467839	56		488	14513	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520087	106520087	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774448553	NA	P-0041092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	35	305	0	ENST00000359195.3:c.2515C>T	p.Arg839Cys	p.R839C	ENST00000359195	NM_002649.2	839	Cgc/Tgc	6/11	0.585121218975813	3	FACETS	0.603	0.497	0.72	0.301	0.248	0.36	SUBCLONAL	1	TRUE	1	0.628015450467839	3		305	243	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240690	55240690	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs772046081	NA	P-0041092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11992	2567	572	0	ENST00000275493.2:c.1934C>G	p.Ser645Cys	p.S645C	ENST00000275493	NM_005228.3	645	tCc/tGc	17/28	0.628015450467839	56	FACETS	1	0.985	1			1	CLONAL	10	TRUE	NA	0.628015450467839	56		572	14559	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913428	NA	P-0041092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11995	383	403	0	ENST00000275493.2:c.2156G>A	p.Gly719Asp	p.G719D	ENST00000275493	NM_005228.3	719	gGc/gAc	18/28	0.628015450467839	56	FACETS	0.885	0.833	0.939			1	CLONAL	2	TRUE	NA	0.628015450467839	56		403	12378	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517553	176517553	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149419025	NA	P-0041092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	41	571	1	ENST00000292408.4:c.254G>A	p.Arg85His	p.R85H	ENST00000292408	NM_213647.1	85	cGc/cAc	3/18	1	2	FACETS	0.235	0.195	0.28	0.235	0.195	0.28	SUBCLONAL	1	TRUE	1	0.628015450467839	2		572	555	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624244	89624245	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs786204881	NA	P-0041092-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	61	131	0	ENST00000371953.3:c.21_22del	p.Glu7AspfsTer3	p.E7Dfs*3	ENST00000371953	NM_000314.4	6	aaAGag/aaag	1/9	0.628015450467839	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.628015450467839	1		131	125	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0041888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	106	545	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.647656047676113	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.647656047676113	1		545	172	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522416	176522416	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519792	NA	P-0041888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	410	884	0	ENST00000292408.4:c.1605C>G	p.Asn535Lys	p.N535K	ENST00000292408	NM_213647.1	535	aaC/aaG	12/18	0.530682656276857	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.647656047676113	1		884	823	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142964	47142964	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	49	626	0	ENST00000409792.3:c.4999C>G	p.Gln1667Glu	p.Q1667E	ENST00000409792	NM_014159.6	1667	Cag/Gag	8/21	0.165461464483866	2	FACETS	0.633	0.541	0.732	0.317	0.27	0.366	INDETERMINATE	1	TRUE	0	0.647656047676113	2		626	239	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11270913	11270913	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs767734840	NA	P-0041888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	76	542	0	ENST00000361445.4:c.3612C>G	p.Ile1204Met	p.I1204M	ENST00000361445	NM_004958.3	1204	atC/atG	24/58	0.329959512346442	3	FACETS	0.956	0.846	1			1	INDETERMINATE	1	TRUE	NA	0.647656047676113	3		542	325	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261928	16261928	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	91	576	0	ENST00000375759.3:c.9193C>A	p.Pro3065Thr	p.P3065T	ENST00000375759	NM_015001.2	3065	Ccc/Acc	11/15	0.329959512346442	3	FACETS	0.501	0.444	0.561			1	INDETERMINATE	1	TRUE	NA	0.647656047676113	3		576	743	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247934	59247934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	176	873	0	ENST00000371222.2:c.809G>A	p.Arg270Gln	p.R270Q	ENST00000371222	NM_002228.3	270	cGa/cAa	1/1	0.464307214244524	4	FACETS	0.79	0.727	0.857	0.198	0.181	0.215	SUBCLONAL	1	TRUE	0	0.647656047676113	4		873	1133	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104377051	104377051	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	97	463	0	ENST00000369902.3:c.1162A>T	p.Arg388Trp	p.R388W	ENST00000369902	NM_016169.3	388	Agg/Tgg	10/12	0.647656047676113	1	FACETS	0.537	0.483	0.594	0.537	0.483	0.594	SUBCLONAL	1	TRUE	0	0.647656047676113	1		463	377	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007732	45007738	+	frameshift_variant	Frame_Shift_Del	DEL	TGAAGAA	TGAAGAA	-	novel	NA	P-0041888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	50	483	0	ENST00000558401.1:c.181_187del	p.Lys61GlufsTer40	p.K61Efs*40	ENST00000558401	NM_004048.2	60	cTGAAGAAt/ct	2/4	0.320320795009105	3	FACETS	0.897	0.769	1	0.448	0.384	0.517	INDETERMINATE	1	TRUE	1	0.647656047676113	3		483	228	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817771	3817771	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	222	752	0	ENST00000262367.5:c.3200G>T	p.Ser1067Ile	p.S1067I	ENST00000262367	NM_004380.2	1067	aGt/aTt	16/31	0.41291220980335	3	FACETS	0.847	0.795	0.899	0.847	0.795	0.899	CLONAL	2	TRUE	1	0.647656047676113	3		752	536	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245859	41245859	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	51	640	0	ENST00000357654.3:c.1689G>C	p.Gln563His	p.Q563H	ENST00000357654	NM_007294.3	563	caG/caC	10/23	0.647656047676113	1	FACETS	0.598	0.517	0.684	0.598	0.517	0.684	SUBCLONAL	1	TRUE	0	0.647656047676113	1		640	178	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166793	32166793	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	126	962	0	ENST00000375023.3:c.4445G>A	p.Trp1482Ter	p.W1482*	ENST00000375023	NM_004557.3	1482	tGg/tAg	24/30	0.647656047676113	3	FACETS	0.46	0.416	0.508	0.23	0.208	0.254	SUBCLONAL	1	TRUE	1	0.647656047676113	3		962	1119	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194815	29194815	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	234	976	1	ENST00000240100.2:c.913G>T	p.Glu305Ter	p.E305*	ENST00000240100	NM_001394.6	305	Gag/Tag	4/4	0.647656047676113	1	FACETS	0.583	0.545	0.622	0.583	0.545	0.622	SUBCLONAL	1	TRUE	0	0.647656047676113	1		977	838	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214865	36214866	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	T	novel	NA	P-0041888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	57	1000	4	ENST00000222270.7:c.3291_3292delinsT	p.Gly1099AlafsTer83	p.G1099Afs*83	ENST00000222270	NM_014727.1	1097	ccCGgg/ccTgg	8/37	0.212713847971836	2	FACETS	0.191	0.163	0.221	0.095	0.081	0.111	INDETERMINATE	1	TRUE	0	0.647656047676113	2		1004	923	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs17849781	NA	P-0041962-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	473	457	1	ENST00000269305.4:c.832C>G	p.Pro278Ala	p.P278A	ENST00000269305	NM_001126112.2	278	Cct/Gct	8/11	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.598367657738973	2		458	685	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380346	14380346	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041962-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	103	202	0	ENST00000256196.4:c.71G>A	p.Gly24Asp	p.G24D	ENST00000256196		24	gGc/gAc	1/6	0.598367657738973	3	FACETS	1	0.981	1	0.69	0.625	0.758	CLONAL	1	TRUE	1	0.598367657738973	3		202	324	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591101	67591101	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041962-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	117	185	0	ENST00000274335.5:c.1694G>T	p.Ser565Ile	p.S565I	ENST00000274335		565	aGc/aTc	12/15	0.598367657738973	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	0	0.598367657738973	2		185	194	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467993	50467993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041962-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	115	423	1	ENST00000331340.3:c.1228G>A	p.Gly410Ser	p.G410S	ENST00000331340	NM_006060.4	410	Ggt/Agt	8/8	0.598367657738973	3	FACETS	0.981	0.888	1	0.491	0.444	0.539	CLONAL	1	TRUE	1	0.598367657738973	3		424	509	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202701	128202701	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0041962-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	142	390	0	ENST00000341105.2:c.1017+2T>G		p.X339_splice	ENST00000341105	NM_032638.4	339			0.526650829737037	5	FACETS	0.903	0.822	0.989	0.226	0.205	0.248	CLONAL	1	TRUE	1	0.598367657738973	5		390	997	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921646	39921646	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041962-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	73	293	0	ENST00000378444.4:c.4174G>C	p.Val1392Leu	p.V1392L	ENST00000378444	NM_001123385.1	1392	Gtg/Ctg	10/15	0.374135177990021	3	FACETS	0.811	0.713	0.915	0.405	0.356	0.458	CLONAL	1	TRUE	1	0.598367657738973	3		293	391	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0042069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	79	294	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.236107291887028	4	FACETS	1	0.96	1	0.596	0.527	0.668	INDETERMINATE	1	TRUE	2	0.551634574081105	4		294	373	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374244	138374244	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	58	467	0	ENST00000289153.2:c.3200A>T	p.Asp1067Val	p.D1067V	ENST00000289153	NM_006219.2	1067	gAc/gTc	22/22	0.0911496896027506	4	FACETS	0.854	0.737	0.981	0.427	0.368	0.491	INDETERMINATE	1	TRUE	2	0.551634574081105	4		467	382	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259250	89259250	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	103	409	0	ENST00000336596.2:c.394G>T	p.Gly132Trp	p.G132W	ENST00000336596	NM_005233.5	132	Ggg/Tgg	3/17	0.551634574081105	4	FACETS	1	0.964	1	0.582	0.523	0.644	CLONAL	1	TRUE	2	0.551634574081105	4		409	498	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372696	81372696	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	64	334	0	ENST00000222390.5:c.838T>A	p.Trp280Arg	p.W280R	ENST00000222390	NM_000601.4	280	Tgg/Agg	7/18	0.276157024826559	5	FACETS	1	0.953	1	0.403	0.35	0.459	INDETERMINATE	1	TRUE	2	0.551634574081105	5		334	351	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932060	39932061	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	AT	novel	NA	P-0042069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	33	776	0	ENST00000378444.4:c.2538_2539delinsAT	p.Gln847Ter	p.Q847*	ENST00000378444	NM_001123385.1	846	ctGCag/ctATag	4/15	1	2	FACETS	0.363	0.296	0.438	0.363	0.296	0.438	SUBCLONAL	1	TRUE	1	0.551634574081105	2		776	330	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040653	47040653	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	50	797	1	ENST00000377604.3:c.1288G>T	p.Glu430Ter	p.E430*	ENST00000377604	NM_001204468.1	430	Gag/Tag	13/24	1	2	FACETS	0.579	0.494	0.672	0.579	0.494	0.672	SUBCLONAL	1	TRUE	1	0.551634574081105	2		798	313	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347185	70347185	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0042069-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	25	572	0	ENST00000374080.3:c.2850-1G>T		p.X950_splice	ENST00000374080		950			1	2	FACETS	0.392	0.31	0.486	0.392	0.31	0.486	SUBCLONAL	1	TRUE	1	0.551634574081105	2		572	231	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0042069-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	49	347	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.263609509885694	3	FACETS	0.869	0.743	1	0.869	0.743	1	CLONAL	2	TRUE	1	0.263609509885694	3		347	242	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186599	108186599	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876658415	NA	P-0042069-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	37	123	0	ENST00000278616.4:c.6056A>G	p.Tyr2019Cys	p.Y2019C	ENST00000278616	NM_000051.3	2019	tAt/tGt	41/63	0.263609509885694	2	FACETS	0.942	0.79	1	0.942	0.79	1	CLONAL	2	TRUE	0	0.263609509885694	2		123	149	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220400	1220400	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1359582062	NA	P-0042069-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	424	658	0	ENST00000326873.7:c.493G>T	p.Glu165Ter	p.E165*	ENST00000326873	NM_000455.4	165	Gag/Tag	4/10	NA	3	FACETS	1	0.978	1			1	INDETERMINATE	4	TRUE	NA	0.263609509885694	3		658	882	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175946	176175947	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0042069-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	17	107	0	ENST00000367669.3:c.168dup	p.Gly57ArgfsTer21	p.G57Rfs*21	ENST00000367669	NM_022457.5	56	-/C	1/20	0.177597388485462	4	FACETS	0.776	0.587	0.993	0.776	0.587	0.993	CLONAL	2	TRUE	2	0.263609509885694	4		107	105	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419973	41419973	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042069-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	70	605	0	ENST00000373198.4:c.348C>G	p.Ser116Arg	p.S116R	ENST00000373198	NM_133170.3	116	agC/agG	3/32	1	2	FACETS	0.942	0.822	1	0.942	0.822	1	CLONAL	1	TRUE	1	0.263609509885694	2		605	564	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443418	187443418	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0042069-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	121	289	0	ENST00000232014.4:c.1709-1G>A		p.X570_splice	ENST00000232014	NM_001130845.1	570			0.107808323233641	5	FACETS	0.97	0.888	1	0.97	0.888	1	INDETERMINATE	4	TRUE	1	0.263609509885694	5		289	330	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143326433	143326433	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042069-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	35	350	0	ENST00000262992.4:c.181A>G	p.Thr61Ala	p.T61A	ENST00000262992	NM_001101669.1	61	Aca/Gca	4/24	1	2	FACETS	0.795	0.653	0.953	0.795	0.653	0.953	CLONAL	1	TRUE	1	0.263609509885694	2		350	334	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295440	1295440	+	upstream_gene_variant	5'Flank	DEL	G	G	-	rs1320348397	NA	P-0042069-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	12	46	0				ENST00000310581	NM_198253.2	-/1132			0.216548856064539	4	FACETS	1	0.752	1	1	0.752	1	CLONAL	2	TRUE	2	0.263609509885694	4		46	55	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974206	2974206	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042069-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	84	692	0	ENST00000396946.4:c.1399C>A	p.Pro467Thr	p.P467T	ENST00000396946	NM_032415.4	467	Ccc/Acc	10/25	0.107808323233641	5	FACETS	1	0.976	1	0.364	0.321	0.409	INDETERMINATE	1	TRUE	1	0.263609509885694	5		692	611	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81399274	81399274	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042069-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	102	606	0	ENST00000222390.5:c.14A>T	p.Lys5Ile	p.K5I	ENST00000222390	NM_000601.4	5	aAa/aTa	1/18	0.107808323233641	5	FACETS	0.863	0.773	0.958	0.431	0.386	0.479	INDETERMINATE	2	TRUE	1	0.263609509885694	5		606	626	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829065	128829065	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042069-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	15	50	0	ENST00000249373.3:c.73G>T	p.Asp25Tyr	p.D25Y	ENST00000249373	NM_005631.4	25	Gac/Tac	1/12	0.107808323233641	5	FACETS	1	0.809	1	0.551	0.412	0.71	INDETERMINATE	2	TRUE	1	0.263609509885694	5		50	72	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717626	89717632	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCCAG	CTGCCAG	-	novel	NA	P-0042711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	80	295	1	ENST00000371953.3:c.653_659del	p.Cys218Ter	p.C218*	ENST00000371953	NM_000314.4	217	gtCTGCCAG/gt	7/9	0.551735589097457	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.551735589097457	1		296	201	SUCCESS
AR	367	MSKCC	GRCh37	X	66931289	66931289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042711-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	55	210	0	ENST00000374690.3:c.1931G>A	p.Gly644Glu	p.G644E	ENST00000374690	NM_000044.3	644	gGa/gAa	4/8	1	1	FACETS	0.642	0.555	0.733	0.642	0.555	0.733	SUBCLONAL	1	TRUE	0	0.551735589097457	1		210	225	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59886067	59886067	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs45459799	NA	P-0042766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	10	424	0	ENST00000259008.2:c.679C>G	p.Gln227Glu	p.Q227E	ENST00000259008	NM_032043.2	227	Caa/Gaa	7/20	0.275000637488311	2	FACETS	1	0.732	1	0.535	0.368	0.736	CLONAL	1	TRUE	0	0.275000637488311	2		424	68	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578275	+	protein_altering_variant	In_Frame_Del	DEL	ATAAGATGCTG	ATAAGATGCTG	CA	novel	NA	P-0042766-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	16	626	2	ENST00000269305.4:c.574_584delinsTG	p.Gln192_Ile195delinsCys	p.Q192_I195delinsC	ENST00000269305	NM_001126112.2	192	CAGCATCTTATc/TGc	6/11	0.275000637488311	2	FACETS	1	0.85	1	1	0.927	1	CLONAL	3	TRUE	0	0.275000637488311	2		628	35	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246414	10246414	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs1331424954	NA	P-0042887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	107	688	0	ENST00000340748.4:c.4723C>T	p.Gln1575Ter	p.Q1575*	ENST00000340748		1575	Cag/Tag	38/40	1	2	FACETS	0.638	0.572	0.708	0.638	0.572	0.708	SUBCLONAL	1	TRUE	1	0.405767255874784	2		688	827	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115953	8115957	+	frameshift_variant	Frame_Shift_Del	DEL	CCACC	CCACC	-	novel	NA	P-0042887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	86	355	1	ENST00000346208.3:c.1301_1305del	p.His434LeufsTer71	p.H434Lfs*71	ENST00000346208		433	caCCACCcc/cacc	6/6	1	2	FACETS	0.912	0.81	1	0.912	0.81	1	CLONAL	1	TRUE	1	0.405767255874784	2		356	465	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0042966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	443	571	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	0.361140319846417	1	FACETS	0.957	0.913	1	0.957	0.913	1	CLONAL	1	TRUE	0	0.514482558180467	1		571	1337	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533652	63533652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779029020	NA	P-0042966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	137	605	0	ENST00000307078.5:c.1502G>A	p.Gly501Glu	p.G501E	ENST00000307078	NM_004655.3	501	gGg/gAg	6/11	0.514482558180467	6	FACETS	0.843	0.764	0.926			1	CLONAL	1	TRUE	NA	0.514482558180467	6		605	1282	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725059	47725059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	147	743	0	ENST00000449228.1:c.685G>A	p.Gly229Ser	p.G229S	ENST00000449228	NM_001127240.2	229	Ggt/Agt	4/4	0.194040869234669	2	FACETS	0.58	0.529	0.634	0.29	0.264	0.317	INDETERMINATE	1	TRUE	0	0.514482558180467	2		743	985	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	249	700	1	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.33597447907356	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.33597447907356	1		701	1101	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACT	novel	NA	P-0043102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1433	471	740	0	ENST00000275493.2:c.2310_2311insTAC	p.Asp770_Asn771insTyr	p.D770_N771insY	ENST00000275493	NM_005228.3	770	gac/gACTac	20/28	0.120055069717041	3	FACETS	0.86	0.819	0.901	0.86	0.819	0.901	INDETERMINATE	2	TRUE	1	0.33597447907356	3		740	1904	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265477	198265477	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043102-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	94	466	0	ENST00000335508.6:c.2680G>A	p.Asp894Asn	p.D894N	ENST00000335508	NM_012433.2	894	Gat/Aat	18/25	1	2	FACETS	0.887	0.79	0.99	0.887	0.79	0.99	CLONAL	1	TRUE	1	0.33597447907356	2		466	631	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	230	750	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.428576904881427	1	FACETS	0.888	0.828	0.949	0.888	0.828	0.949	CLONAL	1	TRUE	0	0.428576904881427	1		750	950	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115736	8115737	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0043231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	44	497	0	ENST00000346208.3:c.1083_1084dup	p.Gln362ProfsTer43	p.Q362Pfs*43	ENST00000346208		361	atc/atCCc	6/6	1	2	FACETS	0.411	0.345	0.485	0.411	0.345	0.485	SUBCLONAL	1	TRUE	1	0.428576904881427	2		497	499	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842647	68842647	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	116	695	0	ENST00000261769.5:c.583C>T	p.Gln195Ter	p.Q195*	ENST00000261769	NM_004360.3	195	Caa/Taa	5/16	0.425871585049709	1	FACETS	0.823	0.745	0.904	0.823	0.745	0.904	CLONAL	1	TRUE	0	0.428576904881427	1		695	517	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264348	46264348	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	104	444	0	ENST00000371998.3:c.1395C>A	p.Ser465Arg	p.S465R	ENST00000371998		465	agC/agA	11/23	1	2	FACETS	0.788	0.707	0.874	0.788	0.707	0.874	SUBCLONAL	1	TRUE	1	0.428576904881427	2		444	616	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176145127	176145127	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043504-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	38	387	0	ENST00000367669.3:c.484C>T	p.Gln162Ter	p.Q162*	ENST00000367669	NM_022457.5	162	Cag/Tag	3/20	1	2	FACETS	0.792	0.659	0.936	0.792	0.659	0.936	CLONAL	1	TRUE	1	0.417447220579592	2		387	230	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0043504-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	157	580	0	ENST00000269305.4:c.672+1G>C		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.287785228616049	1	FACETS	0.699	0.64	0.76	0.699	0.64	0.76	SUBCLONAL	1	TRUE	0	0.417447220579592	1		580	852	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184361	7184361	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043504-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	144	554	0	ENST00000302850.5:c.940G>C	p.Glu314Gln	p.E314Q	ENST00000302850	NM_000208.2	314	Gag/Cag	3/22	1	2	FACETS	0.693	0.631	0.758	0.693	0.631	0.758	SUBCLONAL	1	TRUE	1	0.417447220579592	2		554	996	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551100	41551100	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043504-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	133	475	0	ENST00000263253.7:c.3244C>G	p.Gln1082Glu	p.Q1082E	ENST00000263253	NM_001429.3	1082	Cag/Gag	17/31	1	2	FACETS	0.872	0.793	0.955	0.872	0.793	0.955	CLONAL	1	TRUE	1	0.417447220579592	2		475	731	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553348	41553348	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043504-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	60	525	0	ENST00000263253.7:c.3437C>G	p.Ser1146Cys	p.S1146C	ENST00000263253	NM_001429.3	1146	tCt/tGt	18/31	1	2	FACETS	0.636	0.549	0.73	0.636	0.549	0.73	SUBCLONAL	1	TRUE	1	0.417447220579592	2		525	452	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553371	41553371	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043504-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	62	462	0	ENST00000263253.7:c.3460G>C	p.Asp1154His	p.D1154H	ENST00000263253	NM_001429.3	1154	Gac/Cac	18/31	1	2	FACETS	0.702	0.608	0.803	0.702	0.608	0.803	SUBCLONAL	1	TRUE	1	0.417447220579592	2		462	423	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41554462	41554462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043504-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	82	431	0	ENST00000263253.7:c.3548G>A	p.Cys1183Tyr	p.C1183Y	ENST00000263253	NM_001429.3	1183	tGc/tAc	19/31	1	2	FACETS	0.569	0.502	0.642	0.569	0.502	0.642	SUBCLONAL	1	TRUE	1	0.417447220579592	2		431	690	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170002367	170002367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043504-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	29	212	0	ENST00000295797.4:c.1186G>A	p.Asp396Asn	p.D396N	ENST00000295797	NM_002740.5	396	Gac/Aac	12/18	0.338141620344272	3	FACETS	0.785	0.634	0.954	0.392	0.317	0.477	CLONAL	1	TRUE	1	0.417447220579592	3		212	214	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0043504-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	34	375	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	1	2	FACETS	0.747	0.615	0.893	0.747	0.615	0.893	SUBCLONAL	1	TRUE	1	0.417447220579592	2		375	218	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412506	63412506	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043504-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	148	538	0	ENST00000330258.3:c.661T>A	p.Phe221Ile	p.F221I	ENST00000330258	NM_152424.3	221	Ttc/Atc	2/2	0.34742905735597	1	FACETS	0.663	0.606	0.723	0.663	0.606	0.723	SUBCLONAL	1	TRUE	0	0.417447220579592	1		538	846	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371409680	NA	P-0043597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	717	1121	0	ENST00000269305.4:c.848G>C	p.Arg283Pro	p.R283P	ENST00000269305	NM_001126112.2	283	cGc/cCc	8/11	0.626206825298885	2	FACETS	0.934	0.908	0.961	0.934	0.908	0.961	CLONAL	2	TRUE	0	0.638851645639499	2		1121	1201	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646949	37646949	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1159844816	NA	P-0043597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	339	827	1	ENST00000447079.4:c.2071A>G	p.Ile691Val	p.I691V	ENST00000447079	NM_015083.1	691	Atc/Gtc	3/14	0.626206825298885	2	FACETS	0.953	0.914	0.991	0.953	0.914	0.991	CLONAL	2	TRUE	0	0.638851645639499	2		828	557	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326258	62326258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755300600	NA	P-0043597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	400	1195	0	ENST00000360203.5:c.3274C>T	p.Leu1092Phe	p.L1092F	ENST00000360203	NM_001283009.1	1092	Ctc/Ttc	32/35	0.2795926579418	3	FACETS	0.779	0.743	0.816	0.779	0.743	0.816	INDETERMINATE	2	TRUE	1	0.638851645639499	3		1195	1060	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920102	1920102	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0043597-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	58	1071	0	ENST00000382891.5:c.1162A>T	p.Lys388Ter	p.K388*	ENST00000382891	NM_133335.3	388	Aag/Tag	5/22	0.431529071701592	1	FACETS	0.245	0.21	0.282	0.245	0.21	0.282	SUBCLONAL	1	TRUE	0	0.638851645639499	1		1071	505	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0043728-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	78	241	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.905	0.808	1	1	0.987	1	CLONAL	3	TRUE	1	0.245487542812855	2		241	234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577080	7577087	+	frameshift_variant	Frame_Shift_Del	DEL	TTCCTCTG	TTCCTCTG	-	novel	NA	P-0043728-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	597	735	0	ENST00000269305.4:c.851_858del	p.Thr284ArgfsTer19	p.T284Rfs*19	ENST00000269305	NM_001126112.2	284	aCAGAGGAA/a	8/11	0.245487542812855	2	FACETS	0.951	0.93	0.97	1	0.998	1	CLONAL	7	TRUE	0	0.245487542812855	2		735	731	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937741	76937744	+	frameshift_variant	Frame_Shift_Del	DEL	TTAC	TTAC	-	novel	NA	P-0043728-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	134	495	0	ENST00000373344.5:c.3004_3007del	p.Val1002LeufsTer30	p.V1002Lfs*30	ENST00000373344	NM_000489.3	1002	GTAAtt/tt	9/35	0.245487542812855	1	FACETS	1	0.98	1	1	0.992	1	CLONAL	2	TRUE	0	0.245487542812855	1		495	391	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0043801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	156	545	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.429310596510296	2		545	633	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736583	85736583	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	38	180	0	ENST00000370580.1:c.64G>T	p.Glu22Ter	p.E22*	ENST00000370580	NM_003921.4	22	Gaa/Taa	2/3	1	2	FACETS	0.816	0.68	0.964	0.816	0.68	0.964	CLONAL	1	TRUE	1	0.429310596510296	2		180	217	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562865	21562865	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1216948921	NA	P-0043801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	81	405	0	ENST00000382592.4:c.1054C>T	p.Arg352Trp	p.R352W	ENST00000382592	NM_014572.2	352	Cgg/Tgg	4/8	1	2	FACETS	0.494	0.435	0.558	0.494	0.435	0.558	SUBCLONAL	1	TRUE	1	0.429310596510296	2		405	764	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647254	23647254	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	120	555	0	ENST00000261584.4:c.613G>C	p.Glu205Gln	p.E205Q	ENST00000261584	NM_024675.3	205	Gaa/Caa	4/13	0.429310596510296	1	FACETS	0.697	0.631	0.766	0.697	0.631	0.766	SUBCLONAL	1	TRUE	0	0.429310596510296	1		555	630	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647455	23647455	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	126	470	0	ENST00000261584.4:c.412G>C	p.Glu138Gln	p.E138Q	ENST00000261584	NM_024675.3	138	Gag/Cag	4/13	0.429310596510296	1	FACETS	0.736	0.669	0.808	0.736	0.669	0.808	SUBCLONAL	1	TRUE	0	0.429310596510296	1		470	626	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511639	38511639	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	107	610	0	ENST00000254066.5:c.1137G>A	p.Met379Ile	p.M379I	ENST00000254066	NM_000964.3	379	atG/atA	8/9	1	2	FACETS	0.612	0.549	0.68	0.612	0.549	0.68	SUBCLONAL	1	TRUE	1	0.429310596510296	2		610	814	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511649	38511649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	94	575	0	ENST00000254066.5:c.1147G>A	p.Asp383Asn	p.D383N	ENST00000254066	NM_000964.3	383	Gac/Aac	8/9	1	2	FACETS	0.59	0.525	0.66	0.59	0.525	0.66	SUBCLONAL	1	TRUE	1	0.429310596510296	2		575	742	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246443	41246443	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	165	566	0	ENST00000357654.3:c.1105G>C	p.Asp369His	p.D369H	ENST00000357654	NM_007294.3	369	Gat/Cat	10/23	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.429310596510296	2		566	624	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252856	36252856	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	75	278	0	ENST00000300305.3:c.506G>C	p.Arg169Thr	p.R169T	ENST00000300305		169	aGa/aCa	4/8	1	2	FACETS	0.792	0.697	0.894	0.792	0.697	0.894	SUBCLONAL	1	TRUE	1	0.429310596510296	2		278	441	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442555	52442558	+	frameshift_variant	Frame_Shift_Del	DEL	TAGA	TAGA	-	novel	NA	P-0043801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	190	484	0	ENST00000460680.1:c.187_190del	p.Ser63ProfsTer8	p.S63Pfs*8	ENST00000460680	NM_004656.3	63	TCTAcc/cc	4/17	0.429310596510296	1	FACETS	0.997	0.925	1	0.997	0.925	1	CLONAL	1	TRUE	0	0.429310596510296	1		484	697	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651944	36651947	+	frameshift_variant	Frame_Shift_Del	DEL	CGGC	CGGC	GGA	novel	NA	P-0043801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	179	571	1	ENST00000244741.5:c.66_69delinsGGA	p.Phe22LeufsTer9	p.F22Lfs*9	ENST00000244741	NM_000389.4	22	ttCGGC/ttGGA	2/3	1	2	FACETS	0.903	0.833	0.977	0.903	0.833	0.977	CLONAL	1	TRUE	1	0.429310596510296	2		572	923	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651984	36651985	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0043801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	237	615	0	ENST00000244741.5:c.108_109del	p.Leu37AsnfsTer10	p.L37Nfs*10	ENST00000244741	NM_000389.4	36	GCg/g	2/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.429310596510296	2		615	987	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402728	139402728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554728424	NA	P-0043801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	221	703	1	ENST00000277541.6:c.3281G>A	p.Cys1094Tyr	p.C1094Y	ENST00000277541	NM_017617.3	1094	tGc/tAc	20/34	0.429310596510296	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.429310596510296	1		704	720	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106144	27106155	+	frameshift_variant	Frame_Shift_Del	DEL	TCTAGCACCTTG	TCTAGCACCTTG	C	novel	NA	P-0043801-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	158	461	0	ENST00000324856.7:c.5755_5766delinsC	p.Ser1919HisfsTer6	p.S1919Hfs*6	ENST00000324856	NM_006015.4	1919	TCTAGCACCTTG/C	20/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.429310596510296	2		461	664	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0043813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	160	157	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.70420465472957	2	FACETS	0.842	0.791	0.891	0.842	0.791	0.891	CLONAL	2	TRUE	0	0.70420465472957	2		157	270	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0043813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	166	331	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.70420465472957	3	FACETS	0.99	0.926	1	0.99	0.926	1	CLONAL	2	TRUE	1	0.70420465472957	3		331	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0043813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	377	411	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.70420465472957	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.70420465472957	1		411	568	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515247	106515247	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	81	325	0	ENST00000359195.3:c.2390C>A	p.Ala797Glu	p.A797E	ENST00000359195	NM_002649.2	797	gCa/gAa	5/11	0.302447983220423	3	FACETS	1	0.914	1	0.521	0.46	0.586	CLONAL	1	TRUE	1	0.343715710330218	3		325	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057519990	NA	P-0043844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	198	591	0	ENST00000269305.4:c.796G>T	p.Gly266Ter	p.G266*	ENST00000269305	NM_001126112.2	266	Gga/Tga	8/11	0.343715710330218	1	FACETS	0.762	0.71	0.816	1	0.992	1	SUBCLONAL	2	TRUE	0	0.343715710330218	1		591	626	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873595	35873595	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	66	201	0	ENST00000303115.3:c.551C>A	p.Ser184Tyr	p.S184Y	ENST00000303115	NM_002185.3	184	tCc/tAc	5/8	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.343715710330218	2		201	280	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221284	1221284	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	176	718	0	ENST00000326873.7:c.810del	p.Ser271AlafsTer16	p.S271Afs*16	ENST00000326873	NM_000455.4	269	aaG/aa	6/10	0.343715710330218	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.343715710330218	1		718	669	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843426	156843426	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	153	652	1	ENST00000524377.1:c.852C>A	p.Phe284Leu	p.F284L	ENST00000524377	NM_002529.3	284	ttC/ttA	8/17	0.224826399139764	3	FACETS	1	0.988	1	0.749	0.687	0.814	CLONAL	1	TRUE	1	0.343715710330218	3		653	696	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844410	156844410	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	247	894	1	ENST00000524377.1:c.1243C>A	p.Pro415Thr	p.P415T	ENST00000524377	NM_002529.3	415	Cct/Act	10/17	0.224826399139764	3	FACETS	0.782	0.731	0.835	0.782	0.731	0.835	SUBCLONAL	2	TRUE	1	0.343715710330218	3		895	1077	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175822	176175822	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	69	387	0	ENST00000367669.3:c.293G>A	p.Gly98Asp	p.G98D	ENST00000367669	NM_022457.5	98	gGc/gAc	1/20	0.289625772538804	5	FACETS	1	0.938	1			1	CLONAL	1	TRUE	NA	0.343715710330218	5		387	539	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105624	30105624	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	118	654	0	ENST00000331968.5:c.1062T>G	p.Ser354Arg	p.S354R	ENST00000331968	NM_002742.2	354	agT/agG	7/18	0.339884810603309	2	FACETS	0.962	0.868	1	0.481	0.434	0.53	CLONAL	1	TRUE	0	0.343715710330218	2		654	714	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029410	14029410	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	60	365	1	ENST00000311895.7:c.1621G>T	p.Asp541Tyr	p.D541Y	ENST00000311895	NM_005236.2	541	Gat/Tat	8/11	1	2	FACETS	0.825	0.713	0.947	0.825	0.713	0.947	CLONAL	1	TRUE	1	0.343715710330218	2		366	423	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660581	67660581	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	97	558	0	ENST00000264010.4:c.1481G>T	p.Arg494Leu	p.R494L	ENST00000264010	NM_006565.3	494	cGc/cTc	8/12	0.281132385205337	2	FACETS	0.761	0.678	0.849	0.38	0.339	0.425	SUBCLONAL	1	TRUE	0	0.343715710330218	2		558	742	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951081	17951081	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	210	711	0	ENST00000458235.1:c.1212C>A	p.Ser404Arg	p.S404R	ENST00000458235	NM_000215.3	404	agC/agA	9/24	0.281132385205337	2	FACETS	0.82	0.764	0.878	0.82	0.764	0.878	CLONAL	2	TRUE	0	0.343715710330218	2		711	745	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015675	27015675	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	90	569	0	ENST00000335756.4:c.262G>T	p.Ala88Ser	p.A88S	ENST00000335756	NM_001809.3	88	Gcc/Tcc	3/5	1	2	FACETS	0.879	0.781	0.983	0.879	0.781	0.983	CLONAL	1	TRUE	1	0.343715710330218	2		569	596	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710520	40710520	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0043844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	53	529	0	ENST00000373198.4:c.4329+2T>A		p.X1443_splice	ENST00000373198	NM_133170.3	1443			0.343715710330218	1	FACETS	0.424	0.361	0.493	0.424	0.361	0.493	SUBCLONAL	1	TRUE	0	0.343715710330218	1		529	602	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747950	41747950	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	45	198	0	ENST00000226382.2:c.819G>T	p.Trp273Cys	p.W273C	ENST00000226382	NM_003924.3	273	tgG/tgT	3/3	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.343715710330218	2		198	205	SUCCESS
APC	324	MSKCC	GRCh37	5	112175976	112175976	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	77	228	0	ENST00000257430.4:c.4685A>T	p.Asp1562Val	p.D1562V	ENST00000257430	NM_000038.5	1562	gAc/gTc	16/16	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.343715710330218	2		228	326	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637648	176637648	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	145	513	0	ENST00000439151.2:c.2248G>C	p.Ala750Pro	p.A750P	ENST00000439151	NM_022455.4	750	Gct/Cct	5/23	0.326941907213795	2	FACETS	1	0.985	1	0.676	0.619	0.736	CLONAL	1	TRUE	0	0.343715710330218	2		513	624	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048797	180048797	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs748004441	NA	P-0043844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	88	863	0	ENST00000261937.6:c.1765C>G	p.Arg589Gly	p.R589G	ENST00000261937	NM_182925.4	589	Cgc/Ggc	13/30	0.343715710330218	1	FACETS	0.654	0.58	0.734	0.654	0.58	0.734	SUBCLONAL	1	TRUE	0	0.343715710330218	1		863	648	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978820	13978820	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	88	458	0	ENST00000405192.2:c.287G>A	p.Cys96Tyr	p.C96Y	ENST00000405192	NM_001163147.1	96	tGt/tAt	6/12	0.224826399139764	3	FACETS	0.846	0.75	0.95	0.423	0.375	0.475	CLONAL	1	TRUE	1	0.343715710330218	3		458	709	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877919	151877919	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	48	351	0	ENST00000262189.6:c.7026G>C	p.Met2342Ile	p.M2342I	ENST00000262189	NM_170606.2	2342	atG/atC	36/59	1	2	FACETS	0.63	0.534	0.737	0.63	0.534	0.737	SUBCLONAL	1	TRUE	1	0.343715710330218	2		351	443	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739658	145739658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1010524385	NA	P-0043844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	102	738	0	ENST00000428558.2:c.1793C>T	p.Pro598Leu	p.P598L	ENST00000428558	NM_004260.3	598	cCa/cTa	11/22	0.339884810603309	2	FACETS	0.802	0.717	0.892	0.401	0.358	0.446	CLONAL	1	TRUE	0	0.343715710330218	2		738	740	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5029816	5029816	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	155	446	0	ENST00000381652.3:c.260T>C	p.Leu87Ser	p.L87S	ENST00000381652	NM_004972.3	87	tTa/tCa	4/25	0.323867512534801	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.343715710330218	1		446	579	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521350	8521350	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043844-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	63	431	0	ENST00000356435.5:c.888G>T	p.Gln296His	p.Q296H	ENST00000356435		296	caG/caT	9/35	0.284494833217291	0	FACETS	0.544	0.472	0.622			1	SUBCLONAL	1	TRUE	0	0.343715710330218	0		431	442	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159748	20159748	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043848-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	22	331	0	ENST00000379607.5:c.11A>G	p.Asn4Ser	p.N4S	ENST00000379607	NM_001412.3	4	aAt/aGt	1/7	0.350312552887295	2	FACETS	0.516	0.403	0.644			1	SUBCLONAL	1	TRUE	NA	0.539647327656455	2		331	158	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0044066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	186	347	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA	2	FACETS	0.914	0.868	0.959			1	INDETERMINATE	2	TRUE	NA	0.734498836334973	2		347	277	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920817	NA	P-0044066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	228	537	0	ENST00000269305.4:c.481G>A	p.Ala161Thr	p.A161T	ENST00000269305	NM_001126112.2	161	Gcc/Acc	5/11	0.712726931349019	1	FACETS	0.997	0.946	1	0.997	0.946	1	CLONAL	1	TRUE	0	0.734498836334973	1		537	394	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241084	39241084	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730881024	NA	P-0044066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	51	378	0	ENST00000402219.2:c.1987A>G	p.Ile663Val	p.I663V	ENST00000402219	NM_005633.3	663	Ata/Gta	12/23	0.431658169028075	1	FACETS	0.357	0.306	0.412	0.357	0.306	0.412	INDETERMINATE	1	TRUE	0	0.734498836334973	1		378	246	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739888	41739888	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	202	324	1	ENST00000242208.4:c.85C>A	p.His29Asn	p.H29N	ENST00000242208	NM_002192.2	29	Cac/Aac	2/3	0.6839944085374	2	FACETS	0.887	0.843	0.93	0.887	0.843	0.93	CLONAL	2	TRUE	0	0.734498836334973	2		325	310	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112764448	112764448	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	49	359	0	ENST00000369452.4:c.1057C>T	p.Gln353Ter	p.Q353*	ENST00000369452	NM_007373.3	353	Cag/Tag	5/9	0.431658169028075	1	FACETS	0.306	0.261	0.355	0.306	0.261	0.355	INDETERMINATE	1	TRUE	0	0.734498836334973	1		359	276	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859028	57859028	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766741235	NA	P-0044066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	320	548	1	ENST00000228682.2:c.524C>T	p.Pro175Leu	p.P175L	ENST00000228682	NM_005269.2	175	cCa/cTa	5/12	0.568637436888279	3	FACETS	0.82	0.78	0.861			1	CLONAL	2	TRUE	NA	0.734498836334973	3		549	726	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014071	14014071	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs368281878	NA	P-0044066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	83	498	0	ENST00000311895.7:c.49G>C	p.Glu17Gln	p.E17Q	ENST00000311895	NM_005236.2	17	Gag/Cag	1/11	0.734498836334973	1	FACETS	0.439	0.39	0.489	0.439	0.39	0.489	SUBCLONAL	1	TRUE	0	0.734498836334973	1		498	326	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143994	11143994	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	250	441	0	ENST00000358026.2:c.3575G>T	p.Arg1192Leu	p.R1192L	ENST00000358026	NM_001128849.1	1192	cGc/cTc	26/36	0.659384998139268	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.734498836334973	1		441	397	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218339	36218339	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	202	511	0	ENST00000222270.7:c.4118A>C	p.Asp1373Ala	p.D1373A	ENST00000222270	NM_014727.1	1373	gAt/gCt	16/37	1	2	FACETS	0.987	0.922	1	0.987	0.922	1	CLONAL	1	TRUE	1	0.734498836334973	2		511	557	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219963	36219963	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	265	523	0	ENST00000222270.7:c.4765G>T	p.Asp1589Tyr	p.D1589Y	ENST00000222270	NM_014727.1	1589	Gat/Tat	21/37	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.734498836334973	2		523	710	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594047	158594047	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	69	253	0	ENST00000263640.3:c.1526G>T	p.Cys509Phe	p.C509F	ENST00000263640	NM_001105.4	509	tGt/tTt	11/11	1	2	FACETS	0.85	0.752	0.953	0.85	0.752	0.953	CLONAL	1	TRUE	1	0.734498836334973	2		253	221	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732670	204732670	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	104	339	0	ENST00000302823.3:c.5C>A	p.Ala2Asp	p.A2D	ENST00000302823	NM_005214.4	2	gCt/gAt	1/4	1	2	FACETS	0.902	0.818	0.989	0.902	0.818	0.989	CLONAL	1	TRUE	1	0.734498836334973	2		339	314	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962450	38962450	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs369914112	NA	P-0044066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	69	96	0	ENST00000357387.3:c.1682A>G	p.Asn561Ser	p.N561S	ENST00000357387	NM_152756.3	561	aAt/aGt	19/38	0.269341875570483	2	FACETS	1	0.956	1	0.573	0.511	0.636	INDETERMINATE	1	TRUE	0	0.734498836334973	2		96	164	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137524824	137524824	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0044066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	85	237	0	ENST00000367739.4:c.547-2A>G		p.X183_splice	ENST00000367739	NM_000416.2	183			0.677441776374507	1	FACETS	0.927	0.846	1	0.927	0.846	1	CLONAL	1	TRUE	0	0.734498836334973	1		237	158	SUCCESS
MET	4233	MSKCC	GRCh37	7	116414934	116414934	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0044066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	176	435	2	ENST00000397752.3:c.3029-1G>T		p.X1010_splice	ENST00000397752	NM_000245.2	1010			1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.734498836334973	2		437	476	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145736899	145736899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370069034	NA	P-0044066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	355	570	4	ENST00000428558.2:c.3542G>A	p.Arg1181Gln	p.R1181Q	ENST00000428558	NM_004260.3	1181	cGa/cAa	22/22	0.723171793746459	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.734498836334973	1		574	578	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929245	44929245	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044066-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	72	241	0	ENST00000377967.4:c.2345C>T	p.Ala782Val	p.A782V	ENST00000377967	NM_021140.2	782	gCc/gTc	17/29	0.659384998139268	0	FACETS		NA	1			1	NA	1	TRUE	NA	0.734498836334973	0		241	166	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383360	42383360	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1555843601	NA	P-0044087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	80	545	0	ENST00000221972.3:c.379+1G>A		p.X127_splice	ENST00000221972	NM_021601.3	127			1	2	FACETS	0.441	0.388	0.497	0.441	0.388	0.497	SUBCLONAL	1	TRUE	1	0.615212856788284	2		545	590	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401585	401585	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	164	559	0	ENST00000380956.4:c.907A>T	p.Asn303Tyr	p.N303Y	ENST00000380956	NM_001195286.1	303	Aac/Tac	7/9	1	2	FACETS	0.884	0.815	0.955	0.884	0.815	0.955	CLONAL	1	TRUE	1	0.615212856788284	2		559	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	408	911	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.568397081481136	1	FACETS	0.919	0.877	0.961	0.919	0.877	0.961	CLONAL	1	TRUE	0	0.606301361474768	1		911	1021	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	152	443	0	ENST00000288602.6:c.1397G>T	p.Gly466Val	p.G466V	ENST00000288602	NM_004333.4	466	gGa/gTa	11/18	1	2	FACETS	0.985	0.907	1	0.985	0.907	1	CLONAL	1	TRUE	1	0.606301361474768	2		443	509	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257845	19257845	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	335	1213	0	ENST00000162023.5:c.541G>T	p.Gly181Cys	p.G181C	ENST00000162023		181	Ggc/Tgc	9/13	0.561425917072775	1	FACETS	0.836	0.793	0.88	0.836	0.793	0.88	CLONAL	1	TRUE	0	0.606301361474768	1		1213	921	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222562	69222562	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	212	308	0	ENST00000462284.1:c.535G>T	p.Asp179Tyr	p.D179Y	ENST00000462284	NM_002392.5	179	Gat/Tat	8/11	0.544289489031781	3	FACETS	0.863	0.809	0.918	0.863	0.809	0.918	CLONAL	2	TRUE	1	0.606301361474768	3		308	528	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610405	10610405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	372	1159	0	ENST00000171111.5:c.305C>T	p.Ser102Leu	p.S102L	ENST00000171111	NM_203500.1	102	tCa/tTa	2/6	0.561425917072775	1	FACETS	0.864	0.822	0.906	0.864	0.822	0.906	CLONAL	1	TRUE	0	0.606301361474768	1		1159	990	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725025	47725025	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199804290	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	383	1246	1	ENST00000449228.1:c.719C>T	p.Ser240Leu	p.S240L	ENST00000449228	NM_001127240.2	240	tCg/tTg	4/4	0.561425917072775	1	FACETS	0.867	0.825	0.908	0.867	0.825	0.908	CLONAL	1	TRUE	0	0.606301361474768	1		1247	1016	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230371	46230371	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	198	266	0	ENST00000334344.6:c.706-1G>C		p.X236_splice	ENST00000334344	NM_152641.2	236			0.544289489031781	3	FACETS	0.961	0.901	1	0.961	0.901	1	CLONAL	2	TRUE	1	0.606301361474768	3		266	443	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346659	81346659	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	91	322	0	ENST00000222390.5:c.1294G>T	p.Ala432Ser	p.A432S	ENST00000222390	NM_000601.4	432	Gca/Tca	11/18	1	2	FACETS	0.827	0.74	0.918	0.827	0.74	0.918	CLONAL	1	TRUE	1	0.606301361474768	2		322	363	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193820	106193820	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	159	461	0	ENST00000380013.4:c.4282G>A	p.Glu1428Lys	p.E1428K	ENST00000380013	NM_001127208.2	1428	Gag/Aag	10/11	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.606301361474768	2		461	524	SUCCESS
EED	8726	MSKCC	GRCh37	11	85961469	85961469	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	67	185	0	ENST00000263360.6:c.246C>G	p.Phe82Leu	p.F82L	ENST00000263360	NM_003797.3	82	ttC/ttG	2/12	1	2	FACETS	0.853	0.75	0.962	0.853	0.75	0.962	CLONAL	1	TRUE	1	0.606301361474768	2		185	259	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909282	41909282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	330	987	1	ENST00000372991.4:c.106G>A	p.Glu36Lys	p.E36K	ENST00000372991	NM_001760.3	36	Gag/Aag	1/5	1	2	FACETS	0.953	0.901	1	0.953	0.901	1	CLONAL	1	TRUE	1	0.606301361474768	2		988	1142	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235260	235260	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	161	499	0	ENST00000264932.6:c.1066G>A	p.Gly356Ser	p.G356S	ENST00000264932	NM_004168.2	356	Ggc/Agc	9/15	1	2	FACETS	0.959	0.884	1	0.959	0.884	1	CLONAL	1	TRUE	1	0.606301361474768	2		499	554	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163282	32163282	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	386	1258	0	ENST00000375023.3:c.5944C>T	p.Gln1982Ter	p.Q1982*	ENST00000375023	NM_004557.3	1982	Caa/Taa	30/30	1	2	FACETS	0.913	0.867	0.961	0.913	0.867	0.961	CLONAL	1	TRUE	1	0.606301361474768	2		1258	1394	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243951	46243951	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	173	492	0	ENST00000334344.6:c.2045C>G	p.Ser682Ter	p.S682*	ENST00000334344	NM_152641.2	682	tCa/tGa	15/21	0.544289489031781	3	FACETS	1	0.946	1	0.516	0.476	0.557	CLONAL	1	TRUE	1	0.606301361474768	3		492	721	SUCCESS
ALK	238	MSKCC	GRCh37	2	29448360	29448360	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370049091	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	452	1211	2	ENST00000389048.3:c.3139G>A	p.Ala1047Thr	p.A1047T	ENST00000389048	NM_004304.4	1047	Gcc/Acc	19/29	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.606301361474768	2		1213	1403	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472459	88472459	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	242	771	0	ENST00000360948.2:c.2096del	p.Gly699AlafsTer60	p.G699Afs*60	ENST00000360948	NM_001012338.2	699	gGc/gc	16/19	1	2	FACETS	0.95	0.89	1	0.95	0.89	1	CLONAL	1	TRUE	1	0.606301361474768	2		771	840	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679361	29679361	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	164	570	1	ENST00000356175.3:c.7481G>T	p.Ser2494Ile	p.S2494I	ENST00000356175	NM_000267.3	2494	aGt/aTt	50/57	1	2	FACETS	0.828	0.763	0.896	0.828	0.763	0.896	CLONAL	1	TRUE	1	0.606301361474768	2		571	653	SUCCESS
MET	4233	MSKCC	GRCh37	7	116414999	116414999	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	260	734	0	ENST00000397752.3:c.3093G>T	p.Met1031Ile	p.M1031I	ENST00000397752	NM_000245.2	1031	atG/atT	15/21	1	2	FACETS	0.969	0.91	1	0.969	0.91	1	CLONAL	1	TRUE	1	0.606301361474768	2		734	885	SUCCESS
APC	324	MSKCC	GRCh37	5	112174248	112174248	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs730881243	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	109	335	0	ENST00000257430.4:c.2957A>G	p.Tyr986Cys	p.Y986C	ENST00000257430	NM_000038.5	986	tAt/tGt	16/16	1	2	FACETS	0.812	0.733	0.893	0.812	0.733	0.893	CLONAL	1	TRUE	1	0.606301361474768	2		335	443	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026786	6026786	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	218	413	0	ENST00000265849.7:c.1610A>G	p.Glu537Gly	p.E537G	ENST00000265849	NM_000535.5	537	gAg/gGg	11/15	1	2	FACETS	0.81	0.763	0.856	1	0.994	1	CLONAL	2	TRUE	1	0.606301361474768	2		413	444	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087874	27087874	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	261	743	0	ENST00000324856.7:c.2162-1G>T		p.X721_splice	ENST00000324856	NM_006015.4	721			1	2	FACETS	0.996	0.936	1	0.996	0.936	1	CLONAL	1	TRUE	1	0.606301361474768	2		743	864	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251269	115251269	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	77	369	0	ENST00000369535.4:c.457G>C	p.Glu153Gln	p.E153Q	ENST00000369535	NM_002524.4	153	Gaa/Caa	5/7	1	2	FACETS	0.543	0.478	0.612	0.543	0.478	0.612	SUBCLONAL	1	TRUE	1	0.606301361474768	2		369	468	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725466	162725466	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs889257496	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	234	786	0	ENST00000367921.3:c.578C>G	p.Ser193Cys	p.S193C	ENST00000367921	NM_006182.2	193	tCt/tGt	7/18	0.563493956308771	3	FACETS	0.99	0.924	1			1	CLONAL	1	TRUE	NA	0.606301361474768	3		786	1016	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943329	71943329	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1221876161	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	260	912	0	ENST00000298229.2:c.1661C>A	p.Ser554Ter	p.S554*	ENST00000298229	NM_001567.3	554	tCa/tAa	14/28	1	2	FACETS	0.868	0.814	0.924	0.868	0.814	0.924	CLONAL	1	TRUE	1	0.606301361474768	2		912	988	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103173	119103173	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	178	559	1	ENST00000264033.4:c.211C>T	p.Gln71Ter	p.Q71*	ENST00000264033	NM_005188.3	71	Cag/Tag	2/16	NA	2	FACETS	0.842	0.779	0.908			1	INDETERMINATE	1	TRUE	NA	0.606301361474768	2		560	697	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944797	31944797	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	223	652	0	ENST00000340398.3:c.304G>T	p.Gly102Cys	p.G102C	ENST00000340398	NM_001013699.2	102	Ggt/Tgt	1/1	0.544289489031781	3	FACETS	0.945	0.88	1	0.473	0.44	0.507	CLONAL	1	TRUE	1	0.606301361474768	3		652	1014	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420151	49420151	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	315	914	0	ENST00000301067.7:c.15598C>G	p.His5200Asp	p.H5200D	ENST00000301067	NM_003482.3	5200	Cat/Gat	48/54	0.544289489031781	3	FACETS	1	0.971	1	0.523	0.493	0.554	CLONAL	1	TRUE	1	0.606301361474768	3		914	1294	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445804	49445804	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1344	371	1248	0	ENST00000301067.7:c.1662G>T	p.Leu554Phe	p.L554F	ENST00000301067	NM_003482.3	554	ttG/ttT	10/54	0.544289489031781	3	FACETS	0.93	0.88	0.981	0.465	0.44	0.491	CLONAL	1	TRUE	1	0.606301361474768	3		1248	1715	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222667	69222667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	394	633	0	ENST00000462284.1:c.640G>A	p.Glu214Lys	p.E214K	ENST00000462284	NM_002392.5	214	Gaa/Aaa	8/11	0.544289489031781	3	FACETS	0.902	0.861	0.943	0.902	0.861	0.943	CLONAL	2	TRUE	1	0.606301361474768	3		633	939	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609802	28609802	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	207	574	0	ENST00000241453.7:c.1427A>T	p.Glu476Val	p.E476V	ENST00000241453	NM_004119.2	476	gAa/gTa	12/24	1	2	FACETS	0.967	0.901	1	0.967	0.901	1	CLONAL	1	TRUE	1	0.606301361474768	2		574	706	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281252	49281252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	255	554	1	ENST00000282018.3:c.299G>A	p.Arg100Lys	p.R100K	ENST00000282018	NM_020377.2	100	aGa/aAa	1/1	0.361660880143159	4	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.606301361474768	4		555	908	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434563	110434563	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	268	994	0	ENST00000375856.3:c.3838G>C	p.Asp1280His	p.D1280H	ENST00000375856	NM_003749.2	1280	Gac/Cac	1/2	1	2	FACETS	0.848	0.796	0.902	0.848	0.796	0.902	CLONAL	1	TRUE	1	0.606301361474768	2		994	1042	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95556976	95556976	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	198	625	0	ENST00000393063.1:c.5628del	p.Lys1877ArgfsTer8	p.K1877Rfs*8	ENST00000393063	NM_030621.3	1876	ggG/gg	28/28	1	2	FACETS	0.855	0.794	0.918	0.855	0.794	0.918	CLONAL	1	TRUE	1	0.606301361474768	2		625	764	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295016	91295016	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	42	119	0	ENST00000355112.3:c.800-1G>C		p.X267_splice	ENST00000355112	NM_000057.2	267			1	2	FACETS	0.815	0.691	0.948	0.815	0.691	0.948	CLONAL	1	TRUE	1	0.606301361474768	2		119	170	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295091	91295091	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	93	222	0	ENST00000355112.3:c.874G>C	p.Asp292His	p.D292H	ENST00000355112	NM_000057.2	292	Gat/Cat	4/22	1	2	FACETS	0.913	0.82	1	0.913	0.82	1	CLONAL	1	TRUE	1	0.606301361474768	2		222	336	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646396	23646396	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	195	633	0	ENST00000261584.4:c.1471G>T	p.Ala491Ser	p.A491S	ENST00000261584	NM_024675.3	491	Gct/Tct	4/13	1	2	FACETS	0.818	0.759	0.88	0.818	0.759	0.88	CLONAL	1	TRUE	1	0.606301361474768	2		633	786	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89355016	89355016	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	315	1064	0	ENST00000301030.4:c.664G>T	p.Ala222Ser	p.A222S	ENST00000301030	NM_001256183.1	222	Gct/Tct	7/13	1	2	FACETS	0.882	0.832	0.933	0.882	0.832	0.933	CLONAL	1	TRUE	1	0.606301361474768	2		1064	1178	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40364008	40364008	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1285898420	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	303	1088	0	ENST00000293328.3:c.1674C>G	p.Phe558Leu	p.F558L	ENST00000293328	NM_012448.3	558	ttC/ttG	13/19	1	2	FACETS	0.856	0.807	0.907	0.856	0.807	0.907	CLONAL	1	TRUE	1	0.606301361474768	2		1088	1167	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56801448	56801448	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876659875	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	104	527	0	ENST00000337432.4:c.952G>T	p.Asp318Tyr	p.D318Y	ENST00000337432	NM_058216.2	318	Gac/Tac	7/9	1	2	FACETS	0.719	0.647	0.795	0.719	0.647	0.795	SUBCLONAL	1	TRUE	1	0.606301361474768	2		527	477	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222489	2222489	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	330	1174	0	ENST00000398665.3:c.3322del	p.Arg1108GlufsTer43	p.R1108Efs*43	ENST00000398665	NM_032482.2	1107	cgC/cg	24/28	0.561425917072775	1	FACETS	0.879	0.834	0.925	0.879	0.834	0.925	CLONAL	1	TRUE	0	0.606301361474768	1		1174	863	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218802	5218802	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370343222	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	283	818	0	ENST00000357368.4:c.3931G>A	p.Asp1311Asn	p.D1311N	ENST00000357368	NM_002850.3	1311	Gac/Aac	24/38	0.561425917072775	1	FACETS	0.849	0.802	0.897	0.849	0.802	0.897	CLONAL	1	TRUE	0	0.606301361474768	1		818	766	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221766	36221766	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs200571590	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	329	989	0	ENST00000222270.7:c.5435C>T	p.Ser1812Leu	p.S1812L	ENST00000222270	NM_014727.1	1812	tCa/tTa	26/37	NA	2	FACETS	0.894	0.845	0.945			1	INDETERMINATE	1	TRUE	NA	0.606301361474768	2		989	1214	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965250	25965250	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	182	595	0	ENST00000435504.4:c.3956G>T	p.Ser1319Ile	p.S1319I	ENST00000435504		1319	aGc/aTc	13/13	1	2	FACETS	0.802	0.741	0.864	0.802	0.741	0.864	CLONAL	1	TRUE	1	0.606301361474768	2		595	749	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149922	202149922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	260	791	0	ENST00000358485.4:c.1363G>A	p.Glu455Lys	p.E455K	ENST00000358485	NM_001080125.1	455	Gag/Aag	8/9	1	2	FACETS	0.947	0.889	1	0.947	0.889	1	CLONAL	1	TRUE	1	0.606301361474768	2		791	906	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747109	40747109	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	197	692	0	ENST00000373198.4:c.2973G>C	p.Trp991Cys	p.W991C	ENST00000373198	NM_133170.3	991	tgG/tgC	22/32	1	2	FACETS	0.808	0.75	0.869	0.808	0.75	0.869	CLONAL	1	TRUE	1	0.606301361474768	2		692	804	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790098	40790098	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs6130063	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	232	896	0	ENST00000373198.4:c.2633G>T	p.Ser878Ile	p.S878I	ENST00000373198	NM_133170.3	878	aGc/aTc	18/32	1	2	FACETS	0.792	0.739	0.847	0.792	0.739	0.847	SUBCLONAL	1	TRUE	1	0.606301361474768	2		896	966	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827947	40827948	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	250	781	0	ENST00000373198.4:c.2480_2481insA	p.Thr828HisfsTer9	p.T828Hfs*9	ENST00000373198	NM_133170.3	827	acc/acAc	17/32	1	2	FACETS	0.949	0.89	1	0.949	0.89	1	CLONAL	1	TRUE	1	0.606301361474768	2		781	869	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100910	41100910	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	208	783	0	ENST00000373198.4:c.1446A>T	p.Glu482Asp	p.E482D	ENST00000373198	NM_133170.3	482	gaA/gaT	8/32	1	2	FACETS	0.859	0.799	0.92	0.859	0.799	0.92	CLONAL	1	TRUE	1	0.606301361474768	2		783	799	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41818310	41818310	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	19	42	0	ENST00000373198.4:c.64G>T	p.Gly22Cys	p.G22C	ENST00000373198	NM_133170.3	22	Ggc/Tgc	1/32	1	2	FACETS	0.995	0.78	1	0.995	0.78	1	CLONAL	1	TRUE	1	0.606301361474768	2		42	63	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795478	39795478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs761890055	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	166	695	0	ENST00000288319.7:c.242C>A	p.Ser81Tyr	p.S81Y	ENST00000288319	NM_182918.3	81	tCt/tAt	3/10	0.247058306680408	1	FACETS	0.589	0.543	0.637	0.589	0.543	0.637	INDETERMINATE	1	TRUE	0	0.606301361474768	1		695	648	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713768	30713768	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	264	852	0	ENST00000295754.5:c.1093C>G	p.His365Asp	p.H365D	ENST00000295754	NM_003242.5	365	Cac/Gac	4/7	1	2	FACETS	0.908	0.852	0.965	0.908	0.852	0.965	CLONAL	1	TRUE	1	0.606301361474768	2		852	959	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143324208	143324208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	95	348	0	ENST00000262992.4:c.256-1G>A		p.X86_splice	ENST00000262992	NM_001101669.1	86			1	2	FACETS	0.812	0.728	0.899	0.812	0.728	0.899	CLONAL	1	TRUE	1	0.606301361474768	2		348	386	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444386	50444386	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	166	531	1	ENST00000331340.3:c.316G>T	p.Gly106Ter	p.G106*	ENST00000331340	NM_006060.4	106	Gga/Tga	4/8	1	2	FACETS	0.886	0.817	0.957	0.886	0.817	0.957	CLONAL	1	TRUE	1	0.606301361474768	2		532	618	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69000041	69000041	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044145-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	175	634	0	ENST00000288368.4:c.2110A>G	p.Arg704Gly	p.R704G	ENST00000288368	NM_024870.2	704	Aga/Gga	19/40	0.602183058857329	4	FACETS	0.846	0.778	0.917	0.282	0.259	0.306	CLONAL	1	TRUE	1	0.606301361474768	4		634	1096	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044204-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	107	425	0				ENST00000310581	NM_198253.2	-/1132			0.175961355279858	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.862246892035483	0		425	265	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0044204-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	328	546	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	FALSE	NA	0.862246892035483	2		546	690	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0044204-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	12	457	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.08	0.056	0.11	0.08	0.056	0.11	SUBCLONAL	1	FALSE	1	0.862246892035483	2		457	348	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431898	49431898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044204-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	339	606	0	ENST00000301067.7:c.9241G>A	p.Glu3081Lys	p.E3081K	ENST00000301067	NM_003482.3	3081	Gaa/Aaa	34/54	1	2	FACETS	0.974	0.927	1	0.974	0.927	1	CLONAL	1	FALSE	1	0.862246892035483	2		606	807	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94963999	94963999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318902387	NA	P-0044204-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	172	212	0	ENST00000536441.1:c.26C>T	p.Ser9Leu	p.S9L	ENST00000536441	NM_144665.3	9	tCg/tTg	1/10	1	2	FACETS	0.983	0.916	1	0.983	0.916	1	CLONAL	1	FALSE	1	0.862246892035483	2		212	406	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045806	180045806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1051985552	NA	P-0044204-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	250	565	0	ENST00000261937.6:c.2965G>A	p.Glu989Lys	p.E989K	ENST00000261937	NM_182925.4	989	Gag/Aag	21/30	NA	2	FACETS	0.978	0.922	1			1	INDETERMINATE	1	FALSE	NA	0.862246892035483	2		565	593	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984343	201984344	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044204-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	351	512	0	ENST00000359651.3:c.1009dup	p.Tyr337LeufsTer134	p.Y337Lfs*134	ENST00000359651		336	-/T	8/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.862246892035483	2		512	765	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431430	49431430	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044204-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	311	577	0	ENST00000301067.7:c.9709G>C	p.Glu3237Gln	p.E3237Q	ENST00000301067	NM_003482.3	3237	Gag/Cag	34/54	1	2	FACETS	0.999	0.949	1	0.999	0.949	1	CLONAL	1	FALSE	1	0.862246892035483	2		577	722	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907237	32907237	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044204-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	165	339	0	ENST00000380152.3:c.1622A>G	p.Glu541Gly	p.E541G	ENST00000380152		541	gAa/gGa	10/27	0.214156230316597	1	FACETS	0.561	0.522	0.601	0.561	0.522	0.601	INDETERMINATE	1	FALSE	0	0.862246892035483	1		339	388	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68290342	68290342	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs761684336	NA	P-0044204-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	140	250	0	ENST00000487270.1:c.82C>G	p.Gln28Glu	p.Q28E	ENST00000487270	NM_133509.3	28	Cag/Gag	2/11	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	FALSE	1	0.862246892035483	2		250	324	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574334	95574334	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1182299033	NA	P-0044204-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	96	260	0	ENST00000393063.1:c.2533T>G	p.Leu845Val	p.L845V	ENST00000393063	NM_030621.3	845	Ttg/Gtg	17/28	1	2	FACETS	0.92	0.835	1	0.92	0.835	1	CLONAL	1	FALSE	1	0.862246892035483	2		260	242	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149245664	149245664	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044204-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	337	543	0	ENST00000360632.3:c.864G>C	p.Met288Ile	p.M288I	ENST00000360632	NM_015472.4	288	atG/atC	5/7	1	2	FACETS	0.998	0.95	1	0.998	0.95	1	CLONAL	1	FALSE	1	0.862246892035483	2		543	783	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149310	119149311	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0044204-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	74	436	1	ENST00000264033.4:c.1318_1319delinsTT	p.Gly440Phe	p.G440F	ENST00000264033	NM_005188.3	440	GGc/TTc	9/16	1	2	FACETS	0.273	0.239	0.31	0.273	0.239	0.31	SUBCLONAL	1	FALSE	1	0.862246892035483	2		437	629	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260607	1260607	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044204-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	75	509	0	ENST00000310581.5:c.2952C>A	p.Ser984Arg	p.S984R	ENST00000310581	NM_198253.2	984	agC/agA	12/16	0.813474619692743	1	FACETS	0.206	0.18	0.233	0.206	0.18	0.233	SUBCLONAL	1	FALSE	0	0.862246892035483	1		509	481	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662351	67662351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	197	246	0	ENST00000264010.4:c.1597C>T	p.Arg533Cys	p.R533C	ENST00000264010	NM_006565.3	533	Cgc/Tgc	9/12	0.596976420755771	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	0	0.596976420755771	1		246	439	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044261-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	135	425	0				ENST00000310581	NM_198253.2	-/1132			0.319272379018056	3	FACETS	0.895	0.831	0.959	1	0.991	1	CLONAL	4	TRUE	1	0.329006776334728	3		425	267	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0044261-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	247	383	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	0.319272379018056	3	FACETS	0.926	0.878	0.974	1	0.995	1	CLONAL	4	TRUE	1	0.329006776334728	3		383	472	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0044261-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	16	882	1	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.144	0.106	0.191	0.144	0.106	0.191	SUBCLONAL	1	TRUE	1	0.329006776334728	2		883	675	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602533	10602533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1048289	NA	P-0044261-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	370	550	0	ENST00000171111.5:c.1045G>A	p.Asp349Asn	p.D349N	ENST00000171111	NM_203500.1	349	Gac/Aac	3/6	0.154184264260625	4	FACETS	1	0.991	1	1	0.996	1	INDETERMINATE	3	TRUE	2	0.329006776334728	4		550	868	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197697	123197697	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0044261-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	31	190	0	ENST00000218089.9:c.1822-1G>T		p.X608_splice	ENST00000218089	NM_001042749.1	608			1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.329006776334728	2		190	182	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120293	70120294	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0044261-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	176	519	0	ENST00000245479.2:c.1297_1298dup	p.Pro434ArgfsTer37	p.P434Rfs*37	ENST00000245479	NM_000346.3	432	tac/taCCc	3/3	1	2	FACETS	0.774	0.715	0.835	1	0.99	1	SUBCLONAL	2	TRUE	1	0.329006776334728	2		519	691	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044261-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	29	425	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.833	1	1	0.833	1	CLONAL	1	TRUE	1	0.23440985331167	2		425	239	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0044261-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	57	383	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.23440985331167	2		383	398	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602533	10602533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1048289	NA	P-0044261-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	97	550	0	ENST00000171111.5:c.1045G>A	p.Asp349Asn	p.D349N	ENST00000171111	NM_203500.1	349	Gac/Aac	3/6	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.23440985331167	2		550	703	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120293	70120294	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0044261-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	60	519	0	ENST00000245479.2:c.1297_1298dup	p.Pro434ArgfsTer37	p.P434Rfs*37	ENST00000245479	NM_000346.3	432	tac/taCCc	3/3	1	2	FACETS	0.849	0.731	0.977	0.849	0.731	0.977	CLONAL	1	TRUE	1	0.23440985331167	2		519	603	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0044261-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	85	284	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	0.205041423854791	2	FACETS	0.947	0.843	1	0.947	0.843	1	CLONAL	2	TRUE	0	0.23440985331167	2		284	383	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43767792	43767792	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044261-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	58	325	0	ENST00000382044.4:c.1056G>C	p.Gln352His	p.Q352H	ENST00000382044	NM_001141980.1	352	caG/caC	9/28	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.23440985331167	2		325	465	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823756	3823756	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0044261-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	56	360	0	ENST00000262367.5:c.2459C>G	p.Ser820Ter	p.S820*	ENST00000262367	NM_004380.2	820	tCa/tGa	13/31	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.23440985331167	2		360	420	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339547	81339547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044261-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	37	264	0	ENST00000222390.5:c.1457C>T	p.Ser486Phe	p.S486F	ENST00000222390	NM_000601.4	486	tCt/tTt	13/18	1	2	FACETS	0.818	0.675	0.977	0.818	0.675	0.977	CLONAL	1	TRUE	1	0.23440985331167	2		264	386	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68981273	68981273	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044261-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	14	169	0	ENST00000288368.4:c.1345G>C	p.Asp449His	p.D449H	ENST00000288368	NM_024870.2	449	Gat/Cat	12/40	1	2	FACETS	0.791	0.575	1	0.791	0.575	1	CLONAL	1	TRUE	1	0.23440985331167	2		169	151	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0044345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	270	798	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.685096465176801	2	FACETS	0.959	0.918	0.999	0.959	0.918	0.999	CLONAL	2	FALSE	0	0.695220478549262	2		798	405	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40743901	40743901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761347839	NA	P-0044345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	134	722	2	ENST00000392038.2:c.806G>A	p.Arg269Gln	p.R269Q	ENST00000392038	NM_001626.4	269	cGg/cAg	9/14	0.686785753605949	4	FACETS	0.905	0.824	0.991	0.453	0.412	0.496	CLONAL	1	FALSE	2	0.695220478549262	4		724	722	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728671	190728672	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0044345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	22	382	0	ENST00000441310.2:c.2064_2065dup	p.Arg689LysfsTer16	p.R689Kfs*16	ENST00000441310	NM_000534.4	687	gaa/gAAaa	10/13	0.360679629992661	6	FACETS	0.366	0.283	0.463	0.122	0.094	0.155	INDETERMINATE	1	FALSE	3	0.695220478549262	6		382	413	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728730	190728730	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	18	301	0	ENST00000441310.2:c.2122del	p.Ile708Ter	p.I708*	ENST00000441310	NM_000534.4	706	ttA/tt	10/13	0.360679629992661	6	FACETS	0.407	0.306	0.527	0.136	0.102	0.176	INDETERMINATE	1	FALSE	3	0.695220478549262	6		301	304	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106194038	106194038	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	71	272	0	ENST00000380013.4:c.4500A>T	p.Lys1500Asn	p.K1500N	ENST00000380013	NM_001127208.2	1500	aaA/aaT	10/11	0.195604695034434	3	FACETS	1	0.954	1	0.578	0.512	0.648	INDETERMINATE	1	FALSE	1	0.695220478549262	3		272	238	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220334	98220334	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs746220311	NA	P-0044345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	96	437	0	ENST00000331920.6:c.3129C>G	p.Cys1043Trp	p.C1043W	ENST00000331920	NM_000264.3	1043	tgC/tgG	18/24	1	2	FACETS	0.986	0.891	1	0.986	0.891	1	CLONAL	1	FALSE	1	0.695220478549262	2		437	280	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249013	55249014	+	protein_altering_variant	In_Frame_Ins	INS	AA	AA	GGGTT	novel	NA	P-0044365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	99	595	0	ENST00000275493.2:c.2311_2312delinsGGGTT	p.Asn771delinsGlyPhe	p.N771delinsGF	ENST00000275493	NM_005228.3	771	AAc/GGGTTc	20/28	1	2	FACETS	0.987	0.88	1	0.987	0.88	1	CLONAL	1	TRUE	1	0.243268423047179	2		595	825	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174416	11174416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	100	629	0	ENST00000361445.4:c.7259C>T	p.Ala2420Val	p.A2420V	ENST00000361445	NM_004958.3	2420	gCc/gTc	53/58	1	2	FACETS	0.978	0.872	1	0.978	0.872	1	CLONAL	1	TRUE	1	0.243268423047179	2		629	841	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578371	7578371	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs776167460	NA	P-0044365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	16	578	2	ENST00000269305.4:c.559G>A	p.Gly187Ser	p.G187S	ENST00000269305	NM_001126112.2	187	Ggt/Agt	5/11	0.243268423047179	1	FACETS	0.148	0.108	0.196	0.148	0.108	0.196	SUBCLONAL	1	TRUE	0	0.243268423047179	1		580	780	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022338	26022341	+	frameshift_variant	Frame_Shift_Del	DEL	CTGA	CTGA	-	novel	NA	P-0044365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	30	389	0	ENST00000435504.4:c.316_319del	p.Ser106IlefsTer60	p.S106Ifs*60	ENST00000435504		106	TCAGat/at	5/13	NA	2	FACETS	0.43	0.346	0.527			1	INDETERMINATE	1	TRUE	NA	0.243268423047179	2		389	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0044379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	242	634	0	ENST00000269305.4:c.560-2A>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.38226179019865	2		634	963	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612890	228612890	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	597	824	0	ENST00000366696.1:c.137C>A	p.Thr46Lys	p.T46K	ENST00000366696	NM_003493.2	46	aCg/aAg	1/1	0.38226179019865	3	FACETS	0.886	0.854	0.919	0.886	0.854	0.919	CLONAL	3	TRUE	0	0.38226179019865	3		824	1399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs11575997	NA	P-0044410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	186	612	0	ENST00000269305.4:c.993+1G>T		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.297726068001384	2	FACETS	0.868	0.808	0.93	1	0.988	1	CLONAL	3	TRUE	0	0.27	2		612	529	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914137	32914137	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs80358785	NA	P-0044410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	105	471	0	ENST00000380152.3:c.5645C>A	p.Ser1882Ter	p.S1882*	ENST00000380152		1882	tCa/tAa	11/27	0.268934757717837	2	FACETS	0.972	0.878	1	0.972	0.878	1	CLONAL	2	TRUE	0	0.27	2		471	400	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221961	1221961	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0044410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	143	853	0	ENST00000326873.7:c.876C>G	p.Tyr292Ter	p.Y292*	ENST00000326873	NM_000455.4	292	taC/taG	7/10	0.297726068001384	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.27	1		853	668	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865112	57865112	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	124	1028	0	ENST00000228682.2:c.2592del	p.Tyr865IlefsTer81	p.Y865Ifs*81	ENST00000228682	NM_005269.2	863	ggC/gg	12/12	1	2	FACETS	0.833	0.752	0.919	0.833	0.752	0.919	CLONAL	1	TRUE	1	0.27	2		1028	1103	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030035	36030035	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1224513777	NA	P-0044410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	51	864	0	ENST00000358208.4:c.1070C>G	p.Thr357Arg	p.T357R	ENST00000358208		357	aCa/aGa	9/12	1	2	FACETS	0.512	0.434	0.598	0.512	0.434	0.598	SUBCLONAL	1	TRUE	1	0.27	2		864	738	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509508	149509508	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	104	692	0	ENST00000261799.4:c.1391C>A	p.Thr464Lys	p.T464K	ENST00000261799	NM_002609.3	464	aCg/aAg	10/23	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.27	2		692	728	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402707	20402707	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	41	459	0	ENST00000346618.3:c.244G>C	p.Gly82Arg	p.G82R	ENST00000346618	NM_001949.4	82	Ggc/Cgc	1/7	1	2	FACETS	0.698	0.582	0.827	0.698	0.582	0.827	SUBCLONAL	1	TRUE	1	0.27	2		459	435	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781234	161781256	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGCCTGGGGAAACAAAGAGGAA	AGGCCTGGGGAAACAAAGAGGAA	-	novel	NA	P-0044410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	50	490	0	ENST00000366898.1:c.1168-19_1171del		p.X390_splice	ENST00000366898	NM_004562.2	390		11/12	1	2	FACETS	0.728	0.617	0.849	0.728	0.617	0.849	SUBCLONAL	1	TRUE	1	0.27	2		490	509	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436817	52436820	+	protein_altering_variant	In_Frame_Del	DEL	ACCT	ACCT	G	novel	NA	P-0044410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	82	753	0	ENST00000460680.1:c.1958_1961delinsC	p.Glu653_Val654delinsAla	p.E653_V654delinsA	ENST00000460680	NM_004656.3	653	gAGGTa/gCa	15/17	0.297726068001384	1	FACETS	0.877	0.774	0.987	0.877	0.774	0.987	CLONAL	1	TRUE	0	0.27	1		753	599	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0044431-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	522	870	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.837981121388729	2	FACETS	0.984	0.963	1	0.984	0.963	1	CLONAL	2	TRUE	0	0.845659927453225	2		870	627	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0044459-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	850	707	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.598026681376341	4	FACETS	0.958	0.937	0.978	0.958	0.937	0.978	CLONAL	4	TRUE	0	0.607635172169836	4		708	1174	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942593	17942593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044459-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2830	155	715	2	ENST00000458235.1:c.2695C>T	p.Arg899Trp	p.R899W	ENST00000458235	NM_000215.3	899	Cgg/Tgg	20/24	0.607635172169836	11	FACETS	0.638	0.581	0.699			1	SUBCLONAL	1	TRUE	NA	0.607635172169836	11		717	2985	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0044462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	245	487	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.168677502078691	0	FACETS	0.944	0.904	0.983			1	CLONAL	6	FALSE	0	0.199071942317995	0		487	348	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0044462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	52	240	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.199071942317995	7	FACETS	1	0.901	1	0.841	0.728	0.962	CLONAL	4	FALSE	2	0.199071942317995	7		240	186	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731065	162731065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747307320	NA	P-0044462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	126	452	0	ENST00000367921.3:c.920G>A	p.Arg307His	p.R307H	ENST00000367921	NM_006182.2	307	cGc/cAc	9/18	0.172172633869774	3	FACETS	1	0.94	1	1	0.987	1	CLONAL	3	FALSE	1	0.199071942317995	3		452	447	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741657	17741657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	76	411	0	ENST00000250003.3:c.328C>T	p.Arg110Cys	p.R110C	ENST00000250003	NM_002478.4	110	Cgc/Tgc	1/3	1	2	FACETS	1	0.926	1	1	0.984	1	CLONAL	2	FALSE	1	0.199071942317995	2		411	358	SUCCESS
APC	324	MSKCC	GRCh37	5	112136975	112136975	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs1554076129	NA	P-0044462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	142	324	0	ENST00000257430.4:c.730-1G>C		p.X244_splice	ENST00000257430	NM_000038.5	244			0.199071942317995	7	FACETS	1	0.942	1	1	0.983	1	CLONAL	6	FALSE	2	0.199071942317995	7		324	348	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781844	3781844	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	199	800	0	ENST00000262367.5:c.4823C>G	p.Pro1608Arg	p.P1608R	ENST00000262367	NM_004380.2	1608	cCc/cGc	29/31	0.199071942317995	5	FACETS	0.955	0.886	1	0.716	0.664	0.771	CLONAL	3	FALSE	1	0.199071942317995	5		800	906	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138452234	138452234	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	94	489	0	ENST00000289153.2:c.1019G>T	p.Gly340Val	p.G340V	ENST00000289153	NM_006219.2	340	gGa/gTa	6/22	1	2	FACETS	0.872	0.783	0.966	1	0.989	1	CLONAL	3	FALSE	1	0.199071942317995	2		489	361	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531088	187531088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368431115	NA	P-0044462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	123	434	1	ENST00000441802.2:c.9935C>T	p.Thr3312Met	p.T3312M	ENST00000441802	NM_005245.3	3312	aCg/aTg	15/27	1	2	FACETS	0.976	0.89	1	1	0.992	1	CLONAL	3	FALSE	1	0.199071942317995	2		435	422	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882025	NA	P-0044525-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	264	529	0	ENST00000269305.4:c.646G>C	p.Val216Leu	p.V216L	ENST00000269305	NM_001126112.2	216	Gtg/Ctg	6/11	0.694763816476871	1	FACETS	0.939	0.891	0.988	0.939	0.891	0.988	CLONAL	1	TRUE	0	0.694763816476871	1		529	528	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138294	2138311	+	inframe_deletion	In_Frame_Del	DEL	CGGCTCCGCCACATCAAG	CGGCTCCGCCACATCAAG	-	rs137854218	NA	P-0044525-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	160	629	0	ENST00000219476.3:c.5238_5255del	p.His1746_Arg1751del	p.H1746_R1751del	ENST00000219476	NM_000548.3	1743	CGGCTCCGCCACATCAAG/-	41/42	0.694763816476871	1	FACETS	0.704	0.652	0.757	0.704	0.652	0.757	SUBCLONAL	1	TRUE	0	0.694763816476871	1		629	427	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863251	57863267	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGTGACCACTCCCCG	GCAGTGACCACTCCCCG	-	novel	NA	P-0044569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	212	532	0	ENST00000228682.2:c.1350_1366del	p.Ser450ArgfsTer21	p.S450Rfs*21	ENST00000228682	NM_005269.2	449	aGCAGTGACCACTCCCCG/a	11/12	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.668702966240944	2		532	611	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81904541	81904541	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0044569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	76	232	1	ENST00000359376.3:c.648+1G>A		p.X216_splice	ENST00000359376	NM_002661.3	216			0.668702966240944	3	FACETS	0.729	0.642	0.821	0.365	0.321	0.411	SUBCLONAL	1	TRUE	1	0.668702966240944	3		233	416	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216495	2216495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	211	709	0	ENST00000398665.3:c.2139G>A	p.Met713Ile	p.M713I	ENST00000398665	NM_032482.2	713	atG/atA	20/28	1	2	FACETS	0.733	0.682	0.786	0.733	0.682	0.786	SUBCLONAL	1	TRUE	1	0.668702966240944	2		709	861	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582195	189582195	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	149	365	0	ENST00000264731.3:c.754G>T	p.Glu252Ter	p.E252*	ENST00000264731	NM_003722.4	252	Gaa/Taa	5/14	1	2	FACETS	0.844	0.776	0.915	0.844	0.776	0.915	CLONAL	1	TRUE	1	0.668702966240944	2		365	528	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184634	32184727	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AACCATCAAACACCCACCAATGAACTCTGCCCCAACCCAAATGGAATAAAATATTCTGCCAGTTCTTTCCAGTGCCTCCCCTGTGAACCTGTGA	AACCATCAAACACCCACCAATGAACTCTGCCCCAACCCAAATGGAATAAAATATTCTGCCAGTTCTTTCCAGTGCCTCCCCTGTGAACCTGTGA	-	novel	NA	P-0044569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	139	532	0	ENST00000375023.3:c.1856_1861+88del		p.X619_splice	ENST00000375023	NM_004557.3	619		11/30	1	2	FACETS	0.581	0.529	0.634	0.581	0.529	0.634	SUBCLONAL	1	TRUE	1	0.668702966240944	2		532	716	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878678	151878678	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	148	437	0	ENST00000262189.6:c.6267G>T	p.Gln2089His	p.Q2089H	ENST00000262189	NM_170606.2	2089	caG/caT	36/59	1	2	FACETS	0.988	0.91	1	0.988	0.91	1	CLONAL	1	TRUE	1	0.668702966240944	2		437	448	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	131	425	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.887	0.811	0.966	0.887	0.811	0.966	CLONAL	1	TRUE	1	0.651958794027914	2		425	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	444	519	1	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.62557372872887	2	FACETS	0.976	0.942	1	0.976	0.942	1	CLONAL	2	TRUE	0	0.651958794027914	2		520	698	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81954830	81954830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758623675	NA	P-0044694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	128	423	0	ENST00000359376.3:c.2263G>A	p.Val755Ile	p.V755I	ENST00000359376	NM_002661.3	755	Gtc/Atc	21/33	1	2	FACETS	0.855	0.781	0.933	0.855	0.781	0.933	CLONAL	1	TRUE	1	0.651958794027914	2		423	459	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923045	44923048	+	frameshift_variant	Frame_Shift_Del	DEL	CTAT	CTAT	-	rs398122969	NA	P-0044694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	191	500	0	ENST00000377967.4:c.1909_1912del	p.Ser637ThrfsTer53	p.S637Tfs*53	ENST00000377967	NM_021140.2	636	CTATct/ct	16/29	0.560924338922622	1	FACETS	0.708	0.659	0.758	0.708	0.659	0.758	SUBCLONAL	1	TRUE	0	0.651958794027914	1		500	558	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981764	201981768	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCAGA	CCAGA	-	novel	NA	P-0044694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	233	653	0	ENST00000359651.3:c.479_483del		p.X160_splice	ENST00000359651		160		4/8	1	2	FACETS	0.873	0.816	0.931	0.873	0.816	0.931	CLONAL	1	TRUE	1	0.651958794027914	2		653	819	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984373	201984374	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCC	novel	NA	P-0044694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	312	612	0	ENST00000359651.3:c.1042_1045dup	p.Arg349ProfsTer123	p.R349Pfs*123	ENST00000359651		346	-/GGCC	8/8	1	2	FACETS	0.98	0.926	1	0.98	0.926	1	CLONAL	1	TRUE	1	0.651958794027914	2		612	977	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732609	190732610	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GATCCTCGTCTTACAGCGAATG	novel	NA	P-0044694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	64	352	0	ENST00000441310.2:c.2429_2450dup	p.Phe818SerfsTer20	p.F818Sfs*20	ENST00000441310	NM_000534.4	809	-/GATCCTCGTCTTACAGCGAATG	11/13	1	2	FACETS	0.551	0.48	0.628	0.551	0.48	0.628	SUBCLONAL	1	TRUE	1	0.651958794027914	2		352	356	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802682	135802682	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	133	263	0	ENST00000298552.3:c.116del	p.Pro39LeufsTer4	p.P39Lfs*4	ENST00000298552	NM_001162426.1	39	cCt/ct	4/23	0.651958794027914	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.651958794027914	1		263	227	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	47	425	0				ENST00000310581	NM_198253.2	-/1132			0.184476410940129	5	FACETS	0.823	0.695	0.964	0.206	0.173	0.241	INDETERMINATE	1	TRUE	1	0.383430514119741	5		425	469	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0044754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	200	908	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.222441012963406	4	FACETS	1	0.982	1	0.6	0.555	0.647	INDETERMINATE	1	TRUE	2	0.383430514119741	4		908	1203	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0044754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	502	631	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	0.383430514119741	6	FACETS	0.922	0.887	0.956			1	CLONAL	5	TRUE	NA	0.383430514119741	6		631	1004	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0044754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	77	349	0	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	0.299325105396815	4	FACETS	0.674	0.591	0.764			1	SUBCLONAL	1	TRUE	NA	0.383430514119741	4		349	824	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451860	29451860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	124	670	0	ENST00000389048.3:c.2705G>A	p.Gly902Glu	p.G902E	ENST00000389048	NM_004304.4	902	gGa/gAa	16/29	0.274492816796784	3	FACETS	0.904	0.817	0.995	0.452	0.408	0.498	CLONAL	1	TRUE	1	0.383430514119741	3		670	853	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340408	8340408	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775122610	NA	P-0044754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	91	561	2	ENST00000356435.5:c.5188C>T	p.Arg1730Trp	p.R1730W	ENST00000356435		1730	Cgg/Tgg	31/35	0.290352924601415	4	FACETS	0.651	0.577	0.731			1	SUBCLONAL	1	TRUE	NA	0.383430514119741	4		563	1008	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352582	118352582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	191	557	1	ENST00000534358.1:c.3787C>T	p.Pro1263Ser	p.P1263S	ENST00000534358	NM_005933.3	1263	Cca/Tca	7/36	0.347757963575269	4	FACETS	1	0.989	1	0.722	0.668	0.779	CLONAL	1	TRUE	2	0.383430514119741	4		558	954	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908239	41908239	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1325	146	923	0	ENST00000372991.4:c.283C>G	p.Arg95Gly	p.R95G	ENST00000372991	NM_001760.3	95	Cga/Gga	2/5	0.383430514119741	4	FACETS	0.716	0.651	0.785	0.358	0.325	0.393	SUBCLONAL	1	TRUE	2	0.383430514119741	4		923	1471	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004402	150004402	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	102	475	1	ENST00000253339.5:c.1823A>T	p.Lys608Ile	p.K608I	ENST00000253339		608	aAa/aTa	3/7	0.383430514119741	3	FACETS	0.741	0.662	0.825	0.37	0.331	0.413	SUBCLONAL	1	TRUE	1	0.383430514119741	3		476	856	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401174	139401174	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	99	956	0	ENST00000277541.6:c.3895C>T	p.His1299Tyr	p.H1299Y	ENST00000277541	NM_017617.3	1299	Cac/Tac	23/34	0.383430514119741	4	FACETS	0.578	0.514	0.646	0.193	0.171	0.216	SUBCLONAL	1	TRUE	1	0.383430514119741	4		956	1236	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403440	139403441	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1464	150	999	0	ENST00000277541.6:c.3052dup	p.Cys1018LeufsTer7	p.C1018Lfs*7	ENST00000277541	NM_017617.3	1018	tgc/tTgc	19/34	0.383430514119741	4	FACETS	0.671	0.61	0.734	0.224	0.203	0.245	SUBCLONAL	1	TRUE	1	0.383430514119741	4		999	1614	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407917	139407918	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTGGA	novel	NA	P-0044754-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	465	869	0	ENST00000277541.6:c.2275_2279dup	p.Cys762ThrfsTer12	p.C762Tfs*12	ENST00000277541	NM_017617.3	760	aac/aaTCCAAc	14/34	0.383430514119741	4	FACETS	1	0.994	1	0.811	0.775	0.848	CLONAL	2	TRUE	1	0.383430514119741	4		869	1379	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0044821-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	181	545	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.21076054538456	3	FACETS	1	0.991	1	0.711	0.664	0.759	INDETERMINATE	1	TRUE	1	0.837661021233608	3		545	431	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044821-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	200	305	0	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	0.778852672209124	2	FACETS	0.853	0.813	0.89	0.853	0.813	0.89	CLONAL	2	TRUE	0	0.837661021233608	2		305	280	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662023	227662023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776903727	NA	P-0044821-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	309	690	0	ENST00000305123.5:c.1432G>A	p.Ala478Thr	p.A478T	ENST00000305123	NM_005544.2	478	Gcc/Acc	1/2	1	2	FACETS	0.963	0.913	1	0.963	0.913	1	CLONAL	1	TRUE	1	0.837661021233608	2		690	766	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106644	27106644	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044821-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	309	714	0	ENST00000324856.7:c.6256del	p.Asp2086ThrfsTer49	p.D2086Tfs*49	ENST00000324856	NM_006015.4	2085	ctG/ct	20/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.837661021233608	2		714	735	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439660	140439660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044821-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	68	329	0	ENST00000288602.6:c.2079G>A	p.Met693Ile	p.M693I	ENST00000288602	NM_004333.4	693	atG/atA	17/18	1	2	FACETS	0.503	0.44	0.569	0.503	0.44	0.569	SUBCLONAL	1	TRUE	1	0.837661021233608	2		329	323	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779604	3779605	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0044896-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	413	1003	0	ENST00000262367.5:c.5443_5444del	p.Gly1815LeufsTer150	p.G1815Lfs*150	ENST00000262367	NM_004380.2	1815	GGc/c	31/31	1	2	FACETS	1	0.993	1	1	0.997	1	CLONAL	2	TRUE	1	0.271919071858128	2		1003	1253	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577508	7577508	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1060501201	NA	P-0044922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	58	526	0	ENST00000269305.4:c.773A>C	p.Glu258Ala	p.E258A	ENST00000269305	NM_001126112.2	258	gAa/gCa	7/11	0.517616316087327	4	FACETS	0.502	0.431	0.58	0.251	0.215	0.29	SUBCLONAL	1	TRUE	2	0.582168009742835	4		526	628	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31421465	31421465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044922-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	145	272	0	ENST00000344624.3:c.3439G>A	p.Glu1147Lys	p.E1147K	ENST00000344624		1147	Gaa/Aaa	27/33	0.454217568366354	4	FACETS	0.963	0.888	1	0.963	0.888	1	CLONAL	2	TRUE	2	0.582168009742835	4		272	409	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	97	294	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.249283176680381	3	FACETS	1	0.98	1	0.728	0.651	0.809	CLONAL	1	TRUE	1	0.280472331631129	3		294	542	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144096	11144098	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0044941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	97	521	0	ENST00000358026.2:c.3679_3681del	p.Lys1227del	p.K1227del	ENST00000358026	NM_001128849.1	1226	cAGAag/cag	26/36	0.242692958667077	2	FACETS	0.887	0.79	0.99	0.443	0.395	0.495	CLONAL	1	TRUE	0	0.280472331631129	2		521	780	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602869	10602869	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	242	584	0	ENST00000171111.5:c.709C>G	p.Leu237Val	p.L237V	ENST00000171111	NM_203500.1	237	Ctg/Gtg	3/6	0.242692958667077	2	FACETS	0.901	0.842	0.961	0.901	0.842	0.961	CLONAL	2	TRUE	0	0.280472331631129	2		584	958	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1206984	1206988	+	frameshift_variant	Frame_Shift_Del	DEL	GTTCA	GTTCA	-	novel	NA	P-0044941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	160	387	0	ENST00000326873.7:c.72_76del	p.Phe25ProfsTer136	p.F25Pfs*136	ENST00000326873	NM_000455.4	24	acGTTCAtc/actc	1/10	0.242692958667077	2	FACETS	0.793	0.729	0.86	0.793	0.729	0.86	SUBCLONAL	2	TRUE	0	0.280472331631129	2		387	719	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186763	11186763	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	154	406	0	ENST00000361445.4:c.6442C>T	p.Gln2148Ter	p.Q2148*	ENST00000361445	NM_004958.3	2148	Cag/Tag	46/58	0.280472331631129	5	FACETS	0.868	0.794	0.945	0.578	0.529	0.63	CLONAL	2	TRUE	2	0.280472331631129	5		406	899	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724577	162724586	+	frameshift_variant	Frame_Shift_Del	DEL	ATGTACAAGA	ATGTACAAGA	-	novel	NA	P-0044941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	135	375	0	ENST00000367921.3:c.349_358del	p.Met117SerfsTer33	p.M117Sfs*33	ENST00000367921	NM_006182.2	117	ATGTACAAGAtc/tc	5/18	0.280472331631129	7	FACETS	0.866	0.787	0.95	0.347	0.314	0.38	CLONAL	2	TRUE	2	0.280472331631129	7		375	945	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573302	55573302	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	86	295	0	ENST00000288135.5:c.964A>T	p.Thr322Ser	p.T322S	ENST00000288135	NM_000222.2	322	Aca/Tca	6/21	0.249283176680381	3	FACETS	1	0.976	1	0.709	0.629	0.794	CLONAL	1	TRUE	1	0.280472331631129	3		295	493	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350151	81350151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044941-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	157	248	0	ENST00000222390.5:c.1181G>A	p.Gly394Glu	p.G394E	ENST00000222390	NM_000601.4	394	gGg/gAg	10/18	0.225894525817281	3	FACETS	0.867	0.8	0.935	0.867	0.8	0.935	CLONAL	3	TRUE	0	0.280472331631129	3		248	491	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0044942-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	96	262	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.302056359754628	3	FACETS	0.916	0.817	1	0.458	0.408	0.511	CLONAL	1	TRUE	1	0.3845110263558	3		262	650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0044942-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	141	667	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.361737890485928	1	FACETS	0.816	0.745	0.891	0.816	0.745	0.891	CLONAL	1	TRUE	0	0.3845110263558	1		669	726	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971000	21971000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044942-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	217	476	0	ENST00000304494.5:c.358G>T	p.Glu120Ter	p.E120*	ENST00000304494	NM_000077.4	120	Gag/Tag	2/3	0.177140796328253	2	FACETS	0.792	0.739	0.845	0.792	0.739	0.845	INDETERMINATE	2	TRUE	0	0.3845110263558	2		476	713	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821989	72821989	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044942-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	81	338	0	ENST00000268489.5:c.10186C>A	p.Pro3396Thr	p.P3396T	ENST00000268489	NM_006885.3	3396	Ccc/Acc	10/10	1	2	FACETS	0.765	0.675	0.861	0.765	0.675	0.861	SUBCLONAL	1	TRUE	1	0.3845110263558	2		338	551	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910342	29910342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044942-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	191	660	0	ENST00000376809.5:c.12G>A	p.Met4Ile	p.M4I	ENST00000376809	NM_002116.7	4	atG/atA	1/8	1	2	FACETS	0.997	0.922	1	0.997	0.922	1	CLONAL	1	TRUE	1	0.3845110263558	2		660	996	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0044943-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	126	454	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.972	0.881	1	0.972	0.881	1	CLONAL	1	TRUE	1	0.324333187512847	2		454	799	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20159743	20159743	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044943-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	117	620	0	ENST00000379607.5:c.16G>A	p.Gly6Ser	p.G6S	ENST00000379607	NM_001412.3	6	Ggt/Agt	1/7	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.324333187512847	2		620	701	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132612	67132612	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0044943-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	111	602	0	ENST00000412916.2:c.496-1G>A		p.X166_splice	ENST00000412916		166			0.324333187512847	1	FACETS	0.996	0.898	1	0.996	0.898	1	CLONAL	1	TRUE	0	0.324333187512847	1		602	576	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0044952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	89	403	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.467481413636498	2		403	374	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0044952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	460	634	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.430690489257264	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.467481413636498	3		634	1131	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291075	11291075	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1212283687	NA	P-0044952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	169	578	0	ENST00000361445.4:c.2686C>T	p.Pro896Ser	p.P896S	ENST00000361445	NM_004958.3	896	Cct/Tct	18/58	NA	2	FACETS	0.976	0.899	1			1	INDETERMINATE	1	TRUE	NA	0.467481413636498	2		578	741	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120802537	120802537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	203	735	0	ENST00000257552.2:c.289C>T	p.Pro97Ser	p.P97S	ENST00000257552	NM_002442.3	97	Cct/Tct	5/15	NA	2	FACETS	0.982	0.912	1			1	INDETERMINATE	1	TRUE	NA	0.467481413636498	2		735	884	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910431	32910431	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1555282367	NA	P-0044952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	146	343	0	ENST00000380152.3:c.1939T>G	p.Cys647Gly	p.C647G	ENST00000380152		647	Tgt/Ggt	11/27	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.467481413636498	2		343	502	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639302	3639302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	223	937	1	ENST00000294008.3:c.4337C>T	p.Thr1446Ile	p.T1446I	ENST00000294008	NM_032444.2	1446	aCc/aTc	12/15	1	2	FACETS	0.965	0.898	1	0.965	0.898	1	CLONAL	1	TRUE	1	0.467481413636498	2		938	989	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923479	9923479	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	127	522	0	ENST00000330684.3:c.1808A>G	p.Lys603Arg	p.K603R	ENST00000330684	NM_001134407.1	603	aAa/aGa	9/13	1	2	FACETS	0.913	0.83	1	0.913	0.83	1	CLONAL	1	TRUE	1	0.467481413636498	2		522	595	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274265	10274266	+	start_lost	Translation_Start_Site	DNP	CC	CC	TT	novel	NA	P-0044952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	40	392	0	ENST00000330684.3:c.3_4delinsAA	p.MetGly1_?2	p.MG1_?2	ENST00000330684	NM_001134407.1	1	atGGgc/atAAgc	2/13	1	2	FACETS	0.465	0.387	0.551	0.465	0.387	0.551	SUBCLONAL	1	TRUE	1	0.467481413636498	2		392	368	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351926	89351926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	258	1161	0	ENST00000301030.4:c.1024C>T	p.Pro342Ser	p.P342S	ENST00000301030	NM_001256183.1	342	Ccc/Tcc	9/13	0.467481413636498	1	FACETS	0.961	0.902	1	0.961	0.902	1	CLONAL	1	TRUE	0	0.467481413636498	1		1161	880	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144102	11144102	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	237	911	0	ENST00000358026.2:c.3683T>G	p.Val1228Gly	p.V1228G	ENST00000358026	NM_001128849.1	1228	gTg/gGg	26/36	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.467481413636498	2		911	974	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376236	15376236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	207	715	1	ENST00000263377.2:c.778C>T	p.Pro260Ser	p.P260S	ENST00000263377	NM_058243.2	260	Cca/Tca	5/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.467481413636498	2		716	752	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52729019	52729019	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	280	699	0	ENST00000322088.6:c.1711C>T	p.Gln571Ter	p.Q571*	ENST00000322088	NM_014225.5	571	Cag/Tag	14/15	0.467481413636498	3	FACETS	0.865	0.815	0.916	0.865	0.815	0.916	CLONAL	2	TRUE	1	0.467481413636498	3		699	854	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248674	212248674	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	118	510	0	ENST00000342788.4:c.3593C>G	p.Ala1198Gly	p.A1198G	ENST00000342788	NM_005235.2	1198	gCc/gGc	28/28	1	2	FACETS	0.846	0.765	0.93	0.846	0.765	0.93	CLONAL	1	TRUE	1	0.467481413636498	2		510	597	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561124	9561124	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	96	425	0	ENST00000353224.5:c.658C>T	p.Gln220Ter	p.Q220*	ENST00000353224	NM_177990.2	220	Cag/Tag	4/10	1	2	FACETS	0.955	0.856	1	0.955	0.856	1	CLONAL	1	TRUE	1	0.467481413636498	2		425	430	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710658	40710658	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0044952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	109	485	0	ENST00000373198.4:c.4194-1G>A		p.X1398_splice	ENST00000373198	NM_133170.3	1398			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.467481413636498	NA		485	539	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096114	71096114	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146606219	NA	P-0044952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	126	394	0	ENST00000318789.4:c.643C>T	p.Pro215Ser	p.P215S	ENST00000318789	NM_032682.5	215	Ccc/Tcc	10/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.467481413636498	2		394	486	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156102	106156102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	108	341	0	ENST00000380013.4:c.1003C>T	p.Pro335Ser	p.P335S	ENST00000380013	NM_001127208.2	335	Cct/Tct	3/11	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.467481413636498	2		341	436	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950585	38950585	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	139	451	0	ENST00000357387.3:c.3365C>T	p.Ser1122Phe	p.S1122F	ENST00000357387	NM_152756.3	1122	tCt/tTt	31/38	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.467481413636498	2		451	573	SUCCESS
APC	324	MSKCC	GRCh37	5	112177692	112177692	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	122	320	0	ENST00000257430.4:c.6401C>T	p.Ser2134Phe	p.S2134F	ENST00000257430	NM_000038.5	2134	tCc/tTc	16/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.467481413636498	2		320	463	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169206	32169206	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	207	916	0	ENST00000375023.3:c.3827A>C	p.Glu1276Ala	p.E1276A	ENST00000375023	NM_004557.3	1276	gAg/gCg	22/30	1	2	FACETS	0.932	0.865	1	0.932	0.865	1	CLONAL	1	TRUE	1	0.467481413636498	2		916	950	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69000042	69000042	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	180	543	0	ENST00000288368.4:c.2111G>A	p.Arg704Lys	p.R704K	ENST00000288368	NM_024870.2	704	aGa/aAa	19/40	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.467481413636498	2		543	713	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534962	5534962	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	117	583	0	ENST00000397747.3:c.273A>C	p.Gln91His	p.Q91H	ENST00000397747	NM_025239.3	91	caA/caC	3/7	0.467481413636498	1	FACETS	0.807	0.732	0.886	0.807	0.732	0.886	CLONAL	1	TRUE	0	0.467481413636498	1		583	475	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460420	8460420	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	111	291	0	ENST00000356435.5:c.3866T>G	p.Leu1289Arg	p.L1289R	ENST00000356435		1289	cTt/cGt	22/35	0.467481413636498	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.467481413636498	1		291	319	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93640026	93640026	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	77	331	1	ENST00000375746.1:c.1355A>C	p.Glu452Ala	p.E452A	ENST00000375746	NM_001174167.1	452	gAa/gCa	10/14	1	2	FACETS	0.858	0.758	0.964	0.858	0.758	0.964	CLONAL	1	TRUE	1	0.467481413636498	2		332	384	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0044965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	120	278	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.723744229117365	2		278	270	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578507	7578507	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519977	NA	P-0044965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	1173	734	0	ENST00000269305.4:c.423C>G	p.Cys141Trp	p.C141W	ENST00000269305	NM_001126112.2	141	tgC/tgG	5/11	0.609742084953168	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.723744229117365	1		734	1605	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104353442	104353442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	178	533	0	ENST00000369902.3:c.647G>A	p.Gly216Glu	p.G216E	ENST00000369902	NM_016169.3	216	gGg/gAg	5/12	0.310645877058888	1	FACETS	0.337	0.31	0.365	0.337	0.31	0.365	INDETERMINATE	1	TRUE	0	0.723744229117365	1		533	932	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034471	47034471	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045019-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	80	685	0	ENST00000377604.3:c.556C>T	p.Arg186Ter	p.R186*	ENST00000377604	NM_001204468.1	186	Cga/Tga	6/24	1	2	FACETS	0.829	0.729	0.935	0.829	0.729	0.935	CLONAL	1	TRUE	1	0.272747902763161	2		685	708	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879598	37879599	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCG	novel	NA	P-0045019-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	177	806	0	ENST00000269571.5:c.1973_1974insCCG	p.Val658_Val659insArg	p.V658_V659insR	ENST00000269571		658	gtg/gtCCGg	17/27	0.272747902763161	2	FACETS	0.909	0.84	0.98	0.909	0.84	0.98	CLONAL	2	TRUE	0	0.272747902763161	2		806	714	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591900	48591900	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045019-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	46	389	1	ENST00000342988.3:c.1063G>T	p.Asp355Tyr	p.D355Y	ENST00000342988	NM_005359.5	355	Gac/Tac	9/12	0.211455169710389	1	FACETS	0.872	0.737	1	0.872	0.737	1	CLONAL	1	TRUE	0	0.272747902763161	1		390	334	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983475	90983475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045019-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	41	227	0	ENST00000265433.3:c.628G>A	p.Val210Ile	p.V210I	ENST00000265433	NM_002485.4	210	Gtt/Att	6/16	1	2	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	TRUE	1	0.272747902763161	2		227	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0045040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	420	330	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	0.213526491551425	3	FACETS	0.937	0.895	0.979	1	0.994	1	CLONAL	4	TRUE	0	0.241048329717519	3		330	1042	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465650	8465650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763141884	NA	P-0045040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	29	159	0	ENST00000356435.5:c.3530G>A	p.Arg1177His	p.R1177H	ENST00000356435		1177	cGc/cAc	21/35	0.223926345352571	1	FACETS	0.672	0.54	0.821	0.672	0.54	0.821	SUBCLONAL	1	TRUE	0	0.241048329717519	1		159	315	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119823	70119823	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	280	349	1	ENST00000245479.2:c.825del	p.Ile275MetfsTer4	p.I275Mfs*4	ENST00000245479	NM_000346.3	275	atC/at	3/3	0.187776498814573	3	FACETS	1	0.979	1	1	0.994	1	CLONAL	3	TRUE	1	0.241048329717519	3		350	805	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243615	41243615	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	71	320	0	ENST00000357654.3:c.3933C>A	p.Asn1311Lys	p.N1311K	ENST00000357654	NM_007294.3	1311	aaC/aaA	10/23	0.187776498814573	3	FACETS	0.851	0.741	0.969	0.425	0.37	0.485	CLONAL	1	TRUE	1	0.241048329717519	3		320	776	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228550	36228550	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	107	336	0	ENST00000222270.7:c.7564G>C	p.Asp2522His	p.D2522H	ENST00000222270	NM_014727.1	2522	Gac/Cac	34/37	0.241048329717519	6	FACETS	1	0.968	1	0.201	0.18	0.224	CLONAL	1	TRUE	0	0.241048329717519	6		336	1089	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12043182	12043199	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CAAAGTATAAAGAGCTTC	CAAAGTATAAAGAGCTTC	TT	novel	NA	P-0045040-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	28	116	1	ENST00000353533.5:c.1067_1084delinsTT	p.Pro356LeufsTer2	p.P356Lfs*2	ENST00000353533	NM_003010.3	356	cCAAAGTATAAAGAGCTTCtg/cTTtg	10/11	0.213526491551425	3	FACETS	1	0.857	1	0.362	0.29	0.442	CLONAL	1	TRUE	0	0.241048329717519	3		117	240	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0045057-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	137	242	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.881	0.811	0.953	0.881	0.811	0.953	CLONAL	1	TRUE	1	0.838093456498933	2		242	371	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0045095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	13	354	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.572	0.407	0.774	0.572	0.407	0.774	SUBCLONAL	1	TRUE	1	0.16	2		354	284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0045095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	19	820	0	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	1	2	FACETS	0.344	0.26	0.444	0.344	0.26	0.444	SUBCLONAL	1	TRUE	1	0.16	2		820	690	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111504	8111505	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	110	680	0	ENST00000346208.3:c.992dup	p.Asn331LysfsTer21	p.N331Kfs*21	ENST00000346208		330	-/A	5/6	0.474224880884343	5	FACETS	0.971	0.879	1	0.647	0.586	0.711	CLONAL	2	TRUE	2	0.47189808654623	5		680	410	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748538	40748538	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1203244050	NA	P-0045100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	46	742	0	ENST00000392038.2:c.344C>T	p.Pro115Leu	p.P115L	ENST00000392038	NM_001626.4	115	cCa/cTa	5/14	0.400454804983202	3	FACETS	0.972	0.825	1	0.486	0.412	0.565	CLONAL	1	TRUE	1	0.47189808654623	3		742	248	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553489	106553489	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	27	475	0	ENST00000369096.4:c.1454G>A	p.Arg485Lys	p.R485K	ENST00000369096	NM_001198.3	485	aGg/aAg	5/7	0.447630735471165	3	FACETS	0.837	0.672	1			1	CLONAL	1	TRUE	NA	0.47189808654623	3		475	169	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265613	152265613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	62	493	1	ENST00000206249.3:c.1066C>T	p.His356Tyr	p.H356Y	ENST00000206249	NM_000125.3	356	Cac/Tac	4/8	0.474224880884343	3	FACETS	1	0.96	1	0.634	0.554	0.72	CLONAL	1	TRUE	1	0.47189808654623	3		494	256	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107083	27107097	+	inframe_deletion	In_Frame_Del	DEL	CGGCGGGCTGCCCGC	CGGCGGGCTGCCCGC	-	novel	NA	P-0045100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	62	533	0	ENST00000324856.7:c.6694_6708del	p.Arg2232_Arg2236del	p.R2232_R2236del	ENST00000324856	NM_006015.4	2232	CGGCGGGCTGCCCGC/-	20/20	0.474224880884343	3	FACETS	1	0.965	1	0.444	0.388	0.503	CLONAL	1	TRUE	0	0.47189808654623	3		533	244	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954153	32954153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	41	448	0	ENST00000380152.3:c.9127G>A	p.Glu3043Lys	p.E3043K	ENST00000380152		3043	Gaa/Aaa	24/27	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.47189808654623	2		448	144	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265613	152265613	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	61	494	0	ENST00000206249.3:c.1066C>A	p.His356Asn	p.H356N	ENST00000206249	NM_000125.3	356	Cac/Aac	4/8	0.474224880884343	3	FACETS	1	0.958	1	0.624	0.544	0.709	CLONAL	1	TRUE	1	0.47189808654623	3		494	256	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414400	6414400	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	67	142	0	ENST00000356142.4:c.34G>A	p.Gly12Arg	p.G12R	ENST00000356142	NM_018890.3	12	Gga/Aga	1/7	0.541887718396101	5	FACETS	1	0.956	1	0.305	0.266	0.346	CLONAL	1	TRUE	1	0.588355662885972	5		142	352	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796894	78796894	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	222	453	0	ENST00000306801.3:c.1007T>A	p.Leu336His	p.L336H	ENST00000306801	NM_020761.2	336	cTc/cAc	9/34	0.588355662885972	5	FACETS	1	0.967	1	0.422	0.394	0.45	CLONAL	2	TRUE	0	0.588355662885972	5		453	674	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182927	123182927	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045103-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	39	145	0	ENST00000218089.9:c.892C>T	p.Arg298Cys	p.R298C	ENST00000218089	NM_001042749.1	298	Cgt/Tgt	10/35	0.534056038273461	2	FACETS	0.989	0.837	1			1	CLONAL	1	TRUE	NA	0.588355662885972	2		145	134	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0045104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	13	427	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.62	0.44	0.842	0.62	0.44	0.842	SUBCLONAL	1	TRUE	1	0.08	2		427	524	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0045104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	18	460	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.636	0.476	0.826	0.636	0.476	0.826	SUBCLONAL	1	TRUE	1	0.08	2		460	708	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469669	NA	P-0045104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	24	252	0	ENST00000374080.3:c.130G>A	p.Gly44Ser	p.G44S	ENST00000374080		44	Ggt/Agt	2/45	1	1	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	0	0.08	1		252	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0045105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	296	629	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.364841593982954	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.364841593982954	2		629	747	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637326	47637326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759712763	NA	P-0045105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	159	712	0	ENST00000233146.2:c.460G>A	p.Ala154Thr	p.A154T	ENST00000233146	NM_000251.2	154	Gca/Aca	3/16	0.364841593982954	4	FACETS	0.996	0.911	1	0.498	0.455	0.543	CLONAL	1	TRUE	2	0.364841593982954	4		712	1194	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783334	9783334	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	117	530	0	ENST00000377346.4:c.2578A>C	p.Lys860Gln	p.K860Q	ENST00000377346	NM_005026.3	860	Aag/Cag	20/24	0.364841593982954	3	FACETS	0.916	0.826	1	0.458	0.413	0.506	CLONAL	1	TRUE	1	0.364841593982954	3		530	828	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94922977	94922977	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	98	403	1	ENST00000536441.1:c.491A>G	p.His164Arg	p.H164R	ENST00000536441	NM_144665.3	164	cAt/cGt	4/10	0.364841593982954	3	FACETS	1	0.959	1	0.574	0.514	0.639	CLONAL	1	TRUE	1	0.364841593982954	3		404	553	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504096	123504096	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	99	418	1	ENST00000371139.4:c.272A>C	p.Asp91Ala	p.D91A	ENST00000371139	NM_001114937.2	91	gAt/gCt	3/4	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	1	TRUE	NA	0.364841593982954	2		419	455	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0045106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	52	286	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.16	2		286	558	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0045106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	54	458	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.908	0.774	1	0.908	0.774	1	CLONAL	1	TRUE	1	0.16	2		458	743	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278343	39278343	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	33	545	0	ENST00000402219.2:c.806T>A	p.Met269Lys	p.M269K	ENST00000402219	NM_005633.3	269	aTg/aAg	6/23	1	2	FACETS	0.806	0.655	0.976	0.806	0.655	0.976	CLONAL	1	TRUE	1	0.16	2		545	512	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685289	89685290	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0045106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	21	187	0	ENST00000371953.3:c.187_188del	p.Asn63ProfsTer10	p.N63Pfs*10	ENST00000371953	NM_000314.4	62	AAa/a	3/9	0.16693220754897	3	FACETS	1	0.868	1	0.596	0.46	0.753	CLONAL	1	TRUE	1	0.16	3		187	238	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589151	67589152	+	inframe_insertion	In_Frame_Ins	INS	-	-	AATCAA	novel	NA	P-0045106-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	17	249	0	ENST00000274335.5:c.1143_1148dup	p.Lys382_Ile383dup	p.K382_I383dup	ENST00000274335		382	tta/ttAATCAAa	9/15	1	2	FACETS	0.904	0.676	1	0.904	0.676	1	CLONAL	1	TRUE	1	0.16	2		249	235	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0045107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	189	454	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.925	0.855	0.998	0.925	0.855	0.998	CLONAL	1	TRUE	1	0.416478659257251	2		454	981	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005843	69005843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	100	327	0	ENST00000288368.4:c.2254G>A	p.Asp752Asn	p.D752N	ENST00000288368	NM_024870.2	752	Gat/Aat	21/40	1	2	FACETS	0.883	0.791	0.98	0.883	0.791	0.98	CLONAL	1	TRUE	1	0.416478659257251	2		327	544	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441973	52441973	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs775451516	NA	P-0045107-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	187	383	1	ENST00000460680.1:c.375+1G>A		p.X125_splice	ENST00000460680	NM_004656.3	125			0.416478659257251	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.416478659257251	1		384	611	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0045108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	115	330	0	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	0.294859750363932	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.294859750363932	1		330	533	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149242	119149242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779039234	NA	P-0045108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	122	516	1	ENST00000264033.4:c.1250C>T	p.Pro417Leu	p.P417L	ENST00000264033	NM_005188.3	417	cCt/cTt	9/16	0.294859750363932	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.294859750363932	1		517	651	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169586	27169586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	145	602	0	ENST00000380036.4:c.587G>A	p.Gly196Glu	p.G196E	ENST00000380036	NM_000459.3	196	gGa/gAa	4/23	0.294859750363932	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.294859750363932	1		602	772	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549706	226549706	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	86	417	0	ENST00000366794.5:c.2927C>T	p.Ser976Leu	p.S976L	ENST00000366794	NM_001618.3	976	tCa/tTa	22/23	1	2	FACETS	0.767	0.678	0.862	0.767	0.678	0.862	SUBCLONAL	1	TRUE	1	0.294859750363932	2		417	761	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156486	55156486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756581500	NA	P-0045108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	67	339	0	ENST00000257290.5:c.2887G>A	p.Glu963Lys	p.E963K	ENST00000257290	NM_006206.4	963	Gaa/Aaa	22/23	1	2	FACETS	0.914	0.796	1	0.914	0.796	1	CLONAL	1	TRUE	1	0.294859750363932	2		339	497	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698171	47698171	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs774985655	NA	P-0045108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	65	305	0	ENST00000233146.2:c.1729A>G	p.Ile577Val	p.I577V	ENST00000233146	NM_000251.2	577	Att/Gtt	11/16	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.294859750363932	2		305	402	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743285	162743285	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757836784	NA	P-0045108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	51	283	0	ENST00000367921.3:c.1755G>A	p.Met585Ile	p.M585I	ENST00000367921	NM_006182.2	585	atG/atA	14/18	1	2	FACETS	0.869	0.741	1	0.869	0.741	1	CLONAL	1	TRUE	1	0.294859750363932	2		283	398	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426147	49426147	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	97	532	0	ENST00000301067.7:c.12341G>C	p.Gly4114Ala	p.G4114A	ENST00000301067	NM_003482.3	4114	gGa/gCa	39/54	1	2	FACETS	0.788	0.702	0.88	0.788	0.702	0.88	SUBCLONAL	1	TRUE	1	0.294859750363932	2		532	835	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623821	28623821	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	101	474	0	ENST00000241453.7:c.833A>G	p.Asn278Ser	p.N278S	ENST00000241453	NM_004119.2	278	aAc/aGc	7/24	1	2	FACETS	0.954	0.853	1	0.954	0.853	1	CLONAL	1	TRUE	1	0.294859750363932	2		474	718	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645301	67645301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754178156	NA	P-0045108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	154	519	0	ENST00000264010.4:c.566C>T	p.Pro189Leu	p.P189L	ENST00000264010	NM_006565.3	189	cCt/cTt	3/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.294859750363932	2		519	831	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682416	37682416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777844841	NA	P-0045108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	80	401	0	ENST00000447079.4:c.3607C>T	p.Pro1203Ser	p.P1203S	ENST00000447079	NM_015083.1	1203	Cca/Tca	13/14	0.294859750363932	1	FACETS	0.846	0.746	0.953	0.846	0.746	0.953	CLONAL	1	TRUE	0	0.294859750363932	1		401	547	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223175	36223175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769851153	NA	P-0045108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	192	658	0	ENST00000222270.7:c.5725C>T	p.Pro1909Ser	p.P1909S	ENST00000222270	NM_014727.1	1909	Ccc/Tcc	28/37	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.294859750363932	2		658	1086	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223871	36223871	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	185	608	0	ENST00000222270.7:c.6421C>A	p.Pro2141Thr	p.P2141T	ENST00000222270	NM_014727.1	2141	Ccc/Acc	28/37	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.294859750363932	2		608	1033	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485401	57485401	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	57	282	0	ENST00000371085.3:c.983C>T	p.Pro328Leu	p.P328L	ENST00000371085	NM_000516.4	328	cCc/cTc	12/13	1	2	FACETS	0.776	0.667	0.896	0.776	0.667	0.896	SUBCLONAL	1	TRUE	1	0.294859750363932	2		282	498	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421202	12421202	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0045108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	108	331	0	ENST00000287820.6:c.83-1G>A		p.X28_splice	ENST00000287820	NM_015869.4	28			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.294859750363932	2		331	600	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374815	149374816	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0045108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	35	209	0	ENST00000360632.3:c.278_279delinsTT	p.Ser93Phe	p.S93F	ENST00000360632	NM_015472.4	93	tCC/tTT	2/7	1	2	FACETS	0.61	0.501	0.733	0.61	0.501	0.733	SUBCLONAL	1	TRUE	1	0.294859750363932	2		209	389	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169003	32169003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	196	633	0	ENST00000375023.3:c.4030G>A	p.Gly1344Arg	p.G1344R	ENST00000375023	NM_004557.3	1344	Ggg/Agg	22/30	0.0981336929216718	3	FACETS	1	0.988	1	0.673	0.622	0.726	INDETERMINATE	1	TRUE	1	0.294859750363932	3		633	1134	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725589	117725589	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1386947086	NA	P-0045108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	88	329	0	ENST00000368508.3:c.292A>G	p.Asn98Asp	p.N98D	ENST00000368508	NM_002944.2	98	Aat/Gat	5/43	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.294859750363932	2		329	579	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045146	47045146	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	127	553	0	ENST00000377604.3:c.2387T>G	p.Leu796Trp	p.L796W	ENST00000377604	NM_001204468.1	796	tTg/tGg	21/24	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.294859750363932	2		553	858	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409956	63409956	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	75	386	0	ENST00000330258.3:c.3211C>T	p.Pro1071Ser	p.P1071S	ENST00000330258	NM_152424.3	1071	Cct/Tct	2/2	1	2	FACETS	0.858	0.752	0.971	0.858	0.752	0.971	CLONAL	1	TRUE	1	0.294859750363932	2		386	593	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354975	70354975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	131	511	1	ENST00000374080.3:c.4897G>A	p.Glu1633Lys	p.E1633K	ENST00000374080		1633	Gaa/Aaa	36/45	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.294859750363932	2		512	884	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0045110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	18	309	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		309	307	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520087	106520087	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774448553	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	67	305	0	ENST00000359195.3:c.2515C>T	p.Arg839Cys	p.R839C	ENST00000359195	NM_002649.2	839	Cgc/Tgc	6/11	1	2	FACETS	0.956	0.846	1	0.956	0.846	1	CLONAL	1	TRUE	1	0.718990580787651	2		305	195	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396234	396234	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	62	651	1	ENST00000262320.3:c.792del	p.Gly265GlufsTer149	p.G265Efs*149	ENST00000262320	NM_003502.3	264	ccC/cc	2/11	1	2	FACETS	0.166	0.142	0.191	0.166	0.142	0.191	SUBCLONAL	1	TRUE	1	0.718990580787651	2		652	1041	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	127	373	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	0.718990580787651	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.718990580787651	1		373	224	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	262	568	1	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.989	0.931	1	0.989	0.931	1	CLONAL	1	TRUE	1	0.718990580787651	2		569	737	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	228	606	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.885	0.828	0.943	0.885	0.828	0.943	CLONAL	1	TRUE	1	0.718990580787651	2		610	717	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	41	545	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.198	0.164	0.236	0.198	0.164	0.236	SUBCLONAL	1	TRUE	1	0.718990580787651	2		545	576	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	174	395	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.835	0.773	0.898	0.835	0.773	0.898	CLONAL	1	TRUE	1	0.718990580787651	2		396	580	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151289	202151290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	180	444	0	ENST00000358485.4:c.1596dup	p.Leu533ThrfsTer6	p.L533Tfs*6	ENST00000358485	NM_001080125.1	530	aga/agAa	9/9	1	2	FACETS	0.836	0.775	0.899	0.836	0.775	0.899	CLONAL	1	TRUE	1	0.718990580787651	2		444	599	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070349	37070349	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs63750855	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	189	502	3	ENST00000231790.2:c.1489del	p.Arg497GlyfsTer11	p.R497Gfs*11	ENST00000231790	NM_000249.3	495	aCc/ac	13/19	1	2	FACETS	0.931	0.866	0.997	0.931	0.866	0.997	CLONAL	1	TRUE	1	0.718990580787651	2		505	565	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	179	411	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.924	0.858	0.991	0.924	0.858	0.991	CLONAL	1	TRUE	1	0.718990580787651	2		412	539	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849514	68849514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs36087757	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	55	658	0	ENST00000261769.5:c.1417G>A	p.Val473Ile	p.V473I	ENST00000261769	NM_004360.3	473	Gtc/Atc	10/16	1	2	FACETS	0.144	0.122	0.167	0.144	0.122	0.167	SUBCLONAL	1	TRUE	1	0.718990580787651	2		658	1066	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	284	617	2	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.843	0.794	0.893	0.843	0.794	0.893	CLONAL	1	TRUE	1	0.718990580787651	2		619	937	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069060	5069060	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	106	402	0	ENST00000381652.3:c.1370del	p.Asn457MetfsTer22	p.N457Mfs*22	ENST00000381652	NM_004972.3	455	acA/ac	11/25	1	2	FACETS	0.964	0.875	1	0.964	0.875	1	CLONAL	1	TRUE	1	0.718990580787651	2		402	306	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63760023	63760023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	34	429	0	ENST00000279873.7:c.676C>T	p.Arg226Trp	p.R226W	ENST00000279873	NM_032199.2	226	Cgg/Tgg	4/10	1	2	FACETS	0.168	0.137	0.203	0.168	0.137	0.203	SUBCLONAL	1	TRUE	1	0.718990580787651	2		429	563	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347983	347983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760961378	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	73	787	1	ENST00000262320.3:c.1523del	p.Gly508ValfsTer197	p.G508Vfs*197	ENST00000262320	NM_003502.3	508	gGt/gt	6/11	1	2	FACETS	0.186	0.162	0.213	0.186	0.162	0.213	SUBCLONAL	1	TRUE	1	0.718990580787651	2		788	1090	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829283	72829283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773115759	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	278	756	1	ENST00000268489.5:c.7298C>T	p.Ala2433Val	p.A2433V	ENST00000268489	NM_006885.3	2433	gCg/gTg	9/10	1	2	FACETS	0.784	0.737	0.832	0.784	0.737	0.832	SUBCLONAL	1	TRUE	1	0.718990580787651	2		757	986	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120115	70120115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	54	128	0	ENST00000245479.2:c.1121del	p.Pro374ArgfsTer9	p.P374Rfs*9	ENST00000245479	NM_000346.3	373	Ccc/cc	3/3	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.718990580787651	2		128	148	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143043366	143043366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199940140	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	123	456	0	ENST00000262992.4:c.2050G>A	p.Val684Ile	p.V684I	ENST00000262992	NM_001101669.1	684	Gtt/Att	19/24	1	2	FACETS	0.776	0.707	0.848	0.776	0.707	0.848	SUBCLONAL	1	TRUE	1	0.718990580787651	2		456	441	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489486	40489486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	293	622	0	ENST00000264657.5:c.764C>T	p.Pro255Leu	p.P255L	ENST00000264657	NM_139276.2	255	cCg/cTg	8/24	1	2	FACETS	0.872	0.822	0.922	0.872	0.822	0.922	CLONAL	1	TRUE	1	0.718990580787651	2		622	935	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279860	46279861	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAA	rs753491875	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	29	493	0	ENST00000371998.3:c.3788_3789insACA	p.Gln1276dup	p.Q1276dup	ENST00000371998		1276	-/CAA	20/23	1	2	FACETS	0.141	0.113	0.174	0.141	0.113	0.174	SUBCLONAL	1	TRUE	1	0.718990580787651	2		493	571	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867370	68867370	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	265	510	0	ENST00000261769.5:c.2617G>A	p.Ala873Thr	p.A873T	ENST00000261769	NM_004360.3	873	Gct/Act	16/16	1	2	FACETS	0.908	0.854	0.963	0.908	0.854	0.963	CLONAL	1	TRUE	1	0.718990580787651	2		510	812	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435168	56435168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766439784	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	340	748	3	ENST00000407977.2:c.1969C>T	p.Arg657Trp	p.R657W	ENST00000407977		657	Cgg/Tgg	9/10	1	2	FACETS	0.993	0.942	1	0.993	0.942	1	CLONAL	1	TRUE	1	0.718990580787651	2		751	952	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803111	1803111	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1361311749	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	354	704	4	ENST00000260795.2:c.463C>T	p.Arg155Trp	p.R155W	ENST00000260795		155	Cgg/Tgg	4/17	1	2	FACETS	0.965	0.916	1	0.965	0.916	1	CLONAL	1	TRUE	1	0.718990580787651	2		708	1020	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996200	73996200	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757435411	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	244	510	0	ENST00000318443.5:c.934G>A	p.Ala312Thr	p.A312T	ENST00000318443	NM_001024736.1	312	Gcc/Acc	5/10	1	2	FACETS	0.963	0.904	1	0.963	0.904	1	CLONAL	1	TRUE	1	0.718990580787651	2		510	705	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564680	86564680	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	299	720	0	ENST00000274376.6:c.416del	p.Pro139LeufsTer35	p.P139Lfs*35	ENST00000274376	NM_002890.2	138	Ccc/cc	1/25	1	2	FACETS	0.832	0.784	0.88	0.832	0.784	0.88	CLONAL	1	TRUE	1	0.718990580787651	2		720	1000	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966873	25966873	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1271466699	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	238	609	4	ENST00000435504.4:c.2333del	p.Pro778GlnfsTer21	p.P778Qfs*21	ENST00000435504		778	cCa/ca	13/13	1	2	FACETS	0.856	0.802	0.912	0.856	0.802	0.912	CLONAL	1	TRUE	1	0.718990580787651	2		613	773	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020818	112020819	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	225	482	0	ENST00000368678.4:c.752dup	p.Gln252ThrfsTer7	p.Q252Tfs*7	ENST00000368678		251	cca/ccCa	8/13	1	2	FACETS	0.856	0.8	0.913	0.856	0.8	0.913	CLONAL	1	TRUE	1	0.718990580787651	2		482	731	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759781	133759783	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs1008368368	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	249	655	0	ENST00000318560.5:c.2111_2113del	p.Glu704del	p.E704del	ENST00000318560	NM_005157.4	702	GAG/-	11/11	1	2	FACETS	0.877	0.823	0.932	0.877	0.823	0.932	CLONAL	1	TRUE	1	0.718990580787651	2		655	790	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937603	76937603	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	59	409	1	ENST00000373344.5:c.3145del	p.Ile1049Ter	p.I1049*	ENST00000373344	NM_000489.3	1049	Ata/ta	9/35	0.381545992144056	1	FACETS	0.415	0.361	0.473	0.415	0.361	0.473	INDETERMINATE	1	TRUE	0	0.718990580787651	1		410	253	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	302	780	2	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	0.707	0.666	0.75	0.707	0.666	0.75	SUBCLONAL	1	TRUE	1	0.718990580787651	2		782	1188	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007794	45007797	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	80	495	0	ENST00000558401.1:c.244_247del	p.Phe82IlefsTer20	p.F82Ifs*20	ENST00000558401	NM_004048.2	81	TCTTtc/tc	2/4	1	2	FACETS	0.539	0.477	0.605	0.539	0.477	0.605	SUBCLONAL	1	TRUE	1	0.718990580787651	2		495	413	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589576	67589576	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1289537429	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	68	302	0	ENST00000274335.5:c.1344del	p.Lys448AsnfsTer32	p.K448Nfs*32	ENST00000274335		447	Aaa/aa	10/15	1	2	FACETS	0.778	0.686	0.875	0.778	0.686	0.875	SUBCLONAL	1	TRUE	1	0.718990580787651	2		302	243	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	76	523	10	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.371	0.325	0.42	0.371	0.325	0.42	SUBCLONAL	1	TRUE	1	0.718990580787651	2		533	570	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980558	1980559	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs752037034	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	282	698	21	ENST00000382891.5:c.4028dup	p.Glu1344ArgfsTer91	p.E1344Rfs*91	ENST00000382891	NM_133335.3	1340	-/C	22/22	1	2	FACETS	0.803	0.755	0.851	0.803	0.755	0.851	CLONAL	1	TRUE	1	0.718990580787651	2		719	977	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412124	63412124	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	390	963	0	ENST00000330258.3:c.1043del	p.Gly348AlafsTer16	p.G348Afs*16	ENST00000330258	NM_152424.3	348	gGc/gc	2/2	0.381545992144056	1	FACETS	0.622	0.592	0.653	0.622	0.592	0.653	INDETERMINATE	1	TRUE	0	0.718990580787651	1		963	1117	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578480	7578480	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	449	767	7	ENST00000269305.4:c.450del	p.Pro152ArgfsTer18	p.P152Rfs*18	ENST00000269305	NM_001126112.2	150	acA/ac	5/11	1	2	FACETS	0.956	0.913	1	0.956	0.913	1	CLONAL	1	TRUE	1	0.718990580787651	2		774	1306	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	248	541	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	1	2	FACETS	0.888	0.833	0.944	0.888	0.833	0.944	CLONAL	1	TRUE	1	0.718990580787651	2		541	777	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738829	145738829	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758736784	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1198	110	815	0	ENST00000428558.2:c.2236G>A	p.Ala746Thr	p.A746T	ENST00000428558	NM_004260.3	746	Gcg/Acg	14/22	1	2	FACETS	0.234	0.209	0.26	0.234	0.209	0.26	SUBCLONAL	1	TRUE	1	0.718990580787651	2		815	1308	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426093	47426094	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1431646407	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	261	778	2	ENST00000377045.4:c.619dup	p.Leu207ProfsTer36	p.L207Pfs*36	ENST00000377045	NM_001654.4	205	gcc/gCcc	7/16	0.381545992144056	1	FACETS	0.437	0.41	0.466	0.437	0.41	0.466	INDETERMINATE	1	TRUE	0	0.718990580787651	1		780	1063	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274740	142274741	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	94	399	1	ENST00000350721.4:c.2319_2320del	p.Lys773AsnfsTer3	p.K773Nfs*3	ENST00000350721	NM_001184.3	773	aaAAta/aata	10/47	1	2	FACETS	0.833	0.749	0.919	0.833	0.749	0.919	CLONAL	1	TRUE	1	0.718990580787651	2		400	314	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447334	187447335	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	306	667	0	ENST00000232014.4:c.858dup	p.Ser287LeufsTer11	p.S287Lfs*11	ENST00000232014	NM_001130845.1	286	-/C	5/10	1	2	FACETS	0.884	0.835	0.934	0.884	0.835	0.934	CLONAL	1	TRUE	1	0.718990580787651	2		667	963	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578369	7578369	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	287	649	0	ENST00000269305.4:c.559+2T>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			1	2	FACETS	0.983	0.928	1	0.983	0.928	1	CLONAL	1	TRUE	1	0.718990580787651	2		649	812	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162704	47162704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142723093	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	131	472	0	ENST00000409792.3:c.3422C>T	p.Pro1141Leu	p.P1141L	ENST00000409792	NM_014159.6	1141	cCg/cTg	3/21	1	2	FACETS	0.861	0.789	0.937	0.861	0.789	0.937	CLONAL	1	TRUE	1	0.718990580787651	2		472	423	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46740268	46740268	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs28363243	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	259	528	0	ENST00000371975.4:c.1748T>C	p.Ile583Thr	p.I583T	ENST00000371975	NM_003579.3	583	aTt/aCt	16/18	1	2	FACETS	0.945	0.889	1	0.945	0.889	1	CLONAL	1	TRUE	1	0.718990580787651	2		528	762	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434561	49434562	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	275	704	2	ENST00000301067.7:c.6991dup	p.Leu2331ProfsTer46	p.L2331Pfs*46	ENST00000301067	NM_003482.3	2331	ctg/cCtg	31/54	1	2	FACETS	0.785	0.737	0.833	0.785	0.737	0.833	SUBCLONAL	1	TRUE	1	0.718990580787651	2		706	975	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374711	149374711	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1485853361	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	213	589	0	ENST00000360632.3:c.383del	p.Pro128ArgfsTer5	p.P128Rfs*5	ENST00000360632	NM_015472.4	128	cCg/cg	2/7	1	2	FACETS	0.622	0.578	0.668	0.622	0.578	0.668	SUBCLONAL	1	TRUE	1	0.718990580787651	2		589	952	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467987	50467987	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	275	561	0	ENST00000331340.3:c.1222C>T	p.Arg408Cys	p.R408C	ENST00000331340	NM_006060.4	408	Cgc/Tgc	8/8	1	2	FACETS	0.96	0.905	1	0.96	0.905	1	CLONAL	1	TRUE	1	0.718990580787651	2		561	797	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022880	12022880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	355	710	0	ENST00000396373.4:c.986C>T	p.Ala329Val	p.A329V	ENST00000396373	NM_001987.4	329	gCc/gTc	5/8	0.200064409358526	4	FACETS	0.833	0.791	0.876	0.833	0.791	0.876	INDETERMINATE	2	TRUE	2	0.718990580787651	4		710	1019	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264377	46264378	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	181	458	0	ENST00000371998.3:c.1427dup	p.Asn476LysfsTer11	p.N476Kfs*11	ENST00000371998		475	cca/ccAa	11/23	1	2	FACETS	0.835	0.774	0.897	0.835	0.774	0.897	CLONAL	1	TRUE	1	0.718990580787651	2		458	603	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944151	81944151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	268	652	0	ENST00000359376.3:c.1760G>A	p.Arg587Gln	p.R587Q	ENST00000359376	NM_002661.3	587	cGg/cAg	18/33	1	2	FACETS	0.926	0.872	0.981	0.926	0.872	0.981	CLONAL	1	TRUE	1	0.718990580787651	2		652	805	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987066	36987066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1325836054	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	293	604	1	ENST00000354822.5:c.623G>A	p.Arg208Gln	p.R208Q	ENST00000354822	NM_001079668.2	208	cGa/cAa	3/3	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.718990580787651	2		605	808	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874550	35874550	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1055222075	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	180	500	0	ENST00000303115.3:c.707-1G>A		p.X236_splice	ENST00000303115	NM_002185.3	236			1	2	FACETS	0.988	0.918	1	0.988	0.918	1	CLONAL	1	TRUE	1	0.718990580787651	2		500	507	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599937	10599937	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369083385	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	430	668	2	ENST00000171111.5:c.1639G>A	p.Val547Ile	p.V547I	ENST00000171111	NM_203500.1	547	Gta/Ata	5/6	1	2	FACETS	0.993	0.947	1	0.993	0.947	1	CLONAL	1	TRUE	1	0.718990580787651	2		670	1205	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981438	70981438	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	385	842	0	ENST00000276594.2:c.658C>A	p.His220Asn	p.H220N	ENST00000276594	NM_024504.3	220	Cac/Aac	2/8	1	2	FACETS	0.983	0.935	1	0.983	0.935	1	CLONAL	1	TRUE	1	0.718990580787651	2		842	1090	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404813	404813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368604945	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	244	601	0	ENST00000399788.2:c.4381G>A	p.Glu1461Lys	p.E1461K	ENST00000399788	NM_001042603.1	1461	Gag/Aag	26/28	0.381545992144056	1	FACETS	0.546	0.512	0.581	0.546	0.512	0.581	INDETERMINATE	1	TRUE	0	0.718990580787651	1		601	796	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294672	1294672	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1554043093	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	192	374	0	ENST00000310581.5:c.329del	p.Gly110AlafsTer18	p.G110Afs*18	ENST00000310581	NM_198253.2	110	gGc/gc	2/16	1	2	FACETS	0.898	0.835	0.962	0.898	0.835	0.962	CLONAL	1	TRUE	1	0.718990580787651	2		374	595	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11210190	11210190	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	50	525	0	ENST00000361445.4:c.4563G>T	p.Trp1521Cys	p.W1521C	ENST00000361445	NM_004958.3	1521	tgG/tgT	31/58	1	2	FACETS	0.164	0.139	0.193	0.164	0.139	0.193	SUBCLONAL	1	TRUE	1	0.718990580787651	2		525	847	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101515	27101516	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	409	781	0	ENST00000324856.7:c.4800_4801del	p.Pro1601Ter	p.P1601*	ENST00000324856	NM_006015.4	1599	acCTct/acct	18/20	1	2	FACETS	0.927	0.883	0.972	0.927	0.883	0.972	CLONAL	1	TRUE	1	0.718990580787651	2		781	1227	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309777	65309777	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	300	583	0	ENST00000342505.4:c.2373G>T	p.Glu791Asp	p.E791D	ENST00000342505	NM_002227.2	791	gaG/gaT	17/25	1	2	FACETS	0.945	0.893	0.998	0.945	0.893	0.998	CLONAL	1	TRUE	1	0.718990580787651	2		583	883	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65312411	65312413	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	217	538	0	ENST00000342505.4:c.1906_1908del	p.Phe636del	p.F636del	ENST00000342505	NM_002227.2	636	TTC/-	14/25	1	2	FACETS	0.894	0.836	0.954	0.894	0.836	0.954	CLONAL	1	TRUE	1	0.718990580787651	2		538	675	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282416	115282416	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	181	572	0	ENST00000438362.2:c.234del	p.Lys78AsnfsTer3	p.K78Nfs*3	ENST00000438362	NM_001242891.1	78	aaA/aa	3/20	1	2	FACETS	0.972	0.904	1	0.972	0.904	1	CLONAL	1	TRUE	1	0.718990580787651	2		572	518	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333316	70333316	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	360	756	1	ENST00000373644.4:c.1221G>T	p.Glu407Asp	p.E407D	ENST00000373644	NM_030625.2	407	gaG/gaT	2/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.718990580787651	2		757	951	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711974	89711974	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1554900633	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	103	385	1	ENST00000371953.3:c.592A>G	p.Met198Val	p.M198V	ENST00000371953	NM_000314.4	198	Atg/Gtg	6/9	0.718990580787651	1	FACETS	0.891	0.817	0.964	0.891	0.817	0.964	CLONAL	1	TRUE	0	0.718990580787651	1		386	206	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633581	69633581	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	98	155	0	ENST00000334134.2:c.121G>A	p.Gly41Arg	p.G41R	ENST00000334134	NM_005247.2	41	Ggg/Agg	1/3	1	2	FACETS	0.847	0.764	0.933	0.847	0.764	0.933	CLONAL	1	TRUE	1	0.718990580787651	2		155	322	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71947023	71947024	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	306	816	0	ENST00000298229.2:c.2877dup	p.Arg960GlnfsTer9	p.R960Qfs*9	ENST00000298229	NM_001567.3	958	acc/aCcc	25/28	1	2	FACETS	0.79	0.745	0.836	0.79	0.745	0.836	SUBCLONAL	1	TRUE	1	0.718990580787651	2		816	1078	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307256	118307256	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	126	193	0	ENST00000534358.1:c.29C>T	p.Pro10Leu	p.P10L	ENST00000534358	NM_005933.3	10	cCc/cTc	1/36	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.718990580787651	2		193	267	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307291	118307293	+	inframe_deletion	In_Frame_Del	DEL	GGG	GGG	-	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	12	58	0	ENST00000534358.1:c.67_69del	p.Gly23del	p.G23del	ENST00000534358	NM_005933.3	22	GGG/-	1/36	1	2	FACETS	0.397	0.283	0.534	0.397	0.283	0.534	SUBCLONAL	1	TRUE	1	0.718990580787651	2		58	84	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118365442	118365442	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	119	394	1	ENST00000534358.1:c.5327del	p.Lys1776SerfsTer47	p.K1776Sfs*47	ENST00000534358	NM_005933.3	1775	Aaa/aa	18/36	1	2	FACETS	0.932	0.851	1	0.932	0.851	1	CLONAL	1	TRUE	1	0.718990580787651	2		395	355	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14016051	14016051	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	19	280	1	ENST00000311895.7:c.371C>A	p.Pro124His	p.P124H	ENST00000311895	NM_005236.2	124	cCt/cAt	2/11	1	2	FACETS	0.227	0.172	0.291	0.227	0.172	0.291	SUBCLONAL	1	TRUE	1	0.718990580787651	2		281	233	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993824	72993824	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	168	555	0	ENST00000268489.5:c.221C>A	p.Pro74His	p.P74H	ENST00000268489	NM_006885.3	74	cCc/cAc	2/10	1	2	FACETS	0.76	0.702	0.82	0.76	0.702	0.82	SUBCLONAL	1	TRUE	1	0.718990580787651	2		555	615	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857898	89857904	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCTGG	CAGCTGG	-	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	325	636	0	ENST00000389301.3:c.1266_1272del	p.Cys422TrpfsTer102	p.C422Wfs*102	ENST00000389301	NM_000135.2	422	tgCCAGCTG/tg	14/43	1	2	FACETS	0.903	0.855	0.953	0.903	0.855	0.953	CLONAL	1	TRUE	1	0.718990580787651	2		636	1001	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511582	38511582	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	336	736	0	ENST00000254066.5:c.1080G>T	p.Lys360Asn	p.K360N	ENST00000254066	NM_000964.3	360	aaG/aaT	8/9	1	2	FACETS	0.926	0.878	0.976	0.926	0.878	0.976	CLONAL	1	TRUE	1	0.718990580787651	2		736	1009	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245803	41245803	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786202386	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	176	637	0	ENST00000357654.3:c.1745C>T	p.Thr582Met	p.T582M	ENST00000357654	NM_007294.3	582	aCg/aTg	10/23	1	2	FACETS	0.913	0.847	0.981	0.913	0.847	0.981	CLONAL	1	TRUE	1	0.718990580787651	2		637	536	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78704382	78704382	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	218	477	0	ENST00000306801.3:c.530T>G	p.Leu177Arg	p.L177R	ENST00000306801	NM_020761.2	177	cTg/cGg	5/34	1	2	FACETS	0.933	0.872	0.995	0.933	0.872	0.995	CLONAL	1	TRUE	1	0.718990580787651	2		477	650	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919559	78919559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569635813	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	267	504	0	ENST00000306801.3:c.3118G>A	p.Val1040Ile	p.V1040I	ENST00000306801	NM_020761.2	1040	Gta/Ata	26/34	1	2	FACETS	0.94	0.885	0.996	0.94	0.885	0.996	CLONAL	1	TRUE	1	0.718990580787651	2		504	790	SUCCESS
YES1	7525	MSKCC	GRCh37	18	746034	746034	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	55	478	0	ENST00000314574.4:c.488T>C	p.Met163Thr	p.M163T	ENST00000314574	NM_005433.3	163	aTg/aCg	5/12	0.718990580787651	1	FACETS	0.4	0.345	0.458	0.4	0.345	0.458	SUBCLONAL	1	TRUE	0	0.718990580787651	1		478	245	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5207934	5207934	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	307	632	1	ENST00000357368.4:c.5777A>G	p.Glu1926Gly	p.E1926G	ENST00000357368	NM_002850.3	1926	gAg/gGg	37/38	1	2	FACETS	0.922	0.872	0.974	0.922	0.872	0.974	CLONAL	1	TRUE	1	0.718990580787651	2		633	926	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765647	41765647	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1181583644	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	387	753	2	ENST00000301178.4:c.2528del	p.Pro843GlnfsTer113	p.P843Qfs*113	ENST00000301178	NM_021913.4	841	gaC/ga	20/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.718990580787651	2		755	1004	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967284	25967284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1338721842	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	240	522	0	ENST00000435504.4:c.1922G>A	p.Arg641His	p.R641H	ENST00000435504		641	cGt/cAt	13/13	1	2	FACETS	0.869	0.815	0.925	0.869	0.815	0.925	CLONAL	1	TRUE	1	0.718990580787651	2		522	768	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149569	202149570	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	195	424	0	ENST00000358485.4:c.1014dup	p.Glu339Ter	p.E339*	ENST00000358485	NM_001080125.1	337	cat/caTt	8/9	1	2	FACETS	0.906	0.843	0.969	0.906	0.843	0.969	CLONAL	1	TRUE	1	0.718990580787651	2		424	599	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467529	66467529	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	156	406	0	ENST00000273854.3:c.740T>C	p.Ile247Thr	p.I247T	ENST00000273854	NM_004439.5	247	aTc/aCc	3/18	1	2	FACETS	0.858	0.791	0.926	0.858	0.791	0.926	CLONAL	1	TRUE	1	0.718990580787651	2		406	506	SUCCESS
APC	324	MSKCC	GRCh37	5	112164590	112164590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	133	295	0	ENST00000257430.4:c.1664C>T	p.Ala555Val	p.A555V	ENST00000257430	NM_000038.5	555	gCa/gTa	14/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.718990580787651	2		295	326	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638434	176638434	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773655381	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	360	746	3	ENST00000439151.2:c.3034C>T	p.Arg1012Cys	p.R1012C	ENST00000439151	NM_022455.4	1012	Cgt/Tgt	5/23	1	2	FACETS	0.918	0.871	0.965	0.918	0.871	0.965	CLONAL	1	TRUE	1	0.718990580787651	2		749	1091	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171977	32171977	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	297	543	0	ENST00000375023.3:c.3055G>T	p.Gly1019Cys	p.G1019C	ENST00000375023	NM_004557.3	1019	Ggc/Tgc	19/30	1	2	FACETS	0.981	0.927	1	0.981	0.927	1	CLONAL	1	TRUE	1	0.718990580787651	2		543	842	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864416	162864416	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs770591350	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	272	533	2	ENST00000366898.1:c.97C>T	p.Arg33Ter	p.R33*	ENST00000366898	NM_004562.2	33	Cga/Tga	2/12	1	2	FACETS	0.989	0.932	1	0.989	0.932	1	CLONAL	1	TRUE	1	0.718990580787651	2		535	765	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739831	41739831	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	233	552	0	ENST00000242208.4:c.142C>T	p.Pro48Ser	p.P48S	ENST00000242208	NM_002192.2	48	Ccc/Tcc	2/3	1	2	FACETS	0.876	0.82	0.933	0.876	0.82	0.933	CLONAL	1	TRUE	1	0.718990580787651	2		552	740	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543631	148543631	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	42	481	0	ENST00000320356.2:c.177A>T	p.Glu59Asp	p.E59D	ENST00000320356	NM_004456.4	59	gaA/gaT	3/20	1	2	FACETS	0.177	0.147	0.21	0.177	0.147	0.21	SUBCLONAL	1	TRUE	1	0.718990580787651	2		481	660	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146034	38146034	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	402	714	0	ENST00000317025.8:c.3472G>T	p.Gly1158Cys	p.G1158C	ENST00000317025	NM_023034.1	1158	Ggc/Tgc	19/24	1	2	FACETS	0.98	0.934	1	0.98	0.934	1	CLONAL	1	TRUE	1	0.718990580787651	2		714	1141	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970904	21970904	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	364	612	0	ENST00000304494.5:c.454T>G	p.Ser152Ala	p.S152A	ENST00000304494	NM_000077.4	152	Tca/Gca	2/3	1	2	FACETS	0.942	0.895	0.99	0.942	0.895	0.99	CLONAL	1	TRUE	1	0.718990580787651	2		612	1075	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417382	139417382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	293	678	0	ENST00000277541.6:c.662C>T	p.Pro221Leu	p.P221L	ENST00000277541	NM_017617.3	221	cCc/cTc	4/34	1	2	FACETS	0.865	0.816	0.916	0.865	0.816	0.916	CLONAL	1	TRUE	1	0.718990580787651	2		678	942	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47004874	47004874	+	5_prime_UTR_variant	5'UTR	SNP	G	G	A	rs1207442896	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	267	588	2	ENST00000377604.3:c.-136G>A		p.*46*	ENST00000377604	NM_001204468.1	-/852		1/24	0.381545992144056	1	FACETS	0.543	0.51	0.577	0.543	0.51	0.577	INDETERMINATE	1	TRUE	0	0.718990580787651	1		590	876	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918934	76918934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	243	652	1	ENST00000373344.5:c.4057G>A	p.Gly1353Arg	p.G1353R	ENST00000373344	NM_000489.3	1353	Gga/Aga	12/35	0.381545992144056	1	FACETS	0.685	0.644	0.726	0.685	0.644	0.726	INDETERMINATE	1	TRUE	0	0.718990580787651	1		653	632	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181270	123181270	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	42	392	1	ENST00000218089.9:c.734A>G	p.Gln245Arg	p.Q245R	ENST00000218089	NM_001042749.1	245	cAa/cGa	9/35	0.381545992144056	1	FACETS	0.268	0.225	0.316	0.268	0.225	0.316	INDETERMINATE	1	TRUE	0	0.718990580787651	1		393	279	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0045113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	64	278	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.250362782810569	4	FACETS	1	0.961	1	0.437	0.379	0.499	CLONAL	1	TRUE	1	0.250362782810569	4		278	488	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187527242	187527242	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1227689203	NA	P-0045113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	58	400	0	ENST00000441802.2:c.10332C>G	p.Asn3444Lys	p.N3444K	ENST00000441802	NM_005245.3	3444	aaC/aaG	17/27	1	2	FACETS	0.747	0.642	0.863	0.747	0.642	0.863	SUBCLONAL	1	TRUE	1	0.250362782810569	2		400	620	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188199	32188199	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	57	509	0	ENST00000375023.3:c.1142G>T	p.Cys381Phe	p.C381F	ENST00000375023	NM_004557.3	381	tGc/tTc	6/30	0.111218799771517	4	FACETS	0.962	0.825	1	0.481	0.412	0.556	INDETERMINATE	1	TRUE	2	0.250362782810569	4		509	592	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804358	46804358	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139475791	NA	P-0045135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	307	592	0	ENST00000290295.7:c.649C>T	p.Arg217Cys	p.R217C	ENST00000290295	NM_006361.5	217	Cgc/Tgc	2/2	0.585008283624268	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.568275459888112	1		592	577	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724510	112724510	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	318	446	0	ENST00000369452.4:c.394A>G	p.Ser132Gly	p.S132G	ENST00000369452	NM_007373.3	132	Agt/Ggt	2/9	0.585008283624268	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.568275459888112	2		446	454	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373845	118373845	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	26	251	0	ENST00000534358.1:c.7238G>C	p.Arg2413Thr	p.R2413T	ENST00000534358	NM_005933.3	2413	aGa/aCa	27/36	0.585008283624268	1	FACETS	0.291	0.231	0.359	0.291	0.231	0.359	SUBCLONAL	1	TRUE	0	0.568275459888112	1		251	225	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060992	38060992	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	203	581	0	ENST00000250448.2:c.997C>A	p.Gln333Lys	p.Q333K	ENST00000250448	NM_004496.3	333	Cag/Aag	2/2	0.212448441113551	3	FACETS	1	0.988	1	0.64	0.595	0.686	INDETERMINATE	1	TRUE	1	0.568275459888112	3		581	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577146	7577156	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	TAGATTACCAC	TAGATTACCAC	-	novel	NA	P-0045135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	396	616	0	ENST00000269305.4:c.783-1_792del		p.X261_splice	ENST00000269305	NM_001126112.2	261		8/11	0.585008283624268	1	FACETS	0.899	0.869	0.927	1	0.997	1	CLONAL	2	TRUE	0	0.568275459888112	1		616	555	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554280	29554295	+	frameshift_variant	Frame_Shift_Del	DEL	ATTGAGCATCCCACTG	ATTGAGCATCCCACTG	-	novel	NA	P-0045135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	41	627	0	ENST00000356175.3:c.2296_2311del	p.Ile766GlnfsTer20	p.I766Qfs*20	ENST00000356175	NM_000267.3	766	ATTGAGCATCCCACTGca/ca	19/57	0.585008283624268	1	FACETS	0.172	0.143	0.205	0.172	0.143	0.205	SUBCLONAL	1	TRUE	0	0.568275459888112	1		627	600	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58725420	58725420	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	102	418	0	ENST00000305921.3:c.994C>T	p.Gln332Ter	p.Q332*	ENST00000305921	NM_003620.3	332	Caa/Taa	4/6	0.585008283624268	1	FACETS	0.585	0.527	0.647	0.585	0.527	0.647	SUBCLONAL	1	TRUE	0	0.568275459888112	1		418	439	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378317	15378317	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	29	315	0	ENST00000263377.2:c.469T>G	p.Phe157Val	p.F157V	ENST00000263377	NM_058243.2	157	Ttc/Gtc	4/20	0.437103033085861	4	FACETS	0.292	0.234	0.359			1	SUBCLONAL	1	TRUE	NA	0.568275459888112	4		315	548	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248353	212248353	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	64	228	0	ENST00000342788.4:c.3914A>G	p.Asn1305Ser	p.N1305S	ENST00000342788	NM_005235.2	1305	aAt/aGt	28/28	0.123565602731056	3	FACETS	1	0.939	1			1	INDETERMINATE	1	TRUE	NA	0.568275459888112	3		228	258	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161209	185161247	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TACATGTTTATGTTTTCTTGGAAGGGGTGTTTGTACTCA	TACATGTTTATGTTTTCTTGGAAGGGGTGTTTGTACTCA	-	novel	NA	P-0045135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	209	399	0	ENST00000265026.3:c.660-24_674del		p.X220_splice	ENST00000265026	NM_004721.4	220		4/14	0.370706622132193	3	FACETS	0.946	0.888	1			1	CLONAL	2	TRUE	NA	0.568275459888112	3		399	499	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004454	150004454	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1444466664	NA	P-0045135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	378	417	0	ENST00000253339.5:c.1771G>A	p.Asp591Asn	p.D591N	ENST00000253339		591	Gat/Aat	3/7	0.585008283624268	3	FACETS	1	0.992	1	0.761	0.728	0.794	CLONAL	2	TRUE	0	0.568275459888112	3		417	748	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859713	151859755	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGGTGTGCTCACTGCAGGAGTAGAGGTAGTTTCTGAGATGC	CTGGGTGTGCTCACTGCAGGAGTAGAGGTAGTTTCTGAGATGC	-	novel	NA	P-0045135-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	55	340	0	ENST00000262189.6:c.10907_10949del	p.Gly3636ValfsTer31	p.G3636Vfs*31	ENST00000262189	NM_170606.2	3636	gGCATCTCAGAAACTACCTCTACTCCTGCAGTGAGCACACCCAGt/gt	43/59	0.585008283624268	3	FACETS	0.52	0.445	0.602	0.26	0.222	0.301	SUBCLONAL	1	TRUE	1	0.568275459888112	3		340	478	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	35	425	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.658	0.54	0.791	0.658	0.54	0.791	SUBCLONAL	1	TRUE	1	0.26	2		425	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0045136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	143	770	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.26	2		770	907	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934194	48934194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	34	347	0	ENST00000267163.4:c.649C>T	p.Gln217Ter	p.Q217*	ENST00000267163	NM_000321.2	217	Cag/Tag	7/27	1	2	FACETS	0.8	0.655	0.962	0.8	0.655	0.962	CLONAL	1	TRUE	1	0.26	2		347	327	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426384	49426384	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	140	1043	0	ENST00000301067.7:c.12104C>T	p.Ser4035Leu	p.S4035L	ENST00000301067	NM_003482.3	4035	tCa/tTa	39/54	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.26	2		1043	1071	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434732	49434732	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767236217	NA	P-0045136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	102	1082	1	ENST00000301067.7:c.6821C>T	p.Ser2274Leu	p.S2274L	ENST00000301067	NM_003482.3	2274	tCg/tTg	31/54	1	2	FACETS	0.739	0.659	0.824	0.739	0.659	0.824	SUBCLONAL	1	TRUE	1	0.26	2		1083	1062	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47730006	47730006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	35	625	0	ENST00000449228.1:c.383C>T	p.Ser128Leu	p.S128L	ENST00000449228	NM_001127240.2	128	tCa/tTa	3/4	1	2	FACETS	0.424	0.346	0.512	0.424	0.346	0.512	SUBCLONAL	1	TRUE	1	0.26	2		625	635	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678559	88678559	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764882745	NA	P-0045136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	40	442	0	ENST00000360948.2:c.977G>A	p.Arg326His	p.R326H	ENST00000360948	NM_001012338.2	326	cGt/cAt	9/19	1	2	FACETS	0.722	0.601	0.858	0.722	0.601	0.858	SUBCLONAL	1	TRUE	1	0.26	2		442	426	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143494	108143494	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	37	414	0	ENST00000278616.4:c.3199G>C	p.Asp1067His	p.D1067H	ENST00000278616	NM_000051.3	1067	Gac/Cac	22/63	1	2	FACETS	0.704	0.581	0.842	0.704	0.581	0.842	SUBCLONAL	1	TRUE	1	0.26	2		414	404	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057329	30057329	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs794728682	NA	P-0045136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	56	385	1	ENST00000338641.4:c.810+1G>A		p.X270_splice	ENST00000338641	NM_000268.3	270			0.3	1	FACETS	0.994	0.855	1	0.994	0.855	1	CLONAL	1	TRUE	0	0.26	1		386	377	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432408	49432408	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	88	953	0	ENST00000301067.7:c.8731G>T	p.Glu2911Ter	p.E2911*	ENST00000301067	NM_003482.3	2911	Gag/Tag	34/54	1	2	FACETS	0.772	0.683	0.867	0.772	0.683	0.867	SUBCLONAL	1	TRUE	1	0.26	2		953	877	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432543	49432543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	71	877	0	ENST00000301067.7:c.8596G>A	p.Glu2866Lys	p.E2866K	ENST00000301067	NM_003482.3	2866	Gag/Aag	34/54	1	2	FACETS	0.709	0.618	0.808	0.709	0.618	0.808	SUBCLONAL	1	TRUE	1	0.26	2		877	770	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434129	49434129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1250844847	NA	P-0045136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	77	844	0	ENST00000301067.7:c.7424C>T	p.Pro2475Leu	p.P2475L	ENST00000301067	NM_003482.3	2475	cCt/cTt	31/54	1	2	FACETS	0.788	0.691	0.892	0.788	0.691	0.892	SUBCLONAL	1	TRUE	1	0.26	2		844	752	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934189	48934189	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768305224	NA	P-0045136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	40	339	1	ENST00000267163.4:c.644C>T	p.Ser215Leu	p.S215L	ENST00000267163	NM_000321.2	215	tCa/tTa	7/27	1	2	FACETS	0.971	0.81	1	0.971	0.81	1	CLONAL	1	TRUE	1	0.26	2		340	317	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023403	33023403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	78	691	1	ENST00000300177.4:c.512C>T	p.Thr171Ile	p.T171I	ENST00000300177	NM_001191322.1	171	aCa/aTa	2/2	1	2	FACETS	0.882	0.775	0.998	0.882	0.775	0.998	CLONAL	1	TRUE	1	0.26	2		692	680	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217839	7217839	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	68	632	0	ENST00000380728.2:c.172G>C	p.Glu58Gln	p.E58Q	ENST00000380728		58	Gag/Cag	3/11	1	2	FACETS	0.761	0.662	0.869	0.761	0.662	0.869	SUBCLONAL	1	TRUE	1	0.26	2		632	687	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16097838	16097838	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	82	428	0	ENST00000268712.3:c.46G>A	p.Glu16Lys	p.E16K	ENST00000268712	NM_006311.3	16	Gaa/Aaa	2/46	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.26	2		428	512	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55334471	55334471	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	30	262	0	ENST00000284073.2:c.75C>G	p.Ile25Met	p.I25M	ENST00000284073	NM_138962.2	25	atC/atG	2/14	1	2	FACETS	0.697	0.563	0.849	0.697	0.563	0.849	SUBCLONAL	1	TRUE	1	0.26	2		262	331	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296430	15296430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	98	1123	0	ENST00000263388.2:c.2012C>T	p.Ser671Phe	p.S671F	ENST00000263388	NM_000435.2	671	tCc/tTc	13/33	1	2	FACETS	0.762	0.679	0.852	0.762	0.679	0.852	SUBCLONAL	1	TRUE	1	0.26	2		1123	989	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711078	61711078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	50	360	0	ENST00000401558.2:c.2671G>A	p.Asp891Asn	p.D891N	ENST00000401558	NM_003400.3	891	Gat/Aat	21/25	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.26	2		360	371	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61712912	61712912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	22	290	0	ENST00000401558.2:c.2499G>A	p.Met833Ile	p.M833I	ENST00000401558	NM_003400.3	833	atG/atA	20/25	1	2	FACETS	0.493	0.382	0.623	0.493	0.382	0.623	SUBCLONAL	1	TRUE	1	0.26	2		290	343	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61713016	61713016	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	34	397	0	ENST00000401558.2:c.2395G>A	p.Glu799Lys	p.E799K	ENST00000401558	NM_003400.3	799	Gaa/Aaa	20/25	1	2	FACETS	0.603	0.492	0.727	0.603	0.492	0.727	SUBCLONAL	1	TRUE	1	0.26	2		397	434	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721199	61721199	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	41	352	0	ENST00000401558.2:c.1075G>C	p.Glu359Gln	p.E359Q	ENST00000401558	NM_003400.3	359	Gaa/Caa	12/25	1	2	FACETS	0.773	0.645	0.915	0.773	0.645	0.915	CLONAL	1	TRUE	1	0.26	2		352	408	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024044	31024044	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	88	611	0	ENST00000375687.4:c.3529C>G	p.Leu1177Val	p.L1177V	ENST00000375687	NM_015338.5	1177	Ctt/Gtt	13/13	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.26	2		611	633	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747127	40747127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	74	506	0	ENST00000373198.4:c.2955G>C	p.Glu985Asp	p.E985D	ENST00000373198	NM_133170.3	985	gaG/gaC	22/32	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.26	2		506	557	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968201	134968201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201702941	NA	P-0045136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	96	685	2	ENST00000398015.3:c.2714G>A	p.Arg905His	p.R905H	ENST00000398015	NM_004441.4	905	cGc/cAc	15/16	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.26	2		687	717	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143129620	143129620	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	40	337	0	ENST00000262992.4:c.1030C>G	p.Leu344Val	p.L344V	ENST00000262992	NM_001101669.1	344	Cta/Gta	12/24	1	2	FACETS	0.696	0.579	0.827	0.696	0.579	0.827	SUBCLONAL	1	TRUE	1	0.26	2		337	442	SUCCESS
MET	4233	MSKCC	GRCh37	7	116417487	116417487	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	30	280	0	ENST00000397752.3:c.3304G>A	p.Gly1102Ser	p.G1102S	ENST00000397752	NM_000245.2	1102	Ggc/Agc	16/21	1	2	FACETS	0.73	0.59	0.889	0.73	0.59	0.889	SUBCLONAL	1	TRUE	1	0.26	2		280	316	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140507827	140507827	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	28	389	0	ENST00000288602.6:c.644C>G	p.Ser215Cys	p.S215C	ENST00000288602	NM_004333.4	215	tCc/tGc	5/18	1	2	FACETS	0.44	0.351	0.543	0.44	0.351	0.543	SUBCLONAL	1	TRUE	1	0.26	2		389	489	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0045137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	117	294	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.183646211328051	6	FACETS	1	0.959	1	1	0.959	1	CLONAL	3	TRUE	3	0.22	6		294	464	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581309	48581309	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	41	401	0	ENST00000342988.3:c.613G>T	p.Glu205Ter	p.E205*	ENST00000342988	NM_005359.5	205	Gag/Tag	5/12	1	2	FACETS	0.911	0.76	1	0.911	0.76	1	CLONAL	1	TRUE	1	0.22	2		401	409	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940995	49940997	+	inframe_deletion	In_Frame_Del	DEL	CAG	CAG	-	rs1259473737	NA	P-0045137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	33	775	1	ENST00000296474.3:c.46_48del	p.Leu17del	p.L17del	ENST00000296474	NM_002447.2	16	CTG/-	1/20	0.148751952590976	4	FACETS	0.556	0.452	0.675	0.278	0.226	0.338	SUBCLONAL	1	TRUE	2	0.22	4		776	658	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250782	26250782	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	29	422	0	ENST00000446824.2:c.52C>G	p.Arg18Gly	p.R18G	ENST00000446824	NM_021018.2	18	Cgc/Ggc	1/1	0.248056518650029	1	FACETS	0.51	0.409	0.626	0.51	0.409	0.626	SUBCLONAL	1	TRUE	0	0.22	1		422	460	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913517	NA	P-0045138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	158	357	0	ENST00000288135.5:c.1676T>A	p.Val559Asp	p.V559D	ENST00000288135	NM_000222.2	559	gTt/gAt	11/21	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.785325129655673	2		357	382	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307013	65307013	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	135	274	0	ENST00000342505.4:c.2564T>C	p.Ile855Thr	p.I855T	ENST00000342505	NM_002227.2	855	aTt/aCt	19/25	0.785325129655673	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.785325129655673	1		274	205	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967576	26967576	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	24	392	0	ENST00000381527.3:c.719A>T	p.Asp240Val	p.D240V	ENST00000381527	NM_001260.1	240	gAc/gTc	7/13	1	2	FACETS	0.135	0.105	0.169	0.135	0.105	0.169	SUBCLONAL	1	TRUE	1	0.785325129655673	2		392	454	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0045139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	37	707	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.7	0.575	0.841	0.7	0.575	0.841	SUBCLONAL	1	TRUE	1	0.14	2		708	755	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0045139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	27	294	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.984	0.783	1	0.984	0.783	1	CLONAL	1	TRUE	1	0.14	2		294	392	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136841	2136841	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045139-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	40	735	1	ENST00000219476.3:c.4958C>A	p.Ser1653Tyr	p.S1653Y	ENST00000219476	NM_000548.3	1653	tCc/tAc	38/42	1	2	FACETS	0.833	0.69	0.993	0.833	0.69	0.993	CLONAL	1	TRUE	1	0.14	2		736	686	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759870	133759870	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	37	715	1	ENST00000318560.5:c.2193G>A	p.Trp731Ter	p.W731*	ENST00000318560	NM_005157.4	731	tgG/tgA	11/11	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	FALSE	1	0.271865153844493	2		716	251	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023423	27023423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	38	447	0	ENST00000324856.7:c.529C>T	p.Gln177Ter	p.Q177*	ENST00000324856	NM_006015.4	177	Caa/Taa	1/20	0.271865153844493	3	FACETS	1	0.912	1	0.579	0.481	0.688	CLONAL	1	FALSE	1	0.271865153844493	3		447	274	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111494	8111495	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTGGAGG	novel	NA	P-0045140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	15	510	0	ENST00000346208.3:c.981_987dup	p.Arg330LeufsTer24	p.R330Lfs*24	ENST00000346208		327	ctc/ctCTGGAGGc	5/6	0.271865153844493	3	FACETS	0.798	0.587	1	0.399	0.293	0.525	CLONAL	1	FALSE	1	0.271865153844493	3		510	157	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202427	123202427	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754256233	NA	P-0045140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	12	276	0	ENST00000218089.9:c.2279G>A	p.Arg760His	p.R760H	ENST00000218089	NM_001042749.1	760	cGt/cAt	24/35	1	2	FACETS	0.92	0.654	1	0.92	0.654	1	CLONAL	1	FALSE	1	0.271865153844493	2		276	96	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316352	14316352	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045140-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	15	456	0	ENST00000256196.4:c.253A>C	p.Thr85Pro	p.T85P	ENST00000256196		85	Act/Cct	3/6	0.164778872789746	3	FACETS	1	0.854	1	0.418	0.309	0.544	CLONAL	1	FALSE	0	0.271865153844493	3		456	100	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0045141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	104	262	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.272139802472706	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.274240053186393	4		262	399	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0045141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	77	403	0				ENST00000310581	NM_198253.2	-/1132			0.273803403050402	3	FACETS	0.976	0.872	1	0.976	0.872	1	CLONAL	3	TRUE	0	0.274240053186393	3		403	218	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0045141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	106	677	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	0.274240053186393	4	FACETS	0.786	0.705	0.87	0.524	0.47	0.58	SUBCLONAL	2	TRUE	1	0.274240053186393	4		677	627	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971121	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0045141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	99	515	0	ENST00000304494.5:c.237_238delinsTT	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	79	acCCga/acTTga	2/3	0.274240053186393	2	FACETS	0.948	0.853	1	0.948	0.853	1	CLONAL	2	TRUE	0	0.274240053186393	2		515	381	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39763596	39763596	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	36	214	0	ENST00000288319.7:c.856C>T	p.Gln286Ter	p.Q286*	ENST00000288319	NM_182918.3	286	Cag/Tag	8/10	0.253049008651516	3	FACETS	0.969	0.8	1	0.485	0.4	0.579	CLONAL	1	TRUE	1	0.274240053186393	3		214	308	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992447	72992447	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772706179	NA	P-0045141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	68	626	0	ENST00000268489.5:c.1598C>T	p.Ser533Phe	p.S533F	ENST00000268489	NM_006885.3	533	tCc/tTc	2/10	0.189549515494267	4	FACETS	1	0.92	1	0.539	0.469	0.615	CLONAL	1	TRUE	2	0.274240053186393	4		626	586	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609621	81609621	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	46	346	0	ENST00000298171.2:c.1219C>T	p.Pro407Ser	p.P407S	ENST00000298171	NM_000369.2	407	Ccg/Tcg	10/10	1	2	FACETS	0.885	0.747	1	0.885	0.747	1	CLONAL	1	TRUE	1	0.274240053186393	2		346	379	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212117	142212117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	51	289	0	ENST00000350721.4:c.5935G>A	p.Gly1979Ser	p.G1979S	ENST00000350721	NM_001184.3	1979	Ggt/Agt	35/47	0.274240053186393	3	FACETS	1	0.892	1	0.529	0.45	0.614	CLONAL	1	TRUE	1	0.274240053186393	3		289	400	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988249	36988249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	42	474	0	ENST00000354822.5:c.404G>A	p.Arg135Lys	p.R135K	ENST00000354822	NM_001079668.2	135	aGg/aAg	2/3	1	2	FACETS	0.982	0.823	1	0.982	0.823	1	CLONAL	1	TRUE	1	0.274240053186393	2		474	312	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714274	43714288	+	inframe_deletion	In_Frame_Del	DEL	GGAAACTTCAGTTTC	GGAAACTTCAGTTTC	-	novel	NA	P-0045141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	60	507	0	ENST00000382044.4:c.3865_3879del	p.Glu1289_Ser1293del	p.E1289_S1293del	ENST00000382044	NM_001141980.1	1289	GAAACTGAAGTTTCC/-	19/28	0.274240053186393	3	FACETS	0.803	0.691	0.924	0.401	0.345	0.462	CLONAL	1	TRUE	1	0.274240053186393	3		507	620	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33433410	33433410	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	52	459	0	ENST00000345365.6:c.571C>A	p.Gln191Lys	p.Q191K	ENST00000345365	NM_002878.3	191	Cag/Aag	6/10	0.272139802472706	4	FACETS	1	0.865	1	0.508	0.432	0.59	CLONAL	1	TRUE	2	0.274240053186393	4		459	476	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264257	46264257	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045141-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	35	263	0	ENST00000371998.3:c.1304G>T	p.Gly435Val	p.G435V	ENST00000371998		435	gGt/gTt	11/23	0.253049008651516	3	FACETS	0.974	0.801	1	0.487	0.4	0.583	CLONAL	1	TRUE	1	0.274240053186393	3		263	298	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129169	64129169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746466314	NA	P-0045142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	103	826	1	ENST00000334205.4:c.707C>T	p.Ser236Leu	p.S236L	ENST00000334205	NM_003942.2	236	tCg/tTg	7/17	1	2	FACETS	0.678	0.606	0.754	0.678	0.606	0.754	SUBCLONAL	1	TRUE	1	0.365857359760534	2		827	831	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094273	193094273	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	58	325	0	ENST00000367435.3:c.163T>A	p.Tyr55Asn	p.Y55N	ENST00000367435	NM_024529.4	55	Tac/Aac	2/17	1	2	FACETS	0.824	0.71	0.946	0.824	0.71	0.946	CLONAL	1	TRUE	1	0.365857359760534	2		325	385	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827602	72827602	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	62	556	0	ENST00000268489.5:c.8979G>A	p.Trp2993Ter	p.W2993*	ENST00000268489	NM_006885.3	2993	tgG/tgA	9/10	NA	2	FACETS	0.624	0.539	0.716			1	INDETERMINATE	1	TRUE	NA	0.365857359760534	2		556	543	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618822	37618825	+	frameshift_variant	Frame_Shift_Del	DEL	AGCC	AGCC	-	novel	NA	P-0045142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	328	500	0	ENST00000447079.4:c.499_502del	p.Ala167LysfsTer23	p.A167Kfs*23	ENST00000447079	NM_015083.1	166	gtAGCC/gt	1/14	0.365857359760534	6	FACETS	1	0.953	1			1	CLONAL	3	TRUE	NA	0.365857359760534	6		500	1027	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619240	37619240	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	179	457	0	ENST00000447079.4:c.916del	p.Ser306AlafsTer32	p.S306Afs*32	ENST00000447079	NM_015083.1	306	Agc/gc	1/14	0.365857359760534	6	FACETS	0.87	0.802	0.941			1	CLONAL	2	TRUE	NA	0.365857359760534	6		457	974	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859288	151859288	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	35	246	0	ENST00000262189.6:c.11374C>T	p.Gln3792Ter	p.Q3792*	ENST00000262189	NM_170606.2	3792	Caa/Taa	43/59	1	2	FACETS	0.709	0.584	0.848	0.709	0.584	0.848	SUBCLONAL	1	TRUE	1	0.365857359760534	2		246	270	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061227	38061242	+	protein_altering_variant	In_Frame_Del	DEL	GAACATGTTGCCGGAG	GAACATGTTGCCGGAG	C	novel	NA	P-0045142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	82	698	0	ENST00000250448.2:c.747_762delinsG	p.Asp249_Phe254delinsGlu	p.D249_F254delinsE	ENST00000250448	NM_004496.3	249	gaCTCCGGCAACATGTTC/gaG	2/2	1	2	FACETS	0.64	0.564	0.722	0.64	0.564	0.722	SUBCLONAL	1	TRUE	1	0.365857359760534	2		698	700	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0045143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	504	565	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.886695124346888	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.887071955033087	1		567	606	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988914	41988914	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0045143-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	293	390	0	ENST00000219905.7:c.1706C>G	p.Ser569Ter	p.S569*	ENST00000219905	NM_001164273.1	569	tCa/tGa	3/24	0.887071955033087	1	FACETS	0.996	0.964	1	0.996	0.964	1	CLONAL	1	TRUE	0	0.887071955033087	1		390	369	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390736	139390736	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	239	935	1	ENST00000277541.6:c.7455del	p.Ser2486ArgfsTer103	p.S2486Rfs*103	ENST00000277541	NM_017617.3	2485	ccC/cc	34/34	1	2	FACETS	0.837	0.781	0.895	0.837	0.781	0.895	CLONAL	1	TRUE	1	0.518886566035865	2		936	1100	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796882	42796883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761345552	NA	P-0045144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	216	957	3	ENST00000575354.2:c.3347dup	p.Ser1117LysfsTer34	p.S1117Kfs*34	ENST00000575354	NM_015125.3	1114	gcc/gCcc	14/20	0.503330499294677	1	FACETS	0.845	0.788	0.903	0.845	0.788	0.903	CLONAL	1	TRUE	0	0.518886566035865	1		960	730	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438211	49438211	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	152	529	0	ENST00000301067.7:c.5058del	p.Lys1686AsnfsTer36	p.K1686Nfs*36	ENST00000301067	NM_003482.3	1686	aaA/aa	20/54	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.518886566035865	2		529	567	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639540	3639540	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs17136464	NA	P-0045144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	255	883	1	ENST00000294008.3:c.4099G>A	p.Ala1367Thr	p.A1367T	ENST00000294008	NM_032444.2	1367	Gcc/Acc	12/15	0.491793395478164	1	FACETS	0.918	0.862	0.975	0.918	0.862	0.975	CLONAL	1	TRUE	0	0.518886566035865	1		884	793	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439919	51439919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	94	279	0	ENST00000262662.1:c.488del	p.Gly163GlufsTer24	p.G163Efs*24	ENST00000262662		162	Ggg/gg	4/4	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.518886566035865	2		279	319	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239405	123239405	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	47	327	0	ENST00000358487.5:c.2432A>G	p.Gln811Arg	p.Q811R	ENST00000358487	NM_000141.4	811	cAg/cGg	18/18	1	2	FACETS	0.839	0.716	0.971	0.839	0.716	0.971	CLONAL	1	TRUE	1	0.518886566035865	2		327	216	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560457	65560457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	66	356	0	ENST00000358664.4:c.140G>A	p.Arg47Gln	p.R47Q	ENST00000358664	NM_002382.4	47	cGg/cAg	3/5	1	2	FACETS	0.78	0.682	0.885	0.78	0.682	0.885	SUBCLONAL	1	TRUE	1	0.518886566035865	2		356	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574006	7574007	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0045144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	221	685	0	ENST00000269305.4:c.1020dup	p.Phe341ValfsTer6	p.F341Vfs*6	ENST00000269305	NM_001126112.2	340	-/G	10/11	0.491793395478164	1	FACETS	0.989	0.926	1	0.989	0.926	1	CLONAL	1	TRUE	0	0.518886566035865	1		685	638	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223069	5223069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs906063149	NA	P-0045144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	108	926	1	ENST00000357368.4:c.2734G>A	p.Gly912Ser	p.G912S	ENST00000357368	NM_002850.3	912	Ggc/Agc	18/38	1	2	FACETS	0.428	0.383	0.476	0.428	0.383	0.476	SUBCLONAL	1	TRUE	1	0.518886566035865	2		927	972	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22142579	22142579	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	54	428	0	ENST00000215832.6:c.823T>C	p.Trp275Arg	p.W275R	ENST00000215832	NM_002745.4	275	Tgg/Cgg	6/9	0.491793395478164	1	FACETS	0.811	0.704	0.925	0.811	0.704	0.925	CLONAL	1	TRUE	0	0.518886566035865	1		428	190	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568618	41568618	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	40	416	0	ENST00000263253.7:c.4568A>G	p.Glu1523Gly	p.E1523G	ENST00000263253	NM_001429.3	1523	gAg/gGg	28/31	0.491793395478164	1	FACETS	0.645	0.543	0.755	0.645	0.543	0.755	SUBCLONAL	1	TRUE	0	0.518886566035865	1		416	177	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090092	37090092	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	95	413	0	ENST00000231790.2:c.1981del	p.Ala661ProfsTer4	p.A661Pfs*4	ENST00000231790	NM_000249.3	661	Gcc/cc	17/19	0.308652611821072	2	FACETS	1	0.978	1	0.663	0.599	0.73	INDETERMINATE	1	TRUE	0	0.518886566035865	2		413	276	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630819	187630820	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0045144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	78	447	0	ENST00000441802.2:c.162dup	p.His55AlafsTer26	p.H55Afs*26	ENST00000441802	NM_005245.3	54	-/G	2/27	0.393284679688673	3	FACETS	0.782	0.689	0.881	0.261	0.229	0.294	SUBCLONAL	1	TRUE	0	0.518886566035865	3		447	484	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197219	26197220	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0045144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	95	558	0	ENST00000356476.2:c.259_260del	p.Ser87LeufsTer19	p.S87Lfs*19	ENST00000356476		87	AGc/c	1/1	1	2	FACETS	0.714	0.638	0.794	0.714	0.638	0.794	SUBCLONAL	1	TRUE	1	0.518886566035865	2		558	513	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710624	117710624	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	59	282	0	ENST00000368508.3:c.1648T>G	p.Ser550Ala	p.S550A	ENST00000368508	NM_002944.2	550	Tca/Gca	12/43	1	2	FACETS	0.65	0.562	0.744	0.65	0.562	0.744	SUBCLONAL	1	TRUE	1	0.518886566035865	2		282	350	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578404	7578404	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs967461896	NA	P-0045146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	415	611	0	ENST00000269305.4:c.526T>C	p.Cys176Arg	p.C176R	ENST00000269305	NM_001126112.2	176	Tgc/Cgc	5/11	0.817466190803444	1	FACETS	0.979	0.946	1	0.979	0.946	1	CLONAL	1	TRUE	0	0.817466190803444	1		611	613	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874147	151874148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs747256476	NA	P-0045146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	189	363	5	ENST00000262189.6:c.8390dup	p.Glu2798GlyfsTer11	p.E2798Gfs*11	ENST00000262189	NM_170606.2	2797	aag/aaAg	38/59	1	2	FACETS	0.721	0.67	0.774	0.721	0.67	0.774	SUBCLONAL	1	TRUE	1	0.817466190803444	2		368	641	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72863719	72863719	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	315	443	0	ENST00000268489.5:c.3488C>A	p.Ala1163Asp	p.A1163D	ENST00000268489	NM_006885.3	1163	gCt/gAt	5/10	0.817466190803444	1	FACETS	0.978	0.94	1	0.978	0.94	1	CLONAL	1	TRUE	0	0.817466190803444	1		443	466	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950443	68950443	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	214	343	0	ENST00000288368.4:c.755T>C	p.Leu252Ser	p.L252S	ENST00000288368	NM_024870.2	252	tTa/tCa	7/40	0.817466190803444	3	FACETS	0.859	0.799	0.92	0.429	0.399	0.46	CLONAL	1	TRUE	1	0.817466190803444	3		343	859	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349937	70349937	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045146-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	441	313	0	ENST00000374080.3:c.3920T>C	p.Leu1307Pro	p.L1307P	ENST00000374080		1307	cTg/cCg	28/45	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.817466190803444	1		313	535	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0045148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	127	278	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.393434729334565	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	1	0.393434729334565	3		278	365	SUCCESS
APC	324	MSKCC	GRCh37	5	112175101	112175101	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs587783033	NA	P-0045148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	43	140	0	ENST00000257430.4:c.3814del	p.Ser1272GlnfsTer16	p.S1272Qfs*16	ENST00000257430	NM_000038.5	1270	tgT/tg	16/16	0.393434729334565	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.393434729334565	1		140	155	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99179952	99179952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1394330959	NA	P-0045148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	294	629	0	ENST00000074304.5:c.1895C>T	p.Pro632Leu	p.P632L	ENST00000074304	NM_001134224.1	632	cCg/cTg	19/26	0.156226717506645	5	FACETS	1	0.99	1	0.824	0.777	0.872	INDETERMINATE	2	TRUE	2	0.393434729334565	5		629	961	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117906	70117907	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0045148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	120	494	0	ENST00000245479.2:c.376dup	p.Gln126ProfsTer126	p.Q126Pfs*126	ENST00000245479	NM_000346.3	125	gac/gaCc	1/3	0.393434729334565	3	FACETS	1	0.971	1	0.593	0.536	0.652	CLONAL	1	TRUE	1	0.393434729334565	3		494	616	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989616	212989616	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463950609	NA	P-0045148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	98	201	0	ENST00000342788.4:c.95C>T	p.Thr32Met	p.T32M	ENST00000342788	NM_005235.2	32	aCg/aTg	2/28	0.156226717506645	5	FACETS	1	0.948	1	0.723	0.651	0.799	INDETERMINATE	2	TRUE	2	0.393434729334565	5		201	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0045153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	857	667	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.730825547452093	2	FACETS	0.996	0.975	1	0.996	0.975	1	CLONAL	2	TRUE	0	0.730825547452093	2		669	1177	SUCCESS
APC	324	MSKCC	GRCh37	5	112175162	112175162	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561588104	NA	P-0045153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	72	159	0	ENST00000257430.4:c.3871C>T	p.Gln1291Ter	p.Q1291*	ENST00000257430	NM_000038.5	1291	Cag/Tag	16/16	0.730825547452093	1	FACETS	0.893	0.806	0.98	0.893	0.806	0.98	CLONAL	1	TRUE	0	0.730825547452093	1		159	140	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437614	52437614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755719248	NA	P-0045153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	382	678	4	ENST00000460680.1:c.1547C>T	p.Pro516Leu	p.P516L	ENST00000460680	NM_004656.3	516	cCg/cTg	13/17	1	2	FACETS	0.963	0.916	1	0.963	0.916	1	CLONAL	1	TRUE	1	0.730825547452093	2		682	1086	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808294	99808294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	144	323	3	ENST00000280892.6:c.395G>A	p.Arg132Gln	p.R132Q	ENST00000280892	NM_001130678.1	132	cGa/cAa	5/7	0.507521112761846	1	FACETS	0.658	0.607	0.71	0.658	0.607	0.71	SUBCLONAL	1	TRUE	0	0.730825547452093	1		326	380	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	113	688	1	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	0.476903265295743	3	FACETS	0.828	0.755	0.903	0.552	0.503	0.602	CLONAL	2	TRUE	0	0.555450129891829	3		689	314	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984686	11984687	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0045154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	82	307	0	ENST00000353533.5:c.237_238del	p.His79GlnfsTer3	p.H79Qfs*3	ENST00000353533	NM_003010.3	78	ACa/a	3/11	0.53389477088464	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.555450129891829	2		307	132	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	82	425	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.824	0.732	0.921	0.824	0.732	0.921	CLONAL	1	TRUE	1	0.543971511836404	2		425	366	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	137	545	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.543971511836404	3	FACETS	0.833	0.759	0.911	0.417	0.379	0.456	CLONAL	1	TRUE	1	0.543971511836404	3		545	769	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	181	614	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	1	2	FACETS	0.904	0.836	0.975	0.904	0.836	0.975	CLONAL	1	TRUE	1	0.543971511836404	2		614	736	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	110	349	0	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	0.543971511836404	1	FACETS	0.8	0.726	0.877	0.8	0.726	0.877	SUBCLONAL	1	TRUE	0	0.543971511836404	1		349	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	167	634	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	0.91	0.839	0.983	0.91	0.839	0.983	CLONAL	1	TRUE	1	0.543971511836404	2		634	675	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309857	65309857	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	123	421	0	ENST00000342505.4:c.2293G>C	p.Glu765Gln	p.E765Q	ENST00000342505	NM_002227.2	765	Gag/Cag	17/25	1	2	FACETS	0.887	0.806	0.971	0.887	0.806	0.971	CLONAL	1	TRUE	1	0.543971511836404	2		421	510	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243472	46243472	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	82	330	0	ENST00000334344.6:c.1825C>T	p.Gln609Ter	p.Q609*	ENST00000334344	NM_152641.2	609	Cag/Tag	14/21	1	2	FACETS	0.648	0.574	0.728	0.648	0.574	0.728	SUBCLONAL	1	TRUE	1	0.543971511836404	2		330	465	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664804	138664804	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	178	315	2	ENST00000330315.3:c.761C>T	p.Ser254Leu	p.S254L	ENST00000330315	NM_023067.3	254	tCg/tTg	1/1	0.543971511836404	3	FACETS	0.915	0.852	0.979	0.915	0.852	0.979	CLONAL	2	TRUE	1	0.543971511836404	3		317	455	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061115	38061115	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1016447126	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	66	405	0	ENST00000250448.2:c.874G>A	p.Glu292Lys	p.E292K	ENST00000250448	NM_004496.3	292	Gag/Aag	2/2	1	2	FACETS	0.851	0.746	0.963	0.851	0.746	0.963	CLONAL	1	TRUE	1	0.543971511836404	2		405	285	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212522509	212522509	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs532377012	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	130	365	1	ENST00000342788.4:c.1916C>T	p.Thr639Met	p.T639M	ENST00000342788	NM_005235.2	639	aCg/aTg	16/28	0.543971511836404	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.543971511836404	1		366	348	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855787	45855787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	194	793	0	ENST00000391945.4:c.2023G>T	p.Gly675Cys	p.G675C	ENST00000391945	NM_000400.3	675	Ggc/Tgc	21/23	0.153471504964358	0	FACETS	0.411	0.381	0.442			1	INDETERMINATE	1	TRUE	0	0.543971511836404	0		793	791	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446821	49446821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	120	594	0	ENST00000301067.7:c.989C>T	p.Ser330Leu	p.S330L	ENST00000301067	NM_003482.3	330	tCa/tTa	8/54	1	2	FACETS	0.755	0.684	0.83	0.755	0.684	0.83	SUBCLONAL	1	TRUE	1	0.543971511836404	2		594	584	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023460	27023479	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGGGGCCTGGAGCCCTAC	GCGGGGGCCTGGAGCCCTAC	-	novel	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	141	672	0	ENST00000324856.7:c.572_591del	p.Gly191AlafsTer202	p.G191Afs*202	ENST00000324856	NM_006015.4	189	gGCGGGGGCCTGGAGCCCTAC/g	1/20	0.324209809646367	3	FACETS	0.807	0.736	0.882			1	INDETERMINATE	1	TRUE	NA	0.543971511836404	3		672	817	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451262	70451262	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs551446004	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	212	649	0	ENST00000373644.4:c.6102G>C	p.Glu2034Asp	p.E2034D	ENST00000373644	NM_030625.2	2034	gaG/gaC	12/12	0.515101554414383	1	FACETS	0.938	0.877	1	0.938	0.877	1	CLONAL	1	TRUE	0	0.543971511836404	1		649	605	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26927896	26927896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	102	222	0	ENST00000381527.3:c.335G>A	p.Arg112Lys	p.R112K	ENST00000381527	NM_001260.1	112	aGa/aAa	4/13	0.515731678616371	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.543971511836404	1		222	255	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954229	32954229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	155	406	0	ENST00000380152.3:c.9203C>T	p.Ser3068Phe	p.S3068F	ENST00000380152		3068	tCt/tTt	24/27	0.515101554414383	1	FACETS	0.928	0.858	1	0.928	0.858	1	CLONAL	1	TRUE	0	0.543971511836404	1		406	447	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878185	48878185	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	54	223	0	ENST00000267163.4:c.137G>C	p.Arg46Thr	p.R46T	ENST00000267163	NM_000321.2	46	aGg/aCg	1/27	0.515101554414383	1	FACETS	0.777	0.675	0.885	0.777	0.675	0.885	SUBCLONAL	1	TRUE	0	0.543971511836404	1		223	186	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871761	35871761	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	172	562	1	ENST00000216797.5:c.745C>T	p.Gln249Ter	p.Q249*	ENST00000216797	NM_020529.2	249	Cag/Tag	5/6	1	2	FACETS	0.98	0.906	1	0.98	0.906	1	CLONAL	1	TRUE	1	0.543971511836404	2		563	645	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873685	35873705	+	inframe_deletion	In_Frame_Del	DEL	GCTCGAGGCGGATCTCCTGCA	GCTCGAGGCGGATCTCCTGCA	-	novel	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	158	565	0	ENST00000216797.5:c.146_166del	p.Leu49_Glu55del	p.L49_E55del	ENST00000216797	NM_020529.2	49	cTGCAGGAGATCCGCCTCGAGCcg/ccg	1/6	1	2	FACETS	0.931	0.856	1	0.931	0.856	1	CLONAL	1	TRUE	1	0.543971511836404	2		565	624	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310228	91310228	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	75	281	0	ENST00000355112.3:c.2282A>C	p.Lys761Thr	p.K761T	ENST00000355112	NM_000057.2	761	aAa/aCa	10/22	1	2	FACETS	0.766	0.676	0.862	0.766	0.676	0.862	SUBCLONAL	1	TRUE	1	0.543971511836404	2		281	360	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348891	11348891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760173376	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	282	414	1	ENST00000332029.2:c.445G>A	p.Glu149Lys	p.E149K	ENST00000332029	NM_003745.1	149	Gag/Aag	2/2	0.543971511836404	3	FACETS	1	0.987	1			1	CLONAL	2	TRUE	NA	0.543971511836404	3		415	586	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641505	23641505	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	161	514	0	ENST00000261584.4:c.1970A>C	p.Glu657Ala	p.E657A	ENST00000261584	NM_024675.3	657	gAg/gCg	5/13	1	2	FACETS	0.915	0.842	0.99	0.915	0.842	0.99	CLONAL	1	TRUE	1	0.543971511836404	2		514	647	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55674249	55674249	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	108	321	0	ENST00000284073.2:c.475G>A	p.Glu159Lys	p.E159K	ENST00000284073	NM_138962.2	159	Gag/Aag	8/14	1	2	FACETS	0.939	0.848	1	0.939	0.848	1	CLONAL	1	TRUE	1	0.543971511836404	2		321	423	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492792	56492810	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGATAATAGCTTTCTGT	TCTGATAATAGCTTTCTGT	-	novel	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	125	543	0	ENST00000407977.2:c.129_147del	p.Gln44Ter	p.Q44*	ENST00000407977		43	gaACAGAAAGCTATTATCAGA/ga	2/10	1	2	FACETS	0.742	0.674	0.814	0.742	0.674	0.814	SUBCLONAL	1	TRUE	1	0.543971511836404	2		543	619	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113725	11113725	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	216	615	0	ENST00000358026.2:c.1833G>C	p.Gln611His	p.Q611H	ENST00000358026	NM_001128849.1	611	caG/caC	12/36	1	2	FACETS	0.999	0.931	1	0.999	0.931	1	CLONAL	1	TRUE	1	0.543971511836404	2		615	795	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728700	190728700	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	142	334	0	ENST00000441310.2:c.2088G>T	p.Met696Ile	p.M696I	ENST00000441310	NM_000534.4	696	atG/atT	10/13	0.543971511836404	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.543971511836404	1		334	376	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46275955	46275955	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	137	461	0	ENST00000371998.3:c.3391C>T	p.Gln1131Ter	p.Q1131*	ENST00000371998		1131	Caa/Taa	18/23	1	2	FACETS	0.876	0.8	0.955	0.876	0.8	0.955	CLONAL	1	TRUE	1	0.543971511836404	2		461	575	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513285	41513291	+	frameshift_variant	Frame_Shift_Del	DEL	GCTTCAG	GCTTCAG	-	novel	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	141	457	0	ENST00000263253.7:c.189_195del	p.Leu64GlnfsTer50	p.L64Qfs*50	ENST00000263253	NM_001429.3	63	caGCTTCAG/ca	2/31	1	2	FACETS	0.927	0.849	1	0.927	0.849	1	CLONAL	1	TRUE	1	0.543971511836404	2		457	559	SUCCESS
ATR	545	MSKCC	GRCh37	3	142224066	142224085	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTTTAGAGATGGTTCTGC	TCTTTTAGAGATGGTTCTGC	-	novel	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	96	450	0	ENST00000350721.4:c.5092_5111del	p.Ala1698ThrfsTer4	p.A1698Tfs*4	ENST00000350721	NM_001184.3	1698	GCAGAACCATCTCTAAAAGAa/a	29/47	0.543971511836404	3	FACETS	0.608	0.541	0.678	0.304	0.27	0.339	SUBCLONAL	1	TRUE	1	0.543971511836404	3		450	739	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951953	178951953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	93	324	0	ENST00000263967.3:c.3008C>T	p.Ser1003Leu	p.S1003L	ENST00000263967	NM_006218.2	1003	tCa/tTa	21/21	0.543971511836404	3	FACETS	0.818	0.729	0.911	0.409	0.364	0.456	CLONAL	1	TRUE	1	0.543971511836404	3		324	532	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247229	153247229	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	133	331	0	ENST00000281708.4:c.1573del	p.Val525CysfsTer31	p.V525Cfs*31	ENST00000281708	NM_033632.3	525	Gtg/tg	10/12	0.515101554414383	1	FACETS	0.92	0.844	0.997	0.92	0.844	0.997	CLONAL	1	TRUE	0	0.543971511836404	1		331	387	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526307	31526307	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs746252202	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	217	918	1	ENST00000344624.3:c.733C>G	p.Arg245Gly	p.R245G	ENST00000344624		245	Cgg/Ggg	2/33	1	2	FACETS	0.858	0.798	0.919	0.858	0.798	0.919	CLONAL	1	TRUE	1	0.543971511836404	2		919	930	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202368	138202368	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	125	726	1	ENST00000237289.4:c.2285G>T	p.Cys762Phe	p.C762F	ENST00000237289	NM_001270507.1	762	tGc/tTc	9/9	1	2	FACETS	0.691	0.627	0.759	0.691	0.627	0.759	SUBCLONAL	1	TRUE	1	0.543971511836404	2		727	665	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528510	157528510	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554237982	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	81	545	1	ENST00000346085.5:c.6235C>T	p.Gln2079Ter	p.Q2079*	ENST00000346085	NM_020732.3	2079	Cag/Tag	20/20	1	2	FACETS	0.55	0.486	0.62	0.55	0.486	0.62	SUBCLONAL	1	TRUE	1	0.543971511836404	2		546	541	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874808	151874809	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	78	301	0	ENST00000262189.6:c.7729_7730delinsTT	p.Pro2577Leu	p.P2577L	ENST00000262189	NM_170606.2	2577	CCa/TTa	38/59	1	2	FACETS	0.872	0.772	0.976	0.872	0.772	0.976	CLONAL	1	TRUE	1	0.543971511836404	2		301	329	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391793	139391793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	194	900	0	ENST00000277541.6:c.6398C>T	p.Pro2133Leu	p.P2133L	ENST00000277541	NM_017617.3	2133	cCc/cTc	34/34	1	2	FACETS	0.931	0.864	1	0.931	0.864	1	CLONAL	1	TRUE	1	0.543971511836404	2		900	766	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821577	32821595	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	GCGAGAAGCTCAGCCATTT	GCGAGAAGCTCAGCCATTT	TAA	novel	NA	P-0045155-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	211	863	2	ENST00000354258.4:c.-2_17delinsTTA		p.*1*	ENST00000354258	NM_000593.5	?-6/808		1/11	1	2	FACETS	0.873	0.811	0.936	0.873	0.811	0.936	CLONAL	1	TRUE	1	0.543971511836404	2		865	889	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738211	133738211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370646520	NA	P-0045156-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	515	539	1	ENST00000318560.5:c.611C>T	p.Thr204Met	p.T204M	ENST00000318560	NM_005157.4	204	aCg/aTg	4/11	0.68767742987929	4	FACETS	0.95	0.913	0.987	0.95	0.913	0.987	CLONAL	2	TRUE	2	0.915142772123409	4		540	1135	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218787	66218787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	24	214	0	ENST00000273854.3:c.2271G>T	p.Glu757Asp	p.E757D	ENST00000273854	NM_004439.5	757	gaG/gaT	13/18	0.372127243999122	1	FACETS	0.877	0.699	1	0.877	0.699	1	CLONAL	1	TRUE	0	0.384378895348843	1		214	115	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577494	7577505	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGACCTGGAGT	CTGACCTGGAGT	-	novel	NA	P-0045158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	167	593	0	ENST00000269305.4:c.776_782+5del		p.X259_splice	ENST00000269305	NM_001126112.2	259		7/11	0.105518864541314	4	FACETS	0.943	0.877	1			1	INDETERMINATE	3	TRUE	NA	0.384378895348843	4		593	425	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0045159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	150	403	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.535728393124777	2		403	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0045159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	312	911	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.535728393124777	1	FACETS	0.989	0.937	1	0.989	0.937	1	CLONAL	1	TRUE	0	0.535728393124777	1		911	862	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519893	NA	P-0045159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	37	754	0	ENST00000267101.3:c.310G>T	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ttg	3/28	0.535728393124777	1	FACETS	0.129	0.106	0.156	0.129	0.106	0.156	SUBCLONAL	1	TRUE	0	0.535728393124777	1		754	781	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578463	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371524413	NA	P-0045159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	30	934	0	ENST00000269305.4:c.467G>C	p.Arg156Pro	p.R156P	ENST00000269305	NM_001126112.2	156	cGc/cCc	5/11	0.535728393124777	1	FACETS	0.094	0.075	0.116	0.094	0.075	0.116	SUBCLONAL	1	TRUE	0	0.535728393124777	1		934	873	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526302	189526302	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866938979	NA	P-0045159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	171	447	0	ENST00000264731.3:c.566C>T	p.Ser189Leu	p.S189L	ENST00000264731	NM_003722.4	189	tCg/tTg	4/14	1	2	FACETS	0.973	0.899	1	0.973	0.899	1	CLONAL	1	TRUE	1	0.535728393124777	2		447	656	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589552	67589552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	59	170	0	ENST00000274335.5:c.1315G>A	p.Glu439Lys	p.E439K	ENST00000274335		439	Gaa/Aaa	10/15	1	2	FACETS	0.885	0.769	1	0.885	0.769	1	CLONAL	1	TRUE	1	0.535728393124777	2		170	249	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123683	46123683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	104	395	0	ENST00000334344.6:c.64G>A	p.Glu22Lys	p.E22K	ENST00000334344	NM_152641.2	22	Gag/Aag	1/21	0.365233416574306	1	FACETS	0.643	0.579	0.71	0.643	0.579	0.71	SUBCLONAL	1	TRUE	0	0.535728393124777	1		395	442	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047509	49047510	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0045159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	81	242	0	ENST00000267163.4:c.2505dup	p.Gly836TrpfsTer2	p.G836Wfs*2	ENST00000267163	NM_000321.2	835	att/aTtt	24/27	0.535728393124777	1	FACETS	0.993	0.89	1	0.993	0.89	1	CLONAL	1	TRUE	0	0.535728393124777	1		242	223	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772202	68772202	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	191	848	0	ENST00000261769.5:c.51del	p.Ser18ProfsTer38	p.S18Pfs*38	ENST00000261769	NM_004360.3	17	gtC/gt	2/16	0.535728393124777	1	FACETS	0.811	0.753	0.87	0.811	0.753	0.87	CLONAL	1	TRUE	0	0.535728393124777	1		848	644	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861763	59861763	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	93	330	0	ENST00000259008.2:c.1496A>G	p.Gln499Arg	p.Q499R	ENST00000259008	NM_032043.2	499	cAa/cGa	11/20	1	2	FACETS	0.813	0.727	0.904	0.813	0.727	0.904	CLONAL	1	TRUE	1	0.535728393124777	2		330	427	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027956	48027956	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	40	279	0	ENST00000234420.5:c.2834G>C	p.Arg945Thr	p.R945T	ENST00000234420	NM_000179.2	945	aGa/aCa	4/10	0.365233416574306	1	FACETS	0.342	0.285	0.405	0.342	0.285	0.405	SUBCLONAL	1	TRUE	0	0.535728393124777	1		279	320	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69012073	69012073	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	121	357	0	ENST00000288368.4:c.2710A>G	p.Lys904Glu	p.K904E	ENST00000288368	NM_024870.2	904	Aaa/Gaa	23/40	1	2	FACETS	0.928	0.843	1	0.928	0.843	1	CLONAL	1	TRUE	1	0.535728393124777	2		357	487	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737107	145737107	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	266	928	0	ENST00000428558.2:c.3459G>C	p.Glu1153Asp	p.E1153D	ENST00000428558	NM_004260.3	1153	gaG/gaC	21/22	1	2	FACETS	0.967	0.907	1	0.967	0.907	1	CLONAL	1	TRUE	1	0.535728393124777	2		928	1027	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737362	145737362	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	255	951	0	ENST00000428558.2:c.3325G>C	p.Glu1109Gln	p.E1109Q	ENST00000428558	NM_004260.3	1109	Gag/Cag	20/22	1	2	FACETS	0.898	0.841	0.957	0.898	0.841	0.957	CLONAL	1	TRUE	1	0.535728393124777	2		951	1060	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44911031	44911032	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	166	159	0	ENST00000377967.4:c.732_733insA	p.Val245SerfsTer18	p.V245Sfs*18	ENST00000377967	NM_021140.2	244	-/A	9/29	1	1	FACETS	0.886	0.837	0.934	1	0.993	1	CLONAL	2	TRUE	0	0.535728393124777	1		159	256	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339629	70339629	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045159-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	51	300	0	ENST00000374080.3:c.298G>C	p.Asp100His	p.D100H	ENST00000374080		100	Gat/Cat	3/45	1	1	FACETS	0.306	0.26	0.357	0.306	0.26	0.357	SUBCLONAL	1	TRUE	0	0.535728393124777	1		300	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0045160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	83	763	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.260202692823204	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.260202692823204	1		765	455	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747137	40747137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752831315	NA	P-0045160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	42	378	1	ENST00000373198.4:c.2945C>T	p.Pro982Leu	p.P982L	ENST00000373198	NM_133170.3	982	cCg/cTg	22/32	1	2	FACETS	0.776	0.649	0.917	0.776	0.649	0.917	CLONAL	1	TRUE	1	0.260202692823204	2		379	416	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0045160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	110	294	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.260202692823204	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.260202692823204	4		294	451	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023203	27023222	+	frameshift_variant	Frame_Shift_Del	DEL	GAACGGGAACGCGGGCCCTA	GAACGGGAACGCGGGCCCTA	-	novel	NA	P-0045160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	38	198	0	ENST00000324856.7:c.310_329del	p.Asn104AlafsTer6	p.N104Afs*6	ENST00000324856	NM_006015.4	103	tcGAACGGGAACGCGGGCCCTAgg/tcgg	1/20	0.260202692823204	1	FACETS	0.765	0.642	0.899	1	0.957	1	SUBCLONAL	2	TRUE	0	0.260202692823204	1		198	166	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525943	148525944	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045160-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	43	338	0	ENST00000320356.2:c.513dup	p.Val172CysfsTer11	p.V172Cfs*11	ENST00000320356	NM_004456.4	171	-/T	6/20	1	2	FACETS	0.867	0.728	1	0.867	0.728	1	CLONAL	1	TRUE	1	0.260202692823204	2		338	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0045161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	407	712	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	0.778749473167734	1	FACETS	0.973	0.938	1	0.973	0.938	1	CLONAL	1	TRUE	0	0.792220478828853	1		712	638	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435422	18435422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	130	214	0	ENST00000266497.5:c.407C>T	p.Ala136Val	p.A136V	ENST00000266497		136	gCt/gTt	1/31	0.537395664994851	3	FACETS	0.977	0.892	1	0.488	0.446	0.533	CLONAL	1	TRUE	1	0.792220478828853	3		214	469	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748863	41748906	+	frameshift_variant	Frame_Shift_Del	DEL	GTGTCCTCATCTTGGCTCTCTTCCTTGTCCACCGGCGAAAGAAG	GTGTCCTCATCTTGGCTCTCTTCCTTGTCCACCGGCGAAAGAAG	-	novel	NA	P-0045161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	238	614	0	ENST00000301178.4:c.1389_1432del	p.Cys463Ter	p.C463*	ENST00000301178	NM_021913.4	463	tGTGTCCTCATCTTGGCTCTCTTCCTTGTCCACCGGCGAAAGAAG/t	11/20	1	2	FACETS	0.694	0.649	0.74	0.694	0.649	0.74	SUBCLONAL	1	TRUE	1	0.792220478828853	2		614	866	SUCCESS
MET	4233	MSKCC	GRCh37	7	116381038	116381038	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	56	511	0	ENST00000397752.3:c.1660G>C	p.Gly554Arg	p.G554R	ENST00000397752	NM_000245.2	554	Ggg/Cgg	5/21	1	2	FACETS	0.146	0.124	0.17	0.146	0.124	0.17	SUBCLONAL	1	TRUE	1	0.792220478828853	2		511	967	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221226	1221226	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876661238	NA	P-0045162-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	233	688	0	ENST00000326873.7:c.749C>T	p.Thr250Met	p.T250M	ENST00000326873	NM_000455.4	250	aCg/aTg	6/10	1	2	FACETS	0.901	0.842	0.961	0.901	0.842	0.961	CLONAL	1	TRUE	1	0.629415046393258	2		688	822	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0045163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	17	354	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.645	0.48	0.843	0.645	0.48	0.843	SUBCLONAL	1	TRUE	1	0.12	2		354	439	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286764	212286764	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	20	312	0	ENST00000342788.4:c.2932G>T	p.Ala978Ser	p.A978S	ENST00000342788	NM_005235.2	978	Gct/Tct	24/28	1	2	FACETS	0.923	0.705	1	0.923	0.705	1	CLONAL	1	TRUE	1	0.12	2		312	361	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864721	57864721	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	40	807	0	ENST00000228682.2:c.2198G>T	p.Gly733Val	p.G733V	ENST00000228682	NM_005269.2	733	gGg/gTg	12/12	1	2	FACETS	0.997	0.826	1	0.997	0.826	1	CLONAL	1	TRUE	1	0.12	2		807	669	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600336	10600336	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	27	570	0	ENST00000171111.5:c.1519C>G	p.Arg507Gly	p.R507G	ENST00000171111	NM_203500.1	507	Cga/Gga	4/6	0.137190322138237	1	FACETS	0.833	0.661	1	0.833	0.661	1	CLONAL	1	TRUE	0	0.12	1		570	508	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030473	47030473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	36	955	0	ENST00000377604.3:c.249del	p.Arg84GlyfsTer50	p.R84Gfs*50	ENST00000377604	NM_001204468.1	83	cGg/cg	4/24	0.137190322138237	1	FACETS	0.791	0.648	0.952	0.791	0.648	0.952	CLONAL	1	TRUE	0	0.12	1		955	713	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0045164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	227	454	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.247916659533749	3	FACETS	0.93	0.872	0.989	0.62	0.581	0.659	INDETERMINATE	2	TRUE	0	0.492318851724928	3		454	618	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0045164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	119	403	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.492318851724928	2		403	459	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890221	72890221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752101890	NA	P-0045164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	122	373	2	ENST00000325599.8:c.461G>A	p.Arg154Gln	p.R154Q	ENST00000325599	NM_018130.2	154	cGa/cAa	4/11	1	2	FACETS	0.909	0.825	0.997	0.909	0.825	0.997	CLONAL	1	TRUE	1	0.492318851724928	2		375	545	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523334	9523334	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	157	453	0	ENST00000353224.5:c.1903G>A	p.Glu635Lys	p.E635K	ENST00000353224	NM_177990.2	635	Gaa/Aaa	9/10	1	2	FACETS	0.903	0.83	0.98	0.903	0.83	0.98	CLONAL	1	TRUE	1	0.492318851724928	2		453	706	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950309	17950309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	253	709	0	ENST00000458235.1:c.1418C>T	p.Ser473Phe	p.S473F	ENST00000458235	NM_000215.3	473	tCc/tTc	10/24	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.492318851724928	2		709	1026	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257158	16257158	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	42	416	1	ENST00000375759.3:c.4423C>T	p.Arg1475Ter	p.R1475*	ENST00000375759	NM_015001.2	1475	Cga/Tga	11/15	1	2	FACETS	0.268	0.223	0.318	0.268	0.223	0.318	SUBCLONAL	1	TRUE	1	0.492318851724928	2		417	636	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750695	128750695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	159	586	0	ENST00000377970.2:c.232C>T	p.Pro78Ser	p.P78S	ENST00000377970	NM_002467.4	78	Cct/Tct	2/3	1	2	FACETS	0.871	0.799	0.944	0.871	0.799	0.944	CLONAL	1	TRUE	1	0.492318851724928	2		586	742	SUCCESS
BLM	641	MSKCC	GRCh37	15	91306259	91306259	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	117	294	0	ENST00000355112.3:c.1946T>A	p.Phe649Tyr	p.F649Y	ENST00000355112	NM_000057.2	649	tTt/tAt	8/22	1	2	FACETS	0.885	0.801	0.973	0.885	0.801	0.973	CLONAL	1	TRUE	1	0.492318851724928	2		294	537	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804212	43804212	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs867404262	NA	P-0045164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	263	413	0	ENST00000372470.3:c.213-1G>A		p.X71_splice	ENST00000372470	NM_005373.2	71			0.247916659533749	3	FACETS	1	0.988	1	0.765	0.724	0.807	INDETERMINATE	2	TRUE	0	0.492318851724928	3		413	580	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519347	137519347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747857191	NA	P-0045164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	27	270	0	ENST00000367739.4:c.1291C>T	p.Pro431Ser	p.P431S	ENST00000367739	NM_000416.2	431	Ccc/Tcc	7/7	0.338886953489423	1	FACETS	0.304	0.242	0.374	0.304	0.242	0.374	SUBCLONAL	1	TRUE	0	0.492318851724928	1		270	272	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980798	40980798	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	252	523	0	ENST00000373198.4:c.1688C>T	p.Ser563Phe	p.S563F	ENST00000373198	NM_133170.3	563	tCc/tTc	10/32	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.492318851724928	2		523	778	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795069	242795069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	262	877	0	ENST00000334409.5:c.140G>A	p.Gly47Glu	p.G47E	ENST00000334409	NM_005018.2	47	gGg/gAg	2/5	1	2	FACETS	0.969	0.908	1	0.969	0.908	1	CLONAL	1	TRUE	1	0.492318851724928	2		877	1098	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652476	48652476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	125	872	0	ENST00000376670.3:c.1147C>T	p.Pro383Ser	p.P383S	ENST00000376670	NM_002049.3	383	Cct/Tct	6/6	0.406765620228431	1	FACETS	0.404	0.365	0.445	0.404	0.365	0.445	SUBCLONAL	1	TRUE	0	0.492318851724928	1		872	947	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261281	115261281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	309	459	0	ENST00000438362.2:c.2440C>T	p.Pro814Ser	p.P814S	ENST00000438362	NM_001242891.1	814	Cct/Tct	19/20	0.247916659533749	3	FACETS	1	0.983	1	0.722	0.685	0.759	INDETERMINATE	2	TRUE	0	0.492318851724928	3		459	722	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135641	64135641	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	294	806	1	ENST00000334205.4:c.1109A>T	p.His370Leu	p.H370L	ENST00000334205	NM_003942.2	370	cAc/cTc	10/17	0.492318851724928	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.492318851724928	1		807	847	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953941	32953941	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1566253139	NA	P-0045164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	106	305	0	ENST00000380152.3:c.9008G>A	p.Gly3003Glu	p.G3003E	ENST00000380152		3003	gGa/gAa	23/27	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.492318851724928	2		305	357	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785809	50785809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	65	350	0	ENST00000398568.2:c.799G>A	p.Val267Met	p.V267M	ENST00000398568	NM_001042412.1	267	Gtg/Atg	4/18	1	2	FACETS	0.627	0.546	0.715	0.627	0.546	0.715	SUBCLONAL	1	TRUE	1	0.492318851724928	2		350	421	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740873	58740873	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867112527	NA	P-0045164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	228	406	0	ENST00000305921.3:c.1778C>T	p.Pro593Leu	p.P593L	ENST00000305921	NM_003620.3	593	cCt/cTt	6/6	0.492318851724928	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.492318851724928	1		406	511	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5258054	5258054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	172	524	0	ENST00000357368.4:c.680C>T	p.Ser227Phe	p.S227F	ENST00000357368	NM_002850.3	227	tCc/tTc	8/38	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.492318851724928	2		524	678	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113831	11113831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	170	612	0	ENST00000358026.2:c.1939C>T	p.Pro647Ser	p.P647S	ENST00000358026	NM_001128849.1	647	Ccg/Tcg	12/36	1	2	FACETS	0.917	0.845	0.992	0.917	0.845	0.992	CLONAL	1	TRUE	1	0.492318851724928	2		612	753	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570052	212570052	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	113	304	0	ENST00000342788.4:c.1189G>C	p.Glu397Gln	p.E397Q	ENST00000342788	NM_005235.2	397	Gag/Cag	10/28	1	2	FACETS	0.996	0.902	1	0.996	0.902	1	CLONAL	1	TRUE	1	0.492318851724928	2		304	461	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30664696	30664696	+	intron_variant	Intron	SNP	G	G	T	novel	NA	P-0045164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	61	265	0	ENST00000295754.5:c.94+16227G>T		p.*32*	ENST00000295754	NM_003242.5	34/592			1	2	FACETS	0.818	0.711	0.932	0.818	0.711	0.932	CLONAL	1	TRUE	1	0.492318851724928	2		265	303	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582099	189582099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754080925	NA	P-0045164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	150	442	0	ENST00000264731.3:c.658C>T	p.Pro220Ser	p.P220S	ENST00000264731	NM_003722.4	220	Cct/Tct	5/14	1	2	FACETS	0.942	0.864	1	0.942	0.864	1	CLONAL	1	TRUE	1	0.492318851724928	2		442	647	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807788	1807788	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	98	770	0	ENST00000260795.2:c.1847G>A	p.Arg616Lys	p.R616K	ENST00000260795		616	aGg/aAg	13/17	1	2	FACETS	0.479	0.426	0.534	0.479	0.426	0.534	SUBCLONAL	1	TRUE	1	0.492318851724928	2		770	832	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157314	106157314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	102	345	0	ENST00000380013.4:c.2215C>T	p.Pro739Ser	p.P739S	ENST00000380013	NM_001127208.2	739	Cct/Tct	3/11	1	2	FACETS	0.907	0.815	1	0.907	0.815	1	CLONAL	1	TRUE	1	0.492318851724928	2		345	457	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687446	117687446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767616403	NA	P-0045164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	35	250	0	ENST00000368508.3:c.2605G>A	p.Asp869Asn	p.D869N	ENST00000368508	NM_002944.2	869	Gat/Aat	18/43	0.338886953489423	1	FACETS	0.332	0.272	0.398	0.332	0.272	0.398	SUBCLONAL	1	TRUE	0	0.492318851724928	1		250	323	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68982094	68982094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	78	452	0	ENST00000288368.4:c.1468C>T	p.His490Tyr	p.H490Y	ENST00000288368	NM_024870.2	490	Cat/Tat	13/40	1	2	FACETS	0.632	0.557	0.713	0.632	0.557	0.713	SUBCLONAL	1	TRUE	1	0.492318851724928	2		452	501	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641080	93641080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	197	444	0	ENST00000375746.1:c.1426C>T	p.His476Tyr	p.H476Y	ENST00000375746	NM_001174167.1	476	Cat/Tat	11/14	0.492318851724928	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.492318851724928	1		444	500	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352295	70352295	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	124	623	0	ENST00000374080.3:c.4322G>T	p.Gly1441Val	p.G1441V	ENST00000374080		1441	gGa/gTa	31/45	0.406765620228431	1	FACETS	0.488	0.442	0.537	0.488	0.442	0.537	SUBCLONAL	1	TRUE	0	0.492318851724928	1		623	778	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099423	27099438	+	frameshift_variant	Frame_Shift_Del	DEL	GATGGGGCGCATGTCC	GATGGGGCGCATGTCC	AG	novel	NA	P-0045164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	192	488	2	ENST00000324856.7:c.3660_3675delinsAG	p.Met1220IlefsTer3	p.M1220Ifs*3	ENST00000324856	NM_006015.4	1220	atGATGGGGCGCATGTCC/atAG	14/20	0.247916659533749	3	FACETS	0.841	0.783	0.9	0.561	0.522	0.6	INDETERMINATE	2	TRUE	0	0.492318851724928	3		490	578	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217686	7217686	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	241	447	0	ENST00000380728.2:c.241G>T	p.Glu81Ter	p.E81*	ENST00000380728		81	Gaa/Taa	4/11	0.35445601237573	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	FALSE	0	0.357908281533298	3		447	491	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5225801	5225801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1340374850	NA	P-0045165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	141	866	2	ENST00000357368.4:c.2431G>A	p.Ala811Thr	p.A811T	ENST00000357368	NM_002850.3	811	Gcc/Acc	17/38	0.357908281533298	3	FACETS	1	0.938	1	0.518	0.472	0.567	CLONAL	1	FALSE	1	0.357908281533298	3		868	896	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650850	48650850	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045165-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	255	852	0	ENST00000376670.3:c.719C>G	p.Pro240Arg	p.P240R	ENST00000376670	NM_002049.3	240	cCc/cGc	4/6	0.306468320116127	4	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	FALSE	2	0.357908281533298	4		852	933	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188317	32188317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144492578	NA	P-0045166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	368	843	0	ENST00000375023.3:c.1024G>A	p.Val342Met	p.V342M	ENST00000375023	NM_004557.3	342	Gtg/Atg	6/30	0.709967649094995	3	FACETS	0.93	0.88	0.98	0.465	0.44	0.49	CLONAL	1	TRUE	1	0.709967649094995	3		843	1511	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416393	49416393	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	216	509	3	ENST00000301067.7:c.16318del	p.Glu5440ArgfsTer16	p.E5440Rfs*16	ENST00000301067	NM_003482.3	5440	Gag/ag	51/54	0.709967649094995	3	FACETS	0.978	0.911	1	0.489	0.455	0.524	CLONAL	1	TRUE	1	0.709967649094995	3		512	843	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794511	42794511	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1696	410	949	1	ENST00000575354.2:c.1591G>T	p.Ala531Ser	p.A531S	ENST00000575354	NM_015125.3	531	Gcc/Tcc	10/20	0.516985505672584	4	FACETS	0.938	0.889	0.988	0.469	0.444	0.494	CLONAL	1	TRUE	2	0.709967649094995	4		950	2106	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790075	40790075	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	341	649	1	ENST00000373198.4:c.2656C>A	p.Pro886Thr	p.P886T	ENST00000373198	NM_133170.3	886	Ccc/Acc	18/32	0.709967649094995	3	FACETS	0.994	0.94	1	0.497	0.47	0.525	CLONAL	1	TRUE	1	0.709967649094995	3		650	1309	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259412	89259412	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	122	447	0	ENST00000336596.2:c.556G>A	p.Val186Ile	p.V186I	ENST00000336596	NM_005233.5	186	Gtt/Att	3/17	0.516985505672584	4	FACETS	0.763	0.69	0.84	0.382	0.345	0.42	SUBCLONAL	1	TRUE	2	0.709967649094995	4		447	770	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39003667	39003667	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	185	293	0	ENST00000357387.3:c.253A>G	p.Ile85Val	p.I85V	ENST00000357387	NM_152756.3	85	Ata/Gta	4/38	0.709967649094995	5	FACETS	0.922	0.864	0.981	0.922	0.864	0.981	CLONAL	3	TRUE	2	0.709967649094995	5		293	389	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374429	81374429	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	76	291	2	ENST00000222390.5:c.633C>A	p.Cys211Ter	p.C211*	ENST00000222390	NM_000601.4	211	tgC/tgA	6/18	0.709967649094995	3	FACETS	0.831	0.734	0.934	0.416	0.367	0.467	CLONAL	1	TRUE	1	0.709967649094995	3		293	349	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069649	69069649	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	78	368	2	ENST00000288368.4:c.4324A>G	p.Lys1442Glu	p.K1442E	ENST00000288368	NM_024870.2	1442	Aaa/Gaa	35/40	0.709967649094995	3	FACETS	0.973	0.863	1	0.486	0.431	0.544	CLONAL	1	TRUE	1	0.709967649094995	3		370	306	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8733789	8733789	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	454	541	0	ENST00000356435.5:c.55G>T	p.Asp19Tyr	p.D19Y	ENST00000356435		19	Gat/Tat	1/35	0.708881651030838	4	FACETS	0.981	0.939	1	0.981	0.939	1	CLONAL	2	TRUE	2	0.709967649094995	4		541	1115	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006089	22006089	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1327	915	863	2	ENST00000276925.6:c.314G>T	p.Arg105Leu	p.R105L	ENST00000276925	NM_004936.3	105	cGg/cTg	2/2	0.708881651030838	4	FACETS	0.983	0.953	1	0.983	0.953	1	CLONAL	2	TRUE	2	0.709967649094995	4		865	2242	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652350	48652350	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	942	507	4	ENST00000376670.3:c.1021A>T	p.Ser341Cys	p.S341C	ENST00000376670	NM_002049.3	341	Agc/Tgc	6/6	0.709967649094995	2	FACETS	1	0.998	1			1	CLONAL	2	TRUE	NA	0.709967649094995	2		511	1128	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728636	190728639	+	missense_variant	Missense_Mutation	ONP	AACC	AACC	CACT	novel	NA	P-0045166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	88	404	0	ENST00000441310.2:c.2024_2027delinsCACT	p.Gln675_Pro676delinsProLeu	p.Q675_P676delinsPL	ENST00000441310	NM_000534.4	675	cAACCa/cCACTa	10/13	0.598234053931204	3	FACETS	0.884	0.789	0.984	0.442	0.394	0.492	CLONAL	1	TRUE	1	0.709967649094995	3		404	380	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144049	11144051	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0045184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	92	834	1	ENST00000358026.2:c.3634_3636del	p.Glu1212del	p.E1212del	ENST00000358026	NM_001128849.1	1210	gtGGAg/gtg	26/36	0.34046132804944	1	FACETS	0.718	0.638	0.802	0.718	0.638	0.802	SUBCLONAL	1	TRUE	0	0.34046132804944	1		835	625	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90990538	90990538	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	100	367	0	ENST00000265433.3:c.494T>A	p.Leu165His	p.L165H	ENST00000265433	NM_002485.4	165	cTc/cAc	5/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.34046132804944	2		367	495	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057907	27057908	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGACG	novel	NA	P-0045184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	109	715	0	ENST00000324856.7:c.1616_1620dup	p.Thr541ArgfsTer80	p.T541Rfs*80	ENST00000324856	NM_006015.4	539	tcg/tCGACGcg	3/20	1	2	FACETS	0.821	0.737	0.91	0.821	0.737	0.91	CLONAL	1	TRUE	1	0.34046132804944	2		715	780	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087392	27087392	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	111	656	0	ENST00000324856.7:c.1966G>C	p.Ala656Pro	p.A656P	ENST00000324856	NM_006015.4	656	Gct/Cct	5/20	1	2	FACETS	0.969	0.872	1	0.969	0.872	1	CLONAL	1	TRUE	1	0.34046132804944	2		656	673	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207119	1207120	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0045184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	165	919	3	ENST00000326873.7:c.207_208delinsTT	p.Glu70Ter	p.E70*	ENST00000326873	NM_000455.4	69	tcGGag/tcTTag	1/10	0.34046132804944	1	FACETS	0.954	0.877	1	0.954	0.877	1	CLONAL	1	TRUE	0	0.34046132804944	1		922	843	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602736	10602736	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	181	869	0	ENST00000171111.5:c.842T>A	p.Leu281Gln	p.L281Q	ENST00000171111	NM_203500.1	281	cTg/cAg	3/6	0.34046132804944	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.34046132804944	1		869	767	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296339	15296339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	140	878	0	ENST00000263388.2:c.2103del	p.His701GlnfsTer159	p.H701Qfs*159	ENST00000263388	NM_000435.2	701	caT/ca	13/33	0.34046132804944	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.34046132804944	1		878	605	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876488	35876488	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	87	578	0	ENST00000303115.3:c.1280C>A	p.Thr427Lys	p.T427K	ENST00000303115	NM_002185.3	427	aCa/aAa	8/8	0.136560284416747	3	FACETS	0.96	0.851	1	0.48	0.425	0.539	INDETERMINATE	1	TRUE	1	0.34046132804944	3		578	623	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132458	11132558	+	frameshift_variant	Frame_Shift_Del	DEL	AAGCTGACGCAGGTGCTCAACACGCACTATGTGGCACCCCGCCGCCTGCTGCTGACGGGCACACCGCTGCAGAACAAGCTTCCCGAGCTCTGGGCGCTGCT	AAGCTGACGCAGGTGCTCAACACGCACTATGTGGCACCCCGCCGCCTGCTGCTGACGGGCACACCGCTGCAGAACAAGCTTCCCGAGCTCTGGGCGCTGCT	GGGGTGCCA	novel	NA	P-0045184-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	46	838	2	ENST00000358026.2:c.2674_2774delinsGGGGTGCCA	p.Lys892GlyfsTer22	p.K892Gfs*22	ENST00000358026	NM_001128849.1	892	AAGCTGACGCAGGTGCTCAACACGCACTATGTGGCACCCCGCCGCCTGCTGCTGACGGGCACACCGCTGCAGAACAAGCTTCCCGAGCTCTGGGCGCTGCTc/GGGGTGCCAc	19/36	0.34046132804944	1	FACETS	0.379	0.319	0.446	0.379	0.319	0.446	SUBCLONAL	1	TRUE	0	0.34046132804944	1		840	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0045185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	534	784	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.038776089660868	3	FACETS	1	0.992	1			1	INDETERMINATE	3	TRUE	NA	0.309112672663974	3		784	1199	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168970	32168970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763391002	NA	P-0045185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	424	758	1	ENST00000375023.3:c.4063C>T	p.Arg1355Trp	p.R1355W	ENST00000375023	NM_004557.3	1355	Cgg/Tgg	22/30	0.309112672663974	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	1	0.309112672663974	4		759	1169	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968188	134968188	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	187	593	0	ENST00000398015.3:c.2701C>A	p.Pro901Thr	p.P901T	ENST00000398015	NM_004441.4	901	Ccc/Acc	15/16	0.283416565207382	3	FACETS	0.977	0.905	1	0.977	0.905	1	CLONAL	2	TRUE	1	0.309112672663974	3		593	715	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250849	153250849	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	142	417	0	ENST00000281708.4:c.1211A>C	p.Lys404Thr	p.K404T	ENST00000281708	NM_033632.3	404	aAa/aCa	8/12	0.309112672663974	2	FACETS	0.963	0.884	1	0.963	0.884	1	CLONAL	2	TRUE	0	0.309112672663974	2		417	477	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969193	93969193	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045185-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	29	309	0	ENST00000369303.4:c.1803A>C	p.Lys601Asn	p.K601N	ENST00000369303	NM_004440.3	601	aaA/aaC	10/17	1	2	FACETS	0.463	0.371	0.568	0.463	0.371	0.568	SUBCLONAL	1	TRUE	1	0.309112672663974	2		309	405	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727455	66727455	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs869025608	NA	P-0045185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	111	466	0	ENST00000307102.5:c.171G>T	p.Lys57Asn	p.K57N	ENST00000307102	NM_002755.3	57	aaG/aaT	2/11	0.159020253832246	2	FACETS	1	0.965	1	0.577	0.52	0.637	INDETERMINATE	1	TRUE	0	0.313316409350019	2		466	614	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562982	29562982	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1306237220	NA	P-0045185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	41	491	0	ENST00000356175.3:c.3917G>A	p.Arg1306Gln	p.R1306Q	ENST00000356175	NM_000267.3	1306	cGa/cAa	29/57	0.197674574854686	3	FACETS	0.494	0.41	0.587	0.247	0.205	0.294	SUBCLONAL	1	TRUE	1	0.313316409350019	3		491	613	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021535	31021535	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs757832294	NA	P-0045185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	100	523	0	ENST00000375687.4:c.1534C>T	p.Gln512Ter	p.Q512*	ENST00000375687	NM_015338.5	512	Cag/Tag	12/13	0.16518191531746	5	FACETS	1	0.962	1	0.391	0.349	0.436	INDETERMINATE	1	TRUE	2	0.313316409350019	5		523	800	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976689	55976689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747477930	NA	P-0045185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	42	496	0	ENST00000263923.4:c.1136C>T	p.Ala379Val	p.A379V	ENST00000263923	NM_002253.2	379	gCg/gTg	9/30	0.127143775649216	0	FACETS	0.321	0.267	0.38			1	INDETERMINATE	1	TRUE	0	0.313316409350019	0		496	574	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303709	65303709	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	50	578	0	ENST00000342505.4:c.3046C>T	p.Gln1016Ter	p.Q1016*	ENST00000342505	NM_002227.2	1016	Caa/Taa	22/25	1	2	FACETS	0.426	0.36	0.499	0.426	0.36	0.499	SUBCLONAL	1	TRUE	1	0.313316409350019	2		578	749	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101074	4101074	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	26	308	0	ENST00000262948.5:c.648C>A	p.Ser216Arg	p.S216R	ENST00000262948	NM_030662.3	216	agC/agA	6/11	0.175293644927541	2	FACETS	0.544	0.431	0.673	0.272	0.215	0.337	INDETERMINATE	1	TRUE	0	0.313316409350019	2		308	305	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012230	152012230	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	50	409	0	ENST00000262189.6:c.583C>T	p.Gln195Ter	p.Q195*	ENST00000262189	NM_170606.2	195	Cag/Tag	4/59	0.313316409350019	3	FACETS	0.635	0.539	0.742	0.318	0.269	0.371	SUBCLONAL	1	TRUE	1	0.313316409350019	3		409	581	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221897	98221897	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045185-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	74	530	0	ENST00000331920.6:c.2872G>A	p.Glu958Lys	p.E958K	ENST00000331920	NM_000264.3	958	Gaa/Aaa	17/24	0.313316409350019	3	FACETS	0.622	0.544	0.708	0.207	0.181	0.236	SUBCLONAL	1	TRUE	0	0.313316409350019	3		530	878	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248679	59248679	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	163	909	0	ENST00000371222.2:c.64G>C	p.Glu22Gln	p.E22Q	ENST00000371222	NM_002228.3	22	Gag/Cag	1/1	0.156891575771652	3	FACETS	0.883	0.808	0.961	0.883	0.808	0.961	CLONAL	2	FALSE	1	0.156891575771652	3		909	1269	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654533	29654533	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	44	250	0	ENST00000356175.3:c.5222del	p.Val1741AlafsTer3	p.V1741Afs*3	ENST00000356175	NM_000267.3	1741	gTc/gc	37/57	0.156891575771652	2	FACETS	0.825	0.694	0.968	0.825	0.694	0.968	CLONAL	2	FALSE	0	0.156891575771652	2		250	340	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492910	56492910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	21	262	0	ENST00000407977.2:c.29C>T	p.Ala10Val	p.A10V	ENST00000407977		10	gCt/gTt	2/10	0.156891575771652	2	FACETS	0.663	0.509	0.842	0.331	0.254	0.421	SUBCLONAL	1	FALSE	0	0.156891575771652	2		262	404	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516887	187516887	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	48	490	0	ENST00000441802.2:c.13094T>C	p.Val4365Ala	p.V4365A	ENST00000441802	NM_005245.3	4365	gTg/gCg	26/27	0.156891575771652	1	FACETS	0.924	0.781	1	0.924	0.781	1	CLONAL	1	FALSE	0	0.156891575771652	1		490	610	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31422963	31422963	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	67	531	0	ENST00000344624.3:c.3350T>A	p.Ile1117Asn	p.I1117N	ENST00000344624		1117	aTt/aAt	26/33	0.156891575771652	3	FACETS	1	0.937	1	0.569	0.493	0.651	CLONAL	1	FALSE	1	0.156891575771652	3		531	810	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674247	86674248	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0045189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	42	337	0	ENST00000274376.6:c.2380dup	p.Ala794GlyfsTer36	p.A794Gfs*36	ENST00000274376	NM_002890.2	793	-/G	18/25	0.156891575771652	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	FALSE	0	0.156891575771652	1		337	394	SUCCESS
APC	324	MSKCC	GRCh37	5	112176120	112176126	+	frameshift_variant	Frame_Shift_Del	DEL	GTCAGCT	GTCAGCT	-	novel	NA	P-0045189-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	46	405	0	ENST00000257430.4:c.4830_4836del	p.Gln1611LeufsTer37	p.Q1611Lfs*37	ENST00000257430	NM_000038.5	1610	aGTCAGCTg/ag	16/16	0.156891575771652	1	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	FALSE	0	0.156891575771652	1		405	508	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517201	NA	P-0045191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	40	64	0	ENST00000263967.3:c.1637A>C	p.Gln546Pro	p.Q546P	ENST00000263967	NM_006218.2	546	cAg/cCg	10/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		64	164	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0045191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	14	331	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		331	89	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577146	7577147	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGATTACC	novel	NA	P-0045191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	82	222	0	ENST00000269305.4:c.784_791dup	p.Leu265ValfsTer83	p.L265Vfs*83	ENST00000269305	NM_001126112.2	264	cta/ctGGTAATCTa	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		222	411	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413052	139413052	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	113	550	0	ENST00000277541.6:c.1090G>T	p.Gly364Cys	p.G364C	ENST00000277541	NM_017617.3	364	Ggc/Tgc	6/34	0.167568540356153	3	FACETS	0.835	0.752	0.923	0.278	0.25	0.308	INDETERMINATE	1	TRUE	0	0.426430869563275	3		550	770	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578412	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCGCCTCA	CAGCGCCTCA	-	novel	NA	P-0045208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	293	727	0	ENST00000269305.4:c.518_527del	p.Val173AlafsTer71	p.V173Afs*71	ENST00000269305	NM_001126112.2	173	gTGAGGCGCTGc/gc	5/11	0.409547920827384	2	FACETS	0.813	0.768	0.859	0.813	0.768	0.859	CLONAL	2	TRUE	0	0.426430869563275	2		727	845	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158655999	158655999	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	58	379	0	ENST00000263640.3:c.7G>A	p.Asp3Asn	p.D3N	ENST00000263640	NM_001105.4	3	Gat/Aat	3/11	1	2	FACETS	0.602	0.518	0.693	0.602	0.518	0.693	SUBCLONAL	1	TRUE	1	0.426430869563275	2		379	452	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528726	157528726	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	101	530	0	ENST00000346085.5:c.6451G>A	p.Val2151Met	p.V2151M	ENST00000346085	NM_020732.3	2151	Gtg/Atg	20/20	1	2	FACETS	0.825	0.739	0.916	0.825	0.739	0.916	CLONAL	1	TRUE	1	0.426430869563275	2		530	574	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347985	89347986	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0045213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	68	973	0	ENST00000301030.4:c.4964_4965del	p.Lys1655ArgfsTer12	p.K1655Rfs*12	ENST00000301030	NM_001256183.1	1655	aAA/a	9/13	0.40850099084957	0	FACETS	0.217	0.188	0.248			1	SUBCLONAL	1	TRUE	0	0.40850099084957	0		973	908	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591118	67591135	+	inframe_deletion	In_Frame_Del	DEL	ATCCAGCTGAGAAAGACG	ATCCAGCTGAGAAAGACG	-	novel	NA	P-0045213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	17	286	0	ENST00000274335.5:c.1712_1729del	p.Ile571_Thr576del	p.I571_T576del	ENST00000274335		571	ATCCAGCTGAGAAAGACG/-	12/15	0.402902705951651	0	FACETS	0.168	0.125	0.219			1	SUBCLONAL	1	TRUE	0	0.40850099084957	0		286	293	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760753	133760753	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769680358	NA	P-0045213-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	97	878	2	ENST00000318560.5:c.3076G>A	p.Ala1026Thr	p.A1026T	ENST00000318560	NM_005157.4	1026	Gcc/Acc	11/11	0.40850099084957	1	FACETS	0.421	0.375	0.471	0.421	0.375	0.471	SUBCLONAL	1	TRUE	0	0.40850099084957	1		880	897	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054194	30054194	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	30	453	1	ENST00000338641.4:c.616G>T	p.Glu206Ter	p.E206*	ENST00000338641	NM_000268.3	206	Gaa/Taa	7/16	0.570579005294355	1	FACETS	0.189	0.152	0.231	0.189	0.152	0.231	SUBCLONAL	1	TRUE	0	0.66289975802155	1		454	320	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11182158	11182158	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	438	879	0	ENST00000361445.4:c.6688T>G	p.Leu2230Val	p.L2230V	ENST00000361445	NM_004958.3	2230	Tta/Gta	48/58	0.66289975802155	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.66289975802155	2		879	657	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188322	10188322	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs5030814	NA	P-0045214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	151	519	0	ENST00000256474.2:c.463+2T>C		p.X155_splice	ENST00000256474	NM_000551.3	155			0.661336708956755	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.66289975802155	1		519	301	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598211	52598213	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0045214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	133	513	0	ENST00000394830.3:c.3653_3655del	p.Ser1218del	p.S1218del	ENST00000394830	NM_018313.4	1218	tCCTgc/tgc	24/30	0.66289975802155	1	FACETS	0.928	0.858	0.999	0.928	0.858	0.999	CLONAL	1	TRUE	0	0.66289975802155	1		513	289	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	157	425	0				ENST00000310581	NM_198253.2	-/1132			0.810352671545214	4	FACETS	0.981	0.901	1	0.327	0.3	0.355	CLONAL	1	TRUE	1	0.831894524114959	4		425	705	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578412	7578412	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519747	NA	P-0045215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	684	786	0	ENST00000269305.4:c.518T>C	p.Val173Ala	p.V173A	ENST00000269305	NM_001126112.2	173	gTg/gCg	5/11	0.820811331153398	2	FACETS	0.956	0.936	0.976	0.956	0.936	0.976	CLONAL	2	TRUE	0	0.831894524114959	2		786	860	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151186	202151186	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746684914	NA	P-0045215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	122	228	0	ENST00000358485.4:c.1486G>A	p.Asp496Asn	p.D496N	ENST00000358485	NM_001080125.1	496	Gat/Aat	9/9	0.753107333370738	3	FACETS	0.876	0.811	0.942	0.584	0.54	0.628	CLONAL	2	TRUE	0	0.831894524114959	3		228	237	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510153	187510153	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367799188	NA	P-0045215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	183	570	0	ENST00000441802.2:c.13360G>A	p.Glu4454Lys	p.E4454K	ENST00000441802	NM_005245.3	4454	Gaa/Aaa	27/27	0.228536300299268	3	FACETS	1	0.935	1	0.336	0.311	0.361	INDETERMINATE	1	TRUE	0	0.831894524114959	3		570	618	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092948	29092948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201206424	NA	P-0045215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	306	490	0	ENST00000328354.6:c.1036C>T	p.Arg346Cys	p.R346C	ENST00000328354	NM_007194.3	346	Cgt/Tgt	10/15	0.794563902473755	3	FACETS	0.849	0.819	0.877	1	0.995	1	CLONAL	3	TRUE	1	0.831894524114959	3		490	409	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591077	67591077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	156	278	0	ENST00000274335.5:c.1670G>A	p.Arg557Gln	p.R557Q	ENST00000274335		557	cGa/cAa	12/15	0.768086120014708	2	FACETS	0.919	0.875	0.96	0.919	0.875	0.96	CLONAL	2	TRUE	0	0.831894524114959	2		278	204	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519000	66519000	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	348	507	0	ENST00000358598.2:c.281G>A	p.Arg94Lys	p.R94K	ENST00000358598	NM_212471.2	94	aGg/aAg	3/11	0.621928669010089	4	FACETS	0.975	0.929	1	0.65	0.619	0.681	CLONAL	2	TRUE	1	0.831894524114959	4		507	786	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872197	45872197	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	228	709	0	ENST00000391945.4:c.237G>C	p.Glu79Asp	p.E79D	ENST00000391945	NM_000400.3	79	gaG/gaC	4/23	1	2	FACETS	0.905	0.849	0.961	0.905	0.849	0.961	CLONAL	1	TRUE	1	0.831894524114959	2		709	606	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245907	46245907	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	116	368	0	ENST00000334344.6:c.4001G>A	p.Gly1334Glu	p.G1334E	ENST00000334344	NM_152641.2	1334	gGa/gAa	15/21	0.831894524114959	3	FACETS	0.975	0.886	1	0.488	0.443	0.534	CLONAL	1	TRUE	1	0.831894524114959	3		368	405	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094280	27094280	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0045215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	163	434	0	ENST00000324856.7:c.2989-1G>C		p.X997_splice	ENST00000324856	NM_006015.4	997			0.810433589294568	3	FACETS	1	0.977	1	0.57	0.527	0.614	CLONAL	1	TRUE	1	0.831894524114959	3		434	487	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332913	70332913	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	443	644	0	ENST00000373644.4:c.818T>G	p.Leu273Trp	p.L273W	ENST00000373644	NM_030625.2	273	tTg/tGg	2/12	0.831894524114959	3	FACETS	0.9	0.865	0.935	0.9	0.865	0.935	CLONAL	2	TRUE	1	0.831894524114959	3		644	838	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941029	71941029	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	321	1001	1	ENST00000298229.2:c.905G>T	p.Arg302Leu	p.R302L	ENST00000298229	NM_001567.3	302	cGt/cTt	8/28	0.621928669010089	4	FACETS	1	0.992	1	0.432	0.408	0.457	CLONAL	1	TRUE	1	0.831894524114959	4		1002	1091	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949347	71949347	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	266	871	0	ENST00000298229.2:c.3727G>T	p.Asp1243Tyr	p.D1243Y	ENST00000298229	NM_001567.3	1243	Gac/Tac	28/28	0.621928669010089	4	FACETS	1	0.991	1	0.431	0.404	0.457	CLONAL	1	TRUE	1	0.831894524114959	4		871	907	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18649015	18649015	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	74	366	0	ENST00000266497.5:c.2690C>G	p.Ser897Cys	p.S897C	ENST00000266497		897	tCt/tGt	19/31	0.215405176809371	3	FACETS	0.829	0.732	0.93	0.276	0.244	0.31	INDETERMINATE	1	TRUE	0	0.831894524114959	3		366	304	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103520547	103520547	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	210	357	0	ENST00000355739.4:c.2618C>A	p.Thr873Asn	p.T873N	ENST00000355739	NM_000123.3	873	aCc/aAc	12/15	0.745180483481412	2	FACETS	0.867	0.829	0.904	0.867	0.829	0.904	CLONAL	2	TRUE	0	0.831894524114959	2		357	291	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582968	95582968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	173	349	2	ENST00000393063.1:c.1574G>A	p.Gly525Asp	p.G525D	ENST00000393063	NM_030621.3	525	gGt/gAt	11/28	0.773912201941884	2	FACETS	0.874	0.831	0.914	0.874	0.831	0.914	CLONAL	2	TRUE	0	0.831894524114959	2		351	238	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245971	41245971	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	487	740	1	ENST00000357654.3:c.1577A>G	p.Gln526Arg	p.Q526R	ENST00000357654	NM_007294.3	526	cAa/cGa	10/23	0.621928669010089	4	FACETS	0.87	0.839	0.9	0.87	0.839	0.9	CLONAL	3	TRUE	1	0.831894524114959	4		741	822	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119694	70119694	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1040106193	NA	P-0045215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	194	749	0	ENST00000245479.2:c.696G>C	p.Gln232His	p.Q232H	ENST00000245479	NM_000346.3	232	caG/caC	3/3	0.621928669010089	4	FACETS	0.812	0.751	0.876	0.271	0.25	0.292	CLONAL	1	TRUE	1	0.831894524114959	4		749	1052	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45371778	45371778	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	117	397	0	ENST00000262160.6:c.1213del	p.Val405SerfsTer4	p.V405Sfs*4	ENST00000262160	NM_005901.5	405	Gtc/tc	10/11	0.734135928553029	3	FACETS	0.842	0.764	0.924	0.421	0.382	0.462	CLONAL	1	TRUE	1	0.831894524114959	3		397	473	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130296	11130296	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	503	699	0	ENST00000358026.2:c.2539del	p.Gln847SerfsTer11	p.Q847Sfs*11	ENST00000358026	NM_001128849.1	845	gtC/gt	18/36	0.773912201941884	2	FACETS	0.909	0.885	0.933	0.909	0.885	0.933	CLONAL	2	TRUE	0	0.831894524114959	2		699	665	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953241	17953258	+	inframe_deletion	In_Frame_Del	DEL	CGGCTGGATCCAGCCGCT	CGGCTGGATCCAGCCGCT	-	novel	NA	P-0045215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	608	1053	1	ENST00000458235.1:c.728_745del	p.Glu243_Ala248del	p.E243_A248del	ENST00000458235	NM_000215.3	243	gAGCGGCTGGATCCAGCCGgg/ggg	6/24	0.773912201941884	2	FACETS	0.916	0.894	0.937	0.916	0.894	0.937	CLONAL	2	TRUE	0	0.831894524114959	2		1054	798	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449878	29449878	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	349	1054	0	ENST00000389048.3:c.2977G>C	p.Asp993His	p.D993H	ENST00000389048	NM_004304.4	993	Gac/Cac	18/29	0.753107333370738	3	FACETS	1	0.968	1	0.343	0.325	0.362	CLONAL	1	TRUE	0	0.831894524114959	3		1054	1155	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205850	128205850	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	289	432	0	ENST00000341105.2:c.25C>G	p.Arg9Gly	p.R9G	ENST00000341105	NM_032638.4	9	Cgc/Ggc	2/6	0.794563902473755	3	FACETS	0.976	0.931	1	0.976	0.931	1	CLONAL	2	TRUE	1	0.831894524114959	3		432	504	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456617	138456617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	163	556	0	ENST00000289153.2:c.733G>A	p.Asp245Asn	p.D245N	ENST00000289153	NM_006219.2	245	Gat/Aat	4/22	0.794563902473755	3	FACETS	0.949	0.875	1	0.474	0.437	0.512	CLONAL	1	TRUE	1	0.831894524114959	3		556	585	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540908	187540908	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	194	381	0	ENST00000441802.2:c.6832G>A	p.Asp2278Asn	p.D2278N	ENST00000441802	NM_005245.3	2278	Gat/Aat	10/27	0.228536300299268	3	FACETS	0.888	0.835	0.94	0.592	0.557	0.627	INDETERMINATE	2	TRUE	0	0.831894524114959	3		381	372	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526833	31526833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1314	275	890	0	ENST00000344624.3:c.207del	p.Asn70IlefsTer38	p.N70Ifs*38	ENST00000344624		69	ccC/cc	2/33	0.810352671545214	4	FACETS	0.762	0.713	0.813	0.254	0.237	0.271	SUBCLONAL	1	TRUE	1	0.831894524114959	4		890	1589	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672218	30672218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	252	880	0	ENST00000376406.3:c.4742C>T	p.Ser1581Phe	p.S1581F	ENST00000376406	NM_014641.2	1581	tCc/tTc	10/15	0.485319824610049	4	FACETS	0.918	0.858	0.98	0.459	0.429	0.49	INDETERMINATE	1	TRUE	2	0.831894524114959	4		880	1209	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553413	106553413	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs746589089	NA	P-0045215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	82	491	0	ENST00000369096.4:c.1378A>G	p.Met460Val	p.M460V	ENST00000369096	NM_001198.3	460	Atg/Gtg	5/7	0.485319824610049	4	FACETS	0.751	0.664	0.843	0.375	0.332	0.422	INDETERMINATE	1	TRUE	2	0.831894524114959	4		491	481	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151919139	151919139	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	149	257	0	ENST00000262189.6:c.3446A>G	p.Asp1149Gly	p.D1149G	ENST00000262189	NM_170606.2	1149	gAc/gGc	22/59	0.485319824610049	4	FACETS	0.873	0.807	0.939	0.873	0.807	0.939	INDETERMINATE	2	TRUE	2	0.831894524114959	4		257	376	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772998	135772998	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs397514847	NA	P-0045215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	39	159	0	ENST00000298552.3:c.2626-1G>A		p.X876_splice	ENST00000298552	NM_001162426.1	876			1	2	FACETS	0.852	0.726	0.985	0.852	0.726	0.985	CLONAL	1	TRUE	1	0.831894524114959	2		159	110	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797355	135797355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs952813051	NA	P-0045215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	119	310	2	ENST00000298552.3:c.514G>A	p.Val172Met	p.V172M	ENST00000298552	NM_001162426.1	172	Gtg/Atg	7/23	1	2	FACETS	0.9	0.823	0.978	0.9	0.823	0.978	CLONAL	1	TRUE	1	0.831894524114959	2		312	318	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450758	70450771	+	frameshift_variant	Frame_Shift_Del	DEL	AACAGCCTCATGCG	AACAGCCTCATGCG	T	novel	NA	P-0045215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	147	540	0	ENST00000373644.4:c.5598_5611delinsT	p.Thr1867GlyfsTer47	p.T1867Gfs*47	ENST00000373644	NM_030625.2	1866	gcAACAGCCTCATGCGgg/gcTgg	12/12	0.831894524114959	3	FACETS	0.781	0.715	0.849	0.39	0.357	0.425	SUBCLONAL	1	TRUE	1	0.831894524114959	3		540	641	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525838	148525838	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554498830	NA	P-0045217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	35	277	0	ENST00000320356.2:c.619C>T	p.Arg207Ter	p.R207*	ENST00000320356	NM_004456.4	207	Cga/Tga	6/20	0.458202338678639	5	FACETS	1	0.941	1	0.825	0.702	0.95	CLONAL	2	FALSE	2	0.73400826924574	5		277	81	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420191	88420191	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	256	456	0	ENST00000360948.2:c.2495C>A	p.Pro832Gln	p.P832Q	ENST00000360948	NM_001012338.2	832	cCa/cAa	19/19	0.367759057917388	4	FACETS	0.856	0.813	0.899	1	0.993	1	INDETERMINATE	3	FALSE	2	0.73400826924574	4		456	471	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015347	176015347	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	39	336	0	ENST00000367669.3:c.1391A>G	p.Glu464Gly	p.E464G	ENST00000367669	NM_022457.5	464	gAg/gGg	12/20	0.73400826924574	2	FACETS	0.886	0.784	0.981	0.886	0.784	0.981	CLONAL	2	FALSE	0	0.73400826924574	2		336	60	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196068	67196068	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs756293976	NA	P-0045217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	211	630	0	ENST00000312629.5:c.52G>C	p.Glu18Gln	p.E18Q	ENST00000312629	NM_003952.2	18	Gag/Cag	1/15	0.73400826924574	3	FACETS	0.737	0.684	0.792	0.368	0.342	0.396	SUBCLONAL	1	FALSE	1	0.73400826924574	3		630	1067	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954151	32954151	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786203001	NA	P-0045217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	32	395	0	ENST00000380152.3:c.9125A>G	p.Asp3042Gly	p.D3042G	ENST00000380152		3042	gAt/gGt	24/27	0.73400826924574	3	FACETS	1	0.925	1	0.608	0.507	0.715	CLONAL	1	FALSE	1	0.73400826924574	3		395	98	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647631	23647632	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	30	360	1	ENST00000261584.4:c.235dup	p.Tyr79LeufsTer2	p.Y79Lfs*2	ENST00000261584	NM_024675.3	79	tat/tTat	4/13	0.271658015332916	5	FACETS	0.881	0.743	1	0.881	0.743	1	INDETERMINATE	3	FALSE	2	0.73400826924574	5		361	65	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533517	63533517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145717795	NA	P-0045217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	373	755	1	ENST00000307078.5:c.1637G>A	p.Gly546Asp	p.G546D	ENST00000307078	NM_004655.3	546	gGc/gAc	6/11	0.27972475910825	4	FACETS	0.935	0.891	0.98	0.935	0.891	0.98	INDETERMINATE	2	FALSE	2	0.73400826924574	4		756	942	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464432	25464433	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0045217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	428	430	0	ENST00000264709.3:c.2079_2080dup	p.His694ArgfsTer12	p.H694Rfs*12	ENST00000264709	NM_175629.2	694	cat/cGCat	17/23	0.73400826924574	5	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	FALSE	2	0.73400826924574	5		430	753	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26055512	26056015	+	coding_sequence_variant,3_prime_UTR_variant	In_Frame_Del	DEL	AGAGAAAAGAGGCAAAACTTTTAAGTCACAGTAAAGCAAAAAACACAGAATAAGCAACGTCTTCCACCATCCAATTAAATACAGAATGAAAGTCATGTACTAGAAGAACGGACCAACCCGGGAGCAGGGCGGGACTTTTGAAAATTTTTTAGTCCAATCCGGACATCCCTTTAGACTAAGAAACTGGCTCTTGTTTTGCGGTCTTTTCTGCCGTTCACAGGCCTGGGGCGGGACTGCCATCCCAAAACCATCCGCCAGCGAGAAAAGCCTCCGGTCAGGGACCTAGAAGCCGCAATAAAGGTTTAAATGCTGTAACCTCACCACGGCCACTCTCCAACCCCGTCACCCAATTCGTCTGATACCTCAGTAACTCCCATACGACTAACCTTAAGTAACAGGGCAGAACAAGAAAAGGCAGATAGTAAAGAAATTATCCAGCTCTTTTATTGAGATCAGTGGTGGCTCTGAAAAGAGCCTTTTGGGTTTTAGAAGTAGGCGTTCGCC	AGAGAAAAGAGGCAAAACTTTTAAGTCACAGTAAAGCAAAAAACACAGAATAAGCAACGTCTTCCACCATCCAATTAAATACAGAATGAAAGTCATGTACTAGAAGAACGGACCAACCCGGGAGCAGGGCGGGACTTTTGAAAATTTTTTAGTCCAATCCGGACATCCCTTTAGACTAAGAAACTGGCTCTTGTTTTGCGGTCTTTTCTGCCGTTCACAGGCCTGGGGCGGGACTGCCATCCCAAAACCATCCGCCAGCGAGAAAAGCCTCCGGTCAGGGACCTAGAAGCCGCAATAAAGGTTTAAATGCTGTAACCTCACCACGGCCACTCTCCAACCCCGTCACCCAATTCGTCTGATACCTCAGTAACTCCCATACGACTAACCTTAAGTAACAGGGCAGAACAAGAAAAGGCAGATAGTAAAGAAATTATCCAGCTCTTTTATTGAGATCAGTGGTGGCTCTGAAAAGAGCCTTTTGGGTTTTAGAAGTAGGCGTTCGCC	-	novel	NA	P-0045217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	1	70	0				ENST00000343677	NM_005319.3	214		1/1	0.73400826924574	2	FACETS	0.047	0.01	0.125	0.023	0.005	0.063	SUBCLONAL	1	FALSE	0	0.73400826924574	2		70	58	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026871	6026871	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	644	570	0	ENST00000265849.7:c.1525C>T	p.Pro509Ser	p.P509S	ENST00000265849	NM_000535.5	509	Cca/Tca	11/15	0.73400826924574	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	FALSE	0	0.73400826924574	3		570	759	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995491	68995491	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	15	464	0	ENST00000288368.4:c.1895T>C	p.Val632Ala	p.V632A	ENST00000288368	NM_024870.2	632	gTc/gCc	18/40	0.629738897601589	4	FACETS	0.472	0.347	0.621	0.236	0.173	0.311	SUBCLONAL	1	FALSE	2	0.73400826924574	4		464	150	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430650	80430650	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	33	411	0	ENST00000286548.4:c.358A>G	p.Lys120Glu	p.K120E	ENST00000286548	NM_002072.3	120	Aag/Gag	3/7	0.73400826924574	2	FACETS	0.803	0.669	0.946	0.401	0.334	0.473	CLONAL	1	FALSE	0	0.73400826924574	2		411	112	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342618	87342618	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	128	444	0	ENST00000277120.3:c.903G>C	p.Trp301Cys	p.W301C	ENST00000277120		301	tgG/tgC	9/19	0.73400826924574	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	FALSE	0	0.73400826924574	2		444	174	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564164	139564164	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	413	926	2	ENST00000308874.7:c.304T>C	p.Cys102Arg	p.C102R	ENST00000308874		102	Tgt/Cgt	5/10	0.458202338678639	5	FACETS	0.962	0.916	1	0.641	0.611	0.672	CLONAL	2	FALSE	2	0.73400826924574	5		928	1229	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0045218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	415	798	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.324339173471109	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.330688577619875	2		798	1036	SUCCESS
APC	324	MSKCC	GRCh37	5	112175255	112175255	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	59	255	1	ENST00000257430.4:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000257430	NM_000038.5	1322	Gaa/Taa	16/16	0.151888439225151	3	FACETS	1	0.963	1			1	INDETERMINATE	1	TRUE	NA	0.330688577619875	3		256	307	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300489	11300489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1350423605	NA	P-0045218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	140	893	0	ENST00000361445.4:c.1657C>T	p.Arg553Cys	p.R553C	ENST00000361445	NM_004958.3	553	Cgc/Tgc	11/58	0.330688577619875	1	FACETS	0.848	0.773	0.928	0.848	0.773	0.928	CLONAL	1	TRUE	0	0.330688577619875	1		893	833	SUCCESS
APC	324	MSKCC	GRCh37	5	112151261	112151261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854568	NA	P-0045218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	66	339	0	ENST00000257430.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000257430	NM_000038.5	302	Cga/Tga	9/16	0.151888439225151	3	FACETS	1	0.93	1			1	INDETERMINATE	1	TRUE	NA	0.330688577619875	3		339	421	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948799	71948799	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1254	269	1037	1	ENST00000298229.2:c.3514del	p.Arg1172AlafsTer30	p.R1172Afs*30	ENST00000298229	NM_001567.3	1171	Ccc/cc	26/28	0.330688577619875	3	FACETS	1	0.989	1	0.622	0.582	0.664	CLONAL	1	TRUE	1	0.330688577619875	3		1038	1523	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100093	157100117	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGCGGCGGCGGCAGCAGCAGGAG	GCGGCGGCGGCGGCAGCAGCAGGAG	-	novel	NA	P-0045218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	24	31	0	ENST00000346085.5:c.1044_1068del	p.Ala350MetfsTer11	p.A350Mfs*11	ENST00000346085	NM_020732.3	344	GCGGCGGCGGCGGCAGCAGCAGGAGgc/gc	1/20	0.330688577619875	3	FACETS	0.895	0.73	1	1	0.928	1	CLONAL	3	TRUE	1	0.330688577619875	3		31	63	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981981	70981981	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1693	452	1096	1	ENST00000276594.2:c.115T>C	p.Tyr39His	p.Y39H	ENST00000276594	NM_024504.3	39	Tac/Cac	2/8	0.330688577619875	6	FACETS	1	0.981	1	0.529	0.503	0.556	CLONAL	2	TRUE	2	0.330688577619875	6		1097	2145	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0045219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	175	347	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.318917300351994	4	FACETS	0.858	0.796	0.922	0.858	0.796	0.922	CLONAL	3	TRUE	1	0.339699974245796	4		347	536	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161298205	161298205	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs747828462	NA	P-0045219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	53	459	1	ENST00000367975.2:c.97A>G	p.Thr33Ala	p.T33A	ENST00000367975	NM_003001.3	33	Acg/Gcg	3/6	0.339699974245796	5	FACETS	0.69	0.587	0.802	0.23	0.195	0.268	SUBCLONAL	1	TRUE	2	0.339699974245796	5		460	683	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999279	100999279	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	187	869	0	ENST00000325455.5:c.523A>C	p.Ser175Arg	p.S175R	ENST00000325455	NM_001202474.3	175	Agc/Cgc	1/8	0.259659705679649	4	FACETS	0.925	0.856	0.997	0.925	0.856	0.997	CLONAL	2	TRUE	2	0.339699974245796	4		869	797	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611370	28611370	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	76	486	0	ENST00000241453.7:c.1261G>T	p.Glu421Ter	p.E421*	ENST00000241453	NM_004119.2	421	Gaa/Taa	10/24	0.310337088490372	1	FACETS	0.737	0.648	0.832	0.737	0.648	0.832	SUBCLONAL	1	TRUE	0	0.339699974245796	1		486	504	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130390	29130390	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0045219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	70	433	0	ENST00000328354.6:c.319+1G>T		p.X107_splice	ENST00000328354	NM_007194.3	107			0.249461680150867	1	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	0	0.339699974245796	1		433	329	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936017	49936017	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	87	834	0	ENST00000296474.3:c.1653G>T	p.Met551Ile	p.M551I	ENST00000296474	NM_002447.2	551	atG/atT	4/20	0.146569492508534	3	FACETS	1	0.936	1	0.361	0.32	0.404	INDETERMINATE	1	TRUE	0	0.339699974245796	3		834	554	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356236	66356236	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	169	523	0	ENST00000273854.3:c.1261C>A	p.Leu421Met	p.L421M	ENST00000273854	NM_004439.5	421	Ctg/Atg	5/18	0.267965046431076	3	FACETS	0.988	0.913	1	0.988	0.913	1	CLONAL	2	TRUE	1	0.339699974245796	3		523	589	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519707	176519707	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	108	700	0	ENST00000292408.4:c.979G>C	p.Asp327His	p.D327H	ENST00000292408	NM_213647.1	327	Gac/Cac	8/18	0.131943685291914	4	FACETS	0.824	0.742	0.909	0.824	0.742	0.909	INDETERMINATE	2	TRUE	2	0.339699974245796	4		700	517	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180050998	180050998	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	150	831	0	ENST00000261937.6:c.1485G>T	p.Gln495His	p.Q495H	ENST00000261937	NM_182925.4	495	caG/caT	11/30	0.131943685291914	4	FACETS	0.945	0.867	1	0.945	0.867	1	INDETERMINATE	2	TRUE	2	0.339699974245796	4		831	626	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158689	26158689	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	17	130	0	ENST00000289316.2:c.292G>T	p.Ala98Ser	p.A98S	ENST00000289316	NM_138720.2	98	Gcc/Tcc	1/2	1	2	FACETS	1	0.766	1	1	0.766	1	CLONAL	1	TRUE	1	0.339699974245796	2		130	99	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171979	32171979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	53	543	0	ENST00000375023.3:c.3053C>T	p.Thr1018Ile	p.T1018I	ENST00000375023	NM_004557.3	1018	aCa/aTa	19/30	0.199293321296535	0	FACETS	0.636	0.545	0.734			1	INDETERMINATE	1	TRUE	0	0.339699974245796	0		543	324	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045187	47045187	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	154	585	0	ENST00000377604.3:c.2428G>T	p.Glu810Ter	p.E810*	ENST00000377604	NM_001204468.1	810	Gag/Tag	21/24	0.131943685291914	4	FACETS	1	0.969	1	1	0.969	1	INDETERMINATE	2	TRUE	2	0.339699974245796	4		585	550	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799300	42799300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1158987717	NA	P-0045219-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	114	563	7	ENST00000575354.2:c.4790del	p.Pro1597HisfsTer23	p.P1597Hfs*23	ENST00000575354	NM_015125.3	1595	tCc/tc	20/20	0.174926690924176	3	FACETS	0.872	0.797	0.949	0.872	0.797	0.949	INDETERMINATE	3	TRUE	0	0.339699974245796	3		570	300	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	59	500	1	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.894	0.767	1	0.894	0.767	1	CLONAL	1	TRUE	1	0.15	2		501	880	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121913370	NA	P-0045220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	33	235	0	ENST00000288602.6:c.1742A>G	p.Asn581Ser	p.N581S	ENST00000288602	NM_004333.4	581	aAt/aGt	15/18	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.15	2		235	383	SUCCESS
APC	324	MSKCC	GRCh37	5	112175530	112175530	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	21	328	0	ENST00000257430.4:c.4240del	p.Val1414Ter	p.V1414*	ENST00000257430	NM_000038.5	1413	atG/at	16/16	1	2	FACETS	0.787	0.605	0.998	0.787	0.605	0.998	CLONAL	1	TRUE	1	0.15	2		328	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578404	+	inframe_deletion	In_Frame_Del	DEL	GCA	GCA	-	novel	NA	P-0045220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	63	600	0	ENST00000269305.4:c.526_528del	p.Cys176del	p.C176del	ENST00000269305	NM_001126112.2	176	TGC/-	5/11	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.15	2		600	759	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845229	151845229	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	31	413	0	ENST00000262189.6:c.13783C>T	p.Arg4595Cys	p.R4595C	ENST00000262189	NM_170606.2	4595	Cgc/Tgc	52/59	1	2	FACETS	0.833	0.673	1	0.833	0.673	1	CLONAL	1	TRUE	1	0.15	2		413	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0045221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	305	667	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.471458990242159	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.471458990242159	1		669	956	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0045221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	149	494	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.261686177131277	1	FACETS	0.763	0.7	0.829	0.763	0.7	0.829	INDETERMINATE	1	TRUE	0	0.471458990242159	1		494	633	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604785	48604785	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	133	411	0	ENST00000342988.3:c.1607T>G	p.Leu536Arg	p.L536R	ENST00000342988	NM_005359.5	536	cTa/cGa	12/12	0.471458990242159	1	FACETS	0.956	0.875	1	0.956	0.875	1	CLONAL	1	TRUE	0	0.471458990242159	1		411	451	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808853	3808853	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0045221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	81	439	0	ENST00000262367.5:c.3369+2T>G		p.X1123_splice	ENST00000262367	NM_004380.2	1123			0.261686177131277	1	FACETS	0.46	0.406	0.518	0.46	0.406	0.518	INDETERMINATE	1	TRUE	0	0.471458990242159	1		439	571	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765717	41765717	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1466592724	NA	P-0045221-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	204	663	1	ENST00000301178.4:c.2593C>T	p.Arg865Cys	p.R865C	ENST00000301178	NM_021913.4	865	Cgc/Tgc	20/20	0.471458990242159	1	FACETS	0.936	0.871	1	0.936	0.871	1	CLONAL	1	TRUE	0	0.471458990242159	1		664	707	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	111	278	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.741	0.671	0.813	0.741	0.671	0.813	SUBCLONAL	1	TRUE	1	0.729250124538589	2		278	411	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	370	457	1	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.824	0.791	0.856	1	0.996	1	CLONAL	2	TRUE	1	0.729250124538589	2		458	616	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	521	606	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.811	0.784	0.838	1	0.997	1	CLONAL	2	TRUE	1	0.729250124538589	2		610	881	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	215	354	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.729250124538589	3	FACETS	0.766	0.719	0.814	0.766	0.719	0.814	SUBCLONAL	2	TRUE	1	0.729250124538589	3		354	525	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	190	609	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.778	0.722	0.835	0.778	0.722	0.835	SUBCLONAL	1	TRUE	1	0.729250124538589	2		610	670	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	185	665	3	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.771	0.715	0.829	0.771	0.715	0.829	SUBCLONAL	1	TRUE	1	0.729250124538589	2		668	658	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244156	153244156	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	191	483	0	ENST00000281708.4:c.2001del	p.Ser668ValfsTer39	p.S668Vfs*39	ENST00000281708	NM_033632.3	667	ggG/gg	12/12	1	2	FACETS	0.729	0.676	0.783	0.729	0.676	0.783	SUBCLONAL	1	TRUE	1	0.729250124538589	2		483	719	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495023	56495023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs2271188	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	613	656	1	ENST00000267101.3:c.3380G>A	p.Arg1127His	p.R1127H	ENST00000267101	NM_001982.3	1127	cGc/cAc	27/28	0.729250124538589	3	FACETS	0.993	0.96	1	0.993	0.96	1	CLONAL	2	TRUE	1	0.729250124538589	3		657	1155	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	258	742	0	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	0.729250124538589	3	FACETS	0.766	0.716	0.817	0.383	0.358	0.409	SUBCLONAL	1	TRUE	1	0.729250124538589	3		742	1261	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	56	143	1	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	1	FACETS	0.687	0.604	0.773	0.687	0.604	0.773	SUBCLONAL	1	TRUE	0	0.729250124538589	1		144	142	SUCCESS
APC	324	MSKCC	GRCh37	5	112136980	112136980	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1554076133	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	112	353	0	ENST00000257430.4:c.734C>A	p.Ser245Ter	p.S245*	ENST00000257430	NM_000038.5	245	tCa/tAa	8/16	1	2	FACETS	0.788	0.715	0.863	0.788	0.715	0.863	SUBCLONAL	1	TRUE	1	0.729250124538589	2		353	390	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965666	90965666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	116	321	1	ENST00000265433.3:c.1651del	p.Arg551GlyfsTer8	p.R551Gfs*8	ENST00000265433	NM_002485.4	551	Agg/gg	11/16	1	2	FACETS	0.767	0.696	0.84	0.767	0.696	0.84	SUBCLONAL	1	TRUE	1	0.729250124538589	2		322	415	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	190	429	13	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	0.921	0.857	0.986	0.921	0.857	0.986	CLONAL	1	TRUE	1	0.729250124538589	2		442	566	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255142	16255143	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	rs764595221	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	169	433	4	ENST00000375759.3:c.2417_2418del	p.Arg806ThrfsTer14	p.R806Tfs*14	ENST00000375759	NM_015001.2	803	GAg/g	11/15	1	2	FACETS	0.77	0.711	0.83	0.77	0.711	0.83	SUBCLONAL	1	TRUE	1	0.729250124538589	2		437	602	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411246	63411246	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	286	379	0	ENST00000330258.3:c.1921C>T	p.Arg641Ter	p.R641*	ENST00000330258	NM_152424.3	641	Cga/Tga	2/2	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.729250124538589	1		379	428	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029445	16029446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	144	383	2	ENST00000268712.3:c.1584dup	p.Glu529ArgfsTer7	p.E529Rfs*7	ENST00000268712	NM_006311.3	528	-/A	15/46	1	2	FACETS	0.745	0.683	0.809	0.745	0.683	0.809	SUBCLONAL	1	TRUE	1	0.729250124538589	2		385	530	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864148	57864148	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766159479	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	460	606	0	ENST00000228682.2:c.1625G>A	p.Arg542His	p.R542H	ENST00000228682	NM_005269.2	542	cGc/cAc	12/12	0.729250124538589	3	FACETS	0.867	0.832	0.902	0.867	0.832	0.902	CLONAL	2	TRUE	1	0.729250124538589	3		606	993	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661663	227661664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761880048	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	205	486	5	ENST00000305123.5:c.1791dup	p.His598AlafsTer13	p.H598Afs*13	ENST00000305123	NM_005544.2	597	-/G	1/2	NA	2	FACETS	0.744	0.692	0.797			1	INDETERMINATE	1	TRUE	NA	0.729250124538589	2		491	756	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821638	72821638	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs200561133	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	16	87	0	ENST00000268489.5:c.10537A>G	p.Ser3513Gly	p.S3513G	ENST00000268489	NM_006885.3	3513	Agt/Ggt	10/10	1	2	FACETS	0.472	0.354	0.607	0.472	0.354	0.607	SUBCLONAL	1	TRUE	1	0.729250124538589	2		87	93	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753011	57753012	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	129	346	5	ENST00000274289.3:c.1004dup	p.Leu335PhefsTer12	p.L335Ffs*12	ENST00000274289	NM_006622.3	335	ttg/ttTg	7/14	1	2	FACETS	0.743	0.678	0.811	0.743	0.678	0.811	SUBCLONAL	1	TRUE	1	0.729250124538589	2		351	476	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346157	89346158	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs878855327	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	116	330	0	ENST00000301030.4:c.6792dup	p.Ala2265ArgfsTer8	p.A2265Rfs*8	ENST00000301030	NM_001256183.1	2264	-/C	9/13	1	2	FACETS	0.874	0.796	0.955	0.874	0.796	0.955	CLONAL	1	TRUE	1	0.729250124538589	2		330	364	SUCCESS
APC	324	MSKCC	GRCh37	5	112175969	112175970	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1114167552	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	94	255	0	ENST00000257430.4:c.4682dup	p.Asp1562GlyfsTer5	p.D1562Gfs*5	ENST00000257430	NM_000038.5	1560	gaa/gAaa	16/16	1	2	FACETS	0.728	0.654	0.806	0.728	0.654	0.806	SUBCLONAL	1	TRUE	1	0.729250124538589	2		255	354	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67646013	67646014	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs1470210640	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	160	431	6	ENST00000264010.4:c.950_951del	p.Thr317ArgfsTer91	p.T317Rfs*91	ENST00000264010	NM_006565.3	314	aAC/a	4/12	1	2	FACETS	0.764	0.705	0.826	0.764	0.705	0.826	SUBCLONAL	1	TRUE	1	0.729250124538589	2		437	574	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793253	33793253	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs137852728	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	75	139	0	ENST00000498907.2:c.68del	p.Pro23ArgfsTer137	p.P23Rfs*137	ENST00000498907	NM_004364.3	23	cCg/cg	1/1	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.729250124538589	2		139	177	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936083	178936083	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519927	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	198	580	0	ENST00000263967.3:c.1625A>G	p.Glu542Gly	p.E542G	ENST00000263967	NM_006218.2	542	gAa/gGa	10/21	1	2	FACETS	0.986	0.92	1	0.986	0.92	1	CLONAL	1	TRUE	1	0.729250124538589	2		580	551	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748660	43748661	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	275	863	2	ENST00000382044.4:c.2145dup	p.Glu716ArgfsTer9	p.E716Rfs*9	ENST00000382044	NM_001141980.1	715	-/A	12/28	1	2	FACETS	0.734	0.689	0.779	0.734	0.689	0.779	SUBCLONAL	1	TRUE	1	0.729250124538589	2		865	1028	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519504	137519505	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	147	319	0	ENST00000367739.4:c.1132_1133dup	p.Ser378ArgfsTer6	p.S378Rfs*6	ENST00000367739	NM_000416.2	378	agt/agAGt	7/7	1	2	FACETS	0.795	0.731	0.862	0.795	0.731	0.862	SUBCLONAL	1	TRUE	1	0.729250124538589	2		319	507	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323315	31323315	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	112	439	0	ENST00000412585.2:c.674T>C	p.Leu225Pro	p.L225P	ENST00000412585	NM_005514.6	225	cTg/cCg	4/8	0.63645035839328	1	FACETS	0.593	0.54	0.648	0.593	0.54	0.648	SUBCLONAL	1	TRUE	0	0.729250124538589	1		439	329	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026709	6026709	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587778618	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	332	765	0	ENST00000265849.7:c.1687C>T	p.Arg563Ter	p.R563*	ENST00000265849	NM_000535.5	563	Cga/Tga	11/15	1	2	FACETS	0.973	0.922	1	0.973	0.922	1	CLONAL	1	TRUE	1	0.729250124538589	2		765	936	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800429	32800429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750440758	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	420	940	4	ENST00000374899.4:c.1118G>A	p.Arg373His	p.R373H	ENST00000374899	NM_018833.2	373	cGc/cAc	6/12	1	2	FACETS	0.942	0.898	0.986	0.942	0.898	0.986	CLONAL	1	TRUE	1	0.729250124538589	2		944	1223	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972449	32972449	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	236	554	0	ENST00000380152.3:c.9799A>G	p.Lys3267Glu	p.K3267E	ENST00000380152		3267	Aag/Gag	27/27	1	2	FACETS	0.877	0.822	0.934	0.877	0.822	0.934	CLONAL	1	TRUE	1	0.729250124538589	2		554	738	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991847	72991847	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	253	697	0	ENST00000268489.5:c.2198A>G	p.Tyr733Cys	p.Y733C	ENST00000268489	NM_006885.3	733	tAc/tGc	2/10	1	2	FACETS	0.829	0.778	0.881	0.829	0.778	0.881	CLONAL	1	TRUE	1	0.729250124538589	2		697	837	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254644	10254644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148038464	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	168	498	0	ENST00000340748.4:c.2866G>A	p.Val956Met	p.V956M	ENST00000340748		956	Gtg/Atg	28/40	1	2	FACETS	0.817	0.755	0.88	0.817	0.755	0.88	CLONAL	1	TRUE	1	0.729250124538589	2		498	564	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032293	11032293	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	213	603	0	ENST00000327064.4:c.1687T>C	p.Ser563Pro	p.S563P	ENST00000327064	NM_199141.1	563	Tcc/Ccc	16/16	1	2	FACETS	0.844	0.788	0.902	0.844	0.788	0.902	CLONAL	1	TRUE	1	0.729250124538589	2		603	692	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070926	30070926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	204	573	1	ENST00000338641.4:c.1442A>G	p.Tyr481Cys	p.Y481C	ENST00000338641	NM_000268.3	481	tAc/tGc	13/16	1	2	FACETS	0.822	0.765	0.879	0.822	0.765	0.879	CLONAL	1	TRUE	1	0.729250124538589	2		574	681	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280778	41280778	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	57	465	0	ENST00000349496.5:c.2291A>C	p.Asp764Ala	p.D764A	ENST00000349496	NM_001904.3	764	gAt/gCt	15/15	1	2	FACETS	0.281	0.241	0.325	0.281	0.241	0.325	SUBCLONAL	1	TRUE	1	0.729250124538589	2		465	556	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430208	181430208	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	117	417	0	ENST00000325404.1:c.60del	p.Gly21AlafsTer25	p.G21Afs*25	ENST00000325404	NM_003106.3	20	ggC/gg	1/1	1	2	FACETS	0.771	0.701	0.844	0.771	0.701	0.844	SUBCLONAL	1	TRUE	1	0.729250124538589	2		417	416	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409260	31409260	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	160	446	0	ENST00000344624.3:c.3757A>G	p.Ile1253Val	p.I1253V	ENST00000344624		1253	Att/Gtt	30/33	1	2	FACETS	0.847	0.782	0.914	0.847	0.782	0.914	CLONAL	1	TRUE	1	0.729250124538589	2		446	518	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31421429	31421429	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	162	463	1	ENST00000344624.3:c.3475A>C	p.Thr1159Pro	p.T1159P	ENST00000344624		1159	Aca/Cca	27/33	1	2	FACETS	0.803	0.741	0.867	0.803	0.741	0.867	CLONAL	1	TRUE	1	0.729250124538589	2		464	553	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0045224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	15	354	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.189383276596054	3	FACETS	0.916	0.678	1	0.458	0.339	0.597	INDETERMINATE	1	TRUE	1	0.357596275195562	3		354	108	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0045224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	28	556	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.227714941065467	1	FACETS	0.519	0.416	0.634	0.519	0.416	0.634	SUBCLONAL	1	TRUE	0	0.357596275195562	1		556	248	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420499	49420499	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	33	600	0	ENST00000301067.7:c.15250C>G	p.Leu5084Val	p.L5084V	ENST00000301067	NM_003482.3	5084	Ctg/Gtg	48/54	0.189383276596054	3	FACETS	0.78	0.638	0.939	0.39	0.319	0.47	INDETERMINATE	1	TRUE	1	0.357596275195562	3		600	279	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858369	27858369	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1238244292	NA	P-0045224-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	30	507	0	ENST00000359303.2:c.202T>C	p.Phe68Leu	p.F68L	ENST00000359303	NM_003535.2	68	Ttt/Ctt	1/1	0.343870068377863	4	FACETS	0.772	0.624	0.939	0.386	0.312	0.47	CLONAL	1	TRUE	2	0.357596275195562	4		507	295	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	222	425	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.795	0.745	0.845	1	0.993	1	SUBCLONAL	2	TRUE	1	0.48422694827455	2		425	577	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1343	56	591	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.136079632794098	6	FACETS	0.325	0.277	0.379			1	INDETERMINATE	1	TRUE	NA	0.48422694827455	6		591	1399	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	24	457	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.167	0.13	0.21	0.167	0.13	0.21	SUBCLONAL	1	TRUE	1	0.48422694827455	2		457	592	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123705	11123705	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	58	620	0	ENST00000358026.2:c.2355G>C	p.Lys785Asn	p.K785N	ENST00000358026	NM_001128849.1	785	aaG/aaC	16/36	0.472125145705237	2	FACETS	0.262	0.224	0.303	0.131	0.112	0.152	SUBCLONAL	1	TRUE	0	0.48422694827455	2		620	915	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29107910	29107910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	112	475	0	ENST00000328354.6:c.779C>T	p.Ser260Leu	p.S260L	ENST00000328354	NM_007194.3	260	tCa/tTa	6/15	1	2	FACETS	0.775	0.699	0.855	0.775	0.699	0.855	SUBCLONAL	1	TRUE	1	0.48422694827455	2		475	597	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866444	37866444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	777	856	0	ENST00000269571.5:c.749C>T	p.Ser250Phe	p.S250F	ENST00000269571		250	tCt/tTt	6/27	0.136079632794098	6	FACETS	1	0.983	1			1	INDETERMINATE	4	TRUE	NA	0.48422694827455	6		856	1550	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158626	26158626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772836222	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	102	273	0	ENST00000289316.2:c.229G>A	p.Glu77Lys	p.E77K	ENST00000289316	NM_138720.2	77	Gag/Aag	1/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.48422694827455	2		273	344	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	133	742	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	1	2	FACETS	0.582	0.528	0.639	0.582	0.528	0.639	SUBCLONAL	1	TRUE	1	0.48422694827455	2		742	944	SUCCESS
APC	324	MSKCC	GRCh37	5	112175945	112175945	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	22	277	0	ENST00000257430.4:c.4654G>T	p.Glu1552Ter	p.E1552*	ENST00000257430	NM_000038.5	1552	Gag/Tag	16/16	0.48422694827455	1	FACETS	0.282	0.219	0.355	0.282	0.219	0.355	SUBCLONAL	1	TRUE	0	0.48422694827455	1		277	244	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	163	239	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	1	1	FACETS	0.82	0.768	0.873	1	0.992	1	CLONAL	2	TRUE	0	0.48422694827455	1		239	311	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216125	7216125	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	41	403	1	ENST00000380728.2:c.934C>T	p.Arg312Trp	p.R312W	ENST00000380728		312	Cgg/Tgg	11/11	0.422086558140881	1	FACETS	0.246	0.204	0.292	0.246	0.204	0.292	SUBCLONAL	1	TRUE	0	0.48422694827455	1		404	522	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965728	90965728	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs920311188	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	45	288	0	ENST00000265433.3:c.1589C>A	p.Ser530Tyr	p.S530Y	ENST00000265433	NM_002485.4	530	tCt/tAt	11/16	0.48422694827455	3	FACETS	0.65	0.548	0.762	0.325	0.274	0.381	SUBCLONAL	1	TRUE	1	0.48422694827455	3		288	355	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795066	42795066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537583557	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	101	909	0	ENST00000575354.2:c.2146C>T	p.Arg716Trp	p.R716W	ENST00000575354	NM_015125.3	716	Cgg/Tgg	10/20	0.393691997260904	2	FACETS	0.345	0.307	0.385	0.172	0.153	0.193	SUBCLONAL	1	TRUE	0	0.48422694827455	2		909	1210	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115252327	115252327	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	130	351	0	ENST00000369535.4:c.313G>C	p.Asp105His	p.D105H	ENST00000369535	NM_002524.4	105	Gac/Cac	4/7	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.48422694827455	2		351	475	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373322	118373322	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1414433521	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	127	457	0	ENST00000534358.1:c.6715C>G	p.Leu2239Val	p.L2239V	ENST00000534358	NM_005933.3	2239	Ctt/Gtt	27/36	1	2	FACETS	0.873	0.793	0.956	0.873	0.793	0.956	CLONAL	1	TRUE	1	0.48422694827455	2		457	601	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992171	72992171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	227	665	0	ENST00000268489.5:c.1874C>T	p.Ser625Phe	p.S625F	ENST00000268489	NM_006885.3	625	tCc/tTc	2/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.48422694827455	2		665	894	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202762	108202762	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1555124747	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	91	350	0	ENST00000278616.4:c.7786G>A	p.Glu2596Lys	p.E2596K	ENST00000278616	NM_000051.3	2596	Gag/Aag	52/63	1	2	FACETS	0.847	0.755	0.943	0.847	0.755	0.943	CLONAL	1	TRUE	1	0.48422694827455	2		350	444	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412929	49412929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	130	742	1	ENST00000418115.1:c.94G>A	p.Glu32Lys	p.E32K	ENST00000418115	NM_001664.2	32	Gag/Aag	2/5	1	2	FACETS	0.553	0.501	0.608	0.553	0.501	0.608	SUBCLONAL	1	TRUE	1	0.48422694827455	2		743	971	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991481	72991481	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	276	757	1	ENST00000268489.5:c.2564C>A	p.Ser855Ter	p.S855*	ENST00000268489	NM_006885.3	855	tCa/tAa	2/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.48422694827455	2		758	1047	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100212	30100212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	149	449	0	ENST00000331968.5:c.1408G>A	p.Glu470Lys	p.E470K	ENST00000331968	NM_002742.2	470	Gaa/Aaa	10/18	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.48422694827455	2		449	584	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720711	89720711	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	31	125	0	ENST00000371953.3:c.862G>C	p.Glu288Gln	p.E288Q	ENST00000371953	NM_000314.4	288	Gaa/Caa	8/9	1	2	FACETS	0.831	0.681	0.996	0.831	0.681	0.996	CLONAL	1	TRUE	1	0.48422694827455	2		125	154	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981641	101981641	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	22	91	0	ENST00000282441.5:c.62C>G	p.Ser21Trp	p.S21W	ENST00000282441	NM_001130145.2	21	tCg/tGg	1/9	1	2	FACETS	0.51	0.398	0.639	0.51	0.398	0.639	SUBCLONAL	1	TRUE	1	0.48422694827455	2		91	178	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102196060	102196060	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	103	298	0	ENST00000263464.3:c.820G>C	p.Glu274Gln	p.E274Q	ENST00000263464	NM_001165.4	274	Gag/Cag	2/9	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.48422694827455	2		298	402	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373830	118373830	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	99	288	0	ENST00000534358.1:c.7223C>G	p.Ser2408Cys	p.S2408C	ENST00000534358	NM_005933.3	2408	tCt/tGt	27/36	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.48422694827455	2		288	390	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623777	28623777	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	113	540	0	ENST00000241453.7:c.877G>C	p.Glu293Gln	p.E293Q	ENST00000241453	NM_004119.2	293	Gag/Cag	7/24	1	2	FACETS	0.744	0.671	0.821	0.744	0.671	0.821	SUBCLONAL	1	TRUE	1	0.48422694827455	2		540	627	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32905104	32905104	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	106	348	0	ENST00000380152.3:c.730G>C	p.Asp244His	p.D244H	ENST00000380152		244	Gat/Cat	9/27	1	2	FACETS	0.956	0.862	1	0.956	0.862	1	CLONAL	1	TRUE	1	0.48422694827455	2		348	458	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134335	41134335	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	155	473	0	ENST00000379561.5:c.1293G>C	p.Met431Ile	p.M431I	ENST00000379561	NM_002015.3	431	atG/atC	2/3	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.48422694827455	2		473	627	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436825	110436825	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	68	725	0	ENST00000375856.3:c.1576G>C	p.Glu526Gln	p.E526Q	ENST00000375856	NM_003749.2	526	Gag/Cag	1/2	1	2	FACETS	0.259	0.224	0.297	0.259	0.224	0.297	SUBCLONAL	1	TRUE	1	0.48422694827455	2		725	1085	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66737032	66737032	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	144	427	0	ENST00000307102.5:c.555G>C	p.Lys185Asn	p.K185N	ENST00000307102	NM_002755.3	185	aaG/aaC	5/11	1	2	FACETS	0.867	0.793	0.945	0.867	0.793	0.945	CLONAL	1	TRUE	1	0.48422694827455	2		427	686	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636800	2636800	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	251	708	0	ENST00000342085.4:c.1249C>G	p.His417Asp	p.H417D	ENST00000342085	NM_002613.4	417	Cac/Gac	11/14	1	2	FACETS	0.992	0.928	1	0.992	0.928	1	CLONAL	1	TRUE	1	0.48422694827455	2		708	1045	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640024	3640024	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	185	857	0	ENST00000294008.3:c.3615G>C	p.Gln1205His	p.Q1205H	ENST00000294008	NM_032444.2	1205	caG/caC	12/15	1	2	FACETS	0.769	0.709	0.83	0.769	0.709	0.83	SUBCLONAL	1	TRUE	1	0.48422694827455	2		857	994	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992384	72992384	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	306	866	0	ENST00000268489.5:c.1661C>T	p.Ser554Phe	p.S554F	ENST00000268489	NM_006885.3	554	tCt/tTt	2/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.48422694827455	2		866	1137	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348173	89348173	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	65	841	0	ENST00000301030.4:c.4777G>C	p.Glu1593Gln	p.E1593Q	ENST00000301030	NM_001256183.1	1593	Gag/Cag	9/13	1	2	FACETS	0.276	0.238	0.317	0.276	0.238	0.317	SUBCLONAL	1	TRUE	1	0.48422694827455	2		841	974	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89839793	89839793	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	259	747	0	ENST00000389301.3:c.1901-1G>C		p.X634_splice	ENST00000389301	NM_000135.2	634			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.48422694827455	2		747	1001	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579340	7579340	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	176	755	0	ENST00000269305.4:c.347C>G	p.Ser116Cys	p.S116C	ENST00000269305	NM_001126112.2	116	tCt/tGt	4/11	0.422086558140881	1	FACETS	0.711	0.656	0.768	0.711	0.656	0.768	SUBCLONAL	1	TRUE	0	0.48422694827455	1		755	775	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965012	15965012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	109	546	0	ENST00000268712.3:c.5584G>T	p.Glu1862Ter	p.E1862*	ENST00000268712	NM_006311.3	1862	Gaa/Taa	37/46	0.422086558140881	1	FACETS	0.598	0.538	0.66	0.598	0.538	0.66	SUBCLONAL	1	TRUE	0	0.48422694827455	1		546	571	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541565	29541565	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	64	424	0	ENST00000356175.3:c.1489G>T	p.Val497Leu	p.V497L	ENST00000356175	NM_000267.3	497	Gtg/Ttg	13/57	0.422086558140881	1	FACETS	0.475	0.412	0.542	0.475	0.412	0.542	SUBCLONAL	1	TRUE	0	0.48422694827455	1		424	422	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552123	29552123	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	19	202	0	ENST00000356175.3:c.1856G>A	p.Arg619Lys	p.R619K	ENST00000356175	NM_000267.3	619	aGa/aAa	17/57	0.422086558140881	1	FACETS	0.354	0.27	0.451	0.354	0.27	0.451	SUBCLONAL	1	TRUE	0	0.48422694827455	1		202	168	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534323	63534323	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	172	802	0	ENST00000307078.5:c.1198G>A	p.Glu400Lys	p.E400K	ENST00000307078	NM_004655.3	400	Gag/Aag	5/11	1	2	FACETS	0.713	0.656	0.773	0.713	0.656	0.773	SUBCLONAL	1	TRUE	1	0.48422694827455	2		802	996	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736937	736937	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1007155838	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	100	498	0	ENST00000314574.4:c.1162G>A	p.Glu388Lys	p.E388K	ENST00000314574	NM_005433.3	388	Gaa/Aaa	10/12	0.291038300977757	1	FACETS	0.52	0.465	0.578	0.52	0.465	0.578	SUBCLONAL	1	TRUE	0	0.48422694827455	1		498	602	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743035	743035	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	55	628	0	ENST00000314574.4:c.943G>C	p.Glu315Gln	p.E315Q	ENST00000314574	NM_005433.3	315	Gaa/Caa	8/12	0.291038300977757	1	FACETS	0.235	0.2	0.273	0.235	0.2	0.273	SUBCLONAL	1	TRUE	0	0.48422694827455	1		628	732	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56363704	56363704	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	38	283	0	ENST00000348428.3:c.483C>G	p.Phe161Leu	p.F161L	ENST00000348428	NM_006785.3	161	ttC/ttG	3/17	0.291038300977757	1	FACETS	0.294	0.243	0.351	0.294	0.243	0.351	SUBCLONAL	1	TRUE	0	0.48422694827455	1		283	405	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144122	11144122	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	315	805	0	ENST00000358026.2:c.3703G>C	p.Asp1235His	p.D1235H	ENST00000358026	NM_001128849.1	1235	Gac/Cac	26/36	0.472125145705237	2	FACETS	1	0.992	1	0.638	0.603	0.674	CLONAL	1	TRUE	0	0.48422694827455	2		805	1019	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140146	50140146	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	396	720	0	ENST00000246792.3:c.279G>C	p.Met93Ile	p.M93I	ENST00000246792	NM_006270.3	93	atG/atC	3/6	0.393691997260904	2	FACETS	0.941	0.9	0.983	0.941	0.9	0.983	CLONAL	2	TRUE	0	0.48422694827455	2		720	869	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468144	25468144	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	197	837	0	ENST00000264709.3:c.1532G>C	p.Gly511Ala	p.G511A	ENST00000264709	NM_175629.2	511	gGa/gCa	13/23	1	2	FACETS	0.741	0.685	0.799	0.741	0.685	0.799	SUBCLONAL	1	TRUE	1	0.48422694827455	2		837	1098	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010568	48010568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	202	561	1	ENST00000234420.5:c.196C>T	p.Pro66Ser	p.P66S	ENST00000234420	NM_000179.2	66	Ccg/Tcg	1/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.48422694827455	2		562	719	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99203966	99203966	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	40	405	0	ENST00000074304.5:c.2829G>C	p.Met943Ile	p.M943I	ENST00000074304	NM_001134224.1	943	atG/atC	26/26	1	2	FACETS	0.291	0.241	0.347	0.291	0.241	0.347	SUBCLONAL	1	TRUE	1	0.48422694827455	2		405	567	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273139	198273139	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	243	589	0	ENST00000335508.6:c.1071G>C	p.Lys357Asn	p.K357N	ENST00000335508	NM_012433.2	357	aaG/aaC	8/25	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.48422694827455	2		589	897	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215674278	215674278	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876658234	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	44	588	0	ENST00000260947.4:c.16C>A	p.Gln6Lys	p.Q6K	ENST00000260947	NM_000465.2	6	Cag/Aag	1/11	1	2	FACETS	0.248	0.207	0.294	0.248	0.207	0.294	SUBCLONAL	1	TRUE	1	0.48422694827455	2		588	732	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660838	227660838	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376286000	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	55	610	0	ENST00000305123.5:c.2617C>T	p.Arg873Trp	p.R873W	ENST00000305123	NM_005544.2	873	Cgg/Tgg	1/2	1	2	FACETS	0.309	0.264	0.359	0.309	0.264	0.359	SUBCLONAL	1	TRUE	1	0.48422694827455	2		610	735	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265016	46265016	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	141	530	0	ENST00000371998.3:c.1886C>G	p.Ser629Cys	p.S629C	ENST00000371998		629	tCt/tGt	12/23	1	2	FACETS	0.843	0.769	0.919	0.843	0.769	0.919	CLONAL	1	TRUE	1	0.48422694827455	2		530	691	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125569	47125569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	107	418	0	ENST00000409792.3:c.5701G>A	p.Glu1901Lys	p.E1901K	ENST00000409792	NM_014159.6	1901	Gaa/Aaa	12/21	1	2	FACETS	0.925	0.834	1	0.925	0.834	1	CLONAL	1	TRUE	1	0.48422694827455	2		418	478	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067065	143067065	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	90	423	0	ENST00000262992.4:c.1648G>C	p.Glu550Gln	p.E550Q	ENST00000262992	NM_001101669.1	550	Gaa/Caa	16/24	1	2	FACETS	0.623	0.553	0.697	0.623	0.553	0.697	SUBCLONAL	1	TRUE	1	0.48422694827455	2		423	597	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958612	38958612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	43	248	0	ENST00000357387.3:c.2353C>T	p.His785Tyr	p.H785Y	ENST00000357387	NM_152756.3	785	Cat/Tat	24/38	1	2	FACETS	0.577	0.485	0.678	0.577	0.485	0.678	SUBCLONAL	1	TRUE	1	0.48422694827455	2		248	308	SUCCESS
APC	324	MSKCC	GRCh37	5	112174650	112174650	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	113	378	0	ENST00000257430.4:c.3359G>C	p.Gly1120Ala	p.G1120A	ENST00000257430	NM_000038.5	1120	gGa/gCa	16/16	0.48422694827455	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.48422694827455	1		378	314	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930725	131930725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	140	369	0	ENST00000265335.6:c.1958C>T	p.Ser653Leu	p.S653L	ENST00000265335		653	tCa/tTa	12/25	0.48422694827455	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.48422694827455	1		369	369	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514394	149514394	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	140	623	0	ENST00000261799.4:c.550G>C	p.Glu184Gln	p.E184Q	ENST00000261799	NM_002609.3	184	Gag/Cag	4/23	0.48422694827455	1	FACETS	0.766	0.701	0.834	0.766	0.701	0.834	SUBCLONAL	1	TRUE	0	0.48422694827455	1		623	572	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679797	30679797	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	112	556	0	ENST00000376406.3:c.1922C>G	p.Ser641Ter	p.S641*	ENST00000376406	NM_014641.2	641	tCa/tGa	5/15	1	2	FACETS	0.661	0.595	0.731	0.661	0.595	0.731	SUBCLONAL	1	TRUE	1	0.48422694827455	2		556	700	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652023	36652023	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	234	827	0	ENST00000244741.5:c.145T>C	p.Trp49Arg	p.W49R	ENST00000244741	NM_000389.4	49	Tgg/Cgg	2/3	1	2	FACETS	0.959	0.895	1	0.959	0.895	1	CLONAL	1	TRUE	1	0.48422694827455	2		827	1008	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790729	89790729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	68	828	1	ENST00000336032.3:c.116C>T	p.Pro39Leu	p.P39L	ENST00000336032	NM_006813.2	39	cCg/cTg	1/2	1	2	FACETS	0.266	0.231	0.305	0.266	0.231	0.305	SUBCLONAL	1	TRUE	1	0.48422694827455	2		829	1055	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026467	6026467	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	60	192	0	ENST00000265849.7:c.1929G>C	p.Gln643His	p.Q643H	ENST00000265849	NM_000535.5	643	caG/caC	11/15	1	2	FACETS	0.802	0.696	0.916	0.802	0.696	0.916	CLONAL	1	TRUE	1	0.48422694827455	2		192	309	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874923	151874923	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	77	317	0	ENST00000262189.6:c.7615C>A	p.Gln2539Lys	p.Q2539K	ENST00000262189	NM_170606.2	2539	Cag/Aag	38/59	1	2	FACETS	0.629	0.553	0.709	0.629	0.553	0.709	SUBCLONAL	1	TRUE	1	0.48422694827455	2		317	506	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866422	56866422	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	112	586	0	ENST00000519728.1:c.669G>C	p.Glu223Asp	p.E223D	ENST00000519728	NM_002350.3	223	gaG/gaC	8/13	0.32892303481215	1	FACETS	0.39	0.35	0.433	0.39	0.35	0.433	SUBCLONAL	1	TRUE	0	0.48422694827455	1		586	898	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080239	5080239	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	62	232	0	ENST00000381652.3:c.2142G>C	p.Glu714Asp	p.E714D	ENST00000381652	NM_004972.3	714	gaG/gaC	17/25	0.348539726802334	1	FACETS	0.802	0.701	0.909	0.802	0.701	0.909	CLONAL	1	TRUE	0	0.48422694827455	1		232	242	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197356	27197356	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	123	581	0	ENST00000380036.4:c.1668G>C	p.Gln556His	p.Q556H	ENST00000380036	NM_000459.3	556	caG/caC	12/23	0.429160913942893	0	FACETS	0.413	0.374	0.453			1	SUBCLONAL	1	TRUE	0	0.48422694827455	0		581	635	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776149	135776149	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	262	450	0	ENST00000298552.3:c.2578G>T	p.Glu860Ter	p.E860*	ENST00000298552	NM_001162426.1	860	Gag/Tag	20/23	0.469956391329691	2	FACETS	0.884	0.835	0.933	0.884	0.835	0.933	CLONAL	2	TRUE	0	0.48422694827455	2		450	612	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395206	139395206	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	82	894	0	ENST00000277541.6:c.5732C>G	p.Ser1911Cys	p.S1911C	ENST00000277541	NM_017617.3	1911	tCc/tGc	31/34	0.469956391329691	2	FACETS	0.345	0.303	0.39	0.172	0.151	0.195	SUBCLONAL	1	TRUE	0	0.48422694827455	2		894	983	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347754	70347754	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	33	230	0	ENST00000374080.3:c.2993C>G	p.Ser998Ter	p.S998*	ENST00000374080		998	tCa/tGa	22/45	1	1	FACETS	0.32	0.261	0.386	0.32	0.261	0.386	SUBCLONAL	1	TRUE	0	0.48422694827455	1		230	323	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200282	123200283	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	121	242	0	ENST00000218089.9:c.2264dup	p.Glu756GlyfsTer29	p.E756Gfs*29	ENST00000218089	NM_001042749.1	754	aca/acAa	23/35	1	1	FACETS	0.773	0.714	0.832	1	0.989	1	SUBCLONAL	2	TRUE	0	0.48422694827455	1		242	245	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0045229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	16	454	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.21226383947212	4	FACETS	0.934	0.711	1	0.934	0.711	1	INDETERMINATE	2	FALSE	2	0.381912806479851	4		454	62	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405045	405045	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377483798	NA	P-0045230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	100	331	0	ENST00000380956.4:c.1127G>A	p.Arg376His	p.R376H	ENST00000380956	NM_001195286.1	376	cGc/cAc	8/9	0.260553961812947	5	FACETS	1	0.949	1	0.729	0.654	0.808	CLONAL	2	TRUE	2	0.260553961812947	5		331	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578440	7578440	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs879254249	NA	P-0045230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	205	595	0	ENST00000269305.4:c.490A>G	p.Lys164Glu	p.K164E	ENST00000269305	NM_001126112.2	164	Aag/Gag	5/11	0.193131801474518	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.260553961812947	3		595	751	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720741	89720741	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs371387815	NA	P-0045230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	25	158	0	ENST00000371953.3:c.892C>T	p.Gln298Ter	p.Q298*	ENST00000371953	NM_000314.4	298	Caa/Taa	8/9	0.222151533979272	3	FACETS	1	0.896	1	0.408	0.324	0.503	CLONAL	1	TRUE	0	0.260553961812947	3		158	177	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830914	156830914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	137	487	0	ENST00000524377.1:c.188C>T	p.Pro63Leu	p.P63L	ENST00000524377	NM_002529.3	63	cCc/cTc	1/17	0.2332890914356	3	FACETS	0.981	0.895	1	0.981	0.895	1	CLONAL	2	TRUE	1	0.260553961812947	3		487	606	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55270220	55270220	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	90	585	0	ENST00000275493.2:c.3173G>A	p.Cys1058Tyr	p.C1058Y	ENST00000275493	NM_005228.3	1058	tGt/tAt	27/28	0.260553961812947	7	FACETS	1	0.969	1	0.255	0.225	0.286	CLONAL	1	TRUE	2	0.260553961812947	7		585	896	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391983	139391983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1432074829	NA	P-0045230-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	85	621	1	ENST00000277541.6:c.6208C>T	p.Arg2070Trp	p.R2070W	ENST00000277541	NM_017617.3	2070	Cgg/Tgg	34/34	0.107353730309644	5	FACETS	1	0.967	1	0.421	0.372	0.474	INDETERMINATE	1	TRUE	2	0.260553961812947	5		622	718	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0045232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	231	680	1	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.703442053039188	3	FACETS	0.995	0.961	1			1	CLONAL	3	TRUE	NA	0.763972494338474	3		681	280	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660984	227660984	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045232-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	41	572	1	ENST00000305123.5:c.2471G>T	p.Arg824Met	p.R824M	ENST00000305123	NM_005544.2	824	aGg/aTg	1/2	0.429645029941423	5	FACETS	1	0.904	1	0.369	0.31	0.433	INDETERMINATE	1	TRUE	2	0.763972494338474	5		573	208	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0045233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	231	492	0	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	0.411139762690687	2	FACETS	0.866	0.814	0.92	0.866	0.814	0.92	CLONAL	2	TRUE	0	0.452656683865366	2		492	589	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912656	NA	P-0045233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	237	471	0	ENST00000269305.4:c.734G>C	p.Gly245Ala	p.G245A	ENST00000269305	NM_001126112.2	245	gGc/gCc	7/11	0.411139762690687	2	FACETS	0.914	0.86	0.968	0.914	0.86	0.968	CLONAL	2	TRUE	0	0.452656683865366	2		471	573	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546090	29546091	+	missense_variant	Missense_Mutation	DNP	TG	TG	CT	novel	NA	P-0045233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	347	421	1	ENST00000356175.3:c.1595_1596delinsCT	p.Leu532Pro	p.L532P	ENST00000356175	NM_000267.3	532	cTG/cCT	14/57	0.452656683865366	3	FACETS	0.992	0.949	1	0.992	0.949	1	CLONAL	3	TRUE	0	0.452656683865366	3		422	632	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056647	26056647	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	60	145	0	ENST00000343677.2:c.10A>T	p.Thr4Ser	p.T4S	ENST00000343677	NM_005319.3	4	Act/Tct	1/1	0.35127522353496	6	FACETS	1	0.967	1	0.355	0.307	0.406	CLONAL	1	TRUE	2	0.452656683865366	6		145	356	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0045238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	253	914	0	ENST00000269305.4:c.394A>T	p.Lys132Ter	p.K132*	ENST00000269305	NM_001126112.2	132	Aag/Tag	5/11	0.456694815528639	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.456694815528639	1		914	765	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058948	42058948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144386608	NA	P-0045238-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	77	418	1	ENST00000219905.7:c.8668G>A	p.Val2890Ile	p.V2890I	ENST00000219905	NM_001164273.1	2890	Gtt/Att	24/24	0.456694815528639	1	FACETS	0.891	0.791	0.997	0.891	0.791	0.997	CLONAL	1	TRUE	0	0.456694815528639	1		419	292	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	173	425	0				ENST00000310581	NM_198253.2	-/1132			0.857666887105332	3	FACETS	0.917	0.847	0.988	0.458	0.423	0.494	CLONAL	1	TRUE	1	0.847547888658026	3		425	634	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400902	72400902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1450443698	NA	P-0045239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	88	279	0	ENST00000357731.5:c.269G>A	p.Arg90Gln	p.R90Q	ENST00000357731	NM_173808.2	90	cGa/cAa	2/7	0.605516057667241	1	FACETS	0.418	0.375	0.463	0.418	0.375	0.463	SUBCLONAL	1	TRUE	0	0.847547888658026	1		279	286	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073562	8073562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	102	377	0	ENST00000377482.5:c.1097G>A	p.Arg366Lys	p.R366K	ENST00000377482	NM_018948.3	366	aGa/aAa	4/4	0.605516057667241	1	FACETS	0.319	0.287	0.353	0.319	0.287	0.353	SUBCLONAL	1	TRUE	0	0.847547888658026	1		377	435	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639169	3639169	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	169	873	0	ENST00000294008.3:c.4470G>C	p.Glu1490Asp	p.E1490D	ENST00000294008	NM_032444.2	1490	gaG/gaC	12/15	0.426670969924394	2	FACETS	0.583	0.538	0.63	0.292	0.269	0.315	INDETERMINATE	1	TRUE	0	0.847547888658026	2		873	684	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827295	72827295	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1197	118	698	0	ENST00000268489.5:c.9286C>G	p.Gln3096Glu	p.Q3096E	ENST00000268489	NM_006885.3	3096	Cag/Gag	9/10	0.857666887105332	5	FACETS	0.481	0.432	0.533			1	SUBCLONAL	1	TRUE	NA	0.847547888658026	5		698	1315	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829442	72829442	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs774068826	NA	P-0045239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	100	630	0	ENST00000268489.5:c.7139C>G	p.Ser2380Ter	p.S2380*	ENST00000268489	NM_006885.3	2380	tCa/tGa	9/10	0.857666887105332	5	FACETS	0.485	0.432	0.541			1	SUBCLONAL	1	TRUE	NA	0.847547888658026	5		630	1106	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829754	72829754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	109	683	0	ENST00000268489.5:c.6827C>T	p.Ser2276Phe	p.S2276F	ENST00000268489	NM_006885.3	2276	tCt/tTt	9/10	0.857666887105332	5	FACETS	0.465	0.416	0.517			1	SUBCLONAL	1	TRUE	NA	0.847547888658026	5		683	1257	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414755	56414755	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	187	624	0	ENST00000348428.3:c.2156G>C	p.Arg719Pro	p.R719P	ENST00000348428	NM_006785.3	719	cGa/cCa	17/17	0.857666887105332	1	FACETS	0.56	0.523	0.598	0.56	0.523	0.598	SUBCLONAL	1	TRUE	0	0.847547888658026	1		624	454	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741948	40741948	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	142	927	1	ENST00000392038.2:c.1024G>A	p.Glu342Lys	p.E342K	ENST00000392038	NM_001626.4	342	Gag/Aag	11/14	0.54027864622377	1	FACETS	0.361	0.33	0.393	0.361	0.33	0.393	SUBCLONAL	1	TRUE	0	0.847547888658026	1		928	535	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205804	128205804	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	134	601	0	ENST00000341105.2:c.71C>T	p.Ser24Leu	p.S24L	ENST00000341105	NM_032638.4	24	tCa/tTa	2/6	0.486082468336689	1	FACETS	0.396	0.362	0.431	0.396	0.362	0.431	INDETERMINATE	1	TRUE	0	0.847547888658026	1		601	460	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928291	178928291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	94	489	0	ENST00000263967.3:c.1477G>A	p.Glu493Lys	p.E493K	ENST00000263967	NM_006218.2	493	Gaa/Aaa	9/21	0.40877154549161	1	FACETS	0.308	0.275	0.342	0.308	0.275	0.342	INDETERMINATE	1	TRUE	0	0.847547888658026	1		489	415	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409473	80409473	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	113	426	0	ENST00000286548.4:c.641G>T	p.Arg214Ile	p.R214I	ENST00000286548	NM_002072.3	214	aGa/aTa	5/7	0.54027864622377	1	FACETS	0.337	0.305	0.37	0.337	0.305	0.37	SUBCLONAL	1	TRUE	0	0.847547888658026	1		426	456	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409509	80409509	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0045239-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	158	579	0	ENST00000286548.4:c.606-1G>C		p.X202_splice	ENST00000286548	NM_002072.3	202			0.54027864622377	1	FACETS	0.334	0.306	0.362	0.334	0.306	0.362	SUBCLONAL	1	TRUE	0	0.847547888658026	1		579	644	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0045240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	28	354	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.1225069201087	5	FACETS	0.432	0.344	0.533	0.144	0.114	0.178	INDETERMINATE	1	TRUE	2	0.33	5		354	587	SUCCESS
APC	324	MSKCC	GRCh37	5	112175530	112175530	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	27	328	0	ENST00000257430.4:c.4240del	p.Val1414Ter	p.V1414*	ENST00000257430	NM_000038.5	1413	atG/at	16/16	0.0936306451494196	5	FACETS	0.609	0.484	0.751	0.203	0.161	0.251	INDETERMINATE	1	TRUE	2	0.33	5		328	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0045240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	28	618	0	ENST00000269305.4:c.559+1G>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.210311807455058	3	FACETS	0.372	0.297	0.459	0.186	0.148	0.23	SUBCLONAL	1	TRUE	1	0.33	3		618	531	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0045242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	89	278	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.443648658389011	2		278	391	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0045242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	163	531	0	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	0.443648658389011	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.443648658389011	1		531	527	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003808	45003808	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	108	433	0	ENST00000558401.1:c.64C>T	p.Gln22Ter	p.Q22*	ENST00000558401	NM_004048.2	22	Cag/Tag	1/4	0.443648658389011	1	FACETS	0.957	0.866	1	0.957	0.866	1	CLONAL	1	TRUE	0	0.443648658389011	1		433	396	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398280	25398281	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0045242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	70	343	1	ENST00000311936.3:c.38_39delinsTT	p.Gly13Val	p.G13V	ENST00000311936	NM_004985.3	13	gGC/gTT	2/5	1	2	FACETS	0.73	0.639	0.828	0.73	0.639	0.828	SUBCLONAL	1	TRUE	1	0.443648658389011	2		344	432	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101170	41101170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41279256	NA	P-0045242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	403	550	1	ENST00000373198.4:c.1186G>A	p.Val396Ile	p.V396I	ENST00000373198	NM_133170.3	396	Gta/Ata	8/32	0.443648658389011	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.443648658389011	3		551	923	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2111885	2111885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45517154	NA	P-0045242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	168	666	2	ENST00000219476.3:c.1133C>T	p.Pro378Leu	p.P378L	ENST00000219476	NM_000548.3	378	cCg/cTg	12/42	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.443648658389011	2		668	711	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332643	70332643	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	152	477	0	ENST00000373644.4:c.548G>T	p.Gly183Val	p.G183V	ENST00000373644	NM_030625.2	183	gGt/gTt	2/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.443648658389011	2		477	620	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108286	8108286	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144169786	NA	P-0045242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	199	736	1	ENST00000585124.1:c.938C>T	p.Ser313Leu	p.S313L	ENST00000585124	NM_004217.3	313	tCg/tTg	9/9	0.443648658389011	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.443648658389011	1		737	670	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545774	63545775	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0045242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	95	315	0	ENST00000307078.5:c.819dup	p.Phe274LeufsTer8	p.F274Lfs*8	ENST00000307078	NM_004655.3	273	-/C	3/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.443648658389011	2		315	374	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554161	63554162	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	AAGTCAAAAACATCTGGTAGGCATTTTCCTCCATCACCGACTGGATC	novel	NA	P-0045242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	61	664	0	ENST00000307078.5:c.531_577dup	p.Ser193Ter	p.S193*	ENST00000307078	NM_004655.3	193	tct/tGATCCAGTCGGTGATGGAGGAAAATGCCTACCAGATGTTTTTGACTTct	2/11	1	2	FACETS	0.357	0.307	0.412	0.357	0.307	0.412	SUBCLONAL	1	TRUE	1	0.443648658389011	2		664	770	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681653	78681653	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	131	388	0	ENST00000306801.3:c.361C>T	p.Gln121Ter	p.Q121*	ENST00000306801	NM_020761.2	121	Cag/Tag	4/34	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.443648658389011	2		388	474	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584811	48584812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0045242-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	132	298	0	ENST00000342988.3:c.890_891dup	p.Pro298IlefsTer39	p.P298Ifs*39	ENST00000342988	NM_005359.5	297	cat/cATat	7/12	0.443648658389011	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.443648658389011	1		298	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0045243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	135	667	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.224645666857741	2	FACETS	0.939	0.858	1	0.939	0.858	1	CLONAL	2	FALSE	0	0.278233152579798	2		667	517	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	59	425	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.294754480248549	2		425	342	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0045252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	104	457	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.294754480248549	2		457	705	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0045252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	109	592	1	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.224318648799396	2	FACETS	1	0.978	1	0.657	0.592	0.726	CLONAL	1	TRUE	0	0.294754480248549	2		593	563	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246440	41246440	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	106	590	0	ENST00000357654.3:c.1108G>A	p.Val370Ile	p.V370I	ENST00000357654	NM_007294.3	370	Gtt/Att	10/23	1	2	FACETS	0.964	0.865	1	0.964	0.865	1	CLONAL	1	TRUE	1	0.294754480248549	2		590	746	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106983	27106983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	128	491	0	ENST00000324856.7:c.6595del	p.Leu2199Ter	p.L2199*	ENST00000324856	NM_006015.4	2198	ttC/tt	20/20	0.15322286543006	3	FACETS	0.911	0.829	0.996	0.911	0.829	0.996	INDETERMINATE	2	TRUE	1	0.294754480248549	3		491	547	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2164220	2164220	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045252-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	31	576	0	ENST00000398665.3:c.37G>C	p.Val13Leu	p.V13L	ENST00000398665	NM_032482.2	13	Gtg/Ctg	1/28	1	2	FACETS	0.397	0.32	0.484	0.397	0.32	0.484	SUBCLONAL	1	TRUE	1	0.294754480248549	2		576	530	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	155	425	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.922	0.85	0.996	0.922	0.85	0.996	CLONAL	1	TRUE	1	0.677786479851014	2		425	496	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0045252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	277	457	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.677786479851014	2		457	813	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0045252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	441	592	1	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.667390051986495	2	FACETS	0.971	0.938	1	0.971	0.938	1	CLONAL	2	TRUE	0	0.677786479851014	2		593	670	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246440	41246440	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	257	590	0	ENST00000357654.3:c.1108G>A	p.Val370Ile	p.V370I	ENST00000357654	NM_007294.3	370	Gtt/Att	10/23	1	2	FACETS	0.895	0.841	0.951	0.895	0.841	0.951	CLONAL	1	TRUE	1	0.677786479851014	2		590	847	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106983	27106983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	232	491	0	ENST00000324856.7:c.6595del	p.Leu2199Ter	p.L2199*	ENST00000324856	NM_006015.4	2198	ttC/tt	20/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.677786479851014	2		491	656	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2164220	2164220	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	199	576	0	ENST00000398665.3:c.37G>C	p.Val13Leu	p.V13L	ENST00000398665	NM_032482.2	13	Gtg/Ctg	1/28	1	2	FACETS	0.931	0.867	0.996	0.931	0.867	0.996	CLONAL	1	TRUE	1	0.677786479851014	2		576	631	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001469	150001469	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs752896748	NA	P-0045252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	225	482	0	ENST00000253339.5:c.2135G>C	p.Gly712Ala	p.G712A	ENST00000253339		712	gGa/gCa	4/7	0.607821632692315	4	FACETS	0.843	0.784	0.905	0.422	0.392	0.453	CLONAL	1	TRUE	2	0.677786479851014	4		482	1321	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725085	49725085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1189053822	NA	P-0045252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	271	751	2	ENST00000449682.2:c.259G>A	p.Val87Met	p.V87M	ENST00000449682	NM_020998.3	87	Gtg/Atg	3/18	1	2	FACETS	0.811	0.762	0.862	0.811	0.762	0.862	CLONAL	1	TRUE	1	0.677786479851014	2		753	986	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497530	125497530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	136	241	0	ENST00000428830.2:c.94G>A	p.Glu32Lys	p.E32K	ENST00000428830	NM_001114121.2	32	Gaa/Aaa	3/14	1	2	FACETS	0.972	0.892	1	0.972	0.892	1	CLONAL	1	TRUE	1	0.677786479851014	2		241	413	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264419	16264419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	308	766	0	ENST00000375759.3:c.10622C>T	p.Ser3541Phe	p.S3541F	ENST00000375759	NM_015001.2	3541	tCt/tTt	13/15	1	2	FACETS	0.948	0.895	1	0.948	0.895	1	CLONAL	1	TRUE	1	0.677786479851014	2		766	959	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257194	16257194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753930247	NA	P-0045252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	176	555	0	ENST00000375759.3:c.4459C>T	p.Pro1487Ser	p.P1487S	ENST00000375759	NM_015001.2	1487	Cca/Tca	11/15	1	2	FACETS	0.729	0.674	0.787	0.729	0.674	0.787	SUBCLONAL	1	TRUE	1	0.677786479851014	2		555	712	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263970	16263970	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	398	854	0	ENST00000375759.3:c.10339C>G	p.Leu3447Val	p.L3447V	ENST00000375759	NM_015001.2	3447	Ctt/Gtt	12/15	1	2	FACETS	0.894	0.85	0.939	0.894	0.85	0.939	CLONAL	1	TRUE	1	0.677786479851014	2		854	1314	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858312	59858312	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1209325148	NA	P-0045252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	196	367	0	ENST00000259008.2:c.1683G>C	p.Gln561His	p.Q561H	ENST00000259008	NM_032043.2	561	caG/caC	12/20	1	2	FACETS	0.847	0.787	0.908	0.847	0.787	0.908	CLONAL	1	TRUE	1	0.677786479851014	2		367	683	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265615	198265615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	144	374	0	ENST00000335508.6:c.2542G>A	p.Glu848Lys	p.E848K	ENST00000335508	NM_012433.2	848	Gaa/Aaa	18/25	1	2	FACETS	0.841	0.772	0.913	0.841	0.772	0.913	CLONAL	1	TRUE	1	0.677786479851014	2		374	505	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940269	49940269	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs147876136	NA	P-0045252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	290	757	0	ENST00000296474.3:c.774C>G	p.Phe258Leu	p.F258L	ENST00000296474	NM_002447.2	258	ttC/ttG	1/20	1	2	FACETS	0.942	0.889	0.997	0.942	0.889	0.997	CLONAL	1	TRUE	1	0.677786479851014	2		757	908	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138382849	138382849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774423662	NA	P-0045252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	140	400	0	ENST00000289153.2:c.2695G>A	p.Glu899Lys	p.E899K	ENST00000289153	NM_006219.2	899	Gag/Aag	19/22	1	2	FACETS	0.624	0.57	0.681	0.624	0.57	0.681	SUBCLONAL	1	TRUE	1	0.677786479851014	2		400	662	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562603	176562603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	245	519	0	ENST00000439151.2:c.499G>A	p.Glu167Lys	p.E167K	ENST00000439151	NM_022455.4	167	Gaa/Aaa	2/23	1	2	FACETS	0.944	0.885	1	0.944	0.885	1	CLONAL	1	TRUE	1	0.677786479851014	2		519	766	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141568634	141568634	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	57	682	0	ENST00000220592.5:c.828G>C	p.Lys276Asn	p.K276N	ENST00000220592	NM_012154.3	276	aaG/aaC	7/19	1	2	FACETS	0.187	0.159	0.217	0.187	0.159	0.217	SUBCLONAL	1	TRUE	1	0.677786479851014	2		682	900	SUCCESS
AR	367	MSKCC	GRCh37	X	66766271	66766271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	178	466	1	ENST00000374690.3:c.1283C>T	p.Ser428Leu	p.S428L	ENST00000374690	NM_000044.3	428	tCa/tTa	1/8	1	2	FACETS	0.814	0.754	0.877	0.814	0.754	0.877	CLONAL	1	TRUE	1	0.677786479851014	2		467	645	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351399	70351399	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0045252-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	178	644	0	ENST00000374080.3:c.4048-1G>A		p.X1350_splice	ENST00000374080		1350			1	2	FACETS	0.575	0.53	0.622	0.575	0.53	0.622	SUBCLONAL	1	TRUE	1	0.677786479851014	2		644	913	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs11575997	NA	P-0045256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	50	612	0	ENST00000269305.4:c.993+1G>T		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.554074126632207	1	FACETS	0.198	0.168	0.232	0.198	0.168	0.232	SUBCLONAL	1	TRUE	0	0.554074126632207	1		612	658	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602328	10602328	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	323	821	1	ENST00000171111.5:c.1250G>T	p.Gly417Val	p.G417V	ENST00000171111	NM_203500.1	417	gGg/gTg	3/6	0.554074126632207	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.554074126632207	1		822	778	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220578	1220578	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0045256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	212	635	0	ENST00000326873.7:c.598-2A>C		p.X200_splice	ENST00000326873	NM_000455.4	200			0.554074126632207	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.554074126632207	1		635	540	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2202722	2202722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	293	623	0	ENST00000398665.3:c.731C>T	p.Ala244Val	p.A244V	ENST00000398665	NM_032482.2	244	gCc/gTc	9/28	0.554074126632207	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.554074126632207	1		623	677	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678369	88678370	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	A	novel	NA	P-0045256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	246	772	0	ENST00000360948.2:c.1166_1167delinsT	p.Gln389LeufsTer25	p.Q389Lfs*25	ENST00000360948	NM_001012338.2	389	cAG/cT	9/19	1	2	FACETS	0.855	0.8	0.913	0.855	0.8	0.913	CLONAL	1	TRUE	1	0.554074126632207	2		772	1038	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030412	49030412	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045256-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	218	410	0	ENST00000267163.4:c.1887G>T	p.Glu629Asp	p.E629D	ENST00000267163	NM_000321.2	629	gaG/gaT	19/27	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.554074126632207	2		410	744	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0045258-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	287	294	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.286701966840705	5	FACETS	1	0.966	1			1	CLONAL	4	TRUE	NA	0.286701966840705	5		294	697	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0045258-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	159	798	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.286701966840705	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.286701966840705	1		798	771	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797482	45797482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778538	NA	P-0045258-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	109	817	1	ENST00000450313.1:c.1037C>T	p.Ser346Leu	p.S346L	ENST00000450313	NM_012222.2	346	tCg/tTg	12/16	1	2	FACETS	0.786	0.704	0.872	0.786	0.704	0.872	SUBCLONAL	1	TRUE	1	0.286701966840705	2		818	968	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099315	27099316	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	T	novel	NA	P-0045258-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	88	475	1	ENST00000324856.7:c.3552_3553delinsT	p.Val1185LeufsTer21	p.V1185Lfs*21	ENST00000324856	NM_006015.4	1184	tcAGtt/tcTtt	14/20	1	2	FACETS	0.847	0.75	0.95	0.847	0.75	0.95	CLONAL	1	TRUE	1	0.286701966840705	2		476	725	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971104	21971105	+	inframe_insertion	In_Frame_Ins	INS	-	-	CGT	novel	NA	P-0045258-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	81	358	0	ENST00000304494.5:c.251_253dup	p.Asp84dup	p.D84dup	ENST00000304494	NM_000077.4	84	gct/gACGct	2/3	0.286701966840705	1	FACETS	0.992	0.877	1	0.992	0.877	1	CLONAL	1	TRUE	0	0.286701966840705	1		358	488	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0045260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	163	609	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.440506911899161	5	FACETS	0.813	0.744	0.885	0.271	0.248	0.295	CLONAL	1	TRUE	2	0.544430541442524	5		609	1338	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0045260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	232	316	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.440506911899161	5	FACETS	1	0.98	1	0.739	0.693	0.787	CLONAL	2	TRUE	2	0.544430541442524	5		316	698	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0045260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	460	679	1	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	0.483620843365392	2	FACETS	0.861	0.826	0.896	0.861	0.826	0.896	CLONAL	2	TRUE	0	0.544430541442524	2		680	981	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251182	115251182	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	90	372	0	ENST00000369535.4:c.544A>T	p.Met182Leu	p.M182L	ENST00000369535	NM_002524.4	182	Atg/Ttg	5/7	0.476156791630303	3	FACETS	0.713	0.634	0.797	0.356	0.317	0.399	SUBCLONAL	1	TRUE	1	0.544430541442524	3		372	590	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426860	70426860	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	84	301	0	ENST00000373644.4:c.4520G>T	p.Gly1507Val	p.G1507V	ENST00000373644	NM_030625.2	1507	gGc/gTc	7/12	0.519787104576273	2	FACETS	0.706	0.627	0.791	0.353	0.313	0.396	SUBCLONAL	1	TRUE	0	0.544430541442524	2		301	437	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375310	15375310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	222	607	0	ENST00000263377.2:c.1117G>A	p.Ala373Thr	p.A373T	ENST00000263377	NM_058243.2	373	Gcc/Acc	6/20	0.483620843365392	2	FACETS	0.871	0.812	0.933	0.436	0.406	0.467	CLONAL	1	TRUE	0	0.544430541442524	2		607	936	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680043	30680043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	173	512	0	ENST00000376406.3:c.1676C>T	p.Pro559Leu	p.P559L	ENST00000376406	NM_014641.2	559	cCa/cTa	5/15	0.476156791630303	3	FACETS	0.897	0.826	0.972	0.449	0.413	0.486	CLONAL	1	TRUE	1	0.544430541442524	3		512	901	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904851	101904851	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0045260-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	89	260	0	ENST00000374994.4:c.839C>G	p.Ser280Ter	p.S280*	ENST00000374994	NM_004612.2	280	tCa/tGa	5/9	0.544430541442524	1	FACETS	0.823	0.739	0.911	0.823	0.739	0.911	CLONAL	1	TRUE	0	0.544430541442524	1		260	289	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0045263-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	94	615	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.893	0.795	0.998	0.893	0.795	0.998	CLONAL	1	TRUE	1	0.29	2		615	726	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220578	1220578	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0045263-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	108	760	1	ENST00000326873.7:c.598-2A>T		p.X200_splice	ENST00000326873	NM_000455.4	200			0.3	1	FACETS	0.984	0.885	1	0.984	0.885	1	CLONAL	1	TRUE	0	0.29	1		761	647	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602910	10602910	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045263-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	138	781	0	ENST00000171111.5:c.668T>G	p.Leu223Arg	p.L223R	ENST00000171111	NM_203500.1	223	cTg/cGg	3/6	0.3	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.29	1		781	799	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045266-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	461	879	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.754421959661632	2		879	1187	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512270	38512270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866777491	NA	P-0045266-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	501	1076	0	ENST00000254066.5:c.1181G>A	p.Arg394Gln	p.R394Q	ENST00000254066	NM_000964.3	394	cGg/cAg	9/9	1	2	FACETS	0.946	0.906	0.987	0.946	0.906	0.987	CLONAL	1	TRUE	1	0.754421959661632	2		1076	1404	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115715	8115767	+	frameshift_variant	Frame_Shift_Del	DEL	TGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAA	TGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAA	-	novel	NA	P-0045266-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	255	433	0	ENST00000346208.3:c.1062_1114del	p.Thr355GlnfsTer8	p.T355Qfs*8	ENST00000346208		354	cTGACTATGAAGAAGGAAGGCATCCAGACCAGAAACCGAAAAATGTCTAGCAAA/c	6/6	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.754421959661632	2		433	628	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870388	155870388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045266-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1315	302	710	0	ENST00000368323.3:c.451G>A	p.Ala151Thr	p.A151T	ENST00000368323	NM_006912.5	151	Gcc/Acc	6/6	0.714808400783152	4	FACETS	0.869	0.816	0.923	0.29	0.272	0.308	CLONAL	1	TRUE	1	0.754421959661632	4		710	1617	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070565	67070568	+	frameshift_variant	Frame_Shift_Del	DEL	TCTG	TCTG	-	novel	NA	P-0045266-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	192	375	0	ENST00000412916.2:c.192_195del	p.Leu66SerfsTer22	p.L66Sfs*22	ENST00000412916		63	aaTCTG/aa	3/6	0.754421959661632	1	FACETS	0.871	0.819	0.922	0.871	0.819	0.922	CLONAL	1	TRUE	0	0.754421959661632	1		375	364	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15943798	15943799	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0045266-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	232	408	0	ENST00000268712.3:c.6688_6689dup	p.Gln2230HisfsTer64	p.Q2230Hfs*64	ENST00000268712	NM_006311.3	2230	cag/caCAg	43/46	1	2	FACETS	0.955	0.896	1	0.955	0.896	1	CLONAL	1	TRUE	1	0.754421959661632	2		408	644	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880997	37880998	+	protein_altering_variant	In_Frame_Ins	INS	-	-	TGT	rs397516979	NA	P-0045267-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	1612	666	0	ENST00000269571.5:c.2326_2327insTGT	p.Gly776delinsValCys	p.G776delinsVC	ENST00000269571		776	ggt/gTGTgt	20/27	0.803241692723895	5	FACETS	0.969	0.954	0.985	0.969	0.954	0.985	CLONAL	4	TRUE	1	0.815925045936504	5		666	2266	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279432	1279432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866903055	NA	P-0045267-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1607	894	881	0	ENST00000310581.5:c.2104C>T	p.Pro702Ser	p.P702S	ENST00000310581	NM_198253.2	702	Ccg/Tcg	5/16	0.815925045936504	3	FACETS	1	0.997	1	0.617	0.597	0.637	CLONAL	1	TRUE	1	0.815925045936504	3		881	2501	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966955	25966955	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs773343381	NA	P-0045267-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	187	681	1	ENST00000435504.4:c.2251C>G	p.Gln751Glu	p.Q751E	ENST00000435504		751	Cag/Gag	13/13	0.637809694225425	3	FACETS	0.541	0.499	0.585	0.27	0.249	0.293	SUBCLONAL	1	TRUE	1	0.815925045936504	3		682	1193	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577516	7577517	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0045267-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	644	566	0	ENST00000269305.4:c.764_765del	p.Ile255AsnfsTer8	p.I255Nfs*8	ENST00000269305	NM_001126112.2	255	aTC/a	7/11	0.815925045936504	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.815925045936504	2		566	761	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660574	67660574	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045267-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	817	502	0	ENST00000264010.4:c.1474G>C	p.Glu492Gln	p.E492Q	ENST00000264010	NM_006565.3	492	Gag/Cag	8/12	0.815925045936504	5	FACETS	0.965	0.937	0.993			1	CLONAL	3	TRUE	NA	0.815925045936504	5		502	1538	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55674294	55674294	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045267-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	435	344	0	ENST00000284073.2:c.520G>T	p.Glu174Ter	p.E174*	ENST00000284073	NM_138962.2	174	Gaa/Taa	8/14	0.659474637823141	4	FACETS	0.901	0.869	0.934	0.901	0.869	0.934	CLONAL	3	TRUE	1	0.815925045936504	4		344	716	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812163	212812163	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045267-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	108	240	0	ENST00000342788.4:c.413A>G	p.Asn138Ser	p.N138S	ENST00000342788	NM_005235.2	138	aAc/aGc	3/28	0.110963679779896	4	FACETS	0.88	0.803	0.959	0.88	0.803	0.959	INDETERMINATE	2	TRUE	2	0.815925045936504	4		240	273	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502314	157502314	+	splice_donor_variant	Splice_Site	SNP	T	T	G	rs1404726383	NA	P-0045267-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	400	364	0	ENST00000346085.5:c.3345+2T>G		p.X1115_splice	ENST00000346085	NM_020732.3	1115			0.815925045936504	2	FACETS	0.979	0.951	1	0.979	0.951	1	CLONAL	2	TRUE	0	0.815925045936504	2		364	501	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412888	63412888	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045267-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	710	686	0	ENST00000330258.3:c.279C>A	p.Ser93Arg	p.S93R	ENST00000330258	NM_152424.3	93	agC/agA	2/2	0.637809694225425	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.815925045936504	3		686	1204	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536677	120536677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779170721	NA	P-0045286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	150	769	2	ENST00000229340.5:c.415G>A	p.Ala139Thr	p.A139T	ENST00000229340	NM_006861.6	139	Gcc/Acc	5/6	1	2	FACETS	0.781	0.713	0.852	0.781	0.713	0.852	SUBCLONAL	1	TRUE	1	0.391249473087365	2		771	982	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579380	7579380	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045286-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	173	738	0	ENST00000269305.4:c.307del	p.Tyr103ThrfsTer20	p.Y103Tfs*20	ENST00000269305	NM_001126112.2	103	Tac/ac	4/11	0.360581122934201	1	FACETS	0.831	0.765	0.899	0.831	0.765	0.899	CLONAL	1	TRUE	0	0.391249473087365	1		738	856	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922695	44922695	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	98	429	0	ENST00000377967.4:c.1556del	p.Arg519HisfsTer29	p.R519Hfs*29	ENST00000377967	NM_021140.2	519	cGa/ca	16/29	0.428123491060523	3	FACETS	0.766	0.685	0.853			1	SUBCLONAL	1	TRUE	NA	0.507316115162347	3		429	632	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578236	7578236	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520008	NA	P-0045287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	328	810	0	ENST00000269305.4:c.613T>C	p.Tyr205His	p.Y205H	ENST00000269305	NM_001126112.2	205	Tat/Cat	6/11	0.467810334180359	3	FACETS	0.9	0.853	0.947	0.9	0.853	0.947	CLONAL	2	TRUE	1	0.507316115162347	3		810	901	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752903	57752903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	241	477	0	ENST00000274289.3:c.1025G>A	p.Arg342Lys	p.R342K	ENST00000274289	NM_006622.3	342	aGa/aAa	8/14	0.396447970495821	3	FACETS	0.821	0.771	0.873	0.821	0.771	0.873	CLONAL	2	TRUE	1	0.507316115162347	3		477	725	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576906	7576906	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	94	822	0	ENST00000269305.4:c.940del	p.Ser314ProfsTer31	p.S314Pfs*31	ENST00000269305	NM_001126112.2	314	Tcc/cc	9/11	0.467810334180359	3	FACETS	0.533	0.473	0.596	0.266	0.236	0.298	SUBCLONAL	1	TRUE	1	0.507316115162347	3		822	872	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591121	67591123	+	inframe_deletion	In_Frame_Del	DEL	CAG	CAG	-	novel	NA	P-0045287-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	158	359	0	ENST00000274335.5:c.1715_1717del	p.Gln572del	p.Q572del	ENST00000274335		572	CAG/-	12/15	0.396447970495821	3	FACETS	1	0.989	1	0.748	0.69	0.808	CLONAL	1	TRUE	1	0.507316115162347	3		359	522	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0045288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	40	267	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.713	0.595	0.844	0.713	0.595	0.844	SUBCLONAL	1	TRUE	1	0.348435499214868	2		267	322	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	364577	364577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754764999	NA	P-0045288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	108	866	0	ENST00000262320.3:c.985G>A	p.Asp329Asn	p.D329N	ENST00000262320	NM_003502.3	329	Gat/Aat	3/11	0.348435499214868	1	FACETS	0.682	0.612	0.756	0.682	0.612	0.756	SUBCLONAL	1	TRUE	0	0.348435499214868	1		866	751	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912049	127912049	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	24	403	0	ENST00000373547.4:c.821T>C	p.Phe274Ser	p.F274S	ENST00000373547	NM_002721.4	274	tTc/tCc	7/7	1	2	FACETS	0.301	0.236	0.378	0.301	0.236	0.378	SUBCLONAL	1	TRUE	1	0.348435499214868	2		403	457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578445	7578446	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	C	novel	NA	P-0045288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	244	811	0	ENST00000269305.4:c.484_485delinsG	p.Ile162AlafsTer8	p.I162Afs*8	ENST00000269305	NM_001126112.2	162	ATc/Gc	5/11	0.348435499214868	3	FACETS	0.964	0.903	1	0.964	0.903	1	CLONAL	2	TRUE	1	0.348435499214868	3		811	853	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456365	32456365	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	238	646	1	ENST00000332351.3:c.527G>T	p.Arg176Leu	p.R176L	ENST00000332351	NM_024426.4	176	cGc/cTc	1/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.516415541210766	2		647	883	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0045290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	180	354	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.180343350148524	2	FACETS	1	0.985	1	0.617	0.572	0.662	INDETERMINATE	1	TRUE	0	0.533583293124811	2		354	547	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577595	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CAGT	novel	NA	P-0045290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	188	640	0	ENST00000269305.4:c.683_686dup	p.Cys229Ter	p.C229*	ENST00000269305	NM_001126112.2	229	tgt/tgACTGt	7/11	0.533583293124811	1	FACETS	0.992	0.924	1	0.992	0.924	1	CLONAL	1	TRUE	0	0.533583293124811	1		640	521	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793338	242793338	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	237	951	0	ENST00000334409.5:c.739G>T	p.Glu247Ter	p.E247*	ENST00000334409	NM_005018.2	247	Gag/Tag	5/5	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.533583293124811	2		951	646	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665260	138665260	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	38	750	0	ENST00000330315.3:c.305del	p.Ile102ThrfsTer48	p.I102Tfs*48	ENST00000330315	NM_023067.3	102	aTc/ac	1/1	0.533583293124811	1	FACETS	0.204	0.168	0.244	0.204	0.168	0.244	SUBCLONAL	1	TRUE	0	0.533583293124811	1		750	512	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971123	21971129	+	frameshift_variant	Frame_Shift_Del	DEL	TGAGAGT	TGAGAGT	-	novel	NA	P-0045290-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	232	456	0	ENST00000304494.5:c.229_235del	p.Thr77ProfsTer67	p.T77Pfs*67	ENST00000304494	NM_000077.4	77	ACTCTCAcc/cc	2/3	0.533583293124811	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.533583293124811	1		456	504	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0045291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	19	588	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.163	0.123	0.211	0.163	0.123	0.211	SUBCLONAL	1	TRUE	1	0.337190618244528	2		588	692	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0045291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	18	386	2	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	0.336731438832752	3	FACETS	0.196	0.147	0.256	0.098	0.073	0.128	SUBCLONAL	1	TRUE	1	0.337190618244528	3		388	635	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351422	70351422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	86	377	0	ENST00000374080.3:c.4070G>A	p.Arg1357His	p.R1357H	ENST00000374080		1357	cGc/cAc	29/45	0.0624620022256974	2	FACETS	1	0.934	1			1	INDETERMINATE	1	TRUE	NA	0.337190618244528	2		377	475	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393211	393211	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	37	497	0	ENST00000380956.4:c.59G>T	p.Gly20Val	p.G20V	ENST00000380956	NM_001195286.1	20	gGc/gTc	2/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.337190618244528	NA		497	612	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2185914	2185915	+	inframe_insertion	In_Frame_Ins	INS	-	-	TAT	novel	NA	P-0045291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	33	574	0	ENST00000398665.3:c.187_189dup	p.Tyr63dup	p.Y63dup	ENST00000398665	NM_032482.2	63	-/TAT	3/28	1	2	FACETS	0.327	0.265	0.396	0.327	0.265	0.396	SUBCLONAL	1	TRUE	1	0.337190618244528	2		574	599	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919327	178919327	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	14	187	0	ENST00000263967.3:c.812A>G	p.Lys271Arg	p.K271R	ENST00000263967	NM_006218.2	271	aAg/aGg	4/21	0.336731438832752	3	FACETS	0.359	0.259	0.481	0.18	0.129	0.241	SUBCLONAL	1	TRUE	1	0.337190618244528	3		187	270	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0045292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	203	545	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.386810538681641	4	FACETS	0.945	0.891	0.999			1	CLONAL	4	TRUE	NA	0.386810538681641	4		545	385	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577334	64577334	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	298	662	0	ENST00000312049.6:c.248del	p.Leu83ArgfsTer36	p.L83Rfs*36	ENST00000312049	NM_130799.2	83	cTg/cg	2/10	0.32065623647164	4	FACETS	1	0.982	1	1	0.995	1	CLONAL	3	TRUE	2	0.386810538681641	4		662	662	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612142	189612142	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	279	647	0	ENST00000264731.3:c.1894G>A	p.Glu632Lys	p.E632K	ENST00000264731	NM_003722.4	632	Gag/Aag	14/14	0.386810538681641	4	FACETS	1	0.99	1			1	CLONAL	2	TRUE	NA	0.386810538681641	4		647	810	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121811	2121811	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397515223	NA	P-0045292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	258	577	0	ENST00000219476.3:c.1973A>C	p.Lys658Thr	p.K658T	ENST00000219476	NM_000548.3	658	aAg/aCg	19/42	0.359461087898363	3	FACETS	0.968	0.916	1	0.968	0.916	1	CLONAL	3	TRUE	0	0.386810538681641	3		577	548	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711969	89711969	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	63	408	0	ENST00000371953.3:c.587A>T	p.His196Leu	p.H196L	ENST00000371953	NM_000314.4	196	cAc/cTc	6/9	0.386810538681641	3	FACETS	1	0.914	1	0.534	0.464	0.609	CLONAL	1	TRUE	1	0.386810538681641	3		408	364	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109765	115109765	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	200	644	0	ENST00000257566.3:c.2113T>C	p.Ser705Pro	p.S705P	ENST00000257566	NM_016569.3	705	Tcc/Ccc	8/8	0.226280888296936	3	FACETS	1	0.969	1	0.712	0.664	0.761	INDETERMINATE	2	TRUE	0	0.386810538681641	3		644	578	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472513	88472513	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	203	690	3	ENST00000360948.2:c.2042C>A	p.Ala681Asp	p.A681D	ENST00000360948	NM_001012338.2	681	gCc/gAc	16/19	0.386810538681641	3	FACETS	0.906	0.844	0.971	0.906	0.844	0.971	CLONAL	2	TRUE	1	0.386810538681641	3		693	691	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576843	7576854	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GACTTAGTACCT	GACTTAGTACCT	-	novel	NA	P-0045292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	211	552	0	ENST00000269305.4:c.992_993+10del		p.X331_splice	ENST00000269305	NM_001126112.2	331		9/11	0.352427715011053	3	FACETS	0.88	0.826	0.935	0.88	0.826	0.935	CLONAL	3	TRUE	0	0.386810538681641	3		552	493	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29546029	29546029	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0045292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	209	431	0	ENST00000356175.3:c.1534A>T	p.Arg512Ter	p.R512*	ENST00000356175	NM_000267.3	512	Aga/Tga	14/57	0.352427715011053	3	FACETS	0.941	0.884	0.998	0.941	0.884	0.998	CLONAL	3	TRUE	0	0.386810538681641	3		431	457	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290236	15290236	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs112197217	NA	P-0045292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	383	798	0	ENST00000263388.2:c.3399C>G	p.His1133Gln	p.H1133Q	ENST00000263388	NM_000435.2	1133	caC/caG	21/33	0.359461087898363	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	0	0.386810538681641	3		798	742	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508270	106508270	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	203	424	1	ENST00000359195.3:c.264C>A	p.Tyr88Ter	p.Y88*	ENST00000359195	NM_002649.2	88	taC/taA	2/11	0.386810538681641	4	FACETS	1	0.964	1	0.781	0.732	0.83	CLONAL	3	TRUE	0	0.386810538681641	4		425	466	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0045293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	27	403	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.993	0.791	1	0.993	0.791	1	CLONAL	1	TRUE	1	0.17	2		403	320	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0045293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	90	634	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.17	2		634	706	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232138	98232138	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs863224650	NA	P-0045293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	29	374	0	ENST00000331920.6:c.1804C>T	p.Arg602Ter	p.R602*	ENST00000331920	NM_000264.3	602	Cga/Tga	13/24	1	2	FACETS	0.676	0.541	0.829	0.676	0.541	0.829	SUBCLONAL	1	TRUE	1	0.17	2		374	505	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56409145	56409145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1308397244	NA	P-0045293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	31	389	0	ENST00000348428.3:c.1652G>A	p.Arg551Gln	p.R551Q	ENST00000348428	NM_006785.3	551	cGa/cAa	14/17	1	2	FACETS	0.809	0.653	0.985	0.809	0.653	0.985	CLONAL	1	TRUE	1	0.17	2		389	451	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332595	153332595	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	33	424	0	ENST00000281708.4:c.361G>T	p.Glu121Ter	p.E121*	ENST00000281708	NM_033632.3	121	Gag/Tag	2/12	1	2	FACETS	0.842	0.685	1	0.842	0.685	1	CLONAL	1	TRUE	1	0.17	2		424	461	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145735	61145736	+	stop_gained	Nonsense_Mutation	DNP	GA	GA	TG	novel	NA	P-0045293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	31	302	0	ENST00000295025.8:c.847_848delinsTG	p.Glu283Ter	p.E283*	ENST00000295025	NM_002908.2	283	GAa/TGa	7/11	1	2	FACETS	0.999	0.809	1	0.999	0.809	1	CLONAL	1	TRUE	1	0.17	2		302	365	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790162	40790162	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	37	533	0	ENST00000373198.4:c.2569C>T	p.Leu857Phe	p.L857F	ENST00000373198	NM_133170.3	857	Ctt/Ttt	18/32	0.3	1	FACETS	0.688	0.566	0.825	0.688	0.566	0.825	SUBCLONAL	1	TRUE	0	0.17	1		533	579	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502473	186502473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	31	250	0	ENST00000323963.5:c.196C>T	p.Pro66Ser	p.P66S	ENST00000323963		66	Ccc/Tcc	3/11	0.162325678153858	1	FACETS	0.871	0.705	1	0.871	0.705	1	CLONAL	1	TRUE	0	0.17	1		250	383	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244226	153244226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	38	388	0	ENST00000281708.4:c.1931G>A	p.Gly644Glu	p.G644E	ENST00000281708	NM_033632.3	644	gGa/gAa	12/12	1	2	FACETS	0.81	0.669	0.968	0.81	0.669	0.968	CLONAL	1	TRUE	1	0.17	2		388	552	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184929	32184929	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0045293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	31	585	0	ENST00000375023.3:c.1738+1G>A		p.X580_splice	ENST00000375023	NM_004557.3	580			1	2	FACETS	0.595	0.48	0.726	0.595	0.48	0.726	SUBCLONAL	1	TRUE	1	0.17	2		585	613	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152009023	152009023	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	22	291	0	ENST00000262189.6:c.599C>A	p.Ser200Tyr	p.S200Y	ENST00000262189	NM_170606.2	200	tCt/tAt	5/59	1	2	FACETS	0.799	0.619	1	0.799	0.619	1	CLONAL	1	TRUE	1	0.17	2		291	324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576870	7576870	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs876659384	NA	P-0045294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	125	717	0	ENST00000269305.4:c.976G>T	p.Glu326Ter	p.E326*	ENST00000269305	NM_001126112.2	326	Gaa/Taa	9/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.26645284822131	NA		717	583	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601957	43601957	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	60	774	0	ENST00000355710.3:c.1001G>T	p.Trp334Leu	p.W334L	ENST00000355710	NM_020975.4	334	tGg/tTg	5/20	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.26645284822131	NA		774	445	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298847	46298847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	48	250	1	ENST00000334344.6:c.5494G>A	p.Glu1832Lys	p.E1832K	ENST00000334344	NM_152641.2	1832	Gaa/Aaa	21/21	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.26645284822131	NA		251	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0045299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	117	623	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.203428910468012	2		623	1002	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0045299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	50	427	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.203428910468012	1	FACETS	0.852	0.723	0.994	0.852	0.723	0.994	CLONAL	1	FALSE	0	0.203428910468012	1		427	518	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	56	425	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.207849051135133	2		425	486	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0045300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	1374	591	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.207849051135133	15	FACETS	1	0.99	1			1	CLONAL	14	TRUE	NA	0.207849051135133	15		591	2185	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913381	NA	P-0045300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	48	558	0	ENST00000304494.5:c.322G>A	p.Asp108Asn	p.D108N	ENST00000304494	NM_000077.4	108	Gat/Aat	2/3	0.207849051135133	1	FACETS	0.821	0.694	0.961	0.821	0.694	0.961	CLONAL	1	TRUE	0	0.207849051135133	1		558	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1555525970	NA	P-0045300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	82	806	0	ENST00000269305.4:c.548C>G	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tGa	5/11	0.207849051135133	1	FACETS	0.858	0.756	0.968	0.858	0.756	0.968	CLONAL	1	TRUE	0	0.207849051135133	1		806	824	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106696	2106696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	107	1077	0	ENST00000219476.3:c.700G>A	p.Glu234Lys	p.E234K	ENST00000219476	NM_000548.3	234	Gag/Aag	8/42	0.207849051135133	1	FACETS	0.989	0.886	1	0.989	0.886	1	CLONAL	1	TRUE	0	0.207849051135133	1		1077	933	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742733	39742733	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	85	684	0	ENST00000361337.2:c.1576G>C	p.Glu526Gln	p.E526Q	ENST00000361337	NM_003286.2	526	Gag/Cag	15/21	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.207849051135133	2		684	814	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591035	67591035	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1367776221	NA	P-0045300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	47	341	0	ENST00000274335.5:c.1628G>A	p.Arg543Lys	p.R543K	ENST00000274335		543	aGa/aAa	12/15	0.207849051135133	1	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	0	0.207849051135133	1		341	386	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481417	140481417	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913348	NA	P-0045300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	68	574	0	ENST00000288602.6:c.1391G>C	p.Gly464Ala	p.G464A	ENST00000288602	NM_004333.4	464	gGa/gCa	11/18	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.207849051135133	2		574	602	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977198	85977198	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0045300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	51	528	0	ENST00000263360.6:c.800C>G	p.Ser267Ter	p.S267*	ENST00000263360	NM_003797.3	267	tCa/tGa	8/12	1	2	FACETS	0.902	0.767	1	0.902	0.767	1	CLONAL	1	TRUE	1	0.207849051135133	2		528	544	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44910953	44910953	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0045300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	11	204	0	ENST00000377967.4:c.655-1G>C		p.X219_splice	ENST00000377967	NM_021140.2	219			0.207849051135133	0	FACETS	0.403	0.278	0.558			1	SUBCLONAL	1	TRUE	NA	0.207849051135133	0		204	208	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335148	65335148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	58	641	0	ENST00000342505.4:c.493G>A	p.Asp165Asn	p.D165N	ENST00000342505	NM_002227.2	165	Gat/Aat	6/25	1	2	FACETS	0.912	0.783	1	0.912	0.783	1	CLONAL	1	TRUE	1	0.207849051135133	2		641	612	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600594	43600594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	40	822	3	ENST00000355710.3:c.820G>A	p.Ala274Thr	p.A274T	ENST00000355710	NM_020975.4	274	Gcg/Acg	4/20	1	2	FACETS	0.485	0.401	0.578	0.485	0.401	0.578	SUBCLONAL	1	TRUE	1	0.207849051135133	2		825	794	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426373	49426373	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	112	1115	0	ENST00000301067.7:c.12115G>C	p.Glu4039Gln	p.E4039Q	ENST00000301067	NM_003482.3	4039	Gag/Cag	39/54	1	2	FACETS	0.941	0.844	1	0.941	0.844	1	CLONAL	1	TRUE	1	0.207849051135133	2		1115	1145	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716298	52716298	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	131	875	0	ENST00000322088.6:c.742C>G	p.Leu248Val	p.L248V	ENST00000322088	NM_014225.5	248	Ctg/Gtg	6/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.207849051135133	2		875	875	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098775	178098775	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	40	755	0	ENST00000397062.3:c.270G>C	p.Gln90His	p.Q90H	ENST00000397062	NM_006164.4	90	caG/caC	2/5	1	2	FACETS	0.505	0.418	0.602	0.505	0.418	0.602	SUBCLONAL	1	TRUE	1	0.207849051135133	2		755	762	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742637	39742637	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	47	491	0	ENST00000361337.2:c.1480G>C	p.Glu494Gln	p.E494Q	ENST00000361337	NM_003286.2	494	Gag/Cag	15/21	1	2	FACETS	0.844	0.712	0.989	0.844	0.712	0.989	CLONAL	1	TRUE	1	0.207849051135133	2		491	536	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430248	181430248	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	44	591	0	ENST00000325404.1:c.100C>G	p.Gln34Glu	p.Q34E	ENST00000325404	NM_003106.3	34	Cag/Gag	1/1	0.207849051135133	3	FACETS	0.689	0.577	0.815	0.345	0.288	0.408	SUBCLONAL	1	TRUE	1	0.207849051135133	3		591	678	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659239	86659239	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	35	396	0	ENST00000274376.6:c.1528G>A	p.Glu510Lys	p.E510K	ENST00000274376	NM_002890.2	510	Gaa/Aaa	11/25	0.207849051135133	1	FACETS	0.931	0.766	1	0.931	0.766	1	CLONAL	1	TRUE	0	0.207849051135133	1		396	324	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683989	117683989	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	87	545	0	ENST00000368508.3:c.3158C>G	p.Pro1053Arg	p.P1053R	ENST00000368508	NM_002944.2	1053	cCa/cGa	21/43	0.207849051135133	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.207849051135133	1		545	602	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031732	69031732	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045300-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	82	730	0	ENST00000288368.4:c.3487G>C	p.Glu1163Gln	p.E1163Q	ENST00000288368	NM_024870.2	1163	Gag/Cag	28/40	1	2	FACETS	0.983	0.865	1	0.983	0.865	1	CLONAL	1	TRUE	1	0.207849051135133	2		730	803	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0045301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	97	241	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.436516065412018	2		241	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691022	NA	P-0045301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	525	924	1	ENST00000269305.4:c.1024del	p.Arg342GlufsTer3	p.R342Efs*3	ENST00000269305	NM_001126112.2	342	Cga/ga	10/11	0.436516065412018	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.436516065412018	2		925	1194	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855014	76855017	+	frameshift_variant	Frame_Shift_Del	DEL	CTAT	CTAT	-	novel	NA	P-0045301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	150	656	0	ENST00000373344.5:c.5819_5822del	p.Asp1940ValfsTer14	p.D1940Vfs*14	ENST00000373344	NM_000489.3	1940	gATAGt/gt	25/35	0.255683618958911	1	FACETS	0.843	0.773	0.916	0.843	0.773	0.916	INDETERMINATE	1	TRUE	0	0.436516065412018	1		656	637	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023421	33023421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1190459895	NA	P-0045301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	282	951	1	ENST00000300177.4:c.530G>A	p.Arg177His	p.R177H	ENST00000300177	NM_001191322.1	177	cGt/cAt	2/2	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.436516065412018	2		952	1181	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204512049	204512049	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	207	432	0	ENST00000367182.3:c.649T>C	p.Ser217Pro	p.S217P	ENST00000367182	NM_001278516.1	217	Tca/Cca	8/11	0.102104180931985	5	FACETS	1	0.984	1	0.771	0.722	0.822	INDETERMINATE	2	TRUE	2	0.658830277282474	5		432	540	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067882	30067883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0045303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	372	757	0	ENST00000338641.4:c.1069dup	p.Glu357GlyfsTer22	p.E357Gfs*22	ENST00000338641	NM_000268.3	356	ttg/ttGg	11/16	0.658830277282474	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.658830277282474	1		757	634	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045911	180045911	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045303-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	46	530	1	ENST00000261937.6:c.2860C>A	p.Pro954Thr	p.P954T	ENST00000261937	NM_182925.4	954	Ccc/Acc	21/30	0.112268040054705	4	FACETS	0.39	0.328	0.459	0.195	0.164	0.23	INDETERMINATE	1	TRUE	2	0.658830277282474	4		531	594	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0045304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	15	347	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.16720440403552	3	FACETS	0.649	0.474	0.86	0.325	0.237	0.43	SUBCLONAL	1	TRUE	1	0.16	3		347	312	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610695	52610695	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	119	494	0	ENST00000394830.3:c.3478C>T	p.Arg1160Ter	p.R1160*	ENST00000394830	NM_018313.4	1160	Cga/Tga	23/30	0.483136319827111	1	FACETS	0.965	0.88	1	0.965	0.88	1	CLONAL	1	TRUE	0	0.483136319827111	1		494	387	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831936	72831936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs181722888	NA	P-0045305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	252	964	1	ENST00000268489.5:c.4645G>A	p.Val1549Ile	p.V1549I	ENST00000268489	NM_006885.3	1549	Gtc/Atc	9/10	1	2	FACETS	0.96	0.898	1	0.96	0.898	1	CLONAL	1	TRUE	1	0.483136319827111	2		965	1087	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023095	27023095	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	37	128	0	ENST00000324856.7:c.201del	p.Gln67HisfsTer34	p.Q67Hfs*34	ENST00000324856	NM_006015.4	67	caG/ca	1/20	0.483136319827111	1	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	0	0.483136319827111	1		128	109	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602737	10602737	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	287	1006	0	ENST00000171111.5:c.841del	p.Leu281CysfsTer36	p.L281Cfs*36	ENST00000171111	NM_203500.1	281	Ctg/tg	3/6	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.483136319827111	2		1006	1156	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904880	101904880	+	protein_altering_variant	In_Frame_Ins	INS	G	G	TTTA	novel	NA	P-0045305-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	165	489	0	ENST00000374994.4:c.868delinsTTTA	p.Asp290delinsPheAsn	p.D290delinsFN	ENST00000374994	NM_004612.2	290	Gat/TTTAat	5/9	0.483136319827111	1	FACETS	0.963	0.89	1	0.963	0.89	1	CLONAL	1	TRUE	0	0.483136319827111	1		489	538	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	154	425	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.964	0.891	1	0.964	0.891	1	CLONAL	1	TRUE	1	0.736464190802706	2		425	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0045309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	22	833	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.724249463767637	1	FACETS	0.052	0.039	0.066	0.052	0.039	0.066	SUBCLONAL	1	TRUE	0	0.736464190802706	1		833	729	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937028	48937028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	51	517	0	ENST00000267163.4:c.796C>T	p.Gln266Ter	p.Q266*	ENST00000267163	NM_000321.2	266	Caa/Taa	8/27	0.736464190802706	1	FACETS	0.174	0.147	0.202	0.174	0.147	0.202	SUBCLONAL	1	TRUE	0	0.736464190802706	1		517	504	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951171	48951171	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587778846	NA	P-0045309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	207	460	1	ENST00000267163.4:c.1332+1G>T		p.X444_splice	ENST00000267163	NM_000321.2	444			0.736464190802706	1	FACETS	0.856	0.806	0.906	0.856	0.806	0.906	CLONAL	1	TRUE	0	0.736464190802706	1		461	415	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685314	89685314	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	159	344	0	ENST00000371953.3:c.209T>A	p.Leu70His	p.L70H	ENST00000371953	NM_000314.4	70	cTt/cAt	3/9	0.736464190802706	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.736464190802706	1		344	269	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556485	29556485	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0045309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	180	383	0	ENST00000356175.3:c.2850+2T>C		p.X950_splice	ENST00000356175	NM_000267.3	950			0.736464190802706	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.736464190802706	1		383	305	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151168662	151168662	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045309-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	323	556	0	ENST00000262187.5:c.305A>G	p.Lys102Arg	p.K102R	ENST00000262187	NM_005614.3	102	aAa/aGa	5/8	0.722761538315367	3	FACETS	0.934	0.881	0.988			1	CLONAL	1	TRUE	NA	0.736464190802706	3		556	1285	SUCCESS
APC	324	MSKCC	GRCh37	5	112175100	112175101	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0045310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	10	246	0	ENST00000257430.4:c.3814dup	p.Ser1272PhefsTer4	p.S1272Ffs*4	ENST00000257430	NM_000038.5	1270	tgt/tgTt	16/16	0.195655948136081	3	FACETS	0.345	0.234	0.483	0.172	0.117	0.242	INDETERMINATE	1	TRUE	1	0.513451222709115	3		246	142	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627284	12627284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	12	463	1	ENST00000251849.4:c.1432G>A	p.Glu478Lys	p.E478K	ENST00000251849	NM_002880.3	478	Gaa/Aaa	14/17	0.158073734713913	4	FACETS	0.456	0.322	0.621	0.228	0.161	0.311	INDETERMINATE	1	TRUE	2	0.513451222709115	4		464	155	SUCCESS
ATM	472	MSKCC	GRCh37	11	108218083	108218083	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045310-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	73	381	0	ENST00000278616.4:c.8662A>C	p.Ile2888Leu	p.I2888L	ENST00000278616	NM_000051.3	2888	Ata/Cta	59/63	0.513451222709115	3	FACETS	1	0.965	1	0.629	0.556	0.706	CLONAL	1	TRUE	1	0.513451222709115	3		381	284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0045312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	872	833	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.848674394102397	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.848674394102397	2		833	1003	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109309846	109309846	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs369093694	NA	P-0045312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	337	651	0	ENST00000436639.2:c.1469G>T	p.Arg490Leu	p.R490L	ENST00000436639	NM_014454.2	490	cGt/cTt	9/10	1	2	FACETS	0.965	0.917	1	0.965	0.917	1	CLONAL	1	TRUE	1	0.848674394102397	2		651	823	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	250	812	0	ENST00000397752.3:c.3028G>A	p.Asp1010Asn	p.D1010N	ENST00000397752	NM_000245.2	1010	Gat/Aat	14/21	0.597762064416069	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.631141322203662	1		812	525	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056181	27056181	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	112	712	0	ENST00000324856.7:c.1177C>T	p.Gln393Ter	p.Q393*	ENST00000324856	NM_006015.4	393	Cag/Tag	2/20	1	2	FACETS	0.517	0.465	0.571	0.517	0.465	0.571	SUBCLONAL	1	TRUE	1	0.631141322203662	2		712	687	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435151	18435151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs183245589	NA	P-0045313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	33	477	0	ENST00000266497.5:c.136G>A	p.Glu46Lys	p.E46K	ENST00000266497		46	Gag/Aag	1/31	1	2	FACETS	0.23	0.187	0.278	0.23	0.187	0.278	SUBCLONAL	1	TRUE	1	0.631141322203662	2		477	455	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098884	178099449	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTTTTTTCTGTTTTTCCAGCTCATACTCTTTCCGTCGCTGACTGAAGTCAAATACTTCTCGACTTACTCCAAGATCTATATCTTGCCTCCAAAGTATGTCAATCAAATCCATGTCCTATGTTTAAGACAAAAAAAGGAAGGAGAGAGCTCATGTTTTTTAAATGACAGATACCACATAAATTAATTCACATTATGCCACTGTTGATGGTGGGAAGTGGGGAGATTACAAATACAATCTAAATGAGAACACAGATCCAATGTTCTAGAAGAGCACAGTTAATTCCATTCAATGAATCTATTCATTAAAGACAACAAACAACCTACAAACACATAGCCATCCATTCTAATCACTTGGATCATTAATGATAGGGTGATGGTAGAGGTCACTAAAGGGCAAAGTCACAAATGGTTTGAATGAGAAGAAATCCCACCCTTGTTTAATGGAATATAGAAATTAGAGCAAGCACTCTAAGCCACTGGCTTATATAAGAGAAGTGGGGTCTGGAAAACATTACTGAATACATGGAGTTTTCTTTAAACTTTGCTCAGCAAATATCCAGTTTAT	AGTTTTTTCTGTTTTTCCAGCTCATACTCTTTCCGTCGCTGACTGAAGTCAAATACTTCTCGACTTACTCCAAGATCTATATCTTGCCTCCAAAGTATGTCAATCAAATCCATGTCCTATGTTTAAGACAAAAAAAGGAAGGAGAGAGCTCATGTTTTTTAAATGACAGATACCACATAAATTAATTCACATTATGCCACTGTTGATGGTGGGAAGTGGGGAGATTACAAATACAATCTAAATGAGAACACAGATCCAATGTTCTAGAAGAGCACAGTTAATTCCATTCAATGAATCTATTCATTAAAGACAACAAACAACCTACAAACACATAGCCATCCATTCTAATCACTTGGATCATTAATGATAGGGTGATGGTAGAGGTCACTAAAGGGCAAAGTCACAAATGGTTTGAATGAGAAGAAATCCCACCCTTGTTTAATGGAATATAGAAATTAGAGCAAGCACTCTAAGCCACTGGCTTATATAAGAGAAGTGGGGTCTGGAAAACATTACTGAATACATGGAGTTTTCTTTAAACTTTGCTCAGCAAATATCCAGTTTAT	-	novel	NA	P-0045313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	134	650	0	ENST00000397062.3:c.46-450_161del		p.X16_splice	ENST00000397062	NM_006164.4	16		2/5	1	2	FACETS	0.705	0.643	0.77	0.705	0.643	0.77	SUBCLONAL	1	TRUE	1	0.631141322203662	2		650	602	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713864	30713864	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045313-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	460	724	0	ENST00000295754.5:c.1189G>C	p.Asp397His	p.D397H	ENST00000295754	NM_003242.5	397	Gac/Cac	4/7	0.602437786934714	2	FACETS	0.876	0.843	0.909	0.876	0.843	0.909	CLONAL	2	TRUE	0	0.631141322203662	2		724	832	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	66	425	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.694921317972993	2		425	179	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225060	NA	P-0045314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	269	524	0	ENST00000263967.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000263967	NM_006218.2	104	cCa/cTa	2/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.694921317972993	2		524	743	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0045314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	163	426	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.694921317972993	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.694921317972993	1		426	259	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0045314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9896	236	734	4	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.694921317972993	35	FACETS	0.836	0.773	0.901			1	CLONAL	1	TRUE	NA	0.694921317972993	35		738	10132	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221710	55221710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4761	1260	467	0	ENST00000275493.2:c.754C>T	p.Arg252Cys	p.R252C	ENST00000275493	NM_005228.3	252	Cgc/Tgc	7/28	0.694921317972993	35	FACETS	0.939	0.911	0.967			1	CLONAL	8	TRUE	NA	0.694921317972993	35		467	6021	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031524	11031524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754546102	NA	P-0045314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	154	793	0	ENST00000327064.4:c.1439C>T	p.Thr480Met	p.T480M	ENST00000327064	NM_199141.1	480	aCg/aTg	13/16	0.192767979013877	3	FACETS	1	0.98	1	0.397	0.366	0.43	INDETERMINATE	1	TRUE	0	0.694921317972993	3		793	501	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0045315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	505	563	1	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.840628091871103	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.856527134917705	1		564	668	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720709	89720709	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs863224909	NA	P-0045315-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	116	75	0	ENST00000371953.3:c.860C>A	p.Ser287Ter	p.S287*	ENST00000371953	NM_000314.4	287	tCa/tAa	8/9	0.840628091871103	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.856527134917705	1		75	148	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0045316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	533	663	1	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.886385504718356	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.886385504718356	1		664	656	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115947	8115948	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0045316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	392	430	0	ENST00000346208.3:c.1295dup	p.His433ThrfsTer74	p.H433Tfs*74	ENST00000346208		431	-/C	6/6	1	2	FACETS	0.898	0.856	0.94	0.898	0.856	0.94	CLONAL	1	TRUE	1	0.886385504718356	2		430	985	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684061	29684061	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	78	429	0	ENST00000356175.3:c.7759G>T	p.Glu2587Ter	p.E2587*	ENST00000356175	NM_000267.3	2587	Gaa/Taa	52/57	0.886385504718356	1	FACETS	0.225	0.198	0.253	0.225	0.198	0.253	SUBCLONAL	1	TRUE	0	0.886385504718356	1		429	436	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553672	29553672	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	253	466	0	ENST00000356175.3:c.2223del	p.Phe741LeufsTer7	p.F741Lfs*7	ENST00000356175	NM_000267.3	741	Ttt/tt	18/57	0.886385504718356	1	FACETS	0.696	0.661	0.73	0.696	0.661	0.73	SUBCLONAL	1	TRUE	0	0.886385504718356	1		466	457	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3114958	3114958	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	507	689	0	ENST00000078429.4:c.493G>C	p.Asp165His	p.D165H	ENST00000078429	NM_002067.2	165	Gac/Cac	4/7	1	2	FACETS	0.969	0.93	1	0.969	0.93	1	CLONAL	1	TRUE	1	0.886385504718356	2		689	1181	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645732	12645732	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	323	419	1	ENST00000251849.4:c.737C>A	p.Ser246Ter	p.S246*	ENST00000251849	NM_002880.3	246	tCa/tAa	7/17	0.489710108791658	3	FACETS	0.907	0.856	0.958			1	INDETERMINATE	1	TRUE	NA	0.886385504718356	3		420	1160	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185855	32185855	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045316-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	486	696	0	ENST00000375023.3:c.1541C>G	p.Thr514Ser	p.T514S	ENST00000375023	NM_004557.3	514	aCc/aGc	9/30	0.886385504718356	1	FACETS	0.99	0.964	1	0.99	0.964	1	CLONAL	1	TRUE	0	0.886385504718356	1		696	617	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0045318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	469	752	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.354573811297559	2	FACETS	0.869	0.834	0.904	1	0.995	1	CLONAL	3	TRUE	0	0.354573811297559	2		752	1015	SUCCESS
APC	324	MSKCC	GRCh37	5	112175492	112175493	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0045318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	214	393	0	ENST00000257430.4:c.4203dup	p.Ala1402CysfsTer7	p.A1402Cfs*7	ENST00000257430	NM_000038.5	1401	att/aTtt	16/16	0.354573811297559	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.354573811297559	2		393	547	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466993	18466993	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs370262872	NA	P-0045318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	113	379	0	ENST00000266497.5:c.1132C>T	p.Arg378Ter	p.R378*	ENST00000266497		378	Cga/Tga	5/31	0.320322592975977	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.354573811297559	1		379	430	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741455	39741455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	163	472	0	ENST00000361337.2:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000361337	NM_003286.2	448	Cgg/Tgg	14/21	0.305859912063107	5	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.354573811297559	5		472	1117	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793202	33793202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	40	84	0	ENST00000498907.2:c.119C>T	p.Ala40Val	p.A40V	ENST00000498907	NM_004364.3	40	gCg/gTg	1/1	1	2	FACETS	0.757	0.64	0.882	1	0.96	1	SUBCLONAL	2	TRUE	1	0.354573811297559	2		84	149	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117868	70117868	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1407667250	NA	P-0045318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	375	500	0	ENST00000245479.2:c.336C>A	p.Phe112Leu	p.F112L	ENST00000245479	NM_000346.3	112	ttC/ttA	1/3	0.354573811297559	2	FACETS	0.971	0.93	1	1	0.996	1	CLONAL	3	TRUE	0	0.354573811297559	2		500	726	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281592	49281593	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0045318-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1240	128	750	0	ENST00000282018.3:c.639_640insG	p.Phe214ValfsTer72	p.F214Vfs*72	ENST00000282018	NM_020377.2	213	-/G	1/1	0.354573811297559	4	FACETS	0.715	0.646	0.788	0.357	0.323	0.394	SUBCLONAL	1	TRUE	2	0.354573811297559	4		750	1368	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0045319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	96	262	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.906	0.818	0.995	0.906	0.818	0.995	CLONAL	1	TRUE	1	0.765464292062928	2		262	277	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0045319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	157	403	0				ENST00000310581	NM_198253.2	-/1132			0.765464292062928	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.765464292062928	1		403	249	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566827	212566827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202247795	NA	P-0045319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	137	323	0	ENST00000342788.4:c.1354G>A	p.Glu452Lys	p.E452K	ENST00000342788	NM_005235.2	452	Gaa/Aaa	12/28	0.765464292062928	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.765464292062928	1		323	219	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637711	52637711	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	111	434	0	ENST00000394830.3:c.2605C>T	p.Gln869Ter	p.Q869*	ENST00000394830	NM_018313.4	869	Cag/Tag	18/30	0.765464292062928	1	FACETS	0.918	0.85	0.985	0.918	0.85	0.985	CLONAL	1	TRUE	0	0.765464292062928	1		434	195	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026184	71026184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	124	355	0	ENST00000318789.4:c.1438G>A	p.Glu480Lys	p.E480K	ENST00000318789	NM_032682.5	480	Gaa/Aaa	17/21	0.765464292062928	1	FACETS	0.917	0.853	0.981	0.917	0.853	0.981	CLONAL	1	TRUE	0	0.765464292062928	1		355	218	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517620	176517620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	253	804	1	ENST00000292408.4:c.321G>A	p.Met107Ile	p.M107I	ENST00000292408	NM_213647.1	107	atG/atA	3/18	0.765464292062928	1	FACETS	0.919	0.874	0.964	0.919	0.874	0.964	CLONAL	1	TRUE	0	0.765464292062928	1		805	444	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248702	212248702	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	184	447	0	ENST00000342788.4:c.3565C>T	p.His1189Tyr	p.H1189Y	ENST00000342788	NM_005235.2	1189	Cac/Tac	28/28	0.765464292062928	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.765464292062928	1		447	291	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829797	72829797	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs953863150	NA	P-0045319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	269	680	0	ENST00000268489.5:c.6784G>C	p.Asp2262His	p.D2262H	ENST00000268489	NM_006885.3	2262	Gat/Cat	9/10	0.765464292062928	1	FACETS	0.964	0.919	1	0.964	0.919	1	CLONAL	1	TRUE	0	0.765464292062928	1		680	450	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677899	117677899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	91	410	0	ENST00000368508.3:c.4034C>T	p.Ser1345Phe	p.S1345F	ENST00000368508	NM_002944.2	1345	tCt/tTt	25/43	0.500936928601674	1	FACETS	0.558	0.503	0.615	0.558	0.503	0.615	SUBCLONAL	1	TRUE	0	0.765464292062928	1		410	263	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020387	123020387	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	112	277	0	ENST00000355640.3:c.875T>C	p.Leu292Ser	p.L292S	ENST00000355640		292	tTa/tCa	2/7	0.765464292062928	1	FACETS	0.992	0.923	1	0.992	0.923	1	CLONAL	1	TRUE	0	0.765464292062928	1		277	182	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863319	57863319	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	24	779	1	ENST00000228682.2:c.1418del	p.Gly473AlafsTer40	p.G473Afs*40	ENST00000228682	NM_005269.2	472	Ggg/gg	11/12	0.238148240944734	8	FACETS	0.993	0.785	1	0.496	0.392	0.615	CLONAL	2	FALSE	4	0.238148240944734	8		780	174	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	33	606	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.187169001387765	4	FACETS	0.997	0.822	1	0.997	0.822	1	CLONAL	2	FALSE	2	0.238148240944734	4		610	172	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031919	10031919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs901717931	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	23	735	1	ENST00000330684.3:c.904G>A	p.Ala302Thr	p.A302T	ENST00000330684	NM_001134407.1	302	Gct/Act	3/13	0.188514532669617	1	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	FALSE	0	0.238148240944734	1		736	139	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	53	411	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	0.238148240944734	4	FACETS	0.928	0.803	1	1	0.964	1	CLONAL	3	FALSE	2	0.238148240944734	4		412	198	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	16	672	2	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	0.188514532669617	1	FACETS	0.918	0.684	1	0.918	0.684	1	CLONAL	1	FALSE	0	0.238148240944734	1		674	129	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121791	2121792	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs137854144	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	10	718	0	ENST00000219476.3:c.1959_1960del	p.Gly654LeufsTer2	p.G654Lfs*2	ENST00000219476	NM_000548.3	651	ccAGag/ccag	19/42	0.188514532669617	1	FACETS	0.606	0.413	0.847	0.606	0.413	0.847	SUBCLONAL	1	FALSE	0	0.238148240944734	1		718	122	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308383	15308383	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	24	684	1	ENST00000263388.2:c.125del	p.Pro42LeufsTer194	p.P42Lfs*194	ENST00000263388	NM_000435.2	42	cCt/ct	2/33	0.188514532669617	1	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	FALSE	0	0.238148240944734	1		685	142	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509127	66509127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145126637	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	14	362	0	ENST00000273854.3:c.200G>A	p.Arg67His	p.R67H	ENST00000273854	NM_004439.5	67	cGc/cAc	2/18	0.188514532669617	1	FACETS	1	0.838	1	1	0.838	1	CLONAL	1	FALSE	0	0.238148240944734	1		362	85	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs1057519842	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	29	369	0	ENST00000274335.5:c.1727_1729del	p.Thr576del	p.T576del	ENST00000274335		575	aaGACg/aag	12/15	0.187169001387765	4	FACETS	1	0.852	1	1	0.852	1	CLONAL	2	FALSE	2	0.238148240944734	4		369	143	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29579996	29579996	+	intron_variant	Intron	DEL	A	A	-	rs1567859802	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	32	373	2	ENST00000356175.3:c.4110+3865del		p.*1370*	ENST00000356175	NM_000267.3	1384/2839			1	2	FACETS	0.867	0.713	1	1	0.957	1	CLONAL	2	FALSE	1	0.238148240944734	2		375	155	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508805	106508805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762805000	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	10	585	0	ENST00000359195.3:c.799G>A	p.Glu267Lys	p.E267K	ENST00000359195	NM_002649.2	267	Gaa/Aaa	2/11	0.238148240944734	6	FACETS	0.633	0.428	0.889	0.211	0.142	0.297	SUBCLONAL	1	FALSE	3	0.238148240944734	6		585	196	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119781	70119781	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1274036689	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	33	715	3	ENST00000245479.2:c.788del	p.Gly263AlafsTer16	p.G263Afs*16	ENST00000245479	NM_000346.3	261	gaG/ga	3/3	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	1	0.238148240944734	2		718	221	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627501	37627501	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	21	536	1	ENST00000447079.4:c.1421del	p.Asn474IlefsTer8	p.N474Ifs*8	ENST00000447079	NM_015083.1	472	gtA/gt	2/14	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	FALSE	1	0.238148240944734	2		537	123	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588798	52588798	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1559827261	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	27	688	1	ENST00000394830.3:c.4230del	p.Pro1411LeufsTer21	p.P1411Lfs*21	ENST00000394830	NM_018313.4	1410	ggG/gg	27/30	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	FALSE	1	0.238148240944734	2		689	162	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217557	142217557	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1268253442	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	12	370	1	ENST00000350721.4:c.5440del	p.Arg1814GlufsTer10	p.R1814Efs*10	ENST00000350721	NM_001184.3	1814	Aga/ga	32/47	1	2	FACETS	0.925	0.656	1	0.925	0.656	1	CLONAL	1	FALSE	1	0.238148240944734	2		371	109	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439919	56439919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	98	701	2	ENST00000407977.2:c.673del	p.Arg225AlafsTer194	p.R225Afs*194	ENST00000407977		225	Cgc/gc	6/10	1	2	FACETS	0.844	0.761	0.93	1	0.989	1	CLONAL	3	FALSE	1	0.238148240944734	2		703	325	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416952	416953	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs771545848	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	27	524	6	ENST00000399788.2:c.3597dup	p.Gly1200ArgfsTer7	p.G1200Rfs*7	ENST00000399788	NM_001042603.1	1199	-/A	23/28	NA	2	FACETS	1	0.847	1			1	INDETERMINATE	2	FALSE	NA	0.238148240944734	2		530	108	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303220	15303220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs932099250	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	18	822	1	ENST00000263388.2:c.308G>A	p.Arg103Gln	p.R103Q	ENST00000263388	NM_000435.2	103	cGa/cAa	3/33	0.188514532669617	1	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	FALSE	0	0.238148240944734	1		823	101	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485403	57485403	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1394557997	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	17	368	0	ENST00000371085.3:c.985G>A	p.Gly329Arg	p.G329R	ENST00000371085	NM_000516.4	329	Gga/Aga	12/13	0.180415983928833	0	FACETS	0.761	0.572	0.981			1	CLONAL	1	FALSE	0	0.238148240944734	0		368	143	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054541	42054541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1458609443	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	14	384	2	ENST00000219905.7:c.7731del	p.Asp2578ThrfsTer10	p.D2578Tfs*10	ENST00000219905	NM_001164273.1	2575	agA/ag	22/24	1	2	FACETS	0.852	0.62	1	0.852	0.62	1	CLONAL	1	FALSE	1	0.238148240944734	2		386	138	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384650	31384651	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs756395138	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	15	725	0	ENST00000328111.2:c.1359dup	p.Leu454AlafsTer11	p.L454Afs*11	ENST00000328111	NM_006892.3	451	gag/gaGg	13/23	0.180415983928833	0	FACETS	0.989	0.734	1			1	CLONAL	1	FALSE	0	0.238148240944734	0		725	97	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042077	42042077	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	23	563	1	ENST00000219905.7:c.6276del	p.Ala2093ProfsTer9	p.A2093Pfs*9	ENST00000219905	NM_001164273.1	2091	gAa/ga	17/24	1	2	FACETS	0.76	0.601	0.939	1	0.929	1	CLONAL	2	FALSE	1	0.238148240944734	2		564	127	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366207	15366207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	32	791	0	ENST00000263377.2:c.1948G>A	p.Asp650Asn	p.D650N	ENST00000263377	NM_058243.2	650	Gac/Aac	10/20	0.188514532669617	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	FALSE	0	0.238148240944734	1		791	187	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394902	394902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767879003	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	10	582	0	ENST00000380956.4:c.298G>A	p.Ala100Thr	p.A100T	ENST00000380956	NM_001195286.1	100	Gct/Act	3/9	0.15609161771039	3	FACETS	0.627	0.425	0.878			1	SUBCLONAL	1	FALSE	NA	0.238148240944734	3		582	150	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	13	832	4	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	0.188514532669617	1	FACETS	0.601	0.43	0.808	0.601	0.43	0.808	SUBCLONAL	1	FALSE	0	0.238148240944734	1		836	160	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902297	50902297	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	15	824	0	ENST00000440232.2:c.193del	p.Val65LeufsTer11	p.V65Lfs*11	ENST00000440232	NM_002691.3	63	gaG/ga	2/27	0.188514532669617	1	FACETS	0.982	0.726	1	0.982	0.726	1	CLONAL	1	FALSE	0	0.238148240944734	1		824	113	SUCCESS
APC	324	MSKCC	GRCh37	5	112176395	112176395	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	11	355	0	ENST00000257430.4:c.5104G>T	p.Gly1702Ter	p.G1702*	ENST00000257430	NM_000038.5	1702	Gga/Tga	16/16	0.187169001387765	4	FACETS	1	0.779	1	1	0.779	1	CLONAL	2	FALSE	2	0.238148240944734	4		355	51	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344494	118344495	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs782311054	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	16	300	4	ENST00000534358.1:c.2629_2630del	p.Asp877ProfsTer8	p.D877Pfs*8	ENST00000534358	NM_005933.3	874	AGa/a	3/36	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	FALSE	1	0.238148240944734	2		304	92	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856434	111856434	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs776317487	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	17	235	0	ENST00000341259.2:c.489del	p.Thr165ProfsTer32	p.T165Pfs*32	ENST00000341259	NM_005475.2	162	gCc/gc	2/8	0.238148240944734	1	FACETS	0.998	0.753	1	0.998	0.753	1	CLONAL	1	FALSE	0	0.238148240944734	1		235	126	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866417	37866417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	61	757	0	ENST00000269571.5:c.722C>T	p.Ala241Val	p.A241V	ENST00000269571		241	gCt/gTt	6/27	1	2	FACETS	0.943	0.83	1	1	0.984	1	CLONAL	3	FALSE	1	0.238148240944734	2		757	181	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340270	116340270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749738523	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	49	360	0	ENST00000397752.3:c.1132G>A	p.Val378Ile	p.V378I	ENST00000397752	NM_000245.2	378	Gtc/Atc	2/21	0.238148240944734	6	FACETS	0.899	0.775	1	1	0.944	1	CLONAL	4	FALSE	3	0.238148240944734	6		360	169	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448297	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	T	novel	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	79	765	1	ENST00000407977.2:c.349_350delinsA	p.Arg117ThrfsTer41	p.R117Tfs*41	ENST00000407977		117	CGc/Ac	3/10	1	2	FACETS	1	0.922	1	1	0.985	1	CLONAL	2	FALSE	1	0.238148240944734	2		766	316	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946749	17946749	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1049658753	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	34	778	0	ENST00000458235.1:c.1898A>G	p.Tyr633Cys	p.Y633C	ENST00000458235	NM_000215.3	633	tAc/tGc	14/24	0.188514532669617	1	FACETS	0.932	0.775	1	1	0.963	1	CLONAL	2	FALSE	0	0.238148240944734	1		778	135	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001523	150001523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264217871	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	21	450	0	ENST00000253339.5:c.2081G>A	p.Arg694His	p.R694H	ENST00000253339		694	cGt/cAt	4/7	0.187169001387765	4	FACETS	1	0.918	1	0.743	0.577	0.931	CLONAL	1	FALSE	2	0.238148240944734	4		450	147	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562607	21562607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750798997	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	22	282	0	ENST00000382592.4:c.1312G>A	p.Ala438Thr	p.A438T	ENST00000382592	NM_014572.2	438	Gcg/Acg	4/8	0.226841629162165	0	FACETS	0.749	0.593	0.922			1	CLONAL	2	FALSE	0	0.238148240944734	0		282	94	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363835	118363835	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781787241	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	50	583	0	ENST00000534358.1:c.5068G>A	p.Glu1690Lys	p.E1690K	ENST00000534358	NM_005933.3	1690	Gaa/Aaa	16/36	1	2	FACETS	1	0.886	1	1	0.976	1	CLONAL	2	FALSE	1	0.238148240944734	2		583	203	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879593	151879594	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	rs749417254	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	10	370	0	ENST00000262189.6:c.5349_5351dup	p.Gln1787dup	p.Q1787dup	ENST00000262189	NM_170606.2	1787	caa/caGCAa	36/59	0.188109163764508	3	FACETS	1	0.758	1	0.566	0.388	0.784	CLONAL	1	FALSE	1	0.238148240944734	3		370	83	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465624	99465624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771088781	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	22	600	0	ENST00000268035.6:c.2449G>A	p.Ala817Thr	p.A817T	ENST00000268035	NM_000875.3	817	Gcc/Acc	11/21	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	FALSE	1	0.238148240944734	2		600	126	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782277	56782277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	30	629	3	ENST00000308159.5:c.118G>A	p.Gly40Arg	p.G40R	ENST00000308159	NM_014669.4	40	Gga/Aga	2/22	0.188514532669617	1	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	FALSE	0	0.238148240944734	1		632	189	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426237	49426242	+	inframe_deletion	In_Frame_Del	DEL	GGCTGG	GGCTGG	-	novel	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	48	838	0	ENST00000301067.7:c.12246_12251del	p.Gln4085_Pro4086del	p.Q4085_P4086del	ENST00000301067	NM_003482.3	4082	ccCCAGCCt/cct	39/54	0.199075873520796	5	FACETS	1	0.947	1	0.833	0.712	0.963	CLONAL	2	FALSE	2	0.238148240944734	5		838	219	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120783422	120783422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	30	715	0	ENST00000257552.2:c.1061C>T	p.Ala354Val	p.A354V	ENST00000257552	NM_002442.3	354	gCc/gTc	14/15	0.238148240944734	1	FACETS	0.948	0.78	1	1	0.959	1	CLONAL	2	FALSE	0	0.238148240944734	1		715	117	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435513	110435513	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	26	464	0	ENST00000375856.3:c.2888del	p.Pro963ArgfsTer17	p.P963Rfs*17	ENST00000375856	NM_003749.2	963	cCg/cg	1/2	0.168404150830944	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	FALSE	0	0.238148240944734	1		464	131	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274064	10274064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367543128	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	15	762	1	ENST00000330684.3:c.205G>A	p.Val69Met	p.V69M	ENST00000330684	NM_001134407.1	69	Gtg/Atg	2/13	0.188514532669617	1	FACETS	1	0.847	1	1	0.847	1	CLONAL	1	FALSE	0	0.238148240944734	1		763	91	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865863	56865863	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763617550	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	29	435	0	ENST00000308159.5:c.1195G>A	p.Val399Ile	p.V399I	ENST00000308159	NM_014669.4	399	Gtc/Atc	11/22	0.188514532669617	1	FACETS	0.783	0.638	0.942	1	0.946	1	CLONAL	2	FALSE	0	0.238148240944734	1		435	137	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348062	89348062	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	35	1013	1	ENST00000301030.4:c.4888G>T	p.Gly1630Trp	p.G1630W	ENST00000301030	NM_001256183.1	1630	Ggg/Tgg	9/13	0.188514532669617	1	FACETS	0.78	0.648	0.924	1	0.955	1	CLONAL	2	FALSE	0	0.238148240944734	1		1014	166	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663905	29663905	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1335480997	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	29	401	0	ENST00000356175.3:c.6337T>C	p.Cys2113Arg	p.C2113R	ENST00000356175	NM_000267.3	2113	Tgt/Cgt	41/57	1	2	FACETS	0.916	0.747	1	1	0.955	1	CLONAL	2	FALSE	1	0.238148240944734	2		401	133	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39629551	39629551	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	29	380	0	ENST00000262039.4:c.2245C>A	p.Leu749Ile	p.L749I	ENST00000262039	NM_002647.2	749	Ctt/Att	21/25	1	2	FACETS	1	0.887	1	1	0.963	1	CLONAL	2	FALSE	1	0.238148240944734	2		380	109	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57567417	57567417	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	49	527	0	ENST00000316660.6:c.8G>T	p.Gly3Val	p.G3V	ENST00000316660	NM_021127.2	3	gGg/gTg	1/2	1	2	FACETS	0.854	0.73	0.987	1	0.97	1	CLONAL	2	FALSE	1	0.238148240944734	2		527	241	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285942	39285942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772133124	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	25	336	0	ENST00000402219.2:c.217C>T	p.Arg73Cys	p.R73C	ENST00000402219	NM_005633.3	73	Cgt/Tgt	3/23	1	2	FACETS	0.946	0.759	1	1	0.95	1	CLONAL	2	FALSE	1	0.238148240944734	2		336	111	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149918	99149918	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	16	585	1	ENST00000074304.5:c.230A>G	p.Gln77Arg	p.Q77R	ENST00000074304	NM_001134224.1	77	cAg/cGg	5/26	1	2	FACETS	0.662	0.49	0.866	0.662	0.49	0.866	SUBCLONAL	1	FALSE	1	0.238148240944734	2		586	203	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660165	227660165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1384083792	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	29	713	0	ENST00000305123.5:c.3290G>A	p.Arg1097Gln	p.R1097Q	ENST00000305123	NM_005544.2	1097	cGg/cAg	1/2	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	FALSE	1	0.238148240944734	2		713	172	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961357	54961357	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	38	524	0	ENST00000312783.6:c.275T>C	p.Leu92Pro	p.L92P	ENST00000312783	NM_198436.1	92	cTg/cCg	4/10	0.180415983928833	0	FACETS	0.98	0.829	1			1	CLONAL	2	FALSE	0	0.238148240944734	0		524	124	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37092010	37092010	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	21	491	0	ENST00000231790.2:c.2138del	p.Lys713SerfsTer70	p.K713Sfs*70	ENST00000231790	NM_000249.3	713	Aag/ag	19/19	0.238148240944734	4	FACETS	0.984	0.769	1	0.984	0.769	1	CLONAL	2	FALSE	2	0.238148240944734	4		491	111	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165647	47165647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	13	526	0	ENST00000409792.3:c.479C>T	p.Thr160Ile	p.T160I	ENST00000409792	NM_014159.6	160	aCc/aTc	3/21	0.238148240944734	4	FACETS	0.878	0.637	1	0.878	0.637	1	CLONAL	2	FALSE	2	0.238148240944734	4		526	77	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249501	153249501	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	29	502	0	ENST00000281708.4:c.1277C>A	p.Ser426Ter	p.S426*	ENST00000281708	NM_033632.3	426	tCa/tAa	9/12	0.188514532669617	1	FACETS	0.783	0.638	0.942	1	0.946	1	CLONAL	2	FALSE	0	0.238148240944734	1		502	137	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56854492	56854492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1341743995	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	20	508	0	ENST00000519728.1:c.74G>A	p.Arg25His	p.R25H	ENST00000519728	NM_002350.3	25	cGt/cAt	2/13	1	2	FACETS	0.831	0.639	1	0.831	0.639	1	CLONAL	1	FALSE	1	0.238148240944734	2		508	202	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914713	39914715	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0045320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	25	308	0	ENST00000378444.4:c.4647_4649del	p.Leu1550del	p.L1550del	ENST00000378444	NM_001123385.1	1549	ctTCTc/ctc	12/15	1	1	FACETS	0.934	0.765	1	1	0.963	1	CLONAL	3	FALSE	0	0.238148240944734	1		308	66	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242681	46242682	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0045323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	73	314	0	ENST00000334344.6:c.1645_1646dup	p.Leu550ThrfsTer8	p.L550Tfs*8	ENST00000334344	NM_152641.2	548	gaa/gaATa	13/21	1	2	FACETS	0.796	0.704	0.894	0.796	0.704	0.894	SUBCLONAL	1	TRUE	1	0.652365425623375	2		314	281	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9928080	9928080	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	87	223	0	ENST00000330684.3:c.1659C>A	p.Phe553Leu	p.F553L	ENST00000330684	NM_001134407.1	553	ttC/ttA	8/13	1	2	FACETS	0.949	0.851	1	0.949	0.851	1	CLONAL	1	TRUE	1	0.652365425623375	2		223	281	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061208	38061208	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1292426539	NA	P-0045340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	322	516	0	ENST00000250448.2:c.781C>G	p.Arg261Gly	p.R261G	ENST00000250448	NM_004496.3	261	Cgc/Ggc	2/2	0.683430304294974	3	FACETS	1	0.994	1	0.722	0.685	0.76	CLONAL	1	TRUE	1	0.734990696501576	3		516	830	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998544	100998544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	48	593	1	ENST00000325455.5:c.1258G>A	p.Gly420Arg	p.G420R	ENST00000325455	NM_001202474.3	420	Ggg/Agg	1/8	1	2	FACETS	0.163	0.137	0.192	0.163	0.137	0.192	SUBCLONAL	1	TRUE	1	0.734990696501576	2		594	801	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	69061250	69061250	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	98	119	0	ENST00000487270.1:c.1085A>G	p.Glu362Gly	p.E362G	ENST00000487270	NM_133509.3	362	gAa/gGa	11/11	0.683430304294974	3	FACETS	1	0.975	1	0.624	0.564	0.686	CLONAL	1	TRUE	1	0.734990696501576	3		119	292	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675570	30675570	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	370	594	0	ENST00000376406.3:c.2786A>C	p.Asp929Ala	p.D929A	ENST00000376406	NM_014641.2	929	gAt/gCt	8/15	0.360663116805974	5	FACETS	0.83	0.787	0.874			1	INDETERMINATE	2	TRUE	NA	0.734990696501576	5		594	1275	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835938	151835938	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045340-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	284	353	0	ENST00000262189.6:c.14586del	p.Phe4862LeufsTer43	p.F4862Lfs*43	ENST00000262189	NM_170606.2	4862	ttT/tt	58/59	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.734990696501576	2		353	640	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913400	NA	P-0045341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	14	219	0	ENST00000349496.5:c.98C>A	p.Ser33Tyr	p.S33Y	ENST00000349496	NM_001904.3	33	tCt/tAt	3/15	0.444490725029318	1	FACETS	0.143	0.103	0.192	0.143	0.103	0.192	SUBCLONAL	1	TRUE	0	0.444490725029318	1		219	343	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043407	180043407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757396801	NA	P-0045341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	220	442	0	ENST00000261937.6:c.3179G>A	p.Arg1060Gln	p.R1060Q	ENST00000261937	NM_182925.4	1060	cGg/cAg	23/30	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.444490725029318	2		442	923	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874980	151874980	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1331640479	NA	P-0045341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	73	147	1	ENST00000262189.6:c.7558G>A	p.Val2520Ile	p.V2520I	ENST00000262189	NM_170606.2	2520	Gta/Ata	38/59	1	2	FACETS	0.978	0.861	1	0.978	0.861	1	CLONAL	1	TRUE	1	0.444490725029318	2		148	336	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	108	425	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.973	0.887	1	0.973	0.887	1	CLONAL	1	TRUE	1	0.767903149930201	2		425	289	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0045342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	188	380	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.767903149930201	2		380	482	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926248	112926248	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs121918468	NA	P-0045342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	145	280	0	ENST00000351677.2:c.1381G>A	p.Ala461Thr	p.A461T	ENST00000351677	NM_002834.3	461	Gct/Act	12/16	1	2	FACETS	0.784	0.72	0.849	0.784	0.72	0.849	SUBCLONAL	1	TRUE	1	0.767903149930201	2		280	482	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212152	36212152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	142	298	0	ENST00000222270.7:c.1903C>T	p.Pro635Ser	p.P635S	ENST00000222270	NM_014727.1	635	Cct/Tct	3/37	0.75904897587014	3	FACETS	0.99	0.908	1	0.495	0.454	0.538	CLONAL	1	TRUE	1	0.767903149930201	3		298	517	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719716	61719716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	151	398	0	ENST00000401558.2:c.1552G>A	p.Val518Ile	p.V518I	ENST00000401558	NM_003400.3	518	Gtt/Att	14/25	1	2	FACETS	0.962	0.889	1	0.962	0.889	1	CLONAL	1	TRUE	1	0.767903149930201	2		398	409	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0045343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	50	545	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.508	0.431	0.593	0.508	0.431	0.593	SUBCLONAL	1	TRUE	1	0.396806207292238	2		545	496	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0045343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	27	226	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.298	0.237	0.369	0.298	0.237	0.369	SUBCLONAL	1	TRUE	1	0.396806207292238	2		226	456	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0045343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	28	457	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.31	0.247	0.382	0.31	0.247	0.382	SUBCLONAL	1	TRUE	1	0.396806207292238	2		457	455	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652129	36652129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34916193	NA	P-0045343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	77	649	0	ENST00000244741.5:c.251G>A	p.Arg84Gln	p.R84Q	ENST00000244741	NM_000389.4	84	cGa/cAa	2/3	1	2	FACETS	0.501	0.439	0.568	0.501	0.439	0.568	SUBCLONAL	1	TRUE	1	0.396806207292238	2		649	774	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520017	NA	P-0045343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	57	665	0	ENST00000326873.7:c.647C>T	p.Ser216Phe	p.S216F	ENST00000326873	NM_000455.4	216	tCc/tTc	5/10	0.378995759192663	1	FACETS	0.321	0.274	0.371	0.321	0.274	0.371	SUBCLONAL	1	TRUE	0	0.396806207292238	1		665	718	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102199674	102199674	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0045343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	22	235	0	ENST00000263464.3:c.1079C>G	p.Ser360Ter	p.S360*	ENST00000263464	NM_001165.4	360	tCa/tGa	5/9	1	2	FACETS	0.308	0.238	0.389	0.308	0.238	0.389	SUBCLONAL	1	TRUE	1	0.396806207292238	2		235	360	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945141	32945141	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	35	237	0	ENST00000380152.3:c.8536G>C	p.Glu2846Gln	p.E2846Q	ENST00000380152		2846	Gag/Cag	20/27	1	2	FACETS	0.493	0.404	0.592	0.493	0.404	0.592	SUBCLONAL	1	TRUE	1	0.396806207292238	2		237	358	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572056	95572056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	32	348	0	ENST00000393063.1:c.3052G>A	p.Glu1018Lys	p.E1018K	ENST00000393063	NM_030621.3	1018	Gag/Aag	20/28	1	2	FACETS	0.296	0.24	0.361	0.296	0.24	0.361	SUBCLONAL	1	TRUE	1	0.396806207292238	2		348	544	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610154	10610154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	163	562	0	ENST00000171111.5:c.556G>A	p.Gly186Ser	p.G186S	ENST00000171111	NM_203500.1	186	Ggc/Agc	2/6	0.378995759192663	1	FACETS	0.989	0.911	1	0.989	0.911	1	CLONAL	1	TRUE	0	0.396806207292238	1		562	666	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205316	46205316	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	37	223	0	ENST00000334344.6:c.400C>T	p.Gln134Ter	p.Q134*	ENST00000334344	NM_152641.2	134	Cag/Tag	4/21	0.118984670707618	3	FACETS	0.492	0.406	0.589	0.246	0.203	0.295	INDETERMINATE	1	TRUE	1	0.396806207292238	3		223	454	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99136536	99136536	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781317145	NA	P-0045343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	54	472	0	ENST00000074304.5:c.25C>T	p.Arg9Cys	p.R9C	ENST00000074304	NM_001134224.1	9	Cgc/Tgc	3/26	1	2	FACETS	0.398	0.339	0.462	0.398	0.339	0.462	SUBCLONAL	1	TRUE	1	0.396806207292238	2		472	684	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106829	27106829	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0045343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	130	497	0	ENST00000324856.7:c.6440T>A	p.Leu2147Ter	p.L2147*	ENST00000324856	NM_006015.4	2147	tTg/tAg	20/20	0.396806207292238	1	FACETS	0.982	0.895	1	0.982	0.895	1	CLONAL	1	TRUE	0	0.396806207292238	1		497	535	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226566850	226566850	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	36	315	0	ENST00000366794.5:c.1738G>T	p.Glu580Ter	p.E580*	ENST00000366794	NM_001618.3	580	Gaa/Taa	12/23	1	2	FACETS	0.384	0.316	0.462	0.384	0.316	0.462	SUBCLONAL	1	TRUE	1	0.396806207292238	2		315	472	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402157	402157	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1346692091	NA	P-0045343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	44	351	0	ENST00000399788.2:c.4634C>T	p.Ser1545Leu	p.S1545L	ENST00000399788	NM_001042603.1	1545	tCa/tTa	27/28	NA	2	FACETS	0.371	0.311	0.439			1	INDETERMINATE	1	TRUE	NA	0.396806207292238	2		351	597	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438570	49438570	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	45	487	0	ENST00000301067.7:c.4920G>C	p.Lys1640Asn	p.K1640N	ENST00000301067	NM_003482.3	1640	aaG/aaC	19/54	0.118984670707618	3	FACETS	0.366	0.306	0.432	0.183	0.153	0.216	INDETERMINATE	1	TRUE	1	0.396806207292238	3		487	743	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49054149	49054149	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1360367329	NA	P-0045343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	35	193	0	ENST00000267163.4:c.2729G>A	p.Arg910Gln	p.R910Q	ENST00000267163	NM_000321.2	910	cGa/cAa	27/27	1	2	FACETS	0.437	0.358	0.525	0.437	0.358	0.525	SUBCLONAL	1	TRUE	1	0.396806207292238	2		193	404	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50820796	50820796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	28	229	0	ENST00000398568.2:c.1971G>A	p.Met657Ile	p.M657I	ENST00000398568	NM_001042412.1	657	atG/atA	12/18	1	2	FACETS	0.355	0.284	0.437	0.355	0.284	0.437	SUBCLONAL	1	TRUE	1	0.396806207292238	2		229	397	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670592	67670592	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0045343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	28	234	0	ENST00000264010.4:c.1838-1G>C		p.X613_splice	ENST00000264010	NM_006565.3	613			1	2	FACETS	0.434	0.347	0.533	0.434	0.347	0.533	SUBCLONAL	1	TRUE	1	0.396806207292238	2		234	325	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210624	2210624	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs896640132	NA	P-0045343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	44	487	0	ENST00000398665.3:c.1121C>G	p.Ser374Cys	p.S374C	ENST00000398665	NM_032482.2	374	tCt/tGt	14/28	0.378995759192663	1	FACETS	0.399	0.335	0.471	0.399	0.335	0.471	SUBCLONAL	1	TRUE	0	0.396806207292238	1		487	445	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982553	10982553	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	14	134	0	ENST00000327064.4:c.175G>C	p.Glu59Gln	p.E59Q	ENST00000327064	NM_199141.1	59	Gag/Cag	1/16	0.378995759192663	1	FACETS	0.235	0.169	0.314	0.235	0.169	0.314	SUBCLONAL	1	TRUE	0	0.396806207292238	1		134	241	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459700	149459700	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	56	556	0	ENST00000286301.3:c.507C>A	p.Phe169Leu	p.F169L	ENST00000286301	NM_005211.3	169	ttC/ttA	4/22	1	2	FACETS	0.372	0.318	0.431	0.372	0.318	0.431	SUBCLONAL	1	TRUE	1	0.396806207292238	2		556	759	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940273	31940273	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	46	492	0	ENST00000375333.2:c.415C>G	p.Leu139Val	p.L139V	ENST00000375333	NM_032454.1	139	Ctt/Gtt	2/8	1	2	FACETS	0.334	0.28	0.394	0.334	0.28	0.394	SUBCLONAL	1	TRUE	1	0.396806207292238	2		492	694	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622184	117622184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	33	234	0	ENST00000368508.3:c.6686C>T	p.Ser2229Phe	p.S2229F	ENST00000368508	NM_002944.2	2229	tCc/tTc	42/43	1	2	FACETS	0.453	0.369	0.548	0.453	0.369	0.548	SUBCLONAL	1	TRUE	1	0.396806207292238	2		234	367	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200285	138200285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374368025	NA	P-0045343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	53	414	0	ENST00000237289.4:c.1703C>T	p.Ser568Leu	p.S568L	ENST00000237289	NM_001270507.1	568	tCg/tTg	7/9	1	2	FACETS	0.454	0.386	0.527	0.454	0.386	0.527	SUBCLONAL	1	TRUE	1	0.396806207292238	2		414	589	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971334	13971334	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	32	272	0	ENST00000405192.2:c.595C>G	p.Pro199Ala	p.P199A	ENST00000405192	NM_001163147.1	199	Cct/Gct	8/12	1	2	FACETS	0.307	0.249	0.374	0.307	0.249	0.374	SUBCLONAL	1	TRUE	1	0.396806207292238	2		272	525	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539120	23539120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	39	331	0	ENST00000380871.4:c.319G>A	p.Glu107Lys	p.E107K	ENST00000380871	NM_006167.3	107	Gaa/Aaa	2/2	1	2	FACETS	0.443	0.367	0.527	0.443	0.367	0.527	SUBCLONAL	1	TRUE	1	0.396806207292238	2		331	444	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539153	23539153	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0045343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	30	253	1	ENST00000380871.4:c.287-1G>T		p.X96_splice	ENST00000380871	NM_006167.3	96			1	2	FACETS	0.441	0.355	0.537	0.441	0.355	0.537	SUBCLONAL	1	TRUE	1	0.396806207292238	2		254	343	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891285	101891287	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	novel	NA	P-0045343-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	54	311	0	ENST00000374994.4:c.247_249del	p.Pro83del	p.P83del	ENST00000374994	NM_004612.2	82	agGCCg/agg	2/9	0.396806207292238	1	FACETS	0.512	0.438	0.593	0.512	0.438	0.593	SUBCLONAL	1	TRUE	0	0.396806207292238	1		311	426	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0045344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	68	284	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	1	2	FACETS	0.814	0.71	0.925	0.814	0.71	0.925	CLONAL	1	TRUE	1	0.379907669712884	2		284	440	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0045344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	143	556	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.379907669712884	1	FACETS	0.974	0.891	1	0.974	0.891	1	CLONAL	1	TRUE	0	0.379907669712884	1		556	626	SUCCESS
APC	324	MSKCC	GRCh37	5	112174490	112174493	+	frameshift_variant	Frame_Shift_Del	DEL	CAAT	CAAT	-	rs587779353	NA	P-0045344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	45	212	0	ENST00000257430.4:c.3202_3205del	p.Ser1068GlyfsTer57	p.S1068Gfs*57	ENST00000257430	NM_000038.5	1067	CAATca/ca	16/16	0.379907669712884	1	FACETS	0.969	0.825	1	0.969	0.825	1	CLONAL	1	TRUE	0	0.379907669712884	1		212	198	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920422	114920422	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	119	348	0	ENST00000543371.1:c.1363C>T	p.Arg455Ter	p.R455*	ENST00000543371	NM_001198531.1	455	Cga/Tga	13/14	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.379907669712884	2		348	615	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40500453	40500453	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	110	334	0	ENST00000264657.5:c.82A>G	p.Met28Val	p.M28V	ENST00000264657	NM_139276.2	28	Atg/Gtg	2/24	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.379907669712884	2		334	560	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79952308	79952308	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs149350323	NA	P-0045344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	58	290	0	ENST00000265081.6:c.316C>T	p.Gln106Ter	p.Q106*	ENST00000265081	NM_002439.4	106	Caa/Taa	2/24	0.379907669712884	1	FACETS	0.571	0.492	0.657	0.571	0.492	0.657	SUBCLONAL	1	TRUE	0	0.379907669712884	1		290	433	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795004	242795004	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751637749	NA	P-0045357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	60	1334	3	ENST00000334409.5:c.205C>T	p.Arg69Cys	p.R69C	ENST00000334409	NM_005018.2	69	Cgc/Tgc	2/5	1	2	FACETS	0.425	0.365	0.492	0.425	0.365	0.492	SUBCLONAL	1	FALSE	1	0.258052126054284	2		1337	1093	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0045357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	39	373	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.73	0.606	0.869	0.73	0.606	0.869	SUBCLONAL	1	FALSE	1	0.258052126054284	2		373	414	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391896	139391896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766745955	NA	P-0045357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	161	1323	0	ENST00000277541.6:c.6295G>A	p.Asp2099Asn	p.D2099N	ENST00000277541	NM_017617.3	2099	Gac/Aac	34/34	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	1	0.258052126054284	2		1323	1169	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952006	178952006	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	11	510	0	ENST00000263967.3:c.3061T>C	p.Tyr1021His	p.Y1021H	ENST00000263967	NM_006218.2	1021	Tac/Cac	21/21	0.118418716335325	3	FACETS	0.182	0.125	0.254	0.091	0.062	0.127	INDETERMINATE	1	FALSE	1	0.258052126054284	3		510	528	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0045357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	43	396	2	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.236741694155627	1	FACETS	0.737	0.618	0.868	0.737	0.618	0.868	SUBCLONAL	1	FALSE	0	0.258052126054284	1		398	394	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542201	187542201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs189523191	NA	P-0045357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	51	621	0	ENST00000441802.2:c.5539G>A	p.Val1847Ile	p.V1847I	ENST00000441802	NM_005245.3	1847	Gtc/Atc	10/27	1	2	FACETS	0.724	0.615	0.843	0.724	0.615	0.843	SUBCLONAL	1	FALSE	1	0.258052126054284	2		621	546	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264586	1264586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs547377569	NA	P-0045357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	108	1036	0	ENST00000310581.5:c.2776G>A	p.Gly926Ser	p.G926S	ENST00000310581	NM_198253.2	926	Ggc/Agc	11/16	1	2	FACETS	0.942	0.844	1	0.942	0.844	1	CLONAL	1	FALSE	1	0.258052126054284	2		1036	889	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255883	16255883	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	28	543	2	ENST00000375759.3:c.3154del	p.Ile1052SerfsTer40	p.I1052Sfs*40	ENST00000375759	NM_015001.2	1050	Aaa/aa	11/15	1	2	FACETS	0.392	0.312	0.483	0.392	0.312	0.483	SUBCLONAL	1	FALSE	1	0.258052126054284	2		545	554	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178095	56178095	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374455781	NA	P-0045357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	50	405	0	ENST00000399503.3:c.3068G>A	p.Arg1023His	p.R1023H	ENST00000399503	NM_005921.1	1023	cGc/cAc	14/20	1	2	FACETS	0.839	0.712	0.977	0.839	0.712	0.977	CLONAL	1	FALSE	1	0.258052126054284	2		405	462	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0045357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	48	1085	10	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	1	2	FACETS	0.395	0.332	0.464	0.395	0.332	0.464	SUBCLONAL	1	FALSE	1	0.258052126054284	2		1095	943	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138117	2138117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759420443	NA	P-0045357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	56	1230	2	ENST00000219476.3:c.5137C>T	p.Arg1713Cys	p.R1713C	ENST00000219476	NM_000548.3	1713	Cgc/Tgc	40/42	1	2	FACETS	0.393	0.335	0.456	0.393	0.335	0.456	SUBCLONAL	1	FALSE	1	0.258052126054284	2		1232	1105	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610285	10610285	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	113	1182	1	ENST00000171111.5:c.425C>T	p.Thr142Met	p.T142M	ENST00000171111	NM_203500.1	142	aCg/aTg	2/6	1	2	FACETS	0.786	0.706	0.872	0.786	0.706	0.872	SUBCLONAL	1	FALSE	1	0.258052126054284	2		1183	1114	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55124955	55124955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764472307	NA	P-0045357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	120	929	1	ENST00000257290.5:c.20C>T	p.Ala7Val	p.A7V	ENST00000257290	NM_006206.4	7	gCg/gTg	2/23	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	1	0.258052126054284	2		930	867	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422358	422358	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs371715765	NA	P-0045357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	56	450	0	ENST00000399788.2:c.2900C>T	p.Pro967Leu	p.P967L	ENST00000399788	NM_001042603.1	967	cCg/cTg	20/28	1	2	FACETS	0.891	0.764	1	0.891	0.764	1	CLONAL	1	FALSE	1	0.258052126054284	2		450	487	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288751	11288751	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs770601118	NA	P-0045357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	66	744	2	ENST00000361445.4:c.3004C>T	p.Arg1002Ter	p.R1002*	ENST00000361445	NM_004958.3	1002	Cga/Tga	19/58	1	2	FACETS	0.705	0.611	0.806	0.705	0.611	0.806	SUBCLONAL	1	FALSE	1	0.258052126054284	2		746	726	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402834	20402836	+	inframe_deletion	In_Frame_Del	DEL	GCG	GCG	-	rs746263274	NA	P-0045357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	10	90	0	ENST00000346618.3:c.385_387del	p.Gly129del	p.G129del	ENST00000346618	NM_001949.4	124	aGCGgc/agc	1/7	1	2	FACETS	0.807	0.552	1	0.807	0.552	1	CLONAL	1	FALSE	1	0.258052126054284	2		90	96	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874149	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0045357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	59	579	1	ENST00000262189.6:c.8389_8390del	p.Lys2797GlyfsTer11	p.K2797Gfs*11	ENST00000262189	NM_170606.2	2797	AAg/g	38/59	1	2	FACETS	0.788	0.678	0.908	0.788	0.678	0.908	CLONAL	1	FALSE	1	0.258052126054284	2		580	580	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061228	38061228	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	127	870	0	ENST00000250448.2:c.761del	p.Phe254SerfsTer67	p.F254Sfs*67	ENST00000250448	NM_004496.3	254	tTc/tc	2/2	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.258052126054284	2		870	835	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426151	47426151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	29	604	0	ENST00000377045.4:c.671C>T	p.Thr224Met	p.T224M	ENST00000377045	NM_001654.4	224	aCg/aTg	7/16	1	1	FACETS	0.384	0.307	0.471	0.384	0.307	0.471	SUBCLONAL	1	FALSE	0	0.258052126054284	1		604	510	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571498	95571498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	69	613	1	ENST00000393063.1:c.3179G>A	p.Arg1060His	p.R1060H	ENST00000393063	NM_030621.3	1060	cGc/cAc	21/28	1	2	FACETS	0.686	0.596	0.783	0.686	0.596	0.783	SUBCLONAL	1	FALSE	1	0.258052126054284	2		614	780	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141568624	141568624	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	51	1050	0	ENST00000220592.5:c.838C>T	p.Arg280Cys	p.R280C	ENST00000220592	NM_012154.3	280	Cgc/Tgc	7/19	1	2	FACETS	0.391	0.33	0.457	0.391	0.33	0.457	SUBCLONAL	1	FALSE	1	0.258052126054284	2		1050	1012	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36823851	36823851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772996133	NA	P-0045357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	31	578	2	ENST00000373129.3:c.331G>A	p.Gly111Ser	p.G111S	ENST00000373129	NM_032017.1	111	Ggc/Agc	5/12	1	2	FACETS	0.445	0.359	0.543	0.445	0.359	0.543	SUBCLONAL	1	FALSE	1	0.258052126054284	2		580	540	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106171	27106172	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0045357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	144	786	0	ENST00000324856.7:c.5782_5783del	p.Lys1928GlufsTer16	p.K1928Efs*16	ENST00000324856	NM_006015.4	1928	AAg/g	20/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.258052126054284	2		786	785	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120493446	120493446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	40	518	0	ENST00000256646.2:c.2380G>A	p.Val794Met	p.V794M	ENST00000256646	NM_024408.3	794	Gtg/Atg	15/34	1	2	FACETS	0.562	0.466	0.668	0.562	0.466	0.668	SUBCLONAL	1	FALSE	1	0.258052126054284	2		518	552	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821821	72821821	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	129	727	0	ENST00000268489.5:c.10354del	p.Leu3452SerfsTer33	p.L3452Sfs*33	ENST00000268489	NM_006885.3	3452	Ctc/tc	10/10	0.118418716335325	3	FACETS	1	0.984	1	0.72	0.653	0.79	INDETERMINATE	1	FALSE	1	0.258052126054284	3		727	784	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30954249	30954251	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0045357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	66	471	0	ENST00000375687.4:c.122_124del	p.Glu41del	p.E41del	ENST00000375687	NM_015338.5	40	gcAGAa/gca	2/13	1	2	FACETS	0.867	0.753	0.991	0.867	0.753	0.991	CLONAL	1	FALSE	1	0.258052126054284	2		471	590	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80074643	80074643	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	38	497	0	ENST00000265081.6:c.2423T>C	p.Leu808Pro	p.L808P	ENST00000265081	NM_002439.4	808	cTt/cCt	17/24	1	2	FACETS	0.53	0.437	0.633	0.53	0.437	0.633	SUBCLONAL	1	FALSE	1	0.258052126054284	2		497	556	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410121	63410121	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	33	567	0	ENST00000330258.3:c.3046T>C	p.Ser1016Pro	p.S1016P	ENST00000330258	NM_152424.3	1016	Tct/Cct	2/2	1	1	FACETS	0.463	0.377	0.561	0.463	0.377	0.561	SUBCLONAL	1	FALSE	0	0.258052126054284	1		567	481	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0045359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	276	427	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.54097069898893	3	FACETS	0.829	0.782	0.877	0.829	0.782	0.877	CLONAL	2	TRUE	1	0.54097069898893	3		427	782	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0045359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	87	457	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.54097069898893	2		457	318	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748895	41748895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138883984	NA	P-0045359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	295	822	1	ENST00000301178.4:c.1420C>T	p.Arg474Trp	p.R474W	ENST00000301178	NM_021913.4	474	Cgg/Tgg	11/20	1	2	FACETS	0.969	0.913	1	0.969	0.913	1	CLONAL	1	TRUE	1	0.54097069898893	2		823	1125	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119780	70119781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0045359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	282	798	0	ENST00000245479.2:c.788dup	p.Arg264GlnfsTer32	p.R264Qfs*32	ENST00000245479	NM_000346.3	261	gag/gaGg	3/3	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.54097069898893	2		798	899	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5243984	5243984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173811578	NA	P-0045359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	358	983	1	ENST00000357368.4:c.1498C>T	p.Arg500Trp	p.R500W	ENST00000357368	NM_002850.3	500	Cgg/Tgg	11/38	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.54097069898893	2		984	1263	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843242	128843242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs912880810	NA	P-0045359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	675	991	2	ENST00000249373.3:c.349C>T	p.Arg117Cys	p.R117C	ENST00000249373	NM_005631.4	117	Cgc/Tgc	2/12	0.54097069898893	3	FACETS	0.999	0.964	1	0.999	0.964	1	CLONAL	2	TRUE	1	0.54097069898893	3		993	1587	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117878	70117888	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCAGGCGGC	GCGCAGGCGGC	-	novel	NA	P-0045359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	187	796	1	ENST00000245479.2:c.353_363del	p.Ala118GlufsTer130	p.A118Efs*130	ENST00000245479	NM_000346.3	116	GCGCAGGCGGCg/g	1/3	1	2	FACETS	0.772	0.713	0.832	0.772	0.713	0.832	SUBCLONAL	1	TRUE	1	0.54097069898893	2		797	896	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575186	48575186	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	91	372	0	ENST00000342988.3:c.380G>T	p.Cys127Phe	p.C127F	ENST00000342988	NM_005359.5	127	tGt/tTt	3/12	0.54097069898893	1	FACETS	0.826	0.743	0.913	0.826	0.743	0.913	CLONAL	1	TRUE	0	0.54097069898893	1		372	297	SUCCESS
APC	324	MSKCC	GRCh37	5	112175784	112175799	+	frameshift_variant	Frame_Shift_Del	DEL	ATGGATTTTCTTGTTC	ATGGATTTTCTTGTTC	-	novel	NA	P-0045359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	213	359	0	ENST00000257430.4:c.4495_4510del	p.Gly1499ProfsTer3	p.G1499Pfs*3	ENST00000257430	NM_000038.5	1498	gATGGATTTTCTTGTTCa/ga	16/16	0.54097069898893	2	FACETS	0.949	0.895	1	0.949	0.895	1	CLONAL	2	TRUE	0	0.54097069898893	2		359	415	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114799841	114799841	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	299	739	0	ENST00000543371.1:c.508C>T	p.Gln170Ter	p.Q170*	ENST00000543371	NM_001198531.1	170	Caa/Taa	5/14	1	2	FACETS	0.943	0.888	1	0.943	0.888	1	CLONAL	1	TRUE	1	0.54097069898893	2		739	1172	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0045360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	423	688	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	0.398261341422687	5	FACETS	0.901	0.859	0.944	0.901	0.859	0.944	CLONAL	3	TRUE	2	0.398261341422687	5		688	1255	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683565	162683565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	127	585	0	ENST00000366898.1:c.404G>A	p.Gly135Glu	p.G135E	ENST00000366898	NM_004562.2	135	gGa/gAa	3/12	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.398261341422687	2		585	552	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030847	69030847	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045360-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	119	426	0	ENST00000288368.4:c.3389G>T	p.Ser1130Ile	p.S1130I	ENST00000288368	NM_024870.2	1130	aGc/aTc	27/40	0.331505541394503	4	FACETS	1	0.957	1	0.553	0.499	0.609	CLONAL	1	TRUE	2	0.398261341422687	4		426	756	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs1555525367	NA	P-0045361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	507	533	1	ENST00000269305.4:c.783-1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.498626029566196	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.525237928311646	2		534	928	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550537	29550537	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567845906	NA	P-0045361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	24	316	0	ENST00000356175.3:c.1797G>A	p.Trp599Ter	p.W599*	ENST00000356175	NM_000267.3	599	tgG/tgA	16/57	0.525237928311646	1	FACETS	0.196	0.153	0.245	0.196	0.153	0.245	SUBCLONAL	1	TRUE	0	0.525237928311646	1		316	344	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180985	108180985	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1565489916	NA	P-0045361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	27	311	0	ENST00000278616.4:c.5861C>G	p.Ala1954Gly	p.A1954G	ENST00000278616	NM_000051.3	1954	gCt/gGt	39/63	1	2	FACETS	0.237	0.188	0.294	0.237	0.188	0.294	SUBCLONAL	1	TRUE	1	0.525237928311646	2		311	433	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654761	29654945	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTATCCCCCAACACACCAAGATTCGGCCAAAAGATGTCCCTGGGACACTGCTCAATATCGCATTACTTAATTTAGGCAGTTCTGACCCGAGTTTACGGTAGGTTTTTTAAAATTCTCTTCAGTTTGATTTGGGGTTTGTTGCTTTTAAAATGAGACCATTTAATGAATTTTAAAACAGCCTCTAC	CTATCCCCCAACACACCAAGATTCGGCCAAAAGATGTCCCTGGGACACTGCTCAATATCGCATTACTTAATTTAGGCAGTTCTGACCCGAGTTTACGGTAGGTTTTTTAAAATTCTCTTCAGTTTGATTTGGGGTTTGTTGCTTTTAAAATGAGACCATTTAATGAATTTTAAAACAGCCTCTAC	-	novel	NA	P-0045361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	74	443	0	ENST00000356175.3:c.5452_5546+90del		p.X1818_splice	ENST00000356175	NM_000267.3	1818		37/57	0.525237928311646	1	FACETS	0.372	0.326	0.422	0.372	0.326	0.422	SUBCLONAL	1	TRUE	0	0.525237928311646	1		443	558	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448535	89448535	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	210	442	0	ENST00000336596.2:c.1499A>C	p.Lys500Thr	p.K500T	ENST00000336596	NM_005233.5	500	aAg/aCg	7/17	0.525237928311646	1	FACETS	0.914	0.853	0.976	0.914	0.853	0.976	CLONAL	1	TRUE	0	0.525237928311646	1		442	645	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750522	41750522	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	198	644	0	ENST00000226382.2:c.106T>C	p.Cys36Arg	p.C36R	ENST00000226382	NM_003924.3	36	Tgc/Cgc	1/3	0.525237928311646	1	FACETS	0.846	0.787	0.907	0.846	0.787	0.907	CLONAL	1	TRUE	0	0.525237928311646	1		644	657	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515565	31515570	+	inframe_deletion	In_Frame_Del	DEL	TCACAA	TCACAA	-	novel	NA	P-0045361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	73	285	0	ENST00000344624.3:c.1049_1054del	p.Ile350_Val351del	p.I350_V351del	ENST00000344624		350	aTTGTGAat/aat	4/33	1	2	FACETS	0.604	0.53	0.684	0.604	0.53	0.684	SUBCLONAL	1	TRUE	1	0.525237928311646	2		285	460	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641099	117641099	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045361-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	69	590	0	ENST00000368508.3:c.5872G>T	p.Glu1958Ter	p.E1958*	ENST00000368508	NM_002944.2	1958	Gaa/Taa	36/43	1	2	FACETS	0.287	0.249	0.328	0.287	0.249	0.328	SUBCLONAL	1	TRUE	1	0.525237928311646	2		590	916	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0045362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	179	294	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.92	0.851	0.992	0.92	0.851	0.992	CLONAL	1	TRUE	1	0.540247873092784	2		294	720	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0045362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	218	353	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.540247873092784	3	FACETS	0.906	0.849	0.963	0.906	0.849	0.963	CLONAL	2	TRUE	1	0.540247873092784	3		353	566	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117799	108117799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202160435	NA	P-0045362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	281	368	0	ENST00000278616.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000278616	NM_000051.3	337	cGt/cAt	8/63	0.540247873092784	3	FACETS	0.953	0.901	1	0.953	0.901	1	CLONAL	2	TRUE	1	0.540247873092784	3		368	693	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578262	7578262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352697	NA	P-0045362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	223	730	1	ENST00000269305.4:c.587G>A	p.Arg196Gln	p.R196Q	ENST00000269305	NM_001126112.2	196	cGa/cAa	6/11	0.540247873092784	1	FACETS	0.88	0.823	0.938	0.88	0.823	0.938	CLONAL	1	TRUE	0	0.540247873092784	1		731	685	SUCCESS
APC	324	MSKCC	GRCh37	5	112175147	112175147	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	51	222	0	ENST00000257430.4:c.3856G>T	p.Glu1286Ter	p.E1286*	ENST00000257430	NM_000038.5	1286	Gaa/Taa	16/16	0.540247873092784	3	FACETS	0.603	0.513	0.7	0.301	0.256	0.35	SUBCLONAL	1	TRUE	1	0.540247873092784	3		222	398	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302628	15302628	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1418	84	1026	1	ENST00000263388.2:c.730C>T	p.Arg244Ter	p.R244*	ENST00000263388	NM_000435.2	244	Cga/Tga	5/33	0.540247873092784	3	FACETS	0.263	0.231	0.298	0.131	0.115	0.149	SUBCLONAL	1	TRUE	1	0.540247873092784	3		1027	1502	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200113	128200113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906629	NA	P-0045362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	55	745	1	ENST00000341105.2:c.1192C>T	p.Arg398Trp	p.R398W	ENST00000341105	NM_032638.4	398	Cgg/Tgg	6/6	1	2	FACETS	0.195	0.166	0.228	0.195	0.166	0.228	SUBCLONAL	1	TRUE	1	0.540247873092784	2		746	1042	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900414	32900414	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	131	408	0	ENST00000380152.3:c.511G>T	p.Val171Leu	p.V171L	ENST00000380152		171	Gtg/Ttg	6/27	0.540247873092784	3	FACETS	0.748	0.678	0.82	0.374	0.339	0.41	SUBCLONAL	1	TRUE	1	0.540247873092784	3		408	824	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912173	114912173	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	249	635	0	ENST00000543371.1:c.1243C>A	p.Pro415Thr	p.P415T	ENST00000543371	NM_001198531.1	415	Ccc/Acc	11/14	1	2	FACETS	0.975	0.913	1	0.975	0.913	1	CLONAL	1	TRUE	1	0.540247873092784	2		635	945	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17117050	17117050	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	288	726	0	ENST00000285071.4:c.1659G>A	p.Trp553Ter	p.W553*	ENST00000285071	NM_144997.5	553	tgG/tgA	14/14	0.540247873092784	1	FACETS	0.974	0.92	1	0.974	0.92	1	CLONAL	1	TRUE	0	0.540247873092784	1		726	799	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223278	36223278	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1373	345	1215	0	ENST00000222270.7:c.5828C>G	p.Pro1943Arg	p.P1943R	ENST00000222270	NM_014727.1	1943	cCt/cGt	28/37	0.540247873092784	3	FACETS	0.944	0.891	0.999	0.472	0.445	0.5	CLONAL	1	TRUE	1	0.540247873092784	3		1215	1718	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459782	149459782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs532877119	NA	P-0045362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	100	954	2	ENST00000286301.3:c.425G>A	p.Arg142His	p.R142H	ENST00000286301	NM_005211.3	142	cGt/cAt	4/22	0.540247873092784	3	FACETS	0.366	0.325	0.409	0.183	0.162	0.205	SUBCLONAL	1	TRUE	1	0.540247873092784	3		956	1286	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0045364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	179	354	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.625819335082417	3	FACETS	0.951	0.889	1	0.951	0.889	1	CLONAL	2	TRUE	1	0.638503415264978	3		354	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0045364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	465	823	4	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.586346977888103	3	FACETS	0.939	0.909	0.968	0.939	0.909	0.968	CLONAL	3	TRUE	0	0.638503415264978	3		827	682	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0045364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	158	478	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	0.545592728818549	5	FACETS	0.956	0.882	1	0.637	0.588	0.688	CLONAL	2	TRUE	2	0.638503415264978	5		478	507	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473779	67473779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906850	NA	P-0045364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	132	734	2	ENST00000327367.4:c.859C>T	p.Arg287Trp	p.R287W	ENST00000327367	NM_005902.3	287	Cgg/Tgg	6/9	0.579902499025125	2	FACETS	0.925	0.846	1	0.462	0.423	0.503	CLONAL	1	TRUE	0	0.638503415264978	2		736	447	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394805	45394805	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	144	381	1	ENST00000262160.6:c.544C>T	p.Arg182Ter	p.R182*	ENST00000262160	NM_005901.5	182	Cga/Tga	5/11	0.553286499757124	2	FACETS	0.867	0.81	0.924	0.867	0.81	0.924	CLONAL	2	TRUE	0	0.638503415264978	2		382	260	SUCCESS
APC	324	MSKCC	GRCh37	5	112175746	112175746	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	155	442	3	ENST00000257430.4:c.4455del	p.Asp1486IlefsTer21	p.D1486Ifs*21	ENST00000257430	NM_000038.5	1485	gcT/gc	16/16	0.579902499025125	2	FACETS	0.788	0.735	0.841	0.788	0.735	0.841	SUBCLONAL	2	TRUE	0	0.638503415264978	2		445	308	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	228	626	5	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	0.553286499757124	2	FACETS	0.846	0.801	0.891	0.846	0.801	0.891	CLONAL	2	TRUE	0	0.638503415264978	2		631	422	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517886	187517886	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs373689624	NA	P-0045364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	36	630	0	ENST00000441802.2:c.12808C>T	p.Arg4270Ter	p.R4270*	ENST00000441802	NM_005245.3	4270	Cga/Tga	25/27	0.553286499757124	2	FACETS	0.24	0.197	0.289	0.12	0.098	0.145	SUBCLONAL	1	TRUE	0	0.638503415264978	2		630	469	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133729510	133729510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045364-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	156	614	4	ENST00000318560.5:c.139C>T	p.Arg47Cys	p.R47C	ENST00000318560	NM_005157.4	47	Cgt/Tgt	2/11	0.369682781725408	4	FACETS	0.928	0.85	1	0.464	0.425	0.505	INDETERMINATE	1	TRUE	2	0.638503415264978	4		618	863	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437737	110437737	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0121547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	594	800	0	ENST00000375856.3:c.664T>C	p.Ser222Pro	p.S222P	ENST00000375856	NM_003749.2	222	Tct/Cct	1/2	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	NA	1	0.749229660443879	2		800	1434	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522648	176522648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0121547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	523	1090	1	ENST00000292408.4:c.1745G>A	p.Gly582Glu	p.G582E	ENST00000292408	NM_213647.1	582	gGg/gAg	13/18	1	2	FACETS	0.985	0.945	1	0.985	0.945	1	CLONAL	1	NA	1	0.749229660443879	2		1091	1417	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026694	6026694	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs786204115	NA	P-0121547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	446	828	0	ENST00000265849.7:c.1702C>G	p.Pro568Ala	p.P568A	ENST00000265849	NM_000535.5	568	Cca/Gca	11/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	NA	1	0.749229660443879	2		828	1182	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	179	752	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	0.942	0.869	1	0.942	0.869	1	CLONAL	1	TRUE	1	0.43	2		752	884	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	93	262	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.857	0.764	0.954	0.857	0.764	0.954	CLONAL	1	TRUE	1	0.43	2		262	505	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	321	737	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.888	0.842	0.934	1	0.996	1	CLONAL	2	TRUE	1	0.43	2		742	841	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	306	606	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.845	0.8	0.891	1	0.995	1	CLONAL	2	TRUE	1	0.43	2		610	842	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	116	609	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.806	0.728	0.889	0.806	0.728	0.889	CLONAL	1	TRUE	1	0.43	2		610	669	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	120	665	3	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.803	0.726	0.884	0.803	0.726	0.884	CLONAL	1	TRUE	1	0.43	2		668	695	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	291	752	1	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	0.875	0.828	0.924	1	0.995	1	CLONAL	2	TRUE	1	0.43	2		753	773	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	149	1022	7	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	1	2	FACETS	0.666	0.608	0.728	0.666	0.608	0.728	SUBCLONAL	1	TRUE	1	0.43	2		1029	1040	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383999	84383999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150371881	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	57	544	0	ENST00000321945.7:c.853C>T	p.Arg285Trp	p.R285W	ENST00000321945	NM_139076.2	285	Cgg/Tgg	9/9	1	2	FACETS	0.407	0.349	0.471	0.407	0.349	0.471	SUBCLONAL	1	TRUE	1	0.43	2		544	651	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170792	11170792	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568565971	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	155	1003	4	ENST00000358026.2:c.4936C>T	p.Arg1646Trp	p.R1646W	ENST00000358026	NM_001128849.1	1646	Cgg/Tgg	35/36	1	2	FACETS	0.733	0.67	0.798	0.733	0.67	0.798	SUBCLONAL	1	TRUE	1	0.43	2		1007	984	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	173	841	9	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	1	2	FACETS	0.916	0.844	0.992	0.916	0.844	0.992	CLONAL	1	TRUE	1	0.43	2		850	878	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882049	36882050	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs780753361	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	190	943	3	ENST00000358127.4:c.963dup	p.Ala322ArgfsTer19	p.A322Rfs*19	ENST00000358127	NM_001280556.1	321	-/C	8/10	1	2	FACETS	0.841	0.777	0.908	0.841	0.777	0.908	CLONAL	1	TRUE	1	0.43	2		946	1051	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747889	41747889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772358257	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	154	561	0	ENST00000226382.2:c.880G>A	p.Val294Ile	p.V294I	ENST00000226382	NM_003924.3	294	Gtc/Atc	3/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.43	2		561	632	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249029	55249029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs483352806	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	140	822	2	ENST00000275493.2:c.2327G>A	p.Arg776His	p.R776H	ENST00000275493	NM_005228.3	776	cGc/cAc	20/28	1	2	FACETS	0.8	0.729	0.875	0.8	0.729	0.875	SUBCLONAL	1	TRUE	1	0.43	2		824	814	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991141	41991141	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	142	585	0	ENST00000219905.7:c.2092+2T>C		p.X698_splice	ENST00000219905	NM_001164273.1	698			1	2	FACETS	0.902	0.824	0.985	0.902	0.824	0.985	CLONAL	1	TRUE	1	0.43	2		585	732	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346220	152346220	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	130	551	10	ENST00000359321.1:c.350del	p.Leu117TrpfsTer17	p.L117Wfs*17	ENST00000359321	NM_005431.1	117	tTg/tg	3/3	1	2	FACETS	0.901	0.819	0.987	0.901	0.819	0.987	CLONAL	1	TRUE	1	0.43	2		561	671	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200267	138200267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	131	625	0	ENST00000237289.4:c.1685G>A	p.Arg562His	p.R562H	ENST00000237289	NM_001270507.1	562	cGt/cAt	7/9	1	2	FACETS	0.865	0.787	0.948	0.865	0.787	0.948	CLONAL	1	TRUE	1	0.43	2		625	704	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	86	1163	2	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	1	2	FACETS	0.353	0.311	0.398	0.353	0.311	0.398	SUBCLONAL	1	TRUE	1	0.43	2		1165	1133	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	163	1018	1	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	1	2	FACETS	0.73	0.669	0.793	0.73	0.669	0.793	SUBCLONAL	1	TRUE	1	0.43	2		1019	1039	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286238	66286238	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	83	397	0	ENST00000273854.3:c.1448del	p.Asn483ThrfsTer18	p.N483Tfs*18	ENST00000273854	NM_004439.5	483	aAc/ac	6/18	1	2	FACETS	0.83	0.735	0.931	0.83	0.735	0.931	CLONAL	1	TRUE	1	0.43	2		397	465	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945726	17945726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178958564	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	213	956	0	ENST00000458235.1:c.2134G>A	p.Gly712Ser	p.G712S	ENST00000458235	NM_000215.3	712	Ggc/Agc	16/24	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.43	2		956	984	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127460	55127460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779332376	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	113	541	2	ENST00000257290.5:c.248C>T	p.Thr83Met	p.T83M	ENST00000257290	NM_006206.4	83	aCg/aTg	3/23	1	2	FACETS	0.701	0.631	0.775	0.701	0.631	0.775	SUBCLONAL	1	TRUE	1	0.43	2		543	750	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356281	66356282	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CA	CA	-	novel	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	130	630	0	ENST00000273854.3:c.1215_1216del	p.Cys405Ter	p.C405*	ENST00000273854	NM_004439.5	405	tgTGag/tgag	5/18	1	2	FACETS	0.833	0.756	0.913	0.833	0.756	0.913	CLONAL	1	TRUE	1	0.43	2		630	726	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607487	46607487	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	188	1015	3	ENST00000263734.3:c.1681del	p.Gln561SerfsTer7	p.Q561Sfs*7	ENST00000263734	NM_001430.4	559	aCc/ac	12/16	1	2	FACETS	0.85	0.785	0.918	0.85	0.785	0.918	CLONAL	1	TRUE	1	0.43	2		1018	1029	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118934	70118934	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	71	933	2	ENST00000245479.2:c.506A>G	p.His169Arg	p.H169R	ENST00000245479	NM_000346.3	169	cAc/cGc	2/3	1	2	FACETS	0.352	0.307	0.402	0.352	0.307	0.402	SUBCLONAL	1	TRUE	1	0.43	2		935	937	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038781	47038781	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556777817	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	212	1069	1	ENST00000377604.3:c.788G>A	p.Arg263Gln	p.R263Q	ENST00000377604	NM_001204468.1	263	cGg/cAg	9/24	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.43	2		1070	936	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822330	72822330	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756436707	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	209	1042	1	ENST00000268489.5:c.9845C>T	p.Ala3282Val	p.A3282V	ENST00000268489	NM_006885.3	3282	gCg/gTg	10/10	1	2	FACETS	0.989	0.918	1	0.989	0.918	1	CLONAL	1	TRUE	1	0.43	2		1043	983	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65300294	65300294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	80	358	1	ENST00000342505.4:c.3416G>A	p.Arg1139Gln	p.R1139Q	ENST00000342505	NM_002227.2	1139	cGg/cAg	25/25	1	2	FACETS	0.8	0.707	0.9	0.8	0.707	0.9	SUBCLONAL	1	TRUE	1	0.43	2		359	465	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273060	18273060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	214	1007	0	ENST00000222254.8:c.950C>T	p.Ala317Val	p.A317V	ENST00000222254	NM_005027.3	317	gCc/gTc	8/16	1	2	FACETS	0.944	0.877	1	0.944	0.877	1	CLONAL	1	TRUE	1	0.43	2		1007	1054	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022792	31022792	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	149	735	0	ENST00000375687.4:c.2277C>A	p.Cys759Ter	p.C759*	ENST00000375687	NM_015338.5	759	tgC/tgA	13/13	1	2	FACETS	0.959	0.877	1	0.959	0.877	1	CLONAL	1	TRUE	1	0.43	2		735	723	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421701	49421701	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	151	822	2	ENST00000301067.7:c.14528del	p.Lys4843ArgfsTer15	p.K4843Rfs*15	ENST00000301067	NM_003482.3	4843	aAg/ag	47/54	1	2	FACETS	0.848	0.776	0.924	0.848	0.776	0.924	CLONAL	1	TRUE	1	0.43	2		824	828	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310523	65310525	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	130	736	0	ENST00000342505.4:c.2163_2165del	p.Leu722del	p.L722del	ENST00000342505	NM_002227.2	721	ctCCTg/ctg	16/25	1	2	FACETS	0.809	0.735	0.888	0.809	0.735	0.888	CLONAL	1	TRUE	1	0.43	2		736	747	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690383	117690383	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	110	585	0	ENST00000369458.3:c.746G>C	p.Ser249Thr	p.S249T	ENST00000369458	NM_024626.3	249	aGt/aCt	5/6	1	2	FACETS	0.764	0.687	0.845	0.764	0.687	0.845	SUBCLONAL	1	TRUE	1	0.43	2		585	670	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830733	156830733	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	29	105	0	ENST00000524377.1:c.7C>T	p.Arg3Ter	p.R3*	ENST00000524377	NM_002529.3	3	Cga/Tga	1/17	1	2	FACETS	0.887	0.721	1	0.887	0.721	1	CLONAL	1	TRUE	1	0.43	2		105	152	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022532	12022532	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	157	866	0	ENST00000396373.4:c.641del	p.Pro214ArgfsTer52	p.P214Rfs*52	ENST00000396373	NM_001987.4	213	tCc/tc	5/8	0.3	3	FACETS	1	0.945	1			1	CLONAL	1	TRUE	NA	0.43	3		866	852	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425928	49425928	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	221	1039	1	ENST00000301067.7:c.12560G>T	p.Gly4187Val	p.G4187V	ENST00000301067	NM_003482.3	4187	gGg/gTg	39/54	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.43	2		1040	987	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443547	49443547	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	210	851	0	ENST00000301067.7:c.3824C>G	p.Ala1275Gly	p.A1275G	ENST00000301067	NM_003482.3	1275	gCt/gGt	11/54	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.43	2		851	874	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28631536	28631536	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	94	478	0	ENST00000241453.7:c.432del	p.Phe144LeufsTer15	p.F144Lfs*15	ENST00000241453	NM_004119.2	144	ttT/tt	4/24	1	2	FACETS	0.729	0.649	0.813	0.729	0.649	0.813	SUBCLONAL	1	TRUE	1	0.43	2		478	600	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032303	10032303	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	131	692	0	ENST00000330684.3:c.520A>G	p.Thr174Ala	p.T174A	ENST00000330684	NM_001134407.1	174	Acc/Gcc	3/13	1	2	FACETS	0.837	0.76	0.917	0.837	0.76	0.917	CLONAL	1	TRUE	1	0.43	2		692	728	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857944	89857944	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	144	665	0	ENST00000389301.3:c.1226A>T	p.Asp409Val	p.D409V	ENST00000389301	NM_000135.2	409	gAc/gTc	14/43	1	2	FACETS	0.957	0.874	1	0.957	0.874	1	CLONAL	1	TRUE	1	0.43	2		665	700	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40478219	40478219	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	129	510	0	ENST00000264657.5:c.1282-2A>G		p.X428_splice	ENST00000264657	NM_139276.2	428			1	2	FACETS	0.938	0.852	1	0.938	0.852	1	CLONAL	1	TRUE	1	0.43	2		510	640	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117569	70117576	+	frameshift_variant	Frame_Shift_Del	DEL	GAGCAGGA	GAGCAGGA	-	novel	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	150	819	0	ENST00000245479.2:c.39_46del	p.Gln14GlyfsTer235	p.Q14Gfs*235	ENST00000245479	NM_000346.3	13	GAGCAGGAg/g	1/3	1	2	FACETS	0.819	0.749	0.892	0.819	0.749	0.892	CLONAL	1	TRUE	1	0.43	2		819	852	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633222	12633222	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs886042569	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	90	672	0	ENST00000251849.4:c.1178A>C	p.Glu393Ala	p.E393A	ENST00000251849	NM_002880.3	393	gAg/gCg	11/17	1	2	FACETS	0.509	0.451	0.571	0.509	0.451	0.571	SUBCLONAL	1	TRUE	1	0.43	2		672	823	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250938	153250938	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	58	268	0	ENST00000281708.4:c.1123-1G>A		p.X375_splice	ENST00000281708	NM_033632.3	375			1	2	FACETS	0.943	0.817	1	0.943	0.817	1	CLONAL	1	TRUE	1	0.43	2		268	286	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294642	1294642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	180	697	1	ENST00000310581.5:c.359G>A	p.Arg120His	p.R120H	ENST00000310581	NM_198253.2	120	cGc/cAc	2/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.43	2		698	733	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323322	31323322	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61759950	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	43	230	0	ENST00000412585.2:c.667G>A	p.Ala223Thr	p.A223T	ENST00000412585	NM_005514.6	223	Gcc/Acc	4/8	1	2	FACETS	0.81	0.683	0.948	0.81	0.683	0.948	CLONAL	1	TRUE	1	0.43	2		230	247	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997464	149997464	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	158	519	0	ENST00000253339.5:c.2815A>G	p.Ile939Val	p.I939V	ENST00000253339		939	Att/Gtt	6/7	1	2	FACETS	0.985	0.904	1	0.985	0.904	1	CLONAL	1	TRUE	1	0.43	2		519	746	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859437	151859437	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	118	550	0	ENST00000262189.6:c.11225G>A	p.Ser3742Asn	p.S3742N	ENST00000262189	NM_170606.2	3742	aGt/aAt	43/59	1	2	FACETS	0.797	0.72	0.878	0.797	0.72	0.878	SUBCLONAL	1	TRUE	1	0.43	2		550	689	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863271	56863271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752739111	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	151	635	1	ENST00000519728.1:c.415G>A	p.Ala139Thr	p.A139T	ENST00000519728	NM_002350.3	139	Gca/Aca	6/13	1	2	FACETS	0.792	0.724	0.863	0.792	0.724	0.863	SUBCLONAL	1	TRUE	1	0.43	2		636	887	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900299	101900299	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057524497	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	95	425	0	ENST00000374994.4:c.733G>A	p.Glu245Lys	p.E245K	ENST00000374994	NM_004612.2	245	Gag/Aag	4/9	1	2	FACETS	0.82	0.732	0.913	0.82	0.732	0.913	CLONAL	1	TRUE	1	0.43	2		425	539	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110251317	110251317	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	144	742	0	ENST00000374672.4:c.20A>G	p.Glu7Gly	p.E7G	ENST00000374672	NM_004235.4	7	gAg/gGg	2/5	1	2	FACETS	0.924	0.844	1	0.924	0.844	1	CLONAL	1	TRUE	1	0.43	2		742	725	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939696	76939696	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045366-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	134	723	0	ENST00000373344.5:c.1052A>T	p.Glu351Val	p.E351V	ENST00000373344	NM_000489.3	351	gAg/gTg	9/35	1	2	FACETS	0.864	0.786	0.946	0.864	0.786	0.946	CLONAL	1	TRUE	1	0.43	2		723	721	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	197	882	1	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.55951440413077	2		883	595	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	133	737	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.953	0.871	1	0.953	0.871	1	CLONAL	1	TRUE	1	0.55951440413077	2		742	499	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	121	767	3	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.886	0.805	0.971	0.886	0.805	0.971	CLONAL	1	TRUE	1	0.55951440413077	2		770	488	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	147	892	7	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.55951440413077	2		899	469	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	22	354	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.297688956828989	0	FACETS	0.353	0.279	0.436			1	INDETERMINATE	1	TRUE	0	0.55951440413077	0		354	98	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	133	582	0	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.55951440413077	2		582	411	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	126	475	1	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.55951440413077	2		476	382	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1232964733	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	42	128	0	ENST00000324856.7:c.1015del	p.Ala339LeufsTer24	p.A339Lfs*24	ENST00000324856	NM_006015.4	337	tGg/tg	1/20	1	2	FACETS	0.915	0.777	1	0.915	0.777	1	CLONAL	1	TRUE	1	0.55951440413077	2		128	164	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381472	81381472	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777593933	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	57	393	0	ENST00000222390.5:c.589C>T	p.Arg197Cys	p.R197C	ENST00000222390	NM_000601.4	197	Cgc/Tgc	5/18	0.55951440413077	3	FACETS	0.802	0.692	0.921	0.401	0.346	0.461	CLONAL	1	TRUE	1	0.55951440413077	3		393	325	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549832	187549832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371598532	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	45	550	1	ENST00000441802.2:c.4409C>T	p.Ala1470Val	p.A1470V	ENST00000441802	NM_005245.3	1470	gCg/gTg	8/27	1	2	FACETS	0.773	0.657	0.898	0.773	0.657	0.898	SUBCLONAL	1	TRUE	1	0.55951440413077	2		551	208	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588751	29588751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760703505	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	48	290	1	ENST00000356175.3:c.4537C>T	p.Arg1513Ter	p.R1513*	ENST00000356175	NM_000267.3	1513	Cga/Tga	34/57	1	2	FACETS	0.845	0.724	0.975	0.845	0.724	0.975	CLONAL	1	TRUE	1	0.55951440413077	2		291	203	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26978094	26978094	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1160704856	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	247	676	1	ENST00000381527.3:c.1271G>A	p.Arg424His	p.R424H	ENST00000381527	NM_001260.1	424	cGt/cAt	13/13	0.55951440413077	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.55951440413077	3		677	528	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022442	31022442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs750318549	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	103	497	7	ENST00000375687.4:c.1934del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	643	Ggg/gg	13/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.55951440413077	2		504	279	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799098	42799098	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	159	1044	2	ENST00000575354.2:c.4586del	p.Pro1529LeufsTer91	p.P1529Lfs*91	ENST00000575354	NM_015125.3	1528	Ccc/cc	20/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.55951440413077	2		1046	533	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905546	50905546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144979965	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	171	1249	2	ENST00000440232.2:c.674G>A	p.Arg225His	p.R225H	ENST00000440232	NM_002691.3	225	cGt/cAt	6/27	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.55951440413077	2		1251	559	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160393	99160393	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1360678266	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	150	707	0	ENST00000074304.5:c.872G>A	p.Arg291Gln	p.R291Q	ENST00000074304	NM_001134224.1	291	cGg/cAg	11/26	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.55951440413077	2		707	449	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444659	78444659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs908264837	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	136	427	2	ENST00000370768.2:c.30del	p.Ser11LeufsTer43	p.S11Lfs*43	ENST00000370768	NM_003902.3	10	ccC/cc	1/20	1	2	FACETS	0.897	0.82	0.977	0.897	0.82	0.977	CLONAL	1	TRUE	1	0.55951440413077	2		429	542	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132926	64132926	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	131	763	2	ENST00000334205.4:c.1060C>T	p.Arg354Ter	p.R354*	ENST00000334205	NM_003942.2	354	Cga/Tga	9/17	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.55951440413077	2		765	448	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255142	16255145	+	frameshift_variant	Frame_Shift_Del	DEL	GAGA	GAGA	-	novel	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	55	500	0	ENST00000375759.3:c.2415_2418del	p.Glu805AspfsTer3	p.E805Dfs*3	ENST00000375759	NM_015001.2	803	GAGAga/ga	11/15	1	2	FACETS	0.812	0.702	0.93	0.812	0.702	0.93	CLONAL	1	TRUE	1	0.55951440413077	2		500	242	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523357	176523357	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs775373903	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	126	897	1	ENST00000292408.4:c.2014G>A	p.Val672Met	p.V672M	ENST00000292408	NM_213647.1	672	Gtg/Atg	15/18	1	2	FACETS	0.897	0.817	0.981	0.897	0.817	0.981	CLONAL	1	TRUE	1	0.55951440413077	2		898	502	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8733794	8733794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs949202374	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	104	663	1	ENST00000356435.5:c.50G>A	p.Arg17His	p.R17H	ENST00000356435		17	cGc/cAc	1/35	1	2	FACETS	0.916	0.826	1	0.916	0.826	1	CLONAL	1	TRUE	1	0.55951440413077	2		664	406	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732957	30732957	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs727504421	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	103	528	0	ENST00000295754.5:c.1570G>A	p.Asp524Asn	p.D524N	ENST00000295754	NM_003242.5	524	Gac/Aac	7/7	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.55951440413077	2		528	359	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510560	38510560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	118	656	1	ENST00000254066.5:c.814C>T	p.Arg272Trp	p.R272W	ENST00000254066	NM_000964.3	272	Cgg/Tgg	7/9	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.55951440413077	2		657	382	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845477	72845477	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1395722106	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	135	668	0	ENST00000268489.5:c.3863C>T	p.Thr1288Met	p.T1288M	ENST00000268489	NM_006885.3	1288	aCg/aTg	7/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.55951440413077	2		668	398	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813031	76813031	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	53	278	0	ENST00000373344.5:c.6590G>A	p.Arg2197His	p.R2197H	ENST00000373344	NM_000489.3	2197	cGt/cAt	30/35	1	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.55951440413077	1		278	95	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420245	88420245	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1191745945	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	131	647	0	ENST00000360948.2:c.2441G>A	p.Arg814Gln	p.R814Q	ENST00000360948	NM_001012338.2	814	cGg/cAg	19/19	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.55951440413077	2		647	405	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128028956	128028956	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775316471	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	146	738	0	ENST00000285398.2:c.1901G>A	p.Arg634His	p.R634H	ENST00000285398	NM_000122.1	634	cGt/cAt	12/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.55951440413077	2		738	470	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003782	45003782	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs752758095	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	166	779	0	ENST00000558401.1:c.38T>C	p.Leu13Pro	p.L13P	ENST00000558401	NM_004048.2	13	cTc/cCc	1/4	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.55951440413077	2		779	564	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073616	8073616	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760980466	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	156	581	0	ENST00000377482.5:c.1043C>T	p.Pro348Leu	p.P348L	ENST00000377482	NM_018948.3	348	cCg/cTg	4/4	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.55951440413077	2		581	495	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439931	56439931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748533737	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	184	771	0	ENST00000407977.2:c.661C>T	p.Arg221Trp	p.R221W	ENST00000407977		221	Cgg/Tgg	6/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.55951440413077	2		771	543	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433388	49433388	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555191598	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	139	924	0	ENST00000301067.7:c.8059C>T	p.Arg2687Ter	p.R2687*	ENST00000301067	NM_003482.3	2687	Cga/Tga	32/54	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.55951440413077	2		924	422	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185545	27185545	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1564083506	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	110	735	4	ENST00000380036.4:c.1250del	p.Pro417LeufsTer10	p.P417Lfs*10	ENST00000380036	NM_000459.3	415	ctC/ct	9/23	1	2	FACETS	0.995	0.902	1	0.995	0.902	1	CLONAL	1	TRUE	1	0.55951440413077	2		739	395	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832811	3832811	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555484797	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	124	696	2	ENST00000262367.5:c.1447C>T	p.Arg483Ter	p.R483*	ENST00000262367	NM_004380.2	483	Cga/Tga	6/31	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.55951440413077	2		698	404	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137323821	137323821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769209021	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	156	944	3	ENST00000481739.1:c.1114G>A	p.Ala372Thr	p.A372T	ENST00000481739	NM_002957.4	372	Gcc/Acc	8/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.55951440413077	2		947	499	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934644	9934644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1331671132	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	85	494	0	ENST00000330684.3:c.1511G>A	p.Arg504Gln	p.R504Q	ENST00000330684	NM_001134407.1	504	cGg/cAg	7/13	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.55951440413077	2		494	275	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622369	1622369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143406385	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	164	998	0	ENST00000344749.5:c.595G>A	p.Ala199Thr	p.A199T	ENST00000344749	NM_001136139.2	199	Gcc/Acc	9/19	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.55951440413077	2		998	522	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585516	29585516	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	19	113	0	ENST00000356175.3:c.4265C>G	p.Ser1422Ter	p.S1422*	ENST00000356175	NM_000267.3	1422	tCa/tGa	31/57	1	2	FACETS	1	0.815	1	1	0.815	1	CLONAL	1	TRUE	1	0.55951440413077	2		113	65	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629475	187629475	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765412973	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	128	728	0	ENST00000441802.2:c.1507G>A	p.Ala503Thr	p.A503T	ENST00000441802	NM_005245.3	503	Gca/Aca	2/27	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.55951440413077	2		728	445	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799627	3799627	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs200782888	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	27	501	0	ENST00000262367.5:c.3836+1G>A		p.X1279_splice	ENST00000262367	NM_004380.2	1279			1	2	FACETS	1	0.828	1	1	0.828	1	CLONAL	1	TRUE	1	0.55951440413077	2		501	95	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425302	49425302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	171	1004	0	ENST00000301067.7:c.13186C>T	p.Pro4396Ser	p.P4396S	ENST00000301067	NM_003482.3	4396	Cct/Tct	39/54	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.55951440413077	2		1004	552	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137186	64137186	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752564591	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	114	741	1	ENST00000334205.4:c.1618G>A	p.Asp540Asn	p.D540N	ENST00000334205	NM_003942.2	540	Gac/Aac	14/17	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.55951440413077	2		742	394	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170327	119170327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1393832618	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	110	388	0	ENST00000264033.4:c.2557G>A	p.Ala853Thr	p.A853T	ENST00000264033	NM_005188.3	853	Gcc/Acc	16/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.55951440413077	2		388	345	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279836	46279837	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCAG	rs3830809	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	44	454	6	ENST00000371998.3:c.3786_3791dup	p.Gln1275_Gln1276dup	p.Q1275_Q1276dup	ENST00000371998		1275	-/CAGCAG	20/23	1	2	FACETS	0.461	0.388	0.542	0.461	0.388	0.542	SUBCLONAL	1	TRUE	1	0.55951440413077	2		460	341	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155032	55155032	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1428997941	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	92	606	0	ENST00000257290.5:c.2741G>A	p.Arg914Gln	p.R914Q	ENST00000257290	NM_006206.4	914	cGg/cAg	20/23	1	2	FACETS	0.921	0.826	1	0.921	0.826	1	CLONAL	1	TRUE	1	0.55951440413077	2		606	357	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735635	204735635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	102	510	0	ENST00000302823.3:c.436G>A	p.Gly146Arg	p.G146R	ENST00000302823	NM_005214.4	146	Gga/Aga	2/4	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.55951440413077	2		510	342	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345797	152345797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149186933	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	111	432	0	ENST00000359321.1:c.773G>A	p.Arg258His	p.R258H	ENST00000359321	NM_005431.1	258	cGt/cAt	3/3	0.55951440413077	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.55951440413077	3		432	230	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595972	43595972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529018971	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	156	993	1	ENST00000355710.3:c.139G>A	p.Gly47Ser	p.G47S	ENST00000355710	NM_020975.4	47	Ggc/Agc	2/20	1	2	FACETS	0.996	0.917	1	0.996	0.917	1	CLONAL	1	TRUE	1	0.55951440413077	2		994	560	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774226061	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	140	921	0	ENST00000301067.7:c.3704G>A	p.Gly1235Asp	p.G1235D	ENST00000301067	NM_003482.3	1235	gGt/gAt	11/54	1	2	FACETS	0.977	0.896	1	0.977	0.896	1	CLONAL	1	TRUE	1	0.55951440413077	2		921	512	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444525	49444525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs550306157	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	171	962	0	ENST00000301067.7:c.2846C>T	p.Pro949Leu	p.P949L	ENST00000301067	NM_003482.3	949	cCg/cTg	11/54	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.55951440413077	2		962	540	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639666	47639684	+	frameshift_variant	Frame_Shift_Del	DEL	GAATAGTGCTGTATTGCCA	GAATAGTGCTGTATTGCCA	-	novel	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	35	521	0	ENST00000233146.2:c.762_780del	p.Asn254LysfsTer14	p.N254Kfs*14	ENST00000233146	NM_000251.2	253	atGAATAGTGCTGTATTGCCA/at	4/16	1	2	FACETS	0.665	0.551	0.791	0.665	0.551	0.791	SUBCLONAL	1	TRUE	1	0.55951440413077	2		521	188	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247257	153247259	+	inframe_deletion	In_Frame_Del	DEL	AAC	AAC	-	novel	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	74	465	0	ENST00000281708.4:c.1543_1545del	p.Val515del	p.V515del	ENST00000281708	NM_033632.3	515	GTT/-	10/12	1	2	FACETS	0.804	0.709	0.904	0.804	0.709	0.904	CLONAL	1	TRUE	1	0.55951440413077	2		465	329	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149452968	149452968	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	188	690	0	ENST00000286301.3:c.978G>T	p.Glu326Asp	p.E326D	ENST00000286301	NM_005211.3	326	gaG/gaT	7/22	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.55951440413077	2		690	548	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518088	176518088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	131	862	0	ENST00000292408.4:c.586C>T	p.Arg196Cys	p.R196C	ENST00000292408	NM_213647.1	196	Cgc/Tgc	5/18	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.55951440413077	2		862	457	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638147	176638148	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	85	718	0	ENST00000439151.2:c.2749_2750del	p.Met917AlafsTer2	p.M917Afs*2	ENST00000439151	NM_022455.4	916	gAT/g	5/23	1	2	FACETS	0.944	0.842	1	0.944	0.842	1	CLONAL	1	TRUE	1	0.55951440413077	2		718	322	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051060	180051060	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs768956955	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	149	752	0	ENST00000261937.6:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000261937	NM_182925.4	475	Cgg/Tgg	11/30	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.55951440413077	2		752	436	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555005	106555005	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	113	613	0	ENST00000369096.4:c.2122G>T	p.Gly708Trp	p.G708W	ENST00000369096	NM_001198.3	708	Ggg/Tgg	7/7	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.55951440413077	2		613	386	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207764	29207764	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	129	614	0	ENST00000240100.2:c.32A>G	p.Asp11Gly	p.D11G	ENST00000240100	NM_001394.6	11	gAc/gGc	1/4	1	2	FACETS	0.979	0.894	1	0.979	0.894	1	CLONAL	1	TRUE	1	0.55951440413077	2		614	471	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146027	38146027	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	173	821	0	ENST00000317025.8:c.3479G>T	p.Arg1160Met	p.R1160M	ENST00000317025	NM_023034.1	1160	aGg/aTg	19/24	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.55951440413077	2		821	524	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965473	68965473	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150203239	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	60	702	1	ENST00000288368.4:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000288368	NM_024870.2	362	cGg/cAg	9/40	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.55951440413077	2		703	195	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209526	98209526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374346190	NA	P-0045372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	158	976	1	ENST00000331920.6:c.4012C>T	p.Arg1338Cys	p.R1338C	ENST00000331920	NM_000264.3	1338	Cgc/Tgc	23/24	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.55951440413077	2		977	439	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	137	425	0				ENST00000310581	NM_198253.2	-/1132			0.269333904712303	1	FACETS	0.78	0.715	0.846	0.78	0.715	0.846	INDETERMINATE	1	TRUE	0	0.576359625286625	1		425	434	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	259	455	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	1	2	FACETS	0.934	0.876	0.994	0.934	0.876	0.994	CLONAL	1	TRUE	1	0.576359625286625	2		455	962	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264610	1264610	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	225	902	0	ENST00000310581.5:c.2752G>A	p.Ala918Thr	p.A918T	ENST00000310581	NM_198253.2	918	Gct/Act	11/16	0.269333904712303	1	FACETS	0.436	0.405	0.468	0.436	0.405	0.468	INDETERMINATE	1	TRUE	0	0.576359625286625	1		902	1275	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913255	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	740	563	1	ENST00000369535.4:c.183A>T	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caT	3/7	0.442146840170276	4	FACETS	0.958	0.929	0.987	0.958	0.929	0.987	CLONAL	3	TRUE	1	0.576359625286625	4		564	1408	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339680	116339680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	580	412	0	ENST00000397752.3:c.542G>A	p.Gly181Glu	p.G181E	ENST00000397752	NM_000245.2	181	gGa/gAa	2/21	0.442146840170276	4	FACETS	0.897	0.865	0.929	0.897	0.865	0.929	CLONAL	3	TRUE	1	0.576359625286625	4		412	1179	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391084	89391084	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	643	608	2	ENST00000336596.2:c.1150C>T	p.Pro384Ser	p.P384S	ENST00000336596	NM_005233.5	384	Cct/Tct	5/17	0.576359625286625	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.576359625286625	3		610	1431	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259262	89259262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770780950	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	205	405	0	ENST00000336596.2:c.406C>T	p.Arg136Ter	p.R136*	ENST00000336596	NM_005233.5	136	Cga/Tga	3/17	0.576359625286625	3	FACETS	0.99	0.919	1	0.495	0.459	0.532	CLONAL	1	TRUE	1	0.576359625286625	3		405	926	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285224	198285224	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757758244	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	238	405	0	ENST00000335508.6:c.343C>T	p.Arg115Trp	p.R115W	ENST00000335508	NM_012433.2	115	Cgg/Tgg	4/25	1	2	FACETS	0.996	0.932	1	0.996	0.932	1	CLONAL	1	TRUE	1	0.576359625286625	2		405	829	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376627	8376627	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	228	445	1	ENST00000356435.5:c.4486C>T	p.Arg1496Ter	p.R1496*	ENST00000356435		1496	Cga/Tga	27/35	1	2	FACETS	0.974	0.91	1	0.974	0.91	1	CLONAL	1	TRUE	1	0.576359625286625	2		446	812	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411267	63411267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866313799	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	402	425	0	ENST00000330258.3:c.1900C>T	p.Arg634Cys	p.R634C	ENST00000330258	NM_152424.3	634	Cgt/Tgt	2/2	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.576359625286625	1		425	669	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442536	52442536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	277	503	0	ENST00000460680.1:c.209C>T	p.Ser70Phe	p.S70F	ENST00000460680	NM_004656.3	70	tCc/tTc	4/17	0.576359625286625	3	FACETS	0.986	0.925	1	0.493	0.462	0.525	CLONAL	1	TRUE	1	0.576359625286625	3		503	1256	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871196	35871196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773491081	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	171	360	0	ENST00000303115.3:c.418C>T	p.Arg140Trp	p.R140W	ENST00000303115	NM_002185.3	140	Cgg/Tgg	4/8	0.269333904712303	1	FACETS	0.809	0.75	0.87	0.809	0.75	0.87	INDETERMINATE	1	TRUE	0	0.576359625286625	1		360	522	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254717	16254717	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	310	529	1	ENST00000375759.3:c.1982G>A	p.Trp661Ter	p.W661*	ENST00000375759	NM_015001.2	661	tGg/tAg	11/15	0.576359625286625	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.576359625286625	1		530	664	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509537	106509537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774366285	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	751	626	0	ENST00000359195.3:c.1531G>A	p.Glu511Lys	p.E511K	ENST00000359195	NM_002649.2	511	Gag/Aag	2/11	0.442146840170276	4	FACETS	0.9	0.872	0.928	0.9	0.872	0.928	CLONAL	3	TRUE	1	0.576359625286625	4		626	1522	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38631980	38631981	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	180	516	0	ENST00000299084.4:c.471dup	p.Gln158SerfsTer9	p.Q158Sfs*9	ENST00000299084	NM_152594.2	156	ctt/cTtt	5/7	0.285591023211869	1	FACETS	0.533	0.492	0.576	0.533	0.492	0.576	INDETERMINATE	1	TRUE	0	0.576359625286625	1		516	834	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020458	69020458	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	337	602	0	ENST00000288368.4:c.2830G>A	p.Glu944Lys	p.E944K	ENST00000288368	NM_024870.2	944	Gaa/Aaa	24/40	0.269333904712303	1	FACETS	0.942	0.894	0.99	0.942	0.894	0.99	INDETERMINATE	1	TRUE	0	0.576359625286625	1		602	884	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030850	69030850	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150128151	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	242	436	0	ENST00000288368.4:c.3392C>T	p.Ser1131Leu	p.S1131L	ENST00000288368	NM_024870.2	1131	tCg/tTg	27/40	0.269333904712303	1	FACETS	0.803	0.754	0.854	0.803	0.754	0.854	INDETERMINATE	1	TRUE	0	0.576359625286625	1		436	744	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574718	41574718	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780778684	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	450	875	0	ENST00000263253.7:c.7003C>T	p.Pro2335Ser	p.P2335S	ENST00000263253	NM_001429.3	2335	Cct/Tct	31/31	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.576359625286625	2		875	1509	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257642	16257643	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	270	545	0	ENST00000375759.3:c.4907_4908delinsTT	p.Ser1636Phe	p.S1636F	ENST00000375759	NM_015001.2	1636	tCC/tTT	11/15	0.576359625286625	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.576359625286625	1		545	642	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343829	118343829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781786089	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	243	571	0	ENST00000534358.1:c.1955G>A	p.Arg652Gln	p.R652Q	ENST00000534358	NM_005933.3	652	cGa/cAa	3/36	0.576359625286625	1	FACETS	0.929	0.874	0.985	0.929	0.874	0.985	CLONAL	1	TRUE	0	0.576359625286625	1		571	646	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623873	28623873	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	173	469	0	ENST00000241453.7:c.781T>A	p.Phe261Ile	p.F261I	ENST00000241453	NM_004119.2	261	Ttt/Att	7/24	0.285591023211869	1	FACETS	0.611	0.564	0.66	0.611	0.564	0.66	INDETERMINATE	1	TRUE	0	0.576359625286625	1		469	699	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28971206	28971206	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	141	273	0	ENST00000282397.4:c.1552-1G>A		p.X518_splice	ENST00000282397	NM_002019.4	518			0.285591023211869	1	FACETS	0.802	0.738	0.869	0.802	0.738	0.869	INDETERMINATE	1	TRUE	0	0.576359625286625	1		273	434	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40682076	40682076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	237	617	0	ENST00000249776.8:c.631G>A	p.Glu211Lys	p.E211K	ENST00000249776	NM_033286.3	211	Gag/Aag	6/9	0.285591023211869	1	FACETS	0.568	0.53	0.608	0.568	0.53	0.608	INDETERMINATE	1	TRUE	0	0.576359625286625	1		617	1030	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847232	68847232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1273532012	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	127	488	0	ENST00000261769.5:c.1154C>T	p.Pro385Leu	p.P385L	ENST00000261769	NM_004360.3	385	cCt/cTt	9/16	0.269333904712303	1	FACETS	0.395	0.358	0.434	0.395	0.358	0.434	INDETERMINATE	1	TRUE	0	0.576359625286625	1		488	794	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007147	62007147	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	392	608	0	ENST00000392795.3:c.535T>A	p.Phe179Ile	p.F179I	ENST00000392795	NM_001039933.1	179	Ttc/Atc	4/6	0.371735986834668	3	FACETS	1	0.992	1	0.603	0.573	0.635	CLONAL	1	TRUE	1	0.576359625286625	3		608	1452	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622187	1622187	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	456	884	1	ENST00000344749.5:c.688C>T	p.Pro230Ser	p.P230S	ENST00000344749	NM_001136139.2	230	Ccc/Tcc	10/19	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.576359625286625	2		885	1576	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632347	1632347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	447	863	1	ENST00000344749.5:c.203C>T	p.Ser68Phe	p.S68F	ENST00000344749	NM_001136139.2	68	tCc/tTc	4/19	1	2	FACETS	0.966	0.921	1	0.966	0.921	1	CLONAL	1	TRUE	1	0.576359625286625	2		864	1605	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707833	47707833	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	187	274	0	ENST00000233146.2:c.2459-2A>T		p.X820_splice	ENST00000233146	NM_000251.2	820			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.576359625286625	2		274	567	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728905	190728905	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	151	316	0	ENST00000441310.2:c.2293C>T	p.His765Tyr	p.H765Y	ENST00000441310	NM_000534.4	765	Cat/Tat	10/13	1	2	FACETS	0.926	0.851	1	0.926	0.851	1	CLONAL	1	TRUE	1	0.576359625286625	2		316	566	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023548	31023549	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	552	498	0	ENST00000375687.4:c.3033_3034delinsAA	p.Asp1012Asn	p.D1012N	ENST00000375687	NM_015338.5	1011	gaGGac/gaAAac	13/13	0.576359625286625	3	FACETS	0.943	0.907	0.98	0.943	0.907	0.98	CLONAL	2	TRUE	1	0.576359625286625	3		498	1308	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162863	47162863	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	235	417	1	ENST00000409792.3:c.3263C>A	p.Ser1088Tyr	p.S1088Y	ENST00000409792	NM_014159.6	1088	tCt/tAt	3/21	0.576359625286625	3	FACETS	1	0.972	1	0.536	0.501	0.573	CLONAL	1	TRUE	1	0.576359625286625	3		418	979	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390989	89390989	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	428	450	1	ENST00000336596.2:c.1055G>A	p.Gly352Glu	p.G352E	ENST00000336596	NM_005233.5	352	gGa/gAa	5/17	0.576359625286625	3	FACETS	0.968	0.926	1	0.968	0.926	1	CLONAL	2	TRUE	1	0.576359625286625	3		451	988	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982058	38982058	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	134	492	0	ENST00000357387.3:c.664C>T	p.Arg222Ter	p.R222*	ENST00000357387	NM_152756.3	222	Cga/Tga	8/38	0.269333904712303	1	FACETS	0.459	0.417	0.503	0.459	0.417	0.503	INDETERMINATE	1	TRUE	0	0.576359625286625	1		492	721	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287329	33287329	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1327	323	561	0	ENST00000374542.5:c.1768A>G	p.Arg590Gly	p.R590G	ENST00000374542	NM_001141970.1	590	Agg/Ggg	6/8	0.572972686199586	4	FACETS	1	0.977	1	0.535	0.504	0.568	CLONAL	1	TRUE	2	0.576359625286625	4		561	1650	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172290	38172290	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	78	298	0	ENST00000317025.8:c.2117T>G	p.Ile706Ser	p.I706S	ENST00000317025	NM_023034.1	706	aTt/aGt	12/24	0.269333904712303	1	FACETS	0.324	0.285	0.367	0.324	0.285	0.367	INDETERMINATE	1	TRUE	0	0.576359625286625	1		298	594	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971061	21971062	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGGG	novel	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	183	388	0	ENST00000304494.5:c.296_297insCCCG	p.Ala100ProfsTer21	p.A100Pfs*21	ENST00000304494	NM_000077.4	99	cgg/cgCCCGg	2/3	1	2	FACETS	0.723	0.668	0.781	0.723	0.668	0.781	SUBCLONAL	1	TRUE	1	0.576359625286625	2		388	878	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27220136	27220136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	263	551	0	ENST00000380036.4:c.3193G>A	p.Asp1065Asn	p.D1065N	ENST00000380036	NM_000459.3	1065	Gat/Aat	21/23	1	2	FACETS	0.969	0.909	1	0.969	0.909	1	CLONAL	1	TRUE	1	0.576359625286625	2		551	942	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606258	93606258	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	356	852	1	ENST00000375746.1:c.78A>T	p.Glu26Asp	p.E26D	ENST00000375746	NM_001174167.1	26	gaA/gaT	2/14	1	2	FACETS	0.917	0.868	0.967	0.917	0.868	0.967	CLONAL	1	TRUE	1	0.576359625286625	2		853	1347	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133748257	133748258	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0045374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	294	606	0	ENST00000318560.5:c.918_919delinsTT	p.Arg307Trp	p.R307W	ENST00000318560	NM_005157.4	306	acCCgg/acTTgg	6/11	1	2	FACETS	0.889	0.837	0.943	0.889	0.837	0.943	CLONAL	1	TRUE	1	0.576359625286625	2		606	1147	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696689	47696689	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	26	616	0	ENST00000347630.2:c.259T>G	p.Tyr87Asp	p.Y87D	ENST00000347630	NM_001007230.1	87	Tac/Gac	5/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		616	274	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804317	43804317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750046020	NA	P-0045376-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	463	818	0	ENST00000372470.3:c.317C>T	p.Pro106Leu	p.P106L	ENST00000372470	NM_005373.2	106	cCg/cTg	3/12	0.328464867505479	3	FACETS	1	0.991	1	0.57	0.544	0.597	INDETERMINATE	1	TRUE	1	0.722253888067653	3		818	1530	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0045377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	142	458	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.566629646349143	4	FACETS	1	0.981	1	0.846	0.793	0.898	CLONAL	3	TRUE	0	0.566629646349143	4		458	232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057520006	NA	P-0045377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	199	888	0	ENST00000269305.4:c.821T>G	p.Val274Gly	p.V274G	ENST00000269305	NM_001126112.2	274	gTt/gGt	8/11	0.566629646349143	1	FACETS	0.883	0.824	0.944	0.883	0.824	0.944	CLONAL	1	TRUE	0	0.566629646349143	1		888	570	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233024	55233024	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144943614	NA	P-0045377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	155	688	0	ENST00000275493.2:c.1774G>A	p.Val592Ile	p.V592I	ENST00000275493	NM_005228.3	592	Gtc/Atc	15/28	0.390418477300612	5	FACETS	1	0.98	1	0.406	0.372	0.442	CLONAL	1	TRUE	2	0.566629646349143	5		688	830	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294099	1294099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1268051204	NA	P-0045377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1527	268	1182	1	ENST00000310581.5:c.902G>A	p.Arg301His	p.R301H	ENST00000310581	NM_198253.2	301	cGc/cAc	2/16	0.428456767254395	4	FACETS	0.826	0.771	0.882	0.413	0.385	0.441	CLONAL	1	TRUE	2	0.566629646349143	4		1183	1795	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156077	99156077	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs966111733	NA	P-0045377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	221	906	0	ENST00000074304.5:c.757G>A	p.Val253Met	p.V253M	ENST00000074304	NM_001134224.1	253	Gtg/Atg	10/26	0.47464469926617	3	FACETS	1	0.987	1	0.411	0.383	0.44	CLONAL	1	TRUE	0	0.566629646349143	3		906	812	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50811846	50811846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	58	439	0	ENST00000398568.2:c.1123G>A	p.Asp375Asn	p.D375N	ENST00000398568	NM_001042412.1	375	Gat/Aat	7/18	0.32249515379737	5	FACETS	0.845	0.736	0.961	0.564	0.49	0.641	INDETERMINATE	2	TRUE	2	0.566629646349143	5		439	224	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0045378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	96	397	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.898	1	1	0.986	1	CLONAL	2	TRUE	1	0.15	2		397	636	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0045378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	120	487	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	1	0.905	1	1	0.989	1	CLONAL	2	TRUE	1	0.15	2		487	798	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579331	7579331	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	139	863	0	ENST00000269305.4:c.356C>G	p.Ala119Gly	p.A119G	ENST00000269305	NM_001126112.2	119	gCc/gGc	4/11	1	2	FACETS	1	0.936	1	1	0.991	1	CLONAL	2	TRUE	1	0.15	2		863	895	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164727	36164727	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	178	1027	2	ENST00000300305.3:c.1148C>T	p.Pro383Leu	p.P383L	ENST00000300305		383	cCg/cTg	8/8	1	2	FACETS	0.874	0.803	0.948	1	0.991	1	CLONAL	2	TRUE	1	0.15	2		1029	1358	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867214	68867214	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	56	678	1	ENST00000261769.5:c.2461G>T	p.Asp821Tyr	p.D821Y	ENST00000261769	NM_004360.3	821	Gac/Tac	16/16	1	2	FACETS	0.842	0.719	0.977	0.842	0.719	0.977	CLONAL	1	TRUE	1	0.15	2		679	887	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61712994	61712994	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1276441023	NA	P-0045378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	52	573	0	ENST00000401558.2:c.2417T>C	p.Ile806Thr	p.I806T	ENST00000401558	NM_003400.3	806	aTa/aCa	20/25	1	2	FACETS	0.689	0.584	0.804	0.689	0.584	0.804	SUBCLONAL	1	TRUE	1	0.15	2		573	1007	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0045379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	38	294	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.117385638332793	4	FACETS	0.333	0.274	0.399	0.166	0.137	0.2	INDETERMINATE	1	FALSE	2	0.385783414658181	4		294	821	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0045379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	40	711	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.29	0.24	0.346	0.29	0.24	0.346	SUBCLONAL	1	FALSE	1	0.385783414658181	2		711	715	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs104886003	NA	P-0045379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	27	566	0	ENST00000263967.3:c.1633G>C	p.Glu545Gln	p.E545Q	ENST00000263967	NM_006218.2	545	Gag/Cag	10/21	1	2	FACETS	0.185	0.146	0.23	0.185	0.146	0.23	SUBCLONAL	1	FALSE	1	0.385783414658181	2		566	756	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038526	47038526	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	45	1206	0	ENST00000377604.3:c.688C>T	p.Arg230Ter	p.R230*	ENST00000377604	NM_001204468.1	230	Cga/Tga	8/24	0.385783414658181	1	FACETS	0.307	0.257	0.362	0.307	0.257	0.362	SUBCLONAL	1	FALSE	0	0.385783414658181	1		1206	614	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814571	43814571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1460228184	NA	P-0045379-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	42	973	0	ENST00000372470.3:c.1366C>T	p.Arg456Cys	p.R456C	ENST00000372470	NM_005373.2	456	Cgc/Tgc	9/12	1	2	FACETS	0.301	0.25	0.358	0.301	0.25	0.358	SUBCLONAL	1	FALSE	1	0.385783414658181	2		973	723	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693002	89693003	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	250	451	0	ENST00000371953.3:c.491dup	p.Val166SerfsTer14	p.V166Sfs*14	ENST00000371953	NM_000314.4	162	-/A	5/9	0.698859839804589	2	FACETS	0.806	0.765	0.846	0.806	0.765	0.846	CLONAL	2	TRUE	0	0.698859839804589	2		451	444	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559198	29559198	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0045380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	157	542	0	ENST00000356175.3:c.3305T>G	p.Leu1102Ter	p.L1102*	ENST00000356175	NM_000267.3	1102	tTa/tGa	25/57	0.697750247272576	3	FACETS	0.68	0.623	0.739	0.34	0.311	0.37	SUBCLONAL	1	TRUE	1	0.698859839804589	3		542	892	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662185	227662185	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	757	1092	0	ENST00000305123.5:c.1270G>C	p.Gly424Arg	p.G424R	ENST00000305123	NM_005544.2	424	Ggt/Cgt	1/2	0.697750247272576	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.698859839804589	3		1092	1398	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156362	106156362	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045380-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	176	514	0	ENST00000380013.4:c.1263A>T	p.Glu421Asp	p.E421D	ENST00000380013	NM_001127208.2	421	gaA/gaT	3/11	0.697750247272576	3	FACETS	1	0.953	1	0.52	0.481	0.561	CLONAL	1	TRUE	1	0.698859839804589	3		514	653	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0045381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	239	870	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.201857424799138	2	FACETS	1	0.951	1	1	0.951	1	INDETERMINATE	2	TRUE	0	0.529869140545356	2		870	449	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120612003	120612004	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	rs372504208	NA	P-0045381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	13	55	2	ENST00000256646.2:c.17_18del	p.Pro6ArgfsTer27	p.P6Rfs*27	ENST00000256646	NM_024408.3	6	cCC/c	1/34	1	2	FACETS	0.755	0.551	0.991	0.755	0.551	0.991	CLONAL	1	TRUE	1	0.529869140545356	2		57	65	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856129	68856129	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0045381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	77	585	0	ENST00000261769.5:c.1936+1G>T		p.X646_splice	ENST00000261769	NM_004360.3	646			0.502973533071957	2	FACETS	1	0.889	1	0.501	0.444	0.561	CLONAL	1	TRUE	0	0.529869140545356	2		585	290	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914468	32915490	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTACAAAACGCAAGACAAGTGTTTTCTGAAATAGAAGATAGTACCAAGCAAGTCTTTTCCAAAGTATTGTTTAAAAGTAACGAACATTCAGACCAGCTCACAAGAGAAGAAAATACTGCTATACGTACTCCAGAACATTTAATATCCCAAAAAGGCTTTTCATATAATGTGGTAAATTCATCTGCTTTCTCTGGATTTAGTACAGCAAGTGGAAAGCAAGTTTCCATTTTAGAAAGTTCCTTACACAAAGTTAAGGGAGTGTTAGAGGAATTTGATTTAATCAGAACTGAGCATAGTCTTCACTATTCACCTACGTCTAGACAAAATGTATCAAAAATACTTCCTCGTGTTGATAAGAGAAACCCAGAGCACTGTGTAAACTCAGAAATGGAAAAAACCTGCAGTAAAGAATTTAAATTATCAAATAACTTAAATGTTGAAGGTGGTTCTTCAGAAAATAATCACTCTATTAAAGTTTCTCCATATCTCTCTCAATTTCAACAAGACAAACAACAGTTGGTATTAGGAACCAAAGTGTCACTTGTTGAGAACATTCATGTTTTGGGAAAAGAACAGGCTTCACCTAAAAACGTAAAAATGGAAATTGGTAAAACTGAAACTTTTTCTGATGTTCCTGTGAAAACAAATATAGAAGTTTGTTCTACTTACTCCAAAGATTCAGAAAACTACTTTGAAACAGAAGCAGTAGAAATTGCTAAAGCTTTTATGGAAGATGATGAACTGACAGATTCTAAACTGCCAAGTCATGCCACACATTCTCTTTTTACATGTCCCGAAAATGAGGAAATGGTTTTGTCAAATTCAAGAATTGGAAAAAGAAGAGGAGAGCCCCTTATCTTAGTGGGTAAGTGTTCATTTTTACCTTTCGTGTTGCCAATCACTATTTTTAAAGTGTTTATTCAGTAGACTTGGTATGCTAACAATTAAGAGTGTTATAAACTATGTCTTTTCAGCCATTTTTGTGTAGTCAGTTTGGGGGAGTATGGTTTGATATACAGATA	ATTACAAAACGCAAGACAAGTGTTTTCTGAAATAGAAGATAGTACCAAGCAAGTCTTTTCCAAAGTATTGTTTAAAAGTAACGAACATTCAGACCAGCTCACAAGAGAAGAAAATACTGCTATACGTACTCCAGAACATTTAATATCCCAAAAAGGCTTTTCATATAATGTGGTAAATTCATCTGCTTTCTCTGGATTTAGTACAGCAAGTGGAAAGCAAGTTTCCATTTTAGAAAGTTCCTTACACAAAGTTAAGGGAGTGTTAGAGGAATTTGATTTAATCAGAACTGAGCATAGTCTTCACTATTCACCTACGTCTAGACAAAATGTATCAAAAATACTTCCTCGTGTTGATAAGAGAAACCCAGAGCACTGTGTAAACTCAGAAATGGAAAAAACCTGCAGTAAAGAATTTAAATTATCAAATAACTTAAATGTTGAAGGTGGTTCTTCAGAAAATAATCACTCTATTAAAGTTTCTCCATATCTCTCTCAATTTCAACAAGACAAACAACAGTTGGTATTAGGAACCAAAGTGTCACTTGTTGAGAACATTCATGTTTTGGGAAAAGAACAGGCTTCACCTAAAAACGTAAAAATGGAAATTGGTAAAACTGAAACTTTTTCTGATGTTCCTGTGAAAACAAATATAGAAGTTTGTTCTACTTACTCCAAAGATTCAGAAAACTACTTTGAAACAGAAGCAGTAGAAATTGCTAAAGCTTTTATGGAAGATGATGAACTGACAGATTCTAAACTGCCAAGTCATGCCACACATTCTCTTTTTACATGTCCCGAAAATGAGGAAATGGTTTTGTCAAATTCAAGAATTGGAAAAAGAAGAGGAGAGCCCCTTATCTTAGTGGGTAAGTGTTCATTTTTACCTTTCGTGTTGCCAATCACTATTTTTAAAGTGTTTATTCAGTAGACTTGGTATGCTAACAATTAAGAGTGTTATAAACTATGTCTTTTCAGCCATTTTTGTGTAGTCAGTTTGGGGGAGTATGGTTTGATATACAGATA	-	novel	NA	P-0045381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	31	751	0	ENST00000380152.3:c.5976_6841+157del		p.X1992_splice	ENST00000380152		1992		11/27	0.529869140545356	1	FACETS	0.497	0.406	0.598	0.497	0.406	0.598	SUBCLONAL	1	TRUE	0	0.529869140545356	1		751	173	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349928	89349928	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	125	1073	0	ENST00000301030.4:c.3022G>C	p.Glu1008Gln	p.E1008Q	ENST00000301030	NM_001256183.1	1008	Gag/Cag	9/13	0.529869140545356	4	FACETS	1	0.935	1			1	CLONAL	1	TRUE	NA	0.529869140545356	4		1073	695	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752883	128752884	+	stop_gained	Nonsense_Mutation	DNP	GA	GA	CT	novel	NA	P-0045381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	91	513	1	ENST00000377970.2:c.1044_1045delinsCT	p.Arg349Ter	p.R349*	ENST00000377970	NM_002467.4	348	ctGAga/ctCTga	3/3	0.334371572528282	6	FACETS	0.861	0.763	0.965	0.143	0.127	0.161	CLONAL	1	TRUE	0	0.529869140545356	6		514	822	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530019	63530058	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGACTCTTACCTATAATTTCCCTTTTTGCTGAGCTGCTC	AGGACTCTTACCTATAATTTCCCTTTTTGCTGAGCTGCTC	T	novel	NA	P-0045381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	49	478	0	ENST00000307078.5:c.2377_2405+11delinsA		p.X793_splice	ENST00000307078	NM_004655.3	793		10/11	0.529869140545356	4	FACETS	1	0.901	1	0.357	0.305	0.414	CLONAL	1	TRUE	1	0.529869140545356	4		478	264	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861913	57861913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs114543757	NA	P-0045398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	208	552	1	ENST00000228682.2:c.1214G>A	p.Arg405Gln	p.R405Q	ENST00000228682	NM_005269.2	405	cGg/cAg	10/12	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.672199698138146	2		553	599	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348116	348116	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	286	813	1	ENST00000262320.3:c.1390G>T	p.Glu464Ter	p.E464*	ENST00000262320	NM_003502.3	464	Gag/Tag	6/11	0.672199698138146	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.672199698138146	1		814	538	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295199	1295200	+	upstream_gene_variant	5'Flank	INS	-	-	GGAAGGGGAGGGGCTGGGAGGGCCC	novel	NA	P-0045398-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	48	293	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.406	0.344	0.473	0.406	0.344	0.473	SUBCLONAL	1	TRUE	1	0.672199698138146	2		293	352	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0045399-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	86	556	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.210383396205409	0	FACETS	0.719	0.639	0.804			1	SUBCLONAL	2	TRUE	0	0.210383396205409	0		556	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2544	316	446	0	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	1	2	FACETS	0.861	0.808	0.916	0.861	0.808	0.916	CLONAL	1	TRUE	1	0.256626943808878	2		446	2860	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416976	416976	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2038	270	325	0	ENST00000399788.2:c.3574C>T	p.Pro1192Ser	p.P1192S	ENST00000399788	NM_001042603.1	1192	Cct/Tct	23/28	0.216081538690872	1	FACETS	0.795	0.742	0.85	0.795	0.742	0.85	SUBCLONAL	1	TRUE	0	0.256626943808878	1		325	2308	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1568	252	426	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.256626943808878	1	FACETS	0.941	0.877	1	0.941	0.877	1	CLONAL	1	TRUE	0	0.256626943808878	1		426	1820	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2422	298	503	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	1	2	FACETS	0.854	0.799	0.91	0.854	0.799	0.91	CLONAL	1	TRUE	1	0.256626943808878	2		503	2720	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390982	89390982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1643	223	288	0	ENST00000336596.2:c.1048G>A	p.Asp350Asn	p.D350N	ENST00000336596	NM_005233.5	350	Gac/Aac	5/17	0.256626943808878	1	FACETS	0.812	0.753	0.874	0.812	0.753	0.874	CLONAL	1	TRUE	0	0.256626943808878	1		288	1866	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023408	31023408	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515401	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2144	257	325	0	ENST00000375687.4:c.2893C>T	p.Arg965Ter	p.R965*	ENST00000375687	NM_015338.5	965	Cga/Tga	13/13	1	2	FACETS	0.834	0.777	0.894	0.834	0.777	0.894	CLONAL	1	TRUE	1	0.256626943808878	2		325	2401	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023754	27023754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1321	226	292	0	ENST00000324856.7:c.860C>T	p.Pro287Leu	p.P287L	ENST00000324856	NM_006015.4	287	cCc/cTc	1/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.256626943808878	2		292	1547	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445424	29445424	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762571775	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2833	343	550	0	ENST00000389048.3:c.3409G>A	p.Gly1137Arg	p.G1137R	ENST00000389048	NM_004304.4	1137	Gga/Aga	21/29	1	2	FACETS	0.842	0.792	0.894	0.842	0.792	0.894	CLONAL	1	TRUE	1	0.256626943808878	2		550	3176	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347924	347924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756071423	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2445	321	672	0	ENST00000262320.3:c.1582G>A	p.Gly528Ser	p.G528S	ENST00000262320	NM_003502.3	528	Ggc/Agc	6/11	1	2	FACETS	0.904	0.849	0.962	0.904	0.849	0.962	CLONAL	1	TRUE	1	0.256626943808878	2		672	2766	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576273	88576273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1953	216	294	0	ENST00000360948.2:c.1400C>T	p.Pro467Leu	p.P467L	ENST00000360948	NM_001012338.2	467	cCc/cTc	13/19	1	2	FACETS	0.776	0.718	0.837	0.776	0.718	0.837	SUBCLONAL	1	TRUE	1	0.256626943808878	2		294	2169	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743948	41743948	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751738506	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2695	321	624	0	ENST00000301178.4:c.883C>T	p.Arg295Trp	p.R295W	ENST00000301178	NM_021913.4	295	Cgg/Tgg	7/20	1	2	FACETS	0.829	0.778	0.882	0.829	0.778	0.882	CLONAL	1	TRUE	1	0.256626943808878	2		624	3016	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566478	41566478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1620	442	239	0	ENST00000263253.7:c.4355C>T	p.Pro1452Leu	p.P1452L	ENST00000263253	NM_001429.3	1452	cCt/cTt	27/31	1	2	FACETS	0.835	0.794	0.878	1	0.996	1	CLONAL	2	TRUE	1	0.256626943808878	2		239	2062	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715509	117715509	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	104	182	0	ENST00000368508.3:c.980G>A	p.Gly327Glu	p.G327E	ENST00000368508	NM_002944.2	327	gGa/gAa	10/43	0.149797484462492	0	FACETS	0.571	0.51	0.636			1	INDETERMINATE	1	TRUE	0	0.256626943808878	0		182	1055	SUCCESS
REL	5966	MSKCC	GRCh37	2	61144086	61144086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867470560	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2058	219	382	0	ENST00000295025.8:c.469C>T	p.Pro157Ser	p.P157S	ENST00000295025	NM_002908.2	157	Cct/Tct	5/11	1	2	FACETS	0.75	0.694	0.808	0.75	0.694	0.808	SUBCLONAL	1	TRUE	1	0.256626943808878	2		382	2277	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176715855	176715855	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2291	255	362	0	ENST00000439151.2:c.6187C>T	p.Leu2063Phe	p.L2063F	ENST00000439151	NM_022455.4	2063	Ctt/Ttt	21/23	1	2	FACETS	0.781	0.727	0.837	0.781	0.727	0.837	SUBCLONAL	1	TRUE	1	0.256626943808878	2		362	2546	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865537	57865537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2396	307	578	0	ENST00000228682.2:c.3014G>A	p.Gly1005Glu	p.G1005E	ENST00000228682	NM_005269.2	1005	gGa/gAa	12/12	1	2	FACETS	0.885	0.83	0.943	0.885	0.83	0.943	CLONAL	1	TRUE	1	0.256626943808878	2		578	2703	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55124952	55124952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754092062	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2877	346	445	0	ENST00000257290.5:c.17C>T	p.Pro6Leu	p.P6L	ENST00000257290	NM_006206.4	6	cCg/cTg	2/23	1	2	FACETS	0.837	0.787	0.888	0.837	0.787	0.888	CLONAL	1	TRUE	1	0.256626943808878	2		445	3223	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604240	189604240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2639	320	396	0	ENST00000264731.3:c.1407G>A	p.Met469Ile	p.M469I	ENST00000264731	NM_003722.4	469	atG/atA	11/14	0.18347088732002	3	FACETS	0.951	0.892	1	0.475	0.446	0.506	CLONAL	1	TRUE	1	0.256626943808878	3		396	2959	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857250	9857250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866228360	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2399	288	426	1	ENST00000330684.3:c.4151C>T	p.Ser1384Leu	p.S1384L	ENST00000330684	NM_001134407.1	1384	tCg/tTg	13/13	1	2	FACETS	0.835	0.781	0.892	0.835	0.781	0.892	CLONAL	1	TRUE	1	0.256626943808878	2		427	2687	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046405	69046405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2363	275	415	0	ENST00000288368.4:c.3878G>A	p.Ser1293Asn	p.S1293N	ENST00000288368	NM_024870.2	1293	aGc/aAc	32/40	0.256626943808878	1	FACETS	0.708	0.661	0.757	0.708	0.661	0.757	SUBCLONAL	1	TRUE	0	0.256626943808878	1		415	2638	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937985	36937985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237845502	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2477	292	662	2	ENST00000361632.4:c.851C>T	p.Pro284Leu	p.P284L	ENST00000361632		284	cCc/cTc	7/16	1	2	FACETS	0.822	0.769	0.877	0.822	0.769	0.877	CLONAL	1	TRUE	1	0.256626943808878	2		664	2769	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670237	134670237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2368	256	346	1	ENST00000398015.3:c.148G>A	p.Glu50Lys	p.E50K	ENST00000398015	NM_004441.4	50	Gaa/Aaa	3/16	0.18347088732002	3	FACETS	0.858	0.799	0.92	0.429	0.399	0.46	CLONAL	1	TRUE	1	0.256626943808878	3		347	2624	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109947	115109947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2044	286	481	0	ENST00000257566.3:c.1931C>T	p.Ser644Phe	p.S644F	ENST00000257566	NM_016569.3	644	tCc/tTc	8/8	1	2	FACETS	0.957	0.895	1	0.957	0.895	1	CLONAL	1	TRUE	1	0.256626943808878	2		481	2330	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199414	11199414	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2397	361	396	0	ENST00000361445.4:c.5077C>T	p.His1693Tyr	p.H1693Y	ENST00000361445	NM_004958.3	1693	Cac/Tac	36/58	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.256626943808878	2		396	2758	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295198	1295198	+	upstream_gene_variant	5'Flank	SNP	A	A	C	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	112	197	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.711	0.637	0.789	0.711	0.637	0.789	SUBCLONAL	1	TRUE	1	0.256626943808878	2		197	1228	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742919	17742919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1283019508	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1916	234	546	0	ENST00000250003.3:c.827C>T	p.Ser276Phe	p.S276F	ENST00000250003	NM_002478.4	276	tCt/tTt	3/3	1	2	FACETS	0.848	0.787	0.912	0.848	0.787	0.912	CLONAL	1	TRUE	1	0.256626943808878	2		546	2150	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346775	89346775	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1482843507	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1806	241	342	0	ENST00000301030.4:c.6175C>T	p.Pro2059Ser	p.P2059S	ENST00000301030	NM_001256183.1	2059	Ccc/Tcc	9/13	1	2	FACETS	0.918	0.853	0.985	0.918	0.853	0.985	CLONAL	1	TRUE	1	0.256626943808878	2		342	2047	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528471	157528471	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2277	285	410	0	ENST00000346085.5:c.6196C>T	p.Pro2066Ser	p.P2066S	ENST00000346085	NM_020732.3	2066	Ccc/Tcc	20/20	1	2	FACETS	0.867	0.811	0.926	0.867	0.811	0.926	CLONAL	1	TRUE	1	0.256626943808878	2		410	2562	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853910	59853910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1527	189	251	1	ENST00000259008.2:c.1949C>T	p.Thr650Ile	p.T650I	ENST00000259008	NM_032043.2	650	aCc/aTc	14/20	1	2	FACETS	0.858	0.79	0.93	0.858	0.79	0.93	CLONAL	1	TRUE	1	0.256626943808878	2		252	1716	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783650	50783650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1908	218	311	0	ENST00000398568.2:c.41C>T	p.Pro14Leu	p.P14L	ENST00000398568	NM_001042412.1	14	cCc/cTc	3/18	1	2	FACETS	0.799	0.74	0.861	0.799	0.74	0.861	SUBCLONAL	1	TRUE	1	0.256626943808878	2		311	2126	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752662	128752662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1266	306	170	0	ENST00000377970.2:c.823G>A	p.Glu275Lys	p.E275K	ENST00000377970	NM_002467.4	275	Gaa/Aaa	3/3	0.18347088732002	3	FACETS	0.856	0.804	0.909	0.856	0.804	0.909	CLONAL	2	TRUE	1	0.256626943808878	3		170	1572	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729505	41729505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2380	271	438	0	ENST00000242208.4:c.1024C>T	p.Pro342Ser	p.P342S	ENST00000242208	NM_002192.2	342	Ccc/Tcc	3/3	0.18347088732002	3	FACETS	0.899	0.839	0.962	0.449	0.419	0.481	CLONAL	1	TRUE	1	0.256626943808878	3		438	2651	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937118	36937118	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2405	285	483	0	ENST00000361632.4:c.1201T>C	p.Ser401Pro	p.S401P	ENST00000361632		401	Tca/Cca	9/16	1	2	FACETS	0.826	0.772	0.882	0.826	0.772	0.882	CLONAL	1	TRUE	1	0.256626943808878	2		483	2690	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938246	36938247	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2575	304	625	0	ENST00000361632.4:c.714_715delinsTT	p.Pro239Ser	p.P239S	ENST00000361632		238	agCCct/agTTct	6/16	1	2	FACETS	0.823	0.771	0.877	0.823	0.771	0.877	CLONAL	1	TRUE	1	0.256626943808878	2		625	2879	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115279452	115279452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1884	218	358	1	ENST00000438362.2:c.565C>T	p.Pro189Ser	p.P189S	ENST00000438362	NM_001242891.1	189	Cct/Tct	6/20	1	2	FACETS	0.808	0.748	0.871	0.808	0.748	0.871	CLONAL	1	TRUE	1	0.256626943808878	2		359	2102	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984386	201984386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1300332665	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2435	331	468	1	ENST00000359651.3:c.1051G>A	p.Val351Ile	p.V351I	ENST00000359651		351	Gtc/Atc	8/8	1	2	FACETS	0.933	0.876	0.991	0.933	0.876	0.991	CLONAL	1	TRUE	1	0.256626943808878	2		469	2766	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376055	118376055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1849	271	319	1	ENST00000534358.1:c.9448C>T	p.Pro3150Ser	p.P3150S	ENST00000534358	NM_005933.3	3150	Cct/Tct	27/36	0.256626943808878	1	FACETS	0.868	0.811	0.928	0.868	0.811	0.928	CLONAL	1	TRUE	0	0.256626943808878	1		320	2120	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944821	31944822	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2582	271	579	0	ENST00000340398.3:c.279_280delinsAA	p.Glu94Lys	p.E94K	ENST00000340398	NM_001013699.2	93	caGGag/caAAag	1/1	0.216081538690872	1	FACETS	0.645	0.602	0.691	0.645	0.602	0.691	SUBCLONAL	1	TRUE	0	0.256626943808878	1		579	2853	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444250	49444250	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783711	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2905	347	665	0	ENST00000301067.7:c.3121C>T	p.Gln1041Ter	p.Q1041*	ENST00000301067	NM_003482.3	1041	Cag/Tag	11/54	1	2	FACETS	0.832	0.782	0.883	0.832	0.782	0.883	CLONAL	1	TRUE	1	0.256626943808878	2		665	3252	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445878	49445878	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334315280	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2932	345	754	2	ENST00000301067.7:c.1588C>T	p.Pro530Ser	p.P530S	ENST00000301067	NM_003482.3	530	Cct/Tct	10/54	1	2	FACETS	0.82	0.772	0.871	0.82	0.772	0.871	CLONAL	1	TRUE	1	0.256626943808878	2		756	3277	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495318	56495318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2555	270	512	0	ENST00000267101.3:c.3508C>T	p.Pro1170Ser	p.P1170S	ENST00000267101	NM_001982.3	1170	Ccc/Tcc	28/28	1	2	FACETS	0.745	0.695	0.797	0.745	0.695	0.797	SUBCLONAL	1	TRUE	1	0.256626943808878	2		512	2825	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942700	48942700	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1537	121	163	0	ENST00000267163.4:c.1087G>T	p.Asp363Tyr	p.D363Y	ENST00000267163	NM_000321.2	363	Gat/Tat	11/27	0.18347088732002	3	FACETS	0.642	0.577	0.71	0.321	0.288	0.355	SUBCLONAL	1	TRUE	1	0.256626943808878	3		163	1658	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528102	103528103	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2094	203	223	0	ENST00000355739.4:c.3410_3411delinsTT	p.Pro1137Leu	p.P1137L	ENST00000355739	NM_000123.3	1137	cCC/cTT	15/15	0.18347088732002	3	FACETS	0.777	0.717	0.84	0.389	0.358	0.42	SUBCLONAL	1	TRUE	1	0.256626943808878	3		223	2297	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295161	91295161	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1286	116	188	0	ENST00000355112.3:c.944C>T	p.Ser315Phe	p.S315F	ENST00000355112	NM_000057.2	315	tCt/tTt	4/22	1	2	FACETS	0.645	0.579	0.715	0.645	0.579	0.715	SUBCLONAL	1	TRUE	1	0.256626943808878	2		188	1402	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346858	91346858	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458000028	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1472	158	306	0	ENST00000355112.3:c.3466G>A	p.Asp1156Asn	p.D1156N	ENST00000355112	NM_000057.2	1156	Gat/Aat	18/22	1	2	FACETS	0.755	0.689	0.825	0.755	0.689	0.825	SUBCLONAL	1	TRUE	1	0.256626943808878	2		306	1630	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781318	3781318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766953370	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2648	346	656	0	ENST00000262367.5:c.5047C>T	p.Arg1683Cys	p.R1683C	ENST00000262367	NM_004380.2	1683	Cgc/Tgc	30/31	1	2	FACETS	0.901	0.847	0.956	0.901	0.847	0.956	CLONAL	1	TRUE	1	0.256626943808878	2		656	2994	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857262	9857262	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2389	270	404	0	ENST00000330684.3:c.4139G>C	p.Gly1380Ala	p.G1380A	ENST00000330684	NM_001134407.1	1380	gGg/gCg	13/13	1	2	FACETS	0.791	0.738	0.847	0.791	0.738	0.847	SUBCLONAL	1	TRUE	1	0.256626943808878	2		404	2659	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842665	68842665	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2620	329	509	0	ENST00000261769.5:c.601C>T	p.Pro201Ser	p.P201S	ENST00000261769	NM_004360.3	201	Cct/Tct	5/16	1	2	FACETS	0.869	0.817	0.924	0.869	0.817	0.924	CLONAL	1	TRUE	1	0.256626943808878	2		509	2949	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822630	72822630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2215	286	490	0	ENST00000268489.5:c.9545C>T	p.Thr3182Ile	p.T3182I	ENST00000268489	NM_006885.3	3182	aCc/aTc	10/10	1	2	FACETS	0.891	0.833	0.951	0.891	0.833	0.951	CLONAL	1	TRUE	1	0.256626943808878	2		490	2501	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984526	72984526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2546	304	597	0	ENST00000268489.5:c.3058G>A	p.Glu1020Lys	p.E1020K	ENST00000268489	NM_006885.3	1020	Gag/Aag	3/10	1	2	FACETS	0.831	0.779	0.886	0.831	0.779	0.886	CLONAL	1	TRUE	1	0.256626943808878	2		597	2850	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819620	81819621	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2204	235	375	2	ENST00000359376.3:c.26_27delinsTT	p.Ser9Phe	p.S9F	ENST00000359376	NM_002661.3	9	tCC/tTT	2/33	1	2	FACETS	0.751	0.697	0.807	0.751	0.697	0.807	SUBCLONAL	1	TRUE	1	0.256626943808878	2		377	2439	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347869	89347869	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2057	249	456	0	ENST00000301030.4:c.5081G>A	p.Arg1694Lys	p.R1694K	ENST00000301030	NM_001256183.1	1694	aGg/aAg	9/13	1	2	FACETS	0.842	0.783	0.903	0.842	0.783	0.903	CLONAL	1	TRUE	1	0.256626943808878	2		456	2306	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935711	15935712	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2098	239	325	1	ENST00000268712.3:c.7221_7222delinsAA	p.Val2408Met	p.V2408M	ENST00000268712	NM_006311.3	2407	gcGGtg/gcAAtg	46/46	1	2	FACETS	0.797	0.74	0.856	0.797	0.74	0.856	SUBCLONAL	1	TRUE	1	0.256626943808878	2		326	2337	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983787	15983787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2362	267	328	0	ENST00000268712.3:c.3335C>T	p.Pro1112Leu	p.P1112L	ENST00000268712	NM_006311.3	1112	cCc/cTc	25/46	1	2	FACETS	0.791	0.738	0.847	0.791	0.738	0.847	SUBCLONAL	1	TRUE	1	0.256626943808878	2		328	2629	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864686	37864686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2497	320	517	0	ENST00000269571.5:c.338C>T	p.Ala113Val	p.A113V	ENST00000269571		113	gCc/gTc	3/27	1	2	FACETS	0.885	0.831	0.942	0.885	0.831	0.942	CLONAL	1	TRUE	1	0.256626943808878	2		517	2817	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18943158	18943158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775288936	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	78	115	0	ENST00000262803.5:c.140C>T	p.Pro47Leu	p.P47L	ENST00000262803	NM_002911.3	47	cCc/cTc	1/24	0.256626943808878	1	FACETS	0.923	0.812	1	0.923	0.812	1	CLONAL	1	TRUE	0	0.256626943808878	1		115	574	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211501	36211501	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1372163835	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2186	295	421	0	ENST00000222270.7:c.1252C>T	p.Pro418Ser	p.P418S	ENST00000222270	NM_014727.1	418	Cca/Tca	3/37	1	2	FACETS	0.927	0.868	0.988	0.927	0.868	0.988	CLONAL	1	TRUE	1	0.256626943808878	2		421	2481	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212352	36212353	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2571	296	589	1	ENST00000222270.7:c.2103_2104delinsTT	p.Leu702Phe	p.L702F	ENST00000222270	NM_014727.1	701	caCCtc/caTTtc	3/37	1	2	FACETS	0.805	0.753	0.858	0.805	0.753	0.858	CLONAL	1	TRUE	1	0.256626943808878	2		590	2867	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794581	42794581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs541390632	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2468	304	648	0	ENST00000575354.2:c.1661C>T	p.Ser554Leu	p.S554L	ENST00000575354	NM_015125.3	554	tCa/tTa	10/20	1	2	FACETS	0.855	0.801	0.911	0.855	0.801	0.911	CLONAL	1	TRUE	1	0.256626943808878	2		648	2772	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795067	42795067	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1039062682	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2648	324	698	0	ENST00000575354.2:c.2147G>A	p.Arg716Gln	p.R716Q	ENST00000575354	NM_015125.3	716	cGg/cAg	10/20	1	2	FACETS	0.85	0.798	0.904	0.85	0.798	0.904	CLONAL	1	TRUE	1	0.256626943808878	2		698	2972	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966708	25966708	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2789	268	452	0	ENST00000435504.4:c.2498C>T	p.Pro833Leu	p.P833L	ENST00000435504		833	cCt/cTt	13/13	1	2	FACETS	0.683	0.637	0.732	0.683	0.637	0.732	SUBCLONAL	1	TRUE	1	0.256626943808878	2		452	3057	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462654	29462654	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3143	343	695	0	ENST00000389048.3:c.2247C>G	p.Asn749Lys	p.N749K	ENST00000389048	NM_004304.4	749	aaC/aaG	13/29	1	2	FACETS	0.767	0.721	0.814	0.767	0.721	0.814	SUBCLONAL	1	TRUE	1	0.256626943808878	2		695	3486	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213203	39213203	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3357	345	677	0	ENST00000402219.2:c.3764C>T	p.Pro1255Leu	p.P1255L	ENST00000402219	NM_005633.3	1255	cCc/cTc	23/23	1	2	FACETS	0.726	0.683	0.771	0.726	0.683	0.771	SUBCLONAL	1	TRUE	1	0.256626943808878	2		677	3702	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46588087	46588088	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2857	268	505	1	ENST00000263734.3:c.637_638delinsAA	p.Gly213Asn	p.G213N	ENST00000263734	NM_001430.4	213	GGc/AAc	6/16	1	2	FACETS	0.668	0.623	0.716	0.668	0.623	0.716	SUBCLONAL	1	TRUE	1	0.256626943808878	2		506	3125	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523256	9523256	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2279	288	447	1	ENST00000353224.5:c.1981C>A	p.Pro661Thr	p.P661T	ENST00000353224	NM_177990.2	661	Cca/Aca	9/10	1	2	FACETS	0.874	0.818	0.933	0.874	0.818	0.933	CLONAL	1	TRUE	1	0.256626943808878	2		448	2567	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644718	134644718	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2561	297	302	0	ENST00000398015.3:c.119C>T	p.Ser40Phe	p.S40F	ENST00000398015	NM_004441.4	40	tCc/tTc	2/16	0.18347088732002	3	FACETS	0.914	0.855	0.975	0.457	0.427	0.488	CLONAL	1	TRUE	1	0.256626943808878	3		302	2858	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259762	142259762	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1805	180	258	0	ENST00000350721.4:c.3565C>G	p.Pro1189Ala	p.P1189A	ENST00000350721	NM_001184.3	1189	Cct/Gct	18/47	0.18347088732002	3	FACETS	0.797	0.732	0.866	0.399	0.366	0.433	SUBCLONAL	1	TRUE	1	0.256626943808878	3		258	1985	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170002366	170002367	+	missense_variant	Missense_Mutation	DNP	TG	TG	CT	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	113	147	0	ENST00000295797.4:c.1185_1186delinsCT	p.Asp396Tyr	p.D396Y	ENST00000295797	NM_002740.5	395	acTGac/acCTac	12/18	0.18347088732002	3	FACETS	0.854	0.767	0.948	0.427	0.383	0.474	CLONAL	1	TRUE	1	0.256626943808878	3		147	1163	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170011263	170011263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2619	244	376	0	ENST00000295797.4:c.1384C>T	p.Pro462Ser	p.P462S	ENST00000295797	NM_002740.5	462	Cct/Tct	14/18	0.18347088732002	3	FACETS	0.749	0.696	0.805	0.375	0.348	0.403	SUBCLONAL	1	TRUE	1	0.256626943808878	3		376	2863	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502871	186502872	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2252	165	322	0	ENST00000323963.5:c.329_330delinsTT	p.Thr110Ile	p.T110I	ENST00000323963		110	aCC/aTT	4/11	0.18347088732002	3	FACETS	0.6	0.548	0.655	0.3	0.274	0.328	SUBCLONAL	1	TRUE	1	0.256626943808878	3		322	2417	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1976617	1976618	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2483	305	494	0	ENST00000382891.5:c.3400_3401delinsAA	p.Gly1134Lys	p.G1134K	ENST00000382891	NM_133335.3	1134	GGa/AAa	19/22	1	2	FACETS	0.853	0.799	0.908	0.853	0.799	0.908	CLONAL	1	TRUE	1	0.256626943808878	2		494	2788	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542059	187542059	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1237148796	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1852	209	282	0	ENST00000441802.2:c.5681A>G	p.Lys1894Arg	p.K1894R	ENST00000441802	NM_005245.3	1894	aAa/aGa	10/27	1	2	FACETS	0.79	0.73	0.853	0.79	0.73	0.853	SUBCLONAL	1	TRUE	1	0.256626943808878	2		282	2061	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554979	187554979	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1274	164	189	0	ENST00000441802.2:c.4184-2A>G		p.X1395_splice	ENST00000441802	NM_005245.3	1395			1	2	FACETS	0.889	0.813	0.968	0.889	0.813	0.968	CLONAL	1	TRUE	1	0.256626943808878	2		189	1438	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278792	1278793	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2492	293	520	2	ENST00000310581.5:c.2249_2250delinsTT	p.Ala750Val	p.A750V	ENST00000310581	NM_198253.2	750	gCC/gTT	6/16	1	2	FACETS	0.82	0.767	0.875	0.82	0.767	0.875	CLONAL	1	TRUE	1	0.256626943808878	2		522	2785	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294150	1294150	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2391	323	579	0	ENST00000310581.5:c.851C>A	p.Ser284Tyr	p.S284Y	ENST00000310581	NM_198253.2	284	tCt/tAt	2/16	1	2	FACETS	0.928	0.871	0.986	0.928	0.871	0.986	CLONAL	1	TRUE	1	0.256626943808878	2		579	2714	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520672	176520672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2361	318	638	0	ENST00000292408.4:c.1415C>T	p.Pro472Leu	p.P472L	ENST00000292408	NM_213647.1	472	cCc/cTc	11/18	1	2	FACETS	0.925	0.868	0.984	0.925	0.868	0.984	CLONAL	1	TRUE	1	0.256626943808878	2		638	2679	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706927	117706927	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2245	285	354	1	ENST00000368508.3:c.2223C>A	p.His741Gln	p.H741Q	ENST00000368508	NM_002944.2	741	caC/caA	15/43	0.149797484462492	0	FACETS	0.653	0.61	0.697			1	INDETERMINATE	1	TRUE	0	0.256626943808878	0		355	2530	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519482	137519482	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs770411050	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1669	214	230	0	ENST00000367739.4:c.1156C>T	p.Gln386Ter	p.Q386*	ENST00000367739	NM_000416.2	386	Cag/Tag	7/7	1	2	FACETS	0.886	0.82	0.955	0.886	0.82	0.955	CLONAL	1	TRUE	1	0.256626943808878	2		230	1883	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983890	2983890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2667	301	571	0	ENST00000396946.4:c.640G>A	p.Glu214Lys	p.E214K	ENST00000396946	NM_032415.4	214	Gag/Aag	5/25	0.216081538690872	1	FACETS	0.689	0.645	0.735	0.689	0.645	0.735	SUBCLONAL	1	TRUE	0	0.256626943808878	1		571	2968	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846095	128846095	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2705	344	572	0	ENST00000249373.3:c.1025C>T	p.Ser342Phe	p.S342F	ENST00000249373	NM_005631.4	342	tCc/tTc	5/12	1	2	FACETS	0.879	0.827	0.933	0.879	0.827	0.933	CLONAL	1	TRUE	1	0.256626943808878	2		572	3049	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523549	148523550	+	missense_variant	Missense_Mutation	DNP	AA	AA	TT	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	118	114	0	ENST00000320356.2:c.903_904inv	p.Asn301_Tyr302delinsLysAsn	p.N301_Y302delinsKN	ENST00000320356	NM_004456.4	301	aaTTat/aaAAat	8/20	1	2	FACETS	0.799	0.719	0.884	0.799	0.719	0.884	SUBCLONAL	1	TRUE	1	0.256626943808878	2		114	1151	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873656	151873656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2216	254	355	0	ENST00000262189.6:c.8882C>T	p.Pro2961Leu	p.P2961L	ENST00000262189	NM_170606.2	2961	cCt/cTt	38/59	1	2	FACETS	0.801	0.746	0.859	0.801	0.746	0.859	CLONAL	1	TRUE	1	0.256626943808878	2		355	2470	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878905	117878905	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045400-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2169	195	284	0	ENST00000297338.2:c.64C>T	p.His22Tyr	p.H22Y	ENST00000297338	NM_006265.2	22	Cat/Tat	2/14	0.18347088732002	3	FACETS	0.725	0.668	0.786	0.363	0.334	0.393	SUBCLONAL	1	TRUE	1	0.256626943808878	3		284	2364	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119966	70120018	+	frameshift_variant	Frame_Shift_Del	DEL	GCACCGCGGCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAG	GCACCGCGGCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAG	-	novel	NA	P-0045402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	13	323	0	ENST00000245479.2:c.970_1022del	p.Thr324AlafsTer236	p.T324Afs*236	ENST00000245479	NM_000346.3	323	aGCACCGCGGCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAG/a	3/3	1	2	FACETS	0.258	0.184	0.349	0.258	0.184	0.349	SUBCLONAL	1	TRUE	1	0.433758858466128	2		323	232	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0045402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	164	615	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.342918113127382	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.433758858466128	3		615	412	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592163	67592164	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTAG	novel	NA	P-0045402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	22	151	0	ENST00000274335.5:c.1984_1985+3dup		p.S660fs	ENST00000274335		660	tct/tcTGTAGt	14/15	1	2	FACETS	0.659	0.515	0.822	0.659	0.515	0.822	SUBCLONAL	1	TRUE	1	0.433758858466128	2		151	154	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962554	100962554	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	67	489	0	ENST00000325455.5:c.1843C>A	p.Arg615Ser	p.R615S	ENST00000325455	NM_001202474.3	615	Cgc/Agc	3/8	1	2	FACETS	0.765	0.667	0.869	0.765	0.667	0.869	SUBCLONAL	1	TRUE	1	0.433758858466128	2		489	404	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912331	32912331	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	36	338	0	ENST00000380152.3:c.3839A>C	p.Asp1280Ala	p.D1280A	ENST00000380152		1280	gAt/gCt	11/27	1	2	FACETS	1	0.833	1	1	0.833	1	CLONAL	1	TRUE	1	0.433758858466128	2		338	166	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644707	67644748	+	splice_acceptor_variant,coding_sequence_variant,5_prime_UTR_variant,intron_variant	Splice_Site	DEL	TGTGTTCTCCCTTAATAAAGGCAGGGGAAATGGAAGGTGATG	TGTGTTCTCCCTTAATAAAGGCAGGGGAAATGGAAGGTGATG	-	novel	NA	P-0045402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	36	307	0	ENST00000264010.4:c.-9-20_13del		p.X3_splice	ENST00000264010	NM_006565.3	3		3/12	1	2	FACETS	0.802	0.665	0.952	0.802	0.665	0.952	CLONAL	1	TRUE	1	0.433758858466128	2		307	207	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692956	89692956	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	CG	novel	NA	P-0045402-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	79	478	0	ENST00000371953.3:c.440delinsCG	p.Lys147ThrfsTer33	p.K147Tfs*33	ENST00000371953	NM_000314.4	147	aAg/aCGg	5/9	0.342918113127382	3	FACETS	0.846	0.754	0.942	0.846	0.754	0.942	CLONAL	2	TRUE	1	0.433758858466128	3		478	262	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	107	425	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.665215601807732	2		425	313	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031815	10031815	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs397518465	NA	P-0045404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	149	702	1	ENST00000330684.3:c.1007+1G>A		p.X336_splice	ENST00000330684	NM_001134407.1	336			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.665215601807732	NA		703	501	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717747	89717747	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	72	417	0	ENST00000371953.3:c.773del	p.Phe258SerfsTer8	p.F258Sfs*8	ENST00000371953	NM_000314.4	258	Ttc/tc	7/9	0.665215601807732	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.665215601807732	1		417	138	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509541	29509541	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1567826623	NA	P-0045404-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	23	445	0	ENST00000356175.3:c.746T>G	p.Leu249Arg	p.L249R	ENST00000356175	NM_000267.3	249	cTa/cGa	8/57	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.665215601807732	NA		445	88	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	115	425	0				ENST00000310581	NM_198253.2	-/1132			0.455120424646712	3	FACETS	0.915	0.836	0.995	0.915	0.836	0.995	CLONAL	2	TRUE	1	0.527985980294738	3		425	301	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577548	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0045405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	68	650	1	ENST00000269305.4:c.733_734delinsTT	p.Gly245Phe	p.G245F	ENST00000269305	NM_001126112.2	245	GGc/TTc	7/11	1	2	FACETS	0.671	0.586	0.761	0.671	0.586	0.761	SUBCLONAL	1	TRUE	1	0.527985980294738	2		651	384	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278106	142278106	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	56	431	0	ENST00000350721.4:c.1719G>C	p.Leu573Phe	p.L573F	ENST00000350721	NM_001184.3	573	ttG/ttC	7/47	0.38749792182968	3	FACETS	0.868	0.748	0.996	0.434	0.374	0.498	CLONAL	1	TRUE	1	0.527985980294738	3		431	309	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206593	108206593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	165	290	0	ENST00000278616.4:c.8173G>A	p.Asp2725Asn	p.D2725N	ENST00000278616	NM_000051.3	2725	Gat/Aat	56/63	0.527985980294738	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	3	TRUE	0	0.527985980294738	3		290	262	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435298	18435298	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	51	331	0	ENST00000266497.5:c.283G>C	p.Glu95Gln	p.E95Q	ENST00000266497		95	Gaa/Caa	1/31	0.448327190196369	4	FACETS	0.848	0.724	0.983	0.424	0.362	0.492	CLONAL	1	TRUE	2	0.527985980294738	4		331	348	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435382	18435382	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	47	316	0	ENST00000266497.5:c.367G>C	p.Glu123Gln	p.E123Q	ENST00000266497		123	Gaa/Caa	1/31	0.448327190196369	4	FACETS	0.824	0.699	0.962	0.412	0.349	0.481	CLONAL	1	TRUE	2	0.527985980294738	4		316	330	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265452	198265452	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	65	456	0	ENST00000335508.6:c.2705A>C	p.Glu902Ala	p.E902A	ENST00000335508	NM_012433.2	902	gAa/gCa	18/25	1	2	FACETS	0.879	0.77	0.996	0.879	0.77	0.996	CLONAL	1	TRUE	1	0.527985980294738	2		456	280	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569222	67569222	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	113	398	1	ENST00000274335.5:c.339G>C	p.Leu113Phe	p.L113F	ENST00000274335		113	ttG/ttC	2/15	0.527985980294738	2	FACETS	0.935	0.861	1	0.935	0.861	1	CLONAL	2	TRUE	0	0.527985980294738	2		399	229	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528414	157528414	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045405-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	223	702	0	ENST00000346085.5:c.6140del	p.Pro2047GlnfsTer52	p.P2047Qfs*52	ENST00000346085	NM_020732.3	2047	Cca/ca	20/20	0.527985980294738	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.527985980294738	2		702	379	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	128	425	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.991	0.911	1	0.991	0.911	1	CLONAL	1	TRUE	1	0.810147384905482	2		425	319	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748173	72748174	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CCATC	novel	NA	P-0045406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	125	274	0	ENST00000357731.5:c.-1_4dup	p.Asp2GlyfsTer4	p.D2Gfs*4	ENST00000357731	NM_173808.2	2	gac/gGATGGac	1/7	1	2	FACETS	0.995	0.915	1	0.995	0.915	1	CLONAL	1	TRUE	1	0.810147384905482	2		274	310	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492635	56492635	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759764423	NA	P-0045406-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	193	380	0	ENST00000267101.3:c.2785C>T	p.Arg929Trp	p.R929W	ENST00000267101	NM_001982.3	929	Cgg/Tgg	23/28	1	2	FACETS	0.968	0.904	1	0.968	0.904	1	CLONAL	1	TRUE	1	0.810147384905482	2		380	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882019	NA	P-0045408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	334	661	2	ENST00000269305.4:c.455dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	ccg/ccCg	5/11	0.563226694055406	2	FACETS	0.94	0.898	0.982	0.94	0.898	0.982	CLONAL	2	TRUE	0	0.563226694055406	2		663	631	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905512	50905512	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1200514497	NA	P-0045408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	195	648	1	ENST00000440232.2:c.640G>A	p.Val214Met	p.V214M	ENST00000440232	NM_002691.3	214	Gtg/Atg	6/27	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.563226694055406	2		649	576	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061317	38061317	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	318	566	1	ENST00000250448.2:c.672C>A	p.Phe224Leu	p.F224L	ENST00000250448	NM_004496.3	224	ttC/ttA	2/2	0.563532159479195	5	FACETS	1	0.987	1	0.756	0.716	0.798	CLONAL	2	TRUE	2	0.563226694055406	5		567	918	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444375	50444375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776572250	NA	P-0045408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	73	293	0	ENST00000331340.3:c.305C>T	p.Ser102Leu	p.S102L	ENST00000331340	NM_006060.4	102	tCg/tTg	4/8	0.563532159479195	4	FACETS	0.762	0.667	0.863	0.254	0.222	0.288	SUBCLONAL	1	TRUE	1	0.563226694055406	4		293	532	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406003	70406003	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1006076006	NA	P-0045408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	84	469	2	ENST00000373644.4:c.3517C>T	p.Arg1173Trp	p.R1173W	ENST00000373644	NM_030625.2	1173	Cgg/Tgg	4/12	0.563226694055406	7	FACETS	0.76	0.67	0.857			1	SUBCLONAL	1	TRUE	NA	0.563226694055406	7		471	945	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5064902	5064902	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0045408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	44	224	0	ENST00000381652.3:c.1076T>G	p.Leu359Ter	p.L359*	ENST00000381652	NM_004972.3	359	tTa/tGa	9/25	0.280734850229502	1	FACETS	0.607	0.516	0.704	0.607	0.516	0.704	INDETERMINATE	1	TRUE	0	0.563226694055406	1		224	185	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0045409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	119	706	4	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.554154355217249	1	FACETS	0.748	0.684	0.815	0.748	0.684	0.815	SUBCLONAL	1	TRUE	0	0.638702548684701	1		710	339	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0045409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	66	315	2	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	0.563083388871251	2	FACETS	0.868	0.783	0.952	0.868	0.783	0.952	CLONAL	2	TRUE	0	0.638702548684701	2		317	119	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0045409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	93	638	0	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	0.554154355217249	1	FACETS	0.588	0.528	0.651	0.588	0.528	0.651	SUBCLONAL	1	TRUE	0	0.638702548684701	1		638	337	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141569514	141569514	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045409-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	77	452	1	ENST00000220592.5:c.770A>C	p.Lys257Thr	p.K257T	ENST00000220592	NM_012154.3	257	aAg/aCg	6/19	0.180134627620588	6	FACETS	1	0.958	1			1	INDETERMINATE	1	TRUE	NA	0.638702548684701	6		453	459	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	73	425	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.664052789518056	2		425	208	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220274	55220274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19094	456	618	0	ENST00000275493.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000275493	NM_005228.3	222	Cgc/Tgc	6/28	0.664052789518056	51	FACETS	1	0.991	1	0.024	0.022	0.026	CLONAL	1	TRUE	0	0.664052789518056	51		618	19550	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0045410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	98	330	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.664052789518056	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.664052789518056	1		330	174	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812292	212812292	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778048381	NA	P-0045410-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	48	216	0	ENST00000342788.4:c.284G>A	p.Arg95His	p.R95H	ENST00000342788	NM_005235.2	95	cGt/cAt	3/28	1	2	FACETS	0.761	0.652	0.877	0.761	0.652	0.877	SUBCLONAL	1	TRUE	1	0.664052789518056	2		216	190	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0045412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	289	468	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.637616978147639	1	FACETS	0.922	0.873	0.97	0.922	0.873	0.97	CLONAL	1	TRUE	0	0.637616978147639	1		468	670	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924771	49924771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs541003810	NA	P-0045413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	269	681	1	ENST00000296474.3:c.4172G>A	p.Arg1391Gln	p.R1391Q	ENST00000296474	NM_002447.2	1391	cGg/cAg	20/20	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.313549816809483	2		682	1348	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270100	198270100	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	101	284	0	ENST00000335508.6:c.1336A>T	p.Met446Leu	p.M446L	ENST00000335508	NM_012433.2	446	Atg/Ttg	10/25	1	2	FACETS	0.99	0.886	1	0.99	0.886	1	CLONAL	1	TRUE	1	0.313549816809483	2		284	651	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0045414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	393	608	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.628981818320916	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.628981818320916	2		608	579	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027133	49027133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853292	NA	P-0045414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	62	211	0	ENST00000267163.4:c.1700C>T	p.Ser567Leu	p.S567L	ENST00000267163	NM_000321.2	567	tCa/tTa	18/27	0.627147165757178	5	FACETS	0.754	0.652	0.865	0.189	0.163	0.217	SUBCLONAL	1	TRUE	1	0.628981818320916	5		211	508	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528611	8528611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201846121	NA	P-0045414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	194	317	0	ENST00000356435.5:c.521G>A	p.Arg174His	p.R174H	ENST00000356435		174	cGt/cAt	4/35	0.523887513146371	4	FACETS	0.892	0.832	0.955	0.892	0.832	0.955	CLONAL	2	TRUE	2	0.628981818320916	4		317	563	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448391	49448391	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	243	608	1	ENST00000301067.7:c.320A>G	p.Glu107Gly	p.E107G	ENST00000301067	NM_003482.3	107	gAg/gGg	3/54	0.628981818320916	3	FACETS	1	0.983	1	0.571	0.534	0.609	CLONAL	1	TRUE	1	0.628981818320916	3		609	889	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136277	202136277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	263	392	0	ENST00000358485.4:c.521C>T	p.Ser174Leu	p.S174L	ENST00000358485	NM_001080125.1	174	tCa/tTa	3/9	0.628981818320916	3	FACETS	0.99	0.938	1	0.99	0.938	1	CLONAL	2	TRUE	1	0.628981818320916	3		392	555	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259152	36259156	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCA	GGGCA	-	novel	NA	P-0045414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	144	618	0	ENST00000300305.3:c.335_339del	p.Leu112HisfsTer24	p.L112Hfs*24	ENST00000300305		112	cTGCCC/c	3/8	0.620401537493931	5	FACETS	0.863	0.786	0.944	0.288	0.262	0.315	CLONAL	1	TRUE	2	0.628981818320916	5		618	1031	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565544	41565544	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	456	315	0	ENST00000263253.7:c.4211del	p.Phe1404SerfsTer6	p.F1404Sfs*6	ENST00000263253	NM_001429.3	1404	Ttc/tc	26/31	0.628981818320916	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	4	TRUE	0	0.628981818320916	4		315	562	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665299	138665299	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1226344391	NA	P-0045414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	616	713	1	ENST00000330315.3:c.266C>G	p.Pro89Arg	p.P89R	ENST00000330315	NM_023067.3	89	cCg/cGg	1/1	0.599094252384318	5	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	2	0.628981818320916	5		714	1251	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918557	44918557	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0045414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	266	233	0	ENST00000377967.4:c.1040T>A	p.Leu347Ter	p.L347*	ENST00000377967	NM_021140.2	347	tTg/tAg	12/29	0.611011742020935	2	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.628981818320916	2		233	351	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	527	737	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.959	0.929	0.99	1	0.998	1	CLONAL	2	TRUE	1	0.652366473093833	2		742	842	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	426	568	1	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.967	0.933	1	1	0.997	1	CLONAL	2	TRUE	1	0.652366473093833	2		569	675	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	294	743	6	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	0.346671839761777	3	FACETS	1	0.972	1	0.526	0.495	0.558	INDETERMINATE	1	TRUE	1	0.652366473093833	3		749	1136	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830902	72830903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	157	521	0	ENST00000268489.5:c.5677_5678dup	p.Asp1894GlyfsTer21	p.D1894Gfs*21	ENST00000268489	NM_006885.3	1893	agg/agAGg	9/10	1	2	FACETS	0.737	0.677	0.799	0.737	0.677	0.799	SUBCLONAL	1	TRUE	1	0.652366473093833	2		521	653	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	157	350	1	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.652366473093833	2		351	477	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	221	665	3	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.923	0.862	0.985	0.923	0.862	0.985	CLONAL	1	TRUE	1	0.652366473093833	2		668	734	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444659	78444659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs908264837	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	176	427	2	ENST00000370768.2:c.30del	p.Ser11LeufsTer43	p.S11Lfs*43	ENST00000370768	NM_003902.3	10	ccC/cc	1/20	1	2	FACETS	0.952	0.882	1	0.952	0.882	1	CLONAL	1	TRUE	1	0.652366473093833	2		429	567	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	76	309	3	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.735	0.65	0.824	0.735	0.65	0.824	SUBCLONAL	1	TRUE	1	0.652366473093833	2		312	317	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	85	182	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.941	0.842	1	0.941	0.842	1	CLONAL	1	TRUE	1	0.652366473093833	2		182	277	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209616	98209617	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761353734	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	118	683	3	ENST00000331920.6:c.3921dup	p.Arg1308GlnfsTer17	p.R1308Qfs*17	ENST00000331920	NM_000264.3	1307	-/C	23/24	1	2	FACETS	0.538	0.486	0.592	0.538	0.486	0.592	SUBCLONAL	1	TRUE	1	0.652366473093833	2		686	673	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266970	18266970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757629395	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	80	124	0	ENST00000222254.8:c.281G>A	p.Arg94His	p.R94H	ENST00000222254	NM_005027.3	94	cGc/cAc	2/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.652366473093833	2		124	170	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117753	115117753	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765693432	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	157	284	0	ENST00000257566.3:c.682G>A	p.Ala228Thr	p.A228T	ENST00000257566	NM_016569.3	228	Gct/Act	3/8	0.346671839761777	3	FACETS	1	0.988	1	0.701	0.648	0.756	INDETERMINATE	1	TRUE	1	0.652366473093833	3		284	455	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817489	39817489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763409220	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	188	449	0	ENST00000288319.7:c.74C>T	p.Thr25Met	p.T25M	ENST00000288319	NM_182918.3	25	aCg/aTg	2/10	0.292170199659976	1	FACETS	0.552	0.512	0.594	0.552	0.512	0.594	INDETERMINATE	1	TRUE	0	0.652366473093833	1		449	703	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87322770	87322770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781137734	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	94	241	0	ENST00000277120.3:c.371G>A	p.Arg124Gln	p.R124Q	ENST00000277120		124	cGa/cAa	5/19	1	2	FACETS	0.868	0.78	0.96	0.868	0.78	0.96	CLONAL	1	TRUE	1	0.652366473093833	2		241	332	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274934	38274934	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs774678297	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	159	560	2	ENST00000425967.3:c.1646C>T	p.Ser549Leu	p.S549L	ENST00000425967	NM_001174067.1	549	tCg/tTg	13/19	0.652366473093833	5	FACETS	0.706	0.645	0.77	0.177	0.161	0.193	SUBCLONAL	1	TRUE	1	0.652366473093833	5		562	1366	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551935	150551946	+	inframe_deletion	In_Frame_Del	DEL	GCCGGCCCCCAA	GCCGGCCCCCAA	-	rs779327179	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	166	433	0	ENST00000369026.2:c.61_72del	p.Leu21_Gly24del	p.L21_G24del	ENST00000369026	NM_021960.4	21	TTGGGGGCCGGC/-	1/3	1	2	FACETS	0.939	0.868	1	0.939	0.868	1	CLONAL	1	TRUE	1	0.652366473093833	2		433	542	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173696	108173696	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	70	297	0	ENST00000278616.4:c.5441del	p.Leu1814TrpfsTer14	p.L1814Wfs*14	ENST00000278616	NM_000051.3	1812	gcT/gc	36/63	1	2	FACETS	0.758	0.668	0.854	0.758	0.668	0.854	SUBCLONAL	1	TRUE	1	0.652366473093833	2		297	283	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004255	150004255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1314146200	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	17	198	0	ENST00000253339.5:c.1970G>A	p.Arg657His	p.R657H	ENST00000253339		657	cGt/cAt	3/7	1	2	FACETS	0.191	0.142	0.249	0.191	0.142	0.249	SUBCLONAL	1	TRUE	1	0.652366473093833	2		198	273	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508733	106508733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1207051578	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	213	509	0	ENST00000359195.3:c.727G>A	p.Ala243Thr	p.A243T	ENST00000359195	NM_002649.2	243	Gcc/Acc	2/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.652366473093833	2		509	639	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086016	16086016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057517770	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	209	481	2	ENST00000281043.3:c.1192C>T	p.Arg398Trp	p.R398W	ENST00000281043	NM_005378.4	398	Cgg/Tgg	3/3	1	2	FACETS	0.969	0.904	1	0.969	0.904	1	CLONAL	1	TRUE	1	0.652366473093833	2		483	661	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185544	27185545	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	205	513	0	ENST00000380036.4:c.1250dup	p.Asp418Ter	p.D418*	ENST00000380036	NM_000459.3	415	ctc/ctCc	9/23	1	2	FACETS	0.893	0.831	0.956	0.893	0.831	0.956	CLONAL	1	TRUE	1	0.652366473093833	2		513	704	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647657	3647657	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs774532876	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	258	753	3	ENST00000294008.3:c.1406del	p.Pro469HisfsTer4	p.P469Hfs*4	ENST00000294008	NM_032444.2	469	cCa/ca	7/15	1	2	FACETS	0.819	0.768	0.871	0.819	0.768	0.871	CLONAL	1	TRUE	1	0.652366473093833	2		756	966	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10244964	10244964	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1248265917	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	208	639	0	ENST00000340748.4:c.4745C>T	p.Pro1582Leu	p.P1582L	ENST00000340748		1582	cCg/cTg	39/40	1	2	FACETS	0.862	0.802	0.923	0.862	0.802	0.923	CLONAL	1	TRUE	1	0.652366473093833	2		639	740	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24134057	24134057	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	143	303	0	ENST00000263121.7:c.214del	p.Thr72GlnfsTer13	p.T72Qfs*13	ENST00000263121	NM_003073.3	70	Aaa/aa	2/9	1	2	FACETS	0.921	0.846	0.999	0.921	0.846	0.999	CLONAL	1	TRUE	1	0.652366473093833	2		303	476	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988691	41988691	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	105	339	0	ENST00000219905.7:c.1483C>T	p.Arg495Ter	p.R495*	ENST00000219905	NM_001164273.1	495	Cga/Tga	3/24	1	2	FACETS	0.858	0.776	0.944	0.858	0.776	0.944	CLONAL	1	TRUE	1	0.652366473093833	2		339	375	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015025	27015025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754932895	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	61	320	0	ENST00000335756.4:c.127C>T	p.Arg43Trp	p.R43W	ENST00000335756	NM_001809.3	43	Cgg/Tgg	2/5	1	2	FACETS	0.428	0.37	0.491	0.428	0.37	0.491	SUBCLONAL	1	TRUE	1	0.652366473093833	2		320	437	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199451	16199451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	83	287	0	ENST00000375759.3:c.224G>A	p.Arg75His	p.R75H	ENST00000375759	NM_015001.2	75	cGc/cAc	2/15	1	2	FACETS	0.562	0.498	0.63	0.562	0.498	0.63	SUBCLONAL	1	TRUE	1	0.652366473093833	2		287	453	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918729	50918729	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367680864	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	233	676	0	ENST00000440232.2:c.2599G>A	p.Val867Ile	p.V867I	ENST00000440232	NM_002691.3	867	Gtc/Atc	21/27	1	2	FACETS	0.91	0.851	0.97	0.91	0.851	0.97	CLONAL	1	TRUE	1	0.652366473093833	2		676	785	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191805	123191805	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	108	295	2	ENST00000218089.9:c.1400del	p.Phe467SerfsTer3	p.F467Sfs*3	ENST00000218089	NM_001042749.1	465	gTt/gt	15/35	0.652366473093833	1	FACETS	0.918	0.841	0.996	0.918	0.841	0.996	CLONAL	1	TRUE	0	0.652366473093833	1		297	243	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440135	49440136	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	325	574	0	ENST00000301067.7:c.4490_4491del	p.His1497LeufsTer30	p.H1497Lfs*30	ENST00000301067	NM_003482.3	1497	cAC/c	16/54	0.346671839761777	3	FACETS	1	0.995	1	0.741	0.702	0.78	INDETERMINATE	1	TRUE	1	0.652366473093833	3		574	892	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800903	120800903	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748469666	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	398	586	0	ENST00000257552.2:c.345del	p.Leu116CysfsTer3	p.L116Cfs*3	ENST00000257552	NM_002442.3	115	ggG/gg	6/15	0.346671839761777	3	FACETS	0.812	0.774	0.849	0.812	0.774	0.849	INDETERMINATE	2	TRUE	1	0.652366473093833	3		586	997	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39318077	39318077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	89	373	0	ENST00000373001.3:c.725C>T	p.Thr242Ile	p.T242I	ENST00000373001	NM_022157.3	242	aCc/aTc	4/7	1	2	FACETS	0.737	0.659	0.82	0.737	0.659	0.82	SUBCLONAL	1	TRUE	1	0.652366473093833	2		373	370	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137029	64137029	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	122	483	0	ENST00000334205.4:c.1540G>A	p.Val514Met	p.V514M	ENST00000334205	NM_003942.2	514	Gtg/Atg	13/17	1	2	FACETS	0.567	0.513	0.623	0.567	0.513	0.623	SUBCLONAL	1	TRUE	1	0.652366473093833	2		483	660	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362545	118362545	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	113	370	0	ENST00000534358.1:c.4906C>T	p.Arg1636Ter	p.R1636*	ENST00000534358	NM_005933.3	1636	Cga/Tga	15/36	1	2	FACETS	0.743	0.673	0.817	0.743	0.673	0.817	SUBCLONAL	1	TRUE	1	0.652366473093833	2		370	466	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402259	402259	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	175	519	0	ENST00000399788.2:c.4532A>G	p.Glu1511Gly	p.E1511G	ENST00000399788	NM_001042603.1	1511	gAa/gGa	27/28	0.346671839761777	3	FACETS	0.937	0.865	1	0.469	0.432	0.506	INDETERMINATE	1	TRUE	1	0.652366473093833	3		519	759	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879723	123879723	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	20	32	0	ENST00000330479.4:c.419C>A	p.Thr140Asn	p.T140N	ENST00000330479	NM_020382.3	140	aCt/aAt	4/9	0.346671839761777	3	FACETS	1	0.924	1	0.726	0.578	0.884	INDETERMINATE	1	TRUE	1	0.652366473093833	3		32	56	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039144	49039145	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	111	227	0	ENST00000267163.4:c.2224_2225del	p.Val742PhefsTer8	p.V742Ffs*8	ENST00000267163	NM_000321.2	741	cGT/c	22/27	1	2	FACETS	0.967	0.878	1	0.967	0.878	1	CLONAL	1	TRUE	1	0.652366473093833	2		227	352	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028684	12028684	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	92	284	0	ENST00000353533.5:c.887C>T	p.Thr296Ile	p.T296I	ENST00000353533	NM_003010.3	296	aCa/aTa	8/11	1	2	FACETS	0.792	0.71	0.878	0.792	0.71	0.878	SUBCLONAL	1	TRUE	1	0.652366473093833	2		284	356	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12043175	12043175	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	79	200	0	ENST00000353533.5:c.1063del	p.Arg355GlyfsTer8	p.R355Gfs*8	ENST00000353533	NM_003010.3	354	Aaa/aa	10/11	1	2	FACETS	0.868	0.773	0.968	0.868	0.773	0.968	CLONAL	1	TRUE	1	0.652366473093833	2		200	279	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17120470	17120470	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	121	431	0	ENST00000285071.4:c.1089G>A	p.Met363Ile	p.M363I	ENST00000285071	NM_144997.5	363	atG/atA	10/14	1	2	FACETS	0.535	0.484	0.589	0.535	0.484	0.589	SUBCLONAL	1	TRUE	1	0.652366473093833	2		431	693	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322707	30322707	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	146	347	0	ENST00000322652.5:c.1720C>T	p.Leu574Phe	p.L574F	ENST00000322652	NM_015355.2	574	Ctc/Ttc	14/16	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.652366473093833	2		347	434	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38504654	38504654	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	293	676	0	ENST00000254066.5:c.265T>G	p.Phe89Val	p.F89V	ENST00000254066	NM_000964.3	89	Ttt/Gtt	3/9	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.652366473093833	2		676	868	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526204	63526205	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	179	389	0	ENST00000307078.5:c.2421dup	p.Ala808SerfsTer4	p.A808Sfs*4	ENST00000307078	NM_004655.3	807	-/A	11/11	1	2	FACETS	0.964	0.895	1	0.964	0.895	1	CLONAL	1	TRUE	1	0.652366473093833	2		389	569	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63531775	63531775	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	71	544	0	ENST00000307078.5:c.2206C>G	p.Pro736Ala	p.P736A	ENST00000307078	NM_004655.3	736	Ccc/Gcc	9/11	1	2	FACETS	0.288	0.251	0.328	0.288	0.251	0.328	SUBCLONAL	1	TRUE	1	0.652366473093833	2		544	756	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119257	3119257	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	264	723	0	ENST00000078429.4:c.789G>A	p.Trp263Ter	p.W263*	ENST00000078429	NM_002067.2	263	tgG/tgA	6/7	1	2	FACETS	0.977	0.919	1	0.977	0.919	1	CLONAL	1	TRUE	1	0.652366473093833	2		723	828	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208389	5208389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771526918	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	38	566	0	ENST00000357368.4:c.5501G>A	p.Arg1834Gln	p.R1834Q	ENST00000357368	NM_002850.3	1834	cGg/cAg	36/38	1	2	FACETS	0.19	0.156	0.227	0.19	0.156	0.227	SUBCLONAL	1	TRUE	1	0.652366473093833	2		566	614	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11022899	11022899	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	302	737	0	ENST00000327064.4:c.603del	p.Phe201LeufsTer26	p.F201Lfs*26	ENST00000327064	NM_199141.1	200	Ttt/tt	5/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.652366473093833	2		737	924	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082405	16082406	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	313	844	0	ENST00000281043.3:c.224dup	p.Ser76GlufsTer9	p.S76Efs*9	ENST00000281043	NM_005378.4	73	-/C	2/3	1	2	FACETS	0.974	0.921	1	0.974	0.921	1	CLONAL	1	TRUE	1	0.652366473093833	2		844	985	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051156	128051156	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	232	597	0	ENST00000285398.2:c.167A>G	p.Tyr56Cys	p.Y56C	ENST00000285398	NM_000122.1	56	tAt/tGt	2/15	1	2	FACETS	0.929	0.869	0.99	0.929	0.869	0.99	CLONAL	1	TRUE	1	0.652366473093833	2		597	766	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264328	46264328	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	106	336	0	ENST00000371998.3:c.1375T>C	p.Tyr459His	p.Y459H	ENST00000371998		459	Tat/Cat	11/23	1	2	FACETS	0.798	0.721	0.879	0.798	0.721	0.879	SUBCLONAL	1	TRUE	1	0.652366473093833	2		336	407	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437510	52437510	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755664216	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	260	634	1	ENST00000460680.1:c.1651C>T	p.Arg551Cys	p.R551C	ENST00000460680	NM_004656.3	551	Cgt/Tgt	13/17	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.652366473093833	2		635	756	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268969	55268969	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	199	580	0	ENST00000275493.2:c.3035A>G	p.Asp1012Gly	p.D1012G	ENST00000275493	NM_005228.3	1012	gAt/gGt	25/28	1	2	FACETS	0.794	0.738	0.853	0.794	0.738	0.853	SUBCLONAL	1	TRUE	1	0.652366473093833	2		580	768	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151871235	151871235	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	117	318	0	ENST00000262189.6:c.9355C>A	p.Pro3119Thr	p.P3119T	ENST00000262189	NM_170606.2	3119	Cca/Aca	39/59	1	2	FACETS	0.79	0.717	0.866	0.79	0.717	0.866	SUBCLONAL	1	TRUE	1	0.652366473093833	2		318	454	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29195879	29195879	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs767641023	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1490	270	707	0	ENST00000240100.2:c.719A>G	p.Tyr240Cys	p.Y240C	ENST00000240100	NM_001394.6	240	tAt/tGt	3/4	0.652366473093833	5	FACETS	0.931	0.87	0.993	0.233	0.217	0.249	CLONAL	1	TRUE	1	0.652366473093833	5		707	1760	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279419	38279419	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	228	555	0	ENST00000425967.3:c.1070T>G	p.Leu357Arg	p.L357R	ENST00000425967	NM_001174067.1	357	cTt/cGt	9/19	0.652366473093833	5	FACETS	1	0.969	1	0.268	0.249	0.288	CLONAL	1	TRUE	1	0.652366473093833	5		555	1290	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989656	68989656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	141	378	0	ENST00000288368.4:c.1594G>A	p.Ala532Thr	p.A532T	ENST00000288368	NM_024870.2	532	Gca/Aca	15/40	0.652366473093833	5	FACETS	0.892	0.812	0.976	0.223	0.203	0.244	CLONAL	1	TRUE	1	0.652366473093833	5		378	959	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922118	39922118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768842901	NA	P-0045415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	316	627	0	ENST00000378444.4:c.4054G>A	p.Asp1352Asn	p.D1352N	ENST00000378444	NM_001123385.1	1352	Gac/Aac	9/15	0.607566151697334	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.652366473093833	1		627	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0045416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	272	763	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.546660586195939	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.546660586195939	1		765	600	SUCCESS
APC	324	MSKCC	GRCh37	5	112154723	112154723	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775126020	NA	P-0045416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	105	395	0	ENST00000257430.4:c.994C>T	p.Arg332Ter	p.R332*	ENST00000257430	NM_000038.5	332	Cga/Tga	10/16	0.546660586195939	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.546660586195939	1		395	240	SUCCESS
AR	367	MSKCC	GRCh37	X	66765159	66765185	+	inframe_deletion	In_Frame_Del	DEL	GCAGCAGCAGCAGCAGCAGCAGCAGCA	GCAGCAGCAGCAGCAGCAGCAGCAGCA	-	rs3032358	NA	P-0045416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	10	170	0	ENST00000374690.3:c.213_239del	p.Gln72_Gln80del	p.Q72_Q80del	ENST00000374690	NM_000044.3	57	ctGCAGCAGCAGCAGCAGCAGCAGCAGCAg/ctg	1/8	1	1	FACETS	0.172	0.116	0.241	0.172	0.116	0.241	SUBCLONAL	1	TRUE	0	0.546660586195939	1		170	155	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565538	41565538	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	106	333	0	ENST00000263253.7:c.4204C>G	p.His1402Asp	p.H1402D	ENST00000263253	NM_001429.3	1402	Cat/Gat	26/31	1	2	FACETS	0.787	0.708	0.869	0.787	0.708	0.869	SUBCLONAL	1	TRUE	1	0.546660586195939	2		333	493	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922884	44922884	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0045416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	136	281	0	ENST00000377967.4:c.1745C>G	p.Ser582Ter	p.S582*	ENST00000377967	NM_021140.2	582	tCa/tGa	16/29	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.546660586195939	1		281	258	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152009002	152009002	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138740890	NA	P-0045416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	24	284	0	ENST00000262189.6:c.620C>G	p.Ser207Cys	p.S207C	ENST00000262189	NM_170606.2	207	tCt/tGt	5/59	1	2	FACETS	0.245	0.192	0.307	0.245	0.192	0.307	SUBCLONAL	1	TRUE	1	0.546660586195939	2		284	358	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895698	28895699	+	stop_gained	Nonsense_Mutation	DNP	TC	TC	AA	novel	NA	P-0045416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	30	430	1	ENST00000282397.4:c.3075_3076delinsTT	p.Arg1026Ter	p.R1026*	ENST00000282397	NM_002019.4	1025	gcGAga/gcTTga	23/30	1	2	FACETS	0.205	0.165	0.251	0.205	0.165	0.251	SUBCLONAL	1	TRUE	1	0.546660586195939	2		431	535	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105238701	105238701	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0045416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	120	704	0	ENST00000349310.3:c.1260+1G>T		p.X420_splice	ENST00000349310	NM_001014432.1	420			0.546660586195939	1	FACETS	0.605	0.549	0.664	0.605	0.549	0.664	SUBCLONAL	1	TRUE	0	0.546660586195939	1		704	527	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632645	3632645	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	255	844	0	ENST00000294008.3:c.5203G>C	p.Glu1735Gln	p.E1735Q	ENST00000294008	NM_032444.2	1735	Gag/Cag	15/15	0.546660586195939	3	FACETS	1	0.953	1	0.512	0.478	0.546	CLONAL	1	TRUE	1	0.546660586195939	3		844	1161	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013702	12013702	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	115	269	1	ENST00000353533.5:c.644C>A	p.Ala215Glu	p.A215E	ENST00000353533	NM_003010.3	215	gCa/gAa	6/11	0.546660586195939	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.546660586195939	1		270	281	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600000	10600000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263063249	NA	P-0045416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	165	813	0	ENST00000171111.5:c.1576G>A	p.Asp526Asn	p.D526N	ENST00000171111	NM_203500.1	526	Gat/Aat	5/6	1	2	FACETS	0.721	0.663	0.782	0.721	0.663	0.782	SUBCLONAL	1	TRUE	1	0.546660586195939	2		813	837	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714421	40714421	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	62	454	0	ENST00000373198.4:c.3976G>A	p.Asp1326Asn	p.D1326N	ENST00000373198	NM_133170.3	1326	Gac/Aac	29/32	1	2	FACETS	0.402	0.347	0.462	0.402	0.347	0.462	SUBCLONAL	1	TRUE	1	0.546660586195939	2		454	564	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155352	185155352	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	120	353	0	ENST00000265026.3:c.593G>C	p.Arg198Thr	p.R198T	ENST00000265026	NM_004721.4	198	aGa/aCa	3/14	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.546660586195939	2		353	388	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160759	56160759	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	74	270	0	ENST00000399503.3:c.1033C>G	p.Gln345Glu	p.Q345E	ENST00000399503	NM_005921.1	345	Cag/Gag	4/20	NA	2	FACETS	0.953	0.844	1			1	INDETERMINATE	1	TRUE	NA	0.546660586195939	2		270	284	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449739	8449739	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	161	525	0	ENST00000356435.5:c.3974A>C	p.Asn1325Thr	p.N1325T	ENST00000356435		1325	aAc/aCc	23/35	0.546660586195939	1	FACETS	0.955	0.885	1	0.955	0.885	1	CLONAL	1	TRUE	0	0.546660586195939	1		525	448	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966669	44966669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	93	164	0	ENST00000377967.4:c.3893G>A	p.Arg1298Lys	p.R1298K	ENST00000377967	NM_021140.2	1298	aGa/aAa	27/29	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.546660586195939	1		164	170	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0045417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	190	707	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.991	0.916	1	0.991	0.916	1	CLONAL	1	TRUE	1	0.408419492546353	2		708	939	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579361	7579361	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1064796722	NA	P-0045417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	223	625	0	ENST00000269305.4:c.326T>C	p.Phe109Ser	p.F109S	ENST00000269305	NM_001126112.2	109	tTc/tCc	4/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.408419492546353	2		625	1013	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210692	5210692	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	173	644	0	ENST00000357368.4:c.5359C>T	p.Arg1787Trp	p.R1787W	ENST00000357368	NM_002850.3	1787	Cgg/Tgg	34/38	1	2	FACETS	0.997	0.918	1	0.997	0.918	1	CLONAL	1	TRUE	1	0.408419492546353	2		644	850	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244392	5244392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377318412	NA	P-0045417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	55	735	0	ENST00000357368.4:c.1090G>A	p.Val364Ile	p.V364I	ENST00000357368	NM_002850.3	364	Gtc/Atc	11/38	1	2	FACETS	0.265	0.226	0.309	0.265	0.226	0.309	SUBCLONAL	1	TRUE	1	0.408419492546353	2		735	1016	SUCCESS
APC	324	MSKCC	GRCh37	5	112173590	112173590	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561575998	NA	P-0045417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	75	242	0	ENST00000257430.4:c.2299C>T	p.Gln767Ter	p.Q767*	ENST00000257430	NM_000038.5	767	Cag/Tag	16/16	0.408419492546353	1	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	0	0.408419492546353	1		242	289	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971116	21971116	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	109	279	0	ENST00000304494.5:c.242C>A	p.Pro81His	p.P81H	ENST00000304494	NM_000077.4	81	cCc/cAc	2/3	0.378646777083953	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.408419492546353	1		279	411	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3824585	3824585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045417-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	115	394	0	ENST00000262367.5:c.2268G>A	p.Met756Ile	p.M756I	ENST00000262367	NM_004380.2	756	atG/atA	12/31	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.408419492546353	2		394	552	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0045418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	380	316	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.355125566092798	4	FACETS	0.886	0.845	0.928	0.886	0.845	0.928	INDETERMINATE	2	TRUE	2	0.860890931761335	4		316	927	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578498	7578499	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0045418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	1744	755	0	ENST00000269305.4:c.430_431dup	p.Gln144HisfsTer27	p.Q144Hfs*27	ENST00000269305	NM_001126112.2	144	cag/caCAg	5/11	0.860890931761335	2	FACETS	0.927	0.914	0.939	0.927	0.914	0.939	CLONAL	2	TRUE	0	0.860890931761335	2		755	2186	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99203953	99203953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	86	214	0	ENST00000074304.5:c.2816G>A	p.Arg939Lys	p.R939K	ENST00000074304	NM_001134224.1	939	aGa/aAa	26/26	0.860890931761335	2	FACETS	0.493	0.439	0.551	0.247	0.219	0.276	SUBCLONAL	1	TRUE	0	0.860890931761335	2		214	405	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0045433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	59	359	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.11991042996312	5	FACETS	1	0.958	1	0.437	0.376	0.503	INDETERMINATE	1	TRUE	2	0.25	5		359	495	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0045433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	83	571	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.193021312975468	3	FACETS	0.896	0.795	1	0.896	0.795	1	CLONAL	2	TRUE	1	0.25	3		571	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0045433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	252	863	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.246340106359833	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.25	2		863	942	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874036	151874036	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs138845109	NA	P-0045433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	104	469	0	ENST00000262189.6:c.8502A>T	p.Glu2834Asp	p.E2834D	ENST00000262189	NM_170606.2	2834	gaA/gaT	38/59	0.2427840667897	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.25	2		469	384	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121541	2121541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334081822	NA	P-0045433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	252	1008	0	ENST00000219476.3:c.1870G>A	p.Asp624Asn	p.D624N	ENST00000219476	NM_000548.3	624	Gac/Aac	18/42	0.0605147605040144	4	FACETS	1	0.955	1	1	0.955	1	INDETERMINATE	2	TRUE	2	0.25	4		1008	1226	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66520194	66520194	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs765675434	NA	P-0045433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	92	380	0	ENST00000358598.2:c.478G>T	p.Ala160Ser	p.A160S	ENST00000358598	NM_212471.2	160	Gca/Tca	5/11	0.0623383986717783	3	FACETS	1	0.978	1	0.714	0.635	0.797	INDETERMINATE	1	TRUE	1	0.25	3		380	580	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031939	26031939	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045433-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	44	452	0	ENST00000244661.2:c.350G>C	p.Arg117Pro	p.R117P	ENST00000244661	NM_003537.3	117	cGa/cCa	1/1	NA	3	FACETS	0.81	0.679	0.954			1	INDETERMINATE	1	TRUE	NA	0.25	3		452	489	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0045434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	97	267	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.904	0.81	1	0.904	0.81	1	CLONAL	1	TRUE	1	0.476918237329613	2		267	450	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0045434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	208	427	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.436044953747254	2	FACETS	0.839	0.786	0.893	0.839	0.786	0.893	CLONAL	2	TRUE	0	0.476918237329613	2		427	520	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733279	40733279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201275244	NA	P-0045434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	328	520	0	ENST00000373198.4:c.3527G>A	p.Arg1176His	p.R1176H	ENST00000373198	NM_133170.3	1176	cGt/cAt	26/32	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.476918237329613	2		520	1071	SUCCESS
APC	324	MSKCC	GRCh37	5	112175193	112175193	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1064794042	NA	P-0045434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	91	207	0	ENST00000257430.4:c.3904del	p.Leu1302CysfsTer3	p.L1302Cfs*3	ENST00000257430	NM_000038.5	1301	aCc/ac	16/16	0.436044953747254	2	FACETS	1	0.979	1	0.694	0.625	0.766	CLONAL	1	TRUE	0	0.476918237329613	2		207	275	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846216	156846216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	154	883	1	ENST00000524377.1:c.1657G>A	p.Ala553Thr	p.A553T	ENST00000524377	NM_002529.3	553	Gct/Act	14/17	0.242794419243666	1	FACETS	0.44	0.401	0.48	0.44	0.401	0.48	INDETERMINATE	1	TRUE	0	0.476918237329613	1		884	1119	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114905819	114905820	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0045434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	194	586	0	ENST00000543371.1:c.839dup	p.Tyr280Ter	p.Y280*	ENST00000543371	NM_001198531.1	280	tac/tAac	8/14	1	2	FACETS	0.779	0.721	0.84	0.779	0.721	0.84	SUBCLONAL	1	TRUE	1	0.476918237329613	2		586	1044	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579560	7579563	+	frameshift_variant	Frame_Shift_Del	DEL	AATC	AATC	-	novel	NA	P-0045434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	249	826	0	ENST00000269305.4:c.124_127del	p.Asp42Ter	p.D42*	ENST00000269305	NM_001126112.2	42	GATTtg/tg	4/11	0.476918237329613	1	FACETS	0.891	0.835	0.949	0.891	0.835	0.949	CLONAL	1	TRUE	0	0.476918237329613	1		826	892	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957020	1957020	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045434-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	69	711	0	ENST00000382891.5:c.2471G>A	p.Arg824Gln	p.R824Q	ENST00000382891	NM_133335.3	824	cGa/cAa	13/22	1	2	FACETS	0.23	0.199	0.264	0.23	0.199	0.264	SUBCLONAL	1	TRUE	1	0.476918237329613	2		711	1256	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0045436-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	112	623	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.243369885903089	1	FACETS	0.895	0.804	0.991	0.895	0.804	0.991	CLONAL	1	TRUE	0	0.252320399206644	1		623	867	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	25	425	0				ENST00000310581	NM_198253.2	-/1132			0.3	0	FACETS	0.939	0.741	1			1	CLONAL	1	TRUE	0	0.14	0		425	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0045437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	69	623	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.14	2		623	927	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579420	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783062	NA	P-0045437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	53	712	0	ENST00000269305.4:c.267del	p.Ser90ProfsTer33	p.S90Pfs*33	ENST00000269305	NM_001126112.2	89	ccC/cc	4/11	1	2	FACETS	0.758	0.644	0.884	0.758	0.644	0.884	SUBCLONAL	1	TRUE	1	0.14	2		712	999	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845569	63845569	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	22	191	0	ENST00000279873.7:c.1311del	p.Val438TyrfsTer41	p.V438Yfs*41	ENST00000279873	NM_032199.2	436	acA/ac	9/10	0.3	5	FACETS	0.872	0.675	1			1	CLONAL	1	TRUE	NA	0.14	5		191	436	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0045444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	143	545	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.539923873712462	2		545	521	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835596	68835596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587783047	NA	P-0045444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	166	418	1	ENST00000261769.5:c.187C>T	p.Arg63Ter	p.R63*	ENST00000261769	NM_004360.3	63	Cga/Tga	3/16	0.539923873712462	1	FACETS	0.978	0.907	1	0.978	0.907	1	CLONAL	1	TRUE	0	0.539923873712462	1		419	459	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199627	16199627	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415241290	NA	P-0045444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	43	397	0	ENST00000375759.3:c.400G>A	p.Asp134Asn	p.D134N	ENST00000375759	NM_015001.2	134	Gat/Aat	2/15	1	2	FACETS	0.268	0.223	0.317	0.268	0.223	0.317	SUBCLONAL	1	TRUE	1	0.539923873712462	2		397	595	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004348	150004348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766836005	NA	P-0045444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	79	369	0	ENST00000253339.5:c.1877G>A	p.Arg626Gln	p.R626Q	ENST00000253339		626	cGa/cAa	3/7	1	2	FACETS	0.876	0.777	0.981	0.876	0.777	0.981	CLONAL	1	TRUE	1	0.539923873712462	2		369	334	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307328	118307328	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	13	16	0	ENST00000534358.1:c.101G>T	p.Arg34Leu	p.R34L	ENST00000534358	NM_005933.3	34	cGc/cTc	1/36	0.539923873712462	1	FACETS	0.925	0.692	1	0.925	0.692	1	CLONAL	1	TRUE	0	0.539923873712462	1		16	38	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427975	49427975	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	242	669	0	ENST00000301067.7:c.10615C>G	p.Arg3539Gly	p.R3539G	ENST00000301067	NM_003482.3	3539	Cgg/Ggg	38/54	1	2	FACETS	0.936	0.875	0.998	0.936	0.875	0.998	CLONAL	1	TRUE	1	0.539923873712462	2		669	958	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152864448	152864448	+	synonymous_variant	Silent	SNP	G	G	A	novel	NA	P-0045444-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	79	131	0	ENST00000406277.2:c.78C>T	p.Phe26=	p.F26=	ENST00000406277	NM_152274.4	26	ttC/ttT	3/7	1		FACETS		0.915	1				CLONAL	1	TRUE	1	0.539923873712462	2		131	283	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	61	425	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.85	0.745	0.96	0.85	0.745	0.96	CLONAL	1	TRUE	1	0.700096629438892	2		425	205	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944178	71944178	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs748455961	NA	P-0045445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	171	838	0	ENST00000298229.2:c.2011T>C	p.Tyr671His	p.Y671H	ENST00000298229	NM_001567.3	671	Tat/Cat	17/28	1	2	FACETS	0.973	0.902	1	0.973	0.902	1	CLONAL	1	TRUE	1	0.700096629438892	2		838	502	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653821	89653821	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	160	357	0	ENST00000371953.3:c.121del	p.Arg41AspfsTer13	p.R41Dfs*13	ENST00000371953	NM_000314.4	40	gAa/ga	2/9	0.700096629438892	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.700096629438892	2		357	223	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48942663	48942663	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	121	211	0	ENST00000267163.4:c.1053del	p.Phe351LeufsTer16	p.F351Lfs*16	ENST00000267163	NM_000321.2	350	agT/ag	11/27	0.700096629438892	2	FACETS	0.999	0.938	1	0.999	0.938	1	CLONAL	2	TRUE	0	0.700096629438892	2		211	173	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923689	39923689	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	312	463	0	ENST00000378444.4:c.3402del	p.Lys1135AsnfsTer24	p.K1135Nfs*24	ENST00000378444	NM_001123385.1	1134	agG/ag	7/15	0.700096629438892	2	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.700096629438892	2		463	408	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0045446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	110	331	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.762	0.689	0.839	0.762	0.689	0.839	SUBCLONAL	1	TRUE	1	0.623427265254002	2		331	463	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0045446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	518	588	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.623427265254002	2	FACETS	0.838	0.817	0.858	1	0.997	1	CLONAL	3	TRUE	0	0.623427265254002	2		588	661	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0045446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	362	873	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.623427265254002	2		873	1092	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189846	11189846	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	44	458	0	ENST00000361445.4:c.5663T>C	p.Phe1888Ser	p.F1888S	ENST00000361445	NM_004958.3	1888	tTc/tCc	40/58	1	2	FACETS	0.178	0.149	0.211	0.178	0.149	0.211	SUBCLONAL	1	TRUE	1	0.623427265254002	2		458	791	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259398	11259398	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	152	523	0	ENST00000361445.4:c.4170C>G	p.Cys1390Trp	p.C1390W	ENST00000361445	NM_004958.3	1390	tgC/tgG	28/58	1	2	FACETS	0.686	0.628	0.746	0.686	0.628	0.746	SUBCLONAL	1	TRUE	1	0.623427265254002	2		523	711	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997862	149997862	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142843346	NA	P-0045446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	188	374	0	ENST00000253339.5:c.2605C>T	p.Arg869Trp	p.R869W	ENST00000253339		869	Cgg/Tgg	5/7	1	2	FACETS	0.974	0.905	1	0.974	0.905	1	CLONAL	1	TRUE	1	0.623427265254002	2		374	619	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361161	70361161	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	334	730	0	ENST00000374080.3:c.6349C>T	p.Gln2117Ter	p.Q2117*	ENST00000374080		2117	Cag/Tag	43/45	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.623427265254002	2		730	943	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263992	104263992	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758001170	NA	P-0045447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	24	423	2	ENST00000369902.3:c.83C>T	p.Ser28Leu	p.S28L	ENST00000369902	NM_016169.3	28	tCg/tTg	1/12	0.225801177549494	3	FACETS	0.663	0.521	0.826	0.331	0.26	0.413	SUBCLONAL	1	TRUE	1	0.320717432645818	3		425	262	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025830	1025830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	112	581	0	ENST00000358495.3:c.700C>T	p.Pro234Ser	p.P234S	ENST00000358495	NM_134424.2	234	Ccg/Tcg	8/12	NA	2	FACETS	1	0.913	1			1	INDETERMINATE	2	TRUE	NA	0.320717432645818	2		581	348	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881516	48881516	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0045447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	12	223	0	ENST00000267163.4:c.238A>T	p.Lys80Ter	p.K80*	ENST00000267163	NM_000321.2	80	Aaa/Taa	2/27	0.241438152671632	3	FACETS	0.611	0.432	0.83	0.306	0.216	0.415	SUBCLONAL	1	TRUE	1	0.320717432645818	3		223	142	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039205	49039206	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	AT	novel	NA	P-0045447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	43	478	0	ENST00000267163.4:c.2283_2284delinsAT	p.Met761_Gln762delinsIleTer	p.M761_Q762delinsI*	ENST00000267163	NM_000321.2	761	atGCag/atATag	22/27	0.241438152671632	3	FACETS	1	0.949	1	0.665	0.561	0.778	CLONAL	1	TRUE	1	0.320717432645818	3		478	234	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712772	43712773	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0045447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	46	778	0	ENST00000382044.4:c.4411_4412delinsTT	p.Pro1471Phe	p.P1471F	ENST00000382044	NM_001141980.1	1471	CCt/TTt	21/28	1	2	FACETS	0.672	0.566	0.788	0.672	0.566	0.788	SUBCLONAL	1	TRUE	1	0.320717432645818	2		778	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0045447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	66	609	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.282869209742159	2	FACETS	1	0.959	1	0.624	0.545	0.707	CLONAL	1	TRUE	0	0.320717432645818	2		609	330	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578260	212578260	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	11	362	0	ENST00000342788.4:c.997G>A	p.Ala333Thr	p.A333T	ENST00000342788	NM_005235.2	333	Gct/Act	8/28	0.250417109169758	3	FACETS	0.437	0.302	0.605	0.146	0.1	0.202	SUBCLONAL	1	TRUE	0	0.320717432645818	3		362	182	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29115386	29115386	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	23	392	1	ENST00000328354.6:c.680G>A	p.Gly227Glu	p.G227E	ENST00000328354	NM_007194.3	227	gGa/gAa	5/15	0.0862270885056124	3	FACETS	0.94	0.739	1	0.47	0.369	0.585	INDETERMINATE	1	TRUE	1	0.320717432645818	3		393	177	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096246	71096246	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	11	251	0	ENST00000318789.4:c.511C>A	p.Gln171Lys	p.Q171K	ENST00000318789	NM_032682.5	171	Caa/Aaa	10/21	0.183595880138919	5	FACETS	0.706	0.489	0.972	0.235	0.163	0.324	INDETERMINATE	1	TRUE	2	0.320717432645818	5		251	144	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235401	235401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1386175077	NA	P-0045447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	35	701	0	ENST00000264932.6:c.1207C>T	p.Leu403Phe	p.L403F	ENST00000264932	NM_004168.2	403	Ctc/Ttc	9/15	0.0862270885056124	3	FACETS	0.515	0.421	0.62	0.257	0.21	0.31	INDETERMINATE	1	TRUE	1	0.320717432645818	3		701	492	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56176539	56176539	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs753037944	NA	P-0045447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	13	303	1	ENST00000399503.3:c.2089C>T	p.Arg697Cys	p.R697C	ENST00000399503	NM_005921.1	697	Cgc/Tgc	12/20	0.0862270885056124	3	FACETS	0.452	0.323	0.61	0.226	0.161	0.305	INDETERMINATE	1	TRUE	1	0.320717432645818	3		304	208	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005336	150005336	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	37	614	0	ENST00000253339.5:c.889C>T	p.Gln297Ter	p.Q297*	ENST00000253339		297	Caa/Taa	3/7	0.225801177549494	3	FACETS	0.746	0.616	0.89	0.373	0.308	0.445	SUBCLONAL	1	TRUE	1	0.320717432645818	3		614	359	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980547	70980547	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045447-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	37	696	0	ENST00000276594.2:c.830G>A	p.Gly277Glu	p.G277E	ENST00000276594	NM_024504.3	277	gGa/gAa	4/8	0.183595880138919	5	FACETS	0.784	0.646	0.938	0.261	0.215	0.313	INDETERMINATE	1	TRUE	2	0.320717432645818	5		696	436	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	979	425	0				ENST00000310581	NM_198253.2	-/1132			0.83074128086793	7	FACETS	1	0.997	1	1	0.997	1	CLONAL	5	TRUE	2	0.83074128086793	7		425	1322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0045449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	1279	707	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.83074128086793	4	FACETS	0.996	0.985	1	0.996	0.985	1	CLONAL	4	TRUE	0	0.83074128086793	4		708	1415	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955535	48955535	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	61	259	0	ENST00000267163.4:c.1651G>T	p.Glu551Ter	p.E551*	ENST00000267163	NM_000321.2	551	Gaa/Taa	17/27	NA	2	FACETS	0.941	0.871	1			1	INDETERMINATE	2	TRUE	NA	0.83074128086793	2		259	78	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0045450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	140	262	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.853	0.783	0.925	0.853	0.783	0.925	CLONAL	1	TRUE	1	0.726342842268558	2		262	452	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857875	9857875	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	327	574	0	ENST00000330684.3:c.3526G>A	p.Glu1176Lys	p.E1176K	ENST00000330684	NM_001134407.1	1176	Gag/Aag	13/13	1	2	FACETS	0.982	0.931	1	0.982	0.931	1	CLONAL	1	TRUE	1	0.726342842268558	2		574	917	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650147	206650147	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	377	695	1	ENST00000367120.3:c.667C>T	p.Pro223Ser	p.P223S	ENST00000367120	NM_014002.3	223	Ccc/Tcc	7/22	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.726342842268558	2		696	1030	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720950	176720950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	314	515	0	ENST00000439151.2:c.6581C>T	p.Ser2194Phe	p.S2194F	ENST00000439151	NM_022455.4	2194	tCc/tTc	23/23	0.378687321284855	1	FACETS	0.81	0.77	0.85	0.81	0.77	0.85	INDETERMINATE	1	TRUE	0	0.726342842268558	1		515	680	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106522561	106522561	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0045450-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	170	287	0	ENST00000359195.3:c.2539-1G>A		p.X847_splice	ENST00000359195	NM_002649.2	847			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.726342842268558	2		287	442	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0045451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	21	294	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.747	0.578	0.944	0.747	0.578	0.944	CLONAL	1	TRUE	1	0.260160646060958	2		294	216	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0045451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	99	995	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.260160646060958	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.260160646060958	1		995	597	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0045451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	17	270	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	0.260160646060958	1	FACETS	0.836	0.629	1	0.836	0.629	1	CLONAL	1	TRUE	0	0.260160646060958	1		270	136	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266091	41266099	+	inframe_deletion	In_Frame_Del	DEL	TACCTGGAC	TACCTGGAC	-	novel	NA	P-0045454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	241	339	0	ENST00000349496.5:c.89_97del	p.Tyr30_Asp32del	p.Y30_D32del	ENST00000349496	NM_001904.3	30	TACCTGGAC/-	3/15	0.205046702505185	5	FACETS	1	0.945	1	1	0.994	1	CLONAL	6	FALSE	1	0.205046702505185	5		339	512	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054231	30054232	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTGAACTACTTTGCAACA	novel	NA	P-0045455-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	106	412	0	ENST00000338641.4:c.670_671insCATGTGAACTACTTTGCAA	p.Ile224ThrfsTer10	p.I224Tfs*10	ENST00000338641	NM_000268.3	218	ggt/ggTGTGAACTACTTTGCAACAt	7/16	0.355497644790915	0	FACETS	0.683	0.62	0.749			1	SUBCLONAL	1	TRUE	0	0.487680121104369	0		412	326	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188251	10188251	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs5030813	NA	P-0045457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	129	485	0	ENST00000256474.2:c.394C>T	p.Gln132Ter	p.Q132*	ENST00000256474	NM_000551.3	132	Caa/Taa	2/3	0.351921794282753	1	FACETS	0.892	0.811	0.978	0.892	0.811	0.978	CLONAL	1	TRUE	0	0.351921794282753	1		485	677	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135964	64135964	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	162	916	0	ENST00000334205.4:c.1225G>T	p.Glu409Ter	p.E409*	ENST00000334205	NM_003942.2	409	Gag/Tag	11/17	1	2	FACETS	0.927	0.85	1	0.927	0.85	1	CLONAL	1	TRUE	1	0.351921794282753	2		916	993	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584578	52584579	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0045457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	135	619	0	ENST00000394830.3:c.4434dup	p.Ile1479HisfsTer30	p.I1479Hfs*30	ENST00000394830	NM_018313.4	1478	-/C	29/30	0.351921794282753	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.351921794282753	1		619	602	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2493197	2493197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762075584	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	555	681	1	ENST00000355716.4:c.637G>A	p.Val213Ile	p.V213I	ENST00000355716	NM_003820.2	213	Gtc/Atc	6/8	0.3	2	FACETS	0.987	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.93	2		682	1209	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780827	9780827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs991423011	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	261	790	0	ENST00000377346.4:c.1549C>T	p.Arg517Trp	p.R517W	ENST00000377346	NM_005026.3	517	Cgg/Tgg	13/24	0.3	2	FACETS	0.411	0.384	0.438			1	INDETERMINATE	1	TRUE	NA	0.93	2		790	1367	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257728	16257728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	387	449	0	ENST00000375759.3:c.4993G>A	p.Ala1665Thr	p.A1665T	ENST00000375759	NM_015001.2	1665	Gcg/Acg	11/15	1	2	FACETS	0.972	0.929	1	0.972	0.929	1	CLONAL	1	TRUE	1	0.93	2		449	856	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262082	16262082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763721746	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	291	390	0	ENST00000375759.3:c.9347C>T	p.Ala3116Val	p.A3116V	ENST00000375759	NM_015001.2	3116	gCg/gTg	11/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.93	2		390	617	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089489	27089489	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	568	707	0	ENST00000324856.7:c.2445T>G	p.Tyr815Ter	p.Y815*	ENST00000324856	NM_006015.4	815	taT/taG	8/20	1	2	FACETS	0.986	0.95	1	0.986	0.95	1	CLONAL	1	TRUE	1	0.93	2		707	1239	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100151	27100151	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749727660	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	186	676	0	ENST00000324856.7:c.3947C>T	p.Ser1316Leu	p.S1316L	ENST00000324856	NM_006015.4	1316	tCg/tTg	16/20	1	2	FACETS	0.332	0.306	0.359	0.332	0.306	0.359	SUBCLONAL	1	TRUE	1	0.93	2		676	1205	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101055	27101055	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772939817	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	616	746	0	ENST00000324856.7:c.4337G>A	p.Arg1446Gln	p.R1446Q	ENST00000324856	NM_006015.4	1446	cGa/cAa	18/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.93	2		746	1322	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933510	36933510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754739637	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	703	861	0	ENST00000361632.4:c.1777G>A	p.Ala593Thr	p.A593T	ENST00000361632		593	Gcc/Acc	13/16	1	2	FACETS	0.944	0.912	0.976	0.944	0.912	0.976	CLONAL	1	TRUE	1	0.93	2		861	1601	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812205	43812205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866559375	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	165	574	1	ENST00000372470.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000372470	NM_005373.2	357	cGa/cAa	7/12	1	2	FACETS	0.353	0.324	0.384	0.353	0.324	0.384	SUBCLONAL	1	TRUE	1	0.93	2		575	1005	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798467	45798467	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747993448	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	634	732	1	ENST00000450313.1:c.544C>T	p.Arg182Cys	p.R182C	ENST00000450313	NM_012222.2	182	Cgt/Tgt	7/16	1	2	FACETS	0.982	0.948	1	0.982	0.948	1	CLONAL	1	TRUE	1	0.93	2		733	1388	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46715735	46715735	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs530382665	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	429	526	1	ENST00000371975.4:c.154C>T	p.Arg52Trp	p.R52W	ENST00000371975	NM_003579.3	52	Cgg/Tgg	3/18	1	2	FACETS	0.993	0.951	1	0.993	0.951	1	CLONAL	1	TRUE	1	0.93	2		527	929	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46725710	46725710	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	473	502	1	ENST00000371975.4:c.346G>T	p.Asp116Tyr	p.D116Y	ENST00000371975	NM_003579.3	116	Gat/Tat	5/18	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.93	2		503	1017	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743950	46743950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761304456	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	416	464	0	ENST00000371975.4:c.2240G>A	p.Arg747His	p.R747H	ENST00000371975	NM_003579.3	747	cGc/cAc	18/18	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.93	2		464	888	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310570	65310570	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	97	381	0	ENST00000342505.4:c.2118G>T	p.Glu706Asp	p.E706D	ENST00000342505	NM_002227.2	706	gaG/gaT	16/25	1	2	FACETS	0.32	0.286	0.357	0.32	0.286	0.357	SUBCLONAL	1	TRUE	1	0.93	2		381	651	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330648	65330648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	66	223	0	ENST00000342505.4:c.998C>T	p.Ser333Phe	p.S333F	ENST00000342505	NM_002227.2	333	tCt/tTt	8/25	1	2	FACETS	0.336	0.293	0.383	0.336	0.293	0.383	SUBCLONAL	1	TRUE	1	0.93	2		223	422	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332824	65332824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773295622	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	176	284	0	ENST00000342505.4:c.715C>T	p.Arg239Trp	p.R239W	ENST00000342505	NM_002227.2	239	Cgg/Tgg	7/25	1	2	FACETS	0.819	0.762	0.877	0.819	0.762	0.877	CLONAL	1	TRUE	1	0.93	2		284	462	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261278	115261278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	396	483	0	ENST00000438362.2:c.2443C>T	p.Arg815Cys	p.R815C	ENST00000438362	NM_001242891.1	815	Cgc/Tgc	19/20	1	2	FACETS	0.966	0.923	1	0.966	0.923	1	CLONAL	1	TRUE	1	0.93	2		483	882	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280664	115280664	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	96	455	0	ENST00000438362.2:c.367C>T	p.Arg123Ter	p.R123*	ENST00000438362	NM_001242891.1	123	Cga/Tga	4/20	1	2	FACETS	0.273	0.243	0.305	0.273	0.243	0.305	SUBCLONAL	1	TRUE	1	0.93	2		455	756	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510802	120510802	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1273608383	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	399	427	0	ENST00000256646.2:c.1162G>A	p.Ala388Thr	p.A388T	ENST00000256646	NM_024408.3	388	Gca/Aca	7/34	1	2	FACETS	0.964	0.922	1	0.964	0.922	1	CLONAL	1	TRUE	1	0.93	2		427	890	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843535	156843535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369367198	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	623	723	0	ENST00000524377.1:c.961G>A	p.Val321Met	p.V321M	ENST00000524377	NM_002529.3	321	Gtg/Atg	8/17	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.93	2		723	1274	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846300	156846300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150579345	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	735	942	0	ENST00000524377.1:c.1741G>A	p.Glu581Lys	p.E581K	ENST00000524377	NM_002529.3	581	Gag/Aag	14/17	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.93	2		942	1542	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849143	156849143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775191394	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	641	746	0	ENST00000524377.1:c.2035G>A	p.Asp679Asn	p.D679N	ENST00000524377	NM_002529.3	679	Gac/Aac	15/17	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.93	NA		746	1342	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849863	156849863	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747855434	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	546	715	0	ENST00000524377.1:c.2119G>A	p.Glu707Lys	p.E707K	ENST00000524377	NM_002529.3	707	Gag/Aag	16/17	1	2	FACETS	0.957	0.921	0.993	0.957	0.921	0.993	CLONAL	1	TRUE	1	0.93	2		715	1227	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746017	162746017	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	256	354	0	ENST00000367921.3:c.2140C>T	p.Arg714Ter	p.R714*	ENST00000367921	NM_006182.2	714	Cga/Tga	16/18	1	2	FACETS	0.99	0.936	1	0.99	0.936	1	CLONAL	1	TRUE	1	0.93	2		354	556	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306550	163306550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201079271	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	170	317	0	ENST00000271452.3:c.347G>A	p.Arg116Gln	p.R116Q	ENST00000271452	NM_145697.2	116	cGg/cAg	6/14	1	2	FACETS	0.877	0.816	0.939	0.877	0.816	0.939	CLONAL	1	TRUE	1	0.93	2		317	417	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175706	176175706	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	590	683	0	ENST00000367669.3:c.407+2T>C		p.X136_splice	ENST00000367669	NM_022457.5	136			1	2	FACETS	0.966	0.93	1	0.966	0.93	1	CLONAL	1	TRUE	1	0.93	2		683	1314	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206647794	206647794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	384	453	0	ENST00000367120.3:c.208C>T	p.Leu70Phe	p.L70F	ENST00000367120	NM_014002.3	70	Ctc/Ttc	4/22	1	2	FACETS	0.881	0.84	0.923	0.881	0.84	0.923	CLONAL	1	TRUE	1	0.93	2		453	937	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226551647	226551647	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	361	429	0	ENST00000366794.5:c.2783A>G	p.Asn928Ser	p.N928S	ENST00000366794	NM_001618.3	928	aAc/aGc	20/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.93	2		429	761	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226574031	226574031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201975538	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	317	351	0	ENST00000366794.5:c.830C>T	p.Ser277Leu	p.S277L	ENST00000366794	NM_001618.3	277	tCg/tTg	6/23	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.93	2		351	615	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63829525	63829525	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	257	326	1	ENST00000279873.7:c.1168G>A	p.Ala390Thr	p.A390T	ENST00000279873	NM_032199.2	390	Gct/Act	8/10	1	2	FACETS	0.921	0.87	0.973	0.921	0.87	0.973	CLONAL	1	TRUE	1	0.93	2		327	600	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451273	70451273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	137	671	0	ENST00000373644.4:c.6113G>A	p.Arg2038His	p.R2038H	ENST00000373644	NM_030625.2	2038	cGt/cAt	12/12	1	2	FACETS	0.257	0.233	0.282	0.257	0.233	0.282	SUBCLONAL	1	TRUE	1	0.93	2		671	1147	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690823	89690823	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs747865777	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	99	274	0	ENST00000371953.3:c.230A>G	p.Asp77Gly	p.D77G	ENST00000371953	NM_000314.4	77	gAc/gGc	4/9	1	2	FACETS	0.842	0.764	0.92	0.842	0.764	0.92	CLONAL	1	TRUE	1	0.93	2		274	253	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	197	423	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.898	0.84	0.956	0.898	0.84	0.956	CLONAL	1	TRUE	1	0.93	2		423	472	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712007	89712007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765433422	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	137	196	0	ENST00000371953.3:c.625G>A	p.Gly209Arg	p.G209R	ENST00000371953	NM_000314.4	209	Gga/Aga	6/9	1	2	FACETS	0.898	0.829	0.968	0.898	0.829	0.968	CLONAL	1	TRUE	1	0.93	2		196	328	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720870	89720870	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1554825652	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	248	407	0	ENST00000371953.3:c.1021T>G	p.Phe341Val	p.F341V	ENST00000371953	NM_000314.4	341	Ttt/Gtt	8/9	1	2	FACETS	0.944	0.891	0.997	0.944	0.891	0.997	CLONAL	1	TRUE	1	0.93	2		407	565	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114901057	114901057	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776719680	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	362	419	1	ENST00000543371.1:c.667G>A	p.Asp223Asn	p.D223N	ENST00000543371	NM_001198531.1	223	Gac/Aac	6/14	1	2	FACETS	0.954	0.91	0.999	0.954	0.91	0.999	CLONAL	1	TRUE	1	0.93	2		420	816	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154350	2154350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1268163024	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	850	1062	1	ENST00000434045.2:c.578G>A	p.Arg193His	p.R193H	ENST00000434045	NM_001127598.1	193	cGc/cAc	5/5	0.146227775907956	1	FACETS	0.551	0.535	0.568	0.551	0.535	0.568	INDETERMINATE	1	TRUE	0	0.93	1		1063	1774	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132927	64132927	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145356210	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	481	645	1	ENST00000334205.4:c.1061G>A	p.Arg354Gln	p.R354Q	ENST00000334205	NM_003942.2	354	cGa/cAa	9/17	1	2	FACETS	0.918	0.88	0.956	0.918	0.88	0.956	CLONAL	1	TRUE	1	0.93	2		646	1127	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588196	69588196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201349393	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	505	652	0	ENST00000168712.1:c.502G>A	p.Ala168Thr	p.A168T	ENST00000168712	NM_002007.2	168	Gcc/Acc	3/3	1	2	FACETS	0.985	0.946	1	0.985	0.946	1	CLONAL	1	TRUE	1	0.93	2		652	1103	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939479	71939479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775305188	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1583	361	1035	1	ENST00000298229.2:c.334G>A	p.Ala112Thr	p.A112T	ENST00000298229	NM_001567.3	112	Gcc/Acc	3/28	1	2	FACETS	0.399	0.377	0.423	0.399	0.377	0.423	SUBCLONAL	1	TRUE	1	0.93	2		1036	1944	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940539	71940539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	544	672	0	ENST00000298229.2:c.690G>T	p.Glu230Asp	p.E230D	ENST00000298229	NM_001567.3	230	gaG/gaT	6/28	1	2	FACETS	0.955	0.919	0.992	0.955	0.919	0.992	CLONAL	1	TRUE	1	0.93	2		672	1225	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943672	71943672	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	499	555	0	ENST00000298229.2:c.1715G>T	p.Arg572Met	p.R572M	ENST00000298229	NM_001567.3	572	aGg/aTg	15/28	1	2	FACETS	0.945	0.908	0.983	0.945	0.908	0.983	CLONAL	1	TRUE	1	0.93	2		555	1135	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946224	71946224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	268	688	0	ENST00000298229.2:c.2480C>T	p.Ser827Phe	p.S827F	ENST00000298229	NM_001567.3	827	tCc/tTc	22/28	1	2	FACETS	0.435	0.407	0.464	0.435	0.407	0.464	SUBCLONAL	1	TRUE	1	0.93	2		688	1324	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917655	94917655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746291519	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	240	405	0	ENST00000536441.1:c.866G>A	p.Arg289His	p.R289H	ENST00000536441	NM_144665.3	289	cGt/cAt	6/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.93	2		405	512	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996849	100996849	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	330	450	0	ENST00000325455.5:c.1678G>A	p.Glu560Lys	p.E560K	ENST00000325455	NM_001202474.3	560	Gag/Aag	2/8	1	2	FACETS	0.955	0.909	1	0.955	0.909	1	CLONAL	1	TRUE	1	0.93	2		450	743	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999705	100999705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1481	120	1043	1	ENST00000325455.5:c.97G>A	p.Ala33Thr	p.A33T	ENST00000325455	NM_001202474.3	33	Gca/Aca	1/8	1	2	FACETS	0.161	0.145	0.179	0.161	0.145	0.179	SUBCLONAL	1	TRUE	1	0.93	2		1044	1601	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102080255	102080255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771314689	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	267	361	0	ENST00000282441.5:c.992G>A	p.Arg331Gln	p.R331Q	ENST00000282441	NM_001130145.2	331	cGg/cAg	6/9	1	2	FACETS	0.965	0.913	1	0.965	0.913	1	CLONAL	1	TRUE	1	0.93	2		361	595	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122732	108122732	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057524304	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	67	328	0	ENST00000278616.4:c.1776C>A	p.Ser592Arg	p.S592R	ENST00000278616	NM_000051.3	592	agC/agA	11/63	1	2	FACETS	0.366	0.319	0.416	0.366	0.319	0.416	SUBCLONAL	1	TRUE	1	0.93	2		328	394	SUCCESS
ATM	472	MSKCC	GRCh37	11	108127063	108127063	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs867443346	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	191	259	0	ENST00000278616.4:c.2246C>A	p.Ala749Asp	p.A749D	ENST00000278616	NM_000051.3	749	gCc/gAc	14/63	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.93	2		259	403	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172385	108172385	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764389018	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	163	321	0	ENST00000278616.4:c.5188C>T	p.Arg1730Ter	p.R1730*	ENST00000278616	NM_000051.3	1730	Cga/Tga	35/63	1	2	FACETS	0.963	0.897	1	0.963	0.897	1	CLONAL	1	TRUE	1	0.93	2		321	364	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175528	108175528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs376603775	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	253	356	0	ENST00000278616.4:c.5623C>T	p.Arg1875Ter	p.R1875*	ENST00000278616	NM_000051.3	1875	Cga/Tga	37/63	1	2	FACETS	0.973	0.92	1	0.973	0.92	1	CLONAL	1	TRUE	1	0.93	2		356	559	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216630	108216630	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	117	190	0	ENST00000278616.4:c.8579C>A	p.Ser2860Tyr	p.S2860Y	ENST00000278616	NM_000051.3	2860	tCt/tAt	58/63	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.93	2		190	249	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373178	118373178	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200497972	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	264	363	0	ENST00000534358.1:c.6571C>T	p.Arg2191Ter	p.R2191*	ENST00000534358	NM_005933.3	2191	Cga/Tga	27/36	1	2	FACETS	0.819	0.772	0.867	0.819	0.772	0.867	CLONAL	1	TRUE	1	0.93	2		363	693	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390417	118390417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1342425133	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	497	507	1	ENST00000534358.1:c.11231G>A	p.Arg3744Gln	p.R3744Q	ENST00000534358	NM_005933.3	3744	cGa/cAa	32/36	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.93	2		508	1069	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497584	125497584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	125	233	0	ENST00000428830.2:c.148G>A	p.Glu50Lys	p.E50K	ENST00000428830	NM_001114121.2	50	Gaa/Aaa	3/14	1	2	FACETS	0.933	0.859	1	0.933	0.859	1	CLONAL	1	TRUE	1	0.93	2		233	288	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432864	432864	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	363	421	0	ENST00000399788.2:c.2052T>G	p.Phe684Leu	p.F684L	ENST00000399788	NM_001042603.1	684	ttT/ttG	15/28	1	2	FACETS	0.956	0.911	1	0.956	0.911	1	CLONAL	1	TRUE	1	0.93	2		421	817	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524215	18524215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769408892	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	227	503	0	ENST00000266497.5:c.1727C>T	p.Ala576Val	p.A576V	ENST00000266497		576	gCg/gTg	11/31	0.146227775907956	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		503	483	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719972	18719972	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	24	279	0	ENST00000266497.5:c.3869T>C	p.Val1290Ala	p.V1290A	ENST00000266497		1290	gTa/gCa	27/31	0.146227775907956	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		279	399	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246297	46246297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770601353	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	260	301	0	ENST00000334344.6:c.4391G>A	p.Arg1464His	p.R1464H	ENST00000334344	NM_152641.2	1464	cGc/cAc	15/21	0.0792187390946091	3	FACETS	0.75	0.71	0.79	0.75	0.71	0.79	INDETERMINATE	2	TRUE	1	0.93	3		301	546	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426528	49426528	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	801	927	0	ENST00000301067.7:c.11960C>A	p.Pro3987His	p.P3987H	ENST00000301067	NM_003482.3	3987	cCt/cAt	39/54	0.0792187390946091	3	FACETS	1	0.998	1	0.744	0.721	0.767	INDETERMINATE	1	TRUE	1	0.93	3		927	1696	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444222	49444222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	797	936	0	ENST00000301067.7:c.3149C>T	p.Ser1050Phe	p.S1050F	ENST00000301067	NM_003482.3	1050	tCc/tTc	11/54	0.0792187390946091	3	FACETS	1	0.998	1	0.727	0.704	0.75	INDETERMINATE	1	TRUE	1	0.93	3		936	1727	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480117	50480117	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	358	345	0	ENST00000394963.4:c.351A>C	p.Gln117His	p.Q117H	ENST00000394963	NM_003076.4	117	caA/caC	2/13	0.0792187390946091	3	FACETS	0.787	0.751	0.822	0.787	0.751	0.822	INDETERMINATE	2	TRUE	1	0.93	3		345	717	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480121	50480121	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	293	322	0	ENST00000394963.4:c.355C>T	p.Arg119Ter	p.R119*	ENST00000394963	NM_003076.4	119	Cga/Tga	2/13	0.0792187390946091	3	FACETS	1	0.993	1	0.671	0.636	0.706	INDETERMINATE	1	TRUE	1	0.93	3		322	688	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493497	56493497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	110	370	0	ENST00000267101.3:c.2905G>A	p.Ala969Thr	p.A969T	ENST00000267101	NM_001982.3	969	Gcc/Acc	24/28	0.0792187390946091	3	FACETS	0.455	0.409	0.505	0.228	0.204	0.253	INDETERMINATE	1	TRUE	1	0.93	3		370	761	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863391	57863391	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139792497	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	603	763	1	ENST00000228682.2:c.1486C>T	p.Arg496Cys	p.R496C	ENST00000228682	NM_005269.2	496	Cgc/Tgc	11/12	1	2	FACETS	0.96	0.925	0.995	0.96	0.925	0.995	CLONAL	1	TRUE	1	0.93	2		764	1351	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145099	58145099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3211612	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	497	595	0	ENST00000257904.6:c.245G>A	p.Arg82Gln	p.R82Q	ENST00000257904	NM_000075.3	82	cGa/cAa	3/8	1	2	FACETS	0.969	0.931	1	0.969	0.931	1	CLONAL	1	TRUE	1	0.93	2		595	1103	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891184	112891184	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369155025	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	376	525	1	ENST00000351677.2:c.518G>A	p.Arg173His	p.R173H	ENST00000351677	NM_002834.3	173	cGc/cAc	4/16	1	2	FACETS	0.914	0.871	0.956	0.914	0.871	0.956	CLONAL	1	TRUE	1	0.93	2		526	885	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926915	112926915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	46	455	0	ENST00000351677.2:c.1535G>A	p.Arg512Gln	p.R512Q	ENST00000351677	NM_002834.3	512	cGa/cAa	13/16	1	2	FACETS	0.117	0.098	0.139	0.117	0.098	0.139	SUBCLONAL	1	TRUE	1	0.93	2		455	843	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112939958	112939958	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	235	290	0	ENST00000351677.2:c.1610G>T	p.Arg537Met	p.R537M	ENST00000351677	NM_002834.3	537	aGg/aTg	14/16	1	2	FACETS	0.997	0.94	1	0.997	0.94	1	CLONAL	1	TRUE	1	0.93	2		290	507	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120796847	120796847	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769968859	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1236	258	794	3	ENST00000257552.2:c.412G>A	p.Ala138Thr	p.A138T	ENST00000257552	NM_002442.3	138	Gcc/Acc	7/15	1	2	FACETS	0.371	0.347	0.397	0.371	0.347	0.397	SUBCLONAL	1	TRUE	1	0.93	2		797	1494	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123875263	123875263	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	28	97	0	ENST00000330479.4:c.219G>T	p.Glu73Asp	p.E73D	ENST00000330479	NM_020382.3	73	gaG/gaT	3/9	1	2	FACETS	0.26	0.208	0.317	0.26	0.208	0.317	SUBCLONAL	1	TRUE	1	0.93	2		97	232	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215787	133215787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762000608	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	204	631	0	ENST00000320574.5:c.5476C>T	p.Arg1826Trp	p.R1826W	ENST00000320574	NM_006231.2	1826	Cgg/Tgg	40/49	1	2	FACETS	0.372	0.345	0.401	0.372	0.345	0.401	SUBCLONAL	1	TRUE	1	0.93	2		631	1178	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	429	534	0	ENST00000320574.5:c.1231G>C	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ctg	13/49	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.93	2		534	870	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252014	133252014	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500853	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	136	742	1	ENST00000320574.5:c.1196C>T	p.Ala399Val	p.A399V	ENST00000320574	NM_006231.2	399	gCg/gTg	12/49	1	2	FACETS	0.228	0.206	0.251	0.228	0.206	0.251	SUBCLONAL	1	TRUE	1	0.93	2		743	1283	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257273	133257273	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs773435807	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	252	337	0	ENST00000320574.5:c.205A>G	p.Thr69Ala	p.T69A	ENST00000320574	NM_006231.2	69	Acc/Gcc	3/49	1	2	FACETS	0.919	0.867	0.971	0.919	0.867	0.971	CLONAL	1	TRUE	1	0.93	2		337	590	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562247	21562247	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143741195	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1490	297	960	0	ENST00000382592.4:c.1672C>T	p.Arg558Cys	p.R558C	ENST00000382592	NM_014572.2	558	Cgc/Tgc	4/8	0.3	2	FACETS	0.357	0.335	0.381			1	INDETERMINATE	1	TRUE	NA	0.93	2		960	1787	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562463	21562463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	287	348	1	ENST00000382592.4:c.1456G>A	p.Ala486Thr	p.A486T	ENST00000382592	NM_014572.2	486	Gcc/Acc	4/8	0.3	2	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.93	2		349	590	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21565498	21565498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	539	673	0	ENST00000382592.4:c.388G>A	p.Glu130Lys	p.E130K	ENST00000382592	NM_014572.2	130	Gag/Aag	3/8	0.3	2	FACETS	0.957	0.921	0.994			1	INDETERMINATE	1	TRUE	NA	0.93	2		673	1211	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877366	28877366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1392528455	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	401	465	0	ENST00000282397.4:c.3955G>A	p.Ala1319Thr	p.A1319T	ENST00000282397	NM_002019.4	1319	Gcg/Acg	30/30	0.3	1	FACETS	0.514	0.491	0.537	0.514	0.491	0.537	INDETERMINATE	1	TRUE	0	0.93	1		465	898	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964022	28964022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	207	360	0	ENST00000282397.4:c.1880C>T	p.Ser627Phe	p.S627F	ENST00000282397	NM_002019.4	627	tCc/tTc	13/30	0.3	1	FACETS	0.495	0.464	0.526	0.495	0.464	0.526	INDETERMINATE	1	TRUE	0	0.93	1		360	481	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914664	32914664	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs80358857	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	164	399	0	ENST00000380152.3:c.6172T>A	p.Phe2058Ile	p.F2058I	ENST00000380152		2058	Ttt/Att	11/27	1	2	FACETS	0.897	0.834	0.961	0.897	0.834	0.961	CLONAL	1	TRUE	1	0.93	2		399	393	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32931912	32931912	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs398122587	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	143	277	0	ENST00000380152.3:c.7651A>C	p.Lys2551Gln	p.K2551Q	ENST00000380152		2551	Aaa/Caa	16/27	1	2	FACETS	0.976	0.905	1	0.976	0.905	1	CLONAL	1	TRUE	1	0.93	2		277	315	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133802	41133802	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748924681	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	28	356	0	ENST00000379561.5:c.1826G>A	p.Arg609His	p.R609H	ENST00000379561	NM_002015.3	609	cGc/cAc	2/3	1	2	FACETS	0.114	0.09	0.14	0.114	0.09	0.14	SUBCLONAL	1	TRUE	1	0.93	2		356	530	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916769	48916769	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	147	335	0	ENST00000267163.4:c.299G>A	p.Gly100Glu	p.G100E	ENST00000267163	NM_000321.2	100	gGa/gAa	3/27	1	2	FACETS	0.911	0.844	0.979	0.911	0.844	0.979	CLONAL	1	TRUE	1	0.93	2		335	347	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030478	49030479	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1566234123	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	149	234	0	ENST00000267163.4:c.1959dup	p.Val654SerfsTer14	p.V654Sfs*14	ENST00000267163	NM_000321.2	651	-/A	19/27	1	2	FACETS	0.905	0.839	0.972	0.905	0.839	0.972	CLONAL	1	TRUE	1	0.93	2		234	354	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039374	49039374	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137853293	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	363	569	0	ENST00000267163.4:c.2359C>T	p.Arg787Ter	p.R787*	ENST00000267163	NM_000321.2	787	Cga/Tga	23/27	1	2	FACETS	0.866	0.825	0.908	0.866	0.825	0.908	CLONAL	1	TRUE	1	0.93	2		569	901	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281656	49281656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	566	671	0	ENST00000282018.3:c.703G>A	p.Glu235Lys	p.E235K	ENST00000282018	NM_020377.2	235	Gaa/Aaa	1/1	1	2	FACETS	0.97	0.934	1	0.97	0.934	1	CLONAL	1	TRUE	1	0.93	2		671	1255	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103510736	103510736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56255799	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	149	300	0	ENST00000355739.4:c.640C>T	p.Arg214Cys	p.R214C	ENST00000355739	NM_000123.3	214	Cgc/Tgc	6/15	1	2	FACETS	0.845	0.782	0.91	0.845	0.782	0.91	CLONAL	1	TRUE	1	0.93	2		300	379	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514688	103514688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	221	337	0	ENST00000355739.4:c.1189G>A	p.Asp397Asn	p.D397N	ENST00000355739	NM_000123.3	397	Gat/Aat	8/15	1	2	FACETS	0.859	0.807	0.913	0.859	0.807	0.913	CLONAL	1	TRUE	1	0.93	2		337	553	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524750	103524750	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	177	253	0	ENST00000355739.4:c.2879+2T>C		p.X960_splice	ENST00000355739	NM_000123.3	960			1	2	FACETS	0.979	0.914	1	0.979	0.914	1	CLONAL	1	TRUE	1	0.93	2		253	389	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527789	103527789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41551412	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	208	269	0	ENST00000355739.4:c.3097G>A	p.Glu1033Lys	p.E1033K	ENST00000355739	NM_000123.3	1033	Gaa/Aaa	15/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.93	2		269	430	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436204	110436204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	547	678	0	ENST00000375856.3:c.2197G>A	p.Ala733Thr	p.A733T	ENST00000375856	NM_003749.2	733	Gcc/Acc	1/2	1	2	FACETS	0.975	0.939	1	0.975	0.939	1	CLONAL	1	TRUE	1	0.93	2		678	1206	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436851	110436851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761099871	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	587	891	0	ENST00000375856.3:c.1550G>A	p.Arg517Gln	p.R517Q	ENST00000375856	NM_003749.2	517	cGa/cAa	1/2	1	2	FACETS	0.911	0.877	0.945	0.911	0.877	0.945	CLONAL	1	TRUE	1	0.93	2		891	1386	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437691	110437691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	655	850	1	ENST00000375856.3:c.710C>T	p.Ser237Leu	p.S237L	ENST00000375856	NM_003749.2	237	tCg/tTg	1/2	1	2	FACETS	0.979	0.945	1	0.979	0.945	1	CLONAL	1	TRUE	1	0.93	2		851	1439	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060863	38060863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	652	843	1	ENST00000250448.2:c.1126G>A	p.Ala376Thr	p.A376T	ENST00000250448	NM_004496.3	376	Gca/Aca	2/2	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.93	2		844	1366	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81563024	81563024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	76	326	0	ENST00000298171.2:c.587C>T	p.Ala196Val	p.A196V	ENST00000298171	NM_000369.2	196	gCt/gTt	7/10	1	2	FACETS	0.293	0.257	0.332	0.293	0.257	0.332	SUBCLONAL	1	TRUE	1	0.93	2		326	557	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574253	95574253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149242330	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	151	251	0	ENST00000393063.1:c.2614G>A	p.Ala872Thr	p.A872T	ENST00000393063	NM_030621.3	872	Gct/Act	17/28	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.93	2		251	321	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590765	95590765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886037667	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	227	299	0	ENST00000393063.1:c.1144G>A	p.Glu382Lys	p.E382K	ENST00000393063	NM_030621.3	382	Gaa/Aaa	9/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.93	2		299	451	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961363	41961363	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	340	371	0	ENST00000219905.7:c.271C>T	p.Arg91Ter	p.R91*	ENST00000219905	NM_001164273.1	91	Cga/Tga	2/24	0.3	2	FACETS	1	0.972	1			1	INDETERMINATE	1	TRUE	NA	0.93	2		371	712	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003283	42003283	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	229	507	0	ENST00000219905.7:c.2820G>T	p.Lys940Asn	p.K940N	ENST00000219905	NM_001164273.1	940	aaG/aaT	8/24	0.3	2	FACETS	0.588	0.549	0.628			1	INDETERMINATE	1	TRUE	NA	0.93	2		507	837	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052723	42052723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	139	373	0	ENST00000219905.7:c.7394C>T	p.Thr2465Ile	p.T2465I	ENST00000219905	NM_001164273.1	2465	aCt/aTt	20/24	0.3	2	FACETS	0.442	0.403	0.483			1	INDETERMINATE	1	TRUE	NA	0.93	2		373	676	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748890	43748890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201785039	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	618	634	0	ENST00000382044.4:c.1916G>A	p.Arg639Gln	p.R639Q	ENST00000382044	NM_001141980.1	639	cGa/cAa	12/28	0.3	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.93	2		634	1277	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74003508	74003508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	507	571	1	ENST00000318443.5:c.1579G>A	p.Glu527Lys	p.E527K	ENST00000318443	NM_001024736.1	527	Gaa/Aaa	9/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.93	2		572	1087	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628303	90628303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	711	939	1	ENST00000330062.3:c.1108G>A	p.Ala370Thr	p.A370T	ENST00000330062	NM_002168.2	370	Gcc/Acc	9/11	1	2	FACETS	0.961	0.929	0.993	0.961	0.929	0.993	CLONAL	1	TRUE	1	0.93	2		940	1591	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292628	91292628	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1249086421	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	64	184	0	ENST00000355112.3:c.130G>T	p.Asp44Tyr	p.D44Y	ENST00000355112	NM_000057.2	44	Gat/Tat	3/22	1	2	FACETS	0.399	0.347	0.454	0.399	0.347	0.454	SUBCLONAL	1	TRUE	1	0.93	2		184	345	SUCCESS
BLM	641	MSKCC	GRCh37	15	91352442	91352442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760554566	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	70	301	0	ENST00000355112.3:c.3827C>T	p.Ala1276Val	p.A1276V	ENST00000355112	NM_000057.2	1276	gCg/gTg	20/22	1	2	FACETS	0.266	0.232	0.303	0.266	0.232	0.303	SUBCLONAL	1	TRUE	1	0.93	2		301	566	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250962	99250962	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1455239044	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	176	566	1	ENST00000268035.6:c.266G>A	p.Arg89Gln	p.R89Q	ENST00000268035	NM_000875.3	89	cGa/cAa	2/21	1	2	FACETS	0.341	0.313	0.37	0.341	0.313	0.37	SUBCLONAL	1	TRUE	1	0.93	2		567	1110	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99491879	99491879	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	488	707	0	ENST00000268035.6:c.3664C>A	p.Leu1222Ile	p.L1222I	ENST00000268035	NM_000875.3	1222	Ctt/Att	20/21	1	2	FACETS	0.918	0.881	0.956	0.918	0.881	0.956	CLONAL	1	TRUE	1	0.93	2		707	1143	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112563	2112563	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	691	857	0	ENST00000219476.3:c.1323G>A	p.Trp441Ter	p.W441*	ENST00000219476	NM_000548.3	441	tgG/tgA	13/42	1	2	FACETS	0.983	0.95	1	0.983	0.95	1	CLONAL	1	TRUE	1	0.93	2		857	1512	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223493	2223493	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	678	834	0	ENST00000326181.6:c.1024G>A	p.Glu342Lys	p.E342K	ENST00000326181	NM_032271.2	342	Gaa/Aaa	11/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.93	2		834	1440	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642782	3642782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753926402	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	708	840	0	ENST00000294008.3:c.2245C>T	p.Arg749Cys	p.R749C	ENST00000294008	NM_032444.2	749	Cgc/Tgc	11/15	1	2	FACETS	0.986	0.954	1	0.986	0.954	1	CLONAL	1	TRUE	1	0.93	2		840	1544	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647857	3647857	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773539191	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	732	786	0	ENST00000294008.3:c.1307C>T	p.Ala436Val	p.A436V	ENST00000294008	NM_032444.2	436	gCg/gTg	6/15	1	2	FACETS	0.977	0.945	1	0.977	0.945	1	CLONAL	1	TRUE	1	0.93	2		786	1612	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647906	3647906	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	756	880	0	ENST00000294008.3:c.1258G>A	p.Asp420Asn	p.D420N	ENST00000294008	NM_032444.2	420	Gac/Aac	6/15	1	2	FACETS	0.991	0.959	1	0.991	0.959	1	CLONAL	1	TRUE	1	0.93	2		880	1641	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3827631	3827631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141098117	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	263	328	1	ENST00000262367.5:c.2141G>A	p.Arg714His	p.R714H	ENST00000262367	NM_004380.2	714	cGc/cAc	11/31	1	2	FACETS	0.894	0.844	0.944	0.894	0.844	0.944	CLONAL	1	TRUE	1	0.93	2		329	633	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842080	3842080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	221	255	0	ENST00000262367.5:c.1232C>T	p.Ser411Phe	p.S411F	ENST00000262367	NM_004380.2	411	tCt/tTt	5/31	1	2	FACETS	0.907	0.852	0.962	0.907	0.852	0.962	CLONAL	1	TRUE	1	0.93	2		255	524	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843555	3843555	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	471	486	0	ENST00000262367.5:c.1048A>C	p.Lys350Gln	p.K350Q	ENST00000262367	NM_004380.2	350	Aaa/Caa	4/31	1	2	FACETS	0.97	0.931	1	0.97	0.931	1	CLONAL	1	TRUE	1	0.93	2		486	1044	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892299	9892299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs796052549	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	225	368	0	ENST00000330684.3:c.2191G>A	p.Asp731Asn	p.D731N	ENST00000330684	NM_001134407.1	731	Gat/Aat	11/13	1	2	FACETS	0.923	0.868	0.979	0.923	0.868	0.979	CLONAL	1	TRUE	1	0.93	2		368	524	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031989	10031990	+	missense_variant	Missense_Mutation	DNP	AG	AG	GA	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	433	612	0	ENST00000330684.3:c.833_834delinsTC	p.Ser278Phe	p.S278F	ENST00000330684	NM_001134407.1	278	tCT/tTC	3/13	1	2	FACETS	0.973	0.932	1	0.973	0.932	1	CLONAL	1	TRUE	1	0.93	2		612	957	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032248	10032248	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	404	650	0	ENST00000330684.3:c.575A>G	p.Asp192Gly	p.D192G	ENST00000330684	NM_001134407.1	192	gAc/gGc	3/13	1	2	FACETS	0.951	0.909	0.993	0.951	0.909	0.993	CLONAL	1	TRUE	1	0.93	2		650	914	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274190	10274190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1478469530	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	120	522	1	ENST00000330684.3:c.79G>A	p.Ala27Thr	p.A27T	ENST00000330684	NM_001134407.1	27	Gcg/Acg	2/13	1	2	FACETS	0.314	0.283	0.346	0.314	0.283	0.346	SUBCLONAL	1	TRUE	1	0.93	2		523	823	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029387	14029387	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	101	287	0	ENST00000311895.7:c.1598A>G	p.Glu533Gly	p.E533G	ENST00000311895	NM_005236.2	533	gAa/gGa	8/11	1	2	FACETS	0.416	0.373	0.462	0.416	0.373	0.462	SUBCLONAL	1	TRUE	1	0.93	2		287	522	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041527	14041527	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs756155469	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	288	361	0	ENST00000311895.7:c.2074C>T	p.Arg692Ter	p.R692*	ENST00000311895	NM_005236.2	692	Cga/Tga	11/11	1	2	FACETS	0.884	0.836	0.931	0.884	0.836	0.931	CLONAL	1	TRUE	1	0.93	2		361	701	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133325	30133325	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	480	552	0	ENST00000263025.4:c.173C>T	p.Ser58Leu	p.S58L	ENST00000263025	NM_002746.2	58	tCg/tTg	2/9	1	2	FACETS	0.955	0.916	0.994	0.955	0.916	0.994	CLONAL	1	TRUE	1	0.93	2		552	1081	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116149	67116149	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	331	369	0	ENST00000412916.2:c.433G>T	p.Glu145Ter	p.E145*	ENST00000412916		145	Gag/Tag	5/6	1	2	FACETS	0.948	0.902	0.994	0.948	0.902	0.994	CLONAL	1	TRUE	1	0.93	2		369	751	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847306	68847306	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs187906987	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	415	512	0	ENST00000261769.5:c.1228G>A	p.Glu410Lys	p.E410K	ENST00000261769	NM_004360.3	410	Gag/Aag	9/16	1	2	FACETS	0.959	0.917	1	0.959	0.917	1	CLONAL	1	TRUE	1	0.93	2		512	931	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821437	72821437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371324694	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	145	648	1	ENST00000268489.5:c.10738G>A	p.Asp3580Asn	p.D3580N	ENST00000268489	NM_006885.3	3580	Gat/Aat	10/10	1	2	FACETS	0.246	0.224	0.27	0.246	0.224	0.27	SUBCLONAL	1	TRUE	1	0.93	2		649	1266	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822234	72822234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs988043548	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	605	739	0	ENST00000268489.5:c.9941G>A	p.Gly3314Asp	p.G3314D	ENST00000268489	NM_006885.3	3314	gGc/gAc	10/10	1	2	FACETS	0.98	0.945	1	0.98	0.945	1	CLONAL	1	TRUE	1	0.93	2		739	1328	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828084	72828084	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	579	689	1	ENST00000268489.5:c.8497G>A	p.Asp2833Asn	p.D2833N	ENST00000268489	NM_006885.3	2833	Gat/Aat	9/10	1	2	FACETS	0.985	0.949	1	0.985	0.949	1	CLONAL	1	TRUE	1	0.93	2		690	1264	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830108	72830108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479325725	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	492	584	2	ENST00000268489.5:c.6473G>A	p.Arg2158Gln	p.R2158Q	ENST00000268489	NM_006885.3	2158	cGa/cAa	9/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.93	2		586	1009	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831357	72831358	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTG	rs34918837	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	169	384	4	ENST00000268489.5:c.5221_5223dup	p.Gln1741dup	p.Q1741dup	ENST00000268489	NM_006885.3	1741	-/CAA	9/10	1	2	FACETS	0.579	0.534	0.625	0.579	0.534	0.625	SUBCLONAL	1	TRUE	1	0.93	2		388	628	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831456	72831456	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	396	553	0	ENST00000268489.5:c.5125G>T	p.Glu1709Ter	p.E1709*	ENST00000268489	NM_006885.3	1709	Gag/Tag	9/10	1	2	FACETS	0.953	0.91	0.995	0.953	0.91	0.995	CLONAL	1	TRUE	1	0.93	2		553	894	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845496	72845496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1042149925	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	473	552	0	ENST00000268489.5:c.3844G>A	p.Val1282Met	p.V1282M	ENST00000268489	NM_006885.3	1282	Gtg/Atg	7/10	1	2	FACETS	0.969	0.929	1	0.969	0.929	1	CLONAL	1	TRUE	1	0.93	2		552	1050	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923723	72923723	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	525	632	0	ENST00000268489.5:c.3355C>T	p.Arg1119Ter	p.R1119*	ENST00000268489	NM_006885.3	1119	Cga/Tga	4/10	1	2	FACETS	0.941	0.904	0.978	0.941	0.904	0.978	CLONAL	1	TRUE	1	0.93	2		632	1200	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991896	72991896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374181382	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	579	638	0	ENST00000268489.5:c.2149G>A	p.Glu717Lys	p.E717K	ENST00000268489	NM_006885.3	717	Gag/Aag	2/10	1	2	FACETS	0.999	0.963	1	0.999	0.963	1	CLONAL	1	TRUE	1	0.93	2		638	1246	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992222	72992222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	707	851	1	ENST00000268489.5:c.1823G>A	p.Ser608Asn	p.S608N	ENST00000268489	NM_006885.3	608	aGc/aAc	2/10	1	2	FACETS	0.999	0.966	1	0.999	0.966	1	CLONAL	1	TRUE	1	0.93	2		852	1522	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346918	89346918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775544970	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	352	473	0	ENST00000301030.4:c.6032C>T	p.Ser2011Leu	p.S2011L	ENST00000301030	NM_001256183.1	2011	tCg/tTg	9/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.93	2		473	746	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347980	89347980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749114664	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	636	880	3	ENST00000301030.4:c.4970C>T	p.Ser1657Leu	p.S1657L	ENST00000301030	NM_001256183.1	1657	tCg/tTg	9/13	1	2	FACETS	0.872	0.841	0.904	0.872	0.841	0.904	CLONAL	1	TRUE	1	0.93	2		883	1568	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348674	89348674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs963622923	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	593	693	0	ENST00000301030.4:c.4276G>A	p.Glu1426Lys	p.E1426K	ENST00000301030	NM_001256183.1	1426	Gaa/Aaa	9/13	1	2	FACETS	0.978	0.943	1	0.978	0.943	1	CLONAL	1	TRUE	1	0.93	2		693	1304	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350069	89350069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758856347	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	735	790	0	ENST00000301030.4:c.2881C>T	p.Arg961Cys	p.R961C	ENST00000301030	NM_001256183.1	961	Cgc/Tgc	9/13	1	2	FACETS	0.979	0.947	1	0.979	0.947	1	CLONAL	1	TRUE	1	0.93	2		790	1615	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350432	89350432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761259443	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	596	732	0	ENST00000301030.4:c.2518C>T	p.Arg840Trp	p.R840W	ENST00000301030	NM_001256183.1	840	Cgg/Tgg	9/13	1	2	FACETS	0.967	0.932	1	0.967	0.932	1	CLONAL	1	TRUE	1	0.93	2		732	1325	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350734	89350734	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146294483	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	138	695	0	ENST00000301030.4:c.2216C>T	p.Ser739Leu	p.S739L	ENST00000301030	NM_001256183.1	739	tCg/tTg	9/13	1	2	FACETS	0.237	0.215	0.261	0.237	0.215	0.261	SUBCLONAL	1	TRUE	1	0.93	2		695	1252	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89811407	89811407	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1390620949	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	803	926	0	ENST00000389301.3:c.3586G>T	p.Glu1196Ter	p.E1196*	ENST00000389301	NM_000135.2	1196	Gaa/Taa	36/43	1	2	FACETS	0.994	0.963	1	0.994	0.963	1	CLONAL	1	TRUE	1	0.93	2		926	1737	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	519	556	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.956	0.919	0.994	0.956	0.919	0.994	CLONAL	1	TRUE	1	0.93	2		556	1167	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	298	734	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	1	2	FACETS	0.463	0.435	0.492	0.463	0.435	0.492	SUBCLONAL	1	TRUE	1	0.93	2		734	1385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	770	942	1	ENST00000269305.4:c.388C>A	p.Leu130Ile	p.L130I	ENST00000269305	NM_001126112.2	130	Ctc/Atc	5/11	1	2	FACETS	0.978	0.947	1	0.978	0.947	1	CLONAL	1	TRUE	1	0.93	2		943	1693	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781371	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1467	67	786	0	ENST00000269305.4:c.328C>T	p.Arg110Cys	p.R110C	ENST00000269305	NM_001126112.2	110	Cgt/Tgt	4/11	1	2	FACETS	0.094	0.081	0.108	0.094	0.081	0.108	SUBCLONAL	1	TRUE	1	0.93	2		786	1534	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976593	7976593	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1333287390	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	623	728	0	ENST00000319144.4:c.1799G>A	p.Arg600Gln	p.R600Q	ENST00000319144	NM_001139.2	600	cGg/cAg	14/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.93	2		728	1326	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979527	7979527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064796312	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	521	571	1	ENST00000319144.4:c.1498G>A	p.Asp500Asn	p.D500N	ENST00000319144	NM_001139.2	500	Gat/Aat	11/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.93	2		572	1100	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998898	11998898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	119	163	0	ENST00000353533.5:c.400C>T	p.Arg134Trp	p.R134W	ENST00000353533	NM_003010.3	134	Cgg/Tgg	4/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.93	2		163	252	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016549	12016549	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	160	214	0	ENST00000353533.5:c.686-1G>T		p.X229_splice	ENST00000353533	NM_003010.3	229			1	2	FACETS	0.945	0.879	1	0.945	0.879	1	CLONAL	1	TRUE	1	0.93	2		214	364	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968255	15968255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	65	294	0	ENST00000268712.3:c.5030G>T	p.Arg1677Ile	p.R1677I	ENST00000268712	NM_006311.3	1677	aGa/aTa	34/46	1	2	FACETS	0.335	0.291	0.382	0.335	0.291	0.382	SUBCLONAL	1	TRUE	1	0.93	2		294	417	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15978896	15978896	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	375	490	0	ENST00000268712.3:c.3622G>T	p.Gly1208Cys	p.G1208C	ENST00000268712	NM_006311.3	1208	Ggc/Tgc	27/46	1	2	FACETS	0.92	0.877	0.963	0.92	0.877	0.963	CLONAL	1	TRUE	1	0.93	2		490	877	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989721	15989721	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	256	319	0	ENST00000268712.3:c.3052C>A	p.Leu1018Ile	p.L1018I	ENST00000268712	NM_006311.3	1018	Ctc/Atc	23/46	1	2	FACETS	0.901	0.85	0.952	0.901	0.85	0.952	CLONAL	1	TRUE	1	0.93	2		319	611	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024540	16024540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	417	510	0	ENST00000268712.3:c.1678G>A	p.Glu560Lys	p.E560K	ENST00000268712	NM_006311.3	560	Gaa/Aaa	16/46	1	2	FACETS	0.974	0.932	1	0.974	0.932	1	CLONAL	1	TRUE	1	0.93	2		510	921	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650878	37650878	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	429	507	0	ENST00000447079.4:c.2350C>T	p.Arg784Ter	p.R784*	ENST00000447079	NM_015083.1	784	Cga/Tga	5/14	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.93	2		507	905	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676267	37676267	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	451	521	0	ENST00000447079.4:c.3022C>T	p.Arg1008Trp	p.R1008W	ENST00000447079	NM_015083.1	1008	Cgg/Tgg	11/14	1	2	FACETS	0.968	0.928	1	0.968	0.928	1	CLONAL	1	TRUE	1	0.93	2		521	1002	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353760	40353760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748370281	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	260	606	2	ENST00000293328.3:c.2360C>T	p.Ser787Leu	p.S787L	ENST00000293328	NM_012448.3	787	tCg/tTg	19/19	1	2	FACETS	0.439	0.41	0.468	0.439	0.41	0.468	SUBCLONAL	1	TRUE	1	0.93	2		608	1274	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40368090	40368090	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	550	550	0	ENST00000293328.3:c.1415G>A	p.Gly472Asp	p.G472D	ENST00000293328	NM_012448.3	472	gGc/gAc	12/19	1	2	FACETS	0.983	0.946	1	0.983	0.946	1	CLONAL	1	TRUE	1	0.93	2		550	1203	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40376808	40376808	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	181	521	0	ENST00000293328.3:c.364G>T	p.Glu122Ter	p.E122*	ENST00000293328	NM_012448.3	122	Gaa/Taa	4/19	1	2	FACETS	0.371	0.342	0.402	0.371	0.342	0.402	SUBCLONAL	1	TRUE	1	0.93	2		521	1049	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226387	41226387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28897691	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	414	535	0	ENST00000357654.3:c.4636G>A	p.Asp1546Asn	p.D1546N	ENST00000357654	NM_007294.3	1546	Gat/Aat	14/23	1	2	FACETS	0.95	0.909	0.992	0.95	0.909	0.992	CLONAL	1	TRUE	1	0.93	2		535	937	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772505	56772505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	316	468	2	ENST00000337432.4:c.359C>T	p.Thr120Ile	p.T120I	ENST00000337432	NM_058216.2	120	aCa/aTa	2/9	1	2	FACETS	0.946	0.899	0.994	0.946	0.899	0.994	CLONAL	1	TRUE	1	0.93	2		470	718	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56801452	56801452	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367846829	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	168	324	0	ENST00000337432.4:c.956G>A	p.Arg319Gln	p.R319Q	ENST00000337432	NM_058216.2	319	cGa/cAa	7/9	1	2	FACETS	0.852	0.792	0.913	0.852	0.792	0.913	CLONAL	1	TRUE	1	0.93	2		324	424	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007527	62007527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	627	757	0	ENST00000392795.3:c.340C>T	p.Arg114Trp	p.R114W	ENST00000392795	NM_001039933.1	114	Cgg/Tgg	3/6	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.93	2		757	1345	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545699	63545699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773351166	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	45	528	1	ENST00000307078.5:c.895G>A	p.Asp299Asn	p.D299N	ENST00000307078	NM_004655.3	299	Gac/Aac	3/11	1	2	FACETS	0.115	0.096	0.136	0.115	0.096	0.136	SUBCLONAL	1	TRUE	1	0.93	2		529	841	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66522024	66522024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	177	204	0	ENST00000358598.2:c.679G>A	p.Asp227Asn	p.D227N	ENST00000358598	NM_212471.2	227	Gac/Aac	7/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.93	2		204	353	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775165	73775165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1341	159	738	0	ENST00000254810.4:c.91C>T	p.Pro31Ser	p.P31S	ENST00000254810	NM_005324.3	31	Ccc/Tcc	2/4	1	2	FACETS	0.228	0.208	0.249	0.228	0.208	0.249	SUBCLONAL	1	TRUE	1	0.93	2		738	1500	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78599548	78599548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	399	492	0	ENST00000306801.3:c.220G>A	p.Asp74Asn	p.D74N	ENST00000306801	NM_020761.2	74	Gat/Aat	2/34	1	2	FACETS	0.892	0.851	0.933	0.892	0.851	0.933	CLONAL	1	TRUE	1	0.93	2		492	962	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681707	78681707	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	469	584	0	ENST00000306801.3:c.415C>T	p.Arg139Cys	p.R139C	ENST00000306801	NM_020761.2	139	Cgc/Tgc	4/34	1	2	FACETS	0.959	0.92	0.998	0.959	0.92	0.998	CLONAL	1	TRUE	1	0.93	2		584	1052	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796945	78796945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	397	556	1	ENST00000306801.3:c.1058C>T	p.Ala353Val	p.A353V	ENST00000306801	NM_020761.2	353	gCg/gTg	9/34	1	2	FACETS	0.94	0.898	0.983	0.94	0.898	0.983	CLONAL	1	TRUE	1	0.93	2		557	908	SUCCESS
YES1	7525	MSKCC	GRCh37	18	751726	751726	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1010928891	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	190	324	0	ENST00000314574.4:c.350G>T	p.Arg117Ile	p.R117I	ENST00000314574	NM_005433.3	117	aGa/aTa	3/12	1	2	FACETS	0.808	0.753	0.863	0.808	0.753	0.863	CLONAL	1	TRUE	1	0.93	2		324	506	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609317	39609317	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	182	230	0	ENST00000262039.4:c.1619C>A	p.Ser540Tyr	p.S540Y	ENST00000262039	NM_002647.2	540	tCt/tAt	15/25	1	2	FACETS	0.868	0.809	0.927	0.868	0.809	0.927	CLONAL	1	TRUE	1	0.93	2		230	451	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45396936	45396936	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	161	283	0	ENST00000262160.6:c.237-1G>A		p.X79_splice	ENST00000262160	NM_005901.5	79			1	2	FACETS	0.949	0.883	1	0.949	0.883	1	CLONAL	1	TRUE	1	0.93	2		283	365	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422958	45422958	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	76	321	0	ENST00000262160.6:c.170G>A	p.Arg57Gln	p.R57Q	ENST00000262160	NM_005901.5	57	cGa/cAa	2/11	1	2	FACETS	0.272	0.239	0.309	0.272	0.239	0.309	SUBCLONAL	1	TRUE	1	0.93	2		321	600	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56401614	56401614	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs888212988	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	26	300	2	ENST00000348428.3:c.1475+1G>A		p.X492_splice	ENST00000348428	NM_006785.3	492			1	2	FACETS	0.109	0.086	0.136	0.109	0.086	0.136	SUBCLONAL	1	TRUE	1	0.93	2		302	514	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414715	56414715	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs751472121	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	323	507	0	ENST00000348428.3:c.2116A>C	p.Asn706His	p.N706H	ENST00000348428	NM_006785.3	706	Aat/Cat	17/17	1	2	FACETS	0.949	0.902	0.996	0.949	0.902	0.996	CLONAL	1	TRUE	1	0.93	2		507	732	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615791	1615791	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs562975911	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	563	799	3	ENST00000344749.5:c.1480G>A	p.Ala494Thr	p.A494T	ENST00000344749	NM_001136139.2	494	Gcc/Acc	17/19	1	2	FACETS	0.983	0.946	1	0.983	0.946	1	CLONAL	1	TRUE	1	0.93	2		802	1232	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2202775	2202775	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	518	605	0	ENST00000398665.3:c.784G>T	p.Glu262Ter	p.E262*	ENST00000398665	NM_032482.2	262	Gaa/Taa	9/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.93	2		605	1084	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213597	2213597	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	592	830	1	ENST00000398665.3:c.1617G>T	p.Gln539His	p.Q539H	ENST00000398665	NM_032482.2	539	caG/caT	17/28	1	2	FACETS	0.931	0.896	0.965	0.931	0.896	0.965	CLONAL	1	TRUE	1	0.93	2		831	1368	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216455	2216455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754139005	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1444	96	879	0	ENST00000398665.3:c.2099C>T	p.Ser700Leu	p.S700L	ENST00000398665	NM_032482.2	700	tCg/tTg	20/28	1	2	FACETS	0.134	0.119	0.151	0.134	0.119	0.151	SUBCLONAL	1	TRUE	1	0.93	2		879	1540	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226268	2226268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs927525441	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1511	349	1095	1	ENST00000398665.3:c.3748G>A	p.Asp1250Asn	p.D1250N	ENST00000398665	NM_032482.2	1250	Gac/Aac	27/28	1	2	FACETS	0.404	0.38	0.427	0.404	0.38	0.427	SUBCLONAL	1	TRUE	1	0.93	2		1096	1860	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226674	2226674	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377222686	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	687	934	1	ENST00000398665.3:c.4154G>A	p.Arg1385His	p.R1385H	ENST00000398665	NM_032482.2	1385	cGc/cAc	27/28	1	2	FACETS	0.949	0.917	0.981	0.949	0.917	0.981	CLONAL	1	TRUE	1	0.93	2		935	1557	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3113442	3113442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778757346	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	595	692	4	ENST00000078429.4:c.436G>A	p.Asp146Asn	p.D146N	ENST00000078429	NM_002067.2	146	Gac/Aac	3/7	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.93	2		696	1262	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5206839	5206839	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	492	702	0	ENST00000357368.4:c.5793C>A	p.Phe1931Leu	p.F1931L	ENST00000357368	NM_002850.3	1931	ttC/ttA	38/38	1	2	FACETS	0.946	0.908	0.985	0.946	0.908	0.985	CLONAL	1	TRUE	1	0.93	2		702	1118	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208335	5208335	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148478353	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	599	727	1	ENST00000357368.4:c.5555C>T	p.Ser1852Leu	p.S1852L	ENST00000357368	NM_002850.3	1852	tCg/tTg	36/38	1	2	FACETS	0.963	0.928	0.998	0.963	0.928	0.998	CLONAL	1	TRUE	1	0.93	2		728	1338	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210506	5210506	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	180	621	1	ENST00000357368.4:c.5461C>T	p.Arg1821Ter	p.R1821*	ENST00000357368	NM_002850.3	1821	Cga/Tga	35/38	1	2	FACETS	0.375	0.345	0.406	0.375	0.345	0.406	SUBCLONAL	1	TRUE	1	0.93	2		622	1033	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172315	7172315	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	299	371	0	ENST00000302850.5:c.1254G>T	p.Glu418Asp	p.E418D	ENST00000302850	NM_000208.2	418	gaG/gaT	5/22	1	2	FACETS	0.894	0.848	0.942	0.894	0.848	0.942	CLONAL	1	TRUE	1	0.93	2		371	719	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267389	7267389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767658477	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	126	454	0	ENST00000302850.5:c.619G>A	p.Glu207Lys	p.E207K	ENST00000302850	NM_000208.2	207	Gaa/Aaa	2/22	1	2	FACETS	0.334	0.302	0.367	0.334	0.302	0.367	SUBCLONAL	1	TRUE	1	0.93	2		454	812	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602425	10602425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746815974	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	877	1008	1	ENST00000171111.5:c.1153G>A	p.Asp385Asn	p.D385N	ENST00000171111	NM_203500.1	385	Gac/Aac	3/6	1	2	FACETS	0.998	0.968	1	0.998	0.968	1	CLONAL	1	TRUE	1	0.93	2		1009	1890	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602796	10602796	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	849	886	0	ENST00000171111.5:c.782G>A	p.Arg261Gln	p.R261Q	ENST00000171111	NM_203500.1	261	cGg/cAg	3/6	1	2	FACETS	0.997	0.967	1	0.997	0.967	1	CLONAL	1	TRUE	1	0.93	2		886	1831	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610292	10610292	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201447398	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1451	333	873	3	ENST00000171111.5:c.418G>A	p.Ala140Thr	p.A140T	ENST00000171111	NM_203500.1	140	Gcc/Acc	2/6	1	2	FACETS	0.401	0.378	0.426	0.401	0.378	0.426	SUBCLONAL	1	TRUE	1	0.93	2		876	1784	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11018786	11018786	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762459878	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	855	854	2	ENST00000327064.4:c.418C>T	p.Arg140Trp	p.R140W	ENST00000327064	NM_199141.1	140	Cgg/Tgg	3/16	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.93	2		856	1737	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136115	11136115	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	195	649	0	ENST00000358026.2:c.3099G>T	p.Lys1033Asn	p.K1033N	ENST00000358026	NM_001128849.1	1033	aaG/aaT	22/36	1	2	FACETS	0.338	0.312	0.365	0.338	0.312	0.365	SUBCLONAL	1	TRUE	1	0.93	2		649	1241	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152118	11152118	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	483	558	1	ENST00000358026.2:c.4402G>T	p.Glu1468Ter	p.E1468*	ENST00000358026	NM_001128849.1	1468	Gag/Tag	31/36	1	2	FACETS	0.987	0.948	1	0.987	0.948	1	CLONAL	1	TRUE	1	0.93	2		559	1052	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050870	13050870	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	285	379	0	ENST00000316448.5:c.401C>T	p.Pro134Leu	p.P134L	ENST00000316448	NM_004343.3	134	cCc/cTc	4/9	1	2	FACETS	0.919	0.87	0.968	0.919	0.87	0.968	CLONAL	1	TRUE	1	0.93	2		379	667	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302801	15302801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756520455	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	729	903	2	ENST00000263388.2:c.649G>A	p.Asp217Asn	p.D217N	ENST00000263388	NM_000435.2	217	Gac/Aac	4/33	1	2	FACETS	0.977	0.945	1	0.977	0.945	1	CLONAL	1	TRUE	1	0.93	2		905	1604	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30311638	30311638	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	58	307	1	ENST00000262643.3:c.492G>T	p.Glu164Asp	p.E164D	ENST00000262643	NM_001238.2	164	gaG/gaT	7/12	1	2	FACETS	0.217	0.186	0.251	0.217	0.186	0.251	SUBCLONAL	1	TRUE	1	0.93	2		308	574	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314574	30314574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	425	602	0	ENST00000262643.3:c.1123G>A	p.Ala375Thr	p.A375T	ENST00000262643	NM_001238.2	375	Gca/Aca	12/12	1	2	FACETS	0.93	0.889	0.97	0.93	0.889	0.97	CLONAL	1	TRUE	1	0.93	2		602	983	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212371	36212371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753909605	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	732	869	1	ENST00000222270.7:c.2122G>A	p.Ala708Thr	p.A708T	ENST00000222270	NM_014727.1	708	Gcc/Acc	3/37	1	2	FACETS	0.994	0.962	1	0.994	0.962	1	CLONAL	1	TRUE	1	0.93	2		870	1584	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228564	36228564	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	673	732	0	ENST00000222270.7:c.7578C>A	p.Phe2526Leu	p.F2526L	ENST00000222270	NM_014727.1	2526	ttC/ttA	34/37	1	2	FACETS	0.971	0.938	1	0.971	0.938	1	CLONAL	1	TRUE	1	0.93	2		732	1490	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744405	41744405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	629	860	1	ENST00000301178.4:c.1025C>T	p.Ala342Val	p.A342V	ENST00000301178	NM_021913.4	342	gCt/gTt	8/20	1	2	FACETS	0.977	0.943	1	0.977	0.943	1	CLONAL	1	TRUE	1	0.93	2		861	1384	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754460	41754460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374709166	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	587	749	1	ENST00000301178.4:c.1579C>T	p.Arg527Trp	p.R527W	ENST00000301178	NM_021913.4	527	Cgg/Tgg	13/20	1	2	FACETS	0.943	0.908	0.978	0.943	0.908	0.978	CLONAL	1	TRUE	1	0.93	2		750	1339	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765694	41765694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61737385	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	543	661	0	ENST00000301178.4:c.2570C>T	p.Ala857Val	p.A857V	ENST00000301178	NM_021913.4	857	gCg/gTg	20/20	1	2	FACETS	0.962	0.925	0.999	0.962	0.925	0.999	CLONAL	1	TRUE	1	0.93	2		661	1214	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867304	45867304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1372639983	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1476	290	978	1	ENST00000391945.4:c.889G>A	p.Ala297Thr	p.A297T	ENST00000391945	NM_000400.3	297	Gcc/Acc	10/23	1	2	FACETS	0.353	0.331	0.376	0.353	0.331	0.376	SUBCLONAL	1	TRUE	1	0.93	2		979	1766	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867575	45867575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777291413	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1546	173	1024	0	ENST00000391945.4:c.733G>A	p.Asp245Asn	p.D245N	ENST00000391945	NM_000400.3	245	Gac/Aac	9/23	1	2	FACETS	0.216	0.198	0.236	0.216	0.198	0.236	SUBCLONAL	1	TRUE	1	0.93	2		1024	1719	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714555	52714555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	590	742	0	ENST00000322088.6:c.313C>T	p.Arg105Trp	p.R105W	ENST00000322088	NM_014225.5	105	Cgg/Tgg	4/15	0.3	2	FACETS	0.969	0.934	1			1	INDETERMINATE	1	TRUE	NA	0.93	2		742	1309	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015001	27015001	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs141275453	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	300	308	0	ENST00000335756.4:c.103G>A	p.Ala35Thr	p.A35T	ENST00000335756	NM_001809.3	35	Gct/Act	2/5	1	2	FACETS	0.988	0.938	1	0.988	0.938	1	CLONAL	1	TRUE	1	0.93	2		308	653	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432704	29432704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774360880	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	88	593	0	ENST00000389048.3:c.3784C>T	p.Pro1262Ser	p.P1262S	ENST00000389048	NM_004304.4	1262	Cct/Tct	25/29	1	2	FACETS	0.199	0.176	0.224	0.199	0.176	0.224	SUBCLONAL	1	TRUE	1	0.93	2		593	951	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445257	29445257	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	167	641	0	ENST00000389048.3:c.3468C>A	p.Cys1156Ter	p.C1156*	ENST00000389048	NM_004304.4	1156	tgC/tgA	22/29	1	2	FACETS	0.342	0.314	0.372	0.342	0.314	0.372	SUBCLONAL	1	TRUE	1	0.93	2		641	1049	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39214639	39214639	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1022820895	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	64	454	0	ENST00000402219.2:c.3485C>T	p.Ala1162Val	p.A1162V	ENST00000402219	NM_005633.3	1162	gCc/gTc	22/23	1	2	FACETS	0.157	0.135	0.181	0.157	0.135	0.181	SUBCLONAL	1	TRUE	1	0.93	2		454	876	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39240688	39240688	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	51	328	1	ENST00000402219.2:c.2080C>T	p.Arg694Trp	p.R694W	ENST00000402219	NM_005633.3	694	Cgg/Tgg	13/23	1	2	FACETS	0.301	0.257	0.35	0.301	0.257	0.35	SUBCLONAL	1	TRUE	1	0.93	2		329	364	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46583923	46583923	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	331	360	0	ENST00000263734.3:c.430C>A	p.Arg144Ser	p.R144S	ENST00000263734	NM_001430.4	144	Cgt/Agt	4/16	1	2	FACETS	0.986	0.939	1	0.986	0.939	1	CLONAL	1	TRUE	1	0.93	2		360	722	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657021	47657021	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146567853	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	214	289	0	ENST00000233146.2:c.1217G>A	p.Arg406Gln	p.R406Q	ENST00000233146	NM_000251.2	406	cGa/cAa	7/16	1	2	FACETS	0.99	0.931	1	0.99	0.931	1	CLONAL	1	TRUE	1	0.93	2		289	465	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702340	47702340	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	204	315	0	ENST00000233146.2:c.1936G>T	p.Asp646Tyr	p.D646Y	ENST00000233146	NM_000251.2	646	Gat/Tat	12/16	1	2	FACETS	0.906	0.849	0.964	0.906	0.849	0.964	CLONAL	1	TRUE	1	0.93	2		315	484	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48025824	48025824	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	88	205	0	ENST00000234420.5:c.702G>T	p.Lys234Asn	p.K234N	ENST00000234420	NM_000179.2	234	aaG/aaT	4/10	1	2	FACETS	0.538	0.48	0.598	0.538	0.48	0.598	SUBCLONAL	1	TRUE	1	0.93	2		205	352	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026606	48026606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1358771617	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	249	323	0	ENST00000234420.5:c.1484G>A	p.Arg495Gln	p.R495Q	ENST00000234420	NM_000179.2	495	cGa/cAa	4/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.93	2		323	531	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033753	48033753	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1553333707	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	140	256	0	ENST00000234420.5:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000234420	NM_000179.2	1322	Gaa/Taa	9/10	1	2	FACETS	0.968	0.897	1	0.968	0.897	1	CLONAL	1	TRUE	1	0.93	2		256	311	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99189293	99189293	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766300586	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	360	421	0	ENST00000074304.5:c.2549G>A	p.Arg850His	p.R850H	ENST00000074304	NM_001134224.1	850	cGc/cAc	24/26	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.93	2		421	763	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99203982	99203982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1476692844	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	204	329	0	ENST00000074304.5:c.2845C>T	p.Arg949Cys	p.R949C	ENST00000074304	NM_001134224.1	949	Cgc/Tgc	26/26	1	2	FACETS	0.862	0.807	0.918	0.862	0.807	0.918	CLONAL	1	TRUE	1	0.93	2		329	509	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038195	128038195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	336	443	0	ENST00000285398.2:c.1355G>A	p.Arg452Gln	p.R452Q	ENST00000285398	NM_000122.1	452	cGa/cAa	9/15	1	2	FACETS	0.979	0.932	1	0.979	0.932	1	CLONAL	1	TRUE	1	0.93	2		443	738	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873098	136873098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	314	392	0	ENST00000241393.3:c.400C>T	p.Arg134Cys	p.R134C	ENST00000241393	NM_003467.2	134	Cgc/Tgc	2/2	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.93	2		392	673	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873483	136873483	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	200	275	0	ENST00000241393.3:c.16-1G>A		p.X6_splice	ENST00000241393	NM_003467.2	6			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.93	2		275	406	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622495	158622495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316254232	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	275	413	0	ENST00000263640.3:c.1004G>A	p.Arg335Gln	p.R335Q	ENST00000263640	NM_001105.4	335	cGa/cAa	8/11	1	2	FACETS	0.939	0.888	0.989	0.939	0.888	0.989	CLONAL	1	TRUE	1	0.93	2		413	630	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190670436	190670436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780386003	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	74	350	1	ENST00000441310.2:c.374G>A	p.Gly125Asp	p.G125D	ENST00000441310	NM_000534.4	125	gGc/gAc	4/13	1	2	FACETS	0.374	0.329	0.423	0.374	0.329	0.423	SUBCLONAL	1	TRUE	1	0.93	2		351	425	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265106	198265106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1559265118	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	308	342	1	ENST00000335508.6:c.2771G>A	p.Arg924Gln	p.R924Q	ENST00000335508	NM_012433.2	924	cGa/cAa	19/25	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.93	2		343	640	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273249	198273249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	393	467	0	ENST00000335508.6:c.961G>A	p.Asp321Asn	p.D321N	ENST00000335508	NM_012433.2	321	Gat/Aat	8/25	1	2	FACETS	0.982	0.938	1	0.982	0.938	1	CLONAL	1	TRUE	1	0.93	2		467	861	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131301	202131301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748087575	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	272	380	0	ENST00000358485.4:c.269C>T	p.Pro90Leu	p.P90L	ENST00000358485	NM_001080125.1	90	cCg/cTg	2/9	1	2	FACETS	0.928	0.878	0.979	0.928	0.878	0.979	CLONAL	1	TRUE	1	0.93	2		380	630	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	184	162	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.914	0.854	0.975	0.914	0.854	0.975	CLONAL	1	TRUE	1	0.93	2		162	433	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288934	212288934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	46	362	0	ENST00000342788.4:c.2812C>T	p.Arg938Cys	p.R938C	ENST00000342788	NM_005235.2	938	Cgt/Tgt	23/28	1	2	FACETS	0.213	0.179	0.251	0.213	0.179	0.251	SUBCLONAL	1	TRUE	1	0.93	2		362	464	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812236	212812236	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	179	237	0	ENST00000342788.4:c.340C>T	p.Arg114Ter	p.R114*	ENST00000342788	NM_005235.2	114	Cga/Tga	3/28	1	2	FACETS	0.914	0.853	0.976	0.914	0.853	0.976	CLONAL	1	TRUE	1	0.93	2		237	421	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368379	225368379	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	186	270	0	ENST00000264414.4:c.1367C>A	p.Ser456Tyr	p.S456Y	ENST00000264414	NM_003590.4	456	tCt/tAt	9/16	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.93	2		270	396	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370789	225370789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765785569	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	228	343	0	ENST00000264414.4:c.1090C>T	p.Arg364Cys	p.R364C	ENST00000264414	NM_003590.4	364	Cgt/Tgt	8/16	1	2	FACETS	0.969	0.913	1	0.969	0.913	1	CLONAL	1	TRUE	1	0.93	2		343	506	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378351	225378351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	126	166	2	ENST00000264414.4:c.544G>A	p.Ala182Thr	p.A182T	ENST00000264414	NM_003590.4	182	Gca/Aca	5/16	1	2	FACETS	0.857	0.788	0.928	0.857	0.788	0.928	CLONAL	1	TRUE	1	0.93	2		168	316	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660408	227660408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747700323	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	438	695	0	ENST00000305123.5:c.3047G>A	p.Arg1016Gln	p.R1016Q	ENST00000305123	NM_005544.2	1016	cGa/cAa	1/2	1	2	FACETS	0.968	0.927	1	0.968	0.927	1	CLONAL	1	TRUE	1	0.93	2		695	973	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662433	227662433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751685762	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	567	758	0	ENST00000305123.5:c.1022C>T	p.Ser341Leu	p.S341L	ENST00000305123	NM_005544.2	341	tCg/tTg	1/2	1	2	FACETS	0.99	0.953	1	0.99	0.953	1	CLONAL	1	TRUE	1	0.93	2		758	1232	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663328	227663328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	522	591	1	ENST00000305123.5:c.127C>T	p.Arg43Cys	p.R43C	ENST00000305123	NM_005544.2	43	Cgc/Tgc	1/2	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.93	2		592	1121	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795004	242795004	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751637749	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1529	133	1334	3	ENST00000334409.5:c.205C>T	p.Arg69Cys	p.R69C	ENST00000334409	NM_005018.2	69	Cgc/Tgc	2/5	1	2	FACETS	0.172	0.155	0.19	0.172	0.155	0.19	SUBCLONAL	1	TRUE	1	0.93	2		1337	1662	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024390	31024390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	482	788	1	ENST00000375687.4:c.3875G>A	p.Gly1292Asp	p.G1292D	ENST00000375687	NM_015338.5	1292	gGt/gAt	13/13	1	2	FACETS	0.947	0.909	0.986	0.947	0.909	0.986	CLONAL	1	TRUE	1	0.93	2		789	1094	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730916	40730916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765075213	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	461	570	2	ENST00000373198.4:c.3619C>T	p.Arg1207Cys	p.R1207C	ENST00000373198	NM_133170.3	1207	Cgt/Tgt	27/32	0.3	1	FACETS	0.573	0.551	0.596	0.573	0.551	0.596	INDETERMINATE	1	TRUE	0	0.93	1		572	925	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747137	40747137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752831315	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	327	378	1	ENST00000373198.4:c.2945C>T	p.Pro982Leu	p.P982L	ENST00000373198	NM_133170.3	982	cCg/cTg	22/32	0.3	1	FACETS	0.553	0.527	0.58	0.553	0.527	0.58	INDETERMINATE	1	TRUE	0	0.93	1		379	680	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306602	41306602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1419824411	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	483	661	0	ENST00000373198.4:c.1057G>A	p.Asp353Asn	p.D353N	ENST00000373198	NM_133170.3	353	Gat/Aat	7/32	0.3	1	FACETS	0.566	0.544	0.589	0.566	0.544	0.589	INDETERMINATE	1	TRUE	0	0.93	1		661	981	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264104	46264104	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	213	280	0	ENST00000371998.3:c.1151G>A	p.Gly384Glu	p.G384E	ENST00000371998		384	gGa/gAa	11/23	1	2	FACETS	0.931	0.874	0.988	0.931	0.874	0.988	CLONAL	1	TRUE	1	0.93	2		280	492	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46266401	46266401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	112	240	0	ENST00000371998.3:c.2386G>A	p.Asp796Asn	p.D796N	ENST00000371998		796	Gac/Aac	13/23	1	2	FACETS	0.842	0.769	0.916	0.842	0.769	0.916	CLONAL	1	TRUE	1	0.93	2		240	286	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268783	46268783	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746421427	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	380	497	1	ENST00000371998.3:c.3068G>A	p.Gly1023Asp	p.G1023D	ENST00000371998		1023	gGc/gAc	16/23	1	2	FACETS	0.912	0.87	0.955	0.912	0.87	0.955	CLONAL	1	TRUE	1	0.93	2		498	896	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46271069	46271069	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	77	387	1	ENST00000371998.3:c.3193G>A	p.Asp1065Asn	p.D1065N	ENST00000371998		1065	Gat/Aat	17/23	1	2	FACETS	0.231	0.203	0.262	0.231	0.203	0.262	SUBCLONAL	1	TRUE	1	0.93	2		388	716	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62297363	62297363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	408	459	0	ENST00000360203.5:c.545G>A	p.Ser182Asn	p.S182N	ENST00000360203	NM_001283009.1	182	aGc/aAc	7/35	1	2	FACETS	0.985	0.942	1	0.985	0.942	1	CLONAL	1	TRUE	1	0.93	2		459	891	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326726	62326726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770535334	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	849	1005	0	ENST00000360203.5:c.3545C>T	p.Ser1182Leu	p.S1182L	ENST00000360203	NM_001283009.1	1182	tCg/tTg	34/35	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.93	2		1005	1794	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035126	30035126	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	310	424	0	ENST00000338641.4:c.288C>A	p.Phe96Leu	p.F96L	ENST00000338641	NM_000268.3	96	ttC/ttA	3/16	1	2	FACETS	0.942	0.894	0.989	0.942	0.894	0.989	CLONAL	1	TRUE	1	0.93	2		424	708	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051605	30051605	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	208	316	0	ENST00000338641.4:c.539C>A	p.Thr180Asn	p.T180N	ENST00000338641	NM_000268.3	180	aCt/aAt	6/16	1	2	FACETS	0.828	0.775	0.882	0.828	0.775	0.882	CLONAL	1	TRUE	1	0.93	2		316	540	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125437	47125437	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	270	360	0	ENST00000409792.3:c.5833G>T	p.Glu1945Ter	p.E1945*	ENST00000409792	NM_014159.6	1945	Gaa/Taa	12/21	1	2	FACETS	0.957	0.905	1	0.957	0.905	1	CLONAL	1	TRUE	1	0.93	2		360	607	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436312	52436312	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	563	729	0	ENST00000460680.1:c.2182C>T	p.Arg728Cys	p.R728C	ENST00000460680	NM_004656.3	728	Cgc/Tgc	17/17	1	2	FACETS	0.994	0.957	1	0.994	0.957	1	CLONAL	1	TRUE	1	0.93	2		729	1218	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643668	52643668	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	337	383	0	ENST00000394830.3:c.2228C>A	p.Ser743Tyr	p.S743Y	ENST00000394830	NM_018313.4	743	tCt/tAt	17/30	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.93	2		383	715	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651334	52651334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1394528754	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	328	413	0	ENST00000394830.3:c.1762G>A	p.Glu588Lys	p.E588K	ENST00000394830	NM_018313.4	588	Gaa/Aaa	15/30	1	2	FACETS	0.955	0.908	1	0.955	0.908	1	CLONAL	1	TRUE	1	0.93	2		413	739	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651496	52651496	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	334	405	1	ENST00000394830.3:c.1600C>T	p.Arg534Ter	p.R534*	ENST00000394830	NM_018313.4	534	Cga/Tga	15/30	1	2	FACETS	0.98	0.933	1	0.98	0.933	1	CLONAL	1	TRUE	1	0.93	2		406	733	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678727	52678727	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	247	319	0	ENST00000394830.3:c.892C>T	p.Arg298Ter	p.R298*	ENST00000394830	NM_018313.4	298	Cga/Tga	9/30	1	2	FACETS	0.961	0.907	1	0.961	0.907	1	CLONAL	1	TRUE	1	0.93	2		319	553	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990481	69990481	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs201247895	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	70	271	0	ENST00000394351.3:c.440C>T	p.Thr147Met	p.T147M	ENST00000394351	NM_000248.3	147	aCg/aTg	4/9	1	2	FACETS	0.422	0.37	0.477	0.422	0.37	0.477	SUBCLONAL	1	TRUE	1	0.93	2		271	357	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114584	73114584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	129	197	0	ENST00000356692.5:c.965G>A	p.Arg322Lys	p.R322K	ENST00000356692		322	aGa/aAa	9/9	1	2	FACETS	0.95	0.876	1	0.95	0.876	1	CLONAL	1	TRUE	1	0.93	2		197	292	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138383915	138383915	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	295	368	0	ENST00000289153.2:c.2635G>T	p.Asp879Tyr	p.D879Y	ENST00000289153	NM_006219.2	879	Gat/Tat	18/22	1	2	FACETS	0.926	0.878	0.975	0.926	0.878	0.975	CLONAL	1	TRUE	1	0.93	2		368	685	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426123	138426123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217537873	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	176	248	0	ENST00000289153.2:c.1408G>A	p.Glu470Lys	p.E470K	ENST00000289153	NM_006219.2	470	Gaa/Aaa	9/22	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.93	2		248	378	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478041	138478041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	83	332	0	ENST00000289153.2:c.145G>A	p.Glu49Lys	p.E49K	ENST00000289153	NM_006219.2	49	Gaa/Aaa	1/22	1	2	FACETS	0.306	0.27	0.345	0.306	0.27	0.345	SUBCLONAL	1	TRUE	1	0.93	2		332	583	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664546	138664546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757937453	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	50	277	0	ENST00000330315.3:c.1019C>T	p.Ala340Val	p.A340V	ENST00000330315	NM_023067.3	340	gCg/gTg	1/1	1	2	FACETS	0.244	0.207	0.284	0.244	0.207	0.284	SUBCLONAL	1	TRUE	1	0.93	2		277	441	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176456	142176456	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	172	231	1	ENST00000350721.4:c.7645C>T	p.Pro2549Ser	p.P2549S	ENST00000350721	NM_001184.3	2549	Cct/Tct	45/47	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.93	2		232	357	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587145	189587145	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	230	340	0	ENST00000264731.3:c.1162A>G	p.Thr388Ala	p.T388A	ENST00000264731	NM_003722.4	388	Aca/Gca	9/14	1	2	FACETS	0.886	0.834	0.94	0.886	0.834	0.94	CLONAL	1	TRUE	1	0.93	2		340	558	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801497	1801497	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774962503	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	751	949	0	ENST00000260795.2:c.403G>A	p.Glu135Lys	p.E135K	ENST00000260795		135	Gaa/Aaa	3/17	0.3	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.93	2		949	1582	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803630	1803630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780147591	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	725	865	1	ENST00000260795.2:c.808G>A	p.Asp270Asn	p.D270N	ENST00000260795		270	Gac/Aac	6/17	0.3	2	FACETS	0.967	0.935	0.999			1	INDETERMINATE	1	TRUE	NA	0.93	2		866	1613	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808870	1808870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560280646	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	756	977	2	ENST00000260795.2:c.2302G>A	p.Glu768Lys	p.E768K	ENST00000260795		768	Gag/Aag	17/17	0.3	2	FACETS	0.963	0.932	0.994			1	INDETERMINATE	1	TRUE	NA	0.93	2		979	1688	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808942	1808942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376043260	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1478	87	882	2	ENST00000260795.2:c.2374G>A	p.Asp792Asn	p.D792N	ENST00000260795		792	Gac/Aac	17/17	0.3	2	FACETS	0.12	0.105	0.135			1	INDETERMINATE	1	TRUE	NA	0.93	2		884	1565	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902622	1902622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	556	644	0	ENST00000382891.5:c.241G>A	p.Asp81Asn	p.D81N	ENST00000382891	NM_133335.3	81	Gat/Aat	2/22	0.3	2	FACETS	0.944	0.908	0.98			1	INDETERMINATE	1	TRUE	NA	0.93	2		644	1267	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955099	1955099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	505	670	1	ENST00000382891.5:c.2186G>A	p.Arg729His	p.R729H	ENST00000382891	NM_133335.3	729	cGc/cAc	12/22	0.3	2	FACETS	0.936	0.899	0.974			1	INDETERMINATE	1	TRUE	NA	0.93	2		671	1160	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1959714	1959714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	66	270	0	ENST00000382891.5:c.2936G>A	p.Arg979Gln	p.R979Q	ENST00000382891	NM_133335.3	979	cGa/cAa	16/22	0.3	2	FACETS	0.287	0.25	0.328			1	INDETERMINATE	1	TRUE	NA	0.93	2		270	494	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748309	41748309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs894529129	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	741	834	0	ENST00000226382.2:c.460C>T	p.Arg154Cys	p.R154C	ENST00000226382	NM_003924.3	154	Cgc/Tgc	3/3	0.146227775907956	1	FACETS	0.542	0.524	0.559	0.542	0.524	0.559	INDETERMINATE	1	TRUE	0	0.93	1		834	1574	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155180	55155180	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600187	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	340	489	0	ENST00000257290.5:c.2779G>A	p.Glu927Lys	p.E927K	ENST00000257290	NM_006206.4	927	Gag/Aag	21/23	0.146227775907956	1	FACETS	0.507	0.482	0.531	0.507	0.482	0.531	INDETERMINATE	1	TRUE	0	0.93	1		489	772	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971073	55971073	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs754856383	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	324	453	0	ENST00000263923.4:c.1724G>T	p.Arg575Ile	p.R575I	ENST00000263923	NM_002253.2	575	aGa/aTa	13/30	0.146227775907956	1	FACETS	0.531	0.505	0.557	0.531	0.505	0.557	INDETERMINATE	1	TRUE	0	0.93	1		453	702	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156457	106156457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	237	283	0	ENST00000380013.4:c.1358G>A	p.Gly453Asp	p.G453D	ENST00000380013	NM_001127208.2	453	gGt/gAt	3/11	1	2	FACETS	0.93	0.876	0.984	0.93	0.876	0.984	CLONAL	1	TRUE	1	0.93	2		283	548	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193781	106193781	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	31	231	0	ENST00000380013.4:c.4243C>T	p.Leu1415Phe	p.L1415F	ENST00000380013	NM_001127208.2	1415	Ctt/Ttt	10/11	1	2	FACETS	0.126	0.101	0.153	0.126	0.101	0.153	SUBCLONAL	1	TRUE	1	0.93	2		231	531	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197025	106197025	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	175	246	0	ENST00000380013.4:c.5358G>T	p.Glu1786Asp	p.E1786D	ENST00000380013	NM_001127208.2	1786	gaG/gaT	11/11	1	2	FACETS	0.95	0.887	1	0.95	0.887	1	CLONAL	1	TRUE	1	0.93	2		246	396	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143033717	143033717	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	179	283	0	ENST00000262992.4:c.2254G>T	p.Glu752Ter	p.E752*	ENST00000262992	NM_001101669.1	752	Gaa/Taa	20/24	1	2	FACETS	0.972	0.909	1	0.972	0.909	1	CLONAL	1	TRUE	1	0.93	2		283	396	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143191833	143191833	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	297	396	0	ENST00000262992.4:c.598G>T	p.Asp200Tyr	p.D200Y	ENST00000262992	NM_001101669.1	200	Gat/Tat	8/24	1	2	FACETS	0.907	0.86	0.955	0.907	0.86	0.955	CLONAL	1	TRUE	1	0.93	2		396	704	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258998	153258998	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	109	201	0	ENST00000281708.4:c.817G>T	p.Glu273Ter	p.E273*	ENST00000281708	NM_033632.3	273	Gaa/Taa	5/12	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.93	2		201	224	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332466	153332466	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	207	268	0	ENST00000281708.4:c.490A>C	p.Lys164Gln	p.K164Q	ENST00000281708	NM_033632.3	164	Aaa/Caa	2/12	1	2	FACETS	0.892	0.836	0.949	0.892	0.836	0.949	CLONAL	1	TRUE	1	0.93	2		268	499	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535417	187535417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367986355	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	204	442	1	ENST00000441802.2:c.9157C>T	p.Arg3053Cys	p.R3053C	ENST00000441802	NM_005245.3	3053	Cgc/Tgc	12/27	1	2	FACETS	0.845	0.791	0.9	0.845	0.791	0.9	CLONAL	1	TRUE	1	0.93	2		443	519	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539951	187539951	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs777631605	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	264	321	0	ENST00000441802.2:c.7789C>T	p.Arg2597Ter	p.R2597*	ENST00000441802	NM_005245.3	2597	Cga/Tga	10/27	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.93	2		321	549	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540958	187540958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs189912205	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	228	304	1	ENST00000441802.2:c.6782C>T	p.Thr2261Met	p.T2261M	ENST00000441802	NM_005245.3	2261	aCg/aTg	10/27	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.93	2		305	485	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541765	187541765	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	273	393	1	ENST00000441802.2:c.5975C>A	p.Ser1992Tyr	p.S1992Y	ENST00000441802	NM_005245.3	1992	tCc/tAc	10/27	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.93	2		394	582	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549725	187549725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199516712	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	201	338	0	ENST00000441802.2:c.4516C>T	p.Arg1506Cys	p.R1506C	ENST00000441802	NM_005245.3	1506	Cgt/Tgt	8/27	1	2	FACETS	0.803	0.751	0.857	0.803	0.751	0.857	CLONAL	1	TRUE	1	0.93	2		338	538	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629648	187629648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528553183	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	197	538	1	ENST00000441802.2:c.1334C>T	p.Ala445Val	p.A445V	ENST00000441802	NM_005245.3	445	gCg/gTg	2/27	1	2	FACETS	0.503	0.466	0.541	0.503	0.466	0.541	SUBCLONAL	1	TRUE	1	0.93	2		539	843	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31423029	31423029	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1311212433	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	238	358	0	ENST00000344624.3:c.3284G>A	p.Arg1095Gln	p.R1095Q	ENST00000344624		1095	cGa/cAa	26/33	1	2	FACETS	0.873	0.822	0.926	0.873	0.822	0.926	CLONAL	1	TRUE	1	0.93	2		358	586	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31493364	31493364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	176	270	0	ENST00000344624.3:c.1792G>A	p.Glu598Lys	p.E598K	ENST00000344624		598	Gag/Aag	10/33	1	2	FACETS	0.787	0.731	0.844	0.787	0.731	0.844	SUBCLONAL	1	TRUE	1	0.93	2		270	481	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963006	38963006	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs547757338	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	111	212	0	ENST00000357387.3:c.1538G>A	p.Arg513Gln	p.R513Q	ENST00000357387	NM_152756.3	513	cGa/cAa	17/38	1	2	FACETS	0.929	0.851	1	0.929	0.851	1	CLONAL	1	TRUE	1	0.93	2		212	257	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178394	56178394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	51	269	1	ENST00000399503.3:c.3367G>A	p.Asp1123Asn	p.D1123N	ENST00000399503	NM_005921.1	1123	Gat/Aat	14/20	1	2	FACETS	0.282	0.24	0.328	0.282	0.24	0.328	SUBCLONAL	1	TRUE	1	0.93	2		270	389	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754240	57754240	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	79	308	0	ENST00000274289.3:c.611G>T	p.Arg204Ile	p.R204I	ENST00000274289	NM_006622.3	204	aGa/aTa	4/14	1	2	FACETS	0.361	0.319	0.407	0.361	0.319	0.407	SUBCLONAL	1	TRUE	1	0.93	2		308	470	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86637111	86637111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759265277	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	31	243	0	ENST00000274376.6:c.1022G>A	p.Arg341Gln	p.R341Q	ENST00000274376	NM_002890.2	341	cGg/cAg	6/25	1	2	FACETS	0.264	0.214	0.319	0.264	0.214	0.319	SUBCLONAL	1	TRUE	1	0.93	2		243	253	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86676375	86676375	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	95	160	0	ENST00000274376.6:c.2653T>C	p.Trp885Arg	p.W885R	ENST00000274376	NM_002890.2	885	Tgg/Cgg	20/25	1	2	FACETS	0.968	0.882	1	0.968	0.882	1	CLONAL	1	TRUE	1	0.93	2		160	211	SUCCESS
APC	324	MSKCC	GRCh37	5	112154970	112154970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881233	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	110	601	0	ENST00000257430.4:c.1241G>A	p.Arg414His	p.R414H	ENST00000257430	NM_000038.5	414	cGc/cAc	10/16	1	2	FACETS	0.216	0.193	0.24	0.216	0.193	0.24	SUBCLONAL	1	TRUE	1	0.93	2		601	1097	SUCCESS
APC	324	MSKCC	GRCh37	5	112170825	112170825	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	42	469	0	ENST00000257430.4:c.1921A>G	p.Asn641Asp	p.N641D	ENST00000257430	NM_000038.5	641	Aat/Gat	15/16	1	2	FACETS	0.115	0.095	0.137	0.115	0.095	0.137	SUBCLONAL	1	TRUE	1	0.93	2		469	786	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940521	131940521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs181961360	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	188	253	0	ENST00000265335.6:c.2548C>T	p.Arg850Cys	p.R850C	ENST00000265335		850	Cgt/Tgt	16/25	1	2	FACETS	0.981	0.919	1	0.981	0.919	1	CLONAL	1	TRUE	1	0.93	2		253	412	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131972883	131972883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs535261113	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	71	214	0	ENST00000265335.6:c.3466C>T	p.Arg1156Cys	p.R1156C	ENST00000265335		1156	Cgt/Tgt	22/25	1	2	FACETS	0.314	0.274	0.356	0.314	0.274	0.356	SUBCLONAL	1	TRUE	1	0.93	2		214	487	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631256	176631256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	239	297	0	ENST00000439151.2:c.1199G>A	p.Arg400Lys	p.R400K	ENST00000439151	NM_022455.4	400	aGa/aAa	4/23	1	2	FACETS	0.988	0.933	1	0.988	0.933	1	CLONAL	1	TRUE	1	0.93	2		297	520	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038418	180038418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530977029	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	719	900	0	ENST00000261937.6:c.3599C>T	p.Ser1200Leu	p.S1200L	ENST00000261937	NM_182925.4	1200	tCg/tTg	27/30	1	2	FACETS	0.975	0.943	1	0.975	0.943	1	CLONAL	1	TRUE	1	0.93	2		900	1586	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048655	180048655	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	643	873	0	ENST00000261937.6:c.1907T>A	p.Leu636His	p.L636H	ENST00000261937	NM_182925.4	636	cTc/cAc	13/30	1	2	FACETS	0.982	0.948	1	0.982	0.948	1	CLONAL	1	TRUE	1	0.93	2		873	1408	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401655	401655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201105575	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	414	573	0	ENST00000380956.4:c.977C>T	p.Ala326Val	p.A326V	ENST00000380956	NM_001195286.1	326	gCg/gTg	7/9	1	2	FACETS	0.952	0.911	0.994	0.952	0.911	0.994	CLONAL	1	TRUE	1	0.93	2		573	935	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401693	401693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	410	594	0	ENST00000380956.4:c.1015C>T	p.Pro339Ser	p.P339S	ENST00000380956	NM_001195286.1	339	Ccc/Tcc	7/9	1	2	FACETS	0.936	0.895	0.978	0.936	0.895	0.978	CLONAL	1	TRUE	1	0.93	2		594	942	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20486949	20486949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188266138	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	165	246	1	ENST00000346618.3:c.914G>A	p.Arg305Gln	p.R305Q	ENST00000346618	NM_001949.4	305	cGa/cAa	5/7	1	2	FACETS	0.959	0.893	1	0.959	0.893	1	CLONAL	1	TRUE	1	0.93	2		247	370	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858167	27858167	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1436434441	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	315	397	0	ENST00000359303.2:c.404G>A	p.Arg135Gln	p.R135Q	ENST00000359303	NM_003535.2	135	cGa/cAa	1/1	1	2	FACETS	0.953	0.905	1	0.953	0.905	1	CLONAL	1	TRUE	1	0.93	2		397	711	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189064	32189064	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	498	639	0	ENST00000375023.3:c.490C>T	p.Pro164Ser	p.P164S	ENST00000375023	NM_004557.3	164	Cca/Tca	4/30	1	2	FACETS	0.95	0.912	0.988	0.95	0.912	0.988	CLONAL	1	TRUE	1	0.93	2		639	1127	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798543	32798543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	585	677	0	ENST00000374899.4:c.1313G>A	p.Gly438Glu	p.G438E	ENST00000374899	NM_018833.2	438	gGa/gAa	8/12	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.93	2		677	1213	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288942	33288942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747846898	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	389	473	0	ENST00000374542.5:c.610C>T	p.Arg204Trp	p.R204W	ENST00000374542	NM_001141970.1	204	Cgg/Tgg	3/8	1	2	FACETS	0.992	0.948	1	0.992	0.948	1	CLONAL	1	TRUE	1	0.93	2		473	843	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553111	106553111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	481	585	1	ENST00000369096.4:c.1076C>T	p.Thr359Met	p.T359M	ENST00000369096	NM_001198.3	359	aCg/aTg	5/7	1	2	FACETS	0.998	0.959	1	0.998	0.959	1	CLONAL	1	TRUE	1	0.93	2		586	1036	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020771	112020771	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374907658	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	132	344	0	ENST00000368678.4:c.800C>T	p.Ser267Leu	p.S267L	ENST00000368678		267	tCg/tTg	8/13	1	2	FACETS	0.428	0.389	0.468	0.428	0.389	0.468	SUBCLONAL	1	TRUE	1	0.93	2		344	664	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527318	137527318	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	278	490	1	ENST00000367739.4:c.328G>T	p.Glu110Ter	p.E110*	ENST00000367739	NM_000416.2	110	Gaa/Taa	3/7	1	2	FACETS	0.923	0.873	0.973	0.923	0.873	0.973	CLONAL	1	TRUE	1	0.93	2		491	648	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099344	157099344	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	289	339	0	ENST00000346085.5:c.281A>G	p.His94Arg	p.H94R	ENST00000346085	NM_020732.3	94	cAc/cGc	1/20	1	2	FACETS	0.94	0.891	0.99	0.94	0.891	0.99	CLONAL	1	TRUE	1	0.93	2		339	661	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157406006	157406006	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs797045272	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	363	432	0	ENST00000346085.5:c.2248C>T	p.Arg750Ter	p.R750*	ENST00000346085	NM_020732.3	750	Cga/Tga	6/20	1	2	FACETS	0.923	0.879	0.966	0.923	0.879	0.966	CLONAL	1	TRUE	1	0.93	2		432	846	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517445	157517445	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs773740590	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	340	390	0	ENST00000346085.5:c.4009C>T	p.Arg1337Ter	p.R1337*	ENST00000346085	NM_020732.3	1337	Cga/Tga	16/20	1	2	FACETS	0.998	0.95	1	0.998	0.95	1	CLONAL	1	TRUE	1	0.93	2		390	733	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026643	6026643	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs63750947	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	799	947	1	ENST00000265849.7:c.1753C>A	p.Leu585Ile	p.L585I	ENST00000265849	NM_000535.5	585	Ctt/Att	11/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.93	2		948	1690	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441565	6441565	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	68	107	0	ENST00000356142.4:c.412C>A	p.Leu138Ile	p.L138I	ENST00000356142	NM_018890.3	138	Ctt/Att	6/7	1	2	FACETS	0.897	0.8	0.996	0.897	0.8	0.996	CLONAL	1	TRUE	1	0.93	2		107	163	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13940381	13940381	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	191	268	0	ENST00000405192.2:c.1125G>T	p.Glu375Asp	p.E375D	ENST00000405192	NM_001163147.1	375	gaG/gaT	11/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.93	2		268	391	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946170	13946170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1259444979	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	310	506	1	ENST00000405192.2:c.926G>A	p.Arg309Gln	p.R309Q	ENST00000405192	NM_001163147.1	309	cGa/cAa	10/12	1	2	FACETS	0.921	0.874	0.968	0.921	0.874	0.968	CLONAL	1	TRUE	1	0.93	2		507	724	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50358686	50358686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	136	212	0	ENST00000331340.3:c.29C>T	p.Ser10Phe	p.S10F	ENST00000331340	NM_006060.4	10	tCc/tTc	2/8	0.146227775907956	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		212	289	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92244500	92244500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	265	371	0	ENST00000265734.4:c.935C>T	p.Ser312Phe	p.S312F	ENST00000265734	NM_001259.6	312	tCc/tTc	8/8	1	2	FACETS	0.934	0.883	0.986	0.934	0.883	0.986	CLONAL	1	TRUE	1	0.93	2		371	610	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395569	116395569	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs375951814	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	207	333	0	ENST00000397752.3:c.1862C>T	p.Thr621Ile	p.T621I	ENST00000397752	NM_000245.2	621	aCa/aTa	6/21	1	2	FACETS	0.964	0.905	1	0.964	0.905	1	CLONAL	1	TRUE	1	0.93	2		333	462	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148544317	148544317	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	360	448	1	ENST00000320356.2:c.74G>A	p.Arg25Gln	p.R25Q	ENST00000320356	NM_004456.4	25	cGa/cAa	2/20	1	2	FACETS	0.935	0.891	0.979	0.935	0.891	0.979	CLONAL	1	TRUE	1	0.93	2		449	828	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841854	151841854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	62	310	1	ENST00000262189.6:c.14287C>T	p.Arg4763Trp	p.R4763W	ENST00000262189	NM_170606.2	4763	Cgg/Tgg	55/59	1	2	FACETS	0.249	0.215	0.286	0.249	0.215	0.286	SUBCLONAL	1	TRUE	1	0.93	2		311	535	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842335	151842335	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	215	274	0	ENST00000262189.6:c.14077C>T	p.Arg4693Ter	p.R4693*	ENST00000262189	NM_170606.2	4693	Cga/Tga	54/59	1	2	FACETS	0.898	0.843	0.954	0.898	0.843	0.954	CLONAL	1	TRUE	1	0.93	2		274	515	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853013	151853013	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	193	264	0	ENST00000262189.6:c.11942A>G	p.Asn3981Ser	p.N3981S	ENST00000262189	NM_170606.2	3981	aAc/aGc	46/59	1	2	FACETS	0.956	0.896	1	0.956	0.896	1	CLONAL	1	TRUE	1	0.93	2		264	434	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878862	151878862	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778364715	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	145	471	0	ENST00000262189.6:c.6083G>A	p.Arg2028Gln	p.R2028Q	ENST00000262189	NM_170606.2	2028	cGa/cAa	36/59	1	2	FACETS	0.364	0.332	0.398	0.364	0.332	0.398	SUBCLONAL	1	TRUE	1	0.93	2		471	856	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884448	151884448	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773744238	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	245	290	0	ENST00000262189.6:c.4907C>T	p.Thr1636Met	p.T1636M	ENST00000262189	NM_170606.2	1636	aCg/aTg	33/59	1	2	FACETS	0.936	0.883	0.989	0.936	0.883	0.989	CLONAL	1	TRUE	1	0.93	2		290	563	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38173552	38173552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	286	374	0	ENST00000317025.8:c.1864G>A	p.Glu622Lys	p.E622K	ENST00000317025	NM_023034.1	622	Gag/Aag	10/24	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.93	2		374	556	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187135	38187135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356401338	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	645	688	0	ENST00000317025.8:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000317025	NM_023034.1	448	Cgg/Tgg	6/24	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.93	2		688	1363	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275801	38275801	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	511	614	0	ENST00000425967.3:c.1468G>A	p.Gly490Arg	p.G490R	ENST00000425967	NM_001174067.1	490	Ggg/Agg	11/19	1	2	FACETS	0.972	0.935	1	0.972	0.935	1	CLONAL	1	TRUE	1	0.93	2		614	1130	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287397	38287397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145315779	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	569	709	0	ENST00000425967.3:c.260G>A	p.Arg87His	p.R87H	ENST00000425967	NM_001174067.1	87	cGc/cAc	4/19	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.93	2		709	1223	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129915	69129915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752310428	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	309	389	1	ENST00000288368.4:c.4669C>T	p.Arg1557Cys	p.R1557C	ENST00000288368	NM_024870.2	1557	Cgt/Tgt	38/40	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.93	2		390	660	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970907	70970907	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	368	472	1	ENST00000276594.2:c.1354C>A	p.Leu452Ile	p.L452I	ENST00000276594	NM_024504.3	452	Ctt/Att	6/8	1	2	FACETS	0.949	0.905	0.993	0.949	0.905	0.993	CLONAL	1	TRUE	1	0.93	2		473	834	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141551357	141551357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	796	897	1	ENST00000220592.5:c.1940G>A	p.Arg647His	p.R647H	ENST00000220592	NM_012154.3	647	cGc/cAc	15/19	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.93	2		898	1709	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566300	141566300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	216	427	0	ENST00000220592.5:c.1112C>T	p.Ser371Leu	p.S371L	ENST00000220592	NM_012154.3	371	tCg/tTg	9/19	1	2	FACETS	0.514	0.478	0.551	0.514	0.478	0.551	SUBCLONAL	1	TRUE	1	0.93	2		427	904	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738143	145738143	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	794	926	0	ENST00000428558.2:c.2767T>G	p.Leu923Val	p.L923V	ENST00000428558	NM_004260.3	923	Ttg/Gtg	17/22	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.93	2		926	1594	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741829	145741829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753959069	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	648	891	0	ENST00000428558.2:c.674C>T	p.Ser225Leu	p.S225L	ENST00000428558	NM_004260.3	225	tCg/tTg	5/22	1	2	FACETS	0.92	0.887	0.953	0.92	0.887	0.953	CLONAL	1	TRUE	1	0.93	2		891	1515	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069023	5069023	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs753648225	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	14	177	0	ENST00000381652.3:c.1328G>A	p.Arg443Gln	p.R443Q	ENST00000381652	NM_004972.3	443	cGa/cAa	11/25	1	2	FACETS	0.139	0.1	0.185	0.139	0.1	0.185	SUBCLONAL	1	TRUE	1	0.93	2		177	217	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072541	5072541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368927897	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	154	274	0	ENST00000381652.3:c.1691G>A	p.Arg564Gln	p.R564Q	ENST00000381652	NM_004972.3	564	cGa/cAa	13/25	1	2	FACETS	0.941	0.874	1	0.941	0.874	1	CLONAL	1	TRUE	1	0.93	2		274	352	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5078388	5078388	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	183	319	0	ENST00000381652.3:c.2075C>A	p.Pro692His	p.P692H	ENST00000381652	NM_004972.3	692	cCt/cAt	16/25	1	2	FACETS	0.903	0.843	0.963	0.903	0.843	0.963	CLONAL	1	TRUE	1	0.93	2		319	436	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090807	5090807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	44	196	0	ENST00000381652.3:c.2955G>T	p.Glu985Asp	p.E985D	ENST00000381652	NM_004972.3	985	gaG/gaT	22/25	1	2	FACETS	0.446	0.378	0.52	0.446	0.378	0.52	SUBCLONAL	1	TRUE	1	0.93	2		196	212	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126343	5126343	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41316003	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	103	230	0	ENST00000381652.3:c.3188G>A	p.Arg1063His	p.R1063H	ENST00000381652	NM_004972.3	1063	cGt/cAt	24/25	1	2	FACETS	0.931	0.85	1	0.931	0.85	1	CLONAL	1	TRUE	1	0.93	2		230	238	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126757	5126757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775495966	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	41	336	1	ENST00000381652.3:c.3365G>A	p.Arg1122Gln	p.R1122Q	ENST00000381652	NM_004972.3	1122	cGa/cAa	25/25	1	2	FACETS	0.241	0.201	0.285	0.241	0.201	0.285	SUBCLONAL	1	TRUE	1	0.93	2		337	366	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457399	5457399	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs897885359	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	125	153	0	ENST00000381577.3:c.373C>T	p.Arg125Ter	p.R125*	ENST00000381577	NM_014143.3	125	Cga/Tga	3/7	1	2	FACETS	0.902	0.83	0.975	0.902	0.83	0.975	CLONAL	1	TRUE	1	0.93	2		153	298	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465510	8465510	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	297	439	0	ENST00000356435.5:c.3670G>T	p.Glu1224Ter	p.E1224*	ENST00000356435		1224	Gaa/Taa	21/35	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.93	2		439	610	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521486	8521486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752937985	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	420	513	0	ENST00000356435.5:c.752G>A	p.Gly251Glu	p.G251E	ENST00000356435		251	gGa/gAa	9/35	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.93	2		513	873	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158023	27158023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	407	536	0	ENST00000380036.4:c.247G>A	p.Ala83Thr	p.A83T	ENST00000380036	NM_000459.3	83	Gct/Act	2/23	1	2	FACETS	0.985	0.942	1	0.985	0.942	1	CLONAL	1	TRUE	1	0.93	2		536	889	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27190581	27190581	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	49	513	0	ENST00000380036.4:c.1382C>T	p.Ala461Val	p.A461V	ENST00000380036	NM_000459.3	461	gCt/gTt	10/23	1	2	FACETS	0.116	0.097	0.136	0.116	0.097	0.136	SUBCLONAL	1	TRUE	1	0.93	2		513	911	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342656	87342656	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763671078	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	283	489	1	ENST00000277120.3:c.941C>T	p.Ala314Val	p.A314V	ENST00000277120		314	gCg/gTg	9/19	1	2	FACETS	0.914	0.865	0.963	0.914	0.865	0.963	CLONAL	1	TRUE	1	0.93	2		490	666	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624564	93624564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs968372087	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	355	524	0	ENST00000375746.1:c.655G>A	p.Asp219Asn	p.D219N	ENST00000375746	NM_001174167.1	219	Gac/Aac	4/14	1	2	FACETS	0.928	0.884	0.972	0.928	0.884	0.972	CLONAL	1	TRUE	1	0.93	2		524	823	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209490	98209490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140417636	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	593	849	0	ENST00000331920.6:c.4048C>T	p.Arg1350Trp	p.R1350W	ENST00000331920	NM_000264.3	1350	Cgg/Tgg	23/24	1	2	FACETS	0.979	0.943	1	0.979	0.943	1	CLONAL	1	TRUE	1	0.93	2		849	1303	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220519	98220519	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867973996	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	385	483	1	ENST00000331920.6:c.2944C>T	p.Arg982Trp	p.R982W	ENST00000331920	NM_000264.3	982	Cgg/Tgg	18/24	1	2	FACETS	0.999	0.954	1	0.999	0.954	1	CLONAL	1	TRUE	1	0.93	2		484	829	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98241428	98241428	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs779204091	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	314	361	0	ENST00000331920.6:c.1069G>A	p.Ala357Thr	p.A357T	ENST00000331920	NM_000264.3	357	Gcc/Acc	8/24	1	2	FACETS	0.952	0.905	1	0.952	0.905	1	CLONAL	1	TRUE	1	0.93	2		361	709	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249413	110249413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	928	1078	1	ENST00000374672.4:c.1160C>T	p.Ser387Leu	p.S387L	ENST00000374672	NM_004235.4	387	tCg/tTg	4/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.93	2		1079	1991	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128201272	128201272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779657195	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	421	541	0	ENST00000265960.3:c.1463C>T	p.Ser488Leu	p.S488L	ENST00000265960	NM_001006617.1	488	tCg/tTg	12/12	1	2	FACETS	0.915	0.874	0.955	0.915	0.874	0.955	CLONAL	1	TRUE	1	0.93	2		541	990	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347931	128347931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	665	833	0	ENST00000265960.3:c.574C>T	p.Pro192Ser	p.P192S	ENST00000265960	NM_001006617.1	192	Cca/Tca	5/12	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.93	2		833	1419	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772663	135772663	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	374	470	0	ENST00000298552.3:c.2883G>T	p.Glu961Asp	p.E961D	ENST00000298552	NM_001162426.1	961	gaG/gaT	22/23	1	2	FACETS	0.967	0.923	1	0.967	0.923	1	CLONAL	1	TRUE	1	0.93	2		470	832	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309018	137309018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771883272	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	738	851	1	ENST00000481739.1:c.625C>T	p.Arg209Trp	p.R209W	ENST00000481739	NM_002957.4	209	Cgg/Tgg	5/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.93	2		852	1520	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396824	139396824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356199208	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	713	721	2	ENST00000277541.6:c.5284C>T	p.Arg1762Trp	p.R1762W	ENST00000277541	NM_017617.3	1762	Cgg/Tgg	28/34	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.93	2		723	1503	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404360	139404360	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758642073	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	868	943	0	ENST00000277541.6:c.2794G>A	p.Asp932Asn	p.D932N	ENST00000277541	NM_017617.3	932	Gac/Aac	18/34	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.93	2		943	1838	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409801	139409801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758837712	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	770	928	0	ENST00000277541.6:c.1955C>T	p.Ser652Leu	p.S652L	ENST00000277541	NM_017617.3	652	tCg/tTg	12/34	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.93	2		928	1631	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564084	139564084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759831503	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1489	180	854	0	ENST00000308874.7:c.224G>A	p.Arg75His	p.R75H	ENST00000308874		75	cGc/cAc	5/10	1	2	FACETS	0.232	0.213	0.252	0.232	0.213	0.252	SUBCLONAL	1	TRUE	1	0.93	2		854	1669	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321297	1321297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370445430	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	401	523	1	ENST00000400841.2:c.458G>A	p.Arg153Gln	p.R153Q	ENST00000400841		153	cGg/cAg	4/6	1	2	FACETS	0.988	0.945	1	0.988	0.945	1	CLONAL	1	TRUE	1	0.93	2		524	873	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922974	44922974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs973676174	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	408	525	1	ENST00000377967.4:c.1835G>A	p.Arg612Gln	p.R612Q	ENST00000377967	NM_021140.2	612	cGa/cAa	16/29	1	2	FACETS	0.909	0.869	0.95	0.909	0.869	0.95	CLONAL	1	TRUE	1	0.93	2		526	965	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969346	44969346	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	198	343	0	ENST00000377967.4:c.4028T>G	p.Phe1343Cys	p.F1343C	ENST00000377967	NM_021140.2	1343	tTt/tGt	28/29	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.93	2		343	416	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428125	47428125	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	600	740	0	ENST00000377045.4:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000377045	NM_001654.4	362	cGa/cAa	11/16	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.93	2		740	1216	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227949	53227949	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1331	81	777	1	ENST00000375401.3:c.2365C>T	p.Arg789Cys	p.R789C	ENST00000375401	NM_004187.3	789	Cgc/Tgc	16/26	1	2	FACETS	0.123	0.108	0.14	0.123	0.108	0.14	SUBCLONAL	1	TRUE	1	0.93	2		778	1412	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230752	53230752	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	515	643	1	ENST00000375401.3:c.2041C>T	p.Arg681Ter	p.R681*	ENST00000375401	NM_004187.3	681	Cga/Tga	14/26	1	2	FACETS	0.927	0.89	0.964	0.927	0.89	0.964	CLONAL	1	TRUE	1	0.93	2		644	1195	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339575	70339575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266838743	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	450	492	1	ENST00000374080.3:c.244C>T	p.Arg82Cys	p.R82C	ENST00000374080		82	Cgt/Tgt	3/45	0.146227775907956	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		493	856	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344077	70344077	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	623	767	1	ENST00000374080.3:c.1813C>T	p.Arg605Ter	p.R605*	ENST00000374080		605	Cga/Tga	13/45	0.146227775907956	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		768	1231	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347793	70347793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	388	487	2	ENST00000374080.3:c.3032C>T	p.Ser1011Leu	p.S1011L	ENST00000374080		1011	tCg/tTg	22/45	0.146227775907956	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		489	813	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889093	76889093	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	124	284	0	ENST00000373344.5:c.4917G>T	p.Glu1639Asp	p.E1639D	ENST00000373344	NM_000489.3	1639	gaG/gaT	18/35	0.146227775907956	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		284	305	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940493	76940493	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	145	307	0	ENST00000373344.5:c.600C>A	p.Cys200Ter	p.C200*	ENST00000373344	NM_000489.3	200	tgC/tgA	8/35	0.146227775907956	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		307	382	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76954062	76954062	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045458-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	208	386	0	ENST00000373344.5:c.189G>T	p.Glu63Asp	p.E63D	ENST00000373344	NM_000489.3	63	gaG/gaT	3/35	0.146227775907956	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.93	0		386	429	SUCCESS
APC	324	MSKCC	GRCh37	5	112175015	112175015	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1460397656	NA	P-0045459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	63	166	0	ENST00000257430.4:c.3724C>T	p.Gln1242Ter	p.Q1242*	ENST00000257430	NM_000038.5	1242	Cag/Tag	16/16	0.642709886805439	3	FACETS	0.981	0.876	1	0.981	0.876	1	CLONAL	2	TRUE	1	0.642709886805439	3		166	132	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55228005	55228005	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	26	228	0	ENST00000275493.2:c.1472T>A	p.Ile491Lys	p.I491K	ENST00000275493	NM_005228.3	491	aTa/aAa	12/28	0.642709886805439	4	FACETS	0.642	0.512	0.79	0.321	0.256	0.395	SUBCLONAL	1	TRUE	2	0.642709886805439	4		228	207	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	233	737	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.867	0.81	0.925	0.867	0.81	0.925	CLONAL	1	TRUE	1	0.602789480012413	2		742	892	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	68	267	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.775	0.681	0.875	0.775	0.681	0.875	SUBCLONAL	1	TRUE	1	0.602789480012413	2		267	291	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003786	45003789	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	159	538	0	ENST00000558401.1:c.45_48del	p.Ser16AlafsTer27	p.S16Afs*27	ENST00000558401	NM_004048.2	14	tcTCTT/tc	1/4	1	2	FACETS	0.79	0.726	0.856	0.79	0.726	0.856	SUBCLONAL	1	TRUE	1	0.602789480012413	2		538	668	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs767894241	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	138	474	0	ENST00000358127.4:c.76dup	p.Val26GlyfsTer49	p.V26Gfs*49	ENST00000358127	NM_001280556.1	26	gtt/gGtt	2/10	1	2	FACETS	0.72	0.657	0.786	0.72	0.657	0.786	SUBCLONAL	1	TRUE	1	0.602789480012413	2		474	636	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	246	984	5	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.841	0.787	0.897	0.841	0.787	0.897	CLONAL	1	TRUE	1	0.602789480012413	2		989	970	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852248	63852248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145564601	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	192	554	0	ENST00000279873.7:c.3026C>T	p.Ala1009Val	p.A1009V	ENST00000279873	NM_032199.2	1009	gCg/gTg	10/10	1	2	FACETS	0.929	0.862	0.997	0.929	0.862	0.997	CLONAL	1	TRUE	1	0.602789480012413	2		554	686	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	312	741	3	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	1	2	FACETS	0.979	0.925	1	0.979	0.925	1	CLONAL	1	TRUE	1	0.602789480012413	2		744	1057	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	360	933	4	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.967	0.917	1	0.967	0.917	1	CLONAL	1	TRUE	1	0.602789480012413	2		937	1235	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342967	225342967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	51	292	1	ENST00000264414.4:c.2125C>T	p.Arg709Trp	p.R709W	ENST00000264414	NM_003590.4	709	Cgg/Tgg	15/16	1	2	FACETS	0.32	0.272	0.374	0.32	0.272	0.374	SUBCLONAL	1	TRUE	1	0.602789480012413	2		293	528	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954023	32954023	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507419	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	29	301	0	ENST00000380152.3:c.9097del	p.Thr3033LeufsTer29	p.T3033Lfs*29	ENST00000380152		3030	acA/ac	23/27	1	2	FACETS	0.249	0.199	0.305	0.249	0.199	0.305	SUBCLONAL	1	TRUE	1	0.602789480012413	2		301	387	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100727	8100728	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs771019738	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	203	796	0	ENST00000346208.3:c.708dup	p.Ser237GlnfsTer66	p.S237Qfs*66	ENST00000346208		234	ttc/ttCc	3/6	1	2	FACETS	0.78	0.725	0.838	0.78	0.725	0.838	SUBCLONAL	1	TRUE	1	0.602789480012413	2		796	863	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007825	45007825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	85	298	1	ENST00000558401.1:c.276del	p.Thr93LeufsTer10	p.T93Lfs*10	ENST00000558401	NM_004048.2	91	aCc/ac	2/4	1	2	FACETS	0.797	0.71	0.888	0.797	0.71	0.888	SUBCLONAL	1	TRUE	1	0.602789480012413	2		299	354	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863319	57863319	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	260	779	1	ENST00000228682.2:c.1418del	p.Gly473AlafsTer40	p.G473Afs*40	ENST00000228682	NM_005269.2	472	Ggg/gg	11/12	1	2	FACETS	0.953	0.895	1	0.953	0.895	1	CLONAL	1	TRUE	1	0.602789480012413	2		780	905	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396234	396234	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	248	651	1	ENST00000262320.3:c.792del	p.Gly265GlufsTer149	p.G265Efs*149	ENST00000262320	NM_003502.3	264	ccC/cc	2/11	1	2	FACETS	0.892	0.836	0.951	0.892	0.836	0.951	CLONAL	1	TRUE	1	0.602789480012413	2		652	922	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443617	49443617	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs727503987	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	98	739	1	ENST00000301067.7:c.3754C>T	p.Arg1252Ter	p.R1252*	ENST00000301067	NM_003482.3	1252	Cga/Tga	11/54	1	2	FACETS	0.391	0.348	0.436	0.391	0.348	0.436	SUBCLONAL	1	TRUE	1	0.602789480012413	2		740	832	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225378265	225378266	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	78	197	0	ENST00000264414.4:c.629dup	p.Leu210PhefsTer20	p.L210Ffs*20	ENST00000264414	NM_003590.4	210	ttg/ttTg	5/16	1	2	FACETS	0.868	0.771	0.971	0.868	0.771	0.971	CLONAL	1	TRUE	1	0.602789480012413	2		197	298	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376248	15376248	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	141	561	0	ENST00000263377.2:c.766del	p.Gln256SerfsTer27	p.Q256Sfs*27	ENST00000263377	NM_058243.2	256	Cag/ag	5/20	1	2	FACETS	0.758	0.693	0.826	0.758	0.693	0.826	SUBCLONAL	1	TRUE	1	0.602789480012413	2		561	617	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133898	41133898	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	42	422	0	ENST00000379561.5:c.1730del	p.Gly577AlafsTer5	p.G577Afs*5	ENST00000379561	NM_002015.3	577	gGc/gc	2/3	1	2	FACETS	0.325	0.271	0.384	0.325	0.271	0.384	SUBCLONAL	1	TRUE	1	0.602789480012413	2		422	429	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175759	176175760	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1373807885	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	256	732	1	ENST00000367669.3:c.355dup	p.Leu119ProfsTer23	p.L119Pfs*23	ENST00000367669	NM_022457.5	119	ctc/cCtc	1/20	1	2	FACETS	0.928	0.871	0.987	0.928	0.871	0.987	CLONAL	1	TRUE	1	0.602789480012413	2		733	915	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226016	226016	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	35	93	0	ENST00000264932.6:c.475C>T	p.Pro159Ser	p.P159S	ENST00000264932	NM_004168.2	159	Ccg/Tcg	5/15	1	2	FACETS	0.841	0.702	0.992	0.841	0.702	0.992	CLONAL	1	TRUE	1	0.602789480012413	2		93	138	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515167	31515169	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	rs760849334	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	193	575	0	ENST00000344624.3:c.1216_1218del	p.Glu406del	p.E406del	ENST00000344624		406	GAA/-	5/33	1	2	FACETS	0.726	0.672	0.782	0.726	0.672	0.782	SUBCLONAL	1	TRUE	1	0.602789480012413	2		575	882	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981892	70981892	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	216	886	0	ENST00000276594.2:c.204del	p.Phe69SerfsTer10	p.F69Sfs*10	ENST00000276594	NM_024504.3	68	ccC/cc	2/8	1	2	FACETS	0.788	0.734	0.845	0.788	0.734	0.845	SUBCLONAL	1	TRUE	1	0.602789480012413	2		886	909	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494872	56494872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112651994	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	195	521	1	ENST00000267101.3:c.3229C>T	p.Arg1077Trp	p.R1077W	ENST00000267101	NM_001982.3	1077	Cgg/Tgg	27/28	1	2	FACETS	0.816	0.757	0.877	0.816	0.757	0.877	CLONAL	1	TRUE	1	0.602789480012413	2		522	793	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47685275	47685275	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	81	288	0	ENST00000347630.2:c.675del	p.Phe225LeufsTer30	p.F225Lfs*30	ENST00000347630	NM_001007230.1	225	ttT/tt	8/11	1	2	FACETS	0.814	0.724	0.91	0.814	0.724	0.91	CLONAL	1	TRUE	1	0.602789480012413	2		288	330	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202555	67202555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201231114	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	292	922	0	ENST00000312629.5:c.1364C>T	p.Pro455Leu	p.P455L	ENST00000312629	NM_003952.2	455	cCg/cTg	15/15	1	2	FACETS	0.872	0.821	0.925	0.872	0.821	0.925	CLONAL	1	TRUE	1	0.602789480012413	2		922	1111	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098037	178098037	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	21	269	0	ENST00000397062.3:c.343T>A	p.Tyr115Asn	p.Y115N	ENST00000397062	NM_006164.4	115	Tac/Aac	3/5	1	2	FACETS	0.218	0.167	0.276	0.218	0.167	0.276	SUBCLONAL	1	TRUE	1	0.602789480012413	2		269	320	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469931	25469931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290621612	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	210	635	0	ENST00000264709.3:c.1111G>A	p.Glu371Lys	p.E371K	ENST00000264709	NM_175629.2	371	Gag/Aag	9/23	1	2	FACETS	0.884	0.823	0.947	0.884	0.823	0.947	CLONAL	1	TRUE	1	0.602789480012413	2		635	788	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804993	43804993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	145	495	0	ENST00000372470.3:c.443G>A	p.Gly148Glu	p.G148E	ENST00000372470	NM_005373.2	148	gGg/gAg	4/12	1	2	FACETS	0.798	0.731	0.868	0.798	0.731	0.868	SUBCLONAL	1	TRUE	1	0.602789480012413	2		495	603	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263266	115263266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	216	641	0	ENST00000438362.2:c.2084G>A	p.Gly695Glu	p.G695E	ENST00000438362	NM_001242891.1	695	gGg/gAg	17/20	1	2	FACETS	0.853	0.795	0.913	0.853	0.795	0.913	CLONAL	1	TRUE	1	0.602789480012413	2		641	840	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462092	120462092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148613210	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	229	714	1	ENST00000256646.2:c.5624G>A	p.Arg1875Gln	p.R1875Q	ENST00000256646	NM_024408.3	1875	cGg/cAg	31/34	1	2	FACETS	0.855	0.798	0.913	0.855	0.798	0.913	CLONAL	1	TRUE	1	0.602789480012413	2		715	889	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102196288	102196288	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	68	205	0	ENST00000263464.3:c.945G>A	p.Trp315Ter	p.W315*	ENST00000263464	NM_001165.4	315	tgG/tgA	3/9	1	2	FACETS	0.797	0.7	0.9	0.797	0.7	0.9	SUBCLONAL	1	TRUE	1	0.602789480012413	2		205	283	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376795	118376795	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	140	339	0	ENST00000534358.1:c.10188G>T	p.Gln3396His	p.Q3396H	ENST00000534358	NM_005933.3	3396	caG/caT	27/36	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.602789480012413	2		339	430	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446120	49446121	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	75	882	0	ENST00000301067.7:c.1345dup	p.Leu449ProfsTer6	p.L449Pfs*6	ENST00000301067	NM_003482.3	449	ctg/cCtg	10/54	1	2	FACETS	0.236	0.206	0.268	0.236	0.206	0.268	SUBCLONAL	1	TRUE	1	0.602789480012413	2		882	1056	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914328	32914328	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs80358811	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	93	338	0	ENST00000380152.3:c.5836T>C	p.Ser1946Pro	p.S1946P	ENST00000380152		1946	Tca/Cca	11/27	1	2	FACETS	0.874	0.784	0.968	0.874	0.784	0.968	CLONAL	1	TRUE	1	0.602789480012413	2		338	353	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643701	38643701	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	221	563	0	ENST00000299084.4:c.1171T>C	p.Cys391Arg	p.C391R	ENST00000299084	NM_152594.2	391	Tgt/Cgt	7/7	1	2	FACETS	0.961	0.897	1	0.961	0.897	1	CLONAL	1	TRUE	1	0.602789480012413	2		563	763	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042241	42042242	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	116	331	0	ENST00000219905.7:c.6437_6438del	p.Lys2146SerfsTer7	p.K2146Sfs*7	ENST00000219905	NM_001164273.1	2146	AAa/a	17/24	1	2	FACETS	0.914	0.83	1	0.914	0.83	1	CLONAL	1	TRUE	1	0.602789480012413	2		331	421	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99460036	99460036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777846544	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	180	348	0	ENST00000268035.6:c.2132C>T	p.Ala711Val	p.A711V	ENST00000268035	NM_000875.3	711	gCc/gTc	10/21	1	2	FACETS	0.97	0.899	1	0.97	0.899	1	CLONAL	1	TRUE	1	0.602789480012413	2		348	616	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3645677	3645677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755500401	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	293	767	0	ENST00000294008.3:c.1942G>A	p.Gly648Ser	p.G648S	ENST00000294008	NM_032444.2	648	Ggc/Agc	9/15	1	2	FACETS	0.971	0.915	1	0.971	0.915	1	CLONAL	1	TRUE	1	0.602789480012413	2		767	1001	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032156	10032156	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	176	539	0	ENST00000330684.3:c.667C>A	p.His223Asn	p.H223N	ENST00000330684	NM_001134407.1	223	Cac/Aac	3/13	1	2	FACETS	0.834	0.771	0.9	0.834	0.771	0.9	CLONAL	1	TRUE	1	0.602789480012413	2		539	700	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGG	novel	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	73	735	0	ENST00000285071.4:c.1283_1285dup	p.Pro428dup	p.P428dup	ENST00000285071	NM_144997.5	428	cac/cCCCac	11/14	1	2	FACETS	0.337	0.294	0.383	0.337	0.294	0.383	SUBCLONAL	1	TRUE	1	0.602789480012413	2		735	719	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760927	59760927	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	107	407	0	ENST00000259008.2:c.3480C>A	p.Asn1160Lys	p.N1160K	ENST00000259008	NM_032043.2	1160	aaC/aaA	20/20	1	2	FACETS	0.667	0.601	0.737	0.667	0.601	0.737	SUBCLONAL	1	TRUE	1	0.602789480012413	2		407	532	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271755	15271755	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	327	1190	0	ENST00000263388.2:c.6684C>A	p.Ser2228Arg	p.S2228R	ENST00000263388	NM_000435.2	2228	agC/agA	33/33	1	2	FACETS	0.903	0.853	0.954	0.903	0.853	0.954	CLONAL	1	TRUE	1	0.602789480012413	2		1190	1202	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260136	19260136	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	82	735	1	ENST00000162023.5:c.157C>A	p.Arg53Ser	p.R53S	ENST00000162023		53	Cgc/Agc	7/13	1	2	FACETS	0.274	0.24	0.31	0.274	0.24	0.31	SUBCLONAL	1	TRUE	1	0.602789480012413	2		736	994	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795322	42795322	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	249	921	0	ENST00000575354.2:c.2402G>C	p.Gly801Ala	p.G801A	ENST00000575354	NM_015125.3	801	gGc/gCc	10/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.602789480012413	2		921	814	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905183	50905183	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	109	935	1	ENST00000440232.2:c.463+2T>C		p.X155_splice	ENST00000440232	NM_002691.3	155			1	2	FACETS	0.315	0.282	0.35	0.315	0.282	0.35	SUBCLONAL	1	TRUE	1	0.602789480012413	2		936	1148	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793220	242793220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	274	934	0	ENST00000334409.5:c.857G>T	p.Trp286Leu	p.W286L	ENST00000334409	NM_005018.2	286	tGg/tTg	5/5	1	2	FACETS	0.916	0.86	0.972	0.916	0.86	0.972	CLONAL	1	TRUE	1	0.602789480012413	2		934	993	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026821	71026823	+	inframe_deletion	In_Frame_Del	DEL	TGG	TGG	-	novel	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	41	183	0	ENST00000318789.4:c.1399_1401del	p.Pro467del	p.P467del	ENST00000318789	NM_032682.5	467	CCA/-	16/21	1	2	FACETS	0.553	0.464	0.65	0.553	0.464	0.65	SUBCLONAL	1	TRUE	1	0.602789480012413	2		183	246	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31435883	31435883	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	101	317	0	ENST00000344624.3:c.3031A>G	p.Met1011Val	p.M1011V	ENST00000344624		1011	Atg/Gtg	22/33	1	2	FACETS	0.811	0.73	0.896	0.811	0.73	0.896	CLONAL	1	TRUE	1	0.602789480012413	2		317	413	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721760	176721760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587784216	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	130	452	0	ENST00000439151.2:c.7391G>A	p.Arg2464His	p.R2464H	ENST00000439151	NM_022455.4	2464	cGc/cAc	23/23	1	2	FACETS	0.92	0.84	1	0.92	0.84	1	CLONAL	1	TRUE	1	0.602789480012413	2		452	469	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453142	140453142	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	65	273	0	ENST00000288602.6:c.1793C>T	p.Ala598Val	p.A598V	ENST00000288602	NM_004333.4	598	gCt/gTt	15/18	1	2	FACETS	0.64	0.558	0.727	0.64	0.558	0.727	SUBCLONAL	1	TRUE	1	0.602789480012413	2		273	337	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97887441	97887441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	153	429	1	ENST00000289081.3:c.923C>T	p.Ala308Val	p.A308V	ENST00000289081	NM_000136.2	308	gCc/gTc	10/15	1	2	FACETS	0.819	0.752	0.888	0.819	0.752	0.888	CLONAL	1	TRUE	1	0.602789480012413	2		430	620	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	118	415	2				ENST00000310581	NM_198253.2	-/1132			0.526384159944265	0	FACETS		NA	1			1	NA	1	FALSE	0	0.678097903973063	0		417	303	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	354	651	2	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.678097903973063	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	0	0.678097903973063	1		653	630	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230641	46230641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	13	301	0	ENST00000334344.6:c.890C>T	p.Ser297Phe	p.S297F	ENST00000334344	NM_152641.2	297	tCc/tTc	8/21	0.106611283071471	4	FACETS	0.105	0.074	0.143	0.052	0.037	0.072	INDETERMINATE	1	FALSE	2	0.678097903973063	4		301	615	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588626	28588626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548609046	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	84	349	0	ENST00000241453.7:c.2822C>T	p.Ser941Leu	p.S941L	ENST00000241453	NM_004119.2	941	tCg/tTg	23/24	0.278950352670744	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.678097903973063	0		349	354	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119325	3119325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	190	737	0	ENST00000078429.4:c.857C>T	p.Ser286Leu	p.S286L	ENST00000078429	NM_002067.2	286	tCg/tTg	6/7	0.500299906440373	1	FACETS	0.505	0.468	0.543	0.505	0.468	0.543	SUBCLONAL	1	FALSE	0	0.678097903973063	1		737	734	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18276986	18276986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748211099	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	224	351	0	ENST00000222254.8:c.1433G>A	p.Arg478His	p.R478H	ENST00000222254	NM_005027.3	478	cGt/cAt	12/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.678097903973063	2		351	600	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032793	30032794	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	39	310	0	ENST00000338641.4:c.168_169delinsTT	p.Arg57Ter	p.R57*	ENST00000338641	NM_000268.3	56	ctCCga/ctTTga	2/16	1	2	FACETS	0.196	0.162	0.235	0.196	0.162	0.235	SUBCLONAL	1	FALSE	1	0.678097903973063	2		310	586	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347217	70347217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338758	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	212	281	2	ENST00000374080.3:c.2881C>T	p.Arg961Trp	p.R961W	ENST00000374080		961	Cgg/Tgg	21/45	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	0	0.678097903973063	1		283	360	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117650567	117650567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	125	385	0	ENST00000368508.3:c.5291G>A	p.Gly1764Glu	p.G1764E	ENST00000368508	NM_002944.2	1764	gGg/gAg	32/43	0.60161245558446	1	FACETS	0.511	0.465	0.558	0.511	0.465	0.558	SUBCLONAL	1	FALSE	0	0.678097903973063	1		385	477	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715333	117715333	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	77	198	0	ENST00000368508.3:c.1156G>A	p.Asp386Asn	p.D386N	ENST00000368508	NM_002944.2	386	Gat/Aat	10/43	0.60161245558446	1	FACETS	0.613	0.546	0.683	0.613	0.546	0.683	SUBCLONAL	1	FALSE	0	0.678097903973063	1		198	245	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931862	68931862	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200600940	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	161	447	0	ENST00000288368.4:c.292G>A	p.Glu98Lys	p.E98K	ENST00000288368	NM_024870.2	98	Gaa/Aaa	3/40	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.678097903973063	NA		447	592	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631445	117631445	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs190667369	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	37	231	0	ENST00000368508.3:c.6234-1G>A		p.X2078_splice	ENST00000368508	NM_002944.2	2078			0.60161245558446	1	FACETS	0.236	0.195	0.281	0.236	0.195	0.281	SUBCLONAL	1	FALSE	0	0.678097903973063	1		231	306	SUCCESS
EED	8726	MSKCC	GRCh37	11	85966300	85966300	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745786094	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	127	228	0	ENST00000263360.6:c.397C>T	p.Arg133Trp	p.R133W	ENST00000263360	NM_003797.3	133	Cgg/Tgg	4/12	1	2	FACETS	0.883	0.807	0.962	0.883	0.807	0.962	CLONAL	1	FALSE	1	0.678097903973063	2		228	424	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324580	62324580	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs574134304	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	313	830	1	ENST00000360203.5:c.2936G>A	p.Arg979Gln	p.R979Q	ENST00000360203	NM_001283009.1	979	cGg/cAg	30/35	1	2	FACETS	0.935	0.884	0.988	0.935	0.884	0.988	CLONAL	1	FALSE	1	0.678097903973063	2		831	987	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781643	9781644	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	243	759	3	ENST00000377346.4:c.1953_1954delinsTT	p.Arg652Cys	p.R652C	ENST00000377346	NM_005026.3	651	ctCCgc/ctTTgc	15/24	NA	2	FACETS	0.889	0.833	0.947			1	INDETERMINATE	1	FALSE	NA	0.678097903973063	2		762	806	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458944	120458944	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	262	667	0	ENST00000256646.2:c.6401C>T	p.Ser2134Phe	p.S2134F	ENST00000256646	NM_024408.3	2134	tCt/tTt	34/34	1	2	FACETS	0.981	0.922	1	0.981	0.922	1	CLONAL	1	FALSE	1	0.678097903973063	2		667	788	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243778408	243778409	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	34	260	0	ENST00000263826.5:c.616_617delinsTT	p.Pro206Phe	p.P206F	ENST00000263826	NM_005465.4	206	CCc/TTc	6/13	0.390949027894404	4	FACETS	0.313	0.255	0.379	0.104	0.085	0.127	INDETERMINATE	1	FALSE	1	0.678097903973063	4		260	537	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606800	43606800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs925104163	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	195	822	0	ENST00000355710.3:c.1409C>T	p.Thr470Ile	p.T470I	ENST00000355710	NM_020975.4	470	aCc/aTc	7/20	0.309258118787219	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.678097903973063	0		822	585	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155811	119155811	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs766785320	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	177	481	0	ENST00000264033.4:c.1563+1G>A		p.X521_splice	ENST00000264033	NM_005188.3	521			1	2	FACETS	0.681	0.628	0.735	0.681	0.628	0.735	SUBCLONAL	1	FALSE	1	0.678097903973063	2		481	767	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431693	49431693	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	68	800	0	ENST00000301067.7:c.9446C>T	p.Ser3149Phe	p.S3149F	ENST00000301067	NM_003482.3	3149	tCc/tTc	34/54	0.106611283071471	4	FACETS	0.349	0.302	0.399	0.174	0.151	0.2	INDETERMINATE	1	FALSE	2	0.678097903973063	4		800	965	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21565456	21565456	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	242	680	0	ENST00000382592.4:c.430C>T	p.Pro144Ser	p.P144S	ENST00000382592	NM_014572.2	144	Ccg/Tcg	3/8	0.278950352670744	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.678097903973063	0		680	787	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944571	32944571	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397507981	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	161	411	0	ENST00000380152.3:c.8364G>A	p.Trp2788Ter	p.W2788*	ENST00000380152		2788	tgG/tgA	19/27	NA	2	FACETS	0.84	0.775	0.908			1	INDETERMINATE	1	FALSE	NA	0.678097903973063	2		411	565	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726696	88726697	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	95	430	1	ENST00000360948.2:c.347_348delinsAA	p.Arg116Gln	p.R116Q	ENST00000360948	NM_001012338.2	116	cGG/cAA	4/19	0.620039603690961	1	FACETS	0.516	0.463	0.571	0.516	0.463	0.571	SUBCLONAL	1	FALSE	0	0.678097903973063	1		431	359	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346871	91346871	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	122	322	0	ENST00000355112.3:c.3479A>T	p.Tyr1160Phe	p.Y1160F	ENST00000355112	NM_000057.2	1160	tAt/tTt	18/22	1	2	FACETS	0.711	0.646	0.779	0.711	0.646	0.779	SUBCLONAL	1	FALSE	1	0.678097903973063	2		322	506	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2090014	2090014	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	335	948	0	ENST00000219066.1:c.850G>A	p.Gly284Ser	p.G284S	ENST00000219066	NM_002528.5	284	Ggc/Agc	6/6	0.331739463870824	1	FACETS	0.643	0.609	0.678	0.643	0.609	0.678	INDETERMINATE	1	FALSE	0	0.678097903973063	1		948	1015	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830348	72830348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774246895	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	113	447	1	ENST00000268489.5:c.6233C>T	p.Pro2078Leu	p.P2078L	ENST00000268489	NM_006885.3	2078	cCg/cTg	9/10	1	2	FACETS	0.918	0.835	1	0.918	0.835	1	CLONAL	1	FALSE	1	0.678097903973063	2		448	363	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81922807	81922807	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs530712899	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	187	354	0	ENST00000359376.3:c.796C>G	p.Arg266Gly	p.R266G	ENST00000359376	NM_002661.3	266	Cgt/Ggt	10/33	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.678097903973063	2		354	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577101	7577102	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	326	687	0	ENST00000269305.4:c.836_837delinsAA	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGG/gAA	8/11	0.661732609293653	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	0	0.678097903973063	1		687	624	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16052787	16052787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	168	247	0	ENST00000268712.3:c.887G>A	p.Arg296Lys	p.R296K	ENST00000268712	NM_006311.3	296	aGa/aAa	9/46	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	FALSE	1	0.678097903973063	2		247	489	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530029	63530029	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	123	359	0	ENST00000307078.5:c.2405+1G>C		p.X802_splice	ENST00000307078	NM_004655.3	802			0.331739463870824	1	FACETS	0.602	0.55	0.657	0.602	0.55	0.657	INDETERMINATE	1	FALSE	0	0.678097903973063	1		359	398	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1627395	1627395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	104	826	0	ENST00000344749.5:c.329C>T	p.Ser110Phe	p.S110F	ENST00000344749	NM_001136139.2	110	tCc/tTc	6/19	0.500299906440373	1	FACETS	0.279	0.25	0.31	0.279	0.25	0.31	SUBCLONAL	1	FALSE	0	0.678097903973063	1		826	726	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300158	15300158	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	358	740	0	ENST00000263388.2:c.1118G>A	p.Gly373Asp	p.G373D	ENST00000263388	NM_000435.2	373	gGc/gAc	7/33	1	2	FACETS	0.96	0.911	1	0.96	0.911	1	CLONAL	1	FALSE	1	0.678097903973063	2		740	1100	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223611	36223611	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	101	1029	0	ENST00000222270.7:c.6161G>T	p.Gly2054Val	p.G2054V	ENST00000222270	NM_014727.1	2054	gGa/gTa	28/37	0.219344621160641	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.678097903973063	0		1029	1056	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519876	29519877	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	167	563	1	ENST00000389048.3:c.1694_1695delinsTT	p.Ser565Phe	p.S565F	ENST00000389048	NM_004304.4	565	tCC/tTT	9/29	0.60161245558446	1	FACETS	0.59	0.545	0.636	0.59	0.545	0.636	SUBCLONAL	1	FALSE	0	0.678097903973063	1		564	552	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251637	212251637	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	161	436	0	ENST00000342788.4:c.3422C>G	p.Pro1141Arg	p.P1141R	ENST00000342788	NM_005235.2	1141	cCa/cGa	27/28	1	2	FACETS	0.926	0.855	0.998	0.926	0.855	0.998	CLONAL	1	FALSE	1	0.678097903973063	2		436	513	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215617193	215617193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	91	196	0	ENST00000260947.4:c.1655C>T	p.Ser552Phe	p.S552F	ENST00000260947	NM_000465.2	552	tCc/tTc	7/11	1	2	FACETS	0.904	0.812	0.999	0.904	0.812	0.999	CLONAL	1	FALSE	1	0.678097903973063	2		196	297	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795056	242795057	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	71	972	1	ENST00000334409.5:c.152_153delinsTT	p.Thr51Ile	p.T51I	ENST00000334409	NM_005018.2	51	aCC/aTT	2/5	0.673589064519149	1	FACETS	0.154	0.134	0.176	0.154	0.134	0.176	SUBCLONAL	1	FALSE	0	0.678097903973063	1		973	899	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911664	134911664	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	14	300	0	ENST00000398015.3:c.2129G>A	p.Arg710Lys	p.R710K	ENST00000398015	NM_004441.4	710	aGg/aAg	11/16	0.278950352670744	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.678097903973063	0		300	253	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143226657	143226657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765578505	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	168	306	0	ENST00000262992.4:c.457G>A	p.Gly153Arg	p.G153R	ENST00000262992	NM_001101669.1	153	Gga/Aga	7/24	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	1	0.678097903973063	2		306	486	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525038	187525038	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	202	402	0	ENST00000441802.2:c.10642del	p.Leu3548TrpfsTer31	p.L3548Wfs*31	ENST00000441802	NM_005245.3	3548	Ctg/tg	19/27	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	1	0.678097903973063	2		402	592	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557259	187557259	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	193	419	0	ENST00000441802.2:c.4103T>A	p.Met1368Lys	p.M1368K	ENST00000441802	NM_005245.3	1368	aTg/aAg	6/27	1	2	FACETS	0.873	0.811	0.936	0.873	0.811	0.936	CLONAL	1	FALSE	1	0.678097903973063	2		419	652	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753206	57753206	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	93	224	0	ENST00000274289.3:c.810G>T	p.Met270Ile	p.M270I	ENST00000274289	NM_006622.3	270	atG/atT	7/14	1	2	FACETS	0.768	0.689	0.851	0.768	0.689	0.851	SUBCLONAL	1	FALSE	1	0.678097903973063	2		224	357	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522732	67522732	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs749306548	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	124	189	0	ENST00000274335.5:c.229A>T	p.Ile77Phe	p.I77F	ENST00000274335		77	Att/Ttt	1/15	1	2	FACETS	0.917	0.837	0.999	0.917	0.837	0.999	CLONAL	1	FALSE	1	0.678097903973063	2		189	399	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685209	86685209	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	80	161	0	ENST00000274376.6:c.2926-1G>A		p.X976_splice	ENST00000274376	NM_002890.2	976			1	2	FACETS	0.828	0.737	0.923	0.828	0.737	0.923	CLONAL	1	FALSE	1	0.678097903973063	2		161	285	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858336	27858336	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	232	653	0	ENST00000359303.2:c.235T>A	p.Phe79Ile	p.F79I	ENST00000359303	NM_003535.2	79	Ttc/Atc	1/1	1	2	FACETS	0.831	0.777	0.887	0.831	0.777	0.887	CLONAL	1	FALSE	1	0.678097903973063	2		653	823	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166270	32166270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	367	672	0	ENST00000375023.3:c.4684C>T	p.Pro1562Ser	p.P1562S	ENST00000375023	NM_004557.3	1562	Cct/Tct	26/30	1	2	FACETS	0.99	0.941	1	0.99	0.941	1	CLONAL	1	FALSE	1	0.678097903973063	2		672	1093	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166425	32166425	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	312	651	0	ENST00000375023.3:c.4617+1G>A		p.X1539_splice	ENST00000375023	NM_004557.3	1539			1	2	FACETS	0.908	0.858	0.96	0.908	0.858	0.96	CLONAL	1	FALSE	1	0.678097903973063	2		651	1013	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662375	117662375	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	150	389	0	ENST00000368508.3:c.5002G>A	p.Glu1668Lys	p.E1668K	ENST00000368508	NM_002944.2	1668	Gag/Aag	30/43	0.60161245558446	1	FACETS	0.659	0.607	0.711	0.659	0.607	0.711	SUBCLONAL	1	FALSE	0	0.678097903973063	1		389	444	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935565	13935565	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770880512	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	31	340	0	ENST00000405192.2:c.1291G>A	p.Asp431Asn	p.D431N	ENST00000405192	NM_001163147.1	431	Gat/Aat	12/12	1	2	FACETS	0.157	0.127	0.192	0.157	0.127	0.192	SUBCLONAL	1	FALSE	1	0.678097903973063	2		340	581	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55214409	55214409	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	243	472	0	ENST00000275493.2:c.535G>A	p.Asp179Asn	p.D179N	ENST00000275493	NM_005228.3	179	Gac/Aac	4/28	1	2	FACETS	0.809	0.757	0.862	0.809	0.757	0.862	CLONAL	1	FALSE	1	0.678097903973063	2		472	886	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509672	106509672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	163	495	0	ENST00000359195.3:c.1666G>A	p.Glu556Lys	p.E556K	ENST00000359195	NM_002649.2	556	Gag/Aag	2/11	0.106611283071471	4	FACETS	0.767	0.708	0.827	0.767	0.708	0.827	INDETERMINATE	2	FALSE	2	0.678097903973063	4		495	526	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38194889	38194889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs74585221	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	273	420	1	ENST00000317025.8:c.844C>T	p.Pro282Ser	p.P282S	ENST00000317025	NM_023034.1	282	Cct/Tct	4/24	1	2	FACETS	0.931	0.876	0.987	0.931	0.876	0.987	CLONAL	1	FALSE	1	0.678097903973063	2		421	865	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391595	139391595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	328	1012	0	ENST00000277541.6:c.6596C>T	p.Pro2199Leu	p.P2199L	ENST00000277541	NM_017617.3	2199	cCc/cTc	34/34	1	2	FACETS	0.892	0.844	0.942	0.892	0.844	0.942	CLONAL	1	FALSE	1	0.678097903973063	2		1012	1084	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314940	1314940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	23	431	0	ENST00000400841.2:c.721C>T	p.Leu241Phe	p.L241F	ENST00000400841		241	Ctt/Ttt	6/6	1	1	FACETS	0.101	0.078	0.127	0.101	0.078	0.127	SUBCLONAL	1	FALSE	0	0.678097903973063	1		431	445	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226030	53226030	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	411	550	0	ENST00000375401.3:c.2819C>T	p.Pro940Leu	p.P940L	ENST00000375401	NM_004187.3	940	cCc/cTc	19/26	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	FALSE	0	0.678097903973063	1		550	559	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412033	63412033	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	72	315	0	ENST00000330258.3:c.1134T>G	p.Asp378Glu	p.D378E	ENST00000330258	NM_152424.3	378	gaT/gaG	2/2	1	1	FACETS	0.496	0.438	0.557	0.496	0.438	0.557	SUBCLONAL	1	FALSE	0	0.678097903973063	1		315	283	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525040	187525040	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747985901	NA	P-0045461-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	209	412	0	ENST00000441802.2:c.10640C>T	p.Pro3547Leu	p.P3547L	ENST00000441802	NM_005245.3	3547	cCc/cTc	19/27	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.678097903973063	2		412	595	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519958	NA	P-0045462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	236	738	0	ENST00000481739.1:c.1280C>A	p.Ser427Tyr	p.S427Y	ENST00000481739	NM_002957.4	427	tCc/tAc	10/10	0.32677823402436	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	0	0.32677823402436	1		738	863	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18956876	18956876	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	119	645	0	ENST00000262803.5:c.319G>T	p.Glu107Ter	p.E107*	ENST00000262803	NM_002911.3	107	Gaa/Taa	2/24	1	2	FACETS	0.894	0.806	0.986	0.894	0.806	0.986	CLONAL	1	FALSE	1	0.32677823402436	2		645	815	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18956882	18956882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	113	628	0	ENST00000262803.5:c.325G>A	p.Glu109Lys	p.E109K	ENST00000262803	NM_002911.3	109	Gaa/Aaa	2/24	1	2	FACETS	0.873	0.786	0.966	0.873	0.786	0.966	CLONAL	1	FALSE	1	0.32677823402436	2		628	792	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436687	52436687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	51	595	0	ENST00000460680.1:c.1987G>A	p.Asp663Asn	p.D663N	ENST00000460680	NM_004656.3	663	Gat/Aat	16/17	0.255357552451374	0	FACETS	0.396	0.337	0.462			1	SUBCLONAL	1	FALSE	0	0.32677823402436	0		595	530	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941837	44941837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	68	129	0	ENST00000377967.4:c.3161G>A	p.Arg1054Lys	p.R1054K	ENST00000377967	NM_021140.2	1054	aGa/aAa	21/29	1	1	FACETS	0.814	0.719	0.912	1	0.979	1	CLONAL	2	FALSE	0	0.32677823402436	1		129	214	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941830	44941830	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	CA	novel	NA	P-0045462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	49	129	0	ENST00000377967.4:c.3154delinsCA	p.Glu1052GlnfsTer7	p.E1052Qfs*7	ENST00000377967	NM_021140.2	1052	Gaa/CAaa	21/29	1	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	0	0.32677823402436	1		129	209	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579861	7579861	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs876658627	NA	P-0045465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	52	653	0	ENST00000269305.4:c.52del	p.Thr18HisfsTer26	p.T18Hfs*26	ENST00000269305	NM_001126112.2	18	Aca/ca	2/11	1	2	FACETS	0.991	0.842	1	0.991	0.842	1	CLONAL	1	TRUE	1	0.13	2		653	807	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220378	1220378	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	36	641	0	ENST00000326873.7:c.471C>G	p.Phe157Leu	p.F157L	ENST00000326873	NM_000455.4	157	ttC/ttG	4/10	1	2	FACETS	0.788	0.646	0.948	0.788	0.646	0.948	CLONAL	1	TRUE	1	0.13	2		641	703	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943803	71943803	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	50	600	0	ENST00000298229.2:c.1846A>T	p.Ile616Phe	p.I616F	ENST00000298229	NM_001567.3	616	Atc/Ttc	15/28	1	2	FACETS	0.962	0.814	1	0.962	0.814	1	CLONAL	1	TRUE	1	0.13	2		600	800	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974715	21974737	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGCGCCCCCGCCTCCAGCAGC	GCAGCGCCCCCGCCTCCAGCAGC	-	novel	NA	P-0045465-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	33	413	0	ENST00000304494.5:c.90_112del	p.Leu31GlnfsTer5	p.L31Qfs*5	ENST00000304494	NM_000077.4	30	gcGCTGCTGGAGGCGGGGGCGCTGCcc/gccc	1/3	1	2	FACETS	1	0.833	1	1	0.833	1	CLONAL	1	TRUE	1	0.13	2		413	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs868137297	NA	P-0045466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	70	734	0	ENST00000269305.4:c.376-1G>A		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.332997285394944	1	FACETS	0.855	0.75	0.967	0.855	0.75	0.967	CLONAL	1	TRUE	0	0.364040720531162	1		734	368	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913386	NA	P-0045466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	69	506	0	ENST00000304494.5:c.341C>A	p.Pro114His	p.P114H	ENST00000304494	NM_000077.4	114	cCc/cAc	2/3	0.364040720531162	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.364040720531162	1		506	259	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894876	101894876	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	28	276	1	ENST00000374994.4:c.429G>T	p.Leu143Phe	p.L143F	ENST00000374994	NM_004612.2	143	ttG/ttT	3/9	0.364040720531162	1	FACETS	0.786	0.636	0.954	0.786	0.636	0.954	CLONAL	1	TRUE	0	0.364040720531162	1		277	160	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894934	101894934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	28	259	0	ENST00000374994.4:c.487G>A	p.Asp163Asn	p.D163N	ENST00000374994	NM_004612.2	163	Gac/Aac	3/9	0.364040720531162	1	FACETS	0.946	0.768	1	0.946	0.768	1	CLONAL	1	TRUE	0	0.364040720531162	1		259	133	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894946	101894946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	29	247	0	ENST00000374994.4:c.499G>T	p.Asp167Tyr	p.D167Y	ENST00000374994	NM_004612.2	167	Gat/Tat	3/9	0.364040720531162	1	FACETS	1	0.824	1	1	0.824	1	CLONAL	1	TRUE	0	0.364040720531162	1		247	129	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894964	101894964	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	26	233	0	ENST00000374994.4:c.517G>C	p.Glu173Gln	p.E173Q	ENST00000374994	NM_004612.2	173	Gag/Cag	3/9	0.364040720531162	1	FACETS	0.982	0.791	1	0.982	0.791	1	CLONAL	1	TRUE	0	0.364040720531162	1		233	119	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894982	101894982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	24	203	0	ENST00000374994.4:c.535G>A	p.Asp179Asn	p.D179N	ENST00000374994	NM_004612.2	179	Gac/Aac	3/9	0.364040720531162	1	FACETS	1	0.839	1	1	0.839	1	CLONAL	1	TRUE	0	0.364040720531162	1		203	102	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894994	101894994	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1452337021	NA	P-0045466-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	20	191	0	ENST00000374994.4:c.547G>A	p.Asp183Asn	p.D183N	ENST00000374994	NM_004612.2	183	Gat/Aat	3/9	0.364040720531162	1	FACETS	0.936	0.73	1	0.936	0.73	1	CLONAL	1	TRUE	0	0.364040720531162	1		191	96	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0045467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	41	241	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.91	1	1	0.973	1	CLONAL	2	FALSE	1	0.227922379331538	2		241	162	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0045467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	429	565	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.227922379331538	2	FACETS	1	0.984	1	1	0.997	1	CLONAL	5	FALSE	0	0.227922379331538	2		567	725	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546832	9546832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1018346655	NA	P-0045467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	58	469	1	ENST00000353224.5:c.1190C>T	p.Thr397Met	p.T397M	ENST00000353224	NM_177990.2	397	aCg/aTg	5/10	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	1	0.227922379331538	2		470	450	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76849194	76849194	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045467-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	29	133	0	ENST00000373344.5:c.6082C>T	p.Arg2028Ter	p.R2028*	ENST00000373344	NM_000489.3	2028	Cga/Tga	26/35	NA	2	FACETS	0.95	0.795	1			1	INDETERMINATE	4	FALSE	NA	0.227922379331538	2		133	67	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0045468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	195	501	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.272868467707859	3	FACETS	1	0.99	1	0.711	0.66	0.765	CLONAL	1	TRUE	1	0.419200190842352	3		501	791	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448599	89448599	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs776808297	NA	P-0045468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	67	468	0	ENST00000336596.2:c.1563C>A	p.Ser521Arg	p.S521R	ENST00000336596	NM_005233.5	521	agC/agA	7/17	0.419200190842352	1	FACETS	0.594	0.518	0.676	0.594	0.518	0.676	SUBCLONAL	1	TRUE	0	0.419200190842352	1		468	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577128	7577128	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519987	NA	P-0045468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	286	660	0	ENST00000269305.4:c.810T>G	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	ttT/ttG	8/11	0.328390403966693	2	FACETS	0.908	0.859	0.959	0.908	0.859	0.959	CLONAL	2	TRUE	0	0.419200190842352	2		660	751	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360602	118360602	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	39	309	0	ENST00000534358.1:c.4575G>C	p.Trp1525Cys	p.W1525C	ENST00000534358	NM_005933.3	1525	tgG/tgC	12/36	0.240977361784818	4	FACETS	0.662	0.549	0.787			1	INDETERMINATE	1	TRUE	NA	0.419200190842352	4		309	399	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804207	46804207	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	268	719	0	ENST00000290295.7:c.800del	p.Arg267ProfsTer12	p.R267Pfs*12	ENST00000290295	NM_006361.5	267	cGc/cc	2/2	0.163478216049339	3	FACETS	0.91	0.856	0.965	0.607	0.57	0.643	INDETERMINATE	2	TRUE	0	0.419200190842352	3		719	850	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349924	70349924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045468-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	198	418	0	ENST00000374080.3:c.3907G>A	p.Asp1303Asn	p.D1303N	ENST00000374080		1303	Gac/Aac	28/45	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.419200190842352	1		418	503	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163794	47163794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	147	272	0	ENST00000409792.3:c.2332C>T	p.Pro778Ser	p.P778S	ENST00000409792	NM_014159.6	778	Cca/Tca	3/21	0.571097796456418	4	FACETS	0.873	0.806	0.942	0.873	0.806	0.942	CLONAL	2	TRUE	2	0.726310965457919	4		272	400	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577064	7577070	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTGCG	TCTTGCG	-	novel	NA	P-0045469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	413	687	1	ENST00000269305.4:c.868_874del	p.Arg290LysfsTer53	p.R290Kfs*53	ENST00000269305	NM_001126112.2	290	CGCAAGAaa/aa	8/11	0.610782239749967	2	FACETS	0.776	0.745	0.806	0.776	0.745	0.806	SUBCLONAL	2	TRUE	0	0.726310965457919	2		688	733	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	45	425	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.379155011029317	2		425	226	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0045470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	64	268	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	1	2	FACETS	0.97	0.845	1	0.97	0.845	1	CLONAL	1	TRUE	1	0.379155011029317	2		268	348	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684326	29684326	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201367	NA	P-0045470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	45	380	0	ENST00000356175.3:c.7846C>T	p.Arg2616Ter	p.R2616*	ENST00000356175	NM_000267.3	2616	Cga/Tga	53/57	0.23897183174555	1	FACETS	0.501	0.422	0.588	0.501	0.422	0.588	SUBCLONAL	1	TRUE	0	0.379155011029317	1		380	384	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719252	61719252	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	38	271	0	ENST00000401558.2:c.1805T>G	p.Val602Gly	p.V602G	ENST00000401558	NM_003400.3	602	gTt/gGt	16/25	0.101006440433361	4	FACETS	0.799	0.662	0.951	0.399	0.331	0.476	INDETERMINATE	1	TRUE	2	0.379155011029317	4		271	346	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61760907	61760907	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	42	324	0	ENST00000401558.2:c.126G>C	p.Gln42His	p.Q42H	ENST00000401558	NM_003400.3	42	caG/caC	2/25	0.101006440433361	4	FACETS	0.806	0.675	0.952	0.403	0.337	0.476	INDETERMINATE	1	TRUE	2	0.379155011029317	4		324	379	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0045471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	239	623	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.42036105852777	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.42036105852777	1		623	790	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0045471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	121	363	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.887	0.803	0.975	0.887	0.803	0.975	CLONAL	1	TRUE	1	0.42036105852777	2		365	649	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0045471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	62	309	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	0.819	0.711	0.935	0.819	0.711	0.935	CLONAL	1	TRUE	1	0.42036105852777	2		309	360	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0045471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	82	309	3	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.879	0.778	0.985	0.879	0.778	0.985	CLONAL	1	TRUE	1	0.42036105852777	2		312	444	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0045471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	163	634	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.42036105852777	2		634	593	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788617	3788617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519884	NA	P-0045471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	83	267	0	ENST00000262367.5:c.4337G>A	p.Arg1446His	p.R1446H	ENST00000262367	NM_004380.2	1446	cGc/cAc	26/31	1	2	FACETS	0.849	0.752	0.952	0.849	0.752	0.952	CLONAL	1	TRUE	1	0.42036105852777	2		267	465	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856014	45856014	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751084702	NA	P-0045471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	277	657	2	ENST00000391945.4:c.1892G>A	p.Arg631His	p.R631H	ENST00000391945	NM_000400.3	631	cGc/cAc	20/23	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.42036105852777	2		659	1102	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638456	176638456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750354456	NA	P-0045471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	191	535	1	ENST00000439151.2:c.3056G>A	p.Arg1019His	p.R1019H	ENST00000439151	NM_022455.4	1019	cGc/cAc	5/23	1	2	FACETS	0.935	0.864	1	0.935	0.864	1	CLONAL	1	TRUE	1	0.42036105852777	2		536	972	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0045471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	16	467	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.203	0.149	0.267	0.203	0.149	0.267	SUBCLONAL	1	TRUE	1	0.42036105852777	2		467	375	SUCCESS
APC	324	MSKCC	GRCh37	5	112176008	112176008	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	56	183	0	ENST00000257430.4:c.4717G>T	p.Glu1573Ter	p.E1573*	ENST00000257430	NM_000038.5	1573	Gaa/Taa	16/16	0.42036105852777	1	FACETS	0.931	0.808	1	0.931	0.808	1	CLONAL	1	TRUE	0	0.42036105852777	1		183	226	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0045471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	138	492	0	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	1	2	FACETS	0.753	0.685	0.824	0.753	0.685	0.824	SUBCLONAL	1	TRUE	1	0.42036105852777	2		492	872	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845693	68845694	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	173	443	0	ENST00000261769.5:c.944dup	p.Asn315LysfsTer6	p.N315Kfs*6	ENST00000261769	NM_004360.3	313	-/A	7/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.42036105852777	2		443	760	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035204	6035207	+	frameshift_variant	Frame_Shift_Del	DEL	CTGT	CTGT	-	rs267608154	NA	P-0045471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	81	298	0	ENST00000265849.7:c.861_864del	p.Arg287SerfsTer19	p.R287Sfs*19	ENST00000265849	NM_000535.5	287	agACAG/ag	8/15	1	2	FACETS	0.856	0.758	0.961	0.856	0.758	0.961	CLONAL	1	TRUE	1	0.42036105852777	2		298	450	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196093	138196093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1405321250	NA	P-0045471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	111	217	0	ENST00000237289.4:c.407G>A	p.Arg136His	p.R136H	ENST00000237289	NM_001270507.1	136	cGc/cAc	3/9	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.42036105852777	2		217	474	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635161	87635161	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	125	356	0	ENST00000277120.3:c.2213C>T	p.Pro738Leu	p.P738L	ENST00000277120		738	cCa/cTa	18/19	1	2	FACETS	0.922	0.836	1	0.922	0.836	1	CLONAL	1	TRUE	1	0.42036105852777	2		356	645	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845958	151845959	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0045471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	129	423	0	ENST00000262189.6:c.13053dup	p.Trp4352MetfsTer17	p.W4352Mfs*17	ENST00000262189	NM_170606.2	4351	-/A	52/59	1	2	FACETS	0.933	0.848	1	0.933	0.848	1	CLONAL	1	TRUE	1	0.42036105852777	2		423	658	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40368072	40368072	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555548678	NA	P-0045471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	234	507	1	ENST00000293328.3:c.1433C>T	p.Ala478Val	p.A478V	ENST00000293328	NM_012448.3	478	gCg/gTg	12/19	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.42036105852777	2		508	1049	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018167	48018167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769279475	NA	P-0045471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	187	474	0	ENST00000234420.5:c.362G>A	p.Arg121His	p.R121H	ENST00000234420	NM_000179.2	121	cGc/cAc	2/10	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.42036105852777	2		474	880	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685280	89685280	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060500118	NA	P-0045471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	22	132	2	ENST00000371953.3:c.175T>C	p.Ser59Pro	p.S59P	ENST00000371953	NM_000314.4	59	Tca/Cca	3/9	1	2	FACETS	0.612	0.478	0.765	0.612	0.478	0.765	SUBCLONAL	1	TRUE	1	0.42036105852777	2		134	171	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797375	42797376	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0045471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	290	919	0	ENST00000575354.2:c.3743dup	p.Leu1249ThrfsTer6	p.L1249Tfs*6	ENST00000575354	NM_015125.3	1246	agc/agCc	15/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.42036105852777	2		919	1295	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809530	36809530	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	291	791	0	ENST00000373129.3:c.935T>C	p.Val312Ala	p.V312A	ENST00000373129	NM_032017.1	312	gTc/gCc	10/12	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.42036105852777	2		791	1203	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939827	71939828	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0045471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	296	878	0	ENST00000298229.2:c.459dup	p.Thr154HisfsTer11	p.T154Hfs*11	ENST00000298229	NM_001567.3	152	gcc/gCcc	4/28	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.42036105852777	2		878	1297	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201106	108201106	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	61	269	0	ENST00000278616.4:c.7473G>A	p.Trp2491Ter	p.W2491*	ENST00000278616	NM_000051.3	2491	tgG/tgA	50/63	1	2	FACETS	0.864	0.75	0.986	0.864	0.75	0.986	CLONAL	1	TRUE	1	0.42036105852777	2		269	336	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218374	133218374	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs377461656	NA	P-0045471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	132	627	0	ENST00000320574.5:c.5237A>G	p.Asn1746Ser	p.N1746S	ENST00000320574	NM_006231.2	1746	aAc/aGc	39/49	1	2	FACETS	0.592	0.536	0.651	0.592	0.536	0.651	SUBCLONAL	1	TRUE	1	0.42036105852777	2		627	1061	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219564	133219564	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	236	595	0	ENST00000320574.5:c.4570C>T	p.Pro1524Ser	p.P1524S	ENST00000320574	NM_006231.2	1524	Ccc/Tcc	36/49	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.42036105852777	2		595	931	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007666	45007667	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	82	193	0	ENST00000558401.1:c.116dup	p.Ser40ValfsTer17	p.S40Vfs*17	ENST00000558401	NM_004048.2	38	gga/ggAa	2/4	0.42036105852777	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.42036105852777	1		193	257	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223320	2223320	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	263	711	0	ENST00000326181.6:c.932A>C	p.Glu311Ala	p.E311A	ENST00000326181	NM_032271.2	311	gAg/gCg	10/21	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.42036105852777	2		711	1066	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831426	72831426	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	67	432	0	ENST00000268489.5:c.5155A>T	p.Ile1719Phe	p.I1719F	ENST00000268489	NM_006885.3	1719	Att/Ttt	9/10	1	2	FACETS	0.466	0.404	0.533	0.466	0.404	0.533	SUBCLONAL	1	TRUE	1	0.42036105852777	2		432	684	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627357	14627357	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	197	564	1	ENST00000254322.2:c.713T>A	p.Val238Asp	p.V238D	ENST00000254322	NM_006145.1	238	gTt/gAt	2/3	1	2	FACETS	0.948	0.877	1	0.948	0.877	1	CLONAL	1	TRUE	1	0.42036105852777	2		565	989	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754011	42754011	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	212	587	0	ENST00000222329.4:c.341T>C	p.Val114Ala	p.V114A	ENST00000222329	NM_006494.2	114	gTc/gCc	3/4	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.42036105852777	2		587	887	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99136596	99136596	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	209	593	0	ENST00000074304.5:c.85A>G	p.Met29Val	p.M29V	ENST00000074304	NM_001134224.1	29	Atg/Gtg	3/26	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.42036105852777	2		593	971	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522414	176522414	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	260	803	0	ENST00000292408.4:c.1603A>G	p.Asn535Asp	p.N535D	ENST00000292408	NM_213647.1	535	Aac/Gac	12/18	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.42036105852777	2		803	1151	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410136	139410136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs562413261	NA	P-0045471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	247	830	1	ENST00000277541.6:c.1702G>A	p.Asp568Asn	p.D568N	ENST00000277541	NM_017617.3	568	Gat/Aat	11/34	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.42036105852777	2		831	1122	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0045473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	523	535	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.553193658396758	2	FACETS	0.959	0.926	0.992	0.959	0.926	0.992	CLONAL	2	TRUE	0	0.583869761134531	2		535	934	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954345	48954345	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1131690877	NA	P-0045473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	78	220	0	ENST00000267163.4:c.1466G>A	p.Cys489Tyr	p.C489Y	ENST00000267163	NM_000321.2	489	tGc/tAc	16/27	0.431226227563882	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.583869761134531	1		220	186	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556864	29556886	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	TGATACCAATACTCAATTTGTAG	TGATACCAATACTCAATTTGTAG	CTA	novel	NA	P-0045473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	14	216	0	ENST00000356175.3:c.2862_2884delinsCTA	p.Asp955Ter	p.D955*	ENST00000356175	NM_000267.3	954	acTGATACCAATACTCAATTTGTAGaa/acCTAaa	22/57	0.583869761134531	1	FACETS	0.25	0.181	0.331	0.25	0.181	0.331	SUBCLONAL	1	TRUE	0	0.583869761134531	1		216	136	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	60	425	0				ENST00000310581	NM_198253.2	-/1132			0.24190415860304	1	FACETS	0.862	0.748	0.984	0.862	0.748	0.984	CLONAL	1	TRUE	0	0.376616369477636	1		425	300	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0045489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	50	524	0	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.925	0.79	1	0.925	0.79	1	CLONAL	1	TRUE	1	0.376616369477636	2		524	287	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205807	108205807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782719	NA	P-0045489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	50	376	0	ENST00000278616.4:c.8122G>A	p.Asp2708Asn	p.D2708N	ENST00000278616	NM_000051.3	2708	Gat/Aat	55/63	0.24190415860304	1	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	0	0.376616369477636	1		376	213	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061393	38061393	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	111	583	0	ENST00000250448.2:c.596G>A	p.Trp199Ter	p.W199*	ENST00000250448	NM_004496.3	199	tGg/tAg	2/2	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.376616369477636	2		583	494	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239420	105239420	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	66	571	0	ENST00000349310.3:c.967G>C	p.Asp323His	p.D323H	ENST00000349310	NM_001014432.1	323	Gac/Cac	12/15	1	2	FACETS	0.718	0.625	0.819	0.718	0.625	0.819	SUBCLONAL	1	TRUE	1	0.376616369477636	2		571	488	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254713	16254713	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	60	481	0	ENST00000375759.3:c.1978G>C	p.Glu660Gln	p.E660Q	ENST00000375759	NM_015001.2	660	Gaa/Caa	11/15	1	2	FACETS	0.85	0.735	0.973	0.85	0.735	0.973	CLONAL	1	TRUE	1	0.376616369477636	2		481	375	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730909	40730909	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201064715	NA	P-0045489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	151	598	0	ENST00000373198.4:c.3626G>A	p.Arg1209Gln	p.R1209Q	ENST00000373198	NM_133170.3	1209	cGg/cAg	27/32	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.376616369477636	2		598	704	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396856	396856	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs574168909	NA	P-0045489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	64	719	1	ENST00000262320.3:c.170C>T	p.Ser57Leu	p.S57L	ENST00000262320	NM_003502.3	57	tCg/tTg	2/11	1	2	FACETS	0.445	0.385	0.511	0.445	0.385	0.511	SUBCLONAL	1	TRUE	1	0.376616369477636	2		720	763	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021332	31021332	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373126831	NA	P-0045489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	123	533	0	ENST00000375687.4:c.1331C>T	p.Ser444Leu	p.S444L	ENST00000375687	NM_015338.5	444	tCa/tTa	12/13	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.376616369477636	2		533	528	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495604	56495604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142809206	NA	P-0045489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	45	481	0	ENST00000267101.3:c.3794G>A	p.Arg1265Gln	p.R1265Q	ENST00000267101	NM_001982.3	1265	cGg/cAg	28/28	1	2	FACETS	0.516	0.434	0.607	0.516	0.434	0.607	SUBCLONAL	1	TRUE	1	0.376616369477636	2		481	463	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805222	43805222	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	109	601	0	ENST00000372470.3:c.672G>T	p.Gln224His	p.Q224H	ENST00000372470	NM_005373.2	224	caG/caT	4/12	1	2	FACETS	0.926	0.833	1	0.926	0.833	1	CLONAL	1	TRUE	1	0.376616369477636	2		601	625	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982095	201982096	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0045489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	150	700	0	ENST00000359651.3:c.622dup	p.His208ProfsTer9	p.H208Pfs*9	ENST00000359651		207	tcc/tCcc	5/8	0.24190415860304	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.376616369477636	1		700	625	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690843	89690843	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1554897880	NA	P-0045489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	18	297	0	ENST00000371953.3:c.250A>T	p.Arg84Ter	p.R84*	ENST00000371953	NM_000314.4	84	Aga/Tga	4/9	1	2	FACETS	0.546	0.413	0.701	0.546	0.413	0.701	SUBCLONAL	1	TRUE	1	0.376616369477636	2		297	175	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117703	108117703	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	14	185	0	ENST00000278616.4:c.914del	p.Ser305Ter	p.S305*	ENST00000278616	NM_000051.3	305	tCa/ta	8/63	0.24190415860304	1	FACETS	0.754	0.555	0.986	0.754	0.555	0.986	CLONAL	1	TRUE	0	0.376616369477636	1		185	80	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205818	108205818	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	40	358	0	ENST00000278616.4:c.8133G>C	p.Glu2711Asp	p.E2711D	ENST00000278616	NM_000051.3	2711	gaG/gaC	55/63	0.24190415860304	1	FACETS	0.893	0.751	1	0.893	0.751	1	CLONAL	1	TRUE	0	0.376616369477636	1		358	193	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118360919	118360919	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	27	400	0	ENST00000534358.1:c.4651C>G	p.His1551Asp	p.H1551D	ENST00000534358	NM_005933.3	1551	Cat/Gat	13/36	0.24190415860304	1	FACETS	0.249	0.197	0.308	0.249	0.197	0.308	SUBCLONAL	1	TRUE	0	0.376616369477636	1		400	468	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366520	118366520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	23	342	0	ENST00000534358.1:c.5469G>A	p.Met1823Ile	p.M1823I	ENST00000534358	NM_005933.3	1823	atG/atA	19/36	0.24190415860304	1	FACETS	0.327	0.255	0.41	0.327	0.255	0.41	SUBCLONAL	1	TRUE	0	0.376616369477636	1		342	303	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907259	32907259	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	57	412	0	ENST00000380152.3:c.1644G>C	p.Gln548His	p.Q548H	ENST00000380152		548	caG/caC	10/27	1	2	FACETS	0.814	0.71	0.922	1	0.975	1	CLONAL	2	TRUE	1	0.376616369477636	2		412	186	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061479	38061479	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	135	524	0	ENST00000250448.2:c.510G>C	p.Lys170Asn	p.K170N	ENST00000250448	NM_004496.3	170	aaG/aaC	2/2	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.376616369477636	2		524	567	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304065	91304065	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	39	491	0	ENST00000355112.3:c.1462G>C	p.Glu488Gln	p.E488Q	ENST00000355112	NM_000057.2	488	Gaa/Caa	7/22	1	2	FACETS	0.693	0.577	0.821	0.693	0.577	0.821	SUBCLONAL	1	TRUE	1	0.376616369477636	2		491	299	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99451974	99451974	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	78	376	1	ENST00000268035.6:c.1308C>A	p.His436Gln	p.H436Q	ENST00000268035	NM_000875.3	436	caC/caA	6/21	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.376616369477636	2		377	377	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965032	15965032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1403583301	NA	P-0045489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	81	469	0	ENST00000268712.3:c.5564G>A	p.Ser1855Asn	p.S1855N	ENST00000268712	NM_006311.3	1855	aGc/aAc	37/46	0.376616369477636	1	FACETS	0.973	0.863	1	0.973	0.863	1	CLONAL	1	TRUE	0	0.376616369477636	1		469	359	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029399	16029399	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	14	327	0	ENST00000268712.3:c.1631C>G	p.Ser544Cys	p.S544C	ENST00000268712	NM_006311.3	544	tCc/tGc	15/46	0.376616369477636	1	FACETS	0.292	0.211	0.389	0.292	0.211	0.389	SUBCLONAL	1	TRUE	0	0.376616369477636	1		327	207	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122506	17122506	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	96	569	0	ENST00000285071.4:c.889G>C	p.Glu297Gln	p.E297Q	ENST00000285071	NM_144997.5	297	Gaa/Caa	9/14	0.376616369477636	1	FACETS	0.902	0.807	1	0.902	0.807	1	CLONAL	1	TRUE	0	0.376616369477636	1		569	459	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218158	36218158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1311138959	NA	P-0045489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	93	440	0	ENST00000222270.7:c.4105G>A	p.Glu1369Lys	p.E1369K	ENST00000222270	NM_014727.1	1369	Gag/Aag	15/37	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.376616369477636	2		440	421	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193530	99193530	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	236	727	0	ENST00000074304.5:c.2725G>T	p.Glu909Ter	p.E909*	ENST00000074304	NM_001134224.1	909	Gag/Tag	25/26	0.198075041011406	3	FACETS	0.888	0.83	0.946	0.888	0.83	0.946	INDETERMINATE	2	TRUE	1	0.376616369477636	3		727	839	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160630	56160630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	51	293	0	ENST00000399503.3:c.904G>A	p.Glu302Lys	p.E302K	ENST00000399503	NM_005921.1	302	Gag/Aag	4/20	0.24190415860304	1	FACETS	0.952	0.818	1	0.952	0.818	1	CLONAL	1	TRUE	0	0.376616369477636	1		293	231	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180916	32180916	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	112	517	2	ENST00000375023.3:c.2434G>A	p.Asp812Asn	p.D812N	ENST00000375023	NM_004557.3	812	Gac/Aac	15/30	1	2	FACETS	0.97	0.875	1	0.97	0.875	1	CLONAL	1	TRUE	1	0.376616369477636	2		519	613	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534572	140534572	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1174578809	NA	P-0045489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	42	323	0	ENST00000288602.6:c.341C>G	p.Ser114Cys	p.S114C	ENST00000288602	NM_004333.4	114	tCt/tGt	3/18	1	2	FACETS	0.826	0.694	0.971	0.826	0.694	0.971	CLONAL	1	TRUE	1	0.376616369477636	2		323	270	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123078	5123078	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	54	393	0	ENST00000381652.3:c.3134A>G	p.Tyr1045Cys	p.Y1045C	ENST00000381652	NM_004972.3	1045	tAt/tGt	23/25	0.376616369477636	1	FACETS	0.978	0.844	1	0.978	0.844	1	CLONAL	1	TRUE	0	0.376616369477636	1		393	238	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101909941	101909941	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	12	161	0	ENST00000374994.4:c.1261C>G	p.His421Asp	p.H421D	ENST00000374994	NM_004612.2	421	Cat/Gat	8/9	0.376616369477636	1	FACETS	0.995	0.72	1	0.995	0.72	1	CLONAL	1	TRUE	0	0.376616369477636	1		161	52	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034472	47034475	+	frameshift_variant	Frame_Shift_Del	DEL	GATG	GATG	-	novel	NA	P-0045489-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	142	323	0	ENST00000377604.3:c.563_566del	p.Met188LysfsTer77	p.M188Kfs*77	ENST00000377604	NM_001204468.1	186	cGATGg/cg	6/24	0.204248103910226	2	FACETS	0.933	0.859	1			1	INDETERMINATE	2	TRUE	NA	0.376616369477636	2		323	404	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	45	425	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.673	0.566	0.792	0.673	0.566	0.792	SUBCLONAL	1	TRUE	1	0.27	2		425	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0045490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	39	531	0	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	1	2	FACETS	0.372	0.307	0.445	0.372	0.307	0.445	SUBCLONAL	1	TRUE	1	0.27	2		531	776	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166275	32166275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs967436228	NA	P-0045490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	61	516	1	ENST00000375023.3:c.4679C>T	p.Ala1560Val	p.A1560V	ENST00000375023	NM_004557.3	1560	gCg/gTg	26/30	0.135143197956467	3	FACETS	0.474	0.407	0.547	0.237	0.203	0.274	INDETERMINATE	1	TRUE	1	0.27	3		517	1082	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033813	49033837	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TATTCCCACAGTGTATCGGCTAGCC	TATTCCCACAGTGTATCGGCTAGCC	-	novel	NA	P-0045490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	29	204	0	ENST00000267163.4:c.1961-8_1977del		p.X654_splice	ENST00000267163	NM_000321.2	654		20/27	1	2	FACETS	0.538	0.432	0.66	0.538	0.432	0.66	SUBCLONAL	1	TRUE	1	0.27	2		204	399	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514464	41514464	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	41	380	0	ENST00000373198.4:c.197A>G	p.Asp66Gly	p.D66G	ENST00000373198	NM_133170.3	66	gAc/gGc	2/32	1	2	FACETS	0.428	0.355	0.509	0.428	0.355	0.509	SUBCLONAL	1	TRUE	1	0.27	2		380	710	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458272	12458272	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	55	375	0	ENST00000287820.6:c.889C>T	p.Pro297Ser	p.P297S	ENST00000287820	NM_015869.4	297	Ccc/Tcc	6/7	1	2	FACETS	0.549	0.469	0.637	0.549	0.469	0.637	SUBCLONAL	1	TRUE	1	0.27	2		375	742	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965707	93965707	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045490-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	18	248	0	ENST00000369303.4:c.2221G>T	p.Gly741Ter	p.G741*	ENST00000369303	NM_004440.3	741	Gga/Tga	13/17	1	2	FACETS	0.376	0.282	0.486	0.376	0.282	0.486	SUBCLONAL	1	TRUE	1	0.27	2		248	355	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711879	89711880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	104	331	0	ENST00000371953.3:c.499dup	p.Thr167AsnfsTer13	p.T167Nfs*13	ENST00000371953	NM_000314.4	166	gta/gtAa	6/9	0.439605831412007	1	FACETS	0.838	0.758	0.92	0.838	0.758	0.92	CLONAL	1	TRUE	0	0.536141537603894	1		331	339	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846235	156846235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201564883	NA	P-0045491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	245	694	1	ENST00000524377.1:c.1676G>A	p.Arg559His	p.R559H	ENST00000524377	NM_002529.3	559	cGt/cAt	14/17	1	2	FACETS	0.899	0.84	0.959	0.899	0.84	0.959	CLONAL	1	TRUE	1	0.536141537603894	2		695	1017	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037908	49037909	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATAG	novel	NA	P-0045491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	68	342	0	ENST00000267163.4:c.2150_2153dup	p.Leu719ArgfsTer3	p.L719Rfs*3	ENST00000267163	NM_000321.2	716	-/ATAG	21/27	0.512445353937424	1	FACETS	0.731	0.644	0.823	0.731	0.644	0.823	SUBCLONAL	1	TRUE	0	0.536141537603894	1		342	254	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522605	67522606	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0045491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	132	303	0	ENST00000274335.5:c.105dup	p.Ser36ValfsTer9	p.S36Vfs*9	ENST00000274335		34	-/G	1/15	1	2	FACETS	0.985	0.899	1	0.985	0.899	1	CLONAL	1	TRUE	1	0.536141537603894	2		303	500	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40497663	40497671	+	frameshift_variant	Frame_Shift_Del	DEL	CAAGATACC	CAAGATACC	GG	novel	NA	P-0045491-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	159	422	1	ENST00000264657.5:c.278_286delinsCC	p.Arg93ThrfsTer43	p.R93Tfs*43	ENST00000264657	NM_139276.2	93	aGGTATCTTGag/aCCag	4/24	1	2	FACETS	0.861	0.791	0.933	0.861	0.791	0.933	CLONAL	1	TRUE	1	0.536141537603894	2		423	689	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696689	47696689	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519972	NA	P-0045492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	194	391	0	ENST00000347630.2:c.259T>A	p.Tyr87Asn	p.Y87N	ENST00000347630	NM_001007230.1	87	Tac/Aac	5/11	0.774761848366991	3	FACETS	0.982	0.926	1	0.982	0.926	1	CLONAL	2	TRUE	1	0.773719571260009	3		391	354	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938394	44938394	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	118	138	0	ENST00000377967.4:c.2942T>A	p.Leu981Gln	p.L981Q	ENST00000377967	NM_021140.2	981	cTg/cAg	20/29	0.679945921276165	2	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.773719571260009	2		138	138	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0045493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	377	354	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.441916249253365	6	FACETS	1	0.976	1	1	0.976	1	CLONAL	5	TRUE	1	0.441916249253365	6		354	629	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70412343	70412635	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTAAGTGGGTAAGTATTTCCTATTTATACATTTTTTTGAAGCTTGTTATTCCAGAGCTGATATTTATACATTTACAATAGCCAGAGTGATCTTTATTTTATTTATTCATTTATTTATTTAATTTTTGAGACAGGCTTTGTCGCCCCGGCTGGATTGCAGTGGTGCAATCACACCTCACTGCAGCCTTGATCTCCCAGGCTCAAGCAATCTTTCCACCTTAGCCTCCAAGTACTTAAGACTTGCCACCAAACCCGGCTAATTTTTTTTTTTTTTTTTTTTTTTTTAGTGGAGA	GCTAAGTGGGTAAGTATTTCCTATTTATACATTTTTTTGAAGCTTGTTATTCCAGAGCTGATATTTATACATTTACAATAGCCAGAGTGATCTTTATTTTATTTATTCATTTATTTATTTAATTTTTGAGACAGGCTTTGTCGCCCCGGCTGGATTGCAGTGGTGCAATCACACCTCACTGCAGCCTTGATCTCCCAGGCTCAAGCAATCTTTCCACCTTAGCCTCCAAGTACTTAAGACTTGCCACCAAACCCGGCTAATTTTTTTTTTTTTTTTTTTTTTTTTAGTGGAGA	-	novel	NA	P-0045493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	27	256	0	ENST00000373644.4:c.4456_4461+287del		p.X1486_splice	ENST00000373644	NM_030625.2	1486		6/12	0.372830870060231	3	FACETS	0.474	0.377	0.583	0.237	0.188	0.292	SUBCLONAL	1	TRUE	1	0.441916249253365	3		256	315	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625192	69625192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782556280	NA	P-0045493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	128	756	0	ENST00000334134.2:c.601C>T	p.Pro201Ser	p.P201S	ENST00000334134	NM_005247.2	201	Ccc/Tcc	3/3	0.372830870060231	3	FACETS	0.754	0.683	0.829	0.377	0.341	0.415	SUBCLONAL	1	TRUE	1	0.441916249253365	3		756	938	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968298	18968298	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	48	799	1	ENST00000262803.5:c.2138C>T	p.Ser713Phe	p.S713F	ENST00000262803	NM_002911.3	713	tCc/tTc	15/24	0.154186542285055	3	FACETS	0.318	0.268	0.374	0.159	0.134	0.187	INDETERMINATE	1	TRUE	1	0.441916249253365	3		800	834	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095922	178095922	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	64	394	0	ENST00000397062.3:c.1409T>G	p.Val470Gly	p.V470G	ENST00000397062	NM_006164.4	470	gTa/gGa	5/5	0.441916249253365	5	FACETS	0.678	0.587	0.778	0.226	0.195	0.26	SUBCLONAL	1	TRUE	2	0.441916249253365	5		394	710	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31485062	31485062	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	37	200	0	ENST00000344624.3:c.1922G>A	p.Cys641Tyr	p.C641Y	ENST00000344624		641	tGt/tAt	12/33	0.372830870060231	3	FACETS	0.901	0.748	1	0.45	0.374	0.534	CLONAL	1	TRUE	1	0.441916249253365	3		200	227	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578402	7578402	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519980	NA	P-0045494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	242	577	0	ENST00000269305.4:c.528C>G	p.Cys176Trp	p.C176W	ENST00000269305	NM_001126112.2	176	tgC/tgG	5/11	0.563014460299527	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.563014460299527	1		577	556	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0045495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	71	217	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.705318319331869	3	FACETS	0.626	0.548	0.709	0.313	0.274	0.355	SUBCLONAL	1	TRUE	1	0.716817921781317	3		217	430	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0045495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	137	478	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	0.923	0.848	1	0.923	0.848	1	CLONAL	1	TRUE	1	0.716817921781317	2		478	414	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0045495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	40	656	0	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	1	2	FACETS	0.161	0.133	0.192	0.161	0.133	0.192	SUBCLONAL	1	TRUE	1	0.716817921781317	2		656	695	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0045495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	111	386	2	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	1	2	FACETS	0.796	0.722	0.873	0.796	0.722	0.873	SUBCLONAL	1	TRUE	1	0.716817921781317	2		388	389	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	205	473	0	ENST00000206249.3:c.1609T>G	p.Tyr537Asp	p.Y537D	ENST00000206249	NM_000125.3	537	Tat/Gat	8/8	1	2	FACETS	0.947	0.884	1	0.947	0.884	1	CLONAL	1	TRUE	1	0.716817921781317	2		473	604	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023921	27023922	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0045495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	10	62	0	ENST00000324856.7:c.1027_1028del	p.Ala343SerfsTer56	p.A343Sfs*56	ENST00000324856	NM_006015.4	343	GCa/a	1/20	1	2	FACETS	0.372	0.255	0.514	0.372	0.255	0.514	SUBCLONAL	1	TRUE	1	0.716817921781317	2		62	75	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087963	27087964	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0045495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	116	411	0	ENST00000324856.7:c.2251+1dup		p.-750fs	ENST00000324856	NM_006015.4	750	-/G	6/20	1	2	FACETS	0.621	0.562	0.683	0.621	0.562	0.683	SUBCLONAL	1	TRUE	1	0.716817921781317	2		411	521	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692998	89693051	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGACAAAAAGGTAAGTTATTTTTTGATGTTTTTCCTTTCCTCTTCCTGGATCT	GAGACAAAAAGGTAAGTTATTTTTTGATGTTTTTCCTTTCCTCTTCCTGGATCT	-	novel	NA	P-0045495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	125	299	0	ENST00000371953.3:c.486_492+47del		p.X162_splice	ENST00000371953	NM_000314.4	162		5/9	0.705318319331869	3	FACETS	1	0.914	1	0.502	0.457	0.549	CLONAL	1	TRUE	1	0.716817921781317	3		299	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0045496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	138	623	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.388294908516275	3	FACETS	1	0.985	1	0.691	0.631	0.754	CLONAL	1	TRUE	1	0.388294908516275	3		623	614	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0045496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	38	494	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.316509880663109	2	FACETS	0.915	0.763	1	0.457	0.381	0.541	CLONAL	1	TRUE	0	0.388294908516275	2		494	214	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175480	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	47	267	0	ENST00000257430.4:c.4189G>T	p.Glu1397Ter	p.E1397*	ENST00000257430	NM_000038.5	1397	Gag/Tag	16/16	0.314090059552517	3	FACETS	1	0.936	1	0.597	0.508	0.693	CLONAL	1	TRUE	1	0.388294908516275	3		267	242	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876659802	NA	P-0045496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	76	439	0	ENST00000269305.4:c.833C>A	p.Pro278His	p.P278H	ENST00000269305	NM_001126112.2	278	cCt/cAt	8/11	0.388294908516275	3	FACETS	0.726	0.637	0.822	0.363	0.318	0.411	SUBCLONAL	1	TRUE	1	0.388294908516275	3		439	644	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305347	39305347	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1233347898	NA	P-0045496-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	83	350	0	ENST00000373001.3:c.1078C>T	p.Arg360Ter	p.R360*	ENST00000373001	NM_022157.3	360	Cga/Tga	7/7	0.223711703044502	3	FACETS	0.755	0.672	0.843	0.503	0.448	0.562	INDETERMINATE	2	TRUE	0	0.388294908516275	3		350	338	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442611	52442611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045497-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	181	225	0	ENST00000460680.1:c.134G>A	p.Gly45Glu	p.G45E	ENST00000460680	NM_004656.3	45	gGa/gAa	4/17	0.83787717409485	1	FACETS	0.931	0.885	0.975	0.931	0.885	0.975	CLONAL	1	TRUE	0	0.859372407242679	1		225	258	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0045499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	64	262	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.37	2		262	317	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045499-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	62	425	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.903	0.784	1	0.903	0.784	1	CLONAL	1	TRUE	1	0.37	2		425	371	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188248	10188252	+	frameshift_variant	Frame_Shift_Del	DEL	AACCA	AACCA	-	novel	NA	P-0045506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	115	568	0	ENST00000256474.2:c.394_398del	p.Gln132Ter	p.Q132*	ENST00000256474	NM_000551.3	131	AACCAa/a	2/3	0.277315056343028	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.277315056343028	1		568	567	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940532	49940532	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	186	808	1	ENST00000296474.3:c.511C>T	p.Pro171Ser	p.P171S	ENST00000296474	NM_002447.2	171	Ccc/Tcc	1/20	0.277315056343028	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.277315056343028	1		809	837	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52677269	52677269	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0045506-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	79	443	0	ENST00000394830.3:c.990T>A	p.Tyr330Ter	p.Y330*	ENST00000394830	NM_018313.4	330	taT/taA	10/30	0.277315056343028	1	FACETS	0.953	0.84	1	0.953	0.84	1	CLONAL	1	TRUE	0	0.277315056343028	1		443	515	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0045507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	54	399	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.169	0.144	0.197	0.169	0.144	0.197	SUBCLONAL	1	TRUE	1	0.978610105203767	2		399	652	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0045507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	160	588	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.491	0.451	0.532	0.491	0.451	0.532	SUBCLONAL	1	TRUE	1	0.978610105203767	2		588	666	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105645	11105645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	357	442	0	ENST00000358026.2:c.1561C>T	p.Arg521Trp	p.R521W	ENST00000358026	NM_001128849.1	521	Cgg/Tgg	9/36	1	2	FACETS	0.982	0.937	1	0.982	0.937	1	CLONAL	1	TRUE	1	0.978610105203767	2		442	743	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713171	30713171	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	223	311	0	ENST00000295754.5:c.496C>T	p.Gln166Ter	p.Q166*	ENST00000295754	NM_003242.5	166	Caa/Taa	4/7	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.978610105203767	2		311	377	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952006	178952006	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	11	319	0	ENST00000263967.3:c.3061T>A	p.Tyr1021Asn	p.Y1021N	ENST00000263967	NM_006218.2	1021	Tac/Aac	21/21	1	2	FACETS	0.049	0.033	0.069	0.049	0.033	0.069	SUBCLONAL	1	TRUE	1	0.978610105203767	2		319	459	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971016	21971016	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	16	503	0	ENST00000304494.5:c.342del	p.Val115TrpfsTer31	p.V115Wfs*31	ENST00000304494	NM_000077.4	114	ccC/cc	2/3	0.967830647093962	0	FACETS		NA	1			1	NA	1	TRUE	0	0.978610105203767	0		503	29	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260833	16260833	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	417	498	0	ENST00000375759.3:c.8098C>G	p.Leu2700Val	p.L2700V	ENST00000375759	NM_015001.2	2700	Ctt/Gtt	11/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.978610105203767	2		498	842	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261044	16261044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746961330	NA	P-0045507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	321	468	0	ENST00000375759.3:c.8309C>T	p.Ser2770Leu	p.S2770L	ENST00000375759	NM_015001.2	2770	tCa/tTa	11/15	1	2	FACETS	0.962	0.916	1	0.962	0.916	1	CLONAL	1	TRUE	1	0.978610105203767	2		468	682	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56415066	56415066	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	209	270	0	ENST00000348428.3:c.2467G>C	p.Glu823Gln	p.E823Q	ENST00000348428	NM_006785.3	823	Gaa/Caa	17/17	0.351226428025031	1	FACETS	0.611	0.578	0.643	0.611	0.578	0.643	INDETERMINATE	1	TRUE	0	0.978610105203767	1		270	357	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095987	11095987	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	61	618	0	ENST00000358026.2:c.263del	p.Pro88ArgfsTer6	p.P88Rfs*6	ENST00000358026	NM_001128849.1	87	gaC/ga	3/36	1	2	FACETS	0.131	0.113	0.152	0.131	0.113	0.152	SUBCLONAL	1	TRUE	1	0.978610105203767	2		618	949	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652048	36652049	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACCACTGGAGGGTG	novel	NA	P-0045507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	175	676	0	ENST00000244741.5:c.173_186dup	p.Phe63HisfsTer90	p.F63Hfs*90	ENST00000244741	NM_000389.4	57	aca/acACCACTGGAGGGTGa	2/3	1	2	FACETS	0.486	0.448	0.525	0.486	0.448	0.525	SUBCLONAL	1	TRUE	1	0.978610105203767	2		676	736	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778042	135778042	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs118203680	NA	P-0045507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	23	460	0	ENST00000298552.3:c.2341C>T	p.Gln781Ter	p.Q781*	ENST00000298552	NM_001162426.1	781	Cag/Tag	18/23	0.978610105203767	1	FACETS	0.059	0.046	0.075	0.059	0.046	0.075	SUBCLONAL	1	TRUE	0	0.978610105203767	1		460	406	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786058	135786062	+	frameshift_variant	Frame_Shift_Del	DEL	AGAGG	AGAGG	-	novel	NA	P-0045507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	59	532	0	ENST00000298552.3:c.1159_1163del	p.Pro387GlyfsTer17	p.P387Gfs*17	ENST00000298552	NM_001162426.1	387	CCTCTg/g	12/23	0.978610105203767	1	FACETS	0.157	0.135	0.18	0.157	0.135	0.18	SUBCLONAL	1	TRUE	0	0.978610105203767	1		532	393	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786906	135786907	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0045507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	25	370	0	ENST00000298552.3:c.962dup	p.Asn321LysfsTer20	p.N321Kfs*20	ENST00000298552	NM_001162426.1	321	aat/aaAt	10/23	0.978610105203767	1	FACETS	0.071	0.056	0.089	0.071	0.056	0.089	SUBCLONAL	1	TRUE	0	0.978610105203767	1		370	366	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797265	135797266	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0045507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	13	212	0	ENST00000298552.3:c.603dup	p.Phe202LeufsTer16	p.F202Lfs*16	ENST00000298552	NM_001162426.1	201	-/C	7/23	0.978610105203767	1	FACETS	0.084	0.06	0.113	0.084	0.06	0.113	SUBCLONAL	1	TRUE	0	0.978610105203767	1		212	162	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797301	135797307	+	frameshift_variant	Frame_Shift_Del	DEL	GATGAAA	GATGAAA	-	novel	NA	P-0045507-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	11	216	0	ENST00000298552.3:c.562_568del	p.Phe188AlafsTer20	p.F188Afs*20	ENST00000298552	NM_001162426.1	188	TTTCATCgc/gc	7/23	0.978610105203767	1	FACETS	0.074	0.051	0.103	0.074	0.051	0.103	SUBCLONAL	1	TRUE	0	0.978610105203767	1		216	155	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0045508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	617	707	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.280570089004139	4	FACETS	0.901	0.872	0.929	0.901	0.872	0.929	INDETERMINATE	4	TRUE	0	0.468135869081674	4		708	1074	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680644	88680644	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	117	386	0	ENST00000360948.2:c.613A>G	p.Ser205Gly	p.S205G	ENST00000360948	NM_001012338.2	205	Agt/Ggt	6/19	0.392065174483765	1	FACETS	0.728	0.659	0.8	0.728	0.659	0.8	SUBCLONAL	1	TRUE	0	0.468135869081674	1		386	526	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5258061	5258061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773920614	NA	P-0045508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	171	418	1	ENST00000357368.4:c.673C>T	p.Arg225Cys	p.R225C	ENST00000357368	NM_002850.3	225	Cgc/Tgc	8/38	0.251404033260159	1	FACETS	0.798	0.736	0.862	0.798	0.736	0.862	INDETERMINATE	1	TRUE	0	0.468135869081674	1		419	701	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	77	425	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.823	0.728	0.924			1	INDETERMINATE	1	TRUE	NA	0.516804657043583	2		425	362	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475586	12475586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201781800	NA	P-0045509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	139	396	1	ENST00000287820.6:c.1460C>T	p.Thr487Met	p.T487M	ENST00000287820	NM_015869.4	487	aCg/aTg	7/7	1	2	FACETS	0.829	0.757	0.904	0.829	0.757	0.904	CLONAL	1	TRUE	1	0.516804657043583	2		397	649	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503820	186503820	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045509-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	163	391	1	ENST00000323963.5:c.497T>C	p.Met166Thr	p.M166T	ENST00000323963		166	aTg/aCg	5/11	1	2	FACETS	0.918	0.845	0.994	0.918	0.845	0.994	CLONAL	1	TRUE	1	0.516804657043583	2		392	687	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0045510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	113	403	0				ENST00000310581	NM_198253.2	-/1132			0.172946917292688	2	FACETS	0.754	0.684	0.826	0.754	0.684	0.826	INDETERMINATE	2	TRUE	0	0.376705272684033	2		403	398	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912874	32912874	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	104	331	0	ENST00000380152.3:c.4382C>T	p.Ser1461Phe	p.S1461F	ENST00000380152		1461	tCc/tTc	11/27	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.376705272684033	2		331	394	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0045510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	353	677	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	0.286931931594714	3	FACETS	0.836	0.791	0.882	0.836	0.791	0.882	CLONAL	2	TRUE	1	0.376705272684033	3		677	1332	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068445	16068445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	26	91	0	ENST00000268712.3:c.466C>T	p.Pro156Ser	p.P156S	ENST00000268712	NM_006311.3	156	Cca/Tca	5/46	1	2	FACETS	0.75	0.609	0.903	1	0.94	1	CLONAL	2	TRUE	1	0.376705272684033	2		91	92	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164440	36164440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	83	250	0	ENST00000300305.3:c.1435C>T	p.Pro479Ser	p.P479S	ENST00000300305		479	Ccc/Tcc	8/8	0.286931931594714	3	FACETS	1	0.975	1	0.685	0.609	0.766	CLONAL	1	TRUE	1	0.376705272684033	3		250	382	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162050	47162050	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	123	299	0	ENST00000409792.3:c.4076C>T	p.Ser1359Phe	p.S1359F	ENST00000409792	NM_014159.6	1359	tCc/tTc	3/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.376705272684033	2		299	528	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587167	189587167	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1209841422	NA	P-0045510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	79	319	0	ENST00000264731.3:c.1184C>T	p.Ser395Phe	p.S395F	ENST00000264731	NM_003722.4	395	tCc/tTc	9/14	1	2	FACETS	0.887	0.783	0.998	0.887	0.783	0.998	CLONAL	1	TRUE	1	0.376705272684033	2		319	473	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	CT	rs121913227	NA	P-0045510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	119	349	0	ENST00000288602.6:c.1798_1799delinsAG	p.Val600Arg	p.V600R	ENST00000288602	NM_004333.4	600	GTg/AGg	15/18	0.223199315933142	5	FACETS	1	0.932	1	0.688	0.625	0.754	INDETERMINATE	2	TRUE	2	0.376705272684033	5		349	479	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520159	9520159	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1484691555	NA	P-0045510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	82	412	0	ENST00000353224.5:c.2110G>A	p.Gly704Ser	p.G704S	ENST00000353224	NM_177990.2	704	Ggt/Agt	10/10	0.322385398113235	3	FACETS	0.807	0.712	0.909	0.404	0.356	0.455	CLONAL	1	TRUE	1	0.376705272684033	3		412	641	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775203	73775203	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	113	565	0	ENST00000254810.4:c.53G>T	p.Arg18Leu	p.R18L	ENST00000254810	NM_005324.3	18	cGc/cTc	2/4	1	2	FACETS	0.82	0.738	0.906	0.82	0.738	0.906	CLONAL	1	TRUE	1	0.376705272684033	2		565	732	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612029	189612029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368336834	NA	P-0045510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	148	398	0	ENST00000264731.3:c.1781G>A	p.Arg594Gln	p.R594Q	ENST00000264731	NM_003722.4	594	cGa/cAa	14/14	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.376705272684033	2		398	608	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729162	66729162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519732	NA	P-0045510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	163	537	0	ENST00000307102.5:c.370C>T	p.Pro124Ser	p.P124S	ENST00000307102	NM_002755.3	124	Ccg/Tcg	3/11	0.286931931594714	3	FACETS	1	0.955	1	0.531	0.487	0.577	CLONAL	1	TRUE	1	0.376705272684033	3		537	969	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964332	55964332	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	142	394	0	ENST00000263923.4:c.2481G>A	p.Trp827Ter	p.W827*	ENST00000263923	NM_002253.2	827	tgG/tgA	17/30	0.259778694115799	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.376705272684033	1		394	490	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969150	93969150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1562049937	NA	P-0045510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	115	320	0	ENST00000369303.4:c.1846G>A	p.Asp616Asn	p.D616N	ENST00000369303	NM_004440.3	616	Gac/Aac	10/17	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.376705272684033	2		320	506	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961969	41961969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1306489330	NA	P-0045510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	173	416	2	ENST00000219905.7:c.877C>T	p.Arg293Cys	p.R293C	ENST00000219905	NM_001164273.1	293	Cgt/Tgt	2/24	0.286931931594714	3	FACETS	0.784	0.724	0.846	0.784	0.724	0.846	SUBCLONAL	2	TRUE	1	0.376705272684033	3		418	696	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38314898	38314898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	95	425	0	ENST00000425967.3:c.166C>T	p.Pro56Ser	p.P56S	ENST00000425967	NM_001174067.1	56	Ccg/Tcg	3/19	1	2	FACETS	0.711	0.633	0.794	0.711	0.633	0.794	SUBCLONAL	1	TRUE	1	0.376705272684033	2		425	709	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575379	64575379	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	268	578	0	ENST00000312049.6:c.638C>T	p.Ala213Val	p.A213V	ENST00000312049	NM_130799.2	213	gCc/gTc	3/10	0.154915977959221	2	FACETS	0.759	0.713	0.806	0.759	0.713	0.806	INDETERMINATE	2	TRUE	0	0.376705272684033	2		578	937	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433019	49433019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	80	585	1	ENST00000301067.7:c.8352G>A	p.Met2784Ile	p.M2784I	ENST00000301067	NM_003482.3	2784	atG/atA	33/54	0.172946917292688	2	FACETS	0.496	0.435	0.561	0.248	0.217	0.281	INDETERMINATE	1	TRUE	0	0.376705272684033	2		586	857	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444261	49444261	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	283	734	0	ENST00000301067.7:c.3110C>T	p.Ser1037Phe	p.S1037F	ENST00000301067	NM_003482.3	1037	tCc/tTc	11/54	0.172946917292688	2	FACETS	1	0.993	1	0.725	0.682	0.769	INDETERMINATE	1	TRUE	0	0.376705272684033	2		734	1036	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891678	28891678	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776861138	NA	P-0045510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	192	555	0	ENST00000282397.4:c.3343G>A	p.Glu1115Lys	p.E1115K	ENST00000282397	NM_002019.4	1115	Gaa/Aaa	25/30	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.376705272684033	2		555	761	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243877	41243877	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	119	477	0	ENST00000357654.3:c.3671C>T	p.Pro1224Leu	p.P1224L	ENST00000357654	NM_007294.3	1224	cCc/cTc	10/23	1	2	FACETS	0.943	0.853	1	0.943	0.853	1	CLONAL	1	TRUE	1	0.376705272684033	2		477	670	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78882610	78882610	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0045510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	97	423	0	ENST00000306801.3:c.2402-1G>A		p.X801_splice	ENST00000306801	NM_020761.2	801			1	2	FACETS	0.832	0.743	0.926	0.832	0.743	0.926	CLONAL	1	TRUE	1	0.376705272684033	2		423	619	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170740	11170740	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	298	661	0	ENST00000358026.2:c.4884G>C	p.Lys1628Asn	p.K1628N	ENST00000358026	NM_001128849.1	1628	aaG/aaC	35/36	0.322385398113235	3	FACETS	0.903	0.851	0.956	0.903	0.851	0.956	CLONAL	2	TRUE	1	0.376705272684033	3		661	1041	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308353	15308354	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0045510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	229	677	1	ENST00000263388.2:c.154_155delinsAA	p.Gly52Lys	p.G52K	ENST00000263388	NM_000435.2	52	GGa/AAa	2/33	0.322385398113235	3	FACETS	0.753	0.702	0.806	0.753	0.702	0.806	SUBCLONAL	2	TRUE	1	0.376705272684033	3		678	959	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927092	131927092	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	21	215	0	ENST00000265335.6:c.1629A>C	p.Lys543Asn	p.K543N	ENST00000265335		543	aaA/aaC	10/25	0.172946917292688	2	FACETS	0.555	0.429	0.7	0.277	0.214	0.35	INDETERMINATE	1	TRUE	0	0.376705272684033	2		215	201	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032149	26032149	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	143	445	1	ENST00000244661.2:c.140T>C	p.Val47Ala	p.V47A	ENST00000244661	NM_003537.3	47	gTg/gCg	1/1	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.376705272684033	2		446	669	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729716	41729717	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0045510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	241	467	0	ENST00000242208.4:c.812dup	p.Lys272GlufsTer5	p.K272Efs*5	ENST00000242208	NM_002192.2	271	aag/aaAg	3/3	0.223199315933142	5	FACETS	0.979	0.914	1	0.652	0.609	0.697	INDETERMINATE	2	TRUE	2	0.376705272684033	5		467	1023	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030872	69030872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	76	334	0	ENST00000288368.4:c.3414G>A	p.Met1138Ile	p.M1138I	ENST00000288368	NM_024870.2	1138	atG/atA	27/40	1	2	FACETS	0.804	0.707	0.908	0.804	0.707	0.908	CLONAL	1	TRUE	1	0.376705272684033	2		334	502	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737451	145737451	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0045510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	130	746	0	ENST00000428558.2:c.3237-1G>A		p.X1079_splice	ENST00000428558	NM_004260.3	1079			1	2	FACETS	0.715	0.648	0.786	0.715	0.648	0.786	SUBCLONAL	1	TRUE	1	0.376705272684033	2		746	965	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549434	5549434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045510-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	319	485	0	ENST00000397747.3:c.461C>T	p.Ser154Phe	p.S154F	ENST00000397747	NM_025239.3	154	tCc/tTc	4/7	0.376705272684033	2	FACETS	0.987	0.935	1	0.987	0.935	1	CLONAL	2	TRUE	0	0.376705272684033	2		485	858	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0045511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	246	623	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.258015852561478	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.27336368987235	2		623	843	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0045511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	95	273	2	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.27336368987235	2	FACETS	0.944	0.848	1	0.944	0.848	1	CLONAL	2	TRUE	0	0.27336368987235	2		275	368	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538257	9538257	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs746240534	NA	P-0045511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	161	344	0	ENST00000353224.5:c.1741C>T	p.Arg581Trp	p.R581W	ENST00000353224	NM_177990.2	581	Cgg/Tgg	7/10	0.27336368987235	6	FACETS	1	0.921	1	0.502	0.46	0.546	CLONAL	2	TRUE	2	0.27336368987235	6		344	907	SUCCESS
APC	324	MSKCC	GRCh37	5	112175504	112175504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761966904	NA	P-0045511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	22	296	0	ENST00000257430.4:c.4213G>A	p.Val1405Ile	p.V1405I	ENST00000257430	NM_000038.5	1405	Gtt/Att	16/16	0.27336368987235	2	FACETS	0.434	0.336	0.548	0.217	0.168	0.274	SUBCLONAL	1	TRUE	0	0.27336368987235	2		296	371	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940587	131940587	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1561645666	NA	P-0045511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	62	237	0	ENST00000265335.6:c.2614T>C	p.Ser872Pro	p.S872P	ENST00000265335		872	Tct/Cct	16/25	0.27336368987235	2	FACETS	1	0.935	1	0.566	0.49	0.647	CLONAL	1	TRUE	0	0.27336368987235	2		237	401	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0045513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	6975	1249	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.593671625088542	43	FACETS	0.999	0.995	1	0.999	0.995	1	CLONAL	41	TRUE	2	0.593671625088542	43		1249	7554	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221131	5221131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201447856	NA	P-0045513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	191	626	0	ENST00000357368.4:c.3335C>T	p.Thr1112Met	p.T1112M	ENST00000357368	NM_002850.3	1112	aCg/aTg	20/38	0.593671625088542	4	FACETS	1	0.965	1	0.358	0.33	0.386	CLONAL	1	TRUE	1	0.593671625088542	4		626	956	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577563	7577563	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1567549584	NA	P-0045513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	275	438	0	ENST00000269305.4:c.718A>G	p.Ser240Gly	p.S240G	ENST00000269305	NM_001126112.2	240	Agt/Ggt	7/11	0.593671625088542	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.593671625088542	2		438	432	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266821	198266821	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	319	438	0	ENST00000335508.6:c.2111T>A	p.Ile704Asn	p.I704N	ENST00000335508	NM_012433.2	704	aTc/aAc	15/25	0.408191355762128	3	FACETS	0.96	0.922	0.997	0.96	0.922	0.997	CLONAL	3	TRUE	0	0.593671625088542	3		438	484	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249091	55249091	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519861	NA	P-0045513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	7120	544	0	ENST00000275493.2:c.2389T>A	p.Cys797Ser	p.C797S	ENST00000275493	NM_005228.3	797	Tgc/Agc	20/28	0.593671625088542	43	FACETS	1	0.998	1	0.936	0.931	0.942	CLONAL	38	TRUE	2	0.593671625088542	43		544	8228	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247813	59247815	+	inframe_deletion	In_Frame_Del	DEL	CTG	CTG	-	novel	NA	P-0045513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	417	638	0	ENST00000371222.2:c.928_930del	p.Gln310del	p.Q310del	ENST00000371222	NM_002228.3	310	CAG/-	1/1	0.593671625088542	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.593671625088542	3		638	793	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65349089	65349089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	108	442	0	ENST00000342505.4:c.76G>A	p.Glu26Lys	p.E26K	ENST00000342505	NM_002227.2	26	Gag/Aag	3/25	0.593671625088542	3	FACETS	0.818	0.736	0.904	0.409	0.368	0.452	CLONAL	1	TRUE	1	0.593671625088542	3		442	577	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446460	49446460	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	156	491	0	ENST00000301067.7:c.1145C>A	p.Thr382Asn	p.T382N	ENST00000301067	NM_003482.3	382	aCt/aAt	9/54	0.593671625088542	3	FACETS	1	0.981	1	0.406	0.373	0.439	CLONAL	1	TRUE	0	0.593671625088542	3		491	560	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829145	72829145	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	338	484	0	ENST00000268489.5:c.7436C>A	p.Ser2479Ter	p.S2479*	ENST00000268489	NM_006885.3	2479	tCg/tAg	9/10	0.593671625088542	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.593671625088542	2		484	495	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468453	89468453	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	60	277	0	ENST00000336596.2:c.1987C>G	p.Gln663Glu	p.Q663E	ENST00000336596	NM_005233.5	663	Cag/Gag	11/17	0.593671625088542	3	FACETS	1	0.938	1	0.565	0.493	0.641	CLONAL	1	TRUE	1	0.593671625088542	3		277	232	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948779	55948779	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	84	353	0	ENST00000263923.4:c.3686G>C	p.Arg1229Pro	p.R1229P	ENST00000263923	NM_002253.2	1229	cGa/cCa	28/30	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.593671625088542	2		353	258	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507365	8507365	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045513-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	322	279	0	ENST00000356435.5:c.1613C>A	p.Pro538His	p.P538H	ENST00000356435		538	cCt/cAt	11/35	0.593671625088542	7	FACETS	0.986	0.939	1	0.986	0.939	1	CLONAL	4	TRUE	3	0.593671625088542	7		279	683	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510611	38510611	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	173	598	0	ENST00000254066.5:c.865G>T	p.Gly289Trp	p.G289W	ENST00000254066	NM_000964.3	289	Ggg/Tgg	7/9	0.173804994243285	3	FACETS	1	0.987	1	0.689	0.633	0.748	CLONAL	1	TRUE	1	0.226755230669469	3		598	1233	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0045515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	203	380	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.159862785226157	3	FACETS	1	0.986	1	0.821	0.763	0.882	CLONAL	2	TRUE	0	0.226755230669469	3		380	809	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	244	537	0	ENST00000269305.4:c.853G>T	p.Glu285Ter	p.E285*	ENST00000269305	NM_001126112.2	285	Gag/Tag	8/11	0.173804994243285	3	FACETS	0.908	0.847	0.972	0.908	0.847	0.972	CLONAL	2	TRUE	1	0.226755230669469	3		537	1319	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979365	93979365	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	49	278	0	ENST00000369303.4:c.1463G>T	p.Arg488Leu	p.R488L	ENST00000369303	NM_004440.3	488	cGg/cTg	7/17	0.150606115406314	2	FACETS	0.78	0.665	0.904	0.78	0.665	0.904	CLONAL	2	TRUE	0	0.226755230669469	2		278	277	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636758	8636758	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	101	370	0	ENST00000356435.5:c.151C>A	p.Pro51Thr	p.P51T	ENST00000356435		51	Cca/Aca	2/35	0.199790616929279	4	FACETS	1	0.972	1	0.636	0.568	0.709	CLONAL	1	TRUE	2	0.226755230669469	4		370	859	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040945	47040945	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1447493714	NA	P-0045515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	136	408	0	ENST00000377604.3:c.1475C>T	p.Ser492Leu	p.S492L	ENST00000377604	NM_001204468.1	492	tCg/tTg	14/24	1	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.226755230669469	1		408	856	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549443	187549443	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	73	501	1	ENST00000441802.2:c.4675G>T	p.Ala1559Ser	p.A1559S	ENST00000441802	NM_005245.3	1559	Gcc/Tcc	9/27	1	2	FACETS	0.708	0.617	0.805	0.708	0.617	0.805	SUBCLONAL	1	TRUE	1	0.226755230669469	2		502	910	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741336	17741336	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	235	582	0	ENST00000250003.3:c.7C>A	p.Leu3Ile	p.L3I	ENST00000250003	NM_002478.4	3	Cta/Ata	1/3	0.173804994243285	3	FACETS	0.818	0.762	0.877	0.818	0.762	0.877	CLONAL	2	TRUE	1	0.226755230669469	3		582	1410	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557599	21557599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	188	527	0	ENST00000382592.4:c.2246C>T	p.Pro749Leu	p.P749L	ENST00000382592	NM_014572.2	749	cCt/cTt	5/8	0.150606115406314	2	FACETS	1	0.989	1	0.72	0.664	0.779	CLONAL	1	TRUE	0	0.226755230669469	2		527	1151	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132954	30132954	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	298	486	0	ENST00000331968.5:c.647G>T	p.Arg216Leu	p.R216L	ENST00000331968	NM_002742.2	216	cGc/cTc	4/18	0.226755230669469	6	FACETS	0.954	0.897	1	0.572	0.538	0.608	CLONAL	3	TRUE	1	0.226755230669469	6		486	1335	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679208	88679208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	131	545	0	ENST00000360948.2:c.829G>A	p.Asp277Asn	p.D277N	ENST00000360948	NM_001012338.2	277	Gac/Aac	8/19	0.150606115406314	2	FACETS	1	0.96	1	0.555	0.503	0.61	CLONAL	1	TRUE	0	0.226755230669469	2		545	1041	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3651062	3651062	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	157	542	0	ENST00000294008.3:c.1081G>C	p.Glu361Gln	p.E361Q	ENST00000294008	NM_032444.2	361	Gag/Cag	5/15	0.173804994243285	3	FACETS	1	0.981	1	0.626	0.572	0.683	CLONAL	1	TRUE	1	0.226755230669469	3		542	1231	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662344	67662344	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	55	455	0	ENST00000264010.4:c.1590G>C	p.Lys530Asn	p.K530N	ENST00000264010	NM_006565.3	530	aaG/aaC	9/12	0.150606115406314	2	FACETS	0.527	0.449	0.613	0.264	0.224	0.307	SUBCLONAL	1	TRUE	0	0.226755230669469	2		455	920	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349942	89349942	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	178	719	0	ENST00000301030.4:c.3008A>G	p.His1003Arg	p.H1003R	ENST00000301030	NM_001256183.1	1003	cAc/cGc	9/13	0.150606115406314	2	FACETS	1	0.976	1	0.578	0.531	0.627	CLONAL	1	TRUE	0	0.226755230669469	2		719	1358	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59934439	59934439	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	39	305	0	ENST00000259008.2:c.359G>T	p.Gly120Val	p.G120V	ENST00000259008	NM_032043.2	120	gGc/gTc	4/20	0.173804994243285	3	FACETS	0.738	0.611	0.88	0.369	0.305	0.44	SUBCLONAL	1	TRUE	1	0.226755230669469	3		305	519	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117407	7117407	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	82	527	0	ENST00000302850.5:c.3809G>T	p.Arg1270Leu	p.R1270L	ENST00000302850	NM_000208.2	1270	cGc/cTc	22/22	1	2	FACETS	0.707	0.622	0.799	0.707	0.622	0.799	SUBCLONAL	1	TRUE	1	0.226755230669469	2		527	1023	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24133968	24133969	+	missense_variant	Missense_Mutation	DNP	GA	GA	CT	novel	NA	P-0045515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	30	319	0	ENST00000263121.7:c.119_120delinsCT	p.Arg40Pro	p.R40P	ENST00000263121	NM_003073.3	40	cGA/cCT	2/9	1	2	FACETS	0.455	0.366	0.558	0.455	0.366	0.558	SUBCLONAL	1	TRUE	1	0.226755230669469	2		319	581	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933680	49933680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1267	188	665	0	ENST00000296474.3:c.2597C>T	p.Pro866Leu	p.P866L	ENST00000296474	NM_002447.2	866	cCc/cTc	10/20	0.173804994243285	3	FACETS	1	0.984	1	0.634	0.584	0.687	CLONAL	1	TRUE	1	0.226755230669469	3		665	1455	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272239	142272239	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	87	244	0	ENST00000350721.4:c.2635G>A	p.Ala879Thr	p.A879T	ENST00000350721	NM_001184.3	879	Gcc/Acc	13/47	0.199790616929279	4	FACETS	0.953	0.846	1	0.953	0.846	1	CLONAL	2	TRUE	2	0.226755230669469	4		244	494	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356349	66356349	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	72	371	0	ENST00000273854.3:c.1148C>A	p.Thr383Asn	p.T383N	ENST00000273854	NM_004439.5	383	aCt/aAt	5/18	1	2	FACETS	0.915	0.799	1	0.915	0.799	1	CLONAL	1	TRUE	1	0.226755230669469	2		371	694	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516891	187516891	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	59	417	0	ENST00000441802.2:c.13090G>T	p.Glu4364Ter	p.E4364*	ENST00000441802	NM_005245.3	4364	Gaa/Taa	26/27	1	2	FACETS	0.611	0.524	0.706	0.611	0.524	0.706	SUBCLONAL	1	TRUE	1	0.226755230669469	2		417	852	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752789	57752789	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	103	239	0	ENST00000274289.3:c.1139G>T	p.Arg380Ile	p.R380I	ENST00000274289	NM_006622.3	380	aGa/aTa	8/14	0.226755230669469	3	FACETS	1	0.974	1	0.828	0.747	0.914	CLONAL	2	TRUE	0	0.226755230669469	3		239	407	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514541	149514541	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	107	433	0	ENST00000261799.4:c.403C>A	p.Leu135Ile	p.L135I	ENST00000261799	NM_002609.3	135	Cta/Ata	4/23	0.150606115406314	2	FACETS	1	0.953	1	0.556	0.499	0.618	CLONAL	1	TRUE	0	0.226755230669469	2		433	848	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016209	150016209	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0045515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	69	283	0	ENST00000253339.5:c.496+1G>T		p.X166_splice	ENST00000253339		166			0.150606115406314	2	FACETS	1	0.972	1	0.728	0.637	0.826	CLONAL	1	TRUE	0	0.226755230669469	2		283	418	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771790	135771790	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	138	585	0	ENST00000298552.3:c.3327G>T	p.Met1109Ile	p.M1109I	ENST00000298552	NM_001162426.1	1109	atG/atT	23/23	0.173804994243285	3	FACETS	1	0.936	1	0.52	0.472	0.571	CLONAL	1	TRUE	1	0.226755230669469	3		585	1303	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504171	123504171	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0045515-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	40	188	0	ENST00000371139.4:c.346+1G>A		p.X116_splice	ENST00000371139	NM_001114937.2	116			1	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.226755230669469	1		188	218	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692793	89692793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045516-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	15	278	0	ENST00000371953.3:c.277C>T	p.His93Tyr	p.H93Y	ENST00000371953	NM_000314.4	93	Cat/Tat	5/9	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		278	261	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0045517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	65	294	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.146151440102924	2	FACETS	0.765	0.666	0.871	0.765	0.666	0.871	SUBCLONAL	2	TRUE	0	0.215655995612399	2		294	394	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0045517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	121	820	0	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	0.215655995612399	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.215655995612399	1		820	814	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998483	100998483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	41	472	0	ENST00000325455.5:c.1319C>T	p.Thr440Met	p.T440M	ENST00000325455	NM_001202474.3	440	aCg/aTg	1/8	1	2	FACETS	0.585	0.486	0.695	0.585	0.486	0.695	SUBCLONAL	1	TRUE	1	0.215655995612399	2		472	650	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971133	21971133	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045517-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	65	526	0	ENST00000304494.5:c.225del	p.Ala76ProfsTer70	p.A76Pfs*70	ENST00000304494	NM_000077.4	75	ccC/cc	2/3	1	2	FACETS	0.933	0.809	1	0.933	0.809	1	CLONAL	1	TRUE	1	0.215655995612399	2		526	646	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0045518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	160	354	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.562109259238561	2		354	544	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0045518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	95	353	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.929	0.834	1	0.929	0.834	1	CLONAL	1	TRUE	1	0.562109259238561	2		353	364	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473779	67473779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906850	NA	P-0045518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	411	734	2	ENST00000327367.4:c.859C>T	p.Arg287Trp	p.R287W	ENST00000327367	NM_005902.3	287	Cgg/Tgg	6/9	0.552676607924112	2	FACETS	0.919	0.881	0.956	0.919	0.881	0.956	CLONAL	2	TRUE	0	0.562109259238561	2		736	796	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139774	55139774	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs771567933	NA	P-0045518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	187	516	0	ENST00000257290.5:c.1435C>T	p.Arg479Ter	p.R479*	ENST00000257290	NM_006206.4	479	Cga/Tga	10/23	1	2	FACETS	0.867	0.803	0.934	0.867	0.803	0.934	CLONAL	1	TRUE	1	0.562109259238561	2		516	767	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103162	119103162	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	62	387	0	ENST00000264033.4:c.200T>C	p.Val67Ala	p.V67A	ENST00000264033	NM_005188.3	67	gTg/gCg	2/16	1	2	FACETS	0.325	0.28	0.374	0.325	0.28	0.374	SUBCLONAL	1	TRUE	1	0.562109259238561	2		387	679	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26978147	26978147	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	100	497	0	ENST00000381527.3:c.1324C>T	p.Gln442Ter	p.Q442*	ENST00000381527	NM_001260.1	442	Cag/Tag	13/13	0.38055866552631	3	FACETS	0.48	0.428	0.535	0.24	0.214	0.268	SUBCLONAL	1	TRUE	1	0.562109259238561	3		497	950	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374995	45374996	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0045518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	183	368	0	ENST00000262160.6:c.847_848insC	p.Asn283ThrfsTer38	p.N283Tfs*38	ENST00000262160	NM_005901.5	283	aat/aCat	8/11	0.562109259238561	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.562109259238561	1		368	426	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102789	71102789	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	39	258	0	ENST00000318789.4:c.418C>A	p.Gln140Lys	p.Q140K	ENST00000318789	NM_032682.5	140	Cag/Aag	8/21	1	2	FACETS	0.291	0.241	0.347	0.291	0.241	0.347	SUBCLONAL	1	TRUE	1	0.562109259238561	2		258	477	SUCCESS
APC	324	MSKCC	GRCh37	5	112175782	112175788	+	frameshift_variant	Frame_Shift_Del	DEL	AGATGGA	AGATGGA	-	novel	NA	P-0045518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	107	249	0	ENST00000257430.4:c.4491_4497del	p.Asp1498PhefsTer7	p.D1498Ffs*7	ENST00000257430	NM_000038.5	1497	ccAGATGGA/cc	16/16	1	2	FACETS	0.959	0.867	1	0.959	0.867	1	CLONAL	1	TRUE	1	0.562109259238561	2		249	397	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979457	2979457	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	101	504	0	ENST00000396946.4:c.790G>C	p.Glu264Gln	p.E264Q	ENST00000396946	NM_032415.4	264	Gag/Cag	6/25	0.560776099316818	3	FACETS	0.411	0.366	0.459	0.206	0.183	0.23	SUBCLONAL	1	TRUE	1	0.562109259238561	3		504	1120	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652426	48652426	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	142	339	0	ENST00000376670.3:c.1097G>T	p.Gly366Val	p.G366V	ENST00000376670	NM_002049.3	366	gGc/gTc	6/6	1	1	FACETS	0.638	0.584	0.695	0.638	0.584	0.695	SUBCLONAL	1	TRUE	0	0.562109259238561	1		339	569	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0045519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	35	294	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	0.636	0.521	0.767			1	INDETERMINATE	1	FALSE	NA	0.194327182239422	2		294	566	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs587781702	NA	P-0045519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	139	568	0	ENST00000269305.4:c.920-1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.194327182239422	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	0	0.194327182239422	1		568	977	SUCCESS
APC	324	MSKCC	GRCh37	5	112174745	112174745	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064795228	NA	P-0045519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	29	289	0	ENST00000257430.4:c.3454C>T	p.Gln1152Ter	p.Q1152*	ENST00000257430	NM_000038.5	1152	Cag/Tag	16/16	1	2	FACETS	0.742	0.596	0.909	0.742	0.596	0.909	CLONAL	1	FALSE	1	0.194327182239422	2		289	402	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799648	3799648	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	51	361	0	ENST00000262367.5:c.3816del	p.Asn1272LysfsTer4	p.N1272Kfs*4	ENST00000262367	NM_004380.2	1272	aaT/aa	21/31	1	2	FACETS	0.765	0.649	0.893	0.765	0.649	0.893	SUBCLONAL	1	FALSE	1	0.194327182239422	2		361	686	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256961	41256961	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	76	442	0	ENST00000357654.3:c.225A>C	p.Glu75Asp	p.E75D	ENST00000357654	NM_007294.3	75	gaA/gaC	5/23	0.194327182239422	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	FALSE	0	0.194327182239422	1		442	613	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244288	153244288	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	28	257	0	ENST00000281708.4:c.1869T>G	p.His623Gln	p.H623Q	ENST00000281708	NM_033632.3	623	caT/caG	12/12	1	2	FACETS	0.749	0.598	0.92	0.749	0.598	0.92	CLONAL	1	FALSE	1	0.194327182239422	2		257	385	SUCCESS
APC	324	MSKCC	GRCh37	5	112175274	112175275	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0045519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	29	259	0	ENST00000257430.4:c.3983_3984del	p.Gln1328ProfsTer3	p.Q1328Pfs*3	ENST00000257430	NM_000038.5	1328	cAG/c	16/16	1	2	FACETS	0.756	0.606	0.925	0.756	0.606	0.925	CLONAL	1	FALSE	1	0.194327182239422	2		259	395	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540266	23540266	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	69	437	0	ENST00000380871.4:c.137C>G	p.Thr46Arg	p.T46R	ENST00000380871	NM_006167.3	46	aCg/aGg	1/2	1	2	FACETS	0.99	0.862	1	0.99	0.862	1	CLONAL	1	FALSE	1	0.194327182239422	2		437	717	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032748	30032748	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	192	322	0	ENST00000338641.4:c.123G>A	p.Trp41Ter	p.W41*	ENST00000338641	NM_000268.3	41	tgG/tgA	2/16	0.581996353195982	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.581996353195982	1		322	420	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441319	52441319	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	223	546	0	ENST00000460680.1:c.451del	p.His151ThrfsTer36	p.H151Tfs*36	ENST00000460680	NM_004656.3	151	Cac/ac	7/17	0.581996353195982	1	FACETS	0.975	0.916	1	0.975	0.916	1	CLONAL	1	TRUE	0	0.581996353195982	1		546	557	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0045530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	11	454	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.092	0.063	0.128	0.092	0.063	0.128	SUBCLONAL	1	TRUE	1	0.650527036132208	2		454	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0045530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	470	573	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.650527036132208	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.650527036132208	2		573	710	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0045530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	27	200	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.650527036132208	1	FACETS	0.7	0.575	0.833	0.7	0.575	0.833	SUBCLONAL	1	TRUE	0	0.650527036132208	1		200	80	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259091	89259091	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	32	321	0	ENST00000336596.2:c.235A>T	p.Asn79Tyr	p.N79Y	ENST00000336596	NM_005233.5	79	Aac/Tac	3/17	0.650527036132208	2	FACETS	0.355	0.289	0.429	0.178	0.144	0.215	SUBCLONAL	1	TRUE	0	0.650527036132208	2		321	277	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984058	2984058	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	229	572	0	ENST00000396946.4:c.472del	p.Gln158SerfsTer9	p.Q158Sfs*9	ENST00000396946	NM_032415.4	158	Cag/ag	5/25	0.64061254139559	3	FACETS	1	0.986	1	0.397	0.371	0.423	CLONAL	1	TRUE	0	0.650527036132208	3		572	784	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853293	151853293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	58	393	0	ENST00000262189.6:c.11809G>A	p.Glu3937Lys	p.E3937K	ENST00000262189	NM_170606.2	3937	Gaa/Aaa	45/59	0.64061254139559	3	FACETS	0.582	0.502	0.669	0.194	0.167	0.223	SUBCLONAL	1	TRUE	0	0.650527036132208	3		393	406	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411224	63411224	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	145	628	0	ENST00000330258.3:c.1943A>G	p.Glu648Gly	p.E648G	ENST00000330258	NM_152424.3	648	gAg/gGg	2/2	0.211033895041147	3	FACETS	0.697	0.636	0.761	0.348	0.318	0.381	INDETERMINATE	1	TRUE	1	0.650527036132208	3		628	848	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0045531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	142	262	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.465178654106454	5	FACETS	1	0.921	1	0.67	0.614	0.727	CLONAL	2	TRUE	2	0.465178654106454	5		262	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0045531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	254	763	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.465178654106454	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.465178654106454	2		765	513	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0045531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	146	181	1	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.464735311340204	2	FACETS	0.923	0.855	0.992	0.923	0.855	0.992	CLONAL	2	TRUE	0	0.465178654106454	2		182	340	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238356	98238356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045531-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	179	543	0	ENST00000331920.6:c.1688C>T	p.Ala563Val	p.A563V	ENST00000331920	NM_000264.3	563	gCg/gTg	12/24	0.246362540832103	2	FACETS	0.822	0.765	0.88	0.822	0.765	0.88	INDETERMINATE	2	TRUE	0	0.465178654106454	2		543	468	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	168	457	1	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.949	1	1	0.994	1	CLONAL	3	TRUE	1	0.220510848708217	2		458	493	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	164	443	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	0.171864686192766	3	FACETS	0.91	0.839	0.983			1	CLONAL	3	TRUE	NA	0.220510848708217	3		443	605	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	134	476	1	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	0.220510848708217	0	FACETS	1	0.949	1			1	CLONAL	2	TRUE	0	0.220510848708217	0		477	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573944	7573944	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555524354	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	330	660	1	ENST00000269305.4:c.1083del	p.Ser362AlafsTer8	p.S362Afs*8	ENST00000269305	NM_001126112.2	361	ggG/gg	10/11	0.0838384601079725	3	FACETS	1	0.978	1	1	0.995	1	INDETERMINATE	3	TRUE	1	0.220510848708217	3		661	1043	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	97	473	0	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	0.0838384601079725	3	FACETS	1	0.981	1	0.748	0.667	0.833	INDETERMINATE	1	TRUE	1	0.220510848708217	3		473	653	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	50	309	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.127073327772688	4	FACETS	1	0.89	1	1	0.969	1	INDETERMINATE	3	TRUE	2	0.220510848708217	4		309	178	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098799	178098799	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	291	569	0	ENST00000397062.3:c.246A>T	p.Glu82Asp	p.E82D	ENST00000397062	NM_006164.4	82	gaA/gaT	2/5	1	2	FACETS	1	0.961	1	1	0.996	1	CLONAL	3	TRUE	1	0.220510848708217	2		569	860	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057673	27057673	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	291	505	0	ENST00000324856.7:c.1383del	p.Tyr462MetfsTer157	p.Y462Mfs*157	ENST00000324856	NM_006015.4	461	Ggg/gg	3/20	0.197435996405829	4	FACETS	1	0.987	1			1	CLONAL	3	TRUE	NA	0.220510848708217	4		505	936	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900239	101900239	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564161544	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	76	359	0	ENST00000374994.4:c.673C>T	p.Arg225Trp	p.R225W	ENST00000374994	NM_004612.2	225	Cgg/Tgg	4/9	1	2	FACETS	0.939	0.829	1	1	0.982	1	CLONAL	2	TRUE	1	0.220510848708217	2		359	367	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335079	65335079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	63	458	0	ENST00000342505.4:c.562G>A	p.Glu188Lys	p.E188K	ENST00000342505	NM_002227.2	188	Gag/Aag	6/25	0.0838384601079725	3	FACETS	0.955	0.826	1	0.478	0.413	0.548	INDETERMINATE	1	TRUE	1	0.220510848708217	3		458	664	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	37	475	1	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	0.157136234494917	4	FACETS	0.768	0.633	0.921			1	CLONAL	1	TRUE	NA	0.220510848708217	4		476	533	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661664	227661664	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs761880048	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	253	696	12	ENST00000305123.5:c.1791del	p.His598ThrfsTer38	p.H598Tfs*38	ENST00000305123	NM_005544.2	597	ggG/gg	1/2	1	2	FACETS	0.884	0.829	0.94	1	0.996	1	CLONAL	3	TRUE	1	0.220510848708217	2		708	865	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	129	265	8	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	0.135249311847294	0	FACETS	0.751	0.687	0.816			1	SUBCLONAL	3	TRUE	0	0.220510848708217	0		273	405	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	224	511	2	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	0.197435996405829	4	FACETS	1	0.956	1			1	CLONAL	3	TRUE	NA	0.220510848708217	4		513	802	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	253	665	3	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	0.0838384601079725	3	FACETS	1	0.954	1	1	0.993	1	INDETERMINATE	3	TRUE	1	0.220510848708217	3		668	833	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346158	89346158	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs878855327	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	199	443	0	ENST00000301030.4:c.6792del	p.Ala2265ProfsTer72	p.A2265Pfs*72	ENST00000301030	NM_001256183.1	2264	ccC/cc	9/13	0.0793647716021531	4	FACETS	0.91	0.848	0.974	1	0.993	1	INDETERMINATE	4	TRUE	2	0.220510848708217	4		443	605	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390736	139390736	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1215	105	935	1	ENST00000277541.6:c.7455del	p.Ser2486ArgfsTer103	p.S2486Rfs*103	ENST00000277541	NM_017617.3	2485	ccC/cc	34/34	1	2	FACETS	0.721	0.644	0.804	0.721	0.644	0.804	SUBCLONAL	1	TRUE	1	0.220510848708217	2		936	1320	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795422	39795422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140580933	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	241	668	0	ENST00000288319.7:c.298G>A	p.Val100Ile	p.V100I	ENST00000288319	NM_182918.3	100	Gtt/Att	3/10	1	2	FACETS	0.852	0.798	0.908	1	0.995	1	CLONAL	3	TRUE	1	0.220510848708217	2		668	855	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345759	152345760	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs730882049	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	65	247	0	ENST00000359321.1:c.810dup	p.Ile271TyrfsTer8	p.I271Yfs*8	ENST00000359321	NM_005431.1	270	-/T	3/3	0.220510848708217	1	FACETS	0.982	0.861	1	1	0.981	1	CLONAL	2	TRUE	0	0.220510848708217	1		247	267	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900661	3900661	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	309	675	0	ENST00000262367.5:c.435del	p.Ala146LeufsTer6	p.A146Lfs*6	ENST00000262367	NM_004380.2	145	ccC/cc	2/31	0.0838384601079725	3	FACETS	1	0.979	1	1	0.995	1	INDETERMINATE	3	TRUE	1	0.220510848708217	3		675	967	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65312341	65312341	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368904859	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	204	492	0	ENST00000342505.4:c.1978G>A	p.Asp660Asn	p.D660N	ENST00000342505	NM_002227.2	660	Gac/Aac	14/25	0.0838384601079725	3	FACETS	1	0.941	1	1	0.992	1	INDETERMINATE	3	TRUE	1	0.220510848708217	3		492	677	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158026	27158026	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	194	558	2	ENST00000380036.4:c.255del	p.Val86LeufsTer31	p.V86Lfs*31	ENST00000380036	NM_000459.3	84	Aaa/aa	2/23	0.135249311847294	0	FACETS	1	0.961	1			1	CLONAL	2	TRUE	0	0.220510848708217	0		560	654	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444960	49444960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	274	531	1	ENST00000301067.7:c.2506del	p.Gln836SerfsTer94	p.Q836Sfs*94	ENST00000301067	NM_003482.3	836	Cag/ag	10/54	0.127073327772688	4	FACETS	1	0.984	1	1	0.994	1	INDETERMINATE	3	TRUE	2	0.220510848708217	4		532	898	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799176	42799176	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs762480443	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	259	631	0	ENST00000575354.2:c.4660G>T	p.Ala1554Ser	p.A1554S	ENST00000575354	NM_015125.3	1554	Gca/Tca	20/20	0.0838384601079725	3	FACETS	0.89	0.834	0.947	1	0.991	1	INDETERMINATE	3	TRUE	1	0.220510848708217	3		631	977	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433394	49433394	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783727	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	322	606	2	ENST00000301067.7:c.8053C>T	p.Arg2685Ter	p.R2685*	ENST00000301067	NM_003482.3	2685	Cga/Tga	32/54	0.127073327772688	4	FACETS	1	0.981	1	1	0.995	1	INDETERMINATE	3	TRUE	2	0.220510848708217	4		608	1098	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950344	17950344	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	329	718	1	ENST00000458235.1:c.1383del	p.Leu462CysfsTer3	p.L462Cfs*3	ENST00000458235	NM_000215.3	461	ggG/gg	10/24	0.0838384601079725	3	FACETS	1	0.967	1	1	0.995	1	INDETERMINATE	3	TRUE	1	0.220510848708217	3		719	1073	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948755	71948755	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1565399032	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	413	782	0	ENST00000298229.2:c.3470del	p.Gly1157AspfsTer45	p.G1157Dfs*45	ENST00000298229	NM_001567.3	1156	cGg/cg	26/28	1	2	FACETS	0.939	0.894	0.985	1	0.997	1	CLONAL	3	TRUE	1	0.220510848708217	2		782	1330	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285245	212285245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	96	392	0	ENST00000342788.4:c.3056C>T	p.Ala1019Val	p.A1019V	ENST00000342788	NM_005235.2	1019	gCt/gTt	25/28	1	2	FACETS	0.984	0.888	1	1	0.99	1	CLONAL	3	TRUE	1	0.220510848708217	2		392	295	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003764	45003764	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	314	530	0	ENST00000558401.1:c.20T>A	p.Leu7Ter	p.L7*	ENST00000558401	NM_004048.2	7	tTa/tAa	1/4	0.127073327772688	4	FACETS	1	0.985	1	1	0.995	1	INDETERMINATE	3	TRUE	2	0.220510848708217	4		530	1034	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220899	36220899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555731828	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	152	272	0	ENST00000222270.7:c.4949C>T	p.Thr1650Met	p.T1650M	ENST00000222270	NM_014727.1	1650	aCg/aTg	23/37	0.0838384601079725	3	FACETS	1	0.973	1	1	0.991	1	INDETERMINATE	3	TRUE	1	0.220510848708217	3		272	455	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437401	110437402	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	103	310	0	ENST00000375856.3:c.999dup	p.Ser334GlnfsTer205	p.S334Qfs*205	ENST00000375856	NM_003749.2	333	-/C	1/2	0.135249311847294	0	FACETS	0.816	0.735	0.902			1	CLONAL	2	TRUE	0	0.220510848708217	0		310	446	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263321	115263321	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	218	464	0	ENST00000438362.2:c.2029G>T	p.Val677Phe	p.V677F	ENST00000438362	NM_001242891.1	677	Gtc/Ttc	17/20	0.0838384601079725	3	FACETS	1	0.969	1	1	0.993	1	INDETERMINATE	3	TRUE	1	0.220510848708217	3		464	689	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226568817	226568818	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs779960019	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1225	272	595	0	ENST00000366794.5:c.1251dup	p.Lys418GlufsTer24	p.K418Efs*24	ENST00000366794	NM_001618.3	417	-/G	9/23	0.220510848708217	8	FACETS	0.913	0.854	0.973	0.391	0.366	0.417	CLONAL	3	TRUE	1	0.220510848708217	8		595	1497	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597896	43597898	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs776989694	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	347	723	1	ENST00000355710.3:c.448_450del	p.Phe150del	p.F150del	ENST00000355710	NM_020975.4	148	tcCTTc/tcc	3/20	1	2	FACETS	1	0.973	1	1	0.997	1	CLONAL	3	TRUE	1	0.220510848708217	2		724	1011	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692808	89692813	+	inframe_deletion	In_Frame_Del	DEL	CTAGAA	CTAGAA	-	novel	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	56	253	0	ENST00000371953.3:c.294_299del	p.Glu99_Leu100del	p.E99_L100del	ENST00000371953	NM_000314.4	98	CTAGAA/-	5/9	0.127073327772688	4	FACETS	0.934	0.816	1	1	0.978	1	INDETERMINATE	4	TRUE	2	0.220510848708217	4		253	166	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240622	133240622	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs762629340	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	238	487	0	ENST00000320574.5:c.2674T>C	p.Tyr892His	p.Y892H	ENST00000320574	NM_006231.2	892	Tac/Cac	23/49	1	2	FACETS	1	0.949	1	1	0.996	1	CLONAL	3	TRUE	1	0.220510848708217	2		487	710	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714276	43714276	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	240	643	0	ENST00000382044.4:c.3877del	p.Ser1293ProfsTer74	p.S1293Pfs*74	ENST00000382044	NM_001141980.1	1293	Tcc/cc	19/28	0.127073327772688	4	FACETS	1	0.982	1	1	0.994	1	INDETERMINATE	3	TRUE	2	0.220510848708217	4		643	789	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73995388	73995388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	193	509	0	ENST00000318443.5:c.694C>T	p.His232Tyr	p.H232Y	ENST00000318443	NM_001024736.1	232	Cac/Tac	4/10	NA	2	FACETS	0.926	0.861	0.993			1	INDETERMINATE	3	TRUE	NA	0.220510848708217	2		509	630	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138087	2138087	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	392	767	1	ENST00000219476.3:c.5107G>A	p.Val1703Met	p.V1703M	ENST00000219476	NM_000548.3	1703	Gtg/Atg	40/42	0.0838384601079725	3	FACETS	1	0.988	1	1	0.996	1	INDETERMINATE	3	TRUE	1	0.220510848708217	3		768	1177	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070587	67070587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	129	242	1	ENST00000412916.2:c.211G>A	p.Ala71Thr	p.A71T	ENST00000412916		71	Gcc/Acc	3/6	0.171864686192766	3	FACETS	1	0.942	1			1	CLONAL	3	TRUE	NA	0.220510848708217	3		243	417	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390436	56390436	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	64	293	0	ENST00000348428.3:c.1175G>C	p.Arg392Pro	p.R392P	ENST00000348428	NM_006785.3	392	cGt/cCt	10/17	1	2	FACETS	1	0.929	1	1	0.982	1	CLONAL	2	TRUE	1	0.220510848708217	2		293	266	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229049	36229049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	350	607	1	ENST00000222270.7:c.7829G>A	p.Arg2610His	p.R2610H	ENST00000222270	NM_014727.1	2610	cGc/cAc	36/37	0.0838384601079725	3	FACETS	1	0.962	1	1	0.995	1	INDETERMINATE	3	TRUE	1	0.220510848708217	3		608	1154	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591088	67591105	+	inframe_deletion	In_Frame_Del	DEL	AAACGTATGAACAGCATT	AAACGTATGAACAGCATT	-	novel	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	70	258	0	ENST00000274335.5:c.1685_1702del	p.Arg562_Lys567del	p.R562_K567del	ENST00000274335		561	AAACGTATGAACAGCATT/-	12/15	0.220510848708217	4	FACETS	0.964	0.85	1	1	0.974	1	CLONAL	3	TRUE	2	0.220510848708217	4		258	268	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80168962	80168962	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	97	554	0	ENST00000265081.6:c.3158T>C	p.Val1053Ala	p.V1053A	ENST00000265081	NM_002439.4	1053	gTc/gCc	23/24	1	2	FACETS	1	0.904	1	1	0.987	1	CLONAL	2	TRUE	1	0.220510848708217	2		554	436	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33286944	33286944	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	157	655	0	ENST00000374542.5:c.1993A>G	p.Thr665Ala	p.T665A	ENST00000374542	NM_001141970.1	665	Acc/Gcc	7/8	0.0793647716021531	4	FACETS	0.76	0.694	0.828	0.76	0.694	0.828	INDETERMINATE	2	TRUE	2	0.220510848708217	4		655	1144	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852018	128852018	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	315	798	1	ENST00000249373.3:c.2090C>T	p.Ala697Val	p.A697V	ENST00000249373	NM_005631.4	697	gCc/gTc	12/12	1	2	FACETS	0.91	0.859	0.961	1	0.996	1	CLONAL	3	TRUE	1	0.220510848708217	2		799	1047	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205490	38205490	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	300	626	0	ENST00000317025.8:c.200C>A	p.Pro67His	p.P67H	ENST00000317025	NM_023034.1	67	cCt/cAt	2/24	0.157136234494917	4	FACETS	0.884	0.835	0.935			1	CLONAL	4	TRUE	NA	0.220510848708217	4		626	939	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372487	55372487	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	508	840	0	ENST00000297316.4:c.1180del	p.Ala394ProfsTer60	p.A394Pfs*60	ENST00000297316	NM_022454.3	393	Ggg/gg	2/2	0.157136234494917	4	FACETS	1	0.967	1			1	CLONAL	4	TRUE	NA	0.220510848708217	4		840	1392	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750638	128750638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	297	609	0	ENST00000377970.2:c.175G>A	p.Ala59Thr	p.A59T	ENST00000377970	NM_002467.4	59	Gcg/Acg	2/3	1	2	FACETS	0.932	0.88	0.986	1	0.996	1	CLONAL	3	TRUE	1	0.220510848708217	2		609	963	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090515	5090515	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	44	274	0	ENST00000381652.3:c.2831A>G	p.His944Arg	p.H944R	ENST00000381652	NM_004972.3	944	cAt/cGt	21/25	1	2	FACETS	0.971	0.832	1	1	0.978	1	CLONAL	3	TRUE	1	0.220510848708217	2		274	137	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249343	110249343	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	364	716	0	ENST00000374672.4:c.1230T>G	p.Ser410Arg	p.S410R	ENST00000374672	NM_004235.4	410	agT/agG	4/5	1	2	FACETS	0.959	0.91	1	1	0.997	1	CLONAL	3	TRUE	1	0.220510848708217	2		716	1148	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0045534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	232	545	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.501472829899716	2	FACETS	0.918	0.877	0.957	1	0.994	1	CLONAL	3	FALSE	0	0.501472829899716	2		545	336	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28931588	NA	P-0045534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	125	279	0	ENST00000349496.5:c.94G>C	p.Asp32His	p.D32H	ENST00000349496	NM_001904.3	32	Gac/Cac	3/15	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.501472829899716	2		279	435	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101712	27101712	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0045534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	249	517	0	ENST00000324856.7:c.4993+1G>A		p.X1665_splice	ENST00000324856	NM_006015.4	1665			1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.501472829899716	2		517	806	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27058083	27058083	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	178	364	0	ENST00000324856.7:c.1793del	p.Pro598LeufsTer21	p.P598Lfs*21	ENST00000324856	NM_006015.4	597	ttC/tt	3/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.501472829899716	2		364	568	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648338	206649360	+	splice_donor_variant,intron_variant	Splice_Site	DEL	GTGAGCCCCTCCCTGTCCCTGCCTCCACCCTCAGACCAGCGGCAGGCCTGGGACAGATGCTGACAGGACTCAGGTGTCTGACTCCTGCTAATCATTCCATTTAAAATTCCAACTTAAAAATTAAACCTAAAAAAGATTGTACACCAATGTTCACAGCAGCATTATTTACAATAGCCAAAAGGTGGAAACATCCTAACTGTGAAAACAAAATGTGGGAGGTACCTAAAATAGAATATTATTCAGTCTTAAAAGGAAAGAAATTCTGACACCTGCTACAACATGGATGGACCTTGATGACATTATGTTAAGTGAAAAAAGCCAGACACAGAAGGACAAATCCTGTATGATTCCACTCATACATTCATAGAAACAGAAAGTACCATGGTGGTTTCCAGTGGCTGGGGGCAGAGGAGAATGAGGAGTTGTTTAATAAGTATGGTTTCAAGTTTGAAGAATGAGGCCGGGTGCAGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCCAAGTGGGCGGATCATTTGAGGTTGGGGGTTTGAGACCAGTCTGGCGAACACGGTGAAACCCTGTCTCTACTAAAAAAATACAAAAATTAGCTGGGTGTGGTGGTGCATGCCTGTAGTTCCAGCCACTTGGGAGGCTGAGGCATGAGAATCGATTGAACCTGGGAGGCAGAGATTGCAGTGAGCTGAGATTGCACCACTGTACTCCAGCCTATGTGTCAGAGTGAGACTCTGTCTCCAAAAAAAAAAAAAAAATTGGAGAATGAGAAAAGTTCTAAGATGGATGGTGTGATGGTGGCACAGCAGCGTGGGTGTGCTTAGTGCCAATGAAGTGTACACTTAAAATTGGTTAAAATGGGAAATTTCGTTATGCATATTTTACCACAATTGAACACCTAATCAAAAGAAGTAATACAAAGAGGGGTGCTGCCCTTGAGGACACAGAGCCACCACCCATCTTGGTTTCCTAGAGAATCCAGATGGTACCTCCATACCCTAGTGTCCTTGAGATGCCCCCTA	GTGAGCCCCTCCCTGTCCCTGCCTCCACCCTCAGACCAGCGGCAGGCCTGGGACAGATGCTGACAGGACTCAGGTGTCTGACTCCTGCTAATCATTCCATTTAAAATTCCAACTTAAAAATTAAACCTAAAAAAGATTGTACACCAATGTTCACAGCAGCATTATTTACAATAGCCAAAAGGTGGAAACATCCTAACTGTGAAAACAAAATGTGGGAGGTACCTAAAATAGAATATTATTCAGTCTTAAAAGGAAAGAAATTCTGACACCTGCTACAACATGGATGGACCTTGATGACATTATGTTAAGTGAAAAAAGCCAGACACAGAAGGACAAATCCTGTATGATTCCACTCATACATTCATAGAAACAGAAAGTACCATGGTGGTTTCCAGTGGCTGGGGGCAGAGGAGAATGAGGAGTTGTTTAATAAGTATGGTTTCAAGTTTGAAGAATGAGGCCGGGTGCAGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCCAAGTGGGCGGATCATTTGAGGTTGGGGGTTTGAGACCAGTCTGGCGAACACGGTGAAACCCTGTCTCTACTAAAAAAATACAAAAATTAGCTGGGTGTGGTGGTGCATGCCTGTAGTTCCAGCCACTTGGGAGGCTGAGGCATGAGAATCGATTGAACCTGGGAGGCAGAGATTGCAGTGAGCTGAGATTGCACCACTGTACTCCAGCCTATGTGTCAGAGTGAGACTCTGTCTCCAAAAAAAAAAAAAAAATTGGAGAATGAGAAAAGTTCTAAGATGGATGGTGTGATGGTGGCACAGCAGCGTGGGTGTGCTTAGTGCCAATGAAGTGTACACTTAAAATTGGTTAAAATGGGAAATTTCGTTATGCATATTTTACCACAATTGAACACCTAATCAAAAGAAGTAATACAAAGAGGGGTGCTGCCCTTGAGGACACAGAGCCACCACCCATCTTGGTTTCCTAGAGAATCCAGATGGTACCTCCATACCCTAGTGTCCTTGAGATGCCCCCTA	-	novel	NA	P-0045534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	264	469	0	ENST00000367120.3:c.358+1_359-164del		p.X120_splice	ENST00000367120	NM_014002.3	120			0.501472829899716	3	FACETS	1	0.989	1	0.618	0.579	0.658	CLONAL	1	FALSE	1	0.501472829899716	3		469	1065	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649667	206649667	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553385318	NA	P-0045534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	249	567	0	ENST00000367120.3:c.502G>A	p.Glu168Lys	p.E168K	ENST00000367120	NM_014002.3	168	Gag/Aag	6/22	0.501472829899716	3	FACETS	1	0.986	1	0.59	0.551	0.629	CLONAL	1	FALSE	1	0.501472829899716	3		567	1053	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532695	187532695	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316346360	NA	P-0045534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	162	404	1	ENST00000441802.2:c.9698G>A	p.Arg3233His	p.R3233H	ENST00000441802	NM_005245.3	3233	cGt/cAt	14/27	0.501472829899716	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	0	0.501472829899716	1		405	348	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196738	106196738	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045535-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	24	321	0	ENST00000380013.4:c.5071T>G	p.Ser1691Ala	p.S1691A	ENST00000380013	NM_001127208.2	1691	Tct/Gct	11/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		321	415	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0045536-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	195	348	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	0.360934572699869	3	FACETS	1	0.983	1	0.774	0.722	0.827	CLONAL	2	TRUE	0	0.367375571418738	3		348	541	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881457	48881457	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0045536-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	112	119	0	ENST00000267163.4:c.179T>A	p.Leu60Ter	p.L60*	ENST00000267163	NM_000321.2	60	tTa/tAa	2/27	0.367375571418738	2	FACETS	0.996	0.909	1	0.996	0.909	1	CLONAL	2	TRUE	0	0.367375571418738	2		119	306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574005	7574005	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045536-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	459	619	0	ENST00000269305.4:c.1022T>G	p.Phe341Cys	p.F341C	ENST00000269305	NM_001126112.2	341	tTc/tGc	10/11	0.367375571418738	3	FACETS	1	0.978	1			1	CLONAL	3	TRUE	NA	0.367375571418738	3		619	960	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591096	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAACAGCATTAAACCAGACCTTATCCAGCTGAGAAAGAC	GAACAGCATTAAACCAGACCTTATCCAGCTGAGAAAGAC	-	novel	NA	P-0045536-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	22	245	0	ENST00000274335.5:c.1691_1729del	p.Asn564_Thr576del	p.N564_T576del	ENST00000274335		563	atGAACAGCATTAAACCAGACCTTATCCAGCTGAGAAAGACg/atg	12/15	0.222158867223953	4	FACETS	0.348	0.269	0.441	0.174	0.134	0.221	SUBCLONAL	1	TRUE	2	0.367375571418738	4		245	470	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242494	+	protein_altering_variant	In_Frame_Del	DEL	TAAGAGAAGCAACATCTCCGAAAGC	TAAGAGAAGCAACATCTCCGAAAGC	CGAGAGA	novel	NA	P-0045536-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2869	157	345	1	ENST00000275493.2:c.2240_2264delinsCGAGAGA	p.Leu747_Ala755delinsSerArgAsp	p.L747_A755delinsSRD	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCCGAAAGCc/tCGAGAGAc	19/28	0.367375571418738	32	FACETS	0.919	0.837	1	0.063	0.057	0.07	CLONAL	2	TRUE	3	0.367375571418738	32		346	3026	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0045537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	93	504	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.176290767464645	0	FACETS	0.638	0.569	0.712			1	INDETERMINATE	1	TRUE	0	0.337532927030049	0		504	572	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524613	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0045537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	38	201	0	ENST00000355739.4:c.2750_2751del	p.Lys917IlefsTer12	p.K917Ifs*12	ENST00000355739	NM_000123.3	915	AAa/a	13/15	0.223739225603512	3	FACETS	0.618	0.511	0.737			1	SUBCLONAL	1	TRUE	NA	0.337532927030049	3		201	426	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249013	55249014	+	protein_altering_variant	In_Frame_Ins	INS	AA	AA	GGGTT	novel	NA	P-0045537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	286	595	0	ENST00000275493.2:c.2311_2312delinsGGGTT	p.Asn771delinsGlyPhe	p.N771delinsGF	ENST00000275493	NM_005228.3	771	AAc/GGGTTc	20/28	0.337532927030049	4	FACETS	0.919	0.867	0.972	0.919	0.867	0.972	CLONAL	3	TRUE	1	0.337532927030049	4		595	822	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105966	27105966	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	70	405	1	ENST00000324856.7:c.5577del	p.Phe1859LeufsTer24	p.F1859Lfs*24	ENST00000324856	NM_006015.4	1859	ttC/tt	20/20	0.235623341603573	1	FACETS	0.684	0.598	0.777	0.684	0.598	0.777	SUBCLONAL	1	TRUE	0	0.337532927030049	1		406	504	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599975	28599975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1450092599	NA	P-0045537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	84	560	3	ENST00000253063.3:c.857G>A	p.Arg286His	p.R286H	ENST00000253063	NM_031459.4	286	cGc/cAc	6/10	0.235623341603573	1	FACETS	0.616	0.544	0.693	0.616	0.544	0.693	SUBCLONAL	1	TRUE	0	0.337532927030049	1		563	672	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524718	103524718	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045537-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	29	249	0	ENST00000355739.4:c.2853del	p.Lys952AsnfsTer30	p.K952Nfs*30	ENST00000355739	NM_000123.3	950	tGg/tg	13/15	0.223739225603512	3	FACETS	0.418	0.334	0.512			1	SUBCLONAL	1	TRUE	NA	0.337532927030049	3		249	481	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366931	40366931	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	349	625	2	ENST00000397332.2:c.266G>T	p.Gly89Val	p.G89V	ENST00000397332	NM_001033082.2	89	gGt/gTt	2/3	0.865020795807612	3	FACETS	0.926	0.877	0.976	0.463	0.438	0.488	CLONAL	1	TRUE	1	0.898286693189654	3		627	1216	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444762	49444762	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	354	837	0	ENST00000301067.7:c.2704G>T	p.Glu902Ter	p.E902*	ENST00000301067	NM_003482.3	902	Gag/Tag	10/54	0.847943377525206	3	FACETS	0.918	0.87	0.968	0.459	0.435	0.484	CLONAL	1	TRUE	1	0.898286693189654	3		837	1244	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856205	111856205	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	369	314	2	ENST00000341259.2:c.256G>T	p.Gly86Cys	p.G86C	ENST00000341259	NM_005475.2	86	Ggc/Tgc	2/8	0.865020795807612	3	FACETS	0.968	0.93	1	0.968	0.93	1	CLONAL	2	TRUE	1	0.898286693189654	3		316	615	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885801	111885801	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	547	582	1	ENST00000341259.2:c.1423G>T	p.Val475Phe	p.V475F	ENST00000341259	NM_005475.2	475	Gtc/Ttc	8/8	0.865020795807612	3	FACETS	0.997	0.965	1	0.997	0.965	1	CLONAL	2	TRUE	1	0.898286693189654	3		583	885	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576202	88576202	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1482426106	NA	P-0045542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	247	480	1	ENST00000360948.2:c.1471C>T	p.Pro491Ser	p.P491S	ENST00000360948	NM_001012338.2	491	Ccc/Tcc	13/19	1	2	FACETS	0.897	0.845	0.95	0.897	0.845	0.95	CLONAL	1	TRUE	1	0.898286693189654	2		481	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0045542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	510	469	0	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.890423266507085	2	FACETS	0.986	0.967	1	0.986	0.967	1	CLONAL	2	TRUE	0	0.898286693189654	2		469	576	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664723	138664723	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	146	254	1	ENST00000330315.3:c.842C>A	p.Pro281Gln	p.P281Q	ENST00000330315	NM_023067.3	281	cCg/cAg	1/1	0.842210750028285	5	FACETS	1	0.976	1	0.295	0.27	0.321	CLONAL	1	TRUE	1	0.898286693189654	5		255	647	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157875	106157875	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	149	165	0	ENST00000380013.4:c.2776A>C	p.Asn926His	p.N926H	ENST00000380013	NM_001127208.2	926	Aat/Cat	3/11	0.898286693189654	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.898286693189654	1		165	171	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371845	116371845	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	168	263	0	ENST00000397752.3:c.1324A>T	p.Ile442Leu	p.I442L	ENST00000397752	NM_000245.2	442	Ata/Tta	3/21	1	2	FACETS	0.829	0.77	0.89	0.829	0.77	0.89	CLONAL	1	TRUE	1	0.898286693189654	2		263	451	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970994	70970994	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	340	458	0	ENST00000276594.2:c.1267C>A	p.Pro423Thr	p.P423T	ENST00000276594	NM_024504.3	423	Ccc/Acc	6/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.898286693189654	2		458	712	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485806	8485807	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0045542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	115	194	1	ENST00000356435.5:c.3010_3011delinsAA	p.Pro1004Lys	p.P1004K	ENST00000356435		1004	CCa/AAa	17/35	1	2	FACETS	0.865	0.791	0.94	0.865	0.791	0.94	CLONAL	1	TRUE	1	0.898286693189654	2		195	296	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15833818	15833818	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	564	320	0	ENST00000307771.7:c.576T>G	p.Asn192Lys	p.N192K	ENST00000307771	NM_005089.3	192	aaT/aaG	8/11	0.818810883726685	3	FACETS	0.963	0.932	0.993			1	CLONAL	2	TRUE	NA	0.898286693189654	3		320	945	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841160	15841160	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	464	269	0	ENST00000307771.7:c.1246del	p.Glu416ArgfsTer?	p.E416Rfs*?	ENST00000307771	NM_005089.3	415	cGg/cg	11/11	0.818810883726685	3	FACETS	1	0.975	1			1	CLONAL	2	TRUE	NA	0.898286693189654	3		269	740	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913182	39913182	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	178	276	0	ENST00000378444.4:c.4933C>A	p.Pro1645Thr	p.P1645T	ENST00000378444	NM_001123385.1	1645	Ccc/Acc	14/15	0.818810883726685	3	FACETS	0.805	0.744	0.869			1	CLONAL	1	TRUE	NA	0.898286693189654	3		276	713	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504041	123504041	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	123	116	0	ENST00000371139.4:c.217C>G	p.His73Asp	p.H73D	ENST00000371139	NM_001114937.2	73	Cat/Gat	3/4	0.898286693189654	3	FACETS	0.919	0.837	1	0.459	0.418	0.502	CLONAL	1	TRUE	1	0.898286693189654	3		116	432	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0045543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	117	403	0				ENST00000310581	NM_198253.2	-/1132			0.304514250454016	6	FACETS	0.962	0.873	1	0.481	0.436	0.528	INDETERMINATE	2	TRUE	2	0.540897189860964	6		403	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0045543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	121	614	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	1	2	FACETS	0.775	0.703	0.851	0.775	0.703	0.851	SUBCLONAL	1	TRUE	1	0.540897189860964	2		614	577	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941653	48941653	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0045543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	80	204	0	ENST00000267163.4:c.963C>G	p.Tyr321Ter	p.Y321*	ENST00000267163	NM_000321.2	321	taC/taG	10/27	0.107568287524852	3	FACETS	1	0.974	1			1	INDETERMINATE	2	TRUE	NA	0.540897189860964	3		204	153	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs121913468	NA	P-0045543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	170	403	0	ENST00000269571.5:c.2305G>C	p.Asp769His	p.D769H	ENST00000269571		769	Gac/Cac	19/27	0.207052309854494	3	FACETS	1	0.968	1	0.708	0.66	0.756	INDETERMINATE	2	TRUE	0	0.540897189860964	3		403	376	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0045543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	208	770	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.540897189860964	2		770	636	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910587	29910587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41549014	NA	P-0045543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	345	1186	1	ENST00000376809.5:c.127G>A	p.Glu43Lys	p.E43K	ENST00000376809	NM_002116.7	43	Gag/Aag	2/8	0.134015638979951	5	FACETS	1	0.992	1	0.618	0.587	0.65	INDETERMINATE	2	TRUE	1	0.540897189860964	5		1187	934	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105892	27105892	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	402	510	0	ENST00000324856.7:c.5503C>T	p.Gln1835Ter	p.Q1835*	ENST00000324856	NM_006015.4	1835	Cag/Tag	20/20	0.540897189860964	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	0	0.540897189860964	3		510	626	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10277291	10277291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257025095	NA	P-0045543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	56	673	0	ENST00000340748.4:c.826G>A	p.Glu276Lys	p.E276K	ENST00000340748		276	Gaa/Aaa	10/40	1	2	FACETS	0.322	0.275	0.373	0.322	0.275	0.373	SUBCLONAL	1	TRUE	1	0.540897189860964	2		673	643	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264627	11264627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	230	547	2	ENST00000361445.4:c.3935C>T	p.Pro1312Leu	p.P1312L	ENST00000361445	NM_004958.3	1312	cCg/cTg	26/58	0.497798262723535	3	FACETS	0.935	0.878	0.992	0.623	0.585	0.661	CLONAL	2	TRUE	0	0.540897189860964	3		549	578	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623894	28623894	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	147	420	0	ENST00000241453.7:c.760C>G	p.Gln254Glu	p.Q254E	ENST00000241453	NM_004119.2	254	Cag/Gag	7/24	0.254430135203203	5	FACETS	1	0.98	1	0.798	0.737	0.862	INDETERMINATE	2	TRUE	2	0.540897189860964	5		420	411	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135286	30135286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1179272987	NA	P-0045543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	21	336	0	ENST00000331968.5:c.532G>A	p.Glu178Lys	p.E178K	ENST00000331968	NM_002742.2	178	Gaa/Aaa	3/18	0.2244028292242	2	FACETS	0.199	0.152	0.253	0.099	0.076	0.127	INDETERMINATE	1	TRUE	0	0.540897189860964	2		336	391	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014103	70014103	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs756384799	NA	P-0045543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	68	523	0	ENST00000394351.3:c.964G>C	p.Glu322Gln	p.E322Q	ENST00000394351	NM_000248.3	322	Gag/Cag	9/9	0.2244028292242	2	FACETS	0.54	0.47	0.614	0.27	0.235	0.307	INDETERMINATE	1	TRUE	0	0.540897189860964	2		523	466	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671985	30671985	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	156	675	1	ENST00000376406.3:c.4975G>A	p.Asp1659Asn	p.D1659N	ENST00000376406	NM_014641.2	1659	Gat/Aat	10/15	0.134015638979951	5	FACETS	1	0.987	1	0.352	0.322	0.382	INDETERMINATE	1	TRUE	1	0.540897189860964	5		676	743	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139804433	139804433	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1250915147	NA	P-0045543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	226	676	0	ENST00000247668.2:c.590T>A	p.Ile197Asn	p.I197N	ENST00000247668	NM_021138.3	197	aTc/aAc	6/11	0.254430135203203	5	FACETS	0.997	0.932	1	0.665	0.621	0.709	INDETERMINATE	2	TRUE	2	0.540897189860964	5		676	759	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139804439	139804439	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	221	645	0	ENST00000247668.2:c.596G>C	p.Arg199Pro	p.R199P	ENST00000247668	NM_021138.3	199	cGg/cCg	6/11	0.254430135203203	5	FACETS	1	0.949	1	0.679	0.634	0.725	INDETERMINATE	2	TRUE	2	0.540897189860964	5		645	727	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577591	7577591	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	347	459	0	ENST00000269305.4:c.690del	p.Thr231ProfsTer16	p.T231Pfs*16	ENST00000269305	NM_001126112.2	230	acC/ac	7/11	0.804320110929965	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.804320110929965	2		459	419	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	98	425	0				ENST00000310581	NM_198253.2	-/1132			0.235429555701544	1	FACETS	1	0.95	1	1	0.95	1	INDETERMINATE	1	TRUE	0	0.457410193687233	1		425	305	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615698	1615698	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145878545	NA	P-0045548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	137	733	2	ENST00000344749.5:c.1573C>T	p.Arg525Trp	p.R525W	ENST00000344749	NM_001136139.2	525	Cgg/Tgg	17/19	0.457410193687233	3	FACETS	0.585	0.53	0.642	0.292	0.265	0.321	SUBCLONAL	1	TRUE	1	0.457410193687233	3		735	1259	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28644733	28644733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	18	245	0	ENST00000241453.7:c.60G>A	p.Met20Ile	p.M20I	ENST00000241453	NM_004119.2	20	atG/atA	2/24	0.384372803206796	3	FACETS	0.294	0.221	0.381	0.147	0.11	0.191	SUBCLONAL	1	TRUE	1	0.457410193687233	3		245	329	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981244	201981245	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0045548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	43	665	0	ENST00000359651.3:c.325dup	p.Glu109GlyfsTer26	p.E109Gfs*26	ENST00000359651		108	gag/gaGg	2/8	0.457410193687233	1	FACETS	0.2	0.166	0.237	0.2	0.166	0.237	SUBCLONAL	1	TRUE	0	0.457410193687233	1		665	726	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981874	201981874	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	160	707	0	ENST00000359651.3:c.585del	p.Asp195GlufsTer59	p.D195Efs*59	ENST00000359651		195	gaC/ga	4/8	0.457410193687233	1	FACETS	0.738	0.678	0.801	0.738	0.678	0.801	SUBCLONAL	1	TRUE	0	0.457410193687233	1		707	731	SUCCESS
FH	2271	MSKCC	GRCh37	1	241676910	241676910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	22	272	2	ENST00000366560.3:c.371C>T	p.Ala124Val	p.A124V	ENST00000366560	NM_000143.3	124	gCa/gTa	3/10	1	2	FACETS	0.245	0.19	0.31	0.245	0.19	0.31	SUBCLONAL	1	TRUE	1	0.457410193687233	2		274	392	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344410	118344410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	20	220	1	ENST00000534358.1:c.2536G>A	p.Glu846Lys	p.E846K	ENST00000534358	NM_005933.3	846	Gaa/Aaa	3/36	0.273355795204312	2	FACETS	0.283	0.216	0.361	0.142	0.108	0.181	INDETERMINATE	1	TRUE	0	0.457410193687233	2		221	309	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344830	118344830	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	19	279	0	ENST00000534358.1:c.2956G>T	p.Glu986Ter	p.E986*	ENST00000534358	NM_005933.3	986	Gag/Tag	3/36	0.273355795204312	2	FACETS	0.225	0.17	0.289	0.112	0.085	0.145	INDETERMINATE	1	TRUE	0	0.457410193687233	2		279	370	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438297	49438297	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	43	469	0	ENST00000301067.7:c.4972G>C	p.Glu1658Gln	p.E1658Q	ENST00000301067	NM_003482.3	1658	Gag/Cag	20/54	0.235429555701544	1	FACETS	0.259	0.217	0.307	0.259	0.217	0.307	INDETERMINATE	1	TRUE	0	0.457410193687233	1		469	559	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018211	48018211	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	131	441	1	ENST00000234420.5:c.406G>A	p.Asp136Asn	p.D136N	ENST00000234420	NM_000179.2	136	Gac/Aac	2/10	1	2	FACETS	0.835	0.759	0.915	0.835	0.759	0.915	CLONAL	1	TRUE	1	0.457410193687233	2		442	686	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997455	149997455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	26	401	0	ENST00000253339.5:c.2824G>A	p.Glu942Lys	p.E942K	ENST00000253339		942	Gaa/Aaa	6/7	0.174093126067809	2	FACETS	0.223	0.176	0.278	0.112	0.088	0.139	INDETERMINATE	1	TRUE	0	0.457410193687233	2		401	509	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527541	157527541	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	19	333	0	ENST00000346085.5:c.5266G>C	p.Glu1756Gln	p.E1756Q	ENST00000346085	NM_020732.3	1756	Gaa/Caa	20/20	0.457410193687233	1	FACETS	0.193	0.146	0.248	0.193	0.146	0.248	SUBCLONAL	1	TRUE	0	0.457410193687233	1		333	332	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527885	157527885	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1381000019	NA	P-0045548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	29	427	0	ENST00000346085.5:c.5610G>C	p.Glu1870Asp	p.E1870D	ENST00000346085	NM_020732.3	1870	gaG/gaC	20/20	0.457410193687233	1	FACETS	0.236	0.189	0.29	0.236	0.189	0.29	SUBCLONAL	1	TRUE	0	0.457410193687233	1		427	414	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528303	157528303	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	33	571	0	ENST00000346085.5:c.6028G>A	p.Asp2010Asn	p.D2010N	ENST00000346085	NM_020732.3	2010	Gat/Aat	20/20	0.457410193687233	1	FACETS	0.203	0.164	0.246	0.203	0.164	0.246	SUBCLONAL	1	TRUE	0	0.457410193687233	1		571	549	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528900	157528900	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	23	458	0	ENST00000346085.5:c.6625G>A	p.Asp2209Asn	p.D2209N	ENST00000346085	NM_020732.3	2209	Gac/Aac	20/20	0.457410193687233	1	FACETS	0.173	0.134	0.218	0.173	0.134	0.218	SUBCLONAL	1	TRUE	0	0.457410193687233	1		458	449	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44911001	44911002	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0045548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	56	247	0	ENST00000377967.4:c.705_706del	p.Asn236SerfsTer26	p.N236Sfs*26	ENST00000377967	NM_021140.2	234	acAGag/acag	9/29	0.457410193687233	1	FACETS	0.8	0.693	0.914	0.8	0.693	0.914	CLONAL	1	TRUE	0	0.457410193687233	1		247	236	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528267	157528269	+	missense_variant	Missense_Mutation	TNP	GAG	GAG	AAA	novel	NA	P-0045548-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	26	487	0	ENST00000346085.5:c.5992_5994delinsAAA	p.Glu1998Lys	p.E1998K	ENST00000346085	NM_020732.3	1998	GAG/AAA	20/20	0.457410193687233	1	FACETS	0.17	0.134	0.211	0.17	0.134	0.211	SUBCLONAL	1	TRUE	0	0.457410193687233	1		487	517	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560464	95560464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	104	315	0	ENST00000393063.1:c.5125G>A	p.Asp1709Asn	p.D1709N	ENST00000393063	NM_030621.3	1709	Gat/Aat	25/28	0.490382778004326	1	FACETS	0.977	0.885	1	1	0.988	1	CLONAL	2	TRUE	0	0.28	1		315	327	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0045550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	112	623	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.287956790242738	1	FACETS	0.896	0.806	0.991	0.896	0.806	0.991	CLONAL	1	FALSE	0	0.287956790242738	1		623	743	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0045550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	60	278	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.958	0.828	1	0.958	0.828	1	CLONAL	1	FALSE	1	0.287956790242738	2		278	435	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486587	56486587	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045550-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	72	553	0	ENST00000267101.3:c.1166C>T	p.Thr389Ile	p.T389I	ENST00000267101	NM_001982.3	389	aCa/aTa	10/28	1	2	FACETS	0.673	0.587	0.766	0.673	0.587	0.766	SUBCLONAL	1	FALSE	1	0.287956790242738	2		553	743	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0045551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	171	670	1	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.170925906787247	2	FACETS	1	0.963	1	0.54	0.496	0.585	INDETERMINATE	1	TRUE	0	0.34	2		671	932	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519477	176519477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749248588	NA	P-0045551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	82	734	0	ENST00000292408.4:c.883G>A	p.Gly295Arg	p.G295R	ENST00000292408	NM_213647.1	295	Gga/Aga	7/18	1	2	FACETS	0.562	0.495	0.635	0.562	0.495	0.635	SUBCLONAL	1	TRUE	1	0.34	2		734	858	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573456	48573456	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	18	199	0	ENST00000342988.3:c.40G>T	p.Asp14Tyr	p.D14Y	ENST00000342988	NM_005359.5	14	Gat/Tat	2/12	1	2	FACETS	0.388	0.292	0.501	0.388	0.292	0.501	SUBCLONAL	1	TRUE	1	0.34	2		199	273	SUCCESS
ATR	545	MSKCC	GRCh37	3	142218561	142218561	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0045551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	33	237	1	ENST00000350721.4:c.5289-1G>T		p.X1763_splice	ENST00000350721	NM_001184.3	1763			1	2	FACETS	0.424	0.345	0.513	0.424	0.345	0.513	SUBCLONAL	1	TRUE	1	0.34	2		238	458	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446885	187446893	+	inframe_deletion	In_Frame_Del	DEL	CTCCCCGCT	CTCCCCGCT	-	novel	NA	P-0045551-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	145	574	0	ENST00000232014.4:c.1300_1308del	p.Ser434_Glu436del	p.S434_E436del	ENST00000232014	NM_001130845.1	434	AGCGGGGAG/-	5/10	1	2	FACETS	0.891	0.812	0.974	0.891	0.812	0.974	CLONAL	1	TRUE	1	0.34	2		574	957	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	127	425	0				ENST00000310581	NM_198253.2	-/1132			0.646900650409528	3	FACETS	0.999	0.924	1	0.999	0.924	1	CLONAL	2	TRUE	1	0.646900650409528	3		425	260	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0045552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	220	457	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.489053684788125	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.646900650409528	4		457	517	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807889	1807889	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs78311289	NA	P-0045552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	408	602	0	ENST00000260795.2:c.1948A>G	p.Lys650Glu	p.K650E	ENST00000260795		650	Aag/Gag	13/17	0.637028553918114	3	FACETS	1	0.967	1	0.674	0.645	0.702	CLONAL	2	TRUE	0	0.646900650409528	3		602	826	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543942	41543942	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045552-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	126	430	0	ENST00000263253.7:c.2233C>G	p.Leu745Val	p.L745V	ENST00000263253	NM_001429.3	745	Ctc/Gtc	12/31	0.646900650409528	3	FACETS	0.694	0.629	0.762	0.347	0.314	0.381	SUBCLONAL	1	TRUE	1	0.646900650409528	3		430	743	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997826	149997826	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	118	480	1	ENST00000253339.5:c.2641del	p.Asp881IlefsTer11	p.D881Ifs*11	ENST00000253339		881	Gat/at	5/7	0.237554290887425	5	FACETS	1	0.963	1	0.746	0.678	0.817	CLONAL	2	TRUE	2	0.368773991180813	5		481	444	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280804	41280804	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	12	333	0	ENST00000349496.5:c.2317C>T	p.Gln773Ter	p.Q773*	ENST00000349496	NM_001904.3	773	Cag/Tag	15/15	0.368773991180813	2	FACETS	0.284	0.199	0.389	0.142	0.099	0.195	SUBCLONAL	1	TRUE	0	0.368773991180813	2		333	229	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0045553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	115	592	1	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.356629483578003	2	FACETS	0.951	0.867	1	0.951	0.867	1	CLONAL	2	TRUE	0	0.368773991180813	2		593	328	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578488	7578488	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	150	718	0	ENST00000269305.4:c.442G>C	p.Asp148His	p.D148H	ENST00000269305	NM_001126112.2	148	Gat/Cat	5/11	0.356629483578003	2	FACETS	0.871	0.803	0.941	0.871	0.803	0.941	CLONAL	2	TRUE	0	0.368773991180813	2		718	467	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472600	88472600	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	123	384	0	ENST00000360948.2:c.1955G>T	p.Gly652Val	p.G652V	ENST00000360948	NM_001012338.2	652	gGg/gTg	16/19	0.368773991180813	5	FACETS	1	0.973	1	0.785	0.715	0.857	CLONAL	2	TRUE	2	0.368773991180813	5		384	440	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346876	91346876	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	85	353	0	ENST00000355112.3:c.3484A>G	p.Asn1162Asp	p.N1162D	ENST00000355112	NM_000057.2	1162	Aat/Gat	18/22	0.368773991180813	5	FACETS	0.865	0.769	0.966	0.576	0.512	0.644	CLONAL	2	TRUE	2	0.368773991180813	5		353	414	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488657	212488657	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	103	386	0	ENST00000342788.4:c.2192C>A	p.Thr731Lys	p.T731K	ENST00000342788	NM_005235.2	731	aCg/aAg	18/28	0.237554290887425	5	FACETS	1	0.962	1	0.755	0.681	0.832	CLONAL	2	TRUE	2	0.368773991180813	5		386	383	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530171	212530171	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	70	271	0	ENST00000342788.4:c.1748T>A	p.Phe583Tyr	p.F583Y	ENST00000342788	NM_005235.2	583	tTt/tAt	15/28	0.237554290887425	5	FACETS	0.999	0.88	1	0.666	0.586	0.751	CLONAL	2	TRUE	2	0.368773991180813	5		271	295	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212615390	212615390	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	113	398	0	ENST00000342788.4:c.596del	p.Gly199AspfsTer10	p.G199Dfs*10	ENST00000342788	NM_005235.2	199	gGa/ga	5/28	0.237554290887425	5	FACETS	1	0.95	1	0.716	0.649	0.787	CLONAL	2	TRUE	2	0.368773991180813	5		398	443	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021820	71021820	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	53	192	0	ENST00000318789.4:c.1538T>A	p.Val513Glu	p.V513E	ENST00000318789	NM_032682.5	513	gTg/gAg	18/21	0.368773991180813	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	2	TRUE	0	0.368773991180813	2		192	142	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104579	69104579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	114	533	0	ENST00000288368.4:c.4423C>T	p.Pro1475Ser	p.P1475S	ENST00000288368	NM_024870.2	1475	Cct/Tct	37/40	0.368773991180813	5	FACETS	0.829	0.749	0.914	0.553	0.499	0.609	CLONAL	2	TRUE	2	0.368773991180813	5		533	579	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141570599	141570599	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	166	419	0	ENST00000220592.5:c.529G>T	p.Val177Leu	p.V177L	ENST00000220592	NM_012154.3	177	Gtg/Ttg	5/19	0.368773991180813	5	FACETS	1	0.981	1	1	0.981	1	CLONAL	3	TRUE	2	0.368773991180813	5		419	402	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900200	101900200	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	88	298	1	ENST00000374994.4:c.634G>T	p.Gly212Cys	p.G212C	ENST00000374994	NM_004612.2	212	Ggc/Tgc	4/9	0.356629483578003	2	FACETS	0.943	0.849	1	0.943	0.849	1	CLONAL	2	TRUE	0	0.368773991180813	2		299	253	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410004	63410004	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	104	471	0	ENST00000330258.3:c.3163G>T	p.Val1055Phe	p.V1055F	ENST00000330258	NM_152424.3	1055	Gtt/Ttt	2/2	0.198886187653779	4	FACETS	0.946	0.853	1	0.946	0.853	1	INDETERMINATE	2	TRUE	2	0.368773991180813	4		471	408	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617654	100617654	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	119	496	0	ENST00000308731.7:c.415G>C	p.Val139Leu	p.V139L	ENST00000308731	NM_000061.2	139	Gtt/Ctt	6/19	0.198886187653779	4	FACETS	1	0.956	1	1	0.956	1	INDETERMINATE	2	TRUE	2	0.368773991180813	4		496	408	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288968	212288970	+	frameshift_variant	Frame_Shift_Del	DEL	CGT	CGT	AG	novel	NA	P-0045553-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	88	440	0	ENST00000342788.4:c.2776_2778delinsCT	p.Thr926LeufsTer8	p.T926Lfs*8	ENST00000342788	NM_005235.2	926	ACG/CT	23/28	0.237554290887425	5	FACETS	0.983	0.877	1	0.655	0.585	0.73	CLONAL	2	TRUE	2	0.368773991180813	5		440	377	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	173	500	1	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.464308263655321	2		501	578	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0045554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	138	354	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.751	0.69	0.812	1	0.988	1	SUBCLONAL	2	TRUE	1	0.464308263655321	2		354	396	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916944	178916944	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519933	NA	P-0045554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	94	478	0	ENST00000263967.3:c.331A>G	p.Lys111Glu	p.K111E	ENST00000263967	NM_006218.2	111	Aag/Gag	2/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.464308263655321	2		478	325	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922694	44922694	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397514628	NA	P-0045554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	101	241	1	ENST00000377967.4:c.1555C>T	p.Arg519Ter	p.R519*	ENST00000377967	NM_021140.2	519	Cga/Tga	16/29	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.464308263655321	2		242	343	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089769	27089769	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	74	438	0	ENST00000324856.7:c.2725C>T	p.Gln909Ter	p.Q909*	ENST00000324856	NM_006015.4	909	Caa/Taa	8/20	1	2	FACETS	0.526	0.461	0.596	0.526	0.461	0.596	SUBCLONAL	1	TRUE	1	0.464308263655321	2		438	606	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717777	89717777	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs786204873	NA	P-0045554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	209	239	0	ENST00000371953.3:c.801+1G>A		p.X267_splice	ENST00000371953	NM_000314.4	267			0.464308263655321	1	FACETS	1	0.991	1	1	0.995	1	CLONAL	2	TRUE	0	0.464308263655321	1		239	293	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057652	27057653	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0045554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	239	406	0	ENST00000324856.7:c.1361dup	p.Tyr454Ter	p.Y454*	ENST00000324856	NM_006015.4	454	tat/tAat	3/20	1	2	FACETS	0.988	0.932	1	1	0.995	1	CLONAL	2	TRUE	1	0.464308263655321	2		406	521	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368226	31368226	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773918660	NA	P-0045554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	233	517	0	ENST00000328111.2:c.97G>A	p.Asp33Asn	p.D33N	ENST00000328111	NM_006892.3	33	Gac/Aac	2/23	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.464308263655321	2		517	769	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189845	11189845	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	63	412	0	ENST00000361445.4:c.5664C>G	p.Phe1888Leu	p.F1888L	ENST00000361445	NM_004958.3	1888	ttC/ttG	40/58	0.188876177403276	2	FACETS	0.331	0.286	0.381	0.166	0.143	0.191	INDETERMINATE	1	TRUE	0	0.464308263655321	2		412	819	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633161	3633161	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	81	706	0	ENST00000294008.3:c.5090C>A	p.Pro1697Gln	p.P1697Q	ENST00000294008	NM_032444.2	1697	cCa/cAa	14/15	1	2	FACETS	0.338	0.297	0.383	0.338	0.297	0.383	SUBCLONAL	1	TRUE	1	0.464308263655321	2		706	1032	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211099	36211099	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	120	650	0	ENST00000222270.7:c.850C>G	p.Gln284Glu	p.Q284E	ENST00000222270	NM_014727.1	284	Cag/Gag	3/37	1	2	FACETS	0.521	0.47	0.576	0.521	0.47	0.576	SUBCLONAL	1	TRUE	1	0.464308263655321	2		650	992	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117870627	117870629	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0045554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	110	296	0	ENST00000297338.2:c.443_445del	p.Glu148del	p.E148del	ENST00000297338	NM_006265.2	148	gAAGtt/gtt	5/14	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.464308263655321	2		296	344	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229245	123229245	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045554-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	101	234	0	ENST00000218089.9:c.3729G>T	p.Glu1243Asp	p.E1243D	ENST00000218089	NM_001042749.1	1243	gaG/gaT	34/35	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.464308263655321	2		234	345	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0045555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	84	403	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.953	1			1	INDETERMINATE	1	TRUE	NA	0.523911188382677	2		403	286	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249022	55249022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567477136	NA	P-0045555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7383	6835	547	0	ENST00000275493.2:c.2320G>A	p.Val774Met	p.V774M	ENST00000275493	NM_005228.3	774	Gtg/Atg	20/28	0.523911188382677	59	FACETS	1	0.994	1	0.504	0.498	0.51	CLONAL	29	TRUE	1	0.523911188382677	59		547	14218	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225060	NA	P-0045555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	194	524	0	ENST00000263967.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000263967	NM_006218.2	104	cCa/cTa	2/21	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.523911188382677	2		524	575	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625110	69625110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782454437	NA	P-0045555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	116	623	0	ENST00000334134.2:c.683C>T	p.Ser228Leu	p.S228L	ENST00000334134	NM_005247.2	228	tCg/tTg	3/3	1	2	FACETS	0.952	0.864	1	0.952	0.864	1	CLONAL	1	TRUE	1	0.523911188382677	2		623	465	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052971	180052971	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753074837	NA	P-0045555-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	188	925	3	ENST00000261937.6:c.1319G>A	p.Arg440His	p.R440H	ENST00000261937	NM_182925.4	440	cGc/cAc	10/30	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.523911188382677	2		928	714	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	44	425	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.803	0.685	0.928	0.803	0.685	0.928	CLONAL	1	TRUE	1	0.685112786795637	2		425	160	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624242	89624243	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs121913290	NA	P-0045556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	120	148	0	ENST00000371953.3:c.17_18del	p.Lys6ArgfsTer4	p.K6Rfs*4	ENST00000371953	NM_000314.4	6	AAa/a	1/9	0.665919540951927	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.685112786795637	2		148	171	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683996	29683996	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	33	362	0	ENST00000356175.3:c.7694C>A	p.Ser2565Ter	p.S2565*	ENST00000356175	NM_000267.3	2565	tCa/tAa	52/57	1	2	FACETS	0.22	0.179	0.267	0.22	0.179	0.267	SUBCLONAL	1	TRUE	1	0.685112786795637	2		362	437	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601376	28601376	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	80	207	0	ENST00000241453.7:c.2056C>A	p.Pro686Thr	p.P686T	ENST00000241453	NM_004119.2	686	Cca/Aca	17/24	1	2	FACETS	0.753	0.67	0.841	0.753	0.67	0.841	SUBCLONAL	1	TRUE	1	0.685112786795637	2		207	310	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68758694	68758694	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	78	182	0	ENST00000487270.1:c.850G>C	p.Glu284Gln	p.E284Q	ENST00000487270	NM_133509.3	284	Gaa/Caa	8/11	0.521270593540027	3	FACETS	1	0.887	1	0.502	0.443	0.563	CLONAL	1	TRUE	1	0.521270593540027	3		182	376	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350358	89350358	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	206	492	0	ENST00000301030.4:c.2592C>G	p.Asp864Glu	p.D864E	ENST00000301030	NM_001256183.1	864	gaC/gaG	9/13	0.418185161201318	4	FACETS	1	0.978	1	0.566	0.525	0.609	CLONAL	1	TRUE	2	0.521270593540027	4		492	1062	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099931	157099931	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045557-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	100	221	0	ENST00000346085.5:c.868T>G	p.Tyr290Asp	p.Y290D	ENST00000346085	NM_020732.3	290	Tac/Gac	1/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.521270593540027	2		221	357	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0045558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	61	294	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.95	0.823	1	0.95	0.823	1	CLONAL	1	TRUE	1	0.35	2		294	367	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099226	4099226	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	136	589	0	ENST00000262948.5:c.892C>T	p.Pro298Ser	p.P298S	ENST00000262948	NM_030662.3	298	Ccg/Tcg	7/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.35	2		589	645	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715643	30715643	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	100	217	0	ENST00000295754.5:c.1301T>G	p.Met434Arg	p.M434R	ENST00000295754	NM_003242.5	434	aTg/aGg	5/7	0.321811898250099	2	FACETS	0.904	0.817	0.994	0.904	0.817	0.994	CLONAL	2	TRUE	0	0.35	2		217	316	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33290691	33290691	+	5_prime_UTR_variant	5'UTR	SNP	T	T	C	rs559461877	NA	P-0045558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	94	491	0	ENST00000374542.5:c.-105A>G		p.*35*	ENST00000374542	NM_001141970.1	-/740		1/8	1	2	FACETS	0.914	0.814	1	0.914	0.814	1	CLONAL	1	TRUE	1	0.35	2		491	588	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971178	21971182	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCA	CGCCA	-	novel	NA	P-0045558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	72	306	0	ENST00000304494.5:c.176_180del	p.Val59GlyfsTer59	p.V59Gfs*59	ENST00000304494	NM_000077.4	59	gTGGCG/g	2/3	0.321811898250099	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.35	1		306	317	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	96	425	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.814122856351964	2		425	207	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0045565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	425	618	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.814122856351964	2		619	751	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579408	7579430	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGGGCCAGGAGGGGGCTGGTG	CAGGGGCCAGGAGGGGGCTGGTG	-	rs886041861	NA	P-0045565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	293	652	0	ENST00000269305.4:c.257_279del	p.Ala86ValfsTer55	p.A86Vfs*55	ENST00000269305	NM_001126112.2	86	gCACCAGCCCCCTCCTGGCCCCTG/g	4/11	0.787214595139587	1	FACETS	0.659	0.625	0.693	0.659	0.625	0.693	SUBCLONAL	1	TRUE	0	0.814122856351964	1		652	648	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475550	12475550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479145908	NA	P-0045565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	312	455	0	ENST00000287820.6:c.1424C>T	p.Thr475Met	p.T475M	ENST00000287820	NM_015869.4	475	aCg/aTg	7/7	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.814122856351964	2		455	763	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045030	47045030	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0045565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	435	356	0	ENST00000377604.3:c.2355+1G>T		p.X785_splice	ENST00000377604	NM_001204468.1	785			1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.814122856351964	1		356	536	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421900	49421900	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	806	581	0	ENST00000301067.7:c.14407del	p.Val4803TrpfsTer5	p.V4803Wfs*5	ENST00000301067	NM_003482.3	4803	Gtg/tg	46/54	0.810684162818284	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.814122856351964	2		581	981	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024559	16024559	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	56	410	0	ENST00000268712.3:c.1659G>C	p.Lys553Asn	p.K553N	ENST00000268712	NM_006311.3	553	aaG/aaC	16/46	0.581324236227863	1	FACETS	0.18	0.154	0.208	0.18	0.154	0.208	SUBCLONAL	1	TRUE	0	0.814122856351964	1		410	454	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50139898	50139898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	489	693	1	ENST00000246792.3:c.431C>T	p.Ala144Val	p.A144V	ENST00000246792	NM_006270.3	144	gCa/gTa	4/6	1	2	FACETS	0.977	0.937	1	0.977	0.937	1	CLONAL	1	TRUE	1	0.814122856351964	2		694	1229	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127240	22127240	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs371304428	NA	P-0045565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	286	467	0	ENST00000215832.6:c.888C>G	p.Phe296Leu	p.F296L	ENST00000215832	NM_002745.4	296	ttC/ttG	7/9	1	2	FACETS	0.981	0.928	1	0.981	0.928	1	CLONAL	1	TRUE	1	0.814122856351964	2		467	716	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458392	12458396	+	frameshift_variant	Frame_Shift_Del	DEL	CTTGA	CTTGA	-	rs1553650477	NA	P-0045565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	312	536	0	ENST00000287820.6:c.1014_1018del	p.Asp338GlufsTer25	p.D338Efs*25	ENST00000287820	NM_015869.4	337	CTTGAc/c	6/7	1	2	FACETS	0.888	0.841	0.936	0.888	0.841	0.936	CLONAL	1	TRUE	1	0.814122856351964	2		536	863	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182325	38182325	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	48	378	0	ENST00000396334.3:c.761T>C	p.Leu254Pro	p.L254P	ENST00000396334	NM_002468.4	254	cTc/cCc	4/5	1	2	FACETS	0.183	0.154	0.215	0.183	0.154	0.215	SUBCLONAL	1	TRUE	1	0.814122856351964	2		378	644	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808923	1808924	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0045565-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	402	638	0	ENST00000260795.2:c.2356dup	p.Asp786GlyfsTer31	p.D786Gfs*31	ENST00000260795		785	-/G	17/17	1	2	FACETS	0.87	0.829	0.912	0.87	0.829	0.912	CLONAL	1	TRUE	1	0.814122856351964	2		638	1135	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881594	111881594	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs778682749	NA	P-0045566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	80	217	0	ENST00000393256.3:c.272G>T	p.Arg91Leu	p.R91L	ENST00000393256	NM_006538.4	91	cGa/cTa	2/4	1	2	FACETS	0.735	0.645	0.832	0.735	0.645	0.832	SUBCLONAL	1	TRUE	1	0.216032461228106	2		217	1008	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120794704	120794718	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CCCAGCATGCCGATG	CCCAGCATGCCGATG	-	novel	NA	P-0045566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	59	189	0	ENST00000257552.2:c.639_652+1del		p.X213_splice	ENST00000257552	NM_002442.3	213		9/15	1	2	FACETS	0.743	0.638	0.858	0.743	0.638	0.858	SUBCLONAL	1	TRUE	1	0.216032461228106	2		189	735	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	30	278	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.25	2		278	212	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	39	294	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.25	2		294	308	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	42	238	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.985	0.825	1	0.985	0.825	1	CLONAL	1	TRUE	1	0.25	2		238	341	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	73	498	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	0.885	0.774	1	0.885	0.774	1	CLONAL	1	TRUE	1	0.25	2		498	660	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	27	353	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.857	0.685	1	0.857	0.685	1	CLONAL	1	TRUE	1	0.25	2		353	252	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844747	156844747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771342578	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	100	574	1	ENST00000524377.1:c.1301C>T	p.Thr434Met	p.T434M	ENST00000524377	NM_002529.3	434	aCg/aTg	11/17	1	2	FACETS	0.917	0.819	1	0.917	0.819	1	CLONAL	1	TRUE	1	0.25	2		575	872	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979563	7979563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1221632429	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	80	500	0	ENST00000319144.4:c.1462C>T	p.Arg488Cys	p.R488C	ENST00000319144	NM_001139.2	488	Cgt/Tgt	11/15	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.25	2		500	623	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021441	42021442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	44	377	0	ENST00000219905.7:c.3744dup	p.Glu1249ArgfsTer25	p.E1249Rfs*25	ENST00000219905	NM_001164273.1	1246	cga/cgAa	11/24	1	2	FACETS	0.898	0.755	1	0.898	0.755	1	CLONAL	1	TRUE	1	0.25	2		377	392	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417305	139417305	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	59	355	0	ENST00000277541.6:c.739C>T	p.Pro247Ser	p.P247S	ENST00000277541	NM_017617.3	247	Cca/Tca	4/34	1	2	FACETS	0.975	0.84	1	0.975	0.84	1	CLONAL	1	TRUE	1	0.25	2		355	484	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164773	106164773	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765414159	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	57	364	0	ENST00000380013.4:c.3641G>A	p.Arg1214Gln	p.R1214Q	ENST00000380013	NM_001127208.2	1214	cGg/cAg	6/11	1	2	FACETS	0.923	0.793	1	0.923	0.793	1	CLONAL	1	TRUE	1	0.25	2		364	494	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916463	39916463	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	106	315	0	ENST00000378444.4:c.4540C>T	p.Arg1514Ter	p.R1514*	ENST00000378444	NM_001123385.1	1514	Cga/Tga	11/15	1	1	FACETS	0.928	0.838	1	1	0.987	1	CLONAL	2	TRUE	0	0.25	1		315	400	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893412	32893412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748609599	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	20	263	1	ENST00000380152.3:c.266C>T	p.Pro89Leu	p.P89L	ENST00000380152		89	cCg/cTg	3/27	1	2	FACETS	0.672	0.515	0.855	0.672	0.515	0.855	SUBCLONAL	1	TRUE	1	0.25	2		264	238	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	62	491	0	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	0.941	0.814	1	0.941	0.814	1	CLONAL	1	TRUE	1	0.25	2		491	527	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264357	30264357	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	14	102	0	ENST00000322652.5:c.92T>C	p.Val31Ala	p.V31A	ENST00000322652	NM_015355.2	31	gTg/gCg	1/16	1	2	FACETS	0.691	0.502	0.919	0.691	0.502	0.919	SUBCLONAL	1	TRUE	1	0.25	2		102	162	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275291	41275291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750554859	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	43	323	1	ENST00000349496.5:c.1457G>A	p.Arg486His	p.R486H	ENST00000349496	NM_001904.3	486	cGc/cAc	9/15	1	2	FACETS	0.948	0.795	1	0.948	0.795	1	CLONAL	1	TRUE	1	0.25	2		324	363	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124366	2124366	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs549612492	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	88	703	0	ENST00000219476.3:c.2521G>A	p.Val841Ile	p.V841I	ENST00000219476	NM_000548.3	841	Gtc/Atc	22/42	1	2	FACETS	0.863	0.764	0.969	0.863	0.764	0.969	CLONAL	1	TRUE	1	0.25	2		703	816	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231576	5231576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	52	270	0	ENST00000357368.4:c.1900G>A	p.Ala634Thr	p.A634T	ENST00000357368	NM_002850.3	634	Gcc/Acc	14/38	1	2	FACETS	0.891	0.759	1	0.891	0.759	1	CLONAL	1	TRUE	1	0.25	2		270	467	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355059	15355059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1331196729	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	52	667	0	ENST00000263377.2:c.2564C>T	p.Ala855Val	p.A855V	ENST00000263377	NM_058243.2	855	gCa/gTa	13/20	1	2	FACETS	0.443	0.376	0.517	0.443	0.376	0.517	SUBCLONAL	1	TRUE	1	0.25	2		667	939	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485280	8485280	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329600473	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	42	342	0	ENST00000356435.5:c.3100G>A	p.Val1034Met	p.V1034M	ENST00000356435		1034	Gtg/Atg	18/35	1	2	FACETS	0.884	0.74	1	0.884	0.74	1	CLONAL	1	TRUE	1	0.25	2		342	380	SUCCESS
AR	367	MSKCC	GRCh37	X	66766603	66766603	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	68	287	0	ENST00000374690.3:c.1615C>T	p.Arg539Cys	p.R539C	ENST00000374690	NM_000044.3	539	Cgt/Tgt	1/8	1	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.25	1		287	356	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211779	5211779	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs544687640	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	43	477	0	ENST00000357368.4:c.5056C>T	p.Arg1686Trp	p.R1686W	ENST00000357368	NM_002850.3	1686	Cgg/Tgg	33/38	1	2	FACETS	0.582	0.486	0.689	0.582	0.486	0.689	SUBCLONAL	1	TRUE	1	0.25	2		477	591	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281494	15281494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	27	323	0	ENST00000263388.2:c.4879C>T	p.Arg1627Trp	p.R1627W	ENST00000263388	NM_000435.2	1627	Cgg/Tgg	26/33	1	2	FACETS	0.455	0.361	0.562	0.455	0.361	0.562	SUBCLONAL	1	TRUE	1	0.25	2		323	475	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468079	31468079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	77	435	0	ENST00000344624.3:c.2333G>A	p.Arg778His	p.R778H	ENST00000344624		778	cGc/cAc	15/33	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.25	2		435	491	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797198	45797198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559963863	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	106	603	0	ENST00000450313.1:c.1217C>T	p.Ser406Phe	p.S406F	ENST00000450313	NM_012222.2	406	tCc/tTc	13/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.25	2		603	720	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211939	36211939	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519283	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	103	652	2	ENST00000222270.7:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000222270	NM_014727.1	564	Cga/Tga	3/37	1	2	FACETS	0.95	0.85	1	0.95	0.85	1	CLONAL	1	TRUE	1	0.25	2		654	867	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123721	11123721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	94	450	0	ENST00000358026.2:c.2371G>A	p.Ala791Thr	p.A791T	ENST00000358026	NM_001128849.1	791	Gcg/Acg	16/36	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.25	2		450	631	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11227537	11227537	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	83	387	1	ENST00000361445.4:c.4291G>A	p.Gly1431Arg	p.G1431R	ENST00000361445	NM_004958.3	1431	Gga/Aga	29/58	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.25	2		388	603	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678049	58678049	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1391305414	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	24	177	0	ENST00000305921.3:c.274T>C	p.Cys92Arg	p.C92R	ENST00000305921	NM_003620.3	92	Tgc/Cgc	1/6	1	2	FACETS	0.722	0.567	0.899	0.722	0.567	0.899	SUBCLONAL	1	TRUE	1	0.25	2		177	266	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191157	185191157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs903937665	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	66	383	0	ENST00000265026.3:c.2038C>T	p.Arg680Trp	p.R680W	ENST00000265026	NM_004721.4	680	Cgg/Tgg	11/14	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.25	2		383	460	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532613	63532613	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121908568	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	99	635	0	ENST00000307078.5:c.1966C>T	p.Arg656Ter	p.R656*	ENST00000307078	NM_004655.3	656	Cga/Tga	8/11	1	2	FACETS	0.885	0.789	0.987	0.885	0.789	0.987	CLONAL	1	TRUE	1	0.25	2		635	895	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737370	145737370	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs34236392	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	198	671	2	ENST00000428558.2:c.3317G>A	p.Arg1106His	p.R1106H	ENST00000428558	NM_004260.3	1106	cGc/cAc	20/22	0.222844631815013	3	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	1	0.25	3		673	883	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879458	56879458	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	52	396	0	ENST00000519728.1:c.973+2T>C		p.X325_splice	ENST00000519728	NM_002350.3	325			0.222844631815013	3	FACETS	0.713	0.606	0.831	0.357	0.303	0.416	SUBCLONAL	1	TRUE	1	0.25	3		396	656	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190717447	190717447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	35	235	0	ENST00000441310.2:c.766G>A	p.Glu256Lys	p.E256K	ENST00000441310	NM_000534.4	256	Gaa/Aaa	7/13	1	2	FACETS	0.962	0.792	1	0.962	0.792	1	CLONAL	1	TRUE	1	0.25	2		235	291	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671699	30671699	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	84	525	0	ENST00000376406.3:c.5261G>T	p.Arg1754Met	p.R1754M	ENST00000376406	NM_014641.2	1754	aGg/aTg	10/15	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.25	2		525	640	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485736	40485736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776115471	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	102	387	0	ENST00000264657.5:c.1004G>A	p.Arg335Gln	p.R335Q	ENST00000264657	NM_139276.2	335	cGg/cAg	10/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.25	2		387	677	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119706	17119706	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs911287169	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	46	424	0	ENST00000285071.4:c.1288G>A	p.Val430Met	p.V430M	ENST00000285071	NM_144997.5	430	Gtg/Atg	11/14	1	2	FACETS	0.79	0.665	0.927	0.79	0.665	0.927	CLONAL	1	TRUE	1	0.25	2		424	466	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350824	15350824	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148664288	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	65	508	0	ENST00000263377.2:c.3179G>A	p.Arg1060His	p.R1060H	ENST00000263377	NM_058243.2	1060	cGc/cAc	15/20	1	2	FACETS	0.86	0.745	0.983	0.86	0.745	0.983	CLONAL	1	TRUE	1	0.25	2		508	605	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295788	212295788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1412193732	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	38	408	0	ENST00000342788.4:c.2525G>A	p.Arg842Gln	p.R842Q	ENST00000342788	NM_005235.2	842	cGg/cAg	21/28	1	2	FACETS	0.7	0.579	0.836	0.7	0.579	0.836	SUBCLONAL	1	TRUE	1	0.25	2		408	434	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964415	70964415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777306806	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	106	406	0	ENST00000276594.2:c.1613G>A	p.Arg538His	p.R538H	ENST00000276594	NM_024504.3	538	cGt/cAt	8/8	0.222844631815013	3	FACETS	0.878	0.79	0.971	0.878	0.79	0.971	CLONAL	2	TRUE	1	0.25	3		406	543	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376302	118376302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1052748793	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	41	405	0	ENST00000534358.1:c.9695G>A	p.Arg3232Gln	p.R3232Q	ENST00000534358	NM_005933.3	3232	cGa/cAa	27/36	1	2	FACETS	0.765	0.637	0.906	0.765	0.637	0.906	CLONAL	1	TRUE	1	0.25	2		405	429	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172379	108172379	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	30	303	0	ENST00000278616.4:c.5182A>G	p.Lys1728Glu	p.K1728E	ENST00000278616	NM_000051.3	1728	Aaa/Gaa	35/63	1	2	FACETS	0.87	0.703	1	0.87	0.703	1	CLONAL	1	TRUE	1	0.25	2		303	276	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759593	133759593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1476030646	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	82	614	0	ENST00000318560.5:c.1916G>A	p.Arg639Gln	p.R639Q	ENST00000318560	NM_005157.4	639	cGa/cAa	11/11	1	2	FACETS	0.766	0.675	0.865	0.766	0.675	0.865	SUBCLONAL	1	TRUE	1	0.25	2		614	856	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599288	28599288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769937470	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	46	662	0	ENST00000253063.3:c.734C>T	p.Pro245Leu	p.P245L	ENST00000253063	NM_031459.4	245	cCg/cTg	5/10	1	2	FACETS	0.403	0.338	0.475	0.403	0.338	0.475	SUBCLONAL	1	TRUE	1	0.25	2		662	913	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018201	48018202	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1057524912	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	82	515	0	ENST00000234420.5:c.402dup	p.Asp135Ter	p.D135*	ENST00000234420	NM_000179.2	132	-/T	2/10	1	2	FACETS	0.962	0.848	1	0.962	0.848	1	CLONAL	1	TRUE	1	0.25	2		515	682	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11205026	11205026	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	46	393	0	ENST00000361445.4:c.4763G>A	p.Gly1588Glu	p.G1588E	ENST00000361445	NM_004958.3	1588	gGg/gAg	33/58	1	2	FACETS	0.862	0.727	1	0.862	0.727	1	CLONAL	1	TRUE	1	0.25	2		393	427	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885905	23885905	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	37	232	0	ENST00000374561.5:c.13A>C	p.Ser5Arg	p.S5R	ENST00000374561	NM_002167.4	5	Agc/Cgc	1/3	1	2	FACETS	0.851	0.703	1	0.851	0.703	1	CLONAL	1	TRUE	1	0.25	2		232	348	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739328	46739328	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1020176839	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	57	398	0	ENST00000371975.4:c.1519G>A	p.Val507Met	p.V507M	ENST00000371975	NM_003579.3	507	Gtg/Atg	14/18	1	2	FACETS	0.908	0.78	1	0.908	0.78	1	CLONAL	1	TRUE	1	0.25	2		398	502	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65323407	65323407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375956046	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	67	454	0	ENST00000342505.4:c.1390G>A	p.Val464Met	p.V464M	ENST00000342505	NM_002227.2	464	Gtg/Atg	10/25	1	2	FACETS	0.828	0.72	0.946	0.828	0.72	0.946	CLONAL	1	TRUE	1	0.25	2		454	647	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121513	193121513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	26	170	0	ENST00000367435.3:c.911C>T	p.Thr304Met	p.T304M	ENST00000367435	NM_024529.4	304	aCg/aTg	10/17	1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	1	0.25	2		170	193	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456806	32456806	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	33	419	0	ENST00000332351.3:c.86A>C	p.Glu29Ala	p.E29A	ENST00000332351	NM_024426.4	29	gAg/gCg	1/10	1	2	FACETS	0.452	0.367	0.548	0.452	0.367	0.548	SUBCLONAL	1	TRUE	1	0.25	2		419	584	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155133	108155133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	35	368	0	ENST00000278616.4:c.3926C>T	p.Ala1309Val	p.A1309V	ENST00000278616	NM_000051.3	1309	gCa/gTa	26/63	1	2	FACETS	0.956	0.786	1	0.956	0.786	1	CLONAL	1	TRUE	1	0.25	2		368	293	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343390	118343390	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	37	312	0	ENST00000534358.1:c.1516A>G	p.Thr506Ala	p.T506A	ENST00000534358	NM_005933.3	506	Acc/Gcc	3/36	1	2	FACETS	0.884	0.73	1	0.884	0.73	1	CLONAL	1	TRUE	1	0.25	2		312	335	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871760	12871760	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	24	92	0	ENST00000228872.4:c.478del	p.Ser160LeufsTer65	p.S160Lfs*65	ENST00000228872	NM_004064.3	159	gaT/ga	2/3	1	2	FACETS	0.857	0.675	1	0.857	0.675	1	CLONAL	1	TRUE	1	0.25	2		92	224	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432236	49432236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750788651	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	120	718	0	ENST00000301067.7:c.8903C>T	p.Pro2968Leu	p.P2968L	ENST00000301067	NM_003482.3	2968	cCg/cTg	34/54	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.25	2		718	865	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433742	49433742	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	110	786	0	ENST00000301067.7:c.7811G>A	p.Ser2604Asn	p.S2604N	ENST00000301067	NM_003482.3	2604	aGc/aAc	31/54	1	2	FACETS	0.977	0.877	1	0.977	0.877	1	CLONAL	1	TRUE	1	0.25	2		786	901	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858905	57858905	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	61	587	0	ENST00000228682.2:c.401G>A	p.Gly134Glu	p.G134E	ENST00000228682	NM_005269.2	134	gGa/gAa	5/12	1	2	FACETS	0.629	0.541	0.724	0.629	0.541	0.724	SUBCLONAL	1	TRUE	1	0.25	2		587	776	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112461	115112461	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777764537	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	90	469	0	ENST00000257566.3:c.1279C>T	p.Arg427Trp	p.R427W	ENST00000257566	NM_016569.3	427	Cgg/Tgg	7/8	1	2	FACETS	0.972	0.862	1	0.972	0.862	1	CLONAL	1	TRUE	1	0.25	2		469	741	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245434	133245434	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	78	574	0	ENST00000320574.5:c.1886C>G	p.Ala629Gly	p.A629G	ENST00000320574	NM_006231.2	629	gCc/gGc	17/49	1	2	FACETS	0.89	0.782	1	0.89	0.782	1	CLONAL	1	TRUE	1	0.25	2		574	701	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508740	29508740	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	51	355	0	ENST00000356175.3:c.667T>G	p.Trp223Gly	p.W223G	ENST00000356175	NM_000267.3	223	Tgg/Ggg	7/57	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.25	2		355	312	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370322	40370322	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	110	570	0	ENST00000293328.3:c.1016C>A	p.Pro339His	p.P339H	ENST00000293328	NM_012448.3	339	cCt/cAt	9/19	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.25	2		570	756	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55693418	55693418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769598215	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	84	563	1	ENST00000284073.2:c.625G>A	p.Ala209Thr	p.A209T	ENST00000284073	NM_138962.2	209	Gcg/Acg	9/14	1	2	FACETS	0.914	0.807	1	0.914	0.807	1	CLONAL	1	TRUE	1	0.25	2		564	735	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774127	56774127	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	40	366	0	ENST00000337432.4:c.478A>G	p.Thr160Ala	p.T160A	ENST00000337432	NM_058216.2	160	Aca/Gca	3/9	1	2	FACETS	0.842	0.701	0.999	0.842	0.701	0.999	CLONAL	1	TRUE	1	0.25	2		366	380	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395646	45395646	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	21	310	0	ENST00000262160.6:c.488A>G	p.Asn163Ser	p.N163S	ENST00000262160	NM_005901.5	163	aAc/aGc	4/11	1	2	FACETS	0.491	0.378	0.624	0.491	0.378	0.624	SUBCLONAL	1	TRUE	1	0.25	2		310	342	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223184	36223184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201325543	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	135	816	0	ENST00000222270.7:c.5734C>T	p.Arg1912Cys	p.R1912C	ENST00000222270	NM_014727.1	1912	Cgt/Tgt	28/37	1	2	FACETS	0.92	0.834	1	0.92	0.834	1	CLONAL	1	TRUE	1	0.25	2		816	1174	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793391	242793391	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	73	677	0	ENST00000334409.5:c.686A>G	p.Gln229Arg	p.Q229R	ENST00000334409	NM_005018.2	229	cAg/cGg	5/5	1	2	FACETS	0.75	0.655	0.852	0.75	0.655	0.852	SUBCLONAL	1	TRUE	1	0.25	2		677	779	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686326	30686326	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	59	253	0	ENST00000295754.5:c.182G>A	p.Cys61Tyr	p.C61Y	ENST00000295754	NM_003242.5	61	tGt/tAt	2/7	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.25	2		253	386	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026192	71026192	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	35	237	0	ENST00000318789.4:c.1430C>T	p.Ala477Val	p.A477V	ENST00000318789	NM_032682.5	477	gCc/gTc	17/21	1	2	FACETS	0.9	0.74	1	0.9	0.74	1	CLONAL	1	TRUE	1	0.25	2		237	311	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519435	176519435	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	84	633	0	ENST00000292408.4:c.841A>G	p.Ile281Val	p.I281V	ENST00000292408	NM_213647.1	281	Atc/Gtc	7/18	1	2	FACETS	0.84	0.741	0.946	0.84	0.741	0.946	CLONAL	1	TRUE	1	0.25	2		633	800	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001349	150001349	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	30	438	0	ENST00000253339.5:c.2255del	p.Ala752ValfsTer14	p.A752Vfs*14	ENST00000253339		752	gCt/gt	4/7	1	2	FACETS	0.769	0.621	0.936	0.769	0.621	0.936	CLONAL	1	TRUE	1	0.25	2		438	312	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884915	151884915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	17	185	0	ENST00000262189.6:c.4678C>T	p.Pro1560Ser	p.P1560S	ENST00000262189	NM_170606.2	1560	Cct/Tct	32/59	1	2	FACETS	0.723	0.542	0.937	0.723	0.542	0.937	CLONAL	1	TRUE	1	0.25	2		185	188	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372218	55372218	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	45	161	0	ENST00000297316.4:c.908C>A	p.Pro303His	p.P303H	ENST00000297316	NM_022454.3	303	cCc/cAc	2/2	0.222844631815013	3	FACETS	1	0.942	1	0.633	0.534	0.741	CLONAL	1	TRUE	1	0.25	3		161	320	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089704	5089704	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	13	190	0	ENST00000381652.3:c.2602T>C	p.Tyr868His	p.Y868H	ENST00000381652	NM_004972.3	868	Tat/Cat	20/25	1	2	FACETS	0.414	0.295	0.56	0.414	0.295	0.56	SUBCLONAL	1	TRUE	1	0.25	2		190	251	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15822284	15822284	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045569-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	13	141	0	ENST00000307771.7:c.363G>T	p.Glu121Asp	p.E121D	ENST00000307771	NM_005089.3	121	gaG/gaT	5/11	1	1	FACETS	0.523	0.374	0.704	0.523	0.374	0.704	SUBCLONAL	1	TRUE	0	0.25	1		141	174	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0045571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	49	278	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.743	0.63	0.867	0.743	0.63	0.867	SUBCLONAL	1	TRUE	1	0.28	2		278	471	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921566	178921566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793349	NA	P-0045571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	36	276	0	ENST00000263967.3:c.1048G>A	p.Asp350Asn	p.D350N	ENST00000263967	NM_006218.2	350	Gac/Aac	5/21	1	2	FACETS	0.759	0.625	0.907	0.759	0.625	0.907	CLONAL	1	TRUE	1	0.28	2		276	339	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152571	56152572	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0045571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	41	233	0	ENST00000399503.3:c.629dup	p.Val211CysfsTer9	p.V211Cfs*9	ENST00000399503	NM_005921.1	209	-/C	2/20	0.3	4	FACETS	0.684	0.569	0.812	0.228	0.189	0.271	SUBCLONAL	1	TRUE	1	0.28	4		233	548	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591966	48591966	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	96	310	0	ENST00000342988.3:c.1129G>A	p.Glu377Lys	p.E377K	ENST00000342988	NM_005359.5	377	Gag/Aag	9/12	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.28	2		310	520	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195658	102195658	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	115	338	0	ENST00000263464.3:c.418A>T	p.Asn140Tyr	p.N140Y	ENST00000263464	NM_001165.4	140	Aac/Tac	2/9	0.240788064291078	3	FACETS	1	0.984	1	0.74	0.668	0.816	CLONAL	1	TRUE	1	0.28	3		338	633	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178068	56178069	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045571-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	186	323	0	ENST00000399503.3:c.3042dup	p.Pro1015ThrfsTer21	p.P1015Tfs*21	ENST00000399503	NM_005921.1	1014	ata/atAa	14/20	0.3	4	FACETS	0.991	0.921	1	0.991	0.921	1	CLONAL	3	TRUE	1	0.28	4		323	572	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0045573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	135	403	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.834789761126429	2		403	279	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912075	56912075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	348	491	0	ENST00000519728.1:c.1303G>A	p.Glu435Lys	p.E435K	ENST00000519728	NM_002350.3	435	Gaa/Aaa	12/13	0.834789761126429	4	FACETS	0.999	0.944	1	0.333	0.314	0.352	CLONAL	1	FALSE	1	0.834789761126429	4		491	1531	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521487	8521487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758577045	NA	P-0045573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	259	437	0	ENST00000356435.5:c.751G>A	p.Gly251Arg	p.G251R	ENST00000356435		251	Gga/Aga	9/35	0.355531962057379	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.834789761126429	0		437	578	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858236	59858236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	216	348	0	ENST00000259008.2:c.1759C>T	p.His587Tyr	p.H587Y	ENST00000259008	NM_032043.2	587	Cat/Tat	12/20	1	2	FACETS	0.939	0.88	0.999	0.939	0.88	0.999	CLONAL	1	FALSE	1	0.834789761126429	2		348	551	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0045573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	214	288	1	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.262193192357772	4	FACETS	1	0.991	1	0.621	0.587	0.654	INDETERMINATE	2	FALSE	0	0.834789761126429	4		289	379	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526232	189526232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267599729	NA	P-0045573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	354	467	0	ENST00000264731.3:c.496C>T	p.Pro166Ser	p.P166S	ENST00000264731	NM_003722.4	166	Ccc/Tcc	4/14	1	2	FACETS	0.991	0.943	1	0.991	0.943	1	CLONAL	1	FALSE	1	0.834789761126429	2		467	856	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518175	8518175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1354824749	NA	P-0045573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	180	338	0	ENST00000356435.5:c.1216G>A	p.Glu406Lys	p.E406K	ENST00000356435		406	Gaa/Aaa	10/35	0.355531962057379	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.834789761126429	0		338	381	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749455	41749455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	235	334	0	ENST00000226382.2:c.340G>A	p.Glu114Lys	p.E114K	ENST00000226382	NM_003924.3	114	Gaa/Aaa	2/3	1	2	FACETS	0.937	0.881	0.994	0.937	0.881	0.994	CLONAL	1	FALSE	1	0.834789761126429	2		334	601	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517867	187517867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	219	296	0	ENST00000441802.2:c.12827C>T	p.Ser4276Phe	p.S4276F	ENST00000441802	NM_005245.3	4276	tCt/tTt	25/27	1	2	FACETS	0.973	0.914	1	0.973	0.914	1	CLONAL	1	FALSE	1	0.834789761126429	2		296	539	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002814	69002814	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1213028913	NA	P-0045573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	120	193	0	ENST00000288368.4:c.2114G>A	p.Gly705Glu	p.G705E	ENST00000288368	NM_024870.2	705	gGa/gAa	20/40	0.834789761126429	4	FACETS	1	0.958	1	0.365	0.331	0.4	CLONAL	1	FALSE	1	0.834789761126429	4		193	482	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630033	117630033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780713592	NA	P-0045573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	173	274	0	ENST00000368508.3:c.6493C>T	p.His2165Tyr	p.H2165Y	ENST00000368508	NM_002944.2	2165	Cat/Tat	41/43	0.834789761126429	1	FACETS	0.951	0.901	0.998	0.951	0.901	0.998	CLONAL	1	FALSE	0	0.834789761126429	1		274	254	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923386	9923386	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555492769	NA	P-0045573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	335	413	0	ENST00000330684.3:c.1901G>A	p.Trp634Ter	p.W634*	ENST00000330684	NM_001134407.1	634	tGg/tAg	9/13	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.834789761126429	2		413	778	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458414	120458414	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	276	436	0	ENST00000256646.2:c.6931C>T	p.Pro2311Ser	p.P2311S	ENST00000256646	NM_024408.3	2311	Cct/Tct	34/34	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.834789761126429	2		436	658	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692938	89692938	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs863224666	NA	P-0045573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	213	443	0	ENST00000371953.3:c.422A>C	p.His141Pro	p.H141P	ENST00000371953	NM_000314.4	141	cAt/cCt	5/9	0.834789761126429	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	0	0.834789761126429	1		443	293	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025635	1025635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	276	474	0	ENST00000358495.3:c.740C>T	p.Ser247Phe	p.S247F	ENST00000358495	NM_134424.2	247	tCc/tTc	9/12	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	FALSE	NA	0.834789761126429	2		474	599	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243549	46243549	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	168	208	0	ENST00000334344.6:c.1903del	p.Ser635HisfsTer12	p.S635Hfs*12	ENST00000334344	NM_152641.2	634	ccT/cc	14/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.834789761126429	2		208	362	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244124	46244124	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	227	364	0	ENST00000334344.6:c.2218C>T	p.Gln740Ter	p.Q740*	ENST00000334344	NM_152641.2	740	Cag/Tag	15/21	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	1	0.834789761126429	2		364	544	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442470	49442471	+	missense_variant	Missense_Mutation	DNP	GA	GA	AC	novel	NA	P-0045573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	290	537	0	ENST00000301067.7:c.4102_4103delinsGT	p.Ser1368Val	p.S1368V	ENST00000301067	NM_003482.3	1368	TCc/GTc	13/54	1	2	FACETS	0.961	0.909	1	0.961	0.909	1	CLONAL	1	FALSE	1	0.834789761126429	2		537	723	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934944	9934944	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139033056	NA	P-0045573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	148	254	0	ENST00000330684.3:c.1346G>A	p.Gly449Glu	p.G449E	ENST00000330684	NM_001134407.1	449	gGg/gAg	6/13	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	1	0.834789761126429	2		254	353	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81939050	81939050	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	242	414	0	ENST00000359376.3:c.1405G>A	p.Glu469Lys	p.E469K	ENST00000359376	NM_002661.3	469	Gag/Aag	15/33	1	2	FACETS	0.952	0.896	1	0.952	0.896	1	CLONAL	1	FALSE	1	0.834789761126429	2		414	609	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211876	36211876	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	476	655	0	ENST00000222270.7:c.1630del	p.Arg544GlyfsTer61	p.R544Gfs*61	ENST00000222270	NM_014727.1	543	Ccc/cc	3/37	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.834789761126429	2		655	1086	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40864868	40864868	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0045573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	154	287	0	ENST00000373198.4:c.2399+1G>T		p.X800_splice	ENST00000373198	NM_133170.3	800			1	2	FACETS	0.929	0.861	0.999	0.929	0.861	0.999	CLONAL	1	FALSE	1	0.834789761126429	2		287	397	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157924	106157925	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0045573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	137	230	0	ENST00000380013.4:c.2825_2826delinsTT	p.Pro942Leu	p.P942L	ENST00000380013	NM_001127208.2	942	cCC/cTT	3/11	1	2	FACETS	0.963	0.888	1	0.963	0.888	1	CLONAL	1	FALSE	1	0.834789761126429	2		230	341	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944608	38944608	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	153	321	0	ENST00000357387.3:c.4853G>A	p.Arg1618Lys	p.R1618K	ENST00000357387	NM_152756.3	1618	aGa/aAa	36/38	1	2	FACETS	0.885	0.819	0.953	0.885	0.819	0.953	CLONAL	1	FALSE	1	0.834789761126429	2		321	414	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681113	117681113	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	221	377	0	ENST00000368508.3:c.3507G>A	p.Met1169Ile	p.M1169I	ENST00000368508	NM_002944.2	1169	atG/atA	23/43	0.834789761126429	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	0	0.834789761126429	1		377	298	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528634	157528634	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	329	499	0	ENST00000346085.5:c.6359G>A	p.Gly2120Glu	p.G2120E	ENST00000346085	NM_020732.3	2120	gGg/gAg	20/20	0.834789761126429	1	FACETS	0.969	0.933	1	0.969	0.933	1	CLONAL	1	FALSE	0	0.834789761126429	1		499	474	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367299	50367299	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	237	314	0	ENST00000331340.3:c.106G>A	p.Asp36Asn	p.D36N	ENST00000331340	NM_006060.4	36	Gac/Aac	3/8	0.262193192357772	4	FACETS	1	0.991	1	0.345	0.322	0.367	INDETERMINATE	1	FALSE	0	0.834789761126429	4		314	756	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504354	8504354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	214	383	0	ENST00000356435.5:c.1729C>T	p.Pro577Ser	p.P577S	ENST00000356435		577	Cca/Tca	12/35	0.355531962057379	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.834789761126429	0		383	481	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27209163	27209163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	205	375	1	ENST00000380036.4:c.2620G>A	p.Glu874Lys	p.E874K	ENST00000380036	NM_000459.3	874	Gaa/Aaa	16/23	0.355531962057379	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.834789761126429	0		376	489	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182878	123182878	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	124	180	0	ENST00000218089.9:c.843A>G	p.Ile281Met	p.I281M	ENST00000218089	NM_001042749.1	281	atA/atG	10/35	0.37930869999714	1	FACETS	0.591	0.543	0.639	0.591	0.543	0.639	INDETERMINATE	1	FALSE	0	0.834789761126429	1		180	293	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211877	36211879	+	frameshift_variant	Frame_Shift_Del	DEL	CCC	CCC	TT	novel	NA	P-0045573-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	482	663	1	ENST00000222270.7:c.1628_1630delinsTT	p.Pro543LeufsTer62	p.P543Lfs*62	ENST00000222270	NM_014727.1	543	cCCCgg/cTTgg	3/37	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.834789761126429	2		664	1091	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	55	425	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.662547715964953	2		425	153	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0045574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	202	380	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	0.959	0.893	1	0.959	0.893	1	CLONAL	1	TRUE	1	0.662547715964953	2		380	636	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876305	35876305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778728560	NA	P-0045574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	113	456	0	ENST00000303115.3:c.1097C>T	p.Ser366Phe	p.S366F	ENST00000303115	NM_002185.3	366	tCc/tTc	8/8	1	2	FACETS	0.891	0.809	0.975	0.891	0.809	0.975	CLONAL	1	TRUE	1	0.662547715964953	2		456	383	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913355	NA	P-0045574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	250	285	0	ENST00000288602.6:c.1406G>A	p.Gly469Glu	p.G469E	ENST00000288602	NM_004333.4	469	gGa/gAa	11/18	0.567594135923594	3	FACETS	0.957	0.905	1	0.957	0.905	1	CLONAL	2	TRUE	1	0.662547715964953	3		285	525	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729784	41729784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866082326	NA	P-0045574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	192	371	0	ENST00000242208.4:c.745G>A	p.Glu249Lys	p.E249K	ENST00000242208	NM_002192.2	249	Gag/Aag	3/3	0.567594135923594	3	FACETS	0.899	0.842	0.957	0.899	0.842	0.957	CLONAL	2	TRUE	1	0.662547715964953	3		371	429	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047200	180047200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	170	678	0	ENST00000261937.6:c.2515G>A	p.Glu839Lys	p.E839K	ENST00000261937	NM_182925.4	839	Gaa/Aaa	17/30	1	2	FACETS	0.985	0.912	1	0.985	0.912	1	CLONAL	1	TRUE	1	0.662547715964953	2		678	521	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922655	56922655	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	126	418	0	ENST00000519728.1:c.1525C>T	p.Gln509Ter	p.Q509*	ENST00000519728	NM_002350.3	509	Cag/Tag	13/13	1	2	FACETS	0.808	0.736	0.882	0.808	0.736	0.882	CLONAL	1	TRUE	1	0.662547715964953	2		418	471	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372765	81372765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	76	252	0	ENST00000222390.5:c.769G>A	p.Asp257Asn	p.D257N	ENST00000222390	NM_000601.4	257	Gat/Aat	7/18	0.567594135923594	3	FACETS	0.893	0.789	1	0.447	0.394	0.502	CLONAL	1	TRUE	1	0.662547715964953	3		252	342	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500885	8500885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1193645875	NA	P-0045574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	148	410	0	ENST00000356435.5:c.1997C>T	p.Pro666Leu	p.P666L	ENST00000356435		666	cCt/cTt	13/35	0.662547715964953	1	FACETS	0.868	0.805	0.933	0.868	0.805	0.933	CLONAL	1	TRUE	0	0.662547715964953	1		410	344	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306763	41306763	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	112	385	0	ENST00000373198.4:c.896C>T	p.Ala299Val	p.A299V	ENST00000373198	NM_133170.3	299	gCt/gTt	7/32	0.662455612706534	1	FACETS	0.613	0.556	0.671	0.613	0.556	0.671	SUBCLONAL	1	TRUE	0	0.662547715964953	1		385	369	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332264	70332264	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	119	274	0	ENST00000373644.4:c.169G>A	p.Asp57Asn	p.D57N	ENST00000373644	NM_030625.2	57	Gat/Aat	2/12	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.662547715964953	2		274	342	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130265	2130265	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	204	730	1	ENST00000219476.3:c.3497C>A	p.Pro1166His	p.P1166H	ENST00000219476	NM_000548.3	1166	cCt/cAt	30/42	1	2	FACETS	0.9	0.838	0.964	0.9	0.838	0.964	CLONAL	1	TRUE	1	0.662547715964953	2		731	684	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965968	25965968	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754260178	NA	P-0045574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	228	585	0	ENST00000435504.4:c.3238C>T	p.Leu1080Phe	p.L1080F	ENST00000435504		1080	Ctc/Ttc	13/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.662547715964953	2		585	653	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537906	212537906	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777951183	NA	P-0045574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	151	362	0	ENST00000342788.4:c.1699C>T	p.Leu567Phe	p.L567F	ENST00000342788	NM_005235.2	567	Ctc/Ttc	14/28	1	2	FACETS	0.976	0.9	1	0.976	0.9	1	CLONAL	1	TRUE	1	0.662547715964953	2		362	467	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967210	93967210	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1208917339	NA	P-0045574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	122	298	0	ENST00000369303.4:c.2142G>A	p.Met714Ile	p.M714I	ENST00000369303	NM_004440.3	714	atG/atA	12/17	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.662547715964953	2		298	354	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663708	117663708	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0045574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	83	223	0	ENST00000368508.3:c.4525-1G>A		p.X1509_splice	ENST00000368508	NM_002944.2	1509			1	2	FACETS	0.931	0.833	1	0.931	0.833	1	CLONAL	1	TRUE	1	0.662547715964953	2		223	269	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933821	39933821	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	191	690	0	ENST00000378444.4:c.778T>G	p.Ser260Ala	p.S260A	ENST00000378444	NM_001123385.1	260	Tcc/Gcc	4/15	1	2	FACETS	0.882	0.819	0.946	0.882	0.819	0.946	CLONAL	1	TRUE	1	0.662547715964953	2		690	654	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858068	152858068	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045574-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	128	512	0	ENST00000406277.2:c.547del	p.Arg183AlafsTer161	p.R183Afs*161	ENST00000406277	NM_152274.4	183	Cgc/gc	6/7	1	2	FACETS	0.878	0.802	0.957	0.878	0.802	0.957	CLONAL	1	TRUE	1	0.662547715964953	2		512	440	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0045575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	72	333	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.231123682071197	2		333	473	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0045575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	27	397	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.231123682071197	3	FACETS	0.612	0.486	0.756	0.306	0.243	0.378	SUBCLONAL	1	TRUE	1	0.231123682071197	3		397	426	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366808	40366808	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	31	328	2	ENST00000397332.2:c.389C>A	p.Ser130Ter	p.S130*	ENST00000397332	NM_001033082.2	130	tCg/tAg	2/3	1	2	FACETS	0.519	0.419	0.633	0.519	0.419	0.633	SUBCLONAL	1	TRUE	1	0.231123682071197	2		330	517	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588896	69588896	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0045575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	66	369	0	ENST00000168712.1:c.341-1G>T		p.X114_splice	ENST00000168712	NM_002007.2	114			1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.231123682071197	2		369	485	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592649	28592649	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	64	333	0	ENST00000241453.7:c.2496G>T	p.Leu832Phe	p.L832F	ENST00000241453	NM_004119.2	832	ttG/ttT	20/24	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.231123682071197	2		333	537	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107971	30107971	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779749535	NA	P-0045575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	90	379	0	ENST00000331968.5:c.836C>A	p.Thr279Asn	p.T279N	ENST00000331968	NM_002742.2	279	aCc/aAc	5/18	0.231123682071197	3	FACETS	1	0.968	1	0.63	0.559	0.706	CLONAL	1	TRUE	1	0.231123682071197	3		379	689	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221227	5221227	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs771119355	NA	P-0045575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	167	467	0	ENST00000357368.4:c.3239G>T	p.Arg1080Leu	p.R1080L	ENST00000357368	NM_002850.3	1080	cGt/cTt	20/38	0.231123682071197	3	FACETS	0.976	0.898	1	0.976	0.898	1	CLONAL	2	TRUE	1	0.231123682071197	3		467	826	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905045	50905045	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs750260438	NA	P-0045575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	34	320	0	ENST00000440232.2:c.327G>T	p.Gln109His	p.Q109H	ENST00000440232	NM_002691.3	109	caG/caT	4/27	1	2	FACETS	0.61	0.498	0.737	0.61	0.498	0.737	SUBCLONAL	1	TRUE	1	0.231123682071197	2		320	482	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560843	9560843	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	31	331	0	ENST00000353224.5:c.939C>A	p.Tyr313Ter	p.Y313*	ENST00000353224	NM_177990.2	313	taC/taA	4/10	1	2	FACETS	0.541	0.437	0.659	0.541	0.437	0.659	SUBCLONAL	1	TRUE	1	0.231123682071197	2		331	496	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928631	49928631	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1375529472	NA	P-0045575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	59	458	0	ENST00000296474.3:c.3643A>G	p.Met1215Val	p.M1215V	ENST00000296474	NM_002447.2	1215	Atg/Gtg	17/20	0.189015143251461	2	FACETS	0.754	0.648	0.87	0.377	0.324	0.435	SUBCLONAL	1	TRUE	0	0.231123682071197	2		458	677	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673726	176673726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	23	275	0	ENST00000439151.2:c.4426C>T	p.His1476Tyr	p.H1476Y	ENST00000439151	NM_022455.4	1476	Cat/Tat	10/23	1	2	FACETS	0.478	0.372	0.602	0.478	0.372	0.602	SUBCLONAL	1	TRUE	1	0.231123682071197	2		275	416	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622151	117622151	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	39	211	0	ENST00000368508.3:c.6719A>T	p.Asn2240Ile	p.N2240I	ENST00000368508	NM_002944.2	2240	aAt/aTt	42/43	1	2	FACETS	1	0.84	1	1	0.84	1	CLONAL	1	TRUE	1	0.231123682071197	2		211	334	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935564	13935564	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	37	296	0	ENST00000405192.2:c.1292A>G	p.Asp431Gly	p.D431G	ENST00000405192	NM_001163147.1	431	gAt/gGt	12/12	0.104189782777463	3	FACETS	0.717	0.591	0.859	0.359	0.295	0.43	INDETERMINATE	1	TRUE	1	0.231123682071197	3		296	498	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508604	106508604	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	56	271	0	ENST00000359195.3:c.598C>A	p.Pro200Thr	p.P200T	ENST00000359195	NM_002649.2	200	Ccg/Acg	2/11	0.104189782777463	3	FACETS	1	0.957	1	0.659	0.566	0.76	INDETERMINATE	1	TRUE	1	0.231123682071197	3		271	410	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47004876	47004876	+	5_prime_UTR_variant	5'UTR	SNP	G	G	C	novel	NA	P-0045575-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	107	470	0	ENST00000377604.3:c.-134G>C		p.*45*	ENST00000377604	NM_001204468.1	-/852		1/24	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.231123682071197	2		470	828	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0045576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	502	545	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.336526086207656	5	FACETS	0.934	0.906	0.961			1	CLONAL	5	TRUE	NA	0.553479039183032	5		545	711	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954105	48954336	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAAAAAAAAAAAAAATTCAATGCTGACACAAATAAGGTTTCAATTAAACAACTTCTTTTTTTTTTTTTAAATTATCTGTTTCAGGAAGAAGAACGATTATCCATTCAAAATTTTAGGTAAATTTTTTACTTTTAGTAAAAAATTTTTTTCTTTTTATAGAAGTAAGTATTTTATAATCTTTTTTTTTTTCCTTTAGCAAACTTCTGAATGACAACATTTTTCATATGTCTTT	AAAAAAAAAAAAAAATTCAATGCTGACACAAATAAGGTTTCAATTAAACAACTTCTTTTTTTTTTTTTAAATTATCTGTTTCAGGAAGAAGAACGATTATCCATTCAAAATTTTAGGTAAATTTTTTACTTTTAGTAAAAAATTTTTTTCTTTTTATAGAAGTAAGTATTTTATAATCTTTTTTTTTTTCCTTTAGCAAACTTCTGAATGACAACATTTTTCATATGTCTTT	-	novel	NA	P-0045576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	35	43	0	ENST00000267163.4:c.1390-83_1458del		p.X464_splice	ENST00000267163	NM_000321.2	464		15-16/27	0.415234895866141	4	FACETS	0.367	0.3	0.443	0.184	0.15	0.222	SUBCLONAL	1	TRUE	2	0.553479039183032	4		43	535	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013744	12013744	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0045576-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	121	244	0	ENST00000353533.5:c.685+1G>A		p.X229_splice	ENST00000353533	NM_003010.3	229			0.262398548062766	2	FACETS	0.922	0.853	0.992	0.922	0.853	0.992	INDETERMINATE	2	TRUE	0	0.553479039183032	2		244	237	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584560	48584560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	182	279	1	ENST00000342988.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000342988	NM_005359.5	245	Cag/Tag	6/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.675462802412285	2		280	479	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434976	110434976	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	180	477	0	ENST00000375856.3:c.3425G>A	p.Gly1142Glu	p.G1142E	ENST00000375856	NM_003749.2	1142	gGg/gAg	1/2	0.212505517807008	4	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.675462802412285	4		477	769	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436869	29436869	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	172	458	0	ENST00000389048.3:c.3724G>A	p.Glu1242Lys	p.E1242K	ENST00000389048	NM_004304.4	1242	Gaa/Aaa	24/29	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.675462802412285	2		458	485	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005652	42005652	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	98	232	0	ENST00000219905.7:c.3388G>T	p.Glu1130Ter	p.E1130*	ENST00000219905	NM_001164273.1	1130	Gaa/Taa	9/24	1	2	FACETS	0.885	0.798	0.975	0.885	0.798	0.975	CLONAL	1	TRUE	1	0.675462802412285	2		232	328	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710578	117710578	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142303126	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	80	160	0	ENST00000368508.3:c.1694C>T	p.Ser565Leu	p.S565L	ENST00000368508	NM_002944.2	565	tCg/tTg	12/43	0.150395974896074	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.675462802412285	0		160	203	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164949	47164949	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	19	153	0	ENST00000409792.3:c.1177C>T	p.Arg393Ter	p.R393*	ENST00000409792	NM_014159.6	393	Cga/Tga	3/21	1	2	FACETS	0.191	0.144	0.245	0.191	0.144	0.245	SUBCLONAL	1	TRUE	1	0.675462802412285	2		153	295	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191141	2191141	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	258	605	0	ENST00000398665.3:c.395C>T	p.Ser132Phe	p.S132F	ENST00000398665	NM_032482.2	132	tCc/tTc	5/28	1	2	FACETS	0.976	0.917	1	0.976	0.917	1	CLONAL	1	TRUE	1	0.675462802412285	2		605	783	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70005680	70005680	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	117	247	0	ENST00000394351.3:c.709C>T	p.Pro237Ser	p.P237S	ENST00000394351	NM_000248.3	237	Cca/Tca	7/9	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.675462802412285	2		247	334	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352342	143352342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	219	353	0	ENST00000262992.4:c.71C>T	p.Pro24Leu	p.P24L	ENST00000262992	NM_001101669.1	24	cCc/cTc	2/24	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.675462802412285	2		353	614	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683963	117683963	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761293495	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	161	304	0	ENST00000368508.3:c.3184G>A	p.Glu1062Lys	p.E1062K	ENST00000368508	NM_002944.2	1062	Gaa/Aaa	21/43	0.150395974896074	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.675462802412285	0		304	420	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524124	18524124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1161481962	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	117	216	0	ENST00000266497.5:c.1636C>T	p.Pro546Ser	p.P546S	ENST00000266497		546	Ccc/Tcc	11/31	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.675462802412285	2		216	317	SUCCESS
APC	324	MSKCC	GRCh37	5	112178282	112178282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	119	268	0	ENST00000257430.4:c.6991C>T	p.Pro2331Ser	p.P2331S	ENST00000257430	NM_000038.5	2331	Cct/Tct	16/16	1	2	FACETS	0.963	0.878	1	0.963	0.878	1	CLONAL	1	TRUE	1	0.675462802412285	2		268	366	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665063	29665063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	214	307	0	ENST00000356175.3:c.6662C>T	p.Pro2221Leu	p.P2221L	ENST00000356175	NM_000267.3	2221	cCa/cTa	44/57	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.675462802412285	2		307	587	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814756	139814756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376884527	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	218	609	0	ENST00000247668.2:c.749C>T	p.Ser250Leu	p.S250L	ENST00000247668	NM_021138.3	250	tCg/tTg	8/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.675462802412285	2		609	631	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46270974	46270974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	182	358	0	ENST00000371998.3:c.3098C>T	p.Ser1033Phe	p.S1033F	ENST00000371998		1033	tCc/tTc	17/23	0.675462802412285	3	FACETS	1	0.943	1	0.511	0.473	0.551	CLONAL	1	TRUE	1	0.675462802412285	3		358	705	SUCCESS
APC	324	MSKCC	GRCh37	5	112178712	112178712	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	137	268	0	ENST00000257430.4:c.7421C>T	p.Pro2474Leu	p.P2474L	ENST00000257430	NM_000038.5	2474	cCc/cTc	16/16	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.675462802412285	2		268	401	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442814	187442814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	168	402	0	ENST00000232014.4:c.1892C>T	p.Pro631Leu	p.P631L	ENST00000232014	NM_001130845.1	631	cCc/cTc	9/10	1	2	FACETS	0.993	0.92	1	0.993	0.92	1	CLONAL	1	TRUE	1	0.675462802412285	2		402	501	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570805	226570805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	205	376	0	ENST00000366794.5:c.1091C>T	p.Ser364Phe	p.S364F	ENST00000366794	NM_001618.3	364	tCc/tTc	8/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.675462802412285	2		376	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577499	7577499	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs786203396	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	272	439	0	ENST00000269305.4:c.782G>C	p.Ser261Thr	p.S261T	ENST00000269305	NM_001126112.2	261	aGt/aCt	7/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.675462802412285	2		439	733	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199937	108199937	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	75	112	0	ENST00000278616.4:c.7279C>T	p.Leu2427Phe	p.L2427F	ENST00000278616	NM_000051.3	2427	Ctt/Ttt	49/63	0.656858797096738	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.675462802412285	1		112	145	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76931730	76931730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	161	113	0	ENST00000373344.5:c.3800C>T	p.Pro1267Leu	p.P1267L	ENST00000373344	NM_000489.3	1267	cCt/cTt	10/35	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.675462802412285	1		113	227	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849795	156849795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1302050750	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	144	310	0	ENST00000524377.1:c.2051G>A	p.Gly684Glu	p.G684E	ENST00000524377	NM_002529.3	684	gGa/gAa	16/17	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.675462802412285	2		310	385	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597802	43597802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	183	561	0	ENST00000355710.3:c.350C>T	p.Pro117Leu	p.P117L	ENST00000355710	NM_020975.4	117	cCc/cTc	3/20	0.505234568810279	1	FACETS	0.693	0.644	0.742	0.693	0.644	0.742	SUBCLONAL	1	TRUE	0	0.675462802412285	1		561	518	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925652	114925652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1408225958	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	140	467	0	ENST00000543371.1:c.1730C>T	p.Thr577Ile	p.T577I	ENST00000543371	NM_001198531.1	577	aCt/aTt	14/14	1	2	FACETS	0.768	0.703	0.835	0.768	0.703	0.835	SUBCLONAL	1	TRUE	1	0.675462802412285	2		467	540	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77069966	77069966	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	145	335	0	ENST00000356341.3:c.574C>T	p.Pro192Ser	p.P192S	ENST00000356341	NM_002576.4	192	Cca/Tca	6/15	1	2	FACETS	0.71	0.65	0.772	0.71	0.65	0.772	SUBCLONAL	1	TRUE	1	0.675462802412285	2		335	605	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420280	49420280	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs919085262	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	197	541	0	ENST00000301067.7:c.15469A>G	p.Ile5157Val	p.I5157V	ENST00000301067	NM_003482.3	5157	Att/Gtt	48/54	1	2	FACETS	0.867	0.806	0.929	0.867	0.806	0.929	CLONAL	1	TRUE	1	0.675462802412285	2		541	673	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434924	49434925	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	201	518	1	ENST00000301067.7:c.6628_6629delinsTT	p.Pro2210Leu	p.P2210L	ENST00000301067	NM_003482.3	2210	CCg/TTg	31/54	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.675462802412285	2		519	529	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69229711	69229719	+	inframe_deletion	In_Frame_Del	DEL	GAAGATTAT	GAAGATTAT	-	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	162	204	0	ENST00000462284.1:c.787_795del	p.Glu263_Tyr265del	p.E263_Y265del	ENST00000462284	NM_002392.5	263	GAAGATTAT/-	9/11	1	2	FACETS	0.995	0.921	1	0.995	0.921	1	CLONAL	1	TRUE	1	0.675462802412285	2		204	482	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592609	28592609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	98	255	0	ENST00000241453.7:c.2536G>A	p.Gly846Ser	p.G846S	ENST00000241453	NM_004119.2	846	Ggc/Agc	20/24	0.675462802412285	1	FACETS	0.886	0.808	0.964	0.886	0.808	0.964	CLONAL	1	TRUE	0	0.675462802412285	1		255	217	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936956	48936965	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGTTATAC	GCTGTTATAC	-	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	112	170	0	ENST00000267163.4:c.724_733del	p.Ala242ProfsTer19	p.A242Pfs*19	ENST00000267163	NM_000321.2	242	GCTGTTATACcc/cc	8/27	0.675462802412285	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.675462802412285	1		170	201	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73351571	73351571	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	114	134	0	ENST00000377767.4:c.641T>A	p.Leu214Ter	p.L214*	ENST00000377767	NM_014953.3	214	tTg/tAg	4/21	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.675462802412285	2		134	331	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528072	103528072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	158	260	0	ENST00000355739.4:c.3380C>T	p.Ser1127Leu	p.S1127L	ENST00000355739	NM_000123.3	1127	tCa/tTa	15/15	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.675462802412285	2		260	368	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95599719	95599719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201358110	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	186	304	0	ENST00000393063.1:c.77C>T	p.Pro26Leu	p.P26L	ENST00000393063	NM_030621.3	26	cCt/cTt	3/28	0.357175271197698	4	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.675462802412285	4		304	659	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576853	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	198	485	1	ENST00000269305.4:c.993_993+1delinsAA		p.X331_splice	ENST00000269305	NM_001126112.2	331		9/11	1	2	FACETS	0.892	0.83	0.956	0.892	0.83	0.956	CLONAL	1	TRUE	1	0.675462802412285	2		486	657	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985463	60985463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	172	547	0	ENST00000333681.4:c.437G>A	p.Arg146Lys	p.R146K	ENST00000333681		146	aGg/aAg	2/3	1	2	FACETS	0.846	0.782	0.912	0.846	0.782	0.912	CLONAL	1	TRUE	1	0.675462802412285	2		547	602	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210743	5210744	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	252	666	0	ENST00000357368.4:c.5307_5308delinsAA	p.Trp1769_Glu1770delinsTer	p.W1769_E1770delins*	ENST00000357368	NM_002850.3	1769	tgGGag/tgAAag	34/38	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.675462802412285	2		666	714	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096000	11096000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	274	609	0	ENST00000358026.2:c.274C>T	p.Gln92Ter	p.Q92*	ENST00000358026	NM_001128849.1	92	Cag/Tag	3/36	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.675462802412285	2		609	751	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272291	15272291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866094583	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	196	616	0	ENST00000263388.2:c.6148C>T	p.Leu2050Phe	p.L2050F	ENST00000263388	NM_000435.2	2050	Ctc/Ttc	33/33	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.675462802412285	2		616	569	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355227	15355227	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	190	435	0	ENST00000263377.2:c.2396C>T	p.Pro799Leu	p.P799L	ENST00000263377	NM_058243.2	799	cCc/cTc	13/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.675462802412285	2		435	488	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029196	26029196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	106	222	0	ENST00000435504.4:c.154C>T	p.Pro52Ser	p.P52S	ENST00000435504		52	Cct/Tct	4/13	1	2	FACETS	0.858	0.776	0.942	0.858	0.776	0.942	CLONAL	1	TRUE	1	0.675462802412285	2		222	366	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634681	158634681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	140	281	0	ENST00000263640.3:c.505G>A	p.Gly169Arg	p.G169R	ENST00000263640	NM_001105.4	169	Ggg/Agg	5/11	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.675462802412285	2		281	409	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101064	41101064	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	197	459	2	ENST00000373198.4:c.1292A>G	p.Asn431Ser	p.N431S	ENST00000373198	NM_133170.3	431	aAc/aGc	8/32	0.675462802412285	3	FACETS	1	0.963	1	0.528	0.49	0.567	CLONAL	1	TRUE	1	0.675462802412285	3		461	739	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521613	89521613	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	137	258	0	ENST00000336596.2:c.2691-1G>A		p.X897_splice	ENST00000336596	NM_005233.5	897			NA	2	FACETS	1	0.931	1			1	INDETERMINATE	1	TRUE	NA	0.675462802412285	2		258	400	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627956	187627956	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	207	456	1	ENST00000441802.2:c.3026C>T	p.Pro1009Leu	p.P1009L	ENST00000441802	NM_005245.3	1009	cCa/cTa	2/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.675462802412285	2		457	555	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947542	38947542	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	52	140	0	ENST00000357387.3:c.4138T>A	p.Phe1380Ile	p.F1380I	ENST00000357387	NM_152756.3	1380	Ttc/Atc	32/38	1	2	FACETS	0.74	0.638	0.849	0.74	0.638	0.849	SUBCLONAL	1	TRUE	1	0.675462802412285	2		140	208	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285929	38285929	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs77734798	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	159	337	0	ENST00000425967.3:c.482A>C	p.Asp161Ala	p.D161A	ENST00000425967	NM_001174067.1	161	gAt/gCt	5/19	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.675462802412285	2		337	470	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864543	56864543	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	175	368	0	ENST00000519728.1:c.506T>A	p.Val169Asp	p.V169D	ENST00000519728	NM_002350.3	169	gTc/gAc	7/13	1	2	FACETS	0.967	0.897	1	0.967	0.897	1	CLONAL	1	TRUE	1	0.675462802412285	2		368	536	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753054	128753055	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	118	275	0	ENST00000377970.2:c.1215_1216delinsTT	p.Pro406Ser	p.P406S	ENST00000377970	NM_002467.4	405	gcCCcc/gcTTcc	3/3	1	2	FACETS	0.965	0.88	1	0.965	0.88	1	CLONAL	1	TRUE	1	0.675462802412285	2		275	362	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139818439	139818439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045577-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	211	466	0	ENST00000247668.2:c.1274C>T	p.Pro425Leu	p.P425L	ENST00000247668	NM_021138.3	425	cCc/cTc	10/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.675462802412285	2		466	542	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740242	162740242	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	93	403	0	ENST00000367921.3:c.1444C>G	p.Gln482Glu	p.Q482E	ENST00000367921	NM_006182.2	482	Cag/Gag	12/18	0.305292429520818	1	FACETS	0.366	0.326	0.408	0.366	0.326	0.408	INDETERMINATE	1	TRUE	0	0.656812671437856	1		403	520	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932903	49932903	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	78	683	0	ENST00000296474.3:c.3041G>C	p.Gly1014Ala	p.G1014A	ENST00000296474	NM_002447.2	1014	gGc/gCc	13/20	0.246377374834665	2	FACETS	0.26	0.228	0.295	0.13	0.114	0.148	INDETERMINATE	1	TRUE	0	0.656812671437856	2		683	913	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578461	+	protein_altering_variant	In_Frame_Del	DEL	CCTCCGTCATGTGCTGTGACTGCTTGTAGATGGCCATGGCGCGGAC	CCTCCGTCATGTGCTGTGACTGCTTGTAGATGGCCATGGCGCGGAC	G	novel	NA	P-0045578-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	270	597	0	ENST00000269305.4:c.469_514delinsC	p.Val157_Val172delinsLeu	p.V157_V172delinsL	ENST00000269305	NM_001126112.2	157	GTCCGCGCCATGGCCATCTACAAGCAGTCACAGCACATGACGGAGGtt/Ctt	5/11	0.628960163248576	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.656812671437856	1		597	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0045580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	83	565	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.170160131429917	1	FACETS	0.99	0.872	1	0.99	0.872	1	CLONAL	1	TRUE	0	0.170160131429917	1		567	902	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0045580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	57	316	4	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.170160131429917	2		320	610	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906786	50906786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778843530	NA	P-0045580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	103	690	5	ENST00000440232.2:c.1174G>A	p.Val392Met	p.V392M	ENST00000440232	NM_002691.3	392	Gtg/Atg	10/27	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.170160131429917	2		695	980	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893340	32893340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1566215861	NA	P-0045580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	77	340	3	ENST00000380152.3:c.194C>T	p.Pro65Leu	p.P65L	ENST00000380152		65	cCa/cTa	3/27	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.170160131429917	2		343	614	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638317	117638317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758446263	NA	P-0045580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	57	350	0	ENST00000368508.3:c.6124C>T	p.Arg2042Trp	p.R2042W	ENST00000368508	NM_002944.2	2042	Cgg/Tgg	38/43	0.170160131429917	2	FACETS	1	0.944	1	0.604	0.518	0.697	CLONAL	1	TRUE	0	0.170160131429917	2		350	555	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41962081	41962082	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	32	397	1	ENST00000219905.7:c.990dup	p.Asp331ArgfsTer9	p.D331Rfs*9	ENST00000219905	NM_001164273.1	330	cga/cgAa	2/24	0.170160131429917	1	FACETS	0.587	0.475	0.714	0.587	0.475	0.714	SUBCLONAL	1	TRUE	0	0.170160131429917	1		398	586	SUCCESS
APC	324	MSKCC	GRCh37	5	112175587	112175632	+	frameshift_variant	Frame_Shift_Del	DEL	ACCAAGCAGAAGTAAAACACCTCCACCACCTCCTCAAACAGCTCAA	ACCAAGCAGAAGTAAAACACCTCCACCACCTCCTCAAACAGCTCAA	-	novel	NA	P-0045580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	45	356	1	ENST00000257430.4:c.4303_4348del	p.Arg1435GlufsTer23	p.R1435Efs*23	ENST00000257430	NM_000038.5	1432	ccACCAAGCAGAAGTAAAACACCTCCACCACCTCCTCAAACAGCTCAA/cc	16/16	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.170160131429917	2		357	446	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0045581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	36	359	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.127754875045634	3	FACETS	0.254	0.209	0.306	0.127	0.104	0.153	INDETERMINATE	1	TRUE	1	0.9	3		359	456	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0045583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	311	667	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.278822960538936	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.278822960538936	2		669	927	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484233	8484233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200684369	NA	P-0045584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	132	452	0	ENST00000356435.5:c.3299C>T	p.Thr1100Met	p.T1100M	ENST00000356435		1100	aCg/aTg	19/35	0.470514408035782	6	FACETS	1	0.978	1	0.208	0.188	0.229	CLONAL	1	TRUE	0	0.486232595654663	6		452	858	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577540	7577563	+	inframe_deletion	In_Frame_Del	DEL	GTTCATGCCGCCCATGCAGGAACT	GTTCATGCCGCCCATGCAGGAACT	-	rs397516437	NA	P-0045584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	430	495	0	ENST00000269305.4:c.718_741del	p.Ser240_Asn247del	p.S240_N247del	ENST00000269305	NM_001126112.2	240	AGTTCCTGCATGGGCGGCATGAAC/-	7/11	0.486232595654663	4	FACETS	0.898	0.864	0.931	0.898	0.864	0.931	CLONAL	4	TRUE	0	0.486232595654663	4		495	732	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664535	29664538	+	frameshift_variant	Frame_Shift_Del	DEL	GAGA	GAGA	-	rs1131691084	NA	P-0045584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	448	382	8	ENST00000356175.3:c.6520_6523del	p.Glu2174LeufsTer4	p.E2174Lfs*4	ENST00000356175	NM_000267.3	2172	GAGAga/ga	42/57	0.486232595654663	4	FACETS	0.927	0.893	0.959	0.927	0.893	0.959	CLONAL	4	TRUE	0	0.486232595654663	4		390	739	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509939	106509939	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	371	558	1	ENST00000359195.3:c.1933G>T	p.Val645Phe	p.V645F	ENST00000359195	NM_002649.2	645	Gtt/Ttt	2/11	0.340455418892141	5	FACETS	1	0.992	1	0.87	0.832	0.909	CLONAL	3	TRUE	1	0.486232595654663	5		559	758	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875892	76875892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045584-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	83	386	0	ENST00000373344.5:c.5243G>A	p.Gly1748Glu	p.G1748E	ENST00000373344	NM_000489.3	1748	gGa/gAa	20/35	0.486232595654663	3	FACETS	1	0.923	1	0.525	0.466	0.588	CLONAL	1	TRUE	1	0.486232595654663	3		386	404	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0045587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	119	241	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.689191436367295	2		241	297	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0045587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	424	565	2	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.689191436367295	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.689191436367295	2		567	575	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939950	76939951	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0045587-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	288	289	0	ENST00000373344.5:c.797dup	p.Tyr266Ter	p.Y266*	ENST00000373344	NM_000489.3	266	tac/taAc	9/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.689191436367295	1		289	424	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0045588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	84	278	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.293252422265541	2		278	446	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419986	41419986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372989163	NA	P-0045588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	99	415	0	ENST00000373198.4:c.335G>A	p.Arg112His	p.R112H	ENST00000373198	NM_133170.3	112	cGt/cAt	3/32	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.293252422265541	2		415	652	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057835	27057835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	158	499	0	ENST00000324856.7:c.1543C>T	p.Gln515Ter	p.Q515*	ENST00000324856	NM_006015.4	515	Cag/Tag	3/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.293252422265541	2		499	909	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280062	66280062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	54	169	0	ENST00000273854.3:c.1627C>T	p.Arg543Cys	p.R543C	ENST00000273854	NM_004439.5	543	Cgt/Tgt	7/18	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.293252422265541	2		169	361	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101492	27101492	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	123	570	0	ENST00000324856.7:c.4777del	p.Arg1593GlyfsTer19	p.R1593Gfs*19	ENST00000324856	NM_006015.4	1592	Ccc/cc	18/20	1	2	FACETS	0.853	0.77	0.94	0.853	0.77	0.94	CLONAL	1	TRUE	1	0.293252422265541	2		570	984	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624305	89624305	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	188	385	0	ENST00000371953.3:c.79T>G	p.Tyr27Asp	p.Y27D	ENST00000371953	NM_000314.4	27	Tat/Gat	1/9	0.285872083000673	2	FACETS	0.866	0.803	0.932	0.866	0.803	0.932	CLONAL	2	TRUE	0	0.293252422265541	2		385	740	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143318	108143318	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045588-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	77	300	0	ENST00000278616.4:c.3137T>G	p.Leu1046Arg	p.L1046R	ENST00000278616	NM_000051.3	1046	cTt/cGt	21/63	1	2	FACETS	0.983	0.865	1	0.983	0.865	1	CLONAL	1	TRUE	1	0.293252422265541	2		300	534	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0045589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	603	636	1	ENST00000269305.4:c.376-1G>T		p.X126_splice	ENST00000269305	NM_001126112.2	126			NA	2	FACETS	1	0.987	1			1	INDETERMINATE	2	TRUE	NA	0.646204354230916	2		637	908	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189856	11189856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139043855	NA	P-0045589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	77	515	0	ENST00000361445.4:c.5653G>A	p.Val1885Ile	p.V1885I	ENST00000361445	NM_004958.3	1885	Gtc/Atc	40/58	0.631151366465096	1	FACETS	0.277	0.243	0.313	0.277	0.243	0.313	SUBCLONAL	1	TRUE	0	0.646204354230916	1		515	583	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78923284	78923284	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	110	518	0	ENST00000306801.3:c.3307G>T	p.Glu1103Ter	p.E1103*	ENST00000306801	NM_020761.2	1103	Gaa/Taa	28/34	0.646204354230916	2	FACETS	0.525	0.472	0.58	0.262	0.236	0.29	SUBCLONAL	1	TRUE	0	0.646204354230916	2		518	649	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120502067	120502067	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	125	380	0	ENST00000256646.2:c.1974C>G	p.Ile658Met	p.I658M	ENST00000256646	NM_024408.3	658	atC/atG	12/34	0.435246112280857	4	FACETS	0.709	0.641	0.781	0.355	0.32	0.391	SUBCLONAL	1	TRUE	2	0.646204354230916	4		380	898	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98011454	98011454	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs905858585	NA	P-0045589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	94	499	0	ENST00000289081.3:c.120G>C	p.Gln40His	p.Q40H	ENST00000289081	NM_000136.2	40	caG/caC	2/15	0.307935305332272	1	FACETS	0.294	0.262	0.329	0.294	0.262	0.329	INDETERMINATE	1	TRUE	0	0.646204354230916	1		499	669	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225236	53225236	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	114	448	1	ENST00000375401.3:c.2982G>T	p.Arg994Ser	p.R994S	ENST00000375401	NM_004187.3	994	agG/agT	20/26	NA	2	FACETS	0.527	0.475	0.582			1	INDETERMINATE	1	TRUE	NA	0.646204354230916	2		449	669	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348288	70348288	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	110	473	0	ENST00000374080.3:c.3352G>A	p.Asp1118Asn	p.D1118N	ENST00000374080		1118	Gat/Aat	23/45	0.613383781318524	1	FACETS	0.277	0.25	0.305	0.277	0.25	0.305	SUBCLONAL	1	TRUE	0	0.945053865890562	1		473	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519990	NA	P-0045611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	433	544	0	ENST00000269305.4:c.796G>C	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Cga	8/11	0.676558898364777	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.676558898364777	2		544	602	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160359	108160359	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782442	NA	P-0045611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	57	242	0	ENST00000278616.4:c.4267T>C	p.Cys1423Arg	p.C1423R	ENST00000278616	NM_000051.3	1423	Tgt/Cgt	29/63	0.575538107975732	3	FACETS	0.526	0.452	0.606	0.263	0.226	0.303	SUBCLONAL	1	TRUE	1	0.676558898364777	3		242	429	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874746	151874746	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045611-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	80	346	0	ENST00000262189.6:c.7792G>A	p.Asp2598Asn	p.D2598N	ENST00000262189	NM_170606.2	2598	Gac/Aac	38/59	0.676558898364777	3	FACETS	0.49	0.431	0.553			1	SUBCLONAL	1	TRUE	NA	0.676558898364777	3		346	646	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0045613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	114	223	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	1	2	FACETS	0.945	0.862	1	0.945	0.862	1	CLONAL	1	TRUE	1	0.751678598405908	2		223	321	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602719	55602719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752695117	NA	P-0045613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	141	347	0	ENST00000288135.5:c.2540C>T	p.Thr847Met	p.T847M	ENST00000288135	NM_000222.2	847	aCg/aTg	18/21	0.395422141928802	1	FACETS	0.619	0.571	0.669	0.619	0.571	0.669	INDETERMINATE	1	TRUE	0	0.751678598405908	1		347	378	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0045614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	37	545	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	TRUE	1	0.53	2		545	139	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830806	72830807	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0045614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	176	657	0	ENST00000268489.5:c.5774dup	p.Gly1926TrpfsTer3	p.G1926Wfs*3	ENST00000268489	NM_006885.3	1925	ggt/ggGt	9/10	1	2	FACETS	0.882	0.814	0.952	0.882	0.814	0.952	CLONAL	1	TRUE	1	0.53	2		657	753	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166541	118166547	+	frameshift_variant	Frame_Shift_Del	DEL	ACCAACG	ACCAACG	-	novel	NA	P-0045614-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	76	385	0	ENST00000369448.3:c.1051_1057del	p.Thr351SerfsTer44	p.T351Sfs*44	ENST00000369448	NM_017709.3	351	ACCAACGtc/tc	2/2	1	2	FACETS	0.717	0.632	0.807	0.717	0.632	0.807	SUBCLONAL	1	TRUE	1	0.53	2		385	400	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0045615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	71	294	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.369078187386452	1	FACETS	0.999	0.88	1	0.999	0.88	1	CLONAL	1	TRUE	0	0.369078187386452	1		294	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0045615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	112	823	4	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.369078187386452	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.369078187386452	1		827	408	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048764	180048764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	68	723	1	ENST00000261937.6:c.1798G>A	p.Asp600Asn	p.D600N	ENST00000261937	NM_182925.4	600	Gat/Aat	13/30	NA	2	FACETS	0.578	0.503	0.66			1	INDETERMINATE	1	TRUE	NA	0.369078187386452	2		724	637	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034441	47034441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	45	552	1	ENST00000377604.3:c.526G>A	p.Val176Ile	p.V176I	ENST00000377604	NM_001204468.1	176	Gtc/Atc	6/24	0.200880839234381	0	FACETS	0.321	0.27	0.378			1	INDETERMINATE	1	TRUE	0	0.369078187386452	0		553	479	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031919	10031919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs901717931	NA	P-0045615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	52	735	1	ENST00000330684.3:c.904G>A	p.Ala302Thr	p.A302T	ENST00000330684	NM_001134407.1	302	Gct/Act	3/13	1	2	FACETS	0.517	0.44	0.602	0.517	0.44	0.602	SUBCLONAL	1	TRUE	1	0.369078187386452	2		736	545	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575128	48575128	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	25	257	0	ENST00000342988.3:c.322G>T	p.Glu108Ter	p.E108*	ENST00000342988	NM_005359.5	108	Gaa/Taa	3/12	0.369078187386452	1	FACETS	0.46	0.364	0.57	0.46	0.364	0.57	SUBCLONAL	1	TRUE	0	0.369078187386452	1		257	240	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542923	187542923	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1304611761	NA	P-0045615-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	31	203	0	ENST00000441802.2:c.4817T>C	p.Ile1606Thr	p.I1606T	ENST00000441802	NM_005245.3	1606	aTt/aCt	10/27	0.270395521587546	1	FACETS	0.729	0.595	0.877	0.729	0.595	0.877	SUBCLONAL	1	TRUE	0	0.369078187386452	1		203	188	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912655	NA	P-0045616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	41	478	0	ENST00000269305.4:c.725G>C	p.Cys242Ser	p.C242S	ENST00000269305	NM_001126112.2	242	tGc/tCc	7/11	1	2	FACETS	0.94	0.783	1	0.94	0.783	1	CLONAL	1	TRUE	1	0.17	2		478	513	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0045616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	54	615	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.17	2		615	513	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123353298	123353298	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	52	561	0	ENST00000358487.5:c.34G>T	p.Val12Leu	p.V12L	ENST00000358487	NM_000141.4	12	Gtg/Ttg	2/18	0.139580291111685	1	FACETS	1	0.86	1	1	0.86	1	CLONAL	1	TRUE	0	0.17	1		561	554	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138375072	138375072	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	23	352	0	ENST00000289153.2:c.2987A>C	p.His996Pro	p.H996P	ENST00000289153	NM_006219.2	996	cAt/cCt	21/22	0.139580291111685	1	FACETS	0.697	0.543	0.876	0.697	0.543	0.876	SUBCLONAL	1	TRUE	0	0.17	1		352	355	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143324119	143324119	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs761329945	NA	P-0045616-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	14	189	0	ENST00000262992.4:c.344A>G	p.Tyr115Cys	p.Y115C	ENST00000262992	NM_001101669.1	115	tAt/tGt	5/24	1	2	FACETS	0.672	0.486	0.898	0.672	0.486	0.898	SUBCLONAL	1	TRUE	1	0.17	2		189	245	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0045617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	161	316	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.444240903253518	4	FACETS	1	0.977	1	0.76	0.704	0.818	CLONAL	2	TRUE	1	0.444240903253518	4		316	459	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456533	29456538	+	inframe_deletion	In_Frame_Del	DEL	AATGCA	AATGCA	-	novel	NA	P-0045617-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	89	382	0	ENST00000389048.3:c.2380_2385del	p.Cys794_Ile795del	p.C794_I795del	ENST00000389048	NM_004304.4	794	TGCATT/-	14/29	1	2	FACETS	0.678	0.602	0.759	0.678	0.602	0.759	SUBCLONAL	1	TRUE	1	0.444240903253518	2		382	591	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0045619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	115	377	1	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.681876979670327	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.681876979670327	3		378	216	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0045619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	94	329	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.681876979670327	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.681876979670327	1		329	153	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448297	56448298	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1567880599	NA	P-0045619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	185	811	1	ENST00000407977.2:c.349dup	p.Arg117ProfsTer8	p.R117Pfs*8	ENST00000407977		117	cgc/cCgc	3/10	0.415543571847533	3	FACETS	0.84	0.785	0.896	0.84	0.785	0.896	CLONAL	2	TRUE	1	0.681876979670327	3		812	433	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562443	95562443	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs939314926	NA	P-0045619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	82	434	0	ENST00000393063.1:c.4814C>G	p.Pro1605Arg	p.P1605R	ENST00000393063	NM_030621.3	1605	cCt/cGt	24/28	1	2	FACETS	0.966	0.865	1	0.966	0.865	1	CLONAL	1	TRUE	1	0.681876979670327	2		434	249	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0045620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	131	354	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.222377087303502	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	2	TRUE	0	0.261738650450644	2		354	499	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120403	70120404	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0045620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	135	798	0	ENST00000245479.2:c.1406dup	p.Met469IlefsTer109	p.M469Ifs*109	ENST00000245479	NM_000346.3	469	atg/aTtg	3/3	1	2	FACETS	0.802	0.727	0.882	0.802	0.727	0.882	CLONAL	1	TRUE	1	0.261738650450644	2		798	1286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576851	7576851	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0045620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	94	608	0	ENST00000269305.4:c.993+2T>C		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.20696886499596	1	FACETS	0.811	0.721	0.906	0.811	0.721	0.906	CLONAL	1	TRUE	0	0.261738650450644	1		608	770	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47735820	47736220	+	coding_sequence_variant,5_prime_UTR_variant	Frame_Shift_Del	DEL	GGCATGGACATGCCTGGGCAGACCCCATGCCAAATTTCATCCTGTCTCATAGCTTTCCATTCCGTTTCTTTTTCAGTTTCTCATTGTTACTTCCTGCCCTGCTCTGGTTTGGTGAGTTTTGTCCTTCCTTTTTCCAAAGCCGTGGATTCCTGTCTCCTCTACACTTTCCATCCTTACTGGGTCTCACCCAATCGCAATCGCCTCACCAGAGTGACTCACCTTCCAGTGCCTAGTGTGGGGCTGGCTGAGTAAGGATGTCAGACTTCTCAAACTTGACTGCCTCCAAGTACACACTCTTAGCTCCCCCAAGAGATGCAGGTAATCTATATCTCACGTGAAATCTCCCCATTTGCAACATTGGGAACTCCTCAGCTTTCCTCCCTCTTTCACTTTCCCTCCTC	GGCATGGACATGCCTGGGCAGACCCCATGCCAAATTTCATCCTGTCTCATAGCTTTCCATTCCGTTTCTTTTTCAGTTTCTCATTGTTACTTCCTGCCCTGCTCTGGTTTGGTGAGTTTTGTCCTTCCTTTTTCCAAAGCCGTGGATTCCTGTCTCCTCTACACTTTCCATCCTTACTGGGTCTCACCCAATCGCAATCGCCTCACCAGAGTGACTCACCTTCCAGTGCCTAGTGTGGGGCTGGCTGAGTAAGGATGTCAGACTTCTCAAACTTGACTGCCTCCAAGTACACACTCTTAGCTCCCCCAAGAGATGCAGGTAATCTATATCTCACGTGAAATCTCCCCATTTGCAACATTGGGAACTCCTCAGCTTTCCTCCCTCTTTCACTTTCCCTCCTC	-	novel	NA	P-0045620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	725	82	0				ENST00000449228	NM_001127240.2	?-14/261		1/4	1	2	FACETS	1	0.982	1	1	0.998	1	CLONAL	3	TRUE	1	0.261738650450644	2		82	1803	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974759	21974759	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	67	255	0	ENST00000304494.5:c.68del	p.Gly23ValfsTer3	p.G23Vfs*3	ENST00000304494	NM_000077.4	23	gGt/gt	1/3	0.261738650450644	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.261738650450644	1		255	370	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0045621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	169	333	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.579707535516009	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.579707535516009	3		333	231	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913315	NA	P-0045621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	244	548	0	ENST00000326873.7:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000326873	NM_000455.4	194	Gac/Tac	4/10	0.579707535516009	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.579707535516009	2		548	400	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602619	10602619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	86	699	1	ENST00000171111.5:c.959G>A	p.Arg320Gln	p.R320Q	ENST00000171111	NM_203500.1	320	cGg/cAg	3/6	0.579707535516009	2	FACETS	0.472	0.417	0.53	0.236	0.208	0.265	SUBCLONAL	1	TRUE	0	0.579707535516009	2		700	629	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934713	49934713	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	278	570	0	ENST00000296474.3:c.2183G>T	p.Arg728Leu	p.R728L	ENST00000296474	NM_002447.2	728	cGg/cTg	7/20	0.579707535516009	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.579707535516009	3		570	595	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923710	39923710	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	183	662	0	ENST00000378444.4:c.3381C>A	p.Ser1127Arg	p.S1127R	ENST00000378444	NM_001123385.1	1127	agC/agA	7/15	0.579707535516009	3	FACETS	1	0.962	1	0.532	0.492	0.574	CLONAL	1	TRUE	1	0.579707535516009	3		662	765	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965567	15965567	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	51	184	0	ENST00000268712.3:c.5239C>G	p.Arg1747Gly	p.R1747G	ENST00000268712	NM_006311.3	1747	Cga/Gga	36/46	0.579707535516009	3	FACETS	1	0.946	1	0.604	0.521	0.691	CLONAL	1	TRUE	1	0.579707535516009	3		184	188	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910843	114910843	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	127	416	0	ENST00000543371.1:c.962A>G	p.Gln321Arg	p.Q321R	ENST00000543371	NM_001198531.1	321	cAg/cGg	9/14	0.579707535516009	4	FACETS	0.939	0.852	1	0.313	0.284	0.344	CLONAL	1	TRUE	1	0.579707535516009	4		416	737	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870848	12870854	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCTCG	GCCCTCG	-	novel	NA	P-0045621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	26	228	0	ENST00000228872.4:c.78_84del	p.Ser27AlafsTer13	p.S27Afs*13	ENST00000228872	NM_004064.3	25	aaGCCCTCG/aa	1/3	0.55832217010498	4	FACETS	0.641	0.51	0.789	0.16	0.127	0.198	SUBCLONAL	1	TRUE	0	0.579707535516009	4		228	221	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69230515	69230515	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	57	269	0	ENST00000462284.1:c.904G>C	p.Glu302Gln	p.E302Q	ENST00000462284	NM_002392.5	302	Gaa/Caa	10/11	0.579707535516009	3	FACETS	1	0.891	1	0.516	0.447	0.589	CLONAL	1	TRUE	1	0.579707535516009	3		269	246	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687519	37687519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	48	316	0	ENST00000447079.4:c.4423C>T	p.Pro1475Ser	p.P1475S	ENST00000447079	NM_015083.1	1475	Cct/Tct	14/14	0.579707535516009	3	FACETS	0.527	0.447	0.616	0.264	0.223	0.308	SUBCLONAL	1	TRUE	1	0.579707535516009	3		316	405	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805384	46805384	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	175	765	0	ENST00000290295.7:c.572C>T	p.Pro191Leu	p.P191L	ENST00000290295	NM_006361.5	191	cCa/cTa	1/2	0.579707535516009	3	FACETS	0.916	0.844	0.991	0.458	0.422	0.496	CLONAL	1	TRUE	1	0.579707535516009	3		765	850	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610590	10610605	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCTTGCACTCAGTG	CGCCTTGCACTCAGTG	-	novel	NA	P-0045621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	61	736	0	ENST00000171111.5:c.105_120del	p.Thr36ArgfsTer2	p.T36Rfs*2	ENST00000171111	NM_203500.1	35	tcCACTGAGTGCAAGGCG/tc	2/6	0.579707535516009	2	FACETS	0.353	0.304	0.406	0.177	0.152	0.203	SUBCLONAL	1	TRUE	0	0.579707535516009	2		736	596	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38314960	38314960	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	174	652	1	ENST00000425967.3:c.104G>A	p.Trp35Ter	p.W35*	ENST00000425967	NM_001174067.1	35	tGg/tAg	3/19	0.304415781959516	3	FACETS	1	0.982	1	0.598	0.553	0.645	INDETERMINATE	1	TRUE	1	0.579707535516009	3		653	647	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528761	8528761	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1371428038	NA	P-0045621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	104	329	0	ENST00000356435.5:c.371G>C	p.Gly124Ala	p.G124A	ENST00000356435		124	gGc/gCc	4/35	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.579707535516009	2		329	280	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	21	425	0				ENST00000310581	NM_198253.2	-/1132			0.188769441009649	1	FACETS	0.849	0.659	1	0.849	0.659	1	CLONAL	1	TRUE	0	0.267829247741352	1		425	160	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264678	11264678	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	69	562	1	ENST00000361445.4:c.3884C>T	p.Ser1295Leu	p.S1295L	ENST00000361445	NM_004958.3	1295	tCa/tTa	26/58	NA	2	FACETS	0.721	0.627	0.822			1	INDETERMINATE	1	TRUE	NA	0.267829247741352	2		563	715	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263968	16263968	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	86	712	0	ENST00000375759.3:c.10337C>G	p.Ser3446Cys	p.S3446C	ENST00000375759	NM_015001.2	3446	tCt/tGt	12/15	1	2	FACETS	0.742	0.656	0.836	0.742	0.656	0.836	SUBCLONAL	1	TRUE	1	0.267829247741352	2		712	865	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46543223	46543223	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	55	387	0	ENST00000262741.5:c.278C>G	p.Ser93Ter	p.S93*	ENST00000262741	NM_003629.3	93	tCa/tGa	3/10	1	2	FACETS	0.83	0.71	0.96	0.83	0.71	0.96	CLONAL	1	TRUE	1	0.267829247741352	2		387	495	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115269705	115269705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	31	335	0	ENST00000438362.2:c.1501G>A	p.Glu501Lys	p.E501K	ENST00000438362	NM_001242891.1	501	Gag/Aag	13/20	1	2	FACETS	0.66	0.534	0.801	0.66	0.534	0.801	SUBCLONAL	1	TRUE	1	0.267829247741352	2		335	351	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981298	201981298	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	92	636	0	ENST00000359651.3:c.377G>C	p.Arg126Pro	p.R126P	ENST00000359651		126	cGa/cCa	2/8	1	2	FACETS	0.96	0.853	1	0.96	0.853	1	CLONAL	1	TRUE	1	0.267829247741352	2		636	716	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94923077	94923077	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	46	398	0	ENST00000536441.1:c.391G>C	p.Glu131Gln	p.E131Q	ENST00000536441	NM_144665.3	131	Gaa/Caa	4/10	0.215126910468181	1	FACETS	0.641	0.54	0.752	0.641	0.54	0.752	SUBCLONAL	1	TRUE	0	0.267829247741352	1		398	464	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524633	103524633	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	44	288	0	ENST00000355739.4:c.2764C>G	p.Gln922Glu	p.Q922E	ENST00000355739	NM_000123.3	922	Caa/Gaa	13/15	1	2	FACETS	0.811	0.682	0.954	0.811	0.682	0.954	CLONAL	1	TRUE	1	0.267829247741352	2		288	405	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40685693	40685693	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	51	382	0	ENST00000249776.8:c.846G>A	p.Met282Ile	p.M282I	ENST00000249776	NM_033286.3	282	atG/atA	9/9	1	2	FACETS	0.9	0.767	1	0.9	0.767	1	CLONAL	1	TRUE	1	0.267829247741352	2		382	423	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41001249	41001249	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	78	339	0	ENST00000267868.3:c.370G>T	p.Glu124Ter	p.E124*	ENST00000267868	NM_002875.4	124	Gaa/Taa	5/10	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.267829247741352	2		339	543	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858072	9858072	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs1244209721	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	68	444	0	ENST00000330684.3:c.3329C>G	p.Ser1110Ter	p.S1110*	ENST00000330684	NM_001134407.1	1110	tCa/tGa	13/13	0.267829247741352	1	FACETS	0.973	0.849	1	0.973	0.849	1	CLONAL	1	TRUE	0	0.267829247741352	1		444	452	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835581	68835581	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	60	364	1	ENST00000261769.5:c.172G>T	p.Glu58Ter	p.E58*	ENST00000261769	NM_004360.3	58	Gaa/Taa	3/16	0.267829247741352	1	FACETS	0.835	0.72	0.958	0.835	0.72	0.958	CLONAL	1	TRUE	0	0.267829247741352	1		365	465	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822696	72822696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	79	595	0	ENST00000268489.5:c.9479C>T	p.Pro3160Leu	p.P3160L	ENST00000268489	NM_006885.3	3160	cCt/cTt	10/10	0.267829247741352	1	FACETS	0.766	0.674	0.865	0.766	0.674	0.865	SUBCLONAL	1	TRUE	0	0.267829247741352	1		595	667	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831279	72831279	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	51	404	0	ENST00000268489.5:c.5302C>T	p.Gln1768Ter	p.Q1768*	ENST00000268489	NM_006885.3	1768	Cag/Tag	9/10	0.267829247741352	1	FACETS	0.795	0.677	0.923	0.795	0.677	0.923	CLONAL	1	TRUE	0	0.267829247741352	1		404	415	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683534	29683534	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	33	234	0	ENST00000356175.3:c.7609G>A	p.Glu2537Lys	p.E2537K	ENST00000356175	NM_000267.3	2537	Gaa/Aaa	51/57	1	2	FACETS	0.727	0.593	0.877	0.727	0.593	0.877	SUBCLONAL	1	TRUE	1	0.267829247741352	2		234	339	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097180	11097180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1368858108	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	49	662	0	ENST00000358026.2:c.671C>T	p.Ser224Leu	p.S224L	ENST00000358026	NM_001128849.1	224	tCg/tTg	4/36	0.232754170111036	2	FACETS	0.474	0.4	0.556	0.237	0.2	0.278	SUBCLONAL	1	TRUE	0	0.267829247741352	2		662	772	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129655	11129655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	169	580	0	ENST00000358026.2:c.2461G>A	p.Glu821Lys	p.E821K	ENST00000358026	NM_001128849.1	821	Gag/Aag	17/36	0.232754170111036	2	FACETS	0.849	0.782	0.919	0.849	0.782	0.919	CLONAL	2	TRUE	0	0.267829247741352	2		580	743	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288514	15288514	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1478078695	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	17	82	0	ENST00000263388.2:c.4225G>C	p.Gly1409Arg	p.G1409R	ENST00000263388	NM_000435.2	1409	Ggc/Cgc	24/33	0.232754170111036	2	FACETS	0.992	0.748	1	0.496	0.374	0.638	CLONAL	1	TRUE	0	0.267829247741352	2		82	128	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794835	42794835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	70	643	0	ENST00000575354.2:c.1915G>A	p.Glu639Lys	p.E639K	ENST00000575354	NM_015125.3	639	Gag/Aag	10/20	0.267829247741352	3	FACETS	0.835	0.727	0.951	0.417	0.363	0.476	CLONAL	1	TRUE	1	0.267829247741352	3		643	710	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858941	45858941	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	197	554	0	ENST00000391945.4:c.1525G>C	p.Glu509Gln	p.E509Q	ENST00000391945	NM_000400.3	509	Gag/Cag	16/23	0.267829247741352	3	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	1	0.267829247741352	3		554	824	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213369	39213369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756728233	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	81	504	0	ENST00000402219.2:c.3598G>A	p.Asp1200Asn	p.D1200N	ENST00000402219	NM_005633.3	1200	Gac/Aac	23/23	1	2	FACETS	0.768	0.675	0.867	0.768	0.675	0.867	SUBCLONAL	1	TRUE	1	0.267829247741352	2		504	788	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624798	9624798	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	44	389	0	ENST00000353224.5:c.179C>T	p.Thr60Ile	p.T60I	ENST00000353224	NM_177990.2	60	aCa/aTa	3/10	1	2	FACETS	0.727	0.61	0.856	0.727	0.61	0.856	SUBCLONAL	1	TRUE	1	0.267829247741352	2		389	452	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264413	46264413	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	37	315	0	ENST00000371998.3:c.1460G>T	p.Arg487Leu	p.R487L	ENST00000371998		487	cGt/cTt	11/23	1	2	FACETS	0.614	0.506	0.735	0.614	0.506	0.735	SUBCLONAL	1	TRUE	1	0.267829247741352	2		315	450	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573437	41573437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1315029784	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	97	658	0	ENST00000263253.7:c.5722C>T	p.Pro1908Ser	p.P1908S	ENST00000263253	NM_001429.3	1908	Cca/Tca	31/31	1	2	FACETS	0.92	0.82	1	0.92	0.82	1	CLONAL	1	TRUE	1	0.267829247741352	2		658	787	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178151	142178151	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	66	251	0	ENST00000350721.4:c.7267G>C	p.Val2423Leu	p.V2423L	ENST00000350721	NM_001184.3	2423	Gta/Cta	43/47	0.204852408394085	3	FACETS	0.787	0.687	0.894	0.787	0.687	0.894	SUBCLONAL	2	TRUE	1	0.267829247741352	3		251	355	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916935	+	inframe_deletion	In_Frame_Del	DEL	GCAACC	GCAACC	-	novel	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	96	349	0	ENST00000263967.3:c.318_323del	p.Asn107_Arg108del	p.N107_R108del	ENST00000263967	NM_006218.2	106	gGCAACCgt/ggt	2/21	0.204852408394085	3	FACETS	0.861	0.771	0.956	0.861	0.771	0.956	CLONAL	2	TRUE	1	0.267829247741352	3		349	472	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955084	55955084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	58	393	0	ENST00000263923.4:c.3461C>T	p.Ser1154Leu	p.S1154L	ENST00000263923	NM_002253.2	1154	tCa/tTa	26/30	1	2	FACETS	0.765	0.657	0.883	0.765	0.657	0.883	SUBCLONAL	1	TRUE	1	0.267829247741352	2		393	566	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352382	143352382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	64	478	0	ENST00000262992.4:c.31G>A	p.Glu11Lys	p.E11K	ENST00000262992	NM_001101669.1	11	Gaa/Aaa	2/24	1	2	FACETS	0.721	0.624	0.826	0.721	0.624	0.826	SUBCLONAL	1	TRUE	1	0.267829247741352	2		478	663	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233727	233727	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	85	620	1	ENST00000264932.6:c.1031C>A	p.Ser344Tyr	p.S344Y	ENST00000264932	NM_004168.2	344	tCt/tAt	8/15	0.188769441009649	1	FACETS	0.684	0.604	0.77	0.684	0.604	0.77	SUBCLONAL	1	TRUE	0	0.267829247741352	1		621	804	SUCCESS
APC	324	MSKCC	GRCh37	5	112174218	112174218	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	40	268	0	ENST00000257430.4:c.2927G>C	p.Arg976Thr	p.R976T	ENST00000257430	NM_000038.5	976	aGa/aCa	16/16	1	2	FACETS	0.871	0.726	1	0.871	0.726	1	CLONAL	1	TRUE	1	0.267829247741352	2		268	343	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490417	20490417	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	46	365	0	ENST00000346618.3:c.1154C>G	p.Ser385Ter	p.S385*	ENST00000346618	NM_001949.4	385	tCa/tGa	7/7	1	2	FACETS	0.816	0.688	0.956	0.816	0.688	0.956	CLONAL	1	TRUE	1	0.267829247741352	2		365	421	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287884	33287884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	61	529	0	ENST00000374542.5:c.1369G>A	p.Glu457Lys	p.E457K	ENST00000374542	NM_001141970.1	457	Gag/Aag	5/8	1	2	FACETS	0.717	0.618	0.825	0.717	0.618	0.825	SUBCLONAL	1	TRUE	1	0.267829247741352	2		529	635	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405796	157405796	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	37	290	0	ENST00000346085.5:c.2038G>A	p.Asp680Asn	p.D680N	ENST00000346085	NM_020732.3	680	Gat/Aat	6/20	1	2	FACETS	0.801	0.662	0.956	0.801	0.662	0.956	CLONAL	1	TRUE	1	0.267829247741352	2		290	345	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028127	69028127	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	74	435	1	ENST00000288368.4:c.3286G>A	p.Asp1096Asn	p.D1096N	ENST00000288368	NM_024870.2	1096	Gat/Aat	26/40	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.267829247741352	2		436	484	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782747	135782748	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	55	316	0	ENST00000298552.3:c.1273_1274del	p.Met425GlyfsTer16	p.M425Gfs*16	ENST00000298552	NM_001162426.1	425	ATg/g	13/23	0.267829247741352	1	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	0	0.267829247741352	1		316	351	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226021	53226021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781785252	NA	P-0045622-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	115	410	0	ENST00000375401.3:c.2828G>A	p.Arg943Gln	p.R943Q	ENST00000375401	NM_004187.3	943	cGa/cAa	19/26	1	1	FACETS	0.762	0.69	0.837	1	0.985	1	SUBCLONAL	2	TRUE	0	0.267829247741352	1		410	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579585	7579585	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	299	592	0	ENST00000269305.4:c.102del	p.Leu35CysfsTer9	p.L35Cfs*9	ENST00000269305	NM_001126112.2	34	ccC/cc	4/11	0.823954528242279	1	FACETS	0.93	0.891	0.967	0.93	0.891	0.967	CLONAL	1	TRUE	0	0.823954528242279	1		592	459	SUCCESS
BTK	695	MSKCC	GRCh37	X	100625010	100625010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	283	429	0	ENST00000308731.7:c.367C>T	p.Arg123Trp	p.R123W	ENST00000308731	NM_000061.2	123	Cgg/Tgg	5/19	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.823954528242279	2		429	678	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683557	29683558	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1060500295	NA	P-0045623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	168	252	0	ENST00000356175.3:c.7638dup	p.Lys2547GlnfsTer9	p.K2547Qfs*9	ENST00000356175	NM_000267.3	2544	-/C	51/57	0.823954528242279	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.823954528242279	1		252	230	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562908	95562909	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0045623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	156	228	0	ENST00000393063.1:c.4348dup	p.Ile1450AsnfsTer6	p.I1450Nfs*6	ENST00000393063	NM_030621.3	1450	atc/aAtc	24/28	1	2	FACETS	0.989	0.917	1	0.989	0.917	1	CLONAL	1	TRUE	1	0.823954528242279	2		228	383	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25462078	25462078	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	251	386	0	ENST00000264709.3:c.2329C>G	p.Pro777Ala	p.P777A	ENST00000264709	NM_175629.2	777	Cct/Gct	20/23	0.367200998774515	3	FACETS	1	0.99	1	0.628	0.591	0.666	INDETERMINATE	1	TRUE	1	0.823954528242279	3		386	685	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392170	81392170	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1475550689	NA	P-0045623-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	133	211	1	ENST00000222390.5:c.107G>T	p.Arg36Ile	p.R36I	ENST00000222390	NM_000601.4	36	aGa/aTa	2/18	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.823954528242279	2		212	297	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251991	8251991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760736132	NA	P-0045624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	96	672	1	ENST00000335790.3:c.86G>A	p.Arg29His	p.R29H	ENST00000335790	NM_002315.2	29	cGc/cAc	2/4	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		673	938	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0045624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	34	347	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		347	188	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0045624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	24	397	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		397	206	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851396	63851396	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	66	423	0	ENST00000279873.7:c.2174G>T	p.Arg725Met	p.R725M	ENST00000279873	NM_032199.2	725	aGg/aTg	10/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		423	556	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120833	115120833	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	114	309	0	ENST00000257566.3:c.173G>A	p.Gly58Asp	p.G58D	ENST00000257566	NM_016569.3	58	gGc/gAc	1/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		309	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912655	NA	P-0045625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	177	489	0	ENST00000269305.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000269305	NM_001126112.2	242	tGc/tAc	7/11	0.233132619088222	2	FACETS	0.991	0.915	1	0.991	0.915	1	CLONAL	2	TRUE	0	0.233132619088222	2		489	766	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0045625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	340	235	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.982	1			1	INDETERMINATE	4	TRUE	NA	0.233132619088222	2		235	689	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983076	201983076	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	110	566	1	ENST00000359651.3:c.925G>T	p.Glu309Ter	p.E309*	ENST00000359651		309	Gag/Tag	7/8	1	2	FACETS	0.986	0.885	1	0.986	0.885	1	CLONAL	1	TRUE	1	0.233132619088222	2		567	957	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983098	201983098	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	205	530	1	ENST00000359651.3:c.947G>T	p.Gly316Val	p.G316V	ENST00000359651		316	gGc/gTc	7/8	1	2	FACETS	1	0.952	1	1	0.994	1	CLONAL	2	TRUE	1	0.233132619088222	2		531	852	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106162567	106162567	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	12	229	0	ENST00000380013.4:c.3481A>G	p.Arg1161Gly	p.R1161G	ENST00000380013	NM_001127208.2	1161	Aga/Gga	4/11	1	2	FACETS	0.62	0.437	0.844	0.62	0.437	0.844	SUBCLONAL	1	TRUE	1	0.233132619088222	2		229	166	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339467	81339467	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	30	270	0	ENST00000222390.5:c.1537T>A	p.Tyr513Asn	p.Y513N	ENST00000222390	NM_000601.4	513	Tac/Aac	13/18	1	2	FACETS	0.9	0.727	1	0.9	0.727	1	CLONAL	1	TRUE	1	0.233132619088222	2		270	286	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44894189	44894190	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0045625-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	14	372	0	ENST00000377967.4:c.580_581dup	p.Leu194PhefsTer49	p.L194Ffs*49	ENST00000377967	NM_021140.2	193	gct/gcTTt	7/29	1	2	FACETS	0.616	0.446	0.821	0.616	0.446	0.821	SUBCLONAL	1	TRUE	1	0.233132619088222	2		372	195	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292430	15292430	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs150338460	NA	P-0045626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	217	771	0	ENST00000263388.2:c.2749G>C	p.Gly917Arg	p.G917R	ENST00000263388	NM_000435.2	917	Gga/Cga	17/33	0.81400403047867	3	FACETS	1	0.977	1	0.548	0.512	0.585	CLONAL	1	TRUE	1	0.81400403047867	3		771	684	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100096	157100110	+	inframe_deletion	In_Frame_Del	DEL	GCGGCGGCGGCAGCA	GCGGCGGCGGCAGCA	-	novel	NA	P-0045626-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	35	21	0	ENST00000346085.5:c.1035_1049del	p.Ala346_Ala350del	p.A346_A350del	ENST00000346085	NM_020732.3	345	GCGGCGGCGGCAGCA/-	1/20	0.81400403047867	4	FACETS	0.981	0.863	1	1	0.967	1	CLONAL	3	TRUE	2	0.81400403047867	4		21	53	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0045627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	60	546	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.33	0.283	0.38	0.33	0.283	0.38	SUBCLONAL	1	TRUE	1	0.55	2		546	662	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0045627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	29	270	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	0.283	0.227	0.347	0.283	0.227	0.347	SUBCLONAL	1	TRUE	1	0.55	2		270	372	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218423	1218423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	25	390	3	ENST00000326873.7:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000326873	NM_000455.4	100	Caa/Taa	2/10	0.3	1	FACETS	0.136	0.107	0.171	0.136	0.107	0.171	INDETERMINATE	1	TRUE	0	0.55	1		393	483	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097211	178097211	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	26	251	1	ENST00000397062.3:c.503C>T	p.Ser168Phe	p.S168F	ENST00000397062	NM_006164.4	168	tCt/tTt	4/5	0.3	1	FACETS	0.156	0.123	0.194	0.156	0.123	0.194	INDETERMINATE	1	TRUE	0	0.55	1		252	440	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932275	36932275	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746747614	NA	P-0045627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	65	645	0	ENST00000361632.4:c.2194G>A	p.Asp732Asn	p.D732N	ENST00000361632		732	Gac/Aac	16/16	1	2	FACETS	0.276	0.238	0.317	0.276	0.238	0.317	SUBCLONAL	1	TRUE	1	0.55	2		645	857	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246038	41246038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357445	NA	P-0045627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	20	428	0	ENST00000357654.3:c.1510C>T	p.Arg504Cys	p.R504C	ENST00000357654	NM_007294.3	504	Cgt/Tgt	10/23	1	2	FACETS	0.252	0.192	0.321	0.252	0.192	0.321	SUBCLONAL	1	TRUE	1	0.55	2		428	289	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857250	9857250	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	34	455	0	ENST00000330684.3:c.4151C>G	p.Ser1384Trp	p.S1384W	ENST00000330684	NM_001134407.1	1384	tCg/tGg	13/13	1	2	FACETS	0.241	0.196	0.291	0.241	0.196	0.291	SUBCLONAL	1	TRUE	1	0.55	2		455	513	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670516	246670516	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	31	297	0	ENST00000388985.4:c.4G>C	p.Glu2Gln	p.E2Q	ENST00000388985		2	Gag/Cag	1/12	1	2	FACETS	0.22	0.177	0.269	0.22	0.177	0.269	SUBCLONAL	1	TRUE	1	0.55	2		297	512	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645381	67645381	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	19	309	0	ENST00000264010.4:c.646G>C	p.Glu216Gln	p.E216Q	ENST00000264010	NM_006565.3	216	Gag/Cag	3/12	1	2	FACETS	0.214	0.162	0.275	0.214	0.162	0.275	SUBCLONAL	1	TRUE	1	0.55	2		309	323	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872559	37872559	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	44	394	0	ENST00000269571.5:c.1519G>C	p.Glu507Gln	p.E507Q	ENST00000269571		507	Gag/Cag	13/27	1	2	FACETS	0.273	0.228	0.323	0.273	0.228	0.323	SUBCLONAL	1	TRUE	1	0.55	2		394	586	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967829	18967829	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045627-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	71	668	0	ENST00000262803.5:c.1968G>T	p.Gln656His	p.Q656H	ENST00000262803	NM_002911.3	656	caG/caT	14/24	1	2	FACETS	0.272	0.236	0.311	0.272	0.236	0.311	SUBCLONAL	1	TRUE	1	0.55	2		668	949	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	36	425	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.923	1			1	INDETERMINATE	1	TRUE	NA	0.225902793321167	2		425	260	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527502	29527503	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0045629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	74	312	0	ENST00000356175.3:c.952_953del	p.Glu318LysfsTer11	p.E318Kfs*11	ENST00000356175	NM_000267.3	317	acAGaa/acaa	9/57	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.225902793321167	2		312	470	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698146	47698147	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs63750393	NA	P-0045629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	17	207	0	ENST00000233146.2:c.1705_1706del	p.Glu569IlefsTer2	p.E569Ifs*2	ENST00000233146	NM_000251.2	568	acAGaa/acaa	11/16	0.154314915650468	2	FACETS	0.521	0.388	0.678	0.26	0.194	0.339	SUBCLONAL	1	TRUE	0	0.225902793321167	2		207	289	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176329	24176329	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1568963596	NA	P-0045629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	165	591	1	ENST00000263121.7:c.1120C>T	p.Arg374Trp	p.R374W	ENST00000263121	NM_003073.3	374	Cgg/Tgg	9/9	0.225902793321167	3	FACETS	0.964	0.886	1	0.643	0.591	0.697	CLONAL	2	TRUE	0	0.225902793321167	3		592	843	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275232	115275232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753559097	NA	P-0045629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	34	333	1	ENST00000438362.2:c.1181G>A	p.Arg394Gln	p.R394Q	ENST00000438362	NM_001242891.1	394	cGa/cAa	10/20	0.154314915650468	2	FACETS	0.664	0.543	0.802	0.332	0.271	0.401	SUBCLONAL	1	TRUE	0	0.225902793321167	2		334	453	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653829	89653829	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	75	233	0	ENST00000371953.3:c.127G>C	p.Glu43Gln	p.E43Q	ENST00000371953	NM_000314.4	43	Gaa/Caa	2/9	0.154314915650468	2	FACETS	0.86	0.758	0.969	0.86	0.758	0.969	CLONAL	2	TRUE	0	0.225902793321167	2		233	386	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142009	108142009	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1210518784	NA	P-0045629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	33	325	0	ENST00000278616.4:c.2953G>C	p.Asp985His	p.D985H	ENST00000278616	NM_000051.3	985	Gat/Cat	20/63	1	2	FACETS	0.648	0.527	0.784	0.648	0.527	0.784	SUBCLONAL	1	TRUE	1	0.225902793321167	2		325	451	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459215	99459216	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0045629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	118	484	0	ENST00000268035.6:c.1852_1853del	p.Leu618PhefsTer63	p.L618Ffs*63	ENST00000268035	NM_000875.3	617	gtTCtt/gttt	9/21	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.225902793321167	2		484	707	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051588	30051588	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	60	184	0	ENST00000338641.4:c.524del	p.Asn175IlefsTer5	p.N175Ifs*5	ENST00000338641	NM_000268.3	174	atA/at	6/16	0.225902793321167	3	FACETS	0.833	0.721	0.953	0.555	0.481	0.635	CLONAL	2	TRUE	0	0.225902793321167	3		184	355	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750794	57750795	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0045629-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	19	285	0	ENST00000274289.3:c.1809_1810insA	p.Gln604ThrfsTer6	p.Q604Tfs*6	ENST00000274289	NM_006622.3	603	-/A	13/14	1	2	FACETS	0.443	0.335	0.569	0.443	0.335	0.569	SUBCLONAL	1	TRUE	1	0.225902793321167	2		285	380	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123260385	123260385	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	23	572	0	ENST00000358487.5:c.1516G>C	p.Asp506His	p.D506H	ENST00000358487	NM_000141.4	506	Gac/Cac	11/18	1	2	FACETS	0.332	0.258	0.417	0.332	0.258	0.417	SUBCLONAL	1	TRUE	1	0.369499236542858	2		572	375	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183753	10183753	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	70	774	0	ENST00000256474.2:c.222del	p.Ile75SerfsTer84	p.I75Sfs*84	ENST00000256474	NM_000551.3	74	gtC/gt	1/3	0.369499236542858	1	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	0	0.369499236542858	1		774	307	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0045631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	176	368	1	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	0.52265218174665	4	FACETS	0.932	0.893	0.968	1	0.991	1	CLONAL	5	FALSE	0	0.52265218174665	4		369	220	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252066	226252068	+	inframe_deletion	In_Frame_Del	DEL	AGC	AGC	-	novel	NA	P-0045632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	116	207	0	ENST00000366813.1:c.16_18del	p.Gln6del	p.Q6del	ENST00000366813		5	aAGCag/aag	1/3	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.78	2		207	295	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663315	67663315	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045632-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	95	273	0	ENST00000264010.4:c.1716A>C	p.Arg572Ser	p.R572S	ENST00000264010	NM_006565.3	572	agA/agC	10/12	1	2	FACETS	0.876	0.791	0.964	0.876	0.791	0.964	CLONAL	1	TRUE	1	0.78	2		273	278	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	73	425	0				ENST00000310581	NM_198253.2	-/1132			0.194081623420899	1	FACETS	0.688	0.609	0.77	0.688	0.609	0.77	INDETERMINATE	1	TRUE	0	0.578222450322276	1		425	261	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274115	10274115	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555491518	NA	P-0045633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	104	317	1	ENST00000330684.3:c.154C>T	p.Arg52Ter	p.R52*	ENST00000330684	NM_001134407.1	52	Cga/Tga	2/13	0.421211531596318	0	FACETS	0.435	0.393	0.478			1	SUBCLONAL	1	TRUE	0	0.578222450322276	0		318	349	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	182	264	0	ENST00000304494.5:c.322G>C	p.Asp108His	p.D108H	ENST00000304494	NM_000077.4	108	Gat/Cat	2/3	0.578222450322276	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.578222450322276	1		264	388	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879583	37879583	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	12019	364	0	ENST00000269571.5:c.1958C>G	p.Ser653Cys	p.S653C	ENST00000269571		653	tCc/tGc	17/27	0.578222450322276	31	FACETS	1	0.999	1			1	CLONAL	31	TRUE	NA	0.578222450322276	31		364	12502	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933735	36933735	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763022964	NA	P-0045633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	236	386	2	ENST00000361632.4:c.1664G>A	p.Gly555Glu	p.G555E	ENST00000361632		555	gGg/gAg	12/16	0.347761818879832	1	FACETS	0.842	0.79	0.896	0.842	0.79	0.896	CLONAL	1	TRUE	0	0.578222450322276	1		388	689	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224470	53224470	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	422	155	0	ENST00000375401.3:c.3243G>A	p.Trp1081Ter	p.W1081*	ENST00000375401	NM_004187.3	1081	tgG/tgA	21/26	0.454737868024868	2	FACETS	0.874	0.848	0.898			1	CLONAL	3	TRUE	NA	0.578222450322276	2		155	557	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780711	9780711	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	67	270	0	ENST00000377346.4:c.1513G>C	p.Glu505Gln	p.E505Q	ENST00000377346	NM_005026.3	505	Gag/Cag	12/24	0.347761818879832	1	FACETS	0.391	0.341	0.445	0.391	0.341	0.445	SUBCLONAL	1	TRUE	0	0.578222450322276	1		270	421	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101985061	101985061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748877056	NA	P-0045633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	119	427	0	ENST00000282441.5:c.508G>A	p.Asp170Asn	p.D170N	ENST00000282441	NM_001130145.2	170	Gat/Aat	2/9	0.347761818879832	1	FACETS	0.409	0.369	0.451	0.409	0.369	0.451	SUBCLONAL	1	TRUE	0	0.578222450322276	1		427	715	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443805	18443805	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	49	111	0	ENST00000266497.5:c.778C>G	p.His260Asp	p.H260D	ENST00000266497		260	Cat/Gat	3/31	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.578222450322276	2		111	168	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426667	49426667	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	75	194	0	ENST00000301067.7:c.11821C>A	p.Gln3941Lys	p.Q3941K	ENST00000301067	NM_003482.3	3941	Caa/Aaa	39/54	1	2	FACETS	0.768	0.678	0.863	0.768	0.678	0.863	SUBCLONAL	1	TRUE	1	0.578222450322276	2		194	338	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573964	7573964	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	101	377	0	ENST00000269305.4:c.1063G>C	p.Ala355Pro	p.A355P	ENST00000269305	NM_001126112.2	355	Gct/Cct	10/11	0.578222450322276	1	FACETS	0.586	0.527	0.647	0.586	0.527	0.647	SUBCLONAL	1	TRUE	0	0.578222450322276	1		377	424	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18943139	18943139	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1429628130	NA	P-0045633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	41	167	1	ENST00000262803.5:c.121C>A	p.Pro41Thr	p.P41T	ENST00000262803	NM_002911.3	41	Cct/Act	1/24	0.28793945859181	1	FACETS	0.372	0.311	0.438	0.372	0.311	0.438	INDETERMINATE	1	TRUE	0	0.578222450322276	1		168	271	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524125	187524126	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0045633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	82	323	0	ENST00000441802.2:c.11412_11413dup	p.Cys3805TyrfsTer29	p.C3805Yfs*29	ENST00000441802	NM_005245.3	3805	tgt/tATgt	20/27	0.249540403834594	2	FACETS	0.458	0.404	0.516	0.229	0.202	0.258	INDETERMINATE	1	TRUE	0	0.578222450322276	2		323	619	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109315728	109315728	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	72	292	0	ENST00000436639.2:c.1057C>G	p.Gln353Glu	p.Q353E	ENST00000436639	NM_014454.2	353	Cag/Gag	6/10	0.402068511904749	1	FACETS	0.377	0.33	0.428	0.377	0.33	0.428	SUBCLONAL	1	TRUE	0	0.578222450322276	1		292	469	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845334	151845334	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	239	264	0	ENST00000262189.6:c.13678C>T	p.Gln4560Ter	p.Q4560*	ENST00000262189	NM_170606.2	4560	Cag/Tag	52/59	0.236003860842626	3	FACETS	0.824	0.774	0.874	0.824	0.774	0.874	INDETERMINATE	2	TRUE	1	0.578222450322276	3		264	647	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974792	21974792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141798398	NA	P-0045634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	12	66	0	ENST00000304494.5:c.35C>T	p.Ser12Leu	p.S12L	ENST00000304494	NM_000077.4	12	tCg/tTg	1/3	0.658091430929999	3	FACETS	0.245	0.172	0.334	0.122	0.086	0.167	SUBCLONAL	1	TRUE	1	0.686618289799898	3		66	192	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027203	49027203	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0045634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	104	99	0	ENST00000267163.4:c.1770T>A	p.Cys590Ter	p.C590*	ENST00000267163	NM_000321.2	590	tgT/tgA	18/27	1	2	FACETS	0.907	0.841	0.971	1	0.99	1	CLONAL	2	TRUE	1	0.686618289799898	2		99	167	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805368	46805368	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	185	186	0	ENST00000290295.7:c.588G>T	p.Lys196Asn	p.K196N	ENST00000290295	NM_006361.5	196	aaG/aaT	1/2	1	2	FACETS	0.9	0.835	0.966	0.9	0.835	0.966	CLONAL	1	TRUE	1	0.686618289799898	2		186	599	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006669	62006669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045634-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	162	160	0	ENST00000392795.3:c.610C>A	p.Gln204Lys	p.Q204K	ENST00000392795	NM_001039933.1	204	Cag/Aag	6/6	0.686618289799898	3	FACETS	0.928	0.854	1	0.464	0.427	0.503	CLONAL	1	TRUE	1	0.686618289799898	3		160	683	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0045635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	20	273	2	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.791	0.605	1	0.791	0.605	1	CLONAL	1	TRUE	1	0.16	2		275	316	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141986	108141986	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660628	NA	P-0045635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	22	365	0	ENST00000278616.4:c.2930G>T	p.Cys977Phe	p.C977F	ENST00000278616	NM_000051.3	977	tGt/tTt	20/63	1	2	FACETS	0.643	0.497	0.812	0.643	0.497	0.812	SUBCLONAL	1	TRUE	1	0.16	2		365	428	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076754	72076754	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	30	446	0	ENST00000357731.5:c.743C>A	p.Ala248Glu	p.A248E	ENST00000357731	NM_173808.2	248	gCa/gAa	5/7	1	2	FACETS	0.688	0.553	0.842	0.688	0.553	0.842	SUBCLONAL	1	TRUE	1	0.16	2		446	545	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542258	187542258	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	18	337	0	ENST00000441802.2:c.5482G>C	p.Ala1828Pro	p.A1828P	ENST00000441802	NM_005245.3	1828	Gct/Cct	10/27	0.3	2	FACETS	0.645	0.485	0.834			1	SUBCLONAL	1	TRUE	NA	0.16	2		337	349	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398287	+	missense_variant	Missense_Mutation	ONP	CCAG	CCAG	TCAA	novel	NA	P-0045635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	44	322	0	ENST00000311936.3:c.32_35delinsTTGA	p.Ala11_Gly12delinsValAsp	p.A11_G12delinsVD	ENST00000311936	NM_004985.3	11	gCTGGt/gTTGAt	2/5	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.16	2		322	442	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0045636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	317	588	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.956	0.912	0.999	1	0.996	1	CLONAL	2	TRUE	1	0.566010308762982	2		588	586	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727451	66727451	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519729	NA	P-0045636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	161	431	0	ENST00000307102.5:c.167A>C	p.Gln56Pro	p.Q56P	ENST00000307102	NM_002755.3	56	cAg/cCg	2/11	0.566010308762982	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.566010308762982	1		431	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0045636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	222	595	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.566010308762982	1	FACETS	0.934	0.876	0.994	0.934	0.876	0.994	CLONAL	1	TRUE	0	0.566010308762982	1		595	602	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641221	93641221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	40	304	0	ENST00000375746.1:c.1567G>A	p.Glu523Lys	p.E523K	ENST00000375746	NM_001174167.1	523	Gaa/Aaa	11/14	0.566010308762982	1	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	0	0.566010308762982	1		304	100	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70412256	70412256	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0045636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	22	169	0	ENST00000373644.4:c.4368-2A>T		p.X1456_splice	ENST00000373644	NM_030625.2	1456			1	2	FACETS	0.883	0.701	1	0.883	0.701	1	CLONAL	1	TRUE	1	0.566010308762982	2		169	88	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999450	100999450	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	235	897	0	ENST00000325455.5:c.352C>A	p.Leu118Met	p.L118M	ENST00000325455	NM_001202474.3	118	Ctg/Atg	1/8	1	2	FACETS	0.938	0.877	1	0.938	0.877	1	CLONAL	1	TRUE	1	0.566010308762982	2		897	885	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443670	49443670	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs767521664	NA	P-0045636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	168	683	0	ENST00000301067.7:c.3701G>T	p.Gly1234Val	p.G1234V	ENST00000301067	NM_003482.3	1234	gGg/gTg	11/54	1	2	FACETS	0.836	0.77	0.904	0.836	0.77	0.904	CLONAL	1	TRUE	1	0.566010308762982	2		683	710	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220147	133220147	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0045636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	168	569	0	ENST00000320574.5:c.4291-1G>T		p.X1431_splice	ENST00000320574	NM_006231.2	1431			1	2	FACETS	0.918	0.847	0.991	0.918	0.847	0.991	CLONAL	1	TRUE	1	0.566010308762982	2		569	647	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754479	41754479	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	306	680	0	ENST00000301178.4:c.1598G>T	p.Arg533Leu	p.R533L	ENST00000301178	NM_021913.4	533	cGg/cTg	13/20	0.562931271677186	1	FACETS	0.743	0.701	0.786	0.743	0.701	0.786	SUBCLONAL	1	TRUE	0	0.566010308762982	1		680	1044	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023771	31023771	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	207	626	0	ENST00000375687.4:c.3256G>T	p.Glu1086Ter	p.E1086*	ENST00000375687	NM_015338.5	1086	Gag/Tag	13/13	1	2	FACETS	0.995	0.927	1	0.995	0.927	1	CLONAL	1	TRUE	1	0.566010308762982	2		626	735	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127281	55127282	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0045636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	54	380	0	ENST00000257290.5:c.69_70delinsAA	p.Cys23_Gln24delinsTer	p.C23_Q24delins*	ENST00000257290	NM_006206.4	23	tgCCag/tgAAag	3/23	1	2	FACETS	0.591	0.507	0.681	0.591	0.507	0.681	SUBCLONAL	1	TRUE	1	0.566010308762982	2		380	323	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278901	1278901	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	192	608	0	ENST00000310581.5:c.2141C>A	p.Thr714Lys	p.T714K	ENST00000310581	NM_198253.2	714	aCg/aAg	6/16	1	2	FACETS	0.827	0.766	0.89	0.827	0.766	0.89	CLONAL	1	TRUE	1	0.566010308762982	2		608	820	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38942465	38942465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	41	338	0	ENST00000357387.3:c.5068G>A	p.Glu1690Lys	p.E1690K	ENST00000357387	NM_152756.3	1690	Gag/Aag	38/38	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.566010308762982	2		338	140	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845471	128845471	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	191	664	0	ENST00000249373.3:c.768G>T	p.Trp256Cys	p.W256C	ENST00000249373	NM_005631.4	256	tgG/tgT	4/12	1	2	FACETS	0.811	0.751	0.873	0.811	0.751	0.873	CLONAL	1	TRUE	1	0.566010308762982	2		664	832	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939469	68939469	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	35	297	0	ENST00000288368.4:c.454C>T	p.Leu152Phe	p.L152F	ENST00000288368	NM_024870.2	152	Ctt/Ttt	5/40	1	2	FACETS	0.703	0.583	0.834	0.703	0.583	0.834	SUBCLONAL	1	TRUE	1	0.566010308762982	2		297	176	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117864337	117864337	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0045636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	73	292	0	ENST00000297338.2:c.1322-2A>T		p.X441_splice	ENST00000297338	NM_006265.2	441			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.566010308762982	2		292	233	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0045637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	177	752	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.40184204774158	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.40184204774158	1		752	513	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0045637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	42	225	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.40184204774158	2	FACETS	1	0.952	1	0.67	0.569	0.778	CLONAL	1	TRUE	0	0.40184204774158	2		225	156	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944264	81944264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1009796025	NA	P-0045637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	159	736	0	ENST00000359376.3:c.1873G>A	p.Ala625Thr	p.A625T	ENST00000359376	NM_002661.3	625	Gcc/Acc	18/33	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.40184204774158	2		736	603	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201833	66201833	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778795902	NA	P-0045637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	35	305	0	ENST00000273854.3:c.2669C>T	p.Ala890Val	p.A890V	ENST00000273854	NM_004439.5	890	gCg/gTg	16/18	0.280568760391207	0	FACETS	0.442	0.364	0.527			1	SUBCLONAL	1	TRUE	0	0.40184204774158	0		305	236	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441625	6441625	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	27	571	0	ENST00000356142.4:c.472T>G	p.Tyr158Asp	p.Y158D	ENST00000356142	NM_018890.3	158	Tat/Gat	6/7	0.196759581637928	1	FACETS	0.213	0.169	0.264	0.213	0.169	0.264	INDETERMINATE	1	TRUE	0	0.40184204774158	1		571	503	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8338970	8338970	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	77	382	0	ENST00000356435.5:c.5331C>A	p.Tyr1777Ter	p.Y1777*	ENST00000356435		1777	taC/taA	32/35	0.167786675594853	2	FACETS	1	0.962	1	0.604	0.535	0.677	INDETERMINATE	1	TRUE	0	0.40184204774158	2		382	317	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045143	47045143	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045637-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	15	308	0	ENST00000377604.3:c.2384A>G	p.His795Arg	p.H795R	ENST00000377604	NM_001204468.1	795	cAc/cGc	21/24	0.40184204774158	2	FACETS	0.256	0.186	0.339			1	SUBCLONAL	1	TRUE	NA	0.40184204774158	2		308	292	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0045638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	57	162	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.197678602153232	4	FACETS	1	0.872	1	0.668	0.581	0.76	INDETERMINATE	2	TRUE	1	0.373992924154229	4		162	209	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779811	135779811	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs118203621	NA	P-0045638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	11	261	0	ENST00000298552.3:c.2028G>A	p.Trp676Ter	p.W676*	ENST00000298552	NM_001162426.1	676	tgG/tgA	16/23	0.373992924154229	1	FACETS	0.276	0.191	0.382	0.276	0.191	0.382	SUBCLONAL	1	TRUE	0	0.373992924154229	1		261	173	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637537	52637538	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0045638-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	56	242	0	ENST00000394830.3:c.2778_2779del	p.Glu927SerfsTer2	p.E927Sfs*2	ENST00000394830	NM_018313.4	926	agAGaa/agaa	18/30	0.298427355440373	2	FACETS	0.814	0.709	0.924	0.814	0.709	0.924	CLONAL	2	TRUE	0	0.373992924154229	2		242	184	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215817	133215817	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	89	548	0	ENST00000320574.5:c.5446A>C	p.Asn1816His	p.N1816H	ENST00000320574	NM_006231.2	1816	Aac/Cac	40/49	1	2	FACETS	0.754	0.672	0.841	1	0.98	1	SUBCLONAL	2	TRUE	1	0.27	2		548	437	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593605	215593605	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045639-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	92	278	0	ENST00000260947.4:c.2129A>G	p.Asp710Gly	p.D710G	ENST00000260947	NM_000465.2	710	gAc/gGc	11/11	0.228994572723265	4	FACETS	0.993	0.887	1	0.662	0.591	0.736	CLONAL	2	TRUE	1	0.27	4		278	436	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916928	178916936	+	inframe_deletion	In_Frame_Del	DEL	AGGCAACCG	AGGCAACCG	-	novel	NA	P-0045640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	39	334	0	ENST00000263967.3:c.315_323del	p.Gly106_Arg108del	p.G106_R108del	ENST00000263967	NM_006218.2	105	gtAGGCAACCGt/gtt	2/21	1	2	FACETS	0.769	0.638	0.914	0.769	0.638	0.914	CLONAL	1	FALSE	1	0.256248284134199	2		334	396	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939848	49939848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750979879	NA	P-0045640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	61	681	1	ENST00000296474.3:c.1195G>A	p.Asp399Asn	p.D399N	ENST00000296474	NM_002447.2	399	Gac/Aac	1/20	1	2	FACETS	0.712	0.613	0.819	0.712	0.613	0.819	SUBCLONAL	1	FALSE	1	0.256248284134199	2		682	669	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467862	99467862	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	22	270	0	ENST00000268035.6:c.2731T>C	p.Ser911Pro	p.S911P	ENST00000268035	NM_000875.3	911	Tct/Cct	13/21	1	2	FACETS	0.538	0.417	0.679	0.538	0.417	0.679	SUBCLONAL	1	FALSE	1	0.256248284134199	2		270	319	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168750	56168751	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0045640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	26	353	0	ENST00000399503.3:c.1604_1605del	p.Gln535ArgfsTer5	p.Q535Rfs*5	ENST00000399503	NM_005921.1	535	cAA/c	9/20	1	2	FACETS	0.506	0.4	0.627	0.506	0.4	0.627	SUBCLONAL	1	FALSE	1	0.256248284134199	2		353	401	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180542	56180542	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	30	241	0	ENST00000399503.3:c.3871del	p.Leu1291Ter	p.L1291*	ENST00000399503	NM_005921.1	1291	Cta/ta	16/20	1	2	FACETS	0.933	0.755	1	0.933	0.755	1	CLONAL	1	FALSE	1	0.256248284134199	2		241	251	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836780	151836781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0045640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	31	341	0	ENST00000262189.6:c.14439dup	p.Glu4814ArgfsTer5	p.E4814Rfs*5	ENST00000262189	NM_170606.2	4813	-/A	56/59	1	2	FACETS	0.549	0.443	0.668	0.549	0.443	0.668	SUBCLONAL	1	FALSE	1	0.256248284134199	2		341	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0045641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	263	595	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.737378698956726	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	FALSE	0	0.737378698956726	2		595	323	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187141	38187141	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045641-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	210	718	0	ENST00000317025.8:c.1336G>C	p.Glu446Gln	p.E446Q	ENST00000317025	NM_023034.1	446	Gaa/Caa	6/24	0.737378698956726	7	FACETS	1	0.991	1			1	CLONAL	1	FALSE	NA	0.737378698956726	7		718	1107	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0045642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	35	217	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.710295474800652	1	FACETS	0.993	0.859	1	0.993	0.859	1	CLONAL	1	TRUE	0	0.710295474800652	1		217	64	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424075	49424075	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	168	696	0	ENST00000301067.7:c.13987del	p.Arg4663GlyfsTer3	p.R4663Gfs*3	ENST00000301067	NM_003482.3	4663	Agg/gg	42/54	0.171505048217903	4	FACETS	0.817	0.757	0.879	0.817	0.757	0.879	INDETERMINATE	2	TRUE	2	0.710295474800652	4		696	495	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527913	157527913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs551038862	NA	P-0045642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	114	484	0	ENST00000346085.5:c.5638G>A	p.Val1880Ile	p.V1880I	ENST00000346085	NM_020732.3	1880	Gtc/Atc	20/20	1	2	FACETS	0.917	0.835	1	0.917	0.835	1	CLONAL	1	TRUE	1	0.710295474800652	2		484	350	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459340	99459340	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs45451896	NA	P-0045643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	48	340	0	ENST00000268035.6:c.1976G>T	p.Arg659Leu	p.R659L	ENST00000268035	NM_000875.3	659	cGg/cTg	9/21	0.390759894571812	5	FACETS	0.629	0.532	0.737	0.21	0.177	0.246	SUBCLONAL	1	TRUE	2	0.453686444441345	5		340	565	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256162	41256162	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	88	440	0	ENST00000357654.3:c.418A>T	p.Ser140Cys	p.S140C	ENST00000357654	NM_007294.3	140	Agt/Tgt	6/23	0.352527189512637	2	FACETS	0.651	0.577	0.729	0.325	0.288	0.365	SUBCLONAL	1	TRUE	0	0.453686444441345	2		440	596	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46611785	46611785	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	93	561	0	ENST00000263734.3:c.2599G>T	p.Asp867Tyr	p.D867Y	ENST00000263734	NM_001430.4	867	Gac/Tac	16/16	0.453686444441345	5	FACETS	0.795	0.706	0.89	0.265	0.235	0.297	SUBCLONAL	1	TRUE	2	0.453686444441345	5		561	867	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629834	187629834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs376427037	NA	P-0045643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	76	546	0	ENST00000441802.2:c.1148A>G	p.Asn383Ser	p.N383S	ENST00000441802	NM_005245.3	383	aAc/aGc	2/27	0.453686444441345	5	FACETS	0.504	0.44	0.573			1	SUBCLONAL	1	TRUE	NA	0.453686444441345	5		546	1117	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157431632	157431635	+	frameshift_variant	Frame_Shift_Del	DEL	GGGA	GGGA	TCC	novel	NA	P-0045643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	64	414	2	ENST00000346085.5:c.2308_2311delinsTCC	p.Gly770SerfsTer12	p.G770Sfs*12	ENST00000346085	NM_020732.3	770	GGGAgc/TCCgc	7/20	0.343043889284558	3	FACETS	0.78	0.677	0.89	0.26	0.225	0.297	SUBCLONAL	1	TRUE	0	0.453686444441345	3		416	444	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0045644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	242	359	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.209414313106313	3	FACETS	0.919	0.866	0.973	0.919	0.866	0.973	INDETERMINATE	3	TRUE	0	0.360313842345493	3		359	575	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248621	10248621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	45	838	0	ENST00000340748.4:c.4132C>T	p.Arg1378Trp	p.R1378W	ENST00000340748		1378	Cgg/Tgg	35/40	0.298054956298525	2	FACETS	0.347	0.291	0.41	0.173	0.145	0.205	SUBCLONAL	1	TRUE	0	0.360313842345493	2		838	720	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579355	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519997	NA	P-0045644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	350	862	0	ENST00000269305.4:c.332T>C	p.Leu111Pro	p.L111P	ENST00000269305	NM_001126112.2	111	cTg/cCg	4/11	0.360313842345493	2	FACETS	0.995	0.945	1	0.995	0.945	1	CLONAL	2	TRUE	0	0.360313842345493	2		862	976	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138137	64138137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	321	842	0	ENST00000334205.4:c.2060C>T	p.Thr687Met	p.T687M	ENST00000334205	NM_003942.2	687	aCg/aTg	16/17	0.298054956298525	2	FACETS	0.982	0.93	1	0.982	0.93	1	CLONAL	2	TRUE	0	0.360313842345493	2		842	907	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075446	8075446	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0045644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	54	305	0	ENST00000377482.5:c.126-2A>G		p.X42_splice	ENST00000377482	NM_018948.3	42			0.257656670218074	3	FACETS	1	0.899	1	0.53	0.454	0.611	CLONAL	1	TRUE	1	0.360313842345493	3		305	334	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515270	31515270	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	116	690	0	ENST00000344624.3:c.1115G>A	p.Trp372Ter	p.W372*	ENST00000344624		372	tGg/tAg	5/33	0.178700956038688	4	FACETS	0.781	0.702	0.865	0.391	0.351	0.433	INDETERMINATE	1	TRUE	2	0.360313842345493	4		690	1121	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47004897	47004897	+	intron_variant	Intron	SNP	G	G	A	rs1251032975	NA	P-0045644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	293	739	0	ENST00000377604.3:c.-126+13G>A		p.*42*	ENST00000377604	NM_001204468.1	-/163			1	2	FACETS	0.857	0.808	0.907	1	0.995	1	CLONAL	2	TRUE	1	0.360313842345493	2		739	949	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242478	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAG	TTAAGAGAAG	C	rs727504278	NA	P-0045645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	75	246	0	ENST00000275493.2:c.2239_2248delinsC	p.Leu747_Ala750delinsPro	p.L747_A750delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGca/Cca	19/28	0.219260207068756	4	FACETS	1	0.957	1	0.605	0.531	0.685	CLONAL	1	TRUE	2	0.287425034706393	4		246	555	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821643	72821645	+	inframe_deletion	In_Frame_Del	DEL	CCG	CCG	-	rs762513291	NA	P-0045645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	10	69	0	ENST00000268489.5:c.10530_10532del	p.Gly3512del	p.G3512del	ENST00000268489	NM_006885.3	3510	ggCGGt/ggt	10/10	1	2	FACETS	0.557	0.379	0.778	0.557	0.379	0.778	SUBCLONAL	1	TRUE	1	0.287425034706393	2		69	125	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279579	18279579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1403656005	NA	P-0045645-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	43	428	0	ENST00000222254.8:c.1852G>A	p.Glu618Lys	p.E618K	ENST00000222254	NM_005027.3	618	Gag/Aag	15/16	1	2	FACETS	0.367	0.306	0.435	0.367	0.306	0.435	SUBCLONAL	1	TRUE	1	0.287425034706393	2		428	815	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061213	38061213	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045664-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	44	514	0	ENST00000250448.2:c.776A>C	p.Tyr259Ser	p.Y259S	ENST00000250448	NM_004496.3	259	tAc/tCc	2/2	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		514	426	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207120	1207120	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	354	718	1	ENST00000326873.7:c.208G>T	p.Glu70Ter	p.E70*	ENST00000326873	NM_000455.4	70	Gag/Tag	1/10	0.80078110581077	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	0	0.824978496923419	2		719	428	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729613	41729613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564878978	NA	P-0045665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	109	508	0	ENST00000242208.4:c.916C>T	p.Arg306Cys	p.R306C	ENST00000242208	NM_002192.2	306	Cgc/Tgc	3/3	0.824978496923419	3	FACETS	0.878	0.794	0.966	0.439	0.397	0.483	CLONAL	1	TRUE	1	0.824978496923419	3		508	425	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0045665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	129	369	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			0.814064824164211	3	FACETS	1	0.953	1	0.354	0.323	0.385	CLONAL	1	TRUE	0	0.824978496923419	3		369	416	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177093	56177093	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	144	187	0	ENST00000399503.3:c.2365del	p.Ile789SerfsTer10	p.I789Sfs*10	ENST00000399503	NM_005921.1	788	gAa/ga	13/20	0.824978496923419	5	FACETS	0.981	0.905	1	0.654	0.603	0.707	CLONAL	2	TRUE	2	0.824978496923419	5		187	398	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180633	56180635	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0045665-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	267	271	0	ENST00000399503.3:c.3964_3966del	p.Phe1322del	p.F1322del	ENST00000399503	NM_005921.1	1321	cTCTtc/ctc	16/20	0.824978496923419	5	FACETS	0.928	0.881	0.975	0.928	0.881	0.975	CLONAL	3	TRUE	2	0.824978496923419	5		271	520	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0045667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	192	1249	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.394744258361691	1	FACETS	0.747	0.692	0.803	0.747	0.692	0.803	SUBCLONAL	1	TRUE	0	0.492992445417346	1		1249	786	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456522	29456522	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs563120454	NA	P-0045667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	188	536	0	ENST00000389048.3:c.2396A>G	p.Asn799Ser	p.N799S	ENST00000389048	NM_004304.4	799	aAt/aGt	14/29	1	2	FACETS	0.947	0.877	1	0.947	0.877	1	CLONAL	1	TRUE	1	0.492992445417346	2		536	805	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035983	47035983	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	255	643	0	ENST00000377604.3:c.662del	p.Lys221SerfsTer45	p.K221Sfs*45	ENST00000377604	NM_001204468.1	221	Aag/ag	7/24	NA	2	FACETS	0.865	0.809	0.923			1	INDETERMINATE	1	TRUE	NA	0.492992445417346	2		643	1196	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085968	16085968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746256291	NA	P-0045668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	117	544	1	ENST00000281043.3:c.1144C>T	p.Arg382Cys	p.R382C	ENST00000281043	NM_005378.4	382	Cgt/Tgt	3/3	0.251094493900522	1	FACETS	0.533	0.481	0.587	0.533	0.481	0.587	INDETERMINATE	1	TRUE	0	0.492777865973538	1		545	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0045669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	338	556	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.859765984400437	2	FACETS	0.986	0.965	1	0.986	0.965	1	CLONAL	2	FALSE	0	0.919155711813575	2		556	373	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0045669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	132	361	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	0.739268303350018	5	FACETS	1	0.953	1	1	0.953	1	CLONAL	3	FALSE	2	0.919155711813575	5		361	222	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788671	3788671	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	103	311	0	ENST00000262367.5:c.4283del	p.Arg1428LeufsTer31	p.R1428Lfs*31	ENST00000262367	NM_004380.2	1428	cGt/ct	26/31	0.472732561149431	5	FACETS	1	0.978	1	0.819	0.75	0.888	INDETERMINATE	2	FALSE	2	0.919155711813575	5		311	217	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941844	44941853	+	frameshift_variant	Frame_Shift_Del	DEL	TCATAAAGAC	TCATAAAGAC	-	novel	NA	P-0045669-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2	87	163	0	ENST00000377967.4:c.3168_3177del	p.His1057ThrfsTer23	p.H1057Tfs*23	ENST00000377967	NM_021140.2	1056	caTCATAAAGAC/ca	21/29	0.919155711813575	2	FACETS	1	0.989	1			1	CLONAL	2	FALSE	NA	0.919155711813575	2		163	89	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0045670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	493	1249	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.42117619236768	5	FACETS	1	0.992	1			1	CLONAL	4	TRUE	NA	0.42117619236768	5		1249	872	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs11575997	NA	P-0045670-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	75	612	0	ENST00000269305.4:c.993+1G>T		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.344063616085549	1	FACETS	0.824	0.728	0.927	0.824	0.728	0.927	CLONAL	1	TRUE	0	0.42117619236768	1		612	341	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0045671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	49	436	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	0.600993825003491	2	FACETS	0.28	0.236	0.327	0.14	0.118	0.164	SUBCLONAL	1	TRUE	0	0.600993825003491	2		436	583	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0045671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	38	335	6	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	1	2	FACETS	0.341	0.282	0.406	0.341	0.282	0.406	SUBCLONAL	1	TRUE	1	0.600993825003491	2		341	371	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466022	69466022	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	313	886	0	ENST00000227507.2:c.860C>T	p.Pro287Leu	p.P287L	ENST00000227507	NM_053056.2	287	cCc/cTc	5/5	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.600993825003491	2		886	896	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517201	NA	P-0045671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	147	64	0	ENST00000263967.3:c.1637A>C	p.Gln546Pro	p.Q546P	ENST00000263967	NM_006218.2	546	cAg/cCg	10/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.600993825003491	2		64	392	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0045671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	291	477	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.600993825003491	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.600993825003491	2		477	420	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266107	41266107	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	59	303	0	ENST00000349496.5:c.104T>G	p.Ile35Ser	p.I35S	ENST00000349496	NM_001904.3	35	aTc/aGc	3/15	1	2	FACETS	0.535	0.462	0.613	0.535	0.462	0.613	SUBCLONAL	1	TRUE	1	0.600993825003491	2		303	367	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0045671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	210	743	6	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.885	0.823	0.948	0.885	0.823	0.948	CLONAL	1	TRUE	1	0.600993825003491	2		749	790	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023769	27023769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	25	337	0	ENST00000324856.7:c.879del	p.Thr294ProfsTer69	p.T294Pfs*69	ENST00000324856	NM_006015.4	292	aCc/ac	1/20	1	2	FACETS	0.204	0.16	0.254	0.204	0.16	0.254	SUBCLONAL	1	TRUE	1	0.600993825003491	2		337	408	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	107	432	3	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.828	0.748	0.912	0.828	0.748	0.912	CLONAL	1	TRUE	1	0.600993825003491	2		435	430	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991736	25991736	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs530632623	NA	P-0045671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	35	280	0	ENST00000435504.4:c.506C>T	p.Ala169Val	p.A169V	ENST00000435504		169	gCg/gTg	7/13	1	2	FACETS	0.355	0.292	0.426	0.355	0.292	0.426	SUBCLONAL	1	TRUE	1	0.600993825003491	2		280	328	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830902	72830903	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0045671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	131	521	0	ENST00000268489.5:c.5677_5678dup	p.Asp1894GlyfsTer21	p.D1894Gfs*21	ENST00000268489	NM_006885.3	1893	agg/agAGg	9/10	1	2	FACETS	0.744	0.677	0.813	0.744	0.677	0.813	SUBCLONAL	1	TRUE	1	0.600993825003491	2		521	586	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420204	49420204	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	57	695	0	ENST00000301067.7:c.15545del	p.Gly5182AlafsTer61	p.G5182Afs*61	ENST00000301067	NM_003482.3	5182	gGc/gc	48/54	1	2	FACETS	0.311	0.266	0.36	0.311	0.266	0.36	SUBCLONAL	1	TRUE	1	0.600993825003491	2		695	610	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277511	142277511	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1278516813	NA	P-0045671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	20	291	0	ENST00000350721.4:c.1840G>A	p.Ala614Thr	p.A614T	ENST00000350721	NM_001184.3	614	Gcc/Acc	8/47	1	2	FACETS	0.23	0.175	0.293	0.23	0.175	0.293	SUBCLONAL	1	TRUE	1	0.600993825003491	2		291	290	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847249	68847249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs556110297	NA	P-0045671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	33	415	1	ENST00000261769.5:c.1171G>A	p.Val391Ile	p.V391I	ENST00000261769	NM_004360.3	391	Gtc/Atc	9/16	1	2	FACETS	0.216	0.175	0.262	0.216	0.175	0.262	SUBCLONAL	1	TRUE	1	0.600993825003491	2		416	508	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67196492	67196492	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	54	493	0	ENST00000312629.5:c.118G>T	p.Glu40Ter	p.E40*	ENST00000312629	NM_003952.2	40	Gag/Tag	2/15	1	2	FACETS	0.356	0.304	0.413	0.356	0.304	0.413	SUBCLONAL	1	TRUE	1	0.600993825003491	2		493	505	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660541	67660560	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCTCATCCAGCATCAGAA	GCCCTCATCCAGCATCAGAA	-	novel	NA	P-0045671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	162	449	0	ENST00000264010.4:c.1442_1461del	p.Ala481ValfsTer5	p.A481Vfs*5	ENST00000264010	NM_006565.3	481	GCCCTCATCCAGCATCAGAAg/g	8/12	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.600993825003491	2		449	515	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745144	41745144	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	105	695	0	ENST00000301178.4:c.1210G>A	p.Val404Met	p.V404M	ENST00000301178	NM_021913.4	404	Gtg/Atg	9/20	1	2	FACETS	0.489	0.438	0.543	0.489	0.438	0.543	SUBCLONAL	1	TRUE	1	0.600993825003491	2		695	715	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181951	38181951	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	189	509	0	ENST00000396334.3:c.575T>A	p.Ile192Asn	p.I192N	ENST00000396334	NM_002468.4	192	aTc/aAc	3/5	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.600993825003491	2		509	536	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249483	153249483	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	66	431	0	ENST00000281708.4:c.1295A>G	p.Asn432Ser	p.N432S	ENST00000281708	NM_033632.3	432	aAc/aGc	9/12	1	2	FACETS	0.648	0.566	0.735	0.648	0.566	0.735	SUBCLONAL	1	TRUE	1	0.600993825003491	2		431	339	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637807	176637807	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	107	505	0	ENST00000439151.2:c.2411del	p.Pro804GlnfsTer3	p.P804Qfs*3	ENST00000439151	NM_022455.4	803	Ccc/cc	5/23	1	2	FACETS	0.852	0.77	0.938	0.852	0.77	0.938	CLONAL	1	TRUE	1	0.600993825003491	2		505	418	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016263	150016263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	26	391	0	ENST00000253339.5:c.443G>A	p.Arg148Gln	p.R148Q	ENST00000253339		148	cGa/cAa	2/7	1	2	FACETS	0.218	0.173	0.271	0.218	0.173	0.271	SUBCLONAL	1	TRUE	1	0.600993825003491	2		391	396	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953070	2953070	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	274	900	0	ENST00000396946.4:c.2870del	p.Asn957ThrfsTer108	p.N957Tfs*108	ENST00000396946	NM_032415.4	957	aAc/ac	22/25	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.600993825003491	2		900	805	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181765	56181765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1287268127	NA	P-0045672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	13	258	1	ENST00000399503.3:c.3989C>T	p.Ser1330Leu	p.S1330L	ENST00000399503	NM_005921.1	1330	tCg/tTg	17/20	1	2	FACETS	0.867	0.619	1	0.867	0.619	1	CLONAL	1	TRUE	1	0.15	2		259	200	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238951	5238951	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237159914	NA	P-0045672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	28	546	1	ENST00000357368.4:c.1828C>T	p.Arg610Trp	p.R610W	ENST00000357368	NM_002850.3	610	Cgg/Tgg	13/38	1	2	FACETS	0.759	0.605	0.934	0.759	0.605	0.934	CLONAL	1	TRUE	1	0.15	2		547	492	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101338	27101348	+	frameshift_variant	Frame_Shift_Del	DEL	CCACGAAGGCT	CCACGAAGGCT	-	novel	NA	P-0045672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	42	982	0	ENST00000324856.7:c.4621_4631del	p.His1541ValfsTer27	p.H1541Vfs*27	ENST00000324856	NM_006015.4	1540	aaCCACGAAGGCTcg/aacg	18/20	1	2	FACETS	0.777	0.647	0.922	0.777	0.647	0.922	CLONAL	1	TRUE	1	0.15	2		982	721	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579482	7579482	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	793	737	0	ENST00000269305.4:c.205del	p.Ala69LeufsTer54	p.A69Lfs*54	ENST00000269305	NM_001126112.2	69	Gct/ct	4/11	0.916909408627436	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.924172774866547	2		737	851	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61709603	61709616	+	frameshift_variant	Frame_Shift_Del	DEL	ATGATGTACTTATT	ATGATGTACTTATT	-	novel	NA	P-0045673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	117	228	0	ENST00000401558.2:c.2871_2884del	p.Lys957AsnfsTer8	p.K957Nfs*8	ENST00000401558	NM_003400.3	957	aaAATAAGTACATCATta/aata	23/25	0.901596175619584	3	FACETS	0.836	0.759	0.916	0.418	0.379	0.458	CLONAL	1	TRUE	1	0.924172774866547	3		228	443	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617465	158617465	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	209	415	0	ENST00000263640.3:c.1191T>A	p.Asp397Glu	p.D397E	ENST00000263640	NM_001105.4	397	gaT/gaA	9/11	1	2	FACETS	0.958	0.9	1	0.958	0.9	1	CLONAL	1	TRUE	1	0.924172774866547	2		415	472	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0045686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	140	1249	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.465029454852174	4	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	2	0.467024890055981	4		1249	436	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424114	49424114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370594537	NA	P-0045686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	158	675	0	ENST00000301067.7:c.13948G>A	p.Glu4650Lys	p.E4650K	ENST00000301067	NM_003482.3	4650	Gag/Aag	42/54	0.254210679644237	5	FACETS	1	0.967	1	0.725	0.669	0.783	INDETERMINATE	2	TRUE	2	0.467024890055981	5		675	529	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431339	49431339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	98	492	0	ENST00000301067.7:c.9800C>T	p.Ser3267Leu	p.S3267L	ENST00000301067	NM_003482.3	3267	tCa/tTa	34/54	0.254210679644237	5	FACETS	1	0.912	1	0.676	0.609	0.746	INDETERMINATE	2	TRUE	2	0.467024890055981	5		492	352	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858258	9858258	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	123	339	0	ENST00000330684.3:c.3143G>T	p.Ser1048Ile	p.S1048I	ENST00000330684	NM_001134407.1	1048	aGc/aTc	13/13	0.467024890055981	6	FACETS	0.875	0.799	0.954	0.656	0.599	0.715	CLONAL	3	TRUE	2	0.467024890055981	6		339	388	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832607	72832607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	54	205	0	ENST00000268489.5:c.3974C>T	p.Ser1325Leu	p.S1325L	ENST00000268489	NM_006885.3	1325	tCa/tTa	9/10	0.254210679644237	5	FACETS	0.959	0.831	1	0.639	0.554	0.73	INDETERMINATE	2	TRUE	2	0.467024890055981	5		205	205	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579425	7579425	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	173	692	1	ENST00000269305.4:c.262del	p.Ala88ProfsTer35	p.A88Pfs*35	ENST00000269305	NM_001126112.2	88	Gcc/cc	4/11	0.458042171653595	2	FACETS	0.901	0.84	0.964	0.901	0.84	0.964	CLONAL	2	TRUE	0	0.467024890055981	2		693	411	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272328	15272328	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	251	948	0	ENST00000263388.2:c.6111C>G	p.His2037Gln	p.H2037Q	ENST00000263388	NM_000435.2	2037	caC/caG	33/33	0.388575675250292	4	FACETS	0.951	0.898	1	0.951	0.898	1	CLONAL	3	TRUE	1	0.467024890055981	4		948	553	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367984	15367984	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	193	529	0	ENST00000263377.2:c.1342G>C	p.Asp448His	p.D448H	ENST00000263377	NM_058243.2	448	Gat/Cat	8/20	0.388575675250292	4	FACETS	0.851	0.795	0.907	0.851	0.795	0.907	CLONAL	3	TRUE	1	0.467024890055981	4		529	475	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182631	38182631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	76	246	0	ENST00000396334.3:c.784C>T	p.Gln262Ter	p.Q262*	ENST00000396334	NM_002468.4	262	Cag/Tag	5/5	0.379167548402256	3	FACETS	0.904	0.807	1	0.603	0.538	0.67	CLONAL	2	TRUE	0	0.467024890055981	3		246	222	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0045686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	106	286	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	0.379167548402256	3	FACETS	1	0.979	1	0.826	0.757	0.895	CLONAL	2	TRUE	0	0.467024890055981	3		286	226	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142949964	142949964	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	33	333	0	ENST00000262992.4:c.2746G>C	p.Glu916Gln	p.E916Q	ENST00000262992	NM_001101669.1	916	Gag/Cag	24/24	0.448152346378347	4	FACETS	1	0.927	1	0.632	0.521	0.753	CLONAL	1	TRUE	2	0.467024890055981	4		333	164	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79965934	79965934	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	41	229	0	ENST00000265081.6:c.598C>G	p.Leu200Val	p.L200V	ENST00000265081	NM_002439.4	200	Ctc/Gtc	4/24	0.458042171653595	2	FACETS	0.887	0.764	1	0.887	0.764	1	CLONAL	2	TRUE	0	0.467024890055981	2		229	99	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032069	26032069	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	60	390	0	ENST00000244661.2:c.220G>C	p.Glu74Gln	p.E74Q	ENST00000244661	NM_003537.3	74	Gaa/Caa	1/1	0.467024890055981	8	FACETS	1	0.877	1	0.204	0.175	0.235	CLONAL	1	TRUE	3	0.467024890055981	8		390	605	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910349	29910349	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	434	832	0	ENST00000376809.5:c.19C>T	p.Arg7Ter	p.R7*	ENST00000376809	NM_002116.7	7	Cga/Tga	1/8	0.467024890055981	7	FACETS	1	0.991	1	0.888	0.852	0.925	CLONAL	4	TRUE	2	0.467024890055981	7		832	907	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639929	93639929	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	25	228	0	ENST00000375746.1:c.1258G>C	p.Glu420Gln	p.E420Q	ENST00000375746	NM_001174167.1	420	Gaa/Caa	10/14	0.435819985862611	2	FACETS	0.714	0.569	0.876	0.357	0.284	0.438	SUBCLONAL	1	TRUE	0	0.467024890055981	2		228	150	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504167	123504167	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	12	216	0	ENST00000371139.4:c.343A>C	p.Thr115Pro	p.T115P	ENST00000371139	NM_001114937.2	115	Aca/Cca	3/4	0.43849259011463	5	FACETS	0.533	0.375	0.725	0.178	0.125	0.242	SUBCLONAL	1	TRUE	2	0.467024890055981	5		216	164	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0045687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	988	591	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.3	13	FACETS	1	0.981	1			1	CLONAL	15	TRUE	NA	0.16	13		591	1541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0045687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	40	625	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			1	2	FACETS	0.896	0.744	1	0.896	0.744	1	CLONAL	1	TRUE	1	0.16	2		625	558	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473698	67473698	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	55	585	0	ENST00000327367.4:c.778T>A	p.Phe260Ile	p.F260I	ENST00000327367	NM_005902.3	260	Ttc/Atc	6/9	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.16	2		585	487	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781200	161781200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766915327	NA	P-0045687-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	31	542	0	ENST00000366898.1:c.1205G>A	p.Arg402His	p.R402H	ENST00000366898	NM_004562.2	402	cGt/cAt	11/12	1	2	FACETS	0.703	0.568	0.858	0.703	0.568	0.858	SUBCLONAL	1	TRUE	1	0.16	2		542	551	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	63	425	0				ENST00000310581	NM_198253.2	-/1132			0.544425120348937	1	FACETS	0.957	0.845	1	0.957	0.845	1	CLONAL	1	TRUE	0	0.544425120348937	1		425	176	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561547	9561547	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	165	370	0	ENST00000353224.5:c.235G>A	p.Glu79Lys	p.E79K	ENST00000353224	NM_177990.2	79	Gaa/Aaa	4/10	0.132112268055934	6	FACETS	1	0.983	1	0.812	0.751	0.874	INDETERMINATE	2	TRUE	3	0.544425120348937	6		370	520	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913351	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	129	296	0	ENST00000288602.6:c.1397G>C	p.Gly466Ala	p.G466A	ENST00000288602	NM_004333.4	466	gGa/gCa	11/18	0.454219859643342	4	FACETS	0.946	0.866	1	0.946	0.866	1	CLONAL	2	TRUE	2	0.544425120348937	4		296	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	364	635	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	0.544425120348937	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.544425120348937	2		635	607	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421568	32421568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267602851	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	283	481	1	ENST00000332351.3:c.1024G>A	p.Asp342Asn	p.D342N	ENST00000332351	NM_024426.4	342	Gat/Aat	6/10	0.192000350721733	4	FACETS	1	0.986	1	1	0.986	1	INDETERMINATE	2	TRUE	2	0.544425120348937	4		482	712	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	212	488	0	ENST00000304494.5:c.262G>A	p.Glu88Lys	p.E88K	ENST00000304494	NM_000077.4	88	Gag/Aag	2/3	0.147038090156828	5	FACETS	1	0.975	1	0.726	0.677	0.775	INDETERMINATE	2	TRUE	2	0.544425120348937	5		488	650	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913250	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	184	252	0	ENST00000369535.4:c.34G>T	p.Gly12Cys	p.G12C	ENST00000369535	NM_002524.4	12	Ggt/Tgt	2/7	0.544425120348937	3	FACETS	0.973	0.908	1	0.973	0.908	1	CLONAL	2	TRUE	1	0.544425120348937	3		252	442	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468230	50468230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	277	599	0	ENST00000331340.3:c.1465C>T	p.Pro489Ser	p.P489S	ENST00000331340	NM_006060.4	489	Cct/Tct	8/8	0.454219859643342	4	FACETS	0.894	0.842	0.947	0.894	0.842	0.947	CLONAL	2	TRUE	2	0.544425120348937	4		599	879	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426722	212426722	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	34	415	0	ENST00000342788.4:c.2393T>G	p.Leu798Arg	p.L798R	ENST00000342788	NM_005235.2	798	cTt/cGt	20/28	0.236122274259678	5	FACETS	0.374	0.304	0.452	0.125	0.101	0.151	INDETERMINATE	1	TRUE	2	0.544425120348937	5		415	607	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012441	29012441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55974987	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	109	424	0	ENST00000282397.4:c.430G>A	p.Glu144Lys	p.E144K	ENST00000282397	NM_002019.4	144	Gaa/Aaa	4/30	0.151715202999281	2	FACETS	1	0.982	1	0.67	0.61	0.731	INDETERMINATE	1	TRUE	0	0.544425120348937	2		424	299	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857436	9857436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	176	353	0	ENST00000330684.3:c.3965G>A	p.Gly1322Glu	p.G1322E	ENST00000330684	NM_001134407.1	1322	gGa/gAa	13/13	0.132112268055934	6	FACETS	0.893	0.83	0.958	0.893	0.83	0.958	INDETERMINATE	3	TRUE	3	0.544425120348937	6		353	504	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274352	5274352	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	147	376	0	ENST00000357368.4:c.95C>T	p.Pro32Leu	p.P32L	ENST00000357368	NM_002850.3	32	cCc/cTc	3/38	0.544425120348937	3	FACETS	1	0.985	1	0.667	0.613	0.723	CLONAL	1	TRUE	1	0.544425120348937	3		376	515	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609951	43609951	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377767410	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	188	748	2	ENST00000355710.3:c.1903C>T	p.Arg635Cys	p.R635C	ENST00000355710	NM_020975.4	635	Cgc/Tgc	11/20	0.544425120348937	3	FACETS	1	0.93	1	0.503	0.465	0.542	CLONAL	1	TRUE	1	0.544425120348937	3		750	874	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422151	81422151	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	305	473	1	ENST00000298171.2:c.127G>A	p.Asp43Asn	p.D43N	ENST00000298171	NM_000369.2	43	Gat/Aat	1/10	0.192000350721733	4	FACETS	0.873	0.829	0.916	1	0.993	1	INDETERMINATE	3	TRUE	2	0.544425120348937	4		474	661	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841835	151841835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	118	234	0	ENST00000262189.6:c.14306G>A	p.Trp4769Ter	p.W4769*	ENST00000262189	NM_170606.2	4769	tGg/tAg	55/59	0.454219859643342	4	FACETS	0.888	0.809	0.969	0.888	0.809	0.969	CLONAL	2	TRUE	2	0.544425120348937	4		234	377	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391917	139391917	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	455	988	1	ENST00000277541.6:c.6274C>T	p.His2092Tyr	p.H2092Y	ENST00000277541	NM_017617.3	2092	Cat/Tat	34/34	0.147038090156828	5	FACETS	0.86	0.822	0.898	0.86	0.822	0.898	INDETERMINATE	3	TRUE	2	0.544425120348937	5		989	1177	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535353	187535353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747181352	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	137	339	0	ENST00000441802.2:c.9221C>T	p.Pro3074Leu	p.P3074L	ENST00000441802	NM_005245.3	3074	cCa/cTa	12/27	0.454219859643342	4	FACETS	0.816	0.748	0.887	0.816	0.748	0.887	CLONAL	2	TRUE	2	0.544425120348937	4		339	476	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913867	32913867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	68	257	0	ENST00000380152.3:c.5375C>T	p.Ser1792Phe	p.S1792F	ENST00000380152		1792	tCc/tTc	11/27	0.151715202999281	2	FACETS	1	0.955	1	0.584	0.516	0.654	INDETERMINATE	1	TRUE	0	0.544425120348937	2		257	214	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202696	16202697	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	63	271	0	ENST00000375759.3:c.405-1_405delinsAA		p.X135_splice	ENST00000375759	NM_015001.2	135		3/15	0.544425120348937	3	FACETS	0.956	0.833	1	0.478	0.416	0.544	CLONAL	1	TRUE	1	0.544425120348937	3		271	308	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843493	156843493	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	267	591	1	ENST00000524377.1:c.919G>T	p.Gly307Trp	p.G307W	ENST00000524377	NM_002529.3	307	Ggg/Tgg	8/17	0.236122274259678	5	FACETS	1	0.984	1	0.75	0.706	0.795	INDETERMINATE	2	TRUE	2	0.544425120348937	5		592	792	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022774	12022774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1471948383	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	187	460	0	ENST00000396373.4:c.880G>A	p.Glu294Lys	p.E294K	ENST00000396373	NM_001987.4	294	Gag/Aag	5/8	0.454219859643342	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.544425120348937	4		460	498	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032267	10032267	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	35	451	0	ENST00000330684.3:c.556T>G	p.Phe186Val	p.F186V	ENST00000330684	NM_001134407.1	186	Ttc/Gtc	3/13	0.132112268055934	6	FACETS	0.388	0.316	0.468	0.129	0.105	0.156	INDETERMINATE	1	TRUE	3	0.544425120348937	6		451	693	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663463	29663463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	143	325	0	ENST00000356175.3:c.6056C>T	p.Ser2019Phe	p.S2019F	ENST00000356175	NM_000267.3	2019	tCt/tTt	40/57	0.544425120348937	2	FACETS	0.867	0.805	0.929	0.867	0.805	0.929	CLONAL	2	TRUE	0	0.544425120348937	2		325	303	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945424	17945424	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	111	560	0	ENST00000458235.1:c.2306C>T	p.Ser769Phe	p.S769F	ENST00000458235	NM_000215.3	769	tCc/tTc	17/24	0.544425120348937	3	FACETS	0.79	0.711	0.873	0.395	0.355	0.437	SUBCLONAL	1	TRUE	1	0.544425120348937	3		560	657	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439730	220439730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144941390	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	454	897	0	ENST00000243786.2:c.583G>A	p.Val195Met	p.V195M	ENST00000243786	NM_002191.3	195	Gtg/Atg	2/2	0.236122274259678	5	FACETS	1	0.993	1	0.79	0.755	0.826	INDETERMINATE	2	TRUE	2	0.544425120348937	5		897	1278	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540059	187540059	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1560939856	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	141	321	0	ENST00000441802.2:c.7681G>A	p.Glu2561Lys	p.E2561K	ENST00000441802	NM_005245.3	2561	Gag/Aag	10/27	0.454219859643342	4	FACETS	0.907	0.833	0.983	0.907	0.833	0.983	CLONAL	2	TRUE	2	0.544425120348937	4		321	441	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821569	32821569	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1485432101	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	366	836	1	ENST00000354258.4:c.25G>A	p.Gly9Arg	p.G9R	ENST00000354258	NM_000593.5	9	Gga/Aga	1/11	0.544425120348937	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.544425120348937	2		837	668	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985483	2985483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	193	387	0	ENST00000396946.4:c.328G>A	p.Glu110Lys	p.E110K	ENST00000396946	NM_032415.4	110	Gag/Aag	4/25	0.454219859643342	4	FACETS	0.903	0.841	0.968	0.903	0.841	0.968	CLONAL	2	TRUE	2	0.544425120348937	4		387	606	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346625	81346625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	106	189	0	ENST00000222390.5:c.1328C>T	p.Pro443Leu	p.P443L	ENST00000222390	NM_000601.4	443	cCa/cTa	11/18	0.454219859643342	4	FACETS	0.89	0.806	0.976	0.89	0.806	0.976	CLONAL	2	TRUE	2	0.544425120348937	4		189	338	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508707	106508707	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	269	449	0	ENST00000359195.3:c.701A>C	p.Lys234Thr	p.K234T	ENST00000359195	NM_002649.2	234	aAg/aCg	2/11	0.454219859643342	4	FACETS	0.983	0.926	1	0.983	0.926	1	CLONAL	2	TRUE	2	0.544425120348937	4		449	776	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950485	68950485	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	274	275	2	ENST00000288368.4:c.797T>A	p.Phe266Tyr	p.F266Y	ENST00000288368	NM_024870.2	266	tTt/tAt	7/40	0.544425120348937	6	FACETS	0.927	0.879	0.975	0.927	0.879	0.975	CLONAL	4	TRUE	2	0.544425120348937	6		277	567	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5022160	5022160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	121	408	0	ENST00000381652.3:c.173C>T	p.Pro58Leu	p.P58L	ENST00000381652	NM_004972.3	58	cCa/cTa	3/25	0.147038090156828	5	FACETS	1	0.941	1	0.694	0.633	0.757	INDETERMINATE	2	TRUE	2	0.544425120348937	5		408	388	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485920	8485921	+	missense_variant	Missense_Mutation	DNP	AG	AG	CA	novel	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	83	308	0	ENST00000356435.5:c.2896_2897delinsTG	p.Leu966Cys	p.L966C	ENST00000356435		966	CTc/TGc	17/35	0.147038090156828	5	FACETS	0.829	0.738	0.925	0.553	0.492	0.617	INDETERMINATE	2	TRUE	2	0.544425120348937	5		308	334	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518064	8518064	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	106	376	0	ENST00000356435.5:c.1327G>A	p.Glu443Lys	p.E443K	ENST00000356435		443	Gag/Aag	10/35	0.147038090156828	5	FACETS	0.956	0.865	1	0.637	0.576	0.7	INDETERMINATE	2	TRUE	2	0.544425120348937	5		376	370	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27203090	27203090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	130	384	0	ENST00000380036.4:c.2182G>A	p.Glu728Lys	p.E728K	ENST00000380036	NM_000459.3	728	Gaa/Aaa	13/23	0.147038090156828	5	FACETS	0.868	0.792	0.947	0.578	0.528	0.631	INDETERMINATE	2	TRUE	2	0.544425120348937	5		384	500	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399241	139399242	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0045688-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	395	766	2	ENST00000277541.6:c.4901_4902delinsTT	p.Ala1634Val	p.A1634V	ENST00000277541	NM_017617.3	1634	gCC/gTT	26/34	0.147038090156828	5	FACETS	0.878	0.837	0.919	0.878	0.837	0.919	INDETERMINATE	3	TRUE	2	0.544425120348937	5		768	1001	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0045689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	319	763	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.493078255848736	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.524565993409585	2		765	596	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469925	25469925	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	93	576	0	ENST00000264709.3:c.1117C>G	p.Leu373Val	p.L373V	ENST00000264709	NM_175629.2	373	Ctg/Gtg	9/23	0.493078255848736	2	FACETS	0.742	0.662	0.826	0.371	0.331	0.413	SUBCLONAL	1	TRUE	0	0.524565993409585	2		576	478	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158400	26158400	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs140899305	NA	P-0045689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	113	628	0	ENST00000289316.2:c.3G>A	p.Met1?	p.M1?	ENST00000289316	NM_138720.2	1	atG/atA	1/2	0.17967285308133	3	FACETS	0.846	0.762	0.934	0.423	0.381	0.467	INDETERMINATE	1	TRUE	1	0.524565993409585	3		628	643	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352367	143352367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	198	381	0	ENST00000262992.4:c.46C>T	p.Leu16Phe	p.L16F	ENST00000262992	NM_001101669.1	16	Ctt/Ttt	2/24	0.524565993409585	2	FACETS	1	0.99	1	0.686	0.64	0.733	CLONAL	1	TRUE	0	0.524565993409585	2		381	550	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934051	39934051	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045689-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	46	644	1	ENST00000378444.4:c.548G>T	p.Gly183Val	p.G183V	ENST00000378444	NM_001123385.1	183	gGt/gTt	4/15	0.221760734832338	3	FACETS	0.338	0.284	0.398			1	INDETERMINATE	1	TRUE	NA	0.524565993409585	3		645	655	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968251	134968251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373797543	NA	P-0045690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	99	646	0	ENST00000398015.3:c.2764G>A	p.Ala922Thr	p.A922T	ENST00000398015	NM_004441.4	922	Gcc/Acc	15/16	0.3	1	FACETS	0.862	0.774	0.954	0.862	0.774	0.954	CLONAL	1	TRUE	0	0.42	1		646	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0045692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	108	556	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.107986145072424	3	FACETS	1	0.942	1			1	INDETERMINATE	2	TRUE	NA	0.208256283086159	3		556	538	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0045692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	46	615	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	1	2	FACETS	0.792	0.666	0.93	0.792	0.666	0.93	CLONAL	1	TRUE	1	0.208256283086159	2		615	558	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920465	50920465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779208942	NA	P-0045692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	69	764	0	ENST00000440232.2:c.3157C>T	p.Arg1053Cys	p.R1053C	ENST00000440232	NM_002691.3	1053	Cgc/Tgc	26/27	1	2	FACETS	0.958	0.833	1	0.958	0.833	1	CLONAL	1	TRUE	1	0.208256283086159	2		764	692	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829715	76829715	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	19	231	0	ENST00000373344.5:c.6326G>A	p.Arg2109Lys	p.R2109K	ENST00000373344	NM_000489.3	2109	aGa/aAa	28/35	0.15642545098545	4	FACETS	0.82	0.623	1	0.41	0.311	0.526	CLONAL	1	TRUE	2	0.208256283086159	4		231	269	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589591	67589599	+	inframe_deletion	In_Frame_Del	DEL	TATAACACT	TATAACACT	-	novel	NA	P-0045692-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	10	53	0	ENST00000274335.5:c.1354_1362del	p.Tyr452_Thr454del	p.Y452_T454del	ENST00000274335		452	TATAACACT/-	10/15	0.15642545098545	4	FACETS	0.829	0.571	1	0.829	0.571	1	CLONAL	2	TRUE	2	0.208256283086159	4		53	70	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	59	425	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.842	0.731	0.961	0.842	0.731	0.961	CLONAL	1	TRUE	1	0.498791882603198	2		425	281	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247328	153247328	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	64	237	1	ENST00000281708.4:c.1474C>T	p.Gln492Ter	p.Q492*	ENST00000281708	NM_033632.3	492	Cag/Tag	10/12	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.498791882603198	2		238	246	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	75	322	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	0.708	0.623	0.798	0.708	0.623	0.798	SUBCLONAL	1	TRUE	1	0.498791882603198	2		322	425	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519757	NA	P-0045693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	49	134	0	ENST00000274335.5:c.1126G>C	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Cga	9/15	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.498791882603198	2		134	163	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046482	69046482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	44	369	0	ENST00000288368.4:c.3955C>T	p.His1319Tyr	p.H1319Y	ENST00000288368	NM_024870.2	1319	Cac/Tac	32/40	1	2	FACETS	0.366	0.307	0.432	0.366	0.307	0.432	SUBCLONAL	1	TRUE	1	0.498791882603198	2		369	482	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	47	341	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.315	0.266	0.369	0.315	0.266	0.369	SUBCLONAL	1	TRUE	1	0.683616266542816	2		341	436	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0045696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	81	427	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.414345145418379	2	FACETS	0.931	0.836	1	0.931	0.836	1	CLONAL	2	TRUE	0	0.414345145418379	2		427	210	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0045696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	162	460	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.414345145418379	5	FACETS	0.981	0.909	1	0.981	0.909	1	CLONAL	3	TRUE	2	0.414345145418379	5		460	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0045696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	231	954	2	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.414345145418379	2	FACETS	0.971	0.913	1	0.971	0.913	1	CLONAL	2	TRUE	0	0.414345145418379	2		956	574	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631301	117631301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199882276	NA	P-0045696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	59	359	0	ENST00000368508.3:c.6377G>A	p.Arg2126Gln	p.R2126Q	ENST00000368508	NM_002944.2	2126	cGg/cAg	40/43	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.414345145418379	2		359	232	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936089	71936089	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	15	124	0	ENST00000298229.2:c.61T>C	p.Trp21Arg	p.W21R	ENST00000298229	NM_001567.3	21	Tgg/Cgg	1/28	0.383039120163564	3	FACETS	0.802	0.593	1	0.401	0.296	0.523	CLONAL	1	TRUE	1	0.414345145418379	3		124	109	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178603	32178603	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201560532	NA	P-0045696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	73	783	0	ENST00000375023.3:c.2791G>A	p.Val931Met	p.V931M	ENST00000375023	NM_004557.3	931	Gtg/Atg	18/30	0.414345145418379	4	FACETS	0.828	0.724	0.939	0.276	0.241	0.313	CLONAL	1	TRUE	1	0.414345145418379	4		783	602	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334990	81334990	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	349	334	0	ENST00000222390.5:c.1837A>T	p.Ser613Cys	p.S613C	ENST00000222390	NM_000601.4	613	Agt/Tgt	16/18	0.414345145418379	12	FACETS	1	0.985	1			1	CLONAL	9	TRUE	NA	0.414345145418379	12		334	547	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907019	101907019	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	39	177	0	ENST00000374994.4:c.979C>G	p.Pro327Ala	p.P327A	ENST00000374994	NM_004612.2	327	Cca/Gca	6/9	0.383707980604514	4	FACETS	0.893	0.754	1	0.893	0.754	1	CLONAL	2	TRUE	2	0.414345145418379	4		177	149	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	96	425	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.891	0.805	0.979	0.891	0.805	0.979	CLONAL	1	TRUE	1	0.772418649199827	2		425	279	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0045697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	429	623	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.664262996862691	2	FACETS	0.966	0.937	0.994	0.966	0.937	0.994	CLONAL	2	TRUE	0	0.772418649199827	2		623	575	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0045697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	181	399	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.843	0.783	0.905	0.843	0.783	0.905	CLONAL	1	TRUE	1	0.772418649199827	2		399	556	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0045697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	83	171	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	0.926	0.831	1	0.926	0.831	1	CLONAL	1	TRUE	1	0.772418649199827	2		171	232	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983120	201983121	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	143	565	0	ENST00000359651.3:c.970dup	p.Met324AsnfsTer147	p.M324Nfs*147	ENST00000359651		323	-/A	7/8	1	2	FACETS	0.807	0.741	0.874	0.807	0.741	0.874	CLONAL	1	TRUE	1	0.772418649199827	2		565	459	SUCCESS
APC	324	MSKCC	GRCh37	5	112176017	112176017	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554086134	NA	P-0045697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	76	167	0	ENST00000257430.4:c.4726G>T	p.Glu1576Ter	p.E1576*	ENST00000257430	NM_000038.5	1576	Gaa/Taa	16/16	0.69898982281777	1	FACETS	0.875	0.795	0.954	0.875	0.795	0.954	CLONAL	1	TRUE	0	0.772418649199827	1		167	138	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624301	89624302	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0045697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	136	451	0	ENST00000371953.3:c.75_76insC	p.Thr26HisfsTer18	p.T26Hfs*18	ENST00000371953	NM_000314.4	25	-/C	1/9	0.762405617229099	1	FACETS	0.706	0.653	0.76	0.706	0.653	0.76	SUBCLONAL	1	TRUE	0	0.772418649199827	1		451	306	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611411	28611412	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	89	202	0	ENST00000241453.7:c.1219dup	p.Cys407LeufsTer4	p.C407Lfs*4	ENST00000241453	NM_004119.2	407	tgc/tTgc	10/24	1	2	FACETS	0.743	0.666	0.824	0.743	0.666	0.824	SUBCLONAL	1	TRUE	1	0.772418649199827	2		202	310	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627804	37627805	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	185	549	0	ENST00000447079.4:c.1720dup	p.Ser574LysfsTer67	p.S574Kfs*67	ENST00000447079	NM_015083.1	573	-/A	2/14	1	2	FACETS	0.797	0.74	0.856	0.797	0.74	0.856	SUBCLONAL	1	TRUE	1	0.772418649199827	2		549	601	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021693	69021693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	133	380	0	ENST00000288368.4:c.2981C>T	p.Thr994Ile	p.T994I	ENST00000288368	NM_024870.2	994	aCc/aTc	25/40	1	2	FACETS	0.808	0.741	0.878	0.808	0.741	0.878	CLONAL	1	TRUE	1	0.772418649199827	2		380	426	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412139	63412142	+	frameshift_variant	Frame_Shift_Del	DEL	CTGT	CTGT	-	novel	NA	P-0045697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	256	694	0	ENST00000330258.3:c.1025_1028del	p.Asp342AlafsTer21	p.D342Afs*21	ENST00000330258	NM_152424.3	342	gACAGc/gc	2/2	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.772418649199827	2		694	641	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	119	425	0				ENST00000310581	NM_198253.2	-/1132			0.179985535583281	2	FACETS	1	0.931	1	1	0.986	1	CLONAL	3	FALSE	0	0.179985535583281	2		425	429	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286758	212286758	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	16	234	0	ENST00000342788.4:c.2938G>C	p.Asp980His	p.D980H	ENST00000342788	NM_005235.2	980	Gac/Cac	24/28	0.179985535583281	3	FACETS	0.941	0.697	1	0.47	0.348	0.615	CLONAL	1	FALSE	1	0.179985535583281	3		234	206	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191540	10191540	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	102	437	0	ENST00000256474.2:c.533del	p.Leu178ArgfsTer24	p.L178Rfs*24	ENST00000256474	NM_000551.3	178	cTg/cg	3/3	0.179985535583281	3	FACETS	1	0.933	1	1	0.933	1	CLONAL	2	FALSE	1	0.179985535583281	3		437	586	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441264	52441264	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	133	525	0	ENST00000460680.1:c.506A>C	p.His169Pro	p.H169P	ENST00000460680	NM_004656.3	169	cAc/cCc	7/17	0.179985535583281	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	FALSE	1	0.179985535583281	3		525	687	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52621419	52621419	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0045698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	60	232	0	ENST00000394830.3:c.2998A>T	p.Lys1000Ter	p.K1000*	ENST00000394830	NM_018313.4	1000	Aaa/Taa	20/30	0.179985535583281	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	FALSE	1	0.179985535583281	3		232	297	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391485	139391485	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457252057	NA	P-0045698-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	184	995	0	ENST00000277541.6:c.6706G>A	p.Gly2236Arg	p.G2236R	ENST00000277541	NM_017617.3	2236	Ggg/Agg	34/34	0.179985535583281	2	FACETS	0.911	0.84	0.985	0.911	0.84	0.985	CLONAL	2	FALSE	0	0.179985535583281	2		995	1122	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878143	48878144	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0045699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	86	106	0	ENST00000267163.4:c.98dup	p.Glu34ArgfsTer15	p.E34Rfs*15	ENST00000267163	NM_000321.2	32	gac/gaCc	1/27	0.727484337290673	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.809408866761388	1		106	116	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727168	40727168	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs761148007	NA	P-0045699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	154	496	0	ENST00000373198.4:c.3796G>C	p.Val1266Leu	p.V1266L	ENST00000373198	NM_133170.3	1266	Gtg/Ctg	28/32	1	2	FACETS	0.877	0.81	0.945	0.877	0.81	0.945	CLONAL	1	TRUE	1	0.809408866761388	2		496	434	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090744	5090744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045699-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	54	140	0	ENST00000381652.3:c.2892G>A	p.Met964Ile	p.M964I	ENST00000381652	NM_004972.3	964	atG/atA	22/25	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.809408866761388	2		140	128	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	132	737	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.96	0.878	1	0.96	0.878	1	CLONAL	1	TRUE	1	0.61	2		742	451	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288735	11288735	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	117	419	0	ENST00000361445.4:c.3020C>T	p.Ala1007Val	p.A1007V	ENST00000361445	NM_004958.3	1007	gCc/gTc	19/58	1	2	FACETS	0.981	0.893	1	0.981	0.893	1	CLONAL	1	TRUE	1	0.61	2		419	391	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088659	27088659	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	172	452	0	ENST00000324856.7:c.2272del	p.Gln758ArgfsTer75	p.Q758Rfs*75	ENST00000324856	NM_006015.4	756	aaC/aa	7/20	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.61	2		452	551	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101612	27101612	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	177	883	3	ENST00000324856.7:c.4899del	p.Met1634Ter	p.M1634*	ENST00000324856	NM_006015.4	1632	Ccc/cc	18/20	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.61	2		886	575	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100430	8100430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770601456	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	161	661	0	ENST00000346208.3:c.404C>T	p.Pro135Leu	p.P135L	ENST00000346208		135	cCg/cTg	3/6	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.61	2		661	515	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717720	89717720	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	104	294	0	ENST00000371953.3:c.745del	p.Val249CysfsTer7	p.V249Cfs*7	ENST00000371953	NM_000314.4	249	Gtg/tg	7/9	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.61	2		294	306	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	78	373	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.61	2		373	242	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	99	457	1	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.61	2		458	288	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392850	118392850	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	84	321	0	ENST00000534358.1:c.11882A>G	p.Asn3961Ser	p.N3961S	ENST00000534358	NM_005933.3	3961	aAc/aGc	36/36	1	2	FACETS	0.97	0.867	1	0.97	0.867	1	CLONAL	1	TRUE	1	0.61	2		321	284	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416994	416994	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	109	285	0	ENST00000399788.2:c.3556A>G	p.Asn1186Asp	p.N1186D	ENST00000399788	NM_001042603.1	1186	Aac/Gac	23/28	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.61	2		285	316	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444809	49444809	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	162	729	0	ENST00000301067.7:c.2657del	p.Pro886LeufsTer44	p.P886Lfs*44	ENST00000301067	NM_003482.3	886	cCt/ct	10/54	1	2	FACETS	0.927	0.855	1	0.927	0.855	1	CLONAL	1	TRUE	1	0.61	2		729	573	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	109	767	3	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.703	0.634	0.776	0.703	0.634	0.776	SUBCLONAL	1	TRUE	1	0.61	2		770	508	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445883	49445883	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	251	772	0	ENST00000301067.7:c.1583del	p.Pro528HisfsTer402	p.P528Hfs*402	ENST00000301067	NM_003482.3	528	cCa/ca	10/54	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.61	2		772	768	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874011	123874013	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs780061449	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	13	29	0	ENST00000330479.4:c.62_64del	p.Ala21del	p.A21del	ENST00000330479	NM_020382.3	14	gaGGCg/gag	2/9	1	2	FACETS	0.789	0.607	0.974	1	0.908	1	CLONAL	2	TRUE	1	0.61	2		29	27	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989044	41989044	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	64	323	2	ENST00000219905.7:c.1840del	p.Arg614GlufsTer7	p.R614Efs*7	ENST00000219905	NM_001164273.1	612	ggA/gg	3/24	1	2	FACETS	0.538	0.468	0.614	0.538	0.468	0.614	SUBCLONAL	1	TRUE	1	0.61	2		325	390	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	73	568	1	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.73	0.643	0.821	0.73	0.643	0.821	SUBCLONAL	1	TRUE	1	0.61	2		569	328	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007824	45007825	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	83	262	0	ENST00000558401.1:c.276dup	p.Thr93HisfsTer2	p.T93Hfs*2	ENST00000558401	NM_004048.2	91	acc/aCcc	2/4	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.61	2		262	271	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	82	443	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.815	0.725	0.909	0.815	0.725	0.909	CLONAL	1	TRUE	1	0.61	2		443	330	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687471	37687472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs760014508	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	79	298	0	ENST00000447079.4:c.4382dup	p.Thr1463AsnfsTer50	p.T1463Nfs*50	ENST00000447079	NM_015083.1	1459	tgg/tGgg	14/14	1	2	FACETS	0.912	0.811	1	0.912	0.811	1	CLONAL	1	TRUE	1	0.61	2		298	284	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475061	40475063	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	139	483	0	ENST00000264657.5:c.1847_1849del	p.Glu616del	p.E616del	ENST00000264657	NM_139276.2	616	gAAGga/gga	20/24	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.61	2		483	445	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435313	56435313	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	129	497	0	ENST00000407977.2:c.1824del	p.Arg609GlyfsTer91	p.R609Gfs*91	ENST00000407977		608	ggG/gg	9/10	1	2	FACETS	0.97	0.887	1	0.97	0.887	1	CLONAL	1	TRUE	1	0.61	2		497	436	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492791	56492792	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	152	413	0	ENST00000407977.2:c.147_148del	p.Arg49SerfsTer25	p.R49Sfs*25	ENST00000407977		49	agAGtg/agtg	2/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.61	2		413	421	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533905	63533905	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	84	403	0	ENST00000307078.5:c.1249del	p.Ala417ArgfsTer41	p.A417Rfs*41	ENST00000307078	NM_004655.3	417	Gcg/cg	6/11	1	2	FACETS	0.924	0.825	1	0.924	0.825	1	CLONAL	1	TRUE	1	0.61	2		403	298	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554437	63554438	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	128	457	0	ENST00000307078.5:c.301_302del	p.Arg101GlyfsTer39	p.R101Gfs*39	ENST00000307078	NM_004655.3	101	AGg/g	2/11	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.61	2		457	413	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966753	18966753	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	178	631	0	ENST00000262803.5:c.1564C>A	p.Pro522Thr	p.P522T	ENST00000262803	NM_002911.3	522	Ccg/Acg	12/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.61	2		631	483	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228594	36228594	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs35021476	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	515	644	0	ENST00000222270.7:c.7612del	p.Ala2538ProfsTer76	p.A2538Pfs*76	ENST00000222270	NM_014727.1	2536	gaG/ga	34/37	0.605549942951673	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	1	0.61	4		644	900	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919765	50919765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371628260	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	565	692	2	ENST00000440232.2:c.2933G>A	p.Arg978His	p.R978H	ENST00000440232	NM_002691.3	978	cGt/cAt	23/27	0.605549942951673	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	1	0.61	4		694	951	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085674	16085674	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	124	417	0	ENST00000281043.3:c.850A>T	p.Lys284Ter	p.K284*	ENST00000281043	NM_005378.4	284	Aag/Tag	3/3	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.61	2		417	376	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467064	25467064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759818409	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	137	585	1	ENST00000264709.3:c.1811G>A	p.Arg604Gln	p.R604Q	ENST00000264709	NM_175629.2	604	cGg/cAg	15/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.61	2		586	385	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873263	136873263	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	82	242	0	ENST00000241393.3:c.235C>T	p.His79Tyr	p.H79Y	ENST00000241393	NM_003467.2	79	Cac/Tac	2/2	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.61	2		242	260	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266209	198266209	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	76	283	0	ENST00000335508.6:c.2411A>C	p.Asn804Thr	p.N804T	ENST00000335508	NM_012433.2	804	aAc/aCc	17/25	1	2	FACETS	0.659	0.582	0.742	0.659	0.582	0.742	SUBCLONAL	1	TRUE	1	0.61	2		283	378	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735457	40735457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775419119	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	135	500	0	ENST00000373198.4:c.3416G>A	p.Arg1139Gln	p.R1139Q	ENST00000373198	NM_133170.3	1139	cGg/cAg	25/32	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.61	2		500	411	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478757	57478757	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	90	272	0	ENST00000371085.3:c.348del	p.Val117TrpfsTer16	p.V117Wfs*16	ENST00000371085	NM_000516.4	115	Ccc/cc	5/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.61	2		272	255	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176351	24176351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1387467529	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	159	644	0	ENST00000263121.7:c.1142C>T	p.Thr381Met	p.T381M	ENST00000263121	NM_003073.3	381	aCg/aTg	9/9	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.61	2		644	489	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566525	41566525	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	62	244	0	ENST00000263253.7:c.4408del	p.Met1470CysfsTer26	p.M1470Cfs*26	ENST00000263253	NM_001429.3	1468	Aaa/aa	27/31	1	2	FACETS	0.899	0.788	1	0.899	0.788	1	CLONAL	1	TRUE	1	0.61	2		244	226	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089123	37089125	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs63751247	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	89	294	0	ENST00000231790.2:c.1852_1854del	p.Lys618del	p.K618del	ENST00000231790	NM_000249.3	615	ctGAAg/ctg	16/19	1	2	FACETS	0.89	0.797	0.987	0.89	0.797	0.987	CLONAL	1	TRUE	1	0.61	2		294	328	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	147	500	1	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.996	0.916	1	0.996	0.916	1	CLONAL	1	TRUE	1	0.61	2		501	484	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594212	55594212	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	101	297	0	ENST00000288135.5:c.1915T>A	p.Ser639Thr	p.S639T	ENST00000288135	NM_000222.2	639	Tct/Act	13/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.61	2		297	269	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557909	187557909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564430066	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	140	359	0	ENST00000441802.2:c.3802C>T	p.Arg1268Trp	p.R1268W	ENST00000441802	NM_005245.3	1268	Cgg/Tgg	5/27	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.61	2		359	361	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	138	606	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.943	0.864	1	0.943	0.864	1	CLONAL	1	TRUE	1	0.61	2		610	480	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	123	892	7	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	0.605549942951673	2	FACETS	0.838	0.763	0.917			1	CLONAL	1	TRUE	NA	0.61	2		899	481	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045990	26045990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	88	303	0	ENST00000540144.1:c.352G>A	p.Val118Ile	p.V118I	ENST00000540144	NM_003531.2	118	Gtc/Atc	1/1	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.61	2		303	231	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37141841	37141841	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	129	351	0	ENST00000373509.5:c.916A>C	p.Ser306Arg	p.S306R	ENST00000373509	NM_002648.3	306	Agc/Cgc	6/6	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.61	2		351	360	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017495	112017495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	88	225	0	ENST00000368678.4:c.1018G>A	p.Glu340Lys	p.E340K	ENST00000368678		340	Gag/Aag	9/13	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.61	2		225	267	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983228	149983228	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	109	459	0	ENST00000253339.5:c.3030del	p.Phe1010LeufsTer10	p.F1010Lfs*10	ENST00000253339		1010	ttT/tt	7/7	1	2	FACETS	0.831	0.751	0.914	0.831	0.751	0.914	CLONAL	1	TRUE	1	0.61	2		459	430	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265479	152265479	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766779326	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	89	352	0	ENST00000206249.3:c.932C>T	p.Thr311Met	p.T311M	ENST00000206249	NM_000125.3	311	aCg/aTg	4/8	1	2	FACETS	0.986	0.885	1	0.986	0.885	1	CLONAL	1	TRUE	1	0.61	2		352	296	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012386	152012386	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	75	229	0	ENST00000262189.6:c.427del	p.Ser143ValfsTer3	p.S143Vfs*3	ENST00000262189	NM_170606.2	143	Agt/gt	4/59	1	2	FACETS	0.98	0.87	1	0.98	0.87	1	CLONAL	1	TRUE	1	0.61	2		229	251	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066767	5066768	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	49	178	0	ENST00000381652.3:c.1310dup	p.Leu437PhefsTer12	p.L437Ffs*12	ENST00000381652	NM_004972.3	435	tat/taTt	10/25	0.605549942951673	1	FACETS	0.642	0.553	0.736	0.642	0.553	0.736	SUBCLONAL	1	TRUE	0	0.61	1		178	174	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904875	101904875	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	73	209	0	ENST00000374994.4:c.867del	p.Phe289LeufsTer4	p.F289Lfs*4	ENST00000374994	NM_004612.2	288	cTt/ct	5/9	1	2	FACETS	0.965	0.856	1	0.965	0.856	1	CLONAL	1	TRUE	1	0.61	2		209	248	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417580	139417580	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	212	803	0	ENST00000277541.6:c.464G>C	p.Cys155Ser	p.C155S	ENST00000277541	NM_017617.3	155	tGc/tCc	4/34	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.61	2		803	601	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317421	1317421	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs377299533	NA	P-0045713-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	140	372	1	ENST00000400841.2:c.644G>A	p.Arg215Gln	p.R215Q	ENST00000400841		215	cGg/cAg	5/6	1	1	FACETS	0.792	0.728	0.856	0.792	0.728	0.856	SUBCLONAL	1	TRUE	0	0.61	1		373	403	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600446	10600446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	236	694	0	ENST00000171111.5:c.1409G>A	p.Arg470His	p.R470H	ENST00000171111	NM_203500.1	470	cGt/cAt	4/6	0.128191219243968	6	FACETS	0.87	0.815	0.926	0.87	0.815	0.926	INDETERMINATE	3	TRUE	3	0.474143022215638	6		694	743	SUCCESS
APC	324	MSKCC	GRCh37	5	112173815	112173815	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1561577701	NA	P-0045718-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	50	275	0	ENST00000257430.4:c.2524G>A	p.Asp842Asn	p.D842N	ENST00000257430	NM_000038.5	842	Gat/Aat	16/16	0.474143022215638	3	FACETS	1	0.916	1	0.55	0.472	0.635	CLONAL	1	TRUE	1	0.474143022215638	3		275	237	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0045720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	96	241	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.879	0.794	0.967	0.879	0.794	0.967	CLONAL	1	TRUE	1	0.777265798257855	2		241	281	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0045720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	243	517	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	1	2	FACETS	0.953	0.896	1	0.953	0.896	1	CLONAL	1	TRUE	1	0.777265798257855	2		517	656	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0045720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	173	517	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	1	2	FACETS	0.708	0.654	0.763	0.708	0.654	0.763	SUBCLONAL	1	TRUE	1	0.777265798257855	2		517	629	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939888	76939888	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0045720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	266	412	0	ENST00000373344.5:c.860T>G	p.Leu287Ter	p.L287*	ENST00000373344	NM_000489.3	287	tTa/tGa	9/35	0.777265798257855	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.777265798257855	1		412	407	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940498	29940498	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045720-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	111	331	0	ENST00000389048.3:c.733C>G	p.Leu245Val	p.L245V	ENST00000389048	NM_004304.4	245	Ctc/Gtc	2/29	1	2	FACETS	0.719	0.652	0.789	0.719	0.652	0.789	SUBCLONAL	1	TRUE	1	0.777265798257855	2		331	397	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0045721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	54	609	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.466521135726185	3	FACETS	0.339	0.289	0.395	0.17	0.144	0.198	SUBCLONAL	1	TRUE	1	0.466521135726185	3		609	841	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0045721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	171	294	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.466521135726185	2	FACETS	0.907	0.845	0.97	0.907	0.845	0.97	CLONAL	2	TRUE	0	0.466521135726185	2		294	404	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882019	NA	P-0045721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	230	661	2	ENST00000269305.4:c.455dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	ccg/ccCg	5/11	0.466521135726185	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.466521135726185	1		663	713	SUCCESS
APC	324	MSKCC	GRCh37	5	112175171	112175171	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085373	NA	P-0045721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	31	126	0	ENST00000257430.4:c.3880C>T	p.Gln1294Ter	p.Q1294*	ENST00000257430	NM_000038.5	1294	Cag/Tag	16/16	0.17804346572812	2	FACETS	0.751	0.614	0.903	0.375	0.307	0.452	INDETERMINATE	1	TRUE	0	0.466521135726185	2		126	177	SUCCESS
APC	324	MSKCC	GRCh37	5	112175419	112175419	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0045721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	80	204	3	ENST00000257430.4:c.4128T>A	p.Tyr1376Ter	p.Y1376*	ENST00000257430	NM_000038.5	1376	taT/taA	16/16	0.17804346572812	2	FACETS	1	0.978	1	0.721	0.644	0.8	INDETERMINATE	1	TRUE	0	0.466521135726185	2		207	238	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743762	46743762	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	216	517	7	ENST00000371975.4:c.2052T>G	p.Cys684Trp	p.C684W	ENST00000371975	NM_003579.3	684	tgT/tgG	18/18	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.466521135726185	2		524	751	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170941	99170941	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1337794979	NA	P-0045721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	70	420	6	ENST00000074304.5:c.1570G>A	p.Glu524Lys	p.E524K	ENST00000074304	NM_001134224.1	524	Gag/Aag	16/26	1	2	FACETS	0.531	0.463	0.604	0.531	0.463	0.604	SUBCLONAL	1	TRUE	1	0.466521135726185	2		426	565	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0045723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	41	316	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.789	0.656	0.938	0.789	0.656	0.938	CLONAL	1	TRUE	1	0.17	2		316	611	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0045723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	36	423	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	1	2	FACETS	0.799	0.656	0.96	0.799	0.656	0.96	CLONAL	1	TRUE	1	0.17	2		423	530	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0045723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	41	711	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	1	0.17	2		711	473	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715721	30715721	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs104893816	NA	P-0045723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	32	259	1	ENST00000295754.5:c.1379G>T	p.Arg460Leu	p.R460L	ENST00000295754	NM_003242.5	460	cGc/cTc	5/7	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.17	2		260	309	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0045724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	302	623	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.451787312149973	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.457960657308612	2		623	565	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251991	8251991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760736132	NA	P-0045724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	164	672	1	ENST00000335790.3:c.86G>A	p.Arg29His	p.R29H	ENST00000335790	NM_002315.2	29	cGc/cAc	2/4	0.257868308696886	2	FACETS	0.783	0.718	0.85	0.391	0.359	0.425	INDETERMINATE	1	TRUE	0	0.457960657308612	2		673	915	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859626	57859626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202128734	NA	P-0045724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	106	492	0	ENST00000228682.2:c.680G>A	p.Arg227His	p.R227H	ENST00000228682	NM_005269.2	227	cGt/cAt	7/12	0.457960657308612	3	FACETS	0.988	0.888	1	0.494	0.444	0.547	CLONAL	1	TRUE	1	0.457960657308612	3		492	576	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394444	162394444	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	91	234	0	ENST00000366898.1:c.624T>G	p.Phe208Leu	p.F208L	ENST00000366898	NM_004562.2	208	ttT/ttG	6/12	0.377255678767087	3	FACETS	0.961	0.867	1	0.961	0.867	1	CLONAL	2	TRUE	1	0.457960657308612	3		234	254	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119966	70120018	+	frameshift_variant	Frame_Shift_Del	DEL	GCACCGCGGCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAG	GCACCGCGGCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAG	-	novel	NA	P-0045724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	40	323	0	ENST00000245479.2:c.970_1022del	p.Thr324AlafsTer236	p.T324Afs*236	ENST00000245479	NM_000346.3	323	aGCACCGCGGCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAG/a	3/3	1	2	FACETS	0.719	0.602	0.847	0.719	0.602	0.847	SUBCLONAL	1	TRUE	1	0.457960657308612	2		323	243	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681031	37681031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143648695	NA	P-0045724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	69	355	0	ENST00000447079.4:c.3200G>A	p.Arg1067Gln	p.R1067Q	ENST00000447079	NM_015083.1	1067	cGa/cAa	12/14	1	2	FACETS	0.969	0.851	1	0.969	0.851	1	CLONAL	1	TRUE	1	0.457960657308612	2		355	311	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979271	40979271	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1431106649	NA	P-0045724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	86	410	0	ENST00000373198.4:c.1862T>C	p.Val621Ala	p.V621A	ENST00000373198	NM_133170.3	621	gTc/gCc	11/32	0.103829977730896	6	FACETS	1	0.978	1	0.491	0.435	0.549	INDETERMINATE	1	TRUE	3	0.457960657308612	6		410	489	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46271105	46271105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	131	353	0	ENST00000371998.3:c.3229G>A	p.Gly1077Ser	p.G1077S	ENST00000371998		1077	Ggc/Agc	17/23	0.103829977730896	6	FACETS	0.834	0.763	0.908	0.834	0.763	0.908	INDETERMINATE	3	TRUE	3	0.457960657308612	6		353	438	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0045725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1400	39	294	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.529547277051326	14	FACETS	0.428	0.352	0.512	0.031	0.025	0.037	SUBCLONAL	1	TRUE	0	0.529547277051326	14		294	1439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0045725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	579	465	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.459802784402008	4	FACETS	0.929	0.901	0.957	0.929	0.901	0.957	CLONAL	4	TRUE	0	0.529547277051326	4		465	900	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519920	NA	P-0045725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	79	215	0	ENST00000397062.3:c.85G>C	p.Asp29His	p.D29H	ENST00000397062	NM_006164.4	29	Gat/Cat	2/5	0.401172571954334	4	FACETS	1	0.953	1	0.578	0.511	0.649	CLONAL	1	TRUE	2	0.529547277051326	4		215	395	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046357	69046357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	59	379	0	ENST00000288368.4:c.3830C>T	p.Ala1277Val	p.A1277V	ENST00000288368	NM_024870.2	1277	gCc/gTc	32/40	0.401172571954334	4	FACETS	0.52	0.447	0.6	0.26	0.223	0.3	SUBCLONAL	1	TRUE	2	0.529547277051326	4		379	655	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916505	39916505	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1228402564	NA	P-0045725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	360	653	1	ENST00000378444.4:c.4498G>A	p.Ala1500Thr	p.A1500T	ENST00000378444	NM_001123385.1	1500	Gcc/Acc	11/15	0.466765972544724	2	FACETS	0.9	0.86	0.941	0.9	0.86	0.941	CLONAL	2	TRUE	0	0.529547277051326	2		654	755	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193202184	193202184	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	89	264	0	ENST00000367435.3:c.1216C>T	p.Gln406Ter	p.Q406*	ENST00000367435	NM_024529.4	406	Caa/Taa	14/17	0.177058121272468	6	FACETS	0.834	0.744	0.929	0.556	0.496	0.62	INDETERMINATE	2	TRUE	3	0.529547277051326	6		264	415	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450134	32450145	+	inframe_deletion	In_Frame_Del	DEL	GGGCGTCCCGTC	GGGCGTCCCGTC	-	novel	NA	P-0045725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	72	585	0	ENST00000332351.3:c.667_678del	p.Asp223_Pro226del	p.D223_P226del	ENST00000332351	NM_024426.4	223	GACGGGACGCCC/-	2/10	0.465238735466156	2	FACETS	0.435	0.38	0.495	0.218	0.19	0.248	SUBCLONAL	1	TRUE	0	0.529547277051326	2		585	625	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443985	49443985	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	309	641	0	ENST00000301067.7:c.3386A>T	p.Asp1129Val	p.D1129V	ENST00000301067	NM_003482.3	1129	gAt/gTt	11/54	0.401172571954334	4	FACETS	0.871	0.822	0.92	0.871	0.822	0.92	CLONAL	2	TRUE	2	0.529547277051326	4		641	1025	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913540	32913540	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587782738	NA	P-0045725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	182	307	0	ENST00000380152.3:c.5048A>T	p.Gln1683Leu	p.Q1683L	ENST00000380152		1683	cAg/cTg	11/27	0.466765972544724	2	FACETS	0.907	0.849	0.964	0.907	0.849	0.964	CLONAL	2	TRUE	0	0.529547277051326	2		307	379	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647038	23647038	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778309339	NA	P-0045725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	358	547	0	ENST00000261584.4:c.829G>T	p.Asp277Tyr	p.D277Y	ENST00000261584	NM_024675.3	277	Gac/Tac	4/13	0.445022182270849	3	FACETS	1	0.993	1	0.81	0.774	0.845	CLONAL	2	TRUE	0	0.529547277051326	3		547	704	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676220	29676220	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1555536030	NA	P-0045725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	278	259	0	ENST00000356175.3:c.7211del	p.Asn2404IlefsTer7	p.N2404Ifs*7	ENST00000356175	NM_000267.3	2403	agA/ag	48/57	0.459802784402008	4	FACETS	0.879	0.839	0.918	0.879	0.839	0.918	CLONAL	4	TRUE	0	0.529547277051326	4		259	457	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761171	59761171	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	96	437	1	ENST00000259008.2:c.3236T>G	p.Ile1079Ser	p.I1079S	ENST00000259008	NM_032043.2	1079	aTt/aGt	20/20	0.459802784402008	4	FACETS	0.688	0.612	0.769	0.172	0.153	0.193	SUBCLONAL	1	TRUE	0	0.529547277051326	4		438	806	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021662	31021662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	229	388	0	ENST00000375687.4:c.1661G>T	p.Ser554Ile	p.S554I	ENST00000375687	NM_015338.5	554	aGt/aTt	12/13	0.371318497552369	6	FACETS	0.955	0.891	1	0.478	0.445	0.511	CLONAL	2	TRUE	2	0.529547277051326	6		388	932	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480475	89480475	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	126	214	0	ENST00000336596.2:c.2312T>C	p.Leu771Pro	p.L771P	ENST00000336596	NM_005233.5	771	cTg/cCg	13/17	0.529547277051326	5	FACETS	0.792	0.72	0.867			1	SUBCLONAL	2	TRUE	NA	0.529547277051326	5		214	539	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293677	1293677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780427764	NA	P-0045725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2466	464	862	0	ENST00000310581.5:c.1324G>A	p.Asp442Asn	p.D442N	ENST00000310581	NM_198253.2	442	Gac/Aac	2/16	0.529547277051326	9	FACETS	0.853	0.811	0.897	0.244	0.231	0.257	CLONAL	2	TRUE	2	0.529547277051326	9		862	2930	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528525	157528525	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	144	460	0	ENST00000346085.5:c.6250G>C	p.Glu2084Gln	p.E2084Q	ENST00000346085	NM_020732.3	2084	Gag/Cag	20/20	0.445022182270849	3	FACETS	0.95	0.868	1	0.317	0.289	0.346	CLONAL	1	TRUE	0	0.529547277051326	3		460	724	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22008835	22008835	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	252	530	2	ENST00000276925.6:c.118C>A	p.Pro40Thr	p.P40T	ENST00000276925	NM_004936.3	40	Ccc/Acc	1/2	0.466765972544724	2	FACETS	1	0.988	1	0.609	0.571	0.647	CLONAL	1	TRUE	0	0.529547277051326	2		532	782	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950061	44950061	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs770933595	NA	P-0045725-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	62	339	0	ENST00000377967.4:c.3830T>C	p.Met1277Thr	p.M1277T	ENST00000377967	NM_021140.2	1277	aTg/aCg	26/29	0.466765972544724	2	FACETS	0.584	0.506	0.668	0.292	0.253	0.334	SUBCLONAL	1	TRUE	0	0.529547277051326	2		339	401	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0045728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	32	294	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.232219356794065	5	FACETS	0.911	0.746	1	0.607	0.497	0.73	CLONAL	2	TRUE	2	0.24	5		294	199	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0045728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	100	564	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.232219356794065	5	FACETS	1	0.919	1	0.687	0.615	0.763	CLONAL	2	TRUE	2	0.24	5		564	550	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411411	63411411	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	102	703	1	ENST00000330258.3:c.1756C>T	p.Arg586Ter	p.R586*	ENST00000330258	NM_152424.3	586	Cga/Tga	2/2	0.278314473328832	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.24	2		704	384	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736510	85736511	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs387906351	NA	P-0045728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	21	197	2	ENST00000370580.1:c.136dup	p.Ile46AsnfsTer4	p.I46Nfs*4	ENST00000370580	NM_003921.4	46	ata/aAta	2/3	0.270728941892824	3	FACETS	1	0.863	1	0.583	0.452	0.734	CLONAL	1	TRUE	1	0.24	3		199	168	SUCCESS
APC	324	MSKCC	GRCh37	5	112175754	112175754	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0045728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	26	230	0	ENST00000257430.4:c.4463T>A	p.Leu1488Ter	p.L1488*	ENST00000257430	NM_000038.5	1488	tTa/tAa	16/16	0.232219356794065	5	FACETS	0.944	0.756	1	0.63	0.504	0.77	CLONAL	2	TRUE	2	0.24	5		230	156	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293760	1293760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1471089239	NA	P-0045728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	79	1024	0	ENST00000310581.5:c.1241C>T	p.Pro414Leu	p.P414L	ENST00000310581	NM_198253.2	414	cCg/cTg	2/16	1	2	FACETS	0.94	0.827	1	0.94	0.827	1	CLONAL	1	TRUE	1	0.24	2		1024	700	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26970440	26970441	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	12	34	0	ENST00000381527.3:c.815dup	p.Met273AspfsTer3	p.M273Dfs*3	ENST00000381527	NM_001260.1	270	ata/atAa	8/13	0.199783395968077	5	FACETS	0.925	0.671	1	0.925	0.671	1	CLONAL	3	TRUE	2	0.24	5		34	49	SUCCESS
APC	324	MSKCC	GRCh37	5	112174979	112174979	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs863225344	NA	P-0045728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	17	170	0	ENST00000257430.4:c.3688C>T	p.Gln1230Ter	p.Q1230*	ENST00000257430	NM_000038.5	1230	Cag/Tag	16/16	0.232219356794065	5	FACETS	1	0.902	1	0.498	0.375	0.641	CLONAL	1	TRUE	2	0.24	5		170	129	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579702	7579703	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	66	489	0	ENST00000269305.4:c.93dup	p.Leu32SerfsTer11	p.L32Sfs*11	ENST00000269305	NM_001126112.2	31	-/T	3/11	0.139329606216494	3	FACETS	0.83	0.724	0.943	0.553	0.483	0.629	INDETERMINATE	2	TRUE	0	0.24	3		489	371	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662055	227662055	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	33	599	0	ENST00000305123.5:c.1400G>T	p.Cys467Phe	p.C467F	ENST00000305123	NM_005544.2	467	tGc/tTc	1/2	0.270728941892824	3	FACETS	0.587	0.477	0.711	0.293	0.238	0.356	SUBCLONAL	1	TRUE	1	0.24	3		599	525	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356317	66356317	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	19	309	0	ENST00000273854.3:c.1180G>T	p.Ala394Ser	p.A394S	ENST00000273854	NM_004439.5	394	Gca/Tca	5/18	0.3	1	FACETS	0.608	0.463	0.779	0.608	0.463	0.779	SUBCLONAL	1	TRUE	0	0.24	1		309	229	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178304	56178304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	22	212	0	ENST00000399503.3:c.3277G>A	p.Asp1093Asn	p.D1093N	ENST00000399503	NM_005921.1	1093	Gac/Aac	14/20	0.232219356794065	5	FACETS	1	0.885	1	0.411	0.32	0.516	CLONAL	1	TRUE	2	0.24	5		212	202	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554377	141554377	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1409885719	NA	P-0045728-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	82	807	0	ENST00000220592.5:c.1774A>G	p.Ile592Val	p.I592V	ENST00000220592	NM_012154.3	592	Atc/Gtc	14/19	0.3	5	FACETS	1	0.933	1	0.272	0.239	0.308	CLONAL	1	TRUE	1	0.24	5		807	853	SUCCESS
EED	8726	MSKCC	GRCh37	11	85961337	85961337	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0045729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	46	125	0	ENST00000263360.6:c.115-1G>A		p.X39_splice	ENST00000263360	NM_003797.3	39			0.685483946923479	3	FACETS	1	0.947	1	0.614	0.528	0.704	CLONAL	1	TRUE	1	0.70321407204929	3		125	144	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293167	212293167	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045729-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	61	232	0	ENST00000342788.4:c.2685del	p.Lys896AsnfsTer18	p.K896Nfs*18	ENST00000342788	NM_005235.2	895	agG/ag	22/28	0.526318021359636	4	FACETS	0.906	0.787	1	0.453	0.393	0.517	CLONAL	1	TRUE	2	0.70321407204929	4		232	326	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033890	49033890	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0045730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	289	243	0	ENST00000267163.4:c.2027T>G	p.Leu676Ter	p.L676*	ENST00000267163	NM_000321.2	676	tTa/tGa	20/27	0.91291876454749	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.923101043994249	2		243	300	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281890	142281890	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045730-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	252	235	0	ENST00000350721.4:c.354del	p.Leu118PhefsTer47	p.L118Ffs*47	ENST00000350721	NM_001184.3	118	ttG/tt	4/47	0.89170599604481	3	FACETS	0.955	0.909	0.999	0.955	0.909	0.999	CLONAL	2	TRUE	1	0.923101043994249	3		235	418	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0045734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	62	354	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.225099701080162	2		354	492	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266713	198266713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776846119	NA	P-0045734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	88	327	0	ENST00000335508.6:c.2219G>A	p.Gly740Glu	p.G740E	ENST00000335508	NM_012433.2	740	gGa/gAa	15/25	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.225099701080162	2		327	570	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101278	27101278	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	114	605	0	ENST00000324856.7:c.4563del	p.Ala1522ProfsTer5	p.A1522Pfs*5	ENST00000324856	NM_006015.4	1520	ggC/gg	18/20	0.225099701080162	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.225099701080162	1		605	685	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81927325	81927325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	117	611	0	ENST00000359376.3:c.998G>A	p.Gly333Asp	p.G333D	ENST00000359376	NM_002661.3	333	gGt/gAt	12/33	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.225099701080162	2		611	840	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149440465	149440465	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs184499252	NA	P-0045734-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	113	566	0	ENST00000286301.3:c.1929C>A	p.His643Gln	p.H643Q	ENST00000286301	NM_005211.3	643	caC/caA	14/22	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.225099701080162	2		566	790	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0045737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	195	1249	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.400282034431136	4	FACETS	0.988	0.918	1	0.988	0.918	1	CLONAL	2	TRUE	2	0.40037359486372	4		1249	690	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200108	67200108	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	104	525	0	ENST00000312629.5:c.495C>G	p.Ile165Met	p.I165M	ENST00000312629	NM_003952.2	165	atC/atG	6/15	0.400282034431136	4	FACETS	0.973	0.871	1	0.486	0.435	0.54	CLONAL	1	TRUE	2	0.40037359486372	4		525	748	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912664	NA	P-0045737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	124	590	1	ENST00000269305.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000269305	NM_001126112.2	337	cGc/cAc	10/11	0.40037359486372	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.40037359486372	1		591	490	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591890	48591905	+	frameshift_variant	Frame_Shift_Del	DEL	TGGATACGTGGACCCT	TGGATACGTGGACCCT	-	novel	NA	P-0045737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	68	349	0	ENST00000342988.3:c.1054_1069del	p.Gly352LeufsTer27	p.G352Lfs*27	ENST00000342988	NM_005359.5	351	gaTGGATACGTGGACCCT/ga	9/12	0.40037359486372	1	FACETS	0.921	0.809	1	0.921	0.809	1	CLONAL	1	TRUE	0	0.40037359486372	1		349	295	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030774	48030774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752164796	NA	P-0045737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	47	257	0	ENST00000234420.5:c.3388G>A	p.Val1130Met	p.V1130M	ENST00000234420	NM_000179.2	1130	Gtg/Atg	5/10	0.39751194842959	3	FACETS	0.826	0.7	0.964	0.413	0.35	0.482	CLONAL	1	TRUE	1	0.40037359486372	3		257	341	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441217	52441217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	58	340	0	ENST00000460680.1:c.553G>A	p.Gly185Arg	p.G185R	ENST00000460680	NM_004656.3	185	Ggg/Agg	7/17	1	2	FACETS	0.835	0.721	0.958	0.835	0.721	0.958	CLONAL	1	TRUE	1	0.40037359486372	2		340	347	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460549	8460549	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	80	311	0	ENST00000356435.5:c.3737A>G	p.Tyr1246Cys	p.Y1246C	ENST00000356435		1246	tAc/tGc	22/35	0.40037359486372	1	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	0	0.40037359486372	1		311	315	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039881	47039881	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045737-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	267	334	0	ENST00000377604.3:c.1224del	p.Ala409ArgfsTer76	p.A409Rfs*76	ENST00000377604	NM_001204468.1	408	gcT/gc	12/24	0.40037359486372	2	FACETS	0.853	0.81	0.897			1	CLONAL	3	TRUE	NA	0.40037359486372	2		334	521	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0045739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	22	354	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.168884739082862	1	FACETS	0.731	0.566	0.922	0.731	0.566	0.922	CLONAL	1	TRUE	0	0.17	1		354	324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0045739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	70	539	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	0.168884739082862	1	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	0	0.17	1		539	724	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492536	50492537	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGCT	novel	NA	P-0045739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	69	523	0	ENST00000394963.4:c.1436_1440dup	p.Phe481LeufsTer28	p.F481Lfs*28	ENST00000394963	NM_003076.4	478	cga/cGAGCTga	12/13	0.168884739082862	1	FACETS	0.941	0.819	1	0.941	0.819	1	CLONAL	1	TRUE	0	0.17	1		523	789	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880987	37880988	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTGATGGCTGCT	novel	NA	P-0045740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	132	510	0	ENST00000269571.5:c.2326_2327insCTGTGATGGCTG	p.Ala775_Gly776insAlaValMetAla	p.A775_G776insAVMA	ENST00000269571		772	-/GTGATGGCTGCT	20/27	0.178066341842384	2	FACETS	0.924	0.839	1	0.924	0.839	1	CLONAL	2	FALSE	0	0.178066341842384	2		510	802	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295260	1295260	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs796188588	NA	P-0045740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	144	245	0				ENST00000310581	NM_198253.2	-/1132			0.178066341842384	3	FACETS	1	0.924	1	1	0.988	1	CLONAL	3	FALSE	1	0.178066341842384	3		245	582	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445258	29445258	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045746-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	8	505	0	ENST00000389048.3:c.3467G>T	p.Cys1156Phe	p.C1156F	ENST00000389048	NM_004304.4	1156	tGc/tTc	22/29	1	2	FACETS	0.261	0.167	0.384	0.261	0.167	0.384	SUBCLONAL	1	TRUE	1	0.162772436851133	2		505	376	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0045752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	22	297	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	0.400846543426478	4	FACETS	0.298	0.23	0.377	0.149	0.115	0.189	SUBCLONAL	1	TRUE	2	0.468603898966562	4		297	463	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856529	111856529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	18	238	0	ENST00000341259.2:c.580G>A	p.Glu194Lys	p.E194K	ENST00000341259	NM_005475.2	194	Gag/Aag	2/8	0.400846543426478	4	FACETS	0.329	0.247	0.426	0.164	0.123	0.213	SUBCLONAL	1	TRUE	2	0.468603898966562	4		238	343	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026915	6026915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782602	NA	P-0045752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	10	113	0	ENST00000265849.7:c.1481C>T	p.Ser494Leu	p.S494L	ENST00000265849	NM_000535.5	494	tCg/tTg	11/15	0.419224363062689	5	FACETS	0.475	0.322	0.666	0.158	0.107	0.222	SUBCLONAL	1	TRUE	2	0.468603898966562	5		113	153	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997756	149997756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754664378	NA	P-0045771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	43	283	1	ENST00000253339.5:c.2711G>A	p.Arg904Gln	p.R904Q	ENST00000253339		904	cGa/cAa	5/7	1	2	FACETS	0.297	0.249	0.351	0.297	0.249	0.351	SUBCLONAL	1	TRUE	1	0.68362684886736	2		284	423	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090962	77090962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	117	261	0	ENST00000356341.3:c.268G>A	p.Asp90Asn	p.D90N	ENST00000356341	NM_002576.4	90	Gat/Aat	3/15	1	2	FACETS	0.735	0.666	0.806	0.735	0.666	0.806	SUBCLONAL	1	TRUE	1	0.68362684886736	2		261	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578194	+	missense_variant	Missense_Mutation	ONP	TAGGG	TAGGG	CAGGC	novel	NA	P-0045771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	197	499	0	ENST00000269305.4:c.655_659delinsGCCTG	p.Pro219_Tyr220delinsAlaCys	p.P219_Y220delinsAC	ENST00000269305	NM_001126112.2	219	CCCTAt/GCCTGt	6/11	0.68362684886736	1	FACETS	0.996	0.937	1	0.996	0.937	1	CLONAL	1	TRUE	0	0.68362684886736	1		499	381	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0045774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	33	458	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.749	0.611	0.902	0.749	0.611	0.902	CLONAL	1	TRUE	1	0.291961083745156	2		458	302	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366685	40366692	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGGGTT	GCCGGGTT	-	novel	NA	P-0045774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	49	406	0	ENST00000397332.2:c.505_512del	p.Asn169AlafsTer27	p.N169Afs*27	ENST00000397332	NM_001033082.2	169	AACCCGGCg/g	2/3	1	2	FACETS	0.765	0.649	0.892	0.765	0.649	0.892	SUBCLONAL	1	TRUE	1	0.291961083745156	2		406	439	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	60	425	0				ENST00000310581	NM_198253.2	-/1132			0.426846008582156	5	FACETS	1	0.896	1	0.348	0.3	0.399	CLONAL	1	TRUE	2	0.501205428102263	5		425	402	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231773	36231773	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1569061762	NA	P-0045816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	180	661	0	ENST00000300305.3:c.611G>A	p.Arg204Gln	p.R204Q	ENST00000300305		204	cGa/cAa	5/8	0.501205428102263	2	FACETS	1	0.964	1	0.534	0.494	0.575	CLONAL	1	TRUE	0	0.501205428102263	2		661	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0045816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	304	883	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.453227455733932	2	FACETS	0.946	0.9	0.993	0.946	0.9	0.993	CLONAL	2	TRUE	0	0.501205428102263	2		884	641	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053343	37053343	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63751480	NA	P-0045816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	74	390	0	ENST00000231790.2:c.578C>T	p.Ser193Leu	p.S193L	ENST00000231790	NM_000249.3	193	tCa/tTa	7/19	0.254255972005703	2	FACETS	1	0.93	1	0.535	0.473	0.6	INDETERMINATE	1	TRUE	0	0.501205428102263	2		390	276	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045003	47045003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	275	577	0	ENST00000377604.3:c.2329C>T	p.His777Tyr	p.H777Y	ENST00000377604	NM_001204468.1	777	Cac/Tac	20/24	0.478321185203615	2	FACETS	0.855	0.817	0.891			1	CLONAL	3	TRUE	NA	0.501205428102263	2		577	428	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934223	48934227	+	frameshift_variant	Frame_Shift_Del	DEL	TATTA	TATTA	-	novel	NA	P-0045816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	136	483	0	ENST00000267163.4:c.678_682del	p.Phe226LeufsTer13	p.F226Lfs*13	ENST00000267163	NM_000321.2	226	ttTATTAaa/ttaa	7/27	0.501205428102263	2	FACETS	0.904	0.837	0.973	0.904	0.837	0.973	CLONAL	2	TRUE	0	0.501205428102263	2		483	300	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546866	9546866	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	132	623	0	ENST00000353224.5:c.1156C>A	p.Pro386Thr	p.P386T	ENST00000353224	NM_177990.2	386	Ccc/Acc	5/10	0.48871931059874	3	FACETS	1	0.984	1	0.685	0.626	0.746	CLONAL	1	TRUE	1	0.501205428102263	3		623	481	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157284	106157284	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	37	479	0	ENST00000380013.4:c.2185C>G	p.Gln729Glu	p.Q729E	ENST00000380013	NM_001127208.2	729	Caa/Gaa	3/11	1	2	FACETS	0.506	0.418	0.602	0.506	0.418	0.602	SUBCLONAL	1	TRUE	1	0.501205428102263	2		479	292	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295311	1295311	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0045816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	95	695	0				ENST00000310581	NM_198253.2	-/1132			0.426846008582156	5	FACETS	0.978	0.871	1	0.326	0.29	0.364	CLONAL	1	TRUE	2	0.501205428102263	5		695	679	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576382	67576382	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	11	316	0	ENST00000274335.5:c.661C>T	p.Gln221Ter	p.Q221*	ENST00000274335		221	Cag/Tag	5/15	NA	2	FACETS	0.237	0.164	0.328			1	INDETERMINATE	1	TRUE	NA	0.501205428102263	2		316	185	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575526	64575526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565648547	NA	P-0045817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	465	910	0	ENST00000312049.6:c.491C>T	p.Ala164Val	p.A164V	ENST00000312049	NM_130799.2	164	gCc/gTc	3/10	0.547975018717703	1	FACETS	0.93	0.891	0.969	0.93	0.891	0.969	CLONAL	1	TRUE	0	0.638633835441703	1		910	1066	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692994	89693017	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCAGAGACAAAAAGGTAAGTTAT	ACCAGAGACAAAAAGGTAAGTTAT	-	novel	NA	P-0045817-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	109	482	0	ENST00000371953.3:c.478_492+9del		p.X160_splice	ENST00000371953	NM_000314.4	160		5/9	0.638633835441703	1	FACETS	0.7	0.636	0.766	0.7	0.636	0.766	SUBCLONAL	1	TRUE	0	0.638633835441703	1		482	332	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0045818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	29	460	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		460	803	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225896	2225896	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045818-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	51	972	0	ENST00000326181.6:c.1688A>G	p.Tyr563Cys	p.Y563C	ENST00000326181	NM_032271.2	563	tAc/tGc	18/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		972	899	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830406	72830406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	111	364	3	ENST00000268489.5:c.6175G>A	p.Ala2059Thr	p.A2059T	ENST00000268489	NM_006885.3	2059	Gcg/Acg	9/10	0.877604859705246	2	FACETS	0.939	0.86	1	0.469	0.43	0.509	CLONAL	1	TRUE	0	0.923964721606283	2		367	256	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420092	420092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760930800	NA	P-0045819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	197	601	2	ENST00000399788.2:c.3175C>T	p.Arg1059Trp	p.R1059W	ENST00000399788	NM_001042603.1	1059	Cgg/Tgg	21/28	0.412478183482167	3	FACETS	0.818	0.759	0.879			1	INDETERMINATE	1	TRUE	NA	0.923964721606283	3		603	762	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120795623	120795628	+	inframe_deletion	In_Frame_Del	DEL	TTGTTG	TTGTTG	-	novel	NA	P-0045819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	290	388	11	ENST00000257552.2:c.525_530del	p.Asn175_Asn176del	p.N175_N176del	ENST00000257552	NM_002442.3	175	aaCAACAAa/aaa	8/15	0.861305085332959	3	FACETS	0.916	0.874	0.957	0.611	0.583	0.638	CLONAL	2	TRUE	0	0.923964721606283	3		399	501	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061612	38061612	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	315	584	15	ENST00000250448.2:c.377G>T	p.Gly126Val	p.G126V	ENST00000250448	NM_004496.3	126	gGc/gTc	2/2	0.692879077663185	6	FACETS	0.956	0.909	1	0.956	0.909	1	CLONAL	3	TRUE	3	0.923964721606283	6		599	677	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641709	23641709	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773340677	NA	P-0045819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	120	487	3	ENST00000261584.4:c.1766C>T	p.Thr589Met	p.T589M	ENST00000261584	NM_024675.3	589	aCg/aTg	5/13	0.901619583917264	3	FACETS	0.766	0.695	0.839	0.383	0.347	0.42	SUBCLONAL	1	TRUE	1	0.923964721606283	3		490	496	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505661	186505661	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	106	296	5	ENST00000323963.5:c.1069T>C	p.Tyr357His	p.Y357H	ENST00000323963		357	Tat/Cat	10/11	1	2	FACETS	0.876	0.799	0.954	0.876	0.799	0.954	CLONAL	1	TRUE	1	0.923964721606283	2		301	262	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391045	139391055	+	frameshift_variant	Frame_Shift_Del	DEL	GGTCTGCACCA	GGTCTGCACCA	-	novel	NA	P-0045819-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	188	1224	6	ENST00000277541.6:c.7136_7146del	p.Leu2379ProfsTer124	p.L2379Pfs*124	ENST00000277541	NM_017617.3	2379	cTGGTGCAGACC/c	34/34	0.85396814958526	2	FACETS	0.741	0.69	0.794	0.371	0.345	0.397	SUBCLONAL	1	TRUE	0	0.923964721606283	2		1230	549	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0045820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	13	262	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.49	0.347	0.665	0.49	0.347	0.665	SUBCLONAL	1	TRUE	1	0.09	2		262	590	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145431	58145431	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11547328	NA	P-0045820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	19	627	0	ENST00000257904.6:c.70C>T	p.Arg24Cys	p.R24C	ENST00000257904	NM_000075.3	24	Cgt/Tgt	2/8	1	2	FACETS	0.636	0.48	0.82	0.636	0.48	0.82	SUBCLONAL	1	TRUE	1	0.09	2		627	664	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	117	425	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.872	0.792	0.956	0.872	0.792	0.956	CLONAL	1	TRUE	1	0.594677424862228	2		425	451	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0045821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	19	546	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.071	0.053	0.092	0.071	0.053	0.092	SUBCLONAL	1	TRUE	1	0.594677424862228	2		546	906	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340047	116340047	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1200423161	NA	P-0045821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	76	316	0	ENST00000397752.3:c.909G>C	p.Lys303Asn	p.K303N	ENST00000397752	NM_000245.2	303	aaG/aaC	2/21	1	2	FACETS	0.772	0.683	0.867	0.772	0.683	0.867	SUBCLONAL	1	TRUE	1	0.594677424862228	2		316	331	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201980347	201980347	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	305	842	0	ENST00000359651.3:c.83C>A	p.Ser28Tyr	p.S28Y	ENST00000359651		28	tCt/tAt	1/8	1	2	FACETS	0.931	0.878	0.985	0.931	0.878	0.985	CLONAL	1	TRUE	1	0.594677424862228	2		842	1102	SUCCESS
CALR	811	MSKCC	GRCh37	19	13049522	13049546	+	frameshift_variant	Frame_Shift_Del	DEL	GCCTCCTCGGCCTGGCCGTCGCCGA	GCCTCCTCGGCCTGGCCGTCGCCGA	-	novel	NA	P-0045821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	307	969	0	ENST00000316448.5:c.33_57del	p.Leu12ProfsTer78	p.L12Pfs*78	ENST00000316448	NM_004343.3	10	gGCCTCCTCGGCCTGGCCGTCGCCGAg/gg	1/9	1	2	FACETS	0.934	0.88	0.988	0.934	0.88	0.988	CLONAL	1	TRUE	1	0.594677424862228	2		969	1106	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46275985	46275985	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	176	550	0	ENST00000371998.3:c.3421C>G	p.Gln1141Glu	p.Q1141E	ENST00000371998		1141	Cag/Gag	18/23	0.594677424862228	3	FACETS	0.921	0.849	0.995	0.46	0.424	0.498	CLONAL	1	TRUE	1	0.594677424862228	3		550	834	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754893	57754893	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	42	315	0	ENST00000274289.3:c.297G>T	p.Met99Ile	p.M99I	ENST00000274289	NM_006622.3	99	atG/atT	2/14	1	2	FACETS	0.388	0.325	0.458	0.388	0.325	0.458	SUBCLONAL	1	TRUE	1	0.594677424862228	2		315	364	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075605	8075625	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTCGGCCATTATGTAGAAA	GGCTCGGCCATTATGTAGAAA	TC	novel	NA	P-0045821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	68	521	2	ENST00000377482.5:c.55_75delinsGA	p.Phe19GlufsTer5	p.F19Efs*5	ENST00000377482	NM_018948.3	19	TTTCTACATAATGGCCGAGCC/GA	2/4	1	2	FACETS	0.381	0.331	0.435	0.381	0.331	0.435	SUBCLONAL	1	TRUE	1	0.594677424862228	2		523	600	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212833	27212833	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	213	813	1	ENST00000380036.4:c.2815C>T	p.Gln939Ter	p.Q939*	ENST00000380036	NM_000459.3	939	Cag/Tag	17/23	1	2	FACETS	0.882	0.821	0.946	1	0.993	1	CLONAL	2	TRUE	1	0.271577925370507	2		814	889	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577155	7577171	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTACTCAGGATAGGAA	ACTACTCAGGATAGGAA	-	novel	NA	P-0045822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	131	608	1	ENST00000269305.4:c.783-16_783del		p.X261_splice	ENST00000269305	NM_001126112.2	261		8/11	0.251707219283572	0	FACETS	0.849	0.777	0.922			1	CLONAL	2	TRUE	0	0.271577925370507	0		609	414	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178114	56178114	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045822-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	109	373	0	ENST00000399503.3:c.3088del	p.His1030ThrfsTer52	p.H1030Tfs*52	ENST00000399503	NM_005921.1	1029	ttC/tt	14/20	1	2	FACETS	0.984	0.89	1	1	0.988	1	CLONAL	2	TRUE	1	0.271577925370507	2		373	408	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	73	262	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.767	0.672	0.868	0.767	0.672	0.868	SUBCLONAL	1	TRUE	1	0.396808269592391	2		262	480	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	367	737	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.984	1	1	0.997	1	CLONAL	2	TRUE	1	0.396808269592391	2		742	866	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	165	984	5	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.941	0.864	1	0.941	0.864	1	CLONAL	1	TRUE	1	0.396808269592391	2		989	884	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	145	606	4	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.9	0.822	0.982	0.9	0.822	0.982	CLONAL	1	TRUE	1	0.396808269592391	2		610	812	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526104	63526104	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs562176077	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	196	672	1	ENST00000307078.5:c.2522G>A	p.Arg841Gln	p.R841Q	ENST00000307078	NM_004655.3	841	cGg/cAg	11/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.396808269592391	2		673	921	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114322	143114322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	105	429	0	ENST00000262992.4:c.1099G>A	p.Gly367Arg	p.G367R	ENST00000262992	NM_001101669.1	367	Gga/Aga	13/24	1	2	FACETS	0.991	0.891	1	0.991	0.891	1	CLONAL	1	TRUE	1	0.396808269592391	2		429	534	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	230	959	5	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.396808269592391	2		964	1097	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715979	52715979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786205227	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	22	794	1	ENST00000322088.6:c.544C>T	p.Arg182Trp	p.R182W	ENST00000322088	NM_014225.5	182	Cgg/Tgg	5/15	1	2	FACETS	0.131	0.101	0.166	0.131	0.101	0.166	SUBCLONAL	1	TRUE	1	0.396808269592391	2		795	847	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100420	8100420	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs991194737	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	82	1008	0	ENST00000346208.3:c.394G>A	p.Val132Ile	p.V132I	ENST00000346208		132	Gtc/Atc	3/6	1	2	FACETS	0.42	0.369	0.474	0.42	0.369	0.474	SUBCLONAL	1	TRUE	1	0.396808269592391	2		1008	985	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933593	39933594	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	153	812	0	ENST00000378444.4:c.1005dup	p.Ser336LeufsTer45	p.S336Lfs*45	ENST00000378444	NM_001123385.1	335	-/C	4/15	1	2	FACETS	0.865	0.792	0.943	0.865	0.792	0.943	CLONAL	1	TRUE	1	0.396808269592391	2		812	891	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532654	63532654	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	200	786	4	ENST00000307078.5:c.1925del	p.Lys642ArgfsTer47	p.K642Rfs*47	ENST00000307078	NM_004655.3	642	aAg/ag	8/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.396808269592391	2		790	953	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142446	119142446	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs267602720	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	82	354	0	ENST00000264033.4:c.445C>T	p.Arg149Ter	p.R149*	ENST00000264033	NM_005188.3	149	Cga/Tga	3/16	1	2	FACETS	0.948	0.84	1	0.948	0.84	1	CLONAL	1	TRUE	1	0.396808269592391	2		354	436	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735467	40735467	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776642212	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	165	768	0	ENST00000373198.4:c.3406C>T	p.Arg1136Cys	p.R1136C	ENST00000373198	NM_133170.3	1136	Cgt/Tgt	25/32	1	2	FACETS	0.932	0.856	1	0.932	0.856	1	CLONAL	1	TRUE	1	0.396808269592391	2		768	892	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509082	106509082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144565710	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	176	710	2	ENST00000359195.3:c.1076G>A	p.Arg359His	p.R359H	ENST00000359195	NM_002649.2	359	cGc/cAc	2/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.396808269592391	2		712	834	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526170	189526170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1225645471	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	218	708	2	ENST00000264731.3:c.434C>T	p.Ala145Val	p.A145V	ENST00000264731	NM_003722.4	145	gCg/gTg	4/14	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.396808269592391	2		710	1061	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521525	46521525	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	138	563	2	ENST00000262741.5:c.883del	p.Met295Ter	p.M295*	ENST00000262741	NM_003629.3	295	Atg/tg	7/10	1	2	FACETS	0.856	0.779	0.936	0.856	0.779	0.936	CLONAL	1	TRUE	1	0.396808269592391	2		565	813	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871060	12871070	+	frameshift_variant	Frame_Shift_Del	DEL	AAGGTGCCTGC	AAGGTGCCTGC	-	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	88	405	0	ENST00000228872.4:c.295_305del	p.Cys99GlyfsTer22	p.C99Gfs*22	ENST00000228872	NM_004064.3	96	aAAGGTGCCTGC/a	1/3	1	2	FACETS	0.934	0.831	1	0.934	0.831	1	CLONAL	1	TRUE	1	0.396808269592391	2		405	475	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424178	49424178	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs886040960	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	27	420	3	ENST00000301067.7:c.13884del	p.Thr4629ProfsTer11	p.T4629Pfs*11	ENST00000301067	NM_003482.3	4628	ccC/cc	42/54	1	2	FACETS	0.298	0.236	0.368	0.298	0.236	0.368	SUBCLONAL	1	TRUE	1	0.396808269592391	2		423	457	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344955	118344955	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	21	257	1	ENST00000534358.1:c.3086del	p.Lys1029ArgfsTer65	p.K1029Rfs*65	ENST00000534358	NM_005933.3	1027	ctA/ct	3/36	1	2	FACETS	0.257	0.197	0.327	0.257	0.197	0.327	SUBCLONAL	1	TRUE	1	0.396808269592391	2		258	412	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215610468	215610468	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	101	362	0	ENST00000260947.4:c.1788del	p.Lys596AsnfsTer9	p.K596Nfs*9	ENST00000260947	NM_000465.2	596	aaA/aa	8/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.396808269592391	2		362	483	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511598	38511598	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	198	825	0	ENST00000254066.5:c.1096C>T	p.Arg366Trp	p.R366W	ENST00000254066	NM_000964.3	366	Cgg/Tgg	8/9	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.396808269592391	2		825	892	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69012017	69012017	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	117	621	0	ENST00000288368.4:c.2654T>C	p.Phe885Ser	p.F885S	ENST00000288368	NM_024870.2	885	tTc/tCc	23/40	1	2	FACETS	0.825	0.744	0.91	0.825	0.744	0.91	CLONAL	1	TRUE	1	0.396808269592391	2		621	715	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129350	64129350	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	99	847	1	ENST00000334205.4:c.782T>C	p.Phe261Ser	p.F261S	ENST00000334205	NM_003942.2	261	tTc/tCc	8/17	1	2	FACETS	0.635	0.566	0.708	0.635	0.566	0.708	SUBCLONAL	1	TRUE	1	0.396808269592391	2		848	786	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164839	36164839	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	246	1073	1	ENST00000300305.3:c.1036del	p.Arg346AlafsTer248	p.R346Afs*248	ENST00000300305		346	Cgc/gc	8/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.396808269592391	2		1074	1134	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748089	41748089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779913205	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	10	89	0	ENST00000226382.2:c.680C>T	p.Ala227Val	p.A227V	ENST00000226382	NM_003924.3	227	gCg/gTg	3/3	NA	2	FACETS	0.622	0.427	0.861			1	INDETERMINATE	1	TRUE	NA	0.396808269592391	2		89	81	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001241	150001241	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	99	524	1	ENST00000253339.5:c.2363del	p.Gly788ValfsTer3	p.G788Vfs*3	ENST00000253339		788	gGt/gt	4/7	1	2	FACETS	0.952	0.853	1	0.952	0.853	1	CLONAL	1	TRUE	1	0.396808269592391	2		525	524	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505431	25505431	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	147	803	0	ENST00000264709.3:c.327del	p.Gln110ArgfsTer52	p.Q110Rfs*52	ENST00000264709	NM_175629.2	109	ggG/gg	4/23	1	2	FACETS	0.983	0.898	1	0.983	0.898	1	CLONAL	1	TRUE	1	0.396808269592391	2		803	754	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106805	27106805	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1302295523	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	183	792	1	ENST00000324856.7:c.6416C>A	p.Pro2139His	p.P2139H	ENST00000324856	NM_006015.4	2139	cCc/cAc	20/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.396808269592391	2		793	864	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533094	63533094	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	164	859	2	ENST00000307078.5:c.1800del	p.Gly601AlafsTer88	p.G601Afs*88	ENST00000307078	NM_004655.3	600	ccC/cc	7/11	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.396808269592391	2		861	798	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115269643	115269643	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	58	671	0	ENST00000438362.2:c.1563G>T	p.Lys521Asn	p.K521N	ENST00000438362	NM_001242891.1	521	aaG/aaT	13/20	1	2	FACETS	0.404	0.347	0.467	0.404	0.347	0.467	SUBCLONAL	1	TRUE	1	0.396808269592391	2		671	723	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724540	112724540	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	132	586	0	ENST00000369452.4:c.424G>A	p.Val142Met	p.V142M	ENST00000369452	NM_007373.3	142	Gtg/Atg	2/9	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.396808269592391	2		586	599	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741651	17741651	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1375320913	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	158	615	0	ENST00000250003.3:c.322G>A	p.Ala108Thr	p.A108T	ENST00000250003	NM_002478.4	108	Gcc/Acc	1/3	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.396808269592391	2		615	696	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127694	64127694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1387218415	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	212	995	2	ENST00000334205.4:c.187G>A	p.Ala63Thr	p.A63T	ENST00000334205	NM_003942.2	63	Gcc/Acc	3/17	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.396808269592391	2		997	1000	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118354983	118354983	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	140	488	0	ENST00000534358.1:c.4177del	p.Ile1393PhefsTer28	p.I1393Ffs*28	ENST00000534358	NM_005933.3	1391	cAa/ca	9/36	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.396808269592391	2		488	604	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434747	49434747	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	181	1022	0	ENST00000301067.7:c.6806C>A	p.Ser2269Tyr	p.S2269Y	ENST00000301067	NM_003482.3	2269	tCc/tAc	31/54	1	2	FACETS	0.942	0.869	1	0.942	0.869	1	CLONAL	1	TRUE	1	0.396808269592391	2		1022	968	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857554	57857554	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	120	644	0	ENST00000228682.2:c.84del	p.Ser29ValfsTer49	p.S29Vfs*49	ENST00000228682	NM_005269.2	27	gCc/gc	2/12	1	2	FACETS	0.932	0.843	1	0.932	0.843	1	CLONAL	1	TRUE	1	0.396808269592391	2		644	649	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257788	133257788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1161199196	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	162	672	0	ENST00000320574.5:c.140G>A	p.Arg47Gln	p.R47Q	ENST00000320574	NM_006231.2	47	cGg/cAg	2/49	1	2	FACETS	0.952	0.874	1	0.952	0.874	1	CLONAL	1	TRUE	1	0.396808269592391	2		672	858	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352456	73352456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770796604	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	134	525	1	ENST00000377767.4:c.449G>A	p.Arg150Gln	p.R150Q	ENST00000377767	NM_014953.3	150	cGa/cAa	3/21	1	2	FACETS	0.976	0.888	1	0.976	0.888	1	CLONAL	1	TRUE	1	0.396808269592391	2		526	692	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434549	110434549	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	175	866	0	ENST00000375856.3:c.3852G>T	p.Trp1284Cys	p.W1284C	ENST00000375856	NM_003749.2	1284	tgG/tgT	1/2	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.396808269592391	2		866	853	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782289	56782289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754633729	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	147	631	2	ENST00000308159.5:c.130C>T	p.Arg44Cys	p.R44C	ENST00000308159	NM_014669.4	44	Cgt/Tgt	2/22	1	2	FACETS	0.907	0.828	0.989	0.907	0.828	0.989	CLONAL	1	TRUE	1	0.396808269592391	2		633	817	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644830	67644830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759711695	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	143	545	1	ENST00000264010.4:c.95G>A	p.Gly32Asp	p.G32D	ENST00000264010	NM_006565.3	32	gGc/gAc	3/12	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.396808269592391	2		546	664	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968214	15968214	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	69	278	0	ENST00000268712.3:c.5071A>G	p.Arg1691Gly	p.R1691G	ENST00000268712	NM_006311.3	1691	Agg/Ggg	34/46	1	2	FACETS	0.899	0.787	1	0.899	0.787	1	CLONAL	1	TRUE	1	0.396808269592391	2		278	387	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007581	62007581	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1277301487	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	139	823	1	ENST00000392795.3:c.286C>T	p.Arg96Cys	p.R96C	ENST00000392795	NM_001039933.1	96	Cgc/Tgc	3/6	1	2	FACETS	0.831	0.757	0.909	0.831	0.757	0.909	CLONAL	1	TRUE	1	0.396808269592391	2		824	843	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231450	5231450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	245	852	1	ENST00000357368.4:c.2026C>T	p.Pro676Ser	p.P676S	ENST00000357368	NM_002850.3	676	Ccg/Tcg	14/38	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.396808269592391	2		853	1049	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610502	10610502	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	93	881	0	ENST00000171111.5:c.208C>A	p.Leu70Met	p.L70M	ENST00000171111	NM_203500.1	70	Ctg/Atg	2/6	1	2	FACETS	0.556	0.494	0.623	0.556	0.494	0.623	SUBCLONAL	1	TRUE	1	0.396808269592391	2		881	843	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141624	202141624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	128	423	0	ENST00000358485.4:c.915del	p.Ala306HisfsTer24	p.A306Hfs*24	ENST00000358485	NM_001080125.1	304	gcA/gc	7/9	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.396808269592391	2		423	582	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548004	41548004	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	68	681	0	ENST00000263253.7:c.2985G>T	p.Glu995Asp	p.E995D	ENST00000263253	NM_001429.3	995	gaG/gaT	15/31	1	2	FACETS	0.422	0.366	0.482	0.422	0.366	0.482	SUBCLONAL	1	TRUE	1	0.396808269592391	2		681	813	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572825	41572825	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	66	785	2	ENST00000263253.7:c.5113del	p.Met1705TrpfsTer4	p.M1705Wfs*4	ENST00000263253	NM_001429.3	1704	Aaa/aa	31/31	1	2	FACETS	0.386	0.334	0.443	0.386	0.334	0.443	SUBCLONAL	1	TRUE	1	0.396808269592391	2		787	861	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480324	89480325	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	78	306	0	ENST00000336596.2:c.2163dup	p.Gln722SerfsTer36	p.Q722Sfs*36	ENST00000336596	NM_005233.5	721	att/aTtt	13/17	1	2	FACETS	0.959	0.847	1	0.959	0.847	1	CLONAL	1	TRUE	1	0.396808269592391	2		306	410	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31464411	31464411	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	175	767	1	ENST00000344624.3:c.2506C>T	p.Arg836Ter	p.R836*	ENST00000344624		836	Cga/Tga	17/33	1	2	FACETS	0.862	0.793	0.934	0.862	0.793	0.934	CLONAL	1	TRUE	1	0.396808269592391	2		768	1023	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696683	176696683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	101	394	0	ENST00000439151.2:c.5384C>T	p.Pro1795Leu	p.P1795L	ENST00000439151	NM_022455.4	1795	cCa/cTa	16/23	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.396808269592391	2		394	487	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057308	180057308	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	108	885	0	ENST00000261937.6:c.430G>T	p.Asp144Tyr	p.D144Y	ENST00000261937	NM_182925.4	144	Gac/Tac	4/30	1	2	FACETS	0.706	0.634	0.783	0.706	0.634	0.783	SUBCLONAL	1	TRUE	1	0.396808269592391	2		885	771	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120774	94120774	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	128	534	0	ENST00000369303.4:c.277G>T	p.Gly93Cys	p.G93C	ENST00000369303	NM_004440.3	93	Ggc/Tgc	3/17	1	2	FACETS	0.867	0.787	0.952	0.867	0.787	0.952	CLONAL	1	TRUE	1	0.396808269592391	2		534	744	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124454	94124457	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	68	455	0	ENST00000369303.4:c.126_129del	p.Thr43SerfsTer57	p.T43Sfs*57	ENST00000369303	NM_004440.3	42	caAACA/ca	2/17	1	2	FACETS	0.695	0.606	0.791	0.695	0.606	0.791	SUBCLONAL	1	TRUE	1	0.396808269592391	2		455	493	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109308826	109308826	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	53	225	0	ENST00000436639.2:c.1577T>A	p.Val526Asp	p.V526D	ENST00000436639	NM_014454.2	526	gTt/gAt	10/10	1	2	FACETS	0.876	0.752	1	0.876	0.752	1	CLONAL	1	TRUE	1	0.396808269592391	2		225	305	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6442031	6442031	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	40	112	1	ENST00000356142.4:c.590G>A	p.Cys197Tyr	p.C197Y	ENST00000356142	NM_018890.3	197	tGc/tAc	7/7	1	2	FACETS	0.806	0.686	0.934	1	0.964	1	CLONAL	2	TRUE	1	0.396808269592391	2		113	125	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367259	50367259	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	109	460	0	ENST00000331340.3:c.66T>A	p.Asp22Glu	p.D22E	ENST00000331340	NM_006060.4	22	gaT/gaA	3/8	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.396808269592391	2		460	540	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27109591	27109591	+	start_lost	Translation_Start_Site	SNP	G	G	T	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	166	635	0	ENST00000380036.4:c.3G>T	p.Met1?	p.M1?	ENST00000380036	NM_000459.3	1	atG/atT	1/23	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.396808269592391	2		635	793	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781484	135781484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	121	499	0	ENST00000298552.3:c.1481C>T	p.Ala494Val	p.A494V	ENST00000298552	NM_001162426.1	494	gCa/gTa	15/23	1	2	FACETS	0.916	0.829	1	0.916	0.829	1	CLONAL	1	TRUE	1	0.396808269592391	2		499	666	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0045824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	41	294	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.887	0.738	1	0.887	0.738	1	CLONAL	1	TRUE	1	0.15	2		294	616	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686313	30686313	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0045824-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	49	555	0	ENST00000295754.5:c.169A>T	p.Arg57Ter	p.R57*	ENST00000295754	NM_003242.5	57	Aga/Tga	2/7	1	2	FACETS	0.921	0.779	1	0.921	0.779	1	CLONAL	1	TRUE	1	0.15	2		555	709	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	29	763	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.108	0.086	0.133	0.108	0.086	0.133	SUBCLONAL	1	TRUE	1	0.687792814101576	2		765	784	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	540	737	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.687792814101576	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.687792814101576	2		742	744	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	100	373	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.687792814101576	2		373	274	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	163	443	0	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.91	0.841	0.981	0.91	0.841	0.981	CLONAL	1	TRUE	1	0.687792814101576	2		443	521	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	267	892	7	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.687792814101576	2		899	757	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	106	330	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.876	0.793	0.961	0.876	0.793	0.961	CLONAL	1	TRUE	1	0.687792814101576	2		330	352	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	113	363	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.562	0.507	0.619	0.562	0.507	0.619	SUBCLONAL	1	TRUE	1	0.687792814101576	2		365	585	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	200	350	1	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.687792814101576	2		351	526	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	69	917	0	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	2	FACETS	0.25	0.217	0.285	0.25	0.217	0.285	SUBCLONAL	1	TRUE	1	0.687792814101576	2		917	804	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020768	37020768	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs926053251	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	221	606	0	ENST00000358127.4:c.77T>G	p.Val26Gly	p.V26G	ENST00000358127	NM_001280556.1	26	gTt/gGt	2/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.687792814101576	2		606	635	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	588	498	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.687792814101576	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.687792814101576	2		498	789	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	181	582	0	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	0.966	0.897	1	0.966	0.897	1	CLONAL	1	TRUE	1	0.687792814101576	2		582	545	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777898	3777898	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	380	1064	1	ENST00000262367.5:c.7150del	p.His2384ThrfsTer12	p.H2384Tfs*12	ENST00000262367	NM_004380.2	2384	Cac/ac	31/31	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.687792814101576	2		1065	1009	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664989	138664989	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	130	342	0	ENST00000330315.3:c.576del	p.Lys193SerfsTer78	p.K193Sfs*78	ENST00000330315	NM_023067.3	192	ccC/cc	1/1	1	2	FACETS	0.977	0.895	1	0.977	0.895	1	CLONAL	1	TRUE	1	0.687792814101576	2		342	387	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	147	476	1	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	0.828	0.761	0.898	0.828	0.761	0.898	CLONAL	1	TRUE	1	0.687792814101576	2		477	516	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	200	735	5	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.971	0.905	1	0.971	0.905	1	CLONAL	1	TRUE	1	0.687792814101576	2		740	599	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349641	89349641	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs772267579	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	229	632	6	ENST00000301030.4:c.3309del	p.Asp1104MetfsTer214	p.D1104Mfs*214	ENST00000301030	NM_001256183.1	1103	aaA/aa	9/13	1	2	FACETS	0.901	0.843	0.96	0.901	0.843	0.96	CLONAL	1	TRUE	1	0.687792814101576	2		638	739	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120617	115120617	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	94	719	1	ENST00000257566.3:c.389G>A	p.Arg130Lys	p.R130K	ENST00000257566	NM_016569.3	130	aGg/aAg	1/8	1	2	FACETS	0.419	0.373	0.468	0.419	0.373	0.468	SUBCLONAL	1	TRUE	1	0.687792814101576	2		720	653	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1627369	1627369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35936626	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	72	850	1	ENST00000344749.5:c.355G>A	p.Gly119Ser	p.G119S	ENST00000344749	NM_001136139.2	119	Ggc/Agc	6/19	1	2	FACETS	0.258	0.225	0.294	0.258	0.225	0.294	SUBCLONAL	1	TRUE	1	0.687792814101576	2		851	811	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910426	50910426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368738479	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	254	890	0	ENST00000440232.2:c.1681C>T	p.Arg561Trp	p.R561W	ENST00000440232	NM_002691.3	561	Cgg/Tgg	13/27	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.687792814101576	2		890	725	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187558039	187558039	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	99	230	0	ENST00000441802.2:c.3672del	p.Lys1225AsnfsTer9	p.K1225Nfs*9	ENST00000441802	NM_005245.3	1224	ccC/cc	5/27	1	2	FACETS	0.875	0.79	0.964	0.875	0.79	0.964	CLONAL	1	TRUE	1	0.687792814101576	2		230	329	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074255	8074255	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	180	480	0	ENST00000377482.5:c.404del	p.Asn135ThrfsTer40	p.N135Tfs*40	ENST00000377482	NM_018948.3	135	aAc/ac	4/4	1	2	FACETS	0.936	0.869	1	0.936	0.869	1	CLONAL	1	TRUE	1	0.687792814101576	2		480	559	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266828	198266828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs16865307	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	216	436	1	ENST00000335508.6:c.2104C>T	p.Arg702Trp	p.R702W	ENST00000335508	NM_012433.2	702	Cgg/Tgg	15/25	1	2	FACETS	0.972	0.909	1	0.972	0.909	1	CLONAL	1	TRUE	1	0.687792814101576	2		437	646	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197564	106197564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754215085	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	151	405	0	ENST00000380013.4:c.5897G>A	p.Arg1966His	p.R1966H	ENST00000380013	NM_001127208.2	1966	cGt/cAt	11/11	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.687792814101576	2		405	431	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519505	137519506	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs780346130	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	117	279	3	ENST00000367739.4:c.1132_1133del	p.Ser378PhefsTer6	p.S378Ffs*6	ENST00000367739	NM_000416.2	378	AGt/t	7/7	1	2	FACETS	0.872	0.794	0.954	0.872	0.794	0.954	CLONAL	1	TRUE	1	0.687792814101576	2		282	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578421	7578421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779000871	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	266	985	0	ENST00000269305.4:c.509C>T	p.Thr170Met	p.T170M	ENST00000269305	NM_001126112.2	170	aCg/aTg	5/11	1	2	FACETS	0.921	0.866	0.977	0.921	0.866	0.977	CLONAL	1	TRUE	1	0.687792814101576	2		985	840	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101117	27101117	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	249	897	0	ENST00000324856.7:c.4403del	p.Pro1468LeufsTer13	p.P1468Lfs*13	ENST00000324856	NM_006015.4	1467	Ccc/cc	18/20	1	2	FACETS	0.997	0.937	1	0.997	0.937	1	CLONAL	1	TRUE	1	0.687792814101576	2		897	726	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332699	153332699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780061054	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	193	323	0	ENST00000281708.4:c.257C>T	p.Ser86Leu	p.S86L	ENST00000281708	NM_033632.3	86	tCg/tTg	2/12	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.687792814101576	2		323	515	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235935	108235935	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770641163	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	118	186	0	ENST00000278616.4:c.8977C>T	p.Arg2993Ter	p.R2993*	ENST00000278616	NM_000051.3	2993	Cga/Tga	62/63	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.687792814101576	2		186	333	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413710	138413710	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	193	501	7	ENST00000289153.2:c.1810del	p.Arg604GlyfsTer4	p.R604Gfs*4	ENST00000289153	NM_006219.2	604	Cgg/gg	12/22	1	2	FACETS	0.911	0.847	0.976	0.911	0.847	0.976	CLONAL	1	TRUE	1	0.687792814101576	2		508	616	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	539	1047	9	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.996	0.967	1	1	0.998	1	CLONAL	2	TRUE	1	0.687792814101576	2		1056	787	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110129	8110130	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs745673717	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	220	621	2	ENST00000585124.1:c.475dup	p.Arg159ProfsTer15	p.R159Pfs*15	ENST00000585124	NM_004217.3	159	cgc/cCgc	6/9	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.687792814101576	2		623	630	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955064	17955064	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749334592	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	315	1067	1	ENST00000458235.1:c.163G>A	p.Val55Met	p.V55M	ENST00000458235	NM_000215.3	55	Gtg/Atg	2/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.687792814101576	2		1068	840	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591246	67591246	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	117	149	0	ENST00000274335.5:c.1746-2A>G		p.X582_splice	ENST00000274335		582			0.20809928290302	3	FACETS	1	0.986	1	0.733	0.67	0.797	INDETERMINATE	1	TRUE	1	0.687792814101576	3		149	312	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187329	38187329	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2234552	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	42	460	0	ENST00000317025.8:c.1148G>A	p.Arg383Gln	p.R383Q	ENST00000317025	NM_023034.1	383	cGa/cAa	6/24	1	2	FACETS	0.209	0.174	0.248	0.209	0.174	0.248	SUBCLONAL	1	TRUE	1	0.687792814101576	2		460	584	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879672	151879672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	63	174	0	ENST00000262189.6:c.5273G>A	p.Arg1758His	p.R1758H	ENST00000262189	NM_170606.2	1758	cGt/cAt	36/59	1	2	FACETS	0.814	0.714	0.92	0.814	0.714	0.92	CLONAL	1	TRUE	1	0.687792814101576	2		174	225	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161293415	161293415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767802663	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	149	392	0	ENST00000367975.2:c.32G>A	p.Arg11His	p.R11H	ENST00000367975	NM_003001.3	11	cGt/cAt	2/6	1	2	FACETS	0.886	0.815	0.959	0.886	0.815	0.959	CLONAL	1	TRUE	1	0.687792814101576	2		392	489	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433374	138433374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746292811	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	107	122	0	ENST00000289153.2:c.1238C>T	p.Thr413Met	p.T413M	ENST00000289153	NM_006219.2	413	aCg/aTg	7/22	1	2	FACETS	0.886	0.803	0.972	0.886	0.803	0.972	CLONAL	1	TRUE	1	0.687792814101576	2		122	351	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	159	130	4	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.687792814101576	2		134	383	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155654	56155654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746479827	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	187	388	0	ENST00000399503.3:c.746G>A	p.Arg249His	p.R249H	ENST00000399503	NM_005921.1	249	cGc/cAc	3/20	1	2	FACETS	0.985	0.916	1	0.985	0.916	1	CLONAL	1	TRUE	1	0.687792814101576	2		388	552	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789590	3789591	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	211	502	1	ENST00000262367.5:c.4268dup	p.Pro1424SerfsTer13	p.P1424Sfs*13	ENST00000262367	NM_004380.2	1423	cct/ccCt	25/31	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.687792814101576	2		503	568	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137540464	137540464	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	107	539	0	ENST00000367739.4:c.1A>G	p.Met1?	p.M1?	ENST00000367739	NM_000416.2	1	Atg/Gtg	1/7	1	2	FACETS	0.892	0.808	0.978	0.892	0.808	0.978	CLONAL	1	TRUE	1	0.687792814101576	2		539	349	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148507467	148507467	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	157	308	0	ENST00000320356.2:c.1987T>C	p.Tyr663His	p.Y663H	ENST00000320356	NM_004456.4	663	Tat/Cat	17/20	1	2	FACETS	0.999	0.923	1	0.999	0.923	1	CLONAL	1	TRUE	1	0.687792814101576	2		308	457	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657480	29657480	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1135402880	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	210	224	0	ENST00000356175.3:c.5717del	p.Leu1906TrpfsTer15	p.L1906Wfs*15	ENST00000356175	NM_000267.3	1905	Ttt/tt	38/57	0.687792814101576	2	FACETS	0.948	0.902	0.993	0.948	0.902	0.993	CLONAL	2	TRUE	0	0.687792814101576	2		224	322	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883184	37883186	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	503	917	0	ENST00000269571.5:c.3092_3094del	p.Phe1031del	p.F1031del	ENST00000269571		1029	ggCTTc/ggc	25/27	0.687792814101576	2	FACETS	0.958	0.928	0.988	0.958	0.928	0.988	CLONAL	2	TRUE	0	0.687792814101576	2		917	763	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031859	10031859	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374637415	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	319	795	0	ENST00000330684.3:c.964G>A	p.Gly322Arg	p.G322R	ENST00000330684	NM_001134407.1	322	Ggg/Agg	3/13	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.687792814101576	2		795	821	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228146	36228146	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1232711537	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	292	906	0	ENST00000222270.7:c.7532G>A	p.Arg2511Gln	p.R2511Q	ENST00000222270	NM_014727.1	2511	cGg/cAg	33/37	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.687792814101576	2		906	802	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097224	11097224	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761515593	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	272	906	2	ENST00000358026.2:c.715G>A	p.Gly239Ser	p.G239S	ENST00000358026	NM_001128849.1	239	Ggc/Agc	4/36	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.687792814101576	2		908	756	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18975016	18975016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761111860	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	185	574	0	ENST00000262803.5:c.2813G>A	p.Arg938Gln	p.R938Q	ENST00000262803	NM_002911.3	938	cGg/cAg	20/24	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.687792814101576	2		574	524	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505134	149505134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367543286	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	213	617	2	ENST00000261799.4:c.1681C>T	p.Arg561Cys	p.R561C	ENST00000261799	NM_002609.3	561	Cgt/Tgt	12/23	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.687792814101576	2		619	613	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37628031	37628031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs578052035	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	241	782	0	ENST00000249071.6:c.229G>A	p.Val77Ile	p.V77I	ENST00000249071	NM_002872.4	77	Gtc/Atc	4/7	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.687792814101576	2		782	619	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609027	43609027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1483605155	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	168	741	1	ENST00000355710.3:c.1783G>A	p.Glu595Lys	p.E595K	ENST00000355710	NM_020975.4	595	Gag/Aag	10/20	1	2	FACETS	0.906	0.839	0.976	0.906	0.839	0.976	CLONAL	1	TRUE	1	0.687792814101576	2		742	539	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255248	16255248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752574502	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	184	368	1	ENST00000375759.3:c.2513C>T	p.Thr838Met	p.T838M	ENST00000375759	NM_015001.2	838	aCg/aTg	11/15	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.687792814101576	2		369	532	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349526	89349526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373193679	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	299	943	0	ENST00000301030.4:c.3424G>A	p.Asp1142Asn	p.D1142N	ENST00000301030	NM_001256183.1	1142	Gac/Aac	9/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.687792814101576	2		943	845	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162122	47162122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537154191	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	144	272	0	ENST00000409792.3:c.4004G>A	p.Arg1335His	p.R1335H	ENST00000409792	NM_014159.6	1335	cGt/cAt	3/21	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.687792814101576	2		272	413	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630214	100630214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	173	303	1	ENST00000308731.7:c.59C>T	p.Thr20Ile	p.T20I	ENST00000308731	NM_000061.2	20	aCa/aTa	2/19	1	2	FACETS	0.932	0.863	1	0.932	0.863	1	CLONAL	1	TRUE	1	0.687792814101576	2		304	540	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743580	46743580	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs888235109	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	306	788	2	ENST00000371975.4:c.1961G>A	p.Arg654His	p.R654H	ENST00000371975	NM_003579.3	654	cGc/cAc	17/18	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.687792814101576	2		790	839	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609400	39609400	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	129	219	0	ENST00000262039.4:c.1706del	p.Lys569ArgfsTer15	p.K569Rfs*15	ENST00000262039	NM_002647.2	568	Aaa/aa	15/25	1	2	FACETS	0.766	0.698	0.835	0.766	0.698	0.835	SUBCLONAL	1	TRUE	1	0.687792814101576	2		219	490	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412587	139412587	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	198	929	0	ENST00000277541.6:c.1255+2T>C		p.X419_splice	ENST00000277541	NM_017617.3	419			1	2	FACETS	0.92	0.856	0.985	0.92	0.856	0.985	CLONAL	1	TRUE	1	0.687792814101576	2		929	626	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822005	72822005	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	181	574	0	ENST00000268489.5:c.10170del	p.Val3391CysfsTer94	p.V3391Cfs*94	ENST00000268489	NM_006885.3	3390	aaA/aa	10/10	1	2	FACETS	0.948	0.881	1	0.948	0.881	1	CLONAL	1	TRUE	1	0.687792814101576	2		574	555	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599885	28599885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371066600	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	265	791	2	ENST00000253063.3:c.767G>A	p.Arg256His	p.R256H	ENST00000253063	NM_031459.4	256	cGc/cAc	6/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.687792814101576	2		793	698	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933744	36933744	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	153	982	1	ENST00000361632.4:c.1655del	p.Pro552LeufsTer27	p.P552Lfs*27	ENST00000361632		552	cCt/ct	12/16	1	2	FACETS	0.486	0.444	0.529	0.486	0.444	0.529	SUBCLONAL	1	TRUE	1	0.687792814101576	2		983	916	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363273	40363273	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	249	776	0	ENST00000397332.2:c.956T>C	p.Leu319Pro	p.L319P	ENST00000397332	NM_001033082.2	319	cTg/cCg	3/3	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.687792814101576	2		776	668	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726574	46726574	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145410495	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	262	664	2	ENST00000371975.4:c.653C>T	p.Ser218Leu	p.S218L	ENST00000371975	NM_003579.3	218	tCg/tTg	7/18	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.687792814101576	2		666	634	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998472	100998472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11571150	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	202	724	0	ENST00000325455.5:c.1330G>A	p.Ala444Thr	p.A444T	ENST00000325455	NM_001202474.3	444	Gcc/Acc	1/8	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.687792814101576	2		724	580	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377305	118377307	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	154	409	0	ENST00000534358.1:c.10702_10704del	p.Ser3568del	p.S3568del	ENST00000534358	NM_005933.3	3566	agTTCt/agt	27/36	1	2	FACETS	0.969	0.895	1	0.969	0.895	1	CLONAL	1	TRUE	1	0.687792814101576	2		409	462	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427411	49427411	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	285	932	1	ENST00000301067.7:c.11077G>A	p.Ala3693Thr	p.A3693T	ENST00000301067	NM_003482.3	3693	Gct/Act	39/54	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.687792814101576	2		933	811	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487287	56487287	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1010091317	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	204	583	0	ENST00000267101.3:c.1433C>T	p.Thr478Met	p.T478M	ENST00000267101	NM_001982.3	478	aCg/aTg	12/28	1	2	FACETS	0.942	0.878	1	0.942	0.878	1	CLONAL	1	TRUE	1	0.687792814101576	2		583	630	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856029	111856029	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	262	915	1	ENST00000341259.2:c.80G>A	p.Ser27Asn	p.S27N	ENST00000341259	NM_005475.2	27	aGc/aAc	2/8	1	2	FACETS	0.995	0.936	1	0.995	0.936	1	CLONAL	1	TRUE	1	0.687792814101576	2		916	766	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123892111	123892111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	59	139	0	ENST00000330479.4:c.920C>T	p.Thr307Ile	p.T307I	ENST00000330479	NM_020382.3	307	aCc/aTc	8/9	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.687792814101576	2		139	140	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527876	103527876	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs764475818	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	42	169	0	ENST00000355739.4:c.3184A>G	p.Asn1062Asp	p.N1062D	ENST00000355739	NM_000123.3	1062	Aat/Gat	15/15	1	2	FACETS	0.461	0.387	0.542	0.461	0.387	0.542	SUBCLONAL	1	TRUE	1	0.687792814101576	2		169	265	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435492	110435492	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1475680302	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	248	655	0	ENST00000375856.3:c.2909G>A	p.Arg970Gln	p.R970Q	ENST00000375856	NM_003749.2	970	cGg/cAg	1/2	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.687792814101576	2		655	721	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872027	35872027	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	198	530	0	ENST00000216797.5:c.586C>A	p.Leu196Met	p.L196M	ENST00000216797	NM_020529.2	196	Ctg/Atg	4/6	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.687792814101576	2		530	574	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823912	3823912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754386072	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	292	810	0	ENST00000262367.5:c.2303G>A	p.Arg768Gln	p.R768Q	ENST00000262367	NM_004380.2	768	cGa/cAa	13/31	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.687792814101576	2		810	742	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980498	7980498	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	137	645	0	ENST00000319144.4:c.1085C>A	p.Pro362His	p.P362H	ENST00000319144	NM_001139.2	362	cCt/cAt	9/15	1	2	FACETS	0.778	0.712	0.847	0.778	0.712	0.847	SUBCLONAL	1	TRUE	1	0.687792814101576	2		645	512	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881166	37881166	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	209	776	0	ENST00000269571.5:c.2493+2T>C		p.X831_splice	ENST00000269571		831			0.687792814101576	2	FACETS	1	0.944	1	0.506	0.472	0.54	CLONAL	1	TRUE	0	0.687792814101576	2		776	601	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11031541	11031541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1160510813	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	293	1068	0	ENST00000327064.4:c.1456G>A	p.Gly486Ser	p.G486S	ENST00000327064	NM_199141.1	486	Ggc/Agc	13/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.687792814101576	2		1068	825	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289926	15289926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758961316	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	319	1184	2	ENST00000263388.2:c.3628C>T	p.Arg1210Cys	p.R1210C	ENST00000263388	NM_000435.2	1210	Cgc/Tgc	22/33	1	2	FACETS	0.968	0.916	1	0.968	0.916	1	CLONAL	1	TRUE	1	0.687792814101576	2		1186	958	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366258	15366258	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	291	832	0	ENST00000263377.2:c.1897G>A	p.Val633Met	p.V633M	ENST00000263377	NM_058243.2	633	Gtg/Atg	10/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.687792814101576	2		832	732	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18963105	18963105	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	184	702	0	ENST00000262803.5:c.972G>T	p.Gln324His	p.Q324H	ENST00000262803	NM_002911.3	324	caG/caT	6/24	1	2	FACETS	0.892	0.828	0.958	0.892	0.828	0.958	CLONAL	1	TRUE	1	0.687792814101576	2		702	600	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218462	36218462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762074423	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	252	1039	1	ENST00000222270.7:c.4241G>A	p.Arg1414His	p.R1414H	ENST00000222270	NM_014727.1	1414	cGc/cAc	16/37	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.687792814101576	2		1040	703	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657044	47657061	+	inframe_deletion	In_Frame_Del	DEL	CTACCTAATGTTATACAG	CTACCTAATGTTATACAG	-	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	59	112	0	ENST00000233146.2:c.1240_1257del	p.Leu414_Gln419del	p.L414_Q419del	ENST00000233146	NM_000251.2	414	CTACCTAATGTTATACAG/-	7/16	1	2	FACETS	0.675	0.587	0.769	0.675	0.587	0.769	SUBCLONAL	1	TRUE	1	0.687792814101576	2		112	254	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698103	47698103	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs267607970	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	43	50	0	ENST00000233146.2:c.1662-1G>A		p.X554_splice	ENST00000233146	NM_000251.2	554			1	2	FACETS	0.834	0.711	0.964	0.834	0.711	0.964	CLONAL	1	TRUE	1	0.687792814101576	2		50	150	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636929	158636929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775537696	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	229	588	0	ENST00000263640.3:c.251C>T	p.Pro84Leu	p.P84L	ENST00000263640	NM_001105.4	84	cCg/cTg	4/11	1	2	FACETS	0.955	0.895	1	0.955	0.895	1	CLONAL	1	TRUE	1	0.687792814101576	2		588	697	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273126	198273126	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	242	580	0	ENST00000335508.6:c.1084A>G	p.Thr362Ala	p.T362A	ENST00000335508	NM_012433.2	362	Aca/Gca	8/25	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.687792814101576	2		580	653	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022881	31022881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1386308534	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	158	633	0	ENST00000375687.4:c.2366G>A	p.Cys789Tyr	p.C789Y	ENST00000375687	NM_015338.5	789	tGt/tAt	13/13	1	2	FACETS	0.84	0.774	0.908	0.84	0.774	0.908	CLONAL	1	TRUE	1	0.687792814101576	2		633	547	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375203	31375203	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	281	943	0	ENST00000328111.2:c.600G>A	p.Met200Ile	p.M200I	ENST00000328111	NM_006892.3	200	atG/atA	6/23	1	2	FACETS	0.916	0.863	0.97	0.916	0.863	0.97	CLONAL	1	TRUE	1	0.687792814101576	2		943	892	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573201	41573201	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	277	895	0	ENST00000263253.7:c.5486G>A	p.Arg1829His	p.R1829H	ENST00000263253	NM_001429.3	1829	cGc/cAc	31/31	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.687792814101576	2		895	738	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940492	49940492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	313	1132	0	ENST00000296474.3:c.551C>T	p.Thr184Ile	p.T184I	ENST00000296474	NM_002447.2	184	aCc/aTc	1/20	1	2	FACETS	0.99	0.937	1	0.99	0.937	1	CLONAL	1	TRUE	1	0.687792814101576	2		1132	919	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437609	52437609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775789477	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	274	919	2	ENST00000460680.1:c.1552C>T	p.Arg518Trp	p.R518W	ENST00000460680	NM_004656.3	518	Cgg/Tgg	13/17	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.687792814101576	2		921	794	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747945	41747945	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1214203989	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	22	374	0	ENST00000226382.2:c.824C>T	p.Pro275Leu	p.P275L	ENST00000226382	NM_003924.3	275	cCc/cTc	3/3	1	2	FACETS	0.186	0.144	0.235	0.186	0.144	0.235	SUBCLONAL	1	TRUE	1	0.687792814101576	2		374	344	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164917	106164917	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1455459760	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	177	421	0	ENST00000380013.4:c.3785G>A	p.Arg1262Gln	p.R1262Q	ENST00000380013	NM_001127208.2	1262	cGg/cAg	6/11	1	2	FACETS	0.996	0.924	1	0.996	0.924	1	CLONAL	1	TRUE	1	0.687792814101576	2		421	517	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755734	57755735	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	90	945	0	ENST00000274289.3:c.52_53del	p.Cys18ArgfsTer87	p.C18Rfs*87	ENST00000274289	NM_006622.3	18	TGc/c	1/14	0.20809928290302	3	FACETS	0.436	0.386	0.489	0.218	0.193	0.245	INDETERMINATE	1	TRUE	1	0.687792814101576	3		945	807	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948316	31948316	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	183	641	0	ENST00000375333.2:c.904T>G	p.Phe302Val	p.F302V	ENST00000375333	NM_032454.1	302	Ttt/Gtt	6/8	1	2	FACETS	0.978	0.909	1	0.978	0.909	1	CLONAL	1	TRUE	1	0.687792814101576	2		641	544	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415018	116415018	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	50	475	0	ENST00000397752.3:c.3115del	p.Asp1039ThrfsTer20	p.D1039Tfs*20	ENST00000397752	NM_000245.2	1038	Ggg/gg	15/21	1	2	FACETS	0.269	0.228	0.314	0.269	0.228	0.314	SUBCLONAL	1	TRUE	1	0.687792814101576	2		475	541	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152055689	152055690	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	140	312	0	ENST00000262189.6:c.232_233del	p.Glu78AsnfsTer17	p.E78Nfs*17	ENST00000262189	NM_170606.2	78	GAa/a	2/59	1	2	FACETS	0.746	0.682	0.811	0.746	0.682	0.811	SUBCLONAL	1	TRUE	1	0.687792814101576	2		312	546	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981891	70981892	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	45	1043	2	ENST00000276594.2:c.204dup	p.Phe69LeufsTer59	p.F69Lfs*59	ENST00000276594	NM_024504.3	68	-/C	2/8	1	2	FACETS	0.167	0.14	0.198	0.167	0.14	0.198	SUBCLONAL	1	TRUE	1	0.687792814101576	2		1045	783	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741252	145741252	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	97	988	1	ENST00000428558.2:c.1154A>C	p.Lys385Thr	p.K385T	ENST00000428558	NM_004260.3	385	aAg/aCg	6/22	1	2	FACETS	0.345	0.307	0.385	0.345	0.307	0.385	SUBCLONAL	1	TRUE	1	0.687792814101576	2		989	818	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341967	8341967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	81	239	0	ENST00000356435.5:c.4673G>A	p.Gly1558Asp	p.G1558D	ENST00000356435		1558	gGc/gAc	29/35	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.687792814101576	2		239	232	SUCCESS
AR	367	MSKCC	GRCh37	X	66766141	66766141	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	213	859	0	ENST00000374690.3:c.1153G>A	p.Ala385Thr	p.A385T	ENST00000374690	NM_000044.3	385	Gct/Act	1/8	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.687792814101576	2		859	593	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352370	70352370	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	190	618	0	ENST00000374080.3:c.4397A>G	p.Asp1466Gly	p.D1466G	ENST00000374080		1466	gAt/gGt	31/45	1	2	FACETS	0.981	0.913	1	0.981	0.913	1	CLONAL	1	TRUE	1	0.687792814101576	2		618	563	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0045826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	42	278	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.15	2		278	481	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155721	56155722	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0045826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	44	339	0	ENST00000399503.3:c.816_817del	p.Arg273SerfsTer27	p.R273Sfs*27	ENST00000399503	NM_005921.1	271	agAAaa/agaa	3/20	0.155937194172525	3	FACETS	1	0.933	1	0.615	0.515	0.725	CLONAL	1	TRUE	1	0.15	3		339	513	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231772	36231773	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0045826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	45	676	0	ENST00000300305.3:c.611dup	p.Arg205LysfsTer8	p.R205Kfs*8	ENST00000300305		204	cga/cgGa	5/8	1	2	FACETS	0.861	0.722	1	0.861	0.722	1	CLONAL	1	TRUE	1	0.15	2		676	697	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161318	55161318	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	32	433	0	ENST00000257290.5:c.3149T>A	p.Ile1050Asn	p.I1050N	ENST00000257290	NM_006206.4	1050	aTt/aAt	23/23	1	2	FACETS	0.848	0.688	1	0.848	0.688	1	CLONAL	1	TRUE	1	0.15	2		433	503	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184052	56184052	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0045826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	36	266	0	ENST00000399503.3:c.4258-1G>A		p.X1420_splice	ENST00000399503	NM_005921.1	1420			0.155937194172525	3	FACETS	1	0.919	1	0.611	0.503	0.733	CLONAL	1	TRUE	1	0.15	3		266	422	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945319	151945320	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0045826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	10	113	0	ENST00000262189.6:c.2198_2199dup	p.Thr734LeufsTer4	p.T734Lfs*4	ENST00000262189	NM_170606.2	733	-/CT	14/59	1	2	FACETS	0.959	0.652	1	0.959	0.652	1	CLONAL	1	TRUE	1	0.15	2		113	139	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0045828-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	52	623	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.737008937617701	1	FACETS	0.928	0.825	1	0.928	0.825	1	CLONAL	1	TRUE	0	0.737008937617701	1		623	96	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982123	93982123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769773179	NA	P-0045828-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	36	409	0	ENST00000369303.4:c.1342G>A	p.Gly448Arg	p.G448R	ENST00000369303	NM_004440.3	448	Gga/Aga	6/17	0.429466264946854	1	FACETS	0.518	0.436	0.606	0.518	0.436	0.606	INDETERMINATE	1	TRUE	0	0.737008937617701	1		409	119	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647400	3647400	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763869769	NA	P-0045828-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	31	817	1	ENST00000294008.3:c.1663G>A	p.Val555Met	p.V555M	ENST00000294008	NM_032444.2	555	Gtg/Atg	7/15	0.151145852500366	2	FACETS	0.486	0.397	0.584	0.243	0.198	0.292	INDETERMINATE	1	TRUE	0	0.737008937617701	2		818	173	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881395	37881395	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045828-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1879	1481	874	0	ENST00000269571.5:c.2587G>C	p.Asp863His	p.D863H	ENST00000269571		863	Gac/Cac	21/27	0.737008937617701	60	FACETS	0.991	0.968	1			1	CLONAL	27	TRUE	NA	0.737008937617701	60		874	3360	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259439	55259439	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs397517126	NA	P-0045829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	195	465	0	ENST00000275493.2:c.2497T>G	p.Leu833Val	p.L833V	ENST00000275493	NM_005228.3	833	Ttg/Gtg	21/28	0.274150291157837	4	FACETS	0.883	0.819	0.949	0.883	0.819	0.949	CLONAL	2	TRUE	2	0.388079889030949	4		465	790	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28929495	NA	P-0045829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	222	647	0	ENST00000275493.2:c.2155G>T	p.Gly719Cys	p.G719C	ENST00000275493	NM_005228.3	719	Ggc/Tgc	18/28	0.274150291157837	4	FACETS	0.892	0.832	0.955	0.892	0.832	0.955	CLONAL	2	TRUE	2	0.388079889030949	4		647	890	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632303	215632303	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	169	451	0	ENST00000260947.4:c.1471G>T	p.Gly491Trp	p.G491W	ENST00000260947	NM_000465.2	491	Ggg/Tgg	6/11	0.332394989242744	3	FACETS	0.757	0.698	0.818	0.757	0.698	0.818	SUBCLONAL	2	TRUE	1	0.388079889030949	3		451	687	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069607	69069607	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	28	381	0	ENST00000288368.4:c.4282G>T	p.Glu1428Ter	p.E1428*	ENST00000288368	NM_024870.2	1428	Gaa/Taa	35/40	1	2	FACETS	0.363	0.289	0.446	0.363	0.289	0.446	SUBCLONAL	1	TRUE	1	0.388079889030949	2		381	398	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149917	202149917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	123	514	0	ENST00000358485.4:c.1358C>T	p.Pro453Leu	p.P453L	ENST00000358485	NM_001080125.1	453	cCg/cTg	8/9	1	2	FACETS	0.968	0.879	1	0.968	0.879	1	CLONAL	1	TRUE	1	0.45797387841997	2		514	555	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745987	162745987	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	131	259	0	ENST00000367921.3:c.2110C>T	p.Leu704Phe	p.L704F	ENST00000367921	NM_006182.2	704	Ctt/Ttt	16/18	0.281032116565449	5	FACETS	1	0.925	1	0.676	0.617	0.737	CLONAL	2	TRUE	2	0.45797387841997	5		259	476	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448631	89448631	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0045831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	96	415	0	ENST00000336596.2:c.1594+1G>C		p.X532_splice	ENST00000336596	NM_005233.5	532			0.314277862923919	5	FACETS	1	0.917	1	0.345	0.307	0.385	CLONAL	1	TRUE	2	0.45797387841997	5		415	684	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	350	700	1	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		701	515	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508173	106508173	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1315748037	NA	P-0045833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	220	374	0	ENST00000359195.3:c.167C>T	p.Thr56Met	p.T56M	ENST00000359195	NM_002649.2	56	aCg/aTg	2/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		374	587	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233526	69233526	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	41	367	0	ENST00000462284.1:c.1391T>C	p.Leu464Pro	p.L464P	ENST00000462284	NM_002392.5	464	cTt/cCt	11/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		367	547	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339044	225339044	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	43	450	0	ENST00000264414.4:c.2225A>G	p.Lys742Arg	p.K742R	ENST00000264414	NM_003590.4	742	aAg/aGg	16/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		450	321	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27229216	27229216	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045833-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	51	558	0	ENST00000380036.4:c.3361G>C	p.Glu1121Gln	p.E1121Q	ENST00000380036	NM_000459.3	1121	Gaa/Caa	23/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		558	781	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0045835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	401	294	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.690214029195738	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	1	0.690214029195738	4		294	630	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699369	47699369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	104	380	0	ENST00000347630.2:c.139G>A	p.Glu47Lys	p.E47K	ENST00000347630	NM_001007230.1	47	Gaa/Aaa	4/11	0.690214029195738	3	FACETS	1	0.933	1	0.521	0.47	0.574	CLONAL	1	TRUE	1	0.690214029195738	3		380	389	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576184	88576184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770581794	NA	P-0045835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	262	663	0	ENST00000360948.2:c.1489G>A	p.Gly497Arg	p.G497R	ENST00000360948	NM_001012338.2	497	Ggg/Agg	13/19	0.690214029195738	3	FACETS	1	0.974	1	0.535	0.502	0.569	CLONAL	1	TRUE	1	0.690214029195738	3		663	954	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770613	40770613	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	155	415	0	ENST00000373198.4:c.2769G>A	p.Trp923Ter	p.W923*	ENST00000373198	NM_133170.3	923	tgG/tgA	19/32	0.690214029195738	3	FACETS	1	0.968	1	0.55	0.506	0.595	CLONAL	1	TRUE	1	0.690214029195738	3		415	549	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739734	41739734	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	256	644	0	ENST00000242208.4:c.239A>G	p.Lys80Arg	p.K80R	ENST00000242208	NM_002192.2	80	aAg/aGg	2/3	0.670064458915475	4	FACETS	1	0.959	1	0.517	0.483	0.552	CLONAL	1	TRUE	2	0.690214029195738	4		644	1213	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455225	29455225	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs61754865	NA	P-0045836-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	55	693	0	ENST00000389048.3:c.2577G>C	p.Glu859Asp	p.E859D	ENST00000389048	NM_004304.4	859	gaG/gaC	15/29	0.194637603435145	3	FACETS	0.702	0.599	0.815	0.351	0.299	0.408	SUBCLONAL	1	TRUE	1	0.223508226017597	3		693	779	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	75	425	0				ENST00000310581	NM_198253.2	-/1132			0.237237463121744	3	FACETS	1	0.916	1	0.35	0.308	0.395	INDETERMINATE	1	TRUE	0	0.424480418020644	3		425	408	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143994	11143994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	292	788	0	ENST00000358026.2:c.3575G>A	p.Arg1192His	p.R1192H	ENST00000358026	NM_001128849.1	1192	cGc/cAc	26/36	0.424480418020644	4	FACETS	0.942	0.887	0.998	0.942	0.887	0.998	CLONAL	2	TRUE	2	0.424480418020644	4		788	1040	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048638	6048638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	332	781	0	ENST00000265849.7:c.13G>A	p.Glu5Lys	p.E5K	ENST00000265849	NM_000535.5	5	Gag/Aag	1/15	0.424480418020644	6	FACETS	1	0.985	1	0.557	0.526	0.589	CLONAL	2	TRUE	2	0.424480418020644	6		781	1297	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983111	111983111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	137	618	0	ENST00000368678.4:c.1436G>A	p.Gly479Asp	p.G479D	ENST00000368678		479	gGc/gAc	13/13	0.260970745670878	3	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.424480418020644	3		618	609	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426088	49426089	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0045839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	599	959	1	ENST00000301067.7:c.12399_12400del	p.Leu4134GlyfsTer33	p.L4134Gfs*33	ENST00000301067	NM_003482.3	4133	ctGCtg/cttg	39/54	0.424480418020644	5	FACETS	0.954	0.921	0.987	0.954	0.921	0.987	CLONAL	4	TRUE	1	0.424480418020644	5		960	1211	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060709	38060737	+	frameshift_variant	Frame_Shift_Del	DEL	GAGTATTGCAGTGCCTGTTCGTATGCCTT	GAGTATTGCAGTGCCTGTTCGTATGCCTT	-	novel	NA	P-0045839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	569	1232	0	ENST00000250448.2:c.1252_1280del	p.Lys418AlafsTer130	p.K418Afs*130	ENST00000250448	NM_004496.3	418	AAGGCATACGAACAGGCACTGCAATACTCg/g	2/2	0.424480418020644	4	FACETS	0.917	0.882	0.953	0.917	0.882	0.953	CLONAL	3	TRUE	1	0.424480418020644	4		1232	1388	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99192832	99192832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs745454926	NA	P-0045839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	210	604	0	ENST00000268035.6:c.22G>C	p.Gly8Arg	p.G8R	ENST00000268035	NM_000875.3	8	Ggg/Cgg	1/21	0.373515549341252	5	FACETS	0.885	0.822	0.95	0.354	0.329	0.38	CLONAL	2	TRUE	0	0.424480418020644	5		604	915	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830774	3830786	+	frameshift_variant	Frame_Shift_Del	DEL	TTCGTGCCAGCCT	TTCGTGCCAGCCT	-	novel	NA	P-0045839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	164	537	0	ENST00000262367.5:c.1770_1782del	p.Lys590AsnfsTer11	p.K590Nfs*11	ENST00000262367	NM_004380.2	590	aaAGGCTGGCACGAA/aa	8/31	0.424480418020644	3	FACETS	0.797	0.735	0.86	0.531	0.49	0.574	SUBCLONAL	2	TRUE	0	0.424480418020644	3		537	588	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641038	23641038	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs766396469	NA	P-0045839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	113	713	0	ENST00000261584.4:c.2437A>G	p.Ile813Val	p.I813V	ENST00000261584	NM_024675.3	813	Att/Gtt	5/13	0.424480418020644	4	FACETS	0.872	0.784	0.965			1	CLONAL	1	TRUE	NA	0.424480418020644	4		713	870	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897351	78897351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	179	1084	0	ENST00000306801.3:c.2686C>T	p.Pro896Ser	p.P896S	ENST00000306801	NM_020761.2	896	Ccg/Tcg	23/34	0.424480418020644	3	FACETS	0.955	0.88	1	0.318	0.293	0.345	CLONAL	1	TRUE	0	0.424480418020644	3		1084	1070	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11030601	11030601	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	133	887	0	ENST00000327064.4:c.1155C>A	p.His385Gln	p.H385Q	ENST00000327064	NM_199141.1	385	caC/caA	10/16	0.424480418020644	4	FACETS	0.845	0.766	0.929	0.423	0.383	0.465	CLONAL	1	TRUE	2	0.424480418020644	4		887	1056	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953154	17953154	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs200147096	NA	P-0045839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	234	1042	0	ENST00000458235.1:c.832G>C	p.Gly278Arg	p.G278R	ENST00000458235	NM_000215.3	278	Ggc/Cgc	6/24	0.424480418020644	4	FACETS	1	0.984	1	0.589	0.548	0.631	CLONAL	1	TRUE	2	0.424480418020644	4		1042	1334	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860781	45860781	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	157	850	1	ENST00000391945.4:c.1328C>T	p.Ala443Val	p.A443V	ENST00000391945	NM_000400.3	443	gCc/gTc	14/23	0.424480418020644	4	FACETS	0.966	0.883	1	0.322	0.294	0.351	CLONAL	1	TRUE	1	0.424480418020644	4		851	1091	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149925	99149925	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	73	687	0	ENST00000074304.5:c.237C>G	p.Phe79Leu	p.F79L	ENST00000074304	NM_001134224.1	79	ttC/ttG	5/26	0.424480418020644	4	FACETS	0.514	0.448	0.585	0.171	0.149	0.195	SUBCLONAL	1	TRUE	1	0.424480418020644	4		687	954	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225400359	225400359	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0045839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	91	218	0	ENST00000264414.4:c.265-1G>C		p.X89_splice	ENST00000264414	NM_003590.4	89			0.424480418020644	3	FACETS	0.922	0.829	1	0.922	0.829	1	CLONAL	2	TRUE	1	0.424480418020644	3		218	282	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440393	52440393	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0045839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	208	575	1	ENST00000460680.1:c.660-1G>T		p.X220_splice	ENST00000460680	NM_004656.3	220			0.424480418020644	7	FACETS	0.958	0.889	1	0.383	0.355	0.412	CLONAL	2	TRUE	2	0.424480418020644	7		576	1054	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442075	52442075	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	500	673	0	ENST00000460680.1:c.274G>C	p.Ala92Pro	p.A92P	ENST00000460680	NM_004656.3	92	Gca/Cca	5/17	0.424480418020644	7	FACETS	1	0.989	1	0.859	0.825	0.894	CLONAL	4	TRUE	2	0.424480418020644	7		673	1130	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955572	55955572	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	77	466	0	ENST00000263923.4:c.3373A>C	p.Met1125Leu	p.M1125L	ENST00000263923	NM_002253.2	1125	Atg/Ctg	25/30	0.395413273249292	3	FACETS	0.922	0.812	1	0.307	0.27	0.347	CLONAL	1	TRUE	0	0.424480418020644	3		466	477	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384700	84384700	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	93	436	0	ENST00000321945.7:c.743del	p.Asn248ThrfsTer3	p.N248Tfs*3	ENST00000321945	NM_139076.2	248	aAc/ac	8/9	0.424480418020644	3	FACETS	1	0.905	1	0.339	0.302	0.378	CLONAL	1	TRUE	0	0.424480418020644	3		436	523	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542645	187542645	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	225	478	0	ENST00000441802.2:c.5095T>A	p.Tyr1699Asn	p.Y1699N	ENST00000441802	NM_005245.3	1699	Tat/Aat	10/27	0.424480418020644	3	FACETS	0.983	0.928	1	0.983	0.928	1	CLONAL	3	TRUE	0	0.424480418020644	3		478	436	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751394	57751394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	91	390	0	ENST00000274289.3:c.1597G>A	p.Ala533Thr	p.A533T	ENST00000274289	NM_006622.3	533	Gct/Act	11/14	0.3194832633166	4	FACETS	1	0.97	1	0.627	0.559	0.699	CLONAL	1	TRUE	2	0.424480418020644	4		390	487	SUCCESS
MET	4233	MSKCC	GRCh37	7	116398560	116398560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	252	513	1	ENST00000397752.3:c.2150C>T	p.Ser717Leu	p.S717L	ENST00000397752	NM_000245.2	717	tCa/tTa	9/21	0.424480418020644	6	FACETS	1	0.977	1			1	CLONAL	3	TRUE	NA	0.424480418020644	6		514	681	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044977	47044977	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045839-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	388	1035	0	ENST00000377604.3:c.2303T>A	p.Phe768Tyr	p.F768Y	ENST00000377604	NM_001204468.1	768	tTc/tAc	20/24	0.424480418020644	2	FACETS	0.96	0.916	1	0.96	0.916	1	CLONAL	2	TRUE	0	0.424480418020644	2		1035	952	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443695	29443695	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs863225281	NA	P-0121530-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	284	572	0	ENST00000389048.3:c.3522C>A	p.Phe1174Leu	p.F1174L	ENST00000389048	NM_004304.4	1174	ttC/ttA	23/29	0.334428743227797	2	FACETS	0.987	0.932	1	0.494	0.466	0.522	INDETERMINATE	1	NA	0	0.700630434703832	2		572	821	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0045841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	210	354	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.85169899167012	1	FACETS	0.973	0.93	1	0.973	0.93	1	CLONAL	1	TRUE	0	0.85169899167012	1		354	291	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0045841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	272	278	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.85169899167012	3	FACETS	0.92	0.875	0.964	0.92	0.875	0.964	CLONAL	2	TRUE	1	0.85169899167012	3		278	495	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750684	128750684	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	492	450	0	ENST00000377970.2:c.221C>G	p.Pro74Arg	p.P74R	ENST00000377970	NM_002467.4	74	cCg/cGg	2/3	0.85169899167012	3	FACETS	0.989	0.955	1	0.989	0.955	1	CLONAL	2	TRUE	1	0.85169899167012	3		450	833	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	232	342	0	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	0.85169899167012	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.85169899167012	1		342	308	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519989	NA	P-0045841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	275	386	0	ENST00000269305.4:c.730G>C	p.Gly244Arg	p.G244R	ENST00000269305	NM_001126112.2	244	Ggc/Cgc	7/11	0.85169899167012	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.85169899167012	1		386	364	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66737031	66737031	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs769044712	NA	P-0045841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	223	318	0	ENST00000307102.5:c.554A>G	p.Lys185Arg	p.K185R	ENST00000307102	NM_002755.3	185	aAg/aGg	5/11	1	2	FACETS	0.906	0.85	0.963	0.906	0.85	0.963	CLONAL	1	TRUE	1	0.85169899167012	2		318	578	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922250	39922251	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	94	330	0	ENST00000378444.4:c.3921dup	p.Gln1308SerfsTer18	p.Q1308Sfs*18	ENST00000378444	NM_001123385.1	1307	-/T	9/15	0.85169899167012	1	FACETS	0.427	0.384	0.471	0.427	0.384	0.471	SUBCLONAL	1	TRUE	0	0.85169899167012	1		330	297	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041604	47041604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	40	474	0	ENST00000377604.3:c.1829G>A	p.Gly610Glu	p.G610E	ENST00000377604	NM_001204468.1	610	gGg/gAg	17/24	0.85169899167012	1	FACETS	0.126	0.104	0.15	0.126	0.104	0.15	SUBCLONAL	1	TRUE	0	0.85169899167012	1		474	429	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019927	123019927	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	151	457	2	ENST00000355640.3:c.415T>C	p.Tyr139His	p.Y139H	ENST00000355640		139	Tat/Cat	2/7	0.4552105732978	1	FACETS	0.378	0.348	0.41	0.378	0.348	0.41	INDETERMINATE	1	TRUE	0	0.85169899167012	1		459	538	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	318	500	0	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.686490566410633	3	FACETS	0.809	0.768	0.851	0.539	0.512	0.567	CLONAL	2	TRUE	0	0.686490566410633	3		500	769	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0045843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	344	714	0	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	0.686490566410633	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.686490566410633	2		714	501	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981531	55981531	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35636987	NA	P-0045843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	27	257	1	ENST00000263923.4:c.406G>A	p.Val136Met	p.V136M	ENST00000263923	NM_002253.2	136	Gtg/Atg	4/30	0.686490566410633	3	FACETS	0.277	0.22	0.342	0.138	0.11	0.171	SUBCLONAL	1	TRUE	1	0.686490566410633	3		258	382	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130365	2130365	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045843-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	361	559	0	ENST00000219476.3:c.3598del	p.Arg1200GlyfsTer10	p.R1200Gfs*10	ENST00000219476	NM_000548.3	1199	gtC/gt	30/42	0.686490566410633	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.686490566410633	2		559	504	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	73	425	0				ENST00000310581	NM_198253.2	-/1132			0.320102027023516	1	FACETS	0.804	0.713	0.9	0.804	0.713	0.9	CLONAL	1	TRUE	0	0.532702212310205	1		425	250	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185062	123185062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	23	336	0	ENST00000218089.9:c.1109G>A	p.Arg370Gln	p.R370Q	ENST00000218089	NM_001042749.1	370	cGg/cAg	12/35	0.532702212310205	1	FACETS	0.487	0.385	0.602	0.487	0.385	0.602	SUBCLONAL	1	TRUE	0	0.532702212310205	1		336	130	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974795	21974818	+	inframe_deletion	In_Frame_Del	DEL	GGCTCCATGCTGCTCCCCGCCGCC	GGCTCCATGCTGCTCCCCGCCGCC	-	rs587780668	NA	P-0045844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	10	175	0	ENST00000304494.5:c.9_32del	p.Ala4_Pro11del	p.A4_P11del	ENST00000304494	NM_000077.4	3	ccGGCGGCGGGGAGCAGCATGGAGCCt/cct	1/3	1	2	FACETS	0.204	0.138	0.287	0.204	0.138	0.287	SUBCLONAL	1	TRUE	1	0.532702212310205	2		175	184	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696453	47696453	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	27	334	0	ENST00000347630.2:c.370A>T	p.Arg124Trp	p.R124W	ENST00000347630	NM_001007230.1	124	Agg/Tgg	6/11	0.105331697957323	5	FACETS	0.406	0.323	0.502	0.135	0.107	0.168	INDETERMINATE	1	TRUE	2	0.532702212310205	5		334	449	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610462	10610462	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045844-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	222	572	0	ENST00000171111.5:c.248T>A	p.Val83Asp	p.V83D	ENST00000171111	NM_203500.1	83	gTc/gAc	2/6	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.532702212310205	2		572	792	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0045845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	123	623	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.384259045173899	1	FACETS	0.969	0.88	1	0.969	0.88	1	CLONAL	1	TRUE	0	0.384259045173899	1		623	534	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0045845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	127	354	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.798	0.73	0.869	1	0.988	1	SUBCLONAL	2	TRUE	1	0.384259045173899	2		354	414	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038846	47038846	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	161	270	0	ENST00000377604.3:c.853C>T	p.Gln285Ter	p.Q285*	ENST00000377604	NM_001204468.1	285	Caa/Taa	9/24	1	1	FACETS	0.895	0.832	0.959	1	0.992	1	CLONAL	2	TRUE	0	0.384259045173899	1		270	378	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968823	15968823	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	100	332	0	ENST00000268712.3:c.4927G>T	p.Gly1643Cys	p.G1643C	ENST00000268712	NM_006311.3	1643	Ggt/Tgt	33/46	0.384259045173899	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.384259045173899	1		332	378	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243870	53243870	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0045845-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	125	194	0	ENST00000375401.3:c.1122+1G>A		p.X374_splice	ENST00000375401	NM_004187.3	374			1	1	FACETS	0.787	0.722	0.854	1	0.988	1	SUBCLONAL	2	TRUE	0	0.384259045173899	1		194	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0045847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	165	833	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.449784233208757	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.449784233208757	1		833	552	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214612	5214612	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139132124	NA	P-0045847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	197	514	2	ENST00000357368.4:c.4454C>T	p.Ala1485Val	p.A1485V	ENST00000357368	NM_002850.3	1485	gCg/gTg	29/38	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.449784233208757	2		516	764	SUCCESS
APC	324	MSKCC	GRCh37	5	112174437	112174437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs876658667	NA	P-0045847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	38	152	0	ENST00000257430.4:c.3146G>A	p.Trp1049Ter	p.W1049*	ENST00000257430	NM_000038.5	1049	tGg/tAg	16/16	0.449784233208757	1	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	0	0.449784233208757	1		152	122	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103525619	103525619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs574826021	NA	P-0045847-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	67	196	0	ENST00000355739.4:c.2890C>T	p.Arg964Trp	p.R964W	ENST00000355739	NM_000123.3	964	Cgg/Tgg	14/15	0.170201620468409	5	FACETS	1	0.906	1	0.349	0.304	0.398	INDETERMINATE	1	TRUE	2	0.449784233208757	5		196	476	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0045848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	323	454	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.650504667109833	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.650504667109833	3		454	642	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156732	20156732	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045848-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	131	271	0	ENST00000379607.5:c.25G>C	p.Gly9Arg	p.G9R	ENST00000379607	NM_001412.3	9	Ggt/Cgt	2/7	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.650504667109833	2		271	380	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0045849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	32	354	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.766	0.621	0.929	0.766	0.621	0.929	CLONAL	1	TRUE	1	0.2	2		354	418	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0045849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	34	291	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	1	2	FACETS	0.798	0.652	0.962	0.798	0.652	0.962	CLONAL	1	TRUE	1	0.2	2		291	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579529	7579529	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658483	NA	P-0045849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	65	530	0	ENST00000269305.4:c.158G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tGg/tAg	4/11	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.2	2		530	615	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410072	63410072	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045849-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	48	648	0	ENST00000330258.3:c.3095del	p.Pro1032LeufsTer13	p.P1032Lfs*13	ENST00000330258	NM_152424.3	1032	cCt/ct	2/2	1	2	FACETS	0.714	0.603	0.838	0.714	0.603	0.838	SUBCLONAL	1	TRUE	1	0.2	2		648	672	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0045850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	50	262	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.203263570419254	3	FACETS	1	0.954	1	0.668	0.569	0.776	CLONAL	1	TRUE	1	0.240334271355412	3		262	349	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798968	45798968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781444	NA	P-0045850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	52	459	0	ENST00000450313.1:c.377G>A	p.Arg126Gln	p.R126Q	ENST00000450313	NM_012222.2	126	cGg/cAg	4/16	1	2	FACETS	0.715	0.608	0.833	0.715	0.608	0.833	SUBCLONAL	1	TRUE	1	0.240334271355412	2		459	605	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0045850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	97	833	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.240334271355412	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.240334271355412	1		833	593	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680721	30680721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61748586	NA	P-0045850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	39	346	0	ENST00000376406.3:c.998C>T	p.Ala333Val	p.A333V	ENST00000376406	NM_014641.2	333	gCg/gTg	5/15	1	2	FACETS	0.743	0.616	0.884	0.743	0.616	0.884	SUBCLONAL	1	TRUE	1	0.240334271355412	2		346	437	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247328	153247328	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	88	237	1	ENST00000281708.4:c.1474C>T	p.Gln492Ter	p.Q492*	ENST00000281708	NM_033632.3	492	Cag/Tag	10/12	1	2	FACETS	1	0.921	1	1	0.986	1	CLONAL	2	TRUE	1	0.240334271355412	2		238	353	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247344	153247344	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	31	176	0	ENST00000281708.4:c.1458G>T	p.Trp486Cys	p.W486C	ENST00000281708	NM_033632.3	486	tgG/tgT	10/12	1	2	FACETS	0.779	0.631	0.946	0.779	0.631	0.946	CLONAL	1	TRUE	1	0.240334271355412	2		176	331	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602347	10602347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045850-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	114	599	0	ENST00000171111.5:c.1231G>A	p.Val411Met	p.V411M	ENST00000171111	NM_203500.1	411	Gtg/Atg	3/6	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.240334271355412	2		599	640	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0045857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	42	294	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.34	2		294	239	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467491	25467491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs962805778	NA	P-0045857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	32	467	3	ENST00000264709.3:c.1585G>A	p.Asp529Asn	p.D529N	ENST00000264709	NM_175629.2	529	Gac/Aac	14/23	1	2	FACETS	0.363	0.294	0.442	0.363	0.294	0.442	SUBCLONAL	1	TRUE	1	0.34	2		470	518	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101376	27101377	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	G	novel	NA	P-0045857-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	49	310	2	ENST00000324856.7:c.4658_4659delinsG	p.Pro1553ArgfsTer12	p.P1553Rfs*12	ENST00000324856	NM_006015.4	1553	cCC/cG	18/20	1	2	FACETS	0.743	0.631	0.865	0.743	0.631	0.865	SUBCLONAL	1	TRUE	1	0.34	2		312	388	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0045858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	24	359	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.208423603065466	4	FACETS	0.706	0.553	0.881	0.353	0.276	0.441	SUBCLONAL	1	TRUE	2	0.261637530242294	4		359	328	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610486	81610486	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	25	233	0	ENST00000298171.2:c.2084A>C	p.Lys695Thr	p.K695T	ENST00000298171	NM_000369.2	695	aAg/aCg	10/10	0.261637530242294	3	FACETS	0.639	0.504	0.795	0.213	0.168	0.265	SUBCLONAL	1	TRUE	0	0.261637530242294	3		233	338	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579533	7579533	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	135	488	0	ENST00000269305.4:c.154del	p.Gln52AsnfsTer71	p.Q52Nfs*71	ENST00000269305	NM_001126112.2	52	Caa/aa	4/11	0.16390592933359	3	FACETS	1	0.919	1			1	CLONAL	2	TRUE	NA	0.261637530242294	3		488	579	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264890	46264890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045858-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	25	279	0	ENST00000371998.3:c.1760C>T	p.Ser587Leu	p.S587L	ENST00000371998		587	tCa/tTa	12/23	0.172193570725501	3	FACETS	0.653	0.515	0.811	0.326	0.257	0.406	SUBCLONAL	1	TRUE	1	0.261637530242294	3		279	331	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0045860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	43	347	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.236010781014596	4	FACETS	0.828	0.698	0.969	0.828	0.698	0.969	CLONAL	2	TRUE	2	0.25970528781605	4		347	252	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207077	1207077	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs121913319	NA	P-0045860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	104	461	0	ENST00000326873.7:c.169del	p.Glu57LysfsTer7	p.E57Kfs*7	ENST00000326873	NM_000455.4	55	ctG/ct	1/10	0.25970528781605	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	0	0.25970528781605	2		461	387	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602698	10602698	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	90	588	0	ENST00000171111.5:c.880G>T	p.Asp294Tyr	p.D294Y	ENST00000171111	NM_203500.1	294	Gac/Tac	3/6	0.25970528781605	2	FACETS	0.866	0.774	0.964	0.866	0.774	0.964	CLONAL	2	TRUE	0	0.25970528781605	2		588	400	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212732	27212732	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	76	389	0	ENST00000380036.4:c.2714C>T	p.Ala905Val	p.A905V	ENST00000380036	NM_000459.3	905	gCg/gTg	17/23	0.197715755675602	1	FACETS	0.756	0.668	0.848	1	0.977	1	SUBCLONAL	2	TRUE	0	0.25970528781605	1		389	337	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469530	25469530	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755744291	NA	P-0045860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	81	520	0	ENST00000264709.3:c.1238del	p.Gly413AlafsTer238	p.G413Afs*238	ENST00000264709	NM_175629.2	413	gGc/gc	10/23	0.248064562124355	3	FACETS	1	0.975	1	0.713	0.63	0.802	CLONAL	1	TRUE	1	0.25970528781605	3		520	494	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138548	11138548	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	83	422	0	ENST00000358026.2:c.3304T>C	p.Phe1102Leu	p.F1102L	ENST00000358026	NM_001128849.1	1102	Ttc/Ctc	24/36	0.25970528781605	2	FACETS	0.968	0.862	1	0.968	0.862	1	CLONAL	2	TRUE	0	0.25970528781605	2		422	330	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041722	42041722	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	27	277	0	ENST00000219905.7:c.5917C>T	p.Gln1973Ter	p.Q1973*	ENST00000219905	NM_001164273.1	1973	Cag/Tag	17/24	1	2	FACETS	0.995	0.797	1	0.995	0.797	1	CLONAL	1	TRUE	1	0.25970528781605	2		277	209	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868193	45868193	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs747109257	NA	P-0045860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	367	510	0	ENST00000391945.4:c.497G>C	p.Arg166Pro	p.R166P	ENST00000391945	NM_000400.3	166	cGt/cCt	7/23	0.25970528781605	7	FACETS	0.967	0.923	1	1	0.991	1	CLONAL	6	TRUE	2	0.25970528781605	7		510	803	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714542	52714542	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	87	441	0	ENST00000322088.6:c.300G>C	p.Glu100Asp	p.E100D	ENST00000322088	NM_014225.5	100	gaG/gaC	4/15	NA	2	FACETS	1	0.909	1			1	INDETERMINATE	2	TRUE	NA	0.25970528781605	2		441	329	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050722	5050722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	66	243	2	ENST00000381652.3:c.505C>T	p.Pro169Ser	p.P169S	ENST00000381652	NM_004972.3	169	Cct/Tct	6/25	0.25970528781605	3	FACETS	0.87	0.767	0.978	1	0.967	1	CLONAL	3	TRUE	1	0.25970528781605	3		245	220	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994225	21994225	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	96	452	0	ENST00000579755.1:c.106G>T	p.Ala36Ser	p.A36S	ENST00000579755		36	Gcg/Tcg	1/3	0.197715755675602		FACETS		0.768	0.947				CLONAL	2	TRUE	0	0.25970528781605	1		452	376	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345287	70345289	+	missense_variant	Missense_Mutation	TNP	CAA	CAA	GAG	novel	NA	P-0045860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	27	407	0	ENST00000374080.3:c.2313_2315delinsGAG	p.Ile771_Lys772delinsMetArg	p.I771_K772delinsMR	ENST00000374080		771	atCAAg/atGAGg	16/45	0.25970528781605	3	FACETS	0.626	0.498	0.773	0.313	0.249	0.387	SUBCLONAL	1	TRUE	1	0.25970528781605	3		407	375	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	107	425	0				ENST00000310581	NM_198253.2	-/1132			0.81886304714198	4	FACETS	1	0.952	1	0.363	0.328	0.401	CLONAL	1	TRUE	1	0.81886304714198	4		425	436	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305460	65305460	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	151	289	0	ENST00000342505.4:c.2668G>C	p.Glu890Gln	p.E890Q	ENST00000342505	NM_002227.2	890	Gag/Cag	20/25	0.320264818343179	5	FACETS	0.903	0.833	0.975	0.602	0.555	0.65	INDETERMINATE	2	TRUE	2	0.81886304714198	5		289	455	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484280	120484280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	53	274	0	ENST00000256646.2:c.2850G>A	p.Met950Ile	p.M950I	ENST00000256646	NM_024408.3	950	atG/atA	18/34	0.320264818343179	5	FACETS	0.571	0.487	0.663	0.19	0.162	0.221	INDETERMINATE	1	TRUE	2	0.81886304714198	5		274	505	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163315571	163315571	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	13	228	0	ENST00000271452.3:c.911C>T	p.Ser304Leu	p.S304L	ENST00000271452	NM_145697.2	304	tCa/tTa	11/14	0.535336183955904	3	FACETS	0.187	0.133	0.253	0.062	0.044	0.085	SUBCLONAL	1	TRUE	0	0.81886304714198	3		228	239	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094319	193094319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	74	233	0	ENST00000367435.3:c.209C>T	p.Ser70Phe	p.S70F	ENST00000367435	NM_024529.4	70	tCt/tTt	2/17	0.535336183955904	3	FACETS	0.784	0.692	0.881	0.261	0.23	0.294	SUBCLONAL	1	TRUE	0	0.81886304714198	3		233	325	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981500	201981500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	56	381	0	ENST00000359651.3:c.414G>A	p.Trp138Ter	p.W138*	ENST00000359651		138	tgG/tgA	3/8	0.558821920791791	2	FACETS	0.231	0.197	0.267	0.115	0.098	0.134	SUBCLONAL	1	TRUE	0	0.81886304714198	2		381	593	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981507	201981507	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	51	390	0	ENST00000359651.3:c.421G>T	p.Glu141Ter	p.E141*	ENST00000359651		141	Gag/Tag	3/8	0.558821920791791	2	FACETS	0.2	0.169	0.234	0.1	0.084	0.117	SUBCLONAL	1	TRUE	0	0.81886304714198	2		390	623	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71945363	71945363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	78	466	0	ENST00000298229.2:c.2251G>A	p.Glu751Lys	p.E751K	ENST00000298229	NM_001567.3	751	Gag/Aag	20/28	0.350325918830263	3	FACETS	0.452	0.397	0.511	0.151	0.132	0.171	INDETERMINATE	1	TRUE	0	0.81886304714198	3		466	594	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998292	100998292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	19	93	0	ENST00000325455.5:c.1510G>A	p.Ala504Thr	p.A504T	ENST00000325455	NM_001202474.3	504	Gcc/Acc	1/8	0.350325918830263	3	FACETS	0.394	0.301	0.502	0.131	0.1	0.168	INDETERMINATE	1	TRUE	0	0.81886304714198	3		93	166	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114679	108114679	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs778624615	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	36	130	0	ENST00000278616.4:c.497-1G>C		p.X166_splice	ENST00000278616	NM_000051.3	166			0.350325918830263	3	FACETS	0.925	0.775	1	0.308	0.258	0.362	INDETERMINATE	1	TRUE	0	0.81886304714198	3		130	134	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343550	118343550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	58	281	0	ENST00000534358.1:c.1676C>T	p.Ser559Leu	p.S559L	ENST00000534358	NM_005933.3	559	tCg/tTg	3/36	0.350325918830263	3	FACETS	0.559	0.483	0.642	0.186	0.161	0.214	INDETERMINATE	1	TRUE	0	0.81886304714198	3		281	357	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374867	118374867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	15	197	0	ENST00000534358.1:c.8260G>A	p.Glu2754Lys	p.E2754K	ENST00000534358	NM_005933.3	2754	Gag/Aag	27/36	0.350325918830263	3	FACETS	0.238	0.174	0.315	0.079	0.058	0.105	INDETERMINATE	1	TRUE	0	0.81886304714198	3		197	217	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350198	89350198	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	82	483	0	ENST00000301030.4:c.2752G>C	p.Glu918Gln	p.E918Q	ENST00000301030	NM_001256183.1	918	Gag/Cag	9/13	0.212406762896294	4	FACETS	0.52	0.459	0.587	0.13	0.114	0.147	INDETERMINATE	1	TRUE	0	0.81886304714198	4		483	700	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556179	29556179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	18	89	0	ENST00000356175.3:c.2546G>A	p.Gly849Glu	p.G849E	ENST00000356175	NM_000267.3	849	gGa/gAa	21/57	0.81886304714198	3	FACETS	0.579	0.442	0.736	0.29	0.221	0.368	SUBCLONAL	1	TRUE	1	0.81886304714198	3		89	107	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627371	37627371	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1335078768	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	77	402	0	ENST00000447079.4:c.1286G>C	p.Arg429Thr	p.R429T	ENST00000447079	NM_015083.1	429	aGa/aCa	2/14	0.508476916298347	4	FACETS	0.479	0.42	0.543			1	SUBCLONAL	1	TRUE	NA	0.81886304714198	4		402	714	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740678	58740678	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	90	325	0	ENST00000305921.3:c.1583G>A	p.Arg528Lys	p.R528K	ENST00000305921	NM_003620.3	528	aGa/aAa	6/6	0.277769010032934	6	FACETS	1	0.911	1	0.343	0.304	0.383	INDETERMINATE	1	TRUE	3	0.81886304714198	6		325	564	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466782	25466782	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	58	411	0	ENST00000264709.3:c.1921G>C	p.Asp641His	p.D641H	ENST00000264709	NM_175629.2	641	Gat/Cat	16/23	0.81886304714198	3	FACETS	0.343	0.294	0.396	0.114	0.098	0.132	SUBCLONAL	1	TRUE	0	0.81886304714198	3		411	582	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39249913	39249913	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs267607079	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	72	400	0	ENST00000402219.2:c.1656G>T	p.Arg552Ser	p.R552S	ENST00000402219	NM_005633.3	552	agG/agT	10/23	0.81886304714198	3	FACETS	0.422	0.369	0.48	0.141	0.123	0.16	SUBCLONAL	1	TRUE	0	0.81886304714198	3		400	587	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010415	48010415	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs776745497	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	98	289	0	ENST00000234420.5:c.43C>G	p.Pro15Ala	p.P15A	ENST00000234420	NM_000179.2	15	Ccg/Gcg	1/10	0.81886304714198	3	FACETS	0.441	0.393	0.492	0.147	0.131	0.164	SUBCLONAL	1	TRUE	0	0.81886304714198	3		289	765	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736181	204736181	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	19	216	0	ENST00000302823.3:c.538C>G	p.Leu180Val	p.L180V	ENST00000302823	NM_005214.4	180	Ctc/Gtc	3/4	0.81886304714198	2	FACETS	0.149	0.113	0.192	0.075	0.056	0.096	SUBCLONAL	1	TRUE	0	0.81886304714198	2		216	311	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030058	36030058	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	279	420	0	ENST00000358208.4:c.1093C>T	p.Gln365Ter	p.Q365*	ENST00000358208		365	Cag/Tag	9/12	0.753329232221705	3	FACETS	1	0.992	1	0.659	0.622	0.696	CLONAL	1	TRUE	1	0.81886304714198	3		420	729	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030837	36030837	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	169	242	0	ENST00000358208.4:c.1117-1G>A		p.X373_splice	ENST00000358208		373			0.753329232221705	3	FACETS	1	0.986	1	0.635	0.589	0.682	CLONAL	1	TRUE	1	0.81886304714198	3		242	458	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24129386	24129386	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	55	203	0	ENST00000263121.7:c.30C>A	p.Phe10Leu	p.F10L	ENST00000263121	NM_003073.3	10	ttC/ttA	1/9	0.24471093173206	2	FACETS	0.268	0.229	0.31	0.134	0.114	0.155	INDETERMINATE	1	TRUE	0	0.81886304714198	2		203	502	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133488	55133488	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	76	289	0	ENST00000257290.5:c.792C>G	p.Ile264Met	p.I264M	ENST00000257290	NM_006206.4	264	atC/atG	6/23	0.248547424590739	2	FACETS	0.593	0.525	0.665	0.297	0.262	0.333	INDETERMINATE	1	TRUE	0	0.81886304714198	2		289	313	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968136	55968136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747362899	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	61	318	0	ENST00000263923.4:c.2194G>A	p.Glu732Lys	p.E732K	ENST00000263923	NM_002253.2	732	Gaa/Aaa	15/30	0.248547424590739	2	FACETS	0.356	0.308	0.408	0.178	0.154	0.204	INDETERMINATE	1	TRUE	0	0.81886304714198	2		318	418	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247175	153247175	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	57	215	0	ENST00000281708.4:c.1627A>G	p.Arg543Gly	p.R543G	ENST00000281708	NM_033632.3	543	Aga/Gga	10/12	0.248547424590739	2	FACETS	0.651	0.566	0.74	0.325	0.283	0.37	INDETERMINATE	1	TRUE	0	0.81886304714198	2		215	214	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982103	38982103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	34	216	0	ENST00000357387.3:c.619G>A	p.Gly207Arg	p.G207R	ENST00000357387	NM_152756.3	207	Gga/Aga	8/38	0.81886304714198	4	FACETS	0.268	0.218	0.325	0.089	0.072	0.109	SUBCLONAL	1	TRUE	1	0.81886304714198	4		216	563	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177456	56177456	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	32	262	0	ENST00000399503.3:c.2429C>G	p.Ser810Ter	p.S810*	ENST00000399503	NM_005921.1	810	tCa/tGa	14/20	0.804959348298348	2	FACETS	0.403	0.33	0.484	0.201	0.165	0.242	SUBCLONAL	1	TRUE	0	0.81886304714198	2		262	194	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183067	32183067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	96	458	0	ENST00000375023.3:c.1957G>A	p.Asp653Asn	p.D653N	ENST00000375023	NM_004557.3	653	Gat/Aat	12/30	0.186696227232463	3	FACETS	0.436	0.388	0.487	0.145	0.129	0.163	INDETERMINATE	1	TRUE	0	0.81886304714198	3		458	758	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798510	32798510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746574637	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	94	414	1	ENST00000374899.4:c.1346G>A	p.Arg449Gln	p.R449Q	ENST00000374899	NM_018833.2	449	cGa/cAa	8/12	0.186696227232463	3	FACETS	0.499	0.444	0.557	0.166	0.148	0.186	INDETERMINATE	1	TRUE	0	0.81886304714198	3		415	649	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651978	36651979	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	196	466	0	ENST00000244741.5:c.102_103del	p.Cys34Ter	p.C34*	ENST00000244741	NM_000389.4	34	TGt/t	2/3	0.186696227232463	3	FACETS	1	0.979	1	0.376	0.35	0.403	INDETERMINATE	1	TRUE	0	0.81886304714198	3		466	598	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652048	36652049	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	385	569	0	ENST00000244741.5:c.171dup	p.Pro58ThrfsTer5	p.P58Tfs*5	ENST00000244741	NM_000389.4	57	aca/acAa	2/3	0.186696227232463	3	FACETS	0.955	0.916	0.993	0.637	0.611	0.662	INDETERMINATE	2	TRUE	0	0.81886304714198	3		569	694	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109308755	109308755	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	12	167	0	ENST00000436639.2:c.1648A>G	p.Met550Val	p.M550V	ENST00000436639	NM_014454.2	550	Atg/Gtg	10/10	0.808944073843457	2	FACETS	0.153	0.107	0.209	0.076	0.053	0.105	SUBCLONAL	1	TRUE	0	0.81886304714198	2		167	192	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099233	157099233	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1478614436	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	64	344	0	ENST00000346085.5:c.170C>T	p.Ser57Leu	p.S57L	ENST00000346085	NM_020732.3	57	tCg/tTg	1/20	NA	2	FACETS	0.364	0.316	0.416			1	INDETERMINATE	1	TRUE	NA	0.81886304714198	2		344	429	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92247496	92247496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	18	211	0	ENST00000265734.4:c.724G>A	p.Asp242Asn	p.D242N	ENST00000265734	NM_001259.6	242	Gac/Aac	7/8	0.209924393058462	5	FACETS	0.339	0.255	0.438	0.113	0.085	0.146	INDETERMINATE	1	TRUE	2	0.81886304714198	5		211	289	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836846	151836846	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	191	324	1	ENST00000262189.6:c.14374G>C	p.Glu4792Gln	p.E4792Q	ENST00000262189	NM_170606.2	4792	Gag/Cag	56/59	0.209924393058462	5	FACETS	1	0.986	1	0.795	0.744	0.846	INDETERMINATE	2	TRUE	2	0.81886304714198	5		325	436	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845956	151845956	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	34	351	0	ENST00000262189.6:c.13056G>A	p.Trp4352Ter	p.W4352*	ENST00000262189	NM_170606.2	4352	tgG/tgA	52/59	0.209924393058462	5	FACETS	0.452	0.37	0.546	0.151	0.123	0.182	INDETERMINATE	1	TRUE	2	0.81886304714198	5		351	409	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187266	38187266	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	186	398	0	ENST00000317025.8:c.1211C>T	p.Ser404Phe	p.S404F	ENST00000317025	NM_023034.1	404	tCc/tTc	6/24	0.81886304714198	1	FACETS	0.919	0.87	0.966	0.919	0.87	0.966	CLONAL	1	TRUE	0	0.81886304714198	1		398	292	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37034007	37034007	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1466879183	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	43	255	1	ENST00000358127.4:c.22C>T	p.Pro8Ser	p.P8S	ENST00000358127	NM_001280556.1	8	Ccg/Tcg	1/10	0.808944073843457	2	FACETS	0.369	0.31	0.433	0.184	0.155	0.217	SUBCLONAL	1	TRUE	0	0.81886304714198	2		256	285	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932138	39932138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201595640	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	177	449	0	ENST00000378444.4:c.2461G>A	p.Val821Met	p.V821M	ENST00000378444	NM_001123385.1	821	Gtg/Atg	4/15	0.480364721620067	2	FACETS	0.768	0.712	0.825	0.384	0.356	0.413	INDETERMINATE	1	TRUE	0	0.81886304714198	2		449	563	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778789	76778789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	42	329	0	ENST00000373344.5:c.6790G>A	p.Glu2264Lys	p.E2264K	ENST00000373344	NM_000489.3	2264	Gaa/Aaa	31/35	0.480364721620067	2	FACETS	0.349	0.293	0.411	0.174	0.146	0.206	INDETERMINATE	1	TRUE	0	0.81886304714198	2		329	294	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854957	76854957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	24	398	0	ENST00000373344.5:c.5879C>T	p.Ser1960Leu	p.S1960L	ENST00000373344	NM_000489.3	1960	tCa/tTa	25/35	0.480364721620067	2	FACETS	0.136	0.106	0.171	0.068	0.053	0.086	INDETERMINATE	1	TRUE	0	0.81886304714198	2		398	430	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020196	123020196	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	69	388	0	ENST00000355640.3:c.684C>G	p.Phe228Leu	p.F228L	ENST00000355640		228	ttC/ttG	2/7	0.723282748676016	1	FACETS	0.346	0.304	0.39	0.346	0.304	0.39	SUBCLONAL	1	TRUE	0	0.81886304714198	1		388	288	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971177	21971177	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913382	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	29	300	1	ENST00000304494.5:c.181G>T	p.Glu61Ter	p.E61*	ENST00000304494	NM_000077.4	61	Gag/Tag	2/3	0.309323105323887	1	FACETS	0.523	0.421	0.639	0.523	0.421	0.639	SUBCLONAL	1	TRUE	0	0.309323105323887	1		301	303	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	201	823	4	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.30195650962477	3	FACETS	0.996	0.932	1	0.996	0.932	1	CLONAL	3	TRUE	0	0.309323105323887	3		827	502	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524968	8524968	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	35	201	0	ENST00000356435.5:c.636C>A	p.Ser212Arg	p.S212R	ENST00000356435		212	agC/agA	7/35	0.309323105323887	1	FACETS	0.874	0.722	1	0.874	0.722	1	CLONAL	1	TRUE	0	0.309323105323887	1		201	219	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456932	149456932	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148357861	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	87	338	0	ENST00000286301.3:c.796G>A	p.Asp266Asn	p.D266N	ENST00000286301	NM_005211.3	266	Gat/Aat	6/22	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.309323105323887	2		338	556	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488225	56488225	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	69	373	1	ENST00000267101.3:c.1744G>T	p.Gly582Trp	p.G582W	ENST00000267101	NM_001982.3	582	Ggg/Tgg	15/28	0.247372459718121	3	FACETS	1	0.94	1	0.565	0.493	0.642	CLONAL	1	TRUE	1	0.309323105323887	3		374	456	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727487	88727487	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1352987249	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	103	416	0	ENST00000360948.2:c.292G>T	p.Asp98Tyr	p.D98Y	ENST00000360948	NM_001012338.2	98	Gac/Tac	3/19	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.309323105323887	2		416	505	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790123	40790123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757562149	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	71	411	2	ENST00000373198.4:c.2608C>T	p.Arg870Cys	p.R870C	ENST00000373198	NM_133170.3	870	Cgc/Tgc	18/32	0.12525612763316	3	FACETS	1	0.939	1	0.374	0.327	0.424	INDETERMINATE	1	TRUE	0	0.309323105323887	3		413	473	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371662	55371662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	30	404	0	ENST00000297316.4:c.352G>A	p.Val118Met	p.V118M	ENST00000297316	NM_022454.3	118	Gtg/Atg	2/2	0.12525612763316	3	FACETS	0.423	0.34	0.518	0.141	0.113	0.173	INDETERMINATE	1	TRUE	0	0.309323105323887	3		404	529	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287202	46287202	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	14	220	0	ENST00000334344.6:c.5148-1G>T		p.X1716_splice	ENST00000334344	NM_152641.2	1716			0.247372459718121	3	FACETS	0.381	0.275	0.51	0.191	0.137	0.255	SUBCLONAL	1	TRUE	1	0.309323105323887	3		220	274	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78921093	78921093	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	31	367	1	ENST00000306801.3:c.3207G>T	p.Arg1069Ser	p.R1069S	ENST00000306801	NM_020761.2	1069	agG/agT	27/34	0.309323105323887	4	FACETS	0.434	0.35	0.53	0.145	0.116	0.177	SUBCLONAL	1	TRUE	1	0.309323105323887	4		368	604	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575108	48575108	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	51	223	0	ENST00000342988.3:c.302G>T	p.Trp101Leu	p.W101L	ENST00000342988	NM_005359.5	101	tGg/tTg	3/12	0.309323105323887	2	FACETS	0.789	0.679	0.906	0.789	0.679	0.906	CLONAL	2	TRUE	0	0.309323105323887	2		223	209	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852308	63852308	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	91	366	0	ENST00000279873.7:c.3088del	p.Ala1030GlnfsTer5	p.A1030Qfs*5	ENST00000279873	NM_032199.2	1029	cGg/cg	10/10	0.284438524296639	4	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.309323105323887	4		366	572	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270165	66270165	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	46	203	0	ENST00000273854.3:c.1717C>A	p.Pro573Thr	p.P573T	ENST00000273854	NM_004439.5	573	Cct/Act	8/18	0.274451298568484	3	FACETS	1	0.94	1	0.615	0.522	0.718	CLONAL	1	TRUE	1	0.309323105323887	3		203	279	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945081	31945081	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	83	372	0	ENST00000340398.3:c.20C>A	p.Thr7Asn	p.T7N	ENST00000340398	NM_001013699.2	7	aCt/aAt	1/1	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.309323105323887	2		372	442	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81528511	81528511	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	21	212	0	ENST00000298171.2:c.190C>A	p.Leu64Met	p.L64M	ENST00000298171	NM_000369.2	64	Ctg/Atg	2/10	0.247372459718121	3	FACETS	0.886	0.687	1	0.443	0.343	0.558	CLONAL	1	TRUE	1	0.309323105323887	3		212	177	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356335	66356335	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	50	269	0	ENST00000273854.3:c.1162G>T	p.Asp388Tyr	p.D388Y	ENST00000273854	NM_004439.5	388	Gac/Tac	5/18	0.274451298568484	3	FACETS	0.977	0.832	1	0.489	0.416	0.568	CLONAL	1	TRUE	1	0.309323105323887	3		269	382	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411091	63411091	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	36	191	0	ENST00000330258.3:c.2076G>T	p.Glu692Asp	p.E692D	ENST00000330258	NM_152424.3	692	gaG/gaT	2/2	1	1	FACETS	0.984	0.817	1	0.984	0.817	1	CLONAL	1	TRUE	0	0.309323105323887	1		191	200	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90634797	90634797	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	35	320	0	ENST00000330062.3:c.195C>A	p.Phe65Leu	p.F65L	ENST00000330062	NM_002168.2	65	ttC/ttA	2/11	1	2	FACETS	0.543	0.445	0.653	0.543	0.445	0.653	SUBCLONAL	1	TRUE	1	0.309323105323887	2		320	417	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522014	157522014	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	32	402	0	ENST00000346085.5:c.4286G>T	p.Arg1429Met	p.R1429M	ENST00000346085	NM_020732.3	1429	aGg/aTg	18/20	0.247372459718121	3	FACETS	0.553	0.449	0.671	0.277	0.224	0.336	SUBCLONAL	1	TRUE	1	0.309323105323887	3		402	432	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955906	55955906	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	46	286	0	ENST00000263923.4:c.3256A>T	p.Ser1086Cys	p.S1086C	ENST00000263923	NM_002253.2	1086	Agt/Tgt	24/30	0.274451298568484	3	FACETS	0.987	0.834	1	0.493	0.417	0.577	CLONAL	1	TRUE	1	0.309323105323887	3		286	348	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462852	120462852	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	27	185	0	ENST00000256646.2:c.5479G>T	p.Asp1827Tyr	p.D1827Y	ENST00000256646	NM_024408.3	1827	Gat/Tat	30/34	0.227523453080976	4	FACETS	0.879	0.702	1	0.44	0.351	0.54	CLONAL	1	TRUE	2	0.309323105323887	4		185	260	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156836771	156836771	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	60	443	1	ENST00000524377.1:c.428+1G>T		p.X143_splice	ENST00000524377	NM_002529.3	143			0.309323105323887	3	FACETS	0.634	0.546	0.731	0.317	0.273	0.366	SUBCLONAL	1	TRUE	1	0.309323105323887	3		444	706	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317592	163317592	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	11	191	0	ENST00000271452.3:c.988G>T	p.Glu330Ter	p.E330*	ENST00000271452	NM_145697.2	330	Gaa/Taa	12/14	0.309323105323887	3	FACETS	0.437	0.302	0.604	0.218	0.151	0.302	SUBCLONAL	1	TRUE	1	0.309323105323887	3		191	188	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665871	241665871	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	23	235	0	ENST00000366560.3:c.1109-1G>C		p.X370_splice	ENST00000366560	NM_000143.3	370			0.309323105323887	3	FACETS	0.59	0.46	0.74	0.295	0.23	0.37	SUBCLONAL	1	TRUE	1	0.309323105323887	3		235	291	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406117	70406117	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	24	328	0	ENST00000373644.4:c.3631G>A	p.Gly1211Arg	p.G1211R	ENST00000373644	NM_030625.2	1211	Ggg/Agg	4/12	0.284438524296639	4	FACETS	0.438	0.342	0.548			1	SUBCLONAL	1	TRUE	NA	0.309323105323887	4		328	464	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211474	46211474	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	18	157	0	ENST00000334344.6:c.440G>T	p.Gly147Val	p.G147V	ENST00000334344	NM_152641.2	147	gGg/gTg	5/21	0.247372459718121	3	FACETS	0.851	0.645	1	0.425	0.322	0.545	CLONAL	1	TRUE	1	0.309323105323887	3		157	158	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428372	49428372	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	80	440	0	ENST00000301067.7:c.10433G>T	p.Ser3478Ile	p.S3478I	ENST00000301067	NM_003482.3	3478	aGt/aTt	36/54	0.247372459718121	3	FACETS	1	0.918	1	0.526	0.463	0.593	CLONAL	1	TRUE	1	0.309323105323887	3		440	568	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863354	57863354	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	96	476	0	ENST00000228682.2:c.1449G>T	p.Glu483Asp	p.E483D	ENST00000228682	NM_005269.2	483	gaG/gaT	11/12	0.247372459718121	3	FACETS	1	0.945	1	0.548	0.489	0.611	CLONAL	1	TRUE	1	0.309323105323887	3		476	654	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112412	115112412	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	88	361	0	ENST00000257566.3:c.1328C>A	p.Ser443Ter	p.S443*	ENST00000257566	NM_016569.3	443	tCg/tAg	7/8	0.247372459718121	3	FACETS	1	0.962	1	0.596	0.529	0.667	CLONAL	1	TRUE	1	0.309323105323887	3		361	551	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249278	133249278	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	90	416	0	ENST00000320574.5:c.1621G>T	p.Gly541Trp	p.G541W	ENST00000320574	NM_006231.2	541	Ggg/Tgg	15/49	0.247372459718121	3	FACETS	1	0.937	1	0.541	0.48	0.606	CLONAL	1	TRUE	1	0.309323105323887	3		416	621	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589323	28589323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	28	213	0	ENST00000241453.7:c.2724G>T	p.Met908Ile	p.M908I	ENST00000241453	NM_004119.2	908	atG/atT	22/24	1	2	FACETS	0.739	0.593	0.903	0.739	0.593	0.903	CLONAL	1	TRUE	1	0.309323105323887	2		213	245	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636038	28636038	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	63	401	2	ENST00000241453.7:c.334C>A	p.Leu112Met	p.L112M	ENST00000241453	NM_004119.2	112	Ctg/Atg	3/24	1	2	FACETS	0.865	0.75	0.989	0.865	0.75	0.989	CLONAL	1	TRUE	1	0.309323105323887	2		403	471	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906807	32906807	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	47	397	0	ENST00000380152.3:c.1192C>G	p.Leu398Val	p.L398V	ENST00000380152		398	Cta/Gta	10/27	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.309323105323887	2		397	296	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281089	49281089	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	46	391	0	ENST00000282018.3:c.136C>G	p.Leu46Val	p.L46V	ENST00000282018	NM_020377.2	46	Ctg/Gtg	1/1	1	2	FACETS	0.867	0.733	1	0.867	0.733	1	CLONAL	1	TRUE	1	0.309323105323887	2		391	343	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438155	110438155	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	27	172	0	ENST00000375856.3:c.246G>T	p.Trp82Cys	p.W82C	ENST00000375856	NM_003749.2	82	tgG/tgT	1/2	1	2	FACETS	0.69	0.551	0.848	0.69	0.551	0.848	SUBCLONAL	1	TRUE	1	0.309323105323887	2		172	253	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68292201	68292201	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	34	204	0	ENST00000487270.1:c.105del	p.Leu36TrpfsTer4	p.L36Wfs*4	ENST00000487270	NM_133509.3	35	ccA/cc	3/11	0.247372459718121	3	FACETS	0.916	0.752	1	0.458	0.376	0.55	CLONAL	1	TRUE	1	0.309323105323887	3		204	277	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606159	81606159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	43	326	0	ENST00000298171.2:c.829C>T	p.Leu277Phe	p.L277F	ENST00000298171	NM_000369.2	277	Ctt/Ttt	9/10	0.247372459718121	3	FACETS	0.706	0.591	0.833	0.353	0.295	0.417	SUBCLONAL	1	TRUE	1	0.309323105323887	3		326	455	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610123	81610123	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	45	292	0	ENST00000298171.2:c.1721C>A	p.Thr574Asn	p.T574N	ENST00000298171	NM_000369.2	574	aCc/aAc	10/10	0.247372459718121	3	FACETS	0.851	0.716	0.998	0.425	0.358	0.499	CLONAL	1	TRUE	1	0.309323105323887	3		292	395	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059449	42059450	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	51	272	1	ENST00000219905.7:c.9169_9170delinsTT	p.Gly3057Leu	p.G3057L	ENST00000219905	NM_001164273.1	3057	GGg/TTg	24/24	0.309323105323887	1	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	0	0.309323105323887	1		273	269	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781320	3781320	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	74	539	0	ENST00000262367.5:c.5045G>C	p.Arg1682Pro	p.R1682P	ENST00000262367	NM_004380.2	1682	cGc/cCc	30/31	NA	2	FACETS	0.808	0.708	0.916			1	INDETERMINATE	1	TRUE	NA	0.309323105323887	2		539	592	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857399	9857399	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	38	298	0	ENST00000330684.3:c.4002C>A	p.Ser1334Arg	p.S1334R	ENST00000330684	NM_001134407.1	1334	agC/agA	13/13	NA	2	FACETS	0.7	0.58	0.833			1	INDETERMINATE	1	TRUE	NA	0.309323105323887	2		298	351	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029395	14029395	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	42	227	1	ENST00000311895.7:c.1606G>T	p.Val536Leu	p.V536L	ENST00000311895	NM_005236.2	536	Gta/Tta	8/11	0.156449060090174	3	FACETS	1	0.882	1	0.531	0.446	0.625	INDETERMINATE	1	TRUE	1	0.309323105323887	3		228	295	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641301	23641301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567217931	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	69	413	0	ENST00000261584.4:c.2174C>T	p.Ser725Leu	p.S725L	ENST00000261584	NM_024675.3	725	tCa/tTa	5/13	0.156449060090174	3	FACETS	1	0.913	1	0.529	0.461	0.601	INDETERMINATE	1	TRUE	1	0.309323105323887	3		413	487	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783870	50783870	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	37	395	0	ENST00000398568.2:c.261G>T	p.Lys87Asn	p.K87N	ENST00000398568	NM_001042412.1	87	aaG/aaT	3/18	0.156449060090174	3	FACETS	0.755	0.623	0.901	0.377	0.311	0.451	INDETERMINATE	1	TRUE	1	0.309323105323887	3		395	366	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40874855	40874855	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	43	348	1	ENST00000428826.2:c.445G>T	p.Glu149Ter	p.E149*	ENST00000428826		149	Gag/Tag	6/21	0.309323105323887	4	FACETS	0.8	0.67	0.944	0.267	0.223	0.315	CLONAL	1	TRUE	1	0.309323105323887	4		349	455	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602854	10602854	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1225595719	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	59	505	0	ENST00000171111.5:c.724G>C	p.Glu242Gln	p.E242Q	ENST00000171111	NM_203500.1	242	Gag/Cag	3/6	0.309323105323887	1	FACETS	0.576	0.495	0.663	0.576	0.495	0.663	SUBCLONAL	1	TRUE	0	0.309323105323887	1		505	560	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519785	29519785	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1410352488	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	56	325	0	ENST00000389048.3:c.1786A>G	p.Met596Val	p.M596V	ENST00000389048	NM_004304.4	596	Atg/Gtg	9/29	0.12525612763316	3	FACETS	0.821	0.704	0.949	0.274	0.234	0.317	INDETERMINATE	1	TRUE	0	0.309323105323887	3		325	509	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46588109	46588109	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	177	448	1	ENST00000263734.3:c.659C>A	p.Ser220Tyr	p.S220Y	ENST00000263734	NM_001430.4	220	tCc/tAc	6/16	0.12525612763316	3	FACETS	1	0.978	1	0.762	0.706	0.819	INDETERMINATE	2	TRUE	0	0.309323105323887	3		449	578	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286777	212286777	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	33	237	1	ENST00000342788.4:c.2919G>T	p.Glu973Asp	p.E973D	ENST00000342788	NM_005235.2	973	gaG/gaT	24/28	0.247372459718121	3	FACETS	0.926	0.758	1	0.463	0.379	0.557	CLONAL	1	TRUE	1	0.309323105323887	3		238	266	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286805	212286805	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	36	216	0	ENST00000342788.4:c.2891G>C	p.Arg964Thr	p.R964T	ENST00000342788	NM_005235.2	964	aGa/aCa	24/28	0.247372459718121	3	FACETS	1	0.909	1	0.579	0.479	0.689	CLONAL	1	TRUE	1	0.309323105323887	3		216	232	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439824	220439824	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	98	564	0	ENST00000243786.2:c.677G>T	p.Gly226Val	p.G226V	ENST00000243786	NM_002191.3	226	gGa/gTa	2/2	0.247372459718121	3	FACETS	1	0.898	1	0.503	0.449	0.561	CLONAL	1	TRUE	1	0.309323105323887	3		564	727	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660718	227660718	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	200	486	0	ENST00000305123.5:c.2737G>T	p.Val913Leu	p.V913L	ENST00000305123	NM_005544.2	913	Gtg/Ttg	1/2	0.247372459718121	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.309323105323887	3		486	658	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710554	40710554	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	69	450	1	ENST00000373198.4:c.4297C>A	p.Arg1433Ser	p.R1433S	ENST00000373198	NM_133170.3	1433	Cgt/Agt	31/32	0.12525612763316	3	FACETS	1	0.889	1	0.34	0.296	0.387	INDETERMINATE	1	TRUE	0	0.309323105323887	3		451	505	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46251026	46251026	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	44	202	0	ENST00000371998.3:c.35C>G	p.Ala12Gly	p.A12G	ENST00000371998		12	gCc/gGc	3/23	0.12525612763316	3	FACETS	1	0.904	1	0.367	0.309	0.431	INDETERMINATE	1	TRUE	0	0.309323105323887	3		202	298	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795449	39795449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144012510	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	139	426	1	ENST00000288319.7:c.271G>A	p.Gly91Arg	p.G91R	ENST00000288319	NM_182918.3	91	Ggg/Agg	3/10	0.309323105323887	2	FACETS	0.992	0.91	1	0.992	0.91	1	CLONAL	2	TRUE	0	0.309323105323887	2		427	453	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057222	30057222	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	73	300	0	ENST00000338641.4:c.704G>C	p.Gly235Ala	p.G235A	ENST00000338641	NM_000268.3	235	gGa/gCa	8/16	0.247372459718121	3	FACETS	1	0.951	1	0.586	0.514	0.663	CLONAL	1	TRUE	1	0.309323105323887	3		300	465	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098342	47098342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	43	292	0	ENST00000409792.3:c.6932C>T	p.Pro2311Leu	p.P2311L	ENST00000409792	NM_014159.6	2311	cCt/cTt	15/21	1	2	FACETS	1	0.842	1	1	0.842	1	CLONAL	1	TRUE	1	0.309323105323887	2		292	278	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163851	47163851	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	29	299	0	ENST00000409792.3:c.2275A>T	p.Lys759Ter	p.K759*	ENST00000409792	NM_014159.6	759	Aaa/Taa	3/21	1	2	FACETS	0.679	0.547	0.829	0.679	0.547	0.829	SUBCLONAL	1	TRUE	1	0.309323105323887	2		299	276	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637750	52637750	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	28	211	0	ENST00000394830.3:c.2568-2A>T		p.X856_splice	ENST00000394830	NM_018313.4	856			1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.309323105323887	2		211	151	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127391	55127392	+	missense_variant	Missense_Mutation	DNP	CC	CC	AG	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	69	343	1	ENST00000257290.5:c.179_180delinsAG	p.Pro60Gln	p.P60Q	ENST00000257290	NM_006206.4	60	cCC/cAG	3/23	0.274451298568484	3	FACETS	1	0.928	1	0.547	0.477	0.622	CLONAL	1	TRUE	1	0.309323105323887	3		344	471	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984770	55984770	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	45	249	0	ENST00000263923.4:c.358+1G>C		p.X120_splice	ENST00000263923	NM_002253.2	120			0.274451298568484	3	FACETS	1	0.904	1	0.549	0.463	0.642	CLONAL	1	TRUE	1	0.309323105323887	3		249	306	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233622	233622	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	27	174	0	ENST00000264932.6:c.926A>G	p.Glu309Gly	p.E309G	ENST00000264932	NM_004168.2	309	gAa/gGa	8/15	0.12525612763316	3	FACETS	0.843	0.674	1	0.281	0.224	0.345	INDETERMINATE	1	TRUE	0	0.309323105323887	3		174	239	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449450	31449450	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	40	304	0	ENST00000344624.3:c.2759G>T	p.Cys920Phe	p.C920F	ENST00000344624		920	tGt/tTt	19/33	0.12525612763316	3	FACETS	0.794	0.661	0.942	0.265	0.22	0.314	INDETERMINATE	1	TRUE	0	0.309323105323887	3		304	376	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170970	56170970	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	18	205	0	ENST00000399503.3:c.1798G>T	p.Gly600Trp	p.G600W	ENST00000399503	NM_005921.1	600	Ggg/Tgg	10/20	0.12525612763316	3	FACETS	0.56	0.422	0.722	0.187	0.14	0.241	INDETERMINATE	1	TRUE	0	0.309323105323887	3		205	240	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517519	176517519	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747421596	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	78	530	0	ENST00000292408.4:c.220G>C	p.Ala74Pro	p.A74P	ENST00000292408	NM_213647.1	74	Gca/Cca	3/18	1	2	FACETS	0.897	0.79	1	0.897	0.79	1	CLONAL	1	TRUE	1	0.309323105323887	2		530	562	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056145	26056145	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	62	310	0	ENST00000343677.2:c.512C>A	p.Ala171Asp	p.A171D	ENST00000343677	NM_005319.3	171	gCt/gAt	1/1	0.247372459718121	3	FACETS	1	0.867	1	0.501	0.434	0.574	CLONAL	1	TRUE	1	0.309323105323887	3		310	462	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120222	94120222	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	13	181	0	ENST00000369303.4:c.829G>T	p.Glu277Ter	p.E277*	ENST00000369303	NM_004440.3	277	Gaa/Taa	3/17	0.247372459718121	3	FACETS	0.476	0.34	0.641	0.238	0.17	0.321	SUBCLONAL	1	TRUE	1	0.309323105323887	3		181	204	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163779	152163779	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	48	282	0	ENST00000206249.3:c.500G>T	p.Ser167Ile	p.S167I	ENST00000206249	NM_000125.3	167	aGt/aTt	2/8	0.247372459718121	3	FACETS	1	0.899	1	0.538	0.457	0.627	CLONAL	1	TRUE	1	0.309323105323887	3		282	333	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157454173	157454174	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	38	246	0	ENST00000346085.5:c.2383_2384delinsTT	p.Gly795Phe	p.G795F	ENST00000346085	NM_020732.3	795	GGc/TTc	8/20	0.247372459718121	3	FACETS	0.927	0.769	1	0.464	0.384	0.551	CLONAL	1	TRUE	1	0.309323105323887	3		246	306	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528860	157528860	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	73	363	0	ENST00000346085.5:c.6585G>T	p.Met2195Ile	p.M2195I	ENST00000346085	NM_020732.3	2195	atG/atT	20/20	0.247372459718121	3	FACETS	1	0.954	1	0.592	0.52	0.67	CLONAL	1	TRUE	1	0.309323105323887	3		363	460	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969983	161969983	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	50	351	0	ENST00000366898.1:c.986G>T	p.Gly329Val	p.G329V	ENST00000366898	NM_004562.2	329	gGc/gTc	9/12	0.247372459718121	3	FACETS	0.768	0.652	0.895	0.384	0.326	0.448	SUBCLONAL	1	TRUE	1	0.309323105323887	3		351	486	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268081	55268081	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	106	438	0	ENST00000275493.2:c.2921A>T	p.Asp974Val	p.D974V	ENST00000275493	NM_005228.3	974	gAc/gTc	24/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.309323105323887	2		438	541	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335673	81335673	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	17	260	0	ENST00000222390.5:c.1687C>A	p.Gln563Lys	p.Q563K	ENST00000222390	NM_000601.4	563	Cag/Aag	15/18	0.309323105323887	3	FACETS	0.529	0.395	0.687	0.264	0.197	0.344	SUBCLONAL	1	TRUE	1	0.309323105323887	3		260	240	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339884	116339884	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	33	294	0	ENST00000397752.3:c.746A>T	p.Tyr249Phe	p.Y249F	ENST00000397752	NM_000245.2	249	tAt/tTt	2/21	0.309323105323887	3	FACETS	0.733	0.598	0.885	0.367	0.299	0.443	SUBCLONAL	1	TRUE	1	0.309323105323887	3		294	336	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453143	140453143	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	28	225	0	ENST00000288602.6:c.1792G>A	p.Ala598Thr	p.A598T	ENST00000288602	NM_004333.4	598	Gct/Act	15/18	0.309323105323887	3	FACETS	0.798	0.64	0.976	0.399	0.32	0.488	CLONAL	1	TRUE	1	0.309323105323887	3		225	262	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960208	151960208	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	12	124	0	ENST00000262189.6:c.1192G>T	p.Gly398Ter	p.G398*	ENST00000262189	NM_170606.2	398	Gga/Tga	9/59	0.309323105323887	3	FACETS	0.963	0.685	1	0.482	0.342	0.648	CLONAL	1	TRUE	1	0.309323105323887	3		124	93	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012277	152012277	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	37	318	0	ENST00000262189.6:c.536G>T	p.Gly179Val	p.G179V	ENST00000262189	NM_170606.2	179	gGa/gTa	4/59	0.309323105323887	3	FACETS	0.835	0.69	0.995	0.417	0.345	0.498	CLONAL	1	TRUE	1	0.309323105323887	3		318	331	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507389	8507389	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	30	228	0	ENST00000356435.5:c.1589C>G	p.Thr530Arg	p.T530R	ENST00000356435		530	aCa/aGa	11/35	0.309323105323887	1	FACETS	0.845	0.687	1	0.845	0.687	1	CLONAL	1	TRUE	0	0.309323105323887	1		228	194	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413240	139413240	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	118	545	0	ENST00000277541.6:c.902T>A	p.Leu301Gln	p.L301Q	ENST00000277541	NM_017617.3	301	cTg/cAg	6/34	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.309323105323887	2		545	637	SUCCESS
AR	367	MSKCC	GRCh37	X	66765620	66765620	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs370893700	NA	P-0045862-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	53	247	0	ENST00000374690.3:c.632C>G	p.Ala211Gly	p.A211G	ENST00000374690	NM_000044.3	211	gCg/gGg	1/8	1	1	FACETS	0.969	0.832	1	0.969	0.832	1	CLONAL	1	TRUE	0	0.309323105323887	1		247	299	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0045863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	9	330	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.56931079197496	1	FACETS	0.618	0.425	0.843	0.618	0.425	0.843	SUBCLONAL	1	TRUE	0	0.575752523046358	1		330	36	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0045863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	254	403	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.979	0.918	1	0.979	0.918	1	CLONAL	1	TRUE	1	0.575752523046358	2		403	901	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205286	38205286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045863-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	59	555	1	ENST00000317025.8:c.404C>T	p.Pro135Leu	p.P135L	ENST00000317025	NM_023034.1	135	cCt/cTt	2/24	1	2	FACETS	0.927	0.809	1	0.927	0.809	1	CLONAL	1	TRUE	1	0.575752523046358	2		556	221	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0045865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	146	667	2	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.432127425714207	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.432127425714207	1		669	517	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0045865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	208	545	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.432127425714207	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.432127425714207	3		545	482	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060499964	NA	P-0045865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	165	529	0	ENST00000326873.7:c.667G>A	p.Glu223Lys	p.E223K	ENST00000326873	NM_000455.4	223	Gag/Aag	5/10	0.432127425714207	1	FACETS	0.961	0.886	1	0.961	0.886	1	CLONAL	1	TRUE	0	0.432127425714207	1		529	623	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090482	37090482	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	24	250	0	ENST00000231790.2:c.2077G>C	p.Glu693Gln	p.E693Q	ENST00000231790	NM_000249.3	693	Gag/Cag	18/19	0.432127425714207	1	FACETS	0.295	0.231	0.368	0.295	0.231	0.368	SUBCLONAL	1	TRUE	0	0.432127425714207	1		250	295	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391896	139391896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766745955	NA	P-0045865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	185	1323	0	ENST00000277541.6:c.6295G>A	p.Asp2099Asn	p.D2099N	ENST00000277541	NM_017617.3	2099	Gac/Aac	34/34	0.256428739516431	1	FACETS	0.78	0.721	0.842	0.78	0.721	0.842	INDETERMINATE	1	TRUE	0	0.432127425714207	1		1323	860	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041751	29041751	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	14	208	0	ENST00000282397.4:c.68C>G	p.Ser23Cys	p.S23C	ENST00000282397	NM_002019.4	23	tCt/tGt	2/30	0.432127425714207	1	FACETS	0.235	0.17	0.314	0.235	0.17	0.314	SUBCLONAL	1	TRUE	0	0.432127425714207	1		208	216	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206939	102206939	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	16	144	0	ENST00000263464.3:c.1567G>C	p.Glu523Gln	p.E523Q	ENST00000263464	NM_001165.4	523	Gag/Cag	7/9	1	2	FACETS	0.325	0.24	0.426	0.325	0.24	0.426	SUBCLONAL	1	TRUE	1	0.432127425714207	2		144	228	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16062082	16062082	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	29	257	0	ENST00000268712.3:c.724G>C	p.Glu242Gln	p.E242Q	ENST00000268712	NM_006311.3	242	Gag/Cag	6/46	1	2	FACETS	0.303	0.243	0.372	0.303	0.243	0.372	SUBCLONAL	1	TRUE	1	0.432127425714207	2		257	443	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937906	76937906	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045865-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	28	341	0	ENST00000373344.5:c.2842C>A	p.His948Asn	p.H948N	ENST00000373344	NM_000489.3	948	Cat/Aat	9/35	0.432127425714207	1	FACETS	0.278	0.222	0.342	0.278	0.222	0.342	SUBCLONAL	1	TRUE	0	0.432127425714207	1		341	365	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0045867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	77	189	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	0.451328801383152	2	FACETS	1	0.897	1	0.507	0.449	0.569	CLONAL	1	TRUE	0	0.461338232830209	2		189	329	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACAACCCCC	rs397517115	NA	P-0045867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	418	352	0	ENST00000275493.2:c.2311_2319dup	p.Asn771_His773dup	p.N771_H773dup	ENST00000275493	NM_005228.3	771	gac/gACAACCCCCac	20/28	0.461338232830209	6	FACETS	1	0.991	1	0.85	0.812	0.888	CLONAL	3	TRUE	2	0.461338232830209	6		352	1025	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs760043106	NA	P-0045867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	216	390	0	ENST00000269305.4:c.584T>A	p.Ile195Asn	p.I195N	ENST00000269305	NM_001126112.2	195	aTc/aAc	6/11	0.441117682835056	2	FACETS	0.877	0.822	0.932	0.877	0.822	0.932	CLONAL	2	TRUE	0	0.461338232830209	2		390	534	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444662	78444663	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGA	novel	NA	P-0045867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	159	307	0	ENST00000370768.2:c.24_26dup	p.Pro10dup	p.P10dup	ENST00000370768	NM_003902.3	10	ccc/ccTCCc	1/20	0.142707463197101	6	FACETS	0.923	0.848	1	0.615	0.565	0.667	INDETERMINATE	2	TRUE	3	0.461338232830209	6		307	718	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3841996	3841996	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1487159105	NA	P-0045867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	151	194	0	ENST00000262367.5:c.1316A>T	p.Lys439Met	p.K439M	ENST00000262367	NM_004380.2	439	aAg/aTg	5/31	0.282804360083746	3	FACETS	0.937	0.865	1	0.937	0.865	1	CLONAL	2	TRUE	1	0.461338232830209	3		194	430	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259475	55259475	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	455	264	0	ENST00000275493.2:c.2533G>T	p.Val845Leu	p.V845L	ENST00000275493	NM_005228.3	845	Gtg/Ttg	21/28	0.461338232830209	6	FACETS	1	0.99	1	1	0.99	1	CLONAL	4	TRUE	2	0.461338232830209	6		264	874	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55270181	55270237	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGTAACCTTCCCTCATTTCCTCCTGCAGCTGCAAAGCTGTCCCATCAAGGAAGACA	GAGTAACCTTCCCTCATTTCCTCCTGCAGCTGCAAAGCTGTCCCATCAAGGAAGACA	-	novel	NA	P-0045867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	545	414	0	ENST00000275493.2:c.3163-28_3191del		p.X1055_splice	ENST00000275493	NM_005228.3	1055		27/28	0.461338232830209	6	FACETS	0.929	0.894	0.965	0.929	0.894	0.965	CLONAL	4	TRUE	2	0.461338232830209	6		414	1222	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925498	114925498	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	194	801	0	ENST00000543371.1:c.1576C>A	p.Leu526Met	p.L526M	ENST00000543371	NM_001198531.1	526	Ctg/Atg	14/14	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.503780321954641	2		801	707	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246491	46246491	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200040222	NA	P-0045871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	62	331	0	ENST00000334344.6:c.4585G>A	p.Gly1529Arg	p.G1529R	ENST00000334344	NM_152641.2	1529	Gga/Aga	15/21	1	2	FACETS	0.802	0.698	0.913	0.802	0.698	0.913	CLONAL	1	FALSE	1	0.503780321954641	2		331	307	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765628	41765628	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs377757427	NA	P-0045871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	307	910	0	ENST00000301178.4:c.2504G>T	p.Gly835Val	p.G835V	ENST00000301178	NM_021913.4	835	gGa/gTa	20/20	0.503780321954641	2	FACETS	0.831	0.788	0.875	0.831	0.788	0.875	CLONAL	2	FALSE	0	0.503780321954641	2		910	733	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794863	42794863	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1210172110	NA	P-0045871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	293	874	1	ENST00000575354.2:c.1943C>T	p.Pro648Leu	p.P648L	ENST00000575354	NM_015125.3	648	cCc/cTc	10/20	0.503780321954641	2	FACETS	0.905	0.858	0.951	0.905	0.858	0.951	CLONAL	2	FALSE	0	0.503780321954641	2		875	643	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781244	135781244	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs548002938	NA	P-0045871-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	234	792	0	ENST00000298552.3:c.1721C>G	p.Thr574Ser	p.T574S	ENST00000298552	NM_001162426.1	574	aCt/aGt	15/23	0.503780321954641	3	FACETS	1	0.99	1	0.666	0.622	0.711	CLONAL	1	FALSE	1	0.503780321954641	3		792	873	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241708	55241708	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913428	NA	P-0045873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	165	526	0	ENST00000275493.2:c.2156G>C	p.Gly719Ala	p.G719A	ENST00000275493	NM_005228.3	719	gGc/gCc	18/28	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.342721839305277	2		526	919	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241678	55241678	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517085	NA	P-0045873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	182	552	0	ENST00000275493.2:c.2126A>C	p.Glu709Ala	p.E709A	ENST00000275493	NM_005228.3	709	gAa/gCa	18/28	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.342721839305277	2		552	1022	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856422	111856422	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045873-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	53	294	3	ENST00000341259.2:c.473A>C	p.His158Pro	p.H158P	ENST00000341259	NM_005475.2	158	cAc/cCc	2/8	1	2	FACETS	0.834	0.714	0.964	0.834	0.714	0.964	CLONAL	1	TRUE	1	0.342721839305277	2		297	371	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613209	52613209	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	127	447	1	ENST00000394830.3:c.3319G>T	p.Glu1107Ter	p.E1107*	ENST00000394830	NM_018313.4	1107	Gaa/Taa	22/30	0.180753934927229	2	FACETS	0.813	0.739	0.891	0.813	0.739	0.891	CLONAL	2	TRUE	0	0.259764483822478	2		448	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1555525585	NA	P-0045875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	122	473	0	ENST00000269305.4:c.673-2A>G		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.188593245036722	2	FACETS	0.878	0.797	0.962	0.878	0.797	0.962	CLONAL	2	TRUE	0	0.259764483822478	2		473	535	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115261337	115261337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772339521	NA	P-0045875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	44	364	0	ENST00000438362.2:c.2384G>A	p.Arg795Gln	p.R795Q	ENST00000438362	NM_001242891.1	795	cGa/cAa	19/20	1	2	FACETS	0.627	0.526	0.74	0.627	0.526	0.74	SUBCLONAL	1	TRUE	1	0.259764483822478	2		364	540	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556321	29556322	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0045875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	169	431	0	ENST00000356175.3:c.2688_2689del	p.Asp896GlufsTer9	p.D896Efs*9	ENST00000356175	NM_000267.3	896	gaTCgg/gagg	21/57	0.188593245036722	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.259764483822478	2		431	629	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	175	425	0				ENST00000310581	NM_198253.2	-/1132			0.736710911971329	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.736710911971329	1		425	282	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120377	94120377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	156	333	0	ENST00000369303.4:c.674C>T	p.Ser225Phe	p.S225F	ENST00000369303	NM_004440.3	225	tCc/tTc	3/17	0.367173944790258	1	FACETS	0.794	0.739	0.849	0.794	0.739	0.849	INDETERMINATE	1	TRUE	0	0.736710911971329	1		333	337	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007798	45007801	+	frameshift_variant	Frame_Shift_Del	DEL	TCTA	TCTA	-	novel	NA	P-0045876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	195	362	0	ENST00000558401.1:c.248_251del	p.Tyr83SerfsTer19	p.Y83Sfs*19	ENST00000558401	NM_004048.2	82	tTCTAt/tt	2/4	0.736710911971329	1	FACETS	0.966	0.912	1	0.966	0.912	1	CLONAL	1	TRUE	0	0.736710911971329	1		362	346	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115738	8115738	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	205	409	0	ENST00000346208.3:c.1084C>T	p.Gln362Ter	p.Q362*	ENST00000346208		362	Cag/Tag	6/6	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.736710911971329	2		409	552	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244063	46244064	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0045876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	118	494	0	ENST00000334344.6:c.2157_2158delinsTT	p.Gln720Ter	p.Q720*	ENST00000334344	NM_152641.2	719	atCCag/atTTag	15/21	0.388375045267845	1	FACETS	0.36	0.326	0.396	0.36	0.326	0.396	INDETERMINATE	1	TRUE	0	0.736710911971329	1		494	562	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822445	72822445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774648909	NA	P-0045876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	455	872	0	ENST00000268489.5:c.9730G>A	p.Glu3244Lys	p.E3244K	ENST00000268489	NM_006885.3	3244	Gaa/Aaa	10/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.736710911971329	2		872	1179	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108242	8108242	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369229594	NA	P-0045876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	411	725	1	ENST00000585124.1:c.982C>T	p.Arg328Trp	p.R328W	ENST00000585124	NM_004217.3	328	Cgg/Tgg	9/9	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.736710911971329	2		726	1077	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983742	15983742	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	274	512	0	ENST00000268712.3:c.3380A>G	p.Gln1127Arg	p.Q1127R	ENST00000268712	NM_006311.3	1127	cAa/cGa	25/46	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.736710911971329	2		512	695	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730894	40730894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748653543	NA	P-0045876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	625	649	0	ENST00000373198.4:c.3641G>A	p.Ser1214Asn	p.S1214N	ENST00000373198	NM_133170.3	1214	aGc/aAc	27/32	0.118098886994452	5	FACETS	1	0.978	1			1	INDETERMINATE	3	TRUE	NA	0.736710911971329	5		649	1174	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146601	185146601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	568	564	0	ENST00000265026.3:c.232G>A	p.Asp78Asn	p.D78N	ENST00000265026	NM_004721.4	78	Gac/Aac	2/14	0.736710911971329	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.736710911971329	3		564	1033	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332028	81332028	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	326	306	0	ENST00000222390.5:c.2056A>T	p.Met686Leu	p.M686L	ENST00000222390	NM_000601.4	686	Atg/Ttg	18/18	0.442826954095361	3	FACETS	1	0.994	1	0.806	0.774	0.837	CLONAL	2	TRUE	0	0.736710911971329	3		306	501	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509058	106509058	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	152	609	2	ENST00000359195.3:c.1052C>T	p.Thr351Ile	p.T351I	ENST00000359195	NM_002649.2	351	aCc/aTc	2/11	0.442826954095361	3	FACETS	0.561	0.512	0.612	0.187	0.17	0.204	SUBCLONAL	1	TRUE	0	0.736710911971329	3		611	1007	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	133	425	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.952	0.874	1	0.952	0.874	1	CLONAL	1	TRUE	1	0.735663093068079	2		425	380	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374293	138374293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	270	536	0	ENST00000289153.2:c.3151G>A	p.Glu1051Lys	p.E1051K	ENST00000289153	NM_006219.2	1051	Gaa/Aaa	22/22	1	2	FACETS	0.928	0.874	0.983	0.928	0.874	0.983	CLONAL	1	TRUE	1	0.735663093068079	2		536	791	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131142	55131142	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6780	1759	491	0	ENST00000257290.5:c.685G>A	p.Glu229Lys	p.E229K	ENST00000257290	NM_006206.4	229	Gaa/Aaa	5/23	0.735663093068079	22	FACETS	0.936	0.912	0.96			1	CLONAL	5	TRUE	NA	0.735663093068079	22		491	8539	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508490	106508490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	150	413	0	ENST00000359195.3:c.484G>A	p.Val162Ile	p.V162I	ENST00000359195	NM_002649.2	162	Gtc/Atc	2/11	0.734885602101754	3	FACETS	1	0.942	1	0.516	0.474	0.559	CLONAL	1	TRUE	1	0.735663093068079	3		413	541	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56787259	56787259	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	278	540	0	ENST00000337432.4:c.745C>A	p.Arg249Ser	p.R249S	ENST00000337432	NM_058216.2	249	Cgt/Agt	5/9	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.735663093068079	2		540	744	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184717	185184717	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	40	394	0	ENST00000265026.3:c.1609G>A	p.Gly537Arg	p.G537R	ENST00000265026	NM_004721.4	537	Gga/Aga	10/14	1	2	FACETS	0.194	0.16	0.231	0.194	0.16	0.231	SUBCLONAL	1	TRUE	1	0.735663093068079	2		394	561	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161307	55161308	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0045877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	5089	409	0	ENST00000257290.5:c.3142_3143del	p.Ser1048CysfsTer3	p.S1048Cfs*3	ENST00000257290	NM_006206.4	1046	gaAGag/gaag	23/23	0.735663093068079	22	FACETS	0.986	0.98	0.991			1	CLONAL	21	TRUE	NA	0.735663093068079	22		409	5585	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138584	55138593	+	protein_altering_variant	In_Frame_Del	DEL	GTCGATGATC	GTCGATGATC	TGTG	novel	NA	P-0045877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5815	1419	554	2	ENST00000257290.5:c.1261_1270delinsTGTG	p.Val421_His424delinsCysAsp	p.V421_H424delinsCD	ENST00000257290	NM_006206.4	421	GTCGATGATCac/TGTGac	9/23	0.735663093068079	22	FACETS	1	0.996	1			1	CLONAL	4	TRUE	NA	0.735663093068079	22		556	7234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578508	7578508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781288	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	951	945	1	ENST00000269305.4:c.422G>A	p.Cys141Tyr	p.C141Y	ENST00000269305	NM_001126112.2	141	tGc/tAc	5/11	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.749087356235072	2		946	1219	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033905	49033905	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	352	427	0	ENST00000267163.4:c.2042G>A	p.Trp681Ter	p.W681*	ENST00000267163	NM_000321.2	681	tGg/tAg	20/27	0.729186290259955	2	FACETS	0.967	0.934	0.999	0.967	0.934	0.999	CLONAL	2	TRUE	0	0.749087356235072	2		427	486	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827993	40827993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1328809133	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	282	554	0	ENST00000373198.4:c.2435G>A	p.Gly812Glu	p.G812E	ENST00000373198	NM_133170.3	812	gGa/gAa	17/32	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.749087356235072	2		554	711	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914236	32914236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs4987117	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	211	392	0	ENST00000380152.3:c.5744C>T	p.Thr1915Met	p.T1915M	ENST00000380152		1915	aCg/aTg	11/27	0.729186290259955	2	FACETS	0.992	0.95	1	0.992	0.95	1	CLONAL	2	TRUE	0	0.749087356235072	2		392	284	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641144	117641144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866970127	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	238	637	0	ENST00000368508.3:c.5827G>A	p.Glu1943Lys	p.E1943K	ENST00000368508	NM_002944.2	1943	Gaa/Aaa	36/43	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.749087356235072	2		637	614	SUCCESS
ATR	545	MSKCC	GRCh37	3	142222283	142222283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	193	319	0	ENST00000350721.4:c.5209C>T	p.His1737Tyr	p.H1737Y	ENST00000350721	NM_001184.3	1737	Cat/Tat	30/47	0.67816337313648	3	FACETS	0.833	0.781	0.886	0.833	0.781	0.886	CLONAL	2	TRUE	1	0.749087356235072	3		319	425	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428227	33428227	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1379526157	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	287	608	0	ENST00000345365.6:c.896C>T	p.Ser299Phe	p.S299F	ENST00000345365	NM_002878.3	299	tCc/tTc	9/10	0.749087356235072	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.749087356235072	1		608	456	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162107	22162107	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	185	370	1	ENST00000215832.6:c.148C>T	p.Arg50Ter	p.R50*	ENST00000215832	NM_002745.4	50	Cga/Tga	2/9	0.749087356235072	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.749087356235072	1		371	285	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56912075	56912075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	221	491	0	ENST00000519728.1:c.1303G>A	p.Glu435Lys	p.E435K	ENST00000519728	NM_002350.3	435	Gaa/Aaa	12/13	1	2	FACETS	0.937	0.877	0.997	0.937	0.877	0.997	CLONAL	1	TRUE	1	0.749087356235072	2		491	630	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604769	48604769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766833269	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	191	398	0	ENST00000342988.3:c.1591C>T	p.Arg531Trp	p.R531W	ENST00000342988	NM_005359.5	531	Cgg/Tgg	12/12	0.749087356235072	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.749087356235072	1		398	319	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244595	41244595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555588649	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	196	578	0	ENST00000357654.3:c.2953C>T	p.Pro985Ser	p.P985S	ENST00000357654	NM_007294.3	985	Ccc/Tcc	10/23	0.749087356235072	1	FACETS	0.919	0.867	0.971	0.919	0.867	0.971	CLONAL	1	TRUE	0	0.749087356235072	1		578	356	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528496	157528496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149978361	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	207	655	1	ENST00000346085.5:c.6221C>T	p.Ser2074Leu	p.S2074L	ENST00000346085	NM_020732.3	2074	tCg/tTg	20/20	1	2	FACETS	0.804	0.75	0.861	0.804	0.75	0.861	CLONAL	1	TRUE	1	0.749087356235072	2		656	687	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117074	7117074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	321	608	0	ENST00000302850.5:c.4142C>T	p.Pro1381Leu	p.P1381L	ENST00000302850	NM_000208.2	1381	cCt/cTt	22/22	0.615261042561365	1	FACETS	0.866	0.826	0.906	0.866	0.826	0.906	CLONAL	1	TRUE	0	0.749087356235072	1		608	619	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36265222	36265222	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs781761402	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	40	177	0	ENST00000300305.3:c.97G>A	p.Asp33Asn	p.D33N	ENST00000300305		33	Gat/Aat	2/8	0.128899853595925	4	FACETS	0.708	0.592	0.835	0.177	0.148	0.209	INDETERMINATE	1	TRUE	0	0.749087356235072	4		177	264	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261251	16261251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1188801107	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	264	620	2	ENST00000375759.3:c.8516C>T	p.Pro2839Leu	p.P2839L	ENST00000375759	NM_015001.2	2839	cCg/cTg	11/15	0.67816337313648	3	FACETS	0.983	0.922	1	0.491	0.461	0.523	CLONAL	1	TRUE	1	0.749087356235072	3		622	986	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439622	51439622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	227	419	0	ENST00000262662.1:c.187C>T	p.Pro63Ser	p.P63S	ENST00000262662		63	Ccc/Tcc	4/4	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.749087356235072	2		419	569	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074394	8074394	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	169	398	0	ENST00000377482.5:c.265A>C	p.Lys89Gln	p.K89Q	ENST00000377482	NM_018948.3	89	Aag/Cag	4/4	0.67816337313648	3	FACETS	0.899	0.829	0.971	0.449	0.414	0.486	CLONAL	1	TRUE	1	0.749087356235072	3		398	690	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326502	161326502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	198	408	0	ENST00000367975.2:c.277C>T	p.Pro93Ser	p.P93S	ENST00000367975	NM_003001.3	93	Cct/Tct	5/6	0.50060392269171	3	FACETS	1	0.967	1	0.533	0.495	0.571	CLONAL	1	TRUE	1	0.749087356235072	3		408	682	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716113	243716113	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	179	470	1	ENST00000263826.5:c.1081G>A	p.Glu361Lys	p.E361K	ENST00000263826	NM_005465.4	361	Gaa/Aaa	10/13	0.50060392269171	3	FACETS	1	0.98	1	0.58	0.538	0.624	CLONAL	1	TRUE	1	0.749087356235072	3		471	566	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860059	57860059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	342	869	0	ENST00000228682.2:c.799G>A	p.Glu267Lys	p.E267K	ENST00000228682	NM_005269.2	267	Gag/Aag	8/12	1	2	FACETS	0.944	0.896	0.993	0.944	0.896	0.993	CLONAL	1	TRUE	1	0.749087356235072	2		869	967	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784046	120784047	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	358	1062	1	ENST00000257552.2:c.938_939delinsTT	p.Pro313Leu	p.P313L	ENST00000257552	NM_002442.3	313	cCC/cTT	13/15	1	2	FACETS	0.95	0.903	0.998	0.95	0.903	0.998	CLONAL	1	TRUE	1	0.749087356235072	2		1063	1006	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784047	120784047	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	358	1063	0	ENST00000257552.2:c.938C>T	p.Pro313Leu	p.P313L	ENST00000257552	NM_002442.3	313	cCc/cTc	13/15	1	2	FACETS	0.95	0.903	0.998	0.95	0.903	0.998	CLONAL	1	TRUE	1	0.749087356235072	2		1063	1006	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066945	30066945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	168	363	0	ENST00000331968.5:c.2186G>A	p.Gly729Asp	p.G729D	ENST00000331968	NM_002742.2	729	gGt/gAt	16/18	1	2	FACETS	0.938	0.87	1	0.938	0.87	1	CLONAL	1	TRUE	1	0.749087356235072	2		363	478	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68878231	68878231	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	148	354	0	ENST00000487270.1:c.944C>G	p.Ser315Ter	p.S315*	ENST00000487270	NM_133509.3	315	tCa/tGa	9/11	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.749087356235072	2		354	381	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988707	41988707	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	126	427	0	ENST00000219905.7:c.1499C>G	p.Ser500Cys	p.S500C	ENST00000219905	NM_001164273.1	500	tCt/tGt	3/24	0.749087356235072	1	FACETS	0.726	0.668	0.784	0.726	0.668	0.784	SUBCLONAL	1	TRUE	0	0.749087356235072	1		427	290	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822400	72822400	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	637	891	0	ENST00000268489.5:c.9775A>C	p.Lys3259Gln	p.K3259Q	ENST00000268489	NM_006885.3	3259	Aag/Cag	10/10	0.67137764238844	3	FACETS	0.936	0.905	0.967			1	CLONAL	2	TRUE	NA	0.749087356235072	3		891	1249	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991733	72991733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	346	400	0	ENST00000268489.5:c.2312G>A	p.Gly771Glu	p.G771E	ENST00000268489	NM_006885.3	771	gGg/gAg	2/10	0.67137764238844	3	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.749087356235072	3		400	596	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602385	10602385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	1077	957	0	ENST00000171111.5:c.1193C>T	p.Pro398Leu	p.P398L	ENST00000171111	NM_203500.1	398	cCc/cTc	3/6	0.58788411554632	4	FACETS	0.951	0.93	0.973	0.951	0.93	0.973	CLONAL	3	TRUE	1	0.749087356235072	4		957	1762	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182122	99182123	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	174	451	1	ENST00000074304.5:c.2187_2188delinsAA	p.Glu730Lys	p.E730K	ENST00000074304	NM_001134224.1	729	ctGGag/ctAAag	21/26	1	2	FACETS	0.966	0.897	1	0.966	0.897	1	CLONAL	1	TRUE	1	0.749087356235072	2		452	481	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182123	99182123	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	174	445	0	ENST00000074304.5:c.2188G>A	p.Glu730Lys	p.E730K	ENST00000074304	NM_001134224.1	730	Gag/Aag	21/26	1	2	FACETS	0.966	0.897	1	0.966	0.897	1	CLONAL	1	TRUE	1	0.749087356235072	2		445	481	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570061	212570063	+	missense_variant	Missense_Mutation	TNP	TCC	TCC	ATT	novel	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	139	443	0	ENST00000342788.4:c.1178_1180delinsAAT	p.Arg393_Thr394delinsGlnSer	p.R393_T394delinsQS	ENST00000342788	NM_005235.2	393	cGGAca/cAATca	10/28	0.749087356235072	2	FACETS	0.859	0.789	0.931	0.43	0.394	0.466	CLONAL	1	TRUE	0	0.749087356235072	2		443	432	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750686	39750686	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	115	269	0	ENST00000361337.2:c.2086G>A	p.Glu696Lys	p.E696K	ENST00000361337	NM_003286.2	696	Gaa/Aaa	20/21	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.749087356235072	2		269	281	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527605	41527605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777025732	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	249	477	0	ENST00000263253.7:c.1496C>T	p.Ser499Phe	p.S499F	ENST00000263253	NM_001429.3	499	tCt/tTt	6/31	0.749087356235072	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.749087356235072	1		477	378	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390904	89390904	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	100	283	0	ENST00000336596.2:c.971-1G>A		p.X324_splice	ENST00000336596	NM_005233.5	324			0.67137764238844	3	FACETS	0.796	0.715	0.882			1	SUBCLONAL	1	TRUE	NA	0.749087356235072	3		283	461	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528569	89528569	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	133	267	0	ENST00000336596.2:c.2869A>T	p.Thr957Ser	p.T957S	ENST00000336596	NM_005233.5	957	Acc/Tcc	17/17	0.67137764238844	3	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.749087356235072	3		267	366	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131181	55131181	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1324568225	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	185	446	0	ENST00000257290.5:c.724G>A	p.Val242Met	p.V242M	ENST00000257290	NM_006206.4	242	Gtg/Atg	5/23	0.749087356235072	1	FACETS	0.901	0.847	0.954	0.901	0.847	0.954	CLONAL	1	TRUE	0	0.749087356235072	1		446	343	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526432	31526432	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	397	864	0	ENST00000344624.3:c.608A>T	p.His203Leu	p.H203L	ENST00000344624		203	cAt/cTt	2/33	1	2	FACETS	0.999	0.952	1	0.999	0.952	1	CLONAL	1	TRUE	1	0.749087356235072	2		864	1061	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514352	149514352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1330417953	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	256	538	0	ENST00000261799.4:c.592G>A	p.Glu198Lys	p.E198K	ENST00000261799	NM_002609.3	198	Gag/Aag	4/23	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.749087356235072	2		538	637	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721562	176721562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	318	630	1	ENST00000439151.2:c.7193C>T	p.Pro2398Leu	p.P2398L	ENST00000439151	NM_022455.4	2398	cCc/cTc	23/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.749087356235072	2		631	793	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725505	117725505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	202	443	0	ENST00000368508.3:c.376G>A	p.Gly126Arg	p.G126R	ENST00000368508	NM_002944.2	126	Gga/Aga	5/43	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.749087356235072	2		443	475	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162475202	162475202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	142	356	0	ENST00000366898.1:c.539C>T	p.Pro180Leu	p.P180L	ENST00000366898	NM_004562.2	180	cCa/cTa	5/12	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.749087356235072	2		356	368	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622286	162622286	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	108	358	0	ENST00000366898.1:c.413-2A>G		p.X138_splice	ENST00000366898	NM_004562.2	138			1	2	FACETS	0.866	0.786	0.948	0.866	0.786	0.948	CLONAL	1	TRUE	1	0.749087356235072	2		358	333	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468038	50468038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1459868445	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	294	670	1	ENST00000331340.3:c.1273G>A	p.Gly425Arg	p.G425R	ENST00000331340	NM_006060.4	425	Ggg/Agg	8/8	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.749087356235072	2		671	635	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964515	70964516	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	255	680	1	ENST00000276594.2:c.1512_1513delinsTT	p.Arg505Cys	p.R505C	ENST00000276594	NM_024504.3	504	ctCCgc/ctTTgc	8/8	1	2	FACETS	0.864	0.812	0.917	0.864	0.812	0.917	CLONAL	1	TRUE	1	0.749087356235072	2		681	788	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981501	70981501	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200062567	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	351	971	0	ENST00000276594.2:c.595G>A	p.Glu199Lys	p.E199K	ENST00000276594	NM_024504.3	199	Gag/Aag	2/8	1	2	FACETS	0.923	0.876	0.971	0.923	0.876	0.971	CLONAL	1	TRUE	1	0.749087356235072	2		971	1015	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741476	145741476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1379758021	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1343	420	1068	0	ENST00000428558.2:c.1027C>T	p.Pro343Ser	p.P343S	ENST00000428558	NM_004260.3	343	Cct/Tct	5/22	0.749087356235072	4	FACETS	1	0.987	1	0.371	0.352	0.39	CLONAL	1	TRUE	1	0.749087356235072	4		1068	1763	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050658	30050673	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	GACCCCAGTGTTCACA	GACCCCAGTGTTCACA	TG	novel	NA	P-0045878-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	26	491	1	ENST00000338641.4:c.460_475delinsTG	p.Asp154Ter	p.D154*	ENST00000338641	NM_000268.3	154	GACCCCAGTGTTCACAag/TGag	5/16	0.749087356235072	1	FACETS	0.137	0.108	0.169	0.137	0.108	0.169	SUBCLONAL	1	TRUE	0	0.749087356235072	1		492	318	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098804	178098804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553487942	NA	P-0045880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	247	536	1	ENST00000397062.3:c.241G>A	p.Gly81Ser	p.G81S	ENST00000397062	NM_006164.4	81	Ggt/Agt	2/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.466038692152499	2		537	972	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477854	140477854	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	159	457	0	ENST00000288602.6:c.1454T>G	p.Leu485Trp	p.L485W	ENST00000288602	NM_004333.4	485	tTg/tGg	12/18	1	2	FACETS	0.993	0.913	1	0.993	0.913	1	CLONAL	1	TRUE	1	0.466038692152499	2		457	687	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115831	8115831	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	191	650	0	ENST00000346208.3:c.1177C>A	p.Pro393Thr	p.P393T	ENST00000346208		393	Ccg/Acg	6/6	1	2	FACETS	0.954	0.883	1	0.954	0.883	1	CLONAL	1	TRUE	1	0.466038692152499	2		650	859	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221908	1221947	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTGTGCCCAGCTGACAGGCTCCTCGCCGGCTTCTCCTCAG	CTGTGCCCAGCTGACAGGCTCCTCGCCGGCTTCTCCTCAG	-	novel	NA	P-0045880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	212	621	0	ENST00000326873.7:c.863-40_863-1del		p.X288_splice	ENST00000326873	NM_000455.4	288			0.466038692152499	1	FACETS	0.959	0.894	1	0.959	0.894	1	CLONAL	1	TRUE	0	0.466038692152499	1		621	728	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480084	20480084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761207862	NA	P-0045881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	127	310	0	ENST00000346618.3:c.401G>A	p.Arg134Gln	p.R134Q	ENST00000346618	NM_001949.4	134	cGa/cAa	2/7	1	2	FACETS	1	0.979	1	1	0.992	1	CLONAL	2	TRUE	1	0.26	2		310	396	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619161	37619162	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	212	564	0	ENST00000447079.4:c.839dup	p.Glu281GlyfsTer17	p.E281Gfs*17	ENST00000447079	NM_015083.1	279	-/A	1/14	1	2	FACETS	1	0.983	1	1	0.995	1	CLONAL	2	TRUE	1	0.26	2		564	700	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627610	37627610	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0045881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	183	491	0	ENST00000447079.4:c.1525A>T	p.Lys509Ter	p.K509*	ENST00000447079	NM_015083.1	509	Aaa/Taa	2/14	1	2	FACETS	0.895	0.833	0.959	1	0.994	1	CLONAL	3	TRUE	1	0.26	2		491	524	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412708	63412708	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	240	283	0	ENST00000330258.3:c.459A>T	p.Lys153Asn	p.K153N	ENST00000330258	NM_152424.3	153	aaA/aaT	2/2	1	1	FACETS	0.988	0.949	1	1	0.996	1	CLONAL	5	TRUE	0	0.26	1		283	325	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202482	123202482	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	11	170	0	ENST00000218089.9:c.2334C>G	p.Asn778Lys	p.N778K	ENST00000218089	NM_001042749.1	778	aaC/aaG	24/35	1	1	FACETS	0.751	0.524	1	0.751	0.524	1	CLONAL	1	TRUE	0	0.26	1		170	98	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0045887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	176	554	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	0.248823120183683	2	FACETS	1	0.989	1	0.729	0.673	0.787	CLONAL	1	TRUE	0	0.317230375823389	2		554	761	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242466	55242480	+	inframe_deletion	In_Frame_Del	DEL	GAATTAAGAGAAGCA	GAATTAAGAGAAGCA	-	rs727504233	NA	P-0045887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	68	316	0	ENST00000275493.2:c.2236_2250del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	746	GAATTAAGAGAAGCA/-	19/28	0.317230375823389	1	FACETS	0.986	0.862	1	0.986	0.862	1	CLONAL	1	TRUE	0	0.317230375823389	1		316	366	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584514	48584514	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	117	368	0	ENST00000342988.3:c.692del	p.Gly231AlafsTer10	p.G231Afs*10	ENST00000342988	NM_005359.5	229	ctG/ct	6/12	0.259160079368934	2	FACETS	0.872	0.792	0.955	0.872	0.792	0.955	CLONAL	2	TRUE	0	0.317230375823389	2		368	423	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996782	100996782	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	142	403	0	ENST00000325455.5:c.1745T>A	p.Leu582His	p.L582H	ENST00000325455	NM_001202474.3	582	cTt/cAt	2/8	0.240828402723882	4	FACETS	0.921	0.842	1	0.921	0.842	1	CLONAL	2	TRUE	2	0.317230375823389	4		403	640	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0045888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	115	278	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.547501015865601	2		278	370	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0045888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	210	354	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.530065668985004	2	FACETS	0.811	0.762	0.861	0.811	0.762	0.861	CLONAL	2	TRUE	0	0.547501015865601	2		354	473	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0045888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	145	417	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.547501015865601	2		417	467	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0045888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	88	316	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.207608603896182	3	FACETS	0.926	0.825	1	0.463	0.412	0.517	INDETERMINATE	1	TRUE	1	0.547501015865601	3		316	442	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0045888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	73	157	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.207608603896182	3	FACETS	1	0.971	1	0.661	0.585	0.74	INDETERMINATE	1	TRUE	1	0.547501015865601	3		157	257	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028619	12028619	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	39	302	0	ENST00000353533.5:c.822A>C	p.Arg274Ser	p.R274S	ENST00000353533	NM_003010.3	274	agA/agC	8/11	0.547501015865601	1	FACETS	0.346	0.288	0.41	0.346	0.288	0.41	SUBCLONAL	1	TRUE	0	0.547501015865601	1		302	299	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575162	48575162	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	103	307	0	ENST00000342988.3:c.356T>G	p.Phe119Cys	p.F119C	ENST00000342988	NM_005359.5	119	tTt/tGt	3/12	0.547501015865601	1	FACETS	0.955	0.868	1	0.955	0.868	1	CLONAL	1	TRUE	0	0.547501015865601	1		307	286	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966012	18966012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045888-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	150	495	0	ENST00000262803.5:c.1505C>T	p.Ser502Leu	p.S502L	ENST00000262803	NM_002911.3	502	tCg/tTg	11/24	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.547501015865601	2		495	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912655	NA	P-0045890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	272	478	0	ENST00000269305.4:c.725G>C	p.Cys242Ser	p.C242S	ENST00000269305	NM_001126112.2	242	tGc/tCc	7/11	0.704210143298307	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.760720890889882	1		478	410	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317011	11317011	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	175	369	0	ENST00000361445.4:c.483T>A	p.Asn161Lys	p.N161K	ENST00000361445	NM_004958.3	161	aaT/aaA	4/58	NA	2	FACETS	0.977	0.908	1			1	INDETERMINATE	1	TRUE	NA	0.760720890889882	2		369	471	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41276045	41276051	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTAAG	CTCTAAG	-	novel	NA	P-0045890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	151	349	0	ENST00000357654.3:c.63_69del	p.Leu22ValfsTer7	p.L22Vfs*7	ENST00000357654	NM_007294.3	21	atCTTAGAG/at	2/23	0.760720890889882	1	FACETS	0.898	0.839	0.956	0.898	0.839	0.956	CLONAL	1	TRUE	0	0.760720890889882	1		349	274	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8339049	8339049	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0045890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	151	273	0	ENST00000356435.5:c.5254-2A>T		p.X1752_splice	ENST00000356435		1752			0.547195854975241	3	FACETS	1	0.951	1			1	CLONAL	1	TRUE	NA	0.760720890889882	3		273	524	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0045891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	206	752	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.269208994452046	2	FACETS	0.936	0.872	1	0.936	0.872	1	CLONAL	2	TRUE	0	0.315423022029677	2		752	698	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0045891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	109	354	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.236178674086541	5	FACETS	1	0.96	1	0.746	0.674	0.821	CLONAL	2	TRUE	2	0.315423022029677	5		354	455	SUCCESS
APC	324	MSKCC	GRCh37	5	112175350	112175351	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0045891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	79	247	0	ENST00000257430.4:c.4059_4060del	p.Glu1353AspfsTer21	p.E1353Dfs*21	ENST00000257430	NM_000038.5	1353	gaATtt/gatt	16/16	0.308804494666259	3	FACETS	1	0.969	1	0.826	0.738	0.917	CLONAL	2	TRUE	0	0.315423022029677	3		247	234	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138564	11138564	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	169	520	0	ENST00000358026.2:c.3320C>T	p.Ser1107Phe	p.S1107F	ENST00000358026	NM_001128849.1	1107	tCc/tTc	24/36	0.209267354208391	3	FACETS	0.944	0.871	1	0.944	0.871	1	CLONAL	2	TRUE	1	0.315423022029677	3		520	657	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114799817	114799817	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	131	447	0	ENST00000543371.1:c.484C>T	p.Gln162Ter	p.Q162*	ENST00000543371	NM_001198531.1	162	Cag/Tag	5/14	0.230947536614886	3	FACETS	0.757	0.689	0.829	0.757	0.689	0.829	SUBCLONAL	2	TRUE	1	0.315423022029677	3		447	635	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61213433	61213433	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	58	345	0	ENST00000301761.2:c.391A>G	p.Ile131Val	p.I131V	ENST00000301761	NM_017841.2	131	Ata/Gta	4/4	1	2	FACETS	0.945	0.815	1	0.945	0.815	1	CLONAL	1	TRUE	1	0.315423022029677	2		345	389	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418397	139418397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	186	540	0	ENST00000277541.6:c.175G>A	p.Asp59Asn	p.D59N	ENST00000277541	NM_017617.3	59	Gac/Aac	3/34	0.230947536614886	3	FACETS	0.902	0.835	0.971	0.902	0.835	0.971	CLONAL	2	TRUE	1	0.315423022029677	3		540	757	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279677	123279677	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs79184941	NA	P-0045892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	124	331	0	ENST00000358487.5:c.755C>G	p.Ser252Trp	p.S252W	ENST00000358487	NM_000141.4	252	tCg/tGg	7/18	1	2	FACETS	0.961	0.877	1	0.961	0.877	1	CLONAL	1	TRUE	1	0.6	2		331	430	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0045892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	132	226	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.83	0.757	0.906	0.83	0.757	0.906	CLONAL	1	TRUE	1	0.6	2		226	530	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711973	89711975	+	inframe_deletion	In_Frame_Del	DEL	GAT	GAT	-	rs1064793244	NA	P-0045892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	151	317	0	ENST00000371953.3:c.595_597del	p.Met199del	p.M199del	ENST00000371953	NM_000314.4	197	aaGATg/aag	6/9	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.6	2		317	435	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779814	3779814	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	203	549	1	ENST00000262367.5:c.5234G>A	p.Trp1745Ter	p.W1745*	ENST00000262367	NM_004380.2	1745	tGg/tAg	31/31	1	2	FACETS	0.967	0.9	1	0.967	0.9	1	CLONAL	1	TRUE	1	0.6	2		550	700	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692945	89692946	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAATA	novel	NA	P-0045892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	129	409	1	ENST00000371953.3:c.433_434insAAAAT	p.Phe145Ter	p.F145*	ENST00000371953	NM_000314.4	143	-/AAATA	5/9	1	2	FACETS	0.764	0.695	0.835	0.764	0.695	0.835	SUBCLONAL	1	TRUE	1	0.6	2		410	563	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692959	89692959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	126	382	0	ENST00000371953.3:c.443C>T	p.Ala148Val	p.A148V	ENST00000371953	NM_000314.4	148	gCa/gTa	5/9	1	2	FACETS	0.83	0.756	0.907	0.83	0.756	0.907	CLONAL	1	TRUE	1	0.6	2		382	506	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650724	67650724	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	273	458	0	ENST00000264010.4:c.1029C>A	p.Tyr343Ter	p.Y343*	ENST00000264010	NM_006565.3	343	taC/taA	5/12	1	2	FACETS	0.998	0.938	1	0.998	0.938	1	CLONAL	1	TRUE	1	0.6	2		458	912	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350879	89350879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	298	625	0	ENST00000301030.4:c.2071C>T	p.Arg691Cys	p.R691C	ENST00000301030	NM_001256183.1	691	Cgc/Tgc	9/13	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.6	2		625	971	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589220	67589234	+	inframe_deletion	In_Frame_Del	DEL	AATTAATAAACCACT	AATTAATAAACCACT	-	novel	NA	P-0045892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	89	299	0	ENST00000274335.5:c.1209_1223del	p.Glu403_Tyr408delinsAsp	p.E403_Y408delinsD	ENST00000274335		403	gAATTAATAAACCACTac/gac	9/15	1	2	FACETS	0.976	0.875	1	0.976	0.875	1	CLONAL	1	TRUE	1	0.6	2		299	304	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590394	67590395	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0045892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	31	131	0	ENST00000274335.5:c.1457dup	p.Phe487IlefsTer2	p.F487Ifs*2	ENST00000274335		486	gca/gCca	11/15	1	2	FACETS	0.507	0.413	0.611	0.507	0.413	0.611	SUBCLONAL	1	TRUE	1	0.6	2		131	204	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342629	70342629	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045892-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	245	494	0	ENST00000374080.3:c.1390G>T	p.Asp464Tyr	p.D464Y	ENST00000374080		464	Gac/Tac	10/45	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.6	2		494	781	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0045893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	184	623	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.300794525215547	2	FACETS	0.949	0.882	1	0.949	0.882	1	CLONAL	2	TRUE	0	0.349882806963891	2		623	554	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0045893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	141	294	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.30159187342771	3	FACETS	1	0.979	1	0.793	0.73	0.858	CLONAL	2	TRUE	0	0.349882806963891	3		294	398	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376443	118376444	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0045893-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	61	408	0	ENST00000534358.1:c.9838dup	p.Ser3280PhefsTer14	p.S3280Ffs*14	ENST00000534358	NM_005933.3	3279	act/acTt	27/36	0.300794525215547	2	FACETS	0.789	0.682	0.904	0.394	0.341	0.452	CLONAL	1	TRUE	0	0.349882806963891	2		408	442	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0045894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	115	238	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.569331567314695	2		238	397	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0045894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	91	271	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.99	0.888	1	0.99	0.888	1	CLONAL	1	TRUE	1	0.569331567314695	2		271	323	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0045894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	97	427	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.941	0.847	1	0.941	0.847	1	CLONAL	1	TRUE	1	0.569331567314695	2		427	362	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934576	NA	P-0045894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	217	512	0	ENST00000269305.4:c.818G>C	p.Arg273Pro	p.R273P	ENST00000269305	NM_001126112.2	273	cGt/cCt	8/11	0.529327976381434	1	FACETS	0.934	0.875	0.994	0.934	0.875	0.994	CLONAL	1	TRUE	0	0.569331567314695	1		512	584	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522751	67522751	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	86	223	0	ENST00000274335.5:c.248C>A	p.Ser83Ter	p.S83*	ENST00000274335		83	tCg/tAg	1/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.569331567314695	2		223	246	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435145	18435145	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	87	290	0	ENST00000266497.5:c.130G>C	p.Val44Leu	p.V44L	ENST00000266497		44	Gta/Cta	1/31	1	2	FACETS	0.873	0.78	0.972	0.873	0.78	0.972	CLONAL	1	TRUE	1	0.569331567314695	2		290	350	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159161	143159161	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0045894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	41	190	0	ENST00000262992.4:c.692T>G	p.Leu231Ter	p.L231*	ENST00000262992	NM_001101669.1	231	tTa/tGa	10/24	0.529327976381434	1	FACETS	0.763	0.649	0.884	0.763	0.649	0.884	SUBCLONAL	1	TRUE	0	0.569331567314695	1		190	135	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0045896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	190	629	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.271895904095561	2	FACETS	1	0.988	1	0.672	0.623	0.723	CLONAL	1	FALSE	0	0.382490257609975	2		629	739	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0045896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	47	204	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	0.747	0.633	0.871	0.747	0.633	0.871	SUBCLONAL	1	FALSE	1	0.382490257609975	2		204	329	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0045896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	18	326	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	0.272478381442245	2	FACETS	0.252	0.189	0.327	0.126	0.094	0.164	SUBCLONAL	1	FALSE	0	0.382490257609975	2		326	373	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231106	53231106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556842168	NA	P-0045896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	25	213	1	ENST00000375401.3:c.1796G>A	p.Arg599His	p.R599H	ENST00000375401	NM_004187.3	599	cGt/cAt	13/26	0.267406684799312	2	FACETS	0.274	0.215	0.342			1	SUBCLONAL	1	FALSE	NA	0.382490257609975	2		214	477	SUCCESS
APC	324	MSKCC	GRCh37	5	112175271	112175271	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	41	201	0	ENST00000257430.4:c.3980C>A	p.Ser1327Ter	p.S1327*	ENST00000257430	NM_000038.5	1327	tCa/tAa	16/16	1	2	FACETS	0.712	0.596	0.84	0.712	0.596	0.84	SUBCLONAL	1	FALSE	1	0.382490257609975	2		201	301	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018193	48018193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	101	388	0	ENST00000234420.5:c.388C>T	p.His130Tyr	p.H130Y	ENST00000234420	NM_000179.2	130	Cat/Tat	2/10	0.303621600111466	3	FACETS	0.691	0.617	0.771	0.346	0.308	0.386	SUBCLONAL	1	FALSE	1	0.382490257609975	3		388	910	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535316	66535316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	41	401	1	ENST00000273854.3:c.145G>A	p.Ala49Thr	p.A49T	ENST00000273854	NM_004439.5	49	Gca/Aca	1/18	0.265927805101899	0	FACETS	0.257	0.214	0.305			1	SUBCLONAL	1	FALSE	0	0.382490257609975	0		402	515	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143404	30143404	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	83	349	0	ENST00000389048.3:c.122G>A	p.Arg41Gln	p.R41Q	ENST00000389048	NM_004304.4	41	cGg/cAg	1/29	1	2	FACETS	0.801	0.708	0.9	0.801	0.708	0.9	CLONAL	1	FALSE	1	0.382490257609975	2		349	542	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794374	242794374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763027752	NA	P-0045896-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	144	505	0	ENST00000334409.5:c.568G>A	p.Val190Ile	p.V190I	ENST00000334409	NM_005018.2	190	Gtc/Atc	3/5	0.300292756220082	3	FACETS	0.971	0.885	1	0.485	0.442	0.531	CLONAL	1	FALSE	1	0.382490257609975	3		505	924	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0045897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	88	278	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.905	0.805	1	0.905	0.805	1	CLONAL	1	TRUE	1	0.40006935759756	2		278	486	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0045897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	77	427	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.721	0.634	0.814	0.721	0.634	0.814	SUBCLONAL	1	TRUE	1	0.40006935759756	2		427	534	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0045897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	69	397	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.399490284468315	2	FACETS	0.793	0.693	0.9	0.396	0.346	0.45	SUBCLONAL	1	TRUE	0	0.40006935759756	2		397	435	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0045897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	150	609	1	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.912	0.834	0.994	0.912	0.834	0.994	CLONAL	1	TRUE	1	0.40006935759756	2		610	822	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0045897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	113	288	1	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	1	2	FACETS	0.984	0.888	1	0.984	0.888	1	CLONAL	1	TRUE	1	0.40006935759756	2		289	574	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692851	89692851	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121909230	NA	P-0045897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	46	134	0	ENST00000371953.3:c.335T>C	p.Leu112Pro	p.L112P	ENST00000371953	NM_000314.4	112	cTa/cCa	5/9	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.40006935759756	2		134	218	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106480	27106481	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0045897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	203	476	0	ENST00000324856.7:c.6092dup	p.Tyr2031Ter	p.Y2031*	ENST00000324856	NM_006015.4	2031	tat/tAat	20/20	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.40006935759756	2		476	1013	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050676	30050676	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150667239	NA	P-0045897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	108	364	2	ENST00000338641.4:c.478C>T	p.Arg160Trp	p.R160W	ENST00000338641	NM_000268.3	160	Cgg/Tgg	5/16	1	2	FACETS	0.872	0.784	0.965	0.872	0.784	0.965	CLONAL	1	TRUE	1	0.40006935759756	2		366	619	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729447	41729447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	166	487	0	ENST00000242208.4:c.1082C>T	p.Thr361Met	p.T361M	ENST00000242208	NM_002192.2	361	aCg/aTg	3/3	1	2	FACETS	0.942	0.866	1	0.942	0.866	1	CLONAL	1	TRUE	1	0.40006935759756	2		487	881	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692896	89692904	+	inframe_deletion	In_Frame_Del	DEL	GAAAGGGAC	GAAAGGGAC	-	novel	NA	P-0045897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	61	284	1	ENST00000371953.3:c.383_391del	p.Lys128_Arg130del	p.K128_R130del	ENST00000371953	NM_000314.4	127	gGAAAGGGACga/gga	5/9	1	2	FACETS	0.653	0.564	0.749	0.653	0.564	0.749	SUBCLONAL	1	TRUE	1	0.40006935759756	2		285	467	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472207	472208	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0045897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	124	369	1	ENST00000399788.2:c.593_594delinsAT	p.Ser198Asn	p.S198N	ENST00000399788	NM_001042603.1	198	aGC/aAT	5/28	1	2	FACETS	0.849	0.769	0.934	0.849	0.769	0.934	CLONAL	1	TRUE	1	0.40006935759756	2		370	730	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829322	72829322	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	199	477	0	ENST00000268489.5:c.7259A>C	p.Asn2420Thr	p.N2420T	ENST00000268489	NM_006885.3	2420	aAt/aCt	9/10	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.40006935759756	2		477	951	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502182	157502182	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554231204	NA	P-0045897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	190	406	0	ENST00000346085.5:c.3215G>A	p.Trp1072Ter	p.W1072*	ENST00000346085	NM_020732.3	1072	tGg/tAg	12/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.40006935759756	2		406	836	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0045899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	15	653	0	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	1	2	FACETS	0.068	0.049	0.092	0.068	0.049	0.092	SUBCLONAL	1	FALSE	1	0.704925791696961	2		653	622	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900563	3900563	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	21	710	0	ENST00000262367.5:c.533del	p.Asn178MetfsTer20	p.N178Mfs*20	ENST00000262367	NM_004380.2	178	aAt/at	2/31	1	2	FACETS	0.153	0.117	0.195	0.153	0.117	0.195	SUBCLONAL	1	FALSE	1	0.704925791696961	2		710	389	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038259	30038259	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	74	412	1	ENST00000338641.4:c.432C>A	p.Tyr144Ter	p.Y144*	ENST00000338641	NM_000268.3	144	taC/taA	4/16	0.704925791696961	1	FACETS	0.971	0.879	1	0.971	0.879	1	CLONAL	1	FALSE	0	0.704925791696961	1		413	140	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0045900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	80	545	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.396353524155719	1	FACETS	0.786	0.695	0.882	0.786	0.695	0.882	SUBCLONAL	1	TRUE	0	0.396353524155719	1		545	412	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0045900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	166	255	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	0.282518027370822	2	FACETS	1	0.989	1	0.718	0.663	0.775	CLONAL	1	TRUE	0	0.396353524155719	2		255	583	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809479	36809479	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	53	292	0	ENST00000373129.3:c.986G>T	p.Ser329Ile	p.S329I	ENST00000373129	NM_032017.1	329	aGt/aTt	10/12	0.282518027370822	2	FACETS	0.34	0.289	0.396	0.17	0.144	0.198	SUBCLONAL	1	TRUE	0	0.396353524155719	2		292	786	SUCCESS
APC	324	MSKCC	GRCh37	5	112173964	112173964	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	35	172	0	ENST00000257430.4:c.2673G>T	p.Met891Ile	p.M891I	ENST00000257430	NM_000038.5	891	atG/atT	16/16	1	2	FACETS	0.575	0.473	0.689	0.575	0.473	0.689	SUBCLONAL	1	TRUE	1	0.396353524155719	2		172	307	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380277	25380278	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0045901-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	116	525	1	ENST00000311936.3:c.180_181delinsAA	p.Gln61Lys	p.Q61K	ENST00000311936	NM_004985.3	60	ggTCaa/ggAAaa	3/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		526	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0045902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	422	636	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	0.895164929598654	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.895164929598654	1		636	483	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900410	3900410	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	441	664	0	ENST00000262367.5:c.686del	p.Pro229GlnfsTer15	p.P229Qfs*15	ENST00000262367	NM_004380.2	229	cCa/ca	2/31	0.483100989397802	1	FACETS	0.704	0.678	0.73	0.704	0.678	0.73	INDETERMINATE	1	TRUE	0	0.895164929598654	1		664	773	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692790	89692790	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554898067	NA	P-0045903-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	12	322	0	ENST00000371953.3:c.274G>T	p.Asp92Tyr	p.D92Y	ENST00000371953	NM_000314.4	92	Gac/Tac	5/9	0.883898523386046	1	FACETS	0.117	0.083	0.16	0.117	0.083	0.16	SUBCLONAL	1	TRUE	0	0.883898523386046	1		322	129	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0045908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	510	911	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.771458761907178	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	0	0.767944522371873	3		911	610	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0045908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	881	329	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.767944522371873	6	FACETS	1	0.998	1	1	0.998	1	CLONAL	6	TRUE	0	0.767944522371873	6		329	934	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058705	47058706	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	339	438	2	ENST00000409792.3:c.7572dup	p.Lys2525Ter	p.K2525*	ENST00000409792	NM_014159.6	2524	-/T	21/21	0.771232686991009	3	FACETS	0.949	0.92	0.977	0.949	0.92	0.977	CLONAL	3	TRUE	0	0.767944522371873	3		440	429	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910239	50910239	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0045908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	357	597	0	ENST00000440232.2:c.1495-1G>C		p.X499_splice	ENST00000440232	NM_002691.3	499			0.716282319201462	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.767944522371873	4		597	753	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453578	138453578	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045908-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	55	353	0	ENST00000289153.2:c.870G>C	p.Lys290Asn	p.K290N	ENST00000289153	NM_006219.2	290	aaG/aaC	5/22	0.771458761907178	4	FACETS	0.794	0.683	0.913	0.265	0.227	0.305	CLONAL	1	TRUE	1	0.767944522371873	4		353	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0045909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	132	702	0	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.350001187157687	2		702	748	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199873	128199873	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780263343	NA	P-0045909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	45	500	0	ENST00000341105.2:c.1432G>A	p.Ala478Thr	p.A478T	ENST00000341105	NM_032638.4	478	Gcc/Acc	6/6	1	2	FACETS	0.463	0.389	0.546	0.463	0.389	0.546	SUBCLONAL	1	TRUE	1	0.350001187157687	2		500	555	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81891957	81891957	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768646306	NA	P-0045909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	24	402	0	ENST00000359376.3:c.427G>A	p.Glu143Lys	p.E143K	ENST00000359376	NM_002661.3	143	Gag/Aag	4/33	1	2	FACETS	0.325	0.254	0.407	0.325	0.254	0.407	SUBCLONAL	1	TRUE	1	0.350001187157687	2		402	422	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660789	227660789	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	35	535	0	ENST00000305123.5:c.2666A>G	p.Glu889Gly	p.E889G	ENST00000305123	NM_005544.2	889	gAg/gGg	1/2	0.179432676104656	3	FACETS	0.394	0.322	0.475	0.197	0.161	0.238	INDETERMINATE	1	TRUE	1	0.350001187157687	3		535	597	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0045911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	36	487	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		487	549	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs730881677	NA	P-0045911-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	18	383	0	ENST00000304494.5:c.151-1G>T		p.X51_splice	ENST00000304494	NM_000077.4	51			1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		383	255	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644715	134644715	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs556035012	NA	P-0045918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	91	515	1	ENST00000398015.3:c.116C>T	p.Ala39Val	p.A39V	ENST00000398015	NM_004441.4	39	gCg/gTg	2/16	1	2	FACETS	0.759	0.674	0.849	0.759	0.674	0.849	SUBCLONAL	1	TRUE	1	0.364392388843307	2		516	658	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859593	151859593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	37	470	1	ENST00000262189.6:c.11069C>T	p.Ser3690Leu	p.S3690L	ENST00000262189	NM_170606.2	3690	tCa/tTa	43/59	1	2	FACETS	0.345	0.283	0.414	0.345	0.283	0.414	SUBCLONAL	1	TRUE	1	0.364392388843307	2		471	589	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0045919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	508	752	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.565813954679122	2	FACETS	0.939	0.906	0.972	0.939	0.906	0.972	CLONAL	2	TRUE	0	0.606517724407143	2		752	892	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043438	180043438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373876329	NA	P-0045919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	491	589	0	ENST00000261937.6:c.3148G>A	p.Val1050Met	p.V1050M	ENST00000261937	NM_182925.4	1050	Gtg/Atg	23/30	0.518901161746319	2	FACETS	0.898	0.866	0.931	0.898	0.866	0.931	CLONAL	2	TRUE	0	0.606517724407143	2		589	901	SUCCESS
APC	324	MSKCC	GRCh37	5	112175615	112175615	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	151	265	0	ENST00000257430.4:c.4325del	p.Pro1442LeufsTer31	p.P1442Lfs*31	ENST00000257430	NM_000038.5	1442	Cct/ct	16/16	0.518901161746319	2	FACETS	0.824	0.768	0.881	0.824	0.768	0.881	CLONAL	2	TRUE	0	0.606517724407143	2		265	302	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213494	27213494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	107	333	0	ENST00000380036.4:c.2890G>A	p.Asp964Asn	p.D964N	ENST00000380036	NM_000459.3	964	Gat/Aat	18/23	0.606517724407143	1	FACETS	0.894	0.815	0.975	0.894	0.815	0.975	CLONAL	1	TRUE	0	0.606517724407143	1		333	275	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330656	65330656	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0045919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	88	213	0	ENST00000342505.4:c.991-1G>A		p.X331_splice	ENST00000342505	NM_002227.2	331			0.319924249004435	2	FACETS	1	0.983	1	0.744	0.675	0.814	INDETERMINATE	1	TRUE	0	0.606517724407143	2		213	195	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646102	215646102	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786202500	NA	P-0045919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	74	484	1	ENST00000260947.4:c.496C>T	p.Gln166Ter	p.Q166*	ENST00000260947	NM_000465.2	166	Cag/Tag	4/11	0.248747191243901	3	FACETS	0.684	0.601	0.773	0.228	0.2	0.258	INDETERMINATE	1	TRUE	0	0.606517724407143	3		485	465	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70353052	70353052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	111	358	0	ENST00000374080.3:c.4607G>A	p.Arg1536Gln	p.R1536Q	ENST00000374080		1536	cGg/cAg	33/45	0.606517724407143	3	FACETS	0.617	0.555	0.683	0.309	0.277	0.342	SUBCLONAL	1	TRUE	1	0.606517724407143	3		358	773	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0045921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	203	262	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.285740484391126	3	FACETS	0.847	0.788	0.907	0.847	0.788	0.907	CLONAL	2	FALSE	1	0.410890976138497	3		262	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913343	NA	P-0045921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	315	618	0	ENST00000269305.4:c.817C>G	p.Arg273Gly	p.R273G	ENST00000269305	NM_001126112.2	273	Cgt/Ggt	8/11	0.298967907002191	2	FACETS	0.779	0.736	0.823	0.779	0.736	0.823	SUBCLONAL	2	FALSE	0	0.410890976138497	2		618	984	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145436	58145436	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	288	414	1	ENST00000257904.6:c.65A>T	p.Lys22Met	p.K22M	ENST00000257904	NM_000075.3	22	aAg/aTg	2/8	0.408580693908587	3	FACETS	0.852	0.802	0.903	0.852	0.802	0.903	CLONAL	2	FALSE	1	0.410890976138497	3		415	992	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0045921-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	137	415	2				ENST00000310581	NM_198253.2	-/1132			0.181214518727723	1	FACETS	1	0.964	1	1	0.964	1	INDETERMINATE	1	FALSE	0	0.410890976138497	1		417	484	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019907	123019907	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs918994753	NA	P-0045923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	91	536	2	ENST00000355640.3:c.395C>T	p.Pro132Leu	p.P132L	ENST00000355640		132	cCa/cTa	2/7	0.272717265418714	1	FACETS	0.411	0.37	0.453	0.411	0.37	0.453	INDETERMINATE	1	TRUE	0	0.914537628372041	1		538	263	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178577	56178579	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs750747779	NA	P-0045924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	24	220	0	ENST00000399503.3:c.3560_3562del	p.Glu1187del	p.E1187del	ENST00000399503	NM_005921.1	1184	GAA/-	14/20	0.330496880990476	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		220	384	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849545	68849545	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	67	567	1	ENST00000261769.5:c.1452del	p.Ile485SerfsTer37	p.I485Sfs*37	ENST00000261769	NM_004360.3	483	gCc/gc	10/16	0.165004592441683	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		568	602	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011207	12011207	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	22	264	3	ENST00000353533.5:c.614T>C	p.Leu205Ser	p.L205S	ENST00000353533	NM_003010.3	205	tTa/tCa	5/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		267	318	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964924	25964924	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	43	358	0	ENST00000435504.4:c.4282T>A	p.Cys1428Ser	p.C1428S	ENST00000435504		1428	Tgc/Agc	13/13	0.165004592441683	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		358	469	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294662	1294662	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	27	344	0	ENST00000310581.5:c.339G>T	p.Glu113Asp	p.E113D	ENST00000310581	NM_198253.2	113	gaG/gaT	2/16	0.165004592441683	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		344	357	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167830	56167830	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	54	363	0	ENST00000399503.3:c.1395C>A	p.Asn465Lys	p.N465K	ENST00000399503	NM_005921.1	465	aaC/aaA	7/20	0.330496880990476	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		363	682	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878842	151878842	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1053658283	NA	P-0045924-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	65	491	2	ENST00000262189.6:c.6103C>T	p.Pro2035Ser	p.P2035S	ENST00000262189	NM_170606.2	2035	Cct/Tct	36/59	0.105468032984936	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		493	630	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0045925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	42	262	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.12	2		262	553	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0045925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	39	264	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.871	0.724	1	1	0.962	1	CLONAL	2	TRUE	1	0.12	2		264	373	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851271	156851271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	65	614	0	ENST00000524377.1:c.2228G>A	p.Gly743Glu	p.G743E	ENST00000524377	NM_002529.3	743	gGa/gAa	17/17	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.12	2		614	848	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714445	117714445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1307627482	NA	P-0045925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	40	390	1	ENST00000368508.3:c.1204G>A	p.Glu402Lys	p.E402K	ENST00000368508	NM_002944.2	402	Gaa/Aaa	11/43	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.12	2		391	469	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962271	2962271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867239716	NA	P-0045925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	94	676	0	ENST00000396946.4:c.2266G>A	p.Glu756Lys	p.E756K	ENST00000396946	NM_032415.4	756	Gaa/Aaa	17/25	1	2	FACETS	0.89	0.791	0.996	1	0.984	1	CLONAL	2	TRUE	1	0.12	2		676	880	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256242	16256243	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0045925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	34	497	1	ENST00000375759.3:c.3507_3508delinsTT	p.Arg1170Ter	p.R1170*	ENST00000375759	NM_015001.2	1169	taCCga/taTTga	11/15	1	2	FACETS	0.926	0.755	1	0.926	0.755	1	CLONAL	1	TRUE	1	0.12	2		498	612	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132120	176132120	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	34	332	0	ENST00000367669.3:c.647G>T	p.Gly216Val	p.G216V	ENST00000367669	NM_022457.5	216	gGc/gTc	5/20	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.12	2		332	482	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138155	64138155	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	46	602	1	ENST00000334205.4:c.2078C>T	p.Ser693Phe	p.S693F	ENST00000334205	NM_003942.2	693	tCc/tTc	16/17	1	2	FACETS	0.935	0.785	1	0.935	0.785	1	CLONAL	1	TRUE	1	0.12	2		603	820	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448780	49448780	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	70	570	0	ENST00000301067.7:c.79A>C	p.Ser27Arg	p.S27R	ENST00000301067	NM_003482.3	27	Agt/Cgt	2/54	1	2	FACETS	0.775	0.675	0.883	1	0.974	1	SUBCLONAL	2	TRUE	1	0.12	2		570	753	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265148	5265148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	55	734	1	ENST00000357368.4:c.439G>A	p.Glu147Lys	p.E147K	ENST00000357368	NM_002850.3	147	Gag/Aag	5/38	1	2	FACETS	0.979	0.835	1	0.979	0.835	1	CLONAL	1	TRUE	1	0.12	2		735	936	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755437	39755437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	55	547	1	ENST00000288319.7:c.1328C>T	p.Ser443Phe	p.S443F	ENST00000288319	NM_182918.3	443	tCc/tTc	10/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.12	2		548	656	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0045926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	153	377	1	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.8	0.733	0.87	1	0.989	1	SUBCLONAL	2	TRUE	1	0.254556617624203	2		378	751	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578208	7578208	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519992	NA	P-0045926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	140	579	0	ENST00000269305.4:c.641A>G	p.His214Arg	p.H214R	ENST00000269305	NM_001126112.2	214	cAt/cGt	6/11	0.254556617624203	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.254556617624203	1		579	705	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661485	227661485	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045926-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	82	611	0	ENST00000305123.5:c.1970T>G	p.Val657Gly	p.V657G	ENST00000305123	NM_005544.2	657	gTg/gGg	1/2	1	2	FACETS	0.828	0.729	0.934	0.828	0.729	0.934	CLONAL	1	TRUE	1	0.254556617624203	2		611	778	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242467	55242485	+	protein_altering_variant	In_Frame_Del	DEL	AATTAAGAGAAGCAACATC	AATTAAGAGAAGCAACATC	T	rs727504258	NA	P-0045927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	50	406	0	ENST00000275493.2:c.2237_2255delinsT	p.Glu746_Ser752delinsVal	p.E746_S752delinsV	ENST00000275493	NM_005228.3	746	gAATTAAGAGAAGCAACATCt/gTt	19/28	1	2	FACETS	0.578	0.49	0.675	0.578	0.49	0.675	SUBCLONAL	1	TRUE	1	0.31	2		406	558	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505556	25505556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs756237176	NA	P-0045927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	101	686	0	ENST00000264709.3:c.202G>T	p.Asp68Tyr	p.D68Y	ENST00000264709	NM_175629.2	68	Gac/Tac	4/23	1	2	FACETS	0.606	0.54	0.676	0.606	0.54	0.676	SUBCLONAL	1	TRUE	1	0.31	2		686	1075	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388718	31388718	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045927-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	48	481	0	ENST00000328111.2:c.1983G>T	p.Arg661Ser	p.R661S	ENST00000328111	NM_006892.3	661	agG/agT	18/23	1	2	FACETS	0.501	0.423	0.587	0.501	0.423	0.587	SUBCLONAL	1	TRUE	1	0.31	2		481	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876659802	NA	P-0046005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	308	548	0	ENST00000269305.4:c.833C>G	p.Pro278Arg	p.P278R	ENST00000269305	NM_001126112.2	278	cCt/cGt	8/11	NA	2	FACETS	0.948	0.903	0.992			1	INDETERMINATE	2	TRUE	NA	0.540865059110908	2		548	601	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310883	123310883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	158	462	0	ENST00000358487.5:c.545G>A	p.Gly182Glu	p.G182E	ENST00000358487	NM_000141.4	182	gGg/gAg	5/18	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.540865059110908	2		462	534	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936374	78936374	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	114	544	1	ENST00000306801.3:c.3806C>T	p.Ala1269Val	p.A1269V	ENST00000306801	NM_020761.2	1269	gCa/gTa	32/34	1	2	FACETS	0.985	0.893	1	0.985	0.893	1	CLONAL	1	TRUE	1	0.540865059110908	2		545	428	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872509	136872509	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	80	212	0	ENST00000241393.3:c.989C>T	p.Ser330Phe	p.S330F	ENST00000241393	NM_003467.2	330	tCc/tTc	2/2	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.540865059110908	2		212	272	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266123	41266124	+	missense_variant	Missense_Mutation	DNP	TA	TA	AG	novel	NA	P-0046005-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	37	264	0	ENST00000349496.5:c.120_121delinsAG	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	40	acTAcc/acAGcc	3/15	0.354846911415073	1	FACETS	0.398	0.33	0.473	0.398	0.33	0.473	SUBCLONAL	1	TRUE	0	0.540865059110908	1		264	251	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971177	21971177	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913382	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	53	300	1	ENST00000304494.5:c.181G>T	p.Glu61Ter	p.E61*	ENST00000304494	NM_000077.4	61	Gag/Tag	2/3	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.24	2		301	375	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974730	21974730	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	45	292	0	ENST00000304494.5:c.97G>T	p.Glu33Ter	p.E33*	ENST00000304494	NM_000077.4	33	Gag/Tag	1/3	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.24	2		292	323	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358987	81358987	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381615839	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	57	383	0	ENST00000222390.5:c.974C>T	p.Pro325Leu	p.P325L	ENST00000222390	NM_000601.4	325	cCa/cTa	8/18	1	2	FACETS	0.994	0.854	1	0.994	0.854	1	CLONAL	1	TRUE	1	0.24	2		383	478	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099026	27099026	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	53	403	0	ENST00000324856.7:c.3442C>T	p.Gln1148Ter	p.Q1148*	ENST00000324856	NM_006015.4	1148	Cag/Tag	13/20	1	2	FACETS	0.894	0.763	1	0.894	0.763	1	CLONAL	1	TRUE	1	0.24	2		403	494	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663617	117663617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751502071	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	42	356	0	ENST00000368508.3:c.4615C>T	p.Pro1539Ser	p.P1539S	ENST00000368508	NM_002944.2	1539	Cct/Tct	28/43	1	2	FACETS	0.862	0.721	1	0.862	0.721	1	CLONAL	1	TRUE	1	0.24	2		356	406	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653271	29653271	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	16	176	0	ENST00000356175.3:c.5205+1G>T		p.X1735_splice	ENST00000356175	NM_000267.3	1735			1	2	FACETS	0.587	0.435	0.769	0.587	0.435	0.769	SUBCLONAL	1	TRUE	1	0.24	2		176	227	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223772	53223772	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	130	790	0	ENST00000375401.3:c.3587G>C	p.Gly1196Ala	p.G1196A	ENST00000375401	NM_004187.3	1196	gGg/gCg	23/26	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.24	2		790	799	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683754	162683754	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	64	445	0	ENST00000366898.1:c.215G>T	p.Arg72Ile	p.R72I	ENST00000366898	NM_004562.2	72	aGa/aTa	3/12	1	2	FACETS	0.918	0.795	1	0.918	0.795	1	CLONAL	1	TRUE	1	0.24	2		445	581	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410145	63410145	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	58	649	0	ENST00000330258.3:c.3022C>A	p.Pro1008Thr	p.P1008T	ENST00000330258	NM_152424.3	1008	Cca/Aca	2/2	1	2	FACETS	0.821	0.705	0.947	0.821	0.705	0.947	CLONAL	1	TRUE	1	0.24	2		649	589	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865090	57865090	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	39	776	1	ENST00000228682.2:c.2567C>A	p.Pro856His	p.P856H	ENST00000228682	NM_005269.2	856	cCt/cAt	12/12	1	2	FACETS	0.48	0.397	0.573	0.48	0.397	0.573	SUBCLONAL	1	TRUE	1	0.24	2		777	677	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396469	30396469	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs756773077	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	32	236	0	ENST00000331968.5:c.250A>G	p.Ile84Val	p.I84V	ENST00000331968	NM_002742.2	84	Att/Gtt	1/18	1	2	FACETS	0.844	0.687	1	0.844	0.687	1	CLONAL	1	TRUE	1	0.24	2		236	316	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375007	45375007	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	23	293	0	ENST00000262160.6:c.836A>G	p.Tyr279Cys	p.Y279C	ENST00000262160	NM_005901.5	279	tAt/tGt	8/11	1	2	FACETS	0.531	0.414	0.667	0.531	0.414	0.667	SUBCLONAL	1	TRUE	1	0.24	2		293	361	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480009	50480010	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1302818922	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	69	602	0	ENST00000394963.4:c.249dup	p.Asn84GlufsTer47	p.N84Efs*47	ENST00000394963	NM_003076.4	81	-/G	2/13	1	2	FACETS	0.963	0.839	1	0.963	0.839	1	CLONAL	1	TRUE	1	0.24	2		602	597	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515247	106515247	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	31	325	0	ENST00000359195.3:c.2390C>A	p.Ala797Glu	p.A797E	ENST00000359195	NM_002649.2	797	gCa/gAa	5/11	1	2	FACETS	0.825	0.669	1	0.825	0.669	1	CLONAL	1	TRUE	1	0.24	2		325	313	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11210204	11210204	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	77	450	0	ENST00000361445.4:c.4549G>T	p.Ala1517Ser	p.A1517S	ENST00000361445	NM_004958.3	1517	Gct/Tct	31/58	1	2	FACETS	0.998	0.876	1	0.998	0.876	1	CLONAL	1	TRUE	1	0.24	2		450	643	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28605730	28605756	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCACTTCCGCCACTCAGAGAAGGTAT	GGCACTTCCGCCACTCAGAGAAGGTAT	-	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	42	411	0	ENST00000253063.3:c.1335_1356+5del		p.X445_splice	ENST00000253063	NM_031459.4	445		9/10	1	2	FACETS	0.694	0.58	0.822	0.694	0.58	0.822	SUBCLONAL	1	TRUE	1	0.24	2		411	504	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932401	36932401	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	125	647	0	ENST00000361632.4:c.2068A>T	p.Thr690Ser	p.T690S	ENST00000361632		690	Acg/Tcg	16/16	1	2	FACETS	0.88	0.799	0.964	1	0.988	1	CLONAL	2	TRUE	1	0.24	2		647	592	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650025	206650025	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	81	407	0	ENST00000367120.3:c.545C>T	p.Pro182Leu	p.P182L	ENST00000367120	NM_014002.3	182	cCc/cTc	7/22	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.24	2		407	464	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226590060	226590060	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	66	446	0	ENST00000366794.5:c.141del	p.Val48SerfsTer47	p.V48Sfs*47	ENST00000366794	NM_001618.3	47	aaA/aa	2/23	1	2	FACETS	0.943	0.819	1	0.943	0.819	1	CLONAL	1	TRUE	1	0.24	2		446	583	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135680	64135680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	82	710	0	ENST00000334205.4:c.1148G>A	p.Gly383Asp	p.G383D	ENST00000334205	NM_003942.2	383	gGt/gAt	10/17	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.24	2		710	674	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625228	69625228	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	48	739	0	ENST00000334134.2:c.565G>T	p.Glu189Ter	p.E189*	ENST00000334134	NM_005247.2	189	Gag/Tag	3/3	1	2	FACETS	0.527	0.444	0.619	0.527	0.444	0.619	SUBCLONAL	1	TRUE	1	0.24	2		739	759	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633604	69633604	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	11	55	0	ENST00000334134.2:c.98G>T	p.Gly33Val	p.G33V	ENST00000334134	NM_005247.2	33	gGc/gTc	1/3	1	2	FACETS	1	0.719	1	1	0.719	1	CLONAL	1	TRUE	1	0.24	2		55	89	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420308	88420308	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	47	337	0	ENST00000360948.2:c.2378G>T	p.Arg793Leu	p.R793L	ENST00000360948	NM_001012338.2	793	cGa/cTa	19/19	1	2	FACETS	0.872	0.737	1	0.872	0.737	1	CLONAL	1	TRUE	1	0.24	2		337	449	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678625	88678626	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	28	300	1	ENST00000360948.2:c.910_911delinsAA	p.Pro304Asn	p.P304N	ENST00000360948	NM_001012338.2	304	CCc/AAc	9/19	1	2	FACETS	0.716	0.573	0.878	0.716	0.573	0.878	SUBCLONAL	1	TRUE	1	0.24	2		301	326	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858454	9858454	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	46	415	0	ENST00000330684.3:c.2947C>A	p.Gln983Lys	p.Q983K	ENST00000330684	NM_001134407.1	983	Caa/Aaa	13/13	1	2	FACETS	0.958	0.809	1	0.958	0.809	1	CLONAL	1	TRUE	1	0.24	2		415	400	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849596	68849596	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	76	577	0	ENST00000261769.5:c.1499G>T	p.Gly500Val	p.G500V	ENST00000261769	NM_004360.3	500	gGc/gTc	10/16	1	2	FACETS	0.827	0.724	0.937	0.827	0.724	0.937	CLONAL	1	TRUE	1	0.24	2		577	766	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351936	89351936	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	128	670	1	ENST00000301030.4:c.1014G>T	p.Lys338Asn	p.K338N	ENST00000301030	NM_001256183.1	338	aaG/aaT	9/13	0.3	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.24	1		671	846	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579440	7579441	+	frameshift_variant	Frame_Shift_Ins	INS	CC	CC	AAA	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	89	668	1	ENST00000269305.4:c.246_247delinsTTT	p.Ala83PhefsTer66	p.A83Ffs*66	ENST00000269305	NM_001126112.2	82	ccGGcg/ccTTTcg	4/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.24	2		669	606	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627793	37627794	+	missense_variant	Missense_Mutation	DNP	CA	CA	TT	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	84	593	0	ENST00000447079.4:c.1708_1709delinsTT	p.Gln570Leu	p.Q570L	ENST00000447079	NM_015083.1	570	CAg/TTg	2/14	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.24	2		593	687	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866352	37866353	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	34	602	0	ENST00000269571.5:c.658dup	p.Cys220LeufsTer15	p.C220Lfs*15	ENST00000269571		219	-/T	6/27	1	2	FACETS	0.452	0.368	0.547	0.452	0.368	0.547	SUBCLONAL	1	TRUE	1	0.24	2		602	627	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260238	19260238	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	68	488	0	ENST00000162023.5:c.55G>T	p.Val19Leu	p.V19L	ENST00000162023		19	Gtg/Ttg	7/13	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.24	2		488	549	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795088	242795088	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	84	801	0	ENST00000334409.5:c.121C>A	p.Leu41Met	p.L41M	ENST00000334409	NM_005018.2	41	Ctg/Atg	2/5	1	2	FACETS	0.975	0.861	1	0.975	0.861	1	CLONAL	1	TRUE	1	0.24	2		801	718	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713354	40713354	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	40	578	0	ENST00000373198.4:c.4161C>A	p.Asp1387Glu	p.D1387E	ENST00000373198	NM_133170.3	1387	gaC/gaA	30/32	1	2	FACETS	0.559	0.464	0.666	0.559	0.464	0.666	SUBCLONAL	1	TRUE	1	0.24	2		578	596	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391198	89391198	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1178604557	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	39	334	0	ENST00000336596.2:c.1264C>A	p.Pro422Thr	p.P422T	ENST00000336596	NM_005233.5	422	Cca/Aca	5/17	1	2	FACETS	0.908	0.754	1	0.908	0.754	1	CLONAL	1	TRUE	1	0.24	2		334	358	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720921	119720921	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	70	375	0	ENST00000316626.5:c.254A>G	p.Lys85Arg	p.K85R	ENST00000316626		85	aAg/aGg	2/12	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.24	2		375	495	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231111	142231111	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	63	308	0	ENST00000350721.4:c.4843G>T	p.Asp1615Tyr	p.D1615Y	ENST00000350721	NM_001184.3	1615	Gac/Tac	27/47	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.24	2		308	473	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356332	66356332	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	28	323	0	ENST00000273854.3:c.1165G>T	p.Val389Leu	p.V389L	ENST00000273854	NM_004439.5	389	Gtg/Ttg	5/18	1	2	FACETS	0.638	0.51	0.783	0.638	0.51	0.783	SUBCLONAL	1	TRUE	1	0.24	2		323	366	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143033810	143033811	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	20	288	0	ENST00000262992.4:c.2160_2161delinsAA	p.Leu721Ile	p.L721I	ENST00000262992	NM_001101669.1	720	aaGCtt/aaAAtt	20/24	1	2	FACETS	0.627	0.48	0.798	0.627	0.48	0.798	SUBCLONAL	1	TRUE	1	0.24	2		288	266	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973868	131973868	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	55	254	0	ENST00000265335.6:c.3571G>T	p.Gly1191Ter	p.G1191*	ENST00000265335		1191	Gga/Tga	23/25	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.24	2		254	342	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501453	149501453	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	39	486	0	ENST00000261799.4:c.2334C>A	p.Tyr778Ter	p.Y778*	ENST00000261799	NM_002609.3	778	taC/taA	16/23	1	2	FACETS	0.54	0.446	0.644	0.54	0.446	0.644	SUBCLONAL	1	TRUE	1	0.24	2		486	602	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522725	176522725	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	43	603	0	ENST00000292408.4:c.1821+1G>C		p.X607_splice	ENST00000292408	NM_213647.1	607			1	2	FACETS	0.704	0.589	0.832	0.704	0.589	0.832	SUBCLONAL	1	TRUE	1	0.24	2		603	509	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184966	32184966	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	68	592	0	ENST00000375023.3:c.1702G>T	p.Asp568Tyr	p.D568Y	ENST00000375023	NM_004557.3	568	Gac/Tac	10/30	1	2	FACETS	0.845	0.734	0.964	0.845	0.734	0.964	CLONAL	1	TRUE	1	0.24	2		592	671	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502301	157502301	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	60	383	0	ENST00000346085.5:c.3334G>T	p.Gly1112Cys	p.G1112C	ENST00000346085	NM_020732.3	1112	Ggt/Tgt	12/20	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.24	2		383	458	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969887	161969887	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	32	419	0	ENST00000366898.1:c.1082G>T	p.Gly361Val	p.G361V	ENST00000366898	NM_004562.2	361	gGg/gTg	9/12	1	2	FACETS	0.542	0.439	0.658	0.542	0.439	0.658	SUBCLONAL	1	TRUE	1	0.24	2		419	492	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161990389	161990389	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	39	280	0	ENST00000366898.1:c.931C>A	p.Gln311Lys	p.Q311K	ENST00000366898	NM_004562.2	311	Cag/Aag	8/12	1	2	FACETS	0.962	0.799	1	0.962	0.799	1	CLONAL	1	TRUE	1	0.24	2		280	338	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729391	41729391	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	35	509	0	ENST00000242208.4:c.1138G>T	p.Gly380Cys	p.G380C	ENST00000242208	NM_002192.2	380	Ggc/Tgc	3/3	1	2	FACETS	0.513	0.419	0.618	0.513	0.419	0.618	SUBCLONAL	1	TRUE	1	0.24	2		509	569	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508431	106508431	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	28	305	0	ENST00000359195.3:c.425C>A	p.Pro142Gln	p.P142Q	ENST00000359195	NM_002649.2	142	cCg/cAg	2/11	1	2	FACETS	0.76	0.609	0.932	0.76	0.609	0.932	CLONAL	1	TRUE	1	0.24	2		305	307	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404560	8404560	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs781289256	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	22	171	0	ENST00000356435.5:c.4187G>T	p.Arg1396Leu	p.R1396L	ENST00000356435		1396	cGg/cTg	25/35	1	2	FACETS	0.94	0.733	1	0.94	0.733	1	CLONAL	1	TRUE	1	0.24	2		171	195	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347847	128347847	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	52	479	0	ENST00000265960.3:c.658G>T	p.Glu220Ter	p.E220*	ENST00000265960	NM_001006617.1	220	Gag/Tag	5/12	1	2	FACETS	0.805	0.686	0.937	0.805	0.686	0.937	CLONAL	1	TRUE	1	0.24	2		479	538	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921436	39921436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	33	463	0	ENST00000378444.4:c.4384G>A	p.Ala1462Thr	p.A1462T	ENST00000378444	NM_001123385.1	1462	Gct/Act	10/15	1	2	FACETS	0.574	0.467	0.695	0.574	0.467	0.695	SUBCLONAL	1	TRUE	1	0.24	2		463	479	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934420	39934420	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	33	393	0	ENST00000378444.4:c.179C>A	p.Thr60Lys	p.T60K	ENST00000378444	NM_001123385.1	60	aCg/aAg	4/15	1	2	FACETS	0.547	0.445	0.662	0.547	0.445	0.662	SUBCLONAL	1	TRUE	1	0.24	2		393	503	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028878	47028878	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	36	532	0	ENST00000377604.3:c.182C>G	p.Ser61Cys	p.S61C	ENST00000377604	NM_001204468.1	61	tCt/tGt	3/24	1	2	FACETS	0.484	0.397	0.582	0.484	0.397	0.582	SUBCLONAL	1	TRUE	1	0.24	2		532	620	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412850	63412850	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	53	642	1	ENST00000330258.3:c.317C>A	p.Pro106His	p.P106H	ENST00000330258	NM_152424.3	106	cCt/cAt	2/2	1	2	FACETS	0.706	0.601	0.82	0.706	0.601	0.82	SUBCLONAL	1	TRUE	1	0.24	2		643	626	SUCCESS
AR	367	MSKCC	GRCh37	X	66931521	66931521	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	30	407	0	ENST00000374690.3:c.2163G>T	p.Lys721Asn	p.K721N	ENST00000374690	NM_000044.3	721	aaG/aaT	4/8	1	2	FACETS	0.495	0.398	0.606	0.495	0.398	0.606	SUBCLONAL	1	TRUE	1	0.24	2		407	505	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350054	70350054	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs966195679	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	35	412	0	ENST00000374080.3:c.4037G>T	p.Arg1346Leu	p.R1346L	ENST00000374080		1346	cGc/cTc	28/45	1	2	FACETS	0.705	0.578	0.847	0.705	0.578	0.847	SUBCLONAL	1	TRUE	1	0.24	2		412	414	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845398	76845398	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	21	219	0	ENST00000373344.5:c.6123C>G	p.Ser2041Arg	p.S2041R	ENST00000373344	NM_000489.3	2041	agC/agG	27/35	1	2	FACETS	0.692	0.534	0.875	0.692	0.534	0.875	SUBCLONAL	1	TRUE	1	0.24	2		219	253	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872093	76872093	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	18	260	0	ENST00000373344.5:c.5554G>T	p.Asp1852Tyr	p.D1852Y	ENST00000373344	NM_000489.3	1852	Gat/Tat	22/35	1	2	FACETS	0.526	0.396	0.68	0.526	0.396	0.68	SUBCLONAL	1	TRUE	1	0.24	2		260	285	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358986	81358986	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	58	394	0	ENST00000222390.5:c.975del	p.Cys326ValfsTer14	p.C326Vfs*14	ENST00000222390	NM_000601.4	325	ccA/cc	8/18	1	2	FACETS	0.997	0.858	1	0.997	0.858	1	CLONAL	1	TRUE	1	0.24	2		394	485	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43749707	43749707	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	TC	novel	NA	P-0046008-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	60	367	0	ENST00000523873.1:c.560delinsTC	p.Cys187PhefsTer17	p.C187Ffs*17	ENST00000523873		187	tGc/tTCc	7/8	1	2	FACETS	0.931	0.803	1	0.931	0.803	1	CLONAL	1	TRUE	1	0.24	2		367	537	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106861	27106861	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0046009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	257	576	0	ENST00000324856.7:c.6472C>T	p.Arg2158Ter	p.R2158*	ENST00000324856	NM_006015.4	2158	Cga/Tga	20/20	0.548231049237569	1	FACETS	0.946	0.891	1	0.946	0.891	1	CLONAL	1	TRUE	0	0.5807313240414	1		576	664	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894916	101894916	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060502040	NA	P-0046009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	132	247	0	ENST00000374994.4:c.469C>T	p.Arg157Ter	p.R157*	ENST00000374994	NM_004612.2	157	Cga/Tga	3/9	0.548231049237569	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.5807313240414	1		247	291	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653817	89653817	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	110	266	0	ENST00000371953.3:c.115G>C	p.Ala39Pro	p.A39P	ENST00000371953	NM_000314.4	39	Gca/Cca	2/9	1	2	FACETS	0.798	0.72	0.878	0.798	0.72	0.878	SUBCLONAL	1	TRUE	1	0.5807313240414	2		266	475	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301808	65301809	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	novel	NA	P-0046009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	80	133	0	ENST00000342505.4:c.3230dup	p.Tyr1077Ter	p.Y1077*	ENST00000342505	NM_002227.2	1077	tac/taAc	23/25	0.548231049237569	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.5807313240414	1		133	173	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639962	3639962	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748607152	NA	P-0046009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	324	736	0	ENST00000294008.3:c.3677G>A	p.Arg1226Gln	p.R1226Q	ENST00000294008	NM_032444.2	1226	cGg/cAg	12/15	0.548231049237569	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.5807313240414	1		736	747	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295725	212295725	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	123	389	0	ENST00000342788.4:c.2588G>T	p.Gly863Val	p.G863V	ENST00000342788	NM_005235.2	863	gGg/gTg	21/28	1	2	FACETS	0.735	0.667	0.807	0.735	0.667	0.807	SUBCLONAL	1	TRUE	1	0.5807313240414	2		389	576	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22143007	22143007	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046009-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	143	324	0	ENST00000215832.6:c.700C>G	p.Leu234Val	p.L234V	ENST00000215832	NM_002745.4	234	Ctt/Gtt	5/9	0.548231049237569	1	FACETS	0.889	0.82	0.96	0.889	0.82	0.96	CLONAL	1	TRUE	0	0.5807313240414	1		324	393	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652842	29652842	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0046010-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	61	204	0	ENST00000356175.3:c.4777A>T	p.Lys1593Ter	p.K1593*	ENST00000356175	NM_000267.3	1593	Aaa/Taa	36/57	0.15072120369388	5	FACETS	0.856	0.752	0.964	0.856	0.752	0.964	INDETERMINATE	3	TRUE	2	0.414326794068358	5		204	186	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	58	425	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.422998020789077	2		425	186	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224307	55224307	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1164954595	NA	P-0046011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	107	422	0	ENST00000275493.2:c.1088C>T	p.Thr363Ile	p.T363I	ENST00000275493	NM_005228.3	363	aCc/aTc	9/28	0.422998020789077	3	FACETS	1	0.929	1	0.52	0.468	0.576	CLONAL	1	TRUE	1	0.422998020789077	3		422	589	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690835	89690835	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs876661177	NA	P-0046011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	44	245	0	ENST00000371953.3:c.242T>G	p.Phe81Cys	p.F81C	ENST00000371953	NM_000314.4	81	tTt/tGt	4/9	0.422998020789077	1	FACETS	0.837	0.711	0.973	0.837	0.711	0.973	CLONAL	1	TRUE	0	0.422998020789077	1		245	196	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221780	55221780	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0046011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	93	628	0	ENST00000275493.2:c.824A>T	p.Tyr275Phe	p.Y275F	ENST00000275493	NM_005228.3	275	tAc/tTc	7/28	0.422998020789077	3	FACETS	0.668	0.594	0.748	0.334	0.297	0.374	SUBCLONAL	1	TRUE	1	0.422998020789077	3		628	797	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0046012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	372	599	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.913215558876424	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.913215558876424	1		599	435	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073406	8073406	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	306	380	0	ENST00000377482.5:c.1253A>G	p.Asn418Ser	p.N418S	ENST00000377482	NM_018948.3	418	aAt/aGt	4/4	1	2	FACETS	0.967	0.918	1	0.967	0.918	1	CLONAL	1	TRUE	1	0.913215558876424	2		380	693	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111959609	111959609	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	370	491	0	ENST00000375549.3:c.188C>A	p.Ser63Tyr	p.S63Y	ENST00000375549	NM_003002.3	63	tCt/tAt	3/4	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.913215558876424	2		491	800	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3634858	3634858	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0046012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	254	521	0	ENST00000294008.3:c.4651A>T	p.Lys1551Ter	p.K1551*	ENST00000294008	NM_032444.2	1551	Aag/Tag	13/15	0.434595839019806	1	FACETS	0.461	0.434	0.488	0.461	0.434	0.488	INDETERMINATE	1	TRUE	0	0.913215558876424	1		521	656	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218779	66218779	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0046012-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	90	163	0	ENST00000273854.3:c.2279C>G	p.Ser760Cys	p.S760C	ENST00000273854	NM_004439.5	760	tCt/tGt	13/18	0.913215558876424	1	FACETS	0.948	0.892	0.998	0.948	0.892	0.998	CLONAL	1	TRUE	0	0.913215558876424	1		163	113	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0046013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	40	425	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.865	0.727	1	0.865	0.727	1	CLONAL	1	TRUE	1	0.497445189659362	2		425	186	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0046013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	369	623	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.497445189659362	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.497445189659362	2		623	689	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0046013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	174	399	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.497445189659362	2		399	633	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112892399	112892399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764663951	NA	P-0046013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	112	344	0	ENST00000351677.2:c.557G>A	p.Arg186Gln	p.R186Q	ENST00000351677	NM_002834.3	186	cGg/cAg	5/16	1	2	FACETS	0.968	0.876	1	0.968	0.876	1	CLONAL	1	TRUE	1	0.497445189659362	2		344	465	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136809	55136809	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0046013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1777	423	284	0	ENST00000257290.5:c.1131C>A	p.Ser377Arg	p.S377R	ENST00000257290	NM_006206.4	377	agC/agA	8/23	0.497445189659362	23	FACETS	0.962	0.913	1	0.219	0.207	0.231	CLONAL	5	TRUE	1	0.497445189659362	23		284	2200	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0046014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	398	763	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.35039671429698	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	3	TRUE	0	0.35039671429698	2		765	677	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0046014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	80	241	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.921	0.822	1	1	0.984	1	CLONAL	2	TRUE	1	0.35039671429698	2		241	248	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939473	76939474	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0046014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	180	550	0	ENST00000373344.5:c.1274_1275del	p.Lys425ArgfsTer8	p.K425Rfs*8	ENST00000373344	NM_000489.3	425	aAA/a	9/35	0.316308890945612	0	FACETS	0.706	0.657	0.755			1	SUBCLONAL	2	TRUE	0	0.35039671429698	0		550	473	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99451971	99451972	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0046014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	82	350	0	ENST00000268035.6:c.1305_1306del	p.Asp435GlufsTer34	p.D435Efs*34	ENST00000268035	NM_000875.3	435	gaCCac/gaac	6/21	0.35039671429698	3	FACETS	1	0.963	1	0.607	0.537	0.681	CLONAL	1	TRUE	1	0.35039671429698	3		350	453	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574953	41574953	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0046014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	96	415	0	ENST00000263253.7:c.7238T>C	p.Ile2413Thr	p.I2413T	ENST00000263253	NM_001429.3	2413	aTa/aCa	31/31	0.310868836624327	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.35039671429698	1		415	350	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711894	89711894	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786204865	NA	P-0046015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	24	344	0	ENST00000371953.3:c.512A>G	p.Gln171Arg	p.Q171R	ENST00000371953	NM_000314.4	171	cAg/cGg	6/9	0.64529646583824	1	FACETS	0.153	0.119	0.191	0.153	0.119	0.191	SUBCLONAL	1	TRUE	0	0.64529646583824	1		344	330	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37622732	37622732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1489649391	NA	P-0046015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	141	654	0	ENST00000249071.6:c.560G>A	p.Arg187His	p.R187H	ENST00000249071	NM_002872.4	187	cGc/cAc	6/7	1	2	FACETS	0.519	0.473	0.568	0.519	0.473	0.568	SUBCLONAL	1	TRUE	1	0.64529646583824	2		654	842	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798840	42798840	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0046015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	298	704	0	ENST00000575354.2:c.4412G>T	p.Arg1471Leu	p.R1471L	ENST00000575354	NM_015125.3	1471	cGg/cTg	19/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.64529646583824	2		704	894	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0046016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	20	354	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.229828665598488	3	FACETS	0.918	0.707	1	0.459	0.353	0.581	CLONAL	1	TRUE	1	0.29	3		354	172	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0046016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	58	707	1	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.148115923678378	1	FACETS	0.91	0.785	1	0.91	0.785	1	INDETERMINATE	1	TRUE	0	0.29	1		708	376	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971122	21971123	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0046016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	26	413	2	ENST00000304494.5:c.235dup	p.Thr79AsnfsTer41	p.T79Nfs*41	ENST00000304494	NM_000077.4	79	acc/aAcc	2/3	0.20387003595075	1	FACETS	0.675	0.537	0.832	0.675	0.537	0.832	SUBCLONAL	1	TRUE	0	0.29	1		415	227	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941988	44941988	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0046016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	12	278	0	ENST00000377967.4:c.3238A>T	p.Lys1080Ter	p.K1080*	ENST00000377967	NM_021140.2	1080	Aaa/Taa	22/29	0.289635653419454	1	FACETS	0.536	0.379	0.727	0.536	0.379	0.727	SUBCLONAL	1	TRUE	0	0.29	1		278	132	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479186	50479186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000508-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	66	159	0	ENST00000394963.4:c.34C>T	p.Pro12Ser	p.P12S	ENST00000394963	NM_003076.4	12	Cca/Tca	1/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.439891692686262	2		159	236	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479186	50479186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000508-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	48	159	0	ENST00000394963.4:c.34C>T	p.Pro12Ser	p.P12S	ENST00000394963	NM_003076.4	12	Cca/Tca	1/13	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.771501070396982	2		159	107	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741636	17741636	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1441843696	NA	P-0000508-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	14	164	0	ENST00000250003.3:c.307C>T	p.Arg103Cys	p.R103C	ENST00000250003	NM_002478.4	103	Cgc/Tgc	1/3	0.771501070396982	1	FACETS	0.282	0.207	0.369	0.282	0.207	0.369	SUBCLONAL	1	TRUE	0	0.771501070396982	1		164	79	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128322038	128322038	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000508-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	79	380	0	ENST00000265960.3:c.722T>C	p.Val241Ala	p.V241A	ENST00000265960	NM_001006617.1	241	gTg/gCg	6/12	0.158070133769592	1	FACETS	0.582	0.521	0.645	0.582	0.521	0.645	INDETERMINATE	1	TRUE	0	0.771501070396982	1		380	216	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500549	99500549	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs531850849	NA	P-0001055-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	329	677	2	ENST00000268035.6:c.3982G>A	p.Gly1328Ser	p.G1328S	ENST00000268035	NM_000875.3	1328	Ggc/Agc	21/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.815025640660049	2		679	765	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424490	49424490	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001055-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	129	654	1	ENST00000301067.7:c.13733C>A	p.Pro4578His	p.P4578H	ENST00000301067	NM_003482.3	4578	cCc/cAc	41/54	1	2	FACETS	0.392	0.355	0.43	0.392	0.355	0.43	SUBCLONAL	1	TRUE	1	0.815025640660049	2		655	808	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198262752	198262752	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001055-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	134	432	0	ENST00000335508.6:c.3223A>G	p.Arg1075Gly	p.R1075G	ENST00000335508	NM_012433.2	1075	Aga/Gga	22/25	1	2	FACETS	0.877	0.806	0.95	0.877	0.806	0.95	CLONAL	1	TRUE	1	0.815025640660049	2		432	375	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409370	31409370	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001055-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	36	402	0	ENST00000344624.3:c.3737T>C	p.Phe1246Ser	p.F1246S	ENST00000344624		1246	tTt/tCt	29/33	0.815025640660049	3	FACETS	0.399	0.328	0.476	0.199	0.164	0.238	SUBCLONAL	1	TRUE	1	0.815025640660049	3		402	312	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115873	8115874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0001862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	500	620	0	ENST00000346208.3:c.1220dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tCcg	6/6	0.711787563810548	3	FACETS	0.945	0.91	0.981	0.945	0.91	0.981	CLONAL	2	TRUE	1	0.705550649644003	3		620	1014	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47004877	47004877	+	5_prime_UTR_variant	5'UTR	SNP	C	C	A	novel	NA	P-0001862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	113	658	0	ENST00000377604.3:c.-133C>A		p.*45*	ENST00000377604	NM_001204468.1	-/852		1/24	0.548130486970714	3	FACETS	0.615	0.553	0.679			1	SUBCLONAL	1	TRUE	NA	0.705550649644003	3		658	705	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115873	8115874	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0001862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	214	620	0	ENST00000346208.3:c.1220dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tCcg	6/6	0.458829518882727	3	FACETS	0.943	0.882	1	0.943	0.882	1	CLONAL	2	TRUE	1	0.458829518882727	3		620	608	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47004877	47004877	+	5_prime_UTR_variant	5'UTR	SNP	C	C	A	novel	NA	P-0001862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	117	658	0	ENST00000377604.3:c.-133C>A		p.*45*	ENST00000377604	NM_001204468.1	-/852		1/24	0.458829518882727	3	FACETS	0.998	0.902	1	0.499	0.451	0.55	CLONAL	1	TRUE	1	0.458829518882727	3		658	628	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5246036	5246036	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	75	436	0	ENST00000357368.4:c.739T>G	p.Phe247Val	p.F247V	ENST00000357368	NM_002850.3	247	Ttc/Gtc	10/38	0.458829518882727	3	FACETS	0.99	0.872	1	0.495	0.436	0.558	CLONAL	1	TRUE	1	0.458829518882727	3		436	406	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026843	71026843	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001862-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	14	324	0	ENST00000318789.4:c.1379A>G	p.Lys460Arg	p.K460R	ENST00000318789	NM_032682.5	460	aAg/aGg	16/21	1	2	FACETS	0.227	0.163	0.304	0.227	0.163	0.304	SUBCLONAL	1	TRUE	1	0.458829518882727	2		324	269	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533656	41533656	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002398-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	165	484	0	ENST00000263253.7:c.1623-1G>A		p.X541_splice	ENST00000263253	NM_001429.3	541			1	2	FACETS	0.862	0.795	0.931	0.862	0.795	0.931	CLONAL	1	TRUE	1	0.61355450137229	2		484	624	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046462	69046462	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761455338	NA	P-0002398-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	228	587	2	ENST00000288368.4:c.3935C>T	p.Ala1312Val	p.A1312V	ENST00000288368	NM_024870.2	1312	gCg/gTg	32/40	1	2	FACETS	0.94	0.878	1	0.94	0.878	1	CLONAL	1	TRUE	1	0.61355450137229	2		589	791	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321175	62321175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1003156687	NA	P-0002398-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	230	693	0	ENST00000360203.5:c.2098C>T	p.Arg700Trp	p.R700W	ENST00000360203	NM_001283009.1	700	Cgg/Tgg	24/35	1	2	FACETS	0.953	0.891	1	0.953	0.891	1	CLONAL	1	TRUE	1	0.61355450137229	2		693	787	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555713	21555730	+	frameshift_variant	Frame_Shift_Del	DEL	TGTCCCCACACCGACAGT	TGTCCCCACACCGACAGT	C	novel	NA	P-0002398-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	46	642	0	ENST00000382592.4:c.2540_2557delinsG	p.Asn847ArgfsTer43	p.N847Rfs*43	ENST00000382592	NM_014572.2	847	aACTGTCGGTGTGGGGACAgg/aGgg	6/8	1	2	FACETS	0.175	0.146	0.206	0.175	0.146	0.206	SUBCLONAL	1	TRUE	1	0.61355450137229	2		642	859	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0003963-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1475	237	401	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.285787684078253	5	FACETS	1	0.99	1			1	CLONAL	1	TRUE	NA	0.285787684078253	5		401	1712	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0004313-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	133	217	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.877301852977902	2		217	293	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0004313-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	199	337	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.877301852977902	2		337	445	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0004313-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	282	548	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.902	0.852	0.952	0.902	0.852	0.952	CLONAL	1	TRUE	1	0.877301852977902	2		548	713	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797278	42797278	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs968289754	NA	P-0004313-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	445	828	0	ENST00000575354.2:c.3640C>T	p.Arg1214Ter	p.R1214*	ENST00000575354	NM_015125.3	1214	Cga/Tga	15/20	0.877301852977902	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.877301852977902	1		828	555	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136105	11136105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004313-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	340	533	0	ENST00000358026.2:c.3089G>A	p.Gly1030Asp	p.G1030D	ENST00000358026	NM_001128849.1	1030	gGc/gAc	22/36	1	2	FACETS	0.992	0.945	1	0.992	0.945	1	CLONAL	1	TRUE	1	0.877301852977902	2		533	781	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729874	41729874	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004313-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	225	399	0	ENST00000242208.4:c.655del	p.His219MetfsTer140	p.H219Mfs*140	ENST00000242208	NM_002192.2	219	Cat/at	3/3	0.836446918314088	3	FACETS	0.898	0.838	0.959	0.449	0.419	0.48	CLONAL	1	TRUE	1	0.877301852977902	3		399	822	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0004328-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	1088	602	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.197040634583433	14	FACETS	1	0.988	1	1	0.996	1	CLONAL	13	TRUE	2	0.197040634583433	14		602	1821	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0004328-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	876	722	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.197040634583433	14	FACETS	0.988	0.962	1	1	0.994	1	CLONAL	13	TRUE	2	0.197040634583433	14		722	1511	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0004328-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1284	357	822	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.197040634583433	14	FACETS	0.964	0.911	1	0.402	0.379	0.424	CLONAL	5	TRUE	2	0.197040634583433	14		822	1641	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0004328-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	264	901	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.17842167081948	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	3	TRUE	0	0.197040634583433	3		901	940	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510775	120510775	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004328-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	126	737	1	ENST00000256646.2:c.1189G>T	p.Gly397Trp	p.G397W	ENST00000256646	NM_024408.3	397	Ggg/Tgg	7/34	0.180423338980721	3	FACETS	0.957	0.868	1	0.957	0.868	1	CLONAL	2	TRUE	1	0.197040634583433	3		738	734	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842620	68842620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004328-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	133	784	0	ENST00000261769.5:c.556G>A	p.Gly186Ser	p.G186S	ENST00000261769	NM_004360.3	186	Ggc/Agc	5/16	0.179318446853644	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.197040634583433	3		784	606	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331685	68331752	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAGATTACAGGTCCACCAGGTTGTGGAAAAACTCAG	TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAGATTACAGGTCCACCAGGTTGTGGAAAAACTCAG	-	novel	NA	P-0004328-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	32	55	0	ENST00000487270.1:c.316-31_352del		p.X106_splice	ENST00000487270	NM_133509.3	106		5/11	0.197040634583433	5	FACETS	1	0.861	1	1	0.961	1	CLONAL	5	TRUE	2	0.197040634583433	5		55	82	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974806	21974807	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004328-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	21	152	0	ENST00000304494.5:c.20dup	p.Ser7ArgfsTer8	p.S7Rfs*8	ENST00000304494	NM_000077.4	7	agc/agGc	1/3	0.197040634583433	2	FACETS	1	0.904	1	0.679	0.527	0.852	CLONAL	1	TRUE	0	0.197040634583433	2		152	157	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981761	101981761	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004339-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	146	511	0	ENST00000282441.5:c.182C>G	p.Ser61Trp	p.S61W	ENST00000282441	NM_001130145.2	61	tCg/tGg	1/9	1	2	FACETS	0.814	0.747	0.883	0.814	0.747	0.883	CLONAL	1	TRUE	1	0.684414028603155	2		511	524	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158610	26158610	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004339-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	86	302	0	ENST00000289316.2:c.213C>G	p.Phe71Leu	p.F71L	ENST00000289316	NM_138720.2	71	ttC/ttG	1/2	1	2	FACETS	0.835	0.747	0.927	0.835	0.747	0.927	CLONAL	1	TRUE	1	0.684414028603155	2		302	301	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165695	118165695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745917069	NA	P-0004339-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	175	283	0	ENST00000369448.3:c.205G>A	p.Val69Ile	p.V69I	ENST00000369448	NM_017709.3	69	Gtc/Atc	2/2	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.684414028603155	2		283	427	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164591	47164591	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0004339-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	76	216	0	ENST00000409792.3:c.1535C>G	p.Ser512Ter	p.S512*	ENST00000409792	NM_014159.6	512	tCa/tGa	3/21	0.684414028603155	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.684414028603155	1		216	144	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165153	47165153	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004339-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	81	184	1	ENST00000409792.3:c.973G>T	p.Glu325Ter	p.E325*	ENST00000409792	NM_014159.6	325	Gaa/Taa	3/21	0.684414028603155	1	FACETS	0.938	0.85	1	0.938	0.85	1	CLONAL	1	TRUE	0	0.684414028603155	1		185	166	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165678	47165678	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004339-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	182	346	0	ENST00000409792.3:c.448C>T	p.His150Tyr	p.H150Y	ENST00000409792	NM_014159.6	150	Cat/Tat	3/21	0.684414028603155	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.684414028603155	1		346	308	SUCCESS
APC	324	MSKCC	GRCh37	5	112176386	112176386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004339-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	89	258	0	ENST00000257430.4:c.5095G>A	p.Glu1699Lys	p.E1699K	ENST00000257430	NM_000038.5	1699	Gag/Aag	16/16	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.684414028603155	2		258	255	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117778	108117778	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004339-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	97	220	0	ENST00000278616.4:c.989G>T	p.Gly330Val	p.G330V	ENST00000278616	NM_000051.3	330	gGa/gTa	8/63	1	2	FACETS	0.945	0.853	1	0.945	0.853	1	CLONAL	1	TRUE	1	0.684414028603155	2		220	300	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437836	110437836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004339-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	135	373	0	ENST00000375856.3:c.565C>T	p.Pro189Ser	p.P189S	ENST00000375856	NM_003749.2	189	Ccc/Tcc	1/2	1	2	FACETS	0.946	0.868	1	0.946	0.868	1	CLONAL	1	TRUE	1	0.684414028603155	2		373	417	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68934917	68934917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004339-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	119	287	0	ENST00000487270.1:c.986C>T	p.Pro329Leu	p.P329L	ENST00000487270	NM_133509.3	329	cCc/cTc	10/11	1	2	FACETS	0.93	0.848	1	0.93	0.848	1	CLONAL	1	TRUE	1	0.684414028603155	2		287	374	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591895	48591895	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs377767346	NA	P-0004339-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	157	348	0	ENST00000342988.3:c.1058A>G	p.Tyr353Cys	p.Y353C	ENST00000342988	NM_005359.5	353	tAc/tGc	9/12	0.684414028603155	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.684414028603155	1		348	275	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749520	41749520	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0004339-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	123	388	0	ENST00000301178.4:c.1446-1G>C		p.X482_splice	ENST00000301178	NM_021913.4	482			1	2	FACETS	0.817	0.744	0.892	0.817	0.744	0.892	CLONAL	1	TRUE	1	0.684414028603155	2		388	440	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120795681	120795681	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004339-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	203	399	0	ENST00000257552.2:c.472G>C	p.Glu158Gln	p.E158Q	ENST00000257552	NM_002442.3	158	Gag/Cag	8/15	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.684414028603155	2		399	581	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158564	26158564	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004339-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	154	472	0	ENST00000289316.2:c.167C>G	p.Ser56Cys	p.S56C	ENST00000289316	NM_138720.2	56	tCt/tGt	1/2	1	2	FACETS	0.827	0.761	0.895	0.827	0.761	0.895	CLONAL	1	TRUE	1	0.684414028603155	2		472	544	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323253	31323253	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs45445194	NA	P-0004339-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	160	419	0	ENST00000412585.2:c.736G>T	p.Glu246Ter	p.E246*	ENST00000412585	NM_005514.6	246	Gag/Tag	4/8	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.684414028603155	2		419	454	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653843	89653843	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004339-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	113	188	0	ENST00000371953.3:c.141G>C	p.Arg47Ser	p.R47S	ENST00000371953	NM_000314.4	47	agG/agC	2/9	0.684414028603155	1	FACETS	0.978	0.902	1	0.978	0.902	1	CLONAL	1	TRUE	0	0.684414028603155	1		188	222	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444166	49444166	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004339-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	251	717	0	ENST00000301067.7:c.3205G>T	p.Glu1069Ter	p.E1069*	ENST00000301067	NM_003482.3	1069	Gag/Tag	11/54	1	2	FACETS	0.993	0.933	1	0.993	0.933	1	CLONAL	1	TRUE	1	0.684414028603155	2		717	739	SUCCESS
APC	324	MSKCC	GRCh37	5	112175859	112175859	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004339-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	59	157	0	ENST00000257430.4:c.4568G>C	p.Arg1523Thr	p.R1523T	ENST00000257430	NM_000038.5	1523	aGa/aCa	16/16	1	2	FACETS	0.829	0.724	0.94	0.829	0.724	0.94	CLONAL	1	TRUE	1	0.684414028603155	2		157	208	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323186	31323186	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004339-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	233	533	0	ENST00000412585.2:c.803G>A	p.Trp268Ter	p.W268*	ENST00000412585	NM_005514.6	268	tGg/tAg	4/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.684414028603155	2		533	624	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243859016	243859016	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs397514606	NA	P-0004411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	61	251	0	ENST00000263826.5:c.49G>A	p.Glu17Lys	p.E17K	ENST00000263826	NM_005465.4	17	Gaa/Aaa	2/13	0.145919090923294	1	FACETS	1	0.913	1	1	0.913	1	INDETERMINATE	1	TRUE	0	0.266382754688879	1		251	371	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252690	133252690	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	86	320	0	ENST00000320574.5:c.1010A>C	p.Glu337Ala	p.E337A	ENST00000320574	NM_006231.2	337	gAa/gCa	10/49	NA	2	FACETS	1	0.913	1			1	INDETERMINATE	1	TRUE	NA	0.266382754688879	2		320	623	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81922799	81922799	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	115	541	0	ENST00000359376.3:c.788A>G	p.Asn263Ser	p.N263S	ENST00000359376	NM_002661.3	263	aAc/aGc	10/33	0.266382754688879	1	FACETS	0.968	0.872	1	0.968	0.872	1	CLONAL	1	TRUE	0	0.266382754688879	1		541	773	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0005037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	182	227	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.878	0.811	0.947	0.878	0.811	0.947	CLONAL	1	TRUE	1	0.500312403481711	2		227	829	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0005037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	298	561	0	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	1	2	FACETS	0.997	0.938	1	0.997	0.938	1	CLONAL	1	TRUE	1	0.500312403481711	2		561	1195	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106094	8106094	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	186	389	0	ENST00000346208.3:c.914G>T	p.Arg305Leu	p.R305L	ENST00000346208		305	cGa/cTa	4/6	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.500312403481711	2		389	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576814	7576883	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAAACTTTCCACTTGATAAGAGGTCCCAAGACTTAGTACCTGAAGGGTGAAATATTCTCCATCCAGTGGT	GAAACTTTCCACTTGATAAGAGGTCCCAAGACTTAGTACCTGAAGGGTGAAATATTCTCCATCCAGTGGT	-	novel	NA	P-0005037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	154	504	0	ENST00000269305.4:c.963_993+39del		p.X321_splice	ENST00000269305	NM_001126112.2	321		9/11	0.475632998950437	1	FACETS	0.766	0.704	0.83	0.766	0.704	0.83	SUBCLONAL	1	TRUE	0	0.500312403481711	1		504	603	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871029	12871034	+	frameshift_variant	Frame_Shift_Del	DEL	GAGTTC	GAGTTC	AAGTG	novel	NA	P-0005037-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	224	456	3	ENST00000228872.4:c.256_261delinsAAGTG	p.Glu86LysfsTer33	p.E86Kfs*33	ENST00000228872	NM_004064.3	86	GAGTTC/AAGTG	1/3	0.47393451689662	1	FACETS	0.883	0.825	0.943	0.883	0.825	0.943	CLONAL	1	TRUE	0	0.500312403481711	1		459	760	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0005114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	50	602	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.144603704616988	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		602	438	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259521	55259521	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	52	438	0	ENST00000275493.2:c.2579A>T	p.Lys860Ile	p.K860I	ENST00000275493	NM_005228.3	860	aAa/aTa	21/28	0.144603704616988	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		438	448	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259542	55259542	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	47	435	0	ENST00000275493.2:c.2600A>C	p.Lys867Thr	p.K867T	ENST00000275493	NM_005228.3	867	aAa/aCa	21/28	0.144603704616988	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		435	465	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0005114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	437	602	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		602	1051	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259521	55259521	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	460	438	0	ENST00000275493.2:c.2579A>T	p.Lys860Ile	p.K860I	ENST00000275493	NM_005228.3	860	aAa/aTa	21/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		438	1091	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259542	55259542	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	485	435	0	ENST00000275493.2:c.2600A>C	p.Lys867Thr	p.K867T	ENST00000275493	NM_005228.3	867	aAa/aCa	21/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		435	1140	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0005114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	213	822	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		822	1148	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248506	59248529	+	inframe_deletion	In_Frame_Del	DEL	CAGGCGCTCCAGCTCGGGCGACGC	CAGGCGCTCCAGCTCGGGCGACGC	-	novel	NA	P-0005114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	413	696	1	ENST00000371222.2:c.214_237del	p.Ala72_Leu79del	p.A72_L79del	ENST00000371222	NM_002228.3	72	GCGTCGCCCGAGCTGGAGCGCCTG/-	1/1	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		697	1177	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058868	42058868	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	91	559	0	ENST00000219905.7:c.8588T>A	p.Phe2863Tyr	p.F2863Y	ENST00000219905	NM_001164273.1	2863	tTt/tAt	24/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		559	564	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362505	40362505	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	149	328	0	ENST00000293328.3:c.1691C>G	p.Pro564Arg	p.P564R	ENST00000293328	NM_012448.3	564	cCa/cGa	14/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		328	1059	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017769	31017769	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	259	764	1	ENST00000375687.4:c.631G>T	p.Ala211Ser	p.A211S	ENST00000375687	NM_015338.5	211	Gcc/Tcc	8/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		765	1326	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259537	55259537	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005114-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	481	439	0	ENST00000275493.2:c.2595A>C	p.Glu865Asp	p.E865D	ENST00000275493	NM_005228.3	865	gaA/gaC	21/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		439	1131	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0005114-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	177	602	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.302527823499499	3	FACETS	0.931	0.861	1	0.931	0.861	1	CLONAL	2	TRUE	1	0.32	3		602	689	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259521	55259521	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005114-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	181	438	0	ENST00000275493.2:c.2579A>T	p.Lys860Ile	p.K860I	ENST00000275493	NM_005228.3	860	aAa/aTa	21/28	0.302527823499499	3	FACETS	0.916	0.848	0.987	0.916	0.848	0.987	CLONAL	2	TRUE	1	0.32	3		438	716	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259542	55259542	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005114-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	172	435	0	ENST00000275493.2:c.2600A>C	p.Lys867Thr	p.K867T	ENST00000275493	NM_005228.3	867	aAa/aCa	21/28	0.302527823499499	3	FACETS	0.897	0.828	0.969	0.897	0.828	0.969	CLONAL	2	TRUE	1	0.32	3		435	695	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248506	59248529	+	inframe_deletion	In_Frame_Del	DEL	CAGGCGCTCCAGCTCGGGCGACGC	CAGGCGCTCCAGCTCGGGCGACGC	-	novel	NA	P-0005114-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	130	696	1	ENST00000371222.2:c.214_237del	p.Ala72_Leu79del	p.A72_L79del	ENST00000371222	NM_002228.3	72	GCGTCGCCCGAGCTGGAGCGCCTG/-	1/1	0.302527823499499	3	FACETS	1	0.98	1	0.643	0.584	0.705	CLONAL	1	TRUE	1	0.32	3		697	733	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362505	40362505	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005114-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	72	328	0	ENST00000293328.3:c.1691C>G	p.Pro564Arg	p.P564R	ENST00000293328	NM_012448.3	564	cCa/cGa	14/19	0.302527823499499	3	FACETS	0.861	0.753	0.978	0.287	0.251	0.326	CLONAL	1	TRUE	0	0.32	3		328	606	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259537	55259537	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005114-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	170	439	0	ENST00000275493.2:c.2595A>C	p.Glu865Asp	p.E865D	ENST00000275493	NM_005228.3	865	gaA/gaC	21/28	0.302527823499499	3	FACETS	0.879	0.811	0.95	0.879	0.811	0.95	CLONAL	2	TRUE	1	0.32	3		439	701	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857538	9857538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778951185	NA	P-0005114-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	40	325	0	ENST00000330684.3:c.3863G>A	p.Arg1288His	p.R1288H	ENST00000330684	NM_001134407.1	1288	cGt/cAt	13/13	0.302527823499499	3	FACETS	0.478	0.396	0.569	0.239	0.198	0.285	SUBCLONAL	1	TRUE	1	0.32	3		325	607	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90949269	90949286	+	inframe_deletion	In_Frame_Del	DEL	GCAAGAGACTCTTCTTTT	GCAAGAGACTCTTCTTTT	-	novel	NA	P-0005114-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	20	109	0	ENST00000265433.3:c.2202_2219del	p.Lys735_Ala740del	p.K735_A740del	ENST00000265433	NM_002485.4	734	gcAAAAGAAGAGTCTCTTGCt/gct	15/16	0.302527823499499	4	FACETS	0.415	0.316	0.53	0.138	0.105	0.177	SUBCLONAL	1	TRUE	1	0.32	4		109	398	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038753	47038753	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005114-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	64	606	1	ENST00000377604.3:c.760G>T	p.Asp254Tyr	p.D254Y	ENST00000377604	NM_001204468.1	254	Gat/Tat	9/24	0.302527823499499	4	FACETS	0.573	0.494	0.658	0.191	0.164	0.22	SUBCLONAL	1	TRUE	1	0.32	4		607	922	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0005636-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	339	641	0	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.614757512662431	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.610022871028301	2		641	531	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117626	70117626	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005636-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1304	234	591	0	ENST00000245479.2:c.94G>T	p.Gly32Cys	p.G32C	ENST00000245479	NM_000346.3	32	Ggc/Tgc	1/3	0.610022871028301	7	FACETS	1	0.987	1	0.315	0.293	0.338	CLONAL	1	TRUE	3	0.610022871028301	7		591	1538	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291040	15291040	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368146879	NA	P-0005636-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	320	791	1	ENST00000263388.2:c.3170C>T	p.Ala1057Val	p.A1057V	ENST00000263388	NM_000435.2	1057	gCg/gTg	20/33	0.614757512662431	3	FACETS	1	0.983	1	0.552	0.521	0.584	CLONAL	1	TRUE	1	0.610022871028301	3		792	1240	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195630	123195630	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005636-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	52	90	0	ENST00000218089.9:c.1544A>T	p.Asp515Val	p.D515V	ENST00000218089	NM_001042749.1	515	gAt/gTt	17/35	1	1	FACETS	0.834	0.76	0.902	1	0.981	1	CLONAL	2	TRUE	0	0.610022871028301	1		90	71	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020901	26020901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1026102996	NA	P-0005636-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	135	348	0	ENST00000357647.3:c.184C>T	p.Leu62Phe	p.L62F	ENST00000357647	NM_003529.2	62	Ctt/Ttt	1/1	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.610022871028301	2		348	434	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609156	46609156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1462311206	NA	P-0005636-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	199	705	0	ENST00000263734.3:c.2215C>T	p.Arg739Trp	p.R739W	ENST00000263734	NM_001430.4	739	Cgg/Tgg	14/16	0.614757512662431	4	FACETS	1	0.952	1	0.345	0.319	0.372	CLONAL	1	TRUE	1	0.610022871028301	4		705	1014	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56477546	56477546	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005636-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	149	430	0	ENST00000267101.3:c.94A>T	p.Thr32Ser	p.T32S	ENST00000267101	NM_001982.3	32	Act/Tct	2/28	0.614757512662431	4	FACETS	1	0.972	1	0.381	0.349	0.415	CLONAL	1	TRUE	1	0.610022871028301	4		430	688	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864720	57864720	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005636-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	231	747	0	ENST00000228682.2:c.2201del	p.Gly734AspfsTer63	p.G734Dfs*63	ENST00000228682	NM_005269.2	733	Ggg/gg	12/12	0.614757512662431	4	FACETS	1	0.981	1	0.381	0.355	0.408	CLONAL	1	TRUE	1	0.610022871028301	4		747	1066	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416659	121416682	+	inframe_deletion	In_Frame_Del	DEL	CTGGGTGAGCCGGGGCCCTACCTC	CTGGGTGAGCCGGGGCCCTACCTC	-	novel	NA	P-0005636-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	204	651	0	ENST00000257555.6:c.92_115del	p.Gly31_Leu38del	p.G31_L38del	ENST00000257555		30	CTGGGTGAGCCGGGGCCCTACCTC/-	1/10	0.598203549028163	4	FACETS	1	0.974	1	0.553	0.513	0.595	CLONAL	1	TRUE	2	0.610022871028301	4		651	974	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623771	28623771	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0005636-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	111	455	0	ENST00000241453.7:c.882+1G>C		p.X294_splice	ENST00000241453	NM_004119.2	294			0.329680071239282	5	FACETS	1	0.964	1	0.384	0.346	0.424	INDETERMINATE	1	TRUE	2	0.610022871028301	5		455	605	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633192	3633192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005636-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1512	306	935	0	ENST00000294008.3:c.5059C>T	p.Pro1687Ser	p.P1687S	ENST00000294008	NM_032444.2	1687	Cct/Tct	14/15	0.425698842352745	6	FACETS	1	0.989	1	0.306	0.287	0.326	CLONAL	1	TRUE	2	0.610022871028301	6		935	1818	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984269	7984269	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005636-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	160	534	0	ENST00000319144.4:c.460C>G	p.Pro154Ala	p.P154A	ENST00000319144	NM_001139.2	154	Ccc/Gcc	4/15	0.614757512662431	2	FACETS	0.76	0.699	0.824	0.38	0.349	0.412	SUBCLONAL	1	TRUE	0	0.610022871028301	2		534	690	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55565865	55565865	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005636-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	132	448	0	ENST00000288135.5:c.689C>A	p.Thr230Lys	p.T230K	ENST00000288135	NM_000222.2	230	aCa/aAa	4/21	0.614757512662431	3	FACETS	1	0.922	1	0.506	0.461	0.553	CLONAL	1	TRUE	1	0.610022871028301	3		448	558	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0005662-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	72	401	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.938	0.825	1	0.938	0.825	1	CLONAL	1	TRUE	1	0.43717355083969	2		401	351	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955090	55955090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373562441	NA	P-0005662-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	112	712	1	ENST00000263923.4:c.3455C>T	p.Thr1152Met	p.T1152M	ENST00000263923	NM_002253.2	1152	aCg/aTg	26/30	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.43717355083969	2		713	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005662-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	130	776	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.43717355083969	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.43717355083969	1		776	454	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729607	41729607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005662-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	136	944	6	ENST00000242208.4:c.922C>T	p.Arg308Cys	p.R308C	ENST00000242208	NM_002192.2	308	Cgt/Tgt	3/3	1	2	FACETS	0.75	0.682	0.821	0.75	0.682	0.821	SUBCLONAL	1	TRUE	1	0.43717355083969	2		950	830	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687129	37687129	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005662-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	136	739	0	ENST00000447079.4:c.4033G>C	p.Glu1345Gln	p.E1345Q	ENST00000447079	NM_015083.1	1345	Gaa/Caa	14/14	1	2	FACETS	0.953	0.869	1	0.953	0.869	1	CLONAL	1	TRUE	1	0.43717355083969	2		739	653	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603128	48603128	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005662-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	54	440	0	ENST00000342988.3:c.1429G>T	p.Gly477Ter	p.G477*	ENST00000342988	NM_005359.5	477	Gga/Tga	11/12	0.43717355083969	1	FACETS	0.72	0.62	0.828	0.72	0.62	0.828	SUBCLONAL	1	TRUE	0	0.43717355083969	1		440	268	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320329	30320330	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005662-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	118	687	0	ENST00000322652.5:c.1275dup	p.Leu426IlefsTer10	p.L426Ifs*10	ENST00000322652	NM_015355.2	424	caa/cAaa	11/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.43717355083969	2		687	433	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0005911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	192	433	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.476624431749399	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.476624431749399	1		433	564	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602871	10602871	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	208	456	0	ENST00000171111.5:c.707A>T	p.Asp236Val	p.D236V	ENST00000171111	NM_203500.1	236	gAc/gTc	3/6	0.476624431749399	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.476624431749399	1		456	599	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17355211	17355211	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs140178341	NA	P-0005911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	86	452	0	ENST00000375499.3:c.307A>G	p.Met103Val	p.M103V	ENST00000375499	NM_003000.2	103	Atg/Gtg	4/8	0.231298431270578	1	FACETS	0.488	0.433	0.548	0.488	0.433	0.548	INDETERMINATE	1	TRUE	0	0.476624431749399	1		452	563	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099397	27099397	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	101	559	0	ENST00000324856.7:c.3634C>T	p.Gln1212Ter	p.Q1212*	ENST00000324856	NM_006015.4	1212	Cag/Tag	14/20	0.476624431749399	1	FACETS	0.497	0.444	0.552	0.497	0.444	0.552	SUBCLONAL	1	TRUE	0	0.476624431749399	1		559	650	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105954	27105954	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	90	322	0	ENST00000324856.7:c.5565C>G	p.Ile1855Met	p.I1855M	ENST00000324856	NM_006015.4	1855	atC/atG	20/20	0.476624431749399	1	FACETS	0.551	0.49	0.616	0.551	0.49	0.616	SUBCLONAL	1	TRUE	0	0.476624431749399	1		322	522	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106983	27106983	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	89	383	0	ENST00000324856.7:c.6594C>A	p.Phe2198Leu	p.F2198L	ENST00000324856	NM_006015.4	2198	ttC/ttA	20/20	0.476624431749399	1	FACETS	0.578	0.514	0.646	0.578	0.514	0.646	SUBCLONAL	1	TRUE	0	0.476624431749399	1		383	492	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439611	51439611	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1276265460	NA	P-0005911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	157	434	0	ENST00000262662.1:c.176G>C	p.Arg59Thr	p.R59T	ENST00000262662		59	aGa/aCa	4/4	0.231298431270578	1	FACETS	0.819	0.753	0.887	0.819	0.753	0.887	INDETERMINATE	1	TRUE	0	0.476624431749399	1		434	613	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128036858	128036858	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	200	612	0	ENST00000285398.2:c.1621T>G	p.Phe541Val	p.F541V	ENST00000285398	NM_000122.1	541	Ttt/Gtt	10/15	0.231298431270578	1	FACETS	0.766	0.711	0.824	0.766	0.711	0.824	INDETERMINATE	1	TRUE	0	0.476624431749399	1		612	834	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900314	101900314	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	115	432	0	ENST00000374994.4:c.748C>T	p.Gln250Ter	p.Q250*	ENST00000374994	NM_004612.2	250	Caa/Taa	4/9	0.476624431749399	1	FACETS	0.819	0.742	0.898	0.819	0.742	0.898	CLONAL	1	TRUE	0	0.476624431749399	1		432	449	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287204	46287204	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	73	285	1	ENST00000334344.6:c.5149C>T	p.Gln1717Ter	p.Q1717*	ENST00000334344	NM_152641.2	1717	Cag/Tag	19/21	0.476624431749399	1	FACETS	0.945	0.837	1	0.945	0.837	1	CLONAL	1	TRUE	0	0.476624431749399	1		286	247	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495450	56495450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	197	513	0	ENST00000267101.3:c.3640C>T	p.Pro1214Ser	p.P1214S	ENST00000267101	NM_001982.3	1214	Cca/Tca	28/28	0.476624431749399	1	FACETS	0.921	0.856	0.987	0.921	0.856	0.987	CLONAL	1	TRUE	0	0.476624431749399	1		513	684	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019515	42019515	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	233	624	0	ENST00000219905.7:c.3568C>T	p.Gln1190Ter	p.Q1190*	ENST00000219905	NM_001164273.1	1190	Cag/Tag	10/24	0.476624431749399	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.476624431749399	1		624	736	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058558	42058558	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	268	959	0	ENST00000219905.7:c.8278G>C	p.Glu2760Gln	p.E2760Q	ENST00000219905	NM_001164273.1	2760	Gag/Cag	24/24	0.476624431749399	1	FACETS	0.922	0.866	0.979	0.922	0.866	0.979	CLONAL	1	TRUE	0	0.476624431749399	1		959	929	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791518	42791518	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	294	521	0	ENST00000575354.2:c.499G>T	p.Gly167Ter	p.G167*	ENST00000575354	NM_015125.3	167	Gga/Tga	4/20	0.411956088313481	2	FACETS	0.851	0.806	0.897	0.851	0.806	0.897	CLONAL	2	TRUE	0	0.476624431749399	2		521	725	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5078346	5078348	+	frameshift_variant	Frame_Shift_Del	DEL	ATA	ATA	CT	novel	NA	P-0005911-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	91	345	0	ENST00000381652.3:c.2033_2035delinsCT	p.Asn678ThrfsTer53	p.N678Tfs*53	ENST00000381652	NM_004972.3	678	aATAtt/aCTtt	16/25	0.476624431749399	1	FACETS	0.863	0.774	0.957	0.863	0.774	0.957	CLONAL	1	TRUE	0	0.476624431749399	1		345	337	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264672	11264672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	106	436	1	ENST00000361445.4:c.3890C>T	p.Ser1297Leu	p.S1297L	ENST00000361445	NM_004958.3	1297	tCg/tTg	26/58	1	2	FACETS	0.701	0.631	0.775	0.701	0.631	0.775	SUBCLONAL	1	TRUE	1	0.590521526169808	2		437	512	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099367	27099367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	125	407	2	ENST00000324856.7:c.3604C>T	p.Arg1202Trp	p.R1202W	ENST00000324856	NM_006015.4	1202	Cgg/Tgg	14/20	1	2	FACETS	0.729	0.662	0.799	0.729	0.662	0.799	SUBCLONAL	1	TRUE	1	0.590521526169808	2		409	581	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795076	45795076	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1380281188	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	134	446	0	ENST00000450313.1:c.1552A>C	p.Ser518Arg	p.S518R	ENST00000450313	NM_012222.2	518	Agt/Cgt	16/16	1	2	FACETS	0.792	0.723	0.864	0.792	0.723	0.864	SUBCLONAL	1	TRUE	1	0.590521526169808	2		446	573	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241899	72241899	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	147	591	0	ENST00000357731.5:c.491G>T	p.Gly164Val	p.G164V	ENST00000357731	NM_173808.2	164	gGg/gTg	3/7	1	2	FACETS	0.726	0.664	0.79	0.726	0.664	0.79	SUBCLONAL	1	TRUE	1	0.590521526169808	2		591	686	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800978	243800978	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	112	488	2	ENST00000263826.5:c.496C>T	p.Arg166Ter	p.R166*	ENST00000263826	NM_005465.4	166	Cga/Tga	5/13	1	2	FACETS	0.734	0.663	0.808	0.734	0.663	0.808	SUBCLONAL	1	TRUE	1	0.590521526169808	2		490	517	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268784	41268784	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	162	429	0	ENST00000349496.5:c.1022G>C	p.Ser341Thr	p.S341T	ENST00000349496	NM_001904.3	341	aGc/aCc	7/15	0.471707971497751	2	FACETS	0.936	0.863	1	0.468	0.431	0.506	CLONAL	1	TRUE	0	0.590521526169808	2		429	586	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541795	187541795	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	140	454	0	ENST00000441802.2:c.5945A>G	p.Asp1982Gly	p.D1982G	ENST00000441802	NM_005245.3	1982	gAt/gGt	10/27	1	2	FACETS	0.784	0.716	0.854	0.784	0.716	0.854	SUBCLONAL	1	TRUE	1	0.590521526169808	2		454	605	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946150	13946150	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	346	396	1	ENST00000405192.2:c.946C>T	p.Gln316Ter	p.Q316*	ENST00000405192	NM_001163147.1	316	Cag/Tag	10/12	0.566684307845191	4	FACETS	0.937	0.896	0.979	0.937	0.896	0.979	CLONAL	3	TRUE	1	0.590521526169808	4		397	663	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737877	145737877	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200629599	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	53	328	1	ENST00000428558.2:c.2953G>A	p.Val985Met	p.V985M	ENST00000428558	NM_004260.3	985	Gtg/Atg	18/22	0.590521526169808	3	FACETS	0.358	0.305	0.417	0.179	0.152	0.209	SUBCLONAL	1	TRUE	1	0.590521526169808	3		329	649	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739338	145739338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780282337	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	159	439	2	ENST00000428558.2:c.2032G>A	p.Val678Met	p.V678M	ENST00000428558	NM_004260.3	678	Gtg/Atg	12/22	0.590521526169808	3	FACETS	0.822	0.753	0.893	0.411	0.376	0.447	CLONAL	1	TRUE	1	0.590521526169808	3		441	849	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739628	145739628	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1054865813	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	132	408	1	ENST00000428558.2:c.1823A>C	p.His608Pro	p.H608P	ENST00000428558	NM_004260.3	608	cAc/cCc	11/22	0.590521526169808	3	FACETS	0.625	0.567	0.687	0.313	0.283	0.344	SUBCLONAL	1	TRUE	1	0.590521526169808	3		409	926	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741542	145741542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748212145	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	165	476	0	ENST00000428558.2:c.961G>A	p.Gly321Arg	p.G321R	ENST00000428558	NM_004260.3	321	Gga/Aga	5/22	0.590521526169808	3	FACETS	0.783	0.718	0.849	0.391	0.359	0.425	SUBCLONAL	1	TRUE	1	0.590521526169808	3		476	925	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244416	98244416	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	114	379	0	ENST00000331920.6:c.654G>T	p.Gln218His	p.Q218H	ENST00000331920	NM_000264.3	218	caG/caT	4/24	1	2	FACETS	0.751	0.679	0.826	0.751	0.679	0.826	SUBCLONAL	1	TRUE	1	0.590521526169808	2		379	514	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343832	118343832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	114	402	0	ENST00000534358.1:c.1958C>T	p.Pro653Leu	p.P653L	ENST00000534358	NM_005933.3	653	cCc/cTc	3/36	1	2	FACETS	0.741	0.67	0.815	0.741	0.67	0.815	SUBCLONAL	1	TRUE	1	0.590521526169808	2		402	521	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856128	111856128	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1425524544	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	121	273	0	ENST00000341259.2:c.179C>T	p.Ala60Val	p.A60V	ENST00000341259	NM_005475.2	60	gCc/gTc	2/8	1	2	FACETS	0.852	0.774	0.933	0.852	0.774	0.933	CLONAL	1	TRUE	1	0.590521526169808	2		273	481	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257863	133257863	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	142	338	0	ENST00000320574.5:c.65A>G	p.Asp22Gly	p.D22G	ENST00000320574	NM_006231.2	22	gAt/gGt	2/49	1	2	FACETS	0.911	0.835	0.99	0.911	0.835	0.99	CLONAL	1	TRUE	1	0.590521526169808	2		338	528	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975441	26975441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	108	325	0	ENST00000381527.3:c.1067G>A	p.Arg356Gln	p.R356Q	ENST00000381527	NM_001260.1	356	cGa/cAa	11/13	1	2	FACETS	0.705	0.635	0.778	0.705	0.635	0.778	SUBCLONAL	1	TRUE	1	0.590521526169808	2		325	519	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988590	41988590	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	190	551	0	ENST00000219905.7:c.1382T>C	p.Leu461Ser	p.L461S	ENST00000219905	NM_001164273.1	461	tTa/tCa	3/24	1	2	FACETS	0.87	0.806	0.935	0.87	0.806	0.935	CLONAL	1	TRUE	1	0.590521526169808	2		551	740	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726655	88726655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772754430	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	97	354	0	ENST00000360948.2:c.389G>A	p.Arg130His	p.R130H	ENST00000360948	NM_001012338.2	130	cGt/cAt	4/19	1	2	FACETS	0.777	0.697	0.861	0.777	0.697	0.861	SUBCLONAL	1	TRUE	1	0.590521526169808	2		354	423	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293173	91293173	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	88	398	0	ENST00000355112.3:c.675G>T	p.Lys225Asn	p.K225N	ENST00000355112	NM_000057.2	225	aaG/aaT	3/22	1	2	FACETS	0.668	0.595	0.746	0.668	0.595	0.746	SUBCLONAL	1	TRUE	1	0.590521526169808	2		398	446	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81954827	81954827	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	132	494	0	ENST00000359376.3:c.2260G>A	p.Asp754Asn	p.D754N	ENST00000359376	NM_002661.3	754	Gac/Aac	21/33	1	2	FACETS	0.795	0.725	0.869	0.795	0.725	0.869	SUBCLONAL	1	TRUE	1	0.590521526169808	2		494	562	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578500	7578500	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs757274881	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	178	487	1	ENST00000269305.4:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000269305	NM_001126112.2	144	Cag/Tag	5/11	1	2	FACETS	0.88	0.814	0.948	0.88	0.814	0.948	CLONAL	1	TRUE	1	0.590521526169808	2		488	685	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864757	37864757	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	106	325	0	ENST00000269571.5:c.409C>A	p.Leu137Met	p.L137M	ENST00000269571		137	Ctg/Atg	3/27	1	2	FACETS	0.743	0.67	0.821	0.743	0.67	0.821	SUBCLONAL	1	TRUE	1	0.590521526169808	2		325	483	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489486	40489486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	211	509	1	ENST00000264657.5:c.764C>T	p.Pro255Leu	p.P255L	ENST00000264657	NM_139276.2	255	cCg/cTg	8/24	1	2	FACETS	0.94	0.876	1	0.94	0.876	1	CLONAL	1	TRUE	1	0.590521526169808	2		510	760	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284969	15284969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	130	350	0	ENST00000263388.2:c.4646C>T	p.Ala1549Val	p.A1549V	ENST00000263388	NM_000435.2	1549	gCg/gTg	25/33	1	2	FACETS	0.881	0.803	0.961	0.881	0.803	0.961	CLONAL	1	TRUE	1	0.590521526169808	2		350	500	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478800	57478800	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	135	393	0	ENST00000371085.3:c.386A>G	p.Asp129Gly	p.D129G	ENST00000371085	NM_000516.4	129	gAc/gGc	5/13	1	2	FACETS	0.797	0.727	0.869	0.797	0.727	0.869	SUBCLONAL	1	TRUE	1	0.590521526169808	2		393	574	SUCCESS
AR	367	MSKCC	GRCh37	X	66905965	66905965	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	84	225	0	ENST00000374690.3:c.1882G>T	p.Gly628Ter	p.G628*	ENST00000374690	NM_000044.3	628	Gga/Tga	3/8	1	1	FACETS	0.911	0.82	1	0.911	0.82	1	CLONAL	1	TRUE	0	0.590521526169808	1		225	220	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354958	70354958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759857680	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	177	253	1	ENST00000374080.3:c.4880G>A	p.Arg1627His	p.R1627H	ENST00000374080		1627	cGc/cAc	36/45	1	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.590521526169808	1		254	375	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357745	70357745	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	109	281	0	ENST00000374080.3:c.5996T>C	p.Val1999Ala	p.V1999A	ENST00000374080		1999	gTg/gCg	41/45	1	1	FACETS	0.703	0.637	0.771	0.703	0.637	0.771	SUBCLONAL	1	TRUE	0	0.590521526169808	1		281	370	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298028	15298029	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	169	467	0	ENST00000263388.2:c.1727dup	p.Thr577HisfsTer46	p.T577Hfs*46	ENST00000263388	NM_000435.2	576	ggc/ggGc	11/33	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.590521526169808	2		467	553	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482926	140482927	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs777474487	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	36	444	1	ENST00000288602.6:c.1208dup	p.Ala404CysfsTer9	p.A404Cfs*9	ENST00000288602	NM_004333.4	403	cct/ccCt	10/18	0.295589038648468	3	FACETS	0.289	0.237	0.348	0.145	0.118	0.174	INDETERMINATE	1	TRUE	1	0.590521526169808	3		445	546	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	287	438	1	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.751	0.712	0.791	1	0.994	1	SUBCLONAL	2	TRUE	1	0.590521526169808	2		439	647	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885939	111885939	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	141	481	0	ENST00000341259.2:c.1566del	p.Glu523SerfsTer25	p.E523Sfs*25	ENST00000341259	NM_005475.2	521	Ccc/cc	8/8	1	2	FACETS	0.696	0.635	0.759	0.696	0.635	0.759	SUBCLONAL	1	TRUE	1	0.590521526169808	2		481	686	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	141	474	6	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	0.859	0.786	0.934	0.859	0.786	0.934	CLONAL	1	TRUE	1	0.590521526169808	2		480	556	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606273	93606273	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	144	987	1	ENST00000375746.1:c.98del	p.Gly33AlafsTer2	p.G33Afs*2	ENST00000375746	NM_001174167.1	31	caG/ca	2/14	1	2	FACETS	0.807	0.739	0.878	0.807	0.739	0.878	CLONAL	1	TRUE	1	0.590521526169808	2		988	604	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022999	27022999	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1436957504	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	14	32	0	ENST00000324856.7:c.110del	p.Gly37AlafsTer14	p.G37Afs*14	ENST00000324856	NM_006015.4	35	gcG/gc	1/20	1	2	FACETS	0.948	0.71	1	0.948	0.71	1	CLONAL	1	TRUE	1	0.590521526169808	2		32	50	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074255	8074255	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	176	679	1	ENST00000377482.5:c.404del	p.Asn135ThrfsTer40	p.N135Tfs*40	ENST00000377482	NM_018948.3	135	aAc/ac	4/4	1	2	FACETS	0.744	0.686	0.804	0.744	0.686	0.804	SUBCLONAL	1	TRUE	1	0.590521526169808	2		680	801	SUCCESS
APC	324	MSKCC	GRCh37	5	112175101	112175101	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs587783033	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	89	294	0	ENST00000257430.4:c.3814del	p.Ser1272GlnfsTer16	p.S1272Qfs*16	ENST00000257430	NM_000038.5	1270	tgT/tg	16/16	1	2	FACETS	0.884	0.791	0.981	0.884	0.791	0.981	CLONAL	1	TRUE	1	0.590521526169808	2		294	341	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244311	41244311	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	93	448	0	ENST00000357654.3:c.3237del	p.Lys1079AsnfsTer2	p.K1079Nfs*2	ENST00000357654	NM_007294.3	1079	aaA/aa	10/23	1	2	FACETS	0.754	0.674	0.837	0.754	0.674	0.837	SUBCLONAL	1	TRUE	1	0.590521526169808	2		448	418	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639588	47639588	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63749897	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	149	428	0	ENST00000233146.2:c.687del	p.Ala230LeufsTer16	p.A230Lfs*16	ENST00000233146	NM_000251.2	227	agA/ag	4/16	1	2	FACETS	0.821	0.752	0.891	0.821	0.752	0.891	CLONAL	1	TRUE	1	0.590521526169808	2		428	615	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	106	389	0	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	1	2	FACETS	0.745	0.671	0.822	0.745	0.671	0.822	SUBCLONAL	1	TRUE	1	0.590521526169808	2		389	482	SUCCESS
APC	324	MSKCC	GRCh37	5	112102932	112102932	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554069710	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	112	449	0	ENST00000257430.4:c.271del	p.Met91CysfsTer34	p.M91Cfs*34	ENST00000257430	NM_000038.5	89	tcA/tc	4/16	1	2	FACETS	0.691	0.624	0.762	0.691	0.624	0.762	SUBCLONAL	1	TRUE	1	0.590521526169808	2		449	549	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023860	27023861	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0006365-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	44	91	0	ENST00000324856.7:c.971dup	p.Ala325ArgfsTer75	p.A325Rfs*75	ENST00000324856	NM_006015.4	322	-/G	1/20	1	2	FACETS	0.892	0.761	1	0.892	0.761	1	CLONAL	1	TRUE	1	0.590521526169808	2		91	167	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs876659675	NA	P-0008441-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	140	783	0	ENST00000269305.4:c.764T>G	p.Ile255Ser	p.I255S	ENST00000269305	NM_001126112.2	255	aTc/aGc	7/11	0.266042270590524	1	FACETS	0.987	0.899	1	0.987	0.899	1	CLONAL	1	TRUE	0	0.270966227451981	1		783	905	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950304	15950305	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0008441-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	131	703	0	ENST00000268712.3:c.6639dup	p.Arg2214SerfsTer2	p.R2214Sfs*2	ENST00000268712	NM_006311.3	2213	-/T	42/46	0.266042270590524	1	FACETS	0.918	0.832	1	0.918	0.832	1	CLONAL	1	TRUE	0	0.270966227451981	1		703	911	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100116	157100117	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGC	rs797045268	NA	P-0008769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	32	61	2	ENST00000346085.5:c.1069_1071dup	p.Gly357dup	p.G357dup	ENST00000346085	NM_020732.3	357	-/GGC	1/20	0.117010061126249	3	FACETS	1	0.932	1	0.416	0.347	0.488	INDETERMINATE	1	TRUE	0	0.761914145417959	3		63	93	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954283	32954283	+	splice_donor_variant	Splice_Site	SNP	G	G	C	rs81002883	NA	P-0008769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	173	390	0	ENST00000380152.3:c.9256+1G>C		p.X3086_splice	ENST00000380152		3086			0.761914145417959	1	FACETS	0.99	0.933	1	0.99	0.933	1	CLONAL	1	TRUE	0	0.761914145417959	1		390	284	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312710	91312725	+	frameshift_variant	Frame_Shift_Del	DEL	CTTCGCCAGAAGTTTC	CTTCGCCAGAAGTTTC	-	novel	NA	P-0008769-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	186	423	0	ENST00000355112.3:c.2453_2468del	p.Arg818LeufsTer4	p.R818Lfs*4	ENST00000355112	NM_000057.2	817	CTTCGCCAGAAGTTTCct/ct	12/22	0.314459775828403	1	FACETS	0.488	0.453	0.525	0.488	0.453	0.525	INDETERMINATE	1	TRUE	0	0.761914145417959	1		423	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0009691-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	381	313	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.587023462760337	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.587023462760337	2		313	619	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073323	8073323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009691-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	233	154	0	ENST00000377482.5:c.1336G>T	p.Asp446Tyr	p.D446Y	ENST00000377482	NM_018948.3	446	Gat/Tat	4/4	0.587023462760337	4	FACETS	0.912	0.854	0.97			1	CLONAL	2	TRUE	NA	0.587023462760337	4		154	691	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796865	45796865	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782263	NA	P-0009691-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	166	254	0	ENST00000450313.1:c.1465G>T	p.Ala489Ser	p.A489S	ENST00000450313	NM_012222.2	489	Gcc/Tcc	14/16	0.560417759922362	5	FACETS	0.985	0.903	1			1	CLONAL	1	TRUE	NA	0.587023462760337	5		254	1080	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798613	45798613	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009691-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	151	345	0	ENST00000450313.1:c.481G>T	p.Asp161Tyr	p.D161Y	ENST00000450313	NM_012222.2	161	Gac/Tac	6/16	0.560417759922362	5	FACETS	0.869	0.793	0.949			1	CLONAL	1	TRUE	NA	0.587023462760337	5		345	1113	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166215	118166215	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009691-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	113	187	0	ENST00000369448.3:c.725G>T	p.Gly242Val	p.G242V	ENST00000369448	NM_017709.3	242	gGg/gTg	2/2	0.330888926843031	5	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.587023462760337	5		187	606	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115829	8115829	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009691-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	158	244	0	ENST00000346208.3:c.1175A>T	p.Asn392Ile	p.N392I	ENST00000346208		392	aAc/aTc	6/6	0.582052088271686	3	FACETS	0.893	0.819	0.969	0.446	0.409	0.485	CLONAL	1	TRUE	1	0.587023462760337	3		244	780	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451003	70451003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009691-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	150	253	0	ENST00000373644.4:c.5843C>T	p.Ser1948Phe	p.S1948F	ENST00000373644	NM_030625.2	1948	tCt/tTt	12/12	0.582052088271686	3	FACETS	1	0.977	1	0.585	0.537	0.635	CLONAL	1	TRUE	1	0.587023462760337	3		253	565	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416218	416218	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs368037236	NA	P-0009691-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	168	213	0	ENST00000399788.2:c.3968G>T	p.Arg1323Leu	p.R1323L	ENST00000399788	NM_001042603.1	1323	cGg/cTg	24/28	0.587023462760337	5	FACETS	0.812	0.749	0.877			1	CLONAL	2	TRUE	NA	0.587023462760337	5		213	663	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117759	115117759	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009691-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	173	159	0	ENST00000257566.3:c.676G>T	p.Asp226Tyr	p.D226Y	ENST00000257566	NM_016569.3	226	Gat/Tat	3/8	0.587023462760337	3	FACETS	0.932	0.869	0.996	0.932	0.869	0.996	CLONAL	2	TRUE	1	0.587023462760337	3		159	409	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36989288	36989288	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009691-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	162	360	1	ENST00000354822.5:c.47C>A	p.Ala16Glu	p.A16E	ENST00000354822	NM_001079668.2	16	gCg/gAg	1/3	0.587023462760337	3	FACETS	0.9	0.827	0.977	0.45	0.413	0.489	CLONAL	1	TRUE	1	0.587023462760337	3		361	793	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023013	33023013	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009691-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	138	259	0	ENST00000300177.4:c.122A>C	p.His41Pro	p.H41P	ENST00000300177	NM_001191322.1	41	cAc/cCc	2/2	0.467504619567423	0	FACETS	0.569	0.525	0.614			1	SUBCLONAL	1	TRUE	0	0.587023462760337	0		259	341	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807967	3807967	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009691-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	138	197	0	ENST00000262367.5:c.3452G>A	p.Trp1151Ter	p.W1151*	ENST00000262367	NM_004380.2	1151	tGg/tAg	18/31	0.587023462760337	2	FACETS	0.95	0.87	1	0.475	0.435	0.517	CLONAL	1	TRUE	0	0.587023462760337	2		197	495	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273974	10273974	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009691-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	399	398	0	ENST00000330684.3:c.295G>C	p.Val99Leu	p.V99L	ENST00000330684	NM_001134407.1	99	Gtg/Ctg	2/13	0.587023462760337	2	FACETS	0.912	0.875	0.949	0.912	0.875	0.949	CLONAL	2	TRUE	0	0.587023462760337	2		398	745	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645032	67645032	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009691-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	149	254	0	ENST00000264010.4:c.297G>T	p.Gln99His	p.Q99H	ENST00000264010	NM_006565.3	99	caG/caT	3/12	1	2	FACETS	0.949	0.872	1	0.949	0.872	1	CLONAL	1	TRUE	1	0.587023462760337	2		254	535	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923738	72923738	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009691-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	163	281	0	ENST00000268489.5:c.3340C>G	p.Arg1114Gly	p.R1114G	ENST00000268489	NM_006885.3	1114	Cga/Gga	4/10	1	2	FACETS	0.891	0.822	0.964	0.891	0.822	0.964	CLONAL	1	TRUE	1	0.587023462760337	2		281	623	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533662	63533662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009691-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	155	299	0	ENST00000307078.5:c.1492C>A	p.Pro498Thr	p.P498T	ENST00000307078	NM_004655.3	498	Ccc/Acc	6/11	0.587023462760337	4	FACETS	0.913	0.836	0.994			1	CLONAL	1	TRUE	NA	0.587023462760337	4		299	918	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220488	1220488	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913316	NA	P-0009691-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	502	425	0	ENST00000326873.7:c.581A>T	p.Asp194Val	p.D194V	ENST00000326873	NM_000455.4	194	gAc/gTc	4/10	0.551485092665882	3	FACETS	0.933	0.903	0.963	0.933	0.903	0.963	CLONAL	3	TRUE	0	0.587023462760337	3		425	790	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47607070	47607084	+	inframe_deletion	In_Frame_Del	DEL	GTTGTGGTGATAGCA	GTTGTGGTGATAGCA	-	novel	NA	P-0009691-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	101	223	0	ENST00000263735.4:c.825_839del	p.Val276_Val280del	p.V276_V280del	ENST00000263735	NM_002354.2	274	GTTGTGGTGATAGCA/-	7/9	0.587023462760337	3	FACETS	0.843	0.756	0.935	0.422	0.378	0.468	CLONAL	1	TRUE	1	0.587023462760337	3		223	528	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523275	9523275	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009691-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	141	228	1	ENST00000353224.5:c.1962G>T	p.Arg654Ser	p.R654S	ENST00000353224	NM_177990.2	654	agG/agT	9/10	1	2	FACETS	0.912	0.835	0.991	0.912	0.835	0.991	CLONAL	1	TRUE	1	0.587023462760337	2		229	527	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714387	40714387	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009691-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	113	246	0	ENST00000373198.4:c.4010G>T	p.Arg1337Leu	p.R1337L	ENST00000373198	NM_133170.3	1337	cGc/cTc	29/32	0.438287223233287	4	FACETS	0.947	0.854	1			1	CLONAL	1	TRUE	NA	0.587023462760337	4		246	645	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186504363	186504363	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009691-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	45	150	0	ENST00000323963.5:c.700C>T	p.Arg234Ter	p.R234*	ENST00000323963		234	Cga/Tga	7/11	0.508984470461727	4	FACETS	0.61	0.513	0.716	0.305	0.256	0.358	SUBCLONAL	1	TRUE	2	0.587023462760337	4		150	399	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153657	55153657	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009691-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	259	243	0	ENST00000257290.5:c.2623C>A	p.Leu875Met	p.L875M	ENST00000257290	NM_006206.4	875	Ctg/Atg	19/23	0.587023462760337	8	FACETS	1	0.965	1			1	CLONAL	2	TRUE	NA	0.587023462760337	8		243	1165	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593669	55593669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009691-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	549	182	0	ENST00000288135.5:c.1735G>T	p.Asp579Tyr	p.D579Y	ENST00000288135	NM_000222.2	579	Gat/Tat	11/21	0.587023462760337	8	FACETS	0.918	0.887	0.948			1	CLONAL	6	TRUE	NA	0.587023462760337	8		182	938	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946329	55946329	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009691-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	71	115	0	ENST00000263923.4:c.3850G>C	p.Gly1284Arg	p.G1284R	ENST00000263923	NM_002253.2	1284	Gga/Cga	30/30	NA	2	FACETS	0.934	0.825	1			1	INDETERMINATE	1	TRUE	NA	0.587023462760337	2		115	259	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242776	66242776	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009691-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	163	137	0	ENST00000273854.3:c.1796G>T	p.Cys599Phe	p.C599F	ENST00000273854	NM_004439.5	599	tGc/tTc	9/18	0.587023462760337	4	FACETS	0.901	0.834	0.97			1	CLONAL	2	TRUE	NA	0.587023462760337	4		137	489	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935714	13935716	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TGA	TGA	-	novel	NA	P-0009691-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	59	155	0	ENST00000405192.2:c.1144-4_1144-2del		p.X382_splice	ENST00000405192	NM_001163147.1	382			0.587023462760337	4	FACETS	0.562	0.483	0.647	0.281	0.241	0.324	SUBCLONAL	1	TRUE	2	0.587023462760337	4		155	568	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729968	41729968	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009691-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	347	290	0	ENST00000242208.4:c.561C>A	p.Asp187Glu	p.D187E	ENST00000242208	NM_002192.2	187	gaC/gaA	3/3	0.146084081272464	6	FACETS	1	0.982	1			1	INDETERMINATE	3	TRUE	NA	0.587023462760337	6		290	807	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459467	50459467	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009691-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	156	127	0	ENST00000331340.3:c.756C>G	p.Asp252Glu	p.D252E	ENST00000331340	NM_006060.4	252	gaC/gaG	7/8	0.146084081272464	6	FACETS	1	0.937	1			1	INDETERMINATE	3	TRUE	NA	0.587023462760337	6		127	381	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492867	8492867	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009691-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	298	166	0	ENST00000356435.5:c.2462G>T	p.Gly821Val	p.G821V	ENST00000356435		821	gGg/gTg	16/35	0.550914719944508	5	FACETS	0.877	0.83	0.923	0.877	0.83	0.923	CLONAL	3	TRUE	2	0.587023462760337	5		166	726	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518363	8518363	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009691-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	208	127	0	ENST00000356435.5:c.1028G>T	p.Trp343Leu	p.W343L	ENST00000356435		343	tGg/tTg	10/35	0.550914719944508	5	FACETS	0.901	0.845	0.958	0.901	0.845	0.958	CLONAL	3	TRUE	2	0.587023462760337	5		127	493	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411016	63411016	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009691-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	144	288	0	ENST00000330258.3:c.2151C>A	p.Cys717Ter	p.C717*	ENST00000330258	NM_152424.3	717	tgC/tgA	2/2	0.582052088271686	3	FACETS	0.978	0.894	1	0.489	0.447	0.533	CLONAL	1	TRUE	1	0.587023462760337	3		288	649	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0010011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	657	727	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.477755012155371	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.477755012155371	2		728	1318	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434993	110434993	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	209	347	0	ENST00000375856.3:c.3408C>G	p.Ile1136Met	p.I1136M	ENST00000375856	NM_003749.2	1136	atC/atG	1/2	0.255717511687734	5	FACETS	0.77	0.715	0.827			1	INDETERMINATE	2	TRUE	NA	0.477755012155371	5		347	975	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478103	99478103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	269	483	1	ENST00000268035.6:c.3007C>T	p.Arg1003Trp	p.R1003W	ENST00000268035	NM_000875.3	1003	Cgg/Tgg	16/21	1	2	FACETS	0.93	0.871	0.99	0.93	0.871	0.99	CLONAL	1	TRUE	1	0.477755012155371	2		484	1211	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456636	40456636	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	397	619	0	ENST00000345506.4:c.1346G>C	p.Ser449Thr	p.S449T	ENST00000345506	NM_003152.3	449	aGt/aCt	12/20	0.477755012155371	2	FACETS	1	0.979	1	0.529	0.501	0.556	CLONAL	1	TRUE	0	0.477755012155371	2		619	1572	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805929	46805929	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	459	503	0	ENST00000290295.7:c.27G>C	p.Leu9Phe	p.L9F	ENST00000290295	NM_006361.5	9	ttG/ttC	1/2	0.477755012155371	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.477755012155371	2		503	890	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290926	15290926	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	82	588	0	ENST00000263388.2:c.3284A>T	p.His1095Leu	p.H1095L	ENST00000263388	NM_000435.2	1095	cAt/cTt	20/33	NA	2	FACETS	0.331	0.291	0.374			1	INDETERMINATE	1	TRUE	NA	0.477755012155371	2		588	1037	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279765	46279765	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	422	400	0	ENST00000371998.3:c.3691A>G	p.Arg1231Gly	p.R1231G	ENST00000371998		1231	Aga/Gga	20/23	0.255717511687734	5	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.477755012155371	5		400	1367	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157150359	157150359	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0010579-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	55	480	0	ENST00000346085.5:c.1543-2A>T		p.X515_splice	ENST00000346085	NM_020732.3	515			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		480	992	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0011306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	361	608	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.408433031833773	2	FACETS	0.863	0.825	0.9	1	0.995	1	CLONAL	3	TRUE	0	0.408433031833773	2		611	683	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0011306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	57	120	2	ENST00000257430.4:c.3919dup	p.Ile1307AsnfsTer8	p.I1307Nfs*8	ENST00000257430	NM_000038.5	1306	gaa/gAaa	16/16	0.408433031833773	3	FACETS	0.899	0.774	1	0.449	0.387	0.517	CLONAL	1	TRUE	1	0.408433031833773	3		122	374	SUCCESS
APC	324	MSKCC	GRCh37	5	112170652	112170652	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	180	255	0	ENST00000257430.4:c.1748C>A	p.Ser583Ter	p.S583*	ENST00000257430	NM_000038.5	583	tCa/tAa	15/16	0.408433031833773	3	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	1	0.408433031833773	3		255	497	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193110988	193110988	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	41	115	0	ENST00000367435.3:c.521C>G	p.Ser174Cys	p.S174C	ENST00000367435	NM_024529.4	174	tCt/tGt	7/17	0.408433031833773	3	FACETS	0.703	0.587	0.831	0.351	0.293	0.416	SUBCLONAL	1	TRUE	1	0.408433031833773	3		115	344	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977594	2977594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	222	1019	0	ENST00000396946.4:c.1090C>T	p.Arg364Cys	p.R364C	ENST00000396946	NM_032415.4	364	Cgc/Tgc	8/25	0.324498106472268	5	FACETS	1	0.989	1	0.444	0.412	0.478	CLONAL	1	TRUE	2	0.408433031833773	5		1019	1315	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215591	5215591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760885887	NA	P-0011306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	262	330	0	ENST00000357368.4:c.4112C>T	p.Pro1371Leu	p.P1371L	ENST00000357368	NM_002850.3	1371	cCg/cTg	27/38	0.404387580280259	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.408433031833773	4		330	798	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0013015-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	539	857	1	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	2	TRUE	NA	0.708663934794599	2		858	732	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958804	55958804	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013015-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	215	617	0	ENST00000263923.4:c.3049G>C	p.Glu1017Gln	p.E1017Q	ENST00000263923	NM_002253.2	1017	Gag/Cag	22/30	0.680266482848814	3	FACETS	1	0.936	1	0.502	0.468	0.538	CLONAL	1	TRUE	1	0.708663934794599	3		617	818	SUCCESS
APC	324	MSKCC	GRCh37	5	112090645	112090645	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013015-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	189	455	0	ENST00000257430.4:c.58A>T	p.Asn20Tyr	p.N20Y	ENST00000257430	NM_000038.5	20	Aac/Tac	2/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.708663934794599	2		455	515	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484337	50484338	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0013015-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	219	548	0	ENST00000394963.4:c.1097_1098insAA	p.Met366IlefsTer36	p.M366Ifs*36	ENST00000394963	NM_003076.4	366	atg/atAAg	9/13	0.708663934794599	3	FACETS	1	0.959	1	0.52	0.485	0.556	CLONAL	1	TRUE	1	0.708663934794599	3		548	805	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952139	178952148	+	frameshift_variant	Frame_Shift_Del	DEL	ATGCATTGAA	ATGCATTGAA	TG	novel	NA	P-0013015-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	431	334	1	ENST00000263967.3:c.3194_3203delinsTG	p.His1065LeufsTer5	p.H1065Lfs*5	ENST00000263967	NM_006218.2	1065	cATGCATTGAAc/cTGc	21/21	0.708663934794599	5	FACETS	1	0.994	1	0.887	0.861	0.911	CLONAL	4	TRUE	0	0.708663934794599	5		335	566	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0013855-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	103	452	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.175694765655117	2		452	819	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0013855-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	165	822	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.612158476556137	4	FACETS	1	0.94	1	0.514	0.472	0.557	CLONAL	1	TRUE	2	0.623508654550206	4		822	836	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0013855-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	244	452	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.612158476556137	4	FACETS	0.797	0.747	0.848	0.797	0.747	0.848	SUBCLONAL	2	TRUE	2	0.623508654550206	4		452	797	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609954	81609954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013855-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	95	381	0	ENST00000298171.2:c.1552G>A	p.Glu518Lys	p.E518K	ENST00000298171	NM_000369.2	518	Gag/Aag	10/10	0.621431643517371	3	FACETS	1	0.94	1	0.356	0.319	0.395	CLONAL	1	TRUE	0	0.623508654550206	3		381	374	SUCCESS
EED	8726	MSKCC	GRCh37	11	85961442	85961447	+	stop_gained,inframe_deletion	Nonsense_Mutation	DEL	GAAGTC	GAAGTC	-	novel	NA	P-0013855-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	69	394	0	ENST00000263360.6:c.219_224del	p.Trp73_Ser75delinsTer	p.W73_S75delins*	ENST00000263360	NM_003797.3	73	tgGAAGTCa/tga	2/12	0.623508654550206	3	FACETS	0.71	0.621	0.805	0.355	0.31	0.403	SUBCLONAL	1	TRUE	1	0.623508654550206	3		394	409	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	17	337	0				ENST00000310581	NM_198253.2	-/1132			0.128848627073614	1	FACETS	1	0.8	1	1	0.8	1	CLONAL	1	TRUE	0	0.21	1		337	135	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	13	609	3	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	1	2	FACETS	0.579	0.413	0.78	0.579	0.413	0.78	SUBCLONAL	1	TRUE	1	0.21	2		612	214	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	27	313	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	0.217908311439082	2	FACETS	1	0.906	1	0.624	0.5	0.764	CLONAL	1	TRUE	0	0.21	2		313	206	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020477	14020477	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145402255	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	10	288	1	ENST00000311895.7:c.448C>T	p.Arg150Cys	p.R150C	ENST00000311895	NM_005236.2	150	Cgc/Tgc	3/11	1	2	FACETS	0.56	0.38	0.786	0.56	0.38	0.786	SUBCLONAL	1	TRUE	1	0.21	2		289	170	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528284	157528284	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs749055122	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	27	526	0	ENST00000346085.5:c.6013del	p.Val2005TrpfsTer16	p.V2005Wfs*16	ENST00000346085	NM_020732.3	2003	aaG/aa	20/20	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.21	2		526	215	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090086	37090086	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	37	362	0	ENST00000231790.2:c.1975del	p.Arg659AspfsTer2	p.R659Dfs*2	ENST00000231790	NM_000249.3	659	Cga/ga	17/19	0.217908311439082	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	2	TRUE	0	0.21	2		362	175	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29107989	29107989	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	15	330	0	ENST00000328354.6:c.700G>C	p.Val234Leu	p.V234L	ENST00000328354	NM_007194.3	234	Gta/Cta	6/15	1	2	FACETS	1	0.741	1	1	0.741	1	CLONAL	1	TRUE	1	0.21	2		330	142	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437697	52437697	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1553644922	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	59	626	0	ENST00000460680.1:c.1464del	p.Ser489AlafsTer82	p.S489Afs*82	ENST00000460680	NM_004656.3	488	ccC/cc	13/17	0.217908311439082	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.21	2		626	242	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	34	564	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.21	2		564	240	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952086	178952086	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	28	275	0	ENST00000263967.3:c.3141T>A	p.His1047Gln	p.H1047Q	ENST00000263967	NM_006218.2	1047	caT/caA	21/21	0.387389703672979	3	FACETS	0.909	0.735	1	0.909	0.735	1	CLONAL	2	TRUE	1	0.21	3		275	162	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795103	242795104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768249210	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	24	698	0	ENST00000334409.5:c.105dup	p.Thr36HisfsTer70	p.T36Hfs*70	ENST00000334409	NM_005018.2	35	-/C	2/5	1	2	FACETS	0.914	0.719	1	0.914	0.719	1	CLONAL	1	TRUE	1	0.21	2		698	250	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678783	52678784	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	29	214	0	ENST00000394830.3:c.835dup	p.Ile279AsnfsTer8	p.I279Nfs*8	ENST00000394830	NM_018313.4	279	ata/aAta	9/30	0.217908311439082	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	2	TRUE	0	0.21	2		214	129	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070577	67070578	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	17	241	0	ENST00000412916.2:c.207dup	p.Pro70SerfsTer13	p.P70Sfs*13	ENST00000412916		67	-/T	3/6	1	2	FACETS	0.93	0.698	1	0.93	0.698	1	CLONAL	1	TRUE	1	0.21	2		241	174	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10273405	10273405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200601847	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	26	469	0	ENST00000340748.4:c.898G>A	p.Glu300Lys	p.E300K	ENST00000340748		300	Gaa/Aaa	12/40	0.128848627073614	1	FACETS	0.994	0.791	1	0.994	0.791	1	CLONAL	1	TRUE	0	0.21	1		469	223	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063359	67063359	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	20	276	2	ENST00000412916.2:c.54del	p.Phe18LeufsTer4	p.F18Lfs*4	ENST00000412916		17	Ttt/tt	1/6	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.21	2		278	154	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741541	17741541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773231763	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	17	336	0	ENST00000250003.3:c.212C>T	p.Pro71Leu	p.P71L	ENST00000250003	NM_002478.4	71	cCg/cTg	1/3	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.21	2		336	130	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755470	39755470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	34	410	1	ENST00000288319.7:c.1295C>T	p.Ala432Val	p.A432V	ENST00000288319	NM_182918.3	432	gCg/gTg	10/10	0.285786425934214	1	FACETS	0.906	0.75	1	1	0.961	1	CLONAL	2	TRUE	0	0.21	1		411	160	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099468	157099470	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	rs1429292576	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	29	251	0	ENST00000346085.5:c.413_415del	p.Asn138del	p.N138del	ENST00000346085	NM_020732.3	135	tcCAAc/tcc	1/20	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.21	2		251	230	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755553	39755554	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	16	366	0	ENST00000288319.7:c.1211dup	p.Glu405GlyfsTer61	p.E405Gfs*61	ENST00000288319	NM_182918.3	404	ccg/ccCg	10/10	0.285786425934214	1	FACETS	0.807	0.599	1	0.807	0.599	1	CLONAL	1	TRUE	0	0.21	1		366	169	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829039	128829040	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCTGCT	rs570242755	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	13	14	0	ENST00000249373.3:c.64_69dup	p.Leu22_Leu23dup	p.L22_L23dup	ENST00000249373	NM_005631.4	22	ggg/ggGCTGCTg	1/12	0.3	2	FACETS	1	0.801	1			1	CLONAL	3	TRUE	NA	0.21	2		14	38	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211504	36211504	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	13	470	0	ENST00000222270.7:c.1259del	p.Pro420LeufsTer55	p.P420Lfs*55	ENST00000222270	NM_014727.1	419	Ccc/cc	3/37	0.128848627073614	1	FACETS	0.583	0.417	0.785	0.583	0.417	0.785	SUBCLONAL	1	TRUE	0	0.21	1		470	190	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40874920	40874920	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756635466	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	32	445	0	ENST00000428826.2:c.380C>T	p.Thr127Met	p.T127M	ENST00000428826		127	aCg/aTg	6/21	1	2	FACETS	0.851	0.698	1	1	0.955	1	CLONAL	2	TRUE	1	0.21	2		445	179	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779810	3779810	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	24	611	1	ENST00000262367.5:c.5238del	p.Leu1747TrpfsTer24	p.L1747Wfs*24	ENST00000262367	NM_004380.2	1746	ggG/gg	31/31	1	2	FACETS	0.973	0.766	1	0.973	0.766	1	CLONAL	1	TRUE	1	0.21	2		612	235	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662544	227662544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756485509	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	24	447	0	ENST00000305123.5:c.911G>A	p.Arg304His	p.R304H	ENST00000305123	NM_005544.2	304	cGc/cAc	1/2	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.21	2		447	195	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714732	52714732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	16	429	1	ENST00000322088.6:c.490G>A	p.Ala164Thr	p.A164T	ENST00000322088	NM_014225.5	164	Gcg/Acg	4/15	0.128848627073614	1	FACETS	0.617	0.457	0.808	0.617	0.457	0.808	SUBCLONAL	1	TRUE	0	0.21	1		430	221	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383350	42383350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144006380	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	27	449	0	ENST00000221972.3:c.370C>T	p.Arg124Cys	p.R124C	ENST00000221972	NM_021601.3	124	Cgc/Tgc	2/5	0.128848627073614	1	FACETS	0.988	0.79	1	0.988	0.79	1	CLONAL	1	TRUE	0	0.21	1		449	233	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520260	176520260	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	18	599	0	ENST00000292408.4:c.1179G>T	p.Gln393His	p.Q393H	ENST00000292408	NM_213647.1	393	caG/caT	9/18	1	2	FACETS	0.745	0.562	0.961	0.745	0.562	0.961	CLONAL	1	TRUE	1	0.21	2		599	230	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226568842	226568842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	19	519	0	ENST00000366794.5:c.1227G>T	p.Lys409Asn	p.K409N	ENST00000366794	NM_001618.3	409	aaG/aaT	9/23	0.217908311439082	3	FACETS	1	0.777	1	0.51	0.389	0.651	CLONAL	1	TRUE	1	0.21	3		519	196	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410674	32410674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	21	400	0	ENST00000332351.3:c.1484G>A	p.Arg495Gln	p.R495Q	ENST00000332351	NM_024426.4	495	cGg/cAg	10/10	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.21	2		400	173	SUCCESS
EED	8726	MSKCC	GRCh37	11	85961381	85961381	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	16	225	0	ENST00000263360.6:c.158C>A	p.Pro53His	p.P53H	ENST00000263360	NM_003797.3	53	cCt/cAt	2/12	1	2	FACETS	1	0.815	1	1	0.815	1	CLONAL	1	TRUE	1	0.21	2		225	136	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962544	100962544	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	13	394	1	ENST00000325455.5:c.1853del	p.Asn618ThrfsTer31	p.N618Tfs*31	ENST00000325455	NM_001202474.3	618	aAc/ac	3/8	1	2	FACETS	0.684	0.489	0.921	0.684	0.489	0.921	SUBCLONAL	1	TRUE	1	0.21	2		395	181	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999749	100999749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759568940	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	24	555	1	ENST00000325455.5:c.53C>T	p.Pro18Leu	p.P18L	ENST00000325455	NM_001202474.3	18	cCg/cTg	1/8	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.21	2		556	154	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206856	102206859	+	frameshift_variant	Frame_Shift_Del	DEL	TGAT	TGAT	-	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	17	284	1	ENST00000263464.3:c.1488_1491del	p.Asp497ArgfsTer3	p.D497Rfs*3	ENST00000263464	NM_001165.4	495	cTGATt/ct	7/9	1	2	FACETS	1	0.798	1	1	0.798	1	CLONAL	1	TRUE	1	0.21	2		285	151	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144589	119144589	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	18	257	0	ENST00000264033.4:c.602C>A	p.Pro201His	p.P201H	ENST00000264033	NM_005188.3	201	cCt/cAt	4/16	0.128848627073614	3	FACETS	1	0.858	1	0.603	0.457	0.773	CLONAL	1	TRUE	1	0.21	3		257	157	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415829	49415829	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	22	289	0	ENST00000301067.7:c.16518G>T	p.Glu5506Asp	p.E5506D	ENST00000301067	NM_003482.3	5506	gaG/gaT	53/54	1	2	FACETS	1	0.828	1	1	0.828	1	CLONAL	1	TRUE	1	0.21	2		289	195	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425510	49425510	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	13	620	4	ENST00000301067.7:c.12978del	p.Ser4327AlafsTer57	p.S4327Afs*57	ENST00000301067	NM_003482.3	4326	ccC/cc	39/54	1	2	FACETS	0.484	0.344	0.654	0.484	0.344	0.654	SUBCLONAL	1	TRUE	1	0.21	2		624	256	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431759	49431759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1359665754	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	23	550	1	ENST00000301067.7:c.9380G>A	p.Arg3127His	p.R3127H	ENST00000301067	NM_003482.3	3127	cGc/cAc	34/54	1	2	FACETS	0.936	0.733	1	0.936	0.733	1	CLONAL	1	TRUE	1	0.21	2		551	234	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442483	49442483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375317924	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	37	541	0	ENST00000301067.7:c.4090G>A	p.Val1364Met	p.V1364M	ENST00000301067	NM_003482.3	1364	Gtg/Atg	13/54	1	2	FACETS	0.759	0.631	0.901	1	0.953	1	CLONAL	2	TRUE	1	0.21	2		541	232	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214699	133214699	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	34	376	0	ENST00000320574.5:c.5579G>T	p.Gly1860Val	p.G1860V	ENST00000320574	NM_006231.2	1860	gGg/gTg	41/49	1	2	FACETS	0.76	0.626	0.908	1	0.95	1	CLONAL	2	TRUE	1	0.21	2		376	213	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061255	38061255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200502828	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	12	485	0	ENST00000250448.2:c.734C>T	p.Thr245Met	p.T245M	ENST00000250448	NM_004496.3	245	aCg/aTg	2/2	0.128848627073614	1	FACETS	0.547	0.385	0.746	0.547	0.385	0.746	SUBCLONAL	1	TRUE	0	0.21	1		485	187	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929457	81929457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	21	452	0	ENST00000359376.3:c.1118G>A	p.Gly373Asp	p.G373D	ENST00000359376	NM_002661.3	373	gGc/gAc	13/33	0.128848627073614	1	FACETS	0.856	0.662	1	0.856	0.662	1	CLONAL	1	TRUE	0	0.21	1		452	209	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117387	7117387	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	24	474	0	ENST00000302850.5:c.3829C>G	p.Pro1277Ala	p.P1277A	ENST00000302850	NM_000208.2	1277	Ccc/Gcc	22/22	0.128848627073614	1	FACETS	0.926	0.729	1	0.926	0.729	1	CLONAL	1	TRUE	0	0.21	1		474	221	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117407	7117407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746000108	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	27	425	0	ENST00000302850.5:c.3809G>A	p.Arg1270His	p.R1270H	ENST00000302850	NM_000208.2	1270	cGc/cAc	22/22	0.128848627073614	1	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	0	0.21	1		425	188	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152003	11152005	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	20	465	0	ENST00000358026.2:c.4291_4293del	p.Glu1431del	p.E1431del	ENST00000358026	NM_001128849.1	1429	ctGGAg/ctg	31/36	0.128848627073614	1	FACETS	0.828	0.635	1	0.828	0.635	1	CLONAL	1	TRUE	0	0.21	1		465	206	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050887	13050887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	23	413	0	ENST00000316448.5:c.418G>A	p.Gly140Ser	p.G140S	ENST00000316448	NM_004343.3	140	Ggc/Agc	4/9	0.128848627073614	1	FACETS	0.908	0.711	1	0.908	0.711	1	CLONAL	1	TRUE	0	0.21	1		413	216	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909526	50909526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	33	673	0	ENST00000440232.2:c.1330C>T	p.Arg444Trp	p.R444W	ENST00000440232	NM_002691.3	444	Cgg/Tgg	11/27	0.128848627073614	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.21	1		673	227	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097268	178097268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	26	378	0	ENST00000397062.3:c.446G>A	p.Gly149Asp	p.G149D	ENST00000397062	NM_006164.4	149	gGt/gAt	4/5	0.3	3	FACETS	1	0.913	1			1	CLONAL	1	TRUE	NA	0.21	3		378	209	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281157	46281159	+	inframe_deletion	In_Frame_Del	DEL	ACA	ACA	-	rs758623577	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	18	399	0	ENST00000371998.3:c.3959_3961del	p.Gln1320del	p.Q1320del	ENST00000371998		1318	ggACAa/gga	21/23	0.3	3	FACETS	1	0.766	1			1	CLONAL	1	TRUE	NA	0.21	3		399	187	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945583	54945583	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	13	497	0	ENST00000312783.6:c.987del	p.Phe329LeufsTer24	p.F329Lfs*24	ENST00000312783	NM_198436.1	329	ttT/tt	9/10	0.3	3	FACETS	0.756	0.54	1			1	CLONAL	1	TRUE	NA	0.21	3		497	181	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845366	42845366	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150445636	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	28	569	1	ENST00000398585.3:c.896C>T	p.Ala299Val	p.A299V	ENST00000398585	NM_001135099.1	299	gCg/gTg	9/14	0.285786425934214	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.21	1		570	163	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169999744	169999744	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	19	245	0	ENST00000295797.4:c.1055A>G	p.Glu352Gly	p.E352G	ENST00000295797	NM_002740.5	352	gAa/gGa	11/18	0.387389703672979	3	FACETS	0.901	0.693	1	0.901	0.693	1	CLONAL	2	TRUE	1	0.21	3		245	111	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505350	186505350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	17	305	0	ENST00000323963.5:c.976G>A	p.Val326Ile	p.V326I	ENST00000323963		326	Gtt/Att	9/11	0.387389703672979	3	FACETS	0.683	0.51	0.888	0.341	0.255	0.444	SUBCLONAL	1	TRUE	1	0.21	3		305	262	SUCCESS
APC	324	MSKCC	GRCh37	5	112177585	112177585	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1554087318	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	11	254	0	ENST00000257430.4:c.6294T>G	p.Asn2098Lys	p.N2098K	ENST00000257430	NM_000038.5	2098	aaT/aaG	16/16	0.128848627073614	3	FACETS	0.973	0.677	1	0.486	0.338	0.668	CLONAL	1	TRUE	1	0.21	3		254	119	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457813	149457813	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	17	369	0	ENST00000286301.3:c.593-2A>G		p.X198_splice	ENST00000286301	NM_005211.3	198			1	2	FACETS	1	0.76	1	1	0.76	1	CLONAL	1	TRUE	1	0.21	2		369	160	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522102	157522102	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	30	407	0	ENST00000346085.5:c.4374G>T	p.Glu1458Asp	p.E1458D	ENST00000346085	NM_020732.3	1458	gaG/gaT	18/20	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.21	2		407	224	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	163148692	163148692	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs950518517	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	19	357	0	ENST00000366898.1:c.7+2T>C		p.X3_splice	ENST00000366898	NM_004562.2	3			1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.21	2		357	154	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935652	13935652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	24	346	0	ENST00000405192.2:c.1204G>A	p.Ala402Thr	p.A402T	ENST00000405192	NM_001163147.1	402	Gcc/Acc	12/12	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.21	2		346	161	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511065	148511065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	29	258	0	ENST00000320356.2:c.1837C>T	p.Arg613Trp	p.R613W	ENST00000320356	NM_004456.4	613	Cgg/Tgg	15/20	1	2	FACETS	0.885	0.719	1	1	0.953	1	CLONAL	2	TRUE	1	0.21	2		258	156	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874341	151874341	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	24	285	0	ENST00000262189.6:c.8197G>T	p.Asp2733Tyr	p.D2733Y	ENST00000262189	NM_170606.2	2733	Gat/Tat	38/59	1	2	FACETS	0.853	0.677	1	1	0.941	1	CLONAL	2	TRUE	1	0.21	2		285	134	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132759	152132759	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	30	348	0	ENST00000262189.6:c.113del	p.Gly38AlafsTer67	p.G38Afs*67	ENST00000262189	NM_170606.2	38	gGc/gc	1/59	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.21	2		348	199	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371653	55371653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	18	497	2	ENST00000297316.4:c.343C>T	p.Arg115Trp	p.R115W	ENST00000297316	NM_022454.3	115	Cgg/Tgg	2/2	1	2	FACETS	0.888	0.672	1	0.888	0.672	1	CLONAL	1	TRUE	1	0.21	2		499	193	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752786	128752786	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1051420663	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	12	231	0	ENST00000377970.2:c.947A>G	p.His316Arg	p.H316R	ENST00000377970	NM_002467.4	316	cAc/cGc	3/3	1	2	FACETS	0.592	0.416	0.808	0.592	0.416	0.808	SUBCLONAL	1	TRUE	1	0.21	2		231	193	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737104	145737106	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs1564787405	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	24	781	0	ENST00000428558.2:c.3460_3462del	p.Lys1154del	p.K1154del	ENST00000428558	NM_004260.3	1154	AAG/-	21/22	1	2	FACETS	0.893	0.702	1	0.893	0.702	1	CLONAL	1	TRUE	1	0.21	2		781	256	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347804	70347804	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	11	538	0	ENST00000374080.3:c.3043A>G	p.Met1015Val	p.M1015V	ENST00000374080		1015	Atg/Gtg	22/45	0.285786425934214	1	FACETS	0.536	0.371	0.74	0.536	0.371	0.74	SUBCLONAL	1	TRUE	0	0.21	1		538	175	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651502	206651502	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0013923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	16	263	0	ENST00000367120.3:c.816del		p.X272_splice	ENST00000367120	NM_014002.3	272			0.217908311439082	3	FACETS	0.752	0.562	0.972	0.752	0.562	0.972	CLONAL	2	TRUE	1	0.21	3		263	112	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0015033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	783	399	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.553561526552083	2	FACETS	0.991	0.963	1	0.991	0.963	1	CLONAL	2	TRUE	0	0.553561526552083	2		399	1427	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436940	49436941	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCACTGA	novel	NA	P-0015033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	204	835	0	ENST00000301067.7:c.5562_5563insTCAGTGC	p.Pro1855SerfsTer7	p.P1855Sfs*7	ENST00000301067	NM_003482.3	1854	-/TCAGTGC	25/54	0.47212890858185	1	FACETS	0.607	0.564	0.652	0.607	0.564	0.652	SUBCLONAL	1	TRUE	0	0.553561526552083	1		835	878	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259016	153259063	+	inframe_deletion	In_Frame_Del	DEL	GTTTTACTTGTGTTGGTTCACAACTATCAATGAGTTCATCTAAAGCAA	GTTTTACTTGTGTTGGTTCACAACTATCAATGAGTTCATCTAAAGCAA	-	novel	NA	P-0015033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	69	426	0	ENST00000281708.4:c.752_799del	p.Leu251_Lys266del	p.L251_K266del	ENST00000281708	NM_033632.3	251	cTTGCTTTAGATGAACTCATTGATAGTTGTGAACCAACACAAGTAAAACat/cat	5/12	0.553561526552083	1	FACETS	0.686	0.604	0.772	0.686	0.604	0.772	SUBCLONAL	1	TRUE	0	0.553561526552083	1		426	263	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858361	27858378	+	inframe_deletion	In_Frame_Del	DEL	GCGCTGAAATGGCAGTTT	GCGCTGAAATGGCAGTTT	-	novel	NA	P-0015033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	168	573	0	ENST00000359303.2:c.193_210del	p.Lys65_Arg70del	p.K65_R70del	ENST00000359303	NM_003535.2	65	AAACTGCCATTTCAGCGC/-	1/1	1	2	FACETS	0.746	0.686	0.808	0.746	0.686	0.808	SUBCLONAL	1	TRUE	1	0.553561526552083	2		573	814	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848544	151848550	+	frameshift_variant	Frame_Shift_Del	DEL	GATCTTT	GATCTTT	-	novel	NA	P-0015033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	145	581	0	ENST00000262189.6:c.12643_12649del	p.Lys4215Ter	p.K4215*	ENST00000262189	NM_170606.2	4215	AAAGATCtg/tg	50/59	NA	2	FACETS	0.676	0.617	0.737			1	INDETERMINATE	1	TRUE	NA	0.553561526552083	2		581	775	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738308	145738308	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1264247879	NA	P-0015033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	308	1095	2	ENST00000428558.2:c.2677C>T	p.Pro893Ser	p.P893S	ENST00000428558	NM_004260.3	893	Ccc/Tcc	16/22	0.429462105650594	1	FACETS	0.837	0.791	0.885	0.837	0.791	0.885	CLONAL	1	TRUE	0	0.553561526552083	1		1097	961	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052719	42052719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	108	342	0	ENST00000219905.7:c.7390C>T	p.Leu2464Phe	p.L2464F	ENST00000219905	NM_001164273.1	2464	Ctt/Ttt	20/24	1	2	FACETS	0.481	0.434	0.532	0.481	0.434	0.532	SUBCLONAL	1	FALSE	1	0.851253703116823	2		342	527	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0015678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	79	369	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	0.375	0.33	0.422	0.375	0.33	0.422	SUBCLONAL	1	FALSE	1	0.851253703116823	2		369	495	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673711	176673711	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs570278338	NA	P-0015678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	17	348	1	ENST00000439151.2:c.4411C>T	p.Arg1471Ter	p.R1471*	ENST00000439151	NM_022455.4	1471	Cga/Tga	10/23	NA	2	FACETS	0.121	0.09	0.159			1	INDETERMINATE	1	FALSE	NA	0.851253703116823	2		349	329	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858210	9858210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756930722	NA	P-0015678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	117	417	0	ENST00000330684.3:c.3191C>T	p.Thr1064Met	p.T1064M	ENST00000330684	NM_001134407.1	1064	aCg/aTg	13/13	1	2	FACETS	0.501	0.453	0.551	0.501	0.453	0.551	SUBCLONAL	1	FALSE	1	0.851253703116823	2		417	549	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955176	1955176	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	168	593	1	ENST00000382891.5:c.2263C>T	p.Arg755Ter	p.R755*	ENST00000382891	NM_133335.3	755	Cga/Tga	12/22	1	2	FACETS	0.508	0.467	0.55	0.508	0.467	0.55	SUBCLONAL	1	FALSE	1	0.851253703116823	2		594	777	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444933	49444933	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767415197	NA	P-0015678-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	184	725	2	ENST00000301067.7:c.2533del	p.Arg845GlyfsTer85	p.R845Gfs*85	ENST00000301067	NM_003482.3	845	Cgg/gg	10/54	1	2	FACETS	0.576	0.532	0.62	0.576	0.532	0.62	SUBCLONAL	1	FALSE	1	0.851253703116823	2		727	751	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	470	497	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.72053212452032	3	FACETS	1	0.973	1	0.676	0.65	0.701	CLONAL	2	TRUE	0	0.736032983800172	3		497	862	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11168343	11168343	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	313	495	0	ENST00000361445.4:c.7529G>A	p.Gly2510Asp	p.G2510D	ENST00000361445	NM_004958.3	2510	gGt/gAt	57/58	0.719353762710525	2	FACETS	0.928	0.893	0.963	0.928	0.893	0.963	CLONAL	2	TRUE	0	0.736032983800172	2		495	458	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015302	128015302	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	141	465	1	ENST00000285398.2:c.2219C>T	p.Ala740Val	p.A740V	ENST00000285398	NM_000122.1	740	gCa/gTa	15/15	0.494149252632365	4	FACETS	1	0.981	1	0.419	0.384	0.456	CLONAL	1	TRUE	1	0.736032983800172	4		466	529	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39021160	39021160	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	114	483	0	ENST00000357387.3:c.176A>T	p.His59Leu	p.H59L	ENST00000357387	NM_152756.3	59	cAt/cTt	3/38	0.171660249318684	5	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.736032983800172	5		483	524	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407485	407485	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	340	543	0	ENST00000380956.4:c.1243T>C	p.Tyr415His	p.Y415H	ENST00000380956	NM_001195286.1	415	Tat/Cat	9/9	0.736032983800172	4	FACETS	0.851	0.808	0.896			1	CLONAL	2	TRUE	NA	0.736032983800172	4		543	942	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133994	38133994	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	51	641	0	ENST00000317025.8:c.3892G>C	p.Glu1298Gln	p.E1298Q	ENST00000317025	NM_023034.1	1298	Gag/Cag	23/24	0.621136745748783	4	FACETS	0.282	0.239	0.33	0.141	0.119	0.165	SUBCLONAL	1	TRUE	2	0.736032983800172	4		641	853	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980508	70980508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015902-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	501	955	1	ENST00000276594.2:c.869C>T	p.Ala290Val	p.A290V	ENST00000276594	NM_024504.3	290	gCc/gTc	4/8	0.621136745748783	4	FACETS	0.928	0.889	0.966	0.928	0.889	0.966	CLONAL	2	TRUE	2	0.736032983800172	4		956	1274	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0015934-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	110	269	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.360770910212777	2		269	490	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485926	8485926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770180884	NA	P-0015934-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	36	339	0	ENST00000356435.5:c.2891C>T	p.Pro964Leu	p.P964L	ENST00000356435		964	cCc/cTc	17/35	0.350136431284658	1	FACETS	0.497	0.41	0.595	0.497	0.41	0.595	SUBCLONAL	1	TRUE	0	0.360770910212777	1		339	329	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902592	1902593	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCA	novel	NA	P-0015934-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	65	651	0	ENST00000382891.5:c.211_212insGGCA	p.Leu71ArgfsTer19	p.L71Rfs*19	ENST00000382891	NM_133335.3	71	ctg/cGGCAtg	2/22	1	2	FACETS	0.623	0.541	0.713	0.623	0.541	0.713	SUBCLONAL	1	TRUE	1	0.360770910212777	2		651	578	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356271	66356271	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015934-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	97	491	0	ENST00000273854.3:c.1226G>C	p.Gly409Ala	p.G409A	ENST00000273854	NM_004439.5	409	gGc/gCc	5/18	1	2	FACETS	0.918	0.82	1	0.918	0.82	1	CLONAL	1	TRUE	1	0.360770910212777	2		491	586	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554928	106554928	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015934-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	51	450	0	ENST00000369096.4:c.2045C>T	p.Thr682Ile	p.T682I	ENST00000369096	NM_001198.3	682	aCc/aTc	7/7	1	2	FACETS	0.612	0.521	0.712	0.612	0.521	0.712	SUBCLONAL	1	TRUE	1	0.360770910212777	2		450	462	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778753	76778753	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015934-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	71	381	0	ENST00000373344.5:c.6826G>T	p.Ala2276Ser	p.A2276S	ENST00000373344	NM_000489.3	2276	Gct/Tct	31/35	1	2	FACETS	0.748	0.654	0.85	0.748	0.654	0.85	SUBCLONAL	1	TRUE	1	0.360770910212777	2		381	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912664	NA	P-0016609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	521	557	0	ENST00000269305.4:c.1010G>C	p.Arg337Pro	p.R337P	ENST00000269305	NM_001126112.2	337	cGc/cCc	10/11	0.925249466988516	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.925249466988516	1		557	599	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948133	178948133	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016609-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	211	237	0	ENST00000263967.3:c.2905C>A	p.Gln969Lys	p.Q969K	ENST00000263967	NM_006218.2	969	Caa/Aaa	20/21	0.921511100988549	3	FACETS	0.932	0.869	0.996	0.466	0.434	0.498	CLONAL	1	TRUE	1	0.925249466988516	3		237	716	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0017308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	143	512	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.985	0.899	1	0.985	0.899	1	CLONAL	1	TRUE	1	0.369969939296641	2		512	785	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0017308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	180	687	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.205439980197565	2	FACETS	1	0.98	1	0.592	0.546	0.639	INDETERMINATE	1	TRUE	0	0.369969939296641	2		688	822	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450300	50450300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	81	641	0	ENST00000331340.3:c.484C>T	p.Arg162Trp	p.R162W	ENST00000331340	NM_006060.4	162	Cgg/Tgg	5/8	0.369969939296641	3	FACETS	0.534	0.469	0.604	0.267	0.234	0.302	SUBCLONAL	1	TRUE	1	0.369969939296641	3		641	972	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556250	29556250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199474739	NA	P-0017308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	68	438	2	ENST00000356175.3:c.2617C>T	p.Arg873Cys	p.R873C	ENST00000356175	NM_000267.3	873	Cgt/Tgt	21/57	0.369969939296641	3	FACETS	0.625	0.543	0.714	0.312	0.271	0.357	SUBCLONAL	1	TRUE	1	0.369969939296641	3		440	697	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156541	55156541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368266633	NA	P-0017308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	63	546	0	ENST00000257290.5:c.2942G>A	p.Arg981His	p.R981H	ENST00000257290	NM_006206.4	981	cGt/cAt	22/23	1	2	FACETS	0.438	0.378	0.504	0.438	0.378	0.504	SUBCLONAL	1	TRUE	1	0.369969939296641	2		546	777	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295425	1295425	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0017308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	21	67	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.369969939296641	2		67	90	SUCCESS
APC	324	MSKCC	GRCh37	5	112137018	112137018	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	109	482	0	ENST00000257430.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000257430	NM_000038.5	258	Gag/Tag	8/16	1	2	FACETS	0.949	0.854	1	0.949	0.854	1	CLONAL	1	TRUE	1	0.369969939296641	2		482	621	SUCCESS
APC	324	MSKCC	GRCh37	5	112175581	112175582	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATGCCACCAAGCAG	novel	NA	P-0017308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	40	420	0	ENST00000257430.4:c.4292_4305dup	p.Ser1436CysfsTer42	p.S1436Cfs*42	ENST00000257430	NM_000038.5	1430	-/ATGCCACCAAGCAG	16/16	1	2	FACETS	0.388	0.322	0.462	0.388	0.322	0.462	SUBCLONAL	1	TRUE	1	0.369969939296641	2		420	557	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156487	55156487	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	47	430	0	ENST00000257290.5:c.2888A>T	p.Glu963Val	p.E963V	ENST00000257290	NM_006206.4	963	gAa/gTa	22/23	1	2	FACETS	0.432	0.364	0.507	0.432	0.364	0.507	SUBCLONAL	1	TRUE	1	0.369969939296641	2		430	588	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196044	138196044	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017308-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	50	294	0	ENST00000237289.4:c.358T>G	p.Leu120Val	p.L120V	ENST00000237289	NM_001270507.1	120	Ttg/Gtg	3/9	0.302127088164556	3	FACETS	0.577	0.489	0.674	0.289	0.244	0.337	SUBCLONAL	1	TRUE	1	0.369969939296641	3		294	555	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0017825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	344	381	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.430097835890243	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.430097835890243	3		381	963	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940157	71940157	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	210	614	0	ENST00000298229.2:c.542T>C	p.Val181Ala	p.V181A	ENST00000298229	NM_001567.3	181	gTc/gCc	5/28	0.342019122485075	3	FACETS	0.957	0.887	1			1	CLONAL	1	TRUE	NA	0.430097835890243	3		614	1240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0017825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	145	375	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.430097835890243	1	FACETS	0.856	0.784	0.932	0.856	0.784	0.932	CLONAL	1	TRUE	0	0.430097835890243	1		375	618	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435780	56435780	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	202	296	0	ENST00000407977.2:c.1357G>T	p.Glu453Ter	p.E453*	ENST00000407977		453	Gaa/Taa	9/10	0.406799262908103	2	FACETS	0.962	0.901	1	0.962	0.901	1	CLONAL	2	TRUE	0	0.430097835890243	2		296	488	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0017825-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	44	139	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	0.430097835890243	1	FACETS	0.727	0.615	0.847	0.727	0.615	0.847	SUBCLONAL	1	TRUE	0	0.430097835890243	1		139	221	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0018026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	374	616	0	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.548785434349581	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.548785434349581	2		616	642	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692892	89692892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554898129	NA	P-0018026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	32	380	0	ENST00000371953.3:c.376G>A	p.Ala126Thr	p.A126T	ENST00000371953	NM_000314.4	126	Gct/Act	5/9	0.453604281249721	5	FACETS	0.597	0.485	0.723	0.199	0.161	0.241	SUBCLONAL	1	TRUE	2	0.548785434349581	5		380	356	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105804	27105805	+	missense_variant	Missense_Mutation	DNP	GA	GA	TT	novel	NA	P-0018026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	157	318	0	ENST00000324856.7:c.5415_5416delinsTT	p.Ile1806Phe	p.I1806F	ENST00000324856	NM_006015.4	1805	ctGAtc/ctTTtc	20/20	0.33318137470849	3	FACETS	1	0.987	1	0.832	0.779	0.886	CLONAL	2	TRUE	0	0.548785434349581	3		318	292	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	427594	427594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756567348	NA	P-0018026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	222	429	0	ENST00000399788.2:c.2575C>T	p.Arg859Cys	p.R859C	ENST00000399788	NM_001042603.1	859	Cgt/Tgt	19/28	0.136759059044307	6	FACETS	0.929	0.87	0.988			1	INDETERMINATE	3	TRUE	NA	0.548785434349581	6		429	609	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434042	121434089	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGGACACTGCTTCCCTCTCCAGGTGTGCGCTATGGACAGCCTGCGAC	CAGGACACTGCTTCCCTCTCCAGGTGTGCGCTATGGACAGCCTGCGAC	-	novel	NA	P-0018026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	202	287	0	ENST00000257555.6:c.956-20_983del		p.X319_splice	ENST00000257555		319		5/10	0.548785434349581	5	FACETS	1	0.964	1	0.702	0.654	0.751	CLONAL	2	TRUE	2	0.548785434349581	5		287	637	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290968	15290969	+	missense_variant	Missense_Mutation	DNP	CA	CA	TG	novel	NA	P-0018026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	63	736	0	ENST00000263388.2:c.3241_3242inv	p.Cys1081His	p.C1081H	ENST00000263388	NM_000435.2	1081	TGt/CAt	20/33	0.548785434349581	2	FACETS	0.387	0.335	0.444	0.194	0.167	0.222	SUBCLONAL	1	TRUE	0	0.548785434349581	2		736	593	SUCCESS
ALK	238	MSKCC	GRCh37	2	29450540	29450540	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0018026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	462	464	0	ENST00000389048.3:c.2816-2A>C		p.X939_splice	ENST00000389048	NM_004304.4	939			0.548092026337436	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	4	TRUE	0	0.548785434349581	4		464	645	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444382	50444382	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	109	332	0	ENST00000331340.3:c.312G>C	p.Leu104Phe	p.L104F	ENST00000331340	NM_006060.4	104	ttG/ttC	4/8	0.548785434349581	2	FACETS	1	0.985	1	0.736	0.672	0.801	CLONAL	1	TRUE	0	0.548785434349581	2		332	270	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355317	81355327	+	protein_altering_variant	In_Frame_Del	DEL	AATTTTCTCGT	AATTTTCTCGT	CCCTATTG	novel	NA	P-0018026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	82	249	1	ENST00000222390.5:c.1047_1057delinsCAATAGGG	p.Arg350_Tyr353delinsAsnArgAsp	p.R350_Y353delinsNRD	ENST00000222390	NM_000601.4	349	ctACGAGAAAATTac/ctCAATAGGGac	9/18	0.548785434349581	4	FACETS	0.798	0.712	0.888	0.399	0.356	0.444	SUBCLONAL	2	TRUE	0	0.548785434349581	4		250	290	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624404	140624427	+	inframe_deletion	In_Frame_Del	DEL	CGGCGCCGGCGCCGGCGCCGGCCT	CGGCGCCGGCGCCGGCGCCGGCCT	-	novel	NA	P-0018026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	16	212	0	ENST00000288602.6:c.77_100del	p.Glu26_Ala33del	p.E26_A33del	ENST00000288602	NM_004333.4	26	gAGGCCGGCGCCGGCGCCGGCGCCGcg/gcg	1/18	0.548785434349581	4	FACETS	0.334	0.247	0.439	0.084	0.061	0.11	SUBCLONAL	1	TRUE	0	0.548785434349581	4		212	270	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787841	135787841	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	83	485	0	ENST00000298552.3:c.741G>A	p.Trp247Ter	p.W247*	ENST00000298552	NM_001162426.1	247	tgG/tgA	9/23	0.468071272794132	1	FACETS	0.853	0.76	0.95	0.853	0.76	0.95	CLONAL	1	TRUE	0	0.479002700151734	1		485	309	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350323	15350323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	57	577	0	ENST00000263377.2:c.3456G>A	p.Met1152Ile	p.M1152I	ENST00000263377	NM_058243.2	1152	atG/atA	17/20	1	2	FACETS	0.585	0.503	0.673	0.585	0.503	0.673	SUBCLONAL	1	TRUE	1	0.479002700151734	2		577	407	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161238	56161238	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	98	650	0	ENST00000399503.3:c.1107A>C	p.Glu369Asp	p.E369D	ENST00000399503	NM_005921.1	369	gaA/gaC	5/20	0.468071272794132	1	FACETS	0.817	0.734	0.903	0.817	0.734	0.903	CLONAL	1	TRUE	0	0.479002700151734	1		650	381	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413265	63413265	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0018389-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	22	110	0	ENST00000330258.3:c.-98-1G>C		p.X33_splice	ENST00000330258	NM_152424.3	33			NA	2	FACETS	1	0.926	1			1	INDETERMINATE	1	TRUE	NA	0.479002700151734	2		110	65	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222151	2222151	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760542574	NA	P-0018389-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	144	900	3	ENST00000398665.3:c.2983C>T	p.Arg995Trp	p.R995W	ENST00000398665	NM_032482.2	995	Cgg/Tgg	24/28	1	2	FACETS	0.801	0.729	0.877	0.801	0.729	0.877	CLONAL	1	TRUE	1	0.325815510155654	2		903	1103	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851765	134851765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018389-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	79	559	0	ENST00000398015.3:c.1171G>A	p.Val391Ile	p.V391I	ENST00000398015	NM_004441.4	391	Gtc/Atc	5/16	0.237533809494784	3	FACETS	0.791	0.695	0.894	0.395	0.347	0.447	SUBCLONAL	1	TRUE	1	0.325815510155654	3		559	713	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289638	15289638	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018389-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	143	710	0	ENST00000263388.2:c.3833C>G	p.Ala1278Gly	p.A1278G	ENST00000263388	NM_000435.2	1278	gCc/gGc	23/33	1	2	FACETS	0.82	0.746	0.897	0.82	0.746	0.897	CLONAL	1	TRUE	1	0.325815510155654	2		710	1071	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574077	46574077	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1202116125	NA	P-0018389-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	190	718	0	ENST00000263734.3:c.92C>T	p.Thr31Met	p.T31M	ENST00000263734	NM_001430.4	31	aCg/aTg	2/16	0.266768788101181	3	FACETS	1	0.977	1	0.575	0.531	0.622	CLONAL	1	TRUE	1	0.325815510155654	3		718	1179	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753200	128753200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018389-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	29	251	0	ENST00000377970.2:c.1361C>T	p.Ala454Val	p.A454V	ENST00000377970	NM_002467.4	454	gCg/gTg	3/3	0.234731086818216	4	FACETS	0.55	0.441	0.674	0.275	0.22	0.337	SUBCLONAL	1	TRUE	2	0.325815510155654	4		251	429	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22008925	22008925	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1456670839	NA	P-0018389-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	49	602	0	ENST00000276925.6:c.28A>C	p.Ser10Arg	p.S10R	ENST00000276925	NM_004936.3	10	Agt/Cgt	1/2	1	2	FACETS	0.342	0.289	0.401	0.342	0.289	0.401	SUBCLONAL	1	TRUE	1	0.325815510155654	2		602	879	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93629464	93629464	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018389-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	30	319	0	ENST00000375746.1:c.898A>G	p.Lys300Glu	p.K300E	ENST00000375746	NM_001174167.1	300	Aag/Gag	7/14	0.325815510155654	3	FACETS	0.39	0.313	0.477	0.195	0.156	0.239	SUBCLONAL	1	TRUE	1	0.325815510155654	3		319	549	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911143	40911143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370795038	NA	P-0018568-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	59	384	0	ENST00000373198.4:c.2162G>A	p.Arg721His	p.R721H	ENST00000373198	NM_133170.3	721	cGt/cAt	13/32	0.288444018760927	3	FACETS	0.741	0.637	0.854	0.37	0.318	0.427	SUBCLONAL	1	TRUE	1	0.288444018760927	3		384	632	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1940200	1940200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018568-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	50	148	0	ENST00000382891.5:c.1697C>T	p.Thr566Met	p.T566M	ENST00000382891	NM_133335.3	566	aCg/aTg	8/22	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.288444018760927	2		148	312	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117874084	117874084	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018568-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	32	341	0	ENST00000297338.2:c.370T>G	p.Leu124Val	p.L124V	ENST00000297338	NM_006265.2	124	Tta/Gta	4/14	1	2	FACETS	0.515	0.418	0.625	0.515	0.418	0.625	SUBCLONAL	1	TRUE	1	0.288444018760927	2		341	431	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603080	48603080	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018568-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	124	414	0	ENST00000342988.3:c.1381C>T	p.Gln461Ter	p.Q461*	ENST00000342988	NM_005359.5	461	Cag/Tag	11/12	0.278412028982543	2	FACETS	1	0.961	1	0.558	0.504	0.613	CLONAL	1	TRUE	0	0.288444018760927	2		414	771	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2110704	2110704	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018568-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1239	197	801	0	ENST00000219476.3:c.1009G>C	p.Glu337Gln	p.E337Q	ENST00000219476	NM_000548.3	337	Gag/Cag	11/42	0.249615895834319	2	FACETS	0.951	0.878	1	0.476	0.439	0.514	CLONAL	1	TRUE	0	0.288444018760927	2		801	1436	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198264981	198264981	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018568-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	45	268	0	ENST00000335508.6:c.2896C>G	p.Gln966Glu	p.Q966E	ENST00000335508	NM_012433.2	966	Caa/Gaa	19/25	1	2	FACETS	0.62	0.521	0.73	0.62	0.521	0.73	SUBCLONAL	1	TRUE	1	0.288444018760927	2		268	503	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514778	44514778	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018568-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	86	436	1	ENST00000291552.4:c.469C>T	p.Gln157Ter	p.Q157*	ENST00000291552	NM_006758.2	157	Cag/Tag	6/8	1	2	FACETS	0.744	0.657	0.836	0.744	0.657	0.836	SUBCLONAL	1	TRUE	1	0.288444018760927	2		437	802	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665353	182665353	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018568-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	26	241	0	ENST00000292782.4:c.588G>A	p.Trp196Ter	p.W196*	ENST00000292782	NM_020640.2	196	tgG/tgA	5/7	0.288444018760927	3	FACETS	0.401	0.316	0.498	0.2	0.158	0.249	SUBCLONAL	1	TRUE	1	0.288444018760927	3		241	515	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953643	38953643	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018568-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	22	167	0	ENST00000357387.3:c.2710G>C	p.Glu904Gln	p.E904Q	ENST00000357387	NM_152756.3	904	Gaa/Caa	28/38	0.288444018760927	3	FACETS	0.69	0.536	0.868	0.345	0.268	0.434	SUBCLONAL	1	TRUE	1	0.288444018760927	3		167	253	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577096	7577096	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587781525	NA	P-0019831-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	356	660	0	ENST00000269305.4:c.842A>G	p.Asp281Gly	p.D281G	ENST00000269305	NM_001126112.2	281	gAc/gGc	8/11	0.436277301608172	2	FACETS	0.978	0.935	1	0.978	0.935	1	CLONAL	2	TRUE	0	0.513300642268813	2		660	709	SUCCESS
APC	324	MSKCC	GRCh37	5	112174835	112174835	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0019831-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	94	207	0	ENST00000257430.4:c.3544A>T	p.Lys1182Ter	p.K1182*	ENST00000257430	NM_000038.5	1182	Aaa/Taa	16/16	0.513300642268813	4	FACETS	0.9	0.81	0.993			1	CLONAL	2	TRUE	NA	0.513300642268813	4		207	308	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376670	8376670	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019831-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	85	425	0	ENST00000356435.5:c.4443A>C	p.Gln1481His	p.Q1481H	ENST00000356435		1481	caA/caC	27/35	0.444033943166823	3	FACETS	0.715	0.633	0.803	0.358	0.316	0.402	SUBCLONAL	1	TRUE	1	0.513300642268813	3		425	582	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122518	17122518	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019831-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	247	492	0	ENST00000285071.4:c.877G>T	p.Glu293Ter	p.E293*	ENST00000285071	NM_144997.5	293	Gaa/Taa	9/14	0.436277301608172	2	FACETS	0.917	0.866	0.967	0.917	0.866	0.967	CLONAL	2	TRUE	0	0.513300642268813	2		492	525	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98221909	98221909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019831-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	250	493	0	ENST00000331920.6:c.2860G>T	p.Asp954Tyr	p.D954Y	ENST00000331920	NM_000264.3	954	Gac/Tac	17/24	0.444033943166823	3	FACETS	0.923	0.869	0.978	0.923	0.869	0.978	CLONAL	2	TRUE	1	0.513300642268813	3		493	663	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828539	72828539	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019831-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	130	565	0	ENST00000268489.5:c.8042A>C	p.Lys2681Thr	p.K2681T	ENST00000268489	NM_006885.3	2681	aAg/aCg	9/10	0.38197555303433	4	FACETS	0.779	0.706	0.856	0.389	0.353	0.428	SUBCLONAL	1	TRUE	2	0.513300642268813	4		565	984	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968538	55968538	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019831-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	93	390	0	ENST00000263923.4:c.2125G>T	p.Glu709Ter	p.E709*	ENST00000263923	NM_002253.2	709	Gaa/Taa	14/30	0.444033943166823	3	FACETS	0.955	0.853	1	0.477	0.426	0.532	CLONAL	1	TRUE	1	0.513300642268813	3		390	477	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0020236-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	349	602	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.943327815626329	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.943327815626329	4		602	713	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001231	150001231	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020236-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	324	461	0	ENST00000253339.5:c.2373G>C	p.Met791Ile	p.M791I	ENST00000253339		791	atG/atC	4/7	0.943327815626329	2	FACETS	0.996	0.978	1	0.996	0.978	1	CLONAL	2	TRUE	0	0.943327815626329	2		461	345	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0020591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	257	738	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.452238424187312	5	FACETS	0.956	0.896	1	0.637	0.597	0.678	CLONAL	2	TRUE	2	0.452238424187312	5		738	998	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0020591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	419	510	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	NA	2	FACETS	1	0.963	1			1	INDETERMINATE	2	TRUE	NA	0.452238424187312	2		510	920	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257644	16257644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746087066	NA	P-0020591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	191	848	0	ENST00000375759.3:c.4909G>A	p.Val1637Ile	p.V1637I	ENST00000375759	NM_015001.2	1637	Gtt/Att	11/15	0.415177705021191	4	FACETS	1	0.974	1	0.56	0.517	0.605	CLONAL	1	TRUE	2	0.452238424187312	4		848	1095	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624296	89624296	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786201995	NA	P-0020591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	159	828	0	ENST00000371953.3:c.70G>T	p.Asp24Tyr	p.D24Y	ENST00000371953	NM_000314.4	24	Gac/Tac	1/9	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.452238424187312	2		828	567	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999303	100999303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372324844	NA	P-0020591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	211	1083	1	ENST00000325455.5:c.499C>T	p.Arg167Trp	p.R167W	ENST00000325455	NM_001202474.3	167	Cgg/Tgg	1/8	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.452238424187312	2		1084	896	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028518	42028518	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	191	758	0	ENST00000219905.7:c.4056G>C	p.Leu1352Phe	p.L1352F	ENST00000219905	NM_001164273.1	1352	ttG/ttC	13/24	0.295782410920721	3	FACETS	1	0.984	1	0.608	0.563	0.655	CLONAL	1	TRUE	1	0.452238424187312	3		758	852	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346759	89346759	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs926985506	NA	P-0020591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	125	618	0	ENST00000301030.4:c.6191C>T	p.Ser2064Phe	p.S2064F	ENST00000301030	NM_001256183.1	2064	tCc/tTc	9/13	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.452238424187312	2		618	529	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588778	29588778	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	94	513	0	ENST00000356175.3:c.4564C>G	p.Leu1522Val	p.L1522V	ENST00000356175	NM_000267.3	1522	Ctt/Gtt	34/57	0.452238424187312	3	FACETS	0.798	0.71	0.89	0.399	0.355	0.445	SUBCLONAL	1	TRUE	1	0.452238424187312	3		513	639	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649096	37649096	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	182	782	0	ENST00000447079.4:c.2201G>C	p.Gly734Ala	p.G734A	ENST00000447079	NM_015083.1	734	gGa/gCa	4/14	0.452238424187312	3	FACETS	1	0.957	1	0.527	0.486	0.57	CLONAL	1	TRUE	1	0.452238424187312	3		782	936	SUCCESS
YES1	7525	MSKCC	GRCh37	18	751775	751775	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	134	854	0	ENST00000314574.4:c.301G>C	p.Asp101His	p.D101H	ENST00000314574	NM_005433.3	101	Gat/Cat	3/12	0.415177705021191	4	FACETS	0.821	0.745	0.902	0.411	0.372	0.451	CLONAL	1	TRUE	2	0.452238424187312	4		854	1048	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218092	36218092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	152	617	0	ENST00000222270.7:c.4039G>A	p.Asp1347Asn	p.D1347N	ENST00000222270	NM_014727.1	1347	Gac/Aac	15/37	0.452238424187312	3	FACETS	1	0.952	1	0.528	0.484	0.575	CLONAL	1	TRUE	1	0.452238424187312	3		617	780	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027797	48027797	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	162	611	0	ENST00000234420.5:c.2675C>G	p.Ser892Cys	p.S892C	ENST00000234420	NM_000179.2	892	tCt/tGt	4/10	0.452238424187312	4	FACETS	1	0.96	1	0.359	0.329	0.39	CLONAL	1	TRUE	1	0.452238424187312	4		611	966	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589850	212589850	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	184	1080	0	ENST00000342788.4:c.692A>G	p.His231Arg	p.H231R	ENST00000342788	NM_005235.2	231	cAt/cGt	6/28	0.295782410920721	3	FACETS	0.975	0.9	1	0.488	0.45	0.527	CLONAL	1	TRUE	1	0.452238424187312	3		1080	1023	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574817	41574817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	205	1015	1	ENST00000263253.7:c.7102G>A	p.Asp2368Asn	p.D2368N	ENST00000263253	NM_001429.3	2368	Gac/Aac	31/31	0.310508684268759	6	FACETS	1	0.984	1	0.305	0.282	0.33	CLONAL	1	TRUE	2	0.452238424187312	6		1016	1413	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184635	185184635	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	132	519	0	ENST00000265026.3:c.1527G>C	p.Lys509Asn	p.K509N	ENST00000265026	NM_004721.4	509	aaG/aaC	10/14	0.452238424187312	5	FACETS	0.98	0.888	1	0.327	0.296	0.359	CLONAL	1	TRUE	2	0.452238424187312	5		519	1000	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295040	1295040	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	29	158	1	ENST00000310581.5:c.65T>A	p.Leu22Gln	p.L22Q	ENST00000310581	NM_198253.2	22	cTg/cAg	1/16	0.452238424187312	3	FACETS	0.79	0.639	0.959	0.395	0.319	0.48	CLONAL	1	TRUE	1	0.452238424187312	3		159	199	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515594	31515594	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	52	619	0	ENST00000344624.3:c.1025A>T	p.Asp342Val	p.D342V	ENST00000344624		342	gAt/gTt	4/33	0.452238424187312	3	FACETS	0.387	0.328	0.451	0.193	0.164	0.226	SUBCLONAL	1	TRUE	1	0.452238424187312	3		619	729	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552883	106552883	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0020591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1316	230	1058	0	ENST00000369096.4:c.848T>G	p.Phe283Cys	p.F283C	ENST00000369096	NM_001198.3	283	tTt/tGt	5/7	0.280549514016606	5	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.452238424187312	5		1058	1546	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112035641	112035641	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	80	677	0	ENST00000368678.4:c.253A>G	p.Thr85Ala	p.T85A	ENST00000368678		85	Aca/Gca	4/13	0.280549514016606	5	FACETS	0.618	0.542	0.699			1	SUBCLONAL	1	TRUE	NA	0.452238424187312	5		677	961	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69030873	69030873	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	200	537	0	ENST00000288368.4:c.3415G>A	p.Asp1139Asn	p.D1139N	ENST00000288368	NM_024870.2	1139	Gac/Aac	27/40	0.452238424187312	4	FACETS	0.908	0.845	0.974	0.606	0.563	0.649	CLONAL	2	TRUE	1	0.452238424187312	4		537	707	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911569	101911569	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	148	777	0	ENST00000374994.4:c.1494G>C	p.Gln498His	p.Q498H	ENST00000374994	NM_004612.2	498	caG/caC	9/9	0.278649340159497	3	FACETS	0.991	0.906	1	0.495	0.453	0.54	CLONAL	1	TRUE	1	0.452238424187312	3		777	810	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152864439	152864439	+	synonymous_variant	Silent	SNP	C	C	A	novel	NA	P-0020591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	61	148	0	ENST00000406277.2:c.87G>T	p.Ala29=	p.A29=	ENST00000406277	NM_152274.4	29	gcG/gcT	3/7	0.452238424187312		FACETS		0.92	1				CLONAL	1	TRUE	NA	0.452238424187312	2		148	251	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023078	150023095	+	frameshift_variant	Frame_Shift_Del	DEL	GGATCTTCGGTTGACATT	GGATCTTCGGTTGACATT	A	novel	NA	P-0020591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	168	1005	0	ENST00000253339.5:c.168_185delinsT	p.Lys56AsnfsTer15	p.K56Nfs*15	ENST00000253339		56	aaAATGTCAACCGAAGATCCt/aaTt	1/7	0.452238424187312	3	FACETS	0.88	0.808	0.955	0.44	0.404	0.478	CLONAL	1	TRUE	1	0.452238424187312	3		1005	1035	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939269	71939271	+	frameshift_variant	Frame_Shift_Del	DEL	CTG	CTG	T	novel	NA	P-0020591-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	225	1060	0	ENST00000298229.2:c.218_220delinsT	p.Pro73LeufsTer24	p.P73Lfs*24	ENST00000298229	NM_001567.3	73	cCTGat/cTat	2/28	1	2	FACETS	0.96	0.894	1	0.96	0.894	1	CLONAL	1	TRUE	1	0.452238424187312	2		1060	1037	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073348	8073348	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	161	615	0	ENST00000377482.5:c.1311A>T	p.Glu437Asp	p.E437D	ENST00000377482	NM_018948.3	437	gaA/gaT	4/4	0.862177388297621	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.845069823000548	1		615	195	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272472	11272472	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	198	690	0	ENST00000361445.4:c.3458C>G	p.Ser1153Cys	p.S1153C	ENST00000361445	NM_004958.3	1153	tCc/tGc	23/58	0.862177388297621	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.845069823000548	1		690	232	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023229	27023229	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	237	304	0	ENST00000324856.7:c.337del	p.Leu113Ter	p.L113*	ENST00000324856	NM_006015.4	112	gCc/gc	1/20	0.669280669690066	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.845069823000548	1		304	262	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999149	100999149	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	441	826	0	ENST00000325455.5:c.653C>G	p.Ala218Gly	p.A218G	ENST00000325455	NM_001202474.3	218	gCg/gGg	1/8	0.862177388297621	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.845069823000548	1		826	542	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562525	21562525	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	34	65	0	ENST00000382592.4:c.1394G>A	p.Trp465Ter	p.W465*	ENST00000382592	NM_014572.2	465	tGg/tAg	4/8	0.862177388297621	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.845069823000548	1		65	40	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937558	32937558	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0020719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	170	717	0	ENST00000380152.3:c.8219T>G	p.Leu2740Ter	p.L2740*	ENST00000380152		2740	tTa/tGa	18/27	0.862177388297621	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.845069823000548	1		717	205	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923460	9923460	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	121	667	2	ENST00000330684.3:c.1827G>T	p.Trp609Cys	p.W609C	ENST00000330684	NM_001134407.1	609	tgG/tgT	9/13	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.845069823000548	2		669	270	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320755	30321615	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATTAAAGAGAATATCTCTAATTTGATTTTCCGCTTAAATTTTTTAAACTATTTTTAGAAGTGATATTTAAACAAAATATCTTGTTATGCGTAAATTGGAGATTTGCTTTTTTTTTTTAATTGTTTTTAGTTTCTCTATAACAACAATACAAGGCAACAAACTGAAGCAAGAGATGACCTGCATTGCCCTTGGTGTACTCTGAACTGCCGCAAACTTTATAGTTTACTCAAGCATCTTAAACTCTGCCATAGCAGATTTATCTTCAACTATGTTGTGAGTAATTTTTCATATTTTCTCAATTTGTGTTAAGAAATCTCTTGTACCCCATAAATATATACATCTATGTACCCACAAAAATTTTTTAAATTAAAAAAGGGAAAAAATATGCATTAAGTACAAGATAGCATGACTTTCAAAAATTGTACTTTGTATAAAAAACAAATTTCTGTATTTGATAGATTGCCGTATATATGGATTACAGTGAATGATTCAGAGTTGACATATATTTGGAATTATAATTAATGTTTGTGTAGTGTCTCTAATTGACTCACAAAATCCTCAACCAACTCTTTGAATTAAATGATAATTTTCTTATTCTTGCTCAACCAAGAAATAATTTGTACAAAGTCACCAAGCAATAAATGACATAGTTAAGATTTTAACACATTTTGTTGACCCCAGGTCTTCTGACTGCCTGTTTACCATGCTGGTGTGCCTGGCCTATTTTAGTTTTCTAAATATTAAGAGCCCACAAATTCTTTAATTAAATTGGAGGGATATTTAGGATAGGATACTTAATATATTTTTTTTTTTACATTTTTGTTGCAGTATCATCCAAAAGGTGCTAGGATAGATGTTTCT	ATTAAAGAGAATATCTCTAATTTGATTTTCCGCTTAAATTTTTTAAACTATTTTTAGAAGTGATATTTAAACAAAATATCTTGTTATGCGTAAATTGGAGATTTGCTTTTTTTTTTTAATTGTTTTTAGTTTCTCTATAACAACAATACAAGGCAACAAACTGAAGCAAGAGATGACCTGCATTGCCCTTGGTGTACTCTGAACTGCCGCAAACTTTATAGTTTACTCAAGCATCTTAAACTCTGCCATAGCAGATTTATCTTCAACTATGTTGTGAGTAATTTTTCATATTTTCTCAATTTGTGTTAAGAAATCTCTTGTACCCCATAAATATATACATCTATGTACCCACAAAAATTTTTTAAATTAAAAAAGGGAAAAAATATGCATTAAGTACAAGATAGCATGACTTTCAAAAATTGTACTTTGTATAAAAAACAAATTTCTGTATTTGATAGATTGCCGTATATATGGATTACAGTGAATGATTCAGAGTTGACATATATTTGGAATTATAATTAATGTTTGTGTAGTGTCTCTAATTGACTCACAAAATCCTCAACCAACTCTTTGAATTAAATGATAATTTTCTTATTCTTGCTCAACCAAGAAATAATTTGTACAAAGTCACCAAGCAATAAATGACATAGTTAAGATTTTAACACATTTTGTTGACCCCAGGTCTTCTGACTGCCTGTTTACCATGCTGGTGTGCCTGGCCTATTTTAGTTTTCTAAATATTAAGAGCCCACAAATTCTTTAATTAAATTGGAGGGATATTTAGGATAGGATACTTAATATATTTTTTTTTTTACATTTTTGTTGCAGTATCATCCAAAAGGTGCTAGGATAGATGTTTCT	-	novel	NA	P-0020719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	165	41	0	ENST00000322652.5:c.1294-127_1472del		p.X432_splice	ENST00000322652	NM_015355.2	432		12-13/16	0.200419632770505	4	FACETS	0.924	0.888	0.956	1	0.995	1	INDETERMINATE	4	TRUE	2	0.845069823000548	4		41	195	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19261500	19261500	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	176	725	0	ENST00000162023.5:c.45G>C	p.Arg15Ser	p.R15S	ENST00000162023		15	agG/agC	6/13	0.433448313964483	1	FACETS	0.37	0.342	0.399	0.37	0.342	0.399	INDETERMINATE	1	TRUE	0	0.845069823000548	1		725	650	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436801	52436803	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0020719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	304	696	0	ENST00000460680.1:c.1975_1977del	p.Lys659del	p.K659del	ENST00000460680	NM_004656.3	659	AAG/-	15/17	0.862177388297621	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.845069823000548	1		696	384	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995607	68995607	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0020719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	73	698	0	ENST00000288368.4:c.2011A>C	p.Ser671Arg	p.S671R	ENST00000288368	NM_024870.2	671	Agc/Cgc	18/40	0.862177388297621	4	FACETS	0.648	0.568	0.734			1	SUBCLONAL	1	TRUE	NA	0.845069823000548	4		698	492	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15822304	15822304	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	35	533	1	ENST00000307771.7:c.383A>T	p.Glu128Val	p.E128V	ENST00000307771	NM_005089.3	128	gAg/gTg	5/11	NA	2	FACETS	0.169	0.138	0.204			1	INDETERMINATE	1	TRUE	NA	0.845069823000548	2		534	489	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938788	76938788	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020719-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	165	833	3	ENST00000373344.5:c.1960C>T	p.Arg654Ter	p.R654*	ENST00000373344	NM_000489.3	654	Cga/Tga	9/35	0.233794018320814	3	FACETS	0.8	0.747	0.854	0.8	0.747	0.854	INDETERMINATE	2	TRUE	1	0.845069823000548	3		836	347	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0020986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	296	269	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.241400891021639	5	FACETS	1	0.987	1	0.765	0.722	0.809	INDETERMINATE	2	TRUE	2	0.478347876957874	5		269	926	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0020986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	440	820	1	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.478347876957874	3	FACETS	0.877	0.842	0.912	0.877	0.842	0.912	CLONAL	3	TRUE	0	0.478347876957874	3		821	866	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220640	1220640	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690940	NA	P-0020986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	496	831	0	ENST00000326873.7:c.658C>T	p.Gln220Ter	p.Q220*	ENST00000326873	NM_000455.4	220	Cag/Tag	5/10	0.322345112503256	3	FACETS	0.987	0.952	1			1	CLONAL	3	TRUE	NA	0.478347876957874	3		831	868	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910801	114910801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1336546841	NA	P-0020986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	161	750	1	ENST00000543371.1:c.920C>T	p.Thr307Met	p.T307M	ENST00000543371	NM_001198531.1	307	aCg/aTg	9/14	0.285237626233708	4	FACETS	1	0.978	1	0.593	0.544	0.644	INDETERMINATE	1	TRUE	2	0.478347876957874	4		751	839	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154444	2154444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0020986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	118	729	1	ENST00000434045.2:c.484C>T	p.Pro162Ser	p.P162S	ENST00000434045	NM_001127598.1	162	Ccc/Tcc	5/5	0.478347876957874	3	FACETS	0.978	0.885	1	0.489	0.442	0.539	CLONAL	1	TRUE	1	0.478347876957874	3		730	625	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475197	475203	+	frameshift_variant	Frame_Shift_Del	DEL	CCCAAGC	CCCAAGC	-	novel	NA	P-0020986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	112	911	4	ENST00000399788.2:c.434_440del	p.Arg145HisfsTer12	p.R145Hfs*12	ENST00000399788	NM_001042603.1	145	cGCTTGGGa/ca	4/28	0.241400891021639	5	FACETS	0.826	0.741	0.915	0.275	0.247	0.305	INDETERMINATE	1	TRUE	2	0.478347876957874	5		915	974	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383360	4383360	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	258	769	0	ENST00000261254.3:c.154C>T	p.Gln52Ter	p.Q52*	ENST00000261254	NM_001759.3	52	Caa/Taa	1/5	0.241400891021639	5	FACETS	1	0.958	1	0.684	0.642	0.727	INDETERMINATE	2	TRUE	2	0.478347876957874	5		769	903	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135322	2135322	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0020986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	243	720	0	ENST00000219476.3:c.4661A>G	p.Gln1554Arg	p.Q1554R	ENST00000219476	NM_000548.3	1554	cAg/cGg	36/42	0.478347876957874	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.478347876957874	2		720	493	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554420	63554420	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	153	737	0	ENST00000307078.5:c.319A>T	p.Thr107Ser	p.T107S	ENST00000307078	NM_004655.3	107	Acc/Tcc	2/11	0.478347876957874	3	FACETS	0.998	0.914	1	0.499	0.457	0.543	CLONAL	1	TRUE	1	0.478347876957874	3		737	794	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610094	10610094	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	440	820	0	ENST00000171111.5:c.616T>A	p.Tyr206Asn	p.Y206N	ENST00000171111	NM_203500.1	206	Tac/Aac	2/6	0.478347876957874	3	FACETS	0.955	0.918	0.991	0.955	0.918	0.991	CLONAL	3	TRUE	0	0.478347876957874	3		820	796	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015220	128015220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	383	668	1	ENST00000285398.2:c.2301G>T	p.Lys767Asn	p.K767N	ENST00000285398	NM_000122.1	767	aaG/aaT	15/15	0.478347876957874	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	2	0.478347876957874	4		669	974	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527748	157527760	+	frameshift_variant	Frame_Shift_Del	DEL	GACACCACCGAGC	GACACCACCGAGC	-	novel	NA	P-0020986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	234	609	0	ENST00000346085.5:c.5473_5485del	p.Asp1825ThrfsTer22	p.D1825Tfs*22	ENST00000346085	NM_020732.3	1825	GACACCACCGAGCac/ac	20/20	0.478347876957874	2	FACETS	0.952	0.897	1	0.952	0.897	1	CLONAL	2	TRUE	0	0.478347876957874	2		609	514	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2949690	2949690	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	305	856	0	ENST00000396946.4:c.3254G>T	p.Arg1085Met	p.R1085M	ENST00000396946	NM_032415.4	1085	aGg/aTg	24/25	0.424422415349923	4	FACETS	0.973	0.919	1	0.973	0.919	1	CLONAL	2	TRUE	2	0.478347876957874	4		856	969	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339462	81339463	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	GA	novel	NA	P-0020986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	164	488	2	ENST00000222390.5:c.1541_1541+1delinsTC		p.X514_splice	ENST00000222390	NM_000601.4	514		13/18	0.424422415349923	4	FACETS	0.81	0.746	0.875	0.81	0.746	0.875	CLONAL	2	TRUE	2	0.478347876957874	4		490	626	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526602	106526602	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	208	589	0	ENST00000359195.3:c.2895C>A	p.Phe965Leu	p.F965L	ENST00000359195	NM_002649.2	965	ttC/ttA	10/11	0.424422415349923	4	FACETS	0.899	0.838	0.962	0.899	0.838	0.962	CLONAL	2	TRUE	2	0.478347876957874	4		589	715	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737126	145737126	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0020986-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	317	811	1	ENST00000428558.2:c.3440T>A	p.Leu1147Gln	p.L1147Q	ENST00000428558	NM_004260.3	1147	cTg/cAg	21/22	0.424422415349923	4	FACETS	0.985	0.931	1	0.985	0.931	1	CLONAL	2	TRUE	2	0.478347876957874	4		812	995	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0021014-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1252	123	866	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	1	2	FACETS	0.778	0.701	0.86	0.778	0.701	0.86	SUBCLONAL	1	TRUE	1	0.23	2		866	1375	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0021053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	226	381	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.375780390240524	2	FACETS	0.772	0.723	0.822	0.772	0.723	0.822	SUBCLONAL	2	TRUE	0	0.451892829861822	2		381	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659675	NA	P-0021053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	139	1123	2	ENST00000269305.4:c.764T>C	p.Ile255Thr	p.I255T	ENST00000269305	NM_001126112.2	255	aTc/aCc	7/11	0.451892829861822	1	FACETS	0.827	0.756	0.901	0.827	0.756	0.901	CLONAL	1	TRUE	0	0.451892829861822	1		1125	576	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310820	123310820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747502397	NA	P-0021053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	116	1065	2	ENST00000358487.5:c.608G>A	p.Arg203His	p.R203H	ENST00000358487	NM_000141.4	203	cGc/cAc	5/18	0.246557593492251	1	FACETS	0.576	0.52	0.635	0.576	0.52	0.635	INDETERMINATE	1	TRUE	0	0.451892829861822	1		1067	690	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76814303	76814306	+	frameshift_variant	Frame_Shift_Del	DEL	ATAA	ATAA	-	novel	NA	P-0021053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	75	649	0	ENST00000373344.5:c.6338_6341del	p.Phe2113SerfsTer9	p.F2113Sfs*9	ENST00000373344	NM_000489.3	2113	tTTATc/tc	29/35	0.181726134478716	2	FACETS	0.611	0.536	0.692	0.306	0.268	0.346	INDETERMINATE	1	TRUE	0	0.451892829861822	2		649	543	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483931	212483931	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs182073178	NA	P-0021053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	108	1115	0	ENST00000342788.4:c.2272G>T	p.Gly758Cys	p.G758C	ENST00000342788	NM_005235.2	758	Ggt/Tgt	19/28	0.246557593492251	1	FACETS	0.535	0.481	0.593	0.535	0.481	0.593	INDETERMINATE	1	TRUE	0	0.451892829861822	1		1115	691	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198448	108198448	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0021053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	92	856	0	ENST00000278616.4:c.7052A>G	p.Glu2351Gly	p.E2351G	ENST00000278616	NM_000051.3	2351	gAa/gGa	48/63	1	2	FACETS	0.645	0.574	0.721	0.645	0.574	0.721	SUBCLONAL	1	TRUE	1	0.451892829861822	2		856	631	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	441034	441034	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	52	767	0	ENST00000399788.2:c.1724A>C	p.Asn575Thr	p.N575T	ENST00000399788	NM_001042603.1	575	aAc/aCc	13/28	NA	2	FACETS	0.338	0.287	0.395			1	INDETERMINATE	1	TRUE	NA	0.451892829861822	2		767	680	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425085	49425095	+	frameshift_variant	Frame_Shift_Del	DEL	CGGAGTAGCTT	CGGAGTAGCTT	-	novel	NA	P-0021053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	88	1189	0	ENST00000301067.7:c.13393_13403del	p.Lys4465GlyfsTer18	p.K4465Gfs*18	ENST00000301067	NM_003482.3	4465	AAGCTACTCCGg/g	39/54	0.375780390240524	2	FACETS	0.466	0.412	0.524	0.233	0.206	0.262	SUBCLONAL	1	TRUE	0	0.451892829861822	2		1189	835	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514746	103514746	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	112	614	0	ENST00000355739.4:c.1247C>G	p.Ala416Gly	p.A416G	ENST00000355739	NM_000123.3	416	gCa/gGa	8/15	0.181726134478716	2	FACETS	1	0.935	1	0.522	0.472	0.574	INDETERMINATE	1	TRUE	0	0.451892829861822	2		614	475	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636833	2636833	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0021053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	52	1152	1	ENST00000342085.4:c.1282T>G	p.Leu428Val	p.L428V	ENST00000342085	NM_002613.4	428	Tta/Gta	11/14	0.427700905506587	1	FACETS	0.215	0.182	0.251	0.215	0.182	0.251	SUBCLONAL	1	TRUE	0	0.451892829861822	1		1153	828	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736963	736963	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0021053-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	53	624	0	ENST00000314574.4:c.1138-2A>T		p.X380_splice	ENST00000314574	NM_005433.3	380			0.216290335060038	3	FACETS	0.471	0.401	0.548			1	INDETERMINATE	1	TRUE	NA	0.451892829861822	3		624	610	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0021457-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	134	372	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.88	2		372	303	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0021457-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	366	522	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.16691926824002	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.88	0		522	870	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0021790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	207	813	2	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.411430292633233	2		815	933	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438491	52438491	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	156	699	1	ENST00000460680.1:c.1228C>T	p.Gln410Ter	p.Q410*	ENST00000460680	NM_004656.3	410	Cag/Tag	12/17	1	2	FACETS	0.97	0.889	1	0.97	0.889	1	CLONAL	1	TRUE	1	0.411430292633233	2		700	782	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413610	32413610	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	86	409	0	ENST00000332351.3:c.1340G>T	p.Gly447Val	p.G447V	ENST00000332351	NM_024426.4	447	gGt/gTt	9/10	1	2	FACETS	0.965	0.858	1	0.965	0.858	1	CLONAL	1	TRUE	1	0.411430292633233	2		409	433	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211453	46211481	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	ATTATCTGCGTCAAAGTTATGGGCTGTCC	ATTATCTGCGTCAAAGTTATGGGCTGTCC	-	novel	NA	P-0021790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	29	250	0	ENST00000334344.6:c.421_449del	p.Tyr141GlyfsTer3	p.Y141Gfs*3	ENST00000334344	NM_152641.2	140	gATTATCTGCGTCAAAGTTATGGGCTGTCC/g	5/21	1	2	FACETS	0.701	0.567	0.852	0.701	0.567	0.852	SUBCLONAL	1	TRUE	1	0.411430292633233	2		250	201	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715951	52715951	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1568593911	NA	P-0021790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	111	674	0	ENST00000322088.6:c.516C>G	p.Asn172Lys	p.N172K	ENST00000322088	NM_014225.5	172	aaC/aaG	5/15	1	2	FACETS	0.889	0.801	0.982	0.889	0.801	0.982	CLONAL	1	TRUE	1	0.411430292633233	2		674	607	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162525	47162525	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0021790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	90	411	0	ENST00000409792.3:c.3601G>T	p.Glu1201Ter	p.E1201*	ENST00000409792	NM_014159.6	1201	Gag/Tag	3/21	1	2	FACETS	0.966	0.861	1	0.966	0.861	1	CLONAL	1	TRUE	1	0.411430292633233	2		411	453	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430227	181430227	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0021790-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	136	501	0	ENST00000325404.1:c.79G>T	p.Ala27Ser	p.A27S	ENST00000325404	NM_003106.3	27	Gcg/Tcg	1/1	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.411430292633233	2		501	529	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0021793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	54	566	1	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	0.486251983537411	1	FACETS	0.695	0.599	0.796	0.695	0.599	0.796	SUBCLONAL	1	TRUE	0	0.486251983537411	1		567	242	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0021793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	64	290	2	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.486251983537411	2		292	185	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86658425	86658425	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0021793-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	10	257	0	ENST00000274376.6:c.1390C>T	p.Arg464Cys	p.R464C	ENST00000274376	NM_002890.2	464	Cgt/Tgt	10/25	1	2	FACETS	0.274	0.186	0.384	0.274	0.186	0.384	SUBCLONAL	1	TRUE	1	0.486251983537411	2		257	150	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115973	8115974	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0023797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	55	350	0	ENST00000346208.3:c.1319_1320del	p.Thr440SerfsTer66	p.T440Sfs*66	ENST00000346208		440	aCC/a	6/6	0.303996679410338	1	FACETS	0.511	0.438	0.592	0.511	0.438	0.592	SUBCLONAL	1	TRUE	0	0.341099712708195	1		350	523	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336157	73336157	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	54	220	0	ENST00000377767.4:c.2246T>C	p.Met749Thr	p.M749T	ENST00000377767	NM_014953.3	749	aTg/aCg	17/21	0.341099712708195	1	FACETS	0.732	0.627	0.844	0.732	0.627	0.844	SUBCLONAL	1	TRUE	0	0.341099712708195	1		220	359	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570416	95570416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0023797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	113	234	1	ENST00000393063.1:c.3317C>T	p.Ser1106Phe	p.S1106F	ENST00000393063	NM_030621.3	1106	tCt/tTt	22/28	0.288232008077973	3	FACETS	0.752	0.679	0.827	0.752	0.679	0.827	SUBCLONAL	2	TRUE	1	0.341099712708195	3		235	516	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42026719	42026719	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0023797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	54	337	0	ENST00000219905.7:c.3844-1G>T		p.X1282_splice	ENST00000219905	NM_001164273.1	1282			1	2	FACETS	0.504	0.43	0.585	0.504	0.43	0.585	SUBCLONAL	1	TRUE	1	0.341099712708195	2		337	628	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400015	49400015	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0023797-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	100	580	0	ENST00000418115.1:c.322C>A	p.Pro108Thr	p.P108T	ENST00000418115	NM_001664.2	108	Ccc/Acc	4/5	0.303996679410338	1	FACETS	0.555	0.495	0.618	0.555	0.495	0.618	SUBCLONAL	1	TRUE	0	0.341099712708195	1		580	877	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0024083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	407	607	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.25813051283171	5	FACETS	1	0.98	1	0.838	0.8	0.877	CLONAL	4	FALSE	0	0.25813051283171	5		607	1044	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71936091	71936091	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	35	90	0	ENST00000298229.2:c.63G>A	p.Trp21Ter	p.W21*	ENST00000298229	NM_001567.3	21	tgG/tgA	1/28	0.258501559377217	4	FACETS	0.992	0.823	1	0.992	0.823	1	CLONAL	2	FALSE	2	0.25813051283171	4		90	172	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149793	202149793	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs773127303	NA	P-0024083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	188	712	0	ENST00000358485.4:c.1234A>G	p.Lys412Glu	p.K412E	ENST00000358485	NM_001080125.1	412	Aaa/Gaa	8/9	0.25813051283171	5	FACETS	0.778	0.717	0.842	0.519	0.478	0.562	SUBCLONAL	2	FALSE	2	0.25813051283171	5		712	1298	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730904	40730904	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	211	644	0	ENST00000373198.4:c.3631G>C	p.Glu1211Gln	p.E1211Q	ENST00000373198	NM_133170.3	1211	Gag/Cag	27/32	0.258501559377217	4	FACETS	0.991	0.92	1	0.991	0.92	1	CLONAL	2	FALSE	2	0.25813051283171	4		644	1038	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186507023	186507023	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024083-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	58	283	0	ENST00000323963.5:c.1189G>T	p.Glu397Ter	p.E397*	ENST00000323963		397	Gag/Tag	11/11	0.258501559377217	4	FACETS	1	0.956	1	0.323	0.278	0.372	CLONAL	1	FALSE	0	0.25813051283171	4		283	437	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0025906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	278	372	0				ENST00000310581	NM_198253.2	-/1132			0.496541669643095	3	FACETS	0.973	0.921	1			1	CLONAL	2	TRUE	NA	0.601701619385446	3		372	618	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0025906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	119	377	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.911	0.829	0.997	0.911	0.829	0.997	CLONAL	1	TRUE	1	0.601701619385446	2		377	434	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0025906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	158	522	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.989	0.912	1	0.989	0.912	1	CLONAL	1	TRUE	1	0.601701619385446	2		522	531	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0025906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	192	564	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.601701619385446	2		564	637	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974770	21974775	+	inframe_deletion	In_Frame_Del	DEL	GGCCGT	GGCCGT	-	novel	NA	P-0025906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	76	260	0	ENST00000304494.5:c.52_57del	p.Thr18_Ala19del	p.T18_A19del	ENST00000304494	NM_000077.4	18	ACGGCC/-	1/3	0.601701619385446	1	FACETS	0.93	0.833	1	0.93	0.833	1	CLONAL	1	TRUE	0	0.601701619385446	1		260	190	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557669	95557669	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0025906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	172	437	0	ENST00000393063.1:c.5398G>C	p.Glu1800Gln	p.E1800Q	ENST00000393063	NM_030621.3	1800	Gag/Cag	26/28	1	2	FACETS	0.958	0.886	1	0.958	0.886	1	CLONAL	1	TRUE	1	0.601701619385446	2		437	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574004	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0025906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	324	753	1	ENST00000269305.4:c.1023_1024del	p.Phe341LeufsTer5	p.F341Lfs*5	ENST00000269305	NM_001126112.2	341	ttCCga/ttga	10/11	0.601701619385446	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.601701619385446	1		754	685	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78882682	78882682	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	282	653	0	ENST00000306801.3:c.2473G>C	p.Glu825Gln	p.E825Q	ENST00000306801	NM_020761.2	825	Gag/Cag	21/34	1	2	FACETS	0.965	0.909	1	0.965	0.909	1	CLONAL	1	TRUE	1	0.601701619385446	2		653	971	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298144	15298144	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0025906-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	278	743	0	ENST00000263388.2:c.1612G>T	p.Glu538Ter	p.E538*	ENST00000263388	NM_000435.2	538	Gag/Tag	11/33	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.601701619385446	2		743	841	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0025912-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	116	290	2	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.280875019131372	3	FACETS	0.811	0.735	0.89	0.811	0.735	0.89	CLONAL	2	FALSE	1	0.346042819833708	3		292	485	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349350	89349350	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025912-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	183	687	0	ENST00000301030.4:c.3600A>T	p.Lys1200Asn	p.K1200N	ENST00000301030	NM_001256183.1	1200	aaA/aaT	9/13	0.304373480002715	3	FACETS	1	0.98	1	0.394	0.363	0.426	CLONAL	1	FALSE	0	0.346042819833708	3		687	1050	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577035	7577036	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0025912-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	350	612	0	ENST00000269305.4:c.902dup	p.Gly302ArgfsTer4	p.G302Rfs*4	ENST00000269305	NM_001126112.2	301	cca/ccCa	8/11	0.304373480002715	3	FACETS	0.849	0.806	0.892	0.849	0.806	0.892	CLONAL	3	FALSE	0	0.346042819833708	3		612	932	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252941	36252943	+	inframe_deletion	In_Frame_Del	DEL	AGT	AGT	-	novel	NA	P-0025912-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	73	414	0	ENST00000300305.3:c.419_421del	p.Tyr140del	p.Y140del	ENST00000300305		140	tACTcg/tcg	4/8	0.280875019131372	3	FACETS	0.874	0.766	0.991	0.437	0.383	0.496	CLONAL	1	FALSE	1	0.346042819833708	3		414	566	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696178	52696178	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025912-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	67	498	0	ENST00000394830.3:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000394830	NM_018313.4	167	Caa/Taa	5/30	0.265468378297609	3	FACETS	0.57	0.494	0.652	0.19	0.164	0.218	SUBCLONAL	1	FALSE	0	0.346042819833708	3		498	797	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186826	142186826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025912-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	49	271	0	ENST00000350721.4:c.6637G>A	p.Gly2213Arg	p.G2213R	ENST00000350721	NM_001184.3	2213	Gga/Aga	39/47	0.304373480002715	3	FACETS	0.595	0.504	0.696	0.198	0.168	0.232	SUBCLONAL	1	FALSE	0	0.346042819833708	3		271	558	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526639	106526639	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025912-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	161	383	0	ENST00000359195.3:c.2932A>T	p.Ile978Phe	p.I978F	ENST00000359195	NM_002649.2	978	Att/Ttt	10/11	0.346042819833708	3	FACETS	0.832	0.766	0.901	0.832	0.766	0.901	CLONAL	2	FALSE	1	0.346042819833708	3		383	656	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27172718	27172718	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025912-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	149	453	0	ENST00000380036.4:c.733G>T	p.Gly245Trp	p.G245W	ENST00000380036	NM_000459.3	245	Ggg/Tgg	5/23	0.346042819833708	2	FACETS	0.751	0.69	0.815	0.751	0.69	0.815	SUBCLONAL	2	FALSE	0	0.346042819833708	2		453	573	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223540	53223541	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0025912-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	94	421	0	ENST00000375401.3:c.3818_3819del	p.Pro1273ArgfsTer26	p.P1273Rfs*26	ENST00000375401	NM_004187.3	1273	cCC/c	23/26	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	FALSE	NA	0.346042819833708	2		421	382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0025994-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	346	537	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.568950525242361	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.592661109327719	1		537	813	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9786991	9786991	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025994-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	175	532	0	ENST00000377346.4:c.3022G>A	p.Glu1008Lys	p.E1008K	ENST00000377346	NM_005026.3	1008	Gag/Aag	24/24	1	2	FACETS	0.807	0.745	0.871	0.807	0.745	0.871	CLONAL	1	TRUE	1	0.592661109327719	2		532	732	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417858	138417858	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025994-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	130	413	1	ENST00000289153.2:c.1661A>G	p.Glu554Gly	p.E554G	ENST00000289153	NM_006219.2	554	gAa/gGa	11/22	1	2	FACETS	0.962	0.879	1	0.962	0.879	1	CLONAL	1	TRUE	1	0.592661109327719	2		414	456	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683404	182683404	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025994-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	84	363	0	ENST00000292782.4:c.141T>A	p.Asn47Lys	p.N47K	ENST00000292782	NM_020640.2	47	aaT/aaA	2/7	1	2	FACETS	0.914	0.816	1	0.914	0.816	1	CLONAL	1	TRUE	1	0.592661109327719	2		363	310	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230818	66230818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs910705978	NA	P-0025994-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	83	341	0	ENST00000273854.3:c.2153G>A	p.Arg718His	p.R718H	ENST00000273854	NM_004439.5	718	cGc/cAc	12/18	1	2	FACETS	0.966	0.862	1	0.966	0.862	1	CLONAL	1	TRUE	1	0.592661109327719	2		341	290	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847283	68847283	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026304-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	70	268	0	ENST00000261769.5:c.1205A>T	p.Asp402Val	p.D402V	ENST00000261769	NM_004360.3	402	gAt/gTt	9/16	1	2	FACETS	1	0.938	1	1	0.983	1	CLONAL	2	TRUE	1	0.14	2		268	446	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0026306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	182	287	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.469394329858202	4	FACETS	0.855	0.796	0.915	0.855	0.796	0.915	CLONAL	2	TRUE	2	0.760049528608022	4		287	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0026306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	456	779	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.742608564990152	3	FACETS	0.984	0.959	1			1	CLONAL	3	TRUE	NA	0.760049528608022	3		781	561	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292925	91292942	+	inframe_deletion	In_Frame_Del	DEL	TCTTCACCAGATTCTTTA	TCTTCACCAGATTCTTTA	-	novel	NA	P-0026306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	303	306	0	ENST00000355112.3:c.427_444del	p.Ser144_Ser149del	p.S144_S149del	ENST00000355112	NM_000057.2	143	TCTTCACCAGATTCTTTA/-	3/22	0.752337397402939	3	FACETS	0.978	0.948	1	0.978	0.948	1	CLONAL	3	TRUE	0	0.760049528608022	3		306	375	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798773	42798773	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269420975	NA	P-0026306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	326	357	0	ENST00000575354.2:c.4345G>A	p.Val1449Met	p.V1449M	ENST00000575354	NM_015125.3	1449	Gtg/Atg	19/20	0.529804941831796	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	2	0.760049528608022	4		357	749	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280813	41280813	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	140	140	0	ENST00000349496.5:c.2326T>C	p.Trp776Arg	p.W776R	ENST00000349496	NM_001904.3	776	Tgg/Cgg	15/15	0.694540073430153	3	FACETS	0.985	0.918	1	0.985	0.918	1	CLONAL	2	TRUE	1	0.760049528608022	3		140	258	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0026306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	61	229	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	0.694540073430153	3	FACETS	0.865	0.755	0.983	0.433	0.377	0.492	CLONAL	1	TRUE	1	0.760049528608022	3		229	256	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0026306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	126	266	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	0.694540073430153	3	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	1	0.760049528608022	3		266	227	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123026612	123026612	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026306-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	99	291	2	ENST00000355640.3:c.1088C>A	p.Thr363Asn	p.T363N	ENST00000355640		363	aCt/aAt	5/7	0.749552515569984	5	FACETS	0.63	0.561	0.703			1	SUBCLONAL	1	TRUE	NA	0.760049528608022	5		293	885	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0026653-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	604	399	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.759250224467795	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	FALSE	0	0.77777333212038	3		399	710	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0026653-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	1210	290	2	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.77777333212038	15	FACETS	1	0.997	1			1	CLONAL	13	FALSE	NA	0.77777333212038	15		292	1401	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205217	46205217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026653-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	86	276	0	ENST00000334344.6:c.301G>A	p.Glu101Lys	p.E101K	ENST00000334344	NM_152641.2	101	Gag/Aag	4/21	0.77777333212038	3	FACETS	1	0.942	1	0.539	0.482	0.598	CLONAL	1	FALSE	1	0.77777333212038	3		276	285	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874147	151874148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs747256476	NA	P-0026653-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	83	480	8	ENST00000262189.6:c.8390dup	p.Glu2798GlyfsTer11	p.E2798Gfs*11	ENST00000262189	NM_170606.2	2797	aag/aaAg	38/59	0.77777333212038	3	FACETS	1	0.962	1	0.584	0.522	0.647	CLONAL	1	FALSE	1	0.77777333212038	3		488	254	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030410	49030410	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026653-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	77	352	0	ENST00000267163.4:c.1885G>T	p.Glu629Ter	p.E629*	ENST00000267163	NM_000321.2	629	Gag/Tag	19/27	0.681564142447075	1	FACETS	0.858	0.78	0.936	0.858	0.78	0.936	CLONAL	1	FALSE	0	0.77777333212038	1		352	141	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945054	31945054	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026653-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	184	679	1	ENST00000340398.3:c.47C>A	p.Ala16Asp	p.A16D	ENST00000340398	NM_001013699.2	16	gCc/gAc	1/1	0.77777333212038	3	FACETS	1	0.952	1	0.517	0.48	0.556	CLONAL	1	FALSE	1	0.77777333212038	3		680	635	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744007	41744007	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026653-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	335	775	0	ENST00000301178.4:c.942C>A	p.Ser314Arg	p.S314R	ENST00000301178	NM_021913.4	314	agC/agA	7/20	0.111809593468151	5	FACETS	0.918	0.875	0.96			1	INDETERMINATE	3	FALSE	NA	0.77777333212038	5		775	678	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281684	142281684	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026653-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	75	371	0	ENST00000350721.4:c.560G>C	p.Gly187Ala	p.G187A	ENST00000350721	NM_001184.3	187	gGa/gCa	4/47	0.724514930670685	5	FACETS	0.813	0.714	0.919			1	CLONAL	1	FALSE	NA	0.77777333212038	5		371	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659675	NA	P-0026974-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	136	1123	2	ENST00000269305.4:c.764T>C	p.Ile255Thr	p.I255T	ENST00000269305	NM_001126112.2	255	aTc/aCc	7/11	0.2675544611879	3	FACETS	1	0.931	1	0.514	0.467	0.564	CLONAL	1	FALSE	1	0.367338045903457	3		1125	852	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242442	55242443	+	inframe_insertion	In_Frame_Ins	INS	-	-	TTAAAATTCCCGTCGCTA	novel	NA	P-0026974-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	88	339	0	ENST00000275493.2:c.2214_2231dup	p.Ile740_Lys745dup	p.I740_K745dup	ENST00000275493	NM_005228.3	740	gtt/gTTAAAATTCCCGTCGCTAtt	19/28	0.367338045903457	4	FACETS	0.941	0.834	1	0.471	0.417	0.528	CLONAL	1	FALSE	2	0.367338045903457	4		339	696	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428411	49428411	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026974-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	121	623	0	ENST00000301067.7:c.10394G>C	p.Gly3465Ala	p.G3465A	ENST00000301067	NM_003482.3	3465	gGa/gCa	36/54	0.209053283570068	3	FACETS	0.774	0.698	0.855	0.387	0.349	0.428	INDETERMINATE	1	FALSE	1	0.367338045903457	3		623	1007	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562768	95562768	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026974-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	40	290	0	ENST00000393063.1:c.4489G>T	p.Asp1497Tyr	p.D1497Y	ENST00000393063	NM_030621.3	1497	Gat/Tat	24/28	1	2	FACETS	0.581	0.483	0.689	0.581	0.483	0.689	SUBCLONAL	1	FALSE	1	0.367338045903457	2		290	375	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843416	3843416	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1425065110	NA	P-0026974-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	45	341	0	ENST00000262367.5:c.1187C>T	p.Thr396Met	p.T396M	ENST00000262367	NM_004380.2	396	aCg/aTg	4/31	0.367338045903457	3	FACETS	0.44	0.369	0.519	0.22	0.184	0.26	SUBCLONAL	1	FALSE	1	0.367338045903457	3		341	659	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	103	290	2	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.964	0.863	1	0.964	0.863	1	CLONAL	1	TRUE	1	0.29	2		292	737	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258605	16258605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779248361	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	153	545	0	ENST00000375759.3:c.5870G>A	p.Arg1957His	p.R1957H	ENST00000375759	NM_015001.2	1957	cGc/cAc	11/15	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.29	2		545	903	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263956	16263956	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	181	759	1	ENST00000375759.3:c.10325A>G	p.Asp3442Gly	p.D3442G	ENST00000375759	NM_015001.2	3442	gAc/gGc	12/15	1	2	FACETS	0.926	0.852	1	0.926	0.852	1	CLONAL	1	TRUE	1	0.29	2		760	1348	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023831	27023831	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1415214478	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	86	255	0	ENST00000324856.7:c.941del	p.Gly314AlafsTer49	p.G314Afs*49	ENST00000324856	NM_006015.4	313	Ggg/gg	1/20	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.29	2		255	576	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	146	703	5	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.29	2		708	907	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366679	40366679	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs777173419	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	126	385	0	ENST00000397332.2:c.518C>G	p.Ala173Gly	p.A173G	ENST00000397332	NM_001033082.2	173	gCc/gGc	2/3	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.29	2		385	719	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115266566	115266566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	145	569	0	ENST00000438362.2:c.1949C>T	p.Pro650Leu	p.P650L	ENST00000438362	NM_001242891.1	650	cCc/cTc	16/20	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.29	2		569	996	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166577	118166577	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773285739	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	106	420	0	ENST00000369448.3:c.1087G>A	p.Val363Ile	p.V363I	ENST00000369448	NM_017709.3	363	Gtc/Atc	2/2	1	2	FACETS	0.928	0.831	1	0.928	0.831	1	CLONAL	1	TRUE	1	0.29	2		420	788	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870291	155870291	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	87	604	0	ENST00000368323.3:c.548G>A	p.Arg183His	p.R183H	ENST00000368323	NM_006912.5	183	cGt/cAt	6/6	1	2	FACETS	0.549	0.484	0.618	0.549	0.484	0.618	SUBCLONAL	1	TRUE	1	0.29	2		604	1093	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729693	162729693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139577393	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	168	556	0	ENST00000367921.3:c.779G>A	p.Arg260Gln	p.R260Q	ENST00000367921	NM_006182.2	260	cGg/cAg	8/18	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.29	2		556	1013	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243668615	243668615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	88	506	0	ENST00000263826.5:c.1376G>A	p.Cys459Tyr	p.C459Y	ENST00000263826	NM_005465.4	459	tGc/tAc	13/13	1	2	FACETS	0.828	0.733	0.929	0.828	0.733	0.929	CLONAL	1	TRUE	1	0.29	2		506	733	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100727	8100727	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	151	660	0	ENST00000346208.3:c.701T>C	p.Phe234Ser	p.F234S	ENST00000346208		234	tTc/tCc	3/6	1	2	FACETS	0.942	0.859	1	0.942	0.859	1	CLONAL	1	TRUE	1	0.29	2		660	1106	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625281	69625281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35983315	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	117	671	3	ENST00000334134.2:c.512G>A	p.Arg171His	p.R171H	ENST00000334134	NM_005247.2	171	cGc/cAc	3/3	1	2	FACETS	0.705	0.634	0.78	0.705	0.634	0.78	SUBCLONAL	1	TRUE	1	0.29	2		674	1145	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999083	100999083	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	78	496	0	ENST00000325455.5:c.719A>G	p.Lys240Arg	p.K240R	ENST00000325455	NM_001202474.3	240	aAa/aGa	1/8	1	2	FACETS	0.579	0.508	0.656	0.579	0.508	0.656	SUBCLONAL	1	TRUE	1	0.29	2		496	929	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038899	12038909	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCGCCACTA	CTGCGCCACTA	-	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	127	573	0	ENST00000396373.4:c.1194_1204del	p.Arg399GlnfsTer23	p.R399Qfs*23	ENST00000396373	NM_001987.4	398	CTGCGCCACTAc/c	7/8	1	2	FACETS	0.912	0.826	1	0.912	0.826	1	CLONAL	1	TRUE	1	0.29	2		573	960	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864125	57864125	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	140	565	0	ENST00000228682.2:c.1607del	p.Pro536GlnfsTer77	p.P536Qfs*77	ENST00000228682	NM_005269.2	534	ggC/gg	12/12	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.29	2		565	954	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120947	115120947	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	77	488	0	ENST00000257566.3:c.59T>C	p.Phe20Ser	p.F20S	ENST00000257566	NM_016569.3	20	tTc/tCc	1/8	1	2	FACETS	0.671	0.589	0.761	0.671	0.589	0.761	SUBCLONAL	1	TRUE	1	0.29	2		488	791	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225574	133225574	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	117	676	1	ENST00000320574.5:c.4090del	p.Arg1364ValfsTer5	p.R1364Vfs*5	ENST00000320574	NM_006231.2	1364	Cgt/gt	32/49	1	2	FACETS	0.802	0.722	0.887	0.802	0.722	0.887	CLONAL	1	TRUE	1	0.29	2		677	1006	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041261	29041262	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	96	378	0	ENST00000282397.4:c.166dup	p.Glu56GlyfsTer5	p.E56Gfs*5	ENST00000282397	NM_002019.4	56	gaa/gGaa	3/30	1	2	FACETS	0.929	0.828	1	0.929	0.828	1	CLONAL	1	TRUE	1	0.29	2		378	713	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3634797	3634797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765601038	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	161	731	1	ENST00000294008.3:c.4712C>T	p.Thr1571Met	p.T1571M	ENST00000294008	NM_032444.2	1571	aCg/aTg	13/15	1	2	FACETS	0.928	0.85	1	0.928	0.85	1	CLONAL	1	TRUE	1	0.29	2		732	1196	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858643	9858643	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	74	513	0	ENST00000330684.3:c.2758del	p.Arg920GlufsTer22	p.R920Efs*22	ENST00000330684	NM_001134407.1	920	Aga/ga	13/13	1	2	FACETS	0.61	0.533	0.693	0.61	0.533	0.693	SUBCLONAL	1	TRUE	1	0.29	2		513	837	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038656	14038656	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	112	481	0	ENST00000311895.7:c.1981G>T	p.Ala661Ser	p.A661S	ENST00000311895	NM_005236.2	661	Gca/Tca	10/11	1	2	FACETS	0.978	0.879	1	0.978	0.879	1	CLONAL	1	TRUE	1	0.29	2		481	790	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042106	14042106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	50	407	0	ENST00000311895.7:c.2653A>G	p.Thr885Ala	p.T885A	ENST00000311895	NM_005236.2	885	Acg/Gcg	11/11	1	2	FACETS	0.528	0.447	0.617	0.528	0.447	0.617	SUBCLONAL	1	TRUE	1	0.29	2		407	653	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56867237	56867237	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138281575	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	100	425	0	ENST00000308159.5:c.1456C>T	p.Arg486Cys	p.R486C	ENST00000308159	NM_014669.4	486	Cgc/Tgc	13/22	1	2	FACETS	0.926	0.827	1	0.926	0.827	1	CLONAL	1	TRUE	1	0.29	2		425	745	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	133	464	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.29	2		465	893	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849488	68849491	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	122	566	2	ENST00000261769.5:c.1395_1398del	p.Leu466ProfsTer14	p.L466Pfs*14	ENST00000261769	NM_004360.3	464	gTCTCt/gt	10/16	1	2	FACETS	0.895	0.808	0.987	0.895	0.808	0.987	CLONAL	1	TRUE	1	0.29	2		568	940	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822586	72822586	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	111	447	3	ENST00000268489.5:c.9589del	p.Gln3197SerfsTer44	p.Q3197Sfs*44	ENST00000268489	NM_006885.3	3197	Cag/ag	10/10	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.29	2		450	744	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81960725	81960725	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	164	669	0	ENST00000359376.3:c.2456T>C	p.Phe819Ser	p.F819S	ENST00000359376	NM_002661.3	819	tTc/tCc	23/33	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.29	2		669	1111	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337295	89337295	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	115	477	0	ENST00000301030.4:c.7736G>T	p.Arg2579Leu	p.R2579L	ENST00000301030	NM_001256183.1	2579	cGc/cTc	12/13	1	2	FACETS	0.991	0.893	1	0.991	0.893	1	CLONAL	1	TRUE	1	0.29	2		477	800	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576066	29576066	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	130	609	0	ENST00000356175.3:c.4039T>C	p.Phe1347Leu	p.F1347L	ENST00000356175	NM_000267.3	1347	Ttc/Ctc	30/57	1	2	FACETS	0.822	0.744	0.904	0.822	0.744	0.904	CLONAL	1	TRUE	1	0.29	2		609	1091	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627418	37627418	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	149	695	1	ENST00000447079.4:c.1337del	p.Lys446SerfsTer6	p.K446Sfs*6	ENST00000447079	NM_015083.1	445	Aaa/aa	2/14	1	2	FACETS	0.872	0.795	0.953	0.872	0.795	0.953	CLONAL	1	TRUE	1	0.29	2		696	1179	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370223	40370223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	166	784	1	ENST00000293328.3:c.1115C>T	p.Thr372Ile	p.T372I	ENST00000293328	NM_012448.3	372	aCc/aTc	9/19	1	2	FACETS	0.911	0.835	0.991	0.911	0.835	0.991	CLONAL	1	TRUE	1	0.29	2		785	1256	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804163	46804163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752722523	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	135	584	0	ENST00000290295.7:c.844G>A	p.Ala282Thr	p.A282T	ENST00000290295	NM_006361.5	282	Gct/Act	2/2	1	2	FACETS	0.92	0.835	1	0.92	0.835	1	CLONAL	1	TRUE	1	0.29	2		584	1012	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	178	663	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.29	2		667	1083	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119051	70119051	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	136	535	0	ENST00000245479.2:c.623A>G	p.Gln208Arg	p.Q208R	ENST00000245479	NM_000346.3	208	cAg/cGg	2/3	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.29	2		535	860	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2189772	2189772	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	219	665	1	ENST00000398665.3:c.242C>T	p.Ala81Val	p.A81V	ENST00000398665	NM_032482.2	81	gCc/gTc	4/28	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.29	2		666	1279	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216733	2216733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751291437	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	151	654	2	ENST00000398665.3:c.2377G>A	p.Gly793Ser	p.G793S	ENST00000398665	NM_032482.2	793	Ggc/Agc	20/28	1	2	FACETS	0.976	0.891	1	0.976	0.891	1	CLONAL	1	TRUE	1	0.29	2		656	1067	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211707	5211707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145108936	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	175	676	3	ENST00000357368.4:c.5128C>T	p.Arg1710Cys	p.R1710C	ENST00000357368	NM_002850.3	1710	Cgc/Tgc	33/38	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.29	2		679	1174	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220125	5220125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1471312670	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	128	564	1	ENST00000357368.4:c.3590G>A	p.Arg1197Gln	p.R1197Q	ENST00000357368	NM_002850.3	1197	cGg/cAg	22/38	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.29	2		565	828	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250360	10250360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	97	295	1	ENST00000340748.4:c.3892G>A	p.Val1298Met	p.V1298M	ENST00000340748		1298	Gtg/Atg	33/40	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.29	2		296	602	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602518	10602518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	150	559	0	ENST00000171111.5:c.1060C>T	p.Arg354Trp	p.R354W	ENST00000171111	NM_203500.1	354	Cgg/Tgg	3/6	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.29	2		559	895	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032374	11032374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs909244932	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	195	733	0	ENST00000327064.4:c.1768G>A	p.Ala590Thr	p.A590T	ENST00000327064	NM_199141.1	590	Gcc/Acc	16/16	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.29	2		733	1076	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276630	15276630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1245481086	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	198	687	1	ENST00000263388.2:c.5635G>A	p.Ala1879Thr	p.A1879T	ENST00000263388	NM_000435.2	1879	Gct/Act	30/33	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.29	2		688	1191	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299097	15299097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	188	631	1	ENST00000263388.2:c.1441G>A	p.Gly481Ser	p.G481S	ENST00000263388	NM_000435.2	481	Ggt/Agt	9/33	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.29	2		632	1148	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367969	15367969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759001252	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	157	649	1	ENST00000263377.2:c.1357C>T	p.Arg453Cys	p.R453C	ENST00000263377	NM_058243.2	453	Cgc/Tgc	8/20	1	2	FACETS	0.956	0.874	1	0.956	0.874	1	CLONAL	1	TRUE	1	0.29	2		650	1133	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376278	15376278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	134	624	0	ENST00000263377.2:c.736C>T	p.Pro246Ser	p.P246S	ENST00000263377	NM_058243.2	246	Cca/Tca	5/20	1	2	FACETS	0.916	0.831	1	0.916	0.831	1	CLONAL	1	TRUE	1	0.29	2		624	1009	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271307	18271307	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	193	740	1	ENST00000222254.8:c.349C>T	p.Gln117Ter	p.Q117*	ENST00000222254	NM_005027.3	117	Cag/Tag	3/16	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.29	2		741	1293	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211248	36211248	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1333	253	890	0	ENST00000222270.7:c.999G>T	p.Glu333Asp	p.E333D	ENST00000222270	NM_014727.1	333	gaG/gaT	3/37	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.29	2		890	1586	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219053	36219053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758967458	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	175	624	2	ENST00000222270.7:c.4552C>T	p.Arg1518Trp	p.R1518W	ENST00000222270	NM_014727.1	1518	Cgg/Tgg	19/37	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.29	2		626	1040	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40745984	40745984	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	112	719	0	ENST00000392038.2:c.607del	p.Val203SerfsTer13	p.V203Sfs*13	ENST00000392038	NM_001626.4	203	Gtc/tc	7/14	1	2	FACETS	0.692	0.621	0.768	0.692	0.621	0.768	SUBCLONAL	1	TRUE	1	0.29	2		719	1116	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744455	41744455	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	135	743	0	ENST00000301178.4:c.1078del	p.Leu360CysfsTer6	p.L360Cfs*6	ENST00000301178	NM_021913.4	359	Ccc/cc	8/20	1	2	FACETS	0.771	0.699	0.848	0.771	0.699	0.848	SUBCLONAL	1	TRUE	1	0.29	2		743	1207	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464454	25464454	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1183198167	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	130	535	1	ENST00000264709.3:c.2059G>A	p.Val687Ile	p.V687I	ENST00000264709	NM_175629.2	687	Gtc/Atc	17/23	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.29	2		536	799	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213161	39213161	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1290	187	916	0	ENST00000402219.2:c.3806C>A	p.Thr1269Lys	p.T1269K	ENST00000402219	NM_005633.3	1269	aCa/aAa	23/23	1	2	FACETS	0.873	0.804	0.946	0.873	0.804	0.946	CLONAL	1	TRUE	1	0.29	2		916	1477	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151290	202151290	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	161	323	0	ENST00000358485.4:c.1596del	p.Lys532AsnfsTer73	p.K532Nfs*73	ENST00000358485	NM_001080125.1	530	agA/ag	9/9	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.29	2		323	1005	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225360561	225360561	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	53	234	0	ENST00000264414.4:c.1830del	p.Lys610AsnfsTer44	p.K610Nfs*44	ENST00000264414	NM_003590.4	610	aaA/aa	13/16	1	2	FACETS	0.98	0.839	1	0.98	0.839	1	CLONAL	1	TRUE	1	0.29	2		234	373	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	73	526	3	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	1	2	FACETS	0.569	0.496	0.647	0.569	0.496	0.647	SUBCLONAL	1	TRUE	1	0.29	2		529	885	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021205	31021205	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	152	601	1	ENST00000375687.4:c.1204C>T	p.Arg402Ter	p.R402*	ENST00000375687	NM_015338.5	402	Cga/Tga	12/13	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.29	2		602	1014	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012773	36012773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	66	200	0	ENST00000358208.4:c.217G>A	p.Val73Ile	p.V73I	ENST00000358208		73	Gtc/Atc	2/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.29	2		200	334	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39751914	39751914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	131	474	1	ENST00000361337.2:c.2275G>A	p.Ala759Thr	p.A759T	ENST00000361337	NM_003286.2	759	Gct/Act	21/21	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.29	2		475	833	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710566	40710566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760820896	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	140	638	1	ENST00000373198.4:c.4285G>A	p.Val1429Met	p.V1429M	ENST00000373198	NM_133170.3	1429	Gtg/Atg	31/32	1	2	FACETS	0.925	0.841	1	0.925	0.841	1	CLONAL	1	TRUE	1	0.29	2		639	1044	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62324629	62324629	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	125	489	0	ENST00000360203.5:c.2988del	p.Thr997LeufsTer10	p.T997Lfs*10	ENST00000360203	NM_001283009.1	995	gaC/ga	30/35	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.29	2		489	794	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650828	12650828	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	98	370	0	ENST00000251849.4:c.327del	p.Ala110HisfsTer3	p.A110Hfs*3	ENST00000251849	NM_002880.3	109	aaA/aa	4/17	1	2	FACETS	0.947	0.845	1	0.947	0.845	1	CLONAL	1	TRUE	1	0.29	2		370	714	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713643	30713643	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	117	508	0	ENST00000295754.5:c.968T>C	p.Leu323Pro	p.L323P	ENST00000295754	NM_003242.5	323	cTg/cCg	4/7	1	2	FACETS	0.932	0.84	1	0.932	0.84	1	CLONAL	1	TRUE	1	0.29	2		508	866	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053348	37053348	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs63751653	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	89	482	1	ENST00000231790.2:c.588del	p.Lys196AsnfsTer6	p.K196Nfs*6	ENST00000231790	NM_000249.3	195	Aaa/aa	7/19	1	2	FACETS	0.65	0.575	0.73	0.65	0.575	0.73	SUBCLONAL	1	TRUE	1	0.29	2		483	945	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098351	47098351	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	122	516	0	ENST00000409792.3:c.6923T>C	p.Val2308Ala	p.V2308A	ENST00000409792	NM_014159.6	2308	gTg/gCg	15/21	1	2	FACETS	0.949	0.857	1	0.949	0.857	1	CLONAL	1	TRUE	1	0.29	2		516	887	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103771	47103771	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	161	581	0	ENST00000409792.3:c.6175A>G	p.Arg2059Gly	p.R2059G	ENST00000409792	NM_014159.6	2059	Agg/Ggg	14/21	1	2	FACETS	0.994	0.91	1	0.994	0.91	1	CLONAL	1	TRUE	1	0.29	2		581	1117	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165283	47165283	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	113	369	0	ENST00000409792.3:c.843del	p.Glu282LysfsTer19	p.E282Kfs*19	ENST00000409792	NM_014159.6	281	aaA/aa	3/21	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.29	2		369	756	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932726	49932726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777576135	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	212	784	0	ENST00000296474.3:c.3145G>A	p.Val1049Met	p.V1049M	ENST00000296474	NM_002447.2	1049	Gtg/Atg	14/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.29	2		784	1270	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643942	52643943	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	118	446	0	ENST00000394830.3:c.1953dup	p.Ser652IlefsTer13	p.S652Ifs*13	ENST00000394830	NM_018313.4	651	-/A	17/30	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.29	2		446	804	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851820	134851820	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	133	609	0	ENST00000398015.3:c.1226T>C	p.Ile409Thr	p.I409T	ENST00000398015	NM_004441.4	409	aTc/aCc	5/16	1	2	FACETS	0.849	0.77	0.933	0.849	0.77	0.933	CLONAL	1	TRUE	1	0.29	2		609	1080	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664891	138664891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	37	132	0	ENST00000330315.3:c.674C>T	p.Ala225Val	p.A225V	ENST00000330315	NM_023067.3	225	gCg/gTg	1/1	1	2	FACETS	0.883	0.731	1	0.883	0.731	1	CLONAL	1	TRUE	1	0.29	2		132	289	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176558	142176558	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	122	497	1	ENST00000350721.4:c.7543C>A	p.Leu2515Met	p.L2515M	ENST00000350721	NM_001184.3	2515	Ctg/Atg	45/47	1	2	FACETS	0.876	0.79	0.966	0.876	0.79	0.966	CLONAL	1	TRUE	1	0.29	2		498	961	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182662919	182662919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451035070	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	147	488	0	ENST00000292782.4:c.743G>A	p.Arg248His	p.R248H	ENST00000292782	NM_020640.2	248	cGc/cAc	7/7	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.29	2		488	920	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801059	1801059	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs371729802	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	193	787	2	ENST00000260795.2:c.188C>A	p.Pro63Gln	p.P63Q	ENST00000260795		63	cCg/cAg	2/17	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.29	2		789	1187	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808985	1808985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374547489	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	115	373	1	ENST00000260795.2:c.2417C>T	p.Thr806Met	p.T806M	ENST00000260795		806	aCg/aTg	17/17	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.29	2		374	677	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356248	66356248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202046693	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	118	577	1	ENST00000273854.3:c.1249C>T	p.Arg417Trp	p.R417W	ENST00000273854	NM_004439.5	417	Cgg/Tgg	5/18	1	2	FACETS	0.815	0.734	0.901	0.815	0.734	0.901	CLONAL	1	TRUE	1	0.29	2		578	998	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531115	187531115	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	133	471	0	ENST00000441802.2:c.9908T>G	p.Leu3303Arg	p.L3303R	ENST00000441802	NM_005245.3	3303	cTa/cGa	15/27	0.3	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.29	1		471	702	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295031	1295031	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	36	56	0	ENST00000310581.5:c.74C>T	p.Ala25Val	p.A25V	ENST00000310581	NM_198253.2	25	gCc/gTc	1/16	1	2	FACETS	0.833	0.696	0.981	1	0.96	1	CLONAL	2	TRUE	1	0.29	2		56	149	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79968171	79968171	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	132	571	1	ENST00000265081.6:c.901G>T	p.Gly301Ter	p.G301*	ENST00000265081	NM_002439.4	301	Gga/Tga	5/24	1	2	FACETS	0.975	0.884	1	0.975	0.884	1	CLONAL	1	TRUE	1	0.29	2		572	934	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	362	539	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.949	1	1	0.996	1	CLONAL	2	TRUE	1	0.29	2		544	1247	SUCCESS
APC	324	MSKCC	GRCh37	5	112174047	112174047	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	95	397	0	ENST00000257430.4:c.2756G>T	p.Arg919Ile	p.R919I	ENST00000257430	NM_000038.5	919	aGa/aTa	16/16	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.29	2		397	618	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931468	131931468	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369560280	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	132	500	0	ENST00000265335.6:c.2173C>T	p.Arg725Trp	p.R725W	ENST00000265335		725	Cgg/Tgg	13/25	1	2	FACETS	0.967	0.877	1	0.967	0.877	1	CLONAL	1	TRUE	1	0.29	2		500	941	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499051	149499051	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	159	633	0	ENST00000261799.4:c.2777C>A	p.Pro926His	p.P926H	ENST00000261799	NM_002609.3	926	cCt/cAt	20/23	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.29	2		633	1094	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519695	176519695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767796482	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	156	692	1	ENST00000292408.4:c.967G>A	p.Val323Met	p.V323M	ENST00000292408	NM_213647.1	323	Gtg/Atg	8/18	1	2	FACETS	0.967	0.884	1	0.967	0.884	1	CLONAL	1	TRUE	1	0.29	2		693	1113	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271208	26271208	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	88	389	0	ENST00000305910.3:c.405A>T	p.Arg135Ser	p.R135S	ENST00000305910	NM_003534.2	135	agA/agT	1/1	1	2	FACETS	0.951	0.844	1	0.951	0.844	1	CLONAL	1	TRUE	1	0.29	2		389	638	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	102	455	1	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.29	2		456	693	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324494	31324494	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs9266161	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	154	590	1	ENST00000412585.2:c.314T>C	p.Leu105Pro	p.L105P	ENST00000412585	NM_005514.6	105	cTg/cCg	2/8	1	2	FACETS	0.971	0.894	1	1	0.992	1	CLONAL	2	TRUE	1	0.29	2		591	547	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169196	32169196	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1271587983	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	186	708	1	ENST00000375023.3:c.3837G>A	p.Trp1279Ter	p.W1279*	ENST00000375023	NM_004557.3	1279	tgG/tgA	22/30	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.29	2		709	1191	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805880	32805880	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs772478924	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	117	744	0	ENST00000374899.4:c.131T>C	p.Leu44Pro	p.L44P	ENST00000374899	NM_018833.2	44	cTg/cCg	2/12	1	2	FACETS	0.655	0.589	0.725	0.655	0.589	0.725	SUBCLONAL	1	TRUE	1	0.29	2		744	1232	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288752	33288752	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	90	445	0	ENST00000374542.5:c.800T>C	p.Val267Ala	p.V267A	ENST00000374542	NM_001141970.1	267	gTt/gCt	3/8	1	2	FACETS	0.776	0.688	0.87	0.776	0.688	0.87	SUBCLONAL	1	TRUE	1	0.29	2		445	800	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005111	150005111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	135	538	0	ENST00000253339.5:c.1114C>T	p.Pro372Ser	p.P372S	ENST00000253339		372	Cca/Tca	3/7	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.29	2		538	821	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242442	55242442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	161	581	0	ENST00000275493.2:c.2212G>A	p.Val738Ile	p.V738I	ENST00000275493	NM_005228.3	738	Gtt/Att	19/28	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.29	2		581	1034	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829040	128829042	+	inframe_deletion	In_Frame_Del	DEL	GCT	GCT	-	rs570242755	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	11	52	0	ENST00000249373.3:c.67_69del	p.Leu23del	p.L23del	ENST00000249373	NM_005631.4	16	ggGCTg/ggg	1/12	1	2	FACETS	0.79	0.552	1	0.79	0.552	1	CLONAL	1	TRUE	1	0.29	2		52	96	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346158	152346158	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	134	636	0	ENST00000359321.1:c.412del	p.Cys138ValfsTer9	p.C138Vfs*9	ENST00000359321	NM_005431.1	138	Tgt/gt	3/3	1	2	FACETS	0.84	0.762	0.923	0.84	0.762	0.923	CLONAL	1	TRUE	1	0.29	2		636	1100	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981422	70981422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	123	683	0	ENST00000276594.2:c.674G>A	p.Gly225Asp	p.G225D	ENST00000276594	NM_024504.3	225	gGc/gAc	2/8	1	2	FACETS	0.658	0.593	0.726	0.658	0.593	0.726	SUBCLONAL	1	TRUE	1	0.29	2		683	1290	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141561520	141561520	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	107	449	0	ENST00000220592.5:c.1285A>G	p.Thr429Ala	p.T429A	ENST00000220592	NM_012154.3	429	Acc/Gcc	11/19	1	2	FACETS	0.853	0.764	0.947	0.853	0.764	0.947	CLONAL	1	TRUE	1	0.29	2		449	865	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015190	37015190	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	82	396	0	ENST00000358127.4:c.214T>C	p.Tyr72His	p.Y72H	ENST00000358127	NM_001280556.1	72	Tat/Cat	3/10	1	2	FACETS	0.884	0.78	0.995	0.884	0.78	0.995	CLONAL	1	TRUE	1	0.29	2		396	640	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390944	139390945	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTG	rs762336270	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	151	750	0	ENST00000277541.6:c.7244_7246dup	p.Pro2415dup	p.P2415dup	ENST00000277541	NM_017617.3	2415	cag/cCACag	34/34	1	2	FACETS	0.8	0.729	0.874	0.8	0.729	0.874	SUBCLONAL	1	TRUE	1	0.29	2		750	1302	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391832	139391832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766836819	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	168	575	0	ENST00000277541.6:c.6359G>A	p.Arg2120His	p.R2120H	ENST00000277541	NM_017617.3	2120	cGc/cAc	34/34	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.29	2		575	958	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652243	48652243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	176	297	0	ENST00000376670.3:c.914G>A	p.Arg305Gln	p.R305Q	ENST00000376670	NM_002049.3	305	cGa/cAa	6/6	1	1	FACETS	0.89	0.825	0.957	1	0.992	1	CLONAL	2	TRUE	0	0.29	1		297	583	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245012	53245012	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	54	348	0	ENST00000375401.3:c.928A>G	p.Met310Val	p.M310V	ENST00000375401	NM_004187.3	310	Atg/Gtg	7/26	1	1	FACETS	0.556	0.474	0.645	0.556	0.474	0.645	SUBCLONAL	1	TRUE	0	0.29	1		348	573	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178218	56178218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780012235	NA	P-0027241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	125	385	0	ENST00000399503.3:c.3191G>A	p.Arg1064Lys	p.R1064K	ENST00000399503	NM_005921.1	1064	aGa/aAa	14/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.29	2		385	770	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0027245-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	420	608	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.794865717603976	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.841721232786839	1		611	553	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931471	131931471	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753002904	NA	P-0027245-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	127	420	2	ENST00000265335.6:c.2176C>T	p.Arg726Cys	p.R726C	ENST00000265335		726	Cgt/Tgt	13/25	0.420806639509809	1	FACETS	0.366	0.333	0.399	0.366	0.333	0.399	INDETERMINATE	1	TRUE	0	0.841721232786839	1		422	478	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273231	18273231	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1260910794	NA	P-0027245-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	230	665	0	ENST00000222254.8:c.1024G>A	p.Glu342Lys	p.E342K	ENST00000222254	NM_005027.3	342	Gag/Aag	9/16	0.411264300383589	1	FACETS	0.399	0.372	0.426	0.399	0.372	0.426	INDETERMINATE	1	TRUE	0	0.841721232786839	1		665	794	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690806	89690806	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027245-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	176	360	0	ENST00000371953.3:c.213T>G	p.Cys71Trp	p.C71W	ENST00000371953	NM_000314.4	71	tgT/tgG	4/9	0.75165783091238	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.841721232786839	1		360	242	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701173	29701184	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	AAGCTTGCTTGC	AAGCTTGCTTGC	-	novel	NA	P-0027245-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	73	262	0	ENST00000356175.3:c.8457_*11del		p.*2819*	ENST00000356175	NM_000267.3	2819		57/57	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.841721232786839	NA		262	313	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0027598-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	349	396	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.137560535588862	5	FACETS	1	0.993	1			1	INDETERMINATE	4	TRUE	NA	0.813563182584601	5		396	439	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948136	178948136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0027598-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	217	239	0	ENST00000263967.3:c.2908G>A	p.Glu970Lys	p.E970K	ENST00000263967	NM_006218.2	970	Gaa/Aaa	20/21	0.813563182584601	4	FACETS	0.925	0.868	0.982	0.925	0.868	0.982	CLONAL	2	TRUE	2	0.813563182584601	4		239	523	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599322	55599322	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027598-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	243	478	0	ENST00000288135.5:c.2448C>A	p.Asp816Glu	p.D816E	ENST00000288135	NM_000222.2	816	gaC/gaA	17/21	0.137560535588862	5	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.813563182584601	5		478	597	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599337	55599339	+	missense_variant	Missense_Mutation	TNP	TAA	TAA	CTT	novel	NA	P-0027598-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	197	450	1	ENST00000288135.5:c.2463_2465delinsCTT	p.Asn822Phe	p.N822F	ENST00000288135	NM_000222.2	821	tcTAAt/tcCTTt	17/21	0.137560535588862	5	FACETS	1	0.946	1			1	INDETERMINATE	2	TRUE	NA	0.813563182584601	5		451	530	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170814967	170814967	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027598-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	39	213	2	ENST00000296930.5:c.15G>T	p.Met5Ile	p.M5I	ENST00000296930	NM_002520.6	5	atG/atT	1/11	0.813563182584601	3	FACETS	0.409	0.34	0.485	0.204	0.17	0.243	SUBCLONAL	1	TRUE	1	0.813563182584601	3		215	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0027800-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	440	866	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	0.510808851199293	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.559358481484938	1		866	1044	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0027881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	119	779	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.241905307865462	3	FACETS	0.924	0.832	1	0.462	0.416	0.511	CLONAL	1	TRUE	1	0.274668887436614	3		781	1067	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0027881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	38	120	2	ENST00000257430.4:c.3919dup	p.Ile1307AsnfsTer8	p.I1307Nfs*8	ENST00000257430	NM_000038.5	1306	gaa/gAaa	16/16	0.274668887436614	3	FACETS	0.636	0.525	0.759	0.318	0.262	0.38	SUBCLONAL	1	TRUE	1	0.274668887436614	3		122	495	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976727	2976727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1298741148	NA	P-0027881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	179	659	1	ENST00000396946.4:c.1285G>A	p.Val429Ile	p.V429I	ENST00000396946	NM_032415.4	429	Gtc/Atc	9/25	0.165504145301694	4	FACETS	1	0.989	1	0.733	0.674	0.793	CLONAL	1	TRUE	2	0.274668887436614	4		660	1134	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196917	108196917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	53	574	1	ENST00000278616.4:c.6940C>T	p.Gln2314Ter	p.Q2314*	ENST00000278616	NM_000051.3	2314	Caa/Taa	47/63	0.274668887436614	3	FACETS	0.475	0.404	0.554	0.238	0.202	0.277	SUBCLONAL	1	TRUE	1	0.274668887436614	3		575	924	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911591	114911592	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGAG	novel	NA	P-0027881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	221	839	0	ENST00000543371.1:c.1112_1115dup	p.Cys372Ter	p.C372*	ENST00000543371	NM_001198531.1	370	gct/gcTGAGt	10/14	0.25514538037472	3	FACETS	1	0.99	1	0.706	0.655	0.758	CLONAL	1	TRUE	1	0.274668887436614	3		839	1297	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813882	50813882	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1264	113	779	0	ENST00000398568.2:c.1436C>G	p.Pro479Arg	p.P479R	ENST00000398568	NM_001042412.1	479	cCt/cGt	8/18	0.274668887436614	3	FACETS	0.68	0.609	0.755	0.227	0.203	0.252	SUBCLONAL	1	TRUE	0	0.274668887436614	3		779	1377	SUCCESS
APC	324	MSKCC	GRCh37	5	112174597	112174597	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs879254092	NA	P-0027881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	248	644	0	ENST00000257430.4:c.3306C>G	p.Tyr1102Ter	p.Y1102*	ENST00000257430	NM_000038.5	1102	taC/taG	16/16	0.274668887436614	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.274668887436614	3		644	985	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0028065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	110	753	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.214693975047227	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.214693975047227	2		753	444	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522059	157522059	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770643408	NA	P-0028065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	33	514	0	ENST00000346085.5:c.4331C>T	p.Pro1444Leu	p.P1444L	ENST00000346085	NM_020732.3	1444	cCg/cTg	18/20	0.195089573700854	4	FACETS	0.931	0.759	1	0.31	0.253	0.375	CLONAL	1	TRUE	1	0.214693975047227	4		514	401	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11227521	11227521	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	38	713	0	ENST00000361445.4:c.4307C>G	p.Ala1436Gly	p.A1436G	ENST00000361445	NM_004958.3	1436	gCc/gGc	29/58	0.214693975047227	3	FACETS	0.86	0.711	1	0.43	0.355	0.513	CLONAL	1	TRUE	1	0.214693975047227	3		713	456	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344077	118344082	+	inframe_deletion	In_Frame_Del	DEL	AAAAGG	AAAAGG	-	novel	NA	P-0028065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	27	371	0	ENST00000534358.1:c.2208_2213del	p.Arg738_Lys739del	p.R738_K739del	ENST00000534358	NM_005933.3	735	AAAAGG/-	3/36	0.195935642059813	2	FACETS	0.856	0.682	1	0.428	0.341	0.527	CLONAL	1	TRUE	0	0.214693975047227	2		371	294	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117733	115117733	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	35	574	0	ENST00000257566.3:c.702del	p.Tyr234Ter	p.Y234*	ENST00000257566	NM_016569.3	234	taT/ta	3/8	0.214693975047227	3	FACETS	0.891	0.731	1	0.446	0.365	0.536	CLONAL	1	TRUE	1	0.214693975047227	3		574	405	SUCCESS
BLM	641	MSKCC	GRCh37	15	91298089	91298090	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0028065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	28	429	0	ENST00000355112.3:c.1010_1011del	p.Thr337IlefsTer9	p.T337Ifs*9	ENST00000355112	NM_000057.2	336	agCAca/agca	5/22	0.214693975047227	5	FACETS	0.787	0.629	0.969	0.262	0.209	0.323	CLONAL	1	TRUE	2	0.214693975047227	5		429	438	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109309684	109309793	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTGAAGGAGACTACGAATCATTGCTAAGTTACAAAGTAAATAAGCCACAATAGGCACATACCTTCTCAGAGTGCTTGAACTGCCTCCAGAAGCTATCATACATTCTTTT	GGTGAAGGAGACTACGAATCATTGCTAAGTTACAAAGTAAATAAGCCACAATAGGCACATACCTTCTCAGAGTGCTTGAACTGCCTCCAGAAGCTATCATACATTCTTTT	-	novel	NA	P-0028065-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	18	200	0	ENST00000436639.2:c.1522_1569+62del		p.X508_splice	ENST00000436639	NM_014454.2	508		9/10	0.195089573700854	4	FACETS	1	0.893	1	0.459	0.348	0.587	CLONAL	1	TRUE	1	0.214693975047227	4		200	148	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0028071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	364	494	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	0.338960576043333	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	FALSE	2	0.473165058681142	4		494	1057	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155995	119155995	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0028071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	290	625	1	ENST00000264033.4:c.1660G>T	p.Val554Phe	p.V554F	ENST00000264033	NM_005188.3	554	Gtt/Ttt	11/16	NA	2	FACETS	0.757	0.715	0.799			1	INDETERMINATE	2	FALSE	NA	0.473165058681142	2		626	810	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926856	112926856	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0028071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	95	583	0	ENST00000351677.2:c.1476A>C	p.Lys492Asn	p.K492N	ENST00000351677	NM_002834.3	492	aaA/aaC	13/16	1	2	FACETS	0.436	0.387	0.488	0.436	0.387	0.488	SUBCLONAL	1	FALSE	1	0.473165058681142	2		583	921	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781381	3781381	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	292	637	0	ENST00000262367.5:c.4984G>A	p.Asp1662Asn	p.D1662N	ENST00000262367	NM_004380.2	1662	Gat/Aat	30/31	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	1	FALSE	NA	0.473165058681142	2		637	838	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857363	9857363	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	31	401	2	ENST00000330684.3:c.4038A>T	p.Gln1346His	p.Q1346H	ENST00000330684	NM_001134407.1	1346	caA/caT	13/13	NA	2	FACETS	0.261	0.21	0.318			1	INDETERMINATE	1	FALSE	NA	0.473165058681142	2		403	502	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657693	37657715	+	splice_donor_variant,intron_variant	Splice_Site	DEL	GTAACATAGTAACCAAATAAGAT	GTAACATAGTAACCAAATAAGAT	-	novel	NA	P-0028071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	228	377	0	ENST00000447079.4:c.2609+1_2609+23del		p.X870_splice	ENST00000447079	NM_015083.1	870			1	2	FACETS	0.782	0.734	0.832	1	0.993	1	SUBCLONAL	2	FALSE	1	0.473165058681142	2		377	616	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198264870	198264870	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	87	485	0	ENST00000335508.6:c.2922G>T	p.Leu974Phe	p.L974F	ENST00000335508	NM_012433.2	974	ttG/ttT	20/25	1	2	FACETS	0.424	0.375	0.477	0.424	0.375	0.477	SUBCLONAL	1	FALSE	1	0.473165058681142	2		485	867	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187445	32187445	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	238	595	0	ENST00000375023.3:c.1434G>T	p.Glu478Asp	p.E478D	ENST00000375023	NM_004557.3	478	gaG/gaT	8/30	0.239983037012991	0	FACETS	0.927	0.872	0.981			1	INDETERMINATE	1	FALSE	0	0.473165058681142	0		595	572	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344709	65344709	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	101	268	0	ENST00000342505.4:c.328A>T	p.Arg110Trp	p.R110W	ENST00000342505	NM_002227.2	110	Agg/Tgg	4/25	0.489018936054419	1	FACETS	0.949	0.857	1	0.949	0.857	1	CLONAL	1	TRUE	0	0.489018936054419	1		268	329	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551710	150551710	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	98	246	0	ENST00000369026.2:c.297C>G	p.Phe99Leu	p.F99L	ENST00000369026	NM_021960.4	99	ttC/ttG	1/3	0.489018936054419	3	FACETS	0.932	0.834	1	0.466	0.417	0.518	CLONAL	1	TRUE	1	0.489018936054419	3		246	535	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332336	70332336	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	172	466	0	ENST00000373644.4:c.241C>A	p.Arg81Ser	p.R81S	ENST00000373644	NM_030625.2	81	Cgc/Agc	2/12	1	2	FACETS	0.897	0.827	0.97	0.897	0.827	0.97	CLONAL	1	TRUE	1	0.489018936054419	2		466	784	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495047	56495048	+	missense_variant	Missense_Mutation	DNP	AG	AG	TA	novel	NA	P-0028077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	236	575	1	ENST00000267101.3:c.3404_3405delinsTA	p.Gln1135Leu	p.Q1135L	ENST00000267101	NM_001982.3	1135	cAG/cTA	27/28	1	2	FACETS	0.974	0.909	1	0.974	0.909	1	CLONAL	1	TRUE	1	0.489018936054419	2		576	991	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288484	15288484	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	105	242	0	ENST00000263388.2:c.4255C>G	p.Leu1419Val	p.L1419V	ENST00000263388	NM_000435.2	1419	Ctg/Gtg	24/33	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.489018936054419	2		242	382	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977892	134977894	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0028077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	186	470	0	ENST00000398015.3:c.2891_2893del	p.Lys964del	p.K964del	ENST00000398015	NM_004441.4	962	cAGAag/cag	16/16	0.489018936054419	3	FACETS	0.987	0.912	1	0.494	0.456	0.533	CLONAL	1	TRUE	1	0.489018936054419	3		470	959	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515304	149515304	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1478236512	NA	P-0028077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	173	514	0	ENST00000261799.4:c.178G>T	p.Val60Leu	p.V60L	ENST00000261799	NM_002609.3	60	Gtg/Ttg	3/23	1	2	FACETS	0.883	0.814	0.955	0.883	0.814	0.955	CLONAL	1	TRUE	1	0.489018936054419	2		514	801	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046353	69046353	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0028077-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	157	454	0	ENST00000288368.4:c.3826T>G	p.Cys1276Gly	p.C1276G	ENST00000288368	NM_024870.2	1276	Tgt/Ggt	32/40	1	2	FACETS	0.875	0.803	0.95	0.875	0.803	0.95	CLONAL	1	TRUE	1	0.489018936054419	2		454	734	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0028843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	246	687	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.341155789627769	2	FACETS	0.777	0.729	0.827	0.777	0.729	0.827	SUBCLONAL	2	TRUE	0	0.408273813266192	2		687	775	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0028843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	126	478	2	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.341155789627769	2	FACETS	0.935	0.858	1	0.935	0.858	1	CLONAL	2	TRUE	0	0.408273813266192	2		480	330	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs1057519842	NA	P-0028843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	40	302	0	ENST00000274335.5:c.1727_1729del	p.Thr576del	p.T576del	ENST00000274335		575	aaGACg/aag	12/15	0.360976845559428	3	FACETS	1	0.861	1	0.515	0.431	0.607	CLONAL	1	TRUE	1	0.408273813266192	3		302	229	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711875	89711875	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587782603	NA	P-0028843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	44	366	0	ENST00000371953.3:c.493G>A	p.Gly165Arg	p.G165R	ENST00000371953	NM_000314.4	165	Gga/Aga	6/9	0.279261737020925	1	FACETS	0.802	0.679	0.934	0.802	0.679	0.934	CLONAL	1	TRUE	0	0.408273813266192	1		366	214	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258095	123258095	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	21	416	0	ENST00000358487.5:c.1586C>G	p.Ser529Cys	p.S529C	ENST00000358487	NM_000141.4	529	tCt/tGt	12/18	0.408273813266192	3	FACETS	0.332	0.255	0.422			1	SUBCLONAL	1	TRUE	NA	0.408273813266192	3		416	373	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717690	89717691	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0028843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	43	392	0	ENST00000371953.3:c.717_718dup	p.Tyr240CysfsTer17	p.Y240Cfs*17	ENST00000371953	NM_000314.4	239	atg/aTGtg	7/9	0.279261737020925	1	FACETS	0.428	0.358	0.504	0.428	0.358	0.504	SUBCLONAL	1	TRUE	0	0.408273813266192	1		392	392	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11022936	11022936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1202	90	631	1	ENST00000327064.4:c.635C>T	p.Ala212Val	p.A212V	ENST00000327064	NM_199141.1	212	gCg/gTg	5/16	0.408273813266192	5	FACETS	0.55	0.486	0.619			1	SUBCLONAL	1	TRUE	NA	0.408273813266192	5		632	1292	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719772	190719772	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	12	209	0	ENST00000441310.2:c.1774G>C	p.Glu592Gln	p.E592Q	ENST00000441310	NM_000534.4	592	Gaa/Caa	9/13	0.225744084922032	3	FACETS	0.319	0.224	0.436	0.106	0.074	0.146	INDETERMINATE	1	TRUE	0	0.408273813266192	3		209	222	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178714	32178714	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0028843-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	49	641	0	ENST00000375023.3:c.2681-1G>C		p.X894_splice	ENST00000375023	NM_004557.3	894			0.164342704302656	3	FACETS	0.452	0.382	0.53	0.151	0.127	0.177	INDETERMINATE	1	TRUE	0	0.408273813266192	3		641	639	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814930	139814930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371121908	NA	P-0029161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	215	636	0	ENST00000247668.2:c.923G>A	p.Arg308Gln	p.R308Q	ENST00000247668	NM_021138.3	308	cGg/cAg	8/11	1	2	FACETS	0.474	0.44	0.508	0.474	0.44	0.508	SUBCLONAL	1	TRUE	1	0.905993812645263	2		636	1002	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849851	156849851	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	241	694	0	ENST00000524377.1:c.2107A>G	p.Lys703Glu	p.K703E	ENST00000524377	NM_002529.3	703	Aag/Gag	16/17	0.440434250495044	2	FACETS	0.528	0.493	0.564	0.264	0.246	0.282	INDETERMINATE	1	TRUE	0	0.905993812645263	2		694	1008	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101197	41101197	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568910629	NA	P-0029161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	142	584	1	ENST00000373198.4:c.1159G>A	p.Val387Ile	p.V387I	ENST00000373198	NM_133170.3	387	Gta/Ata	8/32	0.262191247937157	4	FACETS	0.582	0.53	0.638	0.291	0.265	0.319	INDETERMINATE	1	TRUE	2	0.905993812645263	4		585	1026	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484256	57484257	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0029161-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	175	362	0	ENST00000371085.3:c.572_573del	p.Val191AlafsTer18	p.V191Afs*18	ENST00000371085	NM_000516.4	190	taTGtg/tatg	7/13	0.549466521571675	4	FACETS	0.623	0.573	0.676			1	SUBCLONAL	1	TRUE	NA	0.905993812645263	4		362	1181	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0029338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	278	738	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.259276985232384	3	FACETS	0.891	0.846	0.937	0.891	0.846	0.937	INDETERMINATE	2	TRUE	1	0.746193997620599	3		738	574	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0029338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	516	399	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.746193997620599	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.746193997620599	1		399	735	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0029338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	210	358	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.223306273810302	2	FACETS	1	0.991	1	0.648	0.61	0.687	INDETERMINATE	1	TRUE	0	0.746193997620599	2		358	434	SUCCESS
APC	324	MSKCC	GRCh37	5	112173627	112173627	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0029338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	114	437	0	ENST00000257430.4:c.2336T>A	p.Leu779Ter	p.L779*	ENST00000257430	NM_000038.5	779	tTa/tAa	16/16	0.223306273810302	2	FACETS	0.704	0.638	0.773	0.352	0.319	0.387	INDETERMINATE	1	TRUE	0	0.746193997620599	2		437	434	SUCCESS
APC	324	MSKCC	GRCh37	5	112175765	112175765	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691144	NA	P-0029338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	159	345	0	ENST00000257430.4:c.4474del	p.Ala1492ProfsTer15	p.A1492Pfs*15	ENST00000257430	NM_000038.5	1492	Gcc/cc	16/16	0.223306273810302	2	FACETS	1	0.968	1	0.539	0.5	0.579	INDETERMINATE	1	TRUE	0	0.746193997620599	2		345	395	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0029338-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	121	738	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.271715672158968	1	FACETS	0.684	0.624	0.746	0.684	0.624	0.746	INDETERMINATE	1	TRUE	0	0.633217886023771	1		738	382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0029338-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	430	399	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.633217886023771	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.633217886023771	1		399	904	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0029338-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	83	358	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.361807502040458	0	FACETS	0.324	0.289	0.361			1	INDETERMINATE	1	TRUE	0	0.633217886023771	0		358	297	SUCCESS
APC	324	MSKCC	GRCh37	5	112173627	112173627	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0029338-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	130	437	0	ENST00000257430.4:c.2336T>A	p.Leu779Ter	p.L779*	ENST00000257430	NM_000038.5	779	tTa/tAa	16/16	1	2	FACETS	0.971	0.888	1	0.971	0.888	1	CLONAL	1	TRUE	1	0.633217886023771	2		437	423	SUCCESS
APC	324	MSKCC	GRCh37	5	112175765	112175765	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691144	NA	P-0029338-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	89	345	0	ENST00000257430.4:c.4474del	p.Ala1492ProfsTer15	p.A1492Pfs*15	ENST00000257430	NM_000038.5	1492	Gcc/cc	16/16	1	2	FACETS	0.742	0.662	0.825	0.742	0.662	0.825	SUBCLONAL	1	TRUE	1	0.633217886023771	2		345	379	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54956626	54956626	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029338-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	39	390	1	ENST00000312783.6:c.568C>T	p.His190Tyr	p.H190Y	ENST00000312783	NM_198436.1	190	Cat/Tat	7/10	0.633217886023771	4	FACETS	0.369	0.305	0.44	0.123	0.101	0.147	SUBCLONAL	1	TRUE	1	0.633217886023771	4		391	545	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	66	209	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.97	0.852	1	0.97	0.852	1	CLONAL	1	TRUE	1	0.529353559277132	2		209	257	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	19	561	0	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	1	2	FACETS	0.098	0.073	0.127	0.098	0.073	0.127	SUBCLONAL	1	TRUE	1	0.529353559277132	2		561	734	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	196	537	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.529353559277132	2		537	691	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032374	11032374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs909244932	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	46	733	0	ENST00000327064.4:c.1768G>A	p.Ala590Thr	p.A590T	ENST00000327064	NM_199141.1	590	Gcc/Acc	16/16	1	2	FACETS	0.269	0.226	0.317	0.269	0.226	0.317	SUBCLONAL	1	TRUE	1	0.529353559277132	2		733	646	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470573	25470573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553414070	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	161	558	1	ENST00000264709.3:c.901C>T	p.Arg301Trp	p.R301W	ENST00000264709	NM_175629.2	301	Cgg/Tgg	8/23	1	2	FACETS	0.899	0.827	0.973	0.899	0.827	0.973	CLONAL	1	TRUE	1	0.529353559277132	2		559	677	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	142	252	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.529353559277132	2		252	467	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41536164	41536164	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750740148	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	157	396	0	ENST00000263253.7:c.1781C>T	p.Thr594Met	p.T594M	ENST00000263253	NM_001429.3	594	aCg/aTg	9/31	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.529353559277132	2		396	566	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	30	283	2	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	1	1	FACETS	1	0.836	1	1	0.836	1	CLONAL	1	TRUE	0	0.529353559277132	1		285	83	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975472	13975473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs769886672	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	57	287	2	ENST00000405192.2:c.414dup	p.Thr139HisfsTer24	p.T139Hfs*24	ENST00000405192	NM_001163147.1	138	-/C	7/12	1	2	FACETS	0.761	0.658	0.871	0.761	0.658	0.871	SUBCLONAL	1	TRUE	1	0.529353559277132	2		289	283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	172	794	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.529353559277132	2		794	630	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202313	133202313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756301031	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	149	474	1	ENST00000320574.5:c.6575C>T	p.Ala2192Val	p.A2192V	ENST00000320574	NM_006231.2	2192	gCg/gTg	47/49	1	2	FACETS	0.984	0.904	1	0.984	0.904	1	CLONAL	1	TRUE	1	0.529353559277132	2		475	572	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440855	52440855	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553645702	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	35	433	0	ENST00000460680.1:c.649G>A	p.Ala217Thr	p.A217T	ENST00000460680	NM_004656.3	217	Gcc/Acc	8/17	1	2	FACETS	0.236	0.193	0.285	0.236	0.193	0.285	SUBCLONAL	1	TRUE	1	0.529353559277132	2		433	560	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	147	358	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.529353559277132	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.529353559277132	1		358	374	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333863	70333863	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs750883311	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	85	341	1	ENST00000373644.4:c.1768C>T	p.Arg590Ter	p.R590*	ENST00000373644	NM_030625.2	590	Cga/Tga	2/12	1	2	FACETS	0.923	0.823	1	0.923	0.823	1	CLONAL	1	TRUE	1	0.529353559277132	2		342	348	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299832	15299832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465285176	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	38	524	1	ENST00000263388.2:c.1346G>A	p.Arg449His	p.R449H	ENST00000263388	NM_000435.2	449	cGc/cAc	8/33	1	2	FACETS	0.208	0.171	0.249	0.208	0.171	0.249	SUBCLONAL	1	TRUE	1	0.529353559277132	2		525	690	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472142	472142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1309760726	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	146	358	0	ENST00000399788.2:c.659G>A	p.Arg220His	p.R220H	ENST00000399788	NM_001042603.1	220	cGt/cAt	5/28	NA	2	FACETS	1	0.952	1			1	INDETERMINATE	1	TRUE	NA	0.529353559277132	2		358	524	SUCCESS
AR	367	MSKCC	GRCh37	X	66766276	66766276	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755088348	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	17	158	0	ENST00000374690.3:c.1288G>A	p.Ala430Thr	p.A430T	ENST00000374690	NM_000044.3	430	Gcc/Acc	1/8	1	1	FACETS	0.317	0.238	0.409	0.317	0.238	0.409	SUBCLONAL	1	TRUE	0	0.529353559277132	1		158	149	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927019	131927019	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140333740	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	78	303	0	ENST00000265335.6:c.1556G>A	p.Arg519His	p.R519H	ENST00000265335		519	cGt/cAt	10/25	0.529353559277132	1	FACETS	0.999	0.893	1	0.999	0.893	1	CLONAL	1	TRUE	0	0.529353559277132	1		303	217	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428326	33428326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779808083	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	156	436	0	ENST00000345365.6:c.797G>A	p.Arg266His	p.R266H	ENST00000345365	NM_002878.3	266	cGc/cAc	9/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.529353559277132	2		436	544	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90633818	90633818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371777275	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	142	520	0	ENST00000330062.3:c.266G>A	p.Arg89His	p.R89H	ENST00000330062	NM_002168.2	89	cGt/cAt	3/11	1	2	FACETS	0.846	0.774	0.922	0.846	0.774	0.922	CLONAL	1	TRUE	1	0.529353559277132	2		520	634	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	128	480	0	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	0.818	0.744	0.896	0.818	0.744	0.896	CLONAL	1	TRUE	1	0.529353559277132	2		480	591	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215787	98215787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376844749	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	174	357	1	ENST00000331920.6:c.3422C>T	p.Ala1141Val	p.A1141V	ENST00000331920	NM_000264.3	1141	gCg/gTg	20/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.529353559277132	2		358	609	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219579	133219579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542430685	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	21	372	0	ENST00000320574.5:c.4555C>T	p.Arg1519Cys	p.R1519C	ENST00000320574	NM_006231.2	1519	Cgc/Tgc	36/49	1	2	FACETS	0.192	0.147	0.245	0.192	0.147	0.245	SUBCLONAL	1	TRUE	1	0.529353559277132	2		372	413	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435631	149435631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs690016557	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	34	497	2	ENST00000286301.3:c.2512G>A	p.Val838Ile	p.V838I	ENST00000286301	NM_005211.3	838	Gtc/Atc	19/22	0.529353559277132	1	FACETS	0.244	0.199	0.294	0.244	0.199	0.294	SUBCLONAL	1	TRUE	0	0.529353559277132	1		499	387	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448564	89448564	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1184230536	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	141	426	0	ENST00000336596.2:c.1528C>T	p.Arg510Ter	p.R510*	ENST00000336596	NM_005233.5	510	Cga/Tga	7/17	1	2	FACETS	0.876	0.801	0.954	0.876	0.801	0.954	CLONAL	1	TRUE	1	0.529353559277132	2		426	608	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687471	37687472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs760014508	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	66	382	4	ENST00000447079.4:c.4382dup	p.Thr1463AsnfsTer50	p.T1463Nfs*50	ENST00000447079	NM_015083.1	1459	tgg/tGgg	14/14	1	2	FACETS	0.866	0.759	0.98	0.866	0.759	0.98	CLONAL	1	TRUE	1	0.529353559277132	2		386	288	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739479	145739479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748941688	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	140	443	0	ENST00000428558.2:c.1891C>T	p.Arg631Cys	p.R631C	ENST00000428558	NM_004260.3	631	Cgc/Tgc	12/22	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.529353559277132	2		443	493	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562477	21562477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757658067	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	14	128	0	ENST00000382592.4:c.1442C>T	p.Ala481Val	p.A481V	ENST00000382592	NM_014572.2	481	gCg/gTg	4/8	0.511955375537527	2	FACETS	0.372	0.271	0.494	0.186	0.135	0.247	SUBCLONAL	1	TRUE	0	0.529353559277132	2		128	142	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066534	94066534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1402331883	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	106	342	1	ENST00000369303.4:c.1225G>A	p.Ala409Thr	p.A409T	ENST00000369303	NM_004440.3	409	Gct/Act	5/17	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.529353559277132	2		343	376	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412095	63412095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852217	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	170	319	0	ENST00000330258.3:c.1072C>T	p.Arg358Ter	p.R358*	ENST00000330258	NM_152424.3	358	Cga/Tga	2/2	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.529353559277132	1		319	359	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714409	117714409	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	35	371	0	ENST00000368508.3:c.1240del	p.Ile414LeufsTer14	p.I414Lfs*14	ENST00000368508	NM_002944.2	414	Att/tt	11/43	1	2	FACETS	0.275	0.225	0.331	0.275	0.225	0.331	SUBCLONAL	1	TRUE	1	0.529353559277132	2		371	481	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552222	29552222	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778549	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	125	412	0	ENST00000356175.3:c.1955G>A	p.Arg652His	p.R652H	ENST00000356175	NM_000267.3	652	cGt/cAt	17/57	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.529353559277132	2		412	456	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477160	67477160	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs967072552	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	134	389	1	ENST00000327367.4:c.967C>T	p.Arg323Cys	p.R323C	ENST00000327367	NM_005902.3	323	Cgc/Tgc	7/9	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.529353559277132	2		390	504	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098591	11098591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854197	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	165	437	0	ENST00000358026.2:c.1109G>A	p.Arg370His	p.R370H	ENST00000358026	NM_001128849.1	370	cGc/cAc	6/36	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.529353559277132	2		437	607	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95595941	95595941	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749484792	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	101	392	0	ENST00000393063.1:c.602G>A	p.Arg201His	p.R201H	ENST00000393063	NM_030621.3	201	cGc/cAc	7/28	1	2	FACETS	0.848	0.762	0.938	0.848	0.762	0.938	CLONAL	1	TRUE	1	0.529353559277132	2		392	450	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831953	72831953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	60	580	0	ENST00000268489.5:c.4628G>A	p.Arg1543His	p.R1543H	ENST00000268489	NM_006885.3	1543	cGc/cAc	9/10	1	2	FACETS	0.275	0.236	0.318	0.275	0.236	0.318	SUBCLONAL	1	TRUE	1	0.529353559277132	2		580	823	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286237	66286238	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	89	337	0	ENST00000273854.3:c.1448dup	p.Asn483LysfsTer21	p.N483Kfs*21	ENST00000273854	NM_004439.5	483	aac/aaAc	6/18	1	2	FACETS	0.924	0.826	1	0.924	0.826	1	CLONAL	1	TRUE	1	0.529353559277132	2		337	364	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641487	23641487	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1462734899	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	143	564	0	ENST00000261584.4:c.1988G>A	p.Arg663His	p.R663H	ENST00000261584	NM_024675.3	663	cGc/cAc	5/13	1	2	FACETS	0.859	0.786	0.935	0.859	0.786	0.935	CLONAL	1	TRUE	1	0.529353559277132	2		564	629	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090524	71090524	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs914703084	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	82	276	0	ENST00000318789.4:c.824C>T	p.Ala275Val	p.A275V	ENST00000318789	NM_032682.5	275	gCc/gTc	11/21	1	2	FACETS	0.741	0.657	0.831	0.741	0.657	0.831	SUBCLONAL	1	TRUE	1	0.529353559277132	2		276	418	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740840	58740840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149137187	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	157	417	0	ENST00000305921.3:c.1745G>A	p.Arg582His	p.R582H	ENST00000305921	NM_003620.3	582	cGc/cAc	6/6	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.529353559277132	2		417	582	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736510	85736511	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs387906351	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	86	293	1	ENST00000370580.1:c.136dup	p.Ile46AsnfsTer4	p.I46Nfs*4	ENST00000370580	NM_003921.4	46	ata/aAta	2/3	1	2	FACETS	0.84	0.748	0.937	0.84	0.748	0.937	CLONAL	1	TRUE	1	0.529353559277132	2		294	387	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041518	14041518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149364215	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	98	328	1	ENST00000311895.7:c.2065C>T	p.Arg689Cys	p.R689C	ENST00000311895	NM_005236.2	689	Cgt/Tgt	11/11	1	2	FACETS	0.863	0.775	0.956	0.863	0.775	0.956	CLONAL	1	TRUE	1	0.529353559277132	2		329	429	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163554	32163554	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	105	472	1	ENST00000375023.3:c.5672del	p.Gly1891AlafsTer13	p.G1891Afs*13	ENST00000375023	NM_004557.3	1891	gGc/gc	30/30	1	2	FACETS	0.938	0.846	1	0.938	0.846	1	CLONAL	1	TRUE	1	0.529353559277132	2		473	423	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839743	42839743	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs936556491	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	179	503	1	ENST00000398585.3:c.1496G>A	p.Gly499Asp	p.G499D	ENST00000398585	NM_001135099.1	499	gGt/gAt	13/14	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.529353559277132	2		504	626	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134230	11134230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1227826852	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	139	485	1	ENST00000358026.2:c.2896C>T	p.Arg966Trp	p.R966W	ENST00000358026	NM_001128849.1	966	Cgg/Tgg	20/36	1	2	FACETS	0.941	0.861	1	0.941	0.861	1	CLONAL	1	TRUE	1	0.529353559277132	2		486	558	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134885807	134885807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	113	424	0	ENST00000398015.3:c.1718C>T	p.Ala573Val	p.A573V	ENST00000398015	NM_004441.4	573	gCt/gTt	9/16	1	2	FACETS	0.844	0.763	0.928	0.844	0.763	0.928	CLONAL	1	TRUE	1	0.529353559277132	2		424	506	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505508	25505508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753287419	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	34	472	2	ENST00000264709.3:c.250G>A	p.Ala84Thr	p.A84T	ENST00000264709	NM_175629.2	84	Gcc/Acc	4/23	1	2	FACETS	0.232	0.189	0.281	0.232	0.189	0.281	SUBCLONAL	1	TRUE	1	0.529353559277132	2		474	553	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205667	128205667	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	111	431	0	ENST00000341105.2:c.208G>A	p.Val70Ile	p.V70I	ENST00000341105	NM_032638.4	70	Gtc/Atc	2/6	1	2	FACETS	0.953	0.863	1	0.953	0.863	1	CLONAL	1	TRUE	1	0.529353559277132	2		431	440	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112422	115112422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775182377	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	135	395	0	ENST00000257566.3:c.1318G>A	p.Ala440Thr	p.A440T	ENST00000257566	NM_016569.3	440	Gcc/Acc	7/8	1	2	FACETS	0.977	0.893	1	0.977	0.893	1	CLONAL	1	TRUE	1	0.529353559277132	2		395	522	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955111	17955112	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755706305	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	163	571	0	ENST00000458235.1:c.115dup	p.Gln39ProfsTer13	p.Q39Pfs*13	ENST00000458235	NM_000215.3	39	cag/cCag	2/24	1	2	FACETS	0.864	0.795	0.935	0.864	0.795	0.935	CLONAL	1	TRUE	1	0.529353559277132	2		571	713	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631917	90631918	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs747216375	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	167	482	5	ENST00000330062.3:c.435dup	p.Thr146AspfsTer126	p.T146Dfs*126	ENST00000330062	NM_002168.2	145	-/G	4/11	1	2	FACETS	0.952	0.878	1	0.952	0.878	1	CLONAL	1	TRUE	1	0.529353559277132	2		487	663	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228613001	228613001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373549345	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	95	294	0	ENST00000366696.1:c.26G>A	p.Arg9His	p.R9H	ENST00000366696	NM_003493.2	9	cGc/cAc	1/1	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.529353559277132	2		294	315	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481461	20481461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	75	262	0	ENST00000346618.3:c.530C>T	p.Thr177Met	p.T177M	ENST00000346618	NM_001949.4	177	aCg/aTg	3/7	1	2	FACETS	0.856	0.756	0.962	0.856	0.756	0.962	CLONAL	1	TRUE	1	0.529353559277132	2		262	331	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88671959	88671959	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767919095	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	94	321	1	ENST00000360948.2:c.1211C>T	p.Thr404Met	p.T404M	ENST00000360948	NM_001012338.2	404	aCg/aTg	10/19	1	2	FACETS	0.842	0.753	0.934	0.842	0.753	0.934	CLONAL	1	TRUE	1	0.529353559277132	2		322	422	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167550	24167550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749348930	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	157	446	1	ENST00000263121.7:c.934G>A	p.Ala312Thr	p.A312T	ENST00000263121	NM_003073.3	312	Gca/Aca	7/9	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.529353559277132	2		447	564	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277225	41277225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760837728	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	20	356	0	ENST00000349496.5:c.1694G>A	p.Arg565His	p.R565H	ENST00000349496	NM_001904.3	565	cGc/cAc	11/15	1	2	FACETS	0.217	0.165	0.277	0.217	0.165	0.277	SUBCLONAL	1	TRUE	1	0.529353559277132	2		356	349	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101690	27101690	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1442666063	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	145	627	1	ENST00000324856.7:c.4972C>T	p.Arg1658Trp	p.R1658W	ENST00000324856	NM_006015.4	1658	Cgg/Tgg	18/20	1	2	FACETS	0.671	0.613	0.733	0.671	0.613	0.733	SUBCLONAL	1	TRUE	1	0.529353559277132	2		628	816	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217306	123217306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768937075	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	169	245	0	ENST00000218089.9:c.2960C>T	p.Pro987Leu	p.P987L	ENST00000218089	NM_001042749.1	987	cCg/cTg	29/35	1	1	FACETS	0.81	0.761	0.857	1	0.993	1	CLONAL	2	TRUE	0	0.529353559277132	1		245	290	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729844	41729844	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs908163566	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	79	301	0	ENST00000242208.4:c.685C>T	p.Arg229Trp	p.R229W	ENST00000242208	NM_002192.2	229	Cgg/Tgg	3/3	1	2	FACETS	0.873	0.774	0.977	0.873	0.774	0.977	CLONAL	1	TRUE	1	0.529353559277132	2		301	342	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552710	226552710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	102	306	0	ENST00000366794.5:c.2651C>T	p.Ala884Val	p.A884V	ENST00000366794	NM_001618.3	884	gCg/gTg	19/23	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.529353559277132	2		306	374	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129418	64129418	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	184	779	2	ENST00000334205.4:c.850C>T	p.Arg284Ter	p.R284*	ENST00000334205	NM_003942.2	284	Cga/Tga	8/17	1	2	FACETS	0.989	0.916	1	0.989	0.916	1	CLONAL	1	TRUE	1	0.529353559277132	2		781	703	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912349	97912349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs182879858	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	131	311	2	ENST00000289081.3:c.542C>T	p.Ala181Val	p.A181V	ENST00000289081	NM_000136.2	181	gCg/gTg	7/15	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.529353559277132	2		313	468	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277075	18277075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376215289	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	132	419	0	ENST00000222254.8:c.1522C>T	p.Arg508Cys	p.R508C	ENST00000222254	NM_005027.3	508	Cgc/Tgc	12/16	1	2	FACETS	0.902	0.822	0.985	0.902	0.822	0.985	CLONAL	1	TRUE	1	0.529353559277132	2		419	553	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181431	185181431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377513650	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	142	395	0	ENST00000265026.3:c.1372C>T	p.Arg458Cys	p.R458C	ENST00000265026	NM_004721.4	458	Cgc/Tgc	8/14	1	2	FACETS	0.984	0.902	1	0.984	0.902	1	CLONAL	1	TRUE	1	0.529353559277132	2		395	545	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911260	29911260	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs543623321	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	16	280	1	ENST00000376809.5:c.559A>G	p.Thr187Ala	p.T187A	ENST00000376809	NM_002116.7	187	Acg/Gcg	3/8	1	2	FACETS	0.194	0.143	0.255	0.194	0.143	0.255	SUBCLONAL	1	TRUE	1	0.529353559277132	2		281	312	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014298	70014298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142372494	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	135	451	0	ENST00000394351.3:c.1159G>A	p.Gly387Ser	p.G387S	ENST00000394351	NM_000248.3	387	Ggt/Agt	9/9	1	2	FACETS	0.865	0.789	0.944	0.865	0.789	0.944	CLONAL	1	TRUE	1	0.529353559277132	2		451	590	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868072	56868072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771065608	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	26	316	0	ENST00000308159.5:c.1570C>T	p.Arg524Trp	p.R524W	ENST00000308159	NM_014669.4	524	Cgg/Tgg	14/22	1	2	FACETS	0.197	0.156	0.245	0.197	0.156	0.245	SUBCLONAL	1	TRUE	1	0.529353559277132	2		316	498	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509661	106509661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1182076194	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	39	444	1	ENST00000359195.3:c.1655G>A	p.Arg552His	p.R552H	ENST00000359195	NM_002649.2	552	cGc/cAc	2/11	1	2	FACETS	0.294	0.243	0.35	0.294	0.243	0.35	SUBCLONAL	1	TRUE	1	0.529353559277132	2		445	502	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095913	178095914	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1323566743	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	105	352	2	ENST00000397062.3:c.1417dup	p.Ile473AsnfsTer3	p.I473Nfs*3	ENST00000397062	NM_006164.4	473	atc/aAtc	5/5	1	2	FACETS	0.872	0.786	0.962	0.872	0.786	0.962	CLONAL	1	TRUE	1	0.529353559277132	2		354	455	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601228	28601228	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772146579	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	151	379	0	ENST00000241453.7:c.2204C>T	p.Ser735Phe	p.S735F	ENST00000241453	NM_004119.2	735	tCc/tTc	17/24	0.511955375537527	2	FACETS	1	0.967	1	0.549	0.505	0.594	CLONAL	1	TRUE	0	0.529353559277132	2		379	520	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219934	36219934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	32	534	0	ENST00000222270.7:c.4736G>A	p.Arg1579His	p.R1579H	ENST00000222270	NM_014727.1	1579	cGt/cAt	21/37	1	2	FACETS	0.21	0.17	0.256	0.21	0.17	0.256	SUBCLONAL	1	TRUE	1	0.529353559277132	2		534	576	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533839	533839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749674880	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	56	552	0	ENST00000451590.1:c.217C>T	p.Arg73Cys	p.R73C	ENST00000451590	NM_001130442.1	73	Cgc/Tgc	3/5	1	2	FACETS	0.29	0.248	0.336	0.29	0.248	0.336	SUBCLONAL	1	TRUE	1	0.529353559277132	2		552	730	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46727002	46727002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1363172157	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	120	365	1	ENST00000371975.4:c.836G>A	p.Arg279His	p.R279H	ENST00000371975	NM_003579.3	279	cGc/cAc	8/18	1	2	FACETS	0.874	0.793	0.958	0.874	0.793	0.958	CLONAL	1	TRUE	1	0.529353559277132	2		366	519	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705201	52705201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1372727039	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	104	287	1	ENST00000322088.6:c.83G>A	p.Arg28His	p.R28H	ENST00000322088	NM_014225.5	28	cGc/cAc	2/15	1	2	FACETS	0.973	0.878	1	0.973	0.878	1	CLONAL	1	TRUE	1	0.529353559277132	2		288	404	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939413	71939413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148394356	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	70	628	0	ENST00000298229.2:c.268C>T	p.Arg90Cys	p.R90C	ENST00000298229	NM_001567.3	90	Cgc/Tgc	3/28	1	2	FACETS	0.406	0.353	0.462	0.406	0.353	0.462	SUBCLONAL	1	TRUE	1	0.529353559277132	2		628	652	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45396936	45396936	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	22	224	0	ENST00000262160.6:c.237-1G>A		p.X79_splice	ENST00000262160	NM_005901.5	79			1	2	FACETS	0.278	0.215	0.351	0.278	0.215	0.351	SUBCLONAL	1	TRUE	1	0.529353559277132	2		224	299	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606811	43606811	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775842917	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	164	576	2	ENST00000355710.3:c.1420C>T	p.Arg474Trp	p.R474W	ENST00000355710	NM_020975.4	474	Cgg/Tgg	7/20	1	2	FACETS	0.962	0.887	1	0.962	0.887	1	CLONAL	1	TRUE	1	0.529353559277132	2		578	644	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86686625	86686626	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	81	260	0	ENST00000274376.6:c.3074dup	p.Leu1026AlafsTer20	p.L1026Afs*20	ENST00000274376	NM_002890.2	1023	-/A	25/25	0.529353559277132	1	FACETS	0.843	0.752	0.937	0.843	0.752	0.937	CLONAL	1	TRUE	0	0.529353559277132	1		260	267	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550577	29550577	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	88	253	0	ENST00000356175.3:c.1841del	p.Asn614IlefsTer17	p.N614Ifs*17	ENST00000356175	NM_000267.3	613	Aaa/aa	16/57	1	2	FACETS	0.884	0.789	0.984	0.884	0.789	0.984	CLONAL	1	TRUE	1	0.529353559277132	2		253	376	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574405	95574405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	101	239	1	ENST00000393063.1:c.2462G>A	p.Arg821His	p.R821H	ENST00000393063	NM_030621.3	821	cGc/cAc	17/28	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.529353559277132	2		240	343	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524960	187524960	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767643023	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	168	502	0	ENST00000441802.2:c.10720G>A	p.Val3574Met	p.V3574M	ENST00000441802	NM_005245.3	3574	Gtg/Atg	19/27	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.529353559277132	2		502	604	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753276	42753276	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756887571	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	49	563	0	ENST00000222329.4:c.988G>A	p.Ala330Thr	p.A330T	ENST00000222329	NM_006494.2	330	Gcc/Acc	4/4	1	2	FACETS	0.235	0.198	0.276	0.235	0.198	0.276	SUBCLONAL	1	TRUE	1	0.529353559277132	2		563	787	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112326	115112326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1302202171	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	60	149	0	ENST00000257566.3:c.1414G>A	p.Ala472Thr	p.A472T	ENST00000257566	NM_016569.3	472	Gcg/Acg	7/8	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.529353559277132	2		149	205	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716301	52716301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	51	419	0	ENST00000322088.6:c.745C>T	p.Arg249Cys	p.R249C	ENST00000322088	NM_014225.5	249	Cgc/Tgc	6/15	1	2	FACETS	0.377	0.32	0.439	0.377	0.32	0.439	SUBCLONAL	1	TRUE	1	0.529353559277132	2		419	511	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911882	94911882	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1412449950	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	170	452	0	ENST00000536441.1:c.1048C>T	p.Arg350Ter	p.R350*	ENST00000536441	NM_144665.3	350	Cga/Tga	7/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.529353559277132	2		452	608	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520202	176520202	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763979974	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	196	596	1	ENST00000292408.4:c.1121C>T	p.Ala374Val	p.A374V	ENST00000292408	NM_213647.1	374	gCg/gTg	9/18	0.529353559277132	1	FACETS	0.999	0.932	1	0.999	0.932	1	CLONAL	1	TRUE	0	0.529353559277132	1		597	545	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836295	151836295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	149	360	1	ENST00000262189.6:c.14510C>T	p.Ala4837Val	p.A4837V	ENST00000262189	NM_170606.2	4837	gCg/gTg	57/59	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.529353559277132	2		361	560	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712907	43712907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	140	454	0	ENST00000382044.4:c.4277G>A	p.Gly1426Asp	p.G1426D	ENST00000382044	NM_001141980.1	1426	gGc/gAc	21/28	1	2	FACETS	0.958	0.877	1	0.958	0.877	1	CLONAL	1	TRUE	1	0.529353559277132	2		454	552	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023326	27023327	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	55	163	0	ENST00000324856.7:c.437dup	p.Ala147SerfsTer253	p.A147Sfs*253	ENST00000324856	NM_006015.4	144	-/C	1/20	1	2	FACETS	0.976	0.846	1	0.976	0.846	1	CLONAL	1	TRUE	1	0.529353559277132	2		163	213	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164838	36164838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1282562937	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	145	571	0	ENST00000300305.3:c.1037G>A	p.Arg346His	p.R346H	ENST00000300305		346	cGc/cAc	8/8	1	2	FACETS	0.738	0.675	0.805	0.738	0.675	0.805	SUBCLONAL	1	TRUE	1	0.529353559277132	2		571	742	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205805	108205805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	34	352	0	ENST00000278616.4:c.8120C>T	p.Ser2707Phe	p.S2707F	ENST00000278616	NM_000051.3	2707	tCc/tTc	55/63	1	2	FACETS	0.269	0.22	0.325	0.269	0.22	0.325	SUBCLONAL	1	TRUE	1	0.529353559277132	2		352	477	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093411	30093411	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs201154555	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	126	418	1	ENST00000331968.5:c.1852C>T	p.Arg618Ter	p.R618*	ENST00000331968	NM_002742.2	618	Cga/Tga	13/18	1	2	FACETS	0.862	0.784	0.944	0.862	0.784	0.944	CLONAL	1	TRUE	1	0.529353559277132	2		419	552	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781907	9781907	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	131	503	2	ENST00000377346.4:c.2044C>A	p.Leu682Met	p.L682M	ENST00000377346	NM_005026.3	682	Ctg/Atg	16/24	1	2	FACETS	0.965	0.88	1	0.965	0.88	1	CLONAL	1	TRUE	1	0.529353559277132	2		505	513	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298063	11298063	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778348776	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	123	406	0	ENST00000361445.4:c.2045G>A	p.Arg682His	p.R682H	ENST00000361445	NM_004958.3	682	cGc/cAc	13/58	1	2	FACETS	0.817	0.741	0.896	0.817	0.741	0.896	CLONAL	1	TRUE	1	0.529353559277132	2		406	569	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260692	16260692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201348264	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	149	506	0	ENST00000375759.3:c.7957G>A	p.Ala2653Thr	p.A2653T	ENST00000375759	NM_015001.2	2653	Gca/Aca	11/15	1	2	FACETS	0.972	0.892	1	0.972	0.892	1	CLONAL	1	TRUE	1	0.529353559277132	2		506	579	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262304	16262304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	49	176	0	ENST00000375759.3:c.9569C>T	p.Thr3190Ile	p.T3190I	ENST00000375759	NM_015001.2	3190	aCt/aTt	11/15	1	2	FACETS	0.882	0.756	1	0.882	0.756	1	CLONAL	1	TRUE	1	0.529353559277132	2		176	210	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363267	40363267	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748297163	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	166	421	2	ENST00000397332.2:c.962G>A	p.Arg321His	p.R321H	ENST00000397332	NM_001033082.2	321	cGc/cAc	3/3	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.529353559277132	2		423	566	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797401	45797401	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35352891	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	145	530	0	ENST00000450313.1:c.1118C>T	p.Ala373Val	p.A373V	ENST00000450313	NM_012222.2	373	gCc/gTc	12/16	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.529353559277132	2		530	537	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400916	72400916	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	92	354	0	ENST00000357731.5:c.255G>A	p.Trp85Ter	p.W85*	ENST00000357731	NM_173808.2	85	tgG/tgA	2/7	1	2	FACETS	0.873	0.781	0.97	0.873	0.781	0.97	CLONAL	1	TRUE	1	0.529353559277132	2		354	398	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166418	118166418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	108	371	1	ENST00000369448.3:c.928C>T	p.Leu310Phe	p.L310F	ENST00000369448	NM_017709.3	310	Ctt/Ttt	2/2	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.529353559277132	2		372	353	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120478223	120478223	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	96	319	0	ENST00000256646.2:c.3527T>C	p.Val1176Ala	p.V1176A	ENST00000256646	NM_024408.3	1176	gTc/gCc	22/34	1	2	FACETS	0.972	0.874	1	0.972	0.874	1	CLONAL	1	TRUE	1	0.529353559277132	2		319	373	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844722	156844722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs986498490	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	179	597	2	ENST00000524377.1:c.1276G>A	p.Val426Ile	p.V426I	ENST00000524377	NM_002529.3	426	Gtc/Atc	11/17	1	2	FACETS	0.901	0.832	0.971	0.901	0.832	0.971	CLONAL	1	TRUE	1	0.529353559277132	2		599	751	SUCCESS
FH	2271	MSKCC	GRCh37	1	241683013	241683013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	77	411	0	ENST00000366560.3:c.10G>A	p.Ala4Thr	p.A4T	ENST00000366560	NM_000143.3	4	Gca/Aca	1/10	1	2	FACETS	0.715	0.631	0.804	0.715	0.631	0.804	SUBCLONAL	1	TRUE	1	0.529353559277132	2		411	407	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246093240	246093240	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	110	371	0	ENST00000388985.4:c.532-1G>A		p.X178_splice	ENST00000388985		178			1	2	FACETS	0.9	0.813	0.99	0.9	0.813	0.99	CLONAL	1	TRUE	1	0.529353559277132	2		371	462	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450663	70450663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	119	420	0	ENST00000373644.4:c.5503C>T	p.Pro1835Ser	p.P1835S	ENST00000373644	NM_030625.2	1835	Cca/Tca	12/12	1	2	FACETS	0.839	0.76	0.921	0.839	0.76	0.921	CLONAL	1	TRUE	1	0.529353559277132	2		420	536	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	532716	532716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779101895	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	151	545	0	ENST00000451590.1:c.490C>T	p.Arg164Trp	p.R164W	ENST00000451590	NM_001130442.1	164	Cgg/Tgg	5/5	1	2	FACETS	0.883	0.81	0.959	0.883	0.81	0.959	CLONAL	1	TRUE	1	0.529353559277132	2		545	646	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933244	100933244	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	37	423	0	ENST00000325455.5:c.2146A>G	p.Thr716Ala	p.T716A	ENST00000325455	NM_001202474.3	716	Aca/Gca	4/8	1	2	FACETS	0.258	0.212	0.309	0.258	0.212	0.309	SUBCLONAL	1	TRUE	1	0.529353559277132	2		423	542	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098537	108098537	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1488019755	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	117	249	0	ENST00000278616.4:c.107A>G	p.Asp36Gly	p.D36G	ENST00000278616	NM_000051.3	36	gAt/gGt	3/63	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.529353559277132	2		249	411	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362551	118362551	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	128	350	0	ENST00000534358.1:c.4912G>A	p.Ala1638Thr	p.A1638T	ENST00000534358	NM_005933.3	1638	Gcc/Acc	15/36	1	2	FACETS	0.901	0.82	0.985	0.901	0.82	0.985	CLONAL	1	TRUE	1	0.529353559277132	2		350	537	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422242	422242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769792722	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	134	456	1	ENST00000399788.2:c.3016G>A	p.Ala1006Thr	p.A1006T	ENST00000399788	NM_001042603.1	1006	Gct/Act	20/28	NA	2	FACETS	0.887	0.809	0.968			1	INDETERMINATE	1	TRUE	NA	0.529353559277132	2		457	571	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231492	46231492	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	83	272	0	ENST00000334344.6:c.1330+2T>C		p.X444_splice	ENST00000334344	NM_152641.2	444			1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.529353559277132	2		272	312	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244743	46244743	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	152	449	0	ENST00000334344.6:c.2837T>A	p.Ile946Asn	p.I946N	ENST00000334344	NM_152641.2	946	aTt/aAt	15/21	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.529353559277132	2		449	571	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420090	49420090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746471452	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	25	431	1	ENST00000301067.7:c.15659G>A	p.Arg5220His	p.R5220H	ENST00000301067	NM_003482.3	5220	cGc/cAc	48/54	1	2	FACETS	0.196	0.153	0.244	0.196	0.153	0.244	SUBCLONAL	1	TRUE	1	0.529353559277132	2		432	483	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420657	49420657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746837652	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	105	428	0	ENST00000301067.7:c.15092G>A	p.Arg5031His	p.R5031H	ENST00000301067	NM_003482.3	5031	cGc/cAc	48/54	1	2	FACETS	0.918	0.828	1	0.918	0.828	1	CLONAL	1	TRUE	1	0.529353559277132	2		428	432	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442973	49442973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762289838	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	153	436	0	ENST00000301067.7:c.3935G>A	p.Arg1312His	p.R1312H	ENST00000301067	NM_003482.3	1312	cGc/cAc	12/54	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.529353559277132	2		436	571	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445592	49445592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774789138	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	153	777	1	ENST00000301067.7:c.1874G>A	p.Arg625His	p.R625H	ENST00000301067	NM_003482.3	625	cGc/cAc	10/54	1	2	FACETS	0.668	0.611	0.727	0.668	0.611	0.727	SUBCLONAL	1	TRUE	1	0.529353559277132	2		778	866	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447305	49447305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766543419	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	156	456	0	ENST00000301067.7:c.793C>T	p.Arg265Cys	p.R265C	ENST00000301067	NM_003482.3	265	Cgt/Tgt	6/54	1	2	FACETS	0.907	0.833	0.983	0.907	0.833	0.983	CLONAL	1	TRUE	1	0.529353559277132	2		456	650	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856566	111856566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1299251502	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	13	177	0	ENST00000341259.2:c.617C>T	p.Ala206Val	p.A206V	ENST00000341259	NM_005475.2	206	gCc/gTc	2/8	1	2	FACETS	0.202	0.144	0.273	0.202	0.144	0.273	SUBCLONAL	1	TRUE	1	0.529353559277132	2		177	243	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856569	111856569	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	47	174	0	ENST00000341259.2:c.620A>G	p.Asp207Gly	p.D207G	ENST00000341259	NM_005475.2	207	gAc/gGc	2/8	1	2	FACETS	0.749	0.638	0.869	0.749	0.638	0.869	SUBCLONAL	1	TRUE	1	0.529353559277132	2		174	237	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112230	115112230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780531262	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	83	242	1	ENST00000257566.3:c.1510G>A	p.Ala504Thr	p.A504T	ENST00000257566	NM_016569.3	504	Gcc/Acc	7/8	1	2	FACETS	0.989	0.882	1	0.989	0.882	1	CLONAL	1	TRUE	1	0.529353559277132	2		243	317	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879761	123879761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368237921	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	18	180	1	ENST00000330479.4:c.457G>A	p.Ala153Thr	p.A153T	ENST00000330479	NM_020382.3	153	Gcc/Acc	4/9	1	2	FACETS	0.26	0.195	0.335	0.26	0.195	0.335	SUBCLONAL	1	TRUE	1	0.529353559277132	2		181	262	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250204	133250204	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	134	458	0	ENST00000320574.5:c.1316T>C	p.Leu439Pro	p.L439P	ENST00000320574	NM_006231.2	439	cTa/cCa	13/49	1	2	FACETS	0.929	0.848	1	0.929	0.848	1	CLONAL	1	TRUE	1	0.529353559277132	2		458	545	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28903752	28903752	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs953968689	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	89	369	0	ENST00000282397.4:c.2707G>A	p.Gly903Arg	p.G903R	ENST00000282397	NM_002019.4	903	Ggg/Agg	19/30	0.511955375537527	2	FACETS	0.914	0.816	1	0.457	0.408	0.508	CLONAL	1	TRUE	0	0.529353559277132	2		369	368	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434772	110434772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	141	595	0	ENST00000375856.3:c.3629C>T	p.Ala1210Val	p.A1210V	ENST00000375856	NM_003749.2	1210	gCg/gTg	1/2	0.511955375537527	2	FACETS	0.923	0.845	1	0.462	0.422	0.503	CLONAL	1	TRUE	0	0.529353559277132	2		595	577	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435255	110435255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1042990241	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	77	252	0	ENST00000375856.3:c.3146C>T	p.Ala1049Val	p.A1049V	ENST00000375856	NM_003749.2	1049	gCc/gTc	1/2	0.511955375537527	2	FACETS	0.973	0.863	1	0.486	0.431	0.545	CLONAL	1	TRUE	0	0.529353559277132	2		252	299	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066960	30066960	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	90	331	0	ENST00000331968.5:c.2171A>G	p.Lys724Arg	p.K724R	ENST00000331968	NM_002742.2	724	aAa/aGa	16/18	1	2	FACETS	0.966	0.865	1	0.966	0.865	1	CLONAL	1	TRUE	1	0.529353559277132	2		331	352	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986629	36986629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	12	156	0	ENST00000354822.5:c.1060G>A	p.Ala354Thr	p.A354T	ENST00000354822	NM_001079668.2	354	Gca/Aca	3/3	1	2	FACETS	0.268	0.189	0.366	0.268	0.189	0.366	SUBCLONAL	1	TRUE	1	0.529353559277132	2		156	169	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986947	36986947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	163	439	0	ENST00000354822.5:c.742C>T	p.Arg248Cys	p.R248C	ENST00000354822	NM_001079668.2	248	Cgc/Tgc	3/3	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.529353559277132	2		439	595	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239893	105239893	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1340970650	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	140	602	0	ENST00000349310.3:c.727C>T	p.Arg243Cys	p.R243C	ENST00000349310	NM_001014432.1	243	Cgt/Tgt	10/15	1	2	FACETS	0.991	0.907	1	0.991	0.907	1	CLONAL	1	TRUE	1	0.529353559277132	2		602	534	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243056	105243056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771065764	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	170	577	1	ENST00000349310.3:c.227G>A	p.Arg76His	p.R76H	ENST00000349310	NM_001014432.1	76	cGc/cAc	5/15	1	2	FACETS	0.934	0.861	1	0.934	0.861	1	CLONAL	1	TRUE	1	0.529353559277132	2		578	688	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707942	43707942	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	196	524	0	ENST00000382044.4:c.4939T>G	p.Ser1647Ala	p.S1647A	ENST00000382044	NM_001141980.1	1647	Tcc/Gcc	23/28	1	2	FACETS	0.986	0.915	1	0.986	0.915	1	CLONAL	1	TRUE	1	0.529353559277132	2		524	751	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457360	67457360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770798158	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	46	470	0	ENST00000327367.4:c.334G>A	p.Ala112Thr	p.A112T	ENST00000327367	NM_005902.3	112	Gcc/Acc	2/9	1	2	FACETS	0.284	0.239	0.335	0.284	0.239	0.335	SUBCLONAL	1	TRUE	1	0.529353559277132	2		470	611	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994796	73994796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	125	460	1	ENST00000318443.5:c.280G>A	p.Ala94Thr	p.A94T	ENST00000318443	NM_001024736.1	94	Gcc/Acc	3/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.529353559277132	2		461	449	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304100	91304101	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	47	545	1	ENST00000355112.3:c.1500dup	p.Val501CysfsTer3	p.V501Cfs*3	ENST00000355112	NM_000057.2	499	-/T	7/22	1	2	FACETS	0.269	0.226	0.316	0.269	0.226	0.316	SUBCLONAL	1	TRUE	1	0.529353559277132	2		546	660	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126103	2126103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376801256	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	202	579	0	ENST00000219476.3:c.2674G>A	p.Val892Ile	p.V892I	ENST00000219476	NM_000548.3	892	Gtc/Atc	24/42	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.529353559277132	2		579	733	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223286	2223286	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150194608	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	164	627	0	ENST00000326181.6:c.898G>A	p.Glu300Lys	p.E300K	ENST00000326181	NM_032271.2	300	Gag/Aag	10/21	1	2	FACETS	0.982	0.905	1	0.982	0.905	1	CLONAL	1	TRUE	1	0.529353559277132	2		627	631	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642800	3642800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747832147	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	43	566	0	ENST00000294008.3:c.2227G>A	p.Val743Met	p.V743M	ENST00000294008	NM_032444.2	743	Gtg/Atg	11/15	1	2	FACETS	0.198	0.165	0.235	0.198	0.165	0.235	SUBCLONAL	1	TRUE	1	0.529353559277132	2		566	820	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778323	3778323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146514877	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	104	454	0	ENST00000262367.5:c.6725C>T	p.Pro2242Leu	p.P2242L	ENST00000262367	NM_004380.2	2242	cCg/cTg	31/31	1	2	FACETS	0.887	0.799	0.979	0.887	0.799	0.979	CLONAL	1	TRUE	1	0.529353559277132	2		454	443	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857848	9857848	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780354	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	108	428	0	ENST00000330684.3:c.3553A>G	p.Lys1185Glu	p.K1185E	ENST00000330684	NM_001134407.1	1185	Aaa/Gaa	13/13	1	2	FACETS	0.854	0.77	0.941	0.854	0.77	0.941	CLONAL	1	TRUE	1	0.529353559277132	2		428	478	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934602	9934602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397518470	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	112	384	0	ENST00000330684.3:c.1553G>A	p.Arg518His	p.R518H	ENST00000330684	NM_001134407.1	518	cGt/cAt	7/13	1	2	FACETS	0.926	0.838	1	0.926	0.838	1	CLONAL	1	TRUE	1	0.529353559277132	2		384	457	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042019	14042019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	36	295	0	ENST00000311895.7:c.2566C>T	p.Pro856Ser	p.P856S	ENST00000311895	NM_005236.2	856	Cca/Tca	11/11	1	2	FACETS	0.363	0.298	0.435	0.363	0.298	0.435	SUBCLONAL	1	TRUE	1	0.529353559277132	2		295	375	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133247	30133247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	155	492	0	ENST00000263025.4:c.251G>A	p.Arg84His	p.R84H	ENST00000263025	NM_002746.2	84	cGc/cAc	2/9	1	2	FACETS	0.994	0.914	1	0.994	0.914	1	CLONAL	1	TRUE	1	0.529353559277132	2		492	589	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650683	67650683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	189	415	0	ENST00000264010.4:c.988G>A	p.Ala330Thr	p.A330T	ENST00000264010	NM_006565.3	330	Gcc/Acc	5/12	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.529353559277132	2		415	651	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660580	67660580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	178	480	1	ENST00000264010.4:c.1480C>T	p.Arg494Cys	p.R494C	ENST00000264010	NM_006565.3	494	Cgc/Tgc	8/12	1	2	FACETS	0.957	0.884	1	0.957	0.884	1	CLONAL	1	TRUE	1	0.529353559277132	2		481	703	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828486	72828486	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	158	453	0	ENST00000268489.5:c.8095G>T	p.Gly2699Ter	p.G2699*	ENST00000268489	NM_006885.3	2699	Gga/Tga	9/10	1	2	FACETS	0.974	0.896	1	0.974	0.896	1	CLONAL	1	TRUE	1	0.529353559277132	2		453	613	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831656	72831656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	28	474	0	ENST00000268489.5:c.4925G>A	p.Ser1642Asn	p.S1642N	ENST00000268489	NM_006885.3	1642	aGc/aAc	9/10	1	2	FACETS	0.208	0.165	0.256	0.208	0.165	0.256	SUBCLONAL	1	TRUE	1	0.529353559277132	2		474	509	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993822	72993822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374552910	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	18	385	0	ENST00000268489.5:c.223G>A	p.Ala75Thr	p.A75T	ENST00000268489	NM_006885.3	75	Gcc/Acc	2/10	1	2	FACETS	0.199	0.15	0.258	0.199	0.15	0.258	SUBCLONAL	1	TRUE	1	0.529353559277132	2		385	341	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347980	89347980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749114664	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	189	642	1	ENST00000301030.4:c.4970C>T	p.Ser1657Leu	p.S1657L	ENST00000301030	NM_001256183.1	1657	tCg/tTg	9/13	1	2	FACETS	0.921	0.853	0.992	0.921	0.853	0.992	CLONAL	1	TRUE	1	0.529353559277132	2		643	775	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348909	89348911	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs757750566	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	175	695	0	ENST00000301030.4:c.4039_4041del	p.Lys1347del	p.K1347del	ENST00000301030	NM_001256183.1	1347	AAG/-	9/13	1	2	FACETS	0.852	0.786	0.92	0.852	0.786	0.92	CLONAL	1	TRUE	1	0.529353559277132	2		695	776	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217012	7217012	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	136	368	0	ENST00000380728.2:c.509C>A	p.Ala170Asp	p.A170D	ENST00000380728		170	gCt/gAt	7/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.529353559277132	2		368	459	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042379	16042379	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	128	421	0	ENST00000268712.3:c.1295A>C	p.Lys432Thr	p.K432T	ENST00000268712	NM_006311.3	432	aAa/aCa	12/46	1	2	FACETS	0.921	0.839	1	0.921	0.839	1	CLONAL	1	TRUE	1	0.529353559277132	2		421	525	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587387	29587388	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	rs1555618803	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	86	279	0	ENST00000356175.3:c.4373dup	p.Leu1459ProfsTer2	p.L1459Pfs*2	ENST00000356175	NM_000267.3	1456	-/T	33/57	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.529353559277132	2		279	321	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244952	41244952	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41286300	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	40	547	0	ENST00000357654.3:c.2596C>T	p.Arg866Cys	p.R866C	ENST00000357654	NM_007294.3	866	Cgc/Tgc	10/23	1	2	FACETS	0.222	0.183	0.264	0.222	0.183	0.264	SUBCLONAL	1	TRUE	1	0.529353559277132	2		547	682	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245476	41245476	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	226	669	0	ENST00000357654.3:c.2072G>T	p.Arg691Ile	p.R691I	ENST00000357654	NM_007294.3	691	aGa/aTa	10/23	1	2	FACETS	0.981	0.916	1	0.981	0.916	1	CLONAL	1	TRUE	1	0.529353559277132	2		669	870	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41251812	41251812	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782747	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	164	497	1	ENST00000357654.3:c.527C>T	p.Thr176Met	p.T176M	ENST00000357654	NM_007294.3	176	aCg/aTg	7/23	1	2	FACETS	0.817	0.752	0.886	0.817	0.752	0.886	CLONAL	1	TRUE	1	0.529353559277132	2		498	758	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763428	59763428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	157	513	0	ENST00000259008.2:c.2674C>T	p.Leu892Phe	p.L892F	ENST00000259008	NM_032043.2	892	Ctt/Ttt	19/20	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.529353559277132	2		513	588	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78933909	78933909	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1342049284	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	134	479	0	ENST00000306801.3:c.3509C>T	p.Thr1170Met	p.T1170M	ENST00000306801	NM_020761.2	1170	aCg/aTg	30/34	1	2	FACETS	0.882	0.805	0.963	0.882	0.805	0.963	CLONAL	1	TRUE	1	0.529353559277132	2		479	574	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110201	3110201	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	144	548	0	ENST00000078429.4:c.191G>A	p.Gly64Asp	p.G64D	ENST00000078429	NM_002067.2	64	gGc/gAc	2/7	1	2	FACETS	0.953	0.873	1	0.953	0.873	1	CLONAL	1	TRUE	1	0.529353559277132	2		548	571	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244406	5244406	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	45	594	0	ENST00000357368.4:c.1076C>A	p.Pro359His	p.P359H	ENST00000357368	NM_002850.3	359	cCt/cAt	11/38	1	2	FACETS	0.229	0.191	0.27	0.229	0.191	0.27	SUBCLONAL	1	TRUE	1	0.529353559277132	2		594	744	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296433	15296433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	206	696	0	ENST00000263388.2:c.2009G>A	p.Gly670Asp	p.G670D	ENST00000263388	NM_000435.2	670	gGt/gAt	13/33	1	2	FACETS	0.961	0.893	1	0.961	0.893	1	CLONAL	1	TRUE	1	0.529353559277132	2		696	810	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298125	15298125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751284168	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	148	558	0	ENST00000263388.2:c.1631G>A	p.Arg544His	p.R544H	ENST00000263388	NM_000435.2	544	cGc/cAc	11/33	1	2	FACETS	0.883	0.81	0.96	0.883	0.81	0.96	CLONAL	1	TRUE	1	0.529353559277132	2		558	633	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349877	15349877	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1187497598	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	97	367	1	ENST00000263377.2:c.3775C>T	p.Arg1259Cys	p.R1259C	ENST00000263377	NM_058243.2	1259	Cgc/Tgc	18/20	1	2	FACETS	0.928	0.833	1	0.928	0.833	1	CLONAL	1	TRUE	1	0.529353559277132	2		368	395	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354248	15354248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764128043	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	48	615	0	ENST00000263377.2:c.2632G>A	p.Ala878Thr	p.A878T	ENST00000263377	NM_058243.2	878	Gct/Act	14/20	1	2	FACETS	0.22	0.185	0.258	0.22	0.185	0.258	SUBCLONAL	1	TRUE	1	0.529353559277132	2		615	826	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18276985	18276985	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	124	353	0	ENST00000222254.8:c.1432C>T	p.Arg478Cys	p.R478C	ENST00000222254	NM_005027.3	478	Cgt/Tgt	12/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.529353559277132	2		353	410	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965800	18965800	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	169	561	0	ENST00000262803.5:c.1378C>T	p.Pro460Ser	p.P460S	ENST00000262803	NM_002911.3	460	Ccc/Tcc	10/24	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.529353559277132	2		561	619	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257423	19257423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	203	713	0	ENST00000162023.5:c.710C>T	p.Ser237Phe	p.S237F	ENST00000162023		237	tCc/tTc	11/13	1	2	FACETS	0.91	0.845	0.977	0.91	0.845	0.977	CLONAL	1	TRUE	1	0.529353559277132	2		713	843	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303919	30303919	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879397969	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	144	426	0	ENST00000262643.3:c.155C>T	p.Thr52Met	p.T52M	ENST00000262643	NM_001238.2	52	aCg/aTg	4/12	1	2	FACETS	0.989	0.907	1	0.989	0.907	1	CLONAL	1	TRUE	1	0.529353559277132	2		426	550	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792902	33792902	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	16	65	0	ENST00000498907.2:c.419A>G	p.Asp140Gly	p.D140G	ENST00000498907	NM_004364.3	140	gAc/gGc	1/1	1	2	FACETS	0.545	0.407	0.704	0.545	0.407	0.704	SUBCLONAL	1	TRUE	1	0.529353559277132	2		65	111	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211402	36211402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	61	689	0	ENST00000222270.7:c.1153G>A	p.Ala385Thr	p.A385T	ENST00000222270	NM_014727.1	385	Gct/Act	3/37	1	2	FACETS	0.256	0.22	0.296	0.256	0.22	0.296	SUBCLONAL	1	TRUE	1	0.529353559277132	2		689	899	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214711	36214711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779455230	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	109	425	0	ENST00000222270.7:c.3137G>A	p.Arg1046His	p.R1046H	ENST00000222270	NM_014727.1	1046	cGc/cAc	8/37	1	2	FACETS	0.971	0.878	1	0.971	0.878	1	CLONAL	1	TRUE	1	0.529353559277132	2		425	424	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219692	36219692	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	186	534	1	ENST00000222270.7:c.4589C>T	p.Ala1530Val	p.A1530V	ENST00000222270	NM_014727.1	1530	gCg/gTg	20/37	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.529353559277132	2		535	605	SUCCESS
AXL	558	MSKCC	GRCh37	19	41737106	41737106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771116052	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	189	536	0	ENST00000301178.4:c.686G>A	p.Arg229His	p.R229H	ENST00000301178	NM_021913.4	229	cGt/cAt	6/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.529353559277132	2		536	652	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791215	42791215	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	166	535	0	ENST00000575354.2:c.275C>A	p.Ala92Asp	p.A92D	ENST00000575354	NM_015125.3	92	gCt/gAt	3/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.529353559277132	2		535	607	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795541	42795541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1222909601	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	166	588	1	ENST00000575354.2:c.2621G>A	p.Gly874Asp	p.G874D	ENST00000575354	NM_015125.3	874	gGc/gAc	10/20	1	2	FACETS	0.786	0.723	0.852	0.786	0.723	0.852	SUBCLONAL	1	TRUE	1	0.529353559277132	2		589	798	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855885	45855885	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	158	563	0	ENST00000391945.4:c.1925A>G	p.Asp642Gly	p.D642G	ENST00000391945	NM_000400.3	642	gAc/gGc	21/23	1	2	FACETS	0.89	0.818	0.964	0.89	0.818	0.964	CLONAL	1	TRUE	1	0.529353559277132	2		563	671	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470548	25470548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	173	537	1	ENST00000264709.3:c.926G>A	p.Arg309His	p.R309H	ENST00000264709	NM_175629.2	309	cGc/cAc	8/23	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.529353559277132	2		538	625	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607858	46607858	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	144	507	0	ENST00000263734.3:c.2045+2T>C		p.X682_splice	ENST00000263734	NM_001430.4	682			1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.529353559277132	2		507	533	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47643569	47643569	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs267607940	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	95	381	0	ENST00000233146.2:c.1076+1G>A		p.X359_splice	ENST00000233146	NM_000251.2	359			1	2	FACETS	0.847	0.758	0.939	0.847	0.758	0.939	CLONAL	1	TRUE	1	0.529353559277132	2		381	424	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027728	48027728	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395549583	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	65	320	0	ENST00000234420.5:c.2606G>A	p.Cys869Tyr	p.C869Y	ENST00000234420	NM_000179.2	869	tGt/tAt	4/10	1	2	FACETS	0.737	0.644	0.838	0.737	0.644	0.838	SUBCLONAL	1	TRUE	1	0.529353559277132	2		320	333	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920586	96920586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750870974	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	30	299	1	ENST00000258439.3:c.394G>A	p.Ala132Thr	p.A132T	ENST00000258439	NM_001193304.2	132	Gcc/Acc	3/4	1	2	FACETS	0.309	0.249	0.377	0.309	0.249	0.377	SUBCLONAL	1	TRUE	1	0.529353559277132	2		300	367	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170798	99170798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	111	419	0	ENST00000074304.5:c.1427C>T	p.Ala476Val	p.A476V	ENST00000074304	NM_001134224.1	476	gCt/gTt	16/26	1	2	FACETS	0.902	0.815	0.992	0.902	0.815	0.992	CLONAL	1	TRUE	1	0.529353559277132	2		419	465	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047032	128047032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	129	429	0	ENST00000285398.2:c.703G>A	p.Val235Met	p.V235M	ENST00000285398	NM_000122.1	235	Gtg/Atg	6/15	1	2	FACETS	0.795	0.723	0.87	0.795	0.723	0.87	SUBCLONAL	1	TRUE	1	0.529353559277132	2		429	613	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131327	202131327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	36	402	0	ENST00000358485.4:c.295G>A	p.Asp99Asn	p.D99N	ENST00000358485	NM_001080125.1	99	Gat/Aat	2/9	1	2	FACETS	0.275	0.225	0.33	0.275	0.225	0.33	SUBCLONAL	1	TRUE	1	0.529353559277132	2		402	495	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136246	202136246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	87	395	1	ENST00000358485.4:c.490C>T	p.Leu164Phe	p.L164F	ENST00000358485	NM_001080125.1	164	Ctc/Ttc	3/9	1	2	FACETS	0.661	0.587	0.74	0.661	0.587	0.74	SUBCLONAL	1	TRUE	1	0.529353559277132	2		396	497	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660201	227660201	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	148	492	1	ENST00000305123.5:c.3254C>A	p.Ala1085Asp	p.A1085D	ENST00000305123	NM_005544.2	1085	gCc/gAc	1/2	1	2	FACETS	0.876	0.803	0.953	0.876	0.803	0.953	CLONAL	1	TRUE	1	0.529353559277132	2		493	638	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022390	31022391	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	52	229	0	ENST00000375687.4:c.1879dup	p.Ala627GlyfsTer8	p.A627Gfs*8	ENST00000375687	NM_015338.5	625	-/G	13/13	1	2	FACETS	0.744	0.639	0.857	0.744	0.639	0.857	SUBCLONAL	1	TRUE	1	0.529353559277132	2		229	264	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031768	36031768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754707860	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	113	443	0	ENST00000358208.4:c.1597G>A	p.Gly533Arg	p.G533R	ENST00000358208		533	Ggg/Agg	12/12	1	2	FACETS	0.895	0.81	0.984	0.895	0.81	0.984	CLONAL	1	TRUE	1	0.529353559277132	2		443	477	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877345	40877345	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	100	334	0	ENST00000373198.4:c.2351T>C	p.Met784Thr	p.M784T	ENST00000373198	NM_133170.3	784	aTg/aCg	15/32	1	2	FACETS	0.964	0.868	1	0.964	0.868	1	CLONAL	1	TRUE	1	0.529353559277132	2		334	392	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265129	46265129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	112	348	0	ENST00000371998.3:c.1999G>A	p.Val667Ile	p.V667I	ENST00000371998		667	Gta/Ata	12/23	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.529353559277132	2		348	350	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866397	42866397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	173	612	0	ENST00000398585.3:c.235G>A	p.Ala79Thr	p.A79T	ENST00000398585	NM_001135099.1	79	Gct/Act	3/14	1	2	FACETS	0.908	0.838	0.98	0.908	0.838	0.98	CLONAL	1	TRUE	1	0.529353559277132	2		612	720	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514879	44514879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	123	340	0	ENST00000291552.4:c.368C>T	p.Ala123Val	p.A123V	ENST00000291552	NM_006758.2	123	gCg/gTg	6/8	1	2	FACETS	0.941	0.855	1	0.941	0.855	1	CLONAL	1	TRUE	1	0.529353559277132	2		340	494	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715729	30715729	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	86	267	0	ENST00000295754.5:c.1387G>A	p.Ala463Thr	p.A463T	ENST00000295754	NM_003242.5	463	Gca/Aca	5/7	1	2	FACETS	0.928	0.828	1	0.928	0.828	1	CLONAL	1	TRUE	1	0.529353559277132	2		267	350	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163989	47163989	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1478213869	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	90	280	0	ENST00000409792.3:c.2137G>A	p.Ala713Thr	p.A713T	ENST00000409792	NM_014159.6	713	Gca/Aca	3/21	1	2	FACETS	0.974	0.872	1	0.974	0.872	1	CLONAL	1	TRUE	1	0.529353559277132	2		280	349	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722303	49722303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774351535	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	21	69	0	ENST00000449682.2:c.1637C>T	p.Thr546Met	p.T546M	ENST00000449682	NM_020998.3	546	aCg/aTg	15/18	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.529353559277132	2		69	61	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205093	128205093	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	142	541	0	ENST00000341105.2:c.348G>A	p.Trp116Ter	p.W116*	ENST00000341105	NM_032638.4	116	tgG/tgA	3/6	1	2	FACETS	0.891	0.815	0.97	0.891	0.815	0.97	CLONAL	1	TRUE	1	0.529353559277132	2		541	602	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952019	178952019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	9	374	0	ENST00000263967.3:c.3074C>T	p.Thr1025Ile	p.T1025I	ENST00000263967	NM_006218.2	1025	aCc/aTc	21/21	1	2	FACETS	0.089	0.058	0.128	0.089	0.058	0.128	SUBCLONAL	1	TRUE	1	0.529353559277132	2		374	382	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191161	185191161	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	102	346	0	ENST00000265026.3:c.2042G>A	p.Ser681Asn	p.S681N	ENST00000265026	NM_004721.4	681	aGc/aAc	11/14	1	2	FACETS	0.961	0.866	1	0.961	0.866	1	CLONAL	1	TRUE	1	0.529353559277132	2		346	401	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803663	1803663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	208	645	0	ENST00000260795.2:c.841G>A	p.Ala281Thr	p.A281T	ENST00000260795		281	Gca/Aca	6/17	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.529353559277132	2		645	739	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55963921	55963921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	24	311	0	ENST00000263923.4:c.2522G>A	p.Gly841Asp	p.G841D	ENST00000263923	NM_002253.2	841	gGc/gAc	18/30	1	2	FACETS	0.228	0.179	0.286	0.228	0.179	0.286	SUBCLONAL	1	TRUE	1	0.529353559277132	2		311	397	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972857	55972858	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	79	328	0	ENST00000263923.4:c.1532dup	p.Asn511LysfsTer21	p.N511Kfs*21	ENST00000263923	NM_002253.2	511	aac/aaAc	11/30	1	2	FACETS	0.697	0.616	0.784	0.697	0.616	0.784	SUBCLONAL	1	TRUE	1	0.529353559277132	2		328	428	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973936	55973936	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	134	380	0	ENST00000263923.4:c.1380G>A	p.Trp460Ter	p.W460*	ENST00000263923	NM_002253.2	460	tgG/tgA	10/30	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.529353559277132	2		380	469	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467764	66467764	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	76	284	0	ENST00000273854.3:c.505A>T	p.Asn169Tyr	p.N169Y	ENST00000273854	NM_004439.5	169	Aac/Tac	3/18	1	2	FACETS	0.923	0.817	1	0.923	0.817	1	CLONAL	1	TRUE	1	0.529353559277132	2		284	311	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535303	66535303	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	136	504	0	ENST00000273854.3:c.158T>C	p.Leu53Pro	p.L53P	ENST00000273854	NM_004439.5	53	cTc/cCc	1/18	1	2	FACETS	0.837	0.763	0.913	0.837	0.763	0.913	CLONAL	1	TRUE	1	0.529353559277132	2		504	614	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196936	106196936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	82	262	0	ENST00000380013.4:c.5269C>T	p.His1757Tyr	p.H1757Y	ENST00000380013	NM_001127208.2	1757	Cat/Tat	11/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.529353559277132	2		262	271	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159144	143159144	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	63	249	0	ENST00000262992.4:c.709A>G	p.Lys237Glu	p.K237E	ENST00000262992	NM_001101669.1	237	Aaa/Gaa	10/24	1	2	FACETS	0.749	0.652	0.852	0.749	0.652	0.852	SUBCLONAL	1	TRUE	1	0.529353559277132	2		249	318	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253808	153253808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1217890531	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	97	316	0	ENST00000281708.4:c.925C>T	p.Arg309Cys	p.R309C	ENST00000281708	NM_033632.3	309	Cgc/Tgc	6/12	1	2	FACETS	0.879	0.789	0.974	0.879	0.789	0.974	CLONAL	1	TRUE	1	0.529353559277132	2		316	417	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542345	187542345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	79	307	0	ENST00000441802.2:c.5395G>A	p.Ala1799Thr	p.A1799T	ENST00000441802	NM_005245.3	1799	Gct/Act	10/27	1	2	FACETS	0.886	0.785	0.992	0.886	0.785	0.992	CLONAL	1	TRUE	1	0.529353559277132	2		307	337	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628454	187628454	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	178	525	0	ENST00000441802.2:c.2528A>G	p.Gln843Arg	p.Q843R	ENST00000441802	NM_005245.3	843	cAg/cGg	2/27	1	2	FACETS	0.916	0.847	0.988	0.916	0.847	0.988	CLONAL	1	TRUE	1	0.529353559277132	2		525	734	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271300	1271300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	158	481	2	ENST00000310581.5:c.2402C>T	p.Ala801Val	p.A801V	ENST00000310581	NM_198253.2	801	gCc/gTc	8/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.529353559277132	2		483	539	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294643	1294643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1436692848	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	50	411	0	ENST00000310581.5:c.358C>T	p.Arg120Cys	p.R120C	ENST00000310581	NM_198253.2	120	Cgc/Tgc	2/16	1	2	FACETS	0.401	0.34	0.468	0.401	0.34	0.468	SUBCLONAL	1	TRUE	1	0.529353559277132	2		411	471	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31472277	31472277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	155	534	0	ENST00000344624.3:c.2134G>A	p.Ala712Thr	p.A712T	ENST00000344624		712	Gcc/Acc	14/33	1	2	FACETS	0.893	0.82	0.968	0.893	0.82	0.968	CLONAL	1	TRUE	1	0.529353559277132	2		534	656	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871223	35871223	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	98	361	0	ENST00000303115.3:c.445A>G	p.Thr149Ala	p.T149A	ENST00000303115	NM_002185.3	149	Aca/Gca	4/8	1	2	FACETS	0.855	0.767	0.947	0.855	0.767	0.947	CLONAL	1	TRUE	1	0.529353559277132	2		361	433	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950189	38950189	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	66	426	0	ENST00000357387.3:c.3761G>A	p.Ser1254Asn	p.S1254N	ENST00000357387	NM_152756.3	1254	aGc/aAc	31/38	1	2	FACETS	0.576	0.501	0.656	0.576	0.501	0.656	SUBCLONAL	1	TRUE	1	0.529353559277132	2		426	433	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168726	56168727	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	112	307	0	ENST00000399503.3:c.1583dup	p.Leu528PhefsTer13	p.L528Ffs*13	ENST00000399503	NM_005921.1	527	cct/ccTt	9/20	1	2	FACETS	0.895	0.809	0.984	0.895	0.809	0.984	CLONAL	1	TRUE	1	0.529353559277132	2		307	473	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751532	57751532	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	78	246	0	ENST00000274289.3:c.1459C>T	p.Pro487Ser	p.P487S	ENST00000274289	NM_006622.3	487	Ccg/Tcg	11/14	1	2	FACETS	0.933	0.827	1	0.933	0.827	1	CLONAL	1	TRUE	1	0.529353559277132	2		246	316	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590410	67590411	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	82	245	0	ENST00000274335.5:c.1477dup	p.Ile493AsnfsTer3	p.I493Nfs*3	ENST00000274335		491	ata/atAa	11/15	0.529353559277132	1	FACETS	0.93	0.833	1	0.93	0.833	1	CLONAL	1	TRUE	0	0.529353559277132	1		245	245	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449487	149449487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	29	477	1	ENST00000286301.3:c.1459G>A	p.Ala487Thr	p.A487T	ENST00000286301	NM_005211.3	487	Gcc/Acc	10/22	0.529353559277132	1	FACETS	0.2	0.16	0.245	0.2	0.16	0.245	SUBCLONAL	1	TRUE	0	0.529353559277132	1		478	403	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509342	149509342	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	23	333	0	ENST00000261799.4:c.1557G>T	p.Gln519His	p.Q519H	ENST00000261799	NM_002609.3	519	caG/caT	10/23	0.529353559277132	1	FACETS	0.207	0.161	0.261	0.207	0.161	0.261	SUBCLONAL	1	TRUE	0	0.529353559277132	1		333	308	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519324	176519324	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs777010660	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	97	360	1	ENST00000292408.4:c.730C>T	p.Arg244Trp	p.R244W	ENST00000292408	NM_213647.1	244	Cgg/Tgg	7/18	0.529353559277132	1	FACETS	0.809	0.729	0.893	0.809	0.729	0.893	CLONAL	1	TRUE	0	0.529353559277132	1		361	333	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839988	27839988	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs926284215	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	24	393	2	ENST00000328488.2:c.106G>A	p.Val36Ile	p.V36I	ENST00000328488	NM_003533.2	36	Gtc/Atc	1/1	1	2	FACETS	0.196	0.153	0.246	0.196	0.153	0.246	SUBCLONAL	1	TRUE	1	0.529353559277132	2		395	462	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671238	30671238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	212	561	0	ENST00000376406.3:c.5639G>A	p.Ser1880Asn	p.S1880N	ENST00000376406	NM_014641.2	1880	aGc/aAc	11/15	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.529353559277132	2		561	732	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166284	32166284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	183	542	0	ENST00000375023.3:c.4670G>A	p.Gly1557Asp	p.G1557D	ENST00000375023	NM_004557.3	1557	gGc/gAc	26/30	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.529353559277132	2		542	651	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187513	32187513	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	205	565	0	ENST00000375023.3:c.1366C>T	p.Pro456Ser	p.P456S	ENST00000375023	NM_004557.3	456	Cct/Tct	8/30	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.529353559277132	2		565	684	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32813522	32813522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566329319	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	28	359	0	ENST00000354258.4:c.2261G>A	p.Arg754His	p.R754H	ENST00000354258	NM_000593.5	754	cGc/cAc	11/11	1	2	FACETS	0.261	0.208	0.322	0.261	0.208	0.322	SUBCLONAL	1	TRUE	1	0.529353559277132	2		359	405	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818131	32818131	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	169	537	0	ENST00000354258.4:c.1394C>T	p.Ala465Val	p.A465V	ENST00000354258	NM_000593.5	465	gCt/gTt	5/11	1	2	FACETS	0.879	0.811	0.951	0.879	0.811	0.951	CLONAL	1	TRUE	1	0.529353559277132	2		537	726	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43752294	43752294	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771561387	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	27	367	0	ENST00000523873.1:c.694C>T	p.Arg232Trp	p.R232W	ENST00000523873		232	Cgg/Tgg	8/8	1	2	FACETS	0.209	0.165	0.258	0.209	0.165	0.258	SUBCLONAL	1	TRUE	1	0.529353559277132	2		367	489	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024168	112024168	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	110	370	0	ENST00000368678.4:c.617G>A	p.Arg206His	p.R206H	ENST00000368678		206	cGc/cAc	7/13	1	2	FACETS	0.903	0.817	0.994	0.903	0.817	0.994	CLONAL	1	TRUE	1	0.529353559277132	2		370	460	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117746738	117746738	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	116	364	0	ENST00000368508.3:c.82A>G	p.Thr28Ala	p.T28A	ENST00000368508	NM_002944.2	28	Aca/Gca	1/43	1	2	FACETS	0.951	0.862	1	0.951	0.862	1	CLONAL	1	TRUE	1	0.529353559277132	2		364	461	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042169	6042170	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGGG	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	62	423	0	ENST00000265849.7:c.448_451dup	p.Arg151ProfsTer22	p.R151Pfs*22	ENST00000265849	NM_000535.5	151	cgc/cCCCCgc	5/15	1	2	FACETS	0.385	0.332	0.443	0.385	0.332	0.443	SUBCLONAL	1	TRUE	1	0.529353559277132	2		423	608	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508589	106508589	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	24	311	0	ENST00000359195.3:c.583C>T	p.Leu195Phe	p.L195F	ENST00000359195	NM_002649.2	195	Ctc/Ttc	2/11	1	2	FACETS	0.257	0.201	0.321	0.257	0.201	0.321	SUBCLONAL	1	TRUE	1	0.529353559277132	2		311	353	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508601	106508601	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	90	321	0	ENST00000359195.3:c.595C>T	p.His199Tyr	p.H199Y	ENST00000359195	NM_002649.2	199	Cac/Tac	2/11	1	2	FACETS	0.892	0.798	0.992	0.892	0.798	0.992	CLONAL	1	TRUE	1	0.529353559277132	2		321	381	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140500228	140500228	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs547693139	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	177	422	1	ENST00000288602.6:c.914C>T	p.Ala305Val	p.A305V	ENST00000288602	NM_004333.4	305	gCg/gTg	7/18	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.529353559277132	2		423	660	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949128	151949128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	149	435	0	ENST00000262189.6:c.1517C>T	p.Thr506Ile	p.T506I	ENST00000262189	NM_170606.2	506	aCt/aTt	11/59	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.529353559277132	2		435	555	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346449	152346449	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	73	284	0	ENST00000359321.1:c.122-1G>A		p.X41_splice	ENST00000359321	NM_005431.1	41			1	2	FACETS	0.895	0.79	1	0.895	0.79	1	CLONAL	1	TRUE	1	0.529353559277132	2		284	308	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972929	68972929	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	97	358	0	ENST00000288368.4:c.1254G>A	p.Trp418Ter	p.W418*	ENST00000288368	NM_024870.2	418	tgG/tgA	11/40	1	2	FACETS	0.868	0.779	0.962	0.868	0.779	0.962	CLONAL	1	TRUE	1	0.529353559277132	2		358	422	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982685	90982685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs535602436	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	114	316	0	ENST00000265433.3:c.803C>T	p.Thr268Met	p.T268M	ENST00000265433	NM_002485.4	268	aCg/aTg	7/16	1	2	FACETS	0.922	0.835	1	0.922	0.835	1	CLONAL	1	TRUE	1	0.529353559277132	2		316	467	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566042	141566042	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1460562478	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	148	408	0	ENST00000220592.5:c.1222G>A	p.Val408Met	p.V408M	ENST00000220592	NM_012154.3	408	Gtg/Atg	10/19	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.529353559277132	2		408	515	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123045	5123045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	39	341	0	ENST00000381652.3:c.3101C>T	p.Ala1034Val	p.A1034V	ENST00000381652	NM_004972.3	1034	gCc/gTc	23/25	1	2	FACETS	0.336	0.278	0.4	0.336	0.278	0.4	SUBCLONAL	1	TRUE	1	0.529353559277132	2		341	439	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213494	27213494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	96	431	0	ENST00000380036.4:c.2890G>A	p.Asp964Asn	p.D964N	ENST00000380036	NM_000459.3	964	Gat/Aat	18/23	1	2	FACETS	0.806	0.722	0.895	0.806	0.722	0.895	CLONAL	1	TRUE	1	0.529353559277132	2		431	450	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482202	87482202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	131	488	1	ENST00000277120.3:c.1489C>T	p.Leu497Phe	p.L497F	ENST00000277120		497	Ctc/Ttc	14/19	1	2	FACETS	0.792	0.721	0.866	0.792	0.721	0.866	SUBCLONAL	1	TRUE	1	0.529353559277132	2		489	625	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624520	93624520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1435690353	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	113	372	1	ENST00000375746.1:c.611C>T	p.Ala204Val	p.A204V	ENST00000375746	NM_001174167.1	204	gCc/gTc	4/14	1	2	FACETS	0.947	0.857	1	0.947	0.857	1	CLONAL	1	TRUE	1	0.529353559277132	2		373	451	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650842	93650842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	138	376	2	ENST00000375746.1:c.1768C>T	p.Arg590Trp	p.R590W	ENST00000375746	NM_001174167.1	590	Cgg/Tgg	13/14	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.529353559277132	2		378	507	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97933362	97933362	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs781542763	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	44	300	0	ENST00000289081.3:c.520C>T	p.Arg174Ter	p.R174*	ENST00000289081	NM_000136.2	174	Cga/Tga	6/15	1	2	FACETS	0.334	0.28	0.395	0.334	0.28	0.395	SUBCLONAL	1	TRUE	1	0.529353559277132	2		300	497	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891187	101891187	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	66	328	0	ENST00000374994.4:c.148A>G	p.Thr50Ala	p.T50A	ENST00000374994	NM_004612.2	50	Aca/Gca	2/9	1	2	FACETS	0.669	0.583	0.76	0.669	0.583	0.76	SUBCLONAL	1	TRUE	1	0.529353559277132	2		328	373	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412658	139412658	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	185	548	0	ENST00000277541.6:c.1186G>A	p.Ala396Thr	p.A396T	ENST00000277541	NM_017617.3	396	Gcc/Acc	7/34	0.129871141463946	5	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.529353559277132	5		548	866	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417392	139417392	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	45	613	0	ENST00000277541.6:c.652C>T	p.Pro218Ser	p.P218S	ENST00000277541	NM_017617.3	218	Ccc/Tcc	4/34	0.129871141463946	5	FACETS	0.346	0.29	0.409			1	INDETERMINATE	1	TRUE	NA	0.529353559277132	5		613	881	SUCCESS
AR	367	MSKCC	GRCh37	X	66765298	66765298	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	121	273	0	ENST00000374690.3:c.310C>T	p.Pro104Ser	p.P104S	ENST00000374690	NM_000044.3	104	Ccc/Tcc	1/8	1	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.529353559277132	1		273	259	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357450	70357450	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	23	288	0	ENST00000374080.3:c.5791A>G	p.Thr1931Ala	p.T1931A	ENST00000374080		1931	Act/Gct	40/45	1	1	FACETS	0.194	0.151	0.243	0.194	0.151	0.243	SUBCLONAL	1	TRUE	0	0.529353559277132	1		288	330	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251922	8251922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753207049	NA	P-0030265-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	158	488	2	ENST00000335790.3:c.155C>T	p.Ala52Val	p.A52V	ENST00000335790	NM_002315.2	52	gCc/gTc	2/4	1	2	FACETS	0.995	0.916	1	0.995	0.916	1	CLONAL	1	TRUE	1	0.529353559277132	2		490	600	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	20	401	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.274	0.209	0.352	0.274	0.209	0.352	SUBCLONAL	1	TRUE	1	0.273472963127452	2		401	533	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0031216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	80	257	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.965	0.851	1	0.965	0.851	1	CLONAL	1	TRUE	1	0.273472963127452	2		257	606	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143985	11143985	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	57	622	1	ENST00000358026.2:c.3566G>T	p.Arg1189Leu	p.R1189L	ENST00000358026	NM_001128849.1	1189	cGa/cTa	26/36	1	2	FACETS	0.538	0.46	0.623	0.538	0.46	0.623	SUBCLONAL	1	TRUE	1	0.273472963127452	2		623	775	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721541	49721541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772223669	NA	P-0031216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	60	548	0	ENST00000449682.2:c.2098G>A	p.Ala700Thr	p.A700T	ENST00000449682	NM_020998.3	700	Gca/Aca	18/18	1	2	FACETS	0.67	0.577	0.772	0.67	0.577	0.772	SUBCLONAL	1	TRUE	1	0.273472963127452	2		548	655	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30102152	30102152	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs775376594	NA	P-0031216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	36	541	1	ENST00000331968.5:c.1315C>T	p.Arg439Trp	p.R439W	ENST00000331968	NM_002742.2	439	Cgg/Tgg	9/18	1	2	FACETS	0.521	0.428	0.626	0.521	0.428	0.626	SUBCLONAL	1	TRUE	1	0.273472963127452	2		542	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578469	+	inframe_deletion	In_Frame_Del	DEL	CGCGGGTGC	CGCGGGTGC	-	novel	NA	P-0031218-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	385	809	0	ENST00000269305.4:c.461_469del	p.Gly154_Arg156del	p.G154_R156del	ENST00000269305	NM_001126112.2	154	gGCACCCGCGtc/gtc	5/11	0.684961911082378	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.684961911082378	1		809	739	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0031646-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	300	290	2	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.467282589607795	6	FACETS	0.961	0.913	1	0.961	0.913	1	CLONAL	4	FALSE	2	0.467282589607795	6		292	646	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579575	7579575	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555526795	NA	P-0031646-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	387	485	0	ENST00000269305.4:c.112del	p.Gln38LysfsTer6	p.Q38Kfs*6	ENST00000269305	NM_001126112.2	38	Caa/aa	4/11	0.391738494078663	3	FACETS	1	0.993	1	0.811	0.775	0.847	CLONAL	2	FALSE	0	0.467282589607795	3		485	840	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732969	30732969	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031646-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	245	328	0	ENST00000295754.5:c.1582C>G	p.Arg528Gly	p.R528G	ENST00000295754	NM_003242.5	528	Cgt/Ggt	7/7	NA	2	FACETS	0.872	0.822	0.924			1	INDETERMINATE	2	FALSE	NA	0.467282589607795	2		328	601	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928945	49928945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031646-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	464	698	0	ENST00000296474.3:c.3421C>T	p.Pro1141Ser	p.P1141S	ENST00000296474	NM_002447.2	1141	Ccg/Tcg	16/20	0.376330530125276	3	FACETS	1	0.995	1	0.827	0.794	0.861	CLONAL	2	FALSE	0	0.467282589607795	3		698	987	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47088081	47088081	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031646-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	313	374	1	ENST00000409792.3:c.6994C>T	p.Gln2332Ter	p.Q2332*	ENST00000409792	NM_014159.6	2332	Cag/Tag	16/21	0.376330530125276	3	FACETS	1	0.991	1	0.795	0.755	0.835	CLONAL	2	FALSE	0	0.467282589607795	3		375	693	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441430	52441430	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0031646-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	336	461	0	ENST00000460680.1:c.422A>G	p.His141Arg	p.H141R	ENST00000460680	NM_004656.3	141	cAt/cGt	6/17	0.376330530125276	3	FACETS	1	0.992	1	0.806	0.767	0.844	CLONAL	2	FALSE	0	0.467282589607795	3		461	734	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912451	32912451	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0031646-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	141	246	0	ENST00000380152.3:c.3959A>G	p.Glu1320Gly	p.E1320G	ENST00000380152		1320	gAa/gGa	11/27	0.355330846965607	3	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	FALSE	1	0.467282589607795	3		246	370	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813076	76813076	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0031673-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	114	509	0	ENST00000373344.5:c.6545A>T	p.Lys2182Met	p.K2182M	ENST00000373344	NM_000489.3	2182	aAg/aTg	30/35	0.231687489946873	1	FACETS	0.781	0.714	0.85	0.781	0.714	0.85	INDETERMINATE	1	TRUE	0	0.661753494901612	1		509	295	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0031771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	57	738	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.18	2		738	590	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0031771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	72	599	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.18	2		599	789	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002939	69002939	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773432628	NA	P-0031771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	26	255	0	ENST00000288368.4:c.2239C>T	p.Arg747Trp	p.R747W	ENST00000288368	NM_024870.2	747	Cgg/Tgg	20/40	1	2	FACETS	0.739	0.585	0.916	0.739	0.585	0.916	CLONAL	1	TRUE	1	0.18	2		255	391	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205731	128205732	+	stop_gained	Nonsense_Mutation	DNP	GA	GA	TT	novel	NA	P-0031771-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	78	737	2	ENST00000341105.2:c.143_144delinsAA	p.Phe48Ter	p.F48*	ENST00000341105	NM_032638.4	48	tTC/tAA	2/6	1	2	FACETS	0.904	0.792	1	0.904	0.792	1	CLONAL	1	TRUE	1	0.18	2		739	959	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0031776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	11	401	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.066	0.045	0.092	0.066	0.045	0.092	SUBCLONAL	1	TRUE	1	0.634941976570357	2		401	526	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0031776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	352	510	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.634941976570357	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.634941976570357	1		510	731	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0031776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	191	489	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	1	2	FACETS	0.701	0.649	0.755	0.701	0.649	0.755	SUBCLONAL	1	TRUE	1	0.634941976570357	2		489	858	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977883	131977883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561655417	NA	P-0031776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	140	290	1	ENST00000265335.6:c.3766C>T	p.Arg1256Cys	p.R1256C	ENST00000265335		1256	Cgc/Tgc	25/25	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.634941976570357	2		291	427	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020764	37020764	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	245	517	1	ENST00000358127.4:c.81del	p.Phe27LeufsTer2	p.F27Lfs*2	ENST00000358127	NM_001280556.1	27	ttT/tt	2/10	1	2	FACETS	0.869	0.814	0.926	0.869	0.814	0.926	CLONAL	1	TRUE	1	0.634941976570357	2		518	888	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726698	88726698	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375475747	NA	P-0031776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	192	365	3	ENST00000360948.2:c.346C>T	p.Arg116Trp	p.R116W	ENST00000360948	NM_001012338.2	116	Cgg/Tgg	4/19	1	2	FACETS	0.995	0.925	1	0.995	0.925	1	CLONAL	1	TRUE	1	0.634941976570357	2		368	608	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204661	108204661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1565538536	NA	P-0031776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	30	276	0	ENST00000278616.4:c.7976T>C	p.Leu2659Ser	p.L2659S	ENST00000278616	NM_000051.3	2659	tTa/tCa	54/63	0.249609281381469	3	FACETS	0.234	0.188	0.287	0.117	0.094	0.144	INDETERMINATE	1	TRUE	1	0.634941976570357	3		276	532	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448347	49448347	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0031776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	270	549	0	ENST00000301067.7:c.364G>T	p.Glu122Ter	p.E122*	ENST00000301067	NM_003482.3	122	Gag/Tag	3/54	1	2	FACETS	0.959	0.902	1	0.959	0.902	1	CLONAL	1	TRUE	1	0.634941976570357	2		549	887	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351526	89351526	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0031776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	79	595	0	ENST00000301030.4:c.1424A>C	p.Lys475Thr	p.K475T	ENST00000301030	NM_001256183.1	475	aAg/aCg	9/13	1	2	FACETS	0.243	0.213	0.276	0.243	0.213	0.276	SUBCLONAL	1	TRUE	1	0.634941976570357	2		595	1024	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16097835	16097835	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0031776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	46	511	0	ENST00000268712.3:c.49C>T	p.Gln17Ter	p.Q17*	ENST00000268712	NM_006311.3	17	Caa/Taa	2/46	0.634941976570357	1	FACETS	0.174	0.146	0.205	0.174	0.146	0.205	SUBCLONAL	1	TRUE	0	0.634941976570357	1		511	568	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437841	56438206	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGAAGATAAAAAAATGAATCTAACCCCACCCTTCATTGCCATGGGTCTAAAATGAGATAATGCATCCAAAGCACCACTGCAGCCTGGCACGTGGTACACTCTCAACAAACAATAGTGCTCTTTCACTGGAAGGTCAGAAAAGTGACCAAACTTCAGGCTGGTCCCTGATCTCTGCCTCATGCAGGACACATGGGAAACAGATGTAGCCAGGGTACCCATACCAGCCCCTAGGCCTGCCCACCCCTCCCCCAGCTTCAATCTCCCCAGTCTGGTCATGGAGGTGAACCACAAGACCTGCCTTACCTGCCCCTCAGAGAACTCCTCCAGACAGATGGCACACACAGGGGCTGAGCTGCAGCTGCTCCC	TGAAGATAAAAAAATGAATCTAACCCCACCCTTCATTGCCATGGGTCTAAAATGAGATAATGCATCCAAAGCACCACTGCAGCCTGGCACGTGGTACACTCTCAACAAACAATAGTGCTCTTTCACTGGAAGGTCAGAAAAGTGACCAAACTTCAGGCTGGTCCCTGATCTCTGCCTCATGCAGGACACATGGGAAACAGATGTAGCCAGGGTACCCATACCAGCCCCTAGGCCTGCCCACCCCTCCCCCAGCTTCAATCTCCCCAGTCTGGTCATGGAGGTGAACCACAAGACCTGCCTTACCTGCCCCTCAGAGAACTCCTCCAGACAGATGGCACACACAGGGGCTGAGCTGCAGCTGCTCCC	-	novel	NA	P-0031776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3	17	9	0	ENST00000407977.2:c.787_850-229del		p.X263_splice	ENST00000407977		263		7/10	0.634941976570357	1	FACETS	0.914	0.796	0.997	1	0.953	1	CLONAL	2	TRUE	0	0.634941976570357	1		9	20	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50143301	50143301	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	54	99	0	ENST00000246792.3:c.55C>A	p.Pro19Thr	p.P19T	ENST00000246792	NM_006270.3	19	Cct/Act	1/6	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.634941976570357	NA		99	209	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629933	187629933	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031776-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	64	528	0	ENST00000441802.2:c.1049T>G	p.Val350Gly	p.V350G	ENST00000441802	NM_005245.3	350	gTt/gGt	2/27	0.634941976570357	1	FACETS	0.198	0.171	0.227	0.198	0.171	0.227	SUBCLONAL	1	TRUE	0	0.634941976570357	1		528	696	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0031809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	16	372	0				ENST00000310581	NM_198253.2	-/1132			0.31441116665689	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		372	140	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0031809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	19	799	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.266842529371358	4	FACETS		NA	1			1	NA	NA	FALSE	2	NA	4		799	270	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0031809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	23	683	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.31441116665689	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		683	278	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	11	850	2	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	0.195198510946785	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		852	295	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350772	89350775	+	frameshift_variant	Frame_Shift_Del	DEL	TTTG	TTTG	-	rs886039734	NA	P-0031809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	28	1324	0	ENST00000301030.4:c.2175_2178del	p.Asn725LysfsTer23	p.N725Kfs*23	ENST00000301030	NM_001256183.1	725	aaCAAA/aa	9/13	0.31441116665689	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		1324	468	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729400	41729400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0031809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	26	845	0	ENST00000242208.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000242208	NM_002192.2	377	Cgc/Tgc	3/3	0.266842529371358	4	FACETS		NA	1			1	NA	NA	FALSE	2	NA	4		845	319	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797314	135797314	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0031809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	23	383	0	ENST00000298552.3:c.555del	p.Tyr185Ter	p.Y185*	ENST00000298552	NM_001162426.1	185	taC/ta	7/23	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		383	170	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981271	201981272	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	86	1027	0	ENST00000359651.3:c.355dup	p.Asp119GlyfsTer16	p.D119Gfs*16	ENST00000359651		117	ctg/ctGg	2/8	0.266842529371358	4	FACETS		NA	1			1	NA	NA	FALSE	2	NA	4		1027	384	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670657	134670657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1441537601	NA	P-0031809-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	14	1024	0	ENST00000398015.3:c.568C>T	p.Arg190Cys	p.R190C	ENST00000398015	NM_004441.4	190	Cgt/Tgt	3/16	0.266842529371358	4	FACETS		NA	1			1	NA	NA	FALSE	2	NA	4		1024	210	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0031814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	146	217	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.939	0.864	1	0.939	0.864	1	CLONAL	1	TRUE	1	0.672973579081243	2		217	462	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0031814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	65	400	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.265	0.229	0.304	0.265	0.229	0.304	SUBCLONAL	1	TRUE	1	0.672973579081243	2		400	730	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0031814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	51	731	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	0.142	0.12	0.167	0.142	0.12	0.167	SUBCLONAL	1	TRUE	1	0.672973579081243	2		731	1066	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	458	1082	0	ENST00000269305.4:c.404G>C	p.Cys135Ser	p.C135S	ENST00000269305	NM_001126112.2	135	tGc/tCc	5/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.672973579081243	2		1082	1250	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578463	7578463	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs371524413	NA	P-0031814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	356	972	0	ENST00000269305.4:c.467G>C	p.Arg156Pro	p.R156P	ENST00000269305	NM_001126112.2	156	cGc/cCc	5/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.672973579081243	2		972	996	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165918	47165918	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs775039657	NA	P-0031814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	221	735	0	ENST00000409792.3:c.208C>T	p.Arg70Ter	p.R70*	ENST00000409792	NM_014159.6	70	Cga/Tga	3/21	0.57389828070882	1	FACETS	0.745	0.698	0.792	0.745	0.698	0.792	SUBCLONAL	1	TRUE	0	0.672973579081243	1		735	585	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131161	55131161	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	57	728	2	ENST00000257290.5:c.704G>T	p.Cys235Phe	p.C235F	ENST00000257290	NM_006206.4	235	tGt/tTt	5/23	1	2	FACETS	0.189	0.161	0.219	0.189	0.161	0.219	SUBCLONAL	1	TRUE	1	0.672973579081243	2		730	897	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148590	119149255	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACACAAGCTTTAGTATATTCTTTATAGAACTGACAGCATAATTGAATTCATTGGAACCCATTGACTAGATTAGTGAATTTGTGTGTATGTGGTTTCACTTTAAACCCTGGAGCTTAAAATAGGACCCAGACTAGATGCTTTCTGGTTTAATAAAAAATAAACCACTGTTGTGACATTTTTATATAAGCAAAATTTGTATAGGAAACAAGTCTTCACTTTTTCTGTTAACATTTATAATTGCAGTTATTTATTCAACTAATAGTCTTTTAATTTTTTTTAATCAAAGGAACAATATGAATTATACTGTGAGATGGGCTCCACATTCCAACTATGTAAAATATGTGCTGAAAATGATAAGGATGTAAAGATTGAGCCCTGTGGACACCTCATGTGCACATCCTGTCTTACATCCTGGCAGGTACGGATCTAAACAGCGACTTTTTTCAGCTATGTAATAACCTTGGAAAATTCGGTATTATATAGCCTTTACTGATACAAGGGGTGGCCTGGCTTTTGGGGTTAGGTTTAAACTTTTACTTTTTTTTGATCTCTAGGAAATGTATTTTCTAGTAGATTAATATTTTAAGTATTTTCAGATGCATCTGTTACTATCTTTTGCTTCTTCTGCAGGAATCAGAAGGTCAGGGCTGTCCTTTCTGCCGATGT	ACACAAGCTTTAGTATATTCTTTATAGAACTGACAGCATAATTGAATTCATTGGAACCCATTGACTAGATTAGTGAATTTGTGTGTATGTGGTTTCACTTTAAACCCTGGAGCTTAAAATAGGACCCAGACTAGATGCTTTCTGGTTTAATAAAAAATAAACCACTGTTGTGACATTTTTATATAAGCAAAATTTGTATAGGAAACAAGTCTTCACTTTTTCTGTTAACATTTATAATTGCAGTTATTTATTCAACTAATAGTCTTTTAATTTTTTTTAATCAAAGGAACAATATGAATTATACTGTGAGATGGGCTCCACATTCCAACTATGTAAAATATGTGCTGAAAATGATAAGGATGTAAAGATTGAGCCCTGTGGACACCTCATGTGCACATCCTGTCTTACATCCTGGCAGGTACGGATCTAAACAGCGACTTTTTTCAGCTATGTAATAACCTTGGAAAATTCGGTATTATATAGCCTTTACTGATACAAGGGGTGGCCTGGCTTTTGGGGTTAGGTTTAAACTTTTACTTTTTTTTGATCTCTAGGAAATGTATTTTCTAGTAGATTAATATTTTAAGTATTTTCAGATGCATCTGTTACTATCTTTTGCTTCTTCTGCAGGAATCAGAAGGTCAGGGCTGTCCTTTCTGCCGATGT	-	novel	NA	P-0031814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	143	269	0	ENST00000264033.4:c.1095+36_1263del		p.X365_splice	ENST00000264033	NM_005188.3	365		8-9/16	0.22113838671493	2	FACETS	1	0.978	1	0.582	0.537	0.628	INDETERMINATE	1	TRUE	0	0.672973579081243	2		269	365	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872197	76872197	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0031814-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	256	196	0	ENST00000373344.5:c.5450G>A	p.Arg1817Lys	p.R1817K	ENST00000373344	NM_000489.3	1817	aGg/aAg	22/35	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.672973579081243	1		196	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578517	7578517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750600586	NA	P-0031815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	215	868	0	ENST00000269305.4:c.413C>T	p.Ala138Val	p.A138V	ENST00000269305	NM_001126112.2	138	gCc/gTc	5/11	0.189331477516509	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.189331477516509	3		868	1177	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123156523	123156523	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0031815-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	14	208	0	ENST00000218089.9:c.44+2T>C		p.X15_splice	ENST00000218089	NM_001042749.1	15			1	2	FACETS	1	0.816	1	1	0.816	1	CLONAL	1	TRUE	1	0.189331477516509	2		208	127	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0031918-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	57	381	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.916	0.787	1	0.916	0.787	1	CLONAL	1	TRUE	1	0.273664943242798	2		381	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0031918-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	149	688	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.273664943242798	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.273664943242798	1		689	852	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347320	89347320	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0031918-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	87	745	1	ENST00000301030.4:c.5630C>A	p.Pro1877Gln	p.P1877Q	ENST00000301030	NM_001256183.1	1877	cCg/cAg	9/13	0.273664943242798	3	FACETS	0.661	0.584	0.745	0.331	0.292	0.373	SUBCLONAL	1	TRUE	1	0.273664943242798	3		746	1093	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591825	48591825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767342	NA	P-0031918-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	32	325	0	ENST00000342988.3:c.988G>A	p.Glu330Lys	p.E330K	ENST00000342988	NM_005359.5	330	Gaa/Aaa	9/12	0.203151924644303	1	FACETS	0.555	0.45	0.672	0.555	0.45	0.672	SUBCLONAL	1	TRUE	0	0.273664943242798	1		325	364	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455298	29455298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376091121	NA	P-0031918-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	112	493	2	ENST00000389048.3:c.2504C>T	p.Pro835Leu	p.P835L	ENST00000389048	NM_004304.4	835	cCg/cTg	15/29	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.273664943242798	2		495	684	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971204	21971208	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	TGACC	TGACC	-	novel	NA	P-0031918-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	31	456	0	ENST00000304494.5:c.151-1_154del		p.X51_splice	ENST00000304494	NM_000077.4	51		2/3	0.273664943242798	1	FACETS	0.395	0.319	0.482	0.395	0.319	0.482	SUBCLONAL	1	TRUE	0	0.273664943242798	1		456	495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0032174-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	463	648	0	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	0.588521210708722	2	FACETS	0.874	0.842	0.906	0.874	0.842	0.906	CLONAL	2	TRUE	0	0.649781470885318	2		648	815	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0032174-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	341	648	0	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	0.274559061028199	3	FACETS	0.931	0.883	0.981	0.931	0.883	0.981	CLONAL	3	TRUE	0	0.274559061028199	3		648	1011	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0032246-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	3090	621	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.3	23	FACETS	0.989	0.978	1			1	CLONAL	25	TRUE	NA	0.17	23		622	4095	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782289	NA	P-0032246-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	62	583	0	ENST00000269305.4:c.706T>C	p.Tyr236His	p.Y236H	ENST00000269305	NM_001126112.2	236	Tac/Cac	7/11	1	2	FACETS	0.757	0.652	0.872	0.757	0.652	0.872	SUBCLONAL	1	TRUE	1	0.17	2		583	964	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044850	47044850	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	201	755	5	ENST00000377604.3:c.2176C>T	p.Arg726Ter	p.R726*	ENST00000377604	NM_001204468.1	726	Cga/Tga	20/24	0.606603957858407	4	FACETS	0.951	0.881	1			1	CLONAL	1	TRUE	NA	0.650975403787941	4		760	1072	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162829	38162829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773861449	NA	P-0032251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	1254	458	0	ENST00000317025.8:c.2377C>T	p.Arg793Cys	p.R793C	ENST00000317025	NM_023034.1	793	Cgc/Tgc	13/24	0.650975403787941	12	FACETS	0.996	0.974	1			1	CLONAL	8	TRUE	NA	0.650975403787941	12		458	2058	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176105641	176105641	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	109	443	0	ENST00000367669.3:c.874G>T	p.Asp292Tyr	p.D292Y	ENST00000367669	NM_022457.5	292	Gat/Tat	7/20	0.648990242359191	5	FACETS	0.755	0.677	0.837	0.252	0.225	0.279	SUBCLONAL	1	TRUE	2	0.650975403787941	5		443	877	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473650	67473654	+	frameshift_variant	Frame_Shift_Del	DEL	GTCGG	GTCGG	-	novel	NA	P-0032251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	287	519	0	ENST00000327367.4:c.731_735del	p.Val244GlyfsTer65	p.V244Gfs*65	ENST00000327367	NM_005902.3	244	GTCGGg/g	6/9	0.650975403787941	3	FACETS	0.94	0.891	0.988	0.94	0.891	0.988	CLONAL	2	TRUE	1	0.650975403787941	3		519	622	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106228	27106228	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	63	543	0	ENST00000324856.7:c.5839C>T	p.Gln1947Ter	p.Q1947*	ENST00000324856	NM_006015.4	1947	Cag/Tag	20/20	0.262620023808521	2	FACETS	0.776	0.677	0.883	0.776	0.677	0.883	SUBCLONAL	2	FALSE	0	0.262620023808521	2		543	309	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514308	69514308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142959398	NA	P-0032279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	138	534	0	ENST00000294312.3:c.373G>A	p.Glu125Lys	p.E125K	ENST00000294312	NM_005117.2	125	Gag/Aag	3/3	0.262620023808521	4	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	FALSE	2	0.262620023808521	4		534	648	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344314	118344314	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032279-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	31	340	0	ENST00000534358.1:c.2440C>T	p.Gln814Ter	p.Q814*	ENST00000534358	NM_005933.3	814	Cag/Tag	3/36	0.262620023808521	2	FACETS	0.772	0.632	0.924	0.772	0.632	0.924	CLONAL	2	FALSE	0	0.262620023808521	2		340	153	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106228	27106228	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	50	543	0	ENST00000324856.7:c.5839C>T	p.Gln1947Ter	p.Q1947*	ENST00000324856	NM_006015.4	1947	Cag/Tag	20/20	0.603911590502499	1	FACETS	0.808	0.702	0.919	0.808	0.702	0.919	CLONAL	1	TRUE	0	0.603911590502499	1		543	143	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514308	69514308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142959398	NA	P-0032279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	104	534	0	ENST00000294312.3:c.373G>A	p.Glu125Lys	p.E125K	ENST00000294312	NM_005117.2	125	Gag/Aag	3/3	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.603911590502499	2		534	323	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344314	118344314	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032279-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	25	340	0	ENST00000534358.1:c.2440C>T	p.Gln814Ter	p.Q814*	ENST00000534358	NM_005933.3	814	Cag/Tag	3/36	0.603911590502499	1	FACETS	0.98	0.808	1	0.98	0.808	1	CLONAL	1	TRUE	0	0.603911590502499	1		340	59	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108590	8108590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1444417079	NA	P-0032295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	229	643	0	ENST00000585124.1:c.805G>A	p.Gly269Arg	p.G269R	ENST00000585124	NM_004217.3	269	Ggg/Agg	8/9	0.730531941183364	3	FACETS	1	0.966	1	0.526	0.491	0.561	CLONAL	1	TRUE	1	0.730531941183364	3		643	814	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667538	241667539	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0032295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	94	206	0	ENST00000366560.3:c.911dup	p.Val306CysfsTer6	p.V306Cfs*6	ENST00000366560	NM_000143.3	304	cct/ccCt	7/10	1	2	FACETS	0.971	0.877	1	0.971	0.877	1	CLONAL	1	TRUE	1	0.730531941183364	2		206	265	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605803	46605803	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	448	488	0	ENST00000263734.3:c.1451G>T	p.Ser484Ile	p.S484I	ENST00000263734	NM_001430.4	484	aGc/aTc	11/16	0.730531941183364	4	FACETS	0.983	0.948	1	0.983	0.948	1	CLONAL	3	TRUE	1	0.730531941183364	4		488	720	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441987	52441987	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	136	354	0	ENST00000460680.1:c.362G>T	p.Gly121Val	p.G121V	ENST00000460680	NM_004656.3	121	gGt/gTt	5/17	1	2	FACETS	0.91	0.836	0.987	0.91	0.836	0.987	CLONAL	1	TRUE	1	0.730531941183364	2		354	409	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630007	187630007	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	243	637	0	ENST00000441802.2:c.975G>A	p.Trp325Ter	p.W325*	ENST00000441802	NM_005245.3	325	tgG/tgA	2/27	1	2	FACETS	0.991	0.932	1	0.991	0.932	1	CLONAL	1	TRUE	1	0.730531941183364	2		637	671	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0032346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	532	401	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.874508234511986	3	FACETS	0.987	0.954	1	0.987	0.954	1	CLONAL	2	TRUE	1	0.874508234511986	3		401	886	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974792	21974792	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs141798398	NA	P-0032346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	140	126	0	ENST00000304494.5:c.35C>A	p.Ser12Ter	p.S12*	ENST00000304494	NM_000077.4	12	tCg/tAg	1/3	0.873352164285378	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.874508234511986	1		126	166	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578466	7578466	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs786202752	NA	P-0032346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	455	542	1	ENST00000269305.4:c.464C>A	p.Thr155Asn	p.T155N	ENST00000269305	NM_001126112.2	155	aCc/aAc	5/11	0.847414054077354	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.874508234511986	1		543	550	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61706022	61706022	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs756595032	NA	P-0032346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	386	464	0	ENST00000401558.2:c.3149A>G	p.His1050Arg	p.H1050R	ENST00000401558	NM_003400.3	1050	cAt/cGt	25/25	0.457262942451879	3	FACETS	1	0.993	1	0.618	0.588	0.648	INDETERMINATE	1	TRUE	1	0.874508234511986	3		464	1027	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0032348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	135	359	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.649936928921819	1	FACETS	0.922	0.853	0.993	0.922	0.853	0.993	CLONAL	1	TRUE	0	0.649936928921819	1		359	304	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0032348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	131	351	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.925	0.846	1	0.925	0.846	1	CLONAL	1	TRUE	1	0.649936928921819	2		351	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519991	NA	P-0032348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	178	465	0	ENST00000269305.4:c.536A>C	p.His179Pro	p.H179P	ENST00000269305	NM_001126112.2	179	cAt/cCt	5/11	0.649936928921819	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.649936928921819	1		465	359	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828303	50828303	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	165	433	0	ENST00000398568.2:c.2641G>T	p.Ala881Ser	p.A881S	ENST00000398568	NM_001042412.1	881	Gcc/Tcc	17/18	1	2	FACETS	0.913	0.844	0.985	0.913	0.844	0.985	CLONAL	1	TRUE	1	0.649936928921819	2		433	556	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438178	56438178	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032348-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	177	523	1	ENST00000407977.2:c.815G>T	p.Cys272Phe	p.C272F	ENST00000407977		272	tGt/tTt	7/10	0.649936928921819	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.649936928921819	1		524	351	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	325	518	0	ENST00000322088.6:c.767C>A	p.Ser256Tyr	p.S256Y	ENST00000322088	NM_014225.5	256	tCc/tAc	6/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.735753155017358	2		518	828	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057520000	NA	P-0032357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	433	684	0	ENST00000269305.4:c.452C>G	p.Pro151Arg	p.P151R	ENST00000269305	NM_001126112.2	151	cCc/cGc	5/11	0.735753155017358	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.735753155017358	1		684	723	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591259	67591303	+	inframe_deletion	In_Frame_Del	DEL	AAAAAGGTGTTCGGCAAAAGAAGTTGAACGAGTGGTTGGGCAATG	AAAAAGGTGTTCGGCAAAAGAAGTTGAACGAGTGGTTGGGCAATG	-	novel	NA	P-0032357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	68	328	0	ENST00000274335.5:c.1761_1805del	p.Lys587_Glu601del	p.K587_E601del	ENST00000274335		586	cAAAAAGGTGTTCGGCAAAAGAAGTTGAACGAGTGGTTGGGCAATGaa/caa	13/15	0.408141878840968	1	FACETS	0.375	0.328	0.424	0.375	0.328	0.424	INDETERMINATE	1	TRUE	0	0.735753155017358	1		328	312	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202465	123202465	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0032357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	139	265	1	ENST00000218089.9:c.2317C>G	p.Gln773Glu	p.Q773E	ENST00000218089	NM_001042749.1	773	Caa/Gaa	24/35	1	2	FACETS	0.904	0.831	0.979	0.904	0.831	0.979	CLONAL	1	TRUE	1	0.735753155017358	2		266	418	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665814	241665814	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	396	427	0	ENST00000366560.3:c.1165G>T	p.Gly389Trp	p.G389W	ENST00000366560	NM_000143.3	389	Ggg/Tgg	8/10	0.496170783434372	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.496170783434372	2		427	723	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557898	21557898	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	184	490	0	ENST00000382592.4:c.1947C>A	p.Tyr649Ter	p.Y649*	ENST00000382592	NM_014572.2	649	taC/taA	5/8	0.496170783434372	1	FACETS	0.87	0.807	0.935	0.87	0.807	0.935	CLONAL	1	TRUE	0	0.496170783434372	1		490	641	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196685	106196685	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1163200838	NA	P-0032365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	153	425	0	ENST00000380013.4:c.5018C>A	p.Pro1673Gln	p.P1673Q	ENST00000380013	NM_001127208.2	1673	cCa/cAa	11/11	0.285407029503089	1	FACETS	0.716	0.657	0.777	0.716	0.657	0.777	INDETERMINATE	1	TRUE	0	0.496170783434372	1		425	648	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016327	150016328	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032365-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	197	471	0	ENST00000253339.5:c.378dup	p.Asn127Ter	p.N127*	ENST00000253339		126	-/T	2/7	0.496170783434372	1	FACETS	0.989	0.921	1	0.989	0.921	1	CLONAL	1	TRUE	0	0.496170783434372	1		471	604	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665814	241665814	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0032365-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	529	427	0	ENST00000366560.3:c.1165G>T	p.Gly389Trp	p.G389W	ENST00000366560	NM_000143.3	389	Ggg/Tgg	8/10	0.673091490449771	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.673091490449771	2		427	756	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016327	150016328	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032365-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	314	471	0	ENST00000253339.5:c.378dup	p.Asn127Ter	p.N127*	ENST00000253339		126	-/T	2/7	0.673091490449771	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.673091490449771	1		471	591	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235879	108235879	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139379666	NA	P-0032365-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	207	399	1	ENST00000278616.4:c.8921C>T	p.Pro2974Leu	p.P2974L	ENST00000278616	NM_000051.3	2974	cCg/cTg	62/63	1	2	FACETS	0.783	0.728	0.839	0.783	0.728	0.839	SUBCLONAL	1	TRUE	1	0.673091490449771	2		400	786	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074130	8074131	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0032365-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	203	340	0	ENST00000377482.5:c.528dup	p.Ser177LeufsTer14	p.S177Lfs*14	ENST00000377482	NM_018948.3	176	-/C	4/4	0.673091490449771	1	FACETS	0.967	0.909	1	0.967	0.909	1	CLONAL	1	TRUE	0	0.673091490449771	1		340	414	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180302	27180302	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0032365-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	267	525	0	ENST00000380036.4:c.966G>C	p.Met322Ile	p.M322I	ENST00000380036	NM_000459.3	322	atG/atC	7/23	1	2	FACETS	0.94	0.884	0.997	0.94	0.884	0.997	CLONAL	1	TRUE	1	0.673091490449771	2		525	844	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	160	539	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.867	0.8	0.936	0.867	0.8	0.936	CLONAL	1	TRUE	1	0.693993560064187	2		544	532	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	188	540	2	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.855	0.793	0.917	0.855	0.793	0.917	CLONAL	1	TRUE	1	0.693993560064187	2		542	634	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	175	472	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.873	0.808	0.939	0.873	0.808	0.939	CLONAL	1	TRUE	1	0.693993560064187	2		472	578	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	316	428	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.927	0.89	0.964	1	0.996	1	CLONAL	2	TRUE	1	0.693993560064187	2		428	491	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	217	539	6	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.925	0.864	0.987	0.925	0.864	0.987	CLONAL	1	TRUE	1	0.693993560064187	2		545	676	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	194	417	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	1	2	FACETS	0.995	0.927	1	0.995	0.927	1	CLONAL	1	TRUE	1	0.693993560064187	2		417	562	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370235	40370236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs761761205	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	184	712	4	ENST00000293328.3:c.1102dup	p.Gln368ProfsTer9	p.Q368Pfs*9	ENST00000293328	NM_012448.3	368	cag/cCag	9/19	1	2	FACETS	0.66	0.61	0.711	0.66	0.61	0.711	SUBCLONAL	1	TRUE	1	0.693993560064187	2		716	804	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578206	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs886039484	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	226	574	1	ENST00000269305.4:c.643A>G	p.Ser215Gly	p.S215G	ENST00000269305	NM_001126112.2	215	Agt/Ggt	6/11	1	2	FACETS	0.884	0.826	0.943	0.884	0.826	0.943	CLONAL	1	TRUE	1	0.693993560064187	2		575	737	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954643	17954643	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	204	624	1	ENST00000458235.1:c.251del	p.Pro84ArgfsTer63	p.P84Rfs*63	ENST00000458235	NM_000215.3	84	cCg/cg	3/24	1	2	FACETS	0.829	0.772	0.888	0.829	0.772	0.888	CLONAL	1	TRUE	1	0.693993560064187	2		625	709	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604640	55604640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146374006	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	213	499	0	ENST00000288135.5:c.2848G>A	p.Val950Met	p.V950M	ENST00000288135	NM_000222.2	950	Gtg/Atg	21/21	1	2	FACETS	0.907	0.846	0.968	0.907	0.846	0.968	CLONAL	1	TRUE	1	0.693993560064187	2		499	677	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645275	67645276	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	177	477	0	ENST00000264010.4:c.544dup	p.Glu182GlyfsTer9	p.E182Gfs*9	ENST00000264010	NM_006565.3	180	-/G	3/12	1	2	FACETS	0.857	0.794	0.922	0.857	0.794	0.922	CLONAL	1	TRUE	1	0.693993560064187	2		477	595	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099950	27099950	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	243	513	1	ENST00000324856.7:c.3829C>T	p.Gln1277Ter	p.Q1277*	ENST00000324856	NM_006015.4	1277	Cag/Tag	15/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.693993560064187	2		514	633	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692979	89692979	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs398123325	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	105	393	0	ENST00000371953.3:c.463T>A	p.Tyr155Asn	p.Y155N	ENST00000371953	NM_000314.4	155	Tat/Aat	5/9	1	2	FACETS	0.937	0.849	1	0.937	0.849	1	CLONAL	1	TRUE	1	0.693993560064187	2		393	323	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431746	49431748	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs748239185	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	189	575	1	ENST00000301067.7:c.9391_9393del	p.Pro3131del	p.P3131del	ENST00000301067	NM_003482.3	3131	CCT/-	34/54	1	2	FACETS	0.87	0.808	0.934	0.87	0.808	0.934	CLONAL	1	TRUE	1	0.693993560064187	2		576	626	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2090156	2090156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148474733	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	222	609	2	ENST00000219066.1:c.793G>A	p.Ala265Thr	p.A265T	ENST00000219066	NM_002528.5	265	Gcc/Acc	5/6	1	2	FACETS	0.878	0.82	0.937	0.878	0.82	0.937	CLONAL	1	TRUE	1	0.693993560064187	2		611	729	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463271	25463271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770568549	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	156	430	0	ENST00000264709.3:c.2222C>T	p.Ala741Val	p.A741V	ENST00000264709	NM_175629.2	741	gCg/gTg	19/23	1	2	FACETS	0.837	0.771	0.905	0.837	0.771	0.905	CLONAL	1	TRUE	1	0.693993560064187	2		430	537	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258581	16258581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	187	430	2	ENST00000375759.3:c.5846G>A	p.Arg1949Gln	p.R1949Q	ENST00000375759	NM_015001.2	1949	cGg/cAg	11/15	1	2	FACETS	0.989	0.92	1	0.989	0.92	1	CLONAL	1	TRUE	1	0.693993560064187	2		432	545	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598813	28598813	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	206	605	0	ENST00000253063.3:c.373T>C	p.Cys125Arg	p.C125R	ENST00000253063	NM_031459.4	125	Tgt/Cgt	4/10	1	2	FACETS	0.864	0.805	0.925	0.864	0.805	0.925	CLONAL	1	TRUE	1	0.693993560064187	2		605	687	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690810	89690813	+	frameshift_variant	Frame_Shift_Del	DEL	GAAA	GAAA	-	novel	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	94	388	0	ENST00000371953.3:c.219_222del	p.Glu73AspfsTer25	p.E73Dfs*25	ENST00000371953	NM_000314.4	73	GAAAga/ga	4/9	1	2	FACETS	0.957	0.863	1	0.957	0.863	1	CLONAL	1	TRUE	1	0.693993560064187	2		388	283	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865782	57865782	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	212	531	0	ENST00000228682.2:c.3259A>G	p.Asn1087Asp	p.N1087D	ENST00000228682	NM_005269.2	1087	Aac/Gac	12/12	1	2	FACETS	0.941	0.879	1	0.941	0.879	1	CLONAL	1	TRUE	1	0.693993560064187	2		531	649	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254290	133254291	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	161	368	0	ENST00000320574.5:c.593dup	p.Gly199ArgfsTer5	p.G199Rfs*5	ENST00000320574	NM_006231.2	198	ggc/ggGc	7/49	1	2	FACETS	0.917	0.847	0.989	0.917	0.847	0.989	CLONAL	1	TRUE	1	0.693993560064187	2		368	506	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944597	32944597	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	199	590	0	ENST00000380152.3:c.8390A>G	p.Asp2797Gly	p.D2797G	ENST00000380152		2797	gAc/gGc	19/27	1	2	FACETS	0.909	0.846	0.973	0.909	0.846	0.973	CLONAL	1	TRUE	1	0.693993560064187	2		590	631	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632633	3632633	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	249	615	0	ENST00000294008.3:c.5215del	p.Glu1739ArgfsTer18	p.E1739Rfs*18	ENST00000294008	NM_032444.2	1739	Gag/ag	15/15	1	2	FACETS	0.87	0.816	0.925	0.87	0.816	0.925	CLONAL	1	TRUE	1	0.693993560064187	2		615	825	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45396912	45396912	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	104	363	0	ENST00000262160.6:c.260T>G	p.Leu87Arg	p.L87R	ENST00000262160	NM_005901.5	87	cTg/cGg	3/11	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.693993560064187	2		363	289	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621901	1621901	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	200	601	1	ENST00000344749.5:c.891del	p.Gly298GlufsTer96	p.G298Efs*96	ENST00000344749	NM_001136139.2	297	ccC/cc	11/19	1	2	FACETS	0.889	0.828	0.952	0.889	0.828	0.952	CLONAL	1	TRUE	1	0.693993560064187	2		602	648	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252775	10252775	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	250	535	0	ENST00000340748.4:c.3190T>C	p.Tyr1064His	p.Y1064H	ENST00000340748		1064	Tat/Cat	29/40	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.693993560064187	2		535	682	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610345	10610345	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	238	584	0	ENST00000171111.5:c.365T>C	p.Val122Ala	p.V122A	ENST00000171111	NM_203500.1	122	gTg/gCg	2/6	1	2	FACETS	0.902	0.846	0.961	0.902	0.846	0.961	CLONAL	1	TRUE	1	0.693993560064187	2		584	760	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257962	19257962	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1416516735	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	279	724	1	ENST00000162023.5:c.424G>A	p.Val142Met	p.V142M	ENST00000162023		142	Gtg/Atg	9/13	1	2	FACETS	0.991	0.935	1	0.991	0.935	1	CLONAL	1	TRUE	1	0.693993560064187	2		725	811	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213276	36213276	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	198	580	2	ENST00000222270.7:c.2473C>T	p.Gln825Ter	p.Q825*	ENST00000222270	NM_014727.1	825	Cag/Tag	4/37	1	2	FACETS	0.848	0.789	0.909	0.848	0.789	0.909	CLONAL	1	TRUE	1	0.693993560064187	2		582	673	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99154439	99154439	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	138	424	1	ENST00000074304.5:c.579+2T>C		p.X193_splice	ENST00000074304	NM_001134224.1	193			1	2	FACETS	0.812	0.743	0.882	0.812	0.743	0.882	CLONAL	1	TRUE	1	0.693993560064187	2		425	490	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645286	215645286	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs754539312	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	145	379	0	ENST00000260947.4:c.1312A>G	p.Lys438Glu	p.K438E	ENST00000260947	NM_000465.2	438	Aag/Gag	4/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.693993560064187	2		379	412	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017219	31017219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140731196	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	119	283	0	ENST00000375687.4:c.550G>A	p.Val184Met	p.V184M	ENST00000375687	NM_015338.5	184	Gtg/Atg	7/13	1	2	FACETS	0.847	0.771	0.925	0.847	0.771	0.925	CLONAL	1	TRUE	1	0.693993560064187	2		283	405	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29099491	29099491	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	73	246	0	ENST00000328354.6:c.908+2T>C		p.X303_splice	ENST00000328354	NM_007194.3	303			1	2	FACETS	0.873	0.774	0.976	0.873	0.774	0.976	CLONAL	1	TRUE	1	0.693993560064187	2		246	241	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527599	41527599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	180	390	0	ENST00000263253.7:c.1490G>A	p.Gly497Glu	p.G497E	ENST00000263253	NM_001429.3	497	gGg/gAg	6/31	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.693993560064187	2		390	518	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533747	41533747	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	189	490	1	ENST00000263253.7:c.1713G>A	p.Trp571Ter	p.W571*	ENST00000263253	NM_001429.3	571	tgG/tgA	8/31	1	2	FACETS	0.906	0.842	0.972	0.906	0.842	0.972	CLONAL	1	TRUE	1	0.693993560064187	2		491	601	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566541	41566541	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	143	286	0	ENST00000263253.7:c.4418A>G	p.Lys1473Arg	p.K1473R	ENST00000263253	NM_001429.3	1473	aAg/aGg	27/31	1	2	FACETS	0.906	0.833	0.981	0.906	0.833	0.981	CLONAL	1	TRUE	1	0.693993560064187	2		286	455	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164537	47164537	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	109	448	1	ENST00000409792.3:c.1589G>A	p.Cys530Tyr	p.C530Y	ENST00000409792	NM_014159.6	530	tGt/tAt	3/21	1	2	FACETS	0.892	0.81	0.978	0.892	0.81	0.978	CLONAL	1	TRUE	1	0.693993560064187	2		449	352	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953798	55953798	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	194	534	2	ENST00000263923.4:c.3638A>G	p.His1213Arg	p.H1213R	ENST00000263923	NM_002253.2	1213	cAt/cGt	27/30	1	2	FACETS	0.841	0.781	0.902	0.841	0.781	0.902	CLONAL	1	TRUE	1	0.693993560064187	2		536	665	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542660	187542660	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	136	465	1	ENST00000441802.2:c.5080C>T	p.Gln1694Ter	p.Q1694*	ENST00000441802	NM_005245.3	1694	Caa/Taa	10/27	1	2	FACETS	0.86	0.788	0.934	0.86	0.788	0.934	CLONAL	1	TRUE	1	0.693993560064187	2		466	456	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589135	67589136	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	35	291	0	ENST00000274335.5:c.1126_1127del	p.Gly376LysfsTer2	p.G376Kfs*2	ENST00000274335		375	GGg/g	9/15	1	2	FACETS	0.813	0.681	0.955	0.813	0.681	0.955	CLONAL	1	TRUE	1	0.693993560064187	2		291	124	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591125	67591126	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	71	279	0	ENST00000274335.5:c.1718_1719del	p.Leu573GlnfsTer28	p.L573Qfs*28	ENST00000274335		573	cTG/c	12/15	1	2	FACETS	0.874	0.774	0.979	0.874	0.774	0.979	CLONAL	1	TRUE	1	0.693993560064187	2		279	234	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524370	176524370	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	250	596	0	ENST00000292408.4:c.2231A>G	p.Asp744Gly	p.D744G	ENST00000292408	NM_213647.1	744	gAc/gGc	17/18	1	2	FACETS	0.952	0.894	1	0.952	0.894	1	CLONAL	1	TRUE	1	0.693993560064187	2		596	757	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056287	26056287	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147427763	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	32	478	0	ENST00000343677.2:c.370G>A	p.Gly124Ser	p.G124S	ENST00000343677	NM_005319.3	124	Ggc/Agc	1/1	1	2	FACETS	0.183	0.148	0.223	0.183	0.148	0.223	SUBCLONAL	1	TRUE	1	0.693993560064187	2		478	504	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250649	26250649	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	181	523	0	ENST00000446824.2:c.185T>C	p.Leu62Pro	p.L62P	ENST00000446824	NM_021018.2	62	cTg/cCg	1/1	1	2	FACETS	0.943	0.876	1	0.943	0.876	1	CLONAL	1	TRUE	1	0.693993560064187	2		523	553	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109321776	109321776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	160	567	0	ENST00000436639.2:c.647C>T	p.Ala216Val	p.A216V	ENST00000436639	NM_014454.2	216	gCt/gTt	4/10	1	2	FACETS	0.826	0.762	0.893	0.826	0.762	0.893	CLONAL	1	TRUE	1	0.693993560064187	2		567	558	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112015592	112015592	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	214	444	0	ENST00000368678.4:c.1250A>G	p.Tyr417Cys	p.Y417C	ENST00000368678		417	tAc/tGc	11/13	1	2	FACETS	0.942	0.88	1	0.942	0.88	1	CLONAL	1	TRUE	1	0.693993560064187	2		444	655	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506473	148506473	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	93	286	0	ENST00000320356.2:c.2039T>C	p.Val680Ala	p.V680A	ENST00000320356	NM_004456.4	680	gTg/gCg	18/20	1	2	FACETS	0.927	0.835	1	0.927	0.835	1	CLONAL	1	TRUE	1	0.693993560064187	2		286	289	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141570548	141570548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0032495-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	197	532	1	ENST00000220592.5:c.580G>A	p.Gly194Arg	p.G194R	ENST00000220592	NM_012154.3	194	Ggg/Agg	5/19	1	2	FACETS	0.898	0.836	0.962	0.898	0.836	0.962	CLONAL	1	TRUE	1	0.693993560064187	2		533	632	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0032598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	203	690	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	0.353790116494893	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.361514196996859	1		690	888	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692895	89692896	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0032598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	30	556	0	ENST00000371953.3:c.379_380delinsTT	p.Gly127Leu	p.G127L	ENST00000371953	NM_000314.4	127	GGa/TTa	5/9	0.361514196996859	1	FACETS	0.567	0.459	0.687	0.567	0.459	0.687	SUBCLONAL	1	TRUE	0	0.361514196996859	1		556	240	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12043169	12043169	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0032598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	56	301	0	ENST00000353533.5:c.1054G>T	p.Glu352Ter	p.E352*	ENST00000353533	NM_003010.3	352	Gaa/Taa	10/11	0.353790116494893	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.361514196996859	1		301	225	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138197249	138197249	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777456133	NA	P-0032598-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	52	440	0	ENST00000237289.4:c.751G>A	p.Gly251Ser	p.G251S	ENST00000237289	NM_001270507.1	251	Ggc/Agc	5/9	NA	2	FACETS	0.544	0.463	0.633			1	INDETERMINATE	1	TRUE	NA	0.361514196996859	2		440	529	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0032703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	90	621	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.164252175226508	2	FACETS	0.928	0.826	1	0.464	0.413	0.519	INDETERMINATE	1	TRUE	0	0.37	2		622	524	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575671	48575671	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0032703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	58	622	0	ENST00000342988.3:c.431C>G	p.Ser144Ter	p.S144*	ENST00000342988	NM_005359.5	144	tCa/tGa	4/12	1	2	FACETS	0.498	0.428	0.576	0.498	0.428	0.576	SUBCLONAL	1	TRUE	1	0.37	2		622	629	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255887	16255887	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0032703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	30	443	0	ENST00000375759.3:c.3152A>C	p.Lys1051Thr	p.K1051T	ENST00000375759	NM_015001.2	1051	aAa/aCa	11/15	0.3	3	FACETS	0.534	0.43	0.651			1	SUBCLONAL	1	TRUE	NA	0.37	3		443	360	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164659	47164690	+	frameshift_variant	Frame_Shift_Del	DEL	AGAATAGGATGATGTCCTTAGGTCTCTGTAAG	AGAATAGGATGATGTCCTTAGGTCTCTGTAAG	-	novel	NA	P-0032703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	37	470	0	ENST00000409792.3:c.1436_1467del	p.Ser479Ter	p.S479*	ENST00000409792	NM_014159.6	479	tCTTACAGAGACCTAAGGACATCATCCTATTCT/t	3/21	1	2	FACETS	0.543	0.449	0.649	0.543	0.449	0.649	SUBCLONAL	1	TRUE	1	0.37	2		470	368	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613194	52613194	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0032703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	46	651	0	ENST00000394830.3:c.3334G>T	p.Glu1112Ter	p.E1112*	ENST00000394830	NM_018313.4	1112	Gaa/Taa	22/30	1	2	FACETS	0.476	0.401	0.56	0.476	0.401	0.56	SUBCLONAL	1	TRUE	1	0.37	2		651	522	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510779	157510800	+	frameshift_variant	Frame_Shift_Del	DEL	ACTCGGGATCCTTGCAAGGCCC	ACTCGGGATCCTTGCAAGGCCC	-	novel	NA	P-0032703-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	24	460	0	ENST00000346085.5:c.3556_3577del	p.Ser1186ArgfsTer18	p.S1186Rfs*18	ENST00000346085	NM_020732.3	1185	aACTCGGGATCCTTGCAAGGCCCa/aa	14/20	1	2	FACETS	0.316	0.247	0.395	0.316	0.247	0.395	SUBCLONAL	1	TRUE	1	0.37	2		460	411	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781991	NA	P-0032731-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	124	903	2	ENST00000269305.4:c.404G>T	p.Cys135Phe	p.C135F	ENST00000269305	NM_001126112.2	135	tGc/tTc	5/11	0.282736059599038	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.282736059599038	1		905	582	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143324090	143324090	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0032731-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	46	158	0	ENST00000262992.4:c.372+1del		p.X124_splice	ENST00000262992	NM_001101669.1	124			0.17408579001637	2	FACETS	1	0.908	1	0.552	0.467	0.644	CLONAL	1	TRUE	0	0.282736059599038	2		158	295	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248662	10248662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0032731-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	23	528	0	ENST00000340748.4:c.4091C>A	p.Thr1364Asn	p.T1364N	ENST00000340748		1364	aCc/aAc	35/40	0.282736059599038	1	FACETS	0.416	0.324	0.522	0.416	0.324	0.522	SUBCLONAL	1	TRUE	0	0.282736059599038	1		528	336	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465448	99465448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773205989	NA	P-0032997-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	67	466	0	ENST00000268035.6:c.2273C>T	p.Thr758Met	p.T758M	ENST00000268035	NM_000875.3	758	aCg/aTg	11/21	1	2	FACETS	0.527	0.457	0.603	0.527	0.457	0.603	SUBCLONAL	1	TRUE	1	0.336493246311561	2		466	756	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748075	72748075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749574790	NA	P-0032997-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	45	546	0	ENST00000357731.5:c.103G>A	p.Gly35Arg	p.G35R	ENST00000357731	NM_173808.2	35	Gga/Aga	1/7	0.189300391697265	2	FACETS	0.317	0.265	0.375	0.159	0.132	0.188	INDETERMINATE	1	TRUE	0	0.336493246311561	2		546	843	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332795	153332795	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1054734078	NA	P-0032997-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	150	496	0	ENST00000281708.4:c.161C>T	p.Ala54Val	p.A54V	ENST00000281708	NM_033632.3	54	gCa/gTa	2/12	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.336493246311561	2		496	812	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0033203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	48	377	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.26	2		377	324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0033203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	168	582	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.301608206337519	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.26	1		582	934	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0033203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	76	600	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	1	2	FACETS	0.664	0.581	0.754	0.664	0.581	0.754	SUBCLONAL	1	TRUE	1	0.26	2		600	880	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743864	41743864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753706427	NA	P-0033203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	77	668	0	ENST00000301178.4:c.799G>A	p.Asp267Asn	p.D267N	ENST00000301178	NM_021913.4	267	Gat/Aat	7/20	1	2	FACETS	0.572	0.501	0.65	0.572	0.501	0.65	SUBCLONAL	1	TRUE	1	0.26	2		668	1035	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518366	8518366	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754478667	NA	P-0033203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	28	307	0	ENST00000356435.5:c.1025C>T	p.Thr342Met	p.T342M	ENST00000356435		342	aCg/aTg	10/35	1	2	FACETS	0.403	0.321	0.496	0.403	0.321	0.496	SUBCLONAL	1	TRUE	1	0.26	2		307	535	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557750	187557750	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749093377	NA	P-0033203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	66	340	0	ENST00000441802.2:c.3961G>A	p.Asp1321Asn	p.D1321N	ENST00000441802	NM_005245.3	1321	Gat/Aat	5/27	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.26	2		340	447	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666366	206666366	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1164611253	NA	P-0033203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	74	552	0	ENST00000367120.3:c.1846G>A	p.Glu616Lys	p.E616K	ENST00000367120	NM_014002.3	616	Gag/Aag	19/22	1	2	FACETS	0.509	0.444	0.579	0.509	0.444	0.579	SUBCLONAL	1	TRUE	1	0.26	2		552	1119	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39251196	39251196	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	38	695	0	ENST00000402219.2:c.1157G>T	p.Gly386Val	p.G386V	ENST00000402219	NM_005633.3	386	gGt/gTt	9/23	0.301608206337519	1	FACETS	0.501	0.413	0.598	0.501	0.413	0.598	SUBCLONAL	1	TRUE	0	0.26	1		695	508	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0033211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	124	252	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.522446558769718	2		252	425	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0033211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	110	254	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.522446558769718	2		254	353	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0033211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	59	215	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	0.933	0.812	1	0.933	0.812	1	CLONAL	1	TRUE	1	0.522446558769718	2		215	242	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519934	NA	P-0033211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	111	387	0	ENST00000263967.3:c.333G>C	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaC	2/21	1	2	FACETS	0.97	0.878	1	0.97	0.878	1	CLONAL	1	TRUE	1	0.522446558769718	2		387	438	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs397517201	NA	P-0033211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	99	578	0	ENST00000263967.3:c.1637A>T	p.Gln546Leu	p.Q546L	ENST00000263967	NM_006218.2	546	cAg/cTg	10/21	1	2	FACETS	0.638	0.571	0.709	0.638	0.571	0.709	SUBCLONAL	1	TRUE	1	0.522446558769718	2		578	594	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106043	27106044	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0033211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	122	405	0	ENST00000324856.7:c.5655dup	p.Glu1886ArgfsTer15	p.E1886Rfs*15	ENST00000324856	NM_006015.4	1885	gca/gcAa	20/20	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.522446558769718	2		405	428	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653852	89653854	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0033211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	104	380	0	ENST00000371953.3:c.155_157del	p.Asp52del	p.D52del	ENST00000371953	NM_000314.4	50	atTGAt/att	2/9	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.522446558769718	2		380	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579369	7579369	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555526581	NA	P-0033218-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	343	978	0	ENST00000269305.4:c.318C>G	p.Ser106Arg	p.S106R	ENST00000269305	NM_001126112.2	106	agC/agG	4/11	0.669186573162293	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.669186573162293	1		978	668	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223227	41223227	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033218-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	448	554	0	ENST00000357654.3:c.4704del	p.Ser1569AlafsTer32	p.S1569Afs*32	ENST00000357654	NM_007294.3	1568	atC/at	15/23	0.669186573162293	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.669186573162293	2		554	643	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860326	151860326	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs902827242	NA	P-0033218-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	166	503	0	ENST00000262189.6:c.10336A>T	p.Thr3446Ser	p.T3446S	ENST00000262189	NM_170606.2	3446	Aca/Tca	43/59	0.669186573162293	3	FACETS	0.923	0.85	0.999	0.462	0.425	0.5	CLONAL	1	TRUE	1	0.669186573162293	3		503	717	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0033545-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	195	351	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.270427870057087	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	1	0.25749472120781	4		351	562	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118871	61118871	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372213094	NA	P-0033545-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	91	292	0	ENST00000295025.8:c.64C>T	p.Arg22Cys	p.R22C	ENST00000295025	NM_002908.2	22	Cgt/Tgt	2/11	1	2	FACETS	0.854	0.763	0.95	1	0.984	1	CLONAL	2	TRUE	1	0.25749472120781	2		292	414	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981167	201981167	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033545-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	151	995	0	ENST00000359651.3:c.246del	p.Asn83ThrfsTer72	p.N83Tfs*72	ENST00000359651		82	aaG/aa	2/8	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.25749472120781	2		995	789	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828074	243828074	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0033545-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	75	289	1	ENST00000263826.5:c.284G>T	p.Arg95Met	p.R95M	ENST00000263826	NM_005465.4	95	aGg/aTg	3/13	1	2	FACETS	0.769	0.677	0.865	1	0.977	1	SUBCLONAL	2	TRUE	1	0.25749472120781	2		290	379	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604788	48604790	+	frameshift_variant	Frame_Shift_Del	DEL	ACG	ACG	T	novel	NA	P-0033545-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	89	453	0	ENST00000342988.3:c.1610_1612delinsT	p.Asp537ValfsTer39	p.D537Vfs*39	ENST00000342988	NM_005359.5	537	gACGaa/gTaa	12/12	0.25749472120781	1	FACETS	0.997	0.894	1	1	0.986	1	CLONAL	2	TRUE	0	0.25749472120781	1		453	302	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	90	287	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.74101783143495	1	FACETS	0.453	0.406	0.502	0.453	0.406	0.502	SUBCLONAL	1	TRUE	0	0.767946742040104	1		287	319	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	244	379	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	0.727633125063859	2	FACETS	0.943	0.904	0.98	0.943	0.904	0.98	CLONAL	2	TRUE	0	0.767946742040104	2		379	337	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921444	39921444	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199538037	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	280	567	0	ENST00000378444.4:c.4376A>G	p.Asn1459Ser	p.N1459S	ENST00000378444	NM_001123385.1	1459	aAt/aGt	10/15	1	2	FACETS	0.985	0.931	1	0.985	0.931	1	CLONAL	1	TRUE	1	0.767946742040104	2		567	740	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	84	509	1	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	1	2	FACETS	0.337	0.297	0.379	0.337	0.297	0.379	SUBCLONAL	1	TRUE	1	0.767946742040104	2		510	650	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	10	399	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.072	0.048	0.102	0.072	0.048	0.102	SUBCLONAL	1	TRUE	1	0.767946742040104	2		399	362	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	55	680	1	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	1	2	FACETS	0.143	0.122	0.167	0.143	0.122	0.167	SUBCLONAL	1	TRUE	1	0.767946742040104	2		681	1000	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466019	69466019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	342	785	0	ENST00000227507.2:c.857C>T	p.Thr286Ile	p.T286I	ENST00000227507	NM_053056.2	286	aCa/aTa	5/5	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.767946742040104	2		785	837	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553478	29553478	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587781807	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	347	646	5	ENST00000356175.3:c.2033del	p.Pro678ArgfsTer10	p.P678Rfs*10	ENST00000356175	NM_000267.3	676	aCc/ac	18/57	1	2	FACETS	0.936	0.889	0.985	0.936	0.889	0.985	CLONAL	1	TRUE	1	0.767946742040104	2		651	965	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086076	16086076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760647298	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	228	519	0	ENST00000281043.3:c.1252G>A	p.Ala418Thr	p.A418T	ENST00000281043	NM_005378.4	418	Gcc/Acc	3/3	1	2	FACETS	0.921	0.863	0.979	0.921	0.863	0.979	CLONAL	1	TRUE	1	0.767946742040104	2		519	645	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	107	433	5	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.847	0.769	0.928	0.847	0.769	0.928	CLONAL	1	TRUE	1	0.767946742040104	2		438	329	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916728	178916728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	78	369	0	ENST00000263967.3:c.115G>A	p.Glu39Lys	p.E39K	ENST00000263967	NM_006218.2	39	Gag/Aag	2/21	1	2	FACETS	0.972	0.87	1	0.972	0.87	1	CLONAL	1	TRUE	1	0.767946742040104	2		369	209	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991757	72991758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760959844	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	248	513	1	ENST00000268489.5:c.2287dup	p.Glu763GlyfsTer26	p.E763Gfs*26	ENST00000268489	NM_006885.3	763	gag/gGag	2/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.767946742040104	2		514	614	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498235	498235	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	83	295	0	ENST00000399788.2:c.23del	p.Gly8AlafsTer58	p.G8Afs*58	ENST00000399788	NM_001042603.1	8	gGc/gc	1/28	0.128206033987882	4	FACETS	0.845	0.759	0.934	0.845	0.759	0.934	INDETERMINATE	2	TRUE	2	0.767946742040104	4		295	226	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087437	27087437	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	331	712	0	ENST00000324856.7:c.2011G>T	p.Gly671Ter	p.G671*	ENST00000324856	NM_006015.4	671	Gga/Tga	5/20	1	2	FACETS	0.983	0.933	1	0.983	0.933	1	CLONAL	1	TRUE	1	0.767946742040104	2		712	877	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70005612	70005614	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs1553704814	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	95	419	0	ENST00000394351.3:c.649_651del	p.Arg217del	p.R217del	ENST00000394351	NM_000248.3	214	cGAAga/cga	7/9	1	2	FACETS	0.836	0.754	0.921	0.836	0.754	0.921	CLONAL	1	TRUE	1	0.767946742040104	2		419	296	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426093	47426094	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1431646407	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	276	813	0	ENST00000377045.4:c.619dup	p.Leu207ProfsTer36	p.L207Pfs*36	ENST00000377045	NM_001654.4	205	gcc/gCcc	7/16	1	2	FACETS	0.669	0.628	0.711	0.669	0.628	0.711	SUBCLONAL	1	TRUE	1	0.767946742040104	2		813	1075	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581272	48581273	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	34	506	0	ENST00000342988.3:c.579_580del	p.Glu193AspfsTer12	p.E193Dfs*12	ENST00000342988	NM_005359.5	192	acAGag/acag	5/12	1	2	FACETS	0.137	0.111	0.166	0.137	0.111	0.166	SUBCLONAL	1	TRUE	1	0.767946742040104	2		506	648	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738726	145738726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372741479	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	398	826	2	ENST00000428558.2:c.2338C>T	p.Arg780Trp	p.R780W	ENST00000428558	NM_004260.3	780	Cgg/Tgg	15/22	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.767946742040104	2		828	1013	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224532	36224532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759167832	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	368	1102	0	ENST00000222270.7:c.6994C>T	p.Arg2332Cys	p.R2332C	ENST00000222270	NM_014727.1	2332	Cgt/Tgt	29/37	1	2	FACETS	0.9	0.855	0.945	0.9	0.855	0.945	CLONAL	1	TRUE	1	0.767946742040104	2		1102	1065	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28598212	28598212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769648213	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	87	734	2	ENST00000253063.3:c.184G>A	p.Glu62Lys	p.E62K	ENST00000253063	NM_031459.4	62	Gag/Aag	3/10	1	2	FACETS	0.228	0.201	0.257	0.228	0.201	0.257	SUBCLONAL	1	TRUE	1	0.767946742040104	2		736	992	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94964024	94964024	+	start_lost	Translation_Start_Site	SNP	T	T	C	novel	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	78	215	0	ENST00000536441.1:c.1A>G	p.Met1?	p.M1?	ENST00000536441	NM_144665.3	1	Atg/Gtg	1/10	1	2	FACETS	0.876	0.782	0.973	0.876	0.782	0.973	CLONAL	1	TRUE	1	0.767946742040104	2		215	232	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536739	120536739	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	202	621	0	ENST00000229340.5:c.353T>C	p.Val118Ala	p.V118A	ENST00000229340	NM_006861.6	118	gTg/gCg	5/6	0.128206033987882	4	FACETS	1	0.99	1	0.696	0.648	0.745	INDETERMINATE	1	TRUE	2	0.767946742040104	4		621	668	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727528	66727528	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	179	514	0	ENST00000307102.5:c.244G>A	p.Val82Met	p.V82M	ENST00000307102	NM_002755.3	82	Gtg/Atg	2/11	1	2	FACETS	0.759	0.703	0.817	0.759	0.703	0.817	SUBCLONAL	1	TRUE	1	0.767946742040104	2		514	614	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779365	3779365	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	66	743	1	ENST00000262367.5:c.5683C>T	p.Gln1895Ter	p.Q1895*	ENST00000262367	NM_004380.2	1895	Cag/Tag	31/31	1	2	FACETS	0.181	0.157	0.208	0.181	0.157	0.208	SUBCLONAL	1	TRUE	1	0.767946742040104	2		744	948	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585465	29585465	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	156	431	1	ENST00000356175.3:c.4217del	p.Leu1406Ter	p.L1406*	ENST00000356175	NM_000267.3	1405	aTt/at	31/57	1	2	FACETS	0.977	0.904	1	0.977	0.904	1	CLONAL	1	TRUE	1	0.767946742040104	2		432	416	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884217	37884218	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768092215	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	50	509	0	ENST00000269571.5:c.3694dup	p.Ala1232GlyfsTer45	p.A1232Gfs*45	ENST00000269571		1230	cgg/cGgg	27/27	1	2	FACETS	0.223	0.188	0.26	0.223	0.188	0.26	SUBCLONAL	1	TRUE	1	0.767946742040104	2		509	585	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244326	5244326	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	315	812	2	ENST00000357368.4:c.1156C>T	p.Arg386Cys	p.R386C	ENST00000357368	NM_002850.3	386	Cgt/Tgt	11/38	1	2	FACETS	0.786	0.742	0.83	0.786	0.742	0.83	SUBCLONAL	1	TRUE	1	0.767946742040104	2		814	1044	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278101	18278101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1056224197	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	74	678	0	ENST00000222254.8:c.1721G>A	p.Arg574Gln	p.R574Q	ENST00000222254	NM_005027.3	574	cGa/cAa	13/16	1	2	FACETS	0.179	0.156	0.205	0.179	0.156	0.205	SUBCLONAL	1	TRUE	1	0.767946742040104	2		678	1074	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416167	29416167	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748822593	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	256	563	0	ENST00000389048.3:c.4786G>A	p.Ala1596Thr	p.A1596T	ENST00000389048	NM_004304.4	1596	Gct/Act	29/29	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.767946742040104	2		563	646	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99154425	99154426	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	51	471	0	ENST00000074304.5:c.568_569del	p.Val190GlnfsTer10	p.V190Qfs*10	ENST00000074304	NM_001134224.1	189	acTGtc/actc	8/26	1	2	FACETS	0.188	0.159	0.22	0.188	0.159	0.22	SUBCLONAL	1	TRUE	1	0.767946742040104	2		471	707	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955212	1955212	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	241	542	0	ENST00000382891.5:c.2299T>C	p.Cys767Arg	p.C767R	ENST00000382891	NM_133335.3	767	Tgc/Cgc	12/22	1	2	FACETS	0.842	0.79	0.896	0.842	0.79	0.896	CLONAL	1	TRUE	1	0.767946742040104	2		542	745	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332000	81332000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543827901	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	81	315	0	ENST00000222390.5:c.2084G>A	p.Arg695His	p.R695H	ENST00000222390	NM_000601.4	695	cGt/cAt	18/18	1	2	FACETS	0.851	0.761	0.944	0.851	0.761	0.944	CLONAL	1	TRUE	1	0.767946742040104	2		315	248	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412532	80412532	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	29	329	0	ENST00000286548.4:c.509C>A	p.Pro170His	p.P170H	ENST00000286548	NM_002072.3	170	cCt/cAt	4/7	1	2	FACETS	0.159	0.127	0.196	0.159	0.127	0.196	SUBCLONAL	1	TRUE	1	0.767946742040104	2		329	474	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217323	123217323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0033583-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	97	629	0	ENST00000218089.9:c.2977C>T	p.Pro993Ser	p.P993S	ENST00000218089	NM_001042749.1	993	Cca/Tca	29/35	1	2	FACETS	0.523	0.468	0.581	0.523	0.468	0.581	SUBCLONAL	1	TRUE	1	0.767946742040104	2		629	483	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122854	2122854	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs45517220	NA	P-0033709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	59	395	0	ENST00000219476.3:c.2225C>G	p.Ser742Ter	p.S742*	ENST00000219476	NM_000548.3	742	tCa/tGa	21/42	1	2	FACETS	0.495	0.426	0.569	0.495	0.426	0.569	SUBCLONAL	1	TRUE	1	0.472421178722122	2		395	505	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344971	118344971	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	39	225	0	ENST00000534358.1:c.3097C>T	p.Gln1033Ter	p.Q1033*	ENST00000534358	NM_005933.3	1033	Cag/Tag	3/36	0.24003731156159	1	FACETS	0.404	0.336	0.48	0.404	0.336	0.48	INDETERMINATE	1	TRUE	0	0.472421178722122	1		225	312	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43766925	43766925	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	53	239	1	ENST00000382044.4:c.1126C>T	p.Arg376Ter	p.R376*	ENST00000382044	NM_001141980.1	376	Cga/Tga	10/28	0.315140192738847	1	FACETS	0.48	0.411	0.555	0.48	0.411	0.555	SUBCLONAL	1	TRUE	0	0.472421178722122	1		240	357	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347861	89347861	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0033709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	70	512	0	ENST00000301030.4:c.5089C>G	p.Gln1697Glu	p.Q1697E	ENST00000301030	NM_001256183.1	1697	Cag/Gag	9/13	0.24003731156159	1	FACETS	0.445	0.388	0.505	0.445	0.388	0.505	INDETERMINATE	1	TRUE	0	0.472421178722122	1		512	509	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138383915	138383915	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	97	460	0	ENST00000289153.2:c.2635G>C	p.Asp879His	p.D879H	ENST00000289153	NM_006219.2	879	Gat/Cat	18/22	1	2	FACETS	0.484	0.431	0.54	0.484	0.431	0.54	SUBCLONAL	1	TRUE	1	0.472421178722122	2		460	849	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902586	1902586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1401743505	NA	P-0033709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	119	533	0	ENST00000382891.5:c.205G>A	p.Asp69Asn	p.D69N	ENST00000382891	NM_133335.3	69	Gac/Aac	2/22	1	2	FACETS	0.627	0.565	0.691	0.627	0.565	0.691	SUBCLONAL	1	TRUE	1	0.472421178722122	2		533	804	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2972169	2972169	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0033709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	155	494	0	ENST00000396946.4:c.1570G>C	p.Ala524Pro	p.A524P	ENST00000396946	NM_032415.4	524	Gcc/Ccc	11/25	0.423103618766314	1	FACETS	0.691	0.634	0.751	0.691	0.634	0.751	SUBCLONAL	1	TRUE	0	0.472421178722122	1		494	725	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0033980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	28	401	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.400857580591102	NA		401	396	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881001	37881002	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGCTCCCC	rs397516981	NA	P-0034325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	194	786	0	ENST00000269571.5:c.2331_2339dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	gtg/gtGGGCTCCCCg	20/27	0.246931483406098	4	FACETS	0.911	0.843	0.982	0.911	0.843	0.982	CLONAL	2	TRUE	2	0.290049129041515	4		786	947	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118729	115118730	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	278	650	1	ENST00000257566.3:c.611dup	p.His205ProfsTer22	p.H205Pfs*22	ENST00000257566	NM_016569.3	204	ttc/ttTc	2/8	0.290049129041515	3	FACETS	0.946	0.893	1	0.946	0.893	1	CLONAL	3	TRUE	0	0.290049129041515	3		651	773	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681015	117681015	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs774383914	NA	P-0034325-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	44	468	2	ENST00000368508.3:c.3605A>G	p.Asp1202Gly	p.D1202G	ENST00000368508	NM_002944.2	1202	gAc/gGc	23/43	0.213614965553564	2	FACETS	0.639	0.536	0.753	0.319	0.268	0.377	SUBCLONAL	1	TRUE	0	0.290049129041515	2		470	475	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	98	497	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.354050697077495	1	FACETS	0.391	0.35	0.434	0.391	0.35	0.434	INDETERMINATE	1	TRUE	0	0.668184673562899	1		497	500	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489543	40489543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	108	630	7	ENST00000264657.5:c.707C>T	p.Thr236Met	p.T236M	ENST00000264657	NM_139276.2	236	aCg/aTg	8/24	0.35213516250384	3	FACETS	0.583	0.523	0.646	0.194	0.174	0.216	INDETERMINATE	1	TRUE	0	0.668184673562899	3		637	740	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633113	3633113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	122	665	2	ENST00000294008.3:c.5138C>T	p.Ser1713Phe	p.S1713F	ENST00000294008	NM_032444.2	1713	tCc/tTc	14/15	0.35950930399988	3	FACETS	0.564	0.509	0.622	0.282	0.254	0.311	INDETERMINATE	1	TRUE	1	0.668184673562899	3		667	864	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828208	72828209	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0034333-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	108	719	0	ENST00000268489.5:c.8371_8372dup	p.Met2792ProfsTer10	p.M2792Pfs*10	ENST00000268489	NM_006885.3	2791	acc/acACc	9/10	0.35950930399988	3	FACETS	0.506	0.454	0.562	0.253	0.227	0.281	INDETERMINATE	1	TRUE	1	0.668184673562899	3		719	852	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034368-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	818	575	0	ENST00000397752.3:c.3028G>A	p.Asp1010Asn	p.D1010N	ENST00000397752	NM_000245.2	1010	Gat/Aat	14/21	0.40722056695895	7	FACETS	1	0.985	1			1	CLONAL	7	TRUE	NA	0.40722056695895	7		575	1147	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827732	72827732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241554729	NA	P-0034368-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	198	484	1	ENST00000268489.5:c.8849G>A	p.Arg2950His	p.R2950H	ENST00000268489	NM_006885.3	2950	cGc/cAc	9/10	0.40722056695895	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.40722056695895	2		485	470	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423407	116423407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913671	NA	P-0034368-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	137	263	0	ENST00000397752.3:c.3682G>A	p.Asp1228Asn	p.D1228N	ENST00000397752	NM_000245.2	1228	Gac/Aac	19/21	0.40722056695895	7	FACETS	1	0.959	1			1	CLONAL	2	TRUE	NA	0.40722056695895	7		263	624	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867291	45867291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199863965	NA	P-0034368-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	140	693	1	ENST00000391945.4:c.902C>T	p.Thr301Met	p.T301M	ENST00000391945	NM_000400.3	301	aCg/aTg	10/23	0.40722056695895	4	FACETS	1	0.935	1			1	CLONAL	1	TRUE	NA	0.40722056695895	4		694	936	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263331	115263331	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034368-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	99	502	2	ENST00000438362.2:c.2019G>A	p.Met673Ile	p.M673I	ENST00000438362	NM_001242891.1	673	atG/atA	17/20	1	2	FACETS	0.826	0.738	0.918	0.826	0.738	0.918	CLONAL	1	TRUE	1	0.40722056695895	2		504	589	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172404	7172404	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034368-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	90	491	0	ENST00000302850.5:c.1165G>A	p.Glu389Lys	p.E389K	ENST00000302850	NM_000208.2	389	Gaa/Aaa	5/22	1	2	FACETS	0.936	0.834	1	0.936	0.834	1	CLONAL	1	TRUE	1	0.40722056695895	2		491	472	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645900	215645900	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034368-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	220	490	0	ENST00000260947.4:c.698A>C	p.Glu233Ala	p.E233A	ENST00000260947	NM_000465.2	233	gAg/gCg	4/11	0.40722056695895	3	FACETS	0.956	0.894	1	0.956	0.894	1	CLONAL	2	TRUE	1	0.40722056695895	3		490	680	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161825	47161825	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034368-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	71	299	0	ENST00000409792.3:c.4301G>A	p.Gly1434Glu	p.G1434E	ENST00000409792	NM_014159.6	1434	gGa/gAa	3/21	1	2	FACETS	0.789	0.691	0.894	0.789	0.691	0.894	SUBCLONAL	1	TRUE	1	0.40722056695895	2		299	442	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240446	98240446	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs975634341	NA	P-0034368-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	93	381	0	ENST00000331920.6:c.1238A>G	p.Gln413Arg	p.Q413R	ENST00000331920	NM_000264.3	413	cAg/cGg	9/24	0.40722056695895	3	FACETS	0.921	0.82	1	0.46	0.41	0.514	CLONAL	1	TRUE	1	0.40722056695895	3		381	597	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878117	48878198	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCCGCCGCCGCCCCCTCCTGAGGAGGACCCAGAGCAGGACAGCGGCCCGGAGGACCTGCCTCTCGTCAGGTGAGCGAGCAGA	GCCGCCGCCGCCCCCTCCTGAGGAGGACCCAGAGCAGGACAGCGGCCCGGAGGACCTGCCTCTCGTCAGGTGAGCGAGCAGA	-	novel	NA	P-0034368-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	16	119	0	ENST00000267163.4:c.76_137+20del		p.X26_splice	ENST00000267163	NM_000321.2	26		1/27	0.40722056695895	2	FACETS	0.689	0.515	0.892	0.345	0.257	0.446	SUBCLONAL	1	TRUE	0	0.40722056695895	2		119	114	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936768	78936768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs987417975	NA	P-0034876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	29	775	1	ENST00000306801.3:c.3850G>A	p.Gly1284Arg	p.G1284R	ENST00000306801	NM_020761.2	1284	Gga/Aga	33/34	1	2	FACETS	0.372	0.297	0.457	0.372	0.297	0.457	SUBCLONAL	1	TRUE	1	0.28	2		776	557	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512352	149512352	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	75	614	0	ENST00000261799.4:c.1088G>T	p.Gly363Val	p.G363V	ENST00000261799	NM_002609.3	363	gGc/gTc	7/23	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.28	2		614	513	SUCCESS
AR	367	MSKCC	GRCh37	X	66931258	66931258	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0034876-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	44	187	0	ENST00000374690.3:c.1900A>C	p.Lys634Gln	p.K634Q	ENST00000374690	NM_000044.3	634	Aaa/Caa	4/8	NA	2	FACETS	1	0.901	1			1	INDETERMINATE	2	TRUE	NA	0.28	2		187	147	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981098	201981098	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	111	598	0	ENST00000359651.3:c.177G>T	p.Trp59Cys	p.W59C	ENST00000359651		59	tgG/tgT	2/8	0.147443248125079	4	FACETS	1	0.976	1	0.429	0.385	0.474	INDETERMINATE	1	TRUE	1	0.328665749517195	4		598	698	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589171	67589171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	91	239	0	ENST00000274335.5:c.1159G>A	p.Asp387Asn	p.D387N	ENST00000274335		387	Gat/Aat	9/15	0.328665749517195	3	FACETS	0.769	0.687	0.856	0.769	0.687	0.856	SUBCLONAL	2	TRUE	1	0.328665749517195	3		239	419	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	94	585	1	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.933	0.831	1	0.933	0.831	1	CLONAL	1	TRUE	1	0.32	2		586	630	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	77	496	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	0.906	0.797	1	0.906	0.797	1	CLONAL	1	TRUE	1	0.32	2		496	531	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	127	660	1	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.32	2		661	768	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628248	187628248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200097846	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	123	688	0	ENST00000441802.2:c.2734G>A	p.Val912Ile	p.V912I	ENST00000441802	NM_005245.3	912	Gtt/Att	2/27	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.32	2		688	713	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537053	41537053	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1280109939	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	32	235	0	ENST00000263253.7:c.1880C>T	p.Ala627Val	p.A627V	ENST00000263253	NM_001429.3	627	gCg/gTg	10/31	1	2	FACETS	0.855	0.698	1	0.855	0.698	1	CLONAL	1	TRUE	1	0.32	2		235	234	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	123	623	0	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.32	2		623	745	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	105	540	2	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.32	2		542	639	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	101	704	5	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	1	2	FACETS	0.959	0.859	1	0.959	0.859	1	CLONAL	1	TRUE	1	0.32	2		709	658	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121018	29121018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853009	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	98	533	2	ENST00000328354.6:c.539G>A	p.Arg180His	p.R180H	ENST00000328354	NM_007194.3	180	cGc/cAc	4/15	1	2	FACETS	0.875	0.781	0.975	0.875	0.781	0.975	CLONAL	1	TRUE	1	0.32	2		535	700	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54963246	54963246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745894289	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	45	273	2	ENST00000312783.6:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000312783	NM_198436.1	3	cGa/cAa	3/10	1	2	FACETS	0.659	0.554	0.774	0.659	0.554	0.774	SUBCLONAL	1	TRUE	1	0.32	2		275	427	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630605	187630605	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	115	614	0	ENST00000441802.2:c.377del	p.Asn126IlefsTer20	p.N126Ifs*20	ENST00000441802	NM_005245.3	126	aAt/at	2/27	1	2	FACETS	0.987	0.89	1	0.987	0.89	1	CLONAL	1	TRUE	1	0.32	2		614	728	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271747	15271747	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs773656789	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	116	773	1	ENST00000263388.2:c.6692del	p.Pro2231GlnfsTer15	p.P2231Qfs*15	ENST00000263388	NM_000435.2	2231	cCa/ca	33/33	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.32	2		774	720	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557272	187557273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1279779959	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	104	565	0	ENST00000441802.2:c.4089dup	p.Thr1364TyrfsTer8	p.T1364Yfs*8	ENST00000441802	NM_005245.3	1363	-/T	6/27	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.32	2		565	590	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119661	108119661	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1275066585	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	24	164	0	ENST00000278616.4:c.1071del	p.Phe357LeufsTer33	p.F357Lfs*33	ENST00000278616	NM_000051.3	356	gTt/gt	9/63	1	2	FACETS	0.781	0.617	0.969	0.781	0.617	0.969	CLONAL	1	TRUE	1	0.32	2		164	192	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156935	106156936	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs763386429	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	50	427	0	ENST00000380013.4:c.1842dup	p.Leu615AlafsTer23	p.L615Afs*23	ENST00000380013	NM_001127208.2	612	-/G	3/11	1	2	FACETS	0.785	0.668	0.913	0.785	0.668	0.913	CLONAL	1	TRUE	1	0.32	2		427	398	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347553	89347553	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	60	571	0	ENST00000301030.4:c.5397del	p.Glu1800ArgfsTer163	p.E1800Rfs*163	ENST00000301030	NM_001256183.1	1799	ccC/cc	9/13	1	2	FACETS	0.628	0.541	0.723	0.628	0.541	0.723	SUBCLONAL	1	TRUE	1	0.32	2		571	597	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214728	36214728	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	71	446	2	ENST00000222270.7:c.3159del	p.Arg1055GlyfsTer127	p.R1055Gfs*127	ENST00000222270	NM_014727.1	1052	Ggg/gg	8/37	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.32	2		448	396	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937723	44937723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	88	455	2	ENST00000377967.4:c.2911C>T	p.Arg971Cys	p.R971C	ENST00000377967	NM_021140.2	971	Cgt/Tgt	19/29	1	2	FACETS	0.891	0.791	0.999	0.891	0.791	0.999	CLONAL	1	TRUE	1	0.32	2		457	617	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055982	180055982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147644625	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	105	635	1	ENST00000261937.6:c.1003G>A	p.Val335Ile	p.V335I	ENST00000261937	NM_182925.4	335	Gtc/Atc	8/30	1	2	FACETS	0.964	0.864	1	0.964	0.864	1	CLONAL	1	TRUE	1	0.32	2		636	681	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325426	1325426	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	40	587	0	ENST00000400841.2:c.249del	p.Cys84AlafsTer3	p.C84Afs*3	ENST00000400841		83	ggG/gg	3/6	1	2	FACETS	0.379	0.314	0.452	0.379	0.314	0.452	SUBCLONAL	1	TRUE	1	0.32	2		587	659	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210725	36210725	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	121	684	0	ENST00000222270.7:c.481del	p.Leu161PhefsTer6	p.L161Ffs*6	ENST00000222270	NM_014727.1	159	aCc/ac	3/37	1	2	FACETS	0.995	0.9	1	0.995	0.9	1	CLONAL	1	TRUE	1	0.32	2		684	760	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27180244	27180244	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1564080006	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	75	606	0	ENST00000380036.4:c.908A>G	p.His303Arg	p.H303R	ENST00000380036	NM_000459.3	303	cAc/cGc	7/23	1	2	FACETS	0.744	0.652	0.843	0.744	0.652	0.843	SUBCLONAL	1	TRUE	1	0.32	2		606	630	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730099	41730099	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	67	484	1	ENST00000242208.4:c.430G>T	p.Gly144Cys	p.G144C	ENST00000242208	NM_002192.2	144	Ggc/Tgc	3/3	1	2	FACETS	0.735	0.639	0.838	0.735	0.639	0.838	SUBCLONAL	1	TRUE	1	0.32	2		485	570	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106805	27106805	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1302295523	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	106	614	0	ENST00000324856.7:c.6416C>A	p.Pro2139His	p.P2139H	ENST00000324856	NM_006015.4	2139	cCc/cAc	20/20	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.32	2		614	641	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736589	85736589	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	49	269	0	ENST00000370580.1:c.58G>A	p.Ala20Thr	p.A20T	ENST00000370580	NM_003921.4	20	Gcc/Acc	2/3	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.32	2		269	291	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18576885	18576885	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	84	565	0	ENST00000266497.5:c.2293A>G	p.Lys765Glu	p.K765E	ENST00000266497		765	Aag/Gag	16/31	1	2	FACETS	0.885	0.783	0.995	0.885	0.783	0.995	CLONAL	1	TRUE	1	0.32	2		565	593	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134293	2134293	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs878854103	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	104	725	0	ENST00000219476.3:c.4070T>C	p.Ile1357Thr	p.I1357T	ENST00000219476	NM_000548.3	1357	aTc/aCc	34/42	1	2	FACETS	0.983	0.882	1	0.983	0.882	1	CLONAL	1	TRUE	1	0.32	2		725	661	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50816315	50816315	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	51	390	0	ENST00000398568.2:c.1755T>G	p.Ile585Met	p.I585M	ENST00000398568	NM_001042412.1	585	atT/atG	10/18	1	2	FACETS	0.665	0.566	0.774	0.665	0.566	0.774	SUBCLONAL	1	TRUE	1	0.32	2		390	479	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78811723	78811723	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	38	495	0	ENST00000306801.3:c.1138C>A	p.Gln380Lys	p.Q380K	ENST00000306801	NM_020761.2	380	Caa/Aaa	10/34	1	2	FACETS	0.347	0.286	0.415	0.347	0.286	0.415	SUBCLONAL	1	TRUE	1	0.32	2		495	685	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265084	10265084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	117	671	0	ENST00000340748.4:c.1856C>T	p.Thr619Ile	p.T619I	ENST00000340748		619	aCc/aTc	21/40	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.32	2		671	721	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209106798	209106798	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	122	564	0	ENST00000345146.2:c.770A>G	p.Gln257Arg	p.Q257R	ENST00000345146	NM_005896.2	257	cAa/cGa	7/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.32	2		564	720	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478757	57478757	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	92	398	0	ENST00000371085.3:c.348del	p.Val117TrpfsTer16	p.V117Wfs*16	ENST00000371085	NM_000516.4	115	Ccc/cc	5/13	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.32	2		398	487	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525902	41525903	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	80	380	0	ENST00000263253.7:c.1179_1180del	p.Ala394IlefsTer16	p.A394Ifs*16	ENST00000263253	NM_001429.3	393	TGt/t	5/31	1	2	FACETS	0.982	0.867	1	0.982	0.867	1	CLONAL	1	TRUE	1	0.32	2		380	509	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158113	106158113	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	56	346	0	ENST00000380013.4:c.3014A>G	p.Lys1005Arg	p.K1005R	ENST00000380013	NM_001127208.2	1005	aAg/aGg	3/11	1	2	FACETS	0.926	0.796	1	0.926	0.796	1	CLONAL	1	TRUE	1	0.32	2		346	378	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001022	150001022	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	40	370	0	ENST00000253339.5:c.2582A>G	p.Tyr861Cys	p.Y861C	ENST00000253339		861	tAc/tGc	4/7	1	2	FACETS	0.598	0.497	0.71	0.598	0.497	0.71	SUBCLONAL	1	TRUE	1	0.32	2		370	418	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415622	152415622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	97	553	0	ENST00000206249.3:c.1472C>T	p.Ala491Val	p.A491V	ENST00000206249	NM_000125.3	491	gCc/gTc	7/8	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.32	2		553	555	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207642	29207642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	54	262	0	ENST00000240100.2:c.154C>T	p.Pro52Ser	p.P52S	ENST00000240100	NM_001394.6	52	Ccg/Tcg	1/4	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.32	2		262	334	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139804390	139804390	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	41	574	0	ENST00000247668.2:c.547C>A	p.Pro183Thr	p.P183T	ENST00000247668	NM_021138.3	183	Ccc/Acc	6/11	1	2	FACETS	0.324	0.269	0.386	0.324	0.269	0.386	SUBCLONAL	1	TRUE	1	0.32	2		574	791	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412002	63412002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	68	680	0	ENST00000330258.3:c.1165G>A	p.Glu389Lys	p.E389K	ENST00000330258	NM_152424.3	389	Gaa/Aaa	2/2	1	2	FACETS	0.806	0.703	0.918	0.806	0.703	0.918	CLONAL	1	TRUE	1	0.32	2		680	527	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349934	70349934	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0034967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	62	681	0	ENST00000374080.3:c.3917A>T	p.Asp1306Val	p.D1306V	ENST00000374080		1306	gAc/gTc	28/45	1	2	FACETS	0.496	0.427	0.57	0.496	0.427	0.57	SUBCLONAL	1	TRUE	1	0.32	2		681	782	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	368	381	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.853998972883967	2	FACETS	0.966	0.941	0.989	0.966	0.941	0.989	CLONAL	2	TRUE	0	0.869906739796121	2		381	438	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587781845	NA	P-0035301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	571	699	0	ENST00000269305.4:c.511G>T	p.Glu171Ter	p.E171*	ENST00000269305	NM_001126112.2	171	Gag/Tag	5/11	0.847312259325034	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.869906739796121	2		699	652	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67670713	67670713	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	295	458	0	ENST00000264010.4:c.1958G>T	p.Gly653Val	p.G653V	ENST00000264010	NM_006565.3	653	gGa/gTa	11/12	0.502214358142037	3	FACETS	0.932	0.889	0.975	0.932	0.889	0.975	INDETERMINATE	2	TRUE	1	0.869906739796121	3		458	522	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456396	32456396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	261	611	1	ENST00000332351.3:c.496G>A	p.Gly166Ser	p.G166S	ENST00000332351	NM_024426.4	166	Ggc/Agc	1/10	0.765028380713307	3	FACETS	0.961	0.902	1	0.481	0.451	0.511	CLONAL	1	TRUE	1	0.869906739796121	3		612	896	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352388	70352388	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	199	338	0	ENST00000374080.3:c.4415G>A	p.Ser1472Asn	p.S1472N	ENST00000374080		1472	aGc/aAc	31/45	0.363044153762578	5	FACETS	0.935	0.872	0.999			1	INDETERMINATE	2	TRUE	NA	0.869906739796121	5		338	564	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366683	40366683	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	158	314	0	ENST00000397332.2:c.514C>A	p.Pro172Thr	p.P172T	ENST00000397332	NM_001033082.2	172	Ccc/Acc	2/3	0.869911658862109	3	FACETS	1	0.93	1	0.504	0.465	0.545	CLONAL	1	TRUE	1	0.869906739796121	3		314	517	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248692	59248708	+	frameshift_variant	Frame_Shift_Del	DEL	CGAGGCGTTGAGGGCAT	CGAGGCGTTGAGGGCAT	-	novel	NA	P-0035301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	89	821	0	ENST00000371222.2:c.35_51del	p.Asp12ValfsTer13	p.D12Vfs*13	ENST00000371222	NM_002228.3	12	gATGCCCTCAACGCCTCG/g	1/1	0.171370000257452	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.869906739796121	0		821	757	SUCCESS
H3C13	653604	MSKCC	GRCh37	1	149784839	149784839	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	89	208	0	ENST00000331491.1:c.398G>T	p.Gly133Val	p.G133V	ENST00000331491	NM_001123375.2	133	gGg/gTg	1/1	0.765028380713307	3	FACETS	1	0.934	1	0.526	0.473	0.582	CLONAL	1	TRUE	1	0.869906739796121	3		208	279	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727100	243727100	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	364	502	0	ENST00000263826.5:c.870T>A	p.Phe290Leu	p.F290L	ENST00000263826	NM_005465.4	290	ttT/ttA	9/13	0.765028380713307	3	FACETS	0.9	0.862	0.938	0.9	0.862	0.938	CLONAL	2	TRUE	1	0.869906739796121	3		502	667	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047238	77047238	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	417	549	0	ENST00000356341.3:c.1306G>T	p.Val436Leu	p.V436L	ENST00000356341	NM_002576.4	436	Gtg/Ttg	13/15	0.719036186292726	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.869906739796121	4		549	877	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917692	94917692	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0035301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	208	512	0	ENST00000536441.1:c.829G>T	p.Glu277Ter	p.E277*	ENST00000536441	NM_144665.3	277	Gaa/Taa	6/10	0.49907892148902	5	FACETS	1	0.989	1	0.448	0.416	0.481	INDETERMINATE	1	TRUE	2	0.869906739796121	5		512	820	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343376	118343376	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	198	314	0	ENST00000534358.1:c.1502A>T	p.Glu501Val	p.E501V	ENST00000534358	NM_005933.3	501	gAg/gTg	3/36	0.49907892148902	5	FACETS	1	0.981	1	0.746	0.698	0.794	INDETERMINATE	2	TRUE	2	0.869906739796121	5		314	469	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645388	67645388	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	149	283	0	ENST00000264010.4:c.653G>C	p.Gly218Ala	p.G218A	ENST00000264010	NM_006565.3	218	gGc/gCc	3/12	0.502214358142037	3	FACETS	1	0.984	1	0.625	0.578	0.674	INDETERMINATE	1	TRUE	1	0.869906739796121	3		283	393	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351528	89351528	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	493	730	0	ENST00000301030.4:c.1422C>G	p.Asp474Glu	p.D474E	ENST00000301030	NM_001256183.1	474	gaC/gaG	9/13	0.502214358142037	3	FACETS	0.837	0.805	0.868	0.837	0.805	0.868	INDETERMINATE	2	TRUE	1	0.869906739796121	3		730	972	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600006	10600006	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	565	679	0	ENST00000171111.5:c.1570G>T	p.Gly524Cys	p.G524C	ENST00000171111	NM_203500.1	524	Ggc/Tgc	5/6	0.853998972883967	2	FACETS	0.99	0.971	1	0.99	0.971	1	CLONAL	2	TRUE	0	0.869906739796121	2		679	656	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919628	96919628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	205	531	0	ENST00000258439.3:c.635C>T	p.Ser212Leu	p.S212L	ENST00000258439	NM_001193304.2	212	tCa/tTa	4/4	0.719036186292726	4	FACETS	0.983	0.912	1	0.491	0.456	0.528	CLONAL	1	TRUE	2	0.869906739796121	4		531	897	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736160	204736160	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	340	436	1	ENST00000302823.3:c.517G>C	p.Gly173Arg	p.G173R	ENST00000302823	NM_005214.4	173	Ggg/Cgg	3/4	0.719036186292726	4	FACETS	0.938	0.893	0.984	0.938	0.893	0.984	CLONAL	2	TRUE	2	0.869906739796121	4		437	779	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645508	215645508	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	59	610	1	ENST00000260947.4:c.1090T>C	p.Ser364Pro	p.S364P	ENST00000260947	NM_000465.2	364	Tca/Cca	4/11	0.719036186292726	4	FACETS	0.222	0.19	0.257	0.111	0.095	0.129	SUBCLONAL	1	TRUE	2	0.869906739796121	4		611	1143	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267767	46267767	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	244	512	0	ENST00000371998.3:c.2528A>G	p.Gln843Arg	p.Q843R	ENST00000371998		843	cAg/cGg	14/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.869906739796121	2		512	550	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643711	52643712	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0035301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	502	591	0	ENST00000394830.3:c.2184dup	p.Val729CysfsTer5	p.V729Cfs*5	ENST00000394830	NM_018313.4	728	-/T	17/30	0.858197714467767	2	FACETS	0.922	0.899	0.943	0.922	0.899	0.943	CLONAL	2	TRUE	0	0.869906739796121	2		591	626	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31451736	31451736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	241	248	0	ENST00000344624.3:c.2586G>A	p.Met862Ile	p.M862I	ENST00000344624		862	atG/atA	18/33	0.768731944592572	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.869906739796121	4		248	499	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38949832	38949832	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	218	315	0	ENST00000357387.3:c.4118C>G	p.Ser1373Cys	p.S1373C	ENST00000357387	NM_152756.3	1373	tCc/tGc	31/38	0.768731944592572	4	FACETS	0.861	0.808	0.915	0.861	0.808	0.915	CLONAL	2	TRUE	2	0.869906739796121	4		315	544	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527614	157527614	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	81	443	0	ENST00000346085.5:c.5339A>T	p.Gln1780Leu	p.Q1780L	ENST00000346085	NM_020732.3	1780	cAa/cTa	20/20	0.84442581319796	4	FACETS	0.456	0.401	0.515	0.114	0.1	0.129	SUBCLONAL	1	TRUE	0	0.869906739796121	4		443	763	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332040	81332040	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	169	237	1	ENST00000222390.5:c.2044C>T	p.His682Tyr	p.H682Y	ENST00000222390	NM_000601.4	682	Cat/Tat	18/18	0.719036186292726	4	FACETS	0.897	0.835	0.96	0.897	0.835	0.96	CLONAL	2	TRUE	2	0.869906739796121	4		238	405	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129907	69129907	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0035301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	166	282	0	ENST00000288368.4:c.4661del	p.Leu1554ArgfsTer12	p.L1554Rfs*12	ENST00000288368	NM_024870.2	1554	cTg/cg	38/40	0.362026824807072	2	FACETS	1	0.991	1	0.679	0.639	0.719	INDETERMINATE	1	TRUE	0	0.869906739796121	2		282	281	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967554	90967554	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	104	351	0	ENST00000265433.3:c.1354A>G	p.Thr452Ala	p.T452A	ENST00000265433	NM_002485.4	452	Acc/Gcc	10/16	0.488368678147876	6	FACETS	0.81	0.725	0.9	0.202	0.181	0.225	INDETERMINATE	1	TRUE	2	0.869906739796121	6		351	809	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410118	63410118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1357604176	NA	P-0035301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	534	655	0	ENST00000330258.3:c.3049G>T	p.Gly1017Trp	p.G1017W	ENST00000330258	NM_152424.3	1017	Ggg/Tgg	2/2	0.363044153762578	5	FACETS	0.877	0.845	0.91			1	INDETERMINATE	3	TRUE	NA	0.869906739796121	5		655	1075	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577114	7577114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863224451	NA	P-0035559-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	103	901	0	ENST00000269305.4:c.824G>A	p.Cys275Tyr	p.C275Y	ENST00000269305	NM_001126112.2	275	tGt/tAt	8/11	0.318269589161845	2	FACETS	0.859	0.777	0.944	0.859	0.777	0.944	CLONAL	2	TRUE	0	0.34857665469574	2		901	344	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	173	372	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.905	0.838	0.974	0.905	0.838	0.974	CLONAL	1	TRUE	1	0.686491134795966	2		372	557	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0035590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	261	538	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.91	0.855	0.966	0.91	0.855	0.966	CLONAL	1	TRUE	1	0.686491134795966	2		538	836	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023642	27023642	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0035590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	219	365	0	ENST00000324856.7:c.748A>T	p.Lys250Ter	p.K250*	ENST00000324856	NM_006015.4	250	Aag/Tag	1/20	0.636420707116466	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.686491134795966	1		365	396	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544068	18544068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	146	326	0	ENST00000266497.5:c.1885G>A	p.Ala629Thr	p.A629T	ENST00000266497		629	Gct/Act	13/31	1	2	FACETS	0.985	0.907	1	0.985	0.907	1	CLONAL	1	TRUE	1	0.686491134795966	2		326	432	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416720	121416720	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	370	853	0	ENST00000257555.6:c.149G>C	p.Cys50Ser	p.C50S	ENST00000257555		50	tGc/tCc	1/10	1	2	FACETS	0.94	0.892	0.988	0.94	0.892	0.988	CLONAL	1	TRUE	1	0.686491134795966	2		853	1147	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828861	26828861	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	235	442	1	ENST00000381527.3:c.83G>A	p.Gly28Asp	p.G28D	ENST00000381527	NM_001260.1	28	gGc/gAc	1/13	NA	2	FACETS	0.966	0.905	1			1	INDETERMINATE	1	TRUE	NA	0.686491134795966	2		443	709	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988809	41988809	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	249	519	0	ENST00000219905.7:c.1601C>T	p.Ser534Leu	p.S534L	ENST00000219905	NM_001164273.1	534	tCa/tTa	3/24	1	2	FACETS	0.978	0.918	1	0.978	0.918	1	CLONAL	1	TRUE	1	0.686491134795966	2		519	742	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349535	89349535	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	369	754	0	ENST00000301030.4:c.3415G>C	p.Glu1139Gln	p.E1139Q	ENST00000301030	NM_001256183.1	1139	Gag/Cag	9/13	1	2	FACETS	0.943	0.895	0.991	0.943	0.895	0.991	CLONAL	1	TRUE	1	0.686491134795966	2		754	1140	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912842	50912858	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGCTGAAGGTGAGCG	GGCGCTGAAGGTGAGCG	-	novel	NA	P-0035590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	362	809	0	ENST00000440232.2:c.2073_2089del	p.Ala692GlnfsTer41	p.A692Qfs*41	ENST00000440232	NM_002691.3	691	ctGGCGCTGAAGGTGAGCGcc/ctcc	17/27	1	2	FACETS	0.93	0.882	0.978	0.93	0.882	0.978	CLONAL	1	TRUE	1	0.686491134795966	2		809	1134	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149709	202149710	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0035590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	238	581	0	ENST00000358485.4:c.1150_1151delinsTT	p.Gly384Phe	p.G384F	ENST00000358485	NM_001080125.1	384	GGc/TTc	8/9	0.675526918916101	1	FACETS	0.856	0.807	0.905	0.856	0.807	0.905	CLONAL	1	TRUE	0	0.686491134795966	1		581	532	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514648	44514648	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	256	631	0	ENST00000291552.4:c.508A>G	p.Asn170Asp	p.N170D	ENST00000291552	NM_006758.2	170	Aac/Gac	7/8	1	2	FACETS	0.781	0.732	0.831	0.781	0.732	0.831	SUBCLONAL	1	TRUE	1	0.686491134795966	2		631	955	SUCCESS
APC	324	MSKCC	GRCh37	5	112174320	112174320	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs864622584	NA	P-0035590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	174	337	0	ENST00000257430.4:c.3029G>A	p.Ser1010Asn	p.S1010N	ENST00000257430	NM_000038.5	1010	aGt/aAt	16/16	0.197046170167251	3	FACETS	1	0.988	1	0.676	0.627	0.725	INDETERMINATE	1	TRUE	1	0.686491134795966	3		337	504	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662723	117662723	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	203	453	0	ENST00000368508.3:c.4742C>G	p.Ser1581Cys	p.S1581C	ENST00000368508	NM_002944.2	1581	tCt/tGt	29/43	1	2	FACETS	0.996	0.929	1	0.996	0.929	1	CLONAL	1	TRUE	1	0.686491134795966	2		453	594	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233042	55233042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	264	505	0	ENST00000275493.2:c.1792G>A	p.Gly598Arg	p.G598R	ENST00000275493	NM_005228.3	598	Gga/Aga	15/28	1	2	FACETS	0.878	0.825	0.932	0.878	0.825	0.932	CLONAL	1	TRUE	1	0.686491134795966	2		505	876	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938403	44938403	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035590-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	274	230	0	ENST00000377967.4:c.2951T>C	p.Phe984Ser	p.F984S	ENST00000377967	NM_021140.2	984	tTc/tCc	20/29	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.686491134795966	1		230	386	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035780-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	89	381	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.921	0.818	1	0.921	0.818	1	CLONAL	1	TRUE	1	0.335640344805774	2		381	576	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330522	65330522	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035780-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	127	423	0	ENST00000342505.4:c.1124T>G	p.Ile375Ser	p.I375S	ENST00000342505	NM_002227.2	375	aTt/aGt	8/25	0.335640344805774	1	FACETS	0.989	0.898	1	0.989	0.898	1	CLONAL	1	TRUE	0	0.335640344805774	1		423	637	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577134	7577134	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0035780-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	162	613	0	ENST00000269305.4:c.804del	p.Asn268LysfsTer77	p.N268Kfs*77	ENST00000269305	NM_001126112.2	268	aaC/aa	8/11	0.233329257968434	2	FACETS	1	0.957	1	0.533	0.489	0.579	CLONAL	1	TRUE	0	0.335640344805774	2		613	905	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925196	81925196	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0035780-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	94	409	0	ENST00000359376.3:c.986+1G>A		p.X329_splice	ENST00000359376	NM_002661.3	329			1	2	FACETS	0.824	0.733	0.92	0.824	0.733	0.92	CLONAL	1	TRUE	1	0.335640344805774	2		409	680	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0035895-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	101	290	2	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.652747645288481	3	FACETS	0.881	0.791	0.975	0.44	0.395	0.488	CLONAL	1	TRUE	1	0.652747645288481	3		292	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0035895-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	394	653	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.652747645288481	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.652747645288481	2		653	571	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827475	72827475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567512921	NA	P-0035895-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	213	710	0	ENST00000268489.5:c.9106C>T	p.Arg3036Trp	p.R3036W	ENST00000268489	NM_006885.3	3036	Cgg/Tgg	9/10	0.652747645288481	3	FACETS	0.961	0.894	1	0.48	0.447	0.515	CLONAL	1	TRUE	1	0.652747645288481	3		710	901	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692889	89692889	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035895-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	310	375	0	ENST00000371953.3:c.373A>G	p.Lys125Glu	p.K125E	ENST00000371953	NM_000314.4	125	Aaa/Gaa	5/9	0.615877827669436	3	FACETS	0.948	0.912	0.983	0.948	0.912	0.983	CLONAL	3	TRUE	0	0.652747645288481	3		375	443	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554159	63554159	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035895-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	394	741	0	ENST00000307078.5:c.580G>C	p.Asp194His	p.D194H	ENST00000307078	NM_004655.3	194	Gat/Cat	2/11	0.652747645288481	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.652747645288481	2		741	601	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526700	106526700	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035895-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	569	500	0	ENST00000359195.3:c.2993C>G	p.Ser998Cys	p.S998C	ENST00000359195	NM_002649.2	998	tCt/tGt	10/11	0.652747645288481	4	FACETS	0.998	0.974	1			1	CLONAL	4	TRUE	NA	0.652747645288481	4		500	722	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748881	43748881	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035895-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	241	881	0	ENST00000382044.4:c.1925C>A	p.Ala642Glu	p.A642E	ENST00000382044	NM_001141980.1	642	gCa/gAa	12/28	1	2	FACETS	0.909	0.852	0.968	0.909	0.852	0.968	CLONAL	1	TRUE	1	0.652747645288481	2		881	812	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587454	29587454	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035895-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	34	443	0	ENST00000356175.3:c.4435A>C	p.Ser1479Arg	p.S1479R	ENST00000356175	NM_000267.3	1479	Agt/Cgt	33/57	0.652747645288481	2	FACETS	0.235	0.191	0.283	0.117	0.095	0.142	SUBCLONAL	1	TRUE	0	0.652747645288481	2		443	444	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872518	136872518	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035895-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	27	348	0	ENST00000241393.3:c.980A>C	p.Lys327Thr	p.K327T	ENST00000241393	NM_003467.2	327	aAg/aCg	2/2	0.652747645288481	2	FACETS	0.261	0.208	0.322	0.13	0.104	0.161	SUBCLONAL	1	TRUE	0	0.652747645288481	2		348	317	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965753	90965753	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0035895-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	25	306	0	ENST00000265433.3:c.1564T>G	p.Leu522Val	p.L522V	ENST00000265433	NM_002485.4	522	Tta/Gta	11/16	0.506346668467863	3	FACETS	0.285	0.225	0.355	0.143	0.112	0.178	SUBCLONAL	1	TRUE	1	0.652747645288481	3		306	356	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485908	8485908	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0035895-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	25	488	0	ENST00000356435.5:c.2909A>C	p.Gln970Pro	p.Q970P	ENST00000356435		970	cAg/cCg	17/35	0.652747645288481	2	FACETS	0.205	0.161	0.256	0.103	0.08	0.128	SUBCLONAL	1	TRUE	0	0.652747645288481	2		488	373	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0036013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	511	779	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.31078940666286	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.382470731774548	3		781	982	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38176413	38176413	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	146	536	1	ENST00000317025.8:c.1855G>A	p.Gly619Ser	p.G619S	ENST00000317025	NM_023034.1	619	Ggt/Agt	9/24	0.342853282464194	4	FACETS	1	0.916	1	0.503	0.458	0.55	CLONAL	1	TRUE	2	0.382470731774548	4		537	1050	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622301	117622301	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0036013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	85	493	0	ENST00000368508.3:c.6570-1G>A		p.X2190_splice	ENST00000368508	NM_002944.2	2190			0.368224365403672	3	FACETS	0.855	0.757	0.961	0.428	0.378	0.481	CLONAL	1	TRUE	1	0.382470731774548	3		493	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913343	NA	P-0036113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	107	695	0	ENST00000269305.4:c.817C>G	p.Arg273Gly	p.R273G	ENST00000269305	NM_001126112.2	273	Cgt/Ggt	8/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.19	2		695	936	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295220	15295220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568357671	NA	P-0036113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	66	967	1	ENST00000263388.2:c.2452G>A	p.Ala818Thr	p.A818T	ENST00000263388	NM_000435.2	818	Gca/Aca	16/33	0.156174712845271	3	FACETS	0.608	0.525	0.698	0.304	0.262	0.349	SUBCLONAL	1	TRUE	1	0.19	3		968	1252	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341293	89341293	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036113-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	22	259	0	ENST00000301030.4:c.7642C>T	p.Gln2548Ter	p.Q2548*	ENST00000301030	NM_001256183.1	2548	Cag/Tag	11/13	1	2	FACETS	0.667	0.517	0.842	0.667	0.517	0.842	SUBCLONAL	1	TRUE	1	0.19	2		259	347	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578553	7578553	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1555526335	NA	P-0036163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	400	866	0	ENST00000269305.4:c.377A>G	p.Tyr126Cys	p.Y126C	ENST00000269305	NM_001126112.2	126	tAc/tGc	5/11	0.717398712080307	1	FACETS	0.977	0.938	1	0.977	0.938	1	CLONAL	1	TRUE	0	0.717398712080307	1		866	732	SUCCESS
APC	324	MSKCC	GRCh37	5	112179080	112179080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036163-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	147	327	0	ENST00000257430.4:c.7789G>A	p.Gly2597Arg	p.G2597R	ENST00000257430	NM_000038.5	2597	Gga/Aga	16/16	0.237306166119572	5	FACETS	1	0.952	1	0.695	0.641	0.75	INDETERMINATE	2	TRUE	2	0.717398712080307	5		327	408	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0036233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	369	727	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.467211103918796	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.467211103918796	2		728	766	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175679	+	frameshift_variant	Frame_Shift_Del	DEL	AGAG	AGAG	-	rs387906234	NA	P-0036233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	198	349	0	ENST00000257430.4:c.4391_4394del	p.Glu1464ValfsTer8	p.E1464Vfs*8	ENST00000257430	NM_000038.5	1462	aAGAGa/aa	16/16	0.467211103918796	2	FACETS	0.907	0.85	0.966	0.907	0.85	0.966	CLONAL	2	TRUE	0	0.467211103918796	2		349	467	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856130	111856130	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765237130	NA	P-0036233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	164	185	0	ENST00000341259.2:c.181G>A	p.Glu61Lys	p.E61K	ENST00000341259	NM_005475.2	61	Gag/Aag	2/8	0.357288224699162	4	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	2	0.467211103918796	4		185	502	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256790	133256790	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	229	469	0	ENST00000320574.5:c.304C>T	p.Pro102Ser	p.P102S	ENST00000320574	NM_006231.2	102	Ccg/Tcg	4/49	0.357288224699162	4	FACETS	0.953	0.891	1	0.953	0.891	1	CLONAL	2	TRUE	2	0.467211103918796	4		469	755	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528111	29528111	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	297	476	0	ENST00000356175.3:c.1120del	p.Asp374IlefsTer2	p.D374Ifs*2	ENST00000356175	NM_000267.3	373	gtG/gt	10/57	0.467211103918796	2	FACETS	0.959	0.91	1	0.959	0.91	1	CLONAL	2	TRUE	0	0.467211103918796	2		476	663	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40876422	40876423	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	111	552	0	ENST00000428826.2:c.266dup	p.Phe92IlefsTer35	p.F92Ifs*35	ENST00000428826		89	ttc/ttTc	5/21	0.467211103918796	2	FACETS	0.668	0.601	0.739	0.334	0.3	0.37	SUBCLONAL	1	TRUE	0	0.467211103918796	2		552	711	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180225	38180226	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0036233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	197	459	0	ENST00000396334.3:c.77dup	p.Val27GlyfsTer44	p.V27Gfs*44	ENST00000396334	NM_002468.4	25	gcc/gCcc	1/5	0.467211103918796	2	FACETS	0.954	0.894	1	0.954	0.894	1	CLONAL	2	TRUE	0	0.467211103918796	2		459	442	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778023	27778023	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	191	431	0	ENST00000369163.2:c.172T>C	p.Ser58Pro	p.S58P	ENST00000369163	NM_003536.2	58	Tcc/Ccc	1/1	0.467211103918796	2	FACETS	0.921	0.861	0.981	0.921	0.861	0.981	CLONAL	2	TRUE	0	0.467211103918796	2		431	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0036256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	170	753	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.372032018175569	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.372032018175569	1		753	624	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047527	49047527	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0036256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	20	246	0	ENST00000267163.4:c.2520+1G>C		p.X840_splice	ENST00000267163	NM_000321.2	840			NA	2	FACETS	0.309	0.236	0.395			1	INDETERMINATE	1	TRUE	NA	0.372032018175569	2		246	348	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417902	32417902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	41	686	0	ENST00000332351.3:c.1150G>A	p.Glu384Lys	p.E384K	ENST00000332351	NM_024426.4	384	Gag/Aag	7/10	1	2	FACETS	0.275	0.228	0.327	0.275	0.228	0.327	SUBCLONAL	1	TRUE	1	0.372032018175569	2		686	802	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425037	49425037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1480605988	NA	P-0036256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	79	928	1	ENST00000301067.7:c.13451G>A	p.Arg4484Gln	p.R4484Q	ENST00000301067	NM_003482.3	4484	cGa/cAa	39/54	0.091684335596264	4	FACETS	0.527	0.462	0.598	0.264	0.231	0.299	INDETERMINATE	1	TRUE	2	0.372032018175569	4		929	1105	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216704	7216707	+	frameshift_variant	Frame_Shift_Del	DEL	TGAG	TGAG	-	rs758044036	NA	P-0036256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	81	557	0	ENST00000380728.2:c.716_719del	p.Thr239ArgfsTer105	p.T239Rfs*105	ENST00000380728		239	aCTCAg/ag	8/11	0.372032018175569	1	FACETS	0.691	0.61	0.777	0.691	0.61	0.777	SUBCLONAL	1	TRUE	0	0.372032018175569	1		557	513	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55086974	55086974	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	41	312	1	ENST00000275493.2:c.4C>T	p.Arg2Ter	p.R2*	ENST00000275493	NM_005228.3	2	Cga/Tga	1/28	1	2	FACETS	0.639	0.534	0.755	0.639	0.534	0.755	SUBCLONAL	1	TRUE	1	0.372032018175569	2		313	345	SUCCESS
APC	324	MSKCC	GRCh37	5	112111408	112111411	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	-	rs387906231	NA	P-0036499-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	31	284	0	ENST00000257430.4:c.509_512del	p.Asp170ValfsTer4	p.D170Vfs*4	ENST00000257430	NM_000038.5	169	ATAGat/at	5/16	0.360887941495838	1	FACETS	0.314	0.255	0.38	0.314	0.255	0.38	SUBCLONAL	1	TRUE	0	0.586094506821967	1		284	238	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609952	43609952	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776164321	NA	P-0036499-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	653	1050	0	ENST00000355710.3:c.1904G>A	p.Arg635His	p.R635H	ENST00000355710	NM_020975.4	635	cGc/cAc	11/20	0.568879435220957	4	FACETS	0.937	0.902	0.973			1	CLONAL	2	TRUE	NA	0.586094506821967	4		1050	1885	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974744	21974775	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTCCTCTACCCGACCCCGGGCCGCGGCCGT	ACCTCCTCTACCCGACCCCGGGCCGCGGCCGT	-	novel	NA	P-0036499-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	49	404	0	ENST00000304494.5:c.52_83del	p.Thr18AlafsTer15	p.T18Afs*15	ENST00000304494	NM_000077.4	18	ACGGCCGCGGCCCGGGGTCGGGTAGAGGAGGTg/g	1/3	1	2	FACETS	0.653	0.558	0.756	0.653	0.558	0.756	SUBCLONAL	1	TRUE	1	0.586094506821967	2		404	256	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456347	99456347	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036499-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	10757	574	0	ENST00000268035.6:c.1664A>G	p.Asp555Gly	p.D555G	ENST00000268035	NM_000875.3	555	gAc/gGc	8/21	0.586094506821967	43	FACETS	1	0.999	1			1	CLONAL	42	TRUE	NA	0.586094506821967	43		574	11276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587781702	NA	P-0036499-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	490	735	0	ENST00000269305.4:c.920-1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.56859169842324	2	FACETS	0.962	0.928	0.996	0.962	0.928	0.996	CLONAL	2	TRUE	0	0.586094506821967	2		735	869	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120791129	120791129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375034852	NA	P-0036499-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	238	945	2	ENST00000257552.2:c.706G>A	p.Ala236Thr	p.A236T	ENST00000257552	NM_002442.3	236	Gcc/Acc	10/15	0.356792046227669	4	FACETS	0.889	0.828	0.953	0.444	0.414	0.477	CLONAL	1	TRUE	2	0.586094506821967	4		947	1449	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36814333	36814333	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0036499-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	78	694	0	ENST00000373129.3:c.707G>C	p.Ser236Thr	p.S236T	ENST00000373129	NM_032017.1	236	aGc/aCc	8/12	0.56859169842324	2	FACETS	0.31	0.271	0.351	0.155	0.135	0.176	SUBCLONAL	1	TRUE	0	0.586094506821967	2		694	859	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36823905	36823905	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036499-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	270	715	1	ENST00000373129.3:c.277G>A	p.Glu93Lys	p.E93K	ENST00000373129	NM_032017.1	93	Gag/Aag	5/12	0.56859169842324	2	FACETS	0.959	0.901	1	0.479	0.45	0.509	CLONAL	1	TRUE	0	0.586094506821967	2		716	961	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400860	72400860	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0036499-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	222	384	0	ENST00000357731.5:c.311A>C	p.Gln104Pro	p.Q104P	ENST00000357731	NM_173808.2	104	cAg/cCg	2/7	0.572437593158846	2	FACETS	0.954	0.903	1	0.954	0.903	1	CLONAL	2	TRUE	0	0.586094506821967	2		384	397	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88428924	88428924	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0036499-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	336	508	0	ENST00000360948.2:c.2175+1del		p.X725_splice	ENST00000360948	NM_001012338.2	725			0.512037815027872	3	FACETS	1	0.993	1	0.795	0.759	0.83	CLONAL	2	TRUE	0	0.586094506821967	3		508	622	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943638	9943639	+	missense_variant	Missense_Mutation	DNP	GC	GC	CA	novel	NA	P-0036499-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	113	708	1	ENST00000330684.3:c.1302_1303delinsTG	p.Pro435Ala	p.P435A	ENST00000330684	NM_001134407.1	434	gtGCca/gtTGca	5/13	0.572437593158846	2	FACETS	0.511	0.46	0.566	0.256	0.23	0.283	SUBCLONAL	1	TRUE	0	0.586094506821967	2		709	754	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835717	68835717	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555514464	NA	P-0036499-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	296	739	1	ENST00000261769.5:c.308G>A	p.Trp103Ter	p.W103*	ENST00000261769	NM_004360.3	103	tGg/tAg	3/16	0.570967696940127	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.586094506821967	1		740	642	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213786	66213786	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs201970590	NA	P-0036499-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	105	421	0	ENST00000273854.3:c.2644A>G	p.Met882Val	p.M882V	ENST00000273854	NM_004439.5	882	Atg/Gtg	15/18	0.572437593158846	2	FACETS	0.75	0.675	0.828	0.375	0.337	0.414	SUBCLONAL	1	TRUE	0	0.586094506821967	2		421	478	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166260	32166260	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036499-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	93	795	0	ENST00000375023.3:c.4694C>A	p.Ala1565Asp	p.A1565D	ENST00000375023	NM_004557.3	1565	gCc/gAc	26/30	0.586094506821967	3	FACETS	0.314	0.278	0.353	0.105	0.092	0.118	SUBCLONAL	1	TRUE	0	0.586094506821967	3		795	1307	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100455	8100460	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCCA	GGGCCA	T	novel	NA	P-0036499-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1553	138	932	0	ENST00000346208.3:c.429_434delinsT	p.Gly144ArgfsTer157	p.G144Rfs*157	ENST00000346208		143	ggGGGCCAc/ggTc	3/6	0.521144292759228	5	FACETS	0.523	0.474	0.576			1	SUBCLONAL	1	TRUE	NA	0.586094506821967	5		932	1691	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	70	703	5	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.84	0.733	0.957	0.84	0.733	0.957	CLONAL	1	TRUE	1	0.27	2		708	617	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	28	262	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	1	2	FACETS	0.671	0.537	0.823	0.671	0.537	0.823	SUBCLONAL	1	TRUE	1	0.27	2		262	309	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	37	218	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.27	2		218	217	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	24	233	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.797	0.628	0.991	0.797	0.628	0.991	CLONAL	1	TRUE	1	0.27	2		233	223	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	99	780	4	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.27	2		784	731	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665752	29665755	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1555535032	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	29	295	0	ENST00000356175.3:c.6789_6792del	p.Tyr2264ThrfsTer5	p.Y2264Tfs*5	ENST00000356175	NM_000267.3	2263	ACTTac/ac	45/57	1	2	FACETS	0.716	0.576	0.875	0.716	0.576	0.875	SUBCLONAL	1	TRUE	1	0.27	2		295	300	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675571	86675571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1561325048	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	16	271	0	ENST00000274376.6:c.2513del	p.Asn838MetfsTer4	p.N838Mfs*4	ENST00000274376	NM_002890.2	836	gAa/ga	19/25	1	2	FACETS	0.534	0.395	0.699	0.534	0.395	0.699	SUBCLONAL	1	TRUE	1	0.27	2		271	222	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123246935	123246935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113014479	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	55	361	0	ENST00000358487.5:c.1990C>T	p.Arg664Trp	p.R664W	ENST00000358487	NM_000141.4	664	Cgg/Tgg	15/18	1	2	FACETS	0.851	0.729	0.984	0.851	0.729	0.984	CLONAL	1	TRUE	1	0.27	2		361	479	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	124	597	4	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.841	0.759	0.928	0.841	0.759	0.928	CLONAL	1	TRUE	1	0.27	2		601	1092	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099274	4099274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142307980	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	145	753	0	ENST00000262948.5:c.844C>T	p.Pro282Ser	p.P282S	ENST00000262948	NM_030662.3	282	Ccc/Tcc	7/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.27	2		753	1001	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	11	129	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	0.728	0.506	0.998	0.728	0.506	0.998	CLONAL	1	TRUE	1	0.27	2		129	112	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332628	65332628	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748142963	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	35	312	0	ENST00000342505.4:c.911C>T	p.Ser304Leu	p.S304L	ENST00000342505	NM_002227.2	304	tCg/tTg	7/25	1	2	FACETS	0.763	0.626	0.915	0.763	0.626	0.915	CLONAL	1	TRUE	1	0.27	2		312	340	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245024	133245024	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs752846614	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	98	703	2	ENST00000320574.5:c.2091del	p.Leu698CysfsTer94	p.L698Cfs*94	ENST00000320574	NM_006231.2	697	ccC/cc	19/49	1	2	FACETS	0.754	0.671	0.842	0.754	0.671	0.842	SUBCLONAL	1	TRUE	1	0.27	2		705	963	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298120	15298120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376606994	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	118	744	0	ENST00000263388.2:c.1636G>A	p.Val546Met	p.V546M	ENST00000263388	NM_000435.2	546	Gtg/Atg	11/33	1	2	FACETS	0.874	0.787	0.966	0.874	0.787	0.966	CLONAL	1	TRUE	1	0.27	2		744	1000	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933400	39933400	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	94	588	0	ENST00000378444.4:c.1199del	p.Gly400AlafsTer42	p.G400Afs*42	ENST00000378444	NM_001123385.1	400	gGc/gc	4/15	1	2	FACETS	0.885	0.787	0.989	0.885	0.787	0.989	CLONAL	1	TRUE	1	0.27	2		588	787	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28644740	28644741	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	13	246	0	ENST00000241453.7:c.52dup	p.Ser18PhefsTer24	p.S18Ffs*24	ENST00000241453	NM_004119.2	18	tct/tTct	2/24	1	2	FACETS	0.421	0.3	0.568	0.421	0.3	0.568	SUBCLONAL	1	TRUE	1	0.27	2		246	229	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138564	2138564	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1473538868	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	70	647	0	ENST00000219476.3:c.5377C>T	p.Arg1793Trp	p.R1793W	ENST00000219476	NM_000548.3	1793	Cgg/Tgg	42/42	1	2	FACETS	0.527	0.458	0.602	0.527	0.458	0.602	SUBCLONAL	1	TRUE	1	0.27	2		647	984	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225525	133225525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762090058	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	81	589	0	ENST00000320574.5:c.4139C>T	p.Ser1380Leu	p.S1380L	ENST00000320574	NM_006231.2	1380	tCg/tTg	32/49	1	2	FACETS	0.769	0.677	0.868	0.769	0.677	0.868	SUBCLONAL	1	TRUE	1	0.27	2		589	780	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527531	29527532	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	rs1555610893	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	60	461	0	ENST00000356175.3:c.983_984del	p.Cys328Ter	p.C328*	ENST00000356175	NM_000267.3	327	cTG/c	9/57	1	2	FACETS	0.896	0.773	1	0.896	0.773	1	CLONAL	1	TRUE	1	0.27	2		461	496	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440431	49440431	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1240601136	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	119	713	2	ENST00000301067.7:c.4379del	p.Pro1460HisfsTer46	p.P1460Hfs*46	ENST00000301067	NM_003482.3	1460	cCa/ca	15/54	1	2	FACETS	0.822	0.741	0.909	0.822	0.741	0.909	CLONAL	1	TRUE	1	0.27	2		715	1072	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874149	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	34	404	1	ENST00000262189.6:c.8389_8390del	p.Lys2797GlyfsTer11	p.K2797Gfs*11	ENST00000262189	NM_170606.2	2797	AAg/g	38/59	1	2	FACETS	0.631	0.516	0.761	0.631	0.516	0.761	SUBCLONAL	1	TRUE	1	0.27	2		405	399	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774194	66774194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	145	935	1	ENST00000307102.5:c.670G>A	p.Val224Met	p.V224M	ENST00000307102	NM_002755.3	224	Gtg/Atg	6/11	1	2	FACETS	0.854	0.777	0.935	0.854	0.777	0.935	CLONAL	1	TRUE	1	0.27	2		936	1258	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134569	2134569	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs397514939	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	60	782	4	ENST00000219476.3:c.4351del	p.Arg1451AlafsTer25	p.R1451Afs*25	ENST00000219476	NM_000548.3	1449	tCc/tc	34/42	1	2	FACETS	0.447	0.383	0.516	0.447	0.383	0.516	SUBCLONAL	1	TRUE	1	0.27	2		786	995	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226017	133226017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770966534	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	120	774	1	ENST00000320574.5:c.3880C>T	p.Arg1294Cys	p.R1294C	ENST00000320574	NM_006231.2	1294	Cgt/Tgt	31/49	1	2	FACETS	0.938	0.846	1	0.938	0.846	1	CLONAL	1	TRUE	1	0.27	2		775	948	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682702	86682703	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	22	169	0	ENST00000274376.6:c.2912dup	p.Leu971PhefsTer3	p.L971Ffs*3	ENST00000274376	NM_002890.2	969	-/T	23/25	1	2	FACETS	0.867	0.676	1	0.867	0.676	1	CLONAL	1	TRUE	1	0.27	2		169	188	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220899	36220899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555731828	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	28	257	1	ENST00000222270.7:c.4949C>T	p.Thr1650Met	p.T1650M	ENST00000222270	NM_014727.1	1650	aCg/aTg	23/37	1	2	FACETS	0.713	0.571	0.873	0.713	0.571	0.873	SUBCLONAL	1	TRUE	1	0.27	2		258	291	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998441	100998443	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	novel	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	57	424	0	ENST00000325455.5:c.1359_1361del	p.Ser454del	p.S454del	ENST00000325455	NM_001202474.3	453	tcCTCg/tcg	1/8	1	2	FACETS	0.792	0.68	0.914	0.792	0.68	0.914	CLONAL	1	TRUE	1	0.27	2		424	533	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861829	57861829	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	98	546	0	ENST00000228682.2:c.1130G>C	p.Ser377Thr	p.S377T	ENST00000228682	NM_005269.2	377	aGc/aCc	10/12	1	2	FACETS	0.894	0.797	0.997	0.894	0.797	0.997	CLONAL	1	TRUE	1	0.27	2		546	812	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118796	115118797	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	85	501	0	ENST00000257566.3:c.544_545del	p.Lys182GlufsTer44	p.K182Efs*44	ENST00000257566	NM_016569.3	182	AAg/g	2/8	1	2	FACETS	0.849	0.75	0.955	0.849	0.75	0.955	CLONAL	1	TRUE	1	0.27	2		501	742	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43700174	43700174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	62	401	0	ENST00000382044.4:c.5713G>A	p.Val1905Met	p.V1905M	ENST00000382044	NM_001141980.1	1905	Gtg/Atg	27/28	1	2	FACETS	0.827	0.715	0.949	0.827	0.715	0.949	CLONAL	1	TRUE	1	0.27	2		401	555	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935788	15935788	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	55	308	0	ENST00000268712.3:c.7145A>G	p.Gln2382Arg	p.Q2382R	ENST00000268712	NM_006311.3	2382	cAg/cGg	46/46	1	2	FACETS	0.835	0.715	0.966	0.835	0.715	0.966	CLONAL	1	TRUE	1	0.27	2		308	488	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000013	30000013	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	47	395	0	ENST00000338641.4:c.26T>C	p.Met9Thr	p.M9T	ENST00000338641	NM_000268.3	9	aTg/aCg	1/16	1	2	FACETS	0.713	0.602	0.836	0.713	0.602	0.836	SUBCLONAL	1	TRUE	1	0.27	2		395	488	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077457	30077457	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs74315493	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	54	304	0	ENST00000338641.4:c.1604T>C	p.Leu535Pro	p.L535P	ENST00000338641	NM_000268.3	535	cTg/cCg	15/16	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.27	2		304	374	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196745	106196745	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	70	408	0	ENST00000380013.4:c.5078A>G	p.Tyr1693Cys	p.Y1693C	ENST00000380013	NM_001127208.2	1693	tAc/tGc	11/11	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.27	2		408	436	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157431605	157431605	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0036740-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	76	430	0	ENST00000346085.5:c.2282-1G>T		p.X761_splice	ENST00000346085	NM_020732.3	761			1	2	FACETS	0.881	0.773	0.997	0.881	0.773	0.997	CLONAL	1	TRUE	1	0.27	2		430	639	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0036775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	63	377	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.15	2		377	583	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0036775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	24	233	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	0.882	0.691	1	0.882	0.691	1	CLONAL	1	TRUE	1	0.15	2		233	363	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481627	56481627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1429784531	NA	P-0036775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	80	760	2	ENST00000267101.3:c.662C>T	p.Pro221Leu	p.P221L	ENST00000267101	NM_001982.3	221	cCc/cTc	6/28	1	2	FACETS	0.958	0.841	1	0.958	0.841	1	CLONAL	1	TRUE	1	0.15	2		762	1113	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224583	108224583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881329	NA	P-0036775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	28	386	0	ENST00000278616.4:c.8762C>T	p.Thr2921Met	p.T2921M	ENST00000278616	NM_000051.3	2921	aCg/aTg	60/63	1	2	FACETS	0.688	0.548	0.847	0.688	0.548	0.847	SUBCLONAL	1	TRUE	1	0.15	2		386	543	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570397	95570397	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	36	448	0	ENST00000393063.1:c.3336C>G	p.Asn1112Lys	p.N1112K	ENST00000393063	NM_030621.3	1112	aaC/aaG	22/28	1	2	FACETS	0.726	0.595	0.874	0.726	0.595	0.874	SUBCLONAL	1	TRUE	1	0.15	2		448	661	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005437	150005437	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778494156	NA	P-0036775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	56	526	0	ENST00000253339.5:c.788C>T	p.Pro263Leu	p.P263L	ENST00000253339		263	cCa/cTa	3/7	1	2	FACETS	0.924	0.79	1	0.924	0.79	1	CLONAL	1	TRUE	1	0.15	2		526	808	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152864453	152864454	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CACC	novel	NA	P-0036775-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	11	55	0	ENST00000406277.2:c.69_72dup	p.His25GlyfsTer32	p.H25Gfs*32	ENST00000406277	NM_152274.4	24	-/GGTG	3/7	NA		FACETS		NA	1				INDETERMINATE	NA	TRUE	NA	0.15	NA		55	103	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343093	118343093	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs868934108	NA	P-0036781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	232	449	0	ENST00000534358.1:c.1219C>T	p.Arg407Ter	p.R407*	ENST00000534358	NM_005933.3	407	Cga/Tga	3/36	0.268593623648131	3	FACETS	0.852	0.806	0.899	0.852	0.806	0.899	INDETERMINATE	2	TRUE	1	0.856037923255664	3		449	454	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061221	38061241	+	inframe_deletion	In_Frame_Del	DEL	GTTCTCGAACATGTTGCCGGA	GTTCTCGAACATGTTGCCGGA	-	novel	NA	P-0036781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	267	584	0	ENST00000250448.2:c.748_768del	p.Ser250_Asn256del	p.S250_N256del	ENST00000250448	NM_004496.3	250	TCCGGCAACATGTTCGAGAAC/-	2/2	1	2	FACETS	0.941	0.888	0.994	0.941	0.888	0.994	CLONAL	1	TRUE	1	0.856037923255664	2		584	663	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874986	151874993	+	frameshift_variant	Frame_Shift_Del	DEL	CTGATCTT	CTGATCTT	TGC	novel	NA	P-0036781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	68	318	1	ENST00000262189.6:c.7545_7552delinsGCA	p.Arg2516HisfsTer7	p.R2516Hfs*7	ENST00000262189	NM_170606.2	2515	agAAGATCAGta/agGCAta	38/59	0.856037923255664	1	FACETS	0.4	0.353	0.45	0.4	0.353	0.45	SUBCLONAL	1	TRUE	0	0.856037923255664	1		319	227	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0036830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	134	372	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.628787530196731	2		372	385	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520006	NA	P-0036830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	552	725	0	ENST00000269305.4:c.821T>C	p.Val274Ala	p.V274A	ENST00000269305	NM_001126112.2	274	gTt/gCt	8/11	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.628787530196731	2		725	823	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623120	52623134	+	inframe_deletion	In_Frame_Del	DEL	GATATGTGGTTGTAG	GATATGTGGTTGTAG	-	novel	NA	P-0036830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	168	594	0	ENST00000394830.3:c.2917_2931del	p.Leu973_Ile977del	p.L973_I977del	ENST00000394830	NM_018313.4	973	CTACAACCACATATC/-	19/30	1	2	FACETS	0.755	0.695	0.816	0.755	0.695	0.816	SUBCLONAL	1	TRUE	1	0.628787530196731	2		594	708	SUCCESS
APC	324	MSKCC	GRCh37	5	112174270	112174271	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0036830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	134	355	20	ENST00000257430.4:c.2982_2983dup	p.Cys995PhefsTer11	p.C995Ffs*11	ENST00000257430	NM_000038.5	993	-/TT	16/16	1	2	FACETS	0.98	0.898	1	0.98	0.898	1	CLONAL	1	TRUE	1	0.628787530196731	2		375	435	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109319780	109319780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	98	632	0	ENST00000436639.2:c.908G>A	p.Cys303Tyr	p.C303Y	ENST00000436639	NM_014454.2	303	tGt/tAt	5/10	1	2	FACETS	0.424	0.378	0.472	0.424	0.378	0.472	SUBCLONAL	1	TRUE	1	0.628787530196731	2		632	736	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0037046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	217	753	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.354352299154312	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.354352299154312	1		753	958	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0037046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	76	178	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.302708481361925	2	FACETS	1	0.973	1	0.683	0.604	0.766	CLONAL	1	TRUE	0	0.354352299154312	2		178	314	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40678601	40678601	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037046-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	241	705	0	ENST00000249776.8:c.343G>C	p.Val115Leu	p.V115L	ENST00000249776	NM_033286.3	115	Gtt/Ctt	3/9	0.354352299154312	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.354352299154312	1		705	901	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691022	NA	P-0037049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	256	740	1	ENST00000269305.4:c.1024del	p.Arg342GlufsTer3	p.R342Efs*3	ENST00000269305	NM_001126112.2	342	Cga/ga	10/11	0.752871083187966	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.752871083187966	1		741	424	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068315	30068315	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	66	404	0	ENST00000331968.5:c.2084G>C	p.Arg695Pro	p.R695P	ENST00000331968	NM_002742.2	695	cGg/cCg	15/18	0.237092030530008	3	FACETS	0.647	0.564	0.735	0.323	0.282	0.368	INDETERMINATE	1	TRUE	1	0.752871083187966	3		404	373	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779461	3779461	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	83	843	2	ENST00000262367.5:c.5587C>A	p.Gln1863Lys	p.Q1863K	ENST00000262367	NM_004380.2	1863	Cag/Aag	31/31	0.426144089071579	1	FACETS	0.369	0.327	0.412	0.369	0.327	0.412	INDETERMINATE	1	TRUE	0	0.752871083187966	1		845	373	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719542	190719542	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	102	299	0	ENST00000441310.2:c.1544T>A	p.Val515Glu	p.V515E	ENST00000441310	NM_000534.4	515	gTg/gAg	9/13	0.316750645152719	2	FACETS	0.947	0.86	1	0.474	0.43	0.519	INDETERMINATE	1	TRUE	0	0.752871083187966	2		299	286	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664910	138664910	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	23	157	0	ENST00000330315.3:c.655C>A	p.Gln219Lys	p.Q219K	ENST00000330315	NM_023067.3	219	Cag/Aag	1/1	0.752871083187966	4	FACETS	0.38	0.296	0.476	0.127	0.098	0.159	SUBCLONAL	1	TRUE	1	0.752871083187966	4		157	282	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721025	176721025	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	112	547	0	ENST00000439151.2:c.6656G>T	p.Arg2219Leu	p.R2219L	ENST00000439151	NM_022455.4	2219	cGt/cTt	23/23	0.752871083187966	2	FACETS	0.624	0.564	0.686	0.312	0.282	0.343	SUBCLONAL	1	TRUE	0	0.752871083187966	2		547	477	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448089	49448089	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0037069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	169	446	0	ENST00000301067.7:c.510+1G>T		p.X170_splice	ENST00000301067	NM_003482.3	170			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.415430056699937	2		446	698	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061130	38061192	+	inframe_deletion	In_Frame_Del	DEL	CGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGA	CGCCGCTGCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGA	-	novel	NA	P-0037069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	146	76	0	ENST00000250448.2:c.797_859del	p.Phe266_Ala287delinsSer	p.F266_A287delinsS	ENST00000250448	NM_004496.3	266	tTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGCAGCGGCGcc/tcc	2/2	1	2	FACETS	1	0.965	1	1	0.994	1	CLONAL	3	TRUE	1	0.415430056699937	2		76	226	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0037070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	158	857	0	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	0.619059853155311	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.653809076178811	1		857	317	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156051	99156051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776096061	NA	P-0037070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	48	594	1	ENST00000074304.5:c.731G>A	p.Arg244Gln	p.R244Q	ENST00000074304	NM_001134224.1	244	cGg/cAg	10/26	1	2	FACETS	0.259	0.219	0.304	0.259	0.219	0.304	SUBCLONAL	1	TRUE	1	0.653809076178811	2		595	566	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259526	89259526	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	65	449	1	ENST00000336596.2:c.670G>T	p.Val224Leu	p.V224L	ENST00000336596	NM_005233.5	224	Gtg/Ttg	3/17	0.653809076178811	1	FACETS	0.531	0.466	0.6	0.531	0.466	0.6	SUBCLONAL	1	TRUE	0	0.653809076178811	1		450	252	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820917	36820917	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182214010	NA	P-0037070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	109	648	0	ENST00000373129.3:c.460G>A	p.Ala154Thr	p.A154T	ENST00000373129	NM_032017.1	154	Gct/Act	6/12	0.505052644612104	3	FACETS	0.947	0.856	1	0.474	0.428	0.522	CLONAL	1	TRUE	1	0.653809076178811	3		648	467	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615171	43615171	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	67	664	0	ENST00000355710.3:c.2585T>C	p.Met862Thr	p.M862T	ENST00000355710	NM_020975.4	862	aTg/aCg	14/20	0.355796691349801	3	FACETS	0.67	0.584	0.761	0.223	0.194	0.254	INDETERMINATE	1	TRUE	0	0.653809076178811	3		664	406	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047314	77047314	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	37	430	0	ENST00000356341.3:c.1230C>G	p.Phe410Leu	p.F410L	ENST00000356341	NM_002576.4	410	ttC/ttG	13/15	0.505052644612104	3	FACETS	0.417	0.344	0.498	0.209	0.172	0.249	SUBCLONAL	1	TRUE	1	0.653809076178811	3		430	360	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985449	2985484	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTACCCACAATGGTGGAGAATCTCCGAGTGGGCTCT	TTACCCACAATGGTGGAGAATCTCCGAGTGGGCTCT	-	novel	NA	P-0037070-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	32	354	0	ENST00000396946.4:c.327_358+4del		p.X109_splice	ENST00000396946	NM_032415.4	109		4/25	0.323391306507204	5	FACETS	0.487	0.395	0.591	0.162	0.131	0.197	INDETERMINATE	1	TRUE	2	0.653809076178811	5		354	398	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0037073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	24	548	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.393	0.307	0.494	0.393	0.307	0.494	SUBCLONAL	1	TRUE	1	0.13	2		548	939	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0037073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	56	794	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	1	2	FACETS	0.841	0.718	0.976	0.841	0.718	0.976	CLONAL	1	TRUE	1	0.13	2		794	1025	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518099	8518099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764400127	NA	P-0037073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	29	417	0	ENST00000356435.5:c.1292C>T	p.Ser431Leu	p.S431L	ENST00000356435		431	tCg/tTg	10/35	1	2	FACETS	0.602	0.481	0.741	0.602	0.481	0.741	SUBCLONAL	1	TRUE	1	0.13	2		417	741	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	62	815	1	ENST00000394830.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000394830	NM_018313.4	710	Cga/Tga	17/30	1	2	FACETS	0.934	0.804	1	0.934	0.804	1	CLONAL	1	TRUE	1	0.13	2		816	1021	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200218	123200218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764726360	NA	P-0037073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	21	310	0	ENST00000218089.9:c.2197G>A	p.Ala733Thr	p.A733T	ENST00000218089	NM_001042749.1	733	Gca/Aca	23/35	1	1	FACETS	0.803	0.618	1	0.803	0.618	1	CLONAL	1	TRUE	0	0.13	1		310	376	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020225	123020225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	37	354	0	ENST00000355640.3:c.713G>A	p.Arg238Gln	p.R238Q	ENST00000355640		238	cGa/cAa	2/7	1	1	FACETS	0.982	0.809	1	0.982	0.809	1	CLONAL	1	TRUE	0	0.13	1		354	542	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42040967	42040967	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	54	770	0	ENST00000219905.7:c.5345T>G	p.Leu1782Arg	p.L1782R	ENST00000219905	NM_001164273.1	1782	cTt/cGt	16/24	1	2	FACETS	0.815	0.694	0.949	0.815	0.694	0.949	CLONAL	1	TRUE	1	0.13	2		770	1019	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729208	66729208	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	42	746	0	ENST00000307102.5:c.416T>C	p.Ile139Thr	p.I139T	ENST00000307102	NM_002755.3	139	aTc/aCc	3/11	1	2	FACETS	0.8	0.666	0.95	0.8	0.666	0.95	CLONAL	1	TRUE	1	0.13	2		746	808	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117868	70117868	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1407667250	NA	P-0037073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	24	382	0	ENST00000245479.2:c.336C>A	p.Phe112Leu	p.F112L	ENST00000245479	NM_000346.3	112	ttC/ttA	1/3	1	2	FACETS	0.787	0.616	0.986	0.787	0.616	0.986	CLONAL	1	TRUE	1	0.13	2		382	469	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635599	47635599	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	52	595	0	ENST00000233146.2:c.271G>T	p.Asp91Tyr	p.D91Y	ENST00000233146	NM_000251.2	91	Gat/Tat	2/16	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.13	NA		595	1033	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723613	49723613	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	10	140	0	ENST00000449682.2:c.1029G>T	p.Glu343Asp	p.E343D	ENST00000449682	NM_020998.3	343	gaG/gaT	9/18	1	2	FACETS	0.785	0.532	1	0.785	0.532	1	CLONAL	1	TRUE	1	0.13	2		140	196	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114763	73114763	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	11	149	0	ENST00000356692.5:c.1144G>T	p.Glu382Ter	p.E382*	ENST00000356692		382	Gaa/Taa	9/9	1	2	FACETS	0.956	0.662	1	0.956	0.662	1	CLONAL	1	TRUE	1	0.13	2		149	177	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490528	20490528	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	73	645	0	ENST00000346618.3:c.1265T>G	p.Phe422Cys	p.F422C	ENST00000346618	NM_001949.4	422	tTt/tGt	7/7	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.13	2		645	907	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038531	47038531	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	28	354	0	ENST00000377604.3:c.693G>T	p.Glu231Asp	p.E231D	ENST00000377604	NM_001204468.1	231	gaG/gaT	8/24	1	1	FACETS	0.937	0.748	1	0.937	0.748	1	CLONAL	1	TRUE	0	0.13	1		354	430	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247007	53247007	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	39	283	0	ENST00000375401.3:c.493G>T	p.Glu165Ter	p.E165*	ENST00000375401	NM_004187.3	165	Gaa/Taa	4/26	1	1	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	0	0.13	1		283	523	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938710	76938710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037073-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	27	411	0	ENST00000373344.5:c.2038G>A	p.Glu680Lys	p.E680K	ENST00000373344	NM_000489.3	680	Gaa/Aaa	9/35	1	1	FACETS	0.762	0.605	0.942	0.762	0.605	0.942	CLONAL	1	TRUE	0	0.13	1		411	510	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0037075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	120	257	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.481096328119797	2		257	499	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0037075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	143	269	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.891	0.815	0.971	0.891	0.815	0.971	CLONAL	1	TRUE	1	0.481096328119797	2		269	667	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979529	7979529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768784091	NA	P-0037075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	176	694	0	ENST00000319144.4:c.1496G>A	p.Arg499His	p.R499H	ENST00000319144	NM_001139.2	499	cGc/cAc	11/15	0.471804849060556	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.481096328119797	1		694	507	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375016	45375016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226662382	NA	P-0037075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	128	418	0	ENST00000262160.6:c.827C>T	p.Ser276Leu	p.S276L	ENST00000262160	NM_005901.5	276	tCg/tTg	8/11	0.471804849060556	1	FACETS	0.927	0.847	1	0.927	0.847	1	CLONAL	1	TRUE	0	0.481096328119797	1		418	436	SUCCESS
APC	324	MSKCC	GRCh37	5	112175225	112175225	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037075-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	73	299	0	ENST00000257430.4:c.3934G>T	p.Gly1312Ter	p.G1312*	ENST00000257430	NM_000038.5	1312	Gga/Tga	16/16	1	2	FACETS	0.836	0.736	0.943	0.836	0.736	0.943	CLONAL	1	TRUE	1	0.481096328119797	2		299	363	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	89	381	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.888	0.793	0.987	0.888	0.793	0.987	CLONAL	1	TRUE	1	0.534720447608886	2		381	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121912651	NA	P-0037083-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	160	523	0	ENST00000269305.4:c.742C>G	p.Arg248Gly	p.R248G	ENST00000269305	NM_001126112.2	248	Cgg/Ggg	7/11	0.503956467039159	1	FACETS	0.913	0.844	0.984	0.913	0.844	0.984	CLONAL	1	TRUE	0	0.534720447608886	1		523	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0037094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	483	516	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	0.556409122696131	3	FACETS	0.909	0.877	0.94	0.909	0.877	0.94	CLONAL	3	TRUE	0	0.556409122696131	3		516	814	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657039	215657039	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144856889	NA	P-0037094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	104	288	0	ENST00000260947.4:c.346C>T	p.His116Tyr	p.H116Y	ENST00000260947	NM_000465.2	116	Cat/Tat	3/11	0.296993580019182	5	FACETS	1	0.976	1	0.435	0.39	0.481	INDETERMINATE	1	TRUE	2	0.556409122696131	5		288	526	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097304	178097304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763097686	NA	P-0037094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	149	224	0	ENST00000397062.3:c.410C>T	p.Ser137Leu	p.S137L	ENST00000397062	NM_006164.4	137	tCg/tTg	4/5	0.296993580019182	5	FACETS	1	0.975	1	0.758	0.699	0.819	INDETERMINATE	2	TRUE	2	0.556409122696131	5		224	432	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0037094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	142	232	0	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	0.428662720289396	3	FACETS	1	0.978	1	0.758	0.704	0.811	CLONAL	2	TRUE	0	0.556409122696131	3		232	287	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602923	10602923	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	311	639	0	ENST00000171111.5:c.655G>C	p.Glu219Gln	p.E219Q	ENST00000171111	NM_203500.1	219	Gag/Cag	3/6	0.482202868646623	2	FACETS	0.827	0.786	0.868	0.827	0.786	0.868	CLONAL	2	TRUE	0	0.556409122696131	2		639	676	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732494	74732494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	90	132	0	ENST00000359995.5:c.415C>T	p.Arg139Cys	p.R139C	ENST00000359995	NM_001195427.1	139	Cgc/Tgc	2/3	0.490118578127355	3	FACETS	0.889	0.817	0.96	0.889	0.817	0.96	CLONAL	3	TRUE	0	0.556409122696131	3		132	155	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733217	40733217	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	278	461	1	ENST00000373198.4:c.3589G>T	p.Glu1197Ter	p.E1197*	ENST00000373198	NM_133170.3	1197	Gaa/Taa	26/32	0.556409122696131	4	FACETS	0.932	0.879	0.987	0.932	0.879	0.987	CLONAL	2	TRUE	2	0.556409122696131	4		462	834	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021503	31021503	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	253	416	0	ENST00000375687.4:c.1502C>G	p.Ser501Cys	p.S501C	ENST00000375687	NM_015338.5	501	tCt/tGt	12/13	0.556409122696131	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.556409122696131	4		416	679	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409360	31409360	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	98	330	0	ENST00000344624.3:c.3747G>T	p.Leu1249Phe	p.L1249F	ENST00000344624		1249	ttG/ttT	29/33	0.556409122696131	4	FACETS	1	0.976	1	0.654	0.587	0.724	CLONAL	1	TRUE	2	0.556409122696131	4		330	419	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31409384	31409384	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	98	331	0	ENST00000344624.3:c.3723G>A	p.Met1241Ile	p.M1241I	ENST00000344624		1241	atG/atA	29/33	0.556409122696131	4	FACETS	1	0.97	1	0.611	0.547	0.677	CLONAL	1	TRUE	2	0.556409122696131	4		331	449	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5073762	5073762	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	192	366	0	ENST00000381652.3:c.1841G>A	p.Gly614Glu	p.G614E	ENST00000381652	NM_004972.3	614	gGa/gAa	14/25	0.428662720289396	3	FACETS	1	0.989	1	0.815	0.767	0.862	CLONAL	2	TRUE	0	0.556409122696131	3		366	361	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485880	8485880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037094-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	158	320	0	ENST00000356435.5:c.2937G>A	p.Met979Ile	p.M979I	ENST00000356435		979	atG/atA	17/35	0.428662720289396	3	FACETS	1	0.982	1	0.768	0.717	0.819	CLONAL	2	TRUE	0	0.556409122696131	3		320	315	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0037108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	340	738	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.685078414197328	4	FACETS	1	0.993	1	0.452	0.427	0.478	CLONAL	1	TRUE	1	0.685078414197328	4		738	1233	SUCCESS
AR	367	MSKCC	GRCh37	X	66765161	66765161	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs200185441	NA	P-0037108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	10	283	2	ENST00000374690.3:c.173A>T	p.Gln58Leu	p.Q58L	ENST00000374690	NM_000044.3	58	cAg/cTg	1/8	0.158683023812693	3	FACETS	0.14	0.095	0.198	0.047	0.031	0.066	INDETERMINATE	1	TRUE	0	0.685078414197328	3		285	279	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0037108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1279	155	522	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.685078414197328	4	FACETS	0.532	0.485	0.581	0.177	0.161	0.194	SUBCLONAL	1	TRUE	1	0.685078414197328	4		522	1434	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0037108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	173	726	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	1	2	FACETS	0.468	0.43	0.507	0.468	0.43	0.507	SUBCLONAL	1	TRUE	1	0.685078414197328	2		726	1080	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788617	3788617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519884	NA	P-0037108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	71	342	1	ENST00000262367.5:c.4337G>A	p.Arg1446His	p.R1446H	ENST00000262367	NM_004380.2	1446	cGc/cAc	26/31	1	2	FACETS	0.423	0.37	0.48	0.423	0.37	0.48	SUBCLONAL	1	TRUE	1	0.685078414197328	2		343	490	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26959350	26959350	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	142	333	0	ENST00000381527.3:c.517G>C	p.Asp173His	p.D173H	ENST00000381527	NM_001260.1	173	Gac/Cac	6/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.685078414197328	2		333	383	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263974	104263974	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776579	NA	P-0037108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	60	310	0	ENST00000369902.3:c.71del	p.Pro24ArgfsTer72	p.P24Rfs*72	ENST00000369902	NM_016169.3	22	gCc/gc	1/12	1	2	FACETS	0.454	0.392	0.52	0.454	0.392	0.52	SUBCLONAL	1	TRUE	1	0.685078414197328	2		310	386	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524603	176524603	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758782236	NA	P-0037108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	149	579	0	ENST00000292408.4:c.2335G>A	p.Asp779Asn	p.D779N	ENST00000292408	NM_213647.1	779	Gat/Aat	18/18	0.155579370126491	6	FACETS	0.765	0.697	0.837			1	INDETERMINATE	1	TRUE	NA	0.685078414197328	6		579	1348	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0037108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	102	1110	5	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	0.685078414197328	3	FACETS	0.429	0.383	0.479	0.215	0.191	0.24	SUBCLONAL	1	TRUE	1	0.685078414197328	3		1115	931	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137323821	137323821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769209021	NA	P-0037108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	121	799	0	ENST00000481739.1:c.1114G>A	p.Ala372Thr	p.A372T	ENST00000481739	NM_002957.4	372	Gcc/Acc	8/10	0.56192818441933	3	FACETS	0.378	0.34	0.418	0.189	0.17	0.209	SUBCLONAL	1	TRUE	1	0.685078414197328	3		799	1255	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16174647	16174647	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0037108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	44	279	0	ENST00000375759.3:c.83+2T>C		p.X28_splice	ENST00000375759	NM_015001.2	28			1	2	FACETS	0.326	0.274	0.384	0.326	0.274	0.384	SUBCLONAL	1	TRUE	1	0.685078414197328	2		279	394	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222519	157222519	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554265250	NA	P-0037108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	210	612	0	ENST00000346085.5:c.1786C>T	p.Gln596Ter	p.Q596*	ENST00000346085	NM_020732.3	596	Cag/Tag	4/20	0.685078414197328	1	FACETS	0.922	0.868	0.977	0.922	0.868	0.977	CLONAL	1	TRUE	0	0.685078414197328	1		612	437	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348650	89348650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	383	1002	0	ENST00000301030.4:c.4300G>A	p.Glu1434Lys	p.E1434K	ENST00000301030	NM_001256183.1	1434	Gag/Aag	9/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.685078414197328	2		1002	1091	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350807	89350807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	396	986	0	ENST00000301030.4:c.2143G>A	p.Glu715Lys	p.E715K	ENST00000301030	NM_001256183.1	715	Gaa/Aaa	9/13	1	2	FACETS	0.986	0.938	1	0.986	0.938	1	CLONAL	1	TRUE	1	0.685078414197328	2		986	1173	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911113	29911113	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	275	827	0	ENST00000376809.5:c.412C>T	p.Arg138Trp	p.R138W	ENST00000376809	NM_002116.7	138	Cgg/Tgg	3/8	0.319697818139857	2	FACETS	0.843	0.793	0.895	0.422	0.396	0.448	INDETERMINATE	1	TRUE	0	0.685078414197328	2		827	952	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050383	37050383	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1248251121	NA	P-0037108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	80	260	0	ENST00000231790.2:c.532G>T	p.Glu178Ter	p.E178*	ENST00000231790	NM_000249.3	178	Gaa/Taa	6/19	0.685078414197328	1	FACETS	0.718	0.643	0.794	0.718	0.643	0.794	SUBCLONAL	1	TRUE	0	0.685078414197328	1		260	214	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375519	118375521	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	novel	NA	P-0037108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	43	298	0	ENST00000534358.1:c.8916_8918del	p.Ser2973del	p.S2973del	ENST00000534358	NM_005933.3	2971	gCCTcc/gcc	27/36	0.289153369940481	3	FACETS	0.462	0.387	0.544	0.231	0.193	0.272	INDETERMINATE	1	TRUE	1	0.685078414197328	3		298	365	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156232	119156232	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	71	470	0	ENST00000264033.4:c.1897G>C	p.Asp633His	p.D633H	ENST00000264033	NM_005188.3	633	Gat/Cat	11/16	0.289153369940481	3	FACETS	0.438	0.382	0.499	0.219	0.191	0.25	INDETERMINATE	1	TRUE	1	0.685078414197328	3		470	635	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349223	89349223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	437	1085	0	ENST00000301030.4:c.3727G>A	p.Glu1243Lys	p.E1243K	ENST00000301030	NM_001256183.1	1243	Gaa/Aaa	9/13	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.685078414197328	2		1085	1262	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349366	89349366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144199827	NA	P-0037108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	381	940	0	ENST00000301030.4:c.3584G>A	p.Arg1195Lys	p.R1195K	ENST00000301030	NM_001256183.1	1195	aGa/aAa	9/13	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.685078414197328	2		940	1111	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349649	89349649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	353	892	1	ENST00000301030.4:c.3301G>A	p.Glu1101Lys	p.E1101K	ENST00000301030	NM_001256183.1	1101	Gaa/Aaa	9/13	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.685078414197328	2		893	963	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436909	29436909	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs763332339	NA	P-0037108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	100	474	0	ENST00000389048.3:c.3684C>G	p.His1228Gln	p.H1228Q	ENST00000389048	NM_004304.4	1228	caC/caG	24/29	1	2	FACETS	0.475	0.425	0.529	0.475	0.425	0.529	SUBCLONAL	1	TRUE	1	0.685078414197328	2		474	614	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41558756	41558757	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0037108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	163	436	0	ENST00000263253.7:c.3707dup	p.Asn1236LysfsTer2	p.N1236Kfs*2	ENST00000263253	NM_001429.3	1234	aga/agAa	21/31	1	2	FACETS	0.894	0.826	0.965	0.894	0.826	0.965	CLONAL	1	TRUE	1	0.685078414197328	2		436	532	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278281	142278281	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs746970647	NA	P-0037108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	130	551	2	ENST00000350721.4:c.1544G>A	p.Arg515His	p.R515H	ENST00000350721	NM_001184.3	515	cGt/cAt	7/47	0.685078414197328	3	FACETS	0.529	0.479	0.582	0.265	0.239	0.291	SUBCLONAL	1	TRUE	1	0.685078414197328	3		553	963	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638674	176638674	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1562212423	NA	P-0037108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	112	657	0	ENST00000439151.2:c.3274C>T	p.Gln1092Ter	p.Q1092*	ENST00000439151	NM_022455.4	1092	Cag/Tag	5/23	0.155579370126491	6	FACETS	0.668	0.599	0.741			1	INDETERMINATE	1	TRUE	NA	0.685078414197328	6		657	1161	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859283	151859283	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	83	414	0	ENST00000262189.6:c.11379A>C	p.Lys3793Asn	p.K3793N	ENST00000262189	NM_170606.2	3793	aaA/aaC	43/59	1	2	FACETS	0.483	0.427	0.542	0.483	0.427	0.542	SUBCLONAL	1	TRUE	1	0.685078414197328	2		414	502	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129874	69129874	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	32	291	0	ENST00000288368.4:c.4628A>G	p.Glu1543Gly	p.E1543G	ENST00000288368	NM_024870.2	1543	gAg/gGg	38/40	1	2	FACETS	0.284	0.231	0.344	0.284	0.231	0.344	SUBCLONAL	1	TRUE	1	0.685078414197328	2		291	329	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436302	110436302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037108-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	68	289	1	ENST00000375856.3:c.2099C>T	p.Ala700Val	p.A700V	ENST00000375856	NM_003749.2	700	gCc/gTc	1/2	0.325846259935548	5	FACETS	0.768	0.669	0.875	0.256	0.223	0.292	INDETERMINATE	1	TRUE	2	0.685078414197328	5		290	524	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625405	69625440	+	inframe_deletion	In_Frame_Del	DEL	CATACGTATTATAGCCCAGCTCGTGGATCCGCTCCA	CATACGTATTATAGCCCAGCTCGTGGATCCGCTCCA	-	novel	NA	P-0037122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	29	701	0	ENST00000334134.2:c.353_388del	p.Val118_Tyr129del	p.V118_Y129del	ENST00000334134	NM_005247.2	118	gTGGAGCGGATCCACGAGCTGGGCTATAATACGTATGcc/gcc	3/3	1	2	FACETS	0.309	0.248	0.378	0.309	0.248	0.378	SUBCLONAL	1	TRUE	1	0.613214313871964	2		701	306	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396985	396985	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	54	743	0	ENST00000262320.3:c.41C>G	p.Ala14Gly	p.A14G	ENST00000262320	NM_003502.3	14	gCa/gGa	2/11	1	2	FACETS	0.373	0.319	0.432	0.373	0.319	0.432	SUBCLONAL	1	TRUE	1	0.613214313871964	2		743	472	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696748	47696748	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0037122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	20	307	0	ENST00000347630.2:c.201-1G>T		p.X67_splice	ENST00000347630	NM_001007230.1	67			1	2	FACETS	0.302	0.231	0.384	0.302	0.231	0.384	SUBCLONAL	1	TRUE	1	0.613214313871964	2		307	216	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0037147-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	13	405	0	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	0.820765767220446	1	FACETS	0.047	0.033	0.064	0.047	0.033	0.064	SUBCLONAL	1	TRUE	0	0.820765767220446	1		405	399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs878854073	NA	P-0037178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	160	391	0	ENST00000269305.4:c.673-1G>A		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.526475056691776	2	FACETS	0.921	0.859	0.983	0.921	0.859	0.983	CLONAL	2	TRUE	0	0.532872320753198	2		391	326	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485961	40485961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	422	602	0	ENST00000264657.5:c.904C>T	p.Arg302Trp	p.R302W	ENST00000264657	NM_139276.2	302	Cgg/Tgg	9/24	0.532872320753198	3	FACETS	0.969	0.934	1	0.969	0.934	1	CLONAL	3	TRUE	0	0.532872320753198	3		602	690	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228399	228399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	90	499	0	ENST00000264932.6:c.721G>A	p.Asp241Asn	p.D241N	ENST00000264932	NM_004168.2	241	Gac/Aac	6/15	0.532872320753198	3	FACETS	0.749	0.666	0.838	0.375	0.333	0.419	SUBCLONAL	1	TRUE	1	0.532872320753198	3		499	571	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0037181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	27	528	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	0.241023961060684	2	FACETS	0.434	0.344	0.536	0.217	0.172	0.268	SUBCLONAL	1	FALSE	0	0.285627494045176	2		528	436	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0037181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	57	609	3	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	0.285627494045176	1	FACETS	0.475	0.406	0.549	0.475	0.406	0.549	SUBCLONAL	1	FALSE	0	0.285627494045176	1		612	721	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874713	151874713	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	58	523	0	ENST00000262189.6:c.7825C>T	p.Arg2609Ter	p.R2609*	ENST00000262189	NM_170606.2	2609	Cga/Tga	38/59	0.262926264711163	2	FACETS	0.774	0.665	0.892	0.387	0.332	0.446	SUBCLONAL	1	FALSE	0	0.285627494045176	2		523	525	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650114	206650114	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	91	784	1	ENST00000367120.3:c.634T>C	p.Tyr212His	p.Y212H	ENST00000367120	NM_014002.3	212	Tac/Cac	7/22	1	2	FACETS	0.93	0.826	1	0.93	0.826	1	CLONAL	1	FALSE	1	0.285627494045176	2		785	685	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841800	151841800	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	54	234	0	ENST00000262189.6:c.14341C>T	p.Gln4781Ter	p.Q4781*	ENST00000262189	NM_170606.2	4781	Cag/Tag	55/59	0.262926264711163	2	FACETS	1	0.895	1	0.527	0.452	0.608	CLONAL	1	FALSE	0	0.285627494045176	2		234	359	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841819	151841819	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0037181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	71	243	0	ENST00000262189.6:c.14322T>A	p.Tyr4774Ter	p.Y4774*	ENST00000262189	NM_170606.2	4774	taT/taA	55/59	0.262926264711163	2	FACETS	1	0.962	1	0.626	0.549	0.708	CLONAL	1	FALSE	0	0.285627494045176	2		243	397	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0037181-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	28	528	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	0.490104179076337	1	FACETS	0.307	0.246	0.376	0.307	0.246	0.376	SUBCLONAL	1	TRUE	0	0.490104179076337	1		528	281	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0037181-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	184	609	3	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	0.490104179076337	1	FACETS	0.778	0.72	0.837	0.778	0.72	0.837	SUBCLONAL	1	TRUE	0	0.490104179076337	1		612	729	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874713	151874713	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037181-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	42	523	0	ENST00000262189.6:c.7825C>T	p.Arg2609Ter	p.R2609*	ENST00000262189	NM_170606.2	2609	Cga/Tga	38/59	0.490104179076337	1	FACETS	0.299	0.249	0.354	0.299	0.249	0.354	SUBCLONAL	1	TRUE	0	0.490104179076337	1		523	433	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650114	206650114	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037181-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	184	784	1	ENST00000367120.3:c.634T>C	p.Tyr212His	p.Y212H	ENST00000367120	NM_014002.3	212	Tac/Cac	7/22	1	2	FACETS	0.929	0.859	1	0.929	0.859	1	CLONAL	1	TRUE	1	0.490104179076337	2		785	808	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1131691039	NA	P-0037196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	313	674	0	ENST00000269305.4:c.919+1G>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.693987963800434	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.693987963800434	1		674	517	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94163118	94163118	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	59	494	0	ENST00000323929.3:c.2029C>G	p.Gln677Glu	p.Q677E	ENST00000323929	NM_005591.3	677	Cag/Gag	19/20	0.259258229600305	3	FACETS	0.316	0.271	0.365	0.105	0.09	0.122	INDETERMINATE	1	TRUE	0	0.693987963800434	3		494	724	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865189	57865189	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	147	740	0	ENST00000228682.2:c.2666C>T	p.Ser889Phe	p.S889F	ENST00000228682	NM_005269.2	889	tCc/tTc	12/12	0.693987963800434	1	FACETS	0.447	0.409	0.486	0.447	0.409	0.486	SUBCLONAL	1	TRUE	0	0.693987963800434	1		740	619	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239900	41240077	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCGGCTGCCCCGCGAGCGGCCCAGCGGCGGCGGGGGGCACCGGCGGGTGCTGCGACAGCGGCCCGGGCGGCGGGGGCTGCGGTGGCGCTGGGTGCAGGCAGCCCGCCTCCGGGCCCTGGAAGTCCCCGCACAGCCCCCCGGTGGCGGCCGCGGCGGCCGCCGCCGCCACCGCCGCC	GCGCGGCTGCCCCGCGAGCGGCCCAGCGGCGGCGGGGGGCACCGGCGGGTGCTGCGACAGCGGCCCGGGCGGCGGGGGCTGCGGTGGCGCTGGGTGCAGGCAGCCCGCCTCCGGGCCCTGGAAGTCCCCGCACAGCCCCCCGGTGGCGGCCGCGGCGGCCGCCGCCGCCACCGCCGCC	-	novel	NA	P-0037196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	247	207	0	ENST00000379561.5:c.273_450del	p.Ala92ArgfsTer182	p.A92Rfs*182	ENST00000379561	NM_002015.3	91	gcGGCGGCGGTGGCGGCGGCGGCCGCCGCGGCCGCCACCGGGGGGCTGTGCGGGGACTTCCAGGGCCCGGAGGCGGGCTGCCTGCACCCAGCGCCACCGCAGCCCCCGCCGCCCGGGCCGCTGTCGCAGCACCCGCCGGTGCCCCCCGCCGCCGCTGGGCCGCTCGCGGGGCAGCCGCGC/gc	1/3	0.693987963800434	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.693987963800434	1		207	312	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37667847	37667847	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	141	471	0	ENST00000447079.4:c.2732A>T	p.Glu911Val	p.E911V	ENST00000447079	NM_015083.1	911	gAa/gTa	8/14	0.693987963800434	1	FACETS	0.584	0.537	0.634	0.584	0.537	0.634	SUBCLONAL	1	TRUE	0	0.693987963800434	1		471	454	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586253	48586253	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037196-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	162	497	0	ENST00000342988.3:c.922C>G	p.Leu308Val	p.L308V	ENST00000342988	NM_005359.5	308	Ctt/Gtt	8/12	NA	2	FACETS	0.84	0.775	0.907			1	INDETERMINATE	1	TRUE	NA	0.693987963800434	2		497	556	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0037233-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	624	582	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.914633244143013	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.914633244143013	2		582	658	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0037243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	123	287	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.251400654936635	3	FACETS	0.768	0.696	0.844	0.768	0.696	0.844	SUBCLONAL	2	TRUE	1	0.273300772581248	3		287	666	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0037243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	241	399	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.239667334350669	2	FACETS	0.953	0.892	1	0.953	0.892	1	CLONAL	2	TRUE	0	0.273300772581248	2		399	925	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798379	42798379	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	97	575	1	ENST00000575354.2:c.4250G>T	p.Arg1417Leu	p.R1417L	ENST00000575354	NM_015125.3	1417	cGc/cTc	18/20	0.251400654936635	3	FACETS	0.919	0.818	1	0.459	0.409	0.513	CLONAL	1	TRUE	1	0.273300772581248	3		576	878	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658481	3658481	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140876043	NA	P-0037243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	96	658	1	ENST00000294008.3:c.485C>T	p.Thr162Met	p.T162M	ENST00000294008	NM_032444.2	162	aCg/aTg	2/15	0.148872658801414	4	FACETS	0.865	0.769	0.968	0.433	0.384	0.484	INDETERMINATE	1	TRUE	2	0.273300772581248	4		659	1034	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710654	114710655	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0037243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	58	360	0	ENST00000543371.1:c.142_143del	p.Leu48SerfsTer3	p.L48Sfs*3	ENST00000543371	NM_001198531.1	47	TCt/t	1/14	1	2	FACETS	0.793	0.682	0.915	0.793	0.682	0.915	CLONAL	1	TRUE	1	0.273300772581248	2		360	535	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1940187	1940187	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1274132193	NA	P-0037243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	18	138	0	ENST00000382891.5:c.1684A>G	p.Ile562Val	p.I562V	ENST00000382891	NM_133335.3	562	Atc/Gtc	8/22	1	2	FACETS	0.621	0.469	0.8	0.621	0.469	0.8	SUBCLONAL	1	TRUE	1	0.273300772581248	2		138	212	SUCCESS
APC	324	MSKCC	GRCh37	5	112175751	112175752	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0037243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	57	339	0	ENST00000257430.4:c.4462_4463dup	p.Leu1488PhefsTer20	p.L1488Ffs*20	ENST00000257430	NM_000038.5	1487	act/acTTt	16/16	1	2	FACETS	0.979	0.842	1	0.979	0.842	1	CLONAL	1	TRUE	1	0.273300772581248	2		339	426	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782664	NA	P-0037273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	101	530	0	ENST00000269305.4:c.711G>C	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atC	7/11	0.146677561188897	6	FACETS	1	0.961	1			1	CLONAL	2	FALSE	NA	0.146677561188897	6		530	765	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437597	52437610	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTGGAGGGCCGC	GGCTGGAGGGCCGC	-	novel	NA	P-0037273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	95	592	0	ENST00000460680.1:c.1551_1564del	p.Arg518CysfsTer14	p.R518Cfs*14	ENST00000460680	NM_004656.3	517	acGCGGCCCTCCAGCCct/acct	13/17	0.137498242637531	2	FACETS	0.895	0.797	0.999	0.895	0.797	0.999	CLONAL	2	FALSE	0	0.146677561188897	2		592	724	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0037291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	48	351	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.332447743643871	3	FACETS	1	0.95	1	0.646	0.551	0.749	CLONAL	1	FALSE	1	0.354204974526098	3		351	247	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781371	NA	P-0037291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	9	649	1	ENST00000269305.4:c.328C>T	p.Arg110Cys	p.R110C	ENST00000269305	NM_001126112.2	110	Cgt/Tgt	4/11	0.127941577046078	0	FACETS	0.092	0.06	0.132			1	INDETERMINATE	1	FALSE	0	0.354204974526098	0		650	358	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879657	37879657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1377979176	NA	P-0037291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	9	674	1	ENST00000269571.5:c.2032C>T	p.Arg678Trp	p.R678W	ENST00000269571		678	Cgg/Tgg	17/27	0.127941577046078	0	FACETS	0.091	0.06	0.132			1	INDETERMINATE	1	FALSE	0	0.354204974526098	0		675	360	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815655	139815655	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037291-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	46	559	0	ENST00000247668.2:c.1126A>G	p.Ile376Val	p.I376V	ENST00000247668	NM_021138.3	376	Atc/Gtc	9/11	0.354204974526098	1	FACETS	0.638	0.539	0.746	0.638	0.539	0.746	SUBCLONAL	1	FALSE	0	0.354204974526098	1		559	335	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170837	11170837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374648988	NA	P-0037293-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	172	646	0	ENST00000358026.2:c.4981G>A	p.Asp1661Asn	p.D1661N	ENST00000358026	NM_001128849.1	1661	Gat/Aat	35/36	1	2	FACETS	0.843	0.775	0.913	0.843	0.775	0.913	CLONAL	1	FALSE	1	0.406273667955634	2		646	1005	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199627	16199627	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1415241290	NA	P-0037294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	298	549	0	ENST00000375759.3:c.400G>A	p.Asp134Asn	p.D134N	ENST00000375759	NM_015001.2	134	Gat/Aat	2/15	0.388504765981079	1	FACETS	0.617	0.584	0.65	0.617	0.584	0.65	INDETERMINATE	1	TRUE	0	0.783421572403366	1		549	750	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023307	27023358	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCCGCGGCCGCCTTGCCGCCCCCAGCCTACGGCTTCGGGCAACCCTACGG	CAGCCGCGGCCGCCTTGCCGCCCCCAGCCTACGGCTTCGGGCAACCCTACGG	-	novel	NA	P-0037294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	53	47	0	ENST00000324856.7:c.414_465del	p.Ala139GlyfsTer76	p.A139Gfs*76	ENST00000324856	NM_006015.4	138	tCAGCCGCGGCCGCCTTGCCGCCCCCAGCCTACGGCTTCGGGCAACCCTACGGc/tc	1/20	0.388504765981079	1	FACETS	0.648	0.569	0.729	0.648	0.569	0.729	INDETERMINATE	1	TRUE	0	0.783421572403366	1		47	127	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089463	27089476	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GGTGGCTACCCCAG	GGTGGCTACCCCAG	-	novel	NA	P-0037294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	290	649	0	ENST00000324856.7:c.2420_2433del		p.X807_splice	ENST00000324856	NM_006015.4	807		8/20	0.388504765981079	1	FACETS	0.586	0.554	0.619	0.586	0.554	0.619	INDETERMINATE	1	TRUE	0	0.783421572403366	1		649	768	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551514	150551514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	486	810	1	ENST00000369026.2:c.493C>T	p.Pro165Ser	p.P165S	ENST00000369026	NM_021960.4	165	Ccg/Tcg	1/3	1	2	FACETS	0.966	0.925	1	0.966	0.925	1	CLONAL	1	TRUE	1	0.783421572403366	2		811	1285	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012334	176012334	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	358	465	0	ENST00000367669.3:c.1600G>A	p.Asp534Asn	p.D534N	ENST00000367669	NM_022457.5	534	Gat/Aat	14/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.783421572403366	2		465	890	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982408	201982408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	493	744	0	ENST00000359651.3:c.787G>A	p.Gly263Ser	p.G263S	ENST00000359651		263	Ggc/Agc	6/8	0.738548285324946	1	FACETS	0.957	0.925	0.989	0.957	0.925	0.989	CLONAL	1	TRUE	0	0.783421572403366	1		744	800	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982998	201982998	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	509	874	0	ENST00000359651.3:c.847C>G	p.Leu283Val	p.L283V	ENST00000359651		283	Ctc/Gtc	7/8	0.738548285324946	1	FACETS	0.982	0.95	1	0.982	0.95	1	CLONAL	1	TRUE	0	0.783421572403366	1		874	805	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26975687	26975687	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	289	536	0	ENST00000381527.3:c.1199del	p.Pro400ArgfsTer2	p.P400Rfs*2	ENST00000381527	NM_001260.1	399	Ccc/cc	12/13	0.399879234150515	1	FACETS	0.703	0.667	0.74	0.703	0.667	0.74	INDETERMINATE	1	TRUE	0	0.783421572403366	1		536	638	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435277	110435277	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1320480022	NA	P-0037294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	62	147	0	ENST00000375856.3:c.3124T>C	p.Tyr1042His	p.Y1042H	ENST00000375856	NM_003749.2	1042	Tac/Cac	1/2	1	2	FACETS	0.865	0.762	0.972	0.865	0.762	0.972	CLONAL	1	TRUE	1	0.783421572403366	2		147	183	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923397	9923397	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs962487040	NA	P-0037294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	52	779	0	ENST00000330684.3:c.1890G>C	p.Met630Ile	p.M630I	ENST00000330684	NM_001134407.1	630	atG/atC	9/13	0.783421572403366	1	FACETS	0.091	0.077	0.107	0.091	0.077	0.107	SUBCLONAL	1	TRUE	0	0.783421572403366	1		779	888	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831701	72831701	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	162	817	0	ENST00000268489.5:c.4880C>T	p.Ala1627Val	p.A1627V	ENST00000268489	NM_006885.3	1627	gCc/gTc	9/10	0.419347420957454	1	FACETS	0.301	0.276	0.327	0.301	0.276	0.327	INDETERMINATE	1	TRUE	0	0.783421572403366	1		817	836	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216439	7216439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	430	738	1	ENST00000380728.2:c.809C>T	p.Ser270Phe	p.S270F	ENST00000380728		270	tCt/tTt	10/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.783421572403366	2		739	1098	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855787	45855787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	237	698	1	ENST00000391945.4:c.2023G>T	p.Gly675Cys	p.G675C	ENST00000391945	NM_000400.3	675	Ggc/Tgc	21/23	0.399879234150515	1	FACETS	0.428	0.4	0.457	0.428	0.4	0.457	INDETERMINATE	1	TRUE	0	0.783421572403366	1		699	860	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143185	30143185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1190182265	NA	P-0037294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	207	392	0	ENST00000389048.3:c.341C>T	p.Ser114Leu	p.S114L	ENST00000389048	NM_004304.4	114	tCa/tTa	1/29	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.783421572403366	2		392	502	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989584	212989584	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs965744501	NA	P-0037294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	24	409	0	ENST00000342788.4:c.127G>A	p.Glu43Lys	p.E43K	ENST00000342788	NM_005235.2	43	Gaa/Aaa	2/28	0.738548285324946	1	FACETS	0.085	0.066	0.107	0.085	0.066	0.107	SUBCLONAL	1	TRUE	0	0.783421572403366	1		409	439	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225365149	225365149	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	343	621	0	ENST00000264414.4:c.1541C>G	p.Pro514Arg	p.P514R	ENST00000264414	NM_003590.4	514	cCc/cGc	11/16	0.738548285324946	1	FACETS	0.923	0.885	0.961	0.923	0.885	0.961	CLONAL	1	TRUE	0	0.783421572403366	1		621	577	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12393110	12393110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	353	721	0	ENST00000287820.6:c.19G>A	p.Asp7Asn	p.D7N	ENST00000287820	NM_015869.4	7	Gat/Aat	1/7	1	2	FACETS	0.912	0.866	0.959	0.912	0.866	0.959	CLONAL	1	TRUE	1	0.783421572403366	2		721	988	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114806	73114806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1440424261	NA	P-0037294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	25	3	0	ENST00000356692.5:c.1187C>T	p.Ser396Leu	p.S396L	ENST00000356692		396	tCa/tTa	9/9	1	2	FACETS	0.886	0.765	0.995	1	0.962	1	CLONAL	2	TRUE	1	0.783421572403366	2		3	36	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138375052	138375052	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	387	612	0	ENST00000289153.2:c.3007C>G	p.Leu1003Val	p.L1003V	ENST00000289153	NM_006219.2	1003	Ctc/Gtc	21/22	1	2	FACETS	0.917	0.873	0.962	0.917	0.873	0.962	CLONAL	1	TRUE	1	0.783421572403366	2		612	1077	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430354	181430354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	245	365	0	ENST00000325404.1:c.206C>T	p.Ser69Leu	p.S69L	ENST00000325404	NM_003106.3	69	tCg/tTg	1/1	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.783421572403366	2		365	580	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562641	176562641	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs914277077	NA	P-0037294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	188	691	0	ENST00000439151.2:c.537T>A	p.Ser179Arg	p.S179R	ENST00000439151	NM_022455.4	179	agT/agA	2/23	0.419347420957454	1	FACETS	0.331	0.306	0.358	0.331	0.306	0.358	INDETERMINATE	1	TRUE	0	0.783421572403366	1		691	881	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056047	26056047	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	281	499	0	ENST00000343677.2:c.610A>G	p.Lys204Glu	p.K204E	ENST00000343677	NM_005319.3	204	Aag/Gag	1/1	1	2	FACETS	0.998	0.943	1	0.998	0.943	1	CLONAL	1	TRUE	1	0.783421572403366	2		499	719	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908153	41908153	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	192	763	0	ENST00000372991.4:c.369A>C	p.Lys123Asn	p.K123N	ENST00000372991	NM_001760.3	123	aaA/aaC	2/5	1	2	FACETS	0.422	0.389	0.456	0.422	0.389	0.456	SUBCLONAL	1	TRUE	1	0.783421572403366	2		763	1162	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157470057	157470057	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554226145	NA	P-0037294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	109	465	0	ENST00000346085.5:c.2851C>T	p.Gln951Ter	p.Q951*	ENST00000346085	NM_020732.3	951	Cag/Tag	9/20	0.783421572403366	1	FACETS	0.448	0.406	0.492	0.448	0.406	0.492	SUBCLONAL	1	TRUE	0	0.783421572403366	1		465	378	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38172288	38172288	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	104	496	0	ENST00000317025.8:c.2119T>C	p.Cys707Arg	p.C707R	ENST00000317025	NM_023034.1	707	Tgt/Cgt	12/24	0.783421572403366	1	FACETS	0.365	0.328	0.403	0.365	0.328	0.403	SUBCLONAL	1	TRUE	0	0.783421572403366	1		496	443	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38194966	38194966	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	360	588	1	ENST00000317025.8:c.767C>A	p.Ser256Tyr	p.S256Y	ENST00000317025	NM_023034.1	256	tCt/tAt	4/24	0.783421572403366	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.783421572403366	1		589	558	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370837	55370837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1470546998	NA	P-0037294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	458	285	0	ENST00000297316.4:c.139G>A	p.Glu47Lys	p.E47K	ENST00000297316	NM_022454.3	47	Gag/Aag	1/2	0.76273714713557	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	1	0.783421572403366	3		285	715	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750578	128750578	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	724	743	0	ENST00000377970.2:c.115T>C	p.Tyr39His	p.Y39H	ENST00000377970	NM_002467.4	39	Tac/Cac	2/3	0.76273714713557	3	FACETS	0.948	0.92	0.977	0.948	0.92	0.977	CLONAL	2	TRUE	1	0.783421572403366	3		743	1356	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139438531	139438531	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs908111363	NA	P-0037294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	452	825	0	ENST00000277541.6:c.85G>A	p.Glu29Lys	p.E29K	ENST00000277541	NM_017617.3	29	Gag/Aag	2/34	1	2	FACETS	0.999	0.956	1	0.999	0.956	1	CLONAL	1	TRUE	1	0.783421572403366	2		825	1155	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922669	44922669	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037294-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	270	211	0	ENST00000377967.4:c.1530G>A	p.Met510Ile	p.M510I	ENST00000377967	NM_021140.2	510	atG/atA	16/29	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.783421572403366	1		211	352	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	229	372	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.908664206366607	NA		372	480	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0037330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	241	722	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.908664206366607	3	FACETS	0.798	0.746	0.851	0.399	0.373	0.426	SUBCLONAL	1	TRUE	1	0.908664206366607	3		722	967	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0037330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	306	384	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.908664206366607	3	FACETS	1	0.97	1	0.519	0.49	0.549	CLONAL	1	TRUE	1	0.908664206366607	3		384	943	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922294	100922294	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1315135533	NA	P-0037330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	111	402	0	ENST00000325455.5:c.2218C>T	p.Arg740Ter	p.R740*	ENST00000325455	NM_001202474.3	740	Cga/Tga	5/8	1	2	FACETS	0.908	0.831	0.987	0.908	0.831	0.987	CLONAL	1	TRUE	1	0.908664206366607	2		402	269	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817850	3817850	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	375	612	0	ENST00000262367.5:c.3121C>T	p.Gln1041Ter	p.Q1041*	ENST00000262367	NM_004380.2	1041	Cag/Tag	16/31	1	2	FACETS	0.96	0.916	1	0.96	0.916	1	CLONAL	1	TRUE	1	0.908664206366607	2		612	860	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278343	39278343	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs137852813	NA	P-0037330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	306	773	0	ENST00000402219.2:c.806T>C	p.Met269Thr	p.M269T	ENST00000402219	NM_005633.3	269	aTg/aCg	6/23	1	2	FACETS	0.985	0.935	1	0.985	0.935	1	CLONAL	1	TRUE	1	0.908664206366607	2		773	684	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225613	133225613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138443282	NA	P-0037330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	435	610	0	ENST00000320574.5:c.4051G>A	p.Val1351Ile	p.V1351I	ENST00000320574	NM_006231.2	1351	Gtt/Att	32/49	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.908664206366607	2		610	926	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526707	106526707	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	242	450	0	ENST00000359195.3:c.3000G>T	p.Lys1000Asn	p.K1000N	ENST00000359195	NM_002649.2	1000	aaG/aaT	10/11	0.491052417586629	4	FACETS	1	0.988	1	0.412	0.385	0.439	INDETERMINATE	1	TRUE	1	0.908664206366607	4		450	823	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873500	151873500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	381	593	0	ENST00000262189.6:c.9038C>T	p.Thr3013Ile	p.T3013I	ENST00000262189	NM_170606.2	3013	aCt/aTt	38/59	0.491052417586629	4	FACETS	1	0.993	1	0.416	0.394	0.437	INDETERMINATE	1	TRUE	1	0.908664206366607	4		593	1284	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952090	178952090	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913277	NA	P-0037339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	135	302	0	ENST00000263967.3:c.3145G>C	p.Gly1049Arg	p.G1049R	ENST00000263967	NM_006218.2	1049	Ggt/Cgt	21/21	1	2	FACETS	0.932	0.854	1	0.932	0.854	1	CLONAL	1	TRUE	1	0.653971843872505	2		302	443	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881329	37881329	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037339-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	290	575	0	ENST00000269571.5:c.2521C>G	p.Leu841Val	p.L841V	ENST00000269571		841	Ctc/Gtc	21/27	0.653971843872505	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.653971843872505	1		575	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0037342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	474	753	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.592178184106849	4	FACETS	0.951	0.929	0.971			1	CLONAL	4	TRUE	NA	0.792282743210782	4		753	564	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921750	111921750	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs185078669	NA	P-0037342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	180	462	0	ENST00000393256.3:c.539G>A	p.Arg180Gln	p.R180Q	ENST00000393256	NM_006538.4	180	cGa/cAa	4/4	0.313338222062526	3	FACETS	1	0.989	1	0.684	0.637	0.731	INDETERMINATE	1	TRUE	1	0.792282743210782	3		462	464	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980453	7980453	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	154	605	1	ENST00000319144.4:c.1130A>T	p.Asp377Val	p.D377V	ENST00000319144	NM_001139.2	377	gAc/gTc	9/15	0.592178184106849	4	FACETS	0.761	0.702	0.821			1	SUBCLONAL	2	TRUE	NA	0.792282743210782	4		606	458	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635635	47635635	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780688	NA	P-0037342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	213	596	0	ENST00000233146.2:c.307T>C	p.Tyr103His	p.Y103H	ENST00000233146	NM_000251.2	103	Tat/Cat	2/16	0.792282743210782	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.792282743210782	1		596	319	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36024685	36024685	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs769916129	NA	P-0037342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	161	705	0	ENST00000358208.4:c.674G>T	p.Ser225Ile	p.S225I	ENST00000358208		225	aGc/aTc	6/12	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.792282743210782	2		705	329	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927399	49927399	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	153	678	0	ENST00000296474.3:c.3905A>T	p.Gln1302Leu	p.Q1302L	ENST00000296474	NM_002447.2	1302	cAg/cTg	19/20	0.524024923589568	4	FACETS	0.811	0.749	0.874	0.811	0.749	0.874	CLONAL	2	TRUE	2	0.792282743210782	4		678	427	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460432	149460432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037342-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	261	716	0	ENST00000286301.3:c.205C>T	p.Leu69Phe	p.L69F	ENST00000286301	NM_005211.3	69	Ctc/Ttc	3/22	0.748184760573127	3	FACETS	1	0.992	1	0.782	0.748	0.815	CLONAL	2	TRUE	0	0.792282743210782	3		716	392	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0037369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	118	507	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.236323677159485	2	FACETS	0.874	0.791	0.96	0.874	0.791	0.96	CLONAL	2	TRUE	0	0.238223244829089	2		507	567	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249020	55249020	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913432	NA	P-0037369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	272	394	0	ENST00000275493.2:c.2318A>G	p.His773Arg	p.H773R	ENST00000275493	NM_005228.3	773	cAc/cGc	20/28	0.238223244829089	7	FACETS	1	0.981	1	0.904	0.854	0.954	CLONAL	5	TRUE	1	0.238223244829089	7		394	672	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857875	9857875	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	122	549	0	ENST00000330684.3:c.3526G>A	p.Glu1176Lys	p.E1176K	ENST00000330684	NM_001134407.1	1176	Gag/Aag	13/13	0.208082218734894	4	FACETS	0.928	0.841	1	0.928	0.841	1	CLONAL	2	TRUE	2	0.238223244829089	4		549	683	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927659	131927666	+	frameshift_variant	Frame_Shift_Del	DEL	CTTGAAGA	CTTGAAGA	-	novel	NA	P-0037369-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	19	240	0	ENST00000265335.6:c.1728_1735del	p.Glu577AlafsTer3	p.E577Afs*3	ENST00000265335		576	CTTGAAGAc/c	11/25	0.194110719721662	3	FACETS	0.676	0.514	0.867	0.338	0.257	0.434	SUBCLONAL	1	TRUE	1	0.238223244829089	3		240	264	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0037371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	27	522	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		522	440	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217820	7217821	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0037371-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	35	770	0	ENST00000380728.2:c.190dup	p.Glu64GlyfsTer33	p.E64Gfs*33	ENST00000380728		64	gag/gGag	3/11	0.105895808675923	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		770	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578415	7578415	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	337	723	0	ENST00000269305.4:c.515T>A	p.Val172Asp	p.V172D	ENST00000269305	NM_001126112.2	172	gTt/gAt	5/11	0.812078281963353	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.812078281963353	1		723	490	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42002924	42002924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	205	414	0	ENST00000219905.7:c.2461G>A	p.Ala821Thr	p.A821T	ENST00000219905	NM_001164273.1	821	Gct/Act	8/24	0.812078281963353	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.812078281963353	1		414	287	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163587	32163587	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1191585262	NA	P-0037372-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	142	573	0	ENST00000375023.3:c.5639G>C	p.Arg1880Pro	p.R1880P	ENST00000375023	NM_004557.3	1880	cGg/cCg	30/30	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.812078281963353	2		573	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0037374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	41	753	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	0.708	0.59	0.839	0.708	0.59	0.839	SUBCLONAL	1	FALSE	1	0.265737176808049	2		753	436	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	32	381	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.632	0.513	0.766	0.632	0.513	0.766	SUBCLONAL	1	FALSE	1	0.265737176808049	2		381	381	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448310	56448310	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567880628	NA	P-0037374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	47	481	1	ENST00000407977.2:c.337C>T	p.Arg113Ter	p.R113*	ENST00000407977		113	Cga/Tga	3/10	0.265737176808049	1	FACETS	0.739	0.625	0.865	0.739	0.625	0.865	SUBCLONAL	1	FALSE	0	0.265737176808049	1		482	415	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420606	49420606	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037374-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	41	568	1	ENST00000301067.7:c.15143G>T	p.Arg5048Leu	p.R5048L	ENST00000301067	NM_003482.3	5048	cGt/cTt	48/54	1	2	FACETS	0.745	0.622	0.883	0.745	0.622	0.883	SUBCLONAL	1	FALSE	1	0.265737176808049	2		569	414	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0037425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	701	599	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.841564482537447	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.885111875673966	2		599	792	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752651	128752653	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs761021550	NA	P-0037425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	47	231	0	ENST00000377970.2:c.816_818del	p.Glu272del	p.E272del	ENST00000377970	NM_002467.4	271	cAAGaa/caa	3/3	0.245774158347251	5	FACETS	0.725	0.614	0.846	0.145	0.122	0.17	INDETERMINATE	1	TRUE	0	0.885111875673966	5		231	341	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032865	30032869	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTTG	GGTTG	-	novel	NA	P-0037425-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	192	276	0	ENST00000338641.4:c.240+2_240+6del		p.X80_splice	ENST00000338641	NM_000268.3	80		2/16	0.852058912711875	2	FACETS	0.931	0.896	0.963	0.931	0.896	0.963	CLONAL	2	TRUE	0	0.885111875673966	2		276	233	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	36	372	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.808	0.673	0.954	0.808	0.673	0.954	CLONAL	1	TRUE	1	0.54	2		372	165	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880257	37880257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	710	339	0	ENST00000269571.5:c.2301C>G	p.Ile767Met	p.I767M	ENST00000269571		767	atC/atG	19/27	0.3	12	FACETS	0.954	0.93	0.977			1	INDETERMINATE	10	TRUE	NA	0.54	12		339	1020	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820732	3820732	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	252	675	0	ENST00000262367.5:c.2719C>G	p.Pro907Ala	p.P907A	ENST00000262367	NM_004380.2	907	Ccc/Gcc	14/31	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.54	2		675	902	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591115	67591117	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0037446-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	96	210	0	ENST00000274335.5:c.1708_1710del	p.Leu570del	p.L570del	ENST00000274335		570	CTT/-	12/15	1	2	FACETS	0.958	0.861	1	0.958	0.861	1	CLONAL	1	TRUE	1	0.54	2		210	371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0037460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	535	635	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.790041424918246	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	FALSE	0	0.787910189483749	2		635	663	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589738	69589738	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	23	95	0	ENST00000168712.1:c.115C>A	p.Leu39Met	p.L39M	ENST00000168712	NM_002007.2	39	Ctg/Atg	1/3	0.790041424918246	3	FACETS	0.714	0.566	0.879	0.238	0.188	0.293	SUBCLONAL	1	FALSE	0	0.787910189483749	3		95	114	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0037462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	379	687	1	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.73448373543475	2	FACETS	0.995	0.963	1	0.995	0.963	1	CLONAL	2	TRUE	0	0.741415266444885	2		688	514	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087346	27087346	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0037462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	218	373	0	ENST00000324856.7:c.1921-1G>C		p.X641_splice	ENST00000324856	NM_006015.4	641			0.499157412554077	3	FACETS	1	0.956	1			1	CLONAL	2	TRUE	NA	0.741415266444885	3		373	398	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508482	29508482	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0037462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	111	301	0	ENST00000356175.3:c.629T>A	p.Leu210Ter	p.L210*	ENST00000356175	NM_000267.3	210	tTa/tAa	6/57	0.73448373543475	2	FACETS	0.805	0.73	0.882	0.402	0.365	0.441	CLONAL	1	TRUE	0	0.741415266444885	2		301	372	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559859	29559859	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	74	252	0	ENST00000356175.3:c.3456A>C	p.Leu1152Phe	p.L1152F	ENST00000356175	NM_000267.3	1152	ttA/ttC	26/57	0.73448373543475	2	FACETS	0.774	0.686	0.866	0.387	0.343	0.433	SUBCLONAL	1	TRUE	0	0.741415266444885	2		252	258	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041119	180041119	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	198	675	2	ENST00000261937.6:c.3280C>T	p.Gln1094Ter	p.Q1094*	ENST00000261937	NM_182925.4	1094	Cag/Tag	24/30	0.355312562591592	1	FACETS	0.632	0.59	0.675	0.632	0.59	0.675	INDETERMINATE	1	TRUE	0	0.741415266444885	1		677	532	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024168	112024168	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037462-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	137	410	0	ENST00000368678.4:c.617G>T	p.Arg206Leu	p.R206L	ENST00000368678		206	cGc/cTc	7/13	1	2	FACETS	0.899	0.826	0.974	0.899	0.826	0.974	CLONAL	1	TRUE	1	0.741415266444885	2		410	411	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0037469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	138	484	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.431684721813402	2		484	522	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0037469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	78	286	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.846	0.747	0.952	0.846	0.747	0.952	CLONAL	1	TRUE	1	0.431684721813402	2		286	427	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942085	81942085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767040629	NA	P-0037469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	56	692	3	ENST00000359376.3:c.1622C>T	p.Thr541Met	p.T541M	ENST00000359376	NM_002661.3	541	aCg/aTg	17/33	1	2	FACETS	0.253	0.216	0.294	0.253	0.216	0.294	SUBCLONAL	1	TRUE	1	0.431684721813402	2		695	1026	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100916	27100947	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCAGCAGCAGCAGTTGCCCCCAGCCCAGCC	CCTCAGCAGCAGCAGTTGCCCCCAGCCCAGCC	-	novel	NA	P-0037469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	113	670	0	ENST00000324856.7:c.4200_4231del	p.Gln1401AlafsTer33	p.Q1401Afs*33	ENST00000324856	NM_006015.4	1400	CCTCAGCAGCAGCAGTTGCCCCCAGCCCAGCCc/c	18/20	1	2	FACETS	0.655	0.589	0.725	0.655	0.589	0.725	SUBCLONAL	1	TRUE	1	0.431684721813402	2		670	799	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692778	89692778	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	205	338	0	ENST00000371953.3:c.262del	p.Tyr88IlefsTer11	p.Y88Ifs*11	ENST00000371953	NM_000314.4	88	Tat/at	5/9	0.431684721813402	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.431684721813402	3		338	351	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376780	31376780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1422196524	NA	P-0037469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	95	587	2	ENST00000328111.2:c.775C>T	p.Arg259Trp	p.R259W	ENST00000328111	NM_006892.3	259	Cgg/Tgg	7/23	1	2	FACETS	0.507	0.451	0.567	0.507	0.451	0.567	SUBCLONAL	1	TRUE	1	0.431684721813402	2		589	868	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589561	67589614	+	inframe_deletion	In_Frame_Del	DEL	ATTGAAGCTGTAGGGAAAAAATTACATGAATATAACACTCAGTTTCAAGAAAAA	ATTGAAGCTGTAGGGAAAAAATTACATGAATATAACACTCAGTTTCAAGAAAAA	-	novel	NA	P-0037469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	18	126	0	ENST00000274335.5:c.1325_1378del	p.Ile442_Lys459del	p.I442_K459del	ENST00000274335		442	ATTGAAGCTGTAGGGAAAAAATTACATGAATATAACACTCAGTTTCAAGAAAAA/-	10/15	1	2	FACETS	0.563	0.427	0.721	0.563	0.427	0.721	SUBCLONAL	1	TRUE	1	0.431684721813402	2		126	148	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589577	67589582	+	inframe_deletion	In_Frame_Del	DEL	AAAAAT	AAAAAT	-	novel	NA	P-0037469-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	15	154	0	ENST00000274335.5:c.1340_1345del	p.Lys447_Leu449delinsIle	p.K447_L449delinsI	ENST00000274335		447	aAAAAATta/ata	10/15	1	2	FACETS	0.47	0.345	0.617	0.47	0.345	0.617	SUBCLONAL	1	TRUE	1	0.431684721813402	2		154	148	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577600	7577601	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0037478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	226	570	0	ENST00000269305.4:c.680_681del	p.Ser227Ter	p.S227*	ENST00000269305	NM_001126112.2	227	tCT/t	7/11	0.641499652929483	2	FACETS	0.972	0.925	1	0.972	0.925	1	CLONAL	2	TRUE	0	0.654828318589273	2		570	355	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992592	72992592	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	103	569	1	ENST00000268489.5:c.1453G>T	p.Glu485Ter	p.E485*	ENST00000268489	NM_006885.3	485	Gag/Tag	2/10	1	2	FACETS	0.86	0.776	0.946	0.86	0.776	0.946	CLONAL	1	TRUE	1	0.654828318589273	2		570	366	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948759	17948759	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1229	72	753	0	ENST00000458235.1:c.1683G>C	p.Lys561Asn	p.K561N	ENST00000458235	NM_000215.3	561	aaG/aaC	12/24	0.654828318589273	6	FACETS	0.39	0.339	0.446	0.078	0.067	0.09	SUBCLONAL	1	TRUE	1	0.654828318589273	6		753	1301	SUCCESS
AR	367	MSKCC	GRCh37	X	66765800	66765800	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	172	909	1	ENST00000374690.3:c.812C>T	p.Pro271Leu	p.P271L	ENST00000374690	NM_000044.3	271	cCa/cTa	1/8	0.619154777745547	3	FACETS	1	0.949	1	0.518	0.478	0.559	CLONAL	1	TRUE	1	0.654828318589273	3		910	673	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0037482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	132	287	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.352106489463334	4	FACETS	0.841	0.771	0.913	0.841	0.771	0.913	CLONAL	3	TRUE	1	0.352106489463334	4		287	402	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	9	381	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.352106489463334	4	FACETS	0.175	0.115	0.252	0.058	0.038	0.084	SUBCLONAL	1	TRUE	1	0.352106489463334	4		381	396	SUCCESS
APC	324	MSKCC	GRCh37	5	112173299	112173299	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0037482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	23	272	0	ENST00000257430.4:c.2008A>T	p.Lys670Ter	p.K670*	ENST00000257430	NM_000038.5	670	Aaa/Taa	16/16	1	2	FACETS	0.787	0.619	0.978	0.787	0.619	0.978	CLONAL	1	TRUE	1	0.352106489463334	2		272	166	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217330	11217330	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037482-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	183	607	0	ENST00000361445.4:c.4348T>G	p.Tyr1450Asp	p.Y1450D	ENST00000361445	NM_004958.3	1450	Tat/Gat	30/58	0.352106489463334	2	FACETS	0.952	0.885	1	0.952	0.885	1	CLONAL	2	TRUE	0	0.352106489463334	2		607	546	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0037484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	289	400	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	NA	2	FACETS	0.966	0.914	1			1	INDETERMINATE	1	TRUE	NA	0.845029350446376	2		400	708	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0037484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	378	515	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.751047479813491	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.845029350446376	1		515	499	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844181	68844181	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	342	512	0	ENST00000261769.5:c.769G>T	p.Asp257Tyr	p.D257Y	ENST00000261769	NM_004360.3	257	Gac/Tac	6/16	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.845029350446376	2		512	707	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0037484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	172	296	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.845029350446376	1	FACETS	0.963	0.915	1	0.963	0.915	1	CLONAL	1	TRUE	0	0.845029350446376	1		296	244	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223028	41223028	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs200432771	NA	P-0037484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	426	633	1	ENST00000357654.3:c.4903G>T	p.Glu1635Ter	p.E1635*	ENST00000357654	NM_007294.3	1635	Gag/Tag	15/23	0.845029350446376	1	FACETS	0.977	0.946	1	0.977	0.946	1	CLONAL	1	TRUE	0	0.845029350446376	1		634	596	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000387	42000388	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0037484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	229	329	0	ENST00000219905.7:c.2406_2407insC	p.Ser803LeufsTer4	p.S803Lfs*4	ENST00000219905	NM_001164273.1	802	-/C	7/24	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.845029350446376	2		329	542	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652877	29652898	+	frameshift_variant	Frame_Shift_Del	DEL	CCATGTCTTACTGACTTTAAAG	CCATGTCTTACTGACTTTAAAG	-	novel	NA	P-0037484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	200	261	1	ENST00000356175.3:c.4816_4837del	p.Val1606IlefsTer9	p.V1606Ifs*9	ENST00000356175	NM_000267.3	1604	taCCATGTCTTACTGACTTTAAAG/ta	36/57	0.784350818454385	1	FACETS	0.936	0.891	0.98	0.936	0.891	0.98	CLONAL	1	TRUE	0	0.845029350446376	1		262	292	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961340	1961340	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	408	486	1	ENST00000382891.5:c.3128C>T	p.Pro1043Leu	p.P1043L	ENST00000382891	NM_133335.3	1043	cCg/cTg	17/22	0.845029350446376	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.845029350446376	1		487	511	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721264	176721264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	215	321	0	ENST00000439151.2:c.6895C>T	p.Leu2299Phe	p.L2299F	ENST00000439151	NM_022455.4	2299	Ctc/Ttc	23/23	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.845029350446376	2		321	490	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524696	106524696	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037484-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	89	320	0	ENST00000359195.3:c.2857A>G	p.Met953Val	p.M953V	ENST00000359195	NM_002649.2	953	Atg/Gtg	9/11	0.433376602579502	3	FACETS	0.481	0.427	0.539	0.16	0.142	0.18	INDETERMINATE	1	TRUE	0	0.845029350446376	3		320	623	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0037505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	124	287	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.390714226930165	2		287	569	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0037505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	198	399	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.390714226930165	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.390714226930165	1		399	708	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0037505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	163	522	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.390714226930165	2		522	720	SUCCESS
APC	324	MSKCC	GRCh37	5	112170865	112170865	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	G	rs879254032	NA	P-0037505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	114	360	0	ENST00000257430.4:c.1958+3A>G		p.X653_splice	ENST00000257430	NM_000038.5	653			0.390714226930165	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.390714226930165	1		360	413	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117873	70117873	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	192	390	0	ENST00000245479.2:c.341T>C	p.Val114Ala	p.V114A	ENST00000245479	NM_000346.3	114	gTg/gCg	1/3	0.390714226930165	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.390714226930165	2		390	416	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581158	48581158	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	87	265	0	ENST00000342988.3:c.463del	p.Ser155ValfsTer2	p.S155Vfs*2	ENST00000342988	NM_005359.5	154	tcA/tc	5/12	0.390714226930165	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.390714226930165	1		265	292	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250056	39250056	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	59	575	0	ENST00000402219.2:c.1513G>C	p.Asp505His	p.D505H	ENST00000402219	NM_005633.3	505	Gat/Cat	10/23	1	2	FACETS	0.386	0.331	0.446	0.386	0.331	0.446	SUBCLONAL	1	TRUE	1	0.390714226930165	2		575	782	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713733	30713733	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553630235	NA	P-0037508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	71	324	0	ENST00000295754.5:c.1058C>T	p.Ser353Phe	p.S353F	ENST00000295754	NM_003242.5	353	tCc/tTc	4/7	0.16292348892733	2	FACETS	1	0.915	1	0.528	0.462	0.599	INDETERMINATE	1	TRUE	0	0.3	2		324	448	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0037523-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	35	372	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.977	0.805	1	0.977	0.805	1	CLONAL	1	TRUE	1	0.26835000203041	2		372	267	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0037523-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	23	446	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.26835000203041	1	FACETS	0.542	0.423	0.678	0.542	0.423	0.678	SUBCLONAL	1	TRUE	0	0.26835000203041	1		446	274	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220274	55220274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037523-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5510	833	527	0	ENST00000275493.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000275493	NM_005228.3	222	Cgc/Tgc	6/28	0.26835000203041	85	FACETS	0.99	0.952	1			1	CLONAL	12	TRUE	NA	0.26835000203041	85		527	6343	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0037523-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4323	2196	594	1	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.26835000203041	85	FACETS	1	0.989	1			1	CLONAL	30	TRUE	NA	0.26835000203041	85		595	6519	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117753	70117753	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037523-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	59	511	0	ENST00000245479.2:c.221G>C	p.Arg74Pro	p.R74P	ENST00000245479	NM_000346.3	74	cGc/cCc	1/3	1	2	FACETS	0.905	0.78	1	0.905	0.78	1	CLONAL	1	TRUE	1	0.26835000203041	2		511	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0037534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	352	562	0	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	0.265759696802955	2	FACETS	1	0.991	1	1	0.996	1	CLONAL	3	TRUE	0	0.265759696802955	2		562	768	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951156	48951156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060503078	NA	P-0037534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	104	509	0	ENST00000267163.4:c.1318G>A	p.Glu440Lys	p.E440K	ENST00000267163	NM_000321.2	440	Gaa/Aaa	13/27	0.232951930892566	4	FACETS	0.787	0.706	0.873	0.525	0.471	0.582	SUBCLONAL	2	TRUE	1	0.265759696802955	4		509	629	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212615396	212615396	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs921054446	NA	P-0037534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	100	545	0	ENST00000342788.4:c.590G>T	p.Cys197Phe	p.C197F	ENST00000342788	NM_005235.2	197	tGc/tTc	5/28	0.255017530625795	4	FACETS	1	0.978	1	0.69	0.617	0.768	CLONAL	1	TRUE	2	0.265759696802955	4		545	690	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524363	187524363	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774876308	NA	P-0037534-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	140	584	0	ENST00000441802.2:c.11317C>T	p.Arg3773Cys	p.R3773C	ENST00000441802	NM_005245.3	3773	Cgc/Tgc	19/27	1	2	FACETS	0.878	0.803	0.956	1	0.99	1	CLONAL	2	TRUE	1	0.265759696802955	2		584	600	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0037547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	287	522	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.241450692823673	4	FACETS	0.954	0.902	1	0.715	0.676	0.755	CLONAL	3	TRUE	0	0.374027542041395	4		522	737	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743966	41743966	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	170	827	0	ENST00000301178.4:c.901C>G	p.Pro301Ala	p.P301A	ENST00000301178	NM_021913.4	301	Cct/Gct	7/20	0.17790050848199	4	FACETS	0.755	0.695	0.818	0.755	0.695	0.818	INDETERMINATE	2	TRUE	2	0.374027542041395	4		827	827	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515166	149515166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756405938	NA	P-0037547-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	104	732	0	ENST00000261799.4:c.316C>T	p.Arg106Cys	p.R106C	ENST00000261799	NM_002609.3	106	Cgt/Tgt	3/23	0.265634855818391	3	FACETS	0.948	0.85	1	0.474	0.425	0.527	CLONAL	1	TRUE	1	0.374027542041395	3		732	696	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577153	7577153	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs1131691025	NA	P-0037580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	277	461	0	ENST00000269305.4:c.785G>T	p.Gly262Val	p.G262V	ENST00000269305	NM_001126112.2	262	gGt/gTt	8/11	0.535301255437817	3	FACETS	1	0.993	1	0.812	0.777	0.846	CLONAL	2	TRUE	0	0.726467699646304	3		461	427	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136326	2136326	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	164	801	0	ENST00000219476.3:c.4795G>T	p.Val1599Leu	p.V1599L	ENST00000219476	NM_000548.3	1599	Gtg/Ttg	37/42	0.603566276760384	4	FACETS	0.927	0.852	1	0.463	0.426	0.503	CLONAL	1	TRUE	2	0.726467699646304	4		801	841	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565574	41565574	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	70	412	0	ENST00000263253.7:c.4240T>C	p.Tyr1414His	p.Y1414H	ENST00000263253	NM_001429.3	1414	Tat/Cat	26/31	0.147446828539635	3	FACETS	0.9	0.792	1	0.3	0.264	0.338	INDETERMINATE	1	TRUE	0	0.726467699646304	3		412	292	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0037620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	132	290	2	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.962	0.878	1	0.962	0.878	1	CLONAL	1	TRUE	1	0.512706017184676	2		292	535	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349640	89349641	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs772267579	NA	P-0037620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	270	663	14	ENST00000301030.4:c.3309dup	p.Asp1104ArgfsTer2	p.D1104Rfs*2	ENST00000301030	NM_001256183.1	1103	-/A	9/13	0.512706017184676	1	FACETS	0.837	0.786	0.888	0.837	0.786	0.888	CLONAL	1	TRUE	0	0.512706017184676	1		677	936	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2097822	2097822	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037620-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	225	380	1	ENST00000219066.1:c.27G>A	p.Met9Ile	p.M9I	ENST00000219066	NM_002528.5	9	atG/atA	1/6	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.512706017184676	2		381	840	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0037624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	415	635	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.538258912625792	3	FACETS	0.972	0.936	1	0.972	0.936	1	CLONAL	3	TRUE	0	0.53062134028655	3		635	679	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032111	26032111	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs753823527	NA	P-0037624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	101	276	0	ENST00000244661.2:c.178G>T	p.Glu60Ter	p.E60*	ENST00000244661	NM_003537.3	60	Gag/Tag	1/1	0.53062134028655	9	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.53062134028655	9		276	754	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170070	32170070	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	241	687	0	ENST00000375023.3:c.3538G>A	p.Gly1180Ser	p.G1180S	ENST00000375023	NM_004557.3	1180	Ggc/Agc	21/30	0.538258912625792	4	FACETS	1	0.972	1	0.705	0.663	0.749	CLONAL	2	TRUE	1	0.53062134028655	4		687	657	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68989698	68989698	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	67	539	0	ENST00000288368.4:c.1636C>G	p.His546Asp	p.H546D	ENST00000288368	NM_024870.2	546	Cac/Gac	15/40	0.53062134028655	6	FACETS	0.667	0.579	0.763	0.133	0.115	0.153	SUBCLONAL	1	TRUE	1	0.53062134028655	6		539	780	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0037658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	386	1194	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.506461922584166	2	FACETS	0.857	0.82	0.894	0.857	0.82	0.894	CLONAL	2	TRUE	0	0.573193805840754	2		1194	786	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100292	27100292	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0037658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	145	582	0	ENST00000324856.7:c.4005-1G>C		p.X1335_splice	ENST00000324856	NM_006015.4	1335			0.574027563759395	4	FACETS	0.864	0.788	0.944	0.288	0.262	0.315	CLONAL	1	TRUE	1	0.573193805840754	4		582	921	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148474	119148474	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	102	373	0	ENST00000264033.4:c.1015T>C	p.Phe339Leu	p.F339L	ENST00000264033	NM_005188.3	339	Ttt/Ctt	7/16	0.574027563759395	3	FACETS	0.923	0.829	1	0.462	0.414	0.511	CLONAL	1	TRUE	1	0.573193805840754	3		373	496	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152201	11152201	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs141891784	NA	P-0037658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	68	431	0	ENST00000358026.2:c.4485G>T	p.Lys1495Asn	p.K1495N	ENST00000358026	NM_001128849.1	1495	aaG/aaT	31/36	0.509846473643329	4	FACETS	0.457	0.397	0.523	0.229	0.198	0.262	SUBCLONAL	1	TRUE	2	0.573193805840754	4		431	816	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026768	48026768	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs200447622	NA	P-0037658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	99	362	0	ENST00000234420.5:c.1646C>G	p.Ser549Cys	p.S549C	ENST00000234420	NM_000179.2	549	tCt/tGt	4/10	0.571626441170233	3	FACETS	0.776	0.694	0.862	0.259	0.231	0.288	SUBCLONAL	1	TRUE	0	0.573193805840754	3		362	573	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707741	176707741	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587784156	NA	P-0037658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	81	374	0	ENST00000439151.2:c.5798A>G	p.Asn1933Ser	p.N1933S	ENST00000439151	NM_022455.4	1933	aAc/aGc	18/23	0.518024957829707	2	FACETS	0.61	0.54	0.686	0.305	0.27	0.343	SUBCLONAL	1	TRUE	0	0.573193805840754	2		374	463	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852222	128852222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	207	681	0	ENST00000249373.3:c.2294G>A	p.Gly765Asp	p.G765D	ENST00000249373	NM_005631.4	765	gGc/gAc	12/12	0.574027563759395	3	FACETS	0.901	0.836	0.969	0.451	0.418	0.485	CLONAL	1	TRUE	1	0.573193805840754	3		681	1031	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0037675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	281	564	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.923	0.871	0.975	0.923	0.871	0.975	CLONAL	1	TRUE	1	0.798991860202175	2		564	762	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432848	432848	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	38	350	0	ENST00000399788.2:c.2068T>G	p.Cys690Gly	p.C690G	ENST00000399788	NM_001042603.1	690	Tgt/Ggt	15/28	0.561136914785892	1	FACETS	0.1	0.082	0.12	0.1	0.082	0.12	SUBCLONAL	1	TRUE	0	0.798991860202175	1		350	571	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112578	115112579	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0037675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	406	570	0	ENST00000257566.3:c.1161dup	p.Glu388ArgfsTer19	p.E388Rfs*19	ENST00000257566	NM_016569.3	387	-/C	7/8	1	2	FACETS	0.921	0.878	0.964	0.921	0.878	0.964	CLONAL	1	TRUE	1	0.798991860202175	2		570	1104	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853269	68853269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	323	372	0	ENST00000261769.5:c.1652del	p.Glu551GlyfsTer6	p.E551Gfs*6	ENST00000261769	NM_004360.3	551	gAg/gg	11/16	0.798991860202175	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.798991860202175	1		372	461	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	23	779	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.156460713820058	5	FACETS	0.82	0.639	1	0.273	0.213	0.344	CLONAL	1	TRUE	2	0.17	5		781	414	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	45	548	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.156460713820058	5	FACETS	0.706	0.591	0.834	0.235	0.197	0.278	SUBCLONAL	1	TRUE	2	0.17	5		548	941	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277225	41277225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760837728	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	23	356	0	ENST00000349496.5:c.1694G>A	p.Arg565His	p.R565H	ENST00000349496	NM_001904.3	565	cGc/cAc	11/15	0.156460713820058	5	FACETS	0.901	0.702	1	0.3	0.234	0.378	CLONAL	1	TRUE	2	0.17	5		356	377	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	37	660	1	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.156460713820058	5	FACETS	1	0.906	1	0.387	0.318	0.463	CLONAL	1	TRUE	2	0.17	5		661	471	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	27	1110	5	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	0.429142599754643	4	FACETS	0.691	0.548	0.855	0.345	0.274	0.428	SUBCLONAL	1	TRUE	2	0.17	4		1115	538	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1040408	1040408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370272002	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	38	610	2	ENST00000358495.3:c.164G>A	p.Arg55His	p.R55H	ENST00000358495	NM_134424.2	55	cGc/cAc	3/12	0.3	3	FACETS	1	0.893	1			1	CLONAL	1	TRUE	NA	0.17	3		612	436	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	81	880	0	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	0.429142599754643	4	FACETS	0.943	0.832	1	0.943	0.832	1	CLONAL	2	TRUE	2	0.17	4		880	591	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36824418	36824418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767722663	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	32	562	0	ENST00000373129.3:c.118C>T	p.Arg40Cys	p.R40C	ENST00000373129	NM_032017.1	40	Cgt/Tgt	4/12	0.189080174103133	4	FACETS	0.949	0.77	1	0.475	0.385	0.576	CLONAL	1	TRUE	2	0.17	4		562	464	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	44	372	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	0.156460713820058	5	FACETS	1	0.907	1	0.375	0.314	0.442	CLONAL	1	TRUE	2	0.17	5		372	578	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525060	157525060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1215965074	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	35	408	0	ENST00000346085.5:c.4955C>T	p.Thr1652Met	p.T1652M	ENST00000346085	NM_020732.3	1652	aCg/aTg	19/20	0.487441664452982	4	FACETS	0.821	0.671	0.989	0.41	0.335	0.495	CLONAL	1	TRUE	2	0.17	4		408	587	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198272772	198272772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1360040192	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	43	682	0	ENST00000335508.6:c.1189C>T	p.Arg397Cys	p.R397C	ENST00000335508	NM_012433.2	397	Cgc/Tgc	9/25	0.189080174103133	4	FACETS	1	0.882	1	0.534	0.446	0.632	CLONAL	1	TRUE	2	0.17	4		682	554	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380283	25380283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913528	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	58	561	0	ENST00000311936.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000311936	NM_004985.3	59	Gca/Aca	3/5	0.429142599754643	4	FACETS	1	0.933	1	0.577	0.495	0.667	CLONAL	1	TRUE	2	0.17	4		561	692	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593651	215593651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111367604	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	44	415	0	ENST00000260947.4:c.2083G>A	p.Val695Ile	p.V695I	ENST00000260947	NM_000465.2	695	Gtc/Atc	11/11	0.189080174103133	4	FACETS	1	0.953	1	0.703	0.59	0.827	CLONAL	1	TRUE	2	0.17	4		415	431	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	38	367	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.278151731510246	4	FACETS	0.885	0.73	1	0.443	0.365	0.529	CLONAL	1	TRUE	2	0.17	4		367	591	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944947	31944947	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868835690	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	24	437	0	ENST00000340398.3:c.154C>T	p.Arg52Cys	p.R52C	ENST00000340398	NM_001013699.2	52	Cgt/Tgt	1/1	0.429142599754643	4	FACETS	0.77	0.603	0.964	0.385	0.301	0.482	CLONAL	1	TRUE	2	0.17	4		437	429	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262139	10262139	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	44	735	2	ENST00000340748.4:c.2152del	p.Met718CysfsTer59	p.M718Cfs*59	ENST00000340748		718	Atg/tg	23/40	1	2	FACETS	1	0.843	1	1	0.843	1	CLONAL	1	TRUE	1	0.17	2		737	515	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236086	108236086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782292	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	24	523	0	ENST00000278616.4:c.9022C>T	p.Arg3008Cys	p.R3008C	ENST00000278616	NM_000051.3	3008	Cgt/Tgt	63/63	0.189080174103133	4	FACETS	0.908	0.711	1	0.454	0.355	0.567	CLONAL	1	TRUE	2	0.17	4		523	364	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288785	33288785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765273333	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	43	415	0	ENST00000374542.5:c.767G>A	p.Arg256His	p.R256H	ENST00000374542	NM_001141970.1	256	cGc/cAc	3/8	0.380635817543891	4	FACETS	0.764	0.637	0.905	0.382	0.318	0.453	CLONAL	1	TRUE	2	0.17	4		415	775	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235390	235390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878854625	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	41	608	0	ENST00000264932.6:c.1196C>T	p.Pro399Leu	p.P399L	ENST00000264932	NM_004168.2	399	cCg/cTg	9/15	0.3	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.17	1		608	324	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101138	27101138	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1476360310	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	44	648	0	ENST00000324856.7:c.4420C>T	p.Gln1474Ter	p.Q1474*	ENST00000324856	NM_006015.4	1474	Caa/Taa	18/20	0.189080174103133	4	FACETS	1	0.841	1	0.502	0.42	0.593	CLONAL	1	TRUE	2	0.17	4		648	603	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732318	74732318	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	64	297	0	ENST00000359995.5:c.591G>T	p.Lys197Asn	p.K197N	ENST00000359995	NM_001195427.1	197	aaG/aaT	2/3	0.0977108156828079	3	FACETS	1	0.964	1	0.679	0.587	0.777	INDETERMINATE	1	TRUE	1	0.17	3		297	602	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801726	3801726	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs587783483	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	52	464	1	ENST00000262367.5:c.3779+1G>A		p.X1260_splice	ENST00000262367	NM_004380.2	1260			0.0977108156828079	3	FACETS	0.794	0.678	0.921	0.794	0.678	0.921	INDETERMINATE	2	TRUE	1	0.17	3		465	418	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717712	89717712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782350	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	51	455	0	ENST00000371953.3:c.737C>T	p.Pro246Leu	p.P246L	ENST00000371953	NM_000314.4	246	cCg/cTg	7/9	0.278151731510246	4	FACETS	1	0.85	1	0.501	0.425	0.585	CLONAL	1	TRUE	2	0.17	4		455	701	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032123	48032124	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs63751327	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	40	465	0	ENST00000234420.5:c.3514dup	p.Arg1172LysfsTer5	p.R1172Kfs*5	ENST00000234420	NM_000179.2	1171	-/A	6/10	0.156460713820058	5	FACETS	1	0.839	1	0.337	0.279	0.402	CLONAL	1	TRUE	2	0.17	5		465	584	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352354	73352354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	61	655	0	ENST00000377767.4:c.551C>T	p.Ala184Val	p.A184V	ENST00000377767	NM_014953.3	184	gCc/gTc	3/21	0.189080174103133	4	FACETS	1	0.962	1	0.68	0.587	0.782	CLONAL	1	TRUE	2	0.17	4		655	617	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978455	2978455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747972220	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	20	620	0	ENST00000396946.4:c.875G>A	p.Arg292His	p.R292H	ENST00000396946	NM_032415.4	292	cGc/cAc	7/25	0.3	0	FACETS	1	0.843	1			1	CLONAL	1	TRUE	0	0.17	0		620	173	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278407	39278407	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	55	696	2	ENST00000402219.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000402219	NM_005633.3	248	Cgc/Tgc	6/23	0.156460713820058	5	FACETS	1	0.871	1	0.34	0.29	0.396	CLONAL	1	TRUE	2	0.17	5		698	795	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38139044	38139044	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	81	721	1	ENST00000317025.8:c.3559C>T	p.Arg1187Ter	p.R1187*	ENST00000317025	NM_023034.1	1187	Cga/Tga	20/24	0.189080174103133	4	FACETS	1	0.939	1	0.556	0.489	0.629	CLONAL	1	TRUE	2	0.17	4		722	1002	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210754	5210754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768674983	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	18	671	0	ENST00000357368.4:c.5297G>A	p.Arg1766His	p.R1766H	ENST00000357368	NM_002850.3	1766	cGc/cAc	34/38	1	2	FACETS	0.773	0.582	0.998	0.773	0.582	0.998	CLONAL	1	TRUE	1	0.17	2		671	274	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348413	89348413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1289430140	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	20	942	1	ENST00000301030.4:c.4537G>A	p.Val1513Met	p.V1513M	ENST00000301030	NM_001256183.1	1513	Gtg/Atg	9/13	0.156460713820058	0	FACETS	0.535	0.408	0.684			1	SUBCLONAL	1	TRUE	0	0.17	0		943	365	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754886	29754886	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759426382	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	16	464	0	ENST00000389048.3:c.1049C>T	p.Ser350Leu	p.S350L	ENST00000389048	NM_004304.4	350	tCg/tTg	4/29	0.278151731510246	0	FACETS	0.596	0.441	0.782			1	SUBCLONAL	1	TRUE	0	0.17	0		464	262	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720693	89720693	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554825519	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	38	184	0	ENST00000371953.3:c.844G>T	p.Gly282Ter	p.G282*	ENST00000371953	NM_000314.4	282	Gga/Tga	8/9	0.278151731510246	4	FACETS	0.872	0.724	1	0.872	0.724	1	CLONAL	2	TRUE	2	0.17	4		184	300	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445268	29445268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	16	648	0	ENST00000389048.3:c.3457C>T	p.Pro1153Ser	p.P1153S	ENST00000389048	NM_004304.4	1153	Cct/Tct	22/29	0.278151731510246	0	FACETS	0.651	0.482	0.853			1	SUBCLONAL	1	TRUE	0	0.17	0		648	240	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3120995	3120995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1461947710	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	15	424	0	ENST00000078429.4:c.898C>T	p.Arg300Trp	p.R300W	ENST00000078429	NM_002067.2	300	Cgg/Tgg	7/7	1	2	FACETS	0.848	0.622	1	0.848	0.622	1	CLONAL	1	TRUE	1	0.17	2		424	208	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615748	1615748	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139492270	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	17	650	0	ENST00000344749.5:c.1523C>T	p.Thr508Met	p.T508M	ENST00000344749	NM_001136139.2	508	aCg/aTg	17/19	1	2	FACETS	0.595	0.443	0.776	0.595	0.443	0.776	SUBCLONAL	1	TRUE	1	0.17	2		650	336	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940370	49940370	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs891415020	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	45	607	1	ENST00000296474.3:c.673G>A	p.Ala225Thr	p.A225T	ENST00000296474	NM_002447.2	225	Gcc/Acc	1/20	0.156460713820058	5	FACETS	0.863	0.727	1	0.575	0.484	0.675	CLONAL	2	TRUE	2	0.17	5		608	385	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054361	13054361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	89	529	0	ENST00000316448.5:c.971G>A	p.Gly324Asp	p.G324D	ENST00000316448	NM_004343.3	324	gGc/gAc	8/9	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.17	2		529	766	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008503	70008503	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780721280	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	25	313	0	ENST00000394351.3:c.790G>A	p.Ala264Thr	p.A264T	ENST00000394351	NM_000248.3	264	Gca/Aca	8/9	0.156460713820058	5	FACETS	0.775	0.61	0.967	0.258	0.203	0.323	CLONAL	1	TRUE	2	0.17	5		313	476	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36826928	36826928	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	39	554	0	ENST00000373129.3:c.6G>T	p.Lys2Asn	p.K2N	ENST00000373129	NM_032017.1	2	aaG/aaT	3/12	0.189080174103133	4	FACETS	0.99	0.82	1	0.495	0.41	0.591	CLONAL	1	TRUE	2	0.17	4		554	542	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796192	45796192	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793656	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	27	417	0	ENST00000450313.1:c.1514G>A	p.Cys505Tyr	p.C505Y	ENST00000450313	NM_012222.2	505	tGt/tAt	15/16	0.189080174103133	4	FACETS	0.973	0.774	1	0.486	0.387	0.6	CLONAL	1	TRUE	2	0.17	4		417	382	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748052	72748052	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	27	507	0	ENST00000357731.5:c.126G>A	p.Trp42Ter	p.W42*	ENST00000357731	NM_173808.2	42	tgG/tgA	1/7	0.189080174103133	4	FACETS	0.786	0.624	0.971	0.393	0.312	0.486	CLONAL	1	TRUE	2	0.17	4		507	473	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262222	115262222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	51	371	2	ENST00000438362.2:c.2332G>A	p.Ala778Thr	p.A778T	ENST00000438362	NM_001242891.1	778	Gcc/Acc	18/20	0.189080174103133	4	FACETS	1	0.947	1	0.637	0.541	0.742	CLONAL	1	TRUE	2	0.17	4		373	551	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175581	108175581	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	43	340	0	ENST00000278616.4:c.5674+2T>C		p.X1892_splice	ENST00000278616	NM_000051.3	1892			0.189080174103133	4	FACETS	1	0.942	1	0.649	0.543	0.766	CLONAL	1	TRUE	2	0.17	4		340	456	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170327	119170327	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1393832618	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	23	274	1	ENST00000264033.4:c.2557G>A	p.Ala853Thr	p.A853T	ENST00000264033	NM_005188.3	853	Gcc/Acc	16/16	0.189080174103133	4	FACETS	0.816	0.635	1	0.408	0.317	0.513	CLONAL	1	TRUE	2	0.17	4		275	388	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644599	21644599	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	55	612	0	ENST00000421138.2:c.68T>C	p.Ile23Thr	p.I23T	ENST00000421138		23	aTt/aCt	4/16	0.429142599754643	4	FACETS	1	0.952	1	0.643	0.549	0.745	CLONAL	1	TRUE	2	0.17	4		612	589	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888240	112888240	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs925129380	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	29	511	1	ENST00000351677.2:c.256G>A	p.Gly86Arg	p.G86R	ENST00000351677	NM_002834.3	86	Ggg/Agg	3/16	0.3	1	FACETS	0.865	0.694	1	0.865	0.694	1	CLONAL	1	TRUE	0	0.17	1		512	361	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103525652	103525652	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	36	443	0	ENST00000355739.4:c.2923G>A	p.Glu975Lys	p.E975K	ENST00000355739	NM_000123.3	975	Gaa/Aaa	14/15	0.189080174103133	4	FACETS	0.989	0.812	1	0.495	0.406	0.594	CLONAL	1	TRUE	2	0.17	4		443	501	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061021	38061021	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	14	204	0	ENST00000250448.2:c.968C>T	p.Ala323Val	p.A323V	ENST00000250448	NM_004496.3	323	gCg/gTg	2/2	0.189080174103133	3	FACETS	1	0.847	1	0.638	0.464	0.846	CLONAL	1	TRUE	1	0.17	3		204	140	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035347	42035347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746038976	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	47	487	0	ENST00000219905.7:c.5189G>A	p.Ser1730Asn	p.S1730N	ENST00000219905	NM_001164273.1	1730	aGt/aAt	15/24	0.156460713820058	5	FACETS	0.887	0.751	1	0.592	0.5	0.692	CLONAL	2	TRUE	2	0.17	5		487	391	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656571	3656571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766080551	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	39	847	1	ENST00000294008.3:c.664G>A	p.Glu222Lys	p.E222K	ENST00000294008	NM_032444.2	222	Gag/Aag	3/15	0.0977108156828079	3	FACETS	0.8	0.662	0.955	0.4	0.331	0.478	INDETERMINATE	1	TRUE	1	0.17	3		848	622	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984289	7984289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	21	528	0	ENST00000319144.4:c.440G>A	p.Arg147Gln	p.R147Q	ENST00000319144	NM_001139.2	147	cGa/cAa	4/15	0.156460713820058	5	FACETS	0.934	0.719	1	0.311	0.239	0.395	CLONAL	1	TRUE	2	0.17	5		528	332	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78599576	78599576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465623616	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	22	446	0	ENST00000306801.3:c.248G>A	p.Arg83His	p.R83H	ENST00000306801	NM_020761.2	83	cGc/cAc	2/34	0.0977108156828079	3	FACETS	0.812	0.629	1	0.406	0.314	0.512	INDETERMINATE	1	TRUE	1	0.17	3		446	346	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272452	15272452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	40	849	0	ENST00000263388.2:c.5987C>T	p.Ala1996Val	p.A1996V	ENST00000263388	NM_000435.2	1996	gCc/gTc	33/33	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.17	2		849	328	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18960942	18960942	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	28	640	0	ENST00000262803.5:c.520G>A	p.Gly174Arg	p.G174R	ENST00000262803	NM_002911.3	174	Ggg/Agg	4/24	1	2	FACETS	0.688	0.549	0.847	0.688	0.549	0.847	SUBCLONAL	1	TRUE	1	0.17	2		640	479	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968184	18968184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765018756	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	25	574	1	ENST00000262803.5:c.2024C>T	p.Ala675Val	p.A675V	ENST00000262803	NM_002911.3	675	gCg/gTg	15/24	1	2	FACETS	0.868	0.684	1	0.868	0.684	1	CLONAL	1	TRUE	1	0.17	2		575	339	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39214697	39214697	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	37	446	0	ENST00000402219.2:c.3427G>T	p.Gly1143Cys	p.G1143C	ENST00000402219	NM_005633.3	1143	Ggc/Tgc	22/23	0.156460713820058	5	FACETS	0.837	0.688	1	0.279	0.229	0.335	CLONAL	1	TRUE	2	0.17	5		446	653	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39250172	39250172	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	65	797	0	ENST00000402219.2:c.1397G>T	p.Gly466Val	p.G466V	ENST00000402219	NM_005633.3	466	gGc/gTc	10/23	0.156460713820058	5	FACETS	0.886	0.766	1	0.295	0.255	0.34	CLONAL	1	TRUE	2	0.17	5		797	1083	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99163099	99163099	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	27	495	0	ENST00000074304.5:c.1105G>T	p.Gly369Cys	p.G369C	ENST00000074304	NM_001134224.1	369	Ggt/Tgt	13/26	0.238726836472684	0	FACETS	0.714	0.569	0.881			1	SUBCLONAL	1	TRUE	0	0.17	0		495	369	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104638	209104638	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1040177874	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	26	533	2	ENST00000345146.2:c.940C>T	p.Arg314Cys	p.R314C	ENST00000345146	NM_005896.2	314	Cgt/Tgt	8/10	0.189080174103133	4	FACETS	0.706	0.558	0.876	0.353	0.279	0.438	SUBCLONAL	1	TRUE	2	0.17	4		535	507	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259390	36259390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	31	431	2	ENST00000300305.3:c.101C>T	p.Ala34Val	p.A34V	ENST00000300305		34	gCc/gTc	3/8	1	2	FACETS	0.677	0.546	0.825	0.677	0.546	0.825	SUBCLONAL	1	TRUE	1	0.17	2		433	539	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523626	41523626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	32	670	0	ENST00000263253.7:c.1042G>A	p.Ala348Thr	p.A348T	ENST00000263253	NM_001429.3	348	Gct/Act	4/31	0.0977108156828079	3	FACETS	0.71	0.575	0.864	0.355	0.287	0.432	INDETERMINATE	1	TRUE	1	0.17	3		670	575	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572910	41572910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	37	650	1	ENST00000263253.7:c.5195G>A	p.Arg1732His	p.R1732H	ENST00000263253	NM_001429.3	1732	cGc/cAc	31/31	0.0977108156828079	3	FACETS	1	0.843	1	0.512	0.422	0.613	INDETERMINATE	1	TRUE	1	0.17	3		651	461	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277984	41277984	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	21	377	0	ENST00000349496.5:c.1948G>T	p.Gly650Cys	p.G650C	ENST00000349496	NM_001904.3	650	Ggt/Tgt	12/15	0.156460713820058	5	FACETS	1	0.863	1	0.393	0.303	0.498	CLONAL	1	TRUE	2	0.17	5		377	263	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259590	89259590	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	21	430	0	ENST00000336596.2:c.734G>A	p.Ser245Asn	p.S245N	ENST00000336596	NM_005233.5	245	aGt/aAt	3/17	0.156460713820058	5	FACETS	0.838	0.645	1	0.279	0.215	0.355	CLONAL	1	TRUE	2	0.17	5		430	370	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456506	89456506	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs139544432	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	28	509	0	ENST00000336596.2:c.1682A>G	p.Tyr561Cys	p.Y561C	ENST00000336596	NM_005233.5	561	tAt/tGt	8/17	0.156460713820058	5	FACETS	1	0.824	1	0.345	0.275	0.424	CLONAL	1	TRUE	2	0.17	5		509	400	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670256	134670256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	17	455	1	ENST00000398015.3:c.167G>A	p.Arg56His	p.R56H	ENST00000398015	NM_004441.4	56	cGc/cAc	3/16	0.3	0	FACETS	0.722	0.54	0.937			1	CLONAL	1	TRUE	0	0.17	0		456	230	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582062	189582062	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	42	441	0	ENST00000264731.3:c.621G>T	p.Lys207Asn	p.K207N	ENST00000264731	NM_003722.4	207	aaG/aaT	5/14	0.156460713820058	5	FACETS	0.751	0.628	0.887	0.5	0.418	0.592	SUBCLONAL	2	TRUE	2	0.17	5		441	413	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961390	1961390	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	40	525	0	ENST00000382891.5:c.3178C>T	p.Arg1060Cys	p.R1060C	ENST00000382891	NM_133335.3	1060	Cgc/Tgc	17/22	0.156460713820058	0	FACETS	1	0.868	1			1	CLONAL	1	TRUE	0	0.17	0		525	372	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1255462	1255462	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	14	625	0	ENST00000310581.5:c.3097C>A	p.Leu1033Met	p.L1033M	ENST00000310581	NM_198253.2	1033	Ctg/Atg	14/16	0.3	0	FACETS	0.608	0.439	0.811			1	SUBCLONAL	1	TRUE	0	0.17	0		625	225	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31448689	31448689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	45	627	0	ENST00000344624.3:c.2847G>A	p.Met949Ile	p.M949I	ENST00000344624		949	atG/atA	20/33	0.3	1	FACETS	0.911	0.765	1	0.911	0.765	1	CLONAL	1	TRUE	0	0.17	1		627	532	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183226	56183226	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	33	481	0	ENST00000399503.3:c.4136G>T	p.Ser1379Ile	p.S1379I	ENST00000399503	NM_005921.1	1379	aGc/aTc	18/20	0.608786202927387	4	FACETS	0.851	0.692	1	0.425	0.346	0.515	CLONAL	1	TRUE	2	0.17	4		481	534	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687017	176687017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	32	504	0	ENST00000439151.2:c.4994C>T	p.Pro1665Leu	p.P1665L	ENST00000439151	NM_022455.4	1665	cCt/cTt	14/23	0.189080174103133	3	FACETS	0.775	0.628	0.942	0.388	0.314	0.471	CLONAL	1	TRUE	1	0.17	3		504	527	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176710893	176710893	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	29	548	1	ENST00000439151.2:c.6115C>T	p.Arg2039Cys	p.R2039C	ENST00000439151	NM_022455.4	2039	Cgt/Tgt	20/23	0.189080174103133	3	FACETS	0.726	0.581	0.891	0.363	0.29	0.446	SUBCLONAL	1	TRUE	1	0.17	3		549	510	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271234	26271234	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1372616476	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	46	427	0	ENST00000305910.3:c.379C>T	p.Leu127Phe	p.L127F	ENST00000305910	NM_003534.2	127	Ctc/Ttc	1/1	0.3	18	FACETS	1	0.954	1			1	CLONAL	1	TRUE	NA	0.17	18		427	900	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670650	30670650	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748328915	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	44	440	1	ENST00000376406.3:c.5870G>A	p.Arg1957His	p.R1957H	ENST00000376406	NM_014641.2	1957	cGc/cAc	13/15	0.380635817543891	4	FACETS	1	0.924	1	0.591	0.496	0.697	CLONAL	1	TRUE	2	0.17	4		441	512	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673128	30673128	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1464712448	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	32	648	0	ENST00000376406.3:c.3832G>A	p.Val1278Ile	p.V1278I	ENST00000376406	NM_014641.2	1278	Gtc/Atc	10/15	0.380635817543891	4	FACETS	0.719	0.582	0.874	0.359	0.291	0.437	SUBCLONAL	1	TRUE	2	0.17	4		648	613	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287797	33287797	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1545	87	876	2	ENST00000374542.5:c.1456G>T	p.Ala486Ser	p.A486S	ENST00000374542	NM_001141970.1	486	Gca/Tca	5/8	0.380635817543891	4	FACETS	0.734	0.647	0.828	0.367	0.323	0.414	SUBCLONAL	1	TRUE	2	0.17	4		878	1632	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683840	117683840	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	41	600	1	ENST00000368508.3:c.3307G>A	p.Ala1103Thr	p.A1103T	ENST00000368508	NM_002944.2	1103	Gct/Act	21/43	1	2	FACETS	0.929	0.774	1	0.929	0.774	1	CLONAL	1	TRUE	1	0.17	2		601	519	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004998	150004998	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	38	533	0	ENST00000253339.5:c.1227G>A	p.Met409Ile	p.M409I	ENST00000253339		409	atG/atA	3/7	0.487441664452982	4	FACETS	1	0.913	1	0.589	0.487	0.703	CLONAL	1	TRUE	2	0.17	4		533	444	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528505	157528505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	37	588	0	ENST00000346085.5:c.6230C>T	p.Ser2077Leu	p.S2077L	ENST00000346085	NM_020732.3	2077	tCg/tTg	20/20	0.487441664452982	4	FACETS	0.959	0.79	1	0.48	0.395	0.575	CLONAL	1	TRUE	2	0.17	4		588	531	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509723	106509723	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	24	547	0	ENST00000359195.3:c.1717G>A	p.Glu573Lys	p.E573K	ENST00000359195	NM_002649.2	573	Gaa/Aaa	2/11	0.189080174103133	4	FACETS	0.734	0.574	0.919	0.367	0.287	0.46	CLONAL	1	TRUE	2	0.17	4		547	450	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878670	151878670	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs140719911	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	19	523	0	ENST00000262189.6:c.6275A>G	p.Asp2092Gly	p.D2092G	ENST00000262189	NM_170606.2	2092	gAt/gGt	36/59	0.189080174103133	4	FACETS	0.705	0.534	0.906	0.352	0.267	0.453	CLONAL	1	TRUE	2	0.17	4		523	371	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372432	55372432	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	55	756	0	ENST00000297316.4:c.1122G>T	p.Glu374Asp	p.E374D	ENST00000297316	NM_022454.3	374	gaG/gaT	2/2	0.189080174103133	4	FACETS	0.968	0.826	1	0.484	0.413	0.562	CLONAL	1	TRUE	2	0.17	4		756	782	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8460534	8460534	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	27	521	0	ENST00000356435.5:c.3752T>C	p.Val1251Ala	p.V1251A	ENST00000356435		1251	gTg/gCg	22/35	1	2	FACETS	0.629	0.499	0.778	0.629	0.499	0.778	SUBCLONAL	1	TRUE	1	0.17	2		521	505	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243872	53243872	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1261132692	NA	P-0037690-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	33	682	1	ENST00000375401.3:c.1121C>T	p.Ala374Val	p.A374V	ENST00000375401	NM_004187.3	374	gCg/gTg	8/26	0.156460713820058	0	FACETS	0.876	0.714	1			1	CLONAL	1	TRUE	0	0.17	0		683	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0037756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	92	863	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.523433510187668	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.573451389316683	2		863	155	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271819	15271820	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	-	novel	NA	P-0037756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	47	879	0	ENST00000263388.2:c.6619_6620del	p.Arg2207AlafsTer34	p.R2207Afs*34	ENST00000263388	NM_000435.2	2207	CGg/g	33/33	0.523433510187668	2	FACETS	0.891	0.784	0.998	0.891	0.784	0.998	CLONAL	2	TRUE	0	0.573451389316683	2		879	92	SUCCESS
AXL	558	MSKCC	GRCh37	19	41759571	41759571	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037756-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	10	771	1	ENST00000301178.4:c.1994C>A	p.Thr665Asn	p.T665N	ENST00000301178	NM_021913.4	665	aCc/aAc	17/20	0.301776241342169	6	FACETS	0.4	0.271	0.563	0.1	0.067	0.141	INDETERMINATE	1	TRUE	2	0.573451389316683	6		772	187	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0037759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	295	608	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.610464501591503	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.611386782073812	1		611	651	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524595	103524595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756972065	NA	P-0037759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	127	254	0	ENST00000355739.4:c.2726C>T	p.Pro909Leu	p.P909L	ENST00000355739	NM_000123.3	909	cCt/cTt	13/15	0.610464501591503	1	FACETS	0.937	0.862	1	0.937	0.862	1	CLONAL	1	TRUE	0	0.611386782073812	1		254	308	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491669	56491669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	216	405	0	ENST00000267101.3:c.2561G>T	p.Gly854Val	p.G854V	ENST00000267101	NM_001982.3	854	gGt/gTt	21/28	0.610464501591503	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.611386782073812	1		405	470	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993848	72993848	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	226	460	0	ENST00000268489.5:c.197C>G	p.Ala66Gly	p.A66G	ENST00000268489	NM_006885.3	66	gCg/gGg	2/10	0.610464501591503	3	FACETS	1	0.943	1	0.506	0.472	0.542	CLONAL	1	TRUE	1	0.611386782073812	3		460	953	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868412	45868412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770334103	NA	P-0037759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	299	688	0	ENST00000391945.4:c.365C>T	p.Thr122Ile	p.T122I	ENST00000391945	NM_000400.3	122	aCa/aTa	6/23	1	2	FACETS	0.995	0.939	1	0.995	0.939	1	CLONAL	1	TRUE	1	0.611386782073812	2		688	983	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564603	55564603	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	156	678	0	ENST00000288135.5:c.491C>G	p.Pro164Arg	p.P164R	ENST00000288135	NM_000222.2	164	cCt/cGt	3/21	1	2	FACETS	0.569	0.521	0.619	0.569	0.521	0.619	SUBCLONAL	1	TRUE	1	0.611386782073812	2		678	897	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665309	176665309	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	214	366	0	ENST00000439151.2:c.3993C>G	p.Asp1331Glu	p.D1331E	ENST00000439151	NM_022455.4	1331	gaC/gaG	7/23	0.610464501591503	2	FACETS	1	0.95	1	0.51	0.476	0.545	CLONAL	1	TRUE	0	0.611386782073812	2		366	686	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099218	157099218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537376978	NA	P-0037759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	167	508	0	ENST00000346085.5:c.155C>T	p.Ser52Leu	p.S52L	ENST00000346085	NM_020732.3	52	tCg/tTg	1/20	0.610464501591503	3	FACETS	0.839	0.772	0.91	0.42	0.386	0.455	CLONAL	1	TRUE	1	0.611386782073812	3		508	850	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976136	18976172	+	protein_altering_variant	In_Frame_Del	DEL	ATTGGCATGATCAGTGCCGGCCCTAGCCACGTGGCTG	ATTGGCATGATCAGTGCCGGCCCTAGCCACGTGGCTG	C	novel	NA	P-0037759-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	300	934	0	ENST00000262803.5:c.2896_2932delinsC	p.Ile966_Ala978delinsPro	p.I966_A978delinsP	ENST00000262803	NM_002911.3	966	ATTGGCATGATCAGTGCCGGCCCTAGCCACGTGGCTGcc/Ccc	21/24	0.610464501591503	3	FACETS	0.853	0.801	0.906	0.426	0.4	0.453	CLONAL	1	TRUE	1	0.611386782073812	3		934	1503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0037759-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	147	608	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.438547809128829	1	FACETS	0.858	0.787	0.932	0.858	0.787	0.932	CLONAL	1	TRUE	0	0.450542164093758	1		611	589	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524595	103524595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756972065	NA	P-0037759-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	67	254	0	ENST00000355739.4:c.2726C>T	p.Pro909Leu	p.P909L	ENST00000355739	NM_000123.3	909	cCt/cTt	13/15	0.39455654373686	1	FACETS	0.918	0.808	1	0.918	0.808	1	CLONAL	1	TRUE	0	0.450542164093758	1		254	251	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491669	56491669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037759-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	114	405	0	ENST00000267101.3:c.2561G>T	p.Gly854Val	p.G854V	ENST00000267101	NM_001982.3	854	gGt/gTt	21/28	0.259958170606163	2	FACETS	1	0.973	1	0.6	0.544	0.658	INDETERMINATE	1	TRUE	0	0.450542164093758	2		405	422	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993848	72993848	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037759-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	122	460	0	ENST00000268489.5:c.197C>G	p.Ala66Gly	p.A66G	ENST00000268489	NM_006885.3	66	gCg/gGg	2/10	0.450542164093758	3	FACETS	1	0.952	1	0.539	0.489	0.593	CLONAL	1	TRUE	1	0.450542164093758	3		460	615	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868412	45868412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770334103	NA	P-0037759-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	167	688	0	ENST00000391945.4:c.365C>T	p.Thr122Ile	p.T122I	ENST00000391945	NM_000400.3	122	aCa/aTa	6/23	0.195948404441745	3	FACETS	1	0.975	1	0.574	0.528	0.622	INDETERMINATE	1	TRUE	1	0.450542164093758	3		688	791	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665309	176665309	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037759-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	98	366	0	ENST00000439151.2:c.3993C>G	p.Asp1331Glu	p.D1331E	ENST00000439151	NM_022455.4	1331	gaC/gaG	7/23	0.313486145353557	3	FACETS	1	0.97	1	0.406	0.364	0.45	CLONAL	1	TRUE	0	0.450542164093758	3		366	438	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099218	157099218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537376978	NA	P-0037759-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	178	508	0	ENST00000346085.5:c.155C>T	p.Ser52Leu	p.S52L	ENST00000346085	NM_020732.3	52	tCg/tTg	1/20	0.351984896266303	4	FACETS	1	0.975	1	0.57	0.525	0.617	CLONAL	1	TRUE	2	0.450542164093758	4		508	1005	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268503	46268503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777114269	NA	P-0037759-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	46	289	0	ENST00000371998.3:c.2890C>T	p.Arg964Trp	p.R964W	ENST00000371998		964	Cgg/Tgg	15/23	NA	2	FACETS	0.521	0.439	0.61			1	INDETERMINATE	1	TRUE	NA	0.450542164093758	2		289	392	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976137	18976172	+	frameshift_variant	Frame_Shift_Del	DEL	TTGGCATGATCAGTGCCGGCCCTAGCCACGTGGCTG	TTGGCATGATCAGTGCCGGCCCTAGCCACGTGGCTG	C	novel	NA	P-0037759-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	186	707	0	ENST00000262803.5:c.2897_2932delinsC	p.Ile966ThrfsTer57	p.I966Tfs*57	ENST00000262803	NM_002911.3	966	aTTGGCATGATCAGTGCCGGCCCTAGCCACGTGGCTGcc/aCcc	21/24	0.450542164093758	3	FACETS	0.942	0.869	1	0.471	0.434	0.509	CLONAL	1	TRUE	1	0.450542164093758	3		707	1074	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129645	11129645	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	422	538	0	ENST00000358026.2:c.2451C>A	p.Asn817Lys	p.N817K	ENST00000358026	NM_001128849.1	817	aaC/aaA	17/36	1	2	FACETS	0.997	0.953	1	0.997	0.953	1	CLONAL	1	TRUE	1	0.837840780816112	2		538	1010	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799272	42799272	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037772-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	336	598	2	ENST00000575354.2:c.4756C>T	p.Pro1586Ser	p.P1586S	ENST00000575354	NM_015125.3	1586	Cct/Tct	20/20	1	2	FACETS	0.876	0.831	0.921	0.876	0.831	0.921	CLONAL	1	TRUE	1	0.837840780816112	2		600	916	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0037810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	624	728	0	ENST00000269305.4:c.672+1G>C		p.X224_splice	ENST00000269305	NM_001126112.2	224			0.670494800467628	2	FACETS	0.979	0.952	1	0.979	0.952	1	CLONAL	2	TRUE	0	0.684540103345949	2		728	931	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807978	3808016	+	frameshift_variant	Frame_Shift_Del	DEL	GTATTGCCCTGTGTCCAGCTTCCGCTTGATGGTGGAGAG	GTATTGCCCTGTGTCCAGCTTCCGCTTGATGGTGGAGAG	A	novel	NA	P-0037810-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	122	617	0	ENST00000262367.5:c.3403_3441delinsT	p.Leu1135SerfsTer21	p.L1135Sfs*21	ENST00000262367	NM_004380.2	1135	CTCTCCACCATCAAGCGGAAGCTGGACACAGGGCAATAC/T	18/31	0.684540103345949	1	FACETS	0.612	0.559	0.667	0.612	0.559	0.667	SUBCLONAL	1	TRUE	0	0.684540103345949	1		617	383	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0037835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	144	290	2	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.252752363339897	3	FACETS	0.844	0.774	0.916	1	0.982	1	CLONAL	3	TRUE	1	0.252752363339897	3		292	507	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911012	32911012	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	66	496	0	ENST00000380152.3:c.2520G>C	p.Met840Ile	p.M840I	ENST00000380152		840	atG/atC	11/27	0.228893282806448	1	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	0	0.252752363339897	1		496	437	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873738	35873738	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	103	589	0	ENST00000216797.5:c.113A>G	p.Lys38Arg	p.K38R	ENST00000216797	NM_020529.2	38	aAa/aGa	1/6	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.252752363339897	2		589	627	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857460	68857460	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121964874	NA	P-0037835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	112	605	0	ENST00000261769.5:c.2095C>T	p.Gln699Ter	p.Q699*	ENST00000261769	NM_004360.3	699	Cag/Tag	13/16	0.252752363339897	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.252752363339897	1		605	636	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0037860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	349	564	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.826712614346482	2	FACETS	0.982	0.954	1	0.982	0.954	1	CLONAL	2	TRUE	0	0.830363688127645	2		564	428	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0037860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	158	464	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	0.855	0.791	0.921	0.855	0.791	0.921	CLONAL	1	TRUE	1	0.830363688127645	2		465	445	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0037860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	136	270	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	0.952	0.878	1	0.952	0.878	1	CLONAL	1	TRUE	1	0.830363688127645	2		270	344	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439698	51439698	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1216520571	NA	P-0037860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	119	406	0	ENST00000262662.1:c.263C>G	p.Thr88Ser	p.T88S	ENST00000262662		88	aCt/aGt	4/4	1	2	FACETS	0.848	0.775	0.923	0.848	0.775	0.923	CLONAL	1	TRUE	1	0.830363688127645	2		406	338	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222174	5222174	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	256	601	0	ENST00000357368.4:c.3161G>T	p.Trp1054Leu	p.W1054L	ENST00000357368	NM_002850.3	1054	tGg/tTg	19/38	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.830363688127645	2		601	597	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0037864-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	905	790	2	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	0.825714857998703	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.825714857998703	1		792	1166	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210523	36211102	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTAGCCTCTGTCAGTTGCCGAATGTGTTCTGTGTTCAGAGTCCAAGCTAGTCTGGGCAGCGGGGGAAACACACAAGCAAGACTTAGTCCCTGCCCTCCTGGAGCGCCTTCCTCTGTGTGTAGGGCTGGCTTGATCCATCTCCCCACAACTATTCTCCTTTTAGGTCGAGCGCCCCGAGGTCGGGGTCGCAAGCATAAGACGACCCCCCTTCCTCCTCCTCGCCTAGCAGATGTGGCTCCTACCCCCCCAAAGACCCCTGCCCGGAAACGGGGTGAGGAAGGCACAGAACGGATGGTGCAGGCACTGACTGAACTTCTCCGGCGGGCCCAGGCACCCCAAGCACCCCGGAGCCGGGCATGTGAGCCCTCCACCCCCCGGCGGTCTCGGGGACGGCCCCCAGGACGGCCAGCAGGCCCCTGCAGGAGGAAGCAGCAAGCAGTAGTGGTGGCAGAAGCAGCTGTGACAATCCCCAAACCTGAGCCCCCACCTCCTGTGGTTCCAGTGAAACATCAGACTGGCAGCTGGAAATGCAAGGAGGGGCCCGGTCCAGGACCTGGGACCCCCAGGCGTGGAGGACAGT	CTAGCCTCTGTCAGTTGCCGAATGTGTTCTGTGTTCAGAGTCCAAGCTAGTCTGGGCAGCGGGGGAAACACACAAGCAAGACTTAGTCCCTGCCCTCCTGGAGCGCCTTCCTCTGTGTGTAGGGCTGGCTTGATCCATCTCCCCACAACTATTCTCCTTTTAGGTCGAGCGCCCCGAGGTCGGGGTCGCAAGCATAAGACGACCCCCCTTCCTCCTCCTCGCCTAGCAGATGTGGCTCCTACCCCCCCAAAGACCCCTGCCCGGAAACGGGGTGAGGAAGGCACAGAACGGATGGTGCAGGCACTGACTGAACTTCTCCGGCGGGCCCAGGCACCCCAAGCACCCCGGAGCCGGGCATGTGAGCCCTCCACCCCCCGGCGGTCTCGGGGACGGCCCCCAGGACGGCCAGCAGGCCCCTGCAGGAGGAAGCAGCAAGCAGTAGTGGTGGCAGAAGCAGCTGTGACAATCCCCAAACCTGAGCCCCCACCTCCTGTGGTTCCAGTGAAACATCAGACTGGCAGCTGGAAATGCAAGGAGGGGCCCGGTCCAGGACCTGGGACCCCCAGGCGTGGAGGACAGT	-	novel	NA	P-0037881-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	195	237	0	ENST00000222270.7:c.436+81_854del		p.X146_splice	ENST00000222270	NM_014727.1	146		3/37	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		237	352	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843449	156843449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764645590	NA	P-0037891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	236	483	0	ENST00000524377.1:c.875C>T	p.Thr292Met	p.T292M	ENST00000524377	NM_002529.3	292	aCg/aTg	8/17	0.20489116680938	6	FACETS	0.96	0.903	1	0.96	0.903	1	INDETERMINATE	3	TRUE	3	0.584264468218497	6		483	608	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416668	416668	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	102	284	0	ENST00000399788.2:c.3882G>T	p.Lys1294Asn	p.K1294N	ENST00000399788	NM_001042603.1	1294	aaG/aaT	23/28	0.584264468218497	6	FACETS	1	0.972	1	0.313	0.28	0.348	CLONAL	1	TRUE	2	0.584264468218497	6		284	605	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578264	7578268	+	frameshift_variant	Frame_Shift_Del	DEL	GATAA	GATAA	-	novel	NA	P-0037891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	257	529	0	ENST00000269305.4:c.581_585del	p.Leu194ProfsTer13	p.L194Pfs*13	ENST00000269305	NM_001126112.2	194	cTTATC/c	6/11	0.584264468218497	2	FACETS	0.926	0.879	0.972	0.926	0.879	0.972	CLONAL	2	TRUE	0	0.584264468218497	2		529	475	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972860	25972860	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	87	383	0	ENST00000435504.4:c.1565T>G	p.Val522Gly	p.V522G	ENST00000435504		522	gTt/gGt	12/13	0.523171016876777	2	FACETS	0.745	0.663	0.83	0.372	0.331	0.415	SUBCLONAL	1	TRUE	0	0.584264468218497	2		383	400	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39234250	39234250	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	114	403	0	ENST00000402219.2:c.2595G>C	p.Leu865Phe	p.L865F	ENST00000402219	NM_005633.3	865	ttG/ttC	16/23	0.584264468218497	3	FACETS	0.896	0.809	0.986	0.448	0.404	0.493	CLONAL	1	TRUE	1	0.584264468218497	3		403	563	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084153	47084153	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	266	350	0	ENST00000409792.3:c.7136C>G	p.Pro2379Arg	p.P2379R	ENST00000409792	NM_014159.6	2379	cCg/cGg	17/21	0.257859953554612	6	FACETS	0.931	0.889	0.972	0.776	0.741	0.81	INDETERMINATE	5	TRUE	0	0.584264468218497	6		350	424	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876227	35876227	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	99	468	0	ENST00000303115.3:c.1019T>C	p.Leu340Pro	p.L340P	ENST00000303115	NM_002185.3	340	cTt/cCt	8/8	0.584264468218497	3	FACETS	0.982	0.881	1	0.491	0.44	0.544	CLONAL	1	TRUE	1	0.584264468218497	3		468	446	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386621	81386621	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0037891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	46	244	0	ENST00000222390.5:c.368-2A>T		p.X123_splice	ENST00000222390	NM_000601.4	123			0.584264468218497	3	FACETS	0.759	0.644	0.885	0.38	0.322	0.443	SUBCLONAL	1	TRUE	1	0.584264468218497	3		244	268	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859545	151859560	+	frameshift_variant	Frame_Shift_Del	DEL	TTGTCTACTTCTGAAT	TTGTCTACTTCTGAAT	-	novel	NA	P-0037891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	96	373	0	ENST00000262189.6:c.11102_11117del	p.Asn3701SerfsTer13	p.N3701Sfs*13	ENST00000262189	NM_170606.2	3701	aATTCAGAAGTAGACAAg/ag	43/59	0.584264468218497	3	FACETS	0.886	0.793	0.985	0.443	0.396	0.493	CLONAL	1	TRUE	1	0.584264468218497	3		373	479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0037904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	322	727	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.534826409685303	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.534826409685303	2		728	570	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0037904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	344	264	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	0.284831555252615	6	FACETS	0.932	0.9	0.963			1	INDETERMINATE	6	TRUE	NA	0.534826409685303	6		264	476	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508082	106508082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	48	204	0	ENST00000359195.3:c.76C>T	p.Arg26Cys	p.R26C	ENST00000359195	NM_002649.2	26	Cgc/Tgc	2/11	0.4872456116949	3	FACETS	1	0.916	1	0.552	0.472	0.638	CLONAL	1	TRUE	1	0.534826409685303	3		204	206	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861143	57861143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772799269	NA	P-0037904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	331	393	1	ENST00000228682.2:c.940C>T	p.Arg314Cys	p.R314C	ENST00000228682	NM_005269.2	314	Cgc/Tgc	9/12	0.534826409685303	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.534826409685303	3		394	717	SUCCESS
APC	324	MSKCC	GRCh37	5	112175287	112175288	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0037904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	136	206	0	ENST00000257430.4:c.3999dup	p.Ser1334IlefsTer8	p.S1334Ifs*8	ENST00000257430	NM_000038.5	1332	-/A	16/16	0.534826409685303	3	FACETS	0.903	0.842	0.962	0.903	0.842	0.962	CLONAL	3	TRUE	0	0.534826409685303	3		206	238	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446069	49446069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs952760497	NA	P-0037904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	441	694	0	ENST00000301067.7:c.1397G>A	p.Arg466His	p.R466H	ENST00000301067	NM_003482.3	466	cGc/cAc	10/54	0.534826409685303	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.534826409685303	3		694	962	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992051	72992051	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	105	444	0	ENST00000268489.5:c.1994G>T	p.Arg665Leu	p.R665L	ENST00000268489	NM_006885.3	665	cGt/cTt	2/10	0.534826409685303	2	FACETS	0.939	0.848	1	0.47	0.424	0.518	CLONAL	1	TRUE	0	0.534826409685303	2		444	418	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260142	149260142	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	86	345	0	ENST00000360632.3:c.751C>T	p.Gln251Ter	p.Q251*	ENST00000360632	NM_015472.4	251	Caa/Taa	4/7	0.4872456116949	3	FACETS	0.973	0.865	1	0.486	0.432	0.543	CLONAL	1	TRUE	1	0.534826409685303	3		345	419	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1555525857	NA	P-0037909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	301	508	0	ENST00000269305.4:c.596G>T	p.Gly199Val	p.G199V	ENST00000269305	NM_001126112.2	199	gGa/gTa	6/11	NA	2	FACETS	0.999	0.968	1			1	INDETERMINATE	2	TRUE	NA	0.807999709990843	2		508	373	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18975016	18975016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761111860	NA	P-0037909-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	34	345	3	ENST00000262803.5:c.2813G>A	p.Arg938Gln	p.R938Q	ENST00000262803	NM_002911.3	938	cGg/cAg	20/24	0.555154222013201	4	FACETS	0.329	0.269	0.398	0.11	0.089	0.133	SUBCLONAL	1	TRUE	1	0.807999709990843	4		348	462	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543197	65543197	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037918-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	10	289	0	ENST00000358664.4:c.480C>G	p.Ser160Arg	p.S160R	ENST00000358664	NM_002382.4	160	agC/agG	5/5	0.738129640996062	1	FACETS	0.094	0.063	0.132	0.094	0.063	0.132	SUBCLONAL	1	TRUE	0	0.738129640996062	1		289	182	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0037919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	22	242	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.44	0.34	0.555	0.44	0.34	0.555	SUBCLONAL	1	TRUE	1	0.29	2		242	345	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578194	7578195	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAC	novel	NA	P-0037919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	58	780	0	ENST00000269305.4:c.652_654dup	p.Val218dup	p.V218dup	ENST00000269305	NM_001126112.2	218	-/GTG	6/11	1	2	FACETS	0.605	0.519	0.699	0.605	0.519	0.699	SUBCLONAL	1	TRUE	1	0.29	2		780	661	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267351	41267351	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037919-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	19	193	0	ENST00000349496.5:c.935A>T	p.Lys312Met	p.K312M	ENST00000349496	NM_001904.3	312	aAg/aTg	6/15	0.176672012039081	3	FACETS	0.714	0.544	0.913	0.357	0.272	0.457	CLONAL	1	TRUE	1	0.29	3		193	210	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	201	381	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.405831101531377	4	FACETS	0.842	0.787	0.898			1	CLONAL	3	TRUE	NA	0.428052193298887	4		381	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578266	7578266	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs942158624	NA	P-0037920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	213	648	0	ENST00000269305.4:c.583A>T	p.Ile195Phe	p.I195F	ENST00000269305	NM_001126112.2	195	Atc/Ttc	6/11	0.344924738013218	2	FACETS	0.769	0.718	0.821	0.769	0.718	0.821	SUBCLONAL	2	TRUE	0	0.428052193298887	2		648	647	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012389	29012389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161996687	NA	P-0037920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	154	481	2	ENST00000282397.4:c.482C>T	p.Thr161Met	p.T161M	ENST00000282397	NM_002019.4	161	aCg/aTg	4/30	0.239754215750867	4	FACETS	0.872	0.802	0.945	0.872	0.802	0.945	INDETERMINATE	2	TRUE	2	0.428052193298887	4		483	589	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473732	67473732	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	420	695	0	ENST00000327367.4:c.812T>C	p.Leu271Pro	p.L271P	ENST00000327367	NM_005902.3	271	cTa/cCa	6/9	0.361431757371063	4	FACETS	1	0.993	1	0.874	0.838	0.909	CLONAL	3	TRUE	0	0.428052193298887	4		695	802	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176104188	176104188	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	51	290	0	ENST00000367669.3:c.926A>T	p.Asp309Val	p.D309V	ENST00000367669	NM_022457.5	309	gAt/gTt	8/20	0.320980496653848	3	FACETS	0.955	0.817	1	0.477	0.408	0.552	CLONAL	1	TRUE	1	0.428052193298887	3		290	303	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245379	46245425	+	frameshift_variant	Frame_Shift_Del	DEL	ATAGCCCAGCAACCATTTTCCAAGGGACTTCTGGCAACCAGGTAACC	ATAGCCCAGCAACCATTTTCCAAGGGACTTCTGGCAACCAGGTAACC	-	novel	NA	P-0037920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	96	427	0	ENST00000334344.6:c.3476_3522del	p.Ser1159AsnfsTer66	p.S1159Nfs*66	ENST00000334344	NM_152641.2	1158	aATAGCCCAGCAACCATTTTCCAAGGGACTTCTGGCAACCAGGTAACC/a	15/21	0.428052193298887	5	FACETS	1	0.956	1			1	CLONAL	1	TRUE	NA	0.428052193298887	5		427	645	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245427	46245427	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	99	424	0	ENST00000334344.6:c.3521T>C	p.Ile1174Thr	p.I1174T	ENST00000334344	NM_152641.2	1174	aTa/aCa	15/21	0.428052193298887	5	FACETS	1	0.969	1			1	CLONAL	1	TRUE	NA	0.428052193298887	5		424	619	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872564	35872592	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTCTACGAATGCAAGAGAGACCAGAGAA	AGTCTACGAATGCAAGAGAGACCAGAGAA	-	novel	NA	P-0037920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	57	400	0	ENST00000216797.5:c.337-26_339del		p.X113_splice	ENST00000216797	NM_020529.2	113		3/6	0.305434646752992	4	FACETS	0.664	0.569	0.767	0.332	0.284	0.384	SUBCLONAL	1	TRUE	2	0.428052193298887	4		400	573	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021716	69021716	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	163	505	0	ENST00000288368.4:c.3004T>C	p.Ser1002Pro	p.S1002P	ENST00000288368	NM_024870.2	1002	Tct/Cct	25/40	0.428052193298887	5	FACETS	0.828	0.761	0.898	0.552	0.507	0.599	CLONAL	2	TRUE	2	0.428052193298887	5		505	755	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542603	141542603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	447	671	6	ENST00000220592.5:c.2383C>T	p.Arg795Cys	p.R795C	ENST00000220592	NM_012154.3	795	Cgc/Tgc	18/19	0.428052193298887	5	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	2	0.428052193298887	5		677	1050	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411796	139411796	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767042476	NA	P-0037920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	249	1019	3	ENST00000277541.6:c.1483G>A	p.Ala495Thr	p.A495T	ENST00000277541	NM_017617.3	495	Gcc/Acc	9/34	0.305434646752992	4	FACETS	1	0.992	1	0.711	0.664	0.76	CLONAL	1	TRUE	2	0.428052193298887	4		1022	1168	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0037923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	76	351	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.459462182935898	2		351	243	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54959348	54959348	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	48	309	0	ENST00000312783.6:c.352C>T	p.Gln118Ter	p.Q118*	ENST00000312783	NM_198436.1	118	Cag/Tag	5/10	1	2	FACETS	0.908	0.776	1	0.908	0.776	1	CLONAL	1	TRUE	1	0.459462182935898	2		309	230	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028094	69028094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1409727717	NA	P-0037923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	150	591	2	ENST00000288368.4:c.3253G>A	p.Val1085Ile	p.V1085I	ENST00000288368	NM_024870.2	1085	Gta/Ata	26/40	1	2	FACETS	0.946	0.878	1	1	0.992	1	CLONAL	2	TRUE	1	0.459462182935898	2		593	345	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971026	21971300	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCCAGGCATCGCGCACGTCCAGCCGCGCCCCGGCCCGGTGCAGCACCACCAGCGTGTCCAGGAAGCCCTCCCGGGCAGCGTCGTGCACGGGTCGGGTGAGAGTGGCGGGGTCGGCGCAGTTGGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCTGCCCATCATCATGACCTGCCAGAGAGAACAGAATGGTCAGAGCCAGGGTGGGGGCCGGCATGACGGAAAGGAAGCTTGTGTAGAGCCCCCTCACCGCCAAGCAGACCC	CCCCAGGCATCGCGCACGTCCAGCCGCGCCCCGGCCCGGTGCAGCACCACCAGCGTGTCCAGGAAGCCCTCCCGGGCAGCGTCGTGCACGGGTCGGGTGAGAGTGGCGGGGTCGGCGCAGTTGGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCTGCCCATCATCATGACCTGCCAGAGAGAACAGAATGGTCAGAGCCAGGGTGGGGGCCGGCATGACGGAAAGGAAGCTTGTGTAGAGCCCCCTCACCGCCAAGCAGACCC	-	novel	NA	P-0037923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	54	552	0	ENST00000304494.5:c.151-93_332del		p.X51_splice	ENST00000304494	NM_000077.4	51		2/3	0.179005565473607	1	FACETS	1	0.963	1	1	0.963	1	INDETERMINATE	1	TRUE	0	0.459462182935898	1		552	140	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	129	703	5	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.426138196307275	2		708	600	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	150	464	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.426138196307275	2		465	680	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324494	31324494	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs9266161	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	229	590	1	ENST00000412585.2:c.314T>C	p.Leu105Pro	p.L105P	ENST00000412585	NM_005514.6	105	cTg/cCg	2/8	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.426138196307275	2		591	767	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939413	71939413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148394356	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	199	628	0	ENST00000298229.2:c.268C>T	p.Arg90Cys	p.R90C	ENST00000298229	NM_001567.3	90	Cgc/Tgc	3/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.426138196307275	2		628	797	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	175	704	5	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.426138196307275	2		709	702	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	225	597	4	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.426138196307275	2		601	850	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9776630	9776630	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201035266	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	193	660	1	ENST00000377346.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000377346	NM_005026.3	245	Ggc/Agc	6/24	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.426138196307275	2		661	782	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259043	16259043	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	179	518	0	ENST00000375759.3:c.6313del	p.Ala2105LeufsTer33	p.A2105Lfs*33	ENST00000375759	NM_015001.2	2103	aGg/ag	11/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.426138196307275	2		518	690	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367084	40367084	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	171	547	0	ENST00000397332.2:c.113A>G	p.His38Arg	p.H38R	ENST00000397332	NM_001033082.2	38	cAc/cGc	2/3	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.426138196307275	2		547	642	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430850	78430850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	167	523	0	ENST00000370768.2:c.539G>A	p.Gly180Asp	p.G180D	ENST00000370768	NM_003902.3	180	gGc/gAc	8/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.426138196307275	2		523	668	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458252	120458252	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	206	643	0	ENST00000256646.2:c.7093G>T	p.Val2365Leu	p.V2365L	ENST00000256646	NM_024408.3	2365	Gta/Tta	34/34	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.426138196307275	2		643	789	SUCCESS
FH	2271	MSKCC	GRCh37	1	241661268	241661268	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	123	393	0	ENST00000366560.3:c.1393T>C	p.Tyr465His	p.Y465H	ENST00000366560	NM_000143.3	465	Tat/Cat	10/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.426138196307275	2		393	535	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606814	43606814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746512075	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	223	619	0	ENST00000355710.3:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000355710	NM_020975.4	475	Cgg/Tgg	7/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.426138196307275	2		619	833	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851272	63851272	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	216	597	0	ENST00000279873.7:c.2050C>A	p.Pro684Thr	p.P684T	ENST00000279873	NM_032199.2	684	Cca/Aca	10/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.426138196307275	2		597	836	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925318	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	89	425	0	ENST00000543371.1:c.1402_1403del	p.Lys468ValfsTer8	p.K468Vfs*8	ENST00000543371	NM_001198531.1	465	agAAaa/agaa	14/14	1	2	FACETS	0.772	0.686	0.863	0.772	0.686	0.863	SUBCLONAL	1	TRUE	1	0.426138196307275	2		425	541	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925622	114925622	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1189031682	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	194	560	2	ENST00000543371.1:c.1704del	p.Ser569ProfsTer33	p.S569Pfs*33	ENST00000543371	NM_001198531.1	567	gCc/gc	14/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.426138196307275	2		562	791	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202122	67202122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329977977	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	228	733	1	ENST00000312629.5:c.1225C>T	p.Arg409Cys	p.R409C	ENST00000312629	NM_003952.2	409	Cgc/Tgc	14/15	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.426138196307275	2		734	821	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	171	494	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.426138196307275	2		494	670	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443752	49443752	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1207605582	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	242	686	0	ENST00000301067.7:c.3619G>A	p.Glu1207Lys	p.E1207K	ENST00000301067	NM_003482.3	1207	Gag/Aag	11/54	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.426138196307275	2		686	860	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445500	49445500	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs886042284	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	246	710	1	ENST00000301067.7:c.1966del	p.Leu656CysfsTer274	p.L656Cfs*274	ENST00000301067	NM_003482.3	656	Ctg/tg	10/54	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.426138196307275	2		711	880	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436596	110436596	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	222	624	0	ENST00000375856.3:c.1805G>T	p.Arg602Leu	p.R602L	ENST00000375856	NM_003749.2	602	cGg/cTg	1/2	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.426138196307275	2		624	832	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712602	43712602	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	66	756	0	ENST00000382044.4:c.4582T>C	p.Tyr1528His	p.Y1528H	ENST00000382044	NM_001141980.1	1528	Tac/Cac	21/28	1	2	FACETS	0.33	0.285	0.378	0.33	0.285	0.378	SUBCLONAL	1	TRUE	1	0.426138196307275	2		756	939	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	210	679	2	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.426138196307275	2		681	867	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007846	45007846	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	128	378	0	ENST00000558401.1:c.293A>G	p.Tyr98Cys	p.Y98C	ENST00000558401	NM_004048.2	98	tAt/tGt	2/4	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.426138196307275	2		378	499	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472549	88472549	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	111	517	0	ENST00000360948.2:c.2006A>G	p.Tyr669Cys	p.Y669C	ENST00000360948	NM_001012338.2	669	tAc/tGc	16/19	1	2	FACETS	0.927	0.836	1	0.927	0.836	1	CLONAL	1	TRUE	1	0.426138196307275	2		517	562	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456418	99456418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138992740	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	143	480	0	ENST00000268035.6:c.1735G>A	p.Val579Ile	p.V579I	ENST00000268035	NM_000875.3	579	Gtt/Att	8/21	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.426138196307275	2		480	627	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223521	2223521	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	138	651	0	ENST00000326181.6:c.1052T>C	p.Leu351Pro	p.L351P	ENST00000326181	NM_032271.2	351	cTc/cCc	11/21	1	2	FACETS	0.784	0.714	0.858	0.784	0.714	0.858	SUBCLONAL	1	TRUE	1	0.426138196307275	2		651	826	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789591	3789591	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	162	407	0	ENST00000262367.5:c.4268del	p.Pro1423LeufsTer36	p.P1423Lfs*36	ENST00000262367	NM_004380.2	1423	cCt/ct	25/31	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.426138196307275	2		407	562	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790401	3790401	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1480391685	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	128	364	1	ENST00000262367.5:c.4132C>T	p.Arg1378Trp	p.R1378W	ENST00000262367	NM_004380.2	1378	Cgg/Tgg	24/31	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.426138196307275	2		365	473	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	149	395	2	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.426138196307275	2		397	582	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14021987	14021987	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	109	508	0	ENST00000311895.7:c.687A>G	p.Ile229Met	p.I229M	ENST00000311895	NM_005236.2	229	atA/atG	4/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.426138196307275	2		508	430	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821506	72821506	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	165	462	0	ENST00000268489.5:c.10669A>G	p.Thr3557Ala	p.T3557A	ENST00000268489	NM_006885.3	3557	Aca/Gca	10/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.426138196307275	2		462	596	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845640	72845640	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148354034	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	167	539	1	ENST00000268489.5:c.3700G>A	p.Asp1234Asn	p.D1234N	ENST00000268489	NM_006885.3	1234	Gat/Aat	7/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.426138196307275	2		540	730	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346157	89346158	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs878855327	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	102	331	0	ENST00000301030.4:c.6792dup	p.Ala2265ArgfsTer8	p.A2265Rfs*8	ENST00000301030	NM_001256183.1	2264	-/C	9/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.426138196307275	2		331	363	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649018	37649018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1367487092	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	130	383	0	ENST00000447079.4:c.2123G>A	p.Arg708His	p.R708H	ENST00000447079	NM_015083.1	708	cGt/cAt	4/14	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.426138196307275	2		383	520	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59878754	59878754	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs535414791	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	91	407	0	ENST00000259008.2:c.1000G>A	p.Ala334Thr	p.A334T	ENST00000259008	NM_032043.2	334	Gcc/Acc	8/20	1	2	FACETS	0.935	0.834	1	0.935	0.834	1	CLONAL	1	TRUE	1	0.426138196307275	2		407	457	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395664	45395664	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	136	406	1	ENST00000262160.6:c.470del	p.Lys157ArgfsTer6	p.K157Rfs*6	ENST00000262160	NM_005901.5	157	aAg/ag	4/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.426138196307275	2		407	559	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216500	2216500	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	143	615	0	ENST00000398665.3:c.2144G>T	p.Gly715Val	p.G715V	ENST00000398665	NM_032482.2	715	gGc/gTc	20/28	1	2	FACETS	0.877	0.801	0.957	0.877	0.801	0.957	CLONAL	1	TRUE	1	0.426138196307275	2		615	765	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117084	7117084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	192	560	0	ENST00000302850.5:c.4132C>T	p.Arg1378Trp	p.R1378W	ENST00000302850	NM_000208.2	1378	Cgg/Tgg	22/22	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.426138196307275	2		560	714	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250872	10250872	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201497993	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	170	576	1	ENST00000340748.4:c.3608C>T	p.Thr1203Ile	p.T1203I	ENST00000340748		1203	aCc/aTc	32/40	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.426138196307275	2		577	725	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285030	15285030	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	174	597	0	ENST00000263388.2:c.4585G>A	p.Ala1529Thr	p.A1529T	ENST00000263388	NM_000435.2	1529	Gcc/Acc	25/33	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.426138196307275	2		597	754	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289863	15289863	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201680145	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	219	676	2	ENST00000263388.2:c.3691C>T	p.Arg1231Cys	p.R1231C	ENST00000263388	NM_000435.2	1231	Cgt/Tgt	22/33	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.426138196307275	2		678	834	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349882	15349882	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	91	459	0	ENST00000263377.2:c.3770A>T	p.Gln1257Leu	p.Q1257L	ENST00000263377	NM_058243.2	1257	cAg/cTg	18/20	1	2	FACETS	0.706	0.628	0.789	0.706	0.628	0.789	SUBCLONAL	1	TRUE	1	0.426138196307275	2		459	605	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378346	15378346	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	74	239	0	ENST00000263377.2:c.440T>C	p.Val147Ala	p.V147A	ENST00000263377	NM_058243.2	147	gTc/gCc	4/20	1	2	FACETS	0.995	0.877	1	0.995	0.877	1	CLONAL	1	TRUE	1	0.426138196307275	2		239	349	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967091	18967092	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1384543747	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	189	582	0	ENST00000262803.5:c.1814_1815del	p.Glu605AlafsTer17	p.E605Afs*17	ENST00000262803	NM_002911.3	602	gcAGag/gcag	13/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.426138196307275	2		582	730	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210893	36210893	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	192	616	0	ENST00000222270.7:c.649del	p.Arg217GlyfsTer22	p.R217Gfs*22	ENST00000222270	NM_014727.1	215	aCc/ac	3/37	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.426138196307275	2		616	787	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42384740	42384740	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	144	460	0	ENST00000221972.3:c.502C>T	p.Arg168Ter	p.R168*	ENST00000221972	NM_021601.3	168	Cga/Tga	4/5	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.426138196307275	2		460	572	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753068	42753068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	181	573	0	ENST00000222329.4:c.1196C>T	p.Ala399Val	p.A399V	ENST00000222329	NM_006494.2	399	gCt/gTt	4/4	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.426138196307275	2		573	739	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753266	42753266	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	124	684	0	ENST00000222329.4:c.998A>G	p.His333Arg	p.H333R	ENST00000222329	NM_006494.2	333	cAc/cGc	4/4	1	2	FACETS	0.705	0.637	0.776	0.705	0.637	0.776	SUBCLONAL	1	TRUE	1	0.426138196307275	2		684	826	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791859	42791859	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	203	589	1	ENST00000575354.2:c.745T>C	p.Tyr249His	p.Y249H	ENST00000575354	NM_015125.3	249	Tac/Cac	5/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.426138196307275	2		590	797	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868311	45868311	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs151235136	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	226	604	0	ENST00000391945.4:c.466C>T	p.Arg156Ter	p.R156*	ENST00000391945	NM_000400.3	156	Cga/Tga	6/23	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.426138196307275	2		604	815	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905055	50905055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	152	476	1	ENST00000440232.2:c.342del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	113	Ggg/gg	4/27	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.426138196307275	2		477	547	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262363	39262363	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	111	483	1	ENST00000402219.2:c.1064A>G	p.Glu355Gly	p.E355G	ENST00000402219	NM_005633.3	355	gAa/gGa	8/23	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.426138196307275	2		484	515	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	rs267608078	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	98	397	0	ENST00000234420.5:c.3260_3261dup	p.Phe1088ProfsTer3	p.F1088Pfs*3	ENST00000234420	NM_000179.2	1085	acc/aCCcc	5/10	1	2	FACETS	0.722	0.645	0.804	0.722	0.645	0.804	SUBCLONAL	1	TRUE	1	0.426138196307275	2		397	637	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145432	61145432	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	92	283	0	ENST00000295025.8:c.640+2T>C		p.X214_splice	ENST00000295025	NM_002908.2	214			1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.426138196307275	2		283	387	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96930896	96930896	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	217	609	0	ENST00000258439.3:c.224T>C	p.Val75Ala	p.V75A	ENST00000258439	NM_001193304.2	75	gTg/gCg	2/4	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.426138196307275	2		609	768	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182127	99182127	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	123	375	0	ENST00000074304.5:c.2192A>G	p.Asp731Gly	p.D731G	ENST00000074304	NM_001134224.1	731	gAc/gGc	21/26	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.426138196307275	2		375	508	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645985	215645985	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1329441113	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	88	495	0	ENST00000260947.4:c.613A>C	p.Lys205Gln	p.K205Q	ENST00000260947	NM_000465.2	205	Aag/Cag	4/11	1	2	FACETS	0.758	0.673	0.848	0.758	0.673	0.848	SUBCLONAL	1	TRUE	1	0.426138196307275	2		495	545	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661341	227661341	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	94	625	0	ENST00000305123.5:c.2114del	p.Gly705AlafsTer29	p.G705Afs*29	ENST00000305123	NM_005544.2	705	gGc/gc	1/2	1	2	FACETS	0.644	0.573	0.719	0.644	0.573	0.719	SUBCLONAL	1	TRUE	1	0.426138196307275	2		625	685	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	202	648	0	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.426138196307275	2		648	802	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	64	380	2	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.951	0.829	1	0.951	0.829	1	CLONAL	1	TRUE	1	0.426138196307275	2		382	316	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46276064	46276064	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs370656650	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	184	563	0	ENST00000371998.3:c.3500C>A	p.Pro1167His	p.P1167H	ENST00000371998		1167	cCc/cAc	18/23	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.426138196307275	2		563	756	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62325779	62325779	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	173	612	0	ENST00000360203.5:c.3047T>C	p.Leu1016Pro	p.L1016P	ENST00000360203	NM_001283009.1	1016	cTg/cCg	31/35	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.426138196307275	2		612	743	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866364	42866364	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753509316	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	263	643	3	ENST00000398585.3:c.268G>A	p.Ala90Thr	p.A90T	ENST00000398585	NM_001135099.1	90	Gcc/Acc	3/14	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.426138196307275	2		646	884	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092975	29092975	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	138	439	0	ENST00000328354.6:c.1009T>C	p.Tyr337His	p.Y337H	ENST00000328354	NM_007194.3	337	Tac/Cac	10/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.426138196307275	2		439	538	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627274	37627274	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	142	685	0	ENST00000249071.6:c.445A>C	p.Ile149Leu	p.I149L	ENST00000249071	NM_002872.4	149	Att/Ctt	5/7	1	2	FACETS	0.789	0.719	0.862	0.789	0.719	0.862	SUBCLONAL	1	TRUE	1	0.426138196307275	2		685	845	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	252	313	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	0.426138196307275	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.426138196307275	2		313	489	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090096	37090096	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1559591605	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	164	438	0	ENST00000231790.2:c.1985C>T	p.Thr662Ile	p.T662I	ENST00000231790	NM_000249.3	662	aCt/aTt	17/19	0.426138196307275	2	FACETS	1	0.986	1	0.652	0.602	0.705	CLONAL	1	TRUE	0	0.426138196307275	2		438	590	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	264	344	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	0.426138196307275	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.426138196307275	2		344	516	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280799	41280799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	144	330	0	ENST00000349496.5:c.2312G>A	p.Ser771Asn	p.S771N	ENST00000349496	NM_001904.3	771	aGc/aAc	15/15	0.426138196307275	2	FACETS	1	0.984	1	0.663	0.608	0.719	CLONAL	1	TRUE	0	0.426138196307275	2		330	510	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163376	47163377	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	73	361	0	ENST00000409792.3:c.2749dup	p.Ser917LysfsTer18	p.S917Kfs*18	ENST00000409792	NM_014159.6	917	agt/aAgt	3/21	1	2	FACETS	0.789	0.693	0.892	0.789	0.693	0.892	SUBCLONAL	1	TRUE	1	0.426138196307275	2		361	434	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412898	49412898	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519954	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	186	640	0	ENST00000418115.1:c.125A>G	p.Tyr42Cys	p.Y42C	ENST00000418115	NM_001664.2	42	tAt/tGt	2/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.426138196307275	2		640	733	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722906	49722906	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	rs747477010	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	42	136	1	ENST00000449682.2:c.1421del	p.Pro474GlnfsTer52	p.P474Qfs*52	ENST00000449682	NM_020998.3	474	cCa/ca	12/18	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.426138196307275	2		137	183	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119635000	119635000	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs201787969	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	63	254	0	ENST00000316626.5:c.499C>T	p.Arg167Ter	p.R167*	ENST00000316626		167	Cga/Tga	5/12	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.426138196307275	2		254	271	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213846	66213846	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	152	452	0	ENST00000273854.3:c.2584T>C	p.Trp862Arg	p.W862R	ENST00000273854	NM_004439.5	862	Tgg/Cgg	15/18	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.426138196307275	2		452	581	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509085	66509085	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	75	309	0	ENST00000273854.3:c.242del	p.Asn81MetfsTer24	p.N81Mfs*24	ENST00000273854	NM_004439.5	81	aAt/at	2/18	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.426138196307275	2		309	270	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535298	66535298	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	187	502	0	ENST00000273854.3:c.163G>A	p.Ala55Thr	p.A55T	ENST00000273854	NM_004439.5	55	Gcc/Acc	1/18	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.426138196307275	2		502	649	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539104	187539104	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	163	497	0	ENST00000441802.2:c.8636del	p.Lys2879ArgfsTer49	p.K2879Rfs*49	ENST00000441802	NM_005245.3	2879	aAg/ag	10/27	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.426138196307275	2		497	613	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161675	56161675	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	21	409	0	ENST00000399503.3:c.1172A>G	p.Lys391Arg	p.K391R	ENST00000399503	NM_005921.1	391	aAa/aGa	6/20	0.183883417144364	3	FACETS	0.307	0.235	0.39	0.153	0.117	0.195	INDETERMINATE	1	TRUE	1	0.426138196307275	3		409	390	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592171	67592171	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	70	212	1	ENST00000274335.5:c.1985+2T>C		p.X662_splice	ENST00000274335		662			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.426138196307275	2		213	284	SUCCESS
APC	324	MSKCC	GRCh37	5	112151243	112151243	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	142	412	0	ENST00000257430.4:c.886A>G	p.Ser296Gly	p.S296G	ENST00000257430	NM_000038.5	296	Agc/Ggc	9/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.426138196307275	2		412	527	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944382	131944382	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs748536322	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	75	252	6	ENST00000265335.6:c.2801del	p.Asn934IlefsTer6	p.N934Ifs*6	ENST00000265335		932	Aaa/aa	17/25	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.426138196307275	2		258	305	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131972877	131972877	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	117	339	0	ENST00000265335.6:c.3460A>G	p.Thr1154Ala	p.T1154A	ENST00000265335		1154	Acc/Gcc	22/25	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.426138196307275	2		339	489	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149513503	149513503	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs755109587	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	158	570	0	ENST00000261799.4:c.700A>G	p.Met234Val	p.M234V	ENST00000261799	NM_002609.3	234	Atg/Gtg	5/23	1	2	FACETS	0.956	0.877	1	0.956	0.877	1	CLONAL	1	TRUE	1	0.426138196307275	2		570	776	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168761	32168761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	209	584	0	ENST00000375023.3:c.4162G>T	p.Asp1388Tyr	p.D1388Y	ENST00000375023	NM_004557.3	1388	Gat/Tat	23/30	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.426138196307275	2		584	721	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793888	89793888	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	101	335	0	ENST00000336032.3:c.961del	p.Thr321ArgfsTer16	p.T321Rfs*16	ENST00000336032	NM_006813.2	319	ttA/tt	2/2	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.426138196307275	2		335	437	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521848	157521848	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747088591	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	120	406	1	ENST00000346085.5:c.4120C>T	p.Arg1374Cys	p.R1374C	ENST00000346085	NM_020732.3	1374	Cgc/Tgc	18/20	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.426138196307275	2		407	528	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	198	586	5	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.426138196307275	2		591	738	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971292	13971292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772105404	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	153	458	0	ENST00000405192.2:c.637C>T	p.Arg213Cys	p.R213C	ENST00000405192	NM_001163147.1	213	Cgc/Tgc	8/12	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.426138196307275	2		458	664	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266502	55266502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223694747	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	189	472	1	ENST00000275493.2:c.2794C>T	p.Arg932Cys	p.R932C	ENST00000275493	NM_005228.3	932	Cgc/Tgc	23/28	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.426138196307275	2		473	671	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339917	116339917	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	132	435	0	ENST00000397752.3:c.779A>G	p.Tyr260Cys	p.Y260C	ENST00000397752	NM_000245.2	260	tAc/tGc	2/21	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.426138196307275	2		435	516	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	188	600	0	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.426138196307275	2		600	703	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543692	148543692	+	splice_acceptor_variant	Splice_Site	DEL	T	T	-	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	42	278	0	ENST00000320356.2:c.118-2del		p.X40_splice	ENST00000320356	NM_004456.4	40			1	2	FACETS	0.54	0.452	0.637	0.54	0.452	0.637	SUBCLONAL	1	TRUE	1	0.426138196307275	2		278	365	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370958	55370958	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	223	540	0	ENST00000297316.4:c.260C>T	p.Ala87Val	p.A87V	ENST00000297316	NM_022454.3	87	gCg/gTg	1/2	1	2	FACETS	0.764	0.715	0.814	1	0.992	1	SUBCLONAL	2	TRUE	1	0.426138196307275	2		540	685	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141567295	141567295	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	228	604	0	ENST00000220592.5:c.919A>G	p.Thr307Ala	p.T307A	ENST00000220592	NM_012154.3	307	Acg/Gcg	8/19	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.426138196307275	2		604	764	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244261	98244261	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	145	551	1	ENST00000331920.6:c.716C>T	p.Ala239Val	p.A239V	ENST00000331920	NM_000264.3	239	gCg/gTg	5/24	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.426138196307275	2		552	663	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798875	135798875	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	82	242	0	ENST00000298552.3:c.368A>G	p.Asp123Gly	p.D123G	ENST00000298552	NM_001162426.1	123	gAc/gGc	6/23	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.426138196307275	2		242	337	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324892	31324892	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs765875917	NA	P-0037940-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	37	381	0	ENST00000412585.2:c.44del	p.Ala15GlyfsTer5	p.A15Gfs*5	ENST00000412585	NM_005514.6	15	gCg/gg	1/8	1	2	FACETS	0.315	0.259	0.378	0.315	0.259	0.378	SUBCLONAL	1	TRUE	1	0.426138196307275	2		381	551	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0037962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	316	269	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.500729516035996	4	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	2	0.628309257776777	4		269	803	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143985	11143985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	416	544	0	ENST00000358026.2:c.3566G>A	p.Arg1189Gln	p.R1189Q	ENST00000358026	NM_001128849.1	1189	cGa/cAa	26/36	0.614642299628766	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.628309257776777	3		544	838	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630251	187630251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773192852	NA	P-0037962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	160	656	0	ENST00000441802.2:c.731C>T	p.Thr244Met	p.T244M	ENST00000441802	NM_005245.3	244	aCg/aTg	2/27	0.616862693238	2	FACETS	0.887	0.818	0.959	0.444	0.409	0.48	CLONAL	1	TRUE	0	0.628309257776777	2		656	574	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120267	70120267	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	497	783	1	ENST00000245479.2:c.1269C>A	p.Phe423Leu	p.F423L	ENST00000245479	NM_000346.3	423	ttC/ttA	3/3	0.500729516035996	4	FACETS	0.948	0.908	0.989	0.948	0.908	0.989	CLONAL	2	TRUE	2	0.628309257776777	4		784	1358	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051415	13051415	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0037962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	42	593	0	ENST00000316448.5:c.763G>T	p.Glu255Ter	p.E255*	ENST00000316448	NM_004343.3	255	Gaa/Taa	6/9	0.614642299628766	3	FACETS	0.215	0.179	0.256	0.108	0.089	0.128	SUBCLONAL	1	TRUE	1	0.628309257776777	3		593	817	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0037989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	62	381	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.217142890636266	1	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	0	0.217142890636266	1		381	507	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0037989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	123	582	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.217142890636266	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.217142890636266	1		582	970	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971077	21971077	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	22	222	0	ENST00000304494.5:c.281T>C	p.Leu94Pro	p.L94P	ENST00000304494	NM_000077.4	94	cTg/cCg	2/3	1	2	FACETS	0.798	0.62	1	0.798	0.62	1	CLONAL	1	TRUE	1	0.217142890636266	2		222	254	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031215	36031215	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0037989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	132	940	1	ENST00000358208.4:c.1334A>G	p.Lys445Arg	p.K445R	ENST00000358208		445	aAg/aGg	11/12	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.217142890636266	2		941	1074	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713825	30713825	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0037989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	110	792	1	ENST00000295754.5:c.1150A>T	p.Asn384Tyr	p.N384Y	ENST00000295754	NM_003242.5	384	Aat/Tat	4/7	0.217142890636266	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.217142890636266	1		793	768	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004570	150004573	+	frameshift_variant	Frame_Shift_Del	DEL	TAGT	TAGT	-	novel	NA	P-0037989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	110	784	0	ENST00000253339.5:c.1652_1655del	p.Asn551IlefsTer96	p.N551Ifs*96	ENST00000253339		551	aACTAt/at	3/7	0.217142890636266	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.217142890636266	1		784	797	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739873	41739873	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1261664857	NA	P-0037989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	66	544	0	ENST00000242208.4:c.100G>A	p.Asp34Asn	p.D34N	ENST00000242208	NM_002192.2	34	Gac/Aac	2/3	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.217142890636266	2		544	537	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	426	663	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.991	1	1	0.997	1	CLONAL	2	TRUE	1	0.43	2		667	885	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	165	539	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.202614421739192	3	FACETS	1	0.987	1	0.68	0.626	0.735	INDETERMINATE	1	TRUE	1	0.43	3		544	686	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	251	704	5	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.43	2		709	933	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024002	27024002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs875989848	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	46	129	0	ENST00000324856.7:c.1113del	p.Gln372SerfsTer19	p.Q372Sfs*19	ENST00000324856	NM_006015.4	370	Ggg/gg	1/20	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.43	2		129	180	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	267	1110	5	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.43	2		1115	1093	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748661	43748661	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1375740992	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	262	679	2	ENST00000382044.4:c.2145del	p.Glu716AsnfsTer12	p.E716Nfs*12	ENST00000382044	NM_001141980.1	715	aaA/aa	12/28	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.43	2		681	1016	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143985	11143985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	187	544	0	ENST00000358026.2:c.3566G>A	p.Arg1189Gln	p.R1189Q	ENST00000358026	NM_001128849.1	1189	cGa/cAa	26/36	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.43	2		544	742	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	96	317	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.43	2		317	345	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	51	177	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.968	0.831	1	0.968	0.831	1	CLONAL	1	TRUE	1	0.43	2		177	245	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916890	178916890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	117	474	0	ENST00000263967.3:c.277C>T	p.Arg93Trp	p.R93W	ENST00000263967	NM_006218.2	93	Cgg/Tgg	2/21	1	2	FACETS	0.973	0.881	1	0.973	0.881	1	CLONAL	1	TRUE	1	0.43	2		474	559	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	180	472	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.43	2		472	804	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039371	47039371	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	289	756	1	ENST00000377604.3:c.994C>T	p.Arg332Cys	p.R332C	ENST00000377604	NM_001204468.1	332	Cgc/Tgc	10/24	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.43	2		757	985	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	129	275	1	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.43	2		276	481	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	147	499	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	0.92	0.841	1	0.92	0.841	1	CLONAL	1	TRUE	1	0.43	2		499	743	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	214	613	0	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	0.939	0.872	1	0.939	0.872	1	CLONAL	1	TRUE	1	0.43	2		613	1060	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191489	10191489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730882035	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	125	358	0	ENST00000256474.2:c.482G>A	p.Arg161Gln	p.R161Q	ENST00000256474	NM_000551.3	161	cGa/cAa	3/3	1	2	FACETS	0.972	0.883	1	0.972	0.883	1	CLONAL	1	TRUE	1	0.43	2		358	598	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	156	459	2	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.43	2		461	699	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573666	48573666	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	16	236	0	ENST00000342988.3:c.249+1G>A		p.X83_splice	ENST00000342988	NM_005359.5	83			1	2	FACETS	0.266	0.196	0.349	0.266	0.196	0.349	SUBCLONAL	1	TRUE	1	0.43	2		236	280	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796882	42796883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761345552	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	341	834	3	ENST00000575354.2:c.3347dup	p.Ser1117LysfsTer34	p.S1117Kfs*34	ENST00000575354	NM_015125.3	1114	gcc/gCcc	14/20	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.43	2		837	1304	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667635	29667638	+	frameshift_variant	Frame_Shift_Del	DEL	TAGA	TAGA	-	novel	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	143	351	0	ENST00000356175.3:c.6974_6977del	p.Asp2325ValfsTer49	p.D2325Vfs*49	ENST00000356175	NM_000267.3	2324	tTAGAt/tt	46/57	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.43	2		351	635	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	459813	459813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779410726	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	195	590	0	ENST00000399788.2:c.1282C>T	p.Arg428Trp	p.R428W	ENST00000399788	NM_001042603.1	428	Cgg/Tgg	10/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.43	2		590	822	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	257	706	3	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.43	2		709	1050	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682400	52682400	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	96	267	1	ENST00000394830.3:c.773del	p.Asn258MetfsTer25	p.N258Mfs*25	ENST00000394830	NM_018313.4	258	aAt/at	8/30	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.43	2		268	374	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753011	57753012	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	104	298	2	ENST00000274289.3:c.1004dup	p.Leu335PhefsTer12	p.L335Ffs*12	ENST00000274289	NM_006622.3	335	ttg/ttTg	7/14	0.202614421739192	3	FACETS	1	0.972	1	0.616	0.554	0.681	INDETERMINATE	1	TRUE	1	0.43	3		300	477	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118924	70118926	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	277	782	0	ENST00000245479.2:c.499_501del	p.Lys167del	p.K167del	ENST00000245479	NM_000346.3	166	AAG/-	2/3	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.43	2		782	1097	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513268	44513268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761081553	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	267	582	1	ENST00000291552.4:c.667G>A	p.Gly223Arg	p.G223R	ENST00000291552	NM_006758.2	223	Gga/Aga	8/8	0.26296941329303	0	FACETS	1	0.946	1			1	CLONAL	1	TRUE	0	0.43	0		583	706	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690230	47690230	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs63749947	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	105	280	0	ENST00000233146.2:c.1447G>T	p.Glu483Ter	p.E483*	ENST00000233146	NM_000251.2	483	Gaa/Taa	9/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.43	2		280	379	SUCCESS
APC	324	MSKCC	GRCh37	5	112179036	112179036	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	68	236	0	ENST00000257430.4:c.7749del	p.Ala2584GlnfsTer9	p.A2584Qfs*9	ENST00000257430	NM_000038.5	2582	gAa/ga	16/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.43	2		236	268	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	232	748	5	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.43	2		753	977	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3115015	3115015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	293	728	1	ENST00000078429.4:c.550G>A	p.Val184Met	p.V184M	ENST00000078429	NM_002067.2	184	Gtg/Atg	4/7	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.43	2		729	1039	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	294	694	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.43	2		694	1113	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527817	157527817	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	145	447	0	ENST00000346085.5:c.5547del	p.Leu1850Ter	p.L1850*	ENST00000346085	NM_020732.3	1848	Ccc/cc	20/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.43	2		447	564	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620657	52620657	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	151	350	0	ENST00000394830.3:c.3096del	p.Phe1032LeufsTer102	p.F1032Lfs*102	ENST00000394830	NM_018313.4	1032	ttT/tt	21/30	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.43	2		350	554	SUCCESS
H3C13	653604	MSKCC	GRCh37	1	149784842	149784842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	94	217	0	ENST00000331491.1:c.395G>A	p.Arg132His	p.R132H	ENST00000331491	NM_001123375.2	132	cGc/cAc	1/1	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.43	2		217	351	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469530	25469530	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755744291	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	242	758	1	ENST00000264709.3:c.1238del	p.Gly413AlafsTer238	p.G413Afs*238	ENST00000264709	NM_175629.2	413	gGc/gc	10/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.43	2		759	942	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514895	44514895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	149	345	0	ENST00000291552.4:c.352C>T	p.Arg118Cys	p.R118C	ENST00000291552	NM_006758.2	118	Cgc/Tgc	6/8	0.26296941329303	0	FACETS	1	0.968	1			1	CLONAL	1	TRUE	0	0.43	0		345	364	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218764	66218764	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	35	184	0	ENST00000273854.3:c.2294del	p.Leu765Ter	p.L765*	ENST00000273854	NM_004439.5	765	tTg/tg	13/18	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.43	2		184	155	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225542	26225542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755226121	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	183	412	0	ENST00000360408.1:c.160C>T	p.Arg54Cys	p.R54C	ENST00000360408	NM_003532.2	54	Cgc/Tgc	1/1	0.202614421739192	3	FACETS	0.808	0.749	0.869	0.808	0.749	0.869	INDETERMINATE	2	TRUE	1	0.43	3		412	640	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163297308	163297308	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	72	358	0	ENST00000271452.3:c.154G>T	p.Ala52Ser	p.A52S	ENST00000271452	NM_145697.2	52	Gcc/Tcc	3/14	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.43	2		358	331	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946424	71946424	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	270	726	0	ENST00000298229.2:c.2588del	p.Thr863LysfsTer8	p.T863Kfs*8	ENST00000298229	NM_001567.3	863	aCa/aa	23/28	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.43	2		726	1053	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416795	416795	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	138	325	0	ENST00000399788.2:c.3755G>A	p.Arg1252His	p.R1252H	ENST00000399788	NM_001042603.1	1252	cGt/cAt	23/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.43	2		325	516	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536954	120536954	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	199	504	0	ENST00000229340.5:c.232T>C	p.Tyr78His	p.Y78H	ENST00000229340	NM_006861.6	78	Tat/Cat	4/6	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.43	2		504	791	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527698	103527698	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1397787523	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	116	210	0	ENST00000355739.4:c.3006G>T	p.Gln1002His	p.Q1002H	ENST00000355739	NM_000123.3	1002	caG/caT	15/15	0.202614421739192	3	FACETS	0.953	0.869	1	0.953	0.869	1	INDETERMINATE	2	TRUE	1	0.43	3		210	344	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953253	81953253	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	116	269	0	ENST00000359376.3:c.2219T>C	p.Leu740Pro	p.L740P	ENST00000359376	NM_002661.3	740	cTg/cCg	20/33	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.43	2		269	466	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727957	78727957	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	153	429	1	ENST00000306801.3:c.802A>G	p.Thr268Ala	p.T268A	ENST00000306801	NM_020761.2	268	Acc/Gcc	6/34	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.43	2		430	599	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210748	5210748	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	221	699	0	ENST00000357368.4:c.5303T>C	p.Leu1768Pro	p.L1768P	ENST00000357368	NM_002850.3	1768	cTg/cCg	34/38	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.43	2		699	928	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285081	15285081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375087797	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	292	762	0	ENST00000263388.2:c.4534G>A	p.Val1512Met	p.V1512M	ENST00000263388	NM_000435.2	1512	Gtg/Atg	25/33	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.43	2		762	1084	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919939	50919939	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757190258	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	268	719	0	ENST00000440232.2:c.3026G>A	p.Arg1009His	p.R1009H	ENST00000440232	NM_002691.3	1009	cGc/cAc	24/27	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.43	2		719	1038	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662364	227662364	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	194	589	0	ENST00000305123.5:c.1091G>T	p.Arg364Leu	p.R364L	ENST00000305123	NM_005544.2	364	cGg/cTg	1/2	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.43	2		589	873	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713253	30713253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748437880	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	131	317	0	ENST00000295754.5:c.578G>A	p.Arg193Gln	p.R193Q	ENST00000295754	NM_003242.5	193	cGg/cAg	4/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.43	2		317	503	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498405	89498405	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	98	217	0	ENST00000336596.2:c.2377C>A	p.Pro793Thr	p.P793T	ENST00000336596	NM_005233.5	793	Cca/Aca	14/17	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.43	2		217	341	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880963	134880963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773682419	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	194	511	2	ENST00000398015.3:c.1526G>A	p.Arg509His	p.R509H	ENST00000398015	NM_004441.4	509	cGc/cAc	7/16	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.43	2		513	681	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557984	187557984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	110	336	0	ENST00000441802.2:c.3727C>T	p.Pro1243Ser	p.P1243S	ENST00000441802	NM_005245.3	1243	Cct/Tct	5/27	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.43	2		336	455	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528616	157528616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	254	645	1	ENST00000346085.5:c.6341C>T	p.Thr2114Ile	p.T2114I	ENST00000346085	NM_020732.3	2114	aCa/aTa	20/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.43	2		646	963	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741487	145741488	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	330	847	0	ENST00000428558.2:c.1015dup	p.Leu339ProfsTer11	p.L339Pfs*11	ENST00000428558	NM_004260.3	339	ctg/cCtg	5/22	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.43	2		847	1294	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360680	70360685	+	inframe_deletion	In_Frame_Del	DEL	GCAGCA	GCAGCA	-	novel	NA	P-0038015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	50	228	0	ENST00000374080.3:c.6253_6258del	p.Gln2085_Gln2086del	p.Q2085_Q2086del	ENST00000374080		2080	cgGCAGCAg/cgg	42/45	1	2	FACETS	0.768	0.655	0.889	0.768	0.655	0.889	SUBCLONAL	1	TRUE	1	0.43	2		228	303	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0038249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	184	548	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.995	0.923	1	0.995	0.923	1	CLONAL	1	TRUE	1	0.601396659256297	2		548	615	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0038249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	116	422	2	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.895	0.813	0.981	0.895	0.813	0.981	CLONAL	1	TRUE	1	0.601396659256297	2		424	431	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913476	NA	P-0038249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	301	417	0	ENST00000358487.5:c.1647T>A	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaA	12/18	0.601396659256297	3	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	1	0.601396659256297	3		417	647	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420160	420160	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746956221	NA	P-0038249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	288	376	0	ENST00000399788.2:c.3107G>A	p.Arg1036His	p.R1036H	ENST00000399788	NM_001042603.1	1036	cGt/cAt	21/28	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.601396659256297	2		376	697	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692886	89692886	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	237	312	0	ENST00000371953.3:c.370T>A	p.Cys124Ser	p.C124S	ENST00000371953	NM_000314.4	124	Tgt/Agt	5/9	0.601396659256297	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.601396659256297	3		312	448	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630626	158630626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912678	NA	P-0038249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	98	274	0	ENST00000263640.3:c.617G>A	p.Arg206His	p.R206H	ENST00000263640	NM_001105.4	206	cGc/cAc	6/11	0.174799392261242	3	FACETS	1	0.97	1	0.602	0.542	0.665	INDETERMINATE	1	TRUE	1	0.601396659256297	3		274	352	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720851	89720851	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	151	307	0	ENST00000371953.3:c.1003del	p.Arg335AspfsTer9	p.R335Dfs*9	ENST00000371953	NM_000314.4	334	aaC/aa	8/9	0.601396659256297	3	FACETS	1	0.949	1	0.523	0.48	0.568	CLONAL	1	TRUE	1	0.601396659256297	3		307	624	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056333	27056334	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0038249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	44	345	0	ENST00000324856.7:c.1331dup	p.Leu445ProfsTer178	p.L445Pfs*178	ENST00000324856	NM_006015.4	443	-/G	2/20	1	2	FACETS	0.277	0.232	0.327	0.277	0.232	0.327	SUBCLONAL	1	TRUE	1	0.601396659256297	2		345	529	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106872	27106873	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0038249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	368	515	0	ENST00000324856.7:c.6483_6484del	p.Cys2163ProfsTer61	p.C2163Pfs*61	ENST00000324856	NM_006015.4	2161	ccGGtg/cctg	20/20	1	2	FACETS	0.934	0.896	0.973	1	0.997	1	CLONAL	2	TRUE	1	0.601396659256297	2		515	655	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660479	67660480	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	136	348	0	ENST00000264010.4:c.1381dup	p.Ser461PhefsTer4	p.S461Ffs*4	ENST00000264010	NM_006565.3	460	cat/caTt	8/12	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.601396659256297	2		348	431	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581208	48581208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568205010	NA	P-0038249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	64	410	1	ENST00000342988.3:c.512C>T	p.Ser171Leu	p.S171L	ENST00000342988	NM_005359.5	171	tCg/tTg	5/12	1	2	FACETS	0.43	0.373	0.492	0.43	0.373	0.492	SUBCLONAL	1	TRUE	1	0.601396659256297	2		411	495	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10244351	10244351	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1004658637	NA	P-0038249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	230	577	0	ENST00000340748.4:c.4843A>G	p.Lys1615Glu	p.K1615E	ENST00000340748		1615	Aag/Gag	40/40	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.601396659256297	2		577	741	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085990	16085990	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	253	481	0	ENST00000281043.3:c.1166T>G	p.Leu389Arg	p.L389R	ENST00000281043	NM_005378.4	389	cTg/cGg	3/3	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.601396659256297	2		481	722	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672218	86672218	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	54	274	0	ENST00000274376.6:c.2020C>G	p.Arg674Gly	p.R674G	ENST00000274376	NM_002890.2	674	Cgc/Ggc	16/25	0.174799392261242	3	FACETS	0.613	0.525	0.708	0.307	0.262	0.354	INDETERMINATE	1	TRUE	1	0.601396659256297	3		274	381	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	10	327	0	ENST00000263967.3:c.3132T>G	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaG	21/21	1	2	FACETS	0.344	0.232	0.487	0.344	0.232	0.487	SUBCLONAL	1	TRUE	1	0.12	2		327	484	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40743959	40743959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	116	662	0	ENST00000392038.2:c.748G>A	p.Glu250Lys	p.E250K	ENST00000392038	NM_001626.4	250	Gag/Aag	9/14	1	2	FACETS	1	0.971	1	1	0.99	1	CLONAL	2	TRUE	1	0.12	2		662	803	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111475	8111482	+	frameshift_variant	Frame_Shift_Del	DEL	CAGACCAC	CAGACCAC	-	novel	NA	P-0038672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	78	581	0	ENST00000346208.3:c.963_970del	p.Gln321HisfsTer28	p.Q321Hfs*28	ENST00000346208		321	CAGACCACc/c	5/6	1	2	FACETS	0.921	0.809	1	1	0.982	1	CLONAL	2	TRUE	1	0.12	2		581	706	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658809	3658818	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTAAAGTC	CTTTAAAGTC	-	novel	NA	P-0038672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	114	661	0	ENST00000294008.3:c.148_157del	p.Asp50AsnfsTer10	p.D50Nfs*10	ENST00000294008	NM_032444.2	50	GACTTTAAAGaa/aa	2/15	1	2	FACETS	1	0.966	1	1	0.99	1	CLONAL	2	TRUE	1	0.12	2		661	814	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622553	158622553	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	40	465	0	ENST00000263640.3:c.946C>A	p.Leu316Ile	p.L316I	ENST00000263640	NM_001105.4	316	Ctt/Att	8/11	1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	TRUE	1	0.12	2		465	654	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0038694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	29	522	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.782	0.626	0.959	0.782	0.626	0.959	CLONAL	1	TRUE	1	0.14	2		522	530	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087480	27087480	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038694-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	64	750	0	ENST00000324856.7:c.2055del	p.Ser686ProfsTer56	p.S686Pfs*56	ENST00000324856	NM_006015.4	685	aCc/ac	5/20	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.14	2		750	890	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0038797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	107	779	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.150501768296587	1	FACETS	0.975	0.874	1	0.975	0.874	1	CLONAL	1	FALSE	0	0.232425279138117	1		781	835	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266501	198266501	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	10	232	0	ENST00000335508.6:c.2335T>C	p.Ser779Pro	p.S779P	ENST00000335508	NM_012433.2	779	Tct/Cct	16/25	0.150501768296587	1	FACETS	0.639	0.435	0.892	0.639	0.435	0.892	SUBCLONAL	1	FALSE	0	0.232425279138117	1		232	119	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	79	372	0				ENST00000310581	NM_198253.2	-/1132			0.164906607097002	1	FACETS	1	0.936	1	1	0.986	1	CLONAL	2	FALSE	0	0.263902646484453	1		372	243	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572986	7572986	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	77	441	0	ENST00000269305.4:c.1123C>A	p.Gln375Lys	p.Q375K	ENST00000269305	NM_001126112.2	375	Cag/Aag	11/11	1	2	FACETS	0.954	0.845	1	1	0.983	1	CLONAL	2	FALSE	1	0.263902646484453	2		441	306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577103	7577103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555525248	NA	P-0039089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	115	687	0	ENST00000269305.4:c.835G>A	p.Gly279Arg	p.G279R	ENST00000269305	NM_001126112.2	279	Ggg/Agg	8/11	1	2	FACETS	0.977	0.886	1	1	0.989	1	CLONAL	2	FALSE	1	0.263902646484453	2		687	446	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098965	178098965	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	48	252	0	ENST00000397062.3:c.80A>T	p.Asp27Val	p.D27V	ENST00000397062	NM_006164.4	27	gAt/gTt	2/5	0.263902646484453	3	FACETS	1	0.886	1	1	0.886	1	CLONAL	2	FALSE	1	0.263902646484453	3		252	198	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77066720	77066722	+	frameshift_variant	Frame_Shift_Del	DEL	CTC	CTC	TT	novel	NA	P-0039089-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	26	266	0	ENST00000356341.3:c.763_765delinsAA	p.Glu255LysfsTer6	p.E255Kfs*6	ENST00000356341	NM_002576.4	255	GAG/AA	7/15	0.204111508622016	3	FACETS	0.966	0.768	1	0.483	0.384	0.595	CLONAL	1	FALSE	1	0.263902646484453	3		266	231	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	75	381	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.89	0.779	1	0.89	0.779	1	CLONAL	1	TRUE	1	0.23	2		381	733	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0039172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	59	422	2	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.805	0.692	0.929	0.805	0.692	0.929	CLONAL	1	TRUE	1	0.23	2		424	637	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132428	11132428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	138	710	0	ENST00000358026.2:c.2644G>A	p.Glu882Lys	p.E882K	ENST00000358026	NM_001128849.1	882	Gaa/Aaa	19/36	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.23	2		710	1026	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631839	90631839	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519906	NA	P-0039172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	102	582	0	ENST00000330062.3:c.514A>G	p.Arg172Gly	p.R172G	ENST00000330062	NM_002168.2	172	Agg/Ggg	4/11	1	2	FACETS	0.952	0.85	1	0.952	0.85	1	CLONAL	1	TRUE	1	0.23	2		582	932	SUCCESS
APC	324	MSKCC	GRCh37	5	112175788	112175788	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	95	287	0	ENST00000257430.4:c.4497del	p.Ser1501LeufsTer6	p.S1501Lfs*6	ENST00000257430	NM_000038.5	1499	ggA/gg	16/16	0.241240754576465	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	0	0.23	2		287	393	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509873	106509873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375751703	NA	P-0039172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	90	577	0	ENST00000359195.3:c.1867G>A	p.Asp623Asn	p.D623N	ENST00000359195	NM_002649.2	623	Gat/Aat	2/11	1	2	FACETS	0.95	0.842	1	0.95	0.842	1	CLONAL	1	TRUE	1	0.23	2		577	824	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134269	11134269	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	111	620	0	ENST00000358026.2:c.2935C>T	p.Arg979Ter	p.R979*	ENST00000358026	NM_001128849.1	979	Cga/Tga	20/36	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.23	2		620	826	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404650	70404650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769874955	NA	P-0039172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	52	515	0	ENST00000373644.4:c.2164G>A	p.Val722Met	p.V722M	ENST00000373644	NM_030625.2	722	Gtg/Atg	4/12	NA	2	FACETS	0.492	0.417	0.574			1	INDETERMINATE	1	TRUE	NA	0.23	2		515	919	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701191	43701191	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	129	599	0	ENST00000382044.4:c.5504G>C	p.Trp1835Ser	p.W1835S	ENST00000382044	NM_001141980.1	1835	tGg/tCg	26/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.23	2		599	887	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412014	63412014	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0039172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	101	651	0	ENST00000330258.3:c.1153G>T	p.Glu385Ter	p.E385*	ENST00000330258	NM_152424.3	385	Gaa/Taa	2/2	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.23	2		651	847	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0039227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	423	753	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.784893849862184	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.784893849862184	1		753	644	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2090230	2090230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1308474938	NA	P-0039227-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	366	747	2	ENST00000219066.1:c.719C>T	p.Thr240Met	p.T240M	ENST00000219066	NM_002528.5	240	aCg/aTg	5/6	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.784893849862184	2		749	890	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0039289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	387	428	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.752575911094945	2	FACETS	0.974	0.948	0.998	0.974	0.948	0.998	CLONAL	2	TRUE	0	0.847200677426502	2		428	469	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427582	72427582	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	113	301	0	ENST00000477973.2:c.908C>G	p.Ser303Cys	p.S303C	ENST00000477973	NM_012234.5	303	tCc/tGc	4/4	0.676147004329451	4	FACETS	1	0.91	1	0.335	0.303	0.369	CLONAL	1	TRUE	1	0.847200677426502	4		301	490	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	317	372	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		372	503	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375376	118375376	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	86	297	0	ENST00000534358.1:c.8769G>C	p.Gln2923His	p.Q2923H	ENST00000534358	NM_005933.3	2923	caG/caC	27/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		297	276	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863617	68863617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659218	NA	P-0039362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	433	735	0	ENST00000261769.5:c.2356G>A	p.Asp786Asn	p.D786N	ENST00000261769	NM_004360.3	786	Gac/Aac	15/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		735	1097	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0039362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	646	781	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		781	880	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379796	17379796	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	286	907	0	ENST00000359435.4:c.181G>T	p.Gly61Trp	p.G61W	ENST00000359435	NM_001033549.1	61	Ggg/Tgg	2/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		907	1036	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467523	25467523	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs767136883	NA	P-0039362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	362	573	0	ENST00000264709.3:c.1555-2A>G		p.X519_splice	ENST00000264709	NM_175629.2	519			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		573	924	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468125	25468142	+	inframe_deletion	In_Frame_Del	DEL	GCAGTTTTGGCACATTCC	GCAGTTTTGGCACATTCC	-	novel	NA	P-0039362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	351	788	0	ENST00000264709.3:c.1534_1551del	p.Gly512_Cys517del	p.G512_C517del	ENST00000264709	NM_175629.2	512	GGAATGTGCCAAAACTGC/-	13/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		788	1116	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0039362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	133	244	0	ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	4/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		244	324	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611238	100611238	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	259	474	0	ENST00000308731.7:c.1368G>C	p.Lys456Asn	p.K456N	ENST00000308731	NM_000061.2	456	aaG/aaC	15/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		474	603	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0039437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	61	269	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.803	0.693	0.923	0.803	0.693	0.923	CLONAL	1	TRUE	1	0.274149813355893	2		269	554	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0039437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	33	296	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.531	0.432	0.643	0.531	0.432	0.643	SUBCLONAL	1	TRUE	1	0.274149813355893	2		296	453	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0039437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	79	478	2	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.884	0.778	0.998	0.884	0.778	0.998	CLONAL	1	TRUE	1	0.274149813355893	2		480	652	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412110	63412110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137852216	NA	P-0039437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	140	915	3	ENST00000330258.3:c.1057C>T	p.Arg353Ter	p.R353*	ENST00000330258	NM_152424.3	353	Cga/Tga	2/2	1	2	FACETS	0.905	0.823	0.993	0.905	0.823	0.993	CLONAL	1	TRUE	1	0.274149813355893	2		918	1128	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576853	7576853	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	129	555	2	ENST00000269305.4:c.993G>C	p.Gln331His	p.Q331H	ENST00000269305	NM_001126112.2	331	caG/caC	9/11	0.274149813355893	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.274149813355893	1		557	718	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539003	187539003	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	115	488	1	ENST00000441802.2:c.8737G>T	p.Asp2913Tyr	p.D2913Y	ENST00000441802	NM_005245.3	2913	Gat/Tat	10/27	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.274149813355893	2		489	738	SUCCESS
APC	324	MSKCC	GRCh37	5	112173868	112173870	+	frameshift_variant	Frame_Shift_Del	DEL	TCT	TCT	G	novel	NA	P-0039437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	59	334	0	ENST00000257430.4:c.2577_2579delinsG	p.Leu860ArgfsTer51	p.L860Rfs*51	ENST00000257430	NM_000038.5	859	ggTCTa/ggGa	16/16	1	2	FACETS	0.983	0.848	1	0.983	0.848	1	CLONAL	1	TRUE	1	0.274149813355893	2		334	438	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088677	27088677	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0039564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	45	632	0	ENST00000324856.7:c.2286C>G	p.Tyr762Ter	p.Y762*	ENST00000324856	NM_006015.4	762	taC/taG	7/20	1	2	FACETS	0.209	0.175	0.247	0.209	0.175	0.247	SUBCLONAL	1	TRUE	1	0.49	2		632	879	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43771650	43771650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	76	549	1	ENST00000382044.4:c.733G>A	p.Ala245Thr	p.A245T	ENST00000382044	NM_001141980.1	245	Gca/Aca	7/28	1	2	FACETS	0.387	0.339	0.439	0.387	0.339	0.439	SUBCLONAL	1	TRUE	1	0.49	2		550	801	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786890	135786893	+	frameshift_variant	Frame_Shift_Del	DEL	GTAG	GTAG	AGT	novel	NA	P-0039564-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	30	429	1	ENST00000298552.3:c.976_979delinsACT	p.Leu326ThrfsTer5	p.L326Tfs*5	ENST00000298552	NM_001162426.1	326	CTACct/ACTct	10/23	1	2	FACETS	0.212	0.17	0.26	0.212	0.17	0.26	SUBCLONAL	1	TRUE	1	0.49	2		430	577	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0039582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	123	738	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.996	0.909	1	1	0.99	1	CLONAL	2	FALSE	1	0.309631775794054	2		738	399	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	164	553	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	1	0.932	1	1	0.992	1	CLONAL	2	FALSE	1	0.309631775794054	2		553	525	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1327776	1327776	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1465167956	NA	P-0039582-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	86	528	0	ENST00000400841.2:c.105C>G	p.Ile35Met	p.I35M	ENST00000400841		35	atC/atG	2/6	0.178407151081945	2	FACETS	1	0.977	1			1	INDETERMINATE	1	FALSE	NA	0.309631775794054	2		528	390	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891274	101891274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	196	559	0	ENST00000374994.4:c.235C>T	p.Pro79Ser	p.P79S	ENST00000374994	NM_004612.2	79	Cct/Tct	2/9	0.467300897793907	2	FACETS	1	0.983	1	0.59	0.548	0.633	CLONAL	1	TRUE	0	0.469812963355581	2		559	707	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422842	12422842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	98	496	1	ENST00000287820.6:c.332C>T	p.Ala111Val	p.A111V	ENST00000287820	NM_015869.4	111	gCa/gTa	3/7	0.441380341159361	2	FACETS	0.857	0.768	0.951	0.428	0.384	0.476	CLONAL	1	TRUE	0	0.469812963355581	2		497	487	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165719	185165719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	82	408	1	ENST00000265026.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000265026	NM_004721.4	332	Gaa/Aaa	5/14	0.350411396508709	2	FACETS	0.741	0.656	0.832	0.371	0.328	0.416	SUBCLONAL	1	TRUE	0	0.469812963355581	2		409	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577584	7577584	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0039603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	263	664	1	ENST00000269305.4:c.697del	p.His233ThrfsTer14	p.H233Tfs*14	ENST00000269305	NM_001126112.2	233	Cac/ac	7/11	0.440985185614017	2	FACETS	0.841	0.793	0.889	0.841	0.793	0.889	CLONAL	2	TRUE	0	0.469812963355581	2		665	666	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246207	41246207	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	253	559	0	ENST00000357654.3:c.1341del	p.His448ThrfsTer5	p.H448Tfs*5	ENST00000357654	NM_007294.3	447	gtT/gt	10/23	0.440985185614017	2	FACETS	0.858	0.808	0.907	0.858	0.808	0.907	CLONAL	2	TRUE	0	0.469812963355581	2		559	628	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521412	8521412	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	71	643	0	ENST00000356435.5:c.826C>G	p.Leu276Val	p.L276V	ENST00000356435		276	Ctg/Gtg	9/35	0.469812963355581	3	FACETS	0.379	0.329	0.432	0.126	0.109	0.144	SUBCLONAL	1	TRUE	0	0.469812963355581	3		643	986	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937173	39937173	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039603-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	94	880	0	ENST00000378444.4:c.10G>T	p.Ala4Ser	p.A4S	ENST00000378444	NM_001123385.1	4	Gca/Tca	2/15	0.469812963355581	1	FACETS	0.403	0.358	0.451	0.403	0.358	0.451	SUBCLONAL	1	TRUE	0	0.469812963355581	1		880	760	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0039605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	533	794	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.78090416596635	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	FALSE	0	0.781427035592296	2		794	648	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922694	44922694	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397514628	NA	P-0039605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	96	306	0	ENST00000377967.4:c.1555C>T	p.Arg519Ter	p.R519*	ENST00000377967	NM_021140.2	519	Cga/Tga	16/29	0.566820947836183	3	FACETS	0.947	0.851	1			1	CLONAL	1	FALSE	NA	0.781427035592296	3		306	361	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160464	108160464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	140	479	0	ENST00000278616.4:c.4372G>A	p.Gly1458Arg	p.G1458R	ENST00000278616	NM_000051.3	1458	Gga/Aga	29/63	1	2	FACETS	0.998	0.921	1	0.998	0.921	1	CLONAL	1	FALSE	1	0.781427035592296	2		479	359	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411602	63411602	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	394	882	0	ENST00000330258.3:c.1565A>T	p.Asp522Val	p.D522V	ENST00000330258	NM_152424.3	522	gAt/gTt	2/2	0.566820947836183	3	FACETS	0.932	0.894	0.971			1	CLONAL	2	FALSE	NA	0.781427035592296	3		882	752	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0039635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	490	687	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.624786909002427	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.624786909002427	2		687	700	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150267	108150267	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	447	642	2	ENST00000278616.4:c.3335del	p.Pro1112LeufsTer2	p.P1112Lfs*2	ENST00000278616	NM_000051.3	1112	Cct/ct	23/63	0.616208842591534	4	FACETS	0.995	0.967	1	0.995	0.967	1	CLONAL	4	TRUE	0	0.624786909002427	4		644	584	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518308	187518308	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1448411899	NA	P-0039635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	70	361	0	ENST00000441802.2:c.12386A>T	p.Asp4129Val	p.D4129V	ENST00000441802	NM_005245.3	4129	gAc/gTc	25/27	0.624786909002427	2	FACETS	1	0.948	1	0.56	0.497	0.625	CLONAL	1	TRUE	0	0.624786909002427	2		361	200	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331643	8331643	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039635-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	160	688	0	ENST00000356435.5:c.5473G>T	p.Gly1825Cys	p.G1825C	ENST00000356435		1825	Ggc/Tgc	33/35	1	2	FACETS	0.935	0.862	1	0.935	0.862	1	CLONAL	1	TRUE	1	0.624786909002427	2		688	548	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0039667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	53	227	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.35769719087976	2		227	274	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457315	5457315	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	75	223	0	ENST00000381577.3:c.289G>C	p.Ala97Pro	p.A97P	ENST00000381577	NM_014143.3	97	Gct/Cct	3/7	0.35769719087976	1	FACETS	0.981	0.866	1	0.981	0.866	1	CLONAL	1	TRUE	0	0.35769719087976	1		223	351	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260899	16260899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	119	401	0	ENST00000375759.3:c.8164C>T	p.Pro2722Ser	p.P2722S	ENST00000375759	NM_015001.2	2722	Cca/Tca	11/15	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.35769719087976	2		401	624	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115974	8115991	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	CGCCATGGGTTAGAGCCC	CGCCATGGGTTAGAGCCC	AGCA	novel	NA	P-0039667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	54	266	1	ENST00000346208.3:c.1320_*5delinsAGCA		p.*440*	ENST00000346208		440		6/6	1	2	FACETS	0.623	0.532	0.721	0.623	0.532	0.721	SUBCLONAL	1	TRUE	1	0.35769719087976	2		267	485	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435302	18435302	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	91	296	0	ENST00000266497.5:c.287T>G	p.Leu96Arg	p.L96R	ENST00000266497		96	cTc/cGc	1/31	1	2	FACETS	0.986	0.878	1	0.986	0.878	1	CLONAL	1	TRUE	1	0.35769719087976	2		296	516	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125025	46125041	+	frameshift_variant	Frame_Shift_Del	DEL	AAATTGTTGAAGAGTTC	AAATTGTTGAAGAGTTC	-	novel	NA	P-0039667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	35	227	0	ENST00000334344.6:c.214_230del	p.Ile72LeufsTer7	p.I72Lfs*7	ENST00000334344	NM_152641.2	71	gAAATTGTTGAAGAGTTC/g	3/21	1	2	FACETS	0.571	0.468	0.685	0.571	0.468	0.685	SUBCLONAL	1	TRUE	1	0.35769719087976	2		227	343	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665341	138665341	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039667-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	175	527	0	ENST00000330315.3:c.224T>C	p.Leu75Pro	p.L75P	ENST00000330315	NM_023067.3	75	cTc/cCc	1/1	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.35769719087976	2		527	867	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	63	372	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.463701424874807	2		372	241	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0039717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	226	377	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.463701424874807	2		377	936	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474463	40474463	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	160	662	0	ENST00000264657.5:c.1938C>A	p.Asn646Lys	p.N646K	ENST00000264657	NM_139276.2	646	aaC/aaA	21/24	1	2	FACETS	0.814	0.747	0.884	0.814	0.747	0.884	CLONAL	1	TRUE	1	0.463701424874807	2		662	848	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039722-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	68	401	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.245828417205257	3	FACETS	0.947	0.831	1	0.947	0.831	1	CLONAL	2	TRUE	1	0.276104814049804	3		401	296	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0039723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	99	376	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.801	0.714	0.894	0.801	0.714	0.894	CLONAL	1	TRUE	1	0.26	2		377	951	SUCCESS
APC	324	MSKCC	GRCh37	5	112175561	112175561	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	78	456	0	ENST00000257430.4:c.4271del	p.Pro1424GlnfsTer49	p.P1424Qfs*49	ENST00000257430	NM_000038.5	1424	Cca/ca	16/16	1	2	FACETS	0.924	0.813	1	0.924	0.813	1	CLONAL	1	TRUE	1	0.26	2		456	649	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903731	41903731	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	143	634	0	ENST00000372991.4:c.826C>T	p.Gln276Ter	p.Q276*	ENST00000372991	NM_001760.3	276	Caa/Taa	5/5	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.26	2		634	924	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844149	68844149	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	76	775	0	ENST00000261769.5:c.737T>G	p.Met246Arg	p.M246R	ENST00000261769	NM_004360.3	246	aTg/aGg	6/16	1	2	FACETS	0.541	0.473	0.615	0.541	0.473	0.615	SUBCLONAL	1	TRUE	1	0.26	2		775	1081	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577564	7577564	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	360	529	1	ENST00000269305.4:c.717C>A	p.Asn239Lys	p.N239K	ENST00000269305	NM_001126112.2	239	aaC/aaA	7/11	0.551917889164111	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.551917889164111	2		530	633	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604643	43604661	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTCCGTGAGCAGGAGGG	CTCTCCGTGAGCAGGAGGG	-	novel	NA	P-0039726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	136	592	0	ENST00000355710.3:c.1231_1249del	p.Ser411AlafsTer36	p.S411Afs*36	ENST00000355710	NM_020975.4	410	CTCTCCGTGAGCAGGAGGGct/ct	6/20	0.551917889164111	2	FACETS	0.813	0.742	0.888	0.407	0.371	0.444	CLONAL	1	TRUE	0	0.551917889164111	2		592	606	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266873	18266873	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	225	327	1	ENST00000222254.8:c.184G>T	p.Glu62Ter	p.E62*	ENST00000222254	NM_005027.3	62	Gag/Tag	2/16	0.525143578135113	3	FACETS	0.921	0.865	0.978	0.921	0.865	0.978	CLONAL	2	TRUE	1	0.551917889164111	3		328	565	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927000	131927000	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	104	289	0	ENST00000265335.6:c.1537G>C	p.Asp513His	p.D513H	ENST00000265335		513	Gac/Cac	10/25	0.538862682638002	3	FACETS	0.904	0.812	1	0.452	0.406	0.5	CLONAL	1	TRUE	1	0.551917889164111	3		289	532	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608866	100608866	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	120	547	0	ENST00000308731.7:c.1742G>T	p.Trp581Leu	p.W581L	ENST00000308731	NM_000061.2	581	tGg/tTg	17/19	0.551917889164111	1	FACETS	0.548	0.496	0.602	0.548	0.496	0.602	SUBCLONAL	1	TRUE	0	0.551917889164111	1		547	575	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0039739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	47	250	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	0.307186617359735	1	FACETS	0.906	0.769	1	0.906	0.769	1	CLONAL	1	FALSE	0	0.307186617359735	1		250	286	SUCCESS
APC	324	MSKCC	GRCh37	5	112175198	112175198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	70	186	0	ENST00000257430.4:c.3907C>T	p.Gln1303Ter	p.Q1303*	ENST00000257430	NM_000038.5	1303	Caa/Taa	16/16	0.307186617359735	1	FACETS	0.945	0.839	1	1	0.983	1	CLONAL	2	FALSE	0	0.307186617359735	1		186	204	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748595	40748595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750813623	NA	P-0039739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	122	446	0	ENST00000373198.4:c.2921G>A	p.Arg974Gln	p.R974Q	ENST00000373198	NM_133170.3	974	cGg/cAg	21/32	0.26364580124784	4	FACETS	1	0.977	1			1	CLONAL	1	FALSE	NA	0.307186617359735	4		446	818	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205709	108205709	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	65	185	0	ENST00000278616.4:c.8024G>A	p.Gly2675Glu	p.G2675E	ENST00000278616	NM_000051.3	2675	gGa/gAa	55/63	0.24473078250757	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	0	0.307186617359735	1		185	258	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878922	117878922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039739-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	134	317	0	ENST00000297338.2:c.47A>T	p.Lys16Ile	p.K16I	ENST00000297338	NM_006265.2	16	aAa/aTa	2/14	0.307186617359735	5	FACETS	0.901	0.82	0.986	0.451	0.41	0.493	CLONAL	2	FALSE	1	0.307186617359735	5		317	707	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0039752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	232	426	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.610246464943589	3	FACETS	0.755	0.708	0.803	0.755	0.708	0.803	SUBCLONAL	2	TRUE	1	0.610246464943589	3		426	657	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0039752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	268	670	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	0.349568872006107	2	FACETS	0.925	0.88	0.969	0.925	0.88	0.969	INDETERMINATE	2	TRUE	0	0.610246464943589	2		670	475	SUCCESS
APC	324	MSKCC	GRCh37	5	112175411	112175411	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	128	272	0	ENST00000257430.4:c.4120G>T	p.Glu1374Ter	p.E1374*	ENST00000257430	NM_000038.5	1374	Gaa/Taa	16/16	0.583126133454783	3	FACETS	0.936	0.877	0.992	0.936	0.877	0.992	CLONAL	3	TRUE	0	0.610246464943589	3		272	195	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81891943	81891943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771121259	NA	P-0039752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	104	559	0	ENST00000359376.3:c.413C>T	p.Thr138Met	p.T138M	ENST00000359376	NM_002661.3	138	aCg/aTg	4/33	0.610246464943589	4	FACETS	0.935	0.839	1	0.312	0.279	0.346	CLONAL	1	TRUE	1	0.610246464943589	4		559	587	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62305417	62305417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748022323	NA	P-0039752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	121	709	0	ENST00000360203.5:c.890C>T	p.Pro297Leu	p.P297L	ENST00000360203	NM_001283009.1	297	cCg/cTg	10/35	0.610246464943589	7	FACETS	1	0.927	1	0.344	0.31	0.38	CLONAL	1	TRUE	4	0.610246464943589	7		709	970	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715683	18715683	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	48	267	0	ENST00000266497.5:c.3514T>G	p.Leu1172Val	p.L1172V	ENST00000266497		1172	Ttg/Gtg	25/31	0.486919111410122	5	FACETS	0.83	0.704	0.968	0.277	0.234	0.323	CLONAL	1	TRUE	2	0.610246464943589	5		267	363	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539768	187539768	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	93	431	0	ENST00000441802.2:c.7972A>G	p.Lys2658Glu	p.K2658E	ENST00000441802	NM_005245.3	2658	Aag/Gag	10/27	0.610246464943589	3	FACETS	1	0.953	1	0.556	0.498	0.616	CLONAL	1	TRUE	1	0.610246464943589	3		431	358	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410888	31410888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771452865	NA	P-0039752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	122	716	0	ENST00000344624.3:c.3632C>T	p.Ala1211Val	p.A1211V	ENST00000344624		1211	gCg/gTg	28/33	0.543410539423489	3	FACETS	0.744	0.674	0.819	0.372	0.337	0.41	SUBCLONAL	1	TRUE	1	0.610246464943589	3		716	701	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058444	69058444	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	53	245	0	ENST00000288368.4:c.4088A>T	p.Asn1363Ile	p.N1363I	ENST00000288368	NM_024870.2	1363	aAt/aTt	34/40	0.610246464943589	8	FACETS	0.96	0.819	1	0.137	0.117	0.16	CLONAL	1	TRUE	1	0.610246464943589	8		245	512	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0039774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	390	738	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.589352748180998	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.589352748180998	2		738	648	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699360	47699360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	164	396	0	ENST00000347630.2:c.148G>A	p.Glu50Lys	p.E50K	ENST00000347630	NM_001007230.1	50	Gaa/Aaa	4/11	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.589352748180998	2		396	516	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	183	454	0	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	0.123182781291258	3	FACETS	1	0.989	1	0.696	0.646	0.747	INDETERMINATE	1	TRUE	1	0.589352748180998	3		454	578	SUCCESS
ATR	545	MSKCC	GRCh37	3	142216018	142216018	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	111	315	0	ENST00000350721.4:c.5575G>C	p.Glu1859Gln	p.E1859Q	ENST00000350721	NM_001184.3	1859	Gag/Cag	33/47	0.466704915977669	0	FACETS	0.377	0.342	0.414			1	SUBCLONAL	1	TRUE	0	0.589352748180998	0		315	410	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023264	27023267	+	frameshift_variant	Frame_Shift_Del	DEL	GGCG	GGCG	-	novel	NA	P-0039774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	117	147	0	ENST00000324856.7:c.371_374del	p.Gly124ValfsTer107	p.G124Vfs*107	ENST00000324856	NM_006015.4	124	GGCGgt/gt	1/20	0.123182781291258	3	FACETS	0.845	0.774	0.919	0.845	0.774	0.919	INDETERMINATE	2	TRUE	1	0.589352748180998	3		147	304	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426581	49426581	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	188	809	0	ENST00000301067.7:c.11907G>T	p.Gln3969His	p.Q3969H	ENST00000301067	NM_003482.3	3969	caG/caT	39/54	0.589352748180998	4	FACETS	0.758	0.699	0.821			1	SUBCLONAL	1	TRUE	NA	0.589352748180998	4		809	1337	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959099	28959099	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	136	360	0	ENST00000282397.4:c.2039T>C	p.Leu680Ser	p.L680S	ENST00000282397	NM_002019.4	680	tTa/tCa	14/30	0.335512637404251	0	FACETS	0.467	0.428	0.506			1	INDETERMINATE	1	TRUE	0	0.589352748180998	0		360	406	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251546	251554	+	inframe_deletion	In_Frame_Del	DEL	AGGAGTCAC	AGGAGTCAC	-	novel	NA	P-0039774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	167	558	0	ENST00000264932.6:c.1757_1765del	p.Lys586_Ser588del	p.K586_S588del	ENST00000264932	NM_004168.2	586	aAGGAGTCACgg/agg	13/15	0.500566715942545	0	FACETS	0.465	0.431	0.501			1	SUBCLONAL	1	TRUE	0	0.589352748180998	0		558	500	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502286	157502286	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1282312643	NA	P-0039774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	150	547	0	ENST00000346085.5:c.3319G>A	p.Val1107Ile	p.V1107I	ENST00000346085	NM_020732.3	1107	Gtc/Atc	12/20	1	2	FACETS	0.975	0.897	1	0.975	0.897	1	CLONAL	1	TRUE	1	0.589352748180998	2		547	522	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268968	55268968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	229	753	0	ENST00000275493.2:c.3034G>A	p.Asp1012Asn	p.D1012N	ENST00000275493	NM_005228.3	1012	Gat/Aat	25/28	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.589352748180998	2		753	682	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007151	152007153	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	novel	NA	P-0039774-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	204	378	0	ENST00000262189.6:c.747_749del	p.Cys249del	p.C249del	ENST00000262189	NM_170606.2	249	tgTTGg/tgg	6/59	0.123182781291258	3	FACETS	1	0.99	1	0.693	0.646	0.741	INDETERMINATE	1	TRUE	1	0.589352748180998	3		378	647	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0039795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	109	269	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.242585850033028	2	FACETS	0.823	0.742	0.908	0.823	0.742	0.908	CLONAL	2	TRUE	0	0.259103728999543	2		269	511	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230597	46230597	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	65	380	0	ENST00000334344.6:c.846A>C	p.Glu282Asp	p.E282D	ENST00000334344	NM_152641.2	282	gaA/gaC	8/21	0.242585850033028	2	FACETS	0.902	0.783	1	0.451	0.391	0.516	CLONAL	1	TRUE	0	0.259103728999543	2		380	556	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220487	1220487	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913315	NA	P-0039795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	87	746	0	ENST00000326873.7:c.580G>T	p.Asp194Tyr	p.D194Y	ENST00000326873	NM_000455.4	194	Gac/Tac	4/10	0.259103728999543	1	FACETS	0.961	0.852	1	0.961	0.852	1	CLONAL	1	TRUE	0	0.259103728999543	1		746	608	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602326	10602326	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0039795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	99	774	0	ENST00000171111.5:c.1252del	p.Val418TrpfsTer40	p.V418Wfs*40	ENST00000171111	NM_203500.1	418	Gtg/tg	3/6	0.259103728999543	1	FACETS	0.848	0.757	0.946	0.848	0.757	0.946	CLONAL	1	TRUE	0	0.259103728999543	1		774	784	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215674221	215674221	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	87	706	1	ENST00000260947.4:c.73G>T	p.Ala25Ser	p.A25S	ENST00000260947	NM_000465.2	25	Gcc/Tcc	1/11	1	2	FACETS	0.995	0.881	1	0.995	0.881	1	CLONAL	1	TRUE	1	0.259103728999543	2		707	675	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066687	94066687	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	57	396	1	ENST00000369303.4:c.1072G>T	p.Gly358Trp	p.G358W	ENST00000369303	NM_004440.3	358	Ggg/Tgg	5/17	1	2	FACETS	0.809	0.694	0.934	0.809	0.694	0.934	CLONAL	1	TRUE	1	0.259103728999543	2		397	544	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954983	2954983	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	88	569	0	ENST00000396946.4:c.2727G>T	p.Lys909Asn	p.K909N	ENST00000396946	NM_032415.4	909	aaG/aaT	21/25	1	2	FACETS	0.89	0.788	0.999	0.89	0.788	0.999	CLONAL	1	TRUE	1	0.259103728999543	2		569	763	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540370	23540370	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039795-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	65	504	0	ENST00000380871.4:c.33G>T	p.Glu11Asp	p.E11D	ENST00000380871	NM_006167.3	11	gaG/gaT	1/2	0.259103728999543	1	FACETS	0.96	0.834	1	0.96	0.834	1	CLONAL	1	TRUE	0	0.259103728999543	1		504	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0039816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	335	510	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.553136868987039	2	FACETS	0.867	0.826	0.907	0.867	0.826	0.907	CLONAL	2	TRUE	0	0.569365473924079	2		510	679	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426451	47426491	+	frameshift_variant	Frame_Shift_Del	DEL	CGGGGAGGAAGTCCCCACATTCCAAGTCACCAGCAGAGCAG	CGGGGAGGAAGTCCCCACATTCCAAGTCACCAGCAGAGCAG	-	novel	NA	P-0039816-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	32	900	0	ENST00000377045.4:c.796_836del	p.Gly266ArgfsTer8	p.G266Rfs*8	ENST00000377045	NM_001654.4	265	tCGGGGAGGAAGTCCCCACATTCCAAGTCACCAGCAGAGCAG/t	9/16	0.569365473924079	1	FACETS	0.172	0.139	0.209	0.172	0.139	0.209	SUBCLONAL	1	TRUE	0	0.569365473924079	1		900	468	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977594	2977594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1491	116	1019	0	ENST00000396946.4:c.1090C>T	p.Arg364Cys	p.R364C	ENST00000396946	NM_032415.4	364	Cgc/Tgc	8/25	0.196624403153618	6	FACETS	1	0.916	1	0.205	0.183	0.227	CLONAL	1	TRUE	1	0.196624403153618	6		1019	1607	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0039867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	123	298	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	0.196624403153618	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.196624403153618	2		298	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0039867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	149	1033	1	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.196624403153618	2		1034	1183	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578525	7578525	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1185	133	1206	1	ENST00000269305.4:c.405C>A	p.Cys135Ter	p.C135*	ENST00000269305	NM_001126112.2	135	tgC/tgA	5/11	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.196624403153618	2		1207	1318	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856019	111856019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs984848263	NA	P-0039867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	103	424	0	ENST00000341259.2:c.70C>T	p.Arg24Trp	p.R24W	ENST00000341259	NM_005475.2	24	Cgg/Tgg	2/8	0.196624403153618	3	FACETS	0.928	0.832	1	0.928	0.832	1	CLONAL	2	TRUE	1	0.196624403153618	3		424	620	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451272	70451272	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	78	852	1	ENST00000373644.4:c.6112C>T	p.Arg2038Cys	p.R2038C	ENST00000373644	NM_030625.2	2038	Cgt/Tgt	12/12	0.196624403153618	3	FACETS	0.806	0.706	0.914	0.403	0.353	0.457	CLONAL	1	TRUE	1	0.196624403153618	3		853	1081	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959109	2959109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767537938	NA	P-0039867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1424	91	1024	0	ENST00000396946.4:c.2407G>A	p.Val803Ile	p.V803I	ENST00000396946	NM_032415.4	803	Gtc/Atc	18/25	0.196624403153618	6	FACETS	0.851	0.753	0.957	0.17	0.15	0.192	CLONAL	1	TRUE	1	0.196624403153618	6		1024	1515	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25468148	25468148	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751419033	NA	P-0039867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	141	1022	2	ENST00000264709.3:c.1528G>A	p.Val510Ile	p.V510I	ENST00000264709	NM_175629.2	510	Gtt/Att	13/23	0.196624403153618	3	FACETS	1	0.973	1	0.593	0.539	0.651	CLONAL	1	TRUE	1	0.196624403153618	3		1024	1328	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336606	81336606	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	46	344	0	ENST00000222390.5:c.1616G>A	p.Arg539Gln	p.R539Q	ENST00000222390	NM_000601.4	539	cGa/cAa	14/18	0.196624403153618	3	FACETS	1	0.903	1	0.55	0.463	0.646	CLONAL	1	TRUE	1	0.196624403153618	3		344	467	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119791	70119791	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	233	797	0	ENST00000245479.2:c.793C>T	p.Gln265Ter	p.Q265*	ENST00000245479	NM_000346.3	265	Cag/Tag	3/3	0.196624403153618	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.196624403153618	3		797	1126	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163315580	163315580	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	30	407	0	ENST00000271452.3:c.920G>C	p.Arg307Thr	p.R307T	ENST00000271452	NM_145697.2	307	aGg/aCg	11/14	0.196624403153618	3	FACETS	0.648	0.521	0.793	0.324	0.26	0.397	SUBCLONAL	1	TRUE	1	0.196624403153618	3		407	517	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198260798	198260798	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	107	543	0	ENST00000335508.6:c.3521A>G	p.Glu1174Gly	p.E1174G	ENST00000335508	NM_012433.2	1174	gAa/gGa	23/25	0.196624403153618	3	FACETS	0.928	0.834	1	0.928	0.834	1	CLONAL	2	TRUE	1	0.196624403153618	3		543	644	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322571	109322571	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs760307290	NA	P-0039867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	108	765	0	ENST00000436639.2:c.466A>T	p.Ser156Cys	p.S156C	ENST00000436639	NM_014454.2	156	Agt/Tgt	3/10	0.196624403153618	4	FACETS	1	0.959	1	0.381	0.34	0.424	CLONAL	1	TRUE	1	0.196624403153618	4		765	1151	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372064	55372064	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1479921230	NA	P-0039867-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	85	377	0	ENST00000297316.4:c.754A>G	p.Ser252Gly	p.S252G	ENST00000297316	NM_022454.3	252	Agc/Ggc	2/2	0.196624403153618	5	FACETS	0.903	0.799	1	0.602	0.532	0.676	CLONAL	2	TRUE	2	0.196624403153618	5		377	620	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0039885-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	133	642	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.373404328380901	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.373404328380901	1		642	452	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248749	212248749	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039885-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	41	268	0	ENST00000342788.4:c.3518C>G	p.Ser1173Cys	p.S1173C	ENST00000342788	NM_005235.2	1173	tCt/tGt	28/28	0.373404328380901	10	FACETS	0.825	0.685	0.98			1	CLONAL	1	TRUE	NA	0.373404328380901	10		268	664	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399128	139399128	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372830543	NA	P-0039885-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	161	743	0	ENST00000277541.6:c.5015G>A	p.Arg1672His	p.R1672H	ENST00000277541	NM_017617.3	1672	cGc/cAc	26/34	0.370883874803628	4	FACETS	0.957	0.876	1	0.319	0.292	0.348	CLONAL	1	TRUE	1	0.373404328380901	4		743	1237	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629110	14629110	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs768130288	NA	P-0039885-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	78	390	0	ENST00000254322.2:c.52G>T	p.Glu18Ter	p.E18*	ENST00000254322	NM_006145.1	18	Gag/Tag	1/3	0.373404328380901	3	FACETS	0.849	0.747	0.958			1	CLONAL	1	TRUE	NA	0.373404328380901	3		390	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578232	7578232	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039885-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	300	712	0	ENST00000269305.4:c.617del	p.Leu206TrpfsTer41	p.L206Wfs*41	ENST00000269305	NM_001126112.2	206	tTg/tg	6/11	0.362905096532865	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.373404328380901	2		712	778	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118382708	118382708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039885-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	70	337	1	ENST00000534358.1:c.11114C>T	p.Ser3705Leu	p.S3705L	ENST00000534358	NM_005933.3	3705	tCa/tTa	31/36	0.36651224230286	2	FACETS	1	0.933	1	0.548	0.481	0.62	CLONAL	1	TRUE	0	0.373404328380901	2		338	342	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416495	49416495	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0039885-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	266	615	0	ENST00000301067.7:c.16216del	p.Ile5406SerfsTer12	p.I5406Sfs*12	ENST00000301067	NM_003482.3	5406	Atc/tc	51/54	0.313924817832146	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.373404328380901	4		615	909	SUCCESS
APC	324	MSKCC	GRCh37	5	112174434	112174434	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1321678123	NA	P-0039885-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	59	236	0	ENST00000257430.4:c.3143G>C	p.Arg1048Thr	p.R1048T	ENST00000257430	NM_000038.5	1048	aGa/aCa	16/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.373404328380901	2		236	217	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131945040	131945040	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039885-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	26	194	0	ENST00000265335.6:c.2988G>C	p.Lys996Asn	p.K996N	ENST00000265335		996	aaG/aaC	19/25	1	2	FACETS	1	0.821	1	1	0.821	1	CLONAL	1	TRUE	1	0.373404328380901	2		194	136	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0039935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	129	770	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.312070751159625	1	FACETS	0.968	0.879	1	0.968	0.879	1	CLONAL	1	TRUE	0	0.312070751159625	1		770	721	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564447	86564447	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779770765	NA	P-0039935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	101	710	0	ENST00000274376.6:c.179C>T	p.Thr60Ile	p.T60I	ENST00000274376	NM_002890.2	60	aCt/aTt	1/25	0.312070751159625	1	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	0	0.312070751159625	1		710	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	806	863	0	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.602925016678455	3	FACETS	0.906	0.885	0.927	0.906	0.885	0.927	CLONAL	3	TRUE	0	0.705704660206376	3		863	1137	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696435	47696435	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	142	529	0	ENST00000347630.2:c.388G>C	p.Asp130His	p.D130H	ENST00000347630	NM_001007230.1	130	Gac/Cac	6/11	1	2	FACETS	0.811	0.744	0.881	0.811	0.744	0.881	CLONAL	1	TRUE	1	0.705704660206376	2		529	496	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882362	89882362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	387	585	0	ENST00000389301.3:c.112G>A	p.Glu38Lys	p.E38K	ENST00000389301	NM_000135.2	38	Gaa/Aaa	2/43	0.705704660206376	3	FACETS	0.905	0.865	0.945	0.905	0.865	0.945	CLONAL	2	TRUE	1	0.705704660206376	3		585	820	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023903	27023904	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	91	91	0	ENST00000324856.7:c.1015dup	p.Ala339GlyfsTer61	p.A339Gfs*61	ENST00000324856	NM_006015.4	337	tgg/tGgg	1/20	0.557881945085931	5	FACETS	1	0.971	1	0.794	0.719	0.87	CLONAL	2	TRUE	2	0.705704660206376	5		91	223	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039906	47039906	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	512	343	0	ENST00000377604.3:c.1248+1G>T		p.X416_splice	ENST00000377604	NM_001204468.1	416			0.705704660206376	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.705704660206376	2		343	619	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245376	46245376	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	286	425	0	ENST00000334344.6:c.3470C>G	p.Ser1157Ter	p.S1157*	ENST00000334344	NM_152641.2	1157	tCa/tGa	15/21	0.705704660206376	6	FACETS	0.848	0.797	0.9			1	CLONAL	2	TRUE	NA	0.705704660206376	6		425	1153	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950465	38950465	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	107	392	0	ENST00000357387.3:c.3485C>T	p.Ser1162Leu	p.S1162L	ENST00000357387	NM_152756.3	1162	tCa/tTa	31/38	0.64565299640967	3	FACETS	0.848	0.764	0.935	0.424	0.382	0.468	CLONAL	1	TRUE	1	0.705704660206376	3		392	484	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720290	43720290	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	148	569	0	ENST00000382044.4:c.3752T>C	p.Val1251Ala	p.V1251A	ENST00000382044	NM_001141980.1	1251	gTa/gCa	18/28	0.705704660206376	3	FACETS	0.717	0.656	0.782	0.359	0.328	0.391	SUBCLONAL	1	TRUE	1	0.705704660206376	3		569	791	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605131	46605131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762678739	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	168	710	0	ENST00000263734.3:c.1348G>A	p.Glu450Lys	p.E450K	ENST00000263734	NM_001430.4	450	Gag/Aag	10/16	0.557881945085931	5	FACETS	0.818	0.75	0.889	0.273	0.25	0.297	CLONAL	1	TRUE	2	0.705704660206376	5		710	1198	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258542	16258542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs946117307	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	451	627	0	ENST00000375759.3:c.5807G>A	p.Arg1936Gln	p.R1936Q	ENST00000375759	NM_015001.2	1936	cGa/cAa	11/15	0.557881945085931	5	FACETS	1	0.991	1	0.753	0.72	0.786	CLONAL	2	TRUE	2	0.705704660206376	5		627	1165	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087894	27087906	+	frameshift_variant	Frame_Shift_Del	DEL	GCCACCCAGTGGC	GCCACCCAGTGGC	-	novel	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	518	613	0	ENST00000324856.7:c.2181_2193del	p.Pro728SerfsTer10	p.P728Sfs*10	ENST00000324856	NM_006015.4	727	cgGCCACCCAGTGGC/cg	6/20	0.557881945085931	5	FACETS	0.885	0.851	0.92	0.885	0.851	0.92	CLONAL	3	TRUE	2	0.705704660206376	5		613	1138	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105574	27105575	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	359	572	1	ENST00000324856.7:c.5185_5186delinsCT	p.Gly1729Leu	p.G1729L	ENST00000324856	NM_006015.4	1729	GGc/CTc	20/20	0.557881945085931	5	FACETS	1	0.991	1	0.784	0.746	0.822	CLONAL	2	TRUE	2	0.705704660206376	5		573	891	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163306609	163306609	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1335	87	387	0	ENST00000271452.3:c.406G>T	p.Glu136Ter	p.E136*	ENST00000271452	NM_145697.2	136	Gaa/Taa	6/14	0.705704660206376	11	FACETS	0.724	0.638	0.816	0.08	0.07	0.091	SUBCLONAL	1	TRUE	2	0.705704660206376	11		387	1422	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620369	43620369	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	299	600	0	ENST00000355710.3:c.2978A>T	p.Asp993Val	p.D993V	ENST00000355710	NM_020975.4	993	gAc/gTc	18/20	0.64565299640967	3	FACETS	0.831	0.788	0.874	0.831	0.788	0.874	CLONAL	2	TRUE	1	0.705704660206376	3		600	690	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102098228	102098228	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	320	461	0	ENST00000282441.5:c.1192A>G	p.Thr398Ala	p.T398A	ENST00000282441	NM_001130145.2	398	Aca/Gca	8/9	0.705704660206376	3	FACETS	0.974	0.928	1	0.974	0.928	1	CLONAL	2	TRUE	1	0.705704660206376	3		461	630	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027165	49027172	+	frameshift_variant	Frame_Shift_Del	DEL	GACCGAGA	GACCGAGA	-	novel	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	111	426	0	ENST00000267163.4:c.1732_1739del	p.Asp578ArgfsTer4	p.D578Rfs*4	ENST00000267163	NM_000321.2	578	GACCGAGAa/a	18/27	0.610229879477908	2	FACETS	1	0.981	1	0.629	0.577	0.682	CLONAL	1	TRUE	0	0.705704660206376	2		426	250	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68758636	68758636	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	231	402	0	ENST00000487270.1:c.792T>G	p.Ser264Arg	p.S264R	ENST00000487270	NM_133509.3	264	agT/agG	8/11	0.705704660206376	3	FACETS	0.799	0.752	0.847	0.799	0.752	0.847	SUBCLONAL	2	TRUE	1	0.705704660206376	3		402	554	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989217	41989217	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	298	473	1	ENST00000219905.7:c.2009C>G	p.Ser670Ter	p.S670*	ENST00000219905	NM_001164273.1	670	tCa/tGa	3/24	0.705704660206376	3	FACETS	0.962	0.915	1	0.962	0.915	1	CLONAL	2	TRUE	1	0.705704660206376	3		474	594	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292878	91292891	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTAAAGAAATCC	CTGTAAAGAAATCC	-	novel	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	376	529	0	ENST00000355112.3:c.381_394del	p.Val128GlyfsTer10	p.V128Gfs*10	ENST00000355112	NM_000057.2	127	aCTGTAAAGAAATCC/a	3/22	0.705704660206376	3	FACETS	0.97	0.928	1	0.97	0.928	1	CLONAL	2	TRUE	1	0.705704660206376	3		529	743	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622067	1622067	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	287	831	0	ENST00000344749.5:c.808C>G	p.Gln270Glu	p.Q270E	ENST00000344749	NM_001136139.2	270	Cag/Gag	10/19	0.561897029409381	4	FACETS	1	0.98	1	0.366	0.344	0.389	CLONAL	1	TRUE	1	0.705704660206376	4		831	1263	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10257172	10257172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753467933	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	432	524	0	ENST00000340748.4:c.2701G>A	p.Glu901Lys	p.E901K	ENST00000340748		901	Gag/Aag	27/40	0.561897029409381	4	FACETS	0.857	0.824	0.891	0.857	0.824	0.891	CLONAL	3	TRUE	1	0.705704660206376	4		524	812	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095006	11095006	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	312	794	0	ENST00000358026.2:c.179G>T	p.Gly60Val	p.G60V	ENST00000358026	NM_001128849.1	60	gGg/gTg	2/36	0.561897029409381	4	FACETS	1	0.984	1	0.372	0.35	0.395	CLONAL	1	TRUE	1	0.705704660206376	4		794	1350	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096076	11096076	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs759594383	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	101	731	0	ENST00000358026.2:c.350C>G	p.Ser117Cys	p.S117C	ENST00000358026	NM_001128849.1	117	tCc/tGc	3/36	0.561897029409381	4	FACETS	0.413	0.368	0.462	0.138	0.122	0.154	SUBCLONAL	1	TRUE	1	0.705704660206376	4		731	1181	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262317	46262317	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	254	498	0	ENST00000371998.3:c.901A>C	p.Ile301Leu	p.I301L	ENST00000371998		301	Att/Ctt	9/23	0.496944331667745	4	FACETS	0.865	0.813	0.917	0.865	0.813	0.917	CLONAL	2	TRUE	2	0.705704660206376	4		498	710	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278168	41278168	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	185	432	0	ENST00000349496.5:c.2044C>G	p.Leu682Val	p.L682V	ENST00000349496	NM_001904.3	682	Ctc/Gtc	13/15	0.705704660206376	7	FACETS	1	0.987	1	0.266	0.245	0.288	CLONAL	1	TRUE	2	0.705704660206376	7		432	1088	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69788796	69788796	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	189	395	0	ENST00000352241.4:c.48G>C	p.Glu16Asp	p.E16D	ENST00000352241	NM_198159.2	16	gaG/gaC	1/10	0.46886382742983	4	FACETS	0.792	0.736	0.848	0.792	0.736	0.848	SUBCLONAL	2	TRUE	2	0.705704660206376	4		395	577	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72866475	72866476	+	missense_variant	Missense_Mutation	DNP	AG	AG	CC	novel	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	149	385	0	ENST00000325599.8:c.787_788delinsGG	p.Leu263Gly	p.L263G	ENST00000325599	NM_018130.2	263	CTg/GGg	7/11	0.46886382742983	4	FACETS	1	0.988	1	0.725	0.667	0.784	CLONAL	1	TRUE	2	0.705704660206376	4		385	497	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178150	142178150	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	66	348	0	ENST00000350721.4:c.7268T>C	p.Val2423Ala	p.V2423A	ENST00000350721	NM_001184.3	2423	gTa/gCa	43/47	0.557881945085931	5	FACETS	0.716	0.622	0.817	0.239	0.207	0.273	SUBCLONAL	1	TRUE	2	0.705704660206376	5		348	538	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961823	55961823	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	186	374	0	ENST00000263923.4:c.2738T>C	p.Met913Thr	p.M913T	ENST00000263923	NM_002253.2	913	aTg/aCg	20/30	0.64565299640967	3	FACETS	0.874	0.818	0.93	0.874	0.818	0.93	CLONAL	2	TRUE	1	0.705704660206376	3		374	408	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271193	153271193	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	65	238	0	ENST00000281708.4:c.584+1G>T		p.X195_splice	ENST00000281708	NM_033632.3	195			0.610229879477908	2	FACETS	0.845	0.765	0.923	0.845	0.765	0.923	CLONAL	2	TRUE	0	0.705704660206376	2		238	109	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80169025	80169025	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	308	645	0	ENST00000265081.6:c.3221A>G	p.Lys1074Arg	p.K1074R	ENST00000265081	NM_002439.4	1074	aAa/aGa	23/24	0.64565299640967	3	FACETS	0.864	0.821	0.908	0.864	0.821	0.908	CLONAL	2	TRUE	1	0.705704660206376	3		645	683	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721879	176721879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1005975383	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	347	567	1	ENST00000439151.2:c.7510G>A	p.Val2504Ile	p.V2504I	ENST00000439151	NM_022455.4	2504	Gtt/Att	23/23	0.64565299640967	3	FACETS	0.932	0.889	0.974	0.932	0.889	0.974	CLONAL	2	TRUE	1	0.705704660206376	3		568	714	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93953195	93953195	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	207	391	0	ENST00000369303.4:c.2946G>C	p.Gln982His	p.Q982H	ENST00000369303	NM_004440.3	982	caG/caC	17/17	0.46886382742983	4	FACETS	0.847	0.791	0.903	0.847	0.791	0.903	CLONAL	2	TRUE	2	0.705704660206376	4		391	591	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845083	128845083	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	545	839	0	ENST00000249373.3:c.577T>C	p.Cys193Arg	p.C193R	ENST00000249373	NM_005631.4	193	Tgc/Cgc	3/12	0.437749554045618	5	FACETS	1	0.995	1	0.827	0.795	0.86	CLONAL	2	TRUE	2	0.705704660206376	5		839	1281	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453192	140453192	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	138	275	0	ENST00000288602.6:c.1743T>G	p.Asn581Lys	p.N581K	ENST00000288602	NM_004333.4	581	aaT/aaG	15/18	0.437749554045618	5	FACETS	0.941	0.864	1	0.627	0.576	0.68	CLONAL	2	TRUE	2	0.705704660206376	5		275	428	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960110	151960111	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	164	435	0	ENST00000262189.6:c.1289_1290delinsTT	p.Trp430Phe	p.W430F	ENST00000262189	NM_170606.2	430	tGG/tTT	9/59	0.437749554045618	5	FACETS	0.821	0.757	0.886	0.547	0.505	0.591	CLONAL	2	TRUE	2	0.705704660206376	5		435	583	SUCCESS
AR	367	MSKCC	GRCh37	X	66765235	66765235	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039965-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	30	245	0	ENST00000374690.3:c.247A>G	p.Ser83Gly	p.S83G	ENST00000374690	NM_000044.3	83	Agc/Ggc	1/8	0.705704660206376	2	FACETS	0.766	0.631	0.912			1	CLONAL	1	TRUE	NA	0.705704660206376	2		245	111	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578203	7578203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882025	NA	P-0040022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	237	770	0	ENST00000269305.4:c.646G>A	p.Val216Met	p.V216M	ENST00000269305	NM_001126112.2	216	Gtg/Atg	6/11	0.433729069566807	1	FACETS	0.905	0.845	0.966	0.905	0.845	0.966	CLONAL	1	TRUE	0	0.433729069566807	1		770	946	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796868	45796868	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs768222428	NA	P-0040022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	202	603	0	ENST00000450313.1:c.1462A>G	p.Thr488Ala	p.T488A	ENST00000450313	NM_012222.2	488	Acc/Gcc	14/16	1	2	FACETS	0.888	0.823	0.956	0.888	0.823	0.956	CLONAL	1	TRUE	1	0.433729069566807	2		603	1049	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717613	89717625	+	frameshift_variant	Frame_Shift_Del	DEL	CTCAGTTTGTGGT	CTCAGTTTGTGGT	-	novel	NA	P-0040022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	57	430	0	ENST00000371953.3:c.640_652del	p.Gln214AlafsTer3	p.Q214Afs*3	ENST00000371953	NM_000314.4	213	cCTCAGTTTGTGGTc/cc	7/9	0.433729069566807	1	FACETS	0.684	0.591	0.784	0.684	0.591	0.784	SUBCLONAL	1	TRUE	0	0.433729069566807	1		430	301	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47684658	47684658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	49	585	0	ENST00000347630.2:c.791C>T	p.Pro264Leu	p.P264L	ENST00000347630	NM_001007230.1	264	cCa/cTa	9/11	0.433729069566807	1	FACETS	0.323	0.274	0.378	0.323	0.274	0.378	SUBCLONAL	1	TRUE	0	0.433729069566807	1		585	547	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715970	52715970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	183	647	0	ENST00000322088.6:c.535C>T	p.Pro179Ser	p.P179S	ENST00000322088	NM_014225.5	179	Ccc/Tcc	5/15	0.433729069566807	1	FACETS	0.837	0.773	0.902	0.837	0.773	0.902	CLONAL	1	TRUE	0	0.433729069566807	1		647	790	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534805	5534805	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040022-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	146	552	0	ENST00000397747.3:c.116C>A	p.Thr39Asn	p.T39N	ENST00000397747	NM_025239.3	39	aCc/aAc	3/7	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.433729069566807	2		552	630	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0040043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	319	710	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.672837488616537	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.703819756369373	2		710	435	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483087	29483087	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0040043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	74	474	0	ENST00000356175.3:c.147C>G	p.Tyr49Ter	p.Y49*	ENST00000356175	NM_000267.3	49	taC/taG	2/57	0.672837488616537	2	FACETS	0.974	0.896	1	0.974	0.896	1	CLONAL	2	TRUE	0	0.703819756369373	2		474	108	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363363	40363363	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	37	727	1	ENST00000397332.2:c.866C>G	p.Pro289Arg	p.P289R	ENST00000397332	NM_001033082.2	289	cCt/cGt	3/3	0.703819756369373	4	FACETS	0.271	0.223	0.326	0.068	0.055	0.082	SUBCLONAL	1	TRUE	0	0.703819756369373	4		728	660	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852194	63852212	+	frameshift_variant	Frame_Shift_Del	DEL	GCATGGTCCACCCAATCCT	GCATGGTCCACCCAATCCT	-	novel	NA	P-0040043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	28	537	0	ENST00000279873.7:c.2975_2993del	p.Met992ThrfsTer4	p.M992Tfs*4	ENST00000279873	NM_032199.2	991	gGCATGGTCCACCCAATCCTg/gg	10/10	0.703819756369373	4	FACETS	0.283	0.226	0.349	0.142	0.112	0.175	SUBCLONAL	1	TRUE	2	0.703819756369373	4		537	479	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246198	41246198	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	85	459	0	ENST00000357654.3:c.1350del	p.Lys450AsnfsTer3	p.K450Nfs*3	ENST00000357654	NM_007294.3	450	aaA/aa	10/23	0.672837488616537	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	0	0.703819756369373	2		459	118	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164946	47164946	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs368465960	NA	P-0040043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	10	247	0	ENST00000409792.3:c.1180T>C	p.Cys394Arg	p.C394R	ENST00000409792	NM_014159.6	394	Tgt/Cgt	3/21	0.703819756369373	6	FACETS	0.347	0.235	0.488	0.087	0.058	0.122	SUBCLONAL	1	TRUE	2	0.703819756369373	6		247	197	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645338	67645339	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886041997	NA	P-0040058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	230	464	1	ENST00000264010.4:c.610dup	p.Thr204AsnfsTer26	p.T204Nfs*26	ENST00000264010	NM_006565.3	201	-/A	3/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		465	692	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0040058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	141	478	2	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		480	504	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0040058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	45	227	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		227	434	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0040058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	87	254	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		254	434	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087961	27087961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	223	590	0	ENST00000324856.7:c.2248C>T	p.Arg750Ter	p.R750*	ENST00000324856	NM_006015.4	750	Cga/Tga	6/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		590	671	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001303	29001303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201407326	NA	P-0040058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	112	237	0	ENST00000282397.4:c.1429G>A	p.Glu477Lys	p.E477K	ENST00000282397	NM_002019.4	477	Gaa/Aaa	10/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		237	326	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653807	89653807	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	226	308	0	ENST00000371953.3:c.107del	p.Gly36AspfsTer18	p.G36Dfs*18	ENST00000371953	NM_000314.4	35	atG/at	2/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		308	347	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088681	27088682	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0040058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	316	828	1	ENST00000324856.7:c.2296dup	p.Gln766ProfsTer51	p.Q766Pfs*51	ENST00000324856	NM_006015.4	764	tcc/tCcc	7/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		829	957	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593301	67593301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	118	235	0	ENST00000274335.5:c.2047G>A	p.Glu683Lys	p.E683K	ENST00000274335		683	Gag/Aag	15/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		235	380	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828098	243828098	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	161	288	0	ENST00000263826.5:c.260T>A	p.Phe87Tyr	p.F87Y	ENST00000263826	NM_005465.4	87	tTt/tAt	3/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		288	484	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442940	49442940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201530748	NA	P-0040058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	87	548	0	ENST00000301067.7:c.3968G>A	p.Gly1323Asp	p.G1323D	ENST00000301067	NM_003482.3	1323	gGt/gAt	12/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		548	816	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31384664	31384664	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	76	553	0	ENST00000328111.2:c.1366C>T	p.Gln456Ter	p.Q456*	ENST00000328111	NM_006892.3	456	Cag/Tag	13/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		553	837	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356258	66356258	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs780756647	NA	P-0040058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	100	438	0	ENST00000273854.3:c.1239G>T	p.Arg413Ser	p.R413S	ENST00000273854	NM_004439.5	413	agG/agT	5/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		438	706	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020749	26020749	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	87	188	0	ENST00000357647.3:c.32C>G	p.Ser11Cys	p.S11C	ENST00000357647	NM_003529.2	11	tCt/tGt	1/1	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		188	264	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591151	67591154	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	ATGT	ATGT	C	novel	NA	P-0040058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	124	266	0	ENST00000274335.5:c.1744_1745+2delinsC		p.X582_splice	ENST00000274335		582		12/15	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		266	376	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0040061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	93	237	1	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	0.470932991575145	1	FACETS	0.704	0.636	0.775	0.704	0.636	0.775	SUBCLONAL	1	TRUE	0	0.670329905463828	1		238	262	SUCCESS
APC	324	MSKCC	GRCh37	5	112175212	112175216	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAG	AAAAG	-	rs121913224	NA	P-0040061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	18	178	0	ENST00000257430.4:c.3927_3931del	p.Glu1309AspfsTer4	p.E1309Dfs*4	ENST00000257430	NM_000038.5	1307	atAAAAGaa/ataa	16/16	0.470932991575145	1	FACETS	0.187	0.141	0.241	0.187	0.141	0.241	SUBCLONAL	1	TRUE	0	0.670329905463828	1		178	191	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0040061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	492	781	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.670329905463828	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.670329905463828	1		781	907	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907467	32907467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040061-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	153	202	0	ENST00000380152.3:c.1852G>A	p.Ala618Thr	p.A618T	ENST00000380152		618	Gcc/Acc	10/27	0.623325371312015	3	FACETS	0.98	0.913	1	0.98	0.913	1	CLONAL	2	TRUE	1	0.670329905463828	3		202	311	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	195	381	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.296999969594271	1	FACETS	0.691	0.643	0.741	0.691	0.643	0.741	INDETERMINATE	1	TRUE	0	0.613209261531151	1		381	638	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0040062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	374	690	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	0.613209261531151	1	FACETS	0.89	0.848	0.933	0.89	0.848	0.933	CLONAL	1	TRUE	0	0.613209261531151	1		690	950	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603041	48603041	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767361	NA	P-0040062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	79	283	0	ENST00000342988.3:c.1342C>T	p.Gln448Ter	p.Q448*	ENST00000342988	NM_005359.5	448	Cag/Tag	11/12	0.613209261531151	1	FACETS	0.418	0.369	0.47	0.418	0.369	0.47	SUBCLONAL	1	TRUE	0	0.613209261531151	1		283	427	SUCCESS
APC	324	MSKCC	GRCh37	5	112175761	112175761	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	124	273	0	ENST00000257430.4:c.4473del	p.Phe1491LeufsTer16	p.F1491Lfs*16	ENST00000257430	NM_000038.5	1490	caT/ca	16/16	0.250960651295267	1	FACETS	0.639	0.582	0.698	0.639	0.582	0.698	INDETERMINATE	1	TRUE	0	0.613209261531151	1		273	439	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880998	37880998	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs144434331	NA	P-0040062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	399	715	0	ENST00000269571.5:c.2327G>T	p.Gly776Val	p.G776V	ENST00000269571		776	gGt/gTt	20/27	0.250960651295267	1	FACETS	0.767	0.73	0.805	0.767	0.73	0.805	INDETERMINATE	1	TRUE	0	0.613209261531151	1		715	1176	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163325224	163325224	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	42	287	1	ENST00000271452.3:c.1360G>A	p.Glu454Lys	p.E454K	ENST00000271452	NM_145697.2	454	Gaa/Aaa	14/14	1	2	FACETS	0.263	0.219	0.312	0.263	0.219	0.312	SUBCLONAL	1	TRUE	1	0.613209261531151	2		288	521	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218770	66218770	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	96	240	0	ENST00000273854.3:c.2288C>G	p.Thr763Arg	p.T763R	ENST00000273854	NM_004439.5	763	aCa/aGa	13/18	0.613209261531151	1	FACETS	0.901	0.817	0.986	0.901	0.817	0.986	CLONAL	1	TRUE	0	0.613209261531151	1		240	241	SUCCESS
APC	324	MSKCC	GRCh37	5	112173364	112173365	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0040062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	109	271	0	ENST00000257430.4:c.2075dup	p.Lys693Ter	p.K693*	ENST00000257430	NM_000038.5	691	-/C	16/16	0.250960651295267	1	FACETS	0.494	0.445	0.545	0.494	0.445	0.545	INDETERMINATE	1	TRUE	0	0.613209261531151	1		271	499	SUCCESS
APC	324	MSKCC	GRCh37	5	112178345	112178345	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs764311778	NA	P-0040062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	196	366	0	ENST00000257430.4:c.7054A>T	p.Ser2352Cys	p.S2352C	ENST00000257430	NM_000038.5	2352	Agt/Tgt	16/16	0.250960651295267	1	FACETS	0.744	0.693	0.796	0.744	0.693	0.796	INDETERMINATE	1	TRUE	0	0.613209261531151	1		366	596	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967221	93967221	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	122	338	0	ENST00000369303.4:c.2131A>C	p.Ile711Leu	p.I711L	ENST00000369303	NM_004440.3	711	Ata/Cta	12/17	0.585438453648767	2	FACETS	0.804	0.731	0.88	0.402	0.365	0.44	CLONAL	1	TRUE	0	0.613209261531151	2		338	495	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595967	43595967	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763526874	NA	P-0040062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	121	686	0	ENST00000355710.3:c.134C>T	p.Ala45Val	p.A45V	ENST00000355710	NM_020975.4	45	gCa/gTa	2/20	0.296999969594271	1	FACETS	0.257	0.231	0.284	0.257	0.231	0.284	INDETERMINATE	1	TRUE	0	0.613209261531151	1		686	1066	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862749	9862749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150316865	NA	P-0040080-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	259	501	0	ENST00000330684.3:c.2554G>A	p.Val852Met	p.V852M	ENST00000330684	NM_001134407.1	852	Gtg/Atg	12/13	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.70775001219749	2		501	725	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199949	108199949	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0040084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	118	140	0	ENST00000278616.4:c.7291A>T	p.Lys2431Ter	p.K2431*	ENST00000278616	NM_000051.3	2431	Aaa/Taa	49/63	0.673622177353676	4	FACETS	0.86	0.786	0.935	0.86	0.786	0.935	CLONAL	2	TRUE	2	0.73528402056647	4		140	324	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197348	26197348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	173	334	0	ENST00000356476.2:c.131C>T	p.Pro44Leu	p.P44L	ENST00000356476		44	cCc/cTc	1/1	0.603807968551635	5	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.73528402056647	5		334	827	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007746	62007748	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTG	CTG	-	novel	NA	P-0040084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	257	284	0	ENST00000392795.3:c.122-3_122-1del		p.X41_splice	ENST00000392795	NM_001039933.1	41			0.734765134989646	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	2	0.73528402056647	4		284	597	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447337	187447337	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	292	461	0	ENST00000232014.4:c.856C>T	p.Pro286Ser	p.P286S	ENST00000232014	NM_001130845.1	286	Ccc/Tcc	5/10	0.717828373279445	3	FACETS	1	0.989	1	0.59	0.557	0.625	CLONAL	1	TRUE	1	0.73528402056647	3		461	920	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922968	44922968	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040084-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	225	209	0	ENST00000377967.4:c.1829T>G	p.Leu610Arg	p.L610R	ENST00000377967	NM_021140.2	610	cTg/cGg	16/29	0.67334114747113	2	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.73528402056647	2		209	550	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121909224	NA	P-0040122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	53	379	0	ENST00000371953.3:c.388C>G	p.Arg130Gly	p.R130G	ENST00000371953	NM_000314.4	130	Cga/Gga	5/9	1	2	FACETS	0.534	0.455	0.62	0.534	0.455	0.62	SUBCLONAL	1	TRUE	1	0.375496768067572	2		379	529	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967091	18967092	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1384543747	NA	P-0040122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	50	582	0	ENST00000262803.5:c.1814_1815del	p.Glu605AlafsTer17	p.E605Afs*17	ENST00000262803	NM_002911.3	602	gcAGag/gcag	13/24	1	2	FACETS	0.358	0.303	0.419	0.358	0.303	0.419	SUBCLONAL	1	TRUE	1	0.375496768067572	2		582	743	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0040122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	46	748	5	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.4	0.336	0.471	0.4	0.336	0.471	SUBCLONAL	1	TRUE	1	0.375496768067572	2		753	612	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106804	27106804	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	61	636	1	ENST00000324856.7:c.6420del	p.Phe2141SerfsTer59	p.F2141Sfs*59	ENST00000324856	NM_006015.4	2139	Ccc/cc	20/20	1	2	FACETS	0.535	0.461	0.616	0.535	0.461	0.616	SUBCLONAL	1	TRUE	1	0.375496768067572	2		637	607	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0040122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	49	575	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.449	0.38	0.526	0.449	0.38	0.526	SUBCLONAL	1	TRUE	1	0.375496768067572	2		575	581	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	57	600	1	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.546	0.468	0.631	0.546	0.468	0.631	SUBCLONAL	1	TRUE	1	0.375496768067572	2		601	556	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123788	11123788	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1064795105	NA	P-0040122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	29	418	0	ENST00000358026.2:c.2438C>T	p.Ser813Leu	p.S813L	ENST00000358026	NM_001128849.1	813	tCa/tTa	16/36	1	2	FACETS	0.278	0.222	0.341	0.278	0.222	0.341	SUBCLONAL	1	TRUE	1	0.375496768067572	2		418	556	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505443	157505443	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1554231830	NA	P-0040122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	40	432	0	ENST00000346085.5:c.3428del	p.Lys1143SerfsTer68	p.K1143Sfs*68	ENST00000346085	NM_020732.3	1142	Aaa/aa	13/20	1	2	FACETS	0.385	0.319	0.458	0.385	0.319	0.458	SUBCLONAL	1	TRUE	1	0.375496768067572	2		432	554	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952049	178952049	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242945375	NA	P-0040122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	37	269	0	ENST00000263967.3:c.3104C>T	p.Ala1035Val	p.A1035V	ENST00000263967	NM_006218.2	1035	gCt/gTt	21/21	1	2	FACETS	0.479	0.395	0.573	0.479	0.395	0.573	SUBCLONAL	1	TRUE	1	0.375496768067572	2		269	411	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509786	187509786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142057401	NA	P-0040122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	33	259	0	ENST00000441802.2:c.13727C>T	p.Thr4576Met	p.T4576M	ENST00000441802	NM_005245.3	4576	aCg/aTg	27/27	1	2	FACETS	0.596	0.487	0.718	0.596	0.487	0.718	SUBCLONAL	1	TRUE	1	0.375496768067572	2		259	295	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136201	2136201	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	46	491	0	ENST00000219476.3:c.4670G>A	p.Ser1557Asn	p.S1557N	ENST00000219476	NM_000548.3	1557	aGc/aAc	37/42	1	2	FACETS	0.518	0.436	0.608	0.518	0.436	0.608	SUBCLONAL	1	TRUE	1	0.375496768067572	2		491	473	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922306	178922306	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	31	300	0	ENST00000263967.3:c.1075G>C	p.Gly359Arg	p.G359R	ENST00000263967	NM_006218.2	359	Ggt/Cgt	6/21	1	2	FACETS	0.39	0.315	0.475	0.39	0.315	0.475	SUBCLONAL	1	TRUE	1	0.375496768067572	2		300	423	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1255456	1255456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374968697	NA	P-0040122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	77	655	4	ENST00000310581.5:c.3103G>A	p.Val1035Ile	p.V1035I	ENST00000310581	NM_198253.2	1035	Gtc/Atc	14/16	1	2	FACETS	0.618	0.542	0.699	0.618	0.542	0.699	SUBCLONAL	1	TRUE	1	0.375496768067572	2		659	664	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70412340	70412340	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs562629421	NA	P-0040122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	30	249	0	ENST00000373644.4:c.4450A>G	p.Ile1484Val	p.I1484V	ENST00000373644	NM_030625.2	1484	Att/Gtt	6/12	1	2	FACETS	0.431	0.347	0.526	0.431	0.347	0.526	SUBCLONAL	1	TRUE	1	0.375496768067572	2		249	371	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347631	118347631	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	40	433	0	ENST00000534358.1:c.3268A>G	p.Met1090Val	p.M1090V	ENST00000534358	NM_005933.3	1090	Atg/Gtg	4/36	1	2	FACETS	0.378	0.314	0.451	0.378	0.314	0.451	SUBCLONAL	1	TRUE	1	0.375496768067572	2		433	563	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929152	32929152	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1060502390	NA	P-0040122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	28	458	0	ENST00000380152.3:c.7162A>G	p.Thr2388Ala	p.T2388A	ENST00000380152		2388	Aca/Gca	14/27	1	2	FACETS	0.272	0.216	0.335	0.272	0.216	0.335	SUBCLONAL	1	TRUE	1	0.375496768067572	2		458	549	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830071	72830071	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	64	582	1	ENST00000268489.5:c.6510del	p.Ser2171ValfsTer5	p.S2171Vfs*5	ENST00000268489	NM_006885.3	2170	ccC/cc	9/10	1	2	FACETS	0.486	0.42	0.558	0.486	0.42	0.558	SUBCLONAL	1	TRUE	1	0.375496768067572	2		583	701	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831457	72831458	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0040122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	43	496	0	ENST00000268489.5:c.5123_5124del	p.Lys1708ArgfsTer65	p.K1708Rfs*65	ENST00000268489	NM_006885.3	1708	aAA/a	9/10	1	2	FACETS	0.451	0.377	0.533	0.451	0.377	0.533	SUBCLONAL	1	TRUE	1	0.375496768067572	2		496	508	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530121	63530121	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	56	569	0	ENST00000307078.5:c.2314G>T	p.Gly772Trp	p.G772W	ENST00000307078	NM_004655.3	772	Ggg/Tgg	10/11	1	2	FACETS	0.462	0.395	0.535	0.462	0.395	0.535	SUBCLONAL	1	TRUE	1	0.375496768067572	2		569	646	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36220135	36220136	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0040122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	69	682	0	ENST00000222270.7:c.4855_4856del	p.Phe1619ArgfsTer58	p.F1619Rfs*58	ENST00000222270	NM_014727.1	1619	TTc/c	22/37	1	2	FACETS	0.491	0.427	0.561	0.491	0.427	0.561	SUBCLONAL	1	TRUE	1	0.375496768067572	2		682	748	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965845	25965845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	61	550	1	ENST00000435504.4:c.3361G>A	p.Ala1121Thr	p.A1121T	ENST00000435504		1121	Gca/Aca	13/13	1	2	FACETS	0.483	0.416	0.556	0.483	0.416	0.556	SUBCLONAL	1	TRUE	1	0.375496768067572	2		551	673	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274631	198274631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	51	551	1	ENST00000335508.6:c.767C>A	p.Pro256His	p.P256H	ENST00000335508	NM_012433.2	256	cCt/cAt	7/25	1	2	FACETS	0.411	0.349	0.48	0.411	0.349	0.48	SUBCLONAL	1	TRUE	1	0.375496768067572	2		552	661	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526210	31526210	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756928342	NA	P-0040122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	75	745	2	ENST00000344624.3:c.830G>A	p.Arg277His	p.R277H	ENST00000344624		277	cGc/cAc	2/33	1	2	FACETS	0.467	0.408	0.531	0.467	0.408	0.531	SUBCLONAL	1	TRUE	1	0.375496768067572	2		747	855	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176683985	176683985	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	53	430	0	ENST00000439151.2:c.4799G>T	p.Gly1600Val	p.G1600V	ENST00000439151	NM_022455.4	1600	gGg/gTg	13/23	1	2	FACETS	0.407	0.347	0.474	0.407	0.347	0.474	SUBCLONAL	1	TRUE	1	0.375496768067572	2		430	693	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045823	26045823	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	31	446	0	ENST00000540144.1:c.185T>C	p.Leu62Pro	p.L62P	ENST00000540144	NM_003531.2	62	cTg/cCg	1/1	1	2	FACETS	0.371	0.3	0.452	0.371	0.3	0.452	SUBCLONAL	1	TRUE	1	0.375496768067572	2		446	445	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100243	157100253	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGCCGGCTC	GCCGCCGGCTC	-	novel	NA	P-0040122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	21	116	0	ENST00000346085.5:c.1181_1191del	p.Ala394GlyfsTer137	p.A394Gfs*137	ENST00000346085	NM_020732.3	394	GCCGCCGGCTCg/g	1/20	1	2	FACETS	0.805	0.626	1	0.805	0.626	1	CLONAL	1	TRUE	1	0.375496768067572	2		116	139	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs864622237	NA	P-0040123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	305	526	0	ENST00000269305.4:c.700T>G	p.Tyr234Asp	p.Y234D	ENST00000269305	NM_001126112.2	234	Tac/Gac	7/11	0.603452242387326	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.603452242387326	2		526	483	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456470	89456470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147450955	NA	P-0040123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	63	312	0	ENST00000336596.2:c.1646C>T	p.Ala549Val	p.A549V	ENST00000336596	NM_005233.5	549	gCg/gTg	8/17	0.603452242387326	6	FACETS	0.688	0.594	0.789			1	SUBCLONAL	1	TRUE	NA	0.603452242387326	6		312	670	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221236	1221236	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	70	664	0	ENST00000326873.7:c.762del	p.Phe255SerfsTer32	p.F255Sfs*32	ENST00000326873	NM_000455.4	253	taC/ta	6/10	0.603452242387326	2	FACETS	0.362	0.316	0.413	0.181	0.158	0.207	SUBCLONAL	1	TRUE	0	0.603452242387326	2		664	640	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842052	3842052	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	117	369	0	ENST00000262367.5:c.1260G>C	p.Lys420Asn	p.K420N	ENST00000262367	NM_004380.2	420	aaG/aaC	5/31	0.603452242387326	2	FACETS	1	0.96	1	0.546	0.498	0.596	CLONAL	1	TRUE	0	0.603452242387326	2		369	355	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644912	67644920	+	inframe_deletion	In_Frame_Del	DEL	GATGGTGAT	GATGGTGAT	-	novel	NA	P-0040123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	151	510	0	ENST00000264010.4:c.182_190del	p.Val61_Met63del	p.V61_M63del	ENST00000264010	NM_006565.3	59	caGATGGTGATg/cag	3/12	1	2	FACETS	0.972	0.894	1	0.972	0.894	1	CLONAL	1	TRUE	1	0.603452242387326	2		510	515	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59886064	59886064	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	90	410	0	ENST00000259008.2:c.682G>C	p.Glu228Gln	p.E228Q	ENST00000259008	NM_032043.2	228	Gag/Cag	7/20	0.603452242387326	4	FACETS	0.774	0.687	0.866	0.193	0.171	0.217	SUBCLONAL	1	TRUE	0	0.603452242387326	4		410	618	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220498	1220507	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCCGAGGTA	GGCCGAGGTA	-	novel	NA	P-0040123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	54	595	0	ENST00000326873.7:c.594_597+6del		p.X198_splice	ENST00000326873	NM_000455.4	198		4/10	0.603452242387326	2	FACETS	0.32	0.273	0.371	0.16	0.136	0.186	SUBCLONAL	1	TRUE	0	0.603452242387326	2		595	560	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220642	1220661	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGCCCGAGATTGCCAACG	GCCGCCCGAGATTGCCAACG	-	novel	NA	P-0040123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	65	636	0	ENST00000326873.7:c.663_682del	p.Pro222GlyfsTer37	p.P222Gfs*37	ENST00000326873	NM_000455.4	220	caGCCGCCCGAGATTGCCAACGgc/cagc	5/10	0.603452242387326	2	FACETS	0.329	0.285	0.377	0.164	0.142	0.189	SUBCLONAL	1	TRUE	0	0.603452242387326	2		636	655	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39239469	39239469	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	176	352	0	ENST00000402219.2:c.2188G>C	p.Val730Leu	p.V730L	ENST00000402219	NM_005633.3	730	Gtt/Ctt	14/23	0.311402713852497	5	FACETS	1	0.964	1	0.708	0.657	0.761	INDETERMINATE	2	TRUE	2	0.603452242387326	5		352	523	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340267	116340267	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	103	272	0	ENST00000397752.3:c.1129A>C	p.Ile377Leu	p.I377L	ENST00000397752	NM_000245.2	377	Atc/Ctc	2/21	0.603452242387326	7	FACETS	1	0.966	1	0.239	0.214	0.266	CLONAL	1	TRUE	2	0.603452242387326	7		272	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0040154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	471	442	0	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.719292486866476	2	FACETS	0.983	0.953	1	0.983	0.953	1	CLONAL	2	TRUE	0	0.719292486866476	2		442	666	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245948	41245948	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs142074233	NA	P-0040154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	491	454	1	ENST00000357654.3:c.1600C>T	p.Gln534Ter	p.Q534*	ENST00000357654	NM_007294.3	534	Cag/Tag	10/23	0.719292486866476	2	FACETS	0.974	0.945	1	0.974	0.945	1	CLONAL	2	TRUE	0	0.719292486866476	2		455	701	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670488	246670488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	144	355	0	ENST00000388985.4:c.32C>T	p.Thr11Ile	p.T11I	ENST00000388985		11	aCc/aTc	1/12	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.719292486866476	NA		355	556	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268793	98268793	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	222	416	0	ENST00000331920.6:c.290A>C	p.Asn97Thr	p.N97T	ENST00000331920	NM_000264.3	97	aAc/aCc	2/24	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.719292486866476	2		416	617	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0040164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	175	582	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.392652537272844	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.392652537272844	1		582	652	SUCCESS
APC	324	MSKCC	GRCh37	5	112174580	112174580	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	143	325	0	ENST00000257430.4:c.3289G>T	p.Glu1097Ter	p.E1097*	ENST00000257430	NM_000038.5	1097	Gaa/Taa	16/16	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.392652537272844	2		325	502	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	14	340	0	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	0.392652537272844	1	FACETS	0.137	0.098	0.184	0.137	0.098	0.184	SUBCLONAL	1	TRUE	0	0.392652537272844	1		340	418	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920401	114920401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1422891742	NA	P-0040164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	139	425	0	ENST00000543371.1:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000543371	NM_001198531.1	448	Cgg/Tgg	13/14	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.392652537272844	2		425	665	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317267	87317267	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1052977316	NA	P-0040164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	101	335	0	ENST00000277120.3:c.292A>G	p.Ile98Val	p.I98V	ENST00000277120		98	Att/Gtt	4/19	1	2	FACETS	0.956	0.858	1	0.956	0.858	1	CLONAL	1	TRUE	1	0.392652537272844	2		335	538	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457281	67457315	+	frameshift_variant	Frame_Shift_Del	DEL	TGTCATCTACTGCCGCCTGTGGCGATGGCCAGACC	TGTCATCTACTGCCGCCTGTGGCGATGGCCAGACC	-	novel	NA	P-0040164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	43	477	0	ENST00000327367.4:c.257_291del	p.Val86AlafsTer13	p.V86Afs*13	ENST00000327367	NM_005902.3	85	caTGTCATCTACTGCCGCCTGTGGCGATGGCCAGACCtg/catg	2/9	0.392652537272844	1	FACETS	0.303	0.253	0.359	0.303	0.253	0.359	SUBCLONAL	1	TRUE	0	0.392652537272844	1		477	581	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412313	63412314	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	200	602	0	ENST00000330258.3:c.853dup	p.His285ProfsTer2	p.H285Pfs*2	ENST00000330258	NM_152424.3	285	cat/cCat	2/2	0.133917041041494	3	FACETS	0.759	0.705	0.815	0.759	0.705	0.815	INDETERMINATE	2	TRUE	1	0.392652537272844	3		602	803	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	135	290	2	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.54907389360788	4	FACETS	1	0.93	1	0.342	0.311	0.374	CLONAL	1	TRUE	1	0.54907389360788	4		292	743	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531788	46531788	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	126	388	0	ENST00000262741.5:c.559C>T	p.Gln187Ter	p.Q187*	ENST00000262741	NM_003629.3	187	Cag/Tag	5/10	1	2	FACETS	0.855	0.777	0.935	0.855	0.777	0.935	CLONAL	1	TRUE	1	0.54907389360788	2		388	537	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330511	65330511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	182	441	0	ENST00000342505.4:c.1135G>A	p.Glu379Lys	p.E379K	ENST00000342505	NM_002227.2	379	Gag/Aag	8/25	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.54907389360788	2		441	662	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246490544	246490544	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	159	479	0	ENST00000388985.4:c.490C>T	p.Gln164Ter	p.Q164*	ENST00000388985		164	Cag/Tag	5/12	0.54907389360788	4	FACETS	0.88	0.806	0.958	0.293	0.268	0.32	CLONAL	1	TRUE	1	0.54907389360788	4		479	1019	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527795	103527795	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	139	366	0	ENST00000355739.4:c.3103G>C	p.Glu1035Gln	p.E1035Q	ENST00000355739	NM_000123.3	1035	Gaa/Caa	15/15	1	2	FACETS	0.895	0.818	0.974	0.895	0.818	0.974	CLONAL	1	TRUE	1	0.54907389360788	2		366	566	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061461	38061461	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	423	553	0	ENST00000250448.2:c.528C>G	p.Ile176Met	p.I176M	ENST00000250448	NM_004496.3	176	atC/atG	2/2	0.462950440992348	4	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.54907389360788	4		553	1094	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105237107	105237107	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs751976958	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	184	583	0	ENST00000349310.3:c.1338G>T	p.Met446Ile	p.M446I	ENST00000349310	NM_001014432.1	446	atG/atT	14/15	0.108535367737953	6	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.54907389360788	6		583	1035	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658833	3658833	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	192	603	1	ENST00000294008.3:c.133G>A	p.Asp45Asn	p.D45N	ENST00000294008	NM_032444.2	45	Gat/Aat	2/15	1	2	FACETS	0.884	0.819	0.951	0.884	0.819	0.951	CLONAL	1	TRUE	1	0.54907389360788	2		604	791	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835751	68835752	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	192	574	0	ENST00000261769.5:c.343dup	p.Thr115AsnfsTer53	p.T115Nfs*53	ENST00000261769	NM_004360.3	114	-/A	3/16	0.54907389360788	1	FACETS	0.974	0.908	1	0.974	0.908	1	CLONAL	1	TRUE	0	0.54907389360788	1		574	521	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832025	72832025	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	176	567	0	ENST00000268489.5:c.4556C>G	p.Ser1519Ter	p.S1519*	ENST00000268489	NM_006885.3	1519	tCa/tGa	9/10	0.54907389360788	1	FACETS	0.941	0.875	1	0.941	0.875	1	CLONAL	1	TRUE	0	0.54907389360788	1		567	494	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341230	89341230	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	197	498	0	ENST00000301030.4:c.7705G>T	p.Glu2569Ter	p.E2569*	ENST00000301030	NM_001256183.1	2569	Gag/Tag	11/13	0.54907389360788	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.54907389360788	1		498	470	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858892	89858892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773687142	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	220	651	0	ENST00000389301.3:c.1070C>T	p.Ser357Leu	p.S357L	ENST00000389301	NM_000135.2	357	tCa/tTa	12/43	0.54907389360788	1	FACETS	0.982	0.92	1	0.982	0.92	1	CLONAL	1	TRUE	0	0.54907389360788	1		651	592	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011144	12011144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	96	335	0	ENST00000353533.5:c.551C>T	p.Ser184Leu	p.S184L	ENST00000353533	NM_003010.3	184	tCg/tTg	5/11	0.54907389360788	1	FACETS	0.848	0.765	0.934	0.848	0.765	0.934	CLONAL	1	TRUE	0	0.54907389360788	1		335	299	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879583	37879583	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	255	575	0	ENST00000269571.5:c.1958C>G	p.Ser653Cys	p.S653C	ENST00000269571		653	tCc/tGc	17/27	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.54907389360788	2		575	782	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770135	56770135	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	145	481	0	ENST00000337432.4:c.131C>G	p.Ser44Cys	p.S44C	ENST00000337432	NM_058216.2	44	tCc/tGc	1/9	1	2	FACETS	0.804	0.735	0.875	0.804	0.735	0.875	CLONAL	1	TRUE	1	0.54907389360788	2		481	657	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262160	10262160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	220	685	0	ENST00000340748.4:c.2131G>A	p.Glu711Lys	p.E711K	ENST00000340748		711	Gag/Aag	23/40	1	2	FACETS	0.933	0.869	0.998	0.933	0.869	0.998	CLONAL	1	TRUE	1	0.54907389360788	2		685	859	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610242	10610242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	245	773	1	ENST00000171111.5:c.468G>A	p.Met156Ile	p.M156I	ENST00000171111	NM_203500.1	156	atG/atA	2/6	1	2	FACETS	0.868	0.811	0.926	0.868	0.811	0.926	CLONAL	1	TRUE	1	0.54907389360788	2		774	1028	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610505	10610505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	274	621	2	ENST00000171111.5:c.205G>A	p.Glu69Lys	p.E69K	ENST00000171111	NM_203500.1	69	Gag/Aag	2/6	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.54907389360788	2		623	953	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610685	10610685	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187892356	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	215	527	1	ENST00000171111.5:c.25G>A	p.Gly9Arg	p.G9R	ENST00000171111	NM_203500.1	9	Ggg/Agg	2/6	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.54907389360788	2		528	707	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965421	18965421	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	133	388	0	ENST00000262803.5:c.1168G>C	p.Glu390Gln	p.E390Q	ENST00000262803	NM_002911.3	390	Gag/Cag	9/24	1	2	FACETS	0.956	0.873	1	0.956	0.873	1	CLONAL	1	TRUE	1	0.54907389360788	2		388	507	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748850	41748850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138698106	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	237	657	0	ENST00000301178.4:c.1375G>A	p.Val459Met	p.V459M	ENST00000301178	NM_021913.4	459	Gtg/Atg	11/20	1	2	FACETS	0.966	0.903	1	0.966	0.903	1	CLONAL	1	TRUE	1	0.54907389360788	2		657	894	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754685	42754685	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	85	297	0	ENST00000222329.4:c.55G>C	p.Glu19Gln	p.E19Q	ENST00000222329	NM_006494.2	19	Gag/Cag	2/4	0.108535367737953	6	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.54907389360788	6		297	504	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991658	25991658	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	139	422	0	ENST00000435504.4:c.584C>A	p.Ser195Ter	p.S195*	ENST00000435504		195	tCa/tAa	7/13	1	2	FACETS	0.861	0.787	0.938	0.861	0.787	0.938	CLONAL	1	TRUE	1	0.54907389360788	2		422	588	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547861	41547861	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	129	456	0	ENST00000263253.7:c.2842G>A	p.Glu948Lys	p.E948K	ENST00000263253	NM_001429.3	948	Gaa/Aaa	15/31	0.548942197154412	2	FACETS	0.728	0.662	0.798	0.364	0.331	0.399	SUBCLONAL	1	TRUE	0	0.54907389360788	2		456	645	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268787	41268787	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	180	489	0	ENST00000349496.5:c.1025G>C	p.Arg342Thr	p.R342T	ENST00000349496	NM_001904.3	342	aGa/aCa	7/15	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.54907389360788	2		489	638	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610700	52610700	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	80	363	0	ENST00000394830.3:c.3473G>A	p.Trp1158Ter	p.W1158*	ENST00000394830	NM_018313.4	1158	tGg/tAg	23/30	1	2	FACETS	0.671	0.594	0.754	0.671	0.594	0.754	SUBCLONAL	1	TRUE	1	0.54907389360788	2		363	434	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478177	138478177	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	84	374	0	ENST00000289153.2:c.9C>A	p.Phe3Leu	p.F3L	ENST00000289153	NM_006219.2	3	ttC/ttA	1/22	0.54907389360788	4	FACETS	0.602	0.531	0.678	0.201	0.177	0.226	SUBCLONAL	1	TRUE	1	0.54907389360788	4		374	787	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593470	55593470	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	137	358	0	ENST00000288135.5:c.1627C>G	p.Leu543Val	p.L543V	ENST00000288135	NM_000222.2	543	Ctg/Gtg	10/21	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.54907389360788	2		358	493	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680286	30680286	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	260	729	0	ENST00000376406.3:c.1433G>C	p.Arg478Thr	p.R478T	ENST00000376406	NM_014641.2	478	aGa/aCa	5/15	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.54907389360788	2		729	928	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681429	30681429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	101	423	1	ENST00000376406.3:c.583G>A	p.Glu195Lys	p.E195K	ENST00000376406	NM_014641.2	195	Gag/Aag	4/15	1	2	FACETS	0.719	0.645	0.796	0.719	0.645	0.796	SUBCLONAL	1	TRUE	1	0.54907389360788	2		424	512	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163297	32163297	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	254	810	0	ENST00000375023.3:c.5929G>C	p.Glu1977Gln	p.E1977Q	ENST00000375023	NM_004557.3	1977	Gag/Cag	30/30	1	2	FACETS	0.912	0.854	0.972	0.912	0.854	0.972	CLONAL	1	TRUE	1	0.54907389360788	2		810	1014	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138775	37138775	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	188	618	0	ENST00000373509.5:c.208G>C	p.Glu70Gln	p.E70Q	ENST00000373509	NM_002648.3	70	Gag/Cag	3/6	1	2	FACETS	0.952	0.883	1	0.952	0.883	1	CLONAL	1	TRUE	1	0.54907389360788	2		618	719	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001464	150001464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	190	539	1	ENST00000253339.5:c.2140G>A	p.Gly714Arg	p.G714R	ENST00000253339		714	Gga/Aga	4/7	1	2	FACETS	0.908	0.842	0.977	0.908	0.842	0.977	CLONAL	1	TRUE	1	0.54907389360788	2		540	762	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976764	2976764	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	194	667	0	ENST00000396946.4:c.1248G>C	p.Glu416Asp	p.E416D	ENST00000396946	NM_032415.4	416	gaG/gaC	9/25	0.548942197154412	2	FACETS	0.84	0.779	0.904	0.42	0.389	0.452	CLONAL	1	TRUE	0	0.54907389360788	2		667	841	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38139062	38139062	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	179	506	0	ENST00000317025.8:c.3541G>C	p.Glu1181Gln	p.E1181Q	ENST00000317025	NM_023034.1	1181	Gaa/Caa	20/24	1	2	FACETS	0.902	0.834	0.972	0.902	0.834	0.972	CLONAL	1	TRUE	1	0.54907389360788	2		506	723	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742108	145742108	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	248	653	0	ENST00000428558.2:c.395G>A	p.Arg132Lys	p.R132K	ENST00000428558	NM_004260.3	132	aGa/aAa	5/22	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.54907389360788	2		653	828	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974765	21974768	+	frameshift_variant	Frame_Shift_Del	DEL	GCCG	GCCG	AC	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	261	306	1	ENST00000304494.5:c.59_62delinsGT	p.Ala20GlyfsTer23	p.A20Gfs*23	ENST00000304494	NM_000077.4	20	gCGGCc/gGTc	1/3	0.462950440992348	4	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.54907389360788	4		307	626	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97934369	97934369	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	130	377	0	ENST00000289081.3:c.406C>T	p.Gln136Ter	p.Q136*	ENST00000289081	NM_000136.2	136	Caa/Taa	5/15	1	2	FACETS	0.883	0.805	0.965	0.883	0.805	0.965	CLONAL	1	TRUE	1	0.54907389360788	2		377	536	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911378	39911378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	148	420	0	ENST00000378444.4:c.5252C>T	p.Ser1751Leu	p.S1751L	ENST00000378444	NM_001123385.1	1751	tCa/tTa	15/15	1	2	FACETS	0.857	0.785	0.931	0.857	0.785	0.931	CLONAL	1	TRUE	1	0.54907389360788	2		420	629	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945137	44945137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	173	480	0	ENST00000377967.4:c.3461C>T	p.Ser1154Leu	p.S1154L	ENST00000377967	NM_021140.2	1154	tCa/tTa	24/29	1	2	FACETS	0.929	0.858	1	0.929	0.858	1	CLONAL	1	TRUE	1	0.54907389360788	2		480	678	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179110	123179110	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040166-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	164	507	0	ENST00000218089.9:c.559C>T	p.Gln187Ter	p.Q187*	ENST00000218089	NM_001042749.1	187	Caa/Taa	8/35	1	2	FACETS	0.9	0.829	0.973	0.9	0.829	0.973	CLONAL	1	TRUE	1	0.54907389360788	2		507	664	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560463	95560463	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	333	650	1	ENST00000393063.1:c.5126A>T	p.Asp1709Val	p.D1709V	ENST00000393063	NM_030621.3	1709	gAt/gTt	25/28	0.431665077833791	0	FACETS	0.678	0.65	0.706			1	SUBCLONAL	2	TRUE	0	0.472165761617023	0		651	549	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0040195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	141	217	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.991	0.907	1	0.991	0.907	1	CLONAL	1	TRUE	1	0.515683984801969	2		217	552	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0040195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	102	337	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.956	0.861	1	0.956	0.861	1	CLONAL	1	TRUE	1	0.515683984801969	2		337	414	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141502	11141502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	72	912	0	ENST00000358026.2:c.3479G>A	p.Gly1160Glu	p.G1160E	ENST00000358026	NM_001128849.1	1160	gGg/gAg	25/36	1	2	FACETS	0.285	0.248	0.325	0.285	0.248	0.325	SUBCLONAL	1	TRUE	1	0.515683984801969	2		912	979	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444582	78444586	+	frameshift_variant	Frame_Shift_Del	DEL	TGCAG	TGCAG	-	novel	NA	P-0040195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	112	577	0	ENST00000370768.2:c.103_107del	p.Leu35GlufsTer12	p.L35Efs*12	ENST00000370768	NM_003902.3	35	CTGCAg/g	1/20	0.515683984801969	1	FACETS	0.641	0.579	0.706	0.641	0.579	0.706	SUBCLONAL	1	TRUE	0	0.515683984801969	1		577	503	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793444	42793444	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040195-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	37	806	1	ENST00000575354.2:c.1250del	p.Pro417ArgfsTer18	p.P417Rfs*18	ENST00000575354	NM_015125.3	416	Ccc/cc	8/20	0.515683984801969	1	FACETS	0.151	0.124	0.182	0.151	0.124	0.182	SUBCLONAL	1	TRUE	0	0.515683984801969	1		807	703	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846398	128846398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879255280	NA	P-0040210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	263	723	0	ENST00000249373.3:c.1234C>T	p.Leu412Phe	p.L412F	ENST00000249373	NM_005631.4	412	Ctc/Ttc	6/12	1	2	FACETS	0.983	0.924	1	0.983	0.924	1	CLONAL	1	TRUE	1	0.64	2		723	836	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577567	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1567549651	NA	P-0040243-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	501	534	1	ENST00000269305.4:c.714dup	p.Asn239Ter	p.N239*	ENST00000269305	NM_001126112.2	238	-/T	7/11	0.915492857884557	1	FACETS	0.986	0.964	1	0.986	0.964	1	CLONAL	1	TRUE	0	0.915492857884557	1		535	602	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221123	5221123	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769925793	NA	P-0040249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	244	551	0	ENST00000357368.4:c.3343G>A	p.Ala1115Thr	p.A1115T	ENST00000357368	NM_002850.3	1115	Gcc/Acc	20/38	1	2	FACETS	0.84	0.789	0.893	0.84	0.789	0.893	CLONAL	1	TRUE	1	0.79005704930395	2		551	735	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727429	66727429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	33	400	0	ENST00000307102.5:c.145C>T	p.Arg49Cys	p.R49C	ENST00000307102	NM_002755.3	49	Cgc/Tgc	2/11	0.79005704930395	1	FACETS	0.135	0.109	0.163	0.135	0.109	0.163	SUBCLONAL	1	TRUE	0	0.79005704930395	1		400	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574002	7574002	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	882	684	1	ENST00000269305.4:c.1025del	p.Arg342GlnfsTer3	p.R342Qfs*3	ENST00000269305	NM_001126112.2	342	cGa/ca	10/11	NA	2	FACETS	1	0.998	1			1	INDETERMINATE	2	TRUE	NA	0.79005704930395	2		685	1013	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210313	123210313	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	93	243	0	ENST00000218089.9:c.2665T>G	p.Tyr889Asp	p.Y889D	ENST00000218089	NM_001042749.1	889	Tat/Gat	26/35	0.79005704930395	1	FACETS	0.705	0.642	0.769	0.705	0.642	0.769	SUBCLONAL	1	TRUE	0	0.79005704930395	1		243	202	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023401	27023423	+	frameshift_variant	Frame_Shift_Del	DEL	CCACCAACAACATGGCGGACAAC	CCACCAACAACATGGCGGACAAC	-	novel	NA	P-0040249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	59	391	2	ENST00000324856.7:c.507_529del	p.Phe169LeufsTer223	p.F169Lfs*223	ENST00000324856	NM_006015.4	169	ttCCACCAACAACATGGCGGACAACaa/ttaa	1/20	0.79005704930395	1	FACETS	0.502	0.44	0.567	0.502	0.44	0.567	SUBCLONAL	1	TRUE	0	0.79005704930395	1		393	180	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274791	123274791	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	168	506	0	ENST00000358487.5:c.1127T>C	p.Leu376Pro	p.L376P	ENST00000358487	NM_000141.4	376	cTg/cCg	9/18	NA	2	FACETS	0.892	0.827	0.958			1	INDETERMINATE	1	TRUE	NA	0.79005704930395	2		506	477	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281778	49281778	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	48	626	0	ENST00000282018.3:c.825A>T	p.Lys275Asn	p.K275N	ENST00000282018	NM_020377.2	275	aaA/aaT	1/1	0.79005704930395	1	FACETS	0.144	0.121	0.168	0.144	0.121	0.168	SUBCLONAL	1	TRUE	0	0.79005704930395	1		626	512	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984692	72984692	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	55	674	0	ENST00000268489.5:c.2892C>G	p.His964Gln	p.H964Q	ENST00000268489	NM_006885.3	964	caC/caG	3/10	0.79005704930395	1	FACETS	0.182	0.155	0.211	0.182	0.155	0.211	SUBCLONAL	1	TRUE	0	0.79005704930395	1		674	463	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560229	29560447	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGGTAAGTGATTAGAGTAAGCGGGGAAGAAAAGTGCCTGGCACATAGCAAATCCTTCAGAATATATTTGTTCAATAAATGTTTGTTGAATGAATTGATAAAATTTCAGAGCCAGAAGAAAGATGTTTAGTTAGGTGATTTTTCAGCTGTAGGGAAGTGGTTGGCACCACTAGACCTGACTAGTGTTCTGTATCATTTCATCCTACTAAAAAATTCCAT	TGGGTAAGTGATTAGAGTAAGCGGGGAAGAAAAGTGCCTGGCACATAGCAAATCCTTCAGAATATATTTGTTCAATAAATGTTTGTTGAATGAATTGATAAAATTTCAGAGCCAGAAGAAAGATGTTTAGTTAGGTGATTTTTCAGCTGTAGGGAAGTGGTTGGCACCACTAGACCTGACTAGTGTTCTGTATCATTTCATCCTACTAAAAAATTCCAT	-	novel	NA	P-0040249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	13	190	0	ENST00000356175.3:c.3707_3708+217del		p.X1236_splice	ENST00000356175	NM_000267.3	1236		27/57	NA	2	FACETS	0.141	0.1	0.19			1	INDETERMINATE	1	TRUE	NA	0.79005704930395	2		190	234	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56367745	56367745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1266114717	NA	P-0040249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	142	327	0	ENST00000348428.3:c.571C>G	p.Arg191Gly	p.R191G	ENST00000348428	NM_006785.3	191	Cga/Gga	4/17	0.79005704930395	1	FACETS	0.8	0.744	0.854	0.8	0.744	0.854	SUBCLONAL	1	TRUE	0	0.79005704930395	1		327	272	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149309	61149309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	12	309	0	ENST00000295025.8:c.1499C>T	p.Thr500Ile	p.T500I	ENST00000295025	NM_002908.2	500	aCa/aTa	11/11	1	2	FACETS	0.153	0.108	0.21	0.153	0.108	0.21	SUBCLONAL	1	TRUE	1	0.79005704930395	2		309	198	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847252	68847252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141864044	NA	P-0040264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	48	538	1	ENST00000261769.5:c.1174G>A	p.Val392Ile	p.V392I	ENST00000261769	NM_004360.3	392	Gta/Ata	9/16	1	2	FACETS	0.929	0.783	1	0.929	0.783	1	CLONAL	1	TRUE	1	0.13	2		539	795	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0040264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	75	663	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.13	2		667	887	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0040264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	22	317	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.802	0.62	1	0.802	0.62	1	CLONAL	1	TRUE	1	0.13	2		317	422	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088681	27088682	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0040264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	56	828	1	ENST00000324856.7:c.2296dup	p.Gln766ProfsTer51	p.Q766Pfs*51	ENST00000324856	NM_006015.4	764	tcc/tCcc	7/20	1	2	FACETS	0.832	0.711	0.966	0.832	0.711	0.966	CLONAL	1	TRUE	1	0.13	2		829	1035	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399386	139399386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201360886	NA	P-0040264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	59	913	1	ENST00000277541.6:c.4757G>A	p.Arg1586His	p.R1586H	ENST00000277541	NM_017617.3	1586	cGc/cAc	26/34	1	2	FACETS	0.8	0.685	0.925	0.8	0.685	0.925	CLONAL	1	TRUE	1	0.13	2		914	1135	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106078	27106078	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	44	582	0	ENST00000324856.7:c.5693del	p.Pro1898HisfsTer25	p.P1898Hfs*25	ENST00000324856	NM_006015.4	1897	Ccc/cc	20/20	1	2	FACETS	0.953	0.798	1	0.953	0.798	1	CLONAL	1	TRUE	1	0.13	2		582	710	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480483	57480483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	31	340	0	ENST00000371085.3:c.478C>T	p.Arg160Cys	p.R160C	ENST00000371085	NM_000516.4	160	Cgt/Tgt	6/13	1	2	FACETS	0.849	0.685	1	0.849	0.685	1	CLONAL	1	TRUE	1	0.13	2		340	562	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532710	187532710	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1010116749	NA	P-0040264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	39	482	0	ENST00000441802.2:c.9683del	p.Pro3228LeufsTer42	p.P3228Lfs*42	ENST00000441802	NM_005245.3	3228	cCt/ct	14/27	1	2	FACETS	0.799	0.66	0.955	0.799	0.66	0.955	CLONAL	1	TRUE	1	0.13	2		482	751	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354152	15354152	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs868796773	NA	P-0040264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	47	726	2	ENST00000263377.2:c.2728del	p.Gln910LysfsTer39	p.Q910Kfs*39	ENST00000263377	NM_058243.2	910	Caa/aa	14/20	1	2	FACETS	0.858	0.722	1	0.858	0.722	1	CLONAL	1	TRUE	1	0.13	2		728	843	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514777	44514777	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs371246226	NA	P-0040264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	36	494	0	ENST00000291552.4:c.470A>G	p.Gln157Arg	p.Q157R	ENST00000291552	NM_006758.2	157	cAg/cGg	6/8	1	2	FACETS	0.659	0.54	0.794	0.659	0.54	0.794	SUBCLONAL	1	TRUE	1	0.13	2		494	840	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72897475	72897475	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	27	480	0	ENST00000325599.8:c.17T>G	p.Phe6Cys	p.F6C	ENST00000325599	NM_018130.2	6	tTc/tGc	1/11	1	2	FACETS	0.802	0.637	0.992	0.802	0.637	0.992	CLONAL	1	TRUE	1	0.13	2		480	518	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955875	55955875	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	29	351	0	ENST00000263923.4:c.3287G>A	p.Trp1096Ter	p.W1096*	ENST00000263923	NM_002253.2	1096	tGg/tAg	24/30	1	2	FACETS	0.822	0.658	1	0.822	0.658	1	CLONAL	1	TRUE	1	0.13	2		351	543	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656263	18656263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762092026	NA	P-0040264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	29	486	0	ENST00000266497.5:c.2942G>A	p.Arg981His	p.R981H	ENST00000266497		981	cGc/cAc	21/31	1	2	FACETS	0.78	0.624	0.958	0.78	0.624	0.958	CLONAL	1	TRUE	1	0.13	2		486	572	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061720	38061720	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301834713	NA	P-0040264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	30	357	2	ENST00000250448.2:c.269C>T	p.Ala90Val	p.A90V	ENST00000250448	NM_004496.3	90	gCg/gTg	2/2	1	2	FACETS	0.982	0.79	1	0.982	0.79	1	CLONAL	1	TRUE	1	0.13	2		359	470	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716251	52716251	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	52	845	0	ENST00000322088.6:c.695C>A	p.Ala232Asp	p.A232D	ENST00000322088	NM_014225.5	232	gCc/gAc	6/15	1	2	FACETS	0.839	0.712	0.979	0.839	0.712	0.979	CLONAL	1	TRUE	1	0.13	2		845	954	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662683	227662683	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866580419	NA	P-0040264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	60	740	3	ENST00000305123.5:c.772C>T	p.Arg258Trp	p.R258W	ENST00000305123	NM_005544.2	258	Cgg/Tgg	1/2	1	2	FACETS	0.893	0.767	1	0.893	0.767	1	CLONAL	1	TRUE	1	0.13	2		743	1034	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022603	36022603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	64	807	0	ENST00000358208.4:c.476G>A	p.Arg159Gln	p.R159Q	ENST00000358208		159	cGg/cAg	5/12	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.13	2		807	962	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141583024	141583024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200483361	NA	P-0040264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	51	717	1	ENST00000220592.5:c.223G>A	p.Val75Met	p.V75M	ENST00000220592	NM_012154.3	75	Gtg/Atg	3/19	1	2	FACETS	0.818	0.693	0.957	0.818	0.693	0.957	CLONAL	1	TRUE	1	0.13	2		718	959	SUCCESS
AR	367	MSKCC	GRCh37	X	66765409	66765409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs865948546	NA	P-0040264-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	45	847	0	ENST00000374690.3:c.421G>A	p.Ala141Thr	p.A141T	ENST00000374690	NM_000044.3	141	Gcc/Acc	1/8	1	2	FACETS	0.776	0.65	0.917	0.776	0.65	0.917	CLONAL	1	TRUE	1	0.13	2		847	892	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0040281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	198	510	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.256504197123822	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.262748353741591	2		510	732	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432126	49432126	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	75	753	0	ENST00000301067.7:c.9013G>C	p.Asp3005His	p.D3005H	ENST00000301067	NM_003482.3	3005	Gat/Cat	34/54	0.262748353741591	3	FACETS	0.675	0.59	0.767	0.337	0.295	0.384	SUBCLONAL	1	TRUE	1	0.262748353741591	3		753	957	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435432	121435432	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	108	839	0	ENST00000257555.6:c.1465T>C	p.Phe489Leu	p.F489L	ENST00000257555		489	Ttc/Ctc	7/10	0.262748353741591	3	FACETS	1	0.943	1	0.359	0.322	0.399	CLONAL	1	TRUE	0	0.262748353741591	3		839	863	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858359	59858359	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	63	391	0	ENST00000259008.2:c.1636G>A	p.Asp546Asn	p.D546N	ENST00000259008	NM_032043.2	546	Gat/Aat	12/20	0.256504197123822	2	FACETS	1	0.944	1	0.585	0.508	0.668	CLONAL	1	TRUE	0	0.262748353741591	2		391	410	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214390	36214390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	220	727	0	ENST00000222270.7:c.3044G>A	p.Arg1015Gln	p.R1015Q	ENST00000222270	NM_014727.1	1015	cGa/cAa	7/37	0.262748353741591	5	FACETS	1	0.977	1	0.744	0.692	0.798	CLONAL	2	TRUE	2	0.262748353741591	5		727	1046	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010560	48010560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	96	595	0	ENST00000234420.5:c.188C>T	p.Ser63Phe	p.S63F	ENST00000234420	NM_000179.2	63	tCc/tTc	1/10	0.262748353741591	3	FACETS	1	0.962	1	0.59	0.525	0.658	CLONAL	1	TRUE	1	0.262748353741591	3		595	701	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147778	61147778	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0040281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	36	261	0	ENST00000295025.8:c.1087+1G>T		p.X363_splice	ENST00000295025	NM_002908.2	363			0.262748353741591	3	FACETS	0.945	0.779	1	0.473	0.389	0.565	CLONAL	1	TRUE	1	0.262748353741591	3		261	328	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023018	150023018	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	177	619	0	ENST00000253339.5:c.245G>A	p.Arg82Gln	p.R82Q	ENST00000253339		82	cGa/cAa	1/7	0.262748353741591	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.262748353741591	3		619	727	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0040283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	203	687	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.392962403318342	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.392962403318342	1		687	822	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467203	25467203	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040283-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	109	552	0	ENST00000264709.3:c.1672T>C	p.Phe558Leu	p.F558L	ENST00000264709	NM_175629.2	558	Ttt/Ctt	15/23	1	2	FACETS	0.945	0.851	1	0.945	0.851	1	CLONAL	1	TRUE	1	0.392962403318342	2		552	587	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	225	880	0	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.51	2		880	866	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087961	27087961	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	146	590	0	ENST00000324856.7:c.2248C>T	p.Arg750Ter	p.R750*	ENST00000324856	NM_006015.4	750	Cga/Tga	6/20	1	2	FACETS	0.855	0.782	0.93	0.855	0.782	0.93	CLONAL	1	TRUE	1	0.51	2		590	670	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784333	9784333	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	128	627	2	ENST00000377346.4:c.2719-1G>A		p.X907_splice	ENST00000377346	NM_005026.3	907			1	2	FACETS	0.839	0.763	0.919	0.839	0.763	0.919	CLONAL	1	TRUE	1	0.51	2		629	598	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	158	428	0	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	1	2	FACETS	0.988	0.909	1	0.988	0.909	1	CLONAL	1	TRUE	1	0.51	2		428	627	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736557	85736557	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	69	295	0	ENST00000370580.1:c.90G>T	p.Glu30Asp	p.E30D	ENST00000370580	NM_003921.4	30	gaG/gaT	2/3	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.51	2		295	270	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510194	120510194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199565938	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	135	554	0	ENST00000256646.2:c.1315G>A	p.Ala439Thr	p.A439T	ENST00000256646	NM_024408.3	439	Gcc/Acc	8/34	1	2	FACETS	0.903	0.824	0.986	0.903	0.824	0.986	CLONAL	1	TRUE	1	0.51	2		554	586	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870376	155870376	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	144	594	1	ENST00000368323.3:c.463G>T	p.Glu155Ter	p.E155*	ENST00000368323	NM_006912.5	155	Gaa/Taa	6/6	1	2	FACETS	0.964	0.883	1	0.964	0.883	1	CLONAL	1	TRUE	1	0.51	2		595	586	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578316	226578316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs193238922	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	82	462	3	ENST00000366794.5:c.412C>T	p.Arg138Cys	p.R138C	ENST00000366794	NM_001618.3	138	Cgc/Tgc	4/23	1	2	FACETS	0.549	0.484	0.618	0.549	0.484	0.618	SUBCLONAL	1	TRUE	1	0.51	2		465	586	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	244006434	244006434	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	170	664	0	ENST00000263826.5:c.39G>T	p.Gln13His	p.Q13H	ENST00000263826	NM_005465.4	13	caG/caT	1/13	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.51	2		664	660	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845627	63845627	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	77	328	0	ENST00000279873.7:c.1366G>T	p.Glu456Ter	p.E456*	ENST00000279873	NM_032199.2	456	Gaa/Taa	9/10	1	2	FACETS	0.788	0.696	0.886	0.788	0.696	0.886	SUBCLONAL	1	TRUE	1	0.51	2		328	383	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851828	63851828	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs201944744	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	224	770	0	ENST00000279873.7:c.2606C>A	p.Ser869Tyr	p.S869Y	ENST00000279873	NM_032199.2	869	tCt/tAt	10/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.51	2		770	857	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70360773	70360773	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	20	246	0	ENST00000373644.4:c.1950G>T	p.Lys650Asn	p.K650N	ENST00000373644	NM_030625.2	650	aaG/aaT	3/12	1	2	FACETS	0.272	0.208	0.347	0.272	0.208	0.347	SUBCLONAL	1	TRUE	1	0.51	2		246	288	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	106	554	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.932	0.841	1	0.932	0.841	1	CLONAL	1	TRUE	1	0.51	2		554	446	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720683	89720683	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	31	103	0	ENST00000371953.3:c.834C>A	p.Phe278Leu	p.F278L	ENST00000371953	NM_000314.4	278	ttC/ttA	8/9	1	2	FACETS	0.921	0.758	1	0.921	0.758	1	CLONAL	1	TRUE	1	0.51	2		103	132	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720870	89720870	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1554825652	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	137	347	0	ENST00000371953.3:c.1021T>G	p.Phe341Val	p.F341V	ENST00000371953	NM_000314.4	341	Ttt/Gtt	8/9	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.51	2		347	396	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771467	112771467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	166	624	0	ENST00000369452.4:c.1640G>A	p.Ser547Asn	p.S547N	ENST00000369452	NM_007373.3	547	aGt/aAt	9/9	1	2	FACETS	0.903	0.831	0.977	0.903	0.831	0.977	CLONAL	1	TRUE	1	0.51	2		624	721	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239530	123239530	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	289	1005	0	ENST00000358487.5:c.2307C>A	p.Tyr769Ter	p.Y769*	ENST00000358487	NM_000141.4	769	taC/taA	18/18	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.51	2		1005	1106	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102098216	102098216	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	139	499	0	ENST00000282441.5:c.1180C>T	p.Arg394Ter	p.R394*	ENST00000282441	NM_001130145.2	394	Cga/Tga	8/9	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.51	2		499	539	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172385	108172385	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764389018	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	74	486	0	ENST00000278616.4:c.5188C>T	p.Arg1730Ter	p.R1730*	ENST00000278616	NM_000051.3	1730	Cga/Tga	35/63	1	2	FACETS	0.758	0.667	0.854	0.758	0.667	0.854	SUBCLONAL	1	TRUE	1	0.51	2		486	383	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431589	431589	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	140	453	0	ENST00000399788.2:c.2420A>C	p.Lys807Thr	p.K807T	ENST00000399788	NM_001042603.1	807	aAa/aCa	17/28	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.51	2		453	531	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658237	18658238	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	49	550	0	ENST00000266497.5:c.3047dup	p.Tyr1017LeufsTer17	p.Y1017Lfs*17	ENST00000266497		1014	-/T	22/31	1	2	FACETS	0.386	0.327	0.451	0.386	0.327	0.451	SUBCLONAL	1	TRUE	1	0.51	2		550	498	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861838	57861838	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381253752	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	176	811	0	ENST00000228682.2:c.1139G>A	p.Arg380Gln	p.R380Q	ENST00000228682	NM_005269.2	380	cGa/cAa	10/12	1	2	FACETS	0.972	0.898	1	0.972	0.898	1	CLONAL	1	TRUE	1	0.51	2		811	710	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69210685	69210685	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	37	392	0	ENST00000462284.1:c.268G>T	p.Asp90Tyr	p.D90Y	ENST00000462284	NM_002392.5	90	Gat/Tat	4/11	1	2	FACETS	0.359	0.296	0.43	0.359	0.296	0.43	SUBCLONAL	1	TRUE	1	0.51	2		392	404	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123889443	123889443	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756109032	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	40	546	0	ENST00000330479.4:c.670G>A	p.Asp224Asn	p.D224N	ENST00000330479	NM_020382.3	224	Gat/Aat	7/9	1	2	FACETS	0.279	0.231	0.332	0.279	0.231	0.332	SUBCLONAL	1	TRUE	1	0.51	2		546	562	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	160	674	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	0.885	0.813	0.959	0.885	0.813	0.959	CLONAL	1	TRUE	1	0.51	2		674	709	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597505	28597505	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	129	525	0	ENST00000241453.7:c.2400A>C	p.Glu800Asp	p.E800D	ENST00000241453	NM_004119.2	800	gaA/gaC	19/24	1	2	FACETS	0.99	0.903	1	0.99	0.903	1	CLONAL	1	TRUE	1	0.51	2		525	511	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911751	32911751	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	57	524	0	ENST00000380152.3:c.3259A>G	p.Thr1087Ala	p.T1087A	ENST00000380152		1087	Acc/Gcc	11/27	1	2	FACETS	0.474	0.407	0.546	0.474	0.407	0.546	SUBCLONAL	1	TRUE	1	0.51	2		524	472	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911847	32911847	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	118	554	1	ENST00000380152.3:c.3355G>T	p.Glu1119Ter	p.E1119*	ENST00000380152		1119	Gaa/Taa	11/27	1	2	FACETS	0.918	0.833	1	0.918	0.833	1	CLONAL	1	TRUE	1	0.51	2		555	504	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347911	73347911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146500302	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	27	395	0	ENST00000377767.4:c.1150C>T	p.Arg384Cys	p.R384C	ENST00000377767	NM_014953.3	384	Cgc/Tgc	8/21	1	2	FACETS	0.314	0.25	0.387	0.314	0.25	0.387	SUBCLONAL	1	TRUE	1	0.51	2		395	337	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528078	103528078	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368829739	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	143	506	0	ENST00000355739.4:c.3386C>T	p.Ser1129Leu	p.S1129L	ENST00000355739	NM_000123.3	1129	tCg/tTg	15/15	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.51	2		506	561	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068866	30068866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	111	547	0	ENST00000331968.5:c.2063C>T	p.Thr688Ile	p.T688I	ENST00000331968	NM_002742.2	688	aCt/aTt	14/18	1	2	FACETS	0.879	0.794	0.968	0.879	0.794	0.968	CLONAL	1	TRUE	1	0.51	2		547	495	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135385	30135385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	117	451	1	ENST00000331968.5:c.433C>T	p.Arg145Cys	p.R145C	ENST00000331968	NM_002742.2	145	Cgt/Tgt	3/18	1	2	FACETS	0.819	0.741	0.901	0.819	0.741	0.901	CLONAL	1	TRUE	1	0.51	2		452	560	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569922	95569922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1249975103	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	38	506	0	ENST00000393063.1:c.3811C>T	p.Leu1271Phe	p.L1271F	ENST00000393063	NM_030621.3	1271	Ctc/Ttc	22/28	1	2	FACETS	0.289	0.239	0.346	0.289	0.239	0.346	SUBCLONAL	1	TRUE	1	0.51	2		506	515	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473664	67473664	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	97	797	0	ENST00000327367.4:c.744C>A	p.Phe248Leu	p.F248L	ENST00000327367	NM_005902.3	248	ttC/ttA	6/9	1	2	FACETS	0.497	0.442	0.554	0.497	0.442	0.554	SUBCLONAL	1	TRUE	1	0.51	2		797	766	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3841994	3841994	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	61	381	0	ENST00000262367.5:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000262367	NM_004380.2	440	Cga/Tga	5/31	1	2	FACETS	0.466	0.403	0.535	0.466	0.403	0.535	SUBCLONAL	1	TRUE	1	0.51	2		381	513	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858472	9858472	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs776506065	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	154	638	0	ENST00000330684.3:c.2929A>C	p.Asn977His	p.N977H	ENST00000330684	NM_001134407.1	977	Aac/Cac	13/13	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.51	2		638	596	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650710	67650710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243010179	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	218	699	0	ENST00000264010.4:c.1015C>T	p.Arg339Trp	p.R339W	ENST00000264010	NM_006565.3	339	Cgg/Tgg	5/12	1	2	FACETS	0.957	0.892	1	0.957	0.892	1	CLONAL	1	TRUE	1	0.51	2		699	893	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827580	72827580	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	193	727	2	ENST00000268489.5:c.9001G>T	p.Glu3001Ter	p.E3001*	ENST00000268489	NM_006885.3	3001	Gaa/Taa	9/10	1	2	FACETS	0.912	0.845	0.981	0.912	0.845	0.981	CLONAL	1	TRUE	1	0.51	2		729	830	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347828	89347828	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1043713257	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	184	786	0	ENST00000301030.4:c.5122T>C	p.Ser1708Pro	p.S1708P	ENST00000301030	NM_001256183.1	1708	Tcg/Ccg	9/13	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.51	2		786	707	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562747	29562747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137854556	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	143	529	0	ENST00000356175.3:c.3827G>A	p.Arg1276Gln	p.R1276Q	ENST00000356175	NM_000267.3	1276	cGa/cAa	28/57	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.51	2		529	532	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654856	29654856	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1049849034	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	34	299	0	ENST00000356175.3:c.5545C>T	p.Arg1849Trp	p.R1849W	ENST00000356175	NM_000267.3	1849	Cgg/Tgg	37/57	1	2	FACETS	0.419	0.343	0.504	0.419	0.343	0.504	SUBCLONAL	1	TRUE	1	0.51	2		299	318	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	71	394	1	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.859	0.756	0.969	0.859	0.756	0.969	CLONAL	1	TRUE	1	0.51	2		395	324	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322617	30322617	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	120	506	1	ENST00000322652.5:c.1630C>A	p.Leu544Ile	p.L544I	ENST00000322652	NM_015355.2	544	Ctt/Att	14/16	1	2	FACETS	0.955	0.867	1	0.955	0.867	1	CLONAL	1	TRUE	1	0.51	2		507	493	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734107	58734107	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	160	789	0	ENST00000305921.3:c.1165G>A	p.Asp389Asn	p.D389N	ENST00000305921	NM_003620.3	389	Gat/Aat	5/6	1	2	FACETS	0.882	0.811	0.957	0.882	0.811	0.957	CLONAL	1	TRUE	1	0.51	2		789	711	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740668	58740668	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs759850701	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	151	688	0	ENST00000305921.3:c.1573G>T	p.Glu525Ter	p.E525*	ENST00000305921	NM_003620.3	525	Gaa/Taa	6/6	1	2	FACETS	0.903	0.828	0.981	0.903	0.828	0.981	CLONAL	1	TRUE	1	0.51	2		688	656	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60795942	60795942	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	204	678	0	ENST00000333681.4:c.636C>A	p.Phe212Leu	p.F212L	ENST00000333681		212	ttC/ttA	3/3	1	2	FACETS	0.991	0.921	1	0.991	0.921	1	CLONAL	1	TRUE	1	0.51	2		678	807	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122751	7122751	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	174	731	1	ENST00000302850.5:c.3403G>T	p.Glu1135Ter	p.E1135*	ENST00000302850	NM_000208.2	1135	Gag/Tag	19/22	1	2	FACETS	0.918	0.847	0.992	0.918	0.847	0.992	CLONAL	1	TRUE	1	0.51	2		732	743	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18965932	18965932	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	185	792	0	ENST00000262803.5:c.1426-1G>A		p.X476_splice	ENST00000262803	NM_002911.3	476			1	2	FACETS	0.971	0.899	1	0.971	0.899	1	CLONAL	1	TRUE	1	0.51	2		792	747	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216622	36216622	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	176	822	0	ENST00000222270.7:c.3790-2A>G		p.X1264_splice	ENST00000222270	NM_014727.1	1264			1	2	FACETS	0.869	0.802	0.939	0.869	0.802	0.939	CLONAL	1	TRUE	1	0.51	2		822	794	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383220	42383220	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs926961615	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	69	799	0	ENST00000221972.3:c.240C>A	p.Phe80Leu	p.F80L	ENST00000221972	NM_021601.3	80	ttC/ttA	2/5	1	2	FACETS	0.345	0.299	0.394	0.345	0.299	0.394	SUBCLONAL	1	TRUE	1	0.51	2		799	785	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796594	42796594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762323815	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	38	824	1	ENST00000575354.2:c.3151G>A	p.Ala1051Thr	p.A1051T	ENST00000575354	NM_015125.3	1051	Gcc/Acc	13/20	1	2	FACETS	0.204	0.167	0.244	0.204	0.167	0.244	SUBCLONAL	1	TRUE	1	0.51	2		825	732	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716329	52716329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863225094	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	184	765	0	ENST00000322088.6:c.773G>A	p.Arg258His	p.R258H	ENST00000322088	NM_014225.5	258	cGc/cAc	6/15	1	2	FACETS	0.975	0.902	1	0.975	0.902	1	CLONAL	1	TRUE	1	0.51	2		765	740	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027594	48027594	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	88	380	0	ENST00000234420.5:c.2472A>C	p.Lys824Asn	p.K824N	ENST00000234420	NM_000179.2	824	aaA/aaC	4/10	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.51	2		380	305	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715367	61715367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	122	593	0	ENST00000401558.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000401558	NM_003400.3	749	cGa/cAa	19/25	1	2	FACETS	0.938	0.852	1	0.938	0.852	1	CLONAL	1	TRUE	1	0.51	2		593	510	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617581	158617581	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	97	543	0	ENST00000263640.3:c.1075G>A	p.Val359Ile	p.V359I	ENST00000263640	NM_001105.4	359	Gtc/Atc	9/11	1	2	FACETS	0.789	0.707	0.876	0.789	0.707	0.876	SUBCLONAL	1	TRUE	1	0.51	2		543	482	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136322	202136322	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	137	503	0	ENST00000358485.4:c.566A>C	p.Lys189Thr	p.K189T	ENST00000358485	NM_001080125.1	189	aAa/aCa	3/9	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.51	2		503	536	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137487	202137487	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	160	601	0	ENST00000358485.4:c.715G>T	p.Glu239Ter	p.E239*	ENST00000358485	NM_001080125.1	239	Gaa/Taa	4/9	1	2	FACETS	0.93	0.855	1	0.93	0.855	1	CLONAL	1	TRUE	1	0.51	2		601	675	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251595	212251595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1044752647	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	69	538	0	ENST00000342788.4:c.3464G>A	p.Arg1155Gln	p.R1155Q	ENST00000342788	NM_005235.2	1155	cGa/cAa	27/28	1	2	FACETS	0.552	0.482	0.628	0.552	0.482	0.628	SUBCLONAL	1	TRUE	1	0.51	2		538	490	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293161	212293161	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	88	392	0	ENST00000342788.4:c.2691C>A	p.Phe897Leu	p.F897L	ENST00000342788	NM_005235.2	897	ttC/ttA	22/28	1	2	FACETS	0.892	0.795	0.993	0.892	0.795	0.993	CLONAL	1	TRUE	1	0.51	2		392	387	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259192	36259192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	168	761	1	ENST00000300305.3:c.299C>T	p.Ser100Phe	p.S100F	ENST00000300305		100	tCc/tTc	3/8	1	2	FACETS	0.887	0.817	0.959	0.887	0.817	0.959	CLONAL	1	TRUE	1	0.51	2		762	743	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641252	12641252	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	43	583	0	ENST00000251849.4:c.1046T>G	p.Val349Gly	p.V349G	ENST00000251849	NM_002880.3	349	gTg/gGg	10/17	1	2	FACETS	0.291	0.243	0.344	0.291	0.243	0.344	SUBCLONAL	1	TRUE	1	0.51	2		583	580	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180292	38180292	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1319438	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	226	823	0	ENST00000396334.3:c.140C>A	p.Ser47Tyr	p.S47Y	ENST00000396334	NM_002468.4	47	tCt/tAt	1/5	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.51	2		823	821	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266112	41266112	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913228	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	113	408	0	ENST00000349496.5:c.109T>C	p.Ser37Pro	p.S37P	ENST00000349496	NM_001904.3	37	Tct/Cct	3/15	1	2	FACETS	0.963	0.872	1	0.963	0.872	1	CLONAL	1	TRUE	1	0.51	2		408	460	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610695	52610695	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	77	418	1	ENST00000394830.3:c.3478C>T	p.Arg1160Ter	p.R1160*	ENST00000394830	NM_018313.4	1160	Cga/Tga	23/30	1	2	FACETS	0.807	0.713	0.907	0.807	0.713	0.907	CLONAL	1	TRUE	1	0.51	2		419	374	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69788814	69788814	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	99	433	0	ENST00000352241.4:c.66A>C	p.Lys22Asn	p.K22N	ENST00000352241	NM_198159.2	22	aaA/aaC	1/10	1	2	FACETS	0.805	0.722	0.893	0.805	0.722	0.893	CLONAL	1	TRUE	1	0.51	2		433	482	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720985	119720985	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	165	591	0	ENST00000316626.5:c.190A>C	p.Asn64His	p.N64H	ENST00000316626		64	Aat/Cat	2/12	1	2	FACETS	0.988	0.91	1	0.988	0.91	1	CLONAL	1	TRUE	1	0.51	2		591	655	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268448	142268448	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564283952	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	92	508	1	ENST00000350721.4:c.3044G>A	p.Arg1015Gln	p.R1015Q	ENST00000350721	NM_001184.3	1015	cGa/cAa	15/47	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.51	2		509	345	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922363	178922363	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	104	436	0	ENST00000263967.3:c.1132T>C	p.Cys378Arg	p.C378R	ENST00000263967	NM_006218.2	378	Tgt/Cgt	6/21	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.51	2		436	397	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430663	181430663	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	201	802	1	ENST00000325404.1:c.515G>A	p.Ser172Asn	p.S172N	ENST00000325404	NM_003106.3	172	aGc/aAc	1/1	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.51	2		803	758	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136805	55136805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41279521	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	39	284	0	ENST00000257290.5:c.1127G>A	p.Arg376Gln	p.R376Q	ENST00000257290	NM_006206.4	376	cGa/cAa	8/23	1	2	FACETS	0.381	0.316	0.454	0.381	0.316	0.454	SUBCLONAL	1	TRUE	1	0.51	2		284	401	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953916	55953916	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	28	433	0	ENST00000263923.4:c.3520G>T	p.Asp1174Tyr	p.D1174Y	ENST00000263923	NM_002253.2	1174	Gac/Tac	27/30	1	2	FACETS	0.242	0.193	0.299	0.242	0.193	0.299	SUBCLONAL	1	TRUE	1	0.51	2		433	453	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158369	106158369	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	66	360	0	ENST00000380013.4:c.3270G>T	p.Lys1090Asn	p.K1090N	ENST00000380013	NM_001127208.2	1090	aaG/aaT	3/11	1	2	FACETS	0.707	0.617	0.804	0.707	0.617	0.804	SUBCLONAL	1	TRUE	1	0.51	2		360	366	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510192	187510192	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	167	631	0	ENST00000441802.2:c.13321G>T	p.Asp4441Tyr	p.D4441Y	ENST00000441802	NM_005245.3	4441	Gac/Tac	27/27	1	2	FACETS	0.898	0.827	0.972	0.898	0.827	0.972	CLONAL	1	TRUE	1	0.51	2		631	729	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31486602	31486602	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1008113408	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	89	446	0	ENST00000344624.3:c.1910C>T	p.Pro637Leu	p.P637L	ENST00000344624		637	cCg/cTg	11/33	1	2	FACETS	0.79	0.704	0.881	0.79	0.704	0.881	SUBCLONAL	1	TRUE	1	0.51	2		446	442	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	144	223	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	1	0.935	1	1	0.992	1	CLONAL	2	TRUE	1	0.51	2		223	281	SUCCESS
APC	324	MSKCC	GRCh37	5	112177901	112177901	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs752654519	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	111	419	0	ENST00000257430.4:c.6610C>T	p.Arg2204Ter	p.R2204*	ENST00000257430	NM_000038.5	2204	Cga/Tga	16/16	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.51	2		419	424	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637141	176637141	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	149	718	0	ENST00000439151.2:c.1741G>T	p.Glu581Ter	p.E581*	ENST00000439151	NM_022455.4	581	Gaa/Taa	5/23	1	2	FACETS	0.847	0.776	0.921	0.847	0.776	0.921	CLONAL	1	TRUE	1	0.51	2		718	690	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405111	405111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	159	652	0	ENST00000380956.4:c.1193G>T	p.Arg398Ile	p.R398I	ENST00000380956	NM_001195286.1	398	aGa/aTa	8/9	1	2	FACETS	0.896	0.823	0.971	0.896	0.823	0.971	CLONAL	1	TRUE	1	0.51	2		652	696	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109315802	109315802	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	124	517	0	ENST00000436639.2:c.983C>A	p.Ser328Tyr	p.S328Y	ENST00000436639	NM_014454.2	328	tCt/tAt	6/10	1	2	FACETS	0.891	0.809	0.976	0.891	0.809	0.976	CLONAL	1	TRUE	1	0.51	2		517	546	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609759	117609759	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs771164515	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	134	585	0	ENST00000368508.3:c.6940G>T	p.Asp2314Tyr	p.D2314Y	ENST00000368508	NM_002944.2	2314	Gat/Tat	43/43	1	2	FACETS	0.879	0.801	0.96	0.879	0.801	0.96	CLONAL	1	TRUE	1	0.51	2		585	598	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647564	117647564	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	112	559	0	ENST00000368508.3:c.5380A>C	p.Asn1794His	p.N1794H	ENST00000368508	NM_002944.2	1794	Aat/Cat	33/43	1	2	FACETS	0.882	0.797	0.971	0.882	0.797	0.971	CLONAL	1	TRUE	1	0.51	2		559	498	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519589	137519589	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	102	462	0	ENST00000367739.4:c.1049C>A	p.Ser350Tyr	p.S350Y	ENST00000367739	NM_000416.2	350	tCt/tAt	7/7	1	2	FACETS	0.87	0.782	0.962	0.87	0.782	0.962	CLONAL	1	TRUE	1	0.51	2		462	460	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415537	152415537	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519714	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	139	641	0	ENST00000206249.3:c.1387T>C	p.Ser463Pro	p.S463P	ENST00000206249	NM_000125.3	463	Tcc/Ccc	7/8	1	2	FACETS	0.858	0.784	0.936	0.858	0.784	0.936	CLONAL	1	TRUE	1	0.51	2		641	635	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211097	55211097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219568637	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	71	561	0	ENST00000275493.2:c.340G>A	p.Glu114Lys	p.E114K	ENST00000275493	NM_005228.3	114	Gaa/Aaa	3/28	1	2	FACETS	0.493	0.43	0.56	0.493	0.43	0.56	SUBCLONAL	1	TRUE	1	0.51	2		561	565	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513160	106513160	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	92	366	0	ENST00000359195.3:c.2064C>A	p.Asn688Lys	p.N688K	ENST00000359195	NM_002649.2	688	aaC/aaA	4/11	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.51	2		366	338	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339243	116339243	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	118	443	0	ENST00000397752.3:c.105G>T	p.Met35Ile	p.M35I	ENST00000397752	NM_000245.2	35	atG/atT	2/21	1	2	FACETS	0.997	0.905	1	0.997	0.905	1	CLONAL	1	TRUE	1	0.51	2		443	464	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411975	116411975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910937816	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	208	847	2	ENST00000397752.3:c.2960G>A	p.Arg987Gln	p.R987Q	ENST00000397752	NM_000245.2	987	cGa/cAa	14/21	1	2	FACETS	0.932	0.866	1	0.932	0.866	1	CLONAL	1	TRUE	1	0.51	2		849	875	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538874	23538874	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	35	618	0	ENST00000380871.4:c.565G>T	p.Gly189Ter	p.G189*	ENST00000380871	NM_006167.3	189	Gga/Tga	2/2	1	2	FACETS	0.221	0.18	0.266	0.221	0.18	0.266	SUBCLONAL	1	TRUE	1	0.51	2		618	622	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68950493	68950493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760821149	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	35	459	1	ENST00000288368.4:c.805G>A	p.Asp269Asn	p.D269N	ENST00000288368	NM_024870.2	269	Gat/Aat	7/40	1	2	FACETS	0.313	0.256	0.376	0.313	0.256	0.376	SUBCLONAL	1	TRUE	1	0.51	2		460	439	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457177	5457177	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	84	438	0	ENST00000381577.3:c.151G>A	p.Ala51Thr	p.A51T	ENST00000381577	NM_014143.3	51	Gct/Act	3/7	1	2	FACETS	0.883	0.786	0.986	0.883	0.786	0.986	CLONAL	1	TRUE	1	0.51	2		438	373	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341216	8341216	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	39	428	0	ENST00000356435.5:c.5000C>A	p.Pro1667Gln	p.P1667Q	ENST00000356435		1667	cCa/cAa	30/35	1	2	FACETS	0.436	0.362	0.518	0.436	0.362	0.518	SUBCLONAL	1	TRUE	1	0.51	2		428	351	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504401	8504401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757922864	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	118	475	0	ENST00000356435.5:c.1682G>A	p.Arg561Gln	p.R561Q	ENST00000356435		561	cGa/cAa	12/35	1	2	FACETS	0.944	0.857	1	0.944	0.857	1	CLONAL	1	TRUE	1	0.51	2		475	490	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158095	27158095	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	93	685	0	ENST00000380036.4:c.319C>T	p.Arg107Ter	p.R107*	ENST00000380036	NM_000459.3	107	Cga/Tga	2/23	1	2	FACETS	0.498	0.443	0.557	0.498	0.443	0.557	SUBCLONAL	1	TRUE	1	0.51	2		685	732	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342871	87342871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200996090	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	112	453	0	ENST00000277120.3:c.1156G>A	p.Asp386Asn	p.D386N	ENST00000277120		386	Gat/Aat	9/19	1	2	FACETS	0.938	0.849	1	0.938	0.849	1	CLONAL	1	TRUE	1	0.51	2		453	468	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776149	135776149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1169898186	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	134	605	1	ENST00000298552.3:c.2578G>A	p.Glu860Lys	p.E860K	ENST00000298552	NM_001162426.1	860	Gag/Aag	20/23	1	2	FACETS	0.843	0.769	0.922	0.843	0.769	0.922	CLONAL	1	TRUE	1	0.51	2		606	623	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412685	139412694	+	protein_altering_variant	In_Frame_Del	DEL	AGTTGGAGCC	AGTTGGAGCC	G	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	193	969	0	ENST00000277541.6:c.1150_1159delinsC	p.Gly384_Cys387delinsArg	p.G384_C387delinsR	ENST00000277541	NM_017617.3	384	GGCTCCAACTgc/Cgc	7/34	1	2	FACETS	0.85	0.787	0.916	0.85	0.787	0.916	CLONAL	1	TRUE	1	0.51	2		969	890	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932732	39932732	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	237	1086	0	ENST00000378444.4:c.1867G>T	p.Glu623Ter	p.E623*	ENST00000378444	NM_001123385.1	623	Gaa/Taa	4/15	1	2	FACETS	0.837	0.781	0.896	0.837	0.781	0.896	CLONAL	1	TRUE	1	0.51	2		1086	1110	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938415	44938415	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	41	509	0	ENST00000377967.4:c.2963C>A	p.Thr988Asn	p.T988N	ENST00000377967	NM_021140.2	988	aCt/aAt	20/29	1	2	FACETS	0.303	0.252	0.36	0.303	0.252	0.36	SUBCLONAL	1	TRUE	1	0.51	2		509	531	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966775	44966775	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	56	673	0	ENST00000377967.4:c.3999T>G	p.Ile1333Met	p.I1333M	ENST00000377967	NM_021140.2	1333	atT/atG	27/29	1	2	FACETS	0.383	0.328	0.444	0.383	0.328	0.444	SUBCLONAL	1	TRUE	1	0.51	2		673	573	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240792	53240792	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	153	749	0	ENST00000375401.3:c.1288A>C	p.Asn430His	p.N430H	ENST00000375401	NM_004187.3	430	Aat/Cat	10/26	1	2	FACETS	0.84	0.77	0.913	0.84	0.77	0.913	CLONAL	1	TRUE	1	0.51	2		749	714	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410489	63410489	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	178	854	0	ENST00000330258.3:c.2678G>T	p.Ser893Ile	p.S893I	ENST00000330258	NM_152424.3	893	aGc/aTc	2/2	1	2	FACETS	0.946	0.874	1	0.946	0.874	1	CLONAL	1	TRUE	1	0.51	2		854	738	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413008	63413008	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	244	998	0	ENST00000330258.3:c.159G>T	p.Lys53Asn	p.K53N	ENST00000330258	NM_152424.3	53	aaG/aaT	2/2	1	2	FACETS	0.995	0.93	1	0.995	0.93	1	CLONAL	1	TRUE	1	0.51	2		998	962	SUCCESS
AR	367	MSKCC	GRCh37	X	66765778	66765778	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	242	1041	0	ENST00000374690.3:c.790C>T	p.Arg264Trp	p.R264W	ENST00000374690	NM_000044.3	264	Cgg/Tgg	1/8	1	2	FACETS	0.933	0.872	0.996	0.933	0.872	0.996	CLONAL	1	TRUE	1	0.51	2		1041	1017	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344018	70344018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747113641	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	156	805	0	ENST00000374080.3:c.1754G>A	p.Arg585Gln	p.R585Q	ENST00000374080		585	cGa/cAa	13/45	1	2	FACETS	0.758	0.695	0.824	0.758	0.695	0.824	SUBCLONAL	1	TRUE	1	0.51	2		805	807	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829806	76829806	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	72	588	0	ENST00000373344.5:c.6235C>T	p.Arg2079Ter	p.R2079*	ENST00000373344	NM_000489.3	2079	Cga/Tga	28/35	1	2	FACETS	0.646	0.566	0.731	0.646	0.566	0.731	SUBCLONAL	1	TRUE	1	0.51	2		588	437	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920242	76920242	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	74	373	0	ENST00000373344.5:c.3835G>T	p.Glu1279Ter	p.E1279*	ENST00000373344	NM_000489.3	1279	Gaa/Taa	11/35	1	2	FACETS	0.804	0.708	0.905	0.804	0.708	0.905	CLONAL	1	TRUE	1	0.51	2		373	361	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937751	76937751	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	58	542	0	ENST00000373344.5:c.2997G>T	p.Lys999Asn	p.K999N	ENST00000373344	NM_000489.3	999	aaG/aaT	9/35	1	2	FACETS	0.471	0.405	0.543	0.471	0.405	0.543	SUBCLONAL	1	TRUE	1	0.51	2		542	483	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939073	76939073	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040284-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	109	588	0	ENST00000373344.5:c.1675T>C	p.Ser559Pro	p.S559P	ENST00000373344	NM_000489.3	559	Tca/Cca	9/35	1	2	FACETS	0.827	0.746	0.912	0.827	0.746	0.912	CLONAL	1	TRUE	1	0.51	2		588	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576900	7576906	+	frameshift_variant	Frame_Shift_Del	DEL	GAGAGGA	GAGAGGA	-	novel	NA	P-0040319-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	315	537	0	ENST00000269305.4:c.940_946del	p.Ser314ProfsTer29	p.S314Pfs*29	ENST00000269305	NM_001126112.2	314	TCCTCTCcc/cc	9/11	0.333850675993945	4	FACETS	1	0.988	1	0.841	0.799	0.884	CLONAL	3	TRUE	0	0.342528361117697	4		537	734	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920132	76920132	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0040319-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	134	348	0	ENST00000373344.5:c.3943+2T>G		p.X1315_splice	ENST00000373344	NM_000489.3	1315			0.342528361117697	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	0	0.342528361117697	2		348	386	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196812	108196812	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0040335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	23	253	0	ENST00000278616.4:c.6835A>T	p.Lys2279Ter	p.K2279*	ENST00000278616	NM_000051.3	2279	Aaa/Taa	47/63	1	2	FACETS	0.499	0.389	0.626	0.499	0.389	0.626	SUBCLONAL	1	TRUE	1	0.289217677118728	2		253	319	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124309	2124309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	71	812	0	ENST00000219476.3:c.2464G>A	p.Ala822Thr	p.A822T	ENST00000219476	NM_000548.3	822	Gcg/Acg	22/42	1	2	FACETS	0.519	0.452	0.592	0.519	0.452	0.592	SUBCLONAL	1	TRUE	1	0.289217677118728	2		812	946	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470560	25470560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs765341003	NA	P-0040359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	334	552	1	ENST00000264709.3:c.914G>A	p.Trp305Ter	p.W305*	ENST00000264709	NM_175629.2	305	tGg/tAg	8/23	0.758111786580983	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.758111786580983	1		553	474	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593606	55593650	+	inframe_deletion	In_Frame_Del	DEL	AAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGAC	AAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGAC	-	novel	NA	P-0040359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	100	273	0	ENST00000288135.5:c.1672_1716del	p.Lys558_Asp572del	p.K558_D572del	ENST00000288135	NM_000222.2	558	AAGGTTGTTGAGGAGATAAATGGAAACAATTATGTTTACATAGAC/-	11/21	1	2	FACETS	0.871	0.788	0.956	0.871	0.788	0.956	CLONAL	1	TRUE	1	0.758111786580983	2		273	303	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30664701	30664701	+	intron_variant	Intron	SNP	G	G	A	novel	NA	P-0040359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	92	193	0	ENST00000295754.5:c.94+16232G>A		p.*32*	ENST00000295754	NM_003242.5	35/592			1	2	FACETS	0.889	0.801	0.98	0.889	0.801	0.98	CLONAL	1	TRUE	1	0.758111786580983	2		193	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576893	7576893	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	441	546	0	ENST00000269305.4:c.953del	p.Pro318GlnfsTer27	p.P318Qfs*27	ENST00000269305	NM_001126112.2	318	cCa/ca	9/11	0.64095194183391	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.64095194183391	2		546	657	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020290	123020290	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040451-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	196	450	0	ENST00000355640.3:c.778C>G	p.Pro260Ala	p.P260A	ENST00000355640		260	Cca/Gca	2/7	0.443962846793611	5	FACETS	1	0.99	1			1	CLONAL	1	TRUE	NA	0.64095194183391	5		450	832	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856020	68856020	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	130	684	0	ENST00000261769.5:c.1828C>T	p.Gln610Ter	p.Q610*	ENST00000261769	NM_004360.3	610	Cag/Tag	12/16	0.352289017237497	0	FACETS	0.789	0.735	0.842			1	SUBCLONAL	2	TRUE	0	0.424917568813785	0		684	223	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952146	178952147	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587776802	NA	P-0040459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	74	226	0	ENST00000263967.3:c.3203dup	p.Asn1068LysfsTer5	p.N1068Kfs*5	ENST00000263967	NM_006218.2	1067	-/A	21/21	0.325540495058643	5	FACETS	1	0.964	1	0.812	0.722	0.907	CLONAL	2	TRUE	2	0.424917568813785	5		226	234	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426701	121426701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753998395	NA	P-0040459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	145	797	1	ENST00000257555.6:c.392G>A	p.Arg131Gln	p.R131Q	ENST00000257555		131	cGg/cAg	2/10	0.150966182092297	4	FACETS	1	0.945	1	1	0.945	1	INDETERMINATE	2	TRUE	2	0.424917568813785	4		798	470	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572495	64572505	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CTGTCCCTCAC	CTGTCCCTCAC	-	rs764570645	NA	P-0040459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	115	692	0	ENST00000312049.6:c.1350+1_1350+11del		p.X450_splice	ENST00000312049	NM_130799.2	450			0.394920824732931	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.424917568813785	1		692	303	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115459	115115462	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	TATC	TATC	-	novel	NA	P-0040459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	146	470	0	ENST00000257566.3:c.865-1_867del		p.X289_splice	ENST00000257566	NM_016569.3	289		5/8	0.424917568813785	6	FACETS	0.923	0.849	0.999			1	CLONAL	3	TRUE	NA	0.424917568813785	6		470	459	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0040618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	334	517	0	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.540275512938581	4	FACETS	0.941	0.891	0.991	0.941	0.891	0.991	CLONAL	2	TRUE	2	0.550666529254379	4		517	1000	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397517201	NA	P-0040618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	484	518	0	ENST00000263967.3:c.1637A>C	p.Gln546Pro	p.Q546P	ENST00000263967	NM_006218.2	546	cAg/cCg	10/21	0.550666529254379	6	FACETS	1	0.989	1	1	0.989	1	CLONAL	4	TRUE	2	0.550666529254379	6		518	865	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578507	7578507	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519977	NA	P-0040618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	933	635	0	ENST00000269305.4:c.423C>G	p.Cys141Trp	p.C141W	ENST00000269305	NM_001126112.2	141	tgC/tgG	5/11	0.157677416793243	6	FACETS	0.94	0.92	0.958			1	INDETERMINATE	6	TRUE	NA	0.550666529254379	6		635	1263	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165557	47165557	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs563907746	NA	P-0040618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	340	476	0	ENST00000409792.3:c.569C>T	p.Pro190Leu	p.P190L	ENST00000409792	NM_014159.6	190	cCg/cTg	3/21	0.354948061578683	3	FACETS	0.839	0.802	0.875	0.839	0.802	0.875	CLONAL	3	TRUE	0	0.550666529254379	3		476	626	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692950	89692950	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	125	475	0	ENST00000371953.3:c.434T>G	p.Phe145Cys	p.F145C	ENST00000371953	NM_000314.4	145	tTt/tGt	5/9	0.550666529254379	3	FACETS	0.965	0.876	1	0.482	0.438	0.529	CLONAL	1	TRUE	1	0.550666529254379	3		475	600	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0040619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	77	381	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.169648480067739	2	FACETS	0.588	0.517	0.665	0.294	0.258	0.333	INDETERMINATE	1	FALSE	0	0.456056982509525	2		381	574	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0040619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	185	419	1	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.448851649812547	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	FALSE	0	0.456056982509525	2		420	359	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863224683	NA	P-0040619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	214	810	0	ENST00000269305.4:c.388C>G	p.Leu130Val	p.L130V	ENST00000269305	NM_001126112.2	130	Ctc/Gtc	5/11	0.308837438285334	3	FACETS	0.94	0.879	1	0.627	0.586	0.668	CLONAL	2	FALSE	0	0.456056982509525	3		810	613	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959029	28959031	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs1173235571	NA	P-0040619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	45	338	0	ENST00000282397.4:c.2107_2109del	p.Gln703del	p.Q703del	ENST00000282397	NM_002019.4	703	CAA/-	14/30	0.456056982509525	6	FACETS	1	0.861	1	0.256	0.215	0.3	CLONAL	1	FALSE	2	0.456056982509525	6		338	369	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595292	141595292	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040619-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	115	758	0	ENST00000220592.5:c.141G>C	p.Met47Ile	p.M47I	ENST00000220592	NM_012154.3	47	atG/atC	2/19	0.456056982509525	4	FACETS	0.877	0.79	0.97	0.439	0.395	0.485	CLONAL	1	FALSE	2	0.456056982509525	4		758	837	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261788	16261788	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040621-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	108	612	0	ENST00000375759.3:c.9053C>T	p.Ala3018Val	p.A3018V	ENST00000375759	NM_015001.2	3018	gCt/gTt	11/15	1	2	FACETS	0.992	0.895	1	1	0.988	1	CLONAL	2	FALSE	1	0.222642676998871	2		612	489	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0040653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	103	372	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.941	0.855	1	0.941	0.855	1	CLONAL	1	TRUE	1	0.790490576298895	2		372	277	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0040653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	178	518	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.790490576298895	2		518	431	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791715	42791715	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157030312	NA	P-0040653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	21	522	1	ENST00000575354.2:c.601C>T	p.Arg201Trp	p.R201W	ENST00000575354	NM_015125.3	201	Cgg/Tgg	5/20	0.790490576298895	1	FACETS	0.1	0.077	0.127	0.1	0.077	0.127	SUBCLONAL	1	TRUE	0	0.790490576298895	1		523	321	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796777	42796777	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040653-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	225	691	0	ENST00000575354.2:c.3235C>T	p.Gln1079Ter	p.Q1079*	ENST00000575354	NM_015125.3	1079	Cag/Tag	14/20	0.790490576298895	1	FACETS	0.802	0.759	0.846	0.802	0.759	0.846	CLONAL	1	TRUE	0	0.790490576298895	1		691	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0040820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	359	753	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.553976475245511	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.553976475245511	1		753	898	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282710	1282710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	147	655	0	ENST00000310581.5:c.1603C>T	p.Arg535Cys	p.R535C	ENST00000310581	NM_198253.2	535	Cgt/Tgt	3/16	0.21340929876336	2	FACETS	0.563	0.513	0.615	0.281	0.256	0.308	INDETERMINATE	1	TRUE	0	0.553976475245511	2		655	943	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161298200	161298200	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	220	482	1	ENST00000367975.2:c.92G>A	p.Gly31Glu	p.G31E	ENST00000367975	NM_003001.3	31	gGa/gAa	3/6	0.30551973442481	1	FACETS	0.848	0.793	0.905	0.848	0.793	0.905	INDETERMINATE	1	TRUE	0	0.553976475245511	1		483	677	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436612	110436612	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	357	916	1	ENST00000375856.3:c.1789G>C	p.Glu597Gln	p.E597Q	ENST00000375856	NM_003749.2	597	Gaa/Caa	1/2	0.552479244117029	2	FACETS	0.965	0.914	1	0.483	0.457	0.509	CLONAL	1	TRUE	0	0.553976475245511	2		917	1335	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574822	95574822	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	122	346	0	ENST00000393063.1:c.2275G>A	p.Asp759Asn	p.D759N	ENST00000393063	NM_030621.3	759	Gat/Aat	16/28	1	2	FACETS	0.996	0.907	1	0.996	0.907	1	CLONAL	1	TRUE	1	0.553976475245511	2		346	442	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827722	72827722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	226	573	0	ENST00000268489.5:c.8859G>A	p.Met2953Ile	p.M2953I	ENST00000268489	NM_006885.3	2953	atG/atA	9/10	1	2	FACETS	0.959	0.895	1	0.959	0.895	1	CLONAL	1	TRUE	1	0.553976475245511	2		573	851	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980526	1980552	+	inframe_deletion	In_Frame_Del	DEL	GCGGCATCGGTCAGAAGCACCAAGACT	GCGGCATCGGTCAGAAGCACCAAGACT	-	novel	NA	P-0040820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	91	824	0	ENST00000382891.5:c.3989_4015del	p.Ala1330_Thr1338del	p.A1330_T1338del	ENST00000382891	NM_133335.3	1330	GCGGCATCGGTCAGAAGCACCAAGACT/-	22/22	0.317458703375748	1	FACETS	0.223	0.197	0.25	0.223	0.197	0.25	INDETERMINATE	1	TRUE	0	0.553976475245511	1		824	1067	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981143	55981143	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	105	509	0	ENST00000263923.4:c.556A>T	p.Thr186Ser	p.T186S	ENST00000263923	NM_002253.2	186	Act/Tct	5/30	0.317458703375748	1	FACETS	0.487	0.437	0.539	0.487	0.437	0.539	INDETERMINATE	1	TRUE	0	0.553976475245511	1		509	563	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69103963	69103963	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	62	516	0	ENST00000288368.4:c.4353C>G	p.Phe1451Leu	p.F1451L	ENST00000288368	NM_024870.2	1451	ttC/ttG	36/40	0.553976475245511	3	FACETS	0.399	0.344	0.459	0.2	0.172	0.23	SUBCLONAL	1	TRUE	1	0.553976475245511	3		516	716	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0040855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	348	727	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.388849021136149	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.388849021136149	2		728	722	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878863	151878863	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1563288201	NA	P-0040855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	95	420	0	ENST00000262189.6:c.6082C>T	p.Arg2028Ter	p.R2028*	ENST00000262189	NM_170606.2	2028	Cga/Tga	36/59	0.388849021136149	2	FACETS	0.964	0.861	1	0.482	0.43	0.536	CLONAL	1	TRUE	0	0.388849021136149	2		420	507	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27172710	27172710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040855-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	37	483	0	ENST00000380036.4:c.725G>A	p.Cys242Tyr	p.C242Y	ENST00000380036	NM_000459.3	242	tGc/tAc	5/23	0.143349515957358	0	FACETS	0.229	0.189	0.275			1	INDETERMINATE	1	TRUE	0	0.388849021136149	0		483	507	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518306	187518306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs935510544	NA	P-0040861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	120	241	1	ENST00000441802.2:c.12388G>A	p.Glu4130Lys	p.E4130K	ENST00000441802	NM_005245.3	4130	Gag/Aag	25/27	0.649126626576074	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.649126626576074	1		242	203	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949346	71949346	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	259	775	0	ENST00000298229.2:c.3726G>T	p.Gln1242His	p.Q1242H	ENST00000298229	NM_001567.3	1242	caG/caT	28/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.649126626576074	2		775	748	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336681	81336681	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0040861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	117	216	0	ENST00000222390.5:c.1542-1G>A		p.X514_splice	ENST00000222390	NM_000601.4	514			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.649126626576074	2		216	318	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945115	44945115	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040861-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	144	320	0	ENST00000377967.4:c.3439C>T	p.Gln1147Ter	p.Q1147*	ENST00000377967	NM_021140.2	1147	Cag/Tag	24/29	0.338019574648604	1	FACETS	0.712	0.655	0.77	0.712	0.655	0.77	INDETERMINATE	1	TRUE	0	0.649126626576074	1		320	421	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0040891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	11	60	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	0.11557086603857	5	FACETS	1	0.845	1	0.348	0.244	0.472	INDETERMINATE	1	TRUE	1	0.327177263702647	5		60	72	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734152	58734152	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768126695	NA	P-0040891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	240	420	0	ENST00000305921.3:c.1210C>T	p.Gln404Ter	p.Q404*	ENST00000305921	NM_003620.3	404	Caa/Taa	5/6	0.327177263702647	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	4	TRUE	0	0.327177263702647	4		420	444	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926897	112926897	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs397507548	NA	P-0040891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	44	368	0	ENST00000351677.2:c.1517A>C	p.Gln506Pro	p.Q506P	ENST00000351677	NM_002834.3	506	cAg/cCg	13/16	1	2	FACETS	0.758	0.637	0.89	0.758	0.637	0.89	SUBCLONAL	1	TRUE	1	0.327177263702647	2		368	355	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586148	29586148	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0040891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	36	287	0	ENST00000356175.3:c.4367+1G>T		p.X1456_splice	ENST00000356175	NM_000267.3	1456			0.327177263702647	1	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	0	0.327177263702647	1		287	171	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907823	76907827	+	frameshift_variant	Frame_Shift_Del	DEL	CTCTT	CTCTT	-	novel	NA	P-0040891-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	11	122	0	ENST00000373344.5:c.4334_4338del	p.Glu1445GlyfsTer20	p.E1445Gfs*20	ENST00000373344	NM_000489.3	1445	gAAGAG/g	15/35	0.327177263702647	1	FACETS	0.827	0.582	1	0.827	0.582	1	CLONAL	1	TRUE	0	0.327177263702647	1		122	68	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154887	2154887	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1212009594	NA	P-0040963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	109	727	3	ENST00000434045.2:c.334G>A	p.Ala112Thr	p.A112T	ENST00000434045	NM_001127598.1	112	Gca/Aca	4/5	1	2	FACETS	0.307	0.275	0.341	0.307	0.275	0.341	SUBCLONAL	1	TRUE	1	0.913600317024188	2		730	777	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28934577	NA	P-0040980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	494	656	0	ENST00000269305.4:c.770T>C	p.Leu257Pro	p.L257P	ENST00000269305	NM_001126112.2	257	cTg/cCg	7/11	NA	2	FACETS	0.989	0.958	1			1	INDETERMINATE	2	TRUE	NA	0.656073483350169	2		656	761	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348016	348016	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	318	857	0	ENST00000262320.3:c.1490G>T	p.Gly497Val	p.G497V	ENST00000262320	NM_003502.3	497	gGg/gTg	6/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.656073483350169	2		857	949	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631613	119631613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040980-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	79	353	0	ENST00000316626.5:c.653G>A	p.Cys218Tyr	p.C218Y	ENST00000316626		218	tGt/tAt	6/12	1	2	FACETS	0.75	0.666	0.839	0.75	0.666	0.839	SUBCLONAL	1	TRUE	1	0.656073483350169	2		353	321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0040982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	247	753	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.204514426059392	3	FACETS	1	0.989	1	0.817	0.767	0.868	CLONAL	2	TRUE	0	0.31	3		753	751	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0040982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	50	257	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	0.996	0.849	1	0.996	0.849	1	CLONAL	1	TRUE	1	0.31	2		257	324	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0040982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	66	400	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.295451198873179	3	FACETS	0.806	0.706	0.913	0.806	0.706	0.913	CLONAL	2	TRUE	1	0.31	3		400	305	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457303	67457303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768713596	NA	P-0040982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	166	706	1	ENST00000327367.4:c.277C>T	p.Arg93Ter	p.R93*	ENST00000327367	NM_005902.3	93	Cga/Tga	2/9	0.277884790358241	2	FACETS	0.906	0.836	0.978	0.906	0.836	0.978	CLONAL	2	TRUE	0	0.31	2		707	591	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554282	63554283	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCA	novel	NA	P-0040982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	384	700	0	ENST00000307078.5:c.453_456dup	p.Thr153CysfsTer16	p.T153Cfs*16	ENST00000307078	NM_004655.3	152	-/TGCC	2/11	0.295451198873179	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	4	TRUE	0	0.31	4		700	808	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395746	45395746	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	87	451	3	ENST00000262160.6:c.388C>T	p.Arg130Ter	p.R130*	ENST00000262160	NM_005901.5	130	Cga/Tga	4/11	0.277884790358241	2	FACETS	0.985	0.883	1	0.985	0.883	1	CLONAL	2	TRUE	0	0.31	2		454	285	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212401	36212401	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555495072	NA	P-0040982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	119	819	1	ENST00000222270.7:c.2152G>A	p.Glu718Lys	p.E718K	ENST00000222270	NM_014727.1	718	Gag/Aag	3/37	0.275060201325293	3	FACETS	0.932	0.841	1	0.466	0.42	0.515	CLONAL	1	TRUE	1	0.31	3		820	951	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294537	1294537	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	100	631	2	ENST00000310581.5:c.464G>A	p.Arg155His	p.R155H	ENST00000310581	NM_198253.2	155	cGc/cAc	2/16	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.31	2		633	641	SUCCESS
APC	324	MSKCC	GRCh37	5	112175630	112175630	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	42	308	0	ENST00000257430.4:c.4339C>T	p.Gln1447Ter	p.Q1447*	ENST00000257430	NM_000038.5	1447	Caa/Taa	16/16	1	2	FACETS	0.855	0.717	1	0.855	0.717	1	CLONAL	1	TRUE	1	0.31	2		308	317	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502151	157502151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1248514225	NA	P-0040982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	169	557	0	ENST00000346085.5:c.3184G>A	p.Glu1062Lys	p.E1062K	ENST00000346085	NM_020732.3	1062	Gag/Aag	12/20	0.275060201325293	3	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	1	0.31	3		557	626	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55232991	55232991	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040982-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	115	433	2	ENST00000275493.2:c.1741C>G	p.Gln581Glu	p.Q581E	ENST00000275493	NM_005228.3	581	Cag/Gag	15/28	0.275060201325293	3	FACETS	0.874	0.792	0.961	0.874	0.792	0.961	CLONAL	2	TRUE	1	0.31	3		435	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0040982-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	86	753	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	1	2	FACETS	0.874	0.771	0.986	0.874	0.771	0.986	CLONAL	1	TRUE	1	0.17	2		753	1157	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0040982-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	46	400	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.836	0.703	0.984	0.836	0.703	0.984	CLONAL	1	TRUE	1	0.17	2		400	647	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457303	67457303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768713596	NA	P-0040982-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	87	706	1	ENST00000327367.4:c.277C>T	p.Arg93Ter	p.R93*	ENST00000327367	NM_005902.3	93	Cga/Tga	2/9	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.17	2		707	1004	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554282	63554283	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCA	novel	NA	P-0040982-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	115	700	0	ENST00000307078.5:c.453_456dup	p.Thr153CysfsTer16	p.T153Cfs*16	ENST00000307078	NM_004655.3	152	-/TGCC	2/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.17	2		700	1114	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395746	45395746	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040982-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	52	451	3	ENST00000262160.6:c.388C>T	p.Arg130Ter	p.R130*	ENST00000262160	NM_005901.5	130	Cga/Tga	4/11	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.17	2		454	606	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502151	157502151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1248514225	NA	P-0040982-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	58	557	0	ENST00000346085.5:c.3184G>A	p.Glu1062Lys	p.E1062K	ENST00000346085	NM_020732.3	1062	Gag/Aag	12/20	1	2	FACETS	0.766	0.656	0.886	0.766	0.656	0.886	SUBCLONAL	1	TRUE	1	0.17	2		557	891	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	149	474	6	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	0.3	2	FACETS	0.898	0.825	0.974			1	INDETERMINATE	1	TRUE	NA	0.61	2		480	544	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498235	498235	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	67	295	0	ENST00000399788.2:c.23del	p.Gly8AlafsTer58	p.G8Afs*58	ENST00000399788	NM_001042603.1	8	gGc/gc	1/28	0.3	2	FACETS	0.752	0.66	0.851			1	INDETERMINATE	1	TRUE	NA	0.61	2		295	292	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224532	36224532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759167832	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	359	1102	0	ENST00000222270.7:c.6994C>T	p.Arg2332Cys	p.R2332C	ENST00000222270	NM_014727.1	2332	Cgt/Tgt	29/37	1	2	FACETS	0.973	0.922	1	0.973	0.922	1	CLONAL	1	TRUE	1	0.61	2		1102	1210	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	264	575	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.876	0.832	0.92	1	0.995	1	CLONAL	2	TRUE	1	0.61	2		575	494	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	115	428	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.821	0.745	0.902	0.821	0.745	0.902	CLONAL	1	TRUE	1	0.61	2		428	459	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	110	430	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.777	0.702	0.856	0.777	0.702	0.856	SUBCLONAL	1	TRUE	1	0.61	2		430	464	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156720	20156720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	139	450	0	ENST00000379607.5:c.37C>T	p.Arg13Cys	p.R13C	ENST00000379607	NM_001412.3	13	Cgc/Tgc	2/7	1	2	FACETS	0.876	0.802	0.953	0.876	0.802	0.953	CLONAL	1	TRUE	1	0.61	2		450	520	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850705	63850705	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs201178069	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	116	320	0	ENST00000279873.7:c.1489del	p.Ile497Ter	p.I497*	ENST00000279873	NM_032199.2	495	Aaa/aa	10/10	1	2	FACETS	0.903	0.821	0.99	0.903	0.821	0.99	CLONAL	1	TRUE	1	0.61	2		320	421	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	166	498	8	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	0.995	0.92	1	0.995	0.92	1	CLONAL	1	TRUE	1	0.61	2		506	547	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	94	388	6	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	1	2	FACETS	0.937	0.842	1	0.937	0.842	1	CLONAL	1	TRUE	1	0.61	2		394	329	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027998	48027998	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757653982	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	81	354	0	ENST00000234420.5:c.2876G>A	p.Arg959His	p.R959H	ENST00000234420	NM_000179.2	959	cGc/cAc	4/10	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.61	2		354	253	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676268	37676268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	204	611	0	ENST00000447079.4:c.3023G>A	p.Arg1008Gln	p.R1008Q	ENST00000447079	NM_015083.1	1008	cGg/cAg	11/14	1	2	FACETS	0.854	0.794	0.916	0.854	0.794	0.916	CLONAL	1	TRUE	1	0.61	2		611	783	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309887	65309887	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1304838920	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	155	471	0	ENST00000342505.4:c.2263C>T	p.Arg755Ter	p.R755*	ENST00000342505	NM_002227.2	755	Cga/Tga	17/25	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.61	2		471	487	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817414	39817414	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542019196	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	58	553	1	ENST00000288319.7:c.149G>A	p.Arg50His	p.R50H	ENST00000288319	NM_182918.3	50	cGc/cAc	2/10	1	2	FACETS	0.28	0.24	0.324	0.28	0.24	0.324	SUBCLONAL	1	TRUE	1	0.61	2		554	679	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448565	89448565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	158	602	1	ENST00000336596.2:c.1529G>A	p.Arg510Gln	p.R510Q	ENST00000336596	NM_005233.5	510	cGa/cAa	7/17	1	2	FACETS	0.77	0.707	0.834	0.77	0.707	0.834	SUBCLONAL	1	TRUE	1	0.61	2		603	673	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031815	10031815	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs397518465	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	237	665	0	ENST00000330684.3:c.1007+1G>A		p.X336_splice	ENST00000330684	NM_001134407.1	336			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.61	2		665	735	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591246	67591246	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	101	410	0	ENST00000274335.5:c.1746-2A>G		p.X582_splice	ENST00000274335		582			1	2	FACETS	0.858	0.773	0.947	0.858	0.773	0.947	CLONAL	1	TRUE	1	0.61	2		410	386	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843599	156843599	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770090356	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	331	925	2	ENST00000524377.1:c.1025G>A	p.Arg342Gln	p.R342Q	ENST00000524377	NM_002529.3	342	cGg/cAg	8/17	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.61	2		927	968	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243778429	243778429	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	78	366	0	ENST00000263826.5:c.596T>C	p.Val199Ala	p.V199A	ENST00000263826	NM_005465.4	199	gTa/gCa	6/13	1	2	FACETS	0.894	0.795	0.999	0.894	0.795	0.999	CLONAL	1	TRUE	1	0.61	2		366	286	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274773	123274773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519900	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	63	638	1	ENST00000358487.5:c.1145G>A	p.Cys382Tyr	p.C382Y	ENST00000358487	NM_000141.4	382	tGc/tAc	9/18	1	2	FACETS	0.311	0.269	0.357	0.311	0.269	0.357	SUBCLONAL	1	TRUE	1	0.61	2		639	664	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779650	3779650	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	243	948	2	ENST00000262367.5:c.5398C>T	p.Arg1800Trp	p.R1800W	ENST00000262367	NM_004380.2	1800	Cgg/Tgg	31/31	1	2	FACETS	0.923	0.864	0.984	0.923	0.864	0.984	CLONAL	1	TRUE	1	0.61	2		950	863	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106073	8106073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	175	612	2	ENST00000346208.3:c.893G>A	p.Arg298Gln	p.R298Q	ENST00000346208		298	cGg/cAg	4/6	1	2	FACETS	0.814	0.752	0.878	0.814	0.752	0.878	CLONAL	1	TRUE	1	0.61	2		614	705	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262346	16262346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201781067	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	129	343	0	ENST00000375759.3:c.9611C>T	p.Thr3204Met	p.T3204M	ENST00000375759	NM_015001.2	3204	aCg/aTg	11/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.61	2		343	354	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93636535	93636535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs903194537	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	184	555	0	ENST00000375746.1:c.965C>T	p.Pro322Leu	p.P322L	ENST00000375746	NM_001174167.1	322	cCg/cTg	8/14	1	2	FACETS	0.996	0.924	1	0.996	0.924	1	CLONAL	1	TRUE	1	0.61	2		555	606	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098804	178098804	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	219	678	0	ENST00000397062.3:c.241G>T	p.Gly81Cys	p.G81C	ENST00000397062	NM_006164.4	81	Ggt/Tgt	2/5	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.61	2		678	693	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807520	36807520	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	272	803	0	ENST00000373129.3:c.1144C>T	p.Gln382Ter	p.Q382*	ENST00000373129	NM_032017.1	382	Cag/Tag	12/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.61	2		803	875	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483201	120483201	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	150	453	0	ENST00000256646.2:c.3160G>T	p.Gly1054Cys	p.G1054C	ENST00000256646	NM_024408.3	1054	Ggc/Tgc	19/34	1	2	FACETS	0.897	0.825	0.973	0.897	0.825	0.973	CLONAL	1	TRUE	1	0.61	2		453	548	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202492	67202492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs189269522	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	182	914	0	ENST00000312629.5:c.1301G>A	p.Arg434Gln	p.R434Q	ENST00000312629	NM_003952.2	434	cGg/cAg	15/15	1	2	FACETS	0.625	0.576	0.675	0.625	0.576	0.675	SUBCLONAL	1	TRUE	1	0.61	2		914	955	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245297	46245297	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	149	525	0	ENST00000334344.6:c.3391C>A	p.Pro1131Thr	p.P1131T	ENST00000334344	NM_152641.2	1131	Cca/Aca	15/21	1	2	FACETS	0.891	0.819	0.967	0.891	0.819	0.967	CLONAL	1	TRUE	1	0.61	2		525	548	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859016	57859016	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	235	769	0	ENST00000228682.2:c.515del	p.Gly172AspfsTer8	p.G172Dfs*8	ENST00000228682	NM_005269.2	171	cGg/cg	5/12	1	2	FACETS	0.919	0.86	0.981	0.919	0.86	0.981	CLONAL	1	TRUE	1	0.61	2		769	838	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241010	133241010	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	206	776	0	ENST00000320574.5:c.2507G>A	p.Cys836Tyr	p.C836Y	ENST00000320574	NM_006231.2	836	tGc/tAc	22/49	1	2	FACETS	0.893	0.831	0.957	0.893	0.831	0.957	CLONAL	1	TRUE	1	0.61	2		776	756	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601312	28601312	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	116	481	0	ENST00000241453.7:c.2120G>A	p.Arg707Lys	p.R707K	ENST00000241453	NM_004119.2	707	aGa/aAa	17/24	1	2	FACETS	0.899	0.817	0.985	0.899	0.817	0.985	CLONAL	1	TRUE	1	0.61	2		481	423	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655411	67655411	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	157	613	0	ENST00000264010.4:c.1274A>G	p.His425Arg	p.H425R	ENST00000264010	NM_006565.3	425	cAc/cGc	7/12	1	2	FACETS	0.971	0.895	1	0.971	0.895	1	CLONAL	1	TRUE	1	0.61	2		613	530	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579428	7579428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	143	832	1	ENST00000269305.4:c.259C>T	p.Pro87Ser	p.P87S	ENST00000269305	NM_001126112.2	87	Cca/Tca	4/11	1	2	FACETS	0.507	0.462	0.555	0.507	0.462	0.555	SUBCLONAL	1	TRUE	1	0.61	2		833	924	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390322	56390322	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777036725	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	73	358	0	ENST00000348428.3:c.1061G>A	p.Arg354Gln	p.R354Q	ENST00000348428	NM_006785.3	354	cGg/cAg	10/17	1	2	FACETS	0.849	0.75	0.952	0.849	0.75	0.952	CLONAL	1	TRUE	1	0.61	2		358	282	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223108	1223108	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs553752236	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	315	902	0	ENST00000326873.7:c.1045G>A	p.Glu349Lys	p.E349K	ENST00000326873	NM_000455.4	349	Gag/Aag	8/10	1	2	FACETS	0.953	0.9	1	0.953	0.9	1	CLONAL	1	TRUE	1	0.61	2		902	1084	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211825	36211825	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	366	1109	1	ENST00000222270.7:c.1576C>T	p.Gln526Ter	p.Q526*	ENST00000222270	NM_014727.1	526	Cag/Tag	3/37	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.61	2		1110	1174	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446313	29446313	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	235	784	0	ENST00000389048.3:c.3254C>T	p.Thr1085Ile	p.T1085I	ENST00000389048	NM_004304.4	1085	aCc/aTc	20/29	1	2	FACETS	0.835	0.78	0.891	0.835	0.78	0.891	CLONAL	1	TRUE	1	0.61	2		784	923	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656952	47656952	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376934727	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	114	382	0	ENST00000233146.2:c.1148G>A	p.Arg383Gln	p.R383Q	ENST00000233146	NM_000251.2	383	cGa/cAa	7/16	1	2	FACETS	0.997	0.906	1	0.997	0.906	1	CLONAL	1	TRUE	1	0.61	2		382	375	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881387	111881387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1429573443	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	156	579	0	ENST00000393256.3:c.65C>T	p.Ala22Val	p.A22V	ENST00000393256	NM_006538.4	22	gCg/gTg	2/4	1	2	FACETS	0.834	0.767	0.904	0.834	0.767	0.904	CLONAL	1	TRUE	1	0.61	2		579	613	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051213	128051213	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	240	710	0	ENST00000285398.2:c.110C>A	p.Ala37Glu	p.A37E	ENST00000285398	NM_000122.1	37	gCg/gAg	2/15	1	2	FACETS	0.964	0.903	1	0.964	0.903	1	CLONAL	1	TRUE	1	0.61	2		710	816	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873409	136873409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs923351521	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	92	442	0	ENST00000241393.3:c.89G>A	p.Arg30His	p.R30H	ENST00000241393	NM_003467.2	30	cGt/cAt	2/2	1	2	FACETS	0.743	0.664	0.826	0.743	0.664	0.826	SUBCLONAL	1	TRUE	1	0.61	2		442	406	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662227	227662227	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764990052	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	267	845	0	ENST00000305123.5:c.1228C>T	p.Arg410Trp	p.R410W	ENST00000305123	NM_005544.2	410	Cgg/Tgg	1/2	1	2	FACETS	0.856	0.803	0.91	0.856	0.803	0.91	CLONAL	1	TRUE	1	0.61	2		845	1023	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157406028	157406028	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	137	459	0	ENST00000346085.5:c.2270C>T	p.Ala757Val	p.A757V	ENST00000346085	NM_020732.3	757	gCa/gTa	6/20	1	2	FACETS	0.84	0.768	0.914	0.84	0.768	0.914	CLONAL	1	TRUE	1	0.61	2		459	535	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5078434	5078434	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	85	409	0	ENST00000381652.3:c.2121G>T	p.Leu707Phe	p.L707F	ENST00000381652	NM_004972.3	707	ttG/ttT	16/25	1	2	FACETS	0.974	0.872	1	0.974	0.872	1	CLONAL	1	TRUE	1	0.61	2		409	286	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250170	110250170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	245	815	1	ENST00000374672.4:c.505G>A	p.Gly169Arg	p.G169R	ENST00000374672	NM_004235.4	169	Gga/Aga	3/5	1	2	FACETS	0.977	0.916	1	0.977	0.916	1	CLONAL	1	TRUE	1	0.61	2		816	822	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227753	53227753	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040992-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	121	770	0	ENST00000375401.3:c.2435T>A	p.Leu812Gln	p.L812Q	ENST00000375401	NM_004187.3	812	cTg/cAg	17/26	1	2	FACETS	0.467	0.421	0.515	0.467	0.421	0.515	SUBCLONAL	1	TRUE	1	0.61	2		770	850	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267483	198267483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519961	NA	P-0041013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	158	278	0	ENST00000335508.6:c.1874G>A	p.Arg625His	p.R625H	ENST00000335508	NM_012433.2	625	cGt/cAt	14/25	NA	2	FACETS	0.933	0.865	1			1	INDETERMINATE	1	TRUE	NA	0.840364348621051	2		278	403	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29676154	29676155	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0041013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	158	262	0	ENST00000356175.3:c.7145dup	p.Ala2383CysfsTer18	p.A2383Cfs*18	ENST00000356175	NM_000267.3	2381	-/C	48/57	0.835418856439443	2	FACETS	0.95	0.907	0.988	0.95	0.907	0.988	CLONAL	2	TRUE	0	0.840364348621051	2		262	198	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372071	55372071	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	358	502	0	ENST00000297316.4:c.761C>G	p.Ala254Gly	p.A254G	ENST00000297316	NM_022454.3	254	gCg/gGg	2/2	0.293404152922709	1	FACETS	0.718	0.687	0.749	0.718	0.687	0.749	INDETERMINATE	1	TRUE	0	0.840364348621051	1		502	688	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0041071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	203	401	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.639324935230394	3	FACETS	0.929	0.875	0.982	0.929	0.875	0.982	CLONAL	2	FALSE	1	0.778854679065609	3		401	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578416	7578416	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1131691043	NA	P-0041071-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	793	817	0	ENST00000269305.4:c.514G>T	p.Val172Phe	p.V172F	ENST00000269305	NM_001126112.2	172	Gtt/Ttt	5/11	0.766259832330637	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	FALSE	0	0.778854679065609	2		817	1008	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0041204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	51	522	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.219038399052836	7	FACETS	0.905	0.768	1	0.151	0.128	0.177	CLONAL	1	TRUE	1	0.219038399052836	7		522	796	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520017	NA	P-0041204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	235	936	0	ENST00000326873.7:c.647C>T	p.Ser216Phe	p.S216F	ENST00000326873	NM_000455.4	216	tCc/tTc	5/10	0.216147369296565	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.219038399052836	2		936	1044	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18747479	18747479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755020029	NA	P-0041204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	41	412	0	ENST00000266497.5:c.3940G>A	p.Glu1314Lys	p.E1314K	ENST00000266497		1314	Gaa/Aaa	28/31	0.219038399052836	5	FACETS	0.946	0.787	1	0.315	0.262	0.374	CLONAL	1	TRUE	2	0.219038399052836	5		412	526	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934194	48934194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	56	442	0	ENST00000267163.4:c.649C>T	p.Gln217Ter	p.Q217*	ENST00000267163	NM_000321.2	217	Cag/Tag	7/27	0.211286239444415	3	FACETS	1	0.959	1	0.671	0.576	0.773	CLONAL	1	TRUE	1	0.219038399052836	3		442	423	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190937	185190937	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1524	258	896	0	ENST00000265026.3:c.1818G>C	p.Leu606Phe	p.L606F	ENST00000265026	NM_004721.4	606	ttG/ttC	11/14	0.219038399052836	7	FACETS	1	0.951	1	0.341	0.318	0.365	CLONAL	2	TRUE	1	0.219038399052836	7		896	1782	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170135	32170135	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542331250	NA	P-0041204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	221	921	1	ENST00000375023.3:c.3473G>A	p.Arg1158Gln	p.R1158Q	ENST00000375023	NM_004557.3	1158	cGa/cAa	21/30	0.219038399052836	5	FACETS	1	0.958	1	0.418	0.388	0.449	CLONAL	2	TRUE	0	0.219038399052836	5		922	1284	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032002	10032002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs539907710	NA	P-0041204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	164	732	1	ENST00000330684.3:c.821C>T	p.Ser274Leu	p.S274L	ENST00000330684	NM_001134407.1	274	tCg/tTg	3/13	0.219038399052836	5	FACETS	0.933	0.856	1	0.622	0.57	0.676	CLONAL	2	TRUE	2	0.219038399052836	5		733	1066	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190894	185190894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555365583	NA	P-0041204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1491	114	796	1	ENST00000265026.3:c.1775G>A	p.Arg592Gln	p.R592Q	ENST00000265026	NM_004721.4	592	cGa/cAa	11/14	0.219038399052836	7	FACETS	1	0.9	1	0.167	0.15	0.186	CLONAL	1	TRUE	1	0.219038399052836	7		797	1605	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097228	11097228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201600949	NA	P-0041204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	186	732	0	ENST00000358026.2:c.719C>T	p.Pro240Leu	p.P240L	ENST00000358026	NM_001128849.1	240	cCg/cTg	4/36	0.192936301972672	4	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	2	0.219038399052836	4		732	1020	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129932	55129932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760631068	NA	P-0041204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	160	664	0	ENST00000257290.5:c.466G>A	p.Glu156Lys	p.E156K	ENST00000257290	NM_006206.4	156	Gag/Aag	4/23	0.211286239444415	3	FACETS	0.953	0.875	1	0.953	0.875	1	CLONAL	2	TRUE	1	0.219038399052836	3		664	850	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120496275	120496275	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	106	421	0	ENST00000256646.2:c.2256C>G	p.Ile752Met	p.I752M	ENST00000256646	NM_024408.3	752	atC/atG	14/34	0.219038399052836	4	FACETS	0.894	0.802	0.991	0.894	0.802	0.991	CLONAL	2	TRUE	2	0.219038399052836	4		421	660	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94908774	94908774	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	58	503	0	ENST00000536441.1:c.1280A>T	p.Gln427Leu	p.Q427L	ENST00000536441	NM_144665.3	427	cAa/cTa	9/10	0.211286239444415	3	FACETS	0.888	0.762	1	0.444	0.381	0.513	CLONAL	1	TRUE	1	0.219038399052836	3		503	662	SUCCESS
ATM	472	MSKCC	GRCh37	11	108183211	108183211	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	70	259	0	ENST00000278616.4:c.5992G>A	p.Gly1998Arg	p.G1998R	ENST00000278616	NM_000051.3	1998	Gga/Aga	40/63	0.183974785308972	4	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	2	0.219038399052836	4		259	352	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244001	46244001	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	105	517	0	ENST00000334344.6:c.2095C>G	p.Pro699Ala	p.P699A	ENST00000334344	NM_152641.2	699	Cca/Gca	15/21	0.219038399052836	5	FACETS	0.829	0.743	0.921	0.553	0.495	0.614	CLONAL	2	TRUE	2	0.219038399052836	5		517	768	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955535	48955535	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	58	396	0	ENST00000267163.4:c.1651G>C	p.Glu551Gln	p.E551Q	ENST00000267163	NM_000321.2	551	Gaa/Caa	17/27	0.211286239444415	3	FACETS	1	0.958	1	0.656	0.565	0.755	CLONAL	1	TRUE	1	0.219038399052836	3		396	448	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84397825	84397825	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	34	347	0	ENST00000321945.7:c.186G>T	p.Gln62His	p.Q62H	ENST00000321945	NM_139076.2	62	caG/caT	3/9	0.211286239444415	3	FACETS	0.783	0.639	0.944	0.391	0.319	0.472	CLONAL	1	TRUE	1	0.219038399052836	3		347	440	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635269	87635269	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0041204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	65	513	0	ENST00000277120.3:c.2321C>G	p.Ser774Ter	p.S774*	ENST00000277120		774	tCa/tGa	18/19	0.192936301972672	4	FACETS	0.942	0.815	1	0.471	0.407	0.54	CLONAL	1	TRUE	2	0.219038399052836	4		513	768	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937179	76937179	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1557137075	NA	P-0041204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	40	590	0	ENST00000373344.5:c.3569G>C	p.Arg1190Thr	p.R1190T	ENST00000373344	NM_000489.3	1190	aGa/aCa	9/35	0.216147369296565	2	FACETS	0.821	0.682	0.975	0.41	0.341	0.488	CLONAL	1	TRUE	0	0.219038399052836	2		590	445	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238115	133238115	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	27	371	0	ENST00000320574.5:c.2862G>C	p.Lys954Asn	p.K954N	ENST00000320574	NM_006231.2	954	aaG/aaC	24/49	1	2	FACETS	0.249	0.197	0.308	0.249	0.197	0.308	SUBCLONAL	1	TRUE	1	0.505963105107185	2		371	429	SUCCESS
BLM	641	MSKCC	GRCh37	15	91295085	91295085	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	48	344	0	ENST00000355112.3:c.868G>C	p.Glu290Gln	p.E290Q	ENST00000355112	NM_000057.2	290	Gaa/Caa	4/22	0.119206447132304	3	FACETS	0.586	0.496	0.684	0.195	0.165	0.228	INDETERMINATE	1	TRUE	0	0.505963105107185	3		344	406	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667616	29667616	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	99	505	0	ENST00000356175.3:c.6952G>C	p.Glu2318Gln	p.E2318Q	ENST00000356175	NM_000267.3	2318	Gaa/Caa	46/57	0.127367587268729	6	FACETS	0.901	0.803	1	0.3	0.267	0.335	INDETERMINATE	1	TRUE	3	0.505963105107185	6		505	874	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104729	209104730	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TG	TG	-	novel	NA	P-0041209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	46	281	0	ENST00000345146.2:c.851-3_851-2del		p.X284_splice	ENST00000345146	NM_005896.2	284			NA	2	FACETS	0.671	0.569	0.782			1	INDETERMINATE	1	TRUE	NA	0.505963105107185	2		281	271	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275675	41275675	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	58	450	0	ENST00000349496.5:c.1570C>G	p.His524Asp	p.H524D	ENST00000349496	NM_001904.3	524	Cat/Gat	10/15	NA	2	FACETS	0.481	0.413	0.554			1	INDETERMINATE	1	TRUE	NA	0.505963105107185	2		450	477	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437669	52437669	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	94	631	1	ENST00000460680.1:c.1492G>T	p.Glu498Ter	p.E498*	ENST00000460680	NM_004656.3	498	Gag/Tag	13/17	NA	2	FACETS	0.637	0.568	0.711			1	INDETERMINATE	1	TRUE	NA	0.505963105107185	2		632	583	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55960978	55960978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	56	413	0	ENST00000263923.4:c.2962G>A	p.Glu988Lys	p.E988K	ENST00000263923	NM_002253.2	988	Gaa/Aaa	21/30	0.497211154026502	5	FACETS	0.681	0.583	0.787	0.227	0.194	0.263	SUBCLONAL	1	TRUE	2	0.505963105107185	5		413	572	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031891	26031891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	44	277	0	ENST00000244661.2:c.398G>A	p.Gly133Glu	p.G133E	ENST00000244661	NM_003537.3	133	gGa/gAa	1/1	0.12164608223087	5	FACETS	0.84	0.707	0.987	0.28	0.235	0.329	INDETERMINATE	1	TRUE	2	0.505963105107185	5		277	364	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165223	32165223	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	83	702	0	ENST00000375023.3:c.4905G>C	p.Glu1635Asp	p.E1635D	ENST00000375023	NM_004557.3	1635	gaG/gaC	27/30	0.12164608223087	5	FACETS	0.658	0.58	0.742	0.219	0.193	0.248	INDETERMINATE	1	TRUE	2	0.505963105107185	5		702	877	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937950	76937950	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	36	547	0	ENST00000373344.5:c.2798C>A	p.Ser933Tyr	p.S933Y	ENST00000373344	NM_000489.3	933	tCt/tAt	9/35	0.149322505661492	3	FACETS	0.258	0.211	0.31	0.129	0.105	0.155	INDETERMINATE	1	TRUE	1	0.505963105107185	3		547	692	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0041223-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	44	290	2	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.482	0.403	0.569	0.482	0.403	0.569	SUBCLONAL	1	FALSE	1	0.3	2		292	609	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579530	7579531	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1555526748	NA	P-0041225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	317	722	0	ENST00000269305.4:c.156dup	p.Trp53MetfsTer4	p.W53Mfs*4	ENST00000269305	NM_001126112.2	52	-/A	4/11	0.325943867648675	3	FACETS	1	0.985	1	0.739	0.7	0.779	CLONAL	2	TRUE	0	0.379043087951695	3		722	897	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417431	139417431	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs979299004	NA	P-0041225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	268	656	0	ENST00000277541.6:c.613G>A	p.Val205Ile	p.V205I	ENST00000277541	NM_017617.3	205	Gtc/Atc	4/34	0.310118651703932	2	FACETS	0.917	0.864	0.971	0.917	0.864	0.971	CLONAL	2	TRUE	0	0.379043087951695	2		656	771	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576923	7576928	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGTGCT	AGTGCT	-	novel	NA	P-0041285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	360	722	0	ENST00000269305.4:c.920-2_923del		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	0.297857909006273	1	FACETS	1	0.988	1	1	0.988	1	INDETERMINATE	1	TRUE	0	0.507772081139311	1		722	947	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660832	227660832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs767551071	NA	P-0041285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	195	649	0	ENST00000305123.5:c.2623C>G	p.Arg875Gly	p.R875G	ENST00000305123	NM_005544.2	875	Cga/Gga	1/2	1	2	FACETS	0.953	0.884	1	0.953	0.884	1	CLONAL	1	TRUE	1	0.507772081139311	2		649	806	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247579	123247579	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	293	617	0	ENST00000358487.5:c.1912A>C	p.Asn638His	p.N638H	ENST00000358487	NM_000141.4	638	Aat/Cat	14/18	0.507772081139311	3	FACETS	1	0.976	1	0.537	0.504	0.57	CLONAL	1	TRUE	1	0.507772081139311	3		617	1348	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350732	15350732	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	213	838	0	ENST00000263377.2:c.3271C>G	p.Pro1091Ala	p.P1091A	ENST00000263377	NM_058243.2	1091	Cct/Gct	15/20	1	2	FACETS	0.621	0.575	0.668	0.621	0.575	0.668	SUBCLONAL	1	TRUE	1	0.507772081139311	2		838	1351	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551323	29551323	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041285-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	259	707	0	ENST00000389048.3:c.1307C>A	p.Ala436Asp	p.A436D	ENST00000389048	NM_004304.4	436	gCc/gAc	6/29	1	2	FACETS	0.969	0.908	1	0.969	0.908	1	CLONAL	1	TRUE	1	0.507772081139311	2		707	1053	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568503	41568503	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	42	270	0	ENST00000263253.7:c.4453G>C	p.Asp1485His	p.D1485H	ENST00000263253	NM_001429.3	1485	Gat/Cat	28/31	0.182528759807614	4	FACETS	0.921	0.77	1	0.461	0.385	0.545	CLONAL	1	TRUE	2	0.282362080052964	4		270	414	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497711	125497711	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	68	283	0	ENST00000428830.2:c.275T>C	p.Leu92Pro	p.L92P	ENST00000428830	NM_001114121.2	92	cTt/cCt	3/14	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.282362080052964	2		283	362	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435664	110435687	+	inframe_deletion	In_Frame_Del	DEL	GCTCCGGTGGCAGTGGGTACTCGT	GCTCCGGTGGCAGTGGGTACTCGT	-	novel	NA	P-0041345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	45	449	0	ENST00000375856.3:c.2714_2737del	p.His905_Glu912del	p.H905_E912del	ENST00000375856	NM_003749.2	905	cACGAGTACCCACTGCCACCGGAGCcc/ccc	1/2	0.282362080052964	2	FACETS	0.691	0.581	0.813	0.346	0.29	0.407	SUBCLONAL	1	TRUE	0	0.282362080052964	2		449	461	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522515	67522515	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	23	155	0	ENST00000274335.5:c.12G>C	p.Glu4Asp	p.E4D	ENST00000274335		4	gaG/gaC	1/15	0.282362080052964	3	FACETS	0.939	0.736	1	0.469	0.368	0.585	CLONAL	1	TRUE	1	0.282362080052964	3		155	198	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0041356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	78	663	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.55	0.483	0.623	0.55	0.483	0.623	SUBCLONAL	1	TRUE	1	0.363137236894154	2		667	781	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42840410	42840411	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0041356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	134	571	0	ENST00000398585.3:c.1337_1338del	p.Arg446MetfsTer8	p.R446Mfs*8	ENST00000398585	NM_001135099.1	446	aGA/a	12/14	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.363137236894154	2		571	687	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500474	99500474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45475702	NA	P-0041356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	44	766	0	ENST00000268035.6:c.3907G>A	p.Val1303Ile	p.V1303I	ENST00000268035	NM_000875.3	1303	Gtc/Atc	21/21	1	2	FACETS	0.294	0.246	0.348	0.294	0.246	0.348	SUBCLONAL	1	TRUE	1	0.363137236894154	2		766	824	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582168	189582168	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121908835	NA	P-0041356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	51	498	1	ENST00000264731.3:c.727C>T	p.Arg243Trp	p.R243W	ENST00000264731	NM_003722.4	243	Cgg/Tgg	5/14	1	2	FACETS	0.358	0.303	0.418	0.358	0.303	0.418	SUBCLONAL	1	TRUE	1	0.363137236894154	2		499	785	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258894	16258894	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs779191752	NA	P-0041356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	249	937	0	ENST00000375759.3:c.6159C>A	p.Asn2053Lys	p.N2053K	ENST00000375759	NM_015001.2	2053	aaC/aaA	11/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.363137236894154	2		937	1235	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042300	42042301	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs866465268	NA	P-0041356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	115	642	0	ENST00000219905.7:c.6499_6500del	p.Leu2167GlyfsTer27	p.L2167Gfs*27	ENST00000219905	NM_001164273.1	2165	gaCTct/gact	17/24	1	2	FACETS	0.982	0.886	1	0.982	0.886	1	CLONAL	1	TRUE	1	0.363137236894154	2		642	645	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372071	55372071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	48	375	2	ENST00000297316.4:c.761C>T	p.Ala254Val	p.A254V	ENST00000297316	NM_022454.3	254	gCg/gTg	2/2	1	2	FACETS	0.501	0.423	0.586	0.501	0.423	0.586	SUBCLONAL	1	TRUE	1	0.363137236894154	2		377	528	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274018	10274018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1354238435	NA	P-0041356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	215	905	0	ENST00000330684.3:c.251C>T	p.Thr84Met	p.T84M	ENST00000330684	NM_001134407.1	84	aCg/aTg	2/13	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.363137236894154	2		905	1050	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918548	44918548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	18	257	0	ENST00000377967.4:c.1031C>T	p.Ala344Val	p.A344V	ENST00000377967	NM_021140.2	344	gCt/gTt	12/29	1	1	FACETS	0.305	0.23	0.394	0.305	0.23	0.394	SUBCLONAL	1	TRUE	0	0.363137236894154	1		257	266	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793049	33793049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	25	272	1	ENST00000498907.2:c.272C>T	p.Ala91Val	p.A91V	ENST00000498907	NM_004364.3	91	gCc/gTc	1/1	1	2	FACETS	0.349	0.275	0.435	0.349	0.275	0.435	SUBCLONAL	1	TRUE	1	0.363137236894154	2		273	394	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905525	50905525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150010804	NA	P-0041356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	52	965	0	ENST00000440232.2:c.653G>A	p.Arg218His	p.R218H	ENST00000440232	NM_002691.3	218	cGc/cAc	6/27	1	2	FACETS	0.285	0.241	0.333	0.285	0.241	0.333	SUBCLONAL	1	TRUE	1	0.363137236894154	2		965	1006	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720965	176720965	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs932837462	NA	P-0041356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	130	535	0	ENST00000439151.2:c.6596G>A	p.Arg2199His	p.R2199H	ENST00000439151	NM_022455.4	2199	cGt/cAt	23/23	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.363137236894154	2		535	680	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348536	70348536	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387907360	NA	P-0041356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	37	292	0	ENST00000374080.3:c.3443G>A	p.Arg1148His	p.R1148H	ENST00000374080		1148	cGc/cAc	24/45	1	1	FACETS	0.409	0.337	0.489	0.409	0.337	0.489	SUBCLONAL	1	TRUE	0	0.363137236894154	1		292	408	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374338	81374338	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202185530	NA	P-0041356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	64	405	0	ENST00000222390.5:c.724C>T	p.Arg242Trp	p.R242W	ENST00000222390	NM_000601.4	242	Cgg/Tgg	6/18	1	2	FACETS	0.699	0.606	0.8	0.699	0.606	0.8	SUBCLONAL	1	TRUE	1	0.363137236894154	2		405	504	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349948	70349948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	77	433	0	ENST00000374080.3:c.3931G>A	p.Val1311Met	p.V1311M	ENST00000374080		1311	Gtg/Atg	28/45	1	1	FACETS	0.694	0.611	0.783	0.694	0.611	0.783	SUBCLONAL	1	TRUE	0	0.363137236894154	1		433	500	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809821	36809821	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	202	816	0	ENST00000373129.3:c.784G>A	p.Val262Met	p.V262M	ENST00000373129	NM_032017.1	262	Gtg/Atg	9/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.363137236894154	2		816	956	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104359190	104359190	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	36	462	0	ENST00000369902.3:c.911A>G	p.Asp304Gly	p.D304G	ENST00000369902	NM_016169.3	304	gAc/gGc	8/12	1	2	FACETS	0.384	0.315	0.462	0.384	0.315	0.462	SUBCLONAL	1	TRUE	1	0.363137236894154	2		462	516	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572203	64572203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	57	433	0	ENST00000312049.6:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000312049	NM_130799.2	479	cGg/cAg	10/10	1	2	FACETS	0.733	0.631	0.845	0.733	0.631	0.845	SUBCLONAL	1	TRUE	1	0.363137236894154	2		433	428	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870962	12870962	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	33	405	0	ENST00000228872.4:c.192del	p.Gln65ArgfsTer6	p.Q65Rfs*6	ENST00000228872	NM_004064.3	63	gaT/ga	1/3	0.363137236894154	1	FACETS	0.358	0.292	0.434	0.358	0.292	0.434	SUBCLONAL	1	TRUE	0	0.363137236894154	1		405	415	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924325	112924325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	199	863	1	ENST00000351677.2:c.1271C>T	p.Pro424Leu	p.P424L	ENST00000351677	NM_002834.3	424	cCg/cTg	11/16	1	2	FACETS	0.983	0.91	1	0.983	0.91	1	CLONAL	1	TRUE	1	0.363137236894154	2		864	1115	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646376	3646376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371825444	NA	P-0041356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	178	883	0	ENST00000294008.3:c.1702G>A	p.Val568Met	p.V568M	ENST00000294008	NM_032444.2	568	Gtg/Atg	8/15	1	2	FACETS	0.911	0.839	0.987	0.911	0.839	0.987	CLONAL	1	TRUE	1	0.363137236894154	2		883	1076	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274204	10274204	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	44	472	0	ENST00000330684.3:c.65C>T	p.Ala22Val	p.A22V	ENST00000330684	NM_001134407.1	22	gCg/gTg	2/13	1	2	FACETS	0.483	0.405	0.569	0.483	0.405	0.569	SUBCLONAL	1	TRUE	1	0.363137236894154	2		472	502	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127391	17127391	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	65	796	0	ENST00000285071.4:c.463A>G	p.Thr155Ala	p.T155A	ENST00000285071	NM_144997.5	155	Acc/Gcc	6/14	1	2	FACETS	0.366	0.316	0.421	0.366	0.316	0.421	SUBCLONAL	1	TRUE	1	0.363137236894154	2		796	977	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353770	40353770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	169	795	0	ENST00000293328.3:c.2350C>T	p.His784Tyr	p.H784Y	ENST00000293328	NM_012448.3	784	Cac/Tac	19/19	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.363137236894154	2		795	870	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936801	78936801	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753148409	NA	P-0041356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	226	853	0	ENST00000306801.3:c.3883G>A	p.Gly1295Ser	p.G1295S	ENST00000306801	NM_020761.2	1295	Ggc/Agc	33/34	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.363137236894154	2		853	1044	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56409219	56409219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779797395	NA	P-0041356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	112	527	1	ENST00000348428.3:c.1726C>T	p.Arg576Trp	p.R576W	ENST00000348428	NM_006785.3	576	Cgg/Tgg	14/17	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.363137236894154	2		528	608	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47636839	47637373	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGCGGATCACGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCATCTCTACTAAAAATACAAAAATTAGCCAGGCGTGGTGGTGTGCGCCTGTATTCCCAGCTACTGGGGAGGCTGAAGCAGGAGAATCGATTGAACCCTTGAGGCAGAGGTTGCAGTGAGTTGAGATCGCACCATTGCACTCTAGCCTGGGTGACAGAGCAAGACTTCATCTCAAAAAAAAGAGAAAACATTTTATTAATAAGGTTCATAGAGTTTGGATTTTTCCTTTTTGCTTATAAAATTTTAAAGTATGTTCAAGAGTTTGTTAAATTTTTAAAATTTTATTTTTACTTAGGCTTCTCCTGGCAATCTCTCTCAGTTTGAAGACATTCTCTTTGGTAACAATGATATGTCAGCTTCCATTGGTGTTGTGGGTGTTAAAATGTCCGCAGTTGATGGCCAGAGACAGGTTGGAGTTGGGTATGTGGATTCCATA	CTGGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGCGGATCACGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCATCTCTACTAAAAATACAAAAATTAGCCAGGCGTGGTGGTGTGCGCCTGTATTCCCAGCTACTGGGGAGGCTGAAGCAGGAGAATCGATTGAACCCTTGAGGCAGAGGTTGCAGTGAGTTGAGATCGCACCATTGCACTCTAGCCTGGGTGACAGAGCAAGACTTCATCTCAAAAAAAAGAGAAAACATTTTATTAATAAGGTTCATAGAGTTTGGATTTTTCCTTTTTGCTTATAAAATTTTAAAGTATGTTCAAGAGTTTGTTAAATTTTTAAAATTTTATTTTTACTTAGGCTTCTCCTGGCAATCTCTCTCAGTTTGAAGACATTCTCTTTGGTAACAATGATATGTCAGCTTCCATTGGTGTTGTGGGTGTTAAAATGTCCGCAGTTGATGGCCAGAGACAGGTTGGAGTTGGGTATGTGGATTCCATA	-	novel	NA	P-0041356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2	54	0	0	ENST00000233146.2:c.367-393_508del		p.X123_splice	ENST00000233146	NM_000251.2	123		3/16	0.363137236894154	1	FACETS	1	0.982	1	1	0.987	1	CLONAL	4	TRUE	0	0.363137236894154	1		0	56	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090503	5090503	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	53	338	0	ENST00000381652.3:c.2819A>G	p.Tyr940Cys	p.Y940C	ENST00000381652	NM_004972.3	940	tAt/tGt	21/25	1	2	FACETS	0.89	0.763	1	0.89	0.763	1	CLONAL	1	TRUE	1	0.363137236894154	2		338	328	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0041362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	128	298	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.316028601009344	1	FACETS	0.819	0.747	0.893	0.819	0.747	0.893	CLONAL	1	TRUE	0	0.502252891869036	1		298	466	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0041362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	312	687	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.493096341198989	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.502252891869036	1		687	891	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0041362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	247	358	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.143941445167725	5	FACETS	1	0.985	1			1	INDETERMINATE	2	TRUE	NA	0.502252891869036	5		358	745	SUCCESS
APC	324	MSKCC	GRCh37	5	112175788	112175788	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	52	287	0	ENST00000257430.4:c.4497del	p.Ser1501LeufsTer6	p.S1501Lfs*6	ENST00000257430	NM_000038.5	1499	ggA/gg	16/16	0.316028601009344	1	FACETS	0.408	0.348	0.473	0.408	0.348	0.473	SUBCLONAL	1	TRUE	0	0.502252891869036	1		287	380	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670357	134670357	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369940994	NA	P-0041362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	167	522	0	ENST00000398015.3:c.268C>T	p.Arg90Cys	p.R90C	ENST00000398015	NM_004441.4	90	Cgc/Tgc	3/16	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.502252891869036	2		522	638	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411576	63411576	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	245	427	0	ENST00000330258.3:c.1591C>T	p.Arg531Ter	p.R531*	ENST00000330258	NM_152424.3	531	Cga/Tga	2/2	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.502252891869036	1		427	542	SUCCESS
APC	324	MSKCC	GRCh37	5	112174438	112174438	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs863225340	NA	P-0041362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	84	323	0	ENST00000257430.4:c.3147G>A	p.Trp1049Ter	p.W1049*	ENST00000257430	NM_000038.5	1049	tgG/tgA	16/16	0.316028601009344	1	FACETS	0.743	0.662	0.829	0.743	0.662	0.829	SUBCLONAL	1	TRUE	0	0.502252891869036	1		323	337	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101438	27101438	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	212	652	0	ENST00000324856.7:c.4724del	p.Pro1575HisfsTer37	p.P1575Hfs*37	ENST00000324856	NM_006015.4	1574	Ccc/cc	18/20	0.502252891869036	1	FACETS	0.851	0.793	0.91	0.851	0.793	0.91	CLONAL	1	TRUE	0	0.502252891869036	1		652	743	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210710	36210710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745637683	NA	P-0041362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	132	801	1	ENST00000222270.7:c.461G>A	p.Arg154His	p.R154H	ENST00000222270	NM_014727.1	154	cGc/cAc	3/37	0.316028601009344	1	FACETS	0.418	0.379	0.46	0.418	0.379	0.46	SUBCLONAL	1	TRUE	0	0.502252891869036	1		802	941	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527560	41527560	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041362-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	205	551	0	ENST00000263253.7:c.1451C>A	p.Pro484His	p.P484H	ENST00000263253	NM_001429.3	484	cCc/cAc	6/31	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.502252891869036	2		551	816	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0041457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	14	401	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.576	0.415	0.772	0.576	0.415	0.772	SUBCLONAL	1	TRUE	1	0.13	2		401	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0041457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	17	727	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.382	0.283	0.5	0.382	0.283	0.5	SUBCLONAL	1	TRUE	1	0.13	2		728	685	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0041457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	17	227	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.841	0.627	1	0.841	0.627	1	CLONAL	1	TRUE	1	0.13	2		227	311	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243045	105243045	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	37	447	0	ENST00000349310.3:c.238T>C	p.Trp80Arg	p.W80R	ENST00000349310	NM_001014432.1	80	Tgg/Cgg	5/15	1	2	FACETS	0.868	0.714	1	0.868	0.714	1	CLONAL	1	TRUE	1	0.13	2		447	656	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708054	117708054	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	20	241	0	ENST00000368508.3:c.2123C>T	p.Ser708Leu	p.S708L	ENST00000368508	NM_002944.2	708	tCa/tTa	14/43	1	2	FACETS	1	0.82	1	1	0.82	1	CLONAL	1	TRUE	1	0.13	2		241	283	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638352	176638353	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs587784092	NA	P-0041457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	32	410	0	ENST00000439151.2:c.2954_2955del	p.Ser985CysfsTer25	p.S985Cfs*25	ENST00000439151	NM_022455.4	984	gaCTct/gact	5/23	1	2	FACETS	0.823	0.667	1	0.823	0.667	1	CLONAL	1	TRUE	1	0.13	2		410	598	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2214555	2214555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	37	472	2	ENST00000398665.3:c.1883G>A	p.Ser628Asn	p.S628N	ENST00000398665	NM_032482.2	628	aGc/aAc	19/28	1	2	FACETS	0.841	0.691	1	0.841	0.691	1	CLONAL	1	TRUE	1	0.13	2		474	677	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795162	42795162	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	37	533	0	ENST00000575354.2:c.2245del	p.Leu749CysfsTer175	p.L749Cfs*175	ENST00000575354	NM_015125.3	748	Ccc/cc	10/20	1	2	FACETS	0.881	0.725	1	0.881	0.725	1	CLONAL	1	TRUE	1	0.13	2		533	646	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101143	27101145	+	frameshift_variant	Frame_Shift_Del	DEL	CAT	CAT	A	novel	NA	P-0041457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	30	440	0	ENST00000324856.7:c.4425_4427delinsA	p.Asn1475LysfsTer15	p.N1475Kfs*15	ENST00000324856	NM_006015.4	1475	aaCATg/aaAg	18/20	1	2	FACETS	0.799	0.642	0.977	0.799	0.642	0.977	CLONAL	1	TRUE	1	0.13	2		440	578	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229345	36229347	+	frameshift_variant	Frame_Shift_Del	DEL	CGC	CGC	A	novel	NA	P-0041457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	25	350	0	ENST00000222270.7:c.8035_8037delinsA	p.Arg2679AsnfsTer5	p.R2679Nfs*5	ENST00000222270	NM_014727.1	2679	CGC/A	37/37	1	2	FACETS	0.772	0.607	0.963	0.772	0.607	0.963	CLONAL	1	TRUE	1	0.13	2		350	498	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782948	66782948	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	49	370	0	ENST00000307102.5:c.1177G>C	p.Val393Leu	p.V393L	ENST00000307102	NM_002755.3	393	Gtc/Ctc	11/11	NA	2	FACETS	0.472	0.4	0.552			1	INDETERMINATE	1	TRUE	NA	0.399827118679972	2		370	519	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579360	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAAACCGTA	novel	NA	P-0041481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	197	617	0	ENST00000269305.4:c.319_327dup	p.Tyr107_Phe109dup	p.Y107_F109dup	ENST00000269305	NM_001126112.2	107	-/TACGGTTTC	4/11	0.399827118679972	1	FACETS	0.937	0.869	1	0.937	0.869	1	CLONAL	1	TRUE	0	0.399827118679972	1		617	841	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051644	30051645	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACCG	novel	NA	P-0041505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	115	181	0	ENST00000338641.4:c.579_580insCCGA	p.Glu194ProfsTer10	p.E194Pfs*10	ENST00000338641	NM_000268.3	193	gca/gcACCGa	6/16	0.247402748709407	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.247402748709407	2		181	391	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084050	47084050	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs187254090	NA	P-0041505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	100	254	0	ENST00000409792.3:c.7238+1G>A		p.X2413_splice	ENST00000409792	NM_014159.6	2413			0.225186639928197	2	FACETS	0.804	0.721	0.891	0.804	0.721	0.891	CLONAL	2	TRUE	0	0.247402748709407	2		254	503	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613217	52613218	+	splice_acceptor_variant,intron_variant	Splice_Site	DNP	TG	TG	GT	novel	NA	P-0041505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	125	222	0	ENST00000394830.3:c.3313-3_3313-2delinsAC		p.X1105_splice	ENST00000394830	NM_018313.4	1105			0.241440375290212	3	FACETS	1	0.976	1	0.805	0.734	0.88	CLONAL	2	TRUE	0	0.247402748709407	3		222	470	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467748	50467748	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0041505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	163	357	0	ENST00000331340.3:c.983G>C	p.Arg328Pro	p.R328P	ENST00000331340	NM_006060.4	328	cGc/cCc	8/8	0.186063918508936	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.247402748709407	4		357	708	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629299	187629300	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	C	novel	NA	P-0041505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	63	381	0	ENST00000441802.2:c.1682_1683delinsG	p.Asn561SerfsTer2	p.N561Sfs*2	ENST00000441802	NM_005245.3	561	aAC/aG	2/27	1	2	FACETS	0.859	0.743	0.985	0.859	0.743	0.985	CLONAL	1	TRUE	1	0.247402748709407	2		381	593	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0041519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	66	548	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.855	0.74	0.979	0.855	0.74	0.979	CLONAL	1	TRUE	1	0.19	2		548	813	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0041519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	47	748	5	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.72	0.606	0.846	0.72	0.606	0.846	SUBCLONAL	1	TRUE	1	0.19	2		753	687	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0041519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	37	215	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.19	2		215	365	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0041519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	117	617	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	0.149927866305253	2	FACETS	0.904	0.817	0.997	0.904	0.817	0.997	CLONAL	2	TRUE	0	0.19	2		617	681	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71942053	71942053	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	76	854	0	ENST00000298229.2:c.1322del	p.Asn441ThrfsTer2	p.N441Tfs*2	ENST00000298229	NM_001567.3	439	ccA/cc	12/28	1	2	FACETS	0.976	0.854	1	0.976	0.854	1	CLONAL	1	TRUE	1	0.19	2		854	820	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663418	67663418	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0041519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	34	396	0	ENST00000264010.4:c.1819G>T	p.Glu607Ter	p.E607*	ENST00000264010	NM_006565.3	607	Gaa/Taa	10/12	1	2	FACETS	0.726	0.592	0.876	0.726	0.592	0.876	SUBCLONAL	1	TRUE	1	0.19	2		396	493	SUCCESS
H3C13	653604	MSKCC	GRCh37	1	149784863	149784863	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	26	243	0	ENST00000331491.1:c.374T>C	p.Ile125Thr	p.I125T	ENST00000331491	NM_001123375.2	125	aTc/aCc	1/1	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.19	2		243	248	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466035	69466040	+	inframe_deletion	In_Frame_Del	DEL	GGACGT	GGACGT	-	novel	NA	P-0041519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	55	789	2	ENST00000227507.2:c.877_882del	p.Val293_Asp294del	p.V293_D294del	ENST00000227507	NM_053056.2	291	cgGGACGTg/cgg	5/5	1	2	FACETS	0.787	0.672	0.913	0.787	0.672	0.913	CLONAL	1	TRUE	1	0.19	2		791	736	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1627405	1627405	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199628190	NA	P-0041519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	74	829	0	ENST00000344749.5:c.319G>A	p.Ala107Thr	p.A107T	ENST00000344749	NM_001136139.2	107	Gcc/Acc	6/19	1	2	FACETS	0.909	0.794	1	0.909	0.794	1	CLONAL	1	TRUE	1	0.19	2		829	857	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181776	56181832	+	inframe_deletion	In_Frame_Del	DEL	TTGCTGAGTAAATATGGAGCCTTCAAAGAATCAGTAGTTATTAACTACACTGAACAG	TTGCTGAGTAAATATGGAGCCTTCAAAGAATCAGTAGTTATTAACTACACTGAACAG	-	novel	NA	P-0041519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	24	393	0	ENST00000399503.3:c.4002_4058del	p.Ser1336_Leu1354del	p.S1336_L1354del	ENST00000399503	NM_005921.1	1334	TTGCTGAGTAAATATGGAGCCTTCAAAGAATCAGTAGTTATTAACTACACTGAACAG/-	17/20	1	2	FACETS	0.544	0.426	0.682	0.544	0.426	0.682	SUBCLONAL	1	TRUE	1	0.19	2		393	464	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15818025	15818025	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	31	356	0	ENST00000307771.7:c.152C>G	p.Thr51Ser	p.T51S	ENST00000307771	NM_005089.3	51	aCt/aGt	3/11	1	2	FACETS	0.684	0.553	0.833	0.684	0.553	0.833	SUBCLONAL	1	TRUE	1	0.19	2		356	477	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0041529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	47	351	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.719	0.607	0.842	0.719	0.607	0.842	SUBCLONAL	1	TRUE	1	0.281065818532858	2		351	465	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220561	1220582	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGCACGGCACCGCCACAGGCA	CTGCACGGCACCGCCACAGGCA	-	novel	NA	P-0041529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	87	638	0	ENST00000326873.7:c.598-13_606del		p.X200_splice	ENST00000326873	NM_000455.4	200		5/10	0.281065818532858	1	FACETS	0.96	0.852	1	0.96	0.852	1	CLONAL	1	TRUE	0	0.281065818532858	1		638	554	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243777016	243777016	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	58	501	0	ENST00000263826.5:c.653A>T	p.Lys218Ile	p.K218I	ENST00000263826	NM_005465.4	218	aAa/aTa	7/13	1	2	FACETS	0.764	0.657	0.881	0.764	0.657	0.881	SUBCLONAL	1	TRUE	1	0.281065818532858	2		501	540	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317475	1317475	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	90	689	0	ENST00000400841.2:c.590A>T	p.Asp197Val	p.D197V	ENST00000400841		197	gAc/gTc	5/6	0.229962954073978	1	FACETS	0.831	0.738	0.931	0.831	0.738	0.931	CLONAL	1	TRUE	0	0.281065818532858	1		689	662	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606273	93606273	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	182	987	1	ENST00000375746.1:c.98del	p.Gly33AlafsTer2	p.G33Afs*2	ENST00000375746	NM_001174167.1	31	caG/ca	2/14	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.4	2		988	717	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	146	703	5	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.4	2		708	636	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	357	663	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.993	1	1	0.997	1	CLONAL	2	TRUE	1	0.4	2		667	725	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	114	358	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.77	0.7	0.843	1	0.986	1	SUBCLONAL	2	TRUE	1	0.4	2		358	370	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687471	37687472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs760014508	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	80	382	4	ENST00000447079.4:c.4382dup	p.Thr1463AsnfsTer50	p.T1463Nfs*50	ENST00000447079	NM_015083.1	1459	tgg/tGgg	14/14	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.4	2		386	355	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	132	478	2	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.4	2		480	504	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	155	376	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.4	2		377	590	SUCCESS
AXL	558	MSKCC	GRCh37	19	41736935	41736935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776682499	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	192	935	1	ENST00000301178.4:c.650G>A	p.Arg217His	p.R217H	ENST00000301178	NM_021913.4	217	cGc/cAc	5/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.4	2		936	692	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965666	90965666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	109	356	0	ENST00000265433.3:c.1651del	p.Arg551GlyfsTer8	p.R551Gfs*8	ENST00000265433	NM_002485.4	551	Agg/gg	11/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.4	2		356	395	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845830	72845830	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	189	711	2	ENST00000268489.5:c.3637del	p.Thr1213GlnfsTer31	p.T1213Qfs*31	ENST00000268489	NM_006885.3	1213	Aca/ca	6/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.4	2		713	651	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	132	348	7	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	1	2	FACETS	0.797	0.73	0.866	1	0.988	1	SUBCLONAL	2	TRUE	1	0.4	2		355	414	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932085	39932085	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	245	475	1	ENST00000378444.4:c.2514del	p.Lys839SerfsTer17	p.K839Sfs*17	ENST00000378444	NM_001123385.1	838	ccC/cc	4/15	1	1	FACETS	1	0.985	1	1	0.996	1	CLONAL	2	TRUE	0	0.4	1		476	445	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612879	228612879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767647652	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	168	755	0	ENST00000366696.1:c.148C>T	p.Arg50Cys	p.R50C	ENST00000366696	NM_003493.2	50	Cgc/Tgc	1/1	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.4	2		755	586	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	211	1083	3	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.4	2		1086	873	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447773	49447773	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	137	617	0	ENST00000301067.7:c.661del	p.Ala221LeufsTer40	p.A221Lfs*40	ENST00000301067	NM_003482.3	221	Gct/ct	5/54	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.4	2		617	564	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288789	15288789	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	52	240	0	ENST00000263388.2:c.3950del	p.Pro1317GlnfsTer103	p.P1317Qfs*103	ENST00000263388	NM_000435.2	1317	cCa/ca	24/33	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.4	2		240	221	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221667	36221667	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779863547	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	196	1048	3	ENST00000222270.7:c.5336G>A	p.Arg1779Gln	p.R1779Q	ENST00000222270	NM_014727.1	1779	cGa/cAa	26/37	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.4	2		1051	830	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209583	98209583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375998275	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	150	847	0	ENST00000331920.6:c.3955C>T	p.Arg1319Cys	p.R1319C	ENST00000331920	NM_000264.3	1319	Cgc/Tgc	23/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.4	2		847	581	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	163	1086	0	ENST00000220592.5:c.1805_1806dup	p.Ala603ProfsTer93	p.A603Pfs*93	ENST00000220592	NM_012154.3	602	-/CC	14/19	1	2	FACETS	0.814	0.747	0.885	0.814	0.747	0.885	CLONAL	1	TRUE	1	0.4	2		1086	1001	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212439	5212439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150241840	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	148	1008	0	ENST00000357368.4:c.4678G>A	p.Val1560Met	p.V1560M	ENST00000357368	NM_002850.3	1560	Gtg/Atg	31/38	0.580602781700155	1	FACETS	0.873	0.8	0.95	0.873	0.8	0.95	CLONAL	1	TRUE	0	0.4	1		1008	678	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030841	36030841	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs994208712	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	109	481	0	ENST00000358208.4:c.1120G>A	p.Ala374Thr	p.A374T	ENST00000358208		374	Gcc/Acc	10/12	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.4	2		481	449	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625302	69625302	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782573423	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	195	1119	4	ENST00000334134.2:c.491G>A	p.Arg164His	p.R164H	ENST00000334134	NM_005247.2	164	cGc/cAc	3/3	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.4	2		1123	680	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344759	65344759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	116	330	0	ENST00000342505.4:c.278G>A	p.Arg93His	p.R93H	ENST00000342505	NM_002227.2	93	cGc/cAc	4/25	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.4	2		330	433	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77070026	77070026	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	170	556	2	ENST00000356341.3:c.514C>T	p.Pro172Ser	p.P172S	ENST00000356341	NM_002576.4	172	Cca/Tca	6/15	1	2	FACETS	0.759	0.702	0.817	1	0.99	1	SUBCLONAL	2	TRUE	1	0.4	2		558	560	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856274	111856274	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	21	50	0	ENST00000341259.2:c.325G>A	p.Gly109Ser	p.G109S	ENST00000341259	NM_005475.2	109	Ggc/Agc	2/8	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.4	2		50	71	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877417	28877417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758531658	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	190	644	0	ENST00000282397.4:c.3904G>A	p.Glu1302Lys	p.E1302K	ENST00000282397	NM_002019.4	1302	Gaa/Aaa	30/30	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.4	2		644	673	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133730	2133731	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGGTTCCTGTGCTGGT	novel	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	127	998	0	ENST00000219476.3:c.3920_3936dup	p.Glu1313ArgfsTer18	p.E1313Rfs*18	ENST00000219476	NM_000548.3	1306	-/GAGGTTCCTGTGCTGGT	33/42	1	2	FACETS	0.832	0.754	0.914	0.832	0.754	0.914	CLONAL	1	TRUE	1	0.4	2		998	763	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117218	7117218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1432736648	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	190	887	0	ENST00000302850.5:c.3998C>T	p.Ser1333Leu	p.S1333L	ENST00000302850	NM_000208.2	1333	tCg/tTg	22/22	0.580602781700155	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.4	1		887	675	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281350	15281350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1366413619	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	175	1038	0	ENST00000263388.2:c.4906C>T	p.Pro1636Ser	p.P1636S	ENST00000263388	NM_000435.2	1636	Cct/Tct	27/33	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.4	2		1038	681	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955212	17955212	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	185	989	0	ENST00000458235.1:c.15T>G	p.Ser5Arg	p.S5R	ENST00000458235	NM_000215.3	5	agT/agG	2/24	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.4	2		989	760	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44515842	44515842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	138	610	0	ENST00000291552.4:c.211G>A	p.Asp71Asn	p.D71N	ENST00000291552	NM_006758.2	71	Gat/Aat	4/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.4	2		610	612	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447627	187447627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	194	951	1	ENST00000232014.4:c.566C>T	p.Ser189Phe	p.S189F	ENST00000232014	NM_001130845.1	189	tCc/tTc	5/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.4	2		952	715	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680046	30680046	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	148	698	0	ENST00000376406.3:c.1673del	p.Gly558AspfsTer10	p.G558Dfs*10	ENST00000376406	NM_014641.2	558	gGa/ga	5/15	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.4	2		698	636	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265487	152265487	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	179	712	0	ENST00000206249.3:c.940C>G	p.Gln314Glu	p.Q314E	ENST00000206249	NM_000125.3	314	Cag/Gag	4/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.4	2		712	693	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391798	139391799	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	190	974	0	ENST00000277541.6:c.6392dup	p.Thr2132HisfsTer136	p.T2132Hfs*136	ENST00000277541	NM_017617.3	2131	ggc/ggGc	34/34	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.4	2		974	779	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223646	53223646	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041542-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	256	540	0	ENST00000375401.3:c.3713G>A	p.Trp1238Ter	p.W1238*	ENST00000375401	NM_004187.3	1238	tGg/tAg	23/26	1	1	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	TRUE	0	0.4	1		540	432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0041572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	100	779	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.3	1	FACETS	0.986	0.881	1	0.986	0.881	1	CLONAL	1	TRUE	0	0.25	1		781	710	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254839	16254839	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	53	519	0	ENST00000375759.3:c.2104C>T	p.Arg702Ter	p.R702*	ENST00000375759	NM_015001.2	702	Cga/Tga	11/15	1	2	FACETS	0.625	0.532	0.728	0.625	0.532	0.728	SUBCLONAL	1	TRUE	1	0.25	2		519	678	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405927	49405927	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	134	531	0	ENST00000418115.1:c.211C>A	p.Pro71Thr	p.P71T	ENST00000418115	NM_001664.2	71	Ccc/Acc	3/5	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.25	2		531	882	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18943063	18943063	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	49	418	0	ENST00000262803.5:c.45C>G	p.Phe15Leu	p.F15L	ENST00000262803	NM_002911.3	15	ttC/ttG	1/24	1	2	FACETS	0.595	0.503	0.696	0.595	0.503	0.696	SUBCLONAL	1	TRUE	1	0.25	2		418	659	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114074	73114074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	15	150	0	ENST00000356692.5:c.710C>T	p.Ala237Val	p.A237V	ENST00000356692		237	gCt/gTt	8/9	1	2	FACETS	0.536	0.392	0.708	0.536	0.392	0.708	SUBCLONAL	1	TRUE	1	0.25	2		150	224	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204692	128204692	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	60	811	0	ENST00000341105.2:c.749C>A	p.Pro250His	p.P250H	ENST00000341105	NM_032638.4	250	cCc/cAc	3/6	1	2	FACETS	0.507	0.435	0.585	0.507	0.435	0.585	SUBCLONAL	1	TRUE	1	0.25	2		811	947	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227999	55228009	+	frameshift_variant	Frame_Shift_Del	DEL	AAATTATAAGC	AAATTATAAGC	-	novel	NA	P-0041572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	20	278	0	ENST00000275493.2:c.1468_1478del	p.Ile490GlnfsTer3	p.I490Qfs*3	ENST00000275493	NM_005228.3	489	aAAATTATAAGC/a	12/28	1	2	FACETS	0.447	0.341	0.571	0.447	0.341	0.571	SUBCLONAL	1	TRUE	1	0.25	2		278	358	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0041589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	151	512	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.182524512692651	4	FACETS	1	0.98	1	0.814	0.746	0.884	CLONAL	2	TRUE	1	0.227770440238535	4		512	667	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971194	21971194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561034503	NA	P-0041589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	76	328	0	ENST00000304494.5:c.164G>A	p.Gly55Asp	p.G55D	ENST00000304494	NM_000077.4	55	gGc/gAc	2/3	0.227770440238535	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.227770440238535	1		328	398	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106621	27106623	+	frameshift_variant	Frame_Shift_Ins	INS	GAG	GAG	CAAA	novel	NA	P-0041589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	89	518	2	ENST00000324856.7:c.6232_6234delinsCAAA	p.Glu2078GlnfsTer21	p.E2078Qfs*21	ENST00000324856	NM_006015.4	2078	GAG/CAAA	20/20	0.227770440238535	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.227770440238535	1		520	562	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042194	14042194	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	17	172	0	ENST00000311895.7:c.2741G>T	p.Gly914Val	p.G914V	ENST00000311895	NM_005236.2	914	gGg/gTg	11/11	1	2	FACETS	0.524	0.391	0.682	0.524	0.391	0.682	SUBCLONAL	1	TRUE	1	0.227770440238535	2		172	285	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578447	7578464	+	inframe_deletion	In_Frame_Del	DEL	GGCCATGGCGCGGACGCG	GGCCATGGCGCGGACGCG	-	novel	NA	P-0041589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	93	699	1	ENST00000269305.4:c.466_483del	p.Arg156_Ala161del	p.R156_A161del	ENST00000269305	NM_001126112.2	156	CGCGTCCGCGCCATGGCC/-	5/11	0.227770440238535	1	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	0	0.227770440238535	1		700	702	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164039	47164039	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	13	261	0	ENST00000409792.3:c.2087T>A	p.Met696Lys	p.M696K	ENST00000409792	NM_014159.6	696	aTg/aAg	3/21	1	2	FACETS	0.46	0.328	0.622	0.46	0.328	0.622	SUBCLONAL	1	TRUE	1	0.227770440238535	2		261	248	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031856	26031897	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	TGATGAAAAAGTGACTTTACATTTACGCTCTTTCTCCGCGAA	TGATGAAAAAGTGACTTTACATTTACGCTCTTTCTCCGCGAA	-	novel	NA	P-0041589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	31	126	0	ENST00000244661.2:c.392_*22del		p.*131*	ENST00000244661	NM_003537.3	131		1/1	0.227770440238535	3	FACETS	0.811	0.662	0.976	0.811	0.662	0.976	CLONAL	2	TRUE	1	0.227770440238535	3		126	187	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0041606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	55	351	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.865	0.741	1	0.865	0.741	1	CLONAL	1	TRUE	1	0.257845780427216	2		351	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576917	7576918	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	G	novel	NA	P-0041606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	91	715	0	ENST00000269305.4:c.928_929delinsC	p.Asn310ProfsTer35	p.N310Pfs*35	ENST00000269305	NM_001126112.2	310	AAc/Cc	9/11	0.257845780427216	1	FACETS	0.892	0.793	0.999	0.892	0.793	0.999	CLONAL	1	TRUE	0	0.257845780427216	1		715	689	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148526862	148526862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	14	305	0	ENST00000320356.2:c.442G>A	p.Glu148Lys	p.E148K	ENST00000320356	NM_004456.4	148	Gaa/Aaa	5/20	0.649857256966538	2	FACETS	0.484	0.355	0.635	0.242	0.177	0.318	SUBCLONAL	1	TRUE	0	0.649857256966538	2		305	89	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0041650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	58	522	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.200752963330096	4	FACETS	0.7	0.601	0.808	0.35	0.3	0.404	INDETERMINATE	1	TRUE	2	0.369493253195505	4		522	614	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435391	121435391	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193922580	NA	P-0041650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	175	1055	1	ENST00000257555.6:c.1424C>T	p.Pro475Leu	p.P475L	ENST00000257555		475	cCg/cTg	7/10	0.357207544184328	2	FACETS	0.92	0.846	0.996	0.46	0.423	0.498	CLONAL	1	TRUE	0	0.369493253195505	2		1056	1030	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578555	7578555	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0041650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	323	1020	2	ENST00000269305.4:c.376-1G>T		p.X126_splice	ENST00000269305	NM_001126112.2	126			NA	2	FACETS	0.859	0.812	0.906			1	INDETERMINATE	2	TRUE	NA	0.369493253195505	2		1022	1018	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1064795203	NA	P-0041659-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	211	824	0	ENST00000269305.4:c.532C>G	p.His178Asp	p.H178D	ENST00000269305	NM_001126112.2	178	Cac/Gac	5/11	0.501823214283344	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.501823214283344	1		824	594	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0041668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	260	254	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	0.706051657301114	3	FACETS	0.96	0.91	1	0.96	0.91	1	CLONAL	2	TRUE	1	0.706051657301114	3		254	519	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176330	24176330	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1057517825	NA	P-0041668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	350	1044	0	ENST00000263121.7:c.1121G>A	p.Arg374Gln	p.R374Q	ENST00000263121	NM_003073.3	374	cGg/cAg	9/9	0.698866107972989	2	FACETS	1	0.958	1	0.505	0.479	0.531	CLONAL	1	TRUE	0	0.706051657301114	2		1044	982	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777092	9777092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146796121	NA	P-0041668-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	286	1028	2	ENST00000377346.4:c.856C>T	p.Arg286Trp	p.R286W	ENST00000377346	NM_005026.3	286	Cgg/Tgg	7/24	1	2	FACETS	0.787	0.741	0.835	0.787	0.741	0.835	SUBCLONAL	1	TRUE	1	0.706051657301114	2		1030	1029	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0041675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	40	522	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.842	1	1	0.842	1	CLONAL	1	TRUE	1	0.19	2		522	416	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919331	48919331	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1131690874	NA	P-0041675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	22	110	0	ENST00000267163.4:c.496G>T	p.Glu166Ter	p.E166*	ENST00000267163	NM_000321.2	166	Gaa/Taa	4/27	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.19	2		110	183	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572986	7572986	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555524156	NA	P-0041675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	51	497	0	ENST00000269305.4:c.1123C>T	p.Gln375Ter	p.Q375*	ENST00000269305	NM_001126112.2	375	Cag/Tag	11/11	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.19	2		497	490	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604750	48604750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	33	420	0	ENST00000342988.3:c.1572G>T	p.Trp524Cys	p.W524C	ENST00000342988	NM_005359.5	524	tgG/tgT	12/12	1	2	FACETS	0.762	0.62	0.922	0.762	0.62	0.922	CLONAL	1	TRUE	1	0.19	2		420	456	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94918436	94918436	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	39	383	0	ENST00000536441.1:c.746C>T	p.Ser249Leu	p.S249L	ENST00000536441	NM_144665.3	249	tCa/tTa	5/10	1	2	FACETS	0.923	0.765	1	0.923	0.765	1	CLONAL	1	TRUE	1	0.19	2		383	445	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409106	139409106	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	72	893	0	ENST00000277541.6:c.2063A>G	p.His688Arg	p.H688R	ENST00000277541	NM_017617.3	688	cAc/cGc	13/34	NA	2	FACETS	0.891	0.777	1			1	INDETERMINATE	1	TRUE	NA	0.19	2		893	851	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651499	52651499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	30	460	1	ENST00000394830.3:c.1597G>A	p.Ala533Thr	p.A533T	ENST00000394830	NM_018313.4	533	Gct/Act	15/30	1	2	FACETS	0.616	0.495	0.753	0.616	0.495	0.753	SUBCLONAL	1	TRUE	1	0.19	2		461	513	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651514	52651514	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	29	412	0	ENST00000394830.3:c.1582A>G	p.Asn528Asp	p.N528D	ENST00000394830	NM_018313.4	528	Aat/Gat	15/30	1	2	FACETS	0.654	0.524	0.802	0.654	0.524	0.802	SUBCLONAL	1	TRUE	1	0.19	2		412	467	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56167735	56167735	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0041675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	23	276	0	ENST00000399503.3:c.1302-2A>C		p.X434_splice	ENST00000399503	NM_005921.1	434			1	2	FACETS	0.884	0.69	1	0.884	0.69	1	CLONAL	1	TRUE	1	0.19	2		276	274	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56180461	56180613	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAACTTTGTGAACGTGTTTATTTGAAACAGGTGACTTATGTCAGAAACACATCTTCTGAGCAAGAAGAAGTAGTAGAAGCACTAAGAGAAGAGATAAGAATGATGAGCCATCTGAATCATCCAAACATCATTAGGATGTTGGGAGCCACGTGT	AAACTTTGTGAACGTGTTTATTTGAAACAGGTGACTTATGTCAGAAACACATCTTCTGAGCAAGAAGAAGTAGTAGAAGCACTAAGAGAAGAGATAAGAATGATGAGCCATCTGAATCATCCAAACATCATTAGGATGTTGGGAGCCACGTGT	-	novel	NA	P-0041675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	12	167	0	ENST00000399503.3:c.3820-30_3942del		p.X1274_splice	ENST00000399503	NM_005921.1	1274		16/20	1	2	FACETS	0.686	0.483	0.936	0.686	0.483	0.936	SUBCLONAL	1	TRUE	1	0.19	2		167	184	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194901	29194901	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1400455223	NA	P-0041675-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	75	802	0	ENST00000240100.2:c.827T>C	p.Val276Ala	p.V276A	ENST00000240100	NM_001394.6	276	gTg/gCg	4/4	1	2	FACETS	0.986	0.862	1	0.986	0.862	1	CLONAL	1	TRUE	1	0.19	2		802	801	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0041677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	74	522	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.587	0.513	0.667	0.587	0.513	0.667	SUBCLONAL	1	TRUE	1	0.322998847212461	2		522	781	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0041677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	39	602	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	1	2	FACETS	0.391	0.323	0.467	0.391	0.323	0.467	SUBCLONAL	1	TRUE	1	0.322998847212461	2		602	618	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858987	243858987	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0041677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	66	512	0	ENST00000263826.5:c.78C>G	p.Tyr26Ter	p.Y26*	ENST00000263826	NM_005465.4	26	taC/taG	2/13	1	2	FACETS	0.879	0.765	1	0.879	0.765	1	CLONAL	1	TRUE	1	0.322998847212461	2		512	465	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	217	372	0				ENST00000310581	NM_198253.2	-/1132			0.264186107065	5	FACETS	1	0.975	1	1	0.975	1	CLONAL	4	TRUE	1	0.264186107065	5		372	534	SUCCESS
ATM	472	MSKCC	GRCh37	11	108225575	108225575	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	45	354	0	ENST00000278616.4:c.8824C>T	p.Gln2942Ter	p.Q2942*	ENST00000278616	NM_000051.3	2942	Cag/Tag	61/63	0.249855878574674	2	FACETS	1	0.945	1	0.638	0.54	0.745	CLONAL	1	TRUE	0	0.264186107065	2		354	267	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875055	151875055	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	41	196	0	ENST00000262189.6:c.7483C>T	p.Gln2495Ter	p.Q2495*	ENST00000262189	NM_170606.2	2495	Caa/Taa	38/59	0.264186107065	3	FACETS	1	0.939	1	0.639	0.535	0.753	CLONAL	1	TRUE	1	0.264186107065	3		196	275	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312408	91312408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	43	296	0	ENST00000355112.3:c.2353G>A	p.Glu785Lys	p.E785K	ENST00000355112	NM_000057.2	785	Gag/Aag	11/22	0.249855878574674	2	FACETS	1	0.876	1	0.525	0.441	0.617	CLONAL	1	TRUE	0	0.264186107065	2		296	310	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166279	118166279	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	58	353	0	ENST00000369448.3:c.789C>G	p.Ile263Met	p.I263M	ENST00000369448	NM_017709.3	263	atC/atG	2/2	0.192393405806866	4	FACETS	1	0.891	1			1	CLONAL	1	TRUE	NA	0.264186107065	4		353	532	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466528	120466528	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	68	549	0	ENST00000256646.2:c.4591G>A	p.Gly1531Arg	p.G1531R	ENST00000256646	NM_024408.3	1531	Ggg/Agg	26/34	0.192393405806866	4	FACETS	0.749	0.65	0.856			1	SUBCLONAL	1	TRUE	NA	0.264186107065	4		549	869	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426715	49426715	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	79	298	0	ENST00000301067.7:c.11773C>T	p.Gln3925Ter	p.Q3925*	ENST00000301067	NM_003482.3	3925	Caa/Taa	39/54	0.224072050795619	4	FACETS	0.959	0.849	1	0.959	0.849	1	CLONAL	2	TRUE	2	0.264186107065	4		298	394	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911703	26911703	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0041700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	14	198	0	ENST00000381527.3:c.129-1G>A		p.X43_splice	ENST00000381527	NM_001260.1	43			1	2	FACETS	0.716	0.52	0.95	0.716	0.52	0.95	CLONAL	1	TRUE	1	0.264186107065	2		198	148	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256925	41256925	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	72	481	2	ENST00000357654.3:c.261del	p.Ile89SerfsTer30	p.I89Sfs*30	ENST00000357654	NM_007294.3	87	ttG/tt	5/23	0.185860848149107	4	FACETS	0.815	0.715	0.921	0.815	0.715	0.921	CLONAL	2	TRUE	2	0.264186107065	4		483	423	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276837	15276837	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	92	720	0	ENST00000263388.2:c.5428G>C	p.Glu1810Gln	p.E1810Q	ENST00000263388	NM_000435.2	1810	Gag/Cag	30/33	1	2	FACETS	0.735	0.652	0.825	0.735	0.652	0.825	SUBCLONAL	1	TRUE	1	0.264186107065	2		720	947	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698192	47698192	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1236208777	NA	P-0041700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	13	228	0	ENST00000233146.2:c.1750A>G	p.Ile584Val	p.I584V	ENST00000233146	NM_000251.2	584	Att/Gtt	11/16	0.197249920950648	3	FACETS	0.533	0.38	0.719	0.178	0.126	0.24	SUBCLONAL	1	TRUE	0	0.264186107065	3		228	209	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719442	190719442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	25	241	1	ENST00000441310.2:c.1444G>A	p.Glu482Lys	p.E482K	ENST00000441310	NM_000534.4	482	Gag/Aag	9/13	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.264186107065	2		242	147	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143029249	143029249	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1389881866	NA	P-0041700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	49	185	0	ENST00000262992.4:c.2371G>A	p.Asp791Asn	p.D791N	ENST00000262992	NM_001101669.1	791	Gat/Aat	21/24	0.197249920950648	3	FACETS	1	0.94	1	0.786	0.677	0.903	CLONAL	2	TRUE	0	0.264186107065	3		185	178	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922749	44922749	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0041700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	98	204	0	ENST00000377967.4:c.1610C>G	p.Ser537Ter	p.S537*	ENST00000377967	NM_021140.2	537	tCa/tGa	16/29	0.108847754095591	2	FACETS	1	0.952	1			1	INDETERMINATE	2	TRUE	NA	0.264186107065	2		204	339	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039901	47039901	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0041700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	222	358	0	ENST00000377604.3:c.1244C>A	p.Ser415Ter	p.S415*	ENST00000377604	NM_001204468.1	415	tCa/tAa	12/24	0.108847754095591	2	FACETS	0.985	0.924	1			1	INDETERMINATE	3	TRUE	NA	0.264186107065	2		358	569	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210315	123210315	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0041700-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	28	168	0	ENST00000218089.9:c.2667T>A	p.Tyr889Ter	p.Y889*	ENST00000218089	NM_001042749.1	889	taT/taA	26/35	0.264186107065	2	FACETS	1	0.899	1			1	CLONAL	2	TRUE	NA	0.264186107065	2		168	92	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188215	10188215	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs869025642	NA	P-0041707-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	76	326	0	ENST00000256474.2:c.358A>G	p.Arg120Gly	p.R120G	ENST00000256474	NM_000551.3	120	Aga/Gga	2/3	0.502460309552695	1	FACETS	0.961	0.859	1	0.961	0.859	1	CLONAL	1	FALSE	0	0.541376470356169	1		326	213	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578529	7578529	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs780442292	NA	P-0041714-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	547	771	0	ENST00000269305.4:c.401T>G	p.Phe134Cys	p.F134C	ENST00000269305	NM_001126112.2	134	tTt/tGt	5/11	0.599410097044103	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.599410097044103	2		771	825	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345058	73345058	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041714-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	110	261	0	ENST00000377767.4:c.1739G>T	p.Ser580Ile	p.S580I	ENST00000377767	NM_014953.3	580	aGt/aTt	13/21	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.599410097044103	2		261	363	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696430	47696430	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519970	NA	P-0041714-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	271	481	0	ENST00000347630.2:c.393G>T	p.Trp131Cys	p.W131C	ENST00000347630	NM_001007230.1	131	tgG/tgT	6/11	0.599410097044103	2	FACETS	0.95	0.905	0.995	0.95	0.905	0.995	CLONAL	2	TRUE	0	0.599410097044103	2		481	476	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243966	53243966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041714-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	161	335	1	ENST00000375401.3:c.1027G>A	p.Asp343Asn	p.D343N	ENST00000375401	NM_004187.3	343	Gat/Aat	8/26	0.599410097044103	4	FACETS	0.841	0.77	0.914			1	CLONAL	1	TRUE	NA	0.599410097044103	4		336	1022	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002855	69002855	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041714-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1274	82	315	0	ENST00000288368.4:c.2155A>C	p.Ile719Leu	p.I719L	ENST00000288368	NM_024870.2	719	Att/Ctt	20/40	0.599410097044103	11	FACETS	0.746	0.655	0.844			1	SUBCLONAL	1	TRUE	NA	0.599410097044103	11		315	1356	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247149	53247149	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0041714-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	73	154	0	ENST00000375401.3:c.352-1G>C		p.X118_splice	ENST00000375401	NM_004187.3	118			0.599410097044103	4	FACETS	0.822	0.721	0.93			1	CLONAL	1	TRUE	NA	0.599410097044103	4		154	474	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0041716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	20	290	2	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.842	1	1	0.842	1	CLONAL	1	TRUE	1	0.75465550774222	2		292	50	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874459	151874461	+	stop_gained	Nonsense_Mutation	TNP	GTC	GTC	TTA	novel	NA	P-0041716-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	15	466	0	ENST00000262189.6:c.8077_8079delinsTAA	p.Asp2693Ter	p.D2693*	ENST00000262189	NM_170606.2	2693	GAC/TAA	38/59	0.331918859738349	5	FACETS	1	0.777	1	0.349	0.26	0.451	INDETERMINATE	1	TRUE	2	0.75465550774222	5		466	81	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0041731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	24	381	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.87	0.688	1	0.87	0.688	1	CLONAL	1	TRUE	1	0.313365097445376	2		381	176	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0041731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	9	209	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.432	0.287	0.615	0.432	0.287	0.615	SUBCLONAL	1	TRUE	1	0.313365097445376	2		209	133	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0041731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	49	376	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.678	0.575	0.792	0.678	0.575	0.792	SUBCLONAL	1	TRUE	1	0.313365097445376	2		377	461	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920449	114920449	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	41	523	0	ENST00000543371.1:c.1390A>G	p.Arg464Gly	p.R464G	ENST00000543371	NM_001198531.1	464	Agg/Ggg	13/14	1	2	FACETS	0.673	0.561	0.796	0.673	0.561	0.796	SUBCLONAL	1	TRUE	1	0.313365097445376	2		523	389	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729962	30729962	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs104893819	NA	P-0041731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	68	480	1	ENST00000295754.5:c.1483C>T	p.Arg495Ter	p.R495*	ENST00000295754	NM_003242.5	495	Cga/Tga	6/7	1	2	FACETS	0.612	0.532	0.699	0.612	0.532	0.699	SUBCLONAL	1	TRUE	1	0.313365097445376	2		481	709	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489571	56489571	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	32	547	0	ENST00000267101.3:c.2036G>A	p.Arg679Gln	p.R679Q	ENST00000267101	NM_001982.3	679	cGa/cAa	17/28	1	2	FACETS	0.497	0.403	0.603	0.497	0.403	0.603	SUBCLONAL	1	TRUE	1	0.313365097445376	2		547	411	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780921	9780921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1297091785	NA	P-0041731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1228	118	782	1	ENST00000377346.4:c.1643G>A	p.Arg548Gln	p.R548Q	ENST00000377346	NM_005026.3	548	cGg/cAg	13/24	1	2	FACETS	0.56	0.503	0.62	0.56	0.503	0.62	SUBCLONAL	1	TRUE	1	0.313365097445376	2		783	1346	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188271	142188271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202193482	NA	P-0041731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	20	314	0	ENST00000350721.4:c.6460G>A	p.Asp2154Asn	p.D2154N	ENST00000350721	NM_001184.3	2154	Gat/Aat	38/47	1	2	FACETS	0.845	0.652	1	0.845	0.652	1	CLONAL	1	TRUE	1	0.313365097445376	2		314	151	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518013	176518013	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139464025	NA	P-0041731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1266	178	680	0	ENST00000292408.4:c.511C>T	p.Arg171Cys	p.R171C	ENST00000292408	NM_213647.1	171	Cgc/Tgc	5/18	1	2	FACETS	0.787	0.723	0.854	0.787	0.723	0.854	SUBCLONAL	1	TRUE	1	0.313365097445376	2		680	1444	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031926	26031926	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	34	355	0	ENST00000244661.2:c.363G>C	p.Met121Ile	p.M121I	ENST00000244661	NM_003537.3	121	atG/atC	1/1	1	2	FACETS	0.555	0.454	0.669	0.555	0.454	0.669	SUBCLONAL	1	TRUE	1	0.313365097445376	2		355	391	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32191690	32191691	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAA	novel	NA	P-0041731-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	85	722	1	ENST00000375023.3:c.15_16insTTG	p.Leu16dup	p.L16dup	ENST00000375023	NM_004557.3	16	-/TTG	1/30	1	2	FACETS	0.412	0.362	0.465	0.412	0.362	0.465	SUBCLONAL	1	TRUE	1	0.313365097445376	2		723	1317	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646914	37646914	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041868-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	101	663	0	ENST00000447079.4:c.2036A>G	p.Asp679Gly	p.D679G	ENST00000447079	NM_015083.1	679	gAt/gGt	3/14	1	2	FACETS	0.904	0.808	1	0.904	0.808	1	CLONAL	1	FALSE	1	0.3	2		663	745	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	109	663	4	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.393226004329197	2		667	519	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151290	202151290	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	75	323	0	ENST00000358485.4:c.1596del	p.Lys532AsnfsTer73	p.K532Nfs*73	ENST00000358485	NM_001080125.1	530	agA/ag	9/9	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.393226004329197	2		323	378	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323363	31323363	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	84	455	1	ENST00000412585.2:c.626del	p.Pro209GlnfsTer5	p.P209Qfs*5	ENST00000412585	NM_005514.6	209	cCa/ca	4/8	1	2	FACETS	0.975	0.866	1	0.975	0.866	1	CLONAL	1	TRUE	1	0.393226004329197	2		456	438	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	28	600	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	0.393226004329197	3	FACETS	0.281	0.224	0.347	0.141	0.112	0.174	SUBCLONAL	1	TRUE	1	0.393226004329197	3		600	606	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	88	433	5	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.393226004329197	2		438	441	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	84	540	2	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	0.907	0.804	1	0.907	0.804	1	CLONAL	1	TRUE	1	0.393226004329197	2		542	471	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874149	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	50	404	1	ENST00000262189.6:c.8389_8390del	p.Lys2797GlyfsTer11	p.K2797Gfs*11	ENST00000262189	NM_170606.2	2797	AAg/g	38/59	1	2	FACETS	0.695	0.592	0.807	0.695	0.592	0.807	SUBCLONAL	1	TRUE	1	0.393226004329197	2		405	366	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620657	52620657	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	87	350	0	ENST00000394830.3:c.3096del	p.Phe1032LeufsTer102	p.F1032Lfs*102	ENST00000394830	NM_018313.4	1032	ttT/tt	21/30	0.393226004329197	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.393226004329197	1		350	332	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	80	376	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.938	0.829	1	0.938	0.829	1	CLONAL	1	TRUE	1	0.393226004329197	2		377	434	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850705	63850705	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs201178069	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	56	320	0	ENST00000279873.7:c.1489del	p.Ile497Ter	p.I497*	ENST00000279873	NM_032199.2	495	Aaa/aa	10/10	1	2	FACETS	0.919	0.792	1	0.919	0.792	1	CLONAL	1	TRUE	1	0.393226004329197	2		320	310	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779211	3779211	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783507	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	51	429	2	ENST00000262367.5:c.5837del	p.Pro1946HisfsTer30	p.P1946Hfs*30	ENST00000262367	NM_004380.2	1946	cCa/ca	31/31	1	2	FACETS	0.975	0.836	1	0.975	0.836	1	CLONAL	1	TRUE	1	0.393226004329197	2		431	266	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	78	261	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.393226004329197	2		261	316	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578215	28578216	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	70	415	0	ENST00000241453.7:c.2955_2956del	p.Pro986AlafsTer27	p.P986Afs*27	ENST00000241453	NM_004119.2	985	tcTCcg/tccg	24/24	1	2	FACETS	0.651	0.568	0.74	0.651	0.568	0.74	SUBCLONAL	1	TRUE	1	0.393226004329197	2		415	547	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641389	18641389	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1229278001	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	40	189	1	ENST00000266497.5:c.2393del	p.Asn798MetfsTer16	p.N798Mfs*16	ENST00000266497		796	ctA/ct	17/31	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.393226004329197	2		190	166	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101300	27101300	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	41	625	0	ENST00000324856.7:c.4582C>T	p.Arg1528Ter	p.R1528*	ENST00000324856	NM_006015.4	1528	Cga/Tga	18/20	1	2	FACETS	0.392	0.326	0.465	0.392	0.326	0.465	SUBCLONAL	1	TRUE	1	0.393226004329197	2		625	532	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851558	134851558	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs770155473	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	34	337	0	ENST00000398015.3:c.964G>A	p.Val322Ile	p.V322I	ENST00000398015	NM_004441.4	322	Gtc/Atc	5/16	1	2	FACETS	0.567	0.465	0.681	0.567	0.465	0.681	SUBCLONAL	1	TRUE	1	0.393226004329197	2		337	305	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244454	46244454	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs751704736	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	20	419	0	ENST00000334344.6:c.2552del	p.Pro851HisfsTer4	p.P851Hfs*4	ENST00000334344	NM_152641.2	850	Ccc/cc	15/21	1	2	FACETS	0.269	0.205	0.344	0.269	0.205	0.344	SUBCLONAL	1	TRUE	1	0.393226004329197	2		419	378	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	121	682	0	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.393226004329197	2		682	604	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	40	250	1	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	0.896	0.751	1	0.896	0.751	1	CLONAL	1	TRUE	1	0.393226004329197	2		251	227	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	122	683	4	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	1	2	FACETS	0.932	0.844	1	0.932	0.844	1	CLONAL	1	TRUE	1	0.393226004329197	2		687	666	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351359	89351359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756332789	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	144	805	1	ENST00000301030.4:c.1591G>A	p.Ala531Thr	p.A531T	ENST00000301030	NM_001256183.1	531	Gcc/Acc	9/13	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.393226004329197	2		806	673	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724244	52724244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	103	386	0	ENST00000322088.6:c.1376G>A	p.Arg459His	p.R459H	ENST00000322088	NM_014225.5	459	cGc/cAc	12/15	0.393226004329197	3	FACETS	1	0.972	1	0.618	0.555	0.684	CLONAL	1	TRUE	1	0.393226004329197	3		386	507	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	360055	360055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	75	598	0	ENST00000262320.3:c.1034del	p.Pro345HisfsTer69	p.P345Hfs*69	ENST00000262320	NM_003502.3	345	cCa/ca	4/11	1	2	FACETS	0.857	0.754	0.967	0.857	0.754	0.967	CLONAL	1	TRUE	1	0.393226004329197	2		598	445	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562748	21562748	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1225626637	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	45	180	0	ENST00000382592.4:c.1171C>T	p.Arg391Cys	p.R391C	ENST00000382592	NM_014572.2	391	Cgc/Tgc	4/8	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.393226004329197	2		180	194	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914741	39914741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757308049	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	74	394	1	ENST00000378444.4:c.4621G>A	p.Asp1541Asn	p.D1541N	ENST00000378444	NM_001123385.1	1541	Gat/Aat	12/15	1	2	FACETS	0.936	0.824	1	0.936	0.824	1	CLONAL	1	TRUE	1	0.393226004329197	2		395	402	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310207	91310208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs747341586	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	53	231	0	ENST00000355112.3:c.2268dup	p.Asp757ArgfsTer18	p.D757Rfs*18	ENST00000355112	NM_000057.2	754	tca/tcAa	10/22	1	2	FACETS	0.963	0.827	1	0.963	0.827	1	CLONAL	1	TRUE	1	0.393226004329197	2		231	280	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702581	52702581	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	82	309	0	ENST00000394830.3:c.317A>G	p.Tyr106Cys	p.Y106C	ENST00000394830	NM_018313.4	106	tAt/tGt	4/30	0.393226004329197	1	FACETS	0.926	0.822	1	0.926	0.822	1	CLONAL	1	TRUE	0	0.393226004329197	1		309	362	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910368	29910368	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	91	595	0	ENST00000376809.5:c.38T>G	p.Leu13Arg	p.L13R	ENST00000376809	NM_002116.7	13	cTc/cGc	1/8	1	2	FACETS	0.933	0.832	1	0.933	0.832	1	CLONAL	1	TRUE	1	0.393226004329197	2		595	496	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185545	27185545	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1564083506	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	133	574	1	ENST00000380036.4:c.1250del	p.Pro417LeufsTer10	p.P417Lfs*10	ENST00000380036	NM_000459.3	415	ctC/ct	9/23	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.393226004329197	2		575	623	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023982	31023983	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1569336425	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	24	522	0	ENST00000375687.4:c.3473dup	p.Asn1158LysfsTer6	p.N1158Kfs*6	ENST00000375687	NM_015338.5	1156	gga/ggAa	13/13	1	2	FACETS	0.265	0.207	0.333	0.265	0.207	0.333	SUBCLONAL	1	TRUE	1	0.393226004329197	2		522	460	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528375	157528375	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs869312697	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	113	662	0	ENST00000346085.5:c.6100C>T	p.Gln2034Ter	p.Q2034*	ENST00000346085	NM_020732.3	2034	Cag/Tag	20/20	1	2	FACETS	0.936	0.844	1	0.936	0.844	1	CLONAL	1	TRUE	1	0.393226004329197	2		662	614	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993509	72993509	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	89	658	0	ENST00000268489.5:c.536del	p.Gly179AlafsTer22	p.G179Afs*22	ENST00000268489	NM_006885.3	179	gGc/gc	2/10	1	2	FACETS	0.849	0.755	0.949	0.849	0.755	0.949	CLONAL	1	TRUE	1	0.393226004329197	2		658	533	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727403	66727441	+	inframe_deletion	In_Frame_Del	DEL	TAGAGCTTGATGAGCAGCAGCGAAAGCGCCTTGAGGCCT	TAGAGCTTGATGAGCAGCAGCGAAAGCGCCTTGAGGCCT	-	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	71	382	0	ENST00000307102.5:c.120_158del	p.Glu41_Phe53del	p.E41_F53del	ENST00000307102	NM_002755.3	40	cTAGAGCTTGATGAGCAGCAGCGAAAGCGCCTTGAGGCCTtt/ctt	2/11	1	2	FACETS	0.979	0.859	1	0.979	0.859	1	CLONAL	1	TRUE	1	0.393226004329197	2		382	369	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022593	31022593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	81	551	0	ENST00000375687.4:c.2078G>A	p.Arg693Gln	p.R693Q	ENST00000375687	NM_015338.5	693	cGa/cAa	13/13	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.393226004329197	2		551	410	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323315	31323315	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	24	373	0	ENST00000412585.2:c.674T>C	p.Leu225Pro	p.L225P	ENST00000412585	NM_005514.6	225	cTg/cCg	4/8	1	2	FACETS	0.412	0.324	0.515	0.412	0.324	0.515	SUBCLONAL	1	TRUE	1	0.393226004329197	2		373	296	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495375	56495377	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs780883720	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	70	544	0	ENST00000267101.3:c.3573_3575del	p.Glu1191del	p.E1191del	ENST00000267101	NM_001982.3	1189	GAA/-	28/28	1	2	FACETS	0.704	0.615	0.799	0.704	0.615	0.799	SUBCLONAL	1	TRUE	1	0.393226004329197	2		544	506	SUCCESS
AR	367	MSKCC	GRCh37	X	66765127	66765127	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	31	502	0	ENST00000374690.3:c.139G>A	p.Ala47Thr	p.A47T	ENST00000374690	NM_000044.3	47	Gca/Aca	1/8	1	2	FACETS	0.416	0.336	0.506	0.416	0.336	0.506	SUBCLONAL	1	TRUE	1	0.393226004329197	2		502	379	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817415	39817415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148089492	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	72	478	1	ENST00000288319.7:c.148C>T	p.Arg50Cys	p.R50C	ENST00000288319	NM_182918.3	50	Cgc/Tgc	2/10	1	2	FACETS	0.937	0.823	1	0.937	0.823	1	CLONAL	1	TRUE	1	0.393226004329197	2		479	391	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704481	117704481	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs36029166	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	46	235	1	ENST00000368508.3:c.2495del	p.Lys832ArgfsTer2	p.K832Rfs*2	ENST00000368508	NM_002944.2	832	aAg/ag	16/43	1	2	FACETS	0.947	0.804	1	0.947	0.804	1	CLONAL	1	TRUE	1	0.393226004329197	2		236	247	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969982	161969983	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs745647746	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	47	620	0	ENST00000366898.1:c.986dup	p.Val330ArgfsTer17	p.V330Rfs*17	ENST00000366898	NM_004562.2	329	ggc/ggGc	9/12	1	2	FACETS	0.494	0.417	0.579	0.494	0.417	0.579	SUBCLONAL	1	TRUE	1	0.393226004329197	2		620	484	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47079250	47079250	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	24	406	0	ENST00000409792.3:c.7256C>A	p.Pro2419His	p.P2419H	ENST00000409792	NM_014159.6	2419	cCt/cAt	18/21	0.393226004329197	1	FACETS	0.266	0.208	0.332	0.266	0.208	0.332	SUBCLONAL	1	TRUE	0	0.393226004329197	1		406	369	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393304	393304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	21	429	1	ENST00000380956.4:c.152G>A	p.Arg51His	p.R51H	ENST00000380956	NM_001195286.1	51	cGc/cAc	2/9	1	2	FACETS	0.263	0.202	0.335	0.263	0.202	0.335	SUBCLONAL	1	TRUE	1	0.393226004329197	2		430	406	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363406	40363406	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	39	600	1	ENST00000397332.2:c.823del	p.Glu275LysfsTer11	p.E275Kfs*11	ENST00000397332	NM_001033082.2	275	Gaa/aa	3/3	1	2	FACETS	0.387	0.321	0.462	0.387	0.321	0.462	SUBCLONAL	1	TRUE	1	0.393226004329197	2		601	512	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247872	59247872	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	176	785	0	ENST00000371222.2:c.871A>T	p.Asn291Tyr	p.N291Y	ENST00000371222	NM_002228.3	291	Aac/Tac	1/1	1	2	FACETS	0.963	0.887	1	0.963	0.887	1	CLONAL	1	TRUE	1	0.393226004329197	2		785	930	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459193	120459193	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs192122939	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	74	493	0	ENST00000256646.2:c.6152G>A	p.Arg2051Gln	p.R2051Q	ENST00000256646	NM_024408.3	2051	cGg/cAg	34/34	1	2	FACETS	0.813	0.714	0.919	0.813	0.714	0.919	CLONAL	1	TRUE	1	0.393226004329197	2		493	463	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564883	226564883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1387294607	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	88	416	0	ENST00000366794.5:c.1867G>A	p.Gly623Arg	p.G623R	ENST00000366794	NM_001618.3	623	Ggg/Agg	13/23	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.393226004329197	2		416	427	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333282	70333282	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	89	583	0	ENST00000373644.4:c.1187C>A	p.Pro396Gln	p.P396Q	ENST00000373644	NM_030625.2	396	cCa/cAa	2/12	1	2	FACETS	0.826	0.734	0.924	0.826	0.734	0.924	CLONAL	1	TRUE	1	0.393226004329197	2		583	548	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720658	89720659	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	57	220	0	ENST00000371953.3:c.810_811del	p.Met270IlefsTer27	p.M270Ifs*27	ENST00000371953	NM_000314.4	270	aTG/a	8/9	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.393226004329197	2		220	278	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115111969	115111969	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	31	618	1	ENST00000257566.3:c.1770+1G>T		p.X590_splice	ENST00000257566	NM_016569.3	590			1	2	FACETS	0.369	0.298	0.45	0.369	0.298	0.45	SUBCLONAL	1	TRUE	1	0.393226004329197	2		619	427	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120796850	120796850	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424495218	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	103	715	0	ENST00000257552.2:c.409G>A	p.Asp137Asn	p.D137N	ENST00000257552	NM_002442.3	137	Gac/Aac	7/15	1	2	FACETS	0.844	0.756	0.936	0.844	0.756	0.936	CLONAL	1	TRUE	1	0.393226004329197	2		715	621	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250170	133250170	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	30	470	0	ENST00000320574.5:c.1350G>T	p.Glu450Asp	p.E450D	ENST00000320574	NM_006231.2	450	gaG/gaT	13/49	1	2	FACETS	0.41	0.33	0.501	0.41	0.33	0.501	SUBCLONAL	1	TRUE	1	0.393226004329197	2		470	372	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988459	36988459	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	21	377	0	ENST00000354822.5:c.194G>T	p.Gly65Val	p.G65V	ENST00000354822	NM_001079668.2	65	gGg/gTg	2/3	1	2	FACETS	0.332	0.255	0.421	0.332	0.255	0.421	SUBCLONAL	1	TRUE	1	0.393226004329197	2		377	322	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68292200	68292200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1344776272	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	64	288	0	ENST00000487270.1:c.104C>T	p.Pro35Leu	p.P35L	ENST00000487270	NM_133509.3	35	cCa/cTa	3/11	1	2	FACETS	0.957	0.834	1	0.957	0.834	1	CLONAL	1	TRUE	1	0.393226004329197	2		288	340	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68878183	68878183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	56	332	0	ENST00000487270.1:c.896C>T	p.Thr299Ile	p.T299I	ENST00000487270	NM_133509.3	299	aCc/aTc	9/11	1	2	FACETS	0.772	0.664	0.889	0.772	0.664	0.889	SUBCLONAL	1	TRUE	1	0.393226004329197	2		332	369	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712798	43712799	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	115	709	0	ENST00000382044.4:c.4385dup	p.Leu1462PhefsTer4	p.L1462Ffs*4	ENST00000382044	NM_001141980.1	1462	ttg/ttTg	21/28	1	2	FACETS	0.945	0.853	1	0.945	0.853	1	CLONAL	1	TRUE	1	0.393226004329197	2		709	619	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11172464	11172464	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867536416	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	43	633	0	ENST00000358026.2:c.5012G>A	p.Arg1671His	p.R1671H	ENST00000358026	NM_001128849.1	1671	cGc/cAc	36/36	1	2	FACETS	0.371	0.31	0.439	0.371	0.31	0.439	SUBCLONAL	1	TRUE	1	0.393226004329197	2		633	589	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229429	36229429	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1356978354	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	77	463	3	ENST00000222270.7:c.8119G>A	p.Ala2707Thr	p.A2707T	ENST00000222270	NM_014727.1	2707	Gcc/Acc	37/37	0.393226004329197	3	FACETS	0.954	0.84	1	0.477	0.42	0.538	CLONAL	1	TRUE	1	0.393226004329197	3		466	491	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753231	42753231	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	118	787	0	ENST00000222329.4:c.1033C>A	p.Pro345Thr	p.P345T	ENST00000222329	NM_006494.2	345	Cct/Act	4/4	0.393226004329197	3	FACETS	0.874	0.788	0.964	0.437	0.394	0.482	CLONAL	1	TRUE	1	0.393226004329197	3		787	822	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799172	42799172	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	86	732	0	ENST00000575354.2:c.4656C>A	p.Ser1552Arg	p.S1552R	ENST00000575354	NM_015125.3	1552	agC/agA	20/20	0.393226004329197	3	FACETS	0.819	0.725	0.92	0.41	0.362	0.46	CLONAL	1	TRUE	1	0.393226004329197	3		732	639	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919765	50919765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371628260	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	87	639	0	ENST00000440232.2:c.2933G>A	p.Arg978His	p.R978H	ENST00000440232	NM_002691.3	978	cGt/cAt	23/27	0.393226004329197	3	FACETS	0.921	0.817	1	0.46	0.408	0.516	CLONAL	1	TRUE	1	0.393226004329197	3		639	575	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143237	30143237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1331610896	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	97	341	0	ENST00000389048.3:c.289C>T	p.Pro97Ser	p.P97S	ENST00000389048	NM_004304.4	97	Ccg/Tcg	1/29	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.393226004329197	2		341	373	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215633979	215633979	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	83	290	0	ENST00000260947.4:c.1372G>T	p.Asp458Tyr	p.D458Y	ENST00000260947	NM_000465.2	458	Gac/Tac	5/11	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.393226004329197	2		290	400	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39729866	39729868	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	75	354	1	ENST00000361337.2:c.1188_1190del	p.Pro397del	p.P397del	ENST00000361337	NM_003286.2	394	tCTCct/tct	13/21	1	2	FACETS	0.9	0.792	1	0.9	0.792	1	CLONAL	1	TRUE	1	0.393226004329197	2		355	424	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39774491	39774491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	28	416	0	ENST00000288319.7:c.661G>A	p.Ala221Thr	p.A221T	ENST00000288319	NM_182918.3	221	Gct/Act	5/10	1	2	FACETS	0.28	0.223	0.345	0.28	0.223	0.345	SUBCLONAL	1	TRUE	1	0.393226004329197	2		416	509	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884873	134884873	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	82	480	0	ENST00000398015.3:c.1649T>C	p.Val550Ala	p.V550A	ENST00000398015	NM_004441.4	550	gTc/gCc	8/16	1	2	FACETS	0.782	0.691	0.88	0.782	0.691	0.88	SUBCLONAL	1	TRUE	1	0.393226004329197	2		480	533	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955237	1955237	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	90	392	1	ENST00000382891.5:c.2324C>A	p.Pro775Gln	p.P775Q	ENST00000382891	NM_133335.3	775	cCa/cAa	12/22	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.393226004329197	2		393	401	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067034	143067034	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	56	348	0	ENST00000262992.4:c.1679A>G	p.Lys560Arg	p.K560R	ENST00000262992	NM_001101669.1	560	aAg/aGg	16/24	1	2	FACETS	0.885	0.762	1	0.885	0.762	1	CLONAL	1	TRUE	1	0.393226004329197	2		348	322	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592088	67592088	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	52	247	0	ENST00000274335.5:c.1907del	p.Asn636ThrfsTer26	p.N636Tfs*26	ENST00000274335		635	gAa/ga	14/15	1	2	FACETS	0.876	0.75	1	0.876	0.75	1	CLONAL	1	TRUE	1	0.393226004329197	2		247	302	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673754	30673754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	94	531	0	ENST00000376406.3:c.3206C>T	p.Pro1069Leu	p.P1069L	ENST00000376406	NM_014641.2	1069	cCc/cTc	10/15	1	2	FACETS	0.964	0.861	1	0.964	0.861	1	CLONAL	1	TRUE	1	0.393226004329197	2		531	496	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199888	138199888	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766691413	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	50	400	0	ENST00000237289.4:c.1306G>A	p.Gly436Arg	p.G436R	ENST00000237289	NM_001270507.1	436	Ggg/Agg	7/9	1	2	FACETS	0.708	0.603	0.823	0.708	0.603	0.823	SUBCLONAL	1	TRUE	1	0.393226004329197	2		400	359	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945052	151945052	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs768618172	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	28	407	0	ENST00000262189.6:c.2467A>G	p.Ile823Val	p.I823V	ENST00000262189	NM_170606.2	823	Att/Gtt	14/59	1	2	FACETS	0.308	0.245	0.379	0.308	0.245	0.379	SUBCLONAL	1	TRUE	1	0.393226004329197	2		407	463	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994138	21994138	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	89	490	0	ENST00000579755.1:c.193G>T	p.Gly65Cys	p.G65C	ENST00000579755		65	Ggt/Tgt	1/3	1		FACETS		0.903	1				CLONAL	1	TRUE	1	0.393226004329197	2		490	446	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006027	22006027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371415045	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	128	554	0	ENST00000276925.6:c.376C>T	p.Arg126Cys	p.R126C	ENST00000276925	NM_004936.3	126	Cgc/Tgc	2/2	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.393226004329197	2		554	543	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006137	22006137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866457591	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	100	417	1	ENST00000276925.6:c.266G>A	p.Arg89Gln	p.R89Q	ENST00000276925	NM_004936.3	89	cGg/cAg	2/2	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.393226004329197	2		418	447	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904842	101904842	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041983-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	39	247	0	ENST00000374994.4:c.830G>A	p.Trp277Ter	p.W277*	ENST00000374994	NM_004612.2	277	tGg/tAg	5/9	1	2	FACETS	0.757	0.631	0.895	0.757	0.631	0.895	SUBCLONAL	1	TRUE	1	0.393226004329197	2		247	262	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	826	337	0				ENST00000310581	NM_198253.2	-/1132			0.834678295329708	5	FACETS	1	0.997	1	1	0.997	1	CLONAL	5	TRUE	0	0.834678295329708	5		337	866	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874147	151874148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs747256476	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	257	480	8	ENST00000262189.6:c.8390dup	p.Glu2798GlyfsTer11	p.E2798Gfs*11	ENST00000262189	NM_170606.2	2797	aag/aaAg	38/59	0.567379701656963	6	FACETS	1	0.983	1			1	CLONAL	2	TRUE	NA	0.834678295329708	6		488	734	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	217	539	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	0.834678295329708	3	FACETS	1	0.936	1	0.334	0.312	0.357	CLONAL	1	TRUE	0	0.834678295329708	3		544	735	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	1209	910	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	0.795110521773863	4	FACETS	1	0.998	1			1	CLONAL	3	TRUE	NA	0.834678295329708	4		910	1568	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225360671	225360671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	166	261	0	ENST00000264414.4:c.1720G>A	p.Glu574Lys	p.E574K	ENST00000264414	NM_003590.4	574	Gaa/Aaa	13/16	0.596079148625157	4	FACETS	0.914	0.851	0.979	0.914	0.851	0.979	CLONAL	2	TRUE	2	0.834678295329708	4		261	399	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236087	108236087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781894	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	321	500	0	ENST00000278616.4:c.9023G>A	p.Arg3008His	p.R3008H	ENST00000278616	NM_000051.3	3008	cGt/cAt	63/63	0.752705086850418	3	FACETS	0.922	0.881	0.964			1	CLONAL	2	TRUE	NA	0.834678295329708	3		500	591	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196830	123196830	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	298	212	0	ENST00000218089.9:c.1717C>T	p.Gln573Ter	p.Q573*	ENST00000218089	NM_001042749.1	573	Cag/Tag	18/35	0.752307510708532	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.834678295329708	2		212	316	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884028	37884028	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	612	807	0	ENST00000269571.5:c.3499C>G	p.Leu1167Val	p.L1167V	ENST00000269571		1167	Ctg/Gtg	27/27	0.834678295329708	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	1	0.834678295329708	3		807	959	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884834	111884834	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs181079548	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	221	433	2	ENST00000341259.2:c.923G>A	p.Arg308Gln	p.R308Q	ENST00000341259	NM_005475.2	308	cGa/cAa	4/8	0.675823226767339	4	FACETS	0.917	0.861	0.973	0.917	0.861	0.973	CLONAL	2	TRUE	2	0.834678295329708	4		435	530	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481609	56481609	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1256589883	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	502	656	0	ENST00000267101.3:c.644A>G	p.Asn215Ser	p.N215S	ENST00000267101	NM_001982.3	215	aAt/aGt	6/28	0.675823226767339	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.834678295329708	4		656	1056	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748660	43748661	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	127	789	0	ENST00000382044.4:c.2145dup	p.Glu716ArgfsTer9	p.E716Rfs*9	ENST00000382044	NM_001141980.1	715	-/A	12/28	0.834678295329708	3	FACETS	0.495	0.448	0.544	0.247	0.224	0.272	SUBCLONAL	1	TRUE	1	0.834678295329708	3		789	872	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106916	27106917	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	182	570	0	ENST00000324856.7:c.6532dup	p.Asp2178GlyfsTer47	p.D2178Gfs*47	ENST00000324856	NM_006015.4	2176	cag/caGg	20/20	0.675823226767339	4	FACETS	0.97	0.896	1	0.485	0.448	0.523	CLONAL	1	TRUE	2	0.834678295329708	4		570	825	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205808	128205808	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760183425	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	444	631	0	ENST00000341105.2:c.67G>A	p.Asp23Asn	p.D23N	ENST00000341105	NM_032638.4	23	Gac/Aac	2/6	0.834678295329708	5	FACETS	1	0.985	1	0.709	0.677	0.74	CLONAL	2	TRUE	2	0.834678295329708	5		631	1127	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918843	50918843	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759530743	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	714	891	1	ENST00000440232.2:c.2713G>A	p.Glu905Lys	p.E905K	ENST00000440232	NM_002691.3	905	Gag/Aag	21/27	0.834678295329708	6	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	3	0.834678295329708	6		892	1490	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022989	33022990	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	258	473	0	ENST00000300177.4:c.104dup	p.Pro36AlafsTer8	p.P36Afs*8	ENST00000300177	NM_001191322.1	33	atc/atCc	2/2	0.834678295329708	3	FACETS	0.892	0.847	0.938	0.892	0.847	0.938	CLONAL	2	TRUE	1	0.834678295329708	3		473	491	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096202	178096202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	231	438	0	ENST00000397062.3:c.1129G>A	p.Glu377Lys	p.E377K	ENST00000397062	NM_006164.4	377	Gaa/Aaa	5/5	0.834678295329708	3	FACETS	0.947	0.898	0.997	0.947	0.898	0.997	CLONAL	2	TRUE	1	0.834678295329708	3		438	414	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214078	108214078	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	103	303	0	ENST00000278616.4:c.8398C>T	p.Gln2800Ter	p.Q2800*	ENST00000278616	NM_000051.3	2800	Cag/Tag	57/63	0.752705086850418	3	FACETS	1	0.941	1			1	CLONAL	1	TRUE	NA	0.834678295329708	3		303	332	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268359	198268359	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	244	429	0	ENST00000335508.6:c.1669G>C	p.Asp557His	p.D557H	ENST00000335508	NM_012433.2	557	Gat/Cat	12/25	0.834678295329708	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.834678295329708	3		429	403	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204666	128204666	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768133841	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	514	773	0	ENST00000341105.2:c.775G>A	p.Asp259Asn	p.D259N	ENST00000341105	NM_032638.4	259	Gac/Aac	3/6	0.834678295329708	5	FACETS	1	0.974	1	0.681	0.653	0.709	CLONAL	2	TRUE	2	0.834678295329708	5		773	1358	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265573	198265573	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	152	709	0	ENST00000335508.6:c.2584G>A	p.Glu862Lys	p.E862K	ENST00000335508	NM_012433.2	862	Gaa/Aaa	18/25	0.834678295329708	3	FACETS	1	0.969	1	0.549	0.506	0.593	CLONAL	1	TRUE	1	0.834678295329708	3		709	470	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40854926	40854926	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	211	582	0	ENST00000428826.2:c.2152C>T	p.Gln718Ter	p.Q718*	ENST00000428826		718	Caa/Taa	20/21	0.834678295329708	3	FACETS	0.979	0.912	1	0.489	0.456	0.524	CLONAL	1	TRUE	1	0.834678295329708	3		582	732	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11269500	11269500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768134770	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	267	450	0	ENST00000361445.4:c.3670G>A	p.Asp1224Asn	p.D1224N	ENST00000361445	NM_004958.3	1224	Gat/Aat	25/58	0.675823226767339	4	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	2	0.834678295329708	4		450	581	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699531	117699531	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	113	341	0	ENST00000369458.3:c.110T>C	p.Ile37Thr	p.I37T	ENST00000369458	NM_024626.3	37	aTc/aCc	3/6	0.675823226767339	4	FACETS	0.948	0.857	1	0.474	0.428	0.522	CLONAL	1	TRUE	2	0.834678295329708	4		341	524	SUCCESS
RET	5979	MSKCC	GRCh37	10	43598005	43598005	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1048022444	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	58	867	0	ENST00000355710.3:c.553T>C	p.Phe185Leu	p.F185L	ENST00000355710	NM_020975.4	185	Ttc/Ctc	3/20	0.834678295329708	3	FACETS	0.201	0.172	0.234	0.101	0.086	0.117	SUBCLONAL	1	TRUE	1	0.834678295329708	3		867	978	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104386958	104386958	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	116	311	0	ENST00000369902.3:c.1323G>C	p.Glu441Asp	p.E441D	ENST00000369902	NM_016169.3	441	gaG/gaC	11/12	0.834678295329708	3	FACETS	0.968	0.88	1	0.484	0.44	0.53	CLONAL	1	TRUE	1	0.834678295329708	3		311	407	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719902	18719902	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	235	418	0	ENST00000266497.5:c.3799C>A	p.Leu1267Ile	p.L1267I	ENST00000266497		1267	Cta/Ata	27/31	0.675823226767339	4	FACETS	0.771	0.723	0.82	0.771	0.723	0.82	SUBCLONAL	2	TRUE	2	0.834678295329708	4		418	670	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425526	49425526	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs587783688	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	560	987	1	ENST00000301067.7:c.12962C>A	p.Ser4321Ter	p.S4321*	ENST00000301067	NM_003482.3	4321	tCa/tAa	39/54	0.675823226767339	4	FACETS	0.979	0.943	1	0.979	0.943	1	CLONAL	2	TRUE	2	0.834678295329708	4		988	1257	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432641	49432641	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1213240312	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	157	826	0	ENST00000301067.7:c.8498T>C	p.Met2833Thr	p.M2833T	ENST00000301067	NM_003482.3	2833	aTg/aCg	34/54	0.675823226767339	4	FACETS	0.521	0.476	0.569	0.261	0.238	0.285	SUBCLONAL	1	TRUE	2	0.834678295329708	4		826	1324	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431484	121431484	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	431	714	0	ENST00000257555.6:c.688G>C	p.Glu230Gln	p.E230Q	ENST00000257555		230	Gag/Cag	3/10	0.675823226767339	4	FACETS	0.963	0.921	1	0.963	0.921	1	CLONAL	2	TRUE	2	0.834678295329708	4		714	984	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061633	38061633	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	59	222	0	ENST00000250448.2:c.356A>G	p.Gln119Arg	p.Q119R	ENST00000250448	NM_004496.3	119	cAg/cGg	2/2	0.834678295329708	3	FACETS	0.842	0.733	0.957	0.281	0.244	0.32	CLONAL	1	TRUE	0	0.834678295329708	3		222	238	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221263	2221263	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	104	726	1	ENST00000326181.6:c.349-2A>G		p.X117_splice	ENST00000326181	NM_032271.2	117			0.834678295329708	3	FACETS	0.429	0.384	0.477	0.215	0.192	0.239	SUBCLONAL	1	TRUE	1	0.834678295329708	3		727	823	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639882	3639882	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	103	755	0	ENST00000294008.3:c.3757A>G	p.Thr1253Ala	p.T1253A	ENST00000294008	NM_032444.2	1253	Acc/Gcc	12/15	0.834678295329708	3	FACETS	0.442	0.395	0.492	0.221	0.197	0.246	SUBCLONAL	1	TRUE	1	0.834678295329708	3		755	791	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337235	89337235	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	233	617	0	ENST00000301030.4:c.7796A>C	p.Asp2599Ala	p.D2599A	ENST00000301030	NM_001256183.1	2599	gAc/gCc	12/13	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.834678295329708	2		617	542	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719761	190719761	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	157	262	0	ENST00000441310.2:c.1763A>G	p.Gln588Arg	p.Q588R	ENST00000441310	NM_000534.4	588	cAg/cGg	9/13	0.834678295329708	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	1	0.834678295329708	3		262	262	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30954199	30954199	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	96	326	0	ENST00000375687.4:c.70T>G	p.Tyr24Asp	p.Y24D	ENST00000375687	NM_015338.5	24	Tac/Gac	2/13	0.596079148625157	4	FACETS	0.955	0.855	1	0.477	0.427	0.53	CLONAL	1	TRUE	2	0.834678295329708	4		326	442	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205718	128205718	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	543	748	1	ENST00000341105.2:c.157G>T	p.Asp53Tyr	p.D53Y	ENST00000341105	NM_032638.4	53	Gac/Tac	2/6	0.834678295329708	5	FACETS	0.959	0.92	0.999	0.64	0.613	0.666	CLONAL	2	TRUE	2	0.834678295329708	5		749	1527	SUCCESS
APC	324	MSKCC	GRCh37	5	112116599	112116599	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	69	317	0	ENST00000257430.4:c.644A>C	p.Gln215Pro	p.Q215P	ENST00000257430	NM_000038.5	215	cAg/cCg	6/16	0.834678295329708	2	FACETS	0.844	0.749	0.942	0.422	0.374	0.471	CLONAL	1	TRUE	0	0.834678295329708	2		317	196	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680464	30680464	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	165	519	0	ENST00000376406.3:c.1255C>G	p.Leu419Val	p.L419V	ENST00000376406	NM_014641.2	419	Ctg/Gtg	5/15	0.834678295329708		FACETS		0.963	1				CLONAL	1	TRUE	1	0.834678295329708	3		519	525	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665288	117665288	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1286980491	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	53	369	0	ENST00000368508.3:c.4459T>C	p.Tyr1487His	p.Y1487H	ENST00000368508	NM_002944.2	1487	Tac/Cac	27/43	0.834678295329708	2	FACETS	0.508	0.437	0.584	0.254	0.218	0.292	SUBCLONAL	1	TRUE	0	0.834678295329708	2		369	250	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151896483	151896483	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	172	345	0	ENST00000262189.6:c.4154del	p.Asn1385IlefsTer15	p.N1385Ifs*15	ENST00000262189	NM_170606.2	1385	aAt/at	27/59	0.567379701656963	6	FACETS	1	0.973	1			1	CLONAL	2	TRUE	NA	0.834678295329708	6		345	500	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5077456	5077456	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	43	218	0	ENST00000381652.3:c.1868T>G	p.Ile623Ser	p.I623S	ENST00000381652	NM_004972.3	623	aTt/aGt	15/25	0.834678295329708	13	FACETS	0.79	0.659	0.936			1	CLONAL	1	TRUE	NA	0.834678295329708	13		218	729	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128305436	128305436	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	55	622	0	ENST00000265960.3:c.860A>G	p.His287Arg	p.H287R	ENST00000265960	NM_001006617.1	287	cAt/cGt	7/12	0.834678295329708	3	FACETS	0.299	0.255	0.347	0.1	0.085	0.116	SUBCLONAL	1	TRUE	0	0.834678295329708	3		622	625	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035198	6035198	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	CA	novel	NA	P-0042109-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	315	454	0	ENST00000265849.7:c.870delinsTG	p.Phe291ValfsTer8	p.F291Vfs*8	ENST00000265849	NM_000535.5	290	ttC/ttTG	8/15	0.834678295329708	2	FACETS	0.97	0.941	0.998	0.97	0.941	0.998	CLONAL	2	TRUE	0	0.834678295329708	2		454	389	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0042124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	277	522	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.248800869300191	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	1	0.34433271640897	4		522	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0042124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	110	702	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.352707456782499	3	FACETS	1	0.982	1	0.708	0.638	0.781	CLONAL	1	TRUE	1	0.34433271640897	3		702	529	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120823	115120838	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCAGGGCGCCCGGC	GGCCAGGGCGCCCGGC	-	novel	NA	P-0042124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	189	594	0	ENST00000257566.3:c.168_183del	p.Pro57SerfsTer26	p.P57Sfs*26	ENST00000257566	NM_016569.3	56	ctGCCGGGCGCCCTGGCC/ct	1/8	0.164167422755588	3	FACETS	1	0.979	1	1	0.979	1	INDETERMINATE	3	TRUE	0	0.34433271640897	3		594	389	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	25	422	1	ENST00000334344.6:c.940C>A	p.Arg314Ser	p.R314S	ENST00000334344	NM_152641.2	314	Cgt/Agt	8/21	0.34433271640897	5	FACETS	0.332	0.261	0.415	0.111	0.087	0.139	SUBCLONAL	1	TRUE	2	0.34433271640897	5		423	663	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0042150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	40	337	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.844	0.703	1	0.844	0.703	1	CLONAL	1	FALSE	1	0.24872153092774	2		337	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0042150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	76	562	0	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	1	2	FACETS	0.736	0.645	0.835	0.736	0.645	0.835	SUBCLONAL	1	FALSE	1	0.24872153092774	2		562	830	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0042150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	29	454	0	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	0.925	0.746	1	0.925	0.746	1	CLONAL	1	FALSE	1	0.24872153092774	2		454	252	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249510	153249510	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1157879635	NA	P-0042150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	18	662	0	ENST00000281708.4:c.1268G>T	p.Gly423Val	p.G423V	ENST00000281708	NM_033632.3	423	gGa/gTa	9/12	1	2	FACETS	0.3	0.225	0.39	0.3	0.225	0.39	SUBCLONAL	1	FALSE	1	0.24872153092774	2		662	482	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992138	72992138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764598603	NA	P-0042150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	57	746	1	ENST00000268489.5:c.1907C>T	p.Ser636Leu	p.S636L	ENST00000268489	NM_006885.3	636	tCg/tTg	2/10	0.20922324564501	2	FACETS	0.646	0.554	0.748	0.323	0.277	0.374	SUBCLONAL	1	FALSE	0	0.24872153092774	2		747	709	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076889	41076889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	86	732	0	ENST00000373198.4:c.1531G>A	p.Glu511Lys	p.E511K	ENST00000373198	NM_133170.3	511	Gag/Aag	9/32	0.173594828442681	3	FACETS	0.894	0.789	1	0.447	0.394	0.503	CLONAL	1	FALSE	1	0.24872153092774	3		732	870	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488226	56488226	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	54	664	1	ENST00000267101.3:c.1745G>A	p.Gly582Glu	p.G582E	ENST00000267101	NM_001982.3	582	gGg/gAg	15/28	0.173594828442681	3	FACETS	0.637	0.543	0.741	0.319	0.271	0.371	SUBCLONAL	1	FALSE	1	0.24872153092774	3		665	766	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050351	13050351	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	77	803	1	ENST00000316448.5:c.303G>T	p.Gln101His	p.Q101H	ENST00000316448	NM_004343.3	101	caG/caT	3/9	0.189775213385098	4	FACETS	0.621	0.543	0.706	0.207	0.181	0.236	SUBCLONAL	1	FALSE	1	0.24872153092774	4		804	1245	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188187	108188187	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	42	456	0	ENST00000278616.4:c.6286G>C	p.Glu2096Gln	p.E2096Q	ENST00000278616	NM_000051.3	2096	Gaa/Caa	43/63	1	2	FACETS	0.808	0.675	0.955	0.808	0.675	0.955	CLONAL	1	FALSE	1	0.24872153092774	2		456	418	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40747876	40747876	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	82	901	0	ENST00000392038.2:c.542A>C	p.Lys181Thr	p.K181T	ENST00000392038	NM_001626.4	181	aAg/aCg	6/14	1	2	FACETS	0.808	0.712	0.912	0.808	0.712	0.912	CLONAL	1	FALSE	1	0.24872153092774	2		901	816	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31939858	31939858	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042150-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	70	826	0	ENST00000375333.2:c.85A>C	p.Ser29Arg	p.S29R	ENST00000375333	NM_032454.1	29	Agc/Cgc	1/8	0.0858465399251529	3	FACETS	0.693	0.603	0.791	0.347	0.301	0.396	INDETERMINATE	1	FALSE	1	0.24872153092774	3		826	913	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712017	89712017	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0042153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	253	273	0	ENST00000371953.3:c.634+1G>A		p.X212_splice	ENST00000371953	NM_000314.4	212			0.523487752864607	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.872314248836466	1		273	297	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683138	88683138	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	541	542	0	ENST00000372037.3:c.1348G>T	p.Val450Leu	p.V450L	ENST00000372037	NM_004329.2	450	Gtg/Ttg	12/13	0.523487752864607	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.872314248836466	1		542	650	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207024	1207024	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1060499954	NA	P-0042153-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	90	712	0	ENST00000326873.7:c.112C>G	p.Pro38Ala	p.P38A	ENST00000326873	NM_000455.4	38	Ccg/Gcg	1/10	1	2	FACETS	0.175	0.154	0.197	0.175	0.154	0.197	SUBCLONAL	1	TRUE	1	0.872314248836466	2		712	1182	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024001	27024002	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0042198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	16	106	0	ENST00000324856.7:c.1113dup	p.Gln372AlafsTer28	p.Q372Afs*28	ENST00000324856	NM_006015.4	369	-/G	1/20	1	2	FACETS	0.769	0.57	1	0.769	0.57	1	CLONAL	1	TRUE	1	0.23	2		106	181	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183787	10183787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123481	NA	P-0042198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	101	871	0	ENST00000256474.2:c.256C>T	p.Pro86Ser	p.P86S	ENST00000256474	NM_000551.3	86	Ccc/Tcc	1/3	1	2	FACETS	0.831	0.741	0.927	0.831	0.741	0.927	CLONAL	1	TRUE	1	0.23	2		871	1057	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142950	47142950	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042198-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	39	469	0	ENST00000409792.3:c.5013del	p.Tyr1671Ter	p.Y1671*	ENST00000409792	NM_014159.6	1671	taT/ta	8/21	1	2	FACETS	0.535	0.442	0.639	0.535	0.442	0.639	SUBCLONAL	1	TRUE	1	0.23	2		469	634	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223767	2223789	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGCCCTGCCCTTGGCCCTGCAGG	TGCCCTGCCCTTGGCCCTGCAGG	-	novel	NA	P-0042220-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	138	774	0	ENST00000326181.6:c.1087-22_1087del		p.X363_splice	ENST00000326181	NM_032271.2	363		12/21	NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		774	376	SUCCESS
APC	324	MSKCC	GRCh37	5	112175171	112175171	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085373	NA	P-0042225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	68	236	0	ENST00000257430.4:c.3880C>T	p.Gln1294Ter	p.Q1294*	ENST00000257430	NM_000038.5	1294	Cag/Tag	16/16	0.320705759470442	2	FACETS	0.898	0.792	1	0.898	0.792	1	CLONAL	2	TRUE	0	0.320705759470442	2		236	236	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	66	401	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.826	0.719	0.943	0.826	0.719	0.943	CLONAL	1	TRUE	1	0.320705759470442	2		401	498	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0042225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	96	510	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.320705759470442	1	FACETS	0.834	0.744	0.929	0.834	0.744	0.929	CLONAL	1	TRUE	0	0.320705759470442	1		510	603	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518366	8518366	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754478667	NA	P-0042225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	48	307	0	ENST00000356435.5:c.1025C>T	p.Thr342Met	p.T342M	ENST00000356435		342	aCg/aTg	10/35	1	2	FACETS	0.786	0.666	0.917	0.786	0.666	0.917	CLONAL	1	TRUE	1	0.320705759470442	2		307	381	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244392	5244392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377318412	NA	P-0042225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	112	817	0	ENST00000357368.4:c.1090G>A	p.Val364Ile	p.V364I	ENST00000357368	NM_002850.3	364	Gtc/Atc	11/38	1	2	FACETS	0.874	0.786	0.967	0.874	0.786	0.967	CLONAL	1	TRUE	1	0.320705759470442	2		817	799	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945503	17945503	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	87	748	3	ENST00000458235.1:c.2227C>T	p.Gln743Ter	p.Q743*	ENST00000458235	NM_000215.3	743	Cag/Tag	17/24	1	2	FACETS	0.926	0.821	1	0.926	0.821	1	CLONAL	1	TRUE	1	0.320705759470442	2		751	586	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723354	49723354	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	49	465	0	ENST00000449682.2:c.1189A>T	p.Ser397Cys	p.S397C	ENST00000449682	NM_020998.3	397	Agc/Tgc	10/18	0.293331879448519	1	FACETS	0.864	0.736	1	0.864	0.736	1	CLONAL	1	TRUE	0	0.320705759470442	1		465	297	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268210	153268211	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0042225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	30	264	0	ENST00000281708.4:c.596_597dup	p.Val200LeufsTer40	p.V200Lfs*40	ENST00000281708	NM_033632.3	199	-/TT	4/12	1	2	FACETS	0.5	0.403	0.61	0.5	0.403	0.61	SUBCLONAL	1	TRUE	1	0.320705759470442	2		264	374	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119813	70119822	+	protein_altering_variant	In_Frame_Del	DEL	ACGTGGACAT	ACGTGGACAT	G	novel	NA	P-0042225-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	97	860	0	ENST00000245479.2:c.815_824delinsG	p.Asp272_Ile275delinsGly	p.D272_I275delinsG	ENST00000245479	NM_000346.3	272	gACGTGGACATc/gGc	3/3	0.320705759470442	1	FACETS	0.899	0.804	1	0.899	0.804	1	CLONAL	1	TRUE	0	0.320705759470442	1		860	565	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	46	372	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	0.874	0.738	1	0.874	0.738	1	CLONAL	1	TRUE	0	0.23	1		372	405	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0042234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	24	337	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	0.403	0.315	0.505	0.403	0.315	0.505	SUBCLONAL	1	TRUE	0	0.23	1		337	458	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684326	29684326	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201367	NA	P-0042234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	82	540	1	ENST00000356175.3:c.7846C>T	p.Arg2616Ter	p.R2616*	ENST00000356175	NM_000267.3	2616	Cga/Tga	53/57	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.23	2		541	677	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056752	180056752	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368909190	NA	P-0042234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	76	1129	0	ENST00000261937.6:c.760G>A	p.Val254Met	p.V254M	ENST00000261937	NM_182925.4	254	Gtg/Atg	6/30	0.293994725912229	0	FACETS	0.667	0.584	0.756			1	SUBCLONAL	1	TRUE	0	0.23	0		1129	763	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32899268	32899268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	54	386	0	ENST00000380152.3:c.372G>A	p.Met124Ile	p.M124I	ENST00000380152		124	atG/atA	4/27	0.0909441909415047	3	FACETS	1	0.926	1	0.568	0.486	0.658	INDETERMINATE	1	TRUE	1	0.23	3		386	461	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061627	38061627	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756320300	NA	P-0042234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	47	326	0	ENST00000250448.2:c.362C>T	p.Ala121Val	p.A121V	ENST00000250448	NM_004496.3	121	gCg/gTg	2/2	1	2	FACETS	0.811	0.69	0.942	1	0.967	1	CLONAL	2	TRUE	1	0.23	2		326	252	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509543	29509552	+	frameshift_variant	Frame_Shift_Del	DEL	TTTGACTTGG	TTTGACTTGG	-	novel	NA	P-0042234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	56	535	0	ENST00000356175.3:c.749_758del	p.Phe250TrpfsTer28	p.F250Wfs*28	ENST00000356175	NM_000267.3	250	TTTGACTTGGtg/tg	8/57	1	2	FACETS	0.854	0.732	0.988	0.854	0.732	0.988	CLONAL	1	TRUE	1	0.23	2		535	570	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026856	6026856	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854036	NA	P-0042234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	54	726	1	ENST00000265849.7:c.1540C>T	p.His514Tyr	p.H514Y	ENST00000265849	NM_000535.5	514	Cac/Tac	11/15	0.0909441909415047	3	FACETS	0.881	0.752	1	0.441	0.376	0.512	INDETERMINATE	1	TRUE	1	0.23	3		727	594	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864531	56864534	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	novel	NA	P-0042234-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	50	668	0	ENST00000519728.1:c.497_500del	p.Ser166CysfsTer41	p.S166Cfs*41	ENST00000519728	NM_002350.3	165	tTCTCt/tt	7/13	1	2	FACETS	0.584	0.494	0.683	0.584	0.494	0.683	SUBCLONAL	1	TRUE	1	0.23	2		668	745	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042234-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	55	372	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.782	0.673	0.9	0.782	0.673	0.9	SUBCLONAL	1	TRUE	1	0.432715628582845	2		372	325	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684326	29684326	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786201367	NA	P-0042234-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	113	540	1	ENST00000356175.3:c.7846C>T	p.Arg2616Ter	p.R2616*	ENST00000356175	NM_000267.3	2616	Cga/Tga	53/57	1	2	FACETS	0.973	0.879	1	0.973	0.879	1	CLONAL	1	TRUE	1	0.432715628582845	2		541	537	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056752	180056752	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368909190	NA	P-0042234-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	160	1129	0	ENST00000261937.6:c.760G>A	p.Val254Met	p.V254M	ENST00000261937	NM_182925.4	254	Gtg/Atg	6/30	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.432715628582845	2		1129	737	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32899268	32899268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042234-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	81	386	0	ENST00000380152.3:c.372G>A	p.Met124Ile	p.M124I	ENST00000380152		124	atG/atA	4/27	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.432715628582845	2		386	357	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061627	38061627	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756320300	NA	P-0042234-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	67	326	0	ENST00000250448.2:c.362C>T	p.Ala121Val	p.A121V	ENST00000250448	NM_004496.3	121	gCg/gTg	2/2	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.432715628582845	2		326	245	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509543	29509552	+	frameshift_variant	Frame_Shift_Del	DEL	TTTGACTTGG	TTTGACTTGG	-	novel	NA	P-0042234-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	82	535	0	ENST00000356175.3:c.749_758del	p.Phe250TrpfsTer28	p.F250Wfs*28	ENST00000356175	NM_000267.3	250	TTTGACTTGGtg/tg	8/57	1	2	FACETS	0.95	0.843	1	0.95	0.843	1	CLONAL	1	TRUE	1	0.432715628582845	2		535	399	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026856	6026856	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878854036	NA	P-0042234-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	93	726	1	ENST00000265849.7:c.1540C>T	p.His514Tyr	p.H514Y	ENST00000265849	NM_000535.5	514	Cac/Tac	11/15	0.398879911162056	3	FACETS	0.856	0.762	0.955	0.428	0.381	0.478	CLONAL	1	TRUE	1	0.432715628582845	3		727	611	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56864531	56864534	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	novel	NA	P-0042234-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	114	668	0	ENST00000519728.1:c.497_500del	p.Ser166CysfsTer41	p.S166Cfs*41	ENST00000519728	NM_002350.3	165	tTCTCt/tt	7/13	1	2	FACETS	0.941	0.85	1	0.941	0.85	1	CLONAL	1	TRUE	1	0.432715628582845	2		668	560	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0042257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	526	399	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.764077063088793	6	FACETS	0.901	0.874	0.927			1	CLONAL	5	TRUE	NA	0.764077063088793	6		399	773	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0042257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	134	484	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.961	0.884	1	0.961	0.884	1	CLONAL	1	TRUE	1	0.764077063088793	2		484	365	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716327	52716327	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	395	646	0	ENST00000322088.6:c.771G>C	p.Trp257Cys	p.W257C	ENST00000322088	NM_014225.5	257	tgG/tgC	6/15	0.499722098380729	3	FACETS	0.806	0.77	0.843	0.806	0.77	0.843	CLONAL	2	TRUE	1	0.764077063088793	3		646	886	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578537	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs879254214	NA	P-0042257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	371	1327	0	ENST00000269305.4:c.393_395del	p.Asn131del	p.N131del	ENST00000269305	NM_001126112.2	131	aaCAAg/aag	5/11	0.665601921302402	1	FACETS	0.789	0.754	0.824	0.789	0.754	0.824	SUBCLONAL	1	TRUE	0	0.764077063088793	1		1327	761	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593367	67593367	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	81	293	0	ENST00000274335.5:c.2113C>T	p.Gln705Ter	p.Q705*	ENST00000274335		705	Cag/Tag	15/15	1	2	FACETS	0.741	0.661	0.826	0.741	0.661	0.826	SUBCLONAL	1	TRUE	1	0.764077063088793	2		293	286	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589580	67589585	+	inframe_deletion	In_Frame_Del	DEL	AATTAC	AATTAC	-	novel	NA	P-0042257-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	24	166	0	ENST00000274335.5:c.1344_1349del	p.Lys448_His450delinsAsn	p.K448_H450delinsN	ENST00000274335		448	aAATTACat/aat	10/15	1	2	FACETS	0.73	0.588	0.886	0.73	0.588	0.886	SUBCLONAL	1	TRUE	1	0.764077063088793	2		166	86	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0042261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	440	564	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.815727682753213	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.820393258721176	1		564	525	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368211	45368211	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0042261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	92	288	0	ENST00000262160.6:c.1391C>G	p.Ser464Ter	p.S464*	ENST00000262160	NM_005901.5	464	tCa/tGa	11/11	0.820393258721176	1	FACETS	0.932	0.862	0.998	0.932	0.862	0.998	CLONAL	1	TRUE	0	0.820393258721176	1		288	142	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012397	176012397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	85	304	0	ENST00000367669.3:c.1537G>A	p.Glu513Lys	p.E513K	ENST00000367669	NM_022457.5	513	Gag/Aag	14/20	1	2	FACETS	0.836	0.75	0.924	0.836	0.75	0.924	CLONAL	1	TRUE	1	0.820393258721176	2		304	248	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673130	30673130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	210	542	0	ENST00000376406.3:c.3830C>T	p.Ser1277Phe	p.S1277F	ENST00000376406	NM_014641.2	1277	tCt/tTt	10/15	1	2	FACETS	0.968	0.907	1	0.968	0.907	1	CLONAL	1	TRUE	1	0.820393258721176	2		542	529	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528086	29528086	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs864622107	NA	P-0042261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	80	230	0	ENST00000356175.3:c.1094C>G	p.Ser365Ter	p.S365*	ENST00000356175	NM_000267.3	365	tCa/tGa	10/57	0.815727682753213	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.820393258721176	1		230	105	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422703	49422703	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	225	654	0	ENST00000301067.7:c.14290G>C	p.Glu4764Gln	p.E4764Q	ENST00000301067	NM_003482.3	4764	Gag/Cag	45/54	0.815727682753213	1	FACETS	0.96	0.915	1	0.96	0.915	1	CLONAL	1	TRUE	0	0.820393258721176	1		654	337	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10284510	10284546	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CGTAGAACAAAAAGAAAGGTATAGTAACTATTCTTAC	CGTAGAACAAAAAGAAAGGTATAGTAACTATTCTTAC	-	novel	NA	P-0042261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	15	216	0	ENST00000340748.4:c.635+1_635+37del		p.X212_splice	ENST00000340748		212			1	2	FACETS	0.123	0.089	0.163	0.123	0.089	0.163	SUBCLONAL	1	TRUE	1	0.820393258721176	2		216	298	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326306	62326306	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs945952564	NA	P-0042261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	291	869	0	ENST00000360203.5:c.3322G>C	p.Glu1108Gln	p.E1108Q	ENST00000360203	NM_001283009.1	1108	Gag/Cag	32/35	1	2	FACETS	0.885	0.836	0.934	0.885	0.836	0.934	CLONAL	1	TRUE	1	0.820393258721176	2		869	802	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176618953	176618953	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	184	413	0	ENST00000439151.2:c.996G>C	p.Lys332Asn	p.K332N	ENST00000439151	NM_022455.4	332	aaG/aaC	3/23	1	2	FACETS	0.975	0.91	1	0.975	0.91	1	CLONAL	1	TRUE	1	0.820393258721176	2		413	460	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878754	151878754	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0042261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	85	405	0	ENST00000262189.6:c.6191C>G	p.Ser2064Ter	p.S2064*	ENST00000262189	NM_170606.2	2064	tCa/tGa	36/59	1	2	FACETS	0.702	0.628	0.78	0.702	0.628	0.78	SUBCLONAL	1	TRUE	1	0.820393258721176	2		405	295	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949731	151949731	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	147	394	0	ENST00000262189.6:c.1369G>C	p.Asp457His	p.D457H	ENST00000262189	NM_170606.2	457	Gac/Cac	10/59	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.820393258721176	2		394	344	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964526	70964526	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	224	510	0	ENST00000276594.2:c.1502C>G	p.Ser501Cys	p.S501C	ENST00000276594	NM_024504.3	501	tCc/tGc	8/8	0.79140616311975	3	FACETS	1	0.985	1	0.584	0.547	0.622	CLONAL	1	TRUE	1	0.820393258721176	3		510	659	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606214	93606214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	245	608	1	ENST00000375746.1:c.34C>T	p.His12Tyr	p.H12Y	ENST00000375746	NM_001174167.1	12	Cac/Tac	2/14	1	2	FACETS	0.901	0.847	0.956	0.901	0.847	0.956	CLONAL	1	TRUE	1	0.820393258721176	2		609	663	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0042335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	153	422	2	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.991	0.908	1	0.991	0.908	1	CLONAL	1	TRUE	1	0.409495495861395	2		424	754	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380282	25380282	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	168	384	0	ENST00000311936.3:c.176C>G	p.Ala59Gly	p.A59G	ENST00000311936	NM_004985.3	59	gCa/gGa	3/5	1	2	FACETS	0.999	0.92	1	0.999	0.92	1	CLONAL	1	TRUE	1	0.409495495861395	2		384	821	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs199469669	NA	P-0042335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	61	459	0	ENST00000374080.3:c.130G>C	p.Gly44Arg	p.G44R	ENST00000374080		44	Ggt/Cgt	2/45	1	2	FACETS	0.339	0.291	0.391	0.339	0.291	0.391	SUBCLONAL	1	TRUE	1	0.409495495861395	2		459	879	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859693	151859693	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146298908	NA	P-0042335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	114	273	0	ENST00000262189.6:c.10969G>A	p.Asp3657Asn	p.D3657N	ENST00000262189	NM_170606.2	3657	Gac/Aac	43/59	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.409495495861395	2		273	509	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106100	27106100	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	285	424	0	ENST00000324856.7:c.5715del	p.Lys1905AsnfsTer18	p.K1905Nfs*18	ENST00000324856	NM_006015.4	1904	gAa/ga	20/20	NA	2	FACETS	0.937	0.885	0.989			1	INDETERMINATE	2	TRUE	NA	0.409495495861395	2		424	743	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654659	67654659	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	154	397	0	ENST00000264010.4:c.1148del	p.Leu383CysfsTer12	p.L383Cfs*12	ENST00000264010	NM_006565.3	382	agT/ag	6/12	1	2	FACETS	0.911	0.834	0.991	0.911	0.834	0.991	CLONAL	1	TRUE	1	0.409495495861395	2		397	826	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696742	47696742	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0042335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	199	206	0	ENST00000347630.2:c.206T>A	p.Leu69Ter	p.L69*	ENST00000347630	NM_001007230.1	69	tTg/tAg	5/11	0.409495495861395	2	FACETS	0.89	0.831	0.95	0.89	0.831	0.95	CLONAL	2	TRUE	0	0.409495495861395	2		206	546	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589609	67589610	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAA	novel	NA	P-0042335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	95	53	0	ENST00000274335.5:c.1376_1378dup	p.Lys459dup	p.K459dup	ENST00000274335		459	gaa/gAAAaa	10/15	1	2	FACETS	0.845	0.755	0.941	0.845	0.755	0.941	CLONAL	1	TRUE	1	0.409495495861395	2		53	549	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956787	68956787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs934598745	NA	P-0042335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	203	482	2	ENST00000288368.4:c.905C>T	p.Thr302Met	p.T302M	ENST00000288368	NM_024870.2	302	aCg/aTg	8/40	1	2	FACETS	0.926	0.858	0.996	0.926	0.858	0.996	CLONAL	1	TRUE	1	0.409495495861395	2		484	1071	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717653	89717654	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	A	novel	NA	P-0042335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	133	308	0	ENST00000371953.3:c.678_679delinsA	p.Ser227ProfsTer29	p.S227Pfs*29	ENST00000371953	NM_000314.4	226	tcCTcc/tcAcc	7/9	0.402195070798505	3	FACETS	0.61	0.553	0.672	0.305	0.276	0.336	SUBCLONAL	1	TRUE	1	0.409495495861395	3		308	1282	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805683	43805683	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	82	571	1	ENST00000372470.3:c.739C>T	p.Gln247Ter	p.Q247*	ENST00000372470	NM_005373.2	247	Cag/Tag	5/12	1	2	FACETS	0.63	0.556	0.711	0.63	0.556	0.711	SUBCLONAL	1	TRUE	1	0.374877670911513	2		572	694	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42026741	42026741	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	71	369	0	ENST00000219905.7:c.3865C>G	p.Pro1289Ala	p.P1289A	ENST00000219905	NM_001164273.1	1289	Ccc/Gcc	12/24	1	2	FACETS	0.64	0.559	0.727	0.64	0.559	0.727	SUBCLONAL	1	TRUE	1	0.374877670911513	2		369	592	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579315	7579316	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1267047192	NA	P-0042353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	625	600	0	ENST00000269305.4:c.371dup	p.Cys124TrpfsTer25	p.C124Wfs*25	ENST00000269305	NM_001126112.2	124	tgc/tgGc	4/11	0.815142360874125	4	FACETS	0.984	0.967	1	0.984	0.967	1	CLONAL	4	TRUE	0	0.810741869230712	4		600	709	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858477	57858477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760192848	NA	P-0042353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1395	207	509	0	ENST00000228682.2:c.215G>A	p.Arg72Gln	p.R72Q	ENST00000228682	NM_005269.2	72	cGg/cAg	4/12	0.810741869230712	7	FACETS	0.965	0.892	1	0.193	0.178	0.209	CLONAL	1	TRUE	2	0.810741869230712	7		509	1602	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932881	36932881	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	258	746	0	ENST00000361632.4:c.1990G>C	p.Asp664His	p.D664H	ENST00000361632		664	Gac/Cac	15/16	0.815142360874125	3	FACETS	1	0.96	1	0.515	0.483	0.547	CLONAL	1	TRUE	1	0.810741869230712	3		746	869	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986799	36986799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	86	216	0	ENST00000354822.5:c.890G>T	p.Gly297Val	p.G297V	ENST00000354822	NM_001079668.2	297	gGc/gTc	3/3	0.815142360874125	2	FACETS	1	0.959	1	0.555	0.503	0.608	CLONAL	1	TRUE	0	0.810741869230712	2		216	191	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23652436	23652436	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	229	754	0	ENST00000261584.4:c.43G>C	p.Glu15Gln	p.E15Q	ENST00000261584	NM_024675.3	15	Gaa/Caa	1/13	0.815142360874125	5	FACETS	0.939	0.873	1	0.313	0.291	0.336	CLONAL	1	TRUE	2	0.810741869230712	5		754	1333	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483134	29483134	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	71	326	0	ENST00000356175.3:c.194T>C	p.Val65Ala	p.V65A	ENST00000356175	NM_000267.3	65	gTt/gCt	2/57	0.66599497172735	5	FACETS	0.582	0.508	0.662			1	SUBCLONAL	1	TRUE	NA	0.810741869230712	5		326	667	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920381	50920489	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCCAGGTGGGGAGGCGGGGGCGCCCTGCTCAGCCGCTGCCGTCCCCAGGTATCCCATCTGAATGCCCTGGAGGAGCGCTTCTCGCGCCTCTGGACGCAGTGCCAGCGCT	GCCAGGTGGGGAGGCGGGGGCGCCCTGCTCAGCCGCTGCCGTCCCCAGGTATCCCATCTGAATGCCCTGGAGGAGCGCTTCTCGCGCCTCTGGACGCAGTGCCAGCGCT	-	novel	NA	P-0042353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	160	760	0	ENST00000440232.2:c.3120+33_3187del		p.X1040_splice	ENST00000440232	NM_002691.3	1040		26/27	0.568906793512679	2	FACETS	0.756	0.698	0.816	0.378	0.349	0.408	SUBCLONAL	1	TRUE	0	0.810741869230712	2		760	522	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61717848	61717853	+	inframe_deletion	In_Frame_Del	DEL	CTTGTA	CTTGTA	-	novel	NA	P-0042353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	417	559	0	ENST00000401558.2:c.1946_1951del	p.Val649_Gln650del	p.V649_Q650del	ENST00000401558	NM_003400.3	649	gTACAAGaa/gaa	17/25	0.815142360874125	4	FACETS	0.875	0.836	0.915	0.584	0.557	0.61	CLONAL	2	TRUE	1	0.810741869230712	4		559	1064	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21303999	21303999	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	398	464	0	ENST00000354336.3:c.778G>T	p.Val260Phe	p.V260F	ENST00000354336	NM_005207.3	260	Gtt/Ttt	3/3	0.556235114817971	4	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.810741869230712	4		464	781	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574171	41574171	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	50	567	0	ENST00000263253.7:c.6456G>C	p.Gln2152His	p.Q2152H	ENST00000263253	NM_001429.3	2152	caG/caC	31/31	0.556235114817971	4	FACETS	0.347	0.294	0.406			1	SUBCLONAL	1	TRUE	NA	0.810741869230712	4		567	643	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637408	176637408	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	204	461	0	ENST00000439151.2:c.2008G>C	p.Asp670His	p.D670H	ENST00000439151	NM_022455.4	670	Gat/Cat	5/23	0.815142360874125	3	FACETS	1	0.986	1	0.406	0.379	0.434	CLONAL	1	TRUE	0	0.810741869230712	3		461	580	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958177	2958177	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042353-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	137	708	0	ENST00000396946.4:c.2555G>C	p.Arg852Pro	p.R852P	ENST00000396946	NM_032415.4	852	cGa/cCa	19/25	0.815142360874125	3	FACETS	0.572	0.52	0.626	0.286	0.26	0.313	SUBCLONAL	1	TRUE	1	0.810741869230712	3		708	831	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0042359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	320	500	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.257280498575239	2	FACETS	0.843	0.796	0.89	0.843	0.796	0.89	CLONAL	2	TRUE	0	0.340583992020687	2		500	1115	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670255	134670255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1426484610	NA	P-0042359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	279	421	0	ENST00000398015.3:c.166C>T	p.Arg56Cys	p.R56C	ENST00000398015	NM_004441.4	56	Cgc/Tgc	3/16	0.340583992020687	3	FACETS	0.923	0.867	0.98	0.923	0.867	0.98	CLONAL	2	TRUE	1	0.340583992020687	3		421	1039	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245002	41245002	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1567795227	NA	P-0042359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	310	494	0	ENST00000357654.3:c.2546A>G	p.Glu849Gly	p.E849G	ENST00000357654	NM_007294.3	849	gAa/gGa	10/23	0.191864740872262	3	FACETS	0.904	0.852	0.957	0.904	0.852	0.957	INDETERMINATE	2	TRUE	1	0.340583992020687	3		494	1178	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643737	38643737	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1201851975	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	156	634	2	ENST00000299084.4:c.1207C>T	p.Arg403Ter	p.R403*	ENST00000299084	NM_152594.2	403	Cga/Tga	7/7	1	2	FACETS	0.889	0.814	0.967	0.889	0.814	0.967	CLONAL	1	TRUE	1	0.41	2		636	856	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813941	50813941	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1162188229	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	84	457	0	ENST00000398568.2:c.1495G>A	p.Ala499Thr	p.A499T	ENST00000398568	NM_001042412.1	499	Gct/Act	8/18	1	2	FACETS	0.727	0.643	0.816	0.727	0.643	0.816	SUBCLONAL	1	TRUE	1	0.41	2		457	564	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	42	209	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.911	0.767	1	0.911	0.767	1	CLONAL	1	TRUE	1	0.41	2		209	225	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032374	11032374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs909244932	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	174	733	0	ENST00000327064.4:c.1768G>A	p.Ala590Thr	p.A590T	ENST00000327064	NM_199141.1	590	Gcc/Acc	16/16	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.41	2		733	839	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481461	20481461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	38	262	0	ENST00000346618.3:c.530C>T	p.Thr177Met	p.T177M	ENST00000346618	NM_001949.4	177	aCg/aTg	3/7	1	2	FACETS	0.487	0.403	0.58	0.487	0.403	0.58	SUBCLONAL	1	TRUE	1	0.41	2		262	381	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129418	64129418	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	176	779	2	ENST00000334205.4:c.850C>T	p.Arg284Ter	p.R284*	ENST00000334205	NM_003942.2	284	Cga/Tga	8/17	1	2	FACETS	0.929	0.856	1	0.929	0.856	1	CLONAL	1	TRUE	1	0.41	2		781	924	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112230	115112230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780531262	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	79	242	1	ENST00000257566.3:c.1510G>A	p.Ala504Thr	p.A504T	ENST00000257566	NM_016569.3	504	Gcc/Acc	7/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.41	2		243	289	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239893	105239893	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1340970650	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	162	602	0	ENST00000349310.3:c.727C>T	p.Arg243Cys	p.R243C	ENST00000349310	NM_001014432.1	243	Cgt/Tgt	10/15	1	2	FACETS	0.952	0.874	1	0.952	0.874	1	CLONAL	1	TRUE	1	0.41	2		602	830	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	153	600	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	1	2	FACETS	0.989	0.906	1	0.989	0.906	1	CLONAL	1	TRUE	1	0.41	2		600	755	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121018	29121018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853009	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	105	533	2	ENST00000328354.6:c.539G>A	p.Arg180His	p.R180H	ENST00000328354	NM_007194.3	180	cGc/cAc	4/15	1	2	FACETS	0.943	0.848	1	0.943	0.848	1	CLONAL	1	TRUE	1	0.41	2		535	543	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288785	33288785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765273333	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	76	415	0	ENST00000374542.5:c.767G>A	p.Arg256His	p.R256H	ENST00000374542	NM_001141970.1	256	cGc/cAc	3/8	1	2	FACETS	0.739	0.649	0.834	0.739	0.649	0.834	SUBCLONAL	1	TRUE	1	0.41	2		415	502	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952049	178952049	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242945375	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	76	269	0	ENST00000263967.3:c.3104C>T	p.Ala1035Val	p.A1035V	ENST00000263967	NM_006218.2	1035	gCt/gTt	21/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.41	2		269	296	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105553	27105553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1485978447	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	98	428	0	ENST00000324856.7:c.5164C>T	p.Arg1722Ter	p.R1722*	ENST00000324856	NM_006015.4	1722	Cga/Tga	20/20	1	2	FACETS	0.928	0.831	1	0.928	0.831	1	CLONAL	1	TRUE	1	0.41	2		428	515	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578316	226578316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs193238922	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	105	462	3	ENST00000366794.5:c.412C>T	p.Arg138Cys	p.R138C	ENST00000366794	NM_001618.3	138	Cgc/Tgc	4/23	1	2	FACETS	0.867	0.778	0.96	0.867	0.778	0.96	CLONAL	1	TRUE	1	0.41	2		465	591	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136805	55136805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41279521	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	42	284	0	ENST00000257290.5:c.1127G>A	p.Arg376Gln	p.R376Q	ENST00000257290	NM_006206.4	376	cGa/cAa	8/23	1	2	FACETS	0.762	0.64	0.895	0.762	0.64	0.895	SUBCLONAL	1	TRUE	1	0.41	2		284	269	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344759	65344759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	80	330	0	ENST00000342505.4:c.278G>A	p.Arg93His	p.R93H	ENST00000342505	NM_002227.2	93	cGc/cAc	4/25	1	2	FACETS	0.863	0.763	0.97	0.863	0.763	0.97	CLONAL	1	TRUE	1	0.41	2		330	452	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777114	9777114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765061150	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	181	671	0	ENST00000377346.4:c.878C>T	p.Ala293Val	p.A293V	ENST00000377346	NM_005026.3	293	gCc/gTc	7/24	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.41	2		671	869	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780803	9780803	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	149	599	0	ENST00000377346.4:c.1525C>A	p.Leu509Met	p.L509M	ENST00000377346	NM_005026.3	509	Ctg/Atg	13/24	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.41	2		599	712	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780827	9780827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs991423011	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	60	695	1	ENST00000377346.4:c.1549C>T	p.Arg517Trp	p.R517W	ENST00000377346	NM_005026.3	517	Cgg/Tgg	13/24	1	2	FACETS	0.345	0.296	0.399	0.345	0.296	0.399	SUBCLONAL	1	TRUE	1	0.41	2		696	848	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783301	9783301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763402967	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	45	537	0	ENST00000377346.4:c.2545G>A	p.Ala849Thr	p.A849T	ENST00000377346	NM_005026.3	849	Gcc/Acc	20/24	1	2	FACETS	0.293	0.245	0.346	0.293	0.245	0.346	SUBCLONAL	1	TRUE	1	0.41	2		537	749	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188576	11188576	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	88	404	0	ENST00000361445.4:c.5845C>T	p.Pro1949Ser	p.P1949S	ENST00000361445	NM_004958.3	1949	Ccc/Tcc	42/58	1	2	FACETS	0.845	0.751	0.945	0.845	0.751	0.945	CLONAL	1	TRUE	1	0.41	2		404	508	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190747	11190747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759603938	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	203	649	1	ENST00000361445.4:c.5452C>T	p.Arg1818Cys	p.R1818C	ENST00000361445	NM_004958.3	1818	Cgt/Tgt	39/58	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.41	2		650	920	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260332	16260332	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	111	452	0	ENST00000375759.3:c.7597A>G	p.Thr2533Ala	p.T2533A	ENST00000375759	NM_015001.2	2533	Acc/Gcc	11/15	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.41	2		452	537	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261146	16261146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769982439	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	85	404	0	ENST00000375759.3:c.8411C>T	p.Ala2804Val	p.A2804V	ENST00000375759	NM_015001.2	2804	gCg/gTg	11/15	1	2	FACETS	0.743	0.658	0.834	0.743	0.658	0.834	SUBCLONAL	1	TRUE	1	0.41	2		404	558	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264376	16264376	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141170345	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	153	640	0	ENST00000375759.3:c.10579G>A	p.Val3527Ile	p.V3527I	ENST00000375759	NM_015001.2	3527	Gtc/Atc	13/15	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.41	2		640	740	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16265348	16265348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746234410	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	159	664	0	ENST00000375759.3:c.10840G>A	p.Val3614Ile	p.V3614I	ENST00000375759	NM_015001.2	3614	Gtt/Att	14/15	1	2	FACETS	0.885	0.812	0.962	0.885	0.812	0.962	CLONAL	1	TRUE	1	0.41	2		664	876	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17345405	17345405	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs545681543	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	29	458	0	ENST00000375499.3:c.814A>G	p.Thr272Ala	p.T272A	ENST00000375499	NM_003000.2	272	Acc/Gcc	8/8	1	2	FACETS	0.28	0.224	0.344	0.28	0.224	0.344	SUBCLONAL	1	TRUE	1	0.41	2		458	505	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101611	27101612	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	174	793	0	ENST00000324856.7:c.4899dup	p.Met1634HisfsTer14	p.M1634Hfs*14	ENST00000324856	NM_006015.4	1631	-/C	18/20	1	2	FACETS	0.967	0.891	1	0.967	0.891	1	CLONAL	1	TRUE	1	0.41	2		793	878	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28607291	28607291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1234214591	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	133	491	0	ENST00000253063.3:c.1421C>T	p.Ala474Val	p.A474V	ENST00000253063	NM_031459.4	474	gCc/gTc	10/10	1	2	FACETS	0.977	0.889	1	0.977	0.889	1	CLONAL	1	TRUE	1	0.41	2		491	664	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797139	45797139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150792276	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	189	806	0	ENST00000450313.1:c.1276C>T	p.Arg426Cys	p.R426C	ENST00000450313	NM_012222.2	426	Cgt/Tgt	13/16	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.41	2		806	891	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798968	45798968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781444	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	52	724	0	ENST00000450313.1:c.377G>A	p.Arg126Gln	p.R126Q	ENST00000450313	NM_012222.2	126	cGg/cAg	4/16	1	2	FACETS	0.336	0.285	0.391	0.336	0.285	0.391	SUBCLONAL	1	TRUE	1	0.41	2		724	756	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115252323	115252323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs797045795	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	72	293	0	ENST00000369535.4:c.317C>T	p.Ser106Leu	p.S106L	ENST00000369535	NM_002524.4	106	tCg/tTg	4/7	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.41	2		293	348	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262240	115262240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	91	328	0	ENST00000438362.2:c.2314C>T	p.Arg772Cys	p.R772C	ENST00000438362	NM_001242891.1	772	Cgc/Tgc	18/20	1	2	FACETS	0.836	0.744	0.933	0.836	0.744	0.933	CLONAL	1	TRUE	1	0.41	2		328	531	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166467	118166467	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755966473	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	81	307	1	ENST00000369448.3:c.977G>A	p.Arg326His	p.R326H	ENST00000369448	NM_017709.3	326	cGc/cAc	2/2	1	2	FACETS	0.964	0.854	1	0.964	0.854	1	CLONAL	1	TRUE	1	0.41	2		308	410	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458783	120458783	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139052054	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	89	533	0	ENST00000256646.2:c.6562G>A	p.Ala2188Thr	p.A2188T	ENST00000256646	NM_024408.3	2188	Gcc/Acc	34/34	1	2	FACETS	0.754	0.669	0.843	0.754	0.669	0.843	SUBCLONAL	1	TRUE	1	0.41	2		533	576	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471802	120471802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	78	370	0	ENST00000256646.2:c.3689C>T	p.Ala1230Val	p.A1230V	ENST00000256646	NM_024408.3	1230	gCc/gTc	23/34	1	2	FACETS	0.834	0.736	0.939	0.834	0.736	0.939	CLONAL	1	TRUE	1	0.41	2		370	456	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870336	155870336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs938749530	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	106	446	0	ENST00000368323.3:c.503G>A	p.Arg168His	p.R168H	ENST00000368323	NM_006912.5	168	cGc/cAc	6/6	1	2	FACETS	0.922	0.829	1	0.922	0.829	1	CLONAL	1	TRUE	1	0.41	2		446	561	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740170	162740170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1193186486	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	112	446	0	ENST00000367921.3:c.1372C>T	p.Arg458Cys	p.R458C	ENST00000367921	NM_006182.2	458	Cgc/Tgc	12/18	1	2	FACETS	0.877	0.79	0.968	0.877	0.79	0.968	CLONAL	1	TRUE	1	0.41	2		446	623	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317716	163317716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775293541	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	25	227	0	ENST00000271452.3:c.1112G>A	p.Arg371His	p.R371H	ENST00000271452	NM_145697.2	371	cGc/cAc	12/14	1	2	FACETS	0.562	0.445	0.695	0.562	0.445	0.695	SUBCLONAL	1	TRUE	1	0.41	2		227	217	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176054920	176054920	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759451215	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	18	334	0	ENST00000367669.3:c.1133G>A	p.Arg378His	p.R378H	ENST00000367669	NM_022457.5	378	cGt/cAt	10/20	1	2	FACETS	0.3	0.225	0.388	0.3	0.225	0.388	SUBCLONAL	1	TRUE	1	0.41	2		334	293	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204512023	204512023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	57	308	0	ENST00000367182.3:c.623G>A	p.Ser208Asn	p.S208N	ENST00000367182	NM_001278516.1	208	aGc/aAc	8/11	1	2	FACETS	0.828	0.714	0.95	0.828	0.714	0.95	CLONAL	1	TRUE	1	0.41	2		308	336	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649566	206649566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1464747771	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	62	564	1	ENST00000367120.3:c.401G>A	p.Arg134His	p.R134H	ENST00000367120	NM_014002.3	134	cGc/cAc	6/22	1	2	FACETS	0.429	0.37	0.493	0.429	0.37	0.493	SUBCLONAL	1	TRUE	1	0.41	2		565	705	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206667312	206667312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781860835	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	154	590	2	ENST00000367120.3:c.2105G>A	p.Arg702His	p.R702H	ENST00000367120	NM_014002.3	702	cGc/cAc	21/22	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.41	2		592	741	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567817	226567817	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs374389375	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	46	663	0	ENST00000366794.5:c.1349A>G	p.Asn450Ser	p.N450S	ENST00000366794	NM_001618.3	450	aAc/aGc	10/23	1	2	FACETS	0.254	0.212	0.299	0.254	0.212	0.299	SUBCLONAL	1	TRUE	1	0.41	2		663	885	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612974	228612974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756810829	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	103	367	0	ENST00000366696.1:c.53G>A	p.Arg18His	p.R18H	ENST00000366696	NM_003493.2	18	cGc/cAc	1/1	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.41	2		367	479	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736326	243736326	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	74	337	0	ENST00000263826.5:c.721C>T	p.Arg241Trp	p.R241W	ENST00000263826	NM_005465.4	241	Cgg/Tgg	8/13	1	2	FACETS	0.76	0.667	0.859	0.76	0.667	0.859	SUBCLONAL	1	TRUE	1	0.41	2		337	475	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246091314	246091314	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	55	444	0	ENST00000388985.4:c.621C>A	p.Ser207Arg	p.S207R	ENST00000388985		207	agC/agA	7/12	1	2	FACETS	0.467	0.399	0.541	0.467	0.399	0.541	SUBCLONAL	1	TRUE	1	0.41	2		444	575	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097653	8097653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	60	225	0	ENST00000346208.3:c.35G>A	p.Ser12Asn	p.S12N	ENST00000346208		12	aGc/aAc	2/6	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.41	2		225	290	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115837	8115837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200935603	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	140	579	1	ENST00000346208.3:c.1183G>A	p.Ala395Thr	p.A395T	ENST00000346208		395	Gcc/Acc	6/6	1	2	FACETS	0.873	0.796	0.954	0.873	0.796	0.954	CLONAL	1	TRUE	1	0.41	2		580	782	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597831	43597831	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1180613732	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	165	749	0	ENST00000355710.3:c.379C>A	p.Leu127Met	p.L127M	ENST00000355710	NM_020975.4	127	Ctg/Atg	3/20	1	2	FACETS	0.919	0.844	0.997	0.919	0.844	0.997	CLONAL	1	TRUE	1	0.41	2		749	876	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607597	43607597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545625150	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	170	793	1	ENST00000355710.3:c.1573C>T	p.Arg525Trp	p.R525W	ENST00000355710	NM_020975.4	525	Cgg/Tgg	8/20	1	2	FACETS	0.921	0.848	0.998	0.921	0.848	0.998	CLONAL	1	TRUE	1	0.41	2		794	900	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609108	43609108	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	54	782	1	ENST00000355710.3:c.1864C>T	p.Pro622Ser	p.P622S	ENST00000355710	NM_020975.4	622	Ccc/Tcc	10/20	1	2	FACETS	0.301	0.256	0.351	0.301	0.256	0.351	SUBCLONAL	1	TRUE	1	0.41	2		783	875	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332760	70332760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749194238	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	101	480	1	ENST00000373644.4:c.665G>A	p.Arg222His	p.R222H	ENST00000373644	NM_030625.2	222	cGc/cAc	2/12	1	2	FACETS	0.917	0.823	1	0.917	0.823	1	CLONAL	1	TRUE	1	0.41	2		481	537	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88677054	88677054	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	33	477	0	ENST00000372037.3:c.839C>A	p.Thr280Asn	p.T280N	ENST00000372037	NM_004329.2	280	aCt/aAt	9/13	1	2	FACETS	0.295	0.24	0.358	0.295	0.24	0.358	SUBCLONAL	1	TRUE	1	0.41	2		477	545	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624267	89624267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	88	321	0	ENST00000371953.3:c.41G>A	p.Arg14Lys	p.R14K	ENST00000371953	NM_000314.4	14	aGg/aAg	1/9	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.41	2		321	373	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	39	376	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	0.499	0.414	0.594	0.499	0.414	0.594	SUBCLONAL	1	TRUE	1	0.41	2		376	381	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104377135	104377135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779490664	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	65	666	0	ENST00000369902.3:c.1246G>A	p.Ala416Thr	p.A416T	ENST00000369902	NM_016169.3	416	Gcc/Acc	10/12	1	2	FACETS	0.345	0.298	0.397	0.345	0.298	0.397	SUBCLONAL	1	TRUE	1	0.41	2		666	918	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771563	112771563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1185910534	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	76	386	0	ENST00000369452.4:c.1736G>A	p.Arg579His	p.R579H	ENST00000369452	NM_007373.3	579	cGt/cAt	9/9	1	2	FACETS	0.848	0.747	0.956	0.848	0.747	0.956	CLONAL	1	TRUE	1	0.41	2		386	437	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279549	123279549	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	80	698	0	ENST00000358487.5:c.883G>A	p.Glu295Lys	p.E295K	ENST00000358487	NM_000141.4	295	Gaa/Aaa	7/18	1	2	FACETS	0.449	0.394	0.508	0.449	0.394	0.508	SUBCLONAL	1	TRUE	1	0.41	2		698	869	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310860	123310860	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147987917	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	35	483	1	ENST00000358487.5:c.568C>T	p.Arg190Trp	p.R190W	ENST00000358487	NM_000141.4	190	Cgg/Tgg	5/18	1	2	FACETS	0.245	0.2	0.295	0.245	0.2	0.295	SUBCLONAL	1	TRUE	1	0.41	2		484	698	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325146	123325146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199575491	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	145	498	0	ENST00000358487.5:c.182G>A	p.Arg61His	p.R61H	ENST00000358487	NM_000141.4	61	cGc/cAc	3/18	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.41	2		498	664	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	71	228	2	ENST00000256196.4:c.68G>A	p.Gly23Asp	p.G23D	ENST00000256196		23	gGc/gAc	1/6	1	2	FACETS	0.97	0.852	1	0.97	0.852	1	CLONAL	1	TRUE	1	0.41	2		230	357	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137075	64137075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	78	295	1	ENST00000334205.4:c.1586G>A	p.Arg529His	p.R529H	ENST00000334205	NM_003942.2	529	cGc/cAc	13/17	1	2	FACETS	0.993	0.878	1	0.993	0.878	1	CLONAL	1	TRUE	1	0.41	2		296	383	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137357	64137357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	50	649	0	ENST00000334205.4:c.1789G>A	p.Val597Ile	p.V597I	ENST00000334205	NM_003942.2	597	Gtc/Atc	14/17	1	2	FACETS	0.321	0.272	0.376	0.321	0.272	0.376	SUBCLONAL	1	TRUE	1	0.41	2		649	759	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939804	71939804	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773663316	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	179	727	2	ENST00000298229.2:c.431G>A	p.Arg144His	p.R144H	ENST00000298229	NM_001567.3	144	cGc/cAc	4/28	1	2	FACETS	0.928	0.855	1	0.928	0.855	1	CLONAL	1	TRUE	1	0.41	2		729	941	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940586	71940586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1255360958	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	172	640	1	ENST00000298229.2:c.737G>A	p.Arg246His	p.R246H	ENST00000298229	NM_001567.3	246	cGc/cAc	6/28	1	2	FACETS	0.945	0.87	1	0.945	0.87	1	CLONAL	1	TRUE	1	0.41	2		641	888	SUCCESS
EED	8726	MSKCC	GRCh37	11	85961344	85961344	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138343311	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	96	157	0	ENST00000263360.6:c.121G>A	p.Ala41Thr	p.A41T	ENST00000263360	NM_003797.3	41	Gct/Act	2/12	1	2	FACETS	1	0.965	1	1	0.989	1	CLONAL	2	TRUE	1	0.41	2		157	209	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94197307	94197308	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	77	377	0	ENST00000323929.3:c.1196dup	p.Arg400GlnfsTer3	p.R400Qfs*3	ENST00000323929	NM_005591.3	399	ttc/ttTc	11/20	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.41	2		377	359	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102033288	102033288	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	171	540	0	ENST00000282441.5:c.674T>C	p.Met225Thr	p.M225T	ENST00000282441	NM_001130145.2	225	aTg/aCg	3/9	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.41	2		540	763	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102196254	102196254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	64	251	1	ENST00000263464.3:c.911C>T	p.Ser304Phe	p.S304F	ENST00000263464	NM_001165.4	304	tCt/tTt	3/9	1	2	FACETS	0.988	0.862	1	0.988	0.862	1	CLONAL	1	TRUE	1	0.41	2		252	316	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098524	108098524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148061139	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	44	187	0	ENST00000278616.4:c.94C>T	p.Arg32Cys	p.R32C	ENST00000278616	NM_000051.3	32	Cgc/Tgc	3/63	1	2	FACETS	0.813	0.687	0.951	0.813	0.687	0.951	CLONAL	1	TRUE	1	0.41	2		187	264	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121670	108121670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565383235	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	32	401	0	ENST00000278616.4:c.1478G>A	p.Arg493His	p.R493H	ENST00000278616	NM_000051.3	493	cGt/cAt	10/63	1	2	FACETS	0.348	0.282	0.423	0.348	0.282	0.423	SUBCLONAL	1	TRUE	1	0.41	2		401	448	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143471	108143471	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761590782	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	54	376	0	ENST00000278616.4:c.3176C>T	p.Ala1059Val	p.A1059V	ENST00000278616	NM_000051.3	1059	gCc/gTc	22/63	1	2	FACETS	0.697	0.597	0.805	0.697	0.597	0.805	SUBCLONAL	1	TRUE	1	0.41	2		376	378	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373671	118373671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	83	429	0	ENST00000534358.1:c.7064C>T	p.Ala2355Val	p.A2355V	ENST00000534358	NM_005933.3	2355	gCt/gTt	27/36	1	2	FACETS	0.95	0.843	1	0.95	0.843	1	CLONAL	1	TRUE	1	0.41	2		429	426	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373689	118373689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782524513	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	42	413	0	ENST00000534358.1:c.7082C>T	p.Ser2361Leu	p.S2361L	ENST00000534358	NM_005933.3	2361	tCg/tTg	27/36	1	2	FACETS	0.498	0.417	0.589	0.498	0.417	0.589	SUBCLONAL	1	TRUE	1	0.41	2		413	411	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380737	118380737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1425093050	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	33	366	0	ENST00000534358.1:c.10975C>T	p.Arg3659Trp	p.R3659W	ENST00000534358	NM_005933.3	3659	Cgg/Tgg	30/36	1	2	FACETS	0.398	0.324	0.482	0.398	0.324	0.482	SUBCLONAL	1	TRUE	1	0.41	2		366	404	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392025	118392025	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	99	435	1	ENST00000534358.1:c.11536C>A	p.Leu3846Ile	p.L3846I	ENST00000534358	NM_005933.3	3846	Ctt/Att	35/36	1	2	FACETS	0.899	0.805	0.999	0.899	0.805	0.999	CLONAL	1	TRUE	1	0.41	2		436	537	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497562	125497562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	57	239	1	ENST00000428830.2:c.126G>A	p.Met42Ile	p.M42I	ENST00000428830	NM_001114121.2	42	atG/atA	3/14	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.41	2		240	241	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416748	416748	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	55	242	0	ENST00000399788.2:c.3802G>A	p.Glu1268Lys	p.E1268K	ENST00000399788	NM_001042603.1	1268	Gaa/Aaa	23/28	1	2	FACETS	0.773	0.665	0.891	0.773	0.665	0.891	SUBCLONAL	1	TRUE	1	0.41	2		242	347	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022880	12022880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	148	615	0	ENST00000396373.4:c.986C>T	p.Ala329Val	p.A329V	ENST00000396373	NM_001987.4	329	gCc/gTc	5/8	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.41	2		615	702	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435431	18435431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	56	227	1	ENST00000266497.5:c.416C>T	p.Ser139Phe	p.S139F	ENST00000266497		139	tCc/tTc	1/31	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.41	2		228	227	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544061	18544061	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	39	217	0	ENST00000266497.5:c.1878T>A	p.Asp626Glu	p.D626E	ENST00000266497		626	gaT/gaA	13/31	1	2	FACETS	0.951	0.797	1	0.951	0.797	1	CLONAL	1	TRUE	1	0.41	2		217	200	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552608	18552609	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	25	310	0	ENST00000266497.5:c.2023dup	p.Arg675LysfsTer12	p.R675Kfs*12	ENST00000266497		673	-/A	14/31	1	2	FACETS	0.405	0.32	0.503	0.405	0.32	0.503	SUBCLONAL	1	TRUE	1	0.41	2		310	301	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123879	46123879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	74	240	0	ENST00000334344.6:c.145G>A	p.Gly49Ser	p.G49S	ENST00000334344	NM_152641.2	49	Ggt/Agt	2/21	1	2	FACETS	0.868	0.763	0.979	0.868	0.763	0.979	CLONAL	1	TRUE	1	0.41	2		240	416	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427308	49427308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777628634	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	104	498	1	ENST00000301067.7:c.11180G>A	p.Arg3727His	p.R3727H	ENST00000301067	NM_003482.3	3727	cGt/cAt	39/54	1	2	FACETS	0.884	0.794	0.979	0.884	0.794	0.979	CLONAL	1	TRUE	1	0.41	2		499	574	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431810	49431810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769315900	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	102	572	0	ENST00000301067.7:c.9329G>A	p.Arg3110His	p.R3110H	ENST00000301067	NM_003482.3	3110	cGc/cAc	34/54	1	2	FACETS	0.796	0.713	0.884	0.796	0.713	0.884	SUBCLONAL	1	TRUE	1	0.41	2		572	625	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433357	49433357	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774178055	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	86	630	0	ENST00000301067.7:c.8090G>A	p.Arg2697His	p.R2697H	ENST00000301067	NM_003482.3	2697	cGc/cAc	32/54	1	2	FACETS	0.615	0.544	0.691	0.615	0.544	0.691	SUBCLONAL	1	TRUE	1	0.41	2		630	682	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438204	49438204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761386159	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	52	684	1	ENST00000301067.7:c.5065C>T	p.Arg1689Cys	p.R1689C	ENST00000301067	NM_003482.3	1689	Cgt/Tgt	20/54	1	2	FACETS	0.277	0.235	0.324	0.277	0.235	0.324	SUBCLONAL	1	TRUE	1	0.41	2		685	915	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447880	49447880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771025627	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	50	573	0	ENST00000301067.7:c.554G>A	p.Arg185His	p.R185H	ENST00000301067	NM_003482.3	185	cGc/cAc	5/54	1	2	FACETS	0.321	0.271	0.375	0.321	0.271	0.375	SUBCLONAL	1	TRUE	1	0.41	2		573	761	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233239	69233240	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	58	264	0	ENST00000462284.1:c.1111dup	p.Thr371AsnfsTer5	p.T371Nfs*5	ENST00000462284	NM_002392.5	368	-/A	11/11	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.41	2		264	272	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856059	111856059	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242525317	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	85	238	0	ENST00000341259.2:c.110C>T	p.Ala37Val	p.A37V	ENST00000341259	NM_005475.2	37	gCg/gTg	2/8	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.41	2		238	389	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112919959	112919959	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774356443	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	79	371	0	ENST00000351677.2:c.1174G>A	p.Ala392Thr	p.A392T	ENST00000351677	NM_002834.3	392	Gcc/Acc	10/16	1	2	FACETS	0.783	0.691	0.882	0.783	0.691	0.882	SUBCLONAL	1	TRUE	1	0.41	2		371	492	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109974	115109974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1286841573	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	160	653	2	ENST00000257566.3:c.1904G>A	p.Arg635His	p.R635H	ENST00000257566	NM_016569.3	635	cGc/cAc	8/8	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.41	2		655	778	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112022	115112022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773504740	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	194	756	1	ENST00000257566.3:c.1718C>T	p.Ala573Val	p.A573V	ENST00000257566	NM_016569.3	573	gCg/gTg	7/8	1	2	FACETS	0.947	0.876	1	0.947	0.876	1	CLONAL	1	TRUE	1	0.41	2		757	999	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112154	115112154	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	137	584	2	ENST00000257566.3:c.1586del	p.Gly529AlafsTer103	p.G529Afs*103	ENST00000257566	NM_016569.3	529	gGc/gc	7/8	1	2	FACETS	0.879	0.801	0.962	0.879	0.801	0.962	CLONAL	1	TRUE	1	0.41	2		586	760	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112610	115112610	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	180	753	1	ENST00000257566.3:c.1130C>T	p.Ala377Val	p.A377V	ENST00000257566	NM_016569.3	377	gCc/gTc	7/8	1	2	FACETS	0.853	0.786	0.923	0.853	0.786	0.923	CLONAL	1	TRUE	1	0.41	2		754	1029	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118737	115118737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370362658	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	112	500	3	ENST00000257566.3:c.604G>A	p.Val202Ile	p.V202I	ENST00000257566	NM_016569.3	202	Gtc/Atc	2/8	1	2	FACETS	0.899	0.81	0.992	0.899	0.81	0.992	CLONAL	1	TRUE	1	0.41	2		503	608	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118880	115118880	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	72	377	0	ENST00000257566.3:c.461A>G	p.Asp154Gly	p.D154G	ENST00000257566	NM_016569.3	154	gAc/gGc	2/8	1	2	FACETS	0.995	0.875	1	0.995	0.875	1	CLONAL	1	TRUE	1	0.41	2		377	353	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202283	133202283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764457707	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	152	741	0	ENST00000320574.5:c.6605C>T	p.Thr2202Met	p.T2202M	ENST00000320574	NM_006231.2	2202	aCg/aTg	47/49	1	2	FACETS	0.799	0.73	0.871	0.799	0.73	0.871	SUBCLONAL	1	TRUE	1	0.41	2		741	928	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225553	133225553	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs151278283	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	50	570	1	ENST00000320574.5:c.4111C>T	p.Arg1371Ter	p.R1371*	ENST00000320574	NM_006231.2	1371	Cga/Tga	32/49	1	2	FACETS	0.323	0.273	0.378	0.323	0.273	0.378	SUBCLONAL	1	TRUE	1	0.41	2		571	756	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250214	133250214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	115	596	0	ENST00000320574.5:c.1306C>T	p.Pro436Ser	p.P436S	ENST00000320574	NM_006231.2	436	Ccc/Tcc	13/49	1	2	FACETS	0.778	0.701	0.859	0.778	0.701	0.859	SUBCLONAL	1	TRUE	1	0.41	2		596	721	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549352	21549352	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	94	602	0	ENST00000382592.4:c.2924C>T	p.Ala975Val	p.A975V	ENST00000382592	NM_014572.2	975	gCc/gTc	8/8	1	2	FACETS	0.841	0.751	0.937	0.841	0.751	0.937	CLONAL	1	TRUE	1	0.41	2		602	545	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32920978	32920978	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs80358920	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	69	344	1	ENST00000380152.3:c.6952C>T	p.Arg2318Ter	p.R2318*	ENST00000380152		2318	Cga/Tga	13/27	1	2	FACETS	0.879	0.769	0.996	0.879	0.769	0.996	CLONAL	1	TRUE	1	0.41	2		345	383	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972786	32972786	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1412762465	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	94	402	0	ENST00000380152.3:c.10136A>G	p.Tyr3379Cys	p.Y3379C	ENST00000380152		3379	tAt/tGt	27/27	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.41	2		402	409	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955573	48955573	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	19	242	0	ENST00000267163.4:c.1689G>A	p.Trp563Ter	p.W563*	ENST00000267163	NM_000321.2	563	tgG/tgA	17/27	1	2	FACETS	0.377	0.286	0.483	0.377	0.286	0.483	SUBCLONAL	1	TRUE	1	0.41	2		242	246	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73351583	73351583	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372045592	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	43	193	0	ENST00000377767.4:c.629G>A	p.Arg210His	p.R210H	ENST00000377767	NM_014953.3	210	cGt/cAt	4/21	1	2	FACETS	0.69	0.58	0.811	0.69	0.58	0.811	SUBCLONAL	1	TRUE	1	0.41	2		193	304	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514451	103514451	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	41	207	0	ENST00000355739.4:c.952T>C	p.Ser318Pro	p.S318P	ENST00000355739	NM_000123.3	318	Tct/Cct	8/15	1	2	FACETS	0.971	0.817	1	0.971	0.817	1	CLONAL	1	TRUE	1	0.41	2		207	206	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518182	103518182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	40	241	0	ENST00000355739.4:c.2120G>A	p.Arg707Lys	p.R707K	ENST00000355739	NM_000123.3	707	aGg/aAg	9/15	1	2	FACETS	0.559	0.466	0.662	0.559	0.466	0.662	SUBCLONAL	1	TRUE	1	0.41	2		241	349	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519196	103519196	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	54	284	0	ENST00000355739.4:c.2533+1G>A		p.X845_splice	ENST00000355739	NM_000123.3	845			1	2	FACETS	0.951	0.819	1	0.951	0.819	1	CLONAL	1	TRUE	1	0.41	2		284	277	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434905	110434905	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	205	702	2	ENST00000375856.3:c.3496G>A	p.Ala1166Thr	p.A1166T	ENST00000375856	NM_003749.2	1166	Gcc/Acc	1/2	1	2	FACETS	0.999	0.927	1	0.999	0.927	1	CLONAL	1	TRUE	1	0.41	2		704	1001	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435004	110435004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	179	496	1	ENST00000375856.3:c.3397G>A	p.Ala1133Thr	p.A1133T	ENST00000375856	NM_003749.2	1133	Gcc/Acc	1/2	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.41	2		497	677	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437401	110437402	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	44	189	0	ENST00000375856.3:c.999dup	p.Ser334GlnfsTer205	p.S334Qfs*205	ENST00000375856	NM_003749.2	333	-/C	1/2	1	2	FACETS	0.728	0.613	0.852	0.728	0.613	0.852	SUBCLONAL	1	TRUE	1	0.41	2		189	295	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093456	30093456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1008608681	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	60	293	0	ENST00000331968.5:c.1807C>T	p.Arg603Cys	p.R603C	ENST00000331968	NM_002742.2	603	Cgt/Tgt	13/18	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.41	2		293	275	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	69061312	69061313	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	26	117	0	ENST00000487270.1:c.1153dup	p.Ter385LeufsTer15	p.*385Lfs*15	ENST00000487270	NM_133509.3	383	att/aTtt	11/11	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.41	2		117	106	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571498	95571498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	86	343	0	ENST00000393063.1:c.3179G>A	p.Arg1060His	p.R1060H	ENST00000393063	NM_030621.3	1060	cGc/cAc	21/28	1	2	FACETS	0.78	0.691	0.874	0.78	0.691	0.874	SUBCLONAL	1	TRUE	1	0.41	2		343	538	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574729	95574729	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	54	353	0	ENST00000393063.1:c.2368C>T	p.Arg790Trp	p.R790W	ENST00000393063	NM_030621.3	790	Cgg/Tgg	16/28	1	2	FACETS	0.869	0.747	1	0.869	0.747	1	CLONAL	1	TRUE	1	0.41	2		353	303	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582083	95582083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1336108562	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	68	304	0	ENST00000393063.1:c.1828G>A	p.Val610Ile	p.V610I	ENST00000393063	NM_030621.3	610	Gtt/Att	12/28	1	2	FACETS	0.942	0.825	1	0.942	0.825	1	CLONAL	1	TRUE	1	0.41	2		304	352	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059313	42059313	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	32	326	0	ENST00000219905.7:c.9033G>A	p.Met3011Ile	p.M3011I	ENST00000219905	NM_001164273.1	3011	atG/atA	24/24	1	2	FACETS	0.407	0.33	0.493	0.407	0.33	0.493	SUBCLONAL	1	TRUE	1	0.41	2		326	384	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714099	43714099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139105949	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	195	693	0	ENST00000382044.4:c.4054G>A	p.Ala1352Thr	p.A1352T	ENST00000382044	NM_001141980.1	1352	Gca/Aca	19/28	1	2	FACETS	0.924	0.855	0.996	0.924	0.855	0.996	CLONAL	1	TRUE	1	0.41	2		693	1029	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720288	43720288	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1450516978	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	111	483	0	ENST00000382044.4:c.3754C>T	p.Arg1252Cys	p.R1252C	ENST00000382044	NM_001141980.1	1252	Cgc/Tgc	18/28	1	2	FACETS	0.907	0.817	1	0.907	0.817	1	CLONAL	1	TRUE	1	0.41	2		483	597	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43739624	43739624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	67	337	0	ENST00000382044.4:c.2776G>A	p.Ala926Thr	p.A926T	ENST00000382044	NM_001141980.1	926	Gca/Aca	13/28	1	2	FACETS	0.895	0.783	1	0.895	0.783	1	CLONAL	1	TRUE	1	0.41	2		337	365	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996182	73996182	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776412054	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	194	690	0	ENST00000318443.5:c.916G>A	p.Ala306Thr	p.A306T	ENST00000318443	NM_001024736.1	306	Gcc/Acc	5/10	1	2	FACETS	0.999	0.925	1	0.999	0.925	1	CLONAL	1	TRUE	1	0.41	2		690	947	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631661	90631661	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766888561	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	155	651	0	ENST00000330062.3:c.608G>A	p.Gly203Asp	p.G203D	ENST00000330062	NM_002168.2	203	gGt/gAt	5/11	1	2	FACETS	0.876	0.802	0.953	0.876	0.802	0.953	CLONAL	1	TRUE	1	0.41	2		651	863	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456332	99456332	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	86	411	0	ENST00000268035.6:c.1649A>G	p.Asn550Ser	p.N550S	ENST00000268035	NM_000875.3	550	aAc/aGc	8/21	1	2	FACETS	0.796	0.706	0.892	0.796	0.706	0.892	SUBCLONAL	1	TRUE	1	0.41	2		411	527	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99472802	99472802	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	123	373	0	ENST00000268035.6:c.2798T>C	p.Phe933Ser	p.F933S	ENST00000268035	NM_000875.3	933	tTc/tCc	14/21	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.41	2		373	585	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343707	343707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758124815	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	196	866	1	ENST00000262320.3:c.1967C>T	p.Thr656Met	p.T656M	ENST00000262320	NM_003502.3	656	aCg/aTg	8/11	1	2	FACETS	0.965	0.893	1	0.965	0.893	1	CLONAL	1	TRUE	1	0.41	2		867	991	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094737	2094737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750992242	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	201	740	1	ENST00000219066.1:c.443C>T	p.Ala148Val	p.A148V	ENST00000219066	NM_002528.5	148	gCg/gTg	3/6	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.41	2		741	950	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121604	2121604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746677177	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	92	678	0	ENST00000219476.3:c.1933G>A	p.Val645Ile	p.V645I	ENST00000219476	NM_000548.3	645	Gtc/Atc	18/42	1	2	FACETS	0.491	0.435	0.551	0.491	0.435	0.551	SUBCLONAL	1	TRUE	1	0.41	2		678	914	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130244	2130244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45473098	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	183	758	0	ENST00000219476.3:c.3476G>A	p.Arg1159Gln	p.R1159Q	ENST00000219476	NM_000548.3	1159	cGg/cAg	30/42	1	2	FACETS	0.968	0.894	1	0.968	0.894	1	CLONAL	1	TRUE	1	0.41	2		758	922	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130321	2130321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	79	716	1	ENST00000219476.3:c.3553G>A	p.Ala1185Thr	p.A1185T	ENST00000219476	NM_000548.3	1185	Gcc/Acc	30/42	1	2	FACETS	0.425	0.373	0.482	0.425	0.373	0.482	SUBCLONAL	1	TRUE	1	0.41	2		717	906	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213960	2213961	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs753146456	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	149	659	0	ENST00000326181.6:c.45dup	p.Pro16AlafsTer33	p.P16Afs*33	ENST00000326181	NM_032271.2	13	-/G	2/21	1	2	FACETS	0.805	0.735	0.878	0.805	0.735	0.878	CLONAL	1	TRUE	1	0.41	2		659	903	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3634827	3634827	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs543847606	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	51	701	2	ENST00000294008.3:c.4682C>T	p.Thr1561Met	p.T1561M	ENST00000294008	NM_032444.2	1561	aCg/aTg	13/15	1	2	FACETS	0.253	0.214	0.296	0.253	0.214	0.296	SUBCLONAL	1	TRUE	1	0.41	2		703	983	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3634834	3634834	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	169	656	1	ENST00000294008.3:c.4675C>T	p.Pro1559Ser	p.P1559S	ENST00000294008	NM_032444.2	1559	Ccc/Tcc	13/15	1	2	FACETS	0.882	0.81	0.956	0.882	0.81	0.956	CLONAL	1	TRUE	1	0.41	2		657	935	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639566	3639566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	66	797	0	ENST00000294008.3:c.4073C>T	p.Ala1358Val	p.A1358V	ENST00000294008	NM_032444.2	1358	gCt/gTt	12/15	1	2	FACETS	0.324	0.28	0.372	0.324	0.28	0.372	SUBCLONAL	1	TRUE	1	0.41	2		797	994	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656543	3656543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	198	705	0	ENST00000294008.3:c.692G>A	p.Cys231Tyr	p.C231Y	ENST00000294008	NM_032444.2	231	tGc/tAc	3/15	1	2	FACETS	0.985	0.912	1	0.985	0.912	1	CLONAL	1	TRUE	1	0.41	2		705	981	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3656568	3656568	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1306426498	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	203	701	0	ENST00000294008.3:c.667C>T	p.Arg223Cys	p.R223C	ENST00000294008	NM_032444.2	223	Cgt/Tgt	3/15	1	2	FACETS	0.96	0.889	1	0.96	0.889	1	CLONAL	1	TRUE	1	0.41	2		701	1032	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778708	3778708	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139169188	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	137	761	0	ENST00000262367.5:c.6340G>A	p.Gly2114Ser	p.G2114S	ENST00000262367	NM_004380.2	2114	Ggc/Agc	31/31	1	2	FACETS	0.844	0.768	0.923	0.844	0.768	0.923	CLONAL	1	TRUE	1	0.41	2		761	792	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779041	3779041	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1282498604	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	134	578	3	ENST00000262367.5:c.6007C>T	p.Pro2003Ser	p.P2003S	ENST00000262367	NM_004380.2	2003	Ccc/Tcc	31/31	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.41	2		581	598	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900759	3900759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	126	494	0	ENST00000262367.5:c.337G>A	p.Ala113Thr	p.A113T	ENST00000262367	NM_004380.2	113	Gcc/Acc	2/31	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.41	2		494	533	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900861	3900861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752992134	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	98	537	0	ENST00000262367.5:c.235G>A	p.Gly79Ser	p.G79S	ENST00000262367	NM_004380.2	79	Ggc/Agc	2/31	1	2	FACETS	0.737	0.658	0.82	0.737	0.658	0.82	SUBCLONAL	1	TRUE	1	0.41	2		537	649	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020477	14020477	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145402255	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	72	288	1	ENST00000311895.7:c.448C>T	p.Arg150Cys	p.R150C	ENST00000311895	NM_005236.2	150	Cgc/Tgc	3/11	1	2	FACETS	0.937	0.823	1	0.937	0.823	1	CLONAL	1	TRUE	1	0.41	2		289	375	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14042128	14042128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	65	259	0	ENST00000311895.7:c.2675C>T	p.Ala892Val	p.A892V	ENST00000311895	NM_005236.2	892	gCa/gTa	11/11	1	2	FACETS	0.862	0.751	0.98	0.862	0.751	0.98	CLONAL	1	TRUE	1	0.41	2		259	368	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641369	23641369	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730881886	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	178	728	0	ENST00000261584.4:c.2106A>G	p.Ile702Met	p.I702M	ENST00000261584	NM_024675.3	702	atA/atG	5/13	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.41	2		728	746	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647553	23647553	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	110	530	0	ENST00000261584.4:c.314A>G	p.Glu105Gly	p.E105G	ENST00000261584	NM_024675.3	105	gAg/gGg	4/13	1	2	FACETS	0.97	0.875	1	0.97	0.875	1	CLONAL	1	TRUE	1	0.41	2		530	553	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785686	50785686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763792744	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	115	528	0	ENST00000398568.2:c.676G>A	p.Glu226Lys	p.E226K	ENST00000398568	NM_001042412.1	226	Gaa/Aaa	4/18	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.41	2		528	560	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828327	50828327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	75	326	1	ENST00000398568.2:c.2665G>A	p.Ala889Thr	p.A889T	ENST00000398568	NM_001042412.1	889	Gcc/Acc	17/18	1	2	FACETS	0.744	0.653	0.84	0.744	0.653	0.84	SUBCLONAL	1	TRUE	1	0.41	2		327	492	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835737	68835737	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	163	519	0	ENST00000261769.5:c.328T>C	p.Phe110Leu	p.F110L	ENST00000261769	NM_004360.3	110	Ttt/Ctt	3/16	1	2	FACETS	0.952	0.875	1	0.952	0.875	1	CLONAL	1	TRUE	1	0.41	2		519	835	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842740	68842740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	88	394	0	ENST00000261769.5:c.676G>A	p.Ala226Thr	p.A226T	ENST00000261769	NM_004360.3	226	Gcc/Acc	5/16	1	2	FACETS	0.917	0.816	1	0.917	0.816	1	CLONAL	1	TRUE	1	0.41	2		394	468	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822234	72822234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs988043548	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	45	712	0	ENST00000268489.5:c.9941G>A	p.Gly3314Asp	p.G3314D	ENST00000268489	NM_006885.3	3314	gGc/gAc	10/10	1	2	FACETS	0.258	0.215	0.305	0.258	0.215	0.305	SUBCLONAL	1	TRUE	1	0.41	2		712	852	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832176	72832176	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	106	414	0	ENST00000268489.5:c.4405G>A	p.Ala1469Thr	p.A1469T	ENST00000268489	NM_006885.3	1469	Gcc/Acc	9/10	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.41	2		414	499	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845829	72845830	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	139	524	0	ENST00000268489.5:c.3637dup	p.Thr1213AsnfsTer3	p.T1213Nfs*3	ENST00000268489	NM_006885.3	1213	aca/aAca	6/10	1	2	FACETS	0.892	0.813	0.975	0.892	0.813	0.975	CLONAL	1	TRUE	1	0.41	2		524	760	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81960745	81960745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	38	528	0	ENST00000359376.3:c.2476G>A	p.Asp826Asn	p.D826N	ENST00000359376	NM_002661.3	826	Gac/Aac	23/33	1	2	FACETS	0.307	0.253	0.368	0.307	0.253	0.368	SUBCLONAL	1	TRUE	1	0.41	2		528	603	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965192	81965192	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	79	560	0	ENST00000359376.3:c.2672A>G	p.Asp891Gly	p.D891G	ENST00000359376	NM_002661.3	891	gAc/gGc	25/33	1	2	FACETS	0.472	0.415	0.534	0.472	0.415	0.534	SUBCLONAL	1	TRUE	1	0.41	2		560	816	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346867	89346867	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1387729666	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	48	285	0	ENST00000301030.4:c.6083C>T	p.Pro2028Leu	p.P2028L	ENST00000301030	NM_001256183.1	2028	cCc/cTc	9/13	1	2	FACETS	0.867	0.739	1	0.867	0.739	1	CLONAL	1	TRUE	1	0.41	2		285	270	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347732	89347732	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764052859	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	167	573	1	ENST00000301030.4:c.5218G>A	p.Ala1740Thr	p.A1740T	ENST00000301030	NM_001256183.1	1740	Gcc/Acc	9/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.41	2		574	750	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350882	89350882	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751750670	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	177	831	0	ENST00000301030.4:c.2068G>A	p.Asp690Asn	p.D690N	ENST00000301030	NM_001256183.1	690	Gat/Aat	9/13	1	2	FACETS	0.966	0.89	1	0.966	0.89	1	CLONAL	1	TRUE	1	0.41	2		831	894	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351148	89351148	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371119186	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	130	564	1	ENST00000301030.4:c.1802G>A	p.Arg601Gln	p.R601Q	ENST00000301030	NM_001256183.1	601	cGa/cAa	9/13	1	2	FACETS	0.948	0.862	1	0.948	0.862	1	CLONAL	1	TRUE	1	0.41	2		565	669	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805896	89805896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs925649874	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	46	540	0	ENST00000389301.3:c.4000G>A	p.Ala1334Thr	p.A1334T	ENST00000389301	NM_000135.2	1334	Gct/Act	40/43	1	2	FACETS	0.305	0.256	0.36	0.305	0.256	0.36	SUBCLONAL	1	TRUE	1	0.41	2		540	735	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216765	7216765	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	82	365	0	ENST00000380728.2:c.658C>T	p.Gln220Ter	p.Q220*	ENST00000380728		220	Cag/Tag	8/11	1	2	FACETS	0.883	0.782	0.991	0.883	0.782	0.991	CLONAL	1	TRUE	1	0.41	2		365	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579317	7579317	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	140	533	0	ENST00000269305.4:c.370T>C	p.Cys124Arg	p.C124R	ENST00000269305	NM_001126112.2	124	Tgc/Cgc	4/11	1	2	FACETS	0.933	0.851	1	0.933	0.851	1	CLONAL	1	TRUE	1	0.41	2		533	732	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110189	8110189	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753106886	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	101	535	0	ENST00000585124.1:c.416G>A	p.Arg139His	p.R139H	ENST00000585124	NM_004217.3	139	cGt/cAt	6/9	1	2	FACETS	0.735	0.658	0.818	0.735	0.658	0.818	SUBCLONAL	1	TRUE	1	0.41	2		535	670	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15952271	15952271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150237987	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	139	589	0	ENST00000268712.3:c.6424G>A	p.Val2142Ile	p.V2142I	ENST00000268712	NM_006311.3	2142	Gtc/Atc	41/46	1	2	FACETS	0.92	0.839	1	0.92	0.839	1	CLONAL	1	TRUE	1	0.41	2		589	737	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965207	15965207	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	73	245	0	ENST00000268712.3:c.5389C>T	p.Pro1797Ser	p.P1797S	ENST00000268712	NM_006311.3	1797	Cca/Tca	37/46	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.41	2		245	338	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049855	16049855	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	44	233	0	ENST00000268712.3:c.917A>G	p.Lys306Arg	p.K306R	ENST00000268712	NM_006311.3	306	aAa/aGa	10/46	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.41	2		233	212	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557286	29557286	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753082620	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	46	234	0	ENST00000356175.3:c.2999G>A	p.Arg1000His	p.R1000H	ENST00000356175	NM_000267.3	1000	cGt/cAt	23/57	1	2	FACETS	0.959	0.815	1	0.959	0.815	1	CLONAL	1	TRUE	1	0.41	2		234	234	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560097	29560097	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	39	248	0	ENST00000356175.3:c.3574G>T	p.Glu1192Ter	p.E1192*	ENST00000356175	NM_000267.3	1192	Gaa/Taa	27/57	1	2	FACETS	0.518	0.43	0.616	0.518	0.43	0.616	SUBCLONAL	1	TRUE	1	0.41	2		248	367	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562689	29562689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	35	413	0	ENST00000356175.3:c.3769C>T	p.Leu1257Phe	p.L1257F	ENST00000356175	NM_000267.3	1257	Ctc/Ttc	28/57	1	2	FACETS	0.332	0.272	0.4	0.332	0.272	0.4	SUBCLONAL	1	TRUE	1	0.41	2		413	514	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264510	30264510	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	23	373	0	ENST00000322652.5:c.245A>T	p.Asp82Val	p.D82V	ENST00000322652	NM_015355.2	82	gAc/gTc	1/16	1	2	FACETS	0.259	0.201	0.326	0.259	0.201	0.326	SUBCLONAL	1	TRUE	1	0.41	2		373	433	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30326004	30326005	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs769517721	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	51	255	0	ENST00000322652.5:c.2208dup	p.Gln737ThrfsTer20	p.Q737Tfs*20	ENST00000322652	NM_015355.2	734	-/A	16/16	1	2	FACETS	0.808	0.691	0.935	0.808	0.691	0.935	CLONAL	1	TRUE	1	0.41	2		255	308	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510717	38510717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	92	501	1	ENST00000254066.5:c.971C>T	p.Ala324Val	p.A324V	ENST00000254066	NM_000964.3	324	gCg/gTg	7/9	1	2	FACETS	0.84	0.749	0.937	0.84	0.749	0.937	CLONAL	1	TRUE	1	0.41	2		502	534	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353767	40353767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760771231	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	158	611	0	ENST00000293328.3:c.2353G>A	p.Ala785Thr	p.A785T	ENST00000293328	NM_012448.3	785	Gca/Aca	19/19	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.41	2		611	749	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40376882	40376882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766427008	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	61	421	1	ENST00000293328.3:c.290C>T	p.Thr97Met	p.T97M	ENST00000293328	NM_012448.3	97	aCg/aTg	4/19	1	2	FACETS	0.471	0.406	0.542	0.471	0.406	0.542	SUBCLONAL	1	TRUE	1	0.41	2		422	632	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474434	40474434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	44	427	0	ENST00000264657.5:c.1967G>A	p.Gly656Asp	p.G656D	ENST00000264657	NM_139276.2	656	gGc/gAc	21/24	1	2	FACETS	0.361	0.302	0.426	0.361	0.302	0.426	SUBCLONAL	1	TRUE	1	0.41	2		427	595	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40860050	40860050	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201655400	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	193	641	0	ENST00000428826.2:c.1586G>A	p.Arg529His	p.R529H	ENST00000428826		529	cGc/cAc	15/21	1	2	FACETS	0.993	0.919	1	0.993	0.919	1	CLONAL	1	TRUE	1	0.41	2		641	948	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40872289	40872289	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	98	514	0	ENST00000428826.2:c.664+2T>C		p.X222_splice	ENST00000428826		222			1	2	FACETS	0.809	0.723	0.9	0.809	0.723	0.9	CLONAL	1	TRUE	1	0.41	2		514	591	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40872344	40872344	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	138	659	0	ENST00000428826.2:c.611A>G	p.Asp204Gly	p.D204G	ENST00000428826		204	gAc/gGc	7/21	1	2	FACETS	0.922	0.84	1	0.922	0.84	1	CLONAL	1	TRUE	1	0.41	2		659	730	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804268	46804268	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750244360	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	161	665	0	ENST00000290295.7:c.739C>T	p.Arg247Cys	p.R247C	ENST00000290295	NM_006361.5	247	Cgc/Tgc	2/2	1	2	FACETS	0.936	0.859	1	0.936	0.859	1	CLONAL	1	TRUE	1	0.41	2		665	839	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699369	47699369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	54	356	0	ENST00000347630.2:c.139G>A	p.Glu47Lys	p.E47K	ENST00000347630	NM_001007230.1	47	Gaa/Aaa	4/11	1	2	FACETS	0.772	0.663	0.891	0.772	0.663	0.891	SUBCLONAL	1	TRUE	1	0.41	2		356	341	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120500	70120500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1319061093	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	249	884	0	ENST00000245479.2:c.1502C>T	p.Pro501Leu	p.P501L	ENST00000245479	NM_000346.3	501	cCc/cTc	3/3	1	2	FACETS	0.955	0.892	1	0.955	0.892	1	CLONAL	1	TRUE	1	0.41	2		884	1272	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727919	78727919	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	46	483	0	ENST00000306801.3:c.764T>C	p.Ile255Thr	p.I255T	ENST00000306801	NM_020761.2	255	aTc/aCc	6/34	1	2	FACETS	0.35	0.294	0.412	0.35	0.294	0.412	SUBCLONAL	1	TRUE	1	0.41	2		483	641	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78933917	78933917	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	160	607	0	ENST00000306801.3:c.3517T>C	p.Ser1173Pro	p.S1173P	ENST00000306801	NM_020761.2	1173	Tcc/Ccc	30/34	1	2	FACETS	0.943	0.865	1	0.943	0.865	1	CLONAL	1	TRUE	1	0.41	2		607	828	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78933971	78933971	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771723844	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	176	657	0	ENST00000306801.3:c.3571C>T	p.Arg1191Cys	p.R1191C	ENST00000306801	NM_020761.2	1191	Cgc/Tgc	30/34	1	2	FACETS	0.964	0.888	1	0.964	0.888	1	CLONAL	1	TRUE	1	0.41	2		657	891	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591960	48591960	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	29	294	0	ENST00000342988.3:c.1123G>A	p.Ala375Thr	p.A375T	ENST00000342988	NM_005359.5	375	Gcc/Acc	9/12	1	2	FACETS	0.41	0.329	0.502	0.41	0.329	0.502	SUBCLONAL	1	TRUE	1	0.41	2		294	345	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604739	48604739	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	84	363	0	ENST00000342988.3:c.1561A>G	p.Thr521Ala	p.T521A	ENST00000342988	NM_005359.5	521	Aca/Gca	12/12	1	2	FACETS	0.921	0.817	1	0.921	0.817	1	CLONAL	1	TRUE	1	0.41	2		363	445	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207078	1207078	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753252227	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	175	849	0	ENST00000326873.7:c.166G>A	p.Gly56Arg	p.G56R	ENST00000326873	NM_000455.4	56	Ggg/Agg	1/10	1	2	FACETS	0.951	0.876	1	0.951	0.876	1	CLONAL	1	TRUE	1	0.41	2		849	898	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207591	2207591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	143	612	0	ENST00000398665.3:c.875G>A	p.Arg292His	p.R292H	ENST00000398665	NM_032482.2	292	cGc/cAc	11/28	1	2	FACETS	0.928	0.847	1	0.928	0.847	1	CLONAL	1	TRUE	1	0.41	2		612	752	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210815	2210815	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200004531	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	130	472	0	ENST00000398665.3:c.1312G>A	p.Ala438Thr	p.A438T	ENST00000398665	NM_032482.2	438	Gct/Act	14/28	1	2	FACETS	0.965	0.878	1	0.965	0.878	1	CLONAL	1	TRUE	1	0.41	2		472	657	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4090706	4090706	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	62	670	0	ENST00000262948.5:c.1093A>G	p.Asn365Asp	p.N365D	ENST00000262948	NM_030662.3	365	Aac/Gac	11/11	1	2	FACETS	0.331	0.285	0.381	0.331	0.285	0.381	SUBCLONAL	1	TRUE	1	0.41	2		670	914	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101230	4101230	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	118	706	3	ENST00000262948.5:c.577C>T	p.Arg193Ter	p.R193*	ENST00000262948	NM_030662.3	193	Cga/Tga	5/11	1	2	FACETS	0.744	0.671	0.82	0.744	0.671	0.82	SUBCLONAL	1	TRUE	1	0.41	2		709	774	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125515	7125515	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	53	500	1	ENST00000302850.5:c.3037C>T	p.Pro1013Ser	p.P1013S	ENST00000302850	NM_000208.2	1013	Ccg/Tcg	17/22	1	2	FACETS	0.387	0.329	0.45	0.387	0.329	0.45	SUBCLONAL	1	TRUE	1	0.41	2		501	668	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132295	7132295	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs575954707	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	38	612	1	ENST00000302850.5:c.2716G>A	p.Ala906Thr	p.A906T	ENST00000302850	NM_000208.2	906	Gct/Act	14/22	1	2	FACETS	0.266	0.219	0.319	0.266	0.219	0.319	SUBCLONAL	1	TRUE	1	0.41	2		613	696	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267574	7267574	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1210993396	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	153	680	0	ENST00000302850.5:c.434G>A	p.Arg145His	p.R145H	ENST00000302850	NM_000208.2	145	cGc/cAc	2/22	1	2	FACETS	0.88	0.805	0.958	0.88	0.805	0.958	CLONAL	1	TRUE	1	0.41	2		680	848	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246949	10246949	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	200	601	3	ENST00000340748.4:c.4456G>A	p.Asp1486Asn	p.D1486N	ENST00000340748		1486	Gac/Aac	37/40	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.41	2		604	885	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265415	10265415	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568234601	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	159	677	1	ENST00000340748.4:c.1631G>A	p.Arg544His	p.R544H	ENST00000340748		544	cGc/cAc	20/40	1	2	FACETS	0.848	0.777	0.922	0.848	0.777	0.922	CLONAL	1	TRUE	1	0.41	2		678	915	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610306	10610306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	219	789	1	ENST00000171111.5:c.404G>A	p.Arg135His	p.R135H	ENST00000171111	NM_203500.1	135	cGc/cAc	2/6	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.41	2		790	1032	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610427	10610427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	178	648	0	ENST00000171111.5:c.283G>A	p.Ala95Thr	p.A95T	ENST00000171111	NM_203500.1	95	Gcc/Acc	2/6	1	2	FACETS	0.988	0.911	1	0.988	0.911	1	CLONAL	1	TRUE	1	0.41	2		648	879	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097117	11097117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780497718	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	122	607	2	ENST00000358026.2:c.608C>T	p.Ala203Val	p.A203V	ENST00000358026	NM_001128849.1	203	gCg/gTg	4/36	1	2	FACETS	0.887	0.803	0.975	0.887	0.803	0.975	CLONAL	1	TRUE	1	0.41	2		609	671	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097672	11097672	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	151	727	0	ENST00000358026.2:c.852G>A	p.Trp284Ter	p.W284*	ENST00000358026	NM_001128849.1	284	tgG/tgA	5/36	1	2	FACETS	0.834	0.763	0.909	0.834	0.763	0.909	CLONAL	1	TRUE	1	0.41	2		727	883	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118684	11118684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550731833	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	97	667	0	ENST00000358026.2:c.2108C>T	p.Ala703Val	p.A703V	ENST00000358026	NM_001128849.1	703	gCg/gTg	14/36	1	2	FACETS	0.498	0.443	0.557	0.498	0.443	0.557	SUBCLONAL	1	TRUE	1	0.41	2		667	950	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132633	11132633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217938288	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	161	676	0	ENST00000358026.2:c.2849C>T	p.Thr950Ile	p.T950I	ENST00000358026	NM_001128849.1	950	aCc/aTc	19/36	1	2	FACETS	0.879	0.807	0.955	0.879	0.807	0.955	CLONAL	1	TRUE	1	0.41	2		676	893	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138539	11138539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	65	589	1	ENST00000358026.2:c.3295G>A	p.Val1099Met	p.V1099M	ENST00000358026	NM_001128849.1	1099	Gtg/Atg	24/36	1	2	FACETS	0.397	0.343	0.455	0.397	0.343	0.455	SUBCLONAL	1	TRUE	1	0.41	2		590	799	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145759	11145759	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502070	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	139	787	3	ENST00000358026.2:c.4121G>A	p.Arg1374His	p.R1374H	ENST00000358026	NM_001128849.1	1374	cGc/cAc	29/36	1	2	FACETS	0.793	0.722	0.868	0.793	0.722	0.868	SUBCLONAL	1	TRUE	1	0.41	2		790	855	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272378	15272378	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199620476	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	83	863	1	ENST00000263388.2:c.6061G>A	p.Val2021Met	p.V2021M	ENST00000263388	NM_000435.2	2021	Gtg/Atg	33/33	1	2	FACETS	0.383	0.336	0.432	0.383	0.336	0.432	SUBCLONAL	1	TRUE	1	0.41	2		864	1058	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276310	15276310	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369768722	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	60	680	1	ENST00000263388.2:c.5684G>A	p.Arg1895His	p.R1895H	ENST00000263388	NM_000435.2	1895	cGc/cAc	31/33	1	2	FACETS	0.357	0.307	0.412	0.357	0.307	0.412	SUBCLONAL	1	TRUE	1	0.41	2		681	820	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281305	15281305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	95	604	0	ENST00000263388.2:c.4951G>A	p.Ala1651Thr	p.A1651T	ENST00000263388	NM_000435.2	1651	Gct/Act	27/33	1	2	FACETS	0.577	0.513	0.645	0.577	0.513	0.645	SUBCLONAL	1	TRUE	1	0.41	2		604	803	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296155	15296155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754815179	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	162	828	0	ENST00000263388.2:c.2209G>A	p.Ala737Thr	p.A737T	ENST00000263388	NM_000435.2	737	Gcc/Acc	14/33	1	2	FACETS	0.815	0.747	0.885	0.815	0.747	0.885	CLONAL	1	TRUE	1	0.41	2		828	970	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297773	15297773	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	197	713	0	ENST00000263388.2:c.1867G>A	p.Asp623Asn	p.D623N	ENST00000263388	NM_000435.2	623	Gac/Aac	12/33	1	2	FACETS	0.953	0.882	1	0.953	0.882	1	CLONAL	1	TRUE	1	0.41	2		713	1008	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349736	15349736	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755237120	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	131	676	0	ENST00000263377.2:c.3838C>T	p.Arg1280Cys	p.R1280C	ENST00000263377	NM_058243.2	1280	Cgt/Tgt	19/20	1	2	FACETS	0.94	0.854	1	0.94	0.854	1	CLONAL	1	TRUE	1	0.41	2		676	680	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937713	17937713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752088869	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	136	485	0	ENST00000458235.1:c.3214G>A	p.Glu1072Lys	p.E1072K	ENST00000458235	NM_000215.3	1072	Gag/Aag	24/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.41	2		485	591	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274154	18274154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763448968	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	137	626	0	ENST00000222254.8:c.1372C>T	p.Arg458Cys	p.R458C	ENST00000222254	NM_005027.3	458	Cgc/Tgc	11/16	1	2	FACETS	0.756	0.687	0.828	0.756	0.687	0.828	SUBCLONAL	1	TRUE	1	0.41	2		626	884	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257856	19257856	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	200	894	1	ENST00000162023.5:c.530C>T	p.Ala177Val	p.A177V	ENST00000162023		177	gCc/gTc	9/13	1	2	FACETS	0.974	0.902	1	0.974	0.902	1	CLONAL	1	TRUE	1	0.41	2		895	1002	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210440	36210440	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	113	546	0	ENST00000222270.7:c.433C>T	p.Arg145Ter	p.R145*	ENST00000222270	NM_014727.1	145	Cga/Tga	2/37	1	2	FACETS	0.823	0.741	0.909	0.823	0.741	0.909	CLONAL	1	TRUE	1	0.41	2		546	670	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212411	36212412	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	173	718	0	ENST00000222270.7:c.2162_2163insA	p.His722SerfsTer124	p.H722Sfs*124	ENST00000222270	NM_014727.1	721	cct/ccAt	3/37	1	2	FACETS	0.969	0.892	1	0.969	0.892	1	CLONAL	1	TRUE	1	0.41	2		718	871	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215906	36215906	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	186	689	0	ENST00000222270.7:c.3446G>A	p.Gly1149Asp	p.G1149D	ENST00000222270	NM_014727.1	1149	gGc/gAc	10/37	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.41	2		689	887	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216703	36216703	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866662490	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	61	482	2	ENST00000222270.7:c.3869G>A	p.Arg1290His	p.R1290H	ENST00000222270	NM_014727.1	1290	cGc/cAc	13/37	1	2	FACETS	0.438	0.377	0.504	0.438	0.377	0.504	SUBCLONAL	1	TRUE	1	0.41	2		484	680	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726691	41726691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776776986	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	157	691	1	ENST00000301178.4:c.236C>T	p.Ala79Val	p.A79V	ENST00000301178	NM_021913.4	79	gCg/gTg	2/20	1	2	FACETS	0.903	0.828	0.982	0.903	0.828	0.982	CLONAL	1	TRUE	1	0.41	2		692	848	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752649	42752649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	155	586	0	ENST00000222329.4:c.1615G>A	p.Ala539Thr	p.A539T	ENST00000222329	NM_006494.2	539	Gcc/Acc	4/4	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.41	2		586	685	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753836	42753836	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1250639908	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	216	870	1	ENST00000222329.4:c.428G>A	p.Arg143His	p.R143H	ENST00000222329	NM_006494.2	143	cGc/cAc	4/4	1	2	FACETS	0.924	0.858	0.993	0.924	0.858	0.993	CLONAL	1	TRUE	1	0.41	2		871	1140	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794623	42794623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564532974	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	135	675	2	ENST00000575354.2:c.1703C>T	p.Ala568Val	p.A568V	ENST00000575354	NM_015125.3	568	gCg/gTg	10/20	1	2	FACETS	0.826	0.751	0.905	0.826	0.751	0.905	CLONAL	1	TRUE	1	0.41	2		677	797	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794979	42794979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749021269	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	163	641	1	ENST00000575354.2:c.2059G>A	p.Ala687Thr	p.A687T	ENST00000575354	NM_015125.3	687	Gcc/Acc	10/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.41	2		642	738	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905151	50905151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137953986	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	92	870	1	ENST00000440232.2:c.433G>A	p.Ala145Thr	p.A145T	ENST00000440232	NM_002691.3	145	Gct/Act	4/27	1	2	FACETS	0.405	0.359	0.455	0.405	0.359	0.455	SUBCLONAL	1	TRUE	1	0.41	2		871	1107	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909745	50909745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753244422	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	204	846	0	ENST00000440232.2:c.1465G>A	p.Val489Met	p.V489M	ENST00000440232	NM_002691.3	489	Gtg/Atg	12/27	1	2	FACETS	0.98	0.909	1	0.98	0.909	1	CLONAL	1	TRUE	1	0.41	2		846	1015	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918798	50918798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555793052	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	177	852	3	ENST00000440232.2:c.2668G>A	p.Ala890Thr	p.A890T	ENST00000440232	NM_002691.3	890	Gcg/Acg	21/27	1	2	FACETS	0.995	0.917	1	0.995	0.917	1	CLONAL	1	TRUE	1	0.41	2		855	868	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714687	52714687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	45	651	1	ENST00000322088.6:c.445G>A	p.Gly149Ser	p.G149S	ENST00000322088	NM_014225.5	149	Ggc/Agc	4/15	1	2	FACETS	0.258	0.216	0.305	0.258	0.216	0.305	SUBCLONAL	1	TRUE	1	0.41	2		652	850	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965049	25965049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780551383	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	109	424	0	ENST00000435504.4:c.4157C>T	p.Ala1386Val	p.A1386V	ENST00000435504		1386	gCg/gTg	13/13	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.41	2		424	498	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27016049	27016049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756721845	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	112	548	1	ENST00000335756.4:c.325G>A	p.Ala109Thr	p.A109T	ENST00000335756	NM_001809.3	109	Gcc/Acc	4/5	1	2	FACETS	0.779	0.702	0.862	0.779	0.702	0.862	SUBCLONAL	1	TRUE	1	0.41	2		549	701	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445273	29445273	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs113994091	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	106	553	0	ENST00000389048.3:c.3452C>T	p.Thr1151Met	p.T1151M	ENST00000389048	NM_004304.4	1151	aCg/aTg	22/29	1	2	FACETS	0.862	0.774	0.954	0.862	0.774	0.954	CLONAL	1	TRUE	1	0.41	2		553	600	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285891	39285891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	68	392	0	ENST00000402219.2:c.268G>A	p.Ala90Thr	p.A90T	ENST00000402219	NM_005633.3	90	Gcc/Acc	3/23	1	2	FACETS	0.855	0.747	0.97	0.855	0.747	0.97	CLONAL	1	TRUE	1	0.41	2		392	388	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672741	47672741	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs557339938	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	94	474	0	ENST00000233146.2:c.1331G>A	p.Arg444His	p.R444H	ENST00000233146	NM_000251.2	444	cGt/cAt	8/16	1	2	FACETS	0.915	0.817	1	0.915	0.817	1	CLONAL	1	TRUE	1	0.41	2		474	501	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026204	48026204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750440	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	72	309	0	ENST00000234420.5:c.1082G>A	p.Arg361His	p.R361H	ENST00000234420	NM_000179.2	361	cGc/cAc	4/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.41	2		309	314	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030613	48030613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779617676	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	91	431	2	ENST00000234420.5:c.3227G>A	p.Arg1076His	p.R1076H	ENST00000234420	NM_000179.2	1076	cGc/cAc	5/10	1	2	FACETS	0.83	0.739	0.926	0.83	0.739	0.926	CLONAL	1	TRUE	1	0.41	2		433	535	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149023	61149023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	98	338	0	ENST00000295025.8:c.1213G>A	p.Ala405Thr	p.A405T	ENST00000295025	NM_002908.2	405	Gca/Aca	11/11	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.41	2		338	449	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149558	61149558	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	69	316	0	ENST00000295025.8:c.1748G>A	p.Ser583Asn	p.S583N	ENST00000295025	NM_002908.2	583	aGt/aAt	11/11	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.41	2		316	315	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920597	96920597	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779277417	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	88	385	0	ENST00000258439.3:c.383G>A	p.Arg128His	p.R128H	ENST00000258439	NM_001193304.2	128	cGc/cAc	3/4	1	2	FACETS	0.908	0.807	1	0.908	0.807	1	CLONAL	1	TRUE	1	0.41	2		385	473	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128028933	128028933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759338358	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	121	555	0	ENST00000285398.2:c.1924C>T	p.Arg642Trp	p.R642W	ENST00000285398	NM_000122.1	642	Cgg/Tgg	12/15	1	2	FACETS	0.81	0.732	0.891	0.81	0.732	0.891	CLONAL	1	TRUE	1	0.41	2		555	729	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098965	178098965	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	43	239	0	ENST00000397062.3:c.80A>C	p.Asp27Ala	p.D27A	ENST00000397062	NM_006164.4	27	gAt/gCt	2/5	1	2	FACETS	0.819	0.691	0.96	0.819	0.691	0.96	CLONAL	1	TRUE	1	0.41	2		239	256	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719556	190719556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	33	162	0	ENST00000441310.2:c.1558C>T	p.Pro520Ser	p.P520S	ENST00000441310	NM_000534.4	520	Cct/Tct	9/13	1	2	FACETS	0.805	0.661	0.963	0.805	0.661	0.963	CLONAL	1	TRUE	1	0.41	2		162	200	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212530055	212530055	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	61	203	0	ENST00000342788.4:c.1864A>G	p.Thr622Ala	p.T622A	ENST00000342788	NM_005235.2	622	Acc/Gcc	15/28	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.41	2		203	269	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645489	215645489	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881416	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	103	512	1	ENST00000260947.4:c.1109G>A	p.Arg370His	p.R370H	ENST00000260947	NM_000465.2	370	cGt/cAt	4/11	1	2	FACETS	0.915	0.822	1	0.915	0.822	1	CLONAL	1	TRUE	1	0.41	2		513	549	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342967	225342967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	77	409	1	ENST00000264414.4:c.2125C>T	p.Arg709Trp	p.R709W	ENST00000264414	NM_003590.4	709	Cgg/Tgg	15/16	1	2	FACETS	0.874	0.77	0.984	0.874	0.77	0.984	CLONAL	1	TRUE	1	0.41	2		410	430	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370818	225370818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs983814335	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	76	342	1	ENST00000264414.4:c.1061G>A	p.Arg354His	p.R354H	ENST00000264414	NM_003590.4	354	cGc/cAc	8/16	1	2	FACETS	0.934	0.823	1	0.934	0.823	1	CLONAL	1	TRUE	1	0.41	2		343	397	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371691	225371691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	99	478	0	ENST00000264414.4:c.913C>T	p.Arg305Cys	p.R305C	ENST00000264414	NM_003590.4	305	Cgt/Tgt	7/16	1	2	FACETS	0.958	0.859	1	0.958	0.859	1	CLONAL	1	TRUE	1	0.41	2		478	504	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662253	227662253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	149	714	0	ENST00000305123.5:c.1202G>A	p.Gly401Asp	p.G401D	ENST00000305123	NM_005544.2	401	gGc/gAc	1/2	1	2	FACETS	0.934	0.855	1	0.934	0.855	1	CLONAL	1	TRUE	1	0.41	2		714	778	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525054	9525054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	37	383	0	ENST00000353224.5:c.1831G>A	p.Ala611Thr	p.A611T	ENST00000353224	NM_177990.2	611	Gcc/Acc	8/10	1	2	FACETS	0.336	0.276	0.403	0.336	0.276	0.403	SUBCLONAL	1	TRUE	1	0.41	2		383	537	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624936	9624936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760501160	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	88	316	1	ENST00000353224.5:c.41C>T	p.Pro14Leu	p.P14L	ENST00000353224	NM_177990.2	14	cCg/cTg	3/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.41	2		317	394	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023920	31023920	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	47	583	0	ENST00000375687.4:c.3405A>C	p.Gln1135His	p.Q1135H	ENST00000375687	NM_015338.5	1135	caA/caC	13/13	1	2	FACETS	0.362	0.304	0.425	0.362	0.304	0.425	SUBCLONAL	1	TRUE	1	0.41	2		583	634	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374324	31374324	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	126	507	0	ENST00000328111.2:c.323A>G	p.Asn108Ser	p.N108S	ENST00000328111	NM_006892.3	108	aAc/aGc	5/23	1	2	FACETS	0.998	0.906	1	0.998	0.906	1	CLONAL	1	TRUE	1	0.41	2		507	616	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375211	31375211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147945634	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	177	695	1	ENST00000328111.2:c.608C>T	p.Pro203Leu	p.P203L	ENST00000328111	NM_006892.3	203	cCg/cTg	6/23	1	2	FACETS	0.93	0.857	1	0.93	0.857	1	CLONAL	1	TRUE	1	0.41	2		696	928	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388006	31388006	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908943	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	63	332	0	ENST00000328111.2:c.1807G>A	p.Ala603Thr	p.A603T	ENST00000328111	NM_006892.3	603	Gct/Act	17/23	1	2	FACETS	0.73	0.633	0.834	0.73	0.633	0.834	SUBCLONAL	1	TRUE	1	0.41	2		332	421	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012617	36012617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367543238	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	78	301	3	ENST00000358208.4:c.61G>A	p.Ala21Thr	p.A21T	ENST00000358208		21	Gcc/Acc	2/12	1	2	FACETS	0.869	0.767	0.977	0.869	0.767	0.977	CLONAL	1	TRUE	1	0.41	2		304	438	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713386	40713386	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	141	867	0	ENST00000373198.4:c.4129C>T	p.Arg1377Ter	p.R1377*	ENST00000373198	NM_133170.3	1377	Cga/Tga	30/32	1	2	FACETS	0.832	0.758	0.909	0.832	0.758	0.909	CLONAL	1	TRUE	1	0.41	2		867	827	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306640	41306640	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs774033275	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	141	654	0	ENST00000373198.4:c.1019T>C	p.Val340Ala	p.V340A	ENST00000373198	NM_133170.3	340	gTc/gCc	7/32	1	2	FACETS	0.858	0.782	0.937	0.858	0.782	0.937	CLONAL	1	TRUE	1	0.41	2		654	802	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958197	54958197	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752948413	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	74	392	0	ENST00000312783.6:c.410G>A	p.Arg137His	p.R137H	ENST00000312783	NM_198436.1	137	cGc/cAc	6/10	1	2	FACETS	0.808	0.71	0.912	0.808	0.71	0.912	CLONAL	1	TRUE	1	0.41	2		392	447	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62292822	62292822	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1404412328	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	74	313	1	ENST00000360203.5:c.274G>A	p.Ala92Thr	p.A92T	ENST00000360203	NM_001283009.1	92	Gct/Act	3/35	1	2	FACETS	0.909	0.8	1	0.909	0.8	1	CLONAL	1	TRUE	1	0.41	2		314	397	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62320469	62320469	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs535749230	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	137	584	0	ENST00000360203.5:c.1862C>T	p.Ala621Val	p.A621V	ENST00000360203	NM_001283009.1	621	gCg/gTg	22/35	1	2	FACETS	0.937	0.854	1	0.937	0.854	1	CLONAL	1	TRUE	1	0.41	2		584	713	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62325731	62325731	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201560152	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	122	563	1	ENST00000360203.5:c.2999C>T	p.Thr1000Met	p.T1000M	ENST00000360203	NM_001283009.1	1000	aCg/aTg	31/35	1	2	FACETS	0.86	0.778	0.946	0.86	0.778	0.946	CLONAL	1	TRUE	1	0.41	2		564	692	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860344	42860344	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	68	611	0	ENST00000398585.3:c.533G>A	p.Gly178Asp	p.G178D	ENST00000398585	NM_001135099.1	178	gGc/gAc	5/14	1	2	FACETS	0.387	0.335	0.442	0.387	0.335	0.442	SUBCLONAL	1	TRUE	1	0.41	2		611	858	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514850	44514850	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	114	469	0	ENST00000291552.4:c.397C>T	p.Arg133Cys	p.R133C	ENST00000291552	NM_006758.2	133	Cgt/Tgt	6/8	1	2	FACETS	0.85	0.767	0.938	0.85	0.767	0.938	CLONAL	1	TRUE	1	0.41	2		469	654	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655272	45655272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764295138	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	189	699	1	ENST00000407780.3:c.580C>T	p.Arg194Trp	p.R194W	ENST00000407780	NM_001283052.1	194	Cgg/Tgg	4/7	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.41	2		700	917	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288141	21288141	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	93	460	1	ENST00000354336.3:c.386G>A	p.Arg129Gln	p.R129Q	ENST00000354336	NM_005207.3	129	cGg/cAg	2/3	1	2	FACETS	0.8	0.713	0.893	0.8	0.713	0.893	SUBCLONAL	1	TRUE	1	0.41	2		461	567	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627979	37627979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780585104	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	159	669	1	ENST00000249071.6:c.281G>A	p.Arg94His	p.R94H	ENST00000249071	NM_002872.4	94	cGc/cAc	4/7	1	2	FACETS	0.906	0.831	0.985	0.906	0.831	0.985	CLONAL	1	TRUE	1	0.41	2		670	856	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523587	41523587	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	153	489	1	ENST00000263253.7:c.1003C>T	p.Arg335Cys	p.R335C	ENST00000263253	NM_001429.3	335	Cgc/Tgc	4/31	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.41	2		490	736	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41526007	41526007	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs201341021	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	62	319	0	ENST00000263253.7:c.1282C>T	p.Pro428Ser	p.P428S	ENST00000263253	NM_001429.3	428	Cca/Tca	5/31	1	2	FACETS	0.869	0.755	0.991	0.869	0.755	0.991	CLONAL	1	TRUE	1	0.41	2		319	348	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527619	41527619	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	83	366	0	ENST00000263253.7:c.1510C>T	p.Arg504Trp	p.R504W	ENST00000263253	NM_001429.3	504	Cgg/Tgg	6/31	1	2	FACETS	0.863	0.765	0.968	0.863	0.765	0.968	CLONAL	1	TRUE	1	0.41	2		366	469	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458342	12458342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	135	588	1	ENST00000287820.6:c.959C>T	p.Ala320Val	p.A320V	ENST00000287820	NM_015869.4	320	gCt/gTt	6/7	1	2	FACETS	0.853	0.776	0.934	0.853	0.776	0.934	CLONAL	1	TRUE	1	0.41	2		589	772	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641739	12641739	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	132	496	0	ENST00000251849.4:c.902G>A	p.Ser301Asn	p.S301N	ENST00000251849	NM_002880.3	301	aGc/aAc	9/17	1	2	FACETS	0.892	0.811	0.977	0.892	0.811	0.977	CLONAL	1	TRUE	1	0.41	2		496	722	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713667	30713667	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1332138742	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	97	478	0	ENST00000295754.5:c.992G>A	p.Gly331Asp	p.G331D	ENST00000295754	NM_003242.5	331	gGc/gAc	4/7	1	2	FACETS	0.854	0.764	0.95	0.854	0.764	0.95	CLONAL	1	TRUE	1	0.41	2		478	554	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180195	38180195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167556183	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	91	444	0	ENST00000396334.3:c.43G>A	p.Ala15Thr	p.A15T	ENST00000396334	NM_002468.4	15	Gct/Act	1/5	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.41	2		444	432	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098816	47098816	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	163	643	0	ENST00000409792.3:c.6458A>C	p.Asp2153Ala	p.D2153A	ENST00000409792	NM_014159.6	2153	gAc/gCc	15/21	1	2	FACETS	0.948	0.87	1	0.948	0.87	1	CLONAL	1	TRUE	1	0.41	2		643	839	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164763	47164763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	60	324	0	ENST00000409792.3:c.1363G>A	p.Ala455Thr	p.A455T	ENST00000409792	NM_014159.6	455	Gca/Aca	3/21	1	2	FACETS	0.811	0.702	0.928	0.811	0.702	0.928	CLONAL	1	TRUE	1	0.41	2		324	361	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165270	47165270	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1176819692	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	47	295	0	ENST00000409792.3:c.856A>G	p.Ile286Val	p.I286V	ENST00000409792	NM_014159.6	286	Att/Gtt	3/21	1	2	FACETS	0.913	0.777	1	0.913	0.777	1	CLONAL	1	TRUE	1	0.41	2		295	251	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723034	49723034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771296103	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	96	385	0	ENST00000449682.2:c.1382G>A	p.Arg461His	p.R461H	ENST00000449682	NM_020998.3	461	cGc/cAc	11/18	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.41	2		385	450	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932797	49932797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	172	729	0	ENST00000296474.3:c.3074C>T	p.Ala1025Val	p.A1025V	ENST00000296474	NM_002447.2	1025	gCc/gTc	14/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.41	2		729	760	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940385	49940385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771132053	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	98	625	1	ENST00000296474.3:c.658C>T	p.Arg220Cys	p.R220C	ENST00000296474	NM_002447.2	220	Cgt/Tgt	1/20	1	2	FACETS	0.53	0.472	0.592	0.53	0.472	0.592	SUBCLONAL	1	TRUE	1	0.41	2		626	902	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008542	70008542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202020443	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	113	332	0	ENST00000394351.3:c.829G>A	p.Ala277Thr	p.A277T	ENST00000394351	NM_000248.3	277	Gcc/Acc	8/9	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.41	2		332	535	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528645	89528645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	65	200	0	ENST00000336596.2:c.2945C>T	p.Pro982Leu	p.P982L	ENST00000336596	NM_005233.5	982	cCc/cTc	17/17	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.41	2		200	265	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205019	128205019	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	115	572	0	ENST00000341105.2:c.422A>G	p.Tyr141Cys	p.Y141C	ENST00000341105	NM_032638.4	141	tAc/tGc	3/6	1	2	FACETS	0.964	0.871	1	0.964	0.871	1	CLONAL	1	TRUE	1	0.41	2		572	582	SUCCESS
ATR	545	MSKCC	GRCh37	3	142168414	142168414	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	52	305	0	ENST00000350721.4:c.7792C>T	p.Arg2598Ter	p.R2598*	ENST00000350721	NM_001184.3	2598	Cga/Tga	47/47	1	2	FACETS	0.821	0.703	0.948	0.821	0.703	0.948	CLONAL	1	TRUE	1	0.41	2		305	309	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183540	185183540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	53	263	0	ENST00000265026.3:c.1394C>T	p.Ala465Val	p.A465V	ENST00000265026	NM_004721.4	465	gCg/gTg	9/14	1	2	FACETS	0.816	0.7	0.941	0.816	0.7	0.941	CLONAL	1	TRUE	1	0.41	2		263	317	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801476	1801476	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs200300532	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	129	783	0	ENST00000260795.2:c.382G>A	p.Ala128Thr	p.A128T	ENST00000260795		128	Gct/Act	3/17	1	2	FACETS	0.71	0.643	0.781	0.71	0.643	0.781	SUBCLONAL	1	TRUE	1	0.41	2		783	886	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1959734	1959734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	81	263	0	ENST00000382891.5:c.2956C>T	p.Arg986Cys	p.R986C	ENST00000382891	NM_133335.3	986	Cgc/Tgc	16/22	1	2	FACETS	0.957	0.847	1	0.957	0.847	1	CLONAL	1	TRUE	1	0.41	2		263	413	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133523	55133523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142492533	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	114	452	1	ENST00000257290.5:c.827C>T	p.Thr276Met	p.T276M	ENST00000257290	NM_006206.4	276	aCg/aTg	6/23	1	2	FACETS	0.936	0.845	1	0.936	0.845	1	CLONAL	1	TRUE	1	0.41	2		453	594	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133767	55133767	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	100	413	0	ENST00000257290.5:c.980T>C	p.Val327Ala	p.V327A	ENST00000257290	NM_006206.4	327	gTc/gCc	7/23	1	2	FACETS	0.991	0.89	1	0.991	0.89	1	CLONAL	1	TRUE	1	0.41	2		413	492	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55597574	55597574	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	58	333	0	ENST00000288135.5:c.2222C>A	p.Ser741Tyr	p.S741Y	ENST00000288135	NM_000222.2	741	tCt/tAt	15/21	1	2	FACETS	0.818	0.706	0.938	0.818	0.706	0.938	CLONAL	1	TRUE	1	0.41	2		333	346	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953773	55953773	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	80	378	0	ENST00000263923.4:c.3662+1G>A		p.X1221_splice	ENST00000263923	NM_002253.2	1221			1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.41	2		378	379	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979612	55979612	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	97	441	0	ENST00000263923.4:c.835A>C	p.Thr279Pro	p.T279P	ENST00000263923	NM_002253.2	279	Acc/Ccc	7/30	1	2	FACETS	0.905	0.809	1	0.905	0.809	1	CLONAL	1	TRUE	1	0.41	2		441	523	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230823	66230824	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	46	359	0	ENST00000273854.3:c.2147dup	p.Gln717AlafsTer8	p.Q717Afs*8	ENST00000273854	NM_004439.5	716	aag/aaAg	12/18	1	2	FACETS	0.779	0.66	0.909	0.779	0.66	0.909	CLONAL	1	TRUE	1	0.41	2		359	288	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242734	66242734	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	75	297	0	ENST00000273854.3:c.1838C>T	p.Ala613Val	p.A613V	ENST00000273854	NM_004439.5	613	gCc/gTc	9/18	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.41	2		297	363	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280056	66280056	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	16	241	0	ENST00000273854.3:c.1633G>T	p.Ala545Ser	p.A545S	ENST00000273854	NM_004439.5	545	Gca/Tca	7/18	1	2	FACETS	0.286	0.211	0.375	0.286	0.211	0.375	SUBCLONAL	1	TRUE	1	0.41	2		241	273	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467472	66467472	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	22	255	1	ENST00000273854.3:c.797C>A	p.Ser266Tyr	p.S266Y	ENST00000273854	NM_004439.5	266	tCt/tAt	3/18	1	2	FACETS	0.308	0.239	0.389	0.308	0.239	0.389	SUBCLONAL	1	TRUE	1	0.41	2		256	348	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155305	106155305	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	68	343	0	ENST00000380013.4:c.206G>A	p.Ser69Asn	p.S69N	ENST00000380013	NM_001127208.2	69	aGc/aAc	3/11	1	2	FACETS	0.878	0.767	0.995	0.878	0.767	0.995	CLONAL	1	TRUE	1	0.41	2		343	378	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164916	106164916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1361899165	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	93	308	1	ENST00000380013.4:c.3784C>T	p.Arg1262Trp	p.R1262W	ENST00000380013	NM_001127208.2	1262	Cgg/Tgg	6/11	1	2	FACETS	0.898	0.802	1	0.898	0.802	1	CLONAL	1	TRUE	1	0.41	2		309	505	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196249	106196249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	38	211	0	ENST00000380013.4:c.4582C>T	p.Pro1528Ser	p.P1528S	ENST00000380013	NM_001127208.2	1528	Ccc/Tcc	11/11	1	2	FACETS	0.721	0.6	0.855	0.721	0.6	0.855	SUBCLONAL	1	TRUE	1	0.41	2		211	257	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143043320	143043320	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	81	334	0	ENST00000262992.4:c.2096C>T	p.Ala699Val	p.A699V	ENST00000262992	NM_001101669.1	699	gCc/gTc	19/24	1	2	FACETS	0.995	0.882	1	0.995	0.882	1	CLONAL	1	TRUE	1	0.41	2		334	397	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332496	153332496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138477494	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	78	352	0	ENST00000281708.4:c.460G>A	p.Val154Ile	p.V154I	ENST00000281708	NM_033632.3	154	Gtt/Att	2/12	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.41	2		352	374	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539527	187539527	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	67	323	0	ENST00000441802.2:c.8213T>C	p.Val2738Ala	p.V2738A	ENST00000441802	NM_005245.3	2738	gTc/gCc	10/27	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.41	2		323	293	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541826	187541826	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	80	373	0	ENST00000441802.2:c.5914A>T	p.Ser1972Cys	p.S1972C	ENST00000441802	NM_005245.3	1972	Agc/Tgc	10/27	1	2	FACETS	0.881	0.779	0.99	0.881	0.779	0.99	CLONAL	1	TRUE	1	0.41	2		373	443	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541861	187541861	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	38	377	0	ENST00000441802.2:c.5879C>T	p.Ala1960Val	p.A1960V	ENST00000441802	NM_005245.3	1960	gCc/gTc	10/27	1	2	FACETS	0.338	0.278	0.404	0.338	0.278	0.404	SUBCLONAL	1	TRUE	1	0.41	2		377	549	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549695	187549695	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	78	364	0	ENST00000441802.2:c.4546A>G	p.Thr1516Ala	p.T1516A	ENST00000441802	NM_005245.3	1516	Act/Gct	8/27	1	2	FACETS	0.831	0.733	0.935	0.831	0.733	0.935	CLONAL	1	TRUE	1	0.41	2		364	458	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630921	187630921	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	46	427	0	ENST00000441802.2:c.61A>G	p.Ser21Gly	p.S21G	ENST00000441802	NM_005245.3	21	Agt/Ggt	2/27	1	2	FACETS	0.399	0.335	0.469	0.399	0.335	0.469	SUBCLONAL	1	TRUE	1	0.41	2		427	563	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1268689	1268689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	179	777	0	ENST00000310581.5:c.2528G>A	p.Ser843Asn	p.S843N	ENST00000310581	NM_198253.2	843	aGc/aAc	9/16	1	2	FACETS	0.904	0.833	0.978	0.904	0.833	0.978	CLONAL	1	TRUE	1	0.41	2		777	966	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278755	1278755	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	121	538	0	ENST00000310581.5:c.2286+1G>A		p.X762_splice	ENST00000310581	NM_198253.2	762			1	2	FACETS	0.799	0.722	0.879	0.799	0.722	0.879	SUBCLONAL	1	TRUE	1	0.41	2		538	739	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278818	1278818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs939537185	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	169	680	0	ENST00000310581.5:c.2224C>T	p.Arg742Cys	p.R742C	ENST00000310581	NM_198253.2	742	Cgt/Tgt	6/16	1	2	FACETS	0.908	0.835	0.984	0.908	0.835	0.984	CLONAL	1	TRUE	1	0.41	2		680	908	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526339	31526339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747051575	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	218	960	0	ENST00000344624.3:c.701G>A	p.Arg234Gln	p.R234Q	ENST00000344624		234	cGa/cAa	2/33	1	2	FACETS	0.921	0.855	0.989	0.921	0.855	0.989	CLONAL	1	TRUE	1	0.41	2		960	1155	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874605	35874605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	103	422	0	ENST00000303115.3:c.761C>T	p.Ala254Val	p.A254V	ENST00000303115	NM_002185.3	254	gCt/gTt	6/8	1	2	FACETS	0.939	0.843	1	0.939	0.843	1	CLONAL	1	TRUE	1	0.41	2		422	535	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152572	56152572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1376416139	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	63	280	0	ENST00000399503.3:c.628C>T	p.Pro210Ser	p.P210S	ENST00000399503	NM_005921.1	210	Cct/Tct	2/20	1	2	FACETS	0.77	0.669	0.879	0.77	0.669	0.879	SUBCLONAL	1	TRUE	1	0.41	2		280	399	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564738	86564738	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	166	701	0	ENST00000274376.6:c.470A>C	p.Asp157Ala	p.D157A	ENST00000274376	NM_002890.2	157	gAc/gCc	1/25	1	2	FACETS	0.994	0.914	1	0.994	0.914	1	CLONAL	1	TRUE	1	0.41	2		701	815	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645166	86645166	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	25	239	0	ENST00000274376.6:c.1238G>A	p.Gly413Asp	p.G413D	ENST00000274376	NM_002890.2	413	gGc/gAc	8/25	1	2	FACETS	0.689	0.547	0.849	0.689	0.547	0.849	SUBCLONAL	1	TRUE	1	0.41	2		239	177	SUCCESS
APC	324	MSKCC	GRCh37	5	112173495	112173495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147655929	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	40	268	0	ENST00000257430.4:c.2204C>T	p.Ala735Val	p.A735V	ENST00000257430	NM_000038.5	735	gCg/gTg	16/16	1	2	FACETS	0.793	0.664	0.935	0.793	0.664	0.935	CLONAL	1	TRUE	1	0.41	2		268	246	SUCCESS
APC	324	MSKCC	GRCh37	5	112175814	112175814	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	29	225	0	ENST00000257430.4:c.4523C>T	p.Ala1508Val	p.A1508V	ENST00000257430	NM_000038.5	1508	gCt/gTt	16/16	1	2	FACETS	0.652	0.526	0.793	0.652	0.526	0.793	SUBCLONAL	1	TRUE	1	0.41	2		225	217	SUCCESS
APC	324	MSKCC	GRCh37	5	112176605	112176605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554086631	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	43	249	0	ENST00000257430.4:c.5314C>T	p.Pro1772Ser	p.P1772S	ENST00000257430	NM_000038.5	1772	Cca/Tca	16/16	1	2	FACETS	0.823	0.693	0.963	0.823	0.693	0.963	CLONAL	1	TRUE	1	0.41	2		249	255	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915588	131915588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769853458	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	47	190	0	ENST00000265335.6:c.586C>T	p.Arg196Cys	p.R196C	ENST00000265335		196	Cgt/Tgt	5/25	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.41	2		190	214	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459783	149459783	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147811334	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	144	603	0	ENST00000286301.3:c.424C>T	p.Arg142Cys	p.R142C	ENST00000286301	NM_005211.3	142	Cgt/Tgt	4/22	1	2	FACETS	0.922	0.842	1	0.922	0.842	1	CLONAL	1	TRUE	1	0.41	2		603	762	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149511596	149511596	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377445092	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	113	593	0	ENST00000261799.4:c.1189C>T	p.Arg397Trp	p.R397W	ENST00000261799	NM_002609.3	397	Cgg/Tgg	8/23	1	2	FACETS	0.848	0.764	0.936	0.848	0.764	0.936	CLONAL	1	TRUE	1	0.41	2		593	650	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176516607	176516607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545721160	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	181	702	0	ENST00000292408.4:c.4C>T	p.Arg2Trp	p.R2W	ENST00000292408	NM_213647.1	2	Cgg/Tgg	2/18	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.41	2		702	846	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638458	176638458	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	179	649	0	ENST00000439151.2:c.3058A>G	p.Asn1020Asp	p.N1020D	ENST00000439151	NM_022455.4	1020	Aac/Gac	5/23	1	2	FACETS	0.997	0.92	1	0.997	0.92	1	CLONAL	1	TRUE	1	0.41	2		649	876	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707731	176707731	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1468516072	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	121	435	1	ENST00000439151.2:c.5788C>T	p.Arg1930Cys	p.R1930C	ENST00000439151	NM_022455.4	1930	Cgc/Tgc	18/23	1	2	FACETS	0.989	0.896	1	0.989	0.896	1	CLONAL	1	TRUE	1	0.41	2		436	597	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048177	180048177	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762674026	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	178	724	1	ENST00000261937.6:c.2096G>A	p.Cys699Tyr	p.C699Y	ENST00000261937	NM_182925.4	699	tGc/tAc	14/30	1	2	FACETS	0.899	0.828	0.972	0.899	0.828	0.972	CLONAL	1	TRUE	1	0.41	2		725	966	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180050993	180050993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	173	772	4	ENST00000261937.6:c.1490C>T	p.Ala497Val	p.A497V	ENST00000261937	NM_182925.4	497	gCc/gTc	11/30	1	2	FACETS	0.872	0.802	0.945	0.872	0.802	0.945	CLONAL	1	TRUE	1	0.41	2		776	968	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394981	394981	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745876631	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	128	465	0	ENST00000380956.4:c.377G>A	p.Arg126Lys	p.R126K	ENST00000380956	NM_001195286.1	126	aGg/aAg	3/9	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.41	2		465	588	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481454	20481455	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	57	244	0	ENST00000346618.3:c.529dup	p.Thr177AsnfsTer4	p.T177Nfs*4	ENST00000346618	NM_001949.4	175	gaa/gAaa	3/7	1	2	FACETS	0.762	0.656	0.876	0.762	0.656	0.876	SUBCLONAL	1	TRUE	1	0.41	2		244	365	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225435	26225435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	28	245	0	ENST00000360408.1:c.53G>A	p.Arg18His	p.R18H	ENST00000360408	NM_003532.2	18	cGc/cAc	1/1	1	2	FACETS	0.395	0.315	0.485	0.395	0.315	0.485	SUBCLONAL	1	TRUE	1	0.41	2		245	346	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777973	27777973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs576862710	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	75	372	0	ENST00000369163.2:c.122G>A	p.Arg41His	p.R41H	ENST00000369163	NM_003536.2	41	cGc/cAc	1/1	1	2	FACETS	0.847	0.745	0.955	0.847	0.745	0.955	CLONAL	1	TRUE	1	0.41	2		372	432	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858200	27858200	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	98	407	0	ENST00000359303.2:c.371A>G	p.Asp124Gly	p.D124G	ENST00000359303	NM_003535.2	124	gAc/gGc	1/1	1	2	FACETS	0.954	0.855	1	0.954	0.855	1	CLONAL	1	TRUE	1	0.41	2		407	501	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681477	30681477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28986464	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	71	352	0	ENST00000376406.3:c.535C>T	p.Arg179Cys	p.R179C	ENST00000376406	NM_014641.2	179	Cgt/Tgt	4/15	1	2	FACETS	0.872	0.765	0.987	0.872	0.765	0.987	CLONAL	1	TRUE	1	0.41	2		352	397	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139232	37139232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	89	467	0	ENST00000373509.5:c.572C>T	p.Ala191Val	p.A191V	ENST00000373509	NM_002648.3	191	gCg/gTg	4/6	1	2	FACETS	0.861	0.766	0.962	0.861	0.766	0.962	CLONAL	1	TRUE	1	0.41	2		467	504	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43742099	43742099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	176	653	0	ENST00000523873.1:c.88G>A	p.Ala30Thr	p.A30T	ENST00000523873		30	Gca/Aca	2/8	1	2	FACETS	0.977	0.9	1	0.977	0.9	1	CLONAL	1	TRUE	1	0.41	2		653	879	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745233	43745233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1267535717	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	124	559	2	ENST00000523873.1:c.146G>A	p.Arg49His	p.R49H	ENST00000523873		49	cGc/cAc	3/8	1	2	FACETS	0.89	0.806	0.977	0.89	0.806	0.977	CLONAL	1	TRUE	1	0.41	2		561	680	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066471	94066471	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1179484555	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	44	244	0	ENST00000369303.4:c.1288C>T	p.Leu430Phe	p.L430F	ENST00000369303	NM_004440.3	430	Ctc/Ttc	5/17	1	2	FACETS	0.753	0.635	0.882	0.753	0.635	0.882	SUBCLONAL	1	TRUE	1	0.41	2		244	285	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553591	106553591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376600972	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	85	345	0	ENST00000369096.4:c.1556C>T	p.Ala519Val	p.A519V	ENST00000369096	NM_001198.3	519	gCg/gTg	5/7	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.41	2		345	414	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109315715	109315715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	98	533	0	ENST00000436639.2:c.1070C>T	p.Ala357Val	p.A357V	ENST00000436639	NM_014454.2	357	gCt/gTt	6/10	1	2	FACETS	0.806	0.721	0.897	0.806	0.721	0.897	CLONAL	1	TRUE	1	0.41	2		533	593	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017578	112017578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	114	455	0	ENST00000368678.4:c.935C>T	p.Ala312Val	p.A312V	ENST00000368678		312	gCg/gTg	9/13	1	2	FACETS	0.916	0.827	1	0.916	0.827	1	CLONAL	1	TRUE	1	0.41	2		455	607	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112025223	112025223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	108	420	1	ENST00000368678.4:c.526C>T	p.Arg176Cys	p.R176C	ENST00000368678		176	Cgc/Tgc	6/13	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.41	2		421	508	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519461	137519461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777316078	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	53	240	1	ENST00000367739.4:c.1177G>A	p.Ala393Thr	p.A393T	ENST00000367739	NM_000416.2	393	Gct/Act	7/7	1	2	FACETS	0.998	0.859	1	0.998	0.859	1	CLONAL	1	TRUE	1	0.41	2		241	259	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196958	138196958	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	42	208	1	ENST00000237289.4:c.620T>C	p.Ile207Thr	p.I207T	ENST00000237289	NM_001270507.1	207	aTc/aCc	4/9	1	2	FACETS	0.803	0.676	0.943	0.803	0.676	0.943	CLONAL	1	TRUE	1	0.41	2		209	255	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199922	138199922	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778782828	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	91	389	0	ENST00000237289.4:c.1340C>T	p.Ala447Val	p.A447V	ENST00000237289	NM_001270507.1	447	gCg/gTg	7/9	1	2	FACETS	0.951	0.848	1	0.951	0.848	1	CLONAL	1	TRUE	1	0.41	2		389	467	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004222	150004222	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	47	206	0	ENST00000253339.5:c.2003T>C	p.Met668Thr	p.M668T	ENST00000253339		668	aTg/aCg	3/7	1	2	FACETS	0.959	0.817	1	0.959	0.817	1	CLONAL	1	TRUE	1	0.41	2		206	239	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954964	2954964	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	185	671	0	ENST00000396946.4:c.2746A>G	p.Asn916Asp	p.N916D	ENST00000396946	NM_032415.4	916	Aac/Gac	21/25	1	2	FACETS	0.997	0.921	1	0.997	0.921	1	CLONAL	1	TRUE	1	0.41	2		671	905	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026514	6026514	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs63750451	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	142	556	0	ENST00000265849.7:c.1882C>T	p.Arg628Ter	p.R628*	ENST00000265849	NM_000535.5	628	Cga/Tga	11/15	1	2	FACETS	0.948	0.865	1	0.948	0.865	1	CLONAL	1	TRUE	1	0.41	2		556	731	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729639	41729639	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	111	465	0	ENST00000242208.4:c.890C>T	p.Ala297Val	p.A297V	ENST00000242208	NM_002192.2	297	gCc/gTc	3/3	1	2	FACETS	0.972	0.877	1	0.972	0.877	1	CLONAL	1	TRUE	1	0.41	2		465	557	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739717	41739717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	153	685	0	ENST00000242208.4:c.256G>A	p.Ala86Thr	p.A86T	ENST00000242208	NM_002192.2	86	Gcg/Acg	2/3	1	2	FACETS	0.917	0.839	0.998	0.917	0.839	0.998	CLONAL	1	TRUE	1	0.41	2		685	814	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444275	50444275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	65	282	0	ENST00000331340.3:c.205C>T	p.Arg69Cys	p.R69C	ENST00000331340	NM_006060.4	69	Cgt/Tgt	4/8	1	2	FACETS	0.949	0.829	1	0.949	0.829	1	CLONAL	1	TRUE	1	0.41	2		282	334	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468020	50468020	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	111	520	3	ENST00000331340.3:c.1255G>A	p.Ala419Thr	p.A419T	ENST00000331340	NM_006060.4	419	Gcc/Acc	8/8	1	2	FACETS	0.929	0.837	1	0.929	0.837	1	CLONAL	1	TRUE	1	0.41	2		523	583	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240686	55240686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	220	815	0	ENST00000275493.2:c.1930C>T	p.Pro644Ser	p.P644S	ENST00000275493	NM_005228.3	644	Ccg/Tcg	17/28	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.41	2		815	1004	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240786	55240786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756870976	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	189	837	3	ENST00000275493.2:c.2030G>A	p.Arg677His	p.R677H	ENST00000275493	NM_005228.3	677	cGc/cAc	17/28	1	2	FACETS	0.992	0.918	1	0.992	0.918	1	CLONAL	1	TRUE	1	0.41	2		840	929	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508557	106508557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	67	324	1	ENST00000359195.3:c.551G>A	p.Arg184His	p.R184H	ENST00000359195	NM_002649.2	184	cGc/cAc	2/11	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.41	2		325	313	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509082	106509082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144565710	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	155	564	0	ENST00000359195.3:c.1076G>A	p.Arg359His	p.R359H	ENST00000359195	NM_002649.2	359	cGc/cAc	2/11	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.41	2		564	742	SUCCESS
MET	4233	MSKCC	GRCh37	7	116381005	116381005	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763991073	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	123	479	0	ENST00000397752.3:c.1627G>A	p.Asp543Asn	p.D543N	ENST00000397752	NM_000245.2	543	Gac/Aac	5/21	1	2	FACETS	0.701	0.633	0.772	0.701	0.633	0.772	SUBCLONAL	1	TRUE	1	0.41	2		479	856	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850915	128850915	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	141	572	0	ENST00000249373.3:c.1762T>C	p.Ser588Pro	p.S588P	ENST00000249373	NM_005631.4	588	Tcc/Ccc	10/12	1	2	FACETS	0.945	0.862	1	0.945	0.862	1	CLONAL	1	TRUE	1	0.41	2		572	728	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852114	128852114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200751953	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	198	842	3	ENST00000249373.3:c.2186C>T	p.Ala729Val	p.A729V	ENST00000249373	NM_005631.4	729	gCg/gTg	12/12	1	2	FACETS	0.989	0.916	1	0.989	0.916	1	CLONAL	1	TRUE	1	0.41	2		845	977	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512114	148512114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	34	378	0	ENST00000320356.2:c.1564G>A	p.Val522Ile	p.V522I	ENST00000320356	NM_004456.4	522	Gtt/Att	14/20	1	2	FACETS	0.33	0.269	0.399	0.33	0.269	0.399	SUBCLONAL	1	TRUE	1	0.41	2		378	502	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846197	151846197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754010322	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	75	415	0	ENST00000262189.6:c.12815C>T	p.Thr4272Met	p.T4272M	ENST00000262189	NM_170606.2	4272	aCg/aTg	52/59	1	2	FACETS	0.799	0.702	0.902	0.799	0.702	0.902	CLONAL	1	TRUE	1	0.41	2		415	458	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853002	151853002	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	35	204	0	ENST00000262189.6:c.11953G>T	p.Glu3985Ter	p.E3985*	ENST00000262189	NM_170606.2	3985	Gaa/Taa	46/59	1	2	FACETS	0.565	0.465	0.677	0.565	0.465	0.677	SUBCLONAL	1	TRUE	1	0.41	2		204	302	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856027	151856027	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774117324	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	53	417	1	ENST00000262189.6:c.11591G>A	p.Arg3864His	p.R3864H	ENST00000262189	NM_170606.2	3864	cGc/cAc	44/59	1	2	FACETS	0.427	0.363	0.496	0.427	0.363	0.496	SUBCLONAL	1	TRUE	1	0.41	2		418	606	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875037	151875037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	40	165	0	ENST00000262189.6:c.7501C>T	p.Pro2501Ser	p.P2501S	ENST00000262189	NM_170606.2	2501	Cct/Tct	38/59	1	2	FACETS	0.841	0.705	0.99	0.841	0.705	0.99	CLONAL	1	TRUE	1	0.41	2		165	232	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949769	151949769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760928040	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	57	319	0	ENST00000262189.6:c.1331G>A	p.Arg444Gln	p.R444Q	ENST00000262189	NM_170606.2	444	cGg/cAg	10/59	1	2	FACETS	0.801	0.691	0.92	0.801	0.691	0.92	CLONAL	1	TRUE	1	0.41	2		319	347	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38187179	38187179	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	64	663	0	ENST00000317025.8:c.1298C>A	p.Thr433Asn	p.T433N	ENST00000317025	NM_023034.1	433	aCc/aAc	6/24	1	2	FACETS	0.314	0.271	0.361	0.314	0.271	0.361	SUBCLONAL	1	TRUE	1	0.41	2		663	995	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38283754	38283754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	123	528	1	ENST00000425967.3:c.724G>A	p.Ala242Thr	p.A242T	ENST00000425967	NM_001174067.1	242	Gcc/Acc	7/19	1	2	FACETS	0.969	0.879	1	0.969	0.879	1	CLONAL	1	TRUE	1	0.41	2		529	619	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372134	55372134	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	65	286	3	ENST00000297316.4:c.824G>A	p.Gly275Asp	p.G275D	ENST00000297316	NM_022454.3	275	gGc/gAc	2/2	1	2	FACETS	0.832	0.725	0.947	0.832	0.725	0.947	CLONAL	1	TRUE	1	0.41	2		289	381	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372389	55372389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1274955948	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	201	996	0	ENST00000297316.4:c.1079G>A	p.Arg360His	p.R360H	ENST00000297316	NM_022454.3	360	cGc/cAc	2/2	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.41	2		996	955	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981768	70981768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	221	798	0	ENST00000276594.2:c.328G>A	p.Glu110Lys	p.E110K	ENST00000276594	NM_024504.3	110	Gaa/Aaa	2/8	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.41	2		798	1077	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958511	90958511	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	81	289	0	ENST00000265433.3:c.1927C>A	p.Leu643Ile	p.L643I	ENST00000265433	NM_002485.4	643	Ctt/Att	13/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.41	2		289	322	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859836	117859836	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	69	207	0	ENST00000297338.2:c.1799T>C	p.Phe600Ser	p.F600S	ENST00000297338	NM_006265.2	600	tTc/tCc	14/14	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.41	2		207	292	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868981	117868981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs575505257	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	63	259	0	ENST00000297338.2:c.718G>A	p.Gly240Ser	p.G240S	ENST00000297338	NM_006265.2	240	Ggt/Agt	7/14	1	2	FACETS	0.802	0.697	0.916	0.802	0.697	0.916	CLONAL	1	TRUE	1	0.41	2		259	383	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741686	145741686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs34103564	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	120	719	0	ENST00000428558.2:c.817G>A	p.Ala273Thr	p.A273T	ENST00000428558	NM_004260.3	273	Gca/Aca	5/22	1	2	FACETS	0.785	0.709	0.864	0.785	0.709	0.864	SUBCLONAL	1	TRUE	1	0.41	2		719	746	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449745	8449745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1172700321	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	38	520	0	ENST00000356435.5:c.3968G>A	p.Arg1323His	p.R1323H	ENST00000356435		1323	cGc/cAc	23/35	1	2	FACETS	0.268	0.221	0.321	0.268	0.221	0.321	SUBCLONAL	1	TRUE	1	0.41	2		520	691	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465587	8465587	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	108	445	0	ENST00000356435.5:c.3593T>C	p.Val1198Ala	p.V1198A	ENST00000356435		1198	gTc/gCc	21/35	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.41	2		445	450	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507374	8507374	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	27	268	0	ENST00000356435.5:c.1604C>A	p.Ser535Tyr	p.S535Y	ENST00000356435		535	tCt/tAt	11/35	1	2	FACETS	0.345	0.274	0.426	0.345	0.274	0.426	SUBCLONAL	1	TRUE	1	0.41	2		268	382	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518016	8518016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	60	321	0	ENST00000356435.5:c.1375C>T	p.Pro459Ser	p.P459S	ENST00000356435		459	Ccc/Tcc	10/35	1	2	FACETS	0.898	0.778	1	0.898	0.778	1	CLONAL	1	TRUE	1	0.41	2		321	326	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518112	8518112	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs533774328	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	79	386	0	ENST00000356435.5:c.1279C>T	p.Arg427Ter	p.R427*	ENST00000356435		427	Cga/Tga	10/35	1	2	FACETS	0.878	0.775	0.987	0.878	0.775	0.987	CLONAL	1	TRUE	1	0.41	2		386	439	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528596	8528596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	34	323	0	ENST00000356435.5:c.536G>A	p.Arg179Gln	p.R179Q	ENST00000356435		179	cGa/cAa	4/35	1	2	FACETS	0.489	0.4	0.589	0.489	0.4	0.589	SUBCLONAL	1	TRUE	1	0.41	2		323	339	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27203039	27203039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	81	509	0	ENST00000380036.4:c.2131G>A	p.Asp711Asn	p.D711N	ENST00000380036	NM_000459.3	711	Gac/Aac	13/23	1	2	FACETS	0.734	0.648	0.826	0.734	0.648	0.826	SUBCLONAL	1	TRUE	1	0.41	2		509	538	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624558	93624558	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867241355	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	128	497	1	ENST00000375746.1:c.649C>T	p.Arg217Cys	p.R217C	ENST00000375746	NM_001174167.1	217	Cgc/Tgc	4/14	1	2	FACETS	0.982	0.892	1	0.982	0.892	1	CLONAL	1	TRUE	1	0.41	2		498	636	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93636969	93636969	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs200994798	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	74	333	0	ENST00000375746.1:c.1019C>A	p.Ala340Asp	p.A340D	ENST00000375746	NM_001174167.1	340	gCc/gAc	9/14	1	2	FACETS	0.766	0.673	0.866	0.766	0.673	0.866	SUBCLONAL	1	TRUE	1	0.41	2		333	471	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239974	98239974	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	113	358	0	ENST00000331920.6:c.1358C>A	p.Ala453Asp	p.A453D	ENST00000331920	NM_000264.3	453	gCc/gAc	10/24	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.41	2		358	515	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98247997	98247997	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1276503562	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	68	397	0	ENST00000331920.6:c.554C>T	p.Ala185Val	p.A185V	ENST00000331920	NM_000264.3	185	gCc/gTc	3/24	1	2	FACETS	0.633	0.551	0.721	0.633	0.551	0.721	SUBCLONAL	1	TRUE	1	0.41	2		397	524	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908828	101908828	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1327426815	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	38	378	1	ENST00000374994.4:c.1192C>T	p.Arg398Cys	p.R398C	ENST00000374994	NM_004612.2	398	Cgt/Tgt	7/9	1	2	FACETS	0.448	0.37	0.534	0.448	0.37	0.534	SUBCLONAL	1	TRUE	1	0.41	2		379	414	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908850	101908850	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	64	427	0	ENST00000374994.4:c.1214G>A	p.Gly405Asp	p.G405D	ENST00000374994	NM_004612.2	405	gGc/gAc	7/9	1	2	FACETS	0.663	0.575	0.757	0.663	0.575	0.757	SUBCLONAL	1	TRUE	1	0.41	2		427	471	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249413	110249413	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	297	897	0	ENST00000374672.4:c.1160C>T	p.Ser387Leu	p.S387L	ENST00000374672	NM_004235.4	387	tCg/tTg	4/5	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.41	2		897	1262	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760790	133760790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367600262	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	146	658	0	ENST00000318560.5:c.3113C>T	p.Ala1038Val	p.A1038V	ENST00000318560	NM_005157.4	1038	gCg/gTg	11/11	1	2	FACETS	0.996	0.911	1	0.996	0.911	1	CLONAL	1	TRUE	1	0.41	2		658	715	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395186	139395186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	199	775	1	ENST00000277541.6:c.5752G>A	p.Ala1918Thr	p.A1918T	ENST00000277541	NM_017617.3	1918	Gcc/Acc	31/34	1	2	FACETS	0.991	0.918	1	0.991	0.918	1	CLONAL	1	TRUE	1	0.41	2		776	980	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396884	139396884	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760669267	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	144	517	1	ENST00000277541.6:c.5224G>A	p.Ala1742Thr	p.A1742T	ENST00000277541	NM_017617.3	1742	Gcc/Acc	28/34	1	2	FACETS	0.988	0.903	1	0.988	0.903	1	CLONAL	1	TRUE	1	0.41	2		518	711	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400321	139400321	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369654090	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	135	576	0	ENST00000277541.6:c.4027G>A	p.Ala1343Thr	p.A1343T	ENST00000277541	NM_017617.3	1343	Gcc/Acc	25/34	1	2	FACETS	0.913	0.831	0.999	0.913	0.831	0.999	CLONAL	1	TRUE	1	0.41	2		576	721	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403498	139403498	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756840659	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	208	749	0	ENST00000277541.6:c.2995G>A	p.Val999Met	p.V999M	ENST00000277541	NM_017617.3	999	Gtg/Atg	19/34	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.41	2		749	983	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412365	139412365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	129	602	0	ENST00000277541.6:c.1280G>A	p.Gly427Asp	p.G427D	ENST00000277541	NM_017617.3	427	gGc/gAc	8/34	1	2	FACETS	0.899	0.816	0.986	0.899	0.816	0.986	CLONAL	1	TRUE	1	0.41	2		602	700	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412375	139412375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1341448592	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	115	573	1	ENST00000277541.6:c.1270G>A	p.Glu424Lys	p.E424K	ENST00000277541	NM_017617.3	424	Gag/Aag	8/34	1	2	FACETS	0.866	0.781	0.955	0.866	0.781	0.955	CLONAL	1	TRUE	1	0.41	2		574	648	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139563109	139563109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747731431	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	144	587	2	ENST00000308874.7:c.181G>A	p.Ala61Thr	p.A61T	ENST00000308874		61	Gcc/Acc	4/10	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.41	2		589	690	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15838375	15838375	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	105	342	0	ENST00000307771.7:c.873G>A	p.Trp291Ter	p.W291*	ENST00000307771	NM_005089.3	291	tgG/tgA	10/11	1	2	FACETS	0.93	0.836	1	0.93	0.836	1	CLONAL	1	TRUE	1	0.41	2		342	551	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841306	15841306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1196200389	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	58	399	0	ENST00000307771.7:c.1390C>T	p.Arg464Cys	p.R464C	ENST00000307771	NM_005089.3	464	Cgt/Tgt	11/11	1	2	FACETS	0.468	0.401	0.54	0.468	0.401	0.54	SUBCLONAL	1	TRUE	1	0.41	2		399	605	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916463	39916463	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	134	665	0	ENST00000378444.4:c.4540C>T	p.Arg1514Ter	p.R1514*	ENST00000378444	NM_001123385.1	1514	Cga/Tga	11/15	1	2	FACETS	0.73	0.662	0.8	0.73	0.662	0.8	SUBCLONAL	1	TRUE	1	0.41	2		665	896	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916493	39916493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	59	739	0	ENST00000378444.4:c.4510G>A	p.Ala1504Thr	p.A1504T	ENST00000378444	NM_001123385.1	1504	Gct/Act	11/15	1	2	FACETS	0.307	0.263	0.355	0.307	0.263	0.355	SUBCLONAL	1	TRUE	1	0.41	2		739	938	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933871	39933871	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs865796679	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	193	745	0	ENST00000378444.4:c.728G>A	p.Arg243His	p.R243H	ENST00000378444	NM_001123385.1	243	cGc/cAc	4/15	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.41	2		745	940	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922973	44922973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	147	508	3	ENST00000377967.4:c.1834C>T	p.Arg612Ter	p.R612*	ENST00000377967	NM_021140.2	612	Cga/Tga	16/29	1	2	FACETS	0.878	0.802	0.957	0.878	0.802	0.957	CLONAL	1	TRUE	1	0.41	2		511	817	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035918	47035918	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	179	697	0	ENST00000377604.3:c.596G>A	p.Gly199Asp	p.G199D	ENST00000377604	NM_001204468.1	199	gGc/gAc	7/24	1	2	FACETS	0.907	0.836	0.981	0.907	0.836	0.981	CLONAL	1	TRUE	1	0.41	2		697	963	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652476	48652476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	64	742	0	ENST00000376670.3:c.1147C>T	p.Pro383Ser	p.P383S	ENST00000376670	NM_002049.3	383	Cct/Tct	6/6	1	2	FACETS	0.356	0.307	0.409	0.356	0.307	0.409	SUBCLONAL	1	TRUE	1	0.41	2		742	878	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222460	53222460	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	173	792	1	ENST00000375401.3:c.4372C>T	p.Arg1458Trp	p.R1458W	ENST00000375401	NM_004187.3	1458	Cgg/Tgg	26/26	1	2	FACETS	0.917	0.844	0.993	0.917	0.844	0.993	CLONAL	1	TRUE	1	0.41	2		793	920	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226016	53226016	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	199	829	1	ENST00000375401.3:c.2833G>A	p.Gly945Ser	p.G945S	ENST00000375401	NM_004187.3	945	Ggc/Agc	19/26	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.41	2		830	935	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230913	53230913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	150	627	1	ENST00000375401.3:c.1880G>A	p.Arg627His	p.R627H	ENST00000375401	NM_004187.3	627	cGc/cAc	14/26	1	2	FACETS	0.895	0.818	0.974	0.895	0.818	0.974	CLONAL	1	TRUE	1	0.41	2		628	818	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410985	63410985	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	50	603	0	ENST00000330258.3:c.2182T>C	p.Phe728Leu	p.F728L	ENST00000330258	NM_152424.3	728	Ttt/Ctt	2/2	1	2	FACETS	0.387	0.327	0.452	0.387	0.327	0.452	SUBCLONAL	1	TRUE	1	0.41	2		603	631	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411777	63411777	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767567473	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	174	811	1	ENST00000330258.3:c.1390G>A	p.Ala464Thr	p.A464T	ENST00000330258	NM_152424.3	464	Gcc/Acc	2/2	1	2	FACETS	0.933	0.859	1	0.933	0.859	1	CLONAL	1	TRUE	1	0.41	2		812	910	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412185	63412185	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	162	794	0	ENST00000330258.3:c.982T>C	p.Cys328Arg	p.C328R	ENST00000330258	NM_152424.3	328	Tgt/Cgt	2/2	1	2	FACETS	0.961	0.883	1	0.961	0.883	1	CLONAL	1	TRUE	1	0.41	2		794	822	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347241	70347241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	142	562	0	ENST00000374080.3:c.2905C>T	p.Arg969Cys	p.R969C	ENST00000374080		969	Cgc/Tgc	21/45	1	2	FACETS	0.954	0.871	1	0.954	0.871	1	CLONAL	1	TRUE	1	0.41	2		562	726	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348542	70348542	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	172	496	0	ENST00000374080.3:c.3449C>T	p.Ala1150Val	p.A1150V	ENST00000374080		1150	gCt/gTt	24/45	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.41	2		496	716	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349009	70349009	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1405190651	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	61	628	3	ENST00000374080.3:c.3521G>A	p.Arg1174His	p.R1174H	ENST00000374080		1174	cGc/cAc	25/45	1	2	FACETS	0.32	0.275	0.369	0.32	0.275	0.369	SUBCLONAL	1	TRUE	1	0.41	2		631	930	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937794	76937794	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557138509	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	39	450	0	ENST00000373344.5:c.2954G>A	p.Ser985Asn	p.S985N	ENST00000373344	NM_000489.3	985	aGc/aAc	9/35	1	2	FACETS	0.383	0.317	0.456	0.383	0.317	0.456	SUBCLONAL	1	TRUE	1	0.41	2		450	497	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938049	76938049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	84	495	0	ENST00000373344.5:c.2699C>T	p.Thr900Ile	p.T900I	ENST00000373344	NM_000489.3	900	aCc/aTc	9/35	1	2	FACETS	0.816	0.723	0.915	0.816	0.723	0.915	CLONAL	1	TRUE	1	0.41	2		495	502	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27183462	27183462	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042390-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	72	313	0	ENST00000380036.4:c.1036C>T	p.Gln346Ter	p.Q346*	ENST00000380036	NM_000459.3	346	Cag/Tag	8/23	1	2	FACETS	0.965	0.848	1	0.965	0.848	1	CLONAL	1	TRUE	1	0.41	2		313	364	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	106	372	0				ENST00000310581	NM_198253.2	-/1132			0.222872909322693	4	FACETS	0.947	0.852	1	0.947	0.852	1	CLONAL	2	TRUE	2	0.248590640048025	4		372	562	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577595	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0042412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	165	486	0	ENST00000269305.4:c.686_687del	p.Cys229TyrfsTer10	p.C229Yfs*10	ENST00000269305	NM_001126112.2	229	tGT/t	7/11	0.239590909014808	2	FACETS	0.976	0.899	1	0.976	0.899	1	CLONAL	2	TRUE	0	0.248590640048025	2		486	680	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391168	89391168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772463834	NA	P-0042412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	633	405	0	ENST00000336596.2:c.1234G>A	p.Val412Ile	p.V412I	ENST00000336596	NM_005233.5	412	Gtt/Att	5/17	0.248590640048025	11	FACETS	0.982	0.949	1			1	CLONAL	9	TRUE	NA	0.248590640048025	11		405	1221	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244787	46244787	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	102	470	0	ENST00000334344.6:c.2881C>T	p.Gln961Ter	p.Q961*	ENST00000334344	NM_152641.2	961	Cag/Tag	15/21	0.154032536761953	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.248590640048025	1		470	541	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259169	89259169	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	91	267	0	ENST00000336596.2:c.313G>C	p.Asp105His	p.D105H	ENST00000336596	NM_005233.5	105	Gac/Cac	3/17	0.248590640048025	11	FACETS	0.836	0.741	0.938			1	CLONAL	2	TRUE	NA	0.248590640048025	11		267	928	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880261	37880261	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs121913468	NA	P-0042412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	2692	483	2	ENST00000269571.5:c.2305G>A	p.Asp769Asn	p.D769N	ENST00000269571		769	Gac/Aac	19/27	0.248590640048025	49	FACETS	0.993	0.982	1			1	CLONAL	44	TRUE	NA	0.248590640048025	49		485	3391	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422455	47422455	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398289359	NA	P-0042412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	74	569	0	ENST00000377045.4:c.89G>A	p.Arg30His	p.R30H	ENST00000377045	NM_001654.4	30	cGc/cAc	2/16	NA	2	FACETS	0.721	0.63	0.819			1	INDETERMINATE	1	TRUE	NA	0.248590640048025	2		569	826	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094447	27094447	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	155	522	0	ENST00000324856.7:c.3155A>G	p.Tyr1052Cys	p.Y1052C	ENST00000324856	NM_006015.4	1052	tAt/tGt	11/20	0.248590640048025	2	FACETS	0.968	0.889	1	0.968	0.889	1	CLONAL	2	TRUE	0	0.248590640048025	2		522	644	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610036	43610036	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	74	735	2	ENST00000355710.3:c.1988T>C	p.Phe663Ser	p.F663S	ENST00000355710	NM_020975.4	663	tTt/tCt	11/20	0.226201479450803	3	FACETS	0.771	0.674	0.877	0.386	0.337	0.439	SUBCLONAL	1	TRUE	1	0.248590640048025	3		737	868	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991581	72991581	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	200	686	0	ENST00000268489.5:c.2464C>G	p.His822Asp	p.H822D	ENST00000268489	NM_006885.3	822	Cac/Gac	2/10	0.248590640048025	3	FACETS	0.934	0.866	1	0.934	0.866	1	CLONAL	2	TRUE	1	0.248590640048025	3		686	968	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050363	13050363	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	159	514	0	ENST00000316448.5:c.315T>G	p.Cys105Trp	p.C105W	ENST00000316448	NM_004343.3	105	tgT/tgG	3/9	1	2	FACETS	0.752	0.69	0.818	1	0.988	1	SUBCLONAL	2	TRUE	1	0.248590640048025	2		514	850	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145736924	145736924	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042412-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	218	724	0	ENST00000428558.2:c.3517C>T	p.Pro1173Ser	p.P1173S	ENST00000428558	NM_004260.3	1173	Ccg/Tcg	22/22	0.228238846754565	5	FACETS	1	0.979	1	0.756	0.703	0.812	CLONAL	2	TRUE	2	0.248590640048025	5		724	1061	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0042441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	20	753	1	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	1	2	FACETS	0.442	0.336	0.567	0.442	0.336	0.567	SUBCLONAL	1	TRUE	1	0.11	2		754	823	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868185	37868185	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	43	843	0	ENST00000269571.5:c.906C>G	p.Asn302Lys	p.N302K	ENST00000269571		302	aaC/aaG	8/27	1	2	FACETS	1	0.834	1	1	0.834	1	CLONAL	1	TRUE	1	0.11	2		843	782	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0042518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	71	381	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.303956108894149	1	FACETS	0.939	0.824	1	0.939	0.824	1	CLONAL	1	TRUE	0	0.32	1		381	397	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0042518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	28	262	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	1	2	FACETS	0.706	0.566	0.863	0.706	0.566	0.863	SUBCLONAL	1	TRUE	1	0.32	2		262	248	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	69	388	1	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	0.303956108894149	1	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	0	0.32	1		389	362	SUCCESS
APC	324	MSKCC	GRCh37	5	112175351	112175351	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	54	278	0	ENST00000257430.4:c.4063del	p.Ser1355LeufsTer60	p.S1355Lfs*60	ENST00000257430	NM_000038.5	1354	Ttt/tt	16/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.32	2		278	239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578490	7578490	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	226	1041	0	ENST00000269305.4:c.440T>A	p.Val147Asp	p.V147D	ENST00000269305	NM_001126112.2	147	gTt/gAt	5/11	0.219458285416022	2	FACETS	1	0.991	1	0.73	0.68	0.781	CLONAL	1	TRUE	0	0.32	2		1041	968	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535355	66535355	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	63	627	0	ENST00000273854.3:c.106C>T	p.Arg36Ter	p.R36*	ENST00000273854	NM_004439.5	36	Cga/Tga	1/18	0.303956108894149	1	FACETS	0.563	0.486	0.645	0.563	0.486	0.645	SUBCLONAL	1	TRUE	0	0.32	1		627	588	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18958556	18958556	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	61	586	0	ENST00000262803.5:c.375C>A	p.Tyr125Ter	p.Y125*	ENST00000262803	NM_002911.3	125	taC/taA	3/24	1	2	FACETS	0.59	0.509	0.679	0.59	0.509	0.679	SUBCLONAL	1	TRUE	1	0.32	2		586	646	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149452958	149452958	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	717	606	1	ENST00000286301.3:c.988G>A	p.Gly330Ser	p.G330S	ENST00000286301	NM_005211.3	330	Ggc/Agc	7/22	0.303956108894149	9	FACETS	0.962	0.934	0.99			1	CLONAL	8	TRUE	NA	0.32	9		607	1234	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002816	69002816	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042518-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	21	243	0	ENST00000288368.4:c.2116A>C	p.Thr706Pro	p.T706P	ENST00000288368	NM_024870.2	706	Act/Cct	20/40	1	2	FACETS	0.551	0.426	0.697	0.551	0.426	0.697	SUBCLONAL	1	TRUE	1	0.32	2		243	238	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577569	7577569	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519981	NA	P-0042519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	457	589	0	ENST00000269305.4:c.712T>G	p.Cys238Gly	p.C238G	ENST00000269305	NM_001126112.2	238	Tgt/Ggt	7/11	0.545583371778392	2	FACETS	0.846	0.814	0.878	0.846	0.814	0.878	CLONAL	2	TRUE	0	0.634579728637193	2		589	851	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099403	157099426	+	inframe_deletion	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAGCAA	CAGCAGCAGCAGCAGCAGCAGCAA	-	rs770869529	NA	P-0042519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	112	256	0	ENST00000346085.5:c.369_392del	p.Gln124_Gln131del	p.Q124_Q131del	ENST00000346085	NM_020732.3	114	CAGCAGCAGCAGCAGCAGCAGCAA/-	1/20	0.542088417657314	3	FACETS	1	0.955	1	0.546	0.494	0.599	CLONAL	1	TRUE	1	0.634579728637193	3		256	426	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031900	26031900	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	33	221	0	ENST00000244661.2:c.389G>A	p.Arg130His	p.R130H	ENST00000244661	NM_003537.3	130	cGc/cAc	1/1	0.573915131931722	3	FACETS	0.299	0.243	0.362	0.15	0.121	0.181	SUBCLONAL	1	TRUE	1	0.634579728637193	3		221	458	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797119	42797119	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1460	103	949	1	ENST00000575354.2:c.3481A>T	p.Thr1161Ser	p.T1161S	ENST00000575354	NM_015125.3	1161	Acc/Tcc	15/20	0.542088417657314	3	FACETS	0.274	0.243	0.306	0.137	0.121	0.153	SUBCLONAL	1	TRUE	1	0.634579728637193	3		950	1563	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259514	55259515	+	missense_variant	Missense_Mutation	DNP	CT	CT	AG	rs1057519847	NA	P-0042521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	154	576	1	ENST00000275493.2:c.2572_2573inv	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	CTg/AGg	21/28	0.28839153688426	3	FACETS	0.9	0.827	0.975	0.9	0.827	0.975	CLONAL	2	TRUE	1	0.337394335319195	3		577	593	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039614	47039615	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0042521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	100	635	0	ENST00000377604.3:c.1066_1067delinsTT	p.Ala356Leu	p.A356L	ENST00000377604	NM_001204468.1	356	GCa/TTa	11/24	0.107695846291582	5	FACETS	1	0.946	1	0.54	0.486	0.598	INDETERMINATE	2	TRUE	1	0.337394335319195	5		635	413	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132644	11132644	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0042524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	483	744	0	ENST00000358026.2:c.2859+1G>T		p.X953_splice	ENST00000358026	NM_001128849.1	953			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.97	2		744	987	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944620	40944620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	162	325	0	ENST00000373198.4:c.1882G>A	p.Val628Ile	p.V628I	ENST00000373198	NM_133170.3	628	Gtc/Atc	12/32	1	2	FACETS	0.763	0.707	0.82	0.763	0.707	0.82	SUBCLONAL	1	TRUE	1	0.97	2		325	438	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	72	372	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.813253127147504	2		372	169	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0042600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	77	426	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.289	0.253	0.327	0.289	0.253	0.327	SUBCLONAL	1	TRUE	1	0.813253127147504	2		426	655	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0042600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	362	755	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	1	2	FACETS	0.92	0.874	0.965	0.92	0.874	0.965	CLONAL	1	TRUE	1	0.813253127147504	2		755	968	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692818	89692818	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1339631701	NA	P-0042600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	97	214	0	ENST00000371953.3:c.302T>C	p.Ile101Thr	p.I101T	ENST00000371953	NM_000314.4	101	aTc/aCc	5/9	0.813253127147504	1	FACETS	0.937	0.869	1	0.937	0.869	1	CLONAL	1	TRUE	0	0.813253127147504	1		214	151	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932750	39932750	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143744110	NA	P-0042600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	367	787	0	ENST00000378444.4:c.1849G>A	p.Ala617Thr	p.A617T	ENST00000378444	NM_001123385.1	617	Gcc/Acc	4/15	1	2	FACETS	0.965	0.919	1	0.965	0.919	1	CLONAL	1	TRUE	1	0.813253127147504	2		787	935	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913444	NA	P-0042600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	67	507	0	ENST00000275493.2:c.2582T>G	p.Leu861Arg	p.L861R	ENST00000275493	NM_005228.3	861	cTg/cGg	21/28	0.813253127147504	3	FACETS	0.238	0.206	0.273	0.119	0.103	0.137	SUBCLONAL	1	TRUE	1	0.813253127147504	3		507	973	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439701	51439701	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	172	350	0	ENST00000262662.1:c.266T>C	p.Leu89Ser	p.L89S	ENST00000262662		89	tTg/tCg	4/4	1	2	FACETS	0.995	0.926	1	0.995	0.926	1	CLONAL	1	TRUE	1	0.813253127147504	2		350	425	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	DEL	C	C	-	novel	NA	P-0042600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	285	489	0	ENST00000269305.4:c.559+1del		p.X187_splice	ENST00000269305	NM_001126112.2	187			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.813253127147504	2		489	673	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39240664	39240664	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs727505381	NA	P-0042600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	40	319	0	ENST00000402219.2:c.2104T>C	p.Tyr702His	p.Y702H	ENST00000402219	NM_005633.3	702	Tat/Cat	13/23	1	2	FACETS	0.231	0.192	0.275	0.231	0.192	0.275	SUBCLONAL	1	TRUE	1	0.813253127147504	2		319	425	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106094	8106094	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	18	419	0	ENST00000346208.3:c.914G>C	p.Arg305Pro	p.R305P	ENST00000346208		305	cGa/cCa	4/6	0.813253127147504	1	FACETS	0.098	0.073	0.127	0.098	0.073	0.127	SUBCLONAL	1	TRUE	0	0.813253127147504	1		419	268	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39294890	39294890	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	171	247	0	ENST00000402219.2:c.92A>C	p.Gln31Pro	p.Q31P	ENST00000402219	NM_005633.3	31	cAg/cCg	2/23	1	2	FACETS	0.949	0.882	1	0.949	0.882	1	CLONAL	1	TRUE	1	0.813253127147504	2		247	443	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64286814	64286814	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	41	425	0	ENST00000370651.3:c.29T>C	p.Val10Ala	p.V10A	ENST00000370651	NM_003463.4	10	gTg/gCg	2/6	1	2	FACETS	0.187	0.156	0.223	0.187	0.156	0.223	SUBCLONAL	1	TRUE	1	0.813253127147504	2		425	538	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931731	39931731	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	262	588	0	ENST00000378444.4:c.2868del	p.Lys956AsnfsTer65	p.K956Nfs*65	ENST00000378444	NM_001123385.1	956	aaA/aa	4/15	1	2	FACETS	0.883	0.831	0.935	0.883	0.831	0.935	CLONAL	1	TRUE	1	0.813253127147504	2		588	730	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913196	44913196	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	199	429	0	ENST00000377967.4:c.871G>C	p.Gly291Arg	p.G291R	ENST00000377967	NM_021140.2	291	Gga/Cga	10/29	1	2	FACETS	0.915	0.854	0.976	0.915	0.854	0.976	CLONAL	1	TRUE	1	0.813253127147504	2		429	535	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164941	123164941	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	148	269	0	ENST00000218089.9:c.254T>C	p.Phe85Ser	p.F85S	ENST00000218089	NM_001042749.1	85	tTt/tCt	5/35	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.813253127147504	2		269	364	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323957	31323957	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs151341333	NA	P-0042600-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	12	98	0	ENST00000412585.2:c.606G>C	p.Lys202Asn	p.K202N	ENST00000412585	NM_005514.6	202	aaG/aaC	3/8	1	2	FACETS	0.292	0.207	0.394	0.292	0.207	0.394	SUBCLONAL	1	TRUE	1	0.813253127147504	2		98	101	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577086	7577087	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0042631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	245	740	0	ENST00000269305.4:c.851_852del	p.Thr284ArgfsTer21	p.T284Rfs*21	ENST00000269305	NM_001126112.2	284	aCA/a	8/11	0.60037448434885	1	FACETS	0.929	0.876	0.982	0.929	0.876	0.982	CLONAL	1	TRUE	0	0.641905627162841	1		740	558	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506980	186506980	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	91	193	0	ENST00000323963.5:c.1146G>C	p.Lys382Asn	p.K382N	ENST00000323963		382	aaG/aaC	11/11	0.60037448434885	1	FACETS	0.982	0.894	1	0.982	0.894	1	CLONAL	1	TRUE	0	0.641905627162841	1		193	196	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111959729	111959729	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	205	618	0	ENST00000375549.3:c.308G>C	p.Gly103Ala	p.G103A	ENST00000375549	NM_003002.3	103	gGt/gCt	3/4	1	2	FACETS	0.978	0.912	1	0.978	0.912	1	CLONAL	1	TRUE	1	0.641905627162841	2		618	653	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627540	37627540	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	270	508	0	ENST00000447079.4:c.1455G>T	p.Glu485Asp	p.E485D	ENST00000447079	NM_015083.1	485	gaG/gaT	2/14	0.619069222679526	2	FACETS	0.871	0.829	0.913	0.871	0.829	0.913	CLONAL	2	TRUE	0	0.641905627162841	2		508	483	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244372	5244372	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	223	770	0	ENST00000357368.4:c.1110G>C	p.Lys370Asn	p.K370N	ENST00000357368	NM_002850.3	370	aaG/aaC	11/38	1	2	FACETS	0.962	0.9	1	0.962	0.9	1	CLONAL	1	TRUE	1	0.641905627162841	2		770	722	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72873587	72873587	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042631-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	61	343	0	ENST00000325599.8:c.715C>G	p.His239Asp	p.H239D	ENST00000325599	NM_018130.2	239	Cat/Gat	6/11	1	2	FACETS	0.757	0.66	0.86	0.757	0.66	0.86	SUBCLONAL	1	TRUE	1	0.641905627162841	2		343	251	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0042642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	33	337	0				ENST00000310581	NM_198253.2	-/1132			0.083647286711037	0	FACETS	0.482	0.393	0.582			1	INDETERMINATE	1	TRUE	0	0.28	0		337	352	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0042642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	36	389	0	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	1	2	FACETS	0.89	0.735	1	0.89	0.735	1	CLONAL	1	TRUE	1	0.28	2		389	289	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0042642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	96	780	4	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.28	2		784	520	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0042642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	82	1110	5	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.81	0.714	0.913	0.81	0.714	0.913	CLONAL	1	TRUE	1	0.28	2		1115	723	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265573	198265573	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	63	709	0	ENST00000335508.6:c.2584G>A	p.Glu862Lys	p.E862K	ENST00000335508	NM_012433.2	862	Gaa/Aaa	18/25	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.28	2		709	410	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092809	27092809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	71	874	1	ENST00000324856.7:c.2830C>T	p.Gln944Ter	p.Q944*	ENST00000324856	NM_006015.4	944	Cag/Tag	9/20	0.083647286711037	0	FACETS	0.607	0.529	0.69			1	INDETERMINATE	1	TRUE	0	0.28	0		875	602	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346884	73346884	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	24	349	0	ENST00000377767.4:c.1333del	p.Ser445HisfsTer20	p.S445Hfs*20	ENST00000377767	NM_014953.3	445	Tca/ca	9/21	1	2	FACETS	0.705	0.555	0.878	0.705	0.555	0.878	SUBCLONAL	1	TRUE	1	0.28	2		349	243	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742463	17742463	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	65	885	0	ENST00000250003.3:c.650del	p.Pro217ArgfsTer33	p.P217Rfs*33	ENST00000250003	NM_002478.4	215	ggC/gg	2/3	1	2	FACETS	0.879	0.763	1	0.879	0.763	1	CLONAL	1	TRUE	1	0.28	2		885	528	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0042642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	43	491	2	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.821	0.689	0.967	0.821	0.689	0.967	CLONAL	1	TRUE	1	0.28	2		493	374	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646981	23646981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	84	763	2	ENST00000261584.4:c.886del	p.Met296Ter	p.M296*	ENST00000261584	NM_024675.3	296	Atg/tg	4/13	1	2	FACETS	0.997	0.881	1	0.997	0.881	1	CLONAL	1	TRUE	1	0.28	2		765	602	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772950	135772951	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs118203724	NA	P-0042642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	32	555	3	ENST00000298552.3:c.2672dup	p.Asn891LysfsTer13	p.N891Kfs*13	ENST00000298552	NM_001162426.1	891	aac/aaAc	21/23	0.122340789052263	0	FACETS	0.45	0.365	0.545			1	INDETERMINATE	1	TRUE	0	0.28	0		558	366	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099080	157099080	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	27	264	0	ENST00000346085.5:c.17G>C	p.Gly6Ala	p.G6A	ENST00000346085	NM_020732.3	6	gGc/gCc	1/20	1	2	FACETS	0.778	0.621	0.955	0.778	0.621	0.955	CLONAL	1	TRUE	1	0.28	2		264	248	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926603	59926603	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	27	581	0	ENST00000259008.2:c.394del	p.Thr132ProfsTer25	p.T132Pfs*25	ENST00000259008	NM_032043.2	132	Acc/cc	5/20	1	2	FACETS	0.709	0.566	0.872	0.709	0.566	0.872	SUBCLONAL	1	TRUE	1	0.28	2		581	272	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0042642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	85	594	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.122340789052263	0	FACETS	0.702	0.621	0.788			1	INDETERMINATE	1	TRUE	0	0.28	0		594	623	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0042642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	90	539	6	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.28	2		545	617	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300836	137300836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	93	1122	1	ENST00000481739.1:c.481C>T	p.Arg161Trp	p.R161W	ENST00000481739	NM_002957.4	161	Cgg/Tgg	4/10	0.122340789052263	0	FACETS	0.695	0.618	0.777			1	INDETERMINATE	1	TRUE	0	0.28	0		1123	688	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100129	27100129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	67	972	1	ENST00000324856.7:c.3925C>T	p.Leu1309Phe	p.L1309F	ENST00000324856	NM_006015.4	1309	Ctc/Ttc	16/20	0.083647286711037	0	FACETS	0.655	0.57	0.747			1	INDETERMINATE	1	TRUE	0	0.28	0		973	526	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52661290	52661290	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	34	503	1	ENST00000394830.3:c.1540del	p.Ser514ValfsTer5	p.S514Vfs*5	ENST00000394830	NM_018313.4	514	Agt/gt	14/30	1	2	FACETS	0.662	0.541	0.797	0.662	0.541	0.797	SUBCLONAL	1	TRUE	1	0.28	2		504	367	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933839	39933839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749475374	NA	P-0042642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	99	523	1	ENST00000378444.4:c.760G>A	p.Gly254Ser	p.G254S	ENST00000378444	NM_001123385.1	254	Ggt/Agt	4/15	1	1	FACETS	0.798	0.718	0.882	1	0.984	1	SUBCLONAL	2	TRUE	0	0.28	1		524	381	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090446	37090446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs63750217	NA	P-0042642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	70	675	1	ENST00000231790.2:c.2041G>A	p.Ala681Thr	p.A681T	ENST00000231790	NM_000249.3	681	Gct/Act	18/19	1	2	FACETS	0.928	0.81	1	0.928	0.81	1	CLONAL	1	TRUE	1	0.28	2		676	539	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305286	65305286	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	32	617	0	ENST00000342505.4:c.2842G>A	p.Gly948Arg	p.G948R	ENST00000342505	NM_002227.2	948	Gga/Aga	20/25	1	2	FACETS	0.497	0.403	0.603	0.497	0.403	0.603	SUBCLONAL	1	TRUE	1	0.28	2		617	460	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981862	201981862	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	87	1198	0	ENST00000359651.3:c.573del	p.Gly192AlafsTer62	p.G192Afs*62	ENST00000359651		191	ccT/cc	4/8	1	2	FACETS	0.821	0.726	0.922	0.821	0.726	0.922	CLONAL	1	TRUE	1	0.28	2		1198	757	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366603	118366603	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	49	524	0	ENST00000534358.1:c.5555del	p.Leu1852Ter	p.L1852*	ENST00000534358	NM_005933.3	1851	aTt/at	19/36	1	2	FACETS	1	0.853	1	1	0.853	1	CLONAL	1	TRUE	1	0.28	2		524	349	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443641	49443641	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1064794007	NA	P-0042642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	86	945	2	ENST00000301067.7:c.3730del	p.Val1244SerfsTer86	p.V1244Sfs*86	ENST00000301067	NM_003482.3	1244	Gtc/tc	11/54	1	2	FACETS	0.988	0.875	1	0.988	0.875	1	CLONAL	1	TRUE	1	0.28	2		947	622	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576217	88576217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	72	763	1	ENST00000360948.2:c.1456C>T	p.His486Tyr	p.H486Y	ENST00000360948	NM_001012338.2	486	Cac/Tac	13/19	1	2	FACETS	0.894	0.782	1	0.894	0.782	1	CLONAL	1	TRUE	1	0.28	2		764	575	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830780	3830780	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	52	671	0	ENST00000262367.5:c.1776G>A	p.Trp592Ter	p.W592*	ENST00000262367	NM_004380.2	592	tgG/tgA	8/31	1	2	FACETS	0.702	0.598	0.816	0.702	0.598	0.816	SUBCLONAL	1	TRUE	1	0.28	2		671	529	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822005	72822005	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	46	520	0	ENST00000268489.5:c.10170del	p.Val3391CysfsTer94	p.V3391Cfs*94	ENST00000268489	NM_006885.3	3390	aaA/aa	10/10	1	2	FACETS	0.893	0.754	1	0.893	0.754	1	CLONAL	1	TRUE	1	0.28	2		520	368	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346751	89346751	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1567558766	NA	P-0042642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	55	772	0	ENST00000301030.4:c.6199A>G	p.Ser2067Gly	p.S2067G	ENST00000301030	NM_001256183.1	2067	Agc/Ggc	9/13	1	2	FACETS	0.995	0.854	1	0.995	0.854	1	CLONAL	1	TRUE	1	0.28	2		772	395	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051247	128051247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	72	917	0	ENST00000285398.2:c.76G>A	p.Glu26Lys	p.E26K	ENST00000285398	NM_000122.1	26	Gaa/Aaa	2/15	1	2	FACETS	0.802	0.701	0.912	0.802	0.701	0.912	CLONAL	1	TRUE	1	0.28	2		917	641	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945338	54945338	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	48	601	0	ENST00000312783.6:c.1088T>C	p.Leu363Pro	p.L363P	ENST00000312783	NM_198436.1	363	cTg/cCg	10/10	0.083647286711037	0	FACETS	0.625	0.529	0.73			1	INDETERMINATE	1	TRUE	0	0.28	0		601	395	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22142995	22142995	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	42	581	0	ENST00000215832.6:c.712A>G	p.Asn238Asp	p.N238D	ENST00000215832	NM_002745.4	238	Aac/Gac	5/9	0.083647286711037	0	FACETS	0.474	0.395	0.56			1	INDETERMINATE	1	TRUE	0	0.28	0		581	456	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31406984	31406984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	76	890	0	ENST00000344624.3:c.3923G>A	p.Arg1308Lys	p.R1308K	ENST00000344624		1308	aGa/aAa	31/33	1	2	FACETS	0.804	0.705	0.911	0.804	0.705	0.911	CLONAL	1	TRUE	1	0.28	2		890	675	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707830	176707830	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042642-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	22	435	0	ENST00000439151.2:c.5891del	p.Lys1964ArgfsTer5	p.K1964Rfs*5	ENST00000439151	NM_022455.4	1963	Aaa/aa	18/23	1	2	FACETS	0.462	0.358	0.583	0.462	0.358	0.583	SUBCLONAL	1	TRUE	1	0.28	2		435	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0042683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	451	683	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.656496804128264	2	FACETS	0.867	0.837	0.896	0.867	0.837	0.896	CLONAL	2	TRUE	0	0.744423521783091	2		683	699	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61197647	61197647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	697	511	0	ENST00000301761.2:c.29C>T	p.Ser10Leu	p.S10L	ENST00000301761	NM_017841.2	10	tCg/tTg	1/4	0.6042187385291	4	FACETS	0.926	0.906	0.945	0.926	0.906	0.945	CLONAL	4	TRUE	0	0.744423521783091	4		511	882	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944956	31944956	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	199	699	0	ENST00000340398.3:c.145C>T	p.Arg49Ter	p.R49*	ENST00000340398	NM_001013699.2	49	Cga/Tga	1/1	0.681464637043051	3	FACETS	0.953	0.885	1	0.476	0.442	0.512	CLONAL	1	TRUE	1	0.744423521783091	3		699	770	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699300	117699300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	177	457	0	ENST00000369458.3:c.341C>T	p.Ser114Phe	p.S114F	ENST00000369458	NM_024626.3	114	tCt/tTt	3/6	0.575071928319374	3	FACETS	0.85	0.784	0.917			1	CLONAL	1	TRUE	NA	0.744423521783091	3		457	768	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867218	68867218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555518215	NA	P-0042683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	193	552	0	ENST00000261769.5:c.2465C>T	p.Pro822Leu	p.P822L	ENST00000261769	NM_004360.3	822	cCc/cTc	16/16	1	2	FACETS	0.784	0.729	0.842	0.784	0.729	0.842	SUBCLONAL	1	TRUE	1	0.744423521783091	2		552	661	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523578	41523578	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	215	691	0	ENST00000263253.7:c.995del	p.Pro332GlnfsTer30	p.P332Qfs*30	ENST00000263253	NM_001429.3	332	Cca/ca	4/31	0.688943821900534	4	FACETS	0.828	0.768	0.89			1	CLONAL	1	TRUE	NA	0.744423521783091	4		691	1217	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69039640	69039640	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	166	343	0	ENST00000288368.4:c.3752T>C	p.Leu1251Pro	p.L1251P	ENST00000288368	NM_024870.2	1251	cTt/cCt	31/40	0.744423521783091	5	FACETS	0.868	0.802	0.935	0.578	0.535	0.624	CLONAL	2	TRUE	2	0.744423521783091	5		343	544	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	256	401	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.224527731480501	4	FACETS	0.992	0.93	1			1	CLONAL	4	TRUE	NA	0.15	4		401	989	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874547	155874547	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	73	759	3	ENST00000368323.3:c.212T>A	p.Leu71Gln	p.L71Q	ENST00000368323	NM_006912.5	71	cTg/cAg	4/6	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.15	2		762	964	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15365029	15365029	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	101	895	0	ENST00000263377.2:c.2092T>G	p.Phe698Val	p.F698V	ENST00000263377	NM_058243.2	698	Ttc/Gtc	11/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.15	2		895	1153	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702341	47702341	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	40	551	0	ENST00000233146.2:c.1937A>T	p.Asp646Val	p.D646V	ENST00000233146	NM_000251.2	646	gAt/gTt	12/16	1	2	FACETS	0.736	0.61	0.877	0.736	0.61	0.877	SUBCLONAL	1	TRUE	1	0.15	2		551	725	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119624701	119624701	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0042709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	42	423	0	ENST00000316626.5:c.716-2A>T		p.X239_splice	ENST00000316626		239			1	2	FACETS	0.962	0.802	1	0.962	0.802	1	CLONAL	1	TRUE	1	0.15	2		423	582	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564461	55564466	+	inframe_deletion	In_Frame_Del	DEL	CTTTTC	CTTTTC	-	novel	NA	P-0042709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	58	548	0	ENST00000288135.5:c.352_357del	p.Phe118_Leu119del	p.F118_L119del	ENST00000288135	NM_000222.2	117	CTTTTC/-	3/21	1	2	FACETS	0.943	0.808	1	0.943	0.808	1	CLONAL	1	TRUE	1	0.15	2		548	820	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047932	180047932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1504	82	1167	0	ENST00000261937.6:c.2243G>A	p.Cys748Tyr	p.C748Y	ENST00000261937	NM_182925.4	748	tGc/tAc	15/30	0.175014432648796	3	FACETS	0.741	0.65	0.839	0.371	0.325	0.42	SUBCLONAL	1	TRUE	1	0.15	3		1167	1586	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888198	112888198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121918453	NA	P-0042748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	50	516	0	ENST00000351677.2:c.214G>A	p.Ala72Thr	p.A72T	ENST00000351677	NM_002834.3	72	Gcc/Acc	3/16	1	2	FACETS	0.273	0.231	0.32	0.273	0.231	0.32	SUBCLONAL	1	TRUE	1	0.538434644501817	2		516	680	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988128	85988128	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	110	354	0	ENST00000263360.6:c.1073A>G	p.Tyr358Cys	p.Y358C	ENST00000263360	NM_003797.3	358	tAc/tGc	10/12	1	2	FACETS	0.894	0.808	0.984	0.894	0.808	0.984	CLONAL	1	TRUE	1	0.538434644501817	2		354	457	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875985	76875985	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042748-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	87	291	0	ENST00000373344.5:c.5150T>G	p.Val1717Gly	p.V1717G	ENST00000373344	NM_000489.3	1717	gTt/gGt	20/35	1	2	FACETS	0.857	0.764	0.955	0.857	0.764	0.955	CLONAL	1	TRUE	1	0.538434644501817	2		291	377	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0042813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	304	735	0	ENST00000346208.3:c.1220_1221insT	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcTg	6/6	0.304440131649217	5	FACETS	1	0.992	1	0.831	0.788	0.874	INDETERMINATE	2	TRUE	2	0.671764117033693	5		735	729	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510132	120510132	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	212	571	0	ENST00000256646.2:c.1377G>T	p.Glu459Asp	p.E459D	ENST00000256646	NM_024408.3	459	gaG/gaT	8/34	0.671764117033693	3	FACETS	0.997	0.939	1	0.997	0.939	1	CLONAL	2	TRUE	1	0.671764117033693	3		571	423	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161326630	161326630	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs757663926	NA	P-0042813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	95	996	0	ENST00000367975.2:c.405G>C	p.Leu135Phe	p.L135F	ENST00000367975	NM_003001.3	135	ttG/ttC	5/6	0.671764117033693	3	FACETS	0.825	0.738	0.916	0.412	0.369	0.458	CLONAL	1	TRUE	1	0.671764117033693	3		996	458	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371634	89371635	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0042813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	124	835	0	ENST00000301030.4:c.205dup	p.Glu69GlyfsTer13	p.E69Gfs*13	ENST00000301030	NM_001256183.1	69	gag/gGag	4/13	0.671764117033693	2	FACETS	0.932	0.851	1	0.466	0.425	0.508	CLONAL	1	TRUE	0	0.671764117033693	2		835	396	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699308	47699320	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CATTTCAGTTTAT	CATTTCAGTTTAT	-	novel	NA	P-0042813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	105	447	0	ENST00000347630.2:c.188_200del	p.Asp63GlyfsTer5	p.D63Gfs*5	ENST00000347630	NM_001007230.1	63	gATAAACTGAAATGg/gg	4/11	0.671764117033693	3	FACETS	1	0.979	1			1	CLONAL	3	TRUE	NA	0.671764117033693	3		447	129	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940099	31940099	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs759072198	NA	P-0042813-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	300	1010	1	ENST00000375333.2:c.241G>T	p.Val81Leu	p.V81L	ENST00000375333	NM_032454.1	81	Gta/Tta	2/8	0.671764117033693	3	FACETS	0.921	0.874	0.967	0.921	0.874	0.967	CLONAL	2	TRUE	1	0.671764117033693	3		1011	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578537	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs879254214	NA	P-0042831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	853	1327	0	ENST00000269305.4:c.393_395del	p.Asn131del	p.N131del	ENST00000269305	NM_001126112.2	131	aaCAAg/aag	5/11	0.692819997238761	3	FACETS	0.975	0.954	0.994	0.975	0.954	0.994	CLONAL	3	FALSE	0	0.692819997238761	3		1327	1134	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849121	156849121	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	213	1264	0	ENST00000524377.1:c.2013G>C	p.Met671Ile	p.M671I	ENST00000524377	NM_002529.3	671	atG/atC	15/17	0.659900222026222	3	FACETS	0.895	0.832	0.96	0.448	0.416	0.48	CLONAL	1	FALSE	1	0.692819997238761	3		1264	925	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246078920	246078920	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs769267565	NA	P-0042831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	358	721	0	ENST00000388985.4:c.725T>C	p.Met242Thr	p.M242T	ENST00000388985		242	aTg/aCg	8/12	0.387113893374668	3	FACETS	1	0.975	1	0.684	0.654	0.714	INDETERMINATE	2	FALSE	0	0.692819997238761	3		721	678	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170465	119170484	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTCTCCTGCCCATGTAGC	TCTTCTCCTGCCCATGTAGC	-	novel	NA	P-0042831-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	195	505	0	ENST00000264033.4:c.2696_2715del	p.Ser899TyrfsTer15	p.S899Yfs*15	ENST00000264033	NM_005188.3	899	TCTTCTCCTGCCCATGTAGCt/t	16/16	0.692819997238761	4	FACETS	1	0.975	1	0.719	0.673	0.765	CLONAL	2	FALSE	1	0.692819997238761	4		505	442	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042835-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	125	372	0				ENST00000310581	NM_198253.2	-/1132			0.518074415329359	1	FACETS	0.842	0.775	0.91	0.842	0.775	0.91	CLONAL	1	TRUE	0	0.670878170361201	1		372	294	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57569935	57569935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042835-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	97	253	0	ENST00000316660.6:c.115C>T	p.Arg39Trp	p.R39W	ENST00000316660	NM_021127.2	39	Cgg/Tgg	2/2	0.377104067158381	1	FACETS	0.588	0.529	0.648	0.588	0.529	0.648	INDETERMINATE	1	TRUE	0	0.670878170361201	1		253	327	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958789	55958789	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	47	709	1	ENST00000263923.4:c.3064C>T	p.Arg1022Ter	p.R1022*	ENST00000263923	NM_002253.2	1022	Cga/Tga	22/30	1	2	FACETS	0.576	0.484	0.678	0.576	0.484	0.678	SUBCLONAL	1	TRUE	1	0.2	2		710	816	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199864	138199864	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	51	643	0	ENST00000237289.4:c.1282G>C	p.Glu428Gln	p.E428Q	ENST00000237289	NM_001270507.1	428	Gag/Cag	7/9	1	2	FACETS	0.787	0.668	0.918	0.787	0.668	0.918	CLONAL	1	TRUE	1	0.2	2		643	648	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482425	56482425	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	68	805	0	ENST00000267101.3:c.973G>C	p.Gly325Arg	p.G325R	ENST00000267101	NM_001982.3	325	Gga/Cga	8/28	1	2	FACETS	0.816	0.709	0.933	0.816	0.709	0.933	CLONAL	1	TRUE	1	0.2	2		805	833	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809318	243809318	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	40	480	0	ENST00000263826.5:c.306C>G	p.Ile102Met	p.I102M	ENST00000263826	NM_005465.4	102	atC/atG	4/13	1	2	FACETS	0.677	0.561	0.806	0.677	0.561	0.806	SUBCLONAL	1	TRUE	1	0.2	2		480	591	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404566	8404566	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1187703316	NA	P-0042860-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	33	380	0	ENST00000356435.5:c.4181A>T	p.His1394Leu	p.H1394L	ENST00000356435		1394	cAt/cTt	25/35	1	2	FACETS	0.743	0.605	0.899	0.743	0.605	0.899	SUBCLONAL	1	TRUE	1	0.2	2		380	444	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1555525429	NA	P-0042962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	234	617	1	ENST00000269305.4:c.782+1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.400862831968579	1	FACETS	0.981	0.924	1	0.981	0.924	1	CLONAL	1	TRUE	0	0.6141743293293	1		618	538	SUCCESS
BLM	641	MSKCC	GRCh37	15	91306325	91306338	+	frameshift_variant	Frame_Shift_Del	DEL	ATCAGCTAGAGGCG	ATCAGCTAGAGGCG	-	novel	NA	P-0042962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	133	441	0	ENST00000355112.3:c.2016_2029del	p.Leu673CysfsTer6	p.L673Cfs*6	ENST00000355112	NM_000057.2	671	aATCAGCTAGAGGCG/a	8/22	0.615925761043892	3	FACETS	0.866	0.788	0.947	0.433	0.394	0.474	CLONAL	1	TRUE	1	0.6141743293293	3		441	654	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217414	7217414	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	59	570	0	ENST00000380728.2:c.382C>G	p.Leu128Val	p.L128V	ENST00000380728		128	Ctc/Gtc	5/11	0.400862831968579	1	FACETS	0.197	0.169	0.228	0.197	0.169	0.228	SUBCLONAL	1	TRUE	0	0.6141743293293	1		570	675	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560105	29560105	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	174	382	0	ENST00000356175.3:c.3582del	p.Asp1194GlufsTer21	p.D1194Efs*21	ENST00000356175	NM_000267.3	1194	gaC/ga	27/57	0.614472772235493	1	FACETS	0.903	0.84	0.966	0.903	0.84	0.966	CLONAL	1	TRUE	0	0.6141743293293	1		382	435	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350518	15350518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042962-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	184	608	4	ENST00000263377.2:c.3397C>T	p.Pro1133Ser	p.P1133S	ENST00000263377	NM_058243.2	1133	Ccc/Tcc	16/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.6141743293293	2		612	576	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0042999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	94	290	2	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.858	0.768	0.952	0.858	0.768	0.952	CLONAL	1	TRUE	1	0.515755697384198	2		292	425	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717695	89717696	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1060500115	NA	P-0042999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	154	426	0	ENST00000371953.3:c.723dup	p.Glu242Ter	p.E242*	ENST00000371953	NM_000314.4	240	-/T	7/9	0.459164543211153	2	FACETS	1	0.989	1	0.743	0.687	0.799	CLONAL	1	TRUE	0	0.515755697384198	2		426	402	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636750	2636750	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	30	599	0	ENST00000342085.4:c.1199C>T	p.Ser400Phe	p.S400F	ENST00000342085	NM_002613.4	400	tCc/tTc	11/14	0.437307513201365	1	FACETS	0.169	0.135	0.207	0.169	0.135	0.207	SUBCLONAL	1	TRUE	0	0.515755697384198	1		599	511	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348815	11348815	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	42	157	0	ENST00000332029.2:c.521T>A	p.Leu174Gln	p.L174Q	ENST00000332029	NM_003745.1	174	cTg/cAg	2/2	1	2	FACETS	0.952	0.807	1	0.952	0.807	1	CLONAL	1	TRUE	1	0.515755697384198	2		157	171	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554308	29554308	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	174	625	0	ENST00000356175.3:c.2324A>T	p.Glu775Val	p.E775V	ENST00000356175	NM_000267.3	775	gAg/gTg	19/57	0.515755697384198	1	FACETS	0.86	0.797	0.926	0.86	0.797	0.926	CLONAL	1	TRUE	0	0.515755697384198	1		625	582	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15374322	15374322	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042999-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	133	551	0	ENST00000263377.2:c.1250A>G	p.Glu417Gly	p.E417G	ENST00000263377	NM_058243.2	417	gAg/gGg	7/20	0.404530846829168	1	FACETS	0.641	0.584	0.701	0.641	0.584	0.701	SUBCLONAL	1	TRUE	0	0.515755697384198	1		551	597	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0043003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	49	377	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.819	0.695	0.954	0.819	0.695	0.954	CLONAL	1	FALSE	1	0.3	2		377	399	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0043003-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	73	779	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.3	1	FACETS	0.707	0.619	0.802	0.707	0.619	0.802	SUBCLONAL	1	FALSE	0	0.3	1		781	585	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0043004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	40	381	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.787	0.654	0.934	0.787	0.654	0.934	CLONAL	1	TRUE	1	0.236945045154861	2		381	429	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115727	108115727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747727055	NA	P-0043004-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	23	353	0	ENST00000278616.4:c.875C>T	p.Pro292Leu	p.P292L	ENST00000278616	NM_000051.3	292	cCg/cTg	7/63	1	2	FACETS	0.767	0.6	0.96	0.767	0.6	0.96	CLONAL	1	TRUE	1	0.236945045154861	2		353	253	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0043038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	499	639	1	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	0.831946649077198	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.831946649077198	2		640	565	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432741	49432744	+	frameshift_variant	Frame_Shift_Del	DEL	GATA	GATA	-	novel	NA	P-0043038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	372	654	0	ENST00000301067.7:c.8395_8398del	p.Tyr2799SerfsTer51	p.Y2799Sfs*51	ENST00000301067	NM_003482.3	2799	TATCag/ag	34/54	0.825674566673874	2	FACETS	0.983	0.956	1	0.983	0.956	1	CLONAL	2	TRUE	0	0.831946649077198	2		654	455	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862824	9862824	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1404178457	NA	P-0043038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	363	670	0	ENST00000330684.3:c.2479G>A	p.Ala827Thr	p.A827T	ENST00000330684	NM_001134407.1	827	Gcc/Acc	12/13	0.208060426866218	3	FACETS	0.951	0.911	0.99	0.634	0.607	0.66	INDETERMINATE	2	TRUE	0	0.831946649077198	3		670	650	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76936728	76937405	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCATTACTCCAGAGAAAAGCACTAAACATTGATAAAGAAATTTTGTCATTTACTCAACAAATTTGAGATCCCTGATACTGAATACTAGCAATGTTCAAAATATCTTCCAATGGCAGCATAAAAATAAATAGGGAAACTTTTTTTAATAAACTCCTAAATAATTTTTAAGTGGTATTCTCCTAAGTAGTAACCCTAAATTTGATTAGCTTCAGAGGAAATTAAACAATGTAGTAACTCAAGAGGGGGAAGTACAAATTATGAATTTTTTATTTATTTTTGCATACCTGAAGATTGGCAAAATCCAGTATGTGAAGACAGCACTAAATTTTCAGTCACAGGCTTAATTTTCTGTTCATCGCTGCTTCCCTCACCTATAGAATTCTGATCATCATCTTCTATATCAGAAGAAGATGAGGATGTAATGTCAGCTTGCTTCCTTTTAGTGCTTGTTCTTAGGGAGTTTCTCTTTTTCTCCTTGACAATGACTGCCTTCTTTTTAGATGAAGTTCTTTGCTTCTTCTTTTTATTATCTTCAGAACTTTCCTCAGCATCAGATGATGATGAGCCACTTTGTATTTCCTTAGTATTTCTCTTTGAACTTAAATTTCTTCTTTCCCTCAATTCTATTCTTTTCAGTCTCTTATCAGAAGAGTTACAACCATCTTCTTTCATGGAATA	TCATTACTCCAGAGAAAAGCACTAAACATTGATAAAGAAATTTTGTCATTTACTCAACAAATTTGAGATCCCTGATACTGAATACTAGCAATGTTCAAAATATCTTCCAATGGCAGCATAAAAATAAATAGGGAAACTTTTTTTAATAAACTCCTAAATAATTTTTAAGTGGTATTCTCCTAAGTAGTAACCCTAAATTTGATTAGCTTCAGAGGAAATTAAACAATGTAGTAACTCAAGAGGGGGAAGTACAAATTATGAATTTTTTATTTATTTTTGCATACCTGAAGATTGGCAAAATCCAGTATGTGAAGACAGCACTAAATTTTCAGTCACAGGCTTAATTTTCTGTTCATCGCTGCTTCCCTCACCTATAGAATTCTGATCATCATCTTCTATATCAGAAGAAGATGAGGATGTAATGTCAGCTTGCTTCCTTTTAGTGCTTGTTCTTAGGGAGTTTCTCTTTTTCTCCTTGACAATGACTGCCTTCTTTTTAGATGAAGTTCTTTGCTTCTTCTTTTTATTATCTTCAGAACTTTCCTCAGCATCAGATGATGATGAGCCACTTTGTATTTCCTTAGTATTTCTCTTTGAACTTAAATTTCTTCTTTCCCTCAATTCTATTCTTTTCAGTCTCTTATCAGAAGAGTTACAACCATCTTCTTTCATGGAATA	-	novel	NA	P-0043038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	.	122	4	0	ENST00000373344.5:c.3343_3736+284del		p.X1115_splice	ENST00000373344	NM_000489.3	1115		9/35	0.662566525966855	4	FACETS		NA	1			1	NA	NA	TRUE	1	0.831946649077198	4		4	122	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938210	76938211	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCTTTTGTATTTGGAAT	novel	NA	P-0043038-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	124	341	0	ENST00000373344.5:c.2521_2537dup	p.Asp846GlufsTer29	p.D846Efs*29	ENST00000373344	NM_000489.3	846	gat/gaATTCCAAATACAAAAGAt	9/35	0.662566525966855	4	FACETS	1	0.93	1	0.342	0.311	0.375	CLONAL	1	TRUE	1	0.831946649077198	4		341	532	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	130	548	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	FALSE	1	0.272181769540838	2		548	897	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	135	358	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.20213738976287	3	FACETS	0.815	0.743	0.892	0.815	0.743	0.892	CLONAL	2	FALSE	1	0.272181769540838	3		358	691	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	104	857	0	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	1	2	FACETS	0.697	0.623	0.777	0.697	0.623	0.777	SUBCLONAL	1	FALSE	1	0.272181769540838	2		857	1096	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348413	89348413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1289430140	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	158	942	1	ENST00000301030.4:c.4537G>A	p.Val1513Met	p.V1513M	ENST00000301030	NM_001256183.1	1513	Gtg/Atg	9/13	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.272181769540838	2		943	1018	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119791	70119791	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	177	797	0	ENST00000245479.2:c.793C>T	p.Gln265Ter	p.Q265*	ENST00000245479	NM_000346.3	265	Cag/Tag	3/3	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.272181769540838	2		797	884	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202851	16202851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777745414	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	135	625	1	ENST00000375759.3:c.559C>T	p.Arg187Trp	p.R187W	ENST00000375759	NM_015001.2	187	Cgg/Tgg	3/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.272181769540838	2		626	792	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107136	27107137	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	110	552	0	ENST00000324856.7:c.6749_6750del	p.Glu2250ValfsTer27	p.E2250Vfs*27	ENST00000324856	NM_006015.4	2249	tcAGag/tcag	20/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.272181769540838	2		552	687	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807519	36807519	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	181	780	0	ENST00000373129.3:c.1145A>T	p.Gln382Leu	p.Q382L	ENST00000373129	NM_032017.1	382	cAg/cTg	12/12	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.272181769540838	2		780	999	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301104	65301104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs543134894	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	71	294	0	ENST00000342505.4:c.3344C>T	p.Pro1115Leu	p.P1115L	ENST00000342505	NM_002227.2	1115	cCg/cTg	24/25	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.272181769540838	2		294	411	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304164	65304164	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	91	247	0	ENST00000342505.4:c.2951C>T	p.Ala984Val	p.A984V	ENST00000342505	NM_002227.2	984	gCc/gTc	21/25	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	FALSE	1	0.272181769540838	2		247	630	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874197	155874197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375724784	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	188	653	0	ENST00000368323.3:c.334C>T	p.Arg112Cys	p.R112C	ENST00000368323	NM_006912.5	112	Cgt/Tgt	5/6	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.272181769540838	2		653	937	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206646635	206646635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	206	1005	1	ENST00000367120.3:c.65G>A	p.Ser22Asn	p.S22N	ENST00000367120	NM_014002.3	22	aGt/aAt	3/22	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.272181769540838	2		1006	1184	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669326	241669326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147437099	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	105	426	0	ENST00000366560.3:c.881C>T	p.Ala294Val	p.A294V	ENST00000366560	NM_000143.3	294	gCt/gTt	6/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.272181769540838	2		426	640	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375030	104375030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs79299301	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	136	557	0	ENST00000369902.3:c.1028G>A	p.Arg343His	p.R343H	ENST00000369902	NM_016169.3	343	cGc/cAc	9/12	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.272181769540838	2		557	687	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920393	114920393	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	108	489	0	ENST00000543371.1:c.1334A>C	p.Lys445Thr	p.K445T	ENST00000543371	NM_001198531.1	445	aAg/aCg	13/14	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.272181769540838	2		489	721	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925334	114925334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	106	575	0	ENST00000543371.1:c.1412G>A	p.Arg471His	p.R471H	ENST00000543371	NM_001198531.1	471	cGc/cAc	14/14	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	1	0.272181769540838	2		575	720	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380410	14380410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	26	185	0	ENST00000256196.4:c.7G>A	p.Ala3Thr	p.A3T	ENST00000256196		3	Gcg/Acg	1/6	1	2	FACETS	0.816	0.65	1	0.816	0.65	1	CLONAL	1	FALSE	1	0.272181769540838	2		185	234	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572198	64572198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	149	557	1	ENST00000312049.6:c.1441C>T	p.Arg481Trp	p.R481W	ENST00000312049	NM_130799.2	481	Cgg/Tgg	10/10	1	2	FACETS	0.846	0.775	0.92	1	0.99	1	CLONAL	2	FALSE	1	0.272181769540838	2		558	647	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203741	94203741	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372000848	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	72	163	0	ENST00000323929.3:c.913C>T	p.Arg305Trp	p.R305W	ENST00000323929	NM_005591.3	305	Cgg/Tgg	9/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.272181769540838	2		163	427	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376700	118376700	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375852658	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	113	552	1	ENST00000534358.1:c.10093G>A	p.Val3365Ile	p.V3365I	ENST00000534358	NM_005933.3	3365	Gtc/Atc	27/36	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.272181769540838	2		553	617	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404740	404740	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	76	383	0	ENST00000399788.2:c.4454A>G	p.Glu1485Gly	p.E1485G	ENST00000399788	NM_001042603.1	1485	gAg/gGg	26/28	NA	2	FACETS	1	0.956	1			1	INDETERMINATE	1	FALSE	NA	0.272181769540838	2		383	470	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420116	420116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1281370065	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	125	575	0	ENST00000399788.2:c.3151C>T	p.Arg1051Trp	p.R1051W	ENST00000399788	NM_001042603.1	1051	Cgg/Tgg	21/28	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	FALSE	NA	0.272181769540838	2		575	784	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420852	49420852	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	108	629	0	ENST00000301067.7:c.14897G>T	p.Arg4966Leu	p.R4966L	ENST00000301067	NM_003482.3	4966	cGg/cTg	48/54	1	2	FACETS	0.895	0.802	0.993	0.895	0.802	0.993	CLONAL	1	FALSE	1	0.272181769540838	2		629	887	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421893	49421893	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	155	751	0	ENST00000301067.7:c.14414A>C	p.Glu4805Ala	p.E4805A	ENST00000301067	NM_003482.3	4805	gAg/gCg	46/54	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.272181769540838	2		751	856	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433122	49433122	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	168	853	2	ENST00000301067.7:c.8249G>T	p.Gly2750Val	p.G2750V	ENST00000301067	NM_003482.3	2750	gGg/gTg	33/54	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.272181769540838	2		855	857	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	194	924	1	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.272181769540838	2		925	1085	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202740	133202740	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs5745068	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	148	661	0	ENST00000320574.5:c.6494G>A	p.Arg2165His	p.R2165H	ENST00000320574	NM_006231.2	2165	cGc/cAc	46/49	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.272181769540838	2		661	844	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560382	95560382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	142	609	0	ENST00000393063.1:c.5207G>A	p.Arg1736Gln	p.R1736Q	ENST00000393063	NM_030621.3	1736	cGg/cAg	25/28	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.272181769540838	2		609	720	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003191	42003191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs761227360	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	152	540	0	ENST00000219905.7:c.2728C>T	p.Arg910Ter	p.R910*	ENST00000219905	NM_001164273.1	910	Cga/Tga	8/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.272181769540838	2		540	924	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43749302	43749302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1379752908	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	146	405	1	ENST00000382044.4:c.1504C>T	p.Pro502Ser	p.P502S	ENST00000382044	NM_001141980.1	502	Cca/Tca	12/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.272181769540838	2		406	833	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134359	2134359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137854065	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	204	1007	0	ENST00000219476.3:c.4136C>T	p.Ser1379Leu	p.S1379L	ENST00000219476	NM_000548.3	1379	tCg/tTg	34/42	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.272181769540838	2		1007	1087	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916133	9916133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	86	508	0	ENST00000330684.3:c.2156G>A	p.Ser719Asn	p.S719N	ENST00000330684	NM_001134407.1	719	aGc/aAc	10/13	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	FALSE	1	0.272181769540838	2		508	630	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868112	56868112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374706761	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	54	607	0	ENST00000308159.5:c.1610G>A	p.Arg537Gln	p.R537Q	ENST00000308159	NM_014669.4	537	cGg/cAg	14/22	1	2	FACETS	0.434	0.369	0.505	0.434	0.369	0.505	SUBCLONAL	1	FALSE	1	0.272181769540838	2		607	915	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660602	67660602	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	179	629	0	ENST00000264010.4:c.1502A>G	p.Asp501Gly	p.D501G	ENST00000264010	NM_006565.3	501	gAt/gGt	8/12	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.272181769540838	2		629	986	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832404	72832404	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	91	519	0	ENST00000268489.5:c.4177G>T	p.Val1393Leu	p.V1393L	ENST00000268489	NM_006885.3	1393	Gtg/Ttg	9/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.272181769540838	2		519	570	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993863	72993863	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	66	592	0	ENST00000268489.5:c.182T>C	p.Leu61Pro	p.L61P	ENST00000268489	NM_006885.3	61	cTc/cCc	2/10	1	2	FACETS	0.823	0.715	0.941	0.823	0.715	0.941	CLONAL	1	FALSE	1	0.272181769540838	2		592	589	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348221	89348221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1488507469	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	178	906	1	ENST00000301030.4:c.4729G>A	p.Asp1577Asn	p.D1577N	ENST00000301030	NM_001256183.1	1577	Gac/Aac	9/13	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.272181769540838	2		907	992	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118616	17118616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112980409	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	170	511	0	ENST00000285071.4:c.1315G>A	p.Val439Met	p.V439M	ENST00000285071	NM_144997.5	439	Gtg/Atg	12/14	1	2	FACETS	0.823	0.758	0.89	1	0.991	1	CLONAL	2	FALSE	1	0.272181769540838	2		511	759	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40368115	40368115	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	161	626	0	ENST00000293328.3:c.1390C>A	p.Leu464Met	p.L464M	ENST00000293328	NM_012448.3	464	Ctg/Atg	12/19	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.272181769540838	2		626	814	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936850	78936850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	97	430	0	ENST00000306801.3:c.3932C>T	p.Pro1311Leu	p.P1311L	ENST00000306801	NM_020761.2	1311	cCg/cTg	33/34	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.272181769540838	2		430	525	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7119479	7119479	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369102740	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	84	663	0	ENST00000302850.5:c.3775G>A	p.Asp1259Asn	p.D1259N	ENST00000302850	NM_000208.2	1259	Gac/Aac	21/22	1	2	FACETS	0.668	0.589	0.753	0.668	0.589	0.753	SUBCLONAL	1	FALSE	1	0.272181769540838	2		663	924	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247805	10247805	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770535972	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	241	938	0	ENST00000340748.4:c.4397G>A	p.Arg1466His	p.R1466H	ENST00000340748		1466	cGc/cAc	36/40	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.272181769540838	2		938	1252	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600005	10600005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	99	886	0	ENST00000171111.5:c.1571G>A	p.Gly524Asp	p.G524D	ENST00000171111	NM_203500.1	524	gGc/gAc	5/6	1	2	FACETS	0.679	0.605	0.759	0.679	0.605	0.759	SUBCLONAL	1	FALSE	1	0.272181769540838	2		886	1071	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627496	14627496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	174	610	1	ENST00000254322.2:c.574C>T	p.Pro192Ser	p.P192S	ENST00000254322	NM_006145.1	192	Ccc/Tcc	2/3	1	2	FACETS	0.773	0.712	0.836	1	0.99	1	SUBCLONAL	2	FALSE	1	0.272181769540838	2		611	827	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276311	15276311	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754537422	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	170	803	0	ENST00000263388.2:c.5683C>T	p.Arg1895Cys	p.R1895C	ENST00000263388	NM_000435.2	1895	Cgc/Tgc	31/33	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.272181769540838	2		803	887	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212576	36212576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568272454	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	248	1066	0	ENST00000222270.7:c.2327G>A	p.Arg776Gln	p.R776Q	ENST00000222270	NM_014727.1	776	cGg/cAg	3/37	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	1	0.272181769540838	2		1066	1241	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228789	36228789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	194	890	0	ENST00000222270.7:c.7688C>T	p.Ala2563Val	p.A2563V	ENST00000222270	NM_014727.1	2563	gCc/gTc	35/37	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.272181769540838	2		890	1114	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792080	42792080	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141544536	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	142	718	0	ENST00000575354.2:c.884C>T	p.Thr295Met	p.T295M	ENST00000575354	NM_015125.3	295	aCg/aTg	6/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.272181769540838	2		718	833	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796340	42796340	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	91	1029	0	ENST00000575354.2:c.2989C>A	p.Leu997Met	p.L997M	ENST00000575354	NM_015125.3	997	Ctg/Atg	12/20	1	2	FACETS	0.566	0.501	0.636	0.566	0.501	0.636	SUBCLONAL	1	FALSE	1	0.272181769540838	2		1029	1181	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797780	42797780	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771163344	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	167	852	0	ENST00000575354.2:c.3832G>A	p.Val1278Ile	p.V1278I	ENST00000575354	NM_015125.3	1278	Gtc/Atc	16/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.272181769540838	2		852	981	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39283850	39283850	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	73	137	0	ENST00000402219.2:c.503C>T	p.Ala168Val	p.A168V	ENST00000402219	NM_005633.3	168	gCt/gTt	4/23	1	2	FACETS	0.915	0.801	1	0.915	0.801	1	CLONAL	1	FALSE	1	0.272181769540838	2		137	586	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032110	48032111	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	71	344	0	ENST00000234420.5:c.3504_3505dup	p.Pro1169HisfsTer16	p.P1169Hfs*16	ENST00000234420	NM_000179.2	1167	ctc/ctCAc	6/10	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	FALSE	1	0.272181769540838	2		344	492	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719270	61719270	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	119	348	0	ENST00000401558.2:c.1787G>A	p.Arg596His	p.R596H	ENST00000401558	NM_003400.3	596	cGc/cAc	16/25	1	2	FACETS	0.775	0.702	0.852	1	0.986	1	SUBCLONAL	2	FALSE	1	0.272181769540838	2		348	564	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172092	99172092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	135	678	0	ENST00000074304.5:c.1658G>A	p.Arg553Gln	p.R553Q	ENST00000074304	NM_001134224.1	553	cGg/cAg	17/26	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.272181769540838	2		678	718	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202123055	202123055	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	106	530	1	ENST00000358485.4:c.101G>A	p.Gly34Asp	p.G34D	ENST00000358485	NM_001080125.1	34	gGc/gAc	1/9	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.272181769540838	2		531	697	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141584	202141584	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	43	377	0	ENST00000358485.4:c.872C>A	p.Pro291His	p.P291H	ENST00000358485	NM_001080125.1	291	cCt/cAt	7/9	1	2	FACETS	0.505	0.421	0.597	0.505	0.421	0.597	SUBCLONAL	1	FALSE	1	0.272181769540838	2		377	626	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	44	333	0	ENST00000375687.4:c.1933_1934dup	p.Gly646ValfsTer58	p.G646Vfs*58	ENST00000375687	NM_015338.5	642	-/GG	13/13	1	2	FACETS	0.814	0.684	0.958	0.814	0.684	0.958	CLONAL	1	FALSE	1	0.272181769540838	2		333	397	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42845277	42845277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776538081	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	164	805	4	ENST00000398585.3:c.985G>A	p.Val329Met	p.V329M	ENST00000398585	NM_001135099.1	329	Gtg/Atg	9/14	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.272181769540838	2		809	907	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713435	30713435	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863223856	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	136	624	2	ENST00000295754.5:c.760C>T	p.Arg254Cys	p.R254C	ENST00000295754	NM_003242.5	254	Cgc/Tgc	4/7	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.272181769540838	2		626	809	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613079	52613079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	86	393	0	ENST00000394830.3:c.3449G>A	p.Arg1150His	p.R1150H	ENST00000394830	NM_018313.4	1150	cGt/cAt	22/30	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.272181769540838	2		393	530	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928358	69928358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774545277	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	85	345	0	ENST00000352241.4:c.178C>T	p.Arg60Cys	p.R60C	ENST00000352241	NM_198159.2	60	Cgc/Tgc	2/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.272181769540838	2		345	467	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427727	72427727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753080686	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	75	434	0	ENST00000477973.2:c.763G>A	p.Val255Ile	p.V255I	ENST00000477973	NM_012234.5	255	Gtc/Atc	4/4	1	2	FACETS	0.982	0.862	1	0.982	0.862	1	CLONAL	1	FALSE	1	0.272181769540838	2		434	561	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204912	128204912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	220	934	0	ENST00000341105.2:c.529C>T	p.Pro177Ser	p.P177S	ENST00000341105	NM_032638.4	177	Cca/Tca	3/6	0.272181769540838	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	0	0.272181769540838	1		934	1158	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190816	185190816	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	71	787	1	ENST00000265026.3:c.1697C>T	p.Ala566Val	p.A566V	ENST00000265026	NM_004721.4	566	gCa/gTa	11/14	1	2	FACETS	0.555	0.483	0.633	0.555	0.483	0.633	SUBCLONAL	1	FALSE	1	0.272181769540838	2		788	940	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447236	187447236	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	146	674	5	ENST00000232014.4:c.957del	p.Asn320MetfsTer4	p.N320Mfs*4	ENST00000232014	NM_001130845.1	319	ccC/cc	5/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.272181769540838	2		679	832	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1976713	1976713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375277590	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	124	701	0	ENST00000382891.5:c.3496G>A	p.Val1166Ile	p.V1166I	ENST00000382891	NM_133335.3	1166	Gtc/Atc	19/22	0.272181769540838	1	FACETS	0.897	0.811	0.987	0.897	0.811	0.987	CLONAL	1	FALSE	0	0.272181769540838	1		701	878	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524630	187524630	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	118	698	1	ENST00000441802.2:c.11050C>T	p.Gln3684Ter	p.Q3684*	ENST00000441802	NM_005245.3	3684	Cag/Tag	19/27	1	2	FACETS	0.946	0.852	1	0.946	0.852	1	CLONAL	1	FALSE	1	0.272181769540838	2		699	917	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540211	187540211	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	96	407	0	ENST00000441802.2:c.7529T>C	p.Leu2510Pro	p.L2510P	ENST00000441802	NM_005245.3	2510	cTg/cCg	10/27	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.272181769540838	2		407	624	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282628	1282628	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	195	732	0	ENST00000310581.5:c.1685A>G	p.Tyr562Cys	p.Y562C	ENST00000310581	NM_198253.2	562	tAt/tGt	3/16	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.272181769540838	2		732	979	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293661	1293661	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	80	965	0	ENST00000310581.5:c.1340G>T	p.Arg447Leu	p.R447L	ENST00000310581	NM_198253.2	447	cGc/cTc	2/16	1	2	FACETS	0.551	0.483	0.624	0.551	0.483	0.624	SUBCLONAL	1	FALSE	1	0.272181769540838	2		965	1067	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526775	31526775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	116	718	1	ENST00000344624.3:c.265G>A	p.Ala89Thr	p.A89T	ENST00000344624		89	Gcg/Acg	2/33	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.272181769540838	2		719	767	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161221	56161221	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781300314	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	107	329	0	ENST00000399503.3:c.1090C>T	p.Arg364Trp	p.R364W	ENST00000399503	NM_005921.1	364	Cgg/Tgg	5/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.272181769540838	2		329	704	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177584	56177584	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368201444	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	103	421	0	ENST00000399503.3:c.2557C>T	p.Arg853Cys	p.R853C	ENST00000399503	NM_005921.1	853	Cgt/Tgt	14/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.272181769540838	2		421	556	SUCCESS
APC	324	MSKCC	GRCh37	5	112162891	112162891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854580	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	89	252	0	ENST00000257430.4:c.1495C>T	p.Arg499Ter	p.R499*	ENST00000257430	NM_000038.5	499	Cga/Tga	12/16	0.20213738976287	3	FACETS	1	0.959	1	0.589	0.522	0.659	CLONAL	1	FALSE	1	0.272181769540838	3		252	631	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176671242	176671242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	98	230	0	ENST00000439151.2:c.4349C>T	p.Ala1450Val	p.A1450V	ENST00000439151	NM_022455.4	1450	gCc/gTc	9/23	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.272181769540838	2		230	586	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397231	397231	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	165	441	0	ENST00000380956.4:c.616C>T	p.Gln206Ter	p.Q206*	ENST00000380956	NM_001195286.1	206	Caa/Taa	5/9	NA	2	FACETS	0.847	0.785	0.911			1	INDETERMINATE	3	FALSE	NA	0.272181769540838	2		441	477	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839945	27839945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	82	805	0	ENST00000328488.2:c.149G>A	p.Arg50His	p.R50H	ENST00000328488	NM_003533.2	50	cGc/cAc	1/1	0.272181769540838	2	FACETS	0.659	0.58	0.745	0.33	0.29	0.373	SUBCLONAL	1	FALSE	0	0.272181769540838	2		805	914	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818245	32818245	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	149	740	1	ENST00000354258.4:c.1280C>A	p.Ala427Asp	p.A427D	ENST00000354258	NM_000593.5	427	gCc/gAc	5/11	0.272181769540838	2	FACETS	1	0.977	1	0.604	0.551	0.659	CLONAL	1	FALSE	0	0.272181769540838	2		741	907	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818837	32818837	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1336232266	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	157	788	0	ENST00000354258.4:c.1114C>T	p.Arg372Ter	p.R372*	ENST00000354258	NM_000593.5	372	Cga/Tga	4/11	0.272181769540838	2	FACETS	1	0.978	1	0.598	0.548	0.651	CLONAL	1	FALSE	0	0.272181769540838	2		788	964	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821091	32821091	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1344976701	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	184	984	1	ENST00000354258.4:c.503C>A	p.Pro168Gln	p.P168Q	ENST00000354258	NM_000593.5	168	cCg/cAg	1/11	0.272181769540838	2	FACETS	1	0.975	1	0.568	0.523	0.615	CLONAL	1	FALSE	0	0.272181769540838	2		985	1190	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553776	106553776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs941078758	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	37	470	0	ENST00000369096.4:c.1741G>A	p.Ala581Thr	p.A581T	ENST00000369096	NM_001198.3	581	Gcc/Acc	5/7	1	2	FACETS	0.461	0.379	0.553	0.461	0.379	0.553	SUBCLONAL	1	FALSE	1	0.272181769540838	2		470	590	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528907	157528907	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	148	600	0	ENST00000346085.5:c.6632A>G	p.Asn2211Ser	p.N2211S	ENST00000346085	NM_020732.3	2211	aAc/aGc	20/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.272181769540838	2		600	757	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954952	2954952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	62	803	0	ENST00000396946.4:c.2758C>T	p.Arg920Cys	p.R920C	ENST00000396946	NM_032415.4	920	Cgc/Tgc	21/25	1	2	FACETS	0.471	0.405	0.542	0.471	0.405	0.542	SUBCLONAL	1	FALSE	1	0.272181769540838	2		803	968	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508836	106508836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	119	568	0	ENST00000359195.3:c.830G>A	p.Arg277Gln	p.R277Q	ENST00000359195	NM_002649.2	277	cGg/cAg	2/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.272181769540838	2		568	700	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141542548	141542548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	124	632	0	ENST00000220592.5:c.2438C>T	p.Ala813Val	p.A813V	ENST00000220592	NM_012154.3	813	gCc/gTc	18/19	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.272181769540838	2		632	677	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145736900	145736900	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs765804620	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	191	969	1	ENST00000428558.2:c.3541C>T	p.Arg1181Ter	p.R1181*	ENST00000428558	NM_004260.3	1181	Cga/Tga	22/22	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.272181769540838	2		970	1085	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5078342	5078342	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	40	114	0	ENST00000381652.3:c.2033del	p.Asn678IlefsTer53	p.N678Ifs*53	ENST00000381652	NM_004972.3	677	Aaa/aa	16/25	1	2	FACETS	0.601	0.499	0.715	0.601	0.499	0.715	SUBCLONAL	1	FALSE	1	0.272181769540838	2		114	489	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123061	5123061	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	79	414	0	ENST00000381652.3:c.3117C>A	p.Ser1039Arg	p.S1039R	ENST00000381652	NM_004972.3	1039	agC/agA	23/25	1	2	FACETS	0.886	0.78	1	0.886	0.78	1	CLONAL	1	FALSE	1	0.272181769540838	2		414	655	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126730	5126730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1437629509	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	59	278	0	ENST00000381652.3:c.3338G>A	p.Arg1113His	p.R1113H	ENST00000381652	NM_004972.3	1113	cGc/cAc	25/25	1	2	FACETS	0.807	0.695	0.929	0.807	0.695	0.929	CLONAL	1	FALSE	1	0.272181769540838	2		278	537	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157952	27157952	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	103	690	0	ENST00000380036.4:c.176G>T	p.Arg59Met	p.R59M	ENST00000380036	NM_000459.3	59	aGg/aTg	2/23	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	FALSE	1	0.272181769540838	2		690	753	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966665	36966665	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	85	592	1	ENST00000358127.4:c.661C>T	p.Arg221Trp	p.R221W	ENST00000358127	NM_001280556.1	221	Cgg/Tgg	6/10	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	FALSE	1	0.272181769540838	2		593	619	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336333	80336333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	63	423	0	ENST00000286548.4:c.986C>T	p.Thr329Met	p.T329M	ENST00000286548	NM_002072.3	329	aCg/aTg	7/7	1	2	FACETS	0.915	0.792	1	0.915	0.792	1	CLONAL	1	FALSE	1	0.272181769540838	2		423	506	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759416	133759416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774635743	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	134	879	1	ENST00000318560.5:c.1739C>T	p.Pro580Leu	p.P580L	ENST00000318560	NM_005157.4	580	cCg/cTg	11/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.272181769540838	2		880	848	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396836	139396836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777859108	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	158	767	0	ENST00000277541.6:c.5272C>T	p.Arg1758Cys	p.R1758C	ENST00000277541	NM_017617.3	1758	Cgc/Tgc	28/34	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.272181769540838	2		767	854	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139794916	139794916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267602174	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	114	598	0	ENST00000247668.2:c.310C>T	p.Pro104Ser	p.P104S	ENST00000247668	NM_021138.3	104	Ccg/Tcg	4/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.272181769540838	2		598	766	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032572	47032572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	187	401	0	ENST00000377604.3:c.478C>T	p.Arg160Trp	p.R160W	ENST00000377604	NM_001204468.1	160	Cgg/Tgg	5/24	1	1	FACETS	1	0.984	1	1	0.994	1	CLONAL	2	FALSE	0	0.272181769540838	1		401	502	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220555	123220555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	131	296	1	ENST00000218089.9:c.3212G>A	p.Arg1071Gln	p.R1071Q	ENST00000218089	NM_001042749.1	1071	cGg/cAg	30/35	1	1	FACETS	1	0.943	1	1	0.991	1	CLONAL	2	FALSE	0	0.272181769540838	1		297	401	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432116	121432116	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1565885932	NA	P-0043052-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	142	854	0	ENST00000257555.6:c.863G>C	p.Gly288Ala	p.G288A	ENST00000257555		288	gGg/gCg	4/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.272181769540838	2		854	855	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226165	2226165	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043091-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	24	762	0	ENST00000326181.6:c.1862A>C	p.Tyr621Ser	p.Y621S	ENST00000326181	NM_032271.2	621	tAc/tCc	19/21	0.243455259690899	0	FACETS	1	0.896	1			1	CLONAL	1	FALSE	0	0.243455259690899	0		762	122	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0043096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	129	290	2	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.316569038732465	3	FACETS	0.999	0.925	1	0.999	0.925	1	INDETERMINATE	2	TRUE	1	0.653831446594582	3		292	262	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177384	56177418	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTTTCTTTCAGGTATAAGAAGCTGCTGTCCCTC	TTTTTTCTTTCAGGTATAAGAAGCTGCTGTCCCTC	-	novel	NA	P-0043096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	61	237	0	ENST00000399503.3:c.2370-11_2393del		p.X790_splice	ENST00000399503	NM_005921.1	790		14/20	0.198407266844144	3	FACETS	0.848	0.751	0.947	0.848	0.751	0.947	INDETERMINATE	2	TRUE	1	0.653831446594582	3		237	146	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179390	56179391	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	64	203	0	ENST00000399503.3:c.3705dup	p.Pro1236ThrfsTer3	p.P1236Tfs*3	ENST00000399503	NM_005921.1	1235	caa/cAaa	15/20	0.198407266844144	3	FACETS	1	0.97	1	0.676	0.596	0.76	INDETERMINATE	1	TRUE	1	0.653831446594582	3		203	192	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562641	29562641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854562	NA	P-0043117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	142	337	0	ENST00000356175.3:c.3721C>T	p.Arg1241Ter	p.R1241*	ENST00000356175	NM_000267.3	1241	Cga/Tga	28/57	1	2	FACETS	0.84	0.775	0.908	0.84	0.775	0.908	CLONAL	1	TRUE	1	0.873217902299618	2		337	387	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	31	120	2	ENST00000257430.4:c.3919dup	p.Ile1307AsnfsTer8	p.I1307Nfs*8	ENST00000257430	NM_000038.5	1306	gaa/gAaa	16/16	0.309675881308897	2	FACETS	0.823	0.681	0.975	0.823	0.681	0.975	CLONAL	2	TRUE	0	0.345719393973953	2		122	109	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0043144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	164	399	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.309675881308897	2	FACETS	0.84	0.775	0.906	0.84	0.775	0.906	CLONAL	2	TRUE	0	0.345719393973953	2		399	565	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775467	39775467	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1048054600	NA	P-0043144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	112	344	1	ENST00000288319.7:c.553G>A	p.Ala185Thr	p.A185T	ENST00000288319	NM_182918.3	185	Gcc/Acc	4/10	0.309675881308897	2	FACETS	0.816	0.74	0.895	0.816	0.74	0.895	CLONAL	2	TRUE	0	0.345719393973953	2		345	397	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114711012	114711012	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	80	215	0	ENST00000543371.1:c.238del	p.Arg80GlyfsTer28	p.R80Gfs*28	ENST00000543371	NM_001198531.1	79	tCc/tc	2/14	0.322248911611233	3	FACETS	0.762	0.676	0.854	0.762	0.676	0.854	SUBCLONAL	2	TRUE	1	0.345719393973953	3		215	356	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805917	89805917	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043144-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	126	452	0	ENST00000389301.3:c.3979C>G	p.His1327Asp	p.H1327D	ENST00000389301	NM_000135.2	1327	Cac/Gac	40/43	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.345719393973953	2		452	541	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988517	36988517	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043148-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	275	626	0	ENST00000354822.5:c.136A>T	p.Ile46Phe	p.I46F	ENST00000354822	NM_001079668.2	46	Atc/Ttc	2/3	0.270327187501292	4	FACETS	1	0.983	1	1	0.983	1	INDETERMINATE	2	TRUE	2	0.643171422029884	4		626	644	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	150	539	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.367117254090002	2		544	754	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675571	86675571	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1561325048	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	46	271	0	ENST00000274376.6:c.2513del	p.Asn838MetfsTer4	p.N838Mfs*4	ENST00000274376	NM_002890.2	836	gAa/ga	19/25	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.367117254090002	2		271	207	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	39	380	2	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.784	0.653	0.928	0.784	0.653	0.928	CLONAL	1	TRUE	1	0.367117254090002	2		382	271	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713386	40713386	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	176	867	0	ENST00000373198.4:c.4129C>T	p.Arg1377Ter	p.R1377*	ENST00000373198	NM_133170.3	1377	Cga/Tga	30/32	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.367117254090002	2		867	850	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372389	55372389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1274955948	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	180	996	0	ENST00000297316.4:c.1079G>A	p.Arg360His	p.R360H	ENST00000297316	NM_022454.3	360	cGc/cAc	2/2	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.367117254090002	2		996	978	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646981	23646981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	131	763	2	ENST00000261584.4:c.886del	p.Met296Ter	p.M296*	ENST00000261584	NM_024675.3	296	Atg/tg	4/13	1	2	FACETS	0.987	0.897	1	0.987	0.897	1	CLONAL	1	TRUE	1	0.367117254090002	2		765	723	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	84	518	3	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.786	0.695	0.883	0.786	0.695	0.883	SUBCLONAL	1	TRUE	1	0.367117254090002	2		521	582	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951838	2951838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199916182	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	178	840	2	ENST00000396946.4:c.3112G>A	p.Ala1038Thr	p.A1038T	ENST00000396946	NM_032415.4	1038	Gcc/Acc	23/25	1	2	FACETS	0.964	0.888	1	0.964	0.888	1	CLONAL	1	TRUE	1	0.367117254090002	2		842	1006	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372288	55372288	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1170462661	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	156	868	5	ENST00000297316.4:c.983del	p.Pro328ArgfsTer59	p.P328Rfs*59	ENST00000297316	NM_022454.3	326	caC/ca	2/2	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.367117254090002	2		873	836	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909629	76909629	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs919106518	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	60	562	2	ENST00000373344.5:c.4276C>T	p.Arg1426Ter	p.R1426*	ENST00000373344	NM_000489.3	1426	Cga/Tga	14/35	1	2	FACETS	0.663	0.572	0.762	0.663	0.572	0.762	SUBCLONAL	1	TRUE	1	0.367117254090002	2		564	493	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332153	70332153	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1196853334	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	62	285	6	ENST00000373644.4:c.65del	p.Lys22ArgfsTer23	p.K22Rfs*23	ENST00000373644	NM_030625.2	20	Aaa/aa	2/12	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.367117254090002	2		291	310	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216477	108216477	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587782558	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	30	212	2	ENST00000278616.4:c.8432del	p.Lys2811SerfsTer46	p.K2811Sfs*46	ENST00000278616	NM_000051.3	2809	cAa/ca	58/63	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.367117254090002	2		214	152	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440943	56440943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786205215	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	344	593	1	ENST00000407977.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000407977		132	Cga/Tga	4/10	0.367117254090002	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.367117254090002	2		594	825	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	36	201	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.9	0.746	1	0.9	0.746	1	CLONAL	1	TRUE	1	0.367117254090002	2		201	218	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636143	28636143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371663652	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	167	681	0	ENST00000241453.7:c.229G>A	p.Glu77Lys	p.E77K	ENST00000241453	NM_004119.2	77	Gaa/Aaa	3/24	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.367117254090002	2		681	803	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556463	29556463	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1567849208	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	79	450	0	ENST00000356175.3:c.2835del	p.Phe945LeufsTer9	p.F945Lfs*9	ENST00000356175	NM_000267.3	944	Ttt/tt	21/57	1	2	FACETS	0.934	0.824	1	0.934	0.824	1	CLONAL	1	TRUE	1	0.367117254090002	2		450	461	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030479	49030479	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	51	355	0	ENST00000267163.4:c.1959del	p.Val654CysfsTer4	p.V654Cfs*4	ENST00000267163	NM_000321.2	652	Aaa/aa	19/27	1	2	FACETS	0.896	0.766	1	0.896	0.766	1	CLONAL	1	TRUE	1	0.367117254090002	2		355	310	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435153	110435153	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776792996	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	192	914	0	ENST00000375856.3:c.3248C>T	p.Pro1083Leu	p.P1083L	ENST00000375856	NM_003749.2	1083	cCg/cTg	1/2	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.367117254090002	2		914	1018	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119781	70119781	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1274036689	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	335	917	1	ENST00000245479.2:c.788del	p.Gly263AlafsTer16	p.G263Afs*16	ENST00000245479	NM_000346.3	261	gaG/ga	3/3	0.367117254090002	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.367117254090002	2		918	876	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781122	161781122	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	139	588	0	ENST00000366898.1:c.1283del	p.Asn428MetfsTer7	p.N428Mfs*7	ENST00000366898	NM_004562.2	428	aAt/at	11/12	1	2	FACETS	0.985	0.897	1	0.985	0.897	1	CLONAL	1	TRUE	1	0.367117254090002	2		588	769	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099579	157099579	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1562376341	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	14	156	0	ENST00000346085.5:c.521del	p.Pro174ArgfsTer6	p.P174Rfs*6	ENST00000346085	NM_020732.3	172	gaC/ga	1/20	1	2	FACETS	0.393	0.285	0.524	0.393	0.285	0.524	SUBCLONAL	1	TRUE	1	0.367117254090002	2		156	194	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871053	12871053	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	58	413	0	ENST00000228872.4:c.285del	p.Gly97ValfsTer22	p.G97Vfs*22	ENST00000228872	NM_004064.3	94	Ccc/cc	1/3	1	2	FACETS	0.771	0.664	0.886	0.771	0.664	0.886	SUBCLONAL	1	TRUE	1	0.367117254090002	2		413	410	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343537	343537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745327595	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	250	1034	1	ENST00000262320.3:c.2137C>T	p.Arg713Cys	p.R713C	ENST00000262320	NM_003502.3	713	Cgt/Tgt	8/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.367117254090002	2		1035	1154	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116262	209116263	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs754375602	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	29	314	0	ENST00000345146.2:c.13dup	p.Ile5AsnfsTer13	p.I5Nfs*13	ENST00000345146	NM_005896.2	5	atc/aAtc	3/10	1	2	FACETS	0.558	0.449	0.681	0.558	0.449	0.681	SUBCLONAL	1	TRUE	1	0.367117254090002	2		314	283	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526209	189526210	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1462944177	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	173	842	0	ENST00000264731.3:c.480_481del	p.Pro161IlefsTer36	p.P161Ifs*36	ENST00000264731	NM_003722.4	158	gCT/g	4/14	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.367117254090002	2		842	931	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954273	32954273	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs80359752	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	68	470	0	ENST00000380152.3:c.9253del	p.Thr3085GlnfsTer19	p.T3085Qfs*19	ENST00000380152		3083	Aaa/aa	24/27	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.367117254090002	2		470	367	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149057	61149057	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs749726149	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	80	445	0	ENST00000295025.8:c.1247C>G	p.Ala416Gly	p.A416G	ENST00000295025	NM_002908.2	416	gCc/gGc	11/11	1	2	FACETS	0.895	0.79	1	0.895	0.79	1	CLONAL	1	TRUE	1	0.367117254090002	2		445	487	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681120	117681120	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs748436511	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	113	507	0	ENST00000368508.3:c.3500del	p.Leu1167Ter	p.L1167*	ENST00000368508	NM_002944.2	1167	tTa/ta	23/43	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.367117254090002	2		507	519	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098392	11098392	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	153	818	0	ENST00000358026.2:c.914del	p.Pro305ArgfsTer21	p.P305Rfs*21	ENST00000358026	NM_001128849.1	304	Ccc/cc	6/36	1	2	FACETS	0.981	0.898	1	0.981	0.898	1	CLONAL	1	TRUE	1	0.367117254090002	2		818	850	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991697	72991699	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs757316139	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	88	480	5	ENST00000268489.5:c.2346_2348del	p.Ala784del	p.A784del	ENST00000268489	NM_006885.3	782	gcGGCa/gca	2/10	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.367117254090002	2		485	460	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813396	102813396	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1316717107	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	167	673	0	ENST00000307046.8:c.293G>A	p.Arg98Gln	p.R98Q	ENST00000307046	NM_001111285.1	98	cGg/cAg	3/4	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.367117254090002	2		673	682	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956723	68956723	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs750933833	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	136	465	0	ENST00000288368.4:c.841C>T	p.Arg281Trp	p.R281W	ENST00000288368	NM_024870.2	281	Cgg/Tgg	8/40	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.367117254090002	2		465	708	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625110	69625110	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782454437	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	125	830	0	ENST00000334134.2:c.683C>T	p.Ser228Leu	p.S228L	ENST00000334134	NM_005247.2	228	tCg/tTg	3/3	1	2	FACETS	0.958	0.868	1	0.958	0.868	1	CLONAL	1	TRUE	1	0.367117254090002	2		830	711	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661917	29661917	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	78	524	0	ENST00000356175.3:c.5815del	p.Cys1939AlafsTer19	p.C1939Afs*19	ENST00000356175	NM_000267.3	1937	cgT/cg	39/57	1	2	FACETS	0.942	0.831	1	0.942	0.831	1	CLONAL	1	TRUE	1	0.367117254090002	2		524	451	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197713	66197713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238493512	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	76	491	0	ENST00000273854.3:c.2986G>A	p.Ala996Thr	p.A996T	ENST00000273854	NM_004439.5	996	Gct/Act	17/18	1	2	FACETS	0.961	0.846	1	0.961	0.846	1	CLONAL	1	TRUE	1	0.367117254090002	2		491	431	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89811469	89811469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147017625	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	170	775	1	ENST00000389301.3:c.3524C>T	p.Pro1175Leu	p.P1175L	ENST00000389301	NM_000135.2	1175	cCg/cTg	36/43	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.367117254090002	2		776	817	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678720	52678720	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	75	470	0	ENST00000394830.3:c.899G>T	p.Arg300Met	p.R300M	ENST00000394830	NM_018313.4	300	aGg/aTg	9/30	1	2	FACETS	0.75	0.658	0.848	0.75	0.658	0.848	SUBCLONAL	1	TRUE	1	0.367117254090002	2		470	545	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533773	41533773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	112	543	0	ENST00000263253.7:c.1739G>A	p.Arg580Gln	p.R580Q	ENST00000263253	NM_001429.3	580	cGa/cAa	8/31	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.367117254090002	2		543	576	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432249	432249	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	94	451	0	ENST00000399788.2:c.2274del	p.Asp759IlefsTer2	p.D759Ifs*2	ENST00000399788	NM_001042603.1	758	aaA/aa	16/28	NA	2	FACETS	1	0.936	1			1	INDETERMINATE	1	TRUE	NA	0.367117254090002	2		451	480	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933409	39933409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776961342	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	196	737	3	ENST00000378444.4:c.1190C>T	p.Pro397Leu	p.P397L	ENST00000378444	NM_001123385.1	397	cCg/cTg	4/15	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.367117254090002	2		740	821	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528284	157528284	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs749055122	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	185	526	0	ENST00000346085.5:c.6013del	p.Val2005TrpfsTer16	p.V2005Wfs*16	ENST00000346085	NM_020732.3	2003	aaG/aa	20/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.367117254090002	2		526	976	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2193766	2193766	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	178	652	0	ENST00000398665.3:c.572C>T	p.Pro191Leu	p.P191L	ENST00000398665	NM_032482.2	191	cCg/cTg	6/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.367117254090002	2		652	823	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687094	37687094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567586451	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	123	635	1	ENST00000447079.4:c.3998G>A	p.Arg1333His	p.R1333H	ENST00000447079	NM_015083.1	1333	cGt/cAt	14/14	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.367117254090002	2		636	665	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434351	49434351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375115132	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	190	1006	2	ENST00000301067.7:c.7202G>A	p.Arg2401His	p.R2401H	ENST00000301067	NM_003482.3	2401	cGc/cAc	31/54	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.367117254090002	2		1008	940	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136747	2136747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769913589	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	238	939	4	ENST00000219476.3:c.4864G>A	p.Ala1622Thr	p.A1622T	ENST00000219476	NM_000548.3	1622	Gcc/Acc	38/42	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.367117254090002	2		943	1057	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922046	39922046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	206	858	0	ENST00000378444.4:c.4126G>T	p.Gly1376Ter	p.G1376*	ENST00000378444	NM_001123385.1	1376	Gga/Tga	9/15	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.367117254090002	2		858	1026	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729291	41729291	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	81	532	0	ENST00000242208.4:c.1238del	p.Lys413ArgfsTer6	p.K413Rfs*6	ENST00000242208	NM_002192.2	413	aAg/ag	3/3	1	2	FACETS	0.776	0.684	0.873	0.776	0.684	0.873	SUBCLONAL	1	TRUE	1	0.367117254090002	2		532	569	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868076	56868076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141371158	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	101	574	0	ENST00000308159.5:c.1574G>A	p.Arg525Gln	p.R525Q	ENST00000308159	NM_014669.4	525	cGg/cAg	14/22	1	2	FACETS	0.84	0.752	0.934	0.84	0.752	0.934	CLONAL	1	TRUE	1	0.367117254090002	2		574	655	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777670	9777670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760642664	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	189	768	1	ENST00000377346.4:c.1006G>A	p.Asp336Asn	p.D336N	ENST00000377346	NM_005026.3	336	Gac/Aac	8/24	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.367117254090002	2		769	854	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256925	16256925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	139	734	0	ENST00000375759.3:c.4190C>T	p.Ala1397Val	p.A1397V	ENST00000375759	NM_015001.2	1397	gCa/gTa	11/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.367117254090002	2		734	695	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406668	70406668	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	80	624	0	ENST00000373644.4:c.4182T>A	p.Asn1394Lys	p.N1394K	ENST00000373644	NM_030625.2	1394	aaT/aaA	4/12	1	2	FACETS	0.806	0.711	0.907	0.806	0.711	0.907	CLONAL	1	TRUE	1	0.367117254090002	2		624	541	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941900	71941900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1001989178	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	192	906	4	ENST00000298229.2:c.1258G>A	p.Glu420Lys	p.E420K	ENST00000298229	NM_001567.3	420	Gag/Aag	11/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.367117254090002	2		910	932	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256771	133256771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	88	574	1	ENST00000320574.5:c.323C>T	p.Thr108Ile	p.T108I	ENST00000320574	NM_006231.2	108	aCc/aTc	4/49	1	2	FACETS	0.841	0.747	0.942	0.841	0.747	0.942	CLONAL	1	TRUE	1	0.367117254090002	2		575	570	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563261	21563261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763358548	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	222	1097	0	ENST00000382592.4:c.658G>A	p.Gly220Ser	p.G220S	ENST00000382592	NM_014572.2	220	Ggc/Agc	4/8	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.367117254090002	2		1097	966	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434623	110434623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	136	925	0	ENST00000375856.3:c.3778G>A	p.Glu1260Lys	p.E1260K	ENST00000375856	NM_003749.2	1260	Gag/Aag	1/2	1	2	FACETS	0.816	0.741	0.894	0.816	0.741	0.894	CLONAL	1	TRUE	1	0.367117254090002	2		925	908	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43762229	43762231	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	143	820	0	ENST00000382044.4:c.1214_1216del	p.Glu405del	p.E405del	ENST00000382044	NM_001141980.1	405	gAAGga/gga	11/28	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.367117254090002	2		820	756	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821686	72821686	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	55	348	1	ENST00000268489.5:c.10489C>A	p.Leu3497Met	p.L3497M	ENST00000268489	NM_006885.3	3497	Ctg/Atg	10/10	1	2	FACETS	0.774	0.665	0.893	0.774	0.665	0.893	SUBCLONAL	1	TRUE	1	0.367117254090002	2		349	387	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973698	15973698	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755828055	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	117	518	0	ENST00000268712.3:c.4294C>T	p.Arg1432Trp	p.R1432W	ENST00000268712	NM_006311.3	1432	Cgg/Tgg	31/46	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.367117254090002	2		518	613	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733011	74733011	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	62	589	0	ENST00000359995.5:c.232del	p.Ala78ProfsTer154	p.A78Pfs*154	ENST00000359995	NM_001195427.1	78	Gcc/cc	1/3	0.367117254090002	2	FACETS	0.525	0.453	0.604	0.263	0.226	0.302	SUBCLONAL	1	TRUE	0	0.367117254090002	2		589	643	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603015	48603015	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	74	342	0	ENST00000342988.3:c.1316A>G	p.Asp439Gly	p.D439G	ENST00000342988	NM_005359.5	439	gAt/gGt	11/12	1	2	FACETS	0.993	0.874	1	0.993	0.874	1	CLONAL	1	TRUE	1	0.367117254090002	2		342	406	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218684	36218684	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	190	915	0	ENST00000222270.7:c.4388C>A	p.Ser1463Tyr	p.S1463Y	ENST00000222270	NM_014727.1	1463	tCt/tAt	17/37	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.367117254090002	2		915	884	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727883	41727883	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1420427778	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	193	957	1	ENST00000301178.4:c.508G>T	p.Asp170Tyr	p.D170Y	ENST00000301178	NM_021913.4	170	Gac/Tac	4/20	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.367117254090002	2		958	1038	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909748	50909748	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	226	1011	0	ENST00000440232.2:c.1468C>T	p.Gln490Ter	p.Q490*	ENST00000440232	NM_002691.3	490	Cag/Tag	12/27	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.367117254090002	2		1011	1179	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641407	47641407	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	92	392	0	ENST00000233146.2:c.793-1G>T		p.X265_splice	ENST00000233146	NM_000251.2	265			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.367117254090002	2		392	431	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483927	212483927	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs915065015	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	62	521	0	ENST00000342788.4:c.2276C>A	p.Pro759His	p.P759H	ENST00000342788	NM_005235.2	759	cCc/cAc	19/28	1	2	FACETS	0.818	0.709	0.935	0.818	0.709	0.935	CLONAL	1	TRUE	1	0.367117254090002	2		521	413	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288377	21288377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	196	775	0	ENST00000354336.3:c.622G>A	p.Ala208Thr	p.A208T	ENST00000354336	NM_005207.3	208	Gct/Act	2/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.367117254090002	2		775	912	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41554474	41554474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1289132149	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	114	585	0	ENST00000263253.7:c.3560G>A	p.Arg1187His	p.R1187H	ENST00000263253	NM_001429.3	1187	cGt/cAt	19/31	1	2	FACETS	0.9	0.811	0.994	0.9	0.811	0.994	CLONAL	1	TRUE	1	0.367117254090002	2		585	690	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648424	30648424	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	114	739	0	ENST00000295754.5:c.49T>C	p.Trp17Arg	p.W17R	ENST00000295754	NM_003242.5	17	Tgg/Cgg	1/7	1	2	FACETS	0.859	0.774	0.949	0.859	0.774	0.949	CLONAL	1	TRUE	1	0.367117254090002	2		739	723	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014334	70014334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs531830542	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	159	654	2	ENST00000394351.3:c.1195G>A	p.Gly399Arg	p.G399R	ENST00000394351	NM_000248.3	399	Gga/Aga	9/9	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.367117254090002	2		656	707	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027015	71027015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	153	607	0	ENST00000318789.4:c.1312C>T	p.Arg438Trp	p.R438W	ENST00000318789	NM_032682.5	438	Cgg/Tgg	15/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.367117254090002	2		607	690	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948037	178948037	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	35	230	0	ENST00000263967.3:c.2813del	p.Leu938TrpfsTer19	p.L938Wfs*19	ENST00000263967	NM_006218.2	937	Ttt/tt	20/21	1	2	FACETS	0.714	0.588	0.854	0.714	0.588	0.854	SUBCLONAL	1	TRUE	1	0.367117254090002	2		230	267	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806558	1806558	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	123	789	0	ENST00000260795.2:c.1274T>C	p.Leu425Pro	p.L425P	ENST00000260795		425	cTg/cCg	9/17	1	2	FACETS	0.808	0.731	0.89	0.808	0.731	0.89	CLONAL	1	TRUE	1	0.367117254090002	2		789	829	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156072	106156073	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	76	369	0	ENST00000380013.4:c.978dup	p.Ser327IlefsTer4	p.S327Ifs*4	ENST00000380013	NM_001127208.2	325	caa/cAaa	3/11	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.367117254090002	2		369	383	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197289	106197290	+	frameshift_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	59	383	0	ENST00000380013.4:c.5625_5626del	p.Ala1876LysfsTer3	p.A1876Kfs*3	ENST00000380013	NM_001127208.2	1874	gaGTgt/gagt	11/11	1	2	FACETS	0.869	0.751	0.996	0.869	0.751	0.996	CLONAL	1	TRUE	1	0.367117254090002	2		383	370	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538982	187538982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	111	506	0	ENST00000441802.2:c.8758G>A	p.Ala2920Thr	p.A2920T	ENST00000441802	NM_005245.3	2920	Gcc/Acc	10/27	1	2	FACETS	0.897	0.808	0.992	0.897	0.808	0.992	CLONAL	1	TRUE	1	0.367117254090002	2		506	674	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540501	187540501	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	99	433	0	ENST00000441802.2:c.7239del	p.Ala2414ProfsTer9	p.A2414Pfs*9	ENST00000441802	NM_005245.3	2413	aaA/aa	10/27	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.367117254090002	2		433	493	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973793	131973793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782577	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	81	318	2	ENST00000265335.6:c.3496C>T	p.Arg1166Trp	p.R1166W	ENST00000265335		1166	Cgg/Tgg	23/25	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.367117254090002	2		320	368	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987211	2987211	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs950377099	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	55	490	0	ENST00000396946.4:c.218C>T	p.Ala73Val	p.A73V	ENST00000396946	NM_032415.4	73	gCa/gTa	3/25	1	2	FACETS	0.592	0.507	0.685	0.592	0.507	0.685	SUBCLONAL	1	TRUE	1	0.367117254090002	2		490	506	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878011	151878014	+	frameshift_variant	Frame_Shift_Del	DEL	AGTC	AGTC	-	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	96	401	0	ENST00000262189.6:c.6931_6934del	p.Asp2311LeufsTer53	p.D2311Lfs*53	ENST00000262189	NM_170606.2	2311	GACTct/ct	36/59	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.367117254090002	2		401	417	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400291	139400291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761908188	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	217	941	0	ENST00000277541.6:c.4057G>A	p.Gly1353Ser	p.G1353S	ENST00000277541	NM_017617.3	1353	Ggc/Agc	25/34	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.367117254090002	2		941	901	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430825	47430825	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	197	899	2	ENST00000377045.4:c.1790G>A	p.Cys597Tyr	p.C597Y	ENST00000377045	NM_001654.4	597	tGc/tAc	16/16	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.367117254090002	2		901	861	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354996	70354996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	154	818	2	ENST00000374080.3:c.4918C>T	p.Pro1640Ser	p.P1640S	ENST00000374080		1640	Cca/Tca	36/45	1	2	FACETS	0.87	0.796	0.948	0.87	0.796	0.948	CLONAL	1	TRUE	1	0.367117254090002	2		820	964	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360687	70360687	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	35	177	0	ENST00000374080.3:c.6247C>T	p.Gln2083Ter	p.Q2083*	ENST00000374080		2083	Cag/Tag	42/45	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.367117254090002	2		177	177	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191813	123191813	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	57	355	0	ENST00000218089.9:c.1402T>C	p.Phe468Leu	p.F468L	ENST00000218089	NM_001042749.1	468	Ttt/Ctt	15/35	1	2	FACETS	0.756	0.65	0.87	0.756	0.65	0.87	SUBCLONAL	1	TRUE	1	0.367117254090002	2		355	411	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406662	70406662	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043154-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	76	632	0	ENST00000373644.4:c.4176del	p.Asn1394IlefsTer7	p.N1394Ifs*7	ENST00000373644	NM_030625.2	1392	caG/ca	4/12	1	2	FACETS	0.793	0.697	0.896	0.793	0.697	0.896	SUBCLONAL	1	TRUE	1	0.367117254090002	2		632	522	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025982	1025982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	384	450	0	ENST00000358495.3:c.548C>T	p.Pro183Leu	p.P183L	ENST00000358495	NM_134424.2	183	cCt/cTt	8/12	0.764931261014962	3	FACETS	1	0.962	1			1	CLONAL	2	TRUE	NA	0.764931261014962	3		450	692	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589580	67589621	+	inframe_deletion	In_Frame_Del	DEL	AATTACATGAATATAACACTCAGTTTCAAGAAAAAAGTCGAG	AATTACATGAATATAACACTCAGTTTCAAGAAAAAAGTCGAG	-	novel	NA	P-0043171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	18	235	0	ENST00000274335.5:c.1346_1387del	p.Leu449_Glu462del	p.L449_E462del	ENST00000274335		448	aAATTACATGAATATAACACTCAGTTTCAAGAAAAAAGTCGAGaa/aaa	10/15	0.764931261014962	1	FACETS	0.136	0.102	0.175	0.136	0.102	0.175	SUBCLONAL	1	TRUE	0	0.764931261014962	1		235	214	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66779622	66779622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043179-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	91	512	0	ENST00000307102.5:c.952G>A	p.Val318Ile	p.V318I	ENST00000307102	NM_002755.3	318	Gtc/Atc	8/11	1	2	FACETS	0.869	0.774	0.971	0.869	0.774	0.971	CLONAL	1	TRUE	1	0.389815493231347	2		512	537	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	236	548	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.958	0.894	1	0.958	0.894	1	CLONAL	1	TRUE	1	0.468345955549132	2		548	1052	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	313	727	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.468345955549132	2		728	1245	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922294	100922294	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1315135533	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	125	402	0	ENST00000325455.5:c.2218C>T	p.Arg740Ter	p.R740*	ENST00000325455	NM_001202474.3	740	Cga/Tga	5/8	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.468345955549132	2		402	530	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845627	63845627	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	156	328	0	ENST00000279873.7:c.1366G>T	p.Glu456Ter	p.E456*	ENST00000279873	NM_032199.2	456	Gaa/Taa	9/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.468345955549132	2		328	550	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	239	554	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.468345955549132	2		554	913	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	234	674	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	0.963	0.898	1	0.963	0.898	1	CLONAL	1	TRUE	1	0.468345955549132	2		674	1038	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	142	394	1	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	1	2	FACETS	0.931	0.851	1	0.931	0.851	1	CLONAL	1	TRUE	1	0.468345955549132	2		395	651	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132295	7132295	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs575954707	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	278	612	1	ENST00000302850.5:c.2716G>A	p.Ala906Thr	p.A906T	ENST00000302850	NM_000208.2	906	Gct/Act	14/22	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.468345955549132	2		613	1107	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074256	8074256	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	507	540	0	ENST00000377482.5:c.403A>T	p.Asn135Tyr	p.N135Y	ENST00000377482	NM_018948.3	135	Aac/Tac	4/4	0.468345955549132	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.468345955549132	2		540	969	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242628	16242628	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	157	459	0	ENST00000375759.3:c.1249G>T	p.Glu417Ter	p.E417*	ENST00000375759	NM_015001.2	417	Gaa/Taa	6/15	0.468345955549132	2	FACETS	0.987	0.907	1	0.494	0.453	0.536	CLONAL	1	TRUE	0	0.468345955549132	2		459	679	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805081	43805081	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	246	699	0	ENST00000372470.3:c.531G>T	p.Lys177Asn	p.K177N	ENST00000372470	NM_005373.2	177	aaG/aaT	4/12	0.468345955549132	2	FACETS	0.86	0.803	0.92	0.43	0.401	0.46	CLONAL	1	TRUE	0	0.468345955549132	2		699	1221	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429300	78429300	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	236	640	0	ENST00000370768.2:c.1142T>G	p.Phe381Cys	p.F381C	ENST00000370768	NM_003902.3	381	tTt/tGt	13/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.468345955549132	2		640	929	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280681	115280681	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	223	526	0	ENST00000438362.2:c.350T>G	p.Phe117Cys	p.F117C	ENST00000438362	NM_001242891.1	117	tTt/tGt	4/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.468345955549132	2		526	906	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743265	162743265	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	113	330	0	ENST00000367921.3:c.1735C>A	p.Leu579Ile	p.L579I	ENST00000367921	NM_006182.2	579	Ctc/Atc	14/18	1	2	FACETS	0.935	0.845	1	0.935	0.845	1	CLONAL	1	TRUE	1	0.468345955549132	2		330	516	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745452	162745452	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	136	335	0	ENST00000367921.3:c.1867C>A	p.Leu623Ile	p.L623I	ENST00000367921	NM_006182.2	623	Ctt/Att	15/18	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.468345955549132	2		335	495	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163297332	163297332	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1292835761	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	161	531	0	ENST00000271452.3:c.178C>T	p.Arg60Ter	p.R60*	ENST00000271452	NM_145697.2	60	Cga/Tga	3/14	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.468345955549132	2		531	663	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111132	193111132	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	180	475	0	ENST00000367435.3:c.665G>A	p.Arg222Gln	p.R222Q	ENST00000367435	NM_024529.4	222	cGa/cAa	7/17	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.468345955549132	2		475	702	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193116996	193116996	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	160	379	0	ENST00000367435.3:c.730-1G>T		p.X244_splice	ENST00000367435	NM_024529.4	244			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.468345955549132	2		379	614	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667442	241667442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	224	533	0	ENST00000366560.3:c.1008G>A	p.Met336Ile	p.M336I	ENST00000366560	NM_000143.3	336	atG/atA	7/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.468345955549132	2		533	854	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243777040	243777040	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	109	426	0	ENST00000263826.5:c.629C>A	p.Ser210Tyr	p.S210Y	ENST00000263826	NM_005465.4	210	tCc/tAc	7/13	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.468345955549132	2		426	436	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623673	43623673	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	235	596	0	ENST00000355710.3:c.3301C>T	p.Leu1101Phe	p.L1101F	ENST00000355710	NM_020975.4	1101	Ctt/Ttt	20/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.468345955549132	2		596	961	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70442623	70442623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867702783	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	247	620	1	ENST00000373644.4:c.4945C>T	p.Arg1649Trp	p.R1649W	ENST00000373644	NM_030625.2	1649	Cgg/Tgg	10/12	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.468345955549132	2		621	907	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685316	89685316	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs878853937	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	85	319	0	ENST00000371953.3:c.209+2T>C		p.X70_splice	ENST00000371953	NM_000314.4	70			1	2	FACETS	0.992	0.883	1	0.992	0.883	1	CLONAL	1	TRUE	1	0.468345955549132	2		319	366	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112724367	112724367	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	281	637	0	ENST00000369452.4:c.251A>C	p.Lys84Thr	p.K84T	ENST00000369452	NM_007373.3	84	aAa/aCa	2/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.468345955549132	2		637	1144	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112760194	112760194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	99	546	0	ENST00000369452.4:c.863G>A	p.Arg288His	p.R288H	ENST00000369452	NM_007373.3	288	cGt/cAt	4/9	1	2	FACETS	0.549	0.49	0.612	0.549	0.49	0.612	SUBCLONAL	1	TRUE	1	0.468345955549132	2		546	770	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710666	114710666	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	226	557	0	ENST00000543371.1:c.151G>T	p.Glu51Ter	p.E51*	ENST00000543371	NM_001198531.1	51	Gaa/Taa	1/14	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.468345955549132	2		557	951	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989557	85989557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	197	447	0	ENST00000263360.6:c.1316G>A	p.Arg439Gln	p.R439Q	ENST00000263360	NM_003797.3	439	cGa/cAa	12/12	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.468345955549132	2		447	787	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933241	100933241	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	234	678	0	ENST00000325455.5:c.2149A>G	p.Ser717Gly	p.S717G	ENST00000325455	NM_001202474.3	717	Agt/Ggt	4/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.468345955549132	2		678	922	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115681	108115681	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs876660933	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	121	426	0	ENST00000278616.4:c.829G>T	p.Glu277Ter	p.E277*	ENST00000278616	NM_000051.3	277	Gaa/Taa	7/63	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.468345955549132	2		426	485	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202715	108202715	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	155	426	0	ENST00000278616.4:c.7739G>T	p.Arg2580Ile	p.R2580I	ENST00000278616	NM_000051.3	2580	aGa/aTa	52/63	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.468345955549132	2		426	637	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111958652	111958652	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	211	485	1	ENST00000375549.3:c.124G>T	p.Glu42Ter	p.E42*	ENST00000375549	NM_003002.3	42	Gaa/Taa	2/4	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.468345955549132	2		486	880	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342392	118342392	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	111	348	0	ENST00000534358.1:c.518G>A	p.Arg173Gln	p.R173Q	ENST00000534358	NM_005933.3	173	cGa/cAa	3/36	1	2	FACETS	0.86	0.776	0.949	0.86	0.776	0.949	CLONAL	1	TRUE	1	0.468345955549132	2		348	551	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344543	118344543	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	166	495	1	ENST00000534358.1:c.2669A>G	p.Lys890Arg	p.K890R	ENST00000534358	NM_005933.3	890	aAa/aGa	3/36	1	2	FACETS	0.944	0.869	1	0.944	0.869	1	CLONAL	1	TRUE	1	0.468345955549132	2		496	751	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	431664	431664	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	262	646	3	ENST00000399788.2:c.2345G>A	p.Arg782Gln	p.R782Q	ENST00000399788	NM_001042603.1	782	cGa/cAa	17/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.468345955549132	2		649	1003	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435026	18435026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	109	308	0	ENST00000266497.5:c.11C>A	p.Ser4Tyr	p.S4Y	ENST00000266497		4	tCt/tAt	1/31	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.468345955549132	2		308	436	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435082	18435082	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	142	468	1	ENST00000266497.5:c.67G>T	p.Glu23Ter	p.E23*	ENST00000266497		23	Gaa/Taa	1/31	1	2	FACETS	0.926	0.846	1	0.926	0.846	1	CLONAL	1	TRUE	1	0.468345955549132	2		469	655	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18439862	18439862	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	163	369	0	ENST00000266497.5:c.760A>C	p.Lys254Gln	p.K254Q	ENST00000266497		254	Aaa/Caa	2/31	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.468345955549132	2		369	591	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18496266	18496266	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1361917824	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	69	284	0	ENST00000266497.5:c.1401T>G	p.Phe467Leu	p.F467L	ENST00000266497		467	ttT/ttG	9/31	1	2	FACETS	0.807	0.707	0.914	0.807	0.707	0.914	CLONAL	1	TRUE	1	0.468345955549132	2		284	365	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793408	18793408	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs564875319	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	222	578	0	ENST00000266497.5:c.4105C>A	p.Leu1369Ile	p.L1369I	ENST00000266497		1369	Ctt/Att	30/31	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.468345955549132	2		578	869	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25368454	25368454	+	intron_variant	Intron	SNP	C	C	T	rs758575947	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	124	460	0	ENST00000311936.3:c.451-5609G>A		p.*151*	ENST00000311936	NM_004985.3	164/189			1	2	FACETS	0.853	0.773	0.936	0.853	0.773	0.936	CLONAL	1	TRUE	1	0.468345955549132	2		460	621	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479969	50479969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	264	774	0	ENST00000394963.4:c.203G>A	p.Arg68Gln	p.R68Q	ENST00000394963	NM_003076.4	68	cGa/cAa	2/13	1	2	FACETS	0.884	0.828	0.943	0.884	0.828	0.943	CLONAL	1	TRUE	1	0.468345955549132	2		774	1275	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865438	57865438	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	300	875	0	ENST00000228682.2:c.2915A>C	p.Glu972Ala	p.E972A	ENST00000228682	NM_005269.2	972	gAa/gCa	12/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.468345955549132	2		875	1258	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112893859	112893859	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	157	556	0	ENST00000351677.2:c.748G>T	p.Glu250Ter	p.E250*	ENST00000351677	NM_002834.3	250	Gaa/Taa	6/16	1	2	FACETS	0.876	0.804	0.952	0.876	0.804	0.952	CLONAL	1	TRUE	1	0.468345955549132	2		556	765	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915802	112915802	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	165	457	0	ENST00000351677.2:c.1075G>T	p.Glu359Ter	p.E359*	ENST00000351677	NM_002834.3	359	Gaa/Taa	9/16	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.468345955549132	2		457	688	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636073	28636073	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1255132494	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	267	686	0	ENST00000241453.7:c.299A>G	p.Asn100Ser	p.N100S	ENST00000241453	NM_004119.2	100	aAc/aGc	3/24	1	2	FACETS	0.907	0.849	0.966	0.907	0.849	0.966	CLONAL	1	TRUE	1	0.468345955549132	2		686	1257	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008270	29008270	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	171	419	1	ENST00000282397.4:c.601G>T	p.Glu201Ter	p.E201*	ENST00000282397	NM_002019.4	201	Gaa/Taa	5/30	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.468345955549132	2		420	713	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972865	32972865	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1555290072	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	146	445	0	ENST00000380152.3:c.10215G>T	p.Glu3405Asp	p.E3405D	ENST00000380152		3405	gaG/gaT	27/27	1	2	FACETS	0.916	0.838	0.997	0.916	0.838	0.997	CLONAL	1	TRUE	1	0.468345955549132	2		445	681	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919244	48919244	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913296	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	77	225	0	ENST00000267163.4:c.409G>T	p.Glu137Ter	p.E137*	ENST00000267163	NM_000321.2	137	Gaa/Taa	4/27	1	2	FACETS	0.847	0.76	0.937	1	0.983	1	CLONAL	2	TRUE	1	0.468345955549132	2		225	194	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934254	48934254	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1131690904	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	104	478	0	ENST00000267163.4:c.709G>T	p.Glu237Ter	p.E237*	ENST00000267163	NM_000321.2	237	Gaa/Taa	7/27	1	2	FACETS	0.859	0.772	0.95	0.859	0.772	0.95	CLONAL	1	TRUE	1	0.468345955549132	2		478	517	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506669	103506669	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs188898060	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	84	342	1	ENST00000355739.4:c.412C>T	p.Arg138Ter	p.R138*	ENST00000355739	NM_000123.3	138	Cga/Tga	4/15	1	2	FACETS	0.848	0.753	0.949	0.848	0.753	0.949	CLONAL	1	TRUE	1	0.468345955549132	2		343	423	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061531	38061531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	185	322	0	ENST00000250448.2:c.458C>T	p.Ala153Val	p.A153V	ENST00000250448	NM_004496.3	153	gCg/gTg	2/2	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.468345955549132	2		322	601	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81528503	81528503	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	95	378	0	ENST00000298171.2:c.182A>G	p.Glu61Gly	p.E61G	ENST00000298171	NM_000369.2	61	gAg/gGg	2/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.468345955549132	2		378	328	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028405	42028405	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	118	383	0	ENST00000219905.7:c.3943G>T	p.Glu1315Ter	p.E1315*	ENST00000219905	NM_001164273.1	1315	Gaa/Taa	13/24	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.468345955549132	2		383	478	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67459152	67459152	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	289	670	0	ENST00000327367.4:c.568G>T	p.Glu190Ter	p.E190*	ENST00000327367	NM_005902.3	190	Gaa/Taa	4/9	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.468345955549132	2		670	1097	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857197	9857197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866121846	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	261	650	2	ENST00000330684.3:c.4204C>T	p.Arg1402Trp	p.R1402W	ENST00000330684	NM_001134407.1	1402	Cgg/Tgg	13/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.468345955549132	2		652	986	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858504	9858504	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	232	701	0	ENST00000330684.3:c.2897T>G	p.Phe966Cys	p.F966C	ENST00000330684	NM_001134407.1	966	tTt/tGt	13/13	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.468345955549132	2		701	947	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916214	9916214	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	207	605	1	ENST00000330684.3:c.2075G>T	p.Arg692Ile	p.R692I	ENST00000330684	NM_001134407.1	692	aGa/aTa	10/13	1	2	FACETS	0.879	0.815	0.944	0.879	0.815	0.944	CLONAL	1	TRUE	1	0.468345955549132	2		606	1006	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550472	29550473	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs786204255	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	73	220	0	ENST00000356175.3:c.1738dup	p.Tyr580LeufsTer8	p.Y580Lfs*8	ENST00000356175	NM_000267.3	578	ctt/cTtt	16/57	1	2	FACETS	0.906	0.798	1	0.906	0.798	1	CLONAL	1	TRUE	1	0.468345955549132	2		220	344	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627201	37627201	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	193	538	0	ENST00000447079.4:c.1116G>T	p.Lys372Asn	p.K372N	ENST00000447079	NM_015083.1	372	aaG/aaT	2/14	1	2	FACETS	0.977	0.905	1	0.977	0.905	1	CLONAL	1	TRUE	1	0.468345955549132	2		538	844	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627650	37627650	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	295	815	0	ENST00000447079.4:c.1565A>C	p.Glu522Ala	p.E522A	ENST00000447079	NM_015083.1	522	gAa/gCa	2/14	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.468345955549132	2		815	1146	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453472	40453472	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	330	827	0	ENST00000345506.4:c.1169A>C	p.Asn390Thr	p.N390T	ENST00000345506	NM_003152.3	390	aAc/aCc	10/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.468345955549132	2		827	1289	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40876332	40876332	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	228	552	0	ENST00000428826.2:c.357G>T	p.Gln119His	p.Q119H	ENST00000428826		119	caG/caT	5/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.468345955549132	2		552	845	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519919	66519919	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1383865866	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	196	538	0	ENST00000358598.2:c.402G>T	p.Lys134Asn	p.K134N	ENST00000358598	NM_212471.2	134	aaG/aaT	4/11	1	2	FACETS	0.951	0.881	1	0.951	0.881	1	CLONAL	1	TRUE	1	0.468345955549132	2		538	880	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372086	45372086	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	302	693	0	ENST00000262160.6:c.1083T>A	p.Asn361Lys	p.N361K	ENST00000262160	NM_005901.5	361	aaT/aaA	9/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.468345955549132	2		693	1113	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220119	5220119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755452432	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	280	657	0	ENST00000357368.4:c.3596C>T	p.Ser1199Leu	p.S1199L	ENST00000357368	NM_002850.3	1199	tCg/tTg	22/38	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.468345955549132	2		657	1106	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10267124	10267124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751093624	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	259	642	2	ENST00000340748.4:c.1294G>A	p.Glu432Lys	p.E432K	ENST00000340748		432	Gaa/Aaa	17/40	1	2	FACETS	0.974	0.911	1	0.974	0.911	1	CLONAL	1	TRUE	1	0.468345955549132	2		644	1136	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210688	36210688	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	302	690	0	ENST00000222270.7:c.439C>T	p.Arg147Ter	p.R147*	ENST00000222270	NM_014727.1	147	Cga/Tga	3/37	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.468345955549132	2		690	1161	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743855	41743855	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	279	736	0	ENST00000301178.4:c.790C>A	p.Leu264Met	p.L264M	ENST00000301178	NM_021913.4	264	Ctg/Atg	7/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.468345955549132	2		736	1116	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39241973	39241973	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	103	403	1	ENST00000402219.2:c.1873C>T	p.Arg625Trp	p.R625W	ENST00000402219	NM_005633.3	625	Cgg/Tgg	11/23	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.468345955549132	2		404	409	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39262364	39262364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	224	650	0	ENST00000402219.2:c.1063G>A	p.Glu355Lys	p.E355K	ENST00000402219	NM_005633.3	355	Gaa/Aaa	8/23	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.468345955549132	2		650	950	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281838	39281838	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	162	572	1	ENST00000402219.2:c.637C>T	p.Arg213Ter	p.R213*	ENST00000402219	NM_005633.3	213	Cga/Tga	5/23	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.468345955549132	2		573	600	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033396	48033396	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	186	531	0	ENST00000234420.5:c.3700G>T	p.Glu1234Ter	p.E1234*	ENST00000234420	NM_000179.2	1234	Gaa/Taa	8/10	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.468345955549132	2		531	776	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273266	198273266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	259	577	1	ENST00000335508.6:c.944G>A	p.Arg315Gln	p.R315Q	ENST00000335508	NM_012433.2	315	cGa/cAa	8/25	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.468345955549132	2		578	929	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281565	198281565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147879907	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	265	590	1	ENST00000335508.6:c.566C>T	p.Ala189Val	p.A189V	ENST00000335508	NM_012433.2	189	gCg/gTg	6/25	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.468345955549132	2		591	1068	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136264	202136264	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	176	628	0	ENST00000358485.4:c.508G>T	p.Glu170Ter	p.E170*	ENST00000358485	NM_001080125.1	170	Gaa/Taa	3/9	1	2	FACETS	0.915	0.844	0.989	0.915	0.844	0.989	CLONAL	1	TRUE	1	0.468345955549132	2		628	821	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149974	202149974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301592633	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	279	681	3	ENST00000358485.4:c.1415G>A	p.Arg472Gln	p.R472Q	ENST00000358485	NM_001080125.1	472	cGa/cAa	8/9	1	2	FACETS	0.999	0.937	1	0.999	0.937	1	CLONAL	1	TRUE	1	0.468345955549132	2		684	1193	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016212	31016212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	175	443	0	ENST00000375687.4:c.458G>A	p.Arg153Lys	p.R153K	ENST00000375687	NM_015338.5	153	aGa/aAa	6/13	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.468345955549132	2		443	722	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419994	41419994	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	239	648	0	ENST00000373198.4:c.327C>A	p.Phe109Leu	p.F109L	ENST00000373198	NM_133170.3	109	ttC/ttA	3/32	1	2	FACETS	0.979	0.915	1	0.979	0.915	1	CLONAL	1	TRUE	1	0.468345955549132	2		648	1042	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268450	46268450	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	169	468	0	ENST00000371998.3:c.2837A>C	p.Asn946Thr	p.N946T	ENST00000371998		946	aAt/aCt	15/23	1	2	FACETS	0.951	0.876	1	0.951	0.876	1	CLONAL	1	TRUE	1	0.468345955549132	2		468	759	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127263	22127263	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	215	585	0	ENST00000215832.6:c.865T>G	p.Leu289Val	p.L289V	ENST00000215832	NM_002745.4	289	Tta/Gta	7/9	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.468345955549132	2		585	882	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523692	41523692	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	311	834	0	ENST00000263253.7:c.1108C>T	p.Arg370Cys	p.R370C	ENST00000263253	NM_001429.3	370	Cgc/Tgc	4/31	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.468345955549132	2		834	1268	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183610	10183610	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	324	696	0	ENST00000256474.2:c.79G>T	p.Glu27Ter	p.E27*	ENST00000256474	NM_000551.3	27	Gaa/Taa	1/3	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.468345955549132	2		696	1199	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277923	41277923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	185	468	0	ENST00000349496.5:c.1887A>C	p.Glu629Asp	p.E629D	ENST00000349496	NM_001904.3	629	gaA/gaC	12/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.468345955549132	2		468	748	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125374	47125374	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	213	495	0	ENST00000409792.3:c.5896A>G	p.Asn1966Asp	p.N1966D	ENST00000409792	NM_014159.6	1966	Aac/Gac	12/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.468345955549132	2		495	807	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49927995	49927995	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759230802	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	326	827	0	ENST00000296474.3:c.3733C>T	p.Arg1245Cys	p.R1245C	ENST00000296474	NM_002447.2	1245	Cgc/Tgc	18/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.468345955549132	2		827	1274	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595857	52595857	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	289	606	0	ENST00000394830.3:c.4058C>A	p.Ser1353Tyr	p.S1353Y	ENST00000394830	NM_018313.4	1353	tCt/tAt	26/30	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.468345955549132	2		606	1151	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259364	89259364	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	231	554	1	ENST00000336596.2:c.508G>T	p.Glu170Ter	p.E170*	ENST00000336596	NM_005233.5	170	Gaa/Taa	3/17	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.468345955549132	2		555	912	SUCCESS
ATR	545	MSKCC	GRCh37	3	142185176	142185176	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	170	479	0	ENST00000350721.4:c.6887T>C	p.Phe2296Ser	p.F2296S	ENST00000350721	NM_001184.3	2296	tTt/tCt	40/47	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.468345955549132	2		479	691	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936105	178936105	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	259	753	0	ENST00000263967.3:c.1647T>G	p.Asp549Glu	p.D549E	ENST00000263967	NM_006218.2	549	gaT/gaG	10/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.468345955549132	2		753	977	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181425	185181425	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1435276633	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	220	552	0	ENST00000265026.3:c.1366C>T	p.Arg456Ter	p.R456*	ENST00000265026	NM_004721.4	456	Cga/Tga	8/14	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.468345955549132	2		552	874	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183551	185183551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	178	402	0	ENST00000265026.3:c.1405C>T	p.Arg469Cys	p.R469C	ENST00000265026	NM_004721.4	469	Cgt/Tgt	9/14	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.468345955549132	2		402	729	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443345	187443345	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	195	492	0	ENST00000232014.4:c.1781G>A	p.Arg594Gln	p.R594Q	ENST00000232014	NM_001130845.1	594	cGa/cAa	8/10	1	2	FACETS	0.989	0.917	1	0.989	0.917	1	CLONAL	1	TRUE	1	0.468345955549132	2		492	842	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582021	189582021	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	162	448	0	ENST00000264731.3:c.580T>C	p.Tyr194His	p.Y194H	ENST00000264731	NM_003722.4	194	Tat/Cat	5/14	1	2	FACETS	0.965	0.887	1	0.965	0.887	1	CLONAL	1	TRUE	1	0.468345955549132	2		448	717	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361245	66361245	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	170	414	0	ENST00000273854.3:c.927C>A	p.Phe309Leu	p.F309L	ENST00000273854	NM_004439.5	309	ttC/ttA	4/18	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.468345955549132	2		414	682	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467464	66467464	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773032839	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	148	374	0	ENST00000273854.3:c.805G>A	p.Asp269Asn	p.D269N	ENST00000273854	NM_004439.5	269	Gat/Aat	3/18	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.468345955549132	2		374	630	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158454	106158454	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1182812722	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	133	320	0	ENST00000380013.4:c.3355T>G	p.Leu1119Val	p.L1119V	ENST00000380013	NM_001127208.2	1119	Tta/Gta	3/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.468345955549132	2		320	499	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532732	187532732	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	253	645	0	ENST00000441802.2:c.9661C>A	p.Leu3221Ile	p.L3221I	ENST00000441802	NM_005245.3	3221	Ctt/Att	14/27	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.468345955549132	2		645	1034	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627747	187627747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143694311	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	208	507	0	ENST00000441802.2:c.3235G>A	p.Val1079Ile	p.V1079I	ENST00000441802	NM_005245.3	1079	Gtt/Att	2/27	1	2	FACETS	0.984	0.914	1	0.984	0.914	1	CLONAL	1	TRUE	1	0.468345955549132	2		507	903	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628653	187628653	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	299	836	0	ENST00000441802.2:c.2329T>G	p.Leu777Val	p.L777V	ENST00000441802	NM_005245.3	777	Tta/Gta	2/27	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.468345955549132	2		836	1149	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31431770	31431770	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs775775322	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	192	500	5	ENST00000344624.3:c.3058C>T	p.Arg1020Ter	p.R1020*	ENST00000344624		1020	Cga/Tga	23/33	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.468345955549132	2		505	739	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31508822	31508822	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	270	678	0	ENST00000344624.3:c.1493A>C	p.Asp498Ala	p.D498A	ENST00000344624		498	gAc/gCc	7/33	1	2	FACETS	0.93	0.871	0.99	0.93	0.871	0.99	CLONAL	1	TRUE	1	0.468345955549132	2		678	1240	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178139	56178139	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	188	443	0	ENST00000399503.3:c.3112G>T	p.Asp1038Tyr	p.D1038Y	ENST00000399503	NM_005921.1	1038	Gac/Tac	14/20	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.468345955549132	2		443	680	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184173	56184173	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	136	369	0	ENST00000399503.3:c.4378T>G	p.Leu1460Val	p.L1460V	ENST00000399503	NM_005921.1	1460	Ttg/Gtg	19/20	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.468345955549132	2		369	569	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649005	86649005	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	84	387	0	ENST00000274376.6:c.1285G>T	p.Glu429Ter	p.E429*	ENST00000274376	NM_002890.2	429	Gaa/Taa	9/25	1	2	FACETS	0.917	0.815	1	0.917	0.815	1	CLONAL	1	TRUE	1	0.468345955549132	2		387	391	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675628	86675628	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	104	406	0	ENST00000274376.6:c.2564T>G	p.Leu855Arg	p.L855R	ENST00000274376	NM_002890.2	855	cTt/cGt	19/25	1	2	FACETS	0.968	0.871	1	0.968	0.871	1	CLONAL	1	TRUE	1	0.468345955549132	2		406	459	SUCCESS
APC	324	MSKCC	GRCh37	5	112174119	112174119	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1554084512	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	157	409	0	ENST00000257430.4:c.2828C>A	p.Ser943Ter	p.S943*	ENST00000257430	NM_000038.5	943	tCa/tAa	16/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.468345955549132	2		409	600	SUCCESS
APC	324	MSKCC	GRCh37	5	112175925	112175925	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs863225356	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	116	285	0	ENST00000257430.4:c.4634C>A	p.Ser1545Ter	p.S1545*	ENST00000257430	NM_000038.5	1545	tCa/tAa	16/16	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.468345955549132	2		285	481	SUCCESS
APC	324	MSKCC	GRCh37	5	112176033	112176033	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	153	378	1	ENST00000257430.4:c.4742C>A	p.Ser1581Tyr	p.S1581Y	ENST00000257430	NM_000038.5	1581	tCt/tAt	16/16	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.468345955549132	2		379	603	SUCCESS
APC	324	MSKCC	GRCh37	5	112177368	112177368	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	158	377	0	ENST00000257430.4:c.6077C>A	p.Ser2026Tyr	p.S2026Y	ENST00000257430	NM_000038.5	2026	tCt/tAt	16/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.468345955549132	2		377	617	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815404	32815404	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	317	789	0	ENST00000354258.4:c.1969G>T	p.Glu657Ter	p.E657*	ENST00000354258	NM_000593.5	657	Gaa/Taa	9/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.468345955549132	2		789	1234	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818213	32818213	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs143800384	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	324	722	0	ENST00000354258.4:c.1312C>T	p.Arg438Ter	p.R438*	ENST00000354258	NM_000593.5	438	Cga/Tga	5/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.468345955549132	2		722	1285	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956553	93956553	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1035177735	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	163	415	0	ENST00000369303.4:c.2683C>T	p.Arg895Ter	p.R895*	ENST00000369303	NM_004440.3	895	Cga/Tga	15/17	1	2	FACETS	0.997	0.918	1	0.997	0.918	1	CLONAL	1	TRUE	1	0.468345955549132	2		415	698	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683897	117683897	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	214	540	0	ENST00000368508.3:c.3250A>C	p.Ile1084Leu	p.I1084L	ENST00000368508	NM_002944.2	1084	Att/Ctt	21/43	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.468345955549132	2		540	858	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686839	117686839	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	212	552	0	ENST00000368508.3:c.2878G>T	p.Gly960Ter	p.G960*	ENST00000368508	NM_002944.2	960	Gga/Tga	19/43	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.468345955549132	2		552	869	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265314	152265314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781741770	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	144	429	1	ENST00000206249.3:c.767G>A	p.Arg256Gln	p.R256Q	ENST00000206249	NM_000125.3	256	cGa/cAa	4/8	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.468345955549132	2		430	593	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985523	2985523	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	225	625	0	ENST00000396946.4:c.288A>T	p.Glu96Asp	p.E96D	ENST00000396946	NM_032415.4	96	gaA/gaT	4/25	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.468345955549132	2		625	942	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971145	13971145	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	87	323	0	ENST00000405192.2:c.784G>T	p.Asp262Tyr	p.D262Y	ENST00000405192	NM_001163147.1	262	Gat/Tat	8/12	1	2	FACETS	0.672	0.596	0.753	0.672	0.596	0.753	SUBCLONAL	1	TRUE	1	0.468345955549132	2		323	553	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444375	50444375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776572250	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	209	483	0	ENST00000331340.3:c.305C>T	p.Ser102Leu	p.S102L	ENST00000331340	NM_006060.4	102	tCg/tTg	4/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.468345955549132	2		483	830	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508374	106508374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200423506	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	170	396	1	ENST00000359195.3:c.368G>A	p.Arg123His	p.R123H	ENST00000359195	NM_002649.2	123	cGc/cAc	2/11	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.468345955549132	2		397	723	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418850	116418850	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	150	351	0	ENST00000397752.3:c.3361G>T	p.Val1121Phe	p.V1121F	ENST00000397752	NM_000245.2	1121	Gtt/Ttt	17/21	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.468345955549132	2		351	631	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945021	151945021	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs756918375	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	21	91	0	ENST00000262189.6:c.2498G>T	p.Arg833Ile	p.R833I	ENST00000262189	NM_170606.2	833	aGa/aTa	14/59	1	2	FACETS	0.712	0.555	0.889	0.712	0.555	0.889	SUBCLONAL	1	TRUE	1	0.468345955549132	2		91	126	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012244	152012244	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748254163	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	171	535	0	ENST00000262189.6:c.569G>A	p.Arg190Gln	p.R190Q	ENST00000262189	NM_170606.2	190	cGa/cAa	4/59	1	2	FACETS	0.903	0.831	0.977	0.903	0.831	0.977	CLONAL	1	TRUE	1	0.468345955549132	2		535	809	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345798	152345798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759300252	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	184	472	0	ENST00000359321.1:c.772C>T	p.Arg258Cys	p.R258C	ENST00000359321	NM_005431.1	258	Cgt/Tgt	3/3	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.468345955549132	2		472	761	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964351	70964351	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	146	421	0	ENST00000276594.2:c.1677A>C	p.Glu559Asp	p.E559D	ENST00000276594	NM_024504.3	559	gaA/gaC	8/8	1	2	FACETS	0.901	0.824	0.981	0.901	0.824	0.981	CLONAL	1	TRUE	1	0.468345955549132	2		421	692	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970919	70970919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1563439440	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	179	733	1	ENST00000276594.2:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000276594	NM_024504.3	448	Cgg/Tgg	6/8	1	2	FACETS	0.658	0.606	0.713	0.658	0.606	0.713	SUBCLONAL	1	TRUE	1	0.468345955549132	2		734	1161	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982702	90982702	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs372159380	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	200	479	0	ENST00000265433.3:c.786C>A	p.Phe262Leu	p.F262L	ENST00000265433	NM_002485.4	262	ttC/ttA	7/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.468345955549132	2		479	723	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465499	8465499	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	196	531	0	ENST00000356435.5:c.3681C>A	p.Phe1227Leu	p.F1227L	ENST00000356435		1227	ttC/ttA	21/35	1	2	FACETS	0.98	0.909	1	0.98	0.909	1	CLONAL	1	TRUE	1	0.468345955549132	2		531	854	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485782	8485782	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	171	362	0	ENST00000356435.5:c.3035G>T	p.Arg1012Met	p.R1012M	ENST00000356435		1012	aGg/aTg	17/35	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.468345955549132	2		362	624	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500769	8500769	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	189	450	0	ENST00000356435.5:c.2113C>T	p.Arg705Ter	p.R705*	ENST00000356435		705	Cga/Tga	13/35	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.468345955549132	2		450	732	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633425	8633425	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776040231	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	198	476	0	ENST00000356435.5:c.244C>T	p.Leu82Phe	p.L82F	ENST00000356435		82	Ctc/Ttc	3/35	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.468345955549132	2		476	799	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015065	37015065	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	319	680	1	ENST00000358127.4:c.339G>T	p.Glu113Asp	p.E113D	ENST00000358127	NM_001280556.1	113	gaG/gaT	3/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.468345955549132	2		681	1206	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80343462	80343462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	139	433	0	ENST00000286548.4:c.857C>T	p.Ser286Phe	p.S286F	ENST00000286548	NM_002072.3	286	tCc/tTc	6/7	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.468345955549132	2		433	578	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232138	98232138	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs863224650	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	180	514	0	ENST00000331920.6:c.1804C>T	p.Arg602Ter	p.R602*	ENST00000331920	NM_000264.3	602	Cga/Tga	13/24	1	2	FACETS	0.883	0.814	0.953	0.883	0.814	0.953	CLONAL	1	TRUE	1	0.468345955549132	2		514	871	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912136	127912136	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	143	394	0	ENST00000373547.4:c.734A>C	p.Lys245Thr	p.K245T	ENST00000373547	NM_002721.4	245	aAa/aCa	7/7	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.468345955549132	2		394	584	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321286	1321286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780766655	NA	P-0043206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	258	525	0	ENST00000400841.2:c.469G>A	p.Asp157Asn	p.D157N	ENST00000400841		157	Gac/Aac	4/6	0.468345955549132	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.468345955549132	1		525	673	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0043229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	171	727	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.324878923149034	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.324878923149034	1		728	821	SUCCESS
APC	324	MSKCC	GRCh37	5	112175746	112175746	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	48	348	0	ENST00000257430.4:c.4455del	p.Asp1486IlefsTer21	p.D1486Ifs*21	ENST00000257430	NM_000038.5	1485	gcT/gc	16/16	1	2	FACETS	0.754	0.639	0.88	0.754	0.639	0.88	SUBCLONAL	1	TRUE	1	0.324878923149034	2		348	392	SUCCESS
APC	324	MSKCC	GRCh37	5	112174091	112174094	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	rs1131691143	NA	P-0043229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	57	385	0	ENST00000257430.4:c.2802_2805del	p.Tyr935IlefsTer19	p.Y935Ifs*19	ENST00000257430	NM_000038.5	934	ACTTac/ac	16/16	1	2	FACETS	0.835	0.719	0.962	0.835	0.719	0.962	CLONAL	1	TRUE	1	0.324878923149034	2		385	420	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259328	89259328	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	26	442	0	ENST00000336596.2:c.472G>T	p.Gly158Trp	p.G158W	ENST00000336596	NM_005233.5	158	Ggg/Tgg	3/17	1	2	FACETS	0.31	0.244	0.385	0.31	0.244	0.385	SUBCLONAL	1	TRUE	1	0.324878923149034	2		442	517	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249460	153249460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	96	601	1	ENST00000281708.4:c.1318G>A	p.Asp440Asn	p.D440N	ENST00000281708	NM_033632.3	440	Gat/Aat	9/12	0.258208961413918	1	FACETS	0.87	0.777	0.968	0.87	0.777	0.968	CLONAL	1	TRUE	0	0.324878923149034	1		602	569	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964055	28964055	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	66	507	0	ENST00000282397.4:c.1847C>G	p.Ser616Cys	p.S616C	ENST00000282397	NM_002019.4	616	tCc/tGc	13/30	0.285056818828309	4	FACETS	0.755	0.655	0.864	0.252	0.218	0.288	SUBCLONAL	1	TRUE	1	0.324878923149034	4		507	713	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554003	63554003	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043229-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	110	534	0	ENST00000307078.5:c.736A>G	p.Thr246Ala	p.T246A	ENST00000307078	NM_004655.3	246	Acc/Gcc	2/11	1	2	FACETS	0.849	0.762	0.94	0.849	0.762	0.94	CLONAL	1	TRUE	1	0.324878923149034	2		534	798	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578491	7578491	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1567553924	NA	P-0043240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	935	886	0	ENST00000269305.4:c.439del	p.Val147LeufsTer23	p.V147Lfs*23	ENST00000269305	NM_001126112.2	147	Gtt/tt	5/11	0.63616263508479	4	FACETS	0.949	0.931	0.967	0.949	0.931	0.967	CLONAL	4	TRUE	0	0.676327830756524	4		886	1221	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593613	55593614	+	missense_variant	Missense_Mutation	DNP	TT	TT	AG	novel	NA	P-0043241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	280	389	0	ENST00000288135.5:c.1679_1680delinsAG	p.Val560Glu	p.V560E	ENST00000288135	NM_000222.2	560	gTT/gAG	11/21	0.737672593818051	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.737672593818051	1		389	457	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665756	29665756	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	141	301	1	ENST00000356175.3:c.6791del	p.Tyr2264SerfsTer6	p.Y2264Sfs*6	ENST00000356175	NM_000267.3	2264	tAc/tc	45/57	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.737672593818051	2		302	339	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250906	153250906	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043241-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	141	334	0	ENST00000281708.4:c.1154C>G	p.Thr385Arg	p.T385R	ENST00000281708	NM_033632.3	385	aCa/aGa	8/12	0.737672593818051	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.737672593818051	1		334	238	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412884	49412884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	344	555	0	ENST00000418115.1:c.139G>A	p.Glu47Lys	p.E47K	ENST00000418115	NM_001664.2	47	Gag/Aag	2/5	0.358619739746672	7	FACETS	0.992	0.939	1	0.744	0.704	0.785	CLONAL	3	FALSE	3	0.358619739746672	7		555	1222	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879925	44879925	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs189751539	NA	P-0043298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	305	513	0	ENST00000377967.4:c.514C>T	p.Arg172Ter	p.R172*	ENST00000377967	NM_021140.2	172	Cga/Tga	6/29	0.370476156819175	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	FALSE	0	0.358619739746672	2		513	684	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981277	201981278	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0043298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	1213	661	0	ENST00000359651.3:c.358dup	p.Gln120ProfsTer15	p.Q120Pfs*15	ENST00000359651		119	gac/gaCc	2/8	0.358619739746672	7	FACETS	0.968	0.951	0.986			1	CLONAL	8	FALSE	NA	0.358619739746672	7		661	1656	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434346	49434346	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	358	724	0	ENST00000301067.7:c.7207C>G	p.Leu2403Val	p.L2403V	ENST00000301067	NM_003482.3	2403	Ctg/Gtg	31/54	0.156591418707231	6	FACETS	0.907	0.862	0.952			1	INDETERMINATE	4	FALSE	NA	0.358619739746672	6		724	945	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027105	71027105	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1432237560	NA	P-0043298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	193	475	0	ENST00000318789.4:c.1222A>G	p.Thr408Ala	p.T408A	ENST00000318789	NM_032682.5	408	Acg/Gcg	15/21	0.354993273792747	4	FACETS	1	0.99	1			1	CLONAL	1	FALSE	NA	0.358619739746672	4		475	993	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405123	139405123	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	52	619	0	ENST00000277541.6:c.2722A>G	p.Ile908Val	p.I908V	ENST00000277541	NM_017617.3	908	Atc/Gtc	17/34	0.253871865404577	4	FACETS	0.407	0.345	0.475	0.203	0.172	0.238	SUBCLONAL	1	FALSE	2	0.358619739746672	4		619	969	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564651	139564651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	371	746	0	ENST00000308874.7:c.440G>A	p.Gly147Asp	p.G147D	ENST00000308874		147	gGc/gAc	7/10	0.253871865404577	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	FALSE	2	0.358619739746672	4		746	1173	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139565464	139565464	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	155	309	0	ENST00000308874.7:c.634G>A	p.Glu212Lys	p.E212K	ENST00000308874		212	Gag/Aag	8/10	0.253871865404577	4	FACETS	0.956	0.879	1	0.956	0.879	1	CLONAL	2	FALSE	2	0.358619739746672	4		309	614	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426112	47426112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs923182352	NA	P-0043298-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	281	728	0	ENST00000377045.4:c.632G>A	p.Arg211His	p.R211H	ENST00000377045	NM_001654.4	211	cGc/cAc	7/16	0.370476156819175	1	FACETS	0.908	0.859	0.959	1	0.995	1	CLONAL	2	FALSE	0	0.358619739746672	1		728	708	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023831	27023831	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1415214478	NA	P-0043519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	59	255	0	ENST00000324856.7:c.941del	p.Gly314AlafsTer49	p.G314Afs*49	ENST00000324856	NM_006015.4	313	Ggg/gg	1/20	0.208470350585964	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.208470350585964	1		255	389	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	116	648	0	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.208470350585964	2		648	879	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682400	52682400	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	43	267	1	ENST00000394830.3:c.773del	p.Asn258MetfsTer25	p.N258Mfs*25	ENST00000394830	NM_018313.4	258	aAt/at	8/30	0.208470350585964	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.208470350585964	1		268	326	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	123	694	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.208470350585964	2		694	999	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933593	39933594	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0043519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	95	290	0	ENST00000378444.4:c.1005dup	p.Ser336LeufsTer45	p.S336Lfs*45	ENST00000378444	NM_001123385.1	335	-/C	4/15	1	1	FACETS	1	0.901	1	1	0.987	1	CLONAL	2	TRUE	0	0.208470350585964	1		290	406	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907261	32907263	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0043519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	61	323	0	ENST00000380152.3:c.1650_1652del	p.Glu550del	p.E550del	ENST00000380152		549	aAGGag/aag	10/27	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.208470350585964	2		323	408	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222334	2222334	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	126	642	0	ENST00000326181.6:c.622del	p.Arg208GlufsTer38	p.R208Efs*38	ENST00000326181	NM_032271.2	206	gaC/ga	8/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.208470350585964	2		642	924	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859392	151859393	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0043519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	50	373	0	ENST00000262189.6:c.11269_11270del	p.Gln3757GlufsTer18	p.Q3757Efs*18	ENST00000262189	NM_170606.2	3757	CAg/g	43/59	1	2	FACETS	0.854	0.724	0.996	0.854	0.724	0.996	CLONAL	1	TRUE	1	0.208470350585964	2		373	562	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814616	43814617	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	114	432	0	ENST00000372470.3:c.1413dup	p.Gly472ArgfsTer11	p.G472Rfs*11	ENST00000372470	NM_005373.2	471	caa/cAaa	9/12	0.208470350585964	1	FACETS	0.784	0.707	0.864	1	0.985	1	SUBCLONAL	2	TRUE	0	0.208470350585964	1		432	625	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437094	121437094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	123	549	0	ENST00000257555.6:c.1525G>A	p.Val509Met	p.V509M	ENST00000257555		509	Gtg/Atg	8/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.208470350585964	2		549	856	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251109	99251109	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs746570875	NA	P-0043519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	87	513	1	ENST00000268035.6:c.418del	p.Ala140ProfsTer20	p.A140Pfs*20	ENST00000268035	NM_000875.3	138	cGg/cg	2/21	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.208470350585964	2		514	634	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843553	3843553	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	77	422	0	ENST00000262367.5:c.1050del	p.Lys350AsnfsTer4	p.K350Nfs*4	ENST00000262367	NM_004380.2	350	aaA/aa	4/31	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.208470350585964	2		422	695	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534362	187534362	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375701023	NA	P-0043519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	115	450	0	ENST00000441802.2:c.9364G>A	p.Ala3122Thr	p.A3122T	ENST00000441802	NM_005245.3	3122	Gcc/Acc	13/27	1	2	FACETS	0.775	0.699	0.855	1	0.985	1	SUBCLONAL	2	TRUE	1	0.208470350585964	2		450	712	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053186	180053186	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	101	624	0	ENST00000261937.6:c.1183G>T	p.Gly395Cys	p.G395C	ENST00000261937	NM_182925.4	395	Ggc/Tgc	9/30	0.208470350585964	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.208470350585964	1		624	799	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321357	1321357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	80	492	0	ENST00000400841.2:c.398C>T	p.Ala133Val	p.A133V	ENST00000400841		133	gCa/gTa	4/6	1	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.208470350585964	1		492	629	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412595	63412595	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043519-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	63	246	0	ENST00000330258.3:c.572A>G	p.Glu191Gly	p.E191G	ENST00000330258	NM_152424.3	191	gAg/gGg	2/2	1	1	FACETS	0.82	0.714	0.934	1	0.975	1	CLONAL	2	TRUE	0	0.208470350585964	1		246	330	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0043567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	50	229	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	0.963	0.818	1	0.963	0.818	1	CLONAL	1	FALSE	1	0.228143739534992	2		229	455	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453154	140453154	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913338	NA	P-0043567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	46	334	0	ENST00000288602.6:c.1781A>G	p.Asp594Gly	p.D594G	ENST00000288602	NM_004333.4	594	gAt/gGt	15/18	0.228143739534992	3	FACETS	0.899	0.757	1	0.449	0.378	0.528	CLONAL	1	FALSE	1	0.228143739534992	3		334	500	SUCCESS
APC	324	MSKCC	GRCh37	5	112175645	112175645	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	40	339	0	ENST00000257430.4:c.4354del	p.Val1452TyrfsTer21	p.V1452Yfs*21	ENST00000257430	NM_000038.5	1452	Gta/ta	16/16	1	2	FACETS	0.913	0.76	1	0.913	0.76	1	CLONAL	1	FALSE	1	0.228143739534992	2		339	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1555525429	NA	P-0043567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	80	582	0	ENST00000269305.4:c.782+1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.228143739534992	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	FALSE	0	0.228143739534992	1		582	589	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948712	71948712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374001069	NA	P-0043567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	71	712	1	ENST00000298229.2:c.3424C>T	p.Arg1142Cys	p.R1142C	ENST00000298229	NM_001567.3	1142	Cgc/Tgc	26/28	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	FALSE	1	0.228143739534992	2		713	588	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763340	59763340	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	47	660	0	ENST00000259008.2:c.2762A>G	p.Tyr921Cys	p.Y921C	ENST00000259008	NM_032043.2	921	tAt/tGt	19/20	1	2	FACETS	0.6	0.505	0.705	0.6	0.505	0.705	SUBCLONAL	1	FALSE	1	0.228143739534992	2		660	687	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125806	47125808	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0043567-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	50	321	0	ENST00000409792.3:c.5462_5464del	p.Leu1821del	p.L1821del	ENST00000409792	NM_014159.6	1821	cTTCca/cca	12/21	0.228143739534992	1	FACETS	0.94	0.8	1	0.94	0.8	1	CLONAL	1	FALSE	0	0.228143739534992	1		321	413	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	136	372	0				ENST00000310581	NM_198253.2	-/1132			0.19232249001801	5	FACETS	0.986	0.903	1			1	CLONAL	4	FALSE	NA	0.19232249001801	5		372	462	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230641	46230641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	54	462	0	ENST00000334344.6:c.890C>T	p.Ser297Phe	p.S297F	ENST00000334344	NM_152641.2	297	tCc/tTc	8/21	1	2	FACETS	0.897	0.766	1	0.897	0.766	1	CLONAL	1	FALSE	1	0.19232249001801	2		462	626	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524603	176524603	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758782236	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	179	579	0	ENST00000292408.4:c.2335G>A	p.Asp779Asn	p.D779N	ENST00000292408	NM_213647.1	779	Gat/Aat	18/18	0.187071157132918	3	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	FALSE	1	0.19232249001801	3		579	991	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	240484	240484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1205384855	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	61	113	0	ENST00000264932.6:c.1444C>T	p.Pro482Ser	p.P482S	ENST00000264932	NM_004168.2	482	Cct/Tct	11/15	0.19232249001801	5	FACETS	1	0.905	1			1	CLONAL	4	FALSE	NA	0.19232249001801	5		113	197	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	63	559	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.19232249001801	1	FACETS	0.911	0.787	1	0.911	0.787	1	CLONAL	1	FALSE	0	0.19232249001801	1		559	650	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873660	35873660	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs201559094	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	39	282	0	ENST00000303115.3:c.616C>T	p.Arg206Ter	p.R206*	ENST00000303115	NM_002185.3	206	Cga/Tga	5/8	0.187071157132918	3	FACETS	0.917	0.76	1	0.458	0.38	0.546	CLONAL	1	FALSE	1	0.19232249001801	3		282	485	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508727	148508727	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs267601394	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	53	336	0	ENST00000320356.2:c.1937A>T	p.Tyr646Phe	p.Y646F	ENST00000320356	NM_004456.4	646	tAc/tTc	16/20	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	FALSE	1	0.19232249001801	2		336	544	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321372	1321372	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1319865856	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	68	399	0	ENST00000400841.2:c.383C>T	p.Ser128Leu	p.S128L	ENST00000400841		128	tCg/tTg	4/6	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	1	0.19232249001801	2		399	622	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023019	150023019	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	94	439	0	ENST00000253339.5:c.244C>T	p.Arg82Ter	p.R82*	ENST00000253339		82	Cga/Tga	1/7	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.19232249001801	2		439	753	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976817	2976817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	86	559	1	ENST00000396946.4:c.1195G>A	p.Glu399Lys	p.E399K	ENST00000396946	NM_032415.4	399	Gaa/Aaa	9/25	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	FALSE	1	0.19232249001801	2		560	834	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989487	212989487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765191737	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	30	307	0	ENST00000342788.4:c.224C>T	p.Ser75Phe	p.S75F	ENST00000342788	NM_005235.2	75	tCc/tTc	2/28	0.19232249001801	1	FACETS	0.834	0.673	1	0.834	0.673	1	CLONAL	1	FALSE	0	0.19232249001801	1		307	338	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641054	117641054	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1216964547	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	45	437	0	ENST00000368508.3:c.5917G>A	p.Gly1973Arg	p.G1973R	ENST00000368508	NM_002944.2	1973	Gga/Aga	36/43	0.19232249001801	1	FACETS	0.867	0.729	1	0.867	0.729	1	CLONAL	1	FALSE	0	0.19232249001801	1		437	488	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164686	36164686	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	80	574	1	ENST00000300305.3:c.1189C>T	p.Gln397Ter	p.Q397*	ENST00000300305		397	Caa/Taa	8/8	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	FALSE	1	0.19232249001801	2		575	777	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412494	80412494	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	53	297	0	ENST00000286548.4:c.547C>T	p.Arg183Ter	p.R183*	ENST00000286548	NM_002072.3	183	Cga/Tga	4/7	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	FALSE	1	0.19232249001801	2		297	496	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976787	2976787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	100	580	0	ENST00000396946.4:c.1225G>A	p.Glu409Lys	p.E409K	ENST00000396946	NM_032415.4	409	Gag/Aag	9/25	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.19232249001801	2		580	893	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779382	3779382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143180774	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	86	607	0	ENST00000262367.5:c.5666C>T	p.Pro1889Leu	p.P1889L	ENST00000262367	NM_004380.2	1889	cCg/cTg	31/31	1	2	FACETS	0.952	0.841	1	0.952	0.841	1	CLONAL	1	FALSE	1	0.19232249001801	2		607	939	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286760	212286760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763644012	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	38	299	0	ENST00000342788.4:c.2936G>A	p.Arg979Gln	p.R979Q	ENST00000342788	NM_005235.2	979	cGa/cAa	24/28	0.19232249001801	1	FACETS	0.873	0.723	1	0.873	0.723	1	CLONAL	1	FALSE	0	0.19232249001801	1		299	409	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279483	1279483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	97	657	0	ENST00000310581.5:c.2053G>A	p.Asp685Asn	p.D685N	ENST00000310581	NM_198253.2	685	Gat/Aat	5/16	0.19232249001801	5	FACETS	1	0.957	1			1	CLONAL	1	FALSE	NA	0.19232249001801	5		657	1126	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930595	131930595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	86	259	0	ENST00000265335.6:c.1828C>T	p.His610Tyr	p.H610Y	ENST00000265335		610	Cat/Tat	12/25	0.187071157132918	3	FACETS	0.984	0.874	1	0.984	0.874	1	CLONAL	2	FALSE	1	0.19232249001801	3		259	498	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547850	41547850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	40	383	0	ENST00000263253.7:c.2831C>T	p.Ala944Val	p.A944V	ENST00000263253	NM_001429.3	944	gCt/gTt	15/31	1	2	FACETS	0.77	0.639	0.916	0.77	0.639	0.916	CLONAL	1	FALSE	1	0.19232249001801	2		383	540	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907720	76907720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	59	421	0	ENST00000373344.5:c.4441C>T	p.Arg1481Trp	p.R1481W	ENST00000373344	NM_000489.3	1481	Cgg/Tgg	15/35	1	2	FACETS	0.938	0.807	1	0.938	0.807	1	CLONAL	1	FALSE	1	0.19232249001801	2		421	654	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556190	29556190	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	22	97	0	ENST00000356175.3:c.2557C>T	p.Gln853Ter	p.Q853*	ENST00000356175	NM_000267.3	853	Cag/Tag	21/57	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	FALSE	1	0.19232249001801	2		97	192	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781129	161781129	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	54	438	0	ENST00000366898.1:c.1276G>A	p.Glu426Lys	p.E426K	ENST00000366898	NM_004562.2	426	Gaa/Aaa	11/12	1	2	FACETS	0.831	0.708	0.965	0.831	0.708	0.965	CLONAL	1	FALSE	1	0.19232249001801	2		438	676	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291845	15291845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1302833098	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	70	593	0	ENST00000263388.2:c.2921G>A	p.Gly974Glu	p.G974E	ENST00000263388	NM_000435.2	974	gGg/gAg	18/33	1	2	FACETS	0.862	0.751	0.984	0.862	0.751	0.984	CLONAL	1	FALSE	1	0.19232249001801	2		593	844	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426786	212426786	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866491191	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	60	378	0	ENST00000342788.4:c.2329C>T	p.His777Tyr	p.H777Y	ENST00000342788	NM_005235.2	777	Cat/Tat	20/28	0.19232249001801	1	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	FALSE	0	0.19232249001801	1		378	548	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344269	118344269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	40	377	0	ENST00000534358.1:c.2395C>T	p.Pro799Ser	p.P799S	ENST00000534358	NM_005933.3	799	Cct/Tct	3/36	0.19232249001801	1	FACETS	0.695	0.577	0.827	0.695	0.577	0.827	SUBCLONAL	1	FALSE	0	0.19232249001801	1		377	541	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36931999	36931999	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	76	510	0	ENST00000361632.4:c.2470G>A	p.Gly824Arg	p.G824R	ENST00000361632		824	Ggg/Agg	16/16	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	FALSE	1	0.19232249001801	2		510	779	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424188	49424188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750738360	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	43	289	0	ENST00000301067.7:c.13874C>T	p.Ser4625Leu	p.S4625L	ENST00000301067	NM_003482.3	4625	tCg/tTg	42/54	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	FALSE	1	0.19232249001801	2		289	440	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099426	27099427	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	45	450	0	ENST00000324856.7:c.3663_3664delinsTT	p.Met1221_Gly1222delinsIleTrp	p.M1221_G1222delinsIW	ENST00000324856	NM_006015.4	1221	atGGgg/atTTgg	14/20	1	2	FACETS	0.679	0.569	0.801	0.679	0.569	0.801	SUBCLONAL	1	FALSE	1	0.19232249001801	2		450	689	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933476	36933476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	80	568	1	ENST00000361632.4:c.1811G>A	p.Ser604Asn	p.S604N	ENST00000361632		604	aGc/aAc	13/16	1	2	FACETS	0.936	0.822	1	0.936	0.822	1	CLONAL	1	FALSE	1	0.19232249001801	2		569	889	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36945084	36945084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528738573	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	86	528	0	ENST00000361632.4:c.14G>A	p.Gly5Glu	p.G5E	ENST00000361632		5	gGa/gAa	2/16	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	FALSE	1	0.19232249001801	2		528	870	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514263	69514263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745540845	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	75	566	0	ENST00000294312.3:c.418C>T	p.Arg140Cys	p.R140C	ENST00000294312	NM_005117.2	140	Cgc/Tgc	3/3	1	2	FACETS	0.959	0.839	1	0.959	0.839	1	CLONAL	1	FALSE	1	0.19232249001801	2		566	813	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77085411	77085411	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	46	332	0	ENST00000356341.3:c.440-1G>A		p.X147_splice	ENST00000356341	NM_002576.4	147			1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	FALSE	1	0.19232249001801	2		332	455	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421795	49421795	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	109	649	1	ENST00000301067.7:c.14512C>T	p.Pro4838Ser	p.P4838S	ENST00000301067	NM_003482.3	4838	Cct/Tct	46/54	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.19232249001801	2		650	924	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479208	50479208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	60	272	0	ENST00000394963.4:c.56C>T	p.Ser19Leu	p.S19L	ENST00000394963	NM_003076.4	19	tCa/tTa	1/13	1	2	FACETS	0.763	0.659	0.874	1	0.97	1	SUBCLONAL	2	FALSE	1	0.19232249001801	2		272	409	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209084	133209085	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	42	411	0	ENST00000320574.5:c.6146_6147delinsTT	p.Thr2049Ile	p.T2049I	ENST00000320574	NM_006231.2	2049	aCC/aTT	45/49	1	2	FACETS	0.83	0.693	0.983	0.83	0.693	0.983	CLONAL	1	FALSE	1	0.19232249001801	2		411	526	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21565415	21565416	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	62	493	0	ENST00000382592.4:c.470_471delinsTT	p.Ser157Phe	p.S157F	ENST00000382592	NM_014572.2	157	tCC/tTT	3/8	0.19232249001801	1	FACETS	0.886	0.764	1	0.886	0.764	1	CLONAL	1	FALSE	0	0.19232249001801	1		493	658	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713241	43713241	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774610087	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	87	626	0	ENST00000382044.4:c.4232C>T	p.Ser1411Phe	p.S1411F	ENST00000382044	NM_001141980.1	1411	tCt/tTt	20/28	1	2	FACETS	0.977	0.863	1	0.977	0.863	1	CLONAL	1	FALSE	1	0.19232249001801	2		626	926	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639611	3639611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1341974917	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	100	697	0	ENST00000294008.3:c.4028C>T	p.Pro1343Leu	p.P1343L	ENST00000294008	NM_032444.2	1343	cCt/cTt	12/15	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	FALSE	1	0.19232249001801	2		697	943	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346270	89346271	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	32	301	0	ENST00000301030.4:c.6679_6680delinsTT	p.Pro2227Leu	p.P2227L	ENST00000301030	NM_001256183.1	2227	CCg/TTg	9/13	1	2	FACETS	0.79	0.641	0.959	0.79	0.641	0.959	CLONAL	1	FALSE	1	0.19232249001801	2		301	421	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483074	29483075	+	inframe_insertion	In_Frame_Ins	INS	-	-	TATTTCCAAATACAAGTTTTCTTTGGTTATAAGCGGCCTTAC	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	34	400	0	ENST00000356175.3:c.173_174insTACTATTTCCAAATACAAGTTTTCTTTGGTTATAAGCGGCCT	p.Ile46_Thr59dup	p.I46_T59dup	ENST00000356175	NM_000267.3	46	aat/aaTATTTCCAAATACAAGTTTTCTTTGGTTATAAGCGGCCTTACt	2/57	1	2	FACETS	0.592	0.483	0.716	0.592	0.483	0.716	SUBCLONAL	1	FALSE	1	0.19232249001801	2		400	597	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654520	29654521	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	32	213	0	ENST00000356175.3:c.5209_5210delinsAA	p.Gly1737Asn	p.G1737N	ENST00000356175	NM_000267.3	1737	GGt/AAt	37/57	1	2	FACETS	0.924	0.751	1	0.924	0.751	1	CLONAL	1	FALSE	1	0.19232249001801	2		213	360	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857585	78857586	+	missense_variant	Missense_Mutation	DNP	CC	CC	GT	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	53	471	0	ENST00000306801.3:c.1655_1656delinsGT	p.Ala552Gly	p.A552G	ENST00000306801	NM_020761.2	552	gCC/gGT	16/34	0.187071157132918	3	FACETS	0.778	0.661	0.905	0.389	0.33	0.453	CLONAL	1	FALSE	1	0.19232249001801	3		471	777	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897426	78897426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	68	554	1	ENST00000306801.3:c.2761C>T	p.His921Tyr	p.H921Y	ENST00000306801	NM_020761.2	921	Cac/Tac	23/34	0.187071157132918	3	FACETS	0.908	0.788	1	0.454	0.394	0.519	CLONAL	1	FALSE	1	0.19232249001801	3		555	854	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220464	1220464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	79	623	1	ENST00000326873.7:c.557C>T	p.Thr186Ile	p.T186I	ENST00000326873	NM_000455.4	186	aCc/aTc	4/10	1	2	FACETS	0.985	0.865	1	0.985	0.865	1	CLONAL	1	FALSE	1	0.19232249001801	2		624	834	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302911	15302911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1475080033	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	90	641	0	ENST00000263388.2:c.539C>T	p.Ser180Phe	p.S180F	ENST00000263388	NM_000435.2	180	tCc/tTc	4/33	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	FALSE	1	0.19232249001801	2		641	913	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18961603	18961603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	70	529	0	ENST00000262803.5:c.736C>T	p.Pro246Ser	p.P246S	ENST00000262803	NM_002911.3	246	Ccc/Tcc	5/24	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	FALSE	1	0.19232249001801	2		529	689	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210736	36210737	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	62	632	0	ENST00000222270.7:c.487_488delinsTT	p.Pro163Phe	p.P163F	ENST00000222270	NM_014727.1	163	CCt/TTt	3/37	1	2	FACETS	0.837	0.722	0.963	0.837	0.722	0.963	CLONAL	1	FALSE	1	0.19232249001801	2		632	770	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797201	42797202	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	80	622	1	ENST00000575354.2:c.3563_3564delinsTT	p.Pro1188Leu	p.P1188L	ENST00000575354	NM_015125.3	1188	cCC/cTT	15/20	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	FALSE	1	0.19232249001801	2		623	819	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881552	111881552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	62	483	0	ENST00000393256.3:c.230C>T	p.Ser77Phe	p.S77F	ENST00000393256	NM_006538.4	77	tCc/tTc	2/4	0.19232249001801	1	FACETS	0.866	0.747	0.995	0.866	0.747	0.995	CLONAL	1	FALSE	0	0.19232249001801	1		483	673	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24134070	24134070	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	50	366	0	ENST00000263121.7:c.221C>T	p.Pro74Leu	p.P74L	ENST00000263121	NM_003073.3	74	cCt/cTt	2/9	1	2	FACETS	0.903	0.765	1	0.903	0.765	1	CLONAL	1	FALSE	1	0.19232249001801	2		366	576	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968303	134968303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	60	461	0	ENST00000398015.3:c.2816C>T	p.Ser939Phe	p.S939F	ENST00000398015	NM_004441.4	939	tCc/tTc	15/16	1	2	FACETS	0.954	0.821	1	0.954	0.821	1	CLONAL	1	FALSE	1	0.19232249001801	2		461	654	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612233	189612233	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs761624304	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	65	401	0	ENST00000264731.3:c.1985A>G	p.Asn662Ser	p.N662S	ENST00000264731	NM_003722.4	662	aAc/aGc	14/14	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	FALSE	1	0.19232249001801	2		401	591	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356231	66356231	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	67	485	0	ENST00000273854.3:c.1266A>T	p.Lys422Asn	p.K422N	ENST00000273854	NM_004439.5	422	aaA/aaT	5/18	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	FALSE	1	0.19232249001801	2		485	666	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156402	106156402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1462029603	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	42	334	0	ENST00000380013.4:c.1303C>T	p.His435Tyr	p.H435Y	ENST00000380013	NM_001127208.2	435	Cac/Tac	3/11	1	2	FACETS	0.861	0.719	1	0.861	0.719	1	CLONAL	1	FALSE	1	0.19232249001801	2		334	507	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294115	1294115	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1045272001	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	85	668	1	ENST00000310581.5:c.886C>T	p.His296Tyr	p.H296Y	ENST00000310581	NM_198253.2	296	Cac/Tac	2/16	0.19232249001801	5	FACETS	0.967	0.852	1			1	CLONAL	1	FALSE	NA	0.19232249001801	5		669	1178	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435838	149435838	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	66	593	0	ENST00000286301.3:c.2386G>A	p.Asp796Asn	p.D796N	ENST00000286301	NM_005211.3	796	Gac/Aac	18/22	0.187071157132918	3	FACETS	0.836	0.724	0.958	0.418	0.362	0.479	CLONAL	1	FALSE	1	0.19232249001801	3		593	900	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675484	30675485	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AC	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	68	574	1	ENST00000376406.3:c.2871_2872delinsGT	p.Asp957_Gln958delinsGluTer	p.D957_Q958delinsE*	ENST00000376406	NM_014641.2	957	gaCCag/gaGTag	8/15	1	2	FACETS	0.775	0.672	0.886	0.775	0.672	0.886	SUBCLONAL	1	FALSE	1	0.19232249001801	2		575	913	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359018	81359018	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	55	407	0	ENST00000222390.5:c.943G>A	p.Gly315Ser	p.G315S	ENST00000222390	NM_000601.4	315	Ggc/Agc	8/18	1	2	FACETS	0.911	0.778	1	0.911	0.778	1	CLONAL	1	FALSE	1	0.19232249001801	2		407	628	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68993016	68993017	+	missense_variant	Missense_Mutation	DNP	AG	AG	TA	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	25	339	2	ENST00000288368.4:c.1821_1822delinsTA	p.Leu607_Glu608delinsPheLys	p.L607_E608delinsFK	ENST00000288368	NM_024870.2	607	ttAGaa/ttTAaa	17/40	1	2	FACETS	0.579	0.455	0.722	0.579	0.455	0.722	SUBCLONAL	1	FALSE	1	0.19232249001801	2		341	449	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69032512	69032513	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	60	433	0	ENST00000288368.4:c.3586_3587delinsAA	p.Gly1196Lys	p.G1196K	ENST00000288368	NM_024870.2	1196	GGa/AAa	29/40	1	2	FACETS	0.947	0.815	1	0.947	0.815	1	CLONAL	1	FALSE	1	0.19232249001801	2		433	659	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317565	1317565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	43	352	0	ENST00000400841.2:c.500C>T	p.Thr167Ile	p.T167I	ENST00000400841		167	aCc/aTc	5/6	1	2	FACETS	0.981	0.821	1	0.981	0.821	1	CLONAL	1	FALSE	1	0.19232249001801	2		352	456	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041616	47041616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373311677	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	74	623	0	ENST00000377604.3:c.1841C>T	p.Thr614Ile	p.T614I	ENST00000377604	NM_001204468.1	614	aCc/aTc	17/24	1	2	FACETS	0.892	0.779	1	0.892	0.779	1	CLONAL	1	FALSE	1	0.19232249001801	2		623	863	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412214	63412214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	77	672	1	ENST00000330258.3:c.953C>T	p.Ser318Phe	p.S318F	ENST00000330258	NM_152424.3	318	tCc/tTc	2/2	1	2	FACETS	0.817	0.715	0.927	0.817	0.715	0.927	CLONAL	1	FALSE	1	0.19232249001801	2		673	980	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938035	76938035	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	59	546	0	ENST00000373344.5:c.2713A>G	p.Arg905Gly	p.R905G	ENST00000373344	NM_000489.3	905	Aga/Gga	9/35	1	2	FACETS	0.863	0.741	0.996	0.863	0.741	0.996	CLONAL	1	FALSE	1	0.19232249001801	2		546	711	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0043572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	26	218	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.12	2		218	324	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927974	178927974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397517199	NA	P-0043572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	13	199	0	ENST00000263967.3:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000263967	NM_006218.2	418	Gaa/Aaa	8/21	1	2	FACETS	0.722	0.514	0.977	0.722	0.514	0.977	CLONAL	1	TRUE	1	0.12	2		199	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0043572-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	28	555	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	1	2	FACETS	0.53	0.422	0.655	0.53	0.422	0.655	SUBCLONAL	1	TRUE	1	0.12	2		555	880	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577045	7577046	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0043581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	202	709	0	ENST00000269305.4:c.892dup	p.Glu298GlyfsTer8	p.E298Gfs*8	ENST00000269305	NM_001126112.2	298	gag/gGag	8/11	0.486179340151568	1	FACETS	0.939	0.874	1	0.939	0.874	1	CLONAL	1	TRUE	0	0.487912482854334	1		709	667	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628173	187628195	+	frameshift_variant	Frame_Shift_Del	DEL	GGACTTTCACACGATAATTAGGT	GGACTTTCACACGATAATTAGGT	-	novel	NA	P-0043581-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	125	603	0	ENST00000441802.2:c.2787_2809del	p.Pro930ArgfsTer18	p.P930Rfs*18	ENST00000441802	NM_005245.3	929	ccACCTAATTATCGTGTGAAAGTCCga/ccga	2/27	1	2	FACETS	0.793	0.719	0.87	0.793	0.719	0.87	SUBCLONAL	1	TRUE	1	0.487912482854334	2		603	646	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888166	112888166	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121918461	NA	P-0043658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	18	552	0	ENST00000351677.2:c.182A>C	p.Asp61Ala	p.D61A	ENST00000351677	NM_002834.3	61	gAt/gCt	3/16	1	2	FACETS	0.254	0.19	0.33	0.254	0.19	0.33	SUBCLONAL	1	FALSE	1	0.3	2		552	472	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0043717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	155	257	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	0.413275325144654	1	FACETS	0.707	0.657	0.756	0.707	0.657	0.756	INDETERMINATE	1	TRUE	0	0.792881446233736	1		257	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0043717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	253	507	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	0.792881446233736	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.792881446233736	1		507	379	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0043717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	89	296	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.413275325144654	1	FACETS	0.474	0.425	0.524	0.474	0.425	0.524	INDETERMINATE	1	TRUE	0	0.792881446233736	1		296	286	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546721	9546721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	122	234	0	ENST00000353224.5:c.1301C>T	p.Ala434Val	p.A434V	ENST00000353224	NM_177990.2	434	gCg/gTg	5/10	0.755018405673042	4	FACETS	1	0.954	1	0.36	0.327	0.395	CLONAL	1	TRUE	1	0.792881446233736	4		234	511	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412941	63412941	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	445	625	0	ENST00000330258.3:c.226G>T	p.Gly76Ter	p.G76*	ENST00000330258	NM_152424.3	76	Gga/Tga	2/2	0.792881446233736	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.792881446233736	1		625	599	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052632	42052632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779811318	NA	P-0043717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	230	340	0	ENST00000219905.7:c.7303C>T	p.Arg2435Trp	p.R2435W	ENST00000219905	NM_001164273.1	2435	Cgg/Tgg	20/24	0.792881446233736	1	FACETS	0.998	0.951	1	0.998	0.951	1	CLONAL	1	TRUE	0	0.792881446233736	1		340	351	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790072	40790072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61753667	NA	P-0043717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	260	467	2	ENST00000373198.4:c.2659G>A	p.Ala887Thr	p.A887T	ENST00000373198	NM_133170.3	887	Gcc/Acc	18/32	0.755018405673042	4	FACETS	1	0.97	1	0.353	0.33	0.376	CLONAL	1	TRUE	1	0.792881446233736	4		469	1111	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446192	70446192	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043717-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	209	286	0	ENST00000373644.4:c.5132A>G	p.Tyr1711Cys	p.Y1711C	ENST00000373644	NM_030625.2	1711	tAt/tGt	11/12	0.792881446233736	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.792881446233736	1		286	301	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0043812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	81	573	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.19	2		573	702	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059395	42059395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043812-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	37	301	0	ENST00000219905.7:c.9115G>A	p.Glu3039Lys	p.E3039K	ENST00000219905	NM_001164273.1	3039	Gaa/Aaa	24/24	1	2	FACETS	0.914	0.754	1	0.914	0.754	1	CLONAL	1	TRUE	1	0.19	2		301	426	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0043837-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	265	377	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		377	547	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577511	7577511	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs28934577	NA	P-0043875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	91	704	0	ENST00000269305.4:c.770T>A	p.Leu257Gln	p.L257Q	ENST00000269305	NM_001126112.2	257	cTg/cAg	7/11	0.205785538890608	2	FACETS	1	0.956	1	0.577	0.513	0.646	CLONAL	1	TRUE	0	0.240061283277981	2		704	657	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503816	186503816	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	54	423	0	ENST00000323963.5:c.493G>A	p.Asp165Asn	p.D165N	ENST00000323963		165	Gat/Aat	5/11	0.17449307613364	3	FACETS	0.59	0.502	0.686	0.295	0.251	0.343	SUBCLONAL	1	TRUE	1	0.240061283277981	3		423	854	SUCCESS
APC	324	MSKCC	GRCh37	5	112176427	112176428	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043875-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	44	292	0	ENST00000257430.4:c.5138dup	p.Leu1713PhefsTer3	p.L1713Ffs*3	ENST00000257430	NM_000038.5	1712	-/T	16/16	0.240061283277981	1	FACETS	0.938	0.789	1	0.938	0.789	1	CLONAL	1	TRUE	0	0.240061283277981	1		292	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0043877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	269	712	1	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.601271397194625	1	FACETS	0.906	0.855	0.957	0.906	0.855	0.957	CLONAL	1	TRUE	0	0.601271397194625	1		713	691	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105709	27105709	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	64	373	0	ENST00000324856.7:c.5320G>C	p.Glu1774Gln	p.E1774Q	ENST00000324856	NM_006015.4	1774	Gaa/Caa	20/20	0.372030543934391	1	FACETS	0.433	0.377	0.493	0.433	0.377	0.493	SUBCLONAL	1	TRUE	0	0.601271397194625	1		373	344	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602799	10602799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	304	891	0	ENST00000171111.5:c.779G>T	p.Arg260Leu	p.R260L	ENST00000171111	NM_203500.1	260	cGa/cTa	3/6	0.601271397194625	1	FACETS	0.979	0.929	1	0.979	0.929	1	CLONAL	1	TRUE	0	0.601271397194625	1		891	722	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149011	61149011	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	139	322	0	ENST00000295025.8:c.1201C>T	p.His401Tyr	p.H401Y	ENST00000295025	NM_002908.2	401	Cat/Tat	11/11	0.337656046363442	1	FACETS	0.745	0.684	0.808	0.745	0.684	0.808	INDETERMINATE	1	TRUE	0	0.601271397194625	1		322	434	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106159	27106159	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375952330	NA	P-0043877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	111	586	0	ENST00000324856.7:c.5770G>A	p.Glu1924Lys	p.E1924K	ENST00000324856	NM_006015.4	1924	Gag/Aag	20/20	0.372030543934391	1	FACETS	0.489	0.441	0.539	0.489	0.441	0.539	SUBCLONAL	1	TRUE	0	0.601271397194625	1		586	528	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105796	27105796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	53	465	0	ENST00000324856.7:c.5407G>A	p.Glu1803Lys	p.E1803K	ENST00000324856	NM_006015.4	1803	Gag/Aag	20/20	0.372030543934391	1	FACETS	0.289	0.247	0.336	0.289	0.247	0.336	SUBCLONAL	1	TRUE	0	0.601271397194625	1		465	426	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105614	27105614	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	103	508	0	ENST00000324856.7:c.5225G>C	p.Arg1742Thr	p.R1742T	ENST00000324856	NM_006015.4	1742	aGa/aCa	20/20	0.372030543934391	1	FACETS	0.427	0.383	0.474	0.427	0.383	0.474	SUBCLONAL	1	TRUE	0	0.601271397194625	1		508	561	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105727	27105727	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	60	366	0	ENST00000324856.7:c.5338G>C	p.Glu1780Gln	p.E1780Q	ENST00000324856	NM_006015.4	1780	Gaa/Caa	20/20	0.372030543934391	1	FACETS	0.385	0.333	0.44	0.385	0.333	0.44	SUBCLONAL	1	TRUE	0	0.601271397194625	1		366	363	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105895	27105895	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	76	528	0	ENST00000324856.7:c.5506G>C	p.Glu1836Gln	p.E1836Q	ENST00000324856	NM_006015.4	1836	Gag/Cag	20/20	0.372030543934391	1	FACETS	0.321	0.282	0.363	0.321	0.282	0.363	SUBCLONAL	1	TRUE	0	0.601271397194625	1		528	551	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106166	27106166	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	108	576	0	ENST00000324856.7:c.5777G>T	p.Gly1926Val	p.G1926V	ENST00000324856	NM_006015.4	1926	gGa/gTa	20/20	0.372030543934391	1	FACETS	0.468	0.421	0.517	0.468	0.421	0.517	SUBCLONAL	1	TRUE	0	0.601271397194625	1		576	537	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106279	27106279	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	99	657	0	ENST00000324856.7:c.5890G>A	p.Glu1964Lys	p.E1964K	ENST00000324856	NM_006015.4	1964	Gag/Aag	20/20	0.372030543934391	1	FACETS	0.37	0.33	0.411	0.37	0.33	0.411	SUBCLONAL	1	TRUE	0	0.601271397194625	1		657	623	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100664	8100664	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	225	813	0	ENST00000346208.3:c.638C>G	p.Ser213Trp	p.S213W	ENST00000346208		213	tCg/tGg	3/6	0.590228210057662	3	FACETS	0.843	0.784	0.904	0.421	0.392	0.452	CLONAL	1	TRUE	1	0.601271397194625	3		813	1155	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435176	18435176	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	113	318	0	ENST00000266497.5:c.161A>G	p.Tyr54Cys	p.Y54C	ENST00000266497		54	tAc/tGc	1/31	0.196383439916374	3	FACETS	1	0.948	1	0.535	0.484	0.588	INDETERMINATE	1	TRUE	1	0.601271397194625	3		318	457	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705394	43705394	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	260	797	0	ENST00000382044.4:c.5228T>G	p.Met1743Arg	p.M1743R	ENST00000382044	NM_001141980.1	1743	aTg/aGg	24/28	1	2	FACETS	0.901	0.845	0.958	0.901	0.845	0.958	CLONAL	1	TRUE	1	0.601271397194625	2		797	960	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134529	2134529	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	232	906	1	ENST00000219476.3:c.4306G>A	p.Asp1436Asn	p.D1436N	ENST00000219476	NM_000548.3	1436	Gac/Aac	34/42	0.601271397194625	1	FACETS	0.978	0.92	1	0.978	0.92	1	CLONAL	1	TRUE	0	0.601271397194625	1		907	552	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40859977	40859977	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	290	425	0	ENST00000428826.2:c.1659C>G	p.Asp553Glu	p.D553E	ENST00000428826		553	gaC/gaG	15/21	0.550518114038014	2	FACETS	0.895	0.852	0.937	0.895	0.852	0.937	CLONAL	2	TRUE	0	0.601271397194625	2		425	539	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306619	41306619	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	218	740	0	ENST00000373198.4:c.1040T>A	p.Leu347Gln	p.L347Q	ENST00000373198	NM_133170.3	347	cTg/cAg	7/32	0.601271397194625	1	FACETS	0.833	0.78	0.887	0.833	0.78	0.887	CLONAL	1	TRUE	0	0.601271397194625	1		740	609	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050650	30050650	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	145	325	0	ENST00000338641.4:c.452G>T	p.Gly151Val	p.G151V	ENST00000338641	NM_000268.3	151	gGt/gTt	5/16	0.601271397194625	1	FACETS	0.927	0.857	0.998	0.927	0.857	0.998	CLONAL	1	TRUE	0	0.601271397194625	1		325	364	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269060	142269060	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	184	436	0	ENST00000350721.4:c.2890G>T	p.Val964Leu	p.V964L	ENST00000350721	NM_001184.3	964	Gtg/Ttg	14/47	1	2	FACETS	0.8	0.74	0.862	0.8	0.74	0.862	SUBCLONAL	1	TRUE	1	0.601271397194625	2		436	765	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535384	66535384	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs888131597	NA	P-0043877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	127	307	0	ENST00000273854.3:c.77C>G	p.Ala26Gly	p.A26G	ENST00000273854	NM_004439.5	26	gCg/gGg	1/18	0.559324020874286	1	FACETS	0.898	0.825	0.973	0.898	0.825	0.973	CLONAL	1	TRUE	0	0.601271397194625	1		307	329	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539015	187539015	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	177	490	0	ENST00000441802.2:c.8725A>G	p.Thr2909Ala	p.T2909A	ENST00000441802	NM_005245.3	2909	Acc/Gcc	10/27	0.559324020874286	1	FACETS	0.773	0.717	0.83	0.773	0.717	0.83	SUBCLONAL	1	TRUE	0	0.601271397194625	1		490	533	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562666	176562666	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	190	509	0	ENST00000439151.2:c.562C>G	p.Gln188Glu	p.Q188E	ENST00000439151	NM_022455.4	188	Cag/Gag	2/23	0.550518114038014	2	FACETS	1	0.937	1	0.505	0.469	0.542	CLONAL	1	TRUE	0	0.601271397194625	2		509	626	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030317	180030322	+	protein_altering_variant	In_Frame_Del	DEL	CAGGCC	CAGGCC	GAG	novel	NA	P-0043877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	387	763	5	ENST00000261937.6:c.3962_3967delinsCTC	p.Arg1321_Glu1323delinsProGln	p.R1321_E1323delinsPQ	ENST00000261937	NM_182925.4	1321	cGGCCTGag/cCTCag	30/30	0.550518114038014	2	FACETS	0.907	0.869	0.944	0.907	0.869	0.944	CLONAL	2	TRUE	0	0.601271397194625	2		768	710	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346592	81346592	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	87	296	0	ENST00000222390.5:c.1361C>G	p.Thr454Arg	p.T454R	ENST00000222390	NM_000601.4	454	aCg/aGg	11/18	1	2	FACETS	0.583	0.518	0.653	0.583	0.518	0.653	SUBCLONAL	1	TRUE	1	0.601271397194625	2		296	496	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81399214	81399214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	227	576	1	ENST00000222390.5:c.74C>T	p.Ala25Val	p.A25V	ENST00000222390	NM_000601.4	25	gCc/gTc	1/18	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.601271397194625	2		577	729	SUCCESS
AR	367	MSKCC	GRCh37	X	66766355	66766355	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043877-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	38	24	0	ENST00000374690.3:c.1367G>T	p.Gly456Val	p.G456V	ENST00000374690	NM_000044.3	456	gGt/gTt	1/8	0.0694009943500471	2	FACETS	0.958	0.837	1			1	INDETERMINATE	2	TRUE	NA	0.601271397194625	2		24	66	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	555	542	1	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	0.552393292978477	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.592521357197212	2		543	930	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28901639	28901639	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	84	339	0	ENST00000282397.4:c.2756A>G	p.Asn919Ser	p.N919S	ENST00000282397	NM_002019.4	919	aAc/aGc	20/30	0.519208702720459	2	FACETS	0.623	0.553	0.698	0.312	0.276	0.349	SUBCLONAL	1	TRUE	0	0.592521357197212	2		339	455	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440429	49440430	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	400	626	0	ENST00000301067.7:c.4380dup	p.Leu1461ThrfsTer30	p.L1461Tfs*30	ENST00000301067	NM_003482.3	1460	-/A	15/54	0.302575038264999	2	FACETS	1	0.995	1	0.663	0.632	0.694	INDETERMINATE	1	TRUE	0	0.592521357197212	2		626	1018	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923375	9923375	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	148	499	0	ENST00000330684.3:c.1912G>T	p.Ala638Ser	p.A638S	ENST00000330684	NM_001134407.1	638	Gct/Tct	9/13	0.273558286781432	3	FACETS	0.875	0.8	0.953	0.438	0.4	0.477	INDETERMINATE	1	TRUE	1	0.592521357197212	3		499	740	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972031	55972031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778028304	NA	P-0043883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	184	413	0	ENST00000263923.4:c.1613G>A	p.Arg538Lys	p.R538K	ENST00000263923	NM_002253.2	538	aGa/aAa	12/30	0.301098402058167	3	FACETS	1	0.986	1	0.425	0.394	0.457	INDETERMINATE	1	TRUE	0	0.592521357197212	3		413	632	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412717	139412717	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	565	567	0	ENST00000277541.6:c.1127G>T	p.Cys376Phe	p.C376F	ENST00000277541	NM_017617.3	376	tGc/tTc	7/34	0.592521357197212	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.592521357197212	2		567	951	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845358	76845358	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043883-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	84	388	0	ENST00000373344.5:c.6163G>C	p.Glu2055Gln	p.E2055Q	ENST00000373344	NM_000489.3	2055	Gaa/Caa	27/35	0.151819234551272	5	FACETS	1	0.917	1			1	INDETERMINATE	1	TRUE	NA	0.592521357197212	5		388	513	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0043883-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	103	400	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.332723194285774	1	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	0	0.351303439076012	1		400	460	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045788	143045788	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1181059444	NA	P-0043883-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	68	464	1	ENST00000262992.4:c.1846C>T	p.Gln616Ter	p.Q616*	ENST00000262992	NM_001101669.1	616	Cag/Tag	17/24	0.332723194285774	1	FACETS	0.643	0.561	0.732	0.643	0.561	0.732	SUBCLONAL	1	TRUE	0	0.351303439076012	1		465	496	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165603	118165603	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043883-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	81	375	0	ENST00000369448.3:c.113G>C	p.Arg38Pro	p.R38P	ENST00000369448	NM_017709.3	38	cGa/cCa	2/2	1	2	FACETS	0.998	0.883	1	0.998	0.883	1	CLONAL	1	TRUE	1	0.351303439076012	2		375	462	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313220	30313220	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043883-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	86	507	0	ENST00000262643.3:c.914A>T	p.Tyr305Phe	p.Y305F	ENST00000262643	NM_001238.2	305	tAt/tTt	10/12	1	2	FACETS	0.83	0.735	0.931	0.83	0.735	0.931	CLONAL	1	TRUE	1	0.351303439076012	2		507	590	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098406	47098406	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043883-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	63	450	0	ENST00000409792.3:c.6868C>T	p.Gln2290Ter	p.Q2290*	ENST00000409792	NM_014159.6	2290	Cag/Tag	15/21	1	2	FACETS	0.871	0.756	0.994	0.871	0.756	0.994	CLONAL	1	TRUE	1	0.351303439076012	2		450	412	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225482	26225482	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043883-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	52	341	0	ENST00000360408.1:c.100G>T	p.Gly34Cys	p.G34C	ENST00000360408	NM_003532.2	34	Ggc/Tgc	1/1	1	2	FACETS	0.638	0.544	0.741	0.638	0.544	0.741	SUBCLONAL	1	TRUE	1	0.351303439076012	2		341	464	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044559	47044559	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043883-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	111	712	1	ENST00000377604.3:c.2056G>T	p.Glu686Ter	p.E686*	ENST00000377604	NM_001204468.1	686	Gag/Tag	18/24	0.351303439076012	1	FACETS	0.716	0.644	0.792	0.716	0.644	0.792	SUBCLONAL	1	TRUE	0	0.351303439076012	1		713	728	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357730	70357731	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0043883-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	89	603	2	ENST00000374080.3:c.5981_5982delinsAT	p.Arg1994His	p.R1994H	ENST00000374080		1994	cGG/cAT	41/45	0.351303439076012	1	FACETS	0.552	0.489	0.62	0.552	0.489	0.62	SUBCLONAL	1	TRUE	0	0.351303439076012	1		605	756	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797845	45797845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782727	NA	P-0043905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	191	569	3	ENST00000450313.1:c.926G>A	p.Arg309His	p.R309H	ENST00000450313	NM_012222.2	309	cGc/cAc	10/16	0.695936349673492	3	FACETS	1	0.941	1	0.508	0.471	0.546	CLONAL	1	TRUE	1	0.695936349673492	3		572	728	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65351945	65351945	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0043905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	21	317	0	ENST00000342505.4:c.3G>A	p.Met1?	p.M1?	ENST00000342505	NM_002227.2	1	atG/atA	2/25	NA	2	FACETS	0.208	0.16	0.264			1	INDETERMINATE	1	TRUE	NA	0.695936349673492	2		317	290	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425330	49425360	+	frameshift_variant	Frame_Shift_Del	DEL	GGTTTCTGCTAGGTTGTCTGGGGGATCCCAA	GGTTTCTGCTAGGTTGTCTGGGGGATCCCAA	-	novel	NA	P-0043905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	244	664	2	ENST00000301067.7:c.13128_13158del	p.Trp4377ArgfsTer16	p.W4377Rfs*16	ENST00000301067	NM_003482.3	4376	ccTTGGGATCCCCCAGACAACCTAGCAGAAACC/cc	39/54	0.695936349673492	3	FACETS	0.925	0.864	0.987	0.462	0.432	0.494	CLONAL	1	TRUE	1	0.695936349673492	3		666	1022	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061839	38061839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752132466	NA	P-0043905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	282	756	6	ENST00000250448.2:c.150G>A	p.Met50Ile	p.M50I	ENST00000250448	NM_004496.3	50	atG/atA	2/2	0.695936349673492	3	FACETS	1	0.983	1	0.557	0.524	0.591	CLONAL	1	TRUE	1	0.695936349673492	3		762	981	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614896	23614906	+	frameshift_variant	Frame_Shift_Del	DEL	CAGTACACTGA	CAGTACACTGA	-	novel	NA	P-0043905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	268	456	6	ENST00000261584.4:c.3435_3445del	p.Gln1146ProfsTer7	p.Q1146Pfs*7	ENST00000261584	NM_024675.3	1145	ggTCAGTGTACTGcc/ggcc	13/13	0.686108374262545	4	FACETS	0.949	0.896	1			1	CLONAL	2	TRUE	NA	0.695936349673492	4		462	688	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546901	9546901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs924744761	NA	P-0043905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	293	509	8	ENST00000353224.5:c.1121C>T	p.Pro374Leu	p.P374L	ENST00000353224	NM_177990.2	374	cCg/cTg	5/10	0.584853390378366	4	FACETS	0.968	0.916	1	0.968	0.916	1	CLONAL	2	TRUE	2	0.695936349673492	4		517	738	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31369176	31369176	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760640013	NA	P-0043905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	352	522	6	ENST00000328111.2:c.160C>T	p.Arg54Ter	p.R54*	ENST00000328111	NM_006892.3	54	Cga/Tga	3/23	0.584853390378366	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.695936349673492	4		528	783	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202825	128202833	+	inframe_deletion	In_Frame_Del	DEL	CACAGTTGA	CACAGTTGA	-	novel	NA	P-0043905-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	378	614	6	ENST00000341105.2:c.887_895del	p.Val296_Cys298del	p.V296_C298del	ENST00000341105	NM_032638.4	296	gTCAACTGTGgg/ggg	4/6	0.695936349673492	3	FACETS	0.908	0.868	0.949	0.908	0.868	0.949	CLONAL	2	TRUE	1	0.695936349673492	3		620	806	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0043913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	482	582	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.823089474833958	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.823089474833958	1		582	634	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011194	12011194	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	124	242	0	ENST00000353533.5:c.601C>G	p.Pro201Ala	p.P201A	ENST00000353533	NM_003010.3	201	Cca/Gca	5/11	0.823089474833958	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.823089474833958	1		242	170	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818793	170818793	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	91	250	0	ENST00000296930.5:c.342G>C	p.Gln114His	p.Q114H	ENST00000296930	NM_002520.6	114	caG/caC	4/11	0.823089474833958	1	FACETS	0.731	0.667	0.794	0.731	0.667	0.794	SUBCLONAL	1	TRUE	0	0.823089474833958	1		250	178	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518060	176518060	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043913-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	367	612	0	ENST00000292408.4:c.558G>C	p.Lys186Asn	p.K186N	ENST00000292408	NM_213647.1	186	aaG/aaC	5/18	1	2	FACETS	0.915	0.87	0.96	0.915	0.87	0.96	CLONAL	1	TRUE	1	0.823089474833958	2		612	975	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0043931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	277	687	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.501138988221867	2	FACETS	0.911	0.863	0.959	0.911	0.863	0.959	CLONAL	2	TRUE	0	0.505929957071946	2		687	601	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775239	73775239	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	190	506	0	ENST00000254810.4:c.17A>C	p.Gln6Pro	p.Q6P	ENST00000254810	NM_005324.3	6	cAg/cCg	2/4	0.501138988221867	2	FACETS	0.932	0.874	0.99	0.932	0.874	0.99	CLONAL	2	TRUE	0	0.505929957071946	2		506	403	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574020	46574020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376889179	NA	P-0043931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	80	567	0	ENST00000263734.3:c.35C>T	p.Ser12Leu	p.S12L	ENST00000263734	NM_001430.4	12	tCg/tTg	2/16	0.154781021338543	3	FACETS	0.778	0.687	0.876	0.259	0.229	0.292	INDETERMINATE	1	TRUE	0	0.505929957071946	3		567	509	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	127	779	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.879	0.797	0.966	0.879	0.797	0.966	CLONAL	1	TRUE	1	0.363301685207885	2		781	795	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	149	687	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.96	0.878	1	0.96	0.878	1	CLONAL	1	TRUE	1	0.363301685207885	2		687	854	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	75	358	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.363301685207885	2		358	404	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	75	399	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.894	0.786	1	0.894	0.786	1	CLONAL	1	TRUE	1	0.363301685207885	2		399	462	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	138	585	1	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.363301685207885	2		586	679	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	63	296	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.363301685207885	2		296	345	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143985	11143985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	123	544	0	ENST00000358026.2:c.3566G>A	p.Arg1189Gln	p.R1189Q	ENST00000358026	NM_001128849.1	1189	cGa/cAa	26/36	1	2	FACETS	0.991	0.898	1	0.991	0.898	1	CLONAL	1	TRUE	1	0.363301685207885	2		544	683	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	161	376	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.30052552943623	4	FACETS	0.779	0.715	0.845	0.779	0.715	0.845	SUBCLONAL	2	TRUE	2	0.363301685207885	4		377	776	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101611	27101612	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	80	793	0	ENST00000324856.7:c.4899dup	p.Met1634HisfsTer14	p.M1634Hfs*14	ENST00000324856	NM_006015.4	1631	-/C	18/20	0.363301685207885	2	FACETS	0.447	0.392	0.506	0.223	0.196	0.253	SUBCLONAL	1	TRUE	0	0.363301685207885	2		793	986	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612268	189612268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs972760958	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	96	410	0	ENST00000264731.3:c.2020C>T	p.Arg674Cys	p.R674C	ENST00000264731	NM_003722.4	674	Cgc/Tgc	14/14	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.363301685207885	2		410	472	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	99	384	0	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.363301685207885	2		384	517	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588988	67588988	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	24	198	2	ENST00000274335.5:c.1079C>T	p.Ala360Val	p.A360V	ENST00000274335		360	gCg/gTg	8/15	1	2	FACETS	0.539	0.424	0.671	0.539	0.424	0.671	SUBCLONAL	1	TRUE	1	0.363301685207885	2		200	245	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936995	48936995	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587778842	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	74	346	0	ENST00000267163.4:c.763C>T	p.Arg255Ter	p.R255*	ENST00000267163	NM_000321.2	255	Cga/Tga	8/27	1	2	FACETS	0.878	0.771	0.992	0.878	0.771	0.992	CLONAL	1	TRUE	1	0.363301685207885	2		346	464	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469630	25469630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762563426	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	142	687	1	ENST00000264709.3:c.1138G>A	p.Ala380Thr	p.A380T	ENST00000264709	NM_175629.2	380	Gcg/Acg	10/23	1	2	FACETS	0.928	0.846	1	0.928	0.846	1	CLONAL	1	TRUE	1	0.363301685207885	2		688	842	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947629	48947629	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776783	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	38	196	0	ENST00000267163.4:c.1215+1G>A		p.X405_splice	ENST00000267163	NM_000321.2	405			1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.363301685207885	2		196	190	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151583	55151583	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	91	449	0	ENST00000257290.5:c.2369T>G	p.Leu790Arg	p.L790R	ENST00000257290	NM_006206.4	790	cTt/cGt	17/23	1	2	FACETS	0.852	0.758	0.952	0.852	0.758	0.952	CLONAL	1	TRUE	1	0.363301685207885	2		449	588	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625652	1625652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs533848977	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	198	953	1	ENST00000344749.5:c.422C>T	p.Ser141Leu	p.S141L	ENST00000344749	NM_001136139.2	141	tCg/tTg	7/19	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.363301685207885	2		954	1026	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245538	16245538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1362193717	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	57	302	0	ENST00000375759.3:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000375759	NM_015001.2	505	Cgc/Tgc	7/15	0.363301685207885	2	FACETS	0.978	0.844	1	0.489	0.422	0.561	CLONAL	1	TRUE	0	0.363301685207885	2		302	321	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012441	29012441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55974987	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	104	448	0	ENST00000282397.4:c.430G>A	p.Glu144Lys	p.E144K	ENST00000282397	NM_002019.4	144	Gaa/Aaa	4/30	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.363301685207885	2		448	548	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795030	242795030	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	183	1033	3	ENST00000334409.5:c.179C>A	p.Ser60Ter	p.S60*	ENST00000334409	NM_005018.2	60	tCg/tAg	2/5	1	2	FACETS	0.966	0.891	1	0.966	0.891	1	CLONAL	1	TRUE	1	0.363301685207885	2		1036	1043	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351871	89351871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752417963	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	208	849	0	ENST00000301030.4:c.1079C>T	p.Pro360Leu	p.P360L	ENST00000301030	NM_001256183.1	360	cCg/cTg	9/13	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.363301685207885	2		849	1021	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672233	86672233	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554049394	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	45	320	0	ENST00000274376.6:c.2035C>T	p.Arg679Ter	p.R679*	ENST00000274376	NM_002890.2	679	Cga/Tga	16/25	1	2	FACETS	0.726	0.613	0.851	0.726	0.613	0.851	SUBCLONAL	1	TRUE	1	0.363301685207885	2		320	341	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41276095	41276095	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80356994	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	95	371	1	ENST00000357654.3:c.19C>T	p.Arg7Cys	p.R7C	ENST00000357654	NM_007294.3	7	Cgc/Tgc	2/23	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.363301685207885	2		372	463	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209337	133209337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs115452769	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	148	787	1	ENST00000320574.5:c.6049C>T	p.Arg2017Cys	p.R2017C	ENST00000320574	NM_006231.2	2017	Cgc/Tgc	44/49	1	2	FACETS	0.962	0.879	1	0.962	0.879	1	CLONAL	1	TRUE	1	0.363301685207885	2		788	847	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413105	63413105	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374303948	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	165	753	4	ENST00000330258.3:c.62G>A	p.Arg21His	p.R21H	ENST00000330258	NM_152424.3	21	cGt/cAt	2/2	0.363301685207885	3	FACETS	0.981	0.9	1	0.491	0.45	0.533	CLONAL	1	TRUE	1	0.363301685207885	3		757	1094	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437274	220437274	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs980893896	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	184	971	0	ENST00000243786.2:c.178C>T	p.Arg60Ter	p.R60*	ENST00000243786	NM_002191.3	60	Cga/Tga	1/2	1	2	FACETS	0.97	0.895	1	0.97	0.895	1	CLONAL	1	TRUE	1	0.363301685207885	2		971	1044	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909713	50909713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397514632	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	174	915	1	ENST00000440232.2:c.1433G>A	p.Ser478Asn	p.S478N	ENST00000440232	NM_002691.3	478	aGc/aAc	12/27	1	2	FACETS	0.894	0.822	0.969	0.894	0.822	0.969	CLONAL	1	TRUE	1	0.363301685207885	2		916	1072	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266826	41266826	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	68	281	0	ENST00000349496.5:c.497T>C	p.Val166Ala	p.V166A	ENST00000349496	NM_001904.3	166	gTg/gCg	5/15	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.363301685207885	2		281	353	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777892	3777892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1171889477	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	203	1040	0	ENST00000262367.5:c.7156G>A	p.Gly2386Arg	p.G2386R	ENST00000262367	NM_004380.2	2386	Gga/Aga	31/31	1	2	FACETS	0.915	0.846	0.985	0.915	0.846	0.985	CLONAL	1	TRUE	1	0.363301685207885	2		1040	1222	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425038	49425038	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783690	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	219	849	1	ENST00000301067.7:c.13450C>T	p.Arg4484Ter	p.R4484*	ENST00000301067	NM_003482.3	4484	Cga/Tga	39/54	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.363301685207885	2		850	1087	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916935	178916935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	71	355	0	ENST00000263967.3:c.322C>T	p.Arg108Cys	p.R108C	ENST00000263967	NM_006218.2	108	Cgt/Tgt	2/21	1	2	FACETS	0.901	0.789	1	0.901	0.789	1	CLONAL	1	TRUE	1	0.363301685207885	2		355	434	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211820	2211820	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	150	776	0	ENST00000398665.3:c.1536G>T	p.Gln512His	p.Q512H	ENST00000398665	NM_032482.2	512	caG/caT	16/28	1	2	FACETS	0.96	0.878	1	0.96	0.878	1	CLONAL	1	TRUE	1	0.363301685207885	2		776	860	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422464	47422464	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	136	634	0	ENST00000377045.4:c.96+2T>C		p.X32_splice	ENST00000377045	NM_001654.4	32			0.363301685207885	3	FACETS	0.933	0.848	1	0.467	0.424	0.512	CLONAL	1	TRUE	1	0.363301685207885	3		634	948	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074189	30074189	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs141538143	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	91	400	0	ENST00000338641.4:c.1451T>C	p.Met484Thr	p.M484T	ENST00000338641	NM_000268.3	484	aTg/aCg	14/16	1	2	FACETS	0.926	0.824	1	0.926	0.824	1	CLONAL	1	TRUE	1	0.363301685207885	2		400	541	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946337	2946337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759681668	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	172	845	4	ENST00000396946.4:c.3400G>A	p.Val1134Ile	p.V1134I	ENST00000396946	NM_032415.4	1134	Gtt/Att	25/25	0.363301685207885	3	FACETS	0.986	0.906	1	0.493	0.453	0.535	CLONAL	1	TRUE	1	0.363301685207885	3		849	1135	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791796	42791796	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	150	794	0	ENST00000575354.2:c.682C>T	p.Arg228Trp	p.R228W	ENST00000575354	NM_015125.3	228	Cgg/Tgg	5/20	1	2	FACETS	0.881	0.805	0.961	0.881	0.805	0.961	CLONAL	1	TRUE	1	0.363301685207885	2		794	937	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420092	420092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760930800	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	88	532	1	ENST00000399788.2:c.3175C>T	p.Arg1059Trp	p.R1059W	ENST00000399788	NM_001042603.1	1059	Cgg/Tgg	21/28	1	2	FACETS	0.731	0.648	0.819	0.731	0.648	0.819	SUBCLONAL	1	TRUE	1	0.363301685207885	2		533	663	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638534	176638534	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1359539320	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	147	603	1	ENST00000439151.2:c.3134G>A	p.Arg1045His	p.R1045H	ENST00000439151	NM_022455.4	1045	cGt/cAt	5/23	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.363301685207885	2		604	799	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967502	38967502	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	60	292	0	ENST00000357387.3:c.1088G>T	p.Arg363Met	p.R363M	ENST00000357387	NM_152756.3	363	aGg/aTg	13/38	1	2	FACETS	0.865	0.748	0.99	0.865	0.748	0.99	CLONAL	1	TRUE	1	0.363301685207885	2		292	382	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11177144	11177144	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	47	409	0	ENST00000361445.4:c.6934-1G>T		p.X2312_splice	ENST00000361445	NM_004958.3	2312			0.363301685207885	2	FACETS	0.587	0.496	0.687	0.293	0.248	0.344	SUBCLONAL	1	TRUE	0	0.363301685207885	2		409	441	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291009	11291009	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	87	315	0	ENST00000361445.4:c.2752T>C	p.Ser918Pro	p.S918P	ENST00000361445	NM_004958.3	918	Tca/Cca	18/58	0.363301685207885	2	FACETS	1	0.904	1	0.51	0.453	0.57	CLONAL	1	TRUE	0	0.363301685207885	2		315	470	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28607226	28607226	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	64	474	1	ENST00000253063.3:c.1357-1G>T		p.X453_splice	ENST00000253063	NM_031459.4	453			0.363301685207885	2	FACETS	0.545	0.472	0.625	0.273	0.236	0.313	SUBCLONAL	1	TRUE	0	0.363301685207885	2		475	646	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804258	43804258	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	125	524	0	ENST00000372470.3:c.258C>A	p.His86Gln	p.H86Q	ENST00000372470	NM_005373.2	86	caC/caA	3/12	0.363301685207885	2	FACETS	1	0.933	1	0.517	0.469	0.568	CLONAL	1	TRUE	0	0.363301685207885	2		524	665	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798283	45798283	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	146	670	0	ENST00000450313.1:c.653A>G	p.Tyr218Cys	p.Y218C	ENST00000450313	NM_012222.2	218	tAc/tGc	8/16	0.363301685207885	2	FACETS	1	0.953	1	0.532	0.486	0.58	CLONAL	1	TRUE	0	0.363301685207885	2		670	755	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436045	51436045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	79	279	0	ENST00000262662.1:c.5C>T	p.Ala2Val	p.A2V	ENST00000262662		2	gCc/gTc	3/4	0.363301685207885	2	FACETS	1	0.932	1	0.538	0.476	0.605	CLONAL	1	TRUE	0	0.363301685207885	2		279	404	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248224	59248225	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	25	23	0	ENST00000371222.2:c.518dup	p.Ser174GlnfsTer136	p.S174Qfs*136	ENST00000371222	NM_002228.3	173	ctc/ctTc	1/1	0.363301685207885	2	FACETS	0.956	0.78	1	0.956	0.78	1	CLONAL	2	TRUE	0	0.363301685207885	2		23	72	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400864	72400864	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	51	307	0	ENST00000357731.5:c.307C>A	p.Leu103Ile	p.L103I	ENST00000357731	NM_173808.2	103	Ctc/Atc	2/7	0.363301685207885	2	FACETS	0.761	0.649	0.883	0.38	0.324	0.442	SUBCLONAL	1	TRUE	0	0.363301685207885	2		307	369	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166395	118166395	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	81	293	0	ENST00000369448.3:c.905G>T	p.Ser302Ile	p.S302I	ENST00000369448	NM_017709.3	302	aGc/aTc	2/2	0.363301685207885	2	FACETS	1	0.924	1	0.528	0.468	0.593	CLONAL	1	TRUE	0	0.363301685207885	2		293	422	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572544	64572544	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	61	734	0	ENST00000312049.6:c.1312A>G	p.Thr438Ala	p.T438A	ENST00000312049	NM_130799.2	438	Acc/Gcc	9/10	0.263607044647072	1	FACETS	0.358	0.308	0.413	0.358	0.308	0.413	SUBCLONAL	1	TRUE	0	0.363301685207885	1		734	767	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118365025	118365025	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	63	310	0	ENST00000534358.1:c.5201T>G	p.Val1734Gly	p.V1734G	ENST00000534358	NM_005933.3	1734	gTg/gGg	17/36	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.363301685207885	2		310	314	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374489	118374489	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1301598432	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	86	364	0	ENST00000534358.1:c.7882T>C	p.Ser2628Pro	p.S2628P	ENST00000534358	NM_005933.3	2628	Tct/Cct	27/36	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.363301685207885	2		364	437	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992186	11992186	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	98	406	0	ENST00000396373.4:c.276A>C	p.Lys92Asn	p.K92N	ENST00000396373	NM_001987.4	92	aaA/aaC	3/8	1	2	FACETS	0.95	0.85	1	0.95	0.85	1	CLONAL	1	TRUE	1	0.363301685207885	2		406	568	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628424	21628424	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs890315251	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	66	384	0	ENST00000421138.2:c.1194T>A	p.Tyr398Ter	p.Y398*	ENST00000421138		398	taT/taA	11/16	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.363301685207885	2		384	362	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230770	46230770	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	25	211	0	ENST00000334344.6:c.1019C>A	p.Ala340Asp	p.A340D	ENST00000334344	NM_152641.2	340	gCt/gAt	8/21	1	2	FACETS	0.555	0.439	0.687	0.555	0.439	0.687	SUBCLONAL	1	TRUE	1	0.363301685207885	2		211	248	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425881	49425881	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	149	756	0	ENST00000301067.7:c.12607G>T	p.Gly4203Ter	p.G4203*	ENST00000301067	NM_003482.3	4203	Gga/Tga	39/54	1	2	FACETS	0.949	0.868	1	0.949	0.868	1	CLONAL	1	TRUE	1	0.363301685207885	2		756	864	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50483708	50483708	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	103	508	0	ENST00000394963.4:c.813G>T	p.Gln271His	p.Q271H	ENST00000394963	NM_003076.4	271	caG/caT	7/13	1	2	FACETS	0.866	0.776	0.961	0.866	0.776	0.961	CLONAL	1	TRUE	1	0.363301685207885	2		508	655	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225554	133225554	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	146	641	0	ENST00000320574.5:c.4110G>T	p.Gln1370His	p.Q1370H	ENST00000320574	NM_006231.2	1370	caG/caT	32/49	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.363301685207885	2		641	758	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562576	21562576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762484566	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	46	204	0	ENST00000382592.4:c.1343G>A	p.Arg448His	p.R448H	ENST00000382592	NM_014572.2	448	cGt/cAt	4/8	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.363301685207885	2		204	198	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281236	49281236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201100531	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	143	685	0	ENST00000282018.3:c.283G>A	p.Ala95Thr	p.A95T	ENST00000282018	NM_020377.2	95	Gct/Act	1/1	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.363301685207885	2		685	761	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524669	103524669	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs201274165	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	85	341	0	ENST00000355739.4:c.2800G>T	p.Glu934Ter	p.E934*	ENST00000355739	NM_000123.3	934	Gag/Tag	13/15	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.363301685207885	2		341	453	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872918	35872918	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1314076146	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	49	456	0	ENST00000216797.5:c.314A>G	p.Asn105Ser	p.N105S	ENST00000216797	NM_020529.2	105	aAc/aGc	2/6	1	2	FACETS	0.437	0.37	0.512	0.437	0.37	0.512	SUBCLONAL	1	TRUE	1	0.363301685207885	2		456	617	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701924	43701924	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	37	167	0	ENST00000382044.4:c.5321C>A	p.Pro1774His	p.P1774H	ENST00000382044	NM_001141980.1	1774	cCt/cAt	25/28	1	2	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	1	0.363301685207885	2		167	194	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354582	91354582	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201149857	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	57	426	0	ENST00000355112.3:c.4022C>T	p.Ala1341Val	p.A1341V	ENST00000355112	NM_000057.2	1341	gCc/gTc	21/22	1	2	FACETS	0.542	0.465	0.626	0.542	0.465	0.626	SUBCLONAL	1	TRUE	1	0.363301685207885	2		426	579	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094797	2094797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1324289477	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	149	733	0	ENST00000219066.1:c.383G>A	p.Arg128His	p.R128H	ENST00000219066	NM_002528.5	128	cGc/cAc	3/6	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.363301685207885	2		733	742	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2218087	2218087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	163	918	2	ENST00000326181.6:c.149C>T	p.Thr50Ile	p.T50I	ENST00000326181	NM_032271.2	50	aCc/aTc	4/21	1	2	FACETS	0.889	0.815	0.967	0.889	0.815	0.967	CLONAL	1	TRUE	1	0.363301685207885	2		920	1009	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223278	2223278	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755925380	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	194	812	1	ENST00000326181.6:c.890G>A	p.Arg297His	p.R297H	ENST00000326181	NM_032271.2	297	cGc/cAc	10/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.363301685207885	2		813	992	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647379	23647380	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	rs745533713	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	91	475	0	ENST00000261584.4:c.487_488del	p.Val163LeufsTer4	p.V163Lfs*4	ENST00000261584	NM_024675.3	163	GTc/c	4/13	1	2	FACETS	0.825	0.734	0.923	0.825	0.734	0.923	CLONAL	1	TRUE	1	0.363301685207885	2		475	607	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645912	67645912	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	97	532	0	ENST00000264010.4:c.840T>A	p.Asn280Lys	p.N280K	ENST00000264010	NM_006565.3	280	aaT/aaA	4/12	1	2	FACETS	0.834	0.745	0.929	0.834	0.745	0.929	CLONAL	1	TRUE	1	0.363301685207885	2		532	640	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351416	89351416	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767398092	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	66	697	0	ENST00000301030.4:c.1534C>T	p.Pro512Ser	p.P512S	ENST00000301030	NM_001256183.1	512	Ccc/Tcc	9/13	1	2	FACETS	0.458	0.397	0.525	0.458	0.397	0.525	SUBCLONAL	1	TRUE	1	0.363301685207885	2		697	793	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351961	89351961	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	86	1010	0	ENST00000301030.4:c.989A>C	p.Lys330Thr	p.K330T	ENST00000301030	NM_001256183.1	330	aAg/aCg	9/13	1	2	FACETS	0.385	0.339	0.434	0.385	0.339	0.434	SUBCLONAL	1	TRUE	1	0.363301685207885	2		1010	1230	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533538	63533538	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	141	750	0	ENST00000307078.5:c.1616T>C	p.Val539Ala	p.V539A	ENST00000307078	NM_004655.3	539	gTg/gCg	6/11	1	2	FACETS	0.871	0.793	0.953	0.871	0.793	0.953	CLONAL	1	TRUE	1	0.363301685207885	2		750	891	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7167977	7167977	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs797045624	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	106	416	0	ENST00000302850.5:c.1610+2T>C		p.X537_splice	ENST00000302850	NM_000208.2	537			1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.363301685207885	2		416	530	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247847	10247847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	184	814	2	ENST00000340748.4:c.4355C>T	p.Ala1452Val	p.A1452V	ENST00000340748		1452	gCc/gTc	36/40	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.363301685207885	2		816	994	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270380	10270380	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	147	674	0	ENST00000340748.4:c.1186T>G	p.Phe396Val	p.F396V	ENST00000340748		396	Ttt/Gtt	16/40	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.363301685207885	2		674	787	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10288031	10288031	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	63	522	0	ENST00000340748.4:c.458C>A	p.Pro153His	p.P153H	ENST00000340748		153	cCt/cAt	5/40	1	2	FACETS	0.55	0.475	0.631	0.55	0.475	0.631	SUBCLONAL	1	TRUE	1	0.363301685207885	2		522	631	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229021	36229021	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1412510402	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	186	866	1	ENST00000222270.7:c.7801G>A	p.Val2601Ile	p.V2601I	ENST00000222270	NM_014727.1	2601	Gtc/Atc	36/37	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.363301685207885	2		867	992	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754487	42754487	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	150	702	1	ENST00000222329.4:c.253C>A	p.Leu85Met	p.L85M	ENST00000222329	NM_006494.2	85	Ctg/Atg	2/4	1	2	FACETS	0.921	0.841	1	0.921	0.841	1	CLONAL	1	TRUE	1	0.363301685207885	2		703	897	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793218	42793218	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	101	916	0	ENST00000575354.2:c.1110T>G	p.Ser370Arg	p.S370R	ENST00000575354	NM_015125.3	370	agT/agG	7/20	1	2	FACETS	0.544	0.485	0.606	0.544	0.485	0.606	SUBCLONAL	1	TRUE	1	0.363301685207885	2		916	1023	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725046	47725046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755414185	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	178	874	5	ENST00000449228.1:c.698G>A	p.Arg233His	p.R233H	ENST00000449228	NM_001127240.2	233	cGc/cAc	4/4	1	2	FACETS	0.951	0.876	1	0.951	0.876	1	CLONAL	1	TRUE	1	0.363301685207885	2		879	1030	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910671	50910671	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	66	617	0	ENST00000440232.2:c.1774G>T	p.Gly592Trp	p.G592W	ENST00000440232	NM_002691.3	592	Ggg/Tgg	14/27	1	2	FACETS	0.455	0.394	0.521	0.455	0.394	0.521	SUBCLONAL	1	TRUE	1	0.363301685207885	2		617	799	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921166	50921166	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	159	860	0	ENST00000440232.2:c.3286C>A	p.Leu1096Met	p.L1096M	ENST00000440232	NM_002691.3	1096	Ctg/Atg	27/27	1	2	FACETS	0.955	0.875	1	0.955	0.875	1	CLONAL	1	TRUE	1	0.363301685207885	2		860	917	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47601097	47601097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146913093	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	108	524	0	ENST00000263735.4:c.335G>A	p.Gly112Asp	p.G112D	ENST00000263735	NM_002354.2	112	gGc/gAc	3/9	1	2	FACETS	0.957	0.861	1	0.957	0.861	1	CLONAL	1	TRUE	1	0.363301685207885	2		524	621	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033424	48033424	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs878853737	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	73	349	0	ENST00000234420.5:c.3728C>A	p.Thr1243Lys	p.T1243K	ENST00000234420	NM_000179.2	1243	aCa/aAa	8/10	1	2	FACETS	0.941	0.827	1	0.941	0.827	1	CLONAL	1	TRUE	1	0.363301685207885	2		349	427	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645453	215645453	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	114	561	0	ENST00000260947.4:c.1145A>G	p.Asn382Ser	p.N382S	ENST00000260947	NM_000465.2	382	aAc/aGc	4/11	1	2	FACETS	0.941	0.848	1	0.941	0.848	1	CLONAL	1	TRUE	1	0.363301685207885	2		561	667	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546836	9546836	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs146777362	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	145	466	0	ENST00000353224.5:c.1186T>C	p.Ser396Pro	p.S396P	ENST00000353224	NM_177990.2	396	Tcc/Ccc	5/10	0.30052552943623	4	FACETS	0.854	0.782	0.93	0.854	0.782	0.93	CLONAL	2	TRUE	2	0.363301685207885	4		466	637	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309904	30309904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774465563	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	252	538	0	ENST00000307677.4:c.118G>A	p.Gly40Arg	p.G40R	ENST00000307677	NM_138578.1	40	Ggg/Agg	2/3	0.30052552943623	4	FACETS	0.981	0.919	1	0.981	0.919	1	CLONAL	2	TRUE	2	0.363301685207885	4		538	964	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031150	36031150	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	119	665	0	ENST00000358208.4:c.1271-2A>G		p.X424_splice	ENST00000358208		424			0.30052552943623	4	FACETS	0.957	0.863	1	0.479	0.431	0.529	CLONAL	1	TRUE	2	0.363301685207885	4		665	933	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484240	57484240	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	45	368	0	ENST00000371085.3:c.554T>A	p.Ile185Asn	p.I185N	ENST00000371085	NM_000516.4	185	aTc/aAc	7/13	0.30052552943623	4	FACETS	0.48	0.402	0.566	0.24	0.201	0.283	SUBCLONAL	1	TRUE	2	0.363301685207885	4		368	704	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62297434	62297434	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	65	410	0	ENST00000360203.5:c.614+2T>C		p.X205_splice	ENST00000360203	NM_001283009.1	205			0.30052552943623	4	FACETS	0.636	0.55	0.729	0.318	0.275	0.365	SUBCLONAL	1	TRUE	2	0.363301685207885	4		410	767	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764298	39764298	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	130	698	0	ENST00000288319.7:c.814G>T	p.Ala272Ser	p.A272S	ENST00000288319	NM_182918.3	272	Gct/Tct	7/10	1	2	FACETS	0.836	0.758	0.918	0.836	0.758	0.918	CLONAL	1	TRUE	1	0.363301685207885	2		698	856	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12632475	12632475	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	93	386	0	ENST00000251849.4:c.1194-2A>G		p.X398_splice	ENST00000251849	NM_002880.3	398			1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.363301685207885	2		386	504	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620450	52620450	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	82	340	0	ENST00000394830.3:c.3303C>A	p.Asn1101Lys	p.N1101K	ENST00000394830	NM_018313.4	1101	aaC/aaA	21/30	1	2	FACETS	0.916	0.81	1	0.916	0.81	1	CLONAL	1	TRUE	1	0.363301685207885	2		340	493	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73113299	73113299	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	27	126	0	ENST00000356692.5:c.638+2T>G		p.X213_splice	ENST00000356692		213			1	2	FACETS	0.885	0.711	1	0.885	0.711	1	CLONAL	1	TRUE	1	0.363301685207885	2		126	168	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851720	134851720	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs750758313	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	48	545	0	ENST00000398015.3:c.1126A>G	p.Asn376Asp	p.N376D	ENST00000398015	NM_004441.4	376	Aat/Gat	5/16	1	2	FACETS	0.482	0.407	0.565	0.482	0.407	0.565	SUBCLONAL	1	TRUE	1	0.363301685207885	2		545	548	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189585653	189585653	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	79	413	0	ENST00000264731.3:c.914A>C	p.Asn305Thr	p.N305T	ENST00000264731	NM_003722.4	305	aAt/aCt	7/14	1	2	FACETS	0.925	0.817	1	0.925	0.817	1	CLONAL	1	TRUE	1	0.363301685207885	2		413	470	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561887	55561887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	54	243	0	ENST00000288135.5:c.277G>A	p.Gly93Ser	p.G93S	ENST00000288135	NM_000222.2	93	Ggc/Agc	2/21	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.363301685207885	2		243	291	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524353	187524353	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	84	413	0	ENST00000441802.2:c.11327G>T	p.Arg3776Met	p.R3776M	ENST00000441802	NM_005245.3	3776	aGg/aTg	19/27	1	2	FACETS	0.881	0.78	0.988	0.881	0.78	0.988	CLONAL	1	TRUE	1	0.363301685207885	2		413	525	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539210	187539210	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	77	333	0	ENST00000441802.2:c.8530G>T	p.Val2844Phe	p.V2844F	ENST00000441802	NM_005245.3	2844	Gtt/Ttt	10/27	1	2	FACETS	0.977	0.861	1	0.977	0.861	1	CLONAL	1	TRUE	1	0.363301685207885	2		333	434	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871283	35871283	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	55	328	0	ENST00000303115.3:c.505T>C	p.Tyr169His	p.Y169H	ENST00000303115	NM_002185.3	169	Tac/Cac	4/8	1	2	FACETS	0.805	0.691	0.929	0.805	0.691	0.929	CLONAL	1	TRUE	1	0.363301685207885	2		328	376	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80088564	80088564	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	72	270	0	ENST00000265081.6:c.2556A>T	p.Gln852His	p.Q852H	ENST00000265081	NM_002439.4	852	caA/caT	19/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.363301685207885	2		270	307	SUCCESS
APC	324	MSKCC	GRCh37	5	112173292	112173292	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	40	158	0	ENST00000257430.4:c.2001A>C	p.Gln667His	p.Q667H	ENST00000257430	NM_000038.5	667	caA/caC	16/16	1	2	FACETS	0.97	0.813	1	0.97	0.813	1	CLONAL	1	TRUE	1	0.363301685207885	2		158	227	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032204	26032204	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	72	283	0	ENST00000244661.2:c.85A>G	p.Ser29Gly	p.S29G	ENST00000244661	NM_003537.3	29	Agc/Ggc	1/1	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.363301685207885	2		283	354	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367298	50367298	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	88	462	0	ENST00000331340.3:c.105G>T	p.Glu35Asp	p.E35D	ENST00000331340	NM_006060.4	35	gaG/gaT	3/8	0.363301685207885	3	FACETS	0.854	0.757	0.958	0.427	0.378	0.479	CLONAL	1	TRUE	1	0.363301685207885	3		462	670	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545620	106545620	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1446291886	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	53	450	0	ENST00000359195.3:c.3097A>G	p.Met1033Val	p.M1033V	ENST00000359195	NM_002649.2	1033	Atg/Gtg	11/11	0.363301685207885	3	FACETS	0.523	0.445	0.609	0.262	0.222	0.305	SUBCLONAL	1	TRUE	1	0.363301685207885	3		450	659	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148507452	148507452	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	42	327	0	ENST00000320356.2:c.2002T>C	p.Cys668Arg	p.C668R	ENST00000320356	NM_004456.4	668	Tgc/Cgc	17/20	0.363301685207885	3	FACETS	0.51	0.425	0.604	0.255	0.212	0.302	SUBCLONAL	1	TRUE	1	0.363301685207885	3		327	536	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842238	151842238	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	28	226	0	ENST00000262189.6:c.14174G>T	p.Arg4725Met	p.R4725M	ENST00000262189	NM_170606.2	4725	aGg/aTg	54/59	0.363301685207885	3	FACETS	0.495	0.395	0.608	0.247	0.197	0.304	SUBCLONAL	1	TRUE	1	0.363301685207885	3		226	368	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842335	151842335	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	146	296	3	ENST00000262189.6:c.14077C>T	p.Arg4693Ter	p.R4693*	ENST00000262189	NM_170606.2	4693	Cga/Tga	54/59	0.363301685207885	3	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	1	0.363301685207885	3		299	468	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879621	151879621	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	60	237	0	ENST00000262189.6:c.5324A>G	p.Gln1775Arg	p.Q1775R	ENST00000262189	NM_170606.2	1775	cAg/cGg	36/59	0.363301685207885	3	FACETS	1	0.936	1	0.569	0.493	0.651	CLONAL	1	TRUE	1	0.363301685207885	3		237	343	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141568624	141568624	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	110	730	0	ENST00000220592.5:c.838C>T	p.Arg280Cys	p.R280C	ENST00000220592	NM_012154.3	280	Cgc/Tgc	7/19	0.356982505656961	4	FACETS	0.767	0.687	0.851	0.383	0.343	0.426	SUBCLONAL	1	TRUE	2	0.363301685207885	4		730	1077	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738741	145738741	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1246	184	1036	1	ENST00000428558.2:c.2323G>A	p.Gly775Arg	p.G775R	ENST00000428558	NM_004260.3	775	Ggg/Agg	15/22	0.356982505656961	4	FACETS	0.966	0.889	1	0.483	0.444	0.523	CLONAL	1	TRUE	2	0.363301685207885	4		1037	1430	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740761	145740761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	327	803	0	ENST00000428558.2:c.1339G>T	p.Asp447Tyr	p.D447Y	ENST00000428558	NM_004260.3	447	Gac/Tac	7/22	0.356982505656961	4	FACETS	0.967	0.913	1	0.967	0.913	1	CLONAL	2	TRUE	2	0.363301685207885	4		803	1269	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319923	8319923	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	51	278	0	ENST00000356435.5:c.5578G>T	p.Val1860Phe	p.V1860F	ENST00000356435		1860	Gtt/Ttt	34/35	1	2	FACETS	0.945	0.809	1	0.945	0.809	1	CLONAL	1	TRUE	1	0.363301685207885	2		278	297	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020125	123020125	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	160	722	0	ENST00000355640.3:c.613G>T	p.Gly205Ter	p.G205*	ENST00000355640		205	Gga/Tga	2/7	0.363301685207885	3	FACETS	1	0.932	1	0.51	0.467	0.555	CLONAL	1	TRUE	1	0.363301685207885	3		722	1021	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185246	123185246	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	63	316	0	ENST00000218089.9:c.1196+2T>C		p.X399_splice	ENST00000218089	NM_001042749.1	399			0.363301685207885	3	FACETS	0.944	0.819	1	0.472	0.409	0.54	CLONAL	1	TRUE	1	0.363301685207885	3		316	434	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830280	72830282	+	missense_variant	Missense_Mutation	TNP	TCA	TCA	GCG	novel	NA	P-0043967-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	59	334	0	ENST00000268489.5:c.6299_6301delinsCGC	p.Leu2100_Met2101delinsProLeu	p.L2100_M2101delinsPL	ENST00000268489	NM_006885.3	2100	cTGAtg/cCGCtg	9/10	1	2	FACETS	0.859	0.742	0.985	0.859	0.742	0.985	CLONAL	1	TRUE	1	0.363301685207885	2		334	378	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0043972-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	51	407	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	1	2	FACETS	0.757	0.644	0.883	0.757	0.644	0.883	SUBCLONAL	1	TRUE	1	0.242210280350358	2		407	556	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968597	55968597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs34038364	NA	P-0043972-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	87	529	0	ENST00000263923.4:c.2066C>T	p.Thr689Met	p.T689M	ENST00000263923	NM_002253.2	689	aCg/aTg	14/30	0.242210280350358	1	FACETS	0.722	0.638	0.812	0.722	0.638	0.812	SUBCLONAL	1	TRUE	0	0.242210280350358	1		529	875	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038841	47038844	+	frameshift_variant	Frame_Shift_Del	DEL	CCTC	CCTC	-	novel	NA	P-0043972-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	68	367	0	ENST00000377604.3:c.850_853del	p.Ser284LysfsTer23	p.S284Kfs*23	ENST00000377604	NM_001204468.1	283	gCCTCc/gc	9/24	1	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.242210280350358	1		367	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0043977-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	387	510	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.353861772936699	2	FACETS	0.928	0.885	0.971	0.928	0.885	0.971	CLONAL	2	TRUE	0	0.450819009298061	2		510	925	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279522	1279522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368430301	NA	P-0043977-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1275	217	731	0	ENST00000310581.5:c.2014C>T	p.Arg672Cys	p.R672C	ENST00000310581	NM_198253.2	672	Cgc/Tgc	5/16	0.405848583913154	4	FACETS	0.936	0.868	1	0.312	0.289	0.336	CLONAL	1	TRUE	1	0.450819009298061	4		731	1492	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376135	225376135	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043977-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	140	424	0	ENST00000264414.4:c.819G>A	p.Met273Ile	p.M273I	ENST00000264414	NM_003590.4	273	atG/atA	6/16	0.385112185740031	3	FACETS	0.882	0.803	0.965	0.441	0.401	0.483	CLONAL	1	TRUE	1	0.450819009298061	3		424	863	SUCCESS
APC	324	MSKCC	GRCh37	5	112170682	112170682	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1064794226	NA	P-0043977-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	96	358	0	ENST00000257430.4:c.1778G>A	p.Trp593Ter	p.W593*	ENST00000257430	NM_000038.5	593	tGg/tAg	15/16	1	2	FACETS	0.827	0.739	0.92	0.827	0.739	0.92	CLONAL	1	TRUE	1	0.450819009298061	2		358	515	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023073	27023076	+	frameshift_variant	Frame_Shift_Del	DEL	GCCC	GCCC	-	novel	NA	P-0043977-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	45	74	0	ENST00000324856.7:c.179_182del	p.Gly60AlafsTer40	p.G60Afs*40	ENST00000324856	NM_006015.4	60	gGCCCc/gc	1/20	0.385112185740031	3	FACETS	1	0.956	1	0.683	0.583	0.791	CLONAL	1	TRUE	1	0.450819009298061	3		74	179	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607188	189607188	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043977-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1235	175	655	0	ENST00000264731.3:c.1567C>G	p.Gln523Glu	p.Q523E	ENST00000264731	NM_003722.4	523	Cag/Gag	12/14	0.129233762649651	6	FACETS	1	0.95	1	0.349	0.32	0.379	INDETERMINATE	1	TRUE	3	0.450819009298061	6		655	1410	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392053	81392053	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043977-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	49	230	0	ENST00000222390.5:c.224C>G	p.Thr75Ser	p.T75S	ENST00000222390	NM_000601.4	75	aCt/aGt	2/18	0.425200684903464	3	FACETS	0.734	0.624	0.854	0.367	0.312	0.427	SUBCLONAL	1	TRUE	1	0.450819009298061	3		230	363	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519999	NA	P-0044011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	337	569	0	ENST00000269305.4:c.716A>G	p.Asn239Ser	p.N239S	ENST00000269305	NM_001126112.2	239	aAc/aGc	7/11	0.502989696865229	1	FACETS	0.787	0.752	0.822	1	0.996	1	SUBCLONAL	2	TRUE	0	0.502989696865229	1		569	637	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451254	70451254	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	42	709	0	ENST00000373644.4:c.6094C>G	p.Pro2032Ala	p.P2032A	ENST00000373644	NM_030625.2	2032	Cct/Gct	12/12	0.434586187955859	2	FACETS	0.215	0.179	0.256	0.107	0.089	0.128	SUBCLONAL	1	TRUE	0	0.502989696865229	2		709	777	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878184	48878184	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	89	114	0	ENST00000267163.4:c.136del	p.Arg46GlyfsTer19	p.R46Gfs*19	ENST00000267163	NM_000321.2	46	Agg/gg	1/27	0.502989696865229	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.502989696865229	2		114	155	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131976409	131976428	+	frameshift_variant	Frame_Shift_Del	DEL	TGCCTCAACTGTGGCATCAT	TGCCTCAACTGTGGCATCAT	-	novel	NA	P-0044011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	28	540	0	ENST00000265335.6:c.3669_3688del	p.Asn1224GlyfsTer2	p.N1224Gfs*2	ENST00000265335		1222	TGCCTCAACTGTGGCATCATt/t	24/25	0.502989696865229	1	FACETS	0.177	0.141	0.219	0.177	0.141	0.219	SUBCLONAL	1	TRUE	0	0.502989696865229	1		540	470	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399179	139399179	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	75	793	0	ENST00000277541.6:c.4964G>C	p.Gly1655Ala	p.G1655A	ENST00000277541	NM_017617.3	1655	gGt/gCt	26/34	0.502989696865229	2	FACETS	0.446	0.391	0.506	0.223	0.195	0.253	SUBCLONAL	1	TRUE	0	0.502989696865229	2		793	668	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410012	139410012	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044011-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	254	937	0	ENST00000277541.6:c.1826G>T	p.Ser609Ile	p.S609I	ENST00000277541	NM_017617.3	609	aGc/aTc	11/34	0.502989696865229	2	FACETS	1	0.981	1	0.556	0.521	0.592	CLONAL	1	TRUE	0	0.502989696865229	2		937	908	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	50	372	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.2	2		372	394	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230641	46230641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	37	462	0	ENST00000334344.6:c.890C>T	p.Ser297Phe	p.S297F	ENST00000334344	NM_152641.2	297	tCc/tTc	8/21	0.151596599417398	3	FACETS	0.873	0.72	1	0.437	0.36	0.523	CLONAL	1	TRUE	1	0.2	3		462	466	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518099	8518099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764400127	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	66	417	0	ENST00000356435.5:c.1292C>T	p.Ser431Leu	p.S431L	ENST00000356435		431	tCg/tTg	10/35	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.2	2		417	552	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359066	81359066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	44	420	0	ENST00000222390.5:c.895C>T	p.Pro299Ser	p.P299S	ENST00000222390	NM_000601.4	299	Cct/Tct	8/18	0.151596599417398	3	FACETS	1	0.891	1	0.54	0.453	0.636	CLONAL	1	TRUE	1	0.2	3		420	448	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857284	9857284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	49	611	0	ENST00000330684.3:c.4117G>A	p.Asp1373Asn	p.D1373N	ENST00000330684	NM_001134407.1	1373	Gat/Aat	13/13	1	2	FACETS	0.722	0.61	0.845	0.722	0.61	0.845	SUBCLONAL	1	TRUE	1	0.2	2		611	679	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	65	597	1	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	1	2	FACETS	0.804	0.696	0.922	0.804	0.696	0.922	CLONAL	1	TRUE	1	0.2	2		598	808	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055993	180055993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	50	786	1	ENST00000261937.6:c.992C>T	p.Pro331Leu	p.P331L	ENST00000261937	NM_182925.4	331	cCc/cTc	8/30	0.3	1	FACETS	0.554	0.469	0.649	0.554	0.469	0.649	SUBCLONAL	1	TRUE	0	0.2	1		787	812	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913355	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	40	428	1	ENST00000288602.6:c.1406G>A	p.Gly469Glu	p.G469E	ENST00000288602	NM_004333.4	469	gGa/gAa	11/18	0.151596599417398	3	FACETS	1	0.883	1	0.539	0.448	0.64	CLONAL	1	TRUE	1	0.2	3		429	408	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40441451	40441451	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	107	602	1	ENST00000345506.4:c.22C>T	p.Gln8Ter	p.Q8*	ENST00000345506	NM_003152.3	8	Cag/Tag	3/20	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.2	2		603	870	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419837	41419837	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs267605939	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	25	466	0	ENST00000373198.4:c.484C>T	p.Gln162Ter	p.Q162*	ENST00000373198	NM_133170.3	162	Cag/Tag	3/32	0.151596599417398	0	FACETS	0.41	0.322	0.511			1	SUBCLONAL	1	TRUE	0	0.2	0		466	488	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770023	56770023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759759863	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	106	498	0	ENST00000337432.4:c.19C>T	p.Arg7Cys	p.R7C	ENST00000337432	NM_058216.2	7	Cgc/Tgc	1/9	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.2	2		498	759	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575134	64575134	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057521110	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	82	562	0	ENST00000312049.6:c.673G>A	p.Gly225Arg	p.G225R	ENST00000312049	NM_130799.2	225	Gga/Aga	4/10	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.2	2		562	766	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843724	156843724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	92	908	1	ENST00000524377.1:c.1150G>A	p.Glu384Lys	p.E384K	ENST00000524377	NM_002529.3	384	Gag/Aag	8/17	0.151596599417398	3	FACETS	0.815	0.722	0.916	0.408	0.361	0.458	CLONAL	1	TRUE	1	0.2	3		909	1241	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410343	63410343	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1404477878	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	53	838	1	ENST00000330258.3:c.2824C>T	p.Arg942Ter	p.R942*	ENST00000330258	NM_152424.3	942	Cga/Tga	2/2	1	2	FACETS	0.637	0.542	0.742	0.637	0.542	0.742	SUBCLONAL	1	TRUE	1	0.2	2		839	832	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103716	47103716	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs981018402	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	67	405	1	ENST00000409792.3:c.6230G>A	p.Arg2077Gln	p.R2077Q	ENST00000409792	NM_014159.6	2077	cGa/cAa	14/21	0.151596599417398	3	FACETS	1	0.932	1	0.558	0.485	0.638	CLONAL	1	TRUE	1	0.2	3		406	660	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100988	41100988	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	45	653	0	ENST00000373198.4:c.1368G>A	p.Met456Ile	p.M456I	ENST00000373198	NM_133170.3	456	atG/atA	8/32	0.151596599417398	0	FACETS	0.452	0.378	0.533			1	SUBCLONAL	1	TRUE	0	0.2	0		653	797	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197443	106197443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1452689450	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	37	334	0	ENST00000380013.4:c.5776C>T	p.Arg1926Cys	p.R1926C	ENST00000380013	NM_001127208.2	1926	Cgt/Tgt	11/11	1	2	FACETS	0.864	0.713	1	0.864	0.713	1	CLONAL	1	TRUE	1	0.2	2		334	428	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521384	8521384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777779009	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	89	603	0	ENST00000356435.5:c.854G>A	p.Gly285Glu	p.G285E	ENST00000356435		285	gGa/gAa	9/35	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.2	2		603	607	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612176	189612176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	70	674	0	ENST00000264731.3:c.1928G>A	p.Arg643Gln	p.R643Q	ENST00000264731	NM_003722.4	643	cGa/cAa	14/14	1	2	FACETS	0.776	0.675	0.886	0.776	0.675	0.886	SUBCLONAL	1	TRUE	1	0.2	2		674	902	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487641	56487641	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771536549	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	91	625	2	ENST00000267101.3:c.1574G>A	p.Arg525Gln	p.R525Q	ENST00000267101	NM_001982.3	525	cGa/cAa	13/28	0.151596599417398	3	FACETS	1	0.964	1	0.607	0.539	0.681	CLONAL	1	TRUE	1	0.2	3		627	824	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381520	81381520	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	50	382	0	ENST00000222390.5:c.541C>T	p.Arg181Ter	p.R181*	ENST00000222390	NM_000601.4	181	Cga/Tga	5/18	0.151596599417398	3	FACETS	1	0.936	1	0.6	0.51	0.7	CLONAL	1	TRUE	1	0.2	3		382	458	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170193	32170193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	186	874	0	ENST00000375023.3:c.3415C>T	p.Pro1139Ser	p.P1139S	ENST00000375023	NM_004557.3	1139	Cca/Tca	21/30	0.339426843112024	3	FACETS	0.897	0.827	0.969	0.897	0.827	0.969	CLONAL	2	TRUE	1	0.2	3		874	1141	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	131	906	1	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.2	2		907	1098	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857878	9857878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867464241	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	57	667	0	ENST00000330684.3:c.3523G>A	p.Glu1175Lys	p.E1175K	ENST00000330684	NM_001134407.1	1175	Gaa/Aaa	13/13	1	2	FACETS	0.777	0.665	0.899	0.777	0.665	0.899	SUBCLONAL	1	TRUE	1	0.2	2		667	734	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739001	40739001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	46	541	0	ENST00000373198.4:c.3283G>A	p.Glu1095Lys	p.E1095K	ENST00000373198	NM_133170.3	1095	Gaa/Aaa	24/32	0.151596599417398	0	FACETS	0.599	0.504	0.705			1	SUBCLONAL	1	TRUE	0	0.2	0		541	614	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606709	29606709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	48	576	0	ENST00000389048.3:c.1171G>A	p.Gly391Arg	p.G391R	ENST00000389048	NM_004304.4	391	Gga/Aga	5/29	1	2	FACETS	0.738	0.623	0.866	0.738	0.623	0.866	SUBCLONAL	1	TRUE	1	0.2	2		576	650	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195313	102195313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370738985	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	42	422	0	ENST00000263464.3:c.73G>A	p.Asp25Asn	p.D25N	ENST00000263464	NM_001165.4	25	Gac/Aac	2/9	1	2	FACETS	0.899	0.751	1	0.899	0.751	1	CLONAL	1	TRUE	1	0.2	2		422	467	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285902	39285902	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	20	453	0	ENST00000402219.2:c.257C>T	p.Ala86Val	p.A86V	ENST00000402219	NM_005633.3	86	gCa/gTa	3/23	1	2	FACETS	0.629	0.481	0.802	0.629	0.481	0.802	SUBCLONAL	1	TRUE	1	0.2	2		453	318	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539021	23539021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	62	628	0	ENST00000380871.4:c.418G>A	p.Glu140Lys	p.E140K	ENST00000380871	NM_006167.3	140	Gag/Aag	2/2	1	2	FACETS	0.812	0.7	0.933	0.812	0.7	0.933	CLONAL	1	TRUE	1	0.2	2		628	764	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606700	29606700	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775514690	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	52	583	1	ENST00000389048.3:c.1180G>A	p.Gly394Arg	p.G394R	ENST00000389048	NM_004304.4	394	Ggg/Agg	5/29	1	2	FACETS	0.776	0.66	0.904	0.776	0.66	0.904	CLONAL	1	TRUE	1	0.2	2		584	670	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138513	11138513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	80	730	0	ENST00000358026.2:c.3269C>T	p.Pro1090Leu	p.P1090L	ENST00000358026	NM_001128849.1	1090	cCc/cTc	24/36	1	2	FACETS	0.911	0.801	1	0.911	0.801	1	CLONAL	1	TRUE	1	0.2	2		730	878	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629151	187629151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	41	535	0	ENST00000441802.2:c.1831G>A	p.Glu611Lys	p.E611K	ENST00000441802	NM_005245.3	611	Gaa/Aaa	2/27	1	2	FACETS	0.713	0.593	0.847	0.713	0.593	0.847	SUBCLONAL	1	TRUE	1	0.2	2		535	575	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344934	70344934	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	76	771	0	ENST00000374080.3:c.2164C>T	p.Leu722Phe	p.L722F	ENST00000374080		722	Ctt/Ttt	15/45	1	2	FACETS	0.844	0.738	0.957	0.844	0.738	0.957	CLONAL	1	TRUE	1	0.2	2		771	901	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444812	49444812	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775553446	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	91	806	0	ENST00000301067.7:c.2654C>T	p.Pro885Leu	p.P885L	ENST00000301067	NM_003482.3	885	cCc/cTc	10/54	0.151596599417398	3	FACETS	0.847	0.75	0.951	0.423	0.375	0.476	CLONAL	1	TRUE	1	0.2	3		806	1182	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727072	40727072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	43	536	0	ENST00000373198.4:c.3892G>A	p.Asp1298Asn	p.D1298N	ENST00000373198	NM_133170.3	1298	Gac/Aac	28/32	0.151596599417398	0	FACETS	0.572	0.478	0.677			1	SUBCLONAL	1	TRUE	0	0.2	0		536	601	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458329	12458329	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1364613522	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	150	627	0	ENST00000287820.6:c.946C>T	p.Arg316Cys	p.R316C	ENST00000287820	NM_015869.4	316	Cgc/Tgc	6/7	0.151596599417398	3	FACETS	0.872	0.797	0.951	0.872	0.797	0.951	CLONAL	2	TRUE	1	0.2	3		627	946	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50830322	50830322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	54	452	1	ENST00000398568.2:c.2765C>T	p.Ser922Phe	p.S922F	ENST00000398568	NM_001042412.1	922	tCc/tTc	18/18	1	2	FACETS	0.885	0.756	1	0.885	0.756	1	CLONAL	1	TRUE	1	0.2	2		453	610	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161483	2161483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	84	648	0	ENST00000434045.2:c.44C>T	p.Thr15Ile	p.T15I	ENST00000434045	NM_001127598.1	15	aCc/aTc	2/5	1	2	FACETS	0.934	0.824	1	0.934	0.824	1	CLONAL	1	TRUE	1	0.2	2		648	899	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350486	89350486	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	102	860	0	ENST00000301030.4:c.2464C>T	p.Gln822Ter	p.Q822*	ENST00000301030	NM_001256183.1	822	Cag/Tag	9/13	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.2	2		860	909	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463265	25463265	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755673156	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	80	611	1	ENST00000264709.3:c.2228C>T	p.Pro743Leu	p.P743L	ENST00000264709	NM_175629.2	743	cCc/cTc	19/23	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.2	2		612	781	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425646	49425646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	105	773	0	ENST00000301067.7:c.12842C>T	p.Pro4281Leu	p.P4281L	ENST00000301067	NM_003482.3	4281	cCt/cTt	39/54	0.151596599417398	3	FACETS	1	0.974	1	0.647	0.579	0.719	CLONAL	1	TRUE	1	0.2	3		773	893	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678626	88678626	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	36	374	0	ENST00000360948.2:c.910C>T	p.Pro304Ser	p.P304S	ENST00000360948	NM_001012338.2	304	Ccc/Tcc	9/19	1	2	FACETS	0.835	0.687	1	0.835	0.687	1	CLONAL	1	TRUE	1	0.2	2		374	431	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029127	26029127	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	22	416	1	ENST00000435504.4:c.223C>T	p.Pro75Ser	p.P75S	ENST00000435504		75	Cca/Tca	4/13	1	2	FACETS	0.554	0.429	0.7	0.554	0.429	0.7	SUBCLONAL	1	TRUE	1	0.2	2		417	397	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098392	11098392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745462998	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	76	560	1	ENST00000358026.2:c.910C>T	p.Pro304Ser	p.P304S	ENST00000358026	NM_001128849.1	304	Ccc/Tcc	6/36	1	2	FACETS	0.954	0.835	1	0.954	0.835	1	CLONAL	1	TRUE	1	0.2	2		561	797	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965284	25965284	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61745460	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	72	596	0	ENST00000435504.4:c.3922C>T	p.Leu1308Phe	p.L1308F	ENST00000435504		1308	Ctt/Ttt	13/13	1	2	FACETS	0.946	0.826	1	0.946	0.826	1	CLONAL	1	TRUE	1	0.2	2		596	761	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747109	40747109	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	43	596	0	ENST00000373198.4:c.2973G>A	p.Trp991Ter	p.W991*	ENST00000373198	NM_133170.3	991	tgG/tgA	22/32	0.151596599417398	0	FACETS	0.501	0.418	0.594			1	SUBCLONAL	1	TRUE	0	0.2	0		596	686	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332627	70332627	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	44	618	0	ENST00000373644.4:c.532C>T	p.Pro178Ser	p.P178S	ENST00000373644	NM_030625.2	178	Ccc/Tcc	2/12	1	2	FACETS	0.731	0.612	0.863	0.731	0.612	0.863	SUBCLONAL	1	TRUE	1	0.2	2		618	602	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347562	118347562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	56	533	1	ENST00000534358.1:c.3199C>T	p.Arg1067Trp	p.R1067W	ENST00000534358	NM_005933.3	1067	Cgg/Tgg	4/36	1	2	FACETS	0.821	0.702	0.951	0.821	0.702	0.951	CLONAL	1	TRUE	1	0.2	2		534	682	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411660	63411660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	45	781	0	ENST00000330258.3:c.1507G>A	p.Asp503Asn	p.D503N	ENST00000330258	NM_152424.3	503	Gat/Aat	2/2	1	2	FACETS	0.578	0.485	0.683	0.578	0.485	0.683	SUBCLONAL	1	TRUE	1	0.2	2		781	778	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074237	8074237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	66	494	0	ENST00000377482.5:c.422C>T	p.Pro141Leu	p.P141L	ENST00000377482	NM_018948.3	141	cCc/cTc	4/4	0.151596599417398	3	FACETS	1	0.886	1	0.512	0.444	0.586	CLONAL	1	TRUE	1	0.2	3		494	709	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255050	16255050	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1456830366	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	57	398	0	ENST00000375759.3:c.2315C>T	p.Pro772Leu	p.P772L	ENST00000375759	NM_015001.2	772	cCa/cTa	11/15	0.151596599417398	3	FACETS	1	0.912	1	0.543	0.466	0.628	CLONAL	1	TRUE	1	0.2	3		398	577	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264418	16264419	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	78	789	2	ENST00000375759.3:c.10621_10622delinsAT	p.Ser3541Ile	p.S3541I	ENST00000375759	NM_015001.2	3541	TCt/ATt	13/15	0.151596599417398	3	FACETS	0.935	0.82	1	0.467	0.41	0.53	CLONAL	1	TRUE	1	0.2	3		791	918	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937220	36937220	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	88	718	0	ENST00000361632.4:c.1099C>G	p.Arg367Gly	p.R367G	ENST00000361632		367	Cgg/Ggg	9/16	0.151596599417398	3	FACETS	0.974	0.861	1	0.487	0.43	0.548	CLONAL	1	TRUE	1	0.2	3		718	994	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65321198	65321198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	53	415	0	ENST00000342505.4:c.1642C>T	p.Pro548Ser	p.P548S	ENST00000342505	NM_002227.2	548	Ccc/Tcc	11/25	0.151596599417398	3	FACETS	0.849	0.723	0.987	0.424	0.361	0.494	CLONAL	1	TRUE	1	0.2	3		415	687	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830766	156830766	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	16	154	0	ENST00000524377.1:c.40A>C	p.Ser14Arg	p.S14R	ENST00000524377	NM_002529.3	14	Agc/Cgc	1/17	0.151596599417398	3	FACETS	0.664	0.491	0.871	0.332	0.245	0.436	SUBCLONAL	1	TRUE	1	0.2	3		154	265	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70441165	70441165	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	21	407	1	ENST00000373644.4:c.4834C>T	p.Leu1612Phe	p.L1612F	ENST00000373644	NM_030625.2	1612	Ctt/Ttt	9/12	1	2	FACETS	0.525	0.403	0.667	0.525	0.403	0.667	SUBCLONAL	1	TRUE	1	0.2	2		408	400	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94163105	94163105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782166	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	33	452	0	ENST00000323929.3:c.2042C>T	p.Ser681Leu	p.S681L	ENST00000323929	NM_005591.3	681	tCg/tTg	19/20	1	2	FACETS	0.653	0.531	0.791	0.653	0.531	0.791	SUBCLONAL	1	TRUE	1	0.2	2		452	505	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435072	49435072	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	87	778	1	ENST00000301067.7:c.6481C>T	p.Leu2161Phe	p.L2161F	ENST00000301067	NM_003482.3	2161	Ctc/Ttc	31/54	0.151596599417398	3	FACETS	1	0.933	1	0.54	0.477	0.608	CLONAL	1	TRUE	1	0.2	3		779	886	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446117	49446118	+	missense_variant	Missense_Mutation	DNP	GA	GA	AC	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	115	888	1	ENST00000301067.7:c.1348_1349delinsGT	p.Ser450Val	p.S450V	ENST00000301067	NM_003482.3	450	TCc/GTc	10/54	0.151596599417398	3	FACETS	1	0.965	1	0.583	0.524	0.646	CLONAL	1	TRUE	1	0.2	3		889	1084	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117384	115117385	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	30	403	1	ENST00000257566.3:c.789_790delinsTT	p.Pro264Ser	p.P264S	ENST00000257566	NM_016569.3	263	ctCCct/ctTTct	4/8	1	2	FACETS	0.637	0.512	0.779	0.637	0.512	0.779	SUBCLONAL	1	TRUE	1	0.2	2		404	471	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254190	133254190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	91	561	0	ENST00000320574.5:c.694C>T	p.Leu232Phe	p.L232F	ENST00000320574	NM_006231.2	232	Ctc/Ttc	7/49	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.2	2		561	861	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557599	21557599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	67	739	0	ENST00000382592.4:c.2246C>T	p.Pro749Leu	p.P749L	ENST00000382592	NM_014572.2	749	cCt/cTt	5/8	1	2	FACETS	0.801	0.695	0.917	0.801	0.695	0.917	CLONAL	1	TRUE	1	0.2	2		739	836	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28611406	28611406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	22	331	0	ENST00000241453.7:c.1225C>T	p.His409Tyr	p.H409Y	ENST00000241453	NM_004119.2	409	Cat/Tat	10/24	1	2	FACETS	0.561	0.434	0.709	0.561	0.434	0.709	SUBCLONAL	1	TRUE	1	0.2	2		331	392	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930579	32930580	+	missense_variant	Missense_Mutation	DNP	CT	CT	TA	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	30	322	1	ENST00000380152.3:c.7450_7451delinsTA	p.Leu2484Tyr	p.L2484Y	ENST00000380152		2484	CTt/TAt	15/27	1	2	FACETS	0.829	0.668	1	0.829	0.668	1	CLONAL	1	TRUE	1	0.2	2		323	362	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039344	49039344	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	39	573	0	ENST00000267163.4:c.2329C>T	p.Pro777Ser	p.P777S	ENST00000267163	NM_000321.2	777	Cct/Tct	23/27	1	2	FACETS	0.728	0.602	0.868	0.728	0.602	0.868	SUBCLONAL	1	TRUE	1	0.2	2		573	536	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251097	99251097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778243153	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	64	585	0	ENST00000268035.6:c.401G>A	p.Arg134Lys	p.R134K	ENST00000268035	NM_000875.3	134	aGg/aAg	2/21	1	2	FACETS	0.873	0.755	1	0.873	0.755	1	CLONAL	1	TRUE	1	0.2	2		585	733	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857367	9857367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	44	499	0	ENST00000330684.3:c.4034C>T	p.Pro1345Leu	p.P1345L	ENST00000330684	NM_001134407.1	1345	cCc/cTc	13/13	1	2	FACETS	0.824	0.691	0.972	0.824	0.691	0.972	CLONAL	1	TRUE	1	0.2	2		499	534	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9927963	9927963	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	24	415	0	ENST00000330684.3:c.1776A>C	p.Lys592Asn	p.K592N	ENST00000330684	NM_001134407.1	592	aaA/aaC	8/13	1	2	FACETS	0.558	0.437	0.699	0.558	0.437	0.699	SUBCLONAL	1	TRUE	1	0.2	2		415	430	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273994	10273994	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	106	802	0	ENST00000330684.3:c.275G>A	p.Gly92Glu	p.G92E	ENST00000330684	NM_001134407.1	92	gGg/gAg	2/13	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.2	2		802	932	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244924	41244924	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867654871	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	61	678	1	ENST00000357654.3:c.2624C>T	p.Pro875Leu	p.P875L	ENST00000357654	NM_007294.3	875	cCa/cTa	10/23	1	2	FACETS	0.875	0.754	1	0.875	0.754	1	CLONAL	1	TRUE	1	0.2	2		679	697	SUCCESS
YES1	7525	MSKCC	GRCh37	18	732953	732953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	34	511	0	ENST00000314574.4:c.1304C>T	p.Pro435Leu	p.P435L	ENST00000314574	NM_005433.3	435	cCa/cTa	11/12	1	2	FACETS	0.714	0.583	0.862	0.714	0.583	0.862	SUBCLONAL	1	TRUE	1	0.2	2		511	476	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2225413	2225413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	54	522	0	ENST00000398665.3:c.3623C>T	p.Ser1208Phe	p.S1208F	ENST00000398665	NM_032482.2	1208	tCc/tTc	26/28	1	2	FACETS	0.89	0.759	1	0.89	0.759	1	CLONAL	1	TRUE	1	0.2	2		522	607	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231452	5231452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	95	786	0	ENST00000357368.4:c.2024C>T	p.Pro675Leu	p.P675L	ENST00000357368	NM_002850.3	675	cCc/cTc	14/38	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.2	2		786	906	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280003	18280003	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	74	546	0	ENST00000222254.8:c.2086T>C	p.Tyr696His	p.Y696H	ENST00000222254	NM_005027.3	696	Tac/Cac	16/16	1	2	FACETS	0.925	0.809	1	0.925	0.809	1	CLONAL	1	TRUE	1	0.2	2		546	800	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18972844	18972844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	95	577	2	ENST00000262803.5:c.2483C>T	p.Ala828Val	p.A828V	ENST00000262803	NM_002911.3	828	gCc/gTc	18/24	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.2	2		579	895	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211466	36211466	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	115	856	0	ENST00000222270.7:c.1217del	p.Leu406ArgfsTer69	p.L406Rfs*69	ENST00000222270	NM_014727.1	406	cTg/cg	3/37	1	2	FACETS	0.883	0.793	0.979	0.883	0.793	0.979	CLONAL	1	TRUE	1	0.2	2		856	1302	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211950	36211970	+	frameshift_variant	Frame_Shift_Del	DEL	TACCACCTCCCCACCTGTTCC	TACCACCTCCCCACCTGTTCC	ACCA	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	118	988	3	ENST00000222270.7:c.1701_1721delinsACCA	p.Thr568ProfsTer25	p.T568Pfs*25	ENST00000222270	NM_014727.1	567	atTACCACCTCCCCACCTGTTCCc/atACCAc	3/37	1	2	FACETS	0.915	0.823	1	0.915	0.823	1	CLONAL	1	TRUE	1	0.2	2		991	1290	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50138874	50138874	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1229	102	974	0	ENST00000246792.3:c.616C>T	p.Pro206Ser	p.P206S	ENST00000246792	NM_006270.3	206	Ccc/Tcc	6/6	1	2	FACETS	0.766	0.683	0.856	0.766	0.683	0.856	SUBCLONAL	1	TRUE	1	0.2	2		974	1331	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872450	136872450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1344271734	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	17	269	0	ENST00000241393.3:c.1048C>T	p.His350Tyr	p.H350Y	ENST00000241393	NM_003467.2	350	Cac/Tac	2/2	1	2	FACETS	0.541	0.404	0.705	0.541	0.404	0.705	SUBCLONAL	1	TRUE	1	0.2	2		269	314	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538362	9538362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	22	377	0	ENST00000353224.5:c.1636G>A	p.Ala546Thr	p.A546T	ENST00000353224	NM_177990.2	546	Gct/Act	7/10	1	2	FACETS	0.501	0.387	0.634	0.501	0.387	0.634	SUBCLONAL	1	TRUE	1	0.2	2		377	439	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546685	9546685	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	47	417	0	ENST00000353224.5:c.1337G>T	p.Arg446Met	p.R446M	ENST00000353224	NM_177990.2	446	aGg/aTg	5/10	1	2	FACETS	0.969	0.818	1	0.969	0.818	1	CLONAL	1	TRUE	1	0.2	2		417	485	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375078	31375078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	87	729	0	ENST00000328111.2:c.475C>T	p.Pro159Ser	p.P159S	ENST00000328111	NM_006892.3	159	Ccg/Tcg	6/23	1	2	FACETS	0.867	0.765	0.975	0.867	0.765	0.975	CLONAL	1	TRUE	1	0.2	2		729	1004	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100986	41100986	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1443390760	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	43	646	0	ENST00000373198.4:c.1370C>T	p.Thr457Ile	p.T457I	ENST00000373198	NM_133170.3	457	aCc/aTc	8/32	0.151596599417398	0	FACETS	0.432	0.36	0.512			1	SUBCLONAL	1	TRUE	0	0.2	0		646	796	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231857	36231857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	90	594	2	ENST00000300305.3:c.527C>T	p.Thr176Ile	p.T176I	ENST00000300305		176	aCc/aTc	5/8	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.2	2		596	776	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151555	55151555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757362953	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	24	409	0	ENST00000257290.5:c.2341C>T	p.Leu781Phe	p.L781F	ENST00000257290	NM_006206.4	781	Ctc/Ttc	17/23	1	2	FACETS	0.576	0.45	0.72	0.576	0.45	0.72	SUBCLONAL	1	TRUE	1	0.2	2		409	417	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99823085	99823085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	29	328	0	ENST00000280892.6:c.127G>A	p.Glu43Lys	p.E43K	ENST00000280892	NM_001130678.1	43	Gaa/Aaa	2/7	1	2	FACETS	0.767	0.616	0.939	0.767	0.616	0.939	CLONAL	1	TRUE	1	0.2	2		328	378	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158591	26158591	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	59	491	0	ENST00000289316.2:c.194C>T	p.Ser65Phe	p.S65F	ENST00000289316	NM_138720.2	65	tCc/tTc	1/2	0.339426843112024	3	FACETS	0.862	0.74	0.995	0.431	0.37	0.498	CLONAL	1	TRUE	1	0.2	3		491	753	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120423	94120423	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	21	365	0	ENST00000369303.4:c.628G>A	p.Glu210Lys	p.E210K	ENST00000369303	NM_004440.3	210	Gag/Aag	3/17	1	2	FACETS	0.625	0.481	0.793	0.625	0.481	0.793	SUBCLONAL	1	TRUE	1	0.2	2		365	336	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553285	106553285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	65	552	0	ENST00000369096.4:c.1250C>T	p.Pro417Leu	p.P417L	ENST00000369096	NM_001198.3	417	cCc/cTc	5/7	1	2	FACETS	0.931	0.807	1	0.931	0.807	1	CLONAL	1	TRUE	1	0.2	2		552	698	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976691	2976692	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	76	552	0	ENST00000396946.4:c.1320_1321delinsAA	p.Asp441Asn	p.D441N	ENST00000396946	NM_032415.4	440	aaGGac/aaAAac	9/25	0.151596599417398	0	FACETS	0.885	0.776	1			1	CLONAL	1	TRUE	0	0.2	0		552	687	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729824	41729824	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	44	466	0	ENST00000242208.4:c.705G>C	p.Lys235Asn	p.K235N	ENST00000242208	NM_002192.2	235	aaG/aaC	3/3	0.151596599417398	3	FACETS	0.929	0.779	1	0.464	0.389	0.548	CLONAL	1	TRUE	1	0.2	3		466	521	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509270	106509270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	76	677	0	ENST00000359195.3:c.1264G>A	p.Asp422Asn	p.D422N	ENST00000359195	NM_002649.2	422	Gac/Aac	2/11	0.151596599417398	3	FACETS	0.909	0.795	1	0.454	0.397	0.516	CLONAL	1	TRUE	1	0.2	3		677	920	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566089	141566089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	74	660	1	ENST00000220592.5:c.1175C>T	p.Pro392Leu	p.P392L	ENST00000220592	NM_012154.3	392	cCa/cTa	10/19	1	2	FACETS	0.925	0.809	1	0.925	0.809	1	CLONAL	1	TRUE	1	0.2	2		661	800	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5549520	5549520	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	185	860	0	ENST00000397747.3:c.547A>G	p.Lys183Glu	p.K183E	ENST00000397747	NM_025239.3	183	Aag/Gag	4/7	1	2	FACETS	0.858	0.791	0.928	1	0.991	1	CLONAL	2	TRUE	1	0.2	2		860	1078	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500885	8500886	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	42	512	1	ENST00000356435.5:c.1996_1997delinsTT	p.Pro666Phe	p.P666F	ENST00000356435		666	CCt/TTt	13/35	1	2	FACETS	0.669	0.557	0.793	0.669	0.557	0.793	SUBCLONAL	1	TRUE	1	0.2	2		513	628	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500894	8500894	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	47	526	0	ENST00000356435.5:c.1988T>A	p.Leu663Ter	p.L663*	ENST00000356435		663	tTg/tAg	13/35	1	2	FACETS	0.763	0.643	0.896	0.763	0.643	0.896	SUBCLONAL	1	TRUE	1	0.2	2		526	616	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931903	39931903	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	67	791	0	ENST00000378444.4:c.2696C>T	p.Pro899Leu	p.P899L	ENST00000378444	NM_001123385.1	899	cCa/cTa	4/15	1	2	FACETS	0.788	0.683	0.902	0.788	0.683	0.902	CLONAL	1	TRUE	1	0.2	2		791	850	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412829	63412829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	55	724	1	ENST00000330258.3:c.338G>A	p.Gly113Glu	p.G113E	ENST00000330258	NM_152424.3	113	gGa/gAa	2/2	1	2	FACETS	0.667	0.569	0.774	0.667	0.569	0.774	SUBCLONAL	1	TRUE	1	0.2	2		725	825	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441500	6441500	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	45	265	0	ENST00000356142.4:c.347G>T	p.Trp116Leu	p.W116L	ENST00000356142	NM_018890.3	116	tGg/tTg	6/7	0.151596599417398	3	FACETS	1	0.957	1	0.724	0.61	0.848	CLONAL	1	TRUE	1	0.2	3		265	342	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649951	88649951	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	16	687	0	ENST00000372037.3:c.200G>A	p.Cys67Tyr	p.C67Y	ENST00000372037	NM_004329.2	67	tGt/tAt	4/13	1	2	FACETS	0.982	0.73	1	0.982	0.73	1	CLONAL	1	TRUE	1	0.2	2		687	163	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287465	33287480	+	frameshift_variant	Frame_Shift_Del	DEL	ATCTATGCTGGAGGGG	ATCTATGCTGGAGGGG	-	novel	NA	P-0044178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	22	580	0	ENST00000374542.5:c.1617_1632del	p.Pro540LeufsTer11	p.P540Lfs*11	ENST00000374542	NM_001141970.1	539	gcCCCCTCCAGCATAGAT/gc	6/8	0.215368388468808	3	FACETS	1	0.922	1	0.747	0.584	0.933	CLONAL	1	TRUE	1	0.2	3		580	162	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575047	64575065	+	protein_altering_variant	In_Frame_Del	DEL	GCGAGTCGGTGTGCAGGTC	GCGAGTCGGTGTGCAGGTC	T	novel	NA	P-0044178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	21	593	0	ENST00000312049.6:c.742_760delinsA	p.Asp248_Leu254delinsMet	p.D248_L254delinsM	ENST00000312049	NM_130799.2	248	GACCTGCACACCGACTCGCtg/Atg	4/10	1	2	FACETS	0.623	0.48	0.791	0.623	0.48	0.791	SUBCLONAL	1	TRUE	1	0.2	2		593	337	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	175	372	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.910174583387321	NA		372	363	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0044232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	406	468	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	0.910174583387321	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.910174583387321	1		468	478	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953730	48953730	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs3092891	NA	P-0044232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	100	105	0	ENST00000267163.4:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000267163	NM_000321.2	445	Cga/Tga	14/27	0.250468594995339	1	FACETS	0.605	0.554	0.655	0.605	0.554	0.655	INDETERMINATE	1	TRUE	0	0.910174583387321	1		105	198	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999081	100999081	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	440	606	0	ENST00000325455.5:c.721C>G	p.Pro241Ala	p.P241A	ENST00000325455	NM_001202474.3	241	Cct/Gct	1/8	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.910174583387321	2		606	884	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544714	65544714	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044232-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	333	425	0	ENST00000358664.4:c.212T>C	p.Ile71Thr	p.I71T	ENST00000358664	NM_002382.4	71	aTc/aCc	4/5	0.910174583387321	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.910174583387321	1		425	389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691039	NA	P-0044338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	235	456	0	ENST00000269305.4:c.919+1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.545335401984765	2	FACETS	0.833	0.789	0.878	0.833	0.789	0.878	CLONAL	2	TRUE	0	0.632454409993819	2		456	446	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375357	118375357	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555047328	NA	P-0044338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	31	247	0	ENST00000534358.1:c.8750C>G	p.Ser2917Cys	p.S2917C	ENST00000534358	NM_005933.3	2917	tCt/tGt	27/36	0.362574092150112	3	FACETS	0.492	0.4	0.596	0.164	0.133	0.199	INDETERMINATE	1	TRUE	0	0.632454409993819	3		247	262	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255963	16256985	+	inframe_deletion	In_Frame_Del	DEL	TGGCTCAAGGCCCAGCTCAGACCTACAAGCAAGACTGGGAGAACTAGCAGGTGAATCTGTGGAAAATCAAGAAGTCCAATCAAAAAAGCCCATTCCCTCAAAACCACAGCTCAAACAGCTGCAGGTATTAGATGATCAAGGACCAGAGAGAGAAGACGTTAGGAAAAACTATTGCAGTCTTCGTGATGAAACACCTGAACGTAAATCAGGCCAAGAGAAATCACATTCAGTAAATACTGAAGAAAAAATTGGCATTGACATCGATCACACGCAGAGTTACCGAAAACAAATGGAACAGAGTCGTAGGAAACAGCAGATGGAAATGGAAATAGCCAAGTCTGAGAAGTTTGGCAGTCCTAAAAAAGATGTAGATGAATATGAAAGACGTAGCCTCGTTCACGAGGTAGGCAAACCCCCTCAAGATGTCACTGATGACTCTCCTCCTAGCAAAAAGAAAAGGATGGATCATGTCGATTTTGATATCTGCACCAAGCGAGAACGGAATTACAGAAGTTCACGCCAAATCAGCGAAGATTCTGAAAGGACTGGTGGTTCTCCCAGTGTCCGACATGGTTCCTTCCATGAAGATGAGGATCCCATAGGCTCCCCTAGGCTACTGTCAGTAAAAGGGTCTCCTAAAGTAGATGAAAAAGTCCTCCCCTATTCTAACATAACAGTCAGGGAAGAGTCTTTAAAATTTAATCCTTATGATTCTAGCAGGAGAGAACAGATGGCAGATATGGCCAAAATAAAACTATCTGTCTTGAATTCTGAAGATGAACTAAATCGTTGGGACTCTCAGATGAAACAGGATGCTGGCAGATTTGATGTGAGTTTCCCAAACAGCATAATTAAGAGAGATAGCCTTCGAAAAAGGTCTGTACGAGATCTGGAACCTGGTGAGGTGCCTTCTGATTCTGACGAAGATGGTGAACACAAATCCCACTCACCCAGAGCCTCTGCATTATATGAAAGTTCTCGATTGTCTTTTTTATTGAGGGACAGAGAAGACAAGCTACGTGA	TGGCTCAAGGCCCAGCTCAGACCTACAAGCAAGACTGGGAGAACTAGCAGGTGAATCTGTGGAAAATCAAGAAGTCCAATCAAAAAAGCCCATTCCCTCAAAACCACAGCTCAAACAGCTGCAGGTATTAGATGATCAAGGACCAGAGAGAGAAGACGTTAGGAAAAACTATTGCAGTCTTCGTGATGAAACACCTGAACGTAAATCAGGCCAAGAGAAATCACATTCAGTAAATACTGAAGAAAAAATTGGCATTGACATCGATCACACGCAGAGTTACCGAAAACAAATGGAACAGAGTCGTAGGAAACAGCAGATGGAAATGGAAATAGCCAAGTCTGAGAAGTTTGGCAGTCCTAAAAAAGATGTAGATGAATATGAAAGACGTAGCCTCGTTCACGAGGTAGGCAAACCCCCTCAAGATGTCACTGATGACTCTCCTCCTAGCAAAAAGAAAAGGATGGATCATGTCGATTTTGATATCTGCACCAAGCGAGAACGGAATTACAGAAGTTCACGCCAAATCAGCGAAGATTCTGAAAGGACTGGTGGTTCTCCCAGTGTCCGACATGGTTCCTTCCATGAAGATGAGGATCCCATAGGCTCCCCTAGGCTACTGTCAGTAAAAGGGTCTCCTAAAGTAGATGAAAAAGTCCTCCCCTATTCTAACATAACAGTCAGGGAAGAGTCTTTAAAATTTAATCCTTATGATTCTAGCAGGAGAGAACAGATGGCAGATATGGCCAAAATAAAACTATCTGTCTTGAATTCTGAAGATGAACTAAATCGTTGGGACTCTCAGATGAAACAGGATGCTGGCAGATTTGATGTGAGTTTCCCAAACAGCATAATTAAGAGAGATAGCCTTCGAAAAAGGTCTGTACGAGATCTGGAACCTGGTGAGGTGCCTTCTGATTCTGACGAAGATGGTGAACACAAATCCCACTCACCCAGAGCCTCTGCATTATATGAAAGTTCTCGATTGTCTTTTTTATTGAGGGACAGAGAAGACAAGCTACGTGA	-	novel	NA	P-0044338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	176	367	0	ENST00000375759.3:c.3228_4250del	p.Gly1077_Glu1417del	p.G1077_E1417del	ENST00000375759	NM_015001.2	1076	tcTGGCTCAAGGCCCAGCTCAGACCTACAAGCAAGACTGGGAGAACTAGCAGGTGAATCTGTGGAAAATCAAGAAGTCCAATCAAAAAAGCCCATTCCCTCAAAACCACAGCTCAAACAGCTGCAGGTATTAGATGATCAAGGACCAGAGAGAGAAGACGTTAGGAAAAACTATTGCAGTCTTCGTGATGAAACACCTGAACGTAAATCAGGCCAAGAGAAATCACATTCAGTAAATACTGAAGAAAAAATTGGCATTGACATCGATCACACGCAGAGTTACCGAAAACAAATGGAACAGAGTCGTAGGAAACAGCAGATGGAAATGGAAATAGCCAAGTCTGAGAAGTTTGGCAGTCCTAAAAAAGATGTAGATGAATATGAAAGACGTAGCCTCGTTCACGAGGTAGGCAAACCCCCTCAAGATGTCACTGATGACTCTCCTCCTAGCAAAAAGAAAAGGATGGATCATGTCGATTTTGATATCTGCACCAAGCGAGAACGGAATTACAGAAGTTCACGCCAAATCAGCGAAGATTCTGAAAGGACTGGTGGTTCTCCCAGTGTCCGACATGGTTCCTTCCATGAAGATGAGGATCCCATAGGCTCCCCTAGGCTACTGTCAGTAAAAGGGTCTCCTAAAGTAGATGAAAAAGTCCTCCCCTATTCTAACATAACAGTCAGGGAAGAGTCTTTAAAATTTAATCCTTATGATTCTAGCAGGAGAGAACAGATGGCAGATATGGCCAAAATAAAACTATCTGTCTTGAATTCTGAAGATGAACTAAATCGTTGGGACTCTCAGATGAAACAGGATGCTGGCAGATTTGATGTGAGTTTCCCAAACAGCATAATTAAGAGAGATAGCCTTCGAAAAAGGTCTGTACGAGATCTGGAACCTGGTGAGGTGCCTTCTGATTCTGACGAAGATGGTGAACACAAATCCCACTCACCCAGAGCCTCTGCATTATATGAAAGTTCTCGATTGTCTTTTTTATTGAGGGACAGAGAAGACAAGCTACGTGAg/tcg	11/15	0.632454409993819	5	FACETS	1	0.951	1	0.687	0.638	0.738	CLONAL	2	TRUE	2	0.632454409993819	5		367	526	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69210657	69210658	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0044338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	118	220	0	ENST00000462284.1:c.241_242del	p.Val81IlefsTer5	p.V81Ifs*5	ENST00000462284	NM_002392.5	80	atTGta/atta	4/11	0.577497898681927	4	FACETS	0.777	0.707	0.849	0.777	0.707	0.849	SUBCLONAL	2	TRUE	2	0.632454409993819	4		220	392	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745989	745989	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	157	331	0	ENST00000314574.4:c.533A>C	p.Gln178Pro	p.Q178P	ENST00000314574	NM_005433.3	178	cAa/cCa	5/12	0.48441786553444	4	FACETS	0.917	0.848	0.987	0.917	0.848	0.987	CLONAL	2	TRUE	2	0.632454409993819	4		331	442	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965996	25965997	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0044338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	210	461	0	ENST00000435504.4:c.3209_3210del	p.Leu1070HisfsTer69	p.L1070Hfs*69	ENST00000435504		1070	cTC/c	13/13	0.48441786553444	4	FACETS	0.825	0.77	0.881	0.825	0.77	0.881	CLONAL	2	TRUE	2	0.632454409993819	4		461	657	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213191	39213191	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	263	566	0	ENST00000402219.2:c.3776C>T	p.Pro1259Leu	p.P1259L	ENST00000402219	NM_005633.3	1259	cCt/cTt	23/23	0.48441786553444	4	FACETS	0.834	0.784	0.885	0.834	0.784	0.885	CLONAL	2	TRUE	2	0.632454409993819	4		566	814	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518292	187518292	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044338-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	115	185	0	ENST00000441802.2:c.12402C>A	p.Asn4134Lys	p.N4134K	ENST00000441802	NM_005245.3	4134	aaC/aaA	25/27	0.48441786553444	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	2	0.632454409993819	4		185	277	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827724	72827725	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0044377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	529	581	0	ENST00000268489.5:c.8856_8857del	p.Gln2952HisfsTer14	p.Q2952Hfs*14	ENST00000268489	NM_006885.3	2952	caAAtg/catg	9/10	0.838254883744078	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.838254883744078	2		581	628	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212209	5212209	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142364974	NA	P-0044377-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	326	677	3	ENST00000357368.4:c.4822C>T	p.Arg1608Trp	p.R1608W	ENST00000357368	NM_002850.3	1608	Cgg/Tgg	32/38	0.813712792956434	3	FACETS	1	0.986	1	0.559	0.529	0.59	CLONAL	1	TRUE	1	0.838254883744078	3		680	987	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0044394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	178	269	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.253471489428278	6	FACETS	1	0.952	1	0.674	0.635	0.712	INDETERMINATE	4	TRUE	0	0.699609008269899	6		269	302	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163690	72163690	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0044394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	86	251	0	ENST00000357731.5:c.667+1G>A		p.X223_splice	ENST00000357731	NM_173808.2	223			0.513746268104493	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.699609008269899	3		251	158	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115267931	115267931	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	89	338	0	ENST00000438362.2:c.1802G>T	p.Ser601Ile	p.S601I	ENST00000438362	NM_001242891.1	601	aGc/aTc	15/20	0.513746268104493	3	FACETS	1	0.953	1	0.556	0.498	0.616	CLONAL	1	TRUE	1	0.699609008269899	3		338	309	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199881	108199881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881315	NA	P-0044394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	89	130	0	ENST00000278616.4:c.7223C>T	p.Ser2408Leu	p.S2408L	ENST00000278616	NM_000051.3	2408	tCg/tTg	49/63	0.676097624773888	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.699609008269899	2		130	121	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641744	23641744	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	51	205	0	ENST00000261584.4:c.1731T>G	p.Asn577Lys	p.N577K	ENST00000261584	NM_024675.3	577	aaT/aaG	5/13	0.360867898611622	3	FACETS	0.683	0.585	0.79	0.342	0.292	0.395	INDETERMINATE	1	TRUE	1	0.699609008269899	3		205	288	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845733	68845733	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	120	335	0	ENST00000261769.5:c.979A>G	p.Ser327Gly	p.S327G	ENST00000261769	NM_004360.3	327	Agt/Ggt	7/16	0.36293171121556	4	FACETS	0.819	0.748	0.892			1	INDETERMINATE	2	TRUE	NA	0.699609008269899	4		335	356	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52729229	52729229	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs780001633	NA	P-0044394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	229	454	0	ENST00000322088.6:c.1765G>T	p.Ala589Ser	p.A589S	ENST00000322088	NM_014225.5	589	Gcc/Tcc	15/15	0.305128548030277	4	FACETS	0.923	0.866	0.98	0.923	0.866	0.98	INDETERMINATE	2	TRUE	2	0.699609008269899	4		454	603	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266713	198266713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776846119	NA	P-0044394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	158	349	0	ENST00000335508.6:c.2219G>A	p.Gly740Glu	p.G740E	ENST00000335508	NM_012433.2	740	gGa/gAa	15/25	0.513746268104493	3	FACETS	0.983	0.918	1	0.983	0.918	1	CLONAL	2	TRUE	1	0.699609008269899	3		349	310	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755470	39755470	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	206	397	2	ENST00000288319.7:c.1295C>A	p.Ala432Glu	p.A432E	ENST00000288319	NM_182918.3	432	gCg/gAg	10/10	0.513746268104493	3	FACETS	0.901	0.847	0.956	0.901	0.847	0.956	CLONAL	2	TRUE	1	0.699609008269899	3		399	441	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946428	2946428	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	506	656	0	ENST00000396946.4:c.3309C>A	p.Cys1103Ter	p.C1103*	ENST00000396946	NM_032415.4	1103	tgC/tgA	25/25	0.699609008269899	5	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	2	0.699609008269899	5		656	897	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249873	110249873	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	222	580	0	ENST00000374672.4:c.802G>T	p.Gly268Cys	p.G268C	ENST00000374672	NM_004235.4	268	Ggc/Tgc	3/5	0.36293171121556	4	FACETS	0.911	0.854	0.969			1	INDETERMINATE	2	TRUE	NA	0.699609008269899	4		580	592	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613316	100613316	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	174	454	0	ENST00000308731.7:c.1084C>A	p.His362Asn	p.H362N	ENST00000308731	NM_000061.2	362	Cat/Aat	12/19	0.699609008269899	4	FACETS	0.751	0.695	0.808	0.501	0.463	0.539	SUBCLONAL	2	TRUE	1	0.699609008269899	4		454	563	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480557	123480557	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	133	445	0	ENST00000371139.4:c.65C>A	p.Ala22Asp	p.A22D	ENST00000371139	NM_001114937.2	22	gCc/gAc	1/4	0.699609008269899	4	FACETS	0.988	0.9	1	0.329	0.3	0.361	CLONAL	1	TRUE	1	0.699609008269899	4		445	654	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157529020	157529027	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	TTATGACA	TTATGACA	-	novel	NA	P-0044414-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	22	330	0	ENST00000346085.5:c.6746_*3del		p.*2249*	ENST00000346085	NM_020732.3	2249		20/20	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		330	178	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	34	559	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	1	2	FACETS	0.85	0.694	1	0.85	0.694	1	CLONAL	1	TRUE	1	0.16	2		559	500	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056437	26056437	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	26	338	0	ENST00000343677.2:c.220G>C	p.Glu74Gln	p.E74Q	ENST00000343677	NM_005319.3	74	Gag/Cag	1/1	1	2	FACETS	0.988	0.783	1	0.988	0.783	1	CLONAL	1	TRUE	1	0.16	2		338	329	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871782	35871782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	54	595	0	ENST00000216797.5:c.724G>A	p.Asp242Asn	p.D242N	ENST00000216797	NM_020529.2	242	Gat/Aat	5/6	1	2	FACETS	0.94	0.802	1	0.94	0.802	1	CLONAL	1	TRUE	1	0.16	2		595	718	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0044457-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	17	538	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.22	0.163	0.288	0.22	0.163	0.288	SUBCLONAL	1	TRUE	1	0.29	2		538	533	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0044459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	76	727	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.845	0.742	0.956	1	0.979	1	CLONAL	2	TRUE	1	0.153693945953334	2		728	585	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0044459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	58	351	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	NA	3	FACETS	0.917	0.79	1	0.917	0.79	1	INDETERMINATE	2	TRUE	1	0.153693945953334	3		351	443	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0044459-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	31	372	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	0.0246471519800557	4	FACETS	1	0.934	1	0.699	0.566	0.848	INDETERMINATE	1	TRUE	2	0.153693945953334	4		372	333	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0044470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	255	452	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.309107222645672	8	FACETS	1	0.96	1			1	CLONAL	4	TRUE	NA	0.309107222645672	8		452	774	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0044470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	347	1194	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.281854371320747	3	FACETS	1	0.989	1	0.776	0.736	0.818	CLONAL	2	TRUE	0	0.309107222645672	3		1194	1113	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435386	56435386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372159496	NA	P-0044470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	207	1064	3	ENST00000407977.2:c.1751G>A	p.Arg584Gln	p.R584Q	ENST00000407977		584	cGg/cAg	9/10	0.288096869795146	4	FACETS	0.806	0.747	0.867	0.806	0.747	0.867	CLONAL	2	TRUE	2	0.309107222645672	4		1067	1088	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981298	201981298	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	90	871	0	ENST00000359651.3:c.377G>C	p.Arg126Pro	p.R126P	ENST00000359651		126	cGa/cCa	2/8	0.309107222645672	3	FACETS	0.637	0.564	0.716	0.212	0.188	0.239	SUBCLONAL	1	TRUE	0	0.309107222645672	3		871	1055	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804367	46804367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1187061907	NA	P-0044470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	175	609	0	ENST00000290295.7:c.640C>T	p.Arg214Cys	p.R214C	ENST00000290295	NM_006361.5	214	Cgt/Tgt	2/2	0.288096869795146	4	FACETS	0.954	0.88	1	0.954	0.88	1	CLONAL	2	TRUE	2	0.309107222645672	4		609	777	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492853	56492853	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	103	461	0	ENST00000407977.2:c.86del	p.Gly29AspfsTer22	p.G29Dfs*22	ENST00000407977		29	gGa/ga	2/10	0.288096869795146	4	FACETS	1	0.98	1	0.704	0.631	0.781	CLONAL	1	TRUE	2	0.309107222645672	4		461	620	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633382	8633382	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044470-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	136	513	0	ENST00000356435.5:c.287A>T	p.Tyr96Phe	p.Y96F	ENST00000356435		96	tAt/tTt	3/35	0.309107222645672	3	FACETS	0.782	0.712	0.854	0.521	0.475	0.569	SUBCLONAL	2	TRUE	0	0.309107222645672	3		513	650	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0044470-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	257	452	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.328290441892576	10	FACETS	1	0.958	1	1	0.958	1	CLONAL	7	FALSE	3	0.328290441892576	10		452	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0044470-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	111	1194	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.329494937900079	3	FACETS	1	0.91	1	0.669	0.607	0.734	CLONAL	2	FALSE	0	0.328290441892576	3		1194	392	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435386	56435386	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372159496	NA	P-0044470-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	89	1064	3	ENST00000407977.2:c.1751G>A	p.Arg584Gln	p.R584Q	ENST00000407977		584	cGg/cAg	9/10	0.287664008538233	4	FACETS	1	0.978	1	0.723	0.643	0.808	CLONAL	1	FALSE	2	0.328290441892576	4		1067	498	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981298	201981298	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044470-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	136	871	0	ENST00000359651.3:c.377G>C	p.Arg126Pro	p.R126P	ENST00000359651		126	cGa/cCa	2/8	0.328290441892576	6	FACETS	1	0.978	1	0.608	0.555	0.663	CLONAL	2	FALSE	2	0.328290441892576	6		871	564	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804367	46804367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1187061907	NA	P-0044470-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	70	609	0	ENST00000290295.7:c.640C>T	p.Arg214Cys	p.R214C	ENST00000290295	NM_006361.5	214	Cgt/Tgt	2/2	0.287664008538233	4	FACETS	0.95	0.836	1	0.95	0.836	1	CLONAL	2	FALSE	2	0.328290441892576	4		609	298	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492853	56492853	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044470-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	93	461	0	ENST00000407977.2:c.86del	p.Gly29AspfsTer22	p.G29Dfs*22	ENST00000407977		29	gGa/ga	2/10	0.287664008538233	4	FACETS	0.892	0.798	0.991	0.892	0.798	0.991	CLONAL	2	FALSE	2	0.328290441892576	4		461	422	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633382	8633382	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044470-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	44	513	0	ENST00000356435.5:c.287A>T	p.Tyr96Phe	p.Y96F	ENST00000356435		96	tAt/tTt	3/35	0.26236888970585	0	FACETS	0.655	0.552	0.766			1	SUBCLONAL	1	FALSE	0	0.328290441892576	0		513	275	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	109	401	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.290853544725888	3	FACETS	0.908	0.82	1	0.908	0.82	1	CLONAL	2	TRUE	1	0.297735538399888	3		401	463	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577560	7577560	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520002	NA	P-0044478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	170	662	0	ENST00000269305.4:c.721T>C	p.Ser241Pro	p.S241P	ENST00000269305	NM_001126112.2	241	Tcc/Ccc	7/11	0.297735538399888	2	FACETS	0.979	0.906	1	0.979	0.906	1	CLONAL	2	TRUE	0	0.297735538399888	2		662	583	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032156	26032156	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	62	482	0	ENST00000244661.2:c.133G>T	p.Gly45Cys	p.G45C	ENST00000244661	NM_003537.3	45	Ggc/Tgc	1/1	0.145873050667474	5	FACETS	1	0.919	1	0.363	0.314	0.417	INDETERMINATE	1	TRUE	2	0.297735538399888	5		482	553	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444548	49444548	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	186	911	0	ENST00000301067.7:c.2823del	p.Ile942SerfsTer16	p.I942Sfs*16	ENST00000301067	NM_003482.3	941	ccC/cc	11/54	0.290853544725888	3	FACETS	0.853	0.789	0.92	0.853	0.789	0.92	CLONAL	2	TRUE	1	0.297735538399888	3		911	841	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	102	381	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.184463247859398	0	FACETS	0.453	0.409	0.498			1	INDETERMINATE	1	FALSE	0	0.575610747913282	0		381	332	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624293	89624293	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs876661244	NA	P-0044483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	147	579	0	ENST00000371953.3:c.67T>G	p.Leu23Val	p.L23V	ENST00000371953	NM_000314.4	23	Tta/Gta	1/9	0.135900042312729	4	FACETS	0.806	0.741	0.874	0.806	0.741	0.874	INDETERMINATE	2	FALSE	2	0.575610747913282	4		579	499	SUCCESS
APC	324	MSKCC	GRCh37	5	112154935	112154935	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	217	734	0	ENST00000257430.4:c.1206del	p.Glu403LysfsTer51	p.E403Kfs*51	ENST00000257430	NM_000038.5	402	cgT/cg	10/16	0.496145735097597	3	FACETS	0.836	0.791	0.881	0.836	0.791	0.881	CLONAL	3	FALSE	0	0.575610747913282	3		734	387	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920413	114920413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767830105	NA	P-0044483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	278	597	1	ENST00000543371.1:c.1354G>A	p.Gly452Arg	p.G452R	ENST00000543371	NM_001198531.1	452	Ggg/Agg	13/14	0.575610747913282	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	FALSE	0	0.575610747913282	2		598	434	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690835	89690835	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs876661177	NA	P-0044483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	89	286	0	ENST00000371953.3:c.242T>G	p.Phe81Cys	p.F81C	ENST00000371953	NM_000314.4	81	tTt/tGt	4/9	0.135900042312729	4	FACETS	0.846	0.759	0.936	0.846	0.759	0.936	INDETERMINATE	2	FALSE	2	0.575610747913282	4		286	288	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577557	7577557	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519982	NA	P-0044483-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	259	751	0	ENST00000269305.4:c.724T>A	p.Cys242Ser	p.C242S	ENST00000269305	NM_001126112.2	242	Tgc/Agc	7/11	0.483549772666656	3	FACETS	0.929	0.886	0.97	0.929	0.886	0.97	CLONAL	3	FALSE	0	0.575610747913282	3		751	416	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0044492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	245	372	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.377778799546989	3	FACETS	0.914	0.865	0.964	0.914	0.865	0.964	CLONAL	3	TRUE	0	0.444699720547816	3		372	491	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0044492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	221	484	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.437273779368088	2	FACETS	0.87	0.816	0.925	0.87	0.816	0.925	CLONAL	2	TRUE	0	0.444699720547816	2		484	571	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457389	67457389	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	242	1027	0	ENST00000327367.4:c.363C>A	p.Cys121Ter	p.C121*	ENST00000327367	NM_005902.3	121	tgC/tgA	2/9	1	2	FACETS	0.919	0.858	0.983	0.919	0.858	0.983	CLONAL	1	TRUE	1	0.444699720547816	2		1027	1184	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67116155	67116155	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	183	617	0	ENST00000412916.2:c.439C>T	p.Arg147Trp	p.R147W	ENST00000412916		147	Cgg/Tgg	5/6	1	2	FACETS	0.968	0.895	1	0.968	0.895	1	CLONAL	1	TRUE	1	0.444699720547816	2		617	850	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0044492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	258	851	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	0.444699720547816	1	FACETS	0.972	0.912	1	0.972	0.912	1	CLONAL	1	TRUE	0	0.444699720547816	1		851	928	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246167	41246167	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs62625300	NA	P-0044492-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	195	438	0	ENST00000357654.3:c.1381T>C	p.Phe461Leu	p.F461L	ENST00000357654	NM_007294.3	461	Ttt/Ctt	10/23	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.444699720547816	2		438	877	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226576395	226576395	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758314341	NA	P-0044530-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	11	629	1	ENST00000366794.5:c.679G>A	p.Glu227Lys	p.E227K	ENST00000366794	NM_001618.3	227	Gaa/Aaa	5/23	0.848022554741	3	FACETS	0.204	0.141	0.282	0.102	0.07	0.141	SUBCLONAL	1	TRUE	1	0.848022554741	3		630	181	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419049	419049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044530-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	10	603	0	ENST00000399788.2:c.3298G>A	p.Glu1100Lys	p.E1100K	ENST00000399788	NM_001042603.1	1100	Gaa/Aaa	22/28	0.750100312935878	4	FACETS	0.245	0.166	0.344			1	SUBCLONAL	1	TRUE	NA	0.848022554741	4		603	178	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576879	7576880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGGTTTCTTCTTT	novel	NA	P-0044530-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	181	1007	0	ENST00000269305.4:c.954_966dup	p.Leu323LysfsTer18	p.L323Kfs*18	ENST00000269305	NM_001126112.2	322	-/AAAGAAGAAACCA	9/11	0.284771843804324	5	FACETS	0.959	0.902	1			1	INDETERMINATE	3	TRUE	NA	0.848022554741	5		1007	337	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966334	25966334	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044530-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	45	684	0	ENST00000435504.4:c.2872C>G	p.Gln958Glu	p.Q958E	ENST00000435504		958	Caa/Gaa	13/13	0.742802321888703	4	FACETS	1	0.872	1	0.342	0.291	0.397	CLONAL	1	TRUE	1	0.848022554741	4		684	191	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271316	38271323	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GGTACTCC	GGTACTCC	-	novel	NA	P-0044530-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	94	1055	0	ENST00000425967.3:c.2386-1_2392del		p.X796_splice	ENST00000425967	NM_001174067.1	796		19/19	0.577668562819735	3	FACETS	0.829	0.743	0.918			1	CLONAL	1	TRUE	NA	0.848022554741	3		1055	381	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0044533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	488	562	0	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	0.781671771200498	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.781671771200498	3		562	834	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578528	7578528	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	297	605	0	ENST00000269305.4:c.402T>A	p.Phe134Leu	p.F134L	ENST00000269305	NM_001126112.2	134	ttT/ttA	5/11	0.781671771200498	3	FACETS	0.984	0.927	1	0.492	0.463	0.521	CLONAL	1	TRUE	1	0.781671771200498	3		605	1074	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14380349	14380349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	253	237	0	ENST00000256196.4:c.68G>T	p.Gly23Val	p.G23V	ENST00000256196		23	gGc/gTc	1/6	0.347187451437131	4	FACETS	1	0.979	1	1	0.979	1	INDETERMINATE	2	TRUE	2	0.781671771200498	4		237	538	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645681	12645681	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397516830	NA	P-0044533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	214	245	0	ENST00000251849.4:c.788T>C	p.Val263Ala	p.V263A	ENST00000251849	NM_002880.3	263	gTc/gCc	7/17	0.140638990531785	5	FACETS	0.996	0.941	1			1	INDETERMINATE	3	TRUE	NA	0.781671771200498	5		245	398	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058955	42058955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	88	301	0	ENST00000219905.7:c.8675G>A	p.Gly2892Glu	p.G2892E	ENST00000219905	NM_001164273.1	2892	gGg/gAg	24/24	0.687756049030419	3	FACETS	0.751	0.669	0.837	0.375	0.334	0.419	SUBCLONAL	1	TRUE	1	0.781671771200498	3		301	417	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199632	16199632	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0044533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	285	318	0	ENST00000375759.3:c.404+1G>A		p.X135_splice	ENST00000375759	NM_015001.2	135			0.455565855188858	3	FACETS	0.88	0.836	0.925	0.88	0.836	0.925	INDETERMINATE	2	TRUE	1	0.781671771200498	3		318	576	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279587	123279588	+	missense_variant	Missense_Mutation	DNP	CT	CT	AA	novel	NA	P-0044533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	126	468	0	ENST00000358487.5:c.844_845delinsTT	p.Ser282Phe	p.S282F	ENST00000358487	NM_000141.4	282	AGt/TTt	7/18	0.781671771200498	3	FACETS	0.594	0.538	0.653	0.297	0.269	0.327	SUBCLONAL	1	TRUE	1	0.781671771200498	3		468	755	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148547	119148548	+	missense_variant	Missense_Mutation	DNP	TG	TG	AC	novel	NA	P-0044533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	352	260	1	ENST00000264033.4:c.1088_1089delinsAC	p.Val363Asp	p.V363D	ENST00000264033	NM_005188.3	363	gTG/gAC	7/16	0.781671771200498	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.781671771200498	3		261	400	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459432	40459433	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0044533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	113	461	1	ENST00000345506.4:c.1693_1694delinsTT	p.Gly565Phe	p.G565F	ENST00000345506	NM_003152.3	565	GGc/TTc	15/20	0.781671771200498	3	FACETS	0.526	0.473	0.581	0.263	0.236	0.291	SUBCLONAL	1	TRUE	1	0.781671771200498	3		462	765	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389197	31389197	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1666	137	484	0	ENST00000328111.2:c.2110G>T	p.Val704Phe	p.V704F	ENST00000328111	NM_006892.3	704	Gtt/Ttt	19/23	0.781671771200498	6	FACETS	0.498	0.451	0.548	0.1	0.09	0.11	SUBCLONAL	1	TRUE	1	0.781671771200498	6		484	1803	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980568	70980568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	196	461	1	ENST00000276594.2:c.809G>A	p.Cys270Tyr	p.C270Y	ENST00000276594	NM_024504.3	270	tGc/tAc	4/8	0.687756049030419	3	FACETS	0.895	0.831	0.962	0.448	0.415	0.481	CLONAL	1	TRUE	1	0.781671771200498	3		462	779	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976638	90976638	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044533-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	82	252	1	ENST00000265433.3:c.994G>T	p.Gly332Ter	p.G332*	ENST00000265433	NM_002485.4	332	Gga/Tga	8/16	0.687756049030419	3	FACETS	0.813	0.722	0.909	0.406	0.361	0.455	CLONAL	1	TRUE	1	0.781671771200498	3		253	359	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578219	7578220	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	303	545	0	ENST00000269305.4:c.629dup	p.Asn210LysfsTer6	p.N210Kfs*6	ENST00000269305	NM_001126112.2	210	aac/aaAc	6/11	0.499547222682929	2	FACETS	1	0.994	1	0.713	0.677	0.748	CLONAL	1	TRUE	0	0.657132116321018	2		545	647	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990703	7990703	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	167	574	0	ENST00000319144.4:c.58G>T	p.Asp20Tyr	p.D20Y	ENST00000319144	NM_001139.2	20	Gac/Tac	1/15	0.499547222682929	2	FACETS	0.698	0.643	0.756	0.349	0.321	0.378	SUBCLONAL	1	TRUE	0	0.657132116321018	2		574	728	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267785	7267785	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	118	515	0	ENST00000302850.5:c.223G>C	p.Asp75His	p.D75H	ENST00000302850	NM_000208.2	75	Gac/Cac	2/22	0.516410323615447	3	FACETS	0.67	0.605	0.739	0.335	0.302	0.37	SUBCLONAL	1	TRUE	1	0.657132116321018	3		515	712	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447106	187447106	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	129	536	0	ENST00000232014.4:c.1087C>A	p.Pro363Thr	p.P363T	ENST00000232014	NM_001130845.1	363	Cca/Aca	5/10	0.203532622320881	3	FACETS	0.781	0.709	0.856	0.39	0.354	0.428	INDETERMINATE	1	TRUE	1	0.657132116321018	3		536	668	SUCCESS
APC	324	MSKCC	GRCh37	5	112174182	112174182	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0044543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	50	255	0	ENST00000257430.4:c.2891T>A	p.Leu964Ter	p.L964*	ENST00000257430	NM_000038.5	964	tTa/tAa	16/16	0.159345374322519	3	FACETS	1	0.958	1	0.435	0.376	0.496	INDETERMINATE	1	TRUE	0	0.657132116321018	3		255	155	SUCCESS
APC	324	MSKCC	GRCh37	5	112176021	112176021	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044543-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	29	228	1	ENST00000257430.4:c.4731del	p.Glu1577AspfsTer73	p.E1577Dfs*73	ENST00000257430	NM_000038.5	1577	gAa/ga	16/16	0.159345374322519	3	FACETS	0.674	0.546	0.816	0.225	0.182	0.272	INDETERMINATE	1	TRUE	0	0.657132116321018	3		229	174	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263979	16263988	+	frameshift_variant	Frame_Shift_Del	DEL	CAGACTGCCC	CAGACTGCCC	-	novel	NA	P-0044545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	211	615	1	ENST00000375759.3:c.10350_10359del	p.Thr3451AsnfsTer37	p.T3451Nfs*37	ENST00000375759	NM_015001.2	3450	CAGACTGCCCca/ca	12/15	1	2	FACETS	0.922	0.862	0.983	0.922	0.862	0.983	CLONAL	1	TRUE	1	0.765319259072366	2		616	598	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782329	NA	P-0044546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	67	419	0	ENST00000269305.4:c.746G>C	p.Arg249Thr	p.R249T	ENST00000269305	NM_001126112.2	249	aGg/aCg	7/11	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.2	2		419	604	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11204749	11204749	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	43	345	0	ENST00000361445.4:c.4828G>C	p.Glu1610Gln	p.E1610Q	ENST00000361445	NM_004958.3	1610	Gag/Cag	34/58	1	2	FACETS	0.896	0.75	1	0.896	0.75	1	CLONAL	1	TRUE	1	0.2	2		345	480	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245495	153245495	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	44	365	0	ENST00000281708.4:c.1696T>G	p.Trp566Gly	p.W566G	ENST00000281708	NM_033632.3	566	Tgg/Ggg	11/12	1	2	FACETS	0.9	0.755	1	0.9	0.755	1	CLONAL	1	TRUE	1	0.2	2		365	489	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	25	401	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.244982056794621	3	FACETS	0.449	0.355	0.558	0.225	0.177	0.279	INDETERMINATE	1	TRUE	1	0.491485692180824	3		401	282	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0044570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	22	332	0	ENST00000288602.6:c.1397G>T	p.Gly466Val	p.G466V	ENST00000288602	NM_004333.4	466	gGa/gTa	11/18	0.491485692180824	1	FACETS	0.339	0.264	0.426	0.339	0.264	0.426	SUBCLONAL	1	TRUE	0	0.491485692180824	1		332	199	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612638	228612638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146830002	NA	P-0044570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	168	464	0	ENST00000366696.1:c.389G>A	p.Arg130His	p.R130H	ENST00000366696	NM_003493.2	130	cGt/cAt	1/1	0.287219311803296	3	FACETS	0.823	0.755	0.893	0.411	0.377	0.447	INDETERMINATE	1	TRUE	1	0.491485692180824	3		464	1035	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370318	40370319	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	272	662	0	ENST00000293328.3:c.1019dup	p.Val341GlyfsTer36	p.V341Gfs*36	ENST00000293328	NM_012448.3	340	cag/caAg	9/19	0.101309156062243	3	FACETS	1	0.986	1	0.585	0.548	0.622	INDETERMINATE	1	TRUE	1	0.491485692180824	3		662	1179	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042778	42042784	+	stop_gained	Nonsense_Mutation	ONP	GACTACC	GACTACC	AACTAAA	novel	NA	P-0044570-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	62	342	0	ENST00000219905.7:c.6973_6979delinsAACTAAA	p.Asp2325_Gln2327delinsAsnTer	p.D2325_Q2327delinsN*	ENST00000219905	NM_001164273.1	2325	GACTACCag/AACTAAAag	17/24	0.491485692180824	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.491485692180824	1		342	175	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0044612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	293	337	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.985	0.933	1	1	0.996	1	CLONAL	2	TRUE	1	0.420093535885292	2		337	708	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221743	55221743	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519829	NA	P-0044612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	282	512	0	ENST00000275493.2:c.787A>C	p.Thr263Pro	p.T263P	ENST00000275493	NM_005228.3	263	Acc/Ccc	7/28	0.391035833033274	4	FACETS	0.99	0.932	1	0.99	0.932	1	CLONAL	2	TRUE	2	0.420093535885292	4		512	963	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272308	38272308	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs869320694	NA	P-0044612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	78	569	0	ENST00000425967.3:c.2059A>G	p.Lys687Glu	p.K687E	ENST00000425967	NM_001174067.1	687	Aag/Gag	15/19	0.420093535885292	1	FACETS	0.494	0.434	0.558	0.494	0.434	0.558	SUBCLONAL	1	TRUE	0	0.420093535885292	1		569	594	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295274	1295274	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0044612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	327	368	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.977	0.928	1	1	0.996	1	CLONAL	2	TRUE	1	0.420093535885292	2		368	797	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473767	67473767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	179	543	0	ENST00000327367.4:c.847G>A	p.Val283Met	p.V283M	ENST00000327367	NM_005902.3	283	Gtg/Atg	6/9	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.420093535885292	2		543	827	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964956	55964956	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1317482906	NA	P-0044612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	84	331	0	ENST00000263923.4:c.2281A>G	p.Thr761Ala	p.T761A	ENST00000263923	NM_002253.2	761	Acg/Gcg	16/30	1	2	FACETS	0.885	0.785	0.991	0.885	0.785	0.991	CLONAL	1	TRUE	1	0.420093535885292	2		331	452	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975412	13975412	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	300	394	0	ENST00000405192.2:c.475C>G	p.Pro159Ala	p.P159A	ENST00000405192	NM_001163147.1	159	Ccg/Gcg	7/12	0.391035833033274	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.420093535885292	4		394	962	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410987	63410987	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	72	590	0	ENST00000330258.3:c.2180T>A	p.Met727Lys	p.M727K	ENST00000330258	NM_152424.3	727	aTg/aAg	2/2	0.420093535885292	3	FACETS	0.451	0.393	0.514	0.226	0.196	0.257	SUBCLONAL	1	TRUE	1	0.420093535885292	3		590	919	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210173	123210190	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTCTCCAGATGGTCAGC	TTTCTCCAGATGGTCAGC	GA	novel	NA	P-0044612-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	68	419	1	ENST00000218089.9:c.2534-9_2542delinsGA		p.X845_splice	ENST00000218089	NM_001042749.1	845		26/35	0.420093535885292	3	FACETS	0.609	0.53	0.695	0.305	0.265	0.348	SUBCLONAL	1	TRUE	1	0.420093535885292	3		420	643	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0044613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	408	564	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.687816243151372	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.687816243151372	2		564	552	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	149	497	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	1	2	FACETS	0.553	0.506	0.603	0.553	0.506	0.603	SUBCLONAL	1	TRUE	1	0.687816243151372	2		497	783	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266125	41266125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913413	NA	P-0044613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	97	270	0	ENST00000349496.5:c.122C>T	p.Thr41Ile	p.T41I	ENST00000349496	NM_001904.3	41	aCc/aTc	3/15	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.687816243151372	2		270	256	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654642	67654642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	49	373	0	ENST00000264010.4:c.1129C>T	p.Arg377Cys	p.R377C	ENST00000264010	NM_006565.3	377	Cgt/Tgt	6/12	0.687816243151372	1	FACETS	0.396	0.339	0.458	0.396	0.339	0.458	SUBCLONAL	1	TRUE	0	0.687816243151372	1		373	236	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840093	27840093	+	start_lost	Translation_Start_Site	SNP	T	T	C	rs769800748	NA	P-0044613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	69	217	0	ENST00000328488.2:c.1A>G	p.Met1?	p.M1?	ENST00000328488	NM_003533.2	1	Atg/Gtg	1/1	0.117615788903346	4	FACETS	1	0.976	1	0.739	0.653	0.829	INDETERMINATE	1	TRUE	2	0.687816243151372	4		217	229	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123874011	123874013	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs780061449	NA	P-0044613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	10	38	0	ENST00000330479.4:c.62_64del	p.Ala21del	p.A21del	ENST00000330479	NM_020382.3	14	gaGGCg/gag	2/9	1	2	FACETS	0.233	0.158	0.325	0.233	0.158	0.325	SUBCLONAL	1	TRUE	1	0.687816243151372	2		38	125	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522712	67522712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs910474484	NA	P-0044613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	38	193	0	ENST00000274335.5:c.209C>T	p.Pro70Leu	p.P70L	ENST00000274335		70	cCg/cTg	1/15	1	2	FACETS	0.524	0.437	0.619	0.524	0.437	0.619	SUBCLONAL	1	TRUE	1	0.687816243151372	2		193	211	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828142	3828142	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	109	348	0	ENST00000262367.5:c.1983A>G	p.Ile661Met	p.I661M	ENST00000262367	NM_004380.2	661	atA/atG	10/31	1	2	FACETS	0.929	0.844	1	0.929	0.844	1	CLONAL	1	TRUE	1	0.687816243151372	2		348	341	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348022	89348022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147690079	NA	P-0044613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	50	741	2	ENST00000301030.4:c.4928C>T	p.Pro1643Leu	p.P1643L	ENST00000301030	NM_001256183.1	1643	cCg/cTg	9/13	0.687816243151372	1	FACETS	0.132	0.111	0.155	0.132	0.111	0.155	SUBCLONAL	1	TRUE	0	0.687816243151372	1		743	722	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591125	67591133	+	inframe_deletion	In_Frame_Del	DEL	TGAGAAAGA	TGAGAAAGA	-	novel	NA	P-0044613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	42	251	0	ENST00000274335.5:c.1718_1726del	p.Leu573_Thr576delinsPro	p.L573_T576delinsP	ENST00000274335		573	cTGAGAAAGAcg/ccg	12/15	1	2	FACETS	0.842	0.717	0.975	0.842	0.717	0.975	CLONAL	1	TRUE	1	0.687816243151372	2		251	145	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942807	44942807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	21	414	1	ENST00000377967.4:c.3387G>A	p.Met1129Ile	p.M1129I	ENST00000377967	NM_021140.2	1129	atG/atA	23/29	1	2	FACETS	0.202	0.155	0.257	0.202	0.155	0.257	SUBCLONAL	1	TRUE	1	0.687816243151372	2		415	302	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0044640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	91	753	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.349001238080179	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	0	0.375676714385726	1		753	386	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994850	73994850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141119771	NA	P-0044640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	11	116	0	ENST00000318443.5:c.334G>A	p.Val112Met	p.V112M	ENST00000318443	NM_001024736.1	112	Gtg/Atg	3/10	1	2	FACETS	1	0.76	1	1	0.76	1	CLONAL	1	TRUE	1	0.375676714385726	2		116	54	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033959	49033959	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	76	437	0	ENST00000267163.4:c.2096A>C	p.His699Pro	p.H699P	ENST00000267163	NM_000321.2	699	cAt/cCt	20/27	0.295830525458024	2	FACETS	1	0.973	1	0.681	0.603	0.763	CLONAL	1	TRUE	0	0.375676714385726	2		437	297	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654511	29654592	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCCAGGTTGGTTCTACTGCTGTCCAAGTAACTTCAGCAGAGCGAACAAAAGTCCTAGGGCAATCAGTCTTTCTAAATGACA	TTCCAGGTTGGTTCTACTGCTGTCCAAGTAACTTCAGCAGAGCGAACAAAAGTCCTAGGGCAATCAGTCTTTCTAAATGACA	-	novel	NA	P-0044640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	31	222	0	ENST00000356175.3:c.5206-4_5283del		p.X1736_splice	ENST00000356175	NM_000267.3	1736		37/57	0.349001238080179	1	FACETS	0.798	0.653	0.958	0.798	0.653	0.958	CLONAL	1	TRUE	0	0.375676714385726	1		222	168	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131099	202131355	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTAGTAGTTGCAGTAGCCTTTGATGAACAAGCCAGCAAATGGTACTTTTCTTCCTTATCTGAACATACCATTTATTTTGACTTAGATTATATTCTCCTGCCTTTTAAAAAGATGGACTTCAGCAGAAATCTTTATGATATTGGGGAACAACTGGACAGTGAAGATCTGGCCTCCCTCAAGTTCCTGAGCCTGGACTACATTCCGCAAAGGAAGCAAGAACCCATCAAGGATGCCTTGATGTTATTCCAGAGACTCCA	CTAGTAGTTGCAGTAGCCTTTGATGAACAAGCCAGCAAATGGTACTTTTCTTCCTTATCTGAACATACCATTTATTTTGACTTAGATTATATTCTCCTGCCTTTTAAAAAGATGGACTTCAGCAGAAATCTTTATGATATTGGGGAACAACTGGACAGTGAAGATCTGGCCTCCCTCAAGTTCCTGAGCCTGGACTACATTCCGCAAAGGAAGCAAGAACCCATCAAGGATGCCTTGATGTTATTCCAGAGACTCCA	-	novel	NA	P-0044640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	34	99	0	ENST00000358485.4:c.152-85_323del		p.X51_splice	ENST00000358485	NM_001080125.1	51		2/9	1	2	FACETS	1	0.849	1	1	0.967	1	CLONAL	2	TRUE	1	0.375676714385726	2		99	90	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138383922	138383922	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	27	469	1	ENST00000289153.2:c.2628C>A	p.Phe876Leu	p.F876L	ENST00000289153	NM_006219.2	876	ttC/ttA	18/22	0.269205373298609	3	FACETS	0.428	0.34	0.528	0.214	0.17	0.264	SUBCLONAL	1	TRUE	1	0.375676714385726	3		470	399	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056320	180056320	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0044640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	27	843	0	ENST00000261937.6:c.924T>G	p.Tyr308Ter	p.Y308*	ENST00000261937	NM_182925.4	308	taT/taG	7/30	1	2	FACETS	0.315	0.25	0.39	0.315	0.25	0.39	SUBCLONAL	1	TRUE	1	0.375676714385726	2		843	456	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0044650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	45	269	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.234986149327231	2		269	372	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0044735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	29	512	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.109802874804204	3	FACETS	0.603	0.483	0.741	0.302	0.241	0.371	INDETERMINATE	1	TRUE	1	0.19	3		512	554	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0044735-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	43	564	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.967	0.81	1	0.967	0.81	1	CLONAL	1	TRUE	1	0.19	2		564	468	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0044740-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	302	588	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.271585581684239	3	FACETS	0.845	0.797	0.894	0.563	0.531	0.596	CLONAL	2	TRUE	0	0.430378457247584	3		588	1009	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0044743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	196	510	0	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	0.345775714242983	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.345775714242983	1		510	901	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120785275	120785275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778099314	NA	P-0044743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	176	539	1	ENST00000257552.2:c.833C>T	p.Ala278Val	p.A278V	ENST00000257552	NM_002442.3	278	gCg/gTg	12/15	1	2	FACETS	0.877	0.806	0.951	0.877	0.806	0.951	CLONAL	1	TRUE	1	0.345775714242983	2		540	1161	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058462	42058462	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	48	348	0	ENST00000219905.7:c.8182C>A	p.Pro2728Thr	p.P2728T	ENST00000219905	NM_001164273.1	2728	Cca/Aca	24/24	1	2	FACETS	0.485	0.409	0.568	0.485	0.409	0.568	SUBCLONAL	1	TRUE	1	0.345775714242983	2		348	573	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602852	10602852	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1471	257	760	0	ENST00000171111.5:c.726G>C	p.Glu242Asp	p.E242D	ENST00000171111	NM_203500.1	242	gaG/gaC	3/6	1	2	FACETS	0.86	0.803	0.92	0.86	0.803	0.92	CLONAL	1	TRUE	1	0.345775714242983	2		760	1728	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147720	61147720	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	55	226	0	ENST00000295025.8:c.1030G>C	p.Glu344Gln	p.E344Q	ENST00000295025	NM_002908.2	344	Gag/Cag	10/11	0.1560954874073	2	FACETS	0.886	0.761	1	0.443	0.38	0.511	INDETERMINATE	1	TRUE	0	0.345775714242983	2		226	359	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056452	26056453	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGCA	novel	NA	P-0044743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	54	246	0	ENST00000343677.2:c.201_204dup	p.Ala69CysfsTer5	p.A69Cfs*5	ENST00000343677	NM_005319.3	68	-/TGCC	1/1	0.224838344690406	3	FACETS	0.682	0.583	0.791	0.341	0.291	0.396	SUBCLONAL	1	TRUE	1	0.345775714242983	3		246	537	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680500	30680500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141963390	NA	P-0044743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	88	487	0	ENST00000376406.3:c.1219G>A	p.Glu407Lys	p.E407K	ENST00000376406	NM_014641.2	407	Gag/Aag	5/15	0.224838344690406	3	FACETS	0.551	0.486	0.62	0.275	0.243	0.31	SUBCLONAL	1	TRUE	1	0.345775714242983	3		487	1084	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772982	135772983	+	stop_gained	Nonsense_Mutation	DNP	TC	TC	AA	novel	NA	P-0044743-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	42	210	0	ENST00000298552.3:c.2640_2641delinsTT	p.Met880_Lys881delinsIleTer	p.M880_K881delinsI*	ENST00000298552	NM_001162426.1	880	atGAaa/atTTaa	21/23	0.345775714242983	1	FACETS	0.613	0.513	0.722	0.613	0.513	0.722	SUBCLONAL	1	TRUE	0	0.345775714242983	1		210	328	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0044798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	23	738	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.973	0.769	1	0.973	0.769	1	CLONAL	1	TRUE	1	0.381427912355761	2		738	124	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14016029	14016029	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	46	279	0	ENST00000311895.7:c.349G>C	p.Asp117His	p.D117H	ENST00000311895	NM_005236.2	117	Gac/Cac	2/11	0.381427912355761	3	FACETS	0.845	0.723	0.974	0.845	0.723	0.974	CLONAL	2	TRUE	1	0.381427912355761	3		279	170	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830363	72830363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	42	408	0	ENST00000268489.5:c.6218C>T	p.Ser2073Leu	p.S2073L	ENST00000268489	NM_006885.3	2073	tCa/tTa	9/10	0.381427912355761	1	FACETS	0.785	0.661	0.92	0.785	0.661	0.92	CLONAL	1	TRUE	0	0.381427912355761	1		408	227	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972632	76972632	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs122445108	NA	P-0044798-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	38	429	0	ENST00000373344.5:c.109C>T	p.Arg37Ter	p.R37*	ENST00000373344	NM_000489.3	37	Cga/Tga	2/35	0.262528506244024	1	FACETS	0.75	0.626	0.886	0.75	0.626	0.886	SUBCLONAL	1	TRUE	0	0.381427912355761	1		429	215	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619279	23619279	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587776527	NA	P-0044837-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	117	540	1	ENST00000261584.4:c.3256C>T	p.Arg1086Ter	p.R1086*	ENST00000261584	NM_024675.3	1086	Cga/Tga	12/13	0.384220373985409	2	FACETS	0.833	0.752	0.918	0.416	0.376	0.459	CLONAL	1	TRUE	0	0.410835434999924	2		541	684	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0044841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	34	753	1	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	1	2	FACETS	0.682	0.555	0.827	0.682	0.555	0.827	SUBCLONAL	1	TRUE	1	0.1	2		754	997	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0044841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	50	888	1	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	1	2	FACETS	0.85	0.718	0.996	0.85	0.718	0.996	CLONAL	1	TRUE	1	0.1	2		889	1177	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177068	56177068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	10	284	0	ENST00000399503.3:c.2338G>A	p.Asp780Asn	p.D780N	ENST00000399503	NM_005921.1	780	Gat/Aat	13/20	1	2	FACETS	1	0.758	1	1	0.758	1	CLONAL	1	TRUE	1	0.1	2		284	174	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041585	47041585	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044841-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	33	395	0	ENST00000377604.3:c.1810C>T	p.Gln604Ter	p.Q604*	ENST00000377604	NM_001204468.1	604	Cag/Tag	17/24	1	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.1	1		395	471	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0044853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	14	217	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.602	0.438	0.799	0.602	0.438	0.799	SUBCLONAL	1	TRUE	1	0.3273924640946	2		217	142	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938418	44938420	+	inframe_deletion	In_Frame_Del	DEL	TGG	TGG	-	novel	NA	P-0044853-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	15	372	0	ENST00000377967.4:c.2969_2971del	p.Val990del	p.V990del	ENST00000377967	NM_021140.2	989	tTGGtg/ttg	20/29	1	2	FACETS	0.71	0.524	0.93	0.71	0.524	0.93	CLONAL	1	TRUE	1	0.3273924640946	2		372	129	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0044880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	28	472	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		472	439	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061845	38061862	+	inframe_deletion	In_Frame_Del	DEL	CATGTAGGTGTTCATGGA	CATGTAGGTGTTCATGGA	-	novel	NA	P-0044880-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	42	678	1	ENST00000250448.2:c.127_144del	p.Ser43_Met48del	p.S43_M48del	ENST00000250448	NM_004496.3	43	TCCATGAACACCTACATG/-	2/2	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		679	545	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	47	470	0	ENST00000347630.2:c.305T>C	p.Phe102Ser	p.F102S	ENST00000347630	NM_001007230.1	102	tTc/tCc	5/11	0.149260843488547	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	FALSE	0	0.241612653965968	1		470	275	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779205	3779205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs557611780	NA	P-0044899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	22	587	0	ENST00000262367.5:c.5843C>T	p.Pro1948Leu	p.P1948L	ENST00000262367	NM_004380.2	1948	cCg/cTg	31/31	0.149260843488547	1	FACETS	0.805	0.627	1	0.805	0.627	1	CLONAL	1	FALSE	0	0.241612653965968	1		587	199	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112940010	112940024	+	inframe_deletion	In_Frame_Del	DEL	TGGAGATCAGAGCCC	TGGAGATCAGAGCCC	-	novel	NA	P-0044899-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	83	712	0	ENST00000351677.2:c.1663_1677del	p.Gly555_Pro559del	p.G555_P559del	ENST00000351677	NM_002834.3	554	agTGGAGATCAGAGCCCt/agt	14/16	0.150438959638005	3	FACETS	0.784	0.694	0.88	0.784	0.694	0.88	SUBCLONAL	2	FALSE	1	0.241612653965968	3		712	491	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0044900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	46	426	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		426	573	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0044900-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	56	449	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.177274686770387	1	FACETS		NA	1			1	NA	NA	FALSE	0	NA	1		449	465	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412043	116412043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044904-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	237	575	0	ENST00000397752.3:c.3028G>A	p.Asp1010Asn	p.D1010N	ENST00000397752	NM_000245.2	1010	Gat/Aat	14/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		575	922	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0044916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	214	712	1	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.458841362214181	1	FACETS	0.706	0.656	0.758	0.706	0.656	0.758	SUBCLONAL	1	TRUE	0	0.474887727753045	1		713	973	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934578	NA	P-0044916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	174	637	0	ENST00000269305.4:c.524G>T	p.Arg175Leu	p.R175L	ENST00000269305	NM_001126112.2	175	cGc/cTc	5/11	0.458841362214181	1	FACETS	0.715	0.659	0.772	0.715	0.659	0.772	SUBCLONAL	1	TRUE	0	0.474887727753045	1		637	782	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346338	73346338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	101	264	0	ENST00000377767.4:c.1462G>A	p.Asp488Asn	p.D488N	ENST00000377767	NM_014953.3	488	Gat/Aat	10/21	0.26890707617334	4	FACETS	1	0.982	1	0.747	0.672	0.825	INDETERMINATE	1	TRUE	2	0.474887727753045	4		264	420	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665015	138665015	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	54	152	0	ENST00000330315.3:c.550G>A	p.Asp184Asn	p.D184N	ENST00000330315	NM_023067.3	184	Gac/Aac	1/1	0.372650244848521	2	FACETS	0.818	0.704	0.94	0.409	0.352	0.47	CLONAL	1	TRUE	0	0.474887727753045	2		152	278	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815776	32815776	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	118	686	0	ENST00000354258.4:c.1840C>G	p.Leu614Val	p.L614V	ENST00000354258	NM_000593.5	614	Ctg/Gtg	8/11	0.331869294338754	3	FACETS	0.477	0.428	0.528	0.159	0.142	0.176	SUBCLONAL	1	TRUE	0	0.474887727753045	3		686	1290	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813029	76813029	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	37	224	0	ENST00000373344.5:c.6592C>T	p.His2198Tyr	p.H2198Y	ENST00000373344	NM_000489.3	2198	Cat/Tat	30/35	1	1	FACETS	0.455	0.377	0.541	0.455	0.377	0.541	SUBCLONAL	1	TRUE	0	0.474887727753045	1		224	261	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115272884	115272884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	58	463	0	ENST00000438362.2:c.1489G>A	p.Glu497Lys	p.E497K	ENST00000438362	NM_001242891.1	497	Gag/Aag	12/20	0.126401107393396	3	FACETS	0.404	0.346	0.467	0.135	0.115	0.156	INDETERMINATE	1	TRUE	0	0.474887727753045	3		463	748	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100450	8100450	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1547	191	775	0	ENST00000346208.3:c.424T>C	p.Ser142Pro	p.S142P	ENST00000346208		142	Tcg/Ccg	3/6	0.474887727753045	4	FACETS	0.683	0.629	0.739	0.228	0.209	0.247	SUBCLONAL	1	TRUE	1	0.474887727753045	4		775	1738	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742857	17742857	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	200	753	0	ENST00000250003.3:c.765C>G	p.Ile255Met	p.I255M	ENST00000250003	NM_002478.4	255	atC/atG	3/3	0.126401107393396	3	FACETS	0.901	0.834	0.971	0.3	0.278	0.324	INDETERMINATE	1	TRUE	0	0.474887727753045	3		753	1157	SUCCESS
ATM	472	MSKCC	GRCh37	11	108119829	108119829	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	37	175	0	ENST00000278616.4:c.1235G>C	p.Trp412Ser	p.W412S	ENST00000278616	NM_000051.3	412	tGg/tCg	9/63	0.137291990870522	3	FACETS	0.586	0.484	0.699	0.195	0.161	0.233	INDETERMINATE	1	TRUE	0	0.474887727753045	3		175	329	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362546	118362546	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	178	397	0	ENST00000534358.1:c.4907G>T	p.Arg1636Leu	p.R1636L	ENST00000534358	NM_005933.3	1636	cGa/cTa	15/36	0.137291990870522	3	FACETS	1	0.99	1	0.485	0.449	0.523	INDETERMINATE	1	TRUE	0	0.474887727753045	3		397	637	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29068953	29068953	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	41	267	0	ENST00000282397.4:c.28C>A	p.Leu10Met	p.L10M	ENST00000282397	NM_002019.4	10	Ctg/Atg	1/30	0.382357869255429	2	FACETS	0.372	0.31	0.441	0.186	0.155	0.221	SUBCLONAL	1	TRUE	0	0.474887727753045	2		267	464	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867272	68867272	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	137	490	0	ENST00000261769.5:c.2519C>G	p.Ser840Cys	p.S840C	ENST00000261769	NM_004360.3	840	tCc/tGc	16/16	1	2	FACETS	0.696	0.633	0.762	0.696	0.633	0.762	SUBCLONAL	1	TRUE	1	0.474887727753045	2		490	829	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858148	40858148	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0044916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	820	678	0	ENST00000428826.2:c.1716T>A	p.Cys572Ter	p.C572*	ENST00000428826		572	tgT/tgA	16/21	0.474887727753045	3	FACETS	0.966	0.939	0.993	0.966	0.939	0.993	CLONAL	3	TRUE	0	0.474887727753045	3		678	1475	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799528	72799528	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	222	552	0	ENST00000325599.8:c.1641G>C	p.Lys547Asn	p.K547N	ENST00000325599	NM_018130.2	547	aaG/aaC	11/11	0.372650244848521	2	FACETS	1	0.976	1	0.551	0.513	0.589	CLONAL	1	TRUE	0	0.474887727753045	2		552	849	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86658371	86658371	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	36	104	0	ENST00000274376.6:c.1336C>T	p.Gln446Ter	p.Q446*	ENST00000274376	NM_002890.2	446	Caa/Taa	10/25	NA	2	FACETS	0.936	0.78	1			1	INDETERMINATE	1	TRUE	NA	0.474887727753045	2		104	162	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670004	86670004	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0044916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	59	197	0	ENST00000274376.6:c.1801G>T	p.Glu601Ter	p.E601*	ENST00000274376	NM_002890.2	601	Gaa/Taa	14/25	NA	2	FACETS	0.82	0.711	0.937			1	INDETERMINATE	1	TRUE	NA	0.474887727753045	2		197	303	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467771	50467771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	380	524	0	ENST00000331340.3:c.1006G>A	p.Gly336Ser	p.G336S	ENST00000331340	NM_006060.4	336	Ggc/Agc	8/8	0.474887727753045	5	FACETS	0.97	0.92	1	0.646	0.613	0.681	CLONAL	2	TRUE	2	0.474887727753045	5		524	1413	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	235	401	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.398135871235181	5	FACETS	0.938	0.88	0.997	0.938	0.88	0.997	CLONAL	3	TRUE	2	0.398135871235181	5		401	670	SUCCESS
ATM	472	MSKCC	GRCh37	11	108213974	108213974	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	161	323	0	ENST00000278616.4:c.8294G>T	p.Gly2765Val	p.G2765V	ENST00000278616	NM_000051.3	2765	gGt/gTt	57/63	0.398135871235181	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.398135871235181	2		323	368	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038858	47038858	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1556777925	NA	P-0044925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	261	734	1	ENST00000377604.3:c.865C>T	p.Gln289Ter	p.Q289*	ENST00000377604	NM_001204468.1	289	Cag/Tag	9/24	NA	3	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.398135871235181	3		735	651	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282474	115282474	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	106	441	0	ENST00000438362.2:c.176A>T	p.His59Leu	p.H59L	ENST00000438362	NM_001242891.1	59	cAt/cTt	3/20	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.398135871235181	2		441	504	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426663	49426689	+	inframe_deletion	In_Frame_Del	DEL	TGTTGAAGCTGCTGCTGCTGTTGCTGC	TGTTGAAGCTGCTGCTGCTGTTGCTGC	-	rs774577879	NA	P-0044925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	36	418	0	ENST00000301067.7:c.11799_11825del	p.Gln3939_Gln3947del	p.Q3939_Q3947del	ENST00000301067	NM_003482.3	3933	caGCAGCAACAGCAGCAGCAGCTTCAACAa/caa	39/54	0.120254930696482	4	FACETS	0.515	0.423	0.618			1	INDETERMINATE	1	TRUE	NA	0.398135871235181	4		418	491	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566216	95566216	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	150	540	0	ENST00000393063.1:c.4107G>A	p.Met1369Ile	p.M1369I	ENST00000393063	NM_030621.3	1369	atG/atA	23/28	0.398135871235181	3	FACETS	1	0.971	1	0.57	0.521	0.621	CLONAL	1	TRUE	1	0.398135871235181	3		540	793	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420335	88420335	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	64	420	2	ENST00000360948.2:c.2351C>A	p.Thr784Asn	p.T784N	ENST00000360948	NM_001012338.2	784	aCc/aAc	19/19	1	2	FACETS	0.881	0.767	1	0.881	0.767	1	CLONAL	1	TRUE	1	0.398135871235181	2		422	365	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820622	3820622	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	181	754	0	ENST00000262367.5:c.2829G>T	p.Gln943His	p.Q943H	ENST00000262367	NM_004380.2	943	caG/caT	14/31	0.398135871235181	3	FACETS	1	0.983	1	0.617	0.569	0.666	CLONAL	1	TRUE	1	0.398135871235181	3		754	884	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207044	1207073	+	inframe_deletion	In_Frame_Del	DEL	GCTCATCGGCAAGTACCTGATGGGGGACCT	GCTCATCGGCAAGTACCTGATGGGGGACCT	-	novel	NA	P-0044925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	405	725	0	ENST00000326873.7:c.135_164del	p.Ile46_Leu55del	p.I46_L55del	ENST00000326873	NM_000455.4	44	aaGCTCATCGGCAAGTACCTGATGGGGGACCTg/aag	1/10	0.398135871235181	1	FACETS	1	0.991	1	1	0.997	1	CLONAL	2	TRUE	0	0.398135871235181	1		725	736	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272816	18272816	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0044925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	430	626	0	ENST00000222254.8:c.856A>C	p.Lys286Gln	p.K286Q	ENST00000222254	NM_005027.3	286	Aag/Cag	7/16	0.398135871235181	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.398135871235181	3		626	797	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18974251	18974251	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	326	473	1	ENST00000262803.5:c.2605G>T	p.Gly869Cys	p.G869C	ENST00000262803	NM_002911.3	869	Ggc/Tgc	19/24	0.398135871235181	3	FACETS	0.875	0.837	0.912	1	0.992	1	CLONAL	4	TRUE	0	0.398135871235181	3		474	561	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082571	16082571	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1345499308	NA	P-0044925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	85	377	0	ENST00000281043.3:c.385G>C	p.Ala129Pro	p.A129P	ENST00000281043	NM_005378.4	129	Gcc/Ccc	2/3	0.398135871235181	3	FACETS	0.948	0.849	1	0.948	0.849	1	CLONAL	2	TRUE	1	0.398135871235181	3		377	270	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422375	225422375	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0044925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	215	351	0	ENST00000264414.4:c.264+1G>C		p.X88_splice	ENST00000264414	NM_003590.4	88			0.398135871235181	3	FACETS	0.947	0.891	1	1	0.992	1	CLONAL	3	TRUE	1	0.398135871235181	3		351	456	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434171	12434171	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	118	407	0	ENST00000287820.6:c.539G>C	p.Cys180Ser	p.C180S	ENST00000287820	NM_015869.4	180	tGt/tCt	4/7	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.398135871235181	2		407	451	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459846	149459846	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	243	691	0	ENST00000286301.3:c.361C>A	p.Gln121Lys	p.Q121K	ENST00000286301	NM_005211.3	121	Cag/Aag	4/22	0.123310779330153	5	FACETS	1	0.989	1	0.831	0.779	0.884	INDETERMINATE	2	TRUE	2	0.398135871235181	5		691	782	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759379	133759379	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	369	661	0	ENST00000318560.5:c.1702G>T	p.Val568Leu	p.V568L	ENST00000318560	NM_005157.4	568	Gtg/Ttg	11/11	0.398135871235181	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	0	0.398135871235181	3		661	699	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0044930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	163	779	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.185776342189387	2	FACETS	0.958	0.879	1	0.958	0.879	1	CLONAL	2	TRUE	0	0.185776342189387	2		781	916	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696599	47696599	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	188	466	0	ENST00000347630.2:c.349A>G	p.Met117Val	p.M117V	ENST00000347630	NM_001007230.1	117	Atg/Gtg	5/11	0.185776342189387	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	0	0.185776342189387	3		466	681	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120732	94120732	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	42	421	0	ENST00000369303.4:c.319A>T	p.Arg107Trp	p.R107W	ENST00000369303	NM_004440.3	107	Agg/Tgg	3/17	0.172366964258435	2	FACETS	0.742	0.619	0.88	0.371	0.309	0.44	SUBCLONAL	1	TRUE	0	0.185776342189387	2		421	609	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675691	30675691	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1469117613	NA	P-0044930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	232	909	0	ENST00000376406.3:c.2665A>G	p.Ser889Gly	p.S889G	ENST00000376406	NM_014641.2	889	Agt/Ggt	8/15	0.177445730400954	3	FACETS	0.997	0.928	1	0.997	0.928	1	CLONAL	2	TRUE	1	0.185776342189387	3		909	1369	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	80	372	0				ENST00000310581	NM_198253.2	-/1132			0.220913293484919	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.689590048722681	0		372	180	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0044958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	369	1179	2	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.509909921033558	4	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.689590048722681	4		1181	854	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	266	1012	0	ENST00000269305.4:c.517G>C	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ctg	5/11	0.509909921033558	4	FACETS	0.877	0.826	0.929			1	CLONAL	2	TRUE	NA	0.689590048722681	4		1012	743	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0044958-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	133	695	1	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.587389947829047	4	FACETS	0.994	0.905	1	0.497	0.452	0.544	CLONAL	1	TRUE	2	0.689590048722681	4		696	656	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0044963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	310	608	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.438647080229792	2	FACETS	0.836	0.794	0.878	0.836	0.794	0.878	CLONAL	2	TRUE	0	0.538189947064505	2		611	689	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	266	706	2	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	0.331254107384086	3	FACETS	1	0.992	1	0.688	0.646	0.731	CLONAL	1	TRUE	1	0.538189947064505	3		708	912	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513282	44513287	+	inframe_deletion	In_Frame_Del	DEL	CCACCG	CCACCG	-	rs745888281	NA	P-0044963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	117	819	3	ENST00000291552.4:c.648_653del	p.Gly222_Gly223del	p.G222_G223del	ENST00000291552	NM_006758.2	216	ggCGGTGGt/ggt	8/8	0.331254107384086	3	FACETS	0.471	0.423	0.521	0.235	0.211	0.261	SUBCLONAL	1	TRUE	1	0.538189947064505	3		822	1172	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051652	30051652	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555993336	NA	P-0044963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	147	316	0	ENST00000338641.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000338641	NM_000268.3	196	Cga/Tga	6/16	0.438647080229792	2	FACETS	0.785	0.727	0.844	0.785	0.727	0.844	SUBCLONAL	2	TRUE	0	0.538189947064505	2		316	348	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614463	38614463	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	118	402	0	ENST00000299084.4:c.234del	p.Asp79ThrfsTer42	p.D79Tfs*42	ENST00000299084	NM_152594.2	77	Aaa/aa	3/7	0.483553964157677	1	FACETS	0.876	0.798	0.955	0.876	0.798	0.955	CLONAL	1	TRUE	0	0.538189947064505	1		402	366	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204992	128204992	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	274	758	0	ENST00000341105.2:c.449del	p.Gly150GlufsTer68	p.G150Efs*68	ENST00000341105	NM_032638.4	150	gGa/ga	3/6	0.214540656859034	5	FACETS	1	0.961	1	0.685	0.644	0.726	INDETERMINATE	2	TRUE	2	0.538189947064505	5		758	896	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916840	48916841	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	rs1566186125	NA	P-0044963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	205	295	0	ENST00000267163.4:c.371_372del	p.Ile124ArgfsTer6	p.I124Rfs*6	ENST00000267163	NM_000321.2	124	ATa/a	3/27	0.538189947064505	3	FACETS	0.864	0.816	0.912	0.864	0.816	0.912	CLONAL	3	TRUE	0	0.538189947064505	3		295	373	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672317	86672317	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	171	392	2	ENST00000274376.6:c.2119C>T	p.Arg707Cys	p.R707C	ENST00000274376	NM_002890.2	707	Cgt/Tgt	16/25	0.438647080229792	2	FACETS	0.758	0.706	0.812	0.758	0.706	0.812	SUBCLONAL	2	TRUE	0	0.538189947064505	2		394	419	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325125	39325125	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	237	564	0	ENST00000373001.3:c.194T>C	p.Leu65Pro	p.L65P	ENST00000373001	NM_022157.3	65	cTg/cCg	1/7	0.453553712798289	2	FACETS	0.769	0.723	0.814	0.769	0.723	0.814	SUBCLONAL	2	TRUE	0	0.538189947064505	2		564	573	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666693	206666693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782183853	NA	P-0044963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	204	680	0	ENST00000367120.3:c.2027G>A	p.Arg676Gln	p.R676Q	ENST00000367120	NM_014002.3	676	cGa/cAa	20/22	0.331254107384086	3	FACETS	1	0.971	1	0.542	0.503	0.583	CLONAL	1	TRUE	1	0.538189947064505	3		680	887	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114920419	114920419	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs750925453	NA	P-0044963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	214	528	0	ENST00000543371.1:c.1360G>C	p.Asp454His	p.D454H	ENST00000543371	NM_001198531.1	454	Gac/Cac	13/14	0.442351966510081	4	FACETS	1	0.99	1	0.458	0.426	0.491	CLONAL	1	TRUE	1	0.538189947064505	4		528	891	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992080	11992080	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	93	259	0	ENST00000396373.4:c.170A>G	p.Gln57Arg	p.Q57R	ENST00000396373	NM_001987.4	57	cAg/cGg	3/8	0.483553964157677	1	FACETS	0.845	0.76	0.932	0.845	0.76	0.932	CLONAL	1	TRUE	0	0.538189947064505	1		259	299	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446401	49446401	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	185	645	0	ENST00000301067.7:c.1204A>T	p.Thr402Ser	p.T402S	ENST00000301067	NM_003482.3	402	Acc/Tcc	9/54	0.331254107384086	3	FACETS	0.994	0.918	1	0.497	0.459	0.536	CLONAL	1	TRUE	1	0.538189947064505	3		645	878	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495517	56495517	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	87	611	0	ENST00000267101.3:c.3707G>C	p.Gly1236Ala	p.G1236A	ENST00000267101	NM_001982.3	1236	gGc/gCc	28/28	0.331254107384086	3	FACETS	0.581	0.514	0.653	0.291	0.257	0.327	SUBCLONAL	1	TRUE	1	0.538189947064505	3		611	706	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830549	72830549	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	309	586	1	ENST00000268489.5:c.6032C>T	p.Pro2011Leu	p.P2011L	ENST00000268489	NM_006885.3	2011	cCt/cTt	9/10	0.438647080229792	2	FACETS	0.802	0.761	0.843	0.802	0.761	0.843	CLONAL	2	TRUE	0	0.538189947064505	2		587	716	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244589	41244589	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs878854941	NA	P-0044963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	291	600	0	ENST00000357654.3:c.2959A>G	p.Lys987Glu	p.K987E	ENST00000357654	NM_007294.3	987	Aag/Gag	10/23	0.438647080229792	2	FACETS	0.909	0.863	0.954	0.909	0.863	0.954	CLONAL	2	TRUE	0	0.538189947064505	2		600	595	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247935	10247935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	53	654	0	ENST00000340748.4:c.4267G>A	p.Ala1423Thr	p.A1423T	ENST00000340748		1423	Gcc/Acc	36/40	0.267513608378808	4	FACETS	0.342	0.291	0.399	0.171	0.145	0.2	INDETERMINATE	1	TRUE	2	0.538189947064505	4		654	885	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091773	29091773	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555913769	NA	P-0044963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	75	570	0	ENST00000328354.6:c.1184T>C	p.Val395Ala	p.V395A	ENST00000328354	NM_007194.3	395	gTt/gCt	11/15	0.438647080229792	2	FACETS	0.415	0.364	0.471	0.208	0.182	0.236	SUBCLONAL	1	TRUE	0	0.538189947064505	2		570	671	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664964	138664964	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	112	268	0	ENST00000330315.3:c.601A>T	p.Asn201Tyr	p.N201Y	ENST00000330315	NM_023067.3	201	Aac/Tac	1/1	0.214540656859034	5	FACETS	1	0.918	1	0.674	0.612	0.738	INDETERMINATE	2	TRUE	2	0.538189947064505	5		268	372	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6038807	6038807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	59	622	0	ENST00000265849.7:c.637C>T	p.Pro213Ser	p.P213S	ENST00000265849	NM_000535.5	213	Cct/Tct	6/15	0.331254107384086	3	FACETS	0.263	0.225	0.304	0.131	0.112	0.152	SUBCLONAL	1	TRUE	1	0.538189947064505	3		622	1060	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0044970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	145	337	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.889	0.819	0.961	1	0.991	1	CLONAL	2	TRUE	1	0.380305551811459	2		337	429	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098949	47098949	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	50	515	2	ENST00000409792.3:c.6325C>T	p.Arg2109Ter	p.R2109*	ENST00000409792	NM_014159.6	2109	Cga/Tga	15/21	0.336007677452484	1	FACETS	0.286	0.242	0.335	0.286	0.242	0.335	SUBCLONAL	1	TRUE	0	0.380305551811459	1		517	745	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888163	112888163	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507509	NA	P-0044970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	31	531	0	ENST00000351677.2:c.179G>T	p.Gly60Val	p.G60V	ENST00000351677	NM_002834.3	60	gGt/gTt	3/16	1	2	FACETS	0.174	0.14	0.213	0.174	0.14	0.213	SUBCLONAL	1	TRUE	1	0.380305551811459	2		531	936	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125798	47125799	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0044970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	33	297	0	ENST00000409792.3:c.5471_5472insC	p.Gln1825SerfsTer7	p.Q1825Sfs*7	ENST00000409792	NM_014159.6	1824	att/atCt	12/21	0.336007677452484	1	FACETS	0.332	0.27	0.402	0.332	0.27	0.402	SUBCLONAL	1	TRUE	0	0.380305551811459	1		297	423	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931928	39931929	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0044970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	162	684	0	ENST00000378444.4:c.2670_2671del	p.Asn891ProfsTer25	p.N891Pfs*25	ENST00000378444	NM_001123385.1	890	gaGAac/gaac	4/15	1	2	FACETS	0.714	0.654	0.778	0.714	0.654	0.778	SUBCLONAL	1	TRUE	1	0.380305551811459	2		684	1193	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338609	70338609	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866295169	NA	P-0044970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	111	526	2	ENST00000374080.3:c.5C>T	p.Ala2Val	p.A2V	ENST00000374080		2	gCg/gTg	1/45	1	2	FACETS	0.737	0.662	0.816	0.737	0.662	0.816	SUBCLONAL	1	TRUE	1	0.380305551811459	2		528	792	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225684	26225686	+	inframe_deletion	In_Frame_Del	DEL	TGG	TGG	-	rs764871937	NA	P-0044998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	145	523	0	ENST00000360408.1:c.305_307del	p.Val102del	p.V102del	ENST00000360408	NM_003532.2	101	tTGGtg/ttg	1/1	0.660762983426408	9	FACETS	0.938	0.857	1			1	CLONAL	2	TRUE	NA	0.660762983426408	9		523	775	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905576	50905576	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044998-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	224	829	0	ENST00000440232.2:c.704G>A	p.Gly235Asp	p.G235D	ENST00000440232	NM_002691.3	235	gGc/gAc	6/27	0.660762983426408	4	FACETS	1	0.985	1	0.6	0.559	0.642	CLONAL	1	TRUE	2	0.660762983426408	4		829	939	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0045029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	45	381	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	NA	2	FACETS	0.375	0.315	0.441			1	INDETERMINATE	1	FALSE	NA	0.514115422858013	2		381	467	SUCCESS
APC	324	MSKCC	GRCh37	5	112175507	112175507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587782518	NA	P-0045029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	79	266	0	ENST00000257430.4:c.4216C>T	p.Gln1406Ter	p.Q1406*	ENST00000257430	NM_000038.5	1406	Cag/Tag	16/16	0.489288995654655	1	FACETS	0.852	0.759	0.949	0.852	0.759	0.949	CLONAL	1	FALSE	0	0.514115422858013	1		266	268	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0045029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	232	479	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.495160693028189	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	0	0.514115422858013	1		479	615	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149799	202149799	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045029-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	36	397	0	ENST00000358485.4:c.1245del	p.Phe415LeufsTer26	p.F415Lfs*26	ENST00000358485	NM_001080125.1	414	Ttt/tt	8/9	1	2	FACETS	0.238	0.195	0.286	0.238	0.195	0.286	SUBCLONAL	1	FALSE	1	0.514115422858013	2		397	589	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0045030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	590	337	0				ENST00000310581	NM_198253.2	-/1132			0.3	11	FACETS	0.985	0.957	1	1	0.994	1	CLONAL	10	TRUE	2	0.36	11		337	872	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0045030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	316	687	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.165369272695032	4	FACETS	0.92	0.871	0.969	1	0.994	1	INDETERMINATE	3	TRUE	2	0.36	4		687	865	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0045030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	61	608	3	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.165369272695032	4	FACETS	0.595	0.513	0.686	0.298	0.256	0.343	INDETERMINATE	1	TRUE	2	0.36	4		611	774	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0045030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	1617	621	1	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.3	19	FACETS	0.994	0.977	1			1	CLONAL	15	TRUE	NA	0.36	19		622	2446	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245466	16245466	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	148	258	0	ENST00000375759.3:c.1441C>G	p.Leu481Val	p.L481V	ENST00000375759	NM_015001.2	481	Ctg/Gtg	7/15	0.242166007637027	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.36	4		258	455	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057727	27057727	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	388	522	0	ENST00000324856.7:c.1435C>T	p.Gln479Ter	p.Q479*	ENST00000324856	NM_006015.4	479	Cag/Tag	3/20	0.242166007637027	4	FACETS	1	0.988	1	1	0.996	1	CLONAL	3	TRUE	2	0.36	4		522	893	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059176	27059176	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	187	347	0	ENST00000324856.7:c.1813C>T	p.Gln605Ter	p.Q605*	ENST00000324856	NM_006015.4	605	Caa/Taa	4/20	0.242166007637027	4	FACETS	1	0.946	1	1	0.992	1	CLONAL	3	TRUE	2	0.36	4		347	464	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28607296	28607296	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	40	532	0	ENST00000253063.3:c.1426A>G	p.Thr476Ala	p.T476A	ENST00000253063	NM_031459.4	476	Acc/Gcc	10/10	0.242166007637027	4	FACETS	0.378	0.313	0.451	0.189	0.156	0.226	SUBCLONAL	1	TRUE	2	0.36	4		532	799	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981272	201981272	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1356631733	NA	P-0045030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	126	763	0	ENST00000359651.3:c.355del	p.Asp119ThrfsTer36	p.D119Tfs*36	ENST00000359651		117	ctG/ct	2/8	0.161998873091298	2	FACETS	0.816	0.738	0.897	0.408	0.369	0.449	INDETERMINATE	1	TRUE	0	0.36	2		763	858	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170499	108170499	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1565473763	NA	P-0045030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	27	251	0	ENST00000278616.4:c.5064A>G	p.Ile1688Met	p.I1688M	ENST00000278616	NM_000051.3	1688	atA/atG	34/63	0.165369272695032	4	FACETS	0.537	0.427	0.662	0.268	0.213	0.331	INDETERMINATE	1	TRUE	2	0.36	4		251	380	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118370114	118370114	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1167143563	NA	P-0045030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	128	243	0	ENST00000534358.1:c.6058G>C	p.Glu2020Gln	p.E2020Q	ENST00000534358	NM_005933.3	2020	Gaa/Caa	23/36	0.165369272695032	4	FACETS	0.965	0.887	1	1	0.987	1	INDETERMINATE	3	TRUE	2	0.36	4		243	334	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047495	49047495	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0045030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	113	135	0	ENST00000267163.4:c.2490-1G>C		p.X830_splice	ENST00000267163	NM_000321.2	830			NA	2	FACETS	0.957	0.896	1			1	INDETERMINATE	4	TRUE	NA	0.36	2		135	164	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781353	3781353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	163	766	1	ENST00000262367.5:c.5012C>T	p.Ala1671Val	p.A1671V	ENST00000262367	NM_004380.2	1671	gCc/gTc	30/31	0.3	3	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.36	3		767	899	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0045030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	338	1179	2	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.165369272695032	4	FACETS	1	0.991	1	1	0.991	1	INDETERMINATE	2	TRUE	2	0.36	4		1181	1045	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37865651	37865651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	1788	552	0	ENST00000269571.5:c.520C>T	p.His174Tyr	p.H174Y	ENST00000269571		174	Cac/Tac	4/27	0.3	19	FACETS	1	0.993	1			1	CLONAL	15	TRUE	NA	0.36	19		552	2647	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63526161	63526161	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	163	500	1	ENST00000307078.5:c.2465G>A	p.Trp822Ter	p.W822*	ENST00000307078	NM_004655.3	822	tGg/tAg	11/11	0.264690088475224	4	FACETS	1	0.986	1	0.451	0.414	0.49	CLONAL	1	TRUE	1	0.36	4		501	910	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732339	74732356	+	inframe_deletion	In_Frame_Del	DEL	CCTGGACCGAGACCGGGA	CCTGGACCGAGACCGGGA	-	novel	NA	P-0045030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	49	346	0	ENST00000359995.5:c.553_570del	p.Arg186_Ser191del	p.R186_S191del	ENST00000359995	NM_001195427.1	185	TCCCGGTCTCGGTCCAGG/-	2/3	0.264690088475224	4	FACETS	0.663	0.562	0.776	0.221	0.187	0.259	SUBCLONAL	1	TRUE	1	0.36	4		346	558	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356272	66356272	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	30	431	0	ENST00000273854.3:c.1225G>A	p.Gly409Ser	p.G409S	ENST00000273854	NM_004439.5	409	Ggc/Agc	5/18	0.141263439498522	3	FACETS	0.356	0.286	0.435	0.119	0.095	0.145	INDETERMINATE	1	TRUE	0	0.36	3		431	553	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946126	13946126	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	216	376	0	ENST00000405192.2:c.970G>T	p.Asp324Tyr	p.D324Y	ENST00000405192	NM_001163147.1	324	Gac/Tac	10/12	0.165369272695032	4	FACETS	1	0.959	1	1	0.993	1	INDETERMINATE	3	TRUE	2	0.36	4		376	529	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039356	47039358	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0045030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	342	339	0	ENST00000377604.3:c.985_987del	p.Ser329del	p.S329del	ENST00000377604	NM_001204468.1	327	TCC/-	10/24	0.26016332373251	2	FACETS	1	0.977	1			1	CLONAL	4	TRUE	NA	0.36	2		339	468	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775583	39775583	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369318352	NA	P-0045031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	76	366	0	ENST00000288319.7:c.437C>T	p.Ala146Val	p.A146V	ENST00000288319	NM_182918.3	146	gCg/gTg	4/10	1	2	FACETS	0.605	0.53	0.685	0.605	0.53	0.685	SUBCLONAL	1	TRUE	1	0.380671111536308	2		366	660	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625389	69625389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199801193	NA	P-0045031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	92	771	0	ENST00000334134.2:c.404G>A	p.Arg135Gln	p.R135Q	ENST00000334134	NM_005247.2	135	cGg/cAg	3/3	0.309343715032072	1	FACETS	0.309	0.273	0.347	0.309	0.273	0.347	SUBCLONAL	1	TRUE	0	0.380671111536308	1		771	1268	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666438	206666438	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553391067	NA	P-0045031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	153	528	0	ENST00000367120.3:c.1918G>A	p.Glu640Lys	p.E640K	ENST00000367120	NM_014002.3	640	Gag/Aag	19/22	0.368151832494989	2	FACETS	0.827	0.756	0.901	0.413	0.378	0.451	CLONAL	1	TRUE	0	0.380671111536308	2		528	972	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420218	49420218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369189362	NA	P-0045031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	95	605	0	ENST00000301067.7:c.15531G>A	p.Met5177Ile	p.M5177I	ENST00000301067	NM_003482.3	5177	atG/atA	48/54	0.185287211742635	3	FACETS	0.492	0.436	0.551	0.246	0.218	0.276	INDETERMINATE	1	TRUE	1	0.380671111536308	3		605	1208	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29007971	29007971	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	19	237	0	ENST00000282397.4:c.798G>A	p.Trp266Ter	p.W266*	ENST00000282397	NM_002019.4	266	tgG/tgA	6/30	0.380671111536308	1	FACETS	0.326	0.247	0.418	0.326	0.247	0.418	SUBCLONAL	1	TRUE	0	0.380671111536308	1		237	248	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911328	32911328	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs80358534	NA	P-0045031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	15	371	0	ENST00000380152.3:c.2836G>C	p.Asp946His	p.D946H	ENST00000380152		946	Gat/Cat	11/27	0.380671111536308	1	FACETS	0.229	0.167	0.303	0.229	0.167	0.303	SUBCLONAL	1	TRUE	0	0.380671111536308	1		371	279	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913317	32913317	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659201	NA	P-0045031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	19	373	1	ENST00000380152.3:c.4825A>G	p.Thr1609Ala	p.T1609A	ENST00000380152		1609	Act/Gct	11/27	0.380671111536308	1	FACETS	0.356	0.271	0.456	0.356	0.271	0.456	SUBCLONAL	1	TRUE	0	0.380671111536308	1		374	227	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121840	2121840	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1171806400	NA	P-0045031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1284	131	856	0	ENST00000219476.3:c.2002G>T	p.Gly668Trp	p.G668W	ENST00000219476	NM_000548.3	668	Ggg/Tgg	19/42	0.380671111536308	2	FACETS	0.486	0.44	0.536	0.243	0.22	0.268	SUBCLONAL	1	TRUE	0	0.380671111536308	2		856	1415	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300089	15300089	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs863225297	NA	P-0045031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	209	598	0	ENST00000263388.2:c.1187C>G	p.Ser396Cys	p.S396C	ENST00000263388	NM_000435.2	396	tCt/tGt	7/33	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.380671111536308	2		598	1045	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940789	49940789	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1171261301	NA	P-0045031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	114	670	0	ENST00000296474.3:c.254T>C	p.Leu85Pro	p.L85P	ENST00000296474	NM_002447.2	85	cTg/cCg	1/20	1	2	FACETS	0.567	0.509	0.629	0.567	0.509	0.629	SUBCLONAL	1	TRUE	1	0.380671111536308	2		670	1056	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163438	32163438	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	109	808	0	ENST00000375023.3:c.5788A>T	p.Met1930Leu	p.M1930L	ENST00000375023	NM_004557.3	1930	Atg/Ttg	30/30	1	2	FACETS	0.505	0.452	0.561	0.505	0.452	0.561	SUBCLONAL	1	TRUE	1	0.380671111536308	2		808	1134	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922063	39922063	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1354	105	713	0	ENST00000378444.4:c.4109C>A	p.Pro1370His	p.P1370H	ENST00000378444	NM_001123385.1	1370	cCt/cAt	9/15	1	2	FACETS	0.378	0.337	0.422	0.378	0.337	0.422	SUBCLONAL	1	TRUE	1	0.380671111536308	2		713	1459	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227814	53227814	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	169	614	0	ENST00000375401.3:c.2374G>A	p.Glu792Lys	p.E792K	ENST00000375401	NM_004187.3	792	Gaa/Aaa	17/26	1	2	FACETS	0.954	0.877	1	0.954	0.877	1	CLONAL	1	TRUE	1	0.380671111536308	2		614	931	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0045032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	22	400	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	1	0.833	1	1	0.833	1	CLONAL	1	TRUE	1	0.236447477001678	2		400	172	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220717	1220717	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs587782018	NA	P-0045032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	22	682	0	ENST00000326873.7:c.734+1G>T		p.X245_splice	ENST00000326873	NM_000455.4	245			0.236447477001678	0	FACETS	0.575	0.447	0.723			1	SUBCLONAL	1	TRUE	0	0.236447477001678	0		682	247	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120855	115120855	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1565862637	NA	P-0045032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	24	573	0	ENST00000257566.3:c.151G>A	p.Ala51Thr	p.A51T	ENST00000257566	NM_016569.3	51	Gcg/Acg	1/8	0.236447477001678	1	FACETS	0.639	0.502	0.797	0.639	0.502	0.797	SUBCLONAL	1	TRUE	0	0.236447477001678	1		573	280	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332729	70332729	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	28	444	0	ENST00000373644.4:c.634G>C	p.Glu212Gln	p.E212Q	ENST00000373644	NM_030625.2	212	Gag/Cag	2/12	1	2	FACETS	0.874	0.701	1	0.874	0.701	1	CLONAL	1	TRUE	1	0.236447477001678	2		444	271	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914329	32914329	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0045032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	10	365	0	ENST00000380152.3:c.5837C>G	p.Ser1946Ter	p.S1946*	ENST00000380152		1946	tCa/tGa	11/27	0.236447477001678	1	FACETS	0.525	0.357	0.735	0.525	0.357	0.735	SUBCLONAL	1	TRUE	0	0.236447477001678	1		365	142	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577133	7577133	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	43	573	0	ENST00000269305.4:c.805A>T	p.Ser269Cys	p.S269C	ENST00000269305	NM_001126112.2	269	Agc/Tgc	8/11	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.236447477001678	2		573	335	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428015	33428015	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786203144	NA	P-0045032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	30	572	0	ENST00000345365.6:c.944G>T	p.Gly315Val	p.G315V	ENST00000345365	NM_002878.3	315	gGg/gTg	10/10	1	2	FACETS	0.832	0.672	1	0.832	0.672	1	CLONAL	1	TRUE	1	0.236447477001678	2		572	305	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770631	40770631	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	19	289	0	ENST00000373198.4:c.2751G>T	p.Glu917Asp	p.E917D	ENST00000373198	NM_133170.3	917	gaG/gaT	19/32	1	2	FACETS	0.693	0.527	0.887	0.693	0.527	0.887	SUBCLONAL	1	TRUE	1	0.236447477001678	2		289	232	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109315790	109315790	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	11	427	0	ENST00000436639.2:c.995T>A	p.Val332Asp	p.V332D	ENST00000436639	NM_014454.2	332	gTt/gAt	6/10	0.159948754613649	3	FACETS	0.536	0.371	0.742	0.268	0.185	0.371	SUBCLONAL	1	TRUE	1	0.236447477001678	3		427	194	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750711	128750711	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	41	663	0	ENST00000377970.2:c.248G>T	p.Gly83Val	p.G83V	ENST00000377970	NM_002467.4	83	gGg/gTg	2/3	1	2	FACETS	0.848	0.707	1	0.848	0.707	1	CLONAL	1	TRUE	1	0.236447477001678	2		663	409	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0045033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	17	738	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.506	0.38	0.651	0.506	0.38	0.651	SUBCLONAL	1	TRUE	1	0.490776023215196	2		738	137	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0045033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	147	351	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.33015018732427	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.490776023215196	3		351	314	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440943	56440943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786205215	NA	P-0045033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	105	593	1	ENST00000407977.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000407977		132	Cga/Tga	4/10	1	2	FACETS	0.473	0.423	0.527	0.473	0.423	0.527	SUBCLONAL	1	TRUE	1	0.490776023215196	2		594	904	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604697	48604697	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	149	353	0	ENST00000342988.3:c.1519A>G	p.Lys507Glu	p.K507E	ENST00000342988	NM_005359.5	507	Aaa/Gaa	12/12	0.467725509207983	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.490776023215196	1		353	406	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395665	31395665	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1182001726	NA	P-0045033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	153	591	0	ENST00000328111.2:c.2518C>T	p.Arg840Ter	p.R840*	ENST00000328111	NM_006892.3	840	Cga/Tga	23/23	1	2	FACETS	0.74	0.677	0.805	0.74	0.677	0.805	SUBCLONAL	1	TRUE	1	0.490776023215196	2		591	843	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152038	11152038	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	113	475	0	ENST00000358026.2:c.4322C>A	p.Ser1441Ter	p.S1441*	ENST00000358026	NM_001128849.1	1441	tCa/tAa	31/36	1	2	FACETS	0.52	0.467	0.576	0.52	0.467	0.576	SUBCLONAL	1	TRUE	1	0.490776023215196	2		475	886	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578466	7578470	+	frameshift_variant	Frame_Shift_Del	DEL	GTGCC	GTGCC	-	novel	NA	P-0045033-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	257	713	0	ENST00000269305.4:c.460_464del	p.Gly154ProfsTer25	p.G154Pfs*25	ENST00000269305	NM_001126112.2	154	GGCACc/c	5/11	0.467725509207983	1	FACETS	0.798	0.748	0.85	0.798	0.748	0.85	SUBCLONAL	1	TRUE	0	0.490776023215196	1		713	990	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0045034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	69	428	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.21	2		428	630	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114241	115114241	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	42	391	0	ENST00000257566.3:c.976G>C	p.Asp326His	p.D326H	ENST00000257566	NM_016569.3	326	Gat/Cat	6/8	1	2	FACETS	0.839	0.7	0.992	0.839	0.7	0.992	CLONAL	1	TRUE	1	0.21	2		391	477	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831944	72831944	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs868684048	NA	P-0045034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	44	432	0	ENST00000268489.5:c.4637A>G	p.Lys1546Arg	p.K1546R	ENST00000268489	NM_006885.3	1546	aAg/aGg	9/10	1	2	FACETS	0.734	0.615	0.866	0.734	0.615	0.866	SUBCLONAL	1	TRUE	1	0.21	2		432	571	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189025	32189025	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	97	506	0	ENST00000375023.3:c.529C>A	p.Gln177Lys	p.Q177K	ENST00000375023	NM_004557.3	177	Cag/Aag	4/30	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.21	2		506	714	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128230269	128230269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045034-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	38	323	0	ENST00000265960.3:c.1327G>A	p.Ala443Thr	p.A443T	ENST00000265960	NM_001006617.1	443	Gct/Act	10/12	1	2	FACETS	0.678	0.56	0.81	0.678	0.56	0.81	SUBCLONAL	1	TRUE	1	0.21	2		323	534	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0045035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	129	566	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.331185429102426	2		566	596	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0045035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	49	522	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.322456896777183	1	FACETS	0.686	0.583	0.798	0.686	0.583	0.798	SUBCLONAL	1	TRUE	0	0.331185429102426	1		522	360	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570033	95570033	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045035-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	18	332	0	ENST00000393063.1:c.3700G>A	p.Glu1234Lys	p.E1234K	ENST00000393063	NM_030621.3	1234	Gaa/Aaa	22/28	0.331185429102426	1	FACETS	0.442	0.334	0.57	0.442	0.334	0.57	SUBCLONAL	1	TRUE	0	0.331185429102426	1		332	205	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	15	372	0				ENST00000310581	NM_198253.2	-/1132			0.0986235748924961	0	FACETS	0.555	0.405	0.734			1	INDETERMINATE	1	TRUE	0	0.17	0		372	264	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984398	201984399	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0045036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	56	624	0	ENST00000359651.3:c.1064_1065dup	p.Lys356AlafsTer92	p.K356Afs*92	ENST00000359651		355	ggc/gGCgc	8/8	1	2	FACETS	0.998	0.854	1	0.998	0.854	1	CLONAL	1	TRUE	1	0.17	2		624	660	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236215	108236215	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs730881332	NA	P-0045039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	131	403	0	ENST00000278616.4:c.9151G>C	p.Gly3051Arg	p.G3051R	ENST00000278616	NM_000051.3	3051	Gga/Cga	63/63	0.235195078123248	3	FACETS	1	0.984	1	0.697	0.635	0.761	INDETERMINATE	1	FALSE	1	0.421398017458616	3		403	540	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012228	16012228	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0045039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	33	201	0	ENST00000268712.3:c.2056-2A>C		p.X686_splice	ENST00000268712	NM_006311.3	686			0.197390951438722	3	FACETS	0.695	0.568	0.836	0.232	0.189	0.279	INDETERMINATE	1	FALSE	0	0.421398017458616	3		201	273	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085839	16085839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372079635	NA	P-0045039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	104	414	0	ENST00000281043.3:c.1015G>A	p.Val339Met	p.V339M	ENST00000281043	NM_005378.4	339	Gtg/Atg	3/3	0.260720749154059	3	FACETS	0.986	0.885	1	0.493	0.442	0.547	CLONAL	1	FALSE	1	0.421398017458616	3		414	606	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726998	61727332	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGCCAATGTTTGGGCCATTCTTGTTTCAGTATCTAAAACAAGACATGAAATGTTAATCGCACTTCATTTCTCAAAGGCAAATAAAACAAACTTCAAAGAAATTATGTAATGGATAAAGGCAGGAGTAAGGATAAATCACTTTTCATTTTCTCCTCCTTTATTAAAGGAAGAAATGTGCCACCCTCTTCACCCTACTGGGTAGAAAACAAAACACAAAGTCTTTTATCTTAATCACCGCAGGACCCTTTTCAATTATCCTAATGAAAGGTCCAATCCGTCTAATGGGTCTGTCTGTGTATTAGTATCTGCCTGATAGATATGTAGAAATTATTCTA	GGCCAATGTTTGGGCCATTCTTGTTTCAGTATCTAAAACAAGACATGAAATGTTAATCGCACTTCATTTCTCAAAGGCAAATAAAACAAACTTCAAAGAAATTATGTAATGGATAAAGGCAGGAGTAAGGATAAATCACTTTTCATTTTCTCCTCCTTTATTAAAGGAAGAAATGTGCCACCCTCTTCACCCTACTGGGTAGAAAACAAAACACAAAGTCTTTTATCTTAATCACCGCAGGACCCTTTTCAATTATCCTAATGAAAGGTCCAATCCGTCTAATGGGTCTGTCTGTGTATTAGTATCTGCCTGATAGATATGTAGAAATTATTCTA	-	novel	NA	P-0045039-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	26	323	0	ENST00000401558.2:c.409-303_440del		p.X137_splice	ENST00000401558	NM_003400.3	137		7/25	0.260720749154059	3	FACETS	0.501	0.398	0.62	0.251	0.199	0.31	SUBCLONAL	1	FALSE	1	0.421398017458616	3		323	298	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690805	89690805	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	194	173	0	ENST00000371953.3:c.212G>A	p.Cys71Tyr	p.C71Y	ENST00000371953	NM_000314.4	71	tGt/tAt	4/9	0.925947199259332	1	FACETS	0.949	0.913	0.983	0.949	0.913	0.983	CLONAL	1	TRUE	0	0.925947199259332	1		173	237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578176	7578176	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs863224499	NA	P-0045041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	668	432	0	ENST00000269305.4:c.672+1G>T		p.X224_splice	ENST00000269305	NM_001126112.2	224			NA	2	FACETS	0.987	0.973	1			1	INDETERMINATE	2	TRUE	NA	0.925947199259332	2		432	731	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196835	123196835	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045041-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	177	304	0	ENST00000218089.9:c.1722A>T	p.Leu574Phe	p.L574F	ENST00000218089	NM_001042749.1	574	ttA/ttT	18/35	0.925947199259332	1	FACETS	0.597	0.56	0.634	0.597	0.56	0.634	SUBCLONAL	1	TRUE	0	0.925947199259332	1		304	344	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928358	69928358	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774545277	NA	P-0045042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	89	345	0	ENST00000352241.4:c.178C>T	p.Arg60Cys	p.R60C	ENST00000352241	NM_198159.2	60	Cgc/Tgc	2/10	0.361455256670999	3	FACETS	1	0.982	1	0.75	0.677	0.825	INDETERMINATE	1	TRUE	1	0.679798683815735	3		345	234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0045042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	166	502	0	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.558554644312072	2	FACETS	0.848	0.797	0.898	0.848	0.797	0.898	CLONAL	2	TRUE	0	0.679798683815735	2		502	288	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805624	46805624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781117900	NA	P-0045042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	53	621	1	ENST00000290295.7:c.332C>T	p.Ala111Val	p.A111V	ENST00000290295	NM_006361.5	111	gCg/gTg	1/2	0.230962799769309	5	FACETS	0.539	0.459	0.627	0.18	0.153	0.209	INDETERMINATE	1	TRUE	2	0.679798683815735	5		622	584	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375994	8375994	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	29	268	0	ENST00000356435.5:c.4603T>G	p.Leu1535Val	p.L1535V	ENST00000356435		1535	Tta/Gta	28/35	0.238592938457758	3	FACETS	0.344	0.276	0.421	0.172	0.138	0.211	INDETERMINATE	1	TRUE	1	0.679798683815735	3		268	332	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435403	121435403	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	24	632	0	ENST00000257555.6:c.1436C>A	p.Pro479His	p.P479H	ENST00000257555		479	cCt/cAt	7/10	0.59969179749376	3	FACETS	0.232	0.181	0.29	0.116	0.09	0.145	SUBCLONAL	1	TRUE	1	0.679798683815735	3		632	408	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991985	72991985	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	26	422	0	ENST00000268489.5:c.2060A>T	p.Glu687Val	p.E687V	ENST00000268489	NM_006885.3	687	gAg/gTg	2/10	1	2	FACETS	0.277	0.22	0.343	0.277	0.22	0.343	SUBCLONAL	1	TRUE	1	0.679798683815735	2		422	276	SUCCESS
APC	324	MSKCC	GRCh37	5	112175235	112175235	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	88	144	0	ENST00000257430.4:c.3944del	p.Ser1315Ter	p.S1315*	ENST00000257430	NM_000038.5	1315	tCa/ta	16/16	0.552892469112486	2	FACETS	0.893	0.821	0.962	0.893	0.821	0.962	CLONAL	2	TRUE	0	0.679798683815735	2		144	145	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405170	139405170	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199506721	NA	P-0045042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	105	671	0	ENST00000277541.6:c.2675G>A	p.Arg892His	p.R892H	ENST00000277541	NM_017617.3	892	cGc/cAc	17/34	NA	2	FACETS	0.815	0.737	0.897			1	INDETERMINATE	1	TRUE	NA	0.679798683815735	2		671	379	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912259	97912259	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140781259	NA	P-0045043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	26	327	0	ENST00000289081.3:c.632C>T	p.Pro211Leu	p.P211L	ENST00000289081	NM_000136.2	211	cCt/cTt	7/15	1	2	FACETS	0.676	0.537	0.835	0.676	0.537	0.835	SUBCLONAL	1	TRUE	1	0.2838572975637	2		327	271	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0045044-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	112	599	0	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.150890763605324	2	FACETS	0.898	0.809	0.992	0.898	0.809	0.992	CLONAL	2	TRUE	0	0.190391246933302	2		599	655	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0045045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	100	779	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.187719201536178	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.187719201536178	1		781	742	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351548	89351548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs555075240	NA	P-0045045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	68	570	0	ENST00000301030.4:c.1402C>T	p.Arg468Cys	p.R468C	ENST00000301030	NM_001256183.1	468	Cgc/Tgc	9/13	1	2	FACETS	0.822	0.714	0.94	0.822	0.714	0.94	CLONAL	1	TRUE	1	0.187719201536178	2		570	881	SUCCESS
APC	324	MSKCC	GRCh37	5	112173847	112173848	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0045045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	28	266	2	ENST00000257430.4:c.2556_2557delinsTT	p.Leu852_Glu853delinsPheTer	p.L852_E853delinsF*	ENST00000257430	NM_000038.5	852	ttGGag/ttTTag	16/16	0.187719201536178	1	FACETS	0.788	0.63	0.968	0.788	0.63	0.968	CLONAL	1	TRUE	0	0.187719201536178	1		268	343	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411648	63411648	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045045-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	91	565	0	ENST00000330258.3:c.1519G>T	p.Glu507Ter	p.E507*	ENST00000330258	NM_152424.3	507	Gag/Tag	2/2	0.15643306080017	2	FACETS	1	0.95	1	0.564	0.5	0.632	CLONAL	1	TRUE	0	0.187719201536178	2		565	860	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0045047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	21	287	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.505	0.388	0.643	0.505	0.388	0.643	SUBCLONAL	1	TRUE	1	0.193720506531329	2		287	429	SUCCESS
APC	324	MSKCC	GRCh37	5	112164616	112164616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854574	NA	P-0045047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	29	229	0	ENST00000257430.4:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000257430	NM_000038.5	564	Cga/Tga	14/16	1	2	FACETS	0.868	0.697	1	0.868	0.697	1	CLONAL	1	TRUE	1	0.193720506531329	2		229	345	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724379	117724379	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2243380	NA	P-0045047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	82	443	0	ENST00000368508.3:c.500G>A	p.Arg167Gln	p.R167Q	ENST00000368508	NM_002944.2	167	cGa/cAa	6/43	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.193720506531329	2		443	665	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858064	9858064	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	49	378	0	ENST00000330684.3:c.3337C>T	p.Pro1113Ser	p.P1113S	ENST00000330684	NM_001134407.1	1113	Cct/Tct	13/13	1	2	FACETS	0.9	0.762	1	0.9	0.762	1	CLONAL	1	TRUE	1	0.193720506531329	2		378	562	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979589	55979589	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	61	348	0	ENST00000263923.4:c.858G>T	p.Lys286Asn	p.K286N	ENST00000263923	NM_002253.2	286	aaG/aaT	7/30	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.193720506531329	2		348	520	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456449	32456449	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	41	457	0	ENST00000332351.3:c.443G>T	p.Gly148Val	p.G148V	ENST00000332351	NM_024426.4	148	gGc/gTc	1/10	1	2	FACETS	0.79	0.657	0.937	0.79	0.657	0.937	CLONAL	1	TRUE	1	0.193720506531329	2		457	536	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42046695	42046695	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	34	335	0	ENST00000219905.7:c.7069G>A	p.Glu2357Lys	p.E2357K	ENST00000219905	NM_001164273.1	2357	Gag/Aag	18/24	1	2	FACETS	0.83	0.678	1	0.83	0.678	1	CLONAL	1	TRUE	1	0.193720506531329	2		335	423	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579438	7579445	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCGGTG	CGCCGGTG	-	novel	NA	P-0045047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	83	588	0	ENST00000269305.4:c.242_249del	p.Thr81SerfsTer65	p.T81Sfs*65	ENST00000269305	NM_001126112.2	81	aCACCGGCG/a	4/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.193720506531329	2		588	653	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790094	40790094	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	76	481	0	ENST00000373198.4:c.2637C>A	p.Tyr879Ter	p.Y879*	ENST00000373198	NM_133170.3	879	taC/taA	18/32	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.193720506531329	2		481	675	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0045049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	168	401	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.29369964287725	4	FACETS	0.981	0.909	1	0.981	0.909	1	CLONAL	3	TRUE	1	0.29369964287725	4		401	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577569	7577569	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519981	NA	P-0045049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	143	448	0	ENST00000269305.4:c.712T>C	p.Cys238Arg	p.C238R	ENST00000269305	NM_001126112.2	238	Tgt/Cgt	7/11	0.29369964287725	2	FACETS	0.892	0.817	0.969	0.892	0.817	0.969	CLONAL	2	TRUE	0	0.29369964287725	2		448	546	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248358	59248359	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0045049-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	147	325	0	ENST00000371222.2:c.384dup	p.Ser129GlnfsTer181	p.S129Qfs*181	ENST00000371222	NM_002228.3	128	-/C	1/1	0.240712603019647	3	FACETS	0.952	0.879	1	0.952	0.879	1	CLONAL	3	TRUE	0	0.29369964287725	3		325	402	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	124	372	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.869	0.794	0.946	0.869	0.794	0.946	CLONAL	1	TRUE	1	0.739380076390117	2		372	386	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155942	106155943	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0045050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	36	236	0	ENST00000380013.4:c.845_846del	p.Ser282Ter	p.S282*	ENST00000380013	NM_001127208.2	281	aaCTct/aact	3/11	1	2	FACETS	0.206	0.169	0.247	0.206	0.169	0.247	SUBCLONAL	1	TRUE	1	0.739380076390117	2		236	473	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692916	89692916	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045050-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	229	356	0	ENST00000371953.3:c.400A>G	p.Met134Val	p.M134V	ENST00000371953	NM_000314.4	134	Atg/Gtg	5/9	0.739380076390117	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.739380076390117	1		356	385	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	105	372	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.996	0.903	1	0.996	0.903	1	CLONAL	1	TRUE	1	0.640796571720955	2		372	329	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0045054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	161	538	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.886	0.817	0.957	0.886	0.817	0.957	CLONAL	1	TRUE	1	0.640796571720955	2		538	567	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256510	115256510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	193	513	3	ENST00000369535.4:c.201G>A	p.Met67Ile	p.M67I	ENST00000369535	NM_002524.4	67	atG/atA	3/7	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.640796571720955	2		516	541	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922802	44922802	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	176	272	0	ENST00000377967.4:c.1663C>T	p.Gln555Ter	p.Q555*	ENST00000377967	NM_021140.2	555	Cag/Tag	16/29	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.640796571720955	1		272	272	SUCCESS
AR	367	MSKCC	GRCh37	X	66765025	66765025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1335991486	NA	P-0045054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	248	396	0	ENST00000374690.3:c.37C>T	p.Arg13Trp	p.R13W	ENST00000374690	NM_000044.3	13	Cgg/Tgg	1/8	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.640796571720955	1		396	384	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376187	225376187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773927741	NA	P-0045054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	120	442	0	ENST00000264414.4:c.767C>T	p.Thr256Met	p.T256M	ENST00000264414	NM_003590.4	256	aCg/aTg	6/16	1	2	FACETS	0.97	0.885	1	0.97	0.885	1	CLONAL	1	TRUE	1	0.640796571720955	2		442	386	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566444	41566445	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0045054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	118	340	0	ENST00000263253.7:c.4323_4324dup	p.Glu1442ValfsTer55	p.E1442Vfs*55	ENST00000263253	NM_001429.3	1441	agt/aGTgt	27/31	1	2	FACETS	0.932	0.849	1	0.932	0.849	1	CLONAL	1	TRUE	1	0.640796571720955	2		340	395	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80083427	80083427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	137	579	0	ENST00000265081.6:c.2479C>T	p.His827Tyr	p.H827Y	ENST00000265081	NM_002439.4	827	Cac/Tac	18/24	1	2	FACETS	0.85	0.778	0.925	0.85	0.778	0.925	CLONAL	1	TRUE	1	0.640796571720955	2		579	503	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651894	36651895	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGGAT	novel	NA	P-0045054-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	405	763	0	ENST00000244741.5:c.18_22dup	p.Val8GlyfsTer25	p.V8Gfs*25	ENST00000244741	NM_000389.4	6	ggg/gGGGATgg	2/3	0.640796571720955	2	FACETS	0.871	0.836	0.905	0.871	0.836	0.905	CLONAL	2	TRUE	0	0.640796571720955	2		763	726	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89809239	89809239	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs542032916	NA	P-0045055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	12	568	1	ENST00000389301.3:c.3734A>G	p.Gln1245Arg	p.Q1245R	ENST00000389301	NM_000135.2	1245	cAg/cGg	37/43	0.750740380617815	1	FACETS	0.183	0.129	0.248	0.183	0.129	0.248	SUBCLONAL	1	TRUE	0	0.750740380617815	1		569	109	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945517	151945517	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	47	504	2	ENST00000262189.6:c.2002C>A	p.Gln668Lys	p.Q668K	ENST00000262189	NM_170606.2	668	Cag/Aag	14/59	0.234606626953691	3	FACETS	1	0.967	1	0.486	0.422	0.553	INDETERMINATE	1	TRUE	0	0.750740380617815	3		506	118	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636219	87636219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	82	514	0	ENST00000277120.3:c.2384C>T	p.Pro795Leu	p.P795L	ENST00000277120		795	cCc/cTc	19/19	0.129188791207602	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.750740380617815	0		514	177	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	175	372	0				ENST00000310581	NM_198253.2	-/1132			0.710823347184482	3	FACETS	0.948	0.876	1	0.474	0.438	0.511	CLONAL	1	TRUE	1	0.811141719110285	3		372	640	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047507	49047507	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0045056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	55	191	0	ENST00000267163.4:c.2501C>G	p.Ser834Ter	p.S834*	ENST00000267163	NM_000321.2	834	tCa/tGa	24/27	0.811141719110285	1	FACETS	0.916	0.825	1	0.916	0.825	1	CLONAL	1	TRUE	0	0.811141719110285	1		191	88	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519985	NA	P-0045056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	530	612	1	ENST00000269305.4:c.857A>T	p.Glu286Val	p.E286V	ENST00000269305	NM_001126112.2	286	gAa/gTa	8/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.811141719110285	2		613	1305	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577524	7577524	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	429	507	0	ENST00000269305.4:c.757del	p.Thr253ProfsTer92	p.T253Pfs*92	ENST00000269305	NM_001126112.2	253	Acc/cc	7/11	1	2	FACETS	0.979	0.935	1	0.979	0.935	1	CLONAL	1	TRUE	1	0.811141719110285	2		507	1081	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138903	64138943	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCCAAAGGGGCCCCCCGCCGAGCCAACGGCCCCCTGCCC	CCTCCAAAGGGGCCCCCCGCCGAGCCAACGGCCCCCTGCCC	-	novel	NA	P-0045056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	114	544	0	ENST00000334205.4:c.2272_2312del	p.Ser758LeufsTer32	p.S758Lfs*32	ENST00000334205	NM_003942.2	757	gCCTCCAAAGGGGCCCCCCGCCGAGCCAACGGCCCCCTGCCC/g	17/17	1	2	FACETS	0.246	0.221	0.273	0.246	0.221	0.273	SUBCLONAL	1	TRUE	1	0.811141719110285	2		544	1141	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645970	215645970	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	54	372	0	ENST00000260947.4:c.628del	p.Thr210LeufsTer2	p.T210Lfs*2	ENST00000260947	NM_000465.2	210	Act/ct	4/11	0.811141719110285	1	FACETS	0.851	0.761	0.938	0.851	0.761	0.938	CLONAL	1	TRUE	0	0.811141719110285	1		372	93	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439683	220439683	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	52	924	0	ENST00000243786.2:c.536T>A	p.Leu179Gln	p.L179Q	ENST00000243786	NM_002191.3	179	cTg/cAg	2/2	0.811141719110285	1	FACETS	0.095	0.08	0.111	0.095	0.08	0.111	SUBCLONAL	1	TRUE	0	0.811141719110285	1		924	805	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161807891	161807891	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045056-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	155	316	0	ENST00000366898.1:c.1102T>A	p.Cys368Ser	p.C368S	ENST00000366898	NM_004562.2	368	Tgt/Agt	10/12	0.580999596710716	1	FACETS	0.841	0.789	0.893	0.841	0.789	0.893	CLONAL	1	TRUE	0	0.811141719110285	1		316	270	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	52	372	0				ENST00000310581	NM_198253.2	-/1132			0.398820802661216	3	FACETS	0.667	0.568	0.775	0.333	0.284	0.388	SUBCLONAL	1	TRUE	1	0.398820802661216	3		372	469	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410629	32410629	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs775063171	NA	P-0045058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	101	530	0	ENST00000332351.3:c.1529T>C	p.Met510Thr	p.M510T	ENST00000332351	NM_024426.4	510	aTg/aCg	10/10	1	2	FACETS	0.796	0.713	0.885	0.796	0.713	0.885	SUBCLONAL	1	TRUE	1	0.398820802661216	2		530	636	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477070	67477070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	78	383	0	ENST00000327367.4:c.877G>A	p.Gly293Ser	p.G293S	ENST00000327367	NM_005902.3	293	Ggc/Agc	7/9	1	2	FACETS	0.761	0.67	0.858	0.761	0.67	0.858	SUBCLONAL	1	TRUE	1	0.398820802661216	2		383	514	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044971	47044971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	151	406	0	ENST00000377604.3:c.2297G>A	p.Arg766His	p.R766H	ENST00000377604	NM_001204468.1	766	cGc/cAc	20/24	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.398820802661216	1		406	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0045058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	73	410	1	ENST00000269305.4:c.783-1G>C		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.329359026589284	1	FACETS	0.603	0.529	0.683	0.603	0.529	0.683	SUBCLONAL	1	TRUE	0	0.398820802661216	1		411	486	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568881	212568881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	23	337	0	ENST00000342788.4:c.1237G>A	p.Asp413Asn	p.D413N	ENST00000342788	NM_005235.2	413	Gac/Aac	11/28	1	2	FACETS	0.515	0.403	0.643	0.515	0.403	0.643	SUBCLONAL	1	TRUE	1	0.398820802661216	2		337	224	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098427	47098427	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	78	469	0	ENST00000409792.3:c.6847C>T	p.Gln2283Ter	p.Q2283*	ENST00000409792	NM_014159.6	2283	Cag/Tag	15/21	0.267541306799908	3	FACETS	0.809	0.712	0.913	0.404	0.356	0.457	CLONAL	1	TRUE	1	0.398820802661216	3		469	580	SUCCESS
APC	324	MSKCC	GRCh37	5	112179219	112179219	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	64	236	0	ENST00000257430.4:c.7928T>C	p.Leu2643Pro	p.L2643P	ENST00000257430	NM_000038.5	2643	cTa/cCa	16/16	0.398820802661216	3	FACETS	1	0.956	1	0.615	0.536	0.699	CLONAL	1	TRUE	1	0.398820802661216	3		236	313	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401002	139401002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769908800	NA	P-0045058-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	113	661	1	ENST00000277541.6:c.3991G>A	p.Gly1331Arg	p.G1331R	ENST00000277541	NM_017617.3	1331	Ggg/Agg	24/34	1	2	FACETS	0.667	0.599	0.738	0.667	0.599	0.738	SUBCLONAL	1	TRUE	1	0.398820802661216	2		662	850	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0045096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	264	602	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.799279655657347	5	FACETS	0.984	0.935	1	0.984	0.935	1	CLONAL	3	FALSE	2	0.799279655657347	5		602	492	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0045096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	24	822	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.799279655657347	5	FACETS	0.294	0.23	0.368	0.098	0.076	0.123	SUBCLONAL	1	FALSE	2	0.799279655657347	5		822	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0045096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	211	510	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.760285244612127	3	FACETS	0.919	0.883	0.953	0.919	0.883	0.953	CLONAL	3	FALSE	0	0.799279655657347	3		510	268	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878184	48878240	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTGAGCGAGCAGAGCCGCCGTCGCCTCACGCGGGAAGGGCGCCCCGGGTGTGCGT	AGGTGAGCGAGCAGAGCCGCCGTCGCCTCACGCGGGAAGGGCGCCCCGGGTGTGCGT	-	novel	NA	P-0045096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	35	110	0	ENST00000267163.4:c.137+2_137+58del		p.X46_splice	ENST00000267163	NM_000321.2	46		1/27	0.778367492247609	3	FACETS	1	0.954	1	0.801	0.708	0.887	CLONAL	2	FALSE	0	0.799279655657347	3		110	51	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853804	59853804	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045096-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	29	409	0	ENST00000259008.2:c.2055G>C	p.Gln685His	p.Q685H	ENST00000259008	NM_032043.2	685	caG/caC	14/20	0.799279655657347	3	FACETS	0.275	0.22	0.336	0.137	0.11	0.168	SUBCLONAL	1	FALSE	1	0.799279655657347	3		409	370	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	239	337	0				ENST00000310581	NM_198253.2	-/1132			0.204362922154886	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.730816012171918	0		337	574	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082317	16082317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519919	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	372	731	0	ENST00000281043.3:c.131C>T	p.Pro44Leu	p.P44L	ENST00000281043	NM_005378.4	44	cCc/cTc	2/3	1	2	FACETS	0.99	0.942	1	0.99	0.942	1	CLONAL	1	FALSE	1	0.730816012171918	2		731	1028	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30135385	30135385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	106	451	1	ENST00000331968.5:c.433C>T	p.Arg145Cys	p.R145C	ENST00000331968	NM_002742.2	145	Cgt/Tgt	3/18	1	2	FACETS	0.746	0.674	0.82	0.746	0.674	0.82	SUBCLONAL	1	FALSE	1	0.730816012171918	2		452	389	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956723	68956723	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs750933833	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	27	465	0	ENST00000288368.4:c.841C>T	p.Arg281Trp	p.R281W	ENST00000288368	NM_024870.2	281	Cgg/Tgg	8/40	0.240654492971956	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.730816012171918	0		465	467	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489243	2489243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1337132564	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	289	709	0	ENST00000355716.4:c.148G>A	p.Gly50Ser	p.G50S	ENST00000355716	NM_003820.2	50	Ggc/Agc	2/8	1	2	FACETS	0.867	0.818	0.918	0.867	0.818	0.918	CLONAL	1	FALSE	1	0.730816012171918	2		709	912	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260291	16260291	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	237	529	0	ENST00000375759.3:c.7556C>T	p.Pro2519Leu	p.P2519L	ENST00000375759	NM_015001.2	2519	cCc/cTc	11/15	NA	2	FACETS	0.845	0.791	0.899			1	INDETERMINATE	1	FALSE	NA	0.730816012171918	2		529	768	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432368	432368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1362895739	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	48	176	0	ENST00000399788.2:c.2155C>T	p.Arg719Cys	p.R719C	ENST00000399788	NM_001042603.1	719	Cgc/Tgc	16/28	0.109359879444081	4	FACETS	0.789	0.682	0.902	0.789	0.682	0.902	INDETERMINATE	2	FALSE	2	0.730816012171918	4		176	144	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1023656	1023657	+	missense_variant	Missense_Mutation	DNP	GT	GT	AA	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	222	552	1	ENST00000358495.3:c.907_908delinsTT	p.Thr303Phe	p.T303F	ENST00000358495	NM_134424.2	303	ACt/TTt	10/12	0.109359879444081	4	FACETS	1	0.987	1	0.616	0.574	0.659	INDETERMINATE	1	FALSE	2	0.730816012171918	4		553	854	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037463	12037463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	193	471	0	ENST00000396373.4:c.1094C>T	p.Ser365Phe	p.S365F	ENST00000396373	NM_001987.4	365	tCc/tTc	6/8	0.109359879444081	4	FACETS	1	0.99	1	0.697	0.647	0.748	INDETERMINATE	1	FALSE	2	0.730816012171918	4		471	656	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114150	115114150	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765766538	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	327	618	0	ENST00000257566.3:c.1067C>T	p.Ala356Val	p.A356V	ENST00000257566	NM_016569.3	356	gCc/gTc	6/8	1	2	FACETS	0.871	0.824	0.918	0.871	0.824	0.918	CLONAL	1	FALSE	1	0.730816012171918	2		618	1028	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610104	28610104	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	149	528	0	ENST00000241453.7:c.1386G>A	p.Trp462Ter	p.W462*	ENST00000241453	NM_004119.2	462	tgG/tgA	11/24	0.649947669582988	1	FACETS	0.539	0.496	0.583	0.539	0.496	0.583	SUBCLONAL	1	FALSE	0	0.730816012171918	1		528	480	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554338	81554338	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759773701	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	113	377	0	ENST00000298171.2:c.358G>A	p.Asp120Asn	p.D120N	ENST00000298171	NM_000369.2	120	Gat/Aat	4/10	1	2	FACETS	0.708	0.641	0.777	0.708	0.641	0.777	SUBCLONAL	1	FALSE	1	0.730816012171918	2		377	437	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028740	42028741	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	169	529	0	ENST00000219905.7:c.4278_4279delinsAA	p.Met1426_Glu1427delinsIleLys	p.M1426_E1427delinsIK	ENST00000219905	NM_001164273.1	1426	atGGag/atAAag	13/24	1	2	FACETS	0.715	0.66	0.772	0.715	0.66	0.772	SUBCLONAL	1	FALSE	1	0.730816012171918	2		529	647	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132676	67132676	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536749790	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	137	519	0	ENST00000412916.2:c.559C>T	p.Arg187Cys	p.R187C	ENST00000412916		187	Cgt/Tgt	6/6	1	2	FACETS	0.82	0.752	0.891	0.82	0.752	0.891	CLONAL	1	FALSE	1	0.730816012171918	2		519	457	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836354	89836354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762439008	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	268	618	0	ENST00000389301.3:c.2395C>T	p.Pro799Ser	p.P799S	ENST00000389301	NM_000135.2	799	Cca/Tca	26/43	1	2	FACETS	0.871	0.819	0.924	0.871	0.819	0.924	CLONAL	1	FALSE	1	0.730816012171918	2		618	842	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577540	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	rs1555525498	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	293	603	2	ENST00000269305.4:c.741_742delinsTT	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	247	aaCCgg/aaTTgg	7/11	1	2	FACETS	0.855	0.806	0.905	0.855	0.806	0.905	CLONAL	1	FALSE	1	0.730816012171918	2		605	938	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	295	693	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	1	2	FACETS	0.96	0.907	1	0.96	0.907	1	CLONAL	1	FALSE	1	0.730816012171918	2		693	841	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7978952	7978952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139689690	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	237	481	0	ENST00000319144.4:c.1615G>A	p.Glu539Lys	p.E539K	ENST00000319144	NM_001139.2	539	Gaa/Aaa	12/15	1	2	FACETS	0.843	0.79	0.898	0.843	0.79	0.898	CLONAL	1	FALSE	1	0.730816012171918	2		481	769	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588770	29588770	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	126	380	0	ENST00000356175.3:c.4556C>T	p.Ala1519Val	p.A1519V	ENST00000356175	NM_000267.3	1519	gCa/gTa	34/57	0.109359879444081	4	FACETS	1	0.981	1	0.645	0.587	0.704	INDETERMINATE	1	FALSE	2	0.730816012171918	4		380	463	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281256	15281256	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752437137	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	264	696	2	ENST00000263388.2:c.5000G>A	p.Arg1667His	p.R1667H	ENST00000263388	NM_000435.2	1667	cGc/cAc	27/33	1	2	FACETS	0.818	0.769	0.869	0.818	0.769	0.869	CLONAL	1	FALSE	1	0.730816012171918	2		698	883	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367953	15367954	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	337	669	4	ENST00000263377.2:c.1372_1373delinsTT	p.Pro458Leu	p.P458L	ENST00000263377	NM_058243.2	458	CCg/TTg	8/20	1	2	FACETS	0.928	0.879	0.977	0.928	0.879	0.977	CLONAL	1	FALSE	1	0.730816012171918	2		673	994	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945686	17945686	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	275	690	0	ENST00000458235.1:c.2174C>T	p.Pro725Leu	p.P725L	ENST00000458235	NM_000215.3	725	cCc/cTc	16/24	1	2	FACETS	0.831	0.782	0.881	0.831	0.782	0.881	CLONAL	1	FALSE	1	0.730816012171918	2		690	906	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971769	18971769	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	292	574	0	ENST00000262803.5:c.2435C>T	p.Ser812Phe	p.S812F	ENST00000262803	NM_002911.3	812	tCc/tTc	17/24	1	2	FACETS	0.876	0.826	0.927	0.876	0.826	0.927	CLONAL	1	FALSE	1	0.730816012171918	2		574	912	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257396	19257397	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	271	789	2	ENST00000162023.5:c.736_737delinsAA	p.Gly246Lys	p.G246K	ENST00000162023		246	GGg/AAg	11/13	1	2	FACETS	0.679	0.637	0.722	0.679	0.637	0.722	SUBCLONAL	1	FALSE	1	0.730816012171918	2		791	1093	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748472	40748472	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	260	702	0	ENST00000392038.2:c.410A>G	p.Glu137Gly	p.E137G	ENST00000392038	NM_001626.4	137	gAa/gGa	5/14	NA	2	FACETS	0.792	0.744	0.842			1	INDETERMINATE	1	FALSE	NA	0.730816012171918	2		702	898	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42790949	42790949	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	392	647	2	ENST00000575354.2:c.94G>T	p.Val32Leu	p.V32L	ENST00000575354	NM_015125.3	32	Gtg/Ttg	2/20	NA	2	FACETS	0.921	0.876	0.966			1	INDETERMINATE	1	FALSE	NA	0.730816012171918	2		649	1165	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714673	52714673	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs945560047	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	319	663	0	ENST00000322088.6:c.431G>A	p.Arg144His	p.R144H	ENST00000322088	NM_014225.5	144	cGc/cAc	4/15	NA	2	FACETS	0.972	0.921	1			1	INDETERMINATE	1	FALSE	NA	0.730816012171918	2		663	898	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99170923	99170923	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	310	648	0	ENST00000074304.5:c.1552C>A	p.Leu518Met	p.L518M	ENST00000074304	NM_001134224.1	518	Ctg/Atg	16/26	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.730816012171918	2		648	828	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096414	178096414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	193	403	0	ENST00000397062.3:c.917G>A	p.Ser306Asn	p.S306N	ENST00000397062	NM_006164.4	306	aGc/aAc	5/5	1	2	FACETS	0.895	0.833	0.959	0.895	0.833	0.959	CLONAL	1	FALSE	1	0.730816012171918	2		403	590	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326544	62326544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	338	783	0	ENST00000360203.5:c.3469C>T	p.Pro1157Ser	p.P1157S	ENST00000360203	NM_001283009.1	1157	Cct/Tct	33/35	1	2	FACETS	0.901	0.853	0.949	0.901	0.853	0.949	CLONAL	1	FALSE	1	0.730816012171918	2		783	1027	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713274	30713275	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	226	420	0	ENST00000295754.5:c.599_600delinsTT	p.Thr200Ile	p.T200I	ENST00000295754	NM_003242.5	200	aCC/aTT	4/7	1	2	FACETS	0.892	0.835	0.951	0.892	0.835	0.951	CLONAL	1	FALSE	1	0.730816012171918	2		420	693	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015054	71015054	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	171	352	0	ENST00000318789.4:c.1876C>T	p.Pro626Ser	p.P626S	ENST00000318789	NM_032682.5	626	Cct/Tct	20/21	1	2	FACETS	0.86	0.797	0.926	0.86	0.797	0.926	CLONAL	1	FALSE	1	0.730816012171918	2		352	544	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259220	89259220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	105	381	0	ENST00000336596.2:c.364C>A	p.Leu122Met	p.L122M	ENST00000336596	NM_005233.5	122	Ctg/Atg	3/17	0.204362922154886	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.730816012171918	0		381	332	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390172	89390172	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	93	373	0	ENST00000336596.2:c.921G>T	p.Glu307Asp	p.E307D	ENST00000336596	NM_005233.5	307	gaG/gaT	4/17	0.204362922154886	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.730816012171918	0		373	337	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480459	89480460	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	85	386	0	ENST00000336596.2:c.2296_2297delinsAA	p.Gly766Lys	p.G766K	ENST00000336596	NM_005233.5	766	GGa/AAa	13/17	0.204362922154886	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.730816012171918	0		386	321	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153703	55153703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	158	573	0	ENST00000257290.5:c.2669C>T	p.Ser890Phe	p.S890F	ENST00000257290	NM_006206.4	890	tCc/tTc	19/23	0.270218351080419	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.730816012171918	0		573	514	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530954	187530954	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	148	413	0	ENST00000441802.2:c.10068+1G>A		p.X3356_splice	ENST00000441802	NM_005245.3	3356			1	2	FACETS	0.81	0.745	0.877	0.81	0.745	0.877	CLONAL	1	FALSE	1	0.730816012171918	2		413	500	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540918	187540918	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	135	356	0	ENST00000441802.2:c.6822del	p.Asp2274GlufsTer17	p.D2274Efs*17	ENST00000441802	NM_005245.3	2274	gaC/ga	10/27	1	2	FACETS	0.838	0.768	0.91	0.838	0.768	0.91	CLONAL	1	FALSE	1	0.730816012171918	2		356	441	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754607	57754607	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	145	374	0	ENST00000274289.3:c.440A>T	p.His147Leu	p.H147L	ENST00000274289	NM_006622.3	147	cAc/cTc	3/14	0.109359879444081	4	FACETS	1	0.988	1	0.735	0.676	0.796	INDETERMINATE	1	FALSE	2	0.730816012171918	4		374	467	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518061	176518061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	314	715	0	ENST00000292408.4:c.559G>A	p.Asp187Asn	p.D187N	ENST00000292408	NM_213647.1	187	Gat/Aat	5/18	1	2	FACETS	0.927	0.877	0.978	0.927	0.877	0.978	CLONAL	1	FALSE	1	0.730816012171918	2		715	927	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520185	176520186	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	245	706	1	ENST00000292408.4:c.1104_1105delinsAA	p.Asp369Asn	p.D369N	ENST00000292408	NM_213647.1	368	acGGac/acAAac	9/18	1	2	FACETS	0.77	0.721	0.82	0.77	0.721	0.82	SUBCLONAL	1	FALSE	1	0.730816012171918	2		707	871	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665401	176665401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	233	477	0	ENST00000439151.2:c.4085G>A	p.Gly1362Glu	p.G1362E	ENST00000439151	NM_022455.4	1362	gGa/gAa	7/23	NA	2	FACETS	0.943	0.884	1			1	INDETERMINATE	1	FALSE	NA	0.730816012171918	2		477	676	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609813	117609813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761155034	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	150	547	0	ENST00000368508.3:c.6886G>A	p.Glu2296Lys	p.E2296K	ENST00000368508	NM_002944.2	2296	Gaa/Aaa	43/43	0.340762894204108	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.730816012171918	0		547	422	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686853	117686853	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	80	479	0	ENST00000368508.3:c.2864C>T	p.Ser955Leu	p.S955L	ENST00000368508	NM_002944.2	955	tCa/tTa	19/43	0.340762894204108	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.730816012171918	0		479	309	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001331	150001332	+	missense_variant	Missense_Mutation	DNP	GC	GC	TT	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	121	565	1	ENST00000253339.5:c.2272_2273delinsAA	p.Ala758Asn	p.A758N	ENST00000253339		758	GCt/AAt	4/7	0.668245915951156	1	FACETS	0.703	0.645	0.762	0.703	0.645	0.762	SUBCLONAL	1	FALSE	0	0.730816012171918	1		566	299	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509438	106509438	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748511834	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	185	639	1	ENST00000359195.3:c.1432G>A	p.Gly478Arg	p.G478R	ENST00000359195	NM_002649.2	478	Gga/Aga	2/11	1	2	FACETS	0.778	0.721	0.836	0.778	0.721	0.836	SUBCLONAL	1	FALSE	1	0.730816012171918	2		640	651	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738994	145738995	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	277	628	0	ENST00000428558.2:c.2160_2161delinsTT	p.Arg721Ter	p.R721*	ENST00000428558	NM_004260.3	720	ctCCga/ctTTga	13/22	1	2	FACETS	0.889	0.837	0.941	0.889	0.837	0.941	CLONAL	1	FALSE	1	0.730816012171918	2		628	853	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5072544	5072544	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	66	405	0	ENST00000381652.3:c.1694G>A	p.Arg565Lys	p.R565K	ENST00000381652	NM_004972.3	565	aGa/aAa	13/25	NA	2	FACETS	0.714	0.627	0.806			1	INDETERMINATE	1	FALSE	NA	0.730816012171918	2		405	253	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5456166	5456166	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	48	229	0	ENST00000381577.3:c.52+1G>A		p.X18_splice	ENST00000381577	NM_014143.3	18			NA	2	FACETS	0.746	0.641	0.858			1	INDETERMINATE	1	FALSE	NA	0.730816012171918	2		229	176	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229512	98229512	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	194	479	0	ENST00000331920.6:c.2446C>T	p.Gln816Ter	p.Q816*	ENST00000331920	NM_000264.3	816	Cag/Tag	15/24	NA	2	FACETS	0.756	0.702	0.812			1	INDETERMINATE	1	FALSE	NA	0.730816012171918	2		479	702	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240459	98240459	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	307	372	0	ENST00000331920.6:c.1225C>T	p.Gln409Ter	p.Q409*	ENST00000331920	NM_000264.3	409	Cag/Tag	9/24	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	FALSE	NA	0.730816012171918	2		372	751	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222430	53222431	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0045098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	298	360	0	ENST00000375401.3:c.4401_4402delinsAA	p.Glu1468Lys	p.E1468K	ENST00000375401	NM_004187.3	1467	ggGGag/ggAAag	26/26	1	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	0	0.730816012171918	1		360	492	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0045099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	21	472	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	0.935	0.723	1	0.935	0.723	1	CLONAL	1	TRUE	1	0.21	2		472	214	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41209148	41209148	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	40	582	0	ENST00000357654.3:c.5198A>C	p.Asp1733Ala	p.D1733A	ENST00000357654	NM_007294.3	1733	gAt/gCt	19/23	1	2	FACETS	0.825	0.691	0.971	1	0.962	1	CLONAL	2	TRUE	1	0.21	2		582	231	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156949	106156949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1367059281	NA	P-0045099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	34	517	0	ENST00000380013.4:c.1850G>A	p.Arg617Lys	p.R617K	ENST00000380013	NM_001127208.2	617	aGg/aAg	3/11	1	2	FACETS	0.753	0.62	0.9	1	0.949	1	SUBCLONAL	2	TRUE	1	0.21	2		517	215	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149453013	149453013	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	24	560	0	ENST00000286301.3:c.933G>C	p.Gln311His	p.Q311H	ENST00000286301	NM_005211.3	311	caG/caC	7/22	1	2	FACETS	1	0.822	1	1	0.822	1	CLONAL	1	TRUE	1	0.21	2		560	218	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0045101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	715	510	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.622044216729011	3	FACETS	0.887	0.863	0.912	0.887	0.863	0.912	CLONAL	3	TRUE	0	0.622044216729011	3		510	1132	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412059	63412059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	464	371	0	ENST00000330258.3:c.1108G>A	p.Glu370Lys	p.E370K	ENST00000330258	NM_152424.3	370	Gag/Aag	2/2	0.622044216729011	2	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.622044216729011	2		371	665	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215595163	215595163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377227840	NA	P-0045101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	217	353	0	ENST00000260947.4:c.1973G>A	p.Arg658His	p.R658H	ENST00000260947	NM_000465.2	658	cGc/cAc	10/11	0.52258513015752	3	FACETS	0.849	0.796	0.902	0.849	0.796	0.902	CLONAL	2	TRUE	1	0.622044216729011	3		353	539	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361127	66361127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1400810776	NA	P-0045101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	108	312	0	ENST00000273854.3:c.1045C>T	p.Pro349Ser	p.P349S	ENST00000273854	NM_004439.5	349	Cca/Tca	4/18	0.52258513015752	3	FACETS	0.877	0.79	0.968	0.439	0.395	0.484	CLONAL	1	TRUE	1	0.622044216729011	3		312	519	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456593	32456593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	76	66	0	ENST00000332351.3:c.299C>T	p.Ala100Val	p.A100V	ENST00000332351	NM_024426.4	100	gCg/gTg	1/10	0.554377898896325	2	FACETS	0.843	0.764	0.921	0.843	0.764	0.921	CLONAL	2	TRUE	0	0.622044216729011	2		66	145	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118695	11118695	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	214	512	0	ENST00000358026.2:c.2119A>T	p.Ile707Phe	p.I707F	ENST00000358026	NM_001128849.1	707	Att/Ttt	14/36	0.550348870333299	3	FACETS	0.817	0.759	0.878	0.272	0.253	0.293	CLONAL	1	TRUE	0	0.622044216729011	3		512	1104	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46588226	46588226	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	185	389	0	ENST00000263734.3:c.776A>G	p.Asp259Gly	p.D259G	ENST00000263734	NM_001430.4	259	gAc/gGc	6/16	0.556727263660913	4	FACETS	0.904	0.834	0.977	0.301	0.278	0.326	CLONAL	1	TRUE	1	0.622044216729011	4		389	1067	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638721	176638721	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	489	581	0	ENST00000439151.2:c.3321T>A	p.Asp1107Glu	p.D1107E	ENST00000439151	NM_022455.4	1107	gaT/gaA	5/23	0.601619522160262	3	FACETS	0.934	0.896	0.971			1	CLONAL	2	TRUE	NA	0.622044216729011	3		581	1104	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426808	121426808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371759652	NA	P-0045117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	74	607	0	ENST00000257555.6:c.499G>A	p.Val167Ile	p.V167I	ENST00000257555		167	Gtc/Atc	2/10	NA	2	FACETS	0.554	0.485	0.627			1	INDETERMINATE	1	TRUE	NA	0.48856193020089	2		607	547	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775164	73775164	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867543814	NA	P-0045117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	156	607	0	ENST00000254810.4:c.92C>T	p.Pro31Leu	p.P31L	ENST00000254810	NM_005324.3	31	cCc/cTc	2/4	0.233841767063693	3	FACETS	1	0.984	1	0.639	0.587	0.692	INDETERMINATE	1	TRUE	1	0.48856193020089	3		607	622	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085885	16085885	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs185639773	NA	P-0045117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	73	584	1	ENST00000281043.3:c.1061C>T	p.Ala354Val	p.A354V	ENST00000281043	NM_005378.4	354	gCg/gTg	3/3	0.189548238396688	3	FACETS	0.718	0.629	0.813	0.359	0.314	0.407	INDETERMINATE	1	TRUE	1	0.48856193020089	3		585	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1567548929	NA	P-0045118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	503	537	1	ENST00000269305.4:c.775G>T	p.Asp259Tyr	p.D259Y	ENST00000269305	NM_001126112.2	259	Gac/Tac	7/11	0.510244185480663	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	FALSE	0	0.517791620930251	3		538	797	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851678	134851678	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	245	463	0	ENST00000398015.3:c.1084A>C	p.Lys362Gln	p.K362Q	ENST00000398015	NM_004441.4	362	Aag/Cag	5/16	0.401122403076497	5	FACETS	0.947	0.886	1	0.631	0.591	0.673	CLONAL	2	FALSE	2	0.517791620930251	5		463	888	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0045119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	1239	602	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.488898543248958	11	FACETS	0.977	0.957	0.996	0.977	0.957	0.996	CLONAL	9	FALSE	2	0.488898543248958	11		602	1845	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428610	78428610	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	147	296	0	ENST00000370768.2:c.1189G>A	p.Glu397Lys	p.E397K	ENST00000370768	NM_003902.3	397	Gaa/Aaa	14/20	0.489336548873904	4	FACETS	0.861	0.791	0.933			1	CLONAL	2	FALSE	NA	0.488898543248958	4		296	520	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754723	41754723	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045119-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	220	540	0	ENST00000301178.4:c.1709A>G	p.Lys570Arg	p.K570R	ENST00000301178	NM_021913.4	570	aAg/aGg	14/20	0.303210901756838	4	FACETS	0.842	0.785	0.9	0.842	0.785	0.9	CLONAL	2	FALSE	2	0.488898543248958	4		540	796	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0045120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	58	548	0	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.17	2		548	668	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54963246	54963246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745894289	NA	P-0045120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	30	273	2	ENST00000312783.6:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000312783	NM_198436.1	3	cGa/cAa	3/10	1	2	FACETS	0.874	0.704	1	0.874	0.704	1	CLONAL	1	TRUE	1	0.17	2		275	404	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588951	67588951	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520690	NA	P-0045120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	38	223	0	ENST00000274335.5:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000274335		348	Cga/Tga	8/15	1	2	FACETS	0.768	0.638	0.912	1	0.955	1	CLONAL	2	TRUE	1	0.17	2		223	291	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711899	89711899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913293	NA	P-0045120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	38	383	1	ENST00000371953.3:c.517C>T	p.Arg173Cys	p.R173C	ENST00000371953	NM_000314.4	173	Cgc/Tgc	6/9	1	2	FACETS	0.822	0.678	0.982	0.822	0.678	0.982	CLONAL	1	TRUE	1	0.17	2		384	544	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0045120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	14	387	1	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	0.361	0.26	0.485	0.361	0.26	0.485	SUBCLONAL	1	TRUE	1	0.17	2		388	456	SUCCESS
BLM	641	MSKCC	GRCh37	15	91346819	91346819	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140387675	NA	P-0045120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	32	355	0	ENST00000355112.3:c.3427G>A	p.Glu1143Lys	p.E1143K	ENST00000355112	NM_000057.2	1143	Gaa/Aaa	18/22	1	2	FACETS	0.831	0.674	1	0.831	0.674	1	CLONAL	1	TRUE	1	0.17	2		355	453	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519896	NA	P-0045120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	38	317	0	ENST00000281708.4:c.1514G>A	p.Arg505His	p.R505H	ENST00000281708	NM_033632.3	505	cGc/cAc	10/12	1	2	FACETS	0.791	0.653	0.946	0.791	0.653	0.946	CLONAL	1	TRUE	1	0.17	2		317	565	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0045120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	53	393	0	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	1	2	FACETS	0.974	0.83	1	0.974	0.83	1	CLONAL	1	TRUE	1	0.17	2		393	640	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115600	108115600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772821016	NA	P-0045120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	32	361	1	ENST00000278616.4:c.748C>T	p.Arg250Ter	p.R250*	ENST00000278616	NM_000051.3	250	Cga/Tga	7/63	1	2	FACETS	1	0.828	1	1	0.828	1	CLONAL	1	TRUE	1	0.17	2		362	369	SUCCESS
ATM	472	MSKCC	GRCh37	11	108205756	108205756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531980488	NA	P-0045120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	26	316	0	ENST00000278616.4:c.8071C>T	p.Arg2691Cys	p.R2691C	ENST00000278616	NM_000051.3	2691	Cgc/Tgc	55/63	1	2	FACETS	0.734	0.58	0.91	0.734	0.58	0.91	CLONAL	1	TRUE	1	0.17	2		316	417	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81973635	81973635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	62	470	0	ENST00000359376.3:c.3452C>T	p.Ala1151Val	p.A1151V	ENST00000359376	NM_002661.3	1151	gCc/gTc	30/33	1	2	FACETS	0.936	0.807	1	0.936	0.807	1	CLONAL	1	TRUE	1	0.17	2		470	779	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542861	187542861	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1340793072	NA	P-0045120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	42	305	1	ENST00000441802.2:c.4879C>T	p.Arg1627Ter	p.R1627*	ENST00000441802	NM_005245.3	1627	Cga/Tga	10/27	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.17	2		306	463	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513352	41513352	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	47	522	0	ENST00000263253.7:c.256C>T	p.Arg86Ter	p.R86*	ENST00000263253	NM_001429.3	86	Cga/Tga	2/31	1	2	FACETS	0.692	0.582	0.814	0.692	0.582	0.814	SUBCLONAL	1	TRUE	1	0.17	2		522	799	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385357	4385357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	36	290	0	ENST00000261254.3:c.382G>A	p.Asp128Asn	p.D128N	ENST00000261254	NM_001759.3	128	Gac/Aac	2/5	1	2	FACETS	0.811	0.666	0.974	0.811	0.666	0.974	CLONAL	1	TRUE	1	0.17	2		290	522	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934222	39934222	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1358504792	NA	P-0045120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	71	593	0	ENST00000378444.4:c.377C>T	p.Pro126Leu	p.P126L	ENST00000378444	NM_001123385.1	126	cCg/cTg	4/15	1	2	FACETS	0.8	0.696	0.913	0.8	0.696	0.913	CLONAL	1	TRUE	1	0.17	2		593	1044	SUCCESS
BLM	641	MSKCC	GRCh37	15	91290717	91290717	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	33	286	0	ENST00000355112.3:c.95T>G	p.Phe32Cys	p.F32C	ENST00000355112	NM_000057.2	32	tTt/tGt	2/22	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.17	2		286	366	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404911	404911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	58	434	0	ENST00000399788.2:c.4283G>A	p.Arg1428Gln	p.R1428Q	ENST00000399788	NM_001042603.1	1428	cGa/cAa	26/28	1	2	FACETS	0.785	0.673	0.908	0.785	0.673	0.908	CLONAL	1	TRUE	1	0.17	2		434	869	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105688	27105688	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	32	319	0	ENST00000324856.7:c.5299G>T	p.Glu1767Ter	p.E1767*	ENST00000324856	NM_006015.4	1767	Gaa/Taa	20/20	1	2	FACETS	0.708	0.573	0.86	0.708	0.573	0.86	SUBCLONAL	1	TRUE	1	0.17	2		319	532	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707863	43707863	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	61	542	1	ENST00000382044.4:c.5018G>T	p.Arg1673Ile	p.R1673I	ENST00000382044	NM_001141980.1	1673	aGa/aTa	23/28	1	2	FACETS	0.604	0.519	0.697	0.604	0.519	0.697	SUBCLONAL	1	TRUE	1	0.17	2		543	1189	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048821	180048821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368426530	NA	P-0045120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	91	577	3	ENST00000261937.6:c.1741G>A	p.Asp581Asn	p.D581N	ENST00000261937	NM_182925.4	581	Gac/Aac	13/30	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.17	2		580	1043	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712607	52712607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542945393	NA	P-0045120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	28	250	0	ENST00000394830.3:c.145G>A	p.Val49Met	p.V49M	ENST00000394830	NM_018313.4	49	Gtg/Atg	3/30	1	2	FACETS	0.619	0.494	0.763	0.619	0.494	0.763	SUBCLONAL	1	TRUE	1	0.17	2		250	532	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624243	89624243	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	24	153	0	ENST00000371953.3:c.17A>C	p.Lys6Thr	p.K6T	ENST00000371953	NM_000314.4	6	aAa/aCa	1/9	1	2	FACETS	1	0.798	1	1	0.798	1	CLONAL	1	TRUE	1	0.17	2		153	278	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912693	100912693	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	33	291	0	ENST00000325455.5:c.2629C>A	p.Leu877Ile	p.L877I	ENST00000325455	NM_001202474.3	877	Ctt/Att	7/8	1	2	FACETS	0.687	0.558	0.833	0.687	0.558	0.833	SUBCLONAL	1	TRUE	1	0.17	2		291	565	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383277	4383277	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	41	447	0	ENST00000261254.3:c.71A>G	p.Asp24Gly	p.D24G	ENST00000261254	NM_001759.3	24	gAc/gGc	1/5	1	2	FACETS	0.744	0.619	0.885	0.744	0.619	0.885	SUBCLONAL	1	TRUE	1	0.17	2		447	648	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601306	28601306	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	61	382	0	ENST00000241453.7:c.2126A>C	p.Lys709Thr	p.K709T	ENST00000241453	NM_004119.2	709	aAa/aCa	17/24	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.17	2		382	559	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350825	89350825	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	80	575	0	ENST00000301030.4:c.2125G>T	p.Glu709Ter	p.E709*	ENST00000301030	NM_001256183.1	709	Gaa/Taa	9/13	1	2	FACETS	0.858	0.753	0.971	0.858	0.753	0.971	CLONAL	1	TRUE	1	0.17	2		575	1097	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15976820	15976820	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	47	433	0	ENST00000268712.3:c.3734G>A	p.Arg1245Lys	p.R1245K	ENST00000268712	NM_006311.3	1245	aGa/aAa	28/46	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.17	2		433	506	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164388	47164388	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	29	240	1	ENST00000409792.3:c.1738G>T	p.Glu580Ter	p.E580*	ENST00000409792	NM_014159.6	580	Gaa/Taa	3/21	1	2	FACETS	0.995	0.799	1	0.995	0.799	1	CLONAL	1	TRUE	1	0.17	2		241	343	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808250	99808250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs17850950	NA	P-0045120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	51	448	0	ENST00000280892.6:c.439G>A	p.Asp147Asn	p.D147N	ENST00000280892	NM_001130678.1	147	Gat/Aat	5/7	1	2	FACETS	0.932	0.791	1	0.932	0.791	1	CLONAL	1	TRUE	1	0.17	2		448	644	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31431727	31431727	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1003588847	NA	P-0045120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	53	367	3	ENST00000344624.3:c.3101C>T	p.Ser1034Leu	p.S1034L	ENST00000344624		1034	tCg/tTg	23/33	1	2	FACETS	0.807	0.686	0.939	0.807	0.686	0.939	CLONAL	1	TRUE	1	0.17	2		370	773	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481556	20481556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	38	244	0	ENST00000346618.3:c.625G>A	p.Glu209Lys	p.E209K	ENST00000346618	NM_001949.4	209	Gaa/Aaa	3/7	1	2	FACETS	0.871	0.72	1	0.871	0.72	1	CLONAL	1	TRUE	1	0.17	2		244	513	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447739	187447739	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	1096	658	0	ENST00000232014.4:c.454C>G	p.Gln152Glu	p.Q152E	ENST00000232014	NM_001130845.1	152	Caa/Gaa	5/10	0.841833450787301	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.841833450787301	3		658	1228	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007855	45007855	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	167	401	0	ENST00000558401.1:c.302G>C	p.Arg101Pro	p.R101P	ENST00000558401	NM_004048.2	101	cGt/cCt	2/4	0.841833450787301	1	FACETS	0.66	0.616	0.704	0.66	0.616	0.704	SUBCLONAL	1	TRUE	0	0.841833450787301	1		401	348	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027244	49027244	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	179	393	0	ENST00000267163.4:c.1811A>G	p.Asp604Gly	p.D604G	ENST00000267163	NM_000321.2	604	gAt/gGt	18/27	0.841833450787301	1	FACETS	0.966	0.918	1	0.966	0.918	1	CLONAL	1	TRUE	0	0.841833450787301	1		393	255	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs397516439	NA	P-0045121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	374	616	0	ENST00000269305.4:c.920-2A>G		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.841833450787301	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.841833450787301	1		616	507	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448479	49448479	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs941339684	NA	P-0045121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	398	640	0	ENST00000301067.7:c.232G>A	p.Gly78Arg	p.G78R	ENST00000301067	NM_003482.3	78	Ggg/Agg	3/54	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.841833450787301	2		640	933	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256050	16256050	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	281	577	0	ENST00000375759.3:c.3315G>T	p.Lys1105Asn	p.K1105N	ENST00000375759	NM_015001.2	1105	aaG/aaT	11/15	1	2	FACETS	0.901	0.851	0.952	0.901	0.851	0.952	CLONAL	1	TRUE	1	0.841833450787301	2		577	741	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983074	201983074	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	444	700	0	ENST00000359651.3:c.923C>A	p.Ser308Tyr	p.S308Y	ENST00000359651		308	tCc/tAc	7/8	1	2	FACETS	0.956	0.915	0.998	0.956	0.915	0.998	CLONAL	1	TRUE	1	0.841833450787301	2		700	1103	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366492	118366492	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	263	476	0	ENST00000534358.1:c.5441A>T	p.Asn1814Ile	p.N1814I	ENST00000534358	NM_005933.3	1814	aAc/aTc	19/36	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.841833450787301	2		476	604	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863437	57863437	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	410	651	0	ENST00000228682.2:c.1532C>A	p.Pro511Gln	p.P511Q	ENST00000228682	NM_005269.2	511	cCa/cAa	11/12	1	2	FACETS	0.997	0.953	1	0.997	0.953	1	CLONAL	1	TRUE	1	0.841833450787301	2		651	977	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212522543	212522543	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	227	329	0	ENST00000342788.4:c.1882C>A	p.Pro628Thr	p.P628T	ENST00000342788	NM_005235.2	628	Ccc/Acc	16/28	1	2	FACETS	0.993	0.934	1	0.993	0.934	1	CLONAL	1	TRUE	1	0.841833450787301	2		329	543	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213808	66213808	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0045121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	244	489	0	ENST00000273854.3:c.2622T>G	p.Tyr874Ter	p.Y874*	ENST00000273854	NM_004439.5	874	taT/taG	15/18	1	2	FACETS	0.971	0.915	1	0.971	0.915	1	CLONAL	1	TRUE	1	0.841833450787301	2		489	597	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196856	106196856	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	74	395	0	ENST00000380013.4:c.5189A>T	p.Asp1730Val	p.D1730V	ENST00000380013	NM_001127208.2	1730	gAt/gTt	11/11	1	2	FACETS	0.317	0.278	0.36	0.317	0.278	0.36	SUBCLONAL	1	TRUE	1	0.841833450787301	2		395	554	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650733	48650733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045121-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	318	300	0	ENST00000376670.3:c.602C>T	p.Ala201Val	p.A201V	ENST00000376670	NM_002049.3	201	gCc/gTc	4/6	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.841833450787301	1		300	372	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0045122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	71	400	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.79	0.693	0.894	0.79	0.693	0.894	SUBCLONAL	1	TRUE	1	0.448250899374325	2		400	401	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624275	89624275	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204910	NA	P-0045122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	244	354	0	ENST00000371953.3:c.49C>T	p.Gln17Ter	p.Q17*	ENST00000371953	NM_000314.4	17	Caa/Taa	1/9	0.448250899374325	2	FACETS	0.974	0.918	1	0.974	0.918	1	CLONAL	2	TRUE	0	0.448250899374325	2		354	559	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087548	27087548	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	194	580	1	ENST00000324856.7:c.2122C>T	p.Gln708Ter	p.Q708*	ENST00000324856	NM_006015.4	708	Cag/Tag	5/20	1	2	FACETS	0.831	0.769	0.897	0.831	0.769	0.897	CLONAL	1	TRUE	1	0.448250899374325	2		581	1041	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591259	67591261	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	novel	NA	P-0045122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	73	401	0	ENST00000274335.5:c.1759_1761del	p.Lys587del	p.K587del	ENST00000274335		586	cAAAaa/caa	13/15	1	2	FACETS	0.662	0.58	0.75	0.662	0.58	0.75	SUBCLONAL	1	TRUE	1	0.448250899374325	2		401	492	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589607	67589607	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	36	253	0	ENST00000274335.5:c.1370A>C	p.Gln457Pro	p.Q457P	ENST00000274335		457	cAa/cCa	10/15	1	2	FACETS	0.658	0.545	0.784	0.658	0.545	0.784	SUBCLONAL	1	TRUE	1	0.448250899374325	2		253	244	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325882	65325882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1490560356	NA	P-0045122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	185	477	0	ENST00000342505.4:c.1240C>T	p.Arg414Trp	p.R414W	ENST00000342505	NM_002227.2	414	Cgg/Tgg	9/25	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.448250899374325	2		477	794	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40444032	40444032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1331420896	NA	P-0045122-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	214	663	0	ENST00000345506.4:c.328C>T	p.Arg110Trp	p.R110W	ENST00000345506	NM_003152.3	110	Cgg/Tgg	5/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.448250899374325	2		663	886	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0045123-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	103	401	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.33	2		401	467	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0045124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	188	464	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.886	0.819	0.955	0.886	0.819	0.955	CLONAL	1	TRUE	1	0.465465524421488	2		464	912	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0045124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	126	298	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.465465524421488	2		298	540	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188854	32188854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1183058401	NA	P-0045124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	198	547	1	ENST00000375023.3:c.700C>T	p.Arg234Trp	p.R234W	ENST00000375023	NM_004557.3	234	Cgg/Tgg	4/30	1	2	FACETS	0.973	0.903	1	0.973	0.903	1	CLONAL	1	TRUE	1	0.465465524421488	2		548	874	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0045124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	74	207	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	1	2	FACETS	0.938	0.827	1	0.938	0.827	1	CLONAL	1	TRUE	1	0.465465524421488	2		207	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578254	7578254	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567551821	NA	P-0045124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	220	516	1	ENST00000269305.4:c.595G>T	p.Gly199Ter	p.G199*	ENST00000269305	NM_001126112.2	199	Gga/Tga	6/11	0.461608409910458	1	FACETS	0.925	0.863	0.989	0.925	0.863	0.989	CLONAL	1	TRUE	0	0.465465524421488	1		517	784	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022914	27022942	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCCGCCGCCAGCAGCCTGGGCAACCCG	CCGCCGCCGCCAGCAGCCTGGGCAACCCG	-	novel	NA	P-0045124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	22	19	0	ENST00000324856.7:c.31_59del	p.Ser11AlafsTer90	p.S11Afs*90	ENST00000324856	NM_006015.4	7	cCCGCCGCCGCCAGCAGCCTGGGCAACCCG/c	1/20	0.461608409910458	1	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	0	0.465465524421488	1		19	62	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211898	36211899	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs775294431	NA	P-0045124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	264	612	2	ENST00000222270.7:c.1656dup	p.Lys553GlnfsTer46	p.K553Qfs*46	ENST00000222270	NM_014727.1	550	gac/gaCc	3/37	1	2	FACETS	0.931	0.871	0.992	0.931	0.871	0.992	CLONAL	1	TRUE	1	0.465465524421488	2		614	1219	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119683	70119683	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0045124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	192	443	0	ENST00000245479.2:c.686-1G>T		p.X229_splice	ENST00000245479	NM_000346.3	229			1	2	FACETS	0.952	0.881	1	0.952	0.881	1	CLONAL	1	TRUE	1	0.465465524421488	2		443	867	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292591	15292591	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758913191	NA	P-0045124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	247	513	2	ENST00000263388.2:c.2588C>T	p.Ser863Leu	p.S863L	ENST00000263388	NM_000435.2	863	tCg/tTg	17/33	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.465465524421488	2		515	972	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0045126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	487	644	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.732124537257136	2	FACETS	0.92	0.891	0.948	0.92	0.891	0.948	CLONAL	2	TRUE	0	0.737314298609089	2		644	718	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16203161	16203161	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	158	382	0	ENST00000375759.3:c.869C>T	p.Thr290Ile	p.T290I	ENST00000375759	NM_015001.2	290	aCc/aTc	3/15	0.726707609859463	3	FACETS	0.904	0.831	0.979	0.452	0.415	0.49	CLONAL	1	TRUE	1	0.737314298609089	3		382	649	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100877	27100877	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	395	500	0	ENST00000324856.7:c.4159G>C	p.Glu1387Gln	p.E1387Q	ENST00000324856	NM_006015.4	1387	Gag/Cag	18/20	0.726707609859463	3	FACETS	0.894	0.856	0.933	0.894	0.856	0.933	CLONAL	2	TRUE	1	0.737314298609089	3		500	820	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595928	43595928	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0045126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	718	575	0	ENST00000355710.3:c.95C>A	p.Ser32Ter	p.S32*	ENST00000355710	NM_020975.4	32	tCg/tAg	2/20	0.737314298609089	6	FACETS	0.98	0.947	1	0.98	0.947	1	CLONAL	3	TRUE	3	0.737314298609089	6		575	1639	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933424	100933424	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	155	359	0	ENST00000325455.5:c.1966C>G	p.Leu656Val	p.L656V	ENST00000325455	NM_001202474.3	656	Ctc/Gtc	4/8	0.731454677967059	5	FACETS	1	0.917	1	0.334	0.305	0.364	CLONAL	1	TRUE	2	0.737314298609089	5		359	884	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112942537	112942537	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	283	350	0	ENST00000351677.2:c.1751G>T	p.Gly584Val	p.G584V	ENST00000351677	NM_002834.3	584	gGc/gTc	15/16	0.737314298609089	3	FACETS	0.931	0.885	0.978	0.931	0.885	0.978	CLONAL	2	TRUE	1	0.737314298609089	3		350	564	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436201	110436201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1246771759	NA	P-0045126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	204	403	1	ENST00000375856.3:c.2200G>A	p.Glu734Lys	p.E734K	ENST00000375856	NM_003749.2	734	Gag/Aag	1/2	NA	2	FACETS	1	0.943	1			1	INDETERMINATE	1	TRUE	NA	0.737314298609089	2		404	548	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035119	42035119	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	508	617	0	ENST00000219905.7:c.4961C>T	p.Ser1654Phe	p.S1654F	ENST00000219905	NM_001164273.1	1654	tCt/tTt	15/24	0.732124537257136	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.737314298609089	2		617	678	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041025	42041025	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	474	546	1	ENST00000219905.7:c.5403C>G	p.Phe1801Leu	p.F1801L	ENST00000219905	NM_001164273.1	1801	ttC/ttG	16/24	0.732124537257136	2	FACETS	0.943	0.914	0.971	0.943	0.914	0.971	CLONAL	2	TRUE	0	0.737314298609089	2		547	682	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041388	42041388	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	473	525	0	ENST00000219905.7:c.5583C>G	p.Phe1861Leu	p.F1861L	ENST00000219905	NM_001164273.1	1861	ttC/ttG	17/24	0.732124537257136	2	FACETS	0.965	0.936	0.993	0.965	0.936	0.993	CLONAL	2	TRUE	0	0.737314298609089	2		525	665	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041582	42041582	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0045126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	419	497	0	ENST00000219905.7:c.5777C>G	p.Ser1926Ter	p.S1926*	ENST00000219905	NM_001164273.1	1926	tCa/tGa	17/24	0.732124537257136	2	FACETS	0.981	0.951	1	0.981	0.951	1	CLONAL	2	TRUE	0	0.737314298609089	2		497	579	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041671	42041671	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	368	450	0	ENST00000219905.7:c.5866C>A	p.Pro1956Thr	p.P1956T	ENST00000219905	NM_001164273.1	1956	Cct/Act	17/24	0.732124537257136	2	FACETS	0.969	0.936	1	0.969	0.936	1	CLONAL	2	TRUE	0	0.737314298609089	2		450	515	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556253	29556253	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0045126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	294	400	1	ENST00000356175.3:c.2620A>T	p.Lys874Ter	p.K874*	ENST00000356175	NM_000267.3	874	Aag/Tag	21/57	0.737314298609089	2	FACETS	0.959	0.922	0.994	0.959	0.922	0.994	CLONAL	2	TRUE	0	0.737314298609089	2		401	416	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71101768	71101768	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	79	197	0	ENST00000318789.4:c.430C>G	p.Gln144Glu	p.Q144E	ENST00000318789	NM_032682.5	144	Caa/Gaa	9/21	0.732124537257136	2	FACETS	0.868	0.774	0.965	0.434	0.387	0.483	CLONAL	1	TRUE	0	0.737314298609089	2		197	247	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138376532	138376532	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	180	429	0	ENST00000289153.2:c.2942G>C	p.Arg981Pro	p.R981P	ENST00000289153	NM_006219.2	981	cGg/cCg	20/22	0.718390754566473	4	FACETS	0.936	0.864	1	0.234	0.216	0.253	CLONAL	1	TRUE	0	0.737314298609089	4		429	906	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672224	86672224	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	133	253	1	ENST00000274376.6:c.2026C>T	p.Gln676Ter	p.Q676*	ENST00000274376	NM_002890.2	676	Cag/Tag	16/25	0.732124537257136	2	FACETS	0.932	0.856	1	0.466	0.428	0.506	CLONAL	1	TRUE	0	0.737314298609089	2		254	387	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670961	30670961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	126	604	2	ENST00000376406.3:c.5785G>A	p.Asp1929Asn	p.D1929N	ENST00000376406	NM_014641.2	1929	Gat/Aat	12/15	0.737314298609089	3	FACETS	0.448	0.405	0.494	0.224	0.202	0.247	SUBCLONAL	1	TRUE	1	0.737314298609089	3		606	1044	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843411	128843411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147491841	NA	P-0045126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	189	437	3	ENST00000249373.3:c.518G>A	p.Arg173His	p.R173H	ENST00000249373	NM_005631.4	173	cGc/cAc	2/12	0.737314298609089	4	FACETS	0.956	0.883	1			1	CLONAL	1	TRUE	NA	0.737314298609089	4		440	932	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949126	151949126	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	205	416	0	ENST00000262189.6:c.1519C>G	p.Gln507Glu	p.Q507E	ENST00000262189	NM_170606.2	507	Cag/Gag	11/59	0.737314298609089	4	FACETS	0.839	0.777	0.904			1	CLONAL	1	TRUE	NA	0.737314298609089	4		416	1151	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717661	89717661	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0045169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	97	349	0	ENST00000371953.3:c.686C>G	p.Ser229Ter	p.S229*	ENST00000371953	NM_000314.4	229	tCa/tGa	7/9	0.289924477110229	2	FACETS	0.777	0.699	0.859	0.777	0.699	0.859	SUBCLONAL	2	TRUE	0	0.34290667450967	2		349	364	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643737	38643737	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1201851975	NA	P-0045169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	123	634	2	ENST00000299084.4:c.1207C>T	p.Arg403Ter	p.R403*	ENST00000299084	NM_152594.2	403	Cga/Tga	7/7	1	2	FACETS	0.828	0.749	0.913	0.828	0.749	0.913	CLONAL	1	TRUE	1	0.34290667450967	2		636	866	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608102	28608102	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	122	373	0	ENST00000241453.7:c.1864G>C	p.Gly622Arg	p.G622R	ENST00000241453	NM_004119.2	622	Gga/Cga	15/24	0.34290667450967	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.34290667450967	1		373	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576970	7577335	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATAACTGCACCCTTGGTCTCCTCCACCGCTTCTTGTCCTGCTTGCTTACCTCGCTTAGTGCTCCCTGGGGGCAGCTCGTGGTGAGGCTCCCCTTTCTTGCGGAGATTCTCTTCCTCTGTGCGCCGGTCTCTCCCAGGACAGGCACAAACACGCACCTCAAAGCTGTTCCGTCCCAGTAGATTACCACTACTCAGGATAGGAAAAGAGAAGCAAGAGGCAGTAAGGAAATCAGGTCCTACCTGTCCCATTTAAAAAACCAGGCTCCATCTACTCCCAACCACCCTTGTCCTTTCTGGAGCCTAAGCTCCAGCTCCAGGTAGGTGGAGGAGAAGCCACAGGTTAAGAGGTCCCAAAGCCAGAGAAAAG	ATAACTGCACCCTTGGTCTCCTCCACCGCTTCTTGTCCTGCTTGCTTACCTCGCTTAGTGCTCCCTGGGGGCAGCTCGTGGTGAGGCTCCCCTTTCTTGCGGAGATTCTCTTCCTCTGTGCGCCGGTCTCTCCCAGGACAGGCACAAACACGCACCTCAAAGCTGTTCCGTCCCAGTAGATTACCACTACTCAGGATAGGAAAAGAGAAGCAAGAGGCAGTAAGGAAATCAGGTCCTACCTGTCCCATTTAAAAAACCAGGCTCCATCTACTCCCAACCACCCTTGTCCTTTCTGGAGCCTAAGCTCCAGCTCCAGGTAGGTGGAGGAGAAGCCACAGGTTAAGAGGTCCCAAAGCCAGAGAAAAG	-	novel	NA	P-0045169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	126	497	0	ENST00000269305.4:c.782+164_920-44del		p.X261_splice	ENST00000269305	NM_001126112.2	261		8/11	0.257894863032046	2	FACETS	1	0.952	1	0.539	0.489	0.592	CLONAL	1	TRUE	0	0.34290667450967	2		497	682	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285167	212285167	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs202053701	NA	P-0045169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	21	249	0	ENST00000342788.4:c.3134G>C	p.Arg1045Thr	p.R1045T	ENST00000342788	NM_005235.2	1045	aGg/aCg	25/28	1	2	FACETS	0.628	0.486	0.792	0.628	0.486	0.792	SUBCLONAL	1	TRUE	1	0.34290667450967	2		249	195	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338641	70338641	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	208	623	0	ENST00000374080.3:c.40del	p.Leu14Ter	p.L14*	ENST00000374080		13	Ccc/cc	1/45	0.34290667450967	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.34290667450967	1		623	848	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270025	198270025	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	41	252	0	ENST00000335508.6:c.1411G>C	p.Asp471His	p.D471H	ENST00000335508	NM_012433.2	471	Gat/Cat	10/25	1	2	FACETS	0.857	0.718	1	0.857	0.718	1	CLONAL	1	TRUE	1	0.34290667450967	2		252	279	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411888	116411904	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTCTCTGTTTTAAGAT	TCTCTCTGTTTTAAGAT	A	novel	NA	P-0045169-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	360	621	0	ENST00000397752.3:c.2888-15_2889delinsA		p.X963_splice	ENST00000397752	NM_000245.2	963		14/21	0.280320028902132	3	FACETS	0.868	0.825	0.911	0.868	0.825	0.911	CLONAL	3	TRUE	0	0.34290667450967	3		621	945	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717661	89717661	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0045169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	251	349	0	ENST00000371953.3:c.686C>G	p.Ser229Ter	p.S229*	ENST00000371953	NM_000314.4	229	tCa/tGa	7/9	0.599860709601186	2	FACETS	0.794	0.754	0.834	0.794	0.754	0.834	SUBCLONAL	2	TRUE	0	0.697578268281921	2		349	453	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643737	38643737	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1201851975	NA	P-0045169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	530	634	2	ENST00000299084.4:c.1207C>T	p.Arg403Ter	p.R403*	ENST00000299084	NM_152594.2	403	Cga/Tga	7/7	0.599860709601186	2	FACETS	0.857	0.828	0.885	0.857	0.828	0.885	CLONAL	2	TRUE	0	0.697578268281921	2		636	887	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608102	28608102	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	285	373	0	ENST00000241453.7:c.1864G>C	p.Gly622Arg	p.G622R	ENST00000241453	NM_004119.2	622	Gga/Cga	15/24	0.599860709601186	2	FACETS	0.879	0.84	0.917	0.879	0.84	0.917	CLONAL	2	TRUE	0	0.697578268281921	2		373	465	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576970	7577335	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATAACTGCACCCTTGGTCTCCTCCACCGCTTCTTGTCCTGCTTGCTTACCTCGCTTAGTGCTCCCTGGGGGCAGCTCGTGGTGAGGCTCCCCTTTCTTGCGGAGATTCTCTTCCTCTGTGCGCCGGTCTCTCCCAGGACAGGCACAAACACGCACCTCAAAGCTGTTCCGTCCCAGTAGATTACCACTACTCAGGATAGGAAAAGAGAAGCAAGAGGCAGTAAGGAAATCAGGTCCTACCTGTCCCATTTAAAAAACCAGGCTCCATCTACTCCCAACCACCCTTGTCCTTTCTGGAGCCTAAGCTCCAGCTCCAGGTAGGTGGAGGAGAAGCCACAGGTTAAGAGGTCCCAAAGCCAGAGAAAAG	ATAACTGCACCCTTGGTCTCCTCCACCGCTTCTTGTCCTGCTTGCTTACCTCGCTTAGTGCTCCCTGGGGGCAGCTCGTGGTGAGGCTCCCCTTTCTTGCGGAGATTCTCTTCCTCTGTGCGCCGGTCTCTCCCAGGACAGGCACAAACACGCACCTCAAAGCTGTTCCGTCCCAGTAGATTACCACTACTCAGGATAGGAAAAGAGAAGCAAGAGGCAGTAAGGAAATCAGGTCCTACCTGTCCCATTTAAAAAACCAGGCTCCATCTACTCCCAACCACCCTTGTCCTTTCTGGAGCCTAAGCTCCAGCTCCAGGTAGGTGGAGGAGAAGCCACAGGTTAAGAGGTCCCAAAGCCAGAGAAAAG	-	novel	NA	P-0045169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	272	497	0	ENST00000269305.4:c.782+164_920-44del		p.X261_splice	ENST00000269305	NM_001126112.2	261		8/11	0.599860709601186	2	FACETS	1	0.993	1	0.67	0.635	0.705	CLONAL	1	TRUE	0	0.697578268281921	2		497	582	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285167	212285167	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs202053701	NA	P-0045169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	151	249	0	ENST00000342788.4:c.3134G>C	p.Arg1045Thr	p.R1045T	ENST00000342788	NM_005235.2	1045	aGg/aCg	25/28	0.599860709601186	2	FACETS	0.823	0.771	0.875	0.823	0.771	0.875	CLONAL	2	TRUE	0	0.697578268281921	2		249	263	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338641	70338641	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	521	623	0	ENST00000374080.3:c.40del	p.Leu14Ter	p.L14*	ENST00000374080		13	Ccc/cc	1/45	0.602149123421019	2	FACETS	0.844	0.815	0.872	0.844	0.815	0.872	CLONAL	2	TRUE	0	0.697578268281921	2		623	885	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411888	116411904	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTCTCTGTTTTAAGAT	TCTCTCTGTTTTAAGAT	A	novel	NA	P-0045169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	955	621	0	ENST00000397752.3:c.2888-15_2889delinsA		p.X963_splice	ENST00000397752	NM_000245.2	963		14/21	0.567878133508233	4	FACETS	1	0.997	1	0.863	0.844	0.881	CLONAL	3	TRUE	0	0.697578268281921	4		621	1347	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069931	5069931	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0045169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	11	163	0	ENST00000381652.3:c.1520C>G	p.Ser507Ter	p.S507*	ENST00000381652	NM_004972.3	507	tCa/tGa	12/25	0.666108512738479	1	FACETS	0.167	0.116	0.23	0.167	0.116	0.23	SUBCLONAL	1	TRUE	0	0.697578268281921	1		163	123	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52685766	52685766	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	85	272	0	ENST00000394830.3:c.706A>G	p.Arg236Gly	p.R236G	ENST00000394830	NM_018313.4	236	Agg/Ggg	7/30	0.599860709601186	2	FACETS	0.764	0.682	0.85	0.382	0.341	0.425	SUBCLONAL	1	TRUE	0	0.697578268281921	2		272	319	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873218	71873218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374884396	NA	P-0045169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	122	319	1	ENST00000357731.5:c.976G>A	p.Ala326Thr	p.A326T	ENST00000357731	NM_173808.2	326	Gct/Act	7/7	1	2	FACETS	0.817	0.744	0.893	0.817	0.744	0.893	CLONAL	1	TRUE	1	0.697578268281921	2		320	428	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81939092	81939097	+	inframe_deletion	In_Frame_Del	DEL	ATGTGG	ATGTGG	-	novel	NA	P-0045169-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	156	443	0	ENST00000359376.3:c.1447_1452del	p.Met483_Trp484del	p.M483_W484del	ENST00000359376	NM_002661.3	483	ATGTGG/-	15/33	0.598856617593282	4	FACETS	0.733	0.67	0.799	0.244	0.223	0.267	SUBCLONAL	1	TRUE	1	0.697578268281921	4		443	1036	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618691	37618691	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	480	599	0	ENST00000447079.4:c.367del	p.Leu123Ter	p.L123*	ENST00000447079	NM_015083.1	123	Cta/ta	1/14	0.202406950392081	7	FACETS	1	0.989	1			1	CLONAL	8	TRUE	NA	0.202406950392081	7		599	842	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619348	37619349	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0045170-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	243	457	0	ENST00000447079.4:c.1025dup	p.Ser343GlufsTer8	p.S343Efs*8	ENST00000447079	NM_015083.1	342	ctg/cTtg	1/14	0.202406950392081	7	FACETS	0.999	0.938	1			1	CLONAL	5	TRUE	NA	0.202406950392081	7		457	724	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0045172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	80	330	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.179997699212503	4	FACETS	0.894	0.789	1	0.596	0.526	0.671	CLONAL	2	FALSE	1	0.212282354193106	4		330	511	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424696	49424696	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	91	689	0	ENST00000301067.7:c.13651T>G	p.Leu4551Val	p.L4551V	ENST00000301067	NM_003482.3	4551	Ttg/Gtg	40/54	0.17862182303796	3	FACETS	1	0.954	1	0.573	0.508	0.643	CLONAL	1	FALSE	1	0.212282354193106	3		689	827	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045104	47045132	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCTCTTGCAGCAAAACCTTGAGATTCAC	CCCTCTTGCAGCAAAACCTTGAGATTCAC	-	novel	NA	P-0045172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	124	579	0	ENST00000377604.3:c.2356-10_2374del		p.X786_splice	ENST00000377604	NM_001204468.1	786		21/24	0.171325349631813	4	FACETS	0.834	0.754	0.918	0.834	0.754	0.918	CLONAL	2	FALSE	2	0.212282354193106	4		579	849	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0045173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	124	287	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.357802837389359	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	2	0.447876151423704	4		287	340	SUCCESS
APC	324	MSKCC	GRCh37	5	112175171	112175171	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085373	NA	P-0045173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	69	236	0	ENST00000257430.4:c.3880C>T	p.Gln1294Ter	p.Q1294*	ENST00000257430	NM_000038.5	1294	Cag/Tag	16/16	0.447876151423704	3	FACETS	0.879	0.789	0.969	0.879	0.789	0.969	CLONAL	3	TRUE	0	0.447876151423704	3		236	143	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0045173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	38	521	0	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	0.358976454531121	0	FACETS	0.558	0.467	0.655			1	SUBCLONAL	1	TRUE	0	0.447876151423704	0		521	168	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446208	49446208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0045173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	69	729	0	ENST00000301067.7:c.1259-1G>A		p.X420_splice	ENST00000301067	NM_003482.3	420			0.357802837389359	4	FACETS	1	0.961	1	0.625	0.547	0.707	CLONAL	1	TRUE	2	0.447876151423704	4		729	357	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141533	11141534	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0045173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	57	735	1	ENST00000358026.2:c.3512_3513del	p.Val1171AspfsTer4	p.V1171Dfs*4	ENST00000358026	NM_001128849.1	1170	acTGtg/actg	25/36	1	2	FACETS	0.929	0.804	1	0.929	0.804	1	CLONAL	1	TRUE	1	0.447876151423704	2		736	274	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023165	150023165	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	72	498	0	ENST00000253339.5:c.98A>G	p.Glu33Gly	p.E33G	ENST00000253339		33	gAa/gGa	1/7	1	2	FACETS	0.977	0.861	1	0.977	0.861	1	CLONAL	1	TRUE	1	0.447876151423704	2		498	329	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753202	128753202	+	stop_lost	Nonstop_Mutation	SNP	T	T	G	novel	NA	P-0045173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	47	256	0	ENST00000377970.2:c.1363T>G	p.Ter455GluextTer19	p.*455Eext*19	ENST00000377970	NM_002467.4	455	Taa/Gaa	3/3	0.265939748738476	3	FACETS	1	0.948	1	0.633	0.54	0.732	INDETERMINATE	1	TRUE	1	0.447876151423704	3		256	203	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0045175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	73	217	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.497083406938516	4	FACETS	1	0.952	1	0.383	0.338	0.43	INDETERMINATE	1	TRUE	1	0.854278257488688	4		217	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578384	7578401	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCTCATGGTGGGG	GCAGCGCTCATGGTGGGG	-	novel	NA	P-0045175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	585	566	0	ENST00000269305.4:c.529_546del	p.Pro177_Cys182del	p.P177_C182del	ENST00000269305	NM_001126112.2	177	CCCCACCATGAGCGCTGC/-	5/11	0.846645341981076	3	FACETS	0.996	0.979	1	0.996	0.979	1	CLONAL	3	TRUE	0	0.854278257488688	3		566	654	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257606	19257606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764313266	NA	P-0045175-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	491	917	2	ENST00000162023.5:c.620G>A	p.Arg207Gln	p.R207Q	ENST00000162023		207	cGg/cAg	10/13	0.529757131110594	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.854278257488688	4		919	1040	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456394	40456394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	169	795	0	ENST00000345506.4:c.1204G>A	p.Val402Met	p.V402M	ENST00000345506	NM_003152.3	402	Gtg/Atg	11/20	1	2	FACETS	0.879	0.809	0.953	0.879	0.809	0.953	CLONAL	1	TRUE	1	0.434332458850546	2		795	885	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593610	55593610	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913517	NA	P-0045178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	165	364	0	ENST00000288135.5:c.1676T>A	p.Val559Asp	p.V559D	ENST00000288135	NM_000222.2	559	gTt/gAt	11/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.674644021794782	2		364	451	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143994	11143994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	160	672	0	ENST00000358026.2:c.3575G>A	p.Arg1192His	p.R1192H	ENST00000358026	NM_001128849.1	1192	cGc/cAc	26/36	0.60052768825549	3	FACETS	1	0.98	1	0.592	0.546	0.64	CLONAL	1	TRUE	1	0.658714987585251	3		672	545	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	179	372	0				ENST00000310581	NM_198253.2	-/1132			0.531641183549583	6	FACETS	0.907	0.844	0.97	0.907	0.844	0.97	CLONAL	3	TRUE	3	0.658714987585251	6		372	463	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54956529	54956529	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	96	373	0	ENST00000312783.6:c.665T>C	p.Leu222Pro	p.L222P	ENST00000312783	NM_198436.1	222	cTt/cCt	7/10	0.60052768825549	3	FACETS	1	0.959	1	0.565	0.508	0.624	CLONAL	1	TRUE	1	0.658714987585251	3		373	343	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0045181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	283	785	1	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.658714987585251	2	FACETS	0.968	0.926	1	0.968	0.926	1	CLONAL	2	TRUE	0	0.658714987585251	2		786	444	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290966	15290966	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	161	1162	0	ENST00000263388.2:c.3244G>A	p.Glu1082Lys	p.E1082K	ENST00000263388	NM_000435.2	1082	Gag/Aag	20/33	0.60052768825549	3	FACETS	1	0.923	1	0.501	0.461	0.543	CLONAL	1	TRUE	1	0.658714987585251	3		1162	648	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290990	15290990	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	165	1142	0	ENST00000263388.2:c.3220G>C	p.Glu1074Gln	p.E1074Q	ENST00000263388	NM_000435.2	1074	Gag/Cag	20/33	0.60052768825549	3	FACETS	1	0.948	1	0.518	0.477	0.56	CLONAL	1	TRUE	1	0.658714987585251	3		1142	643	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291945	15291945	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	144	1187	0	ENST00000263388.2:c.2821G>C	p.Asp941His	p.D941H	ENST00000263388	NM_000435.2	941	Gac/Cac	18/33	0.60052768825549	3	FACETS	0.803	0.733	0.875	0.401	0.366	0.438	CLONAL	1	TRUE	1	0.658714987585251	3		1187	724	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54956517	54956517	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	93	364	0	ENST00000312783.6:c.677C>A	p.Ser226Ter	p.S226*	ENST00000312783	NM_198436.1	226	tCa/tAa	7/10	0.60052768825549	3	FACETS	1	0.957	1	0.562	0.504	0.622	CLONAL	1	TRUE	1	0.658714987585251	3		364	334	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226010	53226011	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0045181-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	359	1168	0	ENST00000375401.3:c.2837_2838dup	p.Leu947ProfsTer15	p.L947Pfs*15	ENST00000375401	NM_004187.3	946	-/CC	19/26	0.658714987585251	3	FACETS	0.853	0.813	0.894	0.853	0.813	0.894	CLONAL	2	TRUE	1	0.658714987585251	3		1168	849	SUCCESS
FH	2271	MSKCC	GRCh37	1	241671932	241671932	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1553341321	NA	P-0045182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	52	421	0	ENST00000366560.3:c.709C>T	p.Gln237Ter	p.Q237*	ENST00000366560	NM_000143.3	237	Cag/Tag	5/10	NA	2	FACETS	0.635	0.544	0.733			1	INDETERMINATE	1	TRUE	NA	0.546188805047961	2		421	300	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832202	72832202	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	56	581	0	ENST00000268489.5:c.4379T>G	p.Ile1460Ser	p.I1460S	ENST00000268489	NM_006885.3	1460	aTc/aGc	9/10	1	2	FACETS	0.301	0.257	0.349	0.301	0.257	0.349	SUBCLONAL	1	TRUE	1	0.546188805047961	2		581	681	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144049	11144051	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0045184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1272	29	879	0	ENST00000358026.2:c.3634_3636del	p.Glu1212del	p.E1212del	ENST00000358026	NM_001128849.1	1210	gtGGAg/gtg	26/36	1	2	FACETS	0.892	0.712	1	0.892	0.712	1	CLONAL	1	TRUE	1	0.05	2		879	1301	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90990538	90990538	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	12	327	0	ENST00000265433.3:c.494T>A	p.Leu165His	p.L165H	ENST00000265433	NM_002485.4	165	cTc/cAc	5/16	1	2	FACETS	1	0.816	1	1	0.912	1	CLONAL	2	TRUE	1	0.05	2		327	193	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057907	27057908	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGACG	novel	NA	P-0045184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1425	21	692	0	ENST00000324856.7:c.1616_1620dup	p.Thr541ArgfsTer80	p.T541Rfs*80	ENST00000324856	NM_006015.4	539	tcg/tCGACGcg	3/20	1	2	FACETS	0.581	0.444	0.742	0.581	0.444	0.742	SUBCLONAL	1	TRUE	1	0.05	2		692	1446	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087392	27087392	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	10	634	0	ENST00000324856.7:c.1966G>C	p.Ala656Pro	p.A656P	ENST00000324856	NM_006015.4	656	Gct/Cct	5/20	1	2	FACETS	0.459	0.309	0.651	0.459	0.309	0.651	SUBCLONAL	1	TRUE	1	0.05	2		634	871	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207119	1207120	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0045184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1606	20	963	1	ENST00000326873.7:c.207_208delinsTT	p.Glu70Ter	p.E70*	ENST00000326873	NM_000455.4	69	tcGGag/tcTTag	1/10	1	2	FACETS	0.492	0.374	0.633	0.492	0.374	0.633	SUBCLONAL	1	TRUE	1	0.05	2		964	1626	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602736	10602736	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1451	38	1017	0	ENST00000171111.5:c.842T>A	p.Leu281Gln	p.L281Q	ENST00000171111	NM_203500.1	281	cTg/cAg	3/6	1	2	FACETS	1	0.838	1	1	0.838	1	CLONAL	1	TRUE	1	0.05	2		1017	1489	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296339	15296339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0045184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1525	35	1048	0	ENST00000263388.2:c.2103del	p.His701GlnfsTer159	p.H701Qfs*159	ENST00000263388	NM_000435.2	701	caT/ca	13/33	1	2	FACETS	0.897	0.732	1	0.897	0.732	1	CLONAL	1	TRUE	1	0.05	2		1048	1560	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876488	35876488	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045184-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	20	595	2	ENST00000303115.3:c.1280C>A	p.Thr427Lys	p.T427K	ENST00000303115	NM_002185.3	427	aCa/aAa	8/8	1	2	FACETS	0.832	0.633	1	0.832	0.633	1	CLONAL	1	TRUE	1	0.05	2		597	962	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0045185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	214	428	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.227250725167546	2	FACETS	1	0.957	1	1	0.992	1	CLONAL	3	TRUE	0	0.227250725167546	2		428	610	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274172	10274172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567354612	NA	P-0045185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	26	606	2	ENST00000330684.3:c.97G>A	p.Ala33Thr	p.A33T	ENST00000330684	NM_001134407.1	33	Gcg/Acg	2/13	0.210420201292157	2	FACETS	0.511	0.404	0.634	0.255	0.202	0.317	SUBCLONAL	1	TRUE	0	0.227250725167546	2		608	448	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869501	102869501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs527983684	NA	P-0045185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	133	468	1	ENST00000307046.8:c.140C>T	p.Thr47Met	p.T47M	ENST00000307046	NM_001111285.1	47	aCg/aTg	2/4	1	2	FACETS	1	0.965	1	1	0.991	1	CLONAL	2	TRUE	1	0.227250725167546	2		469	527	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847252	68847252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141864044	NA	P-0045185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	220	538	1	ENST00000261769.5:c.1174G>A	p.Val392Ile	p.V392I	ENST00000261769	NM_004360.3	392	Gta/Ata	9/16	0.210420201292157	2	FACETS	0.981	0.918	1	1	0.992	1	CLONAL	3	TRUE	0	0.227250725167546	2		539	658	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416084	49416084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267607238	NA	P-0045185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	45	600	2	ENST00000301067.7:c.16391C>T	p.Thr5464Met	p.T5464M	ENST00000301067	NM_003482.3	5464	aCg/aTg	52/54	0.0490958413555762	4	FACETS	0.694	0.582	0.819	0.347	0.291	0.41	INDETERMINATE	1	TRUE	2	0.227250725167546	4		602	700	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0045186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	122	377	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.945	0.861	1	1	0.989	1	CLONAL	2	FALSE	1	0.314231320527538	2		377	411	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0045186-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	201	337	0				ENST00000310581	NM_198253.2	-/1132			0.314231320527538	3	FACETS	0.867	0.809	0.926	1	0.989	1	CLONAL	3	FALSE	1	0.314231320527538	3		337	569	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230641	46230641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	65	462	0	ENST00000334344.6:c.890C>T	p.Ser297Phe	p.S297F	ENST00000334344	NM_152641.2	297	tCc/tTc	8/21	1	2	FACETS	0.833	0.723	0.953	0.833	0.723	0.953	CLONAL	1	TRUE	1	0.271307835217592	2		462	575	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508539	106508539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	58	422	0	ENST00000359195.3:c.533G>A	p.Arg178His	p.R178H	ENST00000359195	NM_002649.2	178	cGt/cAt	2/11	1	2	FACETS	0.842	0.724	0.97	0.842	0.724	0.97	CLONAL	1	TRUE	1	0.271307835217592	2		422	508	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11194480	11194480	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	62	626	0	ENST00000361445.4:c.5174A>T	p.Gln1725Leu	p.Q1725L	ENST00000361445	NM_004958.3	1725	cAg/cTg	37/58	1	2	FACETS	0.579	0.499	0.667	0.579	0.499	0.667	SUBCLONAL	1	TRUE	1	0.271307835217592	2		626	789	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092729	27092729	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	54	372	0	ENST00000324856.7:c.2750A>T	p.Asn917Ile	p.N917I	ENST00000324856	NM_006015.4	917	aAt/aTt	9/20	1	2	FACETS	0.733	0.626	0.85	0.733	0.626	0.85	SUBCLONAL	1	TRUE	1	0.271307835217592	2		372	543	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480510	120480510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782489357	NA	P-0045188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	62	420	0	ENST00000256646.2:c.3307G>A	p.Val1103Ile	p.V1103I	ENST00000256646	NM_024408.3	1103	Gtc/Atc	20/34	1	2	FACETS	0.877	0.759	1	0.877	0.759	1	CLONAL	1	TRUE	1	0.271307835217592	2		420	521	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027192	49027192	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	49	427	0	ENST00000267163.4:c.1759G>T	p.Glu587Ter	p.E587*	ENST00000267163	NM_000321.2	587	Gaa/Taa	18/27	0.271307835217592	1	FACETS	0.663	0.562	0.774	0.663	0.562	0.774	SUBCLONAL	1	TRUE	0	0.271307835217592	1		427	471	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858010	9858010	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	55	565	0	ENST00000330684.3:c.3391G>C	p.Asp1131His	p.D1131H	ENST00000330684	NM_001134407.1	1131	Gat/Cat	13/13	1	2	FACETS	0.626	0.535	0.726	0.626	0.535	0.726	SUBCLONAL	1	TRUE	1	0.271307835217592	2		565	648	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579494	7579494	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	212	906	0	ENST00000269305.4:c.193del	p.Arg65GlufsTer58	p.R65Efs*58	ENST00000269305	NM_001126112.2	65	Aga/ga	4/11	0.204273373781704	2	FACETS	0.779	0.724	0.836	0.779	0.724	0.836	SUBCLONAL	2	TRUE	0	0.271307835217592	2		906	1003	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306631	41306632	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0045188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	77	770	0	ENST00000373198.4:c.1027_1028delinsAA	p.Pro343Asn	p.P343N	ENST00000373198	NM_133170.3	343	CCc/AAc	7/32	0.271307835217592	1	FACETS	0.698	0.612	0.79	0.698	0.612	0.79	SUBCLONAL	1	TRUE	0	0.271307835217592	1		770	703	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448564	89448564	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	90	505	0	ENST00000336596.2:c.1528C>G	p.Arg510Gly	p.R510G	ENST00000336596	NM_005233.5	510	Cga/Gga	7/17	0.261736547275525	1	FACETS	0.974	0.865	1	0.974	0.865	1	CLONAL	1	TRUE	0	0.271307835217592	1		505	589	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153617	55153617	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	64	458	0	ENST00000257290.5:c.2583G>T	p.Trp861Cys	p.W861C	ENST00000257290	NM_006206.4	861	tgG/tgT	19/23	1	2	FACETS	0.738	0.639	0.846	0.738	0.639	0.846	SUBCLONAL	1	TRUE	1	0.271307835217592	2		458	639	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573449	55573449	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	28	296	0	ENST00000288135.5:c.1111A>G	p.Ile371Val	p.I371V	ENST00000288135	NM_000222.2	371	Atc/Gtc	6/21	1	2	FACETS	0.59	0.472	0.724	0.59	0.472	0.724	SUBCLONAL	1	TRUE	1	0.271307835217592	2		296	350	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554978	187554978	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0045188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	35	226	0	ENST00000441802.2:c.4184-1G>T		p.X1395_splice	ENST00000441802	NM_005245.3	1395			0.271307835217592	1	FACETS	0.832	0.685	0.995	0.832	0.685	0.995	CLONAL	1	TRUE	0	0.271307835217592	1		226	268	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382147	152382148	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0045188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	31	320	0	ENST00000206249.3:c.1257_1258delinsAT	p.Gly420Cys	p.G420C	ENST00000206249	NM_000125.3	419	gaGGgc/gaATgc	6/8	1	2	FACETS	0.559	0.452	0.68	0.559	0.452	0.68	SUBCLONAL	1	TRUE	1	0.271307835217592	2		320	409	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100496	157100496	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	19	159	0	ENST00000346085.5:c.1433A>T	p.Asp478Val	p.D478V	ENST00000346085	NM_020732.3	478	gAc/gTc	1/20	1	2	FACETS	0.683	0.52	0.873	0.683	0.52	0.873	SUBCLONAL	1	TRUE	1	0.271307835217592	2		159	205	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972979	68972979	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs993179244	NA	P-0045188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	51	386	0	ENST00000288368.4:c.1304G>T	p.Gly435Val	p.G435V	ENST00000288368	NM_024870.2	435	gGa/gTa	11/40	1	2	FACETS	0.671	0.57	0.782	0.671	0.57	0.782	SUBCLONAL	1	TRUE	1	0.271307835217592	2		386	560	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136793	69136793	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0045188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	82	357	0	ENST00000288368.4:c.4708-1G>T		p.X1570_splice	ENST00000288368	NM_024870.2	1570			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.271307835217592	2		357	520	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090559	5090559	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0045188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	38	292	0	ENST00000381652.3:c.2875C>T	p.Gln959Ter	p.Q959*	ENST00000381652	NM_004972.3	959	Cag/Tag	21/25	0.239591625828076	1	FACETS	0.774	0.642	0.92	0.774	0.642	0.92	CLONAL	1	TRUE	0	0.271307835217592	1		292	313	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040929	47040929	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	124	1157	0	ENST00000377604.3:c.1462del	p.Ala488ProfsTer216	p.A488Pfs*216	ENST00000377604	NM_001204468.1	487	Ggg/gg	14/24	1	2	FACETS	0.715	0.645	0.79	0.715	0.645	0.79	SUBCLONAL	1	TRUE	1	0.271307835217592	2		1157	1278	SUCCESS
AR	367	MSKCC	GRCh37	X	66766239	66766239	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0045188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	62	593	0	ENST00000374690.3:c.1253del	p.Gly418ValfsTer61	p.G418Vfs*61	ENST00000374690	NM_000044.3	417	gcG/gc	1/8	1	2	FACETS	0.69	0.596	0.793	0.69	0.596	0.793	SUBCLONAL	1	TRUE	1	0.271307835217592	2		593	662	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952171	76952172	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0045188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	46	319	0	ENST00000373344.5:c.262_263dup	p.Tyr89SerfsTer3	p.Y89Sfs*3	ENST00000373344	NM_000489.3	88	aag/aaAAg	5/35	1	2	FACETS	0.742	0.625	0.871	0.742	0.625	0.871	SUBCLONAL	1	TRUE	1	0.271307835217592	2		319	457	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0045190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	104	298	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	0.203278823264824	3	FACETS	0.92	0.831	1	0.92	0.831	1	CLONAL	3	TRUE	0	0.21756940750847	3		298	384	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967350	134967350	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs61736108	NA	P-0045190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	129	413	0	ENST00000398015.3:c.2689G>A	p.Val897Met	p.V897M	ENST00000398015	NM_004441.4	897	Gtg/Atg	14/16	1	2	FACETS	1	0.921	1	1	0.99	1	CLONAL	2	TRUE	1	0.21756940750847	2		413	585	SUCCESS
APC	324	MSKCC	GRCh37	5	112175219	112175219	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0045190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	70	192	1	ENST00000257430.4:c.3928A>T	p.Lys1310Ter	p.K1310*	ENST00000257430	NM_000038.5	1310	Aag/Tag	16/16	0.203278823264824	3	FACETS	0.874	0.771	0.984	0.874	0.771	0.984	CLONAL	3	TRUE	0	0.21756940750847	3		193	272	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351178	89351178	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	85	667	0	ENST00000301030.4:c.1772C>G	p.Pro591Arg	p.P591R	ENST00000301030	NM_001256183.1	591	cCa/cGa	9/13	0.208373184087047	3	FACETS	0.897	0.791	1	0.448	0.395	0.506	CLONAL	1	TRUE	1	0.21756940750847	3		667	966	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577547	+	inframe_deletion	In_Frame_Del	DEL	TGC	TGC	-	novel	NA	P-0045190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	201	580	0	ENST00000269305.4:c.734_736del	p.Gly245_Met246delinsVal	p.G245_M246delinsV	ENST00000269305	NM_001126112.2	245	gGCAtg/gtg	7/11	0.210378281611658	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.21756940750847	2		580	870	SUCCESS
APC	324	MSKCC	GRCh37	5	112175225	112175225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045190-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	70	198	0	ENST00000257430.4:c.3934G>A	p.Gly1312Arg	p.G1312R	ENST00000257430	NM_000038.5	1312	Gga/Aga	16/16	0.203278823264824	3	FACETS	0.859	0.757	0.966	0.859	0.757	0.966	CLONAL	3	TRUE	0	0.21756940750847	3		198	277	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	32	372	0				ENST00000310581	NM_198253.2	-/1132			0.319652189594291	3	FACETS	0.862	0.705	1	0.431	0.352	0.518	CLONAL	1	FALSE	1	0.45607821061503	3		372	200	SUCCESS
ATM	472	MSKCC	GRCh37	11	108200978	108200978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	38	321	0	ENST00000278616.4:c.7345G>A	p.Glu2449Lys	p.E2449K	ENST00000278616	NM_000051.3	2449	Gaa/Aaa	50/63	0.300459665900745	4	FACETS	1	0.953	1	0.722	0.605	0.849	CLONAL	1	FALSE	2	0.45607821061503	4		321	168	SUCCESS
ATM	472	MSKCC	GRCh37	11	108206581	108206581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	22	257	0	ENST00000278616.4:c.8161G>A	p.Asp2721Asn	p.D2721N	ENST00000278616	NM_000051.3	2721	Gac/Aac	56/63	0.300459665900745	4	FACETS	1	0.792	1	0.505	0.396	0.629	CLONAL	1	FALSE	2	0.45607821061503	4		257	139	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608956	100608956	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	24	434	0	ENST00000308731.7:c.1652A>G	p.Tyr551Cys	p.Y551C	ENST00000308731	NM_000061.2	551	tAc/tGc	17/19	0.362599796591824	1	FACETS	0.316	0.248	0.394	0.316	0.248	0.394	SUBCLONAL	1	FALSE	0	0.45607821061503	1		434	257	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471665	120471665	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	53	497	0	ENST00000256646.2:c.3826G>A	p.Glu1276Lys	p.E1276K	ENST00000256646	NM_024408.3	1276	Gag/Aag	23/34	0.295021174253765	3	FACETS	0.87	0.746	1	0.435	0.373	0.503	CLONAL	1	FALSE	1	0.45607821061503	3		497	328	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202762	108202762	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1555124747	NA	P-0045201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	27	346	0	ENST00000278616.4:c.7786G>A	p.Glu2596Lys	p.E2596K	ENST00000278616	NM_000051.3	2596	Gag/Aag	52/63	0.300459665900745	4	FACETS	0.922	0.74	1	0.461	0.37	0.564	CLONAL	1	FALSE	2	0.45607821061503	4		346	187	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102822	71102822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	16	355	0	ENST00000318789.4:c.385C>T	p.Leu129Phe	p.L129F	ENST00000318789	NM_032682.5	129	Ctc/Ttc	8/21	1	2	FACETS	0.244	0.18	0.321	0.244	0.18	0.321	SUBCLONAL	1	FALSE	1	0.45607821061503	2		355	287	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199883	108199883	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	25	220	0	ENST00000278616.4:c.7225G>C	p.Glu2409Gln	p.E2409Q	ENST00000278616	NM_000051.3	2409	Gaa/Caa	49/63	0.300459665900745	4	FACETS	1	0.926	1	0.694	0.557	0.846	CLONAL	1	FALSE	2	0.45607821061503	4		220	115	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432708	49432708	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	34	743	0	ENST00000301067.7:c.8431C>T	p.Gln2811Ter	p.Q2811*	ENST00000301067	NM_003482.3	2811	Cag/Tag	34/54	0.356149392063699	5	FACETS	0.544	0.444	0.656	0.181	0.148	0.219	SUBCLONAL	1	FALSE	2	0.45607821061503	5		743	462	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645253	67645253	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	32	742	0	ENST00000264010.4:c.518G>A	p.Gly173Glu	p.G173E	ENST00000264010	NM_006565.3	173	gGa/gAa	3/12	1	2	FACETS	0.418	0.339	0.506	0.418	0.339	0.506	SUBCLONAL	1	FALSE	1	0.45607821061503	2		742	336	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485234	8485234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	26	424	0	ENST00000356435.5:c.3146C>T	p.Pro1049Leu	p.P1049L	ENST00000356435		1049	cCt/cTt	18/35	0.45607821061503	3	FACETS	0.56	0.445	0.691	0.187	0.148	0.231	SUBCLONAL	1	FALSE	0	0.45607821061503	3		424	250	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409509	80409509	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0045201-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	20	572	0	ENST00000286548.4:c.606-1G>A		p.X202_splice	ENST00000286548	NM_002072.3	202			0.45607821061503	3	FACETS	0.327	0.25	0.418	0.109	0.083	0.14	SUBCLONAL	1	FALSE	0	0.45607821061503	3		572	329	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	163	372	0				ENST00000310581	NM_198253.2	-/1132			0.316252342334037	8	FACETS	1	0.973	1			1	CLONAL	2	TRUE	NA	0.316252342334037	8		372	881	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0045202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	248	753	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.316252342334037	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.316252342334037	2		753	700	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038233	30038233	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	48	394	0	ENST00000338641.4:c.406G>A	p.Glu136Lys	p.E136K	ENST00000338641	NM_000268.3	136	Gag/Aag	4/16	0.102484523996575	4	FACETS	0.715	0.604	0.837	0.357	0.302	0.419	INDETERMINATE	1	TRUE	2	0.316252342334037	4		394	559	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70432749	70432749	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1424143762	NA	P-0045202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	103	478	0	ENST00000373644.4:c.4771G>T	p.Gly1591Cys	p.G1591C	ENST00000373644	NM_030625.2	1591	Ggt/Tgt	8/12	0.273387321951648	3	FACETS	1	0.979	1	0.685	0.614	0.759	CLONAL	1	TRUE	1	0.316252342334037	3		478	551	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185116	99185116	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	137	360	0	ENST00000074304.5:c.2518G>A	p.Val840Ile	p.V840I	ENST00000074304	NM_001134224.1	840	Gtt/Att	23/26	0.257236030828287	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.316252342334037	4		360	511	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057318	180057318	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	179	796	0	ENST00000261937.6:c.420C>G	p.Ile140Met	p.I140M	ENST00000261937	NM_182925.4	140	atC/atG	4/30	0.316252342334037	2	FACETS	0.91	0.843	0.979	0.91	0.843	0.979	CLONAL	2	TRUE	0	0.316252342334037	2		796	622	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032006	26032014	+	inframe_deletion	In_Frame_Del	DEL	CCTGCAGCG	CCTGCAGCG	-	novel	NA	P-0045202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	110	411	0	ENST00000244661.2:c.275_283del	p.Ala92_Gln94del	p.A92_Q94del	ENST00000244661	NM_003537.3	92	gCGCTGCAGGag/gag	1/1	0.146683930274464	5	FACETS	1	0.949	1	0.72	0.65	0.793	INDETERMINATE	2	TRUE	2	0.316252342334037	5		411	475	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974751	21974756	+	inframe_deletion	In_Frame_Del	DEL	CTACCC	CTACCC	-	novel	NA	P-0045202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	102	353	0	ENST00000304494.5:c.71_76del	p.Arg24_Glu26delinsGln	p.R24_E26delinsQ	ENST00000304494	NM_000077.4	24	cGGGTAGag/cag	1/3	0.316252342334037	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	0	0.316252342334037	2		353	309	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034466	123034466	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045202-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	118	436	0	ENST00000355640.3:c.1223A>T	p.Glu408Val	p.E408V	ENST00000355640		408	gAg/gTg	6/7	0.146683930274464	5	FACETS	0.967	0.875	1	0.645	0.583	0.709	INDETERMINATE	2	TRUE	2	0.316252342334037	5		436	569	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	76	372	0				ENST00000310581	NM_198253.2	-/1132			0.378984913638279	1	FACETS	0.868	0.792	0.943	0.868	0.792	0.943	INDETERMINATE	1	TRUE	0	0.808517337640267	1		372	129	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0045203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	106	538	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.378984913638279	1	FACETS	0.73	0.67	0.79	0.73	0.67	0.79	INDETERMINATE	1	TRUE	0	0.808517337640267	1		538	214	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030472	47030472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782522553	NA	P-0045203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	198	934	1	ENST00000377604.3:c.247C>T	p.Arg83Trp	p.R83W	ENST00000377604	NM_001204468.1	83	Cgg/Tgg	4/24	0.416691497927184	1	FACETS	0.851	0.804	0.897	0.851	0.804	0.897	INDETERMINATE	1	TRUE	0	0.808517337640267	1		935	343	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486842	56486842	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	14	503	0	ENST00000267101.3:c.1256G>C	p.Gly419Ala	p.G419A	ENST00000267101	NM_001982.3	419	gGa/gCa	11/28	0.213394414287301	3	FACETS	0.207	0.149	0.277	0.103	0.074	0.139	INDETERMINATE	1	TRUE	1	0.808517337640267	3		503	235	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368395	225368395	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	103	318	0	ENST00000264414.4:c.1351G>C	p.Glu451Gln	p.E451Q	ENST00000264414	NM_003590.4	451	Gaa/Caa	9/16	0.275369506305372	2	FACETS	1	0.984	1	0.664	0.61	0.716	INDETERMINATE	1	TRUE	0	0.808517337640267	2		318	192	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225368404	225368404	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	118	322	0	ENST00000264414.4:c.1342G>A	p.Asp448Asn	p.D448N	ENST00000264414	NM_003590.4	448	Gat/Aat	9/16	0.275369506305372	2	FACETS	1	0.987	1	0.685	0.635	0.735	INDETERMINATE	1	TRUE	0	0.808517337640267	2		322	213	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20152122	20152122	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	96	392	0	ENST00000379607.5:c.208T>G	p.Trp70Gly	p.W70G	ENST00000379607	NM_001412.3	70	Tgg/Ggg	4/7	0.416691497927184	1	FACETS	0.58	0.526	0.635	0.58	0.526	0.635	INDETERMINATE	1	TRUE	0	0.808517337640267	1		392	244	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0045204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	131	372	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.292036788530824	2		372	737	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074080	8074081	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0045204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	43	334	0	ENST00000377482.5:c.578_579del	p.Tyr193Ter	p.Y193*	ENST00000377482	NM_018948.3	193	tAT/t	4/4	1	2	FACETS	0.54	0.452	0.639	0.54	0.452	0.639	SUBCLONAL	1	TRUE	1	0.292036788530824	2		334	545	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444684	49444684	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	411	896	0	ENST00000301067.7:c.2782C>G	p.Gln928Glu	p.Q928E	ENST00000301067	NM_003482.3	928	Cag/Gag	10/54	0.151825267127716	3	FACETS	1	0.973	1	0.69	0.656	0.725	INDETERMINATE	2	TRUE	0	0.292036788530824	3		896	1558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579410	7579420	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGCCAGGAG	GGGGCCAGGAG	-	novel	NA	P-0045204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	159	870	0	ENST00000269305.4:c.267_277del	p.Ser90ValfsTer55	p.S90Vfs*55	ENST00000269305	NM_001126112.2	89	ccCTCCTGGCCCCtg/cctg	4/11	0.292036788530824	1	FACETS	0.814	0.745	0.887	0.814	0.745	0.887	CLONAL	1	TRUE	0	0.292036788530824	1		870	1142	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227647	36227647	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	81	654	0	ENST00000222270.7:c.7216G>A	p.Ala2406Thr	p.A2406T	ENST00000222270	NM_014727.1	2406	Gcc/Acc	31/37	1	2	FACETS	0.556	0.489	0.629	0.556	0.489	0.629	SUBCLONAL	1	TRUE	1	0.292036788530824	2		654	997	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548213	41548213	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	61	266	0	ENST00000263253.7:c.3001A>G	p.Lys1001Glu	p.K1001E	ENST00000263253	NM_001429.3	1001	Aaa/Gaa	16/31	0.292036788530824	1	FACETS	0.892	0.772	1	0.892	0.772	1	CLONAL	1	TRUE	0	0.292036788530824	1		266	400	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952063	178952063	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	109	328	0	ENST00000263967.3:c.3118A>T	p.Met1040Leu	p.M1040L	ENST00000263967	NM_006218.2	1040	Atg/Ttg	21/21	0.236560670355975	2	FACETS	0.88	0.796	0.968	0.88	0.796	0.968	CLONAL	2	TRUE	0	0.292036788530824	2		328	424	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675735	30675735	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1191	81	821	0	ENST00000376406.3:c.2621C>G	p.Ser874Cys	p.S874C	ENST00000376406	NM_014641.2	874	tCt/tGt	8/15	1	2	FACETS	0.436	0.383	0.494	0.436	0.383	0.494	SUBCLONAL	1	TRUE	1	0.292036788530824	2		821	1272	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552770	106552770	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	133	562	0	ENST00000369096.4:c.735G>C	p.Lys245Asn	p.K245N	ENST00000369096	NM_001198.3	245	aaG/aaC	5/7	1	2	FACETS	0.995	0.903	1	0.995	0.903	1	CLONAL	1	TRUE	1	0.292036788530824	2		562	915	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402683	139402683	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0045204-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	179	835	0	ENST00000277541.6:c.3325+1G>T		p.X1109_splice	ENST00000277541	NM_017617.3	1109			0.292036788530824	1	FACETS	0.992	0.914	1	0.992	0.914	1	CLONAL	1	TRUE	0	0.292036788530824	1		835	1055	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	11	470	0	ENST00000347630.2:c.305T>C	p.Phe102Ser	p.F102S	ENST00000347630	NM_001007230.1	102	tTc/tCc	5/11	1	2	FACETS	0.348	0.24	0.484	0.348	0.24	0.484	SUBCLONAL	1	TRUE	1	0.22	2		470	287	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517497	176517497	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	10	794	0	ENST00000292408.4:c.198G>A	p.Trp66Ter	p.W66*	ENST00000292408	NM_213647.1	66	tgG/tgA	3/18	0.091336237205092	3	FACETS	0.551	0.374	0.774	0.276	0.187	0.387	INDETERMINATE	1	TRUE	1	0.22	3		794	183	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0045207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	101	464	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.223795224820414	4	FACETS	0.931	0.835	1	0.931	0.835	1	CLONAL	2	TRUE	2	0.270340393745247	4		464	510	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518437	204518437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201947927	NA	P-0045207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	43	383	0	ENST00000367182.3:c.1100C>T	p.Ser367Leu	p.S367L	ENST00000367182	NM_001278516.1	367	tCg/tTg	11/11	0.223795224820414	4	FACETS	1	0.869	1	0.521	0.436	0.614	CLONAL	1	TRUE	2	0.270340393745247	4		383	388	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231106	53231106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556842168	NA	P-0045207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	167	293	0	ENST00000375401.3:c.1796G>A	p.Arg599His	p.R599H	ENST00000375401	NM_004187.3	599	cGt/cAt	13/26	0.270340393745247	2	FACETS	1	0.944	1			1	CLONAL	3	TRUE	NA	0.270340393745247	2		293	405	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575055	48575055	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0045207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	10	222	0	ENST00000342988.3:c.250-1G>A		p.X84_splice	ENST00000342988	NM_005359.5	84			1	2	FACETS	0.387	0.262	0.544	0.387	0.262	0.544	SUBCLONAL	1	TRUE	1	0.270340393745247	2		222	191	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578460	7578474	+	inframe_deletion	In_Frame_Del	DEL	ACGCGGGTGCCGGGC	ACGCGGGTGCCGGGC	-	novel	NA	P-0045207-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	171	765	0	ENST00000269305.4:c.456_470del	p.Pro153_Val157del	p.P153_V157del	ENST00000269305	NM_001126112.2	152	ccGCCCGGCACCCGCGTc/ccc	5/11	0.270340393745247	2	FACETS	0.847	0.781	0.915	0.847	0.781	0.915	CLONAL	2	TRUE	0	0.270340393745247	2		765	747	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0045210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	32	738	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.463	0.375	0.562	0.463	0.375	0.562	SUBCLONAL	1	TRUE	1	0.26	2		738	532	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835596	68835596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587783047	NA	P-0045210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	35	531	1	ENST00000261769.5:c.187C>T	p.Arg63Ter	p.R63*	ENST00000261769	NM_004360.3	63	Cga/Tga	3/16	1	2	FACETS	0.724	0.594	0.869	0.724	0.594	0.869	SUBCLONAL	1	TRUE	1	0.26	2		532	372	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061312	38061312	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1329067081	NA	P-0045210-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	50	794	0	ENST00000250448.2:c.677A>G	p.Asp226Gly	p.D226G	ENST00000250448	NM_004496.3	226	gAc/gGc	2/2	1	2	FACETS	0.81	0.688	0.944	0.81	0.688	0.944	CLONAL	1	TRUE	1	0.26	2		794	475	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0045211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	90	333	0	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	1	2	FACETS	0.926	0.83	1	0.926	0.83	1	CLONAL	1	TRUE	1	0.607489686698994	2		333	320	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117632191	117632191	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045211-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	105	548	0	ENST00000368508.3:c.6225C>A	p.Phe2075Leu	p.F2075L	ENST00000368508	NM_002944.2	2075	ttC/ttA	39/43	0.607489686698994	1	FACETS	0.704	0.637	0.773	0.704	0.637	0.773	SUBCLONAL	1	TRUE	0	0.607489686698994	1		548	342	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0045212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	54	381	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.803	0.687	0.93	0.803	0.687	0.93	CLONAL	1	TRUE	1	0.280757929451948	2		381	479	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578407	7578407	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs138729528	NA	P-0045212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	95	669	0	ENST00000269305.4:c.523C>G	p.Arg175Gly	p.R175G	ENST00000269305	NM_001126112.2	175	Cgc/Ggc	5/11	0.254041813546935	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.280757929451948	1		669	551	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584533	48584533	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0045212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	49	329	0	ENST00000342988.3:c.706G>T	p.Gly236Ter	p.G236*	ENST00000342988	NM_005359.5	236	Gga/Tga	6/12	0.254041813546935	1	FACETS	0.765	0.65	0.892	0.765	0.65	0.892	SUBCLONAL	1	TRUE	0	0.280757929451948	1		329	392	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051093	13051093	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	58	500	0	ENST00000316448.5:c.529C>G	p.Arg177Gly	p.R177G	ENST00000316448	NM_004343.3	177	Cgg/Ggg	5/9	1	2	FACETS	0.729	0.626	0.841	0.729	0.626	0.841	SUBCLONAL	1	TRUE	1	0.280757929451948	2		500	567	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648412	30648412	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045212-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	67	527	0	ENST00000295754.5:c.37C>G	p.His13Asp	p.H13D	ENST00000295754	NM_003242.5	13	Cac/Gac	1/7	0.254041813546935	1	FACETS	0.832	0.725	0.948	0.832	0.725	0.948	CLONAL	1	TRUE	0	0.280757929451948	1		527	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0045244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	53	644	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.256958478299306	1	FACETS	0.732	0.625	0.85	0.732	0.625	0.85	SUBCLONAL	1	TRUE	0	0.256958478299306	1		644	491	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439656	140439656	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	22	314	0	ENST00000288602.6:c.2083G>C	p.Glu695Gln	p.E695Q	ENST00000288602	NM_004333.4	695	Gag/Cag	17/18	1	2	FACETS	0.505	0.391	0.637	0.505	0.391	0.637	SUBCLONAL	1	TRUE	1	0.256958478299306	2		314	339	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732584	190732584	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	28	380	0	ENST00000441310.2:c.2402G>C	p.Arg801Thr	p.R801T	ENST00000441310	NM_000534.4	801	aGa/aCa	11/13	1	2	FACETS	0.444	0.354	0.547	0.444	0.354	0.547	SUBCLONAL	1	TRUE	1	0.256958478299306	2		380	491	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774125	66774125	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759605592	NA	P-0045244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	48	880	1	ENST00000307102.5:c.601C>T	p.Arg201Cys	p.R201C	ENST00000307102	NM_002755.3	201	Cgt/Tgt	6/11	0.256958478299306	1	FACETS	0.425	0.358	0.498	0.425	0.358	0.498	SUBCLONAL	1	TRUE	0	0.256958478299306	1		881	767	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098973	178098973	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	17	247	0	ENST00000397062.3:c.72G>T	p.Trp24Cys	p.W24C	ENST00000397062	NM_006164.4	24	tgG/tgT	2/5	1	2	FACETS	0.499	0.373	0.65	0.499	0.373	0.65	SUBCLONAL	1	TRUE	1	0.256958478299306	2		247	265	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813941	50813941	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1162188229	NA	P-0045244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	78	457	0	ENST00000398568.2:c.1495G>A	p.Ala499Thr	p.A499T	ENST00000398568	NM_001042412.1	499	Gct/Act	8/18	0.202602835470122	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.256958478299306	1		457	476	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406210	406210	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	52	302	0	ENST00000399788.2:c.4231C>G	p.Gln1411Glu	p.Q1411E	ENST00000399788	NM_001042603.1	1411	Caa/Gaa	25/28	0.169747546789391	0	FACETS	0.964	0.826	1			1	CLONAL	1	TRUE	0	0.256958478299306	0		302	312	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112745386	112745386	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	29	403	0	ENST00000369452.4:c.704G>T	p.Gly235Val	p.G235V	ENST00000369452	NM_007373.3	235	gGt/gTt	3/9	1	2	FACETS	0.551	0.441	0.675	0.551	0.441	0.675	SUBCLONAL	1	TRUE	1	0.256958478299306	2		403	410	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483959	88483959	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	78	544	0	ENST00000360948.2:c.1611C>A	p.Asp537Glu	p.D537E	ENST00000360948	NM_001012338.2	537	gaC/gaA	14/19	0.256958478299306	1	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	0	0.256958478299306	1		544	515	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469630	25469630	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762563426	NA	P-0045244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	41	647	0	ENST00000264709.3:c.1138G>T	p.Ala380Ser	p.A380S	ENST00000264709	NM_175629.2	380	Gcg/Tcg	10/23	1	2	FACETS	0.521	0.433	0.619	0.521	0.433	0.619	SUBCLONAL	1	TRUE	1	0.256958478299306	2		647	613	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982012	38982012	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0045244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	95	372	0	ENST00000357387.3:c.710A>T	p.His237Leu	p.H237L	ENST00000357387	NM_152756.3	237	cAt/cTt	8/38	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.256958478299306	2		372	553	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038369	180038369	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	25	676	1	ENST00000261937.6:c.3648C>G	p.Asp1216Glu	p.D1216E	ENST00000261937	NM_182925.4	1216	gaC/gaG	27/30	1	2	FACETS	0.484	0.381	0.603	0.484	0.381	0.603	SUBCLONAL	1	TRUE	1	0.256958478299306	2		677	402	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670594	30670594	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	49	559	0	ENST00000376406.3:c.5926G>C	p.Glu1976Gln	p.E1976Q	ENST00000376406	NM_014641.2	1976	Gag/Cag	13/15	1	2	FACETS	0.82	0.695	0.957	0.82	0.695	0.957	CLONAL	1	TRUE	1	0.256958478299306	2		559	465	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967225	93967225	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	47	330	0	ENST00000369303.4:c.2127A>G	p.Ile709Met	p.I709M	ENST00000369303	NM_004440.3	709	atA/atG	12/17	0.18661279241563	2	FACETS	1	0.943	1	0.624	0.53	0.727	CLONAL	1	TRUE	0	0.256958478299306	2		330	293	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27192495	27192495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	57	449	0	ENST00000380036.4:c.1498G>A	p.Glu500Lys	p.E500K	ENST00000380036	NM_000459.3	500	Gag/Aag	11/23	0.256975006276645	1	FACETS	0.634	0.543	0.733	0.634	0.543	0.733	SUBCLONAL	1	TRUE	0	0.256958478299306	1		449	610	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759938	133759939	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0045244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	35	818	3	ENST00000318560.5:c.2261_2262delinsTT	p.Gly754Val	p.G754V	ENST00000318560	NM_005157.4	754	gGG/gTT	11/11	0.256975006276645	1	FACETS	0.425	0.347	0.512	0.425	0.347	0.512	SUBCLONAL	1	TRUE	0	0.256958478299306	1		821	559	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348146	70348146	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs863223704	NA	P-0045244-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	55	237	0	ENST00000374080.3:c.3210G>T	p.Arg1070Ser	p.R1070S	ENST00000374080		1070	agG/agT	23/45	0.253651785462822	2	FACETS	0.919	0.795	1			1	CLONAL	2	TRUE	NA	0.256958478299306	2		237	233	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0045245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	367	564	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.512297621620626	10	FACETS	1	0.993	1			1	CLONAL	10	TRUE	NA	0.512297621620626	10		564	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578552	7578552	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	C	rs1567554500	NA	P-0045245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	118	720	0	ENST00000269305.4:c.378C>G	p.Tyr126Ter	p.Y126*	ENST00000269305	NM_001126112.2	126	taC/taG	5/11	0.512297621620626	2	FACETS	0.9	0.828	0.972	0.9	0.828	0.972	CLONAL	2	TRUE	0	0.512297621620626	2		720	256	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699372	47699372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	75	333	0	ENST00000347630.2:c.136G>A	p.Glu46Lys	p.E46K	ENST00000347630	NM_001007230.1	46	Gag/Aag	4/11	0.512297621620626	2	FACETS	0.898	0.809	0.989	0.898	0.809	0.989	CLONAL	2	TRUE	0	0.512297621620626	2		333	163	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874287	155874287	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs869025194	NA	P-0045245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	11	381	0	ENST00000368323.3:c.244T>G	p.Phe82Val	p.F82V	ENST00000368323	NM_006912.5	82	Ttt/Gtt	5/6	0.489793269270477	4	FACETS	0.314	0.216	0.434	0.157	0.108	0.217	SUBCLONAL	1	TRUE	2	0.512297621620626	4		381	207	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226367	2226367	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	18	702	0	ENST00000398665.3:c.3847T>G	p.Ser1283Ala	p.S1283A	ENST00000398665	NM_032482.2	1283	Tct/Gct	27/28	0.437626218689028	3	FACETS	0.356	0.268	0.459	0.178	0.134	0.23	SUBCLONAL	1	TRUE	1	0.512297621620626	3		702	248	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873101	136873101	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	32	358	0	ENST00000241393.3:c.397G>C	p.Asp133His	p.D133H	ENST00000241393	NM_003467.2	133	Gac/Cac	2/2	0.3737982261669	4	FACETS	0.867	0.708	1	0.433	0.354	0.521	CLONAL	1	TRUE	2	0.512297621620626	4		358	218	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30946627	30946627	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	87	160	0	ENST00000375687.4:c.49G>T	p.Ala17Ser	p.A17S	ENST00000375687	NM_015338.5	17	Gcg/Tcg	1/13	0.437626218689028	3	FACETS	0.79	0.709	0.874	0.79	0.709	0.874	SUBCLONAL	2	TRUE	1	0.512297621620626	3		160	270	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186601	108186601	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	36	358	0	ENST00000278616.4:c.6058G>T	p.Gly2020Cys	p.G2020C	ENST00000278616	NM_000051.3	2020	Ggc/Tgc	41/63	0.422752403297882	1	FACETS	0.682	0.566	0.809	0.682	0.566	0.809	SUBCLONAL	1	TRUE	0	0.422752403297882	1		358	197	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156740	20156740	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045246-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	61	367	1	ENST00000379607.5:c.17G>T	p.Gly6Val	p.G6V	ENST00000379607	NM_001412.3	6	gGt/gTt	2/7	0.365321210045715	1	FACETS	0.834	0.726	0.948	0.834	0.726	0.948	CLONAL	1	TRUE	0	0.422752403297882	1		368	273	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212929	94212929	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0045247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	27	236	0	ENST00000323929.3:c.315-2A>T		p.X105_splice	ENST00000323929	NM_005591.3	105			1	2	FACETS	0.956	0.763	1	0.956	0.763	1	CLONAL	1	TRUE	1	0.21	2		236	269	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245424	46245424	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	25	358	0	ENST00000334344.6:c.3519del	p.Ile1174Ter	p.I1174*	ENST00000334344	NM_152641.2	1173	aCc/ac	15/21	1	2	FACETS	0.52	0.409	0.648	0.52	0.409	0.648	SUBCLONAL	1	TRUE	1	0.21	2		358	458	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560534	65560534	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0045247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	59	327	0	ENST00000358664.4:c.64-1G>T		p.X22_splice	ENST00000358664	NM_002382.4	22			1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.21	2		327	425	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371734	89371734	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	55	593	0	ENST00000301030.4:c.106C>G	p.Leu36Val	p.L36V	ENST00000301030	NM_001256183.1	36	Cta/Gta	4/13	1	2	FACETS	0.782	0.668	0.907	0.782	0.668	0.907	CLONAL	1	TRUE	1	0.21	2		593	670	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556445	29556445	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0045247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	29	405	0	ENST00000356175.3:c.2812A>T	p.Lys938Ter	p.K938*	ENST00000356175	NM_000267.3	938	Aag/Tag	21/57	1	2	FACETS	0.519	0.416	0.637	0.519	0.416	0.637	SUBCLONAL	1	TRUE	1	0.21	2		405	532	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557277	29557277	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0045247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	21	234	0	ENST00000356175.3:c.2991-1G>T		p.X997_splice	ENST00000356175	NM_000267.3	997			1	2	FACETS	0.699	0.539	0.886	0.699	0.539	0.886	SUBCLONAL	1	TRUE	1	0.21	2		234	286	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1327796	1327796	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759760274	NA	P-0045247-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	54	481	0	ENST00000400841.2:c.85G>A	p.Gly29Arg	p.G29R	ENST00000400841		29	Gga/Aga	2/6	0.133855364950772	2	FACETS	0.834	0.711	0.967			1	CLONAL	1	TRUE	NA	0.21	2		481	617	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0045248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	97	337	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		337	302	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0045248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	66	426	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		426	380	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741915	162741915	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	35	394	0	ENST00000367921.3:c.1606A>G	p.Asn536Asp	p.N536D	ENST00000367921	NM_006182.2	536	Aac/Gac	13/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		394	232	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653834	89653835	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0045248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	36	342	0	ENST00000371953.3:c.133_134dup	p.Arg47ThrfsTer8	p.R47Tfs*8	ENST00000371953	NM_000314.4	44	-/GT	2/9	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		342	235	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226387	2226387	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1315856588	NA	P-0045248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	81	757	0	ENST00000326181.6:c.1998+2T>C		p.X666_splice	ENST00000326181	NM_032271.2	666			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		757	434	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248345	212248345	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777088560	NA	P-0045248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	21	178	0	ENST00000342788.4:c.3922G>A	p.Val1308Met	p.V1308M	ENST00000342788	NM_005235.2	1308	Gtg/Atg	28/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		178	137	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395614	31395614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	114	651	0	ENST00000328111.2:c.2467C>T	p.Arg823Cys	p.R823C	ENST00000328111	NM_006892.3	823	Cgt/Tgt	23/23	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		651	550	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652124	36652125	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0045248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	66	661	0	ENST00000244741.5:c.246_247delinsAT	p.Arg83Trp	p.R83W	ENST00000244741	NM_000389.4	82	ccCCgg/ccATgg	2/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		661	551	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372747	81372747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045248-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	54	327	0	ENST00000222390.5:c.787C>T	p.Pro263Ser	p.P263S	ENST00000222390	NM_000601.4	263	Ccc/Tcc	7/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		327	285	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0045249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	184	287	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.116902538559287	5	FACETS	0.894	0.829	0.961	0.894	0.829	0.961	INDETERMINATE	3	TRUE	2	0.317278049042357	5		287	638	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187718	11187718	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1291168931	NA	P-0045249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	271	638	0	ENST00000361445.4:c.6179G>A	p.Arg2060Gln	p.R2060Q	ENST00000361445	NM_004958.3	2060	cGg/cAg	44/58	0.113183583973969	3	FACETS	1	0.989	1	0.803	0.756	0.851	INDETERMINATE	2	TRUE	0	0.317278049042357	3		638	822	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846363	156846363	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs763758904	NA	P-0045249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	116	744	0	ENST00000524377.1:c.1804C>T	p.Arg602Ter	p.R602*	ENST00000524377	NM_002529.3	602	Cga/Tga	14/17	0.113183583973969	3	FACETS	1	0.91	1	0.337	0.303	0.373	INDETERMINATE	1	TRUE	0	0.317278049042357	3		744	838	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137065	64137065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767134558	NA	P-0045249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	52	722	1	ENST00000334205.4:c.1576G>A	p.Val526Met	p.V526M	ENST00000334205	NM_003942.2	526	Gtg/Atg	13/17	0.12617479000979	5	FACETS	0.521	0.442	0.609	0.174	0.147	0.203	INDETERMINATE	1	TRUE	2	0.317278049042357	5		723	928	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0045249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	290	779	2	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.317278049042357	2	FACETS	0.883	0.836	0.93	1	0.993	1	CLONAL	3	TRUE	0	0.317278049042357	2		781	690	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118888	70118888	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	255	737	0	ENST00000245479.2:c.461del	p.Phe154SerfsTer29	p.F154Sfs*29	ENST00000245479	NM_000346.3	154	Ttc/tc	2/3	0.17459824653849	2	FACETS	1	0.949	1	1	0.949	1	INDETERMINATE	2	TRUE	0	0.317278049042357	2		737	795	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591903	48591903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	101	449	0	ENST00000342988.3:c.1066C>T	p.Pro356Ser	p.P356S	ENST00000342988	NM_005359.5	356	Cct/Tct	9/12	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.317278049042357	2		449	457	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593539	48593539	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0045249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	48	223	0	ENST00000342988.3:c.1292del	p.Pro431GlnfsTer5	p.P431Qfs*5	ENST00000342988	NM_005359.5	430	taC/ta	10/12	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.317278049042357	2		223	290	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231339	5231339	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1367694603	NA	P-0045249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	115	656	0	ENST00000357368.4:c.2137G>A	p.Val713Ile	p.V713I	ENST00000357368	NM_002850.3	713	Gtc/Atc	14/38	0.12617479000979	5	FACETS	1	0.964	1	0.384	0.345	0.425	INDETERMINATE	1	TRUE	2	0.317278049042357	5		656	929	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792125	42792125	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	91	557	0	ENST00000575354.2:c.929G>T	p.Gly310Val	p.G310V	ENST00000575354	NM_015125.3	310	gGg/gTg	6/20	0.12617479000979	5	FACETS	1	0.971	1	0.428	0.38	0.479	INDETERMINATE	1	TRUE	2	0.317278049042357	5		557	659	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797159	42797159	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs189391255	NA	P-0045249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	170	987	3	ENST00000575354.2:c.3521C>T	p.Pro1174Leu	p.P1174L	ENST00000575354	NM_015125.3	1174	cCg/cTg	15/20	0.12617479000979	5	FACETS	1	0.984	1	0.428	0.393	0.466	INDETERMINATE	1	TRUE	2	0.317278049042357	5		990	1231	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268382	198268382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	94	438	0	ENST00000335508.6:c.1646G>A	p.Arg549His	p.R549H	ENST00000335508	NM_012433.2	549	cGt/cAt	12/25	0.113183583973969	3	FACETS	1	0.969	1	0.413	0.368	0.461	INDETERMINATE	1	TRUE	0	0.317278049042357	3		438	554	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0045249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	58	242	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	1	2	FACETS	0.965	0.832	1	0.965	0.832	1	CLONAL	1	TRUE	1	0.317278049042357	2		242	379	SUCCESS
APC	324	MSKCC	GRCh37	5	112175473	112175474	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0045249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	82	308	0	ENST00000257430.4:c.4183dup	p.Ser1395LysfsTer3	p.S1395Kfs*3	ENST00000257430	NM_000038.5	1394	-/A	16/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.317278049042357	2		308	348	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265445	152265445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149490424	NA	P-0045249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	220	549	0	ENST00000206249.3:c.898C>T	p.Arg300Cys	p.R300C	ENST00000206249	NM_000125.3	300	Cgc/Tgc	4/8	0.116902538559287	5	FACETS	0.881	0.823	0.942	0.881	0.823	0.942	INDETERMINATE	3	TRUE	2	0.317278049042357	5		549	774	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381567	81381567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370760302	NA	P-0045249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	41	245	1	ENST00000222390.5:c.494C>T	p.Ser165Leu	p.S165L	ENST00000222390	NM_000601.4	165	tCg/tTg	5/18	0.317278049042357	5	FACETS	0.944	0.788	1	0.236	0.197	0.28	CLONAL	1	TRUE	1	0.317278049042357	5		246	404	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257201	16257201	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	32	523	0	ENST00000375759.3:c.4466C>G	p.Pro1489Arg	p.P1489R	ENST00000375759	NM_015001.2	1489	cCt/cGt	11/15	1	2	FACETS	0.904	0.735	1	0.904	0.735	1	CLONAL	1	TRUE	1	0.21	2		523	337	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0045250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	18	313	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	0.207	0.155	0.27	0.207	0.155	0.27	SUBCLONAL	1	TRUE	1	0.21	2		313	827	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696435	47696435	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	75	529	0	ENST00000347630.2:c.388G>A	p.Asp130Asn	p.D130N	ENST00000347630	NM_001007230.1	130	Gac/Aac	6/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.21	2		529	514	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696643	47696643	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs193920894	NA	P-0045250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	24	494	0	ENST00000347630.2:c.305T>G	p.Phe102Cys	p.F102C	ENST00000347630	NM_001007230.1	102	tTc/tGc	5/11	1	2	FACETS	0.543	0.425	0.679	0.543	0.425	0.679	SUBCLONAL	1	TRUE	1	0.21	2		494	421	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	230	379	0	ENST00000347630.2:c.399C>A	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttA	6/11	1	2	FACETS	0.947	0.887	1	1	0.994	1	CLONAL	2	FALSE	1	0.350629979148329	2		379	693	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0045251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	230	444	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	0.208886107414591	0	FACETS	0.661	0.62	0.703			1	INDETERMINATE	2	FALSE	0	0.350629979148329	0		444	644	SUCCESS
APC	324	MSKCC	GRCh37	5	112177791	112177791	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0045251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	60	274	0	ENST00000257430.4:c.6500T>G	p.Ile2167Ser	p.I2167S	ENST00000257430	NM_000038.5	2167	aTt/aGt	16/16	0.350629979148329	3	FACETS	1	0.928	1	0.37	0.32	0.424	CLONAL	1	FALSE	0	0.350629979148329	3		274	362	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76931738	76931740	+	inframe_deletion	In_Frame_Del	DEL	GTC	GTC	-	novel	NA	P-0045251-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	133	173	1	ENST00000373344.5:c.3790_3792del	p.Asp1264del	p.D1264del	ENST00000373344	NM_000489.3	1264	GAC/-	10/35	1	1	FACETS	0.993	0.93	1	1	0.993	1	CLONAL	3	FALSE	0	0.350629979148329	1		174	210	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0045254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	45	209	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.882	0.743	1	0.882	0.743	1	CLONAL	1	TRUE	1	0.26920543446032	2		209	379	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023559	27023560	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0045254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	116	471	0	ENST00000324856.7:c.671dup	p.Pro225AlafsTer175	p.P225Afs*175	ENST00000324856	NM_006015.4	222	tac/taCc	1/20	0.26920543446032	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.26920543446032	1		471	674	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984935	9984935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	72	453	0	ENST00000330684.3:c.1030G>A	p.Asp344Asn	p.D344N	ENST00000330684	NM_001134407.1	344	Gat/Aat	4/13	1	2	FACETS	0.713	0.622	0.811	0.713	0.622	0.811	SUBCLONAL	1	TRUE	1	0.26920543446032	2		453	750	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873818	35873818	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555342918	NA	P-0045254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	66	312	0	ENST00000216797.5:c.33G>A	p.Trp11Ter	p.W11*	ENST00000216797	NM_020529.2	11	tgG/tgA	1/6	1	2	FACETS	0.93	0.809	1	0.93	0.809	1	CLONAL	1	TRUE	1	0.26920543446032	2		312	527	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830084	72830084	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	119	525	0	ENST00000268489.5:c.6497T>G	p.Ile2166Ser	p.I2166S	ENST00000268489	NM_006885.3	2166	aTt/aGt	9/10	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.26920543446032	2		525	860	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602328	10602328	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0045256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	57	834	0	ENST00000171111.5:c.1250G>T	p.Gly417Val	p.G417V	ENST00000171111	NM_203500.1	417	gGg/gTg	3/6	0.130921672973152	1	FACETS	0.83	0.71	0.961	0.83	0.71	0.961	CLONAL	1	TRUE	0	0.16	1		834	790	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38631974	38631974	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0045256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	32	530	0	ENST00000299084.4:c.460G>A	p.Asp154Asn	p.D154N	ENST00000299084	NM_152594.2	154	Gat/Aat	5/7	0.130921672973152	1	FACETS	0.647	0.524	0.786	0.647	0.524	0.786	SUBCLONAL	1	TRUE	0	0.16	1		530	569	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220578	1220578	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0045256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	30	764	0	ENST00000326873.7:c.598-2A>C		p.X200_splice	ENST00000326873	NM_000455.4	200			0.130921672973152	1	FACETS	0.671	0.54	0.821	0.671	0.54	0.821	SUBCLONAL	1	TRUE	0	0.16	1		764	514	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2202722	2202722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	34	590	1	ENST00000398665.3:c.731C>T	p.Ala244Val	p.A244V	ENST00000398665	NM_032482.2	244	gCc/gTc	9/28	0.130921672973152	1	FACETS	0.684	0.557	0.826	0.684	0.557	0.826	SUBCLONAL	1	TRUE	0	0.16	1		591	572	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61706062	61706062	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	52	451	0	ENST00000401558.2:c.3109G>C	p.Glu1037Gln	p.E1037Q	ENST00000401558	NM_003400.3	1037	Gag/Cag	25/25	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.16	2		451	611	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678369	88678370	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	A	novel	NA	P-0045256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	55	726	0	ENST00000360948.2:c.1166_1167delinsT	p.Gln389LeufsTer25	p.Q389Lfs*25	ENST00000360948	NM_001012338.2	389	cAG/cT	9/19	1	2	FACETS	0.92	0.786	1	0.92	0.786	1	CLONAL	1	TRUE	1	0.16	2		726	747	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0045273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	66	401	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.701879663365914	2		401	165	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104359302	104359302	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587776578	NA	P-0045273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	36	603	1	ENST00000369902.3:c.1022+1G>A		p.X341_splice	ENST00000369902	NM_016169.3	341			0.214873214621524	1	FACETS	0.408	0.34	0.483	0.408	0.34	0.483	INDETERMINATE	1	TRUE	0	0.701879663365914	1		604	163	SUCCESS
ATM	472	MSKCC	GRCh37	11	108122680	108122680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	55	440	0	ENST00000278616.4:c.1724C>T	p.Ser575Leu	p.S575L	ENST00000278616	NM_000051.3	575	tCa/tTa	11/63	0.214873214621524	1	FACETS	0.678	0.594	0.766	0.678	0.594	0.766	INDETERMINATE	1	TRUE	0	0.701879663365914	1		440	150	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373931	118373931	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0045273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	14	359	0	ENST00000534358.1:c.7324G>C	p.Glu2442Gln	p.E2442Q	ENST00000534358	NM_005933.3	2442	Gaa/Caa	27/36	0.214873214621524	1	FACETS	0.308	0.226	0.404	0.308	0.226	0.404	INDETERMINATE	1	TRUE	0	0.701879663365914	1		359	84	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579285	7579358	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGAAGCCAGCCCCTCAGGGCAACTGACCGTGCAAGTCACAGACTTGGCTGTCCCAGAATGCAAGAAGCCCAGAC	GGAAGCCAGCCCCTCAGGGCAACTGACCGTGCAAGTCACAGACTTGGCTGTCCCAGAATGCAAGAAGCCCAGAC	-	novel	NA	P-0045273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	36	481	0	ENST00000269305.4:c.329_375+27del		p.X110_splice	ENST00000269305	NM_001126112.2	110		4/11	0.571953188939303	1	FACETS	0.876	0.752	1	0.876	0.752	1	CLONAL	1	TRUE	0	0.701879663365914	1		481	76	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286768	212286768	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0045273-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	51	409	0	ENST00000342788.4:c.2928G>C	p.Arg976Ser	p.R976S	ENST00000342788	NM_005235.2	976	agG/agC	24/28	1	2	FACETS	0.975	0.847	1	0.975	0.847	1	CLONAL	1	TRUE	1	0.701879663365914	2		409	149	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579414	7579414	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876660548	NA	P-0045276-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	131	777	0	ENST00000269305.4:c.273G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tgG/tgA	4/11	1	2	FACETS	0.715	0.648	0.786	0.715	0.648	0.786	SUBCLONAL	1	FALSE	1	0.373986101378379	2		777	980	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28929495	NA	P-0045277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	353	695	1	ENST00000275493.2:c.2155G>A	p.Gly719Ser	p.G719S	ENST00000275493	NM_005228.3	719	Ggc/Agc	18/28	0.370765393955661	5	FACETS	0.88	0.837	0.922	1	0.991	1	CLONAL	4	TRUE	2	0.370765393955661	5		696	842	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0045277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	286	722	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.370765393955661	5	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	2	0.370765393955661	5		722	715	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229221	123229221	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0045277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	18	161	0	ENST00000218089.9:c.3706-1G>A		p.X1236_splice	ENST00000218089	NM_001042749.1	1236			0.370765393955661	2	FACETS	0.384	0.289	0.495			1	SUBCLONAL	1	TRUE	NA	0.370765393955661	2		161	253	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192066	108192066	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0045277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	83	552	0	ENST00000278616.4:c.6491A>C	p.Glu2164Ala	p.E2164A	ENST00000278616	NM_000051.3	2164	gAg/gCg	45/63	0.189029752704076	3	FACETS	1	0.939	1	0.547	0.484	0.614	INDETERMINATE	1	TRUE	1	0.370765393955661	3		552	485	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39613904	39613904	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0045277-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	29	419	0	ENST00000262039.4:c.1822A>T	p.Thr608Ser	p.T608S	ENST00000262039	NM_002647.2	608	Aca/Tca	16/25	1	2	FACETS	0.429	0.344	0.525	0.429	0.344	0.525	SUBCLONAL	1	TRUE	1	0.370765393955661	2		419	365	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0045280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	158	401	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.666573526655207	2		401	437	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0045280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	519	688	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.622901318801392	2	FACETS	0.889	0.859	0.918	0.889	0.859	0.918	CLONAL	2	TRUE	0	0.666573526655207	2		689	876	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0045280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	142	359	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.666573526655207	1	FACETS	0.913	0.847	0.981	0.913	0.847	0.981	CLONAL	1	TRUE	0	0.666573526655207	1		359	311	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0045280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	196	372	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.319453875542171	3	FACETS	1	0.945	1	1	0.945	1	INDETERMINATE	2	TRUE	1	0.666573526655207	3		372	390	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0045280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	95	237	1	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	0.319453875542171	3	FACETS	0.945	0.848	1	0.473	0.424	0.524	INDETERMINATE	1	TRUE	1	0.666573526655207	3		238	402	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944608	40944608	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs752116362	NA	P-0045280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	172	416	0	ENST00000373198.4:c.1894C>T	p.Arg632Ter	p.R632*	ENST00000373198	NM_133170.3	632	Cga/Tga	12/32	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.666573526655207	2		416	399	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120502041	120502041	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0045280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	167	435	0	ENST00000256646.2:c.2000G>A	p.Ser667Asn	p.S667N	ENST00000256646	NM_024408.3	667	aGt/aAt	12/34	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.666573526655207	2		435	458	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961328	15961328	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0045280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	374	511	0	ENST00000268712.3:c.6061C>T	p.Gln2021Ter	p.Q2021*	ENST00000268712	NM_006311.3	2021	Cag/Tag	39/46	0.622901318801392	2	FACETS	0.941	0.906	0.977	0.941	0.906	0.977	CLONAL	2	TRUE	0	0.666573526655207	2		511	596	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051056	13051056	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0045280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	104	484	0	ENST00000316448.5:c.493-1G>A		p.X165_splice	ENST00000316448	NM_004343.3	165			0.40548552534307	1	FACETS	0.417	0.375	0.461	0.417	0.375	0.461	SUBCLONAL	1	TRUE	0	0.666573526655207	1		484	499	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478097	138478097	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	230	507	0	ENST00000289153.2:c.89T>C	p.Ile30Thr	p.I30T	ENST00000289153	NM_006219.2	30	aTa/aCa	1/22	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.666573526655207	2		507	689	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016325	150016325	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0045280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	208	419	0	ENST00000253339.5:c.381C>A	p.Asn127Lys	p.N127K	ENST00000253339		127	aaC/aaA	2/7	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.666573526655207	2		419	624	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0045281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	102	217	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.886	0.804	0.971	1	0.987	1	CLONAL	2	TRUE	1	0.391501405204787	2		217	294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0045281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	600	687	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.391501405204787	2	FACETS	1	0.991	1	1	0.998	1	CLONAL	4	TRUE	0	0.391501405204787	2		687	748	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	244006471	244006471	+	start_lost	Translation_Start_Site	SNP	A	A	C	novel	NA	P-0045281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	71	434	0	ENST00000263826.5:c.2T>G	p.Met1?	p.M1?	ENST00000263826	NM_005465.4	1	aTg/aGg	1/13	1	2	FACETS	0.637	0.557	0.724	0.637	0.557	0.724	SUBCLONAL	1	TRUE	1	0.391501405204787	2		434	569	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46240707	46240707	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0045281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	17	293	0	ENST00000334344.6:c.1569del	p.Phe523LeufsTer6	p.F523Lfs*6	ENST00000334344	NM_152641.2	523	Ttt/tt	12/21	1	2	FACETS	0.333	0.248	0.433	0.333	0.248	0.433	SUBCLONAL	1	TRUE	1	0.391501405204787	2		293	261	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058370	42058370	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0045281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	149	298	0	ENST00000219905.7:c.8090A>G	p.Asp2697Gly	p.D2697G	ENST00000219905	NM_001164273.1	2697	gAt/gGt	24/24	1	2	FACETS	1	0.94	1	1	0.992	1	CLONAL	2	TRUE	1	0.391501405204787	2		298	374	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937075	76937075	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0045281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	133	194	0	ENST00000373344.5:c.3673A>G	p.Lys1225Glu	p.K1225E	ENST00000373344	NM_000489.3	1225	Aaa/Gaa	9/35	1	1	FACETS	1	0.985	1	1	0.994	1	CLONAL	3	TRUE	0	0.391501405204787	1		194	166	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938286	76938286	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0045281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	186	268	0	ENST00000373344.5:c.2462T>G	p.Leu821Ter	p.L821*	ENST00000373344	NM_000489.3	821	tTa/tGa	9/35	1	1	FACETS	1	0.985	1	1	0.995	1	CLONAL	3	TRUE	0	0.391501405204787	1		268	239	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441282	52441285	+	frameshift_variant	Frame_Shift_Del	DEL	CGCA	CGCA	-	novel	NA	P-0000159-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	20	400	0	ENST00000460680.1:c.485_488del	p.Val162GlyfsTer24	p.V162Gfs*24	ENST00000460680	NM_004656.3	162	gTGCGg/gg	7/17	0.3	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		400	209	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127383	17127385	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs786203218	NA	P-0000159-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	17	336	0	ENST00000285071.4:c.469_471del	p.Phe157del	p.F157del	ENST00000285071	NM_144997.5	157	TTC/-	6/14	0.173123213140597	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		336	189	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0001391-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	268	781	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.317874568303042	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.317874568303042	2		782	728	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0001391-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	104	614	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.317874568303042	2		614	563	SUCCESS
APC	324	MSKCC	GRCh37	5	112175390	112175390	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913328	NA	P-0001391-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	64	376	0	ENST00000257430.4:c.4099C>T	p.Gln1367Ter	p.Q1367*	ENST00000257430	NM_000038.5	1367	Cag/Tag	16/16	0.317874568303042	3	FACETS	1	0.923	1	0.545	0.473	0.622	CLONAL	1	TRUE	1	0.317874568303042	3		376	428	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0001391-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	58	465	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	0.317874568303042	4	FACETS	0.881	0.757	1	0.294	0.252	0.339	CLONAL	1	TRUE	1	0.317874568303042	4		465	546	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0001391-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	121	191	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	0.317874568303042	4	FACETS	0.899	0.821	0.98	0.899	0.821	0.98	CLONAL	3	TRUE	1	0.317874568303042	4		191	372	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587179	212587179	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001391-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	82	604	0	ENST00000342788.4:c.822A>C	p.Gln274His	p.Q274H	ENST00000342788	NM_005235.2	274	caA/caC	7/28	0.317874568303042	4	FACETS	1	0.936	1	0.273	0.241	0.308	CLONAL	1	TRUE	0	0.317874568303042	4		604	622	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226351	2226351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1331463984	NA	P-0001391-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	146	857	0	ENST00000326181.6:c.1964G>A	p.Arg655Gln	p.R655Q	ENST00000326181	NM_032271.2	655	cGa/cAa	20/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.317874568303042	2		857	867	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197838	66197838	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001391-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	18	328	0	ENST00000273854.3:c.2861A>C	p.Asn954Thr	p.N954T	ENST00000273854	NM_004439.5	954	aAt/aCt	17/18	1	2	FACETS	0.419	0.316	0.542	0.419	0.316	0.542	SUBCLONAL	1	TRUE	1	0.317874568303042	2		328	270	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245723	46245723	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001391-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	84	646	0	ENST00000334344.6:c.3817C>T	p.Arg1273Ter	p.R1273*	ENST00000334344	NM_152641.2	1273	Cga/Tga	15/21	1	2	FACETS	0.99	0.876	1	0.99	0.876	1	CLONAL	1	TRUE	1	0.317874568303042	2		646	534	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073782	8073782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001391-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	101	475	0	ENST00000377482.5:c.877C>T	p.Pro293Ser	p.P293S	ENST00000377482	NM_018948.3	293	Cca/Tca	4/4	0.317874568303042	2	FACETS	0.777	0.699	0.858	0.777	0.699	0.858	SUBCLONAL	2	TRUE	0	0.317874568303042	2		475	409	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249520	153249520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001391-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	150	596	1	ENST00000281708.4:c.1258C>T	p.His420Tyr	p.H420Y	ENST00000281708	NM_033632.3	420	Cat/Tat	9/12	0.317874568303042	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	0	0.317874568303042	2		597	462	SUCCESS
APC	324	MSKCC	GRCh37	5	112175384	112175384	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001391-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	111	361	0	ENST00000257430.4:c.4094del	p.Gly1365ValfsTer50	p.G1365Vfs*50	ENST00000257430	NM_000038.5	1365	Ggt/gt	16/16	0.317874568303042	3	FACETS	0.975	0.883	1	0.975	0.883	1	CLONAL	2	TRUE	1	0.317874568303042	3		361	415	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637069	176637069	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001391-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	86	763	1	ENST00000439151.2:c.1669A>G	p.Ser557Gly	p.S557G	ENST00000439151	NM_022455.4	557	Agc/Ggc	5/23	0.317874568303042	3	FACETS	0.752	0.664	0.846	0.376	0.332	0.423	SUBCLONAL	1	TRUE	1	0.317874568303042	3		764	834	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151750	108151750	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0001403-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	144	297	0	ENST00000278616.4:c.3431T>A	p.Leu1144Ter	p.L1144*	ENST00000278616	NM_000051.3	1144	tTg/tAg	24/63	0.378494306615516	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.382773453271559	2		297	353	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022460	31022460	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001403-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	64	188	0	ENST00000375687.4:c.1945G>A	p.Gly649Arg	p.G649R	ENST00000375687	NM_015338.5	649	Gga/Aga	13/13	0.382773453271559	4	FACETS	1	0.932	1	0.557	0.484	0.636	CLONAL	1	TRUE	2	0.382773453271559	4		188	415	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402537	20402537	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	92	470	0	ENST00000346618.3:c.74T>C	p.Val25Ala	p.V25A	ENST00000346618	NM_001949.4	25	gTc/gCc	1/7	0.0465021450384908	4	FACETS	1	0.929	1	0.531	0.471	0.594	INDETERMINATE	1	TRUE	2	0.305928374467482	4		470	740	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	50	352	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.0465021450384908	4	FACETS	0.951	0.808	1	0.475	0.404	0.554	INDETERMINATE	1	TRUE	2	0.305928374467482	4		352	449	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156742	20156742	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	44	307	0	ENST00000379607.5:c.17-2A>G		p.X6_splice	ENST00000379607	NM_001412.3	6			0.305928374467482	1	FACETS	0.527	0.442	0.621	0.527	0.442	0.621	SUBCLONAL	1	TRUE	0	0.305928374467482	1		307	462	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601972	43601972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774829203	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	151	751	0	ENST00000355710.3:c.1016C>T	p.Ser339Leu	p.S339L	ENST00000355710	NM_020975.4	339	tCg/tTg	5/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.305928374467482	2		751	846	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	53	265	1	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.305928374467482	2		266	300	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106078	27106078	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	108	521	0	ENST00000324856.7:c.5693del	p.Pro1898HisfsTer25	p.P1898Hfs*25	ENST00000324856	NM_006015.4	1897	Ccc/cc	20/20	0.0427495891417404	4	FACETS	1	0.973	1	0.623	0.559	0.691	INDETERMINATE	1	TRUE	2	0.305928374467482	4		521	740	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101099	27101099	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	152	673	1	ENST00000324856.7:c.4381C>T	p.Arg1461Ter	p.R1461*	ENST00000324856	NM_006015.4	1461	Cga/Tga	18/20	0.0427495891417404	4	FACETS	1	0.984	1	0.667	0.609	0.727	INDETERMINATE	1	TRUE	2	0.305928374467482	4		674	973	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	51	400	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.836	0.712	0.97	0.836	0.712	0.97	CLONAL	1	TRUE	1	0.305928374467482	2		400	399	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394805	45394805	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	56	292	0	ENST00000262160.6:c.544C>T	p.Arg182Ter	p.R182*	ENST00000262160	NM_005901.5	182	Cga/Tga	5/11	1	2	FACETS	0.941	0.809	1	0.941	0.809	1	CLONAL	1	TRUE	1	0.305928374467482	2		292	389	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491273	2491273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771419721	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	161	670	0	ENST00000355716.4:c.316C>T	p.Arg106Cys	p.R106C	ENST00000355716	NM_003820.2	106	Cgc/Tgc	4/8	0.305928374467482	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.305928374467482	1		670	889	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11273611	11273611	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	49	324	0	ENST00000361445.4:c.3130A>G	p.Met1044Val	p.M1044V	ENST00000361445	NM_004958.3	1044	Atg/Gtg	21/58	0.305928374467482	1	FACETS	0.817	0.695	0.95	0.817	0.695	0.95	CLONAL	1	TRUE	0	0.305928374467482	1		324	332	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65316543	65316543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs961932195	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	87	456	2	ENST00000342505.4:c.1699G>A	p.Val567Ile	p.V567I	ENST00000342505	NM_002227.2	567	Gtc/Atc	12/25	1	2	FACETS	0.864	0.766	0.97	0.864	0.766	0.97	CLONAL	1	TRUE	1	0.305928374467482	2		458	658	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719178	61719178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	44	286	0	ENST00000401558.2:c.1879C>T	p.Pro627Ser	p.P627S	ENST00000401558	NM_003400.3	627	Cct/Tct	16/25	1	2	FACETS	0.741	0.623	0.872	0.741	0.623	0.872	SUBCLONAL	1	TRUE	1	0.305928374467482	2		286	388	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928347	69928347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	79	372	1	ENST00000352241.4:c.167G>A	p.Arg56His	p.R56H	ENST00000352241	NM_198159.2	56	cGc/cAc	2/10	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.305928374467482	2		373	500	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182681721	182681721	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	103	414	0	ENST00000292782.4:c.337A>C	p.Thr113Pro	p.T113P	ENST00000292782	NM_020640.2	113	Aca/Cca	3/7	1	2	FACETS	0.989	0.886	1	0.989	0.886	1	CLONAL	1	TRUE	1	0.305928374467482	2		414	681	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750572	41750572	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	83	508	0	ENST00000226382.2:c.56C>A	p.Ala19Asp	p.A19D	ENST00000226382	NM_003924.3	19	gCt/gAt	1/3	1	2	FACETS	0.95	0.84	1	0.95	0.84	1	CLONAL	1	TRUE	1	0.305928374467482	2		508	571	SUCCESS
APC	324	MSKCC	GRCh37	5	112154998	112154998	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	110	555	1	ENST00000257430.4:c.1269G>A	p.Trp423Ter	p.W423*	ENST00000257430	NM_000038.5	423	tgG/tgA	10/16	1	2	FACETS	0.918	0.825	1	0.918	0.825	1	CLONAL	1	TRUE	1	0.305928374467482	2		556	783	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509457	149509457	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758072563	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	120	665	1	ENST00000261799.4:c.1442C>T	p.Thr481Met	p.T481M	ENST00000261799	NM_002609.3	481	aCg/aTg	10/23	1	2	FACETS	0.888	0.802	0.98	0.888	0.802	0.98	CLONAL	1	TRUE	1	0.305928374467482	2		666	883	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707573	176707573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554204064	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	112	425	0	ENST00000439151.2:c.5630G>A	p.Arg1877His	p.R1877H	ENST00000439151	NM_022455.4	1877	cGt/cAt	18/23	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.305928374467482	2		425	634	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005337	150005337	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	115	548	1	ENST00000253339.5:c.888G>A	p.Trp296Ter	p.W296*	ENST00000253339		296	tgG/tgA	3/7	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.305928374467482	2		549	682	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419955	152419955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182943916	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	92	568	0	ENST00000206249.3:c.1642C>T	p.Arg548Cys	p.R548C	ENST00000206249	NM_000125.3	548	Cgc/Tgc	8/8	1	2	FACETS	0.809	0.719	0.906	0.809	0.719	0.906	CLONAL	1	TRUE	1	0.305928374467482	2		568	743	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469823	157469823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542660265	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	147	702	0	ENST00000346085.5:c.2617G>A	p.Gly873Ser	p.G873S	ENST00000346085	NM_020732.3	873	Ggt/Agt	9/20	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.305928374467482	2		702	936	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396316	139396316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290643339	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	185	748	1	ENST00000277541.6:c.5522G>A	p.Arg1841Gln	p.R1841Q	ENST00000277541	NM_017617.3	1841	cGg/cAg	30/34	0.305928374467482	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.305928374467482	1		749	1015	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218912	133218912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1011938171	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	171	759	0	ENST00000320574.5:c.5024G>A	p.Arg1675His	p.R1675H	ENST00000320574	NM_006231.2	1675	cGc/cAc	38/49	0.305928374467482	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.305928374467482	1		759	931	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254004	133254004	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1331349861	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	91	503	0	ENST00000320574.5:c.746G>A	p.Arg249Gln	p.R249Q	ENST00000320574	NM_006231.2	249	cGa/cAa	8/49	0.305928374467482	1	FACETS	0.838	0.746	0.937	0.838	0.746	0.937	CLONAL	1	TRUE	0	0.305928374467482	1		503	601	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554314	81554314	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	72	369	1	ENST00000298171.2:c.334A>G	p.Arg112Gly	p.R112G	ENST00000298171	NM_000369.2	112	Agg/Ggg	4/10	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.305928374467482	2		370	446	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89825003	89825003	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	135	495	0	ENST00000389301.3:c.2963T>C	p.Leu988Pro	p.L988P	ENST00000389301	NM_000135.2	988	cTg/cCg	30/43	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.305928374467482	2		495	871	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989529	7989529	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1231568614	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	85	480	0	ENST00000319144.4:c.157T>C	p.Tyr53His	p.Y53H	ENST00000319144	NM_001139.2	53	Tac/Cac	2/15	1	2	FACETS	0.961	0.851	1	0.961	0.851	1	CLONAL	1	TRUE	1	0.305928374467482	2		480	578	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435372	56435372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	169	733	1	ENST00000407977.2:c.1765C>T	p.Pro589Ser	p.P589S	ENST00000407977		589	Cca/Tca	9/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.305928374467482	2		734	904	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440912	56440912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	174	644	0	ENST00000407977.2:c.425C>T	p.Thr142Ile	p.T142I	ENST00000407977		142	aCt/aTt	4/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.305928374467482	2		644	931	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78935205	78935205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138318172	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	120	623	0	ENST00000306801.3:c.3617C>T	p.Thr1206Met	p.T1206M	ENST00000306801	NM_020761.2	1206	aCg/aTg	31/34	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.305928374467482	2		623	770	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395776	45395776	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	56	276	0	ENST00000262160.6:c.358C>T	p.Arg120Ter	p.R120*	ENST00000262160	NM_005901.5	120	Cga/Tga	4/11	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.305928374467482	2		276	363	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216358	2216358	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370276763	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	137	653	1	ENST00000398665.3:c.2002G>A	p.Ala668Thr	p.A668T	ENST00000398665	NM_032482.2	668	Gcc/Acc	20/28	0.305928374467482	1	FACETS	0.861	0.783	0.943	0.861	0.783	0.943	CLONAL	1	TRUE	0	0.305928374467482	1		654	881	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262079	10262079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762172122	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	120	471	0	ENST00000340748.4:c.2212G>A	p.Val738Ile	p.V738I	ENST00000340748		738	Gtc/Atc	23/40	0.305928374467482	1	FACETS	0.97	0.877	1	0.97	0.877	1	CLONAL	1	TRUE	0	0.305928374467482	1		471	685	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290214	15290214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373181668	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	163	805	1	ENST00000263388.2:c.3421G>A	p.Val1141Met	p.V1141M	ENST00000263388	NM_000435.2	1141	Gtg/Atg	21/33	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.305928374467482	2		806	899	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573302	41573302	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1297677732	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	136	781	1	ENST00000263253.7:c.5587C>T	p.Pro1863Ser	p.P1863S	ENST00000263253	NM_001429.3	1863	Cca/Tca	31/31	1	2	FACETS	0.972	0.883	1	0.972	0.883	1	CLONAL	1	TRUE	1	0.305928374467482	2		782	915	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930411	39930411	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs751015767	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	52	276	1	ENST00000378444.4:c.3053G>A	p.Arg1018His	p.R1018H	ENST00000378444	NM_001123385.1	1018	cGt/cAt	6/15	0.305928374467482	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.305928374467482	1		277	245	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48651631	48651631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	147	732	0	ENST00000376670.3:c.797C>T	p.Thr266Met	p.T266M	ENST00000376670	NM_002049.3	266	aCg/aTg	5/6	0.305928374467482	1	FACETS	0.964	0.881	1	0.964	0.881	1	CLONAL	1	TRUE	0	0.305928374467482	1		732	844	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032153	48032154	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	79	280	0	ENST00000234420.5:c.3545_3546dup	p.Ile1183GlufsTer2	p.I1183Efs*2	ENST00000234420	NM_000179.2	1181	-/AG	6/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.305928374467482	2		280	424	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	83	452	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.992	0.877	1	0.992	0.877	1	CLONAL	1	TRUE	1	0.305928374467482	2		457	547	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411864	63411864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767572122	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	136	967	0	ENST00000330258.3:c.1303G>A	p.Gly435Ser	p.G435S	ENST00000330258	NM_152424.3	435	Ggc/Agc	2/2	0.305928374467482	1	FACETS	0.888	0.807	0.973	0.888	0.807	0.973	CLONAL	1	TRUE	0	0.305928374467482	1		967	848	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491390	18491390	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1377942847	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	52	264	1	ENST00000266497.5:c.1309del	p.Ile437TyrfsTer5	p.I437Yfs*5	ENST00000266497		435	Aaa/aa	8/31	0.0901805244202469	6	FACETS	0.854	0.731	0.987	0.569	0.487	0.658	INDETERMINATE	2	TRUE	3	0.305928374467482	6		265	321	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143440	30143440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	75	488	3	ENST00000389048.3:c.86C>T	p.Ala29Val	p.A29V	ENST00000389048	NM_004304.4	29	gCg/gTg	1/29	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.305928374467482	2		491	450	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346832	89346832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772993940	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	26	415	0	ENST00000301030.4:c.6118G>A	p.Gly2040Arg	p.G2040R	ENST00000301030	NM_001256183.1	2040	Gga/Aga	9/13	1	2	FACETS	0.444	0.351	0.55	0.444	0.351	0.55	SUBCLONAL	1	TRUE	1	0.305928374467482	2		415	383	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800127	32800127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374339816	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	57	350	0	ENST00000374899.4:c.1255G>A	p.Val419Met	p.V419M	ENST00000374899	NM_018833.2	419	Gtg/Atg	7/12	0.0465021450384908	4	FACETS	0.874	0.75	1	0.437	0.375	0.505	INDETERMINATE	1	TRUE	2	0.305928374467482	4		350	557	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211090	36211090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776595230	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	233	934	1	ENST00000222270.7:c.841C>T	p.Arg281Cys	p.R281C	ENST00000222270	NM_014727.1	281	Cgt/Tgt	3/37	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.305928374467482	2		935	1161	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905896	50905896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748657880	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	153	793	2	ENST00000440232.2:c.868G>A	p.Val290Met	p.V290M	ENST00000440232	NM_002691.3	290	Gtg/Atg	8/27	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.305928374467482	2		795	874	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246091265	246091265	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs777672375	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	105	453	1	ENST00000388985.4:c.670C>T	p.Arg224Ter	p.R224*	ENST00000388985		224	Cga/Tga	7/12	1	2	FACETS	0.895	0.802	0.994	0.895	0.802	0.994	CLONAL	1	TRUE	1	0.305928374467482	2		454	767	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830895	72830895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770650936	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	119	538	2	ENST00000268489.5:c.5686G>A	p.Ala1896Thr	p.A1896T	ENST00000268489	NM_006885.3	1896	Gcc/Acc	9/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.305928374467482	2		540	665	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775427	39775428	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CT	CT	-	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	58	371	0	ENST00000288319.7:c.592_592+1del		p.X198_splice	ENST00000288319	NM_182918.3	198		4/10	1	2	FACETS	0.788	0.678	0.908	0.788	0.678	0.908	CLONAL	1	TRUE	1	0.305928374467482	2		371	481	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40857171	40857171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1287411309	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	90	336	0	ENST00000428826.2:c.1870G>A	p.Gly624Arg	p.G624R	ENST00000428826		624	Gga/Aga	17/21	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.305928374467482	2		336	545	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121265	29121265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368570187	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	38	654	1	ENST00000328354.6:c.410G>A	p.Arg137Gln	p.R137Q	ENST00000328354	NM_007194.3	137	cGa/cAa	3/15	1	2	FACETS	0.346	0.285	0.415	0.346	0.285	0.415	SUBCLONAL	1	TRUE	1	0.305928374467482	2		655	717	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371709	89371709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1010844836	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	172	636	0	ENST00000301030.4:c.131G>A	p.Arg44His	p.R44H	ENST00000301030	NM_001256183.1	44	cGt/cAt	4/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.305928374467482	2		636	1014	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246027124	246027124	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	104	537	1	ENST00000388985.4:c.878T>A	p.Ile293Asn	p.I293N	ENST00000388985		293	aTt/aAt	9/12	1	2	FACETS	0.882	0.79	0.98	0.882	0.79	0.98	CLONAL	1	TRUE	1	0.305928374467482	2		538	771	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112025283	112025283	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	55	437	0	ENST00000368678.4:c.466C>T	p.Arg156Ter	p.R156*	ENST00000368678		156	Cga/Tga	6/13	1	2	FACETS	0.62	0.53	0.718	0.62	0.53	0.718	SUBCLONAL	1	TRUE	1	0.305928374467482	2		437	580	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11269505	11269505	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	58	435	0	ENST00000361445.4:c.3665T>G	p.Leu1222Arg	p.L1222R	ENST00000361445	NM_004958.3	1222	cTt/cGt	25/58	0.305928374467482	1	FACETS	0.683	0.588	0.787	0.683	0.588	0.787	SUBCLONAL	1	TRUE	0	0.305928374467482	1		435	470	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392082	118392082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200134640	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	116	432	0	ENST00000534358.1:c.11593G>A	p.Val3865Ile	p.V3865I	ENST00000534358	NM_005933.3	3865	Gtc/Atc	35/36	1	2	FACETS	0.984	0.887	1	0.984	0.887	1	CLONAL	1	TRUE	1	0.305928374467482	2		432	771	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435336	121435336	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	100	667	0	ENST00000257555.6:c.1369A>G	p.Thr457Ala	p.T457A	ENST00000257555		457	Acc/Gcc	7/10	0.305928374467482	1	FACETS	0.693	0.619	0.772	0.693	0.619	0.772	SUBCLONAL	1	TRUE	0	0.305928374467482	1		667	799	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250178	133250178	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	99	498	1	ENST00000320574.5:c.1342G>A	p.Ala448Thr	p.A448T	ENST00000320574	NM_006231.2	448	Gcc/Acc	13/49	0.305928374467482	1	FACETS	0.872	0.779	0.969	0.872	0.779	0.969	CLONAL	1	TRUE	0	0.305928374467482	1		499	629	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32905151	32905151	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	69	395	0	ENST00000380152.3:c.777A>T	p.Arg259Ser	p.R259S	ENST00000380152		259	agA/agT	9/27	0.0725802393341555	3	FACETS	0.862	0.751	0.982	0.431	0.375	0.491	INDETERMINATE	1	TRUE	1	0.305928374467482	3		395	603	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2089989	2089989	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	62	765	0	ENST00000219066.1:c.875C>A	p.Pro292His	p.P292H	ENST00000219066	NM_002528.5	292	cCt/cAt	6/6	1	2	FACETS	0.429	0.37	0.495	0.429	0.37	0.495	SUBCLONAL	1	TRUE	1	0.305928374467482	2		765	944	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647427	3647427	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	97	754	1	ENST00000294008.3:c.1636T>C	p.Tyr546His	p.Y546H	ENST00000294008	NM_032444.2	546	Tac/Cac	7/15	1	2	FACETS	0.806	0.718	0.899	0.806	0.718	0.899	CLONAL	1	TRUE	1	0.305928374467482	2		755	787	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830658	72830658	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	94	605	0	ENST00000268489.5:c.5923G>A	p.Asp1975Asn	p.D1975N	ENST00000268489	NM_006885.3	1975	Gac/Aac	9/10	1	2	FACETS	0.809	0.719	0.904	0.809	0.719	0.904	CLONAL	1	TRUE	1	0.305928374467482	2		605	760	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347336	89347336	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	150	798	0	ENST00000301030.4:c.5614G>A	p.Val1872Ile	p.V1872I	ENST00000301030	NM_001256183.1	1872	Gtt/Att	9/13	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.305928374467482	2		798	972	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348152	89348152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1300503919	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	155	779	1	ENST00000301030.4:c.4798C>T	p.Arg1600Trp	p.R1600W	ENST00000301030	NM_001256183.1	1600	Cgg/Tgg	9/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.305928374467482	2		780	884	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40485715	40485715	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	115	564	1	ENST00000264657.5:c.1025G>A	p.Gly342Asp	p.G342D	ENST00000264657	NM_139276.2	342	gGc/gAc	10/24	1	2	FACETS	0.781	0.702	0.864	0.781	0.702	0.864	SUBCLONAL	1	TRUE	1	0.305928374467482	2		565	963	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218080	36218080	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs904640692	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	83	389	0	ENST00000222270.7:c.4027C>T	p.Arg1343Cys	p.R1343C	ENST00000222270	NM_014727.1	1343	Cgc/Tgc	15/37	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.305928374467482	2		389	539	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909490	50909490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774130423	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	159	841	0	ENST00000440232.2:c.1294C>T	p.Arg432Trp	p.R432W	ENST00000440232	NM_002691.3	432	Cgg/Tgg	11/27	1	2	FACETS	0.99	0.906	1	0.99	0.906	1	CLONAL	1	TRUE	1	0.305928374467482	2		841	1050	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265513	198265513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754803736	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	90	449	0	ENST00000335508.6:c.2644G>A	p.Ala882Thr	p.A882T	ENST00000335508	NM_012433.2	882	Gca/Aca	18/25	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.305928374467482	2		449	558	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1978316	1978316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1424067803	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	167	761	0	ENST00000382891.5:c.3736G>A	p.Gly1246Ser	p.G1246S	ENST00000382891	NM_133335.3	1246	Ggt/Agt	21/22	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.305928374467482	2		761	985	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79950715	79950715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	122	182	0	ENST00000265081.6:c.169G>A	p.Ala57Thr	p.A57T	ENST00000265081	NM_002439.4	57	Gcc/Acc	1/24	1	2	FACETS	1	0.942	1	1	0.99	1	CLONAL	2	TRUE	1	0.305928374467482	2		182	383	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675354	30675354	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	134	563	0	ENST00000376406.3:c.3002G>T	p.Arg1001Met	p.R1001M	ENST00000376406	NM_014641.2	1001	aGg/aTg	8/15	0.0465021450384908	4	FACETS	1	0.985	1	0.734	0.668	0.804	INDETERMINATE	1	TRUE	2	0.305928374467482	4		563	779	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633371	8633371	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002049-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	74	422	0	ENST00000356435.5:c.298G>A	p.Ala100Thr	p.A100T	ENST00000356435		100	Gcc/Acc	3/35	0.305928374467482	1	FACETS	0.813	0.713	0.92	0.813	0.713	0.92	CLONAL	1	TRUE	0	0.305928374467482	1		422	504	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554380	63554380	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002119-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	320	586	1	ENST00000307078.5:c.359T>C	p.Met120Thr	p.M120T	ENST00000307078	NM_004655.3	120	aTg/aCg	2/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.67130728503602	2		587	886	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089577	27089589	+	frameshift_variant	Frame_Shift_Del	DEL	CCTGGCATCCCAC	CCTGGCATCCCAC	-	novel	NA	P-0002119-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	376	586	3	ENST00000324856.7:c.2534_2546del	p.Pro845LeufsTer10	p.P845Lfs*10	ENST00000324856	NM_006015.4	845	CCTGGCATCCCACct/ct	8/20	0.627643561901758	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.67130728503602	1		589	719	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713315	30713315	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002344-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	251	282	1	ENST00000295754.5:c.640G>T	p.Glu214Ter	p.E214*	ENST00000295754	NM_003242.5	214	Gag/Tag	4/7	0.560148725401956	3	FACETS	0.992	0.937	1	0.992	0.937	1	CLONAL	2	TRUE	1	0.560148725401956	3		283	578	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670482	134670482	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002344-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	139	362	0	ENST00000398015.3:c.393G>T	p.Glu131Asp	p.E131D	ENST00000398015	NM_004441.4	131	gaG/gaT	3/16	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.560148725401956	2		362	466	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561767	55561767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780349712	NA	P-0002344-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	114	380	0	ENST00000288135.5:c.157G>A	p.Glu53Lys	p.E53K	ENST00000288135	NM_000222.2	53	Gag/Aag	2/21	1	2	FACETS	0.949	0.861	1	0.949	0.861	1	CLONAL	1	TRUE	1	0.560148725401956	2		380	429	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280343	1280343	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002344-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	180	463	0	ENST00000310581.5:c.1880C>A	p.Pro627His	p.P627H	ENST00000310581	NM_198253.2	627	cCt/cAt	4/16	0.32771213155807	6	FACETS	0.948	0.876	1	0.474	0.438	0.511	INDETERMINATE	2	TRUE	2	0.560148725401956	6		463	719	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495460	149495460	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs775520030	NA	P-0002344-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	188	501	0	ENST00000261799.4:c.3187C>A	p.Pro1063Thr	p.P1063T	ENST00000261799	NM_002609.3	1063	Ccc/Acc	23/23	0.485104208171269	3	FACETS	1	0.988	1	0.448	0.415	0.481	CLONAL	1	TRUE	0	0.560148725401956	3		501	640	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043981	180043981	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002344-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	259	357	0	ENST00000261937.6:c.3015G>T	p.Trp1005Cys	p.W1005C	ENST00000261937	NM_182925.4	1005	tgG/tgT	22/30	0.485104208171269	3	FACETS	0.879	0.836	0.921	0.879	0.836	0.921	CLONAL	3	TRUE	0	0.560148725401956	3		357	449	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395881	395881	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002344-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	129	504	0	ENST00000380956.4:c.438G>T	p.Met146Ile	p.M146I	ENST00000380956	NM_001195286.1	146	atG/atT	4/9	0.239485895976201	3	FACETS	0.954	0.868	1			1	INDETERMINATE	1	TRUE	NA	0.560148725401956	3		504	618	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683785	162683785	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002344-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	311	318	0	ENST00000366898.1:c.184G>C	p.Asp62His	p.D62H	ENST00000366898	NM_004562.2	62	Gat/Cat	3/12	0.484177178264789	4	FACETS	1	0.986	1	0.805	0.769	0.84	CLONAL	3	TRUE	0	0.560148725401956	4		318	538	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958466	90958466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002344-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	125	411	0	ENST00000265433.3:c.1972G>A	p.Glu658Lys	p.E658K	ENST00000265433	NM_002485.4	658	Gaa/Aaa	13/16	0.284963216203933	3	FACETS	1	0.984	1	0.683	0.624	0.745	INDETERMINATE	1	TRUE	1	0.560148725401956	3		411	418	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115820	8115820	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002344-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	177	495	0	ENST00000346208.3:c.1166G>T	p.Ser389Ile	p.S389I	ENST00000346208		389	aGc/aTc	6/6	0.32771213155807	6	FACETS	0.785	0.723	0.848	0.392	0.361	0.424	INDETERMINATE	2	TRUE	2	0.560148725401956	6		495	854	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128020	64128020	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs746032255	NA	P-0002344-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	360	377	0	ENST00000334205.4:c.418G>T	p.Val140Leu	p.V140L	ENST00000334205	NM_003942.2	140	Gtg/Ttg	4/17	0.548148870795696	3	FACETS	0.985	0.947	1			1	CLONAL	3	TRUE	NA	0.560148725401956	3		377	557	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335846	73335846	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs746599822	NA	P-0002344-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	61	308	0	ENST00000377767.4:c.2449C>A	p.Leu817Ile	p.L817I	ENST00000377767	NM_014953.3	817	Cta/Ata	18/21	1	2	FACETS	0.679	0.589	0.774	0.679	0.589	0.774	SUBCLONAL	1	TRUE	1	0.560148725401956	2		308	321	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343629	343629	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1192256273	NA	P-0002344-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	336	528	0	ENST00000262320.3:c.2045C>T	p.Ser682Phe	p.S682F	ENST00000262320	NM_003502.3	682	tCc/tTc	8/11	0.271160383838495	4	FACETS	0.898	0.856	0.94	1	0.994	1	INDETERMINATE	3	TRUE	2	0.560148725401956	4		528	695	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862947	9862947	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0002344-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	185	338	0	ENST00000330684.3:c.2357-1G>T		p.X786_splice	ENST00000330684	NM_001134407.1	786			0.271160383838495	4	FACETS	1	0.931	1	1	0.931	1	INDETERMINATE	2	TRUE	2	0.560148725401956	4		338	515	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375002	45375002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002344-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	71	357	0	ENST00000262160.6:c.841G>A	p.Glu281Lys	p.E281K	ENST00000262160	NM_005901.5	281	Gaa/Aaa	8/11	0.475738889774737	2	FACETS	0.65	0.57	0.735	0.325	0.285	0.368	SUBCLONAL	1	TRUE	0	0.560148725401956	2		357	390	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610253	10610253	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002344-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	177	479	1	ENST00000171111.5:c.457C>T	p.Leu153Phe	p.L153F	ENST00000171111	NM_203500.1	153	Ctc/Ttc	2/6	0.560148725401956	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.560148725401956	1		480	429	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55219029	55219030	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002344-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	140	313	0	ENST00000275493.2:c.603dup	p.Ala202CysfsTer29	p.A202Cfs*29	ENST00000275493	NM_005228.3	201	ggt/ggTt	5/28	0.32771213155807	6	FACETS	1	0.987	1	0.374	0.341	0.409	INDETERMINATE	1	TRUE	2	0.560148725401956	6		313	708	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577535	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0002344-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	263	318	0	ENST00000269305.4:c.746_747delinsTT	p.Arg249Ile	p.R249I	ENST00000269305	NM_001126112.2	249	aGG/aTT	7/11	0.474297592600612	3	FACETS	0.949	0.906	0.992	0.949	0.906	0.992	CLONAL	3	TRUE	0	0.560148725401956	3		318	422	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133559	55133559	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002578-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	118	793	0	ENST00000257290.5:c.863A>G	p.Tyr288Cys	p.Y288C	ENST00000257290	NM_006206.4	288	tAc/tGc	6/23	1	2	FACETS	0.547	0.495	0.602	0.547	0.495	0.602	SUBCLONAL	1	TRUE	1	0.726659711834885	2		793	594	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051118	128051118	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002675-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	27	452	0	ENST00000285398.2:c.205G>A	p.Asp69Asn	p.D69N	ENST00000285398	NM_000122.1	69	Gac/Aac	2/15	1	2	FACETS	0.228	0.18	0.282	0.228	0.18	0.282	SUBCLONAL	1	TRUE	1	0.451785170637834	2		452	525	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240637	133240637	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002675-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	189	501	0	ENST00000320574.5:c.2659A>C	p.Lys887Gln	p.K887Q	ENST00000320574	NM_006231.2	887	Aaa/Caa	23/49	0.451785170637834	3	FACETS	1	0.989	1	0.699	0.647	0.752	CLONAL	1	TRUE	1	0.451785170637834	3		501	734	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0003214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	43	207	0	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	0.229999093523527	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.229999093523527	1		207	258	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0003214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	25	261	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.216944069722893	1	FACETS	0.776	0.614	0.961	0.776	0.614	0.961	CLONAL	1	TRUE	0	0.229999093523527	1		261	248	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774968	73774968	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	24	183	0	ENST00000254810.4:c.205C>A	p.Gln69Lys	p.Q69K	ENST00000254810	NM_005324.3	69	Cag/Aag	3/4	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.229999093523527	2		183	175	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556888	29556889	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAAACCATAGCTATAATGAAGAACTTGCTAGATAATCC	novel	NA	P-0003214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	16	151	0	ENST00000356175.3:c.2923_2924insCCAAACCATAGCTATAATGAAGAACTTGCTAGATAATC	p.His975ProfsTer4	p.H975Pfs*4	ENST00000356175	NM_000267.3	962	-/CAAACCATAGCTATAATGAAGAACTTGCTAGATAATCC	22/57	0.229999093523527	1	FACETS	0.729	0.541	0.95	0.729	0.541	0.95	CLONAL	1	TRUE	0	0.229999093523527	1		151	169	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395006	395007	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0003214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	20	143	0	ENST00000380956.4:c.402_403del	p.Gly135SerfsTer76	p.G135Sfs*76	ENST00000380956	NM_001195286.1	134	aaAGga/aaga	3/9	0.215782539374661	3	FACETS	0.994	0.764	1	0.497	0.382	0.631	CLONAL	1	TRUE	1	0.229999093523527	3		143	195	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0003551-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	1912	533	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.535976356970085	11	FACETS	1	0.998	1			1	CLONAL	10	TRUE	NA	0.535976356970085	11		533	2321	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519925	NA	P-0003551-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	42	470	0	ENST00000263967.3:c.1357G>C	p.Glu453Gln	p.E453Q	ENST00000263967	NM_006218.2	453	Gaa/Caa	8/21	0.478292767238646	3	FACETS	0.31	0.258	0.367	0.103	0.086	0.123	SUBCLONAL	1	TRUE	0	0.535976356970085	3		470	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0003551-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	413	684	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.492027509918612	2	FACETS	0.895	0.857	0.933	0.895	0.857	0.933	CLONAL	2	TRUE	0	0.535976356970085	2		684	861	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254863	16254863	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003551-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	89	551	0	ENST00000375759.3:c.2128G>C	p.Glu710Gln	p.E710Q	ENST00000375759	NM_015001.2	710	Gag/Cag	11/15	1	2	FACETS	0.482	0.427	0.54	0.482	0.427	0.54	SUBCLONAL	1	TRUE	1	0.535976356970085	2		551	689	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858570	57858570	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003551-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	125	660	0	ENST00000228682.2:c.308C>G	p.Pro103Arg	p.P103R	ENST00000228682	NM_005269.2	103	cCc/cGc	4/12	0.492027509918612	2	FACETS	0.587	0.531	0.645	0.293	0.265	0.323	SUBCLONAL	1	TRUE	0	0.535976356970085	2		660	795	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875697	56875697	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003551-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	269	532	0	ENST00000308159.5:c.2301T>G	p.Ser767Arg	p.S767R	ENST00000308159	NM_014669.4	767	agT/agG	21/22	0.492027509918612	2	FACETS	0.881	0.834	0.927	0.881	0.834	0.927	CLONAL	2	TRUE	0	0.535976356970085	2		532	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578486	7578486	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003551-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	428	705	0	ENST00000269305.4:c.444T>A	p.Asp148Glu	p.D148E	ENST00000269305	NM_001126112.2	148	gaT/gaA	5/11	0.492027509918612	2	FACETS	0.907	0.87	0.945	0.907	0.87	0.945	CLONAL	2	TRUE	0	0.535976356970085	2		705	880	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0003551-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	2862	533	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.762662105253	19	FACETS	1	0.997	1			1	CLONAL	17	FALSE	NA	0.762662105253	19		533	3272	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519925	NA	P-0003551-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	111	470	0	ENST00000263967.3:c.1357G>C	p.Glu453Gln	p.E453Q	ENST00000263967	NM_006218.2	453	Gaa/Caa	8/21	0.762662105253	4	FACETS	0.894	0.806	0.986	0.223	0.201	0.247	CLONAL	1	FALSE	0	0.762662105253	4		470	574	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0003551-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	775	684	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.762662105253	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	FALSE	0	0.762662105253	3		684	916	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254863	16254863	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003551-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	183	551	0	ENST00000375759.3:c.2128G>C	p.Glu710Gln	p.E710Q	ENST00000375759	NM_015001.2	710	Gag/Cag	11/15	0.762662105253	4	FACETS	1	0.951	1			1	CLONAL	1	FALSE	NA	0.762662105253	4		551	815	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875697	56875697	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003551-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	696	532	0	ENST00000308159.5:c.2301T>G	p.Ser767Arg	p.S767R	ENST00000308159	NM_014669.4	767	agT/agG	21/22	0.762662105253	4	FACETS	1	0.997	1	1	0.997	1	CLONAL	4	FALSE	0	0.762662105253	4		532	763	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578486	7578486	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003551-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	773	705	0	ENST00000269305.4:c.444T>A	p.Asp148Glu	p.D148E	ENST00000269305	NM_001126112.2	148	gaT/gaA	5/11	0.762662105253	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	FALSE	0	0.762662105253	3		705	914	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857186	9857186	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003551-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	135	470	0	ENST00000330684.3:c.4215G>C	p.Leu1405Phe	p.L1405F	ENST00000330684	NM_001134407.1	1405	ttG/ttC	13/13	0.762662105253	5	FACETS	0.689	0.625	0.756	0.23	0.208	0.252	SUBCLONAL	1	FALSE	2	0.762662105253	5		470	1102	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50143203	50143203	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003551-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	161	436	0	ENST00000246792.3:c.153G>C	p.Gln51His	p.Q51H	ENST00000246792	NM_006270.3	51	caG/caC	1/6	0.762662105253	4	FACETS	0.928	0.852	1	0.232	0.213	0.252	CLONAL	1	FALSE	0	0.762662105253	4		436	802	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282633	1282633	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003551-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2851	195	616	0	ENST00000310581.5:c.1680C>G	p.Phe560Leu	p.F560L	ENST00000310581	NM_198253.2	560	ttC/ttG	3/16	0.762662105253	14	FACETS	0.936	0.861	1			1	CLONAL	1	FALSE	NA	0.762662105253	14		616	3046	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003781-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	88	384	0				ENST00000310581	NM_198253.2	-/1132			0.427533333268237	1	FACETS	0.584	0.524	0.646	0.584	0.524	0.646	SUBCLONAL	1	TRUE	0	0.688668226021728	1		384	287	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237686	133237686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142563997	NA	P-0003781-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	201	647	1	ENST00000320574.5:c.2929G>A	p.Gly977Arg	p.G977R	ENST00000320574	NM_006231.2	977	Ggg/Agg	25/49	0.222564600496071	3	FACETS	0.865	0.802	0.93	0.288	0.267	0.31	INDETERMINATE	1	TRUE	0	0.688668226021728	3		648	907	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100460	8100460	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003781-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	220	943	0	ENST00000346208.3:c.434A>C	p.His145Pro	p.H145P	ENST00000346208		145	cAc/cCc	3/6	0.688668226021728	1	FACETS	0.913	0.86	0.965	0.913	0.86	0.965	CLONAL	1	TRUE	0	0.688668226021728	1		943	459	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31390205	31390205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003781-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	184	387	0	ENST00000328111.2:c.2160G>A	p.Met720Ile	p.M720I	ENST00000328111	NM_006892.3	720	atG/atA	20/23	0.688668226021728	3	FACETS	0.987	0.913	1	0.493	0.456	0.532	CLONAL	1	TRUE	1	0.688668226021728	3		387	728	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003866-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	282	469	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.986	0.931	1	0.986	0.931	1	CLONAL	1	TRUE	1	0.78063243301642	2		469	733	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003866-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	63	624	1	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.78063243301642	1	FACETS	0.163	0.141	0.187	0.163	0.141	0.187	SUBCLONAL	1	TRUE	0	0.78063243301642	1		625	604	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870839	12870840	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0003866-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	157	240	0	ENST00000228872.4:c.67dup	p.His23ProfsTer102	p.H23Pfs*102	ENST00000228872	NM_004064.3	22	-/C	1/3	0.78063243301642	1	FACETS	0.879	0.824	0.934	0.879	0.824	0.934	CLONAL	1	TRUE	0	0.78063243301642	1		240	279	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4123815	4123815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003866-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	77	647	1	ENST00000262948.5:c.58G>A	p.Glu20Lys	p.E20K	ENST00000262948	NM_030662.3	20	Gag/Aag	1/11	1	2	FACETS	0.249	0.218	0.283	0.249	0.218	0.283	SUBCLONAL	1	TRUE	1	0.78063243301642	2		648	791	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005333	150005333	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003866-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	54	651	2	ENST00000253339.5:c.892G>C	p.Glu298Gln	p.E298Q	ENST00000253339		298	Gag/Cag	3/7	0.78063243301642	1	FACETS	0.177	0.151	0.205	0.177	0.151	0.205	SUBCLONAL	1	TRUE	0	0.78063243301642	1		653	477	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748278	41748278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003898-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	10	277	2	ENST00000226382.2:c.491C>T	p.Ala164Val	p.A164V	ENST00000226382	NM_003924.3	164	gCg/gTg	3/3	0.297800768735434	3	FACETS	0.233	0.158	0.328			1	INDETERMINATE	1	FALSE	NA	0.658800394512634	3		279	173	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233216	69233216	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003898-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4512	447	404	0	ENST00000462284.1:c.1081G>C	p.Glu361Gln	p.E361Q	ENST00000462284	NM_002392.5	361	Gag/Cag	11/11	0.658800394512634	54	FACETS	0.992	0.94	1			1	CLONAL	5	FALSE	NA	0.658800394512634	54		404	4959	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774181	66774182	+	frameshift_variant	Frame_Shift_Ins	INS	GG	GG	TCT	novel	NA	P-0003898-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	25	333	0	ENST00000307102.5:c.657_658delinsTCT	p.Met219IlefsTer67	p.M219Ifs*67	ENST00000307102	NM_002755.3	219	atGGcc/atTCTcc	6/11	0.664254934441936	4	FACETS	0.359	0.282	0.446			1	SUBCLONAL	1	FALSE	NA	0.658800394512634	4		333	351	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	114	262	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.899	0.819	0.981	0.899	0.819	0.981	CLONAL	1	TRUE	1	0.756901582000485	2		263	335	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	19	469	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.756901582000485	2	FACETS	0.064	0.048	0.083	0.032	0.024	0.042	SUBCLONAL	1	TRUE	0	0.756901582000485	2		469	784	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	34	413	1	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	0.17	0.138	0.206	0.17	0.138	0.206	SUBCLONAL	1	TRUE	1	0.756901582000485	2		414	529	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	311	846	1	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.756901582000485	2		847	730	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	289	712	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.756901582000485	2		712	750	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	277	254	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	0.756901582000485	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.756901582000485	2		254	345	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551591	150551591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	34	543	0	ENST00000369026.2:c.416C>T	p.Ala139Val	p.A139V	ENST00000369026	NM_021960.4	139	gCt/gTt	1/3	1	2	FACETS	0.155	0.126	0.188	0.155	0.126	0.188	SUBCLONAL	1	TRUE	1	0.756901582000485	2		543	580	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337295	89337295	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1250432793	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	47	590	1	ENST00000301030.4:c.7736G>A	p.Arg2579His	p.R2579H	ENST00000301030	NM_001256183.1	2579	cGc/cAc	12/13	1	2	FACETS	0.235	0.198	0.276	0.235	0.198	0.276	SUBCLONAL	1	TRUE	1	0.756901582000485	2		591	529	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16055282	16055282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	246	424	0	ENST00000268712.3:c.820G>A	p.Val274Met	p.V274M	ENST00000268712	NM_006311.3	274	Gtg/Atg	8/46	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.756901582000485	2		424	618	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939549	76939549	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs782242764	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	256	316	0	ENST00000373344.5:c.1199C>G	p.Ala400Gly	p.A400G	ENST00000373344	NM_000489.3	400	gCt/gGt	9/35	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.756901582000485	1		316	331	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939548	76939549	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	C	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	254	321	0	ENST00000373344.5:c.1199_1200delinsG	p.Ala400GlyfsTer14	p.A400Gfs*14	ENST00000373344	NM_000489.3	400	gCT/gG	9/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.756901582000485	1		321	333	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979661	7979661	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1053727821	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	17	427	0	ENST00000319144.4:c.1364G>A	p.Gly455Asp	p.G455D	ENST00000319144	NM_001139.2	455	gGc/gAc	11/15	1	2	FACETS	0.138	0.103	0.181	0.138	0.103	0.181	SUBCLONAL	1	TRUE	1	0.756901582000485	2		427	325	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838323	156838323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1219432341	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	40	883	2	ENST00000524377.1:c.601C>T	p.Pro201Ser	p.P201S	ENST00000524377	NM_002529.3	201	Ccc/Tcc	6/17	1	2	FACETS	0.164	0.136	0.196	0.164	0.136	0.196	SUBCLONAL	1	TRUE	1	0.756901582000485	2		885	643	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051202	128051202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	39	620	1	ENST00000285398.2:c.121G>A	p.Ala41Thr	p.A41T	ENST00000285398	NM_000122.1	41	Gcg/Acg	2/15	1	2	FACETS	0.169	0.139	0.202	0.169	0.139	0.202	SUBCLONAL	1	TRUE	1	0.756901582000485	2		621	610	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347656	89347656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567564452	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	51	679	0	ENST00000301030.4:c.5294C>T	p.Ser1765Phe	p.S1765F	ENST00000301030	NM_001256183.1	1765	tCc/tTc	9/13	1	2	FACETS	0.231	0.196	0.27	0.231	0.196	0.27	SUBCLONAL	1	TRUE	1	0.756901582000485	2		679	583	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564506	86564506	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1352395584	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	32	603	0	ENST00000274376.6:c.238G>A	p.Ala80Thr	p.A80T	ENST00000274376	NM_002890.2	80	Gca/Aca	1/25	1	2	FACETS	0.16	0.129	0.194	0.16	0.129	0.194	SUBCLONAL	1	TRUE	1	0.756901582000485	2		603	530	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29664601	29664601	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1060500345	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	80	448	1	ENST00000356175.3:c.6579+1G>A		p.X2193_splice	ENST00000356175	NM_000267.3	2193			1	2	FACETS	0.376	0.331	0.424	0.376	0.331	0.424	SUBCLONAL	1	TRUE	1	0.756901582000485	2		449	562	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095698	178095698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	31	405	0	ENST00000397062.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000397062	NM_006164.4	545	Gaa/Aaa	5/5	1	2	FACETS	0.133	0.107	0.162	0.133	0.107	0.162	SUBCLONAL	1	TRUE	1	0.756901582000485	2		405	617	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356359	66356359	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199650353	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	30	487	0	ENST00000273854.3:c.1138C>T	p.Pro380Ser	p.P380S	ENST00000273854	NM_004439.5	380	Cct/Tct	5/18	NA	2	FACETS	0.14	0.112	0.172			1	INDETERMINATE	1	TRUE	NA	0.756901582000485	2		487	565	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781156	161781156	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	85	730	1	ENST00000366898.1:c.1249C>T	p.Pro417Ser	p.P417S	ENST00000366898	NM_004562.2	417	Ccc/Tcc	11/12	1	2	FACETS	0.313	0.276	0.353	0.313	0.276	0.353	SUBCLONAL	1	TRUE	1	0.756901582000485	2		731	717	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3632671	3632671	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752633436	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	34	757	3	ENST00000294008.3:c.5177C>T	p.Ala1726Val	p.A1726V	ENST00000294008	NM_032444.2	1726	gCg/gTg	15/15	1	2	FACETS	0.134	0.109	0.162	0.134	0.109	0.162	SUBCLONAL	1	TRUE	1	0.756901582000485	2		760	672	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264427	16264427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	243	816	0	ENST00000375759.3:c.10630G>A	p.Gly3544Arg	p.G3544R	ENST00000375759	NM_015001.2	3544	Ggg/Agg	13/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.756901582000485	2		816	629	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322672	39322672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	45	591	1	ENST00000373001.3:c.320G>A	p.Ser107Asn	p.S107N	ENST00000373001	NM_022157.3	107	aGc/aAc	2/7	1	2	FACETS	0.169	0.141	0.199	0.169	0.141	0.199	SUBCLONAL	1	TRUE	1	0.756901582000485	2		592	705	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206646603	206646603	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	254	875	1	ENST00000367120.3:c.33del	p.Asp12MetfsTer26	p.D12Mfs*26	ENST00000367120	NM_014002.3	11	acA/ac	3/22	1	2	FACETS	0.93	0.874	0.986	0.93	0.874	0.986	CLONAL	1	TRUE	1	0.756901582000485	2		876	722	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332549	70332549	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	39	639	0	ENST00000373644.4:c.454C>T	p.His152Tyr	p.H152Y	ENST00000373644	NM_030625.2	152	Cac/Tac	2/12	1	2	FACETS	0.185	0.153	0.221	0.185	0.153	0.221	SUBCLONAL	1	TRUE	1	0.756901582000485	2		639	557	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112767359	112767359	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	39	449	0	ENST00000369452.4:c.1232C>T	p.Thr411Ile	p.T411I	ENST00000369452	NM_007373.3	411	aCt/aTt	6/9	1	2	FACETS	0.146	0.121	0.175	0.146	0.121	0.175	SUBCLONAL	1	TRUE	1	0.756901582000485	2		449	704	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462876	69462876	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs984643266	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	33	821	0	ENST00000227507.2:c.689C>T	p.Thr230Ile	p.T230I	ENST00000227507	NM_053056.2	230	aCa/aTa	4/5	NA	2	FACETS	0.141	0.114	0.171			1	INDETERMINATE	1	TRUE	NA	0.756901582000485	2		821	620	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944976	31944976	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1428412574	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	36	763	0	ENST00000340398.3:c.125G>A	p.Arg42Lys	p.R42K	ENST00000340398	NM_001013699.2	42	aGg/aAg	1/1	1	2	FACETS	0.152	0.125	0.184	0.152	0.125	0.184	SUBCLONAL	1	TRUE	1	0.756901582000485	2		763	624	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420916	49420916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	31	696	2	ENST00000301067.7:c.14833C>T	p.Pro4945Ser	p.P4945S	ENST00000301067	NM_003482.3	4945	Ccc/Tcc	48/54	0.671239434428707	1	FACETS	0.119	0.096	0.145	0.119	0.096	0.145	SUBCLONAL	1	TRUE	0	0.756901582000485	1		698	429	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427203	49427203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	36	792	0	ENST00000301067.7:c.11285G>A	p.Gly3762Glu	p.G3762E	ENST00000301067	NM_003482.3	3762	gGa/gAa	39/54	0.671239434428707	1	FACETS	0.141	0.115	0.169	0.141	0.115	0.169	SUBCLONAL	1	TRUE	0	0.756901582000485	1		792	420	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478864	56478864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1418372214	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	95	828	1	ENST00000267101.3:c.320G>A	p.Gly107Glu	p.G107E	ENST00000267101	NM_001982.3	107	gGg/gAg	3/28	1	2	FACETS	0.329	0.293	0.368	0.329	0.293	0.368	SUBCLONAL	1	TRUE	1	0.756901582000485	2		829	763	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865639	57865639	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	42	881	1	ENST00000228682.2:c.3116C>T	p.Ser1039Phe	p.S1039F	ENST00000228682	NM_005269.2	1039	tCt/tTt	12/12	1	2	FACETS	0.142	0.118	0.169	0.142	0.118	0.169	SUBCLONAL	1	TRUE	1	0.756901582000485	2		882	780	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913015	32913015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	58	596	0	ENST00000380152.3:c.4523G>A	p.Gly1508Glu	p.G1508E	ENST00000380152		1508	gGa/gAa	11/27	0.735342386946357	3	FACETS	0.187	0.159	0.217	0.093	0.079	0.109	SUBCLONAL	1	TRUE	1	0.756901582000485	3		596	1132	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14028048	14028048	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	33	314	0	ENST00000311895.7:c.1103-1G>A		p.X368_splice	ENST00000311895	NM_005236.2	368			1	2	FACETS	0.228	0.185	0.275	0.228	0.185	0.275	SUBCLONAL	1	TRUE	1	0.756901582000485	2		314	383	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641760	23641760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757397623	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	25	378	0	ENST00000261584.4:c.1715C>T	p.Ser572Phe	p.S572F	ENST00000261584	NM_024675.3	572	tCc/tTc	5/13	1	2	FACETS	0.169	0.133	0.211	0.169	0.133	0.211	SUBCLONAL	1	TRUE	1	0.756901582000485	2		378	390	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8113505	8113505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	267	755	1	ENST00000585124.1:c.38G>A	p.Gly13Asp	p.G13D	ENST00000585124	NM_004217.3	13	gGc/gAc	2/9	1	2	FACETS	0.974	0.919	1	0.974	0.919	1	CLONAL	1	TRUE	1	0.756901582000485	2		756	724	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40461071	40461071	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	246	730	1	ENST00000345506.4:c.2069C>T	p.Ala690Val	p.A690V	ENST00000345506	NM_003152.3	690	gCt/gTt	18/20	1	2	FACETS	0.962	0.904	1	0.962	0.904	1	CLONAL	1	TRUE	1	0.756901582000485	2		731	676	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481616	40481616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	36	577	0	ENST00000264657.5:c.1189G>A	p.Glu397Lys	p.E397K	ENST00000264657	NM_139276.2	397	Gaa/Aaa	13/24	1	2	FACETS	0.146	0.119	0.176	0.146	0.119	0.176	SUBCLONAL	1	TRUE	1	0.756901582000485	2		577	651	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761279	59761279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555572825	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	55	726	0	ENST00000259008.2:c.3128G>A	p.Ser1043Asn	p.S1043N	ENST00000259008	NM_032043.2	1043	aGt/aAt	20/20	1	2	FACETS	0.182	0.155	0.212	0.182	0.155	0.212	SUBCLONAL	1	TRUE	1	0.756901582000485	2		726	798	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609289	39609289	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1278575040	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	19	305	0	ENST00000262039.4:c.1591G>A	p.Gly531Ser	p.G531S	ENST00000262039	NM_002647.2	531	Ggt/Agt	15/25	1	2	FACETS	0.133	0.1	0.171	0.133	0.1	0.171	SUBCLONAL	1	TRUE	1	0.756901582000485	2		305	378	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220709	1220709	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	26	482	1	ENST00000326873.7:c.727G>A	p.Val243Ile	p.V243I	ENST00000326873	NM_000455.4	243	Gtc/Atc	5/10	1	2	FACETS	0.139	0.109	0.172	0.139	0.109	0.172	SUBCLONAL	1	TRUE	1	0.756901582000485	2		483	496	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5238929	5238929	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	13	150	0	ENST00000357368.4:c.1849+1G>A		p.X617_splice	ENST00000357368	NM_002850.3	617			1	2	FACETS	0.24	0.172	0.322	0.24	0.172	0.322	SUBCLONAL	1	TRUE	1	0.756901582000485	2		150	143	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276740	15276740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	103	758	1	ENST00000263388.2:c.5525C>T	p.Ala1842Val	p.A1842V	ENST00000263388	NM_000435.2	1842	gCt/gTt	30/33	1	2	FACETS	0.448	0.401	0.497	0.448	0.401	0.497	SUBCLONAL	1	TRUE	1	0.756901582000485	2		759	608	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256814	19256814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1189180256	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	26	491	0	ENST00000162023.5:c.899G>A	p.Gly300Asp	p.G300D	ENST00000162023		300	gGc/gAc	13/13	1	2	FACETS	0.153	0.121	0.191	0.153	0.121	0.191	SUBCLONAL	1	TRUE	1	0.756901582000485	2		491	448	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743910	41743910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs191926606	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	34	903	2	ENST00000301178.4:c.845C>T	p.Pro282Leu	p.P282L	ENST00000301178	NM_021913.4	282	cCc/cTc	7/20	1	2	FACETS	0.153	0.124	0.185	0.153	0.124	0.185	SUBCLONAL	1	TRUE	1	0.756901582000485	2		905	587	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797387	42797387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747055103	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	35	797	0	ENST00000575354.2:c.3749C>T	p.Pro1250Leu	p.P1250L	ENST00000575354	NM_015125.3	1250	cCc/cTc	15/20	1	2	FACETS	0.147	0.12	0.178	0.147	0.12	0.178	SUBCLONAL	1	TRUE	1	0.756901582000485	2		797	629	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47735826	47735826	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1157731113	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	42	670	0	ENST00000449228.1:c.34C>T	p.Pro12Ser	p.P12S	ENST00000449228	NM_001127240.2	12	Cca/Tca	1/4	0.756901582000485	1	FACETS	0.167	0.139	0.198	0.167	0.139	0.198	SUBCLONAL	1	TRUE	0	0.756901582000485	1		670	413	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754820	29754820	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	27	411	0	ENST00000389048.3:c.1115C>T	p.Ala372Val	p.A372V	ENST00000389048	NM_004304.4	372	gCa/gTa	4/29	0.345880159343612	1	FACETS	0.092	0.073	0.114	0.092	0.073	0.114	INDETERMINATE	1	TRUE	0	0.756901582000485	1		411	482	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607625	46607625	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	244	820	0	ENST00000263734.3:c.1814C>T	p.Ser605Phe	p.S605F	ENST00000263734	NM_001430.4	605	tCc/tTc	12/16	1	2	FACETS	0.951	0.894	1	0.951	0.894	1	CLONAL	1	TRUE	1	0.756901582000485	2		820	678	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607728	46607729	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	199	829	0	ENST00000263734.3:c.1922dup	p.Asp642ArgfsTer74	p.D642Rfs*74	ENST00000263734	NM_001430.4	639	-/C	12/16	1	2	FACETS	0.882	0.822	0.944	0.882	0.822	0.944	CLONAL	1	TRUE	1	0.756901582000485	2		829	596	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607777	46607777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1177530014	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	38	856	0	ENST00000263734.3:c.1966G>A	p.Asp656Asn	p.D656N	ENST00000263734	NM_001430.4	656	Gat/Aat	12/16	1	2	FACETS	0.15	0.124	0.18	0.15	0.124	0.18	SUBCLONAL	1	TRUE	1	0.756901582000485	2		856	668	SUCCESS
REL	5966	MSKCC	GRCh37	2	61121620	61121620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	204	483	0	ENST00000295025.8:c.242G>A	p.Gly81Glu	p.G81E	ENST00000295025	NM_002908.2	81	gGa/gAa	3/11	1	2	FACETS	0.838	0.781	0.897	0.838	0.781	0.897	CLONAL	1	TRUE	1	0.756901582000485	2		483	643	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646066	215646066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1300620941	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	46	627	0	ENST00000260947.4:c.532G>A	p.Asp178Asn	p.D178N	ENST00000260947	NM_000465.2	178	Gac/Aac	4/11	1	2	FACETS	0.168	0.141	0.198	0.168	0.141	0.198	SUBCLONAL	1	TRUE	1	0.756901582000485	2		627	723	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662700	227662700	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542156343	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	291	770	0	ENST00000305123.5:c.755C>T	p.Thr252Ile	p.T252I	ENST00000305123	NM_005544.2	252	aCc/aTc	1/2	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.756901582000485	2		770	733	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663082	227663082	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	30	604	0	ENST00000305123.5:c.373G>A	p.Ala125Thr	p.A125T	ENST00000305123	NM_005544.2	125	Gcg/Acg	1/2	1	2	FACETS	0.168	0.134	0.205	0.168	0.134	0.205	SUBCLONAL	1	TRUE	1	0.756901582000485	2		604	473	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62293948	62293948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	54	831	0	ENST00000360203.5:c.445G>A	p.Glu149Lys	p.E149K	ENST00000360203	NM_001283009.1	149	Gag/Aag	5/35	1	2	FACETS	0.192	0.164	0.224	0.192	0.164	0.224	SUBCLONAL	1	TRUE	1	0.756901582000485	2		831	742	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574490	41574490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374908361	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	214	730	0	ENST00000263253.7:c.6775G>A	p.Ala2259Thr	p.A2259T	ENST00000263253	NM_001429.3	2259	Gcc/Acc	31/31	1	2	FACETS	0.946	0.885	1	0.946	0.885	1	CLONAL	1	TRUE	1	0.756901582000485	2		730	598	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713810	30713810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	30	654	0	ENST00000295754.5:c.1135G>A	p.Asp379Asn	p.D379N	ENST00000295754	NM_003242.5	379	Gac/Aac	4/7	0.756901582000485	1	FACETS	0.132	0.106	0.161	0.132	0.106	0.161	SUBCLONAL	1	TRUE	0	0.756901582000485	1		654	374	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430648	181430648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	92	427	0	ENST00000325404.1:c.500G>A	p.Ser167Asn	p.S167N	ENST00000325404	NM_003106.3	167	aGc/aAc	1/1	0.756901582000485	3	FACETS	0.561	0.499	0.627			1	SUBCLONAL	1	TRUE	NA	0.756901582000485	3		427	597	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515269	31515269	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	58	778	1	ENST00000344624.3:c.1116G>A	p.Trp372Ter	p.W372*	ENST00000344624		372	tgG/tgA	5/33	1	2	FACETS	0.185	0.158	0.214	0.185	0.158	0.214	SUBCLONAL	1	TRUE	1	0.756901582000485	2		779	828	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953151	38953151	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1447929318	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	24	264	0	ENST00000357387.3:c.2833G>A	p.Glu945Lys	p.E945K	ENST00000357387	NM_152756.3	945	Gaa/Aaa	29/38	1	2	FACETS	0.151	0.118	0.19	0.151	0.118	0.19	SUBCLONAL	1	TRUE	1	0.756901582000485	2		264	419	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176710876	176710876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	57	509	0	ENST00000439151.2:c.6098C>T	p.Ser2033Phe	p.S2033F	ENST00000439151	NM_022455.4	2033	tCt/tTt	20/23	1	2	FACETS	0.271	0.233	0.314	0.271	0.233	0.314	SUBCLONAL	1	TRUE	1	0.756901582000485	2		509	555	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250511	26250511	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	238	671	0	ENST00000446824.2:c.323C>T	p.Thr108Ile	p.T108I	ENST00000446824	NM_021018.2	108	aCc/aTc	1/1	0.756901582000485	2	FACETS	1	0.943	1	0.501	0.471	0.532	CLONAL	1	TRUE	0	0.756901582000485	2		671	627	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323172	31323172	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	73	731	0	ENST00000412585.2:c.817G>A	p.Val273Met	p.V273M	ENST00000412585	NM_005514.6	273	Gtg/Atg	4/8	1	2	FACETS	0.283	0.247	0.322	0.283	0.247	0.322	SUBCLONAL	1	TRUE	1	0.756901582000485	2		731	681	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109319957	109319957	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	30	467	0	ENST00000436639.2:c.731G>A	p.Gly244Glu	p.G244E	ENST00000436639	NM_014454.2	244	gGa/gAa	5/10	1	2	FACETS	0.162	0.13	0.199	0.162	0.13	0.199	SUBCLONAL	1	TRUE	1	0.756901582000485	2		467	488	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519608	137519608	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	33	386	0	ENST00000367739.4:c.1030G>A	p.Glu344Lys	p.E344K	ENST00000367739	NM_000416.2	344	Gaa/Aaa	7/7	1	2	FACETS	0.159	0.129	0.194	0.159	0.129	0.194	SUBCLONAL	1	TRUE	1	0.756901582000485	2		386	547	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874952	151874952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	32	293	0	ENST00000262189.6:c.7586C>T	p.Ser2529Leu	p.S2529L	ENST00000262189	NM_170606.2	2529	tCa/tTa	38/59	0.756901582000485	3	FACETS	0.229	0.185	0.278	0.114	0.092	0.139	SUBCLONAL	1	TRUE	1	0.756901582000485	3		293	510	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964436	70964436	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	25	471	0	ENST00000276594.2:c.1592C>T	p.Ala531Val	p.A531V	ENST00000276594	NM_024504.3	531	gCc/gTc	8/8	1	2	FACETS	0.142	0.111	0.177	0.142	0.111	0.177	SUBCLONAL	1	TRUE	1	0.756901582000485	2		471	466	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98241281	98241281	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	38	561	2	ENST00000331920.6:c.1215+1G>A		p.X405_splice	ENST00000331920	NM_000264.3	405			1	2	FACETS	0.181	0.149	0.217	0.181	0.149	0.217	SUBCLONAL	1	TRUE	1	0.756901582000485	2		563	554	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760771	133760771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	57	691	1	ENST00000318560.5:c.3094G>A	p.Val1032Ile	p.V1032I	ENST00000318560	NM_005157.4	1032	Gtc/Atc	11/11	1	2	FACETS	0.271	0.232	0.313	0.271	0.232	0.313	SUBCLONAL	1	TRUE	1	0.756901582000485	2		692	556	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879855	44879855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	201	211	0	ENST00000377967.4:c.444G>A	p.Trp148Ter	p.W148*	ENST00000377967	NM_021140.2	148	tgG/tgA	6/29	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.756901582000485	1		211	274	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942845	44942845	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	26	295	0	ENST00000377967.4:c.3425G>A	p.Arg1142Lys	p.R1142K	ENST00000377967	NM_021140.2	1142	aGa/aAa	23/29	1	1	FACETS	0.127	0.1	0.158	0.127	0.1	0.158	SUBCLONAL	1	TRUE	0	0.756901582000485	1		295	336	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349193	70349193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	31	373	0	ENST00000374080.3:c.3605C>T	p.Ser1202Phe	p.S1202F	ENST00000374080		1202	tCc/tTc	26/45	1	1	FACETS	0.16	0.129	0.194	0.16	0.129	0.194	SUBCLONAL	1	TRUE	0	0.756901582000485	1		373	319	SUCCESS
BTK	695	MSKCC	GRCh37	X	100609617	100609617	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004073-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	16	233	0	ENST00000308731.7:c.1631+1G>A		p.X544_splice	ENST00000308731	NM_000061.2	544			1	1	FACETS	0.098	0.072	0.129	0.098	0.072	0.129	SUBCLONAL	1	TRUE	0	0.756901582000485	1		233	268	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584575	52584575	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	89	257	0	ENST00000394830.3:c.4438C>T	p.Gln1480Ter	p.Q1480*	ENST00000394830	NM_018313.4	1480	Cag/Tag	29/30	0.562638034564138	1	FACETS	0.449	0.399	0.501	0.449	0.399	0.501	SUBCLONAL	1	TRUE	0	0.571390925833132	1		257	496	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439901	52439901	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0004080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	153	211	0	ENST00000460680.1:c.811del	p.Ile271PhefsTer64	p.I271Ffs*64	ENST00000460680	NM_004656.3	271	Att/tt	10/17	0.562638034564138	1	FACETS	0.809	0.746	0.873	0.809	0.746	0.873	CLONAL	1	TRUE	0	0.571390925833132	1		211	473	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759664	133759664	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004089-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	178	150	0	ENST00000318560.5:c.1987A>C	p.Ser663Arg	p.S663R	ENST00000318560	NM_005157.4	663	Agc/Cgc	11/11	1	2	FACETS	0.963	0.895	1	0.963	0.895	1	CLONAL	1	TRUE	1	0.742087557805825	2		150	498	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730921	40730921	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004089-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	123	72	0	ENST00000373198.4:c.3614C>A	p.Thr1205Lys	p.T1205K	ENST00000373198	NM_133170.3	1205	aCa/aAa	27/32	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.742087557805825	2		72	307	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38957774	38957774	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs779631341	NA	P-0004234-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	39	219	0	ENST00000357387.3:c.2479C>T	p.Gln827Ter	p.Q827*	ENST00000357387	NM_152756.3	827	Caa/Taa	25/38	1	2	FACETS	0.819	0.697	0.947	0.819	0.697	0.947	CLONAL	1	TRUE	1	0.842950163851592	2		219	113	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294171	1294171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	54	105	0	ENST00000310581.5:c.830G>A	p.Arg277Lys	p.R277K	ENST00000310581	NM_198253.2	277	aGa/aAa	2/16	0.225718565321171	3	FACETS	0.827	0.71	0.953	0.827	0.71	0.953	CLONAL	2	TRUE	1	0.225718565321171	3		105	322	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724541	162724541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759709680	NA	P-0004252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	88	167	0	ENST00000367921.3:c.313C>T	p.Arg105Cys	p.R105C	ENST00000367921	NM_006182.2	105	Cgc/Tgc	5/18	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.225718565321171	2		167	550	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793442	42793442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748865223	NA	P-0004252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	46	142	0	ENST00000575354.2:c.1244G>A	p.Arg415Gln	p.R415Q	ENST00000575354	NM_015125.3	415	cGg/cAg	8/20	1	2	FACETS	0.957	0.807	1	0.957	0.807	1	CLONAL	1	TRUE	1	0.225718565321171	2		142	426	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952443	38952443	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	104	169	0	ENST00000357387.3:c.2982G>T	p.Arg994Ser	p.R994S	ENST00000357387	NM_152756.3	994	agG/agT	30/38	0.225718565321171	3	FACETS	1	0.982	1	0.75	0.672	0.832	CLONAL	1	TRUE	1	0.225718565321171	3		169	684	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184757	32184757	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	35	187	0	ENST00000375023.3:c.1826G>T	p.Gly609Val	p.G609V	ENST00000375023	NM_004557.3	609	gGa/gTa	11/30	1	2	FACETS	0.742	0.608	0.892	0.742	0.608	0.892	SUBCLONAL	1	TRUE	1	0.225718565321171	2		187	418	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579559	7579559	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	46	153	0	ENST00000269305.4:c.128del	p.Leu43Ter	p.L43*	ENST00000269305	NM_001126112.2	43	tTg/tg	4/11	0.225718565321171	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	0	0.225718565321171	1		153	330	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575142	48575143	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0004252-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	88	193	0	ENST00000342988.3:c.336_337del	p.Lys113IlefsTer7	p.K113Ifs*7	ENST00000342988	NM_005359.5	112	gtTAaa/gtaa	3/12	0.221897831461837	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.225718565321171	1		193	618	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0004535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	48	228	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.387100157572428	2		228	189	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682399	52682400	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	45	599	0	ENST00000394830.3:c.773dup	p.Asn258LysfsTer6	p.N258Kfs*6	ENST00000394830	NM_018313.4	258	aat/aaAt	8/30	0.352835105883436	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.387100157572428	1		599	170	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864984	57864984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	37	722	0	ENST00000228682.2:c.2461C>T	p.Pro821Ser	p.P821S	ENST00000228682	NM_005269.2	821	Cca/Tca	12/12	0.271855906649908	3	FACETS	1	0.889	1	0.546	0.454	0.646	CLONAL	1	TRUE	1	0.387100157572428	3		722	209	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10251517	10251517	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004535-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	30	467	0	ENST00000340748.4:c.3415C>A	p.Leu1139Met	p.L1139M	ENST00000340748		1139	Ctg/Atg	31/40	1	2	FACETS	0.842	0.685	1	0.842	0.685	1	CLONAL	1	TRUE	1	0.387100157572428	2		467	184	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0004654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	137	228	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.837	0.767	0.909	0.837	0.767	0.909	CLONAL	1	TRUE	1	0.725975472609153	2		228	451	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0004654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	320	769	0	ENST00000346208.3:c.1002_1003dup	p.Asp335GlyfsTer21	p.D335Gfs*21	ENST00000346208		333	-/GG	5/6	1	2	FACETS	0.759	0.717	0.803	0.759	0.717	0.803	SUBCLONAL	1	TRUE	1	0.725975472609153	2		769	1161	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442575	52442575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004654-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	275	526	0	ENST00000460680.1:c.170G>A	p.Arg57Gln	p.R57Q	ENST00000460680	NM_004656.3	57	cGg/cAg	4/17	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.725975472609153	2		526	753	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	237	469	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.262363263032847	4	FACETS	0.9	0.845	0.956	0.9	0.845	0.956	INDETERMINATE	2	TRUE	2	0.682484069809197	4		469	649	SUCCESS
BTK	695	MSKCC	GRCh37	X	100625055	100625055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	125	702	0	ENST00000308731.7:c.322G>A	p.Glu108Lys	p.E108K	ENST00000308731	NM_000061.2	108	Gaa/Aaa	5/19	1	2	FACETS	0.823	0.751	0.898	0.823	0.751	0.898	CLONAL	1	TRUE	1	0.682484069809197	2		702	445	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717731	89717732	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1114167661	NA	P-0004768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	223	585	0	ENST00000371953.3:c.757dup	p.Ile253AsnfsTer45	p.I253Nfs*45	ENST00000371953	NM_000314.4	252	-/A	7/9	0.682484069809197	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.682484069809197	1		585	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579329	7579330	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	412	931	0	ENST00000269305.4:c.357dup	p.Lys120GlnfsTer29	p.K120Qfs*29	ENST00000269305	NM_001126112.2	119	-/C	4/11	0.682484069809197	2	FACETS	0.966	0.932	0.999	0.966	0.932	0.999	CLONAL	2	TRUE	0	0.682484069809197	2		931	625	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099896	27099896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149538231	NA	P-0004768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	48	843	0	ENST00000324856.7:c.3775C>T	p.Pro1259Ser	p.P1259S	ENST00000324856	NM_006015.4	1259	Ccc/Tcc	15/20	0.221367740466588	2	FACETS	0.244	0.206	0.286	0.122	0.103	0.143	INDETERMINATE	1	TRUE	0	0.682484069809197	2		843	576	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743828	46743828	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	86	1019	0	ENST00000371975.4:c.2118G>A	p.Trp706Ter	p.W706*	ENST00000371975	NM_003579.3	706	tgG/tgA	18/18	0.221367740466588	2	FACETS	0.367	0.324	0.412	0.183	0.162	0.206	INDETERMINATE	1	TRUE	0	0.682484069809197	2		1019	687	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912996	32912996	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1060502425	NA	P-0004768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	25	780	0	ENST00000380152.3:c.4504C>G	p.Gln1502Glu	p.Q1502E	ENST00000380152		1502	Caa/Gaa	11/27	0.682484069809197	1	FACETS	0.117	0.091	0.146	0.117	0.091	0.146	SUBCLONAL	1	TRUE	0	0.682484069809197	1		780	414	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045806	180045806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1051985552	NA	P-0004768-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	66	1048	0	ENST00000261937.6:c.2965G>A	p.Glu989Lys	p.E989K	ENST00000261937	NM_182925.4	989	Gag/Aag	21/30	1	2	FACETS	0.25	0.216	0.287	0.25	0.216	0.287	SUBCLONAL	1	TRUE	1	0.682484069809197	2		1048	773	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0004883-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	731	734	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.653738337256837	3	FACETS	0.952	0.929	0.975	0.952	0.929	0.975	CLONAL	3	TRUE	0	0.653738337256837	3		734	1039	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599333	55599333	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913682	NA	P-0004883-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	464	490	0	ENST00000288135.5:c.2459A>G	p.Asp820Gly	p.D820G	ENST00000288135	NM_000222.2	820	gAt/gGt	17/21	0.653738337256837	7	FACETS	1	0.973	1			1	CLONAL	3	TRUE	NA	0.653738337256837	7		490	1219	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112064	115112064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757023811	NA	P-0004883-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	348	1034	0	ENST00000257566.3:c.1676C>T	p.Thr559Met	p.T559M	ENST00000257566	NM_016569.3	559	aCg/aTg	7/8	0.653738337256837	3	FACETS	1	0.949	1	0.502	0.474	0.53	CLONAL	1	TRUE	1	0.653738337256837	3		1034	1407	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593580	55593606	+	splice_acceptor_variant,coding_sequence_variant	In_Frame_Del	DEL	AGAAACCCATGTATGAAGTACAGTGGA	AGAAACCCATGTATGAAGTACAGTGGA	-	rs121913234	NA	P-0004883-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	563	353	0	ENST00000288135.5:c.1648_1674del		p.K550_K558del	ENST00000288135	NM_000222.2	550		11/21	0.653738337256837	7	FACETS	1	0.994	1			1	CLONAL	5	TRUE	NA	0.653738337256837	7		353	835	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56409148	56409148	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004883-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	120	361	1	ENST00000348428.3:c.1655G>A	p.Ser552Asn	p.S552N	ENST00000348428	NM_006785.3	552	aGt/aAt	14/17	0.653738337256837	3	FACETS	0.876	0.794	0.962	0.438	0.397	0.481	CLONAL	1	TRUE	1	0.653738337256837	3		362	556	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026653	6026653	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004883-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2119	418	1232	1	ENST00000265849.7:c.1743A>T	p.Lys581Asn	p.K581N	ENST00000265849	NM_000535.5	581	aaA/aaT	11/15	0.538543500342467	4	FACETS	0.834	0.79	0.879	0.417	0.395	0.44	CLONAL	1	TRUE	2	0.653738337256837	4		1233	2537	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0005007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	60	301	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	NA	2	FACETS	0.674	0.58	0.776			1	INDETERMINATE	1	TRUE	NA	0.26	2		301	685	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs80338963	NA	P-0005007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	81	387	0	ENST00000342988.3:c.1081C>A	p.Arg361Ser	p.R361S	ENST00000342988	NM_005359.5	361	Cgc/Agc	9/12	0.205585039333909	1	FACETS	0.798	0.703	0.9	0.798	0.703	0.9	SUBCLONAL	1	TRUE	0	0.26	1		387	679	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0005007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	362	756	1	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	0.3	8	FACETS	1	0.961	1			1	CLONAL	5	TRUE	NA	0.26	8		757	979	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911505	131911505	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005007-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	89	388	0	ENST00000265335.6:c.250C>G	p.Leu84Val	p.L84V	ENST00000265335		84	Ctg/Gtg	3/25	1	2	FACETS	0.939	0.833	1	0.939	0.833	1	CLONAL	1	TRUE	1	0.26	2		388	729	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286235	66286235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746116670	NA	P-0005323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	111	183	0	ENST00000273854.3:c.1451G>A	p.Ser484Asn	p.S484N	ENST00000273854	NM_004439.5	484	aGc/aAc	6/18	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.79772386600693	2		183	261	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710819	117710819	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1422557855	NA	P-0005323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	222	199	0	ENST00000368508.3:c.1453T>C	p.Ser485Pro	p.S485P	ENST00000368508	NM_002944.2	485	Tct/Cct	12/43	0.583583069901527	3	FACETS	1	0.971	1			1	CLONAL	2	TRUE	NA	0.79772386600693	3		199	376	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450405	50450405	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	97	233	0	ENST00000331340.3:c.589G>T	p.Val197Phe	p.V197F	ENST00000331340	NM_006060.4	197	Gtt/Ttt	5/8	0.138541075862816	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.79772386600693	0		233	231	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748684	43748684	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005323-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	35	437	0	ENST00000382044.4:c.2122C>G	p.Leu708Val	p.L708V	ENST00000382044	NM_001141980.1	708	Ctt/Gtt	12/28	1	2	FACETS	0.21	0.172	0.253	0.21	0.172	0.253	SUBCLONAL	1	TRUE	1	0.79772386600693	2		437	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs28934574	NA	P-0005331-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	637	618	0	ENST00000269305.4:c.844C>G	p.Arg282Gly	p.R282G	ENST00000269305	NM_001126112.2	282	Cgg/Ggg	8/11	0.869269988081897	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.871734393178695	2		618	702	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	441002	441002	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1212131069	NA	P-0005331-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	42	306	0	ENST00000399788.2:c.1756T>C	p.Phe586Leu	p.F586L	ENST00000399788	NM_001042603.1	586	Ttc/Ctc	13/28	NA	2	FACETS	0.25	0.208	0.295			1	INDETERMINATE	1	TRUE	NA	0.871734393178695	2		306	386	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422670	49422670	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005331-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	36	556	0	ENST00000301067.7:c.14323G>T	p.Glu4775Ter	p.E4775*	ENST00000301067	NM_003482.3	4775	Gaa/Taa	45/54	0.869269988081897	2	FACETS	0.142	0.116	0.171	0.071	0.058	0.086	SUBCLONAL	1	TRUE	0	0.871734393178695	2		556	582	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70967549	70967549	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005331-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	174	513	0	ENST00000276594.2:c.1474G>C	p.Val492Leu	p.V492L	ENST00000276594	NM_024504.3	492	Gtg/Ctg	7/8	0.773941811239699	4	FACETS	0.896	0.826	0.969	0.299	0.275	0.323	CLONAL	1	TRUE	1	0.871734393178695	4		513	834	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233628	233628	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	57	175	0	ENST00000264932.6:c.932G>T	p.Cys311Phe	p.C311F	ENST00000264932	NM_004168.2	311	tGt/tTt	8/15	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		175	179	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0005471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	554	496	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	0.99	0.963	1			1	INDETERMINATE	2	TRUE	NA	0.747495563039907	2		496	749	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551335	29551335	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	594	501	0	ENST00000389048.3:c.1295G>T	p.Gly432Val	p.G432V	ENST00000389048	NM_004304.4	432	gGc/gTc	6/29	0.445325224730174	3	FACETS	0.977	0.944	1			1	INDETERMINATE	2	TRUE	NA	0.747495563039907	3		501	1117	SUCCESS
APC	324	MSKCC	GRCh37	5	112116494	112116494	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1554072560	NA	P-0005471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	511	365	0	ENST00000257430.4:c.539T>A	p.Leu180Ter	p.L180*	ENST00000257430	NM_000038.5	180	tTa/tAa	6/16	0.723428570135706	2	FACETS	0.926	0.899	0.953	0.926	0.899	0.953	CLONAL	2	TRUE	0	0.747495563039907	2		365	738	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860053	57860053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200444628	NA	P-0005471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	507	711	0	ENST00000228682.2:c.793C>T	p.Arg265Trp	p.R265W	ENST00000228682	NM_005269.2	265	Cgg/Tgg	8/12	0.729038722625731	2	FACETS	0.945	0.905	0.986	0.473	0.452	0.493	CLONAL	1	TRUE	0	0.747495563039907	2		711	1435	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068324	16068324	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1568423601	NA	P-0005471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	52	231	0	ENST00000268712.3:c.587A>G	p.Glu196Gly	p.E196G	ENST00000268712	NM_006311.3	196	gAa/gGa	5/46	0.723428570135706	2	FACETS	0.35	0.298	0.406	0.175	0.149	0.203	SUBCLONAL	1	TRUE	0	0.747495563039907	2		231	398	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974744	21974775	+	frameshift_variant	Frame_Shift_Del	DEL	ACCTCCTCTACCCGACCCCGGGCCGCGGCCGT	ACCTCCTCTACCCGACCCCGGGCCGCGGCCGT	-	novel	NA	P-0005471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	122	213	0	ENST00000304494.5:c.52_83del	p.Thr18AlafsTer15	p.T18Afs*15	ENST00000304494	NM_000077.4	18	ACGGCCGCGGCCCGGGGTCGGGTAGAGGAGGTg/g	1/3	0.687620878463171	1	FACETS	0.877	0.812	0.942	0.877	0.812	0.942	CLONAL	1	TRUE	0	0.747495563039907	1		213	233	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573573	48573574	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AATTGGATTCTTT	novel	NA	P-0005471-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	242	478	0	ENST00000342988.3:c.161_173dup	p.Thr59GlyfsTer15	p.T59Gfs*15	ENST00000342988	NM_005359.5	53	gaa/gAATTGGATTCTTTaa	2/12	0.747495563039907	1	FACETS	0.671	0.632	0.711	0.671	0.632	0.711	SUBCLONAL	1	TRUE	0	0.747495563039907	1		478	604	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0006083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	93	228	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.712	0.632	0.797	0.712	0.632	0.797	SUBCLONAL	1	TRUE	1	0.31	2		228	843	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0006083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	147	536	2	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.759	0.691	0.831	0.759	0.691	0.831	SUBCLONAL	1	TRUE	1	0.31	2		538	1249	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094410	27094413	+	frameshift_variant	Frame_Shift_Del	DEL	AATC	AATC	-	novel	NA	P-0006083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	95	383	0	ENST00000324856.7:c.3118_3121del	p.Asn1040CysfsTer18	p.N1040Cfs*18	ENST00000324856	NM_006015.4	1040	AATCtg/tg	11/20	1	2	FACETS	0.675	0.6	0.755	0.675	0.6	0.755	SUBCLONAL	1	TRUE	1	0.31	2		383	908	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584513	52584516	+	frameshift_variant	Frame_Shift_Del	DEL	TGAG	TGAG	-	novel	NA	P-0006083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	176	524	0	ENST00000394830.3:c.4497_4500del	p.His1499GlnfsTer5	p.H1499Qfs*5	ENST00000394830	NM_018313.4	1499	caCTCA/ca	29/30	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.31	2		524	1134	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0006176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	90	255	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.851	0.756	0.952	0.851	0.756	0.952	CLONAL	1	TRUE	1	0.342866527094322	2		255	617	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481601	20481601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	55	598	1	ENST00000346618.3:c.670G>A	p.Val224Ile	p.V224I	ENST00000346618	NM_001949.4	224	Gtt/Att	3/7	1	2	FACETS	0.422	0.36	0.49	0.422	0.36	0.49	SUBCLONAL	1	TRUE	1	0.342866527094322	2		599	760	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655364	45655364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006176-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	78	644	0	ENST00000407780.3:c.488G>A	p.Gly163Asp	p.G163D	ENST00000407780	NM_001283052.1	163	gGc/gAc	4/7	1	2	FACETS	0.431	0.378	0.489	0.431	0.378	0.489	SUBCLONAL	1	TRUE	1	0.342866527094322	2		644	1055	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0006353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	249	246	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.480169976863578	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.480169976863578	1		246	609	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0006353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	144	228	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.480169976863578	2		228	594	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105918	27105918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	214	346	0	ENST00000324856.7:c.5529del	p.Trp1844GlyfsTer39	p.W1844Gfs*39	ENST00000324856	NM_006015.4	1843	caC/ca	20/20	0.480169976863578	1	FACETS	0.965	0.9	1	0.965	0.9	1	CLONAL	1	TRUE	0	0.480169976863578	1		346	702	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023691	27023692	+	stop_gained	Nonsense_Mutation	DNP	TC	TC	AA	novel	NA	P-0006353-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	163	388	0	ENST00000324856.7:c.797_798delinsAA	p.Phe266Ter	p.F266*	ENST00000324856	NM_006015.4	266	tTC/tAA	1/20	0.480169976863578	1	FACETS	0.829	0.764	0.897	0.829	0.764	0.897	CLONAL	1	TRUE	0	0.480169976863578	1		388	622	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0006450-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	168	492	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.15604122062617	2	FACETS	0.808	0.742	0.877	0.808	0.742	0.877	CLONAL	2	TRUE	0	0.198788932674209	2		492	1046	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123900	46123936	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACTTTAGGCGGATTCGCGAAGGTGAGTGGAAGTTTTA	ACTTTAGGCGGATTCGCGAAGGTGAGTGGAAGTTTTA	-	novel	NA	P-0006450-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	85	356	0	ENST00000334344.6:c.167_186+17del		p.X56_splice	ENST00000334344	NM_152641.2	56		2/21	0.198788932674209	3	FACETS	0.995	0.878	1	0.497	0.439	0.561	CLONAL	1	TRUE	1	0.198788932674209	3		356	945	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564444	86564445	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0006450-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	113	464	0	ENST00000274376.6:c.177_178dup	p.Thr60LysfsTer14	p.T60Kfs*14	ENST00000274376	NM_002890.2	59	gga/ggAAa	1/25	0.15604122062617	2	FACETS	0.98	0.88	1	0.49	0.44	0.544	CLONAL	1	TRUE	0	0.198788932674209	2		464	1160	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941109	36941109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761404285	NA	P-0006450-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	75	533	1	ENST00000361632.4:c.230G>A	p.Arg77His	p.R77H	ENST00000361632		77	cGt/cAt	3/16	0.198788932674209	3	FACETS	0.688	0.601	0.783	0.344	0.3	0.392	SUBCLONAL	1	TRUE	1	0.198788932674209	3		534	1205	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106440	27106467	+	frameshift_variant	Frame_Shift_Del	DEL	GCACCACAAGCACCCAGAACGGAAGCAG	GCACCACAAGCACCCAGAACGGAAGCAG	-	novel	NA	P-0006450-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	124	317	0	ENST00000324856.7:c.6058_6085del	p.Lys2020Ter	p.K2020*	ENST00000324856	NM_006015.4	2017	ctGCACCACAAGCACCCAGAACGGAAGCAG/ct	20/20	0.198788932674209	3	FACETS	0.788	0.713	0.868	0.788	0.713	0.868	SUBCLONAL	2	TRUE	1	0.198788932674209	3		317	870	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	205	384	0				ENST00000310581	NM_198253.2	-/1132			0.467839789213887	3	FACETS	0.924	0.856	0.995	0.462	0.428	0.498	CLONAL	1	TRUE	1	0.49723271529773	3		384	1114	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074111	8074115	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	AAAAG	AAAAG	TTA	novel	NA	P-0006871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	631	784	1	ENST00000377482.5:c.544_548delinsTAA	p.Leu182Ter	p.L182*	ENST00000377482	NM_018948.3	182	CTTTTa/TAAa	4/4	0.49723271529773	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.49723271529773	1		785	1677	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439833	52439834	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0006885-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	119	454	0	ENST00000460680.1:c.878dup	p.Leu294AlafsTer13	p.L294Afs*13	ENST00000460680	NM_004656.3	293	ccg/ccCg	10/17	0.388523731712622	1	FACETS	0.947	0.859	1	0.947	0.859	1	CLONAL	1	TRUE	0	0.388523731712622	1		454	521	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0007016-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	19	486	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	0.959	0.738	1	0.959	0.738	1	CLONAL	1	TRUE	1	0.350555780014807	2		486	113	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0007041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	10	543	0	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.294017026543306	3	FACETS	1	0.742	1	0.545	0.375	0.752	CLONAL	1	TRUE	1	0.29653942172541	3		543	71	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575195	48575195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	23	293	0	ENST00000342988.3:c.389C>T	p.Pro130Leu	p.P130L	ENST00000342988	NM_005359.5	130	cCa/cTa	3/12	0.23877225494551	5	FACETS	0.869	0.686	1	0.579	0.457	0.716	CLONAL	2	TRUE	2	0.29653942172541	5		293	129	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578397	7578397	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1555526004	NA	P-0007041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	10	251	0	ENST00000269305.4:c.533A>C	p.His178Pro	p.H178P	ENST00000269305	NM_001126112.2	178	cAc/cCc	5/11	0.294017026543306	3	FACETS	1	0.742	1	0.545	0.375	0.752	CLONAL	1	TRUE	1	0.29653942172541	3		251	71	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277555	142277555	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	37	289	1	ENST00000350721.4:c.1796T>C	p.Ile599Thr	p.I599T	ENST00000350721	NM_001184.3	599	aTt/aCt	8/47	0.29653942172541	5	FACETS	1	0.917	1	0.775	0.649	0.912	CLONAL	2	TRUE	2	0.29653942172541	5		290	155	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220276	5220276	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	32	339	0	ENST00000357368.4:c.3544G>T	p.Glu1182Ter	p.E1182*	ENST00000357368	NM_002850.3	1182	Gaa/Taa	21/38	0.294017026543306	3	FACETS	0.983	0.814	1	0.983	0.814	1	CLONAL	2	TRUE	1	0.29653942172541	3		339	126	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629206	187629207	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0007041-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	15	265	0	ENST00000441802.2:c.1775_1776del	p.Ser592CysfsTer3	p.S592Cfs*3	ENST00000441802	NM_005245.3	592	tCT/t	2/27	0.297667883481457	1	FACETS	0.979	0.728	1	0.979	0.728	1	CLONAL	1	TRUE	0	0.29653942172541	1		265	88	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0007107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	94	469	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.397387463316815	3	FACETS	0.853	0.759	0.952	0.426	0.379	0.476	CLONAL	1	TRUE	1	0.397387463316815	3		469	665	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0007107-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	110	228	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.849	0.764	0.939	0.849	0.764	0.939	CLONAL	1	TRUE	1	0.397387463316815	2		228	652	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0007205-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	302	228	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.366087250414095	4	FACETS	0.937	0.886	0.989	0.937	0.886	0.989	CLONAL	2	TRUE	2	0.592980114704695	4		228	866	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118355027	118355032	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AAGGTA	AAGGTA	-	novel	NA	P-0007205-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	161	189	0	ENST00000534358.1:c.4218+3_4218+8del		p.X1406_splice	ENST00000534358	NM_005933.3	1406		9/36	0.133257994665288	4	FACETS	0.786	0.725	0.849	0.786	0.725	0.849	INDETERMINATE	2	TRUE	2	0.592980114704695	4		189	550	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0007213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	57	469	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.2575259630334	3	FACETS	0.814	0.703	0.933	0.814	0.703	0.933	CLONAL	2	TRUE	1	0.2575259630334	3		469	307	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105735	27105826	+	frameshift_variant	Frame_Shift_Del	DEL	TGAAAATGATGAGGAGATAGCCTTTTCAGGCAAGGACAAGCCAGCTTCAGAGAATAGTGAGGAGAAGCTGATCAGTAAGTTTGACAAGCTTC	TGAAAATGATGAGGAGATAGCCTTTTCAGGCAAGGACAAGCCAGCTTCAGAGAATAGTGAGGAGAAGCTGATCAGTAAGTTTGACAAGCTTC	-	novel	NA	P-0007213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	198	349	0	ENST00000324856.7:c.5346_5437del	p.Glu1783SerfsTer8	p.E1783Sfs*8	ENST00000324856	NM_006015.4	1782	gtTGAAAATGATGAGGAGATAGCCTTTTCAGGCAAGGACAAGCCAGCTTCAGAGAATAGTGAGGAGAAGCTGATCAGTAAGTTTGACAAGCTTCca/gtca	20/20	0.250591932390844	2	FACETS	0.862	0.799	0.927	0.862	0.799	0.927	CLONAL	2	TRUE	0	0.2575259630334	2		349	892	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160423	108160426	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	novel	NA	P-0007213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	78	314	0	ENST00000278616.4:c.4335_4338del	p.Phe1445LeufsTer5	p.F1445Lfs*5	ENST00000278616	NM_000051.3	1444	cTGTTt/ct	29/63	0.247858834074299	3	FACETS	0.984	0.864	1	0.492	0.432	0.556	CLONAL	1	TRUE	1	0.2575259630334	3		314	695	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114816	108114817	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0007213-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	85	291	2	ENST00000278616.4:c.640dup	p.Ser214PhefsTer40	p.S214Ffs*40	ENST00000278616	NM_000051.3	211	-/T	6/63	0.247858834074299	3	FACETS	0.801	0.711	0.897	0.801	0.711	0.897	CLONAL	2	TRUE	1	0.2575259630334	3		293	465	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14028160	14028160	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0007520-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	289	221	0	ENST00000311895.7:c.1213+1G>T		p.X405_splice	ENST00000311895	NM_005236.2	405			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.748047522211272	2		221	725	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114686	108114687	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTCTGTGTACTTCAGGCTCTATCTGAAA	novel	NA	P-0007520-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	125	192	0	ENST00000278616.4:c.505_532dup	p.Pro178LeufsTer16	p.P178Lfs*16	ENST00000278616	NM_000051.3	168	ttc/ttCTCTGTGTACTTCAGGCTCTATCTGAAAc	6/63	0.748047522211272	1	FACETS	0.615	0.564	0.668	0.615	0.564	0.668	SUBCLONAL	1	TRUE	0	0.748047522211272	1		192	340	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0007599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	22	270	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.235268278099719	2		270	157	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120258	70120259	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	12	645	0	ENST00000245479.2:c.1261dup	p.Ser421LysfsTer157	p.S421Kfs*157	ENST00000245479	NM_000346.3	420	-/A	3/3	1	2	FACETS	0.945	0.67	1	0.945	0.67	1	CLONAL	1	TRUE	1	0.235268278099719	2		645	108	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540730	187540730	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	15	388	0	ENST00000441802.2:c.7010G>A	p.Ser2337Asn	p.S2337N	ENST00000441802	NM_005245.3	2337	aGc/aAc	10/27	1	2	FACETS	1	0.779	1	1	0.779	1	CLONAL	1	TRUE	1	0.235268278099719	2		388	120	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517769	176517769	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs142240686	NA	P-0007599-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	17	546	0	ENST00000292408.4:c.379G>T	p.Asp127Tyr	p.D127Y	ENST00000292408	NM_213647.1	127	Gat/Tat	4/18	1	2	FACETS	1	0.794	1	1	0.794	1	CLONAL	1	TRUE	1	0.235268278099719	2		546	136	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638354	176638354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769137468	NA	P-0007703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	90	340	0	ENST00000439151.2:c.2954C>T	p.Ser985Phe	p.S985F	ENST00000439151	NM_022455.4	985	tCt/tTt	5/23	1	2	FACETS	0.932	0.827	1	0.932	0.827	1	CLONAL	1	TRUE	1	0.272853963628617	2		340	708	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011150	12011150	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	223	361	0	ENST00000353533.5:c.557A>G	p.Asp186Gly	p.D186G	ENST00000353533	NM_003010.3	186	gAt/gGt	5/11	0.228726874840735	2	FACETS	0.852	0.794	0.913	0.852	0.794	0.913	CLONAL	2	TRUE	0	0.272853963628617	2		361	959	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29563039	29563039	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs863224447	NA	P-0007703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	223	467	0	ENST00000356175.3:c.3974G>C	p.Arg1325Thr	p.R1325T	ENST00000356175	NM_000267.3	1325	aGg/aCg	29/57	0.228726874840735	2	FACETS	0.861	0.802	0.922	0.861	0.802	0.922	CLONAL	2	TRUE	0	0.272853963628617	2		467	949	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375032	45375032	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	52	263	0	ENST00000262160.6:c.811C>T	p.Pro271Ser	p.P271S	ENST00000262160	NM_005901.5	271	Cct/Tct	8/11	0.239197839705088	1	FACETS	0.593	0.505	0.69	0.593	0.505	0.69	SUBCLONAL	1	TRUE	0	0.272853963628617	1		263	555	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604778	48604782	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCT	CAGCT	-	novel	NA	P-0007703-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	109	417	0	ENST00000342988.3:c.1601_1605del	p.Gln534ProfsTer41	p.Q534Pfs*41	ENST00000342988	NM_005359.5	534	CAGCTc/c	12/12	0.239197839705088	1	FACETS	0.935	0.84	1	0.935	0.84	1	CLONAL	1	TRUE	0	0.272853963628617	1		417	738	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0007788-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	133	496	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.887719305384375	3	FACETS	0.698	0.636	0.762	0.349	0.318	0.381	SUBCLONAL	1	TRUE	1	0.918114248481445	3		496	606	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0007788-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	532	280	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.918114248481445	6	FACETS	0.96	0.936	0.983			1	CLONAL	5	TRUE	NA	0.918114248481445	6		280	685	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65569036	65569036	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs752477890	NA	P-0007788-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	198	639	0	ENST00000358664.4:c.22G>T	p.Glu8Ter	p.E8*	ENST00000358664	NM_002382.4	8	Gag/Tag	1/5	0.918114248481445	3	FACETS	0.856	0.795	0.919	0.428	0.397	0.46	CLONAL	1	TRUE	1	0.918114248481445	3		639	735	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467197	25467197	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007788-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	164	657	0	ENST00000264709.3:c.1678G>T	p.Val560Leu	p.V560L	ENST00000264709	NM_175629.2	560	Gtg/Ttg	15/23	0.909785149994198	3	FACETS	0.76	0.7	0.822	0.38	0.35	0.411	SUBCLONAL	1	TRUE	1	0.918114248481445	3		657	686	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539493	187539493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007788-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	164	397	0	ENST00000441802.2:c.8247G>T	p.Glu2749Asp	p.E2749D	ENST00000441802	NM_005245.3	2749	gaG/gaT	10/27	0.853635684062691	1	FACETS	0.867	0.824	0.907	0.867	0.824	0.907	CLONAL	1	TRUE	0	0.918114248481445	1		397	223	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344679	70344679	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007788-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	151	665	0	ENST00000374080.3:c.2040del	p.Lys681SerfsTer30	p.K681Sfs*30	ENST00000374080		680	gaG/ga	14/45	0.918114248481445	3	FACETS	0.612	0.56	0.667	0.306	0.28	0.334	SUBCLONAL	1	TRUE	1	0.918114248481445	3		665	784	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489207	2489207	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007788-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	280	1020	0	ENST00000355716.4:c.112G>C	p.Ala38Pro	p.A38P	ENST00000355716	NM_003820.2	38	Gct/Cct	2/8	0.823427836195807	4	FACETS	0.958	0.899	1	0.24	0.224	0.255	CLONAL	1	TRUE	0	0.918114248481445	4		1020	1221	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932152	36932152	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007788-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	222	852	0	ENST00000361632.4:c.2317A>G	p.Thr773Ala	p.T773A	ENST00000361632		773	Act/Gct	16/16	0.894316543347948	3	FACETS	0.874	0.816	0.934	0.291	0.272	0.312	CLONAL	1	TRUE	0	0.918114248481445	3		852	807	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46266444	46266444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007788-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	180	434	0	ENST00000371998.3:c.2429C>T	p.Ser810Phe	p.S810F	ENST00000371998		810	tCt/tTt	13/23	1	2	FACETS	0.901	0.841	0.963	0.901	0.841	0.963	CLONAL	1	TRUE	1	0.918114248481445	2		434	435	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096065	11096068	+	frameshift_variant	Frame_Shift_Del	DEL	GGAC	GGAC	-	novel	NA	P-0007788-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	233	985	0	ENST00000358026.2:c.339_342del	p.Met113IlefsTer189	p.M113Ifs*189	ENST00000358026	NM_001128849.1	113	atGGAC/at	3/36	0.871699624562939	1	FACETS	0.845	0.809	0.879	0.845	0.809	0.879	CLONAL	1	TRUE	0	0.918114248481445	1		985	325	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577562	7577563	+	missense_variant	Missense_Mutation	DNP	CT	CT	AA	novel	NA	P-0007788-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	677	836	1	ENST00000269305.4:c.718_719delinsTT	p.Ser240Phe	p.S240F	ENST00000269305	NM_001126112.2	240	AGt/TTt	7/11	0.894316543347948	3	FACETS	0.941	0.926	0.956	0.941	0.926	0.956	CLONAL	3	TRUE	0	0.918114248481445	3		837	762	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282336	115282336	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007788-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	352	520	0	ENST00000438362.2:c.314A>T	p.Asn105Ile	p.N105I	ENST00000438362	NM_001242891.1	105	aAc/aTc	3/20	0.545322175422028	4	FACETS	1	0.991	1	0.754	0.722	0.787	INDETERMINATE	2	TRUE	1	0.918114248481445	4		520	650	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752830	128752830	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs184271012	NA	P-0007788-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	134	382	0	ENST00000377970.2:c.991C>T	p.Arg331Trp	p.R331W	ENST00000377970	NM_002467.4	331	Cgg/Tgg	3/3	0.918114248481445	6	FACETS	0.76	0.689	0.835	0.127	0.114	0.14	SUBCLONAL	1	TRUE	0	0.918114248481445	6		382	1089	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902197	151902197	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007788-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	226	614	0	ENST00000262189.6:c.3955G>A	p.Asp1319Asn	p.D1319N	ENST00000262189	NM_170606.2	1319	Gat/Aat	25/59	0.791963154421558	4	FACETS	0.83	0.772	0.889	0.415	0.386	0.445	CLONAL	1	TRUE	2	0.918114248481445	4		614	1138	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300812	137300812	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007788-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	246	878	0	ENST00000481739.1:c.457G>T	p.Glu153Ter	p.E153*	ENST00000481739	NM_002957.4	153	Gag/Tag	4/10	0.824848431494311	2	FACETS	0.794	0.746	0.842	0.397	0.373	0.421	SUBCLONAL	1	TRUE	0	0.918114248481445	2		878	675	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0007837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	172	255	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.774253066378944	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.774253066378944	3		255	290	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0007837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	175	652	1	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.429499064285616	1	FACETS	1	0.991	1	1	0.991	1	INDETERMINATE	1	TRUE	0	0.774253066378944	1		653	228	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782654	9782654	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	127	552	2	ENST00000377346.4:c.2416C>A	p.Leu806Met	p.L806M	ENST00000377346	NM_005026.3	806	Ctg/Atg	19/24	0.415720135764003	1	FACETS	0.957	0.893	1	0.957	0.893	1	INDETERMINATE	1	TRUE	0	0.774253066378944	1		554	210	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604787	48604787	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	54	418	4	ENST00000342988.3:c.1609G>C	p.Asp537His	p.D537H	ENST00000342988	NM_005359.5	537	Gac/Cac	12/12	0.774253066378944	1	FACETS	0.814	0.723	0.905	0.814	0.723	0.905	CLONAL	1	TRUE	0	0.774253066378944	1		422	105	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258736	115258736	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	55	403	3	ENST00000369535.4:c.46A>G	p.Lys16Glu	p.K16E	ENST00000369535	NM_002524.4	16	Aaa/Gaa	2/7	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.774253066378944	NA		406	200	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483984	212483984	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	68	514	2	ENST00000342788.4:c.2219A>T	p.Glu740Val	p.E740V	ENST00000342788	NM_005235.2	740	gAa/gTa	19/28	1	2	FACETS	0.949	0.843	1	0.949	0.843	1	CLONAL	1	TRUE	1	0.774253066378944	2		516	185	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754316	57754316	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	83	423	2	ENST00000274289.3:c.535G>T	p.Glu179Ter	p.E179*	ENST00000274289	NM_006622.3	179	Gag/Tag	4/14	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.774253066378944	2		425	179	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93626935	93626935	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	64	491	1	ENST00000375746.1:c.782A>G	p.Lys261Arg	p.K261R	ENST00000375746	NM_001174167.1	261	aAa/aGa	5/14	0.415720135764003	1	FACETS	0.689	0.613	0.766	0.689	0.613	0.766	INDETERMINATE	1	TRUE	0	0.774253066378944	1		492	147	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725087	89725087	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	35	304	1	ENST00000371953.3:c.1070C>A	p.Pro357Gln	p.P357Q	ENST00000371953	NM_000314.4	357	cCa/cAa	9/9	0.415720135764003	1	FACETS	0.894	0.775	1	0.894	0.775	1	INDETERMINATE	1	TRUE	0	0.774253066378944	1		305	62	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480076	50480076	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	92	378	1	ENST00000394963.4:c.310G>T	p.Ala104Ser	p.A104S	ENST00000394963	NM_003076.4	104	Gcc/Tcc	2/13	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.774253066378944	2		379	225	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436185	56436185	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0007837-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	126	352	5	ENST00000407977.2:c.953-1G>A		p.X318_splice	ENST00000407977		318			0.759602691423762	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.774253066378944	2		357	160	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0007864-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	72	800	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.390061418330919	4	FACETS	0.868	0.759	0.986	0.434	0.379	0.493	CLONAL	1	TRUE	2	0.390061418330919	4		800	591	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0007864-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	64	496	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.390061418330919	4	FACETS	1	0.948	1	0.592	0.515	0.675	CLONAL	1	TRUE	2	0.390061418330919	4		496	385	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0007864-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	17	457	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.8	0.605	1	0.8	0.605	1	CLONAL	1	TRUE	1	0.390061418330919	2		457	109	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0007864-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	48	405	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	0.376989393482888	1	FACETS	0.825	0.704	0.956	0.825	0.704	0.956	CLONAL	1	TRUE	0	0.390061418330919	1		405	240	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004270	150004270	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007864-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	22	450	0	ENST00000253339.5:c.1955A>G	p.Lys652Arg	p.K652R	ENST00000253339		652	aAa/aGa	3/7	1	2	FACETS	0.925	0.727	1	0.925	0.727	1	CLONAL	1	TRUE	1	0.390061418330919	2		450	122	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713613	30713613	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007864-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	77	630	0	ENST00000295754.5:c.939del	p.Lys314ArgfsTer10	p.K314Rfs*10	ENST00000295754	NM_003242.5	313	cGg/cg	4/7	0.376989393482888	1	FACETS	0.975	0.863	1	0.975	0.863	1	CLONAL	1	TRUE	0	0.390061418330919	1		630	326	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249092	55249092	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007864-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	73	827	0	ENST00000275493.2:c.2390G>C	p.Cys797Ser	p.C797S	ENST00000275493	NM_005228.3	797	tGc/tCc	20/28	0.390061418330919	4	FACETS	0.879	0.769	0.997	0.439	0.384	0.499	CLONAL	1	TRUE	2	0.390061418330919	4		827	592	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0008020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	108	747	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.286160794076331	3	FACETS	1	0.898	1	0.5	0.449	0.556	CLONAL	1	TRUE	1	0.286160794076331	3		747	862	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872955	136872955	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1160	211	547	2	ENST00000241393.3:c.543T>A	p.Asp181Glu	p.D181E	ENST00000241393	NM_003467.2	181	gaT/gaA	2/2	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.286160794076331	2		549	1371	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441415	52441415	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008020-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	106	364	0	ENST00000460680.1:c.437G>A	p.Arg146Lys	p.R146K	ENST00000460680	NM_004656.3	146	aGg/aAg	6/17	0.286160794076331	1	FACETS	0.903	0.81	1	0.903	0.81	1	CLONAL	1	TRUE	0	0.286160794076331	1		364	703	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051053	180051053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755736057	NA	P-0008025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	29	256	0	ENST00000261937.6:c.1430G>A	p.Arg477Gln	p.R477Q	ENST00000261937	NM_182925.4	477	cGg/cAg	11/30	1	2	FACETS	0.799	0.642	0.978	0.799	0.642	0.978	CLONAL	1	TRUE	1	0.2	2		256	363	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371775	118371775	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782301554	NA	P-0008025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	45	349	0	ENST00000534358.1:c.6232C>T	p.Arg2078Cys	p.R2078C	ENST00000534358	NM_005933.3	2078	Cgt/Tgt	25/36	1	2	FACETS	0.872	0.733	1	0.872	0.733	1	CLONAL	1	TRUE	1	0.2	2		349	516	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223203	5223203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1416280955	NA	P-0008025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	24	280	0	ENST00000357368.4:c.2600G>A	p.Arg867His	p.R867H	ENST00000357368	NM_002850.3	867	cGc/cAc	18/38	1	2	FACETS	0.637	0.499	0.796	0.637	0.499	0.796	SUBCLONAL	1	TRUE	1	0.2	2		280	377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572963	7572963	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	74	443	0	ENST00000269305.4:c.1146del	p.Lys382AsnfsTer40	p.K382Nfs*40	ENST00000269305	NM_001126112.2	382	aaA/aa	11/11	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.2	2		443	705	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089556	27089556	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	50	427	0	ENST00000324856.7:c.2512G>T	p.Gly838Ter	p.G838*	ENST00000324856	NM_006015.4	838	Gga/Tga	8/20	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.2	2		427	444	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836292	151836292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779150118	NA	P-0008025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	26	195	0	ENST00000262189.6:c.14513C>T	p.Thr4838Met	p.T4838M	ENST00000262189	NM_170606.2	4838	aCg/aTg	57/59	1	2	FACETS	0.67	0.53	0.83	0.67	0.53	0.83	SUBCLONAL	1	TRUE	1	0.2	2		195	388	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240450	98240450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370354759	NA	P-0008025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	30	203	0	ENST00000331920.6:c.1234G>A	p.Ala412Thr	p.A412T	ENST00000331920	NM_000264.3	412	Gca/Aca	9/24	1	2	FACETS	0.716	0.577	0.874	0.716	0.577	0.874	SUBCLONAL	1	TRUE	1	0.2	2		203	419	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438067	49438067	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886043414	NA	P-0008025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	62	313	1	ENST00000301067.7:c.5104C>T	p.Arg1702Ter	p.R1702*	ENST00000301067	NM_003482.3	1702	Cga/Tga	21/54	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.2	2		314	553	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219388	1219388	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780717	NA	P-0008025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	34	395	1	ENST00000326873.7:c.440G>A	p.Arg147His	p.R147H	ENST00000326873	NM_000455.4	147	cGt/cAt	3/10	1	2	FACETS	0.637	0.519	0.769	0.637	0.519	0.769	SUBCLONAL	1	TRUE	1	0.2	2		396	534	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265145	5265145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748255589	NA	P-0008025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	48	375	0	ENST00000357368.4:c.442C>T	p.Arg148Trp	p.R148W	ENST00000357368	NM_002850.3	148	Cgg/Tgg	5/38	1	2	FACETS	0.923	0.78	1	0.923	0.78	1	CLONAL	1	TRUE	1	0.2	2		375	520	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023733	31023733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444168328	NA	P-0008025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	38	314	0	ENST00000375687.4:c.3218G>A	p.Arg1073His	p.R1073H	ENST00000375687	NM_015338.5	1073	cGc/cAc	13/13	1	2	FACETS	0.894	0.74	1	0.894	0.74	1	CLONAL	1	TRUE	1	0.2	2		314	425	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682400	52682400	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	69	425	0	ENST00000394830.3:c.773del	p.Asn258MetfsTer25	p.N258Mfs*25	ENST00000394830	NM_018313.4	258	aAt/at	8/30	1	2	FACETS	0.965	0.84	1	0.965	0.84	1	CLONAL	1	TRUE	1	0.2	2		425	715	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510806	157510806	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	26	324	1	ENST00000346085.5:c.3586del	p.Gln1196SerfsTer15	p.Q1196Sfs*15	ENST00000346085	NM_020732.3	1194	aCc/ac	14/20	1	2	FACETS	0.521	0.412	0.647	0.521	0.412	0.647	SUBCLONAL	1	TRUE	1	0.2	2		325	499	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0008237-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	18	357	0	ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	4/10	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		357	136	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877840	151877855	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGTGTATCAGTTAC	TCTGTGTATCAGTTAC	-	novel	NA	P-0008286-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	143	293	0	ENST00000262189.6:c.7090_7105del	p.Val2364IlefsTer3	p.V2364Ifs*3	ENST00000262189	NM_170606.2	2364	GTAACTGATACACAGAat/at	36/59	1	2	FACETS	0.91	0.831	0.993	0.91	0.831	0.993	CLONAL	1	TRUE	1	0.418903348094677	2		293	750	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074249	8074249	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008286-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	313	702	3	ENST00000377482.5:c.410del	p.Pro137LeufsTer38	p.P137Lfs*38	ENST00000377482	NM_018948.3	137	cCt/ct	4/4	0.325467667336959	1	FACETS	0.95	0.896	1	0.95	0.896	1	CLONAL	1	TRUE	0	0.418903348094677	1		705	1243	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845757	68845757	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587780784	NA	P-0008398-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	93	332	0	ENST00000261769.5:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000261769	NM_004360.3	335	Cga/Tga	7/16	0.394409547385142	1	FACETS	0.568	0.509	0.631	0.568	0.509	0.631	SUBCLONAL	1	TRUE	0	0.583861041012951	1		332	397	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259368	89259368	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008398-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	105	459	0	ENST00000336596.2:c.512T>C	p.Val171Ala	p.V171A	ENST00000336596	NM_005233.5	171	gTa/gCa	3/17	1	2	FACETS	0.803	0.724	0.886	0.803	0.724	0.886	CLONAL	1	TRUE	1	0.583861041012951	2		459	448	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845413	156845413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772559075	NA	P-0008398-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1238	174	935	0	ENST00000524377.1:c.1456C>T	p.Leu486Phe	p.L486F	ENST00000524377	NM_002529.3	486	Ctc/Ttc	12/17	0.346503557301678	4	FACETS	0.669	0.614	0.726	0.334	0.307	0.363	INDETERMINATE	1	TRUE	2	0.583861041012951	4		935	1412	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628626	21628626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008398-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	47	474	0	ENST00000421138.2:c.1082C>T	p.Ser361Leu	p.S361L	ENST00000421138		361	tCa/tTa	10/16	1	2	FACETS	0.785	0.671	0.908	0.785	0.671	0.908	CLONAL	1	TRUE	1	0.583861041012951	2		474	205	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58142368	58142368	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008398-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	98	445	0	ENST00000257904.6:c.852C>G	p.Ile284Met	p.I284M	ENST00000257904	NM_000075.3	284	atC/atG	8/8	1	2	FACETS	0.548	0.489	0.61	0.548	0.489	0.61	SUBCLONAL	1	TRUE	1	0.583861041012951	2		445	613	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873518	151873518	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008398-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	153	567	0	ENST00000262189.6:c.9020del	p.Gly3007GlufsTer25	p.G3007Efs*25	ENST00000262189	NM_170606.2	3007	gGa/ga	38/59	1	2	FACETS	0.701	0.642	0.762	0.701	0.642	0.762	SUBCLONAL	1	TRUE	1	0.583861041012951	2		567	748	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99192845	99192845	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs774479139	NA	P-0008398-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	40	427	0	ENST00000268035.6:c.35C>G	p.Ser12Trp	p.S12W	ENST00000268035	NM_000875.3	12	tCg/tGg	1/21	1	2	FACETS	0.208	0.172	0.248	0.208	0.172	0.248	SUBCLONAL	1	TRUE	1	0.583861041012951	2		427	660	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0008601-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	478	533	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.601291626722796	3	FACETS	0.887	0.858	0.916	0.887	0.858	0.916	CLONAL	3	TRUE	0	0.639039697474056	3		533	742	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0008601-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	458	668	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.589142816142634	2	FACETS	0.943	0.91	0.976	0.943	0.91	0.976	CLONAL	2	TRUE	0	0.639039697474056	2		670	760	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210075	55210075	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008601-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	383	487	0	ENST00000275493.2:c.185T>G	p.Leu62Arg	p.L62R	ENST00000275493	NM_005228.3	62	cTt/cGt	2/28	0.601291626722796	3	FACETS	0.9	0.867	0.932	0.9	0.867	0.932	CLONAL	3	TRUE	0	0.639039697474056	3		487	586	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670685	86670685	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008601-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	37	185	0	ENST00000274376.6:c.1963G>C	p.Glu655Gln	p.E655Q	ENST00000274376	NM_002890.2	655	Gaa/Caa	15/25	0.589142816142634	2	FACETS	0.619	0.516	0.732	0.31	0.258	0.366	SUBCLONAL	1	TRUE	0	0.639039697474056	2		185	187	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0008658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	70	434	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.105896690551599	5	FACETS	0.976	0.864	1	0.488	0.432	0.547	INDETERMINATE	2	TRUE	1	0.585672445385862	5		434	230	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495564	56495564	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	234	387	1	ENST00000267101.3:c.3754G>T	p.Ala1252Ser	p.A1252S	ENST00000267101	NM_001982.3	1252	Gca/Tca	28/28	0.198165152094614	4	FACETS	1	0.992	1	0.724	0.677	0.773	INDETERMINATE	1	TRUE	2	0.585672445385862	4		388	875	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133244235	133244235	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0008658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	213	290	0	ENST00000320574.5:c.2174-1G>T		p.X725_splice	ENST00000320574	NM_006231.2	725			0.198165152094614	4	FACETS	0.876	0.818	0.936	0.876	0.818	0.936	INDETERMINATE	2	TRUE	2	0.585672445385862	4		290	658	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061028	38061028	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	88	269	0	ENST00000250448.2:c.961G>C	p.Glu321Gln	p.E321Q	ENST00000250448	NM_004496.3	321	Gag/Cag	2/2	0.198165152094614	4	FACETS	0.809	0.718	0.906	0.405	0.359	0.453	INDETERMINATE	1	TRUE	2	0.585672445385862	4		269	589	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325821	30325869	+	frameshift_variant	Frame_Shift_Del	DEL	AATAGATAAAGCTGTTACCAAGCTCCGTGAAATGCAGCAAAAATTAGAA	AATAGATAAAGCTGTTACCAAGCTCCGTGAAATGCAGCAAAAATTAGAA	-	novel	NA	P-0008921-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	80	360	0	ENST00000322652.5:c.2021_2069del	p.Ile674ArgfsTer12	p.I674Rfs*12	ENST00000322652	NM_015355.2	673	tcAATAGATAAAGCTGTTACCAAGCTCCGTGAAATGCAGCAAAAATTAGAA/tc	16/16	0.421138790836129	1	FACETS	0.817	0.724	0.915	0.817	0.724	0.915	CLONAL	1	TRUE	0	0.421138790836129	1		360	367	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0009024-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	121	314	1	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	0.808944249320357	4	FACETS	0.923	0.837	1	0.462	0.418	0.507	CLONAL	1	TRUE	2	0.827543986946607	4		315	579	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0009061-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	9	496	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.322987677067189	2	FACETS	0.163	0.107	0.235			1	SUBCLONAL	1	TRUE	NA	0.29	2		496	381	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0009061-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	155	328	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.322987677067189	3	FACETS	0.754	0.69	0.82	0.754	0.69	0.82	SUBCLONAL	2	TRUE	1	0.29	3		328	812	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115514	108115514	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0009061-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	102	252	0	ENST00000278616.4:c.663-1G>C		p.X221_splice	ENST00000278616	NM_000051.3	221			0.322987677067189	2	FACETS	1	0.962	1			1	CLONAL	1	TRUE	NA	0.29	2		252	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0009061-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	35	781	1	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.322987677067189	2	FACETS	0.381	0.312	0.46			1	SUBCLONAL	1	TRUE	NA	0.29	2		782	633	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874590	35874591	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0009061-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	150	443	0	ENST00000303115.3:c.752dup	p.Ser252LeufsTer18	p.S252Lfs*18	ENST00000303115	NM_002185.3	249	agt/agTt	6/8	0.107254205723812	3	FACETS	1	0.974	1	0.586	0.535	0.64	INDETERMINATE	1	TRUE	1	0.29	3		443	1011	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974687	+	protein_altering_variant	In_Frame_Del	DEL	GGCC	GGCC	A	novel	NA	P-0009061-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	272	434	0	ENST00000304494.5:c.140_143delinsT	p.Arg47_Pro48delinsMet	p.R47_P48delinsM	ENST00000304494	NM_000077.4	47	aGGCCg/aTg	1/3	0.107254205723812	3	FACETS	0.97	0.915	1	1	0.993	1	INDETERMINATE	3	TRUE	1	0.29	3		434	738	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs11575997	NA	P-0009187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	234	547	0	ENST00000269305.4:c.993+1G>T		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.309776481186275	2	FACETS	0.796	0.745	0.848	0.796	0.745	0.848	SUBCLONAL	2	TRUE	0	0.372200331006173	2		547	790	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662388	67662388	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	118	726	0	ENST00000264010.4:c.1634A>G	p.Tyr545Cys	p.Y545C	ENST00000264010	NM_006565.3	545	tAt/tGt	9/12	0.11206255439837	6	FACETS	0.948	0.853	1			1	INDETERMINATE	1	TRUE	NA	0.372200331006173	6		726	1167	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230757	53230757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782454292	NA	P-0009187-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	149	841	1	ENST00000375401.3:c.2036G>A	p.Arg679His	p.R679H	ENST00000375401	NM_004187.3	679	cGt/cAt	14/26	0.382475844656856	1	FACETS	0.619	0.564	0.676	0.619	0.564	0.676	SUBCLONAL	1	TRUE	0	0.372200331006173	1		842	1053	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	140	868	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.245867981997525	3	FACETS	0.754	0.688	0.822	0.754	0.688	0.822	SUBCLONAL	2	TRUE	1	0.324056102795144	3		869	666	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0009191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	77	498	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	1	2	FACETS	0.805	0.708	0.91	0.805	0.708	0.91	CLONAL	1	TRUE	1	0.324056102795144	2		498	590	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151181857	151181857	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	132	895	1	ENST00000262187.5:c.158A>T	p.Glu53Val	p.E53V	ENST00000262187	NM_005614.3	53	gAa/gTa	3/8	1	2	FACETS	0.894	0.811	0.982	0.894	0.811	0.982	CLONAL	1	TRUE	1	0.324056102795144	2		896	911	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584709	48584709	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0009191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	96	617	2	ENST00000342988.3:c.788-1G>T		p.X263_splice	ENST00000342988	NM_005359.5	263			0.324056102795144	1	FACETS	0.687	0.612	0.766	0.687	0.612	0.766	SUBCLONAL	1	TRUE	0	0.324056102795144	1		619	723	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577569	7577572	+	frameshift_variant	Frame_Shift_Del	DEL	ACAT	ACAT	-	novel	NA	P-0009191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	108	523	0	ENST00000269305.4:c.709_712del	p.Met237ValfsTer9	p.M237Vfs*9	ENST00000269305	NM_001126112.2	237	ATGTgt/gt	7/11	1	2	FACETS	0.881	0.79	0.976	0.881	0.79	0.976	CLONAL	1	TRUE	1	0.324056102795144	2		523	757	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673703	37673703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009401-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	147	513	0	ENST00000447079.4:c.2857G>A	p.Gly953Ser	p.G953S	ENST00000447079	NM_015083.1	953	Ggt/Agt	10/14	0.779892472027262	3	FACETS	0.825	0.756	0.897			1	CLONAL	1	FALSE	NA	0.779892472027262	3		513	635	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944841	31944842	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0009401-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1188	413	924	0	ENST00000340398.3:c.259_260del	p.Ala87SerfsTer9	p.A87Sfs*9	ENST00000340398	NM_001013699.2	87	GCa/a	1/1	1	2	FACETS	0.662	0.628	0.695	0.662	0.628	0.695	SUBCLONAL	1	FALSE	1	0.779892472027262	2		924	1601	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618989	37618990	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0009401-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	530	614	1	ENST00000447079.4:c.670dup	p.His224ProfsTer6	p.H224Pfs*6	ENST00000447079	NM_015083.1	222	agc/agCc	1/14	0.779892472027262	3	FACETS	0.878	0.845	0.91			1	CLONAL	2	FALSE	NA	0.779892472027262	3		615	1076	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579480	7579480	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009679-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	411	578	0	ENST00000269305.4:c.207del	p.Ala70LeufsTer53	p.A70Lfs*53	ENST00000269305	NM_001126112.2	69	gcT/gc	4/11	0.470831552118176	2	FACETS	0.995	0.953	1	0.995	0.953	1	CLONAL	2	TRUE	0	0.470831552118176	2		578	877	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0009694-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	294	712	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.294589755242609	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	FALSE	0	0.294589755242609	2		712	912	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46733212	46733212	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908690	NA	P-0009694-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	128	918	2	ENST00000371975.4:c.973G>A	p.Gly325Arg	p.G325R	ENST00000371975	NM_003579.3	325	Gga/Aga	9/18	0.294589755242609	3	FACETS	0.942	0.852	1	0.471	0.426	0.519	CLONAL	1	FALSE	1	0.294589755242609	3		920	1058	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	75	473	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.157499669332109	3	FACETS	0.915	0.803	1	0.915	0.803	1	CLONAL	2	TRUE	1	0.16	3		473	553	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0009710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	80	1988	1	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.16	2		1989	812	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964310	55964310	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	28	344	0	ENST00000263923.4:c.2503A>G	p.Lys835Glu	p.K835E	ENST00000263923	NM_002253.2	835	Aag/Gag	17/30	1	2	FACETS	0.866	0.692	1	0.866	0.692	1	CLONAL	1	TRUE	1	0.16	2		344	404	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557327	187557327	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	66	680	0	ENST00000441802.2:c.4035G>T	p.Trp1345Cys	p.W1345C	ENST00000441802	NM_005245.3	1345	tgG/tgT	6/27	1	2	FACETS	0.981	0.85	1	0.981	0.85	1	CLONAL	1	TRUE	1	0.16	2		680	841	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047993	180047993	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	113	804	0	ENST00000261937.6:c.2182G>C	p.Asp728His	p.D728H	ENST00000261937	NM_182925.4	728	Gac/Cac	15/30	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.16	2		804	999	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560499	65560499	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	35	504	0	ENST00000358664.4:c.98G>T	p.Arg33Leu	p.R33L	ENST00000358664	NM_002382.4	33	cGa/cTa	3/5	1	2	FACETS	0.76	0.621	0.915	0.76	0.621	0.915	CLONAL	1	TRUE	1	0.16	2		504	576	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041750	14041750	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	40	476	0	ENST00000311895.7:c.2297C>A	p.Pro766His	p.P766H	ENST00000311895	NM_005236.2	766	cCt/cAt	11/11	1	2	FACETS	0.804	0.667	0.957	0.804	0.667	0.957	CLONAL	1	TRUE	1	0.16	2		476	622	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041266	47041266	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0009710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	70	855	1	ENST00000377604.3:c.1693+1G>A		p.X565_splice	ENST00000377604	NM_001204468.1	565			NA	2	FACETS	0.82	0.713	0.937			1	INDETERMINATE	1	TRUE	NA	0.16	2		856	1067	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626635	100626635	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	72	474	1	ENST00000308731.7:c.295C>A	p.Pro99Thr	p.P99T	ENST00000308731	NM_000061.2	99	Cct/Act	4/19	1	2	FACETS	0.764	0.668	0.868	1	0.975	1	SUBCLONAL	2	TRUE	1	0.16	2		475	589	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372693	81372694	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0009710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	31	342	0	ENST00000222390.5:c.840_841delinsTT	p.Trp280_Glu281delinsCysTer	p.W280_E281delinsC*	ENST00000222390	NM_000601.4	280	tgGGag/tgTTag	7/18	1	2	FACETS	0.848	0.685	1	0.848	0.685	1	CLONAL	1	TRUE	1	0.16	2		342	457	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945049	31945050	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0009710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	81	809	2	ENST00000340398.3:c.51_52delinsAA	p.Arg18Ser	p.R18S	ENST00000340398	NM_001013699.2	17	ccCCgc/ccAAgc	1/1	0.157499669332109	3	FACETS	0.994	0.873	1	0.497	0.436	0.563	CLONAL	1	TRUE	1	0.16	3		811	1100	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50490699	50490699	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	52	577	0	ENST00000394963.4:c.1336A>G	p.Arg446Gly	p.R446G	ENST00000394963	NM_003076.4	446	Aga/Gga	11/13	0.157499669332109	3	FACETS	0.881	0.748	1	0.44	0.374	0.514	CLONAL	1	TRUE	1	0.16	3		577	797	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752897	42752897	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376964824	NA	P-0009710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	93	911	0	ENST00000222329.4:c.1367C>T	p.Thr456Met	p.T456M	ENST00000222329	NM_006494.2	456	aCg/aTg	4/4	1	2	FACETS	0.984	0.872	1	0.984	0.872	1	CLONAL	1	TRUE	1	0.16	2		911	1182	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919555	96919555	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	41	585	0	ENST00000258439.3:c.708C>A	p.Tyr236Ter	p.Y236*	ENST00000258439	NM_001193304.2	236	taC/taA	4/4	1	2	FACETS	0.708	0.588	0.842	0.708	0.588	0.842	SUBCLONAL	1	TRUE	1	0.16	2		585	724	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247215	153247215	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009710-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	29	396	0	ENST00000281708.4:c.1587G>C	p.Glu529Asp	p.E529D	ENST00000281708	NM_033632.3	529	gaG/gaC	10/12	1	2	FACETS	0.69	0.553	0.848	0.69	0.553	0.848	SUBCLONAL	1	TRUE	1	0.16	2		396	525	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009825-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	18	384	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.549	0.416	0.704	0.549	0.416	0.704	SUBCLONAL	1	TRUE	1	0.4	2		384	164	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0009825-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	26	457	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.364	0.288	0.451	0.364	0.288	0.451	SUBCLONAL	1	TRUE	1	0.4	2		457	357	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602320	10602320	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1482163272	NA	P-0009825-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	87	463	1	ENST00000171111.5:c.1258del	p.Val420SerfsTer38	p.V420Sfs*38	ENST00000171111	NM_203500.1	420	Gtc/tc	3/6	1	2	FACETS	0.486	0.429	0.547	0.486	0.429	0.547	SUBCLONAL	1	TRUE	1	0.4	2		464	895	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198283298	198283298	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009825-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	85	574	0	ENST00000335508.6:c.430G>A	p.Asp144Asn	p.D144N	ENST00000335508	NM_012433.2	144	Gat/Aat	5/25	1	2	FACETS	0.41	0.361	0.463	0.41	0.361	0.463	SUBCLONAL	1	TRUE	1	0.4	2		574	1036	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509880	106509880	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009825-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	248	653	0	ENST00000359195.3:c.1874G>C	p.Gly625Ala	p.G625A	ENST00000359195	NM_002649.2	625	gGg/gCg	2/11	0.205979613878321	3	FACETS	1	0.962	1	0.523	0.487	0.559	INDETERMINATE	1	TRUE	1	0.4	3		653	1423	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624473	140624473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1225976306	NA	P-0009825-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	36	87	0	ENST00000288602.6:c.31G>A	p.Gly11Ser	p.G11S	ENST00000288602	NM_004333.4	11	Ggc/Agc	1/18	0.205979613878321	3	FACETS	0.854	0.706	1	0.427	0.353	0.509	INDETERMINATE	1	TRUE	1	0.4	3		87	253	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243986	46243986	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009825-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	179	742	0	ENST00000334344.6:c.2080C>T	p.Gln694Ter	p.Q694*	ENST00000334344	NM_152641.2	694	Cag/Tag	15/21	1	2	FACETS	0.687	0.632	0.745	0.687	0.632	0.745	SUBCLONAL	1	TRUE	1	0.4	2		742	1302	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145795	11145795	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009825-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	71	477	0	ENST00000358026.2:c.4157A>T	p.Lys1386Met	p.K1386M	ENST00000358026	NM_001128849.1	1386	aAg/aTg	29/36	1	2	FACETS	0.423	0.368	0.482	0.423	0.368	0.482	SUBCLONAL	1	TRUE	1	0.4	2		477	839	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464443	25464443	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009825-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	68	443	0	ENST00000264709.3:c.2070del	p.Thr691HisfsTer14	p.T691Hfs*14	ENST00000264709	NM_175629.2	690	gtC/gt	17/23	1	2	FACETS	0.378	0.328	0.432	0.378	0.328	0.432	SUBCLONAL	1	TRUE	1	0.4	2		443	900	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40371847	40371848	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0009825-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	72	667	0	ENST00000293328.3:c.563_564insA	p.Leu189AlafsTer30	p.L189Afs*30	ENST00000293328	NM_012448.3	188	ccg/ccAg	6/19	0.3	1	FACETS	0.262	0.228	0.299	0.262	0.228	0.299	SUBCLONAL	1	TRUE	0	0.4	1		667	1098	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0009916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	113	228	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.391330630153534	4	FACETS	0.913	0.827	1	0.913	0.827	1	CLONAL	2	TRUE	2	0.391330630153534	4		228	440	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105639	27105639	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	261	593	0	ENST00000324856.7:c.5250del	p.Phe1750LeufsTer20	p.F1750Lfs*20	ENST00000324856	NM_006015.4	1750	ttC/tt	20/20	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.391330630153534	2		593	571	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405344	70405345	+	inframe_insertion	In_Frame_Ins	INS	-	-	TAA	novel	NA	P-0009916-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	260	687	0	ENST00000373644.4:c.2860_2862dup	p.Asn954dup	p.N954dup	ENST00000373644	NM_030625.2	954	ctt/ctTAAt	4/12	0.337969659468567	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	2	0.391330630153534	4		687	901	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0009948-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	142	398	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	NA	2	FACETS	0.799	0.732	0.868			1	INDETERMINATE	2	TRUE	NA	0.332824541302668	2		398	534	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374701	118374701	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009948-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	119	166	0	ENST00000534358.1:c.8094A>T	p.Glu2698Asp	p.E2698D	ENST00000534358	NM_005933.3	2698	gaA/gaT	27/36	0.277069989838803	5	FACETS	1	0.976	1	0.814	0.74	0.891	CLONAL	2	TRUE	2	0.332824541302668	5		166	439	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81922859	81922859	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009948-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	102	213	0	ENST00000359376.3:c.848C>A	p.Pro283His	p.P283H	ENST00000359376	NM_002661.3	283	cCt/cAt	10/33	0.332824541302668	3	FACETS	0.779	0.7	0.861	0.779	0.7	0.861	SUBCLONAL	2	TRUE	1	0.332824541302668	3		213	459	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965248	81965248	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009948-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	48	262	0	ENST00000359376.3:c.2728A>C	p.Ile910Leu	p.I910L	ENST00000359376	NM_002661.3	910	Att/Ctt	25/33	0.332824541302668	3	FACETS	0.815	0.69	0.951	0.407	0.345	0.476	CLONAL	1	TRUE	1	0.332824541302668	3		262	413	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41909347	41909347	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009948-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	71	277	0	ENST00000372991.4:c.41G>T	p.Arg14Leu	p.R14L	ENST00000372991	NM_001760.3	14	cGg/cTg	1/5	0.171471273049471	5	FACETS	0.804	0.705	0.909	0.536	0.47	0.606	INDETERMINATE	2	TRUE	2	0.332824541302668	5		277	398	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259524	55259524	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913444	NA	P-0009948-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	8024	314	0	ENST00000275493.2:c.2582T>A	p.Leu861Gln	p.L861Q	ENST00000275493	NM_005228.3	861	cTg/cAg	21/28	0.332824541302668	79	FACETS	0.994	0.991	0.998			1	CLONAL	79	TRUE	NA	0.332824541302668	79		314	8481	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381504	81381504	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009948-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	32	150	0	ENST00000222390.5:c.557del	p.Gly186AspfsTer27	p.G186Dfs*27	ENST00000222390	NM_000601.4	186	gGa/ga	5/18	0.332824541302668	3	FACETS	0.634	0.515	0.767	0.317	0.257	0.384	SUBCLONAL	1	TRUE	1	0.332824541302668	3		150	354	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0010299-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	47	324	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.736	0.621	0.863	0.736	0.621	0.863	SUBCLONAL	1	TRUE	1	0.24	2		324	532	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430419	78430419	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010299-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	82	453	0	ENST00000370768.2:c.749T>A	p.Met250Lys	p.M250K	ENST00000370768	NM_003902.3	250	aTg/aAg	10/20	1	2	FACETS	0.767	0.675	0.866	0.767	0.675	0.866	SUBCLONAL	1	TRUE	1	0.24	2		453	891	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224202	98224202	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs971300374	NA	P-0010299-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1171	96	456	0	ENST00000331920.6:c.2639G>T	p.Gly880Val	p.G880V	ENST00000331920	NM_000264.3	880	gGa/gTa	16/24	1	2	FACETS	0.631	0.561	0.707	0.631	0.561	0.707	SUBCLONAL	1	TRUE	1	0.24	2		456	1267	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222326	2222326	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368825067	NA	P-0010299-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	82	312	0	ENST00000398665.3:c.3158C>T	p.Ala1053Val	p.A1053V	ENST00000398665	NM_032482.2	1053	gCg/gTg	24/28	1	2	FACETS	0.733	0.645	0.828	0.733	0.645	0.828	SUBCLONAL	1	TRUE	1	0.24	2		312	932	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302810	15302810	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1191007031	NA	P-0010299-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	71	236	0	ENST00000263388.2:c.640C>A	p.Gln214Lys	p.Q214K	ENST00000263388	NM_000435.2	214	Cag/Aag	4/33	1	2	FACETS	0.801	0.698	0.912	0.801	0.698	0.912	CLONAL	1	TRUE	1	0.24	2		236	739	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208279	5208280	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010299-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1501	130	540	0	ENST00000357368.4:c.5610dup	p.Gly1871TrpfsTer24	p.G1871Wfs*24	ENST00000357368	NM_002850.3	1870	-/T	36/38	1	2	FACETS	0.664	0.6	0.732	0.664	0.6	0.732	SUBCLONAL	1	TRUE	1	0.24	2		540	1631	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097622	27097622	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	59	456	0	ENST00000324856.7:c.3216del	p.Lys1072AsnfsTer21	p.K1072Nfs*21	ENST00000324856	NM_006015.4	1071	Aaa/aa	12/20	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.14	2		456	822	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0010331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	36	300	2	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	0.87	0.714	1	0.87	0.714	1	CLONAL	1	TRUE	1	0.14	2		302	591	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204842	128204842	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs768767517	NA	P-0010331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	71	532	0	ENST00000341105.2:c.599del	p.Gly200ValfsTer18	p.G200Vfs*18	ENST00000341105	NM_032638.4	200	gGt/gt	3/6	1	2	FACETS	0.983	0.855	1	0.983	0.855	1	CLONAL	1	TRUE	1	0.14	2		532	1032	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794422	242794422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758959367	NA	P-0010331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	56	455	0	ENST00000334409.5:c.520G>A	p.Val174Met	p.V174M	ENST00000334409	NM_005018.2	174	Gtg/Atg	3/5	1	2	FACETS	1	0.862	1	1	0.862	1	CLONAL	1	TRUE	1	0.14	2		455	793	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118924	70118926	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	novel	NA	P-0010331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	83	611	0	ENST00000245479.2:c.499_501del	p.Lys167del	p.K167del	ENST00000245479	NM_000346.3	166	AAG/-	2/3	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.14	2		611	1154	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306930	65306930	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	50	371	0	ENST00000342505.4:c.2647G>T	p.Glu883Ter	p.E883*	ENST00000342505	NM_002227.2	883	Gag/Tag	19/25	1	2	FACETS	0.885	0.749	1	0.885	0.749	1	CLONAL	1	TRUE	1	0.14	2		371	807	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098755	47098755	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	57	513	1	ENST00000409792.3:c.6519G>A	p.Met2173Ile	p.M2173I	ENST00000409792	NM_014159.6	2173	atG/atA	15/21	1	2	FACETS	0.863	0.738	1	0.863	0.738	1	CLONAL	1	TRUE	1	0.14	2		514	944	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630275	187630275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	36	292	0	ENST00000441802.2:c.707G>A	p.Gly236Asp	p.G236D	ENST00000441802	NM_005245.3	236	gGc/gAc	2/27	1	2	FACETS	0.884	0.725	1	0.884	0.725	1	CLONAL	1	TRUE	1	0.14	2		292	582	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760526	133760526	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	49	429	1	ENST00000318560.5:c.2849A>G	p.Gln950Arg	p.Q950R	ENST00000318560	NM_005157.4	950	cAg/cGg	11/11	1	2	FACETS	0.91	0.769	1	0.91	0.769	1	CLONAL	1	TRUE	1	0.14	2		430	769	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829617	72829617	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1812	119	1116	2	ENST00000268489.5:c.6964C>T	p.Arg2322Ter	p.R2322*	ENST00000268489	NM_006885.3	2322	Cga/Tga	9/10	0.123650787033593	1	FACETS	0.819	0.735	0.908	0.819	0.735	0.908	CLONAL	1	TRUE	0	0.14	1		1118	1931	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579344	7579344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	42	398	1	ENST00000269305.4:c.343C>T	p.His115Tyr	p.H115Y	ENST00000269305	NM_001126112.2	115	Cat/Tat	4/11	1	2	FACETS	0.758	0.631	0.9	0.758	0.631	0.9	SUBCLONAL	1	TRUE	1	0.14	2		399	792	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121082	11121082	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	57	456	0	ENST00000358026.2:c.2149G>T	p.Glu717Ter	p.E717*	ENST00000358026	NM_001128849.1	717	Gaa/Taa	15/36	1	2	FACETS	0.879	0.752	1	0.879	0.752	1	CLONAL	1	TRUE	1	0.14	2		456	926	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366384	15366384	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	36	246	0	ENST00000263377.2:c.1771A>G	p.Met591Val	p.M591V	ENST00000263377	NM_058243.2	591	Atg/Gtg	10/20	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.14	2		246	448	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52621443	52621445	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0010331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	73	627	0	ENST00000394830.3:c.2972_2974del	p.Glu991del	p.E991del	ENST00000394830	NM_018313.4	991	gAAGtt/gtt	20/30	1	2	FACETS	0.936	0.816	1	0.936	0.816	1	CLONAL	1	TRUE	1	0.14	2		627	1114	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577084	7577084	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121912667	NA	P-0010487-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	97	927	0	ENST00000269305.4:c.854A>T	p.Glu285Val	p.E285V	ENST00000269305	NM_001126112.2	285	gAg/gTg	8/11	1	2	FACETS	0.225	0.199	0.252	0.225	0.199	0.252	SUBCLONAL	1	TRUE	1	0.75	2		927	1152	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249002	55249003	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAGCGTGGA	rs397517109	NA	P-0010487-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	73	642	0	ENST00000275493.2:c.2303_2311dup	p.Ser768_Asp770dup	p.S768_D770dup	ENST00000275493	NM_005228.3	768	gcc/gcCAGCGTGGAc	20/28	1	2	FACETS	0.221	0.192	0.252	0.221	0.192	0.252	SUBCLONAL	1	TRUE	1	0.75	2		642	881	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442788	187442788	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010487-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	50	579	0	ENST00000232014.4:c.1918C>T	p.Arg640Trp	p.R640W	ENST00000232014	NM_001130845.1	640	Cgg/Tgg	9/10	1	2	FACETS	0.172	0.145	0.201	0.172	0.145	0.201	SUBCLONAL	1	TRUE	1	0.75	2		579	777	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0010532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	46	469	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.265287713564793	3	FACETS	0.772	0.657	0.896	0.772	0.657	0.896	SUBCLONAL	2	TRUE	1	0.30684665890346	3		469	224	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381472	81381472	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777593933	NA	P-0010532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	64	642	1	ENST00000222390.5:c.589C>T	p.Arg197Cys	p.R197C	ENST00000222390	NM_000601.4	197	Cgc/Tgc	5/18	1	2	FACETS	0.375	0.323	0.432	0.375	0.323	0.432	SUBCLONAL	1	TRUE	1	0.30684665890346	2		643	1112	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576888	7576893	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTTG	TCTTTG	C	novel	NA	P-0010532-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	106	529	0	ENST00000269305.4:c.953_958delinsG	p.Pro318ArgfsTer17	p.P318Rfs*17	ENST00000269305	NM_001126112.2	318	cCAAAGAag/cGag	9/11	1	2	FACETS	0.76	0.68	0.845	0.76	0.68	0.845	SUBCLONAL	1	TRUE	1	0.30684665890346	2		529	909	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0010615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	90	469	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.327400402935305	2		469	478	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0010615-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	161	228	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.327400402935305	2		228	851	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0010701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1305	44	550	2	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	0.807356649922686	2	FACETS	0.081	0.067	0.096	0.04	0.033	0.048	SUBCLONAL	1	TRUE	0	0.807356649922686	2		552	1349	SUCCESS
ATR	545	MSKCC	GRCh37	3	142218472	142218472	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	466	415	0	ENST00000350721.4:c.5377G>A	p.Ala1793Thr	p.A1793T	ENST00000350721	NM_001184.3	1793	Gca/Aca	31/47	0.807356649922686	2	FACETS	0.987	0.945	1	0.493	0.472	0.515	CLONAL	1	TRUE	0	0.807356649922686	2		415	1170	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528168	157528168	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	464	351	0	ENST00000346085.5:c.5893A>G	p.Met1965Val	p.M1965V	ENST00000346085	NM_020732.3	1965	Atg/Gtg	20/20	1	2	FACETS	0.968	0.926	1	0.968	0.926	1	CLONAL	1	TRUE	1	0.807356649922686	2		351	1188	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67197001	67197001	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	481	592	1	ENST00000312629.5:c.244T>C	p.Phe82Leu	p.F82L	ENST00000312629	NM_003952.2	82	Ttc/Ctc	4/15	1	2	FACETS	0.966	0.925	1	0.966	0.925	1	CLONAL	1	TRUE	1	0.807356649922686	2		593	1234	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004694	16004694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765129231	NA	P-0010701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	1374	675	0	ENST00000268712.3:c.2560G>A	p.Glu854Lys	p.E854K	ENST00000268712	NM_006311.3	854	Gaa/Aaa	20/46	0.807356649922686	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.807356649922686	2		675	1650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577140	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	1057	551	0	ENST00000269305.4:c.798dup	p.Arg267ThrfsTer5	p.R267Tfs*5	ENST00000269305	NM_001126112.2	266	-/A	8/11	0.807356649922686	2	FACETS	0.959	0.942	0.976	0.959	0.942	0.976	CLONAL	2	TRUE	0	0.807356649922686	2		551	1365	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134584	2134586	+	frameshift_variant	Frame_Shift_Del	DEL	GTG	GTG	A	novel	NA	P-0010701-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	478	499	0	ENST00000219476.3:c.4361_4363delinsA	p.Ser1454LysfsTer69	p.S1454Kfs*69	ENST00000219476	NM_000548.3	1454	aGTGgc/aAgc	34/42	0.807356649922686	1	FACETS	0.959	0.928	0.99	0.959	0.928	0.99	CLONAL	1	TRUE	0	0.807356649922686	1		499	736	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0010733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	49	228	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.841	0.71	0.985	0.841	0.71	0.985	CLONAL	1	TRUE	1	0.15	2		228	777	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101468	27101468	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	85	405	1	ENST00000324856.7:c.4750C>T	p.Gln1584Ter	p.Q1584*	ENST00000324856	NM_006015.4	1584	Cag/Tag	18/20	1	2	FACETS	0.975	0.859	1	0.975	0.859	1	CLONAL	1	TRUE	1	0.15	2		406	1162	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	63	273	0	ENST00000394830.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000394830	NM_018313.4	710	Cga/Tga	17/30	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.15	2		273	826	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0010851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	113	270	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.312008316062113	2		270	691	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431635	6431635	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010851-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	137	192	0	ENST00000356142.4:c.188A>G	p.Asp63Gly	p.D63G	ENST00000356142	NM_018890.3	63	gAt/gGt	3/7	0.312008316062113	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.312008316062113	3		192	453	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0011032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	68	228	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.238018245792843	1	FACETS	0.643	0.564	0.727	0.643	0.564	0.727	INDETERMINATE	1	FALSE	0	0.501464598391259	1		228	316	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112379	115112379	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758811184	NA	P-0011032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	106	200	0	ENST00000257566.3:c.1361G>A	p.Arg454His	p.R454H	ENST00000257566	NM_016569.3	454	cGc/cAc	7/8	NA	2	FACETS	1	0.92	1			1	INDETERMINATE	1	FALSE	NA	0.501464598391259	2		200	414	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106228	27106244	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAGCCACCGGAACAT	CAGAGCCACCGGAACAT	-	novel	NA	P-0011032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	190	395	1	ENST00000324856.7:c.5841_5857del	p.Ser1948AspfsTer9	p.S1948Dfs*9	ENST00000324856	NM_006015.4	1947	CAGAGCCACCGGAACATc/c	20/20	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	FALSE	NA	0.501464598391259	2		396	700	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196879	108196880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs773570504	NA	P-0011032-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	64	413	0	ENST00000278616.4:c.6908dup	p.Glu2304GlyfsTer69	p.E2304Gfs*69	ENST00000278616	NM_000051.3	2301	gca/gcAa	47/63	0.315917151591028	0	FACETS	0.573	0.503	0.647			1	SUBCLONAL	1	FALSE	0	0.501464598391259	0		413	222	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0011140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	258	228	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.608674149664531	2		228	766	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71008411	71008411	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	377	589	0	ENST00000318789.4:c.2021A>T	p.Glu674Val	p.E674V	ENST00000318789	NM_032682.5	674	gAg/gTg	21/21	0.608674149664531	1	FACETS	0.992	0.946	1	0.992	0.946	1	CLONAL	1	TRUE	0	0.608674149664531	1		589	869	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157256661	157256661	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1277043745	NA	P-0011140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	382	399	0	ENST00000346085.5:c.1988A>G	p.Asn663Ser	p.N663S	ENST00000346085	NM_020732.3	663	aAc/aGc	5/20	0.608674149664531	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.608674149664531	1		399	752	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668635	52668636	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0011140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	348	424	0	ENST00000394830.3:c.1283dup	p.Ser429IlefsTer15	p.S429Ifs*15	ENST00000394830	NM_018313.4	428	ata/atTa	12/30	0.608674149664531	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.608674149664531	1		424	716	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0011191-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	54	868	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.911	1	1	0.978	1	CLONAL	2	TRUE	1	0.13	2		869	382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0011191-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	36	656	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	1	2	FACETS	0.83	0.681	0.999	0.83	0.681	0.999	CLONAL	1	TRUE	1	0.13	2		656	667	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971094	21971102	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCCGGGC	CTCCCGGGC	A	novel	NA	P-0011191-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	34	519	0	ENST00000304494.5:c.256_264delinsT	p.Ala86TrpfsTer31	p.A86Wfs*31	ENST00000304494	NM_000077.4	86	GCCCGGGAG/T	2/3	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.13	2		519	470	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422611	49422611	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011191-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	55	545	0	ENST00000301067.7:c.14382G>C	p.Lys4794Asn	p.K4794N	ENST00000301067	NM_003482.3	4794	aaG/aaC	45/54	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.13	2		545	568	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681049	30681049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	77	209	0	ENST00000376406.3:c.670G>A	p.Glu224Lys	p.E224K	ENST00000376406	NM_014641.2	224	Gaa/Aaa	5/15	0.194838467902933	3	FACETS	0.936	0.823	1	0.468	0.411	0.529	INDETERMINATE	1	TRUE	1	0.350152418006865	3		209	552	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936768	78936768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs987417975	NA	P-0011194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	117	442	0	ENST00000306801.3:c.3850G>A	p.Gly1284Arg	p.G1284R	ENST00000306801	NM_020761.2	1284	Gga/Aga	33/34	0.298035944098417	1	FACETS	0.899	0.813	0.99	0.899	0.813	0.99	CLONAL	1	TRUE	0	0.350152418006865	1		442	613	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131926976	131926976	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs193921012	NA	P-0011194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	121	293	0	ENST00000265335.6:c.1513A>G	p.Ile505Val	p.I505V	ENST00000265335		505	Ata/Gta	10/25	1	2	FACETS	0.957	0.866	1	0.957	0.866	1	CLONAL	1	TRUE	1	0.350152418006865	2		293	722	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494227	140494227	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	109	505	0	ENST00000288602.6:c.1021C>A	p.Pro341Thr	p.P341T	ENST00000288602	NM_004333.4	341	Cca/Aca	8/18	1	2	FACETS	0.699	0.627	0.775	0.699	0.627	0.775	SUBCLONAL	1	TRUE	1	0.350152418006865	2		505	891	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196125	108196125	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	82	282	0	ENST00000278616.4:c.6661G>A	p.Glu2221Lys	p.E2221K	ENST00000278616	NM_000051.3	2221	Gag/Aag	46/63	0.225624731538539	1	FACETS	0.627	0.553	0.706	0.627	0.553	0.706	SUBCLONAL	1	TRUE	0	0.350152418006865	1		282	616	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0011223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	137	527	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.215412683132505	2		527	946	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261023	16261023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373713516	NA	P-0011223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	69	408	0	ENST00000375759.3:c.8288C>T	p.Ala2763Val	p.A2763V	ENST00000375759	NM_015001.2	2763	gCa/gTa	11/15	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.215412683132505	2		408	548	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018179	48018179	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	98	545	0	ENST00000234420.5:c.374A>G	p.Lys125Arg	p.K125R	ENST00000234420	NM_000179.2	125	aAa/aGa	2/10	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.215412683132505	2		545	884	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103903	209103903	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	88	467	0	ENST00000345146.2:c.1046A>G	p.Asn349Ser	p.N349S	ENST00000345146	NM_005896.2	349	aAt/aGt	9/10	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.215412683132505	2		467	772	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056145	26056145	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	88	449	0	ENST00000343677.2:c.512C>G	p.Ala171Gly	p.A171G	ENST00000343677	NM_005319.3	171	gCt/gGt	1/1	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.215412683132505	2		449	777	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709079	117709079	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	123	632	1	ENST00000368508.3:c.1878C>A	p.Phe626Leu	p.F626L	ENST00000368508	NM_002944.2	626	ttC/ttA	13/43	0.215412683132505	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.215412683132505	1		633	966	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355269	81355269	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	103	637	0	ENST00000222390.5:c.1105G>T	p.Asp369Tyr	p.D369Y	ENST00000222390	NM_000601.4	369	Gat/Tat	9/18	1	2	FACETS	0.954	0.852	1	0.954	0.852	1	CLONAL	1	TRUE	1	0.215412683132505	2		637	1002	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588124	69588124	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	216	749	1	ENST00000168712.1:c.574C>T	p.Arg192Ter	p.R192*	ENST00000168712	NM_002007.2	192	Cga/Tga	3/3	0.211859210083956	2	FACETS	0.873	0.81	0.937	0.873	0.81	0.937	CLONAL	2	TRUE	0	0.215412683132505	2		750	1149	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877391	40877391	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	96	457	0	ENST00000373198.4:c.2305G>T	p.Val769Leu	p.V769L	ENST00000373198	NM_133170.3	769	Gtg/Ttg	15/32	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.215412683132505	2		457	684	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608301	100608301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868967798	NA	P-0011223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	70	718	1	ENST00000308731.7:c.1789C>T	p.Pro597Ser	p.P597S	ENST00000308731	NM_000061.2	597	Cca/Tca	18/19	0.166114772689934	0	FACETS	0.487	0.423	0.556			1	SUBCLONAL	1	TRUE	0	0.215412683132505	0		719	1048	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579449	7579470	+	frameshift_variant	Frame_Shift_Del	DEL	GAGCTGCTGGTGCAGGGGCCAC	GAGCTGCTGGTGCAGGGGCCAC	-	novel	NA	P-0011223-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	100	533	0	ENST00000269305.4:c.217_238del	p.Val73LeufsTer43	p.V73Lfs*43	ENST00000269305	NM_001126112.2	73	GTGGCCCCTGCACCAGCAGCTCct/ct	4/11	0.17998317512	2	FACETS	1	0.981	1	0.737	0.659	0.819	CLONAL	1	TRUE	0	0.215412683132505	2		533	630	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	140	667	0	ENST00000269305.4:c.811G>T	p.Glu271Ter	p.E271*	ENST00000269305	NM_001126112.2	271	Gag/Tag	8/11	0.20638128436706	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.20638128436706	1		667	1170	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464463	25464463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758490363	NA	P-0011240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	113	565	0	ENST00000264709.3:c.2050G>A	p.Val684Ile	p.V684I	ENST00000264709	NM_175629.2	684	Gtc/Atc	17/23	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.20638128436706	2		565	958	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502477	186502477	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	111	504	0	ENST00000323963.5:c.200G>T	p.Cys67Phe	p.C67F	ENST00000323963		67	tGt/tTt	3/11	1	2	FACETS	0.924	0.829	1	0.924	0.829	1	CLONAL	1	TRUE	1	0.20638128436706	2		504	1164	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55270253	55270253	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	149	533	0	ENST00000275493.2:c.3206A>G	p.Tyr1069Cys	p.Y1069C	ENST00000275493	NM_005228.3	1069	tAc/tGc	27/28	0.140461156563731	3	FACETS	1	0.986	1	0.709	0.647	0.775	CLONAL	1	TRUE	1	0.20638128436706	3		533	1123	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430346	47430346	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	62	453	0	ENST00000377045.4:c.1621G>A	p.Ala541Thr	p.A541T	ENST00000377045	NM_001654.4	541	Gcc/Acc	15/16	1	1	FACETS	0.798	0.689	0.917	0.798	0.689	0.917	CLONAL	1	TRUE	0	0.20638128436706	1		453	675	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579525	7579529	+	frameshift_variant	Frame_Shift_Del	DEL	GAACC	GAACC	-	novel	NA	P-0011329-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	289	389	0	ENST00000269305.4:c.158_162del	p.Trp53TyrfsTer2	p.W53Yfs*2	ENST00000269305	NM_001126112.2	53	tGGTTC/t	4/11	0.624129144936455	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.624931862574353	1		389	586	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989508	212989508	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	132	311	0	ENST00000342788.4:c.203T>A	p.Ile68Asn	p.I68N	ENST00000342788	NM_005235.2	68	aTt/aAt	2/28	0.3	1	FACETS	0.768	0.696	0.845	0.768	0.696	0.845	SUBCLONAL	1	TRUE	0	0.27	1		311	1101	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575572	64575572	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1064793672	NA	P-0011394-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	66	228	0	ENST00000312049.6:c.446-1G>A		p.X149_splice	ENST00000312049	NM_130799.2	149			1	2	FACETS	0.643	0.557	0.737	0.643	0.557	0.737	SUBCLONAL	1	TRUE	1	0.27	2		228	760	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	713	584	0	ENST00000206249.3:c.1610A>G	p.Tyr537Cys	p.Y537C	ENST00000206249	NM_000125.3	537	tAt/tGt	8/8	0.854570223504571	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.856424415836453	2		584	829	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115700	8115714	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGATTAACAGACCCC	AGATTAACAGACCCC	G	novel	NA	P-0011415-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	328	305	0	ENST00000346208.3:c.1048-2_1060delinsG		p.X350_splice	ENST00000346208		350		6/6	0.856424415836453	3	FACETS	0.946	0.905	0.987	0.946	0.905	0.987	CLONAL	2	TRUE	1	0.856424415836453	3		305	578	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425329	49425329	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011516-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	85	530	0	ENST00000301067.7:c.13159C>T	p.Gln4387Ter	p.Q4387*	ENST00000301067	NM_003482.3	4387	Cag/Tag	39/54	1	2	FACETS	0.302	0.266	0.341	0.302	0.266	0.341	SUBCLONAL	1	TRUE	1	0.540085105505742	2		530	1041	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339254	70339254	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469672	NA	P-0011516-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	55	622	0	ENST00000374080.3:c.131G>A	p.Gly44Asp	p.G44D	ENST00000374080		44	gGt/gAt	2/45	0.376633583428827	1	FACETS	0.123	0.105	0.144	0.123	0.105	0.144	SUBCLONAL	1	TRUE	0	0.540085105505742	1		622	1205	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267290	41267290	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011516-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	181	421	0	ENST00000349496.5:c.874A>G	p.Lys292Glu	p.K292E	ENST00000349496	NM_001904.3	292	Aaa/Gaa	6/15	1	2	FACETS	0.662	0.61	0.716	0.662	0.61	0.716	SUBCLONAL	1	TRUE	1	0.540085105505742	2		421	1013	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176118152	176118152	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011516-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	126	337	0	ENST00000367669.3:c.821A>T	p.Asn274Ile	p.N274I	ENST00000367669	NM_022457.5	274	aAt/aTt	6/20	0.440984540437854	5	FACETS	0.903	0.817	0.994	0.226	0.204	0.249	CLONAL	1	TRUE	1	0.540085105505742	5		337	935	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165924	47165924	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011516-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	334	500	1	ENST00000409792.3:c.202C>T	p.Gln68Ter	p.Q68*	ENST00000409792	NM_014159.6	68	Cag/Tag	3/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.540085105505742	2		501	1202	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937121	39937121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778129253	NA	P-0011516-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	54	529	1	ENST00000378444.4:c.62G>A	p.Arg21His	p.R21H	ENST00000378444	NM_001123385.1	21	cGc/cAc	2/15	0.376633583428827	1	FACETS	0.136	0.115	0.158	0.136	0.115	0.158	SUBCLONAL	1	TRUE	0	0.540085105505742	1		530	1077	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0011566-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	279	228	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.605323031394292	2	FACETS	0.96	0.916	1	0.96	0.916	1	CLONAL	2	TRUE	0	0.605323031394292	2		228	480	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434595	NA	P-0011566-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	222	579	1	ENST00000369535.4:c.37G>A	p.Gly13Ser	p.G13S	ENST00000369535	NM_002524.4	13	Ggt/Agt	2/7	1	2	FACETS	0.859	0.801	0.919	0.859	0.801	0.919	CLONAL	1	TRUE	1	0.605323031394292	2		580	854	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023205	27023221	+	frameshift_variant	Frame_Shift_Del	DEL	ACGGGAACGCGGGCCCT	ACGGGAACGCGGGCCCT	-	novel	NA	P-0011566-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	100	213	0	ENST00000324856.7:c.312_328del	p.Asn104LysfsTer7	p.N104Kfs*7	ENST00000324856	NM_006015.4	104	aACGGGAACGCGGGCCCT/a	1/20	0.533793173961427	1	FACETS	0.841	0.763	0.921	0.841	0.763	0.921	CLONAL	1	TRUE	0	0.605323031394292	1		213	274	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17349200	17349200	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011566-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	213	543	1	ENST00000375499.3:c.668G>T	p.Arg223Ile	p.R223I	ENST00000375499	NM_003000.2	223	aGa/aTa	7/8	0.533793173961427	1	FACETS	0.862	0.807	0.918	0.862	0.807	0.918	CLONAL	1	TRUE	0	0.605323031394292	1		544	569	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28631574	28631574	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011566-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	222	561	0	ENST00000241453.7:c.394A>C	p.Lys132Gln	p.K132Q	ENST00000241453	NM_004119.2	132	Aaa/Caa	4/24	1	2	FACETS	0.991	0.926	1	0.991	0.926	1	CLONAL	1	TRUE	1	0.605323031394292	2		561	740	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0012003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	890	483	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	0.442532974067454	4	FACETS	1	0.983	1	1	0.998	1	CLONAL	4	TRUE	2	0.518646207630994	4		483	1294	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363313	40363313	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	158	362	0	ENST00000397332.2:c.916G>T	p.Asp306Tyr	p.D306Y	ENST00000397332	NM_001033082.2	306	Gat/Tat	3/3	0.486761130975888	5	FACETS	0.996	0.911	1	0.332	0.303	0.362	CLONAL	1	TRUE	2	0.518646207630994	5		362	1088	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52621370	52621370	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	684	505	0	ENST00000394830.3:c.3047A>G	p.Lys1016Arg	p.K1016R	ENST00000394830	NM_018313.4	1016	aAg/aGg	20/30	0.518646207630994	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.518646207630994	3		505	1089	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224569	224569	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	607	445	0	ENST00000264932.6:c.245A>G	p.Glu82Gly	p.E82G	ENST00000264932	NM_004168.2	82	gAg/gGg	3/15	0.486761130975888	5	FACETS	0.928	0.893	0.963	0.928	0.893	0.963	CLONAL	3	TRUE	2	0.518646207630994	5		445	1495	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0012101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	22	496	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.837	0.651	1	0.837	0.651	1	CLONAL	1	TRUE	1	0.22	2		496	239	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520017	NA	P-0012101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	79	468	0	ENST00000326873.7:c.647C>T	p.Ser216Phe	p.S216F	ENST00000326873	NM_000455.4	216	tCc/tTc	5/10	0.237971543460616	4	FACETS	0.907	0.8	1			1	CLONAL	2	TRUE	NA	0.22	4		468	483	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257770	16257770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779103344	NA	P-0012101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	18	247	0	ENST00000375759.3:c.5035G>A	p.Val1679Ile	p.V1679I	ENST00000375759	NM_015001.2	1679	Gtc/Atc	11/15	0.237971543460616	4	FACETS	0.585	0.44	0.758			1	SUBCLONAL	1	TRUE	NA	0.22	4		247	341	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668826	52668826	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147499494	NA	P-0012101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	20	265	0	ENST00000394830.3:c.1093C>T	p.Arg365Cys	p.R365C	ENST00000394830	NM_018313.4	365	Cgc/Tgc	12/30	NA	2	FACETS	0.532	0.406	0.679			1	INDETERMINATE	1	TRUE	NA	0.22	2		265	342	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446907	18446909	+	inframe_deletion	In_Frame_Del	DEL	ATC	ATC	-	novel	NA	P-0012101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	35	312	0	ENST00000266497.5:c.994_996del	p.His332del	p.H332del	ENST00000266497		331	gATCat/gat	4/31	0.233732346075881	5	FACETS	0.679	0.555	0.819	0.226	0.185	0.273	SUBCLONAL	1	TRUE	2	0.22	5		312	623	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374576	118374576	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012132-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	90	457	0	ENST00000534358.1:c.7969A>C	p.Lys2657Gln	p.K2657Q	ENST00000534358	NM_005933.3	2657	Aag/Cag	27/36	1	2	FACETS	0.818	0.734	0.905	0.818	0.734	0.905	CLONAL	1	TRUE	1	0.710119863757964	2		457	310	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245513	46245513	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs756545426	NA	P-0012132-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	95	368	0	ENST00000334344.6:c.3607A>G	p.Met1203Val	p.M1203V	ENST00000334344	NM_152641.2	1203	Atg/Gtg	15/21	1	2	FACETS	0.874	0.788	0.964	0.874	0.788	0.964	CLONAL	1	TRUE	1	0.710119863757964	2		368	306	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0012132-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	62	263	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	0.694754791761212	1	FACETS	0.887	0.792	0.982	0.887	0.792	0.982	CLONAL	1	TRUE	0	0.710119863757964	1		263	127	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148516743	148516743	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012132-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	79	432	0	ENST00000320356.2:c.944A>G	p.Asn315Ser	p.N315S	ENST00000320356	NM_004456.4	315	aAc/aGc	9/20	1	2	FACETS	0.803	0.715	0.896	0.803	0.715	0.896	CLONAL	1	TRUE	1	0.710119863757964	2		432	277	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121588	2121596	+	frameshift_variant	Frame_Shift_Ins	INS	GTTCAGCCC	GTTCAGCCC	ACTACATGTACGCA	novel	NA	P-0012132-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	249	1074	0	ENST00000219476.3:c.1917_1925delinsACTACATGTACGCA	p.Phe640LeufsTer60	p.F640Lfs*60	ENST00000219476	NM_000548.3	639	cgGTTCAGCCCc/cgACTACATGTACGCAc	18/42	1	2	FACETS	0.867	0.813	0.922	0.867	0.813	0.922	CLONAL	1	TRUE	1	0.710119863757964	2		1074	809	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11269466	11269466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012423-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	20	646	1	ENST00000361445.4:c.3704G>A	p.Arg1235Gln	p.R1235Q	ENST00000361445	NM_004958.3	1235	cGg/cAg	25/58	0.133104034101028	1	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	0	0.19	1		647	154	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248461	59248461	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012423-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	100	412	0	ENST00000371222.2:c.282del	p.Thr95ProfsTer9	p.T95Pfs*9	ENST00000371222	NM_002228.3	94	ccC/cc	1/1	0.133104034101028	1	FACETS	0.884	0.787	0.987	0.884	0.787	0.987	CLONAL	1	TRUE	0	0.19	1		412	1078	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990724	7990724	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775449310	NA	P-0012423-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	43	495	1	ENST00000319144.4:c.37G>A	p.Asp13Asn	p.D13N	ENST00000319144	NM_001139.2	13	Gac/Aac	1/15	0.133104034101028	3	FACETS	0.797	0.666	0.943	0.398	0.333	0.472	CLONAL	1	TRUE	1	0.19	3		496	622	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740544	58740545	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	rs773913732	NA	P-0012423-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	15	713	0	ENST00000305921.3:c.1450_1451del	p.Leu484LysfsTer4	p.L484Kfs*4	ENST00000305921	NM_003620.3	483	acTTta/acta	6/6	0.133104034101028	3	FACETS	1	0.778	1	0.534	0.392	0.702	CLONAL	1	TRUE	1	0.19	3		713	162	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61729409	61729409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749929742	NA	P-0012423-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	15	778	0	ENST00000401558.2:c.338C>T	p.Thr113Met	p.T113M	ENST00000401558	NM_003400.3	113	aCg/aTg	5/25	1	2	FACETS	0.782	0.573	1	0.782	0.573	1	CLONAL	1	TRUE	1	0.19	2		778	202	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023109	31023109	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012423-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	11	620	0	ENST00000375687.4:c.2594A>G	p.Glu865Gly	p.E865G	ENST00000375687	NM_015338.5	865	gAa/gGa	13/13	1	2	FACETS	0.698	0.483	0.963	0.698	0.483	0.963	SUBCLONAL	1	TRUE	1	0.19	2		620	166	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513329	41513330	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0012423-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	15	629	0	ENST00000263253.7:c.234_235del	p.His78GlnfsTer11	p.H78Qfs*11	ENST00000263253	NM_001429.3	78	cAT/c	2/31	1	2	FACETS	0.774	0.567	1	0.774	0.567	1	CLONAL	1	TRUE	1	0.19	2		629	204	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713544	30713546	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0012423-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	22	468	0	ENST00000295754.5:c.871_873del	p.Lys291del	p.K291del	ENST00000295754	NM_003242.5	290	gAGAag/gag	4/7	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.19	2		468	202	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157997	27157997	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012423-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	17	754	0	ENST00000380036.4:c.221T>C	p.Val74Ala	p.V74A	ENST00000380036	NM_000459.3	74	gTt/gCt	2/23	1	2	FACETS	0.84	0.629	1	0.84	0.629	1	CLONAL	1	TRUE	1	0.19	2		754	213	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0012538-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	79	228	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.230671385776535	2		228	676	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023482	27023483	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0012538-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	115	721	0	ENST00000324856.7:c.590_591del	p.Gly197AlafsTer202	p.G197Afs*202	ENST00000324856	NM_006015.4	196	gcGGgg/gcgg	1/20	0.230671385776535	1	FACETS	0.926	0.833	1	0.926	0.833	1	CLONAL	1	TRUE	0	0.230671385776535	1		721	953	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	28	384	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.834	0.667	1	0.834	0.667	1	CLONAL	1	TRUE	1	0.185033924607753	2		384	363	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0012553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	155	549	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	0.185033924607753	3	FACETS	0.897	0.82	0.978	0.897	0.82	0.978	CLONAL	2	TRUE	1	0.185033924607753	3		549	1020	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146653	185146653	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs547600832	NA	P-0012553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	71	409	0	ENST00000265026.3:c.284C>T	p.Thr95Met	p.T95M	ENST00000265026	NM_004721.4	95	aCg/aTg	2/14	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.185033924607753	2		409	605	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557362	187557362	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1223493108	NA	P-0012553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	39	446	0	ENST00000441802.2:c.4000C>T	p.Gln1334Ter	p.Q1334*	ENST00000441802	NM_005245.3	1334	Caa/Taa	6/27	1	2	FACETS	0.746	0.617	0.89	0.746	0.617	0.89	SUBCLONAL	1	TRUE	1	0.185033924607753	2		446	565	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878963	117878963	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	89	644	0	ENST00000297338.2:c.6C>G	p.Phe2Leu	p.F2L	ENST00000297338	NM_006265.2	2	ttC/ttG	2/14	1	2	FACETS	0.869	0.768	0.977	0.869	0.768	0.977	CLONAL	1	TRUE	1	0.185033924607753	2		644	1107	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433575	49433575	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	81	816	0	ENST00000301067.7:c.7978G>T	p.Glu2660Ter	p.E2660*	ENST00000301067	NM_003482.3	2660	Gaa/Taa	31/54	1	2	FACETS	0.949	0.834	1	0.949	0.834	1	CLONAL	1	TRUE	1	0.185033924607753	2		816	923	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488222	56488222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	59	572	2	ENST00000267101.3:c.1741G>A	p.Asp581Asn	p.D581N	ENST00000267101	NM_001982.3	581	Gat/Aat	15/28	1	2	FACETS	0.958	0.823	1	0.958	0.823	1	CLONAL	1	TRUE	1	0.185033924607753	2		574	666	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044711	47044711	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	78	383	0	ENST00000377604.3:c.2112del	p.Glu705ArgfsTer97	p.E705Rfs*97	ENST00000377604	NM_001204468.1	704	gCc/gc	19/24	1	1	FACETS	0.823	0.725	0.926	1	0.98	1	CLONAL	2	TRUE	0	0.185033924607753	1		383	465	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0012606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	232	567	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.247314387764398	2	FACETS	0.894	0.834	0.957	0.894	0.834	0.957	CLONAL	2	TRUE	0	0.247314387764398	2		568	1049	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437606	56437606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886926322	NA	P-0012606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	104	348	2	ENST00000407977.2:c.856C>T	p.Arg286Trp	p.R286W	ENST00000407977		286	Cgg/Tgg	8/10	0.247314387764398	3	FACETS	1	0.956	1	0.565	0.506	0.629	CLONAL	1	TRUE	1	0.247314387764398	3		350	836	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579406	7579406	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0012606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	178	378	0	ENST00000269305.4:c.281C>G	p.Ser94Ter	p.S94*	ENST00000269305	NM_001126112.2	94	tCa/tGa	4/11	0.247314387764398	2	FACETS	0.918	0.848	0.991	0.918	0.848	0.991	CLONAL	2	TRUE	0	0.247314387764398	2		378	784	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509514	149509514	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	105	286	0	ENST00000261799.4:c.1385C>G	p.Pro462Arg	p.P462R	ENST00000261799	NM_002609.3	462	cCg/cGg	10/23	0.247314387764398	3	FACETS	1	0.946	1	0.545	0.487	0.606	CLONAL	1	TRUE	1	0.247314387764398	3		286	876	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344629	118344629	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782424852	NA	P-0012606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1311	158	564	1	ENST00000534358.1:c.2755G>A	p.Glu919Lys	p.E919K	ENST00000534358	NM_005933.3	919	Gaa/Aaa	3/36	0.247314387764398	3	FACETS	0.977	0.893	1	0.489	0.446	0.534	CLONAL	1	TRUE	1	0.247314387764398	3		565	1469	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645327	67645327	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	143	379	0	ENST00000264010.4:c.592C>T	p.Gln198Ter	p.Q198*	ENST00000264010	NM_006565.3	198	Cag/Tag	3/12	0.247314387764398	3	FACETS	1	0.969	1	0.571	0.52	0.626	CLONAL	1	TRUE	1	0.247314387764398	3		379	1137	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948818	17948818	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1287	171	514	0	ENST00000458235.1:c.1624G>C	p.Glu542Gln	p.E542Q	ENST00000458235	NM_000215.3	542	Gag/Cag	12/24	0.247314387764398	3	FACETS	1	0.956	1	0.533	0.488	0.58	CLONAL	1	TRUE	1	0.247314387764398	3		514	1458	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435933	56435934	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0012606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	149	287	0	ENST00000407977.2:c.1202_1203dup	p.Gln402SerfsTer18	p.Q402Sfs*18	ENST00000407977		401	-/AG	9/10	0.247314387764398	3	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	1	0.247314387764398	3		287	662	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974765	21974788	+	inframe_deletion	In_Frame_Del	DEL	GCCGCGGCCGTGGCCAGCCAGTCA	GCCGCGGCCGTGGCCAGCCAGTCA	-	novel	NA	P-0012606-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	147	242	0	ENST00000304494.5:c.39_62del	p.Asp14_Ala21del	p.D14_A21del	ENST00000304494	NM_000077.4	13	gcTGACTGGCTGGCCACGGCCGCGGCc/gcc	1/3	0.247314387764398	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	0	0.247314387764398	2		242	561	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441242	52441243	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012626-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	167	500	0	ENST00000460680.1:c.527dup	p.Thr177HisfsTer6	p.T177Hfs*6	ENST00000460680	NM_004656.3	176	atc/atTc	7/17	0.3	1	FACETS	0.841	0.772	0.914	0.841	0.772	0.914	CLONAL	1	TRUE	0	0.3	1		500	1125	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577130	7577130	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519988	NA	P-0012630-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	254	710	0	ENST00000269305.4:c.808T>C	p.Phe270Leu	p.F270L	ENST00000269305	NM_001126112.2	270	Ttt/Ctt	8/11	0.28506874995063	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.298471923698734	2		710	809	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354369	354369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012630-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	136	806	0	ENST00000262320.3:c.1189G>A	p.Glu397Lys	p.E397K	ENST00000262320	NM_003502.3	397	Gag/Aag	5/11	0.298471923698734	3	FACETS	1	0.943	1	0.526	0.477	0.577	CLONAL	1	TRUE	1	0.298471923698734	3		806	996	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0012639-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	54	228	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.567940745464746	3	FACETS	1	0.928	1	0.557	0.482	0.638	CLONAL	1	TRUE	1	0.567940745464746	3		228	219	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366650	40366650	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012639-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	15	534	0	ENST00000397332.2:c.547A>C	p.Thr183Pro	p.T183P	ENST00000397332	NM_001033082.2	183	Acc/Ccc	2/3	1	2	FACETS	0.307	0.225	0.405	0.307	0.225	0.405	SUBCLONAL	1	TRUE	1	0.567940745464746	2		534	172	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436827	52436827	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0012639-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	87	756	1	ENST00000460680.1:c.1951A>T	p.Lys651Ter	p.K651*	ENST00000460680	NM_004656.3	651	Aag/Tag	15/17	0.567940745464746	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.567940745464746	1		757	206	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339555	339555	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012639-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	42	744	0	ENST00000262320.3:c.2347A>G	p.Ile783Val	p.I783V	ENST00000262320	NM_003502.3	783	Atc/Gtc	10/11	1	2	FACETS	0.787	0.665	0.918	0.787	0.665	0.918	CLONAL	1	TRUE	1	0.567940745464746	2		744	188	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160433	108160433	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012639-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	21	444	1	ENST00000278616.4:c.4343del	p.Leu1448TyrfsTer3	p.L1448Yfs*3	ENST00000278616	NM_000051.3	1447	agT/ag	29/63	0.567940745464746	1	FACETS	0.84	0.671	1	0.84	0.671	1	CLONAL	1	TRUE	0	0.567940745464746	1		445	63	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30648403	30648403	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012644-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	121	449	0	ENST00000295754.5:c.28T>G	p.Trp10Gly	p.W10G	ENST00000295754	NM_003242.5	10	Tgg/Ggg	1/7	0.37602263839842	1	FACETS	0.754	0.682	0.83	0.754	0.682	0.83	SUBCLONAL	1	TRUE	0	0.37602263839842	1		449	693	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964336	55964336	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012644-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	199	717	2	ENST00000263923.4:c.2477A>G	p.Lys826Arg	p.K826R	ENST00000263923	NM_002253.2	826	aAa/aGa	17/30	1	2	FACETS	0.91	0.842	0.981	0.91	0.842	0.981	CLONAL	1	TRUE	1	0.37602263839842	2		719	1163	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878685	151878685	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012644-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	133	376	2	ENST00000262189.6:c.6260A>T	p.His2087Leu	p.H2087L	ENST00000262189	NM_170606.2	2087	cAt/cTt	36/59	0.36803626154716	3	FACETS	1	0.942	1	0.525	0.476	0.575	CLONAL	1	TRUE	1	0.37602263839842	3		378	801	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39661101	39661101	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	novel	NA	P-0012644-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	166	482	0	ENST00000262039.4:c.2664A>G	p.Ter888TrpextTer4	p.*888Wext*4	ENST00000262039	NM_002647.2	888	tgA/tgG	25/25	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.37602263839842	2		482	843	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441976	52441976	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	228	432	2	ENST00000460680.1:c.373G>T	p.Glu125Ter	p.E125*	ENST00000460680	NM_004656.3	125	Gag/Tag	5/17	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	2	TRUE	NA	0.356209178727946	2		434	615	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564102	139564102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	56	569	1	ENST00000308874.7:c.242C>T	p.Pro81Leu	p.P81L	ENST00000308874		81	cCt/cTt	5/10	0.356209178727946	3	FACETS	0.347	0.295	0.403	0.173	0.147	0.202	SUBCLONAL	1	TRUE	1	0.356209178727946	3		570	1069	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235872	108235872	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012666-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	192	498	0	ENST00000278616.4:c.8914C>T	p.Gln2972Ter	p.Q2972*	ENST00000278616	NM_000051.3	2972	Cag/Tag	62/63	0.198581878627561	4	FACETS	0.849	0.786	0.914	0.849	0.786	0.914	INDETERMINATE	2	TRUE	2	0.356209178727946	4		498	861	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0012867-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	295	324	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.525811751371854	2		324	1045	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11194514	11194514	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012867-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	282	496	0	ENST00000361445.4:c.5140T>G	p.Phe1714Val	p.F1714V	ENST00000361445	NM_004958.3	1714	Ttc/Gtc	37/58	0.525811751371854	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.525811751371854	1		496	766	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181605	32181605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012867-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	307	660	0	ENST00000375023.3:c.2180G>A	p.Ser727Asn	p.S727N	ENST00000375023	NM_004557.3	727	aGt/aAt	14/30	1	2	FACETS	0.981	0.925	1	0.981	0.925	1	CLONAL	1	TRUE	1	0.525811751371854	2		660	1190	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982016	93982016	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012867-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	113	544	0	ENST00000369303.4:c.1449A>C	p.Lys483Asn	p.K483N	ENST00000369303	NM_004440.3	483	aaA/aaC	6/17	1	2	FACETS	0.356	0.319	0.396	0.356	0.319	0.396	SUBCLONAL	1	TRUE	1	0.525811751371854	2		544	1206	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120657	115120657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012867-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	419	886	0	ENST00000257566.3:c.349C>T	p.His117Tyr	p.H117Y	ENST00000257566	NM_016569.3	117	Cac/Tac	1/8	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.525811751371854	2		886	1563	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53254060	53254060	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012867-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	306	313	0	ENST00000375401.3:c.12del	p.Ser5ProfsTer68	p.S5Pfs*68	ENST00000375401	NM_004187.3	4	ggG/gg	1/26	1	1	FACETS	0.758	0.723	0.793	1	0.995	1	SUBCLONAL	2	TRUE	0	0.525811751371854	1		313	566	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0012895-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	60	344	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.853	0.739	0.974	0.853	0.739	0.974	CLONAL	1	TRUE	1	0.439844284452345	2		344	320	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061208	38061208	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012895-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	91	393	1	ENST00000250448.2:c.781C>A	p.Arg261Ser	p.R261S	ENST00000250448	NM_004496.3	261	Cgc/Agc	2/2	1	2	FACETS	0.716	0.637	0.8	0.716	0.637	0.8	SUBCLONAL	1	TRUE	1	0.439844284452345	2		394	578	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911445	134911445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs571583026	NA	P-0012895-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	49	422	0	ENST00000398015.3:c.1910G>A	p.Arg637His	p.R637H	ENST00000398015	NM_004441.4	637	cGt/cAt	11/16	1	2	FACETS	0.392	0.331	0.458	0.392	0.331	0.458	SUBCLONAL	1	TRUE	1	0.439844284452345	2		422	569	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867235	68867236	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012895-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	106	462	0	ENST00000261769.5:c.2483dup	p.Asp828GlufsTer7	p.D828Efs*7	ENST00000261769	NM_004360.3	828	gat/gAat	16/16	0.439844284452345	1	FACETS	0.817	0.737	0.902	0.817	0.737	0.902	CLONAL	1	TRUE	0	0.439844284452345	1		462	460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0013152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	172	632	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.503112795119011	1	FACETS	0.984	0.912	1	0.984	0.912	1	CLONAL	1	TRUE	0	0.503112795119011	1		632	520	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	39	473	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.881	0.74	1	0.881	0.74	1	CLONAL	1	TRUE	1	0.503112795119011	2		473	176	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748146	72748146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	213	708	1	ENST00000357731.5:c.32G>A	p.Cys11Tyr	p.C11Y	ENST00000357731	NM_173808.2	11	tGt/tAt	1/7	0.258281148192873	1	FACETS	0.85	0.792	0.909	0.85	0.792	0.909	INDETERMINATE	1	TRUE	0	0.503112795119011	1		709	746	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591923	48591925	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs377767349	NA	P-0013152-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	52	571	0	ENST00000342988.3:c.1088_1090del	p.Cys363del	p.C363del	ENST00000342988	NM_005359.5	362	ttTTGt/ttt	9/12	0.496069811231198	1	FACETS	0.921	0.799	1	0.921	0.799	1	CLONAL	1	TRUE	0	0.503112795119011	1		571	168	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577571	7577571	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs765848205	NA	P-0013174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	29	449	0	ENST00000269305.4:c.710T>A	p.Met237Lys	p.M237K	ENST00000269305	NM_001126112.2	237	aTg/aAg	7/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		449	743	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111513	8111514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0013345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	367	591	0	ENST00000346208.3:c.1003dup	p.Asp335GlyfsTer17	p.D335Gfs*17	ENST00000346208		333	-/G	5/6	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.811860525684156	2		591	872	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878144	48878144	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	64	83	0	ENST00000267163.4:c.96C>A	p.Asp32Glu	p.D32E	ENST00000267163	NM_000321.2	32	gaC/gaA	1/27	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.811860525684156	2		83	135	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522461	187522461	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	138	406	0	ENST00000441802.2:c.11602G>T	p.Val3868Phe	p.V3868F	ENST00000441802	NM_005245.3	3868	Gtc/Ttc	21/27	0.430687627874778	1	FACETS	0.351	0.32	0.382	0.351	0.32	0.382	INDETERMINATE	1	TRUE	0	0.811860525684156	1		406	576	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874147	151874148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs747256476	NA	P-0013345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	174	404	5	ENST00000262189.6:c.8390dup	p.Glu2798GlyfsTer11	p.E2798Gfs*11	ENST00000262189	NM_170606.2	2797	aag/aaAg	38/59	0.811860525684156	2	FACETS	0.608	0.561	0.656	0.304	0.28	0.328	SUBCLONAL	1	TRUE	0	0.811860525684156	2		409	705	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289737	15289737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2769	235	834	0	ENST00000263388.2:c.3734C>T	p.Thr1245Ile	p.T1245I	ENST00000263388	NM_000435.2	1245	aCt/aTt	23/33	0.811860525684156	7	FACETS	0.584	0.541	0.628			1	SUBCLONAL	1	TRUE	NA	0.811860525684156	7		834	3004	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687142	37687142	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1326824402	NA	P-0013405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	357	592	0	ENST00000447079.4:c.4046G>A	p.Ser1349Asn	p.S1349N	ENST00000447079	NM_015083.1	1349	aGt/aAt	14/14	1	2	FACETS	0.947	0.898	0.998	0.947	0.898	0.998	CLONAL	1	TRUE	1	0.633785154066106	2		592	1189	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441991	52441993	+	inframe_deletion	In_Frame_Del	DEL	TGG	TGG	-	novel	NA	P-0013405-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	264	521	2	ENST00000460680.1:c.356_358del	p.Thr119del	p.T119del	ENST00000460680	NM_004656.3	119	aCCAag/aag	5/17	0.633785154066106	1	FACETS	0.884	0.834	0.934	0.884	0.834	0.934	CLONAL	1	TRUE	0	0.633785154066106	1		523	644	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0013713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	53	496	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.417924908813888	1	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	0	0.417924908813888	1		496	199	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0013713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	1826	747	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.417924908813888	21	FACETS	0.999	0.988	1			1	CLONAL	20	TRUE	NA	0.417924908813888	21		747	2173	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46215271	46215271	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0013713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	77	326	0	ENST00000334344.6:c.705+1G>T		p.X235_splice	ENST00000334344	NM_152641.2	235			NA	2	FACETS	1	0.961	1			1	INDETERMINATE	1	TRUE	NA	0.417924908813888	2		326	308	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791695	42791695	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0013713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	39	346	0	ENST00000575354.2:c.583-2A>T		p.X195_splice	ENST00000575354	NM_015125.3	195			1	2	FACETS	0.567	0.472	0.673	0.567	0.472	0.673	SUBCLONAL	1	TRUE	1	0.417924908813888	2		346	329	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0013719-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	48	533	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.200659619857916	2		533	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0013719-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	24	675	1	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.169377856393959	3	FACETS	0.82	0.643	1	0.41	0.321	0.512	CLONAL	1	FALSE	1	0.200659619857916	3		676	321	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023648	31023648	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0013719-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	41	749	11	ENST00000375687.4:c.3133A>T	p.Lys1045Ter	p.K1045*	ENST00000375687	NM_015338.5	1045	Aag/Tag	13/13	0.169377856393959	3	FACETS	1	0.909	1	0.569	0.475	0.674	CLONAL	1	FALSE	1	0.200659619857916	3		760	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660754	NA	P-0013968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	176	722	1	ENST00000269305.4:c.517G>A	p.Val173Met	p.V173M	ENST00000269305	NM_001126112.2	173	Gtg/Atg	5/11	0.4813345127632	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.49	1		723	522	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259012	153259013	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0013968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	273	714	0	ENST00000281708.4:c.802_803del	p.Met268AspfsTer18	p.M268Dfs*18	ENST00000281708	NM_033632.3	268	ATg/g	5/12	1	2	FACETS	0.924	0.866	0.983	0.924	0.866	0.983	CLONAL	1	TRUE	1	0.49	2		714	1206	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0013968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	205	1006	6	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.917	0.852	0.986	0.917	0.852	0.986	CLONAL	1	TRUE	1	0.49	2		1012	912	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355283	81355283	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	332	761	0	ENST00000222390.5:c.1091G>T	p.Trp364Leu	p.W364L	ENST00000222390	NM_000601.4	364	tGg/tTg	9/18	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.49	2		761	1244	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149973	202149973	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1272714323	NA	P-0013968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	282	720	0	ENST00000358485.4:c.1414C>T	p.Arg472Ter	p.R472*	ENST00000358485	NM_001080125.1	472	Cga/Tga	8/9	0.4813345127632	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.49	1		720	846	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435549	56435549	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	250	712	0	ENST00000407977.2:c.1588C>T	p.Pro530Ser	p.P530S	ENST00000407977		530	Cct/Tct	9/10	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.49	2		712	1016	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259480	16259480	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	154	423	1	ENST00000375759.3:c.6750del	p.Ala2251GlnfsTer102	p.A2251Qfs*102	ENST00000375759	NM_015001.2	2249	Ccc/cc	11/15	1	2	FACETS	0.912	0.837	0.991	0.912	0.837	0.991	CLONAL	1	TRUE	1	0.49	2		424	689	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420184	49420184	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555185701	NA	P-0013968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	259	579	1	ENST00000301067.7:c.15565G>A	p.Gly5189Arg	p.G5189R	ENST00000301067	NM_003482.3	5189	Gga/Aga	48/54	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.49	2		580	992	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792016	42792016	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1199661448	NA	P-0013968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	465	700	0	ENST00000575354.2:c.820C>T	p.Arg274Ter	p.R274*	ENST00000575354	NM_015125.3	274	Cga/Tga	6/20	0.4813345127632	2	FACETS	0.944	0.906	0.983	0.944	0.906	0.983	CLONAL	2	TRUE	0	0.49	2		700	1005	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106731	27106732	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGAGACTGGTCT	novel	NA	P-0013968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	194	655	0	ENST00000324856.7:c.6343_6355dup	p.Leu2119SerfsTer35	p.L2119Sfs*35	ENST00000324856	NM_006015.4	2114	-/CAGAGACTGGTCT	20/20	0.4813345127632	1	FACETS	0.736	0.682	0.792	0.736	0.682	0.792	SUBCLONAL	1	TRUE	0	0.49	1		655	812	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998835	100998835	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	306	815	0	ENST00000325455.5:c.967C>A	p.Leu323Met	p.L323M	ENST00000325455	NM_001202474.3	323	Ctg/Atg	1/8	1	2	FACETS	0.97	0.914	1	0.97	0.914	1	CLONAL	1	TRUE	1	0.49	2		815	1287	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4385256	4385256	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1019910889	NA	P-0013968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	250	710	0	ENST00000261254.3:c.281C>T	p.Pro94Leu	p.P94L	ENST00000261254	NM_001759.3	94	cCg/cTg	2/5	1	2	FACETS	0.984	0.921	1	0.984	0.921	1	CLONAL	1	TRUE	1	0.49	2		710	1037	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478789	56478789	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	261	665	0	ENST00000267101.3:c.245A>T	p.Glu82Val	p.E82V	ENST00000267101	NM_001982.3	82	gAa/gTa	3/28	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.49	2		665	1050	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888294	112888294	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747300372	NA	P-0013968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	80	524	0	ENST00000351677.2:c.310T>C	p.Cys104Arg	p.C104R	ENST00000351677	NM_002834.3	104	Tgt/Cgt	3/16	1	2	FACETS	0.36	0.316	0.408	0.36	0.316	0.408	SUBCLONAL	1	TRUE	1	0.49	2		524	906	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221345	2221347	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0013968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	251	724	0	ENST00000326181.6:c.432_434del	p.Thr145del	p.T145del	ENST00000326181	NM_032271.2	143	atCACc/atc	6/21	1	2	FACETS	0.964	0.902	1	0.964	0.902	1	CLONAL	1	TRUE	1	0.49	2		724	1063	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778798	3778798	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	222	552	0	ENST00000262367.5:c.6250C>A	p.Gln2084Lys	p.Q2084K	ENST00000262367	NM_004380.2	2084	Cag/Aag	31/31	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.49	2		552	866	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347108	89347108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs907255990	NA	P-0013968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	285	857	0	ENST00000301030.4:c.5842G>A	p.Val1948Ile	p.V1948I	ENST00000301030	NM_001256183.1	1948	Gtt/Att	9/13	1	2	FACETS	0.974	0.915	1	0.974	0.915	1	CLONAL	1	TRUE	1	0.49	2		857	1194	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347432	89347432	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144003224	NA	P-0013968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	340	952	2	ENST00000301030.4:c.5518G>A	p.Ala1840Thr	p.A1840T	ENST00000301030	NM_001256183.1	1840	Gcg/Acg	9/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.49	2		954	1292	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291921	15291921	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	43	696	0	ENST00000263388.2:c.2845C>A	p.Leu949Met	p.L949M	ENST00000263388	NM_000435.2	949	Ctg/Atg	18/33	0.4813345127632	1	FACETS	0.169	0.14	0.2	0.169	0.14	0.2	SUBCLONAL	1	TRUE	0	0.49	1		696	785	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42384745	42384745	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	575	858	0	ENST00000221972.3:c.507G>A	p.Trp169Ter	p.W169*	ENST00000221972	NM_021601.3	169	tgG/tgA	4/5	0.4813345127632	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.49	2		858	1173	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432703	29432703	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	263	754	1	ENST00000389048.3:c.3785C>A	p.Pro1262His	p.P1262H	ENST00000389048	NM_004304.4	1262	cCt/cAt	25/29	0.4813345127632	1	FACETS	0.937	0.88	0.995	0.937	0.88	0.995	CLONAL	1	TRUE	0	0.49	1		755	865	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634713	158634713	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs781127308	NA	P-0013968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	344	1015	0	ENST00000263640.3:c.473A>G	p.Asn158Ser	p.N158S	ENST00000263640	NM_001105.4	158	aAt/aGt	5/11	0.4813345127632	1	FACETS	0.919	0.87	0.968	0.919	0.87	0.968	CLONAL	1	TRUE	0	0.49	1		1015	1154	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806572	1806572	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1268914552	NA	P-0013968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	193	564	0	ENST00000260795.2:c.1288T>C	p.Ser430Pro	p.S430P	ENST00000260795		430	Tcc/Ccc	9/17	1	2	FACETS	0.933	0.865	1	0.933	0.865	1	CLONAL	1	TRUE	1	0.49	2		564	844	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509954	187509954	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs993828603	NA	P-0013968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	253	649	1	ENST00000441802.2:c.13559C>T	p.Pro4520Leu	p.P4520L	ENST00000441802	NM_005245.3	4520	cCg/cTg	27/27	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.49	2		650	990	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187558038	187558039	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0013968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	201	441	0	ENST00000441802.2:c.3672dup	p.Lys1225GlnfsTer13	p.K1225Qfs*13	ENST00000441802	NM_005245.3	1224	-/C	5/27	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.49	2		441	810	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519505	137519508	+	frameshift_variant	Frame_Shift_Del	DEL	CTCT	CTCT	-	novel	NA	P-0013968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	206	599	0	ENST00000367739.4:c.1130_1133del	p.Glu377ValfsTer5	p.E377Vfs*5	ENST00000367739	NM_000416.2	377	gAGAGt/gt	7/7	1	2	FACETS	0.837	0.777	0.9	0.837	0.777	0.9	CLONAL	1	TRUE	1	0.49	2		599	1004	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845609	151845609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369745886	NA	P-0013968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	240	607	0	ENST00000262189.6:c.13403C>T	p.Thr4468Met	p.T4468M	ENST00000262189	NM_170606.2	4468	aCg/aTg	52/59	1	2	FACETS	0.973	0.909	1	0.973	0.909	1	CLONAL	1	TRUE	1	0.49	2		607	1007	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054856	5054857	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0013968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	248	545	0	ENST00000381652.3:c.909_910del	p.His303GlnfsTer4	p.H303Qfs*4	ENST00000381652	NM_004972.3	303	cAT/c	7/25	0.4813345127632	1	FACETS	0.912	0.855	0.97	0.912	0.855	0.97	CLONAL	1	TRUE	0	0.49	1		545	838	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393401	139393401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544856644	NA	P-0013968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	238	677	0	ENST00000277541.6:c.6130G>A	p.Ala2044Thr	p.A2044T	ENST00000277541	NM_017617.3	2044	Gca/Aca	33/34	1	2	FACETS	0.991	0.926	1	0.991	0.926	1	CLONAL	1	TRUE	1	0.49	2		677	980	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	253	496	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.594	0.556	0.634	0.594	0.556	0.634	SUBCLONAL	1	TRUE	1	0.778205047045648	2		496	1094	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	253	384	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.994	0.937	1	0.994	0.937	1	CLONAL	1	TRUE	1	0.778205047045648	2		384	654	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	139	262	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.925	0.852	1	0.925	0.852	1	CLONAL	1	TRUE	1	0.778205047045648	2		263	386	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702265	47702265	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750508	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	238	360	0	ENST00000233146.2:c.1861C>T	p.Arg621Ter	p.R621*	ENST00000233146	NM_000251.2	621	Cga/Tga	12/16	1	2	FACETS	0.793	0.743	0.845	0.793	0.743	0.845	SUBCLONAL	1	TRUE	1	0.778205047045648	2		360	771	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791372	42791373	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	86	1021	0	ENST00000575354.2:c.436_437del	p.Ser146Ter	p.S146*	ENST00000575354	NM_015125.3	144	acAGag/acag	3/20	0.778205047045648	1	FACETS	0.202	0.178	0.227	0.202	0.178	0.227	SUBCLONAL	1	TRUE	0	0.778205047045648	1		1021	670	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555525857	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	379	657	0	ENST00000269305.4:c.596G>A	p.Gly199Glu	p.G199E	ENST00000269305	NM_001126112.2	199	gGa/gAa	6/11	1	2	FACETS	0.904	0.86	0.949	0.904	0.86	0.949	CLONAL	1	TRUE	1	0.778205047045648	2		657	1077	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979563	7979563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1221632429	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	97	713	0	ENST00000319144.4:c.1462C>T	p.Arg488Cys	p.R488C	ENST00000319144	NM_001139.2	488	Cgt/Tgt	11/15	1	2	FACETS	0.241	0.214	0.27	0.241	0.214	0.27	SUBCLONAL	1	TRUE	1	0.778205047045648	2		713	1035	SUCCESS
ATM	472	MSKCC	GRCh37	11	108236203	108236203	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434219	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	548	412	0	ENST00000278616.4:c.9139C>T	p.Arg3047Ter	p.R3047*	ENST00000278616	NM_000051.3	3047	Cga/Tga	63/63	0.755714951171995	2	FACETS	0.936	0.911	0.961	0.936	0.911	0.961	CLONAL	2	TRUE	0	0.778205047045648	2		412	752	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266699	18266699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142933317	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	137	865	0	ENST00000222254.8:c.10C>T	p.Pro4Ser	p.P4S	ENST00000222254	NM_005027.3	4	Cct/Tct	2/16	1	2	FACETS	0.286	0.259	0.314	0.286	0.259	0.314	SUBCLONAL	1	TRUE	1	0.778205047045648	2		865	1232	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874637	35874637	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	29	278	1	ENST00000303115.3:c.799del	p.Arg267GlyfsTer28	p.R267Gfs*28	ENST00000303115	NM_002185.3	265	Aaa/aa	6/8	1	2	FACETS	0.152	0.121	0.187	0.152	0.121	0.187	SUBCLONAL	1	TRUE	1	0.778205047045648	2		279	490	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484287	8484287	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	75	302	0	ENST00000356435.5:c.3245C>T	p.Ser1082Leu	p.S1082L	ENST00000356435		1082	tCa/tTa	19/35	0.778205047045648	2	FACETS	0.265	0.232	0.301	0.133	0.116	0.151	SUBCLONAL	1	TRUE	0	0.778205047045648	2		302	726	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573321	55573321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	43	258	0	ENST00000288135.5:c.983G>A	p.Gly328Glu	p.G328E	ENST00000288135	NM_000222.2	328	gGa/gAa	6/21	1	2	FACETS	0.224	0.187	0.265	0.224	0.187	0.265	SUBCLONAL	1	TRUE	1	0.778205047045648	2		258	493	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272336	15272337	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs771517374	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1241	119	853	4	ENST00000263388.2:c.6102dup	p.Gly2035ArgfsTer60	p.G2035Rfs*60	ENST00000263388	NM_000435.2	2034	-/C	33/33	1	2	FACETS	0.225	0.202	0.249	0.225	0.202	0.249	SUBCLONAL	1	TRUE	1	0.778205047045648	2		857	1360	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430902	181430902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746642730	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1322	92	709	0	ENST00000325404.1:c.754C>T	p.Pro252Ser	p.P252S	ENST00000325404	NM_003106.3	252	Ccc/Tcc	1/1	1	2	FACETS	0.167	0.148	0.188	0.167	0.148	0.188	SUBCLONAL	1	TRUE	1	0.778205047045648	2		709	1414	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412094	63412094	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374751715	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	110	885	0	ENST00000330258.3:c.1073G>A	p.Arg358Gln	p.R358Q	ENST00000330258	NM_152424.3	358	cGa/cAa	2/2	1	2	FACETS	0.232	0.207	0.258	0.232	0.207	0.258	SUBCLONAL	1	TRUE	1	0.778205047045648	2		885	1220	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645607	215645607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553622313	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	53	390	0	ENST00000260947.4:c.991C>T	p.Pro331Ser	p.P331S	ENST00000260947	NM_000465.2	331	Ccc/Tcc	4/11	1	2	FACETS	0.162	0.138	0.19	0.162	0.138	0.19	SUBCLONAL	1	TRUE	1	0.778205047045648	2		390	839	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39764328	39764328	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747584221	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	279	485	0	ENST00000288319.7:c.784G>A	p.Gly262Ser	p.G262S	ENST00000288319	NM_182918.3	262	Ggt/Agt	7/10	1	2	FACETS	0.718	0.675	0.762	0.718	0.675	0.762	SUBCLONAL	1	TRUE	1	0.778205047045648	2		485	999	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589663	67589663	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587777709	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	43	413	0	ENST00000274335.5:c.1425+1G>A		p.X475_splice	ENST00000274335		475			1	2	FACETS	0.524	0.443	0.611	0.524	0.443	0.611	SUBCLONAL	1	TRUE	1	0.778205047045648	2		413	211	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938931	178938931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	39	310	0	ENST00000263967.3:c.2173G>A	p.Asp725Asn	p.D725N	ENST00000263967	NM_006218.2	725	Gat/Aat	14/21	1	2	FACETS	0.153	0.126	0.183	0.153	0.126	0.183	SUBCLONAL	1	TRUE	1	0.778205047045648	2		310	657	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985877	60985877	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775404824	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	31	349	0	ENST00000333681.4:c.23G>A	p.Gly8Glu	p.G8E	ENST00000333681		8	gGg/gAg	2/3	0.227222006414792	1	FACETS	0.079	0.063	0.097	0.079	0.063	0.097	INDETERMINATE	1	TRUE	0	0.778205047045648	1		349	615	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841201	15841201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1473782265	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	143	244	0	ENST00000307771.7:c.1285C>T	p.Arg429Cys	p.R429C	ENST00000307771	NM_005089.3	429	Cgc/Tgc	11/11	1	2	FACETS	0.692	0.634	0.752	0.692	0.634	0.752	SUBCLONAL	1	TRUE	1	0.778205047045648	2		244	531	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499382	89499382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	202	291	0	ENST00000336596.2:c.2552C>T	p.Ala851Val	p.A851V	ENST00000336596	NM_005233.5	851	gCt/gTt	15/17	1	2	FACETS	0.805	0.75	0.861	0.805	0.75	0.861	CLONAL	1	TRUE	1	0.778205047045648	2		291	645	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274350	5274350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	42	512	0	ENST00000357368.4:c.97C>T	p.Pro33Ser	p.P33S	ENST00000357368	NM_002850.3	33	Ccc/Tcc	3/38	1	2	FACETS	0.131	0.109	0.156	0.131	0.109	0.156	SUBCLONAL	1	TRUE	1	0.778205047045648	2		512	823	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592115	67592115	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	132	185	0	ENST00000274335.5:c.1931G>A	p.Gly644Asp	p.G644D	ENST00000274335		644	gGc/gAc	14/15	1	2	FACETS	0.756	0.691	0.822	0.756	0.691	0.822	SUBCLONAL	1	TRUE	1	0.778205047045648	2		185	449	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009156	27009156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	97	111	0	ENST00000335756.4:c.92C>T	p.Pro31Leu	p.P31L	ENST00000335756	NM_001809.3	31	cCc/cTc	1/5	1	2	FACETS	0.872	0.788	0.958	0.872	0.788	0.958	CLONAL	1	TRUE	1	0.778205047045648	2		111	286	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2132493	2132493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201135184	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	128	1155	1	ENST00000219476.3:c.3871G>A	p.Val1291Ile	p.V1291I	ENST00000219476	NM_000548.3	1291	Gtt/Att	32/42	NA	2	FACETS	0.25	0.226	0.276			1	INDETERMINATE	1	TRUE	NA	0.778205047045648	2		1156	1314	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928067	178928067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	41	283	0	ENST00000263967.3:c.1345C>T	p.Pro449Ser	p.P449S	ENST00000263967	NM_006218.2	449	Cct/Tct	8/21	1	2	FACETS	0.152	0.126	0.181	0.152	0.126	0.181	SUBCLONAL	1	TRUE	1	0.778205047045648	2		283	693	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994324	21994324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554659249	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	108	366	0	ENST00000579755.1:c.7C>T	p.Arg3Cys	p.R3C	ENST00000579755		3	Cgc/Tgc	1/3	0.778205047045648		FACETS		0.298	0.369				SUBCLONAL	1	TRUE	0	0.778205047045648	2		366	835	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397538	116397538	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	65	272	0	ENST00000397752.3:c.1910C>T	p.Ser637Phe	p.S637F	ENST00000397752	NM_000245.2	637	tCc/tTc	7/21	1	2	FACETS	0.246	0.212	0.282	0.246	0.212	0.282	SUBCLONAL	1	TRUE	1	0.778205047045648	2		272	680	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662373	227662373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746340033	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	80	640	0	ENST00000305123.5:c.1082G>A	p.Gly361Asp	p.G361D	ENST00000305123	NM_005544.2	361	gGc/gAc	1/2	1	2	FACETS	0.207	0.182	0.235	0.207	0.182	0.235	SUBCLONAL	1	TRUE	1	0.778205047045648	2		640	991	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265051	10265051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	106	622	0	ENST00000340748.4:c.1889C>T	p.Thr630Ile	p.T630I	ENST00000340748		630	aCt/aTt	21/40	1	2	FACETS	0.279	0.25	0.311	0.279	0.25	0.311	SUBCLONAL	1	TRUE	1	0.778205047045648	2		622	975	SUCCESS
APC	324	MSKCC	GRCh37	5	112116523	112116523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	49	221	0	ENST00000257430.4:c.568G>A	p.Glu190Lys	p.E190K	ENST00000257430	NM_000038.5	190	Gaa/Aaa	6/16	1	2	FACETS	0.256	0.217	0.299	0.256	0.217	0.299	SUBCLONAL	1	TRUE	1	0.778205047045648	2		221	492	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798242	42798242	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	36	889	0	ENST00000575354.2:c.4195+1G>A		p.X1399_splice	ENST00000575354	NM_015125.3	1399			0.778205047045648	1	FACETS	0.082	0.066	0.099	0.082	0.066	0.099	SUBCLONAL	1	TRUE	0	0.778205047045648	1		889	693	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31521249	31521249	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	77	326	0	ENST00000344624.3:c.928G>A	p.Glu310Lys	p.E310K	ENST00000344624		310	Gag/Aag	3/33	1	2	FACETS	0.279	0.244	0.316	0.279	0.244	0.316	SUBCLONAL	1	TRUE	1	0.778205047045648	2		326	710	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563002	21563002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748263686	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	487	721	0	ENST00000382592.4:c.917C>T	p.Pro306Leu	p.P306L	ENST00000382592	NM_014572.2	306	cCc/cTc	4/8	0.773141856927397	1	FACETS	0.917	0.885	0.949	0.917	0.885	0.949	CLONAL	1	TRUE	0	0.778205047045648	1		721	834	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602451	10602451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	62	752	0	ENST00000171111.5:c.1127C>T	p.Ala376Val	p.A376V	ENST00000171111	NM_203500.1	376	gCc/gTc	3/6	1	2	FACETS	0.133	0.114	0.154	0.133	0.114	0.154	SUBCLONAL	1	TRUE	1	0.778205047045648	2		752	1197	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245420	16245420	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	45	200	0	ENST00000375759.3:c.1396-1G>A		p.X466_splice	ENST00000375759	NM_015001.2	466			0.693326830760303	1	FACETS	0.252	0.213	0.295	0.252	0.213	0.295	SUBCLONAL	1	TRUE	0	0.778205047045648	1		200	280	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260293	16260293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	98	568	0	ENST00000375759.3:c.7558C>T	p.Pro2520Ser	p.P2520S	ENST00000375759	NM_015001.2	2520	Cca/Tca	11/15	0.693326830760303	1	FACETS	0.31	0.277	0.344	0.31	0.277	0.344	SUBCLONAL	1	TRUE	0	0.778205047045648	1		568	497	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094479	27094479	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	104	393	0	ENST00000324856.7:c.3187G>A	p.Gly1063Arg	p.G1063R	ENST00000324856	NM_006015.4	1063	Gga/Aga	11/20	0.778205047045648	1	FACETS	0.442	0.4	0.487	0.442	0.4	0.487	SUBCLONAL	1	TRUE	0	0.778205047045648	1		393	369	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799266	45799266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781374	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	59	336	0	ENST00000450313.1:c.167G>A	p.Gly56Glu	p.G56E	ENST00000450313	NM_012222.2	56	gGg/gAg	3/16	0.778205047045648	1	FACETS	0.263	0.227	0.302	0.263	0.227	0.302	SUBCLONAL	1	TRUE	0	0.778205047045648	1		336	352	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076799	72076799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	231	290	0	ENST00000357731.5:c.698G>A	p.Gly233Asp	p.G233D	ENST00000357731	NM_173808.2	233	gGc/gAc	5/7	0.778205047045648	1	FACETS	0.853	0.808	0.898	0.853	0.808	0.898	CLONAL	1	TRUE	0	0.778205047045648	1		290	425	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280091	115280091	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	236	333	0	ENST00000438362.2:c.540+1G>A		p.X180_splice	ENST00000438362	NM_001242891.1	180			0.778205047045648	1	FACETS	0.799	0.755	0.842	0.799	0.755	0.842	SUBCLONAL	1	TRUE	0	0.778205047045648	1		333	464	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466375	120466375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1039437832	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	308	483	1	ENST00000256646.2:c.4744G>A	p.Asp1582Asn	p.D1582N	ENST00000256646	NM_024408.3	1582	Gac/Aac	26/34	0.778205047045648	1	FACETS	0.912	0.872	0.952	0.912	0.872	0.952	CLONAL	1	TRUE	0	0.778205047045648	1		484	530	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740207	162740207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	52	457	0	ENST00000367921.3:c.1409C>T	p.Thr470Ile	p.T470I	ENST00000367921	NM_006182.2	470	aCt/aTt	12/18	1	2	FACETS	0.164	0.139	0.192	0.164	0.139	0.192	SUBCLONAL	1	TRUE	1	0.778205047045648	2		457	814	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518805	204518805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773932299	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	45	130	0	ENST00000367182.3:c.1468G>A	p.Ala490Thr	p.A490T	ENST00000367182	NM_001278516.1	490	Gca/Aca	11/11	1	2	FACETS	0.372	0.314	0.435	0.372	0.314	0.435	SUBCLONAL	1	TRUE	1	0.778205047045648	2		130	311	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405101	70405101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	158	403	0	ENST00000373644.4:c.2615C>T	p.Pro872Leu	p.P872L	ENST00000373644	NM_030625.2	872	cCc/cTc	4/12	0.227222006414792	1	FACETS	0.376	0.345	0.408	0.376	0.345	0.408	INDETERMINATE	1	TRUE	0	0.778205047045648	1		403	660	SUCCESS
EED	8726	MSKCC	GRCh37	11	85963272	85963272	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	90	243	0	ENST00000263360.6:c.350G>A	p.Gly117Glu	p.G117E	ENST00000263360	NM_003797.3	117	gGa/gAa	3/12	0.755714951171995	2	FACETS	0.548	0.489	0.611	0.274	0.244	0.306	SUBCLONAL	1	TRUE	0	0.778205047045648	2		243	422	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201945	102201945	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	14	178	0	ENST00000263464.3:c.1297G>A	p.Glu433Lys	p.E433K	ENST00000263464	NM_001165.4	433	Gaa/Aaa	6/9	0.755714951171995	2	FACETS	0.139	0.1	0.186	0.069	0.05	0.093	SUBCLONAL	1	TRUE	0	0.778205047045648	2		178	259	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121754	108121754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	220	314	0	ENST00000278616.4:c.1562G>A	p.Arg521Lys	p.R521K	ENST00000278616	NM_000051.3	521	aGa/aAa	10/63	0.755714951171995	2	FACETS	0.896	0.839	0.954	0.448	0.419	0.477	CLONAL	1	TRUE	0	0.778205047045648	2		314	631	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628624	21628624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	201	300	0	ENST00000421138.2:c.1084G>A	p.Ala362Thr	p.A362T	ENST00000421138		362	Gcc/Acc	10/16	1	2	FACETS	0.794	0.739	0.849	0.794	0.739	0.849	SUBCLONAL	1	TRUE	1	0.778205047045648	2		300	651	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244797	46244797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	75	455	0	ENST00000334344.6:c.2891G>A	p.Gly964Glu	p.G964E	ENST00000334344	NM_152641.2	964	gGa/gAa	15/21	1	2	FACETS	0.237	0.207	0.269	0.237	0.207	0.269	SUBCLONAL	1	TRUE	1	0.778205047045648	2		455	813	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444686	49444686	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769451984	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1255	156	1097	0	ENST00000301067.7:c.2780C>T	p.Pro927Leu	p.P927L	ENST00000301067	NM_003482.3	927	cCt/cTt	10/54	1	2	FACETS	0.284	0.259	0.311	0.284	0.259	0.311	SUBCLONAL	1	TRUE	1	0.778205047045648	2		1097	1411	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480616	50480616	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	52	410	0	ENST00000394963.4:c.486G>A	p.Met162Ile	p.M162I	ENST00000394963	NM_003076.4	162	atG/atA	4/13	1	2	FACETS	0.218	0.185	0.255	0.218	0.185	0.255	SUBCLONAL	1	TRUE	1	0.778205047045648	2		410	612	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145496	58145496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	43	322	0	ENST00000257904.6:c.5C>T	p.Ala2Val	p.A2V	ENST00000257904	NM_000075.3	2	gCt/gTt	2/8	1	2	FACETS	0.215	0.179	0.254	0.215	0.179	0.254	SUBCLONAL	1	TRUE	1	0.778205047045648	2		322	515	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434389	121434389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	351	758	1	ENST00000257555.6:c.1153G>A	p.Ala385Thr	p.A385T	ENST00000257555		385	Gca/Aca	6/10	1	2	FACETS	0.742	0.703	0.783	0.742	0.703	0.783	SUBCLONAL	1	TRUE	1	0.778205047045648	2		759	1215	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219435	133219435	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	456	927	1	ENST00000320574.5:c.4699G>A	p.Ala1567Thr	p.A1567T	ENST00000320574	NM_006231.2	1567	Gcc/Acc	36/49	1	2	FACETS	0.835	0.797	0.873	0.835	0.797	0.873	CLONAL	1	TRUE	1	0.778205047045648	2		928	1404	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919257	48919257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	16	113	0	ENST00000267163.4:c.422G>A	p.Ser141Asn	p.S141N	ENST00000267163	NM_000321.2	141	aGt/aAt	4/27	0.773141856927397	1	FACETS	0.237	0.177	0.306	0.237	0.177	0.306	SUBCLONAL	1	TRUE	0	0.778205047045648	1		113	106	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281491	49281491	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	107	451	0	ENST00000282018.3:c.538C>T	p.Gln180Ter	p.Q180*	ENST00000282018	NM_020377.2	180	Cag/Tag	1/1	0.773141856927397	1	FACETS	0.301	0.271	0.333	0.301	0.271	0.333	SUBCLONAL	1	TRUE	0	0.778205047045648	1		451	558	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30102124	30102124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777570460	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	226	373	0	ENST00000331968.5:c.1343G>A	p.Ser448Asn	p.S448N	ENST00000331968	NM_002742.2	448	aGc/aAc	9/18	1	2	FACETS	0.765	0.715	0.817	0.765	0.715	0.817	SUBCLONAL	1	TRUE	1	0.778205047045648	2		373	759	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105637	30105637	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	100	456	0	ENST00000331968.5:c.1049G>A	p.Ser350Asn	p.S350N	ENST00000331968	NM_002742.2	350	aGt/aAt	7/18	1	2	FACETS	0.28	0.249	0.312	0.28	0.249	0.312	SUBCLONAL	1	TRUE	1	0.778205047045648	2		456	919	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90645576	90645576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775225193	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	34	143	0	ENST00000330062.3:c.47G>A	p.Gly16Asp	p.G16D	ENST00000330062	NM_002168.2	16	gGc/gAc	1/11	0.227222006414792	1	FACETS	0.191	0.157	0.23	0.191	0.157	0.23	INDETERMINATE	1	TRUE	0	0.778205047045648	1		143	279	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456470	99456470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	42	432	0	ENST00000268035.6:c.1787G>A	p.Gly596Glu	p.G596E	ENST00000268035	NM_000875.3	596	gGg/gAg	8/21	0.227222006414792	1	FACETS	0.104	0.086	0.124	0.104	0.086	0.124	INDETERMINATE	1	TRUE	0	0.778205047045648	1		432	633	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2105521	2105521	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs45460895	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	222	496	0	ENST00000219476.3:c.599+1G>A		p.X200_splice	ENST00000219476	NM_000548.3	200			NA	2	FACETS	0.684	0.638	0.732			1	INDETERMINATE	1	TRUE	NA	0.778205047045648	2		496	834	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129649	2129649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	147	1058	2	ENST00000219476.3:c.3376G>A	p.Asp1126Asn	p.D1126N	ENST00000219476	NM_000548.3	1126	Gat/Aat	29/42	NA	2	FACETS	0.295	0.268	0.323			1	INDETERMINATE	1	TRUE	NA	0.778205047045648	2		1060	1281	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640782	3640782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1185482904	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	104	686	0	ENST00000294008.3:c.2857C>T	p.Leu953Phe	p.L953F	ENST00000294008	NM_032444.2	953	Ctt/Ttt	12/15	1	2	FACETS	0.274	0.244	0.305	0.274	0.244	0.305	SUBCLONAL	1	TRUE	1	0.778205047045648	2		686	976	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646324	3646324	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1252	157	956	0	ENST00000294008.3:c.1754C>T	p.Pro585Leu	p.P585L	ENST00000294008	NM_032444.2	585	cCc/cTc	8/15	1	2	FACETS	0.286	0.261	0.313	0.286	0.261	0.313	SUBCLONAL	1	TRUE	1	0.778205047045648	2		956	1409	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828789	3828789	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	49	469	0	ENST00000262367.5:c.1853C>T	p.Pro618Leu	p.P618L	ENST00000262367	NM_004380.2	618	cCc/cTc	9/31	1	2	FACETS	0.143	0.12	0.168	0.143	0.12	0.168	SUBCLONAL	1	TRUE	1	0.778205047045648	2		469	882	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782338	56782338	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	169	520	0	ENST00000308159.5:c.179C>T	p.Ala60Val	p.A60V	ENST00000308159	NM_014669.4	60	gCg/gTg	2/22	1	2	FACETS	0.518	0.476	0.561	0.518	0.476	0.561	SUBCLONAL	1	TRUE	1	0.778205047045648	2		520	839	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982808	7982808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	280	855	1	ENST00000319144.4:c.977C>T	p.Thr326Ile	p.T326I	ENST00000319144	NM_001139.2	326	aCc/aTc	8/15	1	2	FACETS	0.527	0.494	0.561	0.527	0.494	0.561	SUBCLONAL	1	TRUE	1	0.778205047045648	2		856	1365	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11998962	11998962	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	90	215	0	ENST00000353533.5:c.464G>A	p.Ser155Asn	p.S155N	ENST00000353533	NM_003010.3	155	aGt/aAt	4/11	1	2	FACETS	0.488	0.435	0.545	0.488	0.435	0.545	SUBCLONAL	1	TRUE	1	0.778205047045648	2		215	474	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17120447	17120447	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	283	609	0	ENST00000285071.4:c.1112G>A	p.Gly371Glu	p.G371E	ENST00000285071	NM_144997.5	371	gGg/gAg	10/14	1	2	FACETS	0.795	0.749	0.842	0.795	0.749	0.842	SUBCLONAL	1	TRUE	1	0.778205047045648	2		609	915	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661958	29661958	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	68	328	0	ENST00000356175.3:c.5852C>T	p.Thr1951Ile	p.T1951I	ENST00000356175	NM_000267.3	1951	aCt/aTt	39/57	1	2	FACETS	0.264	0.229	0.301	0.264	0.229	0.301	SUBCLONAL	1	TRUE	1	0.778205047045648	2		328	663	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883759	37883759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	182	1011	1	ENST00000269571.5:c.3371C>T	p.Thr1124Ile	p.T1124I	ENST00000269571		1124	aCt/aTt	26/27	1	2	FACETS	0.345	0.317	0.374	0.345	0.317	0.374	SUBCLONAL	1	TRUE	1	0.778205047045648	2		1012	1357	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362469	40362469	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	76	535	0	ENST00000293328.3:c.1727G>A	p.Gly576Asp	p.G576D	ENST00000293328	NM_012448.3	576	gGt/gAt	14/19	1	2	FACETS	0.202	0.177	0.23	0.202	0.177	0.23	SUBCLONAL	1	TRUE	1	0.778205047045648	2		535	966	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375550	40375550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	94	491	0	ENST00000293328.3:c.400G>A	p.Ala134Thr	p.A134T	ENST00000293328	NM_012448.3	134	Gct/Act	5/19	1	2	FACETS	0.29	0.258	0.325	0.29	0.258	0.325	SUBCLONAL	1	TRUE	1	0.778205047045648	2		491	832	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459654	40459654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	120	726	1	ENST00000345506.4:c.1819C>T	p.Leu607Phe	p.L607F	ENST00000345506	NM_003152.3	607	Ctc/Ttc	16/20	1	2	FACETS	0.28	0.252	0.31	0.28	0.252	0.31	SUBCLONAL	1	TRUE	1	0.778205047045648	2		727	1101	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245557	41245557	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	73	500	0	ENST00000357654.3:c.1991G>A	p.Arg664Lys	p.R664K	ENST00000357654	NM_007294.3	664	aGa/aAa	10/23	1	2	FACETS	0.152	0.132	0.174	0.152	0.132	0.174	SUBCLONAL	1	TRUE	1	0.778205047045648	2		500	1232	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533171	63533171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	362	740	0	ENST00000307078.5:c.1723G>A	p.Gly575Ser	p.G575S	ENST00000307078	NM_004655.3	575	Ggc/Agc	7/11	1	2	FACETS	0.779	0.739	0.82	0.779	0.739	0.82	SUBCLONAL	1	TRUE	1	0.778205047045648	2		740	1194	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221146	5221146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	125	748	1	ENST00000357368.4:c.3320G>A	p.Gly1107Asp	p.G1107D	ENST00000357368	NM_002850.3	1107	gGc/gAc	20/38	1	2	FACETS	0.29	0.262	0.321	0.29	0.262	0.321	SUBCLONAL	1	TRUE	1	0.778205047045648	2		749	1106	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10286248	10286248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1281646304	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	65	519	0	ENST00000340748.4:c.568G>A	p.Asp190Asn	p.D190N	ENST00000340748		190	Gat/Aat	6/40	1	2	FACETS	0.155	0.133	0.178	0.155	0.133	0.178	SUBCLONAL	1	TRUE	1	0.778205047045648	2		519	1081	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097237	11097237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	346	633	0	ENST00000358026.2:c.728G>A	p.Gly243Asp	p.G243D	ENST00000358026	NM_001128849.1	243	gGc/gAc	4/36	1	2	FACETS	0.808	0.765	0.851	0.808	0.765	0.851	CLONAL	1	TRUE	1	0.778205047045648	2		633	1101	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100030	11100030	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	364	729	0	ENST00000358026.2:c.1156G>A	p.Glu386Lys	p.E386K	ENST00000358026	NM_001128849.1	386	Gaa/Aaa	7/36	1	2	FACETS	0.796	0.755	0.838	0.796	0.755	0.838	SUBCLONAL	1	TRUE	1	0.778205047045648	2		729	1175	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311604	15311604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	76	125	0	ENST00000263388.2:c.113C>T	p.Ala38Val	p.A38V	ENST00000263388	NM_000435.2	38	gCt/gTt	1/33	1	2	FACETS	0.769	0.684	0.858	0.769	0.684	0.858	SUBCLONAL	1	TRUE	1	0.778205047045648	2		125	254	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367968	15367968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1232360432	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	95	816	0	ENST00000263377.2:c.1358G>A	p.Arg453His	p.R453H	ENST00000263377	NM_058243.2	453	cGc/cAc	8/20	1	2	FACETS	0.208	0.184	0.233	0.208	0.184	0.233	SUBCLONAL	1	TRUE	1	0.778205047045648	2		816	1175	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082511	16082511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	121	667	1	ENST00000281043.3:c.325C>T	p.Pro109Ser	p.P109S	ENST00000281043	NM_005378.4	109	Ccg/Tcg	2/3	1	2	FACETS	0.269	0.242	0.298	0.269	0.242	0.298	SUBCLONAL	1	TRUE	1	0.778205047045648	2		668	1155	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966208	25966208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	113	487	0	ENST00000435504.4:c.2998G>A	p.Glu1000Lys	p.E1000K	ENST00000435504		1000	Gaa/Aaa	13/13	1	2	FACETS	0.3	0.27	0.333	0.3	0.27	0.333	SUBCLONAL	1	TRUE	1	0.778205047045648	2		487	967	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705545	47705545	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	165	255	0	ENST00000233146.2:c.2345C>T	p.Thr782Ile	p.T782I	ENST00000233146	NM_000251.2	782	aCc/aTc	14/16	1	2	FACETS	0.787	0.727	0.848	0.787	0.727	0.848	SUBCLONAL	1	TRUE	1	0.778205047045648	2		255	539	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033791	48033791	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	24	170	0	ENST00000234420.5:c.4001+1G>A		p.X1334_splice	ENST00000234420	NM_000179.2	1334			1	2	FACETS	0.155	0.121	0.195	0.155	0.121	0.195	SUBCLONAL	1	TRUE	1	0.778205047045648	2		170	397	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61705969	61705969	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	223	308	2	ENST00000401558.2:c.3202G>A	p.Glu1068Lys	p.E1068K	ENST00000401558	NM_003400.3	1068	Gaa/Aaa	25/25	1	2	FACETS	0.816	0.763	0.871	0.816	0.763	0.871	CLONAL	1	TRUE	1	0.778205047045648	2		310	702	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023340	31023340	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	77	516	0	ENST00000375687.4:c.2825G>A	p.Gly942Glu	p.G942E	ENST00000375687	NM_015338.5	942	gGg/gAg	13/13	1	2	FACETS	0.256	0.224	0.29	0.256	0.224	0.29	SUBCLONAL	1	TRUE	1	0.778205047045648	2		516	774	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46251062	46251062	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	41	259	0	ENST00000371998.3:c.71C>T	p.Thr24Ile	p.T24I	ENST00000371998		24	aCt/aTt	3/23	1	2	FACETS	0.162	0.134	0.193	0.162	0.134	0.193	SUBCLONAL	1	TRUE	1	0.778205047045648	2		259	650	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566477	41566477	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	60	303	0	ENST00000263253.7:c.4354C>T	p.Pro1452Ser	p.P1452S	ENST00000263253	NM_001429.3	1452	Cct/Tct	27/31	1	2	FACETS	0.242	0.208	0.279	0.242	0.208	0.279	SUBCLONAL	1	TRUE	1	0.778205047045648	2		303	637	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990447	69990447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	30	195	0	ENST00000394351.3:c.406G>A	p.Gly136Ser	p.G136S	ENST00000394351	NM_000248.3	136	Ggc/Agc	4/9	NA	2	FACETS	0.149	0.119	0.182			1	INDETERMINATE	1	TRUE	NA	0.778205047045648	2		195	519	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71064764	71064764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	69	332	0	ENST00000318789.4:c.910G>A	p.Gly304Arg	p.G304R	ENST00000318789	NM_032682.5	304	Gga/Aga	12/21	NA	2	FACETS	0.237	0.206	0.271			1	INDETERMINATE	1	TRUE	NA	0.778205047045648	2		332	747	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72897458	72897458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759093041	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	225	337	0	ENST00000325599.8:c.34C>T	p.Pro12Ser	p.P12S	ENST00000325599	NM_018130.2	12	Ccg/Tcg	1/11	NA	2	FACETS	0.844	0.79	0.9			1	INDETERMINATE	1	TRUE	NA	0.778205047045648	2		337	685	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456623	138456623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	89	255	0	ENST00000289153.2:c.727C>T	p.Pro243Ser	p.P243S	ENST00000289153	NM_006219.2	243	Ccc/Tcc	4/22	1	2	FACETS	0.305	0.27	0.342	0.305	0.27	0.342	SUBCLONAL	1	TRUE	1	0.778205047045648	2		255	751	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182679116	182679116	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	55	211	0	ENST00000292782.4:c.418C>T	p.Gln140Ter	p.Q140*	ENST00000292782	NM_020640.2	140	Cag/Tag	4/7	1	2	FACETS	0.214	0.182	0.248	0.214	0.182	0.248	SUBCLONAL	1	TRUE	1	0.778205047045648	2		211	662	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1978226	1978226	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1423726760	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	390	803	0	ENST00000382891.5:c.3646G>A	p.Glu1216Lys	p.E1216K	ENST00000382891	NM_133335.3	1216	Gaa/Aaa	21/22	1	2	FACETS	0.801	0.761	0.842	0.801	0.761	0.842	CLONAL	1	TRUE	1	0.778205047045648	2		803	1251	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156319	106156319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1490447732	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	102	236	0	ENST00000380013.4:c.1220C>T	p.Ser407Phe	p.S407F	ENST00000380013	NM_001127208.2	407	tCt/tTt	3/11	1	2	FACETS	0.665	0.6	0.734	0.665	0.6	0.734	SUBCLONAL	1	TRUE	1	0.778205047045648	2		236	394	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193926	106193926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	164	213	0	ENST00000380013.4:c.4388C>T	p.Thr1463Ile	p.T1463I	ENST00000380013	NM_001127208.2	1463	aCt/aTt	10/11	1	2	FACETS	0.947	0.878	1	0.947	0.878	1	CLONAL	1	TRUE	1	0.778205047045648	2		213	445	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521219	187521219	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	227	414	0	ENST00000441802.2:c.11936C>T	p.Ser3979Phe	p.S3979F	ENST00000441802	NM_005245.3	3979	tCc/tTc	22/27	1	2	FACETS	0.627	0.584	0.67	0.627	0.584	0.67	SUBCLONAL	1	TRUE	1	0.778205047045648	2		414	931	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295291	1295291	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs796451171	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	53	494	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.149	0.126	0.174	0.149	0.126	0.174	SUBCLONAL	1	TRUE	1	0.778205047045648	2		494	916	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526789	31526789	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	78	544	1	ENST00000344624.3:c.251C>T	p.Pro84Leu	p.P84L	ENST00000344624		84	cCc/cTc	2/33	1	2	FACETS	0.21	0.184	0.239	0.21	0.184	0.239	SUBCLONAL	1	TRUE	1	0.778205047045648	2		545	953	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111593	56111593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1404916353	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	97	154	0	ENST00000399503.3:c.193G>A	p.Val65Met	p.V65M	ENST00000399503	NM_005921.1	65	Gtg/Atg	1/20	1	2	FACETS	0.626	0.562	0.693	0.626	0.562	0.693	SUBCLONAL	1	TRUE	1	0.778205047045648	2		154	398	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152530	56152530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	57	230	0	ENST00000399503.3:c.586G>A	p.Ala196Thr	p.A196T	ENST00000399503	NM_005921.1	196	Gcc/Acc	2/20	1	2	FACETS	0.317	0.272	0.366	0.317	0.272	0.366	SUBCLONAL	1	TRUE	1	0.778205047045648	2		230	462	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520423	176520423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	401	903	1	ENST00000292408.4:c.1268G>A	p.Gly423Asp	p.G423D	ENST00000292408	NM_213647.1	423	gGc/gAc	10/18	1	2	FACETS	0.823	0.783	0.864	0.823	0.783	0.864	CLONAL	1	TRUE	1	0.778205047045648	2		904	1252	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671670	30671670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	71	582	0	ENST00000376406.3:c.5290G>A	p.Ala1764Thr	p.A1764T	ENST00000376406	NM_014641.2	1764	Gct/Act	10/15	1	2	FACETS	0.189	0.164	0.216	0.189	0.164	0.216	SUBCLONAL	1	TRUE	1	0.778205047045648	2		582	966	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181941	32181941	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	198	676	0	ENST00000375023.3:c.2113A>G	p.Thr705Ala	p.T705A	ENST00000375023	NM_004557.3	705	Acc/Gcc	13/30	1	2	FACETS	0.473	0.438	0.51	0.473	0.438	0.51	SUBCLONAL	1	TRUE	1	0.778205047045648	2		676	1075	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908121	41908121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1485661924	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	118	595	0	ENST00000372991.4:c.401C>T	p.Pro134Leu	p.P134L	ENST00000372991	NM_001760.3	134	cCc/cTc	2/5	1	2	FACETS	0.3	0.27	0.332	0.3	0.27	0.332	SUBCLONAL	1	TRUE	1	0.778205047045648	2		595	1010	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658455	117658455	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771226930	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	195	258	0	ENST00000368508.3:c.5128C>T	p.Pro1710Ser	p.P1710S	ENST00000368508	NM_002944.2	1710	Cct/Tct	31/43	1	2	FACETS	0.738	0.686	0.792	0.738	0.686	0.792	SUBCLONAL	1	TRUE	1	0.778205047045648	2		258	679	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686270	117686270	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	37	185	0	ENST00000368508.3:c.3071G>A	p.Trp1024Ter	p.W1024*	ENST00000368508	NM_002944.2	1024	tGg/tAg	20/43	1	2	FACETS	0.215	0.177	0.258	0.215	0.177	0.258	SUBCLONAL	1	TRUE	1	0.778205047045648	2		185	442	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511282	157511282	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	51	431	0	ENST00000346085.5:c.3800C>T	p.Pro1267Leu	p.P1267L	ENST00000346085	NM_020732.3	1267	cCc/cTc	15/20	1	2	FACETS	0.166	0.14	0.194	0.166	0.14	0.194	SUBCLONAL	1	TRUE	1	0.778205047045648	2		431	790	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528086	157528086	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886041819	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	56	448	0	ENST00000346085.5:c.5811G>A	p.Trp1937Ter	p.W1937*	ENST00000346085	NM_020732.3	1937	tgG/tgA	20/20	1	2	FACETS	0.171	0.146	0.199	0.171	0.146	0.199	SUBCLONAL	1	TRUE	1	0.778205047045648	2		448	842	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455139	50455139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1359632331	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	173	277	0	ENST00000331340.3:c.686G>A	p.Ser229Asn	p.S229N	ENST00000331340	NM_006060.4	229	aGc/aAc	6/8	1	2	FACETS	0.831	0.77	0.893	0.831	0.77	0.893	CLONAL	1	TRUE	1	0.778205047045648	2		277	535	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133864	38133864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	406	649	0	ENST00000317025.8:c.4022G>A	p.Cys1341Tyr	p.C1341Y	ENST00000317025	NM_023034.1	1341	tGt/tAt	23/24	1	2	FACETS	0.814	0.774	0.854	0.814	0.774	0.854	CLONAL	1	TRUE	1	0.778205047045648	2		649	1282	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38153423	38153423	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	96	357	0	ENST00000317025.8:c.2806G>A	p.Glu936Lys	p.E936K	ENST00000317025	NM_023034.1	936	Gaa/Aaa	16/24	1	2	FACETS	0.3	0.267	0.335	0.3	0.267	0.335	SUBCLONAL	1	TRUE	1	0.778205047045648	2		357	823	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287305	38287305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	385	824	0	ENST00000425967.3:c.352G>A	p.Glu118Lys	p.E118K	ENST00000425967	NM_001174067.1	118	Gag/Aag	4/19	1	2	FACETS	0.795	0.755	0.835	0.795	0.755	0.835	SUBCLONAL	1	TRUE	1	0.778205047045648	2		824	1245	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404563	8404563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	17	192	0	ENST00000356435.5:c.4184C>T	p.Ser1395Phe	p.S1395F	ENST00000356435		1395	tCc/tTc	25/35	0.778205047045648	2	FACETS	0.129	0.096	0.168	0.064	0.048	0.084	SUBCLONAL	1	TRUE	0	0.778205047045648	2		192	339	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293487	137293487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1346	145	1358	0	ENST00000481739.1:c.38C>T	p.Thr13Ile	p.T13I	ENST00000481739	NM_002957.4	13	aCc/aTc	2/10	0.126801914595385	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.778205047045648	0		1358	1491	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418229	139418229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	479	1203	0	ENST00000277541.6:c.343G>A	p.Gly115Ser	p.G115S	ENST00000277541	NM_017617.3	115	Ggc/Agc	3/34	0.126801914595385	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.778205047045648	0		1203	1482	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841289	15841289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	61	282	0	ENST00000307771.7:c.1373C>T	p.Ser458Phe	p.S458F	ENST00000307771	NM_005089.3	458	tCc/tTc	11/11	1	2	FACETS	0.206	0.177	0.238	0.206	0.177	0.238	SUBCLONAL	1	TRUE	1	0.778205047045648	2		282	760	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932104	39932104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	141	576	1	ENST00000378444.4:c.2495G>A	p.Gly832Asp	p.G832D	ENST00000378444	NM_001123385.1	832	gGc/gAc	4/15	1	2	FACETS	0.297	0.27	0.326	0.297	0.27	0.326	SUBCLONAL	1	TRUE	1	0.778205047045648	2		577	1220	SUCCESS
AR	367	MSKCC	GRCh37	X	66766240	66766240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	76	399	0	ENST00000374690.3:c.1252G>A	p.Gly418Ser	p.G418S	ENST00000374690	NM_000044.3	418	Ggt/Agt	1/8	1	2	FACETS	0.259	0.226	0.294	0.259	0.226	0.294	SUBCLONAL	1	TRUE	1	0.778205047045648	2		399	755	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939592	76939592	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	78	329	0	ENST00000373344.5:c.1156G>A	p.Ala386Thr	p.A386T	ENST00000373344	NM_000489.3	386	Gct/Act	9/35	1	2	FACETS	0.234	0.205	0.266	0.234	0.205	0.266	SUBCLONAL	1	TRUE	1	0.778205047045648	2		329	855	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019850	123019850	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	85	421	0	ENST00000355640.3:c.338G>A	p.Gly113Asp	p.G113D	ENST00000355640		113	gGt/gAt	2/7	1	2	FACETS	0.272	0.24	0.306	0.272	0.24	0.306	SUBCLONAL	1	TRUE	1	0.778205047045648	2		421	804	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471063	25471063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013991-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	342	850	1	ENST00000264709.3:c.698C>T	p.Pro233Leu	p.P233L	ENST00000264709	NM_175629.2	233	cCc/cTc	7/23	1	2	FACETS	0.776	0.734	0.818	0.776	0.734	0.818	SUBCLONAL	1	TRUE	1	0.778205047045648	2		851	1133	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014155-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	39	384	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		384	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577138	7577138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780075	NA	P-0014310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	151	560	0	ENST00000269305.4:c.800G>A	p.Arg267Gln	p.R267Q	ENST00000269305	NM_001126112.2	267	cGg/cAg	8/11	0.792940960040752	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.792940960040752	1		560	181	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001231	150001231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	80	415	0	ENST00000253339.5:c.2373G>A	p.Met791Ile	p.M791I	ENST00000253339		791	atG/atA	4/7	0.792940960040752	1	FACETS	0.959	0.88	1	0.959	0.88	1	CLONAL	1	TRUE	0	0.792940960040752	1		415	127	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224578	53224579	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TA	novel	NA	P-0014310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	149	615	0	ENST00000375401.3:c.3133_3134dup	p.Pro1046ThrfsTer10	p.P1046Tfs*10	ENST00000375401	NM_004187.3	1045	tac/taTAc	21/26	0.792940960040752	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.792940960040752	1		615	202	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117715	108117715	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	24	197	0	ENST00000278616.4:c.926G>C	p.Arg309Thr	p.R309T	ENST00000278616	NM_000051.3	309	aGa/aCa	8/63	0.792940960040752	3	FACETS	0.748	0.597	0.916	0.374	0.298	0.458	CLONAL	1	TRUE	1	0.792940960040752	3		197	113	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40874891	40874891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	107	525	0	ENST00000428826.2:c.409G>A	p.Asp137Asn	p.D137N	ENST00000428826		137	Gat/Aat	6/21	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.792940960040752	2		525	236	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432682	29432682	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519781	NA	P-0014310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	102	599	0	ENST00000389048.3:c.3806G>C	p.Gly1269Ala	p.G1269A	ENST00000389048	NM_004304.4	1269	gGa/gCa	25/29	1	2	FACETS	0.825	0.747	0.905	0.825	0.747	0.905	CLONAL	1	TRUE	1	0.792940960040752	2		599	312	SUCCESS
ALK	238	MSKCC	GRCh37	2	29445213	29445213	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519698	NA	P-0014310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	80	569	0	ENST00000389048.3:c.3512T>C	p.Ile1171Thr	p.I1171T	ENST00000389048	NM_004304.4	1171	aTc/aCc	22/29	1	2	FACETS	0.961	0.862	1	0.961	0.862	1	CLONAL	1	TRUE	1	0.792940960040752	2		569	210	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446244	29446244	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014310-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	122	574	0	ENST00000389048.3:c.3323T>C	p.Leu1108Pro	p.L1108P	ENST00000389048	NM_004304.4	1108	cTg/cCg	20/29	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.792940960040752	2		574	248	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631129	69631129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs281860303	NA	P-0014385-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	153	825	1	ENST00000334134.2:c.283C>T	p.Arg95Trp	p.R95W	ENST00000334134	NM_005247.2	95	Cgg/Tgg	2/3	0.163422734050146	3	FACETS	1	0.982	1	0.644	0.587	0.703	CLONAL	1	TRUE	1	0.201025104208677	3		826	1301	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443631	29443631	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519784	NA	P-0014385-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	245	771	1	ENST00000389048.3:c.3586C>A	p.Leu1196Met	p.L1196M	ENST00000389048	NM_004304.4	1196	Ctg/Atg	23/29	0.201025104208677	4	FACETS	1	0.982	1	0.766	0.715	0.819	CLONAL	2	TRUE	1	0.201025104208677	4		772	1274	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015218	128015218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372094432	NA	P-0014385-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	62	651	0	ENST00000285398.2:c.2303C>T	p.Ala768Val	p.A768V	ENST00000285398	NM_000122.1	768	gCg/gTg	15/15	0.146481906025447	2	FACETS	0.584	0.502	0.673	0.292	0.251	0.337	SUBCLONAL	1	TRUE	0	0.201025104208677	2		651	1057	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457737	149457737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759467764	NA	P-0014385-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	78	770	1	ENST00000286301.3:c.667G>A	p.Val223Met	p.V223M	ENST00000286301	NM_005211.3	223	Gtg/Atg	5/22	0.201025104208677	3	FACETS	0.67	0.587	0.761	0.335	0.293	0.381	SUBCLONAL	1	TRUE	1	0.201025104208677	3		771	1274	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477837	140477851	+	inframe_deletion	In_Frame_Del	DEL	TAGGTGCTGTCACAT	TAGGTGCTGTCACAT	-	novel	NA	P-0014432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	76	781	0	ENST00000288602.6:c.1457_1471del	p.Asn486_Pro490del	p.N486_P490del	ENST00000288602	NM_004333.4	486	aATGTGACAGCACCTAca/aca	12/18	0.103571151198049	3	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.233294666256867	3		781	553	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257312	16257315	+	frameshift_variant	Frame_Shift_Del	DEL	TTGC	TTGC	-	novel	NA	P-0014432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	62	848	0	ENST00000375759.3:c.4579_4582del	p.Ala1527LeufsTer19	p.A1527Lfs*19	ENST00000375759	NM_015001.2	1526	tTTGCt/tt	11/15	1	2	FACETS	0.813	0.702	0.934	0.813	0.702	0.934	CLONAL	1	TRUE	1	0.233294666256867	2		848	654	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105966	27105979	+	frameshift_variant	Frame_Shift_Del	DEL	CGAGAGCAAGACAG	CGAGAGCAAGACAG	-	novel	NA	P-0014432-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	55	588	0	ENST00000324856.7:c.5577_5590del	p.Phe1859LeufsTer37	p.F1859Lfs*37	ENST00000324856	NM_006015.4	1859	ttCGAGAGCAAGACAGag/ttag	20/20	1	2	FACETS	0.794	0.679	0.92	0.794	0.679	0.92	CLONAL	1	TRUE	1	0.233294666256867	2		588	594	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0014436-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	198	324	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.307812036086532	6	FACETS	0.933	0.87	0.997	0.933	0.87	0.997	CLONAL	4	FALSE	2	0.307812036086532	6		324	557	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715971	52715971	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786205228	NA	P-0014436-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	169	506	1	ENST00000322088.6:c.536C>G	p.Pro179Arg	p.P179R	ENST00000322088	NM_014225.5	179	cCc/cGc	5/15	0.272381682999516	3	FACETS	0.821	0.756	0.888			1	CLONAL	2	FALSE	NA	0.307812036086532	3		507	772	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519985	NA	P-0014436-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	517	621	7	ENST00000269305.4:c.857A>G	p.Glu286Gly	p.E286G	ENST00000269305	NM_001126112.2	286	gAa/gGa	8/11	0.303569824162939	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	4	FALSE	0	0.307812036086532	4		628	1034	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0014436-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	99	352	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.29490774594333	2	FACETS	0.802	0.721	0.887	0.802	0.721	0.887	CLONAL	2	FALSE	0	0.307812036086532	2		352	401	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610322	10610322	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014436-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1326	120	683	3	ENST00000171111.5:c.388C>A	p.Pro130Thr	p.P130T	ENST00000171111	NM_203500.1	130	Ccc/Acc	2/6	0.307812036086532	9	FACETS	1	0.958	1			1	CLONAL	1	FALSE	NA	0.307812036086532	9		686	1446	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0014438-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	23	868	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.422247879616277	3	FACETS	1	0.907	1	0.626	0.503	0.759	CLONAL	1	TRUE	1	0.637691462809717	3		869	76	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0014438-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	248	668	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	NA	2	FACETS	0.86	0.817	0.904			1	INDETERMINATE	2	TRUE	NA	0.637691462809717	2		670	452	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793433	18793433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202143029	NA	P-0014438-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	21	581	0	ENST00000266497.5:c.4130G>A	p.Arg1377His	p.R1377H	ENST00000266497		1377	cGt/cAt	30/31	0.422247879616277	3	FACETS	1	0.922	1	0.701	0.559	0.852	CLONAL	1	TRUE	1	0.637691462809717	3		581	62	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161406	2161406	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014438-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	451	696	0	ENST00000434045.2:c.121G>C	p.Gly41Arg	p.G41R	ENST00000434045	NM_001127598.1	41	Ggc/Cgc	2/5	0.637691462809717	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.637691462809717	1		696	917	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575204	48575207	+	frameshift_variant	Frame_Shift_Del	DEL	ACGA	ACGA	-	novel	NA	P-0014438-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	12	355	0	ENST00000342988.3:c.402_405del	p.Arg135LeufsTer11	p.R135Lfs*11	ENST00000342988	NM_005359.5	133	tACGAa/ta	3/12	0.637691462809717	1	FACETS	0.596	0.435	0.778	0.596	0.435	0.778	SUBCLONAL	1	TRUE	0	0.637691462809717	1		355	43	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0014522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	8	315	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.1	0.064	0.147	0.1	0.064	0.147	SUBCLONAL	1	TRUE	1	0.43	2		315	373	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	27	344	1	ENST00000288602.6:c.1742A>T	p.Asn581Ile	p.N581I	ENST00000288602	NM_004333.4	581	aAt/aTt	15/18	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.17	2		345	239	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437302	52437302	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014762-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	26	493	0	ENST00000460680.1:c.1742del	p.Gly581ValfsTer36	p.G581Vfs*36	ENST00000460680	NM_004656.3	581	gGt/gt	14/17	1	2	FACETS	0.678	0.536	0.841	0.678	0.536	0.841	SUBCLONAL	1	TRUE	1	0.17	2		493	451	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577536	7577536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587782082	NA	P-0014846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	83	487	0	ENST00000269305.4:c.745A>G	p.Arg249Gly	p.R249G	ENST00000269305	NM_001126112.2	249	Agg/Ggg	7/11	0.231746594787071	1	FACETS	0.982	0.867	1	0.982	0.867	1	CLONAL	1	TRUE	0	0.22	1		487	684	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450943	70450943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	64	502	0	ENST00000373644.4:c.5783C>T	p.Thr1928Ile	p.T1928I	ENST00000373644	NM_030625.2	1928	aCt/aTt	12/12	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.22	2		502	542	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273787	18273787	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	60	536	0	ENST00000222254.8:c.1120A>T	p.Asn374Tyr	p.N374Y	ENST00000222254	NM_005027.3	374	Aac/Tac	10/16	1	2	FACETS	0.76	0.654	0.876	0.76	0.654	0.876	SUBCLONAL	1	TRUE	1	0.22	2		536	718	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855831	45855831	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747646421	NA	P-0014846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	64	672	3	ENST00000391945.4:c.1979C>T	p.Ala660Val	p.A660V	ENST00000391945	NM_000400.3	660	gCg/gTg	21/23	1	2	FACETS	0.698	0.603	0.801	0.698	0.603	0.801	SUBCLONAL	1	TRUE	1	0.22	2		675	834	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483991	212483991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1379834725	NA	P-0014846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	40	379	0	ENST00000342788.4:c.2212G>A	p.Val738Ile	p.V738I	ENST00000342788	NM_005235.2	738	Gta/Ata	19/28	1	2	FACETS	0.889	0.74	1	0.889	0.74	1	CLONAL	1	TRUE	1	0.22	2		379	409	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252952	36252952	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	54	440	0	ENST00000300305.3:c.410A>C	p.Asp137Ala	p.D137A	ENST00000300305		137	gAt/gCt	4/8	0.182402727058791	1	FACETS	0.782	0.667	0.906	0.782	0.667	0.906	CLONAL	1	TRUE	0	0.22	1		440	559	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014074	70014074	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	66	535	0	ENST00000394351.3:c.935A>G	p.Asn312Ser	p.N312S	ENST00000394351	NM_000248.3	312	aAt/aGt	9/9	1	2	FACETS	0.987	0.857	1	0.987	0.857	1	CLONAL	1	TRUE	1	0.22	2		535	608	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799636	72799636	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1345725803	NA	P-0014846-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	51	489	0	ENST00000325599.8:c.1533A>C	p.Arg511Ser	p.R511S	ENST00000325599	NM_018130.2	511	agA/agC	11/11	1	2	FACETS	0.773	0.656	0.901	0.773	0.656	0.901	CLONAL	1	TRUE	1	0.22	2		489	600	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	46	868	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.12	2		869	749	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0015028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	45	498	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.3	2	FACETS	0.794	0.665	0.938			1	CLONAL	1	TRUE	NA	0.12	2		498	945	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715660	30715660	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	30	227	0	ENST00000295754.5:c.1318G>A	p.Glu440Lys	p.E440K	ENST00000295754	NM_003242.5	440	Gag/Aag	5/7	1	2	FACETS	1	0.829	1	1	0.829	1	CLONAL	1	TRUE	1	0.12	2		227	484	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0015031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	213	485	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.473	0.439	0.508	0.473	0.439	0.508	SUBCLONAL	1	TRUE	1	0.88	2		485	1024	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593395	48593395	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	34	338	0	ENST00000342988.3:c.1146del	p.His382GlnfsTer2	p.H382Qfs*2	ENST00000342988	NM_005359.5	382	caC/ca	10/12	1	2	FACETS	0.166	0.135	0.201	0.166	0.135	0.201	SUBCLONAL	1	TRUE	1	0.88	2		338	465	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0015288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	129	416	1	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.38	2		417	610	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508312	38508312	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	148	507	0	ENST00000254066.5:c.620A>G	p.Lys207Arg	p.K207R	ENST00000254066	NM_000964.3	207	aAa/aGa	5/9	1	2	FACETS	0.849	0.775	0.926	0.849	0.775	0.926	CLONAL	1	TRUE	1	0.38	2		507	918	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917033	50917033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760638243	NA	P-0015288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	27	416	0	ENST00000440232.2:c.2285G>A	p.Arg762Gln	p.R762Q	ENST00000440232	NM_002691.3	762	cGa/cAa	19/27	1	2	FACETS	0.327	0.26	0.405	0.327	0.26	0.405	SUBCLONAL	1	TRUE	1	0.38	2		416	434	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610622	52610623	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	140	515	0	ENST00000394830.3:c.3550dup	p.Met1184AsnfsTer11	p.M1184Nfs*11	ENST00000394830	NM_018313.4	1184	atg/aAtg	23/30	0.282552738378263	2	FACETS	1	0.964	1	0.552	0.504	0.603	CLONAL	1	TRUE	0	0.38	2		515	667	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852282	128852282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1425442829	NA	P-0015288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	79	518	2	ENST00000249373.3:c.2354C>T	p.Ser785Leu	p.S785L	ENST00000249373	NM_005631.4	785	tCg/tTg	12/12	0.3	3	FACETS	0.609	0.535	0.689	0.305	0.267	0.345	SUBCLONAL	1	TRUE	1	0.38	3		520	812	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020503	69020503	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015288-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	57	647	4	ENST00000288368.4:c.2875G>T	p.Gly959Cys	p.G959C	ENST00000288368	NM_024870.2	959	Ggt/Tgt	24/40	1	2	FACETS	0.326	0.279	0.379	0.326	0.279	0.379	SUBCLONAL	1	TRUE	1	0.38	2		651	919	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59924478	59924478	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015479-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	103	319	0	ENST00000259008.2:c.611C>A	p.Ser204Tyr	p.S204Y	ENST00000259008	NM_032043.2	204	tCc/tAc	6/20	0.752722905725144	4	FACETS	0.979	0.893	1	0.979	0.893	1	CLONAL	2	TRUE	2	0.752722905725144	4		319	245	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs869320707	NA	P-0015601-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	68	680	1	ENST00000397752.3:c.3028+1G>T		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.159255482809365	2	FACETS	0.801	0.698	0.912	0.801	0.698	0.912	CLONAL	2	FALSE	0	0.159255482809365	2		681	533	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821120	72821120	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015601-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	25	674	0	ENST00000268489.5:c.11055del	p.Ser3686AlafsTer8	p.S3686Afs*8	ENST00000268489	NM_006885.3	3685	ccC/cc	10/10	0.159255482809365	1	FACETS	0.683	0.538	0.851	0.683	0.538	0.851	SUBCLONAL	1	FALSE	0	0.159255482809365	1		674	423	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027955	48027986	+	frameshift_variant	Frame_Shift_Del	DEL	AGAGAAAATGAACAGAGCCTCCTGGAATACCT	AGAGAAAATGAACAGAGCCTCCTGGAATACCT	-	novel	NA	P-0015601-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	21	253	0	ENST00000234420.5:c.2840_2871del	p.Asn947ThrfsTer8	p.N947Tfs*8	ENST00000234420	NM_000179.2	945	AGAGAAAATGAACAGAGCCTCCTGGAATACCTa/a	4/10	0.159255482809365	3	FACETS	1	0.897	1	0.662	0.512	0.836	CLONAL	1	FALSE	1	0.159255482809365	3		253	215	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103871	209103871	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015601-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	16	397	0	ENST00000345146.2:c.1078G>C	p.Glu360Gln	p.E360Q	ENST00000345146	NM_005896.2	360	Gaa/Caa	9/10	1	2	FACETS	0.632	0.466	0.83	0.632	0.466	0.83	SUBCLONAL	1	FALSE	1	0.159255482809365	2		397	318	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987275	2987275	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015601-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	22	501	0	ENST00000396946.4:c.154A>G	p.Ile52Val	p.I52V	ENST00000396946	NM_032415.4	52	Att/Gtt	3/25	0.159255482809365	3	FACETS	0.763	0.59	0.964	0.381	0.295	0.482	CLONAL	1	FALSE	1	0.159255482809365	3		501	391	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0015686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	76	228	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.329989473068677	2		228	407	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117054	193117054	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	151	431	1	ENST00000367435.3:c.787C>A	p.Arg263Ser	p.R263S	ENST00000367435	NM_024529.4	263	Cgt/Agt	8/17	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.329989473068677	2		432	781	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448359	49448359	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015686-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	107	645	0	ENST00000301067.7:c.352A>T	p.Ile118Phe	p.I118F	ENST00000301067	NM_003482.3	118	Att/Ttt	3/54	1	2	FACETS	0.806	0.722	0.894	0.806	0.722	0.894	CLONAL	1	TRUE	1	0.329989473068677	2		645	805	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0015738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	136	1988	1	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.289811767335255	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.289811767335255	1		1989	796	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712017	89712017	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	39	731	0	ENST00000371953.3:c.634+1G>A		p.X212_splice	ENST00000371953	NM_000314.4	212			0.289811767335255	1	FACETS	0.726	0.604	0.861	0.726	0.604	0.861	SUBCLONAL	1	TRUE	0	0.289811767335255	1		731	317	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143495	30143495	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775832910	NA	P-0015738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	55	922	0	ENST00000389048.3:c.31C>T	p.Pro11Ser	p.P11S	ENST00000389048	NM_004304.4	11	Ccg/Tcg	1/29	1	2	FACETS	0.908	0.779	1	0.908	0.779	1	CLONAL	1	TRUE	1	0.289811767335255	2		922	418	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755539	133755539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015738-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	111	1856	0	ENST00000318560.5:c.1508C>T	p.Ser503Leu	p.S503L	ENST00000318560	NM_005157.4	503	tCa/tTa	9/11	1	2	FACETS	0.868	0.78	0.962	0.868	0.78	0.962	CLONAL	1	TRUE	1	0.289811767335255	2		1856	882	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0015923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	74	469	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.769011517944272	3	FACETS	1	0.943	1	0.549	0.488	0.613	CLONAL	1	FALSE	1	0.808307580311695	3		469	234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0015923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	452	447	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.798047391869318	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	FALSE	0	0.808307580311695	1		447	599	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022824	31022824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	287	440	0	ENST00000375687.4:c.2309C>T	p.Ser770Leu	p.S770L	ENST00000375687	NM_015338.5	770	tCa/tTa	13/13	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.808307580311695	2		440	660	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348200	348200	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	428	594	0	ENST00000262320.3:c.1306C>T	p.His436Tyr	p.H436Y	ENST00000262320	NM_003502.3	436	Cac/Tac	6/11	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	1	FALSE	NA	0.808307580311695	2		594	1034	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953743	48953743	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs587778847	NA	P-0015923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	98	162	0	ENST00000267163.4:c.1346G>T	p.Gly449Val	p.G449V	ENST00000267163	NM_000321.2	449	gGa/gTa	14/27	0.804220895057889	1	FACETS	0.623	0.567	0.68	0.623	0.567	0.68	SUBCLONAL	1	FALSE	0	0.808307580311695	1		162	232	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745732	745732	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	55	307	0	ENST00000314574.4:c.700C>T	p.Gln234Ter	p.Q234*	ENST00000314574	NM_005433.3	234	Cag/Tag	6/12	0.210084810345546	3	FACETS	1	0.958	1	0.624	0.546	0.706	INDETERMINATE	1	FALSE	1	0.808307580311695	3		307	153	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754037	42754038	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0015923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	365	500	0	ENST00000222329.4:c.314_315del	p.Lys105IlefsTer15	p.K105Ifs*15	ENST00000222329	NM_006494.2	105	aAG/a	3/4	0.311127917074086	1	FACETS	0.703	0.671	0.734	0.703	0.671	0.734	INDETERMINATE	1	FALSE	0	0.808307580311695	1		500	766	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39294846	39294846	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	125	296	0	ENST00000402219.2:c.136C>T	p.Gln46Ter	p.Q46*	ENST00000402219	NM_005633.3	46	Cag/Tag	2/23	1	2	FACETS	0.946	0.868	1	0.946	0.868	1	CLONAL	1	FALSE	1	0.808307580311695	2		296	327	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73113194	73113194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	27	58	0	ENST00000356692.5:c.535C>T	p.Arg179Ter	p.R179*	ENST00000356692		179	Cga/Tga	7/9	0.808307580311695	1	FACETS	0.885	0.755	1	0.885	0.755	1	CLONAL	1	FALSE	0	0.808307580311695	1		58	45	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249433	153249433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	162	367	1	ENST00000281708.4:c.1345G>A	p.Glu449Lys	p.E449K	ENST00000281708	NM_033632.3	449	Gag/Aag	9/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.808307580311695	2		368	376	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647566	117647566	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	56	321	0	ENST00000368508.3:c.5378C>A	p.Ser1793Ter	p.S1793*	ENST00000368508	NM_002944.2	1793	tCa/tAa	33/43	0.372134220487549	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.808307580311695	0		321	154	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738338	145738338	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs555817330	NA	P-0015923-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	509	666	0	ENST00000428558.2:c.2647G>C	p.Glu883Gln	p.E883Q	ENST00000428558	NM_004260.3	883	Gag/Cag	16/22	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	FALSE	NA	0.808307580311695	2		666	1185	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123836	46123837	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	113	320	0	ENST00000334344.6:c.109dup	p.Ile37AsnfsTer29	p.I37Nfs*29	ENST00000334344	NM_152641.2	34	-/A	2/21	0.310173995026983	1	FACETS	0.98	0.888	1	0.98	0.888	1	CLONAL	1	TRUE	0	0.423019827657058	1		320	430	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031885	26031885	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	66	194	0	ENST00000244661.2:c.404G>C	p.Arg135Thr	p.R135T	ENST00000244661	NM_003537.3	135	aGa/aCa	1/1	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.423019827657058	2		194	291	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097641	27097641	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	225	756	1	ENST00000324856.7:c.3230C>A	p.Ala1077Glu	p.A1077E	ENST00000324856	NM_006015.4	1077	gCa/gAa	12/20	0.410395396144269	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.423019827657058	1		757	768	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878053	48878053	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	72	334	0	ENST00000267163.4:c.5C>G	p.Pro2Arg	p.P2R	ENST00000267163	NM_000321.2	2	cCg/cGg	1/27	0.423019827657058	2	FACETS	0.69	0.605	0.783	0.345	0.302	0.392	SUBCLONAL	1	TRUE	0	0.423019827657058	2		334	493	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573545	48573545	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	81	355	0	ENST00000342988.3:c.129G>T	p.Leu43Phe	p.L43F	ENST00000342988	NM_005359.5	43	ttG/ttT	2/12	0.423019827657058	1	FACETS	0.932	0.829	1	0.932	0.829	1	CLONAL	1	TRUE	0	0.423019827657058	1		355	324	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56363625	56363625	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	76	396	0	ENST00000348428.3:c.404C>A	p.Ser135Ter	p.S135*	ENST00000348428	NM_006785.3	135	tCa/tAa	3/17	0.423019827657058	1	FACETS	0.941	0.834	1	0.941	0.834	1	CLONAL	1	TRUE	0	0.423019827657058	1		396	301	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050791	5050791	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	169	649	0	ENST00000381652.3:c.574G>T	p.Glu192Ter	p.E192*	ENST00000381652	NM_004972.3	192	Gaa/Taa	6/25	0.423019827657058	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.423019827657058	1		649	623	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411493	63411493	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015979-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	176	831	0	ENST00000330258.3:c.1674A>C	p.Glu558Asp	p.E558D	ENST00000330258	NM_152424.3	558	gaA/gaC	2/2	1	2	FACETS	0.831	0.765	0.9	0.831	0.765	0.9	CLONAL	1	TRUE	1	0.423019827657058	2		831	1001	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0016549-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	482	533	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.232361167211793	5	FACETS	0.939	0.901	0.976			1	INDETERMINATE	3	TRUE	NA	0.639231878573279	5		533	1049	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0016549-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	150	868	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.639231878573279	2		869	453	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088759	27088759	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016549-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	577	664	2	ENST00000324856.7:c.2368C>T	p.Gln790Ter	p.Q790*	ENST00000324856	NM_006015.4	790	Cag/Tag	7/20	0.208798856594866	3	FACETS	0.87	0.843	0.896			1	INDETERMINATE	3	TRUE	NA	0.639231878573279	3		666	913	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406235	70406235	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016549-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	225	627	0	ENST00000373644.4:c.3749C>T	p.Ser1250Leu	p.S1250L	ENST00000373644	NM_030625.2	1250	tCa/tTa	4/12	1	2	FACETS	0.918	0.858	0.98	0.918	0.858	0.98	CLONAL	1	TRUE	1	0.639231878573279	2		627	767	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592301	29592301	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016549-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	132	329	0	ENST00000356175.3:c.4716del	p.Tyr1573ThrfsTer30	p.Y1573Tfs*30	ENST00000356175	NM_000267.3	1572	ttC/tt	35/57	0.287069426886032	3	FACETS	1	0.979	1	0.614	0.561	0.668	INDETERMINATE	1	TRUE	1	0.639231878573279	3		329	444	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227938	55227938	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	63	497	0	ENST00000275493.2:c.1405T>G	p.Leu469Val	p.L469V	ENST00000275493	NM_005228.3	469	Ttg/Gtg	12/28	0.133208042960999	3	FACETS	0.979	0.86	1	0.979	0.86	1	INDETERMINATE	2	TRUE	1	0.359964845998708	3		497	211	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25457210	25457210	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	51	570	0	ENST00000264709.3:c.2677T>G	p.Trp893Gly	p.W893G	ENST00000264709	NM_175629.2	893	Tgg/Ggg	23/23	1	2	FACETS	0.824	0.703	0.955	0.824	0.703	0.955	CLONAL	1	TRUE	1	0.359964845998708	2		570	344	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442538	52442538	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016640-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	57	539	0	ENST00000460680.1:c.207del	p.Ser70ProfsTer2	p.S70Pfs*2	ENST00000460680	NM_004656.3	69	acG/ac	4/17	0.359964845998708	1	FACETS	0.965	0.836	1	0.965	0.836	1	CLONAL	1	TRUE	0	0.359964845998708	1		539	269	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0016714-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	111	753	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.208643801544475	3	FACETS	1	0.966	1	0.59	0.529	0.654	CLONAL	1	FALSE	1	0.208643801544475	3		754	996	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0016714-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	109	582	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.208643801544475	2		582	744	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941658	48941658	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs765678030	NA	P-0016714-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	12	26	0	ENST00000267163.4:c.968A>G	p.Glu323Gly	p.E323G	ENST00000267163	NM_000321.2	323	gAa/gGa	10/27	0.208643801544475	1	FACETS	1	0.785	1	1	0.785	1	CLONAL	1	FALSE	0	0.208643801544475	1		26	91	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650569	18650569	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750864969	NA	P-0016714-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	55	320	0	ENST00000266497.5:c.2780G>A	p.Arg927His	p.R927H	ENST00000266497		927	cGt/cAt	20/31	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	FALSE	1	0.208643801544475	2		320	415	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432024	121432024	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016714-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	118	884	0	ENST00000257555.6:c.771C>A	p.Asn257Lys	p.N257K	ENST00000257555		257	aaC/aaA	4/10	1	2	FACETS	0.972	0.874	1	0.972	0.874	1	CLONAL	1	FALSE	1	0.208643801544475	2		884	1164	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2114373	2114373	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016714-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	116	899	0	ENST00000219476.3:c.1544del	p.Leu515ArgfsTer20	p.L515Rfs*20	ENST00000219476	NM_000548.3	515	cTg/cg	15/42	0.128213512727781	1	FACETS	0.92	0.828	1	0.92	0.828	1	CLONAL	1	FALSE	0	0.208643801544475	1		899	1082	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943729	9943729	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016714-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	119	740	0	ENST00000330684.3:c.1212C>A	p.Asn404Lys	p.N404K	ENST00000330684	NM_001134407.1	404	aaC/aaA	5/13	0.128213512727781	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	0	0.208643801544475	1		740	915	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976400	18976400	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016714-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	111	948	0	ENST00000262803.5:c.3050G>C	p.Arg1017Pro	p.R1017P	ENST00000262803	NM_002911.3	1017	cGt/cCt	22/24	1	2	FACETS	0.833	0.747	0.926	0.833	0.747	0.926	CLONAL	1	FALSE	1	0.208643801544475	2		948	1277	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158242	47158242	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016714-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	33	138	0	ENST00000409792.3:c.4457A>T	p.Lys1486Met	p.K1486M	ENST00000409792	NM_014159.6	1486	aAg/aTg	4/21	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	FALSE	1	0.208643801544475	2		138	282	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542429	187542429	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs755310203	NA	P-0016714-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	59	380	0	ENST00000441802.2:c.5311A>G	p.Thr1771Ala	p.T1771A	ENST00000441802	NM_005245.3	1771	Aca/Gca	10/27	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	FALSE	1	0.208643801544475	2		380	518	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374390	81374390	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016714-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	50	341	0	ENST00000222390.5:c.672T>A	p.Asp224Glu	p.D224E	ENST00000222390	NM_000601.4	224	gaT/gaA	6/18	1	2	FACETS	0.841	0.713	0.981	0.841	0.713	0.981	CLONAL	1	FALSE	1	0.208643801544475	2		341	570	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39600661	39600661	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0016714-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	17	101	0	ENST00000262039.4:c.1476T>G	p.Tyr492Ter	p.Y492*	ENST00000262039	NM_002647.2	492	taT/taG	13/25	0.208643801544475	5	FACETS	0.856	0.639	1	0.214	0.159	0.278	CLONAL	1	FALSE	1	0.208643801544475	5		101	250	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0016805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	26	228	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.713	0.565	0.882	0.713	0.565	0.882	SUBCLONAL	1	TRUE	1	0.23	2		228	317	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698121	47698121	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016805-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	53	405	0	ENST00000233146.2:c.1679A>G	p.Asn560Ser	p.N560S	ENST00000233146	NM_000251.2	560	aAt/aGt	11/16	1	2	FACETS	0.991	0.846	1	0.991	0.846	1	CLONAL	1	TRUE	1	0.23	2		405	465	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911081	29911082	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0017268-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	163	591	0	ENST00000376809.5:c.383_384dup	p.Ser129GlyfsTer23	p.S129Gfs*23	ENST00000376809	NM_002116.7	127	gtg/gtGGg	3/8	1	2	FACETS	0.905	0.833	0.979	0.905	0.833	0.979	CLONAL	1	FALSE	1	0.538711408340726	2		591	669	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0017322-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	24	242	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.681	0.535	0.848	0.681	0.535	0.848	SUBCLONAL	1	TRUE	1	0.26215441594248	2		242	269	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473723	67473723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863223740	NA	P-0017322-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	40	311	0	ENST00000327367.4:c.803G>A	p.Arg268His	p.R268H	ENST00000327367	NM_005902.3	268	cGc/cAc	6/9	1	2	FACETS	0.52	0.431	0.619	0.52	0.431	0.619	SUBCLONAL	1	TRUE	1	0.26215441594248	2		311	587	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604754	48604754	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017322-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	94	224	0	ENST00000342988.3:c.1576G>T	p.Glu526Ter	p.E526*	ENST00000342988	NM_005359.5	526	Gaa/Taa	12/12	0.218056985084159	2	FACETS	0.901	0.807	0.999	0.901	0.807	0.999	CLONAL	2	TRUE	0	0.26215441594248	2		224	398	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879441	56879441	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017322-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	133	296	0	ENST00000519728.1:c.958G>T	p.Glu320Ter	p.E320*	ENST00000519728	NM_002350.3	320	Gag/Tag	9/13	0.247396095224266	3	FACETS	0.838	0.762	0.917	0.838	0.762	0.917	CLONAL	2	TRUE	1	0.26215441594248	3		296	685	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132970	30132970	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017322-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	52	299	0	ENST00000331968.5:c.631G>T	p.Gly211Trp	p.G211W	ENST00000331968	NM_002742.2	211	Ggg/Tgg	4/18	1	2	FACETS	0.639	0.543	0.744	0.639	0.543	0.744	SUBCLONAL	1	TRUE	1	0.26215441594248	2		299	621	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028883	47028883	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017322-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	63	349	0	ENST00000377604.3:c.187G>T	p.Glu63Ter	p.E63*	ENST00000377604	NM_001204468.1	63	Gag/Tag	3/24	0.26215441594248	1	FACETS	0.876	0.759	1	0.876	0.759	1	CLONAL	1	TRUE	0	0.26215441594248	1		349	477	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462207	120462207	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017322-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	44	258	0	ENST00000256646.2:c.5509C>G	p.Leu1837Val	p.L1837V	ENST00000256646	NM_024408.3	1837	Ctc/Gtc	31/34	1	2	FACETS	0.867	0.729	1	0.867	0.729	1	CLONAL	1	TRUE	1	0.26215441594248	2		258	387	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468097	120468102	+	inframe_deletion	In_Frame_Del	DEL	AGGCAT	AGGCAT	-	novel	NA	P-0017322-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	60	335	0	ENST00000256646.2:c.4337_4342del	p.His1446_Cys1448delinsArg	p.H1446_C1448delinsR	ENST00000256646	NM_024408.3	1446	cATGCCTgc/cgc	25/34	1	2	FACETS	0.76	0.655	0.875	0.76	0.655	0.875	SUBCLONAL	1	TRUE	1	0.26215441594248	2		335	602	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242700	46242700	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017322-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	15	182	0	ENST00000334344.6:c.1662T>A	p.Ser554Arg	p.S554R	ENST00000334344	NM_152641.2	554	agT/agA	13/21	1	2	FACETS	0.456	0.333	0.603	0.456	0.333	0.603	SUBCLONAL	1	TRUE	1	0.26215441594248	2		182	251	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432146	121432146	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017322-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	43	345	0	ENST00000257555.6:c.893C>A	p.Ala298Glu	p.A298E	ENST00000257555		298	gCg/gAg	4/10	1	2	FACETS	0.588	0.491	0.695	0.588	0.491	0.695	SUBCLONAL	1	TRUE	1	0.26215441594248	2		345	558	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586077	29586077	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017322-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	15	162	0	ENST00000356175.3:c.4297C>T	p.Leu1433Phe	p.L1433F	ENST00000356175	NM_000267.3	1433	Ctc/Ttc	32/57	1	2	FACETS	0.493	0.361	0.652	0.493	0.361	0.652	SUBCLONAL	1	TRUE	1	0.26215441594248	2		162	232	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220675	1220677	+	frameshift_variant	Frame_Shift_Del	DEL	CTC	CTC	TT	novel	NA	P-0017322-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	92	438	1	ENST00000326873.7:c.693_695delinsTT	p.Gly233AlafsTer54	p.G233Afs*54	ENST00000326873	NM_000455.4	231	ttCTCc/ttTTc	5/10	1	2	FACETS	0.993	0.882	1	0.993	0.882	1	CLONAL	1	TRUE	1	0.26215441594248	2		439	707	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223066	1223066	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017322-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	73	403	0	ENST00000326873.7:c.1003del	p.Met335Ter	p.M335*	ENST00000326873	NM_000455.4	335	Atg/tg	8/10	1	2	FACETS	0.779	0.681	0.885	0.779	0.681	0.885	SUBCLONAL	1	TRUE	1	0.26215441594248	2		403	715	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172322	7172322	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017322-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	53	227	0	ENST00000302850.5:c.1247G>T	p.Arg416Leu	p.R416L	ENST00000302850	NM_000208.2	416	cGa/cTa	5/22	1	2	FACETS	0.719	0.613	0.836	0.719	0.613	0.836	SUBCLONAL	1	TRUE	1	0.26215441594248	2		227	562	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215593	36215593	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs928165563	NA	P-0017322-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	89	445	0	ENST00000222270.7:c.3390G>T	p.Gln1130His	p.Q1130H	ENST00000222270	NM_014727.1	1130	caG/caT	9/37	1	2	FACETS	0.872	0.772	0.978	0.872	0.772	0.978	CLONAL	1	TRUE	1	0.26215441594248	2		445	779	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141112	55141112	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017322-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	33	185	0	ENST00000257290.5:c.1758G>T	p.Trp586Cys	p.W586C	ENST00000257290	NM_006206.4	586	tgG/tgT	12/23	1	2	FACETS	0.637	0.519	0.77	0.637	0.519	0.77	SUBCLONAL	1	TRUE	1	0.26215441594248	2		185	395	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197106	106197107	+	stop_gained	Nonsense_Mutation	DNP	AG	AG	TT	novel	NA	P-0017322-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	26	163	0	ENST00000380013.4:c.5439_5440delinsTT	p.Gln1813_Gly1814delinsHisTer	p.Q1813_G1814delinsH*	ENST00000380013	NM_001127208.2	1813	caAGga/caTTga	11/11	1	2	FACETS	0.74	0.588	0.914	0.74	0.588	0.914	CLONAL	1	TRUE	1	0.26215441594248	2		163	268	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177579	56177579	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017322-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	47	197	0	ENST00000399503.3:c.2552G>T	p.Arg851Met	p.R851M	ENST00000399503	NM_005921.1	851	aGg/aTg	14/20	1	2	FACETS	0.883	0.747	1	0.883	0.747	1	CLONAL	1	TRUE	1	0.26215441594248	2		197	406	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441315	149441315	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017322-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	67	331	0	ENST00000286301.3:c.1724G>T	p.Trp575Leu	p.W575L	ENST00000286301	NM_005211.3	575	tGg/tTg	12/22	1	2	FACETS	0.82	0.713	0.937	0.82	0.713	0.937	CLONAL	1	TRUE	1	0.26215441594248	2		331	623	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176339	24176339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs387906812	NA	P-0017696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	209	720	1	ENST00000263121.7:c.1130G>A	p.Arg377His	p.R377H	ENST00000263121	NM_003073.3	377	cGt/cAt	9/9	1	2	FACETS	0.954	0.887	1	0.954	0.887	1	CLONAL	1	TRUE	1	0.524328589770126	2		721	836	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0017696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	339	711	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.409252739244283	2	FACETS	0.75	0.712	0.788	0.75	0.712	0.788	SUBCLONAL	2	TRUE	0	0.524328589770126	2		711	862	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0017696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	143	577	2				ENST00000310581	NM_198253.2	-/1132			0.264828146952826	3	FACETS	0.848	0.773	0.926	0.424	0.386	0.463	INDETERMINATE	1	TRUE	1	0.524328589770126	3		579	812	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123789	11123789	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1555774786	NA	P-0017696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	121	336	0	ENST00000358026.2:c.2438+1G>A		p.X813_splice	ENST00000358026	NM_001128849.1	813			0.493017128321264	1	FACETS	0.867	0.79	0.945	0.867	0.79	0.945	CLONAL	1	TRUE	0	0.524328589770126	1		336	393	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971133	21971133	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	148	493	0	ENST00000304494.5:c.225del	p.Ala76ProfsTer70	p.A76Pfs*70	ENST00000304494	NM_000077.4	75	ccC/cc	2/3	0.524328589770126	1	FACETS	0.833	0.766	0.902	0.833	0.766	0.902	CLONAL	1	TRUE	0	0.524328589770126	1		493	500	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250512	110250512	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs772132221	NA	P-0017696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	135	451	0	ENST00000374672.4:c.163C>A	p.Pro55Thr	p.P55T	ENST00000374672	NM_004235.4	55	Ccc/Acc	3/5	0.493017128321264	1	FACETS	0.931	0.855	1	0.931	0.855	1	CLONAL	1	TRUE	0	0.524328589770126	1		451	408	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165783	108165783	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060501627	NA	P-0017764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	84	489	0	ENST00000278616.4:c.4906C>T	p.Gln1636Ter	p.Q1636*	ENST00000278616	NM_000051.3	1636	Cag/Tag	32/63	0.201281731131102	3	FACETS	1	0.974	1	0.687	0.609	0.77	CLONAL	1	TRUE	1	0.287773649674232	3		489	486	SUCCESS
ATM	472	MSKCC	GRCh37	11	108188140	108188140	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587779855	NA	P-0017764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	73	590	0	ENST00000278616.4:c.6239A>G	p.Tyr2080Cys	p.Y2080C	ENST00000278616	NM_000051.3	2080	tAt/tGt	43/63	0.201281731131102	3	FACETS	0.867	0.758	0.985	0.434	0.379	0.493	CLONAL	1	TRUE	1	0.287773649674232	3		590	669	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588858	52588859	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	132	745	0	ENST00000394830.3:c.4169dup	p.Leu1390PhefsTer6	p.L1390Ffs*6	ENST00000394830	NM_018313.4	1390	ttg/ttTg	27/30	0.199052416226112	2	FACETS	0.956	0.873	1	0.956	0.873	1	CLONAL	2	TRUE	0	0.287773649674232	2		745	480	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206915	162206915	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017764-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	89	529	0	ENST00000366898.1:c.760A>G	p.Asn254Asp	p.N254D	ENST00000366898	NM_004562.2	254	Aac/Gac	7/12	NA	2	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.287773649674232	2		529	497	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0017934-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	55	473	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.253517851708803	1	FACETS	0.649	0.555	0.752	0.649	0.555	0.752	SUBCLONAL	1	TRUE	0	0.264803914776115	1		473	555	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0017934-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	80	545	0	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	0.264803914776115	3	FACETS	0.95	0.836	1	0.475	0.418	0.537	CLONAL	1	TRUE	1	0.264803914776115	3		545	720	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579329	7579329	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs121912658	NA	P-0017934-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	98	652	3	ENST00000269305.4:c.358A>T	p.Lys120Ter	p.K120*	ENST00000269305	NM_001126112.2	120	Aag/Tag	4/11	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.264803914776115	2		655	674	SUCCESS
APC	324	MSKCC	GRCh37	5	112155042	112155042	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0017934-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	54	462	0	ENST00000257430.4:c.1312+1G>T		p.X438_splice	ENST00000257430	NM_000038.5	438			0.264803914776115	1	FACETS	0.795	0.68	0.92	0.795	0.68	0.92	CLONAL	1	TRUE	0	0.264803914776115	1		462	445	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151871297	151871297	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017934-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	37	385	0	ENST00000262189.6:c.9293A>C	p.Lys3098Thr	p.K3098T	ENST00000262189	NM_170606.2	3098	aAa/aCa	39/59	1	2	FACETS	0.759	0.627	0.907	0.759	0.627	0.907	CLONAL	1	TRUE	1	0.264803914776115	2		385	368	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983151	201983324	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTGAGCTGGCGGCCAGGACCCTCACGATACAGCCGGACATGGGGACAGGCGCTCACACTCCCACCGCCCTCTTTCTGGCTGCCACTTGGCTTCTTGCAACAGGGCTGAGTCCTTAGAGTGAGGACAACATCTGGGTTGGTCTACTTCATGGATTAAATGACAACATGGAGAA	AGGTGAGCTGGCGGCCAGGACCCTCACGATACAGCCGGACATGGGGACAGGCGCTCACACTCCCACCGCCCTCTTTCTGGCTGCCACTTGGCTTCTTGCAACAGGGCTGAGTCCTTAGAGTGAGGACAACATCTGGGTTGGTCTACTTCATGGATTAAATGACAACATGGAGAA	-	novel	NA	P-0018375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	58	861	0	ENST00000359651.3:c.1001+1_1001+174del		p.X334_splice	ENST00000359651		334		7/8	0.151616261490217	2	FACETS	1	0.962	1	0.687	0.59	0.792	CLONAL	1	TRUE	0	0.151616261490217	2		861	557	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228980	36228980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780852805	NA	P-0018375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	70	928	0	ENST00000222270.7:c.7760G>A	p.Arg2587Gln	p.R2587Q	ENST00000222270	NM_014727.1	2587	cGa/cAa	36/37	1	2	FACETS	0.809	0.706	0.92	1	0.976	1	CLONAL	2	TRUE	1	0.151616261490217	2		928	571	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785929	135786379	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGAGGGATAGCAGACGAGCTGGATCGCACCTTCCTGGGGGGTGTGACTGTGGCCTGGGGGAGTGAAATGTGCACGTAGTCATCCGAATGACAGAGTGGGGCTGGAGGAGGAGAGGTTGCTGGGGTTCCCAGAGGAGTTCCTTTTCCACCTGCTTAGAGACAAGGGCAGAACATATATGAACACTGAGCCCAACTATTAGAAAAACTGCCGATTTTTTTTCAGCCTATAACTATTACTATAAATAAAGCTGCTAGAGTTAACTTTCTGGGGATCTAGATCAGTCTCTCTCTTTTTTGTTTTTAGGTTCACTTTACACATTCTGAAAGCCCCAGGGATTTGCAATAAGTGTCAAAAACAAGTTTACAACAGCAAGTGGTCCCTTAGATCTAAAAGAGAGCTCCTCCTGCCATTAAAGGCAGGCCAAAACCAACTAATCAAATCCAACCTAAGA	AGAGGGATAGCAGACGAGCTGGATCGCACCTTCCTGGGGGGTGTGACTGTGGCCTGGGGGAGTGAAATGTGCACGTAGTCATCCGAATGACAGAGTGGGGCTGGAGGAGGAGAGGTTGCTGGGGTTCCCAGAGGAGTTCCTTTTCCACCTGCTTAGAGACAAGGGCAGAACATATATGAACACTGAGCCCAACTATTAGAAAAACTGCCGATTTTTTTTCAGCCTATAACTATTACTATAAATAAAGCTGCTAGAGTTAACTTTCTGGGGATCTAGATCAGTCTCTCTCTTTTTTGTTTTTAGGTTCACTTTACACATTCTGAAAGCCCCAGGGATTTGCAATAAGTGTCAAAAACAAGTTTACAACAGCAAGTGGTCCCTTAGATCTAAAAGAGAGCTCCTCCTGCCATTAAAGGCAGGCCAAAACCAACTAATCAAATCCAACCTAAGA	-	novel	NA	P-0018375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	30	721	0	ENST00000298552.3:c.1141+10_1263+29del		p.X381_splice	ENST00000298552	NM_001162426.1	381		12/23	0.151616261490217	1	FACETS	0.867	0.698	1	0.867	0.698	1	CLONAL	1	TRUE	0	0.151616261490217	1		721	422	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786465	135786465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878853958	NA	P-0018375-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	50	956	1	ENST00000298552.3:c.1065G>A	p.Met355Ile	p.M355I	ENST00000298552	NM_001162426.1	355	atG/atA	11/23	0.151616261490217	1	FACETS	0.906	0.767	1	0.906	0.767	1	CLONAL	1	TRUE	0	0.151616261490217	1		957	673	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0018420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	264	868	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.433091204022626	2		869	1056	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0018420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	108	270	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.433091204022626	2		270	484	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067824	30067824	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	63	238	0	ENST00000338641.4:c.1009C>T	p.Gln337Ter	p.Q337*	ENST00000338641	NM_000268.3	337	Cag/Tag	11/16	0.433091204022626	1	FACETS	0.651	0.566	0.742	0.651	0.566	0.742	SUBCLONAL	1	TRUE	0	0.433091204022626	1		238	350	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211118	36211118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200835025	NA	P-0018420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	88	545	0	ENST00000222270.7:c.869G>A	p.Arg290His	p.R290H	ENST00000222270	NM_014727.1	290	cGt/cAt	3/37	1	2	FACETS	0.35	0.309	0.395	0.35	0.309	0.395	SUBCLONAL	1	TRUE	1	0.433091204022626	2		545	1160	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223338	36223338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146177906	NA	P-0018420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	67	603	1	ENST00000222270.7:c.5888C>T	p.Pro1963Leu	p.P1963L	ENST00000222270	NM_014727.1	1963	cCg/cTg	28/37	1	2	FACETS	0.261	0.226	0.3	0.261	0.226	0.3	SUBCLONAL	1	TRUE	1	0.433091204022626	2		604	1185	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560910	9560910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766880332	NA	P-0018420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	57	323	0	ENST00000353224.5:c.872G>A	p.Gly291Glu	p.G291E	ENST00000353224	NM_177990.2	291	gGa/gAa	4/10	1	2	FACETS	0.393	0.337	0.455	0.393	0.337	0.455	SUBCLONAL	1	TRUE	1	0.433091204022626	2		323	669	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538326	187538326	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	130	402	0	ENST00000441802.2:c.8908G>A	p.Glu2970Lys	p.E2970K	ENST00000441802	NM_005245.3	2970	Gaa/Aaa	11/27	1	2	FACETS	0.607	0.55	0.668	0.607	0.55	0.668	SUBCLONAL	1	TRUE	1	0.433091204022626	2		402	989	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0018552-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	280	469	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.234356853340805	3	FACETS	1	0.983	1	0.72	0.683	0.757	INDETERMINATE	2	TRUE	0	0.577280249285469	3		469	579	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018552-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	122	573	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	0.544906344703467	2	FACETS	0.581	0.525	0.639	0.29	0.262	0.32	SUBCLONAL	1	TRUE	0	0.577280249285469	2		573	728	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0018552-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	88	498	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.438192662482331	1	FACETS	0.348	0.308	0.39	0.348	0.308	0.39	SUBCLONAL	1	TRUE	0	0.577280249285469	1		498	623	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577144	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs879253942	NA	P-0018552-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	220	551	0	ENST00000269305.4:c.794T>C	p.Leu265Pro	p.L265P	ENST00000269305	NM_001126112.2	265	cTg/cCg	8/11	0.577280249285469	1	FACETS	0.935	0.876	0.994	0.935	0.876	0.994	CLONAL	1	TRUE	0	0.577280249285469	1		551	580	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225896	2225896	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018567-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	55	538	0	ENST00000326181.6:c.1688A>G	p.Tyr563Cys	p.Y563C	ENST00000326181	NM_032271.2	563	tAc/tGc	18/21	0.158567622585531	3	FACETS	1	0.965	1	0.738	0.632	0.854	CLONAL	1	TRUE	1	0.158567622585531	3		538	507	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0019002-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	43	469	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.230863604629897	3	FACETS	0.539	0.45	0.636	0.269	0.225	0.318	SUBCLONAL	1	TRUE	1	0.372128216565489	3		469	509	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861733	59861733	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555603567	NA	P-0019002-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	31	367	0	ENST00000259008.2:c.1526G>A	p.Gly509Asp	p.G509D	ENST00000259008	NM_032043.2	509	gGt/gAt	11/20	1	2	FACETS	0.367	0.296	0.447	0.367	0.296	0.447	SUBCLONAL	1	TRUE	1	0.372128216565489	2		367	454	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053541	37053541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019002-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	42	465	0	ENST00000231790.2:c.628G>A	p.Ala210Thr	p.A210T	ENST00000231790	NM_000249.3	210	Gcc/Acc	8/19	1	2	FACETS	0.362	0.301	0.429	0.362	0.301	0.429	SUBCLONAL	1	TRUE	1	0.372128216565489	2		465	624	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442542	52442542	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1194652468	NA	P-0019194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	101	940	0	ENST00000460680.1:c.203A>G	p.Asp68Gly	p.D68G	ENST00000460680	NM_004656.3	68	gAt/gGt	4/17	0.293656657860403	1	FACETS	0.856	0.766	0.952	0.856	0.766	0.952	CLONAL	1	TRUE	0	0.306735490213303	1		940	651	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867469	35867469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs191585195	NA	P-0019194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	53	778	1	ENST00000303115.3:c.283G>A	p.Glu95Lys	p.E95K	ENST00000303115	NM_002185.3	95	Gag/Aag	3/8	1	2	FACETS	0.718	0.613	0.833	0.718	0.613	0.833	SUBCLONAL	1	TRUE	1	0.306735490213303	2		779	481	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201984385	201984385	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0019194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	144	1259	1	ENST00000359651.3:c.1050del	p.Val351SerfsTer96	p.V351Sfs*96	ENST00000359651		350	ctC/ct	8/8	1	2	FACETS	0.95	0.866	1	0.95	0.866	1	CLONAL	1	TRUE	1	0.306735490213303	2		1260	988	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61720104	61720104	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	46	1128	0	ENST00000401558.2:c.1330T>C	p.Phe444Leu	p.F444L	ENST00000401558	NM_003400.3	444	Ttc/Ctc	13/25	1	2	FACETS	0.382	0.32	0.45	0.382	0.32	0.45	SUBCLONAL	1	TRUE	1	0.306735490213303	2		1128	786	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670750	134670750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019194-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	27	746	0	ENST00000398015.3:c.661G>A	p.Ala221Thr	p.A221T	ENST00000398015	NM_004441.4	221	Gct/Act	3/16	1	2	FACETS	0.358	0.284	0.443	0.358	0.284	0.443	SUBCLONAL	1	TRUE	1	0.306735490213303	2		746	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0019351-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	184	668	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	NA	2	FACETS	0.954	0.902	1			1	INDETERMINATE	2	TRUE	NA	0.649238550554161	2		670	297	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202720	133202720	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019351-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	68	469	0	ENST00000320574.5:c.6514G>C	p.Asp2172His	p.D2172H	ENST00000320574	NM_006231.2	2172	Gac/Cac	46/49	0.649238550554161	2	FACETS	0.935	0.826	1	0.468	0.413	0.525	CLONAL	1	TRUE	0	0.649238550554161	2		469	224	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857152	9857152	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369508378	NA	P-0019351-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	150	352	0	ENST00000330684.3:c.4249C>T	p.Arg1417Trp	p.R1417W	ENST00000330684	NM_001134407.1	1417	Cgg/Tgg	13/13	0.649238550554161	3	FACETS	0.761	0.703	0.82	0.508	0.469	0.547	SUBCLONAL	2	TRUE	0	0.649238550554161	3		352	402	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200270	67200270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201348433	NA	P-0019351-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	100	584	0	ENST00000312629.5:c.578G>A	p.Arg193Gln	p.R193Q	ENST00000312629	NM_003952.2	193	cGg/cAg	7/15	0.649238550554161	2	FACETS	0.883	0.796	0.973	0.441	0.398	0.487	CLONAL	1	TRUE	0	0.649238550554161	2		584	349	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259348	11259348	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019351-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	72	532	0	ENST00000361445.4:c.4220G>T	p.Gly1407Val	p.G1407V	ENST00000361445	NM_004958.3	1407	gGc/gTc	28/58	NA	2	FACETS	0.88	0.779	0.986			1	INDETERMINATE	1	TRUE	NA	0.649238550554161	2		532	252	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552770	226552770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019351-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	89	515	0	ENST00000366794.5:c.2591C>T	p.Ser864Phe	p.S864F	ENST00000366794	NM_001618.3	864	tCc/tTc	19/23	0.649238550554161	3	FACETS	1	0.908	1	0.509	0.455	0.565	CLONAL	1	TRUE	1	0.649238550554161	3		515	357	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212490	5212490	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019351-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	64	520	1	ENST00000357368.4:c.4627G>A	p.Glu1543Lys	p.E1543K	ENST00000357368	NM_002850.3	1543	Gag/Aag	31/38	0.649238550554161	2	FACETS	0.798	0.699	0.902	0.399	0.349	0.451	CLONAL	1	TRUE	0	0.649238550554161	2		521	247	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753057	42753057	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751388026	NA	P-0019351-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	43	662	0	ENST00000222329.4:c.1207G>A	p.Gly403Ser	p.G403S	ENST00000222329	NM_006494.2	403	Ggt/Agt	4/4	0.649238550554161	2	FACETS	0.341	0.286	0.403	0.171	0.143	0.202	SUBCLONAL	1	TRUE	0	0.649238550554161	2		662	388	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242800919	242800919	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019351-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	97	670	0	ENST00000334409.5:c.72C>G	p.Phe24Leu	p.F24L	ENST00000334409	NM_005018.2	24	ttC/ttG	1/5	0.649238550554161	3	FACETS	0.898	0.805	0.995	0.449	0.402	0.498	CLONAL	1	TRUE	1	0.649238550554161	3		670	441	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024761	31024761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019351-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	91	473	0	ENST00000375687.4:c.4246G>A	p.Glu1416Lys	p.E1416K	ENST00000375687	NM_015338.5	1416	Gag/Aag	13/13	0.649238550554161	2	FACETS	1	0.944	1	0.535	0.482	0.59	CLONAL	1	TRUE	0	0.649238550554161	2		473	262	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385172	41385172	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019351-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	93	661	0	ENST00000373198.4:c.789C>G	p.Ser263Arg	p.S263R	ENST00000373198	NM_133170.3	263	agC/agG	6/32	0.649238550554161	8	FACETS	1	0.962	1			1	CLONAL	1	TRUE	NA	0.649238550554161	8		661	710	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430884	181430884	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0019351-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	67	807	0	ENST00000325404.1:c.736T>G	p.Ser246Ala	p.S246A	ENST00000325404	NM_003106.3	246	Tcc/Gcc	1/1	0.638424240570117	4	FACETS	0.557	0.484	0.636	0.186	0.161	0.212	SUBCLONAL	1	TRUE	1	0.649238550554161	4		807	611	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120536	94120536	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0019351-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	79	309	0	ENST00000369303.4:c.515G>C	p.Arg172Thr	p.R172T	ENST00000369303	NM_004440.3	172	aGa/aCa	3/17	0.540537807110234	3	FACETS	1	0.974	1	0.442	0.395	0.492	CLONAL	1	TRUE	0	0.649238550554161	3		309	243	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700262	117700262	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019351-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	87	415	0	ENST00000368508.3:c.2557C>G	p.Gln853Glu	p.Q853E	ENST00000368508	NM_002944.2	853	Caa/Gaa	17/43	0.540537807110234	3	FACETS	0.962	0.858	1	0.321	0.286	0.357	CLONAL	1	TRUE	0	0.649238550554161	3		415	369	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012394	152012394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019351-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	48	248	0	ENST00000262189.6:c.419G>A	p.Gly140Glu	p.G140E	ENST00000262189	NM_170606.2	140	gGg/gAg	4/59	0.649238550554161	3	FACETS	0.771	0.657	0.894	0.386	0.328	0.447	SUBCLONAL	1	TRUE	1	0.649238550554161	3		248	254	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339256	87339256	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019351-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	79	360	0	ENST00000277120.3:c.838A>T	p.Asn280Tyr	p.N280Y	ENST00000277120		280	Aac/Tac	8/19	0.628651035712003	2	FACETS	0.857	0.762	0.956	0.428	0.381	0.478	CLONAL	1	TRUE	0	0.649238550554161	2		360	284	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781236	135781236	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs118203570	NA	P-0019351-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	103	548	0	ENST00000298552.3:c.1729G>T	p.Glu577Ter	p.E577*	ENST00000298552	NM_001162426.1	577	Gag/Tag	15/23	0.628651035712003	2	FACETS	1	0.974	1	0.599	0.545	0.654	CLONAL	1	TRUE	0	0.649238550554161	2		548	265	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399990	139399990	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0019351-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	25	700	0	ENST00000277541.6:c.4358A>G	p.Glu1453Gly	p.E1453G	ENST00000277541	NM_017617.3	1453	gAg/gGg	25/34	0.550215818696142	3	FACETS	0.271	0.213	0.337	0.09	0.071	0.113	SUBCLONAL	1	TRUE	0	0.649238550554161	3		700	377	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248633	59248634	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0019382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	283	1135	0	ENST00000371222.2:c.109_110del	p.Ser37HisfsTer69	p.S37Hfs*69	ENST00000371222	NM_002228.3	37	AGc/c	1/1	0.438099024648262	2	FACETS	0.833	0.787	0.878	0.833	0.787	0.878	CLONAL	2	TRUE	0	0.488399404133464	2		1135	696	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86676412	86676412	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019382-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	83	355	0	ENST00000274376.6:c.2690G>A	p.Ser897Asn	p.S897N	ENST00000274376	NM_002890.2	897	aGt/aAt	20/25	0.125773094227144	5	FACETS	1	0.952	1			1	INDETERMINATE	3	TRUE	NA	0.488399404133464	5		355	181	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600464	10600464	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019765-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	217	408	0	ENST00000171111.5:c.1391G>T	p.Gly464Val	p.G464V	ENST00000171111	NM_203500.1	464	gGc/gTc	4/6	0.3	3	FACETS	1	0.989	1	0.668	0.62	0.717	CLONAL	1	TRUE	1	0.32	3		408	1178	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974799	21974799	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0019765-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	30	66	0	ENST00000304494.5:c.28G>T	p.Glu10Ter	p.E10*	ENST00000304494	NM_000077.4	10	Gag/Tag	1/3	0.217668830025503	3	FACETS	1	0.884	1	0.563	0.458	0.681	CLONAL	1	TRUE	1	0.32	3		66	193	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258581	16258581	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019765-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	142	314	0	ENST00000375759.3:c.5846G>T	p.Arg1949Leu	p.R1949L	ENST00000375759	NM_015001.2	1949	cGg/cTg	11/15	0.25345999253881	3	FACETS	1	0.968	1	0.566	0.516	0.619	CLONAL	1	TRUE	1	0.32	3		314	909	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731181	162731181	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019765-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	71	260	0	ENST00000367921.3:c.1036A>T	p.Ile346Phe	p.I346F	ENST00000367921	NM_006182.2	346	Atc/Ttc	9/18	0.159815576105022	5	FACETS	0.967	0.844	1	0.322	0.281	0.367	INDETERMINATE	1	TRUE	2	0.32	5		260	679	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944122	71944122	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0019765-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	337	393	0	ENST00000298229.2:c.1955A>T	p.Glu652Val	p.E652V	ENST00000298229	NM_001567.3	652	gAg/gTg	17/28	0.272962935347814	5	FACETS	0.856	0.809	0.904	0.642	0.607	0.678	CLONAL	3	TRUE	1	0.32	5		393	1214	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117430	115117430	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0019765-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	53	227	0	ENST00000257566.3:c.744C>G	p.Tyr248Ter	p.Y248*	ENST00000257566	NM_016569.3	248	taC/taG	4/8	0.217668830025503	3	FACETS	0.645	0.549	0.749	0.322	0.274	0.375	SUBCLONAL	1	TRUE	1	0.32	3		227	596	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478604	99478604	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019765-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	101	266	0	ENST00000268035.6:c.3246G>T	p.Met1082Ile	p.M1082I	ENST00000268035	NM_000875.3	1082	atG/atT	17/21	0.25345999253881	3	FACETS	0.957	0.855	1	0.479	0.427	0.533	CLONAL	1	TRUE	1	0.32	3		266	765	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577542	7577561	+	frameshift_variant	Frame_Shift_Del	DEL	TCATGCCGCCCATGCAGGAA	TCATGCCGCCCATGCAGGAA	-	novel	NA	P-0019765-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	63	308	0	ENST00000269305.4:c.720_739del	p.Ser240ArgfsTer17	p.S240Rfs*17	ENST00000269305	NM_001126112.2	240	agTTCCTGCATGGGCGGCATGAac/agac	7/11	0.167255218127881	4	FACETS	0.483	0.416	0.556	0.241	0.208	0.278	INDETERMINATE	1	TRUE	2	0.32	4		308	1077	SUCCESS
YES1	7525	MSKCC	GRCh37	18	739749	739749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0019765-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	122	195	0	ENST00000314574.4:c.1123G>A	p.Asp375Asn	p.D375N	ENST00000314574	NM_005433.3	375	Gat/Aat	9/12	0.25345999253881	3	FACETS	1	0.945	1	0.533	0.482	0.588	CLONAL	1	TRUE	1	0.32	3		195	829	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288740	15288741	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0019765-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	26	24	0	ENST00000263388.2:c.3998_3999delinsTT	p.Gly1333Val	p.G1333V	ENST00000263388	NM_000435.2	1333	gGG/gTT	24/33	0.3	3	FACETS	1	0.867	1	0.558	0.446	0.683	CLONAL	1	TRUE	1	0.32	3		24	169	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379718	17379718	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0019765-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	241	442	1	ENST00000359435.4:c.103G>T	p.Glu35Ter	p.E35*	ENST00000359435	NM_001033549.1	35	Gag/Tag	2/9	0.3	3	FACETS	1	0.986	1	0.611	0.569	0.654	CLONAL	1	TRUE	1	0.32	3		443	1430	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047393	128047393	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019765-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	40	221	0	ENST00000285398.2:c.529G>T	p.Val177Phe	p.V177F	ENST00000285398	NM_000122.1	177	Gtt/Ttt	5/15	1	2	FACETS	0.399	0.33	0.475	0.399	0.33	0.475	SUBCLONAL	1	TRUE	1	0.32	2		221	627	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39772532	39772532	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0019765-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	82	260	0	ENST00000288319.7:c.709T>C	p.Tyr237His	p.Y237H	ENST00000288319	NM_182918.3	237	Tat/Cat	6/10	0.217668830025503	3	FACETS	0.801	0.706	0.903	0.401	0.353	0.452	CLONAL	1	TRUE	1	0.32	3		260	742	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37622769	37622769	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019765-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	154	440	1	ENST00000249071.6:c.523G>T	p.Ala175Ser	p.A175S	ENST00000249071	NM_002872.4	175	Gcc/Tcc	6/7	0.25345999253881	3	FACETS	0.926	0.845	1	0.463	0.422	0.505	CLONAL	1	TRUE	1	0.32	3		441	1206	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946270	55946270	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0019765-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	75	184	0	ENST00000263923.4:c.3909C>G	p.Ser1303Arg	p.S1303R	ENST00000263923	NM_002253.2	1303	agC/agG	30/30	0.3	3	FACETS	0.946	0.83	1	0.473	0.415	0.535	CLONAL	1	TRUE	1	0.32	3		184	575	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818363	170818363	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs11551576	NA	P-0019765-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	50	165	0	ENST00000296930.5:c.193A>G	p.Met65Val	p.M65V	ENST00000296930	NM_002520.6	65	Atg/Gtg	3/11	1	2	FACETS	0.487	0.412	0.569	0.487	0.412	0.569	SUBCLONAL	1	TRUE	1	0.32	2		165	642	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381516	81381516	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0019765-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	46	200	1	ENST00000222390.5:c.545G>T	p.Gly182Val	p.G182V	ENST00000222390	NM_000601.4	182	gGg/gTg	5/18	0.159815576105022	5	FACETS	0.646	0.543	0.76	0.215	0.181	0.254	INDETERMINATE	1	TRUE	2	0.32	5		201	659	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319966	8319966	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0019765-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	33	103	0	ENST00000356435.5:c.5535C>A	p.Ser1845Arg	p.S1845R	ENST00000356435		1845	agC/agA	34/35	0.217668830025503	3	FACETS	0.779	0.637	0.939	0.39	0.318	0.47	CLONAL	1	TRUE	1	0.32	3		103	307	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0020128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	232	747	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.995	0.927	1	0.995	0.927	1	CLONAL	1	TRUE	1	0.42143514956789	2		747	1107	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189585638	189585638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886058222	NA	P-0020128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	233	820	6	ENST00000264731.3:c.899C>T	p.Thr300Met	p.T300M	ENST00000264731	NM_003722.4	300	aCg/aTg	7/14	0.262987783688502	3	FACETS	0.786	0.734	0.838	0.786	0.734	0.838	SUBCLONAL	2	TRUE	1	0.42143514956789	3		826	852	SUCCESS
APC	324	MSKCC	GRCh37	5	112157614	112157615	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	141	907	0	ENST00000257430.4:c.1335dup	p.Ile446AspfsTer14	p.I446Dfs*14	ENST00000257430	NM_000038.5	445	cag/caGg	11/16	0.42143514956789	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.42143514956789	1		907	486	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940684	131940689	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	AGATAA	AGATAA	-	novel	NA	P-0020128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	126	762	0	ENST00000265335.6:c.2713_2718del	p.Ile905_Lys906del	p.I905_K906del	ENST00000265335		904	gAGATAAag/gag	16/25	0.42143514956789	1	FACETS	0.894	0.813	0.978	0.894	0.813	0.978	CLONAL	1	TRUE	0	0.42143514956789	1		762	528	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442567	52442567	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1253151209	NA	P-0020164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	533	728	0	ENST00000460680.1:c.178C>T	p.Arg60Ter	p.R60*	ENST00000460680	NM_004656.3	60	Cga/Tga	4/17	0.772539476721831	2	FACETS	0.911	0.886	0.935	0.911	0.886	0.935	CLONAL	2	TRUE	0	0.81048556646966	2		728	722	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076751	72076751	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020164-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	76	746	0	ENST00000357731.5:c.746G>C	p.Gly249Ala	p.G249A	ENST00000357731	NM_173808.2	249	gGt/gCt	5/7	0.434655423535327	3	FACETS	0.239	0.209	0.272	0.12	0.104	0.136	INDETERMINATE	1	TRUE	1	0.81048556646966	3		746	1101	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0020175-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	13	496	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.537	0.381	0.729	0.537	0.381	0.729	SUBCLONAL	1	TRUE	1	0.1	2		496	484	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806153	1806153	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28931615	NA	P-0020175-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	10	763	0	ENST00000260795.2:c.1172C>T	p.Ala391Val	p.A391V	ENST00000260795		391	gCg/gTg	8/17	1	2	FACETS	0.412	0.277	0.582	0.412	0.277	0.582	SUBCLONAL	1	TRUE	1	0.1	2		763	486	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106782	27106782	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0020175-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	25	710	0	ENST00000324856.7:c.6393del	p.Asn2131LysfsTer4	p.N2131Kfs*4	ENST00000324856	NM_006015.4	2131	aaT/aa	20/20	1	2	FACETS	1	0.813	1	1	0.813	1	CLONAL	1	TRUE	1	0.1	2		710	482	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	110	384	0				ENST00000310581	NM_198253.2	-/1132			0.406049458519997	4	FACETS	0.837	0.751	0.928	0.279	0.25	0.31	CLONAL	1	TRUE	1	0.406049458519997	4		384	910	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589663	67589663	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587777709	NA	P-0020253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	112	413	0	ENST00000274335.5:c.1425+1G>A		p.X475_splice	ENST00000274335		475			0.406049458519997	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.406049458519997	1		413	388	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0020253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	440	775	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.392522102840903	2	FACETS	0.967	0.924	1	0.967	0.924	1	CLONAL	2	TRUE	0	0.406049458519997	2		775	1121	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246116	46246116	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	259	475	0	ENST00000334344.6:c.4210C>T	p.Gln1404Ter	p.Q1404*	ENST00000334344	NM_152641.2	1404	Caa/Taa	15/21	0.392522102840903	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.406049458519997	2		475	619	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396155	396155	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	118	490	0	ENST00000262320.3:c.871G>A	p.Glu291Lys	p.E291K	ENST00000262320	NM_003502.3	291	Gag/Aag	2/11	0.38617394878922	3	FACETS	0.874	0.788	0.964	0.437	0.394	0.482	CLONAL	1	TRUE	1	0.406049458519997	3		490	800	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597451	10597452	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	TT	novel	NA	P-0020253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	486	884	0	ENST00000171111.5:c.1751_1752insAA	p.Tyr584Ter	p.Y584*	ENST00000171111	NM_203500.1	584	tac/taAAc	6/6	0.392522102840903	2	FACETS	0.964	0.924	1	0.964	0.924	1	CLONAL	2	TRUE	0	0.406049458519997	2		884	1241	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020287-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	133	384	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.929	0.854	1	0.929	0.854	1	CLONAL	1	TRUE	1	0.795031357865357	2		384	360	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0020287-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	228	262	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.302659867640025	1	FACETS	0.721	0.68	0.763	0.721	0.68	0.763	INDETERMINATE	1	TRUE	0	0.795031357865357	1		263	479	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921552	178921552	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519938	NA	P-0020287-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	237	494	0	ENST00000263967.3:c.1034A>T	p.Asn345Ile	p.N345I	ENST00000263967	NM_006218.2	345	aAt/aTt	5/21	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.795031357865357	2		494	595	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803153	1803153	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1222728854	NA	P-0020287-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	301	1088	2	ENST00000260795.2:c.505G>A	p.Ala169Thr	p.A169T	ENST00000260795		169	Gcc/Acc	4/17	0.302659867640025	1	FACETS	0.699	0.663	0.734	0.699	0.663	0.734	INDETERMINATE	1	TRUE	0	0.795031357865357	1		1090	653	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429367	78429367	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020287-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	400	716	1	ENST00000370768.2:c.1075C>T	p.Arg359Ter	p.R359*	ENST00000370768	NM_003902.3	359	Cga/Tga	13/20	0.795031357865357	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.795031357865357	1		717	564	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137724	64137724	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020287-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	309	1140	0	ENST00000334205.4:c.1825T>C	p.Phe609Leu	p.F609L	ENST00000334205	NM_003942.2	609	Ttc/Ctc	15/17	1	2	FACETS	0.93	0.88	0.98	0.93	0.88	0.98	CLONAL	1	TRUE	1	0.795031357865357	2		1140	836	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160760	56160761	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0020360-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	276	365	0	ENST00000399503.3:c.1035+1dup		p.Q345fs	ENST00000399503	NM_005921.1	345	cag/caGg	4/20	0.676134035138969	3	FACETS	0.888	0.851	0.924	0.888	0.851	0.924	CLONAL	3	TRUE	0	0.676134035138969	3		365	410	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201059	NA	P-0020360-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	675	993	0	ENST00000269305.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000269305	NM_001126112.2	286	Gaa/Aaa	8/11	0.676134035138969	3	FACETS	0.883	0.86	0.907	0.883	0.86	0.907	CLONAL	3	TRUE	0	0.676134035138969	3		993	1008	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0020592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	397	384	0				ENST00000310581	NM_198253.2	-/1132			0.525220915619709	5	FACETS	0.918	0.886	0.949	1	0.994	1	CLONAL	5	TRUE	1	0.525220915619709	5		384	589	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243708901	243708901	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0020592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	118	361	0	ENST00000263826.5:c.1164-2A>G		p.X388_splice	ENST00000263826	NM_005465.4	388			1	2	FACETS	0.869	0.788	0.954	0.869	0.788	0.954	CLONAL	1	TRUE	1	0.525220915619709	2		361	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579503	7579503	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567556752	NA	P-0020592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	473	767	0	ENST00000269305.4:c.184G>T	p.Glu62Ter	p.E62*	ENST00000269305	NM_001126112.2	62	Gaa/Taa	4/11	0.36863526751766	5	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	2	0.525220915619709	5		767	1029	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651959	36651959	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	1167	673	0	ENST00000244741.5:c.81del	p.Ser27ArgfsTer4	p.S27Rfs*4	ENST00000244741	NM_000389.4	27	agC/ag	2/3	0.525220915619709	5	FACETS	0.955	0.937	0.974	0.955	0.937	0.974	CLONAL	5	TRUE	0	0.525220915619709	5		673	1663	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522588	157522588	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1385677376	NA	P-0020592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	206	685	0	ENST00000346085.5:c.4860G>C	p.Leu1620Phe	p.L1620F	ENST00000346085	NM_020732.3	1620	ttG/ttC	18/20	0.456222449756106	3	FACETS	0.811	0.751	0.874	0.406	0.375	0.437	CLONAL	1	TRUE	1	0.525220915619709	3		685	1221	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974105	2974105	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1286226733	NA	P-0020592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	439	436	0	ENST00000396946.4:c.1500G>A	p.Met500Ile	p.M500I	ENST00000396946	NM_032415.4	500	atG/atA	10/25	0.452549653009712	4	FACETS	0.894	0.856	0.931	0.894	0.856	0.931	CLONAL	3	TRUE	1	0.525220915619709	4		436	951	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938916	76938918	+	missense_variant	Missense_Mutation	TNP	TCT	TCT	ATC	novel	NA	P-0020592-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	153	320	0	ENST00000373344.5:c.1830_1832delinsGAT	p.Asp611Ile	p.D611I	ENST00000373344	NM_000489.3	610	caAGAt/caGATt	9/35	0.361177406846919	2	FACETS	0.923	0.848	1			1	CLONAL	1	TRUE	NA	0.525220915619709	2		320	631	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0020613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	120	868	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.294660638645201	2		869	759	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643942	52643943	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0020613-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	33	783	0	ENST00000394830.3:c.1953dup	p.Ser652IlefsTer13	p.S652Ifs*13	ENST00000394830	NM_018313.4	651	-/A	17/30	1	2	FACETS	0.359	0.291	0.436	0.359	0.291	0.436	SUBCLONAL	1	TRUE	1	0.294660638645201	2		783	624	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645693	12645698	+	inframe_deletion	In_Frame_Del	DEL	GATGTC	GATGTC	-	novel	NA	P-0020726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	26	357	0	ENST00000251849.4:c.771_776del	p.Ser259_Thr260del	p.S259_T260del	ENST00000251849	NM_002880.3	257	tcGACATCc/tcc	7/17	1	2	FACETS	0.497	0.395	0.612	0.497	0.395	0.612	SUBCLONAL	1	TRUE	1	0.457087380170278	2		357	229	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696148	52696148	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0020726-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	19	784	1	ENST00000394830.3:c.528+1G>T		p.X176_splice	ENST00000394830	NM_018313.4	176			1	2	FACETS	0.27	0.204	0.347	0.27	0.204	0.347	SUBCLONAL	1	TRUE	1	0.457087380170278	2		785	308	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	77	473	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.215156015553844	3	FACETS	0.877	0.773	0.988	0.877	0.773	0.988	CLONAL	2	FALSE	1	0.215156015553844	3		473	452	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0020966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	162	562	0	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	0.182032806485542	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	FALSE	0	0.215156015553844	2		562	684	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230752	53230752	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	244	519	0	ENST00000375401.3:c.2041C>T	p.Arg681Ter	p.R681*	ENST00000375401	NM_004187.3	681	Cga/Tga	14/26	0.215156015553844	3	FACETS	0.9	0.845	0.955			1	CLONAL	4	FALSE	NA	0.215156015553844	3		519	698	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378244	15378244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	26	374	0	ENST00000263377.2:c.542G>A	p.Arg181His	p.R181H	ENST00000263377	NM_058243.2	181	cGt/cAt	4/20	0.215156015553844	3	FACETS	0.63	0.498	0.781	0.315	0.249	0.391	SUBCLONAL	1	FALSE	1	0.215156015553844	3		374	425	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222717	53222717	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	80	670	0	ENST00000375401.3:c.4219del	p.Asp1407ThrfsTer5	p.D1407Tfs*5	ENST00000375401	NM_004187.3	1407	Gac/ac	25/26	0.215156015553844	3	FACETS	0.882	0.775	0.998			1	CLONAL	1	FALSE	NA	0.215156015553844	3		670	934	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945660	54945660	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756649666	NA	P-0020966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	58	240	0	ENST00000312783.6:c.910C>T	p.Arg304Trp	p.R304W	ENST00000312783	NM_198436.1	304	Cgg/Tgg	9/10	0.215156015553844	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	FALSE	1	0.215156015553844	3		240	250	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413115	63413115	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	65	547	0	ENST00000330258.3:c.52G>T	p.Gly18Trp	p.G18W	ENST00000330258	NM_152424.3	18	Ggg/Tgg	2/2	0.215156015553844	1	FACETS	0.975	0.846	1	0.975	0.846	1	CLONAL	1	FALSE	0	0.215156015553844	1		547	553	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107231	193107231	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	34	204	0	ENST00000367435.3:c.440G>T	p.Arg147Leu	p.R147L	ENST00000367435	NM_024529.4	147	cGc/cTc	6/17	0.215156015553844	5	FACETS	1	0.908	1	0.395	0.323	0.475	CLONAL	1	FALSE	2	0.215156015553844	5		204	353	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78420991	78420991	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	66	252	0	ENST00000370768.2:c.1729G>C	p.Ala577Pro	p.A577P	ENST00000370768	NM_003902.3	577	Gct/Cct	18/20	0.215156015553844	5	FACETS	0.867	0.754	0.988	0.578	0.503	0.659	CLONAL	2	FALSE	2	0.215156015553844	5		252	468	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012334	176012334	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	122	328	0	ENST00000367669.3:c.1600G>T	p.Asp534Tyr	p.D534Y	ENST00000367669	NM_022457.5	534	Gat/Tat	14/20	0.215156015553844	5	FACETS	1	0.951	1	1	0.951	1	CLONAL	3	FALSE	2	0.215156015553844	5		328	468	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562885	21562885	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	47	558	1	ENST00000382592.4:c.1034A>T	p.Gln345Leu	p.Q345L	ENST00000382592	NM_014572.2	345	cAg/cTg	4/8	0.215156015553844	3	FACETS	0.816	0.688	0.958	0.408	0.344	0.479	CLONAL	1	FALSE	1	0.215156015553844	3		559	593	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352441	73352441	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	66	373	1	ENST00000377767.4:c.464G>A	p.Trp155Ter	p.W155*	ENST00000377767	NM_014953.3	155	tGg/tAg	3/21	0.215156015553844	3	FACETS	1	0.936	1	0.566	0.491	0.647	CLONAL	1	FALSE	1	0.215156015553844	3		374	600	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508245	38508245	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	79	420	0	ENST00000254066.5:c.553G>C	p.Gly185Arg	p.G185R	ENST00000254066	NM_000964.3	185	Ggg/Cgg	5/9	0.197930227498618	5	FACETS	0.918	0.809	1	0.612	0.539	0.69	CLONAL	2	FALSE	2	0.215156015553844	5		420	529	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861680	59861680	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	76	353	0	ENST00000259008.2:c.1579C>G	p.Leu527Val	p.L527V	ENST00000259008	NM_032043.2	527	Ctt/Gtt	11/20	0.197930227498618	5	FACETS	1	0.901	1	0.685	0.603	0.772	CLONAL	2	FALSE	2	0.215156015553844	5		353	455	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946831	17946831	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	51	512	0	ENST00000458235.1:c.1816G>T	p.Gly606Trp	p.G606W	ENST00000458235	NM_000215.3	606	Ggg/Tgg	14/24	0.215156015553844	3	FACETS	0.891	0.757	1	0.446	0.378	0.52	CLONAL	1	FALSE	1	0.215156015553844	3		512	589	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523113	25523113	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0020966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	93	389	0	ENST00000264709.3:c.73-1G>T		p.X25_splice	ENST00000264709	NM_175629.2	25			0.208191852827264	4	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	FALSE	2	0.215156015553844	4		389	454	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288672	198288672	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	88	381	1	ENST00000335508.6:c.55C>T	p.Gln19Ter	p.Q19*	ENST00000335508	NM_012433.2	19	Caa/Taa	2/25	0.208191852827264	4	FACETS	0.954	0.848	1	0.954	0.848	1	CLONAL	2	FALSE	2	0.215156015553844	4		382	521	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720973	119720974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	133	420	0	ENST00000316626.5:c.201dup	p.Gly68TrpfsTer10	p.G68Wfs*10	ENST00000316626		67	-/T	2/12	0.215156015553844	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	FALSE	1	0.215156015553844	3		420	564	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851603	134851603	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1410626849	NA	P-0020966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	25	455	0	ENST00000398015.3:c.1009T>C	p.Ser337Pro	p.S337P	ENST00000398015	NM_004441.4	337	Tcc/Ccc	5/16	0.215156015553844	3	FACETS	0.606	0.477	0.754	0.303	0.238	0.377	SUBCLONAL	1	FALSE	1	0.215156015553844	3		455	425	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497289	149497289	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	108	628	0	ENST00000261799.4:c.3029C>A	p.Thr1010Asn	p.T1010N	ENST00000261799	NM_002609.3	1010	aCt/aAt	22/23	0.208191852827264	4	FACETS	0.981	0.882	1	0.981	0.882	1	CLONAL	2	FALSE	2	0.215156015553844	4		628	622	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555342	106555342	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	58	327	0	ENST00000369096.4:c.2459T>C	p.Val820Ala	p.V820A	ENST00000369096	NM_001198.3	820	gTt/gCt	7/7	0.215156015553844	3	FACETS	0.8	0.691	0.919	0.8	0.691	0.919	CLONAL	2	FALSE	1	0.215156015553844	3		327	373	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044550	47044550	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	117	694	0	ENST00000377604.3:c.2047G>C	p.Glu683Gln	p.E683Q	ENST00000377604	NM_001204468.1	683	Gag/Cag	18/24	0.215156015553844	3	FACETS	0.94	0.849	1			1	CLONAL	2	FALSE	NA	0.215156015553844	3		694	641	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044552	47044553	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	115	707	0	ENST00000377604.3:c.2050dup	p.Arg684LysfsTer36	p.R684Kfs*36	ENST00000377604	NM_001204468.1	683	-/A	18/24	0.215156015553844	3	FACETS	0.907	0.818	1			1	CLONAL	2	FALSE	NA	0.215156015553844	3		707	653	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939871	76939871	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	56	383	1	ENST00000373344.5:c.877C>A	p.Gln293Lys	p.Q293K	ENST00000373344	NM_000489.3	293	Caa/Aaa	9/35	0.215156015553844	3	FACETS	1	0.894	1	0.526	0.451	0.608	CLONAL	1	FALSE	1	0.215156015553844	3		384	548	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164975	123164975	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	31	190	0	ENST00000218089.9:c.288G>T	p.Gln96His	p.Q96H	ENST00000218089	NM_001042749.1	96	caG/caT	5/35	0.215156015553844	3	FACETS	1	0.85	1	0.528	0.428	0.641	CLONAL	1	FALSE	1	0.215156015553844	3		190	302	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224811	123224811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	37	377	0	ENST00000218089.9:c.3575C>T	p.Ala1192Val	p.A1192V	ENST00000218089	NM_001042749.1	1192	gCc/gTc	32/35	0.215156015553844	3	FACETS	0.787	0.648	0.942	0.394	0.324	0.471	CLONAL	1	FALSE	1	0.215156015553844	3		377	484	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23640969	23640969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536644825	NA	P-0020966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	80	381	0	ENST00000261584.4:c.2506G>A	p.Val836Ile	p.V836I	ENST00000261584	NM_024675.3	836	Gtc/Atc	5/13	0.215156015553844	5	FACETS	0.992	0.875	1	0.661	0.583	0.744	CLONAL	2	FALSE	2	0.215156015553844	5		381	496	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270404	10270404	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	74	558	0	ENST00000340748.4:c.1162A>G	p.Ile388Val	p.I388V	ENST00000340748		388	Atc/Gtc	16/40	0.215156015553844	3	FACETS	1	0.945	1	0.572	0.5	0.649	CLONAL	1	FALSE	1	0.215156015553844	3		558	666	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297997	15297997	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754554486	NA	P-0020966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	90	693	1	ENST00000263388.2:c.1759C>T	p.Arg587Cys	p.R587C	ENST00000263388	NM_000435.2	587	Cgc/Tgc	11/33	0.215156015553844	3	FACETS	1	0.967	1	0.623	0.552	0.698	CLONAL	1	FALSE	1	0.215156015553844	3		694	744	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218516	36218516	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	57	460	0	ENST00000222270.7:c.4295G>C	p.Cys1432Ser	p.C1432S	ENST00000222270	NM_014727.1	1432	tGc/tCc	16/37	0.215156015553844	3	FACETS	1	0.912	1	0.543	0.466	0.627	CLONAL	1	FALSE	1	0.215156015553844	3		460	540	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486104	8486104	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	42	435	0	ENST00000356435.5:c.2713G>T	p.Glu905Ter	p.E905*	ENST00000356435		905	Gag/Tag	17/35	0.195687823986469	2	FACETS	1	0.869	1	0.522	0.437	0.616	CLONAL	1	FALSE	0	0.215156015553844	2		435	374	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137323771	137323771	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020966-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	71	694	0	ENST00000481739.1:c.1064C>T	p.Ser355Phe	p.S355F	ENST00000481739	NM_002957.4	355	tCc/tTc	8/10	0.215156015553844	3	FACETS	1	0.915	1	0.532	0.464	0.606	CLONAL	1	FALSE	1	0.215156015553844	3		694	687	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020966-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	55	473	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.996	0.853	1	0.996	0.853	1	CLONAL	1	TRUE	1	0.22	2		473	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574012	7574012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs17882252	NA	P-0020966-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	94	562	0	ENST00000269305.4:c.1015G>T	p.Glu339Ter	p.E339*	ENST00000269305	NM_001126112.2	339	Gag/Tag	10/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.22	2		562	718	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230752	53230752	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020966-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	100	519	0	ENST00000375401.3:c.2041C>T	p.Arg681Ter	p.R681*	ENST00000375401	NM_004187.3	681	Cga/Tga	14/26	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.22	2		519	769	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222717	53222717	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0020966-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	133	670	0	ENST00000375401.3:c.4219del	p.Asp1407ThrfsTer5	p.D1407Tfs*5	ENST00000375401	NM_004187.3	1407	Gac/ac	25/26	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.22	2		670	934	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945660	54945660	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756649666	NA	P-0020966-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	39	240	0	ENST00000312783.6:c.910C>T	p.Arg304Trp	p.R304W	ENST00000312783	NM_198436.1	304	Cgg/Tgg	9/10	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.22	2		240	262	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413115	63413115	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020966-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	52	547	0	ENST00000330258.3:c.52G>T	p.Gly18Trp	p.G18W	ENST00000330258	NM_152424.3	18	Ggg/Tgg	2/2	1	2	FACETS	0.678	0.576	0.79	0.678	0.576	0.79	SUBCLONAL	1	TRUE	1	0.22	2		547	697	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107231	193107231	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020966-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	36	204	0	ENST00000367435.3:c.440G>T	p.Arg147Leu	p.R147L	ENST00000367435	NM_024529.4	147	cGc/cTc	6/17	1	2	FACETS	0.909	0.749	1	0.909	0.749	1	CLONAL	1	TRUE	1	0.22	2		204	360	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78420991	78420991	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020966-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	58	252	0	ENST00000370768.2:c.1729G>C	p.Ala577Pro	p.A577P	ENST00000370768	NM_003902.3	577	Gct/Cct	18/20	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.22	2		252	485	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012334	176012334	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020966-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	64	328	0	ENST00000367669.3:c.1600G>T	p.Asp534Tyr	p.D534Y	ENST00000367669	NM_022457.5	534	Gat/Tat	14/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.22	2		328	475	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562885	21562885	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0020966-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	79	558	1	ENST00000382592.4:c.1034A>T	p.Gln345Leu	p.Q345L	ENST00000382592	NM_014572.2	345	cAg/cTg	4/8	1	2	FACETS	0.988	0.868	1	0.988	0.868	1	CLONAL	1	TRUE	1	0.22	2		559	727	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352441	73352441	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0020966-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	59	373	1	ENST00000377767.4:c.464G>A	p.Trp155Ter	p.W155*	ENST00000377767	NM_014953.3	155	tGg/tAg	3/21	1	2	FACETS	0.824	0.708	0.95	0.824	0.708	0.95	CLONAL	1	TRUE	1	0.22	2		374	651	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508245	38508245	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020966-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	67	420	0	ENST00000254066.5:c.553G>C	p.Gly185Arg	p.G185R	ENST00000254066	NM_000964.3	185	Ggg/Cgg	5/9	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.22	2		420	567	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861680	59861680	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020966-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	35	353	0	ENST00000259008.2:c.1579C>G	p.Leu527Val	p.L527V	ENST00000259008	NM_032043.2	527	Ctt/Gtt	11/20	1	2	FACETS	0.812	0.666	0.975	0.812	0.666	0.975	CLONAL	1	TRUE	1	0.22	2		353	392	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946831	17946831	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020966-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	68	512	0	ENST00000458235.1:c.1816G>T	p.Gly606Trp	p.G606W	ENST00000458235	NM_000215.3	606	Ggg/Tgg	14/24	1	2	FACETS	0.981	0.854	1	0.981	0.854	1	CLONAL	1	TRUE	1	0.22	2		512	630	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523113	25523113	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0020966-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	58	389	0	ENST00000264709.3:c.73-1G>T		p.X25_splice	ENST00000264709	NM_175629.2	25			1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.22	2		389	517	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288672	198288672	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0020966-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	70	381	1	ENST00000335508.6:c.55C>T	p.Gln19Ter	p.Q19*	ENST00000335508	NM_012433.2	19	Caa/Taa	2/25	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.22	2		382	599	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720973	119720974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020966-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	85	420	0	ENST00000316626.5:c.201dup	p.Gly68TrpfsTer10	p.G68Wfs*10	ENST00000316626		67	-/T	2/12	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.22	2		420	683	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851603	134851603	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1410626849	NA	P-0020966-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	52	455	0	ENST00000398015.3:c.1009T>C	p.Ser337Pro	p.S337P	ENST00000398015	NM_004441.4	337	Tcc/Ccc	5/16	1	2	FACETS	0.841	0.716	0.979	0.841	0.716	0.979	CLONAL	1	TRUE	1	0.22	2		455	562	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497289	149497289	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020966-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	75	628	0	ENST00000261799.4:c.3029C>A	p.Thr1010Asn	p.T1010N	ENST00000261799	NM_002609.3	1010	aCt/aAt	22/23	1	2	FACETS	0.95	0.832	1	0.95	0.832	1	CLONAL	1	TRUE	1	0.22	2		628	718	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555342	106555342	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020966-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	42	327	0	ENST00000369096.4:c.2459T>C	p.Val820Ala	p.V820A	ENST00000369096	NM_001198.3	820	gTt/gCt	7/7	1	2	FACETS	0.884	0.739	1	0.884	0.739	1	CLONAL	1	TRUE	1	0.22	2		327	432	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044550	47044550	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020966-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	65	694	0	ENST00000377604.3:c.2047G>C	p.Glu683Gln	p.E683Q	ENST00000377604	NM_001204468.1	683	Gag/Cag	18/24	1	2	FACETS	0.956	0.829	1	0.956	0.829	1	CLONAL	1	TRUE	1	0.22	2		694	618	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044552	47044553	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0020966-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	64	707	0	ENST00000377604.3:c.2050dup	p.Arg684LysfsTer36	p.R684Kfs*36	ENST00000377604	NM_001204468.1	683	-/A	18/24	1	2	FACETS	0.925	0.801	1	0.925	0.801	1	CLONAL	1	TRUE	1	0.22	2		707	629	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939871	76939871	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020966-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	73	383	1	ENST00000373344.5:c.877C>A	p.Gln293Lys	p.Q293K	ENST00000373344	NM_000489.3	293	Caa/Aaa	9/35	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.22	2		384	642	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164975	123164975	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020966-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	18	190	0	ENST00000218089.9:c.288G>T	p.Gln96His	p.Q96H	ENST00000218089	NM_001042749.1	96	caG/caT	5/35	1	2	FACETS	0.584	0.44	0.755	0.584	0.44	0.755	SUBCLONAL	1	TRUE	1	0.22	2		190	280	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224811	123224811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020966-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	53	377	0	ENST00000218089.9:c.3575C>T	p.Ala1192Val	p.A1192V	ENST00000218089	NM_001042749.1	1192	gCc/gTc	32/35	1	2	FACETS	0.939	0.801	1	0.939	0.801	1	CLONAL	1	TRUE	1	0.22	2		377	513	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670615	134670615	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020966-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	86	669	0	ENST00000398015.3:c.526G>T	p.Ala176Ser	p.A176S	ENST00000398015	NM_004441.4	176	Gct/Tct	3/16	1	2	FACETS	0.944	0.834	1	0.944	0.834	1	CLONAL	1	TRUE	1	0.22	2		669	828	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74002007	74002007	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020966-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	91	440	0	ENST00000318443.5:c.1523G>T	p.Gly508Val	p.G508V	ENST00000318443	NM_001024736.1	508	gGg/gTg	8/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.22	2		440	692	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864738	57864738	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020966-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	58	605	0	ENST00000228682.2:c.2215G>T	p.Ala739Ser	p.A739S	ENST00000228682	NM_005269.2	739	Gca/Tca	12/12	0.297955111544336	3	FACETS	0.703	0.603	0.814			1	SUBCLONAL	1	TRUE	NA	0.22	3		605	832	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890351	72890351	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0020966-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	31	246	1	ENST00000325599.8:c.332-1G>T		p.X111_splice	ENST00000325599	NM_018130.2	111			1	2	FACETS	0.839	0.679	1	0.839	0.679	1	CLONAL	1	TRUE	1	0.22	2		247	336	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180314	32180314	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs760538818	NA	P-0020966-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	162	538	0	ENST00000375023.3:c.2617G>T	p.Gly873Ter	p.G873*	ENST00000375023	NM_004557.3	873	Gga/Tga	17/30	0.222168316001527	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.22	2		538	713	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227796	53227796	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0020966-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	139	547	0	ENST00000375401.3:c.2392G>T	p.Glu798Ter	p.E798*	ENST00000375401	NM_004187.3	798	Gag/Tag	17/26	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.22	2		547	864	SUCCESS
BTK	695	MSKCC	GRCh37	X	100629541	100629541	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020966-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	75	490	0	ENST00000308731.7:c.223C>A	p.Pro75Thr	p.P75T	ENST00000308731	NM_000061.2	75	Cca/Aca	3/19	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.22	2		490	648	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0020966-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	142	456	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	0.242324198955023	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.242324198955023	1		456	701	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028850	47028850	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0020966-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	206	647	0	ENST00000377604.3:c.154G>T	p.Glu52Ter	p.E52*	ENST00000377604	NM_001204468.1	52	Gag/Tag	3/24	0.242324198955023	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.242324198955023	2		647	769	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589753	69589753	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020966-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	15	33	0	ENST00000168712.1:c.100G>A	p.Ala34Thr	p.A34T	ENST00000168712	NM_002007.2	34	Gca/Aca	1/3	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.242324198955023	2		33	92	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797837	45797837	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0020966-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	149	446	0	ENST00000450313.1:c.933+1G>T		p.X311_splice	ENST00000450313	NM_012222.2	311			0.192284294150369	4	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	2	0.242324198955023	4		446	743	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865301	57865301	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020966-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	161	630	1	ENST00000228682.2:c.2778G>T	p.Gln926His	p.Q926H	ENST00000228682	NM_005269.2	926	caG/caT	12/12	0.242324198955023	3	FACETS	0.853	0.783	0.927	0.853	0.783	0.927	CLONAL	2	TRUE	1	0.242324198955023	3		631	873	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979548	7979548	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020966-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	187	485	0	ENST00000319144.4:c.1477C>A	p.Leu493Met	p.L493M	ENST00000319144	NM_001139.2	493	Ctg/Atg	11/15	0.242324198955023	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.242324198955023	3		485	837	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271765	15271765	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020966-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	221	670	1	ENST00000263388.2:c.6674G>T	p.Gly2225Val	p.G2225V	ENST00000263388	NM_000435.2	2225	gGg/gTg	33/33	0.242324198955023	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.242324198955023	3		671	906	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942204	17942204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020966-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	94	399	0	ENST00000458235.1:c.2811G>A	p.Met937Ile	p.M937I	ENST00000458235	NM_000215.3	937	atG/atA	21/24	0.242324198955023	3	FACETS	0.825	0.737	0.919	0.825	0.737	0.919	CLONAL	2	TRUE	1	0.242324198955023	3		399	527	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46607814	46607814	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020966-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	219	671	0	ENST00000263734.3:c.2003G>T	p.Gly668Val	p.G668V	ENST00000263734	NM_001430.4	668	gGg/gTg	12/16	0.242324198955023	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.242324198955023	3		671	969	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198272801	198272801	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0020966-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	75	425	0	ENST00000335508.6:c.1160G>C	p.Arg387Pro	p.R387P	ENST00000335508	NM_012433.2	387	cGg/cCg	9/25	0.242324198955023	3	FACETS	0.827	0.724	0.939	0.414	0.362	0.47	CLONAL	1	TRUE	1	0.242324198955023	3		425	839	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215595233	215595233	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0020966-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	65	193	0	ENST00000260947.4:c.1904-1G>T		p.X635_splice	ENST00000260947	NM_000465.2	635			0.242324198955023	3	FACETS	1	0.972	1	0.748	0.651	0.852	CLONAL	1	TRUE	1	0.242324198955023	3		193	402	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645583	215645583	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0020966-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	172	526	0	ENST00000260947.4:c.1015A>G	p.Ser339Gly	p.S339G	ENST00000260947	NM_000465.2	339	Agc/Ggc	4/11	0.242324198955023	3	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	1	0.242324198955023	3		526	790	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73047250	73047250	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020966-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	139	325	0	ENST00000356692.5:c.57G>T	p.Lys19Asn	p.K19N	ENST00000356692		19	aaG/aaT	2/9	0.242324198955023	2	FACETS	0.876	0.799	0.956	0.876	0.799	0.956	CLONAL	2	TRUE	0	0.242324198955023	2		325	655	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217108	66217108	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs763912590	NA	P-0020966-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	141	256	0	ENST00000273854.3:c.2507G>A	p.Arg836Lys	p.R836K	ENST00000273854	NM_004439.5	836	aGg/aAg	14/18	0.242324198955023	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.242324198955023	3		256	547	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225697	26225697	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs200762279	NA	P-0020966-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	178	465	0	ENST00000360408.1:c.315C>A	p.Phe105Leu	p.F105L	ENST00000360408	NM_003532.2	105	ttC/ttA	1/1	0.242324198955023	1	FACETS	0.759	0.701	0.821	1	0.99	1	SUBCLONAL	2	TRUE	0	0.242324198955023	1		465	850	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956635	93956635	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020966-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	57	282	0	ENST00000369303.4:c.2601G>T	p.Gln867His	p.Q867H	ENST00000369303	NM_004440.3	867	caG/caT	15/17	0.242324198955023	3	FACETS	0.905	0.776	1	0.452	0.388	0.523	CLONAL	1	TRUE	1	0.242324198955023	3		282	583	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141567234	141567234	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0020966-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	124	699	0	ENST00000220592.5:c.980G>T	p.Cys327Phe	p.C327F	ENST00000220592	NM_012154.3	327	tGt/tTt	8/19	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.242324198955023	2		699	950	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441246	52441246	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0020976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	235	674	0	ENST00000460680.1:c.524C>G	p.Pro175Arg	p.P175R	ENST00000460680	NM_004656.3	175	cCt/cGt	7/17	0.583207553621231	1	FACETS	0.894	0.842	0.946	0.894	0.842	0.946	CLONAL	1	TRUE	0	0.663957691422261	1		674	529	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041085	112041085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	41	589	0	ENST00000368678.4:c.170G>A	p.Gly57Glu	p.G57E	ENST00000368678		57	gGg/gAg	3/13	1	2	FACETS	0.152	0.125	0.181	0.152	0.125	0.181	SUBCLONAL	1	TRUE	1	0.663957691422261	2		589	815	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622195	117622195	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020976-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	75	684	2	ENST00000368508.3:c.6675C>A	p.Ser2225Arg	p.S2225R	ENST00000368508	NM_002944.2	2225	agC/agA	42/43	1	2	FACETS	0.263	0.23	0.299	0.263	0.23	0.299	SUBCLONAL	1	TRUE	1	0.663957691422261	2		686	858	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0020989-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	17	473	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.10449632372378	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		473	355	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947560	48947560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690846	NA	P-0021358-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	306	296	0	ENST00000267163.4:c.1147C>T	p.Gln383Ter	p.Q383*	ENST00000267163	NM_000321.2	383	Caa/Taa	12/27	0.635504037494985	3	FACETS	0.926	0.889	0.961	0.926	0.889	0.961	CLONAL	3	TRUE	0	0.635504037494985	3		296	457	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24134069	24134069	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021358-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	623	367	0	ENST00000263121.7:c.220C>G	p.Pro74Ala	p.P74A	ENST00000263121	NM_003073.3	74	Cct/Gct	2/9	0.635504037494985	7	FACETS	1	0.991	1			1	CLONAL	4	TRUE	NA	0.635504037494985	7		367	1194	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243404	46243404	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0021358-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	95	223	0	ENST00000334344.6:c.1757C>G	p.Ser586Cys	p.S586C	ENST00000334344	NM_152641.2	586	tCc/tGc	14/21	0.635504037494985	3	FACETS	1	0.956	1	0.56	0.503	0.619	CLONAL	1	TRUE	1	0.635504037494985	3		223	352	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770862	59770862	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0021358-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	123	221	0	ENST00000259008.2:c.2504A>T	p.His835Leu	p.H835L	ENST00000259008	NM_032043.2	835	cAc/cTc	18/20	0.635504037494985	4	FACETS	1	0.949	1	0.534	0.484	0.586	CLONAL	1	TRUE	2	0.635504037494985	4		221	593	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256369	46256369	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0021752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	141	678	0	ENST00000371998.3:c.597G>A	p.Met199Ile	p.M199I	ENST00000371998		199	atG/atA	7/23	0.454117332541169	2	FACETS	0.917	0.838	0.998	0.458	0.419	0.499	CLONAL	1	TRUE	0	0.515295373383181	2		678	597	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974913	+	start_lost,5_prime_UTR_variant	Translation_Start_Site	DEL	GCCAGCCAGTCAGCCGAAGGCTCCATGCTGCTCCCCGCCGCCGGCTCCATGCTGCTCCCCGCCGCCCGCTGCCTGCTCTCCCCCTCTCCGCAGCCGCCGAGCGCACGCGGTCCGCCCCACCCTCTGGTGACCAGCCA	GCCAGCCAGTCAGCCGAAGGCTCCATGCTGCTCCCCGCCGCCGGCTCCATGCTGCTCCCCGCCGCCCGCTGCCTGCTCTCCCCCTCTCCGCAGCCGCCGAGCGCACGCGGTCCGCCCCACCCTCTGGTGACCAGCCA	-	novel	NA	P-0021752-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	100	375	0	ENST00000304494.5:c.-87_50del		p.*29*	ENST00000304494	NM_000077.4	?-17/156		1/3	0.454117332541169	2	FACETS	0.761	0.692	0.832	0.761	0.692	0.832	SUBCLONAL	2	TRUE	0	0.515295373383181	2		375	255	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0022253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	97	228	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.521250695929633	2		228	358	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165910	118165910	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	144	388	0	ENST00000369448.3:c.420G>T	p.Gln140His	p.Q140H	ENST00000369448	NM_017709.3	140	caG/caT	2/2	0.268876171393402	3	FACETS	1	0.988	1	0.733	0.674	0.795	INDETERMINATE	1	TRUE	1	0.521250695929633	3		388	475	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436657	52436673	+	frameshift_variant	Frame_Shift_Del	DEL	CATCGTAGTTGTGGGTC	CATCGTAGTTGTGGGTC	-	novel	NA	P-0022253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	140	657	0	ENST00000460680.1:c.2001_2017del	p.Thr668ValfsTer43	p.T668Vfs*43	ENST00000460680	NM_004656.3	667	agGACCCACAACTACGATGag/agag	16/17	0.521250695929633	1	FACETS	0.794	0.728	0.863	0.794	0.728	0.863	SUBCLONAL	1	TRUE	0	0.521250695929633	1		657	500	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221284	1221284	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	350	1255	1	ENST00000326873.7:c.810del	p.Ser271AlafsTer16	p.S271Afs*16	ENST00000326873	NM_000455.4	269	aaG/aa	6/10	0.282847015275003	2	FACETS	0.84	0.795	0.887	0.84	0.795	0.887	CLONAL	2	FALSE	0	0.305626542574346	2		1256	1363	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874261	155874261	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs483352822	NA	P-0022304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	338	408	0	ENST00000368323.3:c.270G>T	p.Met90Ile	p.M90I	ENST00000368323	NM_006912.5	90	atG/atT	5/6	0.260271179933735	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	FALSE	1	0.305626542574346	3		408	1197	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602767	10602767	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	428	1069	2	ENST00000171111.5:c.811G>T	p.Val271Leu	p.V271L	ENST00000171111	NM_203500.1	271	Gtg/Ttg	3/6	0.262128889900285	2	FACETS	0.901	0.857	0.945	0.901	0.857	0.945	CLONAL	2	FALSE	0	0.305626542574346	2		1071	1555	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438656	49438656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	210	849	4	ENST00000301067.7:c.4834C>T	p.Arg1612Cys	p.R1612C	ENST00000301067	NM_003482.3	1612	Cgc/Tgc	19/54	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.305626542574346	2		853	1322	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663344	67663377	+	frameshift_variant	Frame_Shift_Del	DEL	GCGTAGAGGGGGAAAATGGAGGAGAAACGAAGAA	GCGTAGAGGGGGAAAATGGAGGAGAAACGAAGAA	-	novel	NA	P-0022304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	94	455	0	ENST00000264010.4:c.1746_1779del	p.Glu584AsnfsTer36	p.E584Nfs*36	ENST00000264010	NM_006565.3	582	gGCGTAGAGGGGGAAAATGGAGGAGAAACGAAGAAg/gg	10/12	1	2	FACETS	0.821	0.731	0.918	0.821	0.731	0.918	CLONAL	1	FALSE	1	0.305626542574346	2		455	749	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849556	68849556	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022304-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	134	625	1	ENST00000261769.5:c.1459G>T	p.Val487Leu	p.V487L	ENST00000261769	NM_004360.3	487	Gtg/Ttg	10/16	1	2	FACETS	0.741	0.671	0.814	0.741	0.671	0.814	SUBCLONAL	1	FALSE	1	0.305626542574346	2		626	1184	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0022337-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	16	324	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.117736703826998	4	FACETS	1	0.784	1	1	0.784	1	INDETERMINATE	2	TRUE	2	0.293522613875777	4		324	68	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577095	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519984	NA	P-0022380-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	307	279	0	ENST00000269305.4:c.843C>A	p.Asp281Glu	p.D281E	ENST00000269305	NM_001126112.2	281	gaC/gaA	8/11	0.346623496743267	2	FACETS	0.938	0.887	0.991	0.938	0.887	0.991	CLONAL	2	TRUE	0	0.356091146445443	2		279	919	SUCCESS
AR	367	MSKCC	GRCh37	X	66765173	66765173	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs746341152	NA	P-0022380-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	18	99	1	ENST00000374690.3:c.185A>T	p.Gln62Leu	p.Q62L	ENST00000374690	NM_000044.3	62	cAg/cTg	1/8	0.356091146445443	3	FACETS	0.349	0.262	0.452	0.175	0.131	0.226	SUBCLONAL	1	TRUE	1	0.356091146445443	3		100	341	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272105	15272105	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372833545	NA	P-0022380-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	138	263	0	ENST00000263388.2:c.6334G>A	p.Gly2112Ser	p.G2112S	ENST00000263388	NM_000435.2	2112	Ggt/Agt	33/33	1	2	FACETS	0.923	0.84	1	0.923	0.84	1	CLONAL	1	TRUE	1	0.356091146445443	2		263	840	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729399	41729399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022380-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	134	172	0	ENST00000242208.4:c.1130G>A	p.Arg377His	p.R377H	ENST00000242208	NM_002192.2	377	cGc/cAc	3/3	0.167326477221083	3	FACETS	1	0.934	1	0.517	0.47	0.567	INDETERMINATE	1	TRUE	1	0.356091146445443	3		172	857	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933337	100933337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767006543	NA	P-0022380-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	124	176	0	ENST00000325455.5:c.2053C>T	p.Pro685Ser	p.P685S	ENST00000325455	NM_001202474.3	685	Cca/Tca	4/8	0.356091146445443	4	FACETS	1	0.939	1	0.351	0.317	0.386	CLONAL	1	TRUE	1	0.356091146445443	4		176	898	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40872362	40872362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022380-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	138	246	0	ENST00000428826.2:c.593C>T	p.Ser198Leu	p.S198L	ENST00000428826		198	tCa/tTa	7/21	0.167326477221083	3	FACETS	1	0.925	1	0.51	0.463	0.558	INDETERMINATE	1	TRUE	1	0.356091146445443	3		246	896	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169998189	169998189	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022380-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	92	152	0	ENST00000295797.4:c.880G>C	p.Glu294Gln	p.E294Q	ENST00000295797	NM_002740.5	294	Gag/Cag	9/18	0.356091146445443	3	FACETS	0.768	0.681	0.86	0.384	0.34	0.43	SUBCLONAL	1	TRUE	1	0.356091146445443	3		152	793	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934144	39934144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375342424	NA	P-0022380-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	123	217	0	ENST00000378444.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000378444	NM_001123385.1	152	cCg/cTg	4/15	0.356091146445443	3	FACETS	0.901	0.814	0.993	0.451	0.407	0.497	CLONAL	1	TRUE	1	0.356091146445443	3		217	903	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324067	123324067	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022380-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	100	153	0	ENST00000358487.5:c.403G>T	p.Asp135Tyr	p.D135Y	ENST00000358487	NM_000141.4	135	Gat/Tat	4/18	0.356091146445443	3	FACETS	0.933	0.834	1	0.467	0.417	0.52	CLONAL	1	TRUE	1	0.356091146445443	3		153	709	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370674	225370674	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022380-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	41	112	0	ENST00000264414.4:c.1205G>A	p.Gly402Glu	p.G402E	ENST00000264414	NM_003590.4	402	gGg/gAg	8/16	0.164344454304305	3	FACETS	0.84	0.702	0.992	0.28	0.234	0.331	INDETERMINATE	1	TRUE	0	0.356091146445443	3		112	323	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024096	112024096	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022380-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	95	152	0	ENST00000368678.4:c.689A>T	p.His230Leu	p.H230L	ENST00000368678		230	cAt/cTt	7/13	NA	2	FACETS	0.923	0.824	1			1	INDETERMINATE	1	TRUE	NA	0.356091146445443	2		152	578	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115280684	115280685	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0022380-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	132	157	0	ENST00000438362.2:c.346dup	p.Glu116GlyfsTer3	p.E116Gfs*3	ENST00000438362	NM_001242891.1	116	gaa/gGaa	4/20	0.167326477221083	3	FACETS	1	0.985	1	0.708	0.644	0.774	INDETERMINATE	1	TRUE	1	0.356091146445443	3		157	617	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720850	89720872	+	frameshift_variant	Frame_Shift_Del	DEL	ACCGATACTTTTCTCCAAATTTT	ACCGATACTTTTCTCCAAATTTT	-	novel	NA	P-0022380-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	54	129	0	ENST00000371953.3:c.1002_1024del	p.Asn334LysfsTer19	p.N334Kfs*19	ENST00000371953	NM_000314.4	334	aACCGATACTTTTCTCCAAATTTT/a	8/9	0.356091146445443	4	FACETS	0.769	0.657	0.891	0.256	0.219	0.297	SUBCLONAL	1	TRUE	1	0.356091146445443	4		129	535	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426682	49426682	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0022380-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	63	150	0	ENST00000301067.7:c.11806C>T	p.Gln3936Ter	p.Q3936*	ENST00000301067	NM_003482.3	3936	Cag/Tag	39/54	NA	2	FACETS	0.88	0.764	1			1	INDETERMINATE	1	TRUE	NA	0.356091146445443	2		150	402	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0022394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	60	868	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.536	0.461	0.619	0.536	0.461	0.619	SUBCLONAL	1	TRUE	1	0.233038690654572	2		869	960	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0022394-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	130	636	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.181668548193722	2	FACETS	1	0.982	1	0.684	0.62	0.751	CLONAL	1	TRUE	0	0.233038690654572	2		636	816	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	105	572	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.27	2		578	665	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058747	180058748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755445139	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	60	986	1	ENST00000261937.6:c.89dup	p.Thr31AspfsTer15	p.T31Dfs*15	ENST00000261937	NM_182925.4	30	ccg/ccCg	2/30	0.3	0	FACETS	0.567	0.489	0.653			1	SUBCLONAL	1	TRUE	0	0.27	0		987	572	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	201	161	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.986	0.916	1	1	0.993	1	CLONAL	2	TRUE	1	0.27	2		161	755	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	158	452	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.955	0.878	1	1	0.992	1	CLONAL	2	TRUE	1	0.27	2		457	613	SUCCESS
AXL	558	MSKCC	GRCh37	19	41736935	41736935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776682499	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	68	822	4	ENST00000301178.4:c.650G>A	p.Arg217His	p.R217H	ENST00000301178	NM_021913.4	217	cGc/cAc	5/20	0.172560052671008	1	FACETS	0.745	0.648	0.849	0.745	0.648	0.849	SUBCLONAL	1	TRUE	0	0.27	1		826	585	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	47	436	0	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	1	2	FACETS	0.635	0.536	0.745	0.635	0.536	0.745	SUBCLONAL	1	TRUE	1	0.27	2		436	548	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402577	139402577	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751398945	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	91	943	2	ENST00000277541.6:c.3340C>T	p.Arg1114Cys	p.R1114C	ENST00000277541	NM_017617.3	1114	Cgc/Tgc	21/34	0.172560052671008	0	FACETS	0.939	0.836	1			1	CLONAL	1	TRUE	0	0.27	0		945	524	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932085	39932085	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	80	461	0	ENST00000378444.4:c.2514del	p.Lys839SerfsTer17	p.K839Sfs*17	ENST00000378444	NM_001123385.1	838	ccC/cc	4/15	1	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.27	1		461	377	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	63	532	1	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	1	2	FACETS	0.991	0.859	1	0.991	0.859	1	CLONAL	1	TRUE	1	0.27	2		533	471	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958479	90958480	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs780235686	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	95	663	0	ENST00000265433.3:c.1958dup	p.Leu654AlafsTer5	p.L654Afs*5	ENST00000265433	NM_002485.4	653	aag/aaAg	13/16	1	2	FACETS	0.753	0.669	0.842	0.753	0.669	0.842	SUBCLONAL	1	TRUE	1	0.27	2		663	935	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135246	2135246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1051502900	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	79	1025	2	ENST00000219476.3:c.4585C>T	p.Arg1529Trp	p.R1529W	ENST00000219476	NM_000548.3	1529	Cgg/Tgg	36/42	0.172560052671008	0	FACETS	0.65	0.572	0.734			1	SUBCLONAL	1	TRUE	0	0.27	0		1027	657	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188297	32188297	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs753855314	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	75	1002	6	ENST00000375023.3:c.1044del	p.Gly349AlafsTer49	p.G349Afs*49	ENST00000375023	NM_004557.3	348	ggC/gg	6/30	1	2	FACETS	0.739	0.647	0.838	0.739	0.647	0.838	SUBCLONAL	1	TRUE	1	0.27	2		1008	752	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050707	30050708	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	81	516	0	ENST00000338641.4:c.514dup	p.Arg172LysfsTer31	p.R172Kfs*31	ENST00000338641	NM_000268.3	170	cca/ccAa	5/16	0.172560052671008	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.27	1		516	461	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753368	42753368	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs780487406	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	100	1156	2	ENST00000222329.4:c.896del	p.Gly299GlufsTer12	p.G299Efs*12	ENST00000222329	NM_006494.2	299	gGa/ga	4/4	0.172560052671008	1	FACETS	0.679	0.605	0.757	0.679	0.605	0.757	SUBCLONAL	1	TRUE	0	0.27	1		1158	944	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426774	49426774	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1334139538	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	33	404	3	ENST00000301067.7:c.11714A>T	p.Gln3905Leu	p.Q3905L	ENST00000301067	NM_003482.3	3905	cAg/cTg	39/54	0.0946451004613025	3	FACETS	1	0.825	1	0.504	0.412	0.607	INDETERMINATE	1	TRUE	1	0.27	3		407	275	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325183	39325183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	97	1069	0	ENST00000373001.3:c.136G>A	p.Ala46Thr	p.A46T	ENST00000373001	NM_022157.3	46	Gca/Aca	1/7	1	2	FACETS	0.858	0.765	0.959	0.858	0.765	0.959	CLONAL	1	TRUE	1	0.27	2		1069	837	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436584	110436584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377510110	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	106	1200	2	ENST00000375856.3:c.1817C>T	p.Ser606Leu	p.S606L	ENST00000375856	NM_003749.2	606	tCg/tTg	1/2	0.0946451004613025	3	FACETS	1	0.948	1	0.547	0.49	0.608	INDETERMINATE	1	TRUE	1	0.27	3		1202	814	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90645513	90645513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1005767629	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	10	75	0	ENST00000330062.3:c.110G>A	p.Arg37His	p.R37H	ENST00000330062	NM_002168.2	37	cGc/cAc	1/11	1	2	FACETS	0.892	0.612	1	0.892	0.612	1	CLONAL	1	TRUE	1	0.27	2		75	83	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133780	2133780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397515062	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	73	915	0	ENST00000219476.3:c.3968C>T	p.Ala1323Val	p.A1323V	ENST00000219476	NM_000548.3	1323	gCg/gTg	33/42	0.172560052671008	0	FACETS	0.715	0.626	0.811			1	SUBCLONAL	1	TRUE	0	0.27	0		915	552	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640449	3640449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142079276	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	88	1120	1	ENST00000294008.3:c.3190G>A	p.Gly1064Arg	p.G1064R	ENST00000294008	NM_032444.2	1064	Gga/Aga	12/15	0.172560052671008	0	FACETS	0.637	0.564	0.715			1	SUBCLONAL	1	TRUE	0	0.27	0		1121	747	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273995	10273995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778499284	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	86	1130	2	ENST00000330684.3:c.274G>A	p.Gly92Arg	p.G92R	ENST00000330684	NM_001134407.1	92	Ggg/Agg	2/13	0.172560052671008	0	FACETS	0.634	0.561	0.713			1	SUBCLONAL	1	TRUE	0	0.27	0		1132	733	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110098	8110098	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	98	605	0	ENST00000585124.1:c.507C>G	p.Ser169Arg	p.S169R	ENST00000585124	NM_004217.3	169	agC/agG	6/9	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.27	2		605	619	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526083	66526083	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768253469	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	71	574	0	ENST00000358598.2:c.914G>A	p.Arg305His	p.R305H	ENST00000358598	NM_212471.2	305	cGt/cAt	10/11	1	2	FACETS	0.835	0.729	0.949	0.835	0.729	0.949	CLONAL	1	TRUE	1	0.27	2		574	630	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610505	10610505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	94	891	0	ENST00000171111.5:c.205G>A	p.Glu69Lys	p.E69K	ENST00000171111	NM_203500.1	69	Gag/Aag	2/6	0.172560052671008	1	FACETS	0.928	0.827	1	0.928	0.827	1	CLONAL	1	TRUE	0	0.27	1		891	649	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210785	36210785	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771353672	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	88	1144	3	ENST00000222270.7:c.536G>A	p.Arg179Gln	p.R179Q	ENST00000222270	NM_014727.1	179	cGg/cAg	3/37	0.172560052671008	1	FACETS	0.793	0.703	0.89	0.793	0.703	0.89	SUBCLONAL	1	TRUE	0	0.27	1		1147	711	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214713	36214714	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	22	677	1	ENST00000222270.7:c.3145dup	p.Ala1049GlyfsTer39	p.A1049Gfs*39	ENST00000222270	NM_014727.1	1047	cgg/cGgg	8/37	0.172560052671008	1	FACETS	0.425	0.329	0.536	0.425	0.329	0.536	SUBCLONAL	1	TRUE	0	0.27	1		678	332	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797405	42797405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369992088	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	65	1039	3	ENST00000575354.2:c.3767G>A	p.Arg1256Gln	p.R1256Q	ENST00000575354	NM_015125.3	1256	cGg/cAg	15/20	0.172560052671008	1	FACETS	0.688	0.597	0.788	0.688	0.597	0.788	SUBCLONAL	1	TRUE	0	0.27	1		1042	605	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095881	178095881	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	116	658	1	ENST00000397062.3:c.1450A>T	p.Met484Leu	p.M484L	ENST00000397062	NM_006164.4	484	Atg/Ttg	5/5	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.27	2		659	761	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156918	89156920	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	rs768142526	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	70	763	0	ENST00000336596.2:c.27_29del	p.Leu11del	p.L11del	ENST00000336596	NM_005233.5	7	aTCCtc/atc	1/17	1	2	FACETS	0.69	0.601	0.787	0.69	0.601	0.787	SUBCLONAL	1	TRUE	1	0.27	2		763	751	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984846	55984846	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371800274	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	91	808	2	ENST00000263923.4:c.283G>A	p.Gly95Arg	p.G95R	ENST00000263923	NM_002253.2	95	Gga/Aga	3/30	0.0946451004613025	0	FACETS	0.588	0.521	0.659			1	INDETERMINATE	1	TRUE	0	0.27	0		810	837	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181800	56181800	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	74	535	1	ENST00000399503.3:c.4024A>G	p.Lys1342Glu	p.K1342E	ENST00000399503	NM_005921.1	1342	Aaa/Gaa	17/20	1	2	FACETS	0.832	0.728	0.944	0.832	0.728	0.944	CLONAL	1	TRUE	1	0.27	2		536	659	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265446	152265446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371610514	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	57	665	0	ENST00000206249.3:c.899G>A	p.Arg300His	p.R300H	ENST00000206249	NM_000125.3	300	cGc/cAc	4/8	1	2	FACETS	0.7	0.6	0.809	0.7	0.6	0.809	SUBCLONAL	1	TRUE	1	0.27	2		665	603	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431665	6431665	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	114	885	2	ENST00000356142.4:c.218C>T	p.Pro73Leu	p.P73L	ENST00000356142	NM_018890.3	73	cCg/cTg	3/7	1	2	FACETS	0.928	0.835	1	0.928	0.835	1	CLONAL	1	TRUE	1	0.27	2		887	910	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729731	41729731	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	60	614	0	ENST00000242208.4:c.798G>T	p.Glu266Asp	p.E266D	ENST00000242208	NM_002192.2	266	gaG/gaT	3/3	1	2	FACETS	0.747	0.643	0.86	0.747	0.643	0.86	SUBCLONAL	1	TRUE	1	0.27	2		614	595	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29196013	29196014	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	84	822	1	ENST00000240100.2:c.584dup	p.Pro196SerfsTer42	p.P196Sfs*42	ENST00000240100	NM_001394.6	195	ggt/ggGt	3/4	1	2	FACETS	0.856	0.756	0.963	0.856	0.756	0.963	CLONAL	1	TRUE	1	0.27	2		823	727	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69104706	69104706	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs945657850	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	37	756	0	ENST00000288368.4:c.4550T>C	p.Leu1517Pro	p.L1517P	ENST00000288368	NM_024870.2	1517	cTg/cCg	37/40	1	2	FACETS	0.394	0.323	0.473	0.394	0.323	0.473	SUBCLONAL	1	TRUE	1	0.27	2		756	696	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841048	15841048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0022508-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	39	383	0	ENST00000307771.7:c.1132C>T	p.Arg378Trp	p.R378W	ENST00000307771	NM_005089.3	378	Cgg/Tgg	11/11	1	1	FACETS	0.598	0.496	0.711	0.598	0.496	0.711	SUBCLONAL	1	TRUE	0	0.27	1		383	418	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0022869-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	51	624	1	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	1	2	FACETS	0.564	0.481	0.655	0.564	0.481	0.655	SUBCLONAL	1	TRUE	1	0.467161602281916	2		625	387	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279864	46279866	+	inframe_deletion	In_Frame_Del	DEL	CAA	CAA	-	rs112826888	NA	P-0022869-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	26	99	1	ENST00000371998.3:c.3792_3794del	p.Gln1276del	p.Q1276del	ENST00000371998		1264	CAA/-	20/23	0.467161602281916	5	FACETS	0.401	0.317	0.498	0.1	0.079	0.125	SUBCLONAL	1	TRUE	1	0.467161602281916	5		100	472	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189387	56189387	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0022869-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	139	105	0	ENST00000399503.3:c.4421del	p.Pro1474LeufsTer16	p.P1474Lfs*16	ENST00000399503	NM_005921.1	1473	atC/at	20/20	0.459272010045041	2	FACETS	0.948	0.877	1	0.948	0.877	1	CLONAL	2	TRUE	0	0.467161602281916	2		105	314	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197700	123197700	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0022869-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	42	76	0	ENST00000218089.9:c.1824T>A	p.His608Gln	p.H608Q	ENST00000218089	NM_001042749.1	608	caT/caA	20/35	0.467161602281916	3	FACETS	0.795	0.668	0.935	0.398	0.334	0.468	CLONAL	1	TRUE	1	0.467161602281916	3		76	279	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431811	49431811	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773164595	NA	P-0022869-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	117	135	0	ENST00000301067.7:c.9328C>T	p.Arg3110Cys	p.R3110C	ENST00000301067	NM_003482.3	3110	Cgc/Tgc	34/54	0.467161602281916	3	FACETS	1	0.926	1	0.514	0.465	0.566	CLONAL	1	TRUE	1	0.467161602281916	3		135	601	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0022928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	316	712	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.700552501251467	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.698176557392159	1		712	512	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920469	134920469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	130	796	0	ENST00000398015.3:c.2284G>A	p.Asp762Asn	p.D762N	ENST00000398015	NM_004441.4	762	Gac/Aac	12/16	0.634648060991454	1	FACETS	0.541	0.494	0.589	0.541	0.494	0.589	SUBCLONAL	1	TRUE	0	0.698176557392159	1		796	448	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0022928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	383	743	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.700552501251467	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.698176557392159	1		743	597	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359091	81359091	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0022928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	18	428	0	ENST00000222390.5:c.870C>A	p.Asp290Glu	p.D290E	ENST00000222390	NM_000601.4	290	gaC/gaA	8/18	0.700552501251467	3	FACETS	0.221	0.166	0.286	0.11	0.083	0.143	SUBCLONAL	1	TRUE	1	0.698176557392159	3		428	315	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266053	41266624	+	splice_donor_variant,splice_acceptor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	ACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTA	ACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTA	-	novel	NA	P-0022928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	68	383	0	ENST00000349496.5:c.52_423del		p.X18_splice	ENST00000349496	NM_001904.3	18	gACAGAAAAGCGGCTGTTAGTCACTGGCAGCAACAGTCTTACCTGGACTCTGGAATCCATTCTGGTGCCACTACCACAGCTCCTTCTCTGAGTGGTAAAGGCAATCCTGAGGAAGAGGATGTGGATACCTCCCAAGTCCTGTATGAGTGGGAACAGGGATTTTCTCAGTCCTTCACTCAAGAACAAGTAGCTGGTAAGAGTATTATTTTTCATTGCCTTACTGAAAGTCAGAATGCAGTTTTGAGAACTAAAAAGTTAGTGTATAATAGTTTAAATAAAATGTTGTGGTGAAGAAAAGAGAGTAATAGCAATGTCACTTTTACCATTTAGGATAGCAAATACTTAGGTAAATGCTGAACTGTGGATAGTGAGTGTTGAATTAACCTTTTCCAGATATTGATGGACAGTATGCAATGACTCGAGCTCAGAGGGTACGAGCTGCTATGTTCCCTGAGACATTAGATGAGGGCATGCAGATCCCATCTACACAGTTTGATGCTGCTCATCCCACTAATGTCCAGCGTTTGGCTGAACCATCACAGATGCTGAAACATGCAGTTGTAAACTTGATTAac/gac	3-4/15	1	2	FACETS	0.599	0.525	0.678	0.599	0.525	0.678	SUBCLONAL	1	TRUE	1	0.698176557392159	2		383	325	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938089	76938092	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	novel	NA	P-0022975-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	74	692	0	ENST00000373344.5:c.2656_2659del	p.Glu886LeufsTer18	p.E886Lfs*18	ENST00000373344	NM_000489.3	886	GAGAct/ct	9/35	1	2	FACETS	0.645	0.564	0.734	0.645	0.564	0.734	SUBCLONAL	1	TRUE	1	0.26	2		692	882	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63816982	63816982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0022975-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	38	313	1	ENST00000279873.7:c.953G>A	p.Arg318Lys	p.R318K	ENST00000279873	NM_032199.2	318	aGg/aAg	6/10	1	2	FACETS	0.621	0.513	0.741	0.621	0.513	0.741	SUBCLONAL	1	TRUE	1	0.26	2		314	471	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865848	56865848	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	316	392	1	ENST00000308159.5:c.1180A>G	p.Ile394Val	p.I394V	ENST00000308159	NM_014669.4	394	Att/Gtt	11/22	0.877707269589685	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.877707269589685	1		393	381	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742865	145742865	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1432766447	NA	P-0023458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	284	380	0	ENST00000428558.2:c.146A>G	p.Lys49Arg	p.K49R	ENST00000428558	NM_004260.3	49	aAg/aGg	3/22	0.877707269589685	3	FACETS	0.827	0.777	0.878	0.413	0.388	0.439	CLONAL	1	TRUE	1	0.877707269589685	3		380	1126	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610566	81610566	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0023458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	54	406	0	ENST00000298171.2:c.2164C>T	p.Gln722Ter	p.Q722*	ENST00000298171	NM_000369.2	722	Caa/Taa	10/10	1	2	FACETS	0.209	0.178	0.243	0.209	0.178	0.243	SUBCLONAL	1	TRUE	1	0.877707269589685	2		406	589	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857602	9857602	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0023458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	294	467	0	ENST00000330684.3:c.3799T>A	p.Tyr1267Asn	p.Y1267N	ENST00000330684	NM_001134407.1	1267	Tac/Aac	13/13	0.877707269589685	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.877707269589685	1		467	364	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578411	7578415	+	frameshift_variant	Frame_Shift_Del	DEL	CACAA	CACAA	-	novel	NA	P-0023458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	512	812	1	ENST00000269305.4:c.515_519del	p.Val172GlufsTer7	p.V172Efs*7	ENST00000269305	NM_001126112.2	172	gTTGTG/g	5/11	0.877707269589685	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.877707269589685	1		813	605	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120270	70120270	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1481	95	987	0	ENST00000245479.2:c.1272C>G	p.Asn424Lys	p.N424K	ENST00000245479	NM_000346.3	424	aaC/aaG	3/3	0.877707269589685	2	FACETS	0.137	0.121	0.155	0.069	0.06	0.078	SUBCLONAL	1	TRUE	0	0.877707269589685	2		987	1576	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679084	117679084	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0023458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	227	387	0	ENST00000368508.3:c.3737A>C	p.Gln1246Pro	p.Q1246P	ENST00000368508	NM_002944.2	1246	cAa/cCa	24/43	0.877707269589685	1	FACETS	0.974	0.935	1	0.974	0.935	1	CLONAL	1	TRUE	0	0.877707269589685	1		387	298	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679099	117679099	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1027270934	NA	P-0023458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	219	376	1	ENST00000368508.3:c.3722C>A	p.Ala1241Glu	p.A1241E	ENST00000368508	NM_002944.2	1241	gCa/gAa	24/43	0.877707269589685	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.877707269589685	1		377	280	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222612	157222622	+	frameshift_variant	Frame_Shift_Del	DEL	GCGCAGTATCT	GCGCAGTATCT	-	novel	NA	P-0023458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	106	566	0	ENST00000346085.5:c.1881_1891del	p.Gln628ValfsTer21	p.Q628Vfs*21	ENST00000346085	NM_020732.3	627	GCGCAGTATCTg/g	4/20	0.877707269589685	1	FACETS	0.193	0.173	0.215	0.193	0.173	0.215	SUBCLONAL	1	TRUE	0	0.877707269589685	1		566	702	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969399	44969399	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023458-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	65	558	0	ENST00000377967.4:c.4081T>A	p.Cys1361Ser	p.C1361S	ENST00000377967	NM_021140.2	1361	Tgt/Agt	28/29	NA	2	FACETS	0.208	0.18	0.239			1	INDETERMINATE	1	TRUE	NA	0.877707269589685	2		558	712	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0023556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	25	324	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.888	0.699	1	0.888	0.699	1	CLONAL	1	TRUE	1	0.12	2		324	469	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0023556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	38	856	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	1	2	FACETS	0.922	0.76	1	0.922	0.76	1	CLONAL	1	TRUE	1	0.12	2		856	687	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849565	68849565	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0023556-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	37	814	0	ENST00000261769.5:c.1468G>T	p.Glu490Ter	p.E490*	ENST00000261769	NM_004360.3	490	Gaa/Taa	10/16	1	2	FACETS	0.949	0.78	1	0.949	0.78	1	CLONAL	1	TRUE	1	0.12	2		814	650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0023593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	71	675	1	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.285615756994844	1	FACETS	0.629	0.548	0.715	0.629	0.548	0.715	SUBCLONAL	1	TRUE	0	0.285615756994844	1		676	678	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165786	108165786	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs753870656	NA	P-0023593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	55	419	0	ENST00000278616.4:c.4909G>T	p.Asp1637Tyr	p.D1637Y	ENST00000278616	NM_000051.3	1637	Gat/Tat	32/63	0.285615756994844	1	FACETS	0.807	0.692	0.932	0.807	0.692	0.932	CLONAL	1	TRUE	0	0.285615756994844	1		419	409	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390994	89390994	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779599137	NA	P-0023593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	84	586	1	ENST00000336596.2:c.1060C>T	p.Arg354Trp	p.R354W	ENST00000336596	NM_005233.5	354	Cgg/Tgg	5/17	1	2	FACETS	0.953	0.843	1	0.953	0.843	1	CLONAL	1	TRUE	1	0.285615756994844	2		587	617	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663299	227663301	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs753296153	NA	P-0023593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	86	534	0	ENST00000305123.5:c.154_156del	p.Lys52del	p.K52del	ENST00000305123	NM_005544.2	52	AAG/-	1/2	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.285615756994844	2		534	482	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981167	201981168	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0023593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	73	850	0	ENST00000359651.3:c.248dup	p.Asn83LysfsTer9	p.N83Kfs*9	ENST00000359651		82	-/A	2/8	1	2	FACETS	0.694	0.606	0.788	0.694	0.606	0.788	SUBCLONAL	1	TRUE	1	0.285615756994844	2		850	737	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745518	162745518	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs762535811	NA	P-0023593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	47	597	0	ENST00000367921.3:c.1933A>G	p.Ile645Val	p.I645V	ENST00000367921	NM_006182.2	645	Atc/Gtc	15/18	1	2	FACETS	0.576	0.486	0.676	0.576	0.486	0.676	SUBCLONAL	1	TRUE	1	0.285615756994844	2		597	571	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880947	134880947	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0023593-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	113	630	0	ENST00000398015.3:c.1510G>C	p.Val504Leu	p.V504L	ENST00000398015	NM_004441.4	504	Gta/Cta	7/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.285615756994844	2		630	718	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0023672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	81	228	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.522452664796257	3	FACETS	0.833	0.736	0.935	0.416	0.368	0.468	CLONAL	1	TRUE	1	0.522020597496227	3		228	470	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477837	140477851	+	inframe_deletion	In_Frame_Del	DEL	TAGGTGCTGTCACAT	TAGGTGCTGTCACAT	-	novel	NA	P-0023820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	106	781	0	ENST00000288602.6:c.1457_1471del	p.Asn486_Pro490del	p.N486_P490del	ENST00000288602	NM_004333.4	486	aATGTGACAGCACCTAca/aca	12/18	0.449389689782969	4	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.449389689782969	4		781	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578184	7578185	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCTCAT	novel	NA	P-0023820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	151	373	0	ENST00000269305.4:c.659_664dup	p.Glu221_Pro222insHisGlu	p.E221_P222insHE	ENST00000269305	NM_001126112.2	222	ccg/cATGAGCcg	6/11	0.44007873905693	2	FACETS	0.826	0.763	0.889	0.826	0.763	0.889	CLONAL	2	TRUE	0	0.449389689782969	2		373	407	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220451	1220453	+	inframe_deletion	In_Frame_Del	DEL	CTG	CTG	-	novel	NA	P-0023820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	80	384	0	ENST00000326873.7:c.549_551del	p.Leu184del	p.L184del	ENST00000326873	NM_000455.4	182	CTG/-	4/10	0.449389689782969	1	FACETS	0.955	0.85	1	0.955	0.85	1	CLONAL	1	TRUE	0	0.449389689782969	1		384	289	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319855	8319856	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TG	novel	NA	P-0023820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	17	293	0	ENST00000356435.5:c.5644_5645dup	p.Gln1882HisfsTer21	p.Q1882Hfs*21	ENST00000356435		1882	caa/caCAa	34/35	0.44007873905693	2	FACETS	0.244	0.182	0.318	0.122	0.091	0.159	SUBCLONAL	1	TRUE	0	0.449389689782969	2		293	310	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412763	63412763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1195123555	NA	P-0023820-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	76	294	0	ENST00000330258.3:c.404G>A	p.Gly135Glu	p.G135E	ENST00000330258	NM_152424.3	135	gGg/gAg	2/2	0.348247389289942	2	FACETS	1	0.965	1	0.617	0.548	0.69	CLONAL	1	TRUE	0	0.449389689782969	2		294	274	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0023826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	57	868	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.982	0.85	1	0.982	0.85	1	CLONAL	1	TRUE	1	0.419015995405405	2		869	277	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505396	157505399	+	frameshift_variant	Frame_Shift_Del	DEL	CAAC	CAAC	-	novel	NA	P-0023826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	32	200	0	ENST00000346085.5:c.3382_3385del	p.Asn1128Ter	p.N1128*	ENST00000346085	NM_020732.3	1126	gCAACc/gc	13/20	1	2	FACETS	0.724	0.592	0.87	0.724	0.592	0.87	SUBCLONAL	1	TRUE	1	0.419015995405405	2		200	211	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0023910-T11-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	319	533	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.854188674553954	3	FACETS	1	0.996	1	1	0.997	1	CLONAL	3	TRUE	1	0.854188674553954	3		533	335	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0023910-T11-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	72	800	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.854188674553954	3	FACETS	0.633	0.556	0.715	0.317	0.278	0.358	SUBCLONAL	1	TRUE	1	0.854188674553954	3		800	380	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445007	89445007	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023910-T11-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	116	357	0	ENST00000336596.2:c.1327A>G	p.Ile443Val	p.I443V	ENST00000336596	NM_005233.5	443	Att/Gtt	6/17	0.50492400805801	4	FACETS	0.896	0.821	0.972	0.597	0.547	0.648	INDETERMINATE	2	TRUE	1	0.854188674553954	4		357	281	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280314	1280314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561203868	NA	P-0023910-T11-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	584	1180	0	ENST00000310581.5:c.1909G>A	p.Asp637Asn	p.D637N	ENST00000310581	NM_198253.2	637	Gac/Aac	4/16	0.854188674553954	8	FACETS	0.933	0.902	0.964			1	CLONAL	5	TRUE	NA	0.854188674553954	8		1180	1044	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039380	47039380	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0023910-T11-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	317	866	0	ENST00000377604.3:c.1003A>T	p.Lys335Ter	p.K335*	ENST00000377604	NM_001204468.1	335	Aag/Tag	10/24	0.854188674553954	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.854188674553954	2		866	329	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241704	55241704	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0023910-T11-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	62	692	0	ENST00000275493.2:c.2152C>G	p.Leu718Val	p.L718V	ENST00000275493	NM_005228.3	718	Ctg/Gtg	18/28	0.854188674553954	3	FACETS	0.577	0.501	0.659	0.289	0.25	0.33	SUBCLONAL	1	TRUE	1	0.854188674553954	3		692	359	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241705	55241705	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0023910-T11-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	61	693	0	ENST00000275493.2:c.2153T>A	p.Leu718Gln	p.L718Q	ENST00000275493	NM_005228.3	718	cTg/cAg	18/28	0.854188674553954	3	FACETS	0.563	0.488	0.644	0.282	0.244	0.322	SUBCLONAL	1	TRUE	1	0.854188674553954	3		693	362	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967252	134967252	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0023910-T11-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	65	728	0	ENST00000398015.3:c.2591A>G	p.Asp864Gly	p.D864G	ENST00000398015	NM_004441.4	864	gAc/gGc	14/16	0.50492400805801	4	FACETS	0.709	0.617	0.808	0.236	0.205	0.27	INDETERMINATE	1	TRUE	1	0.854188674553954	4		728	398	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	231001	231001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143484394	NA	P-0024288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	145	707	0	ENST00000264932.6:c.781C>T	p.Arg261Cys	p.R261C	ENST00000264932	NM_004168.2	261	Cgc/Tgc	7/15	0.164641296584615	1	FACETS	1	0.934	1	1	0.991	1	CLONAL	2	TRUE	0	0.2	1		707	637	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101712	27101712	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0024320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	118	801	0	ENST00000324856.7:c.4993+1G>A		p.X1665_splice	ENST00000324856	NM_006015.4	1665			0.265349398849441	1	FACETS	0.99	0.896	1	0.99	0.896	1	CLONAL	1	TRUE	0	0.332377411451178	1		801	598	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88679187	88679187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199476088	NA	P-0024320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	82	267	0	ENST00000372037.3:c.1127G>A	p.Cys376Tyr	p.C376Y	ENST00000372037	NM_004329.2	376	tGc/tAc	10/13	0.32990556369329	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	0	0.332377411451178	2		267	233	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923646	131923646	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	49	410	0	ENST00000265335.6:c.916G>C	p.Asp306His	p.D306H	ENST00000265335		306	Gac/Cac	7/25	0.332377411451178	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.332377411451178	1		410	213	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411926	116412083	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TACGATGCAAGAGTACACACTCCTCATTTGGATAGGCTTGTAAGTGCCCGAAGTGTAAGCCCAACTACAGAAATGGTTTCAAATGAATCTGTAGACTACCGAGCTACTTTTCCAGAAGGTATATTTCAGTTTATTGTTCTGAGAAATACCTATACATA	TACGATGCAAGAGTACACACTCCTCATTTGGATAGGCTTGTAAGTGCCCGAAGTGTAAGCCCAACTACAGAAATGGTTTCAAATGAATCTGTAGACTACCGAGCTACTTTTCCAGAAGGTATATTTCAGTTTATTGTTCTGAGAAATACCTATACATA	-	novel	NA	P-0024320-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	110	884	0	ENST00000397752.3:c.2914_3028+43del		p.X972_splice	ENST00000397752	NM_000245.2	972		14/21	1	2	FACETS	0.952	0.857	1	0.952	0.857	1	CLONAL	1	TRUE	1	0.332377411451178	2		884	695	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735470	40735470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761910971	NA	P-0024678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	352	600	1	ENST00000373198.4:c.3403G>A	p.Val1135Met	p.V1135M	ENST00000373198	NM_133170.3	1135	Gtg/Atg	25/32	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.576612149221704	2		601	1146	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376688	31376688	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0024678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	69	332	0	ENST00000328111.2:c.683T>G	p.Leu228Arg	p.L228R	ENST00000328111	NM_006892.3	228	cTc/cGc	7/23	1	2	FACETS	0.289	0.251	0.33	0.289	0.251	0.33	SUBCLONAL	1	TRUE	1	0.576612149221704	2		332	829	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678784	52678784	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771618422	NA	P-0024678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	200	418	0	ENST00000394830.3:c.835del	p.Ile279TyrfsTer4	p.I279Yfs*4	ENST00000394830	NM_018313.4	279	Ata/ta	9/30	0.576612149221704	1	FACETS	0.833	0.776	0.89	0.833	0.776	0.89	CLONAL	1	TRUE	0	0.576612149221704	1		418	593	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087393	27087394	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0024678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	364	570	0	ENST00000324856.7:c.1969_1970del	p.Leu657GlufsTer18	p.L657Efs*18	ENST00000324856	NM_006015.4	656	gCT/g	5/20	0.576612149221704	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.576612149221704	1		570	854	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567718	226567719	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0024678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	255	447	0	ENST00000366794.5:c.1447dup	p.Ala483GlyfsTer9	p.A483Gfs*9	ENST00000366794	NM_001618.3	483	gca/gGca	10/23	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.576612149221704	2		447	853	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163309259	163309260	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0024678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	79	437	1	ENST00000271452.3:c.604dup	p.Thr202AsnfsTer24	p.T202Nfs*24	ENST00000271452	NM_145697.2	200	caa/cAaa	8/14	1	2	FACETS	0.367	0.322	0.416	0.367	0.322	0.416	SUBCLONAL	1	TRUE	1	0.576612149221704	2		438	746	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567710	226567718	+	missense_variant	Missense_Mutation	ONP	TCACCTCTG	TCACCTCTG	CACCTCTGC	novel	NA	P-0024678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	255	452	1	ENST00000366794.5:c.1448_1456delinsGCAGAGGTG	p.Ala483_Lys486delinsGlyArgGlyGlu	p.A483_K486delinsGRGE	ENST00000366794	NM_001618.3	483	gCAGAGGTGAag/gGCAGAGGTGag	10/23	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.576612149221704	2		453	878	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625086	69625086	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	220	404	0	ENST00000334134.2:c.707C>T	p.Ala236Val	p.A236V	ENST00000334134	NM_005247.2	236	gCc/gTc	3/3	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.576612149221704	2		404	722	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623593	28623593	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1303886643	NA	P-0024678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	319	540	0	ENST00000241453.7:c.964A>G	p.Arg322Gly	p.R322G	ENST00000241453	NM_004119.2	322	Aga/Gga	8/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.576612149221704	2		540	1071	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434674	99434674	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	332	606	0	ENST00000268035.6:c.761A>G	p.Tyr254Cys	p.Y254C	ENST00000268035	NM_000875.3	254	tAc/tGc	3/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.576612149221704	2		606	1051	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273515	5273515	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1222	95	680	0	ENST00000357368.4:c.317A>G	p.Glu106Gly	p.E106G	ENST00000357368	NM_002850.3	106	gAg/gGg	4/38	1	2	FACETS	0.25	0.222	0.281	0.25	0.222	0.281	SUBCLONAL	1	TRUE	1	0.576612149221704	2		680	1317	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184349	7184349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770929673	NA	P-0024678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	351	634	0	ENST00000302850.5:c.952G>A	p.Gly318Arg	p.G318R	ENST00000302850	NM_000208.2	318	Ggg/Agg	3/22	1	2	FACETS	0.989	0.937	1	0.989	0.937	1	CLONAL	1	TRUE	1	0.576612149221704	2		634	1231	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99154357	99154357	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	234	416	0	ENST00000074304.5:c.499A>G	p.Thr167Ala	p.T167A	ENST00000074304	NM_001134224.1	167	Acc/Gcc	8/26	1	2	FACETS	0.954	0.892	1	0.954	0.892	1	CLONAL	1	TRUE	1	0.576612149221704	2		416	851	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158637067	158637068	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	rs141073095	NA	P-0024678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	313	536	1	ENST00000263640.3:c.111_112dup	p.Glu38ValfsTer21	p.E38Vfs*21	ENST00000263640	NM_001105.4	38	gaa/gTGaa	4/11	1	2	FACETS	0.957	0.903	1	0.957	0.903	1	CLONAL	1	TRUE	1	0.576612149221704	2		537	1134	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437564	52437565	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0024678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	305	536	0	ENST00000460680.1:c.1596dup	p.Gly533TrpfsTer4	p.G533Wfs*4	ENST00000460680	NM_004656.3	532	-/T	13/17	0.576612149221704	1	FACETS	0.96	0.91	1	0.96	0.91	1	CLONAL	1	TRUE	0	0.576612149221704	1		536	784	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449399	31449399	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	268	499	0	ENST00000344624.3:c.2810T>C	p.Met937Thr	p.M937T	ENST00000344624		937	aTg/aCg	19/33	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.576612149221704	2		499	909	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715455	117715455	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	283	432	0	ENST00000368508.3:c.1034T>C	p.Ile345Thr	p.I345T	ENST00000368508	NM_002944.2	345	aTa/aCa	10/43	0.576612149221704	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.576612149221704	1		432	657	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412523	116412523	+	intron_variant	Intron	DEL	T	T	-	novel	NA	P-0024678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1268	543	871	0	ENST00000397752.3:c.3028+483del		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.576612149221704	2		871	1811	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635176	87635176	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024678-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	243	426	0	ENST00000277120.3:c.2228A>G	p.Tyr743Cys	p.Y743C	ENST00000277120		743	tAc/tGc	18/19	1	2	FACETS	0.948	0.887	1	0.948	0.887	1	CLONAL	1	TRUE	1	0.576612149221704	2		426	889	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0024693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	117	270	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	1	2	FACETS	0.986	0.894	1	0.986	0.894	1	CLONAL	1	TRUE	1	0.480328225894941	2		270	494	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73108193	73108193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024693-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	35	69	0	ENST00000356692.5:c.293C>T	p.Pro98Leu	p.P98L	ENST00000356692		98	cCt/cTt	4/9	0.480328225894941	1	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	0	0.480328225894941	1		69	104	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0024727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	79	270	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	0.250319346068584	4	FACETS	0.911	0.807	1	0.911	0.807	1	CLONAL	2	TRUE	2	0.331842977630276	4		270	348	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610715	52610715	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0024727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	96	320	0	ENST00000394830.3:c.3459-1G>T		p.X1153_splice	ENST00000394830	NM_018313.4	1153			0.324785348041367	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	2	TRUE	0	0.331842977630276	2		320	278	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578163	226578163	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs143482147	NA	P-0024727-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	51	462	0	ENST00000366794.5:c.565A>G	p.Thr189Ala	p.T189A	ENST00000366794	NM_001618.3	189	Aca/Gca	4/23	0.331842977630276	5	FACETS	0.671	0.569	0.783	0.224	0.189	0.261	SUBCLONAL	1	TRUE	2	0.331842977630276	5		462	686	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	126	572	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.844	0.766	0.926	0.844	0.766	0.926	CLONAL	1	TRUE	1	0.460054066524529	2		578	649	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	103	415	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.601	0.538	0.668	0.601	0.538	0.668	SUBCLONAL	1	TRUE	1	0.460054066524529	2		415	745	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	103	298	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.859	0.772	0.952	0.859	0.772	0.952	CLONAL	1	TRUE	1	0.460054066524529	2		298	521	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	105	479	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.584	0.523	0.648	0.584	0.523	0.648	SUBCLONAL	1	TRUE	1	0.460054066524529	2		481	782	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	165	747	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.460054066524529	2		747	688	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274774	123274774	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913474	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	266	483	0	ENST00000358487.5:c.1144T>C	p.Cys382Arg	p.C382R	ENST00000358487	NM_000141.4	382	Tgc/Cgc	9/18	NA	2	FACETS	0.833	0.786	0.881			1	INDETERMINATE	2	TRUE	NA	0.460054066524529	2		483	694	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161907	47161907	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	98	367	1	ENST00000409792.3:c.4219del	p.Arg1407GlyfsTer5	p.R1407Gfs*5	ENST00000409792	NM_014159.6	1407	Agg/gg	3/21	1	2	FACETS	0.634	0.566	0.706	0.634	0.566	0.706	SUBCLONAL	1	TRUE	1	0.460054066524529	2		368	672	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348846	11348846	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	28	70	0	ENST00000332029.2:c.490del	p.Ala164ProfsTer41	p.A164Pfs*41	ENST00000332029	NM_003745.1	164	Gcc/cc	2/2	1	2	FACETS	0.839	0.68	1	0.839	0.68	1	CLONAL	1	TRUE	1	0.460054066524529	2		70	145	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202313	133202313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756301031	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	107	484	1	ENST00000320574.5:c.6575C>T	p.Ala2192Val	p.A2192V	ENST00000320574	NM_006231.2	2192	gCg/gTg	47/49	0.460054066524529	1	FACETS	0.724	0.652	0.799	0.724	0.652	0.799	SUBCLONAL	1	TRUE	0	0.460054066524529	1		485	495	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	107	231	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.718	0.645	0.795	0.718	0.645	0.795	SUBCLONAL	1	TRUE	1	0.460054066524529	2		231	648	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	41	538	0	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	0.218	0.181	0.26	0.218	0.181	0.26	SUBCLONAL	1	TRUE	1	0.460054066524529	2		538	817	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226573330	226573330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781235145	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	38	362	0	ENST00000366794.5:c.886G>A	p.Glu296Lys	p.E296K	ENST00000366794	NM_001618.3	296	Gag/Aag	7/23	NA	2	FACETS	0.267	0.22	0.32			1	INDETERMINATE	1	TRUE	NA	0.460054066524529	2		362	619	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793212	139793212	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs748531430	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	109	394	3	ENST00000247668.2:c.26del	p.Pro9LeufsTer77	p.P9Lfs*77	ENST00000247668	NM_021138.3	7	aCc/ac	2/11	NA	2	FACETS	0.735	0.661	0.813			1	INDETERMINATE	1	TRUE	NA	0.460054066524529	2		397	645	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446270	187446270	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	108	420	0	ENST00000232014.4:c.1418del	p.Pro473ArgfsTer117	p.P473Rfs*117	ENST00000232014	NM_001130845.1	473	cCg/cg	6/10	1	2	FACETS	0.695	0.624	0.769	0.695	0.624	0.769	SUBCLONAL	1	TRUE	1	0.460054066524529	2		420	676	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799278	88799278	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	90	422	0	ENST00000360948.2:c.107G>A	p.Cys36Tyr	p.C36Y	ENST00000360948	NM_001012338.2	36	tGt/tAt	2/19	0.112958919016444	0	FACETS	0.395	0.351	0.441			1	INDETERMINATE	1	TRUE	0	0.460054066524529	0		422	535	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456857	32456857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	41	365	0	ENST00000332351.3:c.35C>T	p.Pro12Leu	p.P12L	ENST00000332351	NM_024426.4	12	cCg/cTg	1/10	1	2	FACETS	0.403	0.336	0.478	0.403	0.336	0.478	SUBCLONAL	1	TRUE	1	0.460054066524529	2		365	442	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609778	81609778	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762578626	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	39	289	1	ENST00000298171.2:c.1376C>T	p.Ala459Val	p.A459V	ENST00000298171	NM_000369.2	459	gCg/gTg	10/10	1	2	FACETS	0.367	0.304	0.437	0.367	0.304	0.437	SUBCLONAL	1	TRUE	1	0.460054066524529	2		290	462	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446360	70446360	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886762862	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	218	424	0	ENST00000373644.4:c.5300C>T	p.Ala1767Val	p.A1767V	ENST00000373644	NM_030625.2	1767	gCa/gTa	11/12	0.357702387431326	2	FACETS	1	0.992	1	0.735	0.687	0.783	CLONAL	1	TRUE	0	0.460054066524529	2		424	645	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137430	202137431	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	96	304	0	ENST00000358485.4:c.660_661del	p.Arg221SerfsTer17	p.R221Sfs*17	ENST00000358485	NM_001080125.1	220	AAa/a	4/9	1	2	FACETS	0.731	0.653	0.814	0.731	0.653	0.814	SUBCLONAL	1	TRUE	1	0.460054066524529	2		304	571	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193850	106193850	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	91	260	0	ENST00000380013.4:c.4317del	p.Lys1439AsnfsTer9	p.K1439Nfs*9	ENST00000380013	NM_001127208.2	1438	Aaa/aa	10/11	1	2	FACETS	0.84	0.749	0.936	0.84	0.749	0.936	CLONAL	1	TRUE	1	0.460054066524529	2		260	471	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222730	5222731	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs756013055	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	24	388	0	ENST00000357368.4:c.3072dup	p.Val1025ArgfsTer34	p.V1025Rfs*34	ENST00000357368	NM_002850.3	1024	-/C	18/38	0.460054066524529	1	FACETS	0.202	0.158	0.253	0.202	0.158	0.253	SUBCLONAL	1	TRUE	0	0.460054066524529	1		388	398	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733223	74733223	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	80	296	0	ENST00000359995.5:c.20del	p.Pro7LeufsTer7	p.P7Lfs*7	ENST00000359995	NM_001195427.1	7	cCt/ct	1/3	1	2	FACETS	0.646	0.57	0.728	0.646	0.57	0.728	SUBCLONAL	1	TRUE	1	0.460054066524529	2		296	538	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721099	61721099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458439158	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	313	519	1	ENST00000401558.2:c.1175C>T	p.Pro392Leu	p.P392L	ENST00000401558	NM_003400.3	392	cCg/cTg	12/25	0.153641833907834	5	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.460054066524529	5		520	1015	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33430296	33430296	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770250516	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	129	635	0	ENST00000345365.6:c.715C>T	p.Arg239Trp	p.R239W	ENST00000345365	NM_002878.3	239	Cgg/Tgg	8/10	1	2	FACETS	0.665	0.603	0.731	0.665	0.603	0.731	SUBCLONAL	1	TRUE	1	0.460054066524529	2		635	843	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087417	27087417	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	173	600	0	ENST00000324856.7:c.1991C>G	p.Ser664Ter	p.S664*	ENST00000324856	NM_006015.4	664	tCa/tGa	5/20	1	2	FACETS	0.782	0.719	0.847	0.782	0.719	0.847	SUBCLONAL	1	TRUE	1	0.460054066524529	2		600	962	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506209	120506209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	71	249	0	ENST00000256646.2:c.1903C>T	p.Pro635Ser	p.P635S	ENST00000256646	NM_024408.3	635	Cca/Tca	11/34	1	2	FACETS	0.814	0.715	0.921	0.814	0.715	0.921	CLONAL	1	TRUE	1	0.460054066524529	2		249	379	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727080	243727080	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	133	511	0	ENST00000263826.5:c.890T>G	p.Ile297Ser	p.I297S	ENST00000263826	NM_005465.4	297	aTc/aGc	9/13	NA	2	FACETS	0.74	0.673	0.811			1	INDETERMINATE	1	TRUE	NA	0.460054066524529	2		511	781	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123353300	123353300	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	72	568	0	ENST00000358487.5:c.32T>C	p.Val11Ala	p.V11A	ENST00000358487	NM_000141.4	11	gTc/gCc	2/18	NA	2	FACETS	0.381	0.332	0.434			1	INDETERMINATE	1	TRUE	NA	0.460054066524529	2		568	822	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61213523	61213523	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	87	365	0	ENST00000301761.2:c.481C>G	p.Leu161Val	p.L161V	ENST00000301761	NM_017841.2	161	Ctc/Gtc	4/4	1	2	FACETS	0.655	0.581	0.735	0.655	0.581	0.735	SUBCLONAL	1	TRUE	1	0.460054066524529	2		365	577	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137788	64137788	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	194	702	0	ENST00000334205.4:c.1889A>T	p.Glu630Val	p.E630V	ENST00000334205	NM_003942.2	630	gAg/gTg	15/17	1	2	FACETS	0.884	0.818	0.952	0.884	0.818	0.952	CLONAL	1	TRUE	1	0.460054066524529	2		702	954	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444933	49444933	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767415197	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	96	357	2	ENST00000301067.7:c.2533del	p.Arg845GlyfsTer85	p.R845Gfs*85	ENST00000301067	NM_003482.3	845	Cgg/gg	10/54	NA	2	FACETS	0.847	0.757	0.941			1	INDETERMINATE	1	TRUE	NA	0.460054066524529	2		359	493	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008056	29008056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755339233	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	74	316	0	ENST00000282397.4:c.713G>A	p.Arg238His	p.R238H	ENST00000282397	NM_002019.4	238	cGc/cAc	6/30	1	2	FACETS	0.662	0.581	0.749	0.662	0.581	0.749	SUBCLONAL	1	TRUE	1	0.460054066524529	2		316	486	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913953	32913953	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1555284237	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	173	481	0	ENST00000380152.3:c.5465del	p.Asn1822IlefsTer18	p.N1822Ifs*18	ENST00000380152		1821	Aaa/aa	11/27	1	2	FACETS	0.857	0.789	0.927	0.857	0.789	0.927	CLONAL	1	TRUE	1	0.460054066524529	2		481	878	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914205	32914205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	169	456	1	ENST00000380152.3:c.5713C>T	p.His1905Tyr	p.H1905Y	ENST00000380152		1905	Cat/Tat	11/27	1	2	FACETS	0.858	0.79	0.93	0.858	0.79	0.93	CLONAL	1	TRUE	1	0.460054066524529	2		457	856	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929162	32929162	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	138	564	0	ENST00000380152.3:c.7177del	p.Met2393Ter	p.M2393*	ENST00000380152		2391	gAa/ga	14/27	1	2	FACETS	0.671	0.61	0.735	0.671	0.61	0.735	SUBCLONAL	1	TRUE	1	0.460054066524529	2		564	894	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105236728	105236728	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770370100	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	130	405	0	ENST00000349310.3:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000349310	NM_001014432.1	465	Cgc/Tgc	15/15	1	2	FACETS	0.826	0.751	0.905	0.826	0.751	0.905	CLONAL	1	TRUE	1	0.460054066524529	2		405	684	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843468	3843468	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	51	393	0	ENST00000262367.5:c.1135del	p.Ala379ProfsTer10	p.A379Pfs*10	ENST00000262367	NM_004380.2	379	Gcc/cc	4/31	1	2	FACETS	0.357	0.303	0.417	0.357	0.303	0.417	SUBCLONAL	1	TRUE	1	0.460054066524529	2		393	621	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992108	72992108	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	142	379	0	ENST00000268489.5:c.1937A>T	p.Asp646Val	p.D646V	ENST00000268489	NM_006885.3	646	gAc/gTc	2/10	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.460054066524529	2		379	570	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556332	29556332	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	134	449	0	ENST00000356175.3:c.2699C>A	p.Ser900Tyr	p.S900Y	ENST00000356175	NM_000267.3	900	tCc/tAc	21/57	1	2	FACETS	0.879	0.8	0.961	0.879	0.8	0.961	CLONAL	1	TRUE	1	0.460054066524529	2		449	663	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881120	37881120	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	152	503	0	ENST00000269571.5:c.2449C>A	p.Leu817Met	p.L817M	ENST00000269571		817	Ctg/Atg	20/27	1	2	FACETS	0.826	0.756	0.899	0.826	0.756	0.899	CLONAL	1	TRUE	1	0.460054066524529	2		503	800	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688714	47688714	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	86	342	0	ENST00000347630.2:c.586A>G	p.Asn196Asp	p.N196D	ENST00000347630	NM_001007230.1	196	Aat/Gat	7/11	1	2	FACETS	0.72	0.639	0.807	0.72	0.639	0.807	SUBCLONAL	1	TRUE	1	0.460054066524529	2		342	519	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780623	56780623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	147	652	0	ENST00000337432.4:c.638G>A	p.Cys213Tyr	p.C213Y	ENST00000337432	NM_058216.2	213	tGt/tAt	4/9	1	2	FACETS	0.688	0.628	0.751	0.688	0.628	0.751	SUBCLONAL	1	TRUE	1	0.460054066524529	2		652	929	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853809	59853809	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	137	480	0	ENST00000259008.2:c.2050T>C	p.Cys684Arg	p.C684R	ENST00000259008	NM_032043.2	684	Tgc/Cgc	14/20	1	2	FACETS	0.796	0.725	0.871	0.796	0.725	0.871	SUBCLONAL	1	TRUE	1	0.460054066524529	2		480	748	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220146	5220146	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771853690	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	60	319	0	ENST00000357368.4:c.3569G>A	p.Arg1190Gln	p.R1190Q	ENST00000357368	NM_002850.3	1190	cGg/cAg	22/38	0.460054066524529	1	FACETS	0.489	0.422	0.56	0.489	0.422	0.56	SUBCLONAL	1	TRUE	0	0.460054066524529	1		319	411	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210743	36210743	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375544683	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	151	485	0	ENST00000222270.7:c.494G>A	p.Arg165His	p.R165H	ENST00000222270	NM_014727.1	165	cGc/cAc	3/37	1	2	FACETS	0.837	0.766	0.911	0.837	0.766	0.911	CLONAL	1	TRUE	1	0.460054066524529	2		485	784	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211928	36211928	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	181	639	0	ENST00000222270.7:c.1679C>G	p.Ser560Ter	p.S560*	ENST00000222270	NM_014727.1	560	tCa/tGa	3/37	1	2	FACETS	0.866	0.799	0.935	0.866	0.799	0.935	CLONAL	1	TRUE	1	0.460054066524529	2		639	909	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219700	36219700	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	153	624	0	ENST00000222270.7:c.4601del	p.Pro1534HisfsTer112	p.P1534Hfs*112	ENST00000222270	NM_014727.1	1533	Ccc/cc	20/37	1	2	FACETS	0.78	0.714	0.849	0.78	0.714	0.849	SUBCLONAL	1	TRUE	1	0.460054066524529	2		624	853	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229393	36229393	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	86	397	0	ENST00000222270.7:c.8083G>T	p.Glu2695Ter	p.E2695*	ENST00000222270	NM_014727.1	2695	Gag/Tag	37/37	1	2	FACETS	0.705	0.626	0.79	0.705	0.626	0.79	SUBCLONAL	1	TRUE	1	0.460054066524529	2		397	530	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795885	42795886	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	290	553	0	ENST00000575354.2:c.2880dup	p.Ser961GlnfsTer190	p.S961Qfs*190	ENST00000575354	NM_015125.3	958	-/C	11/20	0.264599278232669	4	FACETS	0.818	0.77	0.868			1	INDETERMINATE	2	TRUE	NA	0.460054066524529	4		553	1125	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39285894	39285894	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	168	541	0	ENST00000402219.2:c.265G>C	p.Asp89His	p.D89H	ENST00000402219	NM_005633.3	89	Gat/Cat	3/23	1	2	FACETS	0.795	0.73	0.862	0.795	0.73	0.862	SUBCLONAL	1	TRUE	1	0.460054066524529	2		541	919	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660004	227660004	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	104	390	0	ENST00000305123.5:c.3451C>A	p.Leu1151Met	p.L1151M	ENST00000305123	NM_005544.2	1151	Ctg/Atg	1/2	1	2	FACETS	0.756	0.678	0.838	0.756	0.678	0.838	SUBCLONAL	1	TRUE	1	0.460054066524529	2		390	598	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022802	31022802	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	101	361	1	ENST00000375687.4:c.2287C>A	p.Pro763Thr	p.P763T	ENST00000375687	NM_015338.5	763	Ccc/Acc	13/13	NA	2	FACETS	0.828	0.743	0.919			1	INDETERMINATE	1	TRUE	NA	0.460054066524529	2		362	530	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57470684	57470684	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	28	303	0	ENST00000371085.3:c.160del	p.Ser54AlafsTer4	p.S54Afs*4	ENST00000371085	NM_000516.4	53	Aaa/aa	2/13	1	2	FACETS	0.237	0.189	0.293	0.237	0.189	0.293	SUBCLONAL	1	TRUE	1	0.460054066524529	2		303	513	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62293880	62293880	+	intron_variant	Intron	SNP	C	C	T	rs767850154	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	143	528	0	ENST00000360203.5:c.396-19C>T		p.*132*	ENST00000360203	NM_001283009.1	150/1243			1	2	FACETS	0.802	0.732	0.876	0.802	0.732	0.876	CLONAL	1	TRUE	1	0.460054066524529	2		528	775	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935550	49935550	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	126	471	0	ENST00000296474.3:c.1814G>C	p.Gly605Ala	p.G605A	ENST00000296474	NM_002447.2	605	gGa/gCa	5/20	1	2	FACETS	0.771	0.699	0.847	0.771	0.699	0.847	SUBCLONAL	1	TRUE	1	0.460054066524529	2		471	710	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940567	49940567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747036471	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	32	393	0	ENST00000296474.3:c.476C>T	p.Ala159Val	p.A159V	ENST00000296474	NM_002447.2	159	gCg/gTg	1/20	1	2	FACETS	0.226	0.182	0.275	0.226	0.182	0.275	SUBCLONAL	1	TRUE	1	0.460054066524529	2		393	616	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242908	142242909	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	166	580	0	ENST00000350721.4:c.4078dup	p.Glu1360GlyfsTer16	p.E1360Gfs*16	ENST00000350721	NM_001184.3	1360	gaa/gGaa	22/47	1	2	FACETS	0.767	0.704	0.832	0.767	0.704	0.832	SUBCLONAL	1	TRUE	1	0.460054066524529	2		580	941	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182683390	182683390	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	124	520	0	ENST00000292782.4:c.155T>C	p.Ile52Thr	p.I52T	ENST00000292782	NM_020640.2	52	aTa/aCa	2/7	1	2	FACETS	0.669	0.605	0.736	0.669	0.605	0.736	SUBCLONAL	1	TRUE	1	0.460054066524529	2		520	806	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920154	1920155	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	135	512	0	ENST00000382891.5:c.1217_1218del	p.Cys406Ter	p.C406*	ENST00000382891	NM_133335.3	405	cTG/c	5/22	1	2	FACETS	0.753	0.685	0.825	0.753	0.685	0.825	SUBCLONAL	1	TRUE	1	0.460054066524529	2		512	779	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980410	1980410	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	185	741	0	ENST00000382891.5:c.3872C>G	p.Pro1291Arg	p.P1291R	ENST00000382891	NM_133335.3	1291	cCt/cGt	22/22	1	2	FACETS	0.836	0.772	0.903	0.836	0.772	0.903	CLONAL	1	TRUE	1	0.460054066524529	2		741	962	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289008	33289008	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	120	436	1	ENST00000374542.5:c.544C>A	p.Arg182Ser	p.R182S	ENST00000374542	NM_001141970.1	182	Cgt/Agt	3/8	0.153641833907834	5	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.460054066524529	5		437	763	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93973635	93973635	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	96	405	0	ENST00000369303.4:c.1743-2A>G		p.X581_splice	ENST00000369303	NM_004440.3	581			NA	2	FACETS	0.643	0.573	0.717			1	INDETERMINATE	1	TRUE	NA	0.460054066524529	2		405	649	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983299	149983301	+	inframe_deletion	In_Frame_Del	DEL	TAA	TAA	-	rs758808789	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	64	598	0	ENST00000253339.5:c.2957_2959del	p.Ile986del	p.I986del	ENST00000253339		986	aTTAaa/aaa	7/7	1	2	FACETS	0.299	0.258	0.344	0.299	0.258	0.344	SUBCLONAL	1	TRUE	1	0.460054066524529	2		598	929	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951857	2951857	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	113	631	0	ENST00000396946.4:c.3093del	p.Asn1032ThrfsTer33	p.N1032Tfs*33	ENST00000396946	NM_032415.4	1031	ccC/cc	23/25	1	2	FACETS	0.654	0.589	0.723	0.654	0.589	0.723	SUBCLONAL	1	TRUE	1	0.460054066524529	2		631	751	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035206	6035206	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	131	476	0	ENST00000265849.7:c.862C>T	p.Gln288Ter	p.Q288*	ENST00000265849	NM_000535.5	288	Cag/Tag	8/15	1	2	FACETS	0.779	0.708	0.854	0.779	0.708	0.854	SUBCLONAL	1	TRUE	1	0.460054066524529	2		476	731	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526583	106526583	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	99	391	0	ENST00000359195.3:c.2876A>G	p.Asn959Ser	p.N959S	ENST00000359195	NM_002649.2	959	aAc/aGc	10/11	NA	2	FACETS	0.692	0.619	0.77			1	INDETERMINATE	1	TRUE	NA	0.460054066524529	2		391	622	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38135870	38135870	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	139	499	0	ENST00000317025.8:c.3821A>T	p.His1274Leu	p.H1274L	ENST00000317025	NM_023034.1	1274	cAc/cTc	22/24	0.339482222979215	1	FACETS	0.721	0.658	0.787	0.721	0.658	0.787	SUBCLONAL	1	TRUE	0	0.460054066524529	1		499	645	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90995009	90995009	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	315	503	0	ENST00000265433.3:c.112G>T	p.Asp38Tyr	p.D38Y	ENST00000265433	NM_002485.4	38	Gat/Tat	2/16	0.319305664572788	3	FACETS	0.84	0.794	0.887	0.84	0.794	0.887	CLONAL	2	TRUE	1	0.460054066524529	3		503	1003	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934006	39934006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	141	418	3	ENST00000378444.4:c.593G>A	p.Gly198Asp	p.G198D	ENST00000378444	NM_001123385.1	198	gGt/gAt	4/15	NA	2	FACETS	0.877	0.8	0.957			1	INDETERMINATE	1	TRUE	NA	0.460054066524529	2		421	699	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422682	47422682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024821-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	100	435	1	ENST00000377045.4:c.154C>T	p.Arg52Trp	p.R52W	ENST00000377045	NM_001654.4	52	Cgg/Tgg	3/16	1	2	FACETS	0.692	0.619	0.77	0.692	0.619	0.77	SUBCLONAL	1	TRUE	1	0.460054066524529	2		436	628	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0024836-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	305	712	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.251576970575624	2	FACETS	0.844	0.795	0.894	0.844	0.795	0.894	CLONAL	2	TRUE	0	0.319804931205069	2		712	1130	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259903	16259903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024836-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	90	859	0	ENST00000375759.3:c.7168C>T	p.Pro2390Ser	p.P2390S	ENST00000375759	NM_015001.2	2390	Ccc/Tcc	11/15	1	2	FACETS	0.644	0.57	0.723	0.644	0.57	0.723	SUBCLONAL	1	TRUE	1	0.319804931205069	2		859	874	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785662	50785662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024836-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	146	857	0	ENST00000398568.2:c.652G>A	p.Gly218Ser	p.G218S	ENST00000398568	NM_001042412.1	218	Ggt/Agt	4/18	NA	2	FACETS	0.987	0.9	1			1	INDETERMINATE	1	TRUE	NA	0.319804931205069	2		857	925	SUCCESS
APC	324	MSKCC	GRCh37	5	112175564	112175565	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0024836-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	62	558	0	ENST00000257430.4:c.4275_4276dup	p.Ser1426IlefsTer48	p.S1426Ifs*48	ENST00000257430	NM_000038.5	1425	gat/gATat	16/16	0.319804931205069	1	FACETS	0.676	0.585	0.774	0.676	0.585	0.774	SUBCLONAL	1	TRUE	0	0.319804931205069	1		558	482	SUCCESS
ALK	238	MSKCC	GRCh37	2	29419698	29419698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024836-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	56	718	0	ENST00000389048.3:c.4102C>T	p.His1368Tyr	p.H1368Y	ENST00000389048	NM_004304.4	1368	Cat/Tat	28/29	NA	2	FACETS	0.44	0.376	0.51			1	INDETERMINATE	1	TRUE	NA	0.319804931205069	2		718	796	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251882	153251884	+	splice_donor_variant,coding_sequence_variant	Splice_Site	TNP	ACC	ACC	TCA	novel	NA	P-0024836-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	50	381	0	ENST00000281708.4:c.1122_1122+2delinsTGA		p.X374_splice	ENST00000281708	NM_033632.3	374		7/12	1	2	FACETS	0.506	0.429	0.591	0.506	0.429	0.591	SUBCLONAL	1	TRUE	1	0.319804931205069	2		381	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0024836-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	202	712	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.215383939589222	2	FACETS	0.866	0.802	0.932	0.866	0.802	0.932	CLONAL	2	TRUE	0	0.222203106243486	2		712	1050	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259903	16259903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024836-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	47	859	0	ENST00000375759.3:c.7168C>T	p.Pro2390Ser	p.P2390S	ENST00000375759	NM_015001.2	2390	Ccc/Tcc	11/15	1	2	FACETS	0.535	0.45	0.63	0.535	0.45	0.63	SUBCLONAL	1	TRUE	1	0.222203106243486	2		859	790	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785662	50785662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024836-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	107	857	0	ENST00000398568.2:c.652G>A	p.Gly218Ser	p.G218S	ENST00000398568	NM_001042412.1	218	Ggt/Agt	4/18	0.138978464829493	3	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.222203106243486	3		857	815	SUCCESS
APC	324	MSKCC	GRCh37	5	112175564	112175565	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0024836-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	34	558	0	ENST00000257430.4:c.4275_4276dup	p.Ser1426IlefsTer48	p.S1426Ifs*48	ENST00000257430	NM_000038.5	1425	gat/gATat	16/16	0.222203106243486	1	FACETS	0.538	0.439	0.649	0.538	0.439	0.649	SUBCLONAL	1	TRUE	0	0.222203106243486	1		558	506	SUCCESS
ALK	238	MSKCC	GRCh37	2	29419698	29419698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024836-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	61	718	0	ENST00000389048.3:c.4102C>T	p.His1368Tyr	p.H1368Y	ENST00000389048	NM_004304.4	1368	Cat/Tat	28/29	1	2	FACETS	0.739	0.636	0.851	0.739	0.636	0.851	SUBCLONAL	1	TRUE	1	0.222203106243486	2		718	743	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929142	44929142	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0024836-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	36	422	0	ENST00000377967.4:c.2243del	p.Pro748LeufsTer7	p.P748Lfs*7	ENST00000377967	NM_021140.2	748	Cct/ct	17/29	0.138978464829493	2	FACETS	0.581	0.476	0.698			1	SUBCLONAL	1	TRUE	NA	0.222203106243486	2		422	558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0024836-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	174	712	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.300621264988263	2	FACETS	1	0.989	1	0.732	0.675	0.791	CLONAL	1	TRUE	0	0.308990708011802	2		712	769	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259903	16259903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024836-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	35	859	0	ENST00000375759.3:c.7168C>T	p.Pro2390Ser	p.P2390S	ENST00000375759	NM_015001.2	2390	Ccc/Tcc	11/15	1	2	FACETS	0.391	0.319	0.471	0.391	0.319	0.471	SUBCLONAL	1	TRUE	1	0.308990708011802	2		859	580	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50785662	50785662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024836-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	102	857	0	ENST00000398568.2:c.652G>A	p.Gly218Ser	p.G218S	ENST00000398568	NM_001042412.1	218	Ggt/Agt	4/18	NA	2	FACETS	1	0.954	1			1	INDETERMINATE	1	TRUE	NA	0.308990708011802	2		857	593	SUCCESS
APC	324	MSKCC	GRCh37	5	112175564	112175565	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AT	novel	NA	P-0024836-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	17	558	0	ENST00000257430.4:c.4275_4276dup	p.Ser1426IlefsTer48	p.S1426Ifs*48	ENST00000257430	NM_000038.5	1425	gat/gATat	16/16	0.308990708011802	1	FACETS	0.315	0.235	0.411	0.315	0.235	0.411	SUBCLONAL	1	TRUE	0	0.308990708011802	1		558	295	SUCCESS
ALK	238	MSKCC	GRCh37	2	29419698	29419698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0024836-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	57	718	0	ENST00000389048.3:c.4102C>T	p.His1368Tyr	p.H1368Y	ENST00000389048	NM_004304.4	1368	Cat/Tat	28/29	1	2	FACETS	0.719	0.617	0.83	0.719	0.617	0.83	SUBCLONAL	1	TRUE	1	0.308990708011802	2		718	513	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251882	153251882	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0024836-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	33	521	0	ENST00000281708.4:c.1122+2T>A		p.X374_splice	ENST00000281708	NM_033632.3	374			1	2	FACETS	0.732	0.598	0.881	0.732	0.598	0.881	SUBCLONAL	1	TRUE	1	0.308990708011802	2		521	292	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251884	153251884	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0024836-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	32	526	0	ENST00000281708.4:c.1122G>T	p.Lys374Asn	p.K374N	ENST00000281708	NM_033632.3	374	aaG/aaT	7/12	1	2	FACETS	0.693	0.564	0.837	0.693	0.564	0.837	SUBCLONAL	1	TRUE	1	0.308990708011802	2		526	299	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568860	212568860	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0024836-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	37	673	0	ENST00000342788.4:c.1258C>G	p.Leu420Val	p.L420V	ENST00000342788	NM_005235.2	420	Ctg/Gtg	11/28	1	2	FACETS	0.542	0.447	0.648	0.542	0.447	0.648	SUBCLONAL	1	TRUE	1	0.308990708011802	2		673	442	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244242	5244242	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0025146-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	37	656	0	ENST00000357368.4:c.1240A>C	p.Ser414Arg	p.S414R	ENST00000357368	NM_002850.3	414	Agc/Cgc	11/38	0.264447331273467	3	FACETS	0.437	0.36	0.524	0.219	0.18	0.262	SUBCLONAL	1	TRUE	1	0.37	3		656	542	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0025287-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	95	385	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.991	0.889	1	0.991	0.889	1	CLONAL	1	TRUE	1	0.518349379500105	2		385	370	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692836	89692836	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786204858	NA	P-0025287-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	70	151	0	ENST00000371953.3:c.320A>G	p.Asp107Gly	p.D107G	ENST00000371953	NM_000314.4	107	gAt/gGt	5/9	0.518349379500105	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.518349379500105	1		151	153	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272498	15272498	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200541224	NA	P-0025287-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	120	712	0	ENST00000263388.2:c.5941C>T	p.Arg1981Cys	p.R1981C	ENST00000263388	NM_000435.2	1981	Cgc/Tgc	33/33	1	2	FACETS	0.945	0.858	1	0.945	0.858	1	CLONAL	1	TRUE	1	0.518349379500105	2		712	490	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0025289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	92	708	1	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	1	2	FACETS	0.866	0.768	0.971	0.866	0.768	0.971	CLONAL	1	TRUE	1	0.219537254600321	2		709	968	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39281778	39281778	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519963	NA	P-0025289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	137	404	1	ENST00000402219.2:c.697A>T	p.Asn233Tyr	p.N233Y	ENST00000402219	NM_005633.3	233	Aat/Tat	5/23	0.219537254600321	3	FACETS	0.92	0.838	1	0.92	0.838	1	CLONAL	2	TRUE	1	0.219537254600321	3		405	753	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643601	52643602	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0025289-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	72	467	0	ENST00000394830.3:c.2293_2294dup	p.Asp766GlufsTer10	p.D766Efs*10	ENST00000394830	NM_018313.4	765	gga/ggGGa	17/30	0.219537254600321	1	FACETS	0.863	0.753	0.98	0.863	0.753	0.98	CLONAL	1	TRUE	0	0.219537254600321	1		467	677	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0025330-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	336	398	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.288346708935812	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.464254089110667	1		398	1022	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602748	10602748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025330-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	464	1051	1	ENST00000171111.5:c.830C>T	p.Thr277Met	p.T277M	ENST00000171111	NM_203500.1	277	aCg/aTg	3/6	0.440944176548792	2	FACETS	0.877	0.84	0.915	0.877	0.84	0.915	CLONAL	2	TRUE	0	0.464254089110667	2		1052	1139	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36934797	36934797	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025330-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	269	792	0	ENST00000361632.4:c.1536G>T	p.Met512Ile	p.M512I	ENST00000361632		512	atG/atT	11/16	0.332031419662585	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.464254089110667	1		792	833	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888102	81888102	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025330-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	117	549	1	ENST00000359376.3:c.247G>T	p.Glu83Ter	p.E83*	ENST00000359376	NM_002661.3	83	Gag/Tag	3/33	0.464254089110667	3	FACETS	0.79	0.712	0.872	0.395	0.356	0.436	SUBCLONAL	1	TRUE	1	0.464254089110667	3		550	786	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244550	41244550	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs80357124	NA	P-0025330-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	118	775	0	ENST00000357654.3:c.2998G>C	p.Glu1000Gln	p.E1000Q	ENST00000357654	NM_007294.3	1000	Gag/Cag	10/23	0.464254089110667	3	FACETS	0.632	0.569	0.699	0.316	0.284	0.35	SUBCLONAL	1	TRUE	1	0.464254089110667	3		775	991	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015126	37015126	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025330-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	164	841	0	ENST00000358127.4:c.278C>G	p.Pro93Arg	p.P93R	ENST00000358127	NM_001280556.1	93	cCc/cGc	3/10	1	2	FACETS	0.713	0.654	0.775	0.713	0.654	0.775	SUBCLONAL	1	TRUE	1	0.464254089110667	2		841	991	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615080	100615080	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025330-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	182	595	0	ENST00000308731.7:c.835T>C	p.Tyr279His	p.Y279H	ENST00000308731	NM_000061.2	279	Tat/Cat	9/19	0.464254089110667	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.464254089110667	1		595	578	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675191	40675191	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025330-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	47	904	1	ENST00000249776.8:c.155G>A	p.Gly52Glu	p.G52E	ENST00000249776	NM_033286.3	52	gGg/gAg	1/9	0.464254089110667	1	FACETS	0.169	0.142	0.2	0.169	0.142	0.2	SUBCLONAL	1	TRUE	0	0.464254089110667	1		905	918	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673798	176673798	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0025330-T07-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	76	520	0	ENST00000439151.2:c.4497+1G>A		p.X1499_splice	ENST00000439151	NM_022455.4	1499			1	2	FACETS	0.45	0.394	0.511	0.45	0.394	0.511	SUBCLONAL	1	TRUE	1	0.464254089110667	2		520	727	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0025445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	74	614	0	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	1	0.88	1	1	0.88	1	CLONAL	1	TRUE	1	0.15	2		614	979	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94163112	94163112	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1332059826	NA	P-0025445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	73	579	0	ENST00000323929.3:c.2035C>T	p.Gln679Ter	p.Q679*	ENST00000323929	NM_005591.3	679	Caa/Taa	19/20	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.15	2		579	938	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47142993	47142993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	49	574	0	ENST00000409792.3:c.4970C>T	p.Pro1657Leu	p.P1657L	ENST00000409792	NM_014159.6	1657	cCt/cTt	8/21	1	2	FACETS	0.672	0.567	0.789	0.672	0.567	0.789	SUBCLONAL	1	TRUE	1	0.15	2		574	972	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738678	145738678	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746005466	NA	P-0025445-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	68	640	1	ENST00000428558.2:c.2386G>A	p.Glu796Lys	p.E796K	ENST00000428558	NM_004260.3	796	Gag/Aag	15/22	1	2	FACETS	0.913	0.792	1	0.913	0.792	1	CLONAL	1	TRUE	1	0.15	2		641	993	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913500	NA	P-0025488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	71	270	0	ENST00000345146.2:c.395G>T	p.Arg132Leu	p.R132L	ENST00000345146	NM_005896.2	132	cGt/cTt	4/10	0.248259033844012	3	FACETS	1	0.972	1	0.702	0.617	0.794	CLONAL	1	TRUE	1	0.319433949590406	3		270	367	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097621	27097622	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0025488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	46	437	0	ENST00000324856.7:c.3216dup	p.Trp1073MetfsTer32	p.W1073Mfs*32	ENST00000324856	NM_006015.4	1070	-/A	12/20	1	2	FACETS	0.492	0.414	0.579	0.492	0.414	0.579	SUBCLONAL	1	TRUE	1	0.319433949590406	2		437	585	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610555	52610555	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0025488-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	72	405	0	ENST00000394830.3:c.3616+2T>G		p.X1206_splice	ENST00000394830	NM_018313.4	1206			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.319433949590406	2		405	372	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0025501-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	759	713	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.724995093576776	2	FACETS		NA	1	1	0.998	1	NA	3	FALSE	0	0.724995093576776	2		713	836	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0025501-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	177	262	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.247682118755992	3	FACETS	0.849	0.793	0.905	0.849	0.793	0.905	INDETERMINATE	2	FALSE	1	0.724995093576776	3		263	392	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951172	48951172	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0025501-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	151	397	0	ENST00000267163.4:c.1332+2T>C		p.X444_splice	ENST00000267163	NM_000321.2	444			0.657221506197416	1	FACETS	0.882	0.822	0.942	0.882	0.822	0.942	CLONAL	1	FALSE	0	0.724995093576776	1		397	301	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90995081	90995448	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTCCTGAGATAAATTTTTTTTTAAAAAAAGATAAGTTGATAGACACATACACATGTACACGAACACACACATACATGTAAGTGTATATGATATAGGTATGACAAATATTAAATAAAACACCTTTGTTATTCAAATGTTAGTCAACTTTACATATGTCAAACTTGTGTTTTCAGTAAAGCCTCACTGAAGGCTATCAAAGGTTATCTAACTATGGTGTTTCAGGAGTAACAACAACAAAATTTAAAATACAATAAAAAAGAGAAAAAGAAAAAAAGGTTATCTAAACAGATAGAAGGCTACATCATTTTTCTAAAGGGAAAGCAATGCTGAAAGGAGTCAATGTTCCCTCAAATTAACTTAAAAACTTA	CTCCTGAGATAAATTTTTTTTTAAAAAAAGATAAGTTGATAGACACATACACATGTACACGAACACACACATACATGTAAGTGTATATGATATAGGTATGACAAATATTAAATAAAACACCTTTGTTATTCAAATGTTAGTCAACTTTACATATGTCAAACTTGTGTTTTCAGTAAAGCCTCACTGAAGGCTATCAAAGGTTATCTAACTATGGTGTTTCAGGAGTAACAACAACAAAATTTAAAATACAATAAAAAAGAGAAAAAGAAAAAAAGGTTATCTAAACAGATAGAAGGCTACATCATTTTTCTAAAGGGAAAGCAATGCTGAAAGGAGTCAATGTTCCCTCAAATTAACTTAAAAACTTA	-	novel	NA	P-0025501-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	179	410	0	ENST00000265433.3:c.38-365_40del		p.X13_splice	ENST00000265433	NM_002485.4	13		2/16	1	2	FACETS	0.959	0.891	1	0.959	0.891	1	CLONAL	1	FALSE	1	0.724995093576776	2		410	515	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907690	76907697	+	frameshift_variant	Frame_Shift_Del	DEL	TTCTCAGT	TTCTCAGT	-	novel	NA	P-0025501-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	298	352	0	ENST00000373344.5:c.4464_4471del	p.Lys1488AsnfsTer8	p.K1488Nfs*8	ENST00000373344	NM_000489.3	1488	aaACTGAGAAca/aaca	15/35	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	FALSE	0	0.724995093576776	1		352	375	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438315	110438315	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0025501-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	68	236	2	ENST00000375856.3:c.86A>G	p.His29Arg	p.H29R	ENST00000375856	NM_003749.2	29	cAc/cGc	1/2	NA	2	FACETS	0.619	0.543	0.7			1	INDETERMINATE	1	FALSE	NA	0.724995093576776	2		238	303	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28963937	28963937	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025501-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	124	473	0	ENST00000282397.4:c.1965C>G	p.Ile655Met	p.I655M	ENST00000282397	NM_002019.4	655	atC/atG	13/30	NA	2	FACETS	0.783	0.714	0.855			1	INDETERMINATE	1	FALSE	NA	0.724995093576776	2		473	437	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547389	106547389	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0025501-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	195	480	0	ENST00000369096.4:c.626A>C	p.His209Pro	p.H209P	ENST00000369096	NM_001198.3	209	cAc/cCc	4/7	0.478599226737264	3	FACETS	1	0.97	1	0.541	0.502	0.58	CLONAL	1	FALSE	1	0.724995093576776	3		480	678	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434624	128434624	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0025501-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	259	660	0	ENST00000265960.3:c.230A>T	p.Asp77Val	p.D77V	ENST00000265960	NM_001006617.1	77	gAc/gTc	2/12	0.724995093576776	3	FACETS	0.891	0.835	0.95	0.446	0.417	0.475	CLONAL	1	FALSE	1	0.724995093576776	3		660	1092	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214592	5214592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369295620	NA	P-0025511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1249	194	462	0	ENST00000357368.4:c.4474C>T	p.Arg1492Trp	p.R1492W	ENST00000357368	NM_002850.3	1492	Cgg/Tgg	29/38	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.247901857183175	2		462	1443	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631837	90631837	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519736	NA	P-0025511-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	128	366	0	ENST00000330062.3:c.516G>C	p.Arg172Ser	p.R172S	ENST00000330062	NM_002168.2	172	agG/agC	4/11	1	2	FACETS	0.897	0.811	0.988	0.897	0.811	0.988	CLONAL	1	TRUE	1	0.247901857183175	2		366	1151	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048638	6048638	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs372539944	NA	P-0025738-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	140	590	0	ENST00000265849.7:c.13G>C	p.Glu5Gln	p.E5Q	ENST00000265849	NM_000535.5	5	Gag/Cag	1/15	0.748615463212801	6	FACETS	0.842	0.765	0.923			1	CLONAL	1	TRUE	NA	0.748615463212801	6		590	1109	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0025738-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	696	636	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.748615463212801	3	FACETS	0.997	0.977	1	0.997	0.977	1	CLONAL	3	TRUE	0	0.748615463212801	3		636	854	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0025738-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	191	582	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.495408704405125	1	FACETS	0.998	0.943	1	0.998	0.943	1	CLONAL	1	TRUE	0	0.748615463212801	1		582	320	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2225386	2225386	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0025738-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	99	389	0	ENST00000398665.3:c.3597-1G>A		p.X1199_splice	ENST00000398665	NM_032482.2	1199			0.748615463212801	3	FACETS	0.824	0.74	0.913	0.275	0.246	0.305	CLONAL	1	TRUE	0	0.748615463212801	3		389	441	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602746	10602746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025738-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	800	804	0	ENST00000171111.5:c.832C>T	p.Pro278Ser	p.P278S	ENST00000171111	NM_203500.1	278	Ccg/Tcg	3/6	0.748615463212801	3	FACETS	0.98	0.961	0.998	0.98	0.961	0.998	CLONAL	3	TRUE	0	0.748615463212801	3		804	999	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220579	1220579	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0025738-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	706	672	0	ENST00000326873.7:c.598-1G>T		p.X200_splice	ENST00000326873	NM_000455.4	200			0.748615463212801	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.748615463212801	3		672	846	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257570	19257570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368120349	NA	P-0025738-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	280	735	2	ENST00000162023.5:c.656G>A	p.Arg219Gln	p.R219Q	ENST00000162023		219	cGa/cAa	10/13	0.748615463212801	3	FACETS	1	0.987	1	0.386	0.364	0.41	CLONAL	1	TRUE	0	0.748615463212801	3		737	887	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514650	103514650	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025738-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	64	346	0	ENST00000355739.4:c.1151C>T	p.Ser384Leu	p.S384L	ENST00000355739	NM_000123.3	384	tCa/tTa	8/15	0.309679282391808	5	FACETS	0.698	0.605	0.799	0.14	0.121	0.16	INDETERMINATE	1	TRUE	0	0.748615463212801	5		346	520	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522726	67522726	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0025738-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	243	237	0	ENST00000274335.5:c.223G>T	p.Glu75Ter	p.E75*	ENST00000274335		75	Gaa/Taa	1/15	0.748615463212801	3	FACETS	0.982	0.947	1	0.982	0.947	1	CLONAL	3	TRUE	0	0.748615463212801	3		237	303	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719181	61719181	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0025738-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	38	294	0	ENST00000401558.2:c.1876C>T	p.Gln626Ter	p.Q626*	ENST00000401558	NM_003400.3	626	Cag/Tag	16/25	0.464196139992685	6	FACETS	0.608	0.503	0.725	0.152	0.125	0.182	SUBCLONAL	1	TRUE	2	0.748615463212801	6		294	417	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932930	49932930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0025738-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	664	722	0	ENST00000296474.3:c.3014C>T	p.Ala1005Val	p.A1005V	ENST00000296474	NM_002447.2	1005	gCc/gTc	13/20	0.748615463212801	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.748615463212801	3		722	804	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325153	123325153	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025738-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	102	506	0	ENST00000358487.5:c.175G>A	p.Glu59Lys	p.E59K	ENST00000358487	NM_000141.4	59	Gag/Aag	3/18	0.704453677212141	3	FACETS	0.751	0.674	0.831	0.25	0.224	0.277	SUBCLONAL	1	TRUE	0	0.748615463212801	3		506	499	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865206	57865206	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025738-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	193	697	0	ENST00000228682.2:c.2683G>C	p.Ala895Pro	p.A895P	ENST00000228682	NM_005269.2	895	Gct/Cct	12/12	0.740044263942476	4	FACETS	0.806	0.744	0.87	0.201	0.186	0.218	CLONAL	1	TRUE	0	0.748615463212801	4		697	1119	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2221942	2222463	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGTCCCCTGAGACCCCCATGTCCTTCCCGGCAGGCTTCTCCTACGCTGGCTCGGTGGCCATCAGCGGGGCCTTGGCGGGCAGCCCGGCCTCTCTCACACCTGGAGCCGAGCCGGCCACCTTGGATGAGTCCTCCAGCTCTGGGAGCCTTTTTGCCACCGTGGGGTCCCGCAGCTCCACGCCACAGCACCCCCTGCTGCTGGCACAGCCCCGGAACTCGCTTCCTGCCTCTCCCGCCCACCAGCTCTCCTCCAGTCCCCGGCTTGGTGGGGCCGCCCAGGGCCCGTTGCCCGAGGCCAGCAAGGGAGACCTGCCCTCCGATTCCGGCTTCTCAGATCCTGAGAGTGAAGCCAAGAGGAGGATTGTGTTCACCATCACCACTGGTGCGGGCAGTGCCAAGCAGTCGCCCTCCAGCAAGCACAGCCCCCTGACCGCCAGCGCCCGTGGGGACTGTGTGCCGAGCCACGGGCAGGACAGTCGCAGGCGCGGCCGGCGGAAGCGAGCATCTGCGGGGACGCCCAGCT	TGTCCCCTGAGACCCCCATGTCCTTCCCGGCAGGCTTCTCCTACGCTGGCTCGGTGGCCATCAGCGGGGCCTTGGCGGGCAGCCCGGCCTCTCTCACACCTGGAGCCGAGCCGGCCACCTTGGATGAGTCCTCCAGCTCTGGGAGCCTTTTTGCCACCGTGGGGTCCCGCAGCTCCACGCCACAGCACCCCCTGCTGCTGGCACAGCCCCGGAACTCGCTTCCTGCCTCTCCCGCCCACCAGCTCTCCTCCAGTCCCCGGCTTGGTGGGGCCGCCCAGGGCCCGTTGCCCGAGGCCAGCAAGGGAGACCTGCCCTCCGATTCCGGCTTCTCAGATCCTGAGAGTGAAGCCAAGAGGAGGATTGTGTTCACCATCACCACTGGTGCGGGCAGTGCCAAGCAGTCGCCCTCCAGCAAGCACAGCCCCCTGACCGCCAGCGCCCGTGGGGACTGTGTGCCGAGCCACGGGCAGGACAGTCGCAGGCGCGGCCGGCGGAAGCGAGCATCTGCGGGGACGCCCAGCT	-	novel	NA	P-0025738-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	186	421	0	ENST00000398665.3:c.2807-31_3297del		p.X936_splice	ENST00000398665	NM_032482.2	936		24/28	0.748615463212801	3	FACETS	1	0.986	1	0.417	0.388	0.447	CLONAL	1	TRUE	0	0.748615463212801	3		421	546	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732699	204732699	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0025738-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	111	371	0	ENST00000302823.3:c.34C>T	p.Gln12Ter	p.Q12*	ENST00000302823	NM_005214.4	12	Cag/Tag	1/4	0.71272850422895	5	FACETS	0.975	0.878	1			1	CLONAL	1	TRUE	NA	0.748615463212801	5		371	646	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294698	1294698	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0025738-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1222	143	543	0	ENST00000310581.5:c.303C>G	p.Phe101Leu	p.F101L	ENST00000310581	NM_198253.2	101	ttC/ttG	2/16	0.748615463212801	8	FACETS	0.908	0.826	0.996	0.182	0.165	0.2	CLONAL	1	TRUE	3	0.748615463212801	8		543	1365	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410936	31410936	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0025738-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	915	709	0	ENST00000344624.3:c.3584G>T	p.Gly1195Val	p.G1195V	ENST00000344624		1195	gGc/gTc	28/33	0.748615463212801	8	FACETS	1	0.98	1	1	0.98	1	CLONAL	5	TRUE	3	0.748615463212801	8		709	1576	SUCCESS
APC	324	MSKCC	GRCh37	5	112154951	112154951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025738-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	215	543	0	ENST00000257430.4:c.1222C>T	p.His408Tyr	p.H408Y	ENST00000257430	NM_000038.5	408	Cat/Tat	10/16	0.727305251303614	2	FACETS	1	0.974	1	0.537	0.503	0.571	CLONAL	1	TRUE	0	0.748615463212801	2		543	535	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978565	70978565	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0025738-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	480	551	0	ENST00000276594.2:c.1088T>A	p.Leu363His	p.L363H	ENST00000276594	NM_024504.3	363	cTt/cAt	5/8	0.748615463212801	6	FACETS	1	0.991	1	0.823	0.791	0.855	CLONAL	3	TRUE	2	0.748615463212801	6		551	973	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636271	87636271	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025738-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	155	605	1	ENST00000277120.3:c.2436G>T	p.Met812Ile	p.M812I	ENST00000277120		812	atG/atT	19/19	0.748615463212801	4	FACETS	0.828	0.759	0.902	0.276	0.253	0.301	CLONAL	1	TRUE	1	0.748615463212801	4		606	874	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911571	39911571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751780062	NA	P-0025738-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	165	582	0	ENST00000378444.4:c.5059G>A	p.Val1687Met	p.V1687M	ENST00000378444	NM_001123385.1	1687	Gtg/Atg	15/15	NA	2	FACETS	1	0.927	1			1	INDETERMINATE	1	TRUE	NA	0.748615463212801	2		582	441	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0025978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	65	868	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.674	0.584	0.773	0.674	0.584	0.773	SUBCLONAL	1	TRUE	1	0.27	2		869	714	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891349	101891349	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0025978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	48	547	1	ENST00000374994.4:c.310G>T	p.Asp104Tyr	p.D104Y	ENST00000374994	NM_004612.2	104	Gac/Tac	2/9	0.3	1	FACETS	0.4	0.337	0.47	0.4	0.337	0.47	SUBCLONAL	1	TRUE	0	0.27	1		548	768	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44919400	44919400	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0025978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	33	155	0	ENST00000377967.4:c.1328A>G	p.Gln443Arg	p.Q443R	ENST00000377967	NM_021140.2	443	cAg/cGg	13/29	1	1	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	0	0.27	1		155	193	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578546	7578564	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGGGAGTACTGTAGGAAG	AGGGGAGTACTGTAGGAAG	-	novel	NA	P-0025978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	65	836	0	ENST00000269305.4:c.376-10_384del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	1	2	FACETS	0.485	0.419	0.557	0.485	0.419	0.557	SUBCLONAL	1	TRUE	1	0.27	2		836	992	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845421	151845421	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0025978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	59	558	0	ENST00000262189.6:c.13591G>A	p.Glu4531Lys	p.E4531K	ENST00000262189	NM_170606.2	4531	Gag/Aag	52/59	1	2	FACETS	0.54	0.464	0.624	0.54	0.464	0.624	SUBCLONAL	1	TRUE	1	0.27	2		558	809	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426908	6426908	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	90	348	0	ENST00000356142.4:c.101C>G	p.Pro34Arg	p.P34R	ENST00000356142	NM_018890.3	34	cCt/cGt	2/7	0.396226319412632	3	FACETS	1	0.946	1	0.552	0.491	0.616	CLONAL	1	TRUE	1	0.396226319412632	3		348	493	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264500	30264500	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	87	325	2	ENST00000322652.5:c.235G>T	p.Val79Phe	p.V79F	ENST00000322652	NM_015355.2	79	Gtc/Ttc	1/16	0.367738392239235	3	FACETS	1	0.902	1	0.509	0.452	0.57	CLONAL	1	TRUE	1	0.396226319412632	3		327	517	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197419	26197419	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0026023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	70	299	0	ENST00000356476.2:c.60G>C	p.Gln20His	p.Q20H	ENST00000356476		20	caG/caC	1/1	0.299203945120819	3	FACETS	0.864	0.755	0.981			1	CLONAL	1	TRUE	NA	0.396226319412632	3		299	490	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547187	106547187	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026023-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	35	238	0	ENST00000369096.4:c.424G>A	p.Gly142Arg	p.G142R	ENST00000369096	NM_001198.3	142	Ggg/Agg	4/7	0.270462504501227	3	FACETS	0.676	0.556	0.81	0.225	0.185	0.27	SUBCLONAL	1	TRUE	0	0.396226319412632	3		238	313	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593601	55593606	+	inframe_deletion	In_Frame_Del	DEL	AGTGGA	AGTGGA	-	rs869025568	NA	P-0026214-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	191	191	0	ENST00000288135.5:c.1669_1674del	p.Trp557_Lys558del	p.W557_K558del	ENST00000288135	NM_000222.2	556	cAGTGGAag/cag	11/21	0.884049504375682	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.884049504375682	1		191	241	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599340	55599340	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913514	NA	P-0026214-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	251	142	0	ENST00000288135.5:c.2466T>A	p.Asn822Lys	p.N822K	ENST00000288135	NM_000222.2	822	aaT/aaA	17/21	0.884049504375682	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.884049504375682	1		142	302	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594258	55594258	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913523	NA	P-0026214-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	138	162	0	ENST00000288135.5:c.1961T>C	p.Val654Ala	p.V654A	ENST00000288135	NM_000222.2	654	gTg/gCg	13/21	0.884049504375682	1	FACETS	0.56	0.518	0.603	0.56	0.518	0.603	SUBCLONAL	1	TRUE	0	0.884049504375682	1		162	311	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796748	135796748	+	splice_donor_variant	Splice_Site	SNP	A	A	G	rs1564497308	NA	P-0026214-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	271	74	0	ENST00000298552.3:c.737+2T>C		p.X246_splice	ENST00000298552	NM_001162426.1	246			0.884049504375682	2	FACETS	0.976	0.949	1	0.976	0.949	1	CLONAL	2	TRUE	0	0.884049504375682	2		74	314	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38963081	38963081	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026214-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	21	112	0	ENST00000357387.3:c.1463A>T	p.Lys488Met	p.K488M	ENST00000357387	NM_152756.3	488	aAg/aTg	17/38	1	2	FACETS	0.153	0.118	0.195	0.153	0.118	0.195	SUBCLONAL	1	TRUE	1	0.884049504375682	2		112	310	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100871	27100871	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0026216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	106	444	1	ENST00000324856.7:c.4153G>T	p.Glu1385Ter	p.E1385*	ENST00000324856	NM_006015.4	1385	Gaa/Taa	18/20	0.352027532397875	1	FACETS	0.913	0.824	1	0.913	0.824	1	CLONAL	1	TRUE	0	0.419852586957471	1		445	437	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2107112	2107112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45517130	NA	P-0026216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	84	451	0	ENST00000219476.3:c.781C>T	p.Arg261Trp	p.R261W	ENST00000219476	NM_000548.3	261	Cgg/Tgg	9/42	0.419852586957471	1	FACETS	0.958	0.854	1	0.958	0.854	1	CLONAL	1	TRUE	0	0.419852586957471	1		451	330	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598137	55598142	+	inframe_deletion	In_Frame_Del	DEL	GGGCAT	GGGCAT	-	novel	NA	P-0026216-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	74	384	0	ENST00000288135.5:c.2336_2341del	p.Gly779_Met780del	p.G779_M780del	ENST00000288135	NM_000222.2	778	aaGGGCATg/aag	16/21	0.419852586957471	1	FACETS	0.596	0.524	0.674	0.596	0.524	0.674	SUBCLONAL	1	TRUE	0	0.419852586957471	1		384	467	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245720	46245720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0026408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	63	624	2	ENST00000334344.6:c.3814C>T	p.Arg1272Ter	p.R1272*	ENST00000334344	NM_152641.2	1272	Cga/Tga	15/21	1	2	FACETS	0.383	0.33	0.441	0.383	0.33	0.441	SUBCLONAL	1	TRUE	1	0.306060324869707	2		626	1074	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325878	65325878	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	73	630	0	ENST00000342505.4:c.1244T>C	p.Leu415Pro	p.L415P	ENST00000342505	NM_002227.2	415	cTc/cCc	9/25	1	2	FACETS	0.427	0.372	0.487	0.427	0.372	0.487	SUBCLONAL	1	TRUE	1	0.306060324869707	2		630	1116	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223963	2223963	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	72	774	0	ENST00000326181.6:c.1177G>C	p.Val393Leu	p.V393L	ENST00000326181	NM_032271.2	393	Gtg/Ctg	13/21	0.144998661893065	3	FACETS	0.455	0.396	0.519	0.228	0.198	0.26	INDETERMINATE	1	TRUE	1	0.306060324869707	3		774	1192	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7170745	7170745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	69	751	0	ENST00000302850.5:c.1286C>T	p.Ala429Val	p.A429V	ENST00000302850	NM_000208.2	429	gCc/gTc	6/22	1	2	FACETS	0.353	0.306	0.404	0.353	0.306	0.404	SUBCLONAL	1	TRUE	1	0.306060324869707	2		751	1278	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550550	29550575	+	frameshift_variant	Frame_Shift_Del	DEL	TTGATCTGCAGGAATAAATTTCTTCT	TTGATCTGCAGGAATAAATTTCTTCT	A	novel	NA	P-0026408-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	49	583	0	ENST00000356175.3:c.1810_1835delinsA	p.Leu604IlefsTer19	p.L604Ifs*19	ENST00000356175	NM_000267.3	604	TTGATCTGCAGGAATAAATTTCTTCTt/At	16/57	1	2	FACETS	0.373	0.315	0.438	0.373	0.315	0.438	SUBCLONAL	1	TRUE	1	0.306060324869707	2		583	858	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0026680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	32	496	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	1	2	FACETS	0.681	0.551	0.829	0.681	0.551	0.829	SUBCLONAL	1	TRUE	1	0.13	2		496	723	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717733	89717733	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1554825235	NA	P-0026680-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	31	537	1	ENST00000371953.3:c.758T>A	p.Ile253Asn	p.I253N	ENST00000371953	NM_000314.4	253	aTc/aAc	7/9	1	2	FACETS	0.806	0.65	0.983	0.806	0.65	0.983	CLONAL	1	TRUE	1	0.13	2		538	592	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771828	135771828	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779599439	NA	P-0026700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	128	595	1	ENST00000298552.3:c.3289C>T	p.Arg1097Cys	p.R1097C	ENST00000298552	NM_001162426.1	1097	Cgt/Tgt	23/23	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.229203519314502	2		596	1010	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222006	1222006	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0026700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	100	487	0	ENST00000326873.7:c.920+1G>T		p.X307_splice	ENST00000326873	NM_000455.4	307			0.229203519314502	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.229203519314502	1		487	716	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411779	63411779	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	137	666	0	ENST00000330258.3:c.1388C>T	p.Ser463Phe	p.S463F	ENST00000330258	NM_152424.3	463	tCc/tTc	2/2	0.229203519314502	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.229203519314502	1		666	975	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985757	60985757	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	43	264	0	ENST00000333681.4:c.143T>C	p.Ile48Thr	p.I48T	ENST00000333681		48	aTc/aCc	2/3	1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	TRUE	1	0.229203519314502	2		264	373	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491726	120491726	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0026700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	85	369	0	ENST00000256646.2:c.2503G>T	p.Ala835Ser	p.A835S	ENST00000256646	NM_024408.3	835	Gct/Tct	16/34	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.229203519314502	2		369	671	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913422	32913423	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0026700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	98	465	0	ENST00000380152.3:c.4935dup	p.Glu1646ArgfsTer20	p.E1646Rfs*20	ENST00000380152		1644	gaa/gAaa	11/27	0.229203519314502	3	FACETS	1	0.896	1	0.503	0.448	0.562	CLONAL	1	TRUE	1	0.229203519314502	3		465	947	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913454	32913454	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs886040557	NA	P-0026700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	235	508	0	ENST00000380152.3:c.4963del	p.Tyr1655ThrfsTer15	p.Y1655Tfs*15	ENST00000380152		1654	tgT/tg	11/27	0.229203519314502	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.229203519314502	3		508	1066	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658565	3658565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759574554	NA	P-0026700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	120	656	0	ENST00000294008.3:c.401C>T	p.Ala134Val	p.A134V	ENST00000294008	NM_032444.2	134	gCc/gTc	2/15	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.229203519314502	2		656	1034	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032146	10032146	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	92	604	0	ENST00000330684.3:c.677T>C	p.Val226Ala	p.V226A	ENST00000330684	NM_001134407.1	226	gTc/gCc	3/13	1	2	FACETS	0.87	0.771	0.975	0.87	0.771	0.975	CLONAL	1	TRUE	1	0.229203519314502	2		604	923	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512413	38512413	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0026700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	45	535	0	ENST00000254066.5:c.1324G>T	p.Gly442Cys	p.G442C	ENST00000254066	NM_000964.3	442	Ggc/Tgc	9/9	0.229203519314502	3	FACETS	0.525	0.44	0.62	0.263	0.22	0.31	SUBCLONAL	1	TRUE	1	0.229203519314502	3		535	833	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475608	40475608	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1567708724	NA	P-0026700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	99	467	1	ENST00000264657.5:c.1636T>C	p.Trp546Arg	p.W546R	ENST00000264657	NM_139276.2	546	Tgg/Cgg	18/24	0.229203519314502	3	FACETS	0.974	0.867	1	0.487	0.433	0.544	CLONAL	1	TRUE	1	0.229203519314502	3		468	989	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464504	25464504	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0026700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	113	558	1	ENST00000264709.3:c.2009T>A	p.Ile670Asn	p.I670N	ENST00000264709	NM_175629.2	670	aTc/aAc	17/23	0.229203519314502	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.229203519314502	1		559	817	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794802	242794802	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	65	408	0	ENST00000334409.5:c.407A>G	p.Glu136Gly	p.E136G	ENST00000334409	NM_005018.2	136	gAg/gGg	2/5	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.229203519314502	2		408	532	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936988	178936988	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0026700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	49	384	0	ENST00000263967.3:c.1669T>C	p.Tyr557His	p.Y557H	ENST00000263967	NM_006218.2	557	Tat/Cat	11/21	0.229203519314502	3	FACETS	0.595	0.502	0.697	0.297	0.251	0.349	SUBCLONAL	1	TRUE	1	0.229203519314502	3		384	801	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056221	26056221	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs769775850	NA	P-0026700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	106	427	0	ENST00000343677.2:c.436A>G	p.Thr146Ala	p.T146A	ENST00000343677	NM_005319.3	146	Act/Gct	1/1	0.229203519314502	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.229203519314502	1		427	660	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202296	138202296	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	95	465	0	ENST00000237289.4:c.2213A>G	p.His738Arg	p.H738R	ENST00000237289	NM_001270507.1	738	cAt/cGt	9/9	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.229203519314502	2		465	742	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249119	55249119	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0026700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	120	651	0	ENST00000275493.2:c.2417A>G	p.Lys806Arg	p.K806R	ENST00000275493	NM_005228.3	806	aAa/aGa	20/28	0.229203519314502	1	FACETS	0.99	0.893	1	0.99	0.893	1	CLONAL	1	TRUE	0	0.229203519314502	1		651	936	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279363	38279363	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0026700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	146	673	0	ENST00000425967.3:c.1126A>T	p.Asn376Tyr	p.N376Y	ENST00000425967	NM_001174067.1	376	Aac/Tac	9/19	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.229203519314502	2		673	1138	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371957	55371957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0026700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	89	389	0	ENST00000297316.4:c.647G>A	p.Gly216Asp	p.G216D	ENST00000297316	NM_022454.3	216	gGc/gAc	2/2	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.229203519314502	2		389	603	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325367	1325367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750085547	NA	P-0026700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	100	587	1	ENST00000400841.2:c.308C>T	p.Thr103Met	p.T103M	ENST00000400841		103	aCg/aTg	3/6	0.229203519314502	1	FACETS	0.864	0.771	0.964	0.864	0.771	0.964	CLONAL	1	TRUE	0	0.229203519314502	1		588	894	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182032	38182032	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0027003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	128	906	0	ENST00000396334.3:c.656C>G	p.Ser219Cys	p.S219C	ENST00000396334	NM_002468.4	219	tCt/tGt	3/5	1	2	FACETS	1	0.974	1	1	0.991	1	CLONAL	2	TRUE	1	0.162485089290349	2		906	656	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733596	85733596	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1363762362	NA	P-0027003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	76	337	0	ENST00000370580.1:c.416A>T	p.Asp139Val	p.D139V	ENST00000370580	NM_003921.4	139	gAt/gTt	3/3	1	2	FACETS	0.908	0.798	1	1	0.981	1	CLONAL	2	TRUE	1	0.162485089290349	2		337	515	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023299	33023301	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0027003-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	96	670	0	ENST00000300177.4:c.408_410del	p.Ser137del	p.S137del	ENST00000300177	NM_001191322.1	136	ggTTCc/ggc	2/2	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.162485089290349	2		670	951	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0027016-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	315	496	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.506469696352541	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	0	0.517580929437346	2		496	604	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0027016-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	182	473	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.517580929437346	3	FACETS	0.815	0.757	0.874	0.815	0.757	0.874	CLONAL	2	TRUE	1	0.517580929437346	3		473	543	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027016-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	95	377	0	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	0.517580929437346	1	FACETS	0.835	0.751	0.922	0.835	0.751	0.922	CLONAL	1	TRUE	0	0.517580929437346	1		377	326	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0027016-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	45	347	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	1	2	FACETS	0.698	0.592	0.814	0.698	0.592	0.814	SUBCLONAL	1	TRUE	1	0.517580929437346	2		347	249	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0027016-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	73	223	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	1	2	FACETS	0.893	0.787	1	0.893	0.787	1	CLONAL	1	TRUE	1	0.517580929437346	2		223	316	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94908705	94908705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs547426358	NA	P-0027016-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	176	491	0	ENST00000536441.1:c.1349G>A	p.Arg450His	p.R450H	ENST00000536441	NM_144665.3	450	cGc/cAc	9/10	0.517580929437346	3	FACETS	1	0.952	1	0.521	0.481	0.564	CLONAL	1	TRUE	1	0.517580929437346	3		491	821	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374306	31374306	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0027016-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	175	394	0	ENST00000328111.2:c.307-2A>G		p.X103_splice	ENST00000328111	NM_006892.3	103			0.432659290664424	5	FACETS	0.835	0.771	0.902	0.557	0.514	0.601	CLONAL	2	TRUE	2	0.517580929437346	5		394	719	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355847	73355847	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027016-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	63	464	0	ENST00000377767.4:c.124G>T	p.Ala42Ser	p.A42S	ENST00000377767	NM_014953.3	42	Gcg/Tcg	1/21	0.302268340437215	6	FACETS	0.676	0.584	0.776	0.113	0.097	0.13	INDETERMINATE	1	TRUE	0	0.517580929437346	6		464	733	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46277836	46277836	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027016-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	75	332	0	ENST00000371998.3:c.3634C>A	p.Pro1212Thr	p.P1212T	ENST00000371998		1212	Ccc/Acc	19/23	0.432659290664424	5	FACETS	0.809	0.709	0.917	0.27	0.236	0.306	CLONAL	1	TRUE	2	0.517580929437346	5		332	636	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502805	186502805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027016-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	61	446	0	ENST00000323963.5:c.263C>T	p.Ala88Val	p.A88V	ENST00000323963		88	gCt/gTt	4/11	0.517580929437346	3	FACETS	0.492	0.424	0.566	0.246	0.212	0.283	SUBCLONAL	1	TRUE	1	0.517580929437346	3		446	603	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0027016-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	447	496	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.677890932906446	3	FACETS	0.906	0.879	0.931	0.906	0.879	0.931	CLONAL	3	TRUE	0	0.745464994189415	3		496	606	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0027016-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	182	473	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.245971608902599	3	FACETS	1	0.988	1	0.431	0.401	0.462	INDETERMINATE	1	TRUE	0	0.745464994189415	3		473	518	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027016-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	178	377	0	ENST00000342988.3:c.1067C>T	p.Pro356Leu	p.P356L	ENST00000342988	NM_005359.5	356	cCt/cTt	9/12	0.745464994189415	1	FACETS	0.93	0.875	0.985	0.93	0.875	0.985	CLONAL	1	TRUE	0	0.745464994189415	1		377	322	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0027016-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	59	347	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	NA	2	FACETS	0.765	0.668	0.867			1	INDETERMINATE	1	TRUE	NA	0.745464994189415	2		347	207	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0027016-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	119	223	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.745464994189415	2		223	246	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94908705	94908705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs547426358	NA	P-0027016-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	210	491	0	ENST00000536441.1:c.1349G>A	p.Arg450His	p.R450H	ENST00000536441	NM_144665.3	450	cGc/cAc	9/10	0.745464994189415	3	FACETS	0.917	0.853	0.984	0.459	0.426	0.492	CLONAL	1	TRUE	1	0.745464994189415	3		491	843	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374306	31374306	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0027016-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	136	394	0	ENST00000328111.2:c.307-2A>G		p.X103_splice	ENST00000328111	NM_006892.3	103			0.745464994189415	4	FACETS	0.963	0.878	1	0.321	0.292	0.351	CLONAL	1	TRUE	1	0.745464994189415	4		394	661	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73355847	73355847	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027016-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	241	464	0	ENST00000377767.4:c.124G>T	p.Ala42Ser	p.A42S	ENST00000377767	NM_014953.3	42	Gcg/Tcg	1/21	0.745464994189415	4	FACETS	1	0.992	1	0.48	0.449	0.511	CLONAL	1	TRUE	1	0.745464994189415	4		464	784	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46277836	46277836	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0027016-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	139	332	0	ENST00000371998.3:c.3634C>A	p.Pro1212Thr	p.P1212T	ENST00000371998		1212	Ccc/Acc	19/23	0.745464994189415	4	FACETS	0.95	0.867	1	0.317	0.289	0.346	CLONAL	1	TRUE	1	0.745464994189415	4		332	685	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502805	186502805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0027016-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	112	446	0	ENST00000323963.5:c.263C>T	p.Ala88Val	p.A88V	ENST00000323963		88	gCt/gTt	4/11	0.745464994189415	3	FACETS	0.626	0.564	0.692	0.313	0.282	0.346	SUBCLONAL	1	TRUE	1	0.745464994189415	3		446	659	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435300	110435302	+	inframe_deletion	In_Frame_Del	DEL	GGT	GGT	-	rs765493638	NA	P-0027016-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	23	192	0	ENST00000375856.3:c.3099_3101del	p.Pro1036del	p.P1036del	ENST00000375856	NM_003749.2	1033	ccACCg/ccg	1/2	0.745464994189415	3	FACETS	0.274	0.214	0.344			1	SUBCLONAL	1	TRUE	NA	0.745464994189415	3		192	309	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007752	45007752	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027016-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	161	347	1	ENST00000558401.1:c.199G>T	p.Glu67Ter	p.E67*	ENST00000558401	NM_004048.2	67	Gaa/Taa	2/4	0.567754911655963	2	FACETS	1	0.974	1	0.552	0.513	0.592	CLONAL	1	TRUE	0	0.745464994189415	2		348	391	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945791	17945791	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0027016-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	94	620	0	ENST00000458235.1:c.2069G>A	p.Trp690Ter	p.W690*	ENST00000458235	NM_000215.3	690	tGg/tAg	16/24	0.677890932906446	3	FACETS	0.556	0.495	0.62	0.185	0.165	0.207	SUBCLONAL	1	TRUE	0	0.745464994189415	3		620	623	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0027316-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	131	339	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.96	0.881	1	1	0.994	1	CLONAL	6	TRUE	1	0.12	2		339	379	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023289	27023290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0027316-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	65	149	0	ENST00000324856.7:c.400dup	p.Ala134GlyfsTer266	p.A134Gfs*266	ENST00000324856	NM_006015.4	132	gtg/gtGg	1/20	1	2	FACETS	0.995	0.895	1	1	0.988	1	CLONAL	9	TRUE	1	0.12	2		149	121	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218417	1218417	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027316-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	138	574	1	ENST00000326873.7:c.292G>T	p.Glu98Ter	p.E98*	ENST00000326873	NM_000455.4	98	Gaa/Taa	2/10	1	2	FACETS	0.958	0.884	1	1	0.994	1	CLONAL	7	TRUE	1	0.12	2		575	343	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948409	71948409	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027316-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	129	1035	0	ENST00000298229.2:c.3121G>C	p.Asp1041His	p.D1041H	ENST00000298229	NM_001567.3	1041	Gat/Cat	26/28	0.3	1	FACETS	1	0.954	1	1	0.993	1	CLONAL	5	TRUE	0	0.12	1		1035	381	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100259	157100260	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1554248082	NA	P-0027316-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	27	122	0	ENST00000346085.5:c.1202dup	p.Phe402LeufsTer133	p.F402Lfs*133	ENST00000346085	NM_020732.3	399	gcg/gcGg	1/20	1	2	FACETS	1	0.867	1	1	0.97	1	CLONAL	5	TRUE	1	0.12	2		122	84	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713856	30713856	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	47	589	0	ENST00000295754.5:c.1181G>T	p.Cys394Phe	p.C394F	ENST00000295754	NM_003242.5	394	tGc/tTc	4/7	1	2	FACETS	0.914	0.769	1	0.914	0.769	1	CLONAL	1	TRUE	1	0.14	2		589	735	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023212	27023230	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGGGCCCTAGGCCCGCC	CGCGGGCCCTAGGCCCGCC	-	novel	NA	P-0027385-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	25	306	0	ENST00000324856.7:c.319_337del	p.Ala107Ter	p.A107*	ENST00000324856	NM_006015.4	106	aaCGCGGGCCCTAGGCCCGCC/aa	1/20	1	2	FACETS	0.963	0.759	1	0.963	0.759	1	CLONAL	1	TRUE	1	0.14	2		306	371	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0027449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	89	242	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.101551913003107	4	FACETS	0.993	0.88	1	0.496	0.44	0.557	INDETERMINATE	1	FALSE	2	0.3	4		242	777	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221322	1221322	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	86	773	0	ENST00000326873.7:c.845T>G	p.Leu282Arg	p.L282R	ENST00000326873	NM_000455.4	282	cTc/cGc	6/10	0.18574870581806	0	FACETS	0.656	0.581	0.736			1	SUBCLONAL	1	FALSE	0	0.3	0		773	612	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691828	30691829	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0027449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	86	641	0	ENST00000295754.5:c.333dup	p.Ile112TyrfsTer20	p.I112Yfs*20	ENST00000295754	NM_003242.5	110	-/T	3/7	1	2	FACETS	0.838	0.742	0.942	0.838	0.742	0.942	CLONAL	1	FALSE	1	0.3	2		641	684	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845757	68845757	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587780784	NA	P-0027460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	36	332	0	ENST00000261769.5:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000261769	NM_004360.3	335	Cga/Tga	7/16	1	2	FACETS	0.637	0.524	0.764	0.637	0.524	0.764	SUBCLONAL	1	TRUE	1	0.260309175031871	2		332	434	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0027460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	185	544	0	ENST00000269305.4:c.610G>T	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	204	Gag/Tag	6/11	0.248636139025923	2	FACETS	0.784	0.724	0.846	0.784	0.724	0.846	SUBCLONAL	2	TRUE	0	0.260309175031871	2		544	907	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844155	68844155	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0027460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	170	525	0	ENST00000261769.5:c.743T>A	p.Ile248Asn	p.I248N	ENST00000261769	NM_004360.3	248	aTt/aAt	6/16	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.260309175031871	2		525	932	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100597	67100597	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0027460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	40	364	0	ENST00000412916.2:c.295G>T	p.Ala99Ser	p.A99S	ENST00000412916		99	Gct/Tct	4/6	1	2	FACETS	0.459	0.381	0.547	0.459	0.381	0.547	SUBCLONAL	1	TRUE	1	0.260309175031871	2		364	669	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469941	25469941	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0027460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	73	521	0	ENST00000264709.3:c.1101A>C	p.Lys367Asn	p.K367N	ENST00000264709	NM_175629.2	367	aaA/aaC	9/23	1	2	FACETS	0.677	0.591	0.771	0.677	0.591	0.771	SUBCLONAL	1	TRUE	1	0.260309175031871	2		521	828	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70350018	70350062	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	AGGATGGGGAAAACCCCCAGCGGCAGCGCATAAAGCGCATTCTCC	AGGATGGGGAAAACCCCCAGCGGCAGCGCATAAAGCGCATTCTCC	-	novel	NA	P-0027460-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	70	512	0	ENST00000374080.3:c.4004_4047+1del		p.EDGENPQRQRIKRILQdel	ENST00000374080		1334	gAGGATGGGGAAAACCCCCAGCGGCAGCGCATAAAGCGCATTCTCCag/gag	28/45	1	2	FACETS	0.838	0.73	0.954	0.838	0.73	0.954	CLONAL	1	TRUE	1	0.260309175031871	2		512	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782529	NA	P-0027951-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	322	549	0	ENST00000269305.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000269305	NM_001126112.2	337	Cgc/Tgc	10/11	0.329735154278489	3	FACETS	1	0.988	1	0.75	0.712	0.789	CLONAL	2	TRUE	0	0.429668535591353	3		549	809	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422928	12422928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765206131	NA	P-0027951-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	59	662	0	ENST00000287820.6:c.418C>T	p.Arg140Cys	p.R140C	ENST00000287820	NM_015869.4	140	Cgt/Tgt	3/7	0.284691313946013	3	FACETS	0.522	0.449	0.602	0.261	0.224	0.301	SUBCLONAL	1	TRUE	1	0.429668535591353	3		662	639	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32903616	32903618	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	rs1060502447	NA	P-0027951-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	19	311	0	ENST00000380152.3:c.670_672del	p.Asp224del	p.D224del	ENST00000380152		223	cATGat/cat	8/27	0.19616783007108	3	FACETS	0.465	0.354	0.595	0.233	0.177	0.298	INDETERMINATE	1	TRUE	1	0.429668535591353	3		311	231	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711160	61711160	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs747078799	NA	P-0027951-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	51	554	0	ENST00000401558.2:c.2589C>A	p.Phe863Leu	p.F863L	ENST00000401558	NM_003400.3	863	ttC/ttA	21/25	0.429668535591353	3	FACETS	0.552	0.469	0.644	0.276	0.234	0.322	SUBCLONAL	1	TRUE	1	0.429668535591353	3		554	522	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0028085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	327	496	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.705056416284781	2	FACETS	0.957	0.924	0.989	0.957	0.924	0.989	CLONAL	2	TRUE	0	0.767528211157835	2		496	445	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436081	110436081	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	62	759	2	ENST00000375856.3:c.2320G>A	p.Ala774Thr	p.A774T	ENST00000375856	NM_003749.2	774	Gcg/Acg	1/2	0.767528211157835	3	FACETS	0.231	0.199	0.266	0.077	0.066	0.089	SUBCLONAL	1	TRUE	0	0.767528211157835	3		761	968	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89809315	89809315	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773150877	NA	P-0028085-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	156	483	0	ENST00000389301.3:c.3658C>T	p.Pro1220Ser	p.P1220S	ENST00000389301	NM_000135.2	1220	Ccc/Tcc	37/43	0.734672836601544	3	FACETS	0.99	0.912	1	0.495	0.456	0.536	CLONAL	1	TRUE	1	0.767528211157835	3		483	568	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0028494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	129	255	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.984	0.895	1	0.984	0.895	1	CLONAL	1	TRUE	1	0.429228363475143	2		255	611	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578488	7578488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1131691007	NA	P-0028494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	239	1008	1	ENST00000269305.4:c.442G>A	p.Asp148Asn	p.D148N	ENST00000269305	NM_001126112.2	148	Gat/Aat	5/11	0.429228363475143	1	FACETS	0.869	0.812	0.929	0.869	0.812	0.929	CLONAL	1	TRUE	0	0.429228363475143	1		1009	1006	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936806	32936806	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80359689	NA	P-0028494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	114	491	0	ENST00000380152.3:c.7954del	p.Val2652CysfsTer5	p.V2652Cfs*5	ENST00000380152		2651	aGg/ag	17/27	0.372376544280045	3	FACETS	1	0.937	1			1	CLONAL	1	TRUE	NA	0.429228363475143	3		491	614	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100411	8100411	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0028494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	221	791	0	ENST00000346208.3:c.388del	p.Leu130SerfsTer65	p.L130Sfs*65	ENST00000346208		129	Ccc/cc	3/6	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.429228363475143	2		791	989	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727565	66727576	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TGGCCAGAAAGG	TGGCCAGAAAGG	-	novel	NA	P-0028494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	100	348	2	ENST00000307102.5:c.283_291+3del		p.X95_splice	ENST00000307102	NM_002755.3	95		2/11	1	2	FACETS	0.934	0.838	1	0.934	0.838	1	CLONAL	1	TRUE	1	0.429228363475143	2		350	499	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686324	30686325	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGTGACAACCAGAAATCCTA	novel	NA	P-0028494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	97	524	0	ENST00000295754.5:c.199_200insATGTGACAACCAGAAATCCT	p.Cys67TyrfsTer9	p.C67Yfs*9	ENST00000295754	NM_003242.5	60	-/TGTGACAACCAGAAATCCTA	2/7	0.429228363475143	1	FACETS	0.601	0.536	0.669	0.601	0.536	0.669	SUBCLONAL	1	TRUE	0	0.429228363475143	1		524	591	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156666	20156666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	191	346	0	ENST00000379607.5:c.91G>A	p.Asp31Asn	p.D31N	ENST00000379607	NM_001412.3	31	Gat/Aat	2/7	1	1	FACETS	0.798	0.747	0.85	1	0.992	1	SUBCLONAL	2	TRUE	0	0.429228363475143	1		346	438	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0028522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	10	413	1	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	0.475	0.32	0.671	0.475	0.32	0.671	SUBCLONAL	1	TRUE	1	0.11	2		414	383	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828827	26828827	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0028522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	17	403	0	ENST00000381527.3:c.49G>C	p.Glu17Gln	p.E17Q	ENST00000381527	NM_001260.1	17	Gag/Cag	1/13	1	2	FACETS	1	0.751	1	1	0.751	1	CLONAL	1	TRUE	1	0.11	2		403	307	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481403	140481403	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913357	NA	P-0028522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	22	518	0	ENST00000288602.6:c.1405G>C	p.Gly469Arg	p.G469R	ENST00000288602	NM_004333.4	469	Gga/Cga	11/18	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.11	2		518	346	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798756	135798757	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGACAG	novel	NA	P-0028522-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	14	431	0	ENST00000298552.3:c.481_486dup	p.Leu161_Ser162dup	p.L161_S162dup	ENST00000298552	NM_001162426.1	161	-/CTGTCA	6/23	1	2	FACETS	0.983	0.71	1	0.983	0.71	1	CLONAL	1	TRUE	1	0.11	2		431	259	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631839	90631839	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519906	NA	P-0028605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	154	624	0	ENST00000330062.3:c.514A>T	p.Arg172Trp	p.R172W	ENST00000330062	NM_002168.2	172	Agg/Tgg	4/11	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.416861732476757	2		624	708	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442558	52442562	+	frameshift_variant	Frame_Shift_Del	DEL	AGACC	AGACC	-	novel	NA	P-0028605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	144	645	0	ENST00000460680.1:c.183_187del	p.Lys61AsnfsTer6	p.K61Nfs*6	ENST00000460680	NM_004656.3	61	aaGGTCTct/aact	4/17	0.416861732476757	1	FACETS	0.832	0.761	0.907	0.832	0.761	0.907	CLONAL	1	TRUE	0	0.416861732476757	1		645	657	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180053136	180053137	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	140	643	0	ENST00000261937.6:c.1232dup	p.Asn411LysfsTer16	p.N411Kfs*16	ENST00000261937	NM_182925.4	411	aac/aaAc	9/30	1	2	FACETS	0.985	0.899	1	0.985	0.899	1	CLONAL	1	TRUE	1	0.416861732476757	2		643	682	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869004	117869004	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1392846626	NA	P-0028605-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	149	476	0	ENST00000297338.2:c.695A>G	p.Lys232Arg	p.K232R	ENST00000297338	NM_006265.2	232	aAa/aGa	7/14	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.416861732476757	2		476	711	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0028644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	326	668	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.305673117697235	2	FACETS	0.776	0.734	0.82	0.776	0.734	0.82	SUBCLONAL	2	TRUE	0	0.39023565158547	2		670	1076	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0028644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	31	211	0	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	0.39023565158547	1	FACETS	0.727	0.594	0.873	0.727	0.594	0.873	SUBCLONAL	1	TRUE	0	0.39023565158547	1		211	176	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495022	56495022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763808045	NA	P-0028644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	280	763	2	ENST00000267101.3:c.3379C>T	p.Arg1127Cys	p.R1127C	ENST00000267101	NM_001982.3	1127	Cgc/Tgc	27/28	0.39023565158547	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.39023565158547	1		765	935	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0028644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	120	321	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.39023565158547	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.39023565158547	1		321	418	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544748	65544748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	151	528	0	ENST00000358664.4:c.178C>T	p.Arg60Trp	p.R60W	ENST00000358664	NM_002382.4	60	Cgg/Tgg	4/5	0.39023565158547	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.39023565158547	1		528	537	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662939	52662939	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0028644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	87	389	0	ENST00000394830.3:c.1414C>T	p.Arg472Ter	p.R472*	ENST00000394830	NM_018313.4	472	Cga/Tga	13/30	0.305673117697235	2	FACETS	1	0.956	1	0.573	0.511	0.639	CLONAL	1	TRUE	0	0.39023565158547	2		389	389	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665110	29665110	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658541	NA	P-0028644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	128	655	0	ENST00000356175.3:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000356175	NM_000267.3	2237	Cga/Tga	44/57	0.305673117697235	2	FACETS	1	0.977	1	0.614	0.559	0.672	CLONAL	1	TRUE	0	0.39023565158547	2		655	534	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59793411	59793411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375082407	NA	P-0028644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	84	434	1	ENST00000259008.2:c.2393G>A	p.Arg798Gln	p.R798Q	ENST00000259008	NM_032043.2	798	cGa/cAa	17/20	0.305673117697235	2	FACETS	1	0.979	1	0.732	0.654	0.814	CLONAL	1	TRUE	0	0.39023565158547	2		435	294	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155399	99155399	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1559033620	NA	P-0028644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	164	528	0	ENST00000074304.5:c.625C>T	p.Arg209Ter	p.R209*	ENST00000074304	NM_001134224.1	209	Cga/Tga	9/26	0.39023565158547	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.39023565158547	1		528	620	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445178	49445178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771291128	NA	P-0028644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	302	997	0	ENST00000301067.7:c.2288C>T	p.Pro763Leu	p.P763L	ENST00000301067	NM_003482.3	763	cCg/cTg	10/54	0.39023565158547	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.39023565158547	1		997	1104	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804370	43804370	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0028644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	315	562	0	ENST00000372470.3:c.370G>A	p.Val124Ile	p.V124I	ENST00000372470	NM_005373.2	124	Gtc/Atc	3/12	0.39023565158547	2	FACETS	0.986	0.934	1	0.986	0.934	1	CLONAL	2	TRUE	0	0.39023565158547	2		562	819	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849828	156849828	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121964868	NA	P-0028644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	211	763	0	ENST00000524377.1:c.2084C>T	p.Pro695Leu	p.P695L	ENST00000524377	NM_002529.3	695	cCg/cTg	16/17	0.39023565158547	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.39023565158547	1		763	839	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204506581	204506581	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145156544	NA	P-0028644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	160	544	0	ENST00000367182.3:c.367G>A	p.Ala123Thr	p.A123T	ENST00000367182	NM_001278516.1	123	Gca/Aca	6/11	0.39023565158547	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.39023565158547	1		544	605	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958211	11958211	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0028644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	65	339	0	ENST00000353533.5:c.121C>T	p.Arg41Cys	p.R41C	ENST00000353533	NM_003010.3	41	Cgc/Tgc	2/11	0.305673117697235	2	FACETS	1	0.963	1	0.638	0.559	0.722	CLONAL	1	TRUE	0	0.39023565158547	2		339	261	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58700977	58700977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375732384	NA	P-0028644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	241	678	0	ENST00000305921.3:c.568G>A	p.Val190Ile	p.V190I	ENST00000305921	NM_003620.3	190	Gta/Ata	2/6	0.305673117697235	2	FACETS	0.754	0.706	0.803	0.754	0.706	0.803	SUBCLONAL	2	TRUE	0	0.39023565158547	2		678	819	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971073	55971073	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs754856383	NA	P-0028644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	63	514	1	ENST00000263923.4:c.1724G>T	p.Arg575Ile	p.R575I	ENST00000263923	NM_002253.2	575	aGa/aTa	13/30	0.39023565158547	1	FACETS	0.417	0.36	0.479	0.417	0.36	0.479	SUBCLONAL	1	TRUE	0	0.39023565158547	1		515	623	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360527	70360528	+	missense_variant	Missense_Mutation	DNP	CA	CA	AT	novel	NA	P-0028644-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	68	590	1	ENST00000374080.3:c.6087_6088delinsAT	p.Met2030Leu	p.M2030L	ENST00000374080		2029	acCAtg/acATtg	42/45	0.39023565158547	2	FACETS	0.407	0.353	0.466			1	SUBCLONAL	1	TRUE	NA	0.39023565158547	2		591	856	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0028693-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	11	536	2	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	0.359811869431648	1	FACETS	0.094	0.064	0.131	0.094	0.064	0.131	SUBCLONAL	1	TRUE	0	0.359811869431648	1		538	534	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842075	3842075	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1302427305	NA	P-0028693-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	119	324	0	ENST00000262367.5:c.1237C>T	p.Arg413Ter	p.R413*	ENST00000262367	NM_004380.2	413	Cga/Tga	5/31	1	2	FACETS	1	0.927	1	1	0.99	1	CLONAL	2	TRUE	1	0.359811869431648	2		324	326	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801726	3801726	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs587783483	NA	P-0028693-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	150	434	0	ENST00000262367.5:c.3779+1G>A		p.X1260_splice	ENST00000262367	NM_004380.2	1260			1	2	FACETS	1	0.979	1	1	0.993	1	CLONAL	2	TRUE	1	0.359811869431648	2		434	362	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949128	44949129	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0028693-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	237	448	0	ENST00000377967.4:c.3690dup	p.Ile1231TyrfsTer20	p.I1231Yfs*20	ENST00000377967	NM_021140.2	1230	gct/gcTt	25/29	0.359811869431648	1	FACETS	1	0.977	1	1	0.995	1	CLONAL	2	TRUE	0	0.359811869431648	1		448	507	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035295	42035301	+	frameshift_variant	Frame_Shift_Del	DEL	CCAACTT	CCAACTT	-	novel	NA	P-0028693-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	160	509	0	ENST00000219905.7:c.5138_5144del	p.Pro1713HisfsTer19	p.P1713Hfs*19	ENST00000219905	NM_001164273.1	1713	CCAACTTca/ca	15/24	1	2	FACETS	0.952	0.881	1	1	0.992	1	CLONAL	2	TRUE	1	0.359811869431648	2		509	467	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523614	41523616	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0028693-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	324	716	0	ENST00000263253.7:c.1032_1034del	p.Leu346del	p.L346del	ENST00000263253	NM_001429.3	344	CTC/-	4/31	0.359811869431648	2	FACETS	1	0.987	1	1	0.996	1	CLONAL	3	TRUE	0	0.359811869431648	2		716	556	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266061	41266062	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0028693-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	136	295	0	ENST00000349496.5:c.59dup	p.Ala21GlyfsTer3	p.A21Gfs*3	ENST00000349496	NM_001904.3	20	gcg/gCcg	3/15	1	2	FACETS	1	0.937	1	1	0.991	1	CLONAL	2	TRUE	1	0.359811869431648	2		295	370	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900122	151900122	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0028693-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	138	170	0	ENST00000262189.6:c.3989del	p.Leu1330Ter	p.L1330*	ENST00000262189	NM_170606.2	1330	tTa/ta	26/59	1	2	FACETS	0.999	0.919	1	1	0.991	1	CLONAL	2	TRUE	1	0.359811869431648	2		170	384	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0028777-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	302	753	1	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	NA	2	FACETS	0.952	0.901	1			1	INDETERMINATE	2	TRUE	NA	0.390481384835242	2		754	812	SUCCESS
FH	2271	MSKCC	GRCh37	1	241672003	241672003	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0028777-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	99	484	0	ENST00000366560.3:c.638A>T	p.Lys213Met	p.K213M	ENST00000366560	NM_000143.3	213	aAg/aTg	5/10	1	2	FACETS	0.998	0.895	1	0.998	0.895	1	CLONAL	1	TRUE	1	0.390481384835242	2		484	508	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905483	11905483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1441890339	NA	P-0028777-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	92	373	0	ENST00000396373.4:c.133G>A	p.Glu45Lys	p.E45K	ENST00000396373	NM_001987.4	45	Gaa/Aaa	2/8	1	2	FACETS	0.984	0.878	1	0.984	0.878	1	CLONAL	1	TRUE	1	0.390481384835242	2		373	479	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443820	49443820	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0028777-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	194	880	0	ENST00000301067.7:c.3551A>G	p.Glu1184Gly	p.E1184G	ENST00000301067	NM_003482.3	1184	gAa/gGa	11/54	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.390481384835242	2		880	940	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339582	339582	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0028777-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	157	808	1	ENST00000262320.3:c.2320G>T	p.Gly774Cys	p.G774C	ENST00000262320	NM_003502.3	774	Ggc/Tgc	10/11	1	2	FACETS	0.958	0.879	1	0.958	0.879	1	CLONAL	1	TRUE	1	0.390481384835242	2		809	839	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	165	314	7	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	1	2	FACETS	0.939	0.869	1	0.939	0.869	1	CLONAL	1	TRUE	1	0.678361712902227	2		321	518	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941648	48941648	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913300	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	74	211	0	ENST00000267163.4:c.958C>T	p.Arg320Ter	p.R320*	ENST00000267163	NM_000321.2	320	Cga/Tga	10/27	0.678361712902227	1	FACETS	0.767	0.686	0.85	0.767	0.686	0.85	SUBCLONAL	1	TRUE	0	0.678361712902227	1		211	188	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	342	734	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.957	0.907	1	0.957	0.907	1	CLONAL	1	TRUE	1	0.678361712902227	2		734	1054	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	161	441	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	1	2	FACETS	0.899	0.83	0.97	0.899	0.83	0.97	CLONAL	1	TRUE	1	0.678361712902227	2		441	528	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	187	299	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.678361712902227	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.678361712902227	1		299	364	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030613	48030613	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779617676	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	250	465	1	ENST00000234420.5:c.3227G>A	p.Arg1076His	p.R1076H	ENST00000234420	NM_000179.2	1076	cGc/cAc	5/10	0.678361712902227	1	FACETS	0.909	0.859	0.959	0.909	0.859	0.959	CLONAL	1	TRUE	0	0.678361712902227	1		466	536	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402537	20402537	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	204	470	0	ENST00000346618.3:c.74T>C	p.Val25Ala	p.V25A	ENST00000346618	NM_001949.4	25	gTc/gCc	1/7	1	2	FACETS	0.863	0.803	0.924	0.863	0.803	0.924	CLONAL	1	TRUE	1	0.678361712902227	2		470	697	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206941988	206941988	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376415487	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	150	257	0	ENST00000423557.1:c.530G>A	p.Arg177Gln	p.R177Q	ENST00000423557	NM_000572.2	177	cGa/cAa	5/5	0.643023971071743	3	FACETS	0.972	0.892	1	0.486	0.446	0.528	CLONAL	1	TRUE	1	0.678361712902227	3		257	609	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119709	17119709	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs80338682	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	272	546	9	ENST00000285071.4:c.1285del	p.His429ThrfsTer39	p.H429Tfs*39	ENST00000285071	NM_144997.5	429	Cac/ac	11/14	1	2	FACETS	0.957	0.901	1	0.957	0.901	1	CLONAL	1	TRUE	1	0.678361712902227	2		555	838	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141492	11141492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	342	709	0	ENST00000358026.2:c.3469C>T	p.Arg1157Trp	p.R1157W	ENST00000358026	NM_001128849.1	1157	Cgg/Tgg	25/36	1	2	FACETS	0.97	0.92	1	0.97	0.92	1	CLONAL	1	TRUE	1	0.678361712902227	2		709	1039	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696430	47696430	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	263	488	0	ENST00000347630.2:c.393G>C	p.Trp131Cys	p.W131C	ENST00000347630	NM_001007230.1	131	tgG/tgC	6/11	1	2	FACETS	0.948	0.891	1	0.948	0.891	1	CLONAL	1	TRUE	1	0.678361712902227	2		488	818	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371409680	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	358	734	1	ENST00000269305.4:c.848G>A	p.Arg283His	p.R283H	ENST00000269305	NM_001126112.2	283	cGc/cAc	8/11	1	2	FACETS	0.927	0.88	0.976	0.927	0.88	0.976	CLONAL	1	TRUE	1	0.678361712902227	2		735	1138	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141874	108141874	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587781558	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	171	331	0	ENST00000278616.4:c.2921+1G>A		p.X974_splice	ENST00000278616	NM_000051.3	974			1	2	FACETS	0.951	0.881	1	0.951	0.881	1	CLONAL	1	TRUE	1	0.678361712902227	2		331	530	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909464	50909464	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199576140	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	370	736	3	ENST00000440232.2:c.1268G>A	p.Arg423His	p.R423H	ENST00000440232	NM_002691.3	423	cGt/cAt	11/27	1	2	FACETS	0.949	0.901	0.997	0.949	0.901	0.997	CLONAL	1	TRUE	1	0.678361712902227	2		739	1150	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106459	27106459	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	314	530	0	ENST00000324856.7:c.6070C>T	p.Arg2024Trp	p.R2024W	ENST00000324856	NM_006015.4	2024	Cgg/Tgg	20/20	1	2	FACETS	0.945	0.893	0.997	0.945	0.893	0.997	CLONAL	1	TRUE	1	0.678361712902227	2		530	980	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348857	89348857	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	463	832	1	ENST00000301030.4:c.4093C>T	p.Arg1365Ter	p.R1365*	ENST00000301030	NM_001256183.1	1365	Cga/Tga	9/13	1	2	FACETS	0.992	0.948	1	0.992	0.948	1	CLONAL	1	TRUE	1	0.678361712902227	2		833	1376	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310895	123310895	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141796960	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	262	461	2	ENST00000358487.5:c.533G>A	p.Arg178His	p.R178H	ENST00000358487	NM_000141.4	178	cGc/cAc	5/18	0.678361712902227	1	FACETS	0.93	0.88	0.979	0.93	0.88	0.979	CLONAL	1	TRUE	0	0.678361712902227	1		463	549	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798112	45798112	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587782885	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	380	683	0	ENST00000450313.1:c.739C>T	p.Arg247Ter	p.R247*	ENST00000450313	NM_012222.2	247	Cga/Tga	9/16	1	2	FACETS	0.984	0.935	1	0.984	0.935	1	CLONAL	1	TRUE	1	0.678361712902227	2		683	1139	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851510	63851510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766155061	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	227	472	0	ENST00000279873.7:c.2288C>T	p.Ser763Leu	p.S763L	ENST00000279873	NM_032199.2	763	tCg/tTg	10/10	1	2	FACETS	0.824	0.77	0.88	0.824	0.77	0.88	CLONAL	1	TRUE	1	0.678361712902227	2		472	812	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448147	49448147	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	690	639	0	ENST00000301067.7:c.453del	p.Gln152ArgfsTer56	p.Q152Rfs*56	ENST00000301067	NM_003482.3	151	ggG/gg	4/54	0.678361712902227	3	FACETS	0.992	0.96	1	0.992	0.96	1	CLONAL	2	TRUE	1	0.678361712902227	3		639	1373	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819704	81819704	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	296	568	0	ENST00000359376.3:c.114del	p.Glu39SerfsTer7	p.E39Sfs*7	ENST00000359376	NM_002661.3	37	aCc/ac	2/33	1	2	FACETS	0.867	0.818	0.918	0.867	0.818	0.918	CLONAL	1	TRUE	1	0.678361712902227	2		568	1006	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944584	40944584	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs531404437	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	211	442	0	ENST00000373198.4:c.1918G>T	p.Ala640Ser	p.A640S	ENST00000373198	NM_133170.3	640	Gct/Tct	12/32	1	2	FACETS	0.903	0.842	0.965	0.903	0.842	0.965	CLONAL	1	TRUE	1	0.678361712902227	2		442	689	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815816	32815816	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	380	640	0	ENST00000354258.4:c.1800T>G	p.Asn600Lys	p.N600K	ENST00000354258	NM_000593.5	600	aaT/aaG	8/11	1	2	FACETS	0.984	0.935	1	0.984	0.935	1	CLONAL	1	TRUE	1	0.678361712902227	2		640	1139	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017591	112017591	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	305	504	0	ENST00000368678.4:c.922T>C	p.Phe308Leu	p.F308L	ENST00000368678		308	Ttc/Ctc	9/13	0.678361712902227	1	FACETS	0.966	0.92	1	0.966	0.92	1	CLONAL	1	TRUE	0	0.678361712902227	1		504	615	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489516	56489516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139022684	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	292	525	0	ENST00000267101.3:c.1981G>A	p.Gly661Ser	p.G661S	ENST00000267101	NM_001982.3	661	Ggc/Agc	17/28	0.678361712902227	3	FACETS	0.95	0.894	1	0.475	0.447	0.505	CLONAL	1	TRUE	1	0.678361712902227	3		525	1213	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30132955	30132955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145651161	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	279	518	0	ENST00000331968.5:c.646C>T	p.Arg216Cys	p.R216C	ENST00000331968	NM_002742.2	216	Cgc/Tgc	4/18	1	2	FACETS	0.952	0.897	1	0.952	0.897	1	CLONAL	1	TRUE	1	0.678361712902227	2		518	864	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298659	11298659	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	259	523	0	ENST00000361445.4:c.1802A>G	p.Gln601Arg	p.Q601R	ENST00000361445	NM_004958.3	601	cAa/cGa	12/58	1	2	FACETS	0.862	0.809	0.916	0.862	0.809	0.916	CLONAL	1	TRUE	1	0.678361712902227	2		523	886	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305396	65305396	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	272	485	0	ENST00000342505.4:c.2732A>C	p.Lys911Thr	p.K911T	ENST00000342505	NM_002227.2	911	aAg/aCg	20/25	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.678361712902227	2		485	791	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282379	115282379	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	211	486	0	ENST00000438362.2:c.271C>T	p.Arg91Cys	p.R91C	ENST00000438362	NM_001242891.1	91	Cgt/Tgt	3/20	1	2	FACETS	0.826	0.77	0.884	0.826	0.77	0.884	CLONAL	1	TRUE	1	0.678361712902227	2		486	753	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161298257	161298257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769177037	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	385	380	0	ENST00000367975.2:c.149G>A	p.Arg50His	p.R50H	ENST00000367975	NM_003001.3	50	cGt/cAt	3/6	0.643023971071743	3	FACETS	0.878	0.838	0.918	0.878	0.838	0.918	CLONAL	2	TRUE	1	0.678361712902227	3		380	866	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025632	1025632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	276	556	2	ENST00000358495.3:c.743C>T	p.Ala248Val	p.A248V	ENST00000358495	NM_134424.2	248	gCc/gTc	9/12	1	2	FACETS	0.956	0.901	1	0.956	0.901	1	CLONAL	1	TRUE	1	0.678361712902227	2		558	851	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679184	88679184	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	259	514	0	ENST00000360948.2:c.853A>G	p.Ile285Val	p.I285V	ENST00000360948	NM_001012338.2	285	Att/Gtt	8/19	1	2	FACETS	0.942	0.885	0.999	0.942	0.885	0.999	CLONAL	1	TRUE	1	0.678361712902227	2		514	811	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312704	91312704	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	202	338	0	ENST00000355112.3:c.2443A>G	p.Asn815Asp	p.N815D	ENST00000355112	NM_000057.2	815	Aat/Gat	12/22	1	2	FACETS	0.97	0.904	1	0.97	0.904	1	CLONAL	1	TRUE	1	0.678361712902227	2		338	614	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778932	3778932	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	269	484	0	ENST00000262367.5:c.6116T>C	p.Val2039Ala	p.V2039A	ENST00000262367	NM_004380.2	2039	gTg/gCg	31/31	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.678361712902227	2		484	776	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857053	9857053	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	118	318	0	ENST00000330684.3:c.4348A>G	p.Asn1450Asp	p.N1450D	ENST00000330684	NM_001134407.1	1450	Aat/Gat	13/13	1	2	FACETS	0.913	0.832	0.997	0.913	0.832	0.997	CLONAL	1	TRUE	1	0.678361712902227	2		318	381	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943782	9943782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	258	463	0	ENST00000330684.3:c.1159C>T	p.His387Tyr	p.H387Y	ENST00000330684	NM_001134407.1	387	Cac/Tac	5/13	1	2	FACETS	0.945	0.888	1	0.945	0.888	1	CLONAL	1	TRUE	1	0.678361712902227	2		463	805	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40474492	40474492	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113994139	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	237	422	0	ENST00000264657.5:c.1909G>A	p.Val637Met	p.V637M	ENST00000264657	NM_139276.2	637	Gtg/Atg	21/24	1	2	FACETS	0.961	0.901	1	0.961	0.901	1	CLONAL	1	TRUE	1	0.678361712902227	2		422	727	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867608	78867608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	391	689	0	ENST00000306801.3:c.2344G>A	p.Glu782Lys	p.E782K	ENST00000306801	NM_020761.2	782	Gag/Aag	20/34	1	2	FACETS	0.965	0.917	1	0.965	0.917	1	CLONAL	1	TRUE	1	0.678361712902227	2		689	1195	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39575876	39575876	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	196	374	0	ENST00000262039.4:c.809A>G	p.His270Arg	p.H270R	ENST00000262039	NM_002647.2	270	cAc/cGc	8/25	1	2	FACETS	0.965	0.898	1	0.965	0.898	1	CLONAL	1	TRUE	1	0.678361712902227	2		374	599	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265066	5265066	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	390	760	0	ENST00000357368.4:c.521C>A	p.Pro174His	p.P174H	ENST00000357368	NM_002850.3	174	cCt/cAt	5/38	1	2	FACETS	0.944	0.898	0.991	0.944	0.898	0.991	CLONAL	1	TRUE	1	0.678361712902227	2		760	1218	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279965	18279965	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1483549709	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	316	572	0	ENST00000222254.8:c.2048A>G	p.Tyr683Cys	p.Y683C	ENST00000222254	NM_005027.3	683	tAc/tGc	16/16	1	2	FACETS	0.983	0.93	1	0.983	0.93	1	CLONAL	1	TRUE	1	0.678361712902227	2		572	948	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905615	50905615	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	376	687	2	ENST00000440232.2:c.743T>C	p.Val248Ala	p.V248A	ENST00000440232	NM_002691.3	248	gTc/gCc	6/27	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.678361712902227	2		689	1066	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723765	49723765	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	24	33	0	ENST00000449682.2:c.997C>T	p.Pro333Ser	p.P333S	ENST00000449682	NM_020998.3	333	Cca/Tca	8/18	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.678361712902227	2		33	52	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448520	89448520	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	211	372	0	ENST00000336596.2:c.1484C>A	p.Thr495Asn	p.T495N	ENST00000336596	NM_005233.5	495	aCc/aAc	7/17	1	2	FACETS	0.915	0.854	0.978	0.915	0.854	0.978	CLONAL	1	TRUE	1	0.678361712902227	2		372	680	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155281	106155281	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1478157080	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	216	311	0	ENST00000380013.4:c.182A>G	p.Tyr61Cys	p.Y61C	ENST00000380013	NM_001127208.2	61	tAt/tGt	3/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.678361712902227	2		311	579	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143324125	143324125	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	87	257	0	ENST00000262992.4:c.338C>G	p.Thr113Arg	p.T113R	ENST00000262992	NM_001101669.1	113	aCa/aGa	5/24	1	2	FACETS	0.697	0.622	0.776	0.697	0.622	0.776	SUBCLONAL	1	TRUE	1	0.678361712902227	2		257	368	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518165	187518165	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	183	383	0	ENST00000441802.2:c.12529A>G	p.Ile4177Val	p.I4177V	ENST00000441802	NM_005245.3	4177	Att/Gtt	25/27	1	2	FACETS	0.922	0.856	0.99	0.922	0.856	0.99	CLONAL	1	TRUE	1	0.678361712902227	2		383	585	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521438	187521438	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	184	463	0	ENST00000441802.2:c.11717T>C	p.Val3906Ala	p.V3906A	ENST00000441802	NM_005245.3	3906	gTc/gCc	22/27	1	2	FACETS	0.864	0.801	0.928	0.864	0.801	0.928	CLONAL	1	TRUE	1	0.678361712902227	2		463	628	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512374	149512374	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	298	653	0	ENST00000261799.4:c.1066A>G	p.Thr356Ala	p.T356A	ENST00000261799	NM_002609.3	356	Acc/Gcc	7/23	0.643023971071743	3	FACETS	0.897	0.843	0.952	0.448	0.421	0.476	CLONAL	1	TRUE	1	0.678361712902227	3		653	1312	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553679	106553679	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs971117477	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	214	422	0	ENST00000369096.4:c.1644T>A	p.Asn548Lys	p.N548K	ENST00000369096	NM_001198.3	548	aaT/aaA	5/7	0.678361712902227	1	FACETS	0.881	0.829	0.935	0.881	0.829	0.935	CLONAL	1	TRUE	0	0.678361712902227	1		422	473	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522247	157522247	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs980714829	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	294	610	0	ENST00000346085.5:c.4519A>G	p.Asn1507Asp	p.N1507D	ENST00000346085	NM_020732.3	1507	Aat/Gat	18/20	1	2	FACETS	0.896	0.845	0.949	0.896	0.845	0.949	CLONAL	1	TRUE	1	0.678361712902227	2		610	967	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148516699	148516699	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	162	303	0	ENST00000320356.2:c.988T>C	p.Tyr330His	p.Y330H	ENST00000320356	NM_004456.4	330	Tac/Cac	9/20	0.678361712902227	3	FACETS	0.83	0.762	0.9	0.415	0.381	0.45	CLONAL	1	TRUE	1	0.678361712902227	3		303	771	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891603	151891603	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs746812551	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	161	360	0	ENST00000262189.6:c.4429A>G	p.Asn1477Asp	p.N1477D	ENST00000262189	NM_170606.2	1477	Aat/Gat	29/59	0.678361712902227	3	FACETS	0.904	0.831	0.98	0.452	0.415	0.49	CLONAL	1	TRUE	1	0.678361712902227	3		360	703	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400046	139400047	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	346	742	0	ENST00000277541.6:c.4301dup	p.Gly1435TrpfsTer44	p.G1435Wfs*44	ENST00000277541	NM_017617.3	1434	ggt/ggGt	25/34	1	2	FACETS	0.878	0.831	0.925	0.878	0.831	0.925	CLONAL	1	TRUE	1	0.678361712902227	2		742	1162	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404222	139404222	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029087-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	308	681	0	ENST00000277541.6:c.2932A>G	p.Ile978Val	p.I978V	ENST00000277541	NM_017617.3	978	Atc/Gtc	18/34	1	2	FACETS	0.881	0.831	0.931	0.881	0.831	0.931	CLONAL	1	TRUE	1	0.678361712902227	2		681	1031	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0029295-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	371	459	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	0.239891443272852	14	FACETS	1	0.959	1			1	CLONAL	8	TRUE	NA	0.239891443272852	14		459	936	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0029295-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	287	905	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.23087675089089	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.239891443272852	2		905	1058	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675049	40675049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764271025	NA	P-0029295-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	109	752	2	ENST00000249776.8:c.13G>A	p.Glu5Lys	p.E5K	ENST00000249776	NM_033286.3	5	Gaa/Aaa	1/9	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.239891443272852	2		754	808	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790401	3790401	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1480391685	NA	P-0029295-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	67	413	0	ENST00000262367.5:c.4132C>T	p.Arg1378Trp	p.R1378W	ENST00000262367	NM_004380.2	1378	Cgg/Tgg	24/31	0.239891443272852	3	FACETS	1	0.938	1	0.567	0.493	0.646	CLONAL	1	TRUE	1	0.239891443272852	3		413	552	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056315	27056316	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0029295-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	98	441	0	ENST00000324856.7:c.1314_1315dup	p.Gln439ArgfsTer181	p.Q439Rfs*181	ENST00000324856	NM_006015.4	437	-/GC	2/20	0.215816185162676	3	FACETS	0.87	0.779	0.966	0.87	0.779	0.966	CLONAL	2	TRUE	1	0.239891443272852	3		441	526	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344375	118344375	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029295-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	75	270	0	ENST00000534358.1:c.2501C>T	p.Pro834Leu	p.P834L	ENST00000534358	NM_005933.3	834	cCt/cTt	3/36	0.233682786462161	3	FACETS	1	0.897	1	1	0.897	1	CLONAL	2	TRUE	1	0.239891443272852	3		270	344	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658755	3658755	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029295-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	92	875	0	ENST00000294008.3:c.211T>C	p.Ser71Pro	p.S71P	ENST00000294008	NM_032444.2	71	Tca/Cca	2/15	0.239891443272852	3	FACETS	0.985	0.874	1	0.493	0.437	0.552	CLONAL	1	TRUE	1	0.239891443272852	3		875	872	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281970	49281972	+	stop_gained	Nonsense_Mutation	TNP	GTT	GTT	TTA	novel	NA	P-0029295-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	63	659	0	ENST00000282018.3:c.1017_1019delinsTTA	p.Trp339_Leu340delinsCysTer	p.W339_L340delinsC*	ENST00000282018	NM_020377.2	339	tgGTTg/tgTTAg	1/1	0.239891443272852	1	FACETS	0.663	0.573	0.761	0.663	0.573	0.761	SUBCLONAL	1	TRUE	0	0.239891443272852	1		659	697	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0029312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	108	228	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.997	0.911	1	0.997	0.911	1	CLONAL	1	TRUE	1	0.82062981072273	2		228	264	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481922	56481922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519803	NA	P-0029312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	39	708	1	ENST00000267101.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000267101	NM_001982.3	284	Gga/Aga	7/28	1	2	FACETS	0.123	0.101	0.148	0.123	0.101	0.148	SUBCLONAL	1	TRUE	1	0.82062981072273	2		709	772	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215617178	215617178	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	82	231	0	ENST00000260947.4:c.1670G>T	p.Cys557Phe	p.C557F	ENST00000260947	NM_000465.2	557	tGc/tTc	7/11	1	2	FACETS	0.989	0.891	1	0.989	0.891	1	CLONAL	1	TRUE	1	0.82062981072273	2		231	202	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672276	86672277	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0029312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	195	454	1	ENST00000274376.6:c.2079dup	p.Ser694LeufsTer9	p.S694Lfs*9	ENST00000274376	NM_002890.2	693	agc/agCc	16/25	0.22958291724651	3	FACETS	1	0.988	1	0.632	0.59	0.676	INDETERMINATE	1	TRUE	1	0.82062981072273	3		455	530	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672379	86672420	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGAGGTATTAAATTATTTATCAGTCTTGTTTTTGTTGGAATT	AGAGGTATTAAATTATTTATCAGTCTTGTTTTTGTTGGAATT	-	novel	NA	P-0029312-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	104	244	4	ENST00000274376.6:c.2182_2184+39del		p.X728_splice	ENST00000274376	NM_002890.2	728		16/25	0.22958291724651	3	FACETS	1	0.982	1	0.685	0.624	0.747	INDETERMINATE	1	TRUE	1	0.82062981072273	3		248	261	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243472	46243472	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	187	321	0	ENST00000334344.6:c.1825C>T	p.Gln609Ter	p.Q609*	ENST00000334344	NM_152641.2	609	Cag/Tag	14/21	0.446259558813731	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.446259558813731	1		321	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579705	7579705	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0029335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	190	445	0	ENST00000269305.4:c.91del	p.Val31PhefsTer13	p.V31Ffs*13	ENST00000269305	NM_001126112.2	31	Gtt/tt	3/11	0.446259558813731	1	FACETS	0.998	0.926	1	0.998	0.926	1	CLONAL	1	TRUE	0	0.446259558813731	1		445	663	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930307	39930307	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0029335-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	102	216	0	ENST00000378444.4:c.3157del	p.Arg1053GlyfsTer2	p.R1053Gfs*2	ENST00000378444	NM_001123385.1	1053	Agg/gg	6/15	1	1	FACETS	0.612	0.549	0.679	0.612	0.549	0.679	SUBCLONAL	1	TRUE	0	0.446259558813731	1		216	580	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0029340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	255	228	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.421261186203823	3	FACETS	0.894	0.846	0.942	0.894	0.846	0.942	INDETERMINATE	2	TRUE	1	0.735881031533261	3		228	530	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922294	100922294	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1315135533	NA	P-0029340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	80	237	0	ENST00000325455.5:c.2218C>T	p.Arg740Ter	p.R740*	ENST00000325455	NM_001202474.3	740	Cga/Tga	5/8	1	2	FACETS	0.499	0.441	0.56	0.499	0.441	0.56	SUBCLONAL	1	TRUE	1	0.735881031533261	2		237	436	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599107	28599108	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0029340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	426	808	0	ENST00000253063.3:c.555_556dup	p.Glu186AlafsTer62	p.E186Afs*62	ENST00000253063	NM_031459.4	185	ggc/gGCgc	5/10	0.735881031533261	1	FACETS	0.926	0.89	0.963	0.926	0.89	0.963	CLONAL	1	TRUE	0	0.735881031533261	1		808	790	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252845	10252845	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0029340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	446	702	1	ENST00000340748.4:c.3120C>A	p.Asn1040Lys	p.N1040K	ENST00000340748		1040	aaC/aaA	29/40	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.735881031533261	2		703	1182	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426744	212426744	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs879103900	NA	P-0029340-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	168	605	0	ENST00000342788.4:c.2371A>G	p.Thr791Ala	p.T791A	ENST00000342788	NM_005235.2	791	Acc/Gcc	20/28	0.421261186203823	3	FACETS	0.566	0.519	0.615	0.283	0.259	0.308	INDETERMINATE	1	TRUE	1	0.735881031533261	3		605	1104	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560089	29560089	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1060500271	NA	P-0029386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	55	313	0	ENST00000356175.3:c.3567del	p.Gly1190AlafsTer25	p.G1190Afs*25	ENST00000356175	NM_000267.3	1189	cAa/ca	27/57	0.27894099205235	1	FACETS	0.531	0.454	0.614	0.531	0.454	0.614	SUBCLONAL	1	TRUE	0	0.34	1		313	506	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672234	86672235	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	143	317	0	ENST00000274376.6:c.2036_2037insT	p.Leu680IlefsTer9	p.L680Ifs*9	ENST00000274376	NM_002890.2	679	cga/cgTa	16/25	0.223294763267816	2	FACETS	1	0.984	1	0.675	0.617	0.735	CLONAL	1	TRUE	0	0.34	2		317	623	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0029566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	110	868	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.822	0.741	0.906	0.822	0.741	0.906	CLONAL	1	TRUE	1	0.515774257692106	2		869	519	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882019	NA	P-0029566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	222	884	0	ENST00000269305.4:c.455dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	ccg/ccCg	5/11	0.499610250280419	1	FACETS	0.815	0.761	0.871	0.815	0.761	0.871	CLONAL	1	TRUE	0	0.515774257692106	1		884	784	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48586262	48586262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658694	NA	P-0029566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	111	382	0	ENST00000342988.3:c.931C>T	p.Gln311Ter	p.Q311*	ENST00000342988	NM_005359.5	311	Cag/Tag	8/12	0.499610250280419	1	FACETS	0.907	0.825	0.993	0.907	0.825	0.993	CLONAL	1	TRUE	0	0.515774257692106	1		382	352	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73351564	73351564	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	22	203	1	ENST00000377767.4:c.648A>C	p.Glu216Asp	p.E216D	ENST00000377767	NM_014953.3	216	gaA/gaC	4/21	0.482907198148352	2	FACETS	0.321	0.249	0.404	0.16	0.124	0.202	SUBCLONAL	1	TRUE	0	0.515774257692106	2		204	266	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149998	202149998	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	209	602	0	ENST00000358485.4:c.1439A>T	p.Tyr480Phe	p.Y480F	ENST00000358485	NM_001080125.1	480	tAc/tTc	8/9	1	2	FACETS	0.994	0.925	1	0.994	0.925	1	CLONAL	1	TRUE	1	0.515774257692106	2		602	815	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191455	185191456	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0029566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	216	759	0	ENST00000265026.3:c.2337dup	p.Glu780Ter	p.E780*	ENST00000265026	NM_004721.4	779	aat/aaTt	11/14	1	2	FACETS	0.877	0.816	0.94	0.877	0.816	0.94	CLONAL	1	TRUE	1	0.515774257692106	2		759	955	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80149966	80149966	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	105	346	0	ENST00000265081.6:c.2831A>G	p.Asn944Ser	p.N944S	ENST00000265081	NM_002439.4	944	aAt/aGt	21/24	1	2	FACETS	0.859	0.774	0.949	0.859	0.774	0.949	CLONAL	1	TRUE	1	0.515774257692106	2		346	474	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131911533	131911533	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0029566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	78	419	0	ENST00000265335.6:c.278T>C	p.Leu93Pro	p.L93P	ENST00000265335		93	cTt/cCt	3/25	1	2	FACETS	0.518	0.455	0.585	0.518	0.455	0.585	SUBCLONAL	1	TRUE	1	0.515774257692106	2		419	584	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860257	151860257	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	AA	novel	NA	P-0029566-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	146	463	0	ENST00000262189.6:c.10405delinsTT	p.Leu3469PhefsTer26	p.L3469Ffs*26	ENST00000262189	NM_170606.2	3469	Ctt/TTtt	43/59	1	2	FACETS	0.915	0.838	0.995	0.915	0.838	0.995	CLONAL	1	TRUE	1	0.515774257692106	2		463	619	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0029609-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	198	301	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.549157871122581	4	FACETS	1	0.969	1			1	CLONAL	2	TRUE	NA	0.564547549613279	4		301	517	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80338963	NA	P-0029609-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	169	261	0	ENST00000342988.3:c.1081C>T	p.Arg361Cys	p.R361C	ENST00000342988	NM_005359.5	361	Cgc/Tgc	9/12	0.452090508019307	2	FACETS	0.829	0.774	0.885	0.829	0.774	0.885	CLONAL	2	TRUE	0	0.564547549613279	2		261	361	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799234	42799234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755696593	NA	P-0029609-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	100	588	1	ENST00000575354.2:c.4718C>T	p.Pro1573Leu	p.P1573L	ENST00000575354	NM_015125.3	1573	cCg/cTg	20/20	0.4873510092293	3	FACETS	1	0.903	1	0.503	0.451	0.556	CLONAL	1	TRUE	1	0.564547549613279	3		589	452	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050038	13050038	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0029609-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	73	345	0	ENST00000316448.5:c.182A>T	p.Glu61Val	p.E61V	ENST00000316448	NM_004343.3	61	gAg/gTg	2/9	0.4873510092293	3	FACETS	0.801	0.704	0.905	0.401	0.352	0.453	CLONAL	1	TRUE	1	0.564547549613279	3		345	414	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0029787-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1335	878	800	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.879569911357447	7	FACETS	0.962	0.932	0.992	0.412	0.399	0.426	CLONAL	3	TRUE	0	0.879569911357447	7		800	2213	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0029787-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	981	496	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.879569911357447	7	FACETS	0.966	0.956	0.976	0.966	0.956	0.976	CLONAL	7	TRUE	0	0.879569911357447	7		496	1055	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190345	32190345	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1304701623	NA	P-0029787-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	233	746	0	ENST00000375023.3:c.394C>T	p.Arg132Cys	p.R132C	ENST00000375023	NM_004557.3	132	Cgc/Tgc	3/30	0.436352633888122	3	FACETS	1	0.942	1	0.503	0.471	0.536	INDETERMINATE	1	TRUE	1	0.879569911357447	3		746	758	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249091	55249091	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029787-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1624	661	720	0	ENST00000275493.2:c.2389T>G	p.Cys797Gly	p.C797G	ENST00000275493	NM_005228.3	797	Tgc/Ggc	20/28	0.879569911357447	7	FACETS	1	0.986	1	0.301	0.289	0.313	CLONAL	2	TRUE	0	0.879569911357447	7		720	2285	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445088	89445088	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0029787-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	43	401	0	ENST00000336596.2:c.1408T>G	p.Tyr470Asp	p.Y470D	ENST00000336596	NM_005233.5	470	Tac/Gac	6/17	0.383239375231293	1	FACETS	0.16	0.134	0.189	0.16	0.134	0.189	INDETERMINATE	1	TRUE	0	0.879569911357447	1		401	342	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0029833-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	332	469	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.4706325261821	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.633879391751476	4		469	808	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011150	12011150	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0029833-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	188	361	0	ENST00000353533.5:c.557A>G	p.Asp186Gly	p.D186G	ENST00000353533	NM_003010.3	186	gAt/gGt	5/11	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.633879391751476	2		361	274	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50358670	50358670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0029833-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	93	277	0	ENST00000331340.3:c.13G>A	p.Glu5Lys	p.E5K	ENST00000331340	NM_006060.4	5	Gag/Aag	2/8	0.558558455094673	4	FACETS	0.869	0.774	0.969	0.434	0.387	0.485	CLONAL	1	TRUE	2	0.633879391751476	4		277	552	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175942	176175942	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs964768927	NA	P-0029833-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	50	109	0	ENST00000367669.3:c.173C>T	p.Ser58Leu	p.S58L	ENST00000367669	NM_022457.5	58	tCg/tTg	1/20	0.633879391751476	5	FACETS	1	0.963	1	0.36	0.308	0.414	CLONAL	1	TRUE	1	0.633879391751476	5		109	214	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880827	28880827	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368266056	NA	P-0029833-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	199	696	0	ENST00000282397.4:c.3803C>T	p.Ser1268Leu	p.S1268L	ENST00000282397	NM_002019.4	1268	tCg/tTg	29/30	0.633879391751476	2	FACETS	0.914	0.85	0.98	0.457	0.425	0.49	CLONAL	1	TRUE	0	0.633879391751476	2		696	687	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111496	8111497	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0029833-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	487	678	0	ENST00000346208.3:c.984dup	p.Arg329GlufsTer23	p.R329Efs*23	ENST00000346208		328	tgg/tGgg	5/6	0.633879391751476	5	FACETS	1	0.98	1	0.695	0.664	0.726	CLONAL	2	TRUE	2	0.633879391751476	5		678	1438	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640691	3640694	+	frameshift_variant	Frame_Shift_Del	DEL	TAAT	TAAT	-	novel	NA	P-0029833-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	488	897	0	ENST00000294008.3:c.2945_2948del	p.Asp982AlafsTer18	p.D982Afs*18	ENST00000294008	NM_032444.2	982	gATTAc/gc	12/15	0.633879391751476	5	FACETS	0.934	0.892	0.976	0.623	0.595	0.651	CLONAL	2	TRUE	2	0.633879391751476	5		897	1608	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40368072	40368072	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555548678	NA	P-0029833-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	508	769	3	ENST00000293328.3:c.1433C>T	p.Ala478Val	p.A478V	ENST00000293328	NM_012448.3	478	gCg/gTg	12/19	0.633879391751476	3	FACETS	0.991	0.953	1	0.991	0.953	1	CLONAL	2	TRUE	1	0.633879391751476	3		772	1065	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003260	143003260	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029833-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	203	657	0	ENST00000262992.4:c.2566G>A	p.Glu856Lys	p.E856K	ENST00000262992	NM_001101669.1	856	Gaa/Aaa	23/24	0.633879391751476	3	FACETS	1	0.936	1	0.504	0.468	0.541	CLONAL	1	TRUE	1	0.633879391751476	3		657	837	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410763	63410763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029833-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	211	704	0	ENST00000330258.3:c.2404G>A	p.Glu802Lys	p.E802K	ENST00000330258	NM_152424.3	802	Gag/Aag	2/2	0.633879391751476	3	FACETS	1	0.941	1	0.506	0.471	0.543	CLONAL	1	TRUE	1	0.633879391751476	3		704	866	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623229	52623229	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141067977	NA	P-0029833-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	127	385	0	ENST00000394830.3:c.2822C>T	p.Ser941Leu	p.S941L	ENST00000394830	NM_018313.4	941	tCa/tTa	19/30	0.4706325261821	4	FACETS	1	0.93	1	0.514	0.467	0.564	CLONAL	1	TRUE	2	0.633879391751476	4		385	637	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944377	206944377	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029833-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	153	530	0	ENST00000423557.1:c.253G>C	p.Glu85Gln	p.E85Q	ENST00000423557	NM_000572.2	85	Gag/Cag	3/5	0.633879391751476	5	FACETS	0.909	0.831	0.991	0.227	0.207	0.248	CLONAL	1	TRUE	1	0.633879391751476	5		530	1036	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56338916	56338916	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029833-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	19	41	0	ENST00000348428.3:c.41C>T	p.Ser14Leu	p.S14L	ENST00000348428	NM_006785.3	14	tCg/tTg	1/17	0.633879391751476	3	FACETS	1	0.823	1			1	CLONAL	1	TRUE	NA	0.633879391751476	3		41	74	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443696	49443697	+	missense_variant	Missense_Mutation	DNP	GG	GG	TC	novel	NA	P-0029833-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1181	148	846	1	ENST00000301067.7:c.3674_3675delinsGA	p.Pro1225Arg	p.P1225R	ENST00000301067	NM_003482.3	1225	cCC/cGA	11/54	0.633879391751476	5	FACETS	0.685	0.624	0.75	0.228	0.208	0.25	SUBCLONAL	1	TRUE	2	0.633879391751476	5		847	1329	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347768	347768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029833-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1520	271	1048	0	ENST00000262320.3:c.1738G>A	p.Glu580Lys	p.E580K	ENST00000262320	NM_003502.3	580	Gag/Aag	6/11	0.633879391751476	5	FACETS	0.931	0.871	0.994	0.31	0.29	0.332	CLONAL	1	TRUE	2	0.633879391751476	5		1048	1791	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138246	2138246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029833-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1437	278	1011	0	ENST00000219476.3:c.5179C>T	p.His1727Tyr	p.H1727Y	ENST00000219476	NM_000548.3	1727	Cat/Tat	41/42	0.633879391751476	5	FACETS	0.998	0.934	1	0.333	0.311	0.355	CLONAL	1	TRUE	2	0.633879391751476	5		1011	1715	SUCCESS
CALR	811	MSKCC	GRCh37	19	13049562	13049562	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029833-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	208	865	0	ENST00000316448.5:c.69C>G	p.Phe23Leu	p.F23L	ENST00000316448	NM_004343.3	23	ttC/ttG	1/9	1	2	FACETS	0.826	0.768	0.885	0.826	0.768	0.885	CLONAL	1	TRUE	1	0.633879391751476	2		865	795	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686229	117686229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029833-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	131	305	0	ENST00000368508.3:c.3112G>A	p.Glu1038Lys	p.E1038K	ENST00000368508	NM_002944.2	1038	Gaa/Aaa	20/43	0.633879391751476	3	FACETS	1	0.961	1	0.547	0.499	0.596	CLONAL	1	TRUE	1	0.633879391751476	3		305	498	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866465	56866465	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029833-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1626	164	838	0	ENST00000519728.1:c.712G>C	p.Asp238His	p.D238H	ENST00000519728	NM_002350.3	238	Gat/Cat	8/13	0.633879391751476	6	FACETS	0.656	0.599	0.715	0.219	0.199	0.239	SUBCLONAL	1	TRUE	3	0.633879391751476	6		838	1790	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923169	39923169	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029833-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	110	702	0	ENST00000378444.4:c.3539C>G	p.Ser1180Cys	p.S1180C	ENST00000378444	NM_001123385.1	1180	tCt/tGt	8/15	0.633879391751476	3	FACETS	0.541	0.485	0.6	0.27	0.242	0.3	SUBCLONAL	1	TRUE	1	0.633879391751476	3		702	845	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0029852-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	81	385	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.732	0.646	0.824	0.732	0.646	0.824	SUBCLONAL	1	TRUE	1	0.408919582632722	2		385	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579718	7579718	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029852-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	439	1099	0	ENST00000269305.4:c.78del	p.Pro27LeufsTer17	p.P27Lfs*17	ENST00000269305	NM_001126112.2	26	ctT/ct	3/11	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.408919582632722	2		1099	996	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44894182	44894182	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0029852-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	75	247	0	ENST00000377967.4:c.571C>T	p.Gln191Ter	p.Q191*	ENST00000377967	NM_021140.2	191	Cag/Tag	7/29	1	1	FACETS	0.82	0.735	0.906	1	0.982	1	CLONAL	2	TRUE	0	0.408919582632722	1		247	178	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604332	189604332	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0029852-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	36	580	0	ENST00000264731.3:c.1499G>C	p.Gly500Ala	p.G500A	ENST00000264731	NM_003722.4	500	gGa/gCa	11/14	0.322549206715361	3	FACETS	0.407	0.334	0.489	0.204	0.167	0.245	SUBCLONAL	1	TRUE	1	0.408919582632722	3		580	521	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71949098	71949098	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0029852-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	246	964	0	ENST00000298229.2:c.3565C>A	p.Gln1189Lys	p.Q1189K	ENST00000298229	NM_001567.3	1189	Cag/Aag	27/28	0.324054046601645	2	FACETS	0.779	0.731	0.829	0.779	0.731	0.829	SUBCLONAL	2	TRUE	0	0.408919582632722	2		964	772	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032378	10032378	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029852-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	61	545	0	ENST00000330684.3:c.445G>A	p.Ala149Thr	p.A149T	ENST00000330684	NM_001134407.1	149	Gcg/Acg	3/13	1	2	FACETS	0.566	0.489	0.65	0.566	0.489	0.65	SUBCLONAL	1	TRUE	1	0.408919582632722	2		545	527	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960074	134960075	+	missense_variant	Missense_Mutation	DNP	GG	GG	TC	novel	NA	P-0029852-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	95	926	1	ENST00000398015.3:c.2431_2432delinsTC	p.Gly811Ser	p.G811S	ENST00000398015	NM_004441.4	811	GGg/TCg	13/16	0.322549206715361	3	FACETS	0.664	0.59	0.742	0.332	0.295	0.371	SUBCLONAL	1	TRUE	1	0.408919582632722	3		927	843	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671269	30671269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0029852-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	61	868	0	ENST00000376406.3:c.5608G>A	p.Glu1870Lys	p.E1870K	ENST00000376406	NM_014641.2	1870	Gag/Aag	11/15	0.154134757819315	2	FACETS	0.346	0.298	0.399	0.173	0.149	0.2	INDETERMINATE	1	TRUE	0	0.408919582632722	2		868	862	SUCCESS
PDCD1LG2	80380	MSKCC	GRCh37	9	5534785	5534785	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0029852-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	175	595	0	ENST00000397747.3:c.96del	p.Ile32MetfsTer7	p.I32Mfs*7	ENST00000397747	NM_025239.3	32	atA/at	3/7	0.324054046601645	2	FACETS	0.847	0.787	0.91	0.847	0.787	0.91	CLONAL	2	TRUE	0	0.408919582632722	2		595	505	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155201	108155201	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs200196781	NA	P-0029955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	58	361	0	ENST00000278616.4:c.3993+1G>A		p.X1331_splice	ENST00000278616	NM_000051.3	1331			0.241316572033116	3	FACETS	0.925	0.796	1	0.463	0.398	0.533	CLONAL	1	TRUE	1	0.275977028774358	3		361	517	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597600	28597600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1411473584	NA	P-0029955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	70	505	0	ENST00000241453.7:c.2305G>A	p.Glu769Lys	p.E769K	ENST00000241453	NM_004119.2	769	Gaa/Aaa	19/24	0.235013021455885	4	FACETS	0.772	0.671	0.88	0.257	0.223	0.294	SUBCLONAL	1	TRUE	1	0.275977028774358	4		505	839	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035110	42035110	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0029955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	204	595	0	ENST00000219905.7:c.4952C>G	p.Ser1651Cys	p.S1651C	ENST00000219905	NM_001164273.1	1651	tCt/tGt	15/24	0.241316572033116	3	FACETS	0.904	0.838	0.971	0.904	0.838	0.971	CLONAL	2	TRUE	1	0.275977028774358	3		595	931	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522553	67522554	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0029955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	76	259	0	ENST00000274335.5:c.51_52del	p.Glu19ArgfsTer4	p.E19Rfs*4	ENST00000274335		17	gAA/g	1/15	0.275977028774358	2	FACETS	0.894	0.792	1	0.894	0.792	1	CLONAL	2	TRUE	0	0.275977028774358	2		259	308	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	149	868	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.913	0.84	0.989	0.913	0.84	0.989	CLONAL	1	TRUE	1	0.646111414792782	2		869	505	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	261	452	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	0.756	0.717	0.796	1	0.994	1	SUBCLONAL	2	TRUE	1	0.646111414792782	2		457	534	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	174	500	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.646111414792782	2		500	512	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799299	42799300	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1158987717	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	111	454	0	ENST00000575354.2:c.4790dup	p.Pro1598ThrfsTer16	p.P1598Tfs*16	ENST00000575354	NM_015125.3	1595	tcc/tCcc	20/20	1	2	FACETS	0.733	0.662	0.806	0.733	0.662	0.806	SUBCLONAL	1	TRUE	1	0.646111414792782	2		454	469	SUCCESS
APC	324	MSKCC	GRCh37	5	112175675	112175676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	120	375	0	ENST00000257430.4:c.4393_4394dup	p.Ser1465ArgfsTer9	p.S1465Rfs*9	ENST00000257430	NM_000038.5	1462	aag/aAGag	16/16	1	2	FACETS	0.945	0.861	1	0.945	0.861	1	CLONAL	1	TRUE	1	0.646111414792782	2		375	393	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260606	16260606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200512596	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	219	574	1	ENST00000375759.3:c.7871G>A	p.Arg2624Gln	p.R2624Q	ENST00000375759	NM_015001.2	2624	cGg/cAg	11/15	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.646111414792782	2		575	667	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	62	159	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.95	0.834	1	0.95	0.834	1	CLONAL	1	TRUE	1	0.646111414792782	2		159	202	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119781	70119781	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1274036689	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	264	627	2	ENST00000245479.2:c.788del	p.Gly263AlafsTer16	p.G263Afs*16	ENST00000245479	NM_000346.3	261	gaG/ga	3/3	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.646111414792782	2		629	791	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	178	429	5	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.646111414792782	2		434	538	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760024	133760024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	313	729	0	ENST00000318560.5:c.2352del	p.Arg785GlyfsTer3	p.R785Gfs*3	ENST00000318560	NM_005157.4	783	Ccc/cc	11/11	1	2	FACETS	0.992	0.937	1	0.992	0.937	1	CLONAL	1	TRUE	1	0.646111414792782	2		729	977	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345768	152345769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs759063323	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	102	266	0	ENST00000359321.1:c.801dup	p.His268ThrfsTer11	p.H268Tfs*11	ENST00000359321	NM_005431.1	267	-/A	3/3	1	2	FACETS	0.882	0.796	0.971	0.882	0.796	0.971	CLONAL	1	TRUE	1	0.646111414792782	2		266	358	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178258	56178258	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	99	371	0	ENST00000399503.3:c.3236del	p.Asn1079IlefsTer3	p.N1079Ifs*3	ENST00000399503	NM_005921.1	1077	tcA/tc	14/20	1	2	FACETS	0.92	0.83	1	0.92	0.83	1	CLONAL	1	TRUE	1	0.646111414792782	2		371	333	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967511	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	rs1349928568	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	110	364	0	ENST00000265433.3:c.1396dup	p.Arg466LysfsTer5	p.R466Kfs*5	ENST00000265433	NM_002485.4	466	agg/aAgg	10/16	1	2	FACETS	0.999	0.907	1	0.999	0.907	1	CLONAL	1	TRUE	1	0.646111414792782	2		364	341	SUCCESS
APC	324	MSKCC	GRCh37	5	112174262	112174262	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs786202995	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	108	413	0	ENST00000257430.4:c.2971G>T	p.Glu991Ter	p.E991*	ENST00000257430	NM_000038.5	991	Gaa/Taa	16/16	1	2	FACETS	0.873	0.79	0.959	0.873	0.79	0.959	CLONAL	1	TRUE	1	0.646111414792782	2		413	383	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432347	49432347	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	286	722	1	ENST00000301067.7:c.8792del	p.Pro2931HisfsTer12	p.P2931Hfs*12	ENST00000301067	NM_003482.3	2931	cCa/ca	34/54	1	2	FACETS	0.988	0.931	1	0.988	0.931	1	CLONAL	1	TRUE	1	0.646111414792782	2		723	896	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874713	151874713	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	169	437	0	ENST00000262189.6:c.7825C>T	p.Arg2609Ter	p.R2609*	ENST00000262189	NM_170606.2	2609	Cga/Tga	38/59	1	2	FACETS	0.985	0.912	1	0.985	0.912	1	CLONAL	1	TRUE	1	0.646111414792782	2		437	531	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873248	71873248	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	134	328	0	ENST00000357731.5:c.946A>C	p.Ser316Arg	p.S316R	ENST00000357731	NM_173808.2	316	Agt/Cgt	7/7	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.646111414792782	2		328	393	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130637	29130637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142243299	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	195	492	0	ENST00000328354.6:c.73G>A	p.Val25Ile	p.V25I	ENST00000328354	NM_007194.3	25	Gtt/Att	2/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.646111414792782	2		492	582	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437222	220437223	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1286117855	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	267	707	0	ENST00000243786.2:c.132dup	p.Ala45ArgfsTer29	p.A45Rfs*29	ENST00000243786	NM_002191.3	42	-/C	1/2	1	2	FACETS	0.831	0.78	0.883	0.831	0.78	0.883	CLONAL	1	TRUE	1	0.646111414792782	2		707	995	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349310	11349310	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	224	359	0	ENST00000332029.2:c.26C>T	p.Ala9Val	p.A9V	ENST00000332029	NM_003745.1	9	gCc/gTc	2/2	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.646111414792782	2		359	645	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133268	38133268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770152981	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	235	636	0	ENST00000317025.8:c.4205G>A	p.Arg1402His	p.R1402H	ENST00000317025	NM_023034.1	1402	cGc/cAc	24/24	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.646111414792782	2		636	722	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958168	2958168	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs928782717	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	274	623	4	ENST00000396946.4:c.2564G>A	p.Arg855Gln	p.R855Q	ENST00000396946	NM_032415.4	855	cGg/cAg	19/25	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.646111414792782	2		627	847	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922084	39922085	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	33	328	0	ENST00000378444.4:c.4087_4088del	p.Cys1363GlnfsTer45	p.C1363Qfs*45	ENST00000378444	NM_001123385.1	1363	TGc/c	9/15	1	1	FACETS	0.154	0.125	0.186	0.154	0.125	0.186	SUBCLONAL	1	TRUE	0	0.646111414792782	1		328	450	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104554	193104554	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	169	440	0	ENST00000367435.3:c.341T>C	p.Leu114Ser	p.L114S	ENST00000367435	NM_024529.4	114	tTa/tCa	4/17	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.646111414792782	2		440	467	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944154	71944154	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	278	640	0	ENST00000298229.2:c.1987T>C	p.Tyr663His	p.Y663H	ENST00000298229	NM_001567.3	663	Tat/Cat	17/28	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.646111414792782	2		640	845	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245043	46245043	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	186	614	0	ENST00000334344.6:c.3137A>C	p.Asn1046Thr	p.N1046T	ENST00000334344	NM_152641.2	1046	aAt/aCt	15/21	1	2	FACETS	0.947	0.879	1	0.947	0.879	1	CLONAL	1	TRUE	1	0.646111414792782	2		614	608	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865040	57865040	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	276	704	0	ENST00000228682.2:c.2520del	p.Pro842HisfsTer104	p.P842Hfs*104	ENST00000228682	NM_005269.2	839	gaG/ga	12/12	1	2	FACETS	0.946	0.89	1	0.946	0.89	1	CLONAL	1	TRUE	1	0.646111414792782	2		704	903	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784663	43784664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	175	438	0	ENST00000382044.4:c.10dup	p.Glu4GlyfsTer25	p.E4Gfs*25	ENST00000382044	NM_001141980.1	4	gag/gGag	2/28	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.646111414792782	2		438	484	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830778	3830778	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	210	537	0	ENST00000262367.5:c.1778A>C	p.His593Pro	p.H593P	ENST00000262367	NM_004380.2	593	cAc/cCc	8/31	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.646111414792782	2		537	604	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822580	72822586	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGCTG	GCTGCTG	-	novel	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	142	465	2	ENST00000268489.5:c.9589_9595del	p.Gln3197SerfsTer42	p.Q3197Sfs*42	ENST00000268489	NM_006885.3	3197	CAGCAGCag/ag	10/10	1	2	FACETS	0.815	0.747	0.886	0.815	0.747	0.886	CLONAL	1	TRUE	1	0.646111414792782	2		467	539	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752390	55752390	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	317	682	0	ENST00000284073.2:c.848C>T	p.Ala283Val	p.A283V	ENST00000284073	NM_138962.2	283	gCc/gTc	12/14	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.646111414792782	2		682	973	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602940	10602940	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	309	668	0	ENST00000171111.5:c.640-2A>G		p.X214_splice	ENST00000171111	NM_203500.1	214			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.646111414792782	2		668	914	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976205	18976205	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	112	746	0	ENST00000262803.5:c.2965A>G	p.Met989Val	p.M989V	ENST00000262803	NM_002911.3	989	Atg/Gtg	21/24	1	2	FACETS	0.388	0.349	0.43	0.388	0.349	0.43	SUBCLONAL	1	TRUE	1	0.646111414792782	2		746	893	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976421	18976421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1234132463	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	351	735	1	ENST00000262803.5:c.3071G>A	p.Arg1024His	p.R1024H	ENST00000262803	NM_002911.3	1024	cGc/cAc	22/24	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.646111414792782	2		736	1040	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519814	29519814	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1046338903	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	209	615	1	ENST00000389048.3:c.1757C>T	p.Ala586Val	p.A586V	ENST00000389048	NM_004304.4	586	gCc/gTc	9/29	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.646111414792782	2		616	628	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092892	29092892	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	187	418	1	ENST00000328354.6:c.1092A>G	p.Ile364Met	p.I364M	ENST00000328354	NM_007194.3	364	atA/atG	10/15	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.646111414792782	2		419	532	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37059012	37059012	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs63750691	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	159	406	0	ENST00000231790.2:c.806C>G	p.Ser269Ter	p.S269*	ENST00000231790	NM_000249.3	269	tCa/tGa	10/19	1	2	FACETS	0.87	0.801	0.94	0.87	0.801	0.94	CLONAL	1	TRUE	1	0.646111414792782	2		406	566	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467833	66467834	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	48	343	0	ENST00000273854.3:c.435dup	p.Thr146AspfsTer3	p.T146Dfs*3	ENST00000273854	NM_004439.5	145	-/G	3/18	1	2	FACETS	0.377	0.319	0.44	0.377	0.319	0.44	SUBCLONAL	1	TRUE	1	0.646111414792782	2		343	394	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721039	176721039	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	26	471	1	ENST00000439151.2:c.6674del	p.Pro2225GlnfsTer69	p.P2225Qfs*69	ENST00000439151	NM_022455.4	2224	Ccc/cc	23/23	1	2	FACETS	0.157	0.124	0.196	0.157	0.124	0.196	SUBCLONAL	1	TRUE	1	0.646111414792782	2		472	511	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672096	30672096	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	538	688	0	ENST00000376406.3:c.4864A>G	p.Thr1622Ala	p.T1622A	ENST00000376406	NM_014641.2	1622	Acc/Gcc	10/15	0.646111414792782	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.646111414792782	2		688	781	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157488286	157488286	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs773510355	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	162	389	0	ENST00000346085.5:c.2992A>C	p.Ser998Arg	p.S998R	ENST00000346085	NM_020732.3	998	Agc/Cgc	10/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.646111414792782	2		389	477	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524267	148524269	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	131	389	0	ENST00000320356.2:c.715_717del	p.Glu239del	p.E239del	ENST00000320356	NM_004456.4	239	GAA/-	7/20	1	2	FACETS	0.922	0.843	1	0.922	0.843	1	CLONAL	1	TRUE	1	0.646111414792782	2		389	440	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860907	151860907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	113	291	0	ENST00000262189.6:c.9755G>A	p.Arg3252His	p.R3252H	ENST00000262189	NM_170606.2	3252	cGt/cAt	43/59	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.646111414792782	2		291	333	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400206	139400206	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	245	760	0	ENST00000277541.6:c.4142C>A	p.Pro1381His	p.P1381H	ENST00000277541	NM_017617.3	1381	cCc/cAc	25/34	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.646111414792782	2		760	753	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	230	868	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.932	0.873	0.992	0.932	0.873	0.992	CLONAL	1	TRUE	1	0.73	2		869	676	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661663	227661664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761880048	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	270	578	9	ENST00000305123.5:c.1791dup	p.His598AlafsTer13	p.H598Afs*13	ENST00000305123	NM_005544.2	597	-/G	1/2	1	2	FACETS	0.812	0.763	0.862	0.812	0.763	0.862	CLONAL	1	TRUE	1	0.73	2		587	911	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	302	452	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.73	2		457	805	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182641	38182641	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs387907272	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	26	349	0	ENST00000396334.3:c.794T>C	p.Leu265Pro	p.L265P	ENST00000396334	NM_002468.4	265	cTg/cCg	5/5	1	2	FACETS	0.116	0.091	0.145	0.116	0.091	0.145	SUBCLONAL	1	TRUE	1	0.73	2		349	612	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	277	500	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.925	0.872	0.98	0.925	0.872	0.98	CLONAL	1	TRUE	1	0.73	2		500	820	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799299	42799300	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1158987717	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	197	454	0	ENST00000575354.2:c.4790dup	p.Pro1598ThrfsTer16	p.P1598Tfs*16	ENST00000575354	NM_015125.3	1595	tcc/tCcc	20/20	1	2	FACETS	0.774	0.72	0.831	0.774	0.72	0.831	SUBCLONAL	1	TRUE	1	0.73	2		454	697	SUCCESS
APC	324	MSKCC	GRCh37	5	112175675	112175676	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	202	375	0	ENST00000257430.4:c.4393_4394dup	p.Ser1465ArgfsTer9	p.S1465Rfs*9	ENST00000257430	NM_000038.5	1462	aag/aAGag	16/16	1	2	FACETS	0.83	0.773	0.888	0.83	0.773	0.888	CLONAL	1	TRUE	1	0.73	2		375	667	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260606	16260606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200512596	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	393	574	1	ENST00000375759.3:c.7871G>A	p.Arg2624Gln	p.R2624Q	ENST00000375759	NM_015001.2	2624	cGg/cAg	11/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.73	2		575	1035	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	92	159	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.894	0.805	0.986	0.894	0.805	0.986	CLONAL	1	TRUE	1	0.73	2		159	282	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119781	70119781	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1274036689	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	410	627	2	ENST00000245479.2:c.788del	p.Gly263AlafsTer16	p.G263Afs*16	ENST00000245479	NM_000346.3	261	gaG/ga	3/3	1	2	FACETS	0.986	0.94	1	0.986	0.94	1	CLONAL	1	TRUE	1	0.73	2		629	1139	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	247	429	5	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	0.88	0.826	0.935	0.88	0.826	0.935	CLONAL	1	TRUE	1	0.73	2		434	769	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760024	133760024	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	422	729	0	ENST00000318560.5:c.2352del	p.Arg785GlyfsTer3	p.R785Gfs*3	ENST00000318560	NM_005157.4	783	Ccc/cc	11/11	1	2	FACETS	0.964	0.92	1	0.964	0.92	1	CLONAL	1	TRUE	1	0.73	2		729	1199	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178258	56178258	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	229	371	0	ENST00000399503.3:c.3236del	p.Asn1079IlefsTer3	p.N1079Ifs*3	ENST00000399503	NM_005921.1	1077	tcA/tc	14/20	1	2	FACETS	0.935	0.876	0.995	0.935	0.876	0.995	CLONAL	1	TRUE	1	0.73	2		371	671	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967511	90967512	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	rs1349928568	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	182	364	0	ENST00000265433.3:c.1396dup	p.Arg466LysfsTer5	p.R466Kfs*5	ENST00000265433	NM_002485.4	466	agg/aAgg	10/16	1	2	FACETS	0.873	0.811	0.937	0.873	0.811	0.937	CLONAL	1	TRUE	1	0.73	2		364	571	SUCCESS
APC	324	MSKCC	GRCh37	5	112174262	112174262	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs786202995	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	229	413	0	ENST00000257430.4:c.2971G>T	p.Glu991Ter	p.E991*	ENST00000257430	NM_000038.5	991	Gaa/Taa	16/16	1	2	FACETS	0.958	0.898	1	0.958	0.898	1	CLONAL	1	TRUE	1	0.73	2		413	655	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130637	29130637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142243299	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	342	492	0	ENST00000328354.6:c.73G>A	p.Val25Ile	p.V25I	ENST00000328354	NM_007194.3	25	Gtt/Att	2/15	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.73	2		492	889	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437222	220437223	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1286117855	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	411	707	0	ENST00000243786.2:c.132dup	p.Ala45ArgfsTer29	p.A45Rfs*29	ENST00000243786	NM_002191.3	42	-/C	1/2	1	2	FACETS	0.887	0.844	0.93	0.887	0.844	0.93	CLONAL	1	TRUE	1	0.73	2		707	1270	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133268	38133268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770152981	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	418	636	0	ENST00000317025.8:c.4205G>A	p.Arg1402His	p.R1402H	ENST00000317025	NM_023034.1	1402	cGc/cAc	24/24	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.73	2		636	1094	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958168	2958168	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs928782717	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	389	623	4	ENST00000396946.4:c.2564G>A	p.Arg855Gln	p.R855Q	ENST00000396946	NM_032415.4	855	cGg/cAg	19/25	1	2	FACETS	0.972	0.926	1	0.972	0.926	1	CLONAL	1	TRUE	1	0.73	2		627	1096	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104554	193104554	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	241	440	0	ENST00000367435.3:c.341T>C	p.Leu114Ser	p.L114S	ENST00000367435	NM_024529.4	114	tTa/tCa	4/17	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.73	2		440	636	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944154	71944154	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	405	640	0	ENST00000298229.2:c.1987T>C	p.Tyr663His	p.Y663H	ENST00000298229	NM_001567.3	663	Tat/Cat	17/28	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.73	2		640	1086	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245043	46245043	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	393	614	0	ENST00000334344.6:c.3137A>C	p.Asn1046Thr	p.N1046T	ENST00000334344	NM_152641.2	1046	aAt/aCt	15/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.73	2		614	1062	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865040	57865040	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	454	704	0	ENST00000228682.2:c.2520del	p.Pro842HisfsTer104	p.P842Hfs*104	ENST00000228682	NM_005269.2	839	gaG/ga	12/12	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.73	2		704	1210	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784663	43784664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	281	438	0	ENST00000382044.4:c.10dup	p.Glu4GlyfsTer25	p.E4Gfs*25	ENST00000382044	NM_001141980.1	4	gag/gGag	2/28	1	2	FACETS	0.883	0.832	0.935	0.883	0.832	0.935	CLONAL	1	TRUE	1	0.73	2		438	872	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830778	3830778	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	335	537	0	ENST00000262367.5:c.1778A>C	p.His593Pro	p.H593P	ENST00000262367	NM_004380.2	593	cAc/cCc	8/31	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.73	2		537	903	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822580	72822586	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGCTG	GCTGCTG	-	novel	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	173	465	2	ENST00000268489.5:c.9589_9595del	p.Gln3197SerfsTer42	p.Q3197Sfs*42	ENST00000268489	NM_006885.3	3197	CAGCAGCag/ag	10/10	1	2	FACETS	0.664	0.613	0.717	0.664	0.613	0.717	SUBCLONAL	1	TRUE	1	0.73	2		467	714	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752390	55752390	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	411	682	0	ENST00000284073.2:c.848C>T	p.Ala283Val	p.A283V	ENST00000284073	NM_138962.2	283	gCc/gTc	12/14	1	2	FACETS	0.946	0.902	0.992	0.946	0.902	0.992	CLONAL	1	TRUE	1	0.73	2		682	1190	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976421	18976421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1234132463	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	487	735	1	ENST00000262803.5:c.3071G>A	p.Arg1024His	p.R1024H	ENST00000262803	NM_002911.3	1024	cGc/cAc	22/24	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.73	2		736	1266	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092892	29092892	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	289	418	1	ENST00000328354.6:c.1092A>G	p.Ile364Met	p.I364M	ENST00000328354	NM_007194.3	364	atA/atG	10/15	1	2	FACETS	0.972	0.917	1	0.972	0.917	1	CLONAL	1	TRUE	1	0.73	2		419	815	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37059012	37059012	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs63750691	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	285	406	0	ENST00000231790.2:c.806C>G	p.Ser269Ter	p.S269*	ENST00000231790	NM_000249.3	269	tCa/tGa	10/19	1	2	FACETS	0.941	0.888	0.995	0.941	0.888	0.995	CLONAL	1	TRUE	1	0.73	2		406	830	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672096	30672096	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	407	688	0	ENST00000376406.3:c.4864A>G	p.Thr1622Ala	p.T1622A	ENST00000376406	NM_014641.2	1622	Acc/Gcc	10/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.73	2		688	1063	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157488286	157488286	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs773510355	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	303	389	0	ENST00000346085.5:c.2992A>C	p.Ser998Arg	p.S998R	ENST00000346085	NM_020732.3	998	Agc/Cgc	10/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.73	2		389	789	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524267	148524269	+	inframe_deletion	In_Frame_Del	DEL	TTC	TTC	-	novel	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	162	389	0	ENST00000320356.2:c.715_717del	p.Glu239del	p.E239del	ENST00000320356	NM_004456.4	239	GAA/-	7/20	1	2	FACETS	0.8	0.738	0.863	0.8	0.738	0.863	SUBCLONAL	1	TRUE	1	0.73	2		389	555	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860907	151860907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	231	291	0	ENST00000262189.6:c.9755G>A	p.Arg3252His	p.R3252H	ENST00000262189	NM_170606.2	3252	cGt/cAt	43/59	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.73	2		291	589	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489171	2489171	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1408719996	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	327	546	0	ENST00000355716.4:c.76T>C	p.Tyr26His	p.Y26H	ENST00000355716	NM_003820.2	26	Tat/Cat	2/8	1	2	FACETS	0.926	0.876	0.975	0.926	0.876	0.975	CLONAL	1	TRUE	1	0.73	2		546	968	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275302	115275302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	260	634	0	ENST00000438362.2:c.1111C>T	p.Arg371Cys	p.R371C	ENST00000438362	NM_001242891.1	371	Cgt/Tgt	10/20	1	2	FACETS	0.668	0.625	0.711	0.668	0.625	0.711	SUBCLONAL	1	TRUE	1	0.73	2		634	1067	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380764	118380764	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1479477078	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	40	473	0	ENST00000534358.1:c.11002C>A	p.Pro3668Thr	p.P3668T	ENST00000534358	NM_005933.3	3668	Ccc/Acc	30/36	1	2	FACETS	0.142	0.117	0.17	0.142	0.117	0.17	SUBCLONAL	1	TRUE	1	0.73	2		473	771	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435646	110435646	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	45	298	0	ENST00000375856.3:c.2755T>C	p.Tyr919His	p.Y919H	ENST00000375856	NM_003749.2	919	Tac/Cac	1/2	1	2	FACETS	0.167	0.14	0.198	0.167	0.14	0.198	SUBCLONAL	1	TRUE	1	0.73	2		298	737	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633171	3633171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1218491919	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1286	97	779	1	ENST00000294008.3:c.5080G>A	p.Ala1694Thr	p.A1694T	ENST00000294008	NM_032444.2	1694	Gcc/Acc	14/15	1	2	FACETS	0.192	0.17	0.216	0.192	0.17	0.216	SUBCLONAL	1	TRUE	1	0.73	2		780	1383	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703635	47703635	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	70	472	0	ENST00000233146.2:c.2135T>C	p.Val712Ala	p.V712A	ENST00000233146	NM_000251.2	712	gTa/gCa	13/16	1	2	FACETS	0.192	0.167	0.22	0.192	0.167	0.22	SUBCLONAL	1	TRUE	1	0.73	2		472	998	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309829	30309829	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	89	555	0	ENST00000307677.4:c.193G>T	p.Val65Leu	p.V65L	ENST00000307677	NM_138578.1	65	Gtg/Ttg	2/3	1	2	FACETS	0.241	0.213	0.272	0.241	0.213	0.272	SUBCLONAL	1	TRUE	1	0.73	2		555	1010	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162134	47162134	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	49	449	0	ENST00000409792.3:c.3992T>C	p.Leu1331Pro	p.L1331P	ENST00000409792	NM_014159.6	1331	cTa/cCa	3/21	1	2	FACETS	0.172	0.145	0.202	0.172	0.145	0.202	SUBCLONAL	1	TRUE	1	0.73	2		449	780	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503955	186503955	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	106	314	0	ENST00000323963.5:c.520C>T	p.Pro174Ser	p.P174S	ENST00000323963		174	Cca/Tca	6/11	1	2	FACETS	0.514	0.462	0.569	0.514	0.462	0.569	SUBCLONAL	1	TRUE	1	0.73	2		314	565	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187442803	187442803	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	66	514	0	ENST00000232014.4:c.1903T>C	p.Cys635Arg	p.C635R	ENST00000232014	NM_001130845.1	635	Tgt/Cgt	9/10	1	2	FACETS	0.179	0.154	0.206	0.179	0.154	0.206	SUBCLONAL	1	TRUE	1	0.73	2		514	1011	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176678792	176678792	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	56	479	0	ENST00000439151.2:c.4703T>C	p.Leu1568Pro	p.L1568P	ENST00000439151	NM_022455.4	1568	cTg/cCg	12/23	1	2	FACETS	0.167	0.143	0.195	0.167	0.143	0.195	SUBCLONAL	1	TRUE	1	0.73	2		479	916	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696783	176696783	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	41	375	0	ENST00000439151.2:c.5484A>C	p.Lys1828Asn	p.K1828N	ENST00000439151	NM_022455.4	1828	aaA/aaC	16/23	1	2	FACETS	0.171	0.142	0.204	0.171	0.142	0.204	SUBCLONAL	1	TRUE	1	0.73	2		375	656	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839727	27839727	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	320	548	0	ENST00000328488.2:c.367A>G	p.Lys123Glu	p.K123E	ENST00000328488	NM_003533.2	123	Aaa/Gaa	1/1	0.23263400815314	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.73	0		548	948	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109322513	109322513	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	216	564	0	ENST00000436639.2:c.524A>G	p.Tyr175Cys	p.Y175C	ENST00000436639	NM_014454.2	175	tAt/tGt	3/10	1	2	FACETS	0.636	0.592	0.682	0.636	0.592	0.682	SUBCLONAL	1	TRUE	1	0.73	2		564	930	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683808	117683808	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	67	467	0	ENST00000368508.3:c.3339del	p.Gln1114AsnfsTer5	p.Q1114Nfs*5	ENST00000368508	NM_002944.2	1113	ttT/tt	21/43	1	2	FACETS	0.25	0.217	0.287	0.25	0.217	0.287	SUBCLONAL	1	TRUE	1	0.73	2		467	733	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346596	81346596	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	62	381	0	ENST00000222390.5:c.1357T>C	p.Tyr453His	p.Y453H	ENST00000222390	NM_000601.4	453	Tac/Cac	11/18	1	2	FACETS	0.242	0.208	0.279	0.242	0.208	0.279	SUBCLONAL	1	TRUE	1	0.73	2		381	702	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211549	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030205-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	53	663	2	ENST00000331920.6:c.3606del	p.Ser1203AlafsTer52	p.S1203Afs*52	ENST00000331920	NM_000264.3	1202	ccC/cc	22/24	1	2	FACETS	0.141	0.119	0.165	0.141	0.119	0.165	SUBCLONAL	1	TRUE	1	0.73	2		665	1030	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400906	72400906	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0030378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	45	281	0	ENST00000357731.5:c.265C>A	p.Pro89Thr	p.P89T	ENST00000357731	NM_173808.2	89	Cct/Act	2/7	0.231981202209265	3	FACETS	0.833	0.7	0.98	0.416	0.35	0.49	CLONAL	1	TRUE	1	0.231981202209265	3		281	520	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117838	108117839	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AGAT	novel	NA	P-0030378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	121	282	0	ENST00000278616.4:c.1051_1054dup	p.Ile352ArgfsTer8	p.I352Rfs*8	ENST00000278616	NM_000051.3	350	gca/gcAGATa	8/63	0.228692150605089	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.231981202209265	2		282	465	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218459	1218459	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0030378-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	172	467	1	ENST00000326873.7:c.334C>T	p.Gln112Ter	p.Q112*	ENST00000326873	NM_000455.4	112	Cag/Tag	2/10	0.228692150605089	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	0	0.231981202209265	2		468	722	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0030819-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	55	384	0				ENST00000310581	NM_198253.2	-/1132			0.124204713254587	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.813733098151899	0		384	213	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436167	51436167	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030819-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	10	416	0	ENST00000262662.1:c.127C>A	p.Gln43Lys	p.Q43K	ENST00000262662		43	Cag/Aag	3/4	0.474663136846883	1	FACETS	0.158	0.108	0.22	0.158	0.108	0.22	INDETERMINATE	1	FALSE	0	0.813733098151899	1		416	92	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439800	51439800	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030819-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	141	558	0	ENST00000262662.1:c.365T>C	p.Leu122Pro	p.L122P	ENST00000262662		122	cTg/cCg	4/4	0.474663136846883	1	FACETS	1	0.976	1	1	0.976	1	INDETERMINATE	1	FALSE	0	0.813733098151899	1		558	194	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578493	7578500	+	frameshift_variant	Frame_Shift_Del	DEL	CACAGCTG	CACAGCTG	-	novel	NA	P-0030870-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	384	888	0	ENST00000269305.4:c.430_437del	p.Gln144GlyfsTer2	p.Q144Gfs*2	ENST00000269305	NM_001126112.2	144	CAGCTGTGg/g	5/11	0.46659286844679	3	FACETS	1	0.973	1	0.679	0.651	0.707	CLONAL	2	FALSE	0	0.733094153091356	3		888	703	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0030925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	309	846	1	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.163203225881453	2	FACETS	0.905	0.853	0.958	0.905	0.853	0.958	INDETERMINATE	2	TRUE	0	0.286561384155852	2		847	1192	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425293	49425294	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATGCC	novel	NA	P-0030925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	201	737	0	ENST00000301067.7:c.13190_13194dup	p.Leu4399GlyfsTer6	p.L4399Gfs*6	ENST00000301067	NM_003482.3	4398	-/GGCAT	39/54	0.286561384155852	3	FACETS	1	0.986	1	0.646	0.597	0.696	CLONAL	1	TRUE	1	0.286561384155852	3		737	1242	SUCCESS
BLM	641	MSKCC	GRCh37	15	91290696	91290696	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0030925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	164	390	0	ENST00000355112.3:c.74T>G	p.Leu25Ter	p.L25*	ENST00000355112	NM_000057.2	25	tTa/tGa	2/22	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.286561384155852	2		390	804	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817871	3817871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	204	435	1	ENST00000262367.5:c.3100G>A	p.Glu1034Lys	p.E1034K	ENST00000262367	NM_004380.2	1034	Gaa/Aaa	16/31	0.286561384155852	3	FACETS	0.774	0.718	0.833	0.774	0.718	0.833	SUBCLONAL	2	TRUE	1	0.286561384155852	3		436	1051	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0031005-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1460	196	800	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.578888301359874	6	FACETS	0.882	0.814	0.954	0.176	0.162	0.191	CLONAL	1	TRUE	1	0.578888301359874	6		800	1656	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1427441061	NA	P-0031005-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	402	885	0	ENST00000269305.4:c.560-2A>G		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.547054573617264	2	FACETS	0.966	0.928	1	0.966	0.928	1	CLONAL	2	TRUE	0	0.578888301359874	2		885	719	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242469	55242481	+	protein_altering_variant	In_Frame_Del	DEL	TTAAGAGAAGCAA	TTAAGAGAAGCAA	C	rs397509368	NA	P-0031005-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	534	604	0	ENST00000275493.2:c.2239_2251delinsC	p.Leu747_Thr751delinsPro	p.L747_T751delinsP	ENST00000275493	NM_005228.3	747	TTAAGAGAAGCAAca/Cca	19/28	0.578888301359874	6	FACETS	1	0.989	1	0.843	0.814	0.871	CLONAL	4	TRUE	1	0.578888301359874	6		604	945	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0031102-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	253	652	1	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.271649807755614	2	FACETS	0.96	0.899	1	0.96	0.899	1	CLONAL	2	TRUE	0	0.271649807755614	2		653	970	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0031102-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	96	161	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.248413455409555	3	FACETS	0.873	0.781	0.969	0.873	0.781	0.969	CLONAL	2	TRUE	1	0.271649807755614	3		161	460	SUCCESS
APC	324	MSKCC	GRCh37	5	112175141	112175141	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031102-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	25	277	0	ENST00000257430.4:c.3850G>T	p.Glu1284Ter	p.E1284*	ENST00000257430	NM_000038.5	1284	Gaa/Taa	16/16	0.248413455409555	3	FACETS	0.736	0.581	0.913	0.368	0.29	0.457	CLONAL	1	TRUE	1	0.271649807755614	3		277	284	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201068	108201068	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0031102-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	46	411	0	ENST00000278616.4:c.7435G>T	p.Glu2479Ter	p.E2479*	ENST00000278616	NM_000051.3	2479	Gaa/Taa	50/63	0.248413455409555	3	FACETS	0.803	0.677	0.943	0.402	0.338	0.472	CLONAL	1	TRUE	1	0.271649807755614	3		411	479	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524498	44524498	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0031102-T06-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	52	321	0	ENST00000291552.4:c.59T>G	p.Phe20Cys	p.F20C	ENST00000291552	NM_006758.2	20	tTt/tGt	2/8	0.238571063485387	3	FACETS	1	0.925	1	0.568	0.485	0.658	CLONAL	1	TRUE	1	0.271649807755614	3		321	383	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0031133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	736	324	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.457826111860054	8	FACETS	0.977	0.951	1			1	CLONAL	7	TRUE	NA	0.457826111860054	8		324	1116	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544703	65544703	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs387906650	NA	P-0031133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	195	613	0	ENST00000358664.4:c.223C>T	p.Arg75Ter	p.R75*	ENST00000358664	NM_002382.4	75	Cga/Tga	4/5	0.450787851949715	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.457826111860054	1		613	626	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	252	837	0	ENST00000269305.4:c.398T>A	p.Met133Lys	p.M133K	ENST00000269305	NM_001126112.2	133	aTg/aAg	5/11	0.457826111860054	1	FACETS	0.953	0.893	1	0.953	0.893	1	CLONAL	1	TRUE	0	0.457826111860054	1		837	891	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717661	89717661	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0031133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	130	460	0	ENST00000371953.3:c.686C>G	p.Ser229Ter	p.S229*	ENST00000371953	NM_000314.4	229	tCa/tGa	7/9	0.457826111860054	1	FACETS	0.867	0.791	0.946	0.867	0.791	0.946	CLONAL	1	TRUE	0	0.457826111860054	1		460	505	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983281	149983281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749247753	NA	P-0031133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	168	550	0	ENST00000253339.5:c.2977G>A	p.Glu993Lys	p.E993K	ENST00000253339		993	Gaa/Aaa	7/7	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.457826111860054	2		550	730	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176015387	176015387	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	82	329	0	ENST00000367669.3:c.1351G>C	p.Asp451His	p.D451H	ENST00000367669	NM_022457.5	451	Gac/Cac	12/20	0.457826111860054	3	FACETS	0.805	0.711	0.905	0.268	0.237	0.302	CLONAL	1	TRUE	0	0.457826111860054	3		329	547	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800899	18800899	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0031133-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	90	402	0	ENST00000266497.5:c.4275C>G	p.Ile1425Met	p.I1425M	ENST00000266497		1425	atC/atG	31/31	1	2	FACETS	0.673	0.598	0.753	0.673	0.598	0.753	SUBCLONAL	1	TRUE	1	0.457826111860054	2		402	584	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0031368-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	116	712	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.364639624452618	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.370320967160484	1		712	510	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376234	15376235	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0031368-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	57	602	0	ENST00000263377.2:c.779dup	p.Pro261ThrfsTer41	p.P261Tfs*41	ENST00000263377	NM_058243.2	260	cca/ccCa	5/20	1	2	FACETS	0.587	0.504	0.678	0.587	0.504	0.678	SUBCLONAL	1	TRUE	1	0.370320967160484	2		602	524	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225603	2225603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033021-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	143	1046	1	ENST00000326181.6:c.1606G>A	p.Gly536Ser	p.G536S	ENST00000326181	NM_032271.2	536	Ggc/Agc	17/21	1	2	FACETS	0.951	0.87	1	0.951	0.87	1	CLONAL	1	TRUE	1	0.483564682109513	2		1047	622	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727441	66727441	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519728	NA	P-0033021-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	142	640	0	ENST00000307102.5:c.157T>C	p.Phe53Leu	p.F53L	ENST00000307102	NM_002755.3	53	Ttt/Ctt	2/11	0.483564682109513	2	FACETS	0.987	0.903	1	0.494	0.451	0.537	CLONAL	1	TRUE	0	0.483564682109513	2		640	595	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386430	31386433	+	protein_altering_variant	In_Frame_Del	DEL	GTGA	GTGA	T	novel	NA	P-0033021-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	175	972	1	ENST00000328111.2:c.1655_1658delinsT	p.Ser552_Asp553delinsIle	p.S552_D553delinsI	ENST00000328111	NM_006892.3	552	aGTGAc/aTc	15/23	1	2	FACETS	0.777	0.715	0.841	0.777	0.715	0.841	SUBCLONAL	1	TRUE	1	0.483564682109513	2		973	932	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0033719-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	16	473	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.635	0.468	0.835	0.635	0.468	0.835	SUBCLONAL	1	TRUE	1	0.15	2		473	336	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0033719-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	20	334	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	0.743	0.567	0.949	0.743	0.567	0.949	CLONAL	1	TRUE	1	0.15	2		334	359	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578431	7578431	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555526097	NA	P-0033719-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	36	207	0	ENST00000269305.4:c.499C>T	p.Gln167Ter	p.Q167*	ENST00000269305	NM_001126112.2	167	Cag/Tag	5/11	1	2	FACETS	0.747	0.612	0.898	0.747	0.612	0.898	SUBCLONAL	1	TRUE	1	0.15	2		207	643	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0033719-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	57	246	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	0.878	0.755	1	1	0.974	1	CLONAL	2	TRUE	1	0.15	2		246	433	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0034191-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	158	255	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA	2	FACETS	0.943	0.874	1			1	INDETERMINATE	1	TRUE	NA	0.833810576106912	2		255	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0034191-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	225	709	5	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.833810576106912	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.833810576106912	1		714	289	SUCCESS
APC	324	MSKCC	GRCh37	5	112174490	112174493	+	frameshift_variant	Frame_Shift_Del	DEL	CAAT	CAAT	-	rs587779353	NA	P-0034191-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	110	330	0	ENST00000257430.4:c.3202_3205del	p.Ser1068GlyfsTer57	p.S1068Gfs*57	ENST00000257430	NM_000038.5	1067	CAATca/ca	16/16	0.176804930854315	4	FACETS	0.837	0.764	0.912	0.837	0.764	0.912	INDETERMINATE	2	TRUE	2	0.833810576106912	4		330	289	SUCCESS
APC	324	MSKCC	GRCh37	5	112175650	112175651	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0034191-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	154	388	1	ENST00000257430.4:c.4364dup	p.Asn1455LysfsTer2	p.N1455Kfs*2	ENST00000257430	NM_000038.5	1453	-/A	16/16	0.176804930854315	4	FACETS	0.985	0.915	1	0.985	0.915	1	INDETERMINATE	2	TRUE	2	0.833810576106912	4		389	344	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112283	115112283	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1018135320	NA	P-0034191-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	64	115	0	ENST00000257566.3:c.1457C>T	p.Thr486Met	p.T486M	ENST00000257566	NM_016569.3	486	aCg/aTg	7/8	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.833810576106912	2		115	130	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039183	49039183	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034191-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	171	418	0	ENST00000267163.4:c.2261T>C	p.Val754Ala	p.V754A	ENST00000267163	NM_000321.2	754	gTa/gCa	22/27	0.833810576106912	3	FACETS	0.922	0.852	0.995	0.461	0.426	0.498	CLONAL	1	TRUE	1	0.833810576106912	3		418	630	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222371	2222371	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1419349453	NA	P-0034191-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	370	905	0	ENST00000326181.6:c.655C>T	p.Arg219Trp	p.R219W	ENST00000326181	NM_032271.2	219	Cgg/Tgg	8/21	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.833810576106912	2		905	828	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732923	30732924	+	inframe_insertion	In_Frame_Ins	INS	-	-	GTGTGTGAGACGTTGACTGAGTGCTGGGACCAC	novel	NA	P-0034191-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	77	305	0	ENST00000295754.5:c.1538_1570dup	p.Val513_His523dup	p.V513_H523dup	ENST00000295754	NM_003242.5	513	-/GTGTGTGAGACGTTGACTGAGTGCTGGGACCAC	7/7	0.815316424764553	1	FACETS	0.46	0.41	0.512	0.46	0.41	0.512	SUBCLONAL	1	TRUE	0	0.833810576106912	1		305	234	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348131	348131	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0034191-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	223	1006	0	ENST00000262320.3:c.1375C>G	p.Leu459Val	p.L459V	ENST00000262320	NM_003502.3	459	Ctc/Gtc	6/11	NA	2	FACETS	0.734	0.686	0.783			1	INDETERMINATE	1	TRUE	NA	0.833810576106912	2		1006	729	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137387	202137389	+	inframe_deletion	In_Frame_Del	DEL	GGA	GGA	-	novel	NA	P-0034191-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	137	404	0	ENST00000358485.4:c.616_618del	p.Glu206del	p.E206del	ENST00000358485	NM_001080125.1	205	atGGAg/atg	4/9	0.828470920127927	2	FACETS	0.978	0.902	1	0.489	0.451	0.528	CLONAL	1	TRUE	0	0.833810576106912	2		404	336	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0034225-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	9	998	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	1	2	FACETS	0.831	0.566	1	1	0.857	1	CLONAL	2	TRUE	1	0.246101126334005	2		998	44	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034371-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	52	384	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.262685430784232	2		384	370	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553486	29553487	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0034371-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	145	624	0	ENST00000356175.3:c.2038dup	p.Cys680LeufsTer20	p.C680Lfs*20	ENST00000356175	NM_000267.3	679	att/aTtt	18/57	0.26133504928805	2	FACETS	0.784	0.717	0.854	0.784	0.717	0.854	SUBCLONAL	2	TRUE	0	0.262685430784232	2		624	704	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711976	89711978	+	frameshift_variant	Frame_Shift_Ins	INS	GAT	GAT	AAACC	novel	NA	P-0034371-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	39	103	1	ENST00000371953.3:c.594_596delinsAAACC	p.Met198IlefsTer24	p.M198Ifs*24	ENST00000371953	NM_000314.4	198	atGATg/atAAACCg	6/9	0.262685430784232	1	FACETS	0.782	0.65	0.928	0.782	0.65	0.928	CLONAL	1	TRUE	0	0.262685430784232	1		104	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730882005	NA	P-0034543-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	485	679	0	ENST00000269305.4:c.713G>A	p.Cys238Tyr	p.C238Y	ENST00000269305	NM_001126112.2	238	tGt/tAt	7/11	0.646912295390015	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.653615985251498	2		679	672	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342597	70342597	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0034543-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	347	599	0	ENST00000374080.3:c.1358T>C	p.Ile453Thr	p.I453T	ENST00000374080		453	aTt/aCt	10/45	0.49987985696579	4	FACETS	0.902	0.856	0.949			1	CLONAL	2	TRUE	NA	0.653615985251498	4		599	973	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619416	1619426	+	frameshift_variant	Frame_Shift_Del	DEL	CGGCGTGGCTG	CGGCGTGGCTG	-	novel	NA	P-0034543-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	466	939	0	ENST00000344749.5:c.1215_1225del	p.Ser406GlyfsTer65	p.S406Gfs*65	ENST00000344749	NM_001136139.2	405	cgCAGCCACGCCGtg/cgtg	15/19	0.631423336116673	2	FACETS	0.876	0.844	0.907	0.876	0.844	0.907	CLONAL	2	TRUE	0	0.653615985251498	2		939	814	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0034616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	122	384	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.973	0.89	1			1	INDETERMINATE	1	TRUE	NA	0.712089276157497	2		384	352	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220274	55220274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0034616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3476	182	809	0	ENST00000275493.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000275493	NM_005228.3	222	Cgc/Tgc	6/28	0.712089276157497	11	FACETS	0.588	0.538	0.639			1	SUBCLONAL	1	TRUE	NA	0.712089276157497	11		809	3658	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183725	10183725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs5030826	NA	P-0034616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	14	667	0	ENST00000256474.2:c.194C>T	p.Ser65Leu	p.S65L	ENST00000256474	NM_000551.3	65	tCg/tTg	1/3	1	2	FACETS	0.06	0.043	0.081	0.06	0.043	0.081	SUBCLONAL	1	TRUE	1	0.712089276157497	2		667	656	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724449	162724449	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0034616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	217	581	0	ENST00000367921.3:c.221C>G	p.Pro74Arg	p.P74R	ENST00000367921	NM_006182.2	74	cCt/cGt	5/18	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.712089276157497	2		581	550	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223546	55223551	+	inframe_deletion	In_Frame_Del	DEL	GGCTCG	GGCTCG	-	novel	NA	P-0034616-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10108	1009	761	0	ENST00000275493.2:c.913_918del	p.Gly305_Ser306del	p.G305_S306del	ENST00000275493	NM_005228.3	305	GGCTCG/-	8/28	0.712089276157497	31	FACETS	0.962	0.928	0.997			1	CLONAL	3	TRUE	NA	0.712089276157497	31		761	11117	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0034665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	169	608	1	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.290311678203824	2	FACETS	0.932	0.862	1	0.932	0.862	1	CLONAL	2	FALSE	0	0.326308760575922	2		609	556	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573524	48573524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0034665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	38	227	0	ENST00000342988.3:c.112del	p.Arg38GlufsTer7	p.R38Efs*7	ENST00000342988	NM_005359.5	36	gcA/gc	2/12	1	2	FACETS	0.91	0.757	1	0.91	0.757	1	CLONAL	1	FALSE	1	0.326308760575922	2		227	256	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211843	36211843	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1314550917	NA	P-0034665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	113	1006	0	ENST00000222270.7:c.1594G>T	p.Val532Leu	p.V532L	ENST00000222270	NM_014727.1	532	Gtg/Ttg	3/37	0.143912910892586	2	FACETS	0.572	0.513	0.635	0.286	0.256	0.318	INDETERMINATE	1	FALSE	0	0.326308760575922	2		1006	1210	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55270306	55270306	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0034665-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	80	818	0	ENST00000275493.2:c.3259C>A	p.Leu1087Ile	p.L1087I	ENST00000275493	NM_005228.3	1087	Ctc/Atc	27/28	0.192858624608444	4	FACETS	0.593	0.52	0.671	0.296	0.26	0.336	INDETERMINATE	1	FALSE	2	0.326308760575922	4		818	1097	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0034774-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	209	161	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.410743189247397	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	FALSE	2	0.509270995239265	4		161	546	SUCCESS
APC	324	MSKCC	GRCh37	5	112175529	112175530	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGTAA	novel	NA	P-0034774-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	105	258	0	ENST00000257430.4:c.4240_4244dup	p.Ser1415ArgfsTer2	p.S1415Rfs*2	ENST00000257430	NM_000038.5	1413	atg/atGGTAAg	16/16	0.410743189247397	4	FACETS	0.804	0.726	0.885	0.804	0.726	0.885	CLONAL	2	FALSE	2	0.509270995239265	4		258	387	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434683	99434683	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0034887-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	393	697	0	ENST00000268035.6:c.771del	p.Gly258ValfsTer40	p.G258Vfs*40	ENST00000268035	NM_000875.3	257	gCc/gc	3/21	0.457543825178365	3	FACETS	0.889	0.846	0.933	0.889	0.846	0.933	CLONAL	2	TRUE	1	0.457543825178365	3		697	1187	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681102	37681102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1337640463	NA	P-0035665-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	21	687	0	ENST00000447079.4:c.3271C>T	p.Pro1091Ser	p.P1091S	ENST00000447079	NM_015083.1	1091	Cct/Tct	12/14	0.451257870930156	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.451242114650476	1		687	53	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231202	142231202	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0035665-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	10	534	0	ENST00000350721.4:c.4752G>C	p.Met1584Ile	p.M1584I	ENST00000350721	NM_001184.3	1584	atG/atC	27/47	1	2	FACETS	0.791	0.548	1	0.791	0.548	1	CLONAL	1	TRUE	1	0.451242114650476	2		534	56	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0035785-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	170	527	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.281845767665287	3	FACETS	0.809	0.746	0.874	0.809	0.746	0.874	CLONAL	2	TRUE	1	0.35458778941162	3		527	698	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579350	7579350	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587781642	NA	P-0035785-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	204	674	0	ENST00000269305.4:c.337T>G	p.Phe113Val	p.F113V	ENST00000269305	NM_001126112.2	113	Ttc/Gtc	4/11	0.214500686689641	2	FACETS	1	0.991	1	0.741	0.689	0.795	CLONAL	1	TRUE	0	0.35458778941162	2		674	776	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625159	69625159	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554980306	NA	P-0035785-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	120	707	1	ENST00000334134.2:c.634C>T	p.Arg212Trp	p.R212W	ENST00000334134	NM_005247.2	212	Cgg/Tgg	3/3	0.35458778941162	4	FACETS	0.928	0.837	1	0.464	0.418	0.513	CLONAL	1	TRUE	2	0.35458778941162	4		708	988	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492794	56492794	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1480969068	NA	P-0035785-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	180	557	0	ENST00000407977.2:c.145A>G	p.Arg49Gly	p.R49G	ENST00000407977		49	Aga/Gga	2/10	0.283297483303655	2	FACETS	0.843	0.782	0.907	0.843	0.782	0.907	CLONAL	2	TRUE	0	0.35458778941162	2		557	602	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974744	21974770	+	inframe_deletion	In_Frame_Del	DEL	ACCTCCTCTACCCGACCCCGGGCCGCG	ACCTCCTCTACCCGACCCCGGGCCGCG	-	novel	NA	P-0035785-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	84	325	0	ENST00000304494.5:c.57_83del	p.Ala20_Val28del	p.A20_V28del	ENST00000304494	NM_000077.4	19	gcCGCGGCCCGGGGTCGGGTAGAGGAGGTg/gcg	1/3	0.35458778941162	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.35458778941162	1		325	371	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0035830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	62	868	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.143212262383834	1	FACETS	0.898	0.779	1	1	0.977	1	CLONAL	2	TRUE	0	0.16	1		869	397	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577594	7577595	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0035830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	36	575	0	ENST00000269305.4:c.686_687del	p.Cys229TyrfsTer10	p.C229Yfs*10	ENST00000269305	NM_001126112.2	229	tGT/t	7/11	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.16	2		575	373	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121796	2121796	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0035830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	30	751	0	ENST00000219476.3:c.1958G>C	p.Arg653Thr	p.R653T	ENST00000219476	NM_000548.3	653	aGa/aCa	19/42	1	2	FACETS	0.753	0.606	0.921	0.753	0.606	0.921	CLONAL	1	TRUE	1	0.16	2		751	498	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577156	7577156	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1555525367	NA	P-0035838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	94	425	0	ENST00000269305.4:c.783-1G>A		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.275986541683964	1	FACETS	0.99	0.883	1	0.99	0.883	1	CLONAL	1	TRUE	0	0.275986541683964	1		425	593	SUCCESS
AR	367	MSKCC	GRCh37	X	66863126	66863146	+	inframe_deletion	In_Frame_Del	DEL	CCCATTGACTATTACTTTCCA	CCCATTGACTATTACTTTCCA	-	novel	NA	P-0035838-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	96	504	0	ENST00000374690.3:c.1648_1668del	p.Ile550_Pro556del	p.I550_P556del	ENST00000374690	NM_000044.3	549	CCCATTGACTATTACTTTCCA/-	2/8	0.275986541683964	1	FACETS	0.806	0.718	0.9	0.806	0.718	0.9	CLONAL	1	TRUE	0	0.275986541683964	1		504	744	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38137113	38137113	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035967-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1577	198	808	0	ENST00000317025.8:c.3705G>A	p.Trp1235Ter	p.W1235*	ENST00000317025	NM_023034.1	1235	tgG/tgA	21/24	0.401705087576777	5	FACETS	0.867	0.8	0.938			1	CLONAL	1	TRUE	NA	0.418927622505077	5		808	1775	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397178	397178	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1469969945	NA	P-0035970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	24	356	0	ENST00000380956.4:c.563C>T	p.Pro188Leu	p.P188L	ENST00000380956	NM_001195286.1	188	cCg/cTg	5/9	NA	2	FACETS	0.412	0.323	0.516			1	INDETERMINATE	1	FALSE	NA	0.3	2		356	388	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948780	55948780	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763426023	NA	P-0035970-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	54	705	1	ENST00000263923.4:c.3685C>T	p.Arg1229Ter	p.R1229*	ENST00000263923	NM_002253.2	1229	Cga/Tga	28/30	0.289157990075155	1	FACETS	0.407	0.347	0.474	0.407	0.347	0.474	SUBCLONAL	1	FALSE	0	0.3	1		706	751	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0036055-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	131	385	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.624824406541452	2		385	364	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970971	21970971	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036055-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	260	589	0	ENST00000304494.5:c.387C>A	p.Tyr129Ter	p.Y129*	ENST00000304494	NM_000077.4	129	taC/taA	2/3	0.624824406541452	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.624824406541452	1		589	520	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021706	71021706	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036055-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	46	308	0	ENST00000318789.4:c.1652G>A	p.Gly551Asp	p.G551D	ENST00000318789	NM_032682.5	551	gGt/gAt	18/21	1	2	FACETS	0.272	0.229	0.32	0.272	0.229	0.32	SUBCLONAL	1	TRUE	1	0.624824406541452	2		308	541	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158154	106158154	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036055-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	28	256	0	ENST00000380013.4:c.3055G>C	p.Val1019Leu	p.V1019L	ENST00000380013	NM_001127208.2	1019	Gtg/Ctg	3/11	1	2	FACETS	0.23	0.183	0.283	0.23	0.183	0.283	SUBCLONAL	1	TRUE	1	0.624824406541452	2		256	390	SUCCESS
APC	324	MSKCC	GRCh37	5	112173345	112173345	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	84	281	0	ENST00000257430.4:c.2054G>A	p.Trp685Ter	p.W685*	ENST00000257430	NM_000038.5	685	tGg/tAg	16/16	0.406492147232613	4	FACETS	0.926	0.826	1	0.926	0.826	1	CLONAL	2	TRUE	2	0.411775128713495	4		281	311	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579592	7579592	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs879254212	NA	P-0036060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	142	478	0	ENST00000269305.4:c.97-2A>G		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.305998344885029	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.411775128713495	2		478	333	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281557	198281557	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036060-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	98	493	0	ENST00000335508.6:c.574C>A	p.Pro192Thr	p.P192T	ENST00000335508	NM_012433.2	192	Cct/Act	6/25	0.406492147232613	4	FACETS	1	0.893	1	0.5	0.446	0.557	CLONAL	1	TRUE	2	0.411775128713495	4		493	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs878854073	NA	P-0036062-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	110	373	0	ENST00000269305.4:c.673-1G>A		p.X225_splice	ENST00000269305	NM_001126112.2	225			0.548498857101393	1	FACETS	0.915	0.834	0.999	0.915	0.834	0.999	CLONAL	1	TRUE	0	0.562737814955381	1		373	307	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089730	27089730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036062-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	148	467	0	ENST00000324856.7:c.2686G>A	p.Glu896Lys	p.E896K	ENST00000324856	NM_006015.4	896	Gaa/Aaa	8/20	0.562737814955381	1	FACETS	0.94	0.868	1	0.94	0.868	1	CLONAL	1	TRUE	0	0.562737814955381	1		467	402	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134988	41134988	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0036062-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	55	186	0	ENST00000379561.5:c.640C>A	p.Arg214Ser	p.R214S	ENST00000379561	NM_002015.3	214	Cgt/Agt	2/3	1	2	FACETS	0.846	0.732	0.968	0.846	0.732	0.968	CLONAL	1	TRUE	1	0.562737814955381	2		186	231	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0036128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	45	632	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.115	0.096	0.137	0.115	0.096	0.137	SUBCLONAL	1	TRUE	1	0.783676009866053	2		632	996	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0036128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	120	596	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.527	0.477	0.579	0.527	0.477	0.579	SUBCLONAL	1	TRUE	1	0.783676009866053	2		596	581	SUCCESS
APC	324	MSKCC	GRCh37	5	112175761	112175761	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0036128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	30	417	0	ENST00000257430.4:c.4473del	p.Phe1491LeufsTer16	p.F1491Lfs*16	ENST00000257430	NM_000038.5	1490	caT/ca	16/16	1	2	FACETS	0.176	0.141	0.215	0.176	0.141	0.215	SUBCLONAL	1	TRUE	1	0.783676009866053	2		417	436	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174437	11174437	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1553171141	NA	P-0036128-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	80	757	0	ENST00000361445.4:c.7238G>T	p.Ser2413Ile	p.S2413I	ENST00000361445	NM_004958.3	2413	aGt/aTt	53/58	1	2	FACETS	0.192	0.168	0.217	0.192	0.168	0.217	SUBCLONAL	1	TRUE	1	0.783676009866053	2		757	1066	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411876	116411890	+	intron_variant	Intron	DEL	AAGCTCTTTCTTTCT	AAGCTCTTTCTTTCT	-	novel	NA	P-0036249-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1238	257	792	2	ENST00000397752.3:c.2888-27_2888-13del		p.*963*	ENST00000397752	NM_000245.2	-/1390			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		794	1495	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0036307-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	5	385	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.107	0.06	0.173	0.107	0.06	0.173	SUBCLONAL	1	TRUE	1	0.311729967041777	2		385	300	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249017	55249018	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCA	rs1554350381	NA	P-0036307-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	281	654	0	ENST00000275493.2:c.2317_2319dup	p.His773dup	p.H773dup	ENST00000275493	NM_005228.3	773	ccc/ccCCAc	20/28	0.311729967041777	8	FACETS	1	0.982	1	0.475	0.446	0.504	CLONAL	3	TRUE	1	0.311729967041777	8		654	1050	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0036307-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1451	14	874	1	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.311729967041777	8	FACETS	0.119	0.085	0.16	0.017	0.012	0.023	SUBCLONAL	1	TRUE	1	0.311729967041777	8		875	1465	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762959	40762959	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs387906659	NA	P-0036501-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	204	529	0	ENST00000392038.2:c.49G>A	p.Glu17Lys	p.E17K	ENST00000392038	NM_001626.4	17	Gaa/Aaa	3/14	1	2	FACETS	0.79	0.732	0.851	0.79	0.732	0.851	SUBCLONAL	1	TRUE	1	0.465517944306632	2		529	1109	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911194	29911201	+	frameshift_variant	Frame_Shift_Del	DEL	CAGATCAC	CAGATCAC	-	novel	NA	P-0036501-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	344	659	0	ENST00000376809.5:c.495_502del	p.Ile166AlafsTer8	p.I166Afs*8	ENST00000376809	NM_002116.7	165	CAGATCACc/c	3/8	0.465517944306632	3	FACETS	1	0.99	1	0.595	0.562	0.629	CLONAL	1	TRUE	1	0.465517944306632	3		659	1531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0036557-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	675	1023	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.64104749511113	2		1023	1023	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0036557-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	9207	734	1	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.64104749511113	36	FACETS	0.988	0.984	0.991			1	CLONAL	35	TRUE	NA	0.64104749511113	36		735	9887	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061098	38061098	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0036557-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	118	379	0	ENST00000250448.2:c.891del	p.Ser298LeufsTer23	p.S298Lfs*23	ENST00000250448	NM_004496.3	297	ccC/cc	2/2	0.64104749511113	2	FACETS	0.879	0.799	0.961	0.439	0.399	0.481	CLONAL	1	TRUE	0	0.64104749511113	2		379	419	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845939	72845941	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TAA	TAA	-	novel	NA	P-0036557-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	189	423	0	ENST00000268489.5:c.3530-4_3530-2del		p.X1177_splice	ENST00000268489	NM_006885.3	1177			1	2	FACETS	1	0.97	1	1	0.995	1	CLONAL	2	TRUE	1	0.64104749511113	2		423	286	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619356	1619366	+	frameshift_variant	Frame_Shift_Del	DEL	AACCTGAGGCC	AACCTGAGGCC	-	novel	NA	P-0036557-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1198	295	1218	0	ENST00000344749.5:c.1275_1285del	p.Ala426HisfsTer45	p.A426Hfs*45	ENST00000344749	NM_001136139.2	425	ctGGCCTCAGGTTtc/cttc	15/19	0.64104749511113	3	FACETS	0.814	0.764	0.865	0.407	0.382	0.433	CLONAL	1	TRUE	1	0.64104749511113	3		1218	1493	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0036672-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	51	496	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.126615166752953	3	FACETS	0.872	0.74	1	0.436	0.37	0.508	INDETERMINATE	1	TRUE	1	0.21454004256031	3		496	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0036672-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	142	747	2	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.190224093127967	2	FACETS	0.808	0.737	0.883	0.808	0.737	0.883	CLONAL	2	TRUE	0	0.21454004256031	2		749	819	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050979	49050979	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036672-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	35	218	0	ENST00000267163.4:c.2663G>C	p.Ser888Thr	p.S888T	ENST00000267163	NM_000321.2	888	aGt/aCt	25/27	0.21454004256031	1	FACETS	0.864	0.71	1	0.864	0.71	1	CLONAL	1	TRUE	0	0.21454004256031	1		218	337	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	201	385	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.574760791674493	2		385	590	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262592	16262592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	430	528	0	ENST00000375759.3:c.9857C>A	p.Pro3286His	p.P3286H	ENST00000375759	NM_015001.2	3286	cCt/cAt	11/15	0.195487885236144	6	FACETS	1	0.991	1			1	INDETERMINATE	3	TRUE	NA	0.574760791674493	6		528	959	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023748	27023748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	425	389	0	ENST00000324856.7:c.854G>A	p.Gly285Glu	p.G285E	ENST00000324856	NM_006015.4	285	gGa/gAa	1/20	0.574760791674493	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.574760791674493	3		389	894	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101423	27101423	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	388	517	1	ENST00000324856.7:c.4705C>T	p.Pro1569Ser	p.P1569S	ENST00000324856	NM_006015.4	1569	Cca/Tca	18/20	0.574760791674493	3	FACETS	0.931	0.889	0.975	0.931	0.889	0.975	CLONAL	2	TRUE	1	0.574760791674493	3		518	933	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935268	36935268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	611	752	1	ENST00000361632.4:c.1459G>A	p.Gly487Arg	p.G487R	ENST00000361632		487	Ggg/Agg	10/16	0.574760791674493	3	FACETS	0.992	0.956	1	0.992	0.956	1	CLONAL	2	TRUE	1	0.574760791674493	3		753	1380	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166271	118166271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	147	389	0	ENST00000369448.3:c.781G>A	p.Glu261Lys	p.E261K	ENST00000369448	NM_017709.3	261	Gaa/Aaa	2/2	0.574760791674493	3	FACETS	0.968	0.886	1	0.484	0.443	0.527	CLONAL	1	TRUE	1	0.574760791674493	3		389	680	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849128	156849128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1426	307	830	0	ENST00000524377.1:c.2020G>A	p.Asp674Asn	p.D674N	ENST00000524377	NM_002529.3	674	Gat/Aat	15/17	0.565622370964141	4	FACETS	0.971	0.912	1	0.324	0.304	0.344	CLONAL	1	TRUE	1	0.574760791674493	4		830	1733	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104377181	104377182	+	missense_variant	Missense_Mutation	DNP	TA	TA	CT	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	277	801	0	ENST00000369902.3:c.1292_1293delinsCT	p.Leu431Ser	p.L431S	ENST00000369902	NM_016169.3	431	tTA/tCT	10/12	1	2	FACETS	0.864	0.812	0.919	0.864	0.812	0.919	CLONAL	1	TRUE	1	0.574760791674493	2		801	1115	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256135	123256135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141929882	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	235	655	0	ENST00000358487.5:c.1774C>T	p.Arg592Cys	p.R592C	ENST00000358487	NM_000141.4	592	Cgt/Tgt	13/18	0.574760791674493	3	FACETS	0.96	0.895	1	0.48	0.447	0.514	CLONAL	1	TRUE	1	0.574760791674493	3		655	1097	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324081	123324081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	165	495	1	ENST00000358487.5:c.389C>T	p.Ser130Phe	p.S130F	ENST00000358487	NM_000141.4	130	tCc/tTc	4/18	0.574760791674493	3	FACETS	0.885	0.814	0.96	0.443	0.407	0.48	CLONAL	1	TRUE	1	0.574760791674493	3		496	835	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141997	108141997	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780619	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	180	431	0	ENST00000278616.4:c.2941C>T	p.Arg981Cys	p.R981C	ENST00000278616	NM_000051.3	981	Cgt/Tgt	20/63	0.5465747732957	1	FACETS	0.946	0.88	1	0.946	0.88	1	CLONAL	1	TRUE	0	0.574760791674493	1		431	472	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165730	108165730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765759912	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	147	390	1	ENST00000278616.4:c.4853G>A	p.Arg1618Gln	p.R1618Q	ENST00000278616	NM_000051.3	1618	cGa/cAa	32/63	0.5465747732957	1	FACETS	0.911	0.841	0.983	0.911	0.841	0.983	CLONAL	1	TRUE	0	0.574760791674493	1		391	400	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103398	119103398	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	171	377	0	ENST00000264033.4:c.436C>T	p.Gln146Ter	p.Q146*	ENST00000264033	NM_005188.3	146	Cag/Tag	2/16	0.5465747732957	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.574760791674493	1		377	420	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417041	417041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	146	400	0	ENST00000399788.2:c.3509C>T	p.Ala1170Val	p.A1170V	ENST00000399788	NM_001042603.1	1170	gCc/gTc	23/28	NA	2	FACETS	0.97	0.89	1			1	INDETERMINATE	1	TRUE	NA	0.574760791674493	2		400	524	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431735	49431735	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	296	798	1	ENST00000301067.7:c.9404C>T	p.Thr3135Ile	p.T3135I	ENST00000301067	NM_003482.3	3135	aCc/aTc	34/54	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.574760791674493	2		799	1016	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112892368	112892368	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	165	430	0	ENST00000351677.2:c.526G>A	p.Glu176Lys	p.E176K	ENST00000351677	NM_002834.3	176	Gaa/Aaa	5/16	1	2	FACETS	0.962	0.887	1	0.962	0.887	1	CLONAL	1	TRUE	1	0.574760791674493	2		430	597	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112910803	112910803	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	218	431	0	ENST00000351677.2:c.812A>T	p.Gln271Leu	p.Q271L	ENST00000351677	NM_002834.3	271	cAa/cTa	7/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.574760791674493	2		431	691	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601256	28601256	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	195	530	0	ENST00000241453.7:c.2176T>C	p.Tyr726His	p.Y726H	ENST00000241453	NM_004119.2	726	Tac/Cac	17/24	1	2	FACETS	0.932	0.865	1	0.932	0.865	1	CLONAL	1	TRUE	1	0.574760791674493	2		530	728	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964022	28964022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	162	445	0	ENST00000282397.4:c.1880C>T	p.Ser627Phe	p.S627F	ENST00000282397	NM_002019.4	627	tCc/tTc	13/30	1	2	FACETS	0.957	0.882	1	0.957	0.882	1	CLONAL	1	TRUE	1	0.574760791674493	2		445	589	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005419	29005419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55687105	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	126	345	0	ENST00000282397.4:c.842G>A	p.Arg281Gln	p.R281Q	ENST00000282397	NM_002019.4	281	cGa/cAa	7/30	1	2	FACETS	0.846	0.77	0.926	0.846	0.77	0.926	CLONAL	1	TRUE	1	0.574760791674493	2		345	518	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012452	29012452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	199	552	0	ENST00000282397.4:c.419G>A	p.Ser140Asn	p.S140N	ENST00000282397	NM_002019.4	140	aGt/aAt	4/30	1	2	FACETS	0.977	0.908	1	0.977	0.908	1	CLONAL	1	TRUE	1	0.574760791674493	2		552	709	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944632	32944632	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	238	572	0	ENST00000380152.3:c.8425T>C	p.Phe2809Leu	p.F2809L	ENST00000380152		2809	Ttc/Ctc	19/27	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.574760791674493	2		572	810	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336134	73336134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	131	325	1	ENST00000377767.4:c.2269G>A	p.Gly757Arg	p.G757R	ENST00000377767	NM_014953.3	757	Gga/Aga	17/21	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.574760791674493	2		326	422	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569948	95569948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	171	435	0	ENST00000393063.1:c.3785C>T	p.Pro1262Leu	p.P1262L	ENST00000393063	NM_030621.3	1262	cCt/cTt	22/28	1	2	FACETS	0.925	0.855	0.998	0.925	0.855	0.998	CLONAL	1	TRUE	1	0.574760791674493	2		435	643	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041734	42041734	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	166	450	0	ENST00000219905.7:c.5929C>T	p.Gln1977Ter	p.Q1977*	ENST00000219905	NM_001164273.1	1977	Cag/Tag	17/24	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.574760791674493	2		450	575	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052602	42052602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	229	445	0	ENST00000219905.7:c.7273C>T	p.Arg2425Cys	p.R2425C	ENST00000219905	NM_001164273.1	2425	Cgc/Tgc	20/24	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.574760791674493	2		445	744	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713311	43713311	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	349	858	0	ENST00000382044.4:c.4162C>G	p.Leu1388Val	p.L1388V	ENST00000382044	NM_001141980.1	1388	Ctt/Gtt	20/28	1	2	FACETS	0.981	0.929	1	0.981	0.929	1	CLONAL	1	TRUE	1	0.574760791674493	2		858	1238	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472652	88472652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	151	402	0	ENST00000360948.2:c.1903G>A	p.Asp635Asn	p.D635N	ENST00000360948	NM_001012338.2	635	Gat/Aat	16/19	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.574760791674493	2		402	517	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476280	88476280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	179	624	0	ENST00000360948.2:c.1852G>A	p.Glu618Lys	p.E618K	ENST00000360948	NM_001012338.2	618	Gaa/Aaa	15/19	1	2	FACETS	0.793	0.733	0.856	0.793	0.733	0.856	SUBCLONAL	1	TRUE	1	0.574760791674493	2		624	785	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396431	396431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	306	745	0	ENST00000262320.3:c.595C>T	p.Pro199Ser	p.P199S	ENST00000262320	NM_003502.3	199	Ccc/Tcc	2/11	1	2	FACETS	0.978	0.922	1	0.978	0.922	1	CLONAL	1	TRUE	1	0.574760791674493	2		745	1089	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632744	23632744	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	162	561	0	ENST00000261584.4:c.3052G>T	p.Glu1018Ter	p.E1018*	ENST00000261584	NM_024675.3	1018	Gag/Tag	10/13	1	2	FACETS	0.801	0.736	0.867	0.801	0.736	0.867	CLONAL	1	TRUE	1	0.574760791674493	2		561	704	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671678	67671679	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	217	578	0	ENST00000264010.4:c.2087_2088delinsTT	p.Pro696Leu	p.P696L	ENST00000264010	NM_006565.3	696	cCC/cTT	12/12	1	2	FACETS	0.964	0.899	1	0.964	0.899	1	CLONAL	1	TRUE	1	0.574760791674493	2		578	783	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346081	89346081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	50	144	0	ENST00000301030.4:c.6869C>T	p.Pro2290Leu	p.P2290L	ENST00000301030	NM_001256183.1	2290	cCc/cTc	9/13	1	2	FACETS	0.853	0.733	0.981	0.853	0.733	0.981	CLONAL	1	TRUE	1	0.574760791674493	2		144	204	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350869	89350869	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	372	842	0	ENST00000301030.4:c.2081T>G	p.Phe694Cys	p.F694C	ENST00000301030	NM_001256183.1	694	tTt/tGt	9/13	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.574760791674493	2		842	1215	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958242	11958242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1261150954	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	73	382	0	ENST00000353533.5:c.152C>T	p.Pro51Leu	p.P51L	ENST00000353533	NM_003010.3	51	cCa/cTa	2/11	1	2	FACETS	0.819	0.723	0.921	0.819	0.723	0.921	CLONAL	1	TRUE	1	0.574760791674493	2		382	310	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554601	29554602	+	missense_variant	Missense_Mutation	DNP	AA	AA	GT	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	110	282	0	ENST00000356175.3:c.2386_2387delinsGT	p.Lys796Val	p.K796V	ENST00000356175	NM_000267.3	796	AAa/GTa	20/57	1	2	FACETS	0.936	0.847	1	0.936	0.847	1	CLONAL	1	TRUE	1	0.574760791674493	2		282	409	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576001	29576001	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	126	314	0	ENST00000356175.3:c.3975-1G>A		p.X1325_splice	ENST00000356175	NM_000267.3	1325			1	2	FACETS	0.91	0.829	0.994	0.91	0.829	0.994	CLONAL	1	TRUE	1	0.574760791674493	2		314	482	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653151	29653151	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	154	388	0	ENST00000356175.3:c.5086G>T	p.Glu1696Ter	p.E1696*	ENST00000356175	NM_000267.3	1696	Gag/Tag	36/57	1	2	FACETS	0.945	0.869	1	0.945	0.869	1	CLONAL	1	TRUE	1	0.574760791674493	2		388	567	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864574	37864574	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	174	454	0	ENST00000269571.5:c.226G>A	p.Asp76Asn	p.D76N	ENST00000269571		76	Gat/Aat	3/27	1	2	FACETS	0.919	0.849	0.991	0.919	0.849	0.991	CLONAL	1	TRUE	1	0.574760791674493	2		454	659	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857681	59857681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	166	429	0	ENST00000259008.2:c.1876G>A	p.Glu626Lys	p.E626K	ENST00000259008	NM_032043.2	626	Gaa/Aaa	13/20	1	2	FACETS	0.87	0.802	0.94	0.87	0.802	0.94	CLONAL	1	TRUE	1	0.574760791674493	2		429	664	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222899	36222899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	701	854	0	ENST00000222270.7:c.5528C>T	p.Pro1843Leu	p.P1843L	ENST00000222270	NM_014727.1	1843	cCt/cTt	27/37	0.574760791674493	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.574760791674493	3		854	1542	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792107	42792107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1382074611	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	480	606	1	ENST00000575354.2:c.911G>A	p.Gly304Asp	p.G304D	ENST00000575354	NM_015125.3	304	gGc/gAc	6/20	0.574760791674493	3	FACETS	0.981	0.941	1	0.981	0.941	1	CLONAL	2	TRUE	1	0.574760791674493	3		607	1096	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965017	25965017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	180	512	1	ENST00000435504.4:c.4189C>T	p.Pro1397Ser	p.P1397S	ENST00000435504		1397	Cct/Tct	13/13	0.574760791674493	3	FACETS	0.86	0.793	0.929	0.43	0.396	0.465	CLONAL	1	TRUE	1	0.574760791674493	3		513	938	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185035	99185035	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	336	424	1	ENST00000074304.5:c.2437T>C	p.Phe813Leu	p.F813L	ENST00000074304	NM_001134224.1	813	Ttt/Ctt	23/26	0.574760791674493	3	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	1	0.574760791674493	3		425	752	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538275	9538275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	224	543	0	ENST00000353224.5:c.1723C>T	p.Leu575Phe	p.L575F	ENST00000353224	NM_177990.2	575	Ctc/Ttc	7/10	0.574760791674493	3	FACETS	1	0.97	1	0.537	0.5	0.574	CLONAL	1	TRUE	1	0.574760791674493	3		543	935	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31015959	31015959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	174	457	0	ENST00000375687.4:c.281C>T	p.Pro94Leu	p.P94L	ENST00000375687	NM_015338.5	94	cCa/cTa	5/13	0.574760791674493	3	FACETS	0.974	0.898	1	0.487	0.449	0.527	CLONAL	1	TRUE	1	0.574760791674493	3		457	800	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739115	40739115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	360	627	1	ENST00000373198.4:c.3169G>A	p.Glu1057Lys	p.E1057K	ENST00000373198	NM_133170.3	1057	Gag/Aag	24/32	0.270064228761635	3	FACETS	0.918	0.874	0.963			1	INDETERMINATE	2	TRUE	NA	0.574760791674493	3		628	878	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827900	40827900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767977370	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	203	529	0	ENST00000373198.4:c.2528C>T	p.Ser843Phe	p.S843F	ENST00000373198	NM_133170.3	843	tCt/tTt	17/32	0.270064228761635	3	FACETS	0.958	0.889	1			1	INDETERMINATE	1	TRUE	NA	0.574760791674493	3		529	949	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817438	39817438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748243137	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	191	563	0	ENST00000288319.7:c.125G>A	p.Gly42Glu	p.G42E	ENST00000288319	NM_182918.3	42	gGa/gAa	2/10	1	2	FACETS	0.824	0.763	0.886	0.824	0.763	0.886	CLONAL	1	TRUE	1	0.574760791674493	2		563	807	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852517	42852517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	292	714	0	ENST00000398585.3:c.569G>A	p.Gly190Glu	p.G190E	ENST00000398585	NM_001135099.1	190	gGa/gAa	6/14	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.574760791674493	2		714	1004	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655440	45655440	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	252	635	0	ENST00000407780.3:c.412T>G	p.Phe138Val	p.F138V	ENST00000407780	NM_001283052.1	138	Ttc/Gtc	4/7	1	2	FACETS	0.97	0.909	1	0.97	0.909	1	CLONAL	1	TRUE	1	0.574760791674493	2		635	904	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035181	30035181	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	193	544	0	ENST00000338641.4:c.343C>T	p.Gln115Ter	p.Q115*	ENST00000338641	NM_000268.3	115	Caa/Taa	3/16	0.258940374836489	3	FACETS	1	0.96	1	0.527	0.488	0.567	INDETERMINATE	1	TRUE	1	0.574760791674493	3		544	820	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259116	89259117	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	226	412	0	ENST00000336596.2:c.260_261delinsAT	p.Val87Asp	p.V87D	ENST00000336596	NM_005233.5	87	gTC/gAT	3/17	0.350723759891302	5	FACETS	1	0.956	1	0.685	0.64	0.73	CLONAL	2	TRUE	2	0.574760791674493	5		412	713	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456447	189456447	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	288	375	0	ENST00000264731.3:c.208C>T	p.Gln70Ter	p.Q70*	ENST00000264731	NM_003722.4	70	Cag/Tag	3/14	0.470435335987105	2	FACETS	0.977	0.931	1	0.977	0.931	1	CLONAL	2	TRUE	0	0.574760791674493	2		375	513	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133586	55133586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501507	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	194	552	0	ENST00000257290.5:c.890G>A	p.Arg297Lys	p.R297K	ENST00000257290	NM_006206.4	297	aGg/aAg	6/23	1	2	FACETS	0.955	0.887	1	0.955	0.887	1	CLONAL	1	TRUE	1	0.574760791674493	2		552	707	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156489	55156489	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1290364180	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	164	430	2	ENST00000257290.5:c.2890A>G	p.Lys964Glu	p.K964E	ENST00000257290	NM_006206.4	964	Aaa/Gaa	22/23	1	2	FACETS	0.976	0.9	1	0.976	0.9	1	CLONAL	1	TRUE	1	0.574760791674493	2		432	585	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157485	106157485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747398674	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	111	363	0	ENST00000380013.4:c.2386G>A	p.Glu796Lys	p.E796K	ENST00000380013	NM_001127208.2	796	Gag/Aag	3/11	1	2	FACETS	0.81	0.732	0.891	0.81	0.732	0.891	CLONAL	1	TRUE	1	0.574760791674493	2		363	477	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541439	187541439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1246955615	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	176	455	0	ENST00000441802.2:c.6301C>T	p.Arg2101Cys	p.R2101C	ENST00000441802	NM_005245.3	2101	Cgc/Tgc	10/27	1	2	FACETS	0.96	0.888	1	0.96	0.888	1	CLONAL	1	TRUE	1	0.574760791674493	2		455	638	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295230	1295230	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs796516131	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	190	372	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.574760791674493	2		372	564	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435618	149435618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	230	615	0	ENST00000286301.3:c.2525G>A	p.Gly842Asp	p.G842D	ENST00000286301	NM_005211.3	842	gGc/gAc	19/22	1	2	FACETS	0.937	0.875	1	0.937	0.875	1	CLONAL	1	TRUE	1	0.574760791674493	2		615	854	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500491	149500491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770930584	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	273	672	0	ENST00000261799.4:c.2546G>A	p.Arg849Gln	p.R849Q	ENST00000261799	NM_002609.3	849	cGa/cAa	18/23	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.574760791674493	2		672	923	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250700	26250700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	596	540	0	ENST00000446824.2:c.134G>A	p.Gly45Asp	p.G45D	ENST00000446824	NM_021018.2	45	gGt/gAt	1/1	0.574760791674493	4	FACETS	0.897	0.865	0.928			1	CLONAL	3	TRUE	NA	0.574760791674493	4		540	1214	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797788	32797788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370090254	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	216	582	1	ENST00000374899.4:c.1714G>A	p.Glu572Lys	p.E572K	ENST00000374899	NM_018833.2	572	Gaa/Aaa	10/12	0.53668097541521	4	FACETS	1	0.94	1	0.338	0.313	0.363	CLONAL	1	TRUE	1	0.574760791674493	4		583	1168	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956552	93956552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754119070	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	114	361	0	ENST00000369303.4:c.2684G>A	p.Arg895Gln	p.R895Q	ENST00000369303	NM_004440.3	895	cGa/cAa	15/17	1	2	FACETS	0.849	0.769	0.933	0.849	0.769	0.933	CLONAL	1	TRUE	1	0.574760791674493	2		361	467	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068097	94068097	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	110	383	0	ENST00000369303.4:c.865C>T	p.Gln289Ter	p.Q289*	ENST00000369303	NM_004440.3	289	Caa/Taa	4/17	1	2	FACETS	0.852	0.771	0.938	0.852	0.771	0.938	CLONAL	1	TRUE	1	0.574760791674493	2		383	449	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725567	117725567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767519397	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	175	470	0	ENST00000368508.3:c.314C>T	p.Pro105Leu	p.P105L	ENST00000368508	NM_002944.2	105	cCc/cTc	5/43	NA	2	FACETS	0.937	0.866	1			1	INDETERMINATE	1	TRUE	NA	0.574760791674493	2		470	650	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6037030	6037030	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1562671039	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	429	404	0	ENST00000265849.7:c.730C>T	p.Gln244Ter	p.Q244*	ENST00000265849	NM_000535.5	244	Cag/Tag	7/15	0.574760791674493	3	FACETS	0.998	0.955	1	0.998	0.955	1	CLONAL	2	TRUE	1	0.574760791674493	3		404	963	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220344	55220344	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	433	590	1	ENST00000275493.2:c.734A>G	p.Glu245Gly	p.E245G	ENST00000275493	NM_005228.3	245	gAg/gGg	6/28	0.574760791674493	3	FACETS	0.934	0.894	0.975	0.934	0.894	0.975	CLONAL	2	TRUE	1	0.574760791674493	3		591	1038	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55232974	55232974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1249099747	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	151	360	0	ENST00000275493.2:c.1724G>A	p.Gly575Glu	p.G575E	ENST00000275493	NM_005228.3	575	gGa/gAa	15/28	0.574760791674493	3	FACETS	1	0.942	1	0.517	0.474	0.562	CLONAL	1	TRUE	1	0.574760791674493	3		360	654	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359032	81359032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	852	511	0	ENST00000222390.5:c.929G>A	p.Gly310Glu	p.G310E	ENST00000222390	NM_000601.4	310	gGa/gAa	8/18	0.574760791674493	6	FACETS	1	0.983	1	1	0.983	1	CLONAL	4	TRUE	2	0.574760791674493	6		511	1568	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945093	151945093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746147314	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	57	514	0	ENST00000262189.6:c.2426G>A	p.Gly809Glu	p.G809E	ENST00000262189	NM_170606.2	809	gGa/gAa	14/59	0.574760791674493	6	FACETS	0.516	0.442	0.598	0.129	0.11	0.15	SUBCLONAL	1	TRUE	2	0.574760791674493	6		514	826	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879289	56879289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	218	646	1	ENST00000519728.1:c.806G>A	p.Ser269Asn	p.S269N	ENST00000519728	NM_002350.3	269	aGt/aAt	9/13	0.258940374836489	3	FACETS	1	0.936	1	0.503	0.468	0.54	INDETERMINATE	1	TRUE	1	0.574760791674493	3		647	970	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069575	69069575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	206	458	0	ENST00000288368.4:c.4250G>A	p.Gly1417Glu	p.G1417E	ENST00000288368	NM_024870.2	1417	gGa/gAa	35/40	0.258940374836489	3	FACETS	0.905	0.847	0.963	0.905	0.847	0.963	INDETERMINATE	2	TRUE	1	0.574760791674493	3		458	510	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5055750	5055750	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs771912975	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	193	358	1	ENST00000381652.3:c.1018C>T	p.Arg340Ter	p.R340*	ENST00000381652	NM_004972.3	340	Cga/Tga	8/25	0.574760791674493	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.574760791674493	2		359	334	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524946	8524946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567730036	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	277	398	0	ENST00000356435.5:c.658C>T	p.Pro220Ser	p.P220S	ENST00000356435		220	Cct/Tct	7/35	0.574760791674493	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.574760791674493	2		398	474	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27228284	27228284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	386	574	0	ENST00000380036.4:c.3281G>A	p.Arg1094Lys	p.R1094K	ENST00000380036	NM_000459.3	1094	aGa/aAa	22/23	0.574760791674493	2	FACETS	0.933	0.894	0.971	0.933	0.894	0.971	CLONAL	2	TRUE	0	0.574760791674493	2		574	720	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317533	1317533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199794164	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	222	614	1	ENST00000400841.2:c.532G>A	p.Glu178Lys	p.E178K	ENST00000400841		178	Gag/Aag	5/6	1	1	FACETS	0.518	0.482	0.556	0.518	0.482	0.556	SUBCLONAL	1	TRUE	0	0.574760791674493	1		615	1062	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913538	39913538	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	239	300	0	ENST00000378444.4:c.4790C>T	p.Thr1597Ile	p.T1597I	ENST00000378444	NM_001123385.1	1597	aCt/aTt	13/15	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.574760791674493	1		300	412	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223368	53223368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	270	378	0	ENST00000375401.3:c.3991C>T	p.Pro1331Ser	p.P1331S	ENST00000375401	NM_004187.3	1331	Cct/Tct	23/26	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.574760791674493	1		378	468	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938304	76938304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	235	321	0	ENST00000373344.5:c.2444C>T	p.Ser815Phe	p.S815F	ENST00000373344	NM_000489.3	815	tCt/tTt	9/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.574760791674493	1		321	407	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259116	89259116	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036733-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	226	412	0	ENST00000336596.2:c.260T>A	p.Val87Asp	p.V87D	ENST00000336596	NM_005233.5	87	gTc/gAc	3/17	0.350723759891302	5	FACETS	1	0.956	1	0.685	0.64	0.73	CLONAL	2	TRUE	2	0.574760791674493	5		412	713	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	276	385	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.925344803850053	2		385	492	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262592	16262592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	269	528	0	ENST00000375759.3:c.9857C>A	p.Pro3286His	p.P3286H	ENST00000375759	NM_015001.2	3286	cCt/cAt	11/15	0.894130752197152	3	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.925344803850053	3		528	607	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023748	27023748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	143	389	0	ENST00000324856.7:c.854G>A	p.Gly285Glu	p.G285E	ENST00000324856	NM_006015.4	285	gGa/gAa	1/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.925344803850053	2		389	293	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101423	27101423	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	230	517	1	ENST00000324856.7:c.4705C>T	p.Pro1569Ser	p.P1569S	ENST00000324856	NM_006015.4	1569	Cca/Tca	18/20	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.925344803850053	2		518	490	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935268	36935268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	311	752	1	ENST00000361632.4:c.1459G>A	p.Gly487Arg	p.G487R	ENST00000361632		487	Ggg/Agg	10/16	1	2	FACETS	0.96	0.912	1	0.96	0.912	1	CLONAL	1	TRUE	1	0.925344803850053	2		753	700	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166271	118166271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	219	389	0	ENST00000369448.3:c.781G>A	p.Glu261Lys	p.E261K	ENST00000369448	NM_017709.3	261	Gaa/Aaa	2/2	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.925344803850053	2		389	469	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849128	156849128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	401	830	0	ENST00000524377.1:c.2020G>A	p.Asp674Asn	p.D674N	ENST00000524377	NM_002529.3	674	Gat/Aat	15/17	0.88570123553309	3	FACETS	0.972	0.925	1	0.486	0.462	0.511	CLONAL	1	TRUE	1	0.925344803850053	3		830	1304	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104377181	104377182	+	missense_variant	Missense_Mutation	DNP	TA	TA	CT	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	374	801	0	ENST00000369902.3:c.1292_1293delinsCT	p.Leu431Ser	p.L431S	ENST00000369902	NM_016169.3	431	tTA/tCT	10/12	NA	2	FACETS	0.928	0.885	0.971			1	INDETERMINATE	1	TRUE	NA	0.925344803850053	2		801	871	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256135	123256135	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141929882	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	322	655	0	ENST00000358487.5:c.1774C>T	p.Arg592Cys	p.R592C	ENST00000358487	NM_000141.4	592	Cgt/Tgt	13/18	0.925344803850053	3	FACETS	0.955	0.903	1	0.477	0.451	0.504	CLONAL	1	TRUE	1	0.925344803850053	3		655	1066	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324081	123324081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	254	495	1	ENST00000358487.5:c.389C>T	p.Ser130Phe	p.S130F	ENST00000358487	NM_000141.4	130	tCc/tTc	4/18	0.925344803850053	3	FACETS	0.944	0.885	1	0.472	0.442	0.502	CLONAL	1	TRUE	1	0.925344803850053	3		496	851	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141997	108141997	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780619	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	281	431	0	ENST00000278616.4:c.2941C>T	p.Arg981Cys	p.R981C	ENST00000278616	NM_000051.3	981	Cgt/Tgt	20/63	0.925344803850053	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.925344803850053	1		431	316	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103398	119103398	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	206	377	0	ENST00000264033.4:c.436C>T	p.Gln146Ter	p.Q146*	ENST00000264033	NM_005188.3	146	Cag/Tag	2/16	0.925344803850053	1	FACETS	0.973	0.938	1	0.973	0.938	1	CLONAL	1	TRUE	0	0.925344803850053	1		377	246	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	417041	417041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	198	400	0	ENST00000399788.2:c.3509C>T	p.Ala1170Val	p.A1170V	ENST00000399788	NM_001042603.1	1170	gCc/gTc	23/28	NA	2	FACETS	0.964	0.904	1			1	INDETERMINATE	1	TRUE	NA	0.925344803850053	2		400	444	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431735	49431735	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	272	798	1	ENST00000301067.7:c.9404C>T	p.Thr3135Ile	p.T3135I	ENST00000301067	NM_003482.3	3135	aCc/aTc	34/54	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.925344803850053	2		799	569	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112892368	112892368	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	220	430	0	ENST00000351677.2:c.526G>A	p.Glu176Lys	p.E176K	ENST00000351677	NM_002834.3	176	Gaa/Aaa	5/16	1	2	FACETS	0.972	0.915	1	0.972	0.915	1	CLONAL	1	TRUE	1	0.925344803850053	2		430	489	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112910803	112910803	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	261	431	0	ENST00000351677.2:c.812A>T	p.Gln271Leu	p.Q271L	ENST00000351677	NM_002834.3	271	cAa/cTa	7/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.925344803850053	2		431	541	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601256	28601256	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	253	530	0	ENST00000241453.7:c.2176T>C	p.Tyr726His	p.Y726H	ENST00000241453	NM_004119.2	726	Tac/Cac	17/24	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.925344803850053	2		530	537	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964022	28964022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	194	445	0	ENST00000282397.4:c.1880C>T	p.Ser627Phe	p.S627F	ENST00000282397	NM_002019.4	627	tCc/tTc	13/30	1	2	FACETS	0.949	0.888	1	0.949	0.888	1	CLONAL	1	TRUE	1	0.925344803850053	2		445	442	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005419	29005419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55687105	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	257	345	0	ENST00000282397.4:c.842G>A	p.Arg281Gln	p.R281Q	ENST00000282397	NM_002019.4	281	cGa/cAa	7/30	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.925344803850053	2		345	540	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012452	29012452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	297	552	0	ENST00000282397.4:c.419G>A	p.Ser140Asn	p.S140N	ENST00000282397	NM_002019.4	140	aGt/aAt	4/30	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.925344803850053	2		552	628	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32944632	32944632	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	334	572	0	ENST00000380152.3:c.8425T>C	p.Phe2809Leu	p.F2809L	ENST00000380152		2809	Ttc/Ctc	19/27	1	2	FACETS	0.94	0.894	0.986	0.94	0.894	0.986	CLONAL	1	TRUE	1	0.925344803850053	2		572	768	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336134	73336134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	119	325	1	ENST00000377767.4:c.2269G>A	p.Gly757Arg	p.G757R	ENST00000377767	NM_014953.3	757	Gga/Aga	17/21	1	2	FACETS	0.915	0.84	0.991	0.915	0.84	0.991	CLONAL	1	TRUE	1	0.925344803850053	2		326	281	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569948	95569948	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	251	435	0	ENST00000393063.1:c.3785C>T	p.Pro1262Leu	p.P1262L	ENST00000393063	NM_030621.3	1262	cCt/cTt	22/28	1	2	FACETS	0.977	0.923	1	0.977	0.923	1	CLONAL	1	TRUE	1	0.925344803850053	2		435	555	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041734	42041734	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	269	450	0	ENST00000219905.7:c.5929C>T	p.Gln1977Ter	p.Q1977*	ENST00000219905	NM_001164273.1	1977	Cag/Tag	17/24	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.925344803850053	2		450	536	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052602	42052602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	333	445	0	ENST00000219905.7:c.7273C>T	p.Arg2425Cys	p.R2425C	ENST00000219905	NM_001164273.1	2425	Cgc/Tgc	20/24	1	2	FACETS	0.983	0.936	1	0.983	0.936	1	CLONAL	1	TRUE	1	0.925344803850053	2		445	732	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713311	43713311	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	468	858	0	ENST00000382044.4:c.4162C>G	p.Leu1388Val	p.L1388V	ENST00000382044	NM_001141980.1	1388	Ctt/Gtt	20/28	1	2	FACETS	0.971	0.931	1	0.971	0.931	1	CLONAL	1	TRUE	1	0.925344803850053	2		858	1042	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472652	88472652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	211	402	0	ENST00000360948.2:c.1903G>A	p.Asp635Asn	p.D635N	ENST00000360948	NM_001012338.2	635	Gat/Aat	16/19	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.925344803850053	2		402	444	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476280	88476280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	301	624	0	ENST00000360948.2:c.1852G>A	p.Glu618Lys	p.E618K	ENST00000360948	NM_001012338.2	618	Gaa/Aaa	15/19	1	2	FACETS	0.986	0.936	1	0.986	0.936	1	CLONAL	1	TRUE	1	0.925344803850053	2		624	660	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396431	396431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	349	745	0	ENST00000262320.3:c.595C>T	p.Pro199Ser	p.P199S	ENST00000262320	NM_003502.3	199	Ccc/Tcc	2/11	1	2	FACETS	0.98	0.934	1	0.98	0.934	1	CLONAL	1	TRUE	1	0.925344803850053	2		745	770	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632744	23632744	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	242	561	0	ENST00000261584.4:c.3052G>T	p.Glu1018Ter	p.E1018*	ENST00000261584	NM_024675.3	1018	Gag/Tag	10/13	1	2	FACETS	0.875	0.823	0.927	0.875	0.823	0.927	CLONAL	1	TRUE	1	0.925344803850053	2		561	598	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671678	67671679	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	275	578	0	ENST00000264010.4:c.2087_2088delinsTT	p.Pro696Leu	p.P696L	ENST00000264010	NM_006565.3	696	cCC/cTT	12/12	1	2	FACETS	0.951	0.9	1	0.951	0.9	1	CLONAL	1	TRUE	1	0.925344803850053	2		578	625	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346081	89346081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	38	144	0	ENST00000301030.4:c.6869C>T	p.Pro2290Leu	p.P2290L	ENST00000301030	NM_001256183.1	2290	cCc/cTc	9/13	1	2	FACETS	0.99	0.851	1	0.99	0.851	1	CLONAL	1	TRUE	1	0.925344803850053	2		144	83	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350869	89350869	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	448	842	0	ENST00000301030.4:c.2081T>G	p.Phe694Cys	p.F694C	ENST00000301030	NM_001256183.1	694	tTt/tGt	9/13	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.925344803850053	2		842	958	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958242	11958242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1261150954	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	250	382	0	ENST00000353533.5:c.152C>T	p.Pro51Leu	p.P51L	ENST00000353533	NM_003010.3	51	cCa/cTa	2/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.925344803850053	2		382	502	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554601	29554602	+	missense_variant	Missense_Mutation	DNP	AA	AA	GT	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	166	282	0	ENST00000356175.3:c.2386_2387delinsGT	p.Lys796Val	p.K796V	ENST00000356175	NM_000267.3	796	AAa/GTa	20/57	1	2	FACETS	0.81	0.751	0.869	0.81	0.751	0.869	CLONAL	1	TRUE	1	0.925344803850053	2		282	443	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576001	29576001	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	251	314	0	ENST00000356175.3:c.3975-1G>A		p.X1325_splice	ENST00000356175	NM_000267.3	1325			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.925344803850053	2		314	532	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653151	29653151	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	183	388	0	ENST00000356175.3:c.5086G>T	p.Glu1696Ter	p.E1696*	ENST00000356175	NM_000267.3	1696	Gag/Tag	36/57	1	2	FACETS	0.875	0.816	0.935	0.875	0.816	0.935	CLONAL	1	TRUE	1	0.925344803850053	2		388	452	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864574	37864574	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	233	454	0	ENST00000269571.5:c.226G>A	p.Asp76Asn	p.D76N	ENST00000269571		76	Gat/Aat	3/27	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.925344803850053	2		454	414	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857681	59857681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	284	429	0	ENST00000259008.2:c.1876G>A	p.Glu626Lys	p.E626K	ENST00000259008	NM_032043.2	626	Gaa/Aaa	13/20	1	2	FACETS	0.956	0.906	1	0.956	0.906	1	CLONAL	1	TRUE	1	0.925344803850053	2		429	642	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222899	36222899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	292	854	0	ENST00000222270.7:c.5528C>T	p.Pro1843Leu	p.P1843L	ENST00000222270	NM_014727.1	1843	cCt/cTt	27/37	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.925344803850053	2		854	599	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792107	42792107	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1382074611	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	217	606	1	ENST00000575354.2:c.911G>A	p.Gly304Asp	p.G304D	ENST00000575354	NM_015125.3	304	gGc/gAc	6/20	1	2	FACETS	0.893	0.839	0.949	0.893	0.839	0.949	CLONAL	1	TRUE	1	0.925344803850053	2		607	525	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965017	25965017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	240	512	1	ENST00000435504.4:c.4189C>T	p.Pro1397Ser	p.P1397S	ENST00000435504		1397	Cct/Tct	13/13	1	2	FACETS	0.93	0.876	0.984	0.93	0.876	0.984	CLONAL	1	TRUE	1	0.925344803850053	2		513	558	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99185035	99185035	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	307	424	1	ENST00000074304.5:c.2437T>C	p.Phe813Leu	p.F813L	ENST00000074304	NM_001134224.1	813	Ttt/Ctt	23/26	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.925344803850053	2		425	661	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538275	9538275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	321	543	0	ENST00000353224.5:c.1723C>T	p.Leu575Phe	p.L575F	ENST00000353224	NM_177990.2	575	Ctc/Ttc	7/10	1	2	FACETS	0.912	0.866	0.958	0.912	0.866	0.958	CLONAL	1	TRUE	1	0.925344803850053	2		543	761	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31015959	31015959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	217	457	0	ENST00000375687.4:c.281C>T	p.Pro94Leu	p.P94L	ENST00000375687	NM_015338.5	94	cCa/cTa	5/13	1	2	FACETS	0.893	0.839	0.949	0.893	0.839	0.949	CLONAL	1	TRUE	1	0.925344803850053	2		457	525	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739115	40739115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	209	627	1	ENST00000373198.4:c.3169G>A	p.Glu1057Lys	p.E1057K	ENST00000373198	NM_133170.3	1057	Gag/Aag	24/32	1	2	FACETS	0.943	0.885	1	0.943	0.885	1	CLONAL	1	TRUE	1	0.925344803850053	2		628	479	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827900	40827900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767977370	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	316	529	0	ENST00000373198.4:c.2528C>T	p.Ser843Phe	p.S843F	ENST00000373198	NM_133170.3	843	tCt/tTt	17/32	1	2	FACETS	0.977	0.929	1	0.977	0.929	1	CLONAL	1	TRUE	1	0.925344803850053	2		529	699	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817438	39817438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748243137	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	284	563	0	ENST00000288319.7:c.125G>A	p.Gly42Glu	p.G42E	ENST00000288319	NM_182918.3	42	gGa/gAa	2/10	1	2	FACETS	0.931	0.882	0.981	0.931	0.882	0.981	CLONAL	1	TRUE	1	0.925344803850053	2		563	659	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852517	42852517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	270	714	0	ENST00000398585.3:c.569G>A	p.Gly190Glu	p.G190E	ENST00000398585	NM_001135099.1	190	gGa/gAa	6/14	1	2	FACETS	0.931	0.88	0.982	0.931	0.88	0.982	CLONAL	1	TRUE	1	0.925344803850053	2		714	627	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655440	45655440	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	295	635	0	ENST00000407780.3:c.412T>G	p.Phe138Val	p.F138V	ENST00000407780	NM_001283052.1	138	Ttc/Gtc	4/7	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.925344803850053	2		635	607	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035181	30035181	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	310	544	0	ENST00000338641.4:c.343C>T	p.Gln115Ter	p.Q115*	ENST00000338641	NM_000268.3	115	Caa/Taa	3/16	1	2	FACETS	0.934	0.887	0.982	0.934	0.887	0.982	CLONAL	1	TRUE	1	0.925344803850053	2		544	717	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259116	89259117	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	228	412	0	ENST00000336596.2:c.260_261delinsAT	p.Val87Asp	p.V87D	ENST00000336596	NM_005233.5	87	gTC/gAT	3/17	0.88570123553309	3	FACETS	0.973	0.91	1	0.486	0.455	0.519	CLONAL	1	TRUE	1	0.925344803850053	3		412	741	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456447	189456447	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	538	375	0	ENST00000264731.3:c.208C>T	p.Gln70Ter	p.Q70*	ENST00000264731	NM_003722.4	70	Cag/Tag	3/14	0.911618036451012	2	FACETS	0.996	0.98	1	0.996	0.98	1	CLONAL	2	TRUE	0	0.925344803850053	2		375	584	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133586	55133586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501507	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	271	552	0	ENST00000257290.5:c.890G>A	p.Arg297Lys	p.R297K	ENST00000257290	NM_006206.4	297	aGg/aAg	6/23	1	2	FACETS	0.971	0.92	1	0.971	0.92	1	CLONAL	1	TRUE	1	0.925344803850053	2		552	603	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156489	55156489	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1290364180	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	219	430	2	ENST00000257290.5:c.2890A>G	p.Lys964Glu	p.K964E	ENST00000257290	NM_006206.4	964	Aaa/Gaa	22/23	1	2	FACETS	0.958	0.901	1	0.958	0.901	1	CLONAL	1	TRUE	1	0.925344803850053	2		432	494	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157485	106157485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747398674	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	174	363	0	ENST00000380013.4:c.2386G>A	p.Glu796Lys	p.E796K	ENST00000380013	NM_001127208.2	796	Gag/Aag	3/11	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.925344803850053	2		363	375	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541439	187541439	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1246955615	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	212	455	0	ENST00000441802.2:c.6301C>T	p.Arg2101Cys	p.R2101C	ENST00000441802	NM_005245.3	2101	Cgc/Tgc	10/27	1	2	FACETS	0.871	0.817	0.926	0.871	0.817	0.926	CLONAL	1	TRUE	1	0.925344803850053	2		455	526	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295230	1295230	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs796516131	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	269	372	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.925344803850053	2		372	465	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435618	149435618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	354	615	0	ENST00000286301.3:c.2525G>A	p.Gly842Asp	p.G842D	ENST00000286301	NM_005211.3	842	gGc/gAc	19/22	1	2	FACETS	0.915	0.871	0.959	0.915	0.871	0.959	CLONAL	1	TRUE	1	0.925344803850053	2		615	836	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500491	149500491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770930584	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	358	672	0	ENST00000261799.4:c.2546G>A	p.Arg849Gln	p.R849Q	ENST00000261799	NM_002609.3	849	cGa/cAa	18/23	1	2	FACETS	0.975	0.929	1	0.975	0.929	1	CLONAL	1	TRUE	1	0.925344803850053	2		672	794	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250700	26250700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	408	540	0	ENST00000446824.2:c.134G>A	p.Gly45Asp	p.G45D	ENST00000446824	NM_021018.2	45	gGt/gAt	1/1	0.88570123553309	3	FACETS	0.924	0.889	0.959	0.924	0.889	0.959	CLONAL	2	TRUE	1	0.925344803850053	3		540	698	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797788	32797788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370090254	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	282	582	1	ENST00000374899.4:c.1714G>A	p.Glu572Lys	p.E572K	ENST00000374899	NM_018833.2	572	Gaa/Aaa	10/12	0.88570123553309	3	FACETS	1	0.956	1	0.509	0.479	0.539	CLONAL	1	TRUE	1	0.925344803850053	3		583	876	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956552	93956552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754119070	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	177	361	0	ENST00000369303.4:c.2684G>A	p.Arg895Gln	p.R895Q	ENST00000369303	NM_004440.3	895	cGa/cAa	15/17	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.925344803850053	2		361	381	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068097	94068097	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	215	383	0	ENST00000369303.4:c.865C>T	p.Gln289Ter	p.Q289*	ENST00000369303	NM_004440.3	289	Caa/Taa	4/17	1	2	FACETS	0.978	0.92	1	0.978	0.92	1	CLONAL	1	TRUE	1	0.925344803850053	2		383	475	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725567	117725567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767519397	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	277	470	0	ENST00000368508.3:c.314C>T	p.Pro105Leu	p.P105L	ENST00000368508	NM_002944.2	105	cCc/cTc	5/43	1	2	FACETS	0.943	0.892	0.994	0.943	0.892	0.994	CLONAL	1	TRUE	1	0.925344803850053	2		470	635	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6037030	6037030	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1562671039	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	453	404	0	ENST00000265849.7:c.730C>T	p.Gln244Ter	p.Q244*	ENST00000265849	NM_000535.5	244	Cag/Tag	7/15	0.596602919334621	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.925344803850053	4		404	883	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220344	55220344	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	522	590	1	ENST00000275493.2:c.734A>G	p.Glu245Gly	p.E245G	ENST00000275493	NM_005228.3	245	gAg/gGg	6/28	0.596602919334621	4	FACETS	0.977	0.94	1	0.977	0.94	1	CLONAL	2	TRUE	2	0.925344803850053	4		591	1112	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55232974	55232974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1249099747	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	376	360	0	ENST00000275493.2:c.1724G>A	p.Gly575Glu	p.G575E	ENST00000275493	NM_005228.3	575	gGa/gAa	15/28	0.596602919334621	4	FACETS	0.971	0.927	1	0.971	0.927	1	CLONAL	2	TRUE	2	0.925344803850053	4		360	806	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359032	81359032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	1217	511	0	ENST00000222390.5:c.929G>A	p.Gly310Glu	p.G310E	ENST00000222390	NM_000601.4	310	gGa/gAa	8/18	0.925344803850053	6	FACETS	0.938	0.917	0.958	0.938	0.917	0.958	CLONAL	4	TRUE	2	0.925344803850053	6		511	1999	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945093	151945093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746147314	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	59	514	0	ENST00000262189.6:c.2426G>A	p.Gly809Glu	p.G809E	ENST00000262189	NM_170606.2	809	gGa/gAa	14/59	0.925344803850053	6	FACETS	0.683	0.588	0.787	0.171	0.147	0.197	SUBCLONAL	1	TRUE	2	0.925344803850053	6		514	532	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56879289	56879289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	306	646	1	ENST00000519728.1:c.806G>A	p.Ser269Asn	p.S269N	ENST00000519728	NM_002350.3	269	aGt/aAt	9/13	1	2	FACETS	0.956	0.907	1	0.956	0.907	1	CLONAL	1	TRUE	1	0.925344803850053	2		647	692	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069575	69069575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	281	458	0	ENST00000288368.4:c.4250G>A	p.Gly1417Glu	p.G1417E	ENST00000288368	NM_024870.2	1417	gGa/gAa	35/40	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.925344803850053	2		458	561	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5055750	5055750	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs771912975	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	337	358	1	ENST00000381652.3:c.1018C>T	p.Arg340Ter	p.R340*	ENST00000381652	NM_004972.3	340	Cga/Tga	8/25	0.923801159714194	2	FACETS	0.958	0.936	0.979	0.958	0.936	0.979	CLONAL	2	TRUE	0	0.925344803850053	2		359	380	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524946	8524946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567730036	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	405	398	0	ENST00000356435.5:c.658C>T	p.Pro220Ser	p.P220S	ENST00000356435		220	Cct/Tct	7/35	0.923801159714194	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.925344803850053	2		398	432	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27228284	27228284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	509	574	0	ENST00000380036.4:c.3281G>A	p.Arg1094Lys	p.R1094K	ENST00000380036	NM_000459.3	1094	aGa/aAa	22/23	0.923801159714194	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.925344803850053	2		574	540	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317533	1317533	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199794164	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	187	614	1	ENST00000400841.2:c.532G>A	p.Glu178Lys	p.E178K	ENST00000400841		178	Gag/Aag	5/6	1	1	FACETS	0.433	0.403	0.463	0.433	0.403	0.463	SUBCLONAL	1	TRUE	0	0.925344803850053	1		615	502	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913538	39913538	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	266	300	0	ENST00000378444.4:c.4790C>T	p.Thr1597Ile	p.T1597I	ENST00000378444	NM_001123385.1	1597	aCt/aTt	13/15	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.925344803850053	1		300	280	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223368	53223368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	438	378	0	ENST00000375401.3:c.3991C>T	p.Pro1331Ser	p.P1331S	ENST00000375401	NM_004187.3	1331	Cct/Tct	23/26	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.925344803850053	1		378	461	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938304	76938304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0036733-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	318	321	0	ENST00000373344.5:c.2444C>T	p.Ser815Phe	p.S815F	ENST00000373344	NM_000489.3	815	tCt/tTt	9/35	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.925344803850053	1		321	359	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0036872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	305	747	2	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.62649103489884	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.676589569299861	2		749	432	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770870	59770870	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0036872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	321	340	0	ENST00000259008.2:c.2496T>G	p.Cys832Trp	p.C832W	ENST00000259008	NM_032043.2	832	tgT/tgG	18/20	0.676589569299861	4	FACETS	0.965	0.934	0.995	0.965	0.934	0.995	CLONAL	4	TRUE	0	0.676589569299861	4		340	412	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30051595	30051595	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0036872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	217	415	0	ENST00000338641.4:c.529T>A	p.Tyr177Asn	p.Y177N	ENST00000338641	NM_000268.3	177	Tat/Aat	6/16	0.62649103489884	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.676589569299861	2		415	316	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178614	56178614	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0036872-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	47	337	0	ENST00000399503.3:c.3587C>G	p.Ser1196Ter	p.S1196*	ENST00000399503	NM_005921.1	1196	tCa/tGa	14/20	0.634920958836867	1	FACETS	0.707	0.612	0.806	0.707	0.612	0.806	SUBCLONAL	1	TRUE	0	0.676589569299861	1		337	130	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0036917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	116	543	0	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.18747874988046	2	FACETS	1	0.974	1	0.622	0.56	0.688	CLONAL	1	TRUE	0	0.217795895636198	2		543	856	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242483	55242506	+	inframe_deletion	In_Frame_Del	DEL	ATCTCCGAAAGCCAACAAGGAAAT	ATCTCCGAAAGCCAACAAGGAAAT	-	rs727504232	NA	P-0036917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	48	413	0	ENST00000275493.2:c.2253_2276del	p.Ser752_Ile759del	p.S752_I759del	ENST00000275493	NM_005228.3	751	acATCTCCGAAAGCCAACAAGGAAATc/acc	19/28	0.109318478136878	4	FACETS	0.867	0.732	1	0.434	0.366	0.508	INDETERMINATE	1	TRUE	2	0.217795895636198	4		413	619	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057911	27057911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs892173376	NA	P-0036917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	152	557	1	ENST00000324856.7:c.1619C>T	p.Thr540Met	p.T540M	ENST00000324856	NM_006015.4	540	aCg/aTg	3/20	0.130558647881954	3	FACETS	0.831	0.76	0.906	0.831	0.76	0.906	INDETERMINATE	2	TRUE	1	0.217795895636198	3		558	931	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11206842	11206843	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0036917-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	95	392	0	ENST00000361445.4:c.4576_4577delinsCT	p.Trp1526Leu	p.W1526L	ENST00000361445	NM_004958.3	1526	TGg/CTg	32/58	0.130558647881954	3	FACETS	0.778	0.693	0.867	0.778	0.693	0.867	INDETERMINATE	2	TRUE	1	0.217795895636198	3		392	622	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266472	55266472	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs961150162	NA	P-0037052-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	90	738	0	ENST00000275493.2:c.2764G>A	p.Glu922Lys	p.E922K	ENST00000275493	NM_005228.3	922	Gag/Aag	23/28	0.14051103393178	4	FACETS	0.777	0.692	0.867	0.777	0.692	0.867	INDETERMINATE	2	TRUE	2	0.319779805675484	4		738	478	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0037052-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	113	1023	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.211180854160106	2	FACETS	1	0.982	1	0.694	0.628	0.764	CLONAL	1	TRUE	0	0.319779805675484	2		1023	509	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647745	2647745	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0037052-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	62	708	0	ENST00000342085.4:c.1648C>T	p.His550Tyr	p.H550Y	ENST00000342085	NM_002613.4	550	Cac/Tac	14/14	1	2	FACETS	0.811	0.702	0.929	0.811	0.702	0.929	CLONAL	1	TRUE	1	0.319779805675484	2		708	478	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40442025	40442025	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037052-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	34	842	1	ENST00000345506.4:c.270C>A	p.Tyr90Ter	p.Y90*	ENST00000345506	NM_003152.3	90	taC/taA	4/20	0.300613471309847	3	FACETS	0.415	0.338	0.502	0.138	0.112	0.168	SUBCLONAL	1	TRUE	0	0.319779805675484	3		843	594	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117948	70117948	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037052-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	144	477	0	ENST00000245479.2:c.416T>C	p.Leu139Pro	p.L139P	ENST00000245479	NM_000346.3	139	cTg/cCg	1/3	0.300613471309847	3	FACETS	0.907	0.837	0.978	0.907	0.837	0.978	CLONAL	3	TRUE	0	0.319779805675484	3		477	384	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964968	55964968	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037052-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	17	341	0	ENST00000263923.4:c.2269G>T	p.Ala757Ser	p.A757S	ENST00000263923	NM_002253.2	757	Gcc/Tcc	16/30	1	2	FACETS	0.447	0.334	0.581	0.447	0.334	0.581	SUBCLONAL	1	TRUE	1	0.319779805675484	2		341	238	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020396	69020396	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037052-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	25	598	0	ENST00000288368.4:c.2768C>A	p.Ser923Tyr	p.S923Y	ENST00000288368	NM_024870.2	923	tCt/tAt	24/40	1	2	FACETS	0.395	0.311	0.492	0.395	0.311	0.492	SUBCLONAL	1	TRUE	1	0.319779805675484	2		598	396	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0037164-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2323	85	496	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.363109078333686	13	FACETS	0.583	0.512	0.659	0.049	0.042	0.055	SUBCLONAL	1	TRUE	1	0.363109078333686	13		496	2408	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0037164-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	228	637	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.347795510669141	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.363109078333686	1		637	941	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624296	89624296	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs786201995	NA	P-0037164-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	152	539	1	ENST00000371953.3:c.70G>C	p.Asp24His	p.D24H	ENST00000371953	NM_000314.4	24	Gac/Cac	1/9	0.363109078333686	1	FACETS	0.871	0.797	0.947	0.871	0.797	0.947	CLONAL	1	TRUE	0	0.363109078333686	1		540	787	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604655	48604655	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121912578	NA	P-0037164-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	69	322	0	ENST00000342988.3:c.1477G>C	p.Asp493His	p.D493H	ENST00000342988	NM_005359.5	493	Gat/Cat	12/12	0.363109078333686	1	FACETS	0.772	0.675	0.875	0.772	0.675	0.875	SUBCLONAL	1	TRUE	0	0.363109078333686	1		322	403	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39935769	39935769	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0037164-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	55	448	0	ENST00000378444.4:c.103G>T	p.Asp35Tyr	p.D35Y	ENST00000378444	NM_001123385.1	35	Gat/Tat	3/15	0.238746781191358	1	FACETS	0.311	0.265	0.361	0.311	0.265	0.361	SUBCLONAL	1	TRUE	0	0.363109078333686	1		448	798	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244040	46244040	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037164-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	60	455	0	ENST00000334344.6:c.2134G>A	p.Glu712Lys	p.E712K	ENST00000334344	NM_152641.2	712	Gaa/Aaa	15/21	0.363109078333686	1	FACETS	0.371	0.318	0.427	0.371	0.318	0.427	SUBCLONAL	1	TRUE	0	0.363109078333686	1		455	730	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0037168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	274	352	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.468344942833566	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.468344942833566	2		352	514	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0037168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	175	605	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.468344942833566	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.468344942833566	1		605	511	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827934	40827934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61749502	NA	P-0037168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	270	495	0	ENST00000373198.4:c.2494G>A	p.Ala832Thr	p.A832T	ENST00000373198	NM_133170.3	832	Gcc/Acc	17/32	0.380880216458552	3	FACETS	0.931	0.878	0.986	0.931	0.878	0.986	CLONAL	2	TRUE	1	0.468344942833566	3		495	764	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258983	153258983	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0037168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	55	334	0	ENST00000281708.4:c.832C>T	p.Arg278Ter	p.R278*	ENST00000281708	NM_033632.3	278	Cga/Tga	5/12	1	2	FACETS	0.86	0.742	0.987	0.86	0.742	0.987	CLONAL	1	TRUE	1	0.468344942833566	2		334	273	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245446	153245446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	138	563	1	ENST00000281708.4:c.1745C>T	p.Ser582Leu	p.S582L	ENST00000281708	NM_033632.3	582	tCg/tTg	11/12	1	2	FACETS	0.876	0.799	0.956	0.876	0.799	0.956	CLONAL	1	TRUE	1	0.468344942833566	2		564	673	SUCCESS
APC	324	MSKCC	GRCh37	5	112175706	112175706	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0037168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	202	277	0	ENST00000257430.4:c.4415del	p.Val1472GlufsTer35	p.V1472Efs*35	ENST00000257430	NM_000038.5	1472	gTa/ga	16/16	0.467033222174112	3	FACETS	0.851	0.8	0.902	0.851	0.8	0.902	CLONAL	3	TRUE	0	0.468344942833566	3		277	417	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591904	48591904	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	137	497	0	ENST00000342988.3:c.1067C>G	p.Pro356Arg	p.P356R	ENST00000342988	NM_005359.5	356	cCt/cGt	9/12	0.468344942833566	1	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	0	0.468344942833566	1		497	448	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524637	176524637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	546	838	0	ENST00000292408.4:c.2369G>A	p.Gly790Glu	p.G790E	ENST00000292408	NM_213647.1	790	gGa/gAa	18/18	0.467033222174112	3	FACETS	0.989	0.955	1	0.989	0.955	1	CLONAL	3	TRUE	0	0.468344942833566	3		838	970	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207072	1207073	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0037648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	172	707	0	ENST00000326873.7:c.161dup	p.Leu55AlafsTer108	p.L55Afs*108	ENST00000326873	NM_000455.4	54	ctg/cTtg	1/10	0.505193826926699	1	FACETS	0.888	0.822	0.956	0.888	0.822	0.956	CLONAL	1	TRUE	0	0.505193826926699	1		707	573	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86648972	86648972	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0037648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	66	209	0	ENST00000274376.6:c.1254-2A>T		p.X418_splice	ENST00000274376	NM_002890.2	418			0.505193826926699	1	FACETS	0.957	0.845	1	0.957	0.845	1	CLONAL	1	TRUE	0	0.505193826926699	1		209	204	SUCCESS
APC	324	MSKCC	GRCh37	5	112162861	112162876	+	frameshift_variant	Frame_Shift_Del	DEL	ACTAATGACCACTACA	ACTAATGACCACTACA	-	novel	NA	P-0037648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	105	459	0	ENST00000257430.4:c.1465_1480del	p.Thr489ValfsTer4	p.T489Vfs*4	ENST00000257430	NM_000038.5	489	ACTAATGACCACTACAgt/gt	12/16	0.505193826926699	1	FACETS	0.818	0.739	0.9	0.818	0.739	0.9	CLONAL	1	TRUE	0	0.505193826926699	1		459	380	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0037689-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	953	632	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.877018763298605	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.877018763298605	2		632	1039	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428229	49428229	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs902898516	NA	P-0037689-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	271	757	1	ENST00000301067.7:c.10471C>T	p.Arg3491Cys	p.R3491C	ENST00000301067	NM_003482.3	3491	Cgt/Tgt	37/54	0.447915740298076	1	FACETS	0.343	0.322	0.365	0.343	0.322	0.365	INDETERMINATE	1	TRUE	0	0.877018763298605	1		758	1011	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878177	48878181	+	frameshift_variant	Frame_Shift_Del	DEL	TCTCG	TCTCG	-	novel	NA	P-0037689-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	201	126	0	ENST00000267163.4:c.131_135del	p.Leu44GlnfsTer3	p.L44Qfs*3	ENST00000267163	NM_000321.2	43	ccTCTCGtc/cctc	1/27	0.877018763298605	3	FACETS	0.931	0.9	0.96	0.931	0.9	0.96	CLONAL	3	TRUE	0	0.877018763298605	3		126	236	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349447	73349447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037689-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	628	425	0	ENST00000377767.4:c.889C>T	p.Leu297Phe	p.L297F	ENST00000377767	NM_014953.3	297	Ctc/Ttc	6/21	0.877018763298605	3	FACETS	0.998	0.983	1	0.998	0.983	1	CLONAL	3	TRUE	0	0.877018763298605	3		425	688	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134422	30134422	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037689-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	308	743	0	ENST00000263025.4:c.109G>C	p.Asp37His	p.D37H	ENST00000263025	NM_002746.2	37	Gac/Cac	1/9	0.877018763298605	2	FACETS	0.661	0.623	0.699	0.33	0.311	0.35	SUBCLONAL	1	TRUE	0	0.877018763298605	2		743	1063	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45375007	45375007	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0037689-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	291	425	0	ENST00000262160.6:c.836A>G	p.Tyr279Cys	p.Y279C	ENST00000262160	NM_005901.5	279	tAt/tGt	8/11	0.877018763298605	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.877018763298605	1		425	356	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164458	36164458	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037689-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	89	336	0	ENST00000300305.3:c.1417G>C	p.Glu473Gln	p.E473Q	ENST00000300305		473	Gag/Cag	8/8	0.820708077841241	3	FACETS	0.579	0.515	0.647	0.29	0.257	0.324	SUBCLONAL	1	TRUE	1	0.877018763298605	3		336	504	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31401588	31401588	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037689-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	185	567	0	ENST00000344624.3:c.4076G>C	p.Arg1359Thr	p.R1359T	ENST00000344624		1359	aGa/aCa	33/33	0.627862932733155	4	FACETS	0.63	0.58	0.682	0.21	0.193	0.228	SUBCLONAL	1	TRUE	1	0.877018763298605	4		567	1257	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048638	6048638	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs372539944	NA	P-0037689-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	66	590	0	ENST00000265849.7:c.13G>C	p.Glu5Gln	p.E5Q	ENST00000265849	NM_000535.5	5	Gag/Cag	1/15	0.877018763298605	3	FACETS	0.167	0.144	0.192	0.056	0.048	0.064	SUBCLONAL	1	TRUE	0	0.877018763298605	3		590	1296	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132763	152132763	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0037689-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	51	559	0	ENST00000262189.6:c.109C>T	p.Arg37Trp	p.R37W	ENST00000262189	NM_170606.2	37	Cgg/Tgg	1/59	0.877018763298605	1	FACETS	0.12	0.102	0.141	0.12	0.102	0.141	SUBCLONAL	1	TRUE	0	0.877018763298605	1		559	542	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0037759-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	289	734	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.494101667469402	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.494101667469402	2		734	556	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524595	103524595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756972065	NA	P-0037759-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	147	294	0	ENST00000355739.4:c.2726C>T	p.Pro909Leu	p.P909L	ENST00000355739	NM_000123.3	909	cCt/cTt	13/15	0.494101667469402	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	0	0.494101667469402	2		294	282	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491669	56491669	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0037759-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	252	449	0	ENST00000267101.3:c.2561G>T	p.Gly854Val	p.G854V	ENST00000267101	NM_001982.3	854	gGt/gTt	21/28	0.486767002606749	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.494101667469402	2		449	496	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993848	72993848	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0037759-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	228	463	0	ENST00000268489.5:c.197C>G	p.Ala66Gly	p.A66G	ENST00000268489	NM_006885.3	66	gCg/gGg	2/10	0.494101667469402	6	FACETS	1	0.977	1	0.55	0.513	0.588	CLONAL	2	TRUE	2	0.494101667469402	6		463	834	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868412	45868412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770334103	NA	P-0037759-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	260	693	0	ENST00000391945.4:c.365C>T	p.Thr122Ile	p.T122I	ENST00000391945	NM_000400.3	122	aCa/aTa	6/23	0.487512166684488	4	FACETS	0.89	0.836	0.946	0.89	0.836	0.946	CLONAL	2	TRUE	2	0.494101667469402	4		693	883	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665309	176665309	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0037759-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	189	471	0	ENST00000439151.2:c.3993C>G	p.Asp1331Glu	p.D1331E	ENST00000439151	NM_022455.4	1331	gaC/gaG	7/23	0.494101667469402	4	FACETS	0.815	0.756	0.876	0.408	0.378	0.438	CLONAL	2	TRUE	0	0.494101667469402	4		471	701	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099218	157099218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537376978	NA	P-0037759-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	175	395	0	ENST00000346085.5:c.155C>T	p.Ser52Leu	p.S52L	ENST00000346085	NM_020732.3	52	tCg/tTg	1/20	0.494101667469402	6	FACETS	0.993	0.917	1	0.497	0.458	0.536	CLONAL	2	TRUE	2	0.494101667469402	6		395	709	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253771	30253771	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0037759-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1303	133	492	0	ENST00000307677.4:c.683C>G	p.Ser228Ter	p.S228*	ENST00000307677	NM_138578.1	228	tCa/tGa	3/3	0.494101667469402	7	FACETS	0.838	0.758	0.922			1	CLONAL	1	TRUE	NA	0.494101667469402	7		492	1436	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841926	151842004	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAAATGACTTTGAGGTGCTGGTGCTGTTTAAGGTGTGAGGCCTGCAGACAATGGCATATCAACAGGAAAAAAATACAAG	GAAATGACTTTGAGGTGCTGGTGCTGTTTAAGGTGTGAGGCCTGCAGACAATGGCATATCAACAGGAAAAAAATACAAG	-	novel	NA	P-0037759-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	79	332	0	ENST00000262189.6:c.14175-38_14215del		p.X4725_splice	ENST00000262189	NM_170606.2	4725		55/59	0.494101667469402	7	FACETS	1	0.961	1	0.175	0.154	0.198	CLONAL	1	TRUE	0	0.494101667469402	7		332	583	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949743	151949743	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0037759-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	163	414	0	ENST00000262189.6:c.1357T>G	p.Cys453Gly	p.C453G	ENST00000262189	NM_170606.2	453	Tgc/Ggc	10/59	0.494101667469402	7	FACETS	0.848	0.778	0.92	0.242	0.222	0.263	CLONAL	2	TRUE	0	0.494101667469402	7		414	870	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976136	18976172	+	protein_altering_variant	In_Frame_Del	DEL	ATTGGCATGATCAGTGCCGGCCCTAGCCACGTGGCTG	ATTGGCATGATCAGTGCCGGCCCTAGCCACGTGGCTG	C	novel	NA	P-0037759-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	264	782	0	ENST00000262803.5:c.2896_2932delinsC	p.Ile966_Ala978delinsPro	p.I966_A978delinsP	ENST00000262803	NM_002911.3	966	ATTGGCATGATCAGTGCCGGCCCTAGCCACGTGGCTGcc/Ccc	21/24	0.494101667469402	7	FACETS	0.946	0.885	1	0.378	0.354	0.404	CLONAL	2	TRUE	2	0.494101667469402	7		782	1263	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227998	53227998	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0037815-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	185	380	0	ENST00000375401.3:c.2316del	p.Trp773GlyfsTer22	p.W773Gfs*22	ENST00000375401	NM_004187.3	772	acC/ac	16/26	1	1	FACETS	0.86	0.797	0.924	1	0.992	1	CLONAL	2	FALSE	0	0.278935006756781	1		380	664	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229669	5229669	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0037815-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	18	24	0	ENST00000357368.4:c.2182G>T	p.Glu728Ter	p.E728*	ENST00000357368	NM_002850.3	728	Gag/Tag	15/38	1	2	FACETS	0.978	0.758	1	1	0.936	1	CLONAL	2	FALSE	1	0.278935006756781	2		24	66	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0037818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	59	344	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.915	0.792	1	1	0.977	1	CLONAL	2	FALSE	1	0.192541664413224	2		344	335	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934576	NA	P-0037818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	73	735	0	ENST00000269305.4:c.818G>C	p.Arg273Pro	p.R273P	ENST00000269305	NM_001126112.2	273	cGt/cCt	8/11	1	2	FACETS	0.649	0.566	0.74	0.649	0.566	0.74	SUBCLONAL	1	FALSE	1	0.192541664413224	2		735	1168	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67070631	67070631	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs760230354	NA	P-0037818-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	43	277	0	ENST00000412916.2:c.255T>A	p.Tyr85Ter	p.Y85*	ENST00000412916		85	taT/taA	3/6	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	FALSE	1	0.192541664413224	2		277	349	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0038062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	209	352	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.47133458427165	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.481953693888065	3		352	518	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0038062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	407	712	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.481953693888065	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.481953693888065	2		712	793	SUCCESS
APC	324	MSKCC	GRCh37	5	112175348	112175348	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1114167568	NA	P-0038062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	66	201	0	ENST00000257430.4:c.4057G>T	p.Glu1353Ter	p.E1353*	ENST00000257430	NM_000038.5	1353	Gaa/Taa	16/16	0.481953693888065	3	FACETS	0.854	0.744	0.971	0.427	0.372	0.486	CLONAL	1	TRUE	1	0.481953693888065	3		201	398	SUCCESS
APC	324	MSKCC	GRCh37	5	112173893	112173893	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	226	314	2	ENST00000257430.4:c.2602G>T	p.Glu868Ter	p.E868*	ENST00000257430	NM_000038.5	868	Gaa/Taa	16/16	0.481953693888065	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.481953693888065	3		316	502	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151168479	151168479	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0038062-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	181	318	0	ENST00000262187.5:c.380+1G>T		p.X127_splice	ENST00000262187	NM_005614.3	127			0.425398501542644	4	FACETS	0.886	0.821	0.953	0.886	0.821	0.953	CLONAL	2	TRUE	2	0.481953693888065	4		318	628	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0038171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	221	457	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.629247448654091	3	FACETS	0.973	0.919	1	0.973	0.919	1	CLONAL	2	TRUE	1	0.710925428192041	3		457	433	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166739	32166739	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157907497	NA	P-0038171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1195	246	824	1	ENST00000375023.3:c.4499G>A	p.Arg1500His	p.R1500H	ENST00000375023	NM_004557.3	1500	cGc/cAc	24/30	0.711317167013917	5	FACETS	0.992	0.925	1	0.331	0.308	0.354	CLONAL	1	TRUE	2	0.710925428192041	5		825	1441	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639161	3639161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs565491187	NA	P-0038171-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	185	801	0	ENST00000294008.3:c.4478C>T	p.Ser1493Leu	p.S1493L	ENST00000294008	NM_032444.2	1493	tCg/tTg	12/15	0.564884442914419	5	FACETS	0.937	0.864	1	0.312	0.288	0.338	CLONAL	1	TRUE	2	0.710925428192041	5		801	1148	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356195	66356195	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	149	403	0	ENST00000273854.3:c.1302C>A	p.His434Gln	p.H434Q	ENST00000273854	NM_004439.5	434	caC/caA	5/18	0.283856446741321	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.419849033379767	1		403	550	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	233677	233678	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0038228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	85	275	1	ENST00000264932.6:c.981_982delinsAA	p.Met327_Glu328delinsIleLys	p.M327_E328delinsIK	ENST00000264932	NM_004168.2	327	atGGag/atAAag	8/15	1	2	FACETS	0.81	0.718	0.907	0.81	0.718	0.907	CLONAL	1	TRUE	1	0.419849033379767	2		276	500	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55225377	55225377	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	100	360	1	ENST00000275493.2:c.1229G>T	p.Trp410Leu	p.W410L	ENST00000275493	NM_005228.3	410	tGg/tTg	11/28	0.419849033379767	3	FACETS	0.745	0.665	0.83	0.248	0.221	0.277	SUBCLONAL	1	TRUE	0	0.419849033379767	3		361	774	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411874	116411892	+	intron_variant	Intron	DEL	ACAAGCTCTTTCTTTCTCT	ACAAGCTCTTTCTTTCTCT	-	novel	NA	P-0038228-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	638	680	0	ENST00000397752.3:c.2888-29_2888-11del		p.*963*	ENST00000397752	NM_000245.2	-/1390			0.419849033379767	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	0	0.419849033379767	3		680	1182	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678509	88678509	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373935634	NA	P-0038235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	89	546	0	ENST00000360948.2:c.1027C>T	p.Arg343Trp	p.R343W	ENST00000360948	NM_001012338.2	343	Cgg/Tgg	9/19	0.251269289974746	3	FACETS	1	0.952	1	0.57	0.505	0.639	CLONAL	1	TRUE	1	0.251269289974746	3		546	700	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996188	73996188	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	110	808	0	ENST00000318443.5:c.922G>A	p.Ala308Thr	p.A308T	ENST00000318443	NM_001024736.1	308	Gcc/Acc	5/10	0.251269289974746	3	FACETS	1	0.946	1	0.542	0.486	0.601	CLONAL	1	TRUE	1	0.251269289974746	3		808	909	SUCCESS
AR	367	MSKCC	GRCh37	X	66765744	66765744	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038235-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	144	1083	1	ENST00000374690.3:c.756G>T	p.Glu252Asp	p.E252D	ENST00000374690	NM_000044.3	252	gaG/gaT	1/8	0.251269289974746	3	FACETS	1	0.91	1	0.5	0.455	0.548	CLONAL	1	TRUE	1	0.251269289974746	3		1084	1289	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0038345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	210	734	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.461588061959249	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.461588061959249	1		734	606	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181346	123181346	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038345-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	43	66	0	ENST00000218089.9:c.810G>T	p.Lys270Asn	p.K270N	ENST00000218089	NM_001042749.1	270	aaG/aaT	9/35	1	2	FACETS	0.817	0.69	0.955	0.817	0.69	0.955	CLONAL	1	TRUE	1	0.461588061959249	2		66	228	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0038371-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	266	868	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.530319014636605	5	FACETS	1	0.964	1	1	0.964	1	CLONAL	3	TRUE	2	0.530319014636605	5		869	586	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974696	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs730881673	NA	P-0038371-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	187	459	0	ENST00000304494.5:c.131dup	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	tac/taAc	1/3	0.160246108852148	5	FACETS	1	0.979	1	0.754	0.701	0.808	INDETERMINATE	2	TRUE	2	0.530319014636605	5		459	560	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81971404	81971404	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038371-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	46	465	0	ENST00000359376.3:c.3094G>C	p.Gly1032Arg	p.G1032R	ENST00000359376	NM_002661.3	1032	Ggg/Cgg	28/33	0.32225220853205	3	FACETS	0.452	0.38	0.53	0.226	0.19	0.265	SUBCLONAL	1	TRUE	1	0.530319014636605	3		465	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876660825	NA	P-0038371-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	305	613	0	ENST00000269305.4:c.569C>G	p.Pro190Arg	p.P190R	ENST00000269305	NM_001126112.2	190	cCt/cGt	6/11	0.530319014636605	2	FACETS	0.967	0.921	1	0.967	0.921	1	CLONAL	2	TRUE	0	0.530319014636605	2		613	595	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257170	16257170	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038371-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	60	235	0	ENST00000375759.3:c.4435G>A	p.Asp1479Asn	p.D1479N	ENST00000375759	NM_015001.2	1479	Gat/Aat	11/15	0.430188085298873	5	FACETS	1	0.867	1	0.334	0.289	0.384	CLONAL	1	TRUE	2	0.530319014636605	5		235	405	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584543	48584544	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0038371-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	175	385	0	ENST00000342988.3:c.717_718del	p.Gln239HisfsTer24	p.Q239Hfs*24	ENST00000342988	NM_005359.5	239	cAG/c	6/12	0.515796633492568	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	2	TRUE	0	0.530319014636605	2		385	323	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566300	141566300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038371-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	130	368	1	ENST00000220592.5:c.1112C>T	p.Ser371Leu	p.S371L	ENST00000220592	NM_012154.3	371	tCg/tTg	9/19	0.520111862686068	6	FACETS	0.819	0.745	0.896	0.409	0.372	0.448	CLONAL	2	TRUE	2	0.530319014636605	6		369	617	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971192	21971193	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	GCCCATCATC	novel	NA	P-0038371-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	95	401	0	ENST00000579755.1:c.199_208dup	p.Gln70ArgfsTer2	p.Q70Rfs*2	ENST00000579755		70	cag/cGATGATGGGCag	2/3	0.160246108852148	5	FACETS	1	0.97	1	0.416	0.371	0.463	INDETERMINATE	1	TRUE	2	0.530319014636605	5		401	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	558	496	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.827846792642491	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.837752061537633	2		496	656	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30103666	30103666	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1434071220	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	44	390	0	ENST00000331968.5:c.1272G>A	p.Met424Ile	p.M424I	ENST00000331968	NM_002742.2	424	atG/atA	8/18	0.837752061537633	3	FACETS	0.213	0.178	0.252	0.106	0.089	0.126	SUBCLONAL	1	TRUE	1	0.837752061537633	3		390	701	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435374	18435374	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs369286185	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	126	222	0	ENST00000266497.5:c.359C>A	p.Thr120Lys	p.T120K	ENST00000266497		120	aCg/aAg	1/31	0.837752061537633	3	FACETS	1	0.938	1	0.517	0.472	0.563	CLONAL	1	TRUE	1	0.837752061537633	3		222	413	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229346	36229346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1452431678	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	83	422	4	ENST00000222270.7:c.8036G>A	p.Arg2679His	p.R2679H	ENST00000222270	NM_014727.1	2679	cGc/cAc	37/37	0.210544168587614	5	FACETS	0.534	0.47	0.602	0.107	0.094	0.121	INDETERMINATE	1	TRUE	0	0.837752061537633	5		426	838	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266446	55266446	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	383	420	0	ENST00000275493.2:c.2738A>T	p.Lys913Met	p.K913M	ENST00000275493	NM_005228.3	913	aAg/aTg	23/28	0.395079163838025	3	FACETS	1	0.99	1	0.718	0.692	0.745	INDETERMINATE	2	TRUE	0	0.837752061537633	3		420	602	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076752	72076752	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	457	413	0	ENST00000357731.5:c.745G>T	p.Gly249Cys	p.G249C	ENST00000357731	NM_173808.2	249	Ggt/Tgt	5/7	0.611826112763529	4	FACETS	0.913	0.881	0.944	0.913	0.881	0.944	CLONAL	3	TRUE	1	0.837752061537633	4		413	732	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396362	139396362	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	610	575	0	ENST00000277541.6:c.5476G>T	p.Glu1826Ter	p.E1826*	ENST00000277541	NM_017617.3	1826	Gag/Tag	30/34	0.827846792642491	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.837752061537633	2		575	715	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322688	39322688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	532	364	0	ENST00000373001.3:c.304G>A	p.Asp102Asn	p.D102N	ENST00000373001	NM_022157.3	102	Gat/Aat	2/7	0.837752061537633	5	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	2	0.837752061537633	5		364	851	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161293439	161293439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	130	240	0	ENST00000367975.2:c.56G>A	p.Ser19Asn	p.S19N	ENST00000367975	NM_003001.3	19	aGc/aAc	2/6	0.837752061537633	5	FACETS	0.748	0.678	0.822	0.187	0.169	0.206	SUBCLONAL	1	TRUE	1	0.837752061537633	5		240	936	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724418	162724418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1261100286	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	149	279	0	ENST00000367921.3:c.190G>A	p.Asp64Asn	p.D64N	ENST00000367921	NM_006182.2	64	Gac/Aac	5/18	0.837752061537633	5	FACETS	0.944	0.863	1	0.236	0.215	0.258	CLONAL	1	TRUE	1	0.837752061537633	5		279	850	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748457	162748457	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	620	276	0	ENST00000367921.3:c.2371C>A	p.Gln791Lys	p.Q791K	ENST00000367921	NM_006182.2	791	Cag/Aag	17/18	0.837752061537633	5	FACETS	1	0.976	1	1	0.976	1	CLONAL	4	TRUE	1	0.837752061537633	5		276	834	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136180	64136180	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	477	506	0	ENST00000334205.4:c.1339G>A	p.Glu447Lys	p.E447K	ENST00000334205	NM_003942.2	447	Gag/Aag	12/17	0.837752061537633	3	FACETS	0.768	0.737	0.799			1	SUBCLONAL	2	TRUE	NA	0.837752061537633	3		506	1052	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022660	12022660	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	201	414	0	ENST00000396373.4:c.766T>G	p.Ser256Ala	p.S256A	ENST00000396373	NM_001987.4	256	Tcc/Gcc	5/8	0.837752061537633	3	FACETS	0.929	0.864	0.996	0.464	0.432	0.498	CLONAL	1	TRUE	1	0.837752061537633	3		414	733	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865807	57865807	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	189	470	0	ENST00000228682.2:c.3284T>C	p.Leu1095Pro	p.L1095P	ENST00000228682	NM_005269.2	1095	cTa/cCa	12/12	0.640713099444171	3	FACETS	0.879	0.815	0.946			1	CLONAL	1	TRUE	NA	0.837752061537633	3		470	728	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557717	21557717	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	628	538	0	ENST00000382592.4:c.2128del	p.Val710TrpfsTer35	p.V710Wfs*35	ENST00000382592	NM_014572.2	710	Gtg/tg	5/8	0.80672014992992	4	FACETS	1	0.993	1			1	CLONAL	2	TRUE	NA	0.837752061537633	4		538	1263	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436355	110436355	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	383	361	0	ENST00000375856.3:c.2046C>G	p.Ser682Arg	p.S682R	ENST00000375856	NM_003749.2	682	agC/agG	1/2	0.827846792642491	2	FACETS	0.969	0.942	0.994	0.969	0.942	0.994	CLONAL	2	TRUE	0	0.837752061537633	2		361	472	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093394	30093394	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	273	365	0	ENST00000331968.5:c.1869A>T	p.Gln623His	p.Q623H	ENST00000331968	NM_002742.2	623	caA/caT	13/18	0.837752061537633	3	FACETS	0.907	0.862	0.951	0.907	0.862	0.951	CLONAL	2	TRUE	1	0.837752061537633	3		365	510	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669547	88669547	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	171	323	0	ENST00000360948.2:c.1351G>T	p.Val451Phe	p.V451F	ENST00000360948	NM_001012338.2	451	Gtc/Ttc	12/19	1	2	FACETS	0.911	0.847	0.977	0.911	0.847	0.977	CLONAL	1	TRUE	1	0.837752061537633	2		323	448	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348068	89348068	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	695	716	1	ENST00000301030.4:c.4882G>A	p.Asp1628Asn	p.D1628N	ENST00000301030	NM_001256183.1	1628	Gac/Aac	9/13	0.789071752811808	4	FACETS	0.936	0.904	0.969	0.936	0.904	0.969	CLONAL	2	TRUE	2	0.837752061537633	4		717	1628	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677824	58677824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	525	522	2	ENST00000305921.3:c.49G>A	p.Gly17Arg	p.G17R	ENST00000305921	NM_003620.3	17	Ggg/Agg	1/6	0.789071752811808	4	FACETS	0.908	0.871	0.944	0.908	0.871	0.944	CLONAL	2	TRUE	2	0.837752061537633	4		524	1269	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223020	1223020	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	1155	547	0	ENST00000326873.7:c.957del	p.Val320CysfsTer16	p.V320Cfs*16	ENST00000326873	NM_000455.4	319	ccA/cc	8/10	0.829338010754804	4	FACETS	0.98	0.968	0.991	0.98	0.968	0.991	CLONAL	4	TRUE	0	0.837752061537633	4		547	1293	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152016	11152016	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	563	409	0	ENST00000358026.2:c.4300G>T	p.Glu1434Ter	p.E1434*	ENST00000358026	NM_001128849.1	1434	Gag/Tag	31/36	0.825227832642383	3	FACETS	0.966	0.947	0.984	0.966	0.947	0.984	CLONAL	3	TRUE	0	0.837752061537633	3		409	658	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292444	15292444	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	919	578	0	ENST00000263388.2:c.2735G>T	p.Cys912Phe	p.C912F	ENST00000263388	NM_000435.2	912	tGc/tTc	17/33	0.825227832642383	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	3	TRUE	0	0.837752061537633	3		578	1026	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279578	18279578	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	815	580	0	ENST00000222254.8:c.1851C>A	p.His617Gln	p.H617Q	ENST00000222254	NM_005027.3	617	caC/caA	15/16	0.825227832642383	3	FACETS	0.987	0.972	1	0.987	0.972	1	CLONAL	3	TRUE	0	0.837752061537633	3		580	932	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498270	29498270	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	269	326	1	ENST00000389048.3:c.1910C>A	p.Thr637Asn	p.T637N	ENST00000389048	NM_004304.4	637	aCc/aAc	10/29	0.313912491481099	5	FACETS	1	0.985	1	0.742	0.701	0.784	INDETERMINATE	2	TRUE	2	0.837752061537633	5		327	651	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739118	40739118	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	389	374	0	ENST00000373198.4:c.3166C>T	p.His1056Tyr	p.H1056Y	ENST00000373198	NM_133170.3	1056	Cat/Tat	24/32	0.487277303970928	6	FACETS	0.892	0.851	0.933	0.892	0.851	0.933	INDETERMINATE	3	TRUE	3	0.837752061537633	6		374	929	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143043301	143043301	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	62	234	0	ENST00000262992.4:c.2115G>T	p.Leu705Phe	p.L705F	ENST00000262992	NM_001101669.1	705	ttG/ttT	19/24	0.179574089149004	4	FACETS	0.699	0.606	0.799			1	INDETERMINATE	1	TRUE	NA	0.837752061537633	4		234	389	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628987	187628987	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	75	344	0	ENST00000441802.2:c.1995del	p.Ser666ValfsTer5	p.S666Vfs*5	ENST00000441802	NM_005245.3	665	gcC/gc	2/27	0.837752061537633	1	FACETS	0.776	0.706	0.846	0.776	0.706	0.846	SUBCLONAL	1	TRUE	0	0.837752061537633	1		344	134	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278821	1278821	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150819225	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1441	478	496	0	ENST00000310581.5:c.2221G>A	p.Val741Met	p.V741M	ENST00000310581	NM_198253.2	741	Gtg/Atg	6/16	0.837752061537633	6	FACETS	0.796	0.758	0.834	0.398	0.379	0.417	SUBCLONAL	2	TRUE	2	0.837752061537633	6		496	1919	SUCCESS
APC	324	MSKCC	GRCh37	5	112176343	112176343	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	84	271	0	ENST00000257430.4:c.5052T>A	p.Phe1684Leu	p.F1684L	ENST00000257430	NM_000038.5	1684	ttT/ttA	16/16	NA	2	FACETS	0.689	0.616	0.766			1	INDETERMINATE	1	TRUE	NA	0.837752061537633	2		271	291	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449859	149449859	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	307	580	0	ENST00000286301.3:c.1205C>T	p.Pro402Leu	p.P402L	ENST00000286301	NM_005211.3	402	cCa/cTa	9/22	0.453198351136675	1	FACETS	0.646	0.614	0.679	0.646	0.614	0.679	INDETERMINATE	1	TRUE	0	0.837752061537633	1		580	659	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497230	149497231	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	193	526	0	ENST00000261799.4:c.3087dup	p.Pro1030ThrfsTer5	p.P1030Tfs*5	ENST00000261799	NM_002609.3	1029	-/A	22/23	0.453198351136675	1	FACETS	0.45	0.419	0.482	0.45	0.419	0.482	INDETERMINATE	1	TRUE	0	0.837752061537633	1		526	595	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158731	26158731	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	453	337	1	ENST00000289316.2:c.334G>T	p.Val112Leu	p.V112L	ENST00000289316	NM_138720.2	112	Gtg/Ttg	1/2	0.789071752811808	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	2	0.837752061537633	4		338	909	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041184	112041184	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	187	346	0	ENST00000368678.4:c.71A>G	p.Gln24Arg	p.Q24R	ENST00000368678		24	cAg/cGg	3/13	1	2	FACETS	0.869	0.809	0.929	0.869	0.809	0.929	CLONAL	1	TRUE	1	0.837752061537633	2		346	514	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923478	36923478	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038524-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	483	474	0	ENST00000358127.4:c.784A>G	p.Thr262Ala	p.T262A	ENST00000358127	NM_001280556.1	262	Aca/Gca	7/10	0.827846792642491	2	FACETS	0.996	0.973	1	0.996	0.973	1	CLONAL	2	TRUE	0	0.837752061537633	2		474	579	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	158	402	6	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.39224565417115	2		408	554	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	149	291	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	1	0.985	1	1	0.993	1	CLONAL	2	FALSE	1	0.39224565417115	2		292	308	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	135	572	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.39224565417115	1	FACETS	0.981	0.896	1	0.981	0.896	1	CLONAL	1	FALSE	0	0.39224565417115	1		578	564	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	95	415	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	FALSE	1	0.39224565417115	2		415	443	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	232	735	15	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	0.39224565417115	1	FACETS	0.88	0.829	0.933	1	0.994	1	CLONAL	2	FALSE	0	0.39224565417115	1		750	540	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	38	506	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.427	0.353	0.51	0.427	0.353	0.51	SUBCLONAL	1	FALSE	1	0.39224565417115	2		506	454	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	93	395	2	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.39224565417115	2		397	378	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	140	692	4	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.39224565417115	2		696	637	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524612	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs752661599	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	132	314	7	ENST00000355739.4:c.2751del	p.Lys917AsnfsTer65	p.K917Nfs*65	ENST00000355739	NM_000123.3	915	Aaa/aa	13/15	0.0996888155498346	3	FACETS	0.856	0.783	0.933	0.856	0.783	0.933	INDETERMINATE	2	FALSE	1	0.39224565417115	3		321	470	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339492	339492	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764818271	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	83	754	1	ENST00000262320.3:c.2410G>A	p.Ala804Thr	p.A804T	ENST00000262320	NM_003502.3	804	Gct/Act	10/11	1	2	FACETS	0.638	0.563	0.719	0.638	0.563	0.719	SUBCLONAL	1	FALSE	1	0.39224565417115	2		755	663	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099080	157099080	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	28	116	0	ENST00000346085.5:c.17G>C	p.Gly6Ala	p.G6A	ENST00000346085	NM_020732.3	6	gGc/gCc	1/20	0.114361146037633	3	FACETS	0.746	0.599	0.911	0.249	0.199	0.304	INDETERMINATE	1	FALSE	0	0.39224565417115	3		116	229	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306550	41306550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760520624	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	104	553	0	ENST00000373198.4:c.1109C>T	p.Thr370Met	p.T370M	ENST00000373198	NM_133170.3	370	aCg/aTg	7/32	0.39224565417115	1	FACETS	0.861	0.775	0.952	0.861	0.775	0.952	CLONAL	1	FALSE	0	0.39224565417115	1		553	495	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058747	180058748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755445139	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	115	986	1	ENST00000261937.6:c.89dup	p.Thr31AspfsTer15	p.T31Dfs*15	ENST00000261937	NM_182925.4	30	ccg/ccCg	2/30	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.39224565417115	2		987	536	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519505	137519506	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs780346130	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	128	327	6	ENST00000367739.4:c.1132_1133del	p.Ser378PhefsTer6	p.S378Ffs*6	ENST00000367739	NM_000416.2	378	AGt/t	7/7	0.114361146037633	3	FACETS	1	0.931	1	0.679	0.622	0.738	INDETERMINATE	2	FALSE	0	0.39224565417115	3		333	383	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512402	38512402	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	111	600	5	ENST00000254066.5:c.1319del	p.Pro440ArgfsTer203	p.P440Rfs*203	ENST00000254066	NM_000964.3	438	gCc/gc	9/9	0.39224565417115	1	FACETS	0.914	0.825	1	0.914	0.825	1	CLONAL	1	FALSE	0	0.39224565417115	1		605	498	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73337684	73337684	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771690280	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	79	259	3	ENST00000377767.4:c.2032del	p.Ile678PhefsTer59	p.I678Ffs*59	ENST00000377767	NM_014953.3	678	Att/tt	16/21	0.0996888155498346	3	FACETS	0.842	0.749	0.94	0.842	0.749	0.94	INDETERMINATE	2	FALSE	1	0.39224565417115	3		262	286	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56348561	56348561	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	85	320	0	ENST00000348428.3:c.374del	p.Pro125GlnfsTer3	p.P125Qfs*3	ENST00000348428	NM_006785.3	123	agC/ag	2/17	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.39224565417115	2		320	334	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349353	73349353	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1026175478	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	83	271	0	ENST00000377767.4:c.983G>A	p.Arg328Gln	p.R328Q	ENST00000377767	NM_014953.3	328	cGa/cAa	6/21	0.0996888155498346	3	FACETS	0.793	0.707	0.884	0.793	0.707	0.884	INDETERMINATE	2	FALSE	1	0.39224565417115	3		271	319	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319442	11319442	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769877976	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	149	591	3	ENST00000361445.4:c.25G>A	p.Ala9Thr	p.A9T	ENST00000361445	NM_004958.3	9	Gcc/Acc	2/58	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.39224565417115	2		594	658	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	174	491	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.39224565417115	2		496	698	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141554344	141554345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs748399150	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	130	775	4	ENST00000220592.5:c.1806dup	p.Ala603ArgfsTer71	p.A603Rfs*71	ENST00000220592	NM_012154.3	602	-/C	14/19	0.39224565417115	3	FACETS	0.808	0.732	0.889	0.404	0.366	0.445	CLONAL	1	FALSE	1	0.39224565417115	3		779	981	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096133	2096133	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs763525759	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	132	609	0	ENST00000219066.1:c.374del	p.Pro125GlnfsTer12	p.P125Qfs*12	ENST00000219066	NM_002528.5	125	cCa/ca	2/6	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.39224565417115	2		609	549	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752695	42752695	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1366176199	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	155	648	5	ENST00000222329.4:c.1569del	p.Leu525SerfsTer6	p.L525Sfs*6	ENST00000222329	NM_006494.2	523	ggG/gg	4/4	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.39224565417115	2		653	630	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647657	3647657	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs774532876	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	169	818	5	ENST00000294008.3:c.1406del	p.Pro469HisfsTer4	p.P469Hfs*4	ENST00000294008	NM_032444.2	469	cCa/ca	7/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.39224565417115	2		823	702	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431874	49431874	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	129	635	0	ENST00000301067.7:c.9265del	p.Val3089TrpfsTer30	p.V3089Wfs*30	ENST00000301067	NM_003482.3	3089	Gtg/tg	34/54	0.0996888155498346	3	FACETS	1	0.981	1	0.65	0.591	0.712	INDETERMINATE	1	FALSE	1	0.39224565417115	3		635	605	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845397	151845397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779339485	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	353	613	0	ENST00000262189.6:c.13615G>A	p.Val4539Met	p.V4539M	ENST00000262189	NM_170606.2	4539	Gtg/Atg	52/59	0.39224565417115	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	FALSE	1	0.39224565417115	3		613	864	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	300	447	9	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	0.39224565417115	3	FACETS	1	0.976	1	1	0.995	1	CLONAL	3	FALSE	1	0.39224565417115	3		456	586	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38631981	38631981	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1255149646	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	128	506	0	ENST00000299084.4:c.471del	p.Gln158SerfsTer16	p.Q158Sfs*16	ENST00000299084	NM_152594.2	156	cTt/ct	5/7	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	1	0.39224565417115	2		506	569	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226716	2226716	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs747161883	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	125	503	0	ENST00000398665.3:c.4196C>A	p.Pro1399His	p.P1399H	ENST00000398665	NM_032482.2	1399	cCc/cAc	27/28	0.39224565417115	1	FACETS	0.991	0.902	1	0.991	0.902	1	CLONAL	1	FALSE	0	0.39224565417115	1		503	517	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022358	31022358	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1230703370	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	82	372	0	ENST00000375687.4:c.1843G>A	p.Ala615Thr	p.A615T	ENST00000375687	NM_015338.5	615	Gca/Aca	13/13	0.39224565417115	1	FACETS	0.994	0.884	1	0.994	0.884	1	CLONAL	1	FALSE	0	0.39224565417115	1		372	338	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964922	55964922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199982402	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	135	396	0	ENST00000263923.4:c.2315C>T	p.Ala772Val	p.A772V	ENST00000263923	NM_002253.2	772	gCg/gTg	16/30	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.39224565417115	2		396	547	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202603	67202603	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	123	574	0	ENST00000312629.5:c.1412A>T	p.Lys471Met	p.K471M	ENST00000312629	NM_003952.2	471	aAg/aTg	15/15	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	FALSE	1	0.39224565417115	2		574	617	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245726	46245726	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	92	490	0	ENST00000334344.6:c.3820G>T	p.Gly1274Ter	p.G1274*	ENST00000334344	NM_152641.2	1274	Gga/Tga	15/21	0.0996888155498346	3	FACETS	1	0.965	1	0.599	0.535	0.668	INDETERMINATE	1	FALSE	1	0.39224565417115	3		490	468	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857995	9857995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	118	553	0	ENST00000330684.3:c.3406G>A	p.Val1136Ile	p.V1136I	ENST00000330684	NM_001134407.1	1136	Gtt/Att	13/13	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	FALSE	1	0.39224565417115	2		553	594	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89354959	89354959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	186	607	2	ENST00000301030.4:c.721G>A	p.Ala241Thr	p.A241T	ENST00000301030	NM_001256183.1	241	Gct/Act	7/13	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.39224565417115	2		609	688	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15976751	15976751	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	96	480	0	ENST00000268712.3:c.3803C>T	p.Pro1268Leu	p.P1268L	ENST00000268712	NM_006311.3	1268	cCg/cTg	28/46	0.39224565417115	1	FACETS	0.848	0.759	0.942	0.848	0.759	0.942	CLONAL	1	FALSE	0	0.39224565417115	1		480	464	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439961	56439962	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	183	730	0	ENST00000407977.2:c.630dup	p.Val211CysfsTer48	p.V211Cfs*48	ENST00000407977		210	-/T	6/10	0.39224565417115	1	FACETS	0.917	0.847	0.989	0.917	0.847	0.989	CLONAL	1	FALSE	0	0.39224565417115	1		730	818	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622325	1622325	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	126	680	0	ENST00000344749.5:c.639del	p.Phe214SerfsTer70	p.F214Sfs*70	ENST00000344749	NM_001136139.2	213	ccC/cc	9/19	0.39224565417115	1	FACETS	0.997	0.907	1	0.997	0.907	1	CLONAL	1	FALSE	0	0.39224565417115	1		680	518	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277996	18277996	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs919917611	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	153	622	1	ENST00000222254.8:c.1616G>A	p.Arg539His	p.R539H	ENST00000222254	NM_005027.3	539	cGc/cAc	13/16	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.39224565417115	2		623	582	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214660	36214660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	119	596	1	ENST00000222270.7:c.3086C>T	p.Pro1029Leu	p.P1029L	ENST00000222270	NM_014727.1	1029	cCc/cTc	8/37	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.39224565417115	2		597	476	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797393	42797393	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	156	750	0	ENST00000575354.2:c.3755C>A	p.Pro1252His	p.P1252H	ENST00000575354	NM_015125.3	1252	cCt/cAt	15/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.39224565417115	2		750	653	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47735829	47735829	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	128	631	0	ENST00000449228.1:c.31T>C	p.Cys11Arg	p.C11R	ENST00000449228	NM_001127240.2	11	Tgt/Cgt	1/4	1	2	FACETS	0.874	0.793	0.959	0.874	0.793	0.959	CLONAL	1	FALSE	1	0.39224565417115	2		631	747	SUCCESS
ATR	545	MSKCC	GRCh37	3	142180827	142180827	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	80	379	0	ENST00000350721.4:c.7147A>G	p.Thr2383Ala	p.T2383A	ENST00000350721	NM_001184.3	2383	Act/Gct	42/47	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	FALSE	1	0.39224565417115	2		379	396	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542676	187542676	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754770963	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	108	399	0	ENST00000441802.2:c.5064G>A	p.Met1688Ile	p.M1688I	ENST00000441802	NM_005245.3	1688	atG/atA	10/27	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.39224565417115	2		399	433	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755737	57755738	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	152	584	1	ENST00000274289.3:c.49dup	p.Met17AsnfsTer89	p.M17Nfs*89	ENST00000274289	NM_006622.3	17	atg/aAtg	1/14	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.39224565417115	2		585	682	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27168504	27168504	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	100	418	0	ENST00000380036.4:c.376C>T	p.Pro126Ser	p.P126S	ENST00000380036	NM_000459.3	126	Cca/Tca	3/23	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.39224565417115	2		418	459	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400056	139400056	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	195	780	1	ENST00000277541.6:c.4292G>A	p.Ser1431Asn	p.S1431N	ENST00000277541	NM_017617.3	1431	aGc/aAc	25/34	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.39224565417115	2		781	674	SUCCESS
BTK	695	MSKCC	GRCh37	X	100629610	100629610	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	79	402	0	ENST00000308731.7:c.154A>G	p.Lys52Glu	p.K52E	ENST00000308731	NM_000061.2	52	Aag/Gag	3/19	0.39224565417115	1	FACETS	0.857	0.758	0.961	0.857	0.758	0.961	CLONAL	1	FALSE	0	0.39224565417115	1		402	378	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427251	49427253	+	inframe_deletion	In_Frame_Del	DEL	TGC	TGC	-	rs760816616	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	109	659	2	ENST00000301067.7:c.11235_11237del	p.Gln3745del	p.Q3745del	ENST00000301067	NM_003482.3	3745	caGCAc/cac	39/54	0.0996888155498346	3	FACETS	1	0.984	1	0.747	0.675	0.822	INDETERMINATE	1	FALSE	1	0.39224565417115	3		661	445	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435845	56435845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746548389	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	35	564	1	ENST00000407977.2:c.1292G>A	p.Cys431Tyr	p.C431Y	ENST00000407977		431	tGc/tAc	9/10	0.39224565417115	1	FACETS	0.315	0.257	0.379	0.315	0.257	0.379	SUBCLONAL	1	FALSE	0	0.39224565417115	1		565	456	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935598	49935598	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	39	723	0	ENST00000296474.3:c.1766T>C	p.Leu589Pro	p.L589P	ENST00000296474	NM_002447.2	589	cTg/cCg	5/20	1	2	FACETS	0.342	0.283	0.409	0.342	0.283	0.409	SUBCLONAL	1	FALSE	1	0.39224565417115	2		723	581	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31511140	31511140	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0038612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	49	527	0	ENST00000344624.3:c.1432+2T>C		p.X478_splice	ENST00000344624		478			1	2	FACETS	0.384	0.324	0.449	0.384	0.324	0.449	SUBCLONAL	1	FALSE	1	0.39224565417115	2		527	651	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593607	55593615	+	inframe_deletion	In_Frame_Del	DEL	AGGTTGTTG	AGGTTGTTG	-	novel	NA	P-0038762-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	24	516	0	ENST00000288135.5:c.1676_1684del	p.Val559_Glu561del	p.V559_E561del	ENST00000288135	NM_000222.2	558	aAGGTTGTTGag/aag	11/21	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		516	679	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481657	40481657	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038762-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	48	542	1	ENST00000264657.5:c.1148A>T	p.Lys383Ile	p.K383I	ENST00000264657	NM_139276.2	383	aAa/aTa	13/24	1	2	FACETS		NA	1			1	NA	NA	TRUE	1	NA	2		543	895	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0038821-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	58	242	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.713	0.613	0.823	0.713	0.613	0.823	SUBCLONAL	1	TRUE	1	0.28	2		242	581	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207021	1207021	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913324	NA	P-0038821-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	88	847	0	ENST00000326873.7:c.109C>T	p.Gln37Ter	p.Q37*	ENST00000326873	NM_000455.4	37	Cag/Tag	1/10	0.297963605381932	1	FACETS	0.665	0.588	0.747	0.665	0.588	0.747	SUBCLONAL	1	TRUE	0	0.28	1		847	813	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602493	10602493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038821-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	79	794	0	ENST00000171111.5:c.1085G>A	p.Arg362Gln	p.R362Q	ENST00000171111	NM_203500.1	362	cGg/cAg	3/6	0.297963605381932	1	FACETS	0.73	0.642	0.824	0.73	0.642	0.824	SUBCLONAL	1	TRUE	0	0.28	1		794	665	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180037025	180037025	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038821-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	54	533	2	ENST00000261937.6:c.3687G>T	p.Arg1229Ser	p.R1229S	ENST00000261937	NM_182925.4	1229	agG/agT	28/30	0.298334411370272	1	FACETS	0.532	0.453	0.617	0.532	0.453	0.617	SUBCLONAL	1	TRUE	0	0.28	1		535	624	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009287	69009287	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038821-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	135	389	0	ENST00000288368.4:c.2404G>C	p.Asp802His	p.D802H	ENST00000288368	NM_024870.2	802	Gat/Cat	22/40	0.270909423753304	3	FACETS	0.878	0.8	0.959	0.878	0.8	0.959	CLONAL	2	TRUE	1	0.28	3		389	626	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486014	8486014	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs375803455	NA	P-0038821-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	51	435	0	ENST00000356435.5:c.2803G>T	p.Val935Phe	p.V935F	ENST00000356435		935	Gtc/Ttc	17/35	1	2	FACETS	0.673	0.572	0.784	0.673	0.572	0.784	SUBCLONAL	1	TRUE	1	0.28	2		435	541	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0038955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	627	785	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.557273674323685	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.557273674323685	1		785	1282	SUCCESS
APC	324	MSKCC	GRCh37	5	112175480	112175481	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0038955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	151	235	0	ENST00000257430.4:c.4192_4193del	p.Arg1399PhefsTer9	p.R1399Ffs*9	ENST00000257430	NM_000038.5	1397	GAg/g	16/16	0.557273674323685	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.557273674323685	1		235	359	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856595	111856595	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1454335466	NA	P-0038955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	20	183	0	ENST00000341259.2:c.646C>T	p.Arg216Cys	p.R216C	ENST00000341259	NM_005475.2	216	Cgc/Tgc	2/8	0.368351898737481	1	FACETS	0.141	0.107	0.181	0.141	0.107	0.181	SUBCLONAL	1	TRUE	0	0.557273674323685	1		183	367	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775932	9775932	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	286	700	1	ENST00000377346.4:c.396C>A	p.Cys132Ter	p.C132*	ENST00000377346	NM_005026.3	132	tgC/tgA	5/24	0.557273674323685	1	FACETS	0.872	0.823	0.923	0.872	0.823	0.923	CLONAL	1	TRUE	0	0.557273674323685	1		701	849	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829700	72829700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	239	621	0	ENST00000268489.5:c.6881G>A	p.Arg2294Gln	p.R2294Q	ENST00000268489	NM_006885.3	2294	cGa/cAa	9/10	1	2	FACETS	0.855	0.799	0.913	0.855	0.799	0.913	CLONAL	1	TRUE	1	0.557273674323685	2		621	1003	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414908	56414908	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0038955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	113	458	0	ENST00000348428.3:c.2309A>G	p.Asn770Ser	p.N770S	ENST00000348428	NM_006785.3	770	aAt/aGt	17/17	0.30633473819097	0	FACETS	0.314	0.284	0.347			1	INDETERMINATE	1	TRUE	0	0.557273674323685	0		458	571	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177789	56177789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1486203483	NA	P-0038955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	55	277	0	ENST00000399503.3:c.2762G>A	p.Ser921Asn	p.S921N	ENST00000399503	NM_005921.1	921	aGt/aAt	14/20	0.421418762528021	1	FACETS	0.376	0.322	0.434	0.376	0.322	0.434	SUBCLONAL	1	TRUE	0	0.557273674323685	1		277	379	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79952261	79952261	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	140	300	0	ENST00000265081.6:c.269C>T	p.Pro90Leu	p.P90L	ENST00000265081	NM_002439.4	90	cCa/cTa	2/24	0.557273674323685	1	FACETS	0.835	0.767	0.905	0.835	0.767	0.905	CLONAL	1	TRUE	0	0.557273674323685	1		300	434	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522142	157522143	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0038955-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	191	570	0	ENST00000346085.5:c.4414_4415del	p.Pro1472LeufsTer37	p.P1472Lfs*37	ENST00000346085	NM_020732.3	1472	CCt/t	18/20	0.270054748553142	2	FACETS	0.974	0.903	1	0.487	0.451	0.523	INDETERMINATE	1	TRUE	0	0.557273674323685	2		570	704	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039163-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	179	868	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.204154421478056	2	FACETS	1	0.989	1	0.703	0.651	0.756	INDETERMINATE	1	TRUE	0	0.423207708195884	2		869	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0039163-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	155	605	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.423207708195884	1	FACETS	0.924	0.849	1	0.924	0.849	1	CLONAL	1	TRUE	0	0.423207708195884	1		605	625	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0039163-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	83	344	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	0.95	0.843	1	0.95	0.843	1	CLONAL	1	TRUE	1	0.423207708195884	2		344	413	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542109	187542110	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1560943587	NA	P-0039163-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	23	391	0	ENST00000441802.2:c.5630dup	p.Val1878CysfsTer8	p.V1878Cfs*8	ENST00000441802	NM_005245.3	1877	cct/ccCt	10/27	0.389735190985375	1	FACETS	0.209	0.162	0.263	0.209	0.162	0.263	SUBCLONAL	1	TRUE	0	0.423207708195884	1		391	410	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs770248150	NA	P-0039163-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	25	471	0	ENST00000311936.3:c.351A>T	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaT	4/5	0.204154421478056	2	FACETS	0.196	0.154	0.245	0.098	0.077	0.123	INDETERMINATE	1	TRUE	0	0.423207708195884	2		471	603	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034471	47034471	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039163-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	35	422	0	ENST00000377604.3:c.556C>T	p.Arg186Ter	p.R186*	ENST00000377604	NM_001204468.1	186	Cga/Tga	6/24	0.423207708195884	2	FACETS	0.271	0.221	0.327			1	SUBCLONAL	1	TRUE	NA	0.423207708195884	2		422	610	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110129	8110130	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs745673717	NA	P-0039163-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	40	637	0	ENST00000585124.1:c.475dup	p.Arg159ProfsTer15	p.R159Pfs*15	ENST00000585124	NM_004217.3	159	cgc/cCgc	6/9	0.423207708195884	1	FACETS	0.26	0.215	0.31	0.26	0.215	0.31	SUBCLONAL	1	TRUE	0	0.423207708195884	1		637	573	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748660	43748661	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039163-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	53	879	1	ENST00000382044.4:c.2145dup	p.Glu716ArgfsTer9	p.E716Rfs*9	ENST00000382044	NM_001141980.1	715	-/A	12/28	0.423207708195884	1	FACETS	0.197	0.167	0.23	0.197	0.167	0.23	SUBCLONAL	1	TRUE	0	0.423207708195884	1		880	1002	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158525	26158525	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1222808686	NA	P-0039163-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	31	591	0	ENST00000289316.2:c.128A>G	p.Tyr43Cys	p.Y43C	ENST00000289316	NM_138720.2	43	tAc/tGc	1/2	0.423207708195884	1	FACETS	0.193	0.155	0.235	0.193	0.155	0.235	SUBCLONAL	1	TRUE	0	0.423207708195884	1		591	600	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994829	73994829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751833994	NA	P-0039163-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	15	276	1	ENST00000318443.5:c.313G>A	p.Ala105Thr	p.A105T	ENST00000318443	NM_001024736.1	105	Gca/Aca	3/10	0.423207708195884	1	FACETS	0.195	0.142	0.259	0.195	0.142	0.259	SUBCLONAL	1	TRUE	0	0.423207708195884	1		277	286	SUCCESS
APC	324	MSKCC	GRCh37	5	112137078	112137078	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1554076217	NA	P-0039163-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	67	401	0	ENST00000257430.4:c.832C>T	p.Gln278Ter	p.Q278*	ENST00000257430	NM_000038.5	278	Cag/Tag	8/16	1	2	FACETS	0.704	0.613	0.801	0.704	0.613	0.801	SUBCLONAL	1	TRUE	1	0.423207708195884	2		401	450	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453987	140453987	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs180177040	NA	P-0039163-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	18	308	0	ENST00000288602.6:c.1741A>C	p.Asn581His	p.N581H	ENST00000288602	NM_004333.4	581	Aat/Cat	14/18	0.218167581155801	3	FACETS	0.274	0.206	0.355	0.137	0.103	0.178	INDETERMINATE	1	TRUE	1	0.423207708195884	3		308	376	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412602	63412602	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039163-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	225	308	0	ENST00000330258.3:c.565C>T	p.Gln189Ter	p.Q189*	ENST00000330258	NM_152424.3	189	Caa/Taa	2/2	0.423207708195884	2	FACETS	1	0.987	1			1	CLONAL	2	TRUE	NA	0.423207708195884	2		308	456	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786733	3786734	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039163-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	164	699	0	ENST00000262367.5:c.4477dup	p.Ile1493AsnfsTer26	p.I1493Nfs*26	ENST00000262367	NM_004380.2	1493	ata/aAta	27/31	0.218167581155801	3	FACETS	0.919	0.843	0.998	0.459	0.421	0.499	INDETERMINATE	1	TRUE	1	0.423207708195884	3		699	1022	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118954	70118954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555629169	NA	P-0039163-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	212	739	1	ENST00000245479.2:c.526C>T	p.Pro176Ser	p.P176S	ENST00000245479	NM_000346.3	176	Ccg/Tcg	2/3	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.423207708195884	2		740	893	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451151	70451151	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039163-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	35	733	0	ENST00000373644.4:c.5991T>A	p.Ser1997Arg	p.S1997R	ENST00000373644	NM_030625.2	1997	agT/agA	12/12	0.389735190985375	1	FACETS	0.188	0.153	0.227	0.188	0.153	0.227	SUBCLONAL	1	TRUE	0	0.423207708195884	1		733	693	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133208998	133208998	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039163-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	55	742	1	ENST00000320574.5:c.6233G>T	p.Arg2078Leu	p.R2078L	ENST00000320574	NM_006231.2	2078	cGg/cTg	45/49	0.204154421478056	2	FACETS	0.306	0.261	0.355	0.153	0.13	0.178	INDETERMINATE	1	TRUE	0	0.423207708195884	2		743	850	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72881585	72881586	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0039163-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	30	416	0	ENST00000325599.8:c.533dup	p.Ala179CysfsTer3	p.A179Cfs*3	ENST00000325599	NM_018130.2	178	cct/ccCt	5/11	0.34068757390404	1	FACETS	0.186	0.149	0.228	0.186	0.149	0.228	SUBCLONAL	1	TRUE	0	0.423207708195884	1		416	600	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295330	1295330	+	upstream_gene_variant	5'Flank	SNP	A	A	G	novel	NA	P-0039163-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	22	407	0				ENST00000310581	NM_198253.2	-/1132			0.423207708195884	1	FACETS	0.188	0.145	0.238	0.188	0.145	0.238	SUBCLONAL	1	TRUE	0	0.423207708195884	1		407	437	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030341	180030341	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039163-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	36	797	0	ENST00000261937.6:c.3943T>A	p.Ser1315Thr	p.S1315T	ENST00000261937	NM_182925.4	1315	Tcc/Acc	30/30	0.389735190985375	1	FACETS	0.188	0.154	0.226	0.188	0.154	0.226	SUBCLONAL	1	TRUE	0	0.423207708195884	1		797	714	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706869	117706869	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0039163-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	30	453	0	ENST00000368508.3:c.2281T>G	p.Tyr761Asp	p.Y761D	ENST00000368508	NM_002944.2	761	Tac/Gac	15/43	1	2	FACETS	0.241	0.193	0.295	0.241	0.193	0.295	SUBCLONAL	1	TRUE	1	0.423207708195884	2		453	589	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912301	97912301	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039163-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	37	565	0	ENST00000289081.3:c.590A>G	p.Asp197Gly	p.D197G	ENST00000289081	NM_000136.2	197	gAc/gGc	7/15	0.389735190985375	1	FACETS	0.206	0.169	0.248	0.206	0.169	0.248	SUBCLONAL	1	TRUE	0	0.423207708195884	1		565	668	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15840946	15840946	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039163-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	18	196	0	ENST00000307771.7:c.1030A>G	p.Arg344Gly	p.R344G	ENST00000307771	NM_005089.3	344	Aga/Gga	11/11	0.423207708195884	2	FACETS	0.247	0.186	0.32			1	SUBCLONAL	1	TRUE	NA	0.423207708195884	2		196	344	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932258	39932258	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039163-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	51	527	0	ENST00000378444.4:c.2341A>G	p.Thr781Ala	p.T781A	ENST00000378444	NM_001123385.1	781	Acc/Gcc	4/15	0.423207708195884	2	FACETS	0.315	0.267	0.369			1	SUBCLONAL	1	TRUE	NA	0.423207708195884	2		527	764	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028881	47028881	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039163-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	29	329	0	ENST00000377604.3:c.185A>G	p.Glu62Gly	p.E62G	ENST00000377604	NM_001204468.1	62	gAg/gGg	3/24	0.423207708195884	2	FACETS	0.279	0.223	0.342			1	SUBCLONAL	1	TRUE	NA	0.423207708195884	2		329	492	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347765	70347765	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039163-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	27	318	0	ENST00000374080.3:c.3004A>G	p.Asn1002Asp	p.N1002D	ENST00000374080		1002	Aac/Gac	22/45	0.423207708195884	2	FACETS	0.291	0.231	0.36			1	SUBCLONAL	1	TRUE	NA	0.423207708195884	2		318	438	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932045	36932045	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039163-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	39	712	0	ENST00000361632.4:c.2424G>T	p.Glu808Asp	p.E808D	ENST00000361632		808	gaG/gaT	16/16	0.34068757390404	1	FACETS	0.198	0.163	0.237	0.198	0.163	0.237	SUBCLONAL	1	TRUE	0	0.423207708195884	1		712	734	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0039163-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	73	868	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.693	0.607	0.786	0.693	0.607	0.786	SUBCLONAL	1	TRUE	1	0.376096131206573	2		869	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0039163-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	125	605	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	0.716	0.648	0.789	0.716	0.648	0.789	SUBCLONAL	1	TRUE	1	0.376096131206573	2		605	928	SUCCESS
APC	324	MSKCC	GRCh37	5	112175576	112175576	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs74535574	NA	P-0039163-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	78	344	0	ENST00000257430.4:c.4285C>T	p.Gln1429Ter	p.Q1429*	ENST00000257430	NM_000038.5	1429	Caa/Taa	16/16	1	2	FACETS	0.651	0.572	0.736	0.651	0.572	0.736	SUBCLONAL	1	TRUE	1	0.376096131206573	2		344	637	SUCCESS
APC	324	MSKCC	GRCh37	5	112137078	112137078	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1554076217	NA	P-0039163-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	44	401	0	ENST00000257430.4:c.832C>T	p.Gln278Ter	p.Q278*	ENST00000257430	NM_000038.5	278	Cag/Tag	8/16	1	2	FACETS	0.444	0.372	0.524	0.444	0.372	0.524	SUBCLONAL	1	TRUE	1	0.376096131206573	2		401	527	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412602	63412602	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0039163-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	141	308	0	ENST00000330258.3:c.565C>T	p.Gln189Ter	p.Q189*	ENST00000330258	NM_152424.3	189	Caa/Taa	2/2	0.278431818818812	2	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.376096131206573	2		308	536	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786733	3786734	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0039163-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	126	699	0	ENST00000262367.5:c.4477dup	p.Ile1493AsnfsTer26	p.I1493Nfs*26	ENST00000262367	NM_004380.2	1493	ata/aAta	27/31	0.110873566838567	3	FACETS	0.662	0.597	0.73	0.331	0.298	0.365	INDETERMINATE	1	TRUE	1	0.376096131206573	3		699	1203	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118954	70118954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555629169	NA	P-0039163-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	207	739	1	ENST00000245479.2:c.526C>T	p.Pro176Ser	p.P176S	ENST00000245479	NM_000346.3	176	Ccg/Tcg	2/3	0.110873566838567	3	FACETS	1	0.949	1	0.515	0.477	0.555	INDETERMINATE	1	TRUE	1	0.376096131206573	3		740	1269	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0039168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	322	632	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.443494595455917	3	FACETS	0.848	0.809	0.887	0.848	0.809	0.887	CLONAL	3	FALSE	0	0.510672163089676	3		632	622	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0039168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	886	339	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.510672163089676	15	FACETS	0.968	0.948	0.988			1	CLONAL	13	FALSE	NA	0.510672163089676	15		339	1191	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281304	15281304	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	117	757	0	ENST00000263388.2:c.4952C>A	p.Ala1651Asp	p.A1651D	ENST00000263388	NM_000435.2	1651	gCt/gAt	27/33	0.125164667197874	6	FACETS	1	0.964	1	0.383	0.345	0.423	INDETERMINATE	1	FALSE	3	0.510672163089676	6		757	807	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1920258	1920258	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039168-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	99	717	0	ENST00000382891.5:c.1318G>A	p.Gly440Arg	p.G440R	ENST00000382891	NM_133335.3	440	Ggg/Agg	5/22	0.510672163089676	3	FACETS	0.815	0.729	0.906	0.408	0.364	0.453	CLONAL	1	FALSE	1	0.510672163089676	3		717	597	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0039429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	267	676	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.64741710414963	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.64741710414963	1		676	520	SUCCESS
APC	324	MSKCC	GRCh37	5	112175760	112175760	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	90	303	0	ENST00000257430.4:c.4469del	p.His1490LeufsTer17	p.H1490Lfs*17	ENST00000257430	NM_000038.5	1490	cAt/ct	16/16	1	2	FACETS	0.903	0.81	0.999	0.903	0.81	0.999	CLONAL	1	TRUE	1	0.64741710414963	2		303	308	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229393	36229393	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	70	581	0	ENST00000222270.7:c.8083G>A	p.Glu2695Lys	p.E2695K	ENST00000222270	NM_014727.1	2695	Gag/Aag	37/37	1	2	FACETS	0.307	0.267	0.35	0.307	0.267	0.35	SUBCLONAL	1	TRUE	1	0.64741710414963	2		581	704	SUCCESS
APC	324	MSKCC	GRCh37	5	112173999	112173999	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0039429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	119	281	0	ENST00000257430.4:c.2708del	p.Asp903AlafsTer13	p.D903Afs*13	ENST00000257430	NM_000038.5	903	gAc/gc	16/16	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.64741710414963	2		281	352	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128305388	128305388	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0039429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	190	694	0	ENST00000265960.3:c.908A>T	p.Glu303Val	p.E303V	ENST00000265960	NM_001006617.1	303	gAa/gTa	7/12	1	2	FACETS	0.887	0.823	0.952	0.887	0.823	0.952	CLONAL	1	TRUE	1	0.64741710414963	2		694	662	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589168	67589168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0039608-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	57	342	0	ENST00000274335.5:c.1156C>T	p.Arg386Ter	p.R386*	ENST00000274335		386	Cga/Tga	9/15	0.317367298087725	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.317367298087725	1		342	285	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0039608-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	67	161	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	0.317367298087725	1	FACETS	0.757	0.66	0.862	0.757	0.66	0.862	SUBCLONAL	1	TRUE	0	0.317367298087725	1		161	469	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881000	37881000	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913471	NA	P-0039608-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	142	856	0	ENST00000269571.5:c.2329G>T	p.Val777Leu	p.V777L	ENST00000269571		777	Gtg/Ttg	20/27	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.317367298087725	2		856	864	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424695	49424695	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0039608-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	138	815	0	ENST00000301067.7:c.13652T>A	p.Leu4551Ter	p.L4551*	ENST00000301067	NM_003482.3	4551	tTg/tAg	40/54	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.317367298087725	2		815	758	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578448	7578449	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0039608-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	313	970	0	ENST00000269305.4:c.481_482del	p.Ala161HisfsTer19	p.A161Hfs*19	ENST00000269305	NM_001126112.2	161	GCc/c	5/11	0.313456140735939	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.317367298087725	2		970	980	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252723	10252723	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039608-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	99	826	0	ENST00000340748.4:c.3242A>G	p.Asn1081Ser	p.N1081S	ENST00000340748		1081	aAc/aGc	29/40	0.291938905624626	3	FACETS	0.809	0.722	0.903	0.405	0.361	0.452	CLONAL	1	TRUE	1	0.317367298087725	3		826	893	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678751	52678751	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039608-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	61	413	0	ENST00000394830.3:c.868C>A	p.His290Asn	p.H290N	ENST00000394830	NM_018313.4	290	Cat/Aat	9/30	1	2	FACETS	0.735	0.635	0.844	0.735	0.635	0.844	SUBCLONAL	1	TRUE	1	0.317367298087725	2		413	523	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86667956	86667957	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0039608-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	62	341	0	ENST00000274376.6:c.1721dup	p.Phe575IlefsTer8	p.F575Ifs*8	ENST00000274376	NM_002890.2	574	gca/gCca	13/25	0.317367298087725	1	FACETS	0.916	0.795	1	0.916	0.795	1	CLONAL	1	TRUE	0	0.317367298087725	1		341	359	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683755	162683755	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0039608-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	82	538	0	ENST00000366898.1:c.214A>G	p.Arg72Gly	p.R72G	ENST00000366898	NM_004562.2	72	Aga/Gga	3/12	0.261466948256119	3	FACETS	0.91	0.803	1	0.455	0.401	0.513	CLONAL	1	TRUE	1	0.317367298087725	3		538	658	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46725680	46725680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145938974	NA	P-0039612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	81	588	0	ENST00000371975.4:c.316C>T	p.Arg106Cys	p.R106C	ENST00000371975	NM_003579.3	106	Cgc/Tgc	5/18	0.523806331862174	1	FACETS	0.535	0.473	0.6	0.535	0.473	0.6	SUBCLONAL	1	TRUE	0	0.523806331862174	1		588	427	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81925189	81925189	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0039612-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	53	520	0	ENST00000359376.3:c.980A>T	p.His327Leu	p.H327L	ENST00000359376	NM_002661.3	327	cAt/cTt	11/33	0.116667423280398	3	FACETS	0.436	0.371	0.507	0.218	0.185	0.254	INDETERMINATE	1	TRUE	1	0.523806331862174	3		520	586	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579415	7579415	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0040160-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	419	650	0	ENST00000269305.4:c.272G>A	p.Trp91Ter	p.W91*	ENST00000269305	NM_001126112.2	91	tGg/tAg	4/11	0.354618627818973	3	FACETS	0.932	0.891	0.973	0.932	0.891	0.973	CLONAL	3	TRUE	0	0.354618627818973	3		650	995	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134494	30134494	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0040160-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	59	265	1	ENST00000263025.4:c.37G>T	p.Glu13Ter	p.E13*	ENST00000263025	NM_002746.2	13	Gag/Tag	1/9	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.354618627818973	2		266	330	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416376	49416376	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040160-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	49	401	1	ENST00000301067.7:c.16335G>T	p.Glu5445Asp	p.E5445D	ENST00000301067	NM_003482.3	5445	gaG/gaT	51/54	1	2	FACETS	0.601	0.509	0.701	0.601	0.509	0.701	SUBCLONAL	1	TRUE	1	0.354618627818973	2		402	460	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661970	227662245	+	inframe_deletion	In_Frame_Del	DEL	GGTGCAGCGGTGGCCATTGCCACCCCGAGACAAAATGTAGTGACCGTTGGGGGCGGTCAGGGTGGAGGGCCCCTTGCCACCCATGCAGATATAGTTGCTTAGCTCCTCCTCACCGCGGGCTGGTGGGGTGTGGCCCAGGGAATCCGGAGTGACACTGCGGAAGGAACTCCGGAAATCGCAGGGACTGGAGCCATACTCATCCGAGGAGATGAAACCGCCATCGCTGGGGGAACCAGACACCGAAGCACTAGATCGCCGTGGGAAGAGACAATCCGA	GGTGCAGCGGTGGCCATTGCCACCCCGAGACAAAATGTAGTGACCGTTGGGGGCGGTCAGGGTGGAGGGCCCCTTGCCACCCATGCAGATATAGTTGCTTAGCTCCTCCTCACCGCGGGCTGGTGGGGTGTGGCCCAGGGAATCCGGAGTGACACTGCGGAAGGAACTCCGGAAATCGCAGGGACTGGAGCCATACTCATCCGAGGAGATGAAACCGCCATCGCTGGGGGAACCAGACACCGAAGCACTAGATCGCCGTGGGAAGAGACAATCCGA	-	novel	NA	P-0040160-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	65	640	0	ENST00000305123.5:c.1210_1485del	p.Ser404_Thr495del	p.S404_T495del	ENST00000305123	NM_005544.2	404	TCGGATTGTCTCTTCCCACGGCGATCTAGTGCTTCGGTGTCTGGTTCCCCCAGCGATGGCGGTTTCATCTCCTCGGATGAGTATGGCTCCAGTCCCTGCGATTTCCGGAGTTCCTTCCGCAGTGTCACTCCGGATTCCCTGGGCCACACCCCACCAGCCCGCGGTGAGGAGGAGCTAAGCAACTATATCTGCATGGGTGGCAAGGGGCCCTCCACCCTGACCGCCCCCAACGGTCACTACATTTTGTCTCGGGGTGGCAATGGCCACCGCTGCACC/-	1/2	0.211157237242731	3	FACETS	0.569	0.492	0.652			1	INDETERMINATE	1	TRUE	NA	0.354618627818973	3		640	759	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140549937	140549937	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040160-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	51	357	0	ENST00000288602.6:c.214C>T	p.His72Tyr	p.H72Y	ENST00000288602	NM_004333.4	72	Cat/Tat	2/18	0.354618627818973	7	FACETS	0.704	0.597	0.822			1	SUBCLONAL	1	TRUE	NA	0.354618627818973	7		357	771	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38186916	38186916	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0040160-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	115	430	0	ENST00000317025.8:c.1561C>T	p.Gln521Ter	p.Q521*	ENST00000317025	NM_023034.1	521	Caa/Taa	6/24	0.294850128138999	2	FACETS	1	0.966	1	0.576	0.52	0.634	CLONAL	1	TRUE	0	0.354618627818973	2		430	563	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56922622	56922622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs62515392	NA	P-0040160-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	70	454	0	ENST00000519728.1:c.1492G>A	p.Asp498Asn	p.D498N	ENST00000519728	NM_002350.3	498	Gat/Aat	13/13	0.159622334222282	4	FACETS	0.706	0.615	0.805	0.353	0.307	0.403	INDETERMINATE	1	TRUE	2	0.354618627818973	4		454	757	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514503	41514509	+	frameshift_variant	Frame_Shift_Del	DEL	GTGAACC	GTGAACC	ATTAA	novel	NA	P-0040160-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	68	390	1	ENST00000373198.4:c.152_158delinsTTAAT	p.Gly51ValfsTer7	p.G51Vfs*7	ENST00000373198	NM_133170.3	51	gGGTTCACc/gTTAATc	2/32	0.354618627818973	3	FACETS	0.644	0.56	0.736	0.322	0.28	0.368	SUBCLONAL	1	TRUE	1	0.354618627818973	3		391	701	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0040656-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	46	242	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.16	2		242	568	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259500	89259500	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040656-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	32	521	0	ENST00000336596.2:c.644C>A	p.Thr215Lys	p.T215K	ENST00000336596	NM_005233.5	215	aCg/aAg	3/17	1	2	FACETS	0.778	0.631	0.945	0.778	0.631	0.945	CLONAL	1	TRUE	1	0.16	2		521	514	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259574	89259574	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040656-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	22	405	0	ENST00000336596.2:c.718C>A	p.Pro240Thr	p.P240T	ENST00000336596	NM_005233.5	240	Cca/Aca	3/17	1	2	FACETS	0.664	0.514	0.84	0.664	0.514	0.84	SUBCLONAL	1	TRUE	1	0.16	2		405	414	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372434	118372434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0040656-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	56	624	0	ENST00000534358.1:c.6367C>T	p.Pro2123Ser	p.P2123S	ENST00000534358	NM_005933.3	2123	Cca/Tca	26/36	1	2	FACETS	0.904	0.773	1	0.904	0.773	1	CLONAL	1	TRUE	1	0.16	2		624	774	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645695	215645695	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040656-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	45	566	0	ENST00000260947.4:c.903G>T	p.Glu301Asp	p.E301D	ENST00000260947	NM_000465.2	301	gaG/gaT	4/11	1	2	FACETS	0.93	0.78	1	0.93	0.78	1	CLONAL	1	TRUE	1	0.16	2		566	605	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750346	39750346	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040656-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	34	352	0	ENST00000361337.2:c.1961A>G	p.Lys654Arg	p.K654R	ENST00000361337	NM_003286.2	654	aAg/aGg	19/21	1	2	FACETS	1	0.832	1	1	0.832	1	CLONAL	1	TRUE	1	0.16	2		352	417	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42839812	42839812	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040656-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	26	414	0	ENST00000398585.3:c.1427G>T	p.Gly476Val	p.G476V	ENST00000398585	NM_001135099.1	476	gGt/gTt	13/14	1	2	FACETS	0.823	0.651	1	0.823	0.651	1	CLONAL	1	TRUE	1	0.16	2		414	395	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673827	30673827	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs752754991	NA	P-0040656-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	32	422	0	ENST00000376406.3:c.3133G>T	p.Ala1045Ser	p.A1045S	ENST00000376406	NM_014641.2	1045	Gcc/Tcc	10/15	1	2	FACETS	0.858	0.696	1	0.858	0.696	1	CLONAL	1	TRUE	1	0.16	2		422	466	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965626	93965626	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0040656-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	54	453	0	ENST00000369303.4:c.2302A>T	p.Ser768Cys	p.S768C	ENST00000369303	NM_004440.3	768	Agc/Tgc	13/17	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.16	2		453	593	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528732	157528732	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0040656-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	38	597	0	ENST00000346085.5:c.6457A>G	p.Lys2153Glu	p.K2153E	ENST00000346085	NM_020732.3	2153	Aaa/Gaa	20/20	1	2	FACETS	0.812	0.67	0.971	0.812	0.67	0.971	CLONAL	1	TRUE	1	0.16	2		597	585	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848043	151848043	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0040656-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	28	320	0	ENST00000262189.6:c.12716G>C	p.Ser4239Thr	p.S4239T	ENST00000262189	NM_170606.2	4239	aGt/aCt	51/59	1	2	FACETS	0.825	0.659	1	0.825	0.659	1	CLONAL	1	TRUE	1	0.16	2		320	424	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271167	38271167	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040656-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	32	599	0	ENST00000425967.3:c.2541T>A	p.Asn847Lys	p.N847K	ENST00000425967	NM_001174067.1	847	aaT/aaA	19/19	1	2	FACETS	0.721	0.584	0.876	0.721	0.584	0.876	SUBCLONAL	1	TRUE	1	0.16	2		599	555	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518237	8518237	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0040656-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	27	362	0	ENST00000356435.5:c.1154C>G	p.Pro385Arg	p.P385R	ENST00000356435		385	cCc/cGc	10/35	1	2	FACETS	0.888	0.707	1	0.888	0.707	1	CLONAL	1	TRUE	1	0.16	2		362	380	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045495	47045508	+	frameshift_variant	Frame_Shift_Del	DEL	GCAGAGAAAAGTAT	GCAGAGAAAAGTAT	-	novel	NA	P-0040656-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	45	723	0	ENST00000377604.3:c.2463_2476del	p.Arg822HisfsTer33	p.R822Hfs*33	ENST00000377604	NM_001204468.1	821	cGCAGAGAAAAGTAT/c	22/24	1	2	FACETS	0.788	0.661	0.929	0.788	0.661	0.929	CLONAL	1	TRUE	1	0.16	2		723	714	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611073	100611073	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040656-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	45	821	0	ENST00000308731.7:c.1533C>A	p.Tyr511Ter	p.Y511*	ENST00000308731	NM_000061.2	511	taC/taA	15/19	1	2	FACETS	0.703	0.589	0.83	0.703	0.589	0.83	SUBCLONAL	1	TRUE	1	0.16	2		821	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0040914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	202	608	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.70578145279569	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.743235039405715	1		608	338	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972713	25972713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0040914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	94	412	0	ENST00000435504.4:c.1712C>T	p.Ser571Phe	p.S571F	ENST00000435504		571	tCc/tTc	12/13	0.311419518324026	1	FACETS	0.418	0.375	0.464	0.418	0.375	0.464	INDETERMINATE	1	TRUE	0	0.743235039405715	1		412	380	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592322	29592326	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTG	AGCTG	-	novel	NA	P-0040914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	33	329	0	ENST00000356175.3:c.4737_4741del	p.Ala1580GlufsTer19	p.A1580Efs*19	ENST00000356175	NM_000267.3	1579	aaAGCTGgg/aagg	35/57	0.689408844731822	1	FACETS	0.439	0.365	0.52	0.439	0.365	0.52	SUBCLONAL	1	TRUE	0	0.743235039405715	1		329	127	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511679	66511680	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0040914-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	151	349	0	ENST00000358598.2:c.140dup	p.Met47IlefsTer9	p.M47Ifs*9	ENST00000358598	NM_212471.2	47	atg/aTtg	2/11	0.743235039405715	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.743235039405715	1		349	237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578493	7578493	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1206165503	NA	P-0040966-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	523	623	1	ENST00000269305.4:c.437G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tGg/tAg	5/11	0.764081109866115	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.764081109866115	1		624	835	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039497	49039497	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0040966-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	277	335	0	ENST00000267163.4:c.2482A>T	p.Arg828Ter	p.R828*	ENST00000267163	NM_000321.2	828	Aga/Tga	23/27	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.764081109866115	2		335	715	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941669	48941690	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAATAAAGATCTAGATGCAA	AAAAATAAAGATCTAGATGCAA	-	novel	NA	P-0040966-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	92	231	0	ENST00000267163.4:c.979_1000del	p.Lys327AspfsTer15	p.K327Dfs*15	ENST00000267163	NM_000321.2	327	AAAAATAAAGATCTAGATGCAAga/ga	10/27	1	2	FACETS	0.725	0.651	0.803	0.725	0.651	0.803	SUBCLONAL	1	TRUE	1	0.764081109866115	2		231	332	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752809	42752811	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0040966-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	399	638	0	ENST00000222329.4:c.1453_1455del	p.Lys485del	p.K485del	ENST00000222329	NM_006494.2	485	AAG/-	4/4	0.682616310101284	1	FACETS	0.96	0.924	0.997	0.96	0.924	0.997	CLONAL	1	TRUE	0	0.764081109866115	1		638	672	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193924	106193924	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040966-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	29	265	0	ENST00000380013.4:c.4386G>T	p.Lys1462Asn	p.K1462N	ENST00000380013	NM_001127208.2	1462	aaG/aaT	10/11	0.68786585719644	1	FACETS	0.122	0.097	0.15	0.122	0.097	0.15	SUBCLONAL	1	TRUE	0	0.764081109866115	1		265	385	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508799	106508799	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0040966-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	315	441	0	ENST00000359195.3:c.793C>A	p.Gln265Lys	p.Q265K	ENST00000359195	NM_002649.2	265	Caa/Aaa	2/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.764081109866115	2		441	786	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137323819	137323819	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0040966-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	375	609	0	ENST00000481739.1:c.1112G>T	p.Arg371Leu	p.R371L	ENST00000481739	NM_002957.4	371	cGc/cTc	8/10	1	2	FACETS	0.996	0.948	1	0.996	0.948	1	CLONAL	1	TRUE	1	0.764081109866115	2		609	986	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0041197-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	65	567	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.383915657748296	1	FACETS	0.48	0.418	0.546	0.48	0.418	0.546	SUBCLONAL	1	TRUE	0	0.546859540582736	1		567	360	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs17849781	NA	P-0041197-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	209	721	0	ENST00000269305.4:c.832C>G	p.Pro278Ala	p.P278A	ENST00000269305	NM_001126112.2	278	Cct/Gct	8/11	0.383915657748296	1	FACETS	0.775	0.722	0.829	0.775	0.722	0.829	SUBCLONAL	1	TRUE	0	0.546859540582736	1		721	717	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	protein_altering_variant	In_Frame_Ins	INS	-	-	GTT	rs1554350347	NA	P-0041197-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	227	538	0	ENST00000275493.2:c.2308_2309insGTT	p.Asp770delinsGlyTyr	p.D770delinsGY	ENST00000275493	NM_005228.3	770	gac/gGTTac	20/28	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.546859540582736	2		538	623	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664495	138664495	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041197-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	46	447	0	ENST00000330315.3:c.1070A>G	p.His357Arg	p.H357R	ENST00000330315	NM_023067.3	357	cAt/cGt	1/1	0.383915657748296	1	FACETS	0.251	0.211	0.295	0.251	0.211	0.295	SUBCLONAL	1	TRUE	0	0.546859540582736	1		447	487	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982016	38982016	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0041197-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	26	462	0	ENST00000357387.3:c.706A>C	p.Asn236His	p.N236H	ENST00000357387	NM_152756.3	236	Aat/Cat	8/38	0.295724558239392	3	FACETS	0.36	0.285	0.446	0.18	0.142	0.223	INDETERMINATE	1	TRUE	1	0.546859540582736	3		462	336	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202344	138202344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746478308	NA	P-0041231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	221	666	0	ENST00000237289.4:c.2261C>T	p.Pro754Leu	p.P754L	ENST00000237289	NM_001270507.1	754	cCc/cTc	9/9	0.338715372140461	3	FACETS	1	0.985	1	0.597	0.556	0.639	CLONAL	1	TRUE	1	0.535094729816378	3		666	877	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434842	110434842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	265	650	0	ENST00000375856.3:c.3559G>A	p.Glu1187Lys	p.E1187K	ENST00000375856	NM_003749.2	1187	Gag/Aag	1/2	0.248439923309074	3	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.535094729816378	3		650	983	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588856	69588871	+	frameshift_variant	Frame_Shift_Del	DEL	CTCACCACGCCCCGCT	CTCACCACGCCCCGCT	-	novel	NA	P-0041231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	83	689	0	ENST00000168712.1:c.365_380del	p.Glu122AlafsTer13	p.E122Afs*13	ENST00000168712	NM_002007.2	122	gAGCGGGGCGTGGTGAGc/gc	2/3	0.269566023519804	3	FACETS	0.469	0.413	0.529	0.234	0.206	0.265	INDETERMINATE	1	TRUE	1	0.535094729816378	3		689	839	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027139	49027139	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0041231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	35	367	0	ENST00000267163.4:c.1706T>A	p.Leu569Ter	p.L569*	ENST00000267163	NM_000321.2	569	tTa/tAa	18/27	0.535094729816378	1	FACETS	0.398	0.328	0.475	0.398	0.328	0.475	SUBCLONAL	1	TRUE	0	0.535094729816378	1		367	241	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578554	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	CTTGTTGAGGGCAGGGGAGTA	CTTGTTGAGGGCAGGGGAGTA	-	novel	NA	P-0041231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	189	826	0	ENST00000269305.4:c.376_396del	p.Tyr126_Lys132del	p.Y126_K132del	ENST00000269305	NM_001126112.2	126	TACTCCCCTGCCCTCAACAAG/-	5/11	0.503889323001612	1	FACETS	0.569	0.526	0.613	0.569	0.526	0.613	SUBCLONAL	1	TRUE	0	0.535094729816378	1		826	910	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11095976	11095980	+	frameshift_variant	Frame_Shift_Ins	INS	ATGTC	ATGTC	GAGGCA	novel	NA	P-0041231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	220	841	3	ENST00000358026.2:c.250_254delinsGAGGCA	p.Met84GlufsTer45	p.M84Efs*45	ENST00000358026	NM_001128849.1	84	ATGTCg/GAGGCAg	3/36	0.163363409712691	3	FACETS	0.953	0.886	1	0.476	0.443	0.511	INDETERMINATE	1	TRUE	1	0.535094729816378	3		844	1094	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919329	178919329	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0041231-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	41	216	0	ENST00000263967.3:c.813+1G>C		p.X271_splice	ENST00000263967	NM_006218.2	271			0.535094729816378	3	FACETS	0.725	0.607	0.854	0.362	0.303	0.427	SUBCLONAL	1	TRUE	1	0.535094729816378	3		216	268	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0041288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	77	385	0				ENST00000310581	NM_198253.2	-/1132			0.334200726171614	3	FACETS	1	0.971	1	0.669	0.59	0.753	CLONAL	1	TRUE	1	0.334200726171614	3		385	402	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0041288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	163	469	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.249739599395083	5	FACETS	0.881	0.813	0.951	0.881	0.813	0.951	CLONAL	3	TRUE	2	0.334200726171614	5		469	554	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0041288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	72	499	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA	2	FACETS	1	0.927	1			1	INDETERMINATE	1	TRUE	NA	0.334200726171614	2		499	399	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435317	56435317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200066146	NA	P-0041288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	224	609	0	ENST00000407977.2:c.1820C>T	p.Ser607Leu	p.S607L	ENST00000407977		607	tCg/tTg	9/10	0.277683123806966	4	FACETS	0.942	0.882	1	0.942	0.882	1	CLONAL	3	TRUE	1	0.334200726171614	4		609	633	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245132	46245132	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0041288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	142	428	0	ENST00000334344.6:c.3226A>T	p.Lys1076Ter	p.K1076*	ENST00000334344	NM_152641.2	1076	Aag/Tag	15/21	0.197532289120258	5	FACETS	1	0.977	1	0.789	0.723	0.858	INDETERMINATE	2	TRUE	2	0.334200726171614	5		428	539	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434978	56434978	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0041288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	243	628	0	ENST00000407977.2:c.2159C>G	p.Ser720Ter	p.S720*	ENST00000407977		720	tCa/tGa	9/10	0.277683123806966	4	FACETS	0.921	0.865	0.979	0.921	0.865	0.979	CLONAL	3	TRUE	1	0.334200726171614	4		628	702	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435159	56435159	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0041288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	221	625	0	ENST00000407977.2:c.1978C>A	p.Pro660Thr	p.P660T	ENST00000407977		660	Ccc/Acc	9/10	0.277683123806966	4	FACETS	0.92	0.862	0.981	0.92	0.862	0.981	CLONAL	3	TRUE	1	0.334200726171614	4		625	639	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929252	44929252	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0041288-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	206	317	0	ENST00000377967.4:c.2352del	p.Met785TrpfsTer82	p.M785Wfs*82	ENST00000377967	NM_021140.2	784	ttG/tt	17/29	0.334200726171614	2	FACETS	0.951	0.894	1			1	CLONAL	3	TRUE	NA	0.334200726171614	2		317	432	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0041299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	294	624	1	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.785520169744753	4	FACETS	0.977	0.926	1	0.489	0.463	0.514	CLONAL	2	TRUE	0	0.785520169744753	4		625	684	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0041299-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	353	712	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.785520169744753	2		712	434	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463577	25463577	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1400330086	NA	P-0041301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	299	595	0	ENST00000264709.3:c.2105A>G	p.Asp702Gly	p.D702G	ENST00000264709	NM_175629.2	702	gAt/gGt	18/23	1	2	FACETS	0.915	0.866	0.965	0.915	0.866	0.965	CLONAL	1	TRUE	1	0.851821431769067	2		595	767	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793239	242793239	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	429	846	0	ENST00000334409.5:c.838G>C	p.Glu280Gln	p.E280Q	ENST00000334409	NM_005018.2	280	Gag/Cag	5/5	NA	2	FACETS	0.98	0.937	1			1	INDETERMINATE	1	TRUE	NA	0.851821431769067	2		846	1028	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54956509	54956509	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0041301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	176	403	0	ENST00000312783.6:c.685G>C	p.Asp229His	p.D229H	ENST00000312783	NM_198436.1	229	Gat/Cat	7/10	0.820131146795843	3	FACETS	0.949	0.878	1	0.474	0.439	0.511	CLONAL	1	TRUE	1	0.851821431769067	3		403	621	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272428	11272428	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	323	534	0	ENST00000361445.4:c.3502G>A	p.Glu1168Lys	p.E1168K	ENST00000361445	NM_004958.3	1168	Gaa/Aaa	23/58	0.851821431769067	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.851821431769067	1		534	412	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914571	32914586	+	protein_altering_variant	In_Frame_Del	DEL	AGAGAAGAAAATACTG	AGAGAAGAAAATACTG	GGTA	novel	NA	P-0041301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	243	467	1	ENST00000380152.3:c.6079_6094delinsGGTA	p.Arg2027_Ala2032delinsGlyThr	p.R2027_A2032delinsGT	ENST00000380152		2027	AGAGAAGAAAATACTGct/GGTAct	11/27	0.851821431769067	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.851821431769067	1		468	303	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857208	9857208	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	258	535	0	ENST00000330684.3:c.4193A>G	p.Asp1398Gly	p.D1398G	ENST00000330684	NM_001134407.1	1398	gAc/gGc	13/13	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.851821431769067	2		535	595	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226452	2226452	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0041301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	482	921	0	ENST00000398665.3:c.3932A>C	p.Asn1311Thr	p.N1311T	ENST00000398665	NM_032482.2	1311	aAc/aCc	27/28	0.110611811472904	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.851821431769067	0		921	1108	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556728	41556728	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0041301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	190	305	0	ENST00000263253.7:c.3671+2T>G		p.X1224_splice	ENST00000263253	NM_001429.3	1224			0.851821431769067	4	FACETS	1	0.955	1			1	CLONAL	1	TRUE	NA	0.851821431769067	4		305	792	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25536826	25536832	+	frameshift_variant	Frame_Shift_Del	DEL	CGGGGCC	CGGGGCC	AT	novel	NA	P-0041301-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	347	809	0	ENST00000264709.3:c.22_28delinsAT	p.Gly8MetfsTer55	p.G8Mfs*55	ENST00000264709	NM_175629.2	8	GGCCCCGgg/ATgg	2/23	1	2	FACETS	0.977	0.929	1	0.977	0.929	1	CLONAL	1	TRUE	1	0.851821431769067	2		809	834	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696644	47696644	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519964	NA	P-0041429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	96	575	0	ENST00000347630.2:c.304T>G	p.Phe102Val	p.F102V	ENST00000347630	NM_001007230.1	102	Ttc/Gtc	5/11	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.465823287857009	2		575	374	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650332	48650332	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200599207	NA	P-0041429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	129	468	0	ENST00000376670.3:c.302C>T	p.Thr101Met	p.T101M	ENST00000376670	NM_002049.3	101	aCg/aTg	3/6	0.427271056900401	2	FACETS	1	0.984	1			1	CLONAL	2	TRUE	NA	0.465823287857009	2		468	227	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147513	47147513	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	128	468	0	ENST00000409792.3:c.4813T>A	p.Tyr1605Asn	p.Y1605N	ENST00000409792	NM_014159.6	1605	Tat/Aat	6/21	0.419922659492979	3	FACETS	0.807	0.737	0.878	0.807	0.737	0.878	CLONAL	2	TRUE	1	0.465823287857009	3		468	420	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447845	49447846	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0041429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	103	872	0	ENST00000301067.7:c.588dup	p.Cys197LeufsTer23	p.C197Lfs*23	ENST00000301067	NM_003482.3	196	-/C	5/54	0.157137273727603	4	FACETS	1	0.976	1	0.648	0.582	0.717	INDETERMINATE	1	TRUE	2	0.465823287857009	4		872	500	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198262739	198262739	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041429-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	111	458	0	ENST00000335508.6:c.3236A>G	p.Asn1079Ser	p.N1079S	ENST00000335508	NM_012433.2	1079	aAc/aGc	22/25	0.157137273727603	4	FACETS	0.796	0.72	0.875	0.796	0.72	0.875	INDETERMINATE	2	TRUE	2	0.465823287857009	4		458	439	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0042203-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	84	242	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.0428975635997277	3	FACETS	0.912	0.815	1	0.912	0.815	1	INDETERMINATE	2	TRUE	1	0.361174093533771	3		242	301	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435868	110435868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754439736	NA	P-0042203-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	85	340	0	ENST00000375856.3:c.2533C>T	p.Pro845Ser	p.P845S	ENST00000375856	NM_003749.2	845	Cca/Tca	1/2	1	2	FACETS	0.949	0.842	1	0.949	0.842	1	CLONAL	1	TRUE	1	0.361174093533771	2		340	496	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221341	1221341	+	splice_donor_variant	Splice_Site	SNP	T	T	G	rs730881983	NA	P-0042203-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	60	357	0	ENST00000326873.7:c.862+2T>G		p.X288_splice	ENST00000326873	NM_000455.4	288			0.361174093533771	1	FACETS	0.771	0.668	0.882	0.771	0.668	0.882	SUBCLONAL	1	TRUE	0	0.361174093533771	1		357	353	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0042203-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	235	242	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.162331310872002	3	FACETS	1	0.981	1	1	0.981	1	INDETERMINATE	2	TRUE	1	0.364413541707206	3		242	687	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435868	110435868	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754439736	NA	P-0042203-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	151	340	0	ENST00000375856.3:c.2533C>T	p.Pro845Ser	p.P845S	ENST00000375856	NM_003749.2	845	Cca/Tca	1/2	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.364413541707206	2		340	649	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921622	39921622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761673955	NA	P-0042203-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	67	568	0	ENST00000378444.4:c.4198C>T	p.Arg1400Trp	p.R1400W	ENST00000378444	NM_001123385.1	1400	Cgg/Tgg	10/15	0.364413541707206	1	FACETS	0.594	0.517	0.677	0.594	0.517	0.677	SUBCLONAL	1	TRUE	0	0.364413541707206	1		568	506	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221341	1221341	+	splice_donor_variant	Splice_Site	SNP	T	T	G	rs730881983	NA	P-0042203-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	162	357	0	ENST00000326873.7:c.862+2T>G		p.X288_splice	ENST00000326873	NM_000455.4	288			0.364413541707206	0	FACETS	0.919	0.847	0.994			1	CLONAL	1	TRUE	0	0.364413541707206	0		357	615	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696638	47696638	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042205-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	20	573	0	ENST00000347630.2:c.310T>G	p.Phe104Val	p.F104V	ENST00000347630	NM_001007230.1	104	Ttc/Gtc	5/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		573	298	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0042240-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	69	485	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		485	565	SUCCESS
ATR	545	MSKCC	GRCh37	3	142297500	142297500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042240-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	63	785	0	ENST00000350721.4:c.47G>A	p.Arg16Gln	p.R16Q	ENST00000350721	NM_001184.3	16	cGg/cAg	1/47	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		785	627	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731112	162731112	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042240-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	129	653	0	ENST00000367921.3:c.967G>T	p.Val323Phe	p.V323F	ENST00000367921	NM_006182.2	323	Gtc/Ttc	9/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		653	842	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143263	108143263	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1263930458	NA	P-0042240-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	23	142	0	ENST00000278616.4:c.3082C>G	p.Leu1028Val	p.L1028V	ENST00000278616	NM_000051.3	1028	Cta/Gta	21/63	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		142	317	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564743	41564748	+	inframe_deletion	In_Frame_Del	DEL	GATGGC	GATGGC	-	novel	NA	P-0042240-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	64	834	0	ENST00000263253.7:c.4044_4049del	p.Met1349_Ala1350del	p.M1349_A1350del	ENST00000263253	NM_001429.3	1348	gaGATGGCa/gaa	25/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		834	895	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0042240-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	56	361	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		361	434	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACAACCCCC	rs397517115	NA	P-0042240-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	52	662	0	ENST00000275493.2:c.2311_2319dup	p.Asn771_His773dup	p.N771_H773dup	ENST00000275493	NM_005228.3	771	gac/gACAACCCCCac	20/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		662	523	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21623936	21623936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042240-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	15	81	0	ENST00000421138.2:c.1764G>A	p.Met588Ile	p.M588I	ENST00000421138		588	atG/atA	15/16	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		81	138	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582133	189582133	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042240-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	65	618	0	ENST00000264731.3:c.692A>G	p.Tyr231Cys	p.Y231C	ENST00000264731	NM_003722.4	231	tAc/tGc	5/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		618	566	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0042250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	44	242	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.101301284711724	3	FACETS	0.931	0.785	1	0.466	0.392	0.546	INDETERMINATE	1	TRUE	1	0.375401210453375	3		242	299	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0042250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	169	434	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.375401210453375	3	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	1	0.375401210453375	3		434	529	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71064794	71064794	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	43	270	0	ENST00000318789.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000318789	NM_032682.5	294	Gag/Tag	12/21	1	2	FACETS	0.779	0.655	0.915	0.779	0.655	0.915	CLONAL	1	TRUE	1	0.375401210453375	2		270	294	SUCCESS
APC	324	MSKCC	GRCh37	5	112175672	112175672	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	58	244	0	ENST00000257430.4:c.4381G>T	p.Glu1461Ter	p.E1461*	ENST00000257430	NM_000038.5	1461	Gaa/Taa	16/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.375401210453375	2		244	243	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913343	28913343	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	214	424	0	ENST00000282397.4:c.2450C>A	p.Ala817Asp	p.A817D	ENST00000282397	NM_002019.4	817	gCc/gAc	17/30	0.231132018695168	5	FACETS	1	0.986	1	0.807	0.753	0.863	CLONAL	2	TRUE	2	0.375401210453375	5		424	736	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412002	63412002	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	104	258	0	ENST00000330258.3:c.1165G>T	p.Glu389Ter	p.E389*	ENST00000330258	NM_152424.3	389	Gaa/Taa	2/2	0.170124742491037	2	FACETS	0.947	0.872	1			1	INDETERMINATE	3	TRUE	NA	0.375401210453375	2		258	195	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578382	7578382	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	141	451	0	ENST00000269305.4:c.548C>A	p.Ser183Ter	p.S183*	ENST00000269305	NM_001126112.2	183	tCa/tAa	5/11	0.320139128498201	2	FACETS	0.988	0.911	1	0.988	0.911	1	CLONAL	2	TRUE	0	0.375401210453375	2		451	380	SUCCESS
APC	324	MSKCC	GRCh37	5	112174685	112174685	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	22	200	0	ENST00000257430.4:c.3394G>T	p.Glu1132Ter	p.E1132*	ENST00000257430	NM_000038.5	1132	Gaa/Taa	16/16	1	2	FACETS	0.737	0.576	0.92	0.737	0.576	0.92	CLONAL	1	TRUE	1	0.375401210453375	2		200	159	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468100	120468100	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	78	492	0	ENST00000256646.2:c.4339G>T	p.Ala1447Ser	p.A1447S	ENST00000256646	NM_024408.3	1447	Gcc/Tcc	25/34	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.375401210453375	2		492	393	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88672122	88672122	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	95	430	0	ENST00000372037.3:c.656G>T	p.Gly219Val	p.G219V	ENST00000372037	NM_004329.2	219	gGg/gTg	8/13	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.375401210453375	2		430	434	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243954	46243954	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	60	289	0	ENST00000334344.6:c.2048G>T	p.Arg683Ile	p.R683I	ENST00000334344	NM_152641.2	683	aGa/aTa	15/21	0.101301284711724	3	FACETS	1	0.948	1	0.599	0.519	0.684	INDETERMINATE	1	TRUE	1	0.375401210453375	3		289	317	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223051	5223051	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	85	410	0	ENST00000357368.4:c.2752G>T	p.Ala918Ser	p.A918S	ENST00000357368	NM_002850.3	918	Gcc/Tcc	18/38	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.375401210453375	2		410	441	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024633	11024633	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	54	470	0	ENST00000327064.4:c.750G>C	p.Gln250His	p.Q250H	ENST00000327064	NM_199141.1	250	caG/caC	6/16	1	2	FACETS	0.606	0.518	0.702	0.606	0.518	0.702	SUBCLONAL	1	TRUE	1	0.375401210453375	2		470	475	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744477	41744477	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	138	613	0	ENST00000301178.4:c.1097G>T	p.Gly366Val	p.G366V	ENST00000301178	NM_021913.4	366	gGg/gTg	8/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.375401210453375	2		613	611	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523716	41523716	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	128	536	0	ENST00000263253.7:c.1132C>A	p.His378Asn	p.H378N	ENST00000263253	NM_001429.3	378	Cac/Aac	4/31	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.375401210453375	2		536	555	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802624	135802624	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	103	229	0	ENST00000298552.3:c.174G>T	p.Leu58Phe	p.L58F	ENST00000298552	NM_001162426.1	58	ttG/ttT	4/23	0.375180633517406	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	0	0.375401210453375	2		229	265	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937428	76937428	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042250-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	77	163	0	ENST00000373344.5:c.3320G>T	p.Cys1107Phe	p.C1107F	ENST00000373344	NM_000489.3	1107	tGt/tTt	9/35	0.170124742491037	2	FACETS	0.871	0.787	0.955			1	INDETERMINATE	3	TRUE	NA	0.375401210453375	2		163	157	SUCCESS
APC	324	MSKCC	GRCh37	5	112170720	112170720	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1460191563	NA	P-0042332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	360	381	3	ENST00000257430.4:c.1816A>G	p.Ile606Val	p.I606V	ENST00000257430	NM_000038.5	606	Ata/Gta	15/16	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.667972779317853	2		384	513	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936792	32936792	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	91	348	0	ENST00000380152.3:c.7939del	p.Leu2647Ter	p.L2647*	ENST00000380152		2646	tgC/tg	17/27	NA	2	FACETS	1	0.93	1			1	INDETERMINATE	1	TRUE	NA	0.667972779317853	2		348	262	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741583	145741583	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042332-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	340	723	0	ENST00000428558.2:c.920C>G	p.Pro307Arg	p.P307R	ENST00000428558	NM_004260.3	307	cCa/cGa	5/22	0.667972779317853	3	FACETS	1	0.949	1	0.502	0.474	0.531	CLONAL	1	TRUE	1	0.667972779317853	3		723	1352	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	92	473	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.947	0.847	1	0.947	0.847	1	CLONAL	1	TRUE	1	0.499669951705218	2		473	389	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944812	31944812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866971809	NA	P-0042370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	326	595	0	ENST00000340398.3:c.289G>A	p.Glu97Lys	p.E97K	ENST00000340398	NM_001013699.2	97	Gaa/Aaa	1/1	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.499669951705218	2		595	1286	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42384977	42384977	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782624281	NA	P-0042370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	276	708	2	ENST00000221972.3:c.611G>A	p.Arg204Gln	p.R204Q	ENST00000221972	NM_021601.3	204	cGg/cAg	5/5	1	2	FACETS	0.973	0.914	1	0.973	0.914	1	CLONAL	1	TRUE	1	0.499669951705218	2		710	1135	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363169	40363169	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2046	248	555	0	ENST00000397332.2:c.1060A>C	p.Ser354Arg	p.S354R	ENST00000397332	NM_001033082.2	354	Agc/Cgc	3/3	0.499669951705218	8	FACETS	1	0.971	1			1	CLONAL	1	TRUE	NA	0.499669951705218	8		555	2294	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250541	26250541	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs758973961	NA	P-0042370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1266	239	615	0	ENST00000446824.2:c.293A>G	p.Glu98Gly	p.E98G	ENST00000446824	NM_021018.2	98	gAg/gGg	1/1	0.499669951705218	3	FACETS	0.794	0.74	0.851	0.397	0.37	0.426	SUBCLONAL	1	TRUE	1	0.499669951705218	3		615	1505	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675831	30675831	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	302	726	0	ENST00000376406.3:c.2525G>T	p.Arg842Ile	p.R842I	ENST00000376406	NM_014641.2	842	aGa/aTa	8/15	0.499669951705218	3	FACETS	1	0.957	1	0.511	0.48	0.543	CLONAL	1	TRUE	1	0.499669951705218	3		726	1479	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680166	30680191	+	frameshift_variant	Frame_Shift_Del	DEL	GTGGTGGAGGCTTGGCTTCTCTCCAG	GTGGTGGAGGCTTGGCTTCTCTCCAG	-	novel	NA	P-0042370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1226	269	692	0	ENST00000376406.3:c.1528_1553del	p.Leu510SerfsTer60	p.L510Sfs*60	ENST00000376406	NM_014641.2	510	CTGGAGAGAAGCCAAGCCTCCACCACa/a	5/15	0.499669951705218	3	FACETS	0.9	0.842	0.96	0.45	0.421	0.48	CLONAL	1	TRUE	1	0.499669951705218	3		692	1495	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128321994	128321995	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATG	novel	NA	P-0042370-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	270	711	0	ENST00000265960.3:c.763_765dup	p.His255dup	p.H255dup	ENST00000265960	NM_001006617.1	255	-/CAT	6/12	1	2	FACETS	0.875	0.82	0.932	0.875	0.82	0.932	CLONAL	1	TRUE	1	0.499669951705218	2		711	1235	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863098	56863098	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	118	410	0	ENST00000519728.1:c.365A>C	p.Asn122Thr	p.N122T	ENST00000519728	NM_002350.3	122	aAc/aCc	5/13	0.145386272869149	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.941771635776228	0		410	298	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0042419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	76	255	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.223754409433369	2		255	596	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028615	12028615	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	60	260	0	ENST00000353533.5:c.818A>G	p.Glu273Gly	p.E273G	ENST00000353533	NM_003010.3	273	gAa/gGa	8/11	0.203927433932197	1	FACETS	0.974	0.841	1	0.974	0.841	1	CLONAL	1	TRUE	0	0.223754409433369	1		260	489	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041743	42041743	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	58	290	0	ENST00000219905.7:c.5938G>T	p.Glu1980Ter	p.E1980*	ENST00000219905	NM_001164273.1	1980	Gaa/Taa	17/24	1	2	FACETS	0.934	0.803	1	0.934	0.803	1	CLONAL	1	TRUE	1	0.223754409433369	2		290	555	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47143009	47143010	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0042419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	93	372	0	ENST00000409792.3:c.4953dup	p.Thr1652TyrfsTer14	p.T1652Yfs*14	ENST00000409792	NM_014159.6	1651	-/T	8/21	0.223754409433369	1	FACETS	0.914	0.812	1	0.914	0.812	1	CLONAL	1	TRUE	0	0.223754409433369	1		372	808	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397186	397186	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774593906	NA	P-0042419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	82	314	0	ENST00000380956.4:c.571C>T	p.Pro191Ser	p.P191S	ENST00000380956	NM_001195286.1	191	Ccg/Tcg	5/9	NA	2	FACETS	1	0.944	1			1	INDETERMINATE	1	TRUE	NA	0.223754409433369	2		314	654	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488669	212488669	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	87	318	0	ENST00000342788.4:c.2180G>T	p.Gly727Val	p.G727V	ENST00000342788	NM_005235.2	727	gGt/gTt	18/28	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.223754409433369	2		318	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574029	7574029	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	78	468	0	ENST00000269305.4:c.998G>C	p.Arg333Pro	p.R333P	ENST00000269305	NM_001126112.2	333	cGt/cCt	10/11	0.203927433932197	1	FACETS	0.746	0.654	0.845	0.746	0.654	0.845	SUBCLONAL	1	TRUE	0	0.223754409433369	1		468	830	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184591	11184591	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	95	499	0	ENST00000361445.4:c.6626T>A	p.Leu2209Gln	p.L2209Q	ENST00000361445	NM_004958.3	2209	cTg/cAg	47/58	1	2	FACETS	0.973	0.865	1	0.973	0.865	1	CLONAL	1	TRUE	1	0.223754409433369	2		499	873	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564839	226564839	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	77	423	0	ENST00000366794.5:c.1911G>T	p.Lys637Asn	p.K637N	ENST00000366794	NM_001618.3	637	aaG/aaT	13/23	1	2	FACETS	0.885	0.776	1	0.885	0.776	1	CLONAL	1	TRUE	1	0.223754409433369	2		423	778	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23635391	23635391	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	93	356	1	ENST00000261584.4:c.2773G>T	p.Val925Leu	p.V925L	ENST00000261584	NM_024675.3	925	Gtg/Ttg	8/13	1	2	FACETS	0.986	0.876	1	0.986	0.876	1	CLONAL	1	TRUE	1	0.223754409433369	2		357	843	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281586	142281586	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	83	388	0	ENST00000350721.4:c.658G>C	p.Val220Leu	p.V220L	ENST00000350721	NM_001184.3	220	Gtg/Ctg	4/47	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.223754409433369	2		388	722	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586499	189586499	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0042419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	67	300	0	ENST00000264731.3:c.1123A>T	p.Lys375Ter	p.K375*	ENST00000264731	NM_003722.4	375	Aag/Tag	8/14	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.223754409433369	2		300	521	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161990445	161990446	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0042419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	49	332	1	ENST00000366898.1:c.874_875delinsTT	p.Gly292Phe	p.G292F	ENST00000366898	NM_004562.2	292	GGc/TTc	8/12	0.223754409433369	1	FACETS	0.686	0.581	0.802	0.686	0.581	0.802	SUBCLONAL	1	TRUE	0	0.223754409433369	1		333	567	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240743	55240743	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	151	678	0	ENST00000275493.2:c.1987G>T	p.Gly663Trp	p.G663W	ENST00000275493	NM_005228.3	663	Ggg/Tgg	17/28	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.223754409433369	2		678	1230	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15821821	15821821	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	21	198	0	ENST00000307771.7:c.214C>A	p.His72Asn	p.H72N	ENST00000307771	NM_005089.3	72	Cat/Aat	4/11	NA	2	FACETS	0.56	0.431	0.711			1	INDETERMINATE	1	TRUE	NA	0.223754409433369	2		198	335	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344227	70344228	+	missense_variant	Missense_Mutation	DNP	AG	AG	CT	novel	NA	P-0042419-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	39	220	0	ENST00000374080.3:c.1963_1964inv	p.Ser655Leu	p.S655L	ENST00000374080		655	AGc/CTc	13/45	1	2	FACETS	0.755	0.625	0.899	0.755	0.625	0.899	SUBCLONAL	1	TRUE	1	0.223754409433369	2		220	462	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs760043106	NA	P-0042422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	138	626	0	ENST00000269305.4:c.584T>A	p.Ile195Asn	p.I195N	ENST00000269305	NM_001126112.2	195	aTc/aAc	6/11	0.462640812079342	1	FACETS	0.983	0.901	1	0.983	0.901	1	CLONAL	1	TRUE	0	0.466231152393272	1		626	462	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411624	63411624	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	169	726	0	ENST00000330258.3:c.1543C>G	p.Leu515Val	p.L515V	ENST00000330258	NM_152424.3	515	Ctt/Gtt	2/2	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.466231152393272	2		726	709	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14303205	14303205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	93	560	0	ENST00000256196.4:c.470C>T	p.Ser157Leu	p.S157L	ENST00000256196		157	tCa/tTa	5/6	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.466231152393272	2		560	316	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0042436-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	187	794	3	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.0631456906879917	3	FACETS	0.78	0.721	0.842			1	INDETERMINATE	2	FALSE	NA	0.28944749006627	3		797	948	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0042436-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	58	735	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	0.678	0.582	0.782	0.678	0.582	0.782	SUBCLONAL	1	FALSE	1	0.28944749006627	2		735	591	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912657	NA	P-0042478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	442	998	0	ENST00000269305.4:c.814G>A	p.Val272Met	p.V272M	ENST00000269305	NM_001126112.2	272	Gtg/Atg	8/11	0.831825002576325	1	FACETS	0.976	0.945	1	0.976	0.945	1	CLONAL	1	TRUE	0	0.831825002576325	1		998	636	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543383	65543383	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0042478-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	350	621	0	ENST00000358664.4:c.296-2A>G		p.X99_splice	ENST00000358664	NM_002382.4	99			0.831825002576325	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.831825002576325	1		621	471	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0042481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	117	415	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	0.580116123552004	1	FACETS	0.768	0.699	0.839	0.768	0.699	0.839	SUBCLONAL	1	TRUE	0	0.580116123552004	1		415	373	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821960	72821960	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762108866	NA	P-0042481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	119	395	2	ENST00000268489.5:c.10215del	p.Ala3407LeufsTer78	p.A3407Lfs*78	ENST00000268489	NM_006885.3	3405	ccC/cc	10/10	1	2	FACETS	0.858	0.779	0.941	0.858	0.779	0.941	CLONAL	1	TRUE	1	0.580116123552004	2		397	478	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0042481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	246	1006	6	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	NA	2	FACETS	0.938	0.878	1			1	INDETERMINATE	1	TRUE	NA	0.580116123552004	2		1012	904	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0042481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	249	906	7	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.580116123552004	2		913	851	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450366	50450366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	189	636	0	ENST00000331340.3:c.550C>T	p.Arg184Trp	p.R184W	ENST00000331340	NM_006060.4	184	Cgg/Tgg	5/8	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.580116123552004	2		636	648	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233793	133233794	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1555225149	NA	P-0042481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	224	719	2	ENST00000320574.5:c.3510dup	p.Leu1171ThrfsTer6	p.L1171Tfs*6	ENST00000320574	NM_006231.2	1170	-/A	29/49	1	2	FACETS	0.981	0.916	1	0.981	0.916	1	CLONAL	1	TRUE	1	0.580116123552004	2		721	787	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610695	52610695	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	122	353	0	ENST00000394830.3:c.3478C>T	p.Arg1160Ter	p.R1160*	ENST00000394830	NM_018313.4	1160	Cga/Tga	23/30	1	2	FACETS	0.901	0.819	0.985	0.901	0.819	0.985	CLONAL	1	TRUE	1	0.580116123552004	2		353	467	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781269	3781269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	296	1183	0	ENST00000262367.5:c.5096G>A	p.Gly1699Asp	p.G1699D	ENST00000262367	NM_004380.2	1699	gGc/gAc	30/31	1	2	FACETS	0.994	0.936	1	0.994	0.936	1	CLONAL	1	TRUE	1	0.580116123552004	2		1183	1027	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598101	52598102	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0042481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	175	478	0	ENST00000394830.3:c.3764_3765del	p.Ser1255CysfsTer2	p.S1255Cfs*2	ENST00000394830	NM_018313.4	1255	tCT/t	24/30	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.580116123552004	2		478	596	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526976	31526976	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1485879154	NA	P-0042481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	241	846	3	ENST00000344624.3:c.64C>T	p.Arg22Ter	p.R22*	ENST00000344624		22	Cga/Tga	2/33	1	2	FACETS	0.938	0.877	1	0.938	0.877	1	CLONAL	1	TRUE	1	0.580116123552004	2		849	886	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870336	155870336	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs938749530	NA	P-0042481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	192	702	1	ENST00000368323.3:c.503G>A	p.Arg168His	p.R168H	ENST00000368323	NM_006912.5	168	cGc/cAc	6/6	0.580116123552004	3	FACETS	0.954	0.883	1	0.477	0.441	0.514	CLONAL	1	TRUE	1	0.580116123552004	3		703	895	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448139	49448139	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	206	683	0	ENST00000301067.7:c.461del	p.Gly154AlafsTer54	p.G154Afs*54	ENST00000301067	NM_003482.3	154	gGc/gc	4/54	NA	2	FACETS	0.965	0.898	1			1	INDETERMINATE	1	TRUE	NA	0.580116123552004	2		683	736	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479291	50479291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	186	652	0	ENST00000394963.4:c.139G>A	p.Gly47Arg	p.G47R	ENST00000394963	NM_003076.4	47	Ggg/Agg	1/13	NA	2	FACETS	0.912	0.845	0.981			1	INDETERMINATE	1	TRUE	NA	0.580116123552004	2		652	703	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133234503	133234503	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	152	657	1	ENST00000320574.5:c.3329T>A	p.Leu1110His	p.L1110H	ENST00000320574	NM_006231.2	1110	cTc/cAc	27/49	1	2	FACETS	0.75	0.687	0.815	0.75	0.687	0.815	SUBCLONAL	1	TRUE	1	0.580116123552004	2		658	699	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610657	81610657	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	118	419	0	ENST00000298171.2:c.2255A>G	p.Gln752Arg	p.Q752R	ENST00000298171	NM_000369.2	752	cAa/cGa	10/10	1	2	FACETS	0.796	0.722	0.874	0.796	0.722	0.874	SUBCLONAL	1	TRUE	1	0.580116123552004	2		419	511	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43714194	43714194	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	327	1093	0	ENST00000382044.4:c.3959del	p.Thr1320AsnfsTer47	p.T1320Nfs*47	ENST00000382044	NM_001141980.1	1320	aCa/aa	19/28	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.580116123552004	2		1093	1109	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631962	90631964	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	novel	NA	P-0042481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	187	698	0	ENST00000330062.3:c.389_391del	p.Lys130del	p.K130del	ENST00000330062	NM_002168.2	130	aAGAtg/atg	4/11	1	2	FACETS	0.861	0.797	0.926	0.861	0.797	0.926	CLONAL	1	TRUE	1	0.580116123552004	2		698	749	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953130	81953130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	115	390	0	ENST00000359376.3:c.2096G>A	p.Gly699Asp	p.G699D	ENST00000359376	NM_002661.3	699	gGc/gAc	20/33	1	2	FACETS	0.853	0.773	0.936	0.853	0.773	0.936	CLONAL	1	TRUE	1	0.580116123552004	2		390	465	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979647	7979647	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199880378	NA	P-0042481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	154	571	0	ENST00000319144.4:c.1378G>A	p.Val460Met	p.V460M	ENST00000319144	NM_001139.2	460	Gtg/Atg	11/15	1	2	FACETS	0.908	0.834	0.983	0.908	0.834	0.983	CLONAL	1	TRUE	1	0.580116123552004	2		571	585	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905522	50905522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1408031137	NA	P-0042481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	288	1074	0	ENST00000440232.2:c.650C>T	p.Pro217Leu	p.P217L	ENST00000440232	NM_002691.3	217	cCg/cTg	6/27	0.580116123552004	3	FACETS	1	0.961	1	0.515	0.483	0.547	CLONAL	1	TRUE	1	0.580116123552004	3		1074	1244	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181378	185181378	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	148	373	0	ENST00000265026.3:c.1319T>G	p.Ile440Ser	p.I440S	ENST00000265026	NM_004721.4	440	aTc/aGc	8/14	1	2	FACETS	0.972	0.893	1	0.972	0.893	1	CLONAL	1	TRUE	1	0.580116123552004	2		373	525	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488443	20488443	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	174	536	0	ENST00000346618.3:c.1099G>A	p.Asp367Asn	p.D367N	ENST00000346618	NM_001949.4	367	Gac/Aac	6/7	0.527049658035269	1	FACETS	0.92	0.855	0.986	0.92	0.855	0.986	CLONAL	1	TRUE	0	0.580116123552004	1		536	463	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419886	152419886	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042481-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	185	638	0	ENST00000206249.3:c.1573C>A	p.Leu525Met	p.L525M	ENST00000206249	NM_000125.3	525	Ctg/Atg	8/8	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.580116123552004	2		638	628	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	246	473	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.375106988440389	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.375106988440389	3		473	742	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609674	117609674	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042493-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	125	447	0	ENST00000368508.3:c.7025A>G	p.Tyr2342Cys	p.Y2342C	ENST00000368508	NM_002944.2	2342	tAt/tGt	43/43	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.375106988440389	2		447	516	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0042494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	86	262	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.963	1	1	0.989	1	CLONAL	3	TRUE	1	0.205972644602677	2		263	241	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061102	38061121	+	frameshift_variant	Frame_Shift_Del	DEL	TCCTTGCGGCTCTCAGGGCC	TCCTTGCGGCTCTCAGGGCC	G	novel	NA	P-0042494-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	30	210	0	ENST00000250448.2:c.868_887delinsC	p.Gly290ProfsTer25	p.G290Pfs*25	ENST00000250448	NM_004496.3	290	GGCCCTGAGAGCCGCAAGGAc/Cc	2/2	1	2	FACETS	0.857	0.698	1	1	0.952	1	CLONAL	2	TRUE	1	0.205972644602677	2		210	170	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	194	384	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.622343706728702	2		384	527	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0042502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	363	499	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.622343706728702	2		499	972	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578268	7578268	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519998	NA	P-0042502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	340	667	0	ENST00000269305.4:c.581T>G	p.Leu194Arg	p.L194R	ENST00000269305	NM_001126112.2	194	cTt/cGt	6/11	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.622343706728702	2		667	1008	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971138	21971138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760640852	NA	P-0042502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	254	390	1	ENST00000304494.5:c.220G>A	p.Asp74Asn	p.D74N	ENST00000304494	NM_000077.4	74	Gac/Aac	2/3	0.622343706728702	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.622343706728702	1		391	507	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951994	178951994	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	200	406	0	ENST00000263967.3:c.3049G>C	p.Asp1017His	p.D1017H	ENST00000263967	NM_006218.2	1017	Gat/Cat	21/21	1	2	FACETS	0.936	0.87	1	0.936	0.87	1	CLONAL	1	TRUE	1	0.622343706728702	2		406	687	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938562	76938562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	276	230	0	ENST00000373344.5:c.2186C>T	p.Ser729Leu	p.S729L	ENST00000373344	NM_000489.3	729	tCa/tTa	9/35	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.622343706728702	1		230	423	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796771	135796771	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	134	317	0	ENST00000298552.3:c.716A>T	p.Asp239Val	p.D239V	ENST00000298552	NM_001162426.1	239	gAc/gTc	8/23	0.622343706728702	1	FACETS	0.948	0.875	1	0.948	0.875	1	CLONAL	1	TRUE	0	0.622343706728702	1		317	313	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781932	3781932	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	184	427	0	ENST00000262367.5:c.4735C>T	p.Gln1579Ter	p.Q1579*	ENST00000262367	NM_004380.2	1579	Cag/Tag	29/31	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.622343706728702	2		427	582	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982105	201982105	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0042502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	407	791	0	ENST00000359651.3:c.629C>G	p.Ser210Ter	p.S210*	ENST00000359651		210	tCa/tGa	5/8	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.622343706728702	2		791	1257	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69103963	69103963	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	228	499	0	ENST00000288368.4:c.4353C>G	p.Phe1451Leu	p.F1451L	ENST00000288368	NM_024870.2	1451	ttC/ttG	36/40	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.622343706728702	2		499	725	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260668	16260668	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	323	674	0	ENST00000375759.3:c.7933C>G	p.Gln2645Glu	p.Q2645E	ENST00000375759	NM_015001.2	2645	Caa/Gaa	11/15	1	2	FACETS	0.997	0.943	1	0.997	0.943	1	CLONAL	1	TRUE	1	0.622343706728702	2		674	1041	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445764	49445764	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	565	1060	1	ENST00000301067.7:c.1702G>T	p.Glu568Ter	p.E568*	ENST00000301067	NM_003482.3	568	Gaa/Taa	10/54	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.622343706728702	2		1061	1733	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942901	15942901	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	264	481	0	ENST00000268712.3:c.6801C>G	p.Ile2267Met	p.I2267M	ENST00000268712	NM_006311.3	2267	atC/atG	44/46	0.622343706728702	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.622343706728702	1		481	538	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554045	63554045	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	289	572	0	ENST00000307078.5:c.694G>C	p.Glu232Gln	p.E232Q	ENST00000307078	NM_004655.3	232	Gag/Cag	2/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.622343706728702	2		572	876	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733084	74733084	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	341	610	0	ENST00000359995.5:c.159G>T	p.Glu53Asp	p.E53D	ENST00000359995	NM_001195427.1	53	gaG/gaT	1/3	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.622343706728702	2		610	970	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288904	212288904	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	163	315	0	ENST00000342788.4:c.2842G>T	p.Asp948Tyr	p.D948Y	ENST00000342788	NM_005235.2	948	Gac/Tac	23/28	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.622343706728702	2		315	501	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632287	215632287	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	246	571	0	ENST00000260947.4:c.1487C>T	p.Ser496Leu	p.S496L	ENST00000260947	NM_000465.2	496	tCa/tTa	6/11	1	2	FACETS	0.988	0.927	1	0.988	0.927	1	CLONAL	1	TRUE	1	0.622343706728702	2		571	800	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402488	20402488	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	290	628	0	ENST00000346618.3:c.25C>G	p.Leu9Val	p.L9V	ENST00000346618	NM_001949.4	9	Ctg/Gtg	1/7	1	2	FACETS	0.947	0.892	1	0.947	0.892	1	CLONAL	1	TRUE	1	0.622343706728702	2		628	984	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043343	6043343	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs864622232	NA	P-0042502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	163	366	0	ENST00000265849.7:c.331C>G	p.Leu111Val	p.L111V	ENST00000265849	NM_000535.5	111	Ctg/Gtg	4/15	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.622343706728702	2		366	484	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44911033	44911034	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0042502-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	155	209	0	ENST00000377967.4:c.735_736del	p.Leu246ThrfsTer16	p.L246Tfs*16	ENST00000377967	NM_021140.2	245	gTC/g	9/29	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.622343706728702	1		209	262	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0042505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	30	324	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.849	0.683	1	0.849	0.683	1	CLONAL	1	TRUE	1	0.14	2		324	505	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0042505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	42	379	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.14	2		379	584	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0042505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	45	443	1	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.986	0.827	1	0.986	0.827	1	CLONAL	1	TRUE	1	0.14	2		444	652	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748963963	NA	P-0042505-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	85	752	1	ENST00000396946.4:c.1663C>T	p.Arg555Trp	p.R555W	ENST00000396946	NM_032415.4	555	Cgg/Tgg	13/25	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.14	2		753	995	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403513	139403514	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0042520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	570	415	0	ENST00000277541.6:c.2979dup	p.Asn994GlnfsTer31	p.N994Qfs*31	ENST00000277541	NM_017617.3	993	-/C	19/34	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		415	1037	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578232	7578236	+	frameshift_variant	Frame_Shift_Del	DEL	AAATA	AAATA	T	novel	NA	P-0042520-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	827	359	0	ENST00000269305.4:c.613_617delinsA	p.Tyr205ArgfsTer41	p.Y205Rfs*41	ENST00000269305	NM_001126112.2	205	TATTTg/Ag	6/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		359	1185	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037877	49037877	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913295	NA	P-0042549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	14	141	0	ENST00000267163.4:c.2117G>T	p.Cys706Phe	p.C706F	ENST00000267163	NM_000321.2	706	tGt/tTt	21/27	0.626102532782947	1	FACETS	0.287	0.21	0.377	0.287	0.21	0.377	SUBCLONAL	1	TRUE	0	0.71304007600838	1		141	88	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666391	206666391	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	43	557	0	ENST00000367120.3:c.1871T>C	p.Val624Ala	p.V624A	ENST00000367120	NM_014002.3	624	gTt/gCt	19/22	1		FACETS		0.13	0.186				SUBCLONAL	1	TRUE	1	0.71304007600838	2		557	771	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878124	48878124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	11	31	0	ENST00000267163.4:c.76C>T	p.Pro26Ser	p.P26S	ENST00000267163	NM_000321.2	26	Ccg/Tcg	1/27	0.626102532782947	1	FACETS	0.187	0.13	0.257	0.187	0.13	0.257	SUBCLONAL	1	TRUE	0	0.71304007600838	1		31	106	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916829	48916829	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	21	145	0	ENST00000267163.4:c.359T>C	p.Leu120Pro	p.L120P	ENST00000267163	NM_000321.2	120	cTa/cCa	3/27	0.626102532782947	1	FACETS	0.267	0.207	0.335	0.267	0.207	0.335	SUBCLONAL	1	TRUE	0	0.71304007600838	1		145	142	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65560448	65560448	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	33	263	0	ENST00000358664.4:c.149T>A	p.Val50Asp	p.V50D	ENST00000358664	NM_002382.4	50	gTc/gAc	3/5	0.680334078073669	1	FACETS	0.17	0.138	0.205	0.17	0.138	0.205	SUBCLONAL	1	TRUE	0	0.71304007600838	1		263	351	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798753	135798753	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	36	158	0	ENST00000298552.3:c.490T>A	p.Trp164Arg	p.W164R	ENST00000298552	NM_001162426.1	164	Tgg/Agg	6/23	1	2	FACETS	0.463	0.384	0.551	0.463	0.384	0.551	SUBCLONAL	1	TRUE	1	0.71304007600838	2		158	218	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593602	55593605	+	protein_altering_variant	In_Frame_Del	DEL	GTGG	GTGG	A	novel	NA	P-0042549-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	72	198	0	ENST00000288135.5:c.1668_1671delinsA	p.Trp557del	p.W557del	ENST00000288135	NM_000222.2	556	caGTGG/caA	11/21	1	2	FACETS	0.765	0.676	0.858	0.765	0.676	0.858	SUBCLONAL	1	TRUE	1	0.71304007600838	2		198	264	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242465	55242479	+	inframe_deletion	In_Frame_Del	DEL	GGAATTAAGAGAAGC	GGAATTAAGAGAAGC	-	rs121913421	NA	P-0042558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	134	496	0	ENST00000275493.2:c.2235_2249del	p.Glu746_Ala750del	p.E746_A750del	ENST00000275493	NM_005228.3	745	aaGGAATTAAGAGAAGCa/aaa	19/28	0.233166202103062	2	FACETS	0.802	0.732	0.876	0.802	0.732	0.876	CLONAL	2	TRUE	0	0.29	2		496	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578394	7578394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519991	NA	P-0042558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	214	677	0	ENST00000269305.4:c.536A>G	p.His179Arg	p.H179R	ENST00000269305	NM_001126112.2	179	cAt/cGt	5/11	0.296083768726596	3	FACETS	0.83	0.771	0.891	0.83	0.771	0.891	CLONAL	2	TRUE	1	0.29	3		677	1018	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622061	1622061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756920681	NA	P-0042558-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	103	986	0	ENST00000344749.5:c.814G>A	p.Glu272Lys	p.E272K	ENST00000344749	NM_001136139.2	272	Gag/Aag	10/19	NA	2	FACETS	0.533	0.475	0.595			1	INDETERMINATE	1	TRUE	NA	0.29	2		986	1333	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578474	7578475	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs730882019	NA	P-0042580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1380	283	884	0	ENST00000269305.4:c.455dup	p.Pro153AlafsTer28	p.P153Afs*28	ENST00000269305	NM_001126112.2	152	ccg/ccCg	5/11	0.118854397612842	5	FACETS	0.936	0.877	0.997	0.468	0.438	0.499	INDETERMINATE	2	TRUE	1	0.25	5		884	1663	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717699	89717699	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554825210	NA	P-0042580-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	101	539	0	ENST00000371953.3:c.724G>T	p.Glu242Ter	p.E242*	ENST00000371953	NM_000314.4	242	Gag/Tag	7/9	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.25	2		539	798	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0042589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	176	632	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.467929602994783	1	FACETS	0.951	0.88	1	0.951	0.88	1	CLONAL	1	TRUE	0	0.467929602994783	1		632	606	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0042589-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	97	405	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	0.467929602994783	2	FACETS	0.897	0.804	0.996	0.449	0.402	0.498	CLONAL	1	TRUE	0	0.467929602994783	2		405	462	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0042606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	34	115	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		115	76	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272308	38272308	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs869320694	NA	P-0042606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	295	632	0	ENST00000425967.3:c.2059A>G	p.Lys687Glu	p.K687E	ENST00000425967	NM_001174067.1	687	Aag/Gag	15/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		632	514	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939674	76939674	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0042606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	162	640	0	ENST00000373344.5:c.1074del	p.Lys358AsnfsTer2	p.K358Nfs*2	ENST00000373344	NM_000489.3	358	aaA/aa	9/35	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		640	558	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817415	39817415	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148089492	NA	P-0042606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	137	555	0	ENST00000288319.7:c.148C>T	p.Arg50Cys	p.R50C	ENST00000288319	NM_182918.3	50	Cgc/Tgc	2/10	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		555	599	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106497	108106497	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs772173522	NA	P-0042606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	13	280	0	ENST00000278616.4:c.432A>G	p.Ile144Met	p.I144M	ENST00000278616	NM_000051.3	144	atA/atG	5/63	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		280	199	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556318	29556318	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	392	518	1	ENST00000356175.3:c.2686del	p.Asp896IlefsTer6	p.D896Ifs*6	ENST00000356175	NM_000267.3	895	atG/at	21/57	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		519	560	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916641	178916664	+	inframe_deletion	In_Frame_Del	DEL	CTGTGGGGCATCCACTTGATGCCC	CTGTGGGGCATCCACTTGATGCCC	-	novel	NA	P-0042606-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	159	354	0	ENST00000263967.3:c.29_52del	p.Leu10_Pro17del	p.L10_P17del	ENST00000263967	NM_006218.2	10	CTGTGGGGCATCCACTTGATGCCC/-	2/21	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		354	301	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0042643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	276	821	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	1	2	FACETS	0.987	0.931	1	0.987	0.931	1	CLONAL	1	TRUE	1	0.735034680323347	2		821	761	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0042643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	246	1008	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.735822206832183	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.735034680323347	1		1008	391	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722906	49722906	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	rs747477010	NA	P-0042643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	10	244	1	ENST00000449682.2:c.1421del	p.Pro474GlnfsTer52	p.P474Qfs*52	ENST00000449682	NM_020998.3	474	cCa/ca	12/18	1	2	FACETS	0.184	0.125	0.258	0.184	0.125	0.258	SUBCLONAL	1	TRUE	1	0.735034680323347	2		245	148	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619057	37619057	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	58	898	0	ENST00000447079.4:c.733G>T	p.Asp245Tyr	p.D245Y	ENST00000447079	NM_015083.1	245	Gat/Tat	1/14	1	2	FACETS	0.267	0.229	0.308	0.267	0.229	0.308	SUBCLONAL	1	TRUE	1	0.735034680323347	2		898	592	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0042650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	47	567	1	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.382479845195188	1	FACETS	0.549	0.471	0.631	0.549	0.471	0.631	INDETERMINATE	1	TRUE	0	0.688753734609924	1		568	163	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578201	7578202	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0042650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	117	721	0	ENST00000269305.4:c.647_648del	p.Val216GlyfsTer5	p.V216Gfs*5	ENST00000269305	NM_001126112.2	216	gTG/g	6/11	0.630875012468096	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.688753734609924	1		721	222	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	459813	459813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779410726	NA	P-0042650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	44	676	1	ENST00000399788.2:c.1282C>T	p.Arg428Trp	p.R428W	ENST00000399788	NM_001042603.1	428	Cgg/Tgg	10/28	1	2	FACETS	0.726	0.618	0.842	0.726	0.618	0.842	SUBCLONAL	1	TRUE	1	0.688753734609924	2		677	176	SUCCESS
APC	324	MSKCC	GRCh37	5	112176030	112176030	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs886039682	NA	P-0042650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	35	300	0	ENST00000257430.4:c.4741del	p.Ser1581LeufsTer69	p.S1581Lfs*69	ENST00000257430	NM_000038.5	1580	aTt/at	16/16	1	2	FACETS	0.876	0.735	1	0.876	0.735	1	CLONAL	1	TRUE	1	0.688753734609924	2		300	116	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619835	1619835	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	158	985	0	ENST00000344749.5:c.1111C>T	p.Arg371Ter	p.R371*	ENST00000344749	NM_001136139.2	371	Cga/Tga	14/19	1	2	FACETS	0.964	0.891	1	0.964	0.891	1	CLONAL	1	TRUE	1	0.688753734609924	2		985	476	SUCCESS
APC	324	MSKCC	GRCh37	5	112173387	112173387	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1060503336	NA	P-0042650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	30	307	0	ENST00000257430.4:c.2096G>A	p.Trp699Ter	p.W699*	ENST00000257430	NM_000038.5	699	tGg/tAg	16/16	1	2	FACETS	0.968	0.803	1	0.968	0.803	1	CLONAL	1	TRUE	1	0.688753734609924	2		307	90	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591911	48591911	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	47	440	0	ENST00000342988.3:c.1074del	p.Gly359GlufsTer25	p.G359Efs*25	ENST00000342988	NM_005359.5	358	ggA/gg	9/12	0.630875012468096	1	FACETS	0.973	0.856	1	0.973	0.856	1	CLONAL	1	TRUE	0	0.688753734609924	1		440	92	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	162	384	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.794225502874175	2		384	408	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0042658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	125	262	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.794225502874175	2		263	301	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0042658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	206	557	2	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	1	2	FACETS	0.735	0.684	0.787	0.735	0.684	0.787	SUBCLONAL	1	TRUE	1	0.794225502874175	2		559	706	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589591	67589592	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATA	novel	NA	P-0042658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	70	265	0	ENST00000274335.5:c.1356_1358dup	p.Asn453dup	p.N453dup	ENST00000274335		453	tat/tATAat	10/15	1	2	FACETS	0.641	0.565	0.721	0.641	0.565	0.721	SUBCLONAL	1	TRUE	1	0.794225502874175	2		265	275	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429349	78429349	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	256	561	0	ENST00000370768.2:c.1093C>T	p.Gln365Ter	p.Q365*	ENST00000370768	NM_003902.3	365	Caa/Taa	13/20	0.794225502874175	1	FACETS	0.941	0.897	0.984	0.941	0.897	0.984	CLONAL	1	TRUE	0	0.794225502874175	1		561	413	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795201	42795204	+	frameshift_variant	Frame_Shift_Del	DEL	ACTA	ACTA	-	novel	NA	P-0042658-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	58	755	0	ENST00000575354.2:c.2283_2286del	p.Asn762TyrfsTer161	p.N762Yfs*161	ENST00000575354	NM_015125.3	761	ACTAac/ac	10/20	0.794225502874175	1	FACETS	0.185	0.159	0.213	0.185	0.159	0.213	SUBCLONAL	1	TRUE	0	0.794225502874175	1		755	476	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0042660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	91	291	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.917	0.819	1	0.917	0.819	1	CLONAL	1	TRUE	1	0.476071363621431	2		292	417	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0042660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	153	572	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.476071363621431	2	FACETS	0.867	0.795	0.943	0.434	0.397	0.472	CLONAL	1	TRUE	0	0.476071363621431	2		578	741	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101438	27101438	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	209	522	0	ENST00000324856.7:c.4724del	p.Pro1575HisfsTer37	p.P1575Hfs*37	ENST00000324856	NM_006015.4	1574	Ccc/cc	18/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.476071363621431	2		522	769	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	142	484	1	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.902	0.825	0.984	0.902	0.825	0.984	CLONAL	1	TRUE	1	0.476071363621431	2		485	661	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248477	59248478	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGA	novel	NA	P-0042660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	186	567	0	ENST00000371222.2:c.263_265dup	p.Ile88dup	p.I88dup	ENST00000371222	NM_002228.3	88	acc/aTCAcc	1/1	1	2	FACETS	0.998	0.924	1	0.998	0.924	1	CLONAL	1	TRUE	1	0.476071363621431	2		567	783	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332602	65332602	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	112	313	0	ENST00000342505.4:c.937T>C	p.Tyr313His	p.Y313H	ENST00000342505	NM_002227.2	313	Tac/Cac	7/25	1	2	FACETS	0.974	0.881	1	0.974	0.881	1	CLONAL	1	TRUE	1	0.476071363621431	2		313	483	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324051	123324051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752501698	NA	P-0042660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	203	530	2	ENST00000358487.5:c.419C>T	p.Ala140Val	p.A140V	ENST00000358487	NM_000141.4	140	gCg/gTg	4/18	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.476071363621431	2		532	813	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534289	534289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894229	NA	P-0042660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	131	511	0	ENST00000451590.1:c.34G>A	p.Gly12Ser	p.G12S	ENST00000451590	NM_001130442.1	12	Ggc/Agc	2/5	1	2	FACETS	0.992	0.904	1	0.992	0.904	1	CLONAL	1	TRUE	1	0.476071363621431	2		511	555	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742463	17742463	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	179	515	2	ENST00000250003.3:c.650del	p.Pro217ArgfsTer33	p.P217Rfs*33	ENST00000250003	NM_002478.4	215	ggC/gg	2/3	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.476071363621431	2		517	688	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202177	108202177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754395517	NA	P-0042660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	69	279	0	ENST00000278616.4:c.7522G>A	p.Gly2508Arg	p.G2508R	ENST00000278616	NM_000051.3	2508	Gga/Aga	51/63	1	2	FACETS	0.865	0.759	0.978	0.865	0.759	0.978	CLONAL	1	TRUE	1	0.476071363621431	2		279	335	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422930	49422930	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	179	644	0	ENST00000301067.7:c.14165del	p.Phe4722SerfsTer75	p.F4722Sfs*75	ENST00000301067	NM_003482.3	4722	tTc/tc	44/54	1	2	FACETS	0.941	0.869	1	0.941	0.869	1	CLONAL	1	TRUE	1	0.476071363621431	2		644	799	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487184	56487184	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs771935902	NA	P-0042660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	131	520	3	ENST00000267101.3:c.1330C>T	p.Arg444Ter	p.R444*	ENST00000267101	NM_001982.3	444	Cga/Tga	12/28	1	2	FACETS	0.803	0.73	0.88	0.803	0.73	0.88	CLONAL	1	TRUE	1	0.476071363621431	2		523	685	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	128	407	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.907	0.825	0.993	0.907	0.825	0.993	CLONAL	1	TRUE	1	0.476071363621431	2		407	593	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121925	2121925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45486196	NA	P-0042660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	196	642	1	ENST00000219476.3:c.2087G>A	p.Cys696Tyr	p.C696Y	ENST00000219476	NM_000548.3	696	tGc/tAc	19/42	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.476071363621431	2		643	790	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041743	14041743	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs146764714	NA	P-0042660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	144	411	0	ENST00000311895.7:c.2290A>G	p.Ser764Gly	p.S764G	ENST00000311895	NM_005236.2	764	Agc/Ggc	11/11	1	2	FACETS	0.936	0.857	1	0.936	0.857	1	CLONAL	1	TRUE	1	0.476071363621431	2		411	646	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772302	68772302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555509780	NA	P-0042660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	170	608	0	ENST00000261769.5:c.151G>A	p.Val51Ile	p.V51I	ENST00000261769	NM_004360.3	51	Gtc/Atc	2/16	1	2	FACETS	0.904	0.833	0.978	0.904	0.833	0.978	CLONAL	1	TRUE	1	0.476071363621431	2		608	790	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696731	47696731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	244	354	0	ENST00000347630.2:c.217C>T	p.Pro73Ser	p.P73S	ENST00000347630	NM_001007230.1	73	Ccc/Tcc	5/11	0.476071363621431	2	FACETS	0.969	0.915	1	0.969	0.915	1	CLONAL	2	TRUE	0	0.476071363621431	2		354	529	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732954	74732954	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	93	355	1	ENST00000359995.5:c.289G>T	p.Asp97Tyr	p.D97Y	ENST00000359995	NM_001195427.1	97	Gac/Tac	1/3	0.476071363621431	2	FACETS	0.932	0.834	1	0.466	0.417	0.518	CLONAL	1	TRUE	0	0.476071363621431	2		356	419	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051649	13051649	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	154	534	0	ENST00000316448.5:c.908C>A	p.Pro303His	p.P303H	ENST00000316448	NM_004343.3	303	cCc/cAc	7/9	1	2	FACETS	0.868	0.796	0.944	0.868	0.796	0.944	CLONAL	1	TRUE	1	0.476071363621431	2		534	745	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210908	36210908	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	218	678	0	ENST00000222270.7:c.662del	p.Gly221AspfsTer18	p.G221Dfs*18	ENST00000222270	NM_014727.1	220	cGg/cg	3/37	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.476071363621431	2		678	813	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753324	42753324	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	224	707	0	ENST00000222329.4:c.940C>A	p.Leu314Met	p.L314M	ENST00000222329	NM_006494.2	314	Ctg/Atg	4/4	1	2	FACETS	0.922	0.858	0.987	0.922	0.858	0.987	CLONAL	1	TRUE	1	0.476071363621431	2		707	1021	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919601	96919601	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144326855	NA	P-0042660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	86	548	1	ENST00000258439.3:c.662C>T	p.Pro221Leu	p.P221L	ENST00000258439	NM_001193304.2	221	cCg/cTg	4/4	1	2	FACETS	0.502	0.444	0.564	0.502	0.444	0.564	SUBCLONAL	1	TRUE	1	0.476071363621431	2		549	720	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806162	1806162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747694886	NA	P-0042660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	221	665	0	ENST00000260795.2:c.1181C>T	p.Thr394Met	p.T394M	ENST00000260795		394	aCg/aTg	8/17	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.476071363621431	2		665	837	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143129653	143129653	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	98	446	0	ENST00000262992.4:c.997G>T	p.Gly333Ter	p.G333*	ENST00000262992	NM_001101669.1	333	Gga/Tga	12/24	1	2	FACETS	0.79	0.707	0.878	0.79	0.707	0.878	SUBCLONAL	1	TRUE	1	0.476071363621431	2		446	521	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38978740	38978740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	89	289	1	ENST00000357387.3:c.766C>T	p.Pro256Ser	p.P256S	ENST00000357387	NM_152756.3	256	Ccc/Tcc	9/38	1	2	FACETS	0.854	0.761	0.952	0.854	0.761	0.952	CLONAL	1	TRUE	1	0.476071363621431	2		290	438	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589610	67589612	+	inframe_deletion	In_Frame_Del	DEL	AAA	AAA	-	novel	NA	P-0042660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	70	254	0	ENST00000274335.5:c.1376_1378del	p.Lys459del	p.K459del	ENST00000274335		458	gAAAaa/gaa	10/15	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.476071363621431	2		254	292	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37141751	37141751	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	126	524	0	ENST00000373509.5:c.826T>A	p.Ser276Thr	p.S276T	ENST00000373509	NM_002648.3	276	Tca/Aca	6/6	1	2	FACETS	0.765	0.694	0.84	0.765	0.694	0.84	SUBCLONAL	1	TRUE	1	0.476071363621431	2		524	692	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553257	106553257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	195	490	0	ENST00000369096.4:c.1222G>A	p.Ala408Thr	p.A408T	ENST00000369096	NM_001198.3	408	Gct/Act	5/7	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.476071363621431	2		490	765	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249459	110249459	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	197	824	1	ENST00000374672.4:c.1114G>A	p.Gly372Ser	p.G372S	ENST00000374672	NM_004235.4	372	Ggt/Agt	4/5	1	2	FACETS	0.81	0.749	0.872	0.81	0.749	0.872	CLONAL	1	TRUE	1	0.476071363621431	2		825	1022	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738378	133738378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772834697	NA	P-0042660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	120	496	0	ENST00000318560.5:c.778G>A	p.Val260Met	p.V260M	ENST00000318560	NM_005157.4	260	Gtg/Atg	4/11	1	2	FACETS	0.829	0.751	0.911	0.829	0.751	0.911	CLONAL	1	TRUE	1	0.476071363621431	2		496	608	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0042671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	29	255	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.961	0.79	1	0.961	0.79	1	CLONAL	1	FALSE	1	0.597324004082864	2		255	101	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740544	58740545	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	rs773913732	NA	P-0042671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	18	713	0	ENST00000305921.3:c.1450_1451del	p.Leu484LysfsTer4	p.L484Kfs*4	ENST00000305921	NM_003620.3	483	acTTta/acta	6/6	1	2	FACETS	0.44	0.334	0.562	0.44	0.334	0.562	SUBCLONAL	1	FALSE	1	0.597324004082864	2		713	137	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956546	93956546	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	11	372	0	ENST00000369303.4:c.2690C>A	p.Pro897Gln	p.P897Q	ENST00000369303	NM_004440.3	897	cCa/cAa	15/17	0.164483676009131	4	FACETS	0.784	0.55	1	0.392	0.275	0.533	INDETERMINATE	1	FALSE	2	0.597324004082864	4		372	75	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855932	76855932	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	14	436	1	ENST00000373344.5:c.5668C>T	p.Gln1890Ter	p.Q1890*	ENST00000373344	NM_000489.3	1890	Cag/Tag	23/35	0.353796819850915	0	FACETS	0.207	0.152	0.273			1	INDETERMINATE	1	FALSE	0	0.597324004082864	0		437	91	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434673	110434673	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1048297070	NA	P-0042671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	120	913	3	ENST00000375856.3:c.3728C>T	p.Thr1243Ile	p.T1243I	ENST00000375856	NM_003749.2	1243	aCc/aTc	1/2	0.340791891342419	1	FACETS	0.328	0.295	0.362	0.328	0.295	0.362	INDETERMINATE	1	FALSE	0	0.597324004082864	1		916	860	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0042672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	392	800	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.511693502667055	3	FACETS	0.953	0.91	0.996	0.953	0.91	0.996	CLONAL	2	TRUE	1	0.586873298874256	3		800	907	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0042672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	95	498	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.511693502667055	3	FACETS	1	0.913	1	0.511	0.457	0.567	CLONAL	1	TRUE	1	0.586873298874256	3		498	410	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99491813	99491813	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042672-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	47	570	1	ENST00000268035.6:c.3598G>A	p.Val1200Ile	p.V1200I	ENST00000268035	NM_000875.3	1200	Gtc/Atc	20/21	0.417440203286968	1	FACETS	0.301	0.254	0.352	0.301	0.254	0.352	SUBCLONAL	1	TRUE	0	0.586873298874256	1		571	376	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0042673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	28	498	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	1	2	FACETS	0.48	0.383	0.59	0.48	0.383	0.59	SUBCLONAL	1	TRUE	1	0.286023662066651	2		498	408	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040640	47040640	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	106	843	1	ENST00000377604.3:c.1275G>A	p.Trp425Ter	p.W425*	ENST00000377604	NM_001204468.1	425	tgG/tgA	13/24	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.286023662066651	2		844	710	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240974	53240974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs907851319	NA	P-0042673-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	105	585	1	ENST00000375401.3:c.1237G>A	p.Val413Met	p.V413M	ENST00000375401	NM_004187.3	413	Gtg/Atg	9/26	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.286023662066651	2		586	535	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0042676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	16	191	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	1	2	FACETS	1	0.81	1	1	0.81	1	CLONAL	1	TRUE	1	0.392285470661275	2		191	75	SUCCESS
APC	324	MSKCC	GRCh37	5	112128143	112128143	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs62619935	NA	P-0042676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	11	215	0	ENST00000257430.4:c.646C>T	p.Arg216Ter	p.R216*	ENST00000257430	NM_000038.5	216	Cga/Tga	7/16	0.392285470661275	1	FACETS	0.716	0.505	0.965	0.716	0.505	0.965	CLONAL	1	TRUE	0	0.392285470661275	1		215	63	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578260	7578260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786204041	NA	P-0042676-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	61	816	0	ENST00000269305.4:c.589G>A	p.Val197Met	p.V197M	ENST00000269305	NM_001126112.2	197	Gtg/Atg	6/11	0.154967698939976	1	FACETS	0.753	0.654	0.86	0.753	0.654	0.86	INDETERMINATE	1	TRUE	0	0.392285470661275	1		816	332	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156723	2156723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	53	783	2	ENST00000434045.2:c.199G>A	p.Val67Met	p.V67M	ENST00000434045	NM_001127598.1	67	Gtg/Atg	3/5	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.318751774048854	2		785	224	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267719	198267719	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042677-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	110	305	0	ENST00000335508.6:c.1760A>G	p.Tyr587Cys	p.Y587C	ENST00000335508	NM_012433.2	587	tAc/tGc	13/25	0.318751774048854	0	FACETS	0.792	0.732	0.851			1	SUBCLONAL	3	FALSE	0	0.318751774048854	0		305	198	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0042695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	52	324	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.216020188312304	2		324	470	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909490	50909490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774130423	NA	P-0042695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	98	841	0	ENST00000440232.2:c.1294C>T	p.Arg432Trp	p.R432W	ENST00000440232	NM_002691.3	432	Cgg/Tgg	11/27	1	2	FACETS	0.873	0.777	0.976	0.873	0.777	0.976	CLONAL	1	TRUE	1	0.216020188312304	2		841	1039	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201059	NA	P-0042708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	570	947	2	ENST00000269305.4:c.856G>T	p.Glu286Ter	p.E286*	ENST00000269305	NM_001126112.2	286	Gaa/Taa	8/11	0.707786519673103	1	FACETS	0.995	0.961	1	0.995	0.961	1	CLONAL	1	TRUE	0	0.707786519673103	1		949	1046	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670844	134670844	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773800250	NA	P-0042708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	223	495	0	ENST00000398015.3:c.755G>A	p.Arg252Gln	p.R252Q	ENST00000398015	NM_004441.4	252	cGa/cAa	3/16	1	2	FACETS	0.905	0.847	0.965	0.905	0.847	0.965	CLONAL	1	TRUE	1	0.707786519673103	2		495	696	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923091	48923091	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0042708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	43	311	0	ENST00000267163.4:c.540-1G>A		p.X180_splice	ENST00000267163	NM_000321.2	180			0.707786519673103	1	FACETS	0.902	0.787	1	0.902	0.787	1	CLONAL	1	TRUE	0	0.707786519673103	1		311	87	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912120	32912120	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	288	793	1	ENST00000380152.3:c.3628G>T	p.Asp1210Tyr	p.D1210Y	ENST00000380152		1210	Gat/Tat	11/27	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.707786519673103	2		794	811	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135777994	135777994	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	285	564	0	ENST00000298552.3:c.2389del	p.Gln797ArgfsTer10	p.Q797Rfs*10	ENST00000298552	NM_001162426.1	797	Cag/ag	18/23	1	2	FACETS	0.955	0.901	1	0.955	0.901	1	CLONAL	1	TRUE	1	0.707786519673103	2		564	843	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135802602	135802602	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042708-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	202	389	0	ENST00000298552.3:c.196G>T	p.Glu66Ter	p.E66*	ENST00000298552	NM_001162426.1	66	Gag/Tag	4/23	1	2	FACETS	0.972	0.907	1	0.972	0.907	1	CLONAL	1	TRUE	1	0.707786519673103	2		389	587	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0042750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	113	255	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.386149907395785	6	FACETS	1	0.973	1	0.791	0.719	0.865	CLONAL	2	TRUE	3	0.533750683658986	6		255	369	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0042750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	662	636	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.533750683658986	6	FACETS	0.925	0.902	0.948	1	0.998	1	CLONAL	6	TRUE	2	0.533750683658986	6		636	924	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942745	68942745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781270008	NA	P-0042750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	83	351	0	ENST00000288368.4:c.557G>A	p.Arg186Gln	p.R186Q	ENST00000288368	NM_024870.2	186	cGg/cAg	6/40	0.155399191280204	4	FACETS	0.75	0.668	0.836	0.75	0.668	0.836	INDETERMINATE	2	TRUE	2	0.533750683658986	4		351	318	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020344	69020344	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	77	325	0	ENST00000288368.4:c.2716T>A	p.Phe906Ile	p.F906I	ENST00000288368	NM_024870.2	906	Ttt/Att	24/40	0.155399191280204	4	FACETS	0.979	0.874	1	0.979	0.874	1	INDETERMINATE	2	TRUE	2	0.533750683658986	4		325	226	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	256470	256470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs3211483	NA	P-0042750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1946	132	447	0	ENST00000264932.6:c.1930G>A	p.Val644Met	p.V644M	ENST00000264932	NM_004168.2	644	Gtg/Atg	15/15	0.533750683658986	16	FACETS	1	0.962	1			1	CLONAL	1	TRUE	NA	0.533750683658986	16		447	2078	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255008	16255008	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753511718	NA	P-0042766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	92	500	3	ENST00000375759.3:c.2273G>A	p.Arg758Gln	p.R758Q	ENST00000375759	NM_015001.2	758	cGa/cAa	11/15	0.366425089593144	4	FACETS	1	0.957	1	0.574	0.511	0.641	CLONAL	1	TRUE	2	0.397758042062046	4		503	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578264	7578274	+	protein_altering_variant	In_Frame_Del	DEL	GATAAGATGCT	GATAAGATGCT	CA	novel	NA	P-0042766-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	208	726	3	ENST00000269305.4:c.575_585delinsTG	p.Gln192_Ile195delinsLeu	p.Q192_I195delinsL	ENST00000269305	NM_001126112.2	192	cAGCATCTTATC/cTG	6/11	0.397758042062046	2	FACETS	0.895	0.837	0.955	0.895	0.837	0.955	CLONAL	2	TRUE	0	0.397758042062046	2		729	584	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0042780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	37	50	0	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	0.32825818805048	1	FACETS	0.345	0.284	0.414	0.345	0.284	0.414	SUBCLONAL	1	TRUE	0	0.32825818805048	1		50	546	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711891	89711891	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876660507	NA	P-0042780-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	19	34	0	ENST00000371953.3:c.509G>T	p.Ser170Ile	p.S170I	ENST00000371953	NM_000314.4	170	aGt/aTt	6/9	0.32825818805048	1	FACETS	0.309	0.234	0.397	0.309	0.234	0.397	SUBCLONAL	1	TRUE	0	0.32825818805048	1		34	313	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36209024	36209024	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042781-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	11	24	0	ENST00000222270.7:c.104G>T	p.Gly35Val	p.G35V	ENST00000222270	NM_014727.1	35	gGa/gTa	1/37	0.345615719861911	5	FACETS	1	0.865	1	0.49	0.351	0.65	INDETERMINATE	1	TRUE	2	0.727014822501673	5		24	43	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866775781	NA	P-0042791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	503	638	1	ENST00000269305.4:c.396G>C	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaC	5/11	0.932516544121315	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.946372124206039	1		639	534	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119789	70119789	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	240	577	0	ENST00000245479.2:c.791G>C	p.Arg264Thr	p.R264T	ENST00000245479	NM_000346.3	264	aGa/aCa	3/3	0.511953090603975	1	FACETS	0.358	0.336	0.381	0.358	0.336	0.381	INDETERMINATE	1	TRUE	0	0.946372124206039	1		577	746	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711947	89711947	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1554900615	NA	P-0042791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	309	425	3	ENST00000371953.3:c.565A>T	p.Arg189Ter	p.R189*	ENST00000371953	NM_000314.4	189	Aga/Tga	6/9	0.946372124206039	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.946372124206039	1		428	333	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424459	49424463	+	frameshift_variant	Frame_Shift_Del	DEL	CTGCC	CTGCC	-	novel	NA	P-0042791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	493	520	0	ENST00000301067.7:c.13760_13764del	p.Gly4587GlufsTer17	p.G4587Efs*17	ENST00000301067	NM_003482.3	4587	gGGCAG/g	41/54	NA	2	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.946372124206039	2		520	902	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425363	49425364	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0042791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	383	662	1	ENST00000301067.7:c.13124dup	p.Pro4376ThrfsTer34	p.P4376Tfs*34	ENST00000301067	NM_003482.3	4375	gga/ggGa	39/54	NA	2	FACETS	0.801	0.763	0.84			1	INDETERMINATE	1	TRUE	NA	0.946372124206039	2		663	1010	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256191	133256191	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	329	486	0	ENST00000320574.5:c.470T>C	p.Phe157Ser	p.F157S	ENST00000320574	NM_006231.2	157	tTc/tCc	6/49	0.129827668457523	5	FACETS	0.986	0.936	1	0.493	0.468	0.519	INDETERMINATE	2	TRUE	1	0.946372124206039	5		486	853	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933481	49933481	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042791-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	458	614	1	ENST00000296474.3:c.2709G>C	p.Glu903Asp	p.E903D	ENST00000296474	NM_002447.2	903	gaG/gaC	11/20	0.946372124206039	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.946372124206039	1		615	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578538	7578538	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1131691037	NA	P-0042826-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	353	1098	0	ENST00000269305.4:c.392A>T	p.Asn131Ile	p.N131I	ENST00000269305	NM_001126112.2	131	aAc/aTc	5/11	0.306028366228204	1	FACETS	0.867	0.824	0.911	1	0.996	1	CLONAL	2	TRUE	0	0.353286126872506	1		1098	949	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426784	121426784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765432081	NA	P-0042827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	27	922	1	ENST00000257555.6:c.475C>T	p.Arg159Trp	p.R159W	ENST00000257555		159	Cgg/Tgg	2/10	1	2	FACETS	0.434	0.346	0.533	0.434	0.346	0.533	SUBCLONAL	1	TRUE	1	0.462997219726872	2		923	269	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466420	120466420	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs552225415	NA	P-0042827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	92	801	0	ENST00000256646.2:c.4699C>T	p.Arg1567Trp	p.R1567W	ENST00000256646	NM_024408.3	1567	Cgg/Tgg	26/34	0.32337044935497	3	FACETS	0.73	0.649	0.817	0.365	0.324	0.409	SUBCLONAL	1	TRUE	1	0.462997219726872	3		801	670	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17354249	17354249	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0042827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	46	419	0	ENST00000375499.3:c.535A>T	p.Lys179Ter	p.K179*	ENST00000375499	NM_003000.2	179	Aaa/Taa	5/8	0.32337044935497	3	FACETS	0.431	0.362	0.507	0.215	0.181	0.254	SUBCLONAL	1	TRUE	1	0.462997219726872	3		419	568	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561027	9561027	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	35	515	0	ENST00000353224.5:c.755A>G	p.Tyr252Cys	p.Y252C	ENST00000353224	NM_177990.2	252	tAc/tGc	4/10	0.462997219726872	1	FACETS	0.214	0.174	0.258	0.214	0.174	0.258	SUBCLONAL	1	TRUE	0	0.462997219726872	1		515	544	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026388	6026388	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0042827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	72	584	0	ENST00000265849.7:c.2006+2T>C		p.X669_splice	ENST00000265849	NM_000535.5	669			0.462997219726872	1	FACETS	0.662	0.582	0.747	0.662	0.582	0.747	SUBCLONAL	1	TRUE	0	0.462997219726872	1		584	361	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939579	76939579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367986587	NA	P-0042827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	151	399	0	ENST00000373344.5:c.1169G>A	p.Arg390His	p.R390H	ENST00000373344	NM_000489.3	390	cGt/cAt	9/35	0.235328708894303	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.462997219726872	2		399	511	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0042829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	356	496	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.924907813193522	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.924907813193522	1		496	388	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	285	473	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.299279250027915	2	FACETS	1	0.994	1	0.667	0.637	0.696	INDETERMINATE	1	TRUE	0	0.924907813193522	2		473	462	SUCCESS
APC	324	MSKCC	GRCh37	5	112175423	112175423	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913329	NA	P-0042829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	193	347	0	ENST00000257430.4:c.4132C>T	p.Gln1378Ter	p.Q1378*	ENST00000257430	NM_000038.5	1378	Cag/Tag	16/16	0.919768480842195	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.924907813193522	2		347	208	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	413	593	0	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	0.924907813193522	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.924907813193522	1		593	445	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164508	47164508	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs201756643	NA	P-0042829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	212	430	0	ENST00000409792.3:c.1618C>T	p.Arg540Ter	p.R540*	ENST00000409792	NM_014159.6	540	Cga/Tga	3/21	0.924907813193522	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.924907813193522	1		430	227	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022914	27022945	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCCGCCGCCAGCAGCCTGGGCAACCCGCCG	CCGCCGCCGCCAGCAGCCTGGGCAACCCGCCG	-	novel	NA	P-0042829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	16	53	0	ENST00000324856.7:c.31_62del	p.Ser11LeufsTer89	p.S11Lfs*89	ENST00000324856	NM_006015.4	7	cCCGCCGCCGCCAGCAGCCTGGGCAACCCGCCG/c	1/20	0.481362911110127	1	FACETS	0.286	0.217	0.364	0.286	0.217	0.364	INDETERMINATE	1	TRUE	0	0.924907813193522	1		53	65	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992914	72992914	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	59	1009	0	ENST00000268489.5:c.1131A>C	p.Glu377Asp	p.E377D	ENST00000268489	NM_006885.3	377	gaA/gaC	2/10	0.469234871339483	1	FACETS	0.094	0.08	0.109	0.094	0.08	0.109	INDETERMINATE	1	TRUE	0	0.924907813193522	1		1009	730	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551231	29551231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042829-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	146	753	0	ENST00000389048.3:c.1399G>A	p.Glu467Lys	p.E467K	ENST00000389048	NM_004304.4	467	Gag/Aag	6/29	0.468557738691625	1	FACETS	0.346	0.317	0.375	0.346	0.317	0.375	INDETERMINATE	1	TRUE	0	0.924907813193522	1		753	491	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696426	47696426	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519966	NA	P-0042834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	146	735	0	ENST00000347630.2:c.397T>G	p.Phe133Val	p.F133V	ENST00000347630	NM_001007230.1	133	Ttc/Gtc	6/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.427040612978813	2		735	459	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193202273	193202273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	60	556	0	ENST00000367435.3:c.1305G>A	p.Met435Ile	p.M435I	ENST00000367435	NM_024529.4	435	atG/atA	14/17	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	FALSE	1	0.427040612978813	2		556	240	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416588	121416588	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	87	758	0	ENST00000257555.6:c.17G>C	p.Ser6Thr	p.S6T	ENST00000257555		6	aGc/aCc	1/10	1	2	FACETS	0.511	0.452	0.575	0.511	0.452	0.575	SUBCLONAL	1	FALSE	1	0.427040612978813	2		758	797	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646672	23646672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	29	628	0	ENST00000261584.4:c.1195C>T	p.Pro399Ser	p.P399S	ENST00000261584	NM_024675.3	399	Cct/Tct	4/13	1	2	FACETS	0.453	0.364	0.553	0.453	0.364	0.553	SUBCLONAL	1	FALSE	1	0.427040612978813	2		628	300	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621158	1621168	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCGGAGCTG	CCCCGGAGCTG	-	novel	NA	P-0042834-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	118	1065	0	ENST00000344749.5:c.978_988del	p.Ser327CysfsTer18	p.S327Cfs*18	ENST00000344749	NM_001136139.2	326	ggCAGCTCCGGGGat/ggat	12/19	1	2	FACETS	0.507	0.456	0.56	0.507	0.456	0.56	SUBCLONAL	1	FALSE	1	0.427040612978813	2		1065	1091	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042835-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	123	384	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	FALSE	1	0.555091518376554	2		384	436	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57569935	57569935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042835-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	111	281	1	ENST00000316660.6:c.115C>T	p.Arg39Trp	p.R39W	ENST00000316660	NM_021127.2	39	Cgg/Tgg	2/2	1	2	FACETS	0.966	0.875	1	0.966	0.875	1	CLONAL	1	FALSE	1	0.555091518376554	2		282	414	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	492	384	0				ENST00000310581	NM_198253.2	-/1132			0.715539711605242	6	FACETS	0.941	0.908	0.973	0.941	0.908	0.973	CLONAL	4	TRUE	2	0.822469146921587	6		384	841	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0042854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	276	469	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.822469146921587	3	FACETS	0.993	0.946	1	0.993	0.946	1	CLONAL	2	TRUE	1	0.822469146921587	3		469	477	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0042854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	1269	775	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.407648100141376	3	FACETS	1	0.998	1			1	INDETERMINATE	3	TRUE	NA	0.822469146921587	3		775	1380	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971124	21971125	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0042854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	372	727	2	ENST00000304494.5:c.233_234del	p.Leu78HisfsTer41	p.L78Hfs*41	ENST00000304494	NM_000077.4	78	cTC/c	2/3	0.822469146921587	3	FACETS	0.872	0.834	0.91	0.872	0.834	0.91	CLONAL	2	TRUE	1	0.822469146921587	3		729	732	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955526	48955526	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0042854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	171	440	2	ENST00000267163.4:c.1642A>T	p.Lys548Ter	p.K548*	ENST00000267163	NM_000321.2	548	Aaa/Taa	17/27	0.822469146921587	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.822469146921587	2		442	206	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022380	26022380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	668	563	5	ENST00000435504.4:c.277G>A	p.Glu93Lys	p.E93K	ENST00000435504		93	Gag/Aag	5/13	0.586294207937207	5	FACETS	0.946	0.921	0.97			1	CLONAL	4	TRUE	NA	0.822469146921587	5		568	959	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509107	66509107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	157	362	2	ENST00000273854.3:c.220G>A	p.Gly74Arg	p.G74R	ENST00000273854	NM_004439.5	74	Gga/Aga	2/18	0.822469146921587	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.822469146921587	2		364	187	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859243	151859243	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	101	395	0	ENST00000262189.6:c.11419G>A	p.Asp3807Asn	p.D3807N	ENST00000262189	NM_170606.2	3807	Gat/Aat	43/59	0.822469146921587	3	FACETS	0.9	0.811	0.993	0.45	0.405	0.497	CLONAL	1	TRUE	1	0.822469146921587	3		395	385	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248153	110248153	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0042854-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	246	671	2	ENST00000374672.4:c.1319C>G	p.Ser440Ter	p.S440*	ENST00000374672	NM_004235.4	440	tCa/tGa	5/5	0.822469146921587	3	FACETS	0.927	0.868	0.987	0.463	0.434	0.494	CLONAL	1	TRUE	1	0.822469146921587	3		673	911	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413171	139413172	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0042859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	181	1218	0	ENST00000277541.6:c.970_971del	p.Val324GlnfsTer6	p.V324Qfs*6	ENST00000277541	NM_017617.3	324	GTc/c	6/34	0.368811335177003	1	FACETS	0.75	0.692	0.812	0.75	0.692	0.812	SUBCLONAL	1	TRUE	0	0.382487723309599	1		1218	1020	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579406	7579406	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	171	1039	0	ENST00000269305.4:c.281C>A	p.Ser94Ter	p.S94*	ENST00000269305	NM_001126112.2	94	tCa/tAa	4/11	0.248447209779247	2	FACETS	1	0.984	1	0.632	0.583	0.683	CLONAL	1	TRUE	0	0.382487723309599	2		1039	707	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692805	89692805	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786204928	NA	P-0042859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	73	394	0	ENST00000371953.3:c.289C>T	p.Gln97Ter	p.Q97*	ENST00000371953	NM_000314.4	97	Cag/Tag	5/9	0.382487723309599	2	FACETS	0.884	0.786	0.985	0.884	0.786	0.985	CLONAL	2	TRUE	0	0.382487723309599	2		394	216	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426373	49426373	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	157	1286	0	ENST00000301067.7:c.12115G>T	p.Glu4039Ter	p.E4039*	ENST00000301067	NM_003482.3	4039	Gag/Tag	39/54	0.10043880673071	4	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.382487723309599	4		1286	1002	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445784	49445784	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0042859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	282	1346	0	ENST00000301067.7:c.1682T>A	p.Leu561Ter	p.L561*	ENST00000301067	NM_003482.3	561	tTg/tAg	10/54	0.10043880673071	4	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.382487723309599	4		1346	1384	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698112	47698112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139920308	NA	P-0042859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	22	421	0	ENST00000233146.2:c.1670C>T	p.Thr557Ile	p.T557I	ENST00000233146	NM_000251.2	557	aCt/aTt	11/16	1	2	FACETS	0.767	0.6	0.956	0.767	0.6	0.956	CLONAL	1	TRUE	1	0.382487723309599	2		421	150	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521052	187521052	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042859-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	84	467	0	ENST00000441802.2:c.12103G>T	p.Gly4035Cys	p.G4035C	ENST00000441802	NM_005245.3	4035	Ggt/Tgt	22/27	0.382487723309599	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.382487723309599	1		467	277	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	85	384	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	FALSE	1	0.491884299869023	2		384	342	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0042870-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	17	262	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.671	0.508	0.858	0.671	0.508	0.858	SUBCLONAL	1	FALSE	1	0.491884299869023	2		263	103	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0042897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	17	868	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.453	0.337	0.591	0.453	0.337	0.591	SUBCLONAL	1	TRUE	1	0.202871423381654	2		869	370	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913381	NA	P-0042897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	44	325	0	ENST00000304494.5:c.322G>A	p.Asp108Asn	p.D108N	ENST00000304494	NM_000077.4	108	Gat/Aat	2/3	0.202871423381654	1	FACETS	0.8	0.671	0.943	0.8	0.671	0.943	CLONAL	1	TRUE	0	0.202871423381654	1		325	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577573	7577573	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0042897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	49	526	0	ENST00000269305.4:c.708C>G	p.Tyr236Ter	p.Y236*	ENST00000269305	NM_001126112.2	236	taC/taG	7/11	1	2	FACETS	0.754	0.637	0.882	0.754	0.637	0.882	SUBCLONAL	1	TRUE	1	0.202871423381654	2		526	641	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637690	52637690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239654517	NA	P-0042897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	13	327	2	ENST00000394830.3:c.2626C>T	p.Arg876Cys	p.R876C	ENST00000394830	NM_018313.4	876	Cgt/Tgt	18/30	1	2	FACETS	0.827	0.592	1	0.827	0.592	1	CLONAL	1	TRUE	1	0.202871423381654	2		329	155	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453149	140453149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913361	NA	P-0042897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	15	338	0	ENST00000288602.6:c.1786G>A	p.Gly596Ser	p.G596S	ENST00000288602	NM_004333.4	596	Ggt/Agt	15/18	1	2	FACETS	0.694	0.509	0.917	0.694	0.509	0.917	SUBCLONAL	1	TRUE	1	0.202871423381654	2		338	213	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368223	45368223	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	31	337	0	ENST00000262160.6:c.1379C>A	p.Ser460Ter	p.S460*	ENST00000262160	NM_005901.5	460	tCa/tAa	11/11	0.202871423381654	1	FACETS	0.883	0.716	1	0.883	0.716	1	CLONAL	1	TRUE	0	0.202871423381654	1		337	311	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192710	94192710	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	23	360	0	ENST00000323929.3:c.1364G>T	p.Gly455Val	p.G455V	ENST00000323929	NM_005591.3	455	gGt/gTt	13/20	1	2	FACETS	0.816	0.637	1	0.816	0.637	1	CLONAL	1	TRUE	1	0.202871423381654	2		360	278	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577568	+	missense_variant	Missense_Mutation	TNP	TAC	TAC	GTA	novel	NA	P-0042897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	46	541	1	ENST00000269305.4:c.713_715inv	p.Cys238_Asn239delinsLeuHis	p.C238_N239delinsLH	ENST00000269305	NM_001126112.2	238	tGTAac/tTACac	7/11	1	2	FACETS	0.689	0.579	0.811	0.689	0.579	0.811	SUBCLONAL	1	TRUE	1	0.202871423381654	2		542	658	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253848	30253848	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042897-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	68	537	0	ENST00000307677.4:c.606G>C	p.Glu202Asp	p.E202D	ENST00000307677	NM_138578.1	202	gaG/gaC	3/3	1	2	FACETS	0.96	0.835	1	0.96	0.835	1	CLONAL	1	TRUE	1	0.202871423381654	2		537	698	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830933	72830933	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs927321584	NA	P-0042930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	18	549	0	ENST00000268489.5:c.5648A>G	p.Lys1883Arg	p.K1883R	ENST00000268489	NM_006885.3	1883	aAa/aGa	9/10	0.4763855074167	1	FACETS	0.136	0.102	0.176	0.136	0.102	0.176	SUBCLONAL	1	TRUE	0	0.774740811094199	1		549	209	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888129	81888129	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs768748750	NA	P-0042930-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	57	496	0	ENST00000359376.3:c.274G>C	p.Glu92Gln	p.E92Q	ENST00000359376	NM_002661.3	92	Gaa/Caa	3/33	0.4763855074167	1	FACETS	0.54	0.472	0.61	0.54	0.472	0.61	SUBCLONAL	1	TRUE	0	0.774740811094199	1		496	167	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0042931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	319	775	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.494215370666966	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.509471056195226	2		775	586	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68965475	68965475	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760923944	NA	P-0042931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	222	683	2	ENST00000288368.4:c.1087C>T	p.Arg363Trp	p.R363W	ENST00000288368	NM_024870.2	363	Cgg/Tgg	9/40	0.509471056195226	3	FACETS	0.844	0.79	0.899	0.844	0.79	0.899	CLONAL	2	TRUE	1	0.509471056195226	3		685	648	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551375	150551375	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	168	916	1	ENST00000369026.2:c.632A>T	p.Glu211Val	p.E211V	ENST00000369026	NM_021960.4	211	gAg/gTg	1/3	0.509471056195226	6	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.509471056195226	6		917	1118	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398006	4398006	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0042931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	51	479	0	ENST00000261254.3:c.572-2A>G		p.X191_splice	ENST00000261254	NM_001759.3	191			NA	2	FACETS	0.648	0.554	0.75			1	INDETERMINATE	1	TRUE	NA	0.509471056195226	2		479	309	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432099	49432099	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	158	831	0	ENST00000301067.7:c.9040C>G	p.Leu3014Val	p.L3014V	ENST00000301067	NM_003482.3	3014	Ctg/Gtg	34/54	0.395548690135705	3	FACETS	1	0.987	1	0.457	0.42	0.494	CLONAL	1	TRUE	0	0.509471056195226	3		831	568	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234422	41234422	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1567782959	NA	P-0042931-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	373	475	0	ENST00000357654.3:c.4356del	p.Ala1453GlnfsTer3	p.A1453Qfs*3	ENST00000357654	NM_007294.3	1452	aaA/aa	12/23	0.211330898911488	6	FACETS	1	0.991	1			1	INDETERMINATE	5	TRUE	NA	0.509471056195226	6		475	547	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042934-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	142	384	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		384	316	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0042956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	194	713	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.297103048973941	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.34	1		713	844	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473644	67473644	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042956-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	149	657	0	ENST00000327367.4:c.724C>T	p.Gln242Ter	p.Q242*	ENST00000327367	NM_005902.3	242	Cag/Tag	6/9	0.297103048973941	1	FACETS	0.884	0.808	0.963	0.884	0.808	0.963	CLONAL	1	TRUE	0	0.34	1		657	823	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0042963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	46	396	1	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	0.209585849490736	2	FACETS	0.922	0.777	1	0.461	0.388	0.541	CLONAL	1	TRUE	0	0.209585849490736	2		397	476	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0042963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	50	399	0	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	0.209585849490736	2	FACETS	0.958	0.813	1	0.479	0.406	0.559	CLONAL	1	TRUE	0	0.209585849490736	2		399	498	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575185	64575513	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATGGCCCACCCTGTGCCTGCTTCAGGGAATGACAGCCAGGAAAAGGGGCTCTTCTGTCTTCCCTTCCTATGTGGGTGGTGATGGGAAGAAAGGGGTGTGGCCCAAGAAAATGGAGTCCCTTGGGTGGCTTGGGCTACTACAGTATGAAGGGGACAAGGCTGGGGGGAGGGAACAATACCCGCTCAGCCACACCGGCATTGACTGTCTGGCCCCTGCGGTCCTCGTTGCCCTTGCCGTGCCAGGTGACCTCAGCTGTCTGCTCCCCATTGGGCCCAAACACTACCCAGGCATGATCCTCAGACAGGGCGAGGTGGACATCCCGGAGACCC	ATGGCCCACCCTGTGCCTGCTTCAGGGAATGACAGCCAGGAAAAGGGGCTCTTCTGTCTTCCCTTCCTATGTGGGTGGTGATGGGAAGAAAGGGGTGTGGCCCAAGAAAATGGAGTCCCTTGGGTGGCTTGGGCTACTACAGTATGAAGGGGACAAGGCTGGGGGGAGGGAACAATACCCGCTCAGCCACACCGGCATTGACTGTCTGGCCCCTGCGGTCCTCGTTGCCCTTGCCGTGCCAGGTGACCTCAGCTGTCTGCTCCCCATTGGGCCCAAACACTACCCAGGCATGATCCTCAGACAGGGCGAGGTGGACATCCCGGAGACCC	-	novel	NA	P-0042963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	89	422	0	ENST00000312049.6:c.504_655-33del		p.X168_splice	ENST00000312049	NM_130799.2	168		3/10	0.209585849490736	2	FACETS	0.944	0.841	1	0.944	0.841	1	CLONAL	2	TRUE	0	0.209585849490736	2		422	450	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12660027	12660027	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	44	469	0	ENST00000251849.4:c.194A>G	p.Lys65Arg	p.K65R	ENST00000251849	NM_002880.3	65	aAg/aGg	2/17	0.209585849490736	2	FACETS	0.864	0.725	1	0.432	0.362	0.509	CLONAL	1	TRUE	0	0.209585849490736	2		469	486	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486257	8486257	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042963-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	40	455	0	ENST00000356435.5:c.2560C>T	p.Gln854Ter	p.Q854*	ENST00000356435		854	Cag/Tag	17/35	0.209585849490736	2	FACETS	0.746	0.619	0.887	0.373	0.309	0.444	SUBCLONAL	1	TRUE	0	0.209585849490736	2		455	512	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609639	81609639	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	286	699	1	ENST00000298171.2:c.1237G>T	p.Gly413Cys	p.G413C	ENST00000298171	NM_000369.2	413	Ggc/Tgc	10/10	0.219913194716711	3	FACETS	1	0.988	1	0.588	0.554	0.622	INDETERMINATE	1	TRUE	1	0.76414999978892	3		700	880	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821140	72821153	+	frameshift_variant	Frame_Shift_Del	DEL	CCGGGCTCGCCGGT	CCGGGCTCGCCGGT	-	novel	NA	P-0042990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	39	742	0	ENST00000268489.5:c.11022_11035del	p.Pro3675GlyfsTer51	p.P3675Gfs*51	ENST00000268489	NM_006885.3	3674	ggACCGGCGAGCCCGGtg/ggtg	10/10	0.76414999978892	1	FACETS	0.085	0.07	0.103	0.085	0.07	0.103	SUBCLONAL	1	TRUE	0	0.76414999978892	1		742	738	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578520	7578568	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGA	AGTTGGCAAAACATCTTGTTGAGGGCAGGGGAGTACTGTAGGAAGAGGA	-	novel	NA	P-0042990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	307	990	0	ENST00000269305.4:c.376-14_410del		p.X126_splice	ENST00000269305	NM_001126112.2	126		5/11	0.689763251057773	1	FACETS	0.675	0.64	0.71	0.675	0.64	0.71	SUBCLONAL	1	TRUE	0	0.76414999978892	1		990	736	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402565	20402565	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	171	365	1	ENST00000346618.3:c.102C>A	p.Asp34Glu	p.D34E	ENST00000346618	NM_001949.4	34	gaC/gaA	1/7	0.564331646849841	2	FACETS	0.663	0.612	0.716	0.332	0.306	0.358	SUBCLONAL	1	TRUE	0	0.76414999978892	2		366	675	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271273	38271273	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042990-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	307	958	0	ENST00000425967.3:c.2435C>G	p.Pro812Arg	p.P812R	ENST00000425967	NM_001174067.1	812	cCc/cGc	19/19	1	2	FACETS	0.762	0.719	0.806	0.762	0.719	0.806	SUBCLONAL	1	TRUE	1	0.76414999978892	2		958	1055	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	68	384	0				ENST00000310581	NM_198253.2	-/1132			0.200642223569712	4	FACETS	0.879	0.769	0.997	0.879	0.769	0.997	CLONAL	2	TRUE	2	0.257327262738838	4		384	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0042997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	117	532	1	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	0.183664986680301	3	FACETS	1	0.951	1	0.717	0.65	0.787	CLONAL	2	TRUE	0	0.257327262738838	3		533	477	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671529	30671529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763745278	NA	P-0042997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	98	727	0	ENST00000376406.3:c.5431C>T	p.Arg1811Cys	p.R1811C	ENST00000376406	NM_014641.2	1811	Cgc/Tgc	10/15	0.257327262738838	3	FACETS	1	0.962	1	0.587	0.524	0.655	CLONAL	1	TRUE	1	0.257327262738838	3		727	732	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578471	7578471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	184	758	0	ENST00000269305.4:c.459del	p.Gly154AlafsTer16	p.G154Afs*16	ENST00000269305	NM_001126112.2	153	ccC/cc	5/11	0.183664986680301	3	FACETS	1	0.981	1	0.783	0.725	0.843	CLONAL	2	TRUE	0	0.257327262738838	3		758	687	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012762	36012762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	24	140	0	ENST00000358208.4:c.206C>T	p.Ser69Phe	p.S69F	ENST00000358208		69	tCc/tTc	2/12	0.200642223569712	4	FACETS	1	0.897	1	0.624	0.492	0.773	CLONAL	1	TRUE	2	0.257327262738838	4		140	188	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55607061	55607061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	55	482	0	ENST00000284073.2:c.430G>A	p.Asp144Asn	p.D144N	ENST00000284073	NM_138962.2	144	Gat/Aat	7/14	0.257327262738838	2	FACETS	0.925	0.793	1	0.463	0.396	0.535	CLONAL	1	TRUE	0	0.257327262738838	2		482	462	SUCCESS
REL	5966	MSKCC	GRCh37	2	61148918	61148918	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	22	316	0	ENST00000295025.8:c.1108G>A	p.Asp370Asn	p.D370N	ENST00000295025	NM_002908.2	370	Gat/Aat	11/11	0.257327262738838	4	FACETS	0.56	0.433	0.707	0.187	0.144	0.236	SUBCLONAL	1	TRUE	1	0.257327262738838	4		316	384	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280738	41280738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343763001	NA	P-0042997-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	49	539	0	ENST00000349496.5:c.2251G>A	p.Asp751Asn	p.D751N	ENST00000349496	NM_001904.3	751	Gat/Aat	15/15	0.257327262738838	2	FACETS	0.888	0.753	1	0.444	0.376	0.518	CLONAL	1	TRUE	0	0.257327262738838	2		539	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs786202799	NA	P-0043037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	330	647	4	ENST00000269305.4:c.376-2A>G		p.X126_splice	ENST00000269305	NM_001126112.2	126			0.575154343712737	2	FACETS	0.993	0.952	1	0.993	0.952	1	CLONAL	2	TRUE	0	0.613068259825175	2		651	542	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251169	115251179	+	frameshift_variant	Frame_Shift_Del	DEL	CATGGCAATCC	CATGGCAATCC	-	novel	NA	P-0043037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	56	260	0	ENST00000369535.4:c.547_557del	p.Gly183CysfsTer9	p.G183Cfs*9	ENST00000369535	NM_002524.4	183	GGATTGCCATGt/t	5/7	0.316969077534589	5	FACETS	0.999	0.86	1			1	INDETERMINATE	1	TRUE	NA	0.613068259825175	5		260	351	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421379	12421379	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043037-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	76	358	0	ENST00000287820.6:c.259G>T	p.Asp87Tyr	p.D87Y	ENST00000287820	NM_015869.4	87	Gat/Tat	2/7	0.586349549419573	3	FACETS	0.892	0.788	1	0.446	0.394	0.502	CLONAL	1	TRUE	1	0.613068259825175	3		358	363	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279450	1279450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs973201915	NA	P-0043069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	435	896	0	ENST00000310581.5:c.2086C>T	p.Arg696Cys	p.R696C	ENST00000310581	NM_198253.2	696	Cgt/Tgt	5/16	0.366777413521029	3	FACETS	0.92	0.88	0.96	0.92	0.88	0.96	INDETERMINATE	2	TRUE	1	0.612086982044942	3		896	1009	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281275	46281275	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	127	424	0	ENST00000371998.3:c.4072C>T	p.Gln1358Ter	p.Q1358*	ENST00000371998		1358	Cag/Tag	21/23	0.518614782349742	4	FACETS	0.977	0.886	1	0.326	0.295	0.357	CLONAL	1	TRUE	1	0.612086982044942	4		424	685	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197318	26197318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1347100402	NA	P-0043069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	189	629	1	ENST00000356476.2:c.161G>A	p.Arg54His	p.R54H	ENST00000356476		54	cGc/cAc	1/1	1	2	FACETS	0.906	0.84	0.973	0.906	0.84	0.973	CLONAL	1	TRUE	1	0.612086982044942	2		630	682	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	532660	532660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748639813	NA	P-0043069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	529	861	1	ENST00000451590.1:c.546G>A	p.Met182Ile	p.M182I	ENST00000451590	NM_001130442.1	182	atG/atA	5/5	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.612086982044942	2		862	831	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573194	64573194	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs149383809	NA	P-0043069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	132	678	0	ENST00000312049.6:c.1098A>T	p.Glu366Asp	p.E366D	ENST00000312049	NM_130799.2	366	gaA/gaT	8/10	0.312184798654384	3	FACETS	0.577	0.523	0.633	0.192	0.174	0.211	INDETERMINATE	1	TRUE	0	0.612086982044942	3		678	977	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577137	7577139	+	inframe_deletion	In_Frame_Del	DEL	CCG	CCG	-	novel	NA	P-0043069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	448	714	0	ENST00000269305.4:c.799_801del	p.Arg267del	p.R267del	ENST00000269305	NM_001126112.2	267	CGG/-	8/11	0.612086982044942	2	FACETS	0.943	0.908	0.978	0.943	0.908	0.978	CLONAL	2	TRUE	0	0.612086982044942	2		714	776	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132400	11132400	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0043069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	558	776	0	ENST00000358026.2:c.2617-1G>C		p.X873_splice	ENST00000358026	NM_001128849.1	873			0.612086982044942	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.612086982044942	2		776	848	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651889	36651889	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs4986866	NA	P-0043069-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	192	581	1	ENST00000244741.5:c.11C>T	p.Pro4Leu	p.P4L	ENST00000244741	NM_000389.4	4	cCg/cTg	2/3	1	2	FACETS	0.915	0.849	0.982	0.915	0.849	0.982	CLONAL	1	TRUE	1	0.612086982044942	2		582	686	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	113	384	0				ENST00000310581	NM_198253.2	-/1132			0.606694733223148	3	FACETS	1	0.908	1	0.502	0.454	0.552	CLONAL	1	TRUE	1	0.606694733223148	3		384	484	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808636	1808636	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762888506	NA	P-0043076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	574	975	2	ENST00000260795.2:c.2249G>A	p.Arg750His	p.R750H	ENST00000260795		750	cGt/cAt	16/17	0.606694733223148	6	FACETS	0.852	0.818	0.887			1	CLONAL	3	TRUE	NA	0.606694733223148	6		977	1638	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860470	151860470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746034306	NA	P-0043076-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	138	578	0	ENST00000262189.6:c.10192C>T	p.Arg3398Trp	p.R3398W	ENST00000262189	NM_170606.2	3398	Cgg/Tgg	43/59	1	2	FACETS	0.927	0.849	1	0.927	0.849	1	CLONAL	1	TRUE	1	0.606694733223148	2		578	491	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41021732	41021732	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043088-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	137	374	0	ENST00000267868.3:c.674C>A	p.Thr225Asn	p.T225N	ENST00000267868	NM_002875.4	225	aCc/aAc	8/10	0.104587628838259	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.815622963793946	0		374	370	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390906	139390909	+	frameshift_variant	Frame_Shift_Del	DEL	GGTG	GGTG	-	novel	NA	P-0043104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	96	939	0	ENST00000277541.6:c.7282_7285del	p.His2428TrpfsTer6	p.H2428Wfs*6	ENST00000277541	NM_017617.3	2428	CACCtg/tg	34/34	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		939	652	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820587	44820593	+	frameshift_variant	Frame_Shift_Del	DEL	TCTTTTG	TCTTTTG	-	novel	NA	P-0043104-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	68	496	0	ENST00000377967.4:c.286_292del	p.Phe96AsnfsTer2	p.F96Nfs*2	ENST00000377967	NM_021140.2	95	tTCTTTTGt/tt	3/29	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		496	636	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316390	14316390	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs113954997	NA	P-0043110-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	164	456	0	ENST00000256196.4:c.215A>T	p.Gln72Leu	p.Q72L	ENST00000256196		72	cAa/cTa	3/6	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		456	880	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0043111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	153	928	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.477213258194005	3	FACETS	0.981	0.898	1	0.49	0.449	0.534	CLONAL	1	TRUE	1	0.477213258194005	3		928	810	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911322	32911322	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs80358533	NA	P-0043111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	202	626	0	ENST00000380152.3:c.2830A>T	p.Lys944Ter	p.K944*	ENST00000380152		944	Aaa/Taa	11/27	0.411514038824288	2	FACETS	0.891	0.835	0.948	0.891	0.835	0.948	CLONAL	2	TRUE	0	0.477213258194005	2		626	475	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508727	148508727	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs267601394	NA	P-0043111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	61	1169	1	ENST00000320356.2:c.1937A>T	p.Tyr646Phe	p.Y646F	ENST00000320356	NM_004456.4	646	tAc/tTc	16/20	1	2	FACETS	0.752	0.652	0.859	0.752	0.652	0.859	SUBCLONAL	1	TRUE	1	0.477213258194005	2		1170	340	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577102	7577102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064793881	NA	P-0043111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	265	923	0	ENST00000269305.4:c.836G>A	p.Gly279Glu	p.G279E	ENST00000269305	NM_001126112.2	279	gGg/gAg	8/11	0.477213258194005	3	FACETS	0.848	0.798	0.899	0.848	0.798	0.899	CLONAL	2	TRUE	1	0.477213258194005	3		923	811	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286206	66286206	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138678484	NA	P-0043111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	127	380	0	ENST00000273854.3:c.1480C>T	p.Arg494Cys	p.R494C	ENST00000273854	NM_004439.5	494	Cgt/Tgt	6/18	0.24428209695137	5	FACETS	1	0.923	1			1	INDETERMINATE	2	TRUE	NA	0.477213258194005	5		380	451	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992838	72992838	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758176150	NA	P-0043111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	307	799	0	ENST00000268489.5:c.1207C>T	p.Leu403Phe	p.L403F	ENST00000268489	NM_006885.3	403	Ctt/Ttt	2/10	0.477213258194005	3	FACETS	0.896	0.853	0.938	0.896	0.853	0.938	CLONAL	3	TRUE	0	0.477213258194005	3		799	593	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068079	94068079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375147203	NA	P-0043111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	58	418	0	ENST00000369303.4:c.883C>T	p.Arg295Cys	p.R295C	ENST00000369303	NM_004440.3	295	Cgt/Tgt	4/17	1	2	FACETS	0.789	0.683	0.903	0.789	0.683	0.903	CLONAL	1	TRUE	1	0.477213258194005	2		418	308	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678720	52678720	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	151	494	0	ENST00000394830.3:c.899G>A	p.Arg300Lys	p.R300K	ENST00000394830	NM_018313.4	300	aGg/aAg	9/30	0.411514038824288	2	FACETS	0.785	0.726	0.846	0.785	0.726	0.846	SUBCLONAL	2	TRUE	0	0.477213258194005	2		494	403	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106507	27106508	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0043111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	114	939	2	ENST00000324856.7:c.6118_6119delinsAA	p.Gly2040Lys	p.G2040K	ENST00000324856	NM_006015.4	2040	GGg/AAg	20/20	0.445367905669441	3	FACETS	0.812	0.731	0.897	0.406	0.365	0.449	CLONAL	1	TRUE	1	0.477213258194005	3		941	729	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120463021	120463021	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0043111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	181	438	0	ENST00000256646.2:c.5311-1G>A		p.X1771_splice	ENST00000256646	NM_024408.3	1771			0.477213258194005	5	FACETS	0.921	0.858	0.985	0.921	0.858	0.985	CLONAL	3	TRUE	2	0.477213258194005	5		438	471	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30100170	30100170	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	215	778	0	ENST00000331968.5:c.1450C>T	p.Pro484Ser	p.P484S	ENST00000331968	NM_002742.2	484	Cct/Tct	10/18	0.450893966105962	4	FACETS	0.821	0.764	0.878	0.41	0.382	0.439	CLONAL	2	TRUE	0	0.477213258194005	4		778	811	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650776	37650776	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0043111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	190	654	0	ENST00000447079.4:c.2249-1G>A		p.X750_splice	ENST00000447079	NM_015083.1	750			0.477213258194005	3	FACETS	0.958	0.893	1	0.958	0.893	1	CLONAL	2	TRUE	1	0.477213258194005	3		654	515	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55704629	55704629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285871661	NA	P-0043111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	128	929	1	ENST00000284073.2:c.692C>T	p.Pro231Leu	p.P231L	ENST00000284073	NM_138962.2	231	cCc/cTc	10/14	0.477213258194005	3	FACETS	0.869	0.788	0.954	0.434	0.394	0.477	CLONAL	1	TRUE	1	0.477213258194005	3		930	765	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760883	59760883	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	110	698	1	ENST00000259008.2:c.3524C>A	p.Thr1175Asn	p.T1175N	ENST00000259008	NM_032043.2	1175	aCt/aAt	20/20	0.477213258194005	3	FACETS	0.885	0.797	0.979	0.443	0.398	0.49	CLONAL	1	TRUE	1	0.477213258194005	3		699	645	SUCCESS
AXL	558	MSKCC	GRCh37	19	41737181	41737182	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0043111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	189	867	2	ENST00000301178.4:c.761_762delinsTT	p.Pro254Leu	p.P254L	ENST00000301178	NM_021913.4	254	cCC/cTT	6/20	0.374981011204025	3	FACETS	1	0.991	1	0.741	0.688	0.796	CLONAL	1	TRUE	1	0.477213258194005	3		869	662	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45864824	45864825	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0043111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	290	1237	2	ENST00000391945.4:c.1194_1195delinsTT	p.Leu399Phe	p.L399F	ENST00000391945	NM_000400.3	398	acCCtc/acTTtc	12/23	0.374981011204025	3	FACETS	0.824	0.777	0.872	0.824	0.777	0.872	CLONAL	2	TRUE	1	0.477213258194005	3		1239	913	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757435	40757435	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238347113	NA	P-0043111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	435	825	0	ENST00000373198.4:c.2863G>A	p.Gly955Arg	p.G955R	ENST00000373198	NM_133170.3	955	Gga/Aga	20/32	0.477213258194005	5	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	2	0.477213258194005	5		825	982	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664806	138664807	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0043111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	62	297	1	ENST00000330315.3:c.758_759delinsTT	p.Ala253Val	p.A253V	ENST00000330315	NM_023067.3	253	gCC/gTT	1/1	0.477213258194005	4	FACETS	0.845	0.74	0.956	0.845	0.74	0.956	CLONAL	2	TRUE	2	0.477213258194005	4		298	227	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964877	55964877	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	136	487	0	ENST00000263923.4:c.2360G>C	p.Arg787Pro	p.R787P	ENST00000263923	NM_002253.2	787	cGg/cCg	16/30	0.24428209695137	5	FACETS	1	0.928	1			1	INDETERMINATE	2	TRUE	NA	0.477213258194005	5		487	482	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530972	187530972	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	224	610	0	ENST00000441802.2:c.10051G>T	p.Glu3351Ter	p.E3351*	ENST00000441802	NM_005245.3	3351	Gag/Tag	15/27	0.477213258194005	4	FACETS	0.958	0.895	1	0.958	0.895	1	CLONAL	2	TRUE	2	0.477213258194005	4		610	724	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628661	187628661	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	226	860	0	ENST00000441802.2:c.2321T>G	p.Leu774Arg	p.L774R	ENST00000441802	NM_005245.3	774	cTg/cGg	2/27	0.477213258194005	4	FACETS	0.835	0.779	0.892	0.835	0.779	0.892	CLONAL	2	TRUE	2	0.477213258194005	4		860	838	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721187	176721187	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	56	472	0	ENST00000439151.2:c.6818G>T	p.Cys2273Phe	p.C2273F	ENST00000439151	NM_022455.4	2273	tGt/tTt	23/23	0.477213258194005	5	FACETS	0.718	0.615	0.83	0.179	0.153	0.208	SUBCLONAL	1	TRUE	1	0.477213258194005	5		472	561	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117717424	117717424	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	44	361	0	ENST00000368508.3:c.783T>A	p.Phe261Leu	p.F261L	ENST00000368508	NM_002944.2	261	ttT/ttA	8/43	1	2	FACETS	0.698	0.59	0.817	0.698	0.59	0.817	SUBCLONAL	1	TRUE	1	0.477213258194005	2		361	264	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718211	117718211	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	80	535	0	ENST00000368508.3:c.646G>T	p.Asp216Tyr	p.D216Y	ENST00000368508	NM_002944.2	216	Gat/Tat	7/43	1	2	FACETS	0.977	0.867	1	0.977	0.867	1	CLONAL	1	TRUE	1	0.477213258194005	2		535	343	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5081733	5081733	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	76	241	0	ENST00000381652.3:c.2443C>A	p.Leu815Ile	p.L815I	ENST00000381652	NM_004972.3	815	Cta/Ata	19/25	0.402166148877431	4	FACETS	0.814	0.722	0.911	0.814	0.722	0.911	CLONAL	2	TRUE	2	0.477213258194005	4		241	289	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137320993	137320993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	252	1114	0	ENST00000481739.1:c.950C>T	p.Ser317Phe	p.S317F	ENST00000481739	NM_002957.4	317	tCc/tTc	7/10	0.477213258194005	5	FACETS	0.839	0.785	0.895	0.336	0.314	0.358	CLONAL	2	TRUE	0	0.477213258194005	5		1114	1080	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15833993	15834015	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	GGGAAAGTGATTCAGTTCAAGGT	GGGAAAGTGATTCAGTTCAAGGT	-	novel	NA	P-0043111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	73	406	0	ENST00000307771.7:c.754_771+5del		p.X252_splice	ENST00000307771	NM_005089.3	252		8/11	0.44785614910448	2	FACETS	0.754	0.662	0.851			1	SUBCLONAL	1	TRUE	NA	0.477213258194005	2		406	406	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932010	39932010	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	252	466	0	ENST00000378444.4:c.2589T>G	p.Ser863Arg	p.S863R	ENST00000378444	NM_001123385.1	863	agT/agG	4/15	0.44785614910448	2	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.477213258194005	2		466	432	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396875	139396875	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043111-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	417	817	0	ENST00000277541.6:c.5233del	p.Val1745CysfsTer53	p.V1745Cfs*53	ENST00000277541	NM_017617.3	1745	Gtg/tg	28/34	0.477213258194005	5	FACETS	1	0.99	1	0.86	0.828	0.892	CLONAL	4	TRUE	0	0.477213258194005	5		817	697	SUCCESS
AR	367	MSKCC	GRCh37	X	66931313	66931313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	83	512	0	ENST00000374690.3:c.1955C>T	p.Pro652Leu	p.P652L	ENST00000374690	NM_000044.3	652	cCc/cTc	4/8	1	2	FACETS	0.813	0.72	0.913	0.813	0.72	0.913	CLONAL	1	TRUE	1	0.420783954263828	2		512	485	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441235	52441235	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs910211860	NA	P-0043120-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	99	473	0	ENST00000460680.1:c.535C>T	p.Arg179Trp	p.R179W	ENST00000460680	NM_004656.3	179	Cgg/Tgg	7/17	0.420783954263828	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.420783954263828	1		473	343	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0043124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	77	426	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	0.283218314452058	1	FACETS	0.452	0.398	0.51	0.452	0.398	0.51	INDETERMINATE	1	TRUE	0	0.510279548655411	1		426	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578291	7578291	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs1427441061	NA	P-0043124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	251	885	0	ENST00000269305.4:c.560-2A>G		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.510279548655411	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.510279548655411	1		885	676	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911490	134911490	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1262078917	NA	P-0043124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	237	605	0	ENST00000398015.3:c.1955C>A	p.Thr652Asn	p.T652N	ENST00000398015	NM_004441.4	652	aCc/aAc	11/16	NA	2	FACETS	1	0.953	1			1	INDETERMINATE	1	TRUE	NA	0.510279548655411	2		605	907	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984826	11984831	+	frameshift_variant	Frame_Shift_Del	DEL	TGGGCA	TGGGCA	G	novel	NA	P-0043124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	191	450	0	ENST00000353533.5:c.372_377delinsG	p.Ser124ArgfsTer6	p.S124Rfs*6	ENST00000353533	NM_003010.3	124	agTGGGCAa/agGa	3/11	0.510279548655411	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.510279548655411	1		450	507	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0043126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	252	339	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.278330634292549	3	FACETS	1	0.99	1	1	0.99	1	INDETERMINATE	2	TRUE	1	0.480922878551668	3		339	534	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0043126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	87	361	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.480922878551668	2		361	318	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106512981	106512981	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0043126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	64	232	0	ENST00000359195.3:c.1996-1G>T		p.X666_splice	ENST00000359195	NM_002649.2	666			1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.480922878551668	2		232	252	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46251015	46251015	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	83	319	0	ENST00000371998.3:c.24G>T	p.Leu8Phe	p.L8F	ENST00000371998		8	ttG/ttT	3/23	NA	2	FACETS	0.941	0.836	1			1	INDETERMINATE	1	TRUE	NA	0.480922878551668	2		319	367	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485280	8485280	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	81	445	0	ENST00000356435.5:c.3100G>T	p.Val1034Leu	p.V1034L	ENST00000356435		1034	Gtg/Ttg	18/35	0.480922878551668	1	FACETS	0.8	0.711	0.893	0.8	0.711	0.893	SUBCLONAL	1	TRUE	0	0.480922878551668	1		445	320	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221284	1221284	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	319	1255	1	ENST00000326873.7:c.810del	p.Ser271AlafsTer16	p.S271Afs*16	ENST00000326873	NM_000455.4	269	aaG/aa	6/10	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	2	TRUE	NA	0.480922878551668	2		1256	632	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944895	31944895	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	76	358	2	ENST00000340398.3:c.206G>T	p.Arg69Met	p.R69M	ENST00000340398	NM_001013699.2	69	aGg/aTg	1/1	NA	2	FACETS	1	0.919	1			1	INDETERMINATE	1	TRUE	NA	0.480922878551668	2		360	302	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281360	49281360	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	168	851	0	ENST00000282018.3:c.407G>T	p.Arg136Leu	p.R136L	ENST00000282018	NM_020377.2	136	cGt/cTt	1/1	0.480922878551668	1	FACETS	0.939	0.868	1	0.939	0.868	1	CLONAL	1	TRUE	0	0.480922878551668	1		851	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577543	7577543	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	140	640	0	ENST00000269305.4:c.738G>C	p.Met246Ile	p.M246I	ENST00000269305	NM_001126112.2	246	atG/atC	7/11	0.4714924496607	1	FACETS	0.941	0.863	1	0.941	0.863	1	CLONAL	1	TRUE	0	0.480922878551668	1		640	470	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56390279	56390279	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0043126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	50	167	0	ENST00000348428.3:c.1019-1G>T		p.X340_splice	ENST00000348428	NM_006785.3	340			1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.480922878551668	2		167	207	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216307	2216307	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	125	623	0	ENST00000398665.3:c.1951C>T	p.Gln651Ter	p.Q651*	ENST00000398665	NM_032482.2	651	Cag/Tag	20/28	0.480922878551668	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.480922878551668	1		623	372	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144097	11144097	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	141	754	1	ENST00000358026.2:c.3678G>T	p.Gln1226His	p.Q1226H	ENST00000358026	NM_001128849.1	1226	caG/caT	26/36	0.480922878551668	1	FACETS	0.95	0.872	1	0.95	0.872	1	CLONAL	1	TRUE	0	0.480922878551668	1		755	469	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144527	11144527	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	106	568	0	ENST00000358026.2:c.3859G>T	p.Glu1287Ter	p.E1287*	ENST00000358026	NM_001128849.1	1287	Gag/Tag	27/36	0.480922878551668	1	FACETS	0.886	0.801	0.974	0.886	0.801	0.974	CLONAL	1	TRUE	0	0.480922878551668	1		568	378	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470949	25470949	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	145	711	0	ENST00000264709.3:c.812A>T	p.Asp271Val	p.D271V	ENST00000264709	NM_175629.2	271	gAc/gTc	7/23	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.480922878551668	2		711	579	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416668	29416668	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	95	446	0	ENST00000389048.3:c.4285C>A	p.Gln1429Lys	p.Q1429K	ENST00000389048	NM_004304.4	1429	Cag/Aag	29/29	NA	2	FACETS	0.988	0.886	1			1	INDETERMINATE	1	TRUE	NA	0.480922878551668	2		446	400	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069466	30069466	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0043126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	122	527	1	ENST00000338641.4:c.1331C>G	p.Ser444Ter	p.S444*	ENST00000338641	NM_000268.3	444	tCa/tGa	12/16	0.480922878551668	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.480922878551668	1		528	364	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217307	66217307	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	44	197	0	ENST00000273854.3:c.2308G>A	p.Gly770Arg	p.G770R	ENST00000273854	NM_004439.5	770	Ggg/Agg	14/18	1	2	FACETS	0.839	0.711	0.978	0.839	0.711	0.978	CLONAL	1	TRUE	1	0.480922878551668	2		197	218	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584452	187584452	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0043126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	52	236	0	ENST00000441802.2:c.3580+1G>T		p.X1194_splice	ENST00000441802	NM_005245.3	1194			1	2	FACETS	0.879	0.756	1	0.879	0.756	1	CLONAL	1	TRUE	1	0.480922878551668	2		236	246	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35857128	35857128	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	34	208	0	ENST00000303115.3:c.49G>T	p.Val17Phe	p.V17F	ENST00000303115	NM_002185.3	17	Gtc/Ttc	1/8	1	2	FACETS	0.67	0.552	0.801	0.67	0.552	0.801	SUBCLONAL	1	TRUE	1	0.480922878551668	2		208	211	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418851	116418851	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	66	284	0	ENST00000397752.3:c.3362T>C	p.Val1121Ala	p.V1121A	ENST00000397752	NM_000245.2	1121	gTt/gCt	17/21	1	2	FACETS	0.966	0.847	1	0.966	0.847	1	CLONAL	1	TRUE	1	0.480922878551668	2		284	284	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347930	70347930	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	124	612	0	ENST00000374080.3:c.3169G>T	p.Ala1057Ser	p.A1057S	ENST00000374080		1057	Gcc/Tcc	22/45	1	2	FACETS	0.874	0.793	0.959	0.874	0.793	0.959	CLONAL	1	TRUE	1	0.480922878551668	2		612	590	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617585	100617585	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043126-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	122	593	0	ENST00000308731.7:c.484G>T	p.Ala162Ser	p.A162S	ENST00000308731	NM_000061.2	162	Gct/Tct	6/19	1	2	FACETS	0.938	0.851	1	0.938	0.851	1	CLONAL	1	TRUE	1	0.480922878551668	2		593	541	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0043132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	166	469	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.494	0.454	0.535	0.494	0.454	0.535	SUBCLONAL	1	TRUE	1	0.844031630250972	2		469	797	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0043132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	17	434	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	1	2	FACETS	0.048	0.035	0.064	0.048	0.035	0.064	SUBCLONAL	1	TRUE	1	0.844031630250972	2		434	837	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0043132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	73	499	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.844031630250972	1	FACETS	0.256	0.225	0.29	0.256	0.225	0.29	SUBCLONAL	1	TRUE	0	0.844031630250972	1		499	390	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832031	72832031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144091993	NA	P-0043132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	111	553	0	ENST00000268489.5:c.4550C>T	p.Ser1517Leu	p.S1517L	ENST00000268489	NM_006885.3	1517	tCg/tTg	9/10	0.844031630250972	1	FACETS	0.366	0.332	0.403	0.366	0.332	0.403	SUBCLONAL	1	TRUE	0	0.844031630250972	1		553	415	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333162	70333162	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs889413336	NA	P-0043132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	227	622	0	ENST00000373644.4:c.1067A>G	p.Gln356Arg	p.Q356R	ENST00000373644	NM_030625.2	356	cAg/cGg	2/12	1	2	FACETS	0.65	0.606	0.694	0.65	0.606	0.694	SUBCLONAL	1	TRUE	1	0.844031630250972	2		622	828	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434106	49434122	+	frameshift_variant	Frame_Shift_Del	DEL	ACCCAGCCTTAAAGGCA	ACCCAGCCTTAAAGGCA	-	novel	NA	P-0043132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	365	612	0	ENST00000301067.7:c.7431_7447del	p.Ala2478SerfsTer22	p.A2478Sfs*22	ENST00000301067	NM_003482.3	2477	gtTGCCTTTAAGGCTGGGTct/gtct	31/54	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.844031630250972	2		612	850	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930601	32930601	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	246	369	1	ENST00000380152.3:c.7472A>T	p.Gln2491Leu	p.Q2491L	ENST00000380152		2491	cAg/cTg	15/27	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.844031630250972	2		370	548	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3799684	3800137	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTTGTTTTAAAATAAGAAAACATGTTTTATTAACTAAAATTTATCTGTTGAGTATAAACTATAGGGTCTCTGGAATGTTATTTTGTAACTAGTTCTTCAAACAAAAAGACATGATGGCCCCTTAAAATCTCAAGTACATGTAATAACGGAATGAACAGAAAATTTAATTTCGTAGAACACTACAATGTCTTTTTCTACATATTCCACTATCATTTCTTTTCCTTCTGTTTTTTCAGAGACAAGGTCTTGCTCTGTTGCCCAGGCTGGAGTGCAGTGGCGTGACCATGGCTCACTGCAGCCTTAACCTCCTAGGCTCAAGTGATCCTCCTGGGTAGCTGGGACTATAGGCATGCACCACCAGGACTGGCTAATTTTTTGATTTTTTGTGGAGATGAGGGTCTCATTATGTTGCCAAGGCTGAACTCAAACTCACCCCGGTTCTGAGTAGCTGGG	CCTTGTTTTAAAATAAGAAAACATGTTTTATTAACTAAAATTTATCTGTTGAGTATAAACTATAGGGTCTCTGGAATGTTATTTTGTAACTAGTTCTTCAAACAAAAAGACATGATGGCCCCTTAAAATCTCAAGTACATGTAATAACGGAATGAACAGAAAATTTAATTTCGTAGAACACTACAATGTCTTTTTCTACATATTCCACTATCATTTCTTTTCCTTCTGTTTTTTCAGAGACAAGGTCTTGCTCTGTTGCCCAGGCTGGAGTGCAGTGGCGTGACCATGGCTCACTGCAGCCTTAACCTCCTAGGCTCAAGTGATCCTCCTGGGTAGCTGGGACTATAGGCATGCACCACCAGGACTGGCTAATTTTTTGATTTTTTGTGGAGATGAGGGTCTCATTATGTTGCCAAGGCTGAACTCAAACTCACCCCGGTTCTGAGTAGCTGGG	-	novel	NA	P-0043132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	222	322	0	ENST00000262367.5:c.3780-453_3780del		p.X1260_splice	ENST00000262367	NM_004380.2	1260		21/31	1	2	FACETS	0.985	0.925	1	0.985	0.925	1	CLONAL	1	TRUE	1	0.844031630250972	2		322	534	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965925	25965925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	132	593	0	ENST00000435504.4:c.3281G>A	p.Gly1094Asp	p.G1094D	ENST00000435504		1094	gGt/gAt	13/13	0.558803015145915	2	FACETS	0.351	0.318	0.386	0.176	0.159	0.193	SUBCLONAL	1	TRUE	0	0.844031630250972	2		593	891	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646021	215646021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	39	454	0	ENST00000260947.4:c.577G>A	p.Glu193Lys	p.E193K	ENST00000260947	NM_000465.2	193	Gag/Aag	4/11	0.558803015145915	2	FACETS	0.14	0.115	0.168	0.07	0.057	0.084	SUBCLONAL	1	TRUE	0	0.844031630250972	2		454	660	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707725	176707725	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043132-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	308	448	0	ENST00000439151.2:c.5782G>T	p.Gly1928Ter	p.G1928*	ENST00000439151	NM_022455.4	1928	Gga/Tga	18/23	0.844031630250972	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.844031630250972	1		448	403	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534286	534286	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs104894228	NA	P-0043138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	439	669	0	ENST00000451590.1:c.37G>C	p.Gly13Arg	p.G13R	ENST00000451590	NM_001130442.1	13	Ggt/Cgt	2/5	0.500780156191202	3	FACETS	0.969	0.935	1			1	CLONAL	3	TRUE	NA	0.558480086789039	3		669	692	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858375	27858375	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043138-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	160	634	0	ENST00000359303.2:c.196C>A	p.Leu66Met	p.L66M	ENST00000359303	NM_003535.2	66	Ctg/Atg	1/1	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.558480086789039	2		634	520	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	107	384	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.639465726651178	2		384	334	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917478	178917478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs587777790	NA	P-0043161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	35	254	0	ENST00000263967.3:c.353G>A	p.Gly118Asp	p.G118D	ENST00000263967	NM_006218.2	118	gGt/gAt	3/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.639465726651178	2		254	81	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220274	55220274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043161-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	5229	809	0	ENST00000275493.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000275493	NM_005228.3	222	Cgc/Tgc	6/28	0.639465726651178	23	FACETS	1	0.998	1	0.929	0.922	0.935	CLONAL	20	TRUE	1	0.639465726651178	23		809	6174	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0043178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	726	794	3	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.703038811476895	2	FACETS	0.975	0.951	0.999	0.975	0.951	0.999	CLONAL	2	TRUE	0	0.712692813948008	2		797	1045	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0043178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	148	326	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	1	2	FACETS	0.905	0.833	0.978	0.905	0.833	0.978	CLONAL	1	TRUE	1	0.712692813948008	2		326	459	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266472	55266472	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs961150162	NA	P-0043178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	226	738	0	ENST00000275493.2:c.2764G>A	p.Glu922Lys	p.E922K	ENST00000275493	NM_005228.3	922	Gag/Aag	23/28	1	2	FACETS	0.849	0.794	0.906	0.849	0.794	0.906	CLONAL	1	TRUE	1	0.712692813948008	2		738	747	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063711	67063711	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	217	300	2	ENST00000412916.2:c.160G>T	p.Glu54Ter	p.E54*	ENST00000412916		54	Gaa/Taa	2/6	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.712692813948008	2		302	519	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186874	142186874	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043178-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	127	270	0	ENST00000350721.4:c.6589A>C	p.Ile2197Leu	p.I2197L	ENST00000350721	NM_001184.3	2197	Atc/Ctc	39/47	1	2	FACETS	0.893	0.817	0.972	0.893	0.817	0.972	CLONAL	1	TRUE	1	0.712692813948008	2		270	399	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821643	72821645	+	inframe_deletion	In_Frame_Del	DEL	CCG	CCG	-	rs762513291	NA	P-0043182-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	11	118	1	ENST00000268489.5:c.10530_10532del	p.Gly3512del	p.G3512del	ENST00000268489	NM_006885.3	3510	ggCGGt/ggt	10/10	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		119	140	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0043183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	97	486	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.127847767253751	3	FACETS	0.79	0.704	0.881	0.79	0.704	0.881	SUBCLONAL	2	TRUE	1	0.177015100090863	3		486	755	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254905	16254905	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs949668986	NA	P-0043183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	97	585	1	ENST00000375759.3:c.2170C>T	p.Arg724Ter	p.R724*	ENST00000375759	NM_015001.2	724	Cga/Tga	11/15	1	2	FACETS	0.755	0.673	0.842	1	0.981	1	SUBCLONAL	2	TRUE	1	0.177015100090863	2		586	726	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646856	37646856	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043183-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	109	577	1	ENST00000447079.4:c.1978C>T	p.Gln660Ter	p.Q660*	ENST00000447079	NM_015083.1	660	Cag/Tag	3/14	1	2	FACETS	0.8	0.718	0.886	1	0.984	1	SUBCLONAL	2	TRUE	1	0.177015100090863	2		578	770	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109321716	109321716	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	183	715	0	ENST00000436639.2:c.707T>A	p.Leu236His	p.L236H	ENST00000436639	NM_014454.2	236	cTt/cAt	4/10	1	2	FACETS	0.946	0.876	1	0.946	0.876	1	CLONAL	1	TRUE	1	0.519099954636557	2		715	745	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412869	63412869	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	214	868	0	ENST00000330258.3:c.298A>T	p.Ser100Cys	p.S100C	ENST00000330258	NM_152424.3	100	Agt/Tgt	2/2	1	2	FACETS	0.98	0.913	1	0.98	0.913	1	CLONAL	1	TRUE	1	0.519099954636557	2		868	841	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741660	17741660	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	68	273	0	ENST00000250003.3:c.331C>G	p.Arg111Gly	p.R111G	ENST00000250003	NM_002478.4	111	Cgc/Ggc	1/3	0.416578592326145	2	FACETS	1	0.895	1	0.511	0.448	0.578	CLONAL	1	TRUE	0	0.427730598737319	2		273	311	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431411	121431411	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	171	546	0	ENST00000257555.6:c.615G>C	p.Lys205Asn	p.K205N	ENST00000257555		205	aaG/aaC	3/10	0.159970030977658	4	FACETS	0.958	0.886	1	0.958	0.886	1	INDETERMINATE	2	TRUE	2	0.427730598737319	4		546	596	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21565464	21565464	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	116	628	0	ENST00000382592.4:c.422A>T	p.Tyr141Phe	p.Y141F	ENST00000382592	NM_014572.2	141	tAc/tTc	3/8	0.414229578708287	2	FACETS	0.901	0.814	0.992	0.45	0.407	0.496	CLONAL	1	TRUE	0	0.427730598737319	2		628	602	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030351	49030351	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	82	246	0	ENST00000267163.4:c.1826C>A	p.Pro609His	p.P609H	ENST00000267163	NM_000321.2	609	cCt/cAt	19/27	0.414229578708287	2	FACETS	0.904	0.813	0.998	0.904	0.813	0.998	CLONAL	2	TRUE	0	0.427730598737319	2		246	212	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003165	42003165	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	257	500	0	ENST00000219905.7:c.2702A>T	p.Gln901Leu	p.Q901L	ENST00000219905	NM_001164273.1	901	cAa/cTa	8/24	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	2	TRUE	NA	0.427730598737319	2		500	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578458	7578458	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	269	573	0	ENST00000269305.4:c.472del	p.Arg158AlafsTer12	p.R158Afs*12	ENST00000269305	NM_001126112.2	158	Cgc/gc	5/11	NA	2	FACETS	0.886	0.836	0.937			1	INDETERMINATE	2	TRUE	NA	0.427730598737319	2		573	710	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256900	41256900	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs80357110	NA	P-0043222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	56	431	0	ENST00000357654.3:c.286G>C	p.Asp96His	p.D96H	ENST00000357654	NM_007294.3	96	Gac/Cac	5/23	0.427730598737319	5	FACETS	0.609	0.521	0.705			1	SUBCLONAL	1	TRUE	NA	0.427730598737319	5		431	706	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792609	33792609	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	12	14	0	ENST00000498907.2:c.712G>T	p.Ala238Ser	p.A238S	ENST00000498907	NM_004364.3	238	Gcg/Tcg	1/1	0.386459227516642	3	FACETS	1	0.837	1	0.42	0.303	0.555	CLONAL	1	TRUE	0	0.427730598737319	3		14	54	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228164	36228535	+	splice_acceptor_variant,splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTGAGAGGTCTGGGGTGTGATGCCTGGGTCAGGGCGCCCCTATGAGAGCTCTTGAGGGTGGGAGTTAACTGTAGAGGTTGGAAACTGAGGCCTGGGGAGGAGACACTAGGTCACTTGAAGAGTTATTTCTAGAGTTAGCCAGGCTCCGTGGCTCATGCCTGTAATCCCGCCACTTTGGGAGGCCGAGGCAGGAGGATCGCATGAGCCCAGGAGTTGGAGACCAGCGTAGGCAACATGGCAAAACCCCATCTCTAAAATAAAAATTTAAAAAAGTTATTTCTAGAGCTGACATCAGAAAAATGAACCCCACCCATTTCCCTGTTAGCTCTGTCTTCAACAGTATATTCCTCCTTCCCCTGCTGCCACCTGCA	GGTGAGAGGTCTGGGGTGTGATGCCTGGGTCAGGGCGCCCCTATGAGAGCTCTTGAGGGTGGGAGTTAACTGTAGAGGTTGGAAACTGAGGCCTGGGGAGGAGACACTAGGTCACTTGAAGAGTTATTTCTAGAGTTAGCCAGGCTCCGTGGCTCATGCCTGTAATCCCGCCACTTTGGGAGGCCGAGGCAGGAGGATCGCATGAGCCCAGGAGTTGGAGACCAGCGTAGGCAACATGGCAAAACCCCATCTCTAAAATAAAAATTTAAAAAAGTTATTTCTAGAGCTGACATCAGAAAAATGAACCCCACCCATTTCCCTGTTAGCTCTGTCTTCAACAGTATATTCCTCCTTCCCCTGCTGCCACCTGCA	-	novel	NA	P-0043222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	98	530	0	ENST00000222270.7:c.7550+2_7551del		p.X2517_splice	ENST00000222270	NM_014727.1	2517		33/37	0.386459227516642	3	FACETS	0.685	0.611	0.764	0.228	0.203	0.255	SUBCLONAL	1	TRUE	0	0.427730598737319	3		530	812	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228640	36228754	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACCAGGTATGGAGTGTGAGCTGGGGGGCGGGTGGTGGTCTGGAAGGGTCTTAGAGAGTGAGCAGGGGTGAGAGAGGTCATTCTGAGCACCAGCCTGGGTGACACTGCTGTCCCTC	ACCAGGTATGGAGTGTGAGCTGGGGGGCGGGTGGTGGTCTGGAAGGGTCTTAGAGAGTGAGCAGGGGTGAGAGAGGTCATTCTGAGCACCAGCCTGGGTGACACTGCTGTCCCTC	-	novel	NA	P-0043222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	96	603	0	ENST00000222270.7:c.7658+1_7659-1del		p.X2553_splice	ENST00000222270	NM_014727.1	2553		34/37	0.386459227516642	3	FACETS	0.594	0.528	0.664	0.198	0.176	0.222	SUBCLONAL	1	TRUE	0	0.427730598737319	3		603	918	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228841	36228959	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGGTGAGTGGGGTTGGGGGGGAGGATGCCCCTTGGGTGGACGGACAGGTGCACTGGGTAGGGGGTACTGTCTGGTTTCTGTCCCCCTCCCCCCTGAGTTCCCTGTTCATCCTGCCCTG	CAGGTGAGTGGGGTTGGGGGGGAGGATGCCCCTTGGGTGGACGGACAGGTGCACTGGGTAGGGGGTACTGTCTGGTTTCTGTCCCCCTCCCCCCTGAGTTCCCTGTTCATCCTGCCCTG	-	novel	NA	P-0043222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	111	583	0	ENST00000222270.7:c.7742+1_7743-1del		p.X2581_splice	ENST00000222270	NM_014727.1	2581		35/37	0.386459227516642	3	FACETS	0.746	0.671	0.827	0.249	0.223	0.276	SUBCLONAL	1	TRUE	0	0.427730598737319	3		583	844	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229091	36229180	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTGGGCTCCCAGTGGCTGTGGGAAGACAGTGGGTGAAGCGAGCCTGTCCGCGGGGACAGAGCACCTGATCTCCCCACCTCATCCCTGC	AGGTGGGCTCCCAGTGGCTGTGGGAAGACAGTGGGTGAAGCGAGCCTGTCCGCGGGGACAGAGCACCTGATCTCCCCACCTCATCCCTGC	-	novel	NA	P-0043222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	82	533	0	ENST00000222270.7:c.7872+2_7873del		p.X2624_splice	ENST00000222270	NM_014727.1	2624		36/37	0.386459227516642	3	FACETS	0.544	0.478	0.614	0.181	0.159	0.205	SUBCLONAL	1	TRUE	0	0.427730598737319	3		533	856	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45864782	45864783	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	133	530	0	ENST00000391945.4:c.1236dup	p.Gly413ArgfsTer10	p.G413Rfs*10	ENST00000391945	NM_000400.3	412	-/A	12/23	0.386459227516642	3	FACETS	1	0.928	1	0.341	0.31	0.374	CLONAL	1	TRUE	0	0.427730598737319	3		530	737	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447079	187447079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	302	568	1	ENST00000232014.4:c.1114G>A	p.Ala372Thr	p.A372T	ENST00000232014	NM_001130845.1	372	Gcc/Acc	5/10	0.386459227516642	3	FACETS	0.864	0.821	0.908	0.864	0.821	0.908	CLONAL	3	TRUE	0	0.427730598737319	3		569	661	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630739	187630739	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	101	513	0	ENST00000441802.2:c.243C>A	p.Asn81Lys	p.N81K	ENST00000441802	NM_005245.3	81	aaC/aaA	2/27	0.427730598737319	2	FACETS	1	0.899	1	0.5	0.449	0.554	CLONAL	1	TRUE	0	0.427730598737319	2		513	472	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80088622	80088637	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	GGAGAACAGGATCAAT	GGAGAACAGGATCAAT	TATTG	novel	NA	P-0043222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	37	416	2	ENST00000265081.6:c.2614_2629delinsTATTG	p.Gly872TyrfsTer2	p.G872Yfs*2	ENST00000265081	NM_002439.4	872	GGAGAACAGGATCAATat/TATTGat	19/24	0.381838609195269	2	FACETS	0.524	0.433	0.625	0.262	0.216	0.313	SUBCLONAL	1	TRUE	0	0.427730598737319	2		418	330	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056274	26056274	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs765547166	NA	P-0043222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	68	426	0	ENST00000343677.2:c.383C>G	p.Pro128Arg	p.P128R	ENST00000343677	NM_005319.3	128	cCt/cGt	1/1	1	2	FACETS	0.688	0.6	0.783	0.688	0.6	0.783	SUBCLONAL	1	TRUE	1	0.427730598737319	2		426	462	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324452	31324470	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CGGGGTCACTCACCGGCCT	CGGGGTCACTCACCGGCCT	-	novel	NA	P-0043222-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	18	329	0	ENST00000412585.2:c.338_343+13del		p.X113_splice	ENST00000412585	NM_005514.6	113		2/8	1	2	FACETS	0.268	0.201	0.347	0.268	0.201	0.347	SUBCLONAL	1	TRUE	1	0.427730598737319	2		329	314	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774113	66774113	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043281-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	159	969	0	ENST00000307102.5:c.589C>G	p.Leu197Val	p.L197V	ENST00000307102	NM_002755.3	197	Cta/Gta	6/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		969	936	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910825	114910825	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	22	538	0	ENST00000543371.1:c.944T>A	p.Val315Asp	p.V315D	ENST00000543371	NM_001198531.1	315	gTc/gAc	9/14	1	2	FACETS	0.327	0.253	0.412	0.327	0.253	0.412	SUBCLONAL	1	TRUE	1	0.422012740579586	2		538	319	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	145	384	0				ENST00000310581	NM_198253.2	-/1132			0.367680043573307	3	FACETS	1	0.98	1	0.62	0.567	0.676	CLONAL	1	TRUE	1	0.419483725064089	3		384	674	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0043292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	430	775	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.368586764320603	2	FACETS	0.988	0.945	1	0.988	0.945	1	CLONAL	2	TRUE	0	0.419483725064089	2		775	1037	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	121	495	2	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	0.419483725064089	3	FACETS	0.929	0.84	1	0.465	0.42	0.512	CLONAL	1	TRUE	1	0.419483725064089	3		497	751	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106649	27106649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	366	755	0	ENST00000324856.7:c.6260G>A	p.Gly2087Glu	p.G2087E	ENST00000324856	NM_006015.4	2087	gGa/gAa	20/20	0.368586764320603	2	FACETS	0.967	0.921	1	0.967	0.921	1	CLONAL	2	TRUE	0	0.419483725064089	2		755	902	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100994	27100994	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	157	686	0	ENST00000324856.7:c.4276G>C	p.Asp1426His	p.D1426H	ENST00000324856	NM_006015.4	1426	Gat/Cat	18/20	0.368586764320603	2	FACETS	0.958	0.879	1	0.479	0.439	0.521	CLONAL	1	TRUE	0	0.419483725064089	2		686	781	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105592	27105592	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	288	586	1	ENST00000324856.7:c.5203G>A	p.Glu1735Lys	p.E1735K	ENST00000324856	NM_006015.4	1735	Gag/Aag	20/20	0.368586764320603	2	FACETS	0.929	0.879	0.98	0.929	0.879	0.98	CLONAL	2	TRUE	0	0.419483725064089	2		587	739	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680771	88680771	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	142	666	0	ENST00000360948.2:c.486C>A	p.Phe162Leu	p.F162L	ENST00000360948	NM_001012338.2	162	ttC/ttA	6/19	0.135721814597267	3	FACETS	0.9	0.82	0.984	0.3	0.273	0.328	INDETERMINATE	1	TRUE	0	0.419483725064089	3		666	910	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780661	56780661	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	101	598	0	ENST00000337432.4:c.676C>T	p.Leu226Phe	p.L226F	ENST00000337432	NM_058216.2	226	Ctt/Ttt	4/9	0.120237901113209	3	FACETS	0.855	0.765	0.951	0.285	0.255	0.317	INDETERMINATE	1	TRUE	0	0.419483725064089	3		598	681	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266217	41266217	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	78	484	0	ENST00000349496.5:c.214C>T	p.Gln72Ter	p.Q72*	ENST00000349496	NM_001904.3	72	Cag/Tag	3/15	1	2	FACETS	0.817	0.721	0.92	0.817	0.721	0.92	CLONAL	1	TRUE	1	0.419483725064089	2		484	455	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295092	1295092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	13	114	0	ENST00000310581.5:c.13C>T	p.Pro5Ser	p.P5S	ENST00000310581	NM_198253.2	5	Ccc/Tcc	1/16	0.367680043573307	3	FACETS	0.302	0.215	0.409	0.151	0.107	0.205	SUBCLONAL	1	TRUE	1	0.419483725064089	3		114	248	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287404	33287404	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	134	590	0	ENST00000374542.5:c.1693C>G	p.Gln565Glu	p.Q565E	ENST00000374542	NM_001141970.1	565	Cag/Gag	6/8	1	2	FACETS	0.951	0.866	1	0.951	0.866	1	CLONAL	1	TRUE	1	0.419483725064089	2		590	672	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950032	44950033	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0043292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	273	308	0	ENST00000377967.4:c.3802_3803dup	p.Pro1269TyrfsTer24	p.P1269Yfs*24	ENST00000377967	NM_021140.2	1267	-/GT	26/29	0.139211097780277	3	FACETS	1	0.963	1			1	INDETERMINATE	3	TRUE	NA	0.419483725064089	3		308	517	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0043295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	428	905	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.290839642845717	3	FACETS	1	0.991	1	0.737	0.707	0.768	INDETERMINATE	2	TRUE	0	0.584958609219021	3		905	855	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041426	42041426	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	189	590	0	ENST00000219905.7:c.5621del	p.Ser1874PhefsTer4	p.S1874Ffs*4	ENST00000219905	NM_001164273.1	1874	tCt/tt	17/24	0.446077932488622	2	FACETS	1	0.992	1	0.746	0.698	0.795	CLONAL	1	TRUE	0	0.584958609219021	2		590	433	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982015	93982015	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0043295-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	86	342	1	ENST00000369303.4:c.1449+1G>A		p.X483_splice	ENST00000369303	NM_004440.3	483			0.532713767598096	4	FACETS	1	0.979	1	0.726	0.648	0.807	CLONAL	1	TRUE	2	0.584958609219021	4		343	321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577555	7577555	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0043297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	153	625	3	ENST00000269305.4:c.726C>A	p.Cys242Ter	p.C242*	ENST00000269305	NM_001126112.2	242	tgC/tgA	7/11	0.18379121435009	2	FACETS	1	0.983	1	0.647	0.592	0.706	CLONAL	1	TRUE	0	0.255214432616796	2		628	926	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70971050	70971050	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043297-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	81	616	0	ENST00000276594.2:c.1211G>C	p.Arg404Thr	p.R404T	ENST00000276594	NM_024504.3	404	aGa/aCa	6/8	0.234259018191777	4	FACETS	0.617	0.541	0.698	0.308	0.27	0.349	SUBCLONAL	1	TRUE	2	0.255214432616796	4		616	1292	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0043317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	431	851	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.752584199425808	2		851	1060	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413049	139413049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064795070	NA	P-0043317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	303	699	0	ENST00000277541.6:c.1093C>T	p.Arg365Cys	p.R365C	ENST00000277541	NM_017617.3	365	Cgc/Tgc	6/34	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.752584199425808	2		699	715	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6035204	6035207	+	frameshift_variant	Frame_Shift_Del	DEL	CTGT	CTGT	-	rs267608154	NA	P-0043317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	519	638	0	ENST00000265849.7:c.861_864del	p.Arg287SerfsTer19	p.R287Sfs*19	ENST00000265849	NM_000535.5	287	agACAG/ag	8/15	0.752584199425808	3	FACETS	0.954	0.919	0.988	0.954	0.919	0.988	CLONAL	2	TRUE	1	0.752584199425808	3		638	995	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506303	120506303	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	213	619	0	ENST00000256646.2:c.1809C>G	p.Ile603Met	p.I603M	ENST00000256646	NM_024408.3	603	atC/atG	11/34	1	2	FACETS	0.687	0.639	0.736	0.687	0.639	0.736	SUBCLONAL	1	TRUE	1	0.752584199425808	2		619	824	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951082	48951082	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	156	368	0	ENST00000267163.4:c.1244T>A	p.Ile415Lys	p.I415K	ENST00000267163	NM_000321.2	415	aTa/aAa	13/27	0.752584199425808	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.752584199425808	1		368	210	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699332	47699332	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0043317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	343	556	0	ENST00000347630.2:c.176C>G	p.Ser59Ter	p.S59*	ENST00000347630	NM_001007230.1	59	tCa/tGa	4/11	0.752584199425808	3	FACETS	0.976	0.933	1	0.976	0.933	1	CLONAL	2	TRUE	1	0.752584199425808	3		556	643	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464507	25464507	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	293	865	0	ENST00000264709.3:c.2006C>G	p.Ser669Cys	p.S669C	ENST00000264709	NM_175629.2	669	tCc/tGc	17/23	0.244029762747877	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.752584199425808	0		865	931	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610583	52610583	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	243	570	0	ENST00000394830.3:c.3590A>C	p.Glu1197Ala	p.E1197A	ENST00000394830	NM_018313.4	1197	gAa/gCa	23/30	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.752584199425808	2		570	602	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521651	89521651	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043317-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	230	665	0	ENST00000336596.2:c.2728A>G	p.Ile910Val	p.I910V	ENST00000336596	NM_005233.5	910	Atc/Gtc	16/17	1	2	FACETS	0.664	0.619	0.709	0.664	0.619	0.709	SUBCLONAL	1	TRUE	1	0.752584199425808	2		665	921	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67593323	67593323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	61	436	0	ENST00000274335.5:c.2069C>T	p.Ser690Phe	p.S690F	ENST00000274335		690	tCt/tTt	15/15	1	2	FACETS	0.938	0.81	1	0.938	0.81	1	CLONAL	1	TRUE	1	0.2529642184311	2		436	514	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469562	25469562	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	171	889	0	ENST00000264709.3:c.1206G>C	p.Gln402His	p.Q402H	ENST00000264709	NM_175629.2	402	caG/caC	10/23	0.205888532214094	2	FACETS	1	0.988	1	0.707	0.65	0.767	CLONAL	1	TRUE	0	0.2529642184311	2		889	956	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434656	99434656	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	130	834	0	ENST00000268035.6:c.743G>C	p.Cys248Ser	p.C248S	ENST00000268035	NM_000875.3	248	tGt/tCt	3/21	1	2	FACETS	0.96	0.869	1	0.96	0.869	1	CLONAL	1	TRUE	1	0.2529642184311	2		834	1071	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845571	72845571	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	96	891	0	ENST00000268489.5:c.3769T>G	p.Cys1257Gly	p.C1257G	ENST00000268489	NM_006885.3	1257	Tgc/Ggc	7/10	0.2529642184311	1	FACETS	0.692	0.615	0.774	0.692	0.615	0.774	SUBCLONAL	1	TRUE	0	0.2529642184311	1		891	958	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578506	7578507	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCA	novel	NA	P-0043319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	168	1052	0	ENST00000269305.4:c.421_423dup	p.Cys141dup	p.C141dup	ENST00000269305	NM_001126112.2	141	-/TGC	5/11	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.2529642184311	2		1052	1299	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940757	49940757	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043319-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	86	766	3	ENST00000296474.3:c.286G>A	p.Ala96Thr	p.A96T	ENST00000296474	NM_002447.2	96	Gct/Act	1/20	1	2	FACETS	0.84	0.743	0.945	0.84	0.743	0.945	CLONAL	1	TRUE	1	0.2529642184311	2		769	809	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0043341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	46	242	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.153532157536909	5	FACETS	0.863	0.727	1	0.288	0.242	0.338	INDETERMINATE	1	TRUE	2	0.370075838692997	5		242	448	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0043341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	45	712	0	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	1	2	FACETS	0.751	0.633	0.879	0.751	0.633	0.879	SUBCLONAL	1	TRUE	1	0.370075838692997	2		712	324	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610293	81610293	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	32	544	0	ENST00000298171.2:c.1891T>A	p.Phe631Ile	p.F631I	ENST00000298171	NM_000369.2	631	Ttc/Atc	10/10	0.28078069041635	4	FACETS	0.501	0.406	0.608			1	SUBCLONAL	1	TRUE	NA	0.370075838692997	4		544	473	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95596406	95596406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	29	420	0	ENST00000393063.1:c.562G>A	p.Glu188Lys	p.E188K	ENST00000393063	NM_030621.3	188	Gaa/Aaa	6/28	NA	2	FACETS	0.415	0.333	0.508			1	INDETERMINATE	1	TRUE	NA	0.370075838692997	2		420	378	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437910	52437910	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	62	797	1	ENST00000460680.1:c.1251G>T	p.Arg417Ser	p.R417S	ENST00000460680	NM_004656.3	417	agG/agT	13/17	1	2	FACETS	0.84	0.728	0.96	0.84	0.728	0.96	CLONAL	1	TRUE	1	0.370075838692997	2		798	399	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172165	32172165	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	26	669	0	ENST00000375023.3:c.2867G>C	p.Cys956Ser	p.C956S	ENST00000375023	NM_004557.3	956	tGt/tCt	19/30	0.189246649637397	4	FACETS	0.47	0.371	0.582	0.235	0.185	0.291	INDETERMINATE	1	TRUE	2	0.370075838692997	4		669	410	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563487	87563487	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043341-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	80	682	0	ENST00000277120.3:c.1875G>C	p.Glu625Asp	p.E625D	ENST00000277120		625	gaG/gaC	16/19	1	2	FACETS	0.888	0.784	0.998	0.888	0.784	0.998	CLONAL	1	TRUE	1	0.370075838692997	2		682	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0043345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	268	496	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.284006371659375	2	FACETS	0.928	0.873	0.984	0.928	0.873	0.984	CLONAL	2	TRUE	0	0.349586091788039	2		496	826	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0043345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	73	385	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.349586091788039	2		385	385	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005348	42005348	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1159446559	NA	P-0043345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	62	371	0	ENST00000219905.7:c.3085-1G>A		p.X1029_splice	ENST00000219905	NM_001164273.1	1029			0.343066244343037	1	FACETS	0.813	0.706	0.928	0.813	0.706	0.928	CLONAL	1	TRUE	0	0.349586091788039	1		371	360	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288140	21288140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	84	549	0	ENST00000354336.3:c.385C>T	p.Arg129Trp	p.R129W	ENST00000354336	NM_005207.3	129	Cgg/Tgg	2/3	1	2	FACETS	0.867	0.768	0.974	0.867	0.768	0.974	CLONAL	1	TRUE	1	0.349586091788039	2		549	554	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905869	50905869	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	129	711	0	ENST00000440232.2:c.841G>A	p.Ala281Thr	p.A281T	ENST00000440232	NM_002691.3	281	Gct/Act	8/27	1	2	FACETS	0.851	0.771	0.935	0.851	0.771	0.935	CLONAL	1	TRUE	1	0.349586091788039	2		711	867	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451810	29451810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	109	677	0	ENST00000389048.3:c.2755G>A	p.Gly919Arg	p.G919R	ENST00000389048	NM_004304.4	919	Ggg/Agg	16/29	1	2	FACETS	0.902	0.811	0.999	0.902	0.811	0.999	CLONAL	1	TRUE	1	0.349586091788039	2		677	691	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0043357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	609	851	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		851	840	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179197	123179197	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043357-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	53	431	0	ENST00000218089.9:c.646C>T	p.Arg216Ter	p.R216*	ENST00000218089	NM_001042749.1	216	Cga/Tga	8/35	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		431	515	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118709	115118709	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs756408358	NA	P-0043407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	70	541	0	ENST00000257566.3:c.632A>C	p.Asn211Thr	p.N211T	ENST00000257566	NM_016569.3	211	aAc/aCc	2/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.20737274519115	2		541	480	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849488	68849491	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	novel	NA	P-0043407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	53	668	0	ENST00000261769.5:c.1395_1398del	p.Leu466ProfsTer14	p.L466Pfs*14	ENST00000261769	NM_004360.3	464	gTCTCt/gt	10/16	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.20737274519115	2		668	354	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425634	49425634	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	43	783	0	ENST00000301067.7:c.12854del	p.Gly4285AlafsTer99	p.G4285Afs*99	ENST00000301067	NM_003482.3	4285	gGc/gc	39/54	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.20737274519115	2		783	344	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339270	+	inframe_deletion	In_Frame_Del	DEL	GGTTTCAATAACCAGCCT	GGTTTCAATAACCAGCCT	-	novel	NA	P-0043407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	26	631	0	ENST00000374080.3:c.131_148del	p.Gly44_Pro49del	p.G44_P49del	ENST00000374080		44	GGTTTCAATAACCAGCCT/-	2/45	0.107938080277843	0	FACETS	0.504	0.399	0.625			1	INDETERMINATE	1	TRUE	0	0.20737274519115	0		631	394	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038879	12038879	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	58	278	0	ENST00000396373.4:c.1172A>G	p.Tyr391Cys	p.Y391C	ENST00000396373	NM_001987.4	391	tAt/tGt	7/8	1	2	FACETS	0.846	0.731	0.97	0.846	0.731	0.97	CLONAL	1	TRUE	1	0.401962830875472	2		278	341	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832212	72832212	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0043416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	23	445	0	ENST00000268489.5:c.4369G>T	p.Glu1457Ter	p.E1457*	ENST00000268489	NM_006885.3	1457	Gag/Tag	9/10	0.401962830875472	1	FACETS	0.204	0.158	0.257	0.204	0.158	0.257	SUBCLONAL	1	TRUE	0	0.401962830875472	1		445	449	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42843742	42843827	+	frameshift_variant	Frame_Shift_Del	DEL	TCAGAGGCTTCTGCAGCTTCATCAGCGCAATGTCATTGTTCTTGGTCTTGGAGTCATAATTTGGATGAGAAATCACTTTTTCTACT	TCAGAGGCTTCTGCAGCTTCATCAGCGCAATGTCATTGTTCTTGGTCTTGGAGTCATAATTTGGATGAGAAATCACTTTTTCTACT	-	novel	NA	P-0043416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	92	467	0	ENST00000398585.3:c.1092_1177del	p.Gln364HisfsTer51	p.Q364Hfs*51	ENST00000398585	NM_001135099.1	364	caAGTAGAAAAAGTGATTTCTCATCCAAATTATGACTCCAAGACCAAGAACAATGACATTGCGCTGATGAAGCTGCAGAAGCCTCTGAct/cact	10/14	1	2	FACETS	0.777	0.692	0.868	0.777	0.692	0.868	SUBCLONAL	1	TRUE	1	0.401962830875472	2		467	589	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931588	NA	P-0043421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	32	66	0	ENST00000349496.5:c.94G>T	p.Asp32Tyr	p.D32Y	ENST00000349496	NM_001904.3	32	Gac/Tac	3/15	0.779935910354874	6	FACETS	0.864	0.727	1	0.864	0.727	1	CLONAL	3	TRUE	3	0.779935910354874	6		66	81	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023722	27023722	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	55	146	0	ENST00000324856.7:c.828del	p.Gly277AlafsTer86	p.G277Afs*86	ENST00000324856	NM_006015.4	276	ggA/gg	1/20	0.779935910354874	6	FACETS	1	0.946	1	1	0.946	1	CLONAL	3	TRUE	3	0.779935910354874	6		146	108	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106662	27106669	+	frameshift_variant	Frame_Shift_Del	DEL	GGCAGTTT	GGCAGTTT	-	novel	NA	P-0043421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	48	87	0	ENST00000324856.7:c.6274_6281del	p.Ala2092ProfsTer4	p.A2092Pfs*4	ENST00000324856	NM_006015.4	2091	tgGGCAGTTTgc/tggc	20/20	0.779935910354874	6	FACETS	1	0.937	1	0.767	0.664	0.874	CLONAL	2	TRUE	3	0.779935910354874	6		87	137	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512326	120512326	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	23	61	0	ENST00000256646.2:c.916C>T	p.Pro306Ser	p.P306S	ENST00000256646	NM_024408.3	306	Ccc/Tcc	6/34	0.536435275295821	6	FACETS	1	0.819	1	0.51	0.41	0.618	CLONAL	2	TRUE	2	0.779935910354874	6		61	74	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462833	69462833	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	25	196	0	ENST00000227507.2:c.646A>C	p.Asn216His	p.N216H	ENST00000227507	NM_053056.2	216	Aac/Cac	4/5	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.779935910354874	NA		196	67	SUCCESS
ATM	472	MSKCC	GRCh37	11	108214021	108214021	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1293051732	NA	P-0043421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	16	42	0	ENST00000278616.4:c.8341G>T	p.Val2781Phe	p.V2781F	ENST00000278616	NM_000051.3	2781	Gtt/Ttt	57/63	0.702218684123652	5	FACETS	0.84	0.644	1			1	CLONAL	2	TRUE	NA	0.779935910354874	5		42	53	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871632	35871633	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	31	63	0	ENST00000216797.5:c.873dup	p.Glu292ArgfsTer15	p.E292Rfs*15	ENST00000216797	NM_020529.2	291	-/A	5/6	NA	2	FACETS	0.657	0.542	0.782			1	INDETERMINATE	1	TRUE	NA	0.779935910354874	2		63	121	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871739	35871739	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	40	86	0	ENST00000216797.5:c.767T>A	p.Leu256His	p.L256H	ENST00000216797	NM_020529.2	256	cTc/cAc	5/6	NA	2	FACETS	0.712	0.603	0.829			1	INDETERMINATE	1	TRUE	NA	0.779935910354874	2		86	144	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883608	37883608	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	49	197	0	ENST00000269571.5:c.3220C>A	p.Pro1074Thr	p.P1074T	ENST00000269571		1074	Cca/Aca	26/27	0.779935910354874	7	FACETS	1	0.949	1	0.61	0.527	0.696	CLONAL	2	TRUE	3	0.779935910354874	7		197	152	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856368	45856368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3	34	264	0	ENST00000391945.4:c.1804G>A	p.Gly602Ser	p.G602S	ENST00000391945	NM_000400.3	602	Ggc/Agc	19/23	0.680078918909949	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	3	TRUE	0	0.779935910354874	3		264	37	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361151	66361151	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	12	48	0	ENST00000273854.3:c.1021G>T	p.Asp341Tyr	p.D341Y	ENST00000273854	NM_004439.5	341	Gat/Tat	4/18	NA	2	FACETS	1	0.829	1			1	INDETERMINATE	1	TRUE	NA	0.779935910354874	2		48	27	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099790	157099799	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCCCGGCG	GGCCCCGGCG	-	novel	NA	P-0043421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	26	96	0	ENST00000346085.5:c.728_737del	p.Gly243AlafsTer20	p.G243Afs*20	ENST00000346085	NM_020732.3	243	GGCCCCGGCGgc/gc	1/20	0.779935910354874	4	FACETS	1	0.935	1			1	CLONAL	1	TRUE	NA	0.779935910354874	4		96	84	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141549543	141549543	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043421-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	10	92	0	ENST00000220592.5:c.2045A>T	p.His682Leu	p.H682L	ENST00000220592	NM_012154.3	682	cAc/cTc	16/19	0.779935910354874	4	FACETS	0.815	0.565	1	0.408	0.282	0.557	CLONAL	1	TRUE	2	0.779935910354874	4		92	56	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156742	20156742	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0043422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	44	307	0	ENST00000379607.5:c.17-2A>G		p.X6_splice	ENST00000379607	NM_001412.3	6			1	1	FACETS	0.77	0.659	0.888	1	0.965	1	SUBCLONAL	2	TRUE	0	0.327196253611155	1		307	146	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120146	70120146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043422-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	53	270	0	ENST00000245479.2:c.1148C>T	p.Thr383Ile	p.T383I	ENST00000245479	NM_000346.3	383	aCc/aTc	3/3	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.327196253611155	2		270	262	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035194	30035216	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTTACAGGTACATCAGTCAAGG	TCTTACAGGTACATCAGTCAAGG	-	novel	NA	P-0043423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	16	229	0	ENST00000338641.4:c.356_363+15del		p.X119_splice	ENST00000338641	NM_000268.3	119		3/16	0.477742866842195	1	FACETS	0.836	0.636	1	0.836	0.636	1	CLONAL	1	FALSE	0	0.477742866842195	1		229	61	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321298	1321298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757079410	NA	P-0043423-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	37	290	0	ENST00000400841.2:c.457C>T	p.Arg153Trp	p.R153W	ENST00000400841		153	Cgg/Tgg	4/6	1	1	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	FALSE	0	0.477742866842195	1		290	110	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265618	152265618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043426-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	189	479	0	ENST00000206249.3:c.1071G>A	p.Met357Ile	p.M357I	ENST00000206249	NM_000125.3	357	atG/atA	4/8	0.697635245085779	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.697635245085779	1		479	336	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0043473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	102	868	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.424638772113122	3	FACETS	0.754	0.681	0.831	0.754	0.681	0.831	SUBCLONAL	2	TRUE	1	0.454576726007198	3		869	365	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981791	101981791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	118	588	1	ENST00000282441.5:c.212C>T	p.Ala71Val	p.A71V	ENST00000282441	NM_001130145.2	71	gCc/gTc	1/9	0.454576726007198	3	FACETS	0.915	0.827	1	0.458	0.413	0.505	CLONAL	1	TRUE	1	0.454576726007198	3		589	696	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892253	9892253	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	206	518	0	ENST00000330684.3:c.2237A>G	p.Lys746Arg	p.K746R	ENST00000330684	NM_001134407.1	746	aAg/aGg	11/13	0.319595063308428	4	FACETS	0.923	0.86	0.988	0.923	0.86	0.988	CLONAL	2	TRUE	2	0.454576726007198	4		518	714	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0043473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	319	447	0	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.454576726007198	2	FACETS	0.993	0.944	1	0.993	0.944	1	CLONAL	2	TRUE	0	0.454576726007198	2		447	707	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419991	152419991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745984515	NA	P-0043473-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	134	616	1	ENST00000206249.3:c.1678G>A	p.Val560Met	p.V560M	ENST00000206249	NM_000125.3	560	Gtg/Atg	8/8	0.13238439556752	4	FACETS	1	0.976	1	0.603	0.549	0.66	INDETERMINATE	1	TRUE	2	0.454576726007198	4		617	711	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593603	55593603	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913235	NA	P-0043479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	181	359	0	ENST00000288135.5:c.1669T>A	p.Trp557Arg	p.W557R	ENST00000288135	NM_000222.2	557	Tgg/Agg	11/21	1	2	FACETS	0.917	0.854	0.981	0.917	0.854	0.981	CLONAL	1	TRUE	1	0.834905901755134	2		359	473	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453395	40453395	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1451895133	NA	P-0043479-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	265	713	0	ENST00000345506.4:c.1092G>T	p.Met364Ile	p.M364I	ENST00000345506	NM_003152.3	364	atG/atT	10/20	1	2	FACETS	0.656	0.616	0.698	0.656	0.616	0.698	SUBCLONAL	1	TRUE	1	0.834905901755134	2		713	967	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155385	106155385	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1187881284	NA	P-0043556-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	61	478	0	ENST00000380013.4:c.286C>T	p.Arg96Cys	p.R96C	ENST00000380013	NM_001127208.2	96	Cgc/Tgc	3/11	1	2	FACETS	0.694	0.598	0.798	0.694	0.598	0.798	SUBCLONAL	1	TRUE	1	0.272720363652486	2		478	645	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	668	572	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.926	0.897	0.955	1	0.998	1	CLONAL	2	TRUE	1	0.573410274389233	2		578	1258	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	87	415	0	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	0.867	0.774	0.965	0.867	0.774	0.965	CLONAL	1	TRUE	1	0.573410274389233	2		415	350	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	181	255	3	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.573410274389233	2		258	613	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429978	78429978	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	34	120	2	ENST00000370768.2:c.901del	p.Ile301TyrfsTer22	p.I301Yfs*22	ENST00000370768	NM_003902.3	301	Ata/ta	11/20	1	2	FACETS	0.567	0.467	0.678	0.567	0.467	0.678	SUBCLONAL	1	TRUE	1	0.573410274389233	2		122	209	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	59	255	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.975	0.851	1	0.975	0.851	1	CLONAL	1	TRUE	1	0.573410274389233	2		255	211	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	109	479	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	1	2	FACETS	0.469	0.421	0.521	0.469	0.421	0.521	SUBCLONAL	1	TRUE	1	0.573410274389233	2		481	810	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	345	234	0	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.573410274389233	1		234	683	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	156	357	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.922	0.848	0.999	0.922	0.848	0.999	CLONAL	1	TRUE	1	0.573410274389233	2		357	590	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223796	53223796	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	539	308	0	ENST00000375401.3:c.3563G>C	p.Cys1188Ser	p.C1188S	ENST00000375401	NM_004187.3	1188	tGt/tCt	23/26	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.573410274389233	1		308	912	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965666	90965666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	27	90	0	ENST00000265433.3:c.1651del	p.Arg551GlyfsTer8	p.R551Gfs*8	ENST00000265433	NM_002485.4	551	Agg/gg	11/16	1	2	FACETS	0.766	0.62	0.926	0.766	0.62	0.926	CLONAL	1	TRUE	1	0.573410274389233	2		90	123	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105841	27105841	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	220	320	1	ENST00000324856.7:c.5452C>T	p.Gln1818Ter	p.Q1818*	ENST00000324856	NM_006015.4	1818	Cag/Tag	20/20	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.573410274389233	2		321	760	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631918	90631918	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs747216375	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	382	492	4	ENST00000330062.3:c.435del	p.Thr146LeufsTer15	p.T146Lfs*15	ENST00000330062	NM_002168.2	145	ggG/gg	4/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.573410274389233	2		496	1264	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	329	539	4	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	NA	2	FACETS	0.835	0.788	0.884			1	INDETERMINATE	1	TRUE	NA	0.573410274389233	2		543	1374	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207153	1207155	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs587782056	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1262	435	524	0	ENST00000326873.7:c.250_252del	p.Lys84del	p.K84del	ENST00000326873	NM_000455.4	81	AAG/-	1/10	1	2	FACETS	0.894	0.851	0.939	0.894	0.851	0.939	CLONAL	1	TRUE	1	0.573410274389233	2		524	1697	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023769	27023769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	263	291	0	ENST00000324856.7:c.879del	p.Thr294ProfsTer69	p.T294Pfs*69	ENST00000324856	NM_006015.4	292	aCc/ac	1/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.573410274389233	2		291	898	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792755	33792757	+	inframe_deletion	In_Frame_Del	DEL	GGC	GGC	-	rs746430067	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	10	51	0	ENST00000498907.2:c.564_566del	p.Pro189del	p.P189del	ENST00000498907	NM_004364.3	188	ccGCCc/ccc	1/1	1	2	FACETS	0.317	0.216	0.442	0.317	0.216	0.442	SUBCLONAL	1	TRUE	1	0.573410274389233	2		51	110	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661663	227661664	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761880048	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	227	578	9	ENST00000305123.5:c.1791dup	p.His598AlafsTer13	p.H598Afs*13	ENST00000305123	NM_005544.2	597	-/G	1/2	1	2	FACETS	0.865	0.807	0.925	0.865	0.807	0.925	CLONAL	1	TRUE	1	0.573410274389233	2		587	915	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130702	29130702	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779607427	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	179	234	2	ENST00000328354.6:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000328354	NM_007194.3	3	cGg/cAg	2/15	1	2	FACETS	0.843	0.779	0.909	0.843	0.779	0.909	CLONAL	1	TRUE	1	0.573410274389233	2		236	741	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858337	9858337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs560057284	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	198	249	0	ENST00000330684.3:c.3064C>T	p.Arg1022Cys	p.R1022C	ENST00000330684	NM_001134407.1	1022	Cgc/Tgc	13/13	1	2	FACETS	0.98	0.911	1	0.98	0.911	1	CLONAL	1	TRUE	1	0.573410274389233	2		249	705	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223599	53223599	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556834165	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	314	175	0	ENST00000375401.3:c.3760C>T	p.Arg1254Cys	p.R1254C	ENST00000375401	NM_004187.3	1254	Cgc/Tgc	23/26	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.573410274389233	1		175	540	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332152	70332153	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1196853334	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	92	136	0	ENST00000373644.4:c.65dup	p.Lys23GlufsTer37	p.K23Efs*37	ENST00000373644	NM_030625.2	19	-/A	2/12	1	2	FACETS	0.927	0.832	1	0.927	0.832	1	CLONAL	1	TRUE	1	0.573410274389233	2		136	346	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905061	50905061	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	362	412	2	ENST00000440232.2:c.347del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	115	Ccc/cc	4/27	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.573410274389233	2		414	1238	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346220	152346220	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	87	197	0	ENST00000359321.1:c.350del	p.Leu117TrpfsTer17	p.L117Wfs*17	ENST00000359321	NM_005431.1	117	tTg/tg	3/3	1	2	FACETS	0.985	0.882	1	0.985	0.882	1	CLONAL	1	TRUE	1	0.573410274389233	2		197	308	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123836	46123837	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	143	320	0	ENST00000334344.6:c.109dup	p.Ile37AsnfsTer29	p.I37Nfs*29	ENST00000334344	NM_152641.2	34	-/A	2/21	1	2	FACETS	0.857	0.785	0.932	0.857	0.785	0.932	CLONAL	1	TRUE	1	0.573410274389233	2		320	582	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221765	55221765	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	345	490	0	ENST00000275493.2:c.809A>G	p.Tyr270Cys	p.Y270C	ENST00000275493	NM_005228.3	270	tAc/tGc	7/28	1	2	FACETS	0.948	0.896	1	0.948	0.896	1	CLONAL	1	TRUE	1	0.573410274389233	2		490	1270	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991949	72991949	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs753977275	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	277	353	0	ENST00000268489.5:c.2096del	p.Gly699AlafsTer125	p.G699Afs*125	ENST00000268489	NM_006885.3	699	gGc/gc	2/10	1	2	FACETS	0.904	0.849	0.96	0.904	0.849	0.96	CLONAL	1	TRUE	1	0.573410274389233	2		353	1069	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	343	410	2	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.994	0.941	1	0.994	0.941	1	CLONAL	1	TRUE	1	0.573410274389233	2		412	1203	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213242	39213243	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1558454973	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	363	492	3	ENST00000402219.2:c.3724dup	p.Ser1242LysfsTer2	p.S1242Kfs*2	ENST00000402219	NM_005633.3	1242	agt/aAgt	23/23	NA	2	FACETS	0.862	0.816	0.91			1	INDETERMINATE	1	TRUE	NA	0.573410274389233	2		495	1468	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440861	52440861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1407261660	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	364	487	3	ENST00000460680.1:c.643G>A	p.Gly215Ser	p.G215S	ENST00000460680	NM_004656.3	215	Ggc/Agc	8/17	1	2	FACETS	0.933	0.884	0.983	0.933	0.884	0.983	CLONAL	1	TRUE	1	0.573410274389233	2		490	1361	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012386	152012386	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	57	85	1	ENST00000262189.6:c.427del	p.Ser143ValfsTer3	p.S143Vfs*3	ENST00000262189	NM_170606.2	143	Agt/gt	4/59	1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.573410274389233	2		86	195	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451783	29451784	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs772809305	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	171	457	0	ENST00000389048.3:c.2781dup	p.Cys928ValfsTer20	p.C928Vfs*20	ENST00000389048	NM_004304.4	927	-/G	16/29	NA	2	FACETS	0.485	0.445	0.527			1	INDETERMINATE	1	TRUE	NA	0.573410274389233	2		457	1229	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095625	178095625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765321668	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	55	139	0	ENST00000397062.3:c.1706G>A	p.Arg569His	p.R569H	ENST00000397062	NM_006164.4	569	cGt/cAt	5/5	1	2	FACETS	0.95	0.824	1	0.95	0.824	1	CLONAL	1	TRUE	1	0.573410274389233	2		139	202	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001188	150001188	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	56	153	0	ENST00000253339.5:c.2416C>T	p.Arg806Ter	p.R806*	ENST00000253339		806	Cga/Tga	4/7	0.573410274389233	2	FACETS	0.957	0.832	1	0.479	0.416	0.545	CLONAL	1	TRUE	0	0.573410274389233	2		153	204	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241894	133241894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757051826	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	342	398	1	ENST00000320574.5:c.2462G>A	p.Arg821His	p.R821H	ENST00000320574	NM_006231.2	821	cGc/cAc	21/49	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.573410274389233	2		399	1156	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73047240	73047240	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	35	144	0	ENST00000356692.5:c.51del	p.Lys19ArgfsTer14	p.K19Rfs*14	ENST00000356692		16	aGg/ag	2/9	1	2	FACETS	0.682	0.565	0.81	0.682	0.565	0.81	SUBCLONAL	1	TRUE	1	0.573410274389233	2		144	179	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251216	115251216	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	87	215	0	ENST00000369535.4:c.510del	p.Lys170AsnfsTer19	p.K170Nfs*19	ENST00000369535	NM_002524.4	170	aaA/aa	5/7	1	2	FACETS	0.831	0.742	0.926	0.831	0.742	0.926	CLONAL	1	TRUE	1	0.573410274389233	2		215	365	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988308	36988309	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776709	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	285	303	0	ENST00000354822.5:c.344dup	p.Tyr116LeufsTer323	p.Y116Lfs*323	ENST00000354822	NM_001079668.2	115	ggc/ggGc	2/3	1	2	FACETS	0.943	0.887	1	0.943	0.887	1	CLONAL	1	TRUE	1	0.573410274389233	2		303	1054	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128420046	128420047	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	76	241	0	ENST00000265960.3:c.381dup	p.Ser128IlefsTer28	p.S128Ifs*28	ENST00000265960	NM_001006617.1	127	-/A	4/12	1	2	FACETS	0.615	0.542	0.693	0.615	0.542	0.693	SUBCLONAL	1	TRUE	1	0.573410274389233	2		241	431	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042736	42042736	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	96	187	0	ENST00000219905.7:c.6934del	p.Thr2312LeufsTer23	p.T2312Lfs*23	ENST00000219905	NM_001164273.1	2311	Aaa/aa	17/24	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.573410274389233	2		187	320	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190815	11190815	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	233	294	0	ENST00000361445.4:c.5384T>C	p.Val1795Ala	p.V1795A	ENST00000361445	NM_004958.3	1795	gTg/gCg	39/58	1	2	FACETS	0.986	0.922	1	0.986	0.922	1	CLONAL	1	TRUE	1	0.573410274389233	2		294	824	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45795061	45795061	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	343	443	0	ENST00000450313.1:c.1567del	p.Arg523AlafsTer48	p.R523Afs*48	ENST00000450313	NM_012222.2	523	Cgc/gc	16/16	1	2	FACETS	0.93	0.88	0.982	0.93	0.88	0.982	CLONAL	1	TRUE	1	0.573410274389233	2		443	1286	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410725	32410725	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1564967706	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	166	234	0	ENST00000332351.3:c.1433G>A	p.Ser478Asn	p.S478N	ENST00000332351	NM_024426.4	478	aGt/aAt	10/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.573410274389233	2		234	565	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172450	108172450	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1370155496	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	48	122	0	ENST00000278616.4:c.5253G>T	p.Glu1751Asp	p.E1751D	ENST00000278616	NM_000051.3	1751	gaG/gaT	35/63	1	2	FACETS	0.991	0.852	1	0.991	0.852	1	CLONAL	1	TRUE	1	0.573410274389233	2		122	169	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245483	133245483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200471266	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	340	448	1	ENST00000320574.5:c.1837G>A	p.Val613Ile	p.V613I	ENST00000320574	NM_006231.2	613	Gtt/Att	17/49	1	2	FACETS	0.946	0.895	0.999	0.946	0.895	0.999	CLONAL	1	TRUE	1	0.573410274389233	2		449	1253	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042098	42042098	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	34	177	0	ENST00000219905.7:c.6293T>C	p.Val2098Ala	p.V2098A	ENST00000219905	NM_001164273.1	2098	gTc/gCc	17/24	1	2	FACETS	0.398	0.326	0.478	0.398	0.326	0.478	SUBCLONAL	1	TRUE	1	0.573410274389233	2		177	298	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820686	3820686	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1254	502	593	0	ENST00000262367.5:c.2765C>T	p.Ala922Val	p.A922V	ENST00000262367	NM_004380.2	922	gCc/gTc	14/31	1	2	FACETS	0.997	0.953	1	0.997	0.953	1	CLONAL	1	TRUE	1	0.573410274389233	2		593	1756	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822378	72822378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369772600	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1552	95	601	0	ENST00000268489.5:c.9797C>T	p.Thr3266Met	p.T3266M	ENST00000268489	NM_006885.3	3266	aCg/aTg	10/10	1	2	FACETS	0.201	0.178	0.226	0.201	0.178	0.226	SUBCLONAL	1	TRUE	1	0.573410274389233	2		601	1647	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868240	37868240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	355	502	0	ENST00000269571.5:c.961G>A	p.Glu321Lys	p.E321K	ENST00000269571		321	Gag/Aag	8/27	1	2	FACETS	0.926	0.877	0.977	0.926	0.877	0.977	CLONAL	1	TRUE	1	0.573410274389233	2		502	1337	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508727	38508727	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	323	468	0	ENST00000254066.5:c.775A>G	p.Thr259Ala	p.T259A	ENST00000254066	NM_000964.3	259	Acc/Gcc	6/9	1	2	FACETS	0.853	0.804	0.903	0.853	0.804	0.903	CLONAL	1	TRUE	1	0.573410274389233	2		468	1321	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622310	1622310	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	355	377	0	ENST00000344749.5:c.652+2T>C		p.X218_splice	ENST00000344749	NM_001136139.2	218			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.573410274389233	2		377	1196	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273911	18273911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	329	447	0	ENST00000222254.8:c.1244C>T	p.Ala415Val	p.A415V	ENST00000222254	NM_005027.3	415	gCc/gTc	10/16	1	2	FACETS	0.907	0.857	0.959	0.907	0.857	0.959	CLONAL	1	TRUE	1	0.573410274389233	2		447	1265	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147239	61147239	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	50	175	0	ENST00000295025.8:c.917A>T	p.Asp306Val	p.D306V	ENST00000295025	NM_002908.2	306	gAt/gTt	8/11	1	2	FACETS	0.695	0.595	0.803	0.695	0.595	0.803	SUBCLONAL	1	TRUE	1	0.573410274389233	2		175	251	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326314	62326314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1555814334	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	398	531	1	ENST00000360203.5:c.3334del	p.Leu1112CysfsTer24	p.L1112Cfs*24	ENST00000360203	NM_001283009.1	1110	ttC/tt	32/35	1	2	FACETS	0.941	0.893	0.989	0.941	0.893	0.989	CLONAL	1	TRUE	1	0.573410274389233	2		532	1476	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37061831	37061832	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	204	323	0	ENST00000231790.2:c.917dup	p.Asn306LysfsTer8	p.N306Kfs*8	ENST00000231790	NM_000249.3	305	-/A	11/19	1	2	FACETS	0.981	0.913	1	0.981	0.913	1	CLONAL	1	TRUE	1	0.573410274389233	2		323	725	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169940552	169940552	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	313	458	0	ENST00000295797.4:c.95A>G	p.Tyr32Cys	p.Y32C	ENST00000295797	NM_002740.5	32	tAc/tGc	1/18	1	2	FACETS	0.931	0.878	0.985	0.931	0.878	0.985	CLONAL	1	TRUE	1	0.573410274389233	2		458	1173	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198063	185198063	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs866033821	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	135	201	0	ENST00000265026.3:c.2545A>G	p.Ser849Gly	p.S849G	ENST00000265026	NM_004721.4	849	Agc/Ggc	13/14	1	2	FACETS	0.959	0.877	1	0.959	0.877	1	CLONAL	1	TRUE	1	0.573410274389233	2		201	491	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549406	187549406	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	426	513	0	ENST00000441802.2:c.4712T>C	p.Val1571Ala	p.V1571A	ENST00000441802	NM_005245.3	1571	gTt/gCt	9/27	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.573410274389233	2		513	1371	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628925	187628925	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	235	289	0	ENST00000441802.2:c.2057A>T	p.Lys686Met	p.K686M	ENST00000441802	NM_005245.3	686	aAg/aTg	2/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.573410274389233	2		289	739	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751921	57751921	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs772449059	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	287	398	0	ENST00000274289.3:c.1316A>G	p.Gln439Arg	p.Q439R	ENST00000274289	NM_006622.3	439	cAg/cGg	10/14	1	2	FACETS	0.951	0.895	1	0.951	0.895	1	CLONAL	1	TRUE	1	0.573410274389233	2		398	1053	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672728	86672728	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	41	93	0	ENST00000274376.6:c.2215T>C	p.Tyr739His	p.Y739H	ENST00000274376	NM_002890.2	739	Tat/Cat	17/25	0.137355320369178	0	FACETS	0.462	0.393	0.535			1	INDETERMINATE	1	TRUE	0	0.573410274389233	0		93	132	SUCCESS
APC	324	MSKCC	GRCh37	5	112174049	112174049	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1561579442	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	83	136	0	ENST00000257430.4:c.2758A>G	p.Asn920Asp	p.N920D	ENST00000257430	NM_000038.5	920	Aat/Gat	16/16	0.137355320369178	0	FACETS	0.439	0.392	0.489			1	INDETERMINATE	1	TRUE	0	0.573410274389233	0		136	281	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188914	32188914	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs777281026	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	683	482	0	ENST00000375023.3:c.640A>G	p.Thr214Ala	p.T214A	ENST00000375023	NM_004557.3	214	Acc/Gcc	4/30	0.573410274389233	2	FACETS	0.95	0.92	0.979	0.95	0.92	0.979	CLONAL	2	TRUE	0	0.573410274389233	2		482	1254	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32819922	32819922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1257301662	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	828	543	0	ENST00000354258.4:c.988C>T	p.Arg330Cys	p.R330C	ENST00000354258	NM_000593.5	330	Cgc/Tgc	3/11	0.573410274389233	2	FACETS	0.968	0.941	0.995	0.968	0.941	0.995	CLONAL	2	TRUE	0	0.573410274389233	2		543	1492	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099558	157099558	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	79	120	0	ENST00000346085.5:c.495T>G	p.Ser165Arg	p.S165R	ENST00000346085	NM_020732.3	165	agT/agG	1/20	0.573410274389233	2	FACETS	0.82	0.727	0.918	0.41	0.363	0.459	CLONAL	1	TRUE	0	0.573410274389233	2		120	336	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099581	157099581	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	58	78	1	ENST00000346085.5:c.518C>T	p.Pro173Leu	p.P173L	ENST00000346085	NM_020732.3	173	cCc/cTc	1/20	0.573410274389233	2	FACETS	0.968	0.844	1	0.484	0.422	0.55	CLONAL	1	TRUE	0	0.573410274389233	2		79	209	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331961	81331961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763072412	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	40	95	0	ENST00000222390.5:c.2123G>A	p.Arg708Gln	p.R708Q	ENST00000222390	NM_000601.4	708	cGa/cAa	18/18	1	2	FACETS	0.811	0.684	0.949	0.811	0.684	0.949	CLONAL	1	TRUE	1	0.573410274389233	2		95	172	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945037	151945037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	20	172	0	ENST00000262189.6:c.2482C>T	p.Pro828Ser	p.P828S	ENST00000262189	NM_170606.2	828	Cca/Tca	14/59	1	2	FACETS	0.188	0.143	0.241	0.188	0.143	0.241	SUBCLONAL	1	TRUE	1	0.573410274389233	2		172	371	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624547	93624547	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	286	413	1	ENST00000375746.1:c.638T>C	p.Val213Ala	p.V213A	ENST00000375746	NM_001174167.1	213	gTg/gCg	4/14	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.573410274389233	2		414	978	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93627372	93627372	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	136	248	0	ENST00000375746.1:c.839A>C	p.His280Pro	p.H280P	ENST00000375746	NM_001174167.1	280	cAt/cCt	6/14	1	2	FACETS	0.867	0.792	0.945	0.867	0.792	0.945	CLONAL	1	TRUE	1	0.573410274389233	2		248	547	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328398	137328398	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	419	500	0	ENST00000481739.1:c.1330del	p.Asp444ThrfsTer18	p.D444Tfs*18	ENST00000481739	NM_002957.4	443	Ggg/gg	10/10	1	2	FACETS	0.986	0.938	1	0.986	0.938	1	CLONAL	1	TRUE	1	0.573410274389233	2		500	1482	SUCCESS
AR	367	MSKCC	GRCh37	X	66766016	66766016	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043599-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	403	279	0	ENST00000374690.3:c.1028C>G	p.Ser343Cys	p.S343C	ENST00000374690	NM_000044.3	343	tCt/tGt	1/8	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.573410274389233	1		279	726	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601972	43601972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774829203	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	326	751	0	ENST00000355710.3:c.1016C>T	p.Ser339Leu	p.S339L	ENST00000355710	NM_020975.4	339	tCg/tTg	5/20	NA	2	FACETS	0.944	0.894	0.996			1	INDETERMINATE	1	TRUE	NA	0.704434414386628	2		751	980	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213917	66213917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	114	249	0	ENST00000273854.3:c.2513G>A	p.Gly838Glu	p.G838E	ENST00000273854	NM_004439.5	838	gGa/gAa	15/18	0.529314729597977	1	FACETS	0.736	0.673	0.8	0.736	0.673	0.8	SUBCLONAL	1	TRUE	0	0.704434414386628	1		249	285	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019807	123019807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1174668840	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	208	202	2	ENST00000355640.3:c.295G>A	p.Glu99Lys	p.E99K	ENST00000355640		99	Gaa/Aaa	2/7	1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.704434414386628	1		204	331	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172106	32172106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	307	552	0	ENST00000375023.3:c.2926C>T	p.Pro976Ser	p.P976S	ENST00000375023	NM_004557.3	976	Ccc/Tcc	19/30	0.675367899135234	1	FACETS	0.901	0.857	0.944	0.901	0.857	0.944	CLONAL	1	TRUE	0	0.704434414386628	1		552	627	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021249	31021250	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	127	415	0	ENST00000375687.4:c.1248_1249delinsTT	p.Arg417Ter	p.R417*	ENST00000375687	NM_015338.5	416	ctCCga/ctTTga	12/13	0.345735071437301	1	FACETS	0.385	0.35	0.423	0.385	0.35	0.423	INDETERMINATE	1	TRUE	0	0.704434414386628	1		415	606	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317623	163317623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747173543	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	132	273	0	ENST00000271452.3:c.1019C>T	p.Ser340Leu	p.S340L	ENST00000271452	NM_145697.2	340	tCg/tTg	12/14	1	2	FACETS	0.903	0.827	0.981	0.903	0.827	0.981	CLONAL	1	TRUE	1	0.704434414386628	2		273	415	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433620	49433620	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555191740	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	470	708	2	ENST00000301067.7:c.7933C>T	p.Arg2645Ter	p.R2645*	ENST00000301067	NM_003482.3	2645	Cga/Tga	31/54	0.345735071437301	1	FACETS	0.84	0.806	0.874	0.84	0.806	0.874	INDETERMINATE	1	TRUE	0	0.704434414386628	1		710	1029	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199925	108199925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555122245	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	83	191	0	ENST00000278616.4:c.7267G>A	p.Glu2423Lys	p.E2423K	ENST00000278616	NM_000051.3	2423	Gaa/Aaa	49/63	1	2	FACETS	0.81	0.723	0.901	0.81	0.723	0.901	CLONAL	1	TRUE	1	0.704434414386628	2		191	291	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322714	39322714	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	407	383	0	ENST00000373001.3:c.278T>C	p.Leu93Ser	p.L93S	ENST00000373001	NM_022157.3	93	tTg/tCg	2/7	0.671698630075882	2	FACETS	0.911	0.879	0.943	0.911	0.879	0.943	CLONAL	2	TRUE	0	0.704434414386628	2		383	634	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224504	108224504	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	44	207	0	ENST00000278616.4:c.8683G>C	p.Glu2895Gln	p.E2895Q	ENST00000278616	NM_000051.3	2895	Gaa/Caa	60/63	1	2	FACETS	0.398	0.335	0.467	0.398	0.335	0.467	SUBCLONAL	1	TRUE	1	0.704434414386628	2		207	314	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344692	118344692	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	135	248	0	ENST00000534358.1:c.2818G>A	p.Asp940Asn	p.D940N	ENST00000534358	NM_005933.3	940	Gat/Aat	3/36	1	2	FACETS	0.865	0.793	0.94	0.865	0.793	0.94	CLONAL	1	TRUE	1	0.704434414386628	2		248	443	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287210	46287210	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	163	240	0	ENST00000334344.6:c.5155A>T	p.Thr1719Ser	p.T1719S	ENST00000334344	NM_152641.2	1719	Act/Tct	19/21	0.345735071437301	1	FACETS	0.771	0.716	0.826	0.771	0.716	0.826	INDETERMINATE	1	TRUE	0	0.704434414386628	1		240	389	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32932047	32932047	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398122591	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	110	230	0	ENST00000380152.3:c.7786G>A	p.Gly2596Arg	p.G2596R	ENST00000380152		2596	Gga/Aga	16/27	1	2	FACETS	0.892	0.81	0.977	0.892	0.81	0.977	CLONAL	1	TRUE	1	0.704434414386628	2		230	350	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49054137	49054137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	122	192	0	ENST00000267163.4:c.2717C>T	p.Ser906Phe	p.S906F	ENST00000267163	NM_000321.2	906	tCt/tTt	27/27	1	2	FACETS	0.924	0.844	1	0.924	0.844	1	CLONAL	1	TRUE	1	0.704434414386628	2		192	375	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43738605	43738605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	208	375	0	ENST00000382044.4:c.3020C>T	p.Ser1007Phe	p.S1007F	ENST00000382044	NM_001141980.1	1007	tCt/tTt	14/28	1	2	FACETS	0.991	0.926	1	0.991	0.926	1	CLONAL	1	TRUE	1	0.704434414386628	2		375	596	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477091	67477091	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	243	407	0	ENST00000327367.4:c.898G>A	p.Gly300Arg	p.G300R	ENST00000327367	NM_005902.3	300	Gga/Aga	7/9	1	2	FACETS	0.946	0.888	1	0.946	0.888	1	CLONAL	1	TRUE	1	0.704434414386628	2		407	729	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647748	2647749	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	207	393	1	ENST00000342085.4:c.1651_1652delinsTT	p.Pro551Leu	p.P551L	ENST00000342085	NM_002613.4	551	CCg/TTg	14/14	1	2	FACETS	0.886	0.827	0.948	0.886	0.827	0.948	CLONAL	1	TRUE	1	0.704434414386628	2		394	663	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633395	3633396	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	347	691	1	ENST00000294008.3:c.4855_4856delinsTT	p.Pro1619Leu	p.P1619L	ENST00000294008	NM_032444.2	1619	CCg/TTg	14/15	1	2	FACETS	0.925	0.877	0.974	0.925	0.877	0.974	CLONAL	1	TRUE	1	0.704434414386628	2		692	1065	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640697	3640698	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TA	novel	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	288	507	2	ENST00000294008.3:c.2941_2942delinsTA	p.Gly981Ter	p.G981*	ENST00000294008	NM_032444.2	981	GGg/TAg	12/15	1	2	FACETS	0.903	0.851	0.955	0.903	0.851	0.955	CLONAL	1	TRUE	1	0.704434414386628	2		509	906	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647556	3647557	+	missense_variant	Missense_Mutation	DNP	GT	GT	AA	novel	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	289	610	2	ENST00000294008.3:c.1506_1507delinsTT	p.Leu503Phe	p.L503F	ENST00000294008	NM_032444.2	502	ccACtt/ccTTtt	7/15	1	2	FACETS	0.815	0.767	0.864	0.815	0.767	0.864	CLONAL	1	TRUE	1	0.704434414386628	2		612	1007	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829251	72829252	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	290	593	2	ENST00000268489.5:c.7329_7330delinsTT	p.Gln2444Ter	p.Q2444*	ENST00000268489	NM_006885.3	2443	acCCaa/acTTaa	9/10	0.691005633693879	3	FACETS	0.859	0.807	0.913			1	CLONAL	1	TRUE	NA	0.704434414386628	3		595	1296	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579312	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TA	novel	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	249	397	2	ENST00000269305.4:c.375_375+1delinsTA		p.X125_splice	ENST00000269305	NM_001126112.2	125		4/11	0.64508267047599	1	FACETS	0.937	0.887	0.986	0.937	0.887	0.986	CLONAL	1	TRUE	0	0.704434414386628	1		399	489	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56809867	56809868	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	166	406	0	ENST00000337432.4:c.988_989delinsTT	p.Pro330Phe	p.P330F	ENST00000337432	NM_058216.2	330	CCc/TTc	8/9	1	2	FACETS	0.792	0.731	0.855	0.792	0.731	0.855	SUBCLONAL	1	TRUE	1	0.704434414386628	2		406	595	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566473	41566474	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	354	280	0	ENST00000263253.7:c.4350_4351delinsTT	p.His1451Tyr	p.H1451Y	ENST00000263253	NM_001429.3	1450	tgCCat/tgTTat	27/31	0.241782659037357	4	FACETS	0.911	0.872	0.949			1	INDETERMINATE	3	TRUE	NA	0.704434414386628	4		280	627	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400051	49400052	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	195	349	1	ENST00000418115.1:c.285_286delinsTT	p.Pro96Ser	p.P96S	ENST00000418115	NM_001664.2	95	atCCca/atTTca	4/5	0.675367899135234	1	FACETS	0.881	0.827	0.935	0.881	0.827	0.935	CLONAL	1	TRUE	0	0.704434414386628	1		350	407	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437875	52437875	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	305	555	0	ENST00000460680.1:c.1286del	p.Leu429Ter	p.L429*	ENST00000460680	NM_004656.3	429	tTg/tg	13/17	0.675367899135234	1	FACETS	0.903	0.859	0.947	0.903	0.859	0.947	CLONAL	1	TRUE	0	0.704434414386628	1		555	621	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129962	55129962	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	112	426	0	ENST00000257290.5:c.496G>A	p.Gly166Arg	p.G166R	ENST00000257290	NM_006206.4	166	Ggg/Agg	4/23	0.529314729597977	1	FACETS	0.31	0.279	0.343	0.31	0.279	0.343	SUBCLONAL	1	TRUE	0	0.704434414386628	1		426	665	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245474	153245474	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	111	408	0	ENST00000281708.4:c.1717T>C	p.Cys573Arg	p.C573R	ENST00000281708	NM_033632.3	573	Tgc/Cgc	11/12	0.345735071437301	1	FACETS	0.404	0.365	0.446	0.404	0.365	0.446	INDETERMINATE	1	TRUE	0	0.704434414386628	1		408	505	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251888	153251889	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	147	250	0	ENST00000281708.4:c.1117_1118delinsTT	p.Pro373Phe	p.P373F	ENST00000281708	NM_033632.3	373	CCt/TTt	7/12	0.345735071437301	1	FACETS	0.659	0.608	0.712	0.659	0.608	0.712	INDETERMINATE	1	TRUE	0	0.704434414386628	1		250	410	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439315	149439315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545858226	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	165	481	1	ENST00000286301.3:c.2080G>A	p.Glu694Lys	p.E694K	ENST00000286301	NM_005211.3	694	Gag/Aag	15/22	0.345735071437301	1	FACETS	0.402	0.37	0.436	0.402	0.37	0.436	INDETERMINATE	1	TRUE	0	0.704434414386628	1		482	754	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93953230	93953230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	146	311	0	ENST00000369303.4:c.2911G>A	p.Val971Ile	p.V971I	ENST00000369303	NM_004440.3	971	Gtt/Att	17/17	0.345735071437301	1	FACETS	0.668	0.616	0.721	0.668	0.616	0.721	INDETERMINATE	1	TRUE	0	0.704434414386628	1		311	402	SUCCESS
MET	4233	MSKCC	GRCh37	7	116414220	116414220	+	intron_variant	Intron	SNP	C	C	T	novel	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	590	520	0	ENST00000397752.3:c.3029-715C>T		p.*1010*	ENST00000397752	NM_000245.2	-/1390			NA	2	FACETS	0.981	0.954	1			1	INDETERMINATE	2	TRUE	NA	0.704434414386628	2		520	854	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945478	151945478	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774013500	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	383	672	0	ENST00000262189.6:c.2041G>A	p.Glu681Lys	p.E681K	ENST00000262189	NM_170606.2	681	Gaa/Aaa	14/59	0.669149755907305	1	FACETS	0.904	0.865	0.944	0.904	0.865	0.944	CLONAL	1	TRUE	0	0.704434414386628	1		672	779	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968163	68968163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	230	469	0	ENST00000288368.4:c.1192G>A	p.Asp398Asn	p.D398N	ENST00000288368	NM_024870.2	398	Gac/Aac	10/40	0.215941141458298	1	FACETS	0.608	0.569	0.647	0.608	0.569	0.647	INDETERMINATE	1	TRUE	0	0.704434414386628	1		469	696	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244270	98244270	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	426	404	0	ENST00000331920.6:c.707G>A	p.Trp236Ter	p.W236*	ENST00000331920	NM_000264.3	236	tGg/tAg	5/24	0.683735530868567	2	FACETS	0.884	0.852	0.915	0.884	0.852	0.915	CLONAL	2	TRUE	0	0.704434414386628	2		404	684	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413198	139413198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043618-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	762	640	1	ENST00000277541.6:c.944C>T	p.Thr315Ile	p.T315I	ENST00000277541	NM_017617.3	315	aCc/aTc	6/34	0.683735530868567	2	FACETS	0.956	0.932	0.979	0.956	0.932	0.979	CLONAL	2	TRUE	0	0.704434414386628	2		641	1132	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0043630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	101	496	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.916	0.817	1	0.916	0.817	1	CLONAL	1	TRUE	1	0.224666779113668	2		496	982	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0043630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	93	469	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.145330062450454	3	FACETS	1	0.974	1	0.667	0.593	0.746	CLONAL	1	TRUE	1	0.224666779113668	3		469	690	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247288	153247288	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519896	NA	P-0043630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	46	366	0	ENST00000281708.4:c.1514G>T	p.Arg505Leu	p.R505L	ENST00000281708	NM_033632.3	505	cGc/cTc	10/12	1	2	FACETS	0.68	0.572	0.8	0.68	0.572	0.8	SUBCLONAL	1	TRUE	1	0.224666779113668	2		366	602	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302673	15302673	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1182030881	NA	P-0043630-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	123	991	0	ENST00000263388.2:c.685G>A	p.Glu229Lys	p.E229K	ENST00000263388	NM_000435.2	229	Gag/Aag	5/33	1	2	FACETS	0.895	0.807	0.988	0.895	0.807	0.988	CLONAL	1	TRUE	1	0.224666779113668	2		991	1224	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78599483	78599490	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	GTTTTCAG	GTTTTCAG	-	novel	NA	P-0043643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	178	448	0	ENST00000306801.3:c.163-8_163-1del		p.X55_splice	ENST00000306801	NM_020761.2	55			1	2	FACETS	0.976	0.909	1	0.976	0.909	1	CLONAL	1	TRUE	1	0.794809504502893	2		448	459	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340166	116340487	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCGGGGTGTTCGCACAAAGCAAGCCAGATTCTGCCGAACCAATGGATCGATCTGCCATGTGTGCATTCCCTATCAAATATGTCAACGACTTCTTCAACAAGATCGTCAACAAAAACAATGTGAGATGTCTCCAGCATTTTTACGGACCCAATCATGAGCACTGCTTTAATAGGGTAAGTCACATCAGTTCCCCACTTATAAACTGTGAGGTATAAATTAGAAATAAGTATCAGTCTCAAAAAGAATATCCAGGGCTTCTTTTGTGCTTTGTAAATGGTGTTTATCCAAAATAGTTGCAGATTTTTTCCAAGAAAATTGAGGA	TCGGGGTGTTCGCACAAAGCAAGCCAGATTCTGCCGAACCAATGGATCGATCTGCCATGTGTGCATTCCCTATCAAATATGTCAACGACTTCTTCAACAAGATCGTCAACAAAAACAATGTGAGATGTCTCCAGCATTTTTACGGACCCAATCATGAGCACTGCTTTAATAGGGTAAGTCACATCAGTTCCCCACTTATAAACTGTGAGGTATAAATTAGAAATAAGTATCAGTCTCAAAAAGAATATCCAGGGCTTCTTTTGTGCTTTGTAAATGGTGTTTATCCAAAATAGTTGCAGATTTTTTCCAAGAAAATTGAGGA	-	novel	NA	P-0043643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	35	328	0	ENST00000397752.3:c.1028_1200+149del		p.X343_splice	ENST00000397752	NM_000245.2	343		2/21	1	2	FACETS	0.348	0.287	0.416	0.348	0.287	0.416	SUBCLONAL	1	TRUE	1	0.794809504502893	2		328	253	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210729	2210734	+	frameshift_variant	Frame_Shift_Del	DEL	GCAAGC	GCAAGC	A	novel	NA	P-0043643-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	391	973	1	ENST00000398665.3:c.1226_1231delinsA	p.Arg409GlnfsTer143	p.R409Qfs*143	ENST00000398665	NM_032482.2	409	cGCAAGCgc/cAgc	14/28	1	2	FACETS	0.959	0.914	1	0.959	0.914	1	CLONAL	1	TRUE	1	0.794809504502893	2		974	1026	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419923	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	67	704	0	ENST00000206249.3:c.1610A>C	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAt/tCt	8/8	0.351713903791633	1	FACETS	0.391	0.338	0.447	0.391	0.338	0.447	SUBCLONAL	1	TRUE	0	0.351713903791633	1		704	804	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155721	56155722	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0043644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	64	386	0	ENST00000399503.3:c.816_817del	p.Arg273SerfsTer27	p.R273Sfs*27	ENST00000399503	NM_005921.1	271	agAAaa/agaa	3/20	0.316422689665405	1	FACETS	0.714	0.62	0.815	0.714	0.62	0.815	SUBCLONAL	1	TRUE	0	0.351713903791633	1		386	420	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060773	38060773	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	225	1240	2	ENST00000250448.2:c.1216A>G	p.Met406Val	p.M406V	ENST00000250448	NM_004496.3	406	Atg/Gtg	2/2	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.351713903791633	2		1242	1227	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653205	29653205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043644-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	76	367	0	ENST00000356175.3:c.5140G>A	p.Glu1714Lys	p.E1714K	ENST00000356175	NM_000267.3	1714	Gag/Aag	36/57	1	2	FACETS	0.882	0.776	0.996	0.882	0.776	0.996	CLONAL	1	TRUE	1	0.351713903791633	2		367	490	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0043648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	87	469	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.981	0.871	1	0.981	0.871	1	CLONAL	1	TRUE	1	0.360678204824066	2		469	492	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431635	6431635	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1459952760	NA	P-0043648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	104	563	1	ENST00000356142.4:c.188A>T	p.Asp63Val	p.D63V	ENST00000356142	NM_018890.3	63	gAt/gTt	3/7	0.349186595276754	3	FACETS	0.902	0.807	1	0.451	0.403	0.501	CLONAL	1	TRUE	1	0.360678204824066	3		564	755	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	134	573	0	ENST00000206249.3:c.1609T>A	p.Tyr537Asn	p.Y537N	ENST00000206249	NM_000125.3	537	Tat/Aat	8/8	1	2	FACETS	0.942	0.856	1	0.942	0.856	1	CLONAL	1	TRUE	1	0.360678204824066	2		573	789	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645889	67645890	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACACGTGTC	novel	NA	P-0043648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	107	549	0	ENST00000264010.4:c.818_826dup	p.Cys275_Pro276insHisThrCys	p.C275_P276insHTC	ENST00000264010	NM_006565.3	273	tac/tACACGTGTCac	4/12	0.360678204824066	1	FACETS	0.799	0.718	0.884	0.799	0.718	0.884	SUBCLONAL	1	TRUE	0	0.360678204824066	1		549	609	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56183145	56183211	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTATCTGTCCTTATTTTTGTTTTTAACATACAAGGTCATTTGCTGTGTTTGTTGACAGGTGCCAA	TTTTATCTGTCCTTATTTTTGTTTTTAACATACAAGGTCATTTGCTGTGTTTGTTGACAGGTGCCAA	-	novel	NA	P-0043648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	58	176	0	ENST00000399503.3:c.4115-57_4124del		p.X1372_splice	ENST00000399503	NM_005921.1	1372		18/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.360678204824066	2		176	223	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189433	56189446	+	frameshift_variant	Frame_Shift_Del	DEL	TTAGAACTTCAACC	TTAGAACTTCAACC	-	novel	NA	P-0043648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	82	546	0	ENST00000399503.3:c.4466_4479del	p.Leu1489SerfsTer29	p.L1489Sfs*29	ENST00000399503	NM_005921.1	1489	TTAGAACTTCAACCt/t	20/20	1	2	FACETS	0.724	0.639	0.815	0.724	0.639	0.815	SUBCLONAL	1	TRUE	1	0.360678204824066	2		546	628	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878808	151878808	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043648-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	217	570	0	ENST00000262189.6:c.6137del	p.Pro2046GlnfsTer32	p.P2046Qfs*32	ENST00000262189	NM_170606.2	2046	cCa/ca	36/59	0.360678204824066	3	FACETS	0.936	0.873	1	0.936	0.873	1	CLONAL	2	TRUE	1	0.360678204824066	3		570	759	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	58	384	0				ENST00000310581	NM_198253.2	-/1132			0.265937378815566	3	FACETS	0.764	0.672	0.858	0.764	0.672	0.858	INDETERMINATE	2	TRUE	1	0.671731974112458	3		384	151	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938390	44938390	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0043685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	76	99	0	ENST00000377967.4:c.2939-1G>A		p.X980_splice	ENST00000377967	NM_021140.2	980			1	1	FACETS		NA	1	1	0.987	1	NA	2	TRUE	0	0.671731974112458	1		99	97	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393303	393303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	39	334	1	ENST00000380956.4:c.151C>T	p.Arg51Cys	p.R51C	ENST00000380956	NM_001195286.1	51	Cgc/Tgc	2/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.671731974112458	NA		335	382	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367042	40367042	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	32	534	0	ENST00000397332.2:c.155C>T	p.Ser52Phe	p.S52F	ENST00000397332	NM_001033082.2	52	tCc/tTc	2/3	0.295864308769573	2	FACETS	0.19	0.154	0.231	0.095	0.077	0.116	INDETERMINATE	1	TRUE	0	0.671731974112458	2		534	501	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982992	201982992	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	317	513	0	ENST00000359651.3:c.841G>C	p.Asp281His	p.D281H	ENST00000359651		281	Gac/Cac	7/8	0.295864308769573	2	FACETS	0.887	0.849	0.925	0.887	0.849	0.925	INDETERMINATE	2	TRUE	0	0.671731974112458	2		513	532	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430740	181430740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043685-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	122	412	0	ENST00000325404.1:c.592C>T	p.His198Tyr	p.H198Y	ENST00000325404	NM_003106.3	198	Cac/Tac	1/1	1	2	FACETS	0.908	0.846	0.968	1	0.991	1	CLONAL	2	TRUE	1	0.671731974112458	2		412	200	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	68	384	0				ENST00000310581	NM_198253.2	-/1132			0.310933723041148	5	FACETS	0.906	0.801	1	0.906	0.801	1	CLONAL	3	TRUE	2	0.340274590933885	5		384	222	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983008	201983008	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	76	876	0	ENST00000359651.3:c.857C>A	p.Pro286Gln	p.P286Q	ENST00000359651		286	cCg/cAg	7/8	0.29822965428144	3	FACETS	1	0.958	1	0.601	0.529	0.677	CLONAL	1	TRUE	1	0.340274590933885	3		876	435	SUCCESS
EED	8726	MSKCC	GRCh37	11	85975286	85975286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	63	275	0	ENST00000263360.6:c.707G>A	p.Arg236Lys	p.R236K	ENST00000263360	NM_003797.3	236	aGa/aAa	7/12	0.340274590933885	5	FACETS	0.853	0.742	0.971	0.853	0.742	0.971	CLONAL	2	TRUE	3	0.340274590933885	5		275	328	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369209	118369209	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	77	311	0	ENST00000534358.1:c.5927A>G	p.Tyr1976Cys	p.Y1976C	ENST00000534358	NM_005933.3	1976	tAt/tGt	22/36	0.340274590933885	3	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	1	0.340274590933885	3		311	250	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006496	12006496	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0043697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	43	611	0	ENST00000396373.4:c.463+1G>T		p.X155_splice	ENST00000396373	NM_001987.4	155			0.152038554384591	4	FACETS	0.707	0.592	0.835	0.354	0.296	0.418	INDETERMINATE	1	TRUE	2	0.340274590933885	4		611	479	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426664	49426664	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	73	443	0	ENST00000301067.7:c.11824C>G	p.Gln3942Glu	p.Q3942E	ENST00000301067	NM_003482.3	3942	Caa/Gaa	39/54	0.152038554384591	4	FACETS	1	0.963	1	1	0.963	1	INDETERMINATE	2	TRUE	2	0.340274590933885	4		443	237	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490937	56490937	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	66	631	0	ENST00000267101.3:c.2383C>A	p.Leu795Met	p.L795M	ENST00000267101	NM_001982.3	795	Ctg/Atg	20/28	0.152038554384591	4	FACETS	1	0.964	1	0.661	0.577	0.752	INDETERMINATE	1	TRUE	2	0.340274590933885	4		631	393	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26974688	26974688	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0043697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	62	375	0	ENST00000381527.3:c.1031+1G>A		p.X344_splice	ENST00000381527	NM_001260.1	344			0.340274590933885	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.340274590933885	1		375	264	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32905069	32905069	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs372188754	NA	P-0043697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	18	164	0	ENST00000380152.3:c.695A>G	p.Tyr232Cys	p.Y232C	ENST00000380152		232	tAt/tGt	9/27	0.226312862032022	3	FACETS	0.836	0.635	1	0.418	0.317	0.536	CLONAL	1	TRUE	1	0.340274590933885	3		164	148	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919281	48919281	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs587778870	NA	P-0043697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	29	99	0	ENST00000267163.4:c.446C>G	p.Ser149Ter	p.S149*	ENST00000267163	NM_000321.2	149	tCa/tGa	4/27	0.226312862032022	3	FACETS	1	0.903	1	0.597	0.484	0.722	CLONAL	1	TRUE	1	0.340274590933885	3		99	167	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436222	110436222	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	26	518	0	ENST00000375856.3:c.2179T>A	p.Tyr727Asn	p.Y727N	ENST00000375856	NM_003749.2	727	Tac/Aac	1/2	NA	2	FACETS	0.831	0.663	1			1	INDETERMINATE	1	TRUE	NA	0.340274590933885	2		518	184	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643303	38643303	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	43	375	0	ENST00000299084.4:c.773A>G	p.Tyr258Cys	p.Y258C	ENST00000299084	NM_152594.2	258	tAt/tGt	7/7	1	2	FACETS	0.983	0.829	1	0.983	0.829	1	CLONAL	1	TRUE	1	0.340274590933885	2		375	257	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0043697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	158	667	1	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.340274590933885	3	FACETS	1	0.976	1	1	0.992	1	CLONAL	3	TRUE	1	0.340274590933885	3		668	328	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16046984	16046984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	33	402	0	ENST00000268712.3:c.1109C>T	p.Ser370Leu	p.S370L	ENST00000268712	NM_006311.3	370	tCa/tTa	11/46	0.340274590933885	3	FACETS	0.847	0.693	1	0.423	0.346	0.51	CLONAL	1	TRUE	1	0.340274590933885	3		402	268	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557918	29557918	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	10	94	0	ENST00000356175.3:c.3172G>C	p.Asp1058His	p.D1058H	ENST00000356175	NM_000267.3	1058	Gat/Cat	24/57	0.0786994887232422	4	FACETS	0.812	0.555	1	0.406	0.277	0.564	INDETERMINATE	1	TRUE	2	0.340274590933885	4		94	97	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0043697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	125	747	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.0786994887232422	4	FACETS	1	0.973	1	1	0.973	1	INDETERMINATE	2	TRUE	2	0.340274590933885	4		747	423	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245896	41245896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	102	470	0	ENST00000357654.3:c.1652G>A	p.Ser551Asn	p.S551N	ENST00000357654	NM_007294.3	551	aGt/aAt	10/23	0.0786994887232422	4	FACETS	1	0.946	1	1	0.946	1	INDETERMINATE	2	TRUE	2	0.340274590933885	4		470	374	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872197	45872197	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	52	666	0	ENST00000391945.4:c.237G>C	p.Glu79Asp	p.E79D	ENST00000391945	NM_000400.3	79	gaG/gaC	4/23	0.340274590933885	3	FACETS	1	0.945	1	0.612	0.525	0.707	CLONAL	1	TRUE	1	0.340274590933885	3		666	292	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731659	47731660	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	novel	NA	P-0043697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	56	242	0	ENST00000449228.1:c.131_132dup	p.Pro45SerfsTer185	p.P45Sfs*185	ENST00000449228	NM_001127240.2	44	-/TC	2/4	0.340274590933885	3	FACETS	1	0.911	1	1	0.911	1	CLONAL	2	TRUE	1	0.340274590933885	3		242	182	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719380	190719380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	31	174	0	ENST00000441310.2:c.1382C>T	p.Ser461Phe	p.S461F	ENST00000441310	NM_000534.4	461	tCc/tTc	9/13	0.340274590933885	3	FACETS	1	0.904	1	0.589	0.481	0.708	CLONAL	1	TRUE	1	0.340274590933885	3		174	181	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719828	190719829	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0043697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	38	144	0	ENST00000441310.2:c.1831dup	p.Thr611AsnfsTer4	p.T611Nfs*4	ENST00000441310	NM_000534.4	610	-/A	9/13	0.340274590933885	3	FACETS	0.807	0.677	0.947	0.807	0.677	0.947	CLONAL	2	TRUE	1	0.340274590933885	3		144	162	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521422	187521453	+	frameshift_variant	Frame_Shift_Del	DEL	CCACTGCCCATCATTGACCTGAATGCTCTGAA	CCACTGCCCATCATTGACCTGAATGCTCTGAA	-	novel	NA	P-0043697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	43	456	0	ENST00000441802.2:c.11702_11733del	p.Val3901AlafsTer37	p.V3901Afs*37	ENST00000441802	NM_005245.3	3901	gTTCAGAGCATTCAGGTCAATGATGGGCAGTGG/g	22/27	1	2	FACETS	0.94	0.791	1	0.94	0.791	1	CLONAL	1	TRUE	1	0.340274590933885	2		456	269	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945113	38945114	+	missense_variant	Missense_Mutation	DNP	TC	TC	AG	novel	NA	P-0043697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	52	312	0	ENST00000357387.3:c.4690_4691delinsCT	p.Glu1564Leu	p.E1564L	ENST00000357387	NM_152756.3	1564	GAa/CTa	35/38	0.310933723041148	5	FACETS	1	0.861	1	0.337	0.287	0.391	CLONAL	1	TRUE	2	0.340274590933885	5		312	457	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045711	26045711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1217247868	NA	P-0043697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	30	237	0	ENST00000540144.1:c.73G>A	p.Ala25Thr	p.A25T	ENST00000540144	NM_003531.2	25	Gca/Aca	1/1	0.340274590933885	6	FACETS	0.797	0.648	0.962			1	CLONAL	2	TRUE	NA	0.340274590933885	6		237	186	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672048	30672048	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	58	784	0	ENST00000376406.3:c.4912A>C	p.Thr1638Pro	p.T1638P	ENST00000376406	NM_014641.2	1638	Act/Cct	10/15	0.340274590933885	3	FACETS	0.879	0.757	1	0.439	0.378	0.506	CLONAL	1	TRUE	1	0.340274590933885	3		784	454	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517346	157517346	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	56	498	0	ENST00000346085.5:c.3910A>C	p.Ser1304Arg	p.S1304R	ENST00000346085	NM_020732.3	1304	Agc/Cgc	16/20	0.340274590933885	2	FACETS	1	0.957	1	0.643	0.556	0.736	CLONAL	1	TRUE	0	0.340274590933885	2		498	256	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902241	151902241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	56	394	0	ENST00000262189.6:c.3911G>A	p.Arg1304Lys	p.R1304K	ENST00000262189	NM_170606.2	1304	aGa/aAa	25/59	NA	2	FACETS	1	0.911	1			1	INDETERMINATE	1	TRUE	NA	0.340274590933885	2		394	306	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606412	93606412	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773659676	NA	P-0043697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	77	796	1	ENST00000375746.1:c.232G>A	p.Gly78Ser	p.G78S	ENST00000375746	NM_001174167.1	78	Ggt/Agt	2/14	0.340274590933885	3	FACETS	1	0.977	1	0.74	0.654	0.831	CLONAL	1	TRUE	1	0.340274590933885	3		797	358	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930262	39930262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1365252801	NA	P-0043697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	59	340	1	ENST00000378444.4:c.3202G>A	p.Glu1068Lys	p.E1068K	ENST00000378444	NM_001123385.1	1068	Gag/Aag	6/15	0.277013211056328	2	FACETS	1	0.964	1			1	CLONAL	1	TRUE	NA	0.340274590933885	2		341	258	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223533	53223533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	60	323	0	ENST00000375401.3:c.3826G>A	p.Glu1276Lys	p.E1276K	ENST00000375401	NM_004187.3	1276	Gag/Aag	23/26	0.277013211056328	2	FACETS	0.972	0.867	1			1	CLONAL	3	TRUE	NA	0.340274590933885	2		323	121	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347223	70347223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043697-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	119	284	0	ENST00000374080.3:c.2887G>A	p.Asp963Asn	p.D963N	ENST00000374080		963	Gat/Aat	21/45	0.277013211056328	2	FACETS	1	0.936	1			1	CLONAL	3	TRUE	NA	0.340274590933885	2		284	230	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220502	1220502	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	rs121913317	NA	P-0043700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	192	679	0	ENST00000326873.7:c.595G>T	p.Glu199Ter	p.E199*	ENST00000326873	NM_000455.4	199	Gag/Tag	4/10	0.252861561584508	0	FACETS	0.79	0.738	0.842			1	SUBCLONAL	3	TRUE	0	0.252833786909599	0		679	479	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440573	49440573	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	144	646	0	ENST00000301067.7:c.4237A>G	p.Ile1413Val	p.I1413V	ENST00000301067	NM_003482.3	1413	Atc/Gtc	15/54	1	2	FACETS	0.757	0.692	0.826	1	0.987	1	SUBCLONAL	2	TRUE	1	0.252833786909599	2		646	752	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95577669	95577669	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	109	289	0	ENST00000393063.1:c.2241G>C	p.Gln747His	p.Q747H	ENST00000393063	NM_030621.3	747	caG/caC	15/28	1	2	FACETS	1	0.955	1	1	0.989	1	CLONAL	2	TRUE	1	0.252833786909599	2		289	394	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610577	10610592	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGCGTCACCTCCGC	AGGGCGTCACCTCCGC	-	novel	NA	P-0043700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	181	670	0	ENST00000171111.5:c.118_133del	p.Ala40ProfsTer23	p.A40Pfs*23	ENST00000171111	NM_203500.1	40	GCGGAGGTGACGCCCTcc/cc	2/6	0.252861561584508	0	FACETS	1	0.951	1			1	CLONAL	2	TRUE	0	0.252833786909599	0		670	520	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521763	89521763	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs192800580	NA	P-0043700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	62	220	0	ENST00000336596.2:c.2840C>A	p.Ser947Tyr	p.S947Y	ENST00000336596	NM_005233.5	947	tCc/tAc	16/17	1	2	FACETS	1	0.892	1	1	0.981	1	CLONAL	2	TRUE	1	0.252833786909599	2		220	240	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68995555	68995555	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0043700-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	73	406	0	ENST00000288368.4:c.1959T>G	p.Asp653Glu	p.D653E	ENST00000288368	NM_024870.2	653	gaT/gaG	18/40	0.252833786909599	8	FACETS	0.988	0.866	1	0.282	0.247	0.32	CLONAL	2	TRUE	1	0.252833786909599	8		406	514	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0043701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	79	384	0				ENST00000310581	NM_198253.2	-/1132			0.2323975689552	3	FACETS	1	0.928	1	1	0.928	1	CLONAL	3	FALSE	0	0.23319230475851	3		384	240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0043701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	111	775	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.186817301974768	3	FACETS	0.873	0.786	0.964	0.873	0.786	0.964	CLONAL	2	FALSE	1	0.23319230475851	3		775	609	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350086	81350086	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	26	267	0	ENST00000222390.5:c.1246G>T	p.Asp416Tyr	p.D416Y	ENST00000222390	NM_000601.4	416	Gac/Tac	10/18	1	2	FACETS	0.748	0.594	0.925	0.748	0.594	0.925	CLONAL	1	FALSE	1	0.23319230475851	2		267	298	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040722	47040723	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0043701-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	40	389	0	ENST00000377604.3:c.1360dup	p.Leu454ProfsTer64	p.L454Pfs*64	ENST00000377604	NM_001204468.1	453	tcc/tCcc	13/24	1	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	0	0.23319230475851	1		389	247	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0043702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	52	301	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	1	2	FACETS	0.565	0.481	0.656	0.565	0.481	0.656	SUBCLONAL	1	TRUE	1	0.39	2		301	472	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0043702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	119	385	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.987	0.894	1	0.987	0.894	1	CLONAL	1	TRUE	1	0.39	2		385	618	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900285	101900291	+	frameshift_variant	Frame_Shift_Del	DEL	GTTCGTG	GTTCGTG	-	novel	NA	P-0043702-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	22	140	0	ENST00000374994.4:c.723_729del	p.Trp242ValfsTer9	p.W242Vfs*9	ENST00000374994	NM_004612.2	240	cGTTCGTGg/cg	4/9	0.3	1	FACETS	0.426	0.332	0.535	0.426	0.332	0.535	SUBCLONAL	1	TRUE	0	0.39	1		140	213	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0043704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	46	469	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.836	0.704	0.983	0.836	0.704	0.983	CLONAL	1	TRUE	1	0.201835081979658	2		469	545	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612900	228612900	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	140	510	2	ENST00000366696.1:c.127C>T	p.Arg43Trp	p.R43W	ENST00000366696	NM_003493.2	43	Cgg/Tgg	1/1	0.193261289585077	2	FACETS	0.971	0.886	1	0.971	0.886	1	CLONAL	2	TRUE	0	0.201835081979658	2		512	714	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578476	7578476	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0043704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	118	690	3	ENST00000269305.4:c.454C>A	p.Pro152Thr	p.P152T	ENST00000269305	NM_001126112.2	152	Ccg/Acg	5/11	0.201835081979658	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.201835081979658	1		693	970	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148516774	148516774	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	26	221	0	ENST00000320356.2:c.913C>T	p.His305Tyr	p.H305Y	ENST00000320356	NM_004456.4	305	Cat/Tat	9/20	1	2	FACETS	0.683	0.541	0.847	0.683	0.541	0.847	SUBCLONAL	1	TRUE	1	0.201835081979658	2		221	377	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248799	133248799	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0043704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	59	401	0	ENST00000320574.5:c.1794+2T>C		p.X598_splice	ENST00000320574	NM_006231.2	598			1	2	FACETS	0.954	0.82	1	0.954	0.82	1	CLONAL	1	TRUE	1	0.201835081979658	2		401	613	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600396	10600396	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs780491344	NA	P-0043704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	108	694	0	ENST00000171111.5:c.1459G>C	p.Ala487Pro	p.A487P	ENST00000171111	NM_203500.1	487	Gct/Cct	4/6	0.201835081979658	1	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	0	0.201835081979658	1		694	960	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144095	11144095	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0043704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	104	663	0	ENST00000358026.2:c.3676C>T	p.Gln1226Ter	p.Q1226*	ENST00000358026	NM_001128849.1	1226	Cag/Tag	26/36	0.201835081979658	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.201835081979658	1		663	847	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92404108	92404108	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	42	319	0	ENST00000265734.4:c.271G>A	p.Glu91Lys	p.E91K	ENST00000265734	NM_001259.6	91	Gaa/Aaa	3/8	1	2	FACETS	0.834	0.696	0.987	0.834	0.696	0.987	CLONAL	1	TRUE	1	0.201835081979658	2		319	499	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128206818	128206818	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	57	330	0	ENST00000265960.3:c.1405G>C	p.Glu469Gln	p.E469Q	ENST00000265960	NM_001006617.1	469	Gaa/Caa	11/12	0.201835081979658	4	FACETS	1	0.917	1			1	CLONAL	1	TRUE	NA	0.201835081979658	4		330	617	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68864632	68864632	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0043704-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	16	113	0	ENST00000288368.4:c.3G>A	p.Met1?	p.M1?	ENST00000288368	NM_024870.2	1	atG/atA	1/40	1	2	FACETS	0.973	0.723	1	0.973	0.723	1	CLONAL	1	TRUE	1	0.201835081979658	2		113	163	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0043709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	208	713	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.644759024647814	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.644759024647814	2		713	322	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48939033	48939033	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1131690901	NA	P-0043709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	71	171	1	ENST00000267163.4:c.869del	p.Asn290MetfsTer11	p.N290Mfs*11	ENST00000267163	NM_000321.2	289	Aaa/aa	9/27	0.617055935072166	2	FACETS	0.775	0.699	0.852	0.775	0.699	0.852	SUBCLONAL	2	TRUE	0	0.644759024647814	2		172	142	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431650	6431650	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	74	497	0	ENST00000356142.4:c.203G>A	p.Arg68His	p.R68H	ENST00000356142	NM_018890.3	68	cGc/cAc	3/7	0.268849154004569	2	FACETS	0.844	0.747	0.945	0.422	0.373	0.473	INDETERMINATE	1	TRUE	0	0.644759024647814	2		497	272	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061219	38061243	+	frameshift_variant	Frame_Shift_Del	DEL	CCGTTCTCGAACATGTTGCCGGAGT	CCGTTCTCGAACATGTTGCCGGAGT	-	novel	NA	P-0043709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	461	466	0	ENST00000250448.2:c.746_770del	p.Asp249AlafsTer64	p.D249Afs*64	ENST00000250448	NM_004496.3	249	gACTCCGGCAACATGTTCGAGAACGGc/gc	2/2	0.644759024647814	5	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	2	0.644759024647814	5		466	877	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570263	95570263	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0043709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	99	288	0	ENST00000393063.1:c.3470T>G	p.Leu1157Arg	p.L1157R	ENST00000393063	NM_030621.3	1157	cTc/cGc	22/28	0.644759024647814	5	FACETS	0.921	0.831	1	0.614	0.554	0.676	CLONAL	2	TRUE	2	0.644759024647814	5		288	328	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015194	128015194	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	55	483	0	ENST00000285398.2:c.2327T>C	p.Leu776Pro	p.L776P	ENST00000285398	NM_000122.1	776	cTc/cCc	15/15	0.573020861901436	3	FACETS	0.806	0.695	0.925	0.403	0.347	0.463	CLONAL	1	TRUE	1	0.644759024647814	3		483	280	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92300744	92300744	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1322062789	NA	P-0043709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	37	219	0	ENST00000265734.4:c.643A>G	p.Arg215Gly	p.R215G	ENST00000265734	NM_001259.6	215	Aga/Gga	5/8	0.486132034463129	4	FACETS	1	0.929	1	0.609	0.51	0.716	CLONAL	1	TRUE	2	0.644759024647814	4		219	155	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342862	87342862	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0043709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	112	362	0	ENST00000277120.3:c.1148del	p.Gly383GlufsTer13	p.G383Efs*13	ENST00000277120		383	Gga/ga	9/19	0.644759024647814	5	FACETS	0.817	0.741	0.897	0.545	0.494	0.598	CLONAL	2	TRUE	2	0.644759024647814	5		362	418	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750414	133750414	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0043709-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	256	498	0	ENST00000318560.5:c.1245G>C	p.Lys415Asn	p.K415N	ENST00000318560	NM_005157.4	415	aaG/aaC	7/11	0.644759024647814	5	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	2	0.644759024647814	5		498	489	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696431	47696431	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	16	285	1	ENST00000347630.2:c.392G>T	p.Trp131Leu	p.W131L	ENST00000347630	NM_001007230.1	131	tGg/tTg	6/11	1	2	FACETS	0.488	0.359	0.644	0.488	0.359	0.644	SUBCLONAL	1	TRUE	1	0.13	2		286	504	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125507398	125507398	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043723-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	18	196	0	ENST00000428830.2:c.773A>G	p.Asp258Gly	p.D258G	ENST00000428830	NM_001114121.2	258	gAc/gGc	8/14	1	2	FACETS	0.842	0.633	1	0.842	0.633	1	CLONAL	1	TRUE	1	0.13	2		196	329	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183872	10183872	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs730882032	NA	P-0043724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	112	427	0	ENST00000256474.2:c.340+1G>A		p.X114_splice	ENST00000256474	NM_000551.3	114			0.438153886729629	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	0	0.451474707521678	1		427	383	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28605657	28605657	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0043724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	36	498	0	ENST00000253063.3:c.1261C>G	p.Leu421Val	p.L421V	ENST00000253063	NM_031459.4	421	Ctc/Gtc	9/10	1	2	FACETS	0.279	0.229	0.336	0.279	0.229	0.336	SUBCLONAL	1	TRUE	1	0.451474707521678	2		498	571	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0043762-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	64	652	1	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.150246090548955	2		653	818	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692791	89692791	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1114167623	NA	P-0043762-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	49	240	0	ENST00000371953.3:c.275A>G	p.Asp92Gly	p.D92G	ENST00000371953	NM_000314.4	92	gAc/gGc	5/9	1	2	FACETS	0.841	0.714	0.979	1	0.968	1	CLONAL	2	TRUE	1	0.150246090548955	2		240	388	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955573	48955573	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043762-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	31	174	1	ENST00000267163.4:c.1689G>A	p.Trp563Ter	p.W563*	ENST00000267163	NM_000321.2	563	tgG/tgA	17/27	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.150246090548955	2		175	356	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556443	29556443	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0043762-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	60	343	0	ENST00000356175.3:c.2810T>A	p.Leu937Ter	p.L937*	ENST00000356175	NM_000267.3	937	tTg/tAg	21/57	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.150246090548955	2		343	600	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969400	44969400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043762-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	62	344	0	ENST00000377967.4:c.4082G>A	p.Cys1361Tyr	p.C1361Y	ENST00000377967	NM_021140.2	1361	tGt/tAt	28/29	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.150246090548955	2		344	722	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874302	76874302	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043797-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	75	504	0	ENST00000373344.5:c.5420T>C	p.Leu1807Pro	p.L1807P	ENST00000373344	NM_000489.3	1807	cTc/cCc	21/35	0.390414611086759	1	FACETS	0.603	0.532	0.679	0.603	0.532	0.679	SUBCLONAL	1	TRUE	0	0.517770026433223	1		504	356	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0043823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	185	533	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.18751335480138	5	FACETS	1	0.98	1	0.769	0.713	0.827	INDETERMINATE	2	TRUE	2	0.376329136640671	5		533	667	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290070	15290070	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	375	618	0	ENST00000263388.2:c.3484G>A	p.Asp1162Asn	p.D1162N	ENST00000263388	NM_000435.2	1162	Gat/Aat	22/33	0.123736216200776	6	FACETS	0.891	0.848	0.934			1	INDETERMINATE	4	TRUE	NA	0.376329136640671	6		618	980	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932488	39932488	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0043823-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	91	649	0	ENST00000378444.4:c.2111A>T	p.Tyr704Phe	p.Y704F	ENST00000378444	NM_001123385.1	704	tAt/tTt	4/15	0.284016221384793	3	FACETS	0.652	0.578	0.732	0.326	0.289	0.366	SUBCLONAL	1	TRUE	1	0.376329136640671	3		649	881	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268766	41268766	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0043835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	44	477	0	ENST00000349496.5:c.1004A>T	p.Lys335Ile	p.K335I	ENST00000349496	NM_001904.3	335	aAa/aTa	7/15	0.802967285122369	3	FACETS	0.46	0.387	0.54	0.23	0.193	0.27	SUBCLONAL	1	TRUE	1	0.802967285122369	3		477	334	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266134	41266136	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs587776850	NA	P-0043835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	32	472	0	ENST00000349496.5:c.133_135del	p.Ser45del	p.S45del	ENST00000349496	NM_001904.3	44	cCTTct/cct	3/15	0.802967285122369	3	FACETS	0.337	0.274	0.409	0.169	0.137	0.205	SUBCLONAL	1	TRUE	1	0.802967285122369	3		472	331	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923601	39923601	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0043835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	251	1175	0	ENST00000378444.4:c.3490C>T	p.Arg1164Ter	p.R1164*	ENST00000378444	NM_001123385.1	1164	Cga/Tga	7/15	0.802967285122369	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.802967285122369	1		1175	280	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266711	198266711	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043835-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	137	646	0	ENST00000335508.6:c.2221A>G	p.Lys741Glu	p.K741E	ENST00000335508	NM_012433.2	741	Aag/Gag	15/25	0.711108626990637	4	FACETS	1	0.984	1	0.441	0.404	0.479	CLONAL	1	TRUE	1	0.802967285122369	4		646	465	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720852	89720852	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909231	NA	P-0043851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	60	321	0	ENST00000371953.3:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	335	Cga/Tga	8/9	0.10062518466934	4	FACETS	1	0.969	1	0.733	0.635	0.839	INDETERMINATE	1	TRUE	2	0.29	4		321	364	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	67	357	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.945	0.823	1	0.945	0.823	1	CLONAL	1	TRUE	1	0.29	2		357	489	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0043851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	57	485	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.10062518466934	4	FACETS	1	0.951	1	0.623	0.536	0.717	INDETERMINATE	1	TRUE	2	0.29	4		485	407	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339111	65339111	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	64	459	1	ENST00000342505.4:c.425del	p.Lys142ArgfsTer26	p.K142Rfs*26	ENST00000342505	NM_002227.2	142	aAg/ag	5/25	1	2	FACETS	0.65	0.562	0.745	0.65	0.562	0.745	SUBCLONAL	1	TRUE	1	0.29	2		460	679	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007332	143007332	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	46	317	0	ENST00000262992.4:c.2452del	p.Arg818GlufsTer4	p.R818Efs*4	ENST00000262992	NM_001101669.1	818	Aga/ga	22/24	1	2	FACETS	0.785	0.663	0.92	0.785	0.663	0.92	CLONAL	1	TRUE	1	0.29	2		317	404	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760023	133760024	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1368469090	NA	P-0043851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	106	786	0	ENST00000318560.5:c.2352dup	p.Arg785GlnfsTer7	p.R785Qfs*7	ENST00000318560	NM_005157.4	782	-/C	11/11	1	2	FACETS	0.818	0.732	0.909	0.818	0.732	0.909	CLONAL	1	TRUE	1	0.29	2		786	894	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063359	67063359	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	49	247	0	ENST00000412916.2:c.54del	p.Phe18LeufsTer4	p.F18Lfs*4	ENST00000412916		17	Ttt/tt	1/6	1	2	FACETS	0.654	0.554	0.764	0.654	0.554	0.764	SUBCLONAL	1	TRUE	1	0.29	2		247	517	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988340	36988340	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	53	301	0	ENST00000354822.5:c.313del	p.Val105CysfsTer20	p.V105Cfs*20	ENST00000354822	NM_001079668.2	105	Gtg/tg	2/3	1	2	FACETS	0.887	0.759	1	0.887	0.759	1	CLONAL	1	TRUE	1	0.29	2		301	412	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106480	27106481	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0043851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	124	638	0	ENST00000324856.7:c.6092dup	p.Tyr2031Ter	p.Y2031*	ENST00000324856	NM_006015.4	2031	tat/tAat	20/20	1	2	FACETS	0.991	0.896	1	0.991	0.896	1	CLONAL	1	TRUE	1	0.29	2		638	863	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589576	67589576	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1289537429	NA	P-0043851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	31	237	0	ENST00000274335.5:c.1344del	p.Lys448AsnfsTer32	p.K448Nfs*32	ENST00000274335		447	Aaa/aa	10/15	1	2	FACETS	0.783	0.636	0.948	0.783	0.636	0.948	CLONAL	1	TRUE	1	0.29	2		237	273	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37081709	37081709	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764663152	NA	P-0043851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	72	494	0	ENST00000231790.2:c.1591G>A	p.Val531Met	p.V531M	ENST00000231790	NM_000249.3	531	Gtg/Atg	14/19	1	2	FACETS	0.615	0.537	0.701	0.615	0.537	0.701	SUBCLONAL	1	TRUE	1	0.29	2		494	807	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214871	36214871	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	97	753	4	ENST00000222270.7:c.3302del	p.Pro1101LeufsTer81	p.P1101Lfs*81	ENST00000222270	NM_014727.1	1099	ggC/gg	8/37	1	2	FACETS	0.638	0.567	0.713	0.638	0.567	0.713	SUBCLONAL	1	TRUE	1	0.29	2		757	1049	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391525	84391525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748680448	NA	P-0043851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	24	385	0	ENST00000321945.7:c.307C>T	p.Arg103Cys	p.R103C	ENST00000321945	NM_139076.2	103	Cgt/Tgt	5/9	1	2	FACETS	0.505	0.396	0.63	0.505	0.396	0.63	SUBCLONAL	1	TRUE	1	0.29	2		385	328	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504578	103504578	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	34	353	0	ENST00000355739.4:c.204del	p.Arg69GlufsTer15	p.R69Efs*15	ENST00000355739	NM_000123.3	67	Ttt/tt	2/15	1	2	FACETS	0.644	0.527	0.776	0.644	0.527	0.776	SUBCLONAL	1	TRUE	1	0.29	2		353	364	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958508	175958508	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0043851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	57	365	0	ENST00000367669.3:c.1837A>G	p.Ile613Val	p.I613V	ENST00000367669	NM_022457.5	613	Att/Gtt	16/20	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.29	2		365	369	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143279	58143280	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0043851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	29	326	0	ENST00000257904.6:c.640_641del	p.Phe214LeufsTer5	p.F214Lfs*5	ENST00000257904	NM_000075.3	214	TTc/c	6/8	0.10062518466934	4	FACETS	0.625	0.501	0.765	0.312	0.25	0.383	INDETERMINATE	1	TRUE	2	0.29	4		326	413	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049760	16049760	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	53	420	0	ENST00000268712.3:c.1012del	p.Thr338GlnfsTer65	p.T338Qfs*65	ENST00000268712	NM_006311.3	338	Aca/ca	10/46	1	2	FACETS	0.725	0.619	0.842	0.725	0.619	0.842	SUBCLONAL	1	TRUE	1	0.29	2		420	504	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40879754	40879754	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs749985288	NA	P-0043851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	66	546	0	ENST00000428826.2:c.145G>T	p.Val49Phe	p.V49F	ENST00000428826		49	Gtt/Ttt	4/21	1	2	FACETS	0.8	0.695	0.914	0.8	0.695	0.914	CLONAL	1	TRUE	1	0.29	2		546	569	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573619	48573619	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	23	351	0	ENST00000342988.3:c.203C>A	p.Pro68His	p.P68H	ENST00000342988	NM_005359.5	68	cCt/cAt	2/12	1	2	FACETS	0.54	0.421	0.676	0.54	0.421	0.676	SUBCLONAL	1	TRUE	1	0.29	2		351	294	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855584	45855584	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0043851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	116	697	1	ENST00000391945.4:c.2073del	p.Lys692SerfsTer17	p.K692Sfs*17	ENST00000391945	NM_000400.3	691	ggG/gg	22/23	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.29	2		698	756	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907619	111907619	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0043851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	56	314	0	ENST00000393256.3:c.395-2A>G		p.X132_splice	ENST00000393256	NM_006538.4	132			1	2	FACETS	0.84	0.721	0.969	0.84	0.721	0.969	CLONAL	1	TRUE	1	0.29	2		314	460	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591149	67591251	+	splice_donor_variant,splice_acceptor_variant,frameshift_variant,stop_lost,intron_variant	Splice_Site	DEL	TGATGTAAGTATTTGAAATGGAATCCTATACATGAATAATTGGTGATTGCTACAATTCAGGATGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGG	TGATGTAAGTATTTGAAATGGAATCCTATACATGAATAATTGGTGATTGCTACAATTCAGGATGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGG	-	novel	NA	P-0043851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	33	339	0	ENST00000274335.5:c.1743_1750del		p.X581_splice	ENST00000274335		581	tTGATGTAAGTATTTGAAATGGAATCCTATACATGAATAATTGGTGATTGCTACAATTCAGGATGAGTTAATGCGTTCTCTTTTCAAAACTGTTTTTCAGGTGG/t	12-13/15	1	2	FACETS	0.72	0.588	0.868	0.72	0.588	0.868	SUBCLONAL	1	TRUE	1	0.29	2		339	316	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469946	157469946	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	72	618	0	ENST00000346085.5:c.2740A>G	p.Ser914Gly	p.S914G	ENST00000346085	NM_020732.3	914	Agc/Ggc	9/20	0.10062518466934	4	FACETS	0.914	0.798	1	0.457	0.399	0.52	INDETERMINATE	1	TRUE	2	0.29	4		618	701	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900300	101900300	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	32	397	0	ENST00000374994.4:c.734A>G	p.Glu245Gly	p.E245G	ENST00000374994	NM_004612.2	245	gAg/gGg	4/9	1	2	FACETS	0.622	0.505	0.753	0.622	0.505	0.753	SUBCLONAL	1	TRUE	1	0.29	2		397	355	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778081	135778081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043851-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	88	550	1	ENST00000298552.3:c.2302C>T	p.Arg768Cys	p.R768C	ENST00000298552	NM_001162426.1	768	Cgt/Tgt	18/23	1	2	FACETS	0.805	0.713	0.904	0.805	0.713	0.904	CLONAL	1	TRUE	1	0.29	2		551	754	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0043915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	88	485	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.240537339794032	2	FACETS	0.802	0.713	0.895	0.802	0.713	0.895	CLONAL	2	TRUE	0	0.242339028319865	2		485	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0043915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	209	785	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.240537339794032	2	FACETS	0.954	0.887	1	0.954	0.887	1	CLONAL	2	TRUE	0	0.242339028319865	2		785	904	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528742	8528742	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043915-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	43	294	0	ENST00000356435.5:c.390G>T	p.Met130Ile	p.M130I	ENST00000356435		130	atG/atT	4/35	0.242339028319865	1	FACETS	0.685	0.574	0.809	0.685	0.574	0.809	SUBCLONAL	1	TRUE	0	0.242339028319865	1		294	455	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0043942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	164	538	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		538	312	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884756	111884756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148319611	NA	P-0043942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	90	425	1	ENST00000341259.2:c.845G>A	p.Arg282Gln	p.R282Q	ENST00000341259	NM_005475.2	282	cGg/cAg	4/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		426	500	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268138	153268138	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1406877044	NA	P-0043942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	67	251	0	ENST00000281708.4:c.670C>T	p.Arg224Ter	p.R224*	ENST00000281708	NM_033632.3	224	Cga/Tga	4/12	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		251	371	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964971	25964971	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0043942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	60	334	0	ENST00000435504.4:c.4235G>T	p.Gly1412Val	p.G1412V	ENST00000435504		1412	gGc/gTc	13/13	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		334	435	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620411	43620411	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0043942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	57	346	0	ENST00000355710.3:c.3020A>G	p.Lys1007Arg	p.K1007R	ENST00000355710	NM_020975.4	1007	aAg/aGg	18/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		346	379	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914584	32914584	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs876658761	NA	P-0043942-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	34	154	0	ENST00000380152.3:c.6092C>G	p.Thr2031Ser	p.T2031S	ENST00000380152		2031	aCt/aGt	11/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		154	231	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0043959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	139	496	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.225211101665134	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.269361708815607	1		496	875	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591918	48591918	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs80338963	NA	P-0043959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	33	387	0	ENST00000342988.3:c.1081C>A	p.Arg361Ser	p.R361S	ENST00000342988	NM_005359.5	361	Cgc/Agc	9/12	0.207819345840917	0	FACETS	0.403	0.328	0.488			1	SUBCLONAL	1	TRUE	0	0.269361708815607	0		387	444	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041178	47041178	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0043959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	157	441	0	ENST00000377604.3:c.1608del	p.Lys536AsnfsTer168	p.K536Nfs*168	ENST00000377604	NM_001204468.1	536	Aaa/aa	15/24	1	1	FACETS	0.799	0.735	0.866	1	0.99	1	SUBCLONAL	2	TRUE	0	0.269361708815607	1		441	631	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134598	2134598	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45517340	NA	P-0043959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	188	993	1	ENST00000219476.3:c.4375C>T	p.Arg1459Ter	p.R1459*	ENST00000219476	NM_000548.3	1459	Cga/Tga	34/42	0.269361708815607	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.269361708815607	1		994	1107	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482340	56482341	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0043959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	187	540	1	ENST00000267101.3:c.888_889delinsTT	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	296	gtGGat/gtTTat	8/28	0.269361708815607	2	FACETS	0.979	0.908	1	0.979	0.908	1	CLONAL	2	TRUE	0	0.269361708815607	2		541	709	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105897	27105898	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0043959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	163	594	0	ENST00000324856.7:c.5510_5511dup	p.Asp1838LeufsTer46	p.D1838Lfs*46	ENST00000324856	NM_006015.4	1836	-/TT	20/20	0.210975310042393	2	FACETS	0.768	0.706	0.833	0.768	0.706	0.833	SUBCLONAL	2	TRUE	0	0.269361708815607	2		594	788	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716389	18716389	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0043959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	46	318	0	ENST00000266497.5:c.3736C>T	p.His1246Tyr	p.H1246Y	ENST00000266497		1246	Cac/Tac	26/31	1	2	FACETS	0.657	0.553	0.772	0.657	0.553	0.772	SUBCLONAL	1	TRUE	1	0.269361708815607	2		318	520	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437733	110437733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0043959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	177	862	0	ENST00000375856.3:c.668C>T	p.Ala223Val	p.A223V	ENST00000375856	NM_003749.2	223	gCg/gTg	1/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.269361708815607	2		862	1162	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633679	86633877	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTTACATTTTTCAATATAATACTATCCCTATCCTATTTTGTGGTATATGACTATTCTAATCTCTGTATTTAAAATTTTTAAATTTAATAACTTTAAAATTGCTATTTTCAGTTTCTTAAAAGGAGATATGTTCATTGTTCATAATGAATTAGAAGATGGATGGATGTGGGTTACAAATTTAAGAACAGATGAACAAGG	CCTTACATTTTTCAATATAATACTATCCCTATCCTATTTTGTGGTATATGACTATTCTAATCTCTGTATTTAAAATTTTTAAATTTAATAACTTTAAAATTGCTATTTTCAGTTTCTTAAAAGGAGATATGTTCATTGTTCATAATGAATTAGAAGATGGATGGATGTGGGTTACAAATTTAAGAACAGATGAACAAGG	-	novel	NA	P-0043959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	10	37	0	ENST00000274376.6:c.900-107_991del		p.X300_splice	ENST00000274376	NM_002890.2	300		5/25	0.269361708815607	1	FACETS	0.256	0.173	0.361	0.256	0.173	0.361	SUBCLONAL	1	TRUE	0	0.269361708815607	1		37	251	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69143611	69143611	+	stop_lost	Nonstop_Mutation	SNP	T	T	A	novel	NA	P-0043959-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	58	319	0	ENST00000288368.4:c.4819T>A	p.Ter1607ArgextTer13	p.*1607Rext*13	ENST00000288368	NM_024870.2	1607	Tga/Aga	40/40	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.269361708815607	2		319	424	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846036	68846036	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0043960-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	50	659	0	ENST00000261769.5:c.1009-2A>G		p.X337_splice	ENST00000261769	NM_004360.3	337			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		659	763	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0043966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	223	636	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.16472940718212	3	FACETS	0.868	0.808	0.929	0.868	0.808	0.929	CLONAL	3	TRUE	0	0.189279627942362	3		636	991	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934218	48934218	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0043966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	49	388	0	ENST00000267163.4:c.673del	p.Tyr225IlefsTer39	p.Y225Ifs*39	ENST00000267163	NM_000321.2	225	Tat/at	7/27	0.189279627942362	2	FACETS	1	0.957	1	0.698	0.593	0.812	CLONAL	1	TRUE	0	0.189279627942362	2		388	371	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859262	151859286	+	frameshift_variant	Frame_Shift_Del	DEL	TGAACAAATACTGCCCTCAGGTTTT	TGAACAAATACTGCCCTCAGGTTTT	-	novel	NA	P-0043966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	27	316	0	ENST00000262189.6:c.11376_11400del	p.Pro3794MetfsTer9	p.P3794Mfs*9	ENST00000262189	NM_170606.2	3792	caAAAACCTGAGGGCAGTATTTGTTCA/ca	43/59	1	2	FACETS	0.847	0.674	1	0.847	0.674	1	CLONAL	1	TRUE	1	0.189279627942362	2		316	337	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577290	64577291	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0044031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	450	714	0	ENST00000312049.6:c.291_292del	p.Ile97MetfsTer19	p.I97Mfs*19	ENST00000312049	NM_130799.2	97	atCCga/atga	2/10	0.64008816323592	1	FACETS	0.986	0.945	1	0.986	0.945	1	CLONAL	1	TRUE	0	0.64008816323592	1		714	970	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248356	212248356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760087458	NA	P-0044031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	73	208	0	ENST00000342788.4:c.3911G>A	p.Arg1304Gln	p.R1304Q	ENST00000342788	NM_005235.2	1304	cGg/cAg	28/28	0.249032127595332	1	FACETS	0.443	0.39	0.5	0.443	0.39	0.5	INDETERMINATE	1	TRUE	0	0.64008816323592	1		208	350	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702661	52702662	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	TC	TC	-	novel	NA	P-0044031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	96	207	0	ENST00000394830.3:c.237-1_237del		p.X79_splice	ENST00000394830	NM_018313.4	79		4/30	0.64008816323592	1	FACETS	0.846	0.768	0.926	0.846	0.768	0.926	CLONAL	1	TRUE	0	0.64008816323592	1		207	241	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287355	38287355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358163666	NA	P-0044031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	68	648	0	ENST00000425967.3:c.302G>A	p.Arg101Gln	p.R101Q	ENST00000425967	NM_001174067.1	101	cGg/cAg	4/19	0.337063655635257	2	FACETS	0.173	0.15	0.199	0.087	0.075	0.1	INDETERMINATE	1	TRUE	0	0.64008816323592	2		648	1226	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798741	135798741	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0044031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	116	174	0	ENST00000298552.3:c.502A>T	p.Lys168Ter	p.K168*	ENST00000298552	NM_001162426.1	168	Aaa/Taa	6/23	0.64008816323592	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.64008816323592	1		174	236	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006899	47006899	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0044036-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	592	481	0	ENST00000377604.3:c.17+2T>C		p.X6_splice	ENST00000377604	NM_001204468.1	6			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		481	1245	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339003	225339003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	27	494	1	ENST00000264414.4:c.2266C>T	p.Arg756Ter	p.R756*	ENST00000264414	NM_003590.4	756	Cga/Tga	16/16	1	2	FACETS	0.475	0.378	0.587	0.475	0.378	0.587	SUBCLONAL	1	TRUE	1	0.2752199210362	2		495	413	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006417	12006417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749555964	NA	P-0044042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	52	626	0	ENST00000396373.4:c.385C>T	p.Leu129Phe	p.L129F	ENST00000396373	NM_001987.4	129	Ctt/Ttt	4/8	1	2	FACETS	0.683	0.582	0.795	0.683	0.582	0.795	SUBCLONAL	1	TRUE	1	0.2752199210362	2		626	553	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868332	45868332	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771687310	NA	P-0044042-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	50	1107	0	ENST00000391945.4:c.445G>A	p.Asp149Asn	p.D149N	ENST00000391945	NM_000400.3	149	Gac/Aac	6/23	1	2	FACETS	0.367	0.31	0.43	0.367	0.31	0.43	SUBCLONAL	1	TRUE	1	0.2752199210362	2		1107	990	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0044043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	108	315	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.775808281766478	2		315	265	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645412	67645412	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	158	313	0	ENST00000264010.4:c.677A>G	p.Tyr226Cys	p.Y226C	ENST00000264010	NM_006565.3	226	tAc/tGc	3/12	0.759967840037086	1	FACETS	0.982	0.924	1	0.982	0.924	1	CLONAL	1	TRUE	0	0.775808281766478	1		313	254	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912664	NA	P-0044043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	218	493	0	ENST00000269305.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000269305	NM_001126112.2	337	cGc/cAc	10/11	0.759967840037086	1	FACETS	0.827	0.781	0.873	0.827	0.781	0.873	CLONAL	1	TRUE	0	0.775808281766478	1		493	416	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061312	38061312	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	722	488	0	ENST00000250448.2:c.677A>T	p.Asp226Val	p.D226V	ENST00000250448	NM_004496.3	226	gAc/gTc	2/2	1	2	FACETS	0.791	0.769	0.813	1	0.998	1	SUBCLONAL	2	TRUE	1	0.775808281766478	2		488	1177	SUCCESS
ATM	472	MSKCC	GRCh37	11	108143570	108143570	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0044043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	58	274	0	ENST00000278616.4:c.3275C>G	p.Ser1092Ter	p.S1092*	ENST00000278616	NM_000051.3	1092	tCa/tGa	22/63	NA	2	FACETS	1	0.89	1			1	INDETERMINATE	1	TRUE	NA	0.775808281766478	2		274	148	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225612	2225612	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	238	490	1	ENST00000326181.6:c.1615C>T	p.Gln539Ter	p.Q539*	ENST00000326181	NM_032271.2	539	Cag/Tag	17/21	0.698518154995733	3	FACETS	1	0.968	1	0.527	0.493	0.562	CLONAL	1	TRUE	1	0.775808281766478	3		491	808	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177588	56177622	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGTTTGATGGCTATTGCAGATGAGGTGGAAATT	GCCGTTTGATGGCTATTGCAGATGAGGTGGAAATT	-	novel	NA	P-0044043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	131	283	0	ENST00000399503.3:c.2565_2599del	p.Leu856SerfsTer36	p.L856Sfs*36	ENST00000399503	NM_005921.1	854	cGCCGTTTGATGGCTATTGCAGATGAGGTGGAAATT/c	14/20	0.52689506757187	1	FACETS	0.834	0.774	0.893	0.834	0.774	0.893	CLONAL	1	TRUE	0	0.775808281766478	1		283	248	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239756	53239756	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044043-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	200	416	0	ENST00000375401.3:c.1586G>A	p.Gly529Asp	p.G529D	ENST00000375401	NM_004187.3	529	gGt/gAt	12/26	NA	2	FACETS	0.937	0.875	1			1	INDETERMINATE	1	TRUE	NA	0.775808281766478	2		416	550	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061223	38061228	+	inframe_deletion	In_Frame_Del	DEL	TCTCGA	TCTCGA	-	novel	NA	P-0044055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	45	462	0	ENST00000250448.2:c.761_766del	p.Phe254_Asn256delinsTyr	p.F254_N256delinsY	ENST00000250448	NM_004496.3	254	tTCGAGAac/tac	2/2	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.2	2		462	416	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933782	49933782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769911110	NA	P-0044055-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	15	577	0	ENST00000296474.3:c.2495G>A	p.Arg832Gln	p.R832Q	ENST00000296474	NM_002447.2	832	cGa/cAa	10/20	1	2	FACETS	0.754	0.553	0.994	0.754	0.553	0.994	CLONAL	1	TRUE	1	0.2	2		577	199	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	93	868	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.424877851412685	5	FACETS	0.982	0.88	1	0.655	0.587	0.726	CLONAL	2	FALSE	2	0.424877851412685	5		869	365	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098803	178098803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	118	559	0	ENST00000397062.3:c.242G>A	p.Gly81Asp	p.G81D	ENST00000397062	NM_006164.4	81	gGt/gAt	2/5	0.424877851412685	4	FACETS	1	0.981	1	0.671	0.607	0.738	CLONAL	1	FALSE	2	0.424877851412685	4		559	590	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519920	NA	P-0044116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	13	246	0	ENST00000397062.3:c.85G>C	p.Asp29His	p.D29H	ENST00000397062	NM_006164.4	29	Gat/Cat	2/5	0.424877851412685	4	FACETS	0.324	0.231	0.438	0.162	0.115	0.219	SUBCLONAL	1	FALSE	2	0.424877851412685	4		246	269	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028638	12028638	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	82	344	0	ENST00000353533.5:c.841C>T	p.Arg281Ter	p.R281*	ENST00000353533	NM_003010.3	281	Cga/Tga	8/11	NA	2	FACETS	0.906	0.815	1			1	INDETERMINATE	2	FALSE	NA	0.424877851412685	2		344	213	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098806	178098806	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	31	547	0	ENST00000397062.3:c.239C>T	p.Thr80Ile	p.T80I	ENST00000397062	NM_006164.4	80	aCa/aTa	2/5	0.424877851412685	4	FACETS	0.364	0.293	0.444	0.182	0.146	0.222	SUBCLONAL	1	FALSE	2	0.424877851412685	4		547	572	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591977	48591977	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs377767354	NA	P-0044116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	67	249	0	ENST00000342988.3:c.1139+1G>A		p.X380_splice	ENST00000342988	NM_005359.5	380			0.398212901764903	3	FACETS	1	0.917	1	1	0.917	1	CLONAL	3	FALSE	0	0.424877851412685	3		249	125	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132621	11132621	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	215	847	0	ENST00000358026.2:c.2837C>T	p.Pro946Leu	p.P946L	ENST00000358026	NM_001128849.1	946	cCc/cTc	19/36	0.41566194366267	4	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	FALSE	2	0.424877851412685	4		847	711	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098808	178098808	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	120	555	0	ENST00000397062.3:c.237G>C	p.Glu79Asp	p.E79D	ENST00000397062	NM_006164.4	79	gaG/gaC	2/5	0.424877851412685	4	FACETS	1	0.983	1	0.696	0.631	0.765	CLONAL	1	FALSE	2	0.424877851412685	4		555	578	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651388	52651388	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	110	394	0	ENST00000394830.3:c.1708A>C	p.Ile570Leu	p.I570L	ENST00000394830	NM_018313.4	570	Ata/Cta	15/30	0.424877851412685	5	FACETS	0.844	0.767	0.923	0.844	0.767	0.923	CLONAL	3	FALSE	2	0.424877851412685	5		394	335	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271490	26271491	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0044116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	46	424	0	ENST00000305910.3:c.122_123del	p.Arg41LeufsTer19	p.R41Lfs*19	ENST00000305910	NM_003534.2	41	cGC/c	1/1	0.424877851412685	9	FACETS	0.96	0.808	1	0.24	0.202	0.282	CLONAL	1	FALSE	5	0.424877851412685	9		424	561	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64288346	64288346	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	10	209	0	ENST00000370651.3:c.110T>G	p.Leu37Arg	p.L37R	ENST00000370651	NM_003463.4	37	cTt/cGt	3/6	0.424877851412685	6	FACETS	0.744	0.507	1	0.248	0.169	0.346	CLONAL	1	FALSE	3	0.424877851412685	6		209	117	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038564	47038564	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0044116-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	144	368	0	ENST00000377604.3:c.724+2T>C		p.X242_splice	ENST00000377604	NM_001204468.1	242			0.373695251486402	2	FACETS	0.866	0.808	0.923			1	CLONAL	3	FALSE	NA	0.424877851412685	2		368	261	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	27	868	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.785	0.626	0.966	0.785	0.626	0.966	CLONAL	1	TRUE	1	0.232368535455989	2		869	296	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577554	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	TGCAG	TGCAG	-	novel	NA	P-0044117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	54	704	0	ENST00000269305.4:c.723_727del	p.Cys242GlyfsTer20	p.C242Gfs*20	ENST00000269305	NM_001126112.2	241	tcCTGCAtg/tctg	7/11	0.232368535455989	1	FACETS	0.722	0.616	0.837	0.722	0.616	0.837	SUBCLONAL	1	TRUE	0	0.232368535455989	1		704	569	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581162	48581186	+	frameshift_variant	Frame_Shift_Del	DEL	ATGATGGTGAAGGATGAATATGTGC	ATGATGGTGAAGGATGAATATGTGC	-	novel	NA	P-0044117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	21	307	0	ENST00000342988.3:c.470_494del	p.Met157ThrfsTer37	p.M157Tfs*37	ENST00000342988	NM_005359.5	156	ATGATGGTGAAGGATGAATATGTGCat/at	5/12	1	2	FACETS	1	0.811	1	1	0.811	1	CLONAL	1	TRUE	1	0.232368535455989	2		307	172	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522658	67522670	+	frameshift_variant	Frame_Shift_Del	DEL	AAATTGGCTGGTT	AAATTGGCTGGTT	-	novel	NA	P-0044117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	16	323	0	ENST00000274335.5:c.159_171del	p.Ile53MetfsTer18	p.I53Mfs*18	ENST00000274335		52	gAAATTGGCTGGTTa/ga	1/15	0.116464646658396	4	FACETS	0.738	0.546	0.966	0.369	0.273	0.483	INDETERMINATE	1	TRUE	2	0.232368535455989	4		323	230	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504270	8504270	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	22	485	0	ENST00000356435.5:c.1813A>C	p.Met605Leu	p.M605L	ENST00000356435		605	Atg/Ctg	12/35	0.232368535455989	1	FACETS	0.43	0.333	0.544	0.43	0.333	0.544	SUBCLONAL	1	TRUE	0	0.232368535455989	1		485	389	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652305	48652305	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044117-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	48	578	0	ENST00000376670.3:c.976G>A	p.Ala326Thr	p.A326T	ENST00000376670	NM_002049.3	326	Gca/Aca	6/6	1	1	FACETS	0.878	0.743	1	0.878	0.743	1	CLONAL	1	TRUE	0	0.232368535455989	1		578	416	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0044124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	87	868	1	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.188431616082553	3	FACETS	1	0.96	1	1	0.96	1	INDETERMINATE	2	TRUE	1	0.322637926447697	3		869	274	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0044124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	107	360	4	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	0.23430733674433	3	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	1	0.322637926447697	3		364	375	SUCCESS
APC	324	MSKCC	GRCh37	5	112137036	112137036	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0044124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	147	466	0	ENST00000257430.4:c.790C>T	p.Gln264Ter	p.Q264*	ENST00000257430	NM_000038.5	264	Caa/Taa	8/16	1	2	FACETS	0.965	0.888	1	1	0.991	1	CLONAL	2	TRUE	1	0.322637926447697	2		466	472	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627976	37627976	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	119	543	3	ENST00000447079.4:c.1891C>T	p.Pro631Ser	p.P631S	ENST00000447079	NM_015083.1	631	Ccc/Tcc	2/14	0.322637926447697	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.322637926447697	1		546	464	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120372	70120372	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	779	1363	0	ENST00000245479.2:c.1376del	p.Gly459AlafsTer11	p.G459Afs*11	ENST00000245479	NM_000346.3	458	caG/ca	3/3	0.322637926447697	1	FACETS	1	0.995	1	1	0.998	1	CLONAL	2	TRUE	0	0.322637926447697	1		1363	1795	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149911	202149911	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	257	708	1	ENST00000358485.4:c.1352A>T	p.Tyr451Phe	p.Y451F	ENST00000358485	NM_001080125.1	451	tAt/tTt	8/9	1	2	FACETS	1	0.975	1	1	0.995	1	CLONAL	2	TRUE	1	0.322637926447697	2		709	746	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162062	47162062	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	66	401	0	ENST00000409792.3:c.4064A>T	p.Lys1355Ile	p.K1355I	ENST00000409792	NM_014159.6	1355	aAa/aTa	3/21	0.256917792453087	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.322637926447697	1		401	262	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155209	55155209	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	217	546	0	ENST00000257290.5:c.2808G>T	p.Glu936Asp	p.E936D	ENST00000257290	NM_006206.4	936	gaG/gaT	21/23	1	2	FACETS	0.915	0.854	0.978	1	0.994	1	CLONAL	2	TRUE	1	0.322637926447697	2		546	735	SUCCESS
APC	324	MSKCC	GRCh37	5	112175432	112175433	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TA	novel	NA	P-0044124-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	81	336	1	ENST00000257430.4:c.4141_4142delinsTA	p.Pro1381Ter	p.P1381*	ENST00000257430	NM_000038.5	1381	CCa/TAa	16/16	1	2	FACETS	0.82	0.73	0.915	1	0.982	1	CLONAL	2	TRUE	1	0.322637926447697	2		337	306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0044167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	28	496	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.573	0.456	0.706	0.573	0.456	0.706	SUBCLONAL	1	TRUE	1	0.15	2		496	652	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	22	473	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.792	1	1	0.792	1	CLONAL	1	TRUE	1	0.15	2		473	287	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881535	48881671	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGTATTGGTAAGGATTTTCTTAAAACGTTTTGAAATTTTTTTTTCTCATTTTAAAAACAACTTCAAATCACTATACAAAAATTGAAAGATAGAAAAATATAAAGACAATAAAAGCTAATAATAATTCCATTACCCA	GAGTATTGGTAAGGATTTTCTTAAAACGTTTTGAAATTTTTTTTTCTCATTTTAAAAACAACTTCAAATCACTATACAAAAATTGAAAGATAGAAAAATATAAAGACAATAAAAGCTAATAATAATTCCATTACCCA	-	novel	NA	P-0044176-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	82	194	0	ENST00000267163.4:c.260_264+132del		p.X87_splice	ENST00000267163	NM_000321.2	87		2/27	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		194	181	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0044177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	222	384	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.997	0.939	1	0.997	0.939	1	CLONAL	1	TRUE	1	0.95	2		384	469	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141018	55141018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121908589	NA	P-0044177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	191	284	0	ENST00000257290.5:c.1664A>G	p.Tyr555Cys	p.Y555C	ENST00000257290	NM_006206.4	555	tAt/tGt	12/23	1	2	FACETS	0.976	0.915	1	0.976	0.915	1	CLONAL	1	TRUE	1	0.95	2		284	412	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226252135	226252135	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519903	NA	P-0044177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	62	115	0	ENST00000366813.1:c.83A>T	p.Lys28Met	p.K28M	ENST00000366813		28	aAg/aTg	1/3	1	2	FACETS	0.932	0.829	1	0.932	0.829	1	CLONAL	1	TRUE	1	0.95	2		115	140	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129847	55129996	+	inframe_deletion	In_Frame_Del	DEL	CTTTGTACCTCTAGGAATGACGGATTATTTAGTCATCGTGGAGGATGATGATTCTGCCATTATACCTTGTCGCACAACTGATCCCGAGACTCCTGTAACCTTACACAACAGTGAGGGGGTGGTACCTGCCTCCTACGACAGCAGACAGGG	CTTTGTACCTCTAGGAATGACGGATTATTTAGTCATCGTGGAGGATGATGATTCTGCCATTATACCTTGTCGCACAACTGATCCCGAGACTCCTGTAACCTTACACAACAGTGAGGGGGTGGTACCTGCCTCCTACGACAGCAGACAGGG	-	novel	NA	P-0044177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	128	424	0	ENST00000257290.5:c.385_534del	p.Val129_Phe178del	p.V129_F178del	ENST00000257290	NM_006206.4	127	gcCTTTGTACCTCTAGGAATGACGGATTATTTAGTCATCGTGGAGGATGATGATTCTGCCATTATACCTTGTCGCACAACTGATCCCGAGACTCCTGTAACCTTACACAACAGTGAGGGGGTGGTACCTGCCTCCTACGACAGCAGACAGGGc/gcc	4/23	1	2	FACETS	0.622	0.568	0.678	0.622	0.568	0.678	SUBCLONAL	1	TRUE	1	0.95	2		424	433	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442567	52442567	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1253151209	NA	P-0044191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	134	728	0	ENST00000460680.1:c.178C>T	p.Arg60Ter	p.R60*	ENST00000460680	NM_004656.3	60	Cga/Tga	4/17	0.555168940316622	1	FACETS	0.969	0.891	1	0.969	0.891	1	CLONAL	1	FALSE	0	0.555168940316622	1		728	360	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551085	41551085	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	111	654	0	ENST00000263253.7:c.3229C>A	p.Gln1077Lys	p.Q1077K	ENST00000263253	NM_001429.3	1077	Caa/Aaa	17/31	0.179304941492319	0	FACETS	0.322	0.29	0.355			1	INDETERMINATE	1	FALSE	0	0.555168940316622	0		654	553	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188297	10188309	+	frameshift_variant	Frame_Shift_Del	DEL	TTTTTGCCAATAT	TTTTTGCCAATAT	-	novel	NA	P-0044191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	104	698	0	ENST00000256474.2:c.440_452del	p.Ile147ThrfsTer8	p.I147Tfs*8	ENST00000256474	NM_000551.3	147	aTTTTTGCCAATATc/ac	2/3	0.555168940316622	1	FACETS	0.798	0.723	0.877	0.798	0.723	0.877	SUBCLONAL	1	FALSE	0	0.555168940316622	1		698	339	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802576	139802576	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	276	1168	2	ENST00000247668.2:c.421G>A	p.Gly141Ser	p.G141S	ENST00000247668	NM_021138.3	141	Ggc/Agc	5/11	0.179304941492319	0	FACETS	0.53	0.499	0.562			1	INDETERMINATE	1	FALSE	0	0.555168940316622	0		1170	834	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923606	39923606	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044191-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	240	483	0	ENST00000378444.4:c.3485G>C	p.Arg1162Pro	p.R1162P	ENST00000378444	NM_001123385.1	1162	cGc/cCc	7/15	1	1	FACETS	0.771	0.733	0.809	1	0.994	1	SUBCLONAL	2	FALSE	0	0.555168940316622	1		483	405	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0044209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	40	324	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.861722118825989	3	FACETS	0.301	0.25	0.357	0.15	0.125	0.179	SUBCLONAL	1	FALSE	1	0.861722118825989	3		324	442	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574000	7574000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0044209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	1005	822	0	ENST00000269305.4:c.1027G>T	p.Glu343Ter	p.E343*	ENST00000269305	NM_001126112.2	343	Gag/Tag	10/11	0.861722118825989	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	FALSE	0	0.861722118825989	2		822	1135	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011144	12011144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	202	218	0	ENST00000353533.5:c.551C>T	p.Ser184Leu	p.S184L	ENST00000353533	NM_003010.3	184	tCg/tTg	5/11	0.861722118825989	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	FALSE	0	0.861722118825989	2		218	225	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398285	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0044209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	234	364	0	ENST00000311936.3:c.34_35delinsTT	p.Gly12Phe	p.G12F	ENST00000311936	NM_004985.3	12	GGt/TTt	2/5	0.310200540632484	3	FACETS	1	0.965	1	0.678	0.645	0.711	INDETERMINATE	2	FALSE	0	0.861722118825989	3		364	382	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221297	36221297	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	1032	941	1	ENST00000222270.7:c.5131G>C	p.Glu1711Gln	p.E1711Q	ENST00000222270	NM_014727.1	1711	Gag/Cag	24/37	0.861722118825989	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	FALSE	0	0.861722118825989	2		942	1196	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482345	56482345	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	224	601	0	ENST00000267101.3:c.893A>T	p.Gln298Leu	p.Q298L	ENST00000267101	NM_001982.3	298	cAa/cTa	8/28	0.861722118825989	3	FACETS	0.878	0.819	0.939	0.439	0.409	0.47	CLONAL	1	FALSE	1	0.861722118825989	3		601	847	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95596451	95596451	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	124	266	0	ENST00000393063.1:c.517G>T	p.Val173Leu	p.V173L	ENST00000393063	NM_030621.3	173	Gtg/Ttg	6/28	0.861722118825989	3	FACETS	0.822	0.748	0.899	0.411	0.374	0.45	CLONAL	1	FALSE	1	0.861722118825989	3		266	501	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797870	42797870	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs371145542	NA	P-0044209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	934	934	0	ENST00000575354.2:c.3922G>C	p.Glu1308Gln	p.E1308Q	ENST00000575354	NM_015125.3	1308	Gag/Cag	16/20	0.861722118825989	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	FALSE	0	0.861722118825989	2		934	1083	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248540	212248540	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	301	536	0	ENST00000342788.4:c.3727T>C	p.Trp1243Arg	p.W1243R	ENST00000342788	NM_005235.2	1243	Tgg/Cgg	28/28	0.683428401722405	3	FACETS	1	0.989	1	0.588	0.556	0.621	CLONAL	1	FALSE	1	0.861722118825989	3		536	850	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164790	36164790	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	1068	1008	0	ENST00000300305.3:c.1085C>G	p.Ser362Trp	p.S362W	ENST00000300305		362	tCg/tGg	8/8	1	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	FALSE	1	0.861722118825989	2		1008	1785	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444650	187444650	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0044209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	247	445	0	ENST00000232014.4:c.1577G>T	p.Arg526Leu	p.R526L	ENST00000232014	NM_001130845.1	526	cGc/cTc	7/10	0.861722118825989	3	FACETS	0.998	0.936	1	0.499	0.468	0.531	CLONAL	1	FALSE	1	0.861722118825989	3		445	822	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1957455	1957455	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	313	585	0	ENST00000382891.5:c.2554G>T	p.Ala852Ser	p.A852S	ENST00000382891	NM_133335.3	852	Gcc/Tcc	14/22	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	1	FALSE	NA	0.861722118825989	2		585	712	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968096	55968096	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	196	387	0	ENST00000263923.4:c.2234G>C	p.Cys745Ser	p.C745S	ENST00000263923	NM_002253.2	745	tGt/tCt	15/30	NA	2	FACETS	0.974	0.912	1			1	INDETERMINATE	1	FALSE	NA	0.861722118825989	2		387	467	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508097	106508097	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0044209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	240	241	0	ENST00000359195.3:c.91A>T	p.Ser31Cys	p.S31C	ENST00000359195	NM_002649.2	31	Agc/Tgc	2/11	0.861722118825989	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	FALSE	1	0.861722118825989	3		241	371	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393635	139393635	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0044209-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	1034	899	0	ENST00000277541.6:c.6011G>C	p.Arg2004Pro	p.R2004P	ENST00000277541	NM_017617.3	2004	cGc/cCc	32/34	0.861722118825989	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	FALSE	0	0.861722118825989	2		899	1177	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0044214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	126	242	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.25580332556087	3	FACETS	0.99	0.9	1			1	CLONAL	2	TRUE	NA	0.25580332556087	3		242	561	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0044214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	96	713	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.68	0.605	0.762	0.68	0.605	0.762	SUBCLONAL	1	TRUE	1	0.25580332556087	2		713	1103	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578242	7578242	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882003	NA	P-0044214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	77	658	1	ENST00000269305.4:c.607G>T	p.Val203Leu	p.V203L	ENST00000269305	NM_001126112.2	203	Gtg/Ttg	6/11	1	2	FACETS	0.621	0.543	0.704	0.621	0.543	0.704	SUBCLONAL	1	TRUE	1	0.25580332556087	2		659	970	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940008	76940008	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs797044865	NA	P-0044214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	60	560	0	ENST00000373344.5:c.740A>G	p.Asn247Ser	p.N247S	ENST00000373344	NM_000489.3	247	aAc/aGc	9/35	0.25580332556087	1	FACETS	0.696	0.599	0.801	0.696	0.599	0.801	SUBCLONAL	1	TRUE	0	0.25580332556087	1		560	588	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175996825	175996825	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0044214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	86	392	0	ENST00000367669.3:c.1613-1G>T		p.X538_splice	ENST00000367669	NM_022457.5	538			0.25580332556087	6	FACETS	1	0.973	1	0.342	0.302	0.385	CLONAL	1	TRUE	2	0.25580332556087	6		392	743	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805676	46805676	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0044214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1338	96	735	0	ENST00000290295.7:c.280C>G	p.Arg94Gly	p.R94G	ENST00000290295	NM_006361.5	94	Cgg/Ggg	1/2	0.25580332556087	4	FACETS	0.657	0.583	0.737	0.219	0.194	0.246	SUBCLONAL	1	TRUE	1	0.25580332556087	4		735	1434	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143080	30143080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374276783	NA	P-0044214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	95	782	0	ENST00000389048.3:c.446C>T	p.Ala149Val	p.A149V	ENST00000389048	NM_004304.4	149	gCg/gTg	1/29	1	2	FACETS	0.673	0.597	0.754	0.673	0.597	0.754	SUBCLONAL	1	TRUE	1	0.25580332556087	2		782	1104	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502626	149502626	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044214-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	57	358	0	ENST00000261799.4:c.2162C>A	p.Pro721His	p.P721H	ENST00000261799	NM_002609.3	721	cCc/cAc	15/23	0.220587902503006	3	FACETS	0.719	0.616	0.832	0.36	0.308	0.416	SUBCLONAL	1	TRUE	1	0.25580332556087	3		358	699	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0044215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	29	341	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	0.327329199182715	2	FACETS	1	0.946	1	0.727	0.603	0.857	CLONAL	1	TRUE	0	0.498873932420377	2		341	80	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0044215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	109	632	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.363126576335089	1	FACETS	0.781	0.706	0.859	0.781	0.706	0.859	SUBCLONAL	1	TRUE	0	0.498873932420377	1		632	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577601	7577601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	9	608	0	ENST00000269305.4:c.680C>T	p.Ser227Phe	p.S227F	ENST00000269305	NM_001126112.2	227	tCt/tTt	7/11	0.363126576335089	1	FACETS	0.089	0.058	0.128	0.089	0.058	0.128	SUBCLONAL	1	TRUE	0	0.498873932420377	1		608	304	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40743980	40743980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763896696	NA	P-0044215-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	44	623	0	ENST00000392038.2:c.727C>T	p.Arg243Trp	p.R243W	ENST00000392038	NM_001626.4	243	Cgg/Tgg	9/14	0.219205996555047	6	FACETS	0.469	0.392	0.554			1	INDETERMINATE	1	TRUE	NA	0.498873932420377	6		623	752	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	487	572	6	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.992	1	1	0.998	1	CLONAL	2	TRUE	1	0.458385901568168	2		578	952	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	198	735	15	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.954	0.884	1	0.954	0.884	1	CLONAL	1	TRUE	1	0.458385901568168	2		750	906	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	249	447	9	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	1	2	FACETS	0.889	0.838	0.941	1	0.995	1	CLONAL	2	TRUE	1	0.458385901568168	2		456	611	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255170	16255170	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	155	444	0	ENST00000375759.3:c.2439del	p.Val814TrpfsTer44	p.V814Wfs*44	ENST00000375759	NM_015001.2	812	gAa/ga	11/15	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.458385901568168	2		444	676	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	156	298	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.94	0.863	1	0.94	0.863	1	CLONAL	1	TRUE	1	0.458385901568168	2		298	724	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248049	59248052	+	frameshift_variant	Frame_Shift_Del	DEL	CTGT	CTGT	-	novel	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	115	450	0	ENST00000371222.2:c.691_694del	p.Thr231CysfsTer29	p.T231Cfs*29	ENST00000371222	NM_002228.3	231	ACAGtg/tg	1/1	1	2	FACETS	0.831	0.75	0.915	0.831	0.75	0.915	CLONAL	1	TRUE	1	0.458385901568168	2		450	604	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551935	150551946	+	inframe_deletion	In_Frame_Del	DEL	GCCGGCCCCCAA	GCCGGCCCCCAA	-	rs779327179	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	125	426	0	ENST00000369026.2:c.61_72del	p.Leu21_Gly24del	p.L21_G24del	ENST00000369026	NM_021960.4	21	TTGGGGGCCGGC/-	1/3	1	2	FACETS	0.89	0.808	0.976	0.89	0.808	0.976	CLONAL	1	TRUE	1	0.458385901568168	2		426	613	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999143	100999143	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	234	747	0	ENST00000325455.5:c.659A>G	p.Glu220Gly	p.E220G	ENST00000325455	NM_001202474.3	220	gAg/gGg	1/8	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.458385901568168	2		747	836	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	165	255	3	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.458385901568168	2		258	648	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398279	25398279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894365	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	166	395	1	ENST00000311936.3:c.40G>A	p.Val14Ile	p.V14I	ENST00000311936	NM_004985.3	14	Gta/Ata	2/5	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.458385901568168	2		396	677	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	248	858	1	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.458385901568168	2		859	1003	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863467	57863467	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs990717142	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	185	562	0	ENST00000228682.2:c.1562G>A	p.Ser521Asn	p.S521N	ENST00000228682	NM_005269.2	521	aGc/aAc	11/12	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.458385901568168	2		562	756	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218430	133218431	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	rs1555222376	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	167	641	0	ENST00000320574.5:c.5180_5181del	p.Val1727GlyfsTer57	p.V1727Gfs*57	ENST00000320574	NM_006231.2	1727	gTG/g	39/49	1	2	FACETS	0.871	0.801	0.943	0.871	0.801	0.943	CLONAL	1	TRUE	1	0.458385901568168	2		641	837	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422039	81422040	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	108	379	0	ENST00000298171.2:c.17dup	p.Leu6PhefsTer56	p.L6Ffs*56	ENST00000298171	NM_000369.2	5	-/T	1/10	1	2	FACETS	0.908	0.818	1	0.908	0.818	1	CLONAL	1	TRUE	1	0.458385901568168	2		379	519	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43705410	43705410	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764425387	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	241	875	1	ENST00000382044.4:c.5212G>A	p.Ala1738Thr	p.A1738T	ENST00000382044	NM_001141980.1	1738	Gca/Aca	24/28	1	2	FACETS	0.931	0.869	0.996	0.931	0.869	0.996	CLONAL	1	TRUE	1	0.458385901568168	2		876	1129	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727565	66727565	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	152	387	0	ENST00000307102.5:c.281T>C	p.Met94Thr	p.M94T	ENST00000307102	NM_002755.3	94	aTg/aCg	2/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.458385901568168	2		387	565	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	158	528	3	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.99	0.91	1	0.99	0.91	1	CLONAL	1	TRUE	1	0.458385901568168	2		531	696	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465477	99465477	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	157	516	0	ENST00000268035.6:c.2302C>T	p.Pro768Ser	p.P768S	ENST00000268035	NM_000875.3	768	Ccg/Tcg	11/21	1	2	FACETS	0.966	0.887	1	0.966	0.887	1	CLONAL	1	TRUE	1	0.458385901568168	2		516	709	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	188	615	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	0.877	0.811	0.946	0.877	0.811	0.946	CLONAL	1	TRUE	1	0.458385901568168	2		615	935	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740789	58740789	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	203	600	0	ENST00000305921.3:c.1694G>A	p.Ser565Asn	p.S565N	ENST00000305921	NM_003620.3	565	aGt/aAt	6/6	1	2	FACETS	0.961	0.891	1	0.961	0.891	1	CLONAL	1	TRUE	1	0.458385901568168	2		600	922	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119910	70119910	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1297203260	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	180	535	0	ENST00000245479.2:c.916del	p.Val306CysfsTer77	p.V306Cfs*77	ENST00000245479	NM_000346.3	304	ccG/cc	3/3	1	2	FACETS	0.99	0.915	1	0.99	0.915	1	CLONAL	1	TRUE	1	0.458385901568168	2		535	793	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244358	5244358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	306	788	3	ENST00000357368.4:c.1124C>T	p.Pro375Leu	p.P375L	ENST00000357368	NM_002850.3	375	cCg/cTg	11/38	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.458385901568168	2		791	1236	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10262139	10262139	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	184	739	1	ENST00000340748.4:c.2152del	p.Met718CysfsTer59	p.M718Cfs*59	ENST00000340748		718	Atg/tg	23/40	1	2	FACETS	0.802	0.74	0.867	0.802	0.74	0.867	CLONAL	1	TRUE	1	0.458385901568168	2		740	1001	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945988	17945988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747131454	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	308	876	0	ENST00000458235.1:c.1951C>T	p.Arg651Trp	p.R651W	ENST00000458235	NM_000215.3	651	Cgg/Tgg	15/24	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.458385901568168	2		876	1141	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	288	907	6	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.458385901568168	2		913	1162	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797411	42797411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	207	877	0	ENST00000575354.2:c.3773G>A	p.Ser1258Asn	p.S1258N	ENST00000575354	NM_015125.3	1258	aGc/aAc	15/20	1	2	FACETS	0.88	0.817	0.946	0.88	0.817	0.946	CLONAL	1	TRUE	1	0.458385901568168	2		877	1026	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660306	227660307	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	155	556	0	ENST00000305123.5:c.3148dup	p.Ala1050GlyfsTer31	p.A1050Gfs*31	ENST00000305123	NM_005544.2	1050	gca/gGca	1/2	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.458385901568168	2		556	669	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022485	31022486	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	100	403	0	ENST00000375687.4:c.1973dup	p.Gly659ArgfsTer9	p.G659Rfs*9	ENST00000375687	NM_015338.5	657	gag/gaGg	13/13	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.458385901568168	2		403	409	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012725	36012725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1432190943	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	61	92	0	ENST00000358208.4:c.169G>A	p.Ala57Thr	p.A57T	ENST00000358208		57	Gcg/Acg	2/12	1	2	FACETS	0.778	0.685	0.874	1	0.976	1	SUBCLONAL	2	TRUE	1	0.458385901568168	2		92	171	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713673	30713673	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	172	502	0	ENST00000295754.5:c.998T>C	p.Leu333Pro	p.L333P	ENST00000295754	NM_003242.5	333	cTa/cCa	4/7	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.458385901568168	2		502	707	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934243	49934243	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1407832113	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	234	783	3	ENST00000296474.3:c.2264del	p.Gly755ValfsTer19	p.G755Vfs*19	ENST00000296474	NM_002447.2	755	gGt/gt	8/20	1	2	FACETS	0.96	0.895	1	0.96	0.895	1	CLONAL	1	TRUE	1	0.458385901568168	2		786	1064	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582242	52582242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879167521	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	85	227	0	ENST00000394830.3:c.4586G>A	p.Arg1529His	p.R1529H	ENST00000394830	NM_018313.4	1529	cGc/cAc	30/30	1	2	FACETS	0.963	0.857	1	0.963	0.857	1	CLONAL	1	TRUE	1	0.458385901568168	2		227	385	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247426	71247426	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200643313	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	177	555	0	ENST00000318789.4:c.107G>A	p.Arg36Gln	p.R36Q	ENST00000318789	NM_032682.5	36	cGg/cAg	6/21	1	2	FACETS	0.919	0.848	0.994	0.919	0.848	0.994	CLONAL	1	TRUE	1	0.458385901568168	2		555	840	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119634948	119634948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334056340	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	112	303	0	ENST00000316626.5:c.551C>T	p.Pro184Leu	p.P184L	ENST00000316626		184	cCg/cTg	5/12	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.458385901568168	2		303	461	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964971	55964971	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	22	263	0	ENST00000263923.4:c.2267-1G>T		p.X756_splice	ENST00000263923	NM_002253.2	756			1	2	FACETS	0.244	0.188	0.308	0.244	0.188	0.308	SUBCLONAL	1	TRUE	1	0.458385901568168	2		263	394	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323147	31323147	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	46	712	0	ENST00000412585.2:c.842A>G	p.Tyr281Cys	p.Y281C	ENST00000412585	NM_005514.6	281	tAc/tGc	4/8	0.458250061299376	2	FACETS	0.223	0.186	0.263	0.111	0.093	0.132	SUBCLONAL	1	TRUE	0	0.458385901568168	2		712	902	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815698	32815698	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs1331472742	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	442	776	1	ENST00000354258.4:c.1918C>T	p.Gln640Ter	p.Q640*	ENST00000354258	NM_000593.5	640	Cag/Tag	8/11	0.458250061299376	2	FACETS	0.995	0.954	1	0.995	0.954	1	CLONAL	2	TRUE	0	0.458385901568168	2		777	969	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845228	128845228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	38	509	0	ENST00000249373.3:c.722C>T	p.Thr241Met	p.T241M	ENST00000249373	NM_005631.4	241	aCg/aTg	3/12	1	2	FACETS	0.221	0.182	0.265	0.221	0.182	0.265	SUBCLONAL	1	TRUE	1	0.458385901568168	2		509	751	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929498	44929498	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	215	558	0	ENST00000377967.4:c.2598del	p.Met866IlefsTer32	p.M866Ifs*32	ENST00000377967	NM_021140.2	866	atG/at	17/29	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.458385901568168	2		558	810	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045483	47045483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	214	632	1	ENST00000377604.3:c.2450G>A	p.Arg817His	p.R817H	ENST00000377604	NM_001204468.1	817	cGt/cAt	22/24	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.458385901568168	2		633	853	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412248	63412248	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0044217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	243	935	0	ENST00000330258.3:c.919del	p.Asp307ThrfsTer3	p.D307Tfs*3	ENST00000330258	NM_152424.3	307	Gac/ac	2/2	1	2	FACETS	0.917	0.856	0.98	0.917	0.856	0.98	CLONAL	1	TRUE	1	0.458385901568168	2		935	1156	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0044253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	202	473	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.5346991065315	4	FACETS	0.974	0.909	1	0.974	0.909	1	CLONAL	2	TRUE	2	0.5346991065315	4		473	595	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587511	29587511	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0044253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	71	283	0	ENST00000356175.3:c.4494del	p.Gln1499SerfsTer54	p.Q1499Sfs*54	ENST00000356175	NM_000267.3	1498	Ggg/gg	33/57	0.488409822501607	3	FACETS	0.746	0.653	0.846	0.373	0.326	0.423	SUBCLONAL	1	TRUE	1	0.5346991065315	3		283	451	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601234	28601234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	231	268	0	ENST00000241453.7:c.2198C>T	p.Pro733Leu	p.P733L	ENST00000241453	NM_004119.2	733	cCa/cTa	17/24	0.488409822501607	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.5346991065315	3		268	508	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198281609	198281609	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	292	311	1	ENST00000335508.6:c.522A>T	p.Glu174Asp	p.E174D	ENST00000335508	NM_012433.2	174	gaA/gaT	6/25	0.5346991065315	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.5346991065315	3		312	632	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982787	90982787	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0044253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	110	164	0	ENST00000265433.3:c.703-2A>T		p.X235_splice	ENST00000265433	NM_002485.4	235			0.448118589910758	3	FACETS	1	0.981	1	0.824	0.759	0.888	CLONAL	2	TRUE	0	0.5346991065315	3		164	211	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517949	8517949	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0044253-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	13	296	0	ENST00000356435.5:c.1442A>T	p.Asn481Ile	p.N481I	ENST00000356435		481	aAc/aTc	10/35	0.530051204336042	1	FACETS	0.166	0.118	0.225	0.166	0.118	0.225	SUBCLONAL	1	TRUE	0	0.5346991065315	1		296	214	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578259	7578259	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1567551903	NA	P-0044256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	1017	729	0	ENST00000269305.4:c.590T>A	p.Val197Glu	p.V197E	ENST00000269305	NM_001126112.2	197	gTg/gAg	6/11	0.930537431141017	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.931769091336921	2		729	1074	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720258	43720258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs941291291	NA	P-0044256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	423	588	0	ENST00000382044.4:c.3784G>A	p.Val1262Met	p.V1262M	ENST00000382044	NM_001141980.1	1262	Gtg/Atg	18/28	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	1	TRUE	NA	0.931769091336921	2		588	749	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79965971	79965971	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0044256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	400	576	0	ENST00000265081.6:c.635A>G	p.Asn212Ser	p.N212S	ENST00000265081	NM_002439.4	212	aAt/aGt	4/24	1	2	FACETS	0.965	0.922	1	0.965	0.922	1	CLONAL	1	TRUE	1	0.931769091336921	2		576	890	SUCCESS
MET	4233	MSKCC	GRCh37	7	116371753	116371753	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201154533	NA	P-0044256-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	337	364	1	ENST00000397752.3:c.1232C>T	p.Ala411Val	p.A411V	ENST00000397752	NM_000245.2	411	gCg/gTg	3/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.931769091336921	2		365	708	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115874	8115875	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0044359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	39	821	0	ENST00000346208.3:c.1221dup	p.Pro408AlafsTer99	p.P408Afs*99	ENST00000346208		407	tcg/tcGg	6/6	1	2	FACETS	0.489	0.404	0.584	0.489	0.404	0.584	SUBCLONAL	1	TRUE	1	0.24	2		821	665	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419922	152419922	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0044359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	21	485	0	ENST00000206249.3:c.1609T>G	p.Tyr537Asp	p.Y537D	ENST00000206249	NM_000125.3	537	Tat/Gat	8/8	1	2	FACETS	0.287	0.22	0.366	0.287	0.22	0.366	SUBCLONAL	1	TRUE	1	0.24	2		485	609	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742934	17742934	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0044359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	29	494	0	ENST00000250003.3:c.842G>T	p.Arg281Leu	p.R281L	ENST00000250003	NM_002478.4	281	cGc/cTc	3/3	1	2	FACETS	0.516	0.414	0.633	0.516	0.414	0.633	SUBCLONAL	1	TRUE	1	0.24	2		494	468	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573118	64573119	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0044359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	17	291	0	ENST00000312049.6:c.1173_1174insT	p.Glu392Ter	p.E392*	ENST00000312049	NM_130799.2	391	-/T	8/10	1	2	FACETS	0.44	0.328	0.574	0.44	0.328	0.574	SUBCLONAL	1	TRUE	1	0.24	2		291	322	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022352	26022352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044359-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	36	464	0	ENST00000435504.4:c.305G>A	p.Ser102Asn	p.S102N	ENST00000435504		102	aGt/aAt	5/13	1	2	FACETS	0.434	0.355	0.522	0.434	0.355	0.522	SUBCLONAL	1	TRUE	1	0.24	2		464	692	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870205	155870205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs563231684	NA	P-0044363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	140	379	0	ENST00000368323.3:c.634C>T	p.Arg212Trp	p.R212W	ENST00000368323	NM_006912.5	212	Cgg/Tgg	6/6	0.58812011434295	7	FACETS	0.91	0.836	0.985			1	CLONAL	3	TRUE	NA	0.58812011434295	7		379	431	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0044363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	192	404	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.58812011434295	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.58812011434295	1		404	418	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71940241	71940241	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113909227	NA	P-0044363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	130	528	2	ENST00000298229.2:c.626G>A	p.Arg209His	p.R209H	ENST00000298229	NM_001567.3	209	cGt/cAt	5/28	0.141923504469863	4	FACETS	0.84	0.769	0.913	0.84	0.769	0.913	INDETERMINATE	2	TRUE	2	0.58812011434295	4		530	418	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212878	94212878	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	66	323	0	ENST00000323929.3:c.364G>A	p.Val122Met	p.V122M	ENST00000323929	NM_005591.3	122	Gtg/Atg	5/20	0.141923504469863	4	FACETS	1	0.926	1	0.543	0.475	0.616	INDETERMINATE	1	TRUE	2	0.58812011434295	4		323	328	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420460	49420460	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	173	522	0	ENST00000301067.7:c.15289C>T	p.Arg5097Ter	p.R5097*	ENST00000301067	NM_003482.3	5097	Cga/Tga	48/54	0.406435450482745	4	FACETS	0.967	0.898	1	0.967	0.898	1	CLONAL	2	TRUE	2	0.58812011434295	4		522	483	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422891	49422891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777490835	NA	P-0044363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	186	515	0	ENST00000301067.7:c.14204G>A	p.Arg4735Gln	p.R4735Q	ENST00000301067	NM_003482.3	4735	cGg/cAg	44/54	0.406435450482745	4	FACETS	0.942	0.877	1	0.942	0.877	1	CLONAL	2	TRUE	2	0.58812011434295	4		515	533	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425896	49425896	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783685	NA	P-0044363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	150	615	1	ENST00000301067.7:c.12592C>T	p.Arg4198Ter	p.R4198*	ENST00000301067	NM_003482.3	4198	Cga/Tga	39/54	0.406435450482745	4	FACETS	0.825	0.759	0.892	0.825	0.759	0.892	CLONAL	2	TRUE	2	0.58812011434295	4		616	491	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788617	3788617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519884	NA	P-0044363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	127	497	1	ENST00000262367.5:c.4337G>A	p.Arg1446His	p.R1446H	ENST00000262367	NM_004380.2	1446	cGc/cAc	26/31	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.58812011434295	2		498	384	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842042	3842042	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783464	NA	P-0044363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	104	315	0	ENST00000262367.5:c.1270C>T	p.Arg424Ter	p.R424*	ENST00000262367	NM_004380.2	424	Cga/Tga	5/31	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.58812011434295	2		315	341	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133218	30133218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	140	464	0	ENST00000263025.4:c.280C>T	p.Arg94Cys	p.R94C	ENST00000263025	NM_002746.2	94	Cgc/Tgc	2/9	1	2	FACETS	0.972	0.891	1	0.972	0.891	1	CLONAL	1	TRUE	1	0.58812011434295	2		464	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0044363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	318	496	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	1	0.994	1	1	0.997	1	CLONAL	2	TRUE	1	0.58812011434295	2		496	445	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110127	8110127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772022668	NA	P-0044363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	149	411	1	ENST00000585124.1:c.478G>A	p.Gly160Arg	p.G160R	ENST00000585124	NM_004217.3	160	Ggg/Agg	6/9	1	2	FACETS	0.961	0.884	1	0.961	0.884	1	CLONAL	1	TRUE	1	0.58812011434295	2		412	527	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740836	58740836	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs747668756	NA	P-0044363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	176	400	0	ENST00000305921.3:c.1741C>T	p.Arg581Ter	p.R581*	ENST00000305921	NM_003620.3	581	Cga/Tga	6/6	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.58812011434295	2		400	524	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252721	10252721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1316623288	NA	P-0044363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	124	525	0	ENST00000340748.4:c.3244C>T	p.Arg1082Cys	p.R1082C	ENST00000340748		1082	Cgc/Tgc	29/40	1	2	FACETS	0.897	0.817	0.981	0.897	0.817	0.981	CLONAL	1	TRUE	1	0.58812011434295	2		525	470	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15280905	15280905	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	129	483	0	ENST00000263388.2:c.5191C>T	p.Arg1731Trp	p.R1731W	ENST00000263388	NM_000435.2	1731	Cgg/Tgg	28/33	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.58812011434295	2		483	400	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703631	47703631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750636	NA	P-0044363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	146	368	0	ENST00000233146.2:c.2131C>T	p.Arg711Ter	p.R711*	ENST00000233146	NM_000251.2	711	Cga/Tga	13/16	0.141923504469863	4	FACETS	0.852	0.783	0.922	0.852	0.783	0.922	INDETERMINATE	2	TRUE	2	0.58812011434295	4		368	463	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0044363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	171	402	6	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	0.141923504469863	4	FACETS	0.852	0.789	0.917	0.852	0.789	0.917	INDETERMINATE	2	TRUE	2	0.58812011434295	4		408	542	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47061326	47061326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775780402	NA	P-0044363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	105	263	1	ENST00000409792.3:c.7355C>T	p.Ser2452Leu	p.S2452L	ENST00000409792	NM_014159.6	2452	tCg/tTg	19/21	0.141923504469863	4	FACETS	0.915	0.83	1	0.915	0.83	1	INDETERMINATE	2	TRUE	2	0.58812011434295	4		264	310	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582117	189582117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	200	398	0	ENST00000264731.3:c.676C>T	p.Arg226Cys	p.R226C	ENST00000264731	NM_003722.4	226	Cgc/Tgc	5/14	0.141923504469863	4	FACETS	0.841	0.783	0.901	0.841	0.783	0.901	INDETERMINATE	2	TRUE	2	0.58812011434295	4		398	642	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0044363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	112	350	0	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	0.141923504469863	4	FACETS	0.979	0.893	1	0.979	0.893	1	INDETERMINATE	2	TRUE	2	0.58812011434295	4		350	309	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55958789	55958789	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	128	393	0	ENST00000263923.4:c.3064C>T	p.Arg1022Ter	p.R1022*	ENST00000263923	NM_002253.2	1022	Cga/Tga	22/30	0.141923504469863	4	FACETS	1	0.981	1	0.652	0.594	0.713	INDETERMINATE	1	TRUE	2	0.58812011434295	4		393	530	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0044363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	240	407	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.587009814453949	3	FACETS	0.85	0.808	0.892	0.85	0.808	0.892	CLONAL	3	TRUE	0	0.58812011434295	3		407	414	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508539	106508539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	69	265	0	ENST00000359195.3:c.533G>A	p.Arg178His	p.R178H	ENST00000359195	NM_002649.2	178	cGt/cAt	2/11	0.50351232395966	4	FACETS	1	0.975	1	0.731	0.644	0.822	CLONAL	1	TRUE	2	0.58812011434295	4		265	255	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879229	151879229	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs763438739	NA	P-0044363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	133	413	0	ENST00000262189.6:c.5716C>T	p.Arg1906Ter	p.R1906*	ENST00000262189	NM_170606.2	1906	Cga/Tga	36/59	0.141923504469863	4	FACETS	0.896	0.821	0.972	0.896	0.821	0.972	INDETERMINATE	2	TRUE	2	0.58812011434295	4		413	401	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636794	8636794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	198	443	0	ENST00000356435.5:c.115G>A	p.Gly39Arg	p.G39R	ENST00000356435		39	Gga/Aga	2/35	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.58812011434295	2		443	626	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971156	21971156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0044363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	343	273	1	ENST00000304494.5:c.202G>A	p.Ala68Thr	p.A68T	ENST00000304494	NM_000077.4	68	Gcg/Acg	2/3	1	2	FACETS	0.858	0.83	0.885	1	0.997	1	CLONAL	3	TRUE	1	0.58812011434295	2		274	453	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293667	137293667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0044363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	154	591	1	ENST00000481739.1:c.218G>A	p.Gly73Asp	p.G73D	ENST00000481739	NM_002957.4	73	gGc/gAc	2/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.58812011434295	2		592	458	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411276	63411276	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0044363-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	150	301	0	ENST00000330258.3:c.1891C>T	p.Arg631Ter	p.R631*	ENST00000330258	NM_152424.3	631	Cga/Tga	2/2	0.48929283264052	2	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.58812011434295	2		301	229	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000056-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	161	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.701784008716135	2		422	432	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442579	52442579	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1312611941	NA	P-0000056-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	328	210	0	ENST00000460680.1:c.166C>T	p.Arg56Cys	p.R56C	ENST00000460680	NM_004656.3	56	Cgc/Tgc	4/17	1	2	FACETS	0.989	0.937	1	0.989	0.937	1	CLONAL	1	TRUE	1	0.701784008716135	2		210	945	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517519	176517519	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000056-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	91	281	0	ENST00000292408.4:c.220G>T	p.Ala74Ser	p.A74S	ENST00000292408	NM_213647.1	74	Gca/Tca	3/18	1	2	FACETS	0.27	0.239	0.303	0.27	0.239	0.303	SUBCLONAL	1	TRUE	1	0.701784008716135	2		281	962	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170183	32170183	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000056-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	314	245	0	ENST00000375023.3:c.3425A>G	p.Tyr1142Cys	p.Y1142C	ENST00000375023	NM_004557.3	1142	tAc/tGc	21/30	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.701784008716135	2		245	861	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652074	36652074	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1213488369	NA	P-0000056-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1248	88	348	0	ENST00000244741.5:c.196G>T	p.Glu66Ter	p.E66*	ENST00000244741	NM_000389.4	66	Gag/Tag	2/3	1	2	FACETS	0.188	0.165	0.212	0.188	0.165	0.212	SUBCLONAL	1	TRUE	1	0.701784008716135	2		348	1336	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806092	1806092	+	protein_altering_variant	In_Frame_Ins	INS	A	A	CACT	novel	NA	P-0000056-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	370	339	0	ENST00000260795.2:c.1111delinsCACT	p.Ser371delinsHisCys	p.S371delinsHC	ENST00000260795		371	Agt/CACTgt	8/17	1	2	FACETS	0.889	0.844	0.935	0.889	0.844	0.935	CLONAL	1	TRUE	1	0.701784008716135	2		339	1186	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0000063-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	248	291	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.740646211995138	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.740646211995138	2		292	316	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000063-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	79	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.977	1			1	INDETERMINATE	2	TRUE	NA	0.740646211995138	2		422	97	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670264	134670264	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs750670511	NA	P-0000063-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	220	267	0	ENST00000398015.3:c.175C>T	p.Gln59Ter	p.Q59*	ENST00000398015	NM_004441.4	59	Cag/Tag	3/16	0.740646211995138	3	FACETS	1	0.971	1	0.536	0.5	0.572	CLONAL	1	TRUE	1	0.740646211995138	3		267	760	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806225	1806225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000063-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	194	327	0	ENST00000260795.2:c.1244C>T	p.Ser415Phe	p.S415F	ENST00000260795		415	tCc/tTc	8/17	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.740646211995138	2		327	480	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518888	187518888	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000063-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	375	444	0	ENST00000441802.2:c.12316G>C	p.Asp4106His	p.D4106H	ENST00000441802	NM_005245.3	4106	Gac/Cac	24/27	0.740646211995138	1	FACETS	0.947	0.908	0.986	0.947	0.908	0.986	CLONAL	1	TRUE	0	0.740646211995138	1		444	673	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518921	187518921	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000063-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	317	392	0	ENST00000441802.2:c.12283G>C	p.Asp4095His	p.D4095H	ENST00000441802	NM_005245.3	4095	Gat/Cat	24/27	0.740646211995138	1	FACETS	0.947	0.905	0.989	0.947	0.905	0.989	CLONAL	1	TRUE	0	0.740646211995138	1		392	569	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949063	151949063	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000063-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	255	279	2	ENST00000262189.6:c.1582C>T	p.Gln528Ter	p.Q528*	ENST00000262189	NM_170606.2	528	Cag/Tag	11/59	1	2	FACETS	0.758	0.71	0.806	0.758	0.71	0.806	SUBCLONAL	1	TRUE	1	0.740646211995138	2		281	909	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949168	151949168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000063-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	192	230	0	ENST00000262189.6:c.1477C>T	p.His493Tyr	p.H493Y	ENST00000262189	NM_170606.2	493	Cac/Tac	11/59	1	2	FACETS	0.732	0.68	0.787	0.732	0.68	0.787	SUBCLONAL	1	TRUE	1	0.740646211995138	2		230	708	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913381	NA	P-0000063-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	265	134	0	ENST00000304494.5:c.322G>A	p.Asp108Asn	p.D108N	ENST00000304494	NM_000077.4	108	Gat/Aat	2/3	1	2	FACETS	0.991	0.953	1	1	0.996	1	CLONAL	2	TRUE	1	0.740646211995138	2		134	361	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435083	110435083	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000063-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	246	195	0	ENST00000375856.3:c.3318G>C	p.Lys1106Asn	p.K1106N	ENST00000375856	NM_003749.2	1106	aaG/aaC	1/2	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	2	TRUE	NA	0.740646211995138	2		195	319	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250890	99250890	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000063-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	353	329	0	ENST00000268035.6:c.194C>G	p.Ser65Cys	p.S65C	ENST00000268035	NM_000875.3	65	tCc/tGc	2/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.740646211995138	2		329	880	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89825040	89825040	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000063-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	221	316	0	ENST00000389301.3:c.2926G>C	p.Asp976His	p.D976H	ENST00000389301	NM_000135.2	976	Gac/Cac	30/43	1	2	FACETS	0.903	0.845	0.962	0.903	0.845	0.962	CLONAL	1	TRUE	1	0.740646211995138	2		316	661	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35860998	35861006	+	inframe_deletion	In_Frame_Del	DEL	TATAGCCAG	TATAGCCAG	-	novel	NA	P-0000063-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2481	322	216	0	ENST00000303115.3:c.128_136del	p.Tyr43_Gln45del	p.Y43_Q45del	ENST00000303115	NM_002185.3	43	TATAGCCAG/-	2/8	0.740646211995138	8	FACETS	0.999	0.938	1	0.167	0.156	0.178	CLONAL	1	TRUE	2	0.740646211995138	8		216	2803	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0000065-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	188	479	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.261238414625122	5	FACETS	0.915	0.844	0.99	0.305	0.281	0.33	INDETERMINATE	1	TRUE	2	0.558197900807594	5		480	1352	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000065-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	18	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.759	0.583	0.957			1	INDETERMINATE	1	TRUE	NA	0.558197900807594	2		422	85	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729153	66729153	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519856	NA	P-0000065-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	90	359	0	ENST00000307102.5:c.361T>A	p.Cys121Ser	p.C121S	ENST00000307102	NM_002755.3	121	Tgc/Agc	3/11	0.291753496236821	4	FACETS	0.812	0.721	0.908	0.406	0.36	0.454	INDETERMINATE	1	TRUE	2	0.558197900807594	4		359	619	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16046949	16046949	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000065-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	147	423	0	ENST00000268712.3:c.1144G>T	p.Glu382Ter	p.E382*	ENST00000268712	NM_006311.3	382	Gaa/Taa	11/46	0.232408478107901	3	FACETS	0.563	0.512	0.616	0.281	0.256	0.308	INDETERMINATE	1	TRUE	1	0.558197900807594	3		423	1197	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000068-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	53	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.14	2		422	757	SUCCESS
APC	324	MSKCC	GRCh37	5	112178909	112178909	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000068-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	31	264	0	ENST00000257430.4:c.7618C>T	p.Pro2540Ser	p.P2540S	ENST00000257430	NM_000038.5	2540	Cca/Tca	16/16	1	2	FACETS	0.804	0.649	0.98	0.804	0.649	0.98	CLONAL	1	TRUE	1	0.14	2		264	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0000068-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	82	548	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	1	2	FACETS	0.932	0.819	1	0.932	0.819	1	CLONAL	1	TRUE	1	0.14	2		548	1257	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883173	37883173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000068-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1687	101	427	0	ENST00000269571.5:c.3076C>T	p.Pro1026Ser	p.P1026S	ENST00000269571		1026	Ccc/Tcc	25/27	1	2	FACETS	0.807	0.718	0.903	0.807	0.718	0.903	CLONAL	1	TRUE	1	0.14	2		427	1788	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	51	422	0				ENST00000310581	NM_198253.2	-/1132			0.190824010937161	6	FACETS	0.977	0.838	1	0.977	0.838	1	CLONAL	3	TRUE	3	0.190824010937161	6		422	252	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303178	11303178	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	69	215	0	ENST00000361445.4:c.1405G>C	p.Ala469Pro	p.A469P	ENST00000361445	NM_004958.3	469	Gcc/Ccc	9/58	NA	2	FACETS	1	0.95	1			1	INDETERMINATE	1	TRUE	NA	0.190824010937161	2		215	609	SUCCESS
FIP1L1	81608	MSKCC	GRCh37	4	54292041	54292041	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	29	167	0	ENST00000358575.5:c.881G>A	p.Arg294Lys	p.R294K	ENST00000358575	NM_001134937.1	294	aGa/aAa	11/18	1	2	FACETS	0.732	0.587	0.897	0.732	0.587	0.897	SUBCLONAL	1	TRUE	1	0.190824010937161	2		167	415	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293613	1293613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	136	187	0	ENST00000310581.5:c.1388G>A	p.Gly463Asp	p.G463D	ENST00000310581	NM_198253.2	463	gGc/gAc	2/16	0.190824010937161	5	FACETS	1	0.942	1			1	CLONAL	3	TRUE	NA	0.190824010937161	5		187	587	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252789	133252789	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	100	229	0	ENST00000320574.5:c.911G>A	p.Gly304Asp	p.G304D	ENST00000320574	NM_006231.2	304	gGc/gAc	10/49	0.190824010937161	3	FACETS	0.876	0.784	0.975			1	CLONAL	2	TRUE	NA	0.190824010937161	3		229	655	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047507	49047507	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0000071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	125	404	0	ENST00000267163.4:c.2501C>G	p.Ser834Ter	p.S834*	ENST00000267163	NM_000321.2	834	tCa/tGa	24/27	0.190824010937161	4	FACETS	0.835	0.755	0.92	0.835	0.755	0.92	CLONAL	2	TRUE	2	0.190824010937161	4		404	934	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577113	7577113	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0000071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	191	396	0	ENST00000269305.4:c.825T>A	p.Cys275Ter	p.C275*	ENST00000269305	NM_001126112.2	275	tgT/tgA	8/11	0.190824010937161	2	FACETS	0.983	0.909	1	0.983	0.909	1	CLONAL	2	TRUE	0	0.190824010937161	2		396	1018	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960969	15960969	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0000071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	118	244	0	ENST00000268712.3:c.6251C>G	p.Ser2084Ter	p.S2084*	ENST00000268712	NM_006311.3	2084	tCa/tGa	40/46	0.190824010937161	2	FACETS	0.887	0.801	0.978	0.887	0.801	0.978	CLONAL	2	TRUE	0	0.190824010937161	2		244	697	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40828029	40828029	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0000071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	44	136	0	ENST00000373198.4:c.2400-1G>T		p.X800_splice	ENST00000373198	NM_133170.3	800			0.190824010937161	3	FACETS	0.758	0.638	0.89	0.758	0.638	0.89	SUBCLONAL	2	TRUE	1	0.190824010937161	3		136	333	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950066	44950066	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs863224886	NA	P-0000071-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	145	281	0	ENST00000377967.4:c.3835C>T	p.Arg1279Ter	p.R1279*	ENST00000377967	NM_021140.2	1279	Cga/Tga	26/29	0.190824010937161	2	FACETS	1	0.979	1			1	CLONAL	2	TRUE	NA	0.190824010937161	2		281	624	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000079-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	72	422	0				ENST00000310581	NM_198253.2	-/1132			0.597126906039691	6	FACETS	1	0.964	1	1	0.964	1	CLONAL	4	TRUE	2	0.597126906039691	6		422	118	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521510	46521510	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000079-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	37	153	0	ENST00000262741.5:c.898C>T	p.Pro300Ser	p.P300S	ENST00000262741	NM_003629.3	300	Cct/Tct	7/10	0.412862281800426	5	FACETS	1	0.905	1	0.732	0.62	0.849	CLONAL	2	TRUE	2	0.597126906039691	5		153	107	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878790	151878790	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760572968	NA	P-0000079-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	17	105	0	ENST00000262189.6:c.6155C>T	p.Ser2052Phe	p.S2052F	ENST00000262189	NM_170606.2	2052	tCc/tTc	36/59	0.523967665200994	4	FACETS	0.957	0.726	1	0.319	0.242	0.407	CLONAL	1	TRUE	1	0.597126906039691	4		105	95	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0000079-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	61	400	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.597126906039691	3	FACETS	1	0.918	1	1	0.918	1	CLONAL	3	TRUE	0	0.597126906039691	3		400	88	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000084-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	69	422	0				ENST00000310581	NM_198253.2	-/1132			0.454247480203535	3	FACETS	1	0.934	1	0.55	0.482	0.622	CLONAL	1	TRUE	1	0.454247480203535	3		422	339	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519893	NA	P-0000084-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	415	377	1	ENST00000267101.3:c.310G>T	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ttg	3/28	0.454247480203535	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.454247480203535	3		378	1089	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431787	49431787	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000084-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	225	229	0	ENST00000301067.7:c.9352G>C	p.Val3118Leu	p.V3118L	ENST00000301067	NM_003482.3	3118	Gtg/Ctg	34/54	0.454247480203535	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.454247480203535	3		229	540	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955550	48955550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913304	NA	P-0000084-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	87	220	0	ENST00000267163.4:c.1666C>T	p.Arg556Ter	p.R556*	ENST00000267163	NM_000321.2	556	Cga/Tga	17/27	NA	2	FACETS	0.775	0.697	0.856			1	INDETERMINATE	2	TRUE	NA	0.454247480203535	2		220	247	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735466	40735466	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs182388300	NA	P-0000084-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1979	363	327	1	ENST00000373198.4:c.3407G>A	p.Arg1136His	p.R1136H	ENST00000373198	NM_133170.3	1136	cGt/cAt	25/32	0.454247480203535	11	FACETS	1	0.969	1	0.26	0.245	0.275	CLONAL	2	TRUE	3	0.454247480203535	11		328	2342	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652061	36652061	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000084-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	377	309	0	ENST00000244741.5:c.183del	p.Asp62ThrfsTer86	p.D62Tfs*86	ENST00000244741	NM_000389.4	61	ggT/gg	2/3	0.386276624234413	5	FACETS	1	0.992	1	0.807	0.767	0.848	CLONAL	2	TRUE	2	0.454247480203535	5		309	1153	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579315	7579316	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1267047192	NA	P-0000084-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	236	191	0	ENST00000269305.4:c.371dup	p.Cys124TrpfsTer25	p.C124Wfs*25	ENST00000269305	NM_001126112.2	124	tgc/tgGc	4/11	0.418648754160323	3	FACETS	0.847	0.799	0.894	0.847	0.799	0.894	CLONAL	3	TRUE	0	0.454247480203535	3		191	502	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652129	36652137	+	frameshift_variant	Frame_Shift_Del	DEL	GAGGCCGGG	GAGGCCGGG	A	novel	NA	P-0000084-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	204	300	0	ENST00000244741.5:c.251_259delinsA	p.Arg84GlnfsTer2	p.R84Qfs*2	ENST00000244741	NM_000389.4	84	cGAGGCCGGGat/cAat	2/3	0.386276624234413	5	FACETS	0.909	0.844	0.975	0.606	0.563	0.65	CLONAL	2	TRUE	2	0.454247480203535	5		300	831	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000085-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	15	422	0				ENST00000310581	NM_198253.2	-/1132			0.149866018607294	3	FACETS	0.964	0.705	1	0.482	0.352	0.638	CLONAL	1	TRUE	1	0.13	3		422	255	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs104886003	NA	P-0000085-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	22	492	0	ENST00000263967.3:c.1633G>C	p.Glu545Gln	p.E545Q	ENST00000263967	NM_006218.2	545	Gag/Cag	10/21	1	2	FACETS	0.754	0.583	0.953	0.754	0.583	0.953	CLONAL	1	TRUE	1	0.13	2		492	449	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481806	56481806	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000085-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	57	330	0	ENST00000267101.3:c.734C>T	p.Ala245Val	p.A245V	ENST00000267101	NM_001982.3	245	gCc/gTc	7/28	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.13	2		330	789	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106785	27106785	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000085-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	40	282	0	ENST00000324856.7:c.6397del	p.Asp2133ThrfsTer2	p.D2133Tfs*2	ENST00000324856	NM_006015.4	2132	gtG/gt	20/20	1	2	FACETS	0.829	0.687	0.989	0.829	0.687	0.989	CLONAL	1	TRUE	1	0.13	2		282	742	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000088-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	55	422	0				ENST00000310581	NM_198253.2	-/1132			0.255287936134078	3	FACETS	1	0.957	1	0.658	0.565	0.759	CLONAL	1	TRUE	1	0.255287936134078	3		422	369	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672534	30672534	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs774404458	NA	P-0000088-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	91	486	0	ENST00000376406.3:c.4426G>T	p.Gly1476Ter	p.G1476*	ENST00000376406	NM_014641.2	1476	Gga/Tga	10/15	0.155199983226286	5	FACETS	0.867	0.768	0.974	0.289	0.256	0.325	CLONAL	1	TRUE	2	0.255287936134078	5		486	1137	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741372	145741372	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000088-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	213	516	0	ENST00000428558.2:c.1131G>C	p.Gln377His	p.Q377H	ENST00000428558	NM_004260.3	377	caG/caC	5/22	0.255287936134078	5	FACETS	0.9	0.835	0.968			1	CLONAL	2	TRUE	NA	0.255287936134078	5		516	1282	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579359	7579359	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587780066	NA	P-0000088-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	161	360	0	ENST00000269305.4:c.328del	p.Arg110ValfsTer13	p.R110Vfs*13	ENST00000269305	NM_001126112.2	110	Cgt/gt	4/11	1	2	FACETS	0.759	0.697	0.824	1	0.989	1	SUBCLONAL	2	TRUE	1	0.255287936134078	2		360	831	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254962	16254962	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000088-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	36	255	0	ENST00000375759.3:c.2227C>G	p.Gln743Glu	p.Q743E	ENST00000375759	NM_015001.2	743	Cag/Gag	11/15	0.255287936134078	3	FACETS	0.57	0.468	0.685	0.285	0.234	0.343	SUBCLONAL	1	TRUE	1	0.255287936134078	3		255	558	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537193	80537193	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000088-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	32	217	0	ENST00000286548.4:c.205G>C	p.Asp69His	p.D69H	ENST00000286548	NM_002072.3	69	Gat/Cat	2/7	0.255287936134078	1	FACETS	0.62	0.503	0.75	0.62	0.503	0.75	SUBCLONAL	1	TRUE	0	0.255287936134078	1		217	353	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317111	87317111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000088-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	54	406	0	ENST00000277120.3:c.250G>A	p.Glu84Lys	p.E84K	ENST00000277120		84	Gaa/Aaa	3/19	0.255287936134078	1	FACETS	0.635	0.542	0.737	0.635	0.542	0.737	SUBCLONAL	1	TRUE	0	0.255287936134078	1		406	581	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427354	49427354	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000088-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	63	362	0	ENST00000301067.7:c.11134G>C	p.Asp3712His	p.D3712H	ENST00000301067	NM_003482.3	3712	Gat/Cat	39/54	0.255287936134078	3	FACETS	0.783	0.676	0.899	0.391	0.338	0.45	SUBCLONAL	1	TRUE	1	0.255287936134078	3		362	711	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434839	99434839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1353303081	NA	P-0000088-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	27	244	0	ENST00000268035.6:c.926C>T	p.Ser309Leu	p.S309L	ENST00000268035	NM_000875.3	309	tCg/tTg	3/21	1	2	FACETS	0.536	0.426	0.661	0.536	0.426	0.661	SUBCLONAL	1	TRUE	1	0.255287936134078	2		244	395	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220428	123220428	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000088-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	147	300	0	ENST00000218089.9:c.3085C>T	p.Gln1029Ter	p.Q1029*	ENST00000218089	NM_001042749.1	1029	Cag/Tag	30/35	0.255287936134078	2	FACETS	1	0.962	1			1	CLONAL	2	TRUE	NA	0.255287936134078	2		300	532	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101267	27101268	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0000088-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	57	439	0	ENST00000324856.7:c.4555dup	p.Gln1519ProfsTer13	p.Q1519Pfs*13	ENST00000324856	NM_006015.4	1517	gcc/gCcc	18/20	0.255287936134078	3	FACETS	0.596	0.51	0.69	0.298	0.255	0.345	SUBCLONAL	1	TRUE	1	0.255287936134078	3		439	845	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801734	3801735	+	missense_variant	Missense_Mutation	DNP	GC	GC	AA	novel	NA	P-0000088-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	80	446	1	ENST00000262367.5:c.3771_3772delinsTT	p.Gln1257_Pro1258delinsHisSer	p.Q1257_P1258delinsHS	ENST00000262367	NM_004380.2	1257	caGCcc/caTTcc	20/31	0.255287936134078	1	FACETS	0.734	0.645	0.829	0.734	0.645	0.829	SUBCLONAL	1	TRUE	0	0.255287936134078	1		447	745	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000096-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	136	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.54134055292768	2		422	417	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412884	49412884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000096-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	481	399	0	ENST00000418115.1:c.139G>A	p.Glu47Lys	p.E47K	ENST00000418115	NM_001664.2	47	Gag/Aag	2/5	0.54134055292768	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	0	0.54134055292768	1		399	1159	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0000096-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	785	168	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.54134055292768	7	FACETS	1	0.992	1			1	CLONAL	5	FALSE	NA	0.54134055292768	7		168	1302	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234541	41234541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000096-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	290	346	0	ENST00000357654.3:c.4237G>A	p.Glu1413Lys	p.E1413K	ENST00000357654	NM_007294.3	1413	Gaa/Aaa	12/23	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	FALSE	1	0.54134055292768	2		346	1061	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5246019	5246019	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000096-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	103	227	0	ENST00000357368.4:c.756G>C	p.Met252Ile	p.M252I	ENST00000357368	NM_002850.3	252	atG/atC	10/38	0.54134055292768	1	FACETS	0.493	0.442	0.547	0.493	0.442	0.547	SUBCLONAL	1	FALSE	0	0.54134055292768	1		227	563	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942137	17942137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000096-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	313	331	0	ENST00000458235.1:c.2878G>A	p.Glu960Lys	p.E960K	ENST00000458235	NM_000215.3	960	Gag/Aag	21/24	0.54134055292768	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	0	0.54134055292768	1		331	698	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041582	47041582	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000096-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	486	222	0	ENST00000377604.3:c.1807C>A	p.Gln603Lys	p.Q603K	ENST00000377604	NM_001204468.1	603	Cag/Aag	17/24	1	1	FACETS	0.836	0.808	0.864	1	0.997	1	CLONAL	2	FALSE	0	0.54134055292768	1		222	783	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782749	135782750	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs118203509	NA	P-0000096-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	379	324	0	ENST00000298552.3:c.1271_1272del	p.Arg424AsnfsTer17	p.R424Nfs*17	ENST00000298552	NM_001162426.1	424	aGA/a	13/23	0.319899651991926	1	FACETS	0.982	0.934	1	0.982	0.934	1	INDETERMINATE	1	FALSE	0	0.54134055292768	1		324	1040	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929463	44929466	+	frameshift_variant	Frame_Shift_Del	DEL	AATG	AATG	-	novel	NA	P-0000096-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	427	217	3	ENST00000377967.4:c.2563_2566del	p.Asn855GlufsTer11	p.N855Efs*11	ENST00000377967	NM_021140.2	855	AATGga/ga	17/29	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	FALSE	0	0.54134055292768	1		220	774	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577036	7577036	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs876660726	NA	P-0000122-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	502	744	0	ENST00000269305.4:c.902del	p.Pro301GlnfsTer44	p.P301Qfs*44	ENST00000269305	NM_001126112.2	301	cCa/ca	8/11	0.773845922963807	1	FACETS	0.976	0.943	1	0.976	0.943	1	CLONAL	1	TRUE	0	0.773845922963807	1		744	815	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62316910	62316926	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGTTCCCCAGCAGGG	CTGGTTCCCCAGCAGGG	-	novel	NA	P-0000122-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	290	663	0	ENST00000360203.5:c.1230_1246del	p.Ser411GlyfsTer6	p.S411Gfs*6	ENST00000360203	NM_001283009.1	409	cCTGGTTCCCCAGCAGGG/c	15/35	1	2	FACETS	0.792	0.747	0.839	0.792	0.747	0.839	SUBCLONAL	1	TRUE	1	0.773845922963807	2		663	946	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11318620	11318625	+	inframe_deletion	In_Frame_Del	DEL	CATAGA	CATAGA	-	novel	NA	P-0000122-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	199	429	1	ENST00000361445.4:c.188_193del	p.Phe63_Asp65delinsTyr	p.F63_D65delinsY	ENST00000361445	NM_004958.3	63	tTCTATGac/tac	3/58	1	2	FACETS	0.641	0.595	0.689	0.641	0.595	0.689	SUBCLONAL	1	TRUE	1	0.773845922963807	2		430	802	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195962	102195962	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000122-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	212	306	0	ENST00000263464.3:c.722A>T	p.Asp241Val	p.D241V	ENST00000263464	NM_001165.4	241	gAc/gTc	2/9	1	2	FACETS	0.956	0.895	1	0.956	0.895	1	CLONAL	1	TRUE	1	0.773845922963807	2		306	573	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905395	11905395	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000122-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	220	357	0	ENST00000396373.4:c.45T>G	p.Ile15Met	p.I15M	ENST00000396373	NM_001987.4	15	atT/atG	2/8	NA	2	FACETS	0.937	0.877	0.997			1	INDETERMINATE	1	TRUE	NA	0.773845922963807	2		357	607	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28880829	28880835	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCTTG	GGCCTTG	-	novel	NA	P-0000122-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	280	517	0	ENST00000282397.4:c.3795_3801del	p.Lys1266ArgfsTer6	p.K1266Rfs*6	ENST00000282397	NM_002019.4	1265	ccCAAGGCC/cc	29/30	0.773845922963807	1	FACETS	0.92	0.878	0.963	0.92	0.878	0.963	CLONAL	1	TRUE	0	0.773845922963807	1		517	482	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61715794	61715794	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000122-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	40	328	0	ENST00000401558.2:c.2135G>T	p.Arg712Ile	p.R712I	ENST00000401558	NM_003400.3	712	aGa/aTa	18/25	NA	2	FACETS	0.145	0.12	0.173			1	INDETERMINATE	1	TRUE	NA	0.773845922963807	2		328	713	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719034	61719188	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAAGGAAAAAAGAAAGAAAATTTAATCAGAAACACTTCTATTGGATCCAATAGTTGCCCTCCTATTTCCATTGATACATACAGATTGATACAAGTGTTACTTTCTAAAAATAACATATGCTCAGTGCTTAACATACCTGTTGAGGCTGAAGATCA	CAAGGAAAAAAGAAAGAAAATTTAATCAGAAACACTTCTATTGGATCCAATAGTTGCCCTCCTATTTCCATTGATACATACAGATTGATACAAGTGTTACTTTCTAAAAATAACATATGCTCAGTGCTTAACATACCTGTTGAGGCTGAAGATCA	-	novel	NA	P-0000122-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	11	43	0	ENST00000401558.2:c.1869_1887+136del		p.X623_splice	ENST00000401558	NM_003400.3	623		16/25	NA	2	FACETS	0.258	0.18	0.355			1	INDETERMINATE	1	TRUE	NA	0.773845922963807	2		43	110	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285249	212285249	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000122-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	266	403	0	ENST00000342788.4:c.3052G>C	p.Asp1018His	p.D1018H	ENST00000342788	NM_005235.2	1018	Gat/Cat	25/28	1	2	FACETS	0.863	0.812	0.914	0.863	0.812	0.914	CLONAL	1	TRUE	1	0.773845922963807	2		403	797	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629079	187629092	+	stop_gained,protein_altering_variant	Nonsense_Mutation	DEL	CTAAGCCATCCATT	CTAAGCCATCCATT	ATTAA	novel	NA	P-0000122-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	110	527	1	ENST00000441802.2:c.1890_1903delinsTTAAT	p.Met631_Gly635delinsTer	p.M631_G635delins*	ENST00000441802	NM_005245.3	630	ctAATGGATGGCTTAGgt/ctTTAATgt	2/27	0.773845922963807	1	FACETS	0.296	0.266	0.327	0.296	0.266	0.327	SUBCLONAL	1	TRUE	0	0.773845922963807	1		528	589	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349638	70349651	+	frameshift_variant	Frame_Shift_Del	DEL	ACATCTCTGTGGAG	ACATCTCTGTGGAG	-	novel	NA	P-0000122-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	377	689	0	ENST00000374080.3:c.3803_3816del	p.Ile1268SerfsTer26	p.I1268Sfs*26	ENST00000374080		1267	aACATCTCTGTGGAG/a	27/45	0.734121286552979	1	FACETS	0.93	0.894	0.967	0.93	0.894	0.967	CLONAL	1	TRUE	0	0.773845922963807	1		689	642	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0000137-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	234	302	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	1	0.981	1	1	0.995	1	CLONAL	2	TRUE	1	0.179616287284782	2		302	1145	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0000137-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	51	139	0				ENST00000310581	NM_198253.2	-/1132			0.179616287284782	0	FACETS	1	0.903	1			1	CLONAL	2	TRUE	0	0.179616287284782	0		139	219	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606091	47606091	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0000137-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	166	289	0	ENST00000263735.4:c.556-1G>A		p.X186_splice	ENST00000263735	NM_002354.2	186			0.134778481791099	0	FACETS	0.906	0.833	0.982			1	CLONAL	2	TRUE	0	0.179616287284782	0		289	837	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128015251	128015251	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000137-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	146	309	0	ENST00000285398.2:c.2270T>C	p.Val757Ala	p.V757A	ENST00000285398	NM_000122.1	757	gTg/gCg	15/15	1	2	FACETS	1	0.943	1	1	0.991	1	CLONAL	2	TRUE	1	0.179616287284782	2		309	780	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242800942	242800942	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000137-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	129	402	2	ENST00000334409.5:c.49C>A	p.Leu17Met	p.L17M	ENST00000334409	NM_005018.2	17	Ctg/Atg	1/5	1	2	FACETS	0.859	0.779	0.944	1	0.988	1	CLONAL	2	TRUE	1	0.179616287284782	2		404	836	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37089060	37089060	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs915595144	NA	P-0000137-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	127	270	0	ENST00000231790.2:c.1782G>C	p.Glu594Asp	p.E594D	ENST00000231790	NM_000249.3	594	gaG/gaC	16/19	NA	2	FACETS	1	0.916	1			1	INDETERMINATE	2	TRUE	NA	0.179616287284782	2		270	700	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435049	110435049	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1310757868	NA	P-0000137-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	105	193	1	ENST00000375856.3:c.3352G>A	p.Glu1118Lys	p.E1118K	ENST00000375856	NM_003749.2	1118	Gag/Aag	1/2	1	2	FACETS	1	0.971	1	1	0.989	1	CLONAL	2	TRUE	1	0.179616287284782	2		194	481	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000149-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	117	422	0				ENST00000310581	NM_198253.2	-/1132			0.328395064039923	5	FACETS	0.945	0.874	1			1	CLONAL	5	TRUE	NA	0.328395064039923	5		422	225	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103692	47103692	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000149-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	59	394	0	ENST00000409792.3:c.6254C>G	p.Ser2085Cys	p.S2085C	ENST00000409792	NM_014159.6	2085	tCt/tGt	14/21	0.328395064039923	3	FACETS	0.415	0.355	0.48	0.207	0.177	0.24	SUBCLONAL	1	TRUE	1	0.328395064039923	3		394	1009	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289023	33289023	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000149-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	30	310	0	ENST00000374542.5:c.529C>G	p.Gln177Glu	p.Q177E	ENST00000374542	NM_001141970.1	177	Cag/Gag	3/8	0.31649560810179	4	FACETS	0.461	0.371	0.565	0.154	0.123	0.189	SUBCLONAL	1	TRUE	1	0.328395064039923	4		310	526	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524667	106524667	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000149-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	63	250	0	ENST00000359195.3:c.2828G>C	p.Gly943Ala	p.G943A	ENST00000359195	NM_002649.2	943	gGa/gCa	9/11	0.328395064039923	6	FACETS	0.634	0.547	0.73	0.106	0.091	0.122	SUBCLONAL	1	TRUE	0	0.328395064039923	6		250	1002	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242871	98242871	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0000149-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	47	305	0	ENST00000331920.6:c.747-1G>A		p.X249_splice	ENST00000331920	NM_000264.3	249			0.287178210698317	4	FACETS	0.523	0.44	0.615	0.262	0.22	0.308	SUBCLONAL	1	TRUE	2	0.328395064039923	4		305	727	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781053	135781053	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000149-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	77	560	0	ENST00000298552.3:c.1912G>C	p.Asp638His	p.D638H	ENST00000298552	NM_001162426.1	638	Gat/Cat	15/23	0.287178210698317	4	FACETS	0.542	0.474	0.615	0.271	0.237	0.308	SUBCLONAL	1	TRUE	2	0.328395064039923	4		560	1150	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930688	32930688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358982	NA	P-0000149-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	83	331	0	ENST00000380152.3:c.7559G>A	p.Arg2520Gln	p.R2520Q	ENST00000380152		2520	cGa/cAa	15/27	0.328395064039923	4	FACETS	0.718	0.632	0.811	0.239	0.21	0.271	SUBCLONAL	1	TRUE	1	0.328395064039923	4		331	935	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325430	1325430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000149-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	131	381	0	ENST00000400841.2:c.245C>T	p.Ser82Leu	p.S82L	ENST00000400841		82	tCg/tTg	3/6	0.296834229259573	4	FACETS	1	0.973	1	0.597	0.542	0.656	CLONAL	1	TRUE	2	0.328395064039923	4		381	887	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217613	142217613	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000149-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	210	227	1	ENST00000350721.4:c.5384del	p.Gly1795GlufsTer29	p.G1795Efs*29	ENST00000350721	NM_001184.3	1795	gGa/ga	32/47	0.328395064039923	4	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	2	0.328395064039923	4		228	833	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881001	37881002	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGCTCCCC	rs397516981	NA	P-0000149-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	239	527	0	ENST00000269571.5:c.2331_2339dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	gtg/gtGGGCTCCCCg	20/27	0.328395064039923	6	FACETS	0.837	0.782	0.894	0.628	0.587	0.671	CLONAL	3	TRUE	2	0.328395064039923	6		527	960	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000149-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	56	422	0				ENST00000310581	NM_198253.2	-/1132			0.326522608753314	5	FACETS	1	0.95	1			1	INDETERMINATE	3	TRUE	NA	0.593233323735591	5		422	106	SUCCESS
ATR	545	MSKCC	GRCh37	3	142217613	142217613	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000149-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	70	227	1	ENST00000350721.4:c.5384del	p.Gly1795GlufsTer29	p.G1795Efs*29	ENST00000350721	NM_001184.3	1795	gGa/ga	32/47	0.194859952864362	6	FACETS	1	0.948	1	0.754	0.668	0.845	INDETERMINATE	2	TRUE	3	0.593233323735591	6		228	228	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881001	37881002	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGCTCCCC	rs397516981	NA	P-0000149-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	64	527	0	ENST00000269571.5:c.2331_2339dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	gtg/gtGGGCTCCCCg	20/27	0.492123456249521	4	FACETS	0.847	0.746	0.952	0.564	0.497	0.635	CLONAL	2	TRUE	1	0.593233323735591	4		527	203	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181429	38181429	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758969072	NA	P-0000149-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	11	266	0	ENST00000396334.3:c.442G>A	p.Asp148Asn	p.D148N	ENST00000396334	NM_002468.4	148	Gac/Aac	2/5	NA	2	FACETS	0.218	0.151	0.302			1	INDETERMINATE	1	TRUE	NA	0.593233323735591	2		266	170	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247070	53247070	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000149-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	15	725	0	ENST00000375401.3:c.430C>G	p.Pro144Ala	p.P144A	ENST00000375401	NM_004187.3	144	Cca/Gca	4/26	0.227533160546068	2	FACETS	0.234	0.171	0.31	0.117	0.085	0.155	INDETERMINATE	1	TRUE	0	0.593233323735591	2		725	216	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443600	29443600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000206-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	83	306	0	ENST00000389048.3:c.3617C>T	p.Ser1206Phe	p.S1206F	ENST00000389048	NM_004304.4	1206	tCc/tTc	23/29	0.291140100514742	3	FACETS	0.844	0.744	0.951	0.422	0.372	0.476	CLONAL	1	TRUE	1	0.291140100514742	3		306	774	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0000206-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	558	291	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.291140100514742	NA		291	1262	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971095	21971103	+	inframe_deletion	In_Frame_Del	DEL	TCCCGGGCA	TCCCGGGCA	-	novel	NA	P-0000206-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	77	295	2	ENST00000304494.5:c.255_263del	p.Ala86_Glu88del	p.A86_E88del	ENST00000304494	NM_000077.4	85	gcTGCCCGGGAg/gcg	2/3	NA	2	FACETS	0.983	0.865	1			1	INDETERMINATE	1	TRUE	NA	0.291140100514742	2		297	538	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0000222-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	42	139	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.623	0.528	0.725			1	INDETERMINATE	1	FALSE	NA	0.793305527391973	2		139	170	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9770648	9770648	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000222-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	76	457	0	ENST00000377346.4:c.135C>G	p.Ile45Met	p.I45M	ENST00000377346	NM_005026.3	45	atC/atG	3/24	0.758477990236833	3	FACETS	0.286	0.25	0.325			1	SUBCLONAL	1	FALSE	NA	0.793305527391973	3		457	937	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432773	78432773	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000222-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1502	147	351	1	ENST00000370768.2:c.303G>C	p.Met101Ile	p.M101I	ENST00000370768	NM_003902.3	101	atG/atC	5/20	0.333245561439292	6	FACETS	0.581	0.528	0.637	0.194	0.176	0.213	INDETERMINATE	1	FALSE	3	0.793305527391973	6		352	1649	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155746	106155746	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1445425331	NA	P-0000222-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	101	308	0	ENST00000380013.4:c.647C>G	p.Ser216Cys	p.S216C	ENST00000380013	NM_001127208.2	216	tCt/tGt	3/11	0.395351730213242	5	FACETS	0.497	0.443	0.555	0.166	0.147	0.185	INDETERMINATE	1	FALSE	2	0.793305527391973	5		308	1122	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295243	1295243	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs35550267	NA	P-0000222-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	37	158	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.643	0.539	0.755			1	INDETERMINATE	1	FALSE	NA	0.793305527391973	2		158	145	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505028	149505028	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000222-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	40	310	0	ENST00000261799.4:c.1787C>G	p.Pro596Arg	p.P596R	ENST00000261799	NM_002609.3	596	cCg/cGg	12/23	0.520099239888421	4	FACETS	0.275	0.228	0.328			1	SUBCLONAL	1	FALSE	NA	0.793305527391973	4		310	658	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099136	157099136	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000222-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	21	97	1	ENST00000346085.5:c.73C>G	p.Leu25Val	p.L25V	ENST00000346085	NM_020732.3	25	Ctc/Gtc	1/20	0.333245561439292	6	FACETS	0.5	0.385	0.633	0.167	0.128	0.211	INDETERMINATE	1	FALSE	3	0.793305527391973	6		98	274	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874550	151874550	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0000222-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1215	66	298	4	ENST00000262189.6:c.7988C>G	p.Ser2663Ter	p.S2663*	ENST00000262189	NM_170606.2	2663	tCa/tGa	38/59	0.333245561439292	6	FACETS	0.336	0.29	0.386	0.112	0.096	0.129	INDETERMINATE	1	FALSE	3	0.793305527391973	6		302	1281	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151919140	151919140	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751681971	NA	P-0000222-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	242	213	10	ENST00000262189.6:c.3445G>A	p.Asp1149Asn	p.D1149N	ENST00000262189	NM_170606.2	1149	Gac/Aac	22/59	0.333245561439292	6	FACETS	1	0.992	1	0.498	0.465	0.532	INDETERMINATE	1	FALSE	3	0.793305527391973	6		223	1056	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390892	139390892	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000222-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	40	266	0	ENST00000277541.6:c.7299C>A	p.Phe2433Leu	p.F2433L	ENST00000277541	NM_017617.3	2433	ttC/ttA	34/34	0.142732841371703	3	FACETS	0.417	0.347	0.494	0.139	0.115	0.165	INDETERMINATE	1	FALSE	0	0.793305527391973	3		266	338	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4398124	4398124	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000222-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	103	295	0	ENST00000261254.3:c.688G>C	p.Glu230Gln	p.E230Q	ENST00000261254	NM_001759.3	230	Gag/Cag	4/5	0.486454191689268	5	FACETS	0.633	0.566	0.705			1	SUBCLONAL	1	FALSE	NA	0.793305527391973	5		295	898	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564521	41564521	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000222-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1281	173	440	6	ENST00000263253.7:c.3943C>G	p.His1315Asp	p.H1315D	ENST00000263253	NM_001429.3	1315	Cac/Gac	24/31	0.413139627418976	4	FACETS	0.538	0.493	0.585	0.269	0.246	0.293	INDETERMINATE	1	FALSE	2	0.793305527391973	4		446	1454	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041720	47041720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000222-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	81	180	1	ENST00000377604.3:c.1945C>T	p.Gln649Ter	p.Q649*	ENST00000377604	NM_001204468.1	649	Caa/Taa	17/24	0.793305527391973	2	FACETS	0.615	0.546	0.687			1	SUBCLONAL	1	FALSE	NA	0.793305527391973	2		181	332	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984909	55984910	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0000222-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1215	67	405	0	ENST00000263923.4:c.219_220del	p.Arg73SerfsTer5	p.R73Sfs*5	ENST00000263923	NM_002253.2	73	agGGtg/agtg	3/30	0.259642720228344	5	FACETS	0.289	0.249	0.331	0.096	0.083	0.111	INDETERMINATE	1	FALSE	2	0.793305527391973	5		405	1282	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295209	1295228	+	upstream_gene_variant	5'Flank	DEL	GGGGCTGGGAGGGCCCGGAG	GGGGCTGGGAGGGCCCGGAG	-	novel	NA	P-0000222-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	17	118	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.383	0.289	0.491			1	INDETERMINATE	1	FALSE	NA	0.793305527391973	2		118	112	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	107	403	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	NA	2	FACETS	0.615	0.552	0.683			1	INDETERMINATE	1	TRUE	NA	0.435853674465243	2		404	798	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	70	422	0				ENST00000310581	NM_198253.2	-/1132			0.435853674465243	1	FACETS	0.866	0.778	0.954	1	0.983	1	CLONAL	2	TRUE	0	0.435853674465243	1		422	145	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	204	531	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	NA	2	FACETS	0.792	0.739	0.846			1	INDETERMINATE	2	TRUE	NA	0.435853674465243	2		531	591	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	175	101	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.435853674465243	6	FACETS	1	0.983	1			1	CLONAL	6	TRUE	NA	0.435853674465243	6		101	234	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261434	16261434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	63	190	0	ENST00000375759.3:c.8699C>T	p.Ser2900Leu	p.S2900L	ENST00000375759	NM_015001.2	2900	tCg/tTg	11/15	0.371873216361557	5	FACETS	0.874	0.757	1			1	CLONAL	1	TRUE	NA	0.435853674465243	5		190	547	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695827	117695827	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	200	246	0	ENST00000369458.3:c.610G>A	p.Glu204Lys	p.E204K	ENST00000369458	NM_024626.3	204	Gag/Aag	4/6	1	2	FACETS	0.948	0.888	1	1	0.994	1	CLONAL	2	TRUE	1	0.435853674465243	2		246	484	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699504	117699504	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750009072	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	121	143	0	ENST00000369458.3:c.137G>A	p.Gly46Glu	p.G46E	ENST00000369458	NM_024626.3	46	gGg/gAg	3/6	1	2	FACETS	0.893	0.818	0.969	1	0.989	1	CLONAL	2	TRUE	1	0.435853674465243	2		143	311	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497905	25497905	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	85	274	0	ENST00000264709.3:c.544C>T	p.Gln182Ter	p.Q182*	ENST00000264709	NM_175629.2	182	Cag/Tag	6/23	1	2	FACETS	0.933	0.829	1	0.933	0.829	1	CLONAL	1	TRUE	1	0.435853674465243	2		274	418	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044357	128044357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	200	356	0	ENST00000285398.2:c.1264G>A	p.Glu422Lys	p.E422K	ENST00000285398	NM_000122.1	422	Gag/Aag	8/15	0.249909832281044	3	FACETS	0.921	0.858	0.985			1	INDETERMINATE	2	TRUE	NA	0.435853674465243	3		356	607	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453532	138453532	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1461713437	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	117	325	0	ENST00000289153.2:c.916C>T	p.Arg306Ter	p.R306*	ENST00000289153	NM_006219.2	306	Cga/Tga	5/22	1	2	FACETS	0.68	0.614	0.751	0.68	0.614	0.751	SUBCLONAL	1	TRUE	1	0.435853674465243	2		325	789	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55597518	55597518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	62	288	0	ENST00000288135.5:c.2166G>A	p.Met722Ile	p.M722I	ENST00000288135	NM_000222.2	722	atG/atA	15/21	0.19220380177304	0	FACETS	0.344	0.297	0.394			1	INDETERMINATE	1	TRUE	0	0.435853674465243	0		288	467	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509751	187509751	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	28	76	0	ENST00000441802.2:c.13762G>T	p.Val4588Phe	p.V4588F	ENST00000441802	NM_005245.3	4588	Gtc/Ttc	27/27	0.133816180951428	0	FACETS	0.442	0.357	0.537			1	INDETERMINATE	1	TRUE	0	0.435853674465243	0		76	164	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584555	187584555	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	80	295	0	ENST00000441802.2:c.3478C>T	p.Gln1160Ter	p.Q1160*	ENST00000441802	NM_005245.3	1160	Cag/Tag	3/27	0.133816180951428	0	FACETS	0.361	0.318	0.408			1	INDETERMINATE	1	TRUE	0	0.435853674465243	0		295	573	SUCCESS
APC	324	MSKCC	GRCh37	5	112103041	112103041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	198	227	0	ENST00000257430.4:c.376G>A	p.Gly126Arg	p.G126R	ENST00000257430	NM_000038.5	126	Gga/Aga	4/16	0.435853674465243	2	FACETS	0.92	0.86	0.98	0.92	0.86	0.98	CLONAL	2	TRUE	0	0.435853674465243	2		227	494	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704529	117704529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	168	332	0	ENST00000368508.3:c.2447G>A	p.Gly816Glu	p.G816E	ENST00000368508	NM_002944.2	816	gGg/gAg	16/43	0.249909832281044	3	FACETS	1	0.939	1			1	INDETERMINATE	1	TRUE	NA	0.435853674465243	3		332	916	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163755	152163755	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	84	259	0	ENST00000206249.3:c.476A>T	p.Gln159Leu	p.Q159L	ENST00000206249	NM_000125.3	159	cAg/cTg	2/8	0.425042844462069	4	FACETS	0.891	0.788	1	0.297	0.262	0.334	CLONAL	1	TRUE	1	0.435853674465243	4		259	621	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206831	162206831	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	64	179	0	ENST00000366898.1:c.844C>T	p.Gln282Ter	p.Q282*	ENST00000366898	NM_004562.2	282	Caa/Taa	7/12	0.425042844462069	4	FACETS	0.827	0.717	0.946	0.276	0.239	0.316	CLONAL	1	TRUE	1	0.435853674465243	4		179	510	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341845	8341845	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	499	387	0	ENST00000356435.5:c.4795G>A	p.Glu1599Lys	p.E1599K	ENST00000356435		1599	Gaa/Aaa	29/35	0.138991489035201	6	FACETS	0.945	0.907	0.983			1	INDETERMINATE	4	TRUE	NA	0.435853674465243	6		387	1134	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507315	8507315	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	95	327	0	ENST00000356435.5:c.1663G>A	p.Glu555Lys	p.E555K	ENST00000356435		555	Gag/Aag	11/35	0.138991489035201	6	FACETS	0.871	0.774	0.974			1	INDETERMINATE	1	TRUE	NA	0.435853674465243	6		327	937	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412690	139412690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	140	250	0	ENST00000277541.6:c.1154C>T	p.Ser385Phe	p.S385F	ENST00000277541	NM_017617.3	385	tCc/tTc	7/34	NA	2	FACETS	1	0.934	1			1	INDETERMINATE	2	TRUE	NA	0.435853674465243	2		250	318	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138944	64138944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	79	243	0	ENST00000334205.4:c.2311C>T	p.Pro771Ser	p.P771S	ENST00000334205	NM_003942.2	771	Ccc/Tcc	17/17	0.184495158893225	5	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.435853674465243	5		243	415	SUCCESS
ATM	472	MSKCC	GRCh37	11	108137973	108137973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879254046	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	188	251	0	ENST00000278616.4:c.2542G>A	p.Glu848Lys	p.E848K	ENST00000278616	NM_000051.3	848	Gag/Aag	17/63	0.435853674465243	3	FACETS	0.809	0.751	0.869	0.809	0.751	0.869	CLONAL	2	TRUE	1	0.435853674465243	3		251	649	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110029	115110029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	61	139	0	ENST00000257566.3:c.1849G>A	p.Ala617Thr	p.A617T	ENST00000257566	NM_016569.3	617	Gcg/Acg	8/8	1	2	FACETS	0.912	0.792	1	0.912	0.792	1	CLONAL	1	TRUE	1	0.435853674465243	2		139	307	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912145	32912145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	88	266	0	ENST00000380152.3:c.3653G>A	p.Gly1218Asp	p.G1218D	ENST00000380152		1218	gGc/gAc	11/27	1	2	FACETS	0.728	0.646	0.814	0.728	0.646	0.814	SUBCLONAL	1	TRUE	1	0.435853674465243	2		266	555	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673806	37673806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201661022	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	73	184	0	ENST00000447079.4:c.2960C>T	p.Ser987Phe	p.S987F	ENST00000447079	NM_015083.1	987	tCt/tTt	10/14	0.249909832281044	3	FACETS	1	0.933	1			1	INDETERMINATE	1	TRUE	NA	0.435853674465243	3		184	374	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867298	45867298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760337216	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	148	115	0	ENST00000391945.4:c.895C>T	p.Arg299Trp	p.R299W	ENST00000391945	NM_000400.3	299	Cgg/Tgg	10/23	NA	2	FACETS	0.951	0.893	1			1	INDETERMINATE	3	TRUE	NA	0.435853674465243	2		115	238	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561547	9561547	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	59	155	0	ENST00000353224.5:c.235G>A	p.Glu79Lys	p.E79K	ENST00000353224	NM_177990.2	79	Gaa/Aaa	4/10	0.435853674465243	3	FACETS	0.945	0.817	1	0.472	0.408	0.541	CLONAL	1	TRUE	1	0.435853674465243	3		155	349	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979281	40979281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	48	148	0	ENST00000373198.4:c.1852G>A	p.Gly618Arg	p.G618R	ENST00000373198	NM_133170.3	618	Gga/Aga	11/32	NA	2	FACETS	0.831	0.708	0.964			1	INDETERMINATE	1	TRUE	NA	0.435853674465243	2		148	265	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938533	44938533	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	122	161	0	ENST00000377967.4:c.3081A>C	p.Arg1027Ser	p.R1027S	ENST00000377967	NM_021140.2	1027	agA/agC	20/29	0.184495158893225	2	FACETS	1	0.928	1			1	INDETERMINATE	1	TRUE	NA	0.435853674465243	2		161	546	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332249	70332249	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	94	506	0	ENST00000373644.4:c.155del	p.Leu52Ter	p.L52*	ENST00000373644	NM_030625.2	52	Tta/ta	2/12	1	2	FACETS	0.471	0.418	0.527	0.471	0.418	0.527	SUBCLONAL	1	TRUE	1	0.435853674465243	2		506	916	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627748	37627777	+	inframe_deletion	In_Frame_Del	DEL	CCTCCAATACCAGCTCTTCCACAGCAACCA	CCTCCAATACCAGCTCTTCCACAGCAACCA	-	novel	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	50	503	0	ENST00000447079.4:c.1667_1696del	p.Pro556_Pro565del	p.P556_P565del	ENST00000447079	NM_015083.1	555	CCTCCAATACCAGCTCTTCCACAGCAACCA/-	2/14	0.249909832281044	3	FACETS	0.335	0.283	0.392			1	INDETERMINATE	1	TRUE	NA	0.435853674465243	3		503	834	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462370	89462371	+	frameshift_variant	Frame_Shift_Ins	INS	GG	GG	AGA	novel	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	87	242	0	ENST00000336596.2:c.1842_1843delinsAGA	p.Leu616IlefsTer9	p.L616Ifs*9	ENST00000336596	NM_005233.5	614	aaGGaa/aaAGAaa	10/17	0.435853674465243	3	FACETS	0.701	0.62	0.787	0.35	0.31	0.394	SUBCLONAL	1	TRUE	1	0.435853674465243	3		242	694	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163021	47163023	+	frameshift_variant	Frame_Shift_Del	DEL	ATG	ATG	TA	novel	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	255	341	0	ENST00000409792.3:c.3103_3105delinsTA	p.His1035Ter	p.H1035*	ENST00000409792	NM_014159.6	1035	CAT/TA	3/21	0.118696126562269	3	FACETS	0.88	0.826	0.934			1	INDETERMINATE	2	TRUE	NA	0.435853674465243	3		341	810	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023625	31023626	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0000237-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	78	339	0	ENST00000375687.4:c.3110_3111delinsAA	p.Trp1037Ter	p.W1037*	ENST00000375687	NM_015338.5	1037	tGG/tAA	13/13	0.435853674465243	3	FACETS	0.73	0.642	0.825	0.365	0.321	0.413	SUBCLONAL	1	TRUE	1	0.435853674465243	3		339	597	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000240-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	258	422	0				ENST00000310581	NM_198253.2	-/1132			0.645820496186315	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	3	TRUE	1	0.645820496186315	4		422	430	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0000240-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	124	310	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.645820496186315	4	FACETS	1	0.975	1	0.403	0.366	0.441	CLONAL	1	TRUE	1	0.645820496186315	4		310	523	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0000245-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	99	275	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.185445336172122	2	FACETS	0.909	0.819	1	0.909	0.819	1	CLONAL	2	TRUE	0	0.305074987091383	2		275	357	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672329	86672329	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs863223718	NA	P-0000245-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	117	194	0	ENST00000274376.6:c.2131C>T	p.Arg711Ter	p.R711*	ENST00000274376	NM_002890.2	711	Cga/Tga	16/25	0.244486334251721	5	FACETS	0.822	0.742	0.906	0.548	0.495	0.604	CLONAL	2	TRUE	2	0.305074987091383	5		194	680	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0000245-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	180	298	0	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	0.305074987091383	4	FACETS	0.897	0.828	0.969	0.897	0.828	0.969	CLONAL	2	TRUE	2	0.305074987091383	4		298	858	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487589	56487589	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000245-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	112	322	0	ENST00000267101.3:c.1522G>C	p.Gly508Arg	p.G508R	ENST00000267101	NM_001982.3	508	Gga/Cga	13/28	0.305074987091383	4	FACETS	0.947	0.85	1	0.473	0.425	0.525	CLONAL	1	TRUE	2	0.305074987091383	4		322	1012	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986893	36986893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1310962672	NA	P-0000245-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	20	134	0	ENST00000354822.5:c.796G>A	p.Gly266Ser	p.G266S	ENST00000354822	NM_001079668.2	266	Ggc/Agc	3/3	0.263753624824931	3	FACETS	0.91	0.701	1	0.455	0.35	0.576	CLONAL	1	TRUE	1	0.305074987091383	3		134	166	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579369	7579369	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555526581	NA	P-0000245-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	76	260	0	ENST00000269305.4:c.318C>G	p.Ser106Arg	p.S106R	ENST00000269305	NM_001126112.2	106	agC/agG	4/11	0.185445336172122	2	FACETS	1	0.964	1	0.626	0.552	0.705	CLONAL	1	TRUE	0	0.305074987091383	2		260	398	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123693	11123693	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000245-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	118	312	0	ENST00000358026.2:c.2343G>C	p.Met781Ile	p.M781I	ENST00000358026	NM_001128849.1	781	atG/atC	16/36	0.305074987091383	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.305074987091383	1		312	476	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460376	149460376	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0000245-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	129	330	0	ENST00000286301.3:c.261del	p.Gly88GlufsTer24	p.G88Efs*24	ENST00000286301	NM_005211.3	87	ccT/cc	3/22	0.244486334251721	5	FACETS	0.901	0.818	0.988	0.601	0.545	0.659	CLONAL	2	TRUE	2	0.305074987091383	5		330	684	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914459	32914460	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs80359552	NA	P-0000245-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	262	241	0	ENST00000380152.3:c.5968_5969del	p.Asp1990CysfsTer12	p.D1990Cfs*12	ENST00000380152		1989	tcAGat/tcat	11/27	0.305074987091383	5	FACETS	0.988	0.928	1	0.741	0.696	0.786	CLONAL	3	TRUE	1	0.305074987091383	5		241	845	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0000268-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	45	139	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	TRUE	1	0.19	2		139	472	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458990	120458990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000268-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	60	399	0	ENST00000256646.2:c.6355C>T	p.Leu2119Phe	p.L2119F	ENST00000256646	NM_024408.3	2119	Ctt/Ttt	34/34	1	2	FACETS	0.696	0.598	0.803	0.696	0.598	0.803	SUBCLONAL	1	TRUE	1	0.19	2		399	908	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61722689	61722689	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000268-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	56	387	0	ENST00000401558.2:c.948G>C	p.Gln316His	p.Q316H	ENST00000401558	NM_003400.3	316	caG/caC	11/25	0.164235374271753	3	FACETS	0.615	0.525	0.714	0.307	0.262	0.357	SUBCLONAL	1	TRUE	1	0.19	3		387	1050	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362012	118362012	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000268-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	24	204	0	ENST00000534358.1:c.4798G>T	p.Glu1600Ter	p.E1600*	ENST00000534358	NM_005933.3	1600	Gag/Tag	14/36	1	2	FACETS	0.532	0.416	0.666	0.532	0.416	0.666	SUBCLONAL	1	TRUE	1	0.19	2		204	475	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66781598	66781598	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs754765552	NA	P-0000268-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	107	421	0	ENST00000307102.5:c.1006G>C	p.Asp336His	p.D336H	ENST00000307102	NM_002755.3	336	Gat/Cat	9/11	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.19	2		421	1038	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397516436	NA	P-0000268-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1280	107	531	0	ENST00000269305.4:c.637C>G	p.Arg213Gly	p.R213G	ENST00000269305	NM_001126112.2	213	Cga/Gga	6/11	0.3	2	FACETS	0.812	0.726	0.904			1	CLONAL	1	TRUE	NA	0.19	2		531	1387	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023202	27023202	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000270-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	127	135	0	ENST00000324856.7:c.308C>A	p.Ser103Ter	p.S103*	ENST00000324856	NM_006015.4	103	tCg/tAg	1/20	0.304415312172978	4	FACETS	0.914	0.836	0.994	0.914	0.836	0.994	INDETERMINATE	2	TRUE	2	0.555910536695171	4		135	389	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023616	27023616	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000270-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	205	307	0	ENST00000324856.7:c.722C>G	p.Ser241Cys	p.S241C	ENST00000324856	NM_006015.4	241	tCc/tGc	1/20	0.304415312172978	4	FACETS	0.777	0.723	0.833	0.777	0.723	0.833	INDETERMINATE	2	TRUE	2	0.555910536695171	4		307	738	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2949759	2949759	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000270-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	84	300	0	ENST00000396946.4:c.3185G>C	p.Arg1062Thr	p.R1062T	ENST00000396946	NM_032415.4	1062	aGa/aCa	24/25	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.555910536695171	2		300	242	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971199	21971199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894095	NA	P-0000270-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	42	80	0	ENST00000304494.5:c.159G>A	p.Met53Ile	p.M53I	ENST00000304494	NM_000077.4	53	atG/atA	2/3	NA	2	FACETS	1	0.96	1			1	INDETERMINATE	1	TRUE	NA	0.555910536695171	2		80	108	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63700140	63700140	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000270-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	63	121	0	ENST00000279873.7:c.475G>C	p.Asp159His	p.D159H	ENST00000279873	NM_032199.2	159	Gac/Cac	3/10	0.527279452916697	5	FACETS	1	0.917	1			1	CLONAL	1	TRUE	NA	0.555910536695171	5		121	386	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579364	7579364	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000270-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	86	292	0	ENST00000269305.4:c.323del	p.Gly108ValfsTer15	p.G108Vfs*15	ENST00000269305	NM_001126112.2	108	gGt/gt	4/11	0.419082219162234	2	FACETS	1	0.952	1	0.554	0.497	0.615	CLONAL	1	TRUE	0	0.555910536695171	2		292	279	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0000280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	140	262	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.369602140397393	3	FACETS	0.962	0.887	1	0.962	0.887	1	CLONAL	2	FALSE	1	0.491389845095402	3		262	369	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1315002	1315002	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	48	315	0	ENST00000400841.2:c.659A>G	p.Glu220Gly	p.E220G	ENST00000400841		220	gAg/gGg	6/6	0.298456437101852	3	FACETS	0.632	0.536	0.738	0.316	0.268	0.369	SUBCLONAL	1	FALSE	1	0.491389845095402	3		315	385	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321289	1321289	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	22	197	0	ENST00000400841.2:c.466T>C	p.Phe156Leu	p.F156L	ENST00000400841		156	Ttc/Ctc	4/6	0.298456437101852	3	FACETS	0.415	0.322	0.522	0.207	0.161	0.261	SUBCLONAL	1	FALSE	1	0.491389845095402	3		197	269	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295243	1295243	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs35550267	NA	P-0000283-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	22	158	0				ENST00000310581	NM_198253.2	-/1132			0.244361022290791	1	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	0	0.25699590523172	1		158	126	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023126	27023126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000283-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	18	53	0	ENST00000324856.7:c.232G>A	p.Glu78Lys	p.E78K	ENST00000324856	NM_006015.4	78	Gag/Aag	1/20	0.244361022290791	1	FACETS	0.848	0.655	1	1	0.926	1	CLONAL	2	TRUE	0	0.25699590523172	1		53	72	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729949	30729949	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000283-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	24	120	0	ENST00000295754.5:c.1470C>G	p.Asn490Lys	p.N490K	ENST00000295754	NM_003242.5	490	aaC/aaG	6/7	NA	2	FACETS	0.551	0.432	0.688			1	INDETERMINATE	1	TRUE	NA	0.25699590523172	2		120	339	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272687	142272687	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000283-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	204	537	0	ENST00000350721.4:c.2512G>C	p.Glu838Gln	p.E838Q	ENST00000350721	NM_001184.3	838	Gaa/Caa	11/47	0.247602258139445	3	FACETS	0.817	0.757	0.879	0.817	0.757	0.879	CLONAL	2	TRUE	1	0.25699590523172	3		537	1097	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295242	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0000283-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	22	152	0				ENST00000310581	NM_198253.2	-/1132			0.244361022290791	1	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	0	0.25699590523172	1		152	132	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969986	161969986	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000283-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	62	390	0	ENST00000366898.1:c.983G>T	p.Gly328Val	p.G328V	ENST00000366898	NM_004562.2	328	gGg/gTg	9/12	0.244361022290791	1	FACETS	0.733	0.633	0.841	0.733	0.633	0.841	SUBCLONAL	1	TRUE	0	0.25699590523172	1		390	574	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493443	56493443	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000283-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	25	204	0	ENST00000267101.3:c.2851G>C	p.Asp951His	p.D951H	ENST00000267101	NM_001982.3	951	Gat/Cat	24/28	1	2	FACETS	0.612	0.483	0.76	0.612	0.483	0.76	SUBCLONAL	1	TRUE	1	0.25699590523172	2		204	318	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0000283-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	53	216	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.25699590523172	1	FACETS	0.799	0.689	0.916	1	0.971	1	CLONAL	2	TRUE	0	0.25699590523172	1		216	225	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349886	15349886	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759358078	NA	P-0000283-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	25	89	0	ENST00000263377.2:c.3766C>T	p.Arg1256Trp	p.R1256W	ENST00000263377	NM_058243.2	1256	Cgg/Tgg	18/20	0.197524448385315	1	FACETS	0.865	0.697	1	1	0.947	1	CLONAL	2	TRUE	0	0.25699590523172	1		89	98	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0000284-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	42	200	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.463197371191777	1	FACETS	0.961	0.818	1	0.961	0.818	1	CLONAL	1	TRUE	0	0.463197371191777	1		200	145	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131514	202131514	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000284-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	32	102	0	ENST00000358485.4:c.482G>A	p.Arg161Lys	p.R161K	ENST00000358485	NM_001080125.1	161	aGg/aAg	2/9	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.463197371191777	2		102	117	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539564	187539564	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000284-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	93	253	0	ENST00000441802.2:c.8176C>T	p.Arg2726Ter	p.R2726*	ENST00000441802	NM_005245.3	2726	Cga/Tga	10/27	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.463197371191777	2		253	331	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0000284-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	16	70	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.813	0.612	1	0.813	0.612	1	CLONAL	1	TRUE	1	0.463197371191777	2		70	85	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570141	95570141	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000284-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	62	337	1	ENST00000393063.1:c.3592C>T	p.Gln1198Ter	p.Q1198*	ENST00000393063	NM_030621.3	1198	Caa/Taa	22/28	1	2	FACETS	0.685	0.594	0.783	0.685	0.594	0.783	SUBCLONAL	1	TRUE	1	0.463197371191777	2		338	391	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628137	187628161	+	frameshift_variant	Frame_Shift_Del	DEL	ACCACATGATGACGGTTCCTTCTGG	ACCACATGATGACGGTTCCTTCTGG	-	novel	NA	P-0000284-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	32	358	0	ENST00000441802.2:c.2821_2845del	p.Pro941Ter	p.P941*	ENST00000441802	NM_005245.3	941	CCAGAAGGAACCGTCATCATGTGGTta/ta	2/27	1	2	FACETS	0.382	0.31	0.463	0.382	0.31	0.463	SUBCLONAL	1	TRUE	1	0.463197371191777	2		358	362	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570140	95570141	+	stop_gained,protein_altering_variant	Nonsense_Mutation	INS	-	-	AGCAAA	novel	NA	P-0000284-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	42	338	0	ENST00000393063.1:c.3592_3593insTTTGCT	p.Gln1198delinsLeuCysTer	p.Q1198delinsLC*	ENST00000393063	NM_030621.3	1198	caa/cTTTGCTaa	22/28	1	2	FACETS	0.464	0.388	0.548	0.464	0.388	0.548	SUBCLONAL	1	TRUE	1	0.463197371191777	2		338	391	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000290-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	34	422	0				ENST00000310581	NM_198253.2	-/1132			0.165144091605584	0	FACETS	0.501	0.413	0.597			1	INDETERMINATE	1	TRUE	0	0.411758247261501	0		422	194	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092809	27092809	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000290-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	115	377	0	ENST00000324856.7:c.2830C>T	p.Gln944Ter	p.Q944*	ENST00000324856	NM_006015.4	944	Cag/Tag	9/20	1	2	FACETS	0.755	0.68	0.834	0.755	0.68	0.834	SUBCLONAL	1	TRUE	1	0.411758247261501	2		377	740	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551631	150551631	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000290-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	74	277	0	ENST00000369026.2:c.376C>A	p.Leu126Met	p.L126M	ENST00000369026	NM_021960.4	126	Ctg/Atg	1/3	1	2	FACETS	0.717	0.629	0.812	0.717	0.629	0.812	SUBCLONAL	1	TRUE	1	0.411758247261501	2		277	501	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666657	206666657	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782804652	NA	P-0000290-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	215	455	0	ENST00000367120.3:c.1991C>T	p.Ser664Leu	p.S664L	ENST00000367120	NM_014002.3	664	tCg/tTg	20/22	0.406058737535643	2	FACETS	0.813	0.76	0.868	0.813	0.76	0.868	CLONAL	2	TRUE	0	0.411758247261501	2		455	642	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278117	41278117	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs761565235	NA	P-0000290-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	143	385	0	ENST00000349496.5:c.1993G>T	p.Asp665Tyr	p.D665Y	ENST00000349496	NM_001904.3	665	Gac/Tac	13/15	1	2	FACETS	0.853	0.778	0.932	0.853	0.778	0.932	CLONAL	1	TRUE	1	0.411758247261501	2		385	814	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643488	52643488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000290-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	132	479	0	ENST00000394830.3:c.2408C>T	p.Ser803Phe	p.S803F	ENST00000394830	NM_018313.4	803	tCt/tTt	17/30	1	2	FACETS	0.761	0.69	0.834	0.761	0.69	0.834	SUBCLONAL	1	TRUE	1	0.411758247261501	2		479	843	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468397	89468397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000290-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	85	268	0	ENST00000336596.2:c.1931C>T	p.Ser644Leu	p.S644L	ENST00000336596	NM_005233.5	644	tCa/tTa	11/17	1	2	FACETS	0.763	0.676	0.856	0.763	0.676	0.856	SUBCLONAL	1	TRUE	1	0.411758247261501	2		268	541	SUCCESS
ATR	545	MSKCC	GRCh37	3	142185309	142185309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000290-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	103	310	0	ENST00000350721.4:c.6754G>A	p.Glu2252Lys	p.E2252K	ENST00000350721	NM_001184.3	2252	Gaa/Aaa	40/47	1	2	FACETS	0.803	0.72	0.891	0.803	0.72	0.891	CLONAL	1	TRUE	1	0.411758247261501	2		310	623	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84397806	84397806	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000290-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	118	471	0	ENST00000321945.7:c.205C>G	p.Gln69Glu	p.Q69E	ENST00000321945	NM_139076.2	69	Cag/Gag	3/9	1	2	FACETS	0.704	0.635	0.777	0.704	0.635	0.777	SUBCLONAL	1	TRUE	1	0.411758247261501	2		471	814	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685259	86685259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1324971631	NA	P-0000290-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	108	233	0	ENST00000274376.6:c.2975C>T	p.Ser992Phe	p.S992F	ENST00000274376	NM_002890.2	992	tCc/tTc	24/25	0.157833872165404	4	FACETS	1	0.975	1	0.632	0.568	0.699	INDETERMINATE	1	TRUE	2	0.411758247261501	4		233	586	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004922	150004922	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000290-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	126	399	0	ENST00000253339.5:c.1303C>T	p.Gln435Ter	p.Q435*	ENST00000253339		435	Cag/Tag	3/7	1	2	FACETS	0.857	0.777	0.941	0.857	0.777	0.941	CLONAL	1	TRUE	1	0.411758247261501	2		399	714	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962804	2962804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772900135	NA	P-0000290-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	124	257	0	ENST00000396946.4:c.2104G>A	p.Glu702Lys	p.E702K	ENST00000396946	NM_032415.4	702	Gag/Aag	16/25	1	2	FACETS	0.792	0.724	0.863	1	0.988	1	SUBCLONAL	2	TRUE	1	0.411758247261501	2		257	380	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431634	6431634	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000290-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	86	213	0	ENST00000356142.4:c.187G>C	p.Asp63His	p.D63H	ENST00000356142	NM_018890.3	63	Gat/Cat	3/7	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.411758247261501	2		213	417	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499823	8499823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1273962518	NA	P-0000290-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	93	288	0	ENST00000356435.5:c.2146C>T	p.Arg716Cys	p.R716C	ENST00000356435		716	Cgc/Tgc	14/35	0.341095935597162	2	FACETS	0.875	0.781	0.975	0.438	0.39	0.488	CLONAL	1	TRUE	0	0.411758247261501	2		288	516	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29068980	29068980	+	start_lost	Translation_Start_Site	SNP	T	T	A	novel	NA	P-0000290-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	10	93	0	ENST00000282397.4:c.1A>T	p.Met1?	p.M1?	ENST00000282397	NM_002019.4	1	Atg/Ttg	1/30	0.261980535846552	2	FACETS	0.26	0.176	0.365	0.13	0.088	0.183	SUBCLONAL	1	TRUE	0	0.411758247261501	2		93	187	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950926	32950926	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000290-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	88	262	0	ENST00000380152.3:c.8752G>A	p.Glu2918Lys	p.E2918K	ENST00000380152		2918	Gag/Aag	21/27	0.261980535846552	2	FACETS	1	0.959	1	0.578	0.515	0.643	CLONAL	1	TRUE	0	0.411758247261501	2		262	370	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801779	3801779	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000290-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	152	272	0	ENST00000262367.5:c.3727G>T	p.Glu1243Ter	p.E1243*	ENST00000262367	NM_004380.2	1243	Gag/Tag	20/31	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.411758247261501	2		272	522	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038683	14038683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139782718	NA	P-0000290-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	58	159	0	ENST00000311895.7:c.2008C>T	p.Arg670Trp	p.R670W	ENST00000311895	NM_005236.2	670	Cgg/Tgg	10/11	1	2	FACETS	0.927	0.802	1	0.927	0.802	1	CLONAL	1	TRUE	1	0.411758247261501	2		159	304	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144101	11144101	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000290-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	84	389	0	ENST00000358026.2:c.3682G>T	p.Val1228Leu	p.V1228L	ENST00000358026	NM_001128849.1	1228	Gtg/Ttg	26/36	1	2	FACETS	0.909	0.806	1	0.909	0.806	1	CLONAL	1	TRUE	1	0.411758247261501	2		389	449	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259229	36259229	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1235407698	NA	P-0000290-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	81	276	0	ENST00000300305.3:c.262G>A	p.Glu88Lys	p.E88K	ENST00000300305		88	Gag/Aag	3/8	1	2	FACETS	0.878	0.777	0.986	0.878	0.777	0.986	CLONAL	1	TRUE	1	0.411758247261501	2		276	448	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938447	44938447	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000290-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	489	345	0	ENST00000377967.4:c.2995G>T	p.Glu999Ter	p.E999*	ENST00000377967	NM_021140.2	999	Gaa/Taa	20/29	0.411758247261501	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.411758247261501	2		345	960	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028886	47028886	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000290-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	159	141	0	ENST00000377604.3:c.190C>T	p.Gln64Ter	p.Q64*	ENST00000377604	NM_001204468.1	64	Cag/Tag	3/24	0.411758247261501	2	FACETS	0.968	0.91	1			1	CLONAL	3	TRUE	NA	0.411758247261501	2		141	266	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0000308-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	445	558	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.31	NA		558	791	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0000308-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	152	139	0				ENST00000310581	NM_198253.2	-/1132			0.296526714956899	1	FACETS	1	0.936	1	1	0.992	1	CLONAL	2	TRUE	0	0.31	1		139	409	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242733	16242733	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000308-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	485	623	0	ENST00000375759.3:c.1354C>A	p.His452Asn	p.H452N	ENST00000375759	NM_015001.2	452	Cat/Aat	6/15	0.296526714956899	1	FACETS	1	0.974	1	1	0.997	1	CLONAL	2	TRUE	0	0.31	1		623	1292	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812182	212812182	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000308-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	385	584	0	ENST00000342788.4:c.394C>T	p.Gln132Ter	p.Q132*	ENST00000342788	NM_005235.2	132	Caa/Taa	3/28	0.296526714956899	1	FACETS	0.758	0.72	0.798	1	0.995	1	SUBCLONAL	2	TRUE	0	0.31	1		584	1384	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451011	70451011	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000308-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	47	331	0	ENST00000373644.4:c.5851G>C	p.Asp1951His	p.D1951H	ENST00000373644	NM_030625.2	1951	Gac/Cac	12/12	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.31	NA		331	506	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451110	70451110	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000308-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	54	349	0	ENST00000373644.4:c.5950G>C	p.Glu1984Gln	p.E1984Q	ENST00000373644	NM_030625.2	1984	Gag/Cag	12/12	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.31	NA		349	514	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488324	56488324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143726790	NA	P-0000308-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	174	277	0	ENST00000267101.3:c.1843G>A	p.Glu615Lys	p.E615K	ENST00000267101	NM_001982.3	615	Gag/Aag	15/28	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.31	NA		277	612	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14021928	14021928	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000308-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	137	395	0	ENST00000311895.7:c.628G>T	p.Glu210Ter	p.E210*	ENST00000311895	NM_005236.2	210	Gaa/Taa	4/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.31	NA		395	1066	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063702	67063702	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000308-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	197	344	0	ENST00000412916.2:c.151G>A	p.Gly51Ser	p.G51S	ENST00000412916		51	Ggc/Agc	2/6	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.31	NA		344	669	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619045	37619045	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000308-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	107	456	0	ENST00000447079.4:c.721T>G	p.Ser241Ala	p.S241A	ENST00000447079	NM_015083.1	241	Tct/Gct	1/14	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.31	NA		456	1092	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866444	37866444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000308-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	99	322	0	ENST00000269571.5:c.749C>T	p.Ser250Phe	p.S250F	ENST00000269571		250	tCt/tTt	6/27	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.31	NA		322	852	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000308-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	475	301	0	ENST00000269571.5:c.829G>C	p.Asp277His	p.D277H	ENST00000269571		277	Gac/Cac	7/27	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.31	NA		301	913	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868663	37868663	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1275492389	NA	P-0000308-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	382	216	0	ENST00000269571.5:c.1110C>G	p.Ile370Met	p.I370M	ENST00000269571		370	atC/atG	9/27	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.31	NA		216	680	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226371	41226371	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000308-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1213	141	629	0	ENST00000357654.3:c.4652C>G	p.Ser1551Cys	p.S1551C	ENST00000357654	NM_007294.3	1551	tCt/tGt	14/23	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.31	NA		629	1354	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435317	56435317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200066146	NA	P-0000308-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	46	158	0	ENST00000407977.2:c.1820C>T	p.Ser607Leu	p.S607L	ENST00000407977		607	tCg/tTg	9/10	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.31	NA		158	458	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799105	42799105	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000308-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	131	181	0	ENST00000575354.2:c.4589G>C	p.Gly1530Ala	p.G1530A	ENST00000575354	NM_015125.3	1530	gGa/gCa	20/20	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.31	NA		181	613	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929362	44929362	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0000308-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	443	349	0	ENST00000377967.4:c.2462C>G	p.Ser821Ter	p.S821*	ENST00000377967	NM_021140.2	821	tCa/tGa	17/29	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.31	NA		349	828	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101345	27101354	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTCGTGGC	GGCTCGTGGC	-	novel	NA	P-0000308-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	275	594	0	ENST00000324856.7:c.4627_4636del	p.Gly1543LeufsTer19	p.G1543Lfs*19	ENST00000324856	NM_006015.4	1543	GGCTCGTGGCct/ct	18/20	0.296526714956899	1	FACETS	0.898	0.846	0.951	1	0.995	1	CLONAL	2	TRUE	0	0.31	1		594	835	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000320-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	26	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.86	0.701	1	1	0.95	1	CLONAL	2	FALSE	1	0.359785532978961	2		422	84	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0000320-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	59	310	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.359785532978961	NA		310	140	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000326-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	41	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.983	0.822	1	0.983	0.822	1	CLONAL	1	TRUE	1	0.26	2		422	321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0000326-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	45	240	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	1	2	FACETS	0.587	0.492	0.691	0.587	0.492	0.691	SUBCLONAL	1	TRUE	1	0.26	2		240	590	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101904831	101904831	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000326-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	65	319	0	ENST00000374994.4:c.819G>A	p.Trp273Ter	p.W273*	ENST00000374994	NM_004612.2	273	tgG/tgA	5/9	1	2	FACETS	0.619	0.535	0.71	0.619	0.535	0.71	SUBCLONAL	1	TRUE	1	0.26	2		319	808	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041640	47041640	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000326-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	57	239	0	ENST00000377604.3:c.1865C>A	p.Ser622Ter	p.S622*	ENST00000377604	NM_001204468.1	622	tCg/tAg	17/24	1	1	FACETS	0.783	0.673	0.903	0.783	0.673	0.903	CLONAL	1	TRUE	0	0.26	1		239	487	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000333-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	51	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.913	1			1	INDETERMINATE	5	FALSE	NA	0.200522480505649	2		422	98	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0000333-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	308	310	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.915	0.866	0.965	1	0.997	1	CLONAL	4	FALSE	1	0.200522480505649	2		310	839	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000336-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	47	422	0				ENST00000310581	NM_198253.2	-/1132			0.408984625371655	4	FACETS	0.97	0.822	1			1	CLONAL	1	TRUE	NA	0.408984625371655	4		422	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0000336-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	262	240	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	0.317105713421149	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	0	0.408984625371655	3		240	480	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0000336-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	230	558	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.382521755075514	5	FACETS	1	0.968	1			1	CLONAL	2	TRUE	NA	0.408984625371655	5		558	856	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294275	11294275	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000336-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	94	460	0	ENST00000361445.4:c.2256G>C	p.Gln752His	p.Q752H	ENST00000361445	NM_004958.3	752	caG/caC	14/58	0.258902694443022	1	FACETS	0.676	0.603	0.753	0.676	0.603	0.753	SUBCLONAL	1	TRUE	0	0.408984625371655	1		460	541	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11294291	11294291	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000336-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	92	421	0	ENST00000361445.4:c.2240G>A	p.Gly747Glu	p.G747E	ENST00000361445	NM_004958.3	747	gGa/gAa	14/58	0.258902694443022	1	FACETS	0.695	0.619	0.775	0.695	0.619	0.775	SUBCLONAL	1	TRUE	0	0.408984625371655	1		421	515	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11297992	11297992	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000336-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	84	449	0	ENST00000361445.4:c.2116G>C	p.Glu706Gln	p.E706Q	ENST00000361445	NM_004958.3	706	Gag/Cag	13/58	0.258902694443022	1	FACETS	0.654	0.579	0.733	0.654	0.579	0.733	SUBCLONAL	1	TRUE	0	0.408984625371655	1		449	500	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36826855	36826855	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000336-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	66	611	0	ENST00000373129.3:c.79A>C	p.Asn27His	p.N27H	ENST00000373129	NM_032017.1	27	Aat/Cat	3/12	0.250612575345546	5	FACETS	0.511	0.442	0.586			1	SUBCLONAL	1	TRUE	NA	0.408984625371655	5		611	1019	SUCCESS
FIP1L1	81608	MSKCC	GRCh37	4	54249939	54249939	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0000336-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	73	134	0	ENST00000358575.5:c.184-1G>T		p.X62_splice	ENST00000358575	NM_001134937.1	62			0.393965711029185	3	FACETS	1	0.886	1	0.505	0.443	0.571	CLONAL	1	TRUE	1	0.408984625371655	3		134	426	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361255	66361255	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000336-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	64	191	0	ENST00000273854.3:c.917G>A	p.Arg306Lys	p.R306K	ENST00000273854	NM_004439.5	306	aGa/aAa	4/18	0.393965711029185	3	FACETS	0.962	0.836	1	0.481	0.418	0.548	CLONAL	1	TRUE	1	0.408984625371655	3		191	392	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004226	29004226	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000336-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	172	392	0	ENST00000282397.4:c.1067C>T	p.Ser356Phe	p.S356F	ENST00000282397	NM_002019.4	356	tCt/tTt	8/30	0.393965711029185	3	FACETS	1	0.961	1	0.535	0.492	0.58	CLONAL	1	TRUE	1	0.408984625371655	3		392	946	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868193	37868193	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000336-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	99	438	0	ENST00000269571.5:c.914C>G	p.Ser305Cys	p.S305C	ENST00000269571		305	tCt/tGt	8/27	0.382521755075514	5	FACETS	0.906	0.808	1			1	CLONAL	1	TRUE	NA	0.408984625371655	5		438	862	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699400	47699400	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000336-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	134	451	0	ENST00000347630.2:c.108G>A	p.Trp36Ter	p.W36*	ENST00000347630	NM_001007230.1	36	tgG/tgA	4/11	0.344625391493971	5	FACETS	0.908	0.823	0.997			1	CLONAL	1	TRUE	NA	0.408984625371655	5		451	1165	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023559	27023560	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0000336-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	221	536	0	ENST00000324856.7:c.671dup	p.Pro225AlafsTer175	p.P225Afs*175	ENST00000324856	NM_006015.4	222	tac/taCc	1/20	0.250612575345546	5	FACETS	0.833	0.775	0.893			1	CLONAL	2	TRUE	NA	0.408984625371655	5		536	1047	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878127	48878127	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1276653645	NA	P-0000336-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	27	61	0	ENST00000267163.4:c.83del	p.Pro28LeufsTer37	p.P28Lfs*37	ENST00000267163	NM_000321.2	27	Ccc/cc	1/27	0.258902694443022	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.408984625371655	1		61	81	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749914	162749914	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000363-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	116	187	0	ENST00000367921.3:c.2446C>G	p.Gln816Glu	p.Q816E	ENST00000367921	NM_006182.2	816	Caa/Gaa	18/18	0.399167858328351	8	FACETS	0.811	0.731	0.896			1	CLONAL	2	TRUE	NA	0.399167858328351	8		187	787	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641222	12641222	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000363-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	47	415	0	ENST00000251849.4:c.1076C>G	p.Ser359Cys	p.S359C	ENST00000251849	NM_002880.3	359	tCt/tGt	10/17	0.315702948670623	3	FACETS	0.473	0.399	0.556	0.158	0.133	0.186	SUBCLONAL	1	TRUE	0	0.399167858328351	3		415	597	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146734	185146734	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000363-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	25	226	0	ENST00000265026.3:c.365G>A	p.Arg122Lys	p.R122K	ENST00000265026	NM_004721.4	122	aGg/aAg	2/14	0.286284268278697	6	FACETS	0.461	0.362	0.575	0.077	0.06	0.096	SUBCLONAL	1	TRUE	0	0.399167858328351	6		226	489	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0000363-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	62	536	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	NA	2	FACETS	0.63	0.545	0.722			1	INDETERMINATE	1	TRUE	NA	0.399167858328351	2		536	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578223	7578223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000363-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	89	431	0	ENST00000269305.4:c.626G>A	p.Arg209Lys	p.R209K	ENST00000269305	NM_001126112.2	209	aGa/aAa	6/11	NA	2	FACETS	0.808	0.718	0.903			1	INDETERMINATE	1	TRUE	NA	0.399167858328351	2		431	552	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41231365	41231365	+	intron_variant	Intron	SNP	C	C	T	novel	NA	P-0000363-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	25	48	0	ENST00000357654.3:c.4358-2734G>A		p.*1453*	ENST00000357654	NM_007294.3	-/1863			NA		FACETS		0.619	0.919				INDETERMINATE	2	TRUE	NA	0.399167858328351	2		48	82	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610279	10610279	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000363-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	199	327	0	ENST00000171111.5:c.431C>A	p.Ser144Tyr	p.S144Y	ENST00000171111	NM_203500.1	144	tCc/tAc	2/6	0.399167858328351	1	FACETS	0.801	0.749	0.854	1	0.993	1	CLONAL	2	TRUE	0	0.399167858328351	1		327	498	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791250	42791250	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000363-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	150	199	0	ENST00000575354.2:c.310G>A	p.Glu104Lys	p.E104K	ENST00000575354	NM_015125.3	104	Gag/Aag	3/20	0.399167858328351	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	0	0.399167858328351	2		199	375	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791373	42791373	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000363-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	178	247	0	ENST00000575354.2:c.433G>C	p.Glu145Gln	p.E145Q	ENST00000575354	NM_015125.3	145	Gag/Cag	3/20	0.399167858328351	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.399167858328351	2		247	406	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791790	42791790	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000363-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	209	230	0	ENST00000575354.2:c.676G>C	p.Asp226His	p.D226H	ENST00000575354	NM_015125.3	226	Gac/Cac	5/20	0.399167858328351	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.399167858328351	2		230	493	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576919	7576919	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000363-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	103	222	0	ENST00000269305.4:c.927del	p.Asn310ThrfsTer35	p.N310Tfs*35	ENST00000269305	NM_001126112.2	309	ccC/cc	9/11	NA	2	FACETS	0.824	0.747	0.904			1	INDETERMINATE	2	TRUE	NA	0.399167858328351	2		222	313	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576925	7576927	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	TGC	TGC	-	novel	NA	P-0000363-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	101	219	0	ENST00000269305.4:c.920-1_921del		p.X307_splice	ENST00000269305	NM_001126112.2	307		9/11	NA	2	FACETS	0.882	0.799	0.966			1	INDETERMINATE	2	TRUE	NA	0.399167858328351	2		219	287	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000364-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	71	422	0				ENST00000310581	NM_198253.2	-/1132			0.230418837371689	4	FACETS	0.856	0.756	0.961	1	0.967	1	CLONAL	3	FALSE	2	0.268952351332234	4		422	261	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0000364-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	230	531	1	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.261564974364252	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	FALSE	0	0.268952351332234	2		532	811	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242667	16242667	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000364-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	325	464	0	ENST00000375759.3:c.1288G>C	p.Asp430His	p.D430H	ENST00000375759	NM_015001.2	430	Gat/Cat	6/15	0.23866103791148	3	FACETS	0.845	0.799	0.892			1	CLONAL	3	FALSE	NA	0.268952351332234	3		464	1082	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652171	36652171	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000364-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	232	276	0	ENST00000244741.5:c.293C>A	p.Ser98Ter	p.S98*	ENST00000244741	NM_000389.4	98	tCa/tAa	2/3	0.268952351332234	4	FACETS	0.958	0.901	1	0.958	0.901	1	CLONAL	4	FALSE	0	0.268952351332234	4		276	571	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941643	48941643	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs886050271	NA	P-0000364-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	176	332	0	ENST00000267163.4:c.953C>G	p.Ser318Cys	p.S318C	ENST00000267163	NM_000321.2	318	tCt/tGt	10/27	0.268952351332234	5	FACETS	0.91	0.838	0.986	0.91	0.838	0.986	CLONAL	2	FALSE	3	0.268952351332234	5		332	1009	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033844	49033844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853294	NA	P-0000364-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	288	455	1	ENST00000267163.4:c.1981C>T	p.Arg661Trp	p.R661W	ENST00000267163	NM_000321.2	661	Cgg/Tgg	20/27	0.268952351332234	5	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	FALSE	3	0.268952351332234	5		456	1382	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033948	49033948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1283902639	NA	P-0000364-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	170	306	0	ENST00000267163.4:c.2085G>A	p.Met695Ile	p.M695I	ENST00000267163	NM_000321.2	695	atG/atA	20/27	0.268952351332234	5	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	FALSE	3	0.268952351332234	5		306	811	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919303	48919303	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000364-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	159	262	0	ENST00000267163.4:c.468del	p.Asp156GlufsTer19	p.D156Efs*19	ENST00000267163	NM_000321.2	156	gaT/ga	4/27	0.268952351332234	5	FACETS	0.951	0.872	1	0.951	0.872	1	CLONAL	2	FALSE	3	0.268952351332234	5		262	872	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000365-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	153	422	0				ENST00000310581	NM_198253.2	-/1132			0.641331520449215	3	FACETS	1	0.984	1	0.631	0.582	0.683	CLONAL	1	TRUE	1	0.641331520449215	3		422	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0000365-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	1429	550	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.641331520449215	3	FACETS	1	0.998	1	1	0.998	1	CLONAL	3	TRUE	0	0.641331520449215	3		550	1824	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258179	16258179	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000365-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	584	294	0	ENST00000375759.3:c.5444A>T	p.Asp1815Val	p.D1815V	ENST00000375759	NM_015001.2	1815	gAt/gTt	11/15	0.641331520449215	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.641331520449215	3		294	1176	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253778	153253778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000365-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	26	324	0	ENST00000281708.4:c.955C>T	p.Leu319Phe	p.L319F	ENST00000281708	NM_033632.3	319	Ctt/Ttt	6/12	1	2	FACETS	0.159	0.125	0.198	0.159	0.125	0.198	SUBCLONAL	1	TRUE	1	0.641331520449215	2		324	509	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542201	187542201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs189523191	NA	P-0000365-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	66	379	0	ENST00000441802.2:c.5539G>A	p.Val1847Ile	p.V1847I	ENST00000441802	NM_005245.3	1847	Gtc/Atc	10/27	1	2	FACETS	0.243	0.21	0.279	0.243	0.21	0.279	SUBCLONAL	1	TRUE	1	0.641331520449215	2		379	847	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456463	32456463	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000365-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	98	120	0	ENST00000332351.3:c.429G>T	p.Glu143Asp	p.E143D	ENST00000332351	NM_024426.4	143	gaG/gaT	1/10	0.641331520449215	3	FACETS	0.947	0.851	1	0.474	0.425	0.525	CLONAL	1	TRUE	1	0.641331520449215	3		120	426	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220464	1220464	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000365-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1584	84	520	0	ENST00000326873.7:c.557C>G	p.Thr186Ser	p.T186S	ENST00000326873	NM_000455.4	186	aCc/aGc	4/10	0.641331520449215	3	FACETS	0.207	0.182	0.235	0.104	0.091	0.118	SUBCLONAL	1	TRUE	1	0.641331520449215	3		520	1668	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088807	27088807	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000369-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	26	285	0	ENST00000324856.7:c.2416C>T	p.Gln806Ter	p.Q806*	ENST00000324856	NM_006015.4	806	Caa/Taa	7/20	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		285	510	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0000372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	84	142	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.483771146224843	3	FACETS	1	0.975	1	0.68	0.607	0.757	CLONAL	1	TRUE	1	0.483771146224843	3		142	317	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682459	52682459	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0000372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	229	604	0	ENST00000394830.3:c.715-1G>C		p.X239_splice	ENST00000394830	NM_018313.4	239			0.483771146224843	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.483771146224843	1		604	714	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11227506	11227506	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	150	672	0	ENST00000361445.4:c.4322G>C	p.Gly1441Ala	p.G1441A	ENST00000361445	NM_004958.3	1441	gGa/gCa	29/58	NA	2	FACETS	0.533	0.486	0.583			1	INDETERMINATE	1	TRUE	NA	0.483771146224843	2		672	1163	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965614	25965614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	48	372	0	ENST00000435504.4:c.3592G>A	p.Glu1198Lys	p.E1198K	ENST00000435504		1198	Gag/Aag	13/13	NA	2	FACETS	0.286	0.241	0.336			1	INDETERMINATE	1	TRUE	NA	0.483771146224843	2		372	693	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967135	25967135	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	35	258	0	ENST00000435504.4:c.2071C>G	p.Pro691Ala	p.P691A	ENST00000435504		691	Cca/Gca	13/13	NA	2	FACETS	0.31	0.254	0.373			1	INDETERMINATE	1	TRUE	NA	0.483771146224843	2		258	467	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257791	198257791	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	55	492	0	ENST00000335508.6:c.3661G>C	p.Glu1221Gln	p.E1221Q	ENST00000335508	NM_012433.2	1221	Gag/Cag	24/25	1	2	FACETS	0.244	0.208	0.284	0.244	0.208	0.284	SUBCLONAL	1	TRUE	1	0.483771146224843	2		492	930	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52621435	52621435	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	70	642	0	ENST00000394830.3:c.2982G>C	p.Lys994Asn	p.K994N	ENST00000394830	NM_018313.4	994	aaG/aaC	20/30	0.483771146224843	1	FACETS	0.274	0.238	0.313	0.274	0.238	0.313	SUBCLONAL	1	TRUE	0	0.483771146224843	1		642	800	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138474716	138474716	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	73	443	0	ENST00000289153.2:c.277G>C	p.Glu93Gln	p.E93Q	ENST00000289153	NM_006219.2	93	Gaa/Caa	2/22	0.483771146224843	3	FACETS	0.366	0.319	0.418	0.183	0.159	0.209	SUBCLONAL	1	TRUE	1	0.483771146224843	3		443	1023	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106164902	106164902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs937035385	NA	P-0000372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	24	169	0	ENST00000380013.4:c.3770C>T	p.Thr1257Met	p.T1257M	ENST00000380013	NM_001127208.2	1257	aCg/aTg	6/11	1	2	FACETS	0.236	0.185	0.296	0.236	0.185	0.296	SUBCLONAL	1	TRUE	1	0.483771146224843	2		169	420	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180045776	180045776	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	93	409	0	ENST00000261937.6:c.2995C>G	p.Gln999Glu	p.Q999E	ENST00000261937	NM_182925.4	999	Caa/Gaa	21/30	0.432721279415661	0	FACETS	0.391	0.348	0.436			1	SUBCLONAL	1	TRUE	0	0.483771146224843	0		409	508	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152382201	152382201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781324888	NA	P-0000372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	54	311	0	ENST00000206249.3:c.1311G>A	p.Met437Ile	p.M437I	ENST00000206249	NM_000125.3	437	atG/atA	6/8	NA	2	FACETS	0.36	0.307	0.418			1	INDETERMINATE	1	TRUE	NA	0.483771146224843	2		311	620	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273254	55273254	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	39	316	0	ENST00000275493.2:c.3577G>T	p.Glu1193Ter	p.E1193*	ENST00000275493	NM_005228.3	1193	Gaa/Taa	28/28	1	2	FACETS	0.292	0.241	0.348	0.292	0.241	0.348	SUBCLONAL	1	TRUE	1	0.483771146224843	2		316	553	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845871	151845871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	55	534	0	ENST00000262189.6:c.13141G>A	p.Glu4381Lys	p.E4381K	ENST00000262189	NM_170606.2	4381	Gaa/Aaa	52/59	1	2	FACETS	0.249	0.212	0.289	0.249	0.212	0.289	SUBCLONAL	1	TRUE	1	0.483771146224843	2		534	915	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006024	22006024	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1541	298	333	0	ENST00000276925.6:c.379G>C	p.Asp127His	p.D127H	ENST00000276925	NM_004936.3	127	Gac/Cac	2/2	0.483771146224843	7	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.483771146224843	7		333	1839	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401310	139401310	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	65	422	0	ENST00000277541.6:c.3759C>G	p.Cys1253Trp	p.C1253W	ENST00000277541	NM_017617.3	1253	tgC/tgG	23/34	1	2	FACETS	0.324	0.28	0.372	0.324	0.28	0.372	SUBCLONAL	1	TRUE	1	0.483771146224843	2		422	829	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180574	94180574	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	47	382	0	ENST00000323929.3:c.1594C>G	p.Gln532Glu	p.Q532E	ENST00000323929	NM_005591.3	532	Cag/Gag	15/20	0.346815955853726	1	FACETS	0.225	0.189	0.264	0.225	0.189	0.264	SUBCLONAL	1	TRUE	0	0.483771146224843	1		382	656	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149334	119149334	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	31	284	0	ENST00000264033.4:c.1342G>C	p.Glu448Gln	p.E448Q	ENST00000264033	NM_005188.3	448	Gag/Cag	9/16	0.313694587497024	1	FACETS	0.218	0.176	0.266	0.218	0.176	0.266	SUBCLONAL	1	TRUE	0	0.483771146224843	1		284	446	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609381	81609381	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	173	549	0	ENST00000298171.2:c.979G>A	p.Glu327Lys	p.E327K	ENST00000298171	NM_000369.2	327	Gaa/Aaa	10/10	0.148930613574996	1	FACETS	0.608	0.56	0.658	0.608	0.56	0.658	INDETERMINATE	1	TRUE	0	0.483771146224843	1		549	892	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303880	91303880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768127491	NA	P-0000372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	94	321	1	ENST00000355112.3:c.1277C>T	p.Ser426Leu	p.S426L	ENST00000355112	NM_000057.2	426	tCa/tTa	7/22	NA	2	FACETS	0.67	0.597	0.747			1	INDETERMINATE	1	TRUE	NA	0.483771146224843	2		322	580	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063709	67063709	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	111	289	0	ENST00000412916.2:c.158C>G	p.Ser53Trp	p.S53W	ENST00000412916		53	tCg/tGg	2/6	NA	2	FACETS	0.582	0.523	0.645			1	INDETERMINATE	1	TRUE	NA	0.483771146224843	2		289	788	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559126	29559126	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0000372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	47	137	0	ENST00000356175.3:c.3233C>G	p.Ser1078Ter	p.S1078*	ENST00000356175	NM_000267.3	1078	tCa/tGa	25/57	0.148930613574996	1	FACETS	0.448	0.379	0.523	0.448	0.379	0.523	INDETERMINATE	1	TRUE	0	0.483771146224843	1		137	329	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222116	2222116	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	41	517	0	ENST00000398665.3:c.2948C>G	p.Ser983Cys	p.S983C	ENST00000398665	NM_032482.2	983	tCc/tGc	24/28	0.483771146224843	1	FACETS	0.193	0.16	0.23	0.193	0.16	0.23	SUBCLONAL	1	TRUE	0	0.483771146224843	1		517	665	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727112	41727112	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs765391793	NA	P-0000372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	206	485	0	ENST00000301178.4:c.370C>G	p.Gln124Glu	p.Q124E	ENST00000301178	NM_021913.4	124	Cag/Gag	3/20	0.483771146224843	1	FACETS	0.555	0.514	0.597	0.555	0.514	0.597	SUBCLONAL	1	TRUE	0	0.483771146224843	1		485	1164	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513664	41513664	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	83	261	0	ENST00000263253.7:c.568C>T	p.Gln190Ter	p.Q190*	ENST00000263253	NM_001429.3	190	Caa/Taa	2/31	NA	2	FACETS	0.751	0.665	0.842			1	INDETERMINATE	1	TRUE	NA	0.483771146224843	2		261	457	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030532	47030532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	197	288	0	ENST00000377604.3:c.307C>T	p.Arg103Trp	p.R103W	ENST00000377604	NM_001204468.1	103	Cgg/Tgg	4/24	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.483771146224843	1		288	500	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222319	53222319	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	65	324	0	ENST00000375401.3:c.4513G>T	p.Glu1505Ter	p.E1505*	ENST00000375401	NM_004187.3	1505	Gag/Tag	26/26	0.483771146224843	0	FACETS	0.269	0.233	0.307			1	SUBCLONAL	1	TRUE	NA	0.483771146224843	0		324	516	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222343	53222343	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	58	352	0	ENST00000375401.3:c.4489G>C	p.Glu1497Gln	p.E1497Q	ENST00000375401	NM_004187.3	1497	Gag/Cag	26/26	0.483771146224843	0	FACETS	0.22	0.189	0.254			1	SUBCLONAL	1	TRUE	NA	0.483771146224843	0		352	562	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76953110	76953110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000372-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	45	360	0	ENST00000373344.5:c.203C>T	p.Ser68Leu	p.S68L	ENST00000373344	NM_000489.3	68	tCa/tTa	4/35	0.346815955853726	0	FACETS	0.171	0.143	0.201			1	SUBCLONAL	1	TRUE	NA	0.483771146224843	0		360	563	SUCCESS
FH	2271	MSKCC	GRCh37	1	241682970	241682970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201887750	NA	P-0000377-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	90	721	0	ENST00000366560.3:c.53C>T	p.Pro18Leu	p.P18L	ENST00000366560	NM_000143.3	18	cCa/cTa	1/10	NA	2	FACETS	0.454	0.403	0.508			1	INDETERMINATE	1	TRUE	NA	0.667913453296755	2		721	594	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472199	472199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000377-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1184	162	907	0	ENST00000399788.2:c.602C>T	p.Thr201Ile	p.T201I	ENST00000399788	NM_001042603.1	201	aCc/aTc	5/28	0.315944310814051	6	FACETS	0.842	0.77	0.917	0.21	0.192	0.23	INDETERMINATE	1	TRUE	2	0.667913453296755	6		907	1346	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18747428	18747428	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000377-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	65	355	0	ENST00000266497.5:c.3889A>G	p.Ser1297Gly	p.S1297G	ENST00000266497		1297	Agt/Ggt	28/31	0.315944310814051	6	FACETS	0.747	0.647	0.854	0.187	0.161	0.214	INDETERMINATE	1	TRUE	2	0.667913453296755	6		355	609	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000377-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	325	318	0	ENST00000269305.4:c.313G>T	p.Gly105Cys	p.G105C	ENST00000269305	NM_001126112.2	105	Ggc/Tgc	4/11	0.651241686807619	2	FACETS	0.981	0.942	1	0.981	0.942	1	CLONAL	2	TRUE	0	0.667913453296755	2		318	496	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573321	41573321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000377-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	154	442	0	ENST00000263253.7:c.5606C>T	p.Pro1869Leu	p.P1869L	ENST00000263253	NM_001429.3	1869	cCc/cTc	31/31	0.33573271874393	3	FACETS	0.658	0.602	0.717	0.219	0.2	0.239	INDETERMINATE	1	TRUE	0	0.667913453296755	3		442	935	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447340	49447341	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0000377-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	98	409	0	ENST00000301067.7:c.757_758delinsTT	p.Gly253Leu	p.G253L	ENST00000301067	NM_003482.3	253	GGg/TTg	6/54	NA	2	FACETS	0.452	0.404	0.504			1	INDETERMINATE	1	TRUE	NA	0.667913453296755	2		409	649	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000377-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	174	318	0	ENST00000269305.4:c.313G>T	p.Gly105Cys	p.G105C	ENST00000269305	NM_001126112.2	105	Ggc/Tgc	4/11	NA	2	FACETS	0.915	0.857	0.972			1	INDETERMINATE	3	TRUE	NA	0.374036756411915	2		318	339	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760192	133760192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000377-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	24	318	0	ENST00000318560.5:c.2515G>A	p.Gly839Ser	p.G839S	ENST00000318560	NM_005157.4	839	Ggc/Agc	11/11	0.374036756411915	1	FACETS	0.337	0.264	0.42	0.337	0.264	0.42	SUBCLONAL	1	TRUE	0	0.374036756411915	1		318	310	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915779	112915779	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507534	NA	P-0000377-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	32	260	1	ENST00000351677.2:c.1052G>A	p.Arg351Gln	p.R351Q	ENST00000351677	NM_002834.3	351	cGa/cAa	9/16	1	2	FACETS	0.332	0.268	0.403	0.332	0.268	0.403	SUBCLONAL	1	TRUE	1	0.374036756411915	2		261	516	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579374	7579374	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000377-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	551	318	0	ENST00000269305.4:c.313G>T	p.Gly105Cys	p.G105C	ENST00000269305	NM_001126112.2	105	Ggc/Tgc	4/11	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.570156277353136	2		318	849	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573321	41573321	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000377-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	260	442	0	ENST00000263253.7:c.5606C>T	p.Pro1869Leu	p.P1869L	ENST00000263253	NM_001429.3	1869	cCc/cTc	31/31	0.570156277353136	4	FACETS	1	0.976	1	0.362	0.338	0.387	CLONAL	1	TRUE	1	0.570156277353136	4		442	1318	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447340	49447341	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0000377-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1243	209	409	0	ENST00000301067.7:c.757_758delinsTT	p.Gly253Leu	p.G253L	ENST00000301067	NM_003482.3	253	GGg/TTg	6/54	0.36883650205723	6	FACETS	1	0.968	1			1	CLONAL	1	TRUE	NA	0.570156277353136	6		409	1452	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992106	11992106	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000377-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1514	162	329	0	ENST00000396373.4:c.196G>T	p.Val66Leu	p.V66L	ENST00000396373	NM_001987.4	66	Gta/Tta	3/8	0.570156277353136	9	FACETS	1	0.927	1			1	CLONAL	1	TRUE	NA	0.570156277353136	9		329	1676	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436647	110436647	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000377-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	200	410	0	ENST00000375856.3:c.1754G>C	p.Arg585Pro	p.R585P	ENST00000375856	NM_003749.2	585	cGg/cCg	1/2	0.570156277353136	2	FACETS	1	0.941	1	0.506	0.471	0.543	CLONAL	1	TRUE	0	0.570156277353136	2		410	693	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942492	17942492	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000377-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	201	307	0	ENST00000458235.1:c.2796G>C	p.Gln932His	p.Q932H	ENST00000458235	NM_000215.3	932	caG/caC	20/24	0.570156277353136	4	FACETS	0.957	0.886	1	0.319	0.295	0.344	CLONAL	1	TRUE	1	0.570156277353136	4		307	1157	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36421143	36421143	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000377-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	181	399	0	ENST00000300305.3:c.54G>A	p.Met18Ile	p.M18I	ENST00000300305		18	atG/atA	1/8	0.490021784044547	3	FACETS	1	0.925	1	0.501	0.462	0.54	CLONAL	1	TRUE	1	0.570156277353136	3		399	815	SUCCESS
APC	324	MSKCC	GRCh37	5	112177198	112177208	+	frameshift_variant	Frame_Shift_Del	DEL	GAGTTCTCTCA	GAGTTCTCTCA	-	novel	NA	P-0000377-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	18	321	0	ENST00000257430.4:c.5908_5918del	p.Ser1970Ter	p.S1970*	ENST00000257430	NM_000038.5	1969	ctGAGTTCTCTCAgt/ctgt	16/16	0.415366693562925	3	FACETS	0.265	0.199	0.343			1	SUBCLONAL	1	TRUE	NA	0.570156277353136	3		321	306	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472173	472198	+	frameshift_variant	Frame_Shift_Del	DEL	TTGTGCCTGGCTCTGGGGAAGTTTGG	TTGTGCCTGGCTCTGGGGAAGTTTGG	-	novel	NA	P-0000377-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1314	154	458	0	ENST00000399788.2:c.603_628del	p.Gln202AspfsTer22	p.Q202Dfs*22	ENST00000399788	NM_001042603.1	201	acCCAAACTTCCCCAGAGCCAGGCACAAgg/acgg	5/28	0.570156277353136	6	FACETS	0.788	0.718	0.861			1	SUBCLONAL	1	TRUE	NA	0.570156277353136	6		458	1468	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000378-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	30	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.855	0.702	1			1	INDETERMINATE	1	FALSE	NA	0.580045490720991	2		422	121	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166607	118166607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752308622	NA	P-0000378-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	62	157	0	ENST00000369448.3:c.1117G>A	p.Val373Ile	p.V373I	ENST00000369448	NM_017709.3	373	Gtt/Att	2/2	0.40890685339685	3	FACETS	0.87	0.757	0.991	0.435	0.378	0.496	CLONAL	1	FALSE	1	0.580045490720991	3		157	317	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165534	47165534	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000378-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	153	421	0	ENST00000409792.3:c.592C>T	p.Gln198Ter	p.Q198*	ENST00000409792	NM_014159.6	198	Caa/Taa	3/21	0.143404113146473	0	FACETS	0.395	0.363	0.428			1	INDETERMINATE	1	FALSE	0	0.580045490720991	0		421	561	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220325	55220325	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000378-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3870	1694	331	0	ENST00000275493.2:c.715G>T	p.Gly239Cys	p.G239C	ENST00000275493	NM_005228.3	239	Ggc/Tgc	6/28	0.580045490720991	45	FACETS	1	0.984	1			1	CLONAL	14	FALSE	NA	0.580045490720991	45		331	5564	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs139236063	NA	P-0000378-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7757	425	296	0	ENST00000275493.2:c.1793G>C	p.Gly598Ala	p.G598A	ENST00000275493	NM_005228.3	598	gGa/gCa	15/28	0.580045490720991	45	FACETS	1	0.991	1			1	CLONAL	2	FALSE	NA	0.580045490720991	45		296	8182	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151868410	151868410	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000378-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	218	298	0	ENST00000262189.6:c.9392A>G	p.Gln3131Arg	p.Q3131R	ENST00000262189	NM_170606.2	3131	cAg/cGg	40/59	0.296982735314179	4	FACETS	1	0.986	1	0.613	0.57	0.657	INDETERMINATE	1	FALSE	2	0.580045490720991	4		298	969	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0000384-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	628	139	0				ENST00000310581	NM_198253.2	-/1132			0.413372180473943	6	FACETS	0.964	0.936	0.991	1	0.996	1	CLONAL	6	TRUE	1	0.413372180473943	6		139	960	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259513	16259513	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000384-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	39	204	0	ENST00000375759.3:c.6778G>C	p.Glu2260Gln	p.E2260Q	ENST00000375759	NM_015001.2	2260	Gag/Cag	11/15	1	2	FACETS	0.427	0.354	0.508	0.427	0.354	0.508	SUBCLONAL	1	TRUE	1	0.413372180473943	2		204	442	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643513	52643513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000384-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	120	488	0	ENST00000394830.3:c.2383G>A	p.Asp795Asn	p.D795N	ENST00000394830	NM_018313.4	795	Gat/Aat	17/30	0.236204670937475	3	FACETS	0.589	0.53	0.651	0.196	0.176	0.217	INDETERMINATE	1	TRUE	0	0.413372180473943	3		488	1190	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799677	72799677	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000384-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	125	480	0	ENST00000325599.8:c.1492G>A	p.Glu498Lys	p.E498K	ENST00000325599	NM_018130.2	498	Gaa/Aaa	11/11	1	2	FACETS	0.657	0.594	0.723	0.657	0.594	0.723	SUBCLONAL	1	TRUE	1	0.413372180473943	2		480	921	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238561	142238561	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000384-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	96	387	0	ENST00000350721.4:c.4332G>C	p.Arg1444Ser	p.R1444S	ENST00000350721	NM_001184.3	1444	agG/agC	24/47	0.413372180473943	1	FACETS	0.453	0.403	0.507	0.453	0.403	0.507	SUBCLONAL	1	TRUE	0	0.413372180473943	1		387	813	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108652	8108652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777705809	NA	P-0000384-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	83	466	2	ENST00000585124.1:c.743G>A	p.Arg248His	p.R248H	ENST00000585124	NM_004217.3	248	cGc/cAc	8/9	0.251238469763144	1	FACETS	0.35	0.308	0.395	0.35	0.308	0.395	SUBCLONAL	1	TRUE	0	0.413372180473943	1		468	910	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	498163	498163	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000384-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1653	376	679	0	ENST00000399788.2:c.95del	p.Pro32ArgfsTer34	p.P32Rfs*34	ENST00000399788	NM_001042603.1	32	cCg/cg	1/28	0.356460279612153	3	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.413372180473943	3		679	2029	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143129	24143130	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	novel	NA	P-0000384-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	178	363	1	ENST00000263121.7:c.363-2_363-1del		p.X121_splice	ENST00000263121	NM_003073.3	121			NA	2	FACETS	0.799	0.741	0.858			1	INDETERMINATE	2	TRUE	NA	0.413372180473943	2		364	539	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000386-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	50	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.8	0.698	0.905	1	0.973	1	CLONAL	2	FALSE	1	0.503895772657086	2		422	124	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131375	202131375	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000386-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	23	321	1	ENST00000358485.4:c.343G>T	p.Glu115Ter	p.E115*	ENST00000358485	NM_001080125.1	115	Gaa/Taa	2/9	1	2	FACETS	0.309	0.241	0.388	0.309	0.241	0.388	SUBCLONAL	1	FALSE	1	0.503895772657086	2		322	295	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191448	185191448	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000386-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	44	268	0	ENST00000265026.3:c.2329G>T	p.Glu777Ter	p.E777*	ENST00000265026	NM_004721.4	777	Gaa/Taa	11/14	1	2	FACETS	0.542	0.457	0.636	0.542	0.457	0.636	SUBCLONAL	1	FALSE	1	0.503895772657086	2		268	322	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779654	3779654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000386-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	12	274	0	ENST00000262367.5:c.5394G>A	p.Met1798Ile	p.M1798I	ENST00000262367	NM_004380.2	1798	atG/atA	31/31	0.469821155000126	0	FACETS	0.175	0.123	0.238			1	SUBCLONAL	1	FALSE	0	0.503895772657086	0		274	135	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781791	3781791	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000386-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	12	330	0	ENST00000262367.5:c.4876G>T	p.Glu1626Ter	p.E1626*	ENST00000262367	NM_004380.2	1626	Gag/Tag	29/31	0.469821155000126	0	FACETS	0.103	0.072	0.141			1	SUBCLONAL	1	FALSE	0	0.503895772657086	0		330	229	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166282	7166282	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000386-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	66	593	0	ENST00000302850.5:c.1744G>T	p.Gly582Cys	p.G582C	ENST00000302850	NM_000208.2	582	Ggt/Tgt	8/22	0.174909729212618	4	FACETS	0.663	0.576	0.758	0.166	0.144	0.19	INDETERMINATE	1	FALSE	0	0.503895772657086	4		593	594	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833947	44833948	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0000386-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	245	301	0	ENST00000377967.4:c.372_373insTT	p.Asp125LeufsTer56	p.D125Lfs*56	ENST00000377967	NM_021140.2	124	tct/tcTTt	4/29	1	1	FACETS	0.996	0.952	1	1	0.996	1	CLONAL	2	FALSE	0	0.503895772657086	1		301	365	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	26	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.819563218454328	2		422	44	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177746	56177746	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	118	334	0	ENST00000399503.3:c.2719C>T	p.His907Tyr	p.H907Y	ENST00000399503	NM_005921.1	907	Cat/Tat	14/20	0.255236989779745	2	FACETS	1	0.97	1	0.558	0.513	0.603	INDETERMINATE	1	TRUE	0	0.819563218454328	2		334	258	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189388	56189388	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	150	424	0	ENST00000399503.3:c.4420C>T	p.Pro1474Ser	p.P1474S	ENST00000399503	NM_005921.1	1474	Cct/Tct	20/20	0.255236989779745	2	FACETS	1	0.985	1	0.612	0.57	0.654	INDETERMINATE	1	TRUE	0	0.819563218454328	2		424	299	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341722	8341722	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	116	665	0	ENST00000356435.5:c.4918A>T	p.Asn1640Tyr	p.N1640Y	ENST00000356435		1640	Aat/Tat	29/35	0.699819107281257	4	FACETS	0.974	0.881	1	0.487	0.44	0.535	CLONAL	1	TRUE	2	0.819563218454328	4		665	529	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485860	8485860	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778486665	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	184	529	0	ENST00000356435.5:c.2957C>T	p.Pro986Leu	p.P986L	ENST00000356435		986	cCa/cTa	17/35	0.699819107281257	4	FACETS	0.898	0.838	0.959	0.898	0.838	0.959	CLONAL	2	TRUE	2	0.819563218454328	4		529	455	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8523518	8523518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	223	284	0	ENST00000356435.5:c.686G>A	p.Arg229Gln	p.R229Q	ENST00000356435		229	cGa/cAa	8/35	0.699819107281257	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.819563218454328	4		284	433	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692782	89692782	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	213	244	0	ENST00000371953.3:c.266C>A	p.Pro89His	p.P89H	ENST00000371953	NM_000314.4	89	cCt/cAt	5/9	0.463621750706811	3	FACETS	1	0.984	1	0.727	0.691	0.763	INDETERMINATE	2	TRUE	0	0.819563218454328	3		244	336	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434940	110434940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	110	611	0	ENST00000375856.3:c.3461C>T	p.Ser1154Phe	p.S1154F	ENST00000375856	NM_003749.2	1154	tCc/tTc	1/2	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.819563218454328	2		611	199	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95583017	95583017	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886037672	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	181	326	0	ENST00000393063.1:c.1525C>T	p.Arg509Ter	p.R509*	ENST00000393063	NM_030621.3	509	Cga/Tga	11/28	0.819563218454328	3	FACETS	0.988	0.931	1	0.988	0.931	1	CLONAL	2	TRUE	1	0.819563218454328	3		326	315	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292608	91292608	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	149	405	0	ENST00000355112.3:c.110T>A	p.Phe37Tyr	p.F37Y	ENST00000355112	NM_000057.2	37	tTt/tAt	3/22	0.819563218454328	2	FACETS	1	0.968	1	0.539	0.5	0.579	CLONAL	1	TRUE	0	0.819563218454328	2		405	337	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31020694	31020694	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	124	229	0	ENST00000375687.4:c.991C>T	p.His331Tyr	p.H331Y	ENST00000375687	NM_015338.5	331	Cat/Tat	11/13	0.819563218454328	3	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	1	0.819563218454328	3		229	213	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041380	47041380	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	176	1012	0	ENST00000377604.3:c.1724A>G	p.Asp575Gly	p.D575G	ENST00000377604	NM_001204468.1	575	gAt/gGt	16/24	0.596911882261709	3	FACETS	0.855	0.801	0.91	0.855	0.801	0.91	CLONAL	2	TRUE	1	0.819563218454328	3		1012	354	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696282	52696282	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	129	508	1	ENST00000394830.3:c.395del	p.Pro132LeufsTer42	p.P132Lfs*42	ENST00000394830	NM_018313.4	132	cCt/ct	5/30	0.383896959488383	3	FACETS	1	0.976	1	0.587	0.538	0.638	INDETERMINATE	1	TRUE	1	0.819563218454328	3		509	378	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662902	227662902	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	121	574	0	ENST00000305123.5:c.553C>T	p.Leu185Phe	p.L185F	ENST00000305123	NM_005544.2	185	Ctt/Ttt	1/2	0.543318492944239	5	FACETS	1	0.96	1			1	CLONAL	2	TRUE	NA	0.819563218454328	5		574	305	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663222	227663222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	108	615	0	ENST00000305123.5:c.233C>T	p.Ser78Phe	p.S78F	ENST00000305123	NM_005544.2	78	tCc/tTc	1/2	0.543318492944239	5	FACETS	1	0.955	1			1	CLONAL	2	TRUE	NA	0.819563218454328	5		615	273	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72891463	72891463	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	149	434	0	ENST00000325599.8:c.299C>T	p.Ser100Phe	p.S100F	ENST00000325599	NM_018130.2	100	tCc/tTc	3/11	0.383896959488383	3	FACETS	1	0.983	1	0.615	0.567	0.663	INDETERMINATE	1	TRUE	1	0.819563218454328	3		434	417	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468471	89468471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	141	399	0	ENST00000336596.2:c.2005G>A	p.Gly669Arg	p.G669R	ENST00000336596	NM_005233.5	669	Gga/Aga	11/17	0.383896959488383	3	FACETS	1	0.986	1	0.672	0.62	0.725	INDETERMINATE	1	TRUE	1	0.819563218454328	3		399	361	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801056	1801056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778645659	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	57	463	0	ENST00000260795.2:c.185C>T	p.Pro62Leu	p.P62L	ENST00000260795		62	cCc/cTc	2/17	1	2	FACETS	0.953	0.838	1	0.953	0.838	1	CLONAL	1	TRUE	1	0.819563218454328	2		463	146	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594250	55594250	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	106	469	0	ENST00000288135.5:c.1953G>A	p.Met651Ile	p.M651I	ENST00000288135	NM_000222.2	651	atG/atA	13/21	NA	2	FACETS	1	0.946	1			1	INDETERMINATE	1	TRUE	NA	0.819563218454328	2		469	247	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189926	66189926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145811811	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	109	356	1	ENST00000273854.3:c.3020G>A	p.Arg1007Gln	p.R1007Q	ENST00000273854	NM_004439.5	1007	cGg/cAg	18/18	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.819563218454328	2		357	234	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178253	56178253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	137	435	0	ENST00000399503.3:c.3226C>T	p.Pro1076Ser	p.P1076S	ENST00000399503	NM_005921.1	1076	Ccc/Tcc	14/20	0.255236989779745	2	FACETS	1	0.984	1	0.619	0.575	0.663	INDETERMINATE	1	TRUE	0	0.819563218454328	2		435	270	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2969666	2969666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747866557	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	35	405	0	ENST00000396946.4:c.1613C>T	p.Ser538Phe	p.S538F	ENST00000396946	NM_032415.4	538	tCc/tTc	12/25	NA	2	FACETS	0.637	0.532	0.751			1	INDETERMINATE	1	TRUE	NA	0.819563218454328	2		405	134	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367294	50367294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	65	265	0	ENST00000331340.3:c.101C>T	p.Pro34Leu	p.P34L	ENST00000331340	NM_006060.4	34	cCc/cTc	3/8	0.56662180688611	3	FACETS	1	0.957	1	0.595	0.525	0.667	CLONAL	1	TRUE	1	0.819563218454328	3		265	188	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372744	81372744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168082930	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	107	423	0	ENST00000222390.5:c.790G>A	p.Asp264Asn	p.D264N	ENST00000222390	NM_000601.4	264	Gat/Aat	7/18	0.56662180688611	3	FACETS	1	0.963	1	0.559	0.508	0.613	CLONAL	1	TRUE	1	0.819563218454328	3		423	329	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020658	37020658	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	75	349	0	ENST00000358127.4:c.187G>T	p.Gly63Cys	p.G63C	ENST00000358127	NM_001280556.1	63	Ggt/Tgt	2/10	0.699819107281257	4	FACETS	1	0.916	1	0.522	0.461	0.586	CLONAL	1	TRUE	2	0.819563218454328	4		349	319	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285811	87285811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	27	190	633	0	ENST00000277120.3:c.148C>T	p.Pro50Ser	p.P50S	ENST00000277120		50	Cct/Tct	2/19	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.819563218454328	2		633	217	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912248	97912248	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	285	487	0	ENST00000289081.3:c.643C>A	p.Leu215Ile	p.L215I	ENST00000289081	NM_000136.2	215	Ctc/Atc	7/15	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.819563218454328	2		487	311	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426253	49426253	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	55	578	0	ENST00000301067.7:c.12235C>T	p.Gln4079Ter	p.Q4079*	ENST00000301067	NM_003482.3	4079	Caa/Taa	39/54	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.819563218454328	2		578	131	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433916	49433916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766114622	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	43	242	0	ENST00000301067.7:c.7637C>T	p.Ser2546Phe	p.S2546F	ENST00000301067	NM_003482.3	2546	tCc/tTc	31/54	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.819563218454328	2		242	104	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444358	49444358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	42	278	0	ENST00000301067.7:c.3013C>T	p.Pro1005Ser	p.P1005S	ENST00000301067	NM_003482.3	1005	Cca/Tca	11/54	1	2	FACETS	0.854	0.732	0.982	0.854	0.732	0.982	CLONAL	1	TRUE	1	0.819563218454328	2		278	120	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28901687	28901687	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	57	339	2	ENST00000282397.4:c.2708G>A	p.Gly903Glu	p.G903E	ENST00000282397	NM_002019.4	903	gGg/gAg	20/30	0.527796310102345	1	FACETS	0.54	0.474	0.608	0.54	0.474	0.608	SUBCLONAL	1	TRUE	0	0.819563218454328	1		341	152	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476275	88476275	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	145	363	0	ENST00000360948.2:c.1857C>A	p.Tyr619Ter	p.Y619*	ENST00000360948	NM_001012338.2	619	taC/taA	15/19	0.819563218454328	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.819563218454328	2		363	164	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478082	99478082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1416018269	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	93	353	0	ENST00000268035.6:c.2986C>T	p.Arg996Trp	p.R996W	ENST00000268035	NM_000875.3	996	Cgg/Tgg	16/21	0.819563218454328	2	FACETS	0.95	0.86	1	0.475	0.43	0.521	CLONAL	1	TRUE	0	0.819563218454328	2		353	239	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220715	2220715	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	35	380	0	ENST00000326181.6:c.332A>C	p.Glu111Ala	p.E111A	ENST00000326181	NM_032271.2	111	gAg/gCg	5/21	0.431578233903269	1	FACETS	0.509	0.429	0.593	0.509	0.429	0.593	INDETERMINATE	1	TRUE	0	0.819563218454328	1		380	99	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857539	9857539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	59	380	0	ENST00000330684.3:c.3862C>T	p.Arg1288Cys	p.R1288C	ENST00000330684	NM_001134407.1	1288	Cgt/Tgt	13/13	0.431578233903269	1	FACETS	0.639	0.566	0.713	0.639	0.566	0.713	INDETERMINATE	1	TRUE	0	0.819563218454328	1		380	133	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645210	67645210	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	91	472	0	ENST00000264010.4:c.475C>T	p.Pro159Ser	p.P159S	ENST00000264010	NM_006565.3	159	Cct/Tct	3/12	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.819563218454328	2		472	212	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579529	7579529	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658483	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	70	342	0	ENST00000269305.4:c.158G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tGg/tAg	4/11	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.819563218454328	2		342	152	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108215	8108215	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	93	345	0	ENST00000585124.1:c.1009C>T	p.Pro337Ser	p.P337S	ENST00000585124	NM_004217.3	337	Ccc/Tcc	9/9	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.819563218454328	2		345	214	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661866	29661866	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	112	355	0	ENST00000356175.3:c.5760G>C	p.Leu1920Phe	p.L1920F	ENST00000356175	NM_000267.3	1920	ttG/ttC	39/57	1	2	FACETS	0.959	0.876	1	0.959	0.876	1	CLONAL	1	TRUE	1	0.819563218454328	2		355	285	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873715	37873715	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	121	572	0	ENST00000269571.5:c.1880C>T	p.Pro627Leu	p.P627L	ENST00000269571		627	cCc/cTc	15/27	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.819563218454328	2		572	282	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56798164	56798164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	166	634	0	ENST00000337432.4:c.895C>T	p.Pro299Ser	p.P299S	ENST00000337432	NM_058216.2	299	Cct/Tct	6/9	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.819563218454328	2		634	363	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11170507	11170507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	71	381	0	ENST00000358026.2:c.4810G>A	p.Gly1604Ser	p.G1604S	ENST00000358026	NM_001128849.1	1604	Ggc/Agc	34/36	0.291080088684873	1	FACETS	0.752	0.679	0.825	0.752	0.679	0.825	INDETERMINATE	1	TRUE	0	0.819563218454328	1		381	136	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954668	17954668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	54	371	0	ENST00000458235.1:c.226G>A	p.Glu76Lys	p.E76K	ENST00000458235	NM_000215.3	76	Gag/Aag	3/24	0.291080088684873	1	FACETS	0.612	0.539	0.688	0.612	0.539	0.688	INDETERMINATE	1	TRUE	0	0.819563218454328	1		371	127	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754448	41754448	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	69	628	0	ENST00000301178.4:c.1567A>G	p.Lys523Glu	p.K523E	ENST00000301178	NM_021913.4	523	Aag/Gag	13/20	0.291080088684873	1	FACETS	0.492	0.436	0.55	0.492	0.436	0.55	INDETERMINATE	1	TRUE	0	0.819563218454328	1		628	202	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52722972	52722972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	89	476	0	ENST00000322088.6:c.1157C>T	p.Ser386Phe	p.S386F	ENST00000322088	NM_014225.5	386	tCt/tTt	10/15	0.544951170055934	4	FACETS	1	0.973	1			1	CLONAL	1	TRUE	NA	0.819563218454328	4		476	310	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933781	39933781	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	95	580	0	ENST00000378444.4:c.818C>T	p.Ser273Phe	p.S273F	ENST00000378444	NM_001123385.1	273	tCc/tTc	4/15	0.596911882261709	3	FACETS	1	0.959	1	0.562	0.506	0.619	CLONAL	1	TRUE	1	0.819563218454328	3		580	291	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763945	76763945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	111	812	0	ENST00000373344.5:c.7363G>A	p.Asp2455Asn	p.D2455N	ENST00000373344	NM_000489.3	2455	Gat/Aat	35/35	0.596911882261709	3	FACETS	0.632	0.57	0.698	0.316	0.285	0.349	SUBCLONAL	1	TRUE	1	0.819563218454328	3		812	604	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577106	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	145	655	1	ENST00000269305.4:c.832_833delinsTT	p.Pro278Phe	p.P278F	ENST00000269305	NM_001126112.2	278	CCt/TTt	8/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.819563218454328	2		656	281	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149436936	149436937	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	54	463	0	ENST00000286301.3:c.2232_2233delinsAA	p.Glu745Lys	p.E745K	ENST00000286301	NM_005211.3	744	aaGGag/aaAAag	17/22	0.670292382201725	1	FACETS	0.734	0.651	0.816	0.734	0.651	0.816	SUBCLONAL	1	TRUE	0	0.819563218454328	1		463	106	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289341	33289342	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	44	193	0	ENST00000374542.5:c.210_211delinsTT	p.Leu71Phe	p.L71F	ENST00000374542	NM_001141970.1	70	ttCCtt/ttTTtt	3/8	0.293215706965302	6	FACETS	0.88	0.751	1	0.44	0.375	0.509	INDETERMINATE	2	TRUE	2	0.819563218454328	6		193	161	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807657	1807658	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	46	520	1	ENST00000260795.2:c.1826_1827delinsTT	p.Ala609Val	p.A609V	ENST00000260795		609	gCC/gTT	12/17	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.819563218454328	2		521	111	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128199938	128199939	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	22	331	0	ENST00000341105.2:c.1366_1367delinsTT	p.Pro456Leu	p.P456L	ENST00000341105	NM_032638.4	456	CCg/TTg	6/6	0.383896959488383	3	FACETS	0.749	0.592	0.925	0.375	0.296	0.463	INDETERMINATE	1	TRUE	1	0.819563218454328	3		331	101	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857125	9857126	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	97	569	0	ENST00000330684.3:c.4275_4276delinsAA	p.Glu1426Lys	p.E1426K	ENST00000330684	NM_001134407.1	1425	tcGGag/tcAAag	13/13	0.431578233903269	1	FACETS	0.605	0.55	0.661	0.605	0.55	0.661	INDETERMINATE	1	TRUE	0	0.819563218454328	1		569	231	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550367	39550368	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	116	420	0	ENST00000262039.4:c.478_479delinsTT	p.Pro160Phe	p.P160F	ENST00000262039	NM_002647.2	160	CCt/TTt	4/25	1	2	FACETS	0.976	0.894	1	0.976	0.894	1	CLONAL	1	TRUE	1	0.819563218454328	2		420	290	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231381	98231384	+	frameshift_variant	Frame_Shift_Del	DEL	GTGT	GTGT	TTG	novel	NA	P-0000399-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	208	249	2	ENST00000331920.6:c.1899_1902delinsCAA	p.His634LysfsTer59	p.H634Kfs*59	ENST00000331920	NM_000264.3	633	acACAC/acCAA	14/24	0.443317407856	5	FACETS	1	0.988	1			1	INDETERMINATE	5	TRUE	NA	0.819563218454328	5		251	222	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000402-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	29	422	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		422	244	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000410-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	84	422	0				ENST00000310581	NM_198253.2	-/1132			0.340366829408587	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	2	0.369127666580543	4		422	277	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249503	153249503	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000410-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	151	295	0	ENST00000281708.4:c.1275G>C	p.Trp425Cys	p.W425C	ENST00000281708	NM_033632.3	425	tgG/tgC	9/12	0.369127666580543	3	FACETS	0.824	0.757	0.894	0.824	0.757	0.894	CLONAL	2	TRUE	1	0.369127666580543	3		295	588	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180051053	180051053	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755736057	NA	P-0000410-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	113	313	0	ENST00000261937.6:c.1430G>A	p.Arg477Gln	p.R477Q	ENST00000261937	NM_182925.4	477	cGg/cAg	11/30	0.317133552544163	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.369127666580543	4		313	368	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030350	49030350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000410-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	260	302	0	ENST00000267163.4:c.1825C>T	p.Pro609Ser	p.P609S	ENST00000267163	NM_000321.2	609	Cct/Tct	19/27	0.369127666580543	4	FACETS	0.938	0.889	0.987	0.938	0.889	0.987	CLONAL	4	TRUE	0	0.369127666580543	4		302	514	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037966	49037966	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000410-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	303	270	0	ENST00000267163.4:c.2206C>T	p.Gln736Ter	p.Q736*	ENST00000267163	NM_000321.2	736	Cag/Tag	21/27	0.369127666580543	4	FACETS	0.898	0.854	0.942	0.898	0.854	0.942	CLONAL	4	TRUE	0	0.369127666580543	4		270	626	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039365	49039365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000410-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	657	732	0	ENST00000267163.4:c.2350C>T	p.His784Tyr	p.H784Y	ENST00000267163	NM_000321.2	784	Cac/Tac	23/27	0.369127666580543	4	FACETS	0.972	0.94	1	0.972	0.94	1	CLONAL	4	TRUE	0	0.369127666580543	4		732	1254	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659729	227659743	+	inframe_deletion	In_Frame_Del	DEL	CTGACGGTCCTCTGG	CTGACGGTCCTCTGG	-	novel	NA	P-0000410-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	113	477	0	ENST00000305123.5:c.3712_3726del	p.Pro1238_Gln1242del	p.P1238_Q1242del	ENST00000305123	NM_005544.2	1238	CCAGAGGACCGTCAG/-	1/2	0.33739436267477	4	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.369127666580543	4		477	651	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652134	36652135	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0000410-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	115	354	0	ENST00000244741.5:c.259dup	p.Asp87GlyfsTer2	p.D87Gfs*2	ENST00000244741	NM_000389.4	86	cgg/cGgg	2/3	0.369127666580543	4	FACETS	0.836	0.757	0.919	0.836	0.757	0.919	CLONAL	2	TRUE	2	0.369127666580543	4		354	510	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000415-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	45	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.861	0.741	0.986	0.861	0.741	0.986	CLONAL	1	FALSE	1	0.798028325774484	2		422	131	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0000415-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	104	318	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.555198055772638	1	FACETS	0.847	0.781	0.911	0.847	0.781	0.911	CLONAL	1	FALSE	0	0.798028325774484	1		318	185	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577191	64577206	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTGAGGCTGTTCCA	GGCTGAGGCTGTTCCA	-	novel	NA	P-0000415-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	50	380	0	ENST00000312049.6:c.376_391del	p.Trp126AlafsTer54	p.W126Afs*54	ENST00000312049	NM_130799.2	126	TGGAACAGCCTCAGCCgc/gc	2/10	0.798028325774484	1	FACETS	0.403	0.347	0.462	0.403	0.347	0.462	SUBCLONAL	1	FALSE	0	0.798028325774484	1		380	187	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958123	54958125	+	frameshift_variant	Frame_Shift_Ins	INS	TAA	TAA	GACT	novel	NA	P-0000415-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	79	402	0	ENST00000312783.6:c.482_484delinsAGTC	p.Leu161GlnfsTer6	p.L161Qfs*6	ENST00000312783	NM_198436.1	161	cTTAaa/cAGTCaa	6/10	NA	2	FACETS	0.695	0.618	0.775			1	INDETERMINATE	1	FALSE	NA	0.798028325774484	2		402	285	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000423-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	305	422	0				ENST00000310581	NM_198253.2	-/1132			0.464535572083627	4	FACETS	0.893	0.855	0.931			1	CLONAL	4	TRUE	NA	0.518700848255729	4		422	500	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0000423-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	63	295	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.305679674292234	3	FACETS	1	0.97	1	0.702	0.616	0.792	INDETERMINATE	1	TRUE	1	0.518700848255729	3		295	218	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0000423-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	224	536	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.518700848255729	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.518700848255729	1		536	535	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023086	48023086	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000423-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	128	232	0	ENST00000234420.5:c.511G>A	p.Glu171Lys	p.E171K	ENST00000234420	NM_000179.2	171	Gaa/Aaa	3/10	1	2	FACETS	0.869	0.791	0.951	0.869	0.791	0.951	CLONAL	1	TRUE	1	0.518700848255729	2		232	568	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519925	NA	P-0000423-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	46	229	0	ENST00000263967.3:c.1357G>C	p.Glu453Gln	p.E453Q	ENST00000263967	NM_006218.2	453	Gaa/Caa	8/21	0.305679674292234	3	FACETS	0.322	0.27	0.379	0.161	0.135	0.19	INDETERMINATE	1	TRUE	1	0.518700848255729	3		229	694	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157480	106157480	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1334737410	NA	P-0000423-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	43	177	0	ENST00000380013.4:c.2381C>G	p.Ser794Ter	p.S794*	ENST00000380013	NM_001127208.2	794	tCa/tGa	3/11	0.518700848255729	1	FACETS	0.333	0.279	0.392	0.333	0.279	0.392	SUBCLONAL	1	TRUE	0	0.518700848255729	1		177	369	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117717422	117717422	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000423-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	129	262	0	ENST00000368508.3:c.785C>G	p.Ser262Cys	p.S262C	ENST00000368508	NM_002944.2	262	tCt/tGt	8/43	1	2	FACETS	0.689	0.625	0.756	0.689	0.625	0.756	SUBCLONAL	1	TRUE	1	0.518700848255729	2		262	722	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884912	151884912	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000423-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	90	92	0	ENST00000262189.6:c.4681C>G	p.Leu1561Val	p.L1561V	ENST00000262189	NM_170606.2	1561	Ctc/Gtc	32/59	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.518700848255729	2		92	311	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250088	110250088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237765057	NA	P-0000423-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	110	235	0	ENST00000374672.4:c.587C>T	p.Ser196Leu	p.S196L	ENST00000374672	NM_004235.4	196	tCg/tTg	3/5	0.30505950270311	1	FACETS	0.615	0.555	0.678	0.615	0.555	0.678	INDETERMINATE	1	TRUE	0	0.518700848255729	1		235	511	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450623	70450623	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000423-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	318	529	0	ENST00000373644.4:c.5463C>G	p.Ile1821Met	p.I1821M	ENST00000373644	NM_030625.2	1821	atC/atG	12/12	0.378280109920785	1	FACETS	0.676	0.637	0.716	0.676	0.637	0.716	SUBCLONAL	1	TRUE	0	0.518700848255729	1		529	1344	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450766	70450766	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000423-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	153	269	0	ENST00000373644.4:c.5606C>T	p.Ser1869Leu	p.S1869L	ENST00000373644	NM_030625.2	1869	tCa/tTa	12/12	0.378280109920785	1	FACETS	0.653	0.599	0.709	0.653	0.599	0.709	SUBCLONAL	1	TRUE	0	0.518700848255729	1		269	669	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450886	70450886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000423-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	103	221	0	ENST00000373644.4:c.5726C>T	p.Pro1909Leu	p.P1909L	ENST00000373644	NM_030625.2	1909	cCt/cTt	12/12	0.378280109920785	1	FACETS	0.735	0.663	0.811	0.735	0.663	0.811	SUBCLONAL	1	TRUE	0	0.518700848255729	1		221	400	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451087	70451087	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000423-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	153	269	0	ENST00000373644.4:c.5927C>G	p.Ser1976Cys	p.S1976C	ENST00000373644	NM_030625.2	1976	tCt/tGt	12/12	0.378280109920785	1	FACETS	0.729	0.67	0.791	0.729	0.67	0.791	SUBCLONAL	1	TRUE	0	0.518700848255729	1		269	599	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203553	108203553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000423-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	32	188	0	ENST00000278616.4:c.7853G>A	p.Arg2618Lys	p.R2618K	ENST00000278616	NM_000051.3	2618	aGa/aAa	53/63	1	2	FACETS	0.208	0.168	0.254	0.208	0.168	0.254	SUBCLONAL	1	TRUE	1	0.518700848255729	2		188	592	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95593075	95593075	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000423-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	214	269	0	ENST00000393063.1:c.745C>G	p.Gln249Glu	p.Q249E	ENST00000393063	NM_030621.3	249	Cag/Gag	8/28	0.42330118712505	3	FACETS	1	0.969	1	0.537	0.499	0.577	CLONAL	1	TRUE	1	0.518700848255729	3		269	967	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817754	3817754	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000423-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	73	598	0	ENST00000262367.5:c.3217C>T	p.Gln1073Ter	p.Q1073*	ENST00000262367	NM_004380.2	1073	Cag/Tag	16/31	0.518700848255729	1	FACETS	0.239	0.209	0.273	0.239	0.209	0.273	SUBCLONAL	1	TRUE	0	0.518700848255729	1		598	871	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844151	68844151	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000423-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	159	299	0	ENST00000261769.5:c.739G>T	p.Glu247Ter	p.E247*	ENST00000261769	NM_004360.3	247	Gag/Tag	6/16	0.518700848255729	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.518700848255729	1		299	361	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559149	29559149	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000423-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	85	220	0	ENST00000356175.3:c.3256C>T	p.Gln1086Ter	p.Q1086*	ENST00000356175	NM_000267.3	1086	Cag/Tag	25/57	1	2	FACETS	0.604	0.535	0.677	0.604	0.535	0.677	SUBCLONAL	1	TRUE	1	0.518700848255729	2		220	543	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000425-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	130	422	0				ENST00000310581	NM_198253.2	-/1132			0.383581228460258	4	FACETS	1	0.933	1	1	0.933	1	CLONAL	3	TRUE	1	0.384357119334909	4		422	308	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579716	7579716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1192416464	NA	P-0000425-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	93	354	0	ENST00000269305.4:c.80del	p.Pro27LeufsTer17	p.P27Lfs*17	ENST00000269305	NM_001126112.2	27	cCt/ct	3/11	0.384357119334909	1	FACETS	0.768	0.685	0.856	0.768	0.685	0.856	SUBCLONAL	1	TRUE	0	0.384357119334909	1		354	509	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451339	187451339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200263685	NA	P-0000444-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1651	167	322	0	ENST00000232014.4:c.143C>T	p.Thr48Met	p.T48M	ENST00000232014	NM_001130845.1	48	aCg/aTg	3/10	0.443013958901003	6	FACETS	0.782	0.715	0.852			1	SUBCLONAL	1	TRUE	NA	0.443013958901003	6		322	1818	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971070	21971072	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0000444-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	112	202	0	ENST00000304494.5:c.286_288del	p.Val96del	p.V96del	ENST00000304494	NM_000077.4	96	GTG/-	2/3	1	2	FACETS	0.916	0.827	1	0.916	0.827	1	CLONAL	1	TRUE	1	0.443013958901003	2		202	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578455	7578460	+	inframe_deletion	In_Frame_Del	DEL	CGCGGA	CGCGGA	-	novel	NA	P-0000444-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	184	261	0	ENST00000269305.4:c.470_475del	p.Val157_Arg158del	p.V157_R158del	ENST00000269305	NM_001126112.2	157	gTCCGCGcc/gcc	5/11	NA	2	FACETS	0.827	0.77	0.886			1	INDETERMINATE	2	TRUE	NA	0.443013958901003	2		261	502	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	221	467	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	0.3	3	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.72	3		467	645	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	286	492	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.210915367403693	4	FACETS	0.836	0.789	0.884	0.836	0.789	0.884	INDETERMINATE	2	TRUE	2	0.72	4		492	817	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	185	92	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.72	2		92	488	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262615	16262615	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	126	242	1	ENST00000375759.3:c.9880C>T	p.Gln3294Ter	p.Q3294*	ENST00000375759	NM_015001.2	3294	Cag/Tag	11/15	1	2	FACETS	0.994	0.911	1	0.994	0.911	1	CLONAL	1	TRUE	1	0.72	2		243	352	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087503	27087503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	157	263	0	ENST00000324856.7:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000324856	NM_006015.4	693	Cga/Tga	5/20	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.72	2		263	433	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101212	27101212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	196	356	0	ENST00000324856.7:c.4494G>A	p.Trp1498Ter	p.W1498*	ENST00000324856	NM_006015.4	1498	tgG/tgA	18/20	1	2	FACETS	0.972	0.907	1	0.972	0.907	1	CLONAL	1	TRUE	1	0.72	2		356	560	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105838	27105838	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375250508	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	38	325	0	ENST00000324856.7:c.5449G>A	p.Val1817Ile	p.V1817I	ENST00000324856	NM_006015.4	1817	Gta/Ata	20/20	1	2	FACETS	0.169	0.139	0.203	0.169	0.139	0.203	SUBCLONAL	1	TRUE	1	0.72	2		325	624	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310517	65310517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	154	326	0	ENST00000342505.4:c.2171G>A	p.Arg724His	p.R724H	ENST00000342505	NM_002227.2	724	cGt/cAt	16/25	1	2	FACETS	0.897	0.827	0.968	0.897	0.827	0.968	CLONAL	1	TRUE	1	0.72	2		326	477	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551912	150551912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770152297	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	98	304	0	ENST00000369026.2:c.95G>A	p.Gly32Glu	p.G32E	ENST00000369026	NM_021960.4	32	gGa/gAa	1/3	0.3	9	FACETS	0.758	0.677	0.844			1	INDETERMINATE	2	TRUE	NA	0.72	9		304	632	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843598	156843598	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375878564	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	157	399	3	ENST00000524377.1:c.1024C>T	p.Arg342Trp	p.R342W	ENST00000524377	NM_002529.3	342	Cgg/Tgg	8/17	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.72	2		402	401	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945724	206945724	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	128	241	0	ENST00000423557.1:c.57C>G	p.Ser19Arg	p.S19R	ENST00000423557	NM_000572.2	19	agC/agG	1/5	1	2	FACETS	0.827	0.756	0.901	0.827	0.756	0.901	CLONAL	1	TRUE	1	0.72	2		241	430	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552839	226552839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748109048	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	164	316	0	ENST00000366794.5:c.2522G>A	p.Arg841His	p.R841H	ENST00000366794	NM_001618.3	841	cGt/cAt	19/23	1	2	FACETS	0.955	0.884	1	0.955	0.884	1	CLONAL	1	TRUE	1	0.72	2		316	477	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467108	25467108	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	123	357	0	ENST00000264709.3:c.1767G>T	p.Lys589Asn	p.K589N	ENST00000264709	NM_175629.2	589	aaG/aaT	15/23	1	2	FACETS	0.787	0.717	0.86	0.787	0.717	0.86	SUBCLONAL	1	TRUE	1	0.72	2		357	434	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965143	25965143	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	226	304	0	ENST00000435504.4:c.4063G>T	p.Gly1355Cys	p.G1355C	ENST00000435504		1355	Ggt/Tgt	13/13	1	2	FACETS	0.993	0.931	1	0.993	0.931	1	CLONAL	1	TRUE	1	0.72	2		304	632	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182192	99182192	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763716402	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	171	320	0	ENST00000074304.5:c.2257G>A	p.Ala753Thr	p.A753T	ENST00000074304	NM_001134224.1	753	Gcc/Acc	21/26	1	2	FACETS	0.958	0.888	1	0.958	0.888	1	CLONAL	1	TRUE	1	0.72	2		320	496	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137370	202137370	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	165	256	0	ENST00000358485.4:c.598G>T	p.Asp200Tyr	p.D200Y	ENST00000358485	NM_001080125.1	200	Gat/Tat	4/9	0.142633519984408	3	FACETS	1	0.985	1	0.626	0.579	0.674	INDETERMINATE	1	TRUE	1	0.72	3		256	498	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027093	71027093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200629338	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	125	199	0	ENST00000318789.4:c.1234G>A	p.Ala412Thr	p.A412T	ENST00000318789	NM_032682.5	412	Gcc/Acc	15/21	0.142633519984408	3	FACETS	1	0.961	1	0.548	0.5	0.598	INDETERMINATE	1	TRUE	1	0.72	3		199	431	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72866503	72866503	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs777239706	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	283	323	0	ENST00000325599.8:c.760C>T	p.Arg254Ter	p.R254*	ENST00000325599	NM_018130.2	254	Cga/Tga	7/11	0.142633519984408	3	FACETS	1	0.993	1	0.691	0.652	0.73	INDETERMINATE	1	TRUE	1	0.72	3		323	774	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890207	72890207	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs936760285	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	53	319	0	ENST00000325599.8:c.475C>A	p.Gln159Lys	p.Q159K	ENST00000325599	NM_018130.2	159	Caa/Aaa	4/11	0.142633519984408	3	FACETS	0.254	0.216	0.297	0.127	0.108	0.149	INDETERMINATE	1	TRUE	1	0.72	3		319	787	SUCCESS
ATR	545	MSKCC	GRCh37	3	142285059	142285059	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758564083	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	301	437	0	ENST00000350721.4:c.196G>A	p.Val66Met	p.V66M	ENST00000350721	NM_001184.3	66	Gtg/Atg	3/47	1	2	FACETS	0.981	0.928	1	0.981	0.928	1	CLONAL	1	TRUE	1	0.72	2		437	852	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921548	178921548	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519942	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	241	343	0	ENST00000263967.3:c.1030G>A	p.Val344Met	p.V344M	ENST00000263967	NM_006218.2	344	Gtg/Atg	5/21	1	2	FACETS	0.932	0.875	0.991	0.932	0.875	0.991	CLONAL	1	TRUE	1	0.72	2		343	718	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952018	178952018	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517202	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	291	382	0	ENST00000263967.3:c.3073A>G	p.Thr1025Ala	p.T1025A	ENST00000263967	NM_006218.2	1025	Acc/Gcc	21/21	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.72	2		382	786	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539936	187539936	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	238	351	0	ENST00000441802.2:c.7804G>T	p.Glu2602Ter	p.E2602*	ENST00000441802	NM_005245.3	2602	Gaa/Taa	10/27	1	2	FACETS	0.987	0.926	1	0.987	0.926	1	CLONAL	1	TRUE	1	0.72	2		351	670	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433673	149433673	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1467770819	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	149	346	0	ENST00000286301.3:c.2878G>A	p.Ala960Thr	p.A960T	ENST00000286301	NM_005211.3	960	Gcc/Acc	22/22	1	2	FACETS	0.89	0.82	0.962	0.89	0.82	0.962	CLONAL	1	TRUE	1	0.72	2		346	465	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459879	149459879	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1432099970	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	108	253	0	ENST00000286301.3:c.328G>A	p.Val110Met	p.V110M	ENST00000286301	NM_005211.3	110	Gtg/Atg	4/22	1	2	FACETS	0.938	0.852	1	0.938	0.852	1	CLONAL	1	TRUE	1	0.72	2		253	320	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170832372	170832372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	100	186	0	ENST00000296930.5:c.736G>A	p.Asp246Asn	p.D246N	ENST00000296930	NM_002520.6	246	Gac/Aac	9/11	1	2	FACETS	0.683	0.614	0.754	0.683	0.614	0.754	SUBCLONAL	1	TRUE	1	0.72	2		186	407	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401589	401589	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs756281792	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	99	298	0	ENST00000380956.4:c.911T>C	p.Ile304Thr	p.I304T	ENST00000380956	NM_001195286.1	304	aTt/aCt	7/9	0.3	3	FACETS	0.977	0.879	1			1	INDETERMINATE	1	TRUE	NA	0.72	3		298	383	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652158	36652158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1236971182	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	170	295	0	ENST00000244741.5:c.280C>T	p.Arg94Trp	p.R94W	ENST00000244741	NM_000389.4	94	Cgg/Tgg	2/3	0.210915367403693	5	FACETS	1	0.983	1	0.787	0.732	0.843	INDETERMINATE	2	TRUE	2	0.72	5		295	416	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001304	150001304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779067408	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	293	464	0	ENST00000253339.5:c.2300G>A	p.Arg767His	p.R767H	ENST00000253339		767	cGt/cAt	4/7	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.72	2		464	793	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381472	81381472	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777593933	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	277	433	0	ENST00000222390.5:c.589C>T	p.Arg197Cys	p.R197C	ENST00000222390	NM_000601.4	197	Cgc/Tgc	5/18	1	2	FACETS	0.95	0.895	1	0.95	0.895	1	CLONAL	1	TRUE	1	0.72	2		433	810	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878749	151878749	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1211949081	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	174	274	0	ENST00000262189.6:c.6196C>T	p.Arg2066Ter	p.R2066*	ENST00000262189	NM_170606.2	2066	Cga/Tga	36/59	1	2	FACETS	0.933	0.866	1	0.933	0.866	1	CLONAL	1	TRUE	1	0.72	2		274	518	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371722	55371722	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	152	186	0	ENST00000297316.4:c.412C>G	p.Arg138Gly	p.R138G	ENST00000297316	NM_022454.3	138	Cgg/Ggg	2/2	0.210915367403693	3	FACETS	1	0.989	1	0.72	0.666	0.775	INDETERMINATE	1	TRUE	1	0.72	3		186	399	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484308	8484308	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	62	446	1	ENST00000356435.5:c.3224T>C	p.Leu1075Pro	p.L1075P	ENST00000356435		1075	cTg/cCg	19/35	1	2	FACETS	0.221	0.19	0.255	0.221	0.19	0.255	SUBCLONAL	1	TRUE	1	0.72	2		447	778	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971066	21971066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793953	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	124	188	0	ENST00000304494.5:c.292C>T	p.His98Tyr	p.H98Y	ENST00000304494	NM_000077.4	98	Cac/Tac	2/3	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.72	2		188	324	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93627350	93627350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756047567	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	176	374	0	ENST00000375746.1:c.817C>T	p.Arg273Cys	p.R273C	ENST00000375746	NM_001174167.1	273	Cgt/Tgt	6/14	1	2	FACETS	0.98	0.91	1	0.98	0.91	1	CLONAL	1	TRUE	1	0.72	2		374	499	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248090	110248090	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	56	380	0	ENST00000374672.4:c.1382G>A	p.Cys461Tyr	p.C461Y	ENST00000374672	NM_004235.4	461	tGc/tAc	5/5	1	2	FACETS	0.258	0.221	0.299	0.258	0.221	0.299	SUBCLONAL	1	TRUE	1	0.72	2		380	602	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406043	70406043	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	247	422	0	ENST00000373644.4:c.3557T>C	p.Ile1186Thr	p.I1186T	ENST00000373644	NM_030625.2	1186	aTa/aCa	4/12	1	2	FACETS	0.982	0.922	1	0.982	0.922	1	CLONAL	1	TRUE	1	0.72	2		422	699	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263395	123263395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs536181987	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	212	364	0	ENST00000358487.5:c.1348C>T	p.Arg450Cys	p.R450C	ENST00000358487	NM_000141.4	450	Cgc/Tgc	10/18	1	2	FACETS	0.969	0.906	1	0.969	0.906	1	CLONAL	1	TRUE	1	0.72	2		364	608	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161493	2161493	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs924071547	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	138	395	0	ENST00000434045.2:c.34G>C	p.Ala12Pro	p.A12P	ENST00000434045	NM_001127598.1	12	Gcc/Ccc	2/5	0.10501790905928	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.72	0		395	339	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136190	64136190	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777217932	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	103	296	0	ENST00000334205.4:c.1349C>T	p.Thr450Met	p.T450M	ENST00000334205	NM_003942.2	450	aCg/aTg	12/17	0.10501790905928	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.72	0		296	311	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371775	118371775	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782301554	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	194	332	0	ENST00000534358.1:c.6232C>T	p.Arg2078Cys	p.R2078C	ENST00000534358	NM_005933.3	2078	Cgt/Tgt	25/36	1	2	FACETS	0.915	0.852	0.979	0.915	0.852	0.979	CLONAL	1	TRUE	1	0.72	2		332	589	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155983	119155983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202065722	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	251	449	0	ENST00000264033.4:c.1648C>T	p.Arg550Trp	p.R550W	ENST00000264033	NM_005188.3	550	Cgg/Tgg	11/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.72	2		449	689	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12043940	12043940	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	44	300	0	ENST00000396373.4:c.1319A>T	p.Gln440Leu	p.Q440L	ENST00000396373	NM_001987.4	440	cAg/cTg	8/8	0.3	3	FACETS	0.301	0.252	0.356			1	INDETERMINATE	1	TRUE	NA	0.72	3		300	552	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428627	49428627	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	151	390	0	ENST00000301067.7:c.10323G>T	p.Gln3441His	p.Q3441H	ENST00000301067	NM_003482.3	3441	caG/caT	35/54	0.142633519984408	3	FACETS	1	0.965	1	0.543	0.5	0.588	INDETERMINATE	1	TRUE	1	0.72	3		390	525	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210935	133210935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	143	310	0	ENST00000320574.5:c.5841G>T	p.Glu1947Asp	p.E1947D	ENST00000320574	NM_006231.2	1947	gaG/gaT	43/49	0.142633519984408	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.72	0		310	365	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589834	28589834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201923726	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	108	309	0	ENST00000241453.7:c.2546G>A	p.Arg849His	p.R849H	ENST00000241453	NM_004119.2	849	cGt/cAt	21/24	0.3	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.72	0		309	384	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893641	28893641	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	129	305	0	ENST00000282397.4:c.3205G>T	p.Glu1069Ter	p.E1069*	ENST00000282397	NM_002019.4	1069	Gaa/Taa	24/30	0.3	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.72	0		305	457	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434482	110434482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1178880510	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	106	173	0	ENST00000375856.3:c.3919G>A	p.Gly1307Arg	p.G1307R	ENST00000375856	NM_003749.2	1307	Ggg/Agg	1/2	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.72	2		173	257	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572013	95572013	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	321	393	0	ENST00000393063.1:c.3093+2T>C		p.X1031_splice	ENST00000393063	NM_030621.3	1031			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.72	2		393	868	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130352	2130352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773951533	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	36	344	0	ENST00000219476.3:c.3584C>T	p.Ala1195Val	p.A1195V	ENST00000219476	NM_000548.3	1195	gCg/gTg	30/42	0.142633519984408	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.72	0		344	341	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857299	9857299	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	145	350	0	ENST00000330684.3:c.4102C>A	p.Leu1368Ile	p.L1368I	ENST00000330684	NM_001134407.1	1368	Ctc/Atc	13/13	0.142633519984408	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.72	0		350	446	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660550	67660550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	43	502	0	ENST00000264010.4:c.1450C>T	p.Gln484Ter	p.Q484*	ENST00000264010	NM_006565.3	484	Cag/Tag	8/12	0.10501790905928	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.72	0		502	610	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15976784	15976784	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	270	541	0	ENST00000268712.3:c.3770G>T	p.Gly1257Val	p.G1257V	ENST00000268712	NM_006311.3	1257	gGg/gTg	28/46	1	2	FACETS	0.889	0.836	0.942	0.889	0.836	0.942	CLONAL	1	TRUE	1	0.72	2		541	844	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	130	842	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.3	3	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.72	3		842	381	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512362	38512362	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1400641137	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	16	234	0	ENST00000254066.5:c.1273G>A	p.Gly425Arg	p.G425R	ENST00000254066	NM_000964.3	425	Gga/Aga	9/9	0.10501790905928	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.72	0		234	264	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681708	78681708	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767783333	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	40	360	0	ENST00000306801.3:c.416G>A	p.Arg139His	p.R139H	ENST00000306801	NM_020761.2	139	cGc/cAc	4/34	0.10501790905928	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.72	0		360	484	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796960	78796960	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	177	305	0	ENST00000306801.3:c.1073G>T	p.Arg358Met	p.R358M	ENST00000306801	NM_020761.2	358	aGg/aTg	9/34	0.10501790905928	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.72	0		305	474	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222930	5222930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374990235	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	98	242	2	ENST00000357368.4:c.2873G>A	p.Arg958His	p.R958H	ENST00000357368	NM_002850.3	958	cGc/cAc	18/38	0.281445775392257	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.72	0		244	221	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244098	5244098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs73545312	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	142	523	0	ENST00000357368.4:c.1384G>A	p.Val462Ile	p.V462I	ENST00000357368	NM_002850.3	462	Gtc/Atc	11/38	0.281445775392257	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.72	0		523	343	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297687	15297687	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	77	335	0	ENST00000263388.2:c.1951+2T>C		p.X651_splice	ENST00000263388	NM_000435.2	651			1	2	FACETS	0.615	0.543	0.69	0.615	0.543	0.69	SUBCLONAL	1	TRUE	1	0.72	2		335	348	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303199	15303199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769955930	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	157	375	0	ENST00000263388.2:c.329G>A	p.Arg110His	p.R110H	ENST00000263388	NM_000435.2	110	cGt/cAt	3/33	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.72	2		375	387	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624804	9624804	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	140	268	0	ENST00000353224.5:c.173G>A	p.Cys58Tyr	p.C58Y	ENST00000353224	NM_177990.2	58	tGc/tAc	3/10	0.561850795876232	3	FACETS	1	0.948	1	0.524	0.48	0.569	CLONAL	1	TRUE	1	0.72	3		268	505	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031597	36031597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1484879243	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	143	336	0	ENST00000358208.4:c.1426G>A	p.Asp476Asn	p.D476N	ENST00000358208		476	Gac/Aac	12/12	0.561850795876232	3	FACETS	1	0.975	1	0.576	0.529	0.624	CLONAL	1	TRUE	1	0.72	3		336	469	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948483	54948483	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	207	485	0	ENST00000312783.6:c.835G>C	p.Val279Leu	p.V279L	ENST00000312783	NM_198436.1	279	Gta/Cta	8/10	0.210915367403693	2	FACETS	0.665	0.618	0.713	0.332	0.309	0.357	INDETERMINATE	1	TRUE	0	0.72	2		485	865	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513327	44513327	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755118626	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	184	305	0	ENST00000291552.4:c.608G>A	p.Arg203His	p.R203H	ENST00000291552	NM_006758.2	203	cGt/cAt	8/8	0.3	2	FACETS	0.952	0.885	1			1	INDETERMINATE	1	TRUE	NA	0.72	2		305	537	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000054	30000054	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	190	418	0	ENST00000338641.4:c.67A>G	p.Thr23Ala	p.T23A	ENST00000338641	NM_000268.3	23	Acc/Gcc	1/16	0.3	2	FACETS	0.84	0.781	0.902			1	INDETERMINATE	1	TRUE	NA	0.72	2		418	628	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938475	44938475	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	336	511	0	ENST00000377967.4:c.3023C>T	p.Ala1008Val	p.A1008V	ENST00000377967	NM_021140.2	1008	gCa/gTa	20/29	0.3	1	FACETS	0.624	0.591	0.657	0.624	0.591	0.657	INDETERMINATE	1	TRUE	0	0.72	1		511	958	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429346	47429346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755229896	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	213	469	0	ENST00000377045.4:c.1474G>A	p.Val492Ile	p.V492I	ENST00000377045	NM_001654.4	492	Gtc/Atc	14/16	0.3	1	FACETS	0.741	0.695	0.787	0.741	0.695	0.787	INDETERMINATE	1	TRUE	0	0.72	1		469	511	SUCCESS
AR	367	MSKCC	GRCh37	X	66765883	66765883	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1213709903	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	158	451	0	ENST00000374690.3:c.895G>A	p.Ala299Thr	p.A299T	ENST00000374690	NM_000044.3	299	Gca/Aca	1/8	0.210915367403693	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.72	0		451	525	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215372	123215372	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	49	415	0	ENST00000218089.9:c.2918T>C	p.Leu973Pro	p.L973P	ENST00000218089	NM_001042749.1	973	cTa/cCa	28/35	0.3	1	FACETS	0.104	0.087	0.122	0.104	0.087	0.122	INDETERMINATE	1	TRUE	0	0.72	1		415	838	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363510	40363519	+	frameshift_variant	Frame_Shift_Del	DEL	TGCTGATGGA	TGCTGATGGA	-	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	161	320	0	ENST00000397332.2:c.710_719del	p.Ile237AsnfsTer46	p.I237Nfs*46	ENST00000397332	NM_001033082.2	237	aTCCATCAGCAa/aa	3/3	1	2	FACETS	0.793	0.731	0.857	0.793	0.731	0.857	SUBCLONAL	1	TRUE	1	0.72	2		320	564	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151289	202151290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	221	431	0	ENST00000358485.4:c.1596dup	p.Leu533ThrfsTer6	p.L533Tfs*6	ENST00000358485	NM_001080125.1	530	aga/agAa	9/9	0.142633519984408	3	FACETS	1	0.982	1	0.57	0.533	0.609	INDETERMINATE	1	TRUE	1	0.72	3		431	732	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504296	8504297	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	44	338	0	ENST00000356435.5:c.1786dup	p.Ser596PhefsTer8	p.S596Ffs*8	ENST00000356435		596	tct/tTct	12/35	1	2	FACETS	0.195	0.163	0.231	0.195	0.163	0.231	SUBCLONAL	1	TRUE	1	0.72	2		338	626	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670396	88670396	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	199	401	0	ENST00000360948.2:c.1290del	p.Phe430LeufsTer5	p.F430Lfs*5	ENST00000360948	NM_001012338.2	430	ttT/tt	11/19	0.3	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.72	0		401	590	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760967	59760967	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000448-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	72	476	0	ENST00000259008.2:c.3440del	p.Asn1147MetfsTer3	p.N1147Mfs*3	ENST00000259008	NM_032043.2	1147	aAt/at	20/20	0.10501790905928	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.72	0		476	832	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0000457-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	182	139	0				ENST00000310581	NM_198253.2	-/1132			0.700775817210146	3	FACETS	0.988	0.927	1	0.988	0.927	1	CLONAL	2	TRUE	1	0.700775817210146	3		139	355	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100375	27100375	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000457-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	490	417	0	ENST00000324856.7:c.4087C>T	p.Gln1363Ter	p.Q1363*	ENST00000324856	NM_006015.4	1363	Caa/Taa	17/20	0.67258919662193	4	FACETS	0.986	0.945	1	0.986	0.945	1	CLONAL	2	TRUE	2	0.700775817210146	4		417	1206	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594094	55594094	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs794726675	NA	P-0000457-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	243	430	0	ENST00000288135.5:c.1879+1G>A		p.X627_splice	ENST00000288135	NM_000222.2	627			1	2	FACETS	0.999	0.939	1	0.999	0.939	1	CLONAL	1	TRUE	1	0.700775817210146	2		430	694	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618602	37618602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000457-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	507	290	0	ENST00000447079.4:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000447079	NM_015083.1	93	cGa/cAa	1/14	0.622750419275882	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.700775817210146	4		290	1193	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942738	44942752	+	inframe_deletion	In_Frame_Del	DEL	TCCTGCTTTTGTGCG	TCCTGCTTTTGTGCG	-	novel	NA	P-0000457-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	394	574	0	ENST00000377967.4:c.3319_3333del	p.Pro1107_Arg1111del	p.P1107_R1111del	ENST00000377967	NM_021140.2	1106	ctTCCTGCTTTTGTGCGt/ctt	23/29	NA	2	FACETS	0.764	0.732	0.795			1	INDETERMINATE	2	TRUE	NA	0.700775817210146	2		574	736	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000460-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	41	422	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		422	120	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591247	67591249	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	GGT	GGT	-	rs1131692243	NA	P-0000460-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	169	243	0	ENST00000274335.5:c.1748_1750del		p.X583_splice	ENST00000274335		583		13/15	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		243	532	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0000467-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	174	498	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.172582502004456	5	FACETS	0.961	0.892	1	0.961	0.892	1	INDETERMINATE	3	TRUE	2	0.374885984614187	5		498	503	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000467-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	54	422	0				ENST00000310581	NM_198253.2	-/1132			0.151300005469442	5	FACETS	0.944	0.823	1	0.708	0.617	0.802	INDETERMINATE	3	TRUE	1	0.374885984614187	5		422	159	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254973	16254973	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000475-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	83	255	0	ENST00000375759.3:c.2238G>T	p.Arg746Ser	p.R746S	ENST00000375759	NM_015001.2	746	agG/agT	11/15	1	2	FACETS	0.983	0.886	1	0.983	0.886	1	CLONAL	1	TRUE	1	0.827497293024691	2		255	204	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295249	1295249	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0000475-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	54	239	0				ENST00000310581	NM_198253.2	-/1132			0.823833940652289	4	FACETS	1	0.921	1	0.274	0.236	0.313	CLONAL	1	TRUE	0	0.827497293024691	4		239	218	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166836	32166836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000475-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	109	325	0	ENST00000375023.3:c.4402C>T	p.Leu1468Phe	p.L1468F	ENST00000375023	NM_004557.3	1468	Ctc/Ttc	24/30	0.827497293024691	4	FACETS	1	0.922	1	0.341	0.308	0.376	CLONAL	1	TRUE	1	0.827497293024691	4		325	470	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166917	32166917	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000475-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	52	172	0	ENST00000375023.3:c.4321C>T	p.Pro1441Ser	p.P1441S	ENST00000375023	NM_004557.3	1441	Cct/Tct	24/30	0.827497293024691	4	FACETS	0.873	0.75	1	0.291	0.25	0.336	CLONAL	1	TRUE	1	0.827497293024691	4		172	263	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133748322	133748322	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000475-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	125	484	0	ENST00000318560.5:c.983G>A	p.Arg328Lys	p.R328K	ENST00000318560	NM_005157.4	328	aGg/aAg	6/11	0.827497293024691	2	FACETS	0.65	0.592	0.71	0.325	0.296	0.355	SUBCLONAL	1	TRUE	0	0.827497293024691	2		484	465	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557507	21557507	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000475-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	140	524	0	ENST00000382592.4:c.2338G>T	p.Glu780Ter	p.E780*	ENST00000382592	NM_014572.2	780	Gag/Tag	5/8	0.827497293024691	3	FACETS	0.982	0.901	1	0.491	0.45	0.534	CLONAL	1	TRUE	1	0.827497293024691	3		524	487	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0000486-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	289	314	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.944	0.894	0.994	0.944	0.894	0.994	CLONAL	1	TRUE	1	0.900549351887656	2		314	680	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0000486-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	63	139	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.932	1			1	INDETERMINATE	1	TRUE	NA	0.900549351887656	2		139	132	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201688	66201688	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000486-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	599	575	0	ENST00000273854.3:c.2814C>A	p.Asn938Lys	p.N938K	ENST00000273854	NM_004439.5	938	aaC/aaA	16/18	1	2	FACETS	0.985	0.95	1	0.985	0.95	1	CLONAL	1	TRUE	1	0.900549351887656	2		575	1350	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469991	157469991	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000486-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	56	243	0	ENST00000346085.5:c.2786del	p.Pro929GlnfsTer10	p.P929Qfs*10	ENST00000346085	NM_020732.3	929	Cca/ca	9/20	1	2	FACETS	0.404	0.348	0.464	0.404	0.348	0.464	SUBCLONAL	1	TRUE	1	0.900549351887656	2		243	308	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	82	422	0				ENST00000310581	NM_198253.2	-/1132			0.153520578169542	2	FACETS	1	0.92	1	0.517	0.462	0.573	INDETERMINATE	1	TRUE	0	0.650551525357974	2		422	244	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	52	295	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.575843429701534	3	FACETS	0.699	0.599	0.808	0.233	0.199	0.27	SUBCLONAL	1	TRUE	0	0.650551525357974	3		295	303	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	21	142	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.575843429701534	3	FACETS	0.313	0.241	0.397	0.104	0.08	0.133	SUBCLONAL	1	TRUE	0	0.650551525357974	3		142	273	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122257	2122257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397515241	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	374	529	0	ENST00000219476.3:c.2113G>A	p.Val705Met	p.V705M	ENST00000219476	NM_000548.3	705	Gtg/Atg	20/42	0.650551525357974	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.650551525357974	2		529	560	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	847	531	1	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.650551525357974	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	4	TRUE	0	0.650551525357974	4		532	1033	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2645847	2645847	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1378928701	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	76	352	0	ENST00000342085.4:c.1397G>A	p.Arg466Gln	p.R466Q	ENST00000342085	NM_002613.4	466	cGg/cAg	12/14	0.650551525357974	2	FACETS	0.427	0.375	0.483	0.214	0.187	0.242	SUBCLONAL	1	TRUE	0	0.650551525357974	2		352	547	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254915	16254915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	68	225	0	ENST00000375759.3:c.2180G>A	p.Ser727Asn	p.S727N	ENST00000375759	NM_015001.2	727	aGt/aAt	11/15	0.444865791009574	4	FACETS	0.649	0.565	0.739			1	SUBCLONAL	1	TRUE	NA	0.650551525357974	4		225	532	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248012	59248012	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	609	340	0	ENST00000371222.2:c.731C>T	p.Pro244Leu	p.P244L	ENST00000371222	NM_002228.3	244	cCc/cTc	1/1	0.650551525357974	6	FACETS	1	0.99	1			1	CLONAL	3	TRUE	NA	0.650551525357974	6		340	1346	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204513812	204513812	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	37	102	0	ENST00000367182.3:c.822G>T	p.Lys274Asn	p.K274N	ENST00000367182	NM_001278516.1	274	aaG/aaT	9/11	0.621602490093061	4	FACETS	0.474	0.391	0.567	0.237	0.195	0.284	SUBCLONAL	1	TRUE	2	0.650551525357974	4		102	396	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567730	226567730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	104	480	0	ENST00000366794.5:c.1436C>T	p.Ser479Phe	p.S479F	ENST00000366794	NM_001618.3	479	tCc/tTc	10/23	0.621602490093061	4	FACETS	0.46	0.411	0.513	0.23	0.205	0.257	SUBCLONAL	1	TRUE	2	0.650551525357974	4		480	1146	SUCCESS
FH	2271	MSKCC	GRCh37	1	241671902	241671902	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	69	260	0	ENST00000366560.3:c.738+1G>A		p.X246_splice	ENST00000366560	NM_000143.3	246			0.621602490093061	4	FACETS	0.427	0.371	0.488	0.213	0.185	0.244	SUBCLONAL	1	TRUE	2	0.650551525357974	4		260	820	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469615	25469615	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	90	399	0	ENST00000264709.3:c.1153C>T	p.Pro385Ser	p.P385S	ENST00000264709	NM_175629.2	385	Ccg/Tcg	10/23	0.6071168815327	3	FACETS	0.442	0.392	0.496	0.221	0.196	0.248	SUBCLONAL	1	TRUE	1	0.650551525357974	3		399	829	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416556	29416556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	79	444	0	ENST00000389048.3:c.4397C>T	p.Pro1466Leu	p.P1466L	ENST00000389048	NM_004304.4	1466	cCt/cTt	29/29	0.6071168815327	3	FACETS	0.396	0.347	0.448	0.198	0.173	0.224	SUBCLONAL	1	TRUE	1	0.650551525357974	3		444	813	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635648	47635648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876658935	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	102	333	0	ENST00000233146.2:c.320C>T	p.Ala107Val	p.A107V	ENST00000233146	NM_000251.2	107	gCt/gTt	2/16	0.6071168815327	3	FACETS	0.476	0.425	0.53	0.238	0.212	0.265	SUBCLONAL	1	TRUE	1	0.650551525357974	3		333	873	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027494	48027494	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755587950	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	58	292	0	ENST00000234420.5:c.2372G>A	p.Arg791His	p.R791H	ENST00000234420	NM_000179.2	791	cGt/cAt	4/10	0.6071168815327	3	FACETS	0.409	0.351	0.472	0.204	0.175	0.236	SUBCLONAL	1	TRUE	1	0.650551525357974	3		292	578	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028264	48028264	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200492211	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	86	299	0	ENST00000234420.5:c.3142C>T	p.Gln1048Ter	p.Q1048*	ENST00000234420	NM_000179.2	1048	Cag/Tag	4/10	0.6071168815327	3	FACETS	0.446	0.394	0.502	0.223	0.197	0.251	SUBCLONAL	1	TRUE	1	0.650551525357974	3		299	786	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145338	61145338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	75	287	0	ENST00000295025.8:c.548C>T	p.Thr183Ile	p.T183I	ENST00000295025	NM_002908.2	183	aCt/aTt	6/11	0.6071168815327	3	FACETS	0.346	0.303	0.394	0.173	0.151	0.197	SUBCLONAL	1	TRUE	1	0.650551525357974	3		287	882	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149642	61149642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	40	122	0	ENST00000295025.8:c.1832C>T	p.Ser611Phe	p.S611F	ENST00000295025	NM_002908.2	611	tCc/tTc	11/11	0.6071168815327	3	FACETS	0.529	0.441	0.626	0.265	0.22	0.313	SUBCLONAL	1	TRUE	1	0.650551525357974	3		122	308	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172160	99172160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	347	305	0	ENST00000074304.5:c.1726C>T	p.Pro576Ser	p.P576S	ENST00000074304	NM_001134224.1	576	Ccg/Tcg	17/26	0.6071168815327	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.650551525357974	3		305	650	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172196	99172196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	54	356	0	ENST00000074304.5:c.1762C>T	p.Pro588Ser	p.P588S	ENST00000074304	NM_001134224.1	588	Ccc/Tcc	17/26	0.6071168815327	3	FACETS	0.317	0.27	0.368	0.158	0.135	0.184	SUBCLONAL	1	TRUE	1	0.650551525357974	3		356	695	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190708689	190708689	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	99	303	0	ENST00000441310.2:c.583-1G>A		p.X195_splice	ENST00000441310	NM_000534.4	195			0.650551525357974	1	FACETS	0.528	0.475	0.584	0.528	0.475	0.584	SUBCLONAL	1	TRUE	0	0.650551525357974	1		303	389	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728936	190728936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	50	136	0	ENST00000441310.2:c.2324C>T	p.Pro775Leu	p.P775L	ENST00000441310	NM_000534.4	775	cCa/cTa	10/13	0.650551525357974	1	FACETS	0.48	0.412	0.553	0.48	0.412	0.553	SUBCLONAL	1	TRUE	0	0.650551525357974	1		136	216	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691761	30691761	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	86	269	0	ENST00000295754.5:c.264-1G>A		p.X88_splice	ENST00000295754	NM_003242.5	88			0.621602490093061	4	FACETS	0.493	0.435	0.555	0.247	0.217	0.278	SUBCLONAL	1	TRUE	2	0.650551525357974	4		269	885	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442589	52442589	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	78	254	0	ENST00000460680.1:c.156G>A	p.Trp52Ter	p.W52*	ENST00000460680	NM_004656.3	52	tgG/tgA	4/17	0.621602490093061	4	FACETS	0.504	0.442	0.57	0.252	0.221	0.285	SUBCLONAL	1	TRUE	2	0.650551525357974	4		254	786	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102786	71102786	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	53	90	0	ENST00000318789.4:c.420+1G>A		p.X140_splice	ENST00000318789	NM_032682.5	140			0.621602490093061	4	FACETS	0.61	0.521	0.707	0.305	0.26	0.354	SUBCLONAL	1	TRUE	2	0.650551525357974	4		90	441	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391058	89391058	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	131	367	0	ENST00000336596.2:c.1124C>T	p.Pro375Leu	p.P375L	ENST00000336596	NM_005233.5	375	cCa/cTa	5/17	0.621602490093061	4	FACETS	0.59	0.534	0.649	0.295	0.267	0.325	SUBCLONAL	1	TRUE	2	0.650551525357974	4		367	1127	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391090	89391090	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	88	355	0	ENST00000336596.2:c.1156C>T	p.Gln386Ter	p.Q386*	ENST00000336596	NM_005233.5	386	Cag/Tag	5/17	0.621602490093061	4	FACETS	0.403	0.355	0.453	0.201	0.177	0.227	SUBCLONAL	1	TRUE	2	0.650551525357974	4		355	1109	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1795759	1795759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	126	259	0	ENST00000260795.2:c.98G>A	p.Gly33Glu	p.G33E	ENST00000260795		33	gGg/gAg	1/17	1	2	FACETS	0.971	0.887	1	0.971	0.887	1	CLONAL	1	TRUE	1	0.650551525357974	2		259	399	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294171	1294171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	51	241	0	ENST00000310581.5:c.830G>A	p.Arg277Lys	p.R277K	ENST00000310581	NM_198253.2	277	aGa/aAa	2/16	0.153520578169542	2	FACETS	0.42	0.358	0.488	0.21	0.179	0.244	INDETERMINATE	1	TRUE	0	0.650551525357974	2		241	373	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751934	57751934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200318957	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1174	109	505	0	ENST00000274289.3:c.1303G>A	p.Val435Ile	p.V435I	ENST00000274289	NM_006622.3	435	Gta/Ata	10/14	0.650551525357974	3	FACETS	0.346	0.31	0.385	0.173	0.155	0.193	SUBCLONAL	1	TRUE	1	0.650551525357974	3		505	1283	SUCCESS
APC	324	MSKCC	GRCh37	5	112175373	112175373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060503264	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	60	220	0	ENST00000257430.4:c.4082C>T	p.Pro1361Leu	p.P1361L	ENST00000257430	NM_000038.5	1361	cCc/cTc	16/16	0.650551525357974	3	FACETS	0.418	0.36	0.481	0.209	0.18	0.241	SUBCLONAL	1	TRUE	1	0.650551525357974	3		220	585	SUCCESS
APC	324	MSKCC	GRCh37	5	112179033	112179033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1203301360	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	58	232	0	ENST00000257430.4:c.7742G>A	p.Ser2581Asn	p.S2581N	ENST00000257430	NM_000038.5	2581	aGt/aAt	16/16	0.650551525357974	3	FACETS	0.423	0.364	0.489	0.212	0.182	0.245	SUBCLONAL	1	TRUE	1	0.650551525357974	3		232	558	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131976363	131976363	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	39	320	0	ENST00000265335.6:c.3619-1G>A		p.X1207_splice	ENST00000265335		1207			0.650551525357974	3	FACETS	0.251	0.207	0.3	0.126	0.103	0.15	SUBCLONAL	1	TRUE	1	0.650551525357974	3		320	633	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459734	149459734	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774005430	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	155	293	0	ENST00000286301.3:c.473C>T	p.Pro158Leu	p.P158L	ENST00000286301	NM_005211.3	158	cCc/cTc	4/22	0.650551525357974	3	FACETS	1	0.927	1	0.504	0.463	0.547	CLONAL	1	TRUE	1	0.650551525357974	3		293	626	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638669	176638669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	140	307	0	ENST00000439151.2:c.3269C>T	p.Pro1090Leu	p.P1090L	ENST00000439151	NM_022455.4	1090	cCc/cTc	5/23	0.142911596480408	3	FACETS	1	0.944	1	0.347	0.317	0.378	INDETERMINATE	1	TRUE	0	0.650551525357974	3		307	548	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176678794	176678794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	77	297	0	ENST00000439151.2:c.4705G>A	p.Glu1569Lys	p.E1569K	ENST00000439151	NM_022455.4	1569	Gag/Aag	12/23	0.142911596480408	3	FACETS	0.488	0.428	0.552	0.163	0.142	0.184	INDETERMINATE	1	TRUE	0	0.650551525357974	3		297	643	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052995	180052995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	71	331	0	ENST00000261937.6:c.1295C>T	p.Pro432Leu	p.P432L	ENST00000261937	NM_182925.4	432	cCc/cTc	10/30	0.142911596480408	3	FACETS	0.551	0.482	0.626	0.184	0.16	0.209	INDETERMINATE	1	TRUE	0	0.650551525357974	3		331	525	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673149	30673149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs927536226	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	74	341	0	ENST00000376406.3:c.3811G>A	p.Gly1271Arg	p.G1271R	ENST00000376406	NM_014641.2	1271	Gga/Aga	10/15	0.621602490093061	4	FACETS	0.525	0.459	0.596	0.263	0.229	0.298	SUBCLONAL	1	TRUE	2	0.650551525357974	4		341	715	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680376	30680376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	99	355	0	ENST00000376406.3:c.1343C>T	p.Thr448Ile	p.T448I	ENST00000376406	NM_014641.2	448	aCc/aTc	5/15	0.621602490093061	4	FACETS	0.511	0.455	0.57	0.255	0.227	0.285	SUBCLONAL	1	TRUE	2	0.650551525357974	4		355	984	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188323	32188323	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	96	467	0	ENST00000375023.3:c.1018C>T	p.His340Tyr	p.H340Y	ENST00000375023	NM_004557.3	340	Cac/Tac	6/30	0.303279390102155	4	FACETS	0.542	0.482	0.606			1	INDETERMINATE	1	TRUE	NA	0.650551525357974	4		467	899	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553267	106553267	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	108	388	0	ENST00000369096.4:c.1232C>T	p.Pro411Leu	p.P411L	ENST00000369096	NM_001198.3	411	cCc/cTc	5/7	0.621602490093061	4	FACETS	0.526	0.471	0.585	0.263	0.235	0.293	SUBCLONAL	1	TRUE	2	0.650551525357974	4		388	1041	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553644	106553644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1435567575	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	50	212	0	ENST00000369096.4:c.1609G>A	p.Ala537Thr	p.A537T	ENST00000369096	NM_001198.3	537	Gcg/Acg	5/7	0.621602490093061	4	FACETS	0.405	0.343	0.474	0.203	0.171	0.237	SUBCLONAL	1	TRUE	2	0.650551525357974	4		212	626	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005468	150005468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	70	376	0	ENST00000253339.5:c.757G>A	p.Gly253Ser	p.G253S	ENST00000253339		253	Ggc/Agc	3/7	0.621602490093061	4	FACETS	0.362	0.315	0.414	0.181	0.157	0.207	SUBCLONAL	1	TRUE	2	0.650551525357974	4		376	981	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129216	152129216	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1394	142	698	0	ENST00000206249.3:c.169G>A	p.Gly57Ser	p.G57S	ENST00000206249	NM_000125.3	57	Ggc/Agc	1/8	0.621602490093061	4	FACETS	0.469	0.426	0.515	0.235	0.213	0.258	SUBCLONAL	1	TRUE	2	0.650551525357974	4		698	1536	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510820	157510820	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	54	427	0	ENST00000346085.5:c.3595G>A	p.Gly1199Ser	p.G1199S	ENST00000346085	NM_020732.3	1199	Ggc/Agc	14/20	0.621602490093061	4	FACETS	0.284	0.242	0.331	0.142	0.121	0.166	SUBCLONAL	1	TRUE	2	0.650551525357974	4		427	964	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522401	157522401	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	54	316	0	ENST00000346085.5:c.4673C>T	p.Ser1558Phe	p.S1558F	ENST00000346085	NM_020732.3	1558	tCc/tTc	18/20	0.621602490093061	4	FACETS	0.324	0.276	0.377	0.162	0.138	0.189	SUBCLONAL	1	TRUE	2	0.650551525357974	4		316	845	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946186	13946186	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	67	312	0	ENST00000405192.2:c.910C>T	p.Pro304Ser	p.P304S	ENST00000405192	NM_001163147.1	304	Ccc/Tcc	10/12	0.621602490093061	4	FACETS	0.336	0.291	0.385	0.168	0.145	0.193	SUBCLONAL	1	TRUE	2	0.650551525357974	4		312	1012	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494257	140494257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1181422421	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	63	212	0	ENST00000288602.6:c.991C>T	p.Leu331Phe	p.L331F	ENST00000288602	NM_004333.4	331	Ctc/Ttc	8/18	0.621602490093061	4	FACETS	0.503	0.435	0.578	0.252	0.217	0.289	SUBCLONAL	1	TRUE	2	0.650551525357974	4		212	635	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151866285	151866285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	94	303	0	ENST00000262189.6:c.9503G>A	p.Gly3168Asp	p.G3168D	ENST00000262189	NM_170606.2	3168	gGt/gAt	41/59	0.621602490093061	4	FACETS	0.486	0.432	0.545	0.243	0.216	0.273	SUBCLONAL	1	TRUE	2	0.650551525357974	4		303	981	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751241	128751241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	63	210	0	ENST00000377970.2:c.778C>T	p.Pro260Ser	p.P260S	ENST00000377970	NM_002467.4	260	Ccg/Tcg	2/3	0.650551525357974	4	FACETS	0.651	0.564	0.745	0.326	0.282	0.373	SUBCLONAL	1	TRUE	2	0.650551525357974	4		210	491	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742112	145742112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561427528	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	23	123	0	ENST00000428558.2:c.391G>A	p.Gly131Arg	p.G131R	ENST00000428558	NM_004260.3	131	Gga/Aga	5/22	0.650551525357974	4	FACETS	0.393	0.306	0.493	0.196	0.153	0.247	SUBCLONAL	1	TRUE	2	0.650551525357974	4		123	297	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742871	145742871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1229615549	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	47	190	1	ENST00000428558.2:c.140C>T	p.Thr47Ile	p.T47I	ENST00000428558	NM_004260.3	47	aCt/aTt	3/22	0.650551525357974	4	FACETS	0.369	0.311	0.434	0.185	0.155	0.217	SUBCLONAL	1	TRUE	2	0.650551525357974	4		191	646	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089765	5089765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	129	321	0	ENST00000381652.3:c.2663C>T	p.Thr888Ile	p.T888I	ENST00000381652	NM_004972.3	888	aCt/aTt	20/25	0.650551525357974	2	FACETS	0.517	0.469	0.568	0.259	0.234	0.284	SUBCLONAL	1	TRUE	0	0.650551525357974	2		321	767	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639903	93639903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs551292916	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	53	204	0	ENST00000375746.1:c.1232C>T	p.Pro411Leu	p.P411L	ENST00000375746	NM_001174167.1	411	cCc/cTc	10/14	0.650551525357974	2	FACETS	0.444	0.38	0.514	0.222	0.19	0.257	SUBCLONAL	1	TRUE	0	0.650551525357974	2		204	367	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63760038	63760038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868152271	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	67	215	0	ENST00000279873.7:c.691C>T	p.His231Tyr	p.H231Y	ENST00000279873	NM_032199.2	231	Cac/Tac	4/10	0.650551525357974	4	FACETS	0.592	0.515	0.676			1	SUBCLONAL	1	TRUE	NA	0.650551525357974	4		215	574	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653805	89653805	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659443	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	699	290	0	ENST00000371953.3:c.103A>G	p.Met35Val	p.M35V	ENST00000371953	NM_000314.4	35	Atg/Gtg	2/9	0.650551525357974	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	0	0.650551525357974	3		290	936	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132866	64132866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	139	659	0	ENST00000334205.4:c.1000G>A	p.Glu334Lys	p.E334K	ENST00000334205	NM_003942.2	334	Gaa/Aaa	9/17	0.650551525357974	2	FACETS	0.588	0.536	0.642	0.294	0.268	0.321	SUBCLONAL	1	TRUE	0	0.650551525357974	2		659	727	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137234	64137234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465545014	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	84	501	0	ENST00000334205.4:c.1666C>T	p.Arg556Trp	p.R556W	ENST00000334205	NM_003942.2	556	Cgg/Tgg	14/17	0.650551525357974	2	FACETS	0.365	0.322	0.411	0.183	0.161	0.206	SUBCLONAL	1	TRUE	0	0.650551525357974	2		501	707	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77060283	77060283	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	92	255	0	ENST00000356341.3:c.885+1G>A		p.X295_splice	ENST00000356341	NM_002576.4	295			NA	2	FACETS	0.54	0.481	0.602			1	INDETERMINATE	1	TRUE	NA	0.650551525357974	2		255	524	SUCCESS
EED	8726	MSKCC	GRCh37	11	85979511	85979511	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	108	234	1	ENST00000263360.6:c.874C>T	p.Gln292Ter	p.Q292*	ENST00000263360	NM_003797.3	292	Cag/Tag	9/12	NA	2	FACETS	0.533	0.479	0.59			1	INDETERMINATE	1	TRUE	NA	0.650551525357974	2		235	623	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94209507	94209507	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779246843	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	124	493	0	ENST00000323929.3:c.607C>T	p.Pro203Ser	p.P203S	ENST00000323929	NM_005591.3	203	Cca/Tca	7/20	NA	2	FACETS	0.321	0.29	0.355			1	INDETERMINATE	1	TRUE	NA	0.650551525357974	2		493	1186	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419028	419028	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	648	466	1	ENST00000399788.2:c.3319C>A	p.Leu1107Met	p.L1107M	ENST00000399788	NM_001042603.1	1107	Ctg/Atg	22/28	0.650551525357974	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.650551525357974	2		467	974	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437202	49437202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	96	361	0	ENST00000301067.7:c.5477G>A	p.Gly1826Asp	p.G1826D	ENST00000301067	NM_003482.3	1826	gGt/gAt	24/54	0.647107093233997	2	FACETS	0.49	0.437	0.546	0.245	0.218	0.273	SUBCLONAL	1	TRUE	0	0.650551525357974	2		361	602	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233520	69233520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	438	340	0	ENST00000462284.1:c.1385G>A	p.Gly462Glu	p.G462E	ENST00000462284	NM_002392.5	462	gGa/gAa	11/11	0.647107093233997	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.650551525357974	2		340	614	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112191	115112191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1275992297	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	64	405	0	ENST00000257566.3:c.1549C>T	p.Pro517Ser	p.P517S	ENST00000257566	NM_016569.3	517	Ccg/Tcg	7/8	0.366340539914361	4	FACETS	0.478	0.413	0.548	0.239	0.206	0.274	INDETERMINATE	1	TRUE	2	0.650551525357974	4		405	680	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562457	21562457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554795068	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	24	84	0	ENST00000382592.4:c.1462G>A	p.Glu488Lys	p.E488K	ENST00000382592	NM_014572.2	488	Gag/Aag	4/8	0.650551525357974	1	FACETS	0.449	0.358	0.549	0.449	0.358	0.549	SUBCLONAL	1	TRUE	0	0.650551525357974	1		84	111	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32890661	32890661	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	51	369	1	ENST00000380152.3:c.64G>A	p.Ala22Thr	p.A22T	ENST00000380152		22	Gca/Aca	2/27	0.650551525357974	2	FACETS	0.184	0.156	0.215	0.092	0.078	0.108	SUBCLONAL	1	TRUE	0	0.650551525357974	2		370	852	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906933	32906933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	38	165	0	ENST00000380152.3:c.1318C>T	p.Leu440Phe	p.L440F	ENST00000380152		440	Ctt/Ttt	10/27	0.650551525357974	2	FACETS	0.419	0.348	0.497	0.209	0.174	0.249	SUBCLONAL	1	TRUE	0	0.650551525357974	2		165	279	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913900	32913900	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	116	349	0	ENST00000380152.3:c.5408C>T	p.Thr1803Ile	p.T1803I	ENST00000380152		1803	aCt/aTt	11/27	0.650551525357974	2	FACETS	0.53	0.478	0.584	0.265	0.239	0.292	SUBCLONAL	1	TRUE	0	0.650551525357974	2		349	673	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936983	48936983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690863	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	119	351	0	ENST00000267163.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000267163	NM_000321.2	251	Cga/Tga	8/27	0.650551525357974	2	FACETS	0.563	0.509	0.62	0.281	0.254	0.31	SUBCLONAL	1	TRUE	0	0.650551525357974	2		351	650	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436839	110436839	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	142	292	0	ENST00000375856.3:c.1562C>T	p.Pro521Leu	p.P521L	ENST00000375856	NM_003749.2	521	cCc/cTc	1/2	0.650551525357974	2	FACETS	0.678	0.619	0.739	0.339	0.309	0.37	SUBCLONAL	1	TRUE	0	0.650551525357974	2		292	644	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68290258	68290258	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	76	354	0	ENST00000487270.1:c.-2-1G>A		p.X1_splice	ENST00000487270	NM_133509.3	1			0.621602490093061	4	FACETS	0.323	0.282	0.367	0.161	0.141	0.184	SUBCLONAL	1	TRUE	2	0.650551525357974	4		354	1194	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473605	67473605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	87	318	2	ENST00000327367.4:c.685C>T	p.Pro229Ser	p.P229S	ENST00000327367	NM_005902.3	229	Ccg/Tcg	6/9	0.6071168815327	3	FACETS	0.492	0.435	0.552	0.246	0.217	0.276	SUBCLONAL	1	TRUE	1	0.650551525357974	3		320	721	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74000815	74000815	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	42	346	0	ENST00000318443.5:c.1504+1G>A		p.X502_splice	ENST00000318443	NM_001024736.1	502			0.6071168815327	3	FACETS	0.32	0.267	0.379	0.16	0.133	0.19	SUBCLONAL	1	TRUE	1	0.650551525357974	3		346	535	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630460	90630460	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	96	339	0	ENST00000330062.3:c.851G>A	p.Trp284Ter	p.W284*	ENST00000330062	NM_002168.2	284	tGg/tAg	7/11	0.6071168815327	3	FACETS	0.517	0.46	0.577	0.258	0.23	0.289	SUBCLONAL	1	TRUE	1	0.650551525357974	3		339	757	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129098	2129098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	70	343	0	ENST00000219476.3:c.3032C>T	p.Ala1011Val	p.A1011V	ENST00000219476	NM_000548.3	1011	gCt/gTt	27/42	0.650551525357974	2	FACETS	0.448	0.392	0.509	0.224	0.196	0.255	SUBCLONAL	1	TRUE	0	0.650551525357974	2		343	480	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779832	3779832	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	77	358	0	ENST00000262367.5:c.5216C>T	p.Ala1739Val	p.A1739V	ENST00000262367	NM_004380.2	1739	gCc/gTc	31/31	0.650551525357974	2	FACETS	0.461	0.406	0.521	0.231	0.203	0.261	SUBCLONAL	1	TRUE	0	0.650551525357974	2		358	513	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108284	8108284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	91	312	0	ENST00000585124.1:c.940G>A	p.Glu314Lys	p.E314K	ENST00000585124	NM_004217.3	314	Gaa/Aaa	9/9	0.650551525357974	4	FACETS	0.572	0.507	0.641	0.143	0.126	0.161	SUBCLONAL	1	TRUE	0	0.650551525357974	4		312	807	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11958301	11958301	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	61	175	0	ENST00000353533.5:c.211C>T	p.Pro71Ser	p.P71S	ENST00000353533	NM_003010.3	71	Cca/Tca	2/11	0.650551525357974	4	FACETS	0.517	0.446	0.594	0.129	0.111	0.149	SUBCLONAL	1	TRUE	0	0.650551525357974	4		175	599	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974908	15974908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1448	141	560	0	ENST00000268712.3:c.3967C>T	p.Pro1323Ser	p.P1323S	ENST00000268712	NM_006311.3	1323	Cct/Tct	30/46	0.650551525357974	4	FACETS	0.45	0.408	0.495	0.113	0.102	0.124	SUBCLONAL	1	TRUE	0	0.650551525357974	4		560	1589	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989670	15989670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	123	316	0	ENST00000268712.3:c.3103C>T	p.Pro1035Ser	p.P1035S	ENST00000268712	NM_006311.3	1035	Cct/Tct	23/46	0.650551525357974	4	FACETS	0.595	0.537	0.657	0.149	0.134	0.165	SUBCLONAL	1	TRUE	0	0.650551525357974	4		316	1049	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627775	37627775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1343	82	639	0	ENST00000447079.4:c.1690C>T	p.Pro564Ser	p.P564S	ENST00000447079	NM_015083.1	564	Cca/Tca	2/14	0.444865791009574	4	FACETS	0.292	0.256	0.331			1	SUBCLONAL	1	TRUE	NA	0.650551525357974	4		639	1425	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246661	41246661	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1184	151	484	0	ENST00000357654.3:c.887G>A	p.Arg296Lys	p.R296K	ENST00000357654	NM_007294.3	296	aGa/aAa	10/23	0.444865791009574	4	FACETS	0.574	0.523	0.628			1	SUBCLONAL	1	TRUE	NA	0.650551525357974	4		484	1335	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763410	59763410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	87	426	0	ENST00000259008.2:c.2692G>A	p.Asp898Asn	p.D898N	ENST00000259008	NM_032043.2	898	Gac/Aac	19/20	0.621602490093061	4	FACETS	0.364	0.321	0.411	0.182	0.16	0.206	SUBCLONAL	1	TRUE	2	0.650551525357974	4		426	1212	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857651	59857651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501769	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	96	324	0	ENST00000259008.2:c.1906G>A	p.Glu636Lys	p.E636K	ENST00000259008	NM_032043.2	636	Gag/Aag	13/20	0.621602490093061	4	FACETS	0.457	0.406	0.512	0.229	0.203	0.256	SUBCLONAL	1	TRUE	2	0.650551525357974	4		324	1065	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511676	66511676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	51	214	0	ENST00000358598.2:c.136C>T	p.Pro46Ser	p.P46S	ENST00000358598	NM_212471.2	46	Ccc/Tcc	2/11	0.621602490093061	4	FACETS	0.299	0.253	0.35	0.15	0.126	0.175	SUBCLONAL	1	TRUE	2	0.650551525357974	4		214	865	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119062	70119062	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	103	228	0	ENST00000245479.2:c.634C>T	p.Pro212Ser	p.P212S	ENST00000245479	NM_000346.3	212	Cca/Tca	2/3	0.621602490093061	4	FACETS	0.641	0.573	0.713	0.321	0.286	0.357	SUBCLONAL	1	TRUE	2	0.650551525357974	4		228	815	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207066	1207066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	422	382	0	ENST00000326873.7:c.154G>A	p.Gly52Arg	p.G52R	ENST00000326873	NM_000455.4	52	Ggg/Agg	1/10	0.366340539914361	4	FACETS	1	0.985	1	1	0.985	1	INDETERMINATE	2	TRUE	2	0.650551525357974	4		382	1004	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2185894	2185894	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	138	523	0	ENST00000398665.3:c.166G>A	p.Glu56Lys	p.E56K	ENST00000398665	NM_032482.2	56	Gag/Aag	3/28	0.366340539914361	4	FACETS	0.543	0.493	0.597	0.272	0.246	0.299	INDETERMINATE	1	TRUE	2	0.650551525357974	4		523	1289	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216731	2216731	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1307709868	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	37	217	0	ENST00000398665.3:c.2375C>T	p.Pro792Leu	p.P792L	ENST00000398665	NM_032482.2	792	cCc/cTc	20/28	0.366340539914361	4	FACETS	0.454	0.374	0.542	0.227	0.187	0.271	INDETERMINATE	1	TRUE	2	0.650551525357974	4		217	414	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226593	2226593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	50	353	1	ENST00000398665.3:c.4073G>A	p.Gly1358Asp	p.G1358D	ENST00000398665	NM_032482.2	1358	gGc/gAc	27/28	0.366340539914361	4	FACETS	0.39	0.33	0.456	0.195	0.165	0.228	INDETERMINATE	1	TRUE	2	0.650551525357974	4		354	650	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231522	5231522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	73	477	0	ENST00000357368.4:c.1954G>A	p.Val652Met	p.V652M	ENST00000357368	NM_002850.3	652	Gtg/Atg	14/38	0.359146554307107	3	FACETS	0.301	0.263	0.343	0.151	0.131	0.172	INDETERMINATE	1	TRUE	1	0.650551525357974	3		477	987	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10252841	10252841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	35	252	0	ENST00000340748.4:c.3124C>T	p.Leu1042Phe	p.L1042F	ENST00000340748		1042	Ctc/Ttc	29/40	0.359146554307107	3	FACETS	0.242	0.197	0.292	0.121	0.098	0.146	INDETERMINATE	1	TRUE	1	0.650551525357974	3		252	590	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10259662	10259662	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772216000	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	71	426	0	ENST00000340748.4:c.2570G>A	p.Gly857Glu	p.G857E	ENST00000340748		857	gGg/gAg	26/40	0.359146554307107	3	FACETS	0.358	0.312	0.408	0.179	0.156	0.204	INDETERMINATE	1	TRUE	1	0.650551525357974	3		426	808	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096076	11096076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759594383	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	39	299	1	ENST00000358026.2:c.350C>T	p.Ser117Phe	p.S117F	ENST00000358026	NM_001128849.1	117	tCc/tTc	3/36	0.359146554307107	3	FACETS	0.293	0.242	0.349	0.146	0.121	0.175	INDETERMINATE	1	TRUE	1	0.650551525357974	3		300	543	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097076	11097076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	84	504	1	ENST00000358026.2:c.567G>A	p.Met189Ile	p.M189I	ENST00000358026	NM_001128849.1	189	atG/atA	4/36	0.359146554307107	3	FACETS	0.377	0.332	0.425	0.188	0.166	0.213	INDETERMINATE	1	TRUE	1	0.650551525357974	3		505	908	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290037	15290037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	78	494	0	ENST00000263388.2:c.3517G>A	p.Gly1173Arg	p.G1173R	ENST00000263388	NM_000435.2	1173	Ggg/Agg	22/33	0.359146554307107	3	FACETS	0.324	0.283	0.367	0.162	0.141	0.184	INDETERMINATE	1	TRUE	1	0.650551525357974	3		494	982	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955135	17955135	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	40	313	0	ENST00000458235.1:c.92C>T	p.Pro31Leu	p.P31L	ENST00000458235	NM_000215.3	31	cCc/cTc	2/24	0.407411061962981	4	FACETS	0.382	0.317	0.455	0.191	0.158	0.228	SUBCLONAL	1	TRUE	2	0.650551525357974	4		313	531	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795381	42795381	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	33	264	0	ENST00000575354.2:c.2461G>A	p.Gly821Arg	p.G821R	ENST00000575354	NM_015125.3	821	Gga/Aga	10/20	0.407411061962981	4	FACETS	0.332	0.27	0.403	0.166	0.135	0.202	SUBCLONAL	1	TRUE	2	0.650551525357974	4		264	504	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019389	31019389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	58	378	0	ENST00000375687.4:c.886G>A	p.Gly296Arg	p.G296R	ENST00000375687	NM_015338.5	296	Ggg/Agg	10/13	0.407411061962981	4	FACETS	0.291	0.249	0.338	0.146	0.124	0.169	SUBCLONAL	1	TRUE	2	0.650551525357974	4		378	1010	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400142	41400142	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	50	291	0	ENST00000373198.4:c.617G>A	p.Gly206Glu	p.G206E	ENST00000373198	NM_133170.3	206	gGg/gAg	5/32	0.407411061962981	4	FACETS	0.323	0.273	0.378	0.161	0.136	0.189	SUBCLONAL	1	TRUE	2	0.650551525357974	4		291	786	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41553210	41553210	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	94	396	0	ENST00000263253.7:c.3299C>T	p.Ser1100Phe	p.S1100F	ENST00000263253	NM_001429.3	1100	tCt/tTt	18/31	0.650551525357974	2	FACETS	0.459	0.408	0.512	0.229	0.204	0.256	SUBCLONAL	1	TRUE	0	0.650551525357974	2		396	630	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227057	53227057	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	486	232	0	ENST00000375401.3:c.2518C>T	p.Pro840Ser	p.P840S	ENST00000375401	NM_004187.3	840	Ccc/Tcc	18/26	0.543012780305513	2	FACETS	0.854	0.835	0.873			1	CLONAL	3	TRUE	NA	0.650551525357974	2		232	583	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019967	123019967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	533	261	0	ENST00000355640.3:c.455C>T	p.Thr152Ile	p.T152I	ENST00000355640		152	aCc/aTc	2/7	0.543012780305513	2	FACETS	0.835	0.816	0.854			1	CLONAL	3	TRUE	NA	0.650551525357974	2		261	654	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033955	49033956	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0000500-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	240	253	0	ENST00000267163.4:c.2092_2093del	p.Arg698AlafsTer22	p.R698Afs*22	ENST00000267163	NM_000321.2	698	AGg/g	20/27	0.650551525357974	2	FACETS	0.956	0.91	1	0.956	0.91	1	CLONAL	2	TRUE	0	0.650551525357974	2		253	386	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000506-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	98	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.793253897864617	2		422	216	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789580	3789580	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000506-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	340	281	1	ENST00000262367.5:c.4279A>T	p.Arg1427Trp	p.R1427W	ENST00000262367	NM_004380.2	1427	Agg/Tgg	25/31	0.143467303128614	3	FACETS	0.895	0.854	0.935	0.895	0.854	0.935	INDETERMINATE	2	TRUE	1	0.793253897864617	3		282	669	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835698	68835698	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000506-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	112	483	0	ENST00000261769.5:c.289C>A	p.His97Asn	p.H97N	ENST00000261769	NM_004360.3	97	Cat/Aat	3/16	0.637285680496209	1	FACETS	0.27	0.243	0.298	0.27	0.243	0.298	SUBCLONAL	1	TRUE	0	0.793253897864617	1		483	631	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343516	118343522	+	frameshift_variant	Frame_Shift_Del	DEL	ACTCTAC	ACTCTAC	-	novel	NA	P-0000506-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	120	227	0	ENST00000534358.1:c.1643_1649del	p.Thr548LysfsTer17	p.T548Kfs*17	ENST00000534358	NM_005933.3	548	ACTCTACaa/aa	3/36	1	2	FACETS	0.745	0.679	0.814	0.745	0.679	0.814	SUBCLONAL	1	TRUE	1	0.793253897864617	2		227	406	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0000516-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	115	536	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.27151182315713	3	FACETS	1	0.921	1	0.678	0.615	0.743	CLONAL	2	TRUE	0	0.306249224886873	3		536	426	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519922	NA	P-0000516-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	139	687	0	ENST00000397062.3:c.235G>C	p.Glu79Gln	p.E79Q	ENST00000397062	NM_006164.4	79	Gag/Cag	2/5	0.306249224886873	4	FACETS	1	0.986	1	0.73	0.665	0.799	CLONAL	1	TRUE	2	0.306249224886873	4		687	812	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521613	89521613	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0000516-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	52	271	0	ENST00000336596.2:c.2691-1G>T		p.X897_splice	ENST00000336596	NM_005233.5	897			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.306249224886873	2		271	269	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200118	128200118	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000516-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	73	307	0	ENST00000341105.2:c.1187G>T	p.Arg396Leu	p.R396L	ENST00000341105	NM_032638.4	396	cGg/cTg	6/6	0.306249224886873	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.306249224886873	3		307	244	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193967	106193967	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000516-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	54	275	0	ENST00000380013.4:c.4429G>T	p.Glu1477Ter	p.E1477*	ENST00000380013	NM_001127208.2	1477	Gaa/Taa	10/11	0.306249224886873	3	FACETS	1	0.896	1	0.528	0.452	0.61	CLONAL	1	TRUE	1	0.306249224886873	3		275	385	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931460	131931460	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1173949737	NA	P-0000516-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	47	224	0	ENST00000265335.6:c.2165A>G	p.Lys722Arg	p.K722R	ENST00000265335		722	aAg/aGg	13/25	0.233579590581458	4	FACETS	1	0.956	1	0.691	0.587	0.805	CLONAL	1	TRUE	2	0.306249224886873	4		224	290	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913381	NA	P-0000516-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	105	201	0	ENST00000304494.5:c.322G>T	p.Asp108Tyr	p.D108Y	ENST00000304494	NM_000077.4	108	Gat/Tat	2/3	0.306249224886873	4	FACETS	0.892	0.814	0.971	1	0.974	1	CLONAL	4	TRUE	1	0.306249224886873	4		201	251	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22143028	22143028	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000516-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	86	475	0	ENST00000215832.6:c.679A>T	p.Ile227Phe	p.I227F	ENST00000215832	NM_002745.4	227	Atc/Ttc	5/9	0.306249224886873	5	FACETS	1	0.974	1			1	CLONAL	1	TRUE	NA	0.306249224886873	5		475	596	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911520	39911520	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000516-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	88	353	0	ENST00000378444.4:c.5110A>C	p.Ser1704Arg	p.S1704R	ENST00000378444	NM_001123385.1	1704	Agt/Cgt	15/15	0.22140327318062	2	FACETS	1	0.96	1			1	CLONAL	2	TRUE	NA	0.306249224886873	2		353	253	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000533-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	30	422	0				ENST00000310581	NM_198253.2	-/1132			0.186296632106847	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		422	94	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0000533-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	274	310	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.132141190375613	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		310	820	SUCCESS
ATM	472	MSKCC	GRCh37	11	108224586	108224586	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000533-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	116	346	0	ENST00000278616.4:c.8765G>T	p.Gly2922Val	p.G2922V	ENST00000278616	NM_000051.3	2922	gGt/gTt	60/63	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		346	371	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0000533-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	67	169	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		169	365	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0000580-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	608	262	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.356030729455319	5	FACETS	0.867	0.837	0.897	0.867	0.837	0.897	INDETERMINATE	3	TRUE	2	0.833722102929965	5		262	1262	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0000580-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1303	198	354	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.356030729455319	5	FACETS	0.712	0.657	0.769	0.237	0.219	0.257	INDETERMINATE	1	TRUE	2	0.833722102929965	5		354	1501	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794824	242794824	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000580-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	418	324	0	ENST00000334409.5:c.385G>T	p.Ala129Ser	p.A129S	ENST00000334409	NM_005018.2	129	Gcc/Tcc	2/5	0.423514042648333	2	FACETS	1	0.997	1	0.749	0.722	0.776	INDETERMINATE	1	TRUE	0	0.833722102929965	2		324	669	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295217	1295217	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs796849347	NA	P-0000580-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	76	120	0				ENST00000310581	NM_198253.2	-/1132			0.274344927924656	5	FACETS	0.906	0.797	1			1	INDETERMINATE	1	TRUE	NA	0.833722102929965	5		120	453	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381563	81381563	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000580-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	530	480	0	ENST00000222390.5:c.498C>G	p.Ser166Arg	p.S166R	ENST00000222390	NM_000601.4	166	agC/agG	5/18	0.833722102929965	2	FACETS	0.985	0.946	1	0.492	0.473	0.512	CLONAL	1	TRUE	0	0.833722102929965	2		480	1291	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578538	7578538	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1131691037	NA	P-0000580-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	512	293	0	ENST00000269305.4:c.392A>T	p.Asn131Ile	p.N131I	ENST00000269305	NM_001126112.2	131	aAc/aTc	5/11	0.833722102929965	2	FACETS	0.967	0.944	0.989	0.967	0.944	0.989	CLONAL	2	TRUE	0	0.833722102929965	2		293	635	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576117	29576117	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000580-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2081	582	475	0	ENST00000356175.3:c.4090G>T	p.Val1364Leu	p.V1364L	ENST00000356175	NM_000267.3	1364	Gtg/Ttg	30/57	0.833722102929965	4	FACETS	0.961	0.92	1			1	CLONAL	1	TRUE	NA	0.833722102929965	4		475	2663	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438255	56438255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000580-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	424	294	3	ENST00000407977.2:c.738G>T	p.Arg246Ser	p.R246S	ENST00000407977		246	agG/agT	7/10	0.833722102929965	5	FACETS	1	0.995	1	0.487	0.463	0.511	CLONAL	1	TRUE	2	0.833722102929965	5		297	1568	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105618	11105618	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000580-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	268	279	0	ENST00000358026.2:c.1534G>T	p.Glu512Ter	p.E512*	ENST00000358026	NM_001128849.1	512	Gag/Tag	9/36	0.134764269948317	3	FACETS	1	0.969	1	0.349	0.327	0.37	INDETERMINATE	1	TRUE	0	0.833722102929965	3		279	871	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101152	41101152	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000580-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	107	167	0	ENST00000373198.4:c.1204C>A	p.Gln402Lys	p.Q402K	ENST00000373198	NM_133170.3	402	Cag/Aag	8/32	0.274344927924656	5	FACETS	0.775	0.696	0.86			1	INDETERMINATE	1	TRUE	NA	0.833722102929965	5		167	745	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	145	264	2	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.739114238029009	3	FACETS	0.905	0.841	0.968	0.905	0.841	0.968	CLONAL	2	TRUE	1	0.739114238029009	3		266	297	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	145	139	0				ENST00000310581	NM_198253.2	-/1132			0.556469455584452	5	FACETS	0.971	0.916	1			1	CLONAL	4	TRUE	NA	0.739114238029009	5		139	213	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393656	139393656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196509879	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	117	290	0	ENST00000277541.6:c.5990C>T	p.Thr1997Met	p.T1997M	ENST00000277541	NM_017617.3	1997	aCg/aTg	32/34	0.417434907213397	3	FACETS	0.758	0.695	0.822			1	INDETERMINATE	2	TRUE	NA	0.739114238029009	3		290	286	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16203076	16203076	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	197	186	0	ENST00000375759.3:c.784G>T	p.Ala262Ser	p.A262S	ENST00000375759	NM_015001.2	262	Gca/Tca	3/15	0.739114238029009	3	FACETS	0.951	0.894	1	0.951	0.894	1	CLONAL	2	TRUE	1	0.739114238029009	3		186	384	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468324	120468324	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587610159	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	149	231	0	ENST00000256646.2:c.4115G>A	p.Arg1372Gln	p.R1372Q	ENST00000256646	NM_024408.3	1372	cGg/cAg	25/34	0.739114238029009	3	FACETS	0.908	0.845	0.971	0.908	0.845	0.971	CLONAL	2	TRUE	1	0.739114238029009	3		231	304	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506432	120506432	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	178	327	0	ENST00000256646.2:c.1682-2A>C		p.X561_splice	ENST00000256646	NM_024408.3	561			0.739114238029009	3	FACETS	1	0.965	1	0.535	0.495	0.575	CLONAL	1	TRUE	1	0.739114238029009	3		327	617	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162749986	162749986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	305	386	0	ENST00000367921.3:c.2518C>T	p.Pro840Ser	p.P840S	ENST00000367921	NM_006182.2	840	Ccc/Tcc	18/18	0.31576150320811	6	FACETS	1	0.991	1	0.823	0.779	0.868	INDETERMINATE	2	TRUE	3	0.739114238029009	6		386	828	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828186	243828186	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	257	299	0	ENST00000263826.5:c.173-1G>A		p.X58_splice	ENST00000263826	NM_005465.4	58			0.739114238029009	3	FACETS	1	0.992	1			1	CLONAL	1	TRUE	NA	0.739114238029009	3		299	719	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416302	29416302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	173	408	0	ENST00000389048.3:c.4651C>T	p.Pro1551Ser	p.P1551S	ENST00000389048	NM_004304.4	1551	Ccg/Tcg	29/29	0.739114238029009	3	FACETS	0.954	0.881	1	0.477	0.44	0.515	CLONAL	1	TRUE	1	0.739114238029009	3		408	672	SUCCESS
ALK	238	MSKCC	GRCh37	2	29450440	29450440	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	149	440	0	ENST00000389048.3:c.2914G>A	p.Val972Met	p.V972M	ENST00000389048	NM_004304.4	972	Gtg/Atg	17/29	0.739114238029009	3	FACETS	0.979	0.899	1	0.49	0.449	0.531	CLONAL	1	TRUE	1	0.739114238029009	3		440	564	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098815	178098815	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	645	599	0	ENST00000397062.3:c.230A>G	p.Asp77Gly	p.D77G	ENST00000397062	NM_006164.4	77	gAt/gGt	2/5	0.739114238029009	3	FACETS	0.997	0.965	1	0.997	0.965	1	CLONAL	2	TRUE	1	0.739114238029009	3		599	1199	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141568	202141568	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	349	447	0	ENST00000358485.4:c.856C>T	p.Gln286Ter	p.Q286*	ENST00000358485	NM_001080125.1	286	Caa/Taa	7/9	0.739114238029009	3	FACETS	0.904	0.863	0.946	0.904	0.863	0.946	CLONAL	2	TRUE	1	0.739114238029009	3		447	715	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279214	142279214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371017404	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	458	420	0	ENST00000350721.4:c.1432G>A	p.Glu478Lys	p.E478K	ENST00000350721	NM_001184.3	478	Gaa/Aaa	6/47	0.704044388928957	3	FACETS	0.942	0.905	0.979	0.942	0.905	0.979	CLONAL	2	TRUE	1	0.739114238029009	3		420	901	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526287	189526287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	187	292	0	ENST00000264731.3:c.551C>T	p.Ser184Leu	p.S184L	ENST00000264731	NM_003722.4	184	tCg/tTg	4/14	0.31576150320811	6	FACETS	1	0.936	1	0.672	0.624	0.722	INDETERMINATE	2	TRUE	3	0.739114238029009	6		292	622	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157371	106157371	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs746152042	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	355	221	1	ENST00000380013.4:c.2272C>T	p.Gln758Ter	p.Q758*	ENST00000380013	NM_001127208.2	758	Cag/Tag	3/11	0.739114238029009	4	FACETS	0.914	0.877	0.952	0.914	0.877	0.952	CLONAL	3	TRUE	1	0.739114238029009	4		222	609	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541114	187541114	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748292089	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	347	270	0	ENST00000441802.2:c.6626C>T	p.Pro2209Leu	p.P2209L	ENST00000441802	NM_005245.3	2209	cCg/cTg	10/27	0.598036171795854	4	FACETS	0.99	0.951	1	1	0.996	1	CLONAL	3	TRUE	2	0.739114238029009	4		270	550	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38942955	38942955	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	526	258	0	ENST00000357387.3:c.5032C>T	p.Gln1678Ter	p.Q1678*	ENST00000357387	NM_152756.3	1678	Caa/Taa	37/38	0.739114238029009	6	FACETS	1	0.99	1	0.806	0.776	0.836	CLONAL	3	TRUE	2	0.739114238029009	6		258	1094	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520282	176520282	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	99	292	0	ENST00000292408.4:c.1201C>G	p.Arg401Gly	p.R401G	ENST00000292408	NM_213647.1	401	Cgc/Ggc	9/18	0.739114238029009	3	FACETS	0.838	0.764	0.912	0.838	0.764	0.912	CLONAL	2	TRUE	1	0.739114238029009	3		292	219	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023057	150023057	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1326453282	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	491	563	0	ENST00000253339.5:c.206C>T	p.Pro69Leu	p.P69L	ENST00000253339		69	cCc/cTc	1/7	0.454982776910726	4	FACETS	0.97	0.93	1			1	CLONAL	2	TRUE	NA	0.739114238029009	4		563	1191	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426893	6426893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519948	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	454	383	2	ENST00000356142.4:c.86C>T	p.Pro29Leu	p.P29L	ENST00000356142	NM_018890.3	29	cCt/cTt	2/7	0.704044388928957	3	FACETS	0.985	0.947	1	0.985	0.947	1	CLONAL	2	TRUE	1	0.739114238029009	3		385	854	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341919	8341919	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs747414574	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	1128	419	0	ENST00000356435.5:c.4721A>C	p.Lys1574Thr	p.K1574T	ENST00000356435		1574	aAg/aCg	29/35	0.739114238029009	7	FACETS	1	0.995	1			1	CLONAL	5	TRUE	NA	0.739114238029009	7		419	1650	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485940	8485940	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	1035	473	0	ENST00000356435.5:c.2877G>T	p.Arg959Ser	p.R959S	ENST00000356435		959	agG/agT	17/35	0.739114238029009	7	FACETS	1	0.994	1			1	CLONAL	5	TRUE	NA	0.739114238029009	7		473	1532	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521469	8521469	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	328	359	0	ENST00000356435.5:c.769T>A	p.Cys257Ser	p.C257S	ENST00000356435		257	Tgt/Agt	9/35	0.739114238029009	7	FACETS	0.836	0.788	0.886			1	CLONAL	2	TRUE	NA	0.739114238029009	7		359	1511	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339230	87339230	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	333	287	0	ENST00000277120.3:c.812T>G	p.Leu271Arg	p.L271R	ENST00000277120		271	cTt/cGt	8/19	0.31576150320811	6	FACETS	0.904	0.859	0.95	0.904	0.859	0.95	INDETERMINATE	3	TRUE	3	0.739114238029009	6		287	823	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637098	93637098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	274	287	0	ENST00000375746.1:c.1148G>A	p.Gly383Glu	p.G383E	ENST00000375746	NM_001174167.1	383	gGa/gAa	9/14	0.31576150320811	6	FACETS	0.895	0.846	0.946	0.895	0.846	0.946	INDETERMINATE	3	TRUE	3	0.739114238029009	6		287	684	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750384	133750384	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	281	561	0	ENST00000318560.5:c.1215G>A	p.Trp405Ter	p.W405*	ENST00000318560	NM_005157.4	405	tgG/tgA	7/11	0.31576150320811	6	FACETS	0.917	0.867	0.967	0.917	0.867	0.967	INDETERMINATE	3	TRUE	3	0.739114238029009	6		561	685	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391196	139391196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	126	280	0	ENST00000277541.6:c.6995C>T	p.Pro2332Leu	p.P2332L	ENST00000277541	NM_017617.3	2332	cCa/cTa	34/34	0.417434907213397	3	FACETS	0.765	0.704	0.828			1	INDETERMINATE	2	TRUE	NA	0.739114238029009	3		280	305	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595906	43595906	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	112	443	0	ENST00000355710.3:c.74-1G>A		p.X25_splice	ENST00000355710	NM_020975.4	25			0.704044388928957	3	FACETS	0.956	0.866	1	0.478	0.433	0.525	CLONAL	1	TRUE	1	0.739114238029009	3		443	434	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446209	70446209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	318	438	0	ENST00000373644.4:c.5149G>A	p.Asp1717Asn	p.D1717N	ENST00000373644	NM_030625.2	1717	Gat/Aat	11/12	0.262038689203966	3	FACETS	0.976	0.931	1			1	INDETERMINATE	2	TRUE	NA	0.739114238029009	3		438	604	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451230	70451230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1222112424	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	136	333	1	ENST00000373644.4:c.6070C>T	p.Arg2024Trp	p.R2024W	ENST00000373644	NM_030625.2	2024	Cgg/Tgg	12/12	0.262038689203966	3	FACETS	1	0.947	1			1	INDETERMINATE	1	TRUE	NA	0.739114238029009	3		334	482	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8284891	8284891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	266	569	0	ENST00000335790.3:c.19G>A	p.Glu7Lys	p.E7K	ENST00000335790	NM_002315.2	7	Gag/Aag	1/4	0.704044388928957	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.739114238029009	3		569	483	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246137	46246137	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	345	255	0	ENST00000334344.6:c.4231C>T	p.Gln1411Ter	p.Q1411*	ENST00000334344	NM_152641.2	1411	Caa/Taa	15/21	0.739114238029009	3	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	1	0.739114238029009	3		255	594	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431861	49431861	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	119	263	1	ENST00000301067.7:c.9278C>T	p.Pro3093Leu	p.P3093L	ENST00000301067	NM_003482.3	3093	cCc/cTc	34/54	0.739114238029009	3	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	1	0.739114238029009	3		264	217	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443980	49443980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777323898	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	95	298	0	ENST00000301067.7:c.3391C>T	p.Pro1131Ser	p.P1131S	ENST00000301067	NM_003482.3	1131	Ccg/Tcg	11/54	0.739114238029009	3	FACETS	0.867	0.777	0.962	0.434	0.388	0.481	CLONAL	1	TRUE	1	0.739114238029009	3		298	406	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913332	28913332	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	196	507	0	ENST00000282397.4:c.2461G>A	p.Glu821Lys	p.E821K	ENST00000282397	NM_002019.4	821	Gag/Aag	17/30	0.23391737051251	3	FACETS	0.97	0.9	1	0.323	0.3	0.347	INDETERMINATE	1	TRUE	0	0.739114238029009	3		507	749	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012396	29012396	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1475917029	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	211	407	0	ENST00000282397.4:c.475C>T	p.Arg159Trp	p.R159W	ENST00000282397	NM_002019.4	159	Cgg/Tgg	4/30	0.23391737051251	3	FACETS	1	0.962	1	0.349	0.325	0.374	INDETERMINATE	1	TRUE	0	0.739114238029009	3		407	746	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32930724	32930724	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs967458408	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	128	307	0	ENST00000380152.3:c.7595C>T	p.Pro2532Leu	p.P2532L	ENST00000380152		2532	cCc/cTc	15/27	0.739114238029009	3	FACETS	0.837	0.761	0.915	0.418	0.38	0.458	CLONAL	1	TRUE	1	0.739114238029009	3		307	567	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514007	103514007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	142	298	0	ENST00000355739.4:c.823G>A	p.Glu275Lys	p.E275K	ENST00000355739	NM_000123.3	275	Gag/Aag	7/15	0.739114238029009	3	FACETS	0.971	0.89	1	0.485	0.445	0.528	CLONAL	1	TRUE	1	0.739114238029009	3		298	542	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68353854	68353854	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	489	387	1	ENST00000487270.1:c.689A>G	p.Glu230Gly	p.E230G	ENST00000487270	NM_133509.3	230	gAa/gGa	7/11	0.702915114410787	4	FACETS	0.924	0.886	0.963	0.924	0.886	0.963	CLONAL	2	TRUE	2	0.739114238029009	4		388	1245	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032038	10032038	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	143	578	0	ENST00000330684.3:c.785C>T	p.Ser262Phe	p.S262F	ENST00000330684	NM_001134407.1	262	tCt/tTt	3/13	0.23391737051251	3	FACETS	0.872	0.798	0.949	0.291	0.266	0.317	INDETERMINATE	1	TRUE	0	0.739114238029009	3		578	608	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041849	14041849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs968717590	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	351	457	0	ENST00000311895.7:c.2396G>A	p.Arg799Gln	p.R799Q	ENST00000311895	NM_005236.2	799	cGg/cAg	11/11	0.739114238029009	3	FACETS	0.966	0.924	1			1	CLONAL	2	TRUE	NA	0.739114238029009	3		457	673	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041923	14041923	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	145	346	0	ENST00000311895.7:c.2470G>A	p.Asp824Asn	p.D824N	ENST00000311895	NM_005236.2	824	Gat/Aat	11/11	0.739114238029009	3	FACETS	1	0.921	1			1	CLONAL	1	TRUE	NA	0.739114238029009	3		346	535	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647610	23647610	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	223	408	0	ENST00000261584.4:c.257C>T	p.Thr86Ile	p.T86I	ENST00000261584	NM_024675.3	86	aCc/aTc	4/13	0.739114238029009	3	FACETS	0.98	0.915	1			1	CLONAL	1	TRUE	NA	0.739114238029009	3		408	843	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782006	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	176	484	0	ENST00000269305.4:c.859G>A	p.Glu287Lys	p.E287K	ENST00000269305	NM_001126112.2	287	Gag/Aag	8/11	0.739114238029009	3	FACETS	1	0.982	1	0.591	0.548	0.635	CLONAL	1	TRUE	1	0.739114238029009	3		484	552	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682533	37682533	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	82	212	0	ENST00000447079.4:c.3724C>T	p.Arg1242Ter	p.R1242*	ENST00000447079	NM_015083.1	1242	Cga/Tga	13/14	0.739114238029009	3	FACETS	0.833	0.739	0.931	0.416	0.369	0.466	CLONAL	1	TRUE	1	0.739114238029009	3		212	365	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747087	40747087	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	270	388	0	ENST00000373198.4:c.2995T>G	p.Ser999Ala	p.S999A	ENST00000373198	NM_133170.3	999	Tcc/Gcc	22/32	0.454982776910726	4	FACETS	0.993	0.938	1			1	CLONAL	2	TRUE	NA	0.739114238029009	4		388	640	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40864896	40864896	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	250	337	0	ENST00000373198.4:c.2372G>A	p.Arg791Lys	p.R791K	ENST00000373198	NM_133170.3	791	aGa/aAa	16/32	0.454982776910726	4	FACETS	0.886	0.834	0.939			1	CLONAL	2	TRUE	NA	0.739114238029009	4		337	664	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572413	41572413	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	220	348	0	ENST00000263253.7:c.4942C>T	p.Gln1648Ter	p.Q1648*	ENST00000263253	NM_001429.3	1648	Cag/Tag	30/31	0.573644429554472	4	FACETS	0.973	0.914	1	0.973	0.914	1	CLONAL	2	TRUE	2	0.739114238029009	4		348	532	SUCCESS
AR	367	MSKCC	GRCh37	X	66765779	66765779	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	294	733	0	ENST00000374690.3:c.791G>A	p.Arg264Gln	p.R264Q	ENST00000374690	NM_000044.3	264	cGg/cAg	1/8	0.545637262645188	3	FACETS	1	0.994	1	0.73	0.691	0.77	CLONAL	1	TRUE	1	0.739114238029009	3		733	746	SUCCESS
AR	367	MSKCC	GRCh37	X	66863145	66863145	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	448	760	0	ENST00000374690.3:c.1664C>T	p.Pro555Leu	p.P555L	ENST00000374690	NM_000044.3	555	cCa/cTa	2/8	0.545637262645188	3	FACETS	1	0.996	1	0.728	0.696	0.76	CLONAL	1	TRUE	1	0.739114238029009	3		760	1140	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185190	123185190	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	528	549	0	ENST00000218089.9:c.1142A>G	p.Asp381Gly	p.D381G	ENST00000218089	NM_001042749.1	381	gAc/gGc	13/35	0.535686047556407	4	FACETS	0.838	0.804	0.873			1	CLONAL	2	TRUE	NA	0.739114238029009	4		549	1482	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577536	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	110	262	0	ENST00000269305.4:c.745dup	p.Arg249LysfsTer15	p.R249Kfs*15	ENST00000269305	NM_001126112.2	249	agg/aAgg	7/11	0.739114238029009	3	FACETS	1	0.981	1	0.662	0.603	0.723	CLONAL	1	TRUE	1	0.739114238029009	3		262	308	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227698	53227711	+	frameshift_variant	Frame_Shift_Del	DEL	CAGAGCTCGGGACA	CAGAGCTCGGGACA	-	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	267	646	0	ENST00000375401.3:c.2477_2490del	p.Val826GlyfsTer22	p.V826Gfs*22	ENST00000375401	NM_004187.3	826	gTGTCCCGAGCTCTG/g	17/26	0.545637262645188	3	FACETS	1	0.99	1	0.617	0.58	0.654	CLONAL	1	TRUE	1	0.739114238029009	3		646	802	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971027	21971028	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	670	116	0	ENST00000304494.5:c.330_331delinsAA	p.Trp110_Gly111delinsTer	p.W110_G111delins*	ENST00000304494	NM_000077.4	110	tgGGgc/tgAAgc	2/3	0.739114238029009	11	FACETS	1	0.99	1			1	CLONAL	11	TRUE	NA	0.739114238029009	11		116	711	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233091	69233092	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	134	300	0	ENST00000462284.1:c.956_957delinsTT	p.Pro319Leu	p.P319L	ENST00000462284	NM_002392.5	319	cCC/cTT	11/11	0.739114238029009	3	FACETS	0.864	0.788	0.943	0.432	0.394	0.472	CLONAL	1	TRUE	1	0.739114238029009	3		300	575	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181931	32181932	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	551	423	0	ENST00000375023.3:c.2122_2123delinsTT	p.Pro708Phe	p.P708F	ENST00000375023	NM_004557.3	708	CCc/TTc	13/30	0.739114238029009	5	FACETS	1	0.983	1			1	CLONAL	5	TRUE	NA	0.739114238029009	5		423	628	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38942955	38942955	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	AA	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	502	258	0	ENST00000357387.3:c.5032delinsTT	p.Gln1678LeufsTer10	p.Q1678Lfs*10	ENST00000357387	NM_152756.3	1678	Caa/TTaa	37/38	0.739114238029009	6	FACETS	1	0.978	1	0.769	0.739	0.8	CLONAL	3	TRUE	2	0.739114238029009	6		258	1094	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295794	212295795	+	missense_variant	Missense_Mutation	DNP	AC	AC	CT	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	235	388	0	ENST00000342788.4:c.2518_2519delinsAG	p.Val840Ser	p.V840S	ENST00000342788	NM_005235.2	840	GTt/AGt	21/28	0.739114238029009	3	FACETS	0.904	0.844	0.966	0.452	0.422	0.483	CLONAL	1	TRUE	1	0.739114238029009	3		388	963	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133242010	133242011	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0000582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	178	326	0	ENST00000320574.5:c.2345_2346delinsTT	p.Ala782Val	p.A782V	ENST00000320574	NM_006231.2	782	gCC/gTT	21/49	0.454982776910726	4	FACETS	0.841	0.782	0.902			1	CLONAL	2	TRUE	NA	0.739114238029009	4		326	498	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000587-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	95	422	0				ENST00000310581	NM_198253.2	-/1132			0.662566313115287	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	TRUE	1	0.759421493870063	4		422	136	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0000587-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	212	456	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.220205048783801	5	FACETS	0.913	0.853	0.975	0.609	0.568	0.65	INDETERMINATE	2	TRUE	2	0.759421493870063	5		456	654	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662320	227662320	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000587-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	55	202	0	ENST00000305123.5:c.1135G>C	p.Ala379Pro	p.A379P	ENST00000305123	NM_005544.2	379	Gct/Cct	1/2	0.542352068230337	3	FACETS	0.76	0.656	0.871	0.38	0.328	0.436	SUBCLONAL	1	TRUE	1	0.759421493870063	3		202	263	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934152	48934152	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0000587-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	18	234	0	ENST00000267163.4:c.608-1G>A		p.X203_splice	ENST00000267163	NM_000321.2	203			NA	2	FACETS	0.137	0.102	0.177			1	INDETERMINATE	1	TRUE	NA	0.759421493870063	2		234	347	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73343020	73343020	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000587-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	174	268	0	ENST00000377767.4:c.1786A>G	p.Arg596Gly	p.R596G	ENST00000377767	NM_014953.3	596	Aga/Gga	14/21	0.70389612874007	5	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.759421493870063	5		268	802	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934152	48934152	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0000587-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	170	234	0	ENST00000267163.4:c.610del		p.X204_splice	ENST00000267163	NM_000321.2	204			NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.759421493870063	2		234	347	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	11	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.957	0.673	1			1	INDETERMINATE	1	FALSE	NA	0.333119138268415	2		422	69	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259588	16259588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	96	207	0	ENST00000375759.3:c.6853C>T	p.Pro2285Ser	p.P2285S	ENST00000375759	NM_015001.2	2285	Cca/Tca	11/15	0.298813289293057	3	FACETS	0.849	0.768	0.932	0.849	0.768	0.932	CLONAL	3	FALSE	0	0.333119138268415	3		207	264	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165637	118165638	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	160	252	0	ENST00000369448.3:c.147_148delinsAA	p.Asp50Asn	p.D50N	ENST00000369448	NM_017709.3	49	aaGGac/aaAAac	2/2	0.333119138268415	3	FACETS	0.98	0.903	1	0.98	0.903	1	CLONAL	2	FALSE	1	0.333119138268415	3		252	572	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650148	206650148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	14	239	0	ENST00000367120.3:c.668C>T	p.Pro223Leu	p.P223L	ENST00000367120	NM_014002.3	223	cCc/cTc	7/22	0.333119138268415	3	FACETS	0.404	0.291	0.539	0.202	0.145	0.27	SUBCLONAL	1	FALSE	1	0.333119138268415	3		239	243	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086142	16086142	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	58	230	0	ENST00000281043.3:c.1318C>T	p.Leu440Phe	p.L440F	ENST00000281043	NM_005378.4	440	Ctt/Ttt	3/3	0.182982683280597	4	FACETS	0.886	0.762	1	0.443	0.381	0.511	INDETERMINATE	1	FALSE	2	0.333119138268415	4		230	524	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589913	212589913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	113	165	0	ENST00000342788.4:c.629G>A	p.Arg210Lys	p.R210K	ENST00000342788	NM_005235.2	210	aGg/aAg	6/28	0.219651923536746	5	FACETS	0.833	0.751	0.918	0.555	0.501	0.612	CLONAL	2	FALSE	2	0.333119138268415	5		165	611	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440391	52440391	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	52	179	0	ENST00000460680.1:c.661G>A	p.Glu221Lys	p.E221K	ENST00000460680	NM_004656.3	221	Gag/Aag	9/17	0.219651923536746	5	FACETS	0.956	0.822	1	0.637	0.548	0.733	CLONAL	2	FALSE	2	0.333119138268415	5		179	245	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588887	52588887	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	75	144	0	ENST00000394830.3:c.4141G>A	p.Gly1381Ser	p.G1381S	ENST00000394830	NM_018313.4	1381	Ggt/Agt	27/30	0.219651923536746	5	FACETS	0.999	0.882	1	0.666	0.588	0.749	CLONAL	2	FALSE	2	0.333119138268415	5		144	338	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037146	71037146	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	114	207	0	ENST00000318789.4:c.1145C>T	p.Pro382Leu	p.P382L	ENST00000318789	NM_032682.5	382	cCc/cTc	14/21	0.219651923536746	5	FACETS	1	0.98	1	0.459	0.413	0.508	CLONAL	1	FALSE	2	0.333119138268415	5		207	745	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156690	55156690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444450672	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	38	145	0	ENST00000257290.5:c.3091G>A	p.Glu1031Lys	p.E1031K	ENST00000257290	NM_006206.4	1031	Gag/Aag	22/23	NA	2	FACETS	1	0.898	1			1	INDETERMINATE	1	FALSE	NA	0.333119138268415	2		145	206	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955617	55955617	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	71	447	0	ENST00000263923.4:c.3328A>T	p.Lys1110Ter	p.K1110*	ENST00000263923	NM_002253.2	1110	Aag/Tag	25/30	NA	2	FACETS	0.496	0.432	0.566			1	INDETERMINATE	1	FALSE	NA	0.333119138268415	2		447	859	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149500876	149500876	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	16	242	0	ENST00000261799.4:c.2354G>A	p.Arg785Lys	p.R785K	ENST00000261799	NM_002609.3	785	aGg/aAg	17/23	1	2	FACETS	0.431	0.319	0.564	0.431	0.319	0.564	SUBCLONAL	1	FALSE	1	0.333119138268415	2		242	223	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524625	176524625	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	36	461	0	ENST00000292408.4:c.2357C>T	p.Pro786Leu	p.P786L	ENST00000292408	NM_213647.1	786	cCc/cTc	18/18	1	2	FACETS	0.73	0.603	0.872	0.73	0.603	0.872	SUBCLONAL	1	FALSE	1	0.333119138268415	2		461	296	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631175	176631175	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	53	305	0	ENST00000439151.2:c.1118C>T	p.Ser373Phe	p.S373F	ENST00000439151	NM_022455.4	373	tCt/tTt	4/23	1	2	FACETS	0.498	0.424	0.579	0.498	0.424	0.579	SUBCLONAL	1	FALSE	1	0.333119138268415	2		305	639	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681160	117681160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	155	266	0	ENST00000368508.3:c.3460C>T	p.Pro1154Ser	p.P1154S	ENST00000368508	NM_002944.2	1154	Cct/Tct	23/43	0.250077835486854	2	FACETS	1	0.984	1	0.654	0.6	0.711	CLONAL	1	FALSE	0	0.333119138268415	2		266	711	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161807833	161807833	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	138	379	0	ENST00000366898.1:c.1160C>G	p.Thr387Ser	p.T387S	ENST00000366898	NM_004562.2	387	aCt/aGt	10/12	0.250077835486854	2	FACETS	1	0.984	1	0.678	0.619	0.74	CLONAL	1	FALSE	0	0.333119138268415	2		379	611	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2966373	2966373	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	82	296	0	ENST00000396946.4:c.1807G>A	p.Asp603Asn	p.D603N	ENST00000396946	NM_032415.4	603	Gat/Aat	14/25	0.333119138268415	3	FACETS	1	0.977	1	0.482	0.427	0.54	CLONAL	1	FALSE	0	0.333119138268415	3		296	397	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	219	482	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.333119138268415	3	FACETS	1	0.991	1	0.496	0.461	0.533	CLONAL	1	FALSE	0	0.333119138268415	3		482	1030	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431659	6431659	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	103	206	0	ENST00000356142.4:c.212C>T	p.Ser71Phe	p.S71F	ENST00000356142	NM_018890.3	71	tCc/tTc	3/7	0.333119138268415	3	FACETS	0.811	0.73	0.895	0.54	0.486	0.597	CLONAL	2	FALSE	0	0.333119138268415	3		206	445	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418947	116418947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	262	293	0	ENST00000397752.3:c.3458C>T	p.Pro1153Leu	p.P1153L	ENST00000397752	NM_000245.2	1153	cCg/cTg	17/21	0.333119138268415	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	FALSE	2	0.333119138268415	4		293	998	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080630	5080630	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	187	348	2	ENST00000381652.3:c.2381T>G	p.Phe794Cys	p.F794C	ENST00000381652	NM_004972.3	794	tTc/tGc	18/25	0.318352520620537	3	FACETS	1	0.979	1	0.585	0.539	0.632	CLONAL	1	FALSE	1	0.333119138268415	3		350	1120	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	17	77	0	ENST00000304494.5:c.151-1G>A		p.X51_splice	ENST00000304494	NM_000077.4	51			0.318352520620537	3	FACETS	1	0.845	1	0.584	0.442	0.747	CLONAL	1	FALSE	1	0.333119138268415	3		77	102	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151820	108151820	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	45	310	0	ENST00000278616.4:c.3501C>G	p.Ile1167Met	p.I1167M	ENST00000278616	NM_000051.3	1167	atC/atG	24/63	0.318352520620537	3	FACETS	0.374	0.313	0.442	0.187	0.156	0.221	SUBCLONAL	1	FALSE	1	0.333119138268415	3		310	843	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149229	119149230	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	192	373	0	ENST00000264033.4:c.1237_1238delinsAA	p.Gly413Asn	p.G413N	ENST00000264033	NM_005188.3	413	GGt/AAt	9/16	0.250077835486854	2	FACETS	1	0.987	1	0.649	0.601	0.699	CLONAL	1	FALSE	0	0.333119138268415	2		373	888	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431198	49431198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258642596	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	15	323	0	ENST00000301067.7:c.9941C>T	p.Ser3314Phe	p.S3314F	ENST00000301067	NM_003482.3	3314	tCc/tTc	34/54	0.318352520620537	3	FACETS	0.36	0.263	0.477	0.18	0.131	0.239	SUBCLONAL	1	FALSE	1	0.333119138268415	3		323	292	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619894	21619894	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55842804	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	50	358	0	ENST00000382592.4:c.272C>T	p.Ser91Leu	p.S91L	ENST00000382592	NM_014572.2	91	tCg/tTg	2/8	NA	2	FACETS	0.487	0.412	0.568			1	INDETERMINATE	1	FALSE	NA	0.333119138268415	2		358	617	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40998441	40998441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	231	472	0	ENST00000267868.3:c.292G>A	p.Glu98Lys	p.E98K	ENST00000267868	NM_002875.4	98	Gag/Aag	4/10	0.291757707502528	4	FACETS	0.854	0.796	0.915	0.854	0.796	0.915	CLONAL	2	FALSE	2	0.333119138268415	4		472	1082	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790547	3790547	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	60	252	0	ENST00000262367.5:c.3986T>G	p.Leu1329Arg	p.L1329R	ENST00000262367	NM_004380.2	1329	cTg/cGg	24/31	0.182982683280597	4	FACETS	1	0.933	1	0.568	0.49	0.651	INDETERMINATE	1	FALSE	2	0.333119138268415	4		252	423	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858517	9858517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765370528	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	144	668	0	ENST00000330684.3:c.2884G>A	p.Glu962Lys	p.E962K	ENST00000330684	NM_001134407.1	962	Gaa/Aaa	13/13	0.182982683280597	4	FACETS	0.795	0.726	0.867	0.795	0.726	0.867	INDETERMINATE	2	FALSE	2	0.333119138268415	4		668	725	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274115	10274115	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555491518	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	62	507	0	ENST00000330684.3:c.154C>T	p.Arg52Ter	p.R52*	ENST00000330684	NM_001134407.1	52	Cga/Tga	2/13	0.182982683280597	4	FACETS	0.773	0.672	0.881	0.773	0.672	0.881	INDETERMINATE	2	FALSE	2	0.333119138268415	4		507	321	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831348	89831348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1216426444	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	95	334	0	ENST00000389301.3:c.2728C>T	p.Leu910Phe	p.L910F	ENST00000389301	NM_000135.2	910	Ctc/Ttc	28/43	0.297283028229864	3	FACETS	1	0.977	1	0.679	0.607	0.755	CLONAL	1	FALSE	1	0.333119138268415	3		334	490	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877197	89877197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138744489	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	108	237	0	ENST00000389301.3:c.440C>T	p.Ser147Phe	p.S147F	ENST00000389301	NM_000135.2	147	tCc/tTc	5/43	0.297283028229864	3	FACETS	0.772	0.696	0.851	0.772	0.696	0.851	SUBCLONAL	2	FALSE	1	0.333119138268415	3		237	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576851	7576851	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	64	305	2	ENST00000269305.4:c.993+2T>G		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.170424134223129	2	FACETS	1	0.904	1	0.523	0.455	0.596	INDETERMINATE	1	FALSE	0	0.333119138268415	2		307	367	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	26	211	0	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			0.170424134223129	2	FACETS	0.653	0.519	0.805	0.327	0.259	0.403	INDETERMINATE	1	FALSE	0	0.333119138268415	2		211	239	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559090	29559090	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1223905930	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	42	19	0	ENST00000356175.3:c.3198-1G>A		p.X1066_splice	ENST00000356175	NM_000267.3	1066			0.170424134223129	2	FACETS	1	0.872	1	1	0.968	1	INDETERMINATE	3	FALSE	0	0.333119138268415	2		19	84	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508318	38508321	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CTAC	CTAC	TTA	novel	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	123	353	0	ENST00000254066.5:c.626_629delinsTTA	p.Thr209IlefsTer61	p.T209Ifs*61	ENST00000254066	NM_000964.3	209	aCTACg/aTTAg	5/9	0.298813289293057	3	FACETS	1	0.979	1	0.82	0.751	0.892	CLONAL	2	FALSE	0	0.333119138268415	3		353	350	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419926	41419926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	196	403	0	ENST00000373198.4:c.395G>A	p.Gly132Glu	p.G132E	ENST00000373198	NM_133170.3	132	gGg/gAg	3/32	0.318352520620537	3	FACETS	0.916	0.851	0.984	0.916	0.851	0.984	CLONAL	2	FALSE	1	0.333119138268415	3		403	749	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123025123	123025123	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000596-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	146	212	0	ENST00000355640.3:c.1013A>T	p.Tyr338Phe	p.Y338F	ENST00000355640		338	tAt/tTt	4/7	0.221771113557186	2	FACETS	0.859	0.789	0.932			1	CLONAL	2	FALSE	NA	0.333119138268415	2		212	510	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0000602-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	192	275	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.298510400473595	2	FACETS	0.78	0.722	0.839	0.78	0.722	0.839	SUBCLONAL	2	TRUE	0	0.309006040975227	2		275	797	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0000602-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	74	295	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.252829897328838	4	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	2	0.309006040975227	4		295	294	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0000602-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	241	626	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.298510400473595	2	FACETS	1	0.991	1	0.694	0.648	0.742	CLONAL	1	TRUE	0	0.309006040975227	2		626	1123	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851351	156851351	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764816792	NA	P-0000602-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	128	437	0	ENST00000524377.1:c.2308C>T	p.Gln770Ter	p.Q770*	ENST00000524377	NM_002529.3	770	Caa/Taa	17/17	0.309006040975227	3	FACETS	0.849	0.768	0.936	0.425	0.384	0.468	CLONAL	1	TRUE	1	0.309006040975227	3		437	1126	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641775	12641775	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755977690	NA	P-0000602-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	118	319	0	ENST00000251849.4:c.866C>T	p.Ser289Leu	p.S289L	ENST00000251849	NM_002880.3	289	tCa/tTa	9/17	0.309006040975227	2	FACETS	1	0.94	1	0.527	0.476	0.582	CLONAL	1	TRUE	0	0.309006040975227	2		319	724	SUCCESS
ATR	545	MSKCC	GRCh37	3	142255044	142255044	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0000602-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	79	305	0	ENST00000350721.4:c.3726-1G>T		p.X1242_splice	ENST00000350721	NM_001184.3	1242			NA	2	FACETS	1	0.917	1			1	INDETERMINATE	1	TRUE	NA	0.309006040975227	2		305	487	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218789	66218789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000602-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	136	523	0	ENST00000273854.3:c.2269G>A	p.Glu757Lys	p.E757K	ENST00000273854	NM_004439.5	757	Gag/Aag	13/18	0.309006040975227	3	FACETS	1	0.982	1	0.664	0.604	0.727	CLONAL	1	TRUE	1	0.309006040975227	3		523	765	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875642	35875642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000602-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	200	414	0	ENST00000303115.3:c.829C>T	p.Pro277Ser	p.P277S	ENST00000303115	NM_002185.3	277	Ccc/Tcc	7/8	0.298510400473595	2	FACETS	0.843	0.783	0.905	0.843	0.783	0.905	CLONAL	2	TRUE	0	0.309006040975227	2		414	768	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395007	395007	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000602-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	91	164	0	ENST00000380956.4:c.403G>C	p.Gly135Arg	p.G135R	ENST00000380956	NM_001195286.1	135	Gga/Cga	3/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.309006040975227	2		164	472	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129216	152129216	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000602-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1227	165	816	0	ENST00000206249.3:c.169G>T	p.Gly57Cys	p.G57C	ENST00000206249	NM_000125.3	57	Ggc/Tgc	1/8	1	2	FACETS	0.767	0.702	0.835	0.767	0.702	0.835	SUBCLONAL	1	TRUE	1	0.309006040975227	2		816	1392	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486135	8486135	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000602-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	277	580	2	ENST00000356435.5:c.2682G>C	p.Arg894Ser	p.R894S	ENST00000356435		894	agG/agC	17/35	0.298510400473595	2	FACETS	0.865	0.813	0.919	0.865	0.813	0.919	CLONAL	2	TRUE	0	0.309006040975227	2		582	1036	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006459	12006459	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1316717602	NA	P-0000602-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	211	553	0	ENST00000396373.4:c.427C>G	p.Gln143Glu	p.Q143E	ENST00000396373	NM_001987.4	143	Cag/Gag	4/8	0.309006040975227	5	FACETS	0.848	0.787	0.912	0.566	0.524	0.608	CLONAL	2	TRUE	2	0.309006040975227	5		553	1178	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918694	32918694	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs876658551	NA	P-0000602-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	97	390	0	ENST00000380152.3:c.6842-1G>T		p.X2281_splice	ENST00000380152		2281			1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.309006040975227	2		390	571	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609877	81609877	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000602-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	230	381	0	ENST00000298171.2:c.1475C>A	p.Pro492His	p.P492H	ENST00000298171	NM_000369.2	492	cCt/cAt	10/10	0.20366788965126	4	FACETS	0.939	0.875	1	0.939	0.875	1	CLONAL	2	TRUE	2	0.309006040975227	4		381	1038	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610118	10610118	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000602-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	250	477	0	ENST00000171111.5:c.592G>T	p.Glu198Ter	p.E198*	ENST00000171111	NM_203500.1	198	Gag/Tag	2/6	0.26742635663932	2	FACETS	0.793	0.742	0.846	0.793	0.742	0.846	SUBCLONAL	2	TRUE	0	0.309006040975227	2		477	1020	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276269	15276269	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000602-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	92	408	0	ENST00000263388.2:c.5725G>T	p.Ala1909Ser	p.A1909S	ENST00000263388	NM_000435.2	1909	Gca/Tca	31/33	1	2	FACETS	0.616	0.546	0.691	0.616	0.546	0.691	SUBCLONAL	1	TRUE	1	0.309006040975227	2		408	967	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376260	15376260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000602-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	58	210	0	ENST00000263377.2:c.754C>T	p.Pro252Ser	p.P252S	ENST00000263377	NM_058243.2	252	Cca/Tca	5/20	1	2	FACETS	0.708	0.609	0.817	0.708	0.609	0.817	SUBCLONAL	1	TRUE	1	0.309006040975227	2		210	530	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867276	45867276	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000602-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	42	216	0	ENST00000391945.4:c.917C>G	p.Ala306Gly	p.A306G	ENST00000391945	NM_000400.3	306	gCc/gGc	10/23	0.20366788965126	4	FACETS	0.511	0.425	0.606	0.255	0.212	0.303	SUBCLONAL	1	TRUE	2	0.309006040975227	4		216	697	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561430	9561430	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000602-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	111	385	0	ENST00000353224.5:c.352G>T	p.Gly118Cys	p.G118C	ENST00000353224	NM_177990.2	118	Ggc/Tgc	4/10	0.20366788965126	4	FACETS	0.97	0.87	1	0.485	0.435	0.538	CLONAL	1	TRUE	2	0.309006040975227	4		385	970	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100966	41100966	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000602-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	171	351	0	ENST00000373198.4:c.1390del	p.Leu464CysfsTer27	p.L464Cfs*27	ENST00000373198	NM_133170.3	464	Ctg/tg	8/32	0.309006040975227	5	FACETS	1	0.988	1	0.483	0.444	0.525	CLONAL	1	TRUE	2	0.309006040975227	5		351	1117	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0000621-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	58	275	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.192746458098772	2	FACETS	0.989	0.86	1	0.989	0.86	1	CLONAL	2	TRUE	0	0.252871416319988	2		275	232	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0000621-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	138	474	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.192746458098772	2	FACETS	0.969	0.886	1	0.969	0.886	1	CLONAL	2	TRUE	0	0.252871416319988	2		474	563	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258779	115258779	+	start_lost	Translation_Start_Site	SNP	C	C	G	novel	NA	P-0000621-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	36	303	0	ENST00000369535.4:c.3G>C	p.Met1?	p.M1?	ENST00000369535	NM_002524.4	1	atG/atC	2/7	0.284447442627516	3	FACETS	0.482	0.395	0.58	0.241	0.197	0.29	SUBCLONAL	1	TRUE	1	0.252871416319988	3		303	666	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000653-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	39	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.873	0.73	1			1	INDETERMINATE	1	TRUE	NA	0.386629474731731	2		422	231	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7978975	7978975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769562383	NA	P-0000653-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1213	223	806	0	ENST00000319144.4:c.1592C>T	p.Pro531Leu	p.P531L	ENST00000319144	NM_001139.2	531	cCg/cTg	12/15	1	2	FACETS	0.803	0.746	0.863	0.803	0.746	0.863	CLONAL	1	TRUE	1	0.386629474731731	2		806	1436	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0000653-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	173	143	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.386629474731731	2		143	844	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720649	89720649	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs587782455	NA	P-0000653-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	30	104	1	ENST00000371953.3:c.802-2A>T		p.X268_splice	ENST00000371953	NM_000314.4	268			0.386629474731731	2	FACETS	0.66	0.535	0.801	0.33	0.267	0.401	SUBCLONAL	1	TRUE	0	0.386629474731731	2		105	235	SUCCESS
EED	8726	MSKCC	GRCh37	11	85967457	85967457	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000653-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	222	516	0	ENST00000263360.6:c.455G>A	p.Trp152Ter	p.W152*	ENST00000263360	NM_003797.3	152	tGg/tAg	5/12	0.386629474731731	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.386629474731731	1		516	746	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915523	112915523	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs28933386	NA	P-0000653-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	267	901	0	ENST00000351677.2:c.922A>G	p.Asn308Asp	p.N308D	ENST00000351677	NM_002834.3	308	Aat/Gat	8/16	1	2	FACETS	0.991	0.927	1	0.991	0.927	1	CLONAL	1	TRUE	1	0.386629474731731	2		901	1394	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720648	89720649	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TA	TA	-	novel	NA	P-0000653-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	23	126	0	ENST00000371953.3:c.802-3_802-2del		p.X268_splice	ENST00000371953	NM_000314.4	268			0.386629474731731	2	FACETS	0.456	0.356	0.571	0.228	0.178	0.286	SUBCLONAL	1	TRUE	0	0.386629474731731	2		126	261	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720649	89720649	+	splice_acceptor_variant	Splice_Site	DEL	A	A	-	rs886047397	NA	P-0000653-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	45	105	0	ENST00000371953.3:c.802-2del		p.X268_splice	ENST00000371953	NM_000314.4	268			0.386629474731731	2	FACETS	0.991	0.84	1	0.495	0.42	0.577	CLONAL	1	TRUE	0	0.386629474731731	2		105	235	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	130	142	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.486805951549847	4	FACETS	0.966	0.886	1	0.966	0.886	1	CLONAL	2	TRUE	2	0.573898054948948	4		142	369	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602581	10602581	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	462	193	0	ENST00000171111.5:c.997G>T	p.Gly333Cys	p.G333C	ENST00000171111	NM_203500.1	333	Ggc/Tgc	3/6	0.573898054948948	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	0	0.573898054948948	3		193	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	252	174	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	0.573898054948948	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.573898054948948	2		174	414	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11210250	11210250	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	169	199	0	ENST00000361445.4:c.4503G>A	p.Trp1501Ter	p.W1501*	ENST00000361445	NM_004958.3	1501	tgG/tgA	31/58	1	2	FACETS	0.773	0.712	0.836	0.773	0.712	0.836	SUBCLONAL	1	TRUE	1	0.573898054948948	2		199	762	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458573	120458573	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	142	153	0	ENST00000256646.2:c.6772G>T	p.Glu2258Ter	p.E2258*	ENST00000256646	NM_024408.3	2258	Gag/Tag	34/34	0.573898054948948	3	FACETS	1	0.961	1	0.542	0.496	0.591	CLONAL	1	TRUE	1	0.573898054948948	3		153	587	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809239	243809239	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	669	439	0	ENST00000263826.5:c.385G>T	p.Gly129Ter	p.G129*	ENST00000263826	NM_005465.4	129	Gga/Tga	4/13	0.573898054948948	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.573898054948948	3		439	1476	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251842	212251842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	180	110	0	ENST00000342788.4:c.3217G>T	p.Ala1073Ser	p.A1073S	ENST00000342788	NM_005235.2	1073	Gct/Tct	27/28	0.573898054948948	3	FACETS	0.802	0.746	0.86	0.802	0.746	0.86	CLONAL	2	TRUE	1	0.573898054948948	3		110	503	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537899	212537899	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	323	140	0	ENST00000342788.4:c.1706G>T	p.Cys569Phe	p.C569F	ENST00000342788	NM_005235.2	569	tGc/tTc	14/28	0.573898054948948	3	FACETS	0.97	0.921	1	0.97	0.921	1	CLONAL	2	TRUE	1	0.573898054948948	3		140	747	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597406	52597406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	610	424	0	ENST00000394830.3:c.3904G>A	p.Glu1302Lys	p.E1302K	ENST00000394830	NM_018313.4	1302	Gaa/Aaa	25/30	0.573898054948948	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.573898054948948	2		424	1022	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643510	52643510	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	446	202	0	ENST00000394830.3:c.2386G>T	p.Glu796Ter	p.E796*	ENST00000394830	NM_018313.4	796	Gag/Tag	17/30	0.573898054948948	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.573898054948948	2		202	728	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55130050	55130050	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	207	320	0	ENST00000257290.5:c.584G>T	p.Gly195Val	p.G195V	ENST00000257290	NM_006206.4	195	gGa/gTa	4/23	0.573898054948948	2	FACETS	0.964	0.898	1	0.482	0.449	0.517	CLONAL	1	TRUE	0	0.573898054948948	2		320	748	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	218480	218480	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs778069799	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	48	18	0	ENST00000264932.6:c.10G>T	p.Val4Phe	p.V4F	ENST00000264932	NM_004168.2	4	Gtc/Ttc	1/15	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.573898054948948	NA		18	143	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235272	235272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766779919	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	88	97	0	ENST00000264932.6:c.1078G>A	p.Glu360Lys	p.E360K	ENST00000264932	NM_004168.2	360	Gag/Aag	9/15	0.405235957636349	5	FACETS	1	0.972	1	0.43	0.383	0.481	CLONAL	1	TRUE	2	0.573898054948948	5		97	442	SUCCESS
APC	324	MSKCC	GRCh37	5	112179761	112179761	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	95	106	0	ENST00000257430.4:c.8470G>C	p.Glu2824Gln	p.E2824Q	ENST00000257430	NM_000038.5	2824	Gaa/Caa	16/16	0.562059301292349	1	FACETS	0.855	0.773	0.941	0.855	0.773	0.941	CLONAL	1	TRUE	0	0.573898054948948	1		106	276	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508496	106508496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	32	69	0	ENST00000359195.3:c.490G>A	p.Asp164Asn	p.D164N	ENST00000359195	NM_002649.2	164	Gac/Aac	2/11	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.573898054948948	2		69	105	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971159	21971159	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	46	39	0	ENST00000304494.5:c.199G>T	p.Gly67Cys	p.G67C	ENST00000304494	NM_000077.4	67	Ggc/Tgc	2/3	0.573898054948948	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.573898054948948	1		39	78	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923427	36923427	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	296	190	0	ENST00000358127.4:c.835G>T	p.Ala279Ser	p.A279S	ENST00000358127	NM_001280556.1	279	Gcc/Tcc	7/10	0.573898054948948	2	FACETS	0.906	0.863	0.95	0.906	0.863	0.95	CLONAL	2	TRUE	0	0.573898054948948	2		190	569	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015041	37015041	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	161	241	0	ENST00000358127.4:c.363G>C	p.Glu121Asp	p.E121D	ENST00000358127	NM_001280556.1	121	gaG/gaC	3/10	0.573898054948948	2	FACETS	0.924	0.852	1	0.462	0.426	0.5	CLONAL	1	TRUE	0	0.573898054948948	2		241	607	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1040418	1040418	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	399	315	0	ENST00000358495.3:c.154A>T	p.Ile52Leu	p.I52L	ENST00000358495	NM_134424.2	52	Ata/Tta	3/12	0.573898054948948	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.573898054948948	3		315	894	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435312	49435312	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	125	176	0	ENST00000301067.7:c.6241G>A	p.Glu2081Lys	p.E2081K	ENST00000301067	NM_003482.3	2081	Gag/Aag	31/54	0.573898054948948	3	FACETS	0.941	0.854	1	0.47	0.427	0.516	CLONAL	1	TRUE	1	0.573898054948948	3		176	596	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112123	115112123	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866191482	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	157	268	0	ENST00000257566.3:c.1617G>T	p.Met539Ile	p.M539I	ENST00000257566	NM_016569.3	539	atG/atT	7/8	0.519194450124038	3	FACETS	1	0.957	1	0.532	0.489	0.577	CLONAL	1	TRUE	1	0.573898054948948	3		268	662	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209090	133209090	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	112	140	0	ENST00000320574.5:c.6141G>C	p.Met2047Ile	p.M2047I	ENST00000320574	NM_006231.2	2047	atG/atC	45/49	0.519194450124038	3	FACETS	1	0.975	1	0.614	0.557	0.674	CLONAL	1	TRUE	1	0.573898054948948	3		140	409	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906850	32906850	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876659628	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	357	221	0	ENST00000380152.3:c.1235C>T	p.Pro412Leu	p.P412L	ENST00000380152		412	cCc/cTc	10/27	0.573898054948948	2	FACETS	0.909	0.87	0.949	0.909	0.87	0.949	CLONAL	2	TRUE	0	0.573898054948948	2		221	684	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349484	73349484	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	193	187	0	ENST00000377767.4:c.852C>G	p.Asn284Lys	p.N284K	ENST00000377767	NM_014953.3	284	aaC/aaG	6/21	0.573898054948948	2	FACETS	0.964	0.895	1	0.482	0.447	0.518	CLONAL	1	TRUE	0	0.573898054948948	2		187	698	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790400	3790400	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	124	168	0	ENST00000262367.5:c.4133G>T	p.Arg1378Leu	p.R1378L	ENST00000262367	NM_004380.2	1378	cGg/cTg	24/31	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.573898054948948	2		168	399	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679408	29679408	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	242	263	0	ENST00000356175.3:c.7528C>G	p.Gln2510Glu	p.Q2510E	ENST00000356175	NM_000267.3	2510	Cag/Gag	50/57	0.573898054948948	3	FACETS	0.986	0.92	1	0.493	0.46	0.527	CLONAL	1	TRUE	1	0.573898054948948	3		263	1101	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243626	41243626	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	234	355	0	ENST00000357654.3:c.3922G>T	p.Ala1308Ser	p.A1308S	ENST00000357654	NM_007294.3	1308	Gca/Tca	10/23	0.573898054948948	3	FACETS	0.966	0.901	1	0.483	0.45	0.517	CLONAL	1	TRUE	1	0.573898054948948	3		355	1086	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5207955	5207955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1412878073	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	744	393	0	ENST00000357368.4:c.5756G>A	p.Arg1919Gln	p.R1919Q	ENST00000357368	NM_002850.3	1919	cGg/cAg	37/38	0.573898054948948	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.573898054948948	3		393	1044	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11106898	11106898	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	430	211	0	ENST00000358026.2:c.1603G>T	p.Glu535Ter	p.E535*	ENST00000358026	NM_001128849.1	535	Gag/Tag	10/36	0.573898054948948	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.573898054948948	3		211	616	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867544	45867544	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	534	238	0	ENST00000391945.4:c.764C>G	p.Thr255Ser	p.T255S	ENST00000391945	NM_000400.3	255	aCc/aGc	9/23	0.312451196239534	3	FACETS	0.997	0.967	1			1	INDETERMINATE	3	TRUE	NA	0.573898054948948	3		238	801	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714400	40714400	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	137	153	0	ENST00000373198.4:c.3997C>A	p.His1333Asn	p.H1333N	ENST00000373198	NM_133170.3	1333	Cac/Aac	29/32	0.329010763729708	5	FACETS	1	0.944	1	0.35	0.318	0.384	INDETERMINATE	1	TRUE	2	0.573898054948948	5		153	846	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929446	44929446	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	245	334	0	ENST00000377967.4:c.2546G>T	p.Ser849Ile	p.S849I	ENST00000377967	NM_021140.2	849	aGt/aTt	17/29	0.573898054948948	1	FACETS	0.95	0.894	1	0.95	0.894	1	CLONAL	1	TRUE	0	0.573898054948948	1		334	641	SUCCESS
AR	367	MSKCC	GRCh37	X	66766250	66766250	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	115	169	0	ENST00000374690.3:c.1262G>T	p.Gly421Val	p.G421V	ENST00000374690	NM_000044.3	421	gGa/gTa	1/8	0.523214931179498	1	FACETS	0.774	0.705	0.847	0.774	0.705	0.847	SUBCLONAL	1	TRUE	0	0.573898054948948	1		169	369	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351422	70351422	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	195	390	0	ENST00000374080.3:c.4070G>T	p.Arg1357Leu	p.R1357L	ENST00000374080		1357	cGc/cTc	29/45	0.523214931179498	1	FACETS	0.563	0.521	0.606	0.563	0.521	0.606	SUBCLONAL	1	TRUE	0	0.573898054948948	1		390	861	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092740	27092740	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1557611083	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	183	219	1	ENST00000324856.7:c.2765del	p.Gly922AlafsTer2	p.G922Afs*2	ENST00000324856	NM_006015.4	921	Ggg/gg	9/20	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.573898054948948	2		220	626	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004750	150004761	+	inframe_deletion	In_Frame_Del	DEL	GCTGGTGTAATT	GCTGGTGTAATT	-	novel	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	74	170	0	ENST00000253339.5:c.1464_1475del	p.Ile489_Ala492del	p.I489_A492del	ENST00000253339		488	gcAATTACACCAGCt/gct	3/7	0.519194450124038	3	FACETS	0.615	0.539	0.696	0.307	0.269	0.348	SUBCLONAL	1	TRUE	1	0.573898054948948	3		170	540	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347830	347830	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	245	417	0	ENST00000262320.3:c.1676del	p.Gln559ArgfsTer146	p.Q559Rfs*146	ENST00000262320	NM_003502.3	559	cAg/cg	6/11	NA	2	FACETS	1	0.943	1			1	INDETERMINATE	1	TRUE	NA	0.573898054948948	2		417	848	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961575	54961580	+	inframe_deletion	In_Frame_Del	DEL	AACTGG	AACTGG	-	novel	NA	P-0000671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	70	96	0	ENST00000312783.6:c.52_57del	p.Pro18_Val19del	p.P18_V19del	ENST00000312783	NM_198436.1	18	CCAGTT/-	4/10	0.392166730206683	4	FACETS	0.815	0.713	0.925			1	CLONAL	1	TRUE	NA	0.573898054948948	4		96	471	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0000677-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	190	139	0				ENST00000310581	NM_198253.2	-/1132			0.119263229507249	0	FACETS	0.358	0.333	0.384			1	INDETERMINATE	1	TRUE	0	0.660198268393153	0		139	546	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224461	55224461	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000677-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	11077	335	1	ENST00000275493.2:c.1143C>G	p.Phe381Leu	p.F381L	ENST00000275493	NM_005228.3	381	ttC/ttG	10/28	0.660198268393153	32	FACETS	1	0.999	1			1	CLONAL	31	TRUE	NA	0.660198268393153	32		336	11655	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955448	48955448	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0000677-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	87	240	0	ENST00000267163.4:c.1565del	p.Asn522IlefsTer2	p.N522Ifs*2	ENST00000267163	NM_000321.2	522	Aat/at	17/27	0.660198268393153	1	FACETS	0.883	0.799	0.968	0.883	0.799	0.968	CLONAL	1	TRUE	0	0.660198268393153	1		240	200	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000679-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	59	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.985	0.866	1			1	INDETERMINATE	1	TRUE	NA	0.721641853465133	2		422	166	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578277	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs1555525902	NA	P-0000679-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	51	240	0	ENST00000269305.4:c.572_574del	p.Pro191del	p.P191del	ENST00000269305	NM_001126112.2	191	cCTCag/cag	6/11	1	2	FACETS	0.214	0.181	0.25	0.214	0.181	0.25	SUBCLONAL	1	TRUE	1	0.721641853465133	2		240	660	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593513	215593513	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587780029	NA	P-0000679-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	226	146	0	ENST00000260947.4:c.2221G>C	p.Asp741His	p.D741H	ENST00000260947	NM_000465.2	741	Gat/Cat	11/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.721641853465133	2		146	610	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718193	117718193	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000679-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	294	201	0	ENST00000368508.3:c.664G>T	p.Gly222Cys	p.G222C	ENST00000368508	NM_002944.2	222	Ggt/Tgt	7/43	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.721641853465133	2		201	758	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926900	112926900	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs886039463	NA	P-0000679-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	61	181	0	ENST00000351677.2:c.1520C>A	p.Thr507Lys	p.T507K	ENST00000351677	NM_002834.3	507	aCa/aAa	13/16	0.354509335066279	1	FACETS	0.177	0.152	0.204	0.177	0.152	0.204	INDETERMINATE	1	TRUE	0	0.721641853465133	1		181	611	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755627	39755627	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000679-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	229	223	1	ENST00000288319.7:c.1138A>G	p.Lys380Glu	p.K380E	ENST00000288319	NM_182918.3	380	Aag/Gag	10/10	1	2	FACETS	0.814	0.761	0.868	0.814	0.761	0.868	CLONAL	1	TRUE	1	0.721641853465133	2		224	780	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123026579	123026579	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0000679-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	457	401	0	ENST00000355640.3:c.1057-2A>T		p.X353_splice	ENST00000355640		353			1	2	FACETS	0.918	0.876	0.96	0.918	0.876	0.96	CLONAL	1	TRUE	1	0.721641853465133	2		401	1380	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720838	89720842	+	frameshift_variant	Frame_Shift_Del	DEL	AAGAC	AAGAC	-	novel	NA	P-0000679-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	109	97	0	ENST00000371953.3:c.991_995del	p.Asp331SerfsTer10	p.D331Sfs*10	ENST00000371953	NM_000314.4	330	aAAGAC/a	8/9	0.721641853465133	1	FACETS	0.818	0.75	0.887	0.818	0.75	0.887	CLONAL	1	TRUE	0	0.721641853465133	1		97	236	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	484	403	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.60577344353505	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	0	0.602630302365166	3		404	635	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622240	162622240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	234	268	0	ENST00000366898.1:c.457C>T	p.Pro153Ser	p.P153S	ENST00000366898	NM_004562.2	153	Ccc/Tcc	4/12	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.602630302365166	2		268	344	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	66	139	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.89	0.802	0.978			1	INDETERMINATE	2	TRUE	NA	0.602630302365166	2		139	123	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	490	482	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.60577344353505	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	1	0.602630302365166	4		482	816	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186751	11186751	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752458445	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	345	228	0	ENST00000361445.4:c.6454C>T	p.Arg2152Cys	p.R2152C	ENST00000361445	NM_004958.3	2152	Cgc/Tgc	46/58	0.420283345506965	5	FACETS	1	0.979	1			1	CLONAL	4	TRUE	NA	0.602630302365166	5		228	531	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950061	38950061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	93	239	0	ENST00000357387.3:c.3889C>T	p.Pro1297Ser	p.P1297S	ENST00000357387	NM_152756.3	1297	Cct/Tct	31/38	0.602630302365166	6	FACETS	0.929	0.826	1	0.186	0.165	0.208	CLONAL	1	TRUE	1	0.602630302365166	6		239	733	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912874	32912874	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	100	161	0	ENST00000380152.3:c.4382C>T	p.Ser1461Phe	p.S1461F	ENST00000380152		1461	tCc/tTc	11/27	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.602630302365166	2		161	320	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944607	40944607	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766880457	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	86	125	0	ENST00000373198.4:c.1895G>A	p.Arg632Gln	p.R632Q	ENST00000373198	NM_133170.3	632	cGa/cAa	12/32	0.449054085875611	3	FACETS	0.829	0.747	0.913			1	CLONAL	2	TRUE	NA	0.602630302365166	3		125	224	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11206809	11206809	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1311361793	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	108	253	0	ENST00000361445.4:c.4610C>T	p.Pro1537Leu	p.P1537L	ENST00000361445	NM_004958.3	1537	cCt/cTt	32/58	0.420283345506965	5	FACETS	1	0.967	1			1	CLONAL	1	TRUE	NA	0.602630302365166	5		253	581	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11264678	11264678	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	73	203	0	ENST00000361445.4:c.3884C>T	p.Ser1295Leu	p.S1295L	ENST00000361445	NM_004958.3	1295	tCa/tTa	26/58	0.420283345506965	5	FACETS	1	0.902	1			1	CLONAL	1	TRUE	NA	0.602630302365166	5		203	447	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023652	27023652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780881207	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	145	262	0	ENST00000324856.7:c.758C>T	p.Pro253Leu	p.P253L	ENST00000324856	NM_006015.4	253	cCc/cTc	1/20	0.60577344353505	5	FACETS	1	0.978	1	0.303	0.276	0.33	CLONAL	1	TRUE	1	0.602630302365166	5		262	757	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057772	27057772	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	334	428	0	ENST00000324856.7:c.1480C>T	p.Pro494Ser	p.P494S	ENST00000324856	NM_006015.4	494	Cct/Tct	3/20	0.60577344353505	5	FACETS	0.921	0.871	0.972	0.46	0.435	0.486	CLONAL	2	TRUE	1	0.602630302365166	5		428	1146	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092806	27092806	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	133	283	2	ENST00000324856.7:c.2827C>T	p.Pro943Ser	p.P943S	ENST00000324856	NM_006015.4	943	Cct/Tct	9/20	0.60577344353505	5	FACETS	1	0.972	1	0.292	0.265	0.32	CLONAL	1	TRUE	1	0.602630302365166	5		285	719	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100091	27100091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	372	325	1	ENST00000324856.7:c.3887C>T	p.Pro1296Leu	p.P1296L	ENST00000324856	NM_006015.4	1296	cCt/cTt	16/20	0.60577344353505	5	FACETS	0.95	0.906	0.993	0.712	0.68	0.745	CLONAL	3	TRUE	1	0.602630302365166	5		326	825	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430641	78430641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1344	177	309	0	ENST00000370768.2:c.649G>A	p.Val217Ile	p.V217I	ENST00000370768	NM_003902.3	217	Gtt/Att	9/20	0.602630302365166	7	FACETS	0.968	0.889	1			1	CLONAL	1	TRUE	NA	0.602630302365166	7		309	1521	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166499	118166499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	107	211	0	ENST00000369448.3:c.1009G>A	p.Ala337Thr	p.A337T	ENST00000369448	NM_017709.3	337	Gcc/Acc	2/2	0.60577344353505	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.602630302365166	1		211	203	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120469180	120469180	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	131	281	0	ENST00000256646.2:c.3947G>C	p.Gly1316Ala	p.G1316A	ENST00000256646	NM_024408.3	1316	gGa/gCa	24/34	0.60577344353505	3	FACETS	0.762	0.7	0.827	0.762	0.7	0.827	SUBCLONAL	2	TRUE	1	0.602630302365166	3		281	371	SUCCESS
INSRR	3645	MSKCC	GRCh37	1	156811906	156811906	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	152	359	0	ENST00000368195.3:c.3395G>A	p.Gly1132Glu	p.G1132E	ENST00000368195	NM_014215.2	1132	gGg/gAg	19/22	0.60577344353505	3	FACETS	1	0.968	1	0.553	0.507	0.599	CLONAL	1	TRUE	1	0.602630302365166	3		359	594	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226551660	226551660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1210082971	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	163	269	0	ENST00000366794.5:c.2770G>A	p.Val924Ile	p.V924I	ENST00000366794	NM_001618.3	924	Gtt/Att	20/23	0.60577344353505	3	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	1	0.602630302365166	3		269	352	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086010	16086010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	132	224	0	ENST00000281043.3:c.1186G>A	p.Asp396Asn	p.D396N	ENST00000281043	NM_005378.4	396	Gac/Aac	3/3	0.194345602754622	3	FACETS	0.986	0.912	1			1	INDETERMINATE	2	TRUE	NA	0.602630302365166	3		224	289	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086053	16086053	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	79	248	0	ENST00000281043.3:c.1229A>T	p.Glu410Val	p.E410V	ENST00000281043	NM_005378.4	410	gAg/gTg	3/3	0.194345602754622	3	FACETS	1	0.944	1			1	INDETERMINATE	1	TRUE	NA	0.602630302365166	3		248	309	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519902	29519902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200364883	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	134	299	0	ENST00000389048.3:c.1669C>T	p.Arg557Cys	p.R557C	ENST00000389048	NM_004304.4	557	Cgt/Tgt	9/29	0.60577344353505	3	FACETS	1	0.975	1	0.589	0.539	0.642	CLONAL	1	TRUE	1	0.602630302365166	3		299	491	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635570	47635570	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793491	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	75	165	1	ENST00000233146.2:c.242G>A	p.Ser81Asn	p.S81N	ENST00000233146	NM_000251.2	81	aGt/aAt	2/16	0.60577344353505	3	FACETS	0.89	0.785	1	0.445	0.392	0.501	CLONAL	1	TRUE	1	0.602630302365166	3		166	364	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018151	48018151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502871	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	250	253	0	ENST00000234420.5:c.346G>A	p.Asp116Asn	p.D116N	ENST00000234420	NM_000179.2	116	Gat/Aat	2/10	0.60577344353505	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.602630302365166	3		253	495	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028262	48028262	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1064794302	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	98	187	0	ENST00000234420.5:c.3140G>A	p.Trp1047Ter	p.W1047*	ENST00000234420	NM_000179.2	1047	tGg/tAg	4/10	0.60577344353505	3	FACETS	1	0.963	1	0.577	0.519	0.637	CLONAL	1	TRUE	1	0.602630302365166	3		187	367	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48032756	48032756	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	85	233	0	ENST00000234420.5:c.3557-1G>A		p.X1186_splice	ENST00000234420	NM_000179.2	1186			0.60577344353505	3	FACETS	0.885	0.786	0.989	0.442	0.393	0.495	CLONAL	1	TRUE	1	0.602630302365166	3		233	415	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212522500	212522500	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs987567655	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	137	134	0	ENST00000342788.4:c.1925C>T	p.Ser642Phe	p.S642F	ENST00000342788	NM_005235.2	642	tCc/tTc	16/28	0.232437907028561	4	FACETS	0.855	0.793	0.918	0.855	0.793	0.918	INDETERMINATE	3	TRUE	1	0.602630302365166	4		134	284	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275359	41275359	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	49	127	0	ENST00000349496.5:c.1524+1G>A		p.X508_splice	ENST00000349496	NM_001904.3	508			0.602630302365166	6	FACETS	0.804	0.682	0.938	0.161	0.136	0.188	CLONAL	1	TRUE	1	0.602630302365166	6		127	446	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71161719	71161719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	559	292	0	ENST00000318789.4:c.250C>T	p.Pro84Ser	p.P84S	ENST00000318789	NM_032682.5	84	Ccc/Tcc	7/21	0.602630302365166	6	FACETS	0.964	0.935	0.992	0.964	0.935	0.992	CLONAL	5	TRUE	1	0.602630302365166	6		292	849	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468436	89468436	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	99	176	0	ENST00000336596.2:c.1970T>C	p.Val657Ala	p.V657A	ENST00000336596	NM_005233.5	657	gTt/gCt	11/17	0.602630302365166	6	FACETS	0.973	0.868	1	0.195	0.173	0.217	CLONAL	1	TRUE	1	0.602630302365166	6		176	745	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521763	89521763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	76	136	0	ENST00000336596.2:c.2840C>T	p.Ser947Phe	p.S947F	ENST00000336596	NM_005233.5	947	tCc/tTc	16/17	0.602630302365166	6	FACETS	0.983	0.863	1	0.197	0.172	0.223	CLONAL	1	TRUE	1	0.602630302365166	6		136	566	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911454	134911454	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	97	155	0	ENST00000398015.3:c.1919T>A	p.Leu640Gln	p.L640Q	ENST00000398015	NM_004441.4	640	cTg/cAg	11/16	0.449054085875611	3	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.602630302365166	3		155	281	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181390	185181390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	258	240	0	ENST00000265026.3:c.1331G>A	p.Gly444Glu	p.G444E	ENST00000265026	NM_004721.4	444	gGa/gAa	8/14	0.582409242456992	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	3	TRUE	1	0.602630302365166	4		240	446	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455644	189455644	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772867228	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	78	171	0	ENST00000264731.3:c.178G>A	p.Asp60Asn	p.D60N	ENST00000264731	NM_003722.4	60	Gat/Aat	2/14	0.582409242456992	4	FACETS	1	0.891	1	0.336	0.297	0.379	CLONAL	1	TRUE	1	0.602630302365166	4		171	411	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803570	1803570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373470718	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	195	195	0	ENST00000260795.2:c.748C>T	p.Pro250Ser	p.P250S	ENST00000260795		250	Ccg/Tcg	6/17	0.475748983949017	4	FACETS	0.971	0.915	1			1	CLONAL	3	TRUE	NA	0.602630302365166	4		195	356	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806207	1806207	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1314341121	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	316	417	1	ENST00000260795.2:c.1226C>T	p.Pro409Leu	p.P409L	ENST00000260795		409	cCc/cTc	8/17	0.475748983949017	4	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.602630302365166	4		418	693	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955949	55955949	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	222	287	0	ENST00000263923.4:c.3213G>A	p.Trp1071Ter	p.W1071*	ENST00000263923	NM_002253.2	1071	tgG/tgA	24/30	NA	2	FACETS	0.833	0.787	0.88			1	INDETERMINATE	2	TRUE	NA	0.602630302365166	2		287	442	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973911	55973911	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs941528100	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	61	138	0	ENST00000263923.4:c.1405G>A	p.Glu469Lys	p.E469K	ENST00000263923	NM_002253.2	469	Gag/Aag	10/30	0.60577344353505	2	FACETS	0.739	0.643	0.841	0.369	0.321	0.421	SUBCLONAL	1	TRUE	0	0.602630302365166	2		138	274	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980300	55980300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1438804033	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	207	263	0	ENST00000263923.4:c.791C>T	p.Ser264Phe	p.S264F	ENST00000263923	NM_002253.2	264	tCt/tTt	6/30	0.60577344353505	2	FACETS	0.793	0.746	0.841	0.793	0.746	0.841	SUBCLONAL	2	TRUE	0	0.602630302365166	2		263	433	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196537	106196537	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	316	272	0	ENST00000380013.4:c.4870C>T	p.Gln1624Ter	p.Q1624*	ENST00000380013	NM_001127208.2	1624	Cag/Tag	11/11	0.60577344353505	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.602630302365166	2		272	458	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510207	187510207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	186	253	0	ENST00000441802.2:c.13306C>T	p.Pro4436Ser	p.P4436S	ENST00000441802	NM_005245.3	4436	Cct/Tct	27/27	0.419305059635172	4	FACETS	0.979	0.912	1	0.979	0.912	1	CLONAL	2	TRUE	2	0.602630302365166	4		253	505	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524119	187524119	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	113	210	0	ENST00000441802.2:c.11420C>T	p.Ser3807Phe	p.S3807F	ENST00000441802	NM_005245.3	3807	tCt/tTt	20/27	0.419305059635172	4	FACETS	1	0.978	1	0.639	0.579	0.703	CLONAL	1	TRUE	2	0.602630302365166	4		210	470	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530363	187530363	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	119	280	0	ENST00000441802.2:c.10180G>A	p.Val3394Met	p.V3394M	ENST00000441802	NM_005245.3	3394	Gtg/Atg	16/27	0.419305059635172	4	FACETS	1	0.948	1	0.535	0.484	0.588	CLONAL	1	TRUE	2	0.602630302365166	4		280	592	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532639	187532639	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	89	205	0	ENST00000441802.2:c.9754G>A	p.Val3252Met	p.V3252M	ENST00000441802	NM_005245.3	3252	Gtg/Atg	14/27	0.419305059635172	4	FACETS	0.798	0.709	0.893	0.399	0.354	0.447	SUBCLONAL	1	TRUE	2	0.602630302365166	4		205	593	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294163	1294163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199701877	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	141	294	0	ENST00000310581.5:c.838G>A	p.Glu280Lys	p.E280K	ENST00000310581	NM_198253.2	280	Gaa/Aaa	2/16	NA	2	FACETS	0.807	0.749	0.865			1	INDETERMINATE	2	TRUE	NA	0.602630302365166	2		294	290	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945092	38945092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769767383	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	499	240	0	ENST00000357387.3:c.4712C>T	p.Ser1571Leu	p.S1571L	ENST00000357387	NM_152756.3	1571	tCg/tTg	35/38	0.602630302365166	6	FACETS	1	0.987	1	1	0.987	1	CLONAL	5	TRUE	1	0.602630302365166	6		240	708	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160597	56160597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	314	175	0	ENST00000399503.3:c.871C>T	p.Pro291Ser	p.P291S	ENST00000399503	NM_005921.1	291	Cct/Tct	4/20	0.602630302365166	6	FACETS	0.901	0.863	0.939	0.901	0.863	0.939	CLONAL	5	TRUE	1	0.602630302365166	6		175	510	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589168	67589168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	145	296	0	ENST00000274335.5:c.1156C>T	p.Arg386Ter	p.R386*	ENST00000274335		386	Cga/Tga	9/15	0.602630302365166	7	FACETS	1	0.982	1	0.216	0.197	0.237	CLONAL	1	TRUE	1	0.602630302365166	7		296	929	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441110	149441110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	303	472	1	ENST00000286301.3:c.1802C>T	p.Ala601Val	p.A601V	ENST00000286301	NM_005211.3	601	gCc/gTc	13/22	0.372222878685366	5	FACETS	0.98	0.925	1	0.653	0.616	0.691	CLONAL	2	TRUE	2	0.602630302365166	5		473	977	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456854	149456854	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	147	287	0	ENST00000286301.3:c.874T>C	p.Phe292Leu	p.F292L	ENST00000286301	NM_005211.3	292	Ttc/Ctc	6/22	0.372222878685366	5	FACETS	0.958	0.881	1	0.638	0.587	0.691	CLONAL	2	TRUE	2	0.602630302365166	5		287	485	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495486	149495486	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	250	344	0	ENST00000261799.4:c.3161C>T	p.Thr1054Ile	p.T1054I	ENST00000261799	NM_002609.3	1054	aCc/aTc	23/23	0.372222878685366	5	FACETS	0.954	0.901	1	0.954	0.901	1	CLONAL	3	TRUE	2	0.602630302365166	5		344	552	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501449	149501449	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	289	223	0	ENST00000261799.4:c.2338C>T	p.Pro780Ser	p.P780S	ENST00000261799	NM_002609.3	780	Ccc/Tcc	16/23	0.372222878685366	5	FACETS	1	0.989	1	1	0.989	1	CLONAL	3	TRUE	2	0.602630302365166	5		223	537	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501461	149501461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751904503	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	153	247	0	ENST00000261799.4:c.2326G>A	p.Asp776Asn	p.D776N	ENST00000261799	NM_002609.3	776	Gat/Aat	16/23	0.372222878685366	5	FACETS	0.856	0.787	0.927	0.57	0.524	0.618	CLONAL	2	TRUE	2	0.602630302365166	5		247	565	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501516	149501516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	322	254	0	ENST00000261799.4:c.2271G>A	p.Met757Ile	p.M757I	ENST00000261799	NM_002609.3	757	atG/atA	16/23	0.372222878685366	5	FACETS	1	0.987	1	1	0.987	1	CLONAL	3	TRUE	2	0.602630302365166	5		254	620	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510160	149510160	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772355478	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	90	175	0	ENST00000261799.4:c.1309C>T	p.Arg437Cys	p.R437C	ENST00000261799	NM_002609.3	437	Cgt/Tgt	9/23	0.372222878685366	5	FACETS	0.79	0.707	0.877	0.527	0.471	0.585	SUBCLONAL	2	TRUE	2	0.602630302365166	5		175	360	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176671198	176671198	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	98	280	0	ENST00000439151.2:c.4305C>A	p.Cys1435Ter	p.C1435*	ENST00000439151	NM_022455.4	1435	tgC/tgA	9/23	0.505838204551185	3	FACETS	0.822	0.736	0.913	0.411	0.368	0.457	CLONAL	1	TRUE	1	0.602630302365166	3		280	515	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721157	176721157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373571733	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	170	153	0	ENST00000439151.2:c.6788C>T	p.Ser2263Leu	p.S2263L	ENST00000439151	NM_022455.4	2263	tCg/tTg	23/23	0.505838204551185	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.602630302365166	3		153	328	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057038	180057038	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	95	272	0	ENST00000261937.6:c.581C>T	p.Ser194Phe	p.S194F	ENST00000261937	NM_182925.4	194	tCc/tTc	5/30	0.505838204551185	3	FACETS	1	0.973	1	0.625	0.563	0.691	CLONAL	1	TRUE	1	0.602630302365166	3		272	328	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679726	30679726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	183	361	0	ENST00000376406.3:c.1993G>A	p.Gly665Arg	p.G665R	ENST00000376406	NM_014641.2	665	Gga/Aga	5/15	0.602630302365166	5	FACETS	1	0.964	1			1	CLONAL	1	TRUE	NA	0.602630302365166	5		361	1073	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166333	32166333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1249809881	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	120	240	0	ENST00000375023.3:c.4621G>A	p.Glu1541Lys	p.E1541K	ENST00000375023	NM_004557.3	1541	Gaa/Aaa	26/30	0.602630302365166	5	FACETS	0.996	0.9	1			1	CLONAL	1	TRUE	NA	0.602630302365166	5		240	761	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170021	32170021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	300	430	1	ENST00000375023.3:c.3587G>A	p.Gly1196Glu	p.G1196E	ENST00000375023	NM_004557.3	1196	gGa/gAa	21/30	0.420283345506965	5	FACETS	1	0.969	1			1	CLONAL	2	TRUE	NA	0.602630302365166	5		431	914	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187392	32187392	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	51	155	0	ENST00000375023.3:c.1487C>T	p.Thr496Ile	p.T496I	ENST00000375023	NM_004557.3	496	aCc/aTc	8/30	0.420283345506965	5	FACETS	0.921	0.786	1			1	CLONAL	1	TRUE	NA	0.602630302365166	5		155	350	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189048	32189048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	95	253	0	ENST00000375023.3:c.506G>A	p.Gly169Glu	p.G169E	ENST00000375023	NM_004557.3	169	gGg/gAg	4/30	0.420283345506965	5	FACETS	1	0.926	1			1	CLONAL	1	TRUE	NA	0.602630302365166	5		253	573	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287242	33287242	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	251	221	0	ENST00000374542.5:c.1855C>T	p.Pro619Ser	p.P619S	ENST00000374542	NM_001141970.1	619	Cct/Tct	6/8	0.602630302365166	6	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.602630302365166	6		221	824	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790813	89790813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1192495729	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	212	444	0	ENST00000336032.3:c.200G>A	p.Cys67Tyr	p.C67Y	ENST00000336032	NM_006813.2	67	tGt/tAt	1/2	0.60577344353505	3	FACETS	1	0.976	1	0.368	0.342	0.395	CLONAL	1	TRUE	0	0.602630302365166	3		444	829	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641051	117641051	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	550	350	0	ENST00000368508.3:c.5920G>A	p.Glu1974Lys	p.E1974K	ENST00000368508	NM_002944.2	1974	Gaa/Aaa	36/43	0.60577344353505	3	FACETS	0.876	0.856	0.895	1	0.997	1	CLONAL	4	TRUE	0	0.602630302365166	3		350	678	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662434	117662434	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1421889146	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	497	281	0	ENST00000368508.3:c.4943G>A	p.Ser1648Asn	p.S1648N	ENST00000368508	NM_002944.2	1648	aGt/aAt	30/43	0.60577344353505	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	3	TRUE	0	0.602630302365166	3		281	627	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724410	117724410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	279	177	0	ENST00000368508.3:c.469C>T	p.Pro157Ser	p.P157S	ENST00000368508	NM_002944.2	157	Ccc/Tcc	6/43	0.60577344353505	3	FACETS	0.876	0.847	0.902	1	0.994	1	CLONAL	4	TRUE	0	0.602630302365166	3		177	344	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997796	149997796	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	57	211	0	ENST00000253339.5:c.2671C>G	p.Leu891Val	p.L891V	ENST00000253339		891	Ctg/Gtg	5/7	0.420283345506965	5	FACETS	0.674	0.579	0.779			1	SUBCLONAL	1	TRUE	NA	0.602630302365166	5		211	534	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963951	2963951	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	329	335	0	ENST00000396946.4:c.1856C>T	p.Ser619Phe	p.S619F	ENST00000396946	NM_032415.4	619	tCc/tTc	15/25	0.60577344353505	3	FACETS	0.858	0.822	0.894	1	0.994	1	CLONAL	3	TRUE	1	0.602630302365166	3		335	552	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55238896	55238896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	252	169	0	ENST00000275493.2:c.1909C>T	p.Pro637Ser	p.P637S	ENST00000275493	NM_005228.3	637	Cca/Tca	16/28	0.60577344353505	4	FACETS	1	0.95	1	1	0.95	1	CLONAL	3	TRUE	1	0.602630302365166	4		169	447	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268989	55268989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	85	248	0	ENST00000275493.2:c.3055C>T	p.Pro1019Ser	p.P1019S	ENST00000275493	NM_005228.3	1019	Cca/Tca	25/28	0.60577344353505	4	FACETS	1	0.914	1	0.345	0.306	0.386	CLONAL	1	TRUE	1	0.602630302365166	4		248	437	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359066	81359066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	556	302	1	ENST00000222390.5:c.895C>T	p.Pro299Ser	p.P299S	ENST00000222390	NM_000601.4	299	Cct/Tct	8/18	0.60577344353505	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	3	TRUE	1	0.602630302365166	4		303	866	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829258	128829258	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	50	213	0	ENST00000249373.3:c.266C>T	p.Ser89Phe	p.S89F	ENST00000249373	NM_005631.4	89	tCc/tTc	1/12	NA	2	FACETS	0.615	0.525	0.711			1	INDETERMINATE	1	TRUE	NA	0.602630302365166	2		213	270	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148513845	148513845	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	113	270	0	ENST00000320356.2:c.1436C>T	p.Ser479Phe	p.S479F	ENST00000320356	NM_004456.4	479	tCt/tTt	12/20	0.531367490796922	4	FACETS	1	0.926	1			1	CLONAL	1	TRUE	NA	0.602630302365166	4		270	583	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845246	151845246	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	70	155	0	ENST00000262189.6:c.13766C>T	p.Thr4589Ile	p.T4589I	ENST00000262189	NM_170606.2	4589	aCt/aTt	52/59	0.531367490796922	4	FACETS	0.895	0.784	1			1	CLONAL	1	TRUE	NA	0.602630302365166	4		155	416	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983483	90983483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	134	221	0	ENST00000265433.3:c.620G>A	p.Ser207Asn	p.S207N	ENST00000265433	NM_002485.4	207	aGt/aAt	6/16	0.60577344353505	3	FACETS	1	0.952	1	0.532	0.485	0.58	CLONAL	1	TRUE	1	0.602630302365166	3		221	544	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737576	145737576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	126	271	0	ENST00000428558.2:c.3187G>A	p.Glu1063Lys	p.E1063K	ENST00000428558	NM_004260.3	1063	Gag/Aag	19/22	0.60577344353505	3	FACETS	1	0.946	1	0.527	0.48	0.577	CLONAL	1	TRUE	1	0.602630302365166	3		271	516	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436600	8436600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs888423638	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	150	278	0	ENST00000356435.5:c.4078G>A	p.Glu1360Lys	p.E1360K	ENST00000356435		1360	Gaa/Aaa	24/35	0.225493172156593	5	FACETS	1	0.963	1			1	INDETERMINATE	2	TRUE	NA	0.602630302365166	5		278	442	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486052	8486052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	240	364	0	ENST00000356435.5:c.2765C>T	p.Pro922Leu	p.P922L	ENST00000356435		922	cCt/cTt	17/35	0.225493172156593	5	FACETS	0.885	0.834	0.937			1	INDETERMINATE	3	TRUE	NA	0.602630302365166	5		364	571	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971116	21971116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552823	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	193	210	0	ENST00000304494.5:c.242C>T	p.Pro81Leu	p.P81L	ENST00000304494	NM_000077.4	81	cCc/cTc	2/3	0.194345602754622	3	FACETS	1	0.986	1			1	INDETERMINATE	3	TRUE	NA	0.602630302365166	3		210	257	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87356813	87356813	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs199505477	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	771	418	0	ENST00000277120.3:c.1166A>G	p.Asn389Ser	p.N389S	ENST00000277120		389	aAc/aGc	10/19	0.60577344353505	4	FACETS	0.943	0.921	0.965			1	CLONAL	4	TRUE	NA	0.602630302365166	4		418	1087	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650881	93650881	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200438123	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	43	119	0	ENST00000375746.1:c.1807G>A	p.Asp603Asn	p.D603N	ENST00000375746	NM_001174167.1	603	Gat/Aat	13/14	0.60577344353505	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.602630302365166	1		119	85	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133729515	133729515	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	803	376	0	ENST00000318560.5:c.144G>A	p.Trp48Ter	p.W48*	ENST00000318560	NM_005157.4	48	tgG/tgA	2/11	0.602630302365166	6	FACETS	0.987	0.963	1	0.987	0.963	1	CLONAL	5	TRUE	1	0.602630302365166	6		376	1191	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133747593	133747593	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	54	188	0	ENST00000318560.5:c.900G>C	p.Gln300His	p.Q300H	ENST00000318560	NM_005157.4	300	caG/caC	5/11	0.602630302365166	6	FACETS	0.813	0.695	0.942	0.163	0.139	0.189	CLONAL	1	TRUE	1	0.602630302365166	6		188	486	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787827	135787827	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	83	188	0	ENST00000298552.3:c.755C>T	p.Thr252Ile	p.T252I	ENST00000298552	NM_001162426.1	252	aCt/aTt	9/23	0.602630302365166	6	FACETS	1	0.893	1	0.202	0.178	0.228	CLONAL	1	TRUE	1	0.602630302365166	6		188	601	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801014	135801014	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	457	213	2	ENST00000298552.3:c.323C>T	p.Ser108Phe	p.S108F	ENST00000298552	NM_001162426.1	108	tCt/tTt	5/23	0.602630302365166	6	FACETS	1	0.97	1	1	0.97	1	CLONAL	5	TRUE	1	0.602630302365166	6		215	668	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390557	139390557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	175	507	0	ENST00000277541.6:c.7634C>T	p.Ser2545Phe	p.S2545F	ENST00000277541	NM_017617.3	2545	tCc/tTc	34/34	0.602630302365166	6	FACETS	1	0.946	1	0.208	0.19	0.226	CLONAL	1	TRUE	1	0.602630302365166	6		507	1234	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653790	89653790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	219	192	0	ENST00000371953.3:c.88C>T	p.Pro30Ser	p.P30S	ENST00000371953	NM_000314.4	30	Cca/Tca	2/9	0.60577344353505	4	FACETS	0.966	0.905	1	0.966	0.905	1	CLONAL	2	TRUE	2	0.602630302365166	4		192	603	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123260418	123260418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	90	297	0	ENST00000358487.5:c.1483G>A	p.Val495Met	p.V495M	ENST00000358487	NM_000141.4	495	Gtg/Atg	11/18	0.449054085875611	3	FACETS	0.759	0.676	0.848			1	SUBCLONAL	1	TRUE	NA	0.602630302365166	3		297	512	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310896	123310896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs974173968	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	187	332	0	ENST00000358487.5:c.532C>T	p.Arg178Cys	p.R178C	ENST00000358487	NM_000141.4	178	Cgc/Tgc	5/18	0.449054085875611	3	FACETS	0.878	0.82	0.937			1	CLONAL	2	TRUE	NA	0.602630302365166	3		332	460	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410671	32410671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	393	339	0	ENST00000332351.3:c.1487C>T	p.Ser496Leu	p.S496L	ENST00000332351	NM_024426.4	496	tCa/tTa	10/10	0.340070862868781	5	FACETS	1	0.967	1	0.804	0.774	0.833	INDETERMINATE	4	TRUE	0	0.602630302365166	5		339	618	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32439138	32439138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564987636	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	316	202	0	ENST00000332351.3:c.935G>A	p.Gly312Glu	p.G312E	ENST00000332351	NM_024426.4	312	gGa/gAa	4/10	0.340070862868781	5	FACETS	1	0.972	1	0.813	0.78	0.846	INDETERMINATE	4	TRUE	0	0.602630302365166	5		202	491	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204628	108204628	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	224	139	0	ENST00000278616.4:c.7943C>T	p.Pro2648Leu	p.P2648L	ENST00000278616	NM_000051.3	2648	cCa/cTa	54/63	0.60577344353505	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	3	TRUE	1	0.602630302365166	4		139	361	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216545	108216545	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779872	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	177	332	0	ENST00000278616.4:c.8494C>T	p.Arg2832Cys	p.R2832C	ENST00000278616	NM_000051.3	2832	Cgt/Tgt	58/63	0.60577344353505	4	FACETS	1	0.981	1	0.396	0.365	0.428	CLONAL	1	TRUE	1	0.602630302365166	4		332	792	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374838	118374838	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	76	154	0	ENST00000534358.1:c.8231C>T	p.Pro2744Leu	p.P2744L	ENST00000534358	NM_005933.3	2744	cCa/cTa	27/36	0.60577344353505	4	FACETS	0.951	0.838	1	0.317	0.279	0.358	CLONAL	1	TRUE	1	0.602630302365166	4		154	425	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376488	118376488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	371	302	0	ENST00000534358.1:c.9881C>T	p.Ser3294Phe	p.S3294F	ENST00000534358	NM_005933.3	3294	tCt/tTt	27/36	0.60577344353505	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	1	0.602630302365166	4		302	615	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170450	119170450	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	302	234	2	ENST00000264033.4:c.2680G>T	p.Glu894Ter	p.E894*	ENST00000264033	NM_005188.3	894	Gaa/Taa	16/16	0.60577344353505	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	1	0.602630302365166	4		236	502	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641526	18641526	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1331057234	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	232	227	0	ENST00000266497.5:c.2525G>A	p.Gly842Glu	p.G842E	ENST00000266497		842	gGg/gAg	17/31	0.475748983949017	4	FACETS	0.906	0.857	0.955			1	CLONAL	3	TRUE	NA	0.602630302365166	4		227	454	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644490	18644490	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs181773550	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	111	227	0	ENST00000266497.5:c.2668G>A	p.Asp890Asn	p.D890N	ENST00000266497		890	Gat/Aat	18/31	0.475748983949017	4	FACETS	1	0.975	1			1	CLONAL	1	TRUE	NA	0.602630302365166	4		227	477	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715752	18715752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	126	235	0	ENST00000266497.5:c.3583G>A	p.Glu1195Lys	p.E1195K	ENST00000266497		1195	Gaa/Aaa	25/31	0.475748983949017	4	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.602630302365166	4		235	532	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244227	46244227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	185	185	0	ENST00000334344.6:c.2321C>T	p.Pro774Leu	p.P774L	ENST00000334344	NM_152641.2	774	cCa/cTa	15/21	0.60577344353505	4	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	2	0.602630302365166	4		185	486	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245939	46245939	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	109	188	0	ENST00000334344.6:c.4033G>A	p.Asp1345Asn	p.D1345N	ENST00000334344	NM_152641.2	1345	Gac/Aac	15/21	0.60577344353505	4	FACETS	1	0.962	1	0.567	0.511	0.626	CLONAL	1	TRUE	2	0.602630302365166	4		188	511	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425562	49425562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	197	476	0	ENST00000301067.7:c.12926C>T	p.Pro4309Leu	p.P4309L	ENST00000301067	NM_003482.3	4309	cCt/cTt	39/54	0.60577344353505	4	FACETS	1	0.98	1	0.578	0.535	0.622	CLONAL	1	TRUE	2	0.602630302365166	4		476	907	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426484	49426484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	258	555	1	ENST00000301067.7:c.12004C>T	p.Pro4002Ser	p.P4002S	ENST00000301067	NM_003482.3	4002	Cca/Tca	39/54	0.60577344353505	4	FACETS	1	0.987	1	0.598	0.56	0.638	CLONAL	1	TRUE	2	0.602630302365166	4		556	1147	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431026	49431026	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	108	281	0	ENST00000301067.7:c.10113G>T	p.Gln3371His	p.Q3371H	ENST00000301067	NM_003482.3	3371	caG/caT	34/54	0.60577344353505	4	FACETS	0.964	0.867	1	0.482	0.433	0.533	CLONAL	1	TRUE	2	0.602630302365166	4		281	596	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435231	49435231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	190	221	1	ENST00000301067.7:c.6322C>T	p.Pro2108Ser	p.P2108S	ENST00000301067	NM_003482.3	2108	Ccg/Tcg	31/54	0.60577344353505	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.602630302365166	4		222	445	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436961	49436961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1392313479	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	100	262	0	ENST00000301067.7:c.5542G>A	p.Asp1848Asn	p.D1848N	ENST00000301067	NM_003482.3	1848	Gat/Aat	25/54	0.60577344353505	4	FACETS	0.801	0.716	0.891	0.401	0.358	0.446	CLONAL	1	TRUE	2	0.602630302365166	4		262	664	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445664	49445664	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1242866061	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	357	400	0	ENST00000301067.7:c.1802C>T	p.Pro601Leu	p.P601L	ENST00000301067	NM_003482.3	601	cCa/cTa	10/54	0.60577344353505	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.602630302365166	4		400	840	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445700	49445700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	402	463	0	ENST00000301067.7:c.1766C>T	p.Pro589Leu	p.P589L	ENST00000301067	NM_003482.3	589	cCc/cTc	10/54	0.60577344353505	4	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	2	0.602630302365166	4		463	977	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446157	49446157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	63	122	0	ENST00000301067.7:c.1309G>A	p.Glu437Lys	p.E437K	ENST00000301067	NM_003482.3	437	Gag/Aag	10/54	0.60577344353505	4	FACETS	0.931	0.809	1	0.465	0.404	0.531	CLONAL	1	TRUE	2	0.602630302365166	4		122	360	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416788	121416788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs905788991	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	231	437	0	ENST00000257555.6:c.217G>A	p.Glu73Lys	p.E73K	ENST00000257555		73	Gag/Aag	1/10	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.602630302365166	2		437	626	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21620063	21620063	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	138	412	0	ENST00000382592.4:c.103C>T	p.Gln35Ter	p.Q35*	ENST00000382592	NM_014572.2	35	Cag/Tag	2/8	0.172626997559109	0	FACETS	0.422	0.387	0.458			1	INDETERMINATE	1	TRUE	0	0.602630302365166	0		412	431	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001305	29001305	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	68	217	0	ENST00000282397.4:c.1427C>T	p.Ser476Phe	p.S476F	ENST00000282397	NM_002019.4	476	tCc/tTc	10/30	0.172626997559109	0	FACETS	0.357	0.314	0.402			1	INDETERMINATE	1	TRUE	0	0.602630302365166	0		217	251	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32921026	32921026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	118	258	0	ENST00000380152.3:c.7000C>T	p.Pro2334Ser	p.P2334S	ENST00000380152		2334	Ccc/Tcc	13/27	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.602630302365166	2		258	357	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32969009	32969009	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	162	391	0	ENST00000380152.3:c.9440C>T	p.Ser3147Phe	p.S3147F	ENST00000380152		3147	tCt/tTt	25/27	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.602630302365166	2		391	527	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972596	32972596	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	102	235	0	ENST00000380152.3:c.9946G>A	p.Glu3316Lys	p.E3316K	ENST00000380152		3316	Gaa/Aaa	27/27	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.602630302365166	2		235	329	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346841	73346841	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	123	206	0	ENST00000377767.4:c.1376T>C	p.Ile459Thr	p.I459T	ENST00000377767	NM_014953.3	459	aTt/aCt	9/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.602630302365166	2		206	348	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435291	110435291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	25	44	0	ENST00000375856.3:c.3110C>T	p.Ala1037Val	p.A1037V	ENST00000375856	NM_003749.2	1037	gCc/gTc	1/2	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.602630302365166	2		44	65	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610248	81610248	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	60	218	0	ENST00000298171.2:c.1846G>A	p.Gly616Arg	p.G616R	ENST00000298171	NM_000369.2	616	Ggg/Agg	10/10	0.372222878685366	5	FACETS	0.962	0.832	1	0.321	0.277	0.368	CLONAL	1	TRUE	2	0.602630302365166	5		218	394	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610608	81610608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	228	309	0	ENST00000298171.2:c.2206G>A	p.Glu736Lys	p.E736K	ENST00000298171	NM_000369.2	736	Gaa/Aaa	10/10	0.372222878685366	5	FACETS	1	0.988	1	0.808	0.759	0.859	CLONAL	2	TRUE	2	0.602630302365166	5		309	594	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569702	95569702	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	138	207	0	ENST00000393063.1:c.4031C>T	p.Ser1344Leu	p.S1344L	ENST00000393063	NM_030621.3	1344	tCa/tTa	22/28	0.372222878685366	5	FACETS	0.995	0.914	1	0.664	0.609	0.72	CLONAL	2	TRUE	2	0.602630302365166	5		207	438	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476243	88476243	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	142	231	0	ENST00000360948.2:c.1889G>A	p.Arg630Lys	p.R630K	ENST00000360948	NM_001012338.2	630	aGg/aAg	15/19	0.531367490796922	4	FACETS	0.805	0.739	0.873			1	CLONAL	2	TRUE	NA	0.602630302365166	4		231	469	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99491879	99491879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	215	349	1	ENST00000268035.6:c.3664C>T	p.Leu1222Phe	p.L1222F	ENST00000268035	NM_000875.3	1222	Ctt/Ttt	20/21	0.578258467089025	5	FACETS	0.999	0.933	1			1	CLONAL	2	TRUE	NA	0.602630302365166	5		350	680	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943819	9943819	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	86	108	0	ENST00000330684.3:c.1123-1G>A		p.X375_splice	ENST00000330684	NM_001134407.1	375			0.419305059635172	4	FACETS	1	0.918	1	1	0.918	1	CLONAL	2	TRUE	2	0.602630302365166	4		108	224	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7978952	7978952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139689690	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	241	336	0	ENST00000319144.4:c.1615G>A	p.Glu539Lys	p.E539K	ENST00000319144	NM_001139.2	539	Gaa/Aaa	12/15	0.60577344353505	3	FACETS	1	0.964	1	0.684	0.646	0.722	CLONAL	2	TRUE	0	0.602630302365166	3		336	507	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29508803	29508803	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1567826188	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	89	221	0	ENST00000356175.3:c.730G>A	p.Glu244Lys	p.E244K	ENST00000356175	NM_000267.3	244	Gaa/Aaa	7/57	0.439621286604576	4	FACETS	1	0.961	1			1	CLONAL	1	TRUE	NA	0.602630302365166	4		221	405	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654712	29654712	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	303	226	0	ENST00000356175.3:c.5401C>T	p.Gln1801Ter	p.Q1801*	ENST00000356175	NM_000267.3	1801	Cag/Tag	37/57	0.439621286604576	4	FACETS	0.886	0.844	0.929			1	CLONAL	3	TRUE	NA	0.602630302365166	4		226	606	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33427997	33427997	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	129	365	0	ENST00000345365.6:c.962C>T	p.Ala321Val	p.A321V	ENST00000345365	NM_002878.3	321	gCc/gTc	10/10	0.449054085875611	3	FACETS	0.967	0.88	1			1	CLONAL	1	TRUE	NA	0.602630302365166	3		365	576	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780590	56780590	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	501	402	0	ENST00000337432.4:c.605A>T	p.Asp202Val	p.D202V	ENST00000337432	NM_058216.2	202	gAt/gTt	4/9	0.602630302365166	6	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	3	0.602630302365166	6		402	1170	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59793418	59793418	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	456	357	0	ENST00000259008.2:c.2386C>A	p.Leu796Ile	p.L796I	ENST00000259008	NM_032043.2	796	Cta/Ata	17/20	0.602630302365166	6	FACETS	0.993	0.951	1	0.993	0.951	1	CLONAL	3	TRUE	3	0.602630302365166	6		357	1120	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62009619	62009619	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	315	359	0	ENST00000392795.3:c.3G>A	p.Met1?	p.M1?	ENST00000392795	NM_001039933.1	1	atG/atA	1/6	0.602630302365166	6	FACETS	0.938	0.889	0.988	0.938	0.889	0.988	CLONAL	3	TRUE	3	0.602630302365166	6		359	819	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117597	70117597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	123	332	1	ENST00000245479.2:c.65C>T	p.Pro22Leu	p.P22L	ENST00000245479	NM_000346.3	22	cCc/cTc	1/3	0.602630302365166	6	FACETS	0.962	0.869	1	0.321	0.289	0.354	CLONAL	1	TRUE	3	0.602630302365166	6		333	936	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897297	78897297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776371271	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	76	280	0	ENST00000306801.3:c.2632C>T	p.Pro878Ser	p.P878S	ENST00000306801	NM_020761.2	878	Cct/Tct	23/34	0.602630302365166	6	FACETS	0.823	0.722	0.932	0.274	0.24	0.311	CLONAL	1	TRUE	3	0.602630302365166	6		280	676	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2206752	2206752	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	95	305	0	ENST00000398665.3:c.812C>G	p.Pro271Arg	p.P271R	ENST00000398665	NM_032482.2	271	cCc/cGc	10/28	0.308682382898426	4	FACETS	0.77	0.686	0.859	0.385	0.343	0.43	INDETERMINATE	1	TRUE	2	0.602630302365166	4		305	656	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227103	2227103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	24	63	0	ENST00000398665.3:c.4583G>A	p.Gly1528Glu	p.G1528E	ENST00000398665	NM_032482.2	1528	gGg/gAg	27/28	0.308682382898426	4	FACETS	0.734	0.58	0.908	0.367	0.29	0.454	INDETERMINATE	1	TRUE	2	0.602630302365166	4		63	174	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5245913	5245913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	141	392	0	ENST00000357368.4:c.862G>A	p.Glu288Lys	p.E288K	ENST00000357368	NM_002850.3	288	Gag/Aag	10/38	0.308682382898426	4	FACETS	1	0.979	1	0.614	0.561	0.669	INDETERMINATE	1	TRUE	2	0.602630302365166	4		392	611	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281491	15281491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	142	285	0	ENST00000263388.2:c.4882G>A	p.Asp1628Asn	p.D1628N	ENST00000263388	NM_000435.2	1628	Gac/Aac	26/33	0.232437907028561	4	FACETS	0.899	0.827	0.973	0.599	0.551	0.649	INDETERMINATE	2	TRUE	1	0.602630302365166	4		285	420	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296473	15296473	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	157	276	0	ENST00000263388.2:c.1969G>T	p.Glu657Ter	p.E657*	ENST00000263388	NM_000435.2	657	Gag/Tag	13/33	0.232437907028561	4	FACETS	0.926	0.856	0.997	0.617	0.57	0.665	INDETERMINATE	2	TRUE	1	0.602630302365166	4		276	451	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355266	15355266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770044101	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	46	46	0	ENST00000263377.2:c.2357C>T	p.Pro786Leu	p.P786L	ENST00000263377	NM_058243.2	786	cCg/cTg	13/20	0.439621286604576	4	FACETS	1	0.93	1			1	CLONAL	2	TRUE	NA	0.602630302365166	4		46	110	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937650	17937650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746347398	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	87	259	0	ENST00000458235.1:c.3277C>T	p.Pro1093Ser	p.P1093S	ENST00000458235	NM_000215.3	1093	Ccc/Tcc	24/24	NA	2	FACETS	0.791	0.706	0.881			1	INDETERMINATE	1	TRUE	NA	0.602630302365166	2		259	365	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741836	40741836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	540	330	2	ENST00000392038.2:c.1136C>T	p.Ser379Phe	p.S379F	ENST00000392038	NM_001626.4	379	tCc/tTc	11/14	0.602630302365166	5	FACETS	1	0.977	1			1	CLONAL	4	TRUE	NA	0.602630302365166	5		332	845	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538374	9538374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868564987	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	150	295	0	ENST00000353224.5:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000353224	NM_177990.2	542	Gaa/Aaa	7/10	0.395552731603754	5	FACETS	0.875	0.811	0.94	0.875	0.811	0.94	CLONAL	3	TRUE	2	0.602630302365166	5		295	361	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546931	9546931	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs562732119	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	108	155	0	ENST00000353224.5:c.1091C>T	p.Ser364Leu	p.S364L	ENST00000353224	NM_177990.2	364	tCg/tTg	5/10	0.395552731603754	5	FACETS	1	0.968	1	0.763	0.695	0.834	CLONAL	2	TRUE	2	0.602630302365166	5		155	298	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309465	30309465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	179	413	0	ENST00000307677.4:c.557G>A	p.Gly186Asp	p.G186D	ENST00000307677	NM_138578.1	186	gGc/gAc	2/3	0.395552731603754	5	FACETS	1	0.974	1	0.378	0.348	0.409	CLONAL	1	TRUE	2	0.602630302365166	5		413	998	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730817	40730817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	108	206	0	ENST00000373198.4:c.3718C>T	p.Leu1240Phe	p.L1240F	ENST00000373198	NM_133170.3	1240	Ctt/Ttt	27/32	0.449054085875611	3	FACETS	0.799	0.727	0.872			1	SUBCLONAL	2	TRUE	NA	0.602630302365166	3		206	292	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730818	40730818	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	123	210	0	ENST00000373198.4:c.3717C>A	p.Phe1239Leu	p.F1239L	ENST00000373198	NM_133170.3	1239	ttC/ttA	27/32	0.449054085875611	3	FACETS	0.916	0.842	0.991			1	CLONAL	2	TRUE	NA	0.602630302365166	3		210	290	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40911144	40911144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776134993	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	259	359	0	ENST00000373198.4:c.2161C>T	p.Arg721Cys	p.R721C	ENST00000373198	NM_133170.3	721	Cgt/Tgt	13/32	0.449054085875611	3	FACETS	0.813	0.766	0.861			1	CLONAL	2	TRUE	NA	0.602630302365166	3		359	688	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755572	39755572	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	217	280	0	ENST00000288319.7:c.1193C>T	p.Ala398Val	p.A398V	ENST00000288319	NM_182918.3	398	gCc/gTc	10/10	0.419305059635172	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.602630302365166	4		280	539	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775563	39775563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	98	234	0	ENST00000288319.7:c.457C>T	p.Pro153Ser	p.P153S	ENST00000288319	NM_182918.3	153	Cca/Tca	4/10	0.419305059635172	4	FACETS	1	0.93	1	0.524	0.47	0.582	CLONAL	1	TRUE	2	0.602630302365166	4		234	497	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656818	45656818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	98	260	0	ENST00000407780.3:c.338G>A	p.Cys113Tyr	p.C113Y	ENST00000407780	NM_001283052.1	113	tGc/tAc	3/7	0.419305059635172	4	FACETS	1	0.966	1	0.594	0.533	0.658	CLONAL	1	TRUE	2	0.602630302365166	4		260	439	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30064325	30064325	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	88	220	0	ENST00000338641.4:c.889C>G	p.Leu297Val	p.L297V	ENST00000338641	NM_000268.3	297	Ctc/Gtc	10/16	0.475748983949017	4	FACETS	1	0.947	1			1	CLONAL	1	TRUE	NA	0.602630302365166	4		220	424	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923720	39923720	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	400	318	2	ENST00000378444.4:c.3371T>C	p.Met1124Thr	p.M1124T	ENST00000378444	NM_001123385.1	1124	aTg/aCg	7/15	0.475748983949017	2	FACETS	0.911	0.887	0.933			1	CLONAL	3	TRUE	NA	0.602630302365166	2		320	486	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936022	44936022	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	556	359	0	ENST00000377967.4:c.2783A>G	p.Tyr928Cys	p.Y928C	ENST00000377967	NM_021140.2	928	tAc/tGc	18/29	0.475748983949017	2	FACETS	0.879	0.858	0.899			1	CLONAL	3	TRUE	NA	0.602630302365166	2		359	700	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938405	44938405	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	353	180	0	ENST00000377967.4:c.2953T>A	p.Ser985Thr	p.S985T	ENST00000377967	NM_021140.2	985	Tct/Act	20/29	0.475748983949017	2	FACETS	0.872	0.845	0.897			1	CLONAL	3	TRUE	NA	0.602630302365166	2		180	448	SUCCESS
AR	367	MSKCC	GRCh37	X	66766138	66766138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	218	145	0	ENST00000374690.3:c.1150C>T	p.His384Tyr	p.H384Y	ENST00000374690	NM_000044.3	384	Cac/Tac	1/8	0.475748983949017	2	FACETS	0.931	0.9	0.96			1	CLONAL	3	TRUE	NA	0.602630302365166	2		145	259	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339298	70339298	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	159	179	0	ENST00000374080.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000374080		59	Gcc/Acc	2/45	0.602630302365166	3	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.602630302365166	3		179	524	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344677	70344677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	222	240	0	ENST00000374080.3:c.2038G>A	p.Glu680Lys	p.E680K	ENST00000374080		680	Gag/Aag	14/45	0.602630302365166	3	FACETS	1	0.99	1			1	CLONAL	1	TRUE	NA	0.602630302365166	3		240	710	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345525	70345525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	244	324	0	ENST00000374080.3:c.2384C>T	p.Pro795Leu	p.P795L	ENST00000374080		795	cCt/cTt	17/45	0.602630302365166	3	FACETS	1	0.99	1			1	CLONAL	1	TRUE	NA	0.602630302365166	3		324	827	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050821	5050829	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	AACTCTATC	AACTCTATC	-	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	113	163	0	ENST00000381652.3:c.605_613del	p.Asn202_Ile204del	p.N202_I204del	ENST00000381652	NM_004972.3	202	AACTCTATC/-	6/25	0.60577344353505	4	FACETS	0.775	0.703	0.848			1	SUBCLONAL	2	TRUE	NA	0.602630302365166	4		163	388	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879009	151879010	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	234	183	0	ENST00000262189.6:c.5935_5936delinsAT	p.Pro1979Ile	p.P1979I	ENST00000262189	NM_170606.2	1979	CCc/ATc	36/59	0.531367490796922	4	FACETS	0.96	0.91	1			1	CLONAL	3	TRUE	NA	0.602630302365166	4		183	432	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979539	55979540	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	128	365	0	ENST00000263923.4:c.907_908delinsAA	p.Gly303Lys	p.G303K	ENST00000263923	NM_002253.2	303	GGa/AAa	7/30	0.60577344353505	2	FACETS	0.858	0.782	0.937	0.429	0.391	0.469	CLONAL	1	TRUE	0	0.602630302365166	2		365	495	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139545	47139546	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0000686-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	600	388	0	ENST00000409792.3:c.5041_5042delinsAT	p.Gly1681Ile	p.G1681I	ENST00000409792	NM_014159.6	1681	GGa/ATa	9/21	0.602630302365166	6	FACETS	1	0.974	1	1	0.974	1	CLONAL	5	TRUE	1	0.602630302365166	6		388	877	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	64	339	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	0.119155205555724	4	FACETS	0.613	0.529	0.703	0.306	0.264	0.352	INDETERMINATE	1	TRUE	2	0.348696937158292	4		339	808	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36814315	36814316	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	47	459	0	ENST00000373129.3:c.724_725delinsTT	p.Pro242Phe	p.P242F	ENST00000373129	NM_032017.1	242	CCc/TTc	8/12	1	2	FACETS	0.677	0.573	0.792	0.677	0.573	0.792	SUBCLONAL	1	TRUE	1	0.348696937158292	2		459	398	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695809	117695809	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1042229408	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	50	263	0	ENST00000369458.3:c.628G>A	p.Val210Ile	p.V210I	ENST00000369458	NM_024626.3	210	Gtt/Att	4/6	0.119155205555724	4	FACETS	0.923	0.785	1	0.462	0.392	0.537	INDETERMINATE	1	TRUE	2	0.348696937158292	4		263	419	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551682	150551682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	23	220	0	ENST00000369026.2:c.325G>A	p.Glu109Lys	p.E109K	ENST00000369026	NM_021960.4	109	Gag/Aag	1/3	0.119155205555724	4	FACETS	0.583	0.455	0.732	0.292	0.227	0.366	INDETERMINATE	1	TRUE	2	0.348696937158292	4		220	305	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844786	156844786	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	21	348	0	ENST00000524377.1:c.1340A>G	p.Lys447Arg	p.K447R	ENST00000524377	NM_002529.3	447	aAg/aGg	11/17	1	2	FACETS	0.315	0.242	0.401	0.315	0.242	0.401	SUBCLONAL	1	TRUE	1	0.348696937158292	2		348	382	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846310	156846310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	45	465	0	ENST00000524377.1:c.1751C>T	p.Pro584Leu	p.P584L	ENST00000524377	NM_002529.3	584	cCc/cTc	14/17	1	2	FACETS	0.757	0.638	0.887	0.757	0.638	0.887	SUBCLONAL	1	TRUE	1	0.348696937158292	2		465	341	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578211	226578211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147537486	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	54	376	0	ENST00000366794.5:c.517C>T	p.Arg173Trp	p.R173W	ENST00000366794	NM_001618.3	173	Cgg/Tgg	4/23	1	2	FACETS	0.589	0.503	0.683	0.589	0.503	0.683	SUBCLONAL	1	TRUE	1	0.348696937158292	2		376	526	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101081	26101087	+	frameshift_variant	Frame_Shift_Del	DEL	TTTTCCC	TTTTCCC	AG	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	117	687	0	ENST00000435504.4:c.5_11delinsCT	p.Arg2ThrfsTer4	p.R2Tfs*4	ENST00000435504		2	aGGGAAAAg/aCTg	1/13	0.246932638707968	2	FACETS	0.945	0.853	1	0.473	0.426	0.521	CLONAL	1	TRUE	0	0.348696937158292	2		687	710	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027253	48027253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878853714	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	74	268	0	ENST00000234420.5:c.2131C>T	p.Pro711Ser	p.P711S	ENST00000234420	NM_000179.2	711	Ccc/Tcc	4/10	0.246932638707968	2	FACETS	0.952	0.836	1	0.476	0.418	0.538	CLONAL	1	TRUE	0	0.348696937158292	2		268	446	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027896	48027896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	64	349	0	ENST00000234420.5:c.2774G>A	p.Gly925Glu	p.G925E	ENST00000234420	NM_000179.2	925	gGa/gAa	4/10	0.246932638707968	2	FACETS	0.592	0.512	0.678	0.296	0.256	0.339	SUBCLONAL	1	TRUE	0	0.348696937158292	2		349	620	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028131	48028131	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	187	427	0	ENST00000234420.5:c.3009T>A	p.Cys1003Ter	p.C1003*	ENST00000234420	NM_000179.2	1003	tgT/tgA	4/10	0.246932638707968	2	FACETS	1	0.99	1	0.741	0.686	0.797	CLONAL	1	TRUE	0	0.348696937158292	2		427	724	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033729	48033729	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1416452389	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	56	305	0	ENST00000234420.5:c.3940C>T	p.Gln1314Ter	p.Q1314*	ENST00000234420	NM_000179.2	1314	Caa/Taa	9/10	0.246932638707968	2	FACETS	0.472	0.403	0.546	0.236	0.201	0.273	SUBCLONAL	1	TRUE	0	0.348696937158292	2		305	681	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096498	178096498	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs375627384	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	103	359	0	ENST00000397062.3:c.833A>G	p.Asn278Ser	p.N278S	ENST00000397062	NM_006164.4	278	aAc/aGc	5/5	1	2	FACETS	0.669	0.598	0.745	0.669	0.598	0.745	SUBCLONAL	1	TRUE	1	0.348696937158292	2		359	883	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288978	212288979	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	78	542	0	ENST00000342788.4:c.2767_2768delinsAA	p.Gly923Lys	p.G923K	ENST00000342788	NM_005235.2	923	GGa/AAa	23/28	1	2	FACETS	0.589	0.517	0.666	0.589	0.517	0.666	SUBCLONAL	1	TRUE	1	0.348696937158292	2		542	760	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225365132	225365132	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	115	353	0	ENST00000264414.4:c.1558C>T	p.Pro520Ser	p.P520S	ENST00000264414	NM_003590.4	520	Cca/Tca	11/16	1	2	FACETS	0.659	0.592	0.73	0.659	0.592	0.73	SUBCLONAL	1	TRUE	1	0.348696937158292	2		353	1001	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662526	227662526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	39	188	0	ENST00000305123.5:c.929C>T	p.Ala310Val	p.A310V	ENST00000305123	NM_005544.2	310	gCc/gTc	1/2	1	2	FACETS	0.79	0.658	0.936	0.79	0.658	0.936	CLONAL	1	TRUE	1	0.348696937158292	2		188	283	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806119	1806119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931614	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	48	601	0	ENST00000260795.2:c.1138G>A	p.Gly380Arg	p.G380R	ENST00000260795		380	Ggg/Agg	8/17	1	2	FACETS	0.85	0.722	0.989	0.85	0.722	0.989	CLONAL	1	TRUE	1	0.348696937158292	2		601	324	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808367	1808367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755495007	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	35	372	0	ENST00000260795.2:c.2125G>A	p.Glu709Lys	p.E709K	ENST00000260795		709	Gag/Aag	15/17	1	2	FACETS	0.819	0.676	0.978	0.819	0.676	0.978	CLONAL	1	TRUE	1	0.348696937158292	2		372	245	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293592	1293592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1013341756	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	20	320	0	ENST00000310581.5:c.1409G>A	p.Arg470His	p.R470H	ENST00000310581	NM_198253.2	470	cGc/cAc	2/16	1	2	FACETS	0.594	0.457	0.754	0.594	0.457	0.754	SUBCLONAL	1	TRUE	1	0.348696937158292	2		320	193	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871292	35871292	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	53	339	0	ENST00000303115.3:c.514G>A	p.Glu172Lys	p.E172K	ENST00000303115	NM_002185.3	172	Gaa/Aaa	4/8	0.119155205555724	4	FACETS	0.785	0.67	0.912	0.393	0.335	0.456	INDETERMINATE	1	TRUE	2	0.348696937158292	4		339	522	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637573	176637573	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	66	312	0	ENST00000439151.2:c.2173A>C	p.Thr725Pro	p.T725P	ENST00000439151	NM_022455.4	725	Acg/Ccg	5/23	1	2	FACETS	0.769	0.669	0.878	0.769	0.669	0.878	SUBCLONAL	1	TRUE	1	0.348696937158292	2		312	492	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039532	180039532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745459631	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	43	448	0	ENST00000261937.6:c.3511G>A	p.Asp1171Asn	p.D1171N	ENST00000261937	NM_182925.4	1171	Gac/Aac	26/30	0.348696937158292	0	FACETS	0.648	0.546	0.758			1	SUBCLONAL	1	TRUE	0	0.348696937158292	0		448	248	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048217	180048217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1410033838	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	17	273	0	ENST00000261937.6:c.2056G>A	p.Asp686Asn	p.D686N	ENST00000261937	NM_182925.4	686	Gac/Aac	14/30	0.348696937158292	0	FACETS	0.281	0.21	0.365			1	SUBCLONAL	1	TRUE	0	0.348696937158292	0		273	226	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407570	407570	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	91	362	0	ENST00000380956.4:c.1328C>T	p.Ser443Phe	p.S443F	ENST00000380956	NM_001195286.1	443	tCt/tTt	9/9	0.324575302231636	5	FACETS	0.918	0.814	1	0.306	0.271	0.343	CLONAL	1	TRUE	2	0.348696937158292	5		362	866	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481478	20481478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	98	347	0	ENST00000346618.3:c.547C>T	p.Leu183Phe	p.L183F	ENST00000346618	NM_001949.4	183	Ctt/Ttt	3/7	0.324575302231636	5	FACETS	1	0.959	1	0.385	0.343	0.43	CLONAL	1	TRUE	2	0.348696937158292	5		347	741	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180653	32180653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	45	332	0	ENST00000375023.3:c.2474C>T	p.Pro825Leu	p.P825L	ENST00000375023	NM_004557.3	825	cCt/cTt	16/30	NA	2	FACETS	0.703	0.593	0.825			1	INDETERMINATE	1	TRUE	NA	0.348696937158292	2		332	367	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790687	89790687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	118	878	0	ENST00000336032.3:c.74C>T	p.Ser25Phe	p.S25F	ENST00000336032	NM_006813.2	25	tCc/tTc	1/2	0.324575302231636	5	FACETS	1	0.964	1	0.382	0.344	0.422	CLONAL	1	TRUE	2	0.348696937158292	5		878	899	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555167	106555167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747743863	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	45	179	0	ENST00000369096.4:c.2284G>A	p.Val762Met	p.V762M	ENST00000369096	NM_001198.3	762	Gtg/Atg	7/7	0.324575302231636	5	FACETS	1	0.845	1	0.334	0.281	0.393	CLONAL	1	TRUE	2	0.348696937158292	5		179	392	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674249	117674249	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	94	513	0	ENST00000368508.3:c.4225C>T	p.Gln1409Ter	p.Q1409*	ENST00000368508	NM_002944.2	1409	Cag/Tag	26/43	NA	2	FACETS	0.7	0.623	0.783			1	INDETERMINATE	1	TRUE	NA	0.348696937158292	2		513	770	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005429	150005429	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142352110	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	93	425	0	ENST00000253339.5:c.796C>T	p.Pro266Ser	p.P266S	ENST00000253339		266	Cct/Tct	3/7	1	2	FACETS	0.918	0.818	1	0.918	0.818	1	CLONAL	1	TRUE	1	0.348696937158292	2		425	581	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023124	150023124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	81	574	0	ENST00000253339.5:c.139G>A	p.Ala47Thr	p.A47T	ENST00000253339		47	Gct/Act	1/7	1	2	FACETS	0.585	0.515	0.661	0.585	0.515	0.661	SUBCLONAL	1	TRUE	1	0.348696937158292	2		574	794	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969988	161969988	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	104	657	0	ENST00000366898.1:c.981G>A	p.Met327Ile	p.M327I	ENST00000366898	NM_004562.2	327	atG/atA	9/12	1	2	FACETS	0.808	0.724	0.898	0.808	0.724	0.898	CLONAL	1	TRUE	1	0.348696937158292	2		657	738	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846164	128846164	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	79	616	0	ENST00000249373.3:c.1094G>A	p.Trp365Ter	p.W365*	ENST00000249373	NM_005631.4	365	tGg/tAg	5/12	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.348696937158292	2		616	437	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439617	140439617	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	95	382	0	ENST00000288602.6:c.2122C>T	p.Pro708Ser	p.P708S	ENST00000288602	NM_004333.4	708	Ccc/Tcc	17/18	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.348696937158292	2		382	528	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140500180	140500180	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	119	269	0	ENST00000288602.6:c.962C>T	p.Pro321Leu	p.P321L	ENST00000288602	NM_004333.4	321	cCc/cTc	7/18	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.348696937158292	2		269	630	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012235	152012236	+	stop_gained	Nonsense_Mutation	DNP	CT	CT	TA	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	141	469	0	ENST00000262189.6:c.577_578delinsTA	p.Arg193Ter	p.R193*	ENST00000262189	NM_170606.2	193	AGa/TAa	4/59	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.348696937158292	2		469	802	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971114	21971114	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501269	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	49	179	2	ENST00000304494.5:c.244G>A	p.Val82Met	p.V82M	ENST00000304494	NM_000077.4	82	Gtg/Atg	2/3	0.294860597809886	1	FACETS	0.714	0.608	0.83	0.714	0.608	0.83	SUBCLONAL	1	TRUE	0	0.348696937158292	1		181	325	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399143	139399143	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	29	355	0	ENST00000277541.6:c.5000A>G	p.Asp1667Gly	p.D1667G	ENST00000277541	NM_017617.3	1667	gAc/gGc	26/34	0.246932638707968	2	FACETS	0.832	0.673	1	0.416	0.336	0.505	CLONAL	1	TRUE	0	0.348696937158292	2		355	200	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412203	139412204	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	64	324	1	ENST00000277541.6:c.1441_1441+1delinsAA		p.X481_splice	ENST00000277541	NM_017617.3	481		8/34	0.246932638707968	2	FACETS	1	0.971	1	0.717	0.628	0.811	CLONAL	1	TRUE	0	0.348696937158292	2		325	256	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416840	416840	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	92	453	0	ENST00000399788.2:c.3710C>T	p.Pro1237Leu	p.P1237L	ENST00000399788	NM_001042603.1	1237	cCc/cTc	23/28	0.348696937158292	1	FACETS	0.555	0.493	0.622	0.555	0.493	0.622	SUBCLONAL	1	TRUE	0	0.348696937158292	1		453	785	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46215212	46215212	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	67	299	0	ENST00000334344.6:c.647C>T	p.Ser216Phe	p.S216F	ENST00000334344	NM_152641.2	216	tCc/tTc	6/21	1	2	FACETS	0.572	0.496	0.654	0.572	0.496	0.654	SUBCLONAL	1	TRUE	1	0.348696937158292	2		299	672	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433394	49433394	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783727	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	14	310	0	ENST00000301067.7:c.8053C>T	p.Arg2685Ter	p.R2685*	ENST00000301067	NM_003482.3	2685	Cga/Tga	32/54	1	2	FACETS	0.613	0.446	0.811	0.613	0.446	0.811	SUBCLONAL	1	TRUE	1	0.348696937158292	2		310	131	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484046	50484046	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1400988399	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	74	439	0	ENST00000394963.4:c.896C>T	p.Pro299Leu	p.P299L	ENST00000394963	NM_003076.4	299	cCc/cTc	8/13	1	2	FACETS	0.697	0.61	0.79	0.697	0.61	0.79	SUBCLONAL	1	TRUE	1	0.348696937158292	2		439	609	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869552	102869552	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766508915	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	25	133	0	ENST00000307046.8:c.89C>T	p.Ser30Leu	p.S30L	ENST00000307046	NM_001111285.1	30	tCg/tTg	2/4	1	2	FACETS	0.451	0.355	0.56	0.451	0.355	0.56	SUBCLONAL	1	TRUE	1	0.348696937158292	2		133	318	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133242017	133242017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778288256	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	55	290	2	ENST00000320574.5:c.2339C>T	p.Ser780Leu	p.S780L	ENST00000320574	NM_006231.2	780	tCg/tTg	21/49	0.294860597809886	1	FACETS	0.698	0.6	0.805	0.698	0.6	0.805	SUBCLONAL	1	TRUE	0	0.348696937158292	1		292	373	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126157	2126157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1319146226	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	38	387	0	ENST00000219476.3:c.2728C>T	p.Pro910Ser	p.P910S	ENST00000219476	NM_000548.3	910	Cct/Tct	24/42	0.294860597809886	1	FACETS	0.671	0.558	0.797	0.671	0.558	0.797	SUBCLONAL	1	TRUE	0	0.348696937158292	1		387	268	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779218	3779218	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	11	124	0	ENST00000262367.5:c.5830G>C	p.Ala1944Pro	p.A1944P	ENST00000262367	NM_004380.2	1944	Gcc/Ccc	31/31	0.294860597809886	1	FACETS	0.42	0.292	0.577	0.42	0.292	0.577	SUBCLONAL	1	TRUE	0	0.348696937158292	1		124	124	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779622	3779622	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	34	276	0	ENST00000262367.5:c.5426A>G	p.Lys1809Arg	p.K1809R	ENST00000262367	NM_004380.2	1809	aAa/aGa	31/31	0.294860597809886	1	FACETS	0.691	0.568	0.827	0.691	0.568	0.827	SUBCLONAL	1	TRUE	0	0.348696937158292	1		276	233	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801767	3801767	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567282647	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	80	338	0	ENST00000262367.5:c.3739G>A	p.Glu1247Lys	p.E1247K	ENST00000262367	NM_004380.2	1247	Gag/Aag	20/31	0.294860597809886	1	FACETS	0.601	0.529	0.678	0.601	0.529	0.678	SUBCLONAL	1	TRUE	0	0.348696937158292	1		338	630	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846137	68846137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	58	437	0	ENST00000261769.5:c.1108G>A	p.Asp370Asn	p.D370N	ENST00000261769	NM_004360.3	370	Gat/Aat	8/16	0.294860597809886	1	FACETS	0.564	0.485	0.65	0.564	0.485	0.65	SUBCLONAL	1	TRUE	0	0.348696937158292	1		437	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577123	7577124	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	69	460	0	ENST00000269305.4:c.814_815delinsAA	p.Val272Lys	p.V272K	ENST00000269305	NM_001126112.2	272	GTg/AAg	8/11	1	2	FACETS	0.743	0.648	0.845	0.743	0.648	0.845	SUBCLONAL	1	TRUE	1	0.348696937158292	2		460	533	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15967400	15967400	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567787429	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	74	473	1	ENST00000268712.3:c.5203G>A	p.Asp1735Asn	p.D1735N	ENST00000268712	NM_006311.3	1735	Gac/Aac	35/46	1	2	FACETS	0.555	0.485	0.63	0.555	0.485	0.63	SUBCLONAL	1	TRUE	1	0.348696937158292	2		474	765	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512383	38512383	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1188389540	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	26	182	0	ENST00000254066.5:c.1294C>T	p.Arg432Trp	p.R432W	ENST00000254066	NM_000964.3	432	Cgg/Tgg	9/9	1	2	FACETS	0.806	0.643	0.989	0.806	0.643	0.989	CLONAL	1	TRUE	1	0.348696937158292	2		182	185	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59820400	59820400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	72	457	0	ENST00000259008.2:c.2353C>T	p.Pro785Ser	p.P785S	ENST00000259008	NM_032043.2	785	Cct/Tct	16/20	1	2	FACETS	0.587	0.513	0.668	0.587	0.513	0.668	SUBCLONAL	1	TRUE	1	0.348696937158292	2		457	703	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136162	11136163	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	35	344	0	ENST00000358026.2:c.3146_3147delinsTT	p.Pro1049Leu	p.P1049L	ENST00000358026	NM_001128849.1	1049	cCC/cTT	22/36	0.348696937158292	1	FACETS	0.658	0.542	0.786	0.658	0.542	0.786	SUBCLONAL	1	TRUE	0	0.348696937158292	1		344	252	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944522	40944523	+	missense_variant	Missense_Mutation	DNP	AG	AG	GA	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	32	341	0	ENST00000373198.4:c.1979_1980delinsTC	p.Ser660Phe	p.S660F	ENST00000373198	NM_133170.3	660	tCT/tTC	12/32	1	2	FACETS	0.462	0.375	0.561	0.462	0.375	0.561	SUBCLONAL	1	TRUE	1	0.348696937158292	2		341	397	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164625	36164625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	55	321	0	ENST00000300305.3:c.1250C>T	p.Ser417Phe	p.S417F	ENST00000300305		417	tCc/tTc	8/8	1	2	FACETS	0.886	0.761	1	0.886	0.761	1	CLONAL	1	TRUE	1	0.348696937158292	2		321	356	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344095	70344095	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	84	400	0	ENST00000374080.3:c.1831C>T	p.His611Tyr	p.H611Y	ENST00000374080		611	Cac/Tac	13/45	0.348696937158292	0	FACETS	0.753	0.668	0.842			1	SUBCLONAL	1	TRUE	NA	0.348696937158292	0		400	417	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970915	21970915	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	58	302	0	ENST00000304494.5:c.443del	p.Ala148GlyfsTer45	p.A148Gfs*45	ENST00000304494	NM_000077.4	148	gCg/gg	2/3	0.294860597809886	1	FACETS	0.602	0.518	0.693	0.602	0.518	0.693	SUBCLONAL	1	TRUE	0	0.348696937158292	1		302	456	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	23	221	0	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	0.564	0.441	0.705	0.564	0.441	0.705	SUBCLONAL	1	TRUE	1	0.348696937158292	2		221	234	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579545	7579545	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	21	260	0	ENST00000269305.4:c.142del	p.Asp48ThrfsTer75	p.D48Tfs*75	ENST00000269305	NM_001126112.2	48	Gac/ac	4/11	1	2	FACETS	0.472	0.364	0.598	0.472	0.364	0.598	SUBCLONAL	1	TRUE	1	0.348696937158292	2		260	255	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024637	31024637	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000705-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	47	456	0	ENST00000375687.4:c.4127del	p.Gly1376ValfsTer74	p.G1376Vfs*74	ENST00000375687	NM_015338.5	1374	gtG/gt	13/13	1	2	FACETS	0.513	0.433	0.602	0.513	0.433	0.602	SUBCLONAL	1	TRUE	1	0.348696937158292	2		456	525	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000715-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	98	422	0				ENST00000310581	NM_198253.2	-/1132			0.16983482883875	0	FACETS	1	0.915	1			1	CLONAL	4	FALSE	0	0.16983482883875	0		422	238	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0000715-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	233	318	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.91	0.852	0.969	1	0.996	1	CLONAL	4	FALSE	1	0.16983482883875	2		318	754	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656284	18656284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000715-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	226	387	0	ENST00000266497.5:c.2963C>T	p.Pro988Leu	p.P988L	ENST00000266497		988	cCa/cTa	21/31	0.16983482883875	1	FACETS	1	0.983	1	1	0.996	1	CLONAL	3	FALSE	0	0.16983482883875	1		387	707	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044541	47044548	+	frameshift_variant	Frame_Shift_Del	DEL	CGAGATGA	CGAGATGA	-	novel	NA	P-0000715-T03-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	209	419	0	ENST00000377604.3:c.2043_2050del	p.Asp681GlufsTer36	p.D681Efs*36	ENST00000377604	NM_001204468.1	680	CGAGATGAc/c	18/24	0.16983482883875	0	FACETS	0.946	0.89	1			1	CLONAL	5	FALSE	0	0.16983482883875	0		419	432	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000717-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	21	422	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		422	65	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000721-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	43	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.802	0.685	0.926	1	0.966	1	CLONAL	2	TRUE	1	0.380025658108916	2		422	141	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0000721-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	294	393	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.803	0.757	0.849	1	0.994	1	CLONAL	2	TRUE	1	0.380025658108916	2		393	964	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0000721-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	187	406	0	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	0.167883146092443	3	FACETS	1	0.99	1	0.745	0.689	0.802	INDETERMINATE	1	TRUE	1	0.380025658108916	3		406	786	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430441	181430441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000721-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	215	434	0	ENST00000325404.1:c.293G>A	p.Arg98Gln	p.R98Q	ENST00000325404	NM_003106.3	98	cGa/cAa	1/1	1	2	FACETS	0.754	0.703	0.807	1	0.992	1	SUBCLONAL	2	TRUE	1	0.380025658108916	2		434	750	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138642	55138642	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143344944	NA	P-0000721-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	120	216	0	ENST00000257290.5:c.1319C>T	p.Thr440Met	p.T440M	ENST00000257290	NM_006206.4	440	aCg/aTg	9/23	1	2	FACETS	0.768	0.7	0.839	1	0.986	1	SUBCLONAL	2	TRUE	1	0.380025658108916	2		216	411	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0000721-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	170	271	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	0.167883146092443	3	FACETS	0.769	0.71	0.831	0.769	0.71	0.831	INDETERMINATE	2	TRUE	1	0.380025658108916	3		271	692	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000721-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	22	505	0	ENST00000267101.3:c.310G>C	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ctg	3/28	0.194176836842773	3	FACETS	0.161	0.124	0.205			1	INDETERMINATE	1	TRUE	NA	0.380025658108916	3		505	856	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481671	56481671	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000721-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	132	317	0	ENST00000267101.3:c.706T>C	p.Ser236Pro	p.S236P	ENST00000267101	NM_001982.3	236	Tca/Cca	6/28	0.194176836842773	3	FACETS	0.902	0.825	0.982			1	INDETERMINATE	2	TRUE	NA	0.380025658108916	3		317	458	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000746-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	16	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.351524812159132	2		422	69	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47079260	47079260	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000746-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	42	223	0	ENST00000409792.3:c.7246C>G	p.Gln2416Glu	p.Q2416E	ENST00000409792	NM_014159.6	2416	Cag/Gag	18/21	0.351524812159132	3	FACETS	0.65	0.543	0.769	0.325	0.271	0.385	SUBCLONAL	1	TRUE	1	0.351524812159132	3		223	432	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803463	1803463	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000746-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	24	212	0	ENST00000260795.2:c.732C>A	p.Asp244Glu	p.D244E	ENST00000260795		244	gaC/gaA	5/17	1	2	FACETS	0.763	0.603	0.945	0.763	0.603	0.945	CLONAL	1	TRUE	1	0.351524812159132	2		212	179	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455091	50455091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1422790468	NA	P-0000746-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	41	199	0	ENST00000331340.3:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000331340	NM_006060.4	213	cGa/cAa	6/8	1	2	FACETS	0.755	0.631	0.891	0.755	0.631	0.891	SUBCLONAL	1	TRUE	1	0.351524812159132	2		199	309	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845772	151845772	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000746-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	75	297	0	ENST00000262189.6:c.13240G>A	p.Asp4414Asn	p.D4414N	ENST00000262189	NM_170606.2	4414	Gat/Aat	52/59	0.327766494389425	3	FACETS	1	0.973	1	0.703	0.62	0.791	CLONAL	1	TRUE	1	0.351524812159132	3		297	357	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845780	151845780	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000746-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	76	298	0	ENST00000262189.6:c.13232G>T	p.Gly4411Val	p.G4411V	ENST00000262189	NM_170606.2	4411	gGa/gTa	52/59	0.327766494389425	3	FACETS	1	0.974	1	0.708	0.625	0.796	CLONAL	1	TRUE	1	0.351524812159132	3		298	359	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845880	151845880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000746-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	103	397	1	ENST00000262189.6:c.13132G>A	p.Glu4378Lys	p.E4378K	ENST00000262189	NM_170606.2	4378	Gaa/Aaa	52/59	0.327766494389425	3	FACETS	1	0.981	1	0.724	0.651	0.8	CLONAL	1	TRUE	1	0.351524812159132	3		398	476	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779187	135779187	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000746-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	150	195	0	ENST00000298552.3:c.2059G>T	p.Glu687Ter	p.E687*	ENST00000298552	NM_001162426.1	687	Gag/Tag	17/23	0.299156036350471	3	FACETS	0.981	0.91	1	0.981	0.91	1	CLONAL	3	TRUE	0	0.351524812159132	3		195	341	SUCCESS
EED	8726	MSKCC	GRCh37	11	85956278	85956278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000746-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	46	69	1	ENST00000263360.6:c.7G>A	p.Glu3Lys	p.E3K	ENST00000263360	NM_003797.3	3	Gag/Aag	1/12	0.181699700984987	2	FACETS	1	0.944	1	0.623	0.531	0.723	INDETERMINATE	1	TRUE	0	0.351524812159132	2		70	210	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191099	2191099	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000746-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	61	481	0	ENST00000398665.3:c.353C>T	p.Ser118Leu	p.S118L	ENST00000398665	NM_032482.2	118	tCg/tTg	5/28	0.351524812159132	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.351524812159132	1		481	254	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039347	47039347	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000746-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	88	229	0	ENST00000377604.3:c.970G>C	p.Ala324Pro	p.A324P	ENST00000377604	NM_001204468.1	324	Gcg/Ccg	10/24	1	1	FACETS	1	0.942	1	1	0.988	1	CLONAL	2	TRUE	0	0.351524812159132	1		229	196	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207108	1207109	+	frameshift_variant	Frame_Shift_Ins	INS	GT	GT	AGCACC	novel	NA	P-0000746-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	32	251	0	ENST00000326873.7:c.196_197delinsAGCACC	p.Val66SerfsTer98	p.V66Sfs*98	ENST00000326873	NM_000455.4	66	GTg/AGCACCg	1/10	0.351524812159132	1	FACETS	0.328	0.266	0.399	0.328	0.266	0.399	SUBCLONAL	1	TRUE	0	0.351524812159132	1		251	457	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259247	36259248	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0000746-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	56	184	0	ENST00000300305.3:c.242_243dup	p.Leu82CysfsTer41	p.L82Cfs*41	ENST00000300305		81	-/TG	3/8	0.351524812159132	3	FACETS	0.994	0.855	1	0.497	0.427	0.572	CLONAL	1	TRUE	1	0.351524812159132	3		184	377	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922820	44922830	+	frameshift_variant	Frame_Shift_Del	DEL	GCCTGCCCTGG	GCCTGCCCTGG	-	novel	NA	P-0000746-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	116	240	0	ENST00000377967.4:c.1683_1693del	p.Cys562AlafsTer15	p.C562Afs*15	ENST00000377967	NM_021140.2	561	GCCTGCCCTGGg/g	16/29	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.351524812159132	1		240	366	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000748-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	58	422	0				ENST00000310581	NM_198253.2	-/1132			0.192044662605006	5	FACETS	1	0.952	1	0.788	0.692	0.888	INDETERMINATE	2	TRUE	2	0.548491010617322	5		422	163	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807889	1807889	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs78311289	NA	P-0000748-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	318	448	0	ENST00000260795.2:c.1948A>G	p.Lys650Glu	p.K650E	ENST00000260795		650	Aag/Gag	13/17	0.309561629866414	6	FACETS	0.967	0.927	1	1	0.994	1	INDETERMINATE	5	TRUE	2	0.548491010617322	6		448	503	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	19	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.801	1			1	INDETERMINATE	1	FALSE	NA	0.804902613348176	2		422	47	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0000758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	90	295	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	NA	2	FACETS	1	0.934	1			1	INDETERMINATE	1	FALSE	NA	0.804902613348176	2		295	215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578524	7578524	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555526268	NA	P-0000758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	125	248	0	ENST00000269305.4:c.406C>G	p.Gln136Glu	p.Q136E	ENST00000269305	NM_001126112.2	136	Caa/Gaa	5/11	0.804902613348176	2	FACETS	0.947	0.896	0.994	0.947	0.896	0.994	CLONAL	2	FALSE	0	0.804902613348176	2		248	164	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176455	123176455	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	134	307	0	ENST00000218089.9:c.422A>T	p.Asn141Ile	p.N141I	ENST00000218089	NM_001042749.1	141	aAc/aTc	7/35	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	0	0.804902613348176	1		307	166	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0000759-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	87	191	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.131538683069223	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.825312635490095	0		191	222	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000759-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	17	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.687	0.529	0.86			1	INDETERMINATE	1	TRUE	NA	0.825312635490095	2		422	60	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0000759-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	280	251	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.825312635490095	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.825312635490095	1		251	389	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371709	225371709	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000759-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	244	274	0	ENST00000264414.4:c.895A>G	p.Met299Val	p.M299V	ENST00000264414	NM_003590.4	299	Atg/Gtg	7/16	1	2	FACETS	0.812	0.762	0.863	0.812	0.762	0.863	CLONAL	1	TRUE	1	0.825312635490095	2		274	728	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577140	7577140	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0000759-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	133	406	0	ENST00000269305.4:c.798del	p.Arg267GlyfsTer78	p.R267Gfs*78	ENST00000269305	NM_001126112.2	266	ggA/gg	8/11	0.131538683069223	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.825312635490095	0		406	403	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0000760-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	28	139	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.83	1			1	INDETERMINATE	1	TRUE	NA	0.563308510431073	2		139	98	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720799	89720802	+	frameshift_variant	Frame_Shift_Del	DEL	TACT	TACT	-	rs146650273	NA	P-0000760-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	23	246	0	ENST00000371953.3:c.955_958del	p.Thr319Ter	p.T319*	ENST00000371953	NM_000314.4	317	gTACTt/gt	8/9	0.563308510431073	1	FACETS	0.524	0.415	0.645	0.524	0.415	0.645	SUBCLONAL	1	TRUE	0	0.563308510431073	1		246	112	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220389	98220389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370150142	NA	P-0000760-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	63	652	0	ENST00000331920.6:c.3074G>A	p.Arg1025His	p.R1025H	ENST00000331920	NM_000264.3	1025	cGc/cAc	18/24	1	2	FACETS	0.736	0.641	0.837	0.736	0.641	0.837	SUBCLONAL	1	TRUE	1	0.563308510431073	2		652	304	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235903	108235903	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000760-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	92	690	0	ENST00000278616.4:c.8945C>T	p.Pro2982Leu	p.P2982L	ENST00000278616	NM_000051.3	2982	cCt/cTt	62/63	1	2	FACETS	0.915	0.82	1	0.915	0.82	1	CLONAL	1	TRUE	1	0.563308510431073	2		690	357	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377241	118377241	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782228819	NA	P-0000760-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	99	1155	0	ENST00000534358.1:c.10634G>A	p.Arg3545Gln	p.R3545Q	ENST00000534358	NM_005933.3	3545	cGg/cAg	27/36	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.563308510431073	2		1155	319	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926258	112926258	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121918469	NA	P-0000760-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	72	741	0	ENST00000351677.2:c.1391G>C	p.Gly464Ala	p.G464A	ENST00000351677	NM_002834.3	464	gGc/gCc	12/16	0.163388067662844	0	FACETS	0.318	0.279	0.359			1	INDETERMINATE	1	TRUE	0	0.563308510431073	0		741	351	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683486	29683487	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0000760-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	75	627	0	ENST00000356175.3:c.7563_7564del	p.Ser2522PhefsTer2	p.S2522Ffs*2	ENST00000356175	NM_000267.3	2521	AAa/a	51/57	0.180244439522418	0	FACETS	0.326	0.287	0.367			1	INDETERMINATE	1	TRUE	0	0.563308510431073	0		627	357	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195628	123195631	+	frameshift_variant	Frame_Shift_Del	DEL	AGAT	AGAT	-	novel	NA	P-0000760-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	101	408	0	ENST00000218089.9:c.1544_1547del	p.Asp515GlyfsTer6	p.D515Gfs*6	ENST00000218089	NM_001042749.1	514	acAGAT/ac	17/35	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.563308510431073	1		408	196	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000813-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	73	422	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		422	144	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000818-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	36	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.871	1			1	INDETERMINATE	1	TRUE	NA	0.860682782404351	2		422	82	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0000818-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	324	163	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	0.860682782404351	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.860682782404351	1		163	387	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0000818-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	566	412	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.860682782404351	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.860682782404351	3		412	602	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631413	117631413	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750308356	NA	P-0000818-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	402	365	1	ENST00000368508.3:c.6265G>A	p.Val2089Met	p.V2089M	ENST00000368508	NM_002944.2	2089	Gtg/Atg	40/43	0.601268887286191	3	FACETS	0.858	0.822	0.893	0.858	0.822	0.893	CLONAL	2	TRUE	1	0.860682782404351	3		366	779	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954222	48954222	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0000818-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	1709	503	0	ENST00000267163.4:c.1421+2T>A		p.X474_splice	ENST00000267163	NM_000321.2	474			0.860682782404351	3	FACETS	1	0.997	1	1	0.997	1	CLONAL	3	TRUE	0	0.860682782404351	3		503	1861	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000819-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	39	422	0				ENST00000310581	NM_198253.2	-/1132			0.296906700996861	4	FACETS	1	0.905	1	1	0.905	1	CLONAL	2	TRUE	2	0.402757451967148	4		422	124	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023220	27023220	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1167372383	NA	P-0000819-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	22	321	0	ENST00000324856.7:c.326C>G	p.Pro109Arg	p.P109R	ENST00000324856	NM_006015.4	109	cCt/cGt	1/20	0.39597850842568	3	FACETS	0.702	0.547	0.879	0.351	0.273	0.44	SUBCLONAL	1	TRUE	1	0.402757451967148	3		321	187	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215674203	215674203	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064795053	NA	P-0000819-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	84	504	0	ENST00000260947.4:c.91C>T	p.Arg31Cys	p.R31C	ENST00000260947	NM_000465.2	31	Cgc/Tgc	1/11	0.164892747278325	2	FACETS	1	0.968	1	0.623	0.555	0.694	INDETERMINATE	1	TRUE	0	0.402757451967148	2		504	335	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526152	189526152	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751300168	NA	P-0000819-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	102	384	1	ENST00000264731.3:c.416C>T	p.Ala139Val	p.A139V	ENST00000264731	NM_003722.4	139	gCg/gTg	4/14	0.402757451967148	5	FACETS	0.852	0.771	0.935	1	0.977	1	CLONAL	3	TRUE	3	0.402757451967148	5		385	318	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948738	55948738	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000819-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	100	495	0	ENST00000263923.4:c.3727C>G	p.Pro1243Ala	p.P1243A	ENST00000263923	NM_002253.2	1243	Ccg/Gcg	28/30	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.402757451967148	2		495	385	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979608	55979608	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000819-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	59	509	0	ENST00000263923.4:c.839A>G	p.Gln280Arg	p.Q280R	ENST00000263923	NM_002253.2	280	cAg/cGg	7/30	1	2	FACETS	0.763	0.659	0.875	0.763	0.659	0.875	SUBCLONAL	1	TRUE	1	0.402757451967148	2		509	384	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007298	143007298	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000819-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	74	519	0	ENST00000262992.4:c.2486C>G	p.Thr829Arg	p.T829R	ENST00000262992	NM_001101669.1	829	aCg/aGg	22/24	0.21809985498758	1	FACETS	0.808	0.712	0.911	0.808	0.712	0.911	INDETERMINATE	1	TRUE	0	0.402757451967148	1		519	363	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	228312	228312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765376662	NA	P-0000819-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	40	97	0	ENST00000264932.6:c.634G>A	p.Asp212Asn	p.D212N	ENST00000264932	NM_004168.2	212	Gat/Aat	6/15	0.296906700996861	4	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	2	0.402757451967148	4		97	116	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517911	8517911	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000819-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	63	464	0	ENST00000356435.5:c.1480G>T	p.Ala494Ser	p.A494S	ENST00000356435		494	Gct/Tct	10/35	0.402757451967148	3	FACETS	0.93	0.808	1	0.31	0.269	0.354	CLONAL	1	TRUE	0	0.402757451967148	3		464	404	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117365	115117365	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000819-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	218	378	0	ENST00000257566.3:c.809C>A	p.Thr270Lys	p.T270K	ENST00000257566	NM_016569.3	270	aCa/aAa	4/8	0.402757451967148	4	FACETS	0.93	0.879	0.981	0.93	0.879	0.981	CLONAL	4	TRUE	0	0.402757451967148	4		378	408	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518719	103518719	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000819-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	37	156	0	ENST00000355739.4:c.2307C>A	p.Phe769Leu	p.F769L	ENST00000355739	NM_000123.3	769	ttC/ttA	10/15	0.402757451967148	3	FACETS	1	0.856	1	0.516	0.429	0.611	CLONAL	1	TRUE	1	0.402757451967148	3		156	214	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035920	47035920	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000819-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	111	352	0	ENST00000377604.3:c.598C>T	p.Gln200Ter	p.Q200*	ENST00000377604	NM_001204468.1	200	Cag/Tag	7/24	0.21809985498758	0	FACETS	0.815	0.753	0.876			1	INDETERMINATE	2	TRUE	NA	0.402757451967148	0		352	202	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245188	46245188	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000819-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	154	273	0	ENST00000334344.6:c.3284del	p.Pro1095LeufsTer61	p.P1095Lfs*61	ENST00000334344	NM_152641.2	1094	agC/ag	15/21	0.402757451967148	4	FACETS	0.982	0.92	1	0.982	0.92	1	CLONAL	4	TRUE	0	0.402757451967148	4		273	273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577133	7577150	+	inframe_deletion	In_Frame_Del	DEL	TGTTCCGTCCCAGTAGAT	TGTTCCGTCCCAGTAGAT	-	novel	NA	P-0000819-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	74	496	0	ENST00000269305.4:c.788_805del	p.Asn263_Asn268del	p.N263_N268del	ENST00000269305	NM_001126112.2	263	aATCTACTGGGACGGAACAgc/agc	8/11	0.402757451967148	2	FACETS	1	0.969	1	0.647	0.572	0.725	CLONAL	1	TRUE	0	0.402757451967148	2		496	284	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385044	31385045	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	rs1447560356	NA	P-0000819-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	32	302	0	ENST00000328111.2:c.1430dup	p.Tyr477Ter	p.Y477*	ENST00000328111	NM_006892.3	477	tac/tAac	14/23	0.402757451967148	3	FACETS	0.74	0.603	0.893	0.37	0.301	0.447	SUBCLONAL	1	TRUE	1	0.402757451967148	3		302	258	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295242	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	32	152	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.928	1			1	INDETERMINATE	1	TRUE	NA	0.453484477598277	2		152	113	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272512	11272512	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	55	252	0	ENST00000361445.4:c.3418G>C	p.Asp1140His	p.D1140H	ENST00000361445	NM_004958.3	1140	Gac/Cac	23/58	0.243511058930366	4	FACETS	1	0.959	1	0.66	0.57	0.757	INDETERMINATE	1	TRUE	2	0.453484477598277	4		252	267	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087380	27087380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	108	593	0	ENST00000324856.7:c.1954G>A	p.Gly652Arg	p.G652R	ENST00000324856	NM_006015.4	652	Ggg/Agg	5/20	0.243511058930366	4	FACETS	1	0.976	1	0.641	0.577	0.708	INDETERMINATE	1	TRUE	2	0.453484477598277	4		593	540	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510855	120510855	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	74	254	0	ENST00000256646.2:c.1109G>A	p.Gly370Asp	p.G370D	ENST00000256646	NM_024408.3	370	gGt/gAt	7/34	0.243511058930366	4	FACETS	0.801	0.708	0.899	0.801	0.708	0.899	INDETERMINATE	2	TRUE	2	0.453484477598277	4		254	296	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143141	30143141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553380334	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	69	587	0	ENST00000389048.3:c.385G>A	p.Gly129Ser	p.G129S	ENST00000389048	NM_004304.4	129	Ggc/Agc	1/29	0.182185801503908	4	FACETS	0.816	0.718	0.919	0.816	0.718	0.919	INDETERMINATE	2	TRUE	2	0.453484477598277	4		587	271	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023044	48023044	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	100	364	0	ENST00000234420.5:c.469A>G	p.Lys157Glu	p.K157E	ENST00000234420	NM_000179.2	157	Aag/Gag	3/10	0.182185801503908	4	FACETS	1	0.979	1	0.685	0.615	0.759	INDETERMINATE	1	TRUE	2	0.453484477598277	4		364	468	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156084	99156084	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	92	392	0	ENST00000074304.5:c.764C>T	p.Ser255Phe	p.S255F	ENST00000074304	NM_001134224.1	255	tCc/tTc	10/26	0.364799310831854	4	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.453484477598277	4		392	429	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209108170	209108170	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	85	486	0	ENST00000345146.2:c.679T>G	p.Phe227Val	p.F227V	ENST00000345146	NM_005896.2	227	Ttt/Gtt	6/10	0.182185801503908	4	FACETS	1	0.952	1	0.569	0.504	0.637	INDETERMINATE	1	TRUE	2	0.453484477598277	4		486	479	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488646	212488646	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	108	602	0	ENST00000342788.4:c.2202+1G>A		p.X734_splice	ENST00000342788	NM_005235.2	734			0.182185801503908	4	FACETS	1	0.961	1	0.568	0.511	0.629	INDETERMINATE	1	TRUE	2	0.453484477598277	4		602	609	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215609815	215609815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	111	713	1	ENST00000260947.4:c.1879G>A	p.Gly627Arg	p.G627R	ENST00000260947	NM_000465.2	627	Gga/Aga	9/11	0.182185801503908	4	FACETS	1	0.944	1	0.536	0.482	0.592	INDETERMINATE	1	TRUE	2	0.453484477598277	4		714	664	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467536	66467536	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	103	419	0	ENST00000273854.3:c.733G>A	p.Asp245Asn	p.D245N	ENST00000273854	NM_004439.5	245	Gac/Aac	3/18	NA	2	FACETS	1	0.94	1			1	INDETERMINATE	1	TRUE	NA	0.453484477598277	2		419	428	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114337	143114337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747045725	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	81	459	0	ENST00000262992.4:c.1084G>A	p.Asp362Asn	p.D362N	ENST00000262992	NM_001101669.1	362	Gat/Aat	13/24	0.323805780447555	4	FACETS	1	0.938	1	0.548	0.484	0.615	CLONAL	1	TRUE	2	0.453484477598277	4		459	474	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143235881	143235881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	71	416	0	ENST00000262992.4:c.407C>T	p.Pro136Leu	p.P136L	ENST00000262992	NM_001101669.1	136	cCc/cTc	6/24	0.323805780447555	4	FACETS	0.885	0.774	1	0.443	0.387	0.503	CLONAL	1	TRUE	2	0.453484477598277	4		416	514	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554836	187554836	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	90	493	0	ENST00000441802.2:c.4323+2T>G		p.X1441_splice	ENST00000441802	NM_005245.3	1441			0.339391820504495	1	FACETS	0.816	0.73	0.907	0.816	0.73	0.907	CLONAL	1	TRUE	0	0.453484477598277	1		493	376	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628455	187628455	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	143	599	0	ENST00000441802.2:c.2527C>T	p.Gln843Ter	p.Q843*	ENST00000441802	NM_005245.3	843	Cag/Tag	2/27	0.339391820504495	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.453484477598277	1		599	451	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945138	38945138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	107	458	0	ENST00000357387.3:c.4666G>A	p.Glu1556Lys	p.E1556K	ENST00000357387	NM_152756.3	1556	Gag/Aag	35/38	0.453484477598277	4	FACETS	1	0.957	1	0.56	0.504	0.62	CLONAL	1	TRUE	2	0.453484477598277	4		458	612	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178449	56178449	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	94	399	0	ENST00000399503.3:c.3422C>T	p.Pro1141Leu	p.P1141L	ENST00000399503	NM_005921.1	1141	cCt/cTt	14/20	0.453484477598277	4	FACETS	1	0.976	1	0.667	0.596	0.741	CLONAL	1	TRUE	2	0.453484477598277	4		399	452	SUCCESS
APC	324	MSKCC	GRCh37	5	112111421	112111421	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	91	336	0	ENST00000257430.4:c.518C>T	p.Pro173Leu	p.P173L	ENST00000257430	NM_000038.5	173	cCt/cTt	5/16	0.453484477598277	4	FACETS	1	0.956	1	0.572	0.509	0.638	CLONAL	1	TRUE	2	0.453484477598277	4		336	510	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497317	149497317	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	74	430	0	ENST00000261799.4:c.3001C>T	p.Pro1001Ser	p.P1001S	ENST00000261799	NM_002609.3	1001	Ccc/Tcc	22/23	0.293038263605761	3	FACETS	0.935	0.822	1	0.468	0.411	0.528	CLONAL	1	TRUE	1	0.453484477598277	3		430	428	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499677	149499677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	64	267	1	ENST00000261799.4:c.2596C>T	p.Pro866Ser	p.P866S	ENST00000261799	NM_002609.3	866	Cct/Tct	19/23	0.293038263605761	3	FACETS	1	0.934	1	0.557	0.486	0.633	CLONAL	1	TRUE	1	0.453484477598277	3		268	311	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956929	2956929	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	58	371	0	ENST00000396946.4:c.2698C>T	p.Leu900Phe	p.L900F	ENST00000396946	NM_032415.4	900	Ctt/Ttt	20/25	0.332179273437943	1	FACETS	0.655	0.567	0.75	0.655	0.567	0.75	SUBCLONAL	1	TRUE	0	0.453484477598277	1		371	302	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026699	6026699	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	76	708	1	ENST00000265849.7:c.1697C>A	p.Pro566His	p.P566H	ENST00000265849	NM_000535.5	566	cCt/cAt	11/15	0.332179273437943	1	FACETS	0.485	0.426	0.549	0.485	0.426	0.549	SUBCLONAL	1	TRUE	0	0.453484477598277	1		709	534	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509030	106509030	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	64	274	0	ENST00000359195.3:c.1024C>T	p.His342Tyr	p.H342Y	ENST00000359195	NM_002649.2	342	Cac/Tac	2/11	0.323805780447555	4	FACETS	1	0.962	1	0.647	0.564	0.735	CLONAL	1	TRUE	2	0.453484477598277	4		274	317	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842274	151842274	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	167	360	0	ENST00000262189.6:c.14138C>T	p.Pro4713Leu	p.P4713L	ENST00000262189	NM_170606.2	4713	cCt/cTt	54/59	0.323805780447555	4	FACETS	0.759	0.699	0.821	0.759	0.699	0.821	SUBCLONAL	2	TRUE	2	0.453484477598277	4		360	705	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151850011	151850011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80167870	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	75	220	0	ENST00000262189.6:c.12305C>T	p.Ser4102Phe	p.S4102F	ENST00000262189	NM_170606.2	4102	tCc/tTc	49/59	0.323805780447555	4	FACETS	1	0.975	1	0.726	0.641	0.816	CLONAL	1	TRUE	2	0.453484477598277	4		220	331	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485838	8485838	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	82	449	0	ENST00000356435.5:c.2979A>C	p.Lys993Asn	p.K993N	ENST00000356435		993	aaA/aaC	17/35	0.293038263605761	3	FACETS	0.902	0.798	1	0.451	0.399	0.507	CLONAL	1	TRUE	1	0.453484477598277	3		449	492	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240336	98240336	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	113	222	0	ENST00000331920.6:c.1347+1G>A		p.X449_splice	ENST00000331920	NM_000264.3	449			0.293038263605761	3	FACETS	0.842	0.774	0.911	1	0.982	1	CLONAL	3	TRUE	1	0.453484477598277	3		222	242	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100694	8100694	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1400015722	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	154	772	0	ENST00000346208.3:c.668C>T	p.Pro223Leu	p.P223L	ENST00000346208		223	cCg/cTg	3/6	0.366673284901575	4	FACETS	0.821	0.755	0.89	0.821	0.755	0.89	CLONAL	2	TRUE	2	0.453484477598277	4		772	601	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201099	108201099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759728261	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	70	250	0	ENST00000278616.4:c.7466C>T	p.Ser2489Phe	p.S2489F	ENST00000278616	NM_000051.3	2489	tCc/tTc	50/63	0.243511058930366	4	FACETS	1	0.949	1	0.583	0.511	0.66	INDETERMINATE	1	TRUE	2	0.453484477598277	4		250	385	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438057	438057	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	125	392	0	ENST00000399788.2:c.1912G>A	p.Glu638Lys	p.E638K	ENST00000399788	NM_001042603.1	638	Gaa/Aaa	14/28	NA	2	FACETS	0.833	0.755	0.914			1	INDETERMINATE	1	TRUE	NA	0.453484477598277	2		392	662	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120961	115120961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	87	291	0	ENST00000257566.3:c.45G>A	p.Met15Ile	p.M15I	ENST00000257566	NM_016569.3	15	atG/atA	1/8	1	2	FACETS	0.832	0.74	0.93	0.832	0.74	0.93	CLONAL	1	TRUE	1	0.453484477598277	2		291	461	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041739	29041739	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	175	489	0	ENST00000282397.4:c.80C>T	p.Ser27Leu	p.S27L	ENST00000282397	NM_002019.4	27	tCa/tTa	2/30	0.326963893912818	2	FACETS	1	0.989	1	0.69	0.64	0.742	CLONAL	1	TRUE	0	0.453484477598277	2		489	559	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562459	95562459	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	94	449	0	ENST00000393063.1:c.4798G>A	p.Glu1600Lys	p.E1600K	ENST00000393063	NM_030621.3	1600	Gaa/Aaa	24/28	0.275783586207161	5	FACETS	1	0.906	1	0.34	0.302	0.38	CLONAL	1	TRUE	2	0.453484477598277	5		449	683	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226105	2226105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	85	514	0	ENST00000326181.6:c.1802C>T	p.Thr601Ile	p.T601I	ENST00000326181	NM_032271.2	601	aCc/aTc	19/21	0.339391820504495	1	FACETS	0.85	0.758	0.947	0.85	0.758	0.947	CLONAL	1	TRUE	0	0.453484477598277	1		514	341	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857284	9857284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	73	588	0	ENST00000330684.3:c.4117G>A	p.Asp1373Asn	p.D1373N	ENST00000330684	NM_001134407.1	1373	Gat/Aat	13/13	0.339391820504495	1	FACETS	0.743	0.655	0.837	0.743	0.655	0.837	SUBCLONAL	1	TRUE	0	0.453484477598277	1		588	335	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857240	78857240	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	168	598	0	ENST00000306801.3:c.1606G>C	p.Ala536Pro	p.A536P	ENST00000306801	NM_020761.2	536	Gct/Cct	15/34	0.243511058930366	4	FACETS	0.992	0.917	1	0.992	0.917	1	INDETERMINATE	2	TRUE	2	0.453484477598277	4		598	543	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39593451	39593451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	108	369	0	ENST00000262039.4:c.1216G>A	p.Glu406Lys	p.E406K	ENST00000262039	NM_002647.2	406	Gaa/Aaa	11/25	0.246224534417804	2	FACETS	1	0.973	1	0.606	0.548	0.666	INDETERMINATE	1	TRUE	0	0.453484477598277	2		369	393	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45377692	45377692	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	59	206	0	ENST00000262160.6:c.737C>T	p.Pro246Leu	p.P246L	ENST00000262160	NM_005901.5	246	cCa/cTa	7/11	0.246224534417804	2	FACETS	1	0.927	1	0.549	0.478	0.624	INDETERMINATE	1	TRUE	0	0.453484477598277	2		206	237	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2216983	2216983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329819181	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	48	408	0	ENST00000398665.3:c.2438C>T	p.Pro813Leu	p.P813L	ENST00000398665	NM_032482.2	813	cCc/cTc	21/28	0.122359263038529	0	FACETS	0.447	0.38	0.518			1	INDETERMINATE	1	TRUE	0	0.453484477598277	0		408	259	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222964	5222964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	39	285	0	ENST00000357368.4:c.2839C>T	p.Leu947Phe	p.L947F	ENST00000357368	NM_002850.3	947	Ctt/Ttt	18/38	0.122359263038529	0	FACETS	0.631	0.532	0.737			1	INDETERMINATE	1	TRUE	0	0.453484477598277	0		285	149	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096972	11096972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	68	728	0	ENST00000358026.2:c.463G>A	p.Asp155Asn	p.D155N	ENST00000358026	NM_001128849.1	155	Gat/Aat	4/36	1	2	FACETS	0.785	0.686	0.891	0.785	0.686	0.891	SUBCLONAL	1	TRUE	1	0.453484477598277	2		728	382	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097021	11097021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1378355850	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	81	687	2	ENST00000358026.2:c.512C>T	p.Pro171Leu	p.P171L	ENST00000358026	NM_001128849.1	171	cCa/cTa	4/36	1	2	FACETS	0.99	0.878	1	0.99	0.878	1	CLONAL	1	TRUE	1	0.453484477598277	2		689	361	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271550	15271550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	77	831	0	ENST00000263388.2:c.6889C>T	p.Pro2297Ser	p.P2297S	ENST00000263388	NM_000435.2	2297	Ccc/Tcc	33/33	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.453484477598277	2		831	324	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271898	15271898	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	17	172	0	ENST00000263388.2:c.6541C>T	p.Pro2181Ser	p.P2181S	ENST00000263388	NM_000435.2	2181	Cca/Tca	33/33	1	2	FACETS	0.872	0.663	1	0.872	0.663	1	CLONAL	1	TRUE	1	0.453484477598277	2		172	86	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292409	15292409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	50	291	0	ENST00000263388.2:c.2770G>A	p.Asp924Asn	p.D924N	ENST00000263388	NM_000435.2	924	Gac/Aac	17/33	1	2	FACETS	0.904	0.774	1	0.904	0.774	1	CLONAL	1	TRUE	1	0.453484477598277	2		291	244	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353797	15353797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1326894689	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	26	268	0	ENST00000263377.2:c.3083C>T	p.Pro1028Leu	p.P1028L	ENST00000263377	NM_058243.2	1028	cCa/cTa	14/20	1	2	FACETS	0.925	0.744	1	0.925	0.744	1	CLONAL	1	TRUE	1	0.453484477598277	2		268	124	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741178	40741178	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	76	651	0	ENST00000392038.2:c.1255C>T	p.Gln419Ter	p.Q419*	ENST00000392038	NM_001626.4	419	Cag/Tag	12/14	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.453484477598277	2		651	294	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754693	41754693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	97	516	1	ENST00000301178.4:c.1679C>T	p.Ser560Phe	p.S560F	ENST00000301178	NM_021913.4	560	tCc/tTc	14/20	1	2	FACETS	0.904	0.81	1	0.904	0.81	1	CLONAL	1	TRUE	1	0.453484477598277	2		517	473	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038231	30038231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	129	456	0	ENST00000338641.4:c.404C>T	p.Pro135Leu	p.P135L	ENST00000338641	NM_000268.3	135	cCt/cTt	4/16	0.350451141598267	3	FACETS	1	0.958	1			1	CLONAL	1	TRUE	NA	0.453484477598277	3		456	639	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357143	70357143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	182	645	0	ENST00000374080.3:c.5658G>A	p.Met1886Ile	p.M1886I	ENST00000374080		1886	atG/atA	39/45	1	1	FACETS	0.759	0.709	0.809	1	0.992	1	SUBCLONAL	2	TRUE	0	0.453484477598277	1		645	409	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415001	116415001	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs771679296	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	121	636	1	ENST00000397752.3:c.3099del	p.Ile1034SerfsTer2	p.I1034Sfs*2	ENST00000397752	NM_000245.2	1032	tCc/tc	15/21	0.323805780447555	4	FACETS	0.988	0.893	1	0.494	0.446	0.544	CLONAL	1	TRUE	2	0.453484477598277	4		637	785	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	397000	397001	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	84	536	0	ENST00000262320.3:c.25_26delinsTT	p.Pro9Phe	p.P9F	ENST00000262320	NM_003502.3	9	CCc/TTc	2/11	0.339391820504495	1	FACETS	0.65	0.576	0.727	0.65	0.576	0.727	SUBCLONAL	1	TRUE	0	0.453484477598277	1		536	441	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257375	19257376	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	36	371	0	ENST00000162023.5:c.757_758delinsAT	p.Gly253Ile	p.G253I	ENST00000162023		253	GGa/ATa	11/13	1	2	FACETS	0.827	0.687	0.98	0.827	0.687	0.98	CLONAL	1	TRUE	1	0.453484477598277	2		371	192	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082316	16082317	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	158	704	1	ENST00000281043.3:c.130_131delinsTT	p.Pro44Phe	p.P44F	ENST00000281043	NM_005378.4	44	CCc/TTc	2/3	0.182185801503908	4	FACETS	0.917	0.846	0.992	0.917	0.846	0.992	INDETERMINATE	2	TRUE	2	0.453484477598277	4		705	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577083	7577085	+	missense_variant	Missense_Mutation	TNP	CTC	CTC	TTT	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	149	573	0	ENST00000269305.4:c.853_855delinsAAA	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	GAG/AAA	8/11	0.453484477598277	1	FACETS	0.973	0.895	1	0.973	0.895	1	CLONAL	1	TRUE	0	0.453484477598277	1		573	522	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211395	98211397	+	missense_variant	Missense_Mutation	TNP	CTT	CTT	TTA	novel	NA	P-0000821-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	194	497	0	ENST00000331920.6:c.3758_3760delinsTAA	p.Gln1253_Val1254delinsLeuMet	p.Q1253_V1254delinsLM	ENST00000331920	NM_000264.3	1253	cAAGtg/cTAAtg	22/24	0.293038263605761	3	FACETS	0.841	0.789	0.894	1	0.989	1	CLONAL	3	TRUE	1	0.453484477598277	3		497	416	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000822-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	51	422	0				ENST00000310581	NM_198253.2	-/1132			0.3	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.87	0		422	91	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978465	2978465	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000822-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	67	203	0	ENST00000396946.4:c.865G>A	p.Ala289Thr	p.A289T	ENST00000396946	NM_032415.4	289	Gcc/Acc	7/25	0.290154005179627	1	FACETS	0.414	0.366	0.465	0.414	0.366	0.465	INDETERMINATE	1	TRUE	0	0.87	1		203	210	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094330	27094330	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	65	174	0	ENST00000324856.7:c.3038A>T	p.Glu1013Val	p.E1013V	ENST00000324856	NM_006015.4	1013	gAg/gTg	11/20	NA	2	FACETS	0.645	0.562	0.734			1	INDETERMINATE	1	TRUE	NA	0.526104121019195	2		174	383	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797466	45797466	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	76	242	0	ENST00000450313.1:c.1053G>T	p.Gln351His	p.Q351H	ENST00000450313	NM_012222.2	351	caG/caT	12/16	NA	2	FACETS	0.818	0.723	0.92			1	INDETERMINATE	1	TRUE	NA	0.526104121019195	2		242	353	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737071	162737071	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	221	279	0	ENST00000367921.3:c.1215G>T	p.Leu405Phe	p.L405F	ENST00000367921	NM_006182.2	405	ttG/ttT	11/18	0.357400605669341	3	FACETS	0.761	0.711	0.812	0.761	0.711	0.812	SUBCLONAL	2	TRUE	1	0.526104121019195	3		279	697	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967300	25967300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	178	215	2	ENST00000435504.4:c.1906G>A	p.Val636Ile	p.V636I	ENST00000435504		636	Gtc/Atc	13/13	0.357400605669341	3	FACETS	0.783	0.726	0.841	0.783	0.726	0.841	SUBCLONAL	2	TRUE	1	0.526104121019195	3		217	546	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519873	29519873	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	88	324	0	ENST00000389048.3:c.1698G>C	p.Leu566Phe	p.L566F	ENST00000389048	NM_004304.4	566	ttG/ttC	9/29	0.357400605669341	3	FACETS	0.668	0.592	0.748	0.334	0.296	0.374	SUBCLONAL	1	TRUE	1	0.526104121019195	3		324	633	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251597	212251597	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	111	224	0	ENST00000342788.4:c.3462G>T	p.Met1154Ile	p.M1154I	ENST00000342788	NM_005235.2	1154	atG/atT	27/28	1	2	FACETS	0.672	0.605	0.742	0.672	0.605	0.742	SUBCLONAL	1	TRUE	1	0.526104121019195	2		224	628	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587241	212587241	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	115	206	0	ENST00000342788.4:c.760G>T	p.Asp254Tyr	p.D254Y	ENST00000342788	NM_005235.2	254	Gac/Tac	7/28	1	2	FACETS	0.76	0.687	0.837	0.76	0.687	0.837	SUBCLONAL	1	TRUE	1	0.526104121019195	2		206	575	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71161758	71161758	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	266	270	0	ENST00000318789.4:c.211C>T	p.Gln71Ter	p.Q71*	ENST00000318789	NM_032682.5	71	Cag/Tag	7/21	0.12414275326949	3	FACETS	0.999	0.944	1			1	INDETERMINATE	2	TRUE	NA	0.526104121019195	3		270	639	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911585	134911585	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	54	181	0	ENST00000398015.3:c.2050G>T	p.Glu684Ter	p.E684*	ENST00000398015	NM_004441.4	684	Gag/Tag	11/16	0.526104121019195	3	FACETS	0.524	0.448	0.607	0.262	0.224	0.304	SUBCLONAL	1	TRUE	1	0.526104121019195	3		181	495	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447122	187447122	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	198	216	0	ENST00000232014.4:c.1071G>T	p.Gln357His	p.Q357H	ENST00000232014	NM_001130845.1	357	caG/caT	5/10	0.435011808406149	4	FACETS	1	0.982	1	0.761	0.712	0.812	CLONAL	2	TRUE	1	0.526104121019195	4		216	503	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981071	55981071	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	93	229	0	ENST00000263923.4:c.628C>T	p.Gln210Ter	p.Q210*	ENST00000263923	NM_002253.2	210	Cag/Tag	5/30	0.147511598177178	3	FACETS	0.789	0.703	0.88	0.263	0.234	0.294	INDETERMINATE	1	TRUE	0	0.526104121019195	3		229	566	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467391	66467391	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	85	167	0	ENST00000273854.3:c.878C>A	p.Ala293Glu	p.A293E	ENST00000273854	NM_004439.5	293	gCa/gAa	3/18	0.526104121019195	3	FACETS	0.818	0.725	0.916	0.409	0.362	0.458	CLONAL	1	TRUE	1	0.526104121019195	3		167	499	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143033712	143033712	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	354	364	0	ENST00000262992.4:c.2259G>C	p.Gln753His	p.Q753H	ENST00000262992	NM_001101669.1	753	caG/caC	20/24	0.526104121019195	3	FACETS	0.899	0.855	0.945	0.899	0.855	0.945	CLONAL	2	TRUE	1	0.526104121019195	3		364	945	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576362	67576362	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs764491846	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	91	187	0	ENST00000274335.5:c.641A>T	p.Gln214Leu	p.Q214L	ENST00000274335		214	cAa/cTa	5/15	1	2	FACETS	0.863	0.771	0.959	0.863	0.771	0.959	CLONAL	1	TRUE	1	0.526104121019195	2		187	401	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171648	32171648	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	46	270	0	ENST00000375023.3:c.3130G>C	p.Glu1044Gln	p.E1044Q	ENST00000375023	NM_004557.3	1044	Gag/Cag	20/30	0.336005031288915	2	FACETS	0.519	0.439	0.607	0.259	0.219	0.304	SUBCLONAL	1	TRUE	0	0.526104121019195	2		270	337	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004331	150004331	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	170	459	0	ENST00000253339.5:c.1894C>G	p.Gln632Glu	p.Q632E	ENST00000253339		632	Caa/Gaa	3/7	1	2	FACETS	0.787	0.725	0.852	0.787	0.725	0.852	SUBCLONAL	1	TRUE	1	0.526104121019195	2		459	821	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346592	81346592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764869064	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	158	297	0	ENST00000222390.5:c.1361C>T	p.Thr454Met	p.T454M	ENST00000222390	NM_000601.4	454	aCg/aTg	11/18	1	2	FACETS	0.791	0.726	0.859	0.791	0.726	0.859	SUBCLONAL	1	TRUE	1	0.526104121019195	2		297	759	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5078363	5078363	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	106	204	0	ENST00000381652.3:c.2050G>T	p.Glu684Ter	p.E684*	ENST00000381652	NM_004972.3	684	Gaa/Taa	16/25	0.499415238306784	1	FACETS	0.699	0.631	0.77	0.699	0.631	0.77	SUBCLONAL	1	TRUE	0	0.526104121019195	1		204	425	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249612	110249612	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	100	313	0	ENST00000374672.4:c.1063C>G	p.Gln355Glu	p.Q355E	ENST00000374672	NM_004235.4	355	Cag/Gag	3/5	0.364022785587543	2	FACETS	0.929	0.836	1	0.465	0.418	0.514	CLONAL	1	TRUE	0	0.526104121019195	2		313	409	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133747515	133747515	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	55	210	0	ENST00000318560.5:c.823-1G>C		p.X275_splice	ENST00000318560	NM_005157.4	275			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.526104121019195	NA		210	346	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405353	70405353	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	99	234	0	ENST00000373644.4:c.2867G>C	p.Cys956Ser	p.C956S	ENST00000373644	NM_030625.2	956	tGt/tCt	4/12	0.147511598177178	3	FACETS	0.841	0.753	0.935	0.28	0.251	0.312	INDETERMINATE	1	TRUE	0	0.526104121019195	3		234	565	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154868	2154868	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs768105151	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	52	357	0	ENST00000434045.2:c.353G>T	p.Arg118Leu	p.R118L	ENST00000434045	NM_001127598.1	118	cGc/cTc	4/5	NA	2	FACETS	0.495	0.423	0.575			1	INDETERMINATE	1	TRUE	NA	0.526104121019195	2		357	399	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198862	67198862	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	163	181	0	ENST00000312629.5:c.333G>T	p.Lys111Asn	p.K111N	ENST00000312629	NM_003952.2	111	aaG/aaT	5/15	0.509770798371426	3	FACETS	0.973	0.904	1	0.973	0.904	1	CLONAL	2	TRUE	1	0.526104121019195	3		181	402	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125499297	125499299	+	missense_variant	Missense_Mutation	TNP	TGG	TGG	GGT	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	102	265	0	ENST00000428830.2:c.366_368delinsGGT	p.His122_Gly123delinsGlnVal	p.H122_G123delinsQV	ENST00000428830	NM_001114121.2	122	caTGGt/caGGTt	5/14	1	2	FACETS	0.613	0.549	0.68	0.613	0.549	0.68	SUBCLONAL	1	TRUE	1	0.526104121019195	2		265	633	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18439825	18439825	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	183	281	1	ENST00000266497.5:c.723C>A	p.Ser241Arg	p.S241R	ENST00000266497		241	agC/agA	2/31	0.149049364907272	5	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.526104121019195	5		282	900	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18473908	18473908	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	138	291	0	ENST00000266497.5:c.1150C>A	p.His384Asn	p.H384N	ENST00000266497		384	Cac/Aac	6/31	0.149049364907272	5	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.526104121019195	5		291	657	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945075	31945075	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	39	135	0	ENST00000340398.3:c.26G>T	p.Arg9Leu	p.R9L	ENST00000340398	NM_001013699.2	9	cGt/cTt	1/1	0.287631986867512	1	FACETS	0.316	0.262	0.375	0.316	0.262	0.375	INDETERMINATE	1	TRUE	0	0.526104121019195	1		135	346	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912617	32912617	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1256857369	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	130	215	0	ENST00000380152.3:c.4125G>T	p.Glu1375Asp	p.E1375D	ENST00000380152		1375	gaG/gaT	11/27	0.509770798371426	3	FACETS	0.93	0.846	1	0.465	0.423	0.51	CLONAL	1	TRUE	1	0.526104121019195	3		215	671	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915157	32915157	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	128	401	0	ENST00000380152.3:c.6665A>C	p.Tyr2222Ser	p.Y2222S	ENST00000380152		2222	tAc/tCc	11/27	0.509770798371426	3	FACETS	0.658	0.596	0.724	0.329	0.298	0.362	SUBCLONAL	1	TRUE	1	0.526104121019195	3		401	934	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929041	32929041	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358930	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	89	241	0	ENST00000380152.3:c.7051G>A	p.Ala2351Thr	p.A2351T	ENST00000380152		2351	Gca/Aca	14/27	0.509770798371426	3	FACETS	0.687	0.61	0.769	0.344	0.305	0.385	SUBCLONAL	1	TRUE	1	0.526104121019195	3		241	622	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590930	95590930	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555374797	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	96	209	0	ENST00000393063.1:c.979A>G	p.Arg327Gly	p.R327G	ENST00000393063	NM_030621.3	327	Aga/Gga	9/28	1	2	FACETS	0.71	0.635	0.79	0.71	0.635	0.79	SUBCLONAL	1	TRUE	1	0.526104121019195	2		209	514	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423565	88423565	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	199	361	0	ENST00000360948.2:c.2270G>T	p.Gly757Val	p.G757V	ENST00000360948	NM_001012338.2	757	gGg/gTg	18/19	0.509770798371426	3	FACETS	1	0.99	1	0.69	0.642	0.74	CLONAL	1	TRUE	1	0.526104121019195	3		361	692	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456333	99456333	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	169	173	0	ENST00000268035.6:c.1650C>G	p.Asn550Lys	p.N550K	ENST00000268035	NM_000875.3	550	aaC/aaG	8/21	0.509770798371426	3	FACETS	0.871	0.808	0.935	0.871	0.808	0.935	CLONAL	2	TRUE	1	0.526104121019195	3		173	466	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103346	2103346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777459404	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	102	214	0	ENST00000219476.3:c.229G>A	p.Ala77Thr	p.A77T	ENST00000219476	NM_000548.3	77	Gca/Aca	4/42	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.526104121019195	2		214	357	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126522	2126522	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	119	413	0	ENST00000219476.3:c.2773G>T	p.Asp925Tyr	p.D925Y	ENST00000219476	NM_000548.3	925	Gat/Tat	25/42	1	2	FACETS	0.986	0.895	1	0.986	0.895	1	CLONAL	1	TRUE	1	0.526104121019195	2		413	459	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831417	89831417	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	49	235	0	ENST00000389301.3:c.2659G>A	p.Asp887Asn	p.D887N	ENST00000389301	NM_000135.2	887	Gac/Aac	28/43	0.499415238306784	1	FACETS	0.411	0.349	0.478	0.411	0.349	0.478	SUBCLONAL	1	TRUE	0	0.526104121019195	1		235	334	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28934874	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	82	209	0	ENST00000269305.4:c.451C>A	p.Pro151Thr	p.P151T	ENST00000269305	NM_001126112.2	151	Ccc/Acc	5/11	0.522327995171154	1	FACETS	0.818	0.73	0.909	0.818	0.73	0.909	CLONAL	1	TRUE	0	0.526104121019195	1		209	281	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422971	45422971	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	232	499	0	ENST00000262160.6:c.157A>G	p.Lys53Glu	p.K53E	ENST00000262160	NM_005901.5	53	Aag/Gag	2/11	1	2	FACETS	0.866	0.807	0.926	0.866	0.807	0.926	CLONAL	1	TRUE	1	0.526104121019195	2		499	1019	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218518	5218518	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	107	332	0	ENST00000357368.4:c.3961A>T	p.Thr1321Ser	p.T1321S	ENST00000357368	NM_002850.3	1321	Acc/Tcc	25/38	0.499415238306784	1	FACETS	0.697	0.629	0.768	0.697	0.629	0.768	SUBCLONAL	1	TRUE	0	0.526104121019195	1		332	430	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278061	18278061	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519801	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	21	211	0	ENST00000222254.8:c.1681A>G	p.Asn561Asp	p.N561D	ENST00000222254	NM_005027.3	561	Aac/Gac	13/16	1	2	FACETS	0.294	0.226	0.372	0.294	0.226	0.372	SUBCLONAL	1	TRUE	1	0.526104121019195	2		211	272	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765564	41765564	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	77	388	0	ENST00000301178.4:c.2440C>T	p.Gln814Ter	p.Q814*	ENST00000301178	NM_021913.4	814	Cag/Tag	20/20	1	2	FACETS	0.475	0.417	0.537	0.475	0.417	0.537	SUBCLONAL	1	TRUE	1	0.526104121019195	2		388	616	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794446	42794446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	183	603	0	ENST00000575354.2:c.1526C>T	p.Pro509Leu	p.P509L	ENST00000575354	NM_015125.3	509	cCa/cTa	10/20	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.526104121019195	2		603	696	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317419	1317419	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	72	364	0	ENST00000400841.2:c.646G>T	p.Asp216Tyr	p.D216Y	ENST00000400841		216	Gat/Tat	5/6	0.287631986867512	0	FACETS	0.319	0.279	0.361			1	INDETERMINATE	1	TRUE	NA	0.526104121019195	0		364	407	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317481	1317481	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1192777792	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	121	417	0	ENST00000400841.2:c.584G>T	p.Gly195Val	p.G195V	ENST00000400841		195	gGg/gTg	5/6	0.287631986867512	0	FACETS	0.374	0.339	0.411			1	INDETERMINATE	1	TRUE	NA	0.526104121019195	0		417	583	SUCCESS
AR	367	MSKCC	GRCh37	X	66766228	66766228	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	61	110	0	ENST00000374690.3:c.1240C>A	p.Leu414Met	p.L414M	ENST00000374690	NM_000044.3	414	Ctg/Atg	1/8	0.287631986867512	0	FACETS	0.674	0.595	0.756			1	INDETERMINATE	1	TRUE	NA	0.526104121019195	0		110	163	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918888	76918888	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	220	370	0	ENST00000373344.5:c.4103G>T	p.Gly1368Val	p.G1368V	ENST00000373344	NM_000489.3	1368	gGc/gTc	12/35	0.287631986867512	0	FACETS	0.665	0.623	0.708			1	INDETERMINATE	1	TRUE	NA	0.526104121019195	0		370	596	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11114034	11114036	+	frameshift_variant	Frame_Shift_Del	DEL	GTC	GTC	TG	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	73	223	0	ENST00000358026.2:c.1962_1964delinsTG	p.Arg654SerfsTer120	p.R654Sfs*120	ENST00000358026	NM_001128849.1	654	agGTCt/agTGt	13/36	0.499415238306784	1	FACETS	0.802	0.71	0.898	0.802	0.71	0.898	CLONAL	1	TRUE	0	0.526104121019195	1		223	255	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942528	17942529	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	34	143	0	ENST00000458235.1:c.2759_2760del	p.Arg920ProfsTer47	p.R920Pfs*47	ENST00000458235	NM_000215.3	920	cGC/c	20/24	1	2	FACETS	0.588	0.484	0.702	0.588	0.484	0.702	SUBCLONAL	1	TRUE	1	0.526104121019195	2		143	220	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387095	31387095	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	72	268	0	ENST00000328111.2:c.1722del	p.Ile575PhefsTer15	p.I575Ffs*15	ENST00000328111	NM_006892.3	574	Ccc/cc	16/23	0.50502111018508	3	FACETS	0.752	0.659	0.851	0.251	0.219	0.284	SUBCLONAL	1	TRUE	0	0.526104121019195	3		268	460	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095894	29095894	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000831-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	102	435	0	ENST00000328354.6:c.940del	p.Val314TrpfsTer6	p.V314Wfs*6	ENST00000328354	NM_007194.3	314	Gtg/tg	9/15	0.509770798371426	3	FACETS	0.622	0.556	0.692	0.311	0.278	0.346	SUBCLONAL	1	TRUE	1	0.526104121019195	3		435	788	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000841-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	150	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.682000377779872	2		422	393	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672341	30672341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1461202402	NA	P-0000841-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	302	304	0	ENST00000376406.3:c.4619C>T	p.Ser1540Phe	p.S1540F	ENST00000376406	NM_014641.2	1540	tCc/tTc	10/15	1	2	FACETS	0.963	0.909	1	0.963	0.909	1	CLONAL	1	TRUE	1	0.682000377779872	2		304	920	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950375	17950375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145751599	NA	P-0000841-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	202	194	0	ENST00000458235.1:c.1352G>A	p.Arg451Gln	p.R451Q	ENST00000458235	NM_000215.3	451	cGa/cAa	10/24	1	2	FACETS	0.957	0.892	1	0.957	0.892	1	CLONAL	1	TRUE	1	0.682000377779872	2		194	619	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000866-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	73	422	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		422	249	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0000877-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	72	234	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	0.258924575474465	4	FACETS	0.936	0.819	1	0.468	0.409	0.531	CLONAL	1	TRUE	2	0.421246309548119	4		234	519	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000877-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	83	422	0				ENST00000310581	NM_198253.2	-/1132			0.363410346661813	3	FACETS	0.91	0.815	1	0.91	0.815	1	CLONAL	2	TRUE	1	0.421246309548119	3		422	262	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549229	226549229	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000877-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	119	302	0	ENST00000366794.5:c.2977G>C	p.Asp993His	p.D993H	ENST00000366794	NM_001618.3	993	Gat/Cat	23/23	0.258924575474465	4	FACETS	1	0.985	1	0.745	0.675	0.818	CLONAL	1	TRUE	2	0.421246309548119	4		302	539	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966652	25966652	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1397489883	NA	P-0000877-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	108	253	0	ENST00000435504.4:c.2554G>C	p.Asp852His	p.D852H	ENST00000435504		852	Gat/Cat	13/13	0.191216020295752	3	FACETS	1	0.977	1	0.647	0.583	0.713	INDETERMINATE	1	TRUE	1	0.421246309548119	3		253	480	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420609	49420609	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000877-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	144	212	0	ENST00000301067.7:c.15140C>T	p.Ala5047Val	p.A5047V	ENST00000301067	NM_003482.3	5047	gCc/gTc	48/54	0.258924575474465	4	FACETS	0.927	0.851	1	0.927	0.851	1	CLONAL	2	TRUE	2	0.421246309548119	4		212	524	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955382	48955382	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1485450031	NA	P-0000877-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	92	144	0	ENST00000267163.4:c.1499-1G>A		p.X500_splice	ENST00000267163	NM_000321.2	500			0.404333189831616	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.421246309548119	2		144	204	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121912652	NA	P-0000877-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	219	212	0	ENST00000269305.4:c.772G>T	p.Glu258Ter	p.E258*	ENST00000269305	NM_001126112.2	258	Gaa/Taa	7/11	0.381580475988347	3	FACETS	0.987	0.932	1	0.987	0.932	1	CLONAL	3	TRUE	0	0.421246309548119	3		212	425	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78704381	78704381	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs150208057	NA	P-0000877-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	125	219	0	ENST00000306801.3:c.529C>G	p.Leu177Val	p.L177V	ENST00000306801	NM_020761.2	177	Ctg/Gtg	5/34	0.421246309548119	5	FACETS	1	0.982	1	0.455	0.412	0.5	CLONAL	1	TRUE	2	0.421246309548119	5		219	709	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420908	49420908	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000877-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	160	317	0	ENST00000301067.7:c.14841del	p.Ser4948HisfsTer47	p.S4948Hfs*47	ENST00000301067	NM_003482.3	4947	ccC/cc	48/54	0.258924575474465	4	FACETS	0.862	0.794	0.933	0.862	0.794	0.933	CLONAL	2	TRUE	2	0.421246309548119	4		317	626	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0000879-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	91	310	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.185589284817166	4	FACETS		NA	1			1	NA	NA	FALSE	2	NA	4		310	785	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294175	1294175	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000879-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	24	201	0	ENST00000310581.5:c.826G>A	p.Ala276Thr	p.A276T	ENST00000310581	NM_198253.2	276	Gcc/Acc	2/16	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		201	356	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317437	1317437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000879-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	63	366	0	ENST00000400841.2:c.628C>T	p.Gln210Ter	p.Q210*	ENST00000400841		210	Cag/Tag	5/6	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		366	702	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0000879-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	30	310	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.13	2		310	390	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294175	1294175	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000879-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	20	201	0	ENST00000310581.5:c.826G>A	p.Ala276Thr	p.A276T	ENST00000310581	NM_198253.2	276	Gcc/Acc	2/16	1	2	FACETS	0.799	0.61	1	0.799	0.61	1	CLONAL	1	TRUE	1	0.13	2		201	385	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317437	1317437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000879-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	74	366	0	ENST00000400841.2:c.628C>T	p.Gln210Ter	p.Q210*	ENST00000400841		210	Cag/Tag	5/6	1	2	FACETS	0.802	0.701	0.91	1	0.977	1	CLONAL	2	TRUE	1	0.13	2		366	710	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000880-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	13	422	0				ENST00000310581	NM_198253.2	-/1132			0.208813656789319	4	FACETS	0.886	0.632	1	0.443	0.316	0.599	CLONAL	1	TRUE	2	0.13	4		422	255	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0000880-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	8	295	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.3	3	FACETS	0.544	0.349	0.797			1	SUBCLONAL	1	TRUE	NA	0.13	3		295	241	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936983	48936983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690863	NA	P-0000880-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	44	351	0	ENST00000267163.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000267163	NM_000321.2	251	Cga/Tga	8/27	0.208813656789319	4	FACETS	1	0.911	1	0.568	0.475	0.672	CLONAL	1	TRUE	2	0.13	4		351	673	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38181402	38181402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000880-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	39	243	0	ENST00000396334.3:c.415G>A	p.Glu139Lys	p.E139K	ENST00000396334	NM_002468.4	139	Gag/Aag	2/5	0.208813656789319	4	FACETS	1	0.877	1	0.538	0.445	0.642	CLONAL	1	TRUE	2	0.13	4		243	630	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916759	48916759	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000880-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	32	358	0	ENST00000267163.4:c.289G>T	p.Glu97Ter	p.E97*	ENST00000267163	NM_000321.2	97	Gaa/Taa	3/27	0.208813656789319	4	FACETS	1	0.839	1	0.52	0.421	0.632	CLONAL	1	TRUE	2	0.13	4		358	535	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855984	68855984	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121964877	NA	P-0000880-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	49	554	0	ENST00000261769.5:c.1792C>T	p.Arg598Ter	p.R598*	ENST00000261769	NM_004360.3	598	Cga/Tga	12/16	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.13	2		554	650	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0000880-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	49	489	0	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	0.208813656789319	3	FACETS	1	0.901	1	0.545	0.461	0.639	CLONAL	1	TRUE	1	0.13	3		489	736	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577537	7577538	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0000880-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	11	276	0	ENST00000269305.4:c.743_744delinsAA	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGG/cAA	7/11	0.208813656789319	3	FACETS	0.361	0.248	0.503	0.181	0.124	0.252	SUBCLONAL	1	TRUE	1	0.13	3		276	499	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0000881-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	260	139	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		139	334	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000889-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	296	422	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		422	571	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000891-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	76	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.87	0.768	0.977			1	INDETERMINATE	1	FALSE	NA	0.503754669993505	2		422	347	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0000891-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	47	295	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.774	0.659	0.899	0.774	0.659	0.899	SUBCLONAL	1	FALSE	1	0.503754669993505	2		295	241	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0000891-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	121	168	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.503754669993505	2		168	446	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620446	52620446	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000891-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	102	338	0	ENST00000394830.3:c.3307G>C	p.Glu1103Gln	p.E1103Q	ENST00000394830	NM_018313.4	1103	Gaa/Caa	21/30	NA	2	FACETS	0.498	0.445	0.555			1	INDETERMINATE	1	FALSE	NA	0.503754669993505	2		338	813	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032069	26032069	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000891-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	123	209	0	ENST00000244661.2:c.220G>C	p.Glu74Gln	p.E74Q	ENST00000244661	NM_003537.3	74	Gaa/Caa	1/1	NA	2	FACETS	0.768	0.696	0.843			1	INDETERMINATE	1	FALSE	NA	0.503754669993505	2		209	636	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864266	151864266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000891-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	246	322	0	ENST00000262189.6:c.9715G>A	p.Glu3239Lys	p.E3239K	ENST00000262189	NM_170606.2	3239	Gaa/Aaa	42/59	1	2	FACETS	0.996	0.931	1	0.996	0.931	1	CLONAL	1	FALSE	1	0.503754669993505	2		322	981	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151864386	151864386	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000891-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	216	333	0	ENST00000262189.6:c.9595G>T	p.Glu3199Ter	p.E3199*	ENST00000262189	NM_170606.2	3199	Gaa/Taa	42/59	1	2	FACETS	0.998	0.93	1	0.998	0.93	1	CLONAL	1	FALSE	1	0.503754669993505	2		333	859	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427111	49427111	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000891-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	175	355	0	ENST00000301067.7:c.11377C>T	p.Gln3793Ter	p.Q3793*	ENST00000301067	NM_003482.3	3793	Caa/Taa	39/54	1	2	FACETS	0.831	0.766	0.899	0.831	0.766	0.899	CLONAL	1	FALSE	1	0.503754669993505	2		355	836	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651943	36651944	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGGCCCC	novel	NA	P-0000891-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	85	166	0	ENST00000244741.5:c.71_72insCCGGCCC	p.Val25ArgfsTer13	p.V25Rfs*13	ENST00000244741	NM_000389.4	22	ttc/ttCGGCCCCc	2/3	1	2	FACETS	0.628	0.557	0.705	0.628	0.557	0.705	SUBCLONAL	1	FALSE	1	0.503754669993505	2		166	537	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779018	3779018	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000891-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	79	131	0	ENST00000262367.5:c.6030del	p.Val2012SerfsTer28	p.V2012Sfs*28	ENST00000262367	NM_004380.2	2010	ggG/gg	31/31	NA	2	FACETS	0.965	0.856	1			1	INDETERMINATE	1	FALSE	NA	0.503754669993505	2		131	325	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808922	1808926	+	frameshift_variant	Frame_Shift_Del	DEL	ACGAC	ACGAC	CCG	novel	NA	P-0000891-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	164	454	0	ENST00000260795.2:c.2354_2358delinsCCG	p.Asp785AlafsTer31	p.D785Afs*31	ENST00000260795		785	gACGAC/gCCG	17/17	1	2	FACETS	0.81	0.744	0.878	0.81	0.744	0.878	CLONAL	1	FALSE	1	0.503754669993505	2		454	804	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000892-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	353	422	0				ENST00000310581	NM_198253.2	-/1132			0.577930534663965	6	FACETS	0.97	0.927	1			1	CLONAL	4	FALSE	NA	0.577930534663965	6		422	679	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0000892-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	110	295	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.527677301404739	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	FALSE	2	0.577930534663965	4		295	281	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989592	212989592	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000892-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	248	311	0	ENST00000342788.4:c.119C>T	p.Ser40Phe	p.S40F	ENST00000342788	NM_005235.2	40	tCt/tTt	2/28	0.26966185043021	3	FACETS	0.955	0.901	1	0.637	0.601	0.674	INDETERMINATE	2	FALSE	0	0.577930534663965	3		311	579	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549764	187549764	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000892-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1335	292	516	0	ENST00000441802.2:c.4477C>G	p.Leu1493Val	p.L1493V	ENST00000441802	NM_005245.3	1493	Ctg/Gtg	8/27	0.578501758993384	4	FACETS	0.98	0.919	1	0.327	0.306	0.348	CLONAL	1	FALSE	1	0.577930534663965	4		516	1627	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651917	36651917	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs756319938	NA	P-0000892-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	693	237	0	ENST00000244741.5:c.39C>A	p.Cys13Ter	p.C13*	ENST00000244741	NM_000389.4	13	tgC/tgA	2/3	0.578501758993384	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	4	FALSE	0	0.577930534663965	4		237	926	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339176	87339176	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000892-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	160	356	0	ENST00000277120.3:c.758C>T	p.Thr253Ile	p.T253I	ENST00000277120		253	aCt/aTt	8/19	0.578501758993384	3	FACETS	0.816	0.748	0.886	0.408	0.374	0.443	CLONAL	1	FALSE	1	0.577930534663965	3		356	875	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098542	108098542	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0000892-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	210	286	1	ENST00000278616.4:c.112G>T	p.Glu38Ter	p.E38*	ENST00000278616	NM_000051.3	38	Gaa/Taa	3/63	0.577930534663965	2	FACETS	0.843	0.794	0.893	0.843	0.794	0.893	CLONAL	2	FALSE	0	0.577930534663965	2		287	431	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947596	48947596	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1566196458	NA	P-0000892-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	355	437	0	ENST00000267163.4:c.1183C>T	p.Gln395Ter	p.Q395*	ENST00000267163	NM_000321.2	395	Caa/Taa	12/27	NA	2	FACETS	0.954	0.913	0.994			1	INDETERMINATE	2	FALSE	NA	0.577930534663965	2		437	644	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791024	42791024	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1361309406	NA	P-0000892-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	176	387	0	ENST00000575354.2:c.169G>A	p.Glu57Lys	p.E57K	ENST00000575354	NM_015125.3	57	Gag/Aag	2/20	0.578501758993384	3	FACETS	0.651	0.598	0.706	0.325	0.299	0.353	SUBCLONAL	1	FALSE	1	0.577930534663965	3		387	1206	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106342	27106343	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0000892-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	177	293	0	ENST00000324856.7:c.5955dup	p.Asn1986GlnfsTer13	p.N1986Qfs*13	ENST00000324856	NM_006015.4	1985	tcc/tCcc	20/20	0.378929609415276	3	FACETS	1	0.93	1			1	CLONAL	1	FALSE	NA	0.577930534663965	3		293	783	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0000894-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	184	262	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.482544644399584	4	FACETS	1	0.983	1	0.776	0.724	0.828	CLONAL	2	TRUE	1	0.56080916956291	4		262	440	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223550	55223550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000894-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	215	360	0	ENST00000275493.2:c.917C>T	p.Ser306Leu	p.S306L	ENST00000275493	NM_005228.3	306	tCg/tTg	8/28	0.482544644399584	4	FACETS	1	0.989	1	0.833	0.783	0.883	CLONAL	2	TRUE	1	0.56080916956291	4		360	479	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259551	55259551	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000894-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	143	270	0	ENST00000275493.2:c.2609A>G	p.His870Arg	p.H870R	ENST00000275493	NM_005228.3	870	cAt/cGt	21/28	0.482544644399584	4	FACETS	1	0.97	1	0.735	0.679	0.792	CLONAL	2	TRUE	1	0.56080916956291	4		270	361	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572002	64572002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779413959	NA	P-0000894-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	52	646	0	ENST00000312049.6:c.1637C>T	p.Pro546Leu	p.P546L	ENST00000312049	NM_130799.2	546	cCg/cTg	10/10	0.56080916956291	3	FACETS	0.451	0.384	0.525	0.226	0.192	0.263	SUBCLONAL	1	TRUE	1	0.56080916956291	3		646	526	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244452	46244452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs980692773	NA	P-0000894-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	85	415	0	ENST00000334344.6:c.2546C>T	p.Ala849Val	p.A849V	ENST00000334344	NM_152641.2	849	gCa/gTa	15/21	0.475416938651291	3	FACETS	0.674	0.596	0.756	0.225	0.198	0.252	SUBCLONAL	1	TRUE	0	0.56080916956291	3		415	576	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314925	1314925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000894-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	610	446	0	ENST00000400841.2:c.736C>T	p.Leu246Phe	p.L246F	ENST00000400841		246	Ctc/Ttc	6/6	0.56080916956291	5	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.56080916956291	5		446	1787	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0000895-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	249	139	0				ENST00000310581	NM_198253.2	-/1132			0.716781166892557	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.716781166892557	1		139	414	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0000895-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	636	482	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.376679474605855	3	FACETS	0.879	0.849	0.91	0.879	0.849	0.91	INDETERMINATE	2	TRUE	1	0.716781166892557	3		482	1371	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720720	89720721	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs786204905	NA	P-0000895-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	21	35	0	ENST00000371953.3:c.875dup	p.Asn292LysfsTer6	p.N292Kfs*6	ENST00000371953	NM_000314.4	291	gaa/gAaa	8/9	0.716781166892557	1	FACETS	0.495	0.391	0.608	0.495	0.391	0.608	SUBCLONAL	1	TRUE	0	0.716781166892557	1		35	76	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0000895-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	500	383	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.664658193057082	2	FACETS	0.938	0.909	0.966	0.938	0.909	0.966	CLONAL	2	TRUE	0	0.716781166892557	2		383	744	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857371	9857371	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000895-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	374	397	0	ENST00000330684.3:c.4030T>A	p.Phe1344Ile	p.F1344I	ENST00000330684	NM_001134407.1	1344	Ttc/Atc	13/13	1	2	FACETS	0.915	0.869	0.961	0.915	0.869	0.961	CLONAL	1	TRUE	1	0.716781166892557	2		397	1141	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733217	40733217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000895-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	274	242	1	ENST00000373198.4:c.3589G>A	p.Glu1197Lys	p.E1197K	ENST00000373198	NM_133170.3	1197	Gaa/Aaa	26/32	0.376679474605855	3	FACETS	0.759	0.717	0.802	0.759	0.717	0.802	INDETERMINATE	2	TRUE	1	0.716781166892557	3		243	684	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003759	45003759	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0000895-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	512	327	0	ENST00000558401.1:c.16del	p.Ala6ProfsTer2	p.A6Pfs*2	ENST00000558401	NM_004048.2	5	gtG/gt	1/4	0.716781166892557	1	FACETS	0.92	0.886	0.954	0.92	0.886	0.954	CLONAL	1	TRUE	0	0.716781166892557	1		327	996	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000896-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	54	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.968	0.853	1	0.968	0.853	1	CLONAL	1	TRUE	1	0.922025994754312	2		422	121	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0000896-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	244	314	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.984	0.929	1	0.984	0.929	1	CLONAL	1	TRUE	1	0.922025994754312	2		314	538	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78421016	78421016	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0000896-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	280	378	0	ENST00000370768.2:c.1706-2A>G		p.X569_splice	ENST00000370768	NM_003902.3	569			0.922025994754312	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.922025994754312	1		378	321	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111050	193111050	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000896-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	277	268	0	ENST00000367435.3:c.583T>C	p.Ser195Pro	p.S195P	ENST00000367435	NM_024529.4	195	Tct/Cct	7/17	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.922025994754312	2		268	555	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057936	27057937	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1415146710	NA	P-0000896-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	155	244	0	ENST00000324856.7:c.1650dup	p.Tyr551LeufsTer72	p.Y551Lfs*72	ENST00000324856	NM_006015.4	548	-/C	3/20	0.922025994754312	1	FACETS	0.813	0.769	0.855	0.813	0.769	0.855	CLONAL	1	TRUE	0	0.922025994754312	1		244	223	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000904-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	179	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.811	0.754	0.869	0.811	0.754	0.869	CLONAL	1	TRUE	1	0.867447511184003	2		422	509	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945452	151945452	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000904-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	392	205	0	ENST00000262189.6:c.2067G>A	p.Met689Ile	p.M689I	ENST00000262189	NM_170606.2	689	atG/atA	14/59	1	2	FACETS	0.906	0.863	0.948	0.906	0.863	0.948	CLONAL	1	TRUE	1	0.867447511184003	2		205	998	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692849	89692849	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554898097	NA	P-0000904-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	218	78	0	ENST00000371953.3:c.333G>A	p.Trp111Ter	p.W111*	ENST00000371953	NM_000314.4	111	tgG/tgA	5/9	0.867447511184003	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.867447511184003	1		78	278	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	162	422	0				ENST00000310581	NM_198253.2	-/1132			0.398548806870016	3	FACETS	1	0.988	1	0.677	0.627	0.728	INDETERMINATE	1	FALSE	1	0.738189813596886	3		422	444	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0000908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	416	558	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	FALSE	1	0.738189813596886	2		558	959	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0000908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	385	400	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	1	2	FACETS	0.972	0.925	1	0.972	0.925	1	CLONAL	1	FALSE	1	0.738189813596886	2		400	1073	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0000908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	30	310	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.138258687908824	1	FACETS	0.109	0.087	0.133	0.109	0.087	0.133	INDETERMINATE	1	FALSE	0	0.738189813596886	1		310	471	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246137	46246137	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	205	255	0	ENST00000334344.6:c.4231C>T	p.Gln1411Ter	p.Q1411*	ENST00000334344	NM_152641.2	1411	Caa/Taa	15/21	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	1	0.738189813596886	2		255	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0000908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	239	268	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	1	0.738189813596886	2		268	643	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732639	190732639	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1172503363	NA	P-0000908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	63	272	0	ENST00000441310.2:c.2457G>C	p.Lys819Asn	p.K819N	ENST00000441310	NM_000534.4	819	aaG/aaC	11/13	0.411283749929878	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.738189813596886	0		272	191	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266505	198266505	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	63	333	0	ENST00000335508.6:c.2331C>A	p.Phe777Leu	p.F777L	ENST00000335508	NM_012433.2	777	ttC/ttA	16/25	0.411283749929878	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.738189813596886	0		333	239	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125496	47125496	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	59	471	0	ENST00000409792.3:c.5774C>T	p.Ser1925Leu	p.S1925L	ENST00000409792	NM_014159.6	1925	tCa/tTa	12/21	0.369011289819963	3	FACETS	0.215	0.184	0.249	0.107	0.092	0.125	INDETERMINATE	1	FALSE	1	0.738189813596886	3		471	1018	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247244	153247244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	123	494	0	ENST00000281708.4:c.1558G>A	p.Asp520Asn	p.D520N	ENST00000281708	NM_033632.3	520	Gat/Aat	10/12	0.576318831532546	1	FACETS	0.322	0.292	0.355	0.322	0.292	0.355	SUBCLONAL	1	FALSE	0	0.738189813596886	1		494	652	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247355	153247355	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	226	251	0	ENST00000281708.4:c.1447C>T	p.Leu483Phe	p.L483F	ENST00000281708	NM_033632.3	483	Ctt/Ttt	10/12	0.576318831532546	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	0	0.738189813596886	1		251	331	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576442	67576442	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	269	439	0	ENST00000274335.5:c.721C>T	p.Gln241Ter	p.Q241*	ENST00000274335		241	Cag/Tag	5/15	0.738189813596886	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	0	0.738189813596886	1		439	396	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158626	26158626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772836222	NA	P-0000908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	111	70	0	ENST00000289316.2:c.229G>A	p.Glu77Lys	p.E77K	ENST00000289316	NM_138720.2	77	Gag/Aag	1/2	0.159645351147932	3	FACETS	0.804	0.737	0.873	0.804	0.737	0.873	INDETERMINATE	2	FALSE	1	0.738189813596886	3		70	256	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445737	49445737	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	436	498	1	ENST00000301067.7:c.1729G>C	p.Glu577Gln	p.E577Q	ENST00000301067	NM_003482.3	577	Gag/Cag	10/54	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.738189813596886	2		499	1155	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222581	69222581	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs576062594	NA	P-0000908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	49	379	0	ENST00000462284.1:c.554G>C	p.Arg185Pro	p.R185P	ENST00000462284	NM_002392.5	185	cGa/cCa	8/11	1	2	FACETS	0.198	0.167	0.232	0.198	0.167	0.232	SUBCLONAL	1	FALSE	1	0.738189813596886	2		379	670	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69230488	69230488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	31	276	0	ENST00000462284.1:c.877G>A	p.Asp293Asn	p.D293N	ENST00000462284	NM_002392.5	293	Gat/Aat	10/11	1	2	FACETS	0.26	0.21	0.316	0.26	0.21	0.316	SUBCLONAL	1	FALSE	1	0.738189813596886	2		276	323	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233330	69233330	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs767686947	NA	P-0000908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	30	248	0	ENST00000462284.1:c.1195G>C	p.Asp399His	p.D399H	ENST00000462284	NM_002392.5	399	Gac/Cac	11/11	1	2	FACETS	0.223	0.18	0.273	0.223	0.18	0.273	SUBCLONAL	1	FALSE	1	0.738189813596886	2		248	364	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947563	48947563	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	124	364	0	ENST00000267163.4:c.1150C>T	p.Gln384Ter	p.Q384*	ENST00000267163	NM_000321.2	384	Caa/Taa	12/27	0.162936994396719	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.738189813596886	0		364	272	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027160	49027160	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0000908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	229	449	0	ENST00000267163.4:c.1727C>G	p.Ser576Ter	p.S576*	ENST00000267163	NM_000321.2	576	tCa/tGa	18/27	0.162936994396719	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.738189813596886	0		449	437	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303853	91303853	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	96	214	0	ENST00000355112.3:c.1250A>G	p.Asn417Ser	p.N417S	ENST00000355112	NM_000057.2	417	aAt/aGt	7/22	0.4050425680827	1	FACETS	0.654	0.592	0.717	0.654	0.592	0.717	INDETERMINATE	1	FALSE	0	0.738189813596886	1		214	251	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222967	5222967	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778392508	NA	P-0000908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	79	187	1	ENST00000357368.4:c.2836G>A	p.Val946Ile	p.V946I	ENST00000357368	NM_002850.3	946	Gtc/Atc	18/38	0.389874796814037	1	FACETS	0.326	0.288	0.367	0.326	0.288	0.367	INDETERMINATE	1	FALSE	0	0.738189813596886	1		188	414	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868136	45868136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451258340	NA	P-0000908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	309	422	0	ENST00000391945.4:c.554G>A	p.Arg185Gln	p.R185Q	ENST00000391945	NM_000400.3	185	cGg/cAg	7/23	0.151423407151846	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.738189813596886	0		422	773	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872197	45872197	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	331	267	0	ENST00000391945.4:c.237G>T	p.Glu79Asp	p.E79D	ENST00000391945	NM_000400.3	79	gaG/gaT	4/23	0.151423407151846	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.738189813596886	0		267	705	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22123531	22123531	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	63	619	0	ENST00000215832.6:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000215832	NM_002745.4	349	Gaa/Taa	8/9	0.738189813596886	1	FACETS	0.182	0.157	0.209	0.182	0.157	0.209	SUBCLONAL	1	FALSE	0	0.738189813596886	1		619	593	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338697	70338697	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057521988	NA	P-0000908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	839	327	0	ENST00000374080.3:c.93G>C	p.Gln31His	p.Q31H	ENST00000374080		31	caG/caC	1/45	1	1	FACETS		NA	1	1	0.999	1	NA	2	FALSE	0	0.738189813596886	1		327	913	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341434	70341434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	487	230	1	ENST00000374080.3:c.869C>T	p.Ser290Phe	p.S290F	ENST00000374080		290	tCt/tTt	7/45	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	FALSE	0	0.738189813596886	1		231	606	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781324	3781326	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	rs587783502	NA	P-0000908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	331	305	0	ENST00000262367.5:c.5039_5041del	p.Ser1680del	p.S1680del	ENST00000262367	NM_004380.2	1680	tCCTtg/ttg	30/31	0.369612247734041	1	FACETS	0.822	0.784	0.861	0.822	0.784	0.861	INDETERMINATE	1	FALSE	0	0.738189813596886	1		305	688	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843486	3843493	+	frameshift_variant	Frame_Shift_Del	DEL	CTTGCTCT	CTTGCTCT	-	novel	NA	P-0000908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	67	342	0	ENST00000262367.5:c.1110_1117del	p.Glu371LysfsTer53	p.E371Kfs*53	ENST00000262367	NM_004380.2	370	cgAGAGCAAGca/cgca	4/31	0.369612247734041	1	FACETS	0.141	0.122	0.162	0.141	0.122	0.162	INDETERMINATE	1	FALSE	0	0.738189813596886	1		342	812	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942770	44942772	+	frameshift_variant	Frame_Shift_Ins	INS	ATC	ATC	TGAT	novel	NA	P-0000908-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	366	313	0	ENST00000377967.4:c.3350_3352delinsTGAT	p.Asn1117MetfsTer34	p.N1117Mfs*34	ENST00000377967	NM_021140.2	1117	aATCtt/aTGATtt	23/29	1	1	FACETS		NA	1	1	0.997	1	NA	2	FALSE	0	0.738189813596886	1		313	413	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	30	422	0				ENST00000310581	NM_198253.2	-/1132			0.563316694517077	3	FACETS	0.771	0.628	0.93			1	CLONAL	1	TRUE	NA	0.563316694517077	3		422	177	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0000916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	16	558	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.308615320612117	5	FACETS	0.193	0.142	0.255	0.064	0.047	0.085	INDETERMINATE	1	TRUE	2	0.563316694517077	5		558	542	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251754	212251754	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	76	199	0	ENST00000342788.4:c.3305T>G	p.Phe1102Cys	p.F1102C	ENST00000342788	NM_005235.2	1102	tTt/tGt	27/28	0.563316694517077	3	FACETS	0.804	0.708	0.906	0.268	0.236	0.302	CLONAL	1	TRUE	0	0.563316694517077	3		199	430	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781419	135781419	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	254	224	0	ENST00000298552.3:c.1546C>T	p.Gln516Ter	p.Q516*	ENST00000298552	NM_001162426.1	516	Cag/Tag	15/23	0.477769879595389	3	FACETS	0.935	0.891	0.978	0.935	0.891	0.978	CLONAL	3	TRUE	0	0.563316694517077	3		224	412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0000916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	203	313	0	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	0.481363920024682	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.563316694517077	2		313	358	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303221	15303221	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	57	340	0	ENST00000263388.2:c.307C>T	p.Arg103Ter	p.R103*	ENST00000263388	NM_000435.2	103	Cga/Tga	3/33	0.119036019898225	4	FACETS	0.805	0.693	0.926			1	INDETERMINATE	1	TRUE	NA	0.563316694517077	4		340	393	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743883	41743883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374699228	NA	P-0000916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	278	432	0	ENST00000301178.4:c.818C>T	p.Ala273Val	p.A273V	ENST00000301178	NM_021913.4	273	gCg/gTg	7/20	0.563316694517077	4	FACETS	1	0.976	1			1	CLONAL	2	TRUE	NA	0.563316694517077	4		432	727	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974769	21974770	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGCCGT	rs1563892769	NA	P-0000916-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	41	184	0	ENST00000304494.5:c.52_57dup	p.Thr18_Ala19dup	p.T18_A19dup	ENST00000304494	NM_000077.4	18	-/ACGGCC	1/3	0.548093521447743	1	FACETS	0.515	0.434	0.604	0.515	0.434	0.604	SUBCLONAL	1	TRUE	0	0.563316694517077	1		184	203	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000918-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	55	422	0				ENST00000310581	NM_198253.2	-/1132			0.182603626363731	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.747990382037212	0		422	146	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692844	89692844	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1114167629	NA	P-0000918-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	79	79	0	ENST00000371953.3:c.328C>T	p.Gln110Ter	p.Q110*	ENST00000371953	NM_000314.4	110	Caa/Taa	5/9	0.747990382037212	1	FACETS	0.938	0.854	1	0.938	0.854	1	CLONAL	1	FALSE	0	0.747990382037212	1		79	141	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204511928	204511928	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0000918-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	157	238	2	ENST00000367182.3:c.528A>C	p.Glu176Asp	p.E176D	ENST00000367182	NM_001278516.1	176	gaA/gaC	8/11	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	FALSE	1	0.747990382037212	2		240	409	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584514	189584514	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000918-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	189	321	0	ENST00000264731.3:c.810C>G	p.Asn270Lys	p.N270K	ENST00000264731	NM_003722.4	270	aaC/aaG	6/14	0.226099511130589	3	FACETS	1	0.988	1	0.645	0.601	0.691	INDETERMINATE	1	FALSE	1	0.747990382037212	3		321	538	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0000918-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	6040	492	0	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.747990382037212	24	FACETS	1	0.999	1			1	CLONAL	22	FALSE	NA	0.747990382037212	24		492	6654	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233016	55233016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751570775	NA	P-0000918-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	4227	267	3	ENST00000275493.2:c.1766C>T	p.Pro589Leu	p.P589L	ENST00000275493	NM_005228.3	589	cCc/cTc	15/28	0.747990382037212	24	FACETS	0.982	0.977	0.988			1	CLONAL	23	FALSE	NA	0.747990382037212	24		270	4616	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888210	112888210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121918464	NA	P-0000918-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	28	467	0	ENST00000351677.2:c.226G>A	p.Glu76Lys	p.E76K	ENST00000351677	NM_002834.3	76	Gag/Aag	3/16	0.21359641791028	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.747990382037212	0		467	393	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184562	7184562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770690301	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	87	148	0	ENST00000302850.5:c.739G>A	p.Asp247Asn	p.D247N	ENST00000302850	NM_000208.2	247	Gac/Aac	3/22	0.253311783093991	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.25	1		148	417	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	60	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.98	0.854	1	1	0.979	1	CLONAL	2	TRUE	1	0.25	2		422	245	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	241	558	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.302486352646961	1	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	0	0.25	1		558	695	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295229	1295229	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	59	190	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.967	0.842	1	1	0.979	1	CLONAL	2	TRUE	1	0.25	2		190	244	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484148	120484148	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	154	311	0	ENST00000256646.2:c.2981+1G>T		p.X994_splice	ENST00000256646	NM_024408.3	994			0.153001254778744	5	FACETS	1	0.938	1	0.686	0.628	0.747	CLONAL	2	TRUE	2	0.25	5		311	823	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162741873	162741873	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	139	234	0	ENST00000367921.3:c.1564G>T	p.Ala522Ser	p.A522S	ENST00000367921	NM_006182.2	522	Gca/Tca	13/18	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.25	2		234	769	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555216	226555216	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374662166	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	161	460	0	ENST00000366794.5:c.2371G>A	p.Asp791Asn	p.D791N	ENST00000366794	NM_001618.3	791	Gat/Aat	17/23	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.25	2		460	914	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967135	25967135	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	117	275	0	ENST00000435504.4:c.2071C>T	p.Pro691Ser	p.P691S	ENST00000435504		691	Cca/Tca	13/13	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.25	2		275	673	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285210	212285210	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	110	421	0	ENST00000342788.4:c.3091C>T	p.Pro1031Ser	p.P1031S	ENST00000342788	NM_005235.2	1031	Cca/Tca	25/28	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.25	2		421	847	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215937	142215937	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs141429029	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	96	383	0	ENST00000350721.4:c.5656C>T	p.Arg1886Ter	p.R1886*	ENST00000350721	NM_001184.3	1886	Cga/Tga	33/47	1	2	FACETS	0.918	0.817	1	0.918	0.817	1	CLONAL	1	TRUE	1	0.25	2		383	837	SUCCESS
ATR	545	MSKCC	GRCh37	3	142232396	142232396	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	88	270	0	ENST00000350721.4:c.4588C>T	p.Pro1530Ser	p.P1530S	ENST00000350721	NM_001184.3	1530	Cca/Tca	26/47	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.25	2		270	684	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947844	178947844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	131	401	0	ENST00000263967.3:c.2719G>A	p.Ala907Thr	p.A907T	ENST00000263967	NM_006218.2	907	Gct/Act	19/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.25	2		401	859	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184651	185184651	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	191	544	0	ENST00000265026.3:c.1543T>A	p.Tyr515Asn	p.Y515N	ENST00000265026	NM_004721.4	515	Tac/Aac	10/14	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.25	2		544	1058	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190831	185190831	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	168	383	1	ENST00000265026.3:c.1712G>A	p.Gly571Glu	p.G571E	ENST00000265026	NM_004721.4	571	gGa/gAa	11/14	1	2	FACETS	0.765	0.704	0.83	1	0.989	1	SUBCLONAL	2	TRUE	1	0.25	2		384	878	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231707	66231707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1211795184	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	130	468	0	ENST00000273854.3:c.1993G>A	p.Glu665Lys	p.E665K	ENST00000273854	NM_004439.5	665	Gaa/Aaa	11/18	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.25	2		468	973	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356161	66356161	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	135	315	0	ENST00000273854.3:c.1336G>A	p.Gly446Arg	p.G446R	ENST00000273854	NM_004439.5	446	Gga/Aga	5/18	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.25	2		315	933	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106194024	106194024	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1463638716	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	149	308	0	ENST00000380013.4:c.4486C>T	p.Pro1496Ser	p.P1496S	ENST00000380013	NM_001127208.2	1496	Cca/Tca	10/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.25	2		308	977	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517930	187517930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	111	430	0	ENST00000441802.2:c.12764C>T	p.Ser4255Phe	p.S4255F	ENST00000441802	NM_005245.3	4255	tCc/tTc	25/27	1	2	FACETS	0.909	0.816	1	0.909	0.816	1	CLONAL	1	TRUE	1	0.25	2		430	977	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525029	187525029	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	83	247	0	ENST00000441802.2:c.10651T>C	p.Phe3551Leu	p.F3551L	ENST00000441802	NM_005245.3	3551	Ttc/Ctc	19/27	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.25	2		247	489	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590370	67590370	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	99	196	0	ENST00000274335.5:c.1432C>T	p.Gln478Ter	p.Q478*	ENST00000274335		478	Caa/Taa	11/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.25	2		196	696	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287262	33287262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	122	308	0	ENST00000374542.5:c.1835C>T	p.Ser612Phe	p.S612F	ENST00000374542	NM_001141970.1	612	tCc/tTc	6/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.25	2		308	757	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631322	117631322	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757128233	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	161	629	0	ENST00000368508.3:c.6356G>A	p.Gly2119Glu	p.G2119E	ENST00000368508	NM_002944.2	2119	gGg/gAg	40/43	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.25	2		629	1114	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662626	117662626	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	129	386	0	ENST00000368508.3:c.4839T>A	p.Phe1613Leu	p.F1613L	ENST00000368508	NM_002944.2	1613	ttT/ttA	29/43	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.25	2		386	950	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971029	21971029	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519852	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	139	224	0	ENST00000304494.5:c.329G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tGg/tAg	2/3	0.302486352646961	1	FACETS	1	0.933	1	1	0.991	1	CLONAL	2	TRUE	0	0.25	1		224	477	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399124	139399124	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	84	333	0	ENST00000277541.6:c.5018+1G>A		p.X1673_splice	ENST00000277541	NM_017617.3	1673			0.302486352646961	1	FACETS	0.77	0.684	0.86	1	0.98	1	SUBCLONAL	2	TRUE	0	0.25	1		333	382	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417641	139417641	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	26	277	0	ENST00000277541.6:c.404-1G>A		p.X135_splice	ENST00000277541	NM_017617.3	135			0.302486352646961	1	FACETS	0.48	0.38	0.595	0.48	0.38	0.595	SUBCLONAL	1	TRUE	0	0.25	1		277	379	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503148	125503148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	154	430	0	ENST00000428830.2:c.515C>T	p.Pro172Leu	p.P172L	ENST00000428830	NM_001114121.2	172	cCa/cTa	6/14	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.25	2		430	980	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246464	46246464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	171	367	0	ENST00000334344.6:c.4558G>A	p.Glu1520Lys	p.E1520K	ENST00000334344	NM_152641.2	1520	Gag/Aag	15/21	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.25	2		367	953	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434076	121434076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748148527	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	193	479	0	ENST00000257555.6:c.967G>A	p.Gly323Arg	p.G323R	ENST00000257555		323	Gga/Aga	5/10	1	2	FACETS	0.917	0.849	0.987	1	0.993	1	CLONAL	2	TRUE	1	0.25	2		479	842	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436737	110436737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	115	377	0	ENST00000375856.3:c.1664C>T	p.Ser555Phe	p.S555F	ENST00000375856	NM_003749.2	555	tCc/tTc	1/2	0.251396246770685	4	FACETS	0.859	0.775	0.948	0.859	0.775	0.948	CLONAL	2	TRUE	2	0.25	4		377	669	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678440	88678440	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	167	552	0	ENST00000360948.2:c.1096A>C	p.Asn366His	p.N366H	ENST00000360948	NM_001012338.2	366	Aac/Cac	9/19	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.25	2		552	972	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347204	347204	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	138	449	0	ENST00000262320.3:c.1807A>C	p.Lys603Gln	p.K603Q	ENST00000262320	NM_003502.3	603	Aaa/Caa	7/11	0.191270450222285	0	FACETS	0.685	0.626	0.747			1	SUBCLONAL	2	TRUE	0	0.25	0		449	604	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16068342	16068342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	10	56	0	ENST00000268712.3:c.569G>A	p.Arg190Gln	p.R190Q	ENST00000268712	NM_006311.3	190	cGa/cAa	5/46	0.142481355993136	0	FACETS	0.545	0.372	0.76			1	INDETERMINATE	1	TRUE	0	0.25	0		56	110	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41251794	41251794	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	281	490	0	ENST00000357654.3:c.545T>C	p.Leu182Ser	p.L182S	ENST00000357654	NM_007294.3	182	tTg/tCg	7/23	0.302486352646961	1	FACETS	1	0.985	1	1	0.996	1	CLONAL	2	TRUE	0	0.25	1		490	873	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533791	63533791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779863826	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	189	389	0	ENST00000307078.5:c.1363C>T	p.Pro455Ser	p.P455S	ENST00000307078	NM_004655.3	455	Cca/Tca	6/11	0.302486352646961	3	FACETS	1	0.947	1			1	CLONAL	3	TRUE	NA	0.25	3		389	556	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285130	15285130	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	128	359	0	ENST00000263388.2:c.4485G>A	p.Trp1495Ter	p.W1495*	ENST00000263388	NM_000435.2	1495	tgG/tgA	25/33	0.253311783093991	1	FACETS	0.8	0.728	0.875	1	0.987	1	SUBCLONAL	2	TRUE	0	0.25	1		359	560	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288469	15288469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	25	74	0	ENST00000263388.2:c.4270C>T	p.Pro1424Ser	p.P1424S	ENST00000263388	NM_000435.2	1424	Ccc/Tcc	24/33	0.253311783093991	1	FACETS	0.825	0.664	1	1	0.943	1	CLONAL	2	TRUE	0	0.25	1		74	106	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546847	9546847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	161	279	0	ENST00000353224.5:c.1175C>T	p.Ser392Leu	p.S392L	ENST00000353224	NM_177990.2	392	tCg/tTg	5/10	0.153001254778744	5	FACETS	1	0.977	1	0.779	0.715	0.845	CLONAL	2	TRUE	2	0.25	5		279	758	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41521930	41521930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1188127391	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	142	531	0	ENST00000263253.7:c.792G>T	p.Gln264His	p.Q264H	ENST00000263253	NM_001429.3	264	caG/caT	3/31	0.236584927318668	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.25	1		531	813	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922863	39922863	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	170	317	0	ENST00000378444.4:c.3845A>G	p.Gln1282Arg	p.Q1282R	ENST00000378444	NM_001123385.1	1282	cAa/cGa	8/15	0.302486352646961	0	FACETS	0.739	0.686	0.793			1	SUBCLONAL	3	TRUE	NA	0.25	0		317	460	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198087	185198095	+	inframe_deletion	In_Frame_Del	DEL	GATGGAGAA	GATGGAGAA	-	novel	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	82	351	0	ENST00000265026.3:c.2571_2579del	p.Asp857_Glu859del	p.D857_E859del	ENST00000265026	NM_004721.4	857	GATGGAGAA/-	13/14	1	2	FACETS	0.883	0.778	0.996	0.883	0.778	0.996	CLONAL	1	TRUE	1	0.25	2		351	743	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851784	134851785	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	116	335	0	ENST00000398015.3:c.1190_1191delinsAA	p.Trp397Ter	p.W397*	ENST00000398015	NM_004441.4	397	tGG/tAA	5/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.25	2		335	760	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760346	133760347	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	90	424	0	ENST00000318560.5:c.2669_2670delinsAA	p.Gly890Glu	p.G890E	ENST00000318560	NM_005157.4	890	gGG/gAA	11/11	0.302486352646961	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.25	1		424	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578289	7578290	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0000919-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	103	371	0	ENST00000269305.4:c.560-1_560delinsAA		p.X187_splice	ENST00000269305	NM_001126112.2	187		6/11	0.142481355993136	0	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	0	0.25	0		371	514	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000926-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	35	422	0				ENST00000310581	NM_198253.2	-/1132			0.379822983371465	4	FACETS	0.89	0.748	1	0.89	0.748	1	CLONAL	2	TRUE	2	0.581360868182522	4		422	107	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866075	37866075	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1209871684	NA	P-0000926-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	61	373	0	ENST00000269571.5:c.584G>A	p.Cys195Tyr	p.C195Y	ENST00000269571		195	tGt/tAt	5/27	0.237623498661762	3	FACETS	0.718	0.623	0.822	0.359	0.311	0.411	INDETERMINATE	1	TRUE	1	0.581360868182522	3		373	377	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0000928-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	120	139	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.684594020818063	2		139	285	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577098	7577098	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0000928-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	19	551	1	ENST00000269305.4:c.840A>T	p.Arg280Ser	p.R280S	ENST00000269305	NM_001126112.2	280	agA/agT	8/11	0.684594020818063	2	FACETS	0.067	0.05	0.088	0.034	0.025	0.044	SUBCLONAL	1	TRUE	0	0.684594020818063	2		552	823	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0000936-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	46	479	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.924	0.776	1	0.924	0.776	1	CLONAL	1	TRUE	1	0.13	2		480	766	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0000936-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	37	234	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.926	0.761	1	0.926	0.761	1	CLONAL	1	TRUE	1	0.13	2		234	615	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971124	21971125	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0000936-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	26	99	0	ENST00000304494.5:c.233_234del	p.Leu78HisfsTer41	p.L78Hfs*41	ENST00000304494	NM_000077.4	78	cTC/c	2/3	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.13	2		99	355	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0000939-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	30	185	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.265032381653353	1	FACETS	0.967	0.786	1	0.967	0.786	1	CLONAL	1	FALSE	0	0.265032381653353	1		185	203	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0000939-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	15	70	0				ENST00000310581	NM_198253.2	-/1132			0.265032381653353	1	FACETS	0.893	0.66	1	0.893	0.66	1	CLONAL	1	FALSE	0	0.265032381653353	1		70	110	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911534	101911534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111426349	NA	P-0000939-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	102	234	0	ENST00000374994.4:c.1459C>T	p.Arg487Trp	p.R487W	ENST00000374994	NM_004612.2	487	Cgg/Tgg	9/9	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	FALSE	NA	0.265032381653353	2		234	517	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239878	98239879	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0000939-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	123	200	0	ENST00000331920.6:c.1453dup	p.Leu485ProfsTer12	p.L485Pfs*12	ENST00000331920	NM_000264.3	485	ctg/cCtg	10/24	NA	2	FACETS	0.975	0.887	1			1	INDETERMINATE	2	FALSE	NA	0.265032381653353	2		200	476	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	65	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	FALSE	NA	0.565335857673046	2		422	176	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	9	295	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.105	0.069	0.151	0.105	0.069	0.151	SUBCLONAL	1	FALSE	1	0.565335857673046	2		295	304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	41	277	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.17135760338698	1	FACETS	0.215	0.179	0.255	0.215	0.179	0.255	INDETERMINATE	1	FALSE	0	0.565335857673046	1		277	484	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	113	171	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	1	2	FACETS	0.79	0.725	0.856	1	0.988	1	SUBCLONAL	2	FALSE	1	0.565335857673046	2		171	253	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169419	11169419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	144	462	0	ENST00000361445.4:c.7456G>A	p.Gly2486Ser	p.G2486S	ENST00000361445	NM_004958.3	2486	Ggt/Agt	56/58	0.17135760338698	1	FACETS	0.672	0.616	0.73	0.672	0.616	0.73	INDETERMINATE	1	FALSE	0	0.565335857673046	1		462	544	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11199456	11199456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	132	297	0	ENST00000361445.4:c.5035G>A	p.Val1679Ile	p.V1679I	ENST00000361445	NM_004958.3	1679	Gtt/Att	36/58	0.17135760338698	1	FACETS	0.688	0.628	0.75	0.688	0.628	0.75	INDETERMINATE	1	FALSE	0	0.565335857673046	1		297	487	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258692	16258692	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	43	207	0	ENST00000375759.3:c.5957C>T	p.Ser1986Phe	p.S1986F	ENST00000375759	NM_015001.2	1986	tCc/tTc	11/15	0.17135760338698	1	FACETS	0.29	0.243	0.342	0.29	0.243	0.342	INDETERMINATE	1	FALSE	0	0.565335857673046	1		207	376	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262297	16262297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	17	52	0	ENST00000375759.3:c.9562C>T	p.Pro3188Ser	p.P3188S	ENST00000375759	NM_015001.2	3188	Ccc/Tcc	11/15	0.17135760338698	1	FACETS	0.334	0.252	0.43	0.334	0.252	0.43	INDETERMINATE	1	FALSE	0	0.565335857673046	1		52	129	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023601	27023601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	73	255	0	ENST00000324856.7:c.707G>A	p.Gly236Asp	p.G236D	ENST00000324856	NM_006015.4	236	gGt/gAt	1/20	0.17135760338698	1	FACETS	0.416	0.365	0.471	0.416	0.365	0.471	INDETERMINATE	1	FALSE	0	0.565335857673046	1		255	445	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809495	36809495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374572688	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	128	243	0	ENST00000373129.3:c.970G>A	p.Val324Ile	p.V324I	ENST00000373129	NM_032017.1	324	Gtc/Atc	10/12	0.17135760338698	1	FACETS	0.763	0.697	0.83	0.763	0.697	0.83	INDETERMINATE	1	FALSE	0	0.565335857673046	1		243	426	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805756	43805756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	45	373	0	ENST00000372470.3:c.812C>T	p.Ser271Phe	p.S271F	ENST00000372470	NM_005373.2	271	tCc/tTc	5/12	0.17135760338698	1	FACETS	0.211	0.177	0.248	0.211	0.177	0.248	INDETERMINATE	1	FALSE	0	0.565335857673046	1		373	542	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430016	78430016	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	73	271	0	ENST00000370768.2:c.863G>A	p.Gly288Asp	p.G288D	ENST00000370768	NM_003902.3	288	gGc/gAc	11/20	0.111980567932591	4	FACETS	0.596	0.521	0.677	0.298	0.26	0.339	INDETERMINATE	1	FALSE	2	0.565335857673046	4		271	678	SUCCESS
FH	2271	MSKCC	GRCh37	1	241661238	241661238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	161	321	0	ENST00000366560.3:c.1423G>A	p.Ala475Thr	p.A475T	ENST00000366560	NM_000143.3	475	Gca/Aca	10/10	1	2	FACETS	0.806	0.741	0.873	0.806	0.741	0.873	CLONAL	1	FALSE	1	0.565335857673046	2		321	707	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982467	25982467	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	39	242	0	ENST00000435504.4:c.823G>A	p.Asp275Asn	p.D275N	ENST00000435504		275	Gac/Aac	9/13	0.17135760338698	1	FACETS	0.156	0.129	0.186	0.156	0.129	0.186	INDETERMINATE	1	FALSE	0	0.565335857673046	1		242	635	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606722	29606722	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	132	218	0	ENST00000389048.3:c.1158G>A	p.Trp386Ter	p.W386*	ENST00000389048	NM_004304.4	386	tgG/tgA	5/29	0.17135760338698	1	FACETS	0.72	0.659	0.784	0.72	0.659	0.784	INDETERMINATE	1	FALSE	0	0.565335857673046	1		218	465	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026318	48026318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878853701	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	162	304	0	ENST00000234420.5:c.1196C>T	p.Pro399Leu	p.P399L	ENST00000234420	NM_000179.2	399	cCt/cTt	4/10	0.17135760338698	1	FACETS	0.739	0.682	0.798	0.739	0.682	0.798	INDETERMINATE	1	FALSE	0	0.565335857673046	1		304	556	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027422	48027422	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781462	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	133	205	1	ENST00000234420.5:c.2300C>T	p.Thr767Ile	p.T767I	ENST00000234420	NM_000179.2	767	aCt/aTt	4/10	0.17135760338698	1	FACETS	0.752	0.688	0.818	0.752	0.688	0.818	INDETERMINATE	1	FALSE	0	0.565335857673046	1		206	449	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169283	99169283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767029111	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	75	346	0	ENST00000074304.5:c.1213C>T	p.Pro405Ser	p.P405S	ENST00000074304	NM_001134224.1	405	Ccc/Tcc	15/26	1	2	FACETS	0.448	0.393	0.508	0.448	0.393	0.508	SUBCLONAL	1	FALSE	1	0.565335857673046	2		346	592	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096129	178096129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1397390214	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	59	199	0	ENST00000397062.3:c.1202G>A	p.Gly401Glu	p.G401E	ENST00000397062	NM_006164.4	401	gGg/gAg	5/5	1	2	FACETS	0.378	0.325	0.436	0.378	0.325	0.436	SUBCLONAL	1	FALSE	1	0.565335857673046	2		199	552	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149710	202149710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	53	341	0	ENST00000358485.4:c.1151G>A	p.Gly384Asp	p.G384D	ENST00000358485	NM_001080125.1	384	gGc/gAc	8/9	1	2	FACETS	0.393	0.335	0.456	0.393	0.335	0.456	SUBCLONAL	1	FALSE	1	0.565335857673046	2		341	477	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645505	215645505	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219606203	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	81	395	0	ENST00000260947.4:c.1093C>T	p.Pro365Ser	p.P365S	ENST00000260947	NM_000465.2	365	Cca/Tca	4/11	1	2	FACETS	0.41	0.361	0.463	0.41	0.361	0.463	SUBCLONAL	1	FALSE	1	0.565335857673046	2		395	699	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662419	227662419	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	17	151	0	ENST00000305123.5:c.1036C>T	p.Pro346Ser	p.P346S	ENST00000305123	NM_005544.2	346	Cct/Tct	1/2	1	2	FACETS	0.202	0.15	0.263	0.202	0.15	0.263	SUBCLONAL	1	FALSE	1	0.565335857673046	2		151	298	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663229	227663229	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	200	400	0	ENST00000305123.5:c.226G>A	p.Ala76Thr	p.A76T	ENST00000305123	NM_005544.2	76	Gct/Act	1/2	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	1	0.565335857673046	2		400	686	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437153	52437153	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	54	270	0	ENST00000460680.1:c.1890+1G>A		p.X630_splice	ENST00000460680	NM_004656.3	630			NA	2	FACETS	0.491	0.421	0.568			1	INDETERMINATE	1	FALSE	NA	0.565335857673046	2		270	389	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461440	138461440	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	155	375	0	ENST00000289153.2:c.581G>A	p.Gly194Glu	p.G194E	ENST00000289153	NM_006219.2	194	gGg/gAg	3/22	NA	2	FACETS	0.934	0.859	1			1	INDETERMINATE	1	FALSE	NA	0.565335857673046	2		375	587	SUCCESS
ATR	545	MSKCC	GRCh37	3	142177874	142177874	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	50	245	0	ENST00000350721.4:c.7429C>T	p.His2477Tyr	p.H2477Y	ENST00000350721	NM_001184.3	2477	Cat/Tat	44/47	NA	2	FACETS	0.259	0.219	0.303			1	INDETERMINATE	1	FALSE	NA	0.565335857673046	2		245	684	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447109	187447109	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	63	211	0	ENST00000232014.4:c.1084C>T	p.Pro362Ser	p.P362S	ENST00000232014	NM_001130845.1	362	Cct/Tct	5/10	1	2	FACETS	0.444	0.384	0.508	0.444	0.384	0.508	SUBCLONAL	1	FALSE	1	0.565335857673046	2		211	502	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129905	55129905	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	208	393	0	ENST00000257290.5:c.439A>T	p.Ile147Phe	p.I147F	ENST00000257290	NM_006206.4	147	Att/Ttt	4/23	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	FALSE	1	0.565335857673046	2		393	727	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196448	106196448	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	123	455	0	ENST00000380013.4:c.4781C>T	p.Pro1594Leu	p.P1594L	ENST00000380013	NM_001127208.2	1594	cCt/cTt	11/11	0.111980567932591	4	FACETS	0.766	0.692	0.844	0.383	0.346	0.422	INDETERMINATE	1	FALSE	2	0.565335857673046	4		455	889	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516972	187516972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	69	253	0	ENST00000441802.2:c.13009G>A	p.Val4337Met	p.V4337M	ENST00000441802	NM_005245.3	4337	Gtg/Atg	26/27	NA	2	FACETS	0.422	0.367	0.48			1	INDETERMINATE	1	FALSE	NA	0.565335857673046	2		253	579	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264610	1264610	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	67	487	2	ENST00000310581.5:c.2752G>A	p.Ala918Thr	p.A918T	ENST00000310581	NM_198253.2	918	Gct/Act	11/16	NA	2	FACETS	0.465	0.404	0.53			1	INDETERMINATE	1	FALSE	NA	0.565335857673046	2		489	510	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279432	1279432	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866903055	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	17	257	0	ENST00000310581.5:c.2104C>T	p.Pro702Ser	p.P702S	ENST00000310581	NM_198253.2	702	Ccg/Tcg	5/16	NA	2	FACETS	0.187	0.139	0.245			1	INDETERMINATE	1	FALSE	NA	0.565335857673046	2		257	321	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873581	35873581	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1315265916	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	50	171	0	ENST00000303115.3:c.538-1G>A		p.X180_splice	ENST00000303115	NM_002185.3	180			0.111980567932591	4	FACETS	0.602	0.511	0.701	0.301	0.255	0.351	INDETERMINATE	1	FALSE	2	0.565335857673046	4		171	460	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930671	131930671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	101	190	0	ENST00000265335.6:c.1904G>A	p.Ser635Asn	p.S635N	ENST00000265335		635	aGc/aAc	12/25	0.111980567932591	4	FACETS	1	0.959	1	0.567	0.509	0.629	INDETERMINATE	1	FALSE	2	0.565335857673046	4		190	493	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433908	149433908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs549775847	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	33	334	0	ENST00000286301.3:c.2740G>A	p.Ala914Thr	p.A914T	ENST00000286301	NM_005211.3	914	Gcc/Acc	21/22	0.111980567932591	4	FACETS	0.349	0.284	0.424	0.175	0.142	0.212	INDETERMINATE	1	FALSE	2	0.565335857673046	4		334	523	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637792	176637792	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758781096	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	49	278	0	ENST00000439151.2:c.2392C>T	p.Pro798Ser	p.P798S	ENST00000439151	NM_022455.4	798	Cca/Tca	5/23	0.167879809440707	0	FACETS	0.161	0.136	0.188			1	INDETERMINATE	1	FALSE	0	0.565335857673046	0		278	468	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637903	176637903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1197555000	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	90	199	0	ENST00000439151.2:c.2503G>A	p.Gly835Ser	p.G835S	ENST00000439151	NM_022455.4	835	Ggt/Agt	5/23	0.167879809440707	0	FACETS	0.361	0.323	0.402			1	INDETERMINATE	1	FALSE	0	0.565335857673046	0		199	383	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176666834	176666834	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	38	343	0	ENST00000439151.2:c.4270C>T	p.Pro1424Ser	p.P1424S	ENST00000439151	NM_022455.4	1424	Ccc/Tcc	8/23	0.167879809440707	0	FACETS	0.098	0.08	0.118			1	INDETERMINATE	1	FALSE	0	0.565335857673046	0		343	597	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721094	176721094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	38	276	0	ENST00000439151.2:c.6725G>A	p.Gly2242Glu	p.G2242E	ENST00000439151	NM_022455.4	2242	gGa/gAa	23/23	0.167879809440707	0	FACETS	0.164	0.135	0.195			1	INDETERMINATE	1	FALSE	0	0.565335857673046	0		276	357	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536265	106536265	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	153	195	0	ENST00000369096.4:c.232C>T	p.Gln78Ter	p.Q78*	ENST00000369096	NM_001198.3	78	Cag/Tag	2/7	1	2	FACETS	0.965	0.887	1	0.965	0.887	1	CLONAL	1	FALSE	1	0.565335857673046	2		195	561	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641063	117641063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	205	391	0	ENST00000368508.3:c.5908G>A	p.Val1970Ile	p.V1970I	ENST00000368508	NM_002944.2	1970	Gtt/Att	36/43	1	2	FACETS	0.981	0.913	1	0.981	0.913	1	CLONAL	1	FALSE	1	0.565335857673046	2		391	739	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005691	150005691	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	81	116	0	ENST00000253339.5:c.534G>A	p.Trp178Ter	p.W178*	ENST00000253339		178	tgG/tgA	3/7	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	FALSE	1	0.565335857673046	2		116	278	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157454342	157454342	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	21	94	0	ENST00000346085.5:c.2551+1G>A		p.X851_splice	ENST00000346085	NM_020732.3	851			1	2	FACETS	0.295	0.227	0.373	0.295	0.227	0.373	SUBCLONAL	1	FALSE	1	0.565335857673046	2		94	252	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622242	162622242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	83	269	0	ENST00000366898.1:c.455G>A	p.Gly152Asp	p.G152D	ENST00000366898	NM_004562.2	152	gGc/gAc	4/12	0.565335857673046	1	FACETS	0.409	0.362	0.459	0.409	0.362	0.459	SUBCLONAL	1	FALSE	0	0.565335857673046	1		269	515	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974245	2974245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	32	276	0	ENST00000396946.4:c.1360C>T	p.Pro454Ser	p.P454S	ENST00000396946	NM_032415.4	454	Cca/Tca	10/25	0.273955031243877	4	FACETS	0.329	0.267	0.401	0.165	0.133	0.201	INDETERMINATE	1	FALSE	2	0.565335857673046	4		276	538	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426896	6426896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	161	322	0	ENST00000356142.4:c.89G>A	p.Gly30Glu	p.G30E	ENST00000356142	NM_018890.3	30	gGa/gAa	2/7	0.273955031243877	4	FACETS	0.878	0.805	0.955	0.439	0.402	0.478	INDETERMINATE	1	FALSE	2	0.565335857673046	4		322	1015	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467669	50467669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	44	248	0	ENST00000331340.3:c.904G>A	p.Glu302Lys	p.E302K	ENST00000331340	NM_006060.4	302	Gag/Aag	8/8	0.565335857673046	6	FACETS	0.452	0.378	0.534			1	SUBCLONAL	1	FALSE	NA	0.565335857673046	6		248	734	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273092	55273092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1473630143	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13155	714	313	0	ENST00000275493.2:c.3415C>T	p.Leu1139Phe	p.L1139F	ENST00000275493	NM_005228.3	1139	Ctc/Ttc	28/28	0.565335857673046	43	FACETS	1	0.992	1			1	CLONAL	2	FALSE	NA	0.565335857673046	43		313	13869	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92244566	92244566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	56	182	0	ENST00000265734.4:c.869C>T	p.Ser290Phe	p.S290F	ENST00000265734	NM_001259.6	290	tCt/tTt	8/8	0.549731195328708	4	FACETS	0.351	0.3	0.408	0.176	0.15	0.204	SUBCLONAL	1	FALSE	2	0.565335857673046	4		182	883	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520076	106520076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	79	176	0	ENST00000359195.3:c.2504G>A	p.Gly835Asp	p.G835D	ENST00000359195	NM_002649.2	835	gGt/gAt	6/11	0.549731195328708	4	FACETS	0.58	0.51	0.656	0.29	0.255	0.328	SUBCLONAL	1	FALSE	2	0.565335857673046	4		176	754	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874595	151874595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	142	209	0	ENST00000262189.6:c.7943C>T	p.Thr2648Ile	p.T2648I	ENST00000262189	NM_170606.2	2648	aCt/aTt	38/59	0.549731195328708	4	FACETS	1	0.937	1	0.517	0.471	0.564	CLONAL	1	FALSE	2	0.565335857673046	4		209	761	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884523	151884523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	74	347	0	ENST00000262189.6:c.4832C>T	p.Pro1611Leu	p.P1611L	ENST00000262189	NM_170606.2	1611	cCt/cTt	33/59	0.549731195328708	4	FACETS	0.401	0.35	0.456	0.2	0.175	0.228	SUBCLONAL	1	FALSE	2	0.565335857673046	4		347	1022	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151902217	151902217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	121	272	2	ENST00000262189.6:c.3935C>T	p.Ser1312Phe	p.S1312F	ENST00000262189	NM_170606.2	1312	tCc/tTc	25/59	0.549731195328708	4	FACETS	0.846	0.764	0.932	0.423	0.382	0.466	CLONAL	1	FALSE	2	0.565335857673046	4		274	792	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287460	38287460	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	20	179	0	ENST00000425967.3:c.197C>T	p.Pro66Leu	p.P66L	ENST00000425967	NM_001174067.1	66	cCc/cTc	4/19	0.111980567932591	4	FACETS	0.357	0.273	0.456	0.179	0.136	0.228	INDETERMINATE	1	FALSE	2	0.565335857673046	4		179	310	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38315005	38315005	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1280460663	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	157	287	1	ENST00000425967.3:c.59G>A	p.Arg20Lys	p.R20K	ENST00000425967	NM_001174067.1	20	aGa/aAa	3/19	0.111980567932591	4	FACETS	0.866	0.799	0.935	0.866	0.799	0.935	INDETERMINATE	2	FALSE	2	0.565335857673046	4		288	502	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955489	90955489	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1421870412	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	82	322	1	ENST00000265433.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000265433	NM_002485.4	726	Gaa/Aaa	14/16	0.111980567932591	4	FACETS	0.635	0.56	0.716	0.318	0.28	0.358	INDETERMINATE	1	FALSE	2	0.565335857673046	4		323	715	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90976692	90976692	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs529845940	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	200	377	0	ENST00000265433.3:c.940G>A	p.Val314Met	p.V314M	ENST00000265433	NM_002485.4	314	Gtg/Atg	8/16	0.111980567932591	4	FACETS	1	0.989	1	0.691	0.642	0.742	INDETERMINATE	1	FALSE	2	0.565335857673046	4		377	801	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741605	145741605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764510816	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	62	346	0	ENST00000428558.2:c.898G>A	p.Gly300Arg	p.G300R	ENST00000428558	NM_004260.3	300	Ggg/Agg	5/22	0.111980567932591	4	FACETS	0.653	0.564	0.749	0.326	0.282	0.375	INDETERMINATE	1	FALSE	2	0.565335857673046	4		346	526	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5078421	5078421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	36	193	0	ENST00000381652.3:c.2108G>A	p.Ser703Asn	p.S703N	ENST00000381652	NM_004972.3	703	aGt/aAt	16/25	1	2	FACETS	0.217	0.178	0.262	0.217	0.178	0.262	SUBCLONAL	1	FALSE	1	0.565335857673046	2		193	586	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342641	87342641	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	156	267	0	ENST00000277120.3:c.926G>A	p.Gly309Asp	p.G309D	ENST00000277120		309	gGc/gAc	9/19	1	2	FACETS	0.9	0.828	0.975	0.9	0.828	0.975	CLONAL	1	FALSE	1	0.565335857673046	2		267	613	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93636534	93636534	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	62	307	0	ENST00000375746.1:c.964C>T	p.Pro322Ser	p.P322S	ENST00000375746	NM_001174167.1	322	Ccg/Tcg	8/14	1	2	FACETS	0.362	0.312	0.416	0.362	0.312	0.416	SUBCLONAL	1	FALSE	1	0.565335857673046	2		307	606	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399810	139399810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	108	206	0	ENST00000277541.6:c.4538G>A	p.Gly1513Asp	p.G1513D	ENST00000277541	NM_017617.3	1513	gGc/gAc	25/34	1	2	FACETS	0.975	0.882	1	0.975	0.882	1	CLONAL	1	FALSE	1	0.565335857673046	2		206	392	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205578	61205578	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1060499901	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	50	255	0	ENST00000301761.2:c.363G>A	p.Trp121Ter	p.W121*	ENST00000301761	NM_017841.2	121	tgG/tgA	3/4	0.533859332005032	2	FACETS	0.399	0.339	0.465	0.2	0.169	0.233	SUBCLONAL	1	FALSE	0	0.565335857673046	2		255	443	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989008	85989008	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762517406	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	38	271	0	ENST00000263360.6:c.1174G>A	p.Glu392Lys	p.E392K	ENST00000263360	NM_003797.3	392	Gaa/Aaa	11/12	0.533859332005032	2	FACETS	0.193	0.159	0.232	0.097	0.079	0.116	SUBCLONAL	1	FALSE	0	0.565335857673046	2		271	695	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94211946	94211946	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1263915515	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	85	300	0	ENST00000323929.3:c.499G>A	p.Val167Ile	p.V167I	ENST00000323929	NM_005591.3	167	Gtt/Att	6/20	0.533859332005032	2	FACETS	0.4	0.353	0.451	0.2	0.176	0.226	SUBCLONAL	1	FALSE	0	0.565335857673046	2		300	751	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373311	118373311	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369443279	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	47	388	0	ENST00000534358.1:c.6704C>T	p.Thr2235Ile	p.T2235I	ENST00000534358	NM_005933.3	2235	aCc/aTc	27/36	NA	2	FACETS	0.254	0.213	0.298			1	INDETERMINATE	1	FALSE	NA	0.565335857673046	2		388	655	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374204	118374204	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	124	219	0	ENST00000534358.1:c.7597G>A	p.Glu2533Lys	p.E2533K	ENST00000534358	NM_005933.3	2533	Gaa/Aaa	27/36	NA	2	FACETS	0.96	0.874	1			1	INDETERMINATE	1	FALSE	NA	0.565335857673046	2		219	457	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380764	118380764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	34	234	0	ENST00000534358.1:c.11002C>T	p.Pro3668Ser	p.P3668S	ENST00000534358	NM_005933.3	3668	Ccc/Tcc	30/36	NA	2	FACETS	0.246	0.2	0.297			1	INDETERMINATE	1	FALSE	NA	0.565335857673046	2		234	489	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037486	12037486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	36	141	0	ENST00000396373.4:c.1117C>T	p.Pro373Ser	p.P373S	ENST00000396373	NM_001987.4	373	Ccc/Tcc	6/8	0.565335857673046	4	FACETS	0.487	0.401	0.584			1	SUBCLONAL	1	FALSE	NA	0.565335857673046	4		141	409	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18473963	18473963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	57	297	0	ENST00000266497.5:c.1205C>T	p.Ser402Phe	p.S402F	ENST00000266497		402	tCc/tTc	6/31	0.17257560153325	5	FACETS	0.438	0.374	0.507			1	INDETERMINATE	1	FALSE	NA	0.565335857673046	5		297	851	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534785	18534785	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757768161	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	116	277	0	ENST00000266497.5:c.1843G>A	p.Val615Ile	p.V615I	ENST00000266497		615	Gta/Ata	12/31	0.17257560153325	5	FACETS	1	0.981	1			1	INDETERMINATE	1	FALSE	NA	0.565335857673046	5		277	557	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445802	49445802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	26	295	0	ENST00000301067.7:c.1664C>T	p.Ser555Phe	p.S555F	ENST00000301067	NM_003482.3	555	tCc/tTc	10/54	1	2	FACETS	0.178	0.14	0.221	0.178	0.14	0.221	SUBCLONAL	1	FALSE	1	0.565335857673046	2		295	517	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446464	49446464	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758955636	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	54	148	2	ENST00000301067.7:c.1141C>T	p.Pro381Ser	p.P381S	ENST00000301067	NM_003482.3	381	Ccc/Tcc	9/54	1	2	FACETS	0.549	0.471	0.633	0.549	0.471	0.633	SUBCLONAL	1	FALSE	1	0.565335857673046	2		150	348	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479330	50479330	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	40	185	0	ENST00000394963.4:c.177+1G>A		p.X59_splice	ENST00000394963	NM_003076.4	59			1	2	FACETS	0.404	0.337	0.479	0.404	0.337	0.479	SUBCLONAL	1	FALSE	1	0.565335857673046	2		185	350	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109672	115109672	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	127	343	0	ENST00000257566.3:c.2206G>A	p.Asp736Asn	p.D736N	ENST00000257566	NM_016569.3	736	Gac/Aac	8/8	0.167879809440707	0	FACETS	0.419	0.382	0.458			1	INDETERMINATE	1	FALSE	0	0.565335857673046	0		343	466	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626787	28626787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	76	309	0	ENST00000241453.7:c.509G>A	p.Arg170Lys	p.R170K	ENST00000241453	NM_004119.2	170	aGa/aAa	5/24	NA	2	FACETS	0.41	0.359	0.464			1	INDETERMINATE	1	FALSE	NA	0.565335857673046	2		309	656	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571480	95571480	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1313061695	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	135	113	0	ENST00000393063.1:c.3197C>T	p.Thr1066Ile	p.T1066I	ENST00000393063	NM_030621.3	1066	aCt/aTt	21/28	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.565335857673046	2		113	421	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239871	105239871	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	35	260	1	ENST00000349310.3:c.749C>T	p.Ala250Val	p.A250V	ENST00000349310	NM_001014432.1	250	gCc/gTc	10/15	1	2	FACETS	0.258	0.211	0.311	0.258	0.211	0.311	SUBCLONAL	1	FALSE	1	0.565335857673046	2		261	480	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312709	91312709	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756799764	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	80	442	0	ENST00000355112.3:c.2448G>A	p.Met816Ile	p.M816I	ENST00000355112	NM_000057.2	816	atG/atA	12/22	1	2	FACETS	0.386	0.339	0.436	0.386	0.339	0.436	SUBCLONAL	1	FALSE	1	0.565335857673046	2		442	734	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108749	2108749	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	62	352	0	ENST00000219476.3:c.850G>A	p.Ala284Thr	p.A284T	ENST00000219476	NM_000548.3	284	Gcc/Acc	10/42	0.167879809440707	0	FACETS	0.225	0.195	0.258			1	INDETERMINATE	1	FALSE	0	0.565335857673046	0		352	423	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108811	2108811	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397514884	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	65	407	0	ENST00000219476.3:c.912G>A	p.Trp304Ter	p.W304*	ENST00000219476	NM_000548.3	304	tgG/tgA	10/42	0.167879809440707	0	FACETS	0.21	0.182	0.24			1	INDETERMINATE	1	FALSE	0	0.565335857673046	0		407	476	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129583	2129583	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397514978	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	33	328	0	ENST00000219476.3:c.3310C>T	p.Gln1104Ter	p.Q1104*	ENST00000219476	NM_000548.3	1104	Cag/Tag	29/42	0.167879809440707	0	FACETS	0.111	0.09	0.135			1	INDETERMINATE	1	FALSE	0	0.565335857673046	0		328	458	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777874	3777874	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	40	513	1	ENST00000262367.5:c.7174G>A	p.Ala2392Thr	p.A2392T	ENST00000262367	NM_004380.2	2392	Gcc/Acc	31/31	0.167879809440707	0	FACETS	0.117	0.097	0.14			1	INDETERMINATE	1	FALSE	0	0.565335857673046	0		514	525	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7978925	7978925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397514532	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	117	358	0	ENST00000319144.4:c.1642C>T	p.Arg548Trp	p.R548W	ENST00000319144	NM_001139.2	548	Cgg/Tgg	12/15	0.17135760338698	1	FACETS	0.672	0.61	0.736	0.672	0.61	0.736	INDETERMINATE	1	FALSE	0	0.565335857673046	1		358	442	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980441	7980441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	51	269	0	ENST00000319144.4:c.1142C>T	p.Ala381Val	p.A381V	ENST00000319144	NM_001139.2	381	gCc/gTc	9/15	0.17135760338698	1	FACETS	0.316	0.269	0.367	0.316	0.269	0.367	INDETERMINATE	1	FALSE	0	0.565335857673046	1		269	410	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049754	16049754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	79	483	0	ENST00000268712.3:c.1018G>A	p.Glu340Lys	p.E340K	ENST00000268712	NM_006311.3	340	Gaa/Aaa	10/46	0.17135760338698	1	FACETS	0.263	0.231	0.297	0.263	0.231	0.297	INDETERMINATE	1	FALSE	0	0.565335857673046	1		483	763	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679358	29679358	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	58	382	0	ENST00000356175.3:c.7478C>T	p.Thr2493Ile	p.T2493I	ENST00000356175	NM_000267.3	2493	aCc/aTc	50/57	0.17135760338698	1	FACETS	0.206	0.176	0.238	0.206	0.176	0.238	INDETERMINATE	1	FALSE	0	0.565335857673046	1		382	715	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41247935	41247935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	43	346	0	ENST00000357654.3:c.598G>A	p.Gly200Arg	p.G200R	ENST00000357654	NM_007294.3	200	Gga/Aga	9/23	0.182754911103547	0	FACETS	0.097	0.081	0.116			1	INDETERMINATE	1	FALSE	0	0.565335857673046	0		346	680	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533653	63533653	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567755834	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	141	425	0	ENST00000307078.5:c.1501G>A	p.Gly501Arg	p.G501R	ENST00000307078	NM_004655.3	501	Ggg/Agg	6/11	1	2	FACETS	0.986	0.904	1	0.986	0.904	1	CLONAL	1	FALSE	1	0.565335857673046	2		425	506	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66520182	66520182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	52	309	0	ENST00000358598.2:c.466G>A	p.Val156Ile	p.V156I	ENST00000358598	NM_212471.2	156	Gtc/Atc	5/11	1	2	FACETS	0.328	0.279	0.382	0.328	0.279	0.382	SUBCLONAL	1	FALSE	1	0.565335857673046	2		309	561	SUCCESS
YES1	7525	MSKCC	GRCh37	18	736946	736946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	61	312	0	ENST00000314574.4:c.1153G>A	p.Ala385Thr	p.A385T	ENST00000314574	NM_005433.3	385	Gca/Aca	10/12	1	2	FACETS	0.464	0.401	0.532	0.464	0.401	0.532	SUBCLONAL	1	FALSE	1	0.565335857673046	2		312	465	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213986	2213986	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	20	101	0	ENST00000398665.3:c.1797+1G>A		p.X599_splice	ENST00000398665	NM_032482.2	599			0.221717483307365	3	FACETS	0.39	0.298	0.495	0.13	0.099	0.165	INDETERMINATE	1	FALSE	0	0.565335857673046	3		101	233	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132283	7132283	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	75	231	0	ENST00000302850.5:c.2728G>A	p.Gly910Ser	p.G910S	ENST00000302850	NM_000208.2	910	Ggc/Agc	14/22	0.215915188874446	2	FACETS	0.613	0.539	0.691	0.306	0.269	0.346	INDETERMINATE	1	FALSE	0	0.565335857673046	2		231	433	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254646	10254646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	68	178	0	ENST00000340748.4:c.2864C>T	p.Pro955Leu	p.P955L	ENST00000340748		955	cCc/cTc	28/40	0.215915188874446	2	FACETS	0.697	0.611	0.79	0.349	0.305	0.395	INDETERMINATE	1	FALSE	0	0.565335857673046	2		178	345	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10260544	10260544	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1201583942	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	43	321	0	ENST00000340748.4:c.2318C>T	p.Pro773Leu	p.P773L	ENST00000340748		773	cCg/cTg	24/40	0.215915188874446	2	FACETS	0.294	0.246	0.348	0.147	0.123	0.174	INDETERMINATE	1	FALSE	0	0.565335857673046	2		321	517	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602617	10602617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	27	262	0	ENST00000171111.5:c.961G>A	p.Ala321Thr	p.A321T	ENST00000171111	NM_203500.1	321	Gcg/Acg	3/6	0.215915188874446	2	FACETS	0.212	0.168	0.262	0.106	0.084	0.131	INDETERMINATE	1	FALSE	0	0.565335857673046	2		262	451	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130268	11130268	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	115	262	0	ENST00000358026.2:c.2507G>A	p.Gly836Glu	p.G836E	ENST00000358026	NM_001128849.1	836	gGa/gAa	18/36	0.221717483307365	3	FACETS	1	0.956	1	0.365	0.331	0.402	INDETERMINATE	1	FALSE	0	0.565335857673046	3		262	476	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152232	11152232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555788376	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	28	165	0	ENST00000358026.2:c.4516G>A	p.Asp1506Asn	p.D1506N	ENST00000358026	NM_001128849.1	1506	Gac/Aac	31/36	0.221717483307365	3	FACETS	0.389	0.311	0.477	0.13	0.103	0.159	INDETERMINATE	1	FALSE	0	0.565335857673046	3		165	327	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271756	15271756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1298647086	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	48	179	0	ENST00000263388.2:c.6683G>A	p.Ser2228Asn	p.S2228N	ENST00000263388	NM_000435.2	2228	aGc/aAc	33/33	0.221717483307365	3	FACETS	0.483	0.409	0.565	0.161	0.136	0.189	INDETERMINATE	1	FALSE	0	0.565335857673046	3		179	451	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272339	15272339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	82	205	0	ENST00000263388.2:c.6100C>T	p.Pro2034Ser	p.P2034S	ENST00000263388	NM_000435.2	2034	Ccc/Tcc	33/33	0.221717483307365	3	FACETS	0.926	0.821	1	0.309	0.273	0.346	INDETERMINATE	1	FALSE	0	0.565335857673046	3		205	402	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17949169	17949169	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	109	309	0	ENST00000458235.1:c.1472G>A	p.Gly491Asp	p.G491D	ENST00000458235	NM_000215.3	491	gGt/gAt	11/24	0.221717483307365	3	FACETS	1	0.964	1	0.379	0.342	0.417	INDETERMINATE	1	FALSE	0	0.565335857673046	3		309	435	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741217	40741217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	50	349	0	ENST00000392038.2:c.1216C>T	p.His406Tyr	p.H406Y	ENST00000392038	NM_001626.4	406	Cac/Tac	12/14	0.221717483307365	3	FACETS	0.383	0.325	0.448	0.128	0.108	0.15	INDETERMINATE	1	FALSE	0	0.565335857673046	3		349	592	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795710	42795710	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1355318527	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	69	379	0	ENST00000575354.2:c.2699C>T	p.Ala900Val	p.A900V	ENST00000575354	NM_015125.3	900	gCc/gTc	11/20	0.221717483307365	3	FACETS	0.428	0.372	0.488	0.143	0.124	0.163	INDETERMINATE	1	FALSE	0	0.565335857673046	3		379	732	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858100	45858100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1039034665	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	34	251	0	ENST00000391945.4:c.1553G>A	p.Arg518Gln	p.R518Q	ENST00000391945	NM_000400.3	518	cGg/cAg	17/23	0.221717483307365	3	FACETS	0.344	0.28	0.415	0.115	0.093	0.139	INDETERMINATE	1	FALSE	0	0.565335857673046	3		251	449	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714532	52714532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	103	257	0	ENST00000322088.6:c.290C>T	p.Ala97Val	p.A97V	ENST00000322088	NM_014225.5	97	gCc/gTc	4/15	0.221717483307365	3	FACETS	0.916	0.823	1	0.305	0.274	0.338	INDETERMINATE	1	FALSE	0	0.565335857673046	3		257	510	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36028566	36028566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	34	313	0	ENST00000358208.4:c.908G>A	p.Gly303Asp	p.G303D	ENST00000358208		303	gGc/gAc	8/12	0.519500601010717	3	FACETS	0.264	0.215	0.32	0.132	0.107	0.16	SUBCLONAL	1	FALSE	1	0.565335857673046	3		313	584	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54956527	54956527	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	68	324	0	ENST00000312783.6:c.667C>T	p.Gln223Ter	p.Q223*	ENST00000312783	NM_198436.1	223	Cag/Tag	7/10	0.519500601010717	3	FACETS	0.379	0.329	0.434	0.19	0.164	0.217	SUBCLONAL	1	FALSE	1	0.565335857673046	3		324	814	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484444	57484444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	158	287	0	ENST00000371085.3:c.625G>A	p.Glu209Lys	p.E209K	ENST00000371085	NM_000516.4	209	Gag/Aag	8/13	0.519500601010717	3	FACETS	0.928	0.851	1	0.464	0.425	0.504	CLONAL	1	FALSE	1	0.565335857673046	3		287	773	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655326	45655326	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	49	341	0	ENST00000407780.3:c.526G>A	p.Asp176Asn	p.D176N	ENST00000407780	NM_001283052.1	176	Gac/Aac	4/7	1	2	FACETS	0.375	0.318	0.438	0.375	0.318	0.438	SUBCLONAL	1	FALSE	1	0.565335857673046	2		341	462	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030644	47030644	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	118	284	1	ENST00000377604.3:c.419C>T	p.Ala140Val	p.A140V	ENST00000377604	NM_001204468.1	140	gCc/gTc	4/24	0.235114047238602	0	FACETS	0.44	0.4	0.482			1	INDETERMINATE	1	FALSE	0	0.565335857673046	0		285	412	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222253	53222253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	143	389	0	ENST00000375401.3:c.4579G>A	p.Glu1527Lys	p.E1527K	ENST00000375401	NM_004187.3	1527	Gaa/Aaa	26/26	0.235114047238602	0	FACETS	0.426	0.391	0.463			1	INDETERMINATE	1	FALSE	0	0.565335857673046	0		389	516	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247036	53247036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000944-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	53	466	1	ENST00000375401.3:c.464C>T	p.Ser155Phe	p.S155F	ENST00000375401	NM_004187.3	155	tCc/tTc	4/26	0.235114047238602	0	FACETS	0.119	0.101	0.138			1	INDETERMINATE	1	FALSE	0	0.565335857673046	0		467	687	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295243	1295243	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs35550267	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	50	158	0				ENST00000310581	NM_198253.2	-/1132			0.181772991592092	3	FACETS	0.983	0.859	1	0.983	0.859	1	INDETERMINATE	2	TRUE	1	0.532178486520903	3		158	121	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295242	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	49	152	0				ENST00000310581	NM_198253.2	-/1132			0.181772991592092	3	FACETS	0.933	0.812	1	0.933	0.812	1	INDETERMINATE	2	TRUE	1	0.532178486520903	3		152	125	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578538	7578538	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1131691037	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	69	293	0	ENST00000269305.4:c.392A>T	p.Asn131Ile	p.N131I	ENST00000269305	NM_001126112.2	131	aAc/aTc	5/11	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.532178486520903	2		293	239	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261778	16261778	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1384515929	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	46	277	0	ENST00000375759.3:c.9043C>T	p.His3015Tyr	p.H3015Y	ENST00000375759	NM_015001.2	3015	Cat/Tat	11/15	NA	2	FACETS	0.887	0.756	1			1	INDETERMINATE	1	TRUE	NA	0.532178486520903	2		277	195	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468090	120468090	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	91	352	0	ENST00000256646.2:c.4349G>A	p.Trp1450Ter	p.W1450*	ENST00000256646	NM_024408.3	1450	tGg/tAg	25/34	0.146672372273521	3	FACETS	1	0.952	1	0.558	0.499	0.62	INDETERMINATE	1	TRUE	1	0.532178486520903	3		352	388	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837941	156837941	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	117	379	0	ENST00000524377.1:c.474G>A	p.Trp158Ter	p.W158*	ENST00000524377	NM_002529.3	158	tgG/tgA	5/17	0.146672372273521	3	FACETS	0.782	0.713	0.853	0.782	0.713	0.853	INDETERMINATE	2	TRUE	1	0.532178486520903	3		379	356	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725501	162725501	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	93	383	0	ENST00000367921.3:c.613C>G	p.Pro205Ala	p.P205A	ENST00000367921	NM_006182.2	205	Cct/Gct	7/18	1	2	FACETS	0.85	0.761	0.944	0.85	0.761	0.944	CLONAL	1	TRUE	1	0.532178486520903	2		383	411	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193980	106193980	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1176823597	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	97	305	0	ENST00000380013.4:c.4442C>T	p.Ser1481Phe	p.S1481F	ENST00000380013	NM_001127208.2	1481	tCc/tTc	10/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.532178486520903	2		305	323	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332580	153332580	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	125	475	0	ENST00000281708.4:c.376G>A	p.Asp126Asn	p.D126N	ENST00000281708	NM_033632.3	126	Gat/Aat	2/12	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.532178486520903	2		475	468	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539841	187539841	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	124	455	0	ENST00000441802.2:c.7899T>A	p.Tyr2633Ter	p.Y2633*	ENST00000441802	NM_005245.3	2633	taT/taA	10/27	1	2	FACETS	0.994	0.905	1	0.994	0.905	1	CLONAL	1	TRUE	1	0.532178486520903	2		455	469	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557280	187557280	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	125	389	0	ENST00000441802.2:c.4082C>G	p.Ser1361Ter	p.S1361*	ENST00000441802	NM_005245.3	1361	tCa/tGa	6/27	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.532178486520903	2		389	414	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457716	149457716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	75	321	0	ENST00000286301.3:c.688G>A	p.Asp230Asn	p.D230N	ENST00000286301	NM_005211.3	230	Gat/Aat	5/22	1	2	FACETS	0.824	0.728	0.926	0.824	0.728	0.926	CLONAL	1	TRUE	1	0.532178486520903	2		321	342	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168695	32168695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143103753	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	93	405	0	ENST00000375023.3:c.4228C>T	p.Arg1410Cys	p.R1410C	ENST00000375023	NM_004557.3	1410	Cgc/Tgc	23/30	0.181772991592092	3	FACETS	1	0.981	1	0.728	0.655	0.804	INDETERMINATE	1	TRUE	1	0.532178486520903	3		405	304	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553593	106553593	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369746133	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	67	201	0	ENST00000369096.4:c.1558G>A	p.Gly520Arg	p.G520R	ENST00000369096	NM_001198.3	520	Gga/Aga	5/7	0.181772991592092	3	FACETS	1	0.941	1	0.561	0.492	0.634	INDETERMINATE	1	TRUE	1	0.532178486520903	3		201	284	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509747	106509747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761655879	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	108	350	0	ENST00000359195.3:c.1741G>A	p.Glu581Lys	p.E581K	ENST00000359195	NM_002649.2	581	Gaa/Aaa	2/11	1	2	FACETS	0.995	0.9	1	0.995	0.9	1	CLONAL	1	TRUE	1	0.532178486520903	2		350	408	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845973	151845973	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	98	507	0	ENST00000262189.6:c.13039C>T	p.Pro4347Ser	p.P4347S	ENST00000262189	NM_170606.2	4347	Ccg/Tcg	52/59	1	2	FACETS	0.815	0.731	0.903	0.815	0.731	0.903	CLONAL	1	TRUE	1	0.532178486520903	2		507	452	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945526	151945526	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	53	118	0	ENST00000262189.6:c.1993G>C	p.Glu665Gln	p.E665Q	ENST00000262189	NM_170606.2	665	Gaa/Caa	14/59	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.532178486520903	2		118	161	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965912	90965912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148205441	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	98	309	0	ENST00000265433.3:c.1405G>A	p.Asp469Asn	p.D469N	ENST00000265433	NM_002485.4	469	Gat/Aat	11/16	0.181772991592092	3	FACETS	1	0.966	1	0.589	0.529	0.651	INDETERMINATE	1	TRUE	1	0.532178486520903	3		309	396	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971080	21971080	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	92	246	1	ENST00000304494.5:c.278C>A	p.Thr93Lys	p.T93K	ENST00000304494	NM_000077.4	93	aCg/aAg	2/3	0.532178486520903	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.532178486520903	1		247	202	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911511	101911511	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	126	267	0	ENST00000374994.4:c.1436G>A	p.Gly479Glu	p.G479E	ENST00000374994	NM_004612.2	479	gGa/gAa	9/9	0.532178486520903	3	FACETS	1	0.96	1	0.367	0.333	0.402	CLONAL	1	TRUE	0	0.532178486520903	3		267	545	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412245	139412245	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	262	409	0	ENST00000277541.6:c.1400G>T	p.Cys467Phe	p.C467F	ENST00000277541	NM_017617.3	467	tGc/tTc	8/34	0.532178486520903	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.532178486520903	3		409	359	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850650	63850650	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	74	256	0	ENST00000279873.7:c.1428G>C	p.Glu476Asp	p.E476D	ENST00000279873	NM_032199.2	476	gaG/gaC	10/10	0.146672372273521	3	FACETS	1	0.898	1	0.51	0.45	0.574	INDETERMINATE	1	TRUE	1	0.532178486520903	3		256	345	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173667	108173667	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	98	374	0	ENST00000278616.4:c.5407G>C	p.Asp1803His	p.D1803H	ENST00000278616	NM_000051.3	1803	Gac/Cac	36/63	0.532178486520903	1	FACETS	0.812	0.732	0.895	0.812	0.732	0.895	CLONAL	1	TRUE	0	0.532178486520903	1		374	333	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246177	46246177	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	75	376	0	ENST00000334344.6:c.4271G>A	p.Gly1424Asp	p.G1424D	ENST00000334344	NM_152641.2	1424	gGt/gAt	15/21	1	2	FACETS	0.834	0.736	0.937	0.834	0.736	0.937	CLONAL	1	TRUE	1	0.532178486520903	2		376	338	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549022	21549022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	70	209	0	ENST00000382592.4:c.3254C>T	p.Pro1085Leu	p.P1085L	ENST00000382592	NM_014572.2	1085	cCt/cTt	8/8	0.532178486520903	1	FACETS	0.965	0.857	1	0.965	0.857	1	CLONAL	1	TRUE	0	0.532178486520903	1		209	200	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001970	29001970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	50	314	0	ENST00000282397.4:c.1195G>A	p.Asp399Asn	p.D399N	ENST00000282397	NM_002019.4	399	Gat/Aat	9/30	0.532178486520903	1	FACETS	0.392	0.333	0.455	0.392	0.333	0.455	SUBCLONAL	1	TRUE	0	0.532178486520903	1		314	352	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465531	99465531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	106	399	0	ENST00000268035.6:c.2356G>A	p.Glu786Lys	p.E786K	ENST00000268035	NM_000875.3	786	Gag/Aag	11/21	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.532178486520903	2		399	333	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916193	9916193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	106	495	0	ENST00000330684.3:c.2096C>T	p.Pro699Leu	p.P699L	ENST00000330684	NM_001134407.1	699	cCc/cTc	10/13	0.292069777678407	1	FACETS	0.696	0.628	0.767	0.696	0.628	0.767	INDETERMINATE	1	TRUE	0	0.532178486520903	1		495	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577081	7577081	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1057519985	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	91	444	0	ENST00000269305.4:c.857A>T	p.Glu286Val	p.E286V	ENST00000269305	NM_001126112.2	286	gAa/gTa	8/11	1	2	FACETS	0.958	0.858	1	0.958	0.858	1	CLONAL	1	TRUE	1	0.532178486520903	2		444	357	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15975521	15975521	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1310576129	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	95	393	0	ENST00000268712.3:c.3833C>T	p.Pro1278Leu	p.P1278L	ENST00000268712	NM_006311.3	1278	cCc/cTc	29/46	1	2	FACETS	0.962	0.864	1	0.962	0.864	1	CLONAL	1	TRUE	1	0.532178486520903	2		393	371	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320942	30320942	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	149	561	0	ENST00000322652.5:c.1352C>T	p.Pro451Leu	p.P451L	ENST00000322652	NM_015355.2	451	cCt/cTt	12/16	1	2	FACETS	0.924	0.848	1	0.924	0.848	1	CLONAL	1	TRUE	1	0.532178486520903	2		561	606	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896585	78896585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	114	514	0	ENST00000306801.3:c.2582C>T	p.Pro861Leu	p.P861L	ENST00000306801	NM_020761.2	861	cCc/cTc	22/34	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.532178486520903	2		514	326	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	74	162	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	0.532178486520903	1	FACETS	0.996	0.888	1	0.996	0.888	1	CLONAL	1	TRUE	0	0.532178486520903	1		162	205	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272236	15272236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	51	228	0	ENST00000263388.2:c.6203G>A	p.Gly2068Glu	p.G2068E	ENST00000263388	NM_000435.2	2068	gGg/gAg	33/33	1	2	FACETS	1	0.87	1	1	0.87	1	CLONAL	1	TRUE	1	0.532178486520903	2		228	190	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295180	15295180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	87	384	0	ENST00000263388.2:c.2492G>A	p.Gly831Glu	p.G831E	ENST00000263388	NM_000435.2	831	gGg/gAg	16/33	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.532178486520903	2		384	325	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302560	15302560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	76	377	0	ENST00000263388.2:c.798G>A	p.Trp266Ter	p.W266*	ENST00000263388	NM_000435.2	266	tgG/tgA	5/33	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.532178486520903	2		377	249	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727910	41727910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	117	519	1	ENST00000301178.4:c.535C>T	p.Pro179Ser	p.P179S	ENST00000301178	NM_021913.4	179	Ccc/Tcc	4/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.532178486520903	2		520	411	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52709301	52709301	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	95	311	0	ENST00000322088.6:c.255C>G	p.Tyr85Ter	p.Y85*	ENST00000322088	NM_014225.5	85	taC/taG	3/15	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.532178486520903	2		311	357	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022326	31022326	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	130	490	0	ENST00000375687.4:c.1811C>T	p.Ser604Phe	p.S604F	ENST00000375687	NM_015338.5	604	tCc/tTc	13/13	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.532178486520903	2		490	460	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36014525	36014525	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	37	451	0	ENST00000358208.4:c.298G>C	p.Glu100Gln	p.E100Q	ENST00000358208		100	Gag/Cag	3/12	1	2	FACETS	0.424	0.35	0.506	0.424	0.35	0.506	SUBCLONAL	1	TRUE	1	0.532178486520903	2		451	328	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39725870	39725870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	40	290	0	ENST00000361337.2:c.741G>A	p.Met247Ile	p.M247I	ENST00000361337	NM_003286.2	247	atG/atA	10/21	1	2	FACETS	0.331	0.275	0.394	0.331	0.275	0.394	SUBCLONAL	1	TRUE	1	0.532178486520903	2		290	454	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923133	48923133	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	245	363	0	ENST00000267163.4:c.581del	p.Ser194PhefsTer7	p.S194Ffs*7	ENST00000267163	NM_000321.2	194	tCt/tt	6/27	0.330556485079875	3	FACETS	0.902	0.849	0.957	0.902	0.849	0.957	CLONAL	2	TRUE	1	0.532178486520903	3		363	646	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90971009	90971010	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	130	391	0	ENST00000265433.3:c.1067_1068delinsTT	p.Ala356Val	p.A356V	ENST00000265433	NM_002485.4	356	gCC/gTT	9/16	0.181772991592092	3	FACETS	1	0.98	1	0.634	0.578	0.691	INDETERMINATE	1	TRUE	1	0.532178486520903	3		391	488	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2636819	2636820	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	80	412	0	ENST00000342085.4:c.1268_1269delinsTT	p.Ser423Phe	p.S423F	ENST00000342085	NM_002613.4	423	tCC/tTT	11/14	0.292069777678407	1	FACETS	0.673	0.597	0.752	0.673	0.597	0.752	INDETERMINATE	1	TRUE	0	0.532178486520903	1		412	328	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451031	70451032	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0000951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	82	420	0	ENST00000373644.4:c.5871_5872delinsAA	p.Met1957_Glu1958delinsIleLys	p.M1957_E1958delinsIK	ENST00000373644	NM_030625.2	1957	atGGaa/atAAaa	12/12	0.146672372273521	3	FACETS	1	0.963	1	0.598	0.532	0.668	INDETERMINATE	1	TRUE	1	0.532178486520903	3		420	326	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000954-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	101	422	0				ENST00000310581	NM_198253.2	-/1132			0.379202370417654	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	2	0.399482535852967	4		422	315	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033877	49033877	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1131690903	NA	P-0000954-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	140	364	0	ENST00000267163.4:c.2014G>T	p.Glu672Ter	p.E672*	ENST00000267163	NM_000321.2	672	Gag/Tag	20/27	0.399482535852967	1	FACETS	0.874	0.798	0.953	0.874	0.798	0.953	CLONAL	1	TRUE	0	0.399482535852967	1		364	642	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3795277	3795277	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0000954-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	76	240	0	ENST00000262367.5:c.3914+1G>A		p.X1305_splice	ENST00000262367	NM_004380.2	1305			0.399482535852967	1	FACETS	0.619	0.544	0.699	0.619	0.544	0.699	SUBCLONAL	1	TRUE	0	0.399482535852967	1		240	492	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782329	NA	P-0000954-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	113	187	1	ENST00000269305.4:c.746G>C	p.Arg249Thr	p.R249T	ENST00000269305	NM_001126112.2	249	aGg/aCg	7/11	0.399482535852967	1	FACETS	0.932	0.843	1	0.932	0.843	1	CLONAL	1	TRUE	0	0.399482535852967	1		188	486	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118872	70118872	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0000954-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	164	338	0	ENST00000245479.2:c.444G>C	p.Glu148Asp	p.E148D	ENST00000245479	NM_000346.3	148	gaG/gaC	2/3	0.107411648977017	4	FACETS	1	0.985	1	0.666	0.611	0.722	INDETERMINATE	1	TRUE	2	0.399482535852967	4		338	863	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913381	NA	P-0000957-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	26	134	0	ENST00000304494.5:c.322G>A	p.Asp108Asn	p.D108N	ENST00000304494	NM_000077.4	108	Gat/Aat	2/3	0.335162452803863	1	FACETS	1	0.846	1	1	0.959	1	CLONAL	2	TRUE	0	0.335162452803863	1		134	63	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587782272	NA	P-0000957-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	16	277	0	ENST00000269305.4:c.994-1G>A		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.324052451586007	1	FACETS	0.828	0.638	1	1	0.92	1	CLONAL	2	TRUE	0	0.335162452803863	1		277	48	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951957	178951957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000957-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	61	244	0	ENST00000263967.3:c.3012G>A	p.Met1004Ile	p.M1004I	ENST00000263967	NM_006218.2	1004	atG/atA	21/21	0.335162452803863	3	FACETS	0.951	0.842	1	0.951	0.842	1	CLONAL	3	TRUE	0	0.335162452803863	3		244	149	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643612	52643612	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0000957-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	20	202	0	ENST00000394830.3:c.2284G>C	p.Asp762His	p.D762H	ENST00000394830	NM_018313.4	762	Gac/Cac	17/30	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.335162452803863	2		202	80	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459462	50459462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0000957-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	20	138	0	ENST00000331340.3:c.751G>A	p.Glu251Lys	p.E251K	ENST00000331340	NM_006060.4	251	Gaa/Aaa	7/8	0.247532243765096	4	FACETS	0.857	0.668	1	0.857	0.668	1	CLONAL	2	TRUE	2	0.335162452803863	4		138	93	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559852	29559852	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1555614972	NA	P-0000957-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	26	170	0	ENST00000356175.3:c.3449C>G	p.Ser1150Ter	p.S1150*	ENST00000356175	NM_000267.3	1150	tCa/tGa	26/57	0.324052451586007	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.335162452803863	1		170	95	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548322	41548322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0000957-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	14	124	0	ENST00000263253.7:c.3110C>T	p.Ser1037Leu	p.S1037L	ENST00000263253	NM_001429.3	1037	tCa/tTa	16/31	NA	2	FACETS	1	0.774	1			1	INDETERMINATE	1	TRUE	NA	0.335162452803863	2		124	79	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952148	178952149	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTTT	novel	NA	P-0000957-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	39	110	0	ENST00000263967.3:c.3205_3206insTTCT	p.Ter1069PhefsTer5	p.*1069Ffs*5	ENST00000263967	NM_006218.2	1068	aac/aaCTTTc	21/21	0.335162452803863	3	FACETS	1	0.941	1	0.823	0.701	0.951	CLONAL	2	TRUE	0	0.335162452803863	3		110	110	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000960-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	225	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.678678760841834	2		422	630	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161901	47161901	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0000960-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1567	836	826	0	ENST00000409792.3:c.4225C>T	p.Gln1409Ter	p.Q1409*	ENST00000409792	NM_014159.6	1409	Cag/Tag	3/21	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.678678760841834	2		826	2403	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685314	89685315	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TG	TG	-	rs1564826836	NA	P-0000960-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	408	482	0	ENST00000371953.3:c.209+1_209+2del		p.X70_splice	ENST00000371953	NM_000314.4	70		3/9	0.678678760841834	1	FACETS	0.942	0.902	0.982	0.942	0.902	0.982	CLONAL	1	TRUE	0	0.678678760841834	1		482	843	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000967-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	28	422	0				ENST00000310581	NM_198253.2	-/1132			0.186292182529573	3	FACETS	1	0.859	1	0.531	0.433	0.637	INDETERMINATE	1	TRUE	1	0.6457444189449	3		422	108	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660430	227660430	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369672495	NA	P-0000967-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	33	205	0	ENST00000305123.5:c.3025C>T	p.Pro1009Ser	p.P1009S	ENST00000305123	NM_005544.2	1009	Cct/Tct	1/2	0.6457444189449	1	FACETS	0.412	0.339	0.492	0.412	0.339	0.492	SUBCLONAL	1	TRUE	0	0.6457444189449	1		205	168	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2132444	2132445	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	rs1185513978	NA	P-0000967-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	116	686	0	ENST00000219476.3:c.3823_3824del	p.Phe1275LeufsTer46	p.F1275Lfs*46	ENST00000219476	NM_000548.3	1274	tcTTtc/tctc	32/42	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.6457444189449	2		686	320	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845606	68845611	+	inframe_deletion	In_Frame_Del	DEL	CACAGC	CACAGC	-	novel	NA	P-0000967-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	104	344	0	ENST00000261769.5:c.857_862del	p.Ala286_Thr287del	p.A286_T287del	ENST00000261769	NM_004360.3	284	gtCACAGCc/gtc	7/16	1	2	FACETS	0.959	0.868	1	0.959	0.868	1	CLONAL	1	TRUE	1	0.6457444189449	2		344	336	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0000976-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	38	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.986	0.82	1	0.986	0.82	1	CLONAL	1	TRUE	1	0.3	2		422	257	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0000976-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	158	310	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.874	0.799	0.953	0.874	0.799	0.953	CLONAL	1	TRUE	1	0.3	2		310	1205	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001006-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	180	422	0				ENST00000310581	NM_198253.2	-/1132			0.457685863848586	2	FACETS	0.846	0.789	0.903	0.846	0.789	0.903	CLONAL	2	TRUE	0	0.500863109595547	2		422	425	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553161	106553161	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001006-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	199	360	0	ENST00000369096.4:c.1126T>C	p.Tyr376His	p.Y376H	ENST00000369096	NM_001198.3	376	Tac/Cac	5/7	0.457685863848586	2	FACETS	0.928	0.861	0.998	0.464	0.43	0.499	CLONAL	1	TRUE	0	0.500863109595547	2		360	856	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717777	89717777	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0001006-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	195	155	0	ENST00000371953.3:c.801+1G>T		p.X267_splice	ENST00000371953	NM_000314.4	267			0.496745036089088	2	FACETS	0.859	0.805	0.915	0.859	0.805	0.915	CLONAL	2	TRUE	0	0.500863109595547	2		155	453	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343831	118343831	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001006-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1251	87	444	0	ENST00000534358.1:c.1957C>A	p.Pro653Thr	p.P653T	ENST00000534358	NM_005933.3	653	Ccc/Acc	3/36	0.500863109595547	1	FACETS	0.195	0.171	0.22	0.195	0.171	0.22	SUBCLONAL	1	TRUE	0	0.500863109595547	1		444	1338	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434698	110434698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138549709	NA	P-0001006-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	262	441	2	ENST00000375856.3:c.3703G>A	p.Gly1235Ser	p.G1235S	ENST00000375856	NM_003749.2	1235	Ggt/Agt	1/2	0.500863109595547	1	FACETS	0.932	0.876	0.99	0.932	0.876	0.99	CLONAL	1	TRUE	0	0.500863109595547	1		443	841	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579481	7579494	+	frameshift_variant	Frame_Shift_Del	DEL	GCCTCTGGCATTCT	GCCTCTGGCATTCT	-	novel	NA	P-0001006-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	200	247	0	ENST00000269305.4:c.193_206del	p.Arg65CysfsTer79	p.R65Cfs*79	ENST00000269305	NM_001126112.2	65	AGAATGCCAGAGGCt/t	4/11	0.457685863848586	2	FACETS	1	0.988	1	0.647	0.603	0.692	CLONAL	1	TRUE	0	0.500863109595547	2		247	617	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527502	29527503	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0001006-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	520	316	0	ENST00000356175.3:c.952_953del	p.Glu318LysfsTer11	p.E318Kfs*11	ENST00000356175	NM_000267.3	317	acAGaa/acaa	9/57	0.457685863848586	2	FACETS	0.908	0.873	0.944	0.908	0.873	0.944	CLONAL	2	TRUE	0	0.500863109595547	2		316	1143	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573513	41573514	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0001006-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	73	408	0	ENST00000263253.7:c.5802_5803del	p.Arg1934SerfsTer138	p.R1934Sfs*138	ENST00000263253	NM_001429.3	1933	cAG/c	31/31	0.444724802356421	1	FACETS	0.263	0.229	0.299	0.263	0.229	0.299	SUBCLONAL	1	TRUE	0	0.500863109595547	1		408	832	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0001008-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	258	479	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.548417652808945	2		480	850	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001008-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	75	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.948	1			1	INDETERMINATE	1	TRUE	NA	0.548417652808945	2		422	245	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411726	139411726	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs377535397	NA	P-0001008-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	210	416	0	ENST00000277541.6:c.1553C>T	p.Thr518Met	p.T518M	ENST00000277541	NM_017617.3	518	aCg/aTg	9/34	0.146166944413476	4	FACETS	0.769	0.716	0.824	0.769	0.716	0.824	INDETERMINATE	2	TRUE	2	0.548417652808945	4		416	771	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56492633	56492633	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001008-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	184	328	3	ENST00000267101.3:c.2783A>G	p.Glu928Gly	p.E928G	ENST00000267101	NM_001982.3	928	gAg/gGg	23/28	0.146166944413476	4	FACETS	0.813	0.754	0.874	0.813	0.754	0.874	INDETERMINATE	2	TRUE	2	0.548417652808945	4		331	639	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732963	30732963	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121918714	NA	P-0001008-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	292	315	0	ENST00000295754.5:c.1576G>C	p.Glu526Gln	p.E526Q	ENST00000295754	NM_003242.5	526	Gag/Cag	7/7	0.548417652808945	3	FACETS	0.918	0.869	0.968	0.918	0.869	0.968	CLONAL	2	TRUE	1	0.548417652808945	3		315	739	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162705	47162705	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001008-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	237	519	0	ENST00000409792.3:c.3421C>G	p.Pro1141Ala	p.P1141A	ENST00000409792	NM_014159.6	1141	Ccg/Gcg	3/21	0.548417652808945	3	FACETS	0.913	0.851	0.977	0.457	0.425	0.489	CLONAL	1	TRUE	1	0.548417652808945	3		519	1206	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015040	71015040	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0001008-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	138	278	0	ENST00000318789.4:c.1889+1G>A		p.X630_splice	ENST00000318789	NM_032682.5	630			0.475799719337966	1	FACETS	0.876	0.805	0.949	0.876	0.805	0.949	CLONAL	1	TRUE	0	0.548417652808945	1		278	417	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539330	187539330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001008-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	167	436	0	ENST00000441802.2:c.8410G>A	p.Asp2804Asn	p.D2804N	ENST00000441802	NM_005245.3	2804	Gac/Aac	10/27	1	2	FACETS	0.884	0.815	0.956	0.884	0.815	0.956	CLONAL	1	TRUE	1	0.548417652808945	2		436	689	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39618752	39618752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1331467644	NA	P-0001008-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	97	339	0	ENST00000262039.4:c.1976G>A	p.Arg659Gln	p.R659Q	ENST00000262039	NM_002647.2	659	cGg/cAg	18/25	1	2	FACETS	0.327	0.291	0.366	0.327	0.291	0.366	SUBCLONAL	1	TRUE	1	0.548417652808945	2		339	1081	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023629	27023642	+	frameshift_variant	Frame_Shift_Del	DEL	GGCTGCCGGCTCCA	GGCTGCCGGCTCCA	-	novel	NA	P-0001008-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	300	336	0	ENST00000324856.7:c.735_748del	p.Gly248SerfsTer147	p.G248Sfs*147	ENST00000324856	NM_006015.4	245	gcGGCTGCCGGCTCCAag/gcag	1/20	0.548417652808945	2	FACETS	0.938	0.893	0.983	0.938	0.893	0.983	CLONAL	2	TRUE	0	0.548417652808945	2		336	583	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001018-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	50	422	0				ENST00000310581	NM_198253.2	-/1132			0.162286419147941	4	FACETS	1	0.945	1	1	0.976	1	INDETERMINATE	3	TRUE	2	0.369935781789293	4		422	108	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0001018-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	76	310	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.919	1	1	0.985	1	CLONAL	2	TRUE	1	0.369935781789293	2		310	199	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045667	47045667	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1556782537	NA	P-0001018-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	93	273	0	ENST00000377604.3:c.2548C>T	p.Gln850Ter	p.Q850*	ENST00000377604	NM_001204468.1	850	Cag/Tag	23/24	0.338895291890309	0	FACETS	0.744	0.676	0.813			1	SUBCLONAL	2	TRUE	0	0.369935781789293	0		273	213	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0001028-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	31	403	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.57885246706334	1	FACETS	0.096	0.077	0.118	0.096	0.077	0.118	SUBCLONAL	1	TRUE	0	0.611603218429654	1		404	731	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001028-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	87	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.925	1			1	INDETERMINATE	1	TRUE	NA	0.611603218429654	2		422	274	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001028-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	54	446	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.57885246706334	1	FACETS	0.195	0.166	0.226	0.195	0.166	0.226	SUBCLONAL	1	TRUE	0	0.611603218429654	1		446	630	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005359	150005359	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001028-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	79	653	0	ENST00000253339.5:c.866C>G	p.Ser289Cys	p.S289C	ENST00000253339		289	tCt/tGt	3/7	0.577493023665629	1	FACETS	0.208	0.182	0.236	0.208	0.182	0.236	SUBCLONAL	1	TRUE	0	0.611603218429654	1		653	863	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005408	150005408	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001028-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	79	589	0	ENST00000253339.5:c.817C>G	p.Gln273Glu	p.Q273E	ENST00000253339		273	Caa/Gaa	3/7	0.577493023665629	1	FACETS	0.213	0.186	0.241	0.213	0.186	0.241	SUBCLONAL	1	TRUE	0	0.611603218429654	1		589	843	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211503	46211503	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001028-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1384	80	635	2	ENST00000334344.6:c.469G>C	p.Asp157His	p.D157H	ENST00000334344	NM_152641.2	157	Gat/Cat	5/21	1	2	FACETS	0.179	0.156	0.203	0.179	0.156	0.203	SUBCLONAL	1	TRUE	1	0.611603218429654	2		637	1464	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953787	48953787	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0001028-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	72	413	0	ENST00000267163.4:c.1389+1G>C		p.X463_splice	ENST00000267163	NM_000321.2	463			0.586858862959903	1	FACETS	0.182	0.158	0.207	0.182	0.158	0.207	SUBCLONAL	1	TRUE	0	0.611603218429654	1		413	900	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588751	29588751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760703505	NA	P-0001028-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	359	361	0	ENST00000356175.3:c.4537C>T	p.Arg1513Ter	p.R1513*	ENST00000356175	NM_000267.3	1513	Cga/Tga	34/57	0.57885246706334	1	FACETS	0.88	0.837	0.924	0.88	0.837	0.924	CLONAL	1	TRUE	0	0.611603218429654	1		361	926	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76777766	76777766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001028-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	92	334	0	ENST00000373344.5:c.6950C>T	p.Ser2317Leu	p.S2317L	ENST00000373344	NM_000489.3	2317	tCa/tTa	32/35	0.250044070018488	0	FACETS	0.134	0.119	0.151			1	INDETERMINATE	1	TRUE	NA	0.611603218429654	0		334	871	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001041-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	34	422	0				ENST00000310581	NM_198253.2	-/1132			0.221178887429539	1	FACETS	1	0.922	1	1	0.969	1	CLONAL	2	TRUE	0	0.221178887429539	1		422	115	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0001041-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	176	318	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.842	0.776	0.911	1	0.991	1	CLONAL	2	TRUE	1	0.221178887429539	2		318	945	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	97	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.692498773971962	2		422	272	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397526	116397526	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001049-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	182	573	0	ENST00000397752.3:c.1898A>C	p.His633Pro	p.H633P	ENST00000397752	NM_000245.2	633	cAt/cCt	7/21	0.684938179573436	3	FACETS	1	0.973	1	0.553	0.512	0.595	CLONAL	1	TRUE	1	0.692498773971962	3		573	640	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001052-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	27	422	0				ENST00000310581	NM_198253.2	-/1132			0.197484494760925	1	FACETS	0.598	0.49	0.713	0.598	0.49	0.713	INDETERMINATE	1	TRUE	0	0.699519478495991	1		422	84	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916614	178916614	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0001052-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	65	961	0	ENST00000263967.3:c.1A>G	p.Met1?	p.M1?	ENST00000263967	NM_006218.2	1	Atg/Gtg	2/21	NA	2	FACETS	0.872	0.768	0.981			1	INDETERMINATE	1	TRUE	NA	0.699519478495991	2		961	213	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056335	180056335	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs540014376	NA	P-0001052-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	86	932	3	ENST00000261937.6:c.909C>A	p.His303Gln	p.H303Q	ENST00000261937	NM_182925.4	303	caC/caA	7/30	0.140715599546669	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.699519478495991	0		935	288	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717756	89717756	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730882131	NA	P-0001052-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	100	339	1	ENST00000371953.3:c.781C>T	p.Gln261Ter	p.Q261*	ENST00000371953	NM_000314.4	261	Cag/Tag	7/9	0.699519478495991	1	FACETS	0.801	0.73	0.873	0.801	0.73	0.873	CLONAL	1	TRUE	0	0.699519478495991	1		340	232	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982726	7982726	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001052-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	49	494	0	ENST00000319144.4:c.1059del	p.Ile354SerfsTer27	p.I354Sfs*27	ENST00000319144	NM_001139.2	353	ccC/cc	8/15	1	2	FACETS	0.77	0.662	0.884	0.77	0.662	0.884	SUBCLONAL	1	TRUE	1	0.699519478495991	2		494	182	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001052-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	109	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.954	0.871	1	0.954	0.871	1	CLONAL	1	TRUE	1	0.843159779645869	2		422	271	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916614	178916614	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0001052-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	458	961	0	ENST00000263967.3:c.1A>G	p.Met1?	p.M1?	ENST00000263967	NM_006218.2	1	Atg/Gtg	2/21	1	2	FACETS	0.966	0.924	1	0.966	0.924	1	CLONAL	1	TRUE	1	0.843159779645869	2		961	1125	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056335	180056335	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs540014376	NA	P-0001052-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	458	932	3	ENST00000261937.6:c.909C>A	p.His303Gln	p.H303Q	ENST00000261937	NM_182925.4	303	caC/caA	7/30	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.843159779645869	2		935	1086	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717756	89717756	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730882131	NA	P-0001052-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	201	339	1	ENST00000371953.3:c.781C>T	p.Gln261Ter	p.Q261*	ENST00000371953	NM_000314.4	261	Cag/Tag	7/9	0.843159779645869	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.843159779645869	1		340	274	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7982726	7982726	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001052-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	278	494	0	ENST00000319144.4:c.1059del	p.Ile354SerfsTer27	p.I354Sfs*27	ENST00000319144	NM_001139.2	353	ccC/cc	8/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.843159779645869	2		494	596	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258748	115258748	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913250	NA	P-0001052-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	51	593	2	ENST00000369535.4:c.34G>T	p.Gly12Cys	p.G12C	ENST00000369535	NM_002524.4	12	Ggt/Tgt	2/7	1	2	FACETS	0.149	0.126	0.174	0.149	0.126	0.174	SUBCLONAL	1	TRUE	1	0.843159779645869	2		595	812	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539774	187539774	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001052-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	259	734	0	ENST00000441802.2:c.7966A>G	p.Thr2656Ala	p.T2656A	ENST00000441802	NM_005245.3	2656	Act/Gct	10/27	1	2	FACETS	0.68	0.638	0.723	0.68	0.638	0.723	SUBCLONAL	1	TRUE	1	0.843159779645869	2		734	904	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741668	145741668	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001052-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	66	584	0	ENST00000428558.2:c.835A>G	p.Ser279Gly	p.S279G	ENST00000428558	NM_004260.3	279	Agc/Ggc	5/22	1	2	FACETS	0.189	0.164	0.217	0.189	0.164	0.217	SUBCLONAL	1	TRUE	1	0.843159779645869	2		584	827	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325184	123325184	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001052-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	31	600	0	ENST00000358487.5:c.144A>T	p.Glu48Asp	p.E48D	ENST00000358487	NM_000141.4	48	gaA/gaT	3/18	0.843159779645869	1	FACETS	0.105	0.084	0.128	0.105	0.084	0.128	SUBCLONAL	1	TRUE	0	0.843159779645869	1		600	407	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102098309	102098309	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001052-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	116	605	0	ENST00000282441.5:c.1273A>G	p.Thr425Ala	p.T425A	ENST00000282441	NM_001130145.2	425	Aca/Gca	8/9	1	2	FACETS	0.326	0.294	0.361	0.326	0.294	0.361	SUBCLONAL	1	TRUE	1	0.843159779645869	2		605	843	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495700	56495700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001052-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	184	494	1	ENST00000267101.3:c.3890G>A	p.Gly1297Glu	p.G1297E	ENST00000267101	NM_001982.3	1297	gGg/gAg	28/28	1	2	FACETS	0.709	0.657	0.761	0.709	0.657	0.761	SUBCLONAL	1	TRUE	1	0.843159779645869	2		495	616	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56809907	56809907	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0001052-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	269	714	0	ENST00000337432.4:c.1026+2T>C		p.X342_splice	ENST00000337432	NM_058216.2	342			1	2	FACETS	0.643	0.603	0.683	0.643	0.603	0.683	SUBCLONAL	1	TRUE	1	0.843159779645869	2		714	993	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244453	46244454	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0001052-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	31	753	0	ENST00000334344.6:c.2552dup	p.Gln852ThrfsTer99	p.Q852Tfs*99	ENST00000334344	NM_152641.2	849	-/C	15/21	0.832813996161937	1	FACETS	0.078	0.063	0.096	0.078	0.063	0.096	SUBCLONAL	1	TRUE	0	0.843159779645869	1		753	545	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119634961	119634967	+	frameshift_variant	Frame_Shift_Del	DEL	GATGGCA	GATGGCA	-	novel	NA	P-0001052-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	47	567	0	ENST00000316626.5:c.532_538del	p.Cys178GlyfsTer17	p.C178Gfs*17	ENST00000316626		178	TGCCATCgg/gg	5/12	1	2	FACETS	0.143	0.12	0.168	0.143	0.12	0.168	SUBCLONAL	1	TRUE	1	0.843159779645869	2		567	781	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001074-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	114	422	0				ENST00000310581	NM_198253.2	-/1132			0.329963456897731	3	FACETS	0.88	0.798	0.965	0.88	0.798	0.965	CLONAL	2	TRUE	1	0.357535288052838	3		422	427	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095740	178095740	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001074-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	177	424	0	ENST00000397062.3:c.1591C>G	p.His531Asp	p.H531D	ENST00000397062	NM_006164.4	531	Cat/Gat	5/5	0.214417619624221	4	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.357535288052838	4		424	1065	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793310	242793310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001074-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	130	387	0	ENST00000334409.5:c.767G>A	p.Gly256Glu	p.G256E	ENST00000334409	NM_005018.2	256	gGa/gAa	5/5	1	2	FACETS	0.944	0.857	1	0.944	0.857	1	CLONAL	1	TRUE	1	0.357535288052838	2		387	770	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163667	47163667	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001074-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	109	427	0	ENST00000409792.3:c.2459C>G	p.Ser820Cys	p.S820C	ENST00000409792	NM_014159.6	820	tCt/tGt	3/21	0.278994102103242	3	FACETS	0.898	0.807	0.996	0.449	0.403	0.498	CLONAL	1	TRUE	1	0.357535288052838	3		427	800	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138375113	138375113	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1189503825	NA	P-0001074-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	76	268	0	ENST00000289153.2:c.2946C>A	p.Phe982Leu	p.F982L	ENST00000289153	NM_006219.2	982	ttC/ttA	21/22	0.278994102103242	3	FACETS	0.75	0.658	0.85	0.375	0.329	0.425	SUBCLONAL	1	TRUE	1	0.357535288052838	3		268	668	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176552	142176552	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001074-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	211	509	1	ENST00000350721.4:c.7549C>G	p.His2517Asp	p.H2517D	ENST00000350721	NM_001184.3	2517	Cat/Gat	45/47	0.354898425118122	4	FACETS	0.757	0.702	0.813	0.757	0.702	0.813	SUBCLONAL	2	TRUE	2	0.357535288052838	4		510	1059	SUCCESS
APC	324	MSKCC	GRCh37	5	112174228	112174228	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001074-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	153	517	2	ENST00000257430.4:c.2937G>A	p.Met979Ile	p.M979I	ENST00000257430	NM_000038.5	979	atG/atA	16/16	0.329963456897731	3	FACETS	1	0.968	1	0.56	0.512	0.61	CLONAL	1	TRUE	1	0.357535288052838	3		519	901	SUCCESS
APC	324	MSKCC	GRCh37	5	112174691	112174691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001074-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	150	400	0	ENST00000257430.4:c.3400G>A	p.Asp1134Asn	p.D1134N	ENST00000257430	NM_000038.5	1134	Gac/Aac	16/16	0.329963456897731	3	FACETS	1	0.982	1	0.638	0.584	0.695	CLONAL	1	TRUE	1	0.357535288052838	3		400	775	SUCCESS
APC	324	MSKCC	GRCh37	5	112174700	112174700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001074-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	150	392	0	ENST00000257430.4:c.3409G>A	p.Asp1137Asn	p.D1137N	ENST00000257430	NM_000038.5	1137	Gat/Aat	16/16	0.329963456897731	3	FACETS	1	0.985	1	0.681	0.624	0.741	CLONAL	1	TRUE	1	0.357535288052838	3		392	726	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169174	32169174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001074-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	97	403	0	ENST00000375023.3:c.3859G>A	p.Glu1287Lys	p.E1287K	ENST00000375023	NM_004557.3	1287	Gaa/Aaa	22/30	0.357535288052838	3	FACETS	0.829	0.738	0.925			1	CLONAL	1	TRUE	NA	0.357535288052838	3		403	772	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978843	13978843	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001074-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	193	436	1	ENST00000405192.2:c.264C>G	p.Ile88Met	p.I88M	ENST00000405192	NM_001163147.1	88	atC/atG	6/12	0.235174172383256	3	FACETS	0.807	0.749	0.868	0.538	0.499	0.579	CLONAL	2	TRUE	0	0.357535288052838	3		437	788	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362470	118362470	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001074-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	119	466	0	ENST00000534358.1:c.4831G>T	p.Glu1611Ter	p.E1611*	ENST00000534358	NM_005933.3	1611	Gag/Tag	15/36	0.278994102103242	3	FACETS	1	0.906	1	0.502	0.453	0.553	CLONAL	1	TRUE	1	0.357535288052838	3		466	782	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500332	99500332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001074-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	265	435	0	ENST00000268035.6:c.3765G>A	p.Met1255Ile	p.M1255I	ENST00000268035	NM_000875.3	1255	atG/atA	21/21	0.243064506770678	3	FACETS	0.922	0.865	0.979	0.614	0.577	0.653	CLONAL	2	TRUE	0	0.357535288052838	3		435	948	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032271	10032271	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001074-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	131	260	0	ENST00000330684.3:c.552C>G	p.Ile184Met	p.I184M	ENST00000330684	NM_001134407.1	184	atC/atG	3/13	0.243064506770678	3	FACETS	0.991	0.906	1	0.66	0.604	0.719	CLONAL	2	TRUE	0	0.357535288052838	3		260	436	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577085	+	missense_variant	Missense_Mutation	ONP	CCTC	CCTC	TCTT	novel	NA	P-0001074-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	426	318	0	ENST00000269305.4:c.853_856delinsAAGA	p.Glu285_Glu286delinsLysLys	p.E285_E286delinsKK	ENST00000269305	NM_001126112.2	285	GAGGaa/AAGAaa	8/11	0.240932037650684	4	FACETS	0.976	0.932	1	0.732	0.699	0.765	CLONAL	3	TRUE	0	0.357535288052838	4		318	1105	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735497	40735497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1453093376	NA	P-0001074-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	89	415	0	ENST00000373198.4:c.3376G>A	p.Glu1126Lys	p.E1126K	ENST00000373198	NM_133170.3	1126	Gaa/Aaa	25/32	0.268886189361652	5	FACETS	0.792	0.7	0.89	0.264	0.233	0.297	SUBCLONAL	1	TRUE	2	0.357535288052838	5		415	966	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933127	39933127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs978793874	NA	P-0001074-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	268	283	0	ENST00000378444.4:c.1472G>A	p.Gly491Glu	p.G491E	ENST00000378444	NM_001123385.1	491	gGa/gAa	4/15	0.269232885621306	2	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.357535288052838	2		283	644	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346624	225346625	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0001074-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	98	467	0	ENST00000264414.4:c.2013_2014del	p.Arg671SerfsTer12	p.R671Sfs*12	ENST00000264414	NM_003590.4	671	agAGtc/agtc	14/16	1	2	FACETS	0.79	0.705	0.88	0.79	0.705	0.88	SUBCLONAL	1	TRUE	1	0.357535288052838	2		467	694	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922758	44922774	+	frameshift_variant	Frame_Shift_Del	DEL	GCCAGCAGCCACAGCTT	GCCAGCAGCCACAGCTT	-	novel	NA	P-0001074-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	152	264	0	ENST00000377967.4:c.1621_1637del	p.Gln541SerfsTer6	p.Q541Sfs*6	ENST00000377967	NM_021140.2	540	gGCCAGCAGCCACAGCTT/g	16/29	0.269232885621306	2	FACETS	0.847	0.78	0.916			1	CLONAL	2	TRUE	NA	0.357535288052838	2		264	502	SUCCESS
APC	324	MSKCC	GRCh37	5	112174757	112174762	+	frameshift_variant	Frame_Shift_Del	DEL	GAAGAG	GAAGAG	AAAAA	novel	NA	P-0001074-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	95	399	0	ENST00000257430.4:c.3466_3471delinsAAAAA	p.Glu1156LysfsTer9	p.E1156Kfs*9	ENST00000257430	NM_000038.5	1156	GAAGAG/AAAAA	16/16	0.329963456897731	3	FACETS	1	0.923	1	0.521	0.465	0.581	CLONAL	1	TRUE	1	0.357535288052838	3		399	601	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0001082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	16	139	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.699250466062694	NA		139	65	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539564	187539564	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	65	253	0	ENST00000441802.2:c.8176C>T	p.Arg2726Ter	p.R2726*	ENST00000441802	NM_005245.3	2726	Cga/Tga	10/27	0.619749562419733	3	FACETS	0.779	0.68	0.885			1	SUBCLONAL	1	FALSE	NA	0.699250466062694	3		253	322	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971027	21971028	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0001082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	107	116	0	ENST00000304494.5:c.330_331delinsAA	p.Trp110_Gly111delinsTer	p.W110_G111delins*	ENST00000304494	NM_000077.4	110	tgGGgc/tgAAgc	2/3	0.699250466062694	4	FACETS	1	0.957	1			1	CLONAL	2	FALSE	NA	0.699250466062694	4		116	242	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141586	202141586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760898260	NA	P-0001082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	47	269	0	ENST00000358485.4:c.874C>T	p.Arg292Trp	p.R292W	ENST00000358485	NM_001080125.1	292	Cgg/Tgg	7/9	0.410961526518987	4	FACETS	0.429	0.362	0.504	0.215	0.181	0.252	INDETERMINATE	1	FALSE	2	0.699250466062694	4		269	532	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508499	106508499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752602335	NA	P-0001082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	15	93	0	ENST00000359195.3:c.493G>A	p.Val165Ile	p.V165I	ENST00000359195	NM_002649.2	165	Gtc/Atc	2/11	0.369383104115751	5	FACETS	0.656	0.483	0.86	0.219	0.161	0.287	INDETERMINATE	1	FALSE	2	0.699250466062694	5		93	134	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300489	11300489	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1350423605	NA	P-0001082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	29	340	0	ENST00000361445.4:c.1657C>T	p.Arg553Cys	p.R553C	ENST00000361445	NM_004958.3	553	Cgc/Tgc	11/58	0.446218210583564	4	FACETS	0.395	0.317	0.483			1	SUBCLONAL	1	FALSE	NA	0.699250466062694	4		340	357	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47600674	47600674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771241036	NA	P-0001082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	95	436	0	ENST00000263735.4:c.149C>T	p.Ser50Leu	p.S50L	ENST00000263735	NM_002354.2	50	tCa/tTa	2/9	0.487934652731177	4	FACETS	0.829	0.74	0.923	0.414	0.37	0.462	CLONAL	1	FALSE	2	0.699250466062694	4		436	557	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010443	48010443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786201684	NA	P-0001082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	25	163	0	ENST00000234420.5:c.71C>T	p.Ser24Leu	p.S24L	ENST00000234420	NM_000179.2	24	tCg/tTg	1/10	0.487934652731177	4	FACETS	0.524	0.414	0.648	0.262	0.207	0.324	SUBCLONAL	1	FALSE	2	0.699250466062694	4		163	232	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726020	61726020	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1290743603	NA	P-0001082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	41	280	0	ENST00000401558.2:c.619C>G	p.Gln207Glu	p.Q207E	ENST00000401558	NM_003400.3	207	Caa/Gaa	8/25	0.487934652731177	4	FACETS	0.316	0.263	0.376	0.158	0.131	0.188	SUBCLONAL	1	FALSE	2	0.699250466062694	4		280	630	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149817	202149817	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	84	310	0	ENST00000358485.4:c.1258C>T	p.Gln420Ter	p.Q420*	ENST00000358485	NM_001080125.1	420	Cag/Tag	8/9	0.410961526518987	4	FACETS	0.943	0.837	1	0.471	0.418	0.528	INDETERMINATE	1	FALSE	2	0.699250466062694	4		310	433	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561686	55561686	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs759129060	NA	P-0001082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	29	170	0	ENST00000288135.5:c.76C>G	p.Gln26Glu	p.Q26E	ENST00000288135	NM_000222.2	26	Caa/Gaa	2/21	0.165621355498735	5	FACETS	0.603	0.485	0.736	0.201	0.161	0.246	INDETERMINATE	1	FALSE	2	0.699250466062694	5		170	282	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535344	187535344	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0001082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	37	349	0	ENST00000441802.2:c.9229+1G>C		p.X3077_splice	ENST00000441802	NM_005245.3	3077			0.619749562419733	3	FACETS	0.32	0.264	0.383			1	SUBCLONAL	1	FALSE	NA	0.699250466062694	3		349	446	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628235	187628235	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	36	230	0	ENST00000441802.2:c.2747C>T	p.Ser916Leu	p.S916L	ENST00000441802	NM_005245.3	916	tCa/tTa	2/27	0.619749562419733	3	FACETS	0.502	0.414	0.599			1	SUBCLONAL	1	FALSE	NA	0.699250466062694	3		230	277	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750550	57750550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	39	305	0	ENST00000274289.3:c.1918G>A	p.Glu640Lys	p.E640K	ENST00000274289	NM_006622.3	640	Gaa/Aaa	14/14	0.699250466062694	4	FACETS	0.431	0.357	0.513	0.215	0.178	0.257	SUBCLONAL	1	FALSE	2	0.699250466062694	4		305	440	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176710860	176710860	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	41	371	0	ENST00000439151.2:c.6082G>T	p.Glu2028Ter	p.E2028*	ENST00000439151	NM_022455.4	2028	Gaa/Taa	20/23	0.165621355498735	5	FACETS	0.471	0.392	0.559	0.157	0.13	0.187	INDETERMINATE	1	FALSE	2	0.699250466062694	5		371	510	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339981	116339981	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	53	253	0	ENST00000397752.3:c.843C>G	p.Phe281Leu	p.F281L	ENST00000397752	NM_000245.2	281	ttC/ttG	2/21	0.369383104115751	5	FACETS	0.659	0.563	0.765	0.22	0.187	0.255	INDETERMINATE	1	FALSE	2	0.699250466062694	5		253	471	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750394	133750394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	33	390	0	ENST00000318560.5:c.1225G>A	p.Glu409Lys	p.E409K	ENST00000318560	NM_005157.4	409	Gag/Aag	7/11	0.417063387567675	4	FACETS	0.378	0.308	0.458	0.189	0.154	0.229	INDETERMINATE	1	FALSE	2	0.699250466062694	4		390	424	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410452	139410452	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0001082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	38	386	0	ENST00000277541.6:c.1650C>G	p.Tyr550Ter	p.Y550*	ENST00000277541	NM_017617.3	550	taC/taG	10/34	0.417063387567675	4	FACETS	0.754	0.627	0.893	0.377	0.313	0.447	INDETERMINATE	1	FALSE	2	0.699250466062694	4		386	245	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104357042	104357042	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554852823	NA	P-0001082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	26	163	0	ENST00000369902.3:c.902C>T	p.Ser301Phe	p.S301F	ENST00000369902	NM_016169.3	301	tCt/tTt	7/12	0.699250466062694	4	FACETS	0.417	0.331	0.516	0.209	0.165	0.258	SUBCLONAL	1	FALSE	2	0.699250466062694	4		163	303	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445656	49445656	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	67	329	0	ENST00000301067.7:c.1810G>T	p.Glu604Ter	p.E604*	ENST00000301067	NM_003482.3	604	Gaa/Taa	10/54	0.699250466062694	4	FACETS	1	0.924	1	0.358	0.314	0.406	CLONAL	1	FALSE	1	0.699250466062694	4		329	303	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445869	49445869	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	70	238	0	ENST00000301067.7:c.1597G>C	p.Glu533Gln	p.E533Q	ENST00000301067	NM_003482.3	533	Gag/Cag	10/54	0.699250466062694	4	FACETS	1	0.919	1	0.353	0.31	0.399	CLONAL	1	FALSE	1	0.699250466062694	4		238	321	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913235	32913235	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	30	235	0	ENST00000380152.3:c.4743G>C	p.Glu1581Asp	p.E1581D	ENST00000380152		1581	gaG/gaC	11/27	0.369383104115751	5	FACETS	0.376	0.303	0.46	0.125	0.101	0.154	INDETERMINATE	1	FALSE	2	0.699250466062694	5		235	467	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995188	15995188	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	85	395	0	ENST00000268712.3:c.3005G>C	p.Arg1002Thr	p.R1002T	ENST00000268712	NM_006311.3	1002	aGa/aCa	22/46	0.699250466062694	3	FACETS	0.598	0.529	0.671	0.299	0.264	0.336	SUBCLONAL	1	FALSE	1	0.699250466062694	3		395	549	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76920202	76920202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	35	604	0	ENST00000373344.5:c.3875C>T	p.Ser1292Leu	p.S1292L	ENST00000373344	NM_000489.3	1292	tCa/tTa	11/35	1	2	FACETS	0.162	0.132	0.196	0.162	0.132	0.196	SUBCLONAL	1	FALSE	1	0.699250466062694	2		604	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577555	7577556	+	missense_variant	Missense_Mutation	DNP	GC	GC	CG	novel	NA	P-0001082-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	66	218	0	ENST00000269305.4:c.725_726delinsCG	p.Cys242Ser	p.C242S	ENST00000269305	NM_001126112.2	242	tGC/tCG	7/11	0.699250466062694	3	FACETS	1	0.9	1	0.514	0.451	0.58	CLONAL	1	FALSE	1	0.699250466062694	3		218	248	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0001088-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	47	139	0				ENST00000310581	NM_198253.2	-/1132			0.364679994106837	2	FACETS	0.969	0.863	1			1	CLONAL	3	TRUE	NA	0.42	2		139	77	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469925	157469925	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs1554226079	NA	P-0001088-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	159	202	0	ENST00000346085.5:c.2719A>T	p.Arg907Ter	p.R907*	ENST00000346085	NM_020732.3	907	Aga/Tga	9/20	0.455004568638884	4	FACETS	0.907	0.842	0.974	1	0.988	1	CLONAL	3	TRUE	2	0.42	4		202	395	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001091-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	68	422	0				ENST00000310581	NM_198253.2	-/1132			0.185527525510495	3	FACETS	0.878	0.791	0.963			1	INDETERMINATE	4	TRUE	NA	0.36	3		422	127	SUCCESS
CBL	867	MSKCC	GRCh37	11	119167635	119167635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001091-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	153	278	0	ENST00000264033.4:c.2044C>T	p.Pro682Ser	p.P682S	ENST00000264033	NM_005188.3	682	Cct/Tct	13/16	1	2	FACETS	0.833	0.768	0.901	1	0.99	1	CLONAL	2	TRUE	1	0.36	2		278	510	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104356940	104356940	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001091-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	39	315	0	ENST00000369902.3:c.800del	p.Ser267MetfsTer12	p.S267Mfs*12	ENST00000369902	NM_016169.3	267	aGt/at	7/12	0.3	3	FACETS	0.356	0.294	0.425			1	SUBCLONAL	1	TRUE	NA	0.36	3		315	719	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001099-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	334	143	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.455770255522201	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	1	0.455770255522201	3		143	869	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193920774	NA	P-0001099-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	319	548	0	ENST00000269305.4:c.797G>A	p.Gly266Glu	p.G266E	ENST00000269305	NM_001126112.2	266	gGa/gAa	8/11	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	2	TRUE	NA	0.455770255522201	2		548	633	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920503	134920503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001099-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	99	455	0	ENST00000398015.3:c.2318C>T	p.Thr773Ile	p.T773I	ENST00000398015	NM_004441.4	773	aCc/aTc	12/16	0.455770255522201	3	FACETS	0.844	0.755	0.939	0.422	0.377	0.47	CLONAL	1	TRUE	1	0.455770255522201	3		455	632	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971084	21971084	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001099-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	68	145	0	ENST00000304494.5:c.274G>T	p.Asp92Tyr	p.D92Y	ENST00000304494	NM_000077.4	92	Gac/Tac	2/3	0.441061212547196	3	FACETS	1	0.973	1	0.721	0.635	0.812	CLONAL	1	TRUE	1	0.455770255522201	3		145	254	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001100-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	11	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.896	0.634	1	0.896	0.634	1	CLONAL	1	TRUE	1	0.438375822542563	2		422	56	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0001100-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	116	142	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.438375822542563	3	FACETS	0.993	0.906	1	0.993	0.906	1	CLONAL	2	TRUE	1	0.438375822542563	3		142	325	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5462893	5462893	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001100-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	151	322	0	ENST00000381577.3:c.454G>T	p.Glu152Ter	p.E152*	ENST00000381577	NM_014143.3	152	Gaa/Taa	4/7	0.438375822542563	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.438375822542563	1		322	467	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929157	44929157	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001100-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	66	271	0	ENST00000377967.4:c.2257C>T	p.Gln753Ter	p.Q753*	ENST00000377967	NM_021140.2	753	Cag/Tag	17/29	0.29292892527134	0	FACETS	0.783	0.69	0.88			1	SUBCLONAL	1	TRUE	NA	0.438375822542563	0		271	216	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338683	70338683	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001100-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	51	331	0	ENST00000374080.3:c.79C>G	p.Gln27Glu	p.Q27E	ENST00000374080		27	Cag/Gag	1/45	0.29292892527134	0	FACETS	0.51	0.437	0.589			1	SUBCLONAL	1	TRUE	NA	0.438375822542563	0		331	256	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577468	7577505	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCAGTGTGCAGGGTGGCAAGTGGCTCCTGACCTGGAGT	CCAGTGTGCAGGGTGGCAAGTGGCTCCTGACCTGGAGT	-	novel	NA	P-0001100-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	20	204	0	ENST00000269305.4:c.776_782+31del		p.X259_splice	ENST00000269305	NM_001126112.2	259		7/11	0.438375822542563	1	FACETS	0.648	0.503	0.812	0.648	0.503	0.812	SUBCLONAL	1	TRUE	0	0.438375822542563	1		204	110	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001135-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	21	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	FALSE	1	0.176522121395651	2		422	178	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429945	78429945	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001135-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	67	554	0	ENST00000370768.2:c.934A>G	p.Lys312Glu	p.K312E	ENST00000370768	NM_003902.3	312	Aag/Gag	11/20	0.176522121395651	3	FACETS	0.748	0.648	0.858			1	SUBCLONAL	1	FALSE	NA	0.176522121395651	3		554	1104	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030343	49030343	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs137853297	NA	P-0001135-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	96	336	0	ENST00000267163.4:c.1818T>A	p.Tyr606Ter	p.Y606*	ENST00000267163	NM_000321.2	606	taT/taA	19/27	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.176522121395651	2		336	801	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs786201057	NA	P-0001135-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	78	340	0	ENST00000269305.4:c.374C>G	p.Thr125Arg	p.T125R	ENST00000269305	NM_001126112.2	125	aCg/aGg	4/11	0.176522121395651	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	0	0.176522121395651	1		340	557	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872195	45872195	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001135-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	78	463	0	ENST00000391945.4:c.239T>C	p.Ile80Thr	p.I80T	ENST00000391945	NM_000400.3	80	aTt/aCt	4/23	0.176522121395651	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	FALSE	0	0.176522121395651	1		463	746	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578454	7578454	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526131	NA	P-0001144-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	120	307	2	ENST00000269305.4:c.476C>T	p.Ala159Val	p.A159V	ENST00000269305	NM_001126112.2	159	gCc/gTc	5/11	0.391387509412121	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.391387509412121	1		309	375	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717615	89717615	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909227	NA	P-0001144-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	165	251	0	ENST00000371953.3:c.640C>T	p.Gln214Ter	p.Q214*	ENST00000371953	NM_000314.4	214	Cag/Tag	7/9	0.391387509412121	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.391387509412121	1		251	511	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741661	17741661	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs745342746	NA	P-0001144-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	243	304	0	ENST00000250003.3:c.332G>T	p.Arg111Leu	p.R111L	ENST00000250003	NM_002478.4	111	cGc/cTc	1/3	0.391387509412121	4	FACETS	1	0.957	1	1	0.957	1	CLONAL	3	TRUE	1	0.391387509412121	4		304	566	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191212	2191212	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001144-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	148	480	2	ENST00000398665.3:c.466G>T	p.Asp156Tyr	p.D156Y	ENST00000398665	NM_032482.2	156	Gac/Tac	5/28	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.391387509412121	2		482	642	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971166	21971167	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0001144-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	87	84	0	ENST00000304494.5:c.191dup	p.Leu65AlafsTer55	p.L65Afs*55	ENST00000304494	NM_000077.4	64	ctg/ctTg	2/3	0.380990626437727	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.391387509412121	2		84	206	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001188-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	88	422	0				ENST00000310581	NM_198253.2	-/1132			0.555084636581093	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	FALSE	1	0.555084636581093	3		422	164	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0001188-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	139	706	0	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.555084636581093	2		706	428	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	29	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.751	0.608	0.912			1	INDETERMINATE	1	FALSE	NA	0.397846549154361	2		422	194	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	17	142	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.309529470380744	4	FACETS	0.319	0.237	0.416	0.159	0.118	0.208	SUBCLONAL	1	FALSE	2	0.397846549154361	4		142	375	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577609	7577609	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs878854073	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	70	263	0	ENST00000269305.4:c.673-1G>A		p.X225_splice	ENST00000269305	NM_001126112.2	225			1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	FALSE	1	0.397846549154361	2		263	333	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237746	16237746	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	74	413	0	ENST00000375759.3:c.1193G>A	p.Gly398Glu	p.G398E	ENST00000375759	NM_015001.2	398	gGa/gAa	5/15	0.263283635046082	1	FACETS	0.494	0.433	0.56	0.494	0.433	0.56	SUBCLONAL	1	FALSE	0	0.397846549154361	1		413	603	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309899	65309899	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	57	287	0	ENST00000342505.4:c.2252-1G>C		p.X751_splice	ENST00000342505	NM_002227.2	751			0.2629392046083	3	FACETS	0.762	0.655	0.878	0.381	0.327	0.439	SUBCLONAL	1	FALSE	1	0.397846549154361	3		287	451	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468088	120468088	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	124	383	1	ENST00000256646.2:c.4351G>A	p.Asp1451Asn	p.D1451N	ENST00000256646	NM_024408.3	1451	Gat/Aat	25/34	0.2629392046083	3	FACETS	1	0.97	1	0.583	0.528	0.64	CLONAL	1	FALSE	1	0.397846549154361	3		384	641	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155870314	155870314	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	160	719	0	ENST00000368323.3:c.525C>G	p.Phe175Leu	p.F175L	ENST00000368323	NM_006912.5	175	ttC/ttG	6/6	0.2629392046083	3	FACETS	1	0.971	1	0.563	0.517	0.612	CLONAL	1	FALSE	1	0.397846549154361	3		719	856	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725505	162725505	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	216	476	2	ENST00000367921.3:c.617G>C	p.Gly206Ala	p.G206A	ENST00000367921	NM_006182.2	206	gGa/gCa	7/18	0.2629392046083	3	FACETS	0.855	0.798	0.915	0.855	0.798	0.915	CLONAL	2	FALSE	1	0.397846549154361	3		478	761	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090083	37090083	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	98	461	0	ENST00000231790.2:c.1972C>T	p.Leu658Phe	p.L658F	ENST00000231790	NM_000249.3	658	Ctt/Ttt	17/19	NA	2	FACETS	0.788	0.704	0.877			1	INDETERMINATE	1	FALSE	NA	0.397846549154361	2		461	625	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247436	71247436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1358353721	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	112	512	0	ENST00000318789.4:c.97C>T	p.Arg33Trp	p.R33W	ENST00000318789	NM_032682.5	33	Cgg/Tgg	6/21	NA	2	FACETS	0.897	0.808	0.99			1	INDETERMINATE	1	FALSE	NA	0.397846549154361	2		512	628	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916683	178916683	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	194	354	0	ENST00000263967.3:c.70T>A	p.Cys24Ser	p.C24S	ENST00000263967	NM_006218.2	24	Tgt/Agt	2/21	0.309529470380744	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	FALSE	2	0.397846549154361	4		354	605	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916810	178916810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	177	529	0	ENST00000263967.3:c.197C>T	p.Ser66Phe	p.S66F	ENST00000263967	NM_006218.2	66	tCt/tTt	2/21	0.309529470380744	4	FACETS	1	0.988	1	0.7	0.645	0.757	CLONAL	1	FALSE	2	0.397846549154361	4		529	888	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526119	189526119	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	154	467	1	ENST00000264731.3:c.383C>T	p.Ser128Phe	p.S128F	ENST00000264731	NM_003722.4	128	tCc/tTc	4/14	0.309529470380744	4	FACETS	1	0.987	1	0.718	0.658	0.78	CLONAL	1	FALSE	2	0.397846549154361	4		468	754	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604319	189604319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	160	452	0	ENST00000264731.3:c.1486C>T	p.Pro496Ser	p.P496S	ENST00000264731	NM_003722.4	496	Cct/Tct	11/14	0.309529470380744	4	FACETS	1	0.985	1	0.663	0.608	0.72	CLONAL	1	FALSE	2	0.397846549154361	4		452	848	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114276	143114276	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768222990	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	170	578	0	ENST00000262992.4:c.1145G>A	p.Arg382Gln	p.R382Q	ENST00000262992	NM_001101669.1	382	cGg/cAg	13/24	0.163356080118931	1	FACETS	0.938	0.865	1	0.938	0.865	1	INDETERMINATE	1	FALSE	0	0.397846549154361	1		578	730	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187516921	187516921	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	135	591	0	ENST00000441802.2:c.13060C>T	p.Gln4354Ter	p.Q4354*	ENST00000441802	NM_005245.3	4354	Cag/Tag	26/27	0.163356080118931	1	FACETS	0.926	0.845	1	0.926	0.845	1	INDETERMINATE	1	FALSE	0	0.397846549154361	1		591	587	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521370	187521370	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	142	512	0	ENST00000441802.2:c.11785C>T	p.Gln3929Ter	p.Q3929*	ENST00000441802	NM_005245.3	3929	Caa/Taa	22/27	0.163356080118931	1	FACETS	1	0.934	1	1	0.934	1	INDETERMINATE	1	FALSE	0	0.397846549154361	1		512	559	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294703	1294703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	27	71	0	ENST00000310581.5:c.298G>A	p.Gly100Ser	p.G100S	ENST00000310581	NM_198253.2	100	Ggc/Agc	2/16	NA	2	FACETS	1	0.904	1			1	INDETERMINATE	1	FALSE	NA	0.397846549154361	2		71	113	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564671	86564671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	145	529	0	ENST00000274376.6:c.403C>T	p.Pro135Ser	p.P135S	ENST00000274376	NM_002890.2	135	Ccc/Tcc	1/25	0.206100435030686	3	FACETS	1	0.986	1	0.712	0.652	0.774	INDETERMINATE	1	FALSE	1	0.397846549154361	3		529	614	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056580	26056580	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs535135864	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	104	198	0	ENST00000343677.2:c.77A>T	p.Lys26Ile	p.K26I	ENST00000343677	NM_005319.3	26	aAa/aTa	1/1	0.397846549154361	3	FACETS	1	0.975	1			1	CLONAL	1	FALSE	NA	0.397846549154361	3		198	495	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680770	30680770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	98	565	1	ENST00000376406.3:c.949C>T	p.His317Tyr	p.H317Y	ENST00000376406	NM_014641.2	317	Cat/Tat	5/15	1	2	FACETS	0.792	0.708	0.882	0.792	0.708	0.882	SUBCLONAL	1	FALSE	1	0.397846549154361	2		566	622	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630048	117630048	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	142	475	0	ENST00000368508.3:c.6478C>T	p.Gln2160Ter	p.Q2160*	ENST00000368508	NM_002944.2	2160	Cag/Tag	41/43	NA	2	FACETS	1	0.939	1			1	INDETERMINATE	1	FALSE	NA	0.397846549154361	2		475	690	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953089	2953089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	89	358	0	ENST00000396946.4:c.2851G>A	p.Glu951Lys	p.E951K	ENST00000396946	NM_032415.4	951	Gag/Aag	22/25	NA	2	FACETS	0.981	0.874	1			1	INDETERMINATE	1	FALSE	NA	0.397846549154361	2		358	456	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639995	93639995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	104	250	0	ENST00000375746.1:c.1324G>A	p.Glu442Lys	p.E442K	ENST00000375746	NM_001174167.1	442	Gag/Aag	10/14	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.397846549154361	2		250	451	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250088	110250088	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	103	435	0	ENST00000374672.4:c.587C>G	p.Ser196Trp	p.S196W	ENST00000374672	NM_004235.4	196	tCg/tGg	3/5	1	2	FACETS	0.918	0.824	1	0.918	0.824	1	CLONAL	1	FALSE	1	0.397846549154361	2		435	564	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396827	139396827	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756191146	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	95	460	0	ENST00000277541.6:c.5281C>T	p.Arg1761Trp	p.R1761W	ENST00000277541	NM_017617.3	1761	Cgg/Tgg	28/34	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	FALSE	1	0.397846549154361	2		460	462	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399826	139399826	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	108	479	0	ENST00000277541.6:c.4522C>T	p.Gln1508Ter	p.Q1508*	ENST00000277541	NM_017617.3	1508	Cag/Tag	25/34	1	2	FACETS	0.916	0.824	1	0.916	0.824	1	CLONAL	1	FALSE	1	0.397846549154361	2		479	593	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239426	123239426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	109	291	0	ENST00000358487.5:c.2411C>T	p.Pro804Leu	p.P804L	ENST00000358487	NM_000141.4	804	cCt/cTt	18/18	0.397846549154361	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	FALSE	0	0.397846549154361	1		291	427	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534232	534232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	113	637	0	ENST00000451590.1:c.91G>A	p.Glu31Lys	p.E31K	ENST00000451590	NM_001130442.1	31	Gaa/Aaa	2/5	0.163356080118931	1	FACETS	0.728	0.657	0.803	0.728	0.657	0.803	INDETERMINATE	1	FALSE	0	0.397846549154361	1		637	625	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154851	2154851	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	103	625	0	ENST00000434045.2:c.370G>A	p.Glu124Lys	p.E124K	ENST00000434045	NM_001127598.1	124	Gag/Aag	4/5	0.163356080118931	1	FACETS	0.928	0.835	1	0.928	0.835	1	INDETERMINATE	1	FALSE	0	0.397846549154361	1		625	447	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742918	17742918	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	44	372	0	ENST00000250003.3:c.826T>G	p.Ser276Ala	p.S276A	ENST00000250003	NM_002478.4	276	Tct/Gct	3/3	0.163356080118931	1	FACETS	0.526	0.442	0.617	0.526	0.442	0.617	INDETERMINATE	1	FALSE	0	0.397846549154361	1		372	337	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196825	108196825	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876660730	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	117	333	0	ENST00000278616.4:c.6848C>T	p.Ser2283Leu	p.S2283L	ENST00000278616	NM_000051.3	2283	tCa/tTa	47/63	0.163356080118931	1	FACETS	0.832	0.753	0.916	0.832	0.753	0.916	INDETERMINATE	1	FALSE	0	0.397846549154361	1		333	566	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142491	119142491	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	138	454	0	ENST00000264033.4:c.490G>C	p.Glu164Gln	p.E164Q	ENST00000264033	NM_005188.3	164	Gaa/Caa	3/16	0.163356080118931	1	FACETS	0.739	0.673	0.808	0.739	0.673	0.808	INDETERMINATE	1	FALSE	0	0.397846549154361	1		454	752	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992208	11992208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	579	390	3	ENST00000396373.4:c.298G>A	p.Glu100Lys	p.E100K	ENST00000396373	NM_001987.4	100	Gag/Aag	3/8	0.397846549154361	11	FACETS	1	0.974	1			1	CLONAL	7	FALSE	NA	0.397846549154361	11		393	1147	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552630	18552630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200787716	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	483	548	0	ENST00000266497.5:c.2041C>T	p.Arg681Cys	p.R681C	ENST00000266497		681	Cgc/Tgc	14/31	0.397846549154361	4	FACETS	0.872	0.835	0.91			1	CLONAL	3	FALSE	NA	0.397846549154361	4		548	1297	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435033	49435033	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	60	179	0	ENST00000301067.7:c.6520C>T	p.Gln2174Ter	p.Q2174*	ENST00000301067	NM_003482.3	2174	Cag/Tag	31/54	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	1	0.397846549154361	2		179	259	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218844	133218844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	114	507	0	ENST00000320574.5:c.5092G>A	p.Glu1698Lys	p.E1698K	ENST00000320574	NM_006231.2	1698	Gag/Aag	38/49	1	2	FACETS	0.929	0.838	1	0.929	0.838	1	CLONAL	1	FALSE	1	0.397846549154361	2		507	617	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937326	32937326	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	106	322	0	ENST00000380152.3:c.7987G>C	p.Glu2663Gln	p.E2663Q	ENST00000380152		2663	Gaa/Caa	18/27	1	2	FACETS	0.998	0.898	1	0.998	0.898	1	CLONAL	1	FALSE	1	0.397846549154361	2		322	534	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518076	103518076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	79	318	0	ENST00000355739.4:c.2014G>A	p.Glu672Lys	p.E672K	ENST00000355739	NM_000123.3	672	Gaa/Aaa	9/15	1	2	FACETS	0.688	0.606	0.776	0.688	0.606	0.776	SUBCLONAL	1	FALSE	1	0.397846549154361	2		318	577	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570201	95570201	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	133	460	0	ENST00000393063.1:c.3532C>G	p.Leu1178Val	p.L1178V	ENST00000393063	NM_030621.3	1178	Ctt/Gtt	22/28	1	2	FACETS	0.982	0.893	1	0.982	0.893	1	CLONAL	1	FALSE	1	0.397846549154361	2		460	681	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293262	91293262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	43	177	0	ENST00000355112.3:c.764G>A	p.Ser255Asn	p.S255N	ENST00000355112	NM_000057.2	255	aGt/aAt	3/22	1	2	FACETS	0.619	0.52	0.729	0.619	0.52	0.729	SUBCLONAL	1	FALSE	1	0.397846549154361	2		177	349	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68844238	68844238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	82	319	0	ENST00000261769.5:c.826C>T	p.Leu276Phe	p.L276F	ENST00000261769	NM_004360.3	276	Ctt/Ttt	6/16	0.163356080118931	1	FACETS	0.65	0.575	0.73	0.65	0.575	0.73	INDETERMINATE	1	FALSE	0	0.397846549154361	1		319	508	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577070	7577070	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770374782	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	110	595	0	ENST00000269305.4:c.868C>T	p.Arg290Cys	p.R290C	ENST00000269305	NM_001126112.2	290	Cgc/Tgc	8/11	1	2	FACETS	0.922	0.83	1	0.922	0.83	1	CLONAL	1	FALSE	1	0.397846549154361	2		595	600	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555525857	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	127	608	0	ENST00000269305.4:c.596G>A	p.Gly199Glu	p.G199E	ENST00000269305	NM_001126112.2	199	gGa/gAa	6/11	1	2	FACETS	0.957	0.869	1	0.957	0.869	1	CLONAL	1	FALSE	1	0.397846549154361	2		608	667	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39706221	39706221	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	179	413	0	ENST00000361337.2:c.280-1G>A		p.X94_splice	ENST00000361337	NM_003286.2	94			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.397846549154361	2		413	806	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866378	42866378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	57	307	0	ENST00000398585.3:c.254C>T	p.Pro85Leu	p.P85L	ENST00000398585	NM_001135099.1	85	cCc/cTc	3/14	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.397846549154361	NA		307	401	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341252	70341252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	170	290	0	ENST00000374080.3:c.811G>A	p.Glu271Lys	p.E271K	ENST00000374080		271	Gaa/Aaa	6/45	0.323606299955064	0	FACETS	0.679	0.633	0.725			1	SUBCLONAL	2	FALSE	NA	0.397846549154361	0		290	379	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321638	30321639	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	149	529	0	ENST00000322652.5:c.1493_1494delinsTT	p.Ser498Phe	p.S498F	ENST00000322652	NM_015355.2	498	tCC/tTT	13/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.397846549154361	2		529	660	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946115	55946116	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	99	451	0	ENST00000263923.4:c.4063_4064delinsTT	p.Pro1355Phe	p.P1355F	ENST00000263923	NM_002253.2	1355	CCt/TTt	30/30	0.397846549154361	1	FACETS	0.749	0.671	0.832	0.749	0.671	0.832	SUBCLONAL	1	FALSE	0	0.397846549154361	1		451	532	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442967	49442968	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	83	452	0	ENST00000301067.7:c.3940_3941delinsTT	p.Pro1314Phe	p.P1314F	ENST00000301067	NM_003482.3	1314	CCt/TTt	12/54	1	2	FACETS	0.742	0.656	0.834	0.742	0.656	0.834	SUBCLONAL	1	FALSE	1	0.397846549154361	2		452	562	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418242	139418243	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	113	594	0	ENST00000277541.6:c.329_330delinsTT	p.Pro110Leu	p.P110L	ENST00000277541	NM_017617.3	110	cCC/cTT	3/34	1	2	FACETS	0.981	0.886	1	0.981	0.886	1	CLONAL	1	FALSE	1	0.397846549154361	2		594	579	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178942532	178942533	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	207	299	2	ENST00000263967.3:c.2339_2340delinsAA	p.Trp780Ter	p.W780*	ENST00000263967	NM_006218.2	780	tGG/tAA	16/21	0.309529470380744	4	FACETS	0.952	0.886	1	0.952	0.886	1	CLONAL	2	FALSE	2	0.397846549154361	4		301	764	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215854	142215855	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0001198-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	150	268	0	ENST00000350721.4:c.5738_5738+1delinsAA		p.X1913_splice	ENST00000350721	NM_001184.3	1913		33/47	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	FALSE	NA	0.397846549154361	2		268	580	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001223-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	42	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.742	0.621	0.876			1	INDETERMINATE	1	TRUE	NA	0.306696412562782	2		422	369	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0001223-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	43	148	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.306696412562782	2		148	254	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255467	16255467	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001223-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	102	462	0	ENST00000375759.3:c.2732C>T	p.Ser911Phe	p.S911F	ENST00000375759	NM_015001.2	911	tCt/tTt	11/15	1	2	FACETS	0.932	0.834	1	0.932	0.834	1	CLONAL	1	TRUE	1	0.306696412562782	2		462	714	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256393	16256393	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001223-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	107	479	0	ENST00000375759.3:c.3658G>A	p.Asp1220Asn	p.D1220N	ENST00000375759	NM_015001.2	1220	Gat/Aat	11/15	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.306696412562782	2		479	681	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437746	49437746	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001223-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	162	771	0	ENST00000301067.7:c.5224G>C	p.Glu1742Gln	p.E1742Q	ENST00000301067	NM_003482.3	1742	Gag/Cag	22/54	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.306696412562782	2		771	1035	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437758	49437758	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001223-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	130	661	0	ENST00000301067.7:c.5212G>T	p.Glu1738Ter	p.E1738*	ENST00000301067	NM_003482.3	1738	Gag/Tag	22/54	1	2	FACETS	0.937	0.849	1	0.937	0.849	1	CLONAL	1	TRUE	1	0.306696412562782	2		661	905	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78820291	78820291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001223-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	135	548	0	ENST00000306801.3:c.1231G>A	p.Glu411Lys	p.E411K	ENST00000306801	NM_020761.2	411	Gag/Aag	11/34	1	2	FACETS	0.987	0.897	1	0.987	0.897	1	CLONAL	1	TRUE	1	0.306696412562782	2		548	892	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249012	55249013	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGTTT	novel	NA	P-0001223-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	149	493	0	ENST00000275493.2:c.2310_2311insGGGTTT	p.Asp770_Asn771insGlyPhe	p.D770_N771insGF	ENST00000275493	NM_005228.3	770	-/GGGTTT	20/28	0.306696412562782	3	FACETS	1	0.982	1	0.639	0.584	0.697	CLONAL	1	TRUE	1	0.306696412562782	3		493	877	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001238-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	53	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.534277047989878	2		422	158	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963873	2963873	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001238-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	318	314	0	ENST00000396946.4:c.1934T>A	p.Leu645Gln	p.L645Q	ENST00000396946	NM_032415.4	645	cTg/cAg	15/25	0.528746639455348	4	FACETS	1	0.961	1	0.679	0.643	0.715	CLONAL	2	TRUE	1	0.534277047989878	4		314	897	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4409144	4409144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587777620	NA	P-0001238-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	132	267	1	ENST00000261254.3:c.839C>T	p.Thr280Ile	p.T280I	ENST00000261254	NM_001759.3	280	aCc/aTc	5/5	1	2	FACETS	0.943	0.861	1	0.943	0.861	1	CLONAL	1	TRUE	1	0.534277047989878	2		268	524	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413070	139413072	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0001238-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	150	249	0	ENST00000277541.6:c.1070_1072del	p.Phe357del	p.F357del	ENST00000277541	NM_017617.3	357	tTCTac/tac	6/34	1	2	FACETS	0.945	0.868	1	0.945	0.868	1	CLONAL	1	TRUE	1	0.534277047989878	2		249	594	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001239-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	95	422	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		422	220	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001246-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	35	422	0				ENST00000310581	NM_198253.2	-/1132			0.273413778519768	3	FACETS	0.917	0.791	1	0.917	0.791	1	INDETERMINATE	2	TRUE	1	0.81370339971452	3		422	66	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521543	8521543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868728165	NA	P-0001246-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	31	304	0	ENST00000356435.5:c.695G>A	p.Arg232His	p.R232H	ENST00000356435		232	cGc/cAc	9/35	0.81370339971452	1	FACETS	0.216	0.176	0.261	0.216	0.176	0.261	SUBCLONAL	1	TRUE	0	0.81370339971452	1		304	209	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709162	117709162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867987684	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	171	263	0	ENST00000368508.3:c.1795G>A	p.Glu599Lys	p.E599K	ENST00000368508	NM_002944.2	599	Gaa/Aaa	13/43	0.182345721783729	3	FACETS	0.826	0.771	0.88	0.826	0.771	0.88	INDETERMINATE	2	TRUE	1	0.789270147364037	3		263	366	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40743950	40743950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781527200	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	127	433	0	ENST00000392038.2:c.757C>T	p.Arg253Trp	p.R253W	ENST00000392038	NM_001626.4	253	Cgg/Tgg	9/14	1	2	FACETS	0.896	0.822	0.973	0.896	0.822	0.973	CLONAL	1	TRUE	1	0.789270147364037	2		433	359	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	328	139	0				ENST00000310581	NM_198253.2	-/1132			0.789270147364037	7	FACETS	1	0.991	1			1	CLONAL	6	TRUE	NA	0.789270147364037	7		139	392	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433916	49433916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766114622	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	81	242	0	ENST00000301067.7:c.7637C>T	p.Ser2546Phe	p.S2546F	ENST00000301067	NM_003482.3	2546	tCc/tTc	31/54	0.197221852471082	4	FACETS	0.756	0.676	0.838	0.756	0.676	0.838	INDETERMINATE	2	TRUE	2	0.789270147364037	4		242	243	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11290984	11290984	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	184	359	0	ENST00000361445.4:c.2777C>T	p.Ser926Phe	p.S926F	ENST00000361445	NM_004958.3	926	tCc/tTc	18/58	0.117286065514447	4	FACETS	0.893	0.833	0.954	0.893	0.833	0.954	INDETERMINATE	2	TRUE	2	0.789270147364037	4		359	467	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17349134	17349134	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	152	335	0	ENST00000375499.3:c.734C>T	p.Thr245Ile	p.T245I	ENST00000375499	NM_003000.2	245	aCc/aTc	7/8	0.117286065514447	4	FACETS	0.787	0.726	0.849	0.787	0.726	0.849	INDETERMINATE	2	TRUE	2	0.789270147364037	4		335	438	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812538	43812538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772102737	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	216	355	0	ENST00000372470.3:c.1241C>T	p.Ser414Leu	p.S414L	ENST00000372470	NM_005373.2	414	tCg/tTg	8/12	0.117286065514447	4	FACETS	0.919	0.862	0.976	0.919	0.862	0.976	INDETERMINATE	2	TRUE	2	0.789270147364037	4		355	533	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332875	65332875	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	164	258	0	ENST00000342505.4:c.664C>T	p.Pro222Ser	p.P222S	ENST00000342505	NM_002227.2	222	Cca/Tca	7/25	0.117286065514447	4	FACETS	0.823	0.762	0.884	0.823	0.762	0.884	INDETERMINATE	2	TRUE	2	0.789270147364037	4		258	452	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430793	78430793	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	308	498	0	ENST00000370768.2:c.596T>C	p.Leu199Ser	p.L199S	ENST00000370768	NM_003902.3	199	tTa/tCa	8/20	0.513005125810874	1	FACETS	0.982	0.942	1	0.982	0.942	1	CLONAL	1	TRUE	0	0.789270147364037	1		498	481	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699495	117699495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1239854439	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	199	285	0	ENST00000369458.3:c.146G>A	p.Gly49Glu	p.G49E	ENST00000369458	NM_024626.3	49	gGg/gAg	3/6	0.513005125810874	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.789270147364037	1		285	285	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165825	118165825	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	133	238	0	ENST00000369448.3:c.335T>C	p.Val112Ala	p.V112A	ENST00000369448	NM_017709.3	112	gTt/gCt	2/2	NA	2	FACETS	0.812	0.744	0.882			1	INDETERMINATE	1	TRUE	NA	0.789270147364037	2		238	415	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651156	206651156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782007787	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	96	331	0	ENST00000367120.3:c.766C>T	p.Pro256Ser	p.P256S	ENST00000367120	NM_014002.3	256	Ccc/Tcc	8/22	0.159177479763073	4	FACETS	1	0.981	1	0.704	0.635	0.776	INDETERMINATE	1	TRUE	2	0.789270147364037	4		331	309	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907692	111907692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775080943	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	226	464	0	ENST00000393256.3:c.466G>A	p.Gly156Arg	p.G156R	ENST00000393256	NM_006538.4	156	Gga/Aga	3/4	0.117286065514447	4	FACETS	0.857	0.804	0.911	0.857	0.804	0.911	INDETERMINATE	2	TRUE	2	0.789270147364037	4		464	598	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128030456	128030457	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	193	694	0	ENST00000285398.2:c.1811_1812delinsTT	p.Thr604Ile	p.T604I	ENST00000285398	NM_000122.1	604	aCC/aTT	11/15	0.197221852471082	4	FACETS	0.796	0.741	0.851	0.796	0.741	0.851	INDETERMINATE	2	TRUE	2	0.789270147364037	4		694	550	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295678	212295678	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1198974786	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	259	518	0	ENST00000342788.4:c.2635G>A	p.Gly879Arg	p.G879R	ENST00000342788	NM_005235.2	879	Gga/Aga	21/28	0.197221852471082	4	FACETS	0.853	0.804	0.904	0.853	0.804	0.904	INDETERMINATE	2	TRUE	2	0.789270147364037	4		518	688	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645525	215645525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553622261	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	308	465	0	ENST00000260947.4:c.1073C>T	p.Pro358Leu	p.P358L	ENST00000260947	NM_000465.2	358	cCa/cTa	4/11	0.197221852471082	4	FACETS	0.99	0.94	1	0.99	0.94	1	INDETERMINATE	2	TRUE	2	0.789270147364037	4		465	705	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042536	37042536	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63751221	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	218	411	0	ENST00000231790.2:c.298C>T	p.Arg100Ter	p.R100*	ENST00000231790	NM_000249.3	100	Cga/Tga	3/19	0.197221852471082	4	FACETS	1	0.992	1	0.744	0.696	0.794	INDETERMINATE	1	TRUE	2	0.789270147364037	4		411	664	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437605	52437605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370664836	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	130	281	0	ENST00000460680.1:c.1556C>T	p.Pro519Leu	p.P519L	ENST00000460680	NM_004656.3	519	cCc/cTc	13/17	NA	2	FACETS	0.9	0.826	0.976			1	INDETERMINATE	1	TRUE	NA	0.789270147364037	2		281	366	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72891509	72891509	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	272	466	1	ENST00000325599.8:c.253T>A	p.Phe85Ile	p.F85I	ENST00000325599	NM_018130.2	85	Ttt/Att	3/11	0.197221852471082	4	FACETS	0.837	0.789	0.885	0.837	0.789	0.885	INDETERMINATE	2	TRUE	2	0.789270147364037	4		467	737	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851626	134851627	+	missense_variant	Missense_Mutation	DNP	TC	TC	GT	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	134	337	2	ENST00000398015.3:c.1032_1033delinsGT	p.Pro345Ser	p.P345S	ENST00000398015	NM_004441.4	344	ccTCca/ccGTca	5/16	NA	2	FACETS	0.918	0.844	0.994			1	INDETERMINATE	1	TRUE	NA	0.789270147364037	2		339	370	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279500	1279500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	91	365	0	ENST00000310581.5:c.2036C>T	p.Ser679Phe	p.S679F	ENST00000310581	NM_198253.2	679	tCt/tTt	5/16	0.789270147364037	7	FACETS	0.887	0.787	0.994			1	CLONAL	1	TRUE	NA	0.789270147364037	7		365	773	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295253	1295253	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1232074117	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	331	147	0				ENST00000310581	NM_198253.2	-/1132			0.789270147364037	7	FACETS	1	0.983	1			1	CLONAL	6	TRUE	NA	0.789270147364037	7		147	408	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871199	35871199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	210	369	2	ENST00000303115.3:c.421G>A	p.Glu141Lys	p.E141K	ENST00000303115	NM_002185.3	141	Gaa/Aaa	4/8	0.197221852471082	4	FACETS	0.819	0.766	0.874	0.819	0.766	0.874	INDETERMINATE	2	TRUE	2	0.789270147364037	4		371	581	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875645	35875645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201449880	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	210	393	1	ENST00000303115.3:c.832G>A	p.Asp278Asn	p.D278N	ENST00000303115	NM_002185.3	278	Gat/Aat	7/8	0.197221852471082	4	FACETS	0.77	0.72	0.822	0.77	0.72	0.822	INDETERMINATE	2	TRUE	2	0.789270147364037	4		394	618	SUCCESS
APC	324	MSKCC	GRCh37	5	112177630	112177630	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	179	244	0	ENST00000257430.4:c.6339T>A	p.Ser2113Arg	p.S2113R	ENST00000257430	NM_000038.5	2113	agT/agA	16/16	0.197221852471082	4	FACETS	0.91	0.848	0.973	0.91	0.848	0.973	INDETERMINATE	2	TRUE	2	0.789270147364037	4		244	446	SUCCESS
APC	324	MSKCC	GRCh37	5	112177800	112177800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755786285	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	154	270	0	ENST00000257430.4:c.6509C>T	p.Pro2170Leu	p.P2170L	ENST00000257430	NM_000038.5	2170	cCa/cTa	16/16	0.197221852471082	4	FACETS	1	0.989	1	0.741	0.684	0.8	INDETERMINATE	1	TRUE	2	0.789270147364037	4		270	471	SUCCESS
APC	324	MSKCC	GRCh37	5	112178690	112178690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	267	413	0	ENST00000257430.4:c.7399C>T	p.Pro2467Ser	p.P2467S	ENST00000257430	NM_000038.5	2467	Cca/Tca	16/16	0.197221852471082	4	FACETS	0.923	0.871	0.975	0.923	0.871	0.975	INDETERMINATE	2	TRUE	2	0.789270147364037	4		413	656	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170814993	170814993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	143	144	0	ENST00000296930.5:c.41C>T	p.Pro14Leu	p.P14L	ENST00000296930	NM_002520.6	14	cCc/cTc	1/11	0.197221852471082	4	FACETS	0.787	0.725	0.851	0.787	0.725	0.851	INDETERMINATE	2	TRUE	2	0.789270147364037	4		144	412	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522662	176522662	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs555513735	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	136	580	0	ENST00000292408.4:c.1759C>T	p.Pro587Ser	p.P587S	ENST00000292408	NM_213647.1	587	Cca/Tca	13/18	1	2	FACETS	0.99	0.913	1	0.99	0.913	1	CLONAL	1	TRUE	1	0.789270147364037	2		580	348	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671765	30671765	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1345659672	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	103	298	0	ENST00000376406.3:c.5195C>A	p.Ser1732Tyr	p.S1732Y	ENST00000376406	NM_014641.2	1732	tCc/tAc	10/15	0.691037887623861	4	FACETS	0.942	0.846	1	0.235	0.211	0.261	CLONAL	1	TRUE	0	0.789270147364037	4		298	496	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553761	106553761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	240	332	0	ENST00000369096.4:c.1726G>A	p.Glu576Lys	p.E576K	ENST00000369096	NM_001198.3	576	Gaa/Aaa	5/7	0.366804118280857	4	FACETS	0.831	0.78	0.882			1	INDETERMINATE	2	TRUE	NA	0.789270147364037	4		332	655	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555026	106555026	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	178	244	0	ENST00000369096.4:c.2143G>A	p.Ala715Thr	p.A715T	ENST00000369096	NM_001198.3	715	Gcg/Acg	7/7	0.366804118280857	4	FACETS	0.928	0.865	0.991			1	INDETERMINATE	2	TRUE	NA	0.789270147364037	4		244	435	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677834	117677834	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	195	379	0	ENST00000368508.3:c.4099G>C	p.Gly1367Arg	p.G1367R	ENST00000368508	NM_002944.2	1367	Ggc/Cgc	25/43	0.182345721783729	3	FACETS	1	0.987	1	0.623	0.581	0.666	INDETERMINATE	1	TRUE	1	0.789270147364037	3		379	553	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117737431	117737431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	287	393	0	ENST00000368508.3:c.218C>T	p.Ala73Val	p.A73V	ENST00000368508	NM_002944.2	73	gCt/gTt	3/43	0.182345721783729	3	FACETS	1	0.994	1	0.709	0.671	0.748	INDETERMINATE	1	TRUE	1	0.789270147364037	3		393	715	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522148	157522148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	97	229	0	ENST00000346085.5:c.4420C>T	p.Pro1474Ser	p.P1474S	ENST00000346085	NM_020732.3	1474	Ccc/Tcc	18/20	NA	2	FACETS	0.987	0.896	1			1	INDETERMINATE	1	TRUE	NA	0.789270147364037	2		229	249	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527985	157527985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764604817	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	109	188	0	ENST00000346085.5:c.5710C>T	p.Pro1904Ser	p.P1904S	ENST00000346085	NM_020732.3	1904	Ccc/Tcc	20/20	NA	2	FACETS	1	0.941	1			1	INDETERMINATE	1	TRUE	NA	0.789270147364037	2		188	266	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026913	6026913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	50	78	0	ENST00000265849.7:c.1483G>A	p.Gly495Arg	p.G495R	ENST00000265849	NM_000535.5	495	Ggg/Agg	11/15	0.614270701136425	3	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	1	0.789270147364037	3		78	84	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467858	50467858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	100	265	0	ENST00000331340.3:c.1093G>A	p.Ala365Thr	p.A365T	ENST00000331340	NM_006060.4	365	Gcc/Acc	8/8	0.319423386374729	6	FACETS	0.9	0.811	0.992	0.45	0.405	0.496	INDETERMINATE	2	TRUE	2	0.789270147364037	6		265	363	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515160	106515160	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	524	393	1	ENST00000359195.3:c.2303A>G	p.Lys768Arg	p.K768R	ENST00000359195	NM_002649.2	768	aAa/aGa	5/11	0.319423386374729	6	FACETS	0.889	0.857	0.92	0.889	0.857	0.92	INDETERMINATE	4	TRUE	2	0.789270147364037	6		394	963	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843285	128843285	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	155	459	0	ENST00000249373.3:c.392T>G	p.Met131Arg	p.M131R	ENST00000249373	NM_005631.4	131	aTg/aGg	2/12	0.319423386374729	6	FACETS	0.885	0.815	0.958	0.443	0.407	0.479	INDETERMINATE	2	TRUE	2	0.789270147364037	6		459	572	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845367	151845367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	294	277	0	ENST00000262189.6:c.13645C>T	p.Arg4549Cys	p.R4549C	ENST00000262189	NM_170606.2	4549	Cgc/Tgc	52/59	0.319423386374729	6	FACETS	1	0.977	1	0.786	0.747	0.825	INDETERMINATE	3	TRUE	2	0.789270147364037	6		277	611	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317942	8317942	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	161	234	0	ENST00000356435.5:c.5671G>A	p.Asp1891Asn	p.D1891N	ENST00000356435		1891	Gat/Aat	35/35	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.789270147364037	2		234	368	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376626	8376626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772303653	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	161	287	0	ENST00000356435.5:c.4487G>A	p.Arg1496Gln	p.R1496Q	ENST00000356435		1496	cGa/cAa	27/35	1	2	FACETS	0.746	0.688	0.805	0.746	0.688	0.805	SUBCLONAL	1	TRUE	1	0.789270147364037	2		287	547	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504308	8504308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	174	305	0	ENST00000356435.5:c.1775G>A	p.Gly592Asp	p.G592D	ENST00000356435		592	gGc/gAc	12/35	1	2	FACETS	0.832	0.771	0.894	0.832	0.771	0.894	CLONAL	1	TRUE	1	0.789270147364037	2		305	530	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518055	8518055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	201	489	0	ENST00000356435.5:c.1336G>A	p.Gly446Arg	p.G446R	ENST00000356435		446	Gga/Aga	10/35	1	2	FACETS	0.931	0.87	0.994	0.931	0.87	0.994	CLONAL	1	TRUE	1	0.789270147364037	2		489	547	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971121	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	132	174	0	ENST00000304494.5:c.237_238delinsTT	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	79	acCCga/acTTga	2/3	1	2	FACETS	0.956	0.905	1	1	0.993	1	CLONAL	2	TRUE	1	0.789270147364037	2		174	175	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971121	21971121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	132	174	0	ENST00000579755.1:c.280C>T	p.Pro94Ser	p.P94S	ENST00000579755		94	Ccg/Tcg	2/3	1	2	FACETS	0.967	0.916	1	1	0.993	1	CLONAL	2	TRUE	1	0.789270147364037	2		174	173	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430683	80430683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	108	234	0	ENST00000286548.4:c.325C>T	p.His109Tyr	p.H109Y	ENST00000286548	NM_002072.3	109	Cat/Tat	3/7	1	2	FACETS	0.679	0.614	0.747	0.679	0.614	0.747	SUBCLONAL	1	TRUE	1	0.789270147364037	2		234	403	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133748264	133748264	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	154	375	0	ENST00000318560.5:c.925C>T	p.Pro309Ser	p.P309S	ENST00000318560	NM_005157.4	309	Ccc/Tcc	6/11	1	2	FACETS	0.945	0.874	1	0.945	0.874	1	CLONAL	1	TRUE	1	0.789270147364037	2		375	413	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442748	442748	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	229	400	0	ENST00000399788.2:c.1558G>A	p.Glu520Lys	p.E520K	ENST00000399788	NM_001042603.1	520	Gag/Aag	12/28	NA	2	FACETS	1	0.963	1			1	INDETERMINATE	1	TRUE	NA	0.789270147364037	2		400	562	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	465598	465598	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	266	584	2	ENST00000399788.2:c.778G>T	p.Asp260Tyr	p.D260Y	ENST00000399788	NM_001042603.1	260	Gat/Tat	6/28	NA	2	FACETS	0.93	0.876	0.984			1	INDETERMINATE	1	TRUE	NA	0.789270147364037	2		586	725	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534770	18534770	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	221	304	0	ENST00000266497.5:c.1828C>T	p.Pro610Ser	p.P610S	ENST00000266497		610	Cca/Tca	12/31	0.197221852471082	4	FACETS	0.928	0.871	0.985	0.928	0.871	0.985	INDETERMINATE	2	TRUE	2	0.789270147364037	4		304	540	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420091	49420091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770413324	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	257	446	0	ENST00000301067.7:c.15658C>T	p.Arg5220Cys	p.R5220C	ENST00000301067	NM_003482.3	5220	Cgc/Tgc	48/54	0.197221852471082	4	FACETS	0.949	0.896	1	0.949	0.896	1	INDETERMINATE	2	TRUE	2	0.789270147364037	4		446	614	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888286	112888286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	123	290	0	ENST00000351677.2:c.302C>T	p.Pro101Leu	p.P101L	ENST00000351677	NM_002834.3	101	cCt/cTt	3/16	0.789270147364037	1	FACETS	0.82	0.76	0.88	0.82	0.76	0.88	CLONAL	1	TRUE	0	0.789270147364037	1		290	230	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28885829	28885829	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1432876753	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	107	468	0	ENST00000282397.4:c.3533G>A	p.Gly1178Glu	p.G1178E	ENST00000282397	NM_002019.4	1178	gGa/gAa	27/30	0.789270147364037	1	FACETS	0.72	0.66	0.78	0.72	0.66	0.78	SUBCLONAL	1	TRUE	0	0.789270147364037	1		468	228	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729163	66729163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516792	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	176	325	0	ENST00000307102.5:c.371C>T	p.Pro124Leu	p.P124L	ENST00000307102	NM_002755.3	124	cCg/cTg	3/11	0.197221852471082	4	FACETS	0.945	0.881	1	0.945	0.881	1	INDETERMINATE	2	TRUE	2	0.789270147364037	4		325	422	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690635	88690635	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	171	266	0	ENST00000360948.2:c.396-1G>A		p.X132_splice	ENST00000360948	NM_001012338.2	132			0.197221852471082	4	FACETS	0.843	0.783	0.904	0.843	0.783	0.904	INDETERMINATE	2	TRUE	2	0.789270147364037	4		266	460	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129160	2129160	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45465195	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	161	390	0	ENST00000219476.3:c.3094C>T	p.Arg1032Ter	p.R1032*	ENST00000219476	NM_000548.3	1032	Cga/Tga	27/42	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.789270147364037	2		390	296	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858259	9858259	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	196	486	0	ENST00000330684.3:c.3142A>G	p.Ser1048Gly	p.S1048G	ENST00000330684	NM_001134407.1	1048	Agc/Ggc	13/13	1	2	FACETS	0.893	0.833	0.955	0.893	0.833	0.955	CLONAL	1	TRUE	1	0.789270147364037	2		486	556	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274043	10274043	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	154	443	0	ENST00000330684.3:c.226C>G	p.Arg76Gly	p.R76G	ENST00000330684	NM_001134407.1	76	Cgc/Ggc	2/13	1	2	FACETS	0.978	0.906	1	0.978	0.906	1	CLONAL	1	TRUE	1	0.789270147364037	2		443	399	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857452	68857452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	115	345	0	ENST00000261769.5:c.2087G>A	p.Arg696Lys	p.R696K	ENST00000261769	NM_004360.3	696	aGg/aAg	13/16	1	2	FACETS	0.574	0.519	0.631	0.574	0.519	0.631	SUBCLONAL	1	TRUE	1	0.789270147364037	2		345	508	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17124889	17124889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748031634	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	170	319	0	ENST00000285071.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000285071	NM_144997.5	278	cCg/cTg	8/14	0.596623061880851	1	FACETS	0.931	0.878	0.984	0.931	0.878	0.984	CLONAL	1	TRUE	0	0.789270147364037	1		319	280	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872150	37872150	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs140670446	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	157	431	0	ENST00000269571.5:c.1471C>T	p.Gln491Ter	p.Q491*	ENST00000269571		491	Caa/Taa	12/27	1	2	FACETS	0.923	0.854	0.993	0.923	0.854	0.993	CLONAL	1	TRUE	1	0.789270147364037	2		431	431	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510612	38510612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	219	525	0	ENST00000254066.5:c.866G>A	p.Gly289Glu	p.G289E	ENST00000254066	NM_000964.3	289	gGg/gAg	7/9	1	2	FACETS	0.989	0.928	1	0.989	0.928	1	CLONAL	1	TRUE	1	0.789270147364037	2		525	561	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223230	5223230	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	88	279	0	ENST00000357368.4:c.2573C>T	p.Thr858Ile	p.T858I	ENST00000357368	NM_002850.3	858	aCc/aTc	18/38	0.789270147364037	1	FACETS	0.964	0.889	1	0.964	0.889	1	CLONAL	1	TRUE	0	0.789270147364037	1		279	140	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143018	7143018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753688285	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	158	393	0	ENST00000302850.5:c.2351C>T	p.Ser784Phe	p.S784F	ENST00000302850	NM_000208.2	784	tCc/tTc	12/22	0.789270147364037	1	FACETS	0.901	0.846	0.955	0.901	0.846	0.955	CLONAL	1	TRUE	0	0.789270147364037	1		393	269	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546761	9546761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768724288	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	117	271	0	ENST00000353224.5:c.1261G>A	p.Asp421Asn	p.D421N	ENST00000353224	NM_177990.2	421	Gac/Aac	5/10	0.182345721783729	3	FACETS	1	0.982	1	0.656	0.6	0.714	INDETERMINATE	1	TRUE	1	0.789270147364037	3		271	315	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387101	31387101	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1226308460	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	195	361	2	ENST00000328111.2:c.1726C>T	p.Arg576Ter	p.R576*	ENST00000328111	NM_006892.3	576	Cga/Tga	16/23	0.182345721783729	3	FACETS	1	0.991	1	0.728	0.681	0.776	INDETERMINATE	1	TRUE	1	0.789270147364037	3		363	473	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032794	30032794	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121434259	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	420	337	0	ENST00000338641.4:c.169C>T	p.Arg57Ter	p.R57*	ENST00000338641	NM_000268.3	57	Cga/Tga	2/16	NA	2	FACETS	0.997	0.969	1			1	INDETERMINATE	2	TRUE	NA	0.789270147364037	2		337	534	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040629	47040629	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	178	421	0	ENST00000377604.3:c.1264G>A	p.Glu422Lys	p.E422K	ENST00000377604	NM_001204468.1	422	Gag/Aag	13/24	NA	2	FACETS	0.942	0.876	1			1	INDETERMINATE	1	TRUE	NA	0.789270147364037	2		421	479	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426777	47426777	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	137	380	0	ENST00000377045.4:c.1022C>A	p.Ser341Tyr	p.S341Y	ENST00000377045	NM_001654.4	341	tCc/tAc	10/16	NA	2	FACETS	0.946	0.871	1			1	INDETERMINATE	1	TRUE	NA	0.789270147364037	2		380	367	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430329	47430329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	228	814	1	ENST00000377045.4:c.1604C>T	p.Ser535Phe	p.S535F	ENST00000377045	NM_001654.4	535	tCc/tTc	15/16	NA	2	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.789270147364037	2		815	563	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665145	29665145	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	208	244	0	ENST00000356175.3:c.6744del	p.Ile2249PhefsTer10	p.I2249Ffs*10	ENST00000356175	NM_000267.3	2248	cgT/cg	44/57	0.570043963488609	1	FACETS	0.922	0.874	0.97	0.922	0.874	0.97	CLONAL	1	TRUE	0	0.789270147364037	1		244	346	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798452	42798452	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001251-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	168	337	0	ENST00000575354.2:c.4323del	p.Thr1442GlnfsTer12	p.T1442Qfs*12	ENST00000575354	NM_015125.3	1441	cgT/cg	18/20	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.789270147364037	2		337	423	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913381	NA	P-0001255-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	17	201	0	ENST00000304494.5:c.322G>T	p.Asp108Tyr	p.D108Y	ENST00000304494	NM_000077.4	108	Gat/Tat	2/3	1	2	FACETS	0.755	0.564	0.981	0.755	0.564	0.981	CLONAL	1	TRUE	1	0.19	2		201	237	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001255-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	18	507	0	ENST00000269305.4:c.853G>T	p.Glu285Ter	p.E285*	ENST00000269305	NM_001126112.2	285	Gag/Tag	8/11	1	2	FACETS	0.431	0.323	0.558	0.431	0.323	0.558	SUBCLONAL	1	TRUE	1	0.19	2		507	440	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117008	193117008	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001255-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	31	472	0	ENST00000367435.3:c.741G>T	p.Lys247Asn	p.K247N	ENST00000367435	NM_024529.4	247	aaG/aaT	8/17	1	2	FACETS	0.57	0.46	0.696	0.57	0.46	0.696	SUBCLONAL	1	TRUE	1	0.19	2		472	572	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178511	56178511	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001255-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	27	274	0	ENST00000399503.3:c.3484G>T	p.Glu1162Ter	p.E1162*	ENST00000399503	NM_005921.1	1162	Gaa/Taa	14/20	1	2	FACETS	0.817	0.65	1	0.817	0.65	1	CLONAL	1	TRUE	1	0.19	2		274	348	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534717	18534717	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001255-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	48	262	0	ENST00000266497.5:c.1775C>G	p.Ser592Cys	p.S592C	ENST00000266497		592	tCt/tGt	12/31	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.19	2		262	404	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398262	25398262	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913538	NA	P-0001255-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	52	413	0	ENST00000311936.3:c.57G>T	p.Leu19Phe	p.L19F	ENST00000311936	NM_004985.3	19	ttG/ttT	2/5	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.19	2		413	409	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347864	347864	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001255-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	50	705	0	ENST00000262320.3:c.1642G>T	p.Glu548Ter	p.E548*	ENST00000262320	NM_003502.3	548	Gag/Tag	6/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.19	2		705	444	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322692	30322692	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001255-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	26	309	0	ENST00000322652.5:c.1705G>A	p.Asp569Asn	p.D569N	ENST00000322652	NM_015355.2	569	Gat/Aat	14/16	1	2	FACETS	0.827	0.655	1	0.827	0.655	1	CLONAL	1	TRUE	1	0.19	2		309	331	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603041	48603041	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767361	NA	P-0001255-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	19	153	0	ENST00000342988.3:c.1342C>T	p.Gln448Ter	p.Q448*	ENST00000342988	NM_005359.5	448	Cag/Tag	11/12	1	2	FACETS	0.587	0.445	0.754	0.587	0.445	0.754	SUBCLONAL	1	TRUE	1	0.19	2		153	341	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117318	7117318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001255-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	26	504	0	ENST00000302850.5:c.3898G>A	p.Glu1300Lys	p.E1300K	ENST00000302850	NM_000208.2	1300	Gag/Aag	22/22	1	2	FACETS	0.638	0.505	0.791	0.638	0.505	0.791	SUBCLONAL	1	TRUE	1	0.19	2		504	429	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40745993	40745993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001255-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	21	335	0	ENST00000392038.2:c.598G>A	p.Glu200Lys	p.E200K	ENST00000392038	NM_001626.4	200	Gag/Aag	7/14	1	2	FACETS	0.676	0.52	0.858	0.676	0.52	0.858	SUBCLONAL	1	TRUE	1	0.19	2		335	327	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106321	27106324	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	novel	NA	P-0001255-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	25	297	0	ENST00000324856.7:c.5932_5935del	p.Ala1978SerfsTer36	p.A1978Sfs*36	ENST00000324856	NM_006015.4	1978	GCCAag/ag	20/20	0.155125519040215	1	FACETS	0.63	0.496	0.784	0.63	0.496	0.784	SUBCLONAL	1	TRUE	0	0.19	1		297	378	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001261-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	158	422	0				ENST00000310581	NM_198253.2	-/1132			0.45811394750313	5	FACETS	0.99	0.947	1	1	0.993	1	CLONAL	6	FALSE	1	0.45811394750313	5		422	196	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0001261-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	267	588	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.107696817341817	0	FACETS	0.96	0.906	1			1	INDETERMINATE	1	FALSE	0	0.45811394750313	0		588	658	SUCCESS
APC	324	MSKCC	GRCh37	5	112116592	112116592	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587781392	NA	P-0001261-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	135	190	0	ENST00000257430.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000257430	NM_000038.5	213	Cga/Tga	6/16	1	2	FACETS	0.805	0.741	0.871	1	0.989	1	CLONAL	2	FALSE	1	0.45811394750313	2		190	366	SUCCESS
APC	324	MSKCC	GRCh37	5	112175524	112175524	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001261-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	171	289	0	ENST00000257430.4:c.4233del	p.Ser1411ArgfsTer4	p.S1411Rfs*4	ENST00000257430	NM_000038.5	1411	agT/ag	16/16	1	2	FACETS	0.915	0.852	0.979	1	0.993	1	CLONAL	2	FALSE	1	0.45811394750313	2		289	408	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404381	139404381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775047070	NA	P-0001261-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	114	352	0	ENST00000277541.6:c.2773G>A	p.Gly925Ser	p.G925S	ENST00000277541	NM_017617.3	925	Ggc/Agc	18/34	NA	2	FACETS	0.824	0.753	0.897			1	INDETERMINATE	2	FALSE	NA	0.45811394750313	2		352	302	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625330	69625330	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs143483033	NA	P-0001261-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	120	562	0	ENST00000334134.2:c.463G>T	p.Val155Leu	p.V155L	ENST00000334134	NM_005247.2	155	Gtg/Ttg	3/3	1	2	FACETS	0.813	0.745	0.884	1	0.988	1	CLONAL	2	FALSE	1	0.45811394750313	2		562	322	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662297	67662297	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001261-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	102	297	0	ENST00000264010.4:c.1543C>G	p.Arg515Gly	p.R515G	ENST00000264010	NM_006565.3	515	Cgc/Ggc	9/12	0.148614897853674	0	FACETS	0.943	0.858	1			1	INDETERMINATE	1	FALSE	0	0.45811394750313	0		297	256	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134252	11134252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001261-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	178	394	0	ENST00000358026.2:c.2918G>A	p.Arg973Gln	p.R973Q	ENST00000358026	NM_001128849.1	973	cGg/cAg	20/36	0.148614897853674	0	FACETS	0.984	0.917	1			1	INDETERMINATE	1	FALSE	0	0.45811394750313	0		394	428	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868112	45868112	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001261-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	118	336	0	ENST00000391945.4:c.578T>C	p.Phe193Ser	p.F193S	ENST00000391945	NM_000400.3	193	tTc/tCc	7/23	1	2	FACETS	0.771	0.704	0.84	1	0.987	1	SUBCLONAL	2	FALSE	1	0.45811394750313	2		336	334	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538211	187538212	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TCGCT	novel	NA	P-0001261-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	209	496	0	ENST00000441802.2:c.9018_9022dup	p.Ile3008LysfsTer3	p.I3008Kfs*3	ENST00000441802	NM_005245.3	3008	ata/aAGCGAta	11/27	0.282629672850631	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	0	0.45811394750313	1		496	672	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0001267-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	302	479	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.316995665350356	5	FACETS	0.998	0.938	1	0.499	0.469	0.53	CLONAL	2	TRUE	1	0.316995665350356	5		480	1409	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001267-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	18	422	0				ENST00000310581	NM_198253.2	-/1132			0.316995665350356	0	FACETS	0.626	0.486	0.778			1	SUBCLONAL	2	TRUE	0	0.316995665350356	0		422	62	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262073	16262073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765111467	NA	P-0001267-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	41	89	0	ENST00000375759.3:c.9338G>A	p.Arg3113Gln	p.R3113Q	ENST00000375759	NM_015001.2	3113	cGg/cAg	11/15	1	2	FACETS	1	0.931	1	1	0.975	1	CLONAL	2	TRUE	1	0.316995665350356	2		89	112	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55973944	55973944	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001267-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	125	314	0	ENST00000263923.4:c.1372T>G	p.Trp458Gly	p.W458G	ENST00000263923	NM_002253.2	458	Tgg/Ggg	10/30	0.145652366727122	0	FACETS	1	0.923	1			1	INDETERMINATE	1	TRUE	0	0.316995665350356	0		314	530	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1268741	1268741	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060503009	NA	P-0001267-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	48	292	0	ENST00000310581.5:c.2476G>A	p.Val826Ile	p.V826I	ENST00000310581	NM_198253.2	826	Gtc/Atc	9/16	0.316995665350356	0	FACETS	0.802	0.683	0.93			1	CLONAL	1	TRUE	0	0.316995665350356	0		292	258	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289245	33289245	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001267-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	131	228	0	ENST00000374542.5:c.307G>T	p.Ala103Ser	p.A103S	ENST00000374542	NM_001141970.1	103	Gcg/Tcg	3/8	0.316995665350356	9	FACETS	0.937	0.853	1			1	CLONAL	3	TRUE	NA	0.316995665350356	9		228	620	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557630	95557630	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001267-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	194	426	0	ENST00000393063.1:c.5437G>C	p.Glu1813Gln	p.E1813Q	ENST00000393063	NM_030621.3	1813	Gag/Cag	26/28	1	2	FACETS	0.819	0.76	0.88	1	0.992	1	CLONAL	2	TRUE	1	0.316995665350356	2		426	747	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0001276-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	68	139	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.926	1			1	INDETERMINATE	1	TRUE	NA	0.7	2		139	184	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678076	117678076	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs373090808	NA	P-0001276-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	135	246	0	ENST00000368508.3:c.3857G>A	p.Arg1286His	p.R1286H	ENST00000368508	NM_002944.2	1286	cGc/cAc	25/43	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.7	2		246	380	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161888	47161891	+	frameshift_variant	Frame_Shift_Del	DEL	CTCT	CTCT	-	rs771527963	NA	P-0001276-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	255	606	0	ENST00000409792.3:c.4235_4238del	p.Glu1412ValfsTer19	p.E1412Vfs*19	ENST00000409792	NM_014159.6	1412	gAGAGt/gt	3/21	NA	2	FACETS	0.911	0.855	0.967			1	INDETERMINATE	1	TRUE	NA	0.7	2		606	800	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	86	422	0				ENST00000310581	NM_198253.2	-/1132			0.366938261026025	3	FACETS	0.991	0.898	1	0.991	0.898	1	CLONAL	2	TRUE	1	0.604591737829902	3		422	187	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0001280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	358	270	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.224617982054557	1	FACETS	0.76	0.721	0.8	0.76	0.721	0.8	INDETERMINATE	1	TRUE	0	0.604591737829902	1		270	1087	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577108	7577108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs763098116	NA	P-0001280-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	408	474	0	ENST00000269305.4:c.830G>T	p.Cys277Phe	p.C277F	ENST00000269305	NM_001126112.2	277	tGt/tTt	8/11	0.568036674437166	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.604591737829902	1		474	808	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001281-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	60	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.853	0.743	0.969			1	INDETERMINATE	2	TRUE	NA	0.291975288766039	2		422	241	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168468	56168468	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001281-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	51	201	0	ENST00000399503.3:c.1424G>C	p.Trp475Ser	p.W475S	ENST00000399503	NM_005921.1	475	tGg/tCg	8/20	0.171796709175138	3	FACETS	0.872	0.742	1	0.436	0.371	0.507	INDETERMINATE	1	TRUE	1	0.291975288766039	3		201	459	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956964	2956964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395288944	NA	P-0001281-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	91	292	0	ENST00000396946.4:c.2663G>A	p.Arg888His	p.R888H	ENST00000396946	NM_032415.4	888	cGt/cAt	20/25	0.291975288766039	3	FACETS	1	0.93	1	0.532	0.472	0.595	CLONAL	1	TRUE	1	0.291975288766039	3		292	672	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692995	89692995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554898225	NA	P-0001281-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	40	182	0	ENST00000371953.3:c.479C>T	p.Thr160Ile	p.T160I	ENST00000371953	NM_000314.4	160	aCc/aTc	5/9	0.291975288766039	1	FACETS	0.88	0.735	1	0.88	0.735	1	CLONAL	1	TRUE	0	0.291975288766039	1		182	266	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0001295-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	825	449	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.354981064828173	4	FACETS	0.906	0.883	0.928	0.906	0.883	0.928	CLONAL	4	TRUE	0	0.552906333556542	4		449	1279	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317419	1317419	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001295-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	265	364	0	ENST00000400841.2:c.646G>T	p.Asp216Tyr	p.D216Y	ENST00000400841		216	Gat/Tat	5/6	0.19942213723485	2	FACETS	1	0.992	1	0.665	0.626	0.704	INDETERMINATE	1	TRUE	0	0.552906333556542	2		364	721	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578413	7578413	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs876660754	NA	P-0001295-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	190	268	0	ENST00000269305.4:c.517G>T	p.Val173Leu	p.V173L	ENST00000269305	NM_001126112.2	173	Gtg/Ttg	5/11	0.532769973518834	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	0	0.552906333556542	2		268	342	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0001295-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	497	472	1	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.552906333556542	3	FACETS	0.839	0.808	0.869			1	CLONAL	3	TRUE	NA	0.552906333556542	3		473	912	SUCCESS
APC	324	MSKCC	GRCh37	5	112154942	112154942	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779780	NA	P-0001295-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	585	352	0	ENST00000257430.4:c.1213C>T	p.Arg405Ter	p.R405*	ENST00000257430	NM_000038.5	405	Cga/Tga	10/16	0.552906333556542	3	FACETS	1	0.991	1			1	CLONAL	3	TRUE	NA	0.552906333556542	3		352	861	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781895	9781895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001295-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	33	303	0	ENST00000377346.4:c.2032C>T	p.His678Tyr	p.H678Y	ENST00000377346	NM_005026.3	678	Cac/Tac	16/24	0.552906333556542	1	FACETS	0.27	0.22	0.326	0.27	0.22	0.326	SUBCLONAL	1	TRUE	0	0.552906333556542	1		303	320	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163896	152163896	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001295-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	154	349	0	ENST00000206249.3:c.617A>C	p.Lys206Thr	p.K206T	ENST00000206249	NM_000125.3	206	aAg/aCg	2/8	0.263426333972247	2	FACETS	0.854	0.784	0.927	0.427	0.392	0.464	INDETERMINATE	1	TRUE	0	0.552906333556542	2		349	652	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5078403	5078403	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001295-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	177	303	0	ENST00000381652.3:c.2090T>G	p.Leu697Arg	p.L697R	ENST00000381652	NM_004972.3	697	cTt/cGt	16/25	0.552906333556542	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.552906333556542	1		303	453	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600478	43600478	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001295-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	84	389	0	ENST00000355710.3:c.704A>G	p.Glu235Gly	p.E235G	ENST00000355710	NM_020975.4	235	gAg/gGg	4/20	0.365546424142408	3	FACETS	0.654	0.578	0.735	0.327	0.289	0.368	SUBCLONAL	1	TRUE	1	0.552906333556542	3		389	593	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400097	41400097	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001295-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	170	275	0	ENST00000373198.4:c.662A>C	p.Gln221Pro	p.Q221P	ENST00000373198	NM_133170.3	221	cAg/cCg	5/32	0.551793657728035	4	FACETS	1	0.952	1	0.349	0.321	0.379	CLONAL	1	TRUE	1	0.552906333556542	4		275	911	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589609	67589611	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0001295-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	79	225	0	ENST00000274335.5:c.1372_1374del	p.Glu458del	p.E458del	ENST00000274335		458	GAA/-	10/15	0.525419601458394	2	FACETS	0.885	0.785	0.99	0.442	0.392	0.495	CLONAL	1	TRUE	0	0.552906333556542	2		225	323	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001307-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	38	422	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.465009903511116	NA		422	113	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242766	16242766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001307-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	71	394	0	ENST00000375759.3:c.1387G>A	p.Glu463Lys	p.E463K	ENST00000375759	NM_015001.2	463	Gaa/Aaa	6/15	0.205704303544615	3	FACETS	0.92	0.807	1	0.46	0.403	0.521	INDETERMINATE	1	TRUE	1	0.465009903511116	3		394	409	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165965	118165965	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001307-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	51	223	0	ENST00000369448.3:c.475A>G	p.Asn159Asp	p.N159D	ENST00000369448	NM_017709.3	159	Aac/Gac	2/2	0.205704303544615	3	FACETS	0.939	0.803	1	0.469	0.401	0.543	INDETERMINATE	1	TRUE	1	0.465009903511116	3		223	288	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098974	178098974	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001307-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	92	281	0	ENST00000397062.3:c.71G>C	p.Trp24Ser	p.W24S	ENST00000397062	NM_006164.4	24	tGg/tCg	2/5	1	2	FACETS	0.925	0.826	1	0.925	0.826	1	CLONAL	1	TRUE	1	0.465009903511116	2		281	428	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913396	NA	P-0001307-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	90	270	0	ENST00000349496.5:c.95A>G	p.Asp32Gly	p.D32G	ENST00000349496	NM_001904.3	32	gAc/gGc	3/15	0.205704303544615	3	FACETS	1	0.968	1	0.613	0.548	0.682	INDETERMINATE	1	TRUE	1	0.465009903511116	3		270	389	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871040	12871040	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs532903617	NA	P-0001307-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	64	253	0	ENST00000228872.4:c.267C>G	p.Tyr89Ter	p.Y89*	ENST00000228872	NM_004064.3	89	taC/taG	1/3	0.465009903511116	7	FACETS	1	0.966	1			1	CLONAL	1	TRUE	NA	0.465009903511116	7		253	432	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739073	40739073	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1306943305	NA	P-0001307-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	25	284	0	ENST00000373198.4:c.3211G>C	p.Asp1071His	p.D1071H	ENST00000373198	NM_133170.3	1071	Gac/Cac	24/32	0.465009903511116	1	FACETS	0.432	0.343	0.533	0.432	0.343	0.533	SUBCLONAL	1	TRUE	0	0.465009903511116	1		284	191	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562738	29562739	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555615472	NA	P-0001315-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	390	431	0	ENST00000356175.3:c.3822_3823del	p.Phe1275ProfsTer8	p.F1275Pfs*8	ENST00000356175	NM_000267.3	1273	aCT/a	28/57	1	2	FACETS	0.98	0.934	1	0.98	0.934	1	CLONAL	1	TRUE	1	0.786006554383295	2		431	1013	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0001315-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	286	310	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.786006554383295	3	FACETS	0.849	0.798	0.902	0.425	0.399	0.451	CLONAL	1	TRUE	1	0.786006554383295	3		310	1194	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513547	41513547	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs780440242	NA	P-0001315-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	392	405	0	ENST00000263253.7:c.451A>G	p.Thr151Ala	p.T151A	ENST00000263253	NM_001429.3	151	Aca/Gca	2/31	0.786006554383295	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.786006554383295	1		405	570	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039132	49039133	+	splice_acceptor_variant	Splice_Site	DEL	AG	AG	-	novel	NA	P-0001315-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	147	260	0	ENST00000267163.4:c.2212-1_2212del		p.X738_splice	ENST00000267163	NM_000321.2	738			0.786006554383295	1	FACETS	0.808	0.753	0.862	0.808	0.753	0.862	CLONAL	1	TRUE	0	0.786006554383295	1		260	281	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121805	2121807	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs137854104	NA	P-0001315-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	235	363	0	ENST00000219476.3:c.1973_1975del	p.Lys658del	p.K658del	ENST00000219476	NM_000548.3	656	gAGAag/gag	19/42	1	2	FACETS	0.791	0.741	0.842	0.791	0.741	0.842	SUBCLONAL	1	TRUE	1	0.786006554383295	2		363	756	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486063	29486064	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs771115661	NA	P-0001315-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	281	411	0	ENST00000356175.3:c.246_247del	p.Gln83ValfsTer23	p.Q83Vfs*23	ENST00000356175	NM_000267.3	80	taTCtc/tatc	3/57	1	2	FACETS	0.875	0.825	0.926	0.875	0.825	0.926	CLONAL	1	TRUE	1	0.786006554383295	2		411	817	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001324-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	32	422	0				ENST00000310581	NM_198253.2	-/1132			0.318035130597412	3	FACETS	0.89	0.736	1	0.89	0.736	1	CLONAL	2	TRUE	1	0.318035130597412	3		422	131	SUCCESS
APC	324	MSKCC	GRCh37	5	112174558	112174558	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001324-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	32	317	0	ENST00000257430.4:c.3267C>A	p.Phe1089Leu	p.F1089L	ENST00000257430	NM_000038.5	1089	ttC/ttA	16/16	0.318035130597412	3	FACETS	1	0.932	1	0.663	0.544	0.794	CLONAL	1	TRUE	1	0.318035130597412	3		317	176	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026035	48026035	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001324-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	43	287	0	ENST00000234420.5:c.913A>C	p.Thr305Pro	p.T305P	ENST00000234420	NM_000179.2	305	Act/Cct	4/10	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.318035130597412	2		287	216	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721165	176721165	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0001324-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	28	207	0	ENST00000439151.2:c.6796A>T	p.Lys2266Ter	p.K2266*	ENST00000439151	NM_022455.4	2266	Aaa/Taa	23/23	0.318035130597412	3	FACETS	1	0.835	1	0.521	0.419	0.634	CLONAL	1	TRUE	1	0.318035130597412	3		207	196	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652323	36652323	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001324-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	88	183	0	ENST00000244741.5:c.445G>A	p.Asp149Asn	p.D149N	ENST00000244741	NM_000389.4	149	Gat/Aat	2/3	0.318035130597412	7	FACETS	0.845	0.753	0.941	0.634	0.565	0.706	CLONAL	3	TRUE	3	0.318035130597412	7		183	392	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630409	90630409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1195247848	NA	P-0001324-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	89	327	0	ENST00000330062.3:c.902C>T	p.Ser301Leu	p.S301L	ENST00000330062	NM_002168.2	301	tCg/tTg	7/11	1	2	FACETS	0.797	0.713	0.886	1	0.982	1	SUBCLONAL	2	TRUE	1	0.318035130597412	2		327	351	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611212	100611212	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001324-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	124	155	0	ENST00000308731.7:c.1394C>G	p.Thr465Ser	p.T465S	ENST00000308731	NM_000061.2	465	aCc/aGc	15/19	0.318035130597412	2	FACETS	0.975	0.91	1			1	CLONAL	4	TRUE	NA	0.318035130597412	2		155	200	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652126	36652141	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGAGGCCGGGATGA	GGCGAGGCCGGGATGA	TC	novel	NA	P-0001324-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	43	266	0	ENST00000244741.5:c.248_263delinsTC	p.Arg83LeufsTer41	p.R83Lfs*41	ENST00000244741	NM_000389.4	83	cGGCGAGGCCGGGATGAg/cTCg	2/3	0.318035130597412	7	FACETS	1	0.946	1	0.332	0.278	0.391	CLONAL	1	TRUE	3	0.318035130597412	7		266	366	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793471	89793471	+	splice_acceptor_variant	Splice_Site	INS	G	G	TCC	novel	NA	P-0001324-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	49	159	0	ENST00000336032.3:c.541-1delinsTCC		p.X181_splice	ENST00000336032	NM_006813.2	181			0.318035130597412	7	FACETS	0.898	0.765	1	0.449	0.382	0.522	CLONAL	2	TRUE	3	0.318035130597412	7		159	308	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138068	2138077	+	frameshift_variant	Frame_Shift_Del	DEL	CACCAGCGTG	CACCAGCGTG	-	novel	NA	P-0001342-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	620	914	0	ENST00000219476.3:c.5088_5097del	p.Asp1696GlufsTer127	p.D1696Efs*127	ENST00000219476	NM_000548.3	1696	gaCACCAGCGTG/ga	40/42	0.340723345049208	3	FACETS	1	0.994	1	1	0.997	1	CLONAL	4	TRUE	0	0.340723345049208	3		914	975	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974723	21974723	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs746834149	NA	P-0001352-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	88	386	0	ENST00000304494.5:c.104G>T	p.Gly35Val	p.G35V	ENST00000304494	NM_000077.4	35	gGg/gTg	1/3	0.275961885287467	1	FACETS	0.521	0.461	0.584	0.521	0.461	0.584	SUBCLONAL	1	TRUE	0	0.405801507144286	1		386	664	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578189	7578189	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0001352-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	244	503	2	ENST00000269305.4:c.660T>G	p.Tyr220Ter	p.Y220*	ENST00000269305	NM_001126112.2	220	taT/taG	6/11	0.405801507144286	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.405801507144286	1		505	904	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29557369	29557369	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001352-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	175	233	0	ENST00000356175.3:c.3082G>T	p.Asp1028Tyr	p.D1028Y	ENST00000356175	NM_000267.3	1028	Gac/Tac	23/57	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	1	TRUE	NA	0.405801507144286	2		233	756	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971162	21971172	+	protein_altering_variant	In_Frame_Del	DEL	GGAGCAGCAGC	GGAGCAGCAGC	AG	novel	NA	P-0001352-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	38	74	0	ENST00000304494.5:c.186_196delinsCT	p.Leu63_His66delinsTyr	p.L63_H66delinsY	ENST00000304494	NM_000077.4	62	ctGCTGCTGCTCCac/ctCTac	2/3	0.275961885287467	1	FACETS	0.834	0.698	0.981	0.834	0.698	0.981	CLONAL	1	TRUE	0	0.405801507144286	1		74	179	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001358-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	40	422	0				ENST00000310581	NM_198253.2	-/1132			0.272353891722598	1	FACETS	0.806	0.695	0.918	1	0.968	1	CLONAL	2	TRUE	0	0.436168243271713	1		422	89	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001358-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	92	143	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.211511221976737	2	FACETS	0.959	0.869	1	0.959	0.869	1	INDETERMINATE	2	TRUE	0	0.436168243271713	2		143	220	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0001358-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	121	318	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.319198006083248	1	FACETS	0.786	0.723	0.85	1	0.988	1	SUBCLONAL	2	TRUE	0	0.436168243271713	1		318	276	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001369-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	15	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.503	0.369	0.663	0.503	0.369	0.663	SUBCLONAL	1	FALSE	1	0.3225495542921	2		422	185	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61749788	61749788	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001369-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	94	356	0	ENST00000401558.2:c.259A>G	p.Ile87Val	p.I87V	ENST00000401558	NM_003400.3	87	Ata/Gta	4/25	1	2	FACETS	0.801	0.712	0.895	0.801	0.712	0.895	CLONAL	1	FALSE	1	0.3225495542921	2		356	728	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418833	116418833	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001369-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	124	303	0	ENST00000397752.3:c.3344T>C	p.Ile1115Thr	p.I1115T	ENST00000397752	NM_000245.2	1115	aTc/aCc	17/21	0.2263903887167	3	FACETS	1	0.982	1	0.685	0.621	0.752	CLONAL	1	FALSE	1	0.3225495542921	3		303	652	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852158	63852164	+	frameshift_variant	Frame_Shift_Del	DEL	ACCATGT	ACCATGT	-	novel	NA	P-0001369-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	27	210	0	ENST00000279873.7:c.2936_2942del	p.His979ArgfsTer21	p.H979Rfs*21	ENST00000279873	NM_032199.2	979	cACCATGTg/cg	10/10	1	2	FACETS	0.407	0.324	0.503	0.407	0.324	0.503	SUBCLONAL	1	FALSE	1	0.3225495542921	2		210	411	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001374-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	64	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.809	0.713	0.908	1	0.978	1	CLONAL	2	TRUE	1	0.410124943408805	2		422	193	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0001374-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	33	142	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.847	0.697	1	0.847	0.697	1	CLONAL	1	TRUE	1	0.410124943408805	2		142	190	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683876	117683876	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs781304519	NA	P-0001374-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	144	552	0	ENST00000368508.3:c.3271C>G	p.Gln1091Glu	p.Q1091E	ENST00000368508	NM_002944.2	1091	Caa/Gaa	21/43	1	2	FACETS	0.996	0.91	1	0.996	0.91	1	CLONAL	1	TRUE	1	0.410124943408805	2		552	705	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87366996	87366996	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001374-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	118	495	0	ENST00000277120.3:c.1392G>C	p.Met464Ile	p.M464I	ENST00000277120		464	atG/atC	12/19	0.410124943408805	3	FACETS	0.94	0.848	1	0.47	0.424	0.518	CLONAL	1	TRUE	1	0.410124943408805	3		495	738	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913233	NA	P-0001374-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	176	428	0	ENST00000451590.1:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000451590	NM_001130442.1	61	cAg/cTg	3/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.410124943408805	2		428	710	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952325	17952325	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001374-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	93	393	0	ENST00000458235.1:c.1015C>A	p.Leu339Met	p.L339M	ENST00000458235	NM_000215.3	339	Ctg/Atg	8/24	1	2	FACETS	0.927	0.828	1	0.927	0.828	1	CLONAL	1	TRUE	1	0.410124943408805	2		393	489	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99175952	99175976	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGCCCAGGTACGTGGTTTCCGTTCA	AGCCCAGGTACGTGGTTTCCGTTCA	-	novel	NA	P-0001374-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	54	451	0	ENST00000074304.5:c.1866_1870+20del		p.X622_splice	ENST00000074304	NM_001134224.1	622		18/26	1	2	FACETS	0.517	0.442	0.6	0.517	0.442	0.6	SUBCLONAL	1	TRUE	1	0.410124943408805	2		451	509	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517696	187517697	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0001374-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	34	137	0	ENST00000441802.2:c.12996_12997dup	p.Asp4333ValfsTer17	p.D4333Vfs*17	ENST00000441802	NM_005245.3	4333	gac/gTGac	25/27	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.410124943408805	2		137	146	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628977	187628987	+	frameshift_variant	Frame_Shift_Del	DEL	GCTTGTGACTG	GCTTGTGACTG	-	novel	NA	P-0001374-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	111	389	0	ENST00000441802.2:c.1995_2005del	p.Ser666GlyfsTer6	p.S666Gfs*6	ENST00000441802	NM_005245.3	665	gcCAGTCACAAGCtg/gctg	2/27	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.410124943408805	2		389	484	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399551	139399552	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0001374-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	151	238	0	ENST00000277541.6:c.4591dup	p.Leu1531ProfsTer79	p.L1531Pfs*79	ENST00000277541	NM_017617.3	1531	ctg/cCtg	26/34	0.410124943408805	3	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	1	0.410124943408805	3		238	430	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412315	139412341	+	inframe_deletion	In_Frame_Del	DEL	AGCCCTGCAGACACTGGCACTCGAAGG	AGCCCTGCAGACACTGGCACTCGAAGG	-	novel	NA	P-0001374-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	80	477	0	ENST00000277541.6:c.1304_1330del	p.Ser435_Gly443del	p.S435_G443del	ENST00000277541	NM_017617.3	435	tCCTTCGAGTGCCAGTGTCTGCAGGGCTac/tac	8/34	0.410124943408805	3	FACETS	0.615	0.541	0.695	0.308	0.27	0.348	SUBCLONAL	1	TRUE	1	0.410124943408805	3		477	764	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137360	202137360	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0001374-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	88	217	0	ENST00000358485.4:c.589-1G>A		p.X197_splice	ENST00000358485	NM_001080125.1	197			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.410124943408805	2		217	321	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204494705	204494705	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001375-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	65	283	0	ENST00000367182.3:c.59C>G	p.Ser20Cys	p.S20C	ENST00000367182	NM_001278516.1	20	tCt/tGt	2/11	1	2	FACETS	0.939	0.814	1	0.939	0.814	1	CLONAL	1	TRUE	1	0.21	2		283	659	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564570	55564570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001375-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	20	303	0	ENST00000288135.5:c.458G>A	p.Gly153Glu	p.G153E	ENST00000288135	NM_000222.2	153	gGg/gAg	3/21	1	2	FACETS	0.477	0.364	0.61	0.477	0.364	0.61	SUBCLONAL	1	TRUE	1	0.21	2		303	399	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170819954	170819954	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001375-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	40	187	1	ENST00000296930.5:c.496G>T	p.Asp166Tyr	p.D166Y	ENST00000296930	NM_002520.6	166	Gat/Tat	6/11	0.234515347856482	1	FACETS	0.787	0.655	0.935	0.787	0.655	0.935	CLONAL	1	TRUE	0	0.21	1		188	433	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176719042	176719042	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001375-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	24	213	0	ENST00000439151.2:c.6346G>T	p.Glu2116Ter	p.E2116*	ENST00000439151	NM_022455.4	2116	Gag/Tag	22/23	0.234515347856482	1	FACETS	0.495	0.388	0.62	0.495	0.388	0.62	SUBCLONAL	1	TRUE	0	0.21	1		213	413	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099173	157099173	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001375-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	22	227	1	ENST00000346085.5:c.110C>A	p.Ser37Tyr	p.S37Y	ENST00000346085	NM_020732.3	37	tCc/tAc	1/20	0.234515347856482	1	FACETS	1	0.782	1	1	0.782	1	CLONAL	1	TRUE	0	0.21	1		228	187	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359014	81359014	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001375-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	81	509	0	ENST00000222390.5:c.947C>A	p.Thr316Asn	p.T316N	ENST00000222390	NM_000601.4	316	aCt/aAt	8/18	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.21	2		509	559	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81399208	81399208	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1353786409	NA	P-0001375-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	63	172	0	ENST00000222390.5:c.80C>A	p.Pro27His	p.P27H	ENST00000222390	NM_000601.4	27	cCc/cAc	1/18	0.3	5	FACETS	1	0.947	1			1	CLONAL	2	TRUE	NA	0.21	5		172	336	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604679	43604679	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0001375-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	18	227	0	ENST00000355710.3:c.1263+1G>T		p.X421_splice	ENST00000355710	NM_020975.4	421			0.3	1	FACETS	0.803	0.607	1	0.803	0.607	1	CLONAL	1	TRUE	0	0.21	1		227	191	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285807	46285807	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0001375-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	84	201	0	ENST00000334344.6:c.5075C>G	p.Ser1692Ter	p.S1692*	ENST00000334344	NM_152641.2	1692	tCa/tGa	18/21	0.1703464591886	3	FACETS	0.915	0.811	1	0.915	0.811	1	CLONAL	2	TRUE	1	0.21	3		201	483	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777991	3777991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771546273	NA	P-0001375-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	31	418	0	ENST00000262367.5:c.7057C>T	p.Arg2353Trp	p.R2353W	ENST00000262367	NM_004380.2	2353	Cgg/Tgg	31/31	0.1703464591886	0	FACETS	0.724	0.587	0.879			1	SUBCLONAL	1	TRUE	0	0.21	0		418	322	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579494	7579494	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs1555526721	NA	P-0001375-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	12	188	0	ENST00000269305.4:c.193A>T	p.Arg65Ter	p.R65*	ENST00000269305	NM_001126112.2	65	Aga/Tga	4/11	1	2	FACETS	0.539	0.379	0.736	0.539	0.379	0.736	SUBCLONAL	1	TRUE	1	0.21	2		188	212	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317472	1317472	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001375-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	48	453	0	ENST00000400841.2:c.593C>A	p.Thr198Lys	p.T198K	ENST00000400841		198	aCa/aAa	5/6	0.3	2	FACETS	1	0.908	1			1	CLONAL	1	TRUE	NA	0.21	2		453	414	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602901	10602908	+	frameshift_variant	Frame_Shift_Del	DEL	CAGTGGGA	CAGTGGGA	-	novel	NA	P-0001375-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	20	276	0	ENST00000171111.5:c.670_677del	p.Ser224ProfsTer123	p.S224Pfs*123	ENST00000171111	NM_203500.1	224	TCCCACTGc/c	3/6	0.234515347856482	1	FACETS	0.669	0.512	0.851	0.669	0.512	0.851	SUBCLONAL	1	TRUE	0	0.21	1		276	255	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001388-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	43	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.41584097984253	2		422	175	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455631	189455631	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001388-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	95	386	0	ENST00000264731.3:c.165C>A	p.Phe55Leu	p.F55L	ENST00000264731	NM_003722.4	55	ttC/ttA	2/14	1	2	FACETS	0.97	0.868	1	0.97	0.868	1	CLONAL	1	TRUE	1	0.41584097984253	2		386	471	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720825	89720825	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001388-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	98	249	0	ENST00000371953.3:c.976G>T	p.Asp326Tyr	p.D326Y	ENST00000371953	NM_000314.4	326	Gac/Tac	8/9	0.41584097984253	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.41584097984253	1		249	285	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240645	133240645	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001388-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	118	648	0	ENST00000320574.5:c.2651A>G	p.Lys884Arg	p.K884R	ENST00000320574	NM_006231.2	884	aAg/aGg	23/49	NA	2	FACETS	0.911	0.824	1			1	INDETERMINATE	1	TRUE	NA	0.41584097984253	2		648	623	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060971	38060971	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001388-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	17	325	0	ENST00000250448.2:c.1018G>T	p.Ala340Ser	p.A340S	ENST00000250448	NM_004496.3	340	Gcg/Tcg	2/2	0.414627829511147	1	FACETS	0.247	0.184	0.322	0.247	0.184	0.322	SUBCLONAL	1	TRUE	0	0.41584097984253	1		325	262	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520248	9520248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759137045	NA	P-0001388-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	99	384	0	ENST00000353224.5:c.2021G>A	p.Arg674Gln	p.R674Q	ENST00000353224	NM_177990.2	674	cGg/cAg	10/10	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.41584097984253	2		384	441	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	127	422	0				ENST00000310581	NM_198253.2	-/1132			0.64360041090233	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.655505221104452	2		422	156	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0001392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	1644	393	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.655505221104452	5	FACETS	0.966	0.953	0.979			1	CLONAL	5	TRUE	NA	0.655505221104452	5		393	2060	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715983	52715983	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519947	NA	P-0001392-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	184	593	0	ENST00000322088.6:c.548G>A	p.Arg183Gln	p.R183Q	ENST00000322088	NM_014225.5	183	cGg/cAg	5/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.655505221104452	2		593	530	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001406-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	45	422	0				ENST00000310581	NM_198253.2	-/1132			0.164758403131418	1	FACETS	0.558	0.478	0.643	0.558	0.478	0.643	INDETERMINATE	1	TRUE	0	0.702037847180225	1		422	149	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185195158	185195158	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001406-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	224	497	0	ENST00000265026.3:c.2475T>G	p.Ser825Arg	p.S825R	ENST00000265026	NM_004721.4	825	agT/agG	12/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.702037847180225	2		497	578	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439721	51439722	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TT	novel	NA	P-0001406-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	718	381	0	ENST00000262662.1:c.287_288dup	p.Asn97LeufsTer28	p.N97Lfs*28	ENST00000262662		96	gtt/gTTtt	4/4	0.68410161149521	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.702037847180225	2		381	1022	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0001408-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	32	139	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.722	0.594	0.863	0.722	0.594	0.863	SUBCLONAL	1	TRUE	1	0.564501975198423	2		139	157	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588751	29588751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760703505	NA	P-0001408-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	211	361	0	ENST00000356175.3:c.4537C>T	p.Arg1513Ter	p.R1513*	ENST00000356175	NM_000267.3	1513	Cga/Tga	34/57	1	2	FACETS	0.938	0.873	1	0.938	0.873	1	CLONAL	1	TRUE	1	0.564501975198423	2		361	797	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591132	67591134	+	inframe_deletion	In_Frame_Del	DEL	GAC	GAC	-	rs1057519842	NA	P-0001408-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	109	296	0	ENST00000274335.5:c.1727_1729del	p.Thr576del	p.T576del	ENST00000274335		575	aaGACg/aag	12/15	1	2	FACETS	0.81	0.731	0.892	0.81	0.731	0.892	CLONAL	1	TRUE	1	0.564501975198423	2		296	477	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556438	29556439	+	inframe_insertion	In_Frame_Ins	INS	-	-	AAATTGAAG	novel	NA	P-0001408-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	80	332	0	ENST00000356175.3:c.2808_2816dup	p.Lys936_Lys938dup	p.K936_K938dup	ENST00000356175	NM_000267.3	936	-/AAATTGAAG	21/57	1	2	FACETS	0.624	0.552	0.702	0.624	0.552	0.702	SUBCLONAL	1	TRUE	1	0.564501975198423	2		332	454	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001409-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	101	422	0				ENST00000310581	NM_198253.2	-/1132			0.799907265595162	3	FACETS	1	0.945	1	0.534	0.482	0.588	CLONAL	1	TRUE	1	0.799907265595162	3		422	331	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267489	198267489	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1039242157	NA	P-0001409-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	104	336	0	ENST00000335508.6:c.1868A>G	p.Tyr623Cys	p.Y623C	ENST00000335508	NM_012433.2	623	tAt/tGt	14/25	1	2	FACETS	0.831	0.753	0.911	0.831	0.753	0.911	CLONAL	1	TRUE	1	0.799907265595162	2		336	313	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0001412-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	335	314	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.90566729770649	2		314	694	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0001412-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	45	139	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.90566729770649	2		139	89	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413171	139413172	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0001412-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	21	308	0	ENST00000277541.6:c.970_971del	p.Val324GlnfsTer6	p.V324Qfs*6	ENST00000277541	NM_017617.3	324	GTc/c	6/34	1	2	FACETS	0.115	0.088	0.146	0.115	0.088	0.146	SUBCLONAL	1	TRUE	1	0.90566729770649	2		308	405	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983146	149983146	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001412-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	407	304	0	ENST00000253339.5:c.3112A>G	p.Asn1038Asp	p.N1038D	ENST00000253339		1038	Aat/Gat	7/7	0.159594376504762	3	FACETS	0.76	0.727	0.793	0.76	0.727	0.793	INDETERMINATE	2	TRUE	1	0.90566729770649	3		304	859	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144113	11144113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001412-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	141	334	0	ENST00000358026.2:c.3694G>A	p.Gly1232Ser	p.G1232S	ENST00000358026	NM_001128849.1	1232	Ggc/Agc	26/36	0.282011453326954	1	FACETS	0.574	0.532	0.615	0.574	0.532	0.615	INDETERMINATE	1	TRUE	0	0.90566729770649	1		334	297	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78444577	78444578	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0001412-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	162	227	0	ENST00000370768.2:c.111_112del	p.Arg37SerfsTer11	p.R37Sfs*11	ENST00000370768	NM_003902.3	37	agAGcc/agcc	1/20	0.90566729770649	1	FACETS	0.652	0.611	0.694	0.652	0.611	0.694	SUBCLONAL	1	TRUE	0	0.90566729770649	1		227	300	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457939	69457941	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0001412-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	176	506	0	ENST00000227507.2:c.340_342del	p.Lys114del	p.K114del	ENST00000227507	NM_053056.2	113	atGAAg/atg	2/5	0.829714421249724	3	FACETS	0.649	0.598	0.702	0.325	0.299	0.351	SUBCLONAL	1	TRUE	1	0.90566729770649	3		506	870	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001418-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	77	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.969	1			1	INDETERMINATE	2	TRUE	NA	0.627362226265514	2		422	111	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0001418-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	11	142	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.527019899714218	3	FACETS	0.165	0.113	0.229	0.055	0.037	0.077	SUBCLONAL	1	TRUE	0	0.627362226265514	3		142	280	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426751	49426751	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001418-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	20	206	0	ENST00000301067.7:c.11737C>T	p.Gln3913Ter	p.Q3913*	ENST00000301067	NM_003482.3	3913	Cag/Tag	39/54	0.544000260729072	3	FACETS	0.317	0.243	0.404	0.106	0.081	0.135	SUBCLONAL	1	TRUE	0	0.627362226265514	3		206	264	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711913	89711913	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0001418-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	89	436	0	ENST00000371953.3:c.531T>A	p.Tyr177Ter	p.Y177*	ENST00000371953	NM_000314.4	177	taT/taA	6/9	0.625922633110521	2	FACETS	0.518	0.46	0.579	0.259	0.23	0.29	SUBCLONAL	1	TRUE	0	0.627362226265514	2		436	548	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033905	49033905	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001418-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	389	519	2	ENST00000267163.4:c.2042G>A	p.Trp681Ter	p.W681*	ENST00000267163	NM_000321.2	681	tGg/tAg	20/27	0.493525078637155	3	FACETS	1	0.995	1	0.825	0.793	0.857	CLONAL	2	TRUE	0	0.627362226265514	3		521	658	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73991983	73991983	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0001418-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	281	452	0	ENST00000318443.5:c.3G>A	p.Met1?	p.M1?	ENST00000318443	NM_001024736.1	1	atG/atA	2/10	0.607246099667732	2	FACETS	0.914	0.871	0.956	0.914	0.871	0.956	CLONAL	2	TRUE	0	0.627362226265514	2		452	490	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559899	29559899	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001418-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	273	228	1	ENST00000356175.3:c.3496G>A	p.Gly1166Ser	p.G1166S	ENST00000356175	NM_000267.3	1166	Ggc/Agc	26/57	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.627362226265514	2		229	406	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870816	12870816	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001418-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	189	185	0	ENST00000228872.4:c.43del	p.Arg15GlyfsTer27	p.R15Gfs*27	ENST00000228872	NM_004064.3	15	Cgg/gg	1/3	0.627362226265514	3	FACETS	1	0.988	1	0.792	0.747	0.837	CLONAL	2	TRUE	0	0.627362226265514	3		185	333	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	26	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.822	1			1	INDETERMINATE	1	TRUE	NA	0.731642522179265	2		422	71	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	215	314	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.731642522179265	2		314	572	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175857	24175859	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs875989800	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	92	537	0	ENST00000263121.7:c.1091_1093del	p.Lys364del	p.K364del	ENST00000263121	NM_003073.3	362	gAGAag/gag	8/9	1	2	FACETS	0.814	0.731	0.9	0.814	0.731	0.9	CLONAL	1	TRUE	1	0.731642522179265	2		537	309	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805236	43805236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	10	585	0	ENST00000372470.3:c.686G>A	p.Arg229Lys	p.R229K	ENST00000372470	NM_005373.2	229	aGa/aAa	4/12	0.729063883324684	1	FACETS	0.098	0.066	0.138	0.098	0.066	0.138	SUBCLONAL	1	TRUE	0	0.731642522179265	1		585	177	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566799	212566799	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	47	574	0	ENST00000342788.4:c.1382C>T	p.Thr461Ile	p.T461I	ENST00000342788	NM_005235.2	461	aCt/aTt	12/28	1	2	FACETS	0.183	0.154	0.215	0.183	0.154	0.215	SUBCLONAL	1	TRUE	1	0.731642522179265	2		574	702	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794464	242794464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	39	656	0	ENST00000334409.5:c.478C>T	p.Pro160Ser	p.P160S	ENST00000334409	NM_005018.2	160	Ccc/Tcc	3/5	1	2	FACETS	0.404	0.336	0.478	0.404	0.336	0.478	SUBCLONAL	1	TRUE	1	0.731642522179265	2		656	264	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139486	47139486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	143	1377	0	ENST00000409792.3:c.5101G>A	p.Gly1701Arg	p.G1701R	ENST00000409792	NM_014159.6	1701	Gga/Aga	9/21	0.16563695853394	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.731642522179265	0		1377	864	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69788852	69788852	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs763445398	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	19	411	0	ENST00000352241.4:c.104G>A	p.Ser35Asn	p.S35N	ENST00000352241	NM_198159.2	35	aGc/aAc	1/10	1	2	FACETS	0.176	0.133	0.226	0.176	0.133	0.226	SUBCLONAL	1	TRUE	1	0.731642522179265	2		411	295	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119562168	119562168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	144	482	0	ENST00000316626.5:c.1168C>T	p.Leu390Phe	p.L390F	ENST00000316626		390	Ctt/Ttt	11/12	1	2	FACETS	0.802	0.736	0.869	0.802	0.736	0.869	CLONAL	1	TRUE	1	0.731642522179265	2		482	491	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447306	187447306	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	32	353	0	ENST00000232014.4:c.887G>A	p.Cys296Tyr	p.C296Y	ENST00000232014	NM_001130845.1	296	tGt/tAt	5/10	1	2	FACETS	0.35	0.285	0.422	0.35	0.285	0.422	SUBCLONAL	1	TRUE	1	0.731642522179265	2		353	250	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562265	176562265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	40	687	0	ENST00000439151.2:c.161G>A	p.Ser54Asn	p.S54N	ENST00000439151	NM_022455.4	54	aGt/aAt	2/23	0.198492248785631	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.731642522179265	0		687	432	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638735	176638735	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs901175981	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	86	619	1	ENST00000439151.2:c.3335G>A	p.Ser1112Asn	p.S1112N	ENST00000439151	NM_022455.4	1112	aGc/aAc	5/23	0.198492248785631	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.731642522179265	0		620	488	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555054	106555054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	62	373	0	ENST00000369096.4:c.2171C>T	p.Thr724Ile	p.T724I	ENST00000369096	NM_001198.3	724	aCc/aTc	7/7	1	2	FACETS	0.575	0.5	0.654	0.575	0.5	0.654	SUBCLONAL	1	TRUE	1	0.731642522179265	2		373	295	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412040	116412040	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	66	409	0	ENST00000397752.3:c.3025G>T	p.Glu1009Ter	p.E1009*	ENST00000397752	NM_000245.2	1009	Gaa/Taa	14/21	1	2	FACETS	0.362	0.315	0.414	0.362	0.315	0.414	SUBCLONAL	1	TRUE	1	0.731642522179265	2		409	498	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456885	32456885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	10	131	0	ENST00000332351.3:c.7G>A	p.Asp3Asn	p.D3N	ENST00000332351	NM_024426.4	3	Gac/Aac	1/10	1	2	FACETS	0.427	0.294	0.587	0.427	0.294	0.587	SUBCLONAL	1	TRUE	1	0.731642522179265	2		131	64	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577197	64577197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	72	827	0	ENST00000312049.6:c.385C>T	p.Leu129Phe	p.L129F	ENST00000312049	NM_130799.2	129	Ctc/Ttc	2/10	1	2	FACETS	0.46	0.403	0.52	0.46	0.403	0.52	SUBCLONAL	1	TRUE	1	0.731642522179265	2		827	428	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514089	69514089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	117	635	0	ENST00000294312.3:c.592G>A	p.Asp198Asn	p.D198N	ENST00000294312	NM_005117.2	198	Gac/Aac	3/3	1	2	FACETS	0.906	0.826	0.988	0.906	0.826	0.988	CLONAL	1	TRUE	1	0.731642522179265	2		635	353	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153465	108153465	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	74	767	0	ENST00000278616.4:c.3605G>A	p.Gly1202Glu	p.G1202E	ENST00000278616	NM_000051.3	1202	gGa/gAa	25/63	1	2	FACETS	0.25	0.218	0.285	0.25	0.218	0.285	SUBCLONAL	1	TRUE	1	0.731642522179265	2		767	808	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245448	46245448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	34	463	0	ENST00000334344.6:c.3542G>A	p.Ser1181Asn	p.S1181N	ENST00000334344	NM_152641.2	1181	aGt/aAt	15/21	1	2	FACETS	0.208	0.169	0.251	0.208	0.169	0.251	SUBCLONAL	1	TRUE	1	0.731642522179265	2		463	447	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435167	49435167	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1232307242	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	10	273	1	ENST00000301067.7:c.6386C>T	p.Pro2129Leu	p.P2129L	ENST00000301067	NM_003482.3	2129	cCc/cTc	31/54	1	2	FACETS	0.232	0.157	0.324	0.232	0.157	0.324	SUBCLONAL	1	TRUE	1	0.731642522179265	2		274	118	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436031	49436031	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	43	399	0	ENST00000301067.7:c.5950C>T	p.Pro1984Ser	p.P1984S	ENST00000301067	NM_003482.3	1984	Ccc/Tcc	28/54	1	2	FACETS	0.773	0.659	0.895	0.773	0.659	0.895	SUBCLONAL	1	TRUE	1	0.731642522179265	2		399	152	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444956	49444956	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	14	194	0	ENST00000301067.7:c.2510C>T	p.Ser837Phe	p.S837F	ENST00000301067	NM_003482.3	837	tCt/tTt	10/54	1	2	FACETS	0.379	0.277	0.499	0.379	0.277	0.499	SUBCLONAL	1	TRUE	1	0.731642522179265	2		194	101	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039467	49039467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	105	809	0	ENST00000267163.4:c.2452G>A	p.Gly818Ser	p.G818S	ENST00000267163	NM_000321.2	818	Ggt/Agt	23/27	0.172398584294948	3	FACETS	0.61	0.547	0.676	0.305	0.273	0.338	INDETERMINATE	1	TRUE	1	0.731642522179265	3		809	643	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129197	2129197	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397515302	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	14	718	0	ENST00000219476.3:c.3131G>A	p.Arg1044Lys	p.R1044K	ENST00000219476	NM_000548.3	1044	aGg/aAg	27/42	0.16563695853394	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.731642522179265	0		718	249	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041770	14041770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	42	737	0	ENST00000311895.7:c.2317G>A	p.Gly773Ser	p.G773S	ENST00000311895	NM_005236.2	773	Ggt/Agt	11/11	0.16563695853394	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.731642522179265	0		737	508	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632765	23632765	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	84	847	0	ENST00000261584.4:c.3031G>A	p.Glu1011Lys	p.E1011K	ENST00000261584	NM_024675.3	1011	Gag/Aag	10/13	0.16563695853394	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.731642522179265	0		847	492	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132613	67132613	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	209	781	0	ENST00000412916.2:c.496G>A	p.Ala166Thr	p.A166T	ENST00000412916		166	Gca/Aca	6/6	0.16563695853394	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.731642522179265	0		781	651	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868289	37868289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	59	434	0	ENST00000269571.5:c.1010C>T	p.Pro337Leu	p.P337L	ENST00000269571		337	cCc/cTc	8/27	1	2	FACETS	0.911	0.799	1	0.911	0.799	1	CLONAL	1	TRUE	1	0.731642522179265	2		434	177	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56798144	56798144	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	58	1037	0	ENST00000337432.4:c.875G>A	p.Arg292Lys	p.R292K	ENST00000337432	NM_058216.2	292	aGa/aAa	6/9	1	2	FACETS	0.259	0.222	0.3	0.259	0.222	0.3	SUBCLONAL	1	TRUE	1	0.731642522179265	2		1037	611	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096996	11096996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	32	963	0	ENST00000358026.2:c.487G>A	p.Gly163Arg	p.G163R	ENST00000358026	NM_001128849.1	163	Ggg/Agg	4/36	0.224551110907045	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.731642522179265	0		963	335	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730795	40730795	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	104	481	0	ENST00000373198.4:c.3740C>T	p.Ser1247Phe	p.S1247F	ENST00000373198	NM_133170.3	1247	tCc/tTc	27/32	1	2	FACETS	0.994	0.903	1	0.994	0.903	1	CLONAL	1	TRUE	1	0.731642522179265	2		481	286	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564477	41564477	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	231	787	0	ENST00000263253.7:c.3899C>T	p.Thr1300Ile	p.T1300I	ENST00000263253	NM_001429.3	1300	aCc/aTc	24/31	1	2	FACETS	0.971	0.911	1	0.971	0.911	1	CLONAL	1	TRUE	1	0.731642522179265	2		787	650	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574571	41574571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1338889339	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	32	859	0	ENST00000263253.7:c.6856C>T	p.Pro2286Ser	p.P2286S	ENST00000263253	NM_001429.3	2286	Cca/Tca	31/31	1	2	FACETS	0.233	0.189	0.283	0.233	0.189	0.283	SUBCLONAL	1	TRUE	1	0.731642522179265	2		859	375	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222169	53222169	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	32	557	0	ENST00000375401.3:c.4663C>T	p.Pro1555Ser	p.P1555S	ENST00000375401	NM_004187.3	1555	Ccg/Tcg	26/26	0.731642522179265	1	FACETS	0.37	0.304	0.442	0.37	0.304	0.442	SUBCLONAL	1	TRUE	0	0.731642522179265	1		557	150	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439690	51439691	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	191	512	0	ENST00000262662.1:c.256_257del	p.Leu86ThrfsTer9	p.L86Tfs*9	ENST00000262662		85	acTTta/acta	4/4	0.729063883324684	1	FACETS	0.892	0.839	0.946	0.892	0.839	0.946	CLONAL	1	TRUE	0	0.731642522179265	1		512	371	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794730	42794731	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs35068781	NA	P-0001420-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	109	692	0	ENST00000575354.2:c.1813dup	p.Ser605LysfsTer85	p.S605Kfs*85	ENST00000575354	NM_015125.3	604	gaa/gAaa	10/20	0.731642522179265	1	FACETS	0.863	0.793	0.932	0.863	0.793	0.932	CLONAL	1	TRUE	0	0.731642522179265	1		692	219	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001425-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	50	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.266271754709448	2		422	294	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0001425-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	213	434	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.266271754709448	2	FACETS	0.925	0.861	0.991	0.925	0.861	0.991	CLONAL	2	TRUE	0	0.266271754709448	2		434	865	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579845	7579845	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001425-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	165	666	0	ENST00000269305.4:c.68G>A	p.Trp23Ter	p.W23*	ENST00000269305	NM_001126112.2	23	tGg/tAg	2/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.266271754709448	2		666	1188	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931740	39931740	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001425-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1469	337	997	0	ENST00000378444.4:c.2859A>T	p.Lys953Asn	p.K953N	ENST00000378444	NM_001123385.1	953	aaA/aaT	4/15	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.266271754709448	2		997	1806	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667633	29667633	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001425-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	212	593	0	ENST00000356175.3:c.6971del	p.Leu2324Ter	p.L2324*	ENST00000356175	NM_000267.3	2323	acT/ac	46/57	0.266271754709448	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.266271754709448	1		593	1155	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001434-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	96	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.919	0.833	1	1	0.987	1	CLONAL	2	TRUE	1	0.42118953223591	2		422	248	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0001434-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	138	1091	1	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	0.414159657070465	1	FACETS	0.854	0.78	0.931	0.854	0.78	0.931	CLONAL	1	TRUE	0	0.42118953223591	1		1092	606	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578424	7578425	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0001434-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	194	836	0	ENST00000269305.4:c.505_506del	p.Met169AspfsTer11	p.M169Dfs*11	ENST00000269305	NM_001126112.2	169	ATg/g	5/11	0.414159657070465	1	FACETS	0.801	0.749	0.853	1	0.993	1	CLONAL	2	TRUE	0	0.42118953223591	1		836	454	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001453-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	130	422	0				ENST00000310581	NM_198253.2	-/1132			0.773726125065191	6	FACETS	0.986	0.921	1			1	CLONAL	4	TRUE	NA	0.773726125065191	6		422	217	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251668	212251668	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1401131440	NA	P-0001453-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	182	402	0	ENST00000342788.4:c.3391G>A	p.Asp1131Asn	p.D1131N	ENST00000342788	NM_005235.2	1131	Gac/Aac	27/28	0.773726125065191	2	FACETS	0.69	0.639	0.743	0.345	0.319	0.372	SUBCLONAL	1	TRUE	0	0.773726125065191	2		402	682	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376288	225376288	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001453-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	160	450	0	ENST00000264414.4:c.666G>C	p.Gln222His	p.Q222H	ENST00000264414	NM_003590.4	222	caG/caC	6/16	0.773726125065191	2	FACETS	0.546	0.501	0.592	0.273	0.25	0.296	SUBCLONAL	1	TRUE	0	0.773726125065191	2		450	758	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584437	52584437	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001453-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	69	269	0	ENST00000394830.3:c.4576G>C	p.Ala1526Pro	p.A1526P	ENST00000394830	NM_018313.4	1526	Gct/Cct	29/30	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.773726125065191	NA		269	847	SUCCESS
APC	324	MSKCC	GRCh37	5	112111409	112111409	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001453-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	249	415	0	ENST00000257430.4:c.506T>C	p.Ile169Thr	p.I169T	ENST00000257430	NM_000038.5	169	aTa/aCa	5/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.773726125065191	2		415	622	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860620	151860620	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001453-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	285	567	0	ENST00000262189.6:c.10042C>A	p.Pro3348Thr	p.P3348T	ENST00000262189	NM_170606.2	3348	Cct/Act	43/59	0.773726125065191	3	FACETS	0.919	0.864	0.975	0.459	0.432	0.488	CLONAL	1	TRUE	1	0.773726125065191	3		567	1112	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133738211	133738211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370646520	NA	P-0001453-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	82	385	0	ENST00000318560.5:c.611C>T	p.Thr204Met	p.T204M	ENST00000318560	NM_005157.4	204	aCg/aTg	4/11	0.773726125065191	3	FACETS	0.422	0.372	0.476	0.211	0.186	0.238	SUBCLONAL	1	TRUE	1	0.773726125065191	3		385	697	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593519	48593519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001453-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	43	314	0	ENST00000342988.3:c.1270G>A	p.Asp424Asn	p.D424N	ENST00000342988	NM_005359.5	424	Gat/Aat	10/12	0.773726125065191	3	FACETS	0.193	0.16	0.229	0.096	0.08	0.115	SUBCLONAL	1	TRUE	1	0.773726125065191	3		314	800	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168953	11168953	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1303255317	NA	P-0001453-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	109	274	0	ENST00000358026.2:c.4543G>A	p.Glu1515Lys	p.E1515K	ENST00000358026	NM_001128849.1	1515	Gag/Aag	32/36	0.773726125065191	3	FACETS	0.972	0.88	1	0.486	0.44	0.534	CLONAL	1	TRUE	1	0.773726125065191	3		274	402	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879961	44879961	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001453-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	350	253	0	ENST00000377967.4:c.550G>C	p.Glu184Gln	p.E184Q	ENST00000377967	NM_021140.2	184	Gag/Cag	6/29	0.43407044513663	2	FACETS	0.75	0.719	0.781			1	INDETERMINATE	2	TRUE	NA	0.773726125065191	2		253	603	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247360	153247361	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0001453-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	35	251	0	ENST00000281708.4:c.1441_1442del	p.Ala481HisfsTer3	p.A481Hfs*3	ENST00000281708	NM_033632.3	481	GCc/c	10/12	0.773726125065191	3	FACETS	0.199	0.162	0.24	0.099	0.081	0.12	SUBCLONAL	1	TRUE	1	0.773726125065191	3		251	631	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	39	139	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.236065205817	2		139	243	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	38	101	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.236065205817	1	FACETS	0.83	0.696	0.976	1	0.962	1	CLONAL	2	TRUE	0	0.236065205817	1		101	171	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871292	35871292	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	39	339	0	ENST00000303115.3:c.514G>A	p.Glu172Lys	p.E172K	ENST00000303115	NM_002185.3	172	Gaa/Aaa	4/8	1	2	FACETS	0.789	0.654	0.938	0.789	0.654	0.938	CLONAL	1	TRUE	1	0.236065205817	2		339	419	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533791	63533791	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779863826	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	75	389	0	ENST00000307078.5:c.1363C>T	p.Pro455Ser	p.P455S	ENST00000307078	NM_004655.3	455	Cca/Tca	6/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.236065205817	2		389	526	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466293	120466293	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866874822	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	47	372	0	ENST00000256646.2:c.4826C>T	p.Ser1609Phe	p.S1609F	ENST00000256646	NM_024408.3	1609	tCc/tTc	26/34	1	2	FACETS	0.785	0.663	0.921	0.785	0.663	0.921	CLONAL	1	TRUE	1	0.236065205817	2		372	507	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837913	156837913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	50	390	0	ENST00000524377.1:c.446C>T	p.Pro149Leu	p.P149L	ENST00000524377	NM_002529.3	149	cCt/cTt	5/17	0.134913372358493	3	FACETS	0.594	0.503	0.695	0.198	0.167	0.232	INDETERMINATE	1	TRUE	0	0.236065205817	3		390	797	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25990587	25990587	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	41	322	0	ENST00000435504.4:c.640G>A	p.Glu214Lys	p.E214K	ENST00000435504		214	Gaa/Aaa	8/13	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.236065205817	2		322	330	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190717435	190717435	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	82	463	0	ENST00000441310.2:c.754C>T	p.Leu252Phe	p.L252F	ENST00000441310	NM_000534.4	252	Ctt/Ttt	7/13	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.236065205817	2		463	628	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735407	204735407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs606231422	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	62	253	0	ENST00000302823.3:c.208C>T	p.Arg70Trp	p.R70W	ENST00000302823	NM_005214.4	70	Cgg/Tgg	2/4	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.236065205817	2		253	428	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248738	212248738	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	60	354	0	ENST00000342788.4:c.3529A>T	p.Asn1177Tyr	p.N1177Y	ENST00000342788	NM_005235.2	1177	Aat/Tat	28/28	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.236065205817	2		354	505	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670400	134670400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	53	409	0	ENST00000398015.3:c.311G>A	p.Gly104Glu	p.G104E	ENST00000398015	NM_004441.4	104	gGa/gAa	3/16	0.214207192742454	1	FACETS	0.784	0.669	0.91	0.784	0.669	0.91	CLONAL	1	TRUE	0	0.236065205817	1		409	505	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188397	142188397	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1169255490	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	44	324	1	ENST00000350721.4:c.6334C>T	p.Arg2112Cys	p.R2112C	ENST00000350721	NM_001184.3	2112	Cgt/Tgt	38/47	0.214207192742454	1	FACETS	0.852	0.716	1	0.852	0.716	1	CLONAL	1	TRUE	0	0.236065205817	1		325	386	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146382	185146382	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	42	210	0	ENST00000265026.3:c.13C>T	p.Gln5Ter	p.Q5*	ENST00000265026	NM_004721.4	5	Cag/Tag	2/14	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.236065205817	2		210	324	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161310	185161310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764242255	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	69	500	0	ENST00000265026.3:c.737G>A	p.Arg246Gln	p.R246Q	ENST00000265026	NM_004721.4	246	cGa/cAa	4/14	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.236065205817	2		500	552	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586482	189586482	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	26	159	0	ENST00000264731.3:c.1106A>T	p.Lys369Met	p.K369M	ENST00000264731	NM_003722.4	369	aAg/aTg	8/14	1	2	FACETS	0.737	0.584	0.911	0.737	0.584	0.911	CLONAL	1	TRUE	1	0.236065205817	2		159	299	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587118	189587118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761885185	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	54	352	2	ENST00000264731.3:c.1135C>T	p.Arg379Cys	p.R379C	ENST00000264731	NM_003722.4	379	Cgt/Tgt	9/14	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.236065205817	2		354	436	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1800980	1800980	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	90	438	1	ENST00000260795.2:c.110-1G>A		p.X37_splice	ENST00000260795		37			1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.236065205817	2		439	677	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948209	55948209	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	46	450	0	ENST00000263923.4:c.3763-1G>A		p.X1255_splice	ENST00000263923	NM_002253.2	1255			1	2	FACETS	0.904	0.763	1	0.904	0.763	1	CLONAL	1	TRUE	1	0.236065205817	2		450	431	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106162522	106162522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	52	341	0	ENST00000380013.4:c.3436C>T	p.Pro1146Ser	p.P1146S	ENST00000380013	NM_001127208.2	1146	Cct/Tct	4/11	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.236065205817	2		341	425	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557896	187557896	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	96	547	0	ENST00000441802.2:c.3815A>C	p.Tyr1272Ser	p.Y1272S	ENST00000441802	NM_005245.3	1272	tAt/tCt	5/27	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.236065205817	2		547	749	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295253	1295253	+	upstream_gene_variant	5'Flank	SNP	G	G	C	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	41	142	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.236065205817	2		142	262	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867535	35867535	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	29	380	0	ENST00000303115.3:c.349A>G	p.Thr117Ala	p.T117A	ENST00000303115	NM_002185.3	117	Acc/Gcc	3/8	1	2	FACETS	0.494	0.396	0.607	0.494	0.396	0.607	SUBCLONAL	1	TRUE	1	0.236065205817	2		380	497	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155705	56155705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	48	280	0	ENST00000399503.3:c.797C>T	p.Ser266Phe	p.S266F	ENST00000399503	NM_005921.1	266	tCt/tTt	3/20	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.236065205817	2		280	379	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505141	149505141	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	87	443	0	ENST00000261799.4:c.1675-1G>A		p.X559_splice	ENST00000261799	NM_002609.3	559			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.236065205817	2		443	640	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673367	30673367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	112	579	0	ENST00000376406.3:c.3593C>T	p.Thr1198Ile	p.T1198I	ENST00000376406	NM_014641.2	1198	aCc/aTc	10/15	0.236065205817	3	FACETS	1	0.956	1	0.558	0.501	0.618	CLONAL	1	TRUE	1	0.236065205817	3		579	951	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675160	30675161	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	122	457	0	ENST00000376406.3:c.3084_3084+1delinsAA		p.X1028_splice	ENST00000376406	NM_014641.2	1028		9/15	0.236065205817	3	FACETS	0.762	0.689	0.839	0.762	0.689	0.839	SUBCLONAL	2	TRUE	1	0.236065205817	3		457	758	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679804	30679804	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	80	434	0	ENST00000376406.3:c.1915C>T	p.Pro639Ser	p.P639S	ENST00000376406	NM_014641.2	639	Cct/Tct	5/15	0.236065205817	3	FACETS	1	0.934	1	0.547	0.481	0.617	CLONAL	1	TRUE	1	0.236065205817	3		434	693	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170217	32170217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	119	274	0	ENST00000375023.3:c.3391C>T	p.Pro1131Ser	p.P1131S	ENST00000375023	NM_004557.3	1131	Cct/Tct	21/30	0.236065205817	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.236065205817	3		274	482	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710822	117710822	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	54	432	0	ENST00000368508.3:c.1450G>A	p.Gly484Ser	p.G484S	ENST00000368508	NM_002944.2	484	Ggc/Agc	12/43	0.236065205817	1	FACETS	0.753	0.643	0.873	0.753	0.643	0.873	SUBCLONAL	1	TRUE	0	0.236065205817	1		432	536	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622275	162622275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	75	364	0	ENST00000366898.1:c.422C>T	p.Ser141Leu	p.S141L	ENST00000366898	NM_004562.2	141	tCa/tTa	4/12	0.127161256387049	3	FACETS	1	0.974	1	0.722	0.634	0.816	INDETERMINATE	1	TRUE	1	0.236065205817	3		364	492	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152009005	152009005	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	51	343	0	ENST00000262189.6:c.617T>C	p.Val206Ala	p.V206A	ENST00000262189	NM_170606.2	206	gTa/gCa	5/59	0.236065205817	3	FACETS	0.901	0.766	1	0.451	0.383	0.525	CLONAL	1	TRUE	1	0.236065205817	3		343	536	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528768	8528768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	54	326	0	ENST00000356435.5:c.364C>T	p.Pro122Ser	p.P122S	ENST00000356435		122	Ccc/Tcc	4/35	0.236065205817	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	0	0.236065205817	1		326	377	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636794	8636794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	51	407	0	ENST00000356435.5:c.115G>A	p.Gly39Arg	p.G39R	ENST00000356435		39	Gga/Aga	2/35	0.236065205817	1	FACETS	0.82	0.697	0.953	0.82	0.697	0.953	CLONAL	1	TRUE	0	0.236065205817	1		407	465	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36846865	36846866	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	61	378	0	ENST00000358127.4:c.1073_1074delinsAA	p.Trp358Ter	p.W358*	ENST00000358127	NM_001280556.1	358	tGG/tAA	9/10	0.236065205817	1	FACETS	0.952	0.822	1	0.952	0.822	1	CLONAL	1	TRUE	0	0.236065205817	1		378	479	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115783	8115783	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	104	739	0	ENST00000346208.3:c.1129A>T	p.Lys377Ter	p.K377*	ENST00000346208		377	Aaa/Taa	6/6	1	2	FACETS	0.939	0.84	1	0.939	0.84	1	CLONAL	1	TRUE	1	0.236065205817	2		739	938	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852470	63852470	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	82	359	0	ENST00000279873.7:c.3248C>T	p.Ser1083Phe	p.S1083F	ENST00000279873	NM_032199.2	1083	tCc/tTc	10/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.236065205817	2		359	563	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194200	94194200	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1431841510	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	123	561	0	ENST00000323929.3:c.1228G>A	p.Glu410Lys	p.E410K	ENST00000323929	NM_005591.3	410	Gaa/Aaa	12/20	0.236065205817	2	FACETS	0.832	0.755	0.914	0.832	0.755	0.914	CLONAL	2	TRUE	0	0.236065205817	2		561	626	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442485	49442485	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	69	560	0	ENST00000301067.7:c.4088C>T	p.Thr1363Ile	p.T1363I	ENST00000301067	NM_003482.3	1363	aCc/aTc	13/54	1	2	FACETS	0.886	0.771	1	0.886	0.771	1	CLONAL	1	TRUE	1	0.236065205817	2		560	660	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444514	49444514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	55	224	0	ENST00000301067.7:c.2857C>T	p.Pro953Ser	p.P953S	ENST00000301067	NM_003482.3	953	Cct/Tct	11/54	1	2	FACETS	0.963	0.825	1	0.963	0.825	1	CLONAL	1	TRUE	1	0.236065205817	2		224	484	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446060	49446060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs971609864	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	67	350	0	ENST00000301067.7:c.1406C>T	p.Pro469Leu	p.P469L	ENST00000301067	NM_003482.3	469	cCa/cTa	10/54	1	2	FACETS	0.913	0.793	1	0.913	0.793	1	CLONAL	1	TRUE	1	0.236065205817	2		350	622	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56477676	56477676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	64	366	0	ENST00000267101.3:c.224C>T	p.Ser75Phe	p.S75F	ENST00000267101	NM_001982.3	75	tCc/tTc	2/28	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.236065205817	2		366	501	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110068	115110068	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs971835561	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	36	209	0	ENST00000257566.3:c.1810C>T	p.Pro604Ser	p.P604S	ENST00000257566	NM_016569.3	604	Ccc/Tcc	8/8	NA	2	FACETS	0.944	0.779	1			1	INDETERMINATE	1	TRUE	NA	0.236065205817	2		209	323	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110091	115110091	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	26	189	0	ENST00000257566.3:c.1787C>T	p.Pro596Leu	p.P596L	ENST00000257566	NM_016569.3	596	cCt/cTt	8/8	NA	2	FACETS	0.878	0.698	1			1	INDETERMINATE	1	TRUE	NA	0.236065205817	2		189	251	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877480	28877480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	49	308	0	ENST00000282397.4:c.3841G>A	p.Glu1281Lys	p.E1281K	ENST00000282397	NM_002019.4	1281	Gag/Aag	30/30	0.236065205817	1	FACETS	0.889	0.754	1	0.889	0.754	1	CLONAL	1	TRUE	0	0.236065205817	1		308	412	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465501	99465501	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	155	398	1	ENST00000268035.6:c.2326C>T	p.Pro776Ser	p.P776S	ENST00000268035	NM_000875.3	776	Cct/Tct	11/21	1	2	FACETS	0.926	0.85	1	1	0.991	1	CLONAL	2	TRUE	1	0.236065205817	2		399	709	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347900	347900	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	154	767	0	ENST00000262320.3:c.1606C>T	p.His536Tyr	p.H536Y	ENST00000262320	NM_003502.3	536	Cac/Tac	6/11	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.236065205817	2		767	918	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226314	2226314	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	93	345	1	ENST00000326181.6:c.1927C>T	p.Gln643Ter	p.Q643*	ENST00000326181	NM_032271.2	643	Cag/Tag	20/21	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.236065205817	2		346	691	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807367	3807367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	57	227	0	ENST00000262367.5:c.3620C>T	p.Ser1207Phe	p.S1207F	ENST00000262367	NM_004380.2	1207	tCc/tTc	19/31	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.236065205817	2		227	482	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560175	29560175	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	45	263	0	ENST00000356175.3:c.3652C>T	p.Gln1218Ter	p.Q1218*	ENST00000356175	NM_000267.3	1218	Caa/Taa	27/57	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.236065205817	2		263	363	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670026	29670026	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	70	392	0	ENST00000356175.3:c.7000-1G>A		p.X2334_splice	ENST00000356175	NM_000267.3	2334			1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.236065205817	2		392	509	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682333	37682333	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	64	467	0	ENST00000447079.4:c.3524C>T	p.Pro1175Leu	p.P1175L	ENST00000447079	NM_015083.1	1175	cCa/cTa	13/14	1	2	FACETS	0.997	0.864	1	0.997	0.864	1	CLONAL	1	TRUE	1	0.236065205817	2		467	544	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876557	59876557	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	54	456	0	ENST00000259008.2:c.1244T>C	p.Leu415Pro	p.L415P	ENST00000259008	NM_032043.2	415	cTt/cCt	9/20	1	2	FACETS	0.86	0.735	0.997	0.86	0.735	0.997	CLONAL	1	TRUE	1	0.236065205817	2		456	532	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550301	39550301	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	51	408	0	ENST00000262039.4:c.412C>A	p.Gln138Lys	p.Q138K	ENST00000262039	NM_002647.2	138	Caa/Aaa	4/25	1	2	FACETS	0.915	0.779	1	0.915	0.779	1	CLONAL	1	TRUE	1	0.236065205817	2		408	472	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57567469	57567469	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	45	233	0	ENST00000316660.6:c.58+2T>C		p.X20_splice	ENST00000316660	NM_021127.2	20			1	2	FACETS	0.885	0.744	1	0.885	0.744	1	CLONAL	1	TRUE	1	0.236065205817	2		233	431	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222230	2222230	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759868765	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	163	462	0	ENST00000398665.3:c.3062C>T	p.Pro1021Leu	p.P1021L	ENST00000398665	NM_032482.2	1021	cCc/cTc	24/28	0.182500383867572	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	2	TRUE	0	0.236065205817	2		462	687	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226953	2226953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	32	217	0	ENST00000398665.3:c.4433C>T	p.Pro1478Leu	p.P1478L	ENST00000398665	NM_032482.2	1478	cCc/cTc	27/28	0.182500383867572	2	FACETS	0.566	0.459	0.687	0.283	0.229	0.344	SUBCLONAL	1	TRUE	0	0.236065205817	2		217	479	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210733	5210733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779302415	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	171	490	0	ENST00000357368.4:c.5318C>T	p.Ser1773Leu	p.S1773L	ENST00000357368	NM_002850.3	1773	tCg/tTg	34/38	0.182500383867572	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	2	TRUE	0	0.236065205817	2		490	718	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248611	10248611	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	138	386	0	ENST00000340748.4:c.4142C>T	p.Ala1381Val	p.A1381V	ENST00000340748		1381	gCc/gTc	35/40	0.182500383867572	2	FACETS	0.878	0.801	0.958	0.878	0.801	0.958	CLONAL	2	TRUE	0	0.236065205817	2		386	666	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141523	11141523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1192589668	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	50	432	1	ENST00000358026.2:c.3500C>T	p.Ser1167Leu	p.S1167L	ENST00000358026	NM_001128849.1	1167	tCg/tTg	25/36	0.182500383867572	2	FACETS	0.601	0.509	0.703	0.3	0.254	0.352	SUBCLONAL	1	TRUE	0	0.236065205817	2		433	705	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292570	15292570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	131	308	0	ENST00000263388.2:c.2609C>T	p.Ser870Phe	p.S870F	ENST00000263388	NM_000435.2	870	tCc/tTc	17/33	0.182500383867572	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	0	0.236065205817	2		308	492	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741880	40741880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	169	475	0	ENST00000392038.2:c.1092G>A	p.Met364Ile	p.M364I	ENST00000392038	NM_001626.4	364	atG/atA	11/14	0.182500383867572	2	FACETS	0.894	0.823	0.968	0.894	0.823	0.968	CLONAL	2	TRUE	0	0.236065205817	2		475	801	SUCCESS
AXL	558	MSKCC	GRCh37	19	41736898	41736898	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	198	548	0	ENST00000301178.4:c.613T>A	p.Cys205Ser	p.C205S	ENST00000301178	NM_021913.4	205	Tgc/Agc	5/20	0.182500383867572	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.236065205817	2		548	796	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561418	9561418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	50	374	0	ENST00000353224.5:c.364G>A	p.Glu122Lys	p.E122K	ENST00000353224	NM_177990.2	122	Gaa/Aaa	4/10	1	2	FACETS	0.78	0.662	0.91	0.78	0.662	0.91	CLONAL	1	TRUE	1	0.236065205817	2		374	543	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899063	40899063	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	86	642	0	ENST00000373198.4:c.2207G>T	p.Gly736Val	p.G736V	ENST00000373198	NM_133170.3	736	gGg/gTg	14/32	1	2	FACETS	0.975	0.862	1	0.975	0.862	1	CLONAL	1	TRUE	1	0.236065205817	2		642	747	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944374	40944374	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	52	317	0	ENST00000373198.4:c.2128A>C	p.Lys710Gln	p.K710Q	ENST00000373198	NM_133170.3	710	Aaa/Caa	12/32	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.236065205817	2		317	382	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306689	41306689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868376470	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	80	350	0	ENST00000373198.4:c.970G>A	p.Glu324Lys	p.E324K	ENST00000373198	NM_133170.3	324	Gaa/Aaa	7/32	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.236065205817	2		350	578	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817359	39817359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142996574	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	45	414	0	ENST00000288319.7:c.204G>A	p.Met68Ile	p.M68I	ENST00000288319	NM_182918.3	68	atG/atA	2/10	0.127161256387049	3	FACETS	0.743	0.623	0.875	0.371	0.311	0.438	INDETERMINATE	1	TRUE	1	0.236065205817	3		414	574	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817382	39817382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	56	402	0	ENST00000288319.7:c.181C>T	p.Pro61Ser	p.P61S	ENST00000288319	NM_182918.3	61	Cca/Tca	2/10	0.127161256387049	3	FACETS	0.946	0.81	1	0.473	0.405	0.547	INDETERMINATE	1	TRUE	1	0.236065205817	3		402	561	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357199	70357199	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001485-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	89	312	0	ENST00000374080.3:c.5714T>G	p.Val1905Gly	p.V1905G	ENST00000374080		1905	gTg/gGg	39/45	0.236065205817	0	FACETS	1	0.971	1			1	CLONAL	1	TRUE	NA	0.236065205817	0		312	452	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001487-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	20	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.845	1			1	INDETERMINATE	1	TRUE	NA	0.557270813751958	2		422	66	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416417	49416417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565753611	NA	P-0001487-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	63	481	0	ENST00000301067.7:c.16294C>T	p.Arg5432Trp	p.R5432W	ENST00000301067	NM_003482.3	5432	Cgg/Tgg	51/54	1	2	FACETS	0.86	0.751	0.975	0.86	0.751	0.975	CLONAL	1	TRUE	1	0.557270813751958	2		481	263	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913371	28913371	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001487-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	54	590	1	ENST00000282397.4:c.2422G>T	p.Glu808Ter	p.E808*	ENST00000282397	NM_002019.4	808	Gag/Tag	17/30	0.139146008119405	0	FACETS	0.401	0.347	0.459			1	INDETERMINATE	1	TRUE	0	0.557270813751958	0		591	214	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0001497-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	27	275	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	1	2	FACETS	0.445	0.355	0.548	0.445	0.355	0.548	SUBCLONAL	1	TRUE	1	0.432934059250557	2		275	280	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0001497-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	159	479	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.254172257117214	3	FACETS	1	0.966	1	1	0.966	1	INDETERMINATE	2	TRUE	1	0.432934059250557	3		480	417	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936095	178936095	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397517201	NA	P-0001497-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	31	116	0	ENST00000263967.3:c.1637A>G	p.Gln546Arg	p.Q546R	ENST00000263967	NM_006218.2	546	cAg/cGg	10/21	0.112415397606615	5	FACETS	1	0.943	1			1	INDETERMINATE	1	TRUE	NA	0.432934059250557	5		116	161	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001501-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	47	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.95	1			1	INDETERMINATE	1	TRUE	NA	0.618201247070521	2		422	124	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0001501-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	89	244	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.618201247070521	1	FACETS	0.938	0.85	1	0.938	0.85	1	CLONAL	1	TRUE	0	0.618201247070521	1		244	212	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249010	55249011	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACAACCCCC	rs397517115	NA	P-0001501-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	269	324	0	ENST00000275493.2:c.2311_2319dup	p.Asn771_His773dup	p.N771_H773dup	ENST00000275493	NM_005228.3	771	gac/gACAACCCCCac	20/28	0.582789843919114	4	FACETS	0.914	0.861	0.968	0.61	0.574	0.646	CLONAL	2	TRUE	1	0.618201247070521	4		324	770	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023039	27023039	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001501-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	55	25	0	ENST00000324856.7:c.145G>T	p.Glu49Ter	p.E49*	ENST00000324856	NM_006015.4	49	Gaa/Taa	1/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.618201247070521	2		25	135	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431640	6431640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001501-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	253	268	0	ENST00000356142.4:c.193G>A	p.Asp65Asn	p.D65N	ENST00000356142	NM_018890.3	65	Gac/Aac	3/7	0.582789843919114	4	FACETS	0.786	0.737	0.835	0.524	0.491	0.557	SUBCLONAL	2	TRUE	1	0.618201247070521	4		268	843	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958409	90958409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881856	NA	P-0001501-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	111	429	0	ENST00000265433.3:c.2029G>A	p.Asp677Asn	p.D677N	ENST00000265433	NM_002485.4	677	Gat/Aat	13/16	0.260899236613613	4	FACETS	0.613	0.55	0.68	0.306	0.275	0.34	INDETERMINATE	1	TRUE	2	0.618201247070521	4		429	948	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427975	49427975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001501-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	277	428	0	ENST00000301067.7:c.10615C>T	p.Arg3539Trp	p.R3539W	ENST00000301067	NM_003482.3	3539	Cgg/Tgg	38/54	0.195573159108464	4	FACETS	1	0.965	1	1	0.965	1	INDETERMINATE	2	TRUE	2	0.618201247070521	4		428	705	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447019	49447019	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001501-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	194	328	0	ENST00000301067.7:c.925G>T	p.Glu309Ter	p.E309*	ENST00000301067	NM_003482.3	309	Gaa/Taa	7/54	0.195573159108464	4	FACETS	0.885	0.824	0.947	0.885	0.824	0.947	INDETERMINATE	2	TRUE	2	0.618201247070521	4		328	574	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574580	41574580	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001501-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	80	525	2	ENST00000263253.7:c.6865G>T	p.Ala2289Ser	p.A2289S	ENST00000263253	NM_001429.3	2289	Gcc/Tcc	31/31	1	2	FACETS	0.383	0.337	0.432	0.383	0.337	0.432	SUBCLONAL	1	TRUE	1	0.618201247070521	2		527	676	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651953	36651974	+	frameshift_variant	Frame_Shift_Del	DEL	GGACAGCGAGCAGCTGAGCCGC	GGACAGCGAGCAGCTGAGCCGC	-	novel	NA	P-0001501-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	39	253	0	ENST00000244741.5:c.76_97del	p.Asp26ThrfsTer5	p.D26Tfs*5	ENST00000244741	NM_000389.4	25	gtGGACAGCGAGCAGCTGAGCCGC/gt	2/3	0.618201247070521	4	FACETS	0.409	0.339	0.488			1	SUBCLONAL	1	TRUE	NA	0.618201247070521	4		253	499	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652147	36652148	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0001501-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	199	342	0	ENST00000244741.5:c.270dup	p.Gly91ArgfsTer38	p.G91Rfs*38	ENST00000244741	NM_000389.4	90	gga/ggAa	2/3	0.618201247070521	4	FACETS	0.919	0.857	0.982			1	CLONAL	2	TRUE	NA	0.618201247070521	4		342	567	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426069	49426070	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0001501-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	116	314	0	ENST00000301067.7:c.12418dup	p.Ser4140PhefsTer28	p.S4140Ffs*28	ENST00000301067	NM_003482.3	4140	tcc/tTcc	39/54	0.195573159108464	4	FACETS	0.87	0.793	0.949	0.87	0.793	0.949	INDETERMINATE	2	TRUE	2	0.618201247070521	4		314	349	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651921	36651933	+	protein_altering_variant	In_Frame_Del	DEL	AGCAAGGCCTGCC	AGCAAGGCCTGCC	G	novel	NA	P-0001501-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	24	224	0	ENST00000244741.5:c.43_55delinsG	p.Ser15_Arg19delinsGly	p.S15_R19delinsG	ENST00000244741	NM_000389.4	15	AGCAAGGCCTGCCgc/Ggc	2/3	0.618201247070521	4	FACETS	0.267	0.209	0.335			1	SUBCLONAL	1	TRUE	NA	0.618201247070521	4		224	470	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001519-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	27	422	0				ENST00000310581	NM_198253.2	-/1132			0.190343028570111	4	FACETS	0.902	0.729	1	0.902	0.729	1	CLONAL	2	TRUE	2	0.305244399937702	4		422	128	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268200	153268200	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239394845	NA	P-0001519-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	98	346	0	ENST00000281708.4:c.608C>T	p.Ser203Leu	p.S203L	ENST00000281708	NM_033632.3	203	tCa/tTa	4/12	0.138869307986147	3	FACETS	0.916	0.817	1	0.305	0.272	0.341	INDETERMINATE	1	TRUE	0	0.305244399937702	3		346	808	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681925	30681925	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1347359920	NA	P-0001519-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	20	117	0	ENST00000376406.3:c.172C>T	p.Arg58Ter	p.R58*	ENST00000376406	NM_014641.2	58	Cga/Tga	3/15	0.261972463638861	3	FACETS	0.779	0.598	0.987	0.389	0.299	0.494	CLONAL	1	TRUE	1	0.305244399937702	3		117	194	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192371	138192371	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001519-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	36	111	0	ENST00000237289.4:c.7G>A	p.Glu3Lys	p.E3K	ENST00000237289	NM_001270507.1	3	Gaa/Aaa	2/9	0.146633440780631	3	FACETS	0.874	0.721	1	0.437	0.36	0.523	INDETERMINATE	1	TRUE	1	0.305244399937702	3		111	311	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161519	2161519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001519-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	117	447	0	ENST00000434045.2:c.8C>T	p.Ser3Phe	p.S3F	ENST00000434045	NM_001127598.1	3	tCc/tTc	2/5	0.278589987114052	1	FACETS	0.868	0.791	0.949	1	0.988	1	CLONAL	2	TRUE	0	0.305244399937702	1		447	374	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420670	49420670	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs797045659	NA	P-0001519-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	59	218	0	ENST00000301067.7:c.15079C>T	p.Arg5027Ter	p.R5027*	ENST00000301067	NM_003482.3	5027	Cga/Tga	48/54	0.290812339731115	3	FACETS	1	0.97	1	0.743	0.644	0.849	CLONAL	1	TRUE	1	0.305244399937702	3		218	300	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226421	133226421	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001519-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	64	441	0	ENST00000320574.5:c.3637G>C	p.Glu1213Gln	p.E1213Q	ENST00000320574	NM_006231.2	1213	Gag/Cag	30/49	1	2	FACETS	0.896	0.778	1	0.896	0.778	1	CLONAL	1	TRUE	1	0.305244399937702	2		441	468	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579521	7579521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001519-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	74	247	0	ENST00000269305.4:c.166G>T	p.Glu56Ter	p.E56*	ENST00000269305	NM_001126112.2	56	Gaa/Taa	4/11	0.233114565639666	2	FACETS	0.78	0.689	0.876	0.78	0.689	0.876	SUBCLONAL	2	TRUE	0	0.305244399937702	2		247	311	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433381	49433381	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001519-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	30	203	0	ENST00000301067.7:c.8066del	p.Leu2689ArgfsTer2	p.L2689Rfs*2	ENST00000301067	NM_003482.3	2689	cTg/cg	32/54	0.290812339731115	3	FACETS	1	0.863	1	0.539	0.438	0.653	CLONAL	1	TRUE	1	0.305244399937702	3		203	210	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001523-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	30	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.168154039983333	2		422	254	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0001523-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	32	353	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	0.168154039983333	3	FACETS	0.942	0.764	1	0.471	0.382	0.572	CLONAL	1	TRUE	1	0.168154039983333	3		353	438	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131505	202131505	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001523-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	32	230	0	ENST00000358485.4:c.473C>T	p.Ser158Phe	p.S158F	ENST00000358485	NM_001080125.1	158	tCt/tTt	2/9	0.168154039983333	1	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	0	0.168154039983333	1		230	310	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894230	NA	P-0001523-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	156	350	0	ENST00000451590.1:c.35G>A	p.Gly12Asp	p.G12D	ENST00000451590	NM_001130442.1	12	gGc/gAc	2/5	1	2	FACETS	1	0.955	1	1	0.994	1	CLONAL	3	TRUE	1	0.168154039983333	2		350	586	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417814	32417814	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001523-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	83	379	0	ENST00000332351.3:c.1238G>A	p.Arg413Lys	p.R413K	ENST00000332351	NM_024426.4	413	aGg/aAg	7/10	1	2	FACETS	0.958	0.848	1	1	0.984	1	CLONAL	2	TRUE	1	0.168154039983333	2		379	515	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001527-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	30	422	0				ENST00000310581	NM_198253.2	-/1132			0.3	0	FACETS	0.931	0.784	1			1	CLONAL	3	TRUE	0	0.24	0		422	68	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0001527-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	97	259	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.976	0.891	1	1	0.991	1	CLONAL	4	TRUE	1	0.24	2		259	207	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0001530-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	142	139	0				ENST00000310581	NM_198253.2	-/1132			0.374396505905935	3	FACETS	0.944	0.881	1	0.944	0.881	1	INDETERMINATE	2	TRUE	1	0.837209234481394	3		139	255	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0001530-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	542	270	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.837209234481394	2	FACETS	0.993	0.971	1	0.993	0.971	1	CLONAL	2	TRUE	0	0.837209234481394	2		270	652	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459710	149459710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1187678502	NA	P-0001530-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	334	363	2	ENST00000286301.3:c.497G>A	p.Arg166Lys	p.R166K	ENST00000286301	NM_005211.3	166	aGg/aAg	4/22	0.374396505905935	3	FACETS	0.788	0.751	0.826	0.788	0.751	0.826	INDETERMINATE	2	TRUE	1	0.837209234481394	3		365	718	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735476	204735476	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001530-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	361	369	0	ENST00000302823.3:c.277A>T	p.Asn93Tyr	p.N93Y	ENST00000302823	NM_005214.4	93	Aat/Tat	2/4	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.837209234481394	2		369	821	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562873	176562873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001530-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	515	380	3	ENST00000439151.2:c.769C>T	p.Pro257Ser	p.P257S	ENST00000439151	NM_022455.4	257	Ccc/Tcc	2/23	0.374396505905935	3	FACETS	0.858	0.826	0.89	0.858	0.826	0.89	INDETERMINATE	2	TRUE	1	0.837209234481394	3		383	1017	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575521	64575521	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1565648511	NA	P-0001530-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	434	336	1	ENST00000312049.6:c.496C>T	p.Gln166Ter	p.Q166*	ENST00000312049	NM_130799.2	166	Cag/Tag	3/10	NA	2	FACETS	0.974	0.95	0.998			1	INDETERMINATE	2	TRUE	NA	0.837209234481394	2		337	532	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194142	94194142	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs141293060	NA	P-0001530-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	542	455	2	ENST00000323929.3:c.1286T>C	p.Val429Ala	p.V429A	ENST00000323929	NM_005591.3	429	gTa/gCa	12/20	0.803452380988938	2	FACETS	0.961	0.938	0.982	0.961	0.938	0.982	CLONAL	2	TRUE	0	0.837209234481394	2		457	674	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425424	49425424	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001530-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	431	444	0	ENST00000301067.7:c.13064C>T	p.Pro4355Leu	p.P4355L	ENST00000301067	NM_003482.3	4355	cCt/cTt	39/54	0.357353563844043	3	FACETS	1	0.987	1	0.699	0.673	0.723	INDETERMINATE	2	TRUE	0	0.837209234481394	3		444	697	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290187	15290187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1337527315	NA	P-0001530-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	317	354	0	ENST00000263388.2:c.3448C>T	p.Pro1150Ser	p.P1150S	ENST00000263388	NM_000435.2	1150	Cca/Tca	21/33	0.418163032679003	2	FACETS	1	0.995	1	0.727	0.696	0.757	INDETERMINATE	1	TRUE	0	0.837209234481394	2		354	521	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355050	15355050	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001530-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	225	186	1	ENST00000263377.2:c.2573C>T	p.Ser858Phe	p.S858F	ENST00000263377	NM_058243.2	858	tCt/tTt	13/20	0.418163032679003	2	FACETS	0.772	0.735	0.808	0.772	0.735	0.808	INDETERMINATE	2	TRUE	0	0.837209234481394	2		187	348	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772901	135772902	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0001530-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	651	416	4	ENST00000298552.3:c.2721dup	p.Arg908ThrfsTer42	p.R908Tfs*42	ENST00000298552	NM_001162426.1	907	-/A	21/23	NA	2	FACETS	0.925	0.903	0.945			1	INDETERMINATE	2	TRUE	NA	0.837209234481394	2		420	841	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138507	2138510	+	frameshift_variant	Frame_Shift_Del	DEL	AGCA	AGCA	-	novel	NA	P-0001530-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	250	430	0	ENST00000219476.3:c.5321_5324del	p.Ser1774LysfsTer51	p.S1774Kfs*51	ENST00000219476	NM_000548.3	1774	AGCAaa/aa	42/42	NA	2	FACETS	0.92	0.866	0.975			1	INDETERMINATE	1	TRUE	NA	0.837209234481394	2		430	649	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0001538-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	42	139	0				ENST00000310581	NM_198253.2	-/1132			0.124782104767992	5	FACETS	1	0.953	1			1	INDETERMINATE	1	TRUE	NA	0.360261649275551	5		139	256	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295773	212295773	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1299031105	NA	P-0001538-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	128	492	1	ENST00000342788.4:c.2540G>A	p.Arg847His	p.R847H	ENST00000342788	NM_005235.2	847	cGt/cAt	21/28	0.360261649275551	3	FACETS	1	0.932	1	0.517	0.468	0.568	CLONAL	1	TRUE	1	0.360261649275551	3		493	811	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046357	180046357	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771222400	NA	P-0001538-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	58	271	0	ENST00000261937.6:c.2657C>T	p.Thr886Met	p.T886M	ENST00000261937	NM_182925.4	886	aCg/aTg	19/30	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.360261649275551	2		271	294	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28631594	28631594	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001538-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	54	322	0	ENST00000241453.7:c.374T>A	p.Val125Asp	p.V125D	ENST00000241453	NM_004119.2	125	gTt/gAt	4/24	NA	2	FACETS	0.642	0.549	0.743			1	INDETERMINATE	1	TRUE	NA	0.360261649275551	2		322	467	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15378269	15378269	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs752951417	NA	P-0001538-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	120	686	0	ENST00000263377.2:c.517A>G	p.Ile173Val	p.I173V	ENST00000263377	NM_058243.2	173	Ata/Gta	4/20	1	2	FACETS	0.934	0.845	1	0.934	0.845	1	CLONAL	1	TRUE	1	0.360261649275551	2		686	713	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001557-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	43	422	0				ENST00000310581	NM_198253.2	-/1132			0.44143102963242	6	FACETS	1	0.944	1			1	CLONAL	1	TRUE	NA	0.44143102963242	6		422	283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577018	7577018	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691039	NA	P-0001557-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	198	300	0	ENST00000269305.4:c.919+1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.44143102963242	3	FACETS	1	0.988	1	0.82	0.769	0.872	CLONAL	2	TRUE	0	0.44143102963242	3		300	445	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973259	25973259	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001557-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	47	224	0	ENST00000435504.4:c.1166C>G	p.Ser389Cys	p.S389C	ENST00000435504		389	tCt/tGt	12/13	0.385271700662096	4	FACETS	0.599	0.506	0.703	0.2	0.168	0.235	SUBCLONAL	1	TRUE	1	0.44143102963242	4		224	512	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261571	142261571	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001557-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	280	353	0	ENST00000350721.4:c.3386G>A	p.Gly1129Asp	p.G1129D	ENST00000350721	NM_001184.3	1129	gGc/gAc	17/47	0.44143102963242	7	FACETS	0.959	0.902	1	0.719	0.677	0.762	CLONAL	3	TRUE	3	0.44143102963242	7		353	928	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917537	178917537	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001557-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	55	322	0	ENST00000263967.3:c.412G>T	p.Asp138Tyr	p.D138Y	ENST00000263967	NM_006218.2	138	Gac/Tac	3/21	0.44143102963242	7	FACETS	0.624	0.532	0.725	0.156	0.133	0.182	SUBCLONAL	1	TRUE	3	0.44143102963242	7		322	840	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189874	66189874	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001557-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	64	371	0	ENST00000273854.3:c.3072A>T	p.Gln1024His	p.Q1024H	ENST00000273854	NM_004439.5	1024	caA/caT	18/18	0.44143102963242	3	FACETS	0.581	0.503	0.666			1	SUBCLONAL	1	TRUE	NA	0.44143102963242	3		371	609	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372716	81372716	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001557-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	208	340	0	ENST00000222390.5:c.818C>G	p.Thr273Ser	p.T273S	ENST00000222390	NM_000601.4	273	aCt/aGt	7/18	0.44143102963242	5	FACETS	1	0.96	1	0.696	0.648	0.746	CLONAL	2	TRUE	2	0.44143102963242	5		340	750	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59820373	59820373	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0001557-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	49	347	0	ENST00000259008.2:c.2379+1G>C		p.X793_splice	ENST00000259008	NM_032043.2	793			0.156245480244021	3	FACETS	0.565	0.478	0.659			1	INDETERMINATE	1	TRUE	NA	0.44143102963242	3		347	480	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938389	44938389	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0001557-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	199	219	0	ENST00000377967.4:c.2939-2A>T		p.X980_splice	ENST00000377967	NM_021140.2	980			0.44143102963242	2	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.44143102963242	2		219	369	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089694	27089712	+	frameshift_variant	Frame_Shift_Del	DEL	TGTCCCCCACCAGGGGGCA	TGTCCCCCACCAGGGGGCA	-	novel	NA	P-0001557-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	24	311	0	ENST00000324856.7:c.2652_2670del	p.Cys884Ter	p.C884*	ENST00000324856	NM_006015.4	884	TGTCCCCCACCAGGGGGCAtg/tg	8/20	0.429786453178377	3	FACETS	0.278	0.217	0.349	0.139	0.108	0.175	SUBCLONAL	1	TRUE	1	0.44143102963242	3		311	477	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288659	198288661	+	missense_variant	Missense_Mutation	TNP	GCC	GCC	AAA	novel	NA	P-0001557-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	44	422	0	ENST00000335508.6:c.66_68delinsTTT	p.Lys22_Ala23delinsAsnLeu	p.K22_A23delinsNL	ENST00000335508	NM_012433.2	22	aaGGCa/aaTTTa	2/25	1	2	FACETS	0.41	0.344	0.484	0.41	0.344	0.484	SUBCLONAL	1	TRUE	1	0.44143102963242	2		422	486	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157256627	157256628	+	missense_variant	Missense_Mutation	DNP	AG	AG	TT	novel	NA	P-0001557-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	50	380	0	ENST00000346085.5:c.1954_1955delinsTT	p.Arg652Leu	p.R652L	ENST00000346085	NM_020732.3	652	AGa/TTa	5/20	0.385271700662096	4	FACETS	0.494	0.418	0.577	0.165	0.139	0.193	SUBCLONAL	1	TRUE	1	0.44143102963242	4		380	661	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001560-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	113	422	0				ENST00000310581	NM_198253.2	-/1132			0.207463154074556	2	FACETS	1	0.973	1	0.584	0.533	0.636	INDETERMINATE	1	TRUE	0	0.644855415434621	2		422	300	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519990	NA	P-0001560-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	779	531	1	ENST00000269305.4:c.796G>A	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	266	Gga/Aga	8/11	0.619597247468647	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.644855415434621	2		532	1177	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0001560-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	779	270	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.644855415434621	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.644855415434621	3		270	1489	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057724	27057724	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001560-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	979	710	1	ENST00000324856.7:c.1432C>T	p.Pro478Ser	p.P478S	ENST00000324856	NM_006015.4	478	Cct/Tct	3/20	0.644855415434621	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	1	0.644855415434621	3		711	1840	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304216	65304216	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001560-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	938	592	2	ENST00000342505.4:c.2899T>C	p.Tyr967His	p.Y967H	ENST00000342505	NM_002227.2	967	Tat/Cat	21/25	0.644855415434621	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	1	0.644855415434621	3		594	1707	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026826	71026826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001560-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1314	754	603	0	ENST00000318789.4:c.1396C>T	p.Pro466Ser	p.P466S	ENST00000318789	NM_032682.5	466	Cca/Tca	16/21	0.565662377560572	4	FACETS	0.93	0.898	0.962			1	CLONAL	2	TRUE	NA	0.644855415434621	4		603	2068	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119562125	119562125	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001560-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	944	493	0	ENST00000316626.5:c.1211C>T	p.Pro404Leu	p.P404L	ENST00000316626		404	cCc/cTc	11/12	0.644855415434621	3	FACETS	0.93	0.91	0.951	0.93	0.91	0.951	CLONAL	3	TRUE	0	0.644855415434621	3		493	1387	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612137	189612137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001560-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1649	387	552	0	ENST00000264731.3:c.1889C>T	p.Ser630Phe	p.S630F	ENST00000264731	NM_003722.4	630	tCc/tTc	14/14	0.644855415434621	4	FACETS	0.97	0.918	1	0.323	0.306	0.341	CLONAL	1	TRUE	1	0.644855415434621	4		552	2036	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612205	189612205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001560-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1531	360	516	0	ENST00000264731.3:c.1957C>T	p.Pro653Ser	p.P653S	ENST00000264731	NM_003722.4	653	Cca/Tca	14/14	0.644855415434621	4	FACETS	0.971	0.917	1	0.324	0.305	0.343	CLONAL	1	TRUE	1	0.644855415434621	4		516	1891	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873660	35873660	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs201559094	NA	P-0001560-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	351	368	0	ENST00000303115.3:c.616C>T	p.Arg206Ter	p.R206*	ENST00000303115	NM_002185.3	206	Cga/Tga	5/8	0.207463154074556	2	FACETS	1	0.981	1	0.533	0.506	0.561	INDETERMINATE	1	TRUE	0	0.644855415434621	2		368	1021	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047194	180047194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001560-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	292	435	0	ENST00000261937.6:c.2521C>T	p.Pro841Ser	p.P841S	ENST00000261937	NM_182925.4	841	Ccc/Tcc	17/30	0.379945975352666	1	FACETS	0.798	0.754	0.842	0.798	0.754	0.842	INDETERMINATE	1	TRUE	0	0.644855415434621	1		435	769	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513006	106513006	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001560-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	638	444	0	ENST00000359195.3:c.2020G>A	p.Asp674Asn	p.D674N	ENST00000359195	NM_002649.2	674	Gat/Aat	3/11	0.644855415434621	4	FACETS	0.886	0.852	0.92	0.886	0.852	0.92	CLONAL	2	TRUE	2	0.644855415434621	4		444	1837	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859534	151859534	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145646770	NA	P-0001560-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1220	752	560	0	ENST00000262189.6:c.11128G>A	p.Glu3710Lys	p.E3710K	ENST00000262189	NM_170606.2	3710	Gaa/Aaa	43/59	0.644855415434621	4	FACETS	0.973	0.939	1	0.973	0.939	1	CLONAL	2	TRUE	2	0.644855415434621	4		560	1972	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639976	93639976	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001560-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	112	414	0	ENST00000375746.1:c.1305G>A	p.Met435Ile	p.M435I	ENST00000375746	NM_001174167.1	435	atG/atA	10/14	0.619597247468647	2	FACETS	0.398	0.357	0.441	0.199	0.178	0.221	SUBCLONAL	1	TRUE	0	0.644855415434621	2		414	873	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100543	8100543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001560-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	656	545	0	ENST00000346208.3:c.517G>A	p.Ala173Thr	p.A173T	ENST00000346208		173	Gcc/Acc	3/6	0.37096594353204	3	FACETS	0.853	0.828	0.877			1	INDETERMINATE	3	TRUE	NA	0.644855415434621	3		545	1052	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230717	46230717	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001560-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	804	632	0	ENST00000334344.6:c.966T>G	p.Ser322Arg	p.S322R	ENST00000334344	NM_152641.2	322	agT/agG	8/21	0.29100321028388	4	FACETS	0.872	0.846	0.898			1	INDETERMINATE	3	TRUE	NA	0.644855415434621	4		632	1568	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210961	133210961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001560-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	592	465	0	ENST00000320574.5:c.5815G>A	p.Asp1939Asn	p.D1939N	ENST00000320574	NM_006231.2	1939	Gac/Aac	43/49	0.60602923307956	2	FACETS	0.992	0.963	1	0.992	0.963	1	CLONAL	2	TRUE	0	0.644855415434621	2		465	925	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41021723	41021723	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001560-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	460	477	0	ENST00000267868.3:c.665A>C	p.Asp222Ala	p.D222A	ENST00000267868	NM_002875.4	222	gAc/gCc	8/10	0.341644653103889	5	FACETS	0.958	0.914	1	0.639	0.609	0.668	INDETERMINATE	2	TRUE	2	0.644855415434621	5		477	1465	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680721	88680721	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001560-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	319	500	0	ENST00000360948.2:c.536A>T	p.Glu179Val	p.E179V	ENST00000360948	NM_001012338.2	179	gAg/gTg	6/19	0.41764117763426	3	FACETS	1	0.981	1	0.545	0.514	0.576	CLONAL	1	TRUE	1	0.644855415434621	3		500	1201	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743864	41743864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753706427	NA	P-0001560-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	304	501	0	ENST00000301178.4:c.799G>A	p.Asp267Asn	p.D267N	ENST00000301178	NM_021913.4	267	Gat/Aat	7/20	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.644855415434621	2		501	804	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755548	39755548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001560-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	519	496	0	ENST00000288319.7:c.1217C>T	p.Ser406Leu	p.S406L	ENST00000288319	NM_182918.3	406	tCa/tTa	10/10	0.568585960018422	2	FACETS	0.826	0.797	0.856	0.826	0.797	0.856	CLONAL	2	TRUE	0	0.644855415434621	2		496	974	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101053	27101054	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AT	novel	NA	P-0001560-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1277	187	555	0	ENST00000324856.7:c.4335_4336delinsAT	p.Arg1446Ter	p.R1446*	ENST00000324856	NM_006015.4	1445	cgCCga/cgATga	18/20	0.644855415434621	3	FACETS	0.524	0.482	0.567	0.262	0.241	0.284	SUBCLONAL	1	TRUE	1	0.644855415434621	3		555	1464	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201525	133201526	+	missense_variant	Missense_Mutation	DNP	CA	CA	GC	novel	NA	P-0001560-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	539	457	0	ENST00000320574.5:c.6712_6713delinsGC	p.Cys2238Ala	p.C2238A	ENST00000320574	NM_006231.2	2238	TGc/GCc	48/49	0.60602923307956	2	FACETS	0.936	0.905	0.966	0.936	0.905	0.966	CLONAL	2	TRUE	0	0.644855415434621	2		457	893	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001578-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	130	422	0				ENST00000310581	NM_198253.2	-/1132			0.369143392901525	3	FACETS	0.788	0.72	0.859	0.788	0.72	0.859	SUBCLONAL	2	TRUE	1	0.441648248226027	3		422	456	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001578-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	566	368	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	0.368033403198797	5	FACETS	1	0.993	1	0.669	0.644	0.695	CLONAL	3	TRUE	0	0.441648248226027	5		368	1273	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0001578-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	295	394	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.441648248226027	4	FACETS	0.939	0.884	0.994	0.469	0.442	0.497	CLONAL	2	TRUE	0	0.441648248226027	4		396	1026	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0001578-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	268	367	0	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.441648248226027	4	FACETS	0.906	0.85	0.962	0.453	0.425	0.481	CLONAL	2	TRUE	0	0.441648248226027	4		367	966	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46715729	46715729	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001578-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1453	131	590	0	ENST00000371975.4:c.148C>G	p.Pro50Ala	p.P50A	ENST00000371975	NM_003579.3	50	Cct/Gct	3/18	0.243432968244789	5	FACETS	0.623	0.563	0.686			1	INDETERMINATE	1	TRUE	NA	0.441648248226027	5		590	1584	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845408	156845408	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001578-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1321	132	411	0	ENST00000524377.1:c.1451C>G	p.Ser484Cys	p.S484C	ENST00000524377	NM_002529.3	484	tCt/tGt	12/17	0.441648248226027	4	FACETS	0.593	0.536	0.653			1	SUBCLONAL	1	TRUE	NA	0.441648248226027	4		411	1453	SUCCESS
REL	5966	MSKCC	GRCh37	2	61128147	61128147	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1016724251	NA	P-0001578-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	115	325	2	ENST00000295025.8:c.323G>A	p.Arg108Gln	p.R108Q	ENST00000295025	NM_002908.2	108	cGa/cAa	4/11	0.381747882139394	4	FACETS	0.681	0.612	0.754	0.34	0.306	0.377	SUBCLONAL	1	TRUE	2	0.441648248226027	4		327	1103	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61713052	61713052	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001578-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	141	499	0	ENST00000401558.2:c.2359G>A	p.Asp787Asn	p.D787N	ENST00000401558	NM_003400.3	787	Gat/Aat	20/25	0.381747882139394	4	FACETS	0.703	0.639	0.771	0.352	0.319	0.386	SUBCLONAL	1	TRUE	2	0.441648248226027	4		499	1309	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601999	43601999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751518221	NA	P-0001578-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	591	382	0	ENST00000355710.3:c.1043G>A	p.Arg348Gln	p.R348Q	ENST00000355710	NM_020975.4	348	cGg/cAg	5/20	0.441648248226027	4	FACETS	1	0.995	1	0.864	0.834	0.893	CLONAL	3	TRUE	0	0.441648248226027	4		382	1117	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425847	49425847	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0001578-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	740	373	0	ENST00000301067.7:c.12641T>G	p.Leu4214Ter	p.L4214*	ENST00000301067	NM_003482.3	4214	tTa/tGa	39/54	0.368033403198797	5	FACETS	1	0.996	1	0.899	0.873	0.924	CLONAL	4	TRUE	0	0.441648248226027	5		373	1240	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941653	48941653	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0001578-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	413	449	0	ENST00000267163.4:c.963C>G	p.Tyr321Ter	p.Y321*	ENST00000267163	NM_000321.2	321	taC/taG	10/27	0.220611614532222	4	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.441648248226027	4		449	1129	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001579-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	54	422	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	0.95	0.829	1	1	0.978	1	CLONAL	2	FALSE	0	0.3	1		422	161	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577095	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519984	NA	P-0001579-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	53	451	0	ENST00000269305.4:c.843C>A	p.Asp281Glu	p.D281E	ENST00000269305	NM_001126112.2	281	gaC/gaA	8/11	0.260924740607898	0	FACETS	0.337	0.286	0.392			1	SUBCLONAL	1	FALSE	0	0.3	0		451	734	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	53	422	0				ENST00000310581	NM_198253.2	-/1132			0.147332553272977	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.805413228748868	0		422	112	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0001582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	122	321	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	0.42428642811889	3	FACETS	1	0.98	1	0.621	0.568	0.676	INDETERMINATE	1	TRUE	1	0.805413228748868	3		321	342	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223540	55223540	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4211	785	416	0	ENST00000275493.2:c.907G>C	p.Asp303His	p.D303H	ENST00000275493	NM_005228.3	303	Gat/Cat	8/28	0.805413228748868	28	FACETS	1	0.993	1			1	CLONAL	4	TRUE	NA	0.805413228748868	28		416	4996	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562355	95562355	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	145	490	0	ENST00000393063.1:c.4902del	p.Asp1636ThrfsTer7	p.D1636Tfs*7	ENST00000393063	NM_030621.3	1634	ttG/tt	24/28	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.805413228748868	2		490	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0001603-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	207	403	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.275246286690607	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.431235404294557	1		404	666	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001603-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	63	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.431235404294557	2		422	289	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971116	21971116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552823	NA	P-0001603-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	132	210	0	ENST00000304494.5:c.242C>T	p.Pro81Leu	p.P81L	ENST00000304494	NM_000077.4	81	cCc/cTc	2/3	0.431235404294557	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.431235404294557	1		210	441	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538374	9538374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868564987	NA	P-0001603-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	72	295	0	ENST00000353224.5:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000353224	NM_177990.2	542	Gaa/Aaa	7/10	0.431235404294557	1	FACETS	0.834	0.735	0.939	0.834	0.735	0.939	CLONAL	1	TRUE	0	0.431235404294557	1		295	314	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0001603-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	162	270	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.351129482879173	2	FACETS	0.793	0.733	0.853	0.793	0.733	0.853	SUBCLONAL	2	TRUE	0	0.431235404294557	2		270	474	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0001603-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	155	180	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.275246286690607	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.431235404294557	1		180	511	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804263	43804263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778516	NA	P-0001603-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	63	391	0	ENST00000372470.3:c.263G>A	p.Gly88Glu	p.G88E	ENST00000372470	NM_005373.2	88	gGa/gAa	3/12	0.351129482879173	2	FACETS	0.388	0.334	0.445	0.194	0.167	0.223	SUBCLONAL	1	TRUE	0	0.431235404294557	2		391	754	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873669	35873669	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748643880	NA	P-0001603-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	110	440	0	ENST00000303115.3:c.625C>T	p.Pro209Ser	p.P209S	ENST00000303115	NM_002185.3	209	Cct/Tct	5/8	0.431235404294557	1	FACETS	0.857	0.774	0.943	0.857	0.774	0.943	CLONAL	1	TRUE	0	0.431235404294557	1		440	467	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553585	106553585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001603-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	47	231	0	ENST00000369096.4:c.1550C>T	p.Pro517Leu	p.P517L	ENST00000369096	NM_001198.3	517	cCc/cTc	5/7	NA	2	FACETS	0.438	0.369	0.513			1	INDETERMINATE	1	TRUE	NA	0.431235404294557	2		231	498	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196107	138196107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1324560863	NA	P-0001603-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	54	375	0	ENST00000237289.4:c.421C>T	p.Arg141Cys	p.R141C	ENST00000237289	NM_001270507.1	141	Cgc/Tgc	3/9	0.309112787363871	1	FACETS	0.369	0.315	0.428	0.369	0.315	0.428	SUBCLONAL	1	TRUE	0	0.431235404294557	1		375	533	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90971052	90971052	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001603-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	71	393	0	ENST00000265433.3:c.1025T>A	p.Leu342His	p.L342H	ENST00000265433	NM_002485.4	342	cTt/cAt	9/16	0.431235404294557	6	FACETS	0.593	0.515	0.676			1	SUBCLONAL	1	TRUE	NA	0.431235404294557	6		393	1035	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446314	70446314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868773920	NA	P-0001603-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	164	413	0	ENST00000373644.4:c.5254C>T	p.Pro1752Ser	p.P1752S	ENST00000373644	NM_030625.2	1752	Ccc/Tcc	11/12	0.431235404294557	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.431235404294557	1		413	538	SUCCESS
ATM	472	MSKCC	GRCh37	11	108204678	108204678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001603-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	15	242	0	ENST00000278616.4:c.7993C>T	p.Pro2665Ser	p.P2665S	ENST00000278616	NM_000051.3	2665	Cct/Tct	54/63	0.353495536010858	1	FACETS	0.194	0.142	0.258	0.194	0.142	0.258	SUBCLONAL	1	TRUE	0	0.431235404294557	1		242	281	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891030	112891030	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001603-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	133	289	0	ENST00000351677.2:c.364G>A	p.Ala122Thr	p.A122T	ENST00000351677	NM_002834.3	122	Gca/Aca	4/16	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.431235404294557	2		289	498	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610071	28610071	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0001603-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	124	432	0	ENST00000241453.7:c.1418+1G>A		p.X473_splice	ENST00000241453	NM_004119.2	473			1	2	FACETS	0.971	0.882	1	0.971	0.882	1	CLONAL	1	TRUE	1	0.431235404294557	2		432	592	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857197	9857197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866121846	NA	P-0001603-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	159	452	1	ENST00000330684.3:c.4204C>T	p.Arg1402Trp	p.R1402W	ENST00000330684	NM_001134407.1	1402	Cgg/Tgg	13/13	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.431235404294557	2		453	640	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743897	41743897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748294158	NA	P-0001603-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	140	380	0	ENST00000301178.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000301178	NM_021913.4	278	Ccc/Tcc	7/20	1	2	FACETS	0.883	0.806	0.965	0.883	0.806	0.965	CLONAL	1	TRUE	1	0.431235404294557	2		380	735	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765528	41765528	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001603-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	169	388	0	ENST00000301178.4:c.2404G>A	p.Asp802Asn	p.D802N	ENST00000301178	NM_021913.4	802	Gat/Aat	20/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.431235404294557	2		388	724	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611248	100611248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782457670	NA	P-0001603-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	92	165	0	ENST00000308731.7:c.1358C>T	p.Ser453Phe	p.S453F	ENST00000308731	NM_000061.2	453	tCc/tTc	15/19	1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.431235404294557	1		165	242	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184066	123184066	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001603-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	94	228	0	ENST00000218089.9:c.924C>A	p.Cys308Ter	p.C308*	ENST00000218089	NM_001042749.1	308	tgC/tgA	11/35	1	1	FACETS	0.864	0.787	0.94	1	0.987	1	CLONAL	2	TRUE	0	0.431235404294557	1		228	198	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001621-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	32	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.87	1	1	0.964	1	CLONAL	2	TRUE	1	0.192656780175436	2		422	155	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs876659675	NA	P-0001621-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	102	358	1	ENST00000269305.4:c.764T>A	p.Ile255Asn	p.I255N	ENST00000269305	NM_001126112.2	255	aTc/aAc	7/11	0.192656780175436	1	FACETS	1	0.953	1	1	0.988	1	CLONAL	2	TRUE	0	0.192656780175436	1		359	434	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882959	89882959	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs761341952	NA	P-0001621-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	51	85	0	ENST00000389301.3:c.65G>A	p.Trp22Ter	p.W22*	ENST00000389301	NM_000135.2	22	tGg/tAg	1/43	0.192656780175436	1	FACETS	1	0.944	1	1	0.983	1	CLONAL	3	TRUE	0	0.192656780175436	1		85	137	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001638-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	131	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.954	0.871	1	0.954	0.871	1	CLONAL	1	TRUE	1	0.537300572549828	2		422	511	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123247530	123247530	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1404851539	NA	P-0001638-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	333	600	0	ENST00000358487.5:c.1961T>C	p.Ile654Thr	p.I654T	ENST00000358487	NM_000141.4	654	aTa/aCa	14/18	0.432150100773775	1	FACETS	0.874	0.828	0.922	0.874	0.828	0.922	CLONAL	1	TRUE	0	0.537300572549828	1		600	1037	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106782	27106783	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0001638-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	242	570	0	ENST00000324856.7:c.6395_6396del	p.Val2132GlyfsTer17	p.V2132Gfs*17	ENST00000324856	NM_006015.4	2131	aaTGtg/aatg	20/20	0.468004400607947	1	FACETS	0.729	0.682	0.777	0.729	0.682	0.777	SUBCLONAL	1	TRUE	0	0.537300572549828	1		570	904	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001641-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	47	422	0				ENST00000310581	NM_198253.2	-/1132			0.187810093131567	3	FACETS	0.942	0.813	1	0.942	0.813	1	INDETERMINATE	2	TRUE	1	0.43752739558776	3		422	139	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120496238	120496238	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001641-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	113	589	0	ENST00000256646.2:c.2293C>A	p.Pro765Thr	p.P765T	ENST00000256646	NM_024408.3	765	Cca/Aca	14/34	1	2	FACETS	0.894	0.807	0.985	0.894	0.807	0.985	CLONAL	1	TRUE	1	0.43752739558776	2		589	578	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629589	187629589	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001641-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	129	555	0	ENST00000441802.2:c.1393C>T	p.Gln465Ter	p.Q465*	ENST00000441802	NM_005245.3	465	Cag/Tag	2/27	0.43752739558776	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.43752739558776	1		555	425	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246410	41246410	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001641-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	53	616	0	ENST00000357654.3:c.1138C>G	p.Gln380Glu	p.Q380E	ENST00000357654	NM_007294.3	380	Cag/Gag	10/23	1	2	FACETS	0.512	0.437	0.594	0.512	0.437	0.594	SUBCLONAL	1	TRUE	1	0.43752739558776	2		616	473	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001654-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	40	422	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		422	174	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001654-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	111	422	0				ENST00000310581	NM_198253.2	-/1132			0.17473602893026	1	FACETS	0.605	0.55	0.662	0.605	0.55	0.662	INDETERMINATE	1	TRUE	0	0.687913434828561	1		422	350	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420053	41420053	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs547588566	NA	P-0001654-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	198	400	0	ENST00000373198.4:c.268C>T	p.Leu90Phe	p.L90F	ENST00000373198	NM_133170.3	90	Ctt/Ttt	3/32	0.242368402188534	3	FACETS	0.917	0.85	0.985	0.306	0.283	0.329	INDETERMINATE	1	TRUE	0	0.687913434828561	3		400	844	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0001671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	267	498	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.545122952712849	2	FACETS	0.94	0.892	0.988	0.94	0.892	0.988	CLONAL	2	TRUE	0	0.545122952712849	2		498	521	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	103	422	0				ENST00000310581	NM_198253.2	-/1132			0.52488864797263	3	FACETS	0.761	0.689	0.835	0.761	0.689	0.835	SUBCLONAL	2	TRUE	1	0.545122952712849	3		422	316	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0001671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	146	318	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.545122952712849	4	FACETS	0.932	0.858	1	0.932	0.858	1	CLONAL	2	TRUE	2	0.545122952712849	4		318	444	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595803	52595803	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	241	561	0	ENST00000394830.3:c.4112C>G	p.Ala1371Gly	p.A1371G	ENST00000394830	NM_018313.4	1371	gCc/gGc	26/30	0.49575586290401	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.545122952712849	4		561	624	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462410	89462410	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	115	365	0	ENST00000336596.2:c.1882G>T	p.Gly628Ter	p.G628*	ENST00000336596	NM_005233.5	628	Gga/Tga	10/17	0.49575586290401	4	FACETS	0.903	0.822	0.987	0.903	0.822	0.987	CLONAL	2	TRUE	2	0.545122952712849	4		365	361	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001680-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	77	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.405861768025419	2		422	379	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433394	49433394	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783727	NA	P-0001680-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	56	310	0	ENST00000301067.7:c.8053C>T	p.Arg2685Ter	p.R2685*	ENST00000301067	NM_003482.3	2685	Cga/Tga	32/54	1	2	FACETS	0.812	0.699	0.933	0.812	0.699	0.933	CLONAL	1	TRUE	1	0.405861768025419	2		310	340	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0001680-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	159	451	0	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	1	2	FACETS	0.923	0.846	1	0.923	0.846	1	CLONAL	1	TRUE	1	0.405861768025419	2		451	849	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145398	61145398	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001680-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	98	376	1	ENST00000295025.8:c.608A>G	p.Glu203Gly	p.E203G	ENST00000295025	NM_002908.2	203	gAa/gGa	6/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.405861768025419	2		377	363	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136258	202136258	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001680-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	144	435	0	ENST00000358485.4:c.502T>C	p.Ser168Pro	p.S168P	ENST00000358485	NM_001080125.1	168	Tca/Cca	3/9	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.405861768025419	2		435	649	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001680-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	123	465	1	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	1	2	FACETS	0.824	0.745	0.906	0.824	0.745	0.906	CLONAL	1	TRUE	1	0.405861768025419	2		466	736	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589586	67589591	+	inframe_deletion	In_Frame_Del	DEL	ATGAAT	ATGAAT	-	novel	NA	P-0001680-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	55	336	2	ENST00000274335.5:c.1351_1356del	p.Glu451_Tyr452del	p.E451_Y452del	ENST00000274335		450	cATGAATat/cat	10/15	1	2	FACETS	0.941	0.811	1	0.941	0.811	1	CLONAL	1	TRUE	1	0.405861768025419	2		338	288	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974782	21974783	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CAGT	novel	NA	P-0001680-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	173	211	0	ENST00000304494.5:c.41_44dup	p.Trp15Ter	p.W15*	ENST00000304494	NM_000077.4	15	tgg/tgACTGg	1/3	0.339572823667801	3	FACETS	0.921	0.853	0.99	0.921	0.853	0.99	CLONAL	2	TRUE	1	0.405861768025419	3		211	557	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001680-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	58	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.928	1	1	0.98	1	CLONAL	2	TRUE	1	0.197959115471246	2		422	264	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099173	157099173	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001680-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	119	227	1	ENST00000346085.5:c.110C>A	p.Ser37Tyr	p.S37Y	ENST00000346085	NM_020732.3	37	tCc/tAc	1/20	0.197959115471246	3	FACETS	0.931	0.846	1			1	CLONAL	3	TRUE	NA	0.197959115471246	3		228	473	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0001680-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	190	451	0	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	1	2	FACETS	0.836	0.775	0.9	1	0.994	1	CLONAL	3	TRUE	1	0.197959115471246	2		451	765	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145398	61145398	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001680-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	138	376	1	ENST00000295025.8:c.608A>G	p.Glu203Gly	p.E203G	ENST00000295025	NM_002908.2	203	gAa/gGa	6/11	0.154893582575203	2	FACETS	0.914	0.832	0.999	0.914	0.832	0.999	CLONAL	2	TRUE	0	0.197959115471246	2		377	763	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136258	202136258	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001680-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	187	435	0	ENST00000358485.4:c.502T>C	p.Ser168Pro	p.S168P	ENST00000358485	NM_001080125.1	168	Tca/Cca	3/9	1	2	FACETS	1	0.945	1	1	0.993	1	CLONAL	2	TRUE	1	0.197959115471246	2		435	920	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251907	153251907	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001680-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	135	465	1	ENST00000281708.4:c.1099C>T	p.Arg367Ter	p.R367*	ENST00000281708	NM_033632.3	367	Cga/Tga	7/12	1	2	FACETS	0.766	0.696	0.84	1	0.986	1	SUBCLONAL	2	TRUE	1	0.197959115471246	2		466	890	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589586	67589591	+	inframe_deletion	In_Frame_Del	DEL	ATGAAT	ATGAAT	-	novel	NA	P-0001680-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	114	336	2	ENST00000274335.5:c.1351_1356del	p.Glu451_Tyr452del	p.E451_Y452del	ENST00000274335		450	cATGAATat/cat	10/15	0.197959115471246	3	FACETS	0.915	0.824	1	0.915	0.824	1	CLONAL	2	TRUE	1	0.197959115471246	3		338	692	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974782	21974783	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	CAGT	novel	NA	P-0001680-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	162	211	0	ENST00000304494.5:c.41_44dup	p.Trp15Ter	p.W15*	ENST00000304494	NM_000077.4	15	tgg/tgACTGg	1/3	0.197959115471246	3	FACETS	1	0.934	1	1	0.993	1	CLONAL	4	TRUE	1	0.197959115471246	3		211	446	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753175	57753175	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001680-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	96	383	0	ENST00000274289.3:c.841G>C	p.Glu281Gln	p.E281Q	ENST00000274289	NM_006622.3	281	Gaa/Caa	7/14	0.197959115471246	3	FACETS	1	0.972	1	0.645	0.574	0.721	CLONAL	1	TRUE	1	0.197959115471246	3		383	826	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553550	106553550	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001680-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	44	265	0	ENST00000369096.4:c.1515G>A	p.Met505Ile	p.M505I	ENST00000369096	NM_001198.3	505	atG/atA	5/7	0.197959115471246	4	FACETS	0.68	0.569	0.804	0.227	0.189	0.268	SUBCLONAL	1	TRUE	1	0.197959115471246	4		265	783	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554952	106554952	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001680-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	239	392	0	ENST00000369096.4:c.2069C>A	p.Ser690Tyr	p.S690Y	ENST00000369096	NM_001198.3	690	tCc/tAc	7/7	0.197959115471246	4	FACETS	0.97	0.906	1	0.97	0.906	1	CLONAL	3	TRUE	1	0.197959115471246	4		392	994	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	125	155	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.48	2		156	407	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433394	49433394	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783727	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	79	310	0	ENST00000301067.7:c.8053C>T	p.Arg2685Ter	p.R2685*	ENST00000301067	NM_003482.3	2685	Cga/Tga	32/54	1	2	FACETS	0.894	0.792	1	0.894	0.792	1	CLONAL	1	TRUE	1	0.48	2		310	368	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817721	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	rs1378599948	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	319	522	4	ENST00000262367.5:c.3250del	p.Ile1084SerfsTer15	p.I1084Sfs*15	ENST00000262367	NM_004380.2	1084	Atc/tc	16/31	0.120666786554146	0	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	0	0.48	0		526	680	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465373	120465373	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	201	437	0	ENST00000256646.2:c.4888C>T	p.Arg1630Cys	p.R1630C	ENST00000256646	NM_024408.3	1630	Cgc/Tgc	27/34	0.120666786554146	3	FACETS	1	0.99	1	0.718	0.668	0.77	INDETERMINATE	1	TRUE	1	0.48	3		437	723	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438647	49438647	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	169	557	0	ENST00000301067.7:c.4843C>T	p.Arg1615Ter	p.R1615*	ENST00000301067	NM_003482.3	1615	Cga/Tga	19/54	1	2	FACETS	0.969	0.893	1	0.969	0.893	1	CLONAL	1	TRUE	1	0.48	2		557	727	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606646	29606646	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147102592	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	183	606	0	ENST00000389048.3:c.1234C>T	p.Arg412Cys	p.R412C	ENST00000389048	NM_004304.4	412	Cgc/Tgc	5/29	1	2	FACETS	0.989	0.915	1	0.989	0.915	1	CLONAL	1	TRUE	1	0.48	2		606	771	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103755	47103756	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	186	701	1	ENST00000409792.3:c.6190_6191del	p.Asp2064ProfsTer8	p.D2064Pfs*8	ENST00000409792	NM_014159.6	2064	GAc/c	14/21	0.120666786554146	0	FACETS	0.461	0.426	0.498			1	INDETERMINATE	1	TRUE	0	0.48	0		702	874	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214594	5214594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768496731	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	207	625	0	ENST00000357368.4:c.4472C>T	p.Thr1491Met	p.T1491M	ENST00000357368	NM_002850.3	1491	aCg/aTg	29/38	0.120666786554146	0	FACETS	0.65	0.606	0.696			1	INDETERMINATE	1	TRUE	0	0.48	0		625	690	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553257	106553257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	60	614	0	ENST00000369096.4:c.1222G>A	p.Ala408Thr	p.A408T	ENST00000369096	NM_001198.3	408	Gct/Act	5/7	0.120666786554146	3	FACETS	0.37	0.318	0.427	0.185	0.159	0.214	INDETERMINATE	1	TRUE	1	0.48	3		614	838	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495360	149495360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs114435947	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	50	518	2	ENST00000261799.4:c.3287C>T	p.Ala1096Val	p.A1096V	ENST00000261799	NM_002609.3	1096	gCg/gTg	23/23	1	2	FACETS	0.299	0.253	0.35	0.299	0.253	0.35	SUBCLONAL	1	TRUE	1	0.48	2		520	696	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11270918	11270918	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	148	531	1	ENST00000361445.4:c.3607C>T	p.Arg1203Ter	p.R1203*	ENST00000361445	NM_004958.3	1203	Cga/Tga	24/58	0.120666786554146	0	FACETS	0.498	0.456	0.542			1	INDETERMINATE	1	TRUE	0	0.48	0		532	644	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11301656	11301656	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	131	488	0	ENST00000361445.4:c.1495C>T	p.Gln499Ter	p.Q499*	ENST00000361445	NM_004958.3	499	Cag/Tag	10/58	0.120666786554146	0	FACETS	0.409	0.371	0.448			1	INDETERMINATE	1	TRUE	0	0.48	0		488	694	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255500	16255500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140341054	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	191	438	0	ENST00000375759.3:c.2765C>T	p.Thr922Met	p.T922M	ENST00000375759	NM_015001.2	922	aCg/aTg	11/15	0.120666786554146	0	FACETS	0.567	0.526	0.61			1	INDETERMINATE	1	TRUE	0	0.48	0		438	730	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023699	27023699	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	94	356	0	ENST00000324856.7:c.805C>T	p.Gln269Ter	p.Q269*	ENST00000324856	NM_006015.4	269	Cag/Tag	1/20	0.3	2	FACETS	0.679	0.605	0.757			1	SUBCLONAL	1	TRUE	NA	0.48	2		356	577	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097631	27097631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	55	612	0	ENST00000324856.7:c.3220C>T	p.Arg1074Trp	p.R1074W	ENST00000324856	NM_006015.4	1074	Cgg/Tgg	12/20	0.3	2	FACETS	0.29	0.247	0.337			1	SUBCLONAL	1	TRUE	NA	0.48	2		612	790	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509485	46509485	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748855044	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	33	434	0	ENST00000262741.5:c.1246G>A	p.Ala416Thr	p.A416T	ENST00000262741	NM_003629.3	416	Gca/Aca	10/10	0.3	2	FACETS	0.217	0.176	0.263			1	SUBCLONAL	1	TRUE	NA	0.48	2		434	634	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462051	120462051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750477480	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	228	527	2	ENST00000256646.2:c.5665C>T	p.Arg1889Trp	p.R1889W	ENST00000256646	NM_024408.3	1889	Cgg/Tgg	31/34	0.120666786554146	3	FACETS	0.775	0.725	0.827	0.775	0.725	0.827	INDETERMINATE	2	TRUE	1	0.48	3		529	760	SUCCESS
ALK	238	MSKCC	GRCh37	2	29420492	29420492	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	173	497	0	ENST00000389048.3:c.3989A>G	p.Tyr1330Cys	p.Y1330C	ENST00000389048	NM_004304.4	1330	tAc/tGc	27/29	1	2	FACETS	0.857	0.79	0.927	0.857	0.79	0.927	CLONAL	1	TRUE	1	0.48	2		497	841	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639626	47639626	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	164	493	1	ENST00000233146.2:c.719A>T	p.Asp240Val	p.D240V	ENST00000233146	NM_000251.2	240	gAc/gTc	4/16	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.48	2		494	642	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639661	47639661	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63750347	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	152	447	1	ENST00000233146.2:c.754C>T	p.Gln252Ter	p.Q252*	ENST00000233146	NM_000251.2	252	Cag/Tag	4/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.48	2		448	567	SUCCESS
REL	5966	MSKCC	GRCh37	2	61144120	61144120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs900673506	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	132	619	0	ENST00000295025.8:c.503C>T	p.Pro168Leu	p.P168L	ENST00000295025	NM_002908.2	168	cCt/cTt	5/11	1	2	FACETS	0.659	0.598	0.723	0.659	0.598	0.723	SUBCLONAL	1	TRUE	1	0.48	2		619	835	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61711081	61711081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs996736538	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	165	443	1	ENST00000401558.2:c.2668G>A	p.Ala890Thr	p.A890T	ENST00000401558	NM_003400.3	890	Gca/Aca	21/25	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.48	2		444	618	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149945	99149945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	129	444	0	ENST00000074304.5:c.257C>T	p.Thr86Met	p.T86M	ENST00000074304	NM_001134224.1	86	aCg/aTg	5/26	1	2	FACETS	0.744	0.676	0.817	0.744	0.676	0.817	SUBCLONAL	1	TRUE	1	0.48	2		444	722	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661531	227661531	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1174719439	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	57	589	0	ENST00000305123.5:c.1924G>A	p.Ala642Thr	p.A642T	ENST00000305123	NM_005544.2	642	Gcc/Acc	1/2	1	2	FACETS	0.248	0.212	0.288	0.248	0.212	0.288	SUBCLONAL	1	TRUE	1	0.48	2		589	957	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793269	242793269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1381223113	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	143	511	0	ENST00000334409.5:c.808G>A	p.Gly270Ser	p.G270S	ENST00000334409	NM_005018.2	270	Ggc/Agc	5/5	1	2	FACETS	0.908	0.83	0.989	0.908	0.83	0.989	CLONAL	1	TRUE	1	0.48	2		511	656	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713688	30713688	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752866783	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	32	336	0	ENST00000295754.5:c.1013C>T	p.Thr338Met	p.T338M	ENST00000295754	NM_003242.5	338	aCg/aTg	4/7	1	2	FACETS	0.245	0.198	0.298	0.245	0.198	0.298	SUBCLONAL	1	TRUE	1	0.48	2		336	544	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52436414	52436414	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	119	436	0	ENST00000460680.1:c.2080C>T	p.Gln694Ter	p.Q694*	ENST00000460680	NM_004656.3	694	Cag/Tag	17/17	0.120666786554146	0	FACETS	0.432	0.391	0.475			1	INDETERMINATE	1	TRUE	0	0.48	0		436	597	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090510	71090510	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	163	564	1	ENST00000318789.4:c.838C>T	p.Gln280Ter	p.Q280*	ENST00000318789	NM_032682.5	280	Cag/Tag	11/21	1	2	FACETS	0.723	0.663	0.785	0.723	0.663	0.785	SUBCLONAL	1	TRUE	1	0.48	2		565	940	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749500	41749500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	147	531	2	ENST00000226382.2:c.295C>T	p.Arg99Trp	p.R99W	ENST00000226382	NM_003924.3	99	Cgg/Tgg	2/3	1	2	FACETS	0.914	0.837	0.995	0.914	0.837	0.995	CLONAL	1	TRUE	1	0.48	2		533	670	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630753	187630753	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377496399	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	52	749	0	ENST00000441802.2:c.229G>A	p.Gly77Arg	p.G77R	ENST00000441802	NM_005245.3	77	Gga/Aga	2/27	0.3	2	FACETS	0.234	0.198	0.273			1	SUBCLONAL	1	TRUE	NA	0.48	2		749	926	SUCCESS
APC	324	MSKCC	GRCh37	5	112176329	112176329	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs754122018	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	59	405	0	ENST00000257430.4:c.5038C>T	p.Gln1680Ter	p.Q1680*	ENST00000257430	NM_000038.5	1680	Cag/Tag	16/16	1	2	FACETS	0.325	0.279	0.376	0.325	0.279	0.376	SUBCLONAL	1	TRUE	1	0.48	2		405	756	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709523	176709523	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs797045057	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	165	541	0	ENST00000439151.2:c.5950C>T	p.Arg1984Ter	p.R1984*	ENST00000439151	NM_022455.4	1984	Cga/Tga	19/23	0.120666786554146	0	FACETS	0.517	0.476	0.56			1	INDETERMINATE	1	TRUE	0	0.48	0		541	691	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552918	106552918	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	63	669	0	ENST00000369096.4:c.883C>A	p.Pro295Thr	p.P295T	ENST00000369096	NM_001198.3	295	Cct/Act	5/7	0.120666786554146	3	FACETS	0.341	0.294	0.393	0.171	0.147	0.197	INDETERMINATE	1	TRUE	1	0.48	3		669	954	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220349	55220349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780001754	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	101	334	0	ENST00000275493.2:c.739G>A	p.Asp247Asn	p.D247N	ENST00000275493	NM_005228.3	247	Gac/Aac	6/28	1	2	FACETS	0.8	0.718	0.887	0.8	0.718	0.887	SUBCLONAL	1	TRUE	1	0.48	2		334	526	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501317	140501317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1325951163	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	111	371	0	ENST00000288602.6:c.755G>A	p.Arg252Gln	p.R252Q	ENST00000288602	NM_004333.4	252	cGa/cAa	6/18	1	2	FACETS	0.744	0.67	0.821	0.744	0.67	0.821	SUBCLONAL	1	TRUE	1	0.48	2		371	622	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372044	55372044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	98	281	0	ENST00000297316.4:c.734G>A	p.Cys245Tyr	p.C245Y	ENST00000297316	NM_022454.3	245	tGc/tAc	2/2	0.3	2	FACETS	1	0.959	1			1	CLONAL	1	TRUE	NA	0.48	2		281	362	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372405	55372405	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	53	623	0	ENST00000297316.4:c.1095G>C	p.Gln365His	p.Q365H	ENST00000297316	NM_022454.3	365	caG/caC	2/2	0.3	2	FACETS	0.281	0.239	0.328			1	SUBCLONAL	1	TRUE	NA	0.48	2		623	785	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248030	98248030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772368023	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	207	573	0	ENST00000331920.6:c.521C>T	p.Ala174Val	p.A174V	ENST00000331920	NM_000264.3	174	gCg/gTg	3/24	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.48	2		573	766	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390539	139390539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774680812	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	152	679	0	ENST00000277541.6:c.7652C>T	p.Pro2551Leu	p.P2551L	ENST00000277541	NM_017617.3	2551	cCg/cTg	34/34	1	2	FACETS	0.782	0.716	0.851	0.782	0.716	0.851	SUBCLONAL	1	TRUE	1	0.48	2		679	810	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391986	139391986	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs567909904	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	115	452	0	ENST00000277541.6:c.6205G>A	p.Ala2069Thr	p.A2069T	ENST00000277541	NM_017617.3	2069	Gcc/Acc	34/34	1	2	FACETS	0.899	0.813	0.989	0.899	0.813	0.989	CLONAL	1	TRUE	1	0.48	2		452	533	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399889	139399889	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	48	581	0	ENST00000277541.6:c.4459T>C	p.Trp1487Arg	p.W1487R	ENST00000277541	NM_017617.3	1487	Tgg/Cgg	25/34	1	2	FACETS	0.289	0.244	0.34	0.289	0.244	0.34	SUBCLONAL	1	TRUE	1	0.48	2		581	691	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412321	139412321	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	119	458	0	ENST00000277541.6:c.1324C>T	p.Gln442Ter	p.Q442*	ENST00000277541	NM_017617.3	442	Cag/Tag	8/34	1	2	FACETS	0.853	0.773	0.938	0.853	0.773	0.938	CLONAL	1	TRUE	1	0.48	2		458	581	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70442645	70442645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	201	559	0	ENST00000373644.4:c.4967G>A	p.Arg1656His	p.R1656H	ENST00000373644	NM_030625.2	1656	cGt/cAt	10/12	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.48	2		559	788	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572612	64572612	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446518998	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	175	461	0	ENST00000312049.6:c.1244G>A	p.Arg415Gln	p.R415Q	ENST00000312049	NM_130799.2	415	cGa/cAa	9/10	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.48	2		461	693	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342391	118342391	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555035511	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	165	548	0	ENST00000534358.1:c.517C>T	p.Arg173Ter	p.R173*	ENST00000534358	NM_005933.3	173	Cga/Tga	3/36	1	2	FACETS	0.96	0.884	1	0.96	0.884	1	CLONAL	1	TRUE	1	0.48	2		548	716	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1036353	1036353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	62	646	0	ENST00000358495.3:c.425C>T	p.Ala142Val	p.A142V	ENST00000358495	NM_134424.2	142	gCa/gTa	6/12	0.3	2	FACETS	0.37	0.319	0.425			1	SUBCLONAL	1	TRUE	NA	0.48	2		646	699	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230620	46230620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	185	532	0	ENST00000334344.6:c.869C>T	p.Ala290Val	p.A290V	ENST00000334344	NM_152641.2	290	gCa/gTa	8/21	1	2	FACETS	0.833	0.77	0.9	0.833	0.77	0.9	CLONAL	1	TRUE	1	0.48	2		532	925	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112919975	112919975	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767503386	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	98	304	0	ENST00000351677.2:c.1190C>T	p.Thr397Met	p.T397M	ENST00000351677	NM_002834.3	397	aCg/aTg	10/16	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.48	2		304	395	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435408	121435408	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	55	612	1	ENST00000257555.6:c.1441C>T	p.Gln481Ter	p.Q481*	ENST00000257555		481	Cag/Tag	7/10	1	2	FACETS	0.344	0.294	0.399	0.344	0.294	0.399	SUBCLONAL	1	TRUE	1	0.48	2		613	666	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631878	90631878	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1319035463	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	178	567	0	ENST00000330062.3:c.475C>T	p.Arg159Cys	p.R159C	ENST00000330062	NM_002168.2	159	Cgc/Tgc	4/11	1	2	FACETS	0.967	0.893	1	0.967	0.893	1	CLONAL	1	TRUE	1	0.48	2		567	767	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251016	99251016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763743119	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	58	613	0	ENST00000268035.6:c.320G>A	p.Arg107His	p.R107H	ENST00000268035	NM_000875.3	107	cGc/cAc	2/21	1	2	FACETS	0.304	0.26	0.351	0.304	0.26	0.351	SUBCLONAL	1	TRUE	1	0.48	2		613	796	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	359972	359972	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	148	615	0	ENST00000262320.3:c.1116+1G>A		p.X372_splice	ENST00000262320	NM_003502.3	372			0.120666786554146	0	FACETS	0.498	0.456	0.542			1	INDETERMINATE	1	TRUE	0	0.48	0		615	644	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106741	2106741	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750649974	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	120	651	0	ENST00000219476.3:c.745G>A	p.Val249Ile	p.V249I	ENST00000219476	NM_000548.3	249	Gtc/Atc	8/42	0.120666786554146	0	FACETS	0.381	0.344	0.42			1	INDETERMINATE	1	TRUE	0	0.48	0		651	682	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89862403	89862403	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs370852532	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	82	510	0	ENST00000389301.3:c.917C>G	p.Thr306Arg	p.T306R	ENST00000389301	NM_000135.2	306	aCg/aGg	11/43	0.3	1	FACETS	0.483	0.426	0.543	0.483	0.426	0.543	SUBCLONAL	1	TRUE	0	0.48	1		510	538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577069	7577069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55819519	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	153	559	0	ENST00000269305.4:c.869G>A	p.Arg290His	p.R290H	ENST00000269305	NM_001126112.2	290	cGc/cAc	8/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.48	2		559	588	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983316	15983316	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	57	628	0	ENST00000268712.3:c.3463G>A	p.Val1155Met	p.V1155M	ENST00000268712	NM_006311.3	1155	Gtg/Atg	26/46	1	2	FACETS	0.26	0.222	0.302	0.26	0.222	0.302	SUBCLONAL	1	TRUE	1	0.48	2		628	912	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627715	37627715	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	54	746	0	ENST00000447079.4:c.1630C>A	p.Pro544Thr	p.P544T	ENST00000447079	NM_015083.1	544	Cct/Act	2/14	1	2	FACETS	0.281	0.239	0.327	0.281	0.239	0.327	SUBCLONAL	1	TRUE	1	0.48	2		746	800	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63545650	63545650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747647668	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	184	502	0	ENST00000307078.5:c.944C>T	p.Thr315Met	p.T315M	ENST00000307078	NM_004655.3	315	aCg/aTg	3/11	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.48	2		502	725	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119006	70119006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	51	584	0	ENST00000245479.2:c.578C>T	p.Thr193Met	p.T193M	ENST00000245479	NM_000346.3	193	aCg/aTg	2/3	1	2	FACETS	0.301	0.255	0.352	0.301	0.255	0.352	SUBCLONAL	1	TRUE	1	0.48	2		584	706	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099262	4099262	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	34	615	0	ENST00000262948.5:c.856G>T	p.Gly286Trp	p.G286W	ENST00000262948	NM_030662.3	286	Ggg/Tgg	7/11	0.120666786554146	0	FACETS	0.132	0.107	0.16			1	INDETERMINATE	1	TRUE	0	0.48	0		615	559	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172376	7172376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1383713230	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	105	561	0	ENST00000302850.5:c.1193G>A	p.Arg398His	p.R398H	ENST00000302850	NM_000208.2	398	cGc/cAc	5/22	0.120666786554146	0	FACETS	0.379	0.34	0.42			1	INDETERMINATE	1	TRUE	0	0.48	0		561	600	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107000	11107000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141090393	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	125	491	0	ENST00000358026.2:c.1705C>T	p.Arg569Trp	p.R569W	ENST00000358026	NM_001128849.1	569	Cgg/Tgg	10/36	0.120666786554146	0	FACETS	0.512	0.465	0.561			1	INDETERMINATE	1	TRUE	0	0.48	0		491	529	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266835	18266835	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778690366	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	22	256	0	ENST00000222254.8:c.146G>A	p.Arg49His	p.R49H	ENST00000222254	NM_005027.3	49	cGc/cAc	2/16	1	2	FACETS	0.231	0.179	0.293	0.231	0.179	0.293	SUBCLONAL	1	TRUE	1	0.48	2		256	396	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375168	31375168	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147591633	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	127	514	1	ENST00000328111.2:c.565G>A	p.Ala189Thr	p.A189T	ENST00000328111	NM_006892.3	189	Gcc/Acc	6/23	1	2	FACETS	0.773	0.701	0.848	0.773	0.701	0.848	SUBCLONAL	1	TRUE	1	0.48	2		515	685	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317461	1317461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781459586	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	177	595	0	ENST00000400841.2:c.604G>A	p.Asp202Asn	p.D202N	ENST00000400841		202	Gac/Aac	5/6	1	2	FACETS	0.993	0.917	1	0.993	0.917	1	CLONAL	1	TRUE	1	0.48	2		595	743	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006883	47006883	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	70	579	0	ENST00000377604.3:c.3G>A	p.Met1?	p.M1?	ENST00000377604	NM_001204468.1	1	atG/atA	2/24	1	2	FACETS	0.37	0.322	0.422	0.37	0.322	0.422	SUBCLONAL	1	TRUE	1	0.48	2		579	789	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649679	48649679	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150572851	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	234	691	1	ENST00000376670.3:c.163G>A	p.Ala55Thr	p.A55T	ENST00000376670	NM_002049.3	55	Gct/Act	2/6	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.48	2		692	902	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223743	53223743	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	134	670	0	ENST00000375401.3:c.3616C>T	p.Gln1206Ter	p.Q1206*	ENST00000375401	NM_004187.3	1206	Cag/Tag	23/26	1	2	FACETS	0.753	0.685	0.825	0.753	0.685	0.825	SUBCLONAL	1	TRUE	1	0.48	2		670	741	SUCCESS
AR	367	MSKCC	GRCh37	X	66905930	66905930	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754201976	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	245	618	0	ENST00000374690.3:c.1847G>A	p.Arg616His	p.R616H	ENST00000374690	NM_000044.3	616	cGt/cAt	3/8	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.48	2		618	997	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158447	106158447	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	137	472	0	ENST00000380013.4:c.3353del	p.Asn1118IlefsTer19	p.N1118Ifs*19	ENST00000380013	NM_001127208.2	1116	atA/at	3/11	1	2	FACETS	0.681	0.62	0.746	0.681	0.62	0.746	SUBCLONAL	1	TRUE	1	0.48	2		472	838	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753988	57753988	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	144	438	1	ENST00000274289.3:c.636del	p.Phe212LeufsTer8	p.F212Lfs*8	ENST00000274289	NM_006622.3	212	ttT/tt	5/14	0.120666786554146	3	FACETS	0.879	0.802	0.96	0.44	0.401	0.48	INDETERMINATE	1	TRUE	1	0.48	3		439	846	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637165	176637168	+	frameshift_variant	Frame_Shift_Del	DEL	TCTT	TCTT	-	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	131	413	0	ENST00000439151.2:c.1766_1769del	p.Ser589TyrfsTer9	p.S589Yfs*9	ENST00000439151	NM_022455.4	589	TCTTta/ta	5/23	0.120666786554146	0	FACETS	0.471	0.428	0.515			1	INDETERMINATE	1	TRUE	0	0.48	0		413	603	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965665	90965666	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs766044684	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	174	704	0	ENST00000265433.3:c.1651dup	p.Arg551LysfsTer5	p.R551Kfs*5	ENST00000265433	NM_002485.4	551	agg/aAgg	11/16	0.120666786554146	3	FACETS	0.898	0.826	0.973	0.449	0.413	0.487	INDETERMINATE	1	TRUE	1	0.48	3		704	1001	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475164	475164	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	125	604	0	ENST00000399788.2:c.473del	p.Leu158Ter	p.L158*	ENST00000399788	NM_001042603.1	158	tTg/tg	4/28	0.3	2	FACETS	0.683	0.618	0.751			1	SUBCLONAL	1	TRUE	NA	0.48	2		604	763	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289665	15289665	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	105	626	0	ENST00000263388.2:c.3806del	p.Gly1269ValfsTer3	p.G1269Vfs*3	ENST00000263388	NM_000435.2	1269	gGt/gt	23/33	0.120666786554146	0	FACETS	0.326	0.292	0.362			1	INDETERMINATE	1	TRUE	0	0.48	0		626	698	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937164	39937164	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	173	727	0	ENST00000378444.4:c.19del	p.Leu7CysfsTer9	p.L7Cfs*9	ENST00000378444	NM_001123385.1	7	Ctg/tg	2/15	1	2	FACETS	0.796	0.732	0.861	0.796	0.732	0.861	SUBCLONAL	1	TRUE	1	0.48	2		727	906	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929383	44929385	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0001703-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	67	693	0	ENST00000377967.4:c.2485_2487del	p.Ser829del	p.S829del	ENST00000377967	NM_021140.2	828	cCTTct/cct	17/29	1	2	FACETS	0.25	0.216	0.287	0.25	0.216	0.287	SUBCLONAL	1	TRUE	1	0.48	2		693	1117	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0001709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	91	275	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.204530537492463	1	FACETS	0.764	0.68	0.852	1	0.98	1	SUBCLONAL	2	TRUE	0	0.204530537492463	1		275	523	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	37	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.204530537492463	2		422	288	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140624411	140624420	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGCCGGCG	GGCGCCGGCG	-	novel	NA	P-0001709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	34	122	0	ENST00000288602.6:c.84_93del	p.Gly30ProfsTer21	p.G30Pfs*21	ENST00000288602	NM_004333.4	28	ggCGCCGGCGCC/gg	1/18	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.204530537492463	2		122	259	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578491	7578491	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1567553924	NA	P-0001709-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	45	491	0	ENST00000269305.4:c.439del	p.Val147LeufsTer23	p.V147Lfs*23	ENST00000269305	NM_001126112.2	147	Gtt/tt	5/11	1	2	FACETS	0.701	0.588	0.826	0.701	0.588	0.826	SUBCLONAL	1	TRUE	1	0.204530537492463	2		491	628	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0001710-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	55	139	0				ENST00000310581	NM_198253.2	-/1132			0.317221821645971	3	FACETS	1	0.88	1	1	0.88	1	CLONAL	2	TRUE	1	0.317221821645971	3		139	198	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0001710-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	277	310	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.317221821645971	8	FACETS	0.953	0.911	0.995			1	CLONAL	8	TRUE	NA	0.317221821645971	8		310	447	SUCCESS
APC	324	MSKCC	GRCh37	5	112175930	112175930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001710-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	33	343	0	ENST00000257430.4:c.4639G>A	p.Glu1547Lys	p.E1547K	ENST00000257430	NM_000038.5	1547	Gaa/Aaa	16/16	0.317221821645971	2	FACETS	0.874	0.716	1	0.437	0.358	0.525	CLONAL	1	TRUE	0	0.317221821645971	2		343	238	SUCCESS
APC	324	MSKCC	GRCh37	5	112176526	112176526	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001710-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	29	427	0	ENST00000257430.4:c.5235G>C	p.Lys1745Asn	p.K1745N	ENST00000257430	NM_000038.5	1745	aaG/aaC	16/16	0.317221821645971	2	FACETS	0.709	0.571	0.864	0.354	0.285	0.432	SUBCLONAL	1	TRUE	0	0.317221821645971	2		427	258	SUCCESS
APC	324	MSKCC	GRCh37	5	112176587	112176587	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001710-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	37	433	0	ENST00000257430.4:c.5296G>C	p.Asp1766His	p.D1766H	ENST00000257430	NM_000038.5	1766	Gat/Cat	16/16	0.317221821645971	2	FACETS	0.948	0.787	1	0.474	0.393	0.563	CLONAL	1	TRUE	0	0.317221821645971	2		433	246	SUCCESS
APC	324	MSKCC	GRCh37	5	112176601	112176601	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001710-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	34	471	0	ENST00000257430.4:c.5310G>C	p.Lys1770Asn	p.K1770N	ENST00000257430	NM_000038.5	1770	aaG/aaC	16/16	0.317221821645971	2	FACETS	0.861	0.707	1	0.43	0.353	0.516	CLONAL	1	TRUE	0	0.317221821645971	2		471	249	SUCCESS
APC	324	MSKCC	GRCh37	5	112176660	112176660	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1158503665	NA	P-0001710-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	51	546	0	ENST00000257430.4:c.5369G>C	p.Arg1790Thr	p.R1790T	ENST00000257430	NM_000038.5	1790	aGa/aCa	16/16	0.317221821645971	2	FACETS	1	0.909	1	0.543	0.464	0.628	CLONAL	1	TRUE	0	0.317221821645971	2		546	296	SUCCESS
APC	324	MSKCC	GRCh37	5	112176699	112176699	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1454330915	NA	P-0001710-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	47	476	0	ENST00000257430.4:c.5408G>C	p.Arg1803Thr	p.R1803T	ENST00000257430	NM_000038.5	1803	aGa/aCa	16/16	0.317221821645971	2	FACETS	1	0.861	1	0.507	0.431	0.591	CLONAL	1	TRUE	0	0.317221821645971	2		476	292	SUCCESS
APC	324	MSKCC	GRCh37	5	112176719	112176719	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001710-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	37	418	1	ENST00000257430.4:c.5428G>T	p.Asp1810Tyr	p.D1810Y	ENST00000257430	NM_000038.5	1810	Gat/Tat	16/16	0.317221821645971	2	FACETS	0.867	0.719	1	0.434	0.359	0.516	CLONAL	1	TRUE	0	0.317221821645971	2		419	269	SUCCESS
APC	324	MSKCC	GRCh37	5	112176812	112176812	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001710-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	28	467	0	ENST00000257430.4:c.5521G>C	p.Asp1841His	p.D1841H	ENST00000257430	NM_000038.5	1841	Gat/Cat	16/16	0.317221821645971	2	FACETS	0.733	0.588	0.895	0.366	0.294	0.448	SUBCLONAL	1	TRUE	0	0.317221821645971	2		467	241	SUCCESS
APC	324	MSKCC	GRCh37	5	112176839	112176839	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001710-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	38	492	0	ENST00000257430.4:c.5548G>A	p.Glu1850Lys	p.E1850K	ENST00000257430	NM_000038.5	1850	Gaa/Aaa	16/16	0.317221821645971	2	FACETS	0.904	0.752	1	0.452	0.376	0.536	CLONAL	1	TRUE	0	0.317221821645971	2		492	265	SUCCESS
APC	324	MSKCC	GRCh37	5	112177115	112177115	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001710-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	26	559	0	ENST00000257430.4:c.5824G>C	p.Asp1942His	p.D1942H	ENST00000257430	NM_000038.5	1942	Gac/Cac	16/16	0.317221821645971	2	FACETS	0.645	0.513	0.796	0.323	0.256	0.398	SUBCLONAL	1	TRUE	0	0.317221821645971	2		559	254	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508805	106508805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762805000	NA	P-0001710-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	63	533	0	ENST00000359195.3:c.799G>A	p.Glu267Lys	p.E267K	ENST00000359195	NM_002649.2	267	Gaa/Aaa	2/11	0.317221821645971	5	FACETS	0.93	0.805	1	0.186	0.161	0.214	CLONAL	1	TRUE	0	0.317221821645971	5		533	630	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298003	15298003	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752404540	NA	P-0001710-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	51	524	0	ENST00000263388.2:c.1753G>A	p.Glu585Lys	p.E585K	ENST00000263388	NM_000435.2	585	Gaa/Aaa	11/33	1	2	FACETS	0.992	0.848	1	0.992	0.848	1	CLONAL	1	TRUE	1	0.317221821645971	2		524	324	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932018	39932018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367736022	NA	P-0001710-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	60	325	0	ENST00000378444.4:c.2581C>T	p.Arg861Cys	p.R861C	ENST00000378444	NM_001123385.1	861	Cgc/Tgc	4/15	1	1	FACETS	0.874	0.768	0.986	1	0.978	1	CLONAL	2	TRUE	0	0.317221821645971	1		325	182	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175951	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001710-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	22	345	0	ENST00000257430.4:c.4660del	p.Glu1554LysfsTer11	p.E1554Kfs*11	ENST00000257430	NM_000038.5	1554	Gaa/aa	16/16	0.317221821645971	2	FACETS	0.622	0.484	0.781	0.311	0.242	0.391	SUBCLONAL	1	TRUE	0	0.317221821645971	2		345	223	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001727-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	83	422	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		422	343	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0001743-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	109	139	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		139	229	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808411	1808411	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0001743-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	197	378	0	ENST00000260795.2:c.2168+1G>C		p.X723_splice	ENST00000260795		723			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		378	415	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001753-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	71	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.919	0.808	1	0.919	0.808	1	CLONAL	1	TRUE	1	0.48	2		422	322	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226924	142226924	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001753-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	139	371	0	ENST00000350721.4:c.4880A>T	p.Gln1627Leu	p.Q1627L	ENST00000350721	NM_001184.3	1627	cAg/cTg	28/47	1	2	FACETS	0.948	0.866	1	0.948	0.866	1	CLONAL	1	TRUE	1	0.48	2		371	611	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	75	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.978	0.877	1			1	INDETERMINATE	1	TRUE	NA	0.852277346953717	2		422	180	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119634954	119634954	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs201450363	NA	P-0001755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	415	330	0	ENST00000316626.5:c.545T>C	p.Ile182Thr	p.I182T	ENST00000316626		182	aTt/aCt	5/12	0.115600601897263	5	FACETS	1	0.989	1	0.735	0.702	0.768	INDETERMINATE	2	TRUE	2	0.852277346953717	5		330	1006	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913273	NA	P-0001755-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	240	181	0	ENST00000263967.3:c.1624G>C	p.Glu542Gln	p.E542Q	ENST00000263967	NM_006218.2	542	Gaa/Caa	10/21	0.298927459381639	4	FACETS	0.966	0.911	1	0.966	0.911	1	INDETERMINATE	2	TRUE	2	0.852277346953717	4		181	540	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913351	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	178	469	0	ENST00000288602.6:c.1397G>A	p.Gly466Glu	p.G466E	ENST00000288602	NM_004333.4	466	gGa/gAa	11/18	0.29118325647395	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.480375581167401	4		469	497	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	38	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.480375581167401	2		422	122	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	218	482	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.480375581167401	2		482	637	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874285	155874285	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs730881014	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	175	330	0	ENST00000368323.3:c.246T>A	p.Phe82Leu	p.F82L	ENST00000368323	NM_006912.5	82	ttT/ttA	5/6	0.480375581167401	4	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.480375581167401	4		330	463	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284907	15284907	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs551991530	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	82	399	0	ENST00000263388.2:c.4708C>T	p.Arg1570Cys	p.R1570C	ENST00000263388	NM_000435.2	1570	Cgt/Tgt	25/33	0.452913427600244	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.480375581167401	1		399	224	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778899	9778899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	113	419	0	ENST00000377346.4:c.1168C>T	p.Leu390Phe	p.L390F	ENST00000377346	NM_005026.3	390	Ctc/Ttc	9/24	NA	2	FACETS	0.792	0.723	0.862			1	INDETERMINATE	2	TRUE	NA	0.480375581167401	2		419	297	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805121	43805121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	122	504	0	ENST00000372470.3:c.571G>A	p.Glu191Lys	p.E191K	ENST00000372470	NM_005373.2	191	Gaa/Aaa	4/12	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.480375581167401	2		504	391	SUCCESS
INSRR	3645	MSKCC	GRCh37	1	156811930	156811930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	110	522	0	ENST00000368195.3:c.3371C>T	p.Ser1124Phe	p.S1124F	ENST00000368195	NM_014215.2	1124	tCc/tTc	19/22	0.2336117768704	4	FACETS	1	0.958	1	1	0.958	1	INDETERMINATE	2	TRUE	2	0.480375581167401	4		522	311	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725057	162725057	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	139	378	0	ENST00000367921.3:c.529T>G	p.Cys177Gly	p.C177G	ENST00000367921	NM_006182.2	177	Tgt/Ggt	6/18	0.2336117768704	4	FACETS	0.927	0.851	1	0.927	0.851	1	INDETERMINATE	2	TRUE	2	0.480375581167401	4		378	462	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729737	162729737	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	209	389	0	ENST00000367921.3:c.823T>A	p.Phe275Ile	p.F275I	ENST00000367921	NM_006182.2	275	Ttt/Att	8/18	0.2336117768704	4	FACETS	1	0.983	1	1	0.983	1	INDETERMINATE	2	TRUE	2	0.480375581167401	4		389	561	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567300	226567300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	194	433	0	ENST00000366794.5:c.1586G>A	p.Gly529Glu	p.G529E	ENST00000366794	NM_001618.3	529	gGa/gAa	11/23	0.2336117768704	4	FACETS	1	0.986	1	1	0.986	1	INDETERMINATE	2	TRUE	2	0.480375581167401	4		433	498	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578181	226578181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	171	429	0	ENST00000366794.5:c.547G>A	p.Gly183Ser	p.G183S	ENST00000366794	NM_001618.3	183	Ggc/Agc	4/23	0.2336117768704	4	FACETS	1	0.984	1	1	0.984	1	INDETERMINATE	2	TRUE	2	0.480375581167401	4		429	439	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390946	89390946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	226	436	0	ENST00000336596.2:c.1012G>A	p.Glu338Lys	p.E338K	ENST00000336596	NM_005233.5	338	Gag/Aag	5/17	0.29118325647395	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.480375581167401	4		436	598	SUCCESS
APC	324	MSKCC	GRCh37	5	112175216	112175216	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1321583762	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	136	249	0	ENST00000257430.4:c.3925G>A	p.Glu1309Lys	p.E1309K	ENST00000257430	NM_000038.5	1309	Gaa/Aaa	16/16	0.2336117768704	4	FACETS	1	0.967	1	1	0.967	1	INDETERMINATE	2	TRUE	2	0.480375581167401	4		249	382	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043441	180043441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56310180	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	75	405	0	ENST00000261937.6:c.3145G>A	p.Asp1049Asn	p.D1049N	ENST00000261937	NM_182925.4	1049	Gac/Aac	23/30	0.452913427600244	1	FACETS	0.976	0.868	1	0.976	0.868	1	CLONAL	1	TRUE	0	0.480375581167401	1		405	243	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673803	30673803	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1387652060	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	172	263	0	ENST00000376406.3:c.3157C>T	p.Leu1053Phe	p.L1053F	ENST00000376406	NM_014641.2	1053	Ctt/Ttt	10/15	0.351784499777446	6	FACETS	0.929	0.867	0.991			1	CLONAL	4	TRUE	NA	0.480375581167401	6		263	378	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188814	32188814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754461878	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	80	399	0	ENST00000375023.3:c.740G>A	p.Gly247Asp	p.G247D	ENST00000375023	NM_004557.3	247	gGc/gAc	4/30	NA	2	FACETS	1	0.953	1			1	INDETERMINATE	1	TRUE	NA	0.480375581167401	2		399	294	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435763	116435763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267601244	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	187	519	0	ENST00000397752.3:c.3853C>T	p.Pro1285Ser	p.P1285S	ENST00000397752	NM_000245.2	1285	Cct/Tct	20/21	0.29118325647395	4	FACETS	0.936	0.869	1	0.936	0.869	1	CLONAL	2	TRUE	2	0.480375581167401	4		519	616	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140434555	140434555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	124	260	0	ENST00000288602.6:c.2143G>A	p.Glu715Lys	p.E715K	ENST00000288602	NM_004333.4	715	Gag/Aag	18/18	0.29118325647395	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.480375581167401	4		260	331	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492889	8492889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778370224	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	178	453	1	ENST00000356435.5:c.2440C>T	p.Pro814Ser	p.P814S	ENST00000356435		814	Ccc/Tcc	16/35	0.255523175301407	3	FACETS	0.972	0.904	1	0.972	0.904	1	INDETERMINATE	2	TRUE	1	0.480375581167401	3		454	473	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507381	8507381	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	193	480	0	ENST00000356435.5:c.1597T>A	p.Leu533Met	p.L533M	ENST00000356435		533	Ttg/Atg	11/35	0.255523175301407	3	FACETS	0.84	0.782	0.9	0.84	0.782	0.9	INDETERMINATE	2	TRUE	1	0.480375581167401	3		480	593	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589784	69589784	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	10	22	0	ENST00000168712.1:c.69G>A	p.Trp23Ter	p.W23*	ENST00000168712	NM_002007.2	23	tgG/tgA	1/3	NA	2	FACETS	1	0.768	1			1	INDETERMINATE	2	TRUE	NA	0.480375581167401	2		22	20	SUCCESS
EED	8726	MSKCC	GRCh37	11	85967550	85967550	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	158	329	1	ENST00000263360.6:c.548T>A	p.Ile183Lys	p.I183K	ENST00000263360	NM_003797.3	183	aTa/aAa	5/12	0.214301528285907	4	FACETS	0.99	0.914	1			1	INDETERMINATE	2	TRUE	NA	0.480375581167401	4		330	492	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375152	118375152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	197	478	0	ENST00000534358.1:c.8545C>T	p.Pro2849Ser	p.P2849S	ENST00000534358	NM_005933.3	2849	Cct/Tct	27/36	0.480375581167401	1	FACETS	0.916	0.866	0.966	1	0.994	1	CLONAL	2	TRUE	0	0.480375581167401	1		478	340	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375923	118375923	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	155	448	0	ENST00000534358.1:c.9316C>T	p.Gln3106Ter	p.Q3106*	ENST00000534358	NM_005933.3	3106	Caa/Taa	27/36	0.480375581167401	1	FACETS	0.791	0.738	0.844	1	0.991	1	SUBCLONAL	2	TRUE	0	0.480375581167401	1		448	310	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230638	46230638	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	221	515	0	ENST00000334344.6:c.887T>C	p.Leu296Pro	p.L296P	ENST00000334344	NM_152641.2	296	cTt/cCt	8/21	0.2336117768704	4	FACETS	1	0.977	1	1	0.977	1	INDETERMINATE	2	TRUE	2	0.480375581167401	4		515	624	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230641	46230641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	229	483	0	ENST00000334344.6:c.890C>T	p.Ser297Phe	p.S297F	ENST00000334344	NM_152641.2	297	tCc/tTc	8/21	0.2336117768704	4	FACETS	1	0.982	1	1	0.982	1	INDETERMINATE	2	TRUE	2	0.480375581167401	4		483	631	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32971122	32971122	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	250	464	0	ENST00000380152.3:c.9589G>A	p.Asp3197Asn	p.D3197N	ENST00000380152		3197	Gac/Aac	26/27	0.371034537287334	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.480375581167401	4		464	739	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352667	68352667	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	222	426	1	ENST00000487270.1:c.534T>A	p.His178Gln	p.H178Q	ENST00000487270	NM_133509.3	178	caT/caA	6/11	0.2336117768704	4	FACETS	1	0.94	1	1	0.94	1	INDETERMINATE	2	TRUE	2	0.480375581167401	4		427	681	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857482	9857482	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148827608	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	121	454	0	ENST00000330684.3:c.3919C>T	p.Pro1307Ser	p.P1307S	ENST00000330684	NM_001134407.1	1307	Ccc/Tcc	13/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.480375581167401	2		454	356	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984848	9984848	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	148	406	0	ENST00000330684.3:c.1117G>A	p.Glu373Lys	p.E373K	ENST00000330684	NM_001134407.1	373	Gaa/Aaa	4/13	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.480375581167401	2		406	419	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979989	7979989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	58	310	0	ENST00000319144.4:c.1348G>A	p.Gly450Arg	p.G450R	ENST00000319144	NM_001139.2	450	Ggg/Agg	10/15	0.168221204335273	4	FACETS	0.77	0.67	0.877	0.77	0.67	0.877	INDETERMINATE	2	TRUE	2	0.480375581167401	4		310	232	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528489	29528489	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764079291	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	278	574	0	ENST00000356175.3:c.1246C>T	p.Arg416Ter	p.R416*	ENST00000356175	NM_000267.3	416	Cga/Tga	11/57	0.168221204335273	4	FACETS	1	0.977	1	1	0.977	1	INDETERMINATE	2	TRUE	2	0.480375581167401	4		574	801	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271976	15271976	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	42	192	0	ENST00000263388.2:c.6463G>A	p.Gly2155Arg	p.G2155R	ENST00000263388	NM_000435.2	2155	Gga/Aga	33/33	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.480375581167401	2		192	156	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520168	9520168	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	181	431	0	ENST00000353224.5:c.2101A>T	p.Lys701Ter	p.K701*	ENST00000353224	NM_177990.2	701	Aaa/Taa	10/10	0.2336117768704	4	FACETS	1	0.987	1	1	0.987	1	INDETERMINATE	2	TRUE	2	0.480375581167401	4		431	447	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561439	9561439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	171	420	0	ENST00000353224.5:c.343C>T	p.His115Tyr	p.H115Y	ENST00000353224	NM_177990.2	115	Cac/Tac	4/10	0.2336117768704	4	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	2	TRUE	2	0.480375581167401	4		420	466	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827993	40827993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1328809133	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	114	336	0	ENST00000373198.4:c.2435G>A	p.Gly812Glu	p.G812E	ENST00000373198	NM_133170.3	812	gGa/gAa	17/32	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.480375581167401	2		336	347	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171760	36171760	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	132	295	0	ENST00000300305.3:c.806-1G>A		p.X269_splice	ENST00000300305		269			0.371034537287334	4	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	2	0.480375581167401	4		295	386	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195669	123195669	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1231750099	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	210	231	0	ENST00000218089.9:c.1583C>T	p.Thr528Ile	p.T528I	ENST00000218089	NM_001042749.1	528	aCc/aTc	17/35	0.214301528285907	2	FACETS	0.925	0.881	0.968			1	INDETERMINATE	3	TRUE	NA	0.480375581167401	2		231	315	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41201146	41201146	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1064794662	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	160	541	0	ENST00000357654.3:c.5398del	p.Gly1801AlafsTer33	p.G1801Afs*33	ENST00000357654	NM_007294.3	1800	Ctt/tt	21/23	0.168221204335273	4	FACETS	1	0.968	1	1	0.968	1	INDETERMINATE	2	TRUE	2	0.480375581167401	4		541	454	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560230	29560231	+	stop_gained,splice_region_variant	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0001756-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	114	227	0	ENST00000356175.3:c.3707_3708delinsAA	p.Trp1236Ter	p.W1236*	ENST00000356175	NM_000267.3	1236	tGG/tAA	27/57	0.168221204335273	4	FACETS	0.984	0.896	1	0.984	0.896	1	INDETERMINATE	2	TRUE	2	0.480375581167401	4		227	357	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001759-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	179	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.799524871556756	2		422	362	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0001759-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	684	310	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.795233053756143	3	FACETS	0.901	0.872	0.93			1	CLONAL	2	TRUE	NA	0.799524871556756	3		310	1329	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226573297	226573297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377195931	NA	P-0001759-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	95	463	0	ENST00000366794.5:c.919G>A	p.Asp307Asn	p.D307N	ENST00000366794	NM_001618.3	307	Gat/Aat	7/23	0.799524871556756	3	FACETS	0.251	0.222	0.281	0.125	0.111	0.141	SUBCLONAL	1	TRUE	1	0.799524871556756	3		463	1327	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379489	225379489	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001759-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	74	327	0	ENST00000264414.4:c.379G>A	p.Asp127Asn	p.D127N	ENST00000264414	NM_003590.4	127	Gac/Aac	4/16	NA	2	FACETS	0.199	0.174	0.227			1	INDETERMINATE	1	TRUE	NA	0.799524871556756	2		327	929	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259241	89259241	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201357801	NA	P-0001759-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	371	433	0	ENST00000336596.2:c.385G>A	p.Asp129Asn	p.D129N	ENST00000336596	NM_005233.5	129	Gat/Aat	3/17	1	2	FACETS	0.844	0.802	0.887	0.844	0.802	0.887	CLONAL	1	TRUE	1	0.799524871556756	2		433	1099	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	14017064	14017064	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001759-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	273	295	0	ENST00000405192.2:c.223C>G	p.Gln75Glu	p.Q75E	ENST00000405192	NM_001163147.1	75	Cag/Gag	5/12	0.799524871556756	3	FACETS	0.81	0.76	0.862	0.405	0.38	0.431	CLONAL	1	TRUE	1	0.799524871556756	3		295	1180	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70412313	70412313	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1351215230	NA	P-0001759-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	415	517	0	ENST00000373644.4:c.4423G>C	p.Glu1475Gln	p.E1475Q	ENST00000373644	NM_030625.2	1475	Gaa/Caa	6/12	NA	2	FACETS	0.843	0.803	0.884			1	INDETERMINATE	1	TRUE	NA	0.799524871556756	2		517	1231	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134691	2134691	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001759-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	168	275	0	ENST00000219476.3:c.4468G>C	p.Glu1490Gln	p.E1490Q	ENST00000219476	NM_000548.3	1490	Gag/Cag	34/42	1	2	FACETS	0.914	0.848	0.981	0.914	0.848	0.981	CLONAL	1	TRUE	1	0.799524871556756	2		275	460	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215930	41215930	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs80356858	NA	P-0001759-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	351	514	1	ENST00000357654.3:c.5113C>G	p.Leu1705Val	p.L1705V	ENST00000357654	NM_007294.3	1705	Cta/Gta	17/23	NA	2	FACETS	0.909	0.863	0.955			1	INDETERMINATE	1	TRUE	NA	0.799524871556756	2		515	966	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53241055	53241055	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001759-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	470	640	0	ENST00000375401.3:c.1156G>C	p.Glu386Gln	p.E386Q	ENST00000375401	NM_004187.3	386	Gag/Cag	9/26	0.193674944063891	1	FACETS	0.616	0.59	0.642	0.616	0.59	0.642	INDETERMINATE	1	TRUE	0	0.799524871556756	1		640	1146	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379349	225379350	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0001759-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	71	507	0	ENST00000264414.4:c.518_519delinsAA	p.Arg173Gln	p.R173Q	ENST00000264414	NM_003590.4	173	cGG/cAA	4/16	NA	2	FACETS	0.147	0.127	0.168			1	INDETERMINATE	1	TRUE	NA	0.799524871556756	2		507	1211	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0001764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	359	92	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.303762556209544	5	FACETS	1	0.986	1	0.856	0.82	0.893	CLONAL	4	TRUE	0	0.405588919539231	5		92	665	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147590	61147590	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	34	114	0	ENST00000295025.8:c.995C>G	p.Ala332Gly	p.A332G	ENST00000295025	NM_002908.2	332	gCc/gGc	9/11	0.35901222023727	4	FACETS	0.854	0.71	1	0.569	0.473	0.673	CLONAL	2	TRUE	1	0.405588919539231	4		114	138	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564521	55564521	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	62	586	0	ENST00000288135.5:c.409C>A	p.Pro137Thr	p.P137T	ENST00000288135	NM_000222.2	137	Cct/Act	3/21	NA	2	FACETS	0.608	0.526	0.697			1	INDETERMINATE	1	TRUE	NA	0.405588919539231	2		586	503	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759943	63759943	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	75	475	0	ENST00000279873.7:c.596C>G	p.Ser199Cys	p.S199C	ENST00000279873	NM_032199.2	199	tCt/tGt	4/10	0.384507330096085	4	FACETS	0.757	0.663	0.858	0.252	0.221	0.286	SUBCLONAL	1	TRUE	1	0.405588919539231	4		475	687	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971160	21971165	+	inframe_deletion	In_Frame_Del	DEL	GTGGAG	GTGGAG	-	novel	NA	P-0001764-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	88	174	0	ENST00000304494.5:c.193_198del	p.Leu65_His66del	p.L65_H66del	ENST00000304494	NM_000077.4	65	CTCCAC/-	2/3	0.405588919539231	4	FACETS	0.941	0.851	1	0.941	0.851	1	CLONAL	3	TRUE	1	0.405588919539231	4		174	216	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0001773-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	49	139	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.800259212044777	2		139	88	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0001773-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	417	310	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.790412207321651	5	FACETS	0.944	0.913	0.975			1	CLONAL	4	TRUE	NA	0.800259212044777	5		310	607	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374244	138374244	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001773-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	132	390	0	ENST00000289153.2:c.3200A>T	p.Asp1067Val	p.D1067V	ENST00000289153	NM_006219.2	1067	gAc/gTc	22/22	0.425425046206787	4	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.800259212044777	4		390	456	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193121548	193121548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001773-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	299	345	0	ENST00000367435.3:c.946C>T	p.His316Tyr	p.H316Y	ENST00000367435	NM_024529.4	316	Cat/Tat	10/17	0.800259212044777	7	FACETS	1	0.978	1	0.429	0.404	0.455	CLONAL	2	TRUE	2	0.800259212044777	7		345	1045	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693886	47693886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750029	NA	P-0001773-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	224	432	0	ENST00000233146.2:c.1600C>T	p.Arg534Cys	p.R534C	ENST00000233146	NM_000251.2	534	Cgt/Tgt	10/16	0.800259212044777	4	FACETS	0.875	0.821	0.93	0.583	0.547	0.62	CLONAL	2	TRUE	1	0.800259212044777	4		432	576	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119642237	119642237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001773-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	134	348	0	ENST00000316626.5:c.460C>T	p.Pro154Ser	p.P154S	ENST00000316626		154	Cct/Tct	4/12	0.738091246563101	4	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.800259212044777	4		348	480	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672149	30672149	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001773-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	66	344	0	ENST00000376406.3:c.4811C>T	p.Ser1604Phe	p.S1604F	ENST00000376406	NM_014641.2	1604	tCc/tTc	10/15	0.800259212044777	6	FACETS	0.897	0.781	1	0.224	0.195	0.256	CLONAL	1	TRUE	2	0.800259212044777	6		344	478	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403120	116403120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001773-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	280	343	0	ENST00000397752.3:c.2381C>T	p.Ser794Phe	p.S794F	ENST00000397752	NM_000245.2	794	tCt/tTt	11/21	0.800259212044777	7	FACETS	0.911	0.86	0.963	0.456	0.43	0.482	CLONAL	3	TRUE	1	0.800259212044777	7		343	768	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156008	119156008	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001773-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	138	456	0	ENST00000264033.4:c.1673C>T	p.Ser558Phe	p.S558F	ENST00000264033	NM_005188.3	558	tCc/tTc	11/16	0.800259212044777	3	FACETS	1	0.954	1	0.529	0.485	0.575	CLONAL	1	TRUE	1	0.800259212044777	3		456	456	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145431	58145431	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11547328	NA	P-0001773-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	438	315	0	ENST00000257904.6:c.70C>T	p.Arg24Cys	p.R24C	ENST00000257904	NM_000075.3	24	Cgt/Tgt	2/8	0.800259212044777	6	FACETS	1	0.989	1	0.847	0.818	0.876	CLONAL	4	TRUE	1	0.800259212044777	6		315	672	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636182	28636182	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376895552	NA	P-0001773-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	90	318	0	ENST00000241453.7:c.190G>A	p.Gly64Arg	p.G64R	ENST00000241453	NM_004119.2	64	Ggg/Agg	3/24	0.350953318710791	3	FACETS	0.946	0.847	1			1	INDETERMINATE	1	TRUE	NA	0.800259212044777	3		318	333	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670433	88670433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001773-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	219	332	0	ENST00000360948.2:c.1253C>T	p.Pro418Leu	p.P418L	ENST00000360948	NM_001012338.2	418	cCt/cTt	11/19	0.800259212044777	3	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	1	0.800259212044777	3		332	383	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892205	9892205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001773-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	95	427	0	ENST00000330684.3:c.2285G>A	p.Gly762Glu	p.G762E	ENST00000330684	NM_001134407.1	762	gGa/gAa	11/13	0.742850575289548	3	FACETS	1	0.909	1	0.505	0.454	0.558	CLONAL	1	TRUE	1	0.800259212044777	3		427	329	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435653	56435653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001773-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	75	199	0	ENST00000407977.2:c.1484C>T	p.Ser495Phe	p.S495F	ENST00000407977		495	tCt/tTt	9/10	0.426931455637537	6	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.800259212044777	6		199	338	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354124	15354124	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780441323	NA	P-0001773-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	102	104	0	ENST00000263377.2:c.2756C>T	p.Pro919Leu	p.P919L	ENST00000263377	NM_058243.2	919	cCt/cTt	14/20	0.800259212044777	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	3	TRUE	0	0.800259212044777	3		104	112	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001805-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	80	422	0				ENST00000310581	NM_198253.2	-/1132			0.166286999645904	4	FACETS	0.978	0.881	1			1	INDETERMINATE	2	TRUE	NA	0.748525689361909	4		422	191	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs104886003	NA	P-0001805-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	4970	492	0	ENST00000263967.3:c.1633G>C	p.Glu545Gln	p.E545Q	ENST00000263967	NM_006218.2	545	Gag/Cag	10/21	0.748525689361909	30	FACETS	0.983	0.977	0.989			1	CLONAL	28	TRUE	NA	0.748525689361909	30		492	5538	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300550	11300550	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001805-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	81	413	0	ENST00000361445.4:c.1596G>C	p.Lys532Asn	p.K532N	ENST00000361445	NM_004958.3	532	aaG/aaC	11/58	0.166286999645904	4	FACETS	0.627	0.552	0.706			1	INDETERMINATE	1	TRUE	NA	0.748525689361909	4		413	604	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518315	204518315	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001805-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	113	472	0	ENST00000367182.3:c.978G>C	p.Leu326Phe	p.L326F	ENST00000367182	NM_001278516.1	326	ttG/ttC	11/11	0.427196767051053	2	FACETS	0.468	0.422	0.517	0.234	0.211	0.259	INDETERMINATE	1	TRUE	0	0.748525689361909	2		472	645	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61725918	61725918	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001805-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	524	418	0	ENST00000401558.2:c.649C>G	p.Gln217Glu	p.Q217E	ENST00000401558	NM_003400.3	217	Caa/Gaa	9/25	0.748525689361909	3	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.748525689361909	3		418	828	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881409	111881409	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001805-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	408	403	0	ENST00000393256.3:c.87A>T	p.Arg29Ser	p.R29S	ENST00000393256	NM_006538.4	29	agA/agT	2/4	NA	2	FACETS	0.856	0.825	0.886			1	INDETERMINATE	2	TRUE	NA	0.748525689361909	2		403	637	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528276	157528276	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001805-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	102	337	0	ENST00000346085.5:c.6001G>A	p.Glu2001Lys	p.E2001K	ENST00000346085	NM_020732.3	2001	Gag/Aag	20/20	0.324678928421374	1	FACETS	0.407	0.366	0.45	0.407	0.366	0.45	INDETERMINATE	1	TRUE	0	0.748525689361909	1		337	419	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126756	5126756	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0001805-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	105	336	0	ENST00000381652.3:c.3364C>T	p.Arg1122Ter	p.R1122*	ENST00000381652	NM_004972.3	1122	Cga/Tga	25/25	0.748525689361909	1	FACETS	0.444	0.401	0.49	0.444	0.401	0.49	SUBCLONAL	1	TRUE	0	0.748525689361909	1		336	395	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12038859	12038859	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0001805-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	153	436	0	ENST00000396373.4:c.1153-1G>A		p.X385_splice	ENST00000396373	NM_001987.4	385			0.748525689361909	4	FACETS	0.881	0.807	0.959			1	CLONAL	1	TRUE	NA	0.748525689361909	4		436	811	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597498	28597498	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001805-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	78	503	0	ENST00000241453.7:c.2407G>C	p.Glu803Gln	p.E803Q	ENST00000241453	NM_004119.2	803	Gaa/Caa	19/24	0.600948755234434	1	FACETS	0.305	0.269	0.344	0.305	0.269	0.344	SUBCLONAL	1	TRUE	0	0.748525689361909	1		503	427	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99192845	99192845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774479139	NA	P-0001805-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	391	339	0	ENST00000268035.6:c.35C>T	p.Ser12Leu	p.S12L	ENST00000268035	NM_000875.3	12	tCg/tTg	1/21	0.725819375928549	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.748525689361909	2		339	498	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274169	10274169	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001805-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	77	298	0	ENST00000330684.3:c.100C>G	p.Leu34Val	p.L34V	ENST00000330684	NM_001134407.1	34	Cta/Gta	2/13	0.257436323885705	2	FACETS	0.625	0.553	0.701	0.313	0.276	0.351	INDETERMINATE	1	TRUE	0	0.748525689361909	2		298	329	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0001805-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	204	377	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.748525689361909	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.748525689361909	1		377	307	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66523994	66523994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001805-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	97	265	0	ENST00000358598.2:c.722G>A	p.Arg241Lys	p.R241K	ENST00000358598	NM_212471.2	241	aGa/aAa	8/11	1	2	FACETS	0.439	0.392	0.488	0.439	0.392	0.488	SUBCLONAL	1	TRUE	1	0.748525689361909	2		265	591	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143073	7143073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774340801	NA	P-0001805-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	54	270	0	ENST00000302850.5:c.2296G>A	p.Asp766Asn	p.D766N	ENST00000302850	NM_000208.2	766	Gat/Aat	12/22	0.272737568675511	1	FACETS	0.216	0.185	0.25	0.216	0.185	0.25	INDETERMINATE	1	TRUE	0	0.748525689361909	1		270	418	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271774	15271774	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1489373939	NA	P-0001805-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	33	274	0	ENST00000263388.2:c.6665C>T	p.Pro2222Leu	p.P2222L	ENST00000263388	NM_000435.2	2222	cCg/cTg	33/33	0.272737568675511	1	FACETS	0.183	0.149	0.221	0.183	0.149	0.221	INDETERMINATE	1	TRUE	0	0.748525689361909	1		274	301	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719914	52719914	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1247831715	NA	P-0001805-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	69	354	0	ENST00000322088.6:c.1126G>A	p.Glu376Lys	p.E376K	ENST00000322088	NM_014225.5	376	Gag/Aag	9/15	0.748525689361909	7	FACETS	0.435	0.377	0.498	0.109	0.094	0.125	SUBCLONAL	1	TRUE	3	0.748525689361909	7		354	1216	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551013	41551013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001805-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	345	402	0	ENST00000263253.7:c.3157G>A	p.Glu1053Lys	p.E1053K	ENST00000263253	NM_001429.3	1053	Gaa/Aaa	17/31	0.469342532806653	4	FACETS	0.918	0.872	0.964			1	CLONAL	2	TRUE	NA	0.748525689361909	4		402	878	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573896	41573896	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001805-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	86	392	0	ENST00000263253.7:c.6181C>A	p.Pro2061Thr	p.P2061T	ENST00000263253	NM_001429.3	2061	Ccc/Acc	31/31	0.469342532806653	4	FACETS	0.534	0.472	0.601			1	SUBCLONAL	1	TRUE	NA	0.748525689361909	4		392	752	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001809-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	135	422	0				ENST00000310581	NM_198253.2	-/1132			0.285680616846543	1	FACETS	1	0.982	1	1	0.992	1	CLONAL	2	TRUE	0	0.285680616846543	1		422	331	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0001809-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	388	384	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	1	2	FACETS	0.967	0.923	1	1	0.997	1	CLONAL	3	TRUE	1	0.285680616846543	2		384	936	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001819-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	68	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.694639143975878	2		422	177	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0001819-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	183	387	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.694639143975878	2		387	516	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451427	187451427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001819-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	254	456	0	ENST00000232014.4:c.55C>T	p.Leu19Phe	p.L19F	ENST00000232014	NM_001130845.1	19	Ctt/Ttt	3/10	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.694639143975878	2		456	699	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221743	55221743	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519829	NA	P-0001819-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8329	466	462	0	ENST00000275493.2:c.787A>C	p.Thr263Pro	p.T263P	ENST00000275493	NM_005228.3	263	Acc/Ccc	7/28	0.694639143975878	26	FACETS	1	0.995	1			1	CLONAL	1	TRUE	NA	0.694639143975878	26		462	8795	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0001819-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7602	1041	487	0	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.694639143975878	26	FACETS	1	0.992	1			1	CLONAL	3	TRUE	NA	0.694639143975878	26		487	8643	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0001819-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	8434	436	355	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.694639143975878	26	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.694639143975878	26		355	8870	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112910835	112910835	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs397507529	NA	P-0001819-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	41	181	0	ENST00000351677.2:c.844A>G	p.Ile282Val	p.I282V	ENST00000351677	NM_002834.3	282	Atc/Gtc	7/16	1	2	FACETS	0.291	0.242	0.345	0.291	0.242	0.345	SUBCLONAL	1	TRUE	1	0.694639143975878	2		181	406	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253820	30253820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs577055474	NA	P-0001819-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	300	497	0	ENST00000307677.4:c.634C>T	p.Arg212Cys	p.R212C	ENST00000307677	NM_138578.1	212	Cgc/Tgc	3/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.694639143975878	2		497	801	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577142	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057519990	NA	P-0001836-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	262	702	0	ENST00000269305.4:c.796G>T	p.Gly266Ter	p.G266*	ENST00000269305	NM_001126112.2	266	Gga/Tga	8/11	0.291206066196887	2	FACETS	0.923	0.869	0.978	0.923	0.869	0.978	CLONAL	2	TRUE	0	0.391996625863894	2		702	724	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857784	9857784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145861983	NA	P-0001836-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	260	727	0	ENST00000330684.3:c.3617G>A	p.Arg1206Gln	p.R1206Q	ENST00000330684	NM_001134407.1	1206	cGa/cAa	13/13	0.244091688523858	2	FACETS	0.924	0.87	0.979	0.924	0.87	0.979	CLONAL	2	TRUE	0	0.391996625863894	2		727	718	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967065	25967065	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001836-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	298	608	0	ENST00000435504.4:c.2141G>T	p.Ser714Ile	p.S714I	ENST00000435504		714	aGt/aTt	13/13	0.282593457865889	2	FACETS	0.929	0.879	0.981	0.929	0.879	0.981	CLONAL	2	TRUE	0	0.391996625863894	2		608	818	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498275	29498275	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001836-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	162	465	0	ENST00000389048.3:c.1905C>A	p.Tyr635Ter	p.Y635*	ENST00000389048	NM_004304.4	635	taC/taA	10/29	0.282593457865889	2	FACETS	0.812	0.75	0.875	0.812	0.75	0.875	CLONAL	2	TRUE	0	0.391996625863894	2		465	509	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566718	212566718	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001836-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	243	605	0	ENST00000342788.4:c.1463G>T	p.Arg488Leu	p.R488L	ENST00000342788	NM_005235.2	488	cGg/cTg	12/28	1	2	FACETS	0.752	0.705	0.801	1	0.993	1	SUBCLONAL	2	TRUE	1	0.391996625863894	2		605	824	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913403	NA	P-0001836-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	135	596	0	ENST00000349496.5:c.110C>G	p.Ser37Cys	p.S37C	ENST00000349496	NM_001904.3	37	tCt/tGt	3/15	0.369230082505724	2	FACETS	1	0.916	1	0.503	0.458	0.55	CLONAL	1	TRUE	0	0.391996625863894	2		596	685	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217236	66217236	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001836-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	309	554	0	ENST00000273854.3:c.2379C>A	p.Asp793Glu	p.D793E	ENST00000273854	NM_004439.5	793	gaC/gaA	14/18	0.391996625863894	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	0	0.391996625863894	2		554	660	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111651	56111651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001836-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	49	117	0	ENST00000399503.3:c.251C>T	p.Pro84Leu	p.P84L	ENST00000399503	NM_005921.1	84	cCg/cTg	1/20	0.285998123507955	2	FACETS	1	0.958	1	0.668	0.575	0.768	CLONAL	1	TRUE	0	0.391996625863894	2		117	187	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389366	8389366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001836-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	199	660	0	ENST00000356435.5:c.4252G>T	p.Gly1418Trp	p.G1418W	ENST00000356435		1418	Ggg/Tgg	26/35	0.391996625863894	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.391996625863894	1		660	574	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971138	21971138	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs760640852	NA	P-0001836-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	70	105	0	ENST00000304494.5:c.220G>T	p.Asp74Tyr	p.D74Y	ENST00000304494	NM_000077.4	74	Gac/Tac	2/3	0.285998123507955	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	0	0.391996625863894	2		105	169	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109819	115109819	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001836-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	60	350	0	ENST00000257566.3:c.2059G>C	p.Asp687His	p.D687H	ENST00000257566	NM_016569.3	687	Gac/Cac	8/8	1	2	FACETS	0.769	0.665	0.881	0.769	0.665	0.881	SUBCLONAL	1	TRUE	1	0.391996625863894	2		350	398	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29004289	29004289	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001836-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	172	575	0	ENST00000282397.4:c.1004C>A	p.Thr335Asn	p.T335N	ENST00000282397	NM_002019.4	335	aCt/aAt	8/30	0.391996625863894	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.391996625863894	1		575	570	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81557474	81557474	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001836-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	139	717	0	ENST00000298171.2:c.454A>G	p.Ile152Val	p.I152V	ENST00000298171	NM_000369.2	152	Ata/Gta	5/10	NA	2	FACETS	0.919	0.837	1			1	INDETERMINATE	1	TRUE	NA	0.391996625863894	2		717	772	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858060	9858060	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555482504	NA	P-0001836-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	59	790	0	ENST00000330684.3:c.3341G>C	p.Arg1114Thr	p.R1114T	ENST00000330684	NM_001134407.1	1114	aGa/aCa	13/13	0.244091688523858	2	FACETS	0.419	0.36	0.484	0.21	0.18	0.242	SUBCLONAL	1	TRUE	0	0.391996625863894	2		790	718	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007210	62007210	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001836-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	90	510	0	ENST00000392795.3:c.472C>G	p.Leu158Val	p.L158V	ENST00000392795	NM_001039933.1	158	Ctg/Gtg	4/6	0.391996625863894	5	FACETS	0.78	0.691	0.876	0.195	0.172	0.219	SUBCLONAL	1	TRUE	1	0.391996625863894	5		510	935	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637845	39637845	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0001836-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	47	545	0	ENST00000262039.4:c.2264-2A>T		p.X755_splice	ENST00000262039	NM_002647.2	755			0.219961042384182	3	FACETS	0.413	0.348	0.486	0.138	0.116	0.162	INDETERMINATE	1	TRUE	0	0.391996625863894	3		545	694	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604710	48604710	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001836-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	128	606	0	ENST00000342988.3:c.1532C>G	p.Pro511Arg	p.P511R	ENST00000342988	NM_005359.5	511	cCg/cGg	12/12	0.219961042384182	3	FACETS	1	0.972	1	0.392	0.355	0.429	INDETERMINATE	1	TRUE	0	0.391996625863894	3		606	665	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610198	10610198	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001836-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	510	759	0	ENST00000171111.5:c.512G>T	p.Cys171Phe	p.C171F	ENST00000171111	NM_203500.1	171	tGc/tTc	2/6	0.391996625863894	2	FACETS	0.854	0.822	0.886	1	0.996	1	CLONAL	3	TRUE	0	0.391996625863894	2		759	1016	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245114	53245114	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001836-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	237	732	0	ENST00000375401.3:c.826G>T	p.Glu276Ter	p.E276*	ENST00000375401	NM_004187.3	276	Gag/Tag	7/26	0.391996625863894	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.391996625863894	1		732	733	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200274	123200274	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0001836-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	211	756	0	ENST00000218089.9:c.2253C>G	p.Ser751Arg	p.S751R	ENST00000218089	NM_001042749.1	751	agC/agG	23/35	0.205864357223056	3	FACETS	1	0.987	1	0.632	0.586	0.679	INDETERMINATE	1	TRUE	1	0.391996625863894	3		756	1019	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101557	27101558	+	stop_gained	Nonsense_Mutation	DNP	GC	GC	TT	novel	NA	P-0001836-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	131	709	0	ENST00000324856.7:c.4839_4840delinsTT	p.Met1613_Gln1614delinsIleTer	p.M1613_Q1614delinsI*	ENST00000324856	NM_006015.4	1613	atGCag/atTTag	18/20	0.205864357223056	3	FACETS	0.972	0.883	1	0.486	0.441	0.534	INDETERMINATE	1	TRUE	1	0.391996625863894	3		709	822	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0001841-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	236	139	0				ENST00000310581	NM_198253.2	-/1132			0.452245371163311	1	FACETS	1	0.972	1	1	0.996	1	CLONAL	2	TRUE	0	0.503431714730442	1		139	343	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268766	41268766	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0001841-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	840	731	0	ENST00000349496.5:c.1004A>T	p.Lys335Ile	p.K335I	ENST00000349496	NM_001904.3	335	aAa/aTa	7/15	0.503431714730442	4	FACETS	0.944	0.915	0.972			1	CLONAL	3	TRUE	NA	0.503431714730442	4		731	1772	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213837	66213837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001841-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	591	944	0	ENST00000273854.3:c.2593G>A	p.Gly865Arg	p.G865R	ENST00000273854	NM_004439.5	865	Gga/Aga	15/18	1	2	FACETS	0.944	0.91	0.977	1	0.998	1	CLONAL	2	TRUE	1	0.503431714730442	2		944	1244	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539927	187539927	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0001841-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	428	577	0	ENST00000441802.2:c.7813A>C	p.Ile2605Leu	p.I2605L	ENST00000441802	NM_005245.3	2605	Atc/Ctc	10/27	1	2	FACETS	0.924	0.885	0.963	1	0.997	1	CLONAL	2	TRUE	1	0.503431714730442	2		577	920	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339680	116339680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001841-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1548	226	485	1	ENST00000397752.3:c.542G>A	p.Gly181Glu	p.G181E	ENST00000397752	NM_000245.2	181	gGa/gAa	2/21	0.503431714730442	5	FACETS	0.888	0.824	0.955	0.222	0.206	0.239	CLONAL	1	TRUE	1	0.503431714730442	5		486	1774	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680680	88680680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001841-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	364	625	0	ENST00000360948.2:c.577G>A	p.Asp193Asn	p.D193N	ENST00000360948	NM_001012338.2	193	Gat/Aat	6/19	1	2	FACETS	0.895	0.854	0.936	1	0.996	1	CLONAL	2	TRUE	1	0.503431714730442	2		625	808	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2225401	2225401	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0001841-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	499	617	1	ENST00000398665.3:c.3611T>A	p.Ile1204Asn	p.I1204N	ENST00000398665	NM_032482.2	1204	aTt/aAt	26/28	1	2	FACETS	0.861	0.827	0.896	1	0.997	1	CLONAL	2	TRUE	1	0.503431714730442	2		618	1151	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0001841-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	1189	627	1	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.503431714730442	5	FACETS	0.943	0.924	0.961	1	0.998	1	CLONAL	5	TRUE	1	0.503431714730442	5		628	1759	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0001843-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	29	139	0				ENST00000310581	NM_198253.2	-/1132			0.300518304508103	4	FACETS	0.913	0.753	1	0.913	0.753	1	INDETERMINATE	2	TRUE	2	0.51005381263905	4		139	94	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577515	7577517	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	rs1064794309	NA	P-0001843-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	239	274	0	ENST00000269305.4:c.764_766del	p.Ile255del	p.I255del	ENST00000269305	NM_001126112.2	255	aTCAca/aca	7/11	0.51005381263905	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	4	TRUE	0	0.51005381263905	4		274	336	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259145	89259145	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001843-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	37	351	0	ENST00000336596.2:c.289G>C	p.Val97Leu	p.V97L	ENST00000336596	NM_005233.5	97	Gtg/Ctg	3/17	0.51005381263905	4	FACETS	0.65	0.537	0.776	0.325	0.268	0.388	SUBCLONAL	1	TRUE	2	0.51005381263905	4		351	337	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719881	18719881	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0001843-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	103	400	0	ENST00000266497.5:c.3780-2A>T		p.X1260_splice	ENST00000266497		1260			0.495147999122725	3	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	1	0.51005381263905	3		400	244	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711984	89711984	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0001843-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	67	201	0	ENST00000371953.3:c.604del	p.Thr202LeufsTer19	p.T202Lfs*19	ENST00000371953	NM_000314.4	201	gAa/ga	6/9	0.51005381263905	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	2	TRUE	0	0.51005381263905	2		201	131	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001853-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	27	422	0				ENST00000310581	NM_198253.2	-/1132			0.370428481359095	4	FACETS	1	0.889	1	1	0.954	1	CLONAL	3	TRUE	2	0.370428481359095	4		422	61	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654854	29654854	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0001853-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	47	2238	0	ENST00000356175.3:c.5543T>G	p.Leu1848Ter	p.L1848*	ENST00000356175	NM_000267.3	1848	tTa/tGa	37/57	0.370428481359095	2	FACETS	0.919	0.809	1	1	0.967	1	CLONAL	3	TRUE	0	0.370428481359095	2		2238	92	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032778	30032778	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0001853-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	11	3095	1	ENST00000338641.4:c.153C>A	p.Cys51Ter	p.C51*	ENST00000338641	NM_000268.3	51	tgC/tgA	2/16	0.262025707834145	3	FACETS	0.554	0.385	0.762	0.185	0.128	0.254	SUBCLONAL	1	TRUE	0	0.370428481359095	3		3096	127	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602707	10602707	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001853-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	74	3164	1	ENST00000171111.5:c.871del	p.Leu291CysfsTer26	p.L291Cfs*26	ENST00000171111	NM_203500.1	291	Ctg/tg	3/6	0.370428481359095	2	FACETS	1	0.909	1	1	0.982	1	CLONAL	3	TRUE	0	0.370428481359095	2		3165	133	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032768	30032769	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0001853-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	11	3148	0	ENST00000338641.4:c.146dup	p.Leu49PhefsTer37	p.L49Ffs*37	ENST00000338641	NM_000268.3	48	gat/gaTt	2/16	0.262025707834145	3	FACETS	0.55	0.382	0.756	0.183	0.127	0.252	SUBCLONAL	1	TRUE	0	0.370428481359095	3		3148	128	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001866-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	47	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.378808821233709	2		422	178	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0001866-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	53	310	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.914	0.785	1	0.914	0.785	1	CLONAL	1	TRUE	1	0.378808821233709	2		310	306	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307254	118307254	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001866-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	25	76	0	ENST00000534358.1:c.27C>A	p.Phe9Leu	p.F9L	ENST00000534358	NM_005933.3	9	ttC/ttA	1/36	0.378808821233709	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.378808821233709	1		76	84	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307502	118307502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782112520	NA	P-0001866-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	53	469	0	ENST00000534358.1:c.275C>T	p.Ser92Leu	p.S92L	ENST00000534358	NM_005933.3	92	tCg/tTg	1/36	0.378808821233709	1	FACETS	0.777	0.667	0.895	0.777	0.667	0.895	SUBCLONAL	1	TRUE	0	0.378808821233709	1		469	292	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307508	118307508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782775993	NA	P-0001866-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	58	491	0	ENST00000534358.1:c.281C>T	p.Ser94Leu	p.S94L	ENST00000534358	NM_005933.3	94	tCg/tTg	1/36	0.378808821233709	1	FACETS	0.811	0.702	0.929	0.811	0.702	0.929	CLONAL	1	TRUE	0	0.378808821233709	1		491	306	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0001868-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	63	139	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.819506733539796	2		139	144	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653820	89653820	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0001868-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	243	443	1	ENST00000371953.3:c.118del	p.Glu40LysfsTer14	p.E40Kfs*14	ENST00000371953	NM_000314.4	40	Gaa/aa	2/9	0.819506733539796	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.819506733539796	1		444	326	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001882-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	140	422	0				ENST00000310581	NM_198253.2	-/1132			0.78077682455966	1	FACETS	0.849	0.802	0.893	0.849	0.802	0.893	CLONAL	1	TRUE	0	0.91402118531105	1		422	196	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0001882-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	276	314	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.45033096062393	1	FACETS	0.344	0.324	0.366	0.344	0.324	0.366	INDETERMINATE	1	TRUE	0	0.91402118531105	1		314	952	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038231	30038231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	301	456	0	ENST00000338641.4:c.404C>T	p.Pro135Leu	p.P135L	ENST00000338641	NM_000268.3	135	cCt/cTt	4/16	NA	2	FACETS	0.535	0.504	0.568			1	INDETERMINATE	1	TRUE	NA	0.91402118531105	2		456	1230	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781509	9781509	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	160	334	0	ENST00000377346.4:c.1819G>A	p.Glu607Lys	p.E607K	ENST00000377346	NM_005026.3	607	Gag/Aag	15/24	0.91402118531105	1	FACETS	0.502	0.466	0.538	0.502	0.466	0.538	SUBCLONAL	1	TRUE	0	0.91402118531105	1		334	379	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543620	29543620	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	231	408	0	ENST00000389048.3:c.1543C>T	p.Gln515Ter	p.Q515*	ENST00000389048	NM_004304.4	515	Caa/Taa	7/29	0.538694965535743	1	FACETS	0.338	0.316	0.361	0.338	0.316	0.361	INDETERMINATE	1	TRUE	0	0.91402118531105	1		408	811	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595851	52595851	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	355	455	0	ENST00000394830.3:c.4064G>A	p.Gly1355Glu	p.G1355E	ENST00000394830	NM_018313.4	1355	gGg/gAg	26/30	NA	2	FACETS	0.713	0.676	0.75			1	INDETERMINATE	1	TRUE	NA	0.91402118531105	2		455	1090	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447294	187447294	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	197	306	0	ENST00000232014.4:c.899G>A	p.Ser300Asn	p.S300N	ENST00000232014	NM_001130845.1	300	aGc/aAc	5/10	0.538694965535743	1	FACETS	0.36	0.335	0.386	0.36	0.335	0.386	INDETERMINATE	1	TRUE	0	0.91402118531105	1		306	650	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638522	176638522	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001882-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	281	341	0	ENST00000439151.2:c.3122A>G	p.Asn1041Ser	p.N1041S	ENST00000439151	NM_022455.4	1041	aAc/aGc	5/23	0.451296922757671	1	FACETS	0.396	0.373	0.419	0.396	0.373	0.419	INDETERMINATE	1	TRUE	0	0.91402118531105	1		341	843	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405092	405092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	263	390	0	ENST00000380956.4:c.1174C>T	p.Pro392Ser	p.P392S	ENST00000380956	NM_001195286.1	392	Cca/Tca	8/9	NA	2	FACETS	0.522	0.489	0.556			1	INDETERMINATE	1	TRUE	NA	0.91402118531105	2		390	1102	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166452	32166452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	286	512	0	ENST00000375023.3:c.4591C>T	p.Pro1531Ser	p.P1531S	ENST00000375023	NM_004557.3	1531	Cct/Tct	25/30	NA	2	FACETS	0.488	0.458	0.519			1	INDETERMINATE	1	TRUE	NA	0.91402118531105	2		512	1282	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157519986	157519986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	251	356	0	ENST00000346085.5:c.4055C>T	p.Pro1352Leu	p.P1352L	ENST00000346085	NM_020732.3	1352	cCc/cTc	17/20	NA	2	FACETS	0.546	0.511	0.582			1	INDETERMINATE	1	TRUE	NA	0.91402118531105	2		356	1006	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683626	162683626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs529360617	NA	P-0001882-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	209	357	0	ENST00000366898.1:c.343G>A	p.Asp115Asn	p.D115N	ENST00000366898	NM_004562.2	115	Gac/Aac	3/12	NA	2	FACETS	0.487	0.452	0.523			1	INDETERMINATE	1	TRUE	NA	0.91402118531105	2		357	940	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971375	13971375	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0001882-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	245	223	0	ENST00000405192.2:c.555-1G>A		p.X185_splice	ENST00000405192	NM_001163147.1	185			0.147838254192764	4	FACETS	1	0.965	1	0.524	0.49	0.559	INDETERMINATE	1	TRUE	2	0.91402118531105	4		223	979	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415138	116415138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	283	358	0	ENST00000397752.3:c.3232G>A	p.Val1078Met	p.V1078M	ENST00000397752	NM_000245.2	1078	Gtg/Atg	15/21	1	2	FACETS	0.497	0.466	0.528	0.497	0.466	0.528	SUBCLONAL	1	TRUE	1	0.91402118531105	2		358	1247	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277118	38277118	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	275	424	0	ENST00000425967.3:c.1310G>A	p.Ser437Asn	p.S437N	ENST00000425967	NM_001174067.1	437	aGt/aAt	10/19	0.538694965535743	1	FACETS	0.395	0.372	0.419	0.395	0.372	0.419	INDETERMINATE	1	TRUE	0	0.91402118531105	1		424	827	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400047	139400047	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	185	322	1	ENST00000277541.6:c.4301G>A	p.Gly1434Asp	p.G1434D	ENST00000277541	NM_017617.3	1434	gGt/gAt	25/34	1	2	FACETS	0.524	0.485	0.565	0.524	0.485	0.565	SUBCLONAL	1	TRUE	1	0.91402118531105	2		323	772	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871249	12871249	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0001882-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	70	90	0	ENST00000228872.4:c.475+1G>A		p.X159_splice	ENST00000228872	NM_004064.3	159			NA	2	FACETS	0.541	0.477	0.61			1	INDETERMINATE	1	TRUE	NA	0.91402118531105	2		90	283	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231362	46231362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	261	298	0	ENST00000334344.6:c.1202G>A	p.Arg401Lys	p.R401K	ENST00000334344	NM_152641.2	401	aGa/aAa	10/21	NA	2	FACETS	0.472	0.442	0.504			1	INDETERMINATE	1	TRUE	NA	0.91402118531105	2		298	1209	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442480	49442480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	404	448	0	ENST00000301067.7:c.4093G>A	p.Val1365Ile	p.V1365I	ENST00000301067	NM_003482.3	1365	Gtt/Att	13/54	0.219584667751444	4	FACETS	1	0.983	1	0.539	0.512	0.567	INDETERMINATE	1	TRUE	2	0.91402118531105	4		448	1569	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445163	49445163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	172	200	0	ENST00000301067.7:c.2303C>T	p.Pro768Leu	p.P768L	ENST00000301067	NM_003482.3	768	cCa/cTa	10/54	0.219584667751444	4	FACETS	0.958	0.883	1	0.479	0.441	0.518	INDETERMINATE	1	TRUE	2	0.91402118531105	4		200	752	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448200	49448200	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0001882-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	275	322	0	ENST00000301067.7:c.401-1G>A		p.X134_splice	ENST00000301067	NM_003482.3	134			0.219584667751444	4	FACETS	0.91	0.853	0.968	0.455	0.426	0.484	INDETERMINATE	1	TRUE	2	0.91402118531105	4		322	1266	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926528	59926528	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1297	353	484	0	ENST00000259008.2:c.469G>A	p.Glu157Lys	p.E157K	ENST00000259008	NM_032043.2	157	Gag/Aag	5/20	NA	2	FACETS	0.468	0.442	0.495			1	INDETERMINATE	1	TRUE	NA	0.91402118531105	2		484	1650	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422953	45422953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	466	517	0	ENST00000262160.6:c.175G>A	p.Asp59Asn	p.D59N	ENST00000262160	NM_005901.5	59	Gat/Aat	2/11	0.451296922757671	1	FACETS	0.381	0.363	0.399	0.381	0.363	0.399	INDETERMINATE	1	TRUE	0	0.91402118531105	1		517	1454	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573460	48573460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	294	313	0	ENST00000342988.3:c.44C>T	p.Ala15Val	p.A15V	ENST00000342988	NM_005359.5	15	gCc/gTc	2/12	0.451296922757671	1	FACETS	0.385	0.363	0.407	0.385	0.363	0.407	INDETERMINATE	1	TRUE	0	0.91402118531105	1		313	908	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223021	1223021	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	250	354	0	ENST00000326873.7:c.958G>A	p.Val320Met	p.V320M	ENST00000326873	NM_000455.4	320	Gtg/Atg	8/10	NA	2	FACETS	0.532	0.498	0.568			1	INDETERMINATE	1	TRUE	NA	0.91402118531105	2		354	1028	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291034	15291034	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	151	395	0	ENST00000263388.2:c.3176G>A	p.Gly1059Glu	p.G1059E	ENST00000263388	NM_000435.2	1059	gGg/gAg	20/33	0.623571283296882	1	FACETS	0.263	0.241	0.286	0.263	0.241	0.286	SUBCLONAL	1	TRUE	0	0.91402118531105	1		395	682	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376428	15376428	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001882-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	231	496	0	ENST00000263377.2:c.586G>A	p.Val196Ile	p.V196I	ENST00000263377	NM_058243.2	196	Gta/Ata	5/20	NA	2	FACETS	0.495	0.461	0.53			1	INDETERMINATE	1	TRUE	NA	0.91402118531105	2		496	1021	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791757	42791757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568504941	NA	P-0001882-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	614	339	0	ENST00000575354.2:c.643C>T	p.Arg215Trp	p.R215W	ENST00000575354	NM_015125.3	215	Cgg/Tgg	5/20	0.91402118531105	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.91402118531105	1		339	679	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931990	39931990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	281	253	0	ENST00000378444.4:c.2609C>T	p.Thr870Ile	p.T870I	ENST00000378444	NM_001123385.1	870	aCt/aTt	4/15	1	1	FACETS	0.534	0.506	0.563	0.534	0.506	0.563	SUBCLONAL	1	TRUE	0	0.91402118531105	1		253	625	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035968	47035968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	325	233	0	ENST00000377604.3:c.646G>A	p.Asp216Asn	p.D216N	ENST00000377604	NM_001204468.1	216	Gac/Aac	7/24	1	1	FACETS	0.541	0.514	0.567	0.541	0.514	0.567	SUBCLONAL	1	TRUE	0	0.91402118531105	1		233	714	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123190057	123190057	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001882-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	380	259	0	ENST00000218089.9:c.1276G>A	p.Val426Ile	p.V426I	ENST00000218089	NM_001042749.1	426	Gta/Ata	14/35	1	1	FACETS	0.555	0.53	0.58	0.555	0.53	0.58	SUBCLONAL	1	TRUE	0	0.91402118531105	1		259	813	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433867	78433870	+	frameshift_variant	Frame_Shift_Del	DEL	CTTT	CTTT	-	novel	NA	P-0001882-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	618	392	2	ENST00000370768.2:c.229_232del	p.Lys77LeufsTer23	p.K77Lfs*23	ENST00000370768	NM_003902.3	77	AAAGtt/tt	3/20	0.91402118531105	1	FACETS	0.925	0.903	0.945	0.925	0.903	0.945	CLONAL	1	TRUE	0	0.91402118531105	1		394	794	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0001904-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	40	65	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.323078567660487	3	FACETS	0.275	0.228	0.327	0.137	0.114	0.164	INDETERMINATE	1	TRUE	1	0.842865282765541	3		65	491	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001904-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	63	422	0				ENST00000310581	NM_198253.2	-/1132			0.141391753564	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.842865282765541	0		422	150	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001904-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	219	143	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.323078567660487	3	FACETS	0.877	0.828	0.926	0.877	0.828	0.926	INDETERMINATE	2	TRUE	1	0.842865282765541	3		143	421	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0001904-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	218	370	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	NA	2	FACETS	1	0.942	1			1	INDETERMINATE	1	TRUE	NA	0.842865282765541	2		370	516	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638026	176638026	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779998560	NA	P-0001904-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	192	386	0	ENST00000439151.2:c.2626G>A	p.Val876Ile	p.V876I	ENST00000439151	NM_022455.4	876	Gtc/Atc	5/23	0.323078567660487	3	FACETS	0.765	0.717	0.814	0.765	0.717	0.814	INDETERMINATE	2	TRUE	1	0.842865282765541	3		386	423	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928992	44928993	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0001904-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	262	723	0	ENST00000377967.4:c.2093dup	p.His698GlnfsTer32	p.H698Qfs*32	ENST00000377967	NM_021140.2	698	cac/cAac	17/29	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.842865282765541	2		723	511	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209513	98209513	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0001904-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	55	373	2	ENST00000331920.6:c.4025G>T	p.Arg1342Leu	p.R1342L	ENST00000331920	NM_000264.3	1342	cGc/cTc	23/24	0.842865282765541	2	FACETS	0.563	0.487	0.643	0.281	0.243	0.322	SUBCLONAL	1	TRUE	0	0.842865282765541	2		375	232	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40990990	40990990	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0001904-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	109	608	0	ENST00000267868.3:c.34G>C	p.Asp12His	p.D12H	ENST00000267868	NM_002875.4	12	Gat/Cat	2/10	0.615198160819599	3	FACETS	0.458	0.411	0.508	0.229	0.205	0.254	SUBCLONAL	1	TRUE	1	0.842865282765541	3		608	802	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860394	151860396	+	frameshift_variant	Frame_Shift_Del	DEL	CTT	CTT	AG	novel	NA	P-0001904-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	53	406	0	ENST00000262189.6:c.10266_10268delinsCT	p.Gln3422HisfsTer2	p.Q3422Hfs*2	ENST00000262189	NM_170606.2	3422	caAAGa/caCTa	43/59	1	2	FACETS	0.346	0.296	0.401	0.346	0.296	0.401	SUBCLONAL	1	TRUE	1	0.842865282765541	2		406	363	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0001914-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	33	139	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.927	1			1	INDETERMINATE	1	TRUE	NA	0.350547145273488	2		139	150	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048866	180048866	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757667364	NA	P-0001914-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	53	245	0	ENST00000261937.6:c.1696G>A	p.Glu566Lys	p.E566K	ENST00000261937	NM_182925.4	566	Gag/Aag	13/30	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.350547145273488	2		245	270	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241726	55241726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767505234	NA	P-0001914-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	63	212	0	ENST00000275493.2:c.2174C>T	p.Thr725Met	p.T725M	ENST00000275493	NM_005228.3	725	aCg/aTg	18/28	0.350547145273488	3	FACETS	0.822	0.712	0.941	0.411	0.356	0.471	CLONAL	1	TRUE	1	0.350547145273488	3		212	514	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249022	55249022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567477136	NA	P-0001914-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	76	258	1	ENST00000275493.2:c.2320G>A	p.Val774Met	p.V774M	ENST00000275493	NM_005228.3	774	Gtg/Atg	20/28	0.350547145273488	3	FACETS	0.982	0.863	1	0.491	0.431	0.555	CLONAL	1	TRUE	1	0.350547145273488	3		259	519	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001928-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	33	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.933	1			1	INDETERMINATE	1	TRUE	NA	0.88096151547087	2		422	64	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218769	66218769	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0001928-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	41	305	0	ENST00000273854.3:c.2289del	p.Leu765Ter	p.L765*	ENST00000273854	NM_004439.5	763	acA/ac	13/18	1	2	FACETS	0.142	0.118	0.169	0.142	0.118	0.169	SUBCLONAL	1	TRUE	1	0.88096151547087	2		305	656	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589590	67589591	+	inframe_insertion	In_Frame_Ins	INS	-	-	TAT	novel	NA	P-0001928-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	173	176	0	ENST00000274335.5:c.1354_1356dup	p.Tyr452dup	p.Y452dup	ENST00000274335		452	-/TAT	10/15	0.169200918157802	3	FACETS	1	0.959	1	0.526	0.487	0.566	INDETERMINATE	1	TRUE	1	0.88096151547087	3		176	538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578480	+	inframe_deletion	In_Frame_Del	DEL	GGT	GGT	-	novel	NA	P-0001928-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	28	174	0	ENST00000269305.4:c.450_452del	p.Pro153del	p.P153del	ENST00000269305	NM_001126112.2	150	acACCc/acc	5/11	0.836574180414924	1	FACETS	0.194	0.156	0.237	0.194	0.156	0.237	SUBCLONAL	1	TRUE	0	0.88096151547087	1		174	183	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001947-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	11	422	0				ENST00000310581	NM_198253.2	-/1132			0.3	0	FACETS	0.75	0.536	0.995			1	CLONAL	2	TRUE	0	0.25	0		422	44	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638390	176638390	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001947-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	156	343	0	ENST00000439151.2:c.2990G>T	p.Gly997Val	p.G997V	ENST00000439151	NM_022455.4	997	gGc/gTc	5/23	0.3	2	FACETS	0.844	0.779	0.911			1	CLONAL	3	TRUE	NA	0.25	2		343	493	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453134	140453136	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	rs397516897	NA	P-0001963-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	190	377	0	ENST00000288602.6:c.1799_1801del	p.Val600_Lys601delinsGlu	p.V600_K601delinsE	ENST00000288602	NM_004333.4	600	gTGAaa/gaa	15/18	1	2	FACETS	0.945	0.879	1	1	0.995	1	CLONAL	4	TRUE	1	0.171905250113945	2		377	585	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001970-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	71	422	0				ENST00000310581	NM_198253.2	-/1132			0.633365298557083	5	FACETS	1	0.97	1	0.823	0.74	0.905	CLONAL	2	FALSE	2	0.964193361155954	5		422	146	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0001970-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	484	314	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.559412597128879	6	FACETS	0.992	0.954	1	0.992	0.954	1	INDETERMINATE	3	FALSE	3	0.964193361155954	6		314	988	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0001970-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	61	306	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	0.559412597128879	6	FACETS	0.338	0.291	0.391	0.113	0.097	0.131	INDETERMINATE	1	FALSE	3	0.964193361155954	6		306	1095	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39762961	39762961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0001970-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	108	363	0	ENST00000288319.7:c.875C>T	p.Pro292Leu	p.P292L	ENST00000288319	NM_182918.3	292	cCt/cTt	9/10	0.642893101612878	6	FACETS	0.564	0.505	0.627	0.188	0.168	0.209	SUBCLONAL	1	FALSE	3	0.964193361155954	6		363	1163	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798163	42798164	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0001970-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	238	379	0	ENST00000575354.2:c.4122dup	p.Thr1375HisfsTer66	p.T1375Hfs*66	ENST00000575354	NM_015125.3	1373	tcc/tCcc	17/20	0.935794282667983	2	FACETS	1	0.989	1	0.582	0.552	0.612	CLONAL	1	FALSE	0	0.964193361155954	2		379	424	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798384	42798393	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTGCAGCT	AGCTGCAGCT	-	novel	NA	P-0001970-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	72	329	0	ENST00000575354.2:c.4255_4264del	p.Ser1419ArgfsTer32	p.S1419Rfs*32	ENST00000575354	NM_015125.3	1419	AGCTGCAGCTcg/cg	18/20	0.935794282667983	2	FACETS	0.305	0.267	0.346	0.153	0.133	0.173	SUBCLONAL	1	FALSE	0	0.964193361155954	2		329	489	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001971-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	14	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.841	1	1	0.841	1	CLONAL	1	TRUE	1	0.190967409794323	2		422	118	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0001971-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	59	355	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.190967409794323	3	FACETS	1	0.929	1	0.566	0.487	0.652	CLONAL	1	TRUE	1	0.190967409794323	3		355	598	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0001978-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	209	535	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.490365349581808	2		536	770	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0001978-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	221	143	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.490365349581808	2		143	755	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0001978-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	344	251	0	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.490365349581808	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	FALSE	0	0.490365349581808	2		251	619	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246482	105246482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001978-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	124	387	0	ENST00000349310.3:c.118G>A	p.Glu40Lys	p.E40K	ENST00000349310	NM_001014432.1	40	Gag/Aag	4/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.490365349581808	2		387	413	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519674	176519674	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0001978-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	97	228	0	ENST00000292408.4:c.946G>T	p.Glu316Ter	p.E316*	ENST00000292408	NM_213647.1	316	Gag/Tag	8/18	0.171447784464662	0	FACETS	0.62	0.559	0.684			1	INDETERMINATE	1	FALSE	0	0.490365349581808	0		228	325	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106332	27106333	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0001978-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	260	292	0	ENST00000324856.7:c.5944_5945insGG	p.Val1982GlyfsTer34	p.V1982Gfs*34	ENST00000324856	NM_006015.4	1981	-/GG	20/20	NA	2	FACETS	0.968	0.916	1			1	INDETERMINATE	2	FALSE	NA	0.490365349581808	2		292	548	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432409	49432412	+	frameshift_variant	Frame_Shift_Del	DEL	ACTT	ACTT	-	novel	NA	P-0001978-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	107	344	0	ENST00000301067.7:c.8727_8730del	p.Ser2910ArgfsTer32	p.S2910Rfs*32	ENST00000301067	NM_003482.3	2909	gtAAGT/gt	34/54	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.490365349581808	2		344	347	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0001991-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	69	422	0				ENST00000310581	NM_198253.2	-/1132			0.394706282222687	1	FACETS	0.762	0.686	0.837	0.762	0.686	0.837	INDETERMINATE	1	TRUE	0	0.806786222984165	1		422	134	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0001991-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	152	327	1	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.806786222984165	2		328	368	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471644	120471644	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0001991-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	17	326	0	ENST00000256646.2:c.3847C>T	p.Gln1283Ter	p.Q1283*	ENST00000256646	NM_024408.3	1283	Cag/Tag	23/34	0.806786222984165	1	FACETS	0.137	0.102	0.177	0.137	0.102	0.177	SUBCLONAL	1	TRUE	0	0.806786222984165	1		326	184	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658567	206658567	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0001991-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	65	299	0	ENST00000367120.3:c.1540A>G	p.Thr514Ala	p.T514A	ENST00000367120	NM_014002.3	514	Acg/Gcg	15/22	1	2	FACETS	0.471	0.411	0.536	0.471	0.411	0.536	SUBCLONAL	1	TRUE	1	0.806786222984165	2		299	342	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512036	148512036	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0001991-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	160	287	0	ENST00000320356.2:c.1642T>G	p.Cys548Gly	p.C548G	ENST00000320356	NM_004456.4	548	Tgt/Ggt	14/20	0.181919300977941	3	FACETS	1	0.987	1	0.663	0.614	0.712	INDETERMINATE	1	TRUE	1	0.806786222984165	3		287	420	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655383	67655383	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0001991-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	21	381	0	ENST00000264010.4:c.1246T>C	p.Phe416Leu	p.F416L	ENST00000264010	NM_006565.3	416	Ttt/Ctt	7/12	0.178697112972589	2	FACETS	0.125	0.096	0.159	0.063	0.048	0.08	INDETERMINATE	1	TRUE	0	0.806786222984165	2		381	416	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437531	56437531	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0001991-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	67	303	0	ENST00000407977.2:c.931C>A	p.Leu311Ile	p.L311I	ENST00000407977		311	Ctc/Atc	8/10	0.582782446141969	3	FACETS	0.595	0.519	0.676	0.297	0.259	0.338	SUBCLONAL	1	TRUE	1	0.806786222984165	3		303	392	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871932	45871932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001991-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	17	415	0	ENST00000391945.4:c.316G>A	p.Gly106Arg	p.G106R	ENST00000391945	NM_000400.3	106	Gga/Aga	5/23	0.806786222984165	1	FACETS	0.106	0.079	0.138	0.106	0.079	0.138	SUBCLONAL	1	TRUE	0	0.806786222984165	1		415	237	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561120	9561120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0001991-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	68	294	0	ENST00000353224.5:c.662G>A	p.Arg221Lys	p.R221K	ENST00000353224	NM_177990.2	221	aGa/aAa	4/10	1	2	FACETS	0.528	0.463	0.598	0.528	0.463	0.598	SUBCLONAL	1	TRUE	1	0.806786222984165	2		294	319	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631717	90631718	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0001991-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	84	336	0	ENST00000330062.3:c.551_552del	p.Phe184CysfsTer87	p.F184Cfs*87	ENST00000330062	NM_002168.2	184	tTT/t	5/11	1	2	FACETS	0.548	0.487	0.612	0.548	0.487	0.612	SUBCLONAL	1	TRUE	1	0.806786222984165	2		336	380	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002002-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	21	422	0				ENST00000310581	NM_198253.2	-/1132			0.607928961995077	1	FACETS	1	0.828	1	1	0.828	1	CLONAL	1	TRUE	0	0.639334340657161	1		422	44	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0002002-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	68	310	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA	2	FACETS	1	0.919	1			1	INDETERMINATE	1	TRUE	NA	0.639334340657161	2		310	203	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470480	25470480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760854242	NA	P-0002002-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	46	598	0	ENST00000264709.3:c.994G>A	p.Gly332Arg	p.G332R	ENST00000264709	NM_175629.2	332	Gga/Aga	8/23	0.229752646208774	3	FACETS	0.785	0.679	0.894	0.785	0.679	0.894	INDETERMINATE	2	TRUE	1	0.639334340657161	3		598	121	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123184126	123184137	+	inframe_deletion	In_Frame_Del	DEL	TTTAAAATATGT	TTTAAAATATGT	-	novel	NA	P-0002002-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	69	697	0	ENST00000218089.9:c.985_996del	p.Leu329_Val332del	p.L329_V332del	ENST00000218089	NM_001042749.1	328	taTTTAAAATATGTt/tat	11/35	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.639334340657161	2		697	162	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002015-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	189	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.945	0.884	1			1	INDETERMINATE	1	TRUE	NA	0.91713632809219	2		422	436	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817412	39817412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200306085	NA	P-0002015-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	339	512	0	ENST00000288319.7:c.151G>A	p.Val51Ile	p.V51I	ENST00000288319	NM_182918.3	51	Gtc/Atc	2/10	1	2	FACETS	0.971	0.925	1	0.971	0.925	1	CLONAL	1	TRUE	1	0.91713632809219	2		512	761	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295243	1295243	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs35550267	NA	P-0002018-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	359	158	0				ENST00000310581	NM_198253.2	-/1132			0.911465376426704	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.918589455697173	2		158	369	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0002018-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	558	310	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.881482087560726	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	1	0.918589455697173	3		310	814	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295242	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0002018-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	345	152	0				ENST00000310581	NM_198253.2	-/1132			0.911465376426704	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.918589455697173	2		152	357	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123245021	123245021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002018-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	218	440	0	ENST00000358487.5:c.2083G>A	p.Glu695Lys	p.E695K	ENST00000358487	NM_000141.4	695	Gag/Aag	16/18	0.911465376426704	2	FACETS	0.949	0.892	1	0.475	0.446	0.504	CLONAL	1	TRUE	0	0.918589455697173	2		440	500	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144588	119144588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002018-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	245	480	0	ENST00000264033.4:c.601C>T	p.Pro201Ser	p.P201S	ENST00000264033	NM_005188.3	201	Cct/Tct	4/16	0.881482087560726	3	FACETS	0.936	0.877	0.996	0.468	0.438	0.498	CLONAL	1	TRUE	1	0.918589455697173	3		480	832	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288281	21288281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002018-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	576	594	0	ENST00000354336.3:c.526C>T	p.Pro176Ser	p.P176S	ENST00000354336	NM_005207.3	176	Cct/Tct	2/3	0.881482087560726	3	FACETS	0.961	0.931	0.991	0.961	0.931	0.991	CLONAL	2	TRUE	1	0.918589455697173	3		594	952	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0002021-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	295	92	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.504205786320881	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.504205786320881	2		92	565	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678508	88678508	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs183806623	NA	P-0002021-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	108	312	0	ENST00000360948.2:c.1028G>A	p.Arg343Gln	p.R343Q	ENST00000360948	NM_001012338.2	343	cGg/cAg	9/19	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.504205786320881	2		312	365	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971087	21971087	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002021-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	204	208	0	ENST00000304494.5:c.271del	p.Leu91TrpfsTer55	p.L91Wfs*55	ENST00000304494	NM_000077.4	91	Ctg/tg	2/3	0.504205786320881	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.504205786320881	2		208	356	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002029-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	11	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.496	0.343	0.684	0.496	0.343	0.684	SUBCLONAL	1	FALSE	1	0.264243255761907	2		422	168	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0002029-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	28	370	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	0.463	0.369	0.57	0.463	0.369	0.57	SUBCLONAL	1	FALSE	1	0.264243255761907	2		370	458	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577100	7577100	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753660142	NA	P-0002029-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	61	389	0	ENST00000269305.4:c.838A>G	p.Arg280Gly	p.R280G	ENST00000269305	NM_001126112.2	280	Aga/Gga	8/11	1	2	FACETS	0.547	0.471	0.631	0.547	0.471	0.631	SUBCLONAL	1	FALSE	1	0.264243255761907	2		389	844	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463191	25463191	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002029-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	52	378	1	ENST00000264709.3:c.2302G>A	p.Asp768Asn	p.D768N	ENST00000264709	NM_175629.2	768	Gac/Aac	19/23	1	2	FACETS	0.516	0.438	0.602	0.516	0.438	0.602	SUBCLONAL	1	FALSE	1	0.264243255761907	2		379	763	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941859	44941862	+	frameshift_variant	Frame_Shift_Del	DEL	AGAT	AGAT	-	rs1556346208	NA	P-0002029-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	86	281	0	ENST00000377967.4:c.3185_3188del	p.Asp1062ValfsTer20	p.D1062Vfs*20	ENST00000377967	NM_021140.2	1061	tcAGAT/tc	21/29	1	1	FACETS	0.786	0.695	0.883	0.786	0.695	0.883	SUBCLONAL	1	FALSE	0	0.264243255761907	1		281	719	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002030-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	117	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.913205783975775	2		422	225	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0002030-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	383	327	1	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	0.524793270119403	4	FACETS	0.999	0.955	1			1	INDETERMINATE	2	FALSE	NA	0.913205783975775	4		328	803	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0002030-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	472	432	2	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	FALSE	1	0.913205783975775	2		434	989	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180921	106180921	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1163224618	NA	P-0002030-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	205	335	0	ENST00000380013.4:c.3949A>G	p.Lys1317Glu	p.K1317E	ENST00000380013	NM_001127208.2	1317	Aaa/Gaa	7/11	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.913205783975775	NA		335	434	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589220	67589222	+	inframe_deletion	In_Frame_Del	DEL	AAT	AAT	-	novel	NA	P-0002030-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	516	458	0	ENST00000274335.5:c.1208_1210del	p.Glu403_Leu404delinsVal	p.E403_L404delinsV	ENST00000274335		403	gAATta/gta	9/15	0.812659081771133	6	FACETS	0.962	0.925	0.999			1	CLONAL	3	FALSE	NA	0.913205783975775	6		458	1107	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412337	139412339	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0002030-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	711	343	0	ENST00000277541.6:c.1306_1308del	p.Phe436del	p.F436del	ENST00000277541	NM_017617.3	436	TTC/-	8/34	0.697218597696628	4	FACETS	0.911	0.88	0.942	0.911	0.88	0.942	CLONAL	2	FALSE	2	0.913205783975775	4		343	1635	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799252	42799253	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0002030-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	438	246	0	ENST00000575354.2:c.4736_4737del	p.Pro1579ArgfsTer34	p.P1579Rfs*34	ENST00000575354	NM_015125.3	1579	cCA/c	20/20	0.372639095031729	3	FACETS	0.847	0.824	0.868			1	INDETERMINATE	3	FALSE	NA	0.913205783975775	3		246	550	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022440	31022441	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0002030-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	34	255	0	ENST00000375687.4:c.1926_1927del	p.Gly645TrpfsTer12	p.G645Wfs*12	ENST00000375687	NM_015338.5	642	gGA/g	13/13	0.149848209945557	4	FACETS	0.291	0.237	0.351	0.145	0.118	0.176	INDETERMINATE	1	FALSE	2	0.913205783975775	4		255	490	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022441	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002030-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	135	231	0	ENST00000375687.4:c.1926del	p.Gly645ValfsTer58	p.G645Vfs*58	ENST00000375687	NM_015338.5	642	ggA/gg	13/13	0.149848209945557	4	FACETS	1	0.979	1	0.61	0.558	0.663	INDETERMINATE	1	FALSE	2	0.913205783975775	4		231	464	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0002044-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	100	275	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.334262450142572	3	FACETS	1	0.971	1	0.615	0.552	0.682	CLONAL	1	TRUE	1	0.412781735629709	3		275	475	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0002044-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	143	180	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.1952335696009	3	FACETS	0.787	0.722	0.855	0.525	0.481	0.57	INDETERMINATE	2	TRUE	0	0.412781735629709	3		180	531	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371749	55371749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138778434	NA	P-0002044-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	110	222	1	ENST00000297316.4:c.439C>T	p.Arg147Trp	p.R147W	ENST00000297316	NM_022454.3	147	Cgg/Tgg	2/2	0.375670726389496	4	FACETS	0.986	0.894	1	0.657	0.596	0.721	CLONAL	2	TRUE	1	0.412781735629709	4		223	382	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432722	49432722	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002044-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	33	268	0	ENST00000301067.7:c.8417G>C	p.Gly2806Ala	p.G2806A	ENST00000301067	NM_003482.3	2806	gGg/gCg	34/54	NA	2	FACETS	0.379	0.308	0.458			1	INDETERMINATE	1	TRUE	NA	0.412781735629709	2		268	422	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954605	17954605	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002044-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	86	357	0	ENST00000458235.1:c.289G>C	p.Val97Leu	p.V97L	ENST00000458235	NM_000215.3	97	Gtc/Ctc	3/24	0.339763240233326	4	FACETS	0.674	0.595	0.758	0.337	0.297	0.379	SUBCLONAL	1	TRUE	2	0.412781735629709	4		357	874	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0002055-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	88	139	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.871	0.792	0.951	1	0.989	1	CLONAL	3	TRUE	1	0.362014100034915	2		139	186	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0002055-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	220	291	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	1	0.982	1	1	0.995	1	CLONAL	2	TRUE	1	0.362014100034915	2		291	542	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148727	20148727	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0002055-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	155	281	0	ENST00000379607.5:c.338-2A>G		p.X113_splice	ENST00000379607	NM_001412.3	113			0.305800079361583	0	FACETS	0.67	0.627	0.711			1	SUBCLONAL	3	TRUE	0	0.362014100034915	0		281	272	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002063-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	40	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.704429794841844	2		422	93	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779823	135779832	+	frameshift_variant	Frame_Shift_Del	DEL	CTTGCTGGGT	CTTGCTGGGT	-	novel	NA	P-0002063-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	107	341	0	ENST00000298552.3:c.2007_2016del	p.Leu669PhefsTer52	p.L669Ffs*52	ENST00000298552	NM_001162426.1	669	ttACCCAGCAAG/tt	16/23	0.704429794841844	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.704429794841844	1		341	183	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0002068-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	333	479	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.396614445573894	2	FACETS	0.931	0.884	0.98	0.931	0.884	0.98	CLONAL	2	TRUE	0	0.398543401668218	2		480	897	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0002068-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	109	139	0				ENST00000310581	NM_198253.2	-/1132			0.398543401668218	3	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	1	0.398543401668218	3		139	320	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858356	9858356	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002068-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	94	351	0	ENST00000330684.3:c.3045G>T	p.Lys1015Asn	p.K1015N	ENST00000330684	NM_001134407.1	1015	aaG/aaT	13/13	1	2	FACETS	0.975	0.871	1	0.975	0.871	1	CLONAL	1	TRUE	1	0.398543401668218	2		351	484	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480538	123480538	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002068-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	86	404	0	ENST00000371139.4:c.46G>A	p.Gly16Ser	p.G16S	ENST00000371139	NM_001114937.2	16	Ggc/Agc	1/4	0.362764416891125	1	FACETS	0.576	0.51	0.646	0.576	0.51	0.646	SUBCLONAL	1	TRUE	0	0.398543401668218	1		404	600	SUCCESS
APC	324	MSKCC	GRCh37	5	112174094	112174095	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	AA	novel	NA	P-0002068-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	129	398	0	ENST00000257430.4:c.2804_2805insAA	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	tac/tAAac	16/16	1	2	FACETS	0.941	0.855	1	0.941	0.855	1	CLONAL	1	TRUE	1	0.398543401668218	2		398	688	SUCCESS
APC	324	MSKCC	GRCh37	5	112175779	112175788	+	frameshift_variant	Frame_Shift_Del	DEL	TCCAGATGGA	TCCAGATGGA	-	novel	NA	P-0002068-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	118	359	0	ENST00000257430.4:c.4489_4498del	p.Pro1497PhefsTer7	p.P1497Ffs*7	ENST00000257430	NM_000038.5	1496	acTCCAGATGGA/ac	16/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.398543401668218	2		359	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0002073-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	264	291	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.381212315445828	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	0	0.440659787448664	2		292	598	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002073-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	37	422	0				ENST00000310581	NM_198253.2	-/1132			0.440659787448664	3	FACETS	0.683	0.565	0.814	0.342	0.282	0.407	SUBCLONAL	1	TRUE	1	0.440659787448664	3		422	300	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532867	187532867	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002073-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	374	394	0	ENST00000441802.2:c.9526G>T	p.Glu3176Ter	p.E3176*	ENST00000441802	NM_005245.3	3176	Gaa/Taa	14/27	0.38586778421884	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.440659787448664	2		394	836	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405608	139405608	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1293804194	NA	P-0002073-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	87	334	0	ENST00000277541.6:c.2583G>A	p.Trp861Ter	p.W861*	ENST00000277541	NM_017617.3	861	tgG/tgA	16/34	0.435519492321065	2	FACETS	0.617	0.546	0.692	0.308	0.273	0.346	SUBCLONAL	1	TRUE	0	0.440659787448664	2		334	640	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0002076-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	124	139	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.98	1	1	0.992	1	CLONAL	2	TRUE	1	0.409997059787692	2		139	253	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0002076-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	300	270	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.409997059787692	2		270	636	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289269	33289269	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002076-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	283	263	0	ENST00000374542.5:c.283G>C	p.Ala95Pro	p.A95P	ENST00000374542	NM_001141970.1	95	Gcc/Ccc	3/8	1	2	FACETS	0.904	0.861	0.947	1	0.996	1	CLONAL	3	TRUE	1	0.409997059787692	2		263	509	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148726	20148726	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0002076-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	228	420	0	ENST00000379607.5:c.338-1G>A		p.X113_splice	ENST00000379607	NM_001412.3	113			0.409997059787692	1	FACETS	0.853	0.803	0.904	1	0.994	1	CLONAL	2	TRUE	0	0.409997059787692	1		420	518	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400056	139400063	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTAGTC	CTGTAGTC	T	novel	NA	P-0002076-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	150	300	0	ENST00000277541.6:c.4285_4292delinsA	p.Asp1429ThrfsTer14	p.D1429Tfs*14	ENST00000277541	NM_017617.3	1429	GACTACAGc/Ac	25/34	1	2	FACETS	1	0.97	1	1	0.993	1	CLONAL	2	TRUE	1	0.409997059787692	2		300	337	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	24	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.341149706868222	2		422	110	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888210	112888210	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121918464	NA	P-0002083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	132	467	0	ENST00000351677.2:c.226G>A	p.Glu76Lys	p.E76K	ENST00000351677	NM_002834.3	76	Gag/Aag	3/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.341149706868222	2		467	662	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711883	89711884	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0002083-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	126	396	0	ENST00000371953.3:c.502_503del	p.Ile168SerfsTer11	p.I168Sfs*11	ENST00000371953	NM_000314.4	167	acTAtt/actt	6/9	0.341149706868222	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.341149706868222	1		396	565	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002093-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	25	422	0				ENST00000310581	NM_198253.2	-/1132			0.230482856975827	1	FACETS	0.509	0.407	0.623	0.509	0.407	0.623	INDETERMINATE	1	TRUE	0	0.536324030435607	1		422	134	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262087	16262087	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1449357349	NA	P-0002093-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	73	129	0	ENST00000375759.3:c.9352C>T	p.His3118Tyr	p.H3118Y	ENST00000375759	NM_015001.2	3118	Cac/Tac	11/15	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.536324030435607	2		129	257	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527778	157527778	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002093-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	67	260	0	ENST00000346085.5:c.5503G>C	p.Glu1835Gln	p.E1835Q	ENST00000346085	NM_020732.3	1835	Gag/Cag	20/20	NA	2	FACETS	0.702	0.613	0.796			1	INDETERMINATE	1	TRUE	NA	0.536324030435607	2		260	356	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527847	157527847	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002093-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	75	321	0	ENST00000346085.5:c.5572G>C	p.Glu1858Gln	p.E1858Q	ENST00000346085	NM_020732.3	1858	Gag/Cag	20/20	NA	2	FACETS	0.627	0.551	0.708			1	INDETERMINATE	1	TRUE	NA	0.536324030435607	2		321	446	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459551	50459551	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002093-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	110	245	2	ENST00000331340.3:c.840G>T	p.Gln280His	p.Q280H	ENST00000331340	NM_006060.4	280	caG/caT	7/8	0.314880211011069	5	FACETS	1	0.975	1			1	INDETERMINATE	1	TRUE	NA	0.536324030435607	5		247	590	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852042	128852042	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002093-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	298	438	0	ENST00000249373.3:c.2114C>T	p.Pro705Leu	p.P705L	ENST00000249373	NM_005631.4	705	cCt/cTt	12/12	0.290373514154361	3	FACETS	1	0.991	1	0.794	0.755	0.832	INDETERMINATE	2	TRUE	0	0.536324030435607	3		438	592	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801105	135801105	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002093-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	151	294	0	ENST00000298552.3:c.232G>T	p.Glu78Ter	p.E78*	ENST00000298552	NM_001162426.1	78	Gaa/Taa	5/23	0.536324030435607	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.536324030435607	1		294	347	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745837	745837	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1050998183	NA	P-0002093-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	88	499	0	ENST00000314574.4:c.595C>T	p.Arg199Cys	p.R199C	ENST00000314574	NM_005433.3	199	Cgt/Tgt	6/12	0.536324030435607	1	FACETS	0.593	0.528	0.661	0.593	0.528	0.661	SUBCLONAL	1	TRUE	0	0.536324030435607	1		499	405	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271969	18271969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1418268495	NA	P-0002093-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	56	98	0	ENST00000222254.8:c.572C>T	p.Ser191Leu	p.S191L	ENST00000222254	NM_005027.3	191	tCg/tTg	5/16	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.536324030435607	2		98	172	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044466	47044466	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002093-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	253	182	0	ENST00000377604.3:c.1963A>G	p.Met655Val	p.M655V	ENST00000377604	NM_001204468.1	655	Atg/Gtg	18/24	0.402245887930975	2	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.536324030435607	2		182	395	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974721	21974721	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002093-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	133	306	0	ENST00000304494.5:c.106del	p.Ala36ArgfsTer17	p.A36Rfs*17	ENST00000304494	NM_000077.4	36	Gcg/cg	1/3	0.536324030435607	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.536324030435607	1		306	322	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002098-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	33	422	0				ENST00000310581	NM_198253.2	-/1132			0.196485797742146	1	FACETS	0.924	0.791	1	1	0.976	1	CLONAL	5	TRUE	0	0.195259539934476	1		422	66	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391346	139391346	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002098-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	67	448	0	ENST00000277541.6:c.6845C>G	p.Thr2282Ser	p.T2282S	ENST00000277541	NM_017617.3	2282	aCc/aGc	34/34	0.196485797742146	0	FACETS	0.837	0.745	0.931			1	CLONAL	4	TRUE	0	0.195259539934476	0		448	165	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922966	44922966	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0002098-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	202	350	0	ENST00000377967.4:c.1827C>G	p.Tyr609Ter	p.Y609*	ENST00000377967	NM_021140.2	609	taC/taG	16/29	1	1	FACETS	1	0.984	1	1	0.996	1	CLONAL	7	TRUE	0	0.195259539934476	1		350	254	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0002109-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	11	139	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.879	0.611	1	0.879	0.611	1	CLONAL	1	TRUE	1	0.201936352020518	2		139	124	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577022	7577022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913344	NA	P-0002109-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	84	481	0	ENST00000269305.4:c.916C>T	p.Arg306Ter	p.R306*	ENST00000269305	NM_001126112.2	306	Cga/Tga	8/11	0.201936352020518	0	FACETS	0.905	0.799	1			1	CLONAL	1	TRUE	0	0.201936352020518	0		481	734	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059260	27059260	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002109-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	183	492	0	ENST00000324856.7:c.1897C>T	p.Gln633Ter	p.Q633*	ENST00000324856	NM_006015.4	633	Cag/Tag	4/20	1	2	FACETS	0.902	0.832	0.975	1	0.992	1	CLONAL	2	TRUE	1	0.201936352020518	2		492	1005	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699369	47699369	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002109-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1224	224	557	0	ENST00000347630.2:c.139G>A	p.Glu47Lys	p.E47K	ENST00000347630	NM_001007230.1	47	Gaa/Aaa	4/11	0.174742462722073	3	FACETS	0.843	0.783	0.906	0.843	0.783	0.906	CLONAL	2	TRUE	1	0.201936352020518	3		557	1448	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510805	157510806	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs1289067120	NA	P-0002109-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	260	537	0	ENST00000346085.5:c.3586dup	p.Gln1196ProfsTer14	p.Q1196Pfs*14	ENST00000346085	NM_020732.3	1194	acc/aCcc	14/20	0.174742462722073	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.201936352020518	3		537	1157	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429978	78429978	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	81	794	3	ENST00000370768.2:c.901del	p.Ile301TyrfsTer22	p.I301Yfs*22	ENST00000370768	NM_003902.3	301	Ata/ta	11/20	1	2	FACETS	0.841	0.743	0.946	0.841	0.743	0.946	CLONAL	1	TRUE	1	0.375466088220361	2		797	513	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	50	1167	4	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.399	0.337	0.466	0.399	0.337	0.466	SUBCLONAL	1	TRUE	1	0.375466088220361	2		1171	668	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1040408	1040408	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370272002	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	96	925	1	ENST00000358495.3:c.164G>A	p.Arg55His	p.R55H	ENST00000358495	NM_134424.2	55	cGc/cAc	3/12	1	2	FACETS	0.97	0.867	1	0.97	0.867	1	CLONAL	1	TRUE	1	0.375466088220361	2		926	527	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	68	581	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.375466088220361	2		581	357	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	57	576	0	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.923	0.796	1	0.923	0.796	1	CLONAL	1	TRUE	1	0.375466088220361	2		576	329	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	119	907	2	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.375466088220361	2		909	612	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779211	3779211	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs587783507	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	37	447	0	ENST00000262367.5:c.5837del	p.Pro1946HisfsTer30	p.P1946Hfs*30	ENST00000262367	NM_004380.2	1946	cCa/ca	31/31	1	2	FACETS	0.738	0.612	0.878	0.738	0.612	0.878	SUBCLONAL	1	TRUE	1	0.375466088220361	2		447	267	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339111	65339111	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	90	817	4	ENST00000342505.4:c.425del	p.Lys142ArgfsTer26	p.K142Rfs*26	ENST00000342505	NM_002227.2	142	aAg/ag	5/25	1	2	FACETS	0.859	0.764	0.96	0.859	0.764	0.96	CLONAL	1	TRUE	1	0.375466088220361	2		821	558	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	138	799	2	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	0.358636715525972	2	FACETS	0.89	0.818	0.964	0.89	0.818	0.964	CLONAL	2	TRUE	0	0.375466088220361	2		801	413	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	220	936	31	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.938	0.878	0.998	1	0.994	1	CLONAL	2	TRUE	1	0.375466088220361	2		967	625	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	70	676	2	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	1	2	FACETS	0.928	0.812	1	0.928	0.812	1	CLONAL	1	TRUE	1	0.375466088220361	2		678	402	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434005	49434005	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	138	1173	1	ENST00000301067.7:c.7548del	p.Asn2517IlefsTer26	p.N2517Ifs*26	ENST00000301067	NM_003482.3	2516	ccC/cc	31/54	1	2	FACETS	0.999	0.91	1	0.999	0.91	1	CLONAL	1	TRUE	1	0.375466088220361	2		1174	736	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	81	760	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	0.816	0.72	0.918	0.816	0.72	0.918	CLONAL	1	TRUE	1	0.375466088220361	2		760	529	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451784	29451784	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs772809305	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	112	1095	3	ENST00000389048.3:c.2781del	p.Cys928AlafsTer11	p.C928Afs*11	ENST00000389048	NM_004304.4	927	ggG/gg	16/29	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.375466088220361	2		1098	583	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307603	118307603	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	128	1059	0	ENST00000534358.1:c.376C>A	p.Leu126Met	p.L126M	ENST00000534358	NM_005933.3	126	Ctg/Atg	1/36	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.375466088220361	2		1059	675	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097604	27097615	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATACAGGTCAAC	ATACAGGTCAAC	-	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	168	930	0	ENST00000324856.7:c.3199-5_3205del		p.X1067_splice	ENST00000324856	NM_006015.4	1067		12/20	0.358636715525972	2	FACETS	0.854	0.79	0.919	0.854	0.79	0.919	CLONAL	2	TRUE	0	0.375466088220361	2		930	524	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	134	980	2	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.375466088220361	2		982	659	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170313	32170313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201260854	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	130	155	0	ENST00000375023.3:c.3295G>A	p.Gly1099Arg	p.G1099R	ENST00000375023	NM_004557.3	1099	Gga/Aga	21/30	1	2	FACETS	0.963	0.875	1	0.963	0.875	1	CLONAL	1	TRUE	1	0.375466088220361	2		155	719	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	84	883	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	1	2	FACETS	0.884	0.783	0.992	0.884	0.783	0.992	CLONAL	1	TRUE	1	0.375466088220361	2		883	506	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740624	58740624	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs763475304	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	120	1047	0	ENST00000305921.3:c.1535del	p.Asn512IlefsTer2	p.N512Ifs*2	ENST00000305921	NM_003620.3	510	cAa/ca	6/6	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.375466088220361	2		1047	565	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	176	841	5	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.954	1	1	0.993	1	CLONAL	2	TRUE	1	0.375466088220361	2		846	454	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347725	89347725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759287339	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	129	782	0	ENST00000301030.4:c.5225C>T	p.Ser1742Leu	p.S1742L	ENST00000301030	NM_001256183.1	1742	tCg/tTg	9/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.375466088220361	2		782	584	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219487	133219487	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	129	1054	3	ENST00000320574.5:c.4647del	p.Lys1550AsnfsTer12	p.K1550Nfs*12	ENST00000320574	NM_006231.2	1549	ccC/cc	36/49	1	2	FACETS	0.925	0.839	1	0.925	0.839	1	CLONAL	1	TRUE	1	0.375466088220361	2		1057	743	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	76	640	2	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.375466088220361	2		642	401	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807363	3807364	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	68	867	0	ENST00000262367.5:c.3623dup	p.Gln1209ThrfsTer25	p.Q1209Tfs*25	ENST00000262367	NM_004380.2	1208	cca/ccCa	19/31	1	2	FACETS	0.651	0.567	0.742	0.651	0.567	0.742	SUBCLONAL	1	TRUE	1	0.375466088220361	2		867	556	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426729	49426730	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs576788910	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	19	292	0	ENST00000301067.7:c.11756_11758dup	p.Gln3919dup	p.Q3919dup	ENST00000301067	NM_003482.3	3919	cta/cAGCta	39/54	1	2	FACETS	0.582	0.444	0.741	0.582	0.444	0.741	SUBCLONAL	1	TRUE	1	0.375466088220361	2		292	174	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806180	1806181	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs760502257	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	110	1088	1	ENST00000260795.2:c.1206dup	p.Lys403GlnfsTer93	p.K403Qfs*93	ENST00000260795		400	agc/agCc	8/17	1	2	FACETS	0.757	0.68	0.838	0.757	0.68	0.838	SUBCLONAL	1	TRUE	1	0.375466088220361	2		1089	774	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120031	70120031	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	11	150	0	ENST00000245479.2:c.1037del	p.Pro346ArgfsTer37	p.P346Rfs*37	ENST00000245479	NM_000346.3	345	Ccc/cc	3/3	1	2	FACETS	0.742	0.52	1	0.742	0.52	1	CLONAL	1	TRUE	1	0.375466088220361	2		150	79	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670949	30670949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1259392922	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	125	1083	6	ENST00000376406.3:c.5797C>T	p.Arg1933Trp	p.R1933W	ENST00000376406	NM_014641.2	1933	Cgg/Tgg	12/15	1	2	FACETS	0.994	0.901	1	0.994	0.901	1	CLONAL	1	TRUE	1	0.375466088220361	2		1089	670	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858292	9858292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	56	590	0	ENST00000330684.3:c.3109G>A	p.Ala1037Thr	p.A1037T	ENST00000330684	NM_001134407.1	1037	Gca/Aca	13/13	1	2	FACETS	0.877	0.756	1	0.877	0.756	1	CLONAL	1	TRUE	1	0.375466088220361	2		590	340	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745962	745963	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	28	954	0	ENST00000314574.4:c.559_560del	p.Ser187Ter	p.S187*	ENST00000314574	NM_005433.3	187	AGt/t	5/12	1	2	FACETS	0.324	0.258	0.399	0.324	0.258	0.399	SUBCLONAL	1	TRUE	1	0.375466088220361	2		954	461	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984672	11984672	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	52	652	0	ENST00000353533.5:c.219-1G>C		p.X73_splice	ENST00000353533	NM_003010.3	73			1	2	FACETS	0.863	0.739	0.997	0.863	0.739	0.997	CLONAL	1	TRUE	1	0.375466088220361	2		652	321	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933617	39933617	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	97	794	1	ENST00000378444.4:c.982del	p.Asp328ThrfsTer50	p.D328Tfs*50	ENST00000378444	NM_001123385.1	328	Gac/ac	4/15	0.375466088220361	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.375466088220361	1		795	409	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	145	1174	6	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.956	0.873	1	0.956	0.873	1	CLONAL	1	TRUE	1	0.375466088220361	2		1180	808	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357102	89357102	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1286864966	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	127	941	2	ENST00000301030.4:c.532C>T	p.Arg178Cys	p.R178C	ENST00000301030	NM_001256183.1	178	Cgc/Tgc	6/13	1	2	FACETS	0.92	0.835	1	0.92	0.835	1	CLONAL	1	TRUE	1	0.375466088220361	2		943	735	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199447	16199447	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	76	721	1	ENST00000375759.3:c.220C>A	p.Leu74Ile	p.L74I	ENST00000375759	NM_015001.2	74	Cta/Ata	2/15	0.358636715525972	2	FACETS	1	0.902	1	0.512	0.452	0.577	CLONAL	1	TRUE	0	0.375466088220361	2		722	395	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820994	36820994	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs145487256	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	48	1092	0	ENST00000373129.3:c.383G>T	p.Arg128Leu	p.R128L	ENST00000373129	NM_032017.1	128	cGg/cTg	6/12	0.358636715525972	2	FACETS	0.404	0.341	0.474	0.202	0.17	0.237	SUBCLONAL	1	TRUE	0	0.375466088220361	2		1092	633	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322657	39322657	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	91	1089	2	ENST00000373001.3:c.335T>C	p.Phe112Ser	p.F112S	ENST00000373001	NM_022157.3	112	tTc/tCc	2/7	0.358636715525972	2	FACETS	0.787	0.7	0.88	0.393	0.35	0.44	SUBCLONAL	1	TRUE	0	0.375466088220361	2		1091	616	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161456	2161456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs970922682	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	151	1010	0	ENST00000434045.2:c.71G>A	p.Arg24His	p.R24H	ENST00000434045	NM_001127598.1	24	cGc/cAc	2/5	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.375466088220361	2		1010	793	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456294	32456294	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	155	1151	1	ENST00000332351.3:c.598C>A	p.Pro200Thr	p.P200T	ENST00000332351	NM_024426.4	200	Ccc/Acc	1/10	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.375466088220361	2		1152	776	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138765	64138765	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	151	1060	0	ENST00000334205.4:c.2135del	p.Gly712AlafsTer8	p.G712Afs*8	ENST00000334205	NM_003942.2	711	cGg/cg	17/17	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.375466088220361	2		1060	719	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998684	100998684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	140	1023	3	ENST00000325455.5:c.1118C>T	p.Ala373Val	p.A373V	ENST00000325455	NM_001202474.3	373	gCg/gTg	1/8	1	2	FACETS	0.937	0.854	1	0.937	0.854	1	CLONAL	1	TRUE	1	0.375466088220361	2		1026	796	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342634	118342634	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1565278132	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	75	639	0	ENST00000534358.1:c.766del	p.Ile256LeufsTer18	p.I256Lfs*18	ENST00000534358	NM_005933.3	254	Aaa/aa	3/36	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.375466088220361	2		639	389	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719883	18719884	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	28	734	0	ENST00000266497.5:c.3783dup	p.Pro1262SerfsTer32	p.P1262Sfs*32	ENST00000266497		1260	-/T	27/31	1	2	FACETS	0.371	0.296	0.456	0.371	0.296	0.456	SUBCLONAL	1	TRUE	1	0.375466088220361	2		734	402	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644555	21644555	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	87	928	1	ENST00000421138.2:c.112A>G	p.Lys38Glu	p.K38E	ENST00000421138		38	Aaa/Gaa	4/16	1	2	FACETS	0.936	0.832	1	0.936	0.832	1	CLONAL	1	TRUE	1	0.375466088220361	2		929	495	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246026	46246026	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	63	791	0	ENST00000334344.6:c.4124del	p.Asn1375ThrfsTer11	p.N1375Tfs*11	ENST00000334344	NM_152641.2	1374	Aaa/aa	15/21	1	2	FACETS	0.791	0.687	0.904	0.791	0.687	0.904	CLONAL	1	TRUE	1	0.375466088220361	2		791	424	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911976	32911976	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878853570	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	97	1034	2	ENST00000380152.3:c.3484G>A	p.Ala1162Thr	p.A1162T	ENST00000380152		1162	Gct/Act	11/27	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.375466088220361	2		1036	512	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524612	103524613	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	63	665	0	ENST00000355739.4:c.2750_2751del	p.Lys917IlefsTer12	p.K917Ifs*12	ENST00000355739	NM_000123.3	915	AAa/a	13/15	1	2	FACETS	0.82	0.712	0.937	0.82	0.712	0.937	CLONAL	1	TRUE	1	0.375466088220361	2		665	409	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396495	30396495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	65	832	1	ENST00000331968.5:c.224C>T	p.Ala75Val	p.A75V	ENST00000331968	NM_002742.2	75	gCg/gTg	1/18	1	2	FACETS	0.571	0.495	0.654	0.571	0.495	0.654	SUBCLONAL	1	TRUE	1	0.375466088220361	2		833	606	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500549	99500549	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	93	825	0	ENST00000268035.6:c.3982G>T	p.Gly1328Cys	p.G1328C	ENST00000268035	NM_000875.3	1328	Ggc/Tgc	21/21	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.375466088220361	2		825	459	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2096133	2096133	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs763525759	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	103	969	3	ENST00000219066.1:c.374del	p.Pro125GlnfsTer12	p.P125Qfs*12	ENST00000219066	NM_002528.5	125	cCa/ca	2/6	1	2	FACETS	0.948	0.85	1	0.948	0.85	1	CLONAL	1	TRUE	1	0.375466088220361	2		972	579	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213961	2213961	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs753146456	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	37	994	4	ENST00000326181.6:c.45del	p.Ser17AlafsTer111	p.S17Afs*111	ENST00000326181	NM_032271.2	14	Ggg/gg	2/21	1	2	FACETS	0.273	0.224	0.328	0.273	0.224	0.328	SUBCLONAL	1	TRUE	1	0.375466088220361	2		998	721	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3817720	3817721	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	68	683	0	ENST00000262367.5:c.3250dup	p.Ile1084AsnfsTer3	p.I1084Nfs*3	ENST00000262367	NM_004380.2	1084	atc/aAtc		1	2	FACETS	0.838	0.732	0.953	0.838	0.732	0.953	CLONAL	1	TRUE	1	0.375466088220361	2		683	432	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835613	68835613	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	124	904	0	ENST00000261769.5:c.208del	p.Ser70ProfsTer13	p.S70Pfs*13	ENST00000261769	NM_004360.3	68	taT/ta	3/16	1	2	FACETS	0.996	0.903	1	0.996	0.903	1	CLONAL	1	TRUE	1	0.375466088220361	2		904	663	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829595	72829595	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1394970712	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	110	966	0	ENST00000268489.5:c.6986A>G	p.Gln2329Arg	p.Q2329R	ENST00000268489	NM_006885.3	2329	cAg/cGg	9/10	1	2	FACETS	0.867	0.78	0.959	0.867	0.78	0.959	CLONAL	1	TRUE	1	0.375466088220361	2		966	676	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984826	72984826	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376414532	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	82	748	2	ENST00000268489.5:c.2758G>A	p.Gly920Arg	p.G920R	ENST00000268489	NM_006885.3	920	Ggg/Agg	3/10	1	2	FACETS	0.91	0.805	1	0.91	0.805	1	CLONAL	1	TRUE	1	0.375466088220361	2		750	480	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990343	81990343	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	124	937	0	ENST00000359376.3:c.3614G>T	p.Arg1205Met	p.R1205M	ENST00000359376	NM_002661.3	1205	aGg/aTg	32/33	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.375466088220361	2		937	593	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346661	89346661	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	68	611	0	ENST00000301030.4:c.6289C>T	p.Pro2097Ser	p.P2097S	ENST00000301030	NM_001256183.1	2097	Ccc/Tcc	9/13	1	2	FACETS	0.971	0.849	1	0.971	0.849	1	CLONAL	1	TRUE	1	0.375466088220361	2		611	373	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11924240	11924240	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1462414385	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	11	50	0	ENST00000353533.5:c.41del	p.Gly14AlafsTer11	p.G14Afs*11	ENST00000353533	NM_003010.3	13	Ggg/gg	1/11	1	2	FACETS	1	0.824	1	1	0.824	1	CLONAL	1	TRUE	1	0.375466088220361	2		50	47	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315331	30315331	+	splice_region_variant,intron_variant	Splice_Region	DEL	T	T	-	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	52	488	0	ENST00000322652.5:c.1024-3del		p.X342_splice	ENST00000322652	NM_015355.2	342			1	2	FACETS	0.86	0.736	0.994	0.86	0.736	0.994	CLONAL	1	TRUE	1	0.375466088220361	2		488	322	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462640	40462656	+	frameshift_variant	Frame_Shift_Del	DEL	TCGCCCCCTGCCGGTCT	TCGCCCCCTGCCGGTCT	-	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	89	925	0	ENST00000345506.4:c.2339_2355del	p.Ser780PhefsTer13	p.S780Ffs*13	ENST00000345506	NM_003152.3	780	TCGCCCCCTGCCGGTCTt/t	20/20	1	2	FACETS	0.797	0.707	0.892	0.797	0.707	0.892	SUBCLONAL	1	TRUE	1	0.375466088220361	2		925	595	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756802	756802	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	74	686	0	ENST00000314574.4:c.26A>C	p.Asn9Thr	p.N9T	ENST00000314574	NM_005433.3	9	aAc/aCc	2/12	1	2	FACETS	0.89	0.782	1	0.89	0.782	1	CLONAL	1	TRUE	1	0.375466088220361	2		686	443	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45396849	45396849	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	66	710	0	ENST00000262160.6:c.323C>G	p.Thr108Ser	p.T108S	ENST00000262160	NM_005901.5	108	aCc/aGc	3/11	1	2	FACETS	0.847	0.738	0.964	0.847	0.738	0.964	CLONAL	1	TRUE	1	0.375466088220361	2		710	415	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222730	5222731	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs756013055	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	127	1025	4	ENST00000357368.4:c.3072dup	p.Val1025ArgfsTer34	p.V1025Rfs*34	ENST00000357368	NM_002850.3	1024	-/C	18/38	1	2	FACETS	0.964	0.874	1	0.964	0.874	1	CLONAL	1	TRUE	1	0.375466088220361	2		1029	702	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267805	7267805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	77	1074	1	ENST00000302850.5:c.203C>T	p.Thr68Met	p.T68M	ENST00000302850	NM_000208.2	68	aCg/aTg	2/22	1	2	FACETS	0.55	0.482	0.623	0.55	0.482	0.623	SUBCLONAL	1	TRUE	1	0.375466088220361	2		1075	746	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626865	14626865	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	134	1087	2	ENST00000254322.2:c.910del	p.Leu304SerfsTer17	p.L304Sfs*17	ENST00000254322	NM_006145.1	304	Ctc/tc	3/3	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.375466088220361	2		1089	702	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17949137	17949137	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	45	1352	1	ENST00000458235.1:c.1504C>T	p.Pro502Ser	p.P502S	ENST00000458235	NM_000215.3	502	Ccc/Tcc	11/24	1	2	FACETS	0.274	0.229	0.324	0.274	0.229	0.324	SUBCLONAL	1	TRUE	1	0.375466088220361	2		1353	875	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258542	19258542	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	159	1156	1	ENST00000162023.5:c.358G>T	p.Gly120Trp	p.G120W	ENST00000162023		120	Ggg/Tgg	8/13	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.375466088220361	2		1157	845	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216455	36216455	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	130	1189	0	ENST00000222270.7:c.3718del	p.His1240IlefsTer115	p.H1240Ifs*115	ENST00000222270	NM_014727.1	1240	Cat/at	12/37	1	2	FACETS	0.878	0.796	0.963	0.878	0.796	0.963	CLONAL	1	TRUE	1	0.375466088220361	2		1189	789	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228005	36228005	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	95	1048	0	ENST00000222270.7:c.7391T>A	p.Leu2464His	p.L2464H	ENST00000222270	NM_014727.1	2464	cTc/cAc	33/37	1	2	FACETS	0.883	0.788	0.984	0.883	0.788	0.984	CLONAL	1	TRUE	1	0.375466088220361	2		1048	573	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921163	50921163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	132	1113	1	ENST00000440232.2:c.3283C>T	p.Leu1095Phe	p.L1095F	ENST00000440232	NM_002691.3	1095	Ctc/Ttc	27/27	1	2	FACETS	0.97	0.882	1	0.97	0.882	1	CLONAL	1	TRUE	1	0.375466088220361	2		1114	725	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370803	225370803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	69	1019	1	ENST00000264414.4:c.1076C>T	p.Ser359Leu	p.S359L	ENST00000264414	NM_003590.4	359	tCa/tTa	8/16	1	2	FACETS	0.627	0.546	0.714	0.627	0.546	0.714	SUBCLONAL	1	TRUE	1	0.375466088220361	2		1020	586	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561289	9561289	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985722631	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	55	685	0	ENST00000353224.5:c.493G>A	p.Ala165Thr	p.A165T	ENST00000353224	NM_177990.2	165	Gca/Aca	4/10	1	2	FACETS	0.927	0.798	1	0.927	0.798	1	CLONAL	1	TRUE	1	0.375466088220361	2		685	316	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309742	30309742	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	76	771	0	ENST00000307677.4:c.280G>T	p.Gly94Cys	p.G94C	ENST00000307677	NM_138578.1	94	Ggc/Tgc	2/3	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.375466088220361	2		771	400	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069268	30069268	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	90	849	1	ENST00000338641.4:c.1133A>G	p.Glu378Gly	p.E378G	ENST00000338641	NM_000268.3	378	gAg/gGg	12/16	1	2	FACETS	0.946	0.842	1	0.946	0.842	1	CLONAL	1	TRUE	1	0.375466088220361	2		850	507	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928645	49928645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1234878460	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	147	934	0	ENST00000296474.3:c.3629C>T	p.Ala1210Val	p.A1210V	ENST00000296474	NM_002447.2	1210	gCt/gTt	17/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.375466088220361	2		934	749	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390926	89390926	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	64	731	0	ENST00000336596.2:c.992A>T	p.Asn331Ile	p.N331I	ENST00000336596	NM_005233.5	331	aAt/aTt	5/17	1	2	FACETS	0.897	0.781	1	0.897	0.781	1	CLONAL	1	TRUE	1	0.375466088220361	2		731	380	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152038	55152038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370600501	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	69	774	0	ENST00000257290.5:c.2470G>A	p.Val824Ile	p.V824I	ENST00000257290	NM_006206.4	824	Gtc/Atc	18/23	1	2	FACETS	0.658	0.573	0.749	0.658	0.573	0.749	SUBCLONAL	1	TRUE	1	0.375466088220361	2		774	559	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356279	66356279	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	122	910	1	ENST00000273854.3:c.1218G>T	p.Glu406Asp	p.E406D	ENST00000273854	NM_004439.5	406	gaG/gaT	5/18	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.375466088220361	2		911	540	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294264	1294264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377315722	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	152	938	4	ENST00000310581.5:c.737C>T	p.Pro246Leu	p.P246L	ENST00000310581	NM_198253.2	246	cCg/cTg	2/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.375466088220361	2		942	645	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800190	32800190	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	62	634	1	ENST00000374899.4:c.1192C>T	p.Gln398Ter	p.Q398*	ENST00000374899	NM_018833.2	398	Cag/Tag	7/12	1	2	FACETS	0.84	0.729	0.96	0.84	0.729	0.96	CLONAL	1	TRUE	1	0.375466088220361	2		635	393	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805788	32805788	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	127	1128	3	ENST00000374899.4:c.223del	p.Leu75Ter	p.L75*	ENST00000374899	NM_018833.2	75	Ctg/tg	2/12	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.375466088220361	2		1131	638	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805803	32805803	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	111	1188	0	ENST00000374899.4:c.208T>C	p.Cys70Arg	p.C70R	ENST00000374899	NM_018833.2	70	Tgt/Cgt	2/12	1	2	FACETS	0.892	0.803	0.986	0.892	0.803	0.986	CLONAL	1	TRUE	1	0.375466088220361	2		1188	663	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729772	41729772	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	14	520	2	ENST00000242208.4:c.757A>T	p.Ser253Cys	p.S253C	ENST00000242208	NM_002192.2	253	Agc/Tgc	3/3	1	2	FACETS	0.288	0.208	0.385	0.288	0.208	0.385	SUBCLONAL	1	TRUE	1	0.375466088220361	2		522	259	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38196103	38196103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	77	1199	0	ENST00000317025.8:c.698C>T	p.Thr233Ile	p.T233I	ENST00000317025	NM_023034.1	233	aCt/aTt	3/24	0.375466088220361	3	FACETS	0.607	0.532	0.688	0.304	0.266	0.344	SUBCLONAL	1	TRUE	1	0.375466088220361	3		1199	802	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931858	68931858	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	130	1252	0	ENST00000288368.4:c.291del	p.Glu98AsnfsTer42	p.E98Nfs*42	ENST00000288368	NM_024870.2	96	caC/ca	3/40	0.375466088220361	3	FACETS	0.961	0.871	1	0.48	0.435	0.528	CLONAL	1	TRUE	1	0.375466088220361	3		1252	856	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145736828	145736828	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs748047415	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	71	803	1	ENST00000428558.2:c.3613C>T	p.Gln1205Ter	p.Q1205*	ENST00000428558	NM_004260.3	1205	Cag/Tag	22/22	0.375466088220361	3	FACETS	0.679	0.592	0.772	0.339	0.296	0.386	SUBCLONAL	1	TRUE	1	0.375466088220361	3		804	662	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485327	8485327	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	rs760429760	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	69	646	0	ENST00000356435.5:c.3056-3C>T		p.X1019_splice	ENST00000356435		1019			1	2	FACETS	0.892	0.78	1	0.892	0.78	1	CLONAL	1	TRUE	1	0.375466088220361	2		646	412	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641176	93641176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	87	925	1	ENST00000375746.1:c.1522G>A	p.Ala508Thr	p.A508T	ENST00000375746	NM_001174167.1	508	Gcc/Acc	11/14	1	2	FACETS	0.805	0.713	0.902	0.805	0.713	0.902	CLONAL	1	TRUE	1	0.375466088220361	2		926	576	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248136	110248136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	86	841	0	ENST00000374672.4:c.1336C>T	p.His446Tyr	p.H446Y	ENST00000374672	NM_004235.4	446	Cac/Tac	5/5	1	2	FACETS	0.824	0.73	0.924	0.824	0.73	0.924	CLONAL	1	TRUE	1	0.375466088220361	2		841	556	SUCCESS
AR	367	MSKCC	GRCh37	X	66943627	66943627	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002113-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	138	1030	0	ENST00000374690.3:c.2707C>T	p.Gln903Ter	p.Q903*	ENST00000374690	NM_000044.3	903	Caa/Taa	8/8	0.375466088220361	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.375466088220361	1		1030	564	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295216	1295216	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs35733142	NA	P-0002134-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	130	125	0				ENST00000310581	NM_198253.2	-/1132			0.20758610680312	6	FACETS	0.917	0.859	0.974			1	INDETERMINATE	5	FALSE	NA	0.632493004871411	6		125	203	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921468	39921468	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773750414	NA	P-0002134-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	203	545	0	ENST00000378444.4:c.4352C>T	p.Pro1451Leu	p.P1451L	ENST00000378444	NM_001123385.1	1451	cCg/cTg	10/15	0.486743117127129	4	FACETS	1	0.963	1	0.53	0.491	0.571	CLONAL	1	FALSE	2	0.632493004871411	4		545	988	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224599	123224599	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002134-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	238	611	0	ENST00000218089.9:c.3452C>A	p.Thr1151Lys	p.T1151K	ENST00000218089	NM_001042749.1	1151	aCa/aAa	31/35	NA		FACETS		NA	1			1	INDETERMINATE	NA	FALSE	NA	0.632493004871411	NA		611	1150	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295216	1295216	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs35733142	NA	P-0002134-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	128	125	0				ENST00000310581	NM_198253.2	-/1132			0.684472232123209	2	FACETS	0.85	0.801	0.898	0.85	0.801	0.898	CLONAL	2	FALSE	0	0.827033536062787	2		125	182	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30314583	30314583	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1463404926	NA	P-0002134-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	59	392	0	ENST00000262643.3:c.1132G>T	p.Ala378Ser	p.A378S	ENST00000262643	NM_001238.2	378	Gcc/Tcc	12/12	0.454330564969237	6	FACETS	0.906	0.782	1	0.226	0.195	0.26	INDETERMINATE	1	FALSE	2	0.827033536062787	6		392	418	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	60	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.787	0.701	0.873			1	INDETERMINATE	2	TRUE	NA	0.620055203530087	2		422	123	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954198	48954198	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123331	NA	P-0002138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	141	549	0	ENST00000267163.4:c.1399C>T	p.Arg467Ter	p.R467*	ENST00000267163	NM_000321.2	467	Cga/Tga	15/27	0.622225212507488	1	FACETS	0.618	0.566	0.671	0.618	0.566	0.671	SUBCLONAL	1	TRUE	0	0.620055203530087	1		549	508	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711927	89711928	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1554900593	NA	P-0002138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	332	519	2	ENST00000371953.3:c.548dup	p.Asn184GlufsTer6	p.N184Efs*6	ENST00000371953	NM_000314.4	182	tta/ttAa	6/9	0.60758572025738	1	FACETS	0.994	0.946	1	0.994	0.946	1	CLONAL	1	TRUE	0	0.620055203530087	1		521	743	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030783	48030783	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	63	400	0	ENST00000234420.5:c.3397A>G	p.Thr1133Ala	p.T1133A	ENST00000234420	NM_000179.2	1133	Act/Gct	5/10	1	2	FACETS	0.32	0.276	0.367	0.32	0.276	0.367	SUBCLONAL	1	TRUE	1	0.620055203530087	2		400	635	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538178	187538178	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	170	592	0	ENST00000441802.2:c.9056A>G	p.Asn3019Ser	p.N3019S	ENST00000441802	NM_005245.3	3019	aAc/aGc	11/27	NA	2	FACETS	0.53	0.487	0.575			1	INDETERMINATE	1	TRUE	NA	0.620055203530087	2		592	1035	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684004	29684004	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555536689	NA	P-0002138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	406	650	0	ENST00000356175.3:c.7702C>T	p.Gln2568Ter	p.Q2568*	ENST00000356175	NM_000267.3	2568	Cag/Tag	52/57	0.622225212507488	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.620055203530087	1		650	721	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579448	7579448	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002138-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	105	427	0	ENST00000269305.4:c.239del	p.Pro80LeufsTer43	p.P80Lfs*43	ENST00000269305	NM_001126112.2	80	cCt/ct	4/11	0.111168046448641	5	FACETS	0.974	0.874	1			1	INDETERMINATE	1	TRUE	NA	0.620055203530087	5		427	671	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002141-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	41	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.984	0.841	1			1	INDETERMINATE	1	TRUE	NA	0.718664725051689	2		422	116	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0002141-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	263	310	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.972	0.915	1	0.972	0.915	1	CLONAL	1	TRUE	1	0.718664725051689	2		310	753	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024290	31024290	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002141-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	117	406	0	ENST00000375687.4:c.3775C>G	p.Pro1259Ala	p.P1259A	ENST00000375687	NM_015338.5	1259	Cca/Gca	13/13	1	2	FACETS	0.529	0.478	0.582	0.529	0.478	0.582	SUBCLONAL	1	TRUE	1	0.718664725051689	2		406	616	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044973	47044986	+	frameshift_variant	Frame_Shift_Del	DEL	CAGTTCCCCAGCAA	CAGTTCCCCAGCAA	-	novel	NA	P-0002141-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	232	188	0	ENST00000377604.3:c.2299_2312del	p.Gln767ArgfsTer18	p.Q767Rfs*18	ENST00000377604	NM_001204468.1	767	CAGTTCCCCAGCAAa/a	20/24	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.718664725051689	1		188	315	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002145-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	49	422	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	1	0.894	1	1	0.976	1	CLONAL	2	TRUE	0	0.23	1		422	180	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866552	78866552	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs781747303	NA	P-0002145-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	281	349	0	ENST00000306801.3:c.2125C>G	p.Arg709Gly	p.R709G	ENST00000306801	NM_020761.2	709	Cga/Gga	19/34	0.184671862999742	2	FACETS	0.947	0.893	1	1	0.993	1	CLONAL	3	TRUE	0	0.23	2		349	860	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302313	15302313	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002145-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	252	366	0	ENST00000263388.2:c.958A>G	p.Thr320Ala	p.T320A	ENST00000263388	NM_000435.2	320	Aca/Gca	6/33	0.3	1	FACETS	0.835	0.784	0.887	1	0.996	1	CLONAL	3	TRUE	0	0.23	1		366	774	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002146-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	21	422	0				ENST00000310581	NM_198253.2	-/1132			0.3	2	FACETS	1	0.823	1			1	CLONAL	2	TRUE	NA	0.18	2		422	110	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912656	NA	P-0002146-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	27	403	0	ENST00000269305.4:c.734G>T	p.Gly245Val	p.G245V	ENST00000269305	NM_001126112.2	245	gGc/gTc	7/11	1	2	FACETS	0.767	0.61	0.947	0.767	0.61	0.947	CLONAL	1	TRUE	1	0.18	2		403	391	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170271	32170271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148269570	NA	P-0002146-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	24	310	0	ENST00000375023.3:c.3337C>T	p.Arg1113Cys	p.R1113C	ENST00000375023	NM_004557.3	1113	Cgc/Tgc	21/30	1	2	FACETS	0.691	0.541	0.864	0.691	0.541	0.864	SUBCLONAL	1	TRUE	1	0.18	2		310	386	SUCCESS
BLM	641	MSKCC	GRCh37	15	91306343	91306343	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs745922014	NA	P-0002146-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	35	464	0	ENST00000355112.3:c.2030A>G	p.Asn677Ser	p.N677S	ENST00000355112	NM_000057.2	677	aAt/aGt	8/22	0.0939885575265432	0	FACETS	0.579	0.473	0.697			1	INDETERMINATE	1	TRUE	0	0.18	0		464	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577508	7577508	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1060501201	NA	P-0002146-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	22	347	0	ENST00000269305.4:c.773A>C	p.Glu258Ala	p.E258A	ENST00000269305	NM_001126112.2	258	gAa/gCa	7/11	1	2	FACETS	0.687	0.532	0.867	0.687	0.532	0.867	SUBCLONAL	1	TRUE	1	0.18	2		347	356	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36653555	36653556	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0002146-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	45	465	0	ENST00000244741.5:c.474dup	p.Phe159LeufsTer38	p.F159Lfs*38	ENST00000244741	NM_000389.4	158	atc/atCc	3/3	0.205807833708715	4	FACETS	1	0.88	1	0.529	0.444	0.623	CLONAL	1	TRUE	2	0.18	4		465	558	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937091	48937091	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002146-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	54	259	0	ENST00000267163.4:c.859del	p.Glu287ArgfsTer2	p.E287Rfs*2	ENST00000267163	NM_000321.2	287	Gag/ag	8/27	0.205807833708715	3	FACETS	1	0.964	1	0.733	0.627	0.849	CLONAL	1	TRUE	1	0.18	3		259	446	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518261	204518261	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002163-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	193	478	0	ENST00000367182.3:c.924A>T	p.Glu308Asp	p.E308D	ENST00000367182	NM_001278516.1	308	gaA/gaT	11/11	1	2	FACETS	0.734	0.678	0.794	0.734	0.678	0.794	SUBCLONAL	1	TRUE	1	0.407078812340905	2		478	1291	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505492	25505492	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002163-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	257	567	1	ENST00000264709.3:c.266C>G	p.Pro89Arg	p.P89R	ENST00000264709	NM_175629.2	89	cCc/cGc	4/23	NA	2	FACETS	1	0.953	1			1	INDETERMINATE	1	TRUE	NA	0.407078812340905	2		568	1235	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994400	25994400	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002163-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	242	505	0	ENST00000435504.4:c.413C>A	p.Ser138Tyr	p.S138Y	ENST00000435504		138	tCc/tAc	6/13	NA	2	FACETS	1	0.933	1			1	INDETERMINATE	1	TRUE	NA	0.407078812340905	2		505	1189	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158719	26158719	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002163-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	48	148	0	ENST00000289316.2:c.322G>C	p.Ala108Pro	p.A108P	ENST00000289316	NM_138720.2	108	Gcc/Ccc	1/2	NA	2	FACETS	0.68	0.577	0.792			1	INDETERMINATE	1	TRUE	NA	0.407078812340905	2		148	347	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946195	13946195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1433178930	NA	P-0002163-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	168	392	0	ENST00000405192.2:c.901C>T	p.Arg301Trp	p.R301W	ENST00000405192	NM_001163147.1	301	Cgg/Tgg	10/12	1	2	FACETS	0.838	0.77	0.909	0.838	0.77	0.909	CLONAL	1	TRUE	1	0.407078812340905	2		392	985	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468045	50468045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002163-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	143	342	0	ENST00000331340.3:c.1280C>T	p.Ser427Leu	p.S427L	ENST00000331340	NM_006060.4	427	tCg/tTg	8/8	1	2	FACETS	0.765	0.697	0.837	0.765	0.697	0.837	SUBCLONAL	1	TRUE	1	0.407078812340905	2		342	918	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386575	81386575	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002163-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	315	550	0	ENST00000222390.5:c.412G>T	p.Gly138Ter	p.G138*	ENST00000222390	NM_000601.4	138	Gga/Tga	4/18	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.407078812340905	2		550	1394	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151917668	151917668	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002163-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	136	240	0	ENST00000262189.6:c.3652C>G	p.Gln1218Glu	p.Q1218E	ENST00000262189	NM_170606.2	1218	Cag/Gag	23/59	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.407078812340905	2		240	598	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499832	8499832	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002163-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	207	467	0	ENST00000356435.5:c.2137G>T	p.Gly713Cys	p.G713C	ENST00000356435		713	Ggt/Tgt	14/35	0.407078812340905	1	FACETS	0.832	0.772	0.894	0.832	0.772	0.894	CLONAL	1	TRUE	0	0.407078812340905	1		467	974	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913385	NA	P-0002163-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	127	155	0	ENST00000304494.5:c.247C>G	p.His83Asp	p.H83D	ENST00000304494	NM_000077.4	83	Cac/Gac	2/3	0.407078812340905	1	FACETS	0.996	0.907	1	0.996	0.907	1	CLONAL	1	TRUE	0	0.407078812340905	1		155	499	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456810	32456810	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002163-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	97	205	0	ENST00000332351.3:c.82C>A	p.Pro28Thr	p.P28T	ENST00000332351	NM_024426.4	28	Cca/Aca	1/10	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.407078812340905	2		205	471	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912252	32912252	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771112270	NA	P-0002163-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	134	491	0	ENST00000380152.3:c.3760G>A	p.Glu1254Lys	p.E1254K	ENST00000380152		1254	Gag/Aag	11/27	0.222348056433049	0	FACETS	0.39	0.354	0.428			1	INDETERMINATE	1	TRUE	0	0.407078812340905	0		491	1001	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138048	2138048	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs45517389	NA	P-0002163-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	225	376	0	ENST00000219476.3:c.5069-1G>C		p.X1690_splice	ENST00000219476	NM_000548.3	1690			0.407078812340905	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.407078812340905	1		376	817	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778472	3778472	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002163-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	239	494	0	ENST00000262367.5:c.6576G>A	p.Met2192Ile	p.M2192I	ENST00000262367	NM_004380.2	2192	atG/atA	31/31	0.407078812340905	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.407078812340905	1		494	815	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519989	NA	P-0002163-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	217	412	0	ENST00000269305.4:c.730G>A	p.Gly244Ser	p.G244S	ENST00000269305	NM_001126112.2	244	Ggc/Agc	7/11	0.407078812340905	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.407078812340905	1		412	792	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509683	29509683	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002163-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	215	373	0	ENST00000356175.3:c.888G>C	p.Lys296Asn	p.K296N	ENST00000356175	NM_000267.3	296	aaG/aaC	8/57	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.407078812340905	2		373	976	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226474	41226474	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs137894496	NA	P-0002163-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	306	509	0	ENST00000357654.3:c.4549C>G	p.Leu1517Val	p.L1517V	ENST00000357654	NM_007294.3	1517	Ctt/Gtt	14/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.407078812340905	2		509	1318	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034482	47034482	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002163-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	121	497	0	ENST00000377604.3:c.567A>T	p.Glu189Asp	p.E189D	ENST00000377604	NM_001204468.1	189	gaA/gaT	6/24	0.222348056433049	0	FACETS	0.335	0.302	0.371			1	INDETERMINATE	1	TRUE	0	0.407078812340905	0		497	1051	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038529	47038529	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002163-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	150	597	0	ENST00000377604.3:c.691G>T	p.Glu231Ter	p.E231*	ENST00000377604	NM_001204468.1	231	Gag/Tag	8/24	0.222348056433049	0	FACETS	0.432	0.394	0.472			1	INDETERMINATE	1	TRUE	0	0.407078812340905	0		597	1011	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652285	48652285	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002163-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	127	633	0	ENST00000376670.3:c.956C>G	p.Ser319Cys	p.S319C	ENST00000376670	NM_002049.3	319	tCc/tGc	6/6	0.222348056433049	0	FACETS	0.314	0.283	0.346			1	INDETERMINATE	1	TRUE	0	0.407078812340905	0		633	1179	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47688743	47688744	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCCG	novel	NA	P-0002163-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	274	469	0	ENST00000347630.2:c.553_556dup	p.Leu186ProfsTer5	p.L186Pfs*5	ENST00000347630	NM_001007230.1	186	ctg/cCGGCtg	7/11	1	2	FACETS	0.957	0.896	1	0.957	0.896	1	CLONAL	1	TRUE	1	0.407078812340905	2		469	1407	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602290	10602306	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCGACGGCATAGATG	CGCCGACGGCATAGATG	-	novel	NA	P-0002163-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	158	404	0	ENST00000171111.5:c.1272_1288del	p.His424GlnfsTer15	p.H424Qfs*15	ENST00000171111	NM_203500.1	424	caCATCTATGCCGTCGGCGgc/cagc	3/6	0.407078812340905	1	FACETS	0.977	0.898	1	0.977	0.898	1	CLONAL	1	TRUE	0	0.407078812340905	1		404	633	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002166-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	128	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.831114441845606	2		422	300	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0002166-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	410	142	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.433713272172472	4	FACETS	0.914	0.88	0.947			1	INDETERMINATE	3	TRUE	NA	0.831114441845606	4		142	659	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0002166-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	225	168	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA	2	FACETS	1	0.947	1			1	INDETERMINATE	1	TRUE	NA	0.831114441845606	2		168	537	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972916	25972916	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002166-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	353	383	0	ENST00000435504.4:c.1509G>C	p.Lys503Asn	p.K503N	ENST00000435504		503	aaG/aaC	12/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.831114441845606	2		383	796	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3827617	3827617	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002166-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	355	373	0	ENST00000262367.5:c.2155C>T	p.Gln719Ter	p.Q719*	ENST00000262367	NM_004380.2	719	Caa/Taa	11/31	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.831114441845606	2		373	792	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565532	41565532	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002166-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	449	464	0	ENST00000263253.7:c.4198A>T	p.Ser1400Cys	p.S1400C	ENST00000263253	NM_001429.3	1400	Agt/Tgt	26/31	NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.831114441845606	2		464	1025	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44894169	44894177	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTGCAGCA	CTTGCAGCA	-	novel	NA	P-0002166-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	591	274	1	ENST00000377967.4:c.565-7_566del		p.X189_splice	ENST00000377967	NM_021140.2	189		7/29	1	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.831114441845606	1		275	665	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039356	47039358	+	inframe_deletion	In_Frame_Del	DEL	TCC	TCC	-	novel	NA	P-0002166-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	399	242	0	ENST00000377604.3:c.985_987del	p.Ser329del	p.S329del	ENST00000377604	NM_001204468.1	327	TCC/-	10/24	1	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.831114441845606	1		242	552	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123199759	123199760	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0002166-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	448	221	0	ENST00000218089.9:c.2059_2060insCA	p.Val687AlafsTer6	p.V687Afs*6	ENST00000218089	NM_001042749.1	687	gta/gCAta	21/35	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.831114441845606	1		221	561	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002168-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	44	422	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		422	234	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0002181-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	136	139	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.798290222283724	2		139	282	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0002181-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	246	196	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	0.989	0.931	1	0.989	0.931	1	CLONAL	1	TRUE	1	0.798290222283724	2		196	623	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389149	31389149	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002181-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	73	332	0	ENST00000328111.2:c.2062G>T	p.Asp688Tyr	p.D688Y	ENST00000328111	NM_006892.3	688	Gat/Tat	19/23	1	2	FACETS	0.224	0.195	0.255	0.224	0.195	0.255	SUBCLONAL	1	TRUE	1	0.798290222283724	2		332	818	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002185-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	51	422	0				ENST00000310581	NM_198253.2	-/1132			0.226308454163073	1	FACETS	0.787	0.675	0.907	1	0.968	1	CLONAL	2	TRUE	0	0.226308454163073	1		422	254	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0002185-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	70	239	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	0.18818356963896	3	FACETS	1	0.968	1	0.68	0.594	0.773	CLONAL	1	TRUE	1	0.226308454163073	3		239	506	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782664	NA	P-0002185-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	142	299	0	ENST00000269305.4:c.711G>T	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atT	7/11	0.124484667382448	3	FACETS	1	0.967	1			1	INDETERMINATE	2	TRUE	NA	0.226308454163073	3		299	627	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120502080	120502080	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002185-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	76	316	0	ENST00000256646.2:c.1961G>T	p.Cys654Phe	p.C654F	ENST00000256646	NM_024408.3	654	tGt/tTt	12/34	0.111202207373247	3	FACETS	0.956	0.838	1	0.478	0.419	0.542	INDETERMINATE	1	TRUE	1	0.226308454163073	3		316	782	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533841	63533841	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002185-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	60	313	0	ENST00000307078.5:c.1313T>C	p.Ile438Thr	p.I438T	ENST00000307078	NM_004655.3	438	aTa/aCa	6/11	0.226308454163073	2	FACETS	1	0.875	1	0.508	0.438	0.584	CLONAL	1	TRUE	0	0.226308454163073	2		313	522	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584728	187584743	+	frameshift_variant	Frame_Shift_Del	DEL	GTCGATTCACGGTCCA	GTCGATTCACGGTCCA	-	novel	NA	P-0002185-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	60	337	0	ENST00000441802.2:c.3290_3305del	p.Leu1097ProfsTer6	p.L1097Pfs*6	ENST00000441802	NM_005245.3	1097	cTGGACCGTGAATCGACc/cc	3/27	0.226308454163073	1	FACETS	0.964	0.832	1	0.964	0.832	1	CLONAL	1	TRUE	0	0.226308454163073	1		337	488	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	562	422	0				ENST00000310581	NM_198253.2	-/1132			0.444275262256897	6	FACETS	1	0.993	1	1	0.993	1	CLONAL	5	TRUE	1	0.444275262256897	6		422	889	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	223	344	0	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.444275262256897	2		344	966	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	233	558	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.444275262256897	2	FACETS	1	0.969	1	0.532	0.496	0.569	CLONAL	1	TRUE	0	0.444275262256897	2		558	986	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250088	110250088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237765057	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	145	235	0	ENST00000374672.4:c.587C>T	p.Ser196Leu	p.S196L	ENST00000374672	NM_004235.4	196	tCg/tTg	3/5	0.444275262256897	3	FACETS	0.877	0.799	0.958	0.438	0.399	0.479	CLONAL	1	TRUE	1	0.444275262256897	3		235	910	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618602	37618602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	179	290	0	ENST00000447079.4:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000447079	NM_015083.1	93	cGa/cAa	1/14	0.444275262256897	3	FACETS	0.918	0.845	0.994	0.459	0.422	0.497	CLONAL	1	TRUE	1	0.444275262256897	3		290	1073	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306689	41306689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868376470	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	176	350	0	ENST00000373198.4:c.970G>A	p.Glu324Lys	p.E324K	ENST00000373198	NM_133170.3	324	Gaa/Aaa	7/32	0.444275262256897	4	FACETS	0.893	0.821	0.969	0.298	0.273	0.323	CLONAL	1	TRUE	1	0.444275262256897	4		350	1281	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057682	27057682	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520585	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	572	472	0	ENST00000324856.7:c.1390C>T	p.Gln464Ter	p.Q464*	ENST00000324856	NM_006015.4	464	Caa/Taa	3/20	0.444275262256897	3	FACETS	0.977	0.938	1	0.977	0.938	1	CLONAL	2	TRUE	1	0.444275262256897	3		472	1610	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100871	27100871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761500441	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	218	321	0	ENST00000324856.7:c.4153G>A	p.Glu1385Lys	p.E1385K	ENST00000324856	NM_006015.4	1385	Gaa/Aaa	18/20	0.444275262256897	3	FACETS	1	0.936	1	0.504	0.468	0.542	CLONAL	1	TRUE	1	0.444275262256897	3		321	1189	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814544	43814544	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs550268500	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	187	269	0	ENST00000372470.3:c.1339G>A	p.Gly447Arg	p.G447R	ENST00000372470	NM_005373.2	447	Ggg/Agg	9/12	0.444275262256897	3	FACETS	0.992	0.916	1	0.496	0.458	0.536	CLONAL	1	TRUE	1	0.444275262256897	3		269	1037	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731205	162731205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	175	326	0	ENST00000367921.3:c.1060G>A	p.Asp354Asn	p.D354N	ENST00000367921	NM_006182.2	354	Gat/Aat	9/18	0.444275262256897	3	FACETS	0.845	0.777	0.917	0.423	0.388	0.459	CLONAL	1	TRUE	1	0.444275262256897	3		326	1139	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018218	48018218	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	176	272	0	ENST00000234420.5:c.413C>T	p.Pro138Leu	p.P138L	ENST00000234420	NM_000179.2	138	cCa/cTa	2/10	0.387791244450136	4	FACETS	1	0.954	1	0.526	0.484	0.571	CLONAL	1	TRUE	2	0.444275262256897	4		272	1087	SUCCESS
ATR	545	MSKCC	GRCh37	3	142232468	142232468	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	180	242	0	ENST00000350721.4:c.4516C>T	p.Leu1506Phe	p.L1506F	ENST00000350721	NM_001184.3	1506	Ctt/Ttt	26/47	0.218567850833665	5	FACETS	1	0.984	1	0.424	0.39	0.459	INDETERMINATE	1	TRUE	2	0.444275262256897	5		242	1062	SUCCESS
ATR	545	MSKCC	GRCh37	3	142286983	142286983	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1353411105	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	174	326	0	ENST00000350721.4:c.73G>A	p.Glu25Lys	p.E25K	ENST00000350721	NM_001184.3	25	Gaa/Aaa	2/47	0.218567850833665	5	FACETS	1	0.973	1	0.378	0.347	0.41	INDETERMINATE	1	TRUE	2	0.444275262256897	5		326	1152	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430396	181430396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1413	210	366	0	ENST00000325404.1:c.248C>T	p.Ser83Leu	p.S83L	ENST00000325404	NM_003106.3	83	tCg/tTg	1/1	0.444275262256897	5	FACETS	0.971	0.898	1	0.324	0.299	0.349	CLONAL	1	TRUE	2	0.444275262256897	5		366	1623	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444632	187444632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	156	235	0	ENST00000232014.4:c.1595C>T	p.Ser532Leu	p.S532L	ENST00000232014	NM_001130845.1	532	tCa/tTa	7/10	0.444275262256897	5	FACETS	0.927	0.847	1	0.309	0.282	0.338	CLONAL	1	TRUE	2	0.444275262256897	5		235	1262	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247207	153247207	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1179476070	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	85	377	0	ENST00000281708.4:c.1595C>T	p.Thr532Ile	p.T532I	ENST00000281708	NM_033632.3	532	aCc/aTc	10/12	0.151884961100001	3	FACETS	0.679	0.6	0.763	0.226	0.2	0.255	INDETERMINATE	1	TRUE	0	0.444275262256897	3		377	689	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199744	138199744	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	242	361	0	ENST00000237289.4:c.1162G>A	p.Glu388Lys	p.E388K	ENST00000237289	NM_001270507.1	388	Gaa/Aaa	7/9	0.27985136859204	3	FACETS	1	0.988	1	0.413	0.385	0.441	CLONAL	1	TRUE	0	0.444275262256897	3		361	1075	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875060	151875060	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	126	120	0	ENST00000262189.6:c.7478C>G	p.Pro2493Arg	p.P2493R	ENST00000262189	NM_170606.2	2493	cCg/cGg	38/59	0.387791244450136	4	FACETS	1	0.962	1	0.56	0.507	0.615	CLONAL	1	TRUE	2	0.444275262256897	4		120	732	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538982	23538982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	240	352	0	ENST00000380871.4:c.457G>A	p.Glu153Lys	p.E153K	ENST00000380871	NM_006167.3	153	Gaa/Aaa	2/2	0.444275262256897	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.444275262256897	1		352	831	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372080	55372080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	76	126	0	ENST00000297316.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000297316	NM_022454.3	257	tCg/tTg	2/2	0.4032512574563	4	FACETS	0.912	0.801	1	0.228	0.2	0.258	CLONAL	1	TRUE	0	0.444275262256897	4		126	542	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069964	5069964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	124	364	0	ENST00000381652.3:c.1553C>T	p.Ser518Phe	p.S518F	ENST00000381652	NM_004972.3	518	tCt/tTt	12/25	0.444275262256897	3	FACETS	0.804	0.727	0.885	0.402	0.363	0.443	CLONAL	1	TRUE	1	0.444275262256897	3		364	849	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852095	63852095	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	138	209	0	ENST00000279873.7:c.2873C>T	p.Ser958Leu	p.S958L	ENST00000279873	NM_032199.2	958	tCa/tTa	10/10	1	2	FACETS	0.96	0.876	1	0.96	0.876	1	CLONAL	1	TRUE	1	0.444275262256897	2		209	647	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572586	64572586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1114167477	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	238	259	0	ENST00000312049.6:c.1270G>A	p.Glu424Lys	p.E424K	ENST00000312049	NM_130799.2	424	Gag/Aag	9/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.444275262256897	2		259	845	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518527	69518527	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	133	166	0	ENST00000294312.3:c.118G>A	p.Asp40Asn	p.D40N	ENST00000294312	NM_005117.2	40	Gac/Aac	1/3	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.444275262256897	2		166	556	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022388	12022388	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	266	420	0	ENST00000396373.4:c.494C>G	p.Ser165Cys	p.S165C	ENST00000396373	NM_001987.4	165	tCc/tGc	5/8	0.437405133522894	3	FACETS	0.985	0.922	1	0.328	0.307	0.351	CLONAL	1	TRUE	0	0.444275262256897	3		420	1485	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125035	46125035	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	198	358	0	ENST00000334344.6:c.222A>C	p.Glu74Asp	p.E74D	ENST00000334344	NM_152641.2	74	gaA/gaC	3/21	0.444275262256897	3	FACETS	0.989	0.915	1	0.494	0.457	0.533	CLONAL	1	TRUE	1	0.444275262256897	3		358	1102	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46125060	46125060	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	196	316	0	ENST00000334344.6:c.247T>C	p.Ser83Pro	p.S83P	ENST00000334344	NM_152641.2	83	Tct/Cct	3/21	0.444275262256897	3	FACETS	1	0.957	1	0.524	0.485	0.565	CLONAL	1	TRUE	1	0.444275262256897	3		316	1029	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245696	46245696	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	213	336	0	ENST00000334344.6:c.3790G>A	p.Glu1264Lys	p.E1264K	ENST00000334344	NM_152641.2	1264	Gaa/Aaa	15/21	0.444275262256897	3	FACETS	1	0.932	1	0.502	0.466	0.54	CLONAL	1	TRUE	1	0.444275262256897	3		336	1167	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911628	32911628	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	74	291	0	ENST00000380152.3:c.3136G>C	p.Glu1046Gln	p.E1046Q	ENST00000380152		1046	Gaa/Caa	11/27	0.218567850833665	5	FACETS	0.815	0.713	0.925	0.272	0.237	0.309	INDETERMINATE	1	TRUE	2	0.444275262256897	5		291	681	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911711	32911711	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	91	282	0	ENST00000380152.3:c.3219G>C	p.Gln1073His	p.Q1073H	ENST00000380152		1073	caG/caC	11/27	0.218567850833665	5	FACETS	0.971	0.862	1	0.324	0.287	0.363	INDETERMINATE	1	TRUE	2	0.444275262256897	5		282	703	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912756	32912756	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	71	265	0	ENST00000380152.3:c.4264G>C	p.Glu1422Gln	p.E1422Q	ENST00000380152		1422	Gag/Cag	11/27	0.218567850833665	5	FACETS	0.828	0.723	0.942	0.276	0.241	0.314	INDETERMINATE	1	TRUE	2	0.444275262256897	5		265	643	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033971	49033971	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	304	252	0	ENST00000267163.4:c.2106+2T>A		p.X702_splice	ENST00000267163	NM_000321.2	702			0.218567850833665	5	FACETS	1	0.983	1	0.734	0.693	0.777	INDETERMINATE	2	TRUE	2	0.444275262256897	5		252	1035	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422112	81422112	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	204	269	0	ENST00000298171.2:c.88G>A	p.Glu30Lys	p.E30K	ENST00000298171	NM_000369.2	30	Gag/Aag	1/10	0.444275262256897	3	FACETS	1	0.967	1	0.536	0.497	0.577	CLONAL	1	TRUE	1	0.444275262256897	3		269	1046	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590677	95590677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	237	471	0	ENST00000393063.1:c.1232C>T	p.Ser411Leu	p.S411L	ENST00000393063	NM_030621.3	411	tCa/tTa	9/28	0.444275262256897	3	FACETS	0.907	0.845	0.972	0.454	0.422	0.486	CLONAL	1	TRUE	1	0.444275262256897	3		471	1437	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16005065	16005065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	140	189	1	ENST00000268712.3:c.2189C>T	p.Ala730Val	p.A730V	ENST00000268712	NM_006311.3	730	gCt/gTt	20/46	1	2	FACETS	0.925	0.845	1	0.925	0.845	1	CLONAL	1	TRUE	1	0.444275262256897	2		190	681	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552170	29552170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	117	374	0	ENST00000356175.3:c.1903C>T	p.Pro635Ser	p.P635S	ENST00000356175	NM_000267.3	635	Cct/Tct	17/57	0.444275262256897	3	FACETS	0.712	0.641	0.787	0.356	0.32	0.394	SUBCLONAL	1	TRUE	1	0.444275262256897	3		374	904	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619040	37619040	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	201	342	0	ENST00000447079.4:c.716G>C	p.Gly239Ala	p.G239A	ENST00000447079	NM_015083.1	239	gGa/gCa	1/14	0.444275262256897	3	FACETS	1	0.961	1	0.529	0.489	0.569	CLONAL	1	TRUE	1	0.444275262256897	3		342	1046	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223117	1223117	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	235	323	0	ENST00000326873.7:c.1054G>A	p.Asp352Asn	p.D352N	ENST00000326873	NM_000455.4	352	Gac/Aac	8/10	0.444275262256897	2	FACETS	1	0.967	1	0.529	0.493	0.566	CLONAL	1	TRUE	0	0.444275262256897	2		323	1000	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130342	11130342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	257	374	0	ENST00000358026.2:c.2581G>A	p.Glu861Lys	p.E861K	ENST00000358026	NM_001128849.1	861	Gag/Aag	18/36	0.444275262256897	2	FACETS	1	0.972	1	0.533	0.499	0.568	CLONAL	1	TRUE	0	0.444275262256897	2		374	1085	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144143	11144143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555784586	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	180	284	0	ENST00000358026.2:c.3724G>A	p.Glu1242Lys	p.E1242K	ENST00000358026	NM_001128849.1	1242	Gag/Aag	26/36	0.444275262256897	2	FACETS	1	0.95	1	0.518	0.478	0.559	CLONAL	1	TRUE	0	0.444275262256897	2		284	782	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873797	45873797	+	start_lost	Translation_Start_Site	SNP	A	A	C	rs764073718	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	202	290	0	ENST00000391945.4:c.2T>G	p.Met1?	p.M1?	ENST00000391945	NM_000400.3	1	aTg/aGg	1/23	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.444275262256897	2		290	906	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52693404	52693404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	189	269	0	ENST00000322088.6:c.55G>A	p.Glu19Lys	p.E19K	ENST00000322088	NM_014225.5	19	Gaa/Aaa	1/15	0.396937802793995	3	FACETS	0.955	0.882	1			1	CLONAL	1	TRUE	NA	0.444275262256897	3		269	1089	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750363	39750363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	158	247	0	ENST00000361337.2:c.1978G>A	p.Asp660Asn	p.D660N	ENST00000361337	NM_003286.2	660	Gat/Aat	19/21	0.444275262256897	4	FACETS	0.886	0.811	0.966	0.295	0.27	0.322	CLONAL	1	TRUE	1	0.444275262256897	4		247	1159	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044550	47044550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1556781510	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	267	180	0	ENST00000377604.3:c.2047G>A	p.Glu683Lys	p.E683K	ENST00000377604	NM_001204468.1	683	Gag/Aag	18/24	0.402414835765788	2	FACETS	0.786	0.74	0.832			1	SUBCLONAL	2	TRUE	NA	0.444275262256897	2		180	765	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426513	47426513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376276271	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	269	196	0	ENST00000377045.4:c.856G>A	p.Asp286Asn	p.D286N	ENST00000377045	NM_001654.4	286	Gat/Aat	9/16	0.402414835765788	2	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.444275262256897	2		196	841	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357444	70357444	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	245	229	0	ENST00000374080.3:c.5785C>T	p.Gln1929Ter	p.Q1929*	ENST00000374080		1929	Cag/Tag	40/45	0.402414835765788	2	FACETS	1	0.99	1			1	CLONAL	1	TRUE	NA	0.444275262256897	2		229	853	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039452	49039461	+	frameshift_variant	Frame_Shift_Del	DEL	TATAAAATTT	TATAAAATTT	-	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	391	326	0	ENST00000267163.4:c.2437_2446del	p.Tyr813GlnfsTer10	p.Y813Qfs*10	ENST00000267163	NM_000321.2	813	TATAAAATTTca/ca	23/27	0.218567850833665	5	FACETS	1	0.986	1	0.731	0.694	0.768	INDETERMINATE	2	TRUE	2	0.444275262256897	5		326	1338	SUCCESS
AR	367	MSKCC	GRCh37	X	66765308	66765332	+	stop_gained	Nonsense_Mutation	DEL	ACCTGGTCCTGGATGAGGAACAGCA	ACCTGGTCCTGGATGAGGAACAGCA	G	novel	NA	P-0002186-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	207	155	0	ENST00000374690.3:c.320_344delinsG	p.Tyr107_Gln115delinsTer	p.Y107_Q115delins*	ENST00000374690	NM_000044.3	107	tACCTGGTCCTGGATGAGGAACAGCAa/tGa	1/8	0.402414835765788	2	FACETS	1	0.99	1			1	CLONAL	1	TRUE	NA	0.444275262256897	2		155	673	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0002189-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	93	139	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		139	493	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002194-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	66	422	0				ENST00000310581	NM_198253.2	-/1132			0.156321492713156	0	FACETS	0.575	0.506	0.648			1	INDETERMINATE	1	TRUE	0	0.496302746907233	0		422	233	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937233	76937233	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002194-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1182	322	494	0	ENST00000373344.5:c.3515C>A	p.Thr1172Asn	p.T1172N	ENST00000373344	NM_000489.3	1172	aCt/aAt	9/35	0.127131570421132	0	FACETS	0.435	0.409	0.461			1	INDETERMINATE	1	TRUE	0	0.496302746907233	0		494	1504	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002204-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	74	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.996	0.875	1			1	INDETERMINATE	1	FALSE	NA	0.334663924911606	2		422	444	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288764	11288764	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002204-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	148	347	0	ENST00000361445.4:c.2991C>A	p.Phe997Leu	p.F997L	ENST00000361445	NM_004958.3	997	ttC/ttA	19/58	0.305986269286404	1	FACETS	0.833	0.761	0.909	0.833	0.761	0.909	CLONAL	1	FALSE	0	0.334663924911606	1		347	884	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098445	47098445	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002204-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	158	390	0	ENST00000409792.3:c.6829C>T	p.Gln2277Ter	p.Q2277*	ENST00000409792	NM_014159.6	2277	Caa/Taa	15/21	0.334663924911606	0	FACETS	0.865	0.795	0.939			1	CLONAL	1	FALSE	0	0.334663924911606	0		390	726	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390099	89390099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002204-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	190	371	0	ENST00000336596.2:c.848G>A	p.Gly283Asp	p.G283D	ENST00000336596	NM_005233.5	283	gGt/gAt	4/17	NA	2	FACETS	0.956	0.882	1			1	INDETERMINATE	1	FALSE	NA	0.334663924911606	2		371	1188	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873678	35873678	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002204-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1273	208	409	0	ENST00000303115.3:c.634T>A	p.Tyr212Asn	p.Y212N	ENST00000303115	NM_002185.3	212	Tat/Aat	5/8	1	2	FACETS	0.839	0.777	0.905	0.839	0.777	0.905	CLONAL	1	FALSE	1	0.334663924911606	2		409	1481	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738617	145738617	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002204-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	83	143	0	ENST00000428558.2:c.2447T>G	p.Leu816Arg	p.L816R	ENST00000428558	NM_004260.3	816	cTc/cGc	15/22	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.334663924911606	2		143	414	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610300	81610300	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002204-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	128	353	0	ENST00000298171.2:c.1898A>C	p.Asp633Ala	p.D633A	ENST00000298171	NM_000369.2	633	gAc/gCc	10/10	1	2	FACETS	0.663	0.599	0.73	0.663	0.599	0.73	SUBCLONAL	1	FALSE	1	0.334663924911606	2		353	1154	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610313	81610313	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002204-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	139	357	0	ENST00000298171.2:c.1911G>T	p.Met637Ile	p.M637I	ENST00000298171	NM_000369.2	637	atG/atT	10/10	1	2	FACETS	0.662	0.601	0.727	0.662	0.601	0.727	SUBCLONAL	1	FALSE	1	0.334663924911606	2		357	1254	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808012	3808012	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002204-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	144	268	0	ENST00000262367.5:c.3407C>A	p.Ser1136Tyr	p.S1136Y	ENST00000262367	NM_004380.2	1136	tCc/tAc	18/31	0.123364493431537	0	FACETS	0.706	0.644	0.771			1	INDETERMINATE	1	FALSE	0	0.334663924911606	0		268	811	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782329	NA	P-0002204-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	115	310	0	ENST00000269305.4:c.746G>A	p.Arg249Lys	p.R249K	ENST00000269305	NM_001126112.2	249	aGg/aAg	7/11	0.334663924911606	1	FACETS	0.965	0.872	1	0.965	0.872	1	CLONAL	1	FALSE	0	0.334663924911606	1		310	593	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610674	52610674	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002204-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	211	427	0	ENST00000394830.3:c.3499del	p.Tyr1167MetfsTer26	p.Y1167Mfs*26	ENST00000394830	NM_018313.4	1167	Tat/at	23/30	0.334663924911606	0	FACETS	0.973	0.905	1			1	CLONAL	1	FALSE	0	0.334663924911606	0		427	862	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0002210-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	241	139	0				ENST00000310581	NM_198253.2	-/1132			0.386218993888557	6	FACETS	0.951	0.901	1	1	0.99	1	CLONAL	5	TRUE	2	0.386218993888557	6		139	465	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0002210-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	237	310	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA	2	FACETS	0.811	0.759	0.863			1	INDETERMINATE	2	TRUE	NA	0.386218993888557	2		310	757	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937151	76937151	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002210-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	226	655	4	ENST00000373344.5:c.3597C>A	p.Asp1199Glu	p.D1199E	ENST00000373344	NM_000489.3	1199	gaC/gaA	9/35	0.236388007307679	3	FACETS	1	0.979	1	0.565	0.525	0.606	CLONAL	1	TRUE	1	0.386218993888557	3		659	1236	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577569	7577580	+	inframe_deletion	In_Frame_Del	DEL	ACATGTAGTTGT	ACATGTAGTTGT	-	novel	NA	P-0002210-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	298	409	0	ENST00000269305.4:c.701_712del	p.Tyr234_Met237del	p.Y234_M237del	ENST00000269305	NM_001126112.2	234	tACAACTACATGTgt/tgt	7/11	0.386218993888557	3	FACETS	0.892	0.846	0.939	0.892	0.846	0.939	CLONAL	3	TRUE	0	0.386218993888557	3		409	688	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032821	30032837	+	frameshift_variant	Frame_Shift_Del	DEL	TACACAATCAAGGACAC	TACACAATCAAGGACAC	ATT	novel	NA	P-0002210-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	241	444	0	ENST00000338641.4:c.196_212delinsATT	p.Tyr66IlefsTer15	p.Y66Ifs*15	ENST00000338641	NM_000268.3	66	TACACAATCAAGGACACa/ATTa	2/16	0.199553497155764	1	FACETS	0.757	0.711	0.804	1	0.993	1	INDETERMINATE	2	TRUE	0	0.386218993888557	1		444	665	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002212-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	160	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.817	0.756	0.879	1	0.991	1	CLONAL	2	FALSE	1	0.439187028194072	2		422	446	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0002212-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	203	318	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.391483961184851	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	FALSE	0	0.439187028194072	2		318	396	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002216-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	89	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.905153077934391	2		422	184	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0002216-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	657	314	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.905153077934391	2		314	1404	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662253	227662253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002216-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	64	409	0	ENST00000305123.5:c.1202G>A	p.Gly401Asp	p.G401D	ENST00000305123	NM_005544.2	401	gGc/gAc	1/2	1	2	FACETS	0.138	0.118	0.159	0.138	0.118	0.159	SUBCLONAL	1	TRUE	1	0.905153077934391	2		409	1027	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70005639	70005639	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763119975	NA	P-0002216-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1255	300	431	0	ENST00000394351.3:c.668G>A	p.Arg223His	p.R223H	ENST00000394351	NM_000248.3	223	cGc/cAc	7/9	1	2	FACETS	0.426	0.4	0.453	0.426	0.4	0.453	SUBCLONAL	1	TRUE	1	0.905153077934391	2		431	1555	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0002220-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	55	139	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.29	2		139	377	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0002220-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	189	310	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.29	2		310	1206	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971124	21971125	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0002220-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	85	99	0	ENST00000304494.5:c.233_234del	p.Leu78HisfsTer41	p.L78Hfs*41	ENST00000304494	NM_000077.4	78	cTC/c	2/3	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.29	2		99	531	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860385	42860385	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002220-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	160	536	0	ENST00000398585.3:c.492C>G	p.Ile164Met	p.I164M	ENST00000398585	NM_001135099.1	164	atC/atG	5/14	1	2	FACETS	0.945	0.865	1	0.945	0.865	1	CLONAL	1	TRUE	1	0.29	2		536	1168	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167467	24167467	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0002220-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	163	446	0	ENST00000263121.7:c.851C>G	p.Ser284Ter	p.S284*	ENST00000263121	NM_003073.3	284	tCa/tGa	7/9	0.3	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.29	1		446	919	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002221-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	99	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.768969988700858	2		422	236	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0002221-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	263	310	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.768969988700858	2		310	625	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720839	176720839	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002221-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	200	500	0	ENST00000439151.2:c.6470G>A	p.Trp2157Ter	p.W2157*	ENST00000439151	NM_022455.4	2157	tGg/tAg	23/23	1	2	FACETS	0.991	0.926	1	0.991	0.926	1	CLONAL	1	TRUE	1	0.768969988700858	2		500	525	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962846	2962846	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002221-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	55	503	0	ENST00000396946.4:c.2062C>T	p.Arg688Ter	p.R688*	ENST00000396946	NM_032415.4	688	Cga/Tga	16/25	1	2	FACETS	0.2	0.17	0.232	0.2	0.17	0.232	SUBCLONAL	1	TRUE	1	0.768969988700858	2		503	716	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574572	64574572	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0002221-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	180	478	2	ENST00000312049.6:c.825-2A>T		p.X275_splice	ENST00000312049	NM_130799.2	275			0.768969988700858	1	FACETS	0.948	0.894	1	0.948	0.894	1	CLONAL	1	TRUE	0	0.768969988700858	1		480	304	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002224-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	224	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.908771571495738	2		422	433	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0002224-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	363	327	1	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	0.892	0.849	0.935	0.892	0.849	0.935	CLONAL	1	TRUE	1	0.908771571495738	2		328	896	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0002224-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	502	424	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.908771571495738	2		424	1076	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491679	120491680	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0002224-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	46	354	0	ENST00000256646.2:c.2549_2550del	p.Glu850ValfsTer5	p.E850Vfs*5	ENST00000256646	NM_024408.3	850	gAG/g	16/34	0.908771571495738	1	FACETS	0.088	0.074	0.104	0.088	0.074	0.104	SUBCLONAL	1	TRUE	0	0.908771571495738	1		354	628	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400022	139400023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0002224-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	441	293	5	ENST00000277541.6:c.4325dup	p.Pro1443AlafsTer36	p.P1443Afs*36	ENST00000277541	NM_017617.3	1442	ccg/ccCg	25/34	0.908771571495738	1	FACETS	0.704	0.678	0.73	0.704	0.678	0.73	SUBCLONAL	1	TRUE	0	0.908771571495738	1		298	752	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002258-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	85	422	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		422	345	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002263-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	122	422	0				ENST00000310581	NM_198253.2	-/1132			0.292277605234904	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	2	0.416999009639883	4		422	383	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0002263-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	131	310	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.297231915512013	3	FACETS	1	0.973	1	0.591	0.538	0.647	CLONAL	1	TRUE	1	0.416999009639883	3		310	642	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579476	7579476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567556576	NA	P-0002263-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	296	417	0	ENST00000269305.4:c.211C>T	p.Pro71Ser	p.P71S	ENST00000269305	NM_001126112.2	71	Ccc/Tcc	4/11	0.416999009639883	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.416999009639883	2		417	629	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921532	39921532	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1309687666	NA	P-0002263-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	392	321	1	ENST00000378444.4:c.4288C>T	p.Gln1430Ter	p.Q1430*	ENST00000378444	NM_001123385.1	1430	Cag/Tag	10/15	0.322658465002629	2	FACETS	0.937	0.9	0.973			1	CLONAL	3	TRUE	NA	0.416999009639883	2		322	669	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002265-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	95	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.767350426585147	2		422	225	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271744	18271744	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002265-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	176	453	0	ENST00000222254.8:c.431C>G	p.Ser144Cys	p.S144C	ENST00000222254	NM_005027.3	144	tCt/tGt	4/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.767350426585147	2		453	433	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	66	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.893	0.782	1			1	INDETERMINATE	1	TRUE	NA	0.511599085162692	2		422	289	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	22	492	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.08	0.061	0.102	0.08	0.061	0.102	SUBCLONAL	1	TRUE	1	0.511599085162692	2		492	1076	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6299	7173	492	0	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.511599085162692	25	FACETS	1	0.998	1			1	CLONAL	14	TRUE	NA	0.511599085162692	25		492	13472	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271744	18271744	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	210	453	0	ENST00000222254.8:c.431C>G	p.Ser144Cys	p.S144C	ENST00000222254	NM_005027.3	144	tCt/tGt	4/16	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.511599085162692	2		453	690	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	23	575	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.084	0.065	0.107	0.084	0.065	0.107	SUBCLONAL	1	TRUE	1	0.511599085162692	2		575	1066	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170565	108170565	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	157	458	0	ENST00000278616.4:c.5130G>A	p.Trp1710Ter	p.W1710*	ENST00000278616	NM_000051.3	1710	tgG/tgA	34/63	1	2	FACETS	0.571	0.523	0.623	0.571	0.523	0.623	SUBCLONAL	1	TRUE	1	0.511599085162692	2		458	1074	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132438	11132438	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794284	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	70	607	2	ENST00000358026.2:c.2654G>A	p.Arg885His	p.R885H	ENST00000358026	NM_001128849.1	885	cGc/cAc	19/36	1	2	FACETS	0.296	0.257	0.338	0.296	0.257	0.338	SUBCLONAL	1	TRUE	1	0.511599085162692	2		609	924	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38064108	38064108	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	90	432	1	ENST00000250448.2:c.70G>A	p.Glu24Lys	p.E24K	ENST00000250448	NM_004496.3	24	Gag/Aag	1/2	1	2	FACETS	0.383	0.339	0.431	0.383	0.339	0.431	SUBCLONAL	1	TRUE	1	0.511599085162692	2		433	918	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448320	49448320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	58	616	1	ENST00000301067.7:c.391G>A	p.Glu131Lys	p.E131K	ENST00000301067	NM_003482.3	131	Gaa/Aaa	3/54	0.121460618590672	4	FACETS	0.314	0.269	0.364	0.157	0.134	0.182	INDETERMINATE	1	TRUE	2	0.511599085162692	4		617	1091	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661500	227661500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757021553	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	106	570	2	ENST00000305123.5:c.1955G>A	p.Arg652His	p.R652H	ENST00000305123	NM_005544.2	652	cGc/cAc	1/2	1	2	FACETS	0.42	0.376	0.468	0.42	0.376	0.468	SUBCLONAL	1	TRUE	1	0.511599085162692	2		572	986	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs149840192	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15474	612	780	0	ENST00000275493.2:c.866C>A	p.Ala289Asp	p.A289D	ENST00000275493	NM_005228.3	289	gCc/gAc	7/28	0.511599085162692	25	FACETS	1	0.971	1			1	CLONAL	1	TRUE	NA	0.511599085162692	25		780	16086	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965188	25965188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	97	452	0	ENST00000435504.4:c.4018G>A	p.Asp1340Asn	p.D1340N	ENST00000435504		1340	Gac/Aac	13/13	1	2	FACETS	0.461	0.41	0.515	0.461	0.41	0.515	SUBCLONAL	1	TRUE	1	0.511599085162692	2		452	823	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50917023	50917023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145473716	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	135	646	3	ENST00000440232.2:c.2275G>A	p.Val759Ile	p.V759I	ENST00000440232	NM_002691.3	759	Gtc/Atc	19/27	1	2	FACETS	0.483	0.438	0.53	0.483	0.438	0.53	SUBCLONAL	1	TRUE	1	0.511599085162692	2		649	1093	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576027	29576027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878853892	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	69	518	0	ENST00000356175.3:c.4000G>A	p.Glu1334Lys	p.E1334K	ENST00000356175	NM_000267.3	1334	Gaa/Aaa	30/57	1	2	FACETS	0.241	0.209	0.276	0.241	0.209	0.276	SUBCLONAL	1	TRUE	1	0.511599085162692	2		518	1118	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199945	138199945	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	45	279	0	ENST00000237289.4:c.1368del	p.Pro457LeufsTer20	p.P457Lfs*20	ENST00000237289	NM_001270507.1	455	Ggg/gg	7/9	1	2	FACETS	0.37	0.311	0.436	0.37	0.311	0.436	SUBCLONAL	1	TRUE	1	0.511599085162692	2		279	475	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32936831	32936831	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs81002873	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	73	420	0	ENST00000380152.3:c.7976+1G>A		p.X2659_splice	ENST00000380152		2659			1	2	FACETS	0.338	0.295	0.384	0.338	0.295	0.384	SUBCLONAL	1	TRUE	1	0.511599085162692	2		420	845	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738638	145738638	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs550469990	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	28	231	0	ENST00000428558.2:c.2426G>A	p.Gly809Glu	p.G809E	ENST00000428558	NM_004260.3	809	gGg/gAg	15/22	1	2	FACETS	0.315	0.251	0.387	0.315	0.251	0.387	SUBCLONAL	1	TRUE	1	0.511599085162692	2		231	348	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865591	57865591	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	100	745	0	ENST00000228682.2:c.3068C>T	p.Pro1023Leu	p.P1023L	ENST00000228682	NM_005269.2	1023	cCt/cTt	12/12	0.121460618590672	4	FACETS	0.469	0.418	0.525	0.235	0.209	0.263	INDETERMINATE	1	TRUE	2	0.511599085162692	4		745	1259	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945066	31945066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	59	628	0	ENST00000340398.3:c.35C>T	p.Thr12Ile	p.T12I	ENST00000340398	NM_001013699.2	12	aCc/aTc	1/1	0.121460618590672	4	FACETS	0.334	0.286	0.386	0.167	0.143	0.193	INDETERMINATE	1	TRUE	2	0.511599085162692	4		628	1045	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410460	63410460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	88	333	0	ENST00000330258.3:c.2707G>A	p.Glu903Lys	p.E903K	ENST00000330258	NM_152424.3	903	Gag/Aag	2/2	1	1	FACETS	0.521	0.463	0.583	0.521	0.463	0.583	SUBCLONAL	1	TRUE	0	0.511599085162692	1		333	491	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146563	185146563	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	64	448	1	ENST00000265026.3:c.194C>T	p.Thr65Ile	p.T65I	ENST00000265026	NM_004721.4	65	aCc/aTc	2/14	1	2	FACETS	0.314	0.271	0.361	0.314	0.271	0.361	SUBCLONAL	1	TRUE	1	0.511599085162692	2		449	797	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467932	66467932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756748785	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	119	578	0	ENST00000273854.3:c.337C>T	p.Leu113Phe	p.L113F	ENST00000273854	NM_004439.5	113	Ctt/Ttt	3/18	1	2	FACETS	0.449	0.405	0.497	0.449	0.405	0.497	SUBCLONAL	1	TRUE	1	0.511599085162692	2		578	1035	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149436881	149436881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	87	545	0	ENST00000286301.3:c.2288C>T	p.Ala763Val	p.A763V	ENST00000286301	NM_005211.3	763	gCc/gTc	17/22	1	2	FACETS	0.413	0.365	0.465	0.413	0.365	0.465	SUBCLONAL	1	TRUE	1	0.511599085162692	2		545	823	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036936	180036936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	77	667	0	ENST00000261937.6:c.3776C>T	p.Pro1259Leu	p.P1259L	ENST00000261937	NM_182925.4	1259	cCc/cTc	28/30	1	2	FACETS	0.347	0.304	0.393	0.347	0.304	0.393	SUBCLONAL	1	TRUE	1	0.511599085162692	2		667	868	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056979	180056979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1297682245	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	92	616	1	ENST00000261937.6:c.640G>A	p.Asp214Asn	p.D214N	ENST00000261937	NM_182925.4	214	Gac/Aac	5/30	1	2	FACETS	0.426	0.378	0.478	0.426	0.378	0.478	SUBCLONAL	1	TRUE	1	0.511599085162692	2		617	844	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41904338	41904338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	42	357	0	ENST00000372991.4:c.670G>A	p.Glu224Lys	p.E224K	ENST00000372991	NM_001760.3	224	Gag/Aag	4/5	1	2	FACETS	0.301	0.251	0.357	0.301	0.251	0.357	SUBCLONAL	1	TRUE	1	0.511599085162692	2		357	546	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553561	106553561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	48	276	0	ENST00000369096.4:c.1526C>T	p.Ala509Val	p.A509V	ENST00000369096	NM_001198.3	509	gCc/gTc	5/7	NA	2	FACETS	0.494	0.418	0.576			1	INDETERMINATE	1	TRUE	NA	0.511599085162692	2		276	380	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469812	157469812	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	134	632	0	ENST00000346085.5:c.2606G>A	p.Gly869Asp	p.G869D	ENST00000346085	NM_020732.3	869	gGc/gAc	9/20	1	2	FACETS	0.497	0.45	0.545	0.497	0.45	0.545	SUBCLONAL	1	TRUE	1	0.511599085162692	2		632	1055	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161807882	161807882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	105	497	0	ENST00000366898.1:c.1111G>A	p.Ala371Thr	p.A371T	ENST00000366898	NM_004562.2	371	Gcg/Acg	10/12	1	2	FACETS	0.425	0.38	0.473	0.425	0.38	0.473	SUBCLONAL	1	TRUE	1	0.511599085162692	2		497	966	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537201	80537201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	50	238	0	ENST00000286548.4:c.197G>A	p.Gly66Glu	p.G66E	ENST00000286548	NM_002072.3	66	gGa/gAa	2/7	0.511599085162692	2	FACETS	0.393	0.334	0.459	0.197	0.167	0.23	SUBCLONAL	1	TRUE	0	0.511599085162692	2		238	497	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760300	133760300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	65	448	0	ENST00000318560.5:c.2623G>A	p.Val875Met	p.V875M	ENST00000318560	NM_005157.4	875	Gtg/Atg	11/11	0.511599085162692	2	FACETS	0.448	0.389	0.513	0.224	0.194	0.257	SUBCLONAL	1	TRUE	0	0.511599085162692	2		448	567	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022546	12022546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	113	529	0	ENST00000396373.4:c.652G>A	p.Ala218Thr	p.A218T	ENST00000396373	NM_001987.4	218	Gct/Act	5/8	1	2	FACETS	0.44	0.395	0.488	0.44	0.395	0.488	SUBCLONAL	1	TRUE	1	0.511599085162692	2		529	1004	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46233280	46233280	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	68	371	0	ENST00000334344.6:c.1498+1G>A		p.X500_splice	ENST00000334344	NM_152641.2	500			0.121460618590672	4	FACETS	0.427	0.37	0.488	0.213	0.185	0.244	INDETERMINATE	1	TRUE	2	0.511599085162692	4		371	942	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871698	35871698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1328	166	740	2	ENST00000216797.5:c.808G>A	p.Gly270Ser	p.G270S	ENST00000216797	NM_020529.2	270	Ggc/Agc	5/6	1	2	FACETS	0.434	0.397	0.473	0.434	0.397	0.473	SUBCLONAL	1	TRUE	1	0.511599085162692	2		742	1494	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65543331	65543331	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1186625283	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1227	109	763	0	ENST00000358664.4:c.346C>T	p.Pro116Ser	p.P116S	ENST00000358664	NM_002382.4	116	Ccc/Tcc	5/5	1	2	FACETS	0.319	0.285	0.355	0.319	0.285	0.355	SUBCLONAL	1	TRUE	1	0.511599085162692	2		763	1336	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680643	88680643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	70	532	0	ENST00000360948.2:c.614G>A	p.Ser205Asn	p.S205N	ENST00000360948	NM_001012338.2	205	aGt/aAt	6/19	1	2	FACETS	0.326	0.283	0.372	0.326	0.283	0.372	SUBCLONAL	1	TRUE	1	0.511599085162692	2		532	840	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993584	72993584	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	113	699	1	ENST00000268489.5:c.461G>A	p.Gly154Glu	p.G154E	ENST00000268489	NM_006885.3	154	gGg/gAg	2/10	1	2	FACETS	0.412	0.37	0.457	0.412	0.37	0.457	SUBCLONAL	1	TRUE	1	0.511599085162692	2		700	1072	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131240	17131240	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555611399	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	118	610	2	ENST00000285071.4:c.212C>T	p.Ser71Phe	p.S71F	ENST00000285071	NM_144997.5	71	tCc/tTc	4/14	1	2	FACETS	0.445	0.401	0.493	0.445	0.401	0.493	SUBCLONAL	1	TRUE	1	0.511599085162692	2		612	1036	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654521	29654521	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	96	458	1	ENST00000356175.3:c.5210G>A	p.Gly1737Asp	p.G1737D	ENST00000356175	NM_000267.3	1737	gGt/gAt	37/57	1	2	FACETS	0.347	0.308	0.389	0.347	0.308	0.389	SUBCLONAL	1	TRUE	1	0.511599085162692	2		459	1081	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897358	78897358	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780000343	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	106	530	2	ENST00000306801.3:c.2693G>A	p.Ser898Asn	p.S898N	ENST00000306801	NM_020761.2	898	aGc/aAc	23/34	1	2	FACETS	0.458	0.41	0.51	0.458	0.41	0.51	SUBCLONAL	1	TRUE	1	0.511599085162692	2		532	904	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024701	31024701	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	96	627	0	ENST00000375687.4:c.4186G>A	p.Val1396Met	p.V1396M	ENST00000375687	NM_015338.5	1396	Gtg/Atg	13/13	1	2	FACETS	0.37	0.328	0.414	0.37	0.328	0.414	SUBCLONAL	1	TRUE	1	0.511599085162692	2		627	1015	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375117	31375117	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	90	609	0	ENST00000328111.2:c.514G>A	p.Asp172Asn	p.D172N	ENST00000328111	NM_006892.3	172	Gac/Aac	6/23	1	2	FACETS	0.395	0.35	0.443	0.395	0.35	0.443	SUBCLONAL	1	TRUE	1	0.511599085162692	2		609	891	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376669	31376669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	59	334	0	ENST00000328111.2:c.664G>A	p.Glu222Lys	p.E222K	ENST00000328111	NM_006892.3	222	Gag/Aag	7/23	1	2	FACETS	0.342	0.293	0.394	0.342	0.293	0.394	SUBCLONAL	1	TRUE	1	0.511599085162692	2		334	675	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57470691	57470691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	94	419	0	ENST00000371085.3:c.164C>T	p.Thr55Ile	p.T55I	ENST00000371085	NM_000516.4	55	aCc/aTc	2/13	NA	2	FACETS	0.423	0.376	0.474			1	INDETERMINATE	1	TRUE	NA	0.511599085162692	2		419	868	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485416	57485416	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1418870137	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	86	351	0	ENST00000371085.3:c.998G>A	p.Arg333His	p.R333H	ENST00000371085	NM_000516.4	333	cGc/cAc	12/13	NA	2	FACETS	0.406	0.358	0.457			1	INDETERMINATE	1	TRUE	NA	0.511599085162692	2		351	828	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41489027	41489027	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	78	445	0	ENST00000263253.7:c.19G>A	p.Glu7Lys	p.E7K	ENST00000263253	NM_001429.3	7	Gaa/Aaa	1/31	0.438976579912459	1	FACETS	0.373	0.327	0.421	0.373	0.327	0.421	SUBCLONAL	1	TRUE	0	0.511599085162692	1		445	609	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742907	17742907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	25	301	0	ENST00000250003.3:c.815C>T	p.Ala272Val	p.A272V	ENST00000250003	NM_002478.4	272	gCg/gTg	3/3	1	2	FACETS	0.304	0.239	0.377	0.304	0.239	0.377	SUBCLONAL	1	TRUE	1	0.511599085162692	2		301	322	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319375	11319375	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	85	460	0	ENST00000361445.4:c.92G>A	p.Ser31Asn	p.S31N	ENST00000361445	NM_004958.3	31	aGc/aAc	2/58	1	2	FACETS	0.413	0.365	0.465	0.413	0.365	0.465	SUBCLONAL	1	TRUE	1	0.511599085162692	2		460	804	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16203146	16203146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	74	374	0	ENST00000375759.3:c.854G>A	p.Ser285Asn	p.S285N	ENST00000375759	NM_015001.2	285	aGc/aAc	3/15	1	2	FACETS	0.382	0.334	0.434	0.382	0.334	0.434	SUBCLONAL	1	TRUE	1	0.511599085162692	2		374	757	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099344	27099344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	77	443	0	ENST00000324856.7:c.3581G>A	p.Gly1194Glu	p.G1194E	ENST00000324856	NM_006015.4	1194	gGa/gAa	14/20	1	2	FACETS	0.358	0.313	0.406	0.358	0.313	0.406	SUBCLONAL	1	TRUE	1	0.511599085162692	2		443	841	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941269	36941269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867425152	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	75	675	0	ENST00000361632.4:c.70G>A	p.Glu24Lys	p.E24K	ENST00000361632		24	Gag/Aag	3/16	1	2	FACETS	0.314	0.274	0.357	0.314	0.274	0.357	SUBCLONAL	1	TRUE	1	0.511599085162692	2		675	935	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804330	43804330	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	70	571	1	ENST00000372470.3:c.330G>A	p.Trp110Ter	p.W110*	ENST00000372470	NM_005373.2	110	tgG/tgA	3/12	1	2	FACETS	0.274	0.238	0.313	0.274	0.238	0.313	SUBCLONAL	1	TRUE	1	0.511599085162692	2		572	999	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436153	51436153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	59	288	0	ENST00000262662.1:c.113G>A	p.Gly38Glu	p.G38E	ENST00000262662		38	gGa/gAa	3/4	1	2	FACETS	0.304	0.261	0.351	0.304	0.261	0.351	SUBCLONAL	1	TRUE	1	0.511599085162692	2		288	759	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471649	120471649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	46	535	1	ENST00000256646.2:c.3842G>A	p.Cys1281Tyr	p.C1281Y	ENST00000256646	NM_024408.3	1281	tGt/tAt	23/34	1	2	FACETS	0.22	0.184	0.259	0.22	0.184	0.259	SUBCLONAL	1	TRUE	1	0.511599085162692	2		536	818	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965305	25965305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763602575	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	50	467	2	ENST00000435504.4:c.3901C>T	p.Pro1301Ser	p.P1301S	ENST00000435504		1301	Ccc/Tcc	13/13	1	2	FACETS	0.234	0.198	0.274	0.234	0.198	0.274	SUBCLONAL	1	TRUE	1	0.511599085162692	2		469	835	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029130	26029130	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	96	569	1	ENST00000435504.4:c.220G>A	p.Val74Ile	p.V74I	ENST00000435504		74	Gtt/Att	4/13	1	2	FACETS	0.305	0.271	0.342	0.305	0.271	0.342	SUBCLONAL	1	TRUE	1	0.511599085162692	2		570	1229	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873227	136873227	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1328	76	774	0	ENST00000241393.3:c.271C>T	p.Leu91Phe	p.L91F	ENST00000241393	NM_003467.2	91	Ctt/Ttt	2/2	1	2	FACETS	0.212	0.184	0.241	0.212	0.184	0.241	SUBCLONAL	1	TRUE	1	0.511599085162692	2		774	1404	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660777	227660777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569587604	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	40	420	0	ENST00000305123.5:c.2678C>T	p.Pro893Leu	p.P893L	ENST00000305123	NM_005544.2	893	cCg/cTg	1/2	1	2	FACETS	0.229	0.19	0.274	0.229	0.19	0.274	SUBCLONAL	1	TRUE	1	0.511599085162692	2		420	682	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928039	49928039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	92	714	1	ENST00000296474.3:c.3689C>T	p.Ala1230Val	p.A1230V	ENST00000296474	NM_002447.2	1230	gCc/gTc	18/20	0.510722155010479	1	FACETS	0.314	0.278	0.352	0.314	0.278	0.352	SUBCLONAL	1	TRUE	0	0.511599085162692	1		715	852	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960013	134960013	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	79	421	1	ENST00000398015.3:c.2370G>A	p.Trp790Ter	p.W790*	ENST00000398015	NM_004441.4	790	tgG/tgA	13/16	1	2	FACETS	0.393	0.345	0.445	0.393	0.345	0.445	SUBCLONAL	1	TRUE	1	0.511599085162692	2		422	786	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277519	142277519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	80	395	0	ENST00000350721.4:c.1832C>T	p.Thr611Ile	p.T611I	ENST00000350721	NM_001184.3	611	aCc/aTc	8/47	1	2	FACETS	0.337	0.296	0.382	0.337	0.296	0.382	SUBCLONAL	1	TRUE	1	0.511599085162692	2		395	928	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55603345	55603345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	51	464	0	ENST00000288135.5:c.2701G>A	p.Asp901Asn	p.D901N	ENST00000288135	NM_000222.2	901	Gac/Aac	20/21	1	2	FACETS	0.232	0.196	0.271	0.232	0.196	0.271	SUBCLONAL	1	TRUE	1	0.511599085162692	2		464	860	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156411	106156411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759106664	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	74	555	1	ENST00000380013.4:c.1312C>T	p.Pro438Ser	p.P438S	ENST00000380013	NM_001127208.2	438	Ccc/Tcc	3/11	1	2	FACETS	0.271	0.237	0.309	0.271	0.237	0.309	SUBCLONAL	1	TRUE	1	0.511599085162692	2		556	1066	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196477	106196477	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	80	558	0	ENST00000380013.4:c.4810G>A	p.Ala1604Thr	p.A1604T	ENST00000380013	NM_001127208.2	1604	Gct/Act	11/11	1	2	FACETS	0.272	0.239	0.309	0.272	0.239	0.309	SUBCLONAL	1	TRUE	1	0.511599085162692	2		558	1148	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539660	187539660	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	123	536	0	ENST00000441802.2:c.8080C>T	p.Leu2694Phe	p.L2694F	ENST00000441802	NM_005245.3	2694	Ctt/Ttt	10/27	1	2	FACETS	0.417	0.376	0.461	0.417	0.376	0.461	SUBCLONAL	1	TRUE	1	0.511599085162692	2		536	1152	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295191	1295191	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	12	141	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.251	0.176	0.342			1	INDETERMINATE	1	TRUE	NA	0.511599085162692	2		141	187	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982121	38982121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1561489588	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	71	353	0	ENST00000357387.3:c.601G>A	p.Val201Met	p.V201M	ENST00000357387	NM_152756.3	201	Gtg/Atg	8/38	1	2	FACETS	0.315	0.274	0.36	0.315	0.274	0.36	SUBCLONAL	1	TRUE	1	0.511599085162692	2		353	880	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564773	86564773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	61	690	2	ENST00000274376.6:c.505G>A	p.Val169Met	p.V169M	ENST00000274376	NM_002890.2	169	Gtg/Atg	1/25	1	2	FACETS	0.216	0.185	0.25	0.216	0.185	0.25	SUBCLONAL	1	TRUE	1	0.511599085162692	2		692	1104	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515193	149515193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	89	549	0	ENST00000261799.4:c.289G>A	p.Glu97Lys	p.E97K	ENST00000261799	NM_002609.3	97	Gaa/Aaa	3/23	1	2	FACETS	0.301	0.266	0.339	0.301	0.266	0.339	SUBCLONAL	1	TRUE	1	0.511599085162692	2		549	1156	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180049733	180049733	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1247073464	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	54	582	0	ENST00000261937.6:c.1655C>T	p.Thr552Ile	p.T552I	ENST00000261937	NM_182925.4	552	aCc/aTc	12/30	1	2	FACETS	0.26	0.221	0.302	0.26	0.221	0.302	SUBCLONAL	1	TRUE	1	0.511599085162692	2		582	813	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671469	30671469	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	111	602	0	ENST00000376406.3:c.5491G>A	p.Glu1831Lys	p.E1831K	ENST00000376406	NM_014641.2	1831	Gaa/Aaa	10/15	1	2	FACETS	0.354	0.317	0.393	0.354	0.317	0.393	SUBCLONAL	1	TRUE	1	0.511599085162692	2		602	1226	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287830	33287830	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769768112	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1252	103	691	0	ENST00000374542.5:c.1423G>A	p.Glu475Lys	p.E475K	ENST00000374542	NM_001141970.1	475	Gag/Aag	5/8	1	2	FACETS	0.297	0.265	0.332	0.297	0.265	0.332	SUBCLONAL	1	TRUE	1	0.511599085162692	2		691	1355	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287896	33287896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	53	471	0	ENST00000374542.5:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000374542	NM_001141970.1	453	Gaa/Aaa	5/8	1	2	FACETS	0.219	0.186	0.256	0.219	0.186	0.256	SUBCLONAL	1	TRUE	1	0.511599085162692	2		471	945	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652257	36652257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1463561308	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	47	364	0	ENST00000244741.5:c.379G>A	p.Ala127Thr	p.A127T	ENST00000244741	NM_000389.4	127	Gct/Act	2/3	1	2	FACETS	0.266	0.224	0.313	0.266	0.224	0.313	SUBCLONAL	1	TRUE	1	0.511599085162692	2		364	691	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718139	117718139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	86	465	0	ENST00000368508.3:c.718G>A	p.Asp240Asn	p.D240N	ENST00000368508	NM_002944.2	240	Gat/Aat	7/43	1	2	FACETS	0.347	0.306	0.391	0.347	0.306	0.391	SUBCLONAL	1	TRUE	1	0.511599085162692	2		465	969	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983190	149983190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	63	503	1	ENST00000253339.5:c.3068C>T	p.Ser1023Phe	p.S1023F	ENST00000253339		1023	tCt/tTt	7/7	1	2	FACETS	0.282	0.243	0.325	0.282	0.243	0.325	SUBCLONAL	1	TRUE	1	0.511599085162692	2		504	872	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157519979	157519979	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	53	514	1	ENST00000346085.5:c.4048G>T	p.Gly1350Cys	p.G1350C	ENST00000346085	NM_020732.3	1350	Ggc/Tgc	17/20	1	2	FACETS	0.24	0.204	0.28	0.24	0.204	0.28	SUBCLONAL	1	TRUE	1	0.511599085162692	2		515	864	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2957015	2957015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	38	270	0	ENST00000396946.4:c.2612C>T	p.Thr871Ile	p.T871I	ENST00000396946	NM_032415.4	871	aCc/aTc	20/25	1	2	FACETS	0.277	0.228	0.331	0.277	0.228	0.331	SUBCLONAL	1	TRUE	1	0.511599085162692	2		270	537	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983947	2983947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747351557	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1415	75	778	2	ENST00000396946.4:c.583G>A	p.Val195Ile	p.V195I	ENST00000396946	NM_032415.4	195	Gtc/Atc	5/25	1	2	FACETS	0.197	0.171	0.224	0.197	0.171	0.224	SUBCLONAL	1	TRUE	1	0.511599085162692	2		780	1490	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242508	55242508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10748	1339	397	0	ENST00000275493.2:c.2278C>T	p.Leu760Phe	p.L760F	ENST00000275493	NM_005228.3	760	Ctc/Ttc	19/28	0.511599085162692	25	FACETS	0.994	0.963	1			1	CLONAL	3	TRUE	NA	0.511599085162692	25		397	12087	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55269041	55269041	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9113	648	347	0	ENST00000275493.2:c.3107G>A	p.Ser1036Asn	p.S1036N	ENST00000275493	NM_005228.3	1036	aGc/aAc	25/28	0.511599085162692	25	FACETS	0.893	0.853	0.934			1	CLONAL	2	TRUE	NA	0.511599085162692	25		347	9761	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856090	151856090	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	138	654	1	ENST00000262189.6:c.11528G>A	p.Gly3843Glu	p.G3843E	ENST00000262189	NM_170606.2	3843	gGa/gAa	44/59	1	2	FACETS	0.407	0.369	0.447	0.407	0.369	0.447	SUBCLONAL	1	TRUE	1	0.511599085162692	2		655	1325	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859716	151859716	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	59	485	1	ENST00000262189.6:c.10946C>T	p.Pro3649Leu	p.P3649L	ENST00000262189	NM_170606.2	3649	cCc/cTc	43/59	1	2	FACETS	0.258	0.221	0.298	0.258	0.221	0.298	SUBCLONAL	1	TRUE	1	0.511599085162692	2		486	895	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90955551	90955551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	63	490	1	ENST00000265433.3:c.2114G>A	p.Gly705Glu	p.G705E	ENST00000265433	NM_002485.4	705	gGa/gAa	14/16	1	2	FACETS	0.232	0.2	0.268	0.232	0.2	0.268	SUBCLONAL	1	TRUE	1	0.511599085162692	2		491	1060	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126774	5126774	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	65	431	0	ENST00000381652.3:c.3382G>A	p.Asp1128Asn	p.D1128N	ENST00000381652	NM_004972.3	1128	Gat/Aat	25/25	0.511599085162692	2	FACETS	0.28	0.242	0.322	0.14	0.121	0.161	SUBCLONAL	1	TRUE	0	0.511599085162692	2		431	906	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5463065	5463065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	65	312	1	ENST00000381577.3:c.626G>A	p.Cys209Tyr	p.C209Y	ENST00000381577	NM_014143.3	209	tGc/tAc	4/7	0.511599085162692	2	FACETS	0.337	0.291	0.386	0.168	0.145	0.193	SUBCLONAL	1	TRUE	0	0.511599085162692	2		313	755	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87322799	87322799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1182	67	515	0	ENST00000277120.3:c.400C>T	p.His134Tyr	p.H134Y	ENST00000277120		134	Cat/Tat	5/19	0.511599085162692	2	FACETS	0.21	0.181	0.241	0.105	0.09	0.121	SUBCLONAL	1	TRUE	0	0.511599085162692	2		515	1249	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93636574	93636574	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	46	365	1	ENST00000375746.1:c.1003+1G>A		p.X335_splice	ENST00000375746	NM_001174167.1	335			0.511599085162692	2	FACETS	0.27	0.227	0.319	0.135	0.113	0.16	SUBCLONAL	1	TRUE	0	0.511599085162692	2		366	665	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405108	139405108	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	56	459	0	ENST00000277541.6:c.2737C>T	p.Pro913Ser	p.P913S	ENST00000277541	NM_017617.3	913	Ccc/Tcc	17/34	0.511599085162692	2	FACETS	0.273	0.233	0.317	0.137	0.116	0.159	SUBCLONAL	1	TRUE	0	0.511599085162692	2		459	801	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405410	70405410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	51	559	0	ENST00000373644.4:c.2924C>T	p.Thr975Ile	p.T975I	ENST00000373644	NM_030625.2	975	aCt/aTt	4/12	0.510722155010479	1	FACETS	0.177	0.15	0.208	0.177	0.15	0.208	SUBCLONAL	1	TRUE	0	0.511599085162692	1		559	836	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573810	64573810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	74	392	0	ENST00000312049.6:c.943G>A	p.Asp315Asn	p.D315N	ENST00000312049	NM_130799.2	315	Gat/Aat	7/10	1	2	FACETS	0.419	0.366	0.475	0.419	0.366	0.475	SUBCLONAL	1	TRUE	1	0.511599085162692	2		392	691	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124566	108124566	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	44	329	0	ENST00000278616.4:c.1924G>A	p.Glu642Lys	p.E642K	ENST00000278616	NM_000051.3	642	Gaa/Aaa	13/63	1	2	FACETS	0.212	0.177	0.251	0.212	0.177	0.251	SUBCLONAL	1	TRUE	1	0.511599085162692	2		329	811	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192092	108192092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	106	464	0	ENST00000278616.4:c.6517C>T	p.Leu2173Phe	p.L2173F	ENST00000278616	NM_000051.3	2173	Ctt/Ttt	45/63	1	2	FACETS	0.36	0.321	0.401	0.36	0.321	0.401	SUBCLONAL	1	TRUE	1	0.511599085162692	2		464	1152	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199901	108199901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	63	421	0	ENST00000278616.4:c.7243G>A	p.Ala2415Thr	p.A2415T	ENST00000278616	NM_000051.3	2415	Gct/Act	49/63	1	2	FACETS	0.245	0.211	0.283	0.245	0.211	0.283	SUBCLONAL	1	TRUE	1	0.511599085162692	2		421	1004	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307447	118307447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	29	228	0	ENST00000534358.1:c.220G>A	p.Val74Ile	p.V74I	ENST00000534358	NM_005933.3	74	Gtt/Att	1/36	1	2	FACETS	0.345	0.277	0.422	0.345	0.277	0.422	SUBCLONAL	1	TRUE	1	0.511599085162692	2		228	329	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402040	402040	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	73	552	0	ENST00000399788.2:c.4751G>A	p.Arg1584Lys	p.R1584K	ENST00000399788	NM_001042603.1	1584	aGa/aAa	27/28	1	2	FACETS	0.274	0.239	0.313	0.274	0.239	0.313	SUBCLONAL	1	TRUE	1	0.511599085162692	2		552	1041	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	443536	443536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	66	445	1	ENST00000399788.2:c.1361C>T	p.Ser454Phe	p.S454F	ENST00000399788	NM_001042603.1	454	tCt/tTt	11/28	1	2	FACETS	0.245	0.211	0.281	0.245	0.211	0.281	SUBCLONAL	1	TRUE	1	0.511599085162692	2		446	1054	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022570	12022570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	93	540	0	ENST00000396373.4:c.676G>A	p.Glu226Lys	p.E226K	ENST00000396373	NM_001987.4	226	Gag/Aag	5/8	1	2	FACETS	0.375	0.333	0.421	0.375	0.333	0.421	SUBCLONAL	1	TRUE	1	0.511599085162692	2		540	969	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644464	18644464	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1047715402	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	91	410	0	ENST00000266497.5:c.2642C>T	p.Ala881Val	p.A881V	ENST00000266497		881	gCc/gTc	18/31	NA	2	FACETS	0.363	0.321	0.407			1	INDETERMINATE	1	TRUE	NA	0.511599085162692	2		410	981	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421003	49421003	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	86	494	1	ENST00000301067.7:c.14746C>T	p.Pro4916Ser	p.P4916S	ENST00000301067	NM_003482.3	4916	Ccg/Tcg	48/54	0.121460618590672	4	FACETS	0.658	0.582	0.74	0.329	0.291	0.37	INDETERMINATE	1	TRUE	2	0.511599085162692	4		495	772	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446837	49446837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	70	387	0	ENST00000301067.7:c.973G>A	p.Ala325Thr	p.A325T	ENST00000301067	NM_003482.3	325	Gcc/Acc	8/54	0.121460618590672	4	FACETS	0.559	0.487	0.637	0.279	0.243	0.319	INDETERMINATE	1	TRUE	2	0.511599085162692	4		387	740	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447023	49447023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1127	67	590	0	ENST00000301067.7:c.921G>A	p.Met307Ile	p.M307I	ENST00000301067	NM_003482.3	307	atG/atA	7/54	0.121460618590672	4	FACETS	0.332	0.287	0.38	0.166	0.143	0.19	INDETERMINATE	1	TRUE	2	0.511599085162692	4		590	1194	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864919	57864919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	114	786	0	ENST00000228682.2:c.2396C>T	p.Thr799Ile	p.T799I	ENST00000228682	NM_005269.2	799	aCc/aTc	12/12	0.121460618590672	4	FACETS	0.522	0.468	0.579	0.261	0.234	0.29	INDETERMINATE	1	TRUE	2	0.511599085162692	4		786	1290	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432098	121432098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	44	521	1	ENST00000257555.6:c.845C>T	p.Ala282Val	p.A282V	ENST00000257555		282	gCc/gTc	4/10	1	2	FACETS	0.217	0.181	0.258	0.217	0.181	0.258	SUBCLONAL	1	TRUE	1	0.511599085162692	2		522	791	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563392	21563392	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1231214682	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	58	683	1	ENST00000382592.4:c.527C>T	p.Thr176Ile	p.T176I	ENST00000382592	NM_014572.2	176	aCc/aTc	4/8	1	2	FACETS	0.205	0.175	0.238	0.205	0.175	0.238	SUBCLONAL	1	TRUE	1	0.511599085162692	2		684	1105	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28599076	28599076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146649334	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	82	318	1	ENST00000241453.7:c.2212C>T	p.Pro738Ser	p.P738S	ENST00000241453	NM_004119.2	738	Cct/Tct	18/24	1	2	FACETS	0.455	0.401	0.513	0.455	0.401	0.513	SUBCLONAL	1	TRUE	1	0.511599085162692	2		319	705	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872508	35872508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1311	163	674	0	ENST00000216797.5:c.395G>A	p.Gly132Glu	p.G132E	ENST00000216797	NM_020529.2	132	gGa/gAa	3/6	1	2	FACETS	0.432	0.395	0.471	0.432	0.395	0.471	SUBCLONAL	1	TRUE	1	0.511599085162692	2		674	1474	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961310	41961310	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1246067553	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1323	161	775	1	ENST00000219905.7:c.218G>A	p.Gly73Asp	p.G73D	ENST00000219905	NM_001164273.1	73	gGt/gAt	2/24	NA	2	FACETS	0.424	0.387	0.463			1	INDETERMINATE	1	TRUE	NA	0.511599085162692	2		776	1484	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019531	42019531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1391	97	737	0	ENST00000219905.7:c.3584C>T	p.Ser1195Phe	p.S1195F	ENST00000219905	NM_001164273.1	1195	tCt/tTt	10/24	NA	2	FACETS	0.255	0.226	0.286			1	INDETERMINATE	1	TRUE	NA	0.511599085162692	2		737	1488	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42026768	42026768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1332	112	619	0	ENST00000219905.7:c.3892G>A	p.Glu1298Lys	p.E1298K	ENST00000219905	NM_001164273.1	1298	Gag/Aag	12/24	NA	2	FACETS	0.303	0.271	0.337			1	INDETERMINATE	1	TRUE	NA	0.511599085162692	2		619	1444	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434622	99434622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	63	438	0	ENST00000268035.6:c.709G>A	p.Gly237Ser	p.G237S	ENST00000268035	NM_000875.3	237	Ggc/Agc	3/21	1	2	FACETS	0.307	0.264	0.353	0.307	0.264	0.353	SUBCLONAL	1	TRUE	1	0.511599085162692	2		438	803	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343567	343567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1369221706	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	92	625	0	ENST00000262320.3:c.2107C>T	p.Pro703Ser	p.P703S	ENST00000262320	NM_003502.3	703	Ccc/Tcc	8/11	1	2	FACETS	0.415	0.368	0.466	0.415	0.368	0.466	SUBCLONAL	1	TRUE	1	0.511599085162692	2		625	866	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131638	2131638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	65	566	0	ENST00000219476.3:c.3653C>T	p.Pro1218Leu	p.P1218L	ENST00000219476	NM_000548.3	1218	cCt/cTt	31/42	1	2	FACETS	0.286	0.247	0.329	0.286	0.247	0.329	SUBCLONAL	1	TRUE	1	0.511599085162692	2		566	888	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220717	2220717	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	53	318	0	ENST00000326181.6:c.334G>A	p.Glu112Lys	p.E112K	ENST00000326181	NM_032271.2	112	Gag/Aag	5/21	1	2	FACETS	0.385	0.328	0.447	0.385	0.328	0.447	SUBCLONAL	1	TRUE	1	0.511599085162692	2		318	538	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56839503	56839503	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769878224	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1445	89	744	2	ENST00000308159.5:c.448G>A	p.Ala150Thr	p.A150T	ENST00000308159	NM_014669.4	150	Gca/Aca	5/22	1	2	FACETS	0.227	0.2	0.256	0.227	0.2	0.256	SUBCLONAL	1	TRUE	1	0.511599085162692	2		746	1534	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993500	72993500	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1234634202	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	134	770	1	ENST00000268489.5:c.545G>A	p.Gly182Glu	p.G182E	ENST00000268489	NM_006885.3	182	gGg/gAg	2/10	1	2	FACETS	0.405	0.367	0.446	0.405	0.367	0.446	SUBCLONAL	1	TRUE	1	0.511599085162692	2		771	1293	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89865617	89865617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	59	438	1	ENST00000389301.3:c.850G>A	p.Gly284Arg	p.G284R	ENST00000389301	NM_000135.2	284	Gga/Aga	10/43	NA	2	FACETS	0.334	0.287	0.386			1	INDETERMINATE	1	TRUE	NA	0.511599085162692	2		439	690	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108590	8108590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1444417079	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	55	489	1	ENST00000585124.1:c.805G>A	p.Gly269Arg	p.G269R	ENST00000585124	NM_004217.3	269	Ggg/Agg	8/9	1	2	FACETS	0.245	0.209	0.285	0.245	0.209	0.285	SUBCLONAL	1	TRUE	1	0.511599085162692	2		490	878	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122443	17122443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756787389	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	74	679	0	ENST00000285071.4:c.952G>A	p.Glu318Lys	p.E318K	ENST00000285071	NM_144997.5	318	Gaa/Aaa	9/14	1	2	FACETS	0.292	0.254	0.332	0.292	0.254	0.332	SUBCLONAL	1	TRUE	1	0.511599085162692	2		679	992	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556358	29556358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	61	480	0	ENST00000356175.3:c.2725G>A	p.Val909Met	p.V909M	ENST00000356175	NM_000267.3	909	Gtg/Atg	21/57	1	2	FACETS	0.243	0.208	0.28	0.243	0.208	0.28	SUBCLONAL	1	TRUE	1	0.511599085162692	2		480	983	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29687632	29687632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1284	92	686	0	ENST00000356175.3:c.8225C>T	p.Pro2742Leu	p.P2742L	ENST00000356175	NM_000267.3	2742	cCt/cTt	56/57	1	2	FACETS	0.261	0.231	0.294	0.261	0.231	0.294	SUBCLONAL	1	TRUE	1	0.511599085162692	2		686	1376	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805444	46805444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	98	843	0	ENST00000290295.7:c.512C>T	p.Ser171Phe	p.S171F	ENST00000290295	NM_006361.5	171	tCt/tTt	1/2	1	2	FACETS	0.31	0.276	0.348	0.31	0.276	0.348	SUBCLONAL	1	TRUE	1	0.511599085162692	2		843	1234	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434913	56434913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773941703	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	63	500	0	ENST00000407977.2:c.2224G>A	p.Glu742Lys	p.E742K	ENST00000407977		742	Gag/Aag	9/10	1	2	FACETS	0.3	0.259	0.345	0.3	0.259	0.345	SUBCLONAL	1	TRUE	1	0.511599085162692	2		500	821	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435445	56435445	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	42	364	0	ENST00000407977.2:c.1692G>A	p.Trp564Ter	p.W564*	ENST00000407977		564	tgG/tgA	9/10	1	2	FACETS	0.279	0.232	0.331	0.279	0.232	0.331	SUBCLONAL	1	TRUE	1	0.511599085162692	2		364	588	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007499	62007499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	110	639	0	ENST00000392795.3:c.368G>A	p.Cys123Tyr	p.C123Y	ENST00000392795	NM_001039933.1	123	tGt/tAt	3/6	1	2	FACETS	0.4	0.359	0.445	0.4	0.359	0.445	SUBCLONAL	1	TRUE	1	0.511599085162692	2		639	1074	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573618	48573618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	41	300	0	ENST00000342988.3:c.202C>T	p.Pro68Ser	p.P68S	ENST00000342988	NM_005359.5	68	Cct/Tct	2/12	1	2	FACETS	0.242	0.201	0.288	0.242	0.201	0.288	SUBCLONAL	1	TRUE	1	0.511599085162692	2		300	662	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611732	1611732	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	59	658	2	ENST00000344749.5:c.1930G>A	p.Ala644Thr	p.A644T	ENST00000344749	NM_001136139.2	644	Gcc/Acc	19/19	1	2	FACETS	0.201	0.172	0.233	0.201	0.172	0.233	SUBCLONAL	1	TRUE	1	0.511599085162692	2		660	1145	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099208	4099208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	42	387	0	ENST00000262948.5:c.910C>T	p.Pro304Ser	p.P304S	ENST00000262948	NM_030662.3	304	Ccc/Tcc	7/11	1	2	FACETS	0.3	0.25	0.355	0.3	0.25	0.355	SUBCLONAL	1	TRUE	1	0.511599085162692	2		387	548	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953217	17953217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	39	423	1	ENST00000458235.1:c.769G>A	p.Gly257Ser	p.G257S	ENST00000458235	NM_000215.3	257	Ggc/Agc	6/24	1	2	FACETS	0.273	0.225	0.326	0.273	0.225	0.326	SUBCLONAL	1	TRUE	1	0.511599085162692	2		424	559	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795160	42795160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	76	612	0	ENST00000575354.2:c.2240G>A	p.Gly747Glu	p.G747E	ENST00000575354	NM_015125.3	747	gGa/gAa	10/20	1	2	FACETS	0.326	0.285	0.37	0.326	0.285	0.37	SUBCLONAL	1	TRUE	1	0.511599085162692	2		612	912	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796882	42796882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	72	608	1	ENST00000575354.2:c.3340G>A	p.Ala1114Thr	p.A1114T	ENST00000575354	NM_015125.3	1114	Gcc/Acc	14/20	1	2	FACETS	0.3	0.261	0.343	0.3	0.261	0.343	SUBCLONAL	1	TRUE	1	0.511599085162692	2		609	937	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375198	31375198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	64	506	0	ENST00000328111.2:c.595G>A	p.Gly199Ser	p.G199S	ENST00000328111	NM_006892.3	199	Ggc/Agc	6/23	1	2	FACETS	0.315	0.272	0.362	0.315	0.272	0.362	SUBCLONAL	1	TRUE	1	0.511599085162692	2		506	795	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395668	31395668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	91	536	1	ENST00000328111.2:c.2521C>T	p.His841Tyr	p.H841Y	ENST00000328111	NM_006892.3	841	Cac/Tac	23/23	1	2	FACETS	0.414	0.367	0.464	0.414	0.367	0.464	SUBCLONAL	1	TRUE	1	0.511599085162692	2		537	860	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264845	46264845	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374724210	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1471	107	903	2	ENST00000371998.3:c.1715G>A	p.Gly572Asp	p.G572D	ENST00000371998		572	gGc/gAc	12/23	NA	2	FACETS	0.265	0.236	0.296			1	INDETERMINATE	1	TRUE	NA	0.511599085162692	2		905	1578	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564768	41564768	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	100	597	0	ENST00000263253.7:c.4069A>G	p.Thr1357Ala	p.T1357A	ENST00000263253	NM_001429.3	1357	Acc/Gcc	25/31	0.438976579912459	1	FACETS	0.323	0.288	0.361	0.323	0.288	0.361	SUBCLONAL	1	TRUE	0	0.511599085162692	1		597	900	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918653	44918653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	74	309	0	ENST00000377967.4:c.1136C>T	p.Thr379Ile	p.T379I	ENST00000377967	NM_021140.2	379	aCt/aTt	12/29	1	1	FACETS	0.366	0.32	0.414	0.366	0.32	0.414	SUBCLONAL	1	TRUE	0	0.511599085162692	1		309	589	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649539	48649539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	29	344	0	ENST00000376670.3:c.23C>T	p.Ser8Phe	p.S8F	ENST00000376670	NM_002049.3	8	tCc/tTc	2/6	1	1	FACETS	0.158	0.126	0.194	0.158	0.126	0.194	SUBCLONAL	1	TRUE	0	0.511599085162692	1		344	534	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650850	48650850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	55	365	0	ENST00000376670.3:c.719C>T	p.Pro240Leu	p.P240L	ENST00000376670	NM_002049.3	240	cCc/cTc	4/6	1	1	FACETS	0.287	0.245	0.332	0.287	0.245	0.332	SUBCLONAL	1	TRUE	0	0.511599085162692	1		365	558	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76952130	76952130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	126	351	0	ENST00000373344.5:c.305C>T	p.Thr102Ile	p.T102I	ENST00000373344	NM_000489.3	102	aCt/aTt	5/35	1	1	FACETS	0.44	0.398	0.484	0.44	0.398	0.484	SUBCLONAL	1	TRUE	0	0.511599085162692	1		351	834	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164824	123164824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002265-T04-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	46	267	0	ENST00000218089.9:c.137G>A	p.Gly46Asp	p.G46D	ENST00000218089	NM_001042749.1	46	gGc/gAc	5/35	1	1	FACETS	0.203	0.17	0.239	0.203	0.17	0.239	SUBCLONAL	1	TRUE	0	0.511599085162692	1		267	659	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002267-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	49	422	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		422	275	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002292-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	32	422	0				ENST00000310581	NM_198253.2	-/1132			0.144053083217353	4	FACETS	1	0.909	1	1	0.909	1	INDETERMINATE	2	TRUE	2	0.32371058348282	4		422	113	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0002292-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	205	558	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.271966893285992	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.32371058348282	4		558	692	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0002292-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	165	489	0	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	0.271966893285992	4	FACETS	0.956	0.88	1	0.956	0.88	1	CLONAL	2	TRUE	2	0.32371058348282	4		489	706	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954210	48954210	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1354030520	NA	P-0002292-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	317	421	0	ENST00000267163.4:c.1411C>T	p.Gln471Ter	p.Q471*	ENST00000267163	NM_000321.2	471	Caa/Taa	15/27	0.316690076165082	2	FACETS	0.846	0.799	0.895	0.846	0.799	0.895	CLONAL	2	TRUE	0	0.32371058348282	2		421	1157	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0002292-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	157	409	0	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.271966893285992	4	FACETS	0.889	0.816	0.965	0.889	0.816	0.965	CLONAL	2	TRUE	2	0.32371058348282	4		409	722	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059264	27059264	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0002292-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	206	401	0	ENST00000324856.7:c.1901C>G	p.Ser634Ter	p.S634*	ENST00000324856	NM_006015.4	634	tCa/tGa	4/20	0.311391760439424	4	FACETS	0.968	0.9	1	0.968	0.9	1	CLONAL	2	TRUE	2	0.32371058348282	4		401	870	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118368735	118368735	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002292-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	244	365	0	ENST00000534358.1:c.5749G>A	p.Asp1917Asn	p.D1917N	ENST00000534358	NM_005933.3	1917	Gat/Aat	21/36	0.32371058348282	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.32371058348282	2		365	736	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431549	49431549	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1239691307	NA	P-0002292-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	150	386	0	ENST00000301067.7:c.9590C>T	p.Thr3197Ile	p.T3197I	ENST00000301067	NM_003482.3	3197	aCc/aTc	34/54	0.316690076165082	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.32371058348282	2		386	405	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755527	39755527	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0002292-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	106	351	0	ENST00000288319.7:c.1238C>G	p.Ser413Ter	p.S413*	ENST00000288319	NM_182918.3	413	tCa/tGa	10/10	0.165464125059144	5	FACETS	0.773	0.694	0.857	0.516	0.463	0.571	INDETERMINATE	2	TRUE	2	0.32371058348282	5		351	629	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30061031	30061031	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0002292-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	120	438	0	ENST00000338641.4:c.863C>G	p.Ser288Ter	p.S288*	ENST00000338641	NM_000268.3	288	tCa/tGa	9/16	0.315943553970105	2	FACETS	0.954	0.862	1	0.477	0.431	0.526	CLONAL	1	TRUE	0	0.32371058348282	2		438	777	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525914	41525914	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs773503228	NA	P-0002292-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	258	437	0	ENST00000263253.7:c.1189C>T	p.Arg397Ter	p.R397*	ENST00000263253	NM_001429.3	397	Cga/Tga	5/31	0.315943553970105	2	FACETS	0.919	0.863	0.977	0.919	0.863	0.977	CLONAL	2	TRUE	0	0.32371058348282	2		437	867	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020251	123020251	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002292-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	337	255	0	ENST00000355640.3:c.739G>A	p.Asp247Asn	p.D247N	ENST00000355640		247	Gat/Aat	2/7	0.32371058348282	2	FACETS	1	0.978	1			1	CLONAL	3	TRUE	NA	0.32371058348282	2		255	668	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651942	36651942	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002292-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	158	331	0	ENST00000244741.5:c.65del	p.Phe22SerfsTer9	p.F22Sfs*9	ENST00000244741	NM_000389.4	22	Ttc/tc	2/3	0.32371058348282	7	FACETS	0.917	0.843	0.993			1	CLONAL	3	TRUE	NA	0.32371058348282	7		331	642	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002331-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	160	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.787	0.724	0.852	0.787	0.724	0.852	SUBCLONAL	1	TRUE	1	0.627666742312736	2		422	648	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080534	5080534	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002331-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	120	433	0	ENST00000381652.3:c.2285A>G	p.Lys762Arg	p.K762R	ENST00000381652	NM_004972.3	762	aAg/aGg	18/25	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.627666742312736	2		433	361	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715662	18715662	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002331-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	91	401	0	ENST00000266497.5:c.3493T>C	p.Phe1165Leu	p.F1165L	ENST00000266497		1165	Ttc/Ctc	25/31	0.627666742312736	3	FACETS	0.884	0.789	0.984	0.442	0.394	0.492	CLONAL	1	TRUE	1	0.627666742312736	3		401	431	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175836	24175837	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555881563	NA	P-0002331-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	407	368	0	ENST00000263121.7:c.1066_1067del	p.Leu356AspfsTer4	p.L356Dfs*4	ENST00000263121	NM_003073.3	355	aCT/a	8/9	0.627666742312736	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.627666742312736	1		368	823	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002347-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	36	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.657	0.544	0.782			1	INDETERMINATE	1	TRUE	NA	0.458300870538729	2		422	239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0002347-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	61	531	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.321	0.276	0.37	0.321	0.276	0.37	SUBCLONAL	1	TRUE	1	0.458300870538729	2		531	829	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782144	NA	P-0002347-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	161	240	0	ENST00000269305.4:c.473G>A	p.Arg158His	p.R158H	ENST00000269305	NM_001126112.2	158	cGc/cAc	5/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.458300870538729	2		240	631	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743932	41743933	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs778012871	NA	P-0002347-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	131	302	1	ENST00000301178.4:c.874dup	p.His292ProfsTer47	p.H292Pfs*47	ENST00000301178	NM_021913.4	289	-/C	7/20	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.458300870538729	2		303	548	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190321	32190321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1033015617	NA	P-0002347-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	84	233	0	ENST00000375023.3:c.418C>T	p.Arg140Cys	p.R140C	ENST00000375023	NM_004557.3	140	Cgc/Tgc	3/30	0.176293962375391	3	FACETS	1	0.932	1	0.535	0.475	0.599	INDETERMINATE	1	TRUE	1	0.458300870538729	3		233	421	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0002347-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	229	542	2	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	0.176293962375391	3	FACETS	1	0.987	1	0.622	0.579	0.665	INDETERMINATE	1	TRUE	1	0.458300870538729	3		544	988	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553477	29553478	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587781807	NA	P-0002347-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	154	220	2	ENST00000356175.3:c.2033dup	p.Ile679AspfsTer21	p.I679Dfs*21	ENST00000356175	NM_000267.3	676	acc/aCcc	18/57	1	2	FACETS	0.768	0.703	0.836	0.768	0.703	0.836	SUBCLONAL	1	TRUE	1	0.458300870538729	2		222	875	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639700	47639700	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs267607934	NA	P-0002347-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	175	276	0	ENST00000233146.2:c.792+1G>A		p.X264_splice	ENST00000233146	NM_000251.2	264			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.458300870538729	2		276	670	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397677	49397677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002347-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	203	355	0	ENST00000418115.1:c.547C>T	p.Arg183Cys	p.R183C	ENST00000418115	NM_001664.2	183	Cgt/Tgt	5/5	0.176293962375391	3	FACETS	1	0.985	1	0.614	0.57	0.66	INDETERMINATE	1	TRUE	1	0.458300870538729	3		355	886	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961104	55961104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371148535	NA	P-0002347-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	223	358	0	ENST00000263923.4:c.2836C>T	p.Arg946Cys	p.R946C	ENST00000263923	NM_002253.2	946	Cgt/Tgt	21/30	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.458300870538729	2		358	915	SUCCESS
APC	324	MSKCC	GRCh37	5	112154969	112154969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137854567	NA	P-0002347-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	226	313	1	ENST00000257430.4:c.1240C>T	p.Arg414Cys	p.R414C	ENST00000257430	NM_000038.5	414	Cgc/Tgc	10/16	0.249413830949702	3	FACETS	1	0.989	1	0.646	0.602	0.691	INDETERMINATE	1	TRUE	1	0.458300870538729	3		314	939	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572649	64572649	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746135199	NA	P-0002347-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	107	189	1	ENST00000312049.6:c.1207G>A	p.Ala403Thr	p.A403T	ENST00000312049	NM_130799.2	403	Gcc/Acc	9/10	1	2	FACETS	0.903	0.813	0.997	0.903	0.813	0.997	CLONAL	1	TRUE	1	0.458300870538729	2		190	517	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344192	118344192	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002347-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	224	388	0	ENST00000534358.1:c.2318C>T	p.Pro773Leu	p.P773L	ENST00000534358	NM_005933.3	773	cCg/cTg	3/36	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.458300870538729	2		388	883	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446800	49446800	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200245957	NA	P-0002347-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	206	278	0	ENST00000301067.7:c.1010C>T	p.Ser337Leu	p.S337L	ENST00000301067	NM_003482.3	337	tCg/tTg	8/54	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.458300870538729	2		278	764	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888199	112888199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918454	NA	P-0002347-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	72	365	0	ENST00000351677.2:c.215C>T	p.Ala72Val	p.A72V	ENST00000351677	NM_002834.3	72	gCc/gTc	3/16	1	2	FACETS	0.403	0.352	0.459	0.403	0.352	0.459	SUBCLONAL	1	TRUE	1	0.458300870538729	2		365	779	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496908	29496908	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002347-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	191	299	0	ENST00000356175.3:c.480-1G>A		p.X160_splice	ENST00000356175	NM_000267.3	160			1	2	FACETS	0.932	0.863	1	0.932	0.863	1	CLONAL	1	TRUE	1	0.458300870538729	2		299	894	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129679	11129679	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002347-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	152	304	0	ENST00000358026.2:c.2485G>A	p.Val829Met	p.V829M	ENST00000358026	NM_001128849.1	829	Gtg/Atg	17/36	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.458300870538729	2		304	649	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349730	15349730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750347317	NA	P-0002347-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	66	161	0	ENST00000263377.2:c.3844C>T	p.Arg1282Cys	p.R1282C	ENST00000263377	NM_058243.2	1282	Cgc/Tgc	19/20	1	2	FACETS	0.881	0.77	0.999	0.881	0.77	0.999	CLONAL	1	TRUE	1	0.458300870538729	2		161	327	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266948	18266948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1270183802	NA	P-0002347-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	78	84	0	ENST00000222254.8:c.259G>A	p.Gly87Ser	p.G87S	ENST00000222254	NM_005027.3	87	Ggc/Agc	2/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.458300870538729	2		84	274	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342433	70342433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs5981075	NA	P-0002347-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	183	314	0	ENST00000374080.3:c.1324G>A	p.Asp442Asn	p.D442N	ENST00000374080		442	Gat/Aat	9/45	0.16568396809205	0	FACETS	0.6	0.555	0.646			1	INDETERMINATE	1	TRUE	0	0.458300870538729	0		314	721	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021276	31021277	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs886042532	NA	P-0002347-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	34	295	0	ENST00000375687.4:c.1281dup	p.Gln428ThrfsTer10	p.Q428Tfs*10	ENST00000375687	NM_015338.5	425	-/A	12/13	1	2	FACETS	0.238	0.194	0.288	0.238	0.194	0.288	SUBCLONAL	1	TRUE	1	0.458300870538729	2		295	623	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934126	39934127	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002347-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	57	421	0	ENST00000378444.4:c.472dup	p.Ser158LysfsTer28	p.S158Kfs*28	ENST00000378444	NM_001123385.1	158	agt/aAgt	4/15	0.16568396809205	0	FACETS	0.187	0.16	0.217			1	INDETERMINATE	1	TRUE	0	0.458300870538729	0		421	719	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332751	65332751	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375997338	NA	P-0002347-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	53	351	0	ENST00000342505.4:c.788C>T	p.Thr263Met	p.T263M	ENST00000342505	NM_002227.2	263	aCg/aTg	7/25	0.176293962375391	3	FACETS	0.305	0.259	0.355	0.152	0.129	0.178	INDETERMINATE	1	TRUE	1	0.458300870538729	3		351	933	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0002353-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	414	318	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	FALSE	1	0.632047555917127	2		318	1291	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0002353-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	59	139	0				ENST00000310581	NM_198253.2	-/1132			0.632047555917127	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	0	0.632047555917127	1		139	112	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230641	46230641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002353-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	225	483	0	ENST00000334344.6:c.890C>T	p.Ser297Phe	p.S297F	ENST00000334344	NM_152641.2	297	tCc/tTc	8/21	NA	2	FACETS	0.607	0.565	0.652			1	INDETERMINATE	1	FALSE	NA	0.632047555917127	2		483	1172	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206941988	206941988	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376415487	NA	P-0002353-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	279	280	0	ENST00000423557.1:c.530G>A	p.Arg177Gln	p.R177Q	ENST00000423557	NM_000572.2	177	cGa/cAa	5/5	1	2	FACETS	0.929	0.874	0.985	0.929	0.874	0.985	CLONAL	1	FALSE	1	0.632047555917127	2		280	950	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029126	26029126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002353-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	201	458	0	ENST00000435504.4:c.224C>T	p.Pro75Leu	p.P75L	ENST00000435504		75	cCa/cTa	4/13	0.336769825849088	1	FACETS	0.37	0.342	0.399	0.37	0.342	0.399	INDETERMINATE	1	FALSE	0	0.632047555917127	1		458	1176	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167830	185167830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002353-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	314	417	0	ENST00000265026.3:c.1153C>T	p.Leu385Phe	p.L385F	ENST00000265026	NM_004721.4	385	Ctt/Ttt	6/14	1	2	FACETS	0.97	0.917	1	0.97	0.917	1	CLONAL	1	FALSE	1	0.632047555917127	2		417	1024	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612083	189612083	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002353-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	258	510	0	ENST00000264731.3:c.1835C>T	p.Ser612Phe	p.S612F	ENST00000264731	NM_003722.4	612	tCc/tTc	14/14	0.445854015537334	1	FACETS	0.649	0.609	0.689	0.649	0.609	0.689	SUBCLONAL	1	FALSE	0	0.632047555917127	1		510	861	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827844	170827844	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs544573727	NA	P-0002353-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	322	332	0	ENST00000296930.5:c.584C>T	p.Ser195Phe	p.S195F	ENST00000296930	NM_002520.6	195	tCt/tTt	8/11	0.579701456930676	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	0	0.632047555917127	1		332	670	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246447	46246447	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002353-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	202	457	0	ENST00000334344.6:c.4541C>T	p.Thr1514Ile	p.T1514I	ENST00000334344	NM_152641.2	1514	aCt/aTt	15/21	NA	2	FACETS	0.618	0.572	0.665			1	INDETERMINATE	1	FALSE	NA	0.632047555917127	2		457	1035	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557476	21557476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002353-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	352	435	4	ENST00000382592.4:c.2369G>A	p.Arg790Gln	p.R790Q	ENST00000382592	NM_014572.2	790	cGa/cAa	5/8	NA	2	FACETS	0.946	0.897	0.997			1	INDETERMINATE	1	FALSE	NA	0.632047555917127	2		439	1177	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986544	36986544	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002353-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	170	346	0	ENST00000354822.5:c.1145C>T	p.Ser382Phe	p.S382F	ENST00000354822	NM_001079668.2	382	tCc/tTc	3/3	0.101867325042197	0	FACETS	0.387	0.359	0.417			1	INDETERMINATE	1	FALSE	0	0.632047555917127	0		346	511	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574426	95574426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002353-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	153	183	0	ENST00000393063.1:c.2441C>T	p.Pro814Leu	p.P814L	ENST00000393063	NM_030621.3	814	cCa/cTa	17/28	NA	2	FACETS	0.9	0.828	0.974			1	INDETERMINATE	1	FALSE	NA	0.632047555917127	2		183	538	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579395	7579395	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002353-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	221	308	0	ENST00000269305.4:c.292C>T	p.Pro98Ser	p.P98S	ENST00000269305	NM_001126112.2	98	Cct/Tct	4/11	0.632047555917127	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	0	0.632047555917127	1		308	476	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5260824	5260824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774744361	NA	P-0002353-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	158	265	0	ENST00000357368.4:c.587C>T	p.Pro196Leu	p.P196L	ENST00000357368	NM_002850.3	196	cCg/cTg	7/38	0.273532212601497	1	FACETS	0.632	0.583	0.683	0.632	0.583	0.683	INDETERMINATE	1	FALSE	0	0.632047555917127	1		265	541	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733211	40733211	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002353-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	146	298	0	ENST00000373198.4:c.3595C>T	p.Gln1199Ter	p.Q1199*	ENST00000373198	NM_133170.3	1199	Cag/Tag	26/32	0.632047555917127	1	FACETS	0.533	0.488	0.579	0.533	0.488	0.579	SUBCLONAL	1	FALSE	0	0.632047555917127	1		298	593	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980844	40980844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002353-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	157	325	0	ENST00000373198.4:c.1642G>A	p.Glu548Lys	p.E548K	ENST00000373198	NM_133170.3	548	Gaa/Aaa	10/32	0.632047555917127	1	FACETS	0.569	0.524	0.616	0.569	0.524	0.616	SUBCLONAL	1	FALSE	0	0.632047555917127	1		325	597	SUCCESS
AR	367	MSKCC	GRCh37	X	66766595	66766595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002353-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	215	479	0	ENST00000374690.3:c.1607G>A	p.Gly536Glu	p.G536E	ENST00000374690	NM_000044.3	536	gGg/gAg	1/8	0.568285940169726	1	FACETS	0.516	0.48	0.553	0.516	0.48	0.553	SUBCLONAL	1	FALSE	0	0.632047555917127	1		479	902	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180395	32180396	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0002353-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	151	246	0	ENST00000375023.3:c.2535_2536delinsAA	p.Met845_Asp846delinsIleAsn	p.M845_D846delinsIN	ENST00000375023	NM_004557.3	845	atGGac/atAAac	17/30	NA	2	FACETS	0.686	0.628	0.745			1	INDETERMINATE	1	FALSE	NA	0.632047555917127	2		246	697	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002367-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	16	422	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	0.826	0.626	1	1	0.914	1	CLONAL	2	TRUE	0	0.24	1		422	71	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0002367-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	48	394	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.3	1	FACETS	0.871	0.738	1	0.871	0.738	1	CLONAL	1	TRUE	0	0.24	1		396	404	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0002367-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	23	235	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.267347525184769	3	FACETS	0.704	0.549	0.882	0.352	0.274	0.441	SUBCLONAL	1	TRUE	1	0.24	3		235	305	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0002396-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	23	139	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.794	0.619	0.995	0.794	0.619	0.995	CLONAL	1	TRUE	1	0.19	2		139	305	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0002396-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	91	542	2	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.777	0.687	0.873	0.777	0.687	0.873	SUBCLONAL	1	TRUE	1	0.19	2		544	1233	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954188	48954188	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002396-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	130	549	0	ENST00000267163.4:c.1390-1G>A		p.X464_splice	ENST00000267163	NM_000321.2	464			0.223479336275533	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.19	1		549	1155	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483145	29483145	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs886039548	NA	P-0002396-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	68	360	0	ENST00000356175.3:c.204+1G>A		p.X68_splice	ENST00000356175	NM_000267.3	68			0.148324473383691	1	FACETS	0.976	0.848	1	0.976	0.848	1	CLONAL	1	TRUE	0	0.19	1		360	664	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717715	89717716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587782341	NA	P-0002396-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	93	365	0	ENST00000371953.3:c.741dup	p.Pro248ThrfsTer5	p.P248Tfs*5	ENST00000371953	NM_000314.4	247	tta/ttAa	7/9	0.148324473383691	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.19	1		365	827	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0002400-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	126	275	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.668124999122648	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.668124999122648	1		275	244	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0002400-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	41	139	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.758	0.641	0.882			1	INDETERMINATE	1	TRUE	NA	0.668124999122648	2		139	162	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0002400-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	168	417	1	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.6288610188133	1	FACETS	0.968	0.904	1	0.968	0.904	1	CLONAL	1	TRUE	0	0.668124999122648	1		418	346	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685307	89685307	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123317	NA	P-0002400-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	82	218	0	ENST00000371953.3:c.202T>C	p.Tyr68His	p.Y68H	ENST00000371953	NM_000314.4	68	Tac/Cac	3/9	0.668124999122648	1	FACETS	0.929	0.841	1	0.929	0.841	1	CLONAL	1	TRUE	0	0.668124999122648	1		218	176	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0002403-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	184	262	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.256118377544205	3	FACETS	0.905	0.837	0.975	0.905	0.837	0.975	CLONAL	2	TRUE	1	0.306179240370751	3		262	766	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0002403-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	138	536	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.306179240370751	1	FACETS	0.864	0.786	0.946	0.864	0.786	0.946	CLONAL	1	TRUE	0	0.306179240370751	1		536	884	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002403-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	54	270	0	ENST00000304494.5:c.322G>C	p.Asp108His	p.D108H	ENST00000304494	NM_000077.4	108	Gat/Cat	2/3	1	2	FACETS	0.757	0.654	0.867	1	0.969	1	SUBCLONAL	2	TRUE	1	0.306179240370751	2		270	233	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663036	227663036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002403-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	101	270	0	ENST00000305123.5:c.419C>T	p.Ser140Phe	p.S140F	ENST00000305123	NM_005544.2	140	tCc/tTc	1/2	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.306179240370751	2		270	573	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215964	142215964	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002403-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	108	370	0	ENST00000350721.4:c.5629C>G	p.Gln1877Glu	p.Q1877E	ENST00000350721	NM_001184.3	1877	Caa/Gaa	33/47	1	2	FACETS	0.764	0.685	0.849	0.764	0.685	0.849	SUBCLONAL	1	TRUE	1	0.306179240370751	2		370	923	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636899	176636899	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002403-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	105	310	0	ENST00000439151.2:c.1499G>C	p.Arg500Thr	p.R500T	ENST00000439151	NM_022455.4	500	aGa/aCa	5/23	1	2	FACETS	0.878	0.787	0.975	0.878	0.787	0.975	CLONAL	1	TRUE	1	0.306179240370751	2		310	781	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246748	41246748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002403-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	129	426	0	ENST00000357654.3:c.800C>T	p.Ser267Leu	p.S267L	ENST00000357654	NM_007294.3	267	tCa/tTa	10/23	0.305586916244486	3	FACETS	0.82	0.742	0.903	0.41	0.371	0.452	CLONAL	1	TRUE	1	0.306179240370751	3		426	1185	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760719	59760719	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	TTG	novel	NA	P-0002403-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	167	574	0	ENST00000259008.2:c.3688delinsCAA	p.Glu1230GlnfsTer3	p.E1230Qfs*3	ENST00000259008	NM_032043.2	1230	Gaa/CAAaa	20/20	0.305586916244486	3	FACETS	0.981	0.899	1	0.491	0.449	0.534	CLONAL	1	TRUE	1	0.306179240370751	3		574	1282	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002405-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	80	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.92	2		422	174	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0002405-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	327	309	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	0.3	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.92	0		310	505	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436839	110436839	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002405-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	364	292	0	ENST00000375856.3:c.1562C>T	p.Pro521Leu	p.P521L	ENST00000375856	NM_003749.2	521	cCc/cTc	1/2	1	2	FACETS	0.898	0.855	0.941	0.898	0.855	0.941	CLONAL	1	TRUE	1	0.92	2		292	881	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107125	27107125	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002405-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	221	175	0	ENST00000324856.7:c.6736G>T	p.Glu2246Ter	p.E2246*	ENST00000324856	NM_006015.4	2246	Gag/Tag	20/20	0.127856764376583	4	FACETS	0.872	0.819	0.925	0.872	0.819	0.925	INDETERMINATE	2	TRUE	2	0.92	4		175	529	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002410-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	32	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.919	0.76	1			1	INDETERMINATE	2	TRUE	NA	0.276273245635017	2		422	126	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544169	18544169	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002410-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	78	457	0	ENST00000266497.5:c.1986G>C	p.Gln662His	p.Q662H	ENST00000266497		662	caG/caC	13/31	0.262156177973613	3	FACETS	0.617	0.541	0.7	0.309	0.27	0.35	SUBCLONAL	1	TRUE	1	0.276273245635017	3		457	1041	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579592	7579592	+	splice_acceptor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0002410-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	88	304	0	ENST00000269305.4:c.97-2A>C		p.X33_splice	ENST00000269305	NM_001126112.2	33			0.276273245635017	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.276273245635017	1		304	491	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030524	47030524	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002410-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	136	229	0	ENST00000377604.3:c.299G>C	p.Gly100Ala	p.G100A	ENST00000377604	NM_001204468.1	100	gGc/gCc	4/24	0.133044440996378	2	FACETS	1	0.967	1			1	INDETERMINATE	2	TRUE	NA	0.276273245635017	2		229	444	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47061302	47061303	+	frameshift_variant	Frame_Shift_Del	DEL	GC	GC	-	novel	NA	P-0002410-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	182	506	1	ENST00000409792.3:c.7378_7379del	p.Ala2460ArgfsTer5	p.A2460Rfs*5	ENST00000409792	NM_014159.6	2460	GCa/a	19/21	0.269802126042751	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.276273245635017	1		507	1013	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30038257	30038258	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0002410-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	191	485	0	ENST00000338641.4:c.431dup	p.Tyr144Ter	p.Y144*	ENST00000338641	NM_000268.3	144	tac/tAac	4/16	0.269802126042751	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.276273245635017	1		485	962	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002440-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	147	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.956	0.891	1			1	INDETERMINATE	2	TRUE	NA	0.555354651648904	2		422	277	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729163	66729163	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516792	NA	P-0002440-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	338	325	0	ENST00000307102.5:c.371C>T	p.Pro124Leu	p.P124L	ENST00000307102	NM_002755.3	124	cCg/cTg	3/11	0.555354651648904	4	FACETS	0.997	0.946	1	0.997	0.946	1	CLONAL	2	TRUE	2	0.555354651648904	4		325	949	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873660	35873660	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs201559094	NA	P-0002440-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	150	368	0	ENST00000303115.3:c.616C>T	p.Arg206Ter	p.R206*	ENST00000303115	NM_002185.3	206	Cga/Tga	5/8	0.555354651648904	3	FACETS	1	0.939	1	0.515	0.472	0.56	CLONAL	1	TRUE	1	0.555354651648904	3		368	670	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0002440-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	299	383	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	0.555354651648904	5	FACETS	0.97	0.921	1	0.97	0.921	1	CLONAL	3	TRUE	2	0.555354651648904	5		383	678	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913255	NA	P-0002440-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	383	344	0	ENST00000369535.4:c.183A>T	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caT	3/7	0.445233699549518	3	FACETS	1	0.994	1	0.829	0.794	0.863	CLONAL	2	TRUE	0	0.555354651648904	3		344	709	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750437	41750437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002440-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	343	279	0	ENST00000226382.2:c.191C>T	p.Ser64Phe	p.S64F	ENST00000226382	NM_003924.3	64	tCc/tTc	1/3	0.536924651914132	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.555354651648904	3		279	785	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0002440-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	123	79	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.998	0.926	1			1	INDETERMINATE	2	TRUE	NA	0.555354651648904	2		79	222	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055993	180055993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002440-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	113	302	0	ENST00000261937.6:c.992C>T	p.Pro331Leu	p.P331L	ENST00000261937	NM_182925.4	331	cCc/cTc	8/30	1	2	FACETS	0.949	0.86	1	0.949	0.86	1	CLONAL	1	TRUE	1	0.555354651648904	2		302	429	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710651	117710651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002440-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	198	316	0	ENST00000368508.3:c.1621G>A	p.Gly541Arg	p.G541R	ENST00000368508	NM_002944.2	541	Ggg/Agg	12/43	NA	2	FACETS	0.995	0.924	1			1	INDETERMINATE	1	TRUE	NA	0.555354651648904	2		316	717	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718093	117718093	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002440-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	139	367	0	ENST00000368508.3:c.764C>T	p.Pro255Leu	p.P255L	ENST00000368508	NM_002944.2	255	cCa/cTa	7/43	NA	2	FACETS	1	0.957	1			1	INDETERMINATE	1	TRUE	NA	0.555354651648904	2		367	469	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367321	50367321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002440-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	260	224	0	ENST00000331340.3:c.128G>A	p.Gly43Glu	p.G43E	ENST00000331340	NM_006060.4	43	gGa/gAa	3/8	0.555354651648904	3	FACETS	0.817	0.769	0.866	0.817	0.769	0.866	CLONAL	2	TRUE	1	0.555354651648904	3		224	732	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509235	106509235	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002440-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	185	349	0	ENST00000359195.3:c.1229G>A	p.Trp410Ter	p.W410*	ENST00000359195	NM_002649.2	410	tGg/tAg	2/11	0.555354651648904	3	FACETS	0.889	0.821	0.96	0.445	0.41	0.48	CLONAL	1	TRUE	1	0.555354651648904	3		349	957	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500886	8500886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002440-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	263	336	0	ENST00000356435.5:c.1996C>T	p.Pro666Ser	p.P666S	ENST00000356435		666	Cct/Tct	13/35	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	2	TRUE	NA	0.555354651648904	2		336	457	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913384	NA	P-0002440-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	244	163	0	ENST00000304494.5:c.262G>T	p.Glu88Ter	p.E88*	ENST00000304494	NM_000077.4	88	Gag/Tag	2/3	0.555354651648904	2	FACETS	0.994	0.943	1	0.994	0.943	1	CLONAL	2	TRUE	0	0.555354651648904	2		163	442	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417418	139417418	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002440-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	240	293	0	ENST00000277541.6:c.626C>T	p.Thr209Ile	p.T209I	ENST00000277541	NM_017617.3	209	aCc/aTc	4/34	0.555354651648904	2	FACETS	0.868	0.82	0.916	0.868	0.82	0.916	CLONAL	2	TRUE	0	0.555354651648904	2		293	498	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514094	125514094	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002440-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	374	391	0	ENST00000428830.2:c.1032T>G	p.Phe344Leu	p.F344L	ENST00000428830	NM_001114121.2	344	ttT/ttG	10/14	0.555354651648904	4	FACETS	0.948	0.901	0.996	0.948	0.901	0.996	CLONAL	2	TRUE	2	0.555354651648904	4		391	1105	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591835	48591835	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002440-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	292	352	0	ENST00000342988.3:c.998T>C	p.Val333Ala	p.V333A	ENST00000342988	NM_005359.5	333	gTt/gCt	9/12	NA	2	FACETS	0.979	0.933	1			1	INDETERMINATE	2	TRUE	NA	0.555354651648904	2		352	537	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272287	15272287	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002440-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	110	236	0	ENST00000263388.2:c.6152C>T	p.Pro2051Leu	p.P2051L	ENST00000263388	NM_000435.2	2051	cCt/cTt	33/33	0.536924651914132	3	FACETS	1	0.91	1	0.504	0.455	0.556	CLONAL	1	TRUE	1	0.555354651648904	3		236	502	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30313214	30313214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002440-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	160	371	0	ENST00000262643.3:c.908C>T	p.Ala303Val	p.A303V	ENST00000262643	NM_001238.2	303	gCc/gTc	10/12	0.555354651648904	3	FACETS	0.949	0.871	1	0.474	0.435	0.515	CLONAL	1	TRUE	1	0.555354651648904	3		371	776	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39772546	39772546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002440-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	200	276	0	ENST00000288319.7:c.695C>T	p.Pro232Leu	p.P232L	ENST00000288319	NM_182918.3	232	cCa/cTa	6/10	0.471558400131552	5	FACETS	1	0.985	1	0.793	0.74	0.847	CLONAL	2	TRUE	2	0.555354651648904	5		276	555	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548241	41548241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002440-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	321	350	0	ENST00000263253.7:c.3029C>T	p.Thr1010Ile	p.T1010I	ENST00000263253	NM_001429.3	1010	aCc/aTc	16/31	0.555354651648904	4	FACETS	0.993	0.941	1			1	CLONAL	2	TRUE	NA	0.555354651648904	4		350	905	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002450-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	64	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.752	0.671	0.834	1	0.978	1	SUBCLONAL	2	TRUE	1	0.616467599078222	2		422	138	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249022	55249022	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567477136	NA	P-0002450-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	273	258	1	ENST00000275493.2:c.2320G>A	p.Val774Met	p.V774M	ENST00000275493	NM_005228.3	774	Gtg/Atg	20/28	0.616467599078222	3	FACETS	0.857	0.81	0.905	0.857	0.81	0.905	CLONAL	2	TRUE	1	0.616467599078222	3		259	676	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685307	89685307	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs398123317	NA	P-0002450-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	112	218	0	ENST00000371953.3:c.202T>C	p.Tyr68His	p.Y68H	ENST00000371953	NM_000314.4	68	Tac/Cac	3/9	0.616467599078222	1	FACETS	0.931	0.852	1	0.931	0.852	1	CLONAL	1	TRUE	0	0.616467599078222	1		218	270	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164654	36164667	+	frameshift_variant	Frame_Shift_Del	DEL	GTAGTACAGGTGGT	GTAGTACAGGTGGT	-	novel	NA	P-0002450-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	61	276	0	ENST00000300305.3:c.1208_1221del	p.Tyr403TrpfsTer192	p.Y403Wfs*192	ENST00000300305		403	tACCACCTGTACTAC/t	8/8	0.103730319267689	4	FACETS	0.851	0.737	0.973	0.425	0.368	0.487	INDETERMINATE	1	TRUE	2	0.616467599078222	4		276	376	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002452-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	102	422	0				ENST00000310581	NM_198253.2	-/1132			0.392538330934613	3	FACETS	1	0.947	1	1	0.947	1	INDETERMINATE	2	TRUE	1	0.686194596152144	3		422	192	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47607002	47607002	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs748065050	NA	P-0002452-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	192	281	0	ENST00000263735.4:c.752A>G	p.Tyr251Cys	p.Y251C	ENST00000263735	NM_002354.2	251	tAt/tGt	7/9	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.686194596152144	2		281	473	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0002472-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	67	403	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.355782407216786	1	FACETS	0.725	0.632	0.825	0.725	0.632	0.825	SUBCLONAL	1	TRUE	0	0.355782407216786	1		404	427	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002472-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	21	422	0				ENST00000310581	NM_198253.2	-/1132			0.309595753550827	0	FACETS	0.629	0.49	0.785			1	SUBCLONAL	1	TRUE	0	0.355782407216786	0		422	121	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47596714	47596714	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002472-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	85	240	0	ENST00000263735.4:c.70C>G	p.Gln24Glu	p.Q24E	ENST00000263735	NM_002354.2	24	Cag/Gag	1/9	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.355782407216786	2		240	395	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002474-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	25	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.809	1	1	0.809	1	CLONAL	1	TRUE	1	0.18	2		422	271	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402100	402100	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002474-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1251	109	512	0	ENST00000399788.2:c.4691A>T	p.Lys1564Met	p.K1564M	ENST00000399788	NM_001042603.1	1564	aAg/aTg	27/28	0.3	2	FACETS	0.891	0.797	0.991			1	CLONAL	1	TRUE	NA	0.18	2		512	1360	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002483-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	32	422	0				ENST00000310581	NM_198253.2	-/1132			0.471490460441205	1	FACETS	0.902	0.748	1	0.902	0.748	1	CLONAL	1	TRUE	0	0.471490460441205	1		422	115	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183725	10183725	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs5030826	NA	P-0002483-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	120	341	0	ENST00000256474.2:c.194C>T	p.Ser65Leu	p.S65L	ENST00000256474	NM_000551.3	65	tCg/tTg	1/3	0.426633380379024	1	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	0	0.471490460441205	1		341	387	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623085	52623085	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0002483-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	112	370	0	ENST00000394830.3:c.2965+1G>C		p.X989_splice	ENST00000394830	NM_018313.4	989			0.426633380379024	1	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	0	0.471490460441205	1		370	363	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976635	55976635	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002483-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	95	424	0	ENST00000263923.4:c.1190C>G	p.Thr397Ser	p.T397S	ENST00000263923	NM_002253.2	397	aCt/aGt	9/30	NA	2	FACETS	0.824	0.737	0.916			1	INDETERMINATE	1	TRUE	NA	0.471490460441205	2		424	489	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89811422	89811422	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1321489026	NA	P-0002483-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	49	324	0	ENST00000389301.3:c.3571A>G	p.Ser1191Gly	p.S1191G	ENST00000389301	NM_000135.2	1191	Agc/Ggc	36/43	0.240320742694503	1	FACETS	0.401	0.34	0.468	0.401	0.34	0.468	INDETERMINATE	1	TRUE	0	0.471490460441205	1		324	396	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135804235	135804235	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002483-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	99	318	0	ENST00000298552.3:c.25del	p.Glu9SerfsTer17	p.E9Sfs*17	ENST00000298552	NM_001162426.1	9	Gag/ag	3/23	0.471490460441205	1	FACETS	0.854	0.768	0.943	0.854	0.768	0.943	CLONAL	1	TRUE	0	0.471490460441205	1		318	376	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	1077	393	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.652072193085329	4	FACETS	1	0.996	1			1	CLONAL	3	TRUE	NA	0.728133254423712	4		393	1580	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	145	139	0				ENST00000310581	NM_198253.2	-/1132			0.51971908392642	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.728133254423712	3		139	261	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245843	46245843	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	225	378	0	ENST00000334344.6:c.3937C>T	p.Gln1313Ter	p.Q1313*	ENST00000334344	NM_152641.2	1313	Caa/Taa	15/21	0.127523222297183	4	FACETS	0.785	0.735	0.837	0.785	0.735	0.837	INDETERMINATE	2	TRUE	2	0.728133254423712	4		378	680	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223550	55223550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	160	360	0	ENST00000275493.2:c.917C>T	p.Ser306Leu	p.S306L	ENST00000275493	NM_005228.3	306	tCg/tTg	8/28	NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.728133254423712	2		360	425	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867535	35867535	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	146	380	0	ENST00000303115.3:c.349A>G	p.Thr117Ala	p.T117A	ENST00000303115	NM_002185.3	117	Acc/Gcc	3/8	0.254714594509009	1	FACETS	0.443	0.406	0.481	0.443	0.406	0.481	INDETERMINATE	1	TRUE	0	0.728133254423712	1		380	576	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780815	9780815	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	158	321	0	ENST00000377346.4:c.1537G>A	p.Glu513Lys	p.E513K	ENST00000377346	NM_005026.3	513	Gaa/Aaa	13/24	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.728133254423712	2		321	427	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258308	16258308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	206	458	1	ENST00000375759.3:c.5573C>T	p.Pro1858Leu	p.P1858L	ENST00000375759	NM_015001.2	1858	cCt/cTt	11/15	1	2	FACETS	0.994	0.929	1	0.994	0.929	1	CLONAL	1	TRUE	1	0.728133254423712	2		459	569	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101669	27101669	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761598513	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	230	376	0	ENST00000324856.7:c.4951C>T	p.Pro1651Ser	p.P1651S	ENST00000324856	NM_006015.4	1651	Cct/Tct	18/20	1	2	FACETS	0.969	0.909	1	0.969	0.909	1	CLONAL	1	TRUE	1	0.728133254423712	2		376	652	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805013	43805013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	179	398	0	ENST00000372470.3:c.463G>A	p.Glu155Lys	p.E155K	ENST00000372470	NM_005373.2	155	Gag/Aag	4/12	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.728133254423712	2		398	487	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812522	43812522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	182	411	0	ENST00000372470.3:c.1225G>A	p.Glu409Lys	p.E409K	ENST00000372470	NM_005373.2	409	Gag/Aag	8/12	1	2	FACETS	0.911	0.846	0.977	0.911	0.846	0.977	CLONAL	1	TRUE	1	0.728133254423712	2		411	549	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510100	120510100	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1252425034	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	251	414	0	ENST00000256646.2:c.1409C>T	p.Thr470Ile	p.T470I	ENST00000256646	NM_024408.3	470	aCc/aTc	8/34	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.728133254423712	2		414	674	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849083	156849083	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	172	398	0	ENST00000524377.1:c.1975G>A	p.Gly659Ser	p.G659S	ENST00000524377	NM_002529.3	659	Ggc/Agc	15/17	1	2	FACETS	0.919	0.852	0.988	0.919	0.852	0.988	CLONAL	1	TRUE	1	0.728133254423712	2		398	514	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104551	193104551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868045207	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	299	419	0	ENST00000367435.3:c.338C>T	p.Pro113Leu	p.P113L	ENST00000367435	NM_024529.4	113	cCc/cTc	4/17	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.728133254423712	2		419	735	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082751	16082751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	28	43	0	ENST00000281043.3:c.565C>T	p.Pro189Ser	p.P189S	ENST00000281043	NM_005378.4	189	Ccc/Tcc	2/3	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.728133254423712	2		43	61	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551307	29551307	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	176	416	0	ENST00000389048.3:c.1323C>A	p.Phe441Leu	p.F441L	ENST00000389048	NM_004304.4	441	ttC/ttA	6/29	1	2	FACETS	0.997	0.926	1	0.997	0.926	1	CLONAL	1	TRUE	1	0.728133254423712	2		416	485	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61709543	61709543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	264	450	0	ENST00000401558.2:c.2944C>T	p.Leu982Phe	p.L982F	ENST00000401558	NM_003400.3	982	Ctt/Ttt	23/25	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.728133254423712	2		450	642	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726878	61726878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	292	520	0	ENST00000401558.2:c.560C>T	p.Thr187Ile	p.T187I	ENST00000401558	NM_003400.3	187	aCc/aTc	7/25	1	2	FACETS	0.996	0.941	1	0.996	0.941	1	CLONAL	1	TRUE	1	0.728133254423712	2		520	805	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160374	99160374	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	166	356	0	ENST00000074304.5:c.853C>T	p.Pro285Ser	p.P285S	ENST00000074304	NM_001134224.1	285	Cct/Tct	11/26	1	2	FACETS	0.894	0.827	0.962	0.894	0.827	0.962	CLONAL	1	TRUE	1	0.728133254423712	2		356	510	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736133	204736133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	234	479	0	ENST00000302823.3:c.490C>T	p.Leu164Phe	p.L164F	ENST00000302823	NM_005214.4	164	Ctc/Ttc	3/4	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.728133254423712	2		479	638	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286761	212286761	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	195	380	2	ENST00000342788.4:c.2935C>T	p.Arg979Ter	p.R979*	ENST00000342788	NM_005235.2	979	Cga/Tga	24/28	0.728133254423712	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.728133254423712	1		382	317	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568893	212568893	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	176	438	0	ENST00000342788.4:c.1225C>T	p.Pro409Ser	p.P409S	ENST00000342788	NM_005235.2	409	Cca/Tca	11/28	0.728133254423712	1	FACETS	0.899	0.843	0.955	0.899	0.843	0.955	CLONAL	1	TRUE	0	0.728133254423712	1		438	342	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812340	212812340	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	175	288	1	ENST00000342788.4:c.236C>T	p.Ser79Phe	p.S79F	ENST00000342788	NM_005235.2	79	tCt/tTt	3/28	0.728133254423712	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.728133254423712	1		289	296	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713801	30713801	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	161	323	0	ENST00000295754.5:c.1126G>T	p.Val376Leu	p.V376L	ENST00000295754	NM_003242.5	376	Gtg/Ttg	4/7	1	2	FACETS	0.884	0.817	0.953	0.884	0.817	0.953	CLONAL	1	TRUE	1	0.728133254423712	2		323	500	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595830	52595831	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	235	463	1	ENST00000394830.3:c.4084_4085delinsAA	p.Gly1362Lys	p.G1362K	ENST00000394830	NM_018313.4	1362	GGg/AAg	26/30	1	2	FACETS	0.869	0.814	0.925	0.869	0.814	0.925	CLONAL	1	TRUE	1	0.728133254423712	2		464	743	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498379	89498379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866959883	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	143	320	0	ENST00000336596.2:c.2351G>A	p.Gly784Glu	p.G784E	ENST00000336596	NM_005233.5	784	gGg/gAg	14/17	1	2	FACETS	0.967	0.891	1	0.967	0.891	1	CLONAL	1	TRUE	1	0.728133254423712	2		320	406	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851706	134851706	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1164993873	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	137	336	0	ENST00000398015.3:c.1112C>T	p.Ser371Phe	p.S371F	ENST00000398015	NM_004441.4	371	tCc/tTc	5/16	1	2	FACETS	0.95	0.874	1	0.95	0.874	1	CLONAL	1	TRUE	1	0.728133254423712	2		336	396	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403591	138403591	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	267	524	0	ENST00000289153.2:c.2191G>C	p.Val731Leu	p.V731L	ENST00000289153	NM_006219.2	731	Gtg/Ctg	15/22	1	2	FACETS	0.998	0.94	1	0.998	0.94	1	CLONAL	1	TRUE	1	0.728133254423712	2		524	735	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	181	433	0	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.728133254423712	2		433	488	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955632	55955632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	167	408	0	ENST00000263923.4:c.3313C>T	p.Pro1105Ser	p.P1105S	ENST00000263923	NM_002253.2	1105	Cca/Tca	25/30	0.172608752309232	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.728133254423712	0		408	513	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972949	55972949	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	216	408	0	ENST00000263923.4:c.1441C>T	p.Pro481Ser	p.P481S	ENST00000263923	NM_002253.2	481	Cct/Tct	11/30	0.172608752309232	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.728133254423712	0		408	593	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530398	187530398	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778500047	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	243	460	0	ENST00000441802.2:c.10145C>T	p.Ser3382Leu	p.S3382L	ENST00000441802	NM_005245.3	3382	tCg/tTg	16/27	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.728133254423712	2		460	665	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557782	187557782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200252550	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	246	458	0	ENST00000441802.2:c.3929C>T	p.Ser1310Leu	p.S1310L	ENST00000441802	NM_005245.3	1310	tCg/tTg	5/27	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.728133254423712	2		458	645	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557785	187557785	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	274	462	0	ENST00000441802.2:c.3926T>C	p.Val1309Ala	p.V1309A	ENST00000441802	NM_005245.3	1309	gTt/gCt	5/27	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.728133254423712	2		462	650	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254488	1254488	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	197	320	0	ENST00000310581.5:c.3290G>A	p.Arg1097Lys	p.R1097K	ENST00000310581	NM_198253.2	1097	aGg/aAg	15/16	0.51971908392642	3	FACETS	0.79	0.74	0.841	0.79	0.74	0.841	SUBCLONAL	2	TRUE	1	0.728133254423712	3		320	467	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293683	1293683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	108	232	0	ENST00000310581.5:c.1318G>A	p.Glu440Lys	p.E440K	ENST00000310581	NM_198253.2	440	Gag/Aag	2/16	0.51971908392642	3	FACETS	0.957	0.865	1	0.478	0.432	0.527	CLONAL	1	TRUE	1	0.728133254423712	3		232	423	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876145	35876145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	144	496	0	ENST00000303115.3:c.937G>A	p.Asp313Asn	p.D313N	ENST00000303115	NM_002185.3	313	Gac/Aac	8/8	0.254714594509009	1	FACETS	0.487	0.447	0.529	0.487	0.447	0.529	INDETERMINATE	1	TRUE	0	0.728133254423712	1		496	516	SUCCESS
APC	324	MSKCC	GRCh37	5	112177203	112177203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	218	360	0	ENST00000257430.4:c.5912C>T	p.Ser1971Phe	p.S1971F	ENST00000257430	NM_000038.5	1971	tCt/tTt	16/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.728133254423712	2		360	552	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131940657	131940657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	253	448	0	ENST00000265335.6:c.2684C>T	p.Ser895Phe	p.S895F	ENST00000265335		895	tCc/tTc	16/25	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.728133254423712	2		448	695	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441131	149441131	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	222	476	0	ENST00000286301.3:c.1781G>A	p.Gly594Glu	p.G594E	ENST00000286301	NM_005211.3	594	gGg/gAg	13/22	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.728133254423712	2		476	591	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441313	149441313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	181	427	0	ENST00000286301.3:c.1726G>A	p.Glu576Lys	p.E576K	ENST00000286301	NM_005211.3	576	Gag/Aag	12/22	1	2	FACETS	0.911	0.846	0.977	0.911	0.846	0.977	CLONAL	1	TRUE	1	0.728133254423712	2		427	546	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149450022	149450022	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	156	286	0	ENST00000286301.3:c.1195C>T	p.Arg399Ter	p.R399*	ENST00000286301	NM_005211.3	399	Cga/Tga	8/22	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.728133254423712	2		286	426	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497239	149497239	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1283951256	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	194	375	0	ENST00000261799.4:c.3079G>A	p.Asp1027Asn	p.D1027N	ENST00000261799	NM_002609.3	1027	Gac/Aac	22/23	1	2	FACETS	0.917	0.854	0.982	0.917	0.854	0.982	CLONAL	1	TRUE	1	0.728133254423712	2		375	581	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515210	149515210	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	179	465	1	ENST00000261799.4:c.272C>T	p.Thr91Ile	p.T91I	ENST00000261799	NM_002609.3	91	aCt/aTt	3/23	1	2	FACETS	0.87	0.807	0.935	0.87	0.807	0.935	CLONAL	1	TRUE	1	0.728133254423712	2		466	565	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515291	149515291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1244128395	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	178	348	1	ENST00000261799.4:c.191G>A	p.Arg64Gln	p.R64Q	ENST00000261799	NM_002609.3	64	cGg/cAg	3/23	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.728133254423712	2		349	481	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480084	20480084	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761207862	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	201	346	0	ENST00000346618.3:c.401G>A	p.Arg134Gln	p.R134Q	ENST00000346618	NM_001949.4	134	cGa/cAa	2/7	0.504468939838827	5	FACETS	0.762	0.708	0.817			1	SUBCLONAL	2	TRUE	NA	0.728133254423712	5		346	758	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480103	20480103	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	229	400	0	ENST00000346618.3:c.420A>T	p.Glu140Asp	p.E140D	ENST00000346618	NM_001949.4	140	gaA/gaT	2/7	0.504468939838827	5	FACETS	0.818	0.765	0.873			1	CLONAL	2	TRUE	NA	0.728133254423712	5		400	804	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672809	30672809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	236	504	0	ENST00000376406.3:c.4151C>T	p.Thr1384Ile	p.T1384I	ENST00000376406	NM_014641.2	1384	aCc/aTc	10/15	0.728133254423712	3	FACETS	0.986	0.921	1	0.493	0.46	0.526	CLONAL	1	TRUE	1	0.728133254423712	3		504	897	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673581	30673581	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1267237231	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	238	512	0	ENST00000376406.3:c.3379C>T	p.Pro1127Ser	p.P1127S	ENST00000376406	NM_014641.2	1127	Ccc/Tcc	10/15	0.728133254423712	3	FACETS	0.955	0.892	1	0.477	0.446	0.51	CLONAL	1	TRUE	1	0.728133254423712	3		512	934	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188818	32188818	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	158	372	0	ENST00000375023.3:c.736G>A	p.Gly246Arg	p.G246R	ENST00000375023	NM_004557.3	246	Ggg/Agg	4/30	0.728133254423712	3	FACETS	0.926	0.852	1	0.463	0.426	0.502	CLONAL	1	TRUE	1	0.728133254423712	3		372	639	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553410	106553410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	134	259	0	ENST00000369096.4:c.1375C>T	p.Pro459Ser	p.P459S	ENST00000369096	NM_001198.3	459	Ccc/Tcc	5/7	0.599483596084788	1	FACETS	0.839	0.777	0.901	0.839	0.777	0.901	CLONAL	1	TRUE	0	0.728133254423712	1		259	279	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641144	117641144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866970127	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	201	470	0	ENST00000368508.3:c.5827G>A	p.Glu1943Lys	p.E1943K	ENST00000368508	NM_002944.2	1943	Gaa/Aaa	36/43	0.728133254423712	1	FACETS	0.967	0.913	1	0.967	0.913	1	CLONAL	1	TRUE	0	0.728133254423712	1		470	363	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662691	117662691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368206665	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	183	407	0	ENST00000368508.3:c.4774C>T	p.Arg1592Cys	p.R1592C	ENST00000368508	NM_002944.2	1592	Cgt/Tgt	29/43	0.728133254423712	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.728133254423712	1		407	318	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771243	161771243	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs760223151	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	133	308	0	ENST00000366898.1:c.1286G>A	p.Gly429Glu	p.G429E	ENST00000366898	NM_004562.2	429	gGa/gAa	12/12	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.728133254423712	NA		308	249	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962842	2962842	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	145	348	0	ENST00000396946.4:c.2066G>A	p.Gly689Glu	p.G689E	ENST00000396946	NM_032415.4	689	gGg/gAg	16/25	NA	2	FACETS	0.753	0.691	0.817			1	INDETERMINATE	1	TRUE	NA	0.728133254423712	2		348	529	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455090	50455090	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	173	348	0	ENST00000331340.3:c.637C>T	p.Arg213Ter	p.R213*	ENST00000331340	NM_006060.4	213	Cga/Tga	6/8	NA	2	FACETS	0.912	0.846	0.98			1	INDETERMINATE	1	TRUE	NA	0.728133254423712	2		348	521	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467616	50467616	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	95	200	0	ENST00000331340.3:c.851G>A	p.Gly284Glu	p.G284E	ENST00000331340	NM_006060.4	284	gGg/gAg	8/8	NA	2	FACETS	0.85	0.766	0.937			1	INDETERMINATE	1	TRUE	NA	0.728133254423712	2		200	307	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467675	50467675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759124417	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	159	357	0	ENST00000331340.3:c.910G>A	p.Glu304Lys	p.E304K	ENST00000331340	NM_006060.4	304	Gaa/Aaa	8/8	NA	2	FACETS	0.933	0.863	1			1	INDETERMINATE	1	TRUE	NA	0.728133254423712	2		357	468	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467721	50467721	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	140	384	0	ENST00000331340.3:c.956T>C	p.Ile319Thr	p.I319T	ENST00000331340	NM_006060.4	319	aTc/aCc	8/8	NA	2	FACETS	0.894	0.822	0.969			1	INDETERMINATE	1	TRUE	NA	0.728133254423712	2		384	430	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227873	55227873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	217	390	0	ENST00000275493.2:c.1340C>T	p.Ser447Phe	p.S447F	ENST00000275493	NM_005228.3	447	tCc/tTc	12/28	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.728133254423712	2		390	541	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508797	106508797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	207	413	0	ENST00000359195.3:c.791G>A	p.Ser264Asn	p.S264N	ENST00000359195	NM_002649.2	264	aGc/aAc	2/11	1	2	FACETS	0.875	0.816	0.935	0.875	0.816	0.935	CLONAL	1	TRUE	1	0.728133254423712	2		413	650	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878341	151878341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760297553	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	218	462	0	ENST00000262189.6:c.6604C>T	p.Pro2202Ser	p.P2202S	ENST00000262189	NM_170606.2	2202	Cca/Tca	36/59	1	2	FACETS	0.98	0.917	1	0.98	0.917	1	CLONAL	1	TRUE	1	0.728133254423712	2		462	611	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370880	55370880	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	101	311	0	ENST00000297316.4:c.182G>A	p.Arg61Gln	p.R61Q	ENST00000297316	NM_022454.3	61	cGa/cAa	1/2	1	2	FACETS	0.806	0.728	0.888	0.806	0.728	0.888	CLONAL	1	TRUE	1	0.728133254423712	2		311	344	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020793	37020793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	181	401	0	ENST00000358127.4:c.52G>A	p.Gly18Arg	p.G18R	ENST00000358127	NM_001280556.1	18	Gga/Aga	2/10	NA	2	FACETS	0.988	0.919	1			1	INDETERMINATE	1	TRUE	NA	0.728133254423712	2		401	503	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342574	87342574	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	162	386	0	ENST00000277120.3:c.859C>T	p.Pro287Ser	p.P287S	ENST00000277120		287	Cca/Tca	9/19	NA	2	FACETS	0.991	0.918	1			1	INDETERMINATE	1	TRUE	NA	0.728133254423712	2		386	449	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229611	98229611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502293	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	230	405	1	ENST00000331920.6:c.2347C>T	p.Arg783Trp	p.R783W	ENST00000331920	NM_000264.3	783	Cgg/Tgg	15/24	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.728133254423712	2		406	596	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759367	133759367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	212	443	0	ENST00000318560.5:c.1690C>T	p.His564Tyr	p.H564Y	ENST00000318560	NM_005157.4	564	Cat/Tat	11/11	1	2	FACETS	0.997	0.933	1	0.997	0.933	1	CLONAL	1	TRUE	1	0.728133254423712	2		443	584	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781460	135781460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	138	335	0	ENST00000298552.3:c.1505G>A	p.Gly502Asp	p.G502D	ENST00000298552	NM_001162426.1	502	gGc/gAc	15/23	1	2	FACETS	0.916	0.841	0.992	0.916	0.841	0.992	CLONAL	1	TRUE	1	0.728133254423712	2		335	414	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100379	8100379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	141	468	0	ENST00000346208.3:c.353C>T	p.Ser118Phe	p.S118F	ENST00000346208		118	tCc/tTc	3/6	NA	2	FACETS	0.886	0.815	0.96			1	INDETERMINATE	1	TRUE	NA	0.728133254423712	2		468	437	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128987	64128988	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	220	386	1	ENST00000334205.4:c.617_618delinsTT	p.Pro206Leu	p.P206L	ENST00000334205	NM_003942.2	206	cCC/cTT	6/17	NA	2	FACETS	1	0.95	1			1	INDETERMINATE	1	TRUE	NA	0.728133254423712	2		387	595	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342464	118342464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	262	496	1	ENST00000534358.1:c.590C>T	p.Ser197Phe	p.S197F	ENST00000534358	NM_005933.3	197	tCc/tTc	3/36	1	2	FACETS	0.979	0.922	1	0.979	0.922	1	CLONAL	1	TRUE	1	0.728133254423712	2		497	735	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006426	12006426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	995	501	3	ENST00000396373.4:c.394C>T	p.Pro132Ser	p.P132S	ENST00000396373	NM_001987.4	132	Cca/Tca	4/8	0.728133254423712	6	FACETS	0.973	0.949	0.998			1	CLONAL	4	TRUE	NA	0.728133254423712	6		504	1724	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435407	18435407	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	207	445	0	ENST00000266497.5:c.392G>A	p.Gly131Glu	p.G131E	ENST00000266497		131	gGa/gAa	1/31	0.652072193085329	4	FACETS	0.88	0.815	0.946			1	CLONAL	1	TRUE	NA	0.728133254423712	4		445	1117	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491360	18491360	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	602	297	0	ENST00000266497.5:c.1273G>A	p.Glu425Lys	p.E425K	ENST00000266497		425	Gaa/Aaa	8/31	0.652072193085329	4	FACETS	1	0.995	1			1	CLONAL	3	TRUE	NA	0.728133254423712	4		297	860	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691241	18691241	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	98	290	0	ENST00000266497.5:c.3352G>A	p.Glu1118Lys	p.E1118K	ENST00000266497		1118	Gaa/Aaa	23/31	0.652072193085329	4	FACETS	0.697	0.623	0.777			1	SUBCLONAL	1	TRUE	NA	0.728133254423712	4		290	667	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716344	18716344	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778895247	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	234	438	1	ENST00000266497.5:c.3691G>A	p.Glu1231Lys	p.E1231K	ENST00000266497		1231	Gaa/Aaa	26/31	0.652072193085329	4	FACETS	1	0.935	1			1	CLONAL	1	TRUE	NA	0.728133254423712	4		439	1107	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944997	31944997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	164	275	0	ENST00000340398.3:c.104G>A	p.Gly35Glu	p.G35E	ENST00000340398	NM_001013699.2	35	gGg/gAg	1/1	0.652072193085329	4	FACETS	0.843	0.774	0.916			1	CLONAL	1	TRUE	NA	0.728133254423712	4		275	923	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424958105	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	273	498	0	ENST00000334344.6:c.940C>T	p.Arg314Cys	p.R314C	ENST00000334344	NM_152641.2	314	Cgt/Tgt	8/21	0.127523222297183	4	FACETS	0.888	0.837	0.938	0.888	0.837	0.938	INDETERMINATE	2	TRUE	2	0.728133254423712	4		498	730	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424170	49424170	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	158	269	0	ENST00000301067.7:c.13892C>T	p.Pro4631Leu	p.P4631L	ENST00000301067	NM_003482.3	4631	cCc/cTc	42/54	0.127523222297183	4	FACETS	0.959	0.89	1	0.959	0.89	1	INDETERMINATE	2	TRUE	2	0.728133254423712	4		269	391	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486836	56486836	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	273	453	0	ENST00000267101.3:c.1250C>T	p.Thr417Ile	p.T417I	ENST00000267101	NM_001982.3	417	aCc/aTc	11/28	0.127523222297183	4	FACETS	0.877	0.827	0.927	0.877	0.827	0.927	INDETERMINATE	2	TRUE	2	0.728133254423712	4		453	739	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69210710	69210710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	217	360	0	ENST00000462284.1:c.293C>T	p.Ser98Phe	p.S98F	ENST00000462284	NM_002392.5	98	tCt/tTt	4/11	0.127523222297183	4	FACETS	0.827	0.773	0.881	0.827	0.773	0.881	INDETERMINATE	2	TRUE	2	0.728133254423712	4		360	623	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924330	112924330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	230	420	0	ENST00000351677.2:c.1276C>T	p.His426Tyr	p.H426Y	ENST00000351677	NM_002834.3	426	Cac/Tac	11/16	0.728133254423712	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.728133254423712	1		420	357	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109863	115109863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	109	218	0	ENST00000257566.3:c.2015G>A	p.Gly672Asp	p.G672D	ENST00000257566	NM_016569.3	672	gGc/gAc	8/8	0.728133254423712	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.728133254423712	1		218	187	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118751	115118751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	167	496	2	ENST00000257566.3:c.590G>A	p.Trp197Ter	p.W197*	ENST00000257566	NM_016569.3	197	tGg/tAg	2/8	0.728133254423712	1	FACETS	0.831	0.776	0.886	0.831	0.776	0.886	CLONAL	1	TRUE	0	0.728133254423712	1		498	351	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416884	121416884	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	171	291	0	ENST00000257555.6:c.313G>A	p.Glu105Lys	p.E105K	ENST00000257555		105	Gag/Aag	1/10	0.728133254423712	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.728133254423712	1		291	248	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001303	29001303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201407326	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	382	390	1	ENST00000282397.4:c.1429G>A	p.Glu477Lys	p.E477K	ENST00000282397	NM_002019.4	477	Gaa/Aaa	10/30	NA	2	FACETS	0.961	0.928	0.993			1	INDETERMINATE	2	TRUE	NA	0.728133254423712	2		391	546	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918787	32918787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	449	414	0	ENST00000380152.3:c.6934G>A	p.Asp2312Asn	p.D2312N	ENST00000380152		2312	Gat/Aat	12/27	0.728133254423712	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.728133254423712	2		414	609	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437106	110437106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	43	19	0	ENST00000375856.3:c.1295C>T	p.Ser432Phe	p.S432F	ENST00000375856	NM_003749.2	432	tCc/tTc	1/2	0.728133254423712	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	2	TRUE	0	0.728133254423712	2		19	59	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986565	36986565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	85	266	0	ENST00000354822.5:c.1124C>T	p.Ser375Phe	p.S375F	ENST00000354822	NM_001079668.2	375	tCc/tTc	3/3	NA	2	FACETS	0.855	0.766	0.948			1	INDETERMINATE	1	TRUE	NA	0.728133254423712	2		266	273	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023037	33023037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	142	316	0	ENST00000300177.4:c.146C>T	p.Ser49Leu	p.S49L	ENST00000300177	NM_001191322.1	49	tCg/tTg	2/2	0.722449906665625	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.728133254423712	1		316	243	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465483	99465483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1270131506	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	226	500	0	ENST00000268035.6:c.2308G>A	p.Glu770Lys	p.E770K	ENST00000268035	NM_000875.3	770	Gag/Aag	11/21	0.655318020175875	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.728133254423712	1		500	371	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892266	9892266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868291959	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	168	403	3	ENST00000330684.3:c.2224G>A	p.Asp742Asn	p.D742N	ENST00000330684	NM_001134407.1	742	Gat/Aat	11/13	0.599483596084788	1	FACETS	0.649	0.602	0.697	0.649	0.602	0.697	SUBCLONAL	1	TRUE	0	0.728133254423712	1		406	452	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032069	10032069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868215122	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	155	458	0	ENST00000330684.3:c.754G>A	p.Asp252Asn	p.D252N	ENST00000330684	NM_001134407.1	252	Gat/Aat	3/13	0.599483596084788	1	FACETS	0.568	0.524	0.613	0.568	0.524	0.613	SUBCLONAL	1	TRUE	0	0.728133254423712	1		458	477	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645286	67645286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	198	393	0	ENST00000264010.4:c.551C>T	p.Pro184Leu	p.P184L	ENST00000264010	NM_006565.3	184	cCa/cTa	3/12	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.728133254423712	2		393	525	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849467	68849469	+	missense_variant	Missense_Mutation	TNP	CGA	CGA	TGG	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	204	440	0	ENST00000261769.5:c.1370_1372delinsTGG	p.Thr457_Asn458delinsMetAsp	p.T457_N458delinsMD	ENST00000261769	NM_004360.3	457	aCGAat/aTGGat	10/16	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.728133254423712	2		440	543	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578179	7578179	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	205	423	0	ENST00000269305.4:c.670G>T	p.Glu224Ter	p.E224*	ENST00000269305	NM_001126112.2	224	Gag/Tag	6/11	0.186016543867344	1	FACETS	0.655	0.612	0.698	0.655	0.612	0.698	INDETERMINATE	1	TRUE	0	0.728133254423712	1		423	547	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	107	260	0	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.186016543867344	1	FACETS	0.5	0.452	0.549	0.5	0.452	0.549	INDETERMINATE	1	TRUE	0	0.728133254423712	1		260	374	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984090	7984090	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	170	327	0	ENST00000319144.4:c.536G>A	p.Gly179Asp	p.G179D	ENST00000319144	NM_001139.2	179	gGc/gAc	5/15	0.186016543867344	1	FACETS	0.712	0.663	0.762	0.712	0.663	0.762	INDETERMINATE	1	TRUE	0	0.728133254423712	1		327	417	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984096	7984096	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs959284348	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	113	313	0	ENST00000319144.4:c.530G>A	p.Trp177Ter	p.W177*	ENST00000319144	NM_001139.2	177	tGg/tAg	5/15	0.186016543867344	1	FACETS	0.493	0.448	0.541	0.493	0.448	0.541	INDETERMINATE	1	TRUE	0	0.728133254423712	1		313	400	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17120483	17120483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	136	325	0	ENST00000285071.4:c.1076C>T	p.Pro359Leu	p.P359L	ENST00000285071	NM_144997.5	359	cCt/cTt	10/14	0.186016543867344	1	FACETS	0.552	0.507	0.6	0.552	0.507	0.6	INDETERMINATE	1	TRUE	0	0.728133254423712	1		325	430	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122376	17122376	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	143	392	0	ENST00000285071.4:c.1019C>T	p.Pro340Leu	p.P340L	ENST00000285071	NM_144997.5	340	cCc/cTc	9/14	0.186016543867344	1	FACETS	0.541	0.497	0.586	0.541	0.497	0.586	INDETERMINATE	1	TRUE	0	0.728133254423712	1		392	462	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657405	29657405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	186	457	0	ENST00000356175.3:c.5638C>T	p.Pro1880Ser	p.P1880S	ENST00000356175	NM_000267.3	1880	Cct/Tct	38/57	1	2	FACETS	0.784	0.727	0.842	0.784	0.727	0.842	SUBCLONAL	1	TRUE	1	0.728133254423712	2		457	652	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435284	56435284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	126	194	1	ENST00000407977.2:c.1853C>T	p.Ala618Val	p.A618V	ENST00000407977		618	gCc/gTc	9/10	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.728133254423712	2		195	332	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760790	59760790	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	249	542	0	ENST00000259008.2:c.3617T>G	p.Ile1206Ser	p.I1206S	ENST00000259008	NM_032043.2	1206	aTt/aGt	20/20	1	2	FACETS	0.912	0.856	0.969	0.912	0.856	0.969	CLONAL	1	TRUE	1	0.728133254423712	2		542	750	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519032	66519032	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	266	408	0	ENST00000358598.2:c.313T>A	p.Tyr105Asn	p.Y105N	ENST00000358598	NM_212471.2	105	Tac/Aac	3/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.728133254423712	2		408	676	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919518	78919518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	185	390	0	ENST00000306801.3:c.3077C>T	p.Pro1026Leu	p.P1026L	ENST00000306801	NM_020761.2	1026	cCc/cTc	26/34	1	2	FACETS	0.922	0.857	0.989	0.922	0.857	0.989	CLONAL	1	TRUE	1	0.728133254423712	2		390	551	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4102441	4102441	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1291541587	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	194	328	0	ENST00000262948.5:c.461C>T	p.Ser154Phe	p.S154F	ENST00000262948	NM_030662.3	154	tCc/tTc	4/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.728133254423712	2		328	510	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743898	41743898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	213	404	0	ENST00000301178.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000301178	NM_021913.4	278	cCc/cTc	7/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.728133254423712	2		404	540	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795520	42795520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	203	365	0	ENST00000575354.2:c.2600C>T	p.Pro867Leu	p.P867L	ENST00000575354	NM_015125.3	867	cCa/cTa	10/20	1	2	FACETS	0.936	0.873	0.999	0.936	0.873	0.999	CLONAL	1	TRUE	1	0.728133254423712	2		365	596	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375076	31375076	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	182	347	0	ENST00000328111.2:c.473G>T	p.Trp158Leu	p.W158L	ENST00000328111	NM_006892.3	158	tGg/tTg	6/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.728133254423712	2		347	472	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730850	40730850	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	151	351	1	ENST00000373198.4:c.3685G>A	p.Asp1229Asn	p.D1229N	ENST00000373198	NM_133170.3	1229	Gac/Aac	27/32	0.543702029924716	1	FACETS	0.619	0.572	0.668	0.619	0.572	0.668	SUBCLONAL	1	TRUE	0	0.728133254423712	1		352	426	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656822	45656822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	351	340	0	ENST00000407780.3:c.334C>T	p.His112Tyr	p.H112Y	ENST00000407780	NM_001283052.1	112	Cac/Tac	3/7	NA	2	FACETS	0.974	0.94	1			1	INDETERMINATE	2	TRUE	NA	0.728133254423712	2		340	495	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349017	70349017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	250	234	0	ENST00000374080.3:c.3529C>T	p.Leu1177Phe	p.L1177F	ENST00000374080		1177	Ctt/Ttt	25/45	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.728133254423712	1		234	333	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260837	16260837	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002490-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	149	278	0	ENST00000375759.3:c.8102del	p.Thr2701ArgfsTer4	p.T2701Rfs*4	ENST00000375759	NM_015001.2	2701	aCg/ag	11/15	1	2	FACETS	0.986	0.91	1	0.986	0.91	1	CLONAL	1	TRUE	1	0.728133254423712	2		278	415	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002492-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	42	422	0				ENST00000310581	NM_198253.2	-/1132			0.601254700153423	3	FACETS	1	0.867	1	0.513	0.434	0.598	CLONAL	1	TRUE	1	0.601254700153423	3		422	177	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266063	41266064	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002492-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	62	516	0	ENST00000349496.5:c.60_61insT	p.Ala21CysfsTer3	p.A21Cfs*3	ENST00000349496	NM_001904.3	20	-/T	3/15	1	2	FACETS	0.446	0.386	0.511	0.446	0.386	0.511	SUBCLONAL	1	TRUE	1	0.601254700153423	2		516	462	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	170	139	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.967	1			1	INDETERMINATE	2	TRUE	NA	0.602740744798269	2		139	272	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121242	29121242	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137853007	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	530	557	1	ENST00000328354.6:c.433C>T	p.Arg145Trp	p.R145W	ENST00000328354	NM_007194.3	145	Cgg/Tgg	3/15	0.602740744798269	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.602740744798269	4		558	1400	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244997	46244997	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs868082376	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	417	574	0	ENST00000334344.6:c.3091C>T	p.Gln1031Ter	p.Q1031*	ENST00000334344	NM_152641.2	1031	Cag/Tag	15/21	0.563195789098457	2	FACETS	0.897	0.862	0.933	0.897	0.862	0.933	CLONAL	2	TRUE	0	0.602740744798269	2		574	771	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12629100	12629100	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	450	434	0	ENST00000251849.4:c.1407G>A	p.Met469Ile	p.M469I	ENST00000251849	NM_002880.3	469	atG/atA	13/17	0.602740744798269	3	FACETS	0.974	0.933	1	0.974	0.933	1	CLONAL	2	TRUE	1	0.602740744798269	3		434	998	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275290	41275290	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs113411271	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	226	376	0	ENST00000349496.5:c.1456C>T	p.Arg486Cys	p.R486C	ENST00000349496	NM_001904.3	486	Cgc/Tgc	9/15	0.602740744798269	3	FACETS	1	0.977	1	0.553	0.516	0.592	CLONAL	1	TRUE	1	0.602740744798269	3		376	882	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102920	71102920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	372	273	0	ENST00000318789.4:c.287C>T	p.Pro96Leu	p.P96L	ENST00000318789	NM_032682.5	96	cCc/cTc	8/21	0.602740744798269	3	FACETS	0.999	0.954	1	0.999	0.954	1	CLONAL	2	TRUE	1	0.602740744798269	3		273	804	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133561	55133561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs958381664	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	100	466	0	ENST00000257290.5:c.865G>A	p.Glu289Lys	p.E289K	ENST00000257290	NM_006206.4	289	Gaa/Aaa	6/23	0.34148991500781	1	FACETS	0.363	0.324	0.404	0.363	0.324	0.404	INDETERMINATE	1	TRUE	0	0.602740744798269	1		466	639	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549725	187549725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199516712	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	67	429	0	ENST00000441802.2:c.4516C>T	p.Arg1506Cys	p.R1506C	ENST00000441802	NM_005245.3	1506	Cgt/Tgt	8/27	1	2	FACETS	0.274	0.237	0.314	0.274	0.237	0.314	SUBCLONAL	1	TRUE	1	0.602740744798269	2		429	811	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631124	176631124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	338	438	0	ENST00000439151.2:c.1067C>T	p.Ser356Phe	p.S356F	ENST00000439151	NM_022455.4	356	tCc/tTc	4/23	0.573312358921155	2	FACETS	0.89	0.851	0.929	0.89	0.851	0.929	CLONAL	2	TRUE	0	0.602740744798269	2		438	630	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180614	32180615	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	373	478	0	ENST00000375023.3:c.2512_2513delinsAT	p.Gly838Ile	p.G838I	ENST00000375023	NM_004557.3	838	GGa/ATa	16/30	0.602740744798269	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.602740744798269	4		478	952	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190371	32190371	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1238773797	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	282	389	0	ENST00000375023.3:c.368C>T	p.Pro123Leu	p.P123L	ENST00000375023	NM_004557.3	123	cCt/cTt	3/30	0.602740744798269	4	FACETS	0.916	0.864	0.969	0.916	0.864	0.969	CLONAL	2	TRUE	2	0.602740744798269	4		389	819	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704527	117704527	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	225	520	0	ENST00000368508.3:c.2449G>A	p.Glu817Lys	p.E817K	ENST00000368508	NM_002944.2	817	Gaa/Aaa	16/43	0.602740744798269	3	FACETS	0.917	0.853	0.982	0.458	0.426	0.491	CLONAL	1	TRUE	1	0.602740744798269	3		520	1060	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959055	2959055	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	83	369	0	ENST00000396946.4:c.2461C>T	p.Pro821Ser	p.P821S	ENST00000396946	NM_032415.4	821	Cct/Tct	18/25	0.333835144580036	3	FACETS	0.525	0.463	0.591	0.175	0.154	0.197	INDETERMINATE	1	TRUE	0	0.602740744798269	3		369	683	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740797	145740797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769553486	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	419	453	0	ENST00000428558.2:c.1303C>T	p.Pro435Ser	p.P435S	ENST00000428558	NM_004260.3	435	Cct/Tct	7/22	0.602740744798269	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	2	0.602740744798269	4		453	1067	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485830	8485830	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367882615	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	556	492	0	ENST00000356435.5:c.2987C>T	p.Ala996Val	p.A996V	ENST00000356435		996	gCt/gTt	17/35	0.532899489181909	3	FACETS	0.916	0.887	0.944	0.916	0.887	0.944	CLONAL	3	TRUE	0	0.602740744798269	3		492	874	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115709	8115709	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	390	413	0	ENST00000346208.3:c.1055G>A	p.Arg352Lys	p.R352K	ENST00000346208		352	aGa/aAa	6/6	0.563712056585297	2	FACETS	0.946	0.908	0.983	0.946	0.908	0.983	CLONAL	2	TRUE	0	0.602740744798269	2		413	684	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202158	67202158	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	172	345	0	ENST00000312629.5:c.1261C>T	p.Pro421Ser	p.P421S	ENST00000312629	NM_003952.2	421	Ccc/Tcc	14/15	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.602740744798269	2		345	563	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870811	12870811	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	265	193	0	ENST00000228872.4:c.38T>A	p.Leu13Gln	p.L13Q	ENST00000228872	NM_004064.3	13	cTg/cAg	1/3	0.401637821376494	4	FACETS	0.983	0.935	1			1	CLONAL	3	TRUE	NA	0.602740744798269	4		193	478	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001405	29001405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	156	349	0	ENST00000282397.4:c.1327C>T	p.Leu443Phe	p.L443F	ENST00000282397	NM_002019.4	443	Ctc/Ttc	10/30	0.185680994945221	3	FACETS	1	0.974	1	0.57	0.524	0.617	INDETERMINATE	1	TRUE	1	0.602740744798269	3		349	591	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858184	9858184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	196	559	0	ENST00000330684.3:c.3217G>A	p.Glu1073Lys	p.E1073K	ENST00000330684	NM_001134407.1	1073	Gaa/Aaa	13/13	1	2	FACETS	0.869	0.807	0.934	0.869	0.807	0.934	CLONAL	1	TRUE	1	0.602740744798269	2		559	748	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041612	14041612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	223	541	0	ENST00000311895.7:c.2159C>T	p.Pro720Leu	p.P720L	ENST00000311895	NM_005236.2	720	cCa/cTa	11/11	1	2	FACETS	0.902	0.842	0.964	0.902	0.842	0.964	CLONAL	1	TRUE	1	0.602740744798269	2		541	820	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29679274	29679274	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	349	422	0	ENST00000356175.3:c.7395-1G>A		p.X2465_splice	ENST00000356175	NM_000267.3	2465			0.533663058525488	2	FACETS	0.857	0.818	0.895	0.857	0.818	0.895	CLONAL	2	TRUE	0	0.602740744798269	2		422	676	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245197	41245197	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55914168	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	252	546	0	ENST00000357654.3:c.2351C>T	p.Ser784Leu	p.S784L	ENST00000357654	NM_007294.3	784	tCg/tTg	10/23	0.585720249086886	2	FACETS	0.98	0.92	1	0.49	0.46	0.522	CLONAL	1	TRUE	0	0.602740744798269	2		546	853	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858236	59858236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	482	538	2	ENST00000259008.2:c.1759C>T	p.His587Tyr	p.H587Y	ENST00000259008	NM_032043.2	587	Cat/Tat	12/20	0.401637821376494	4	FACETS	0.94	0.899	0.981			1	CLONAL	2	TRUE	NA	0.602740744798269	4		540	1364	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2225386	2225386	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	197	472	0	ENST00000398665.3:c.3597-1G>A		p.X1199_splice	ENST00000398665	NM_032482.2	1199			0.303491239176517	4	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.602740744798269	4		472	906	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289973	15289973	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759742938	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	165	474	0	ENST00000263388.2:c.3581C>T	p.Pro1194Leu	p.P1194L	ENST00000263388	NM_000435.2	1194	cCc/cTc	22/33	0.439238358748874	3	FACETS	0.942	0.867	1	0.471	0.433	0.511	CLONAL	1	TRUE	1	0.602740744798269	3		474	756	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292609	15292609	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	247	292	0	ENST00000263388.2:c.2570C>T	p.Pro857Leu	p.P857L	ENST00000263388	NM_000435.2	857	cCa/cTa	17/33	0.439238358748874	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.602740744798269	3		292	506	SUCCESS
AXL	558	MSKCC	GRCh37	19	41736901	41736901	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201799923	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	225	453	0	ENST00000301178.4:c.616G>A	p.Glu206Lys	p.E206K	ENST00000301178	NM_021913.4	206	Gaa/Aaa	5/20	0.602740744798269	3	FACETS	1	0.963	1	0.525	0.489	0.561	CLONAL	1	TRUE	1	0.602740744798269	3		453	926	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873428	45873428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759037835	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	182	443	0	ENST00000391945.4:c.68C>T	p.Ser23Phe	p.S23F	ENST00000391945	NM_000400.3	23	tCc/tTc	2/23	0.602740744798269	3	FACETS	0.938	0.866	1	0.469	0.433	0.506	CLONAL	1	TRUE	1	0.602740744798269	3		443	838	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561151	9561151	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	179	433	0	ENST00000353224.5:c.631G>A	p.Glu211Lys	p.E211K	ENST00000353224	NM_177990.2	211	Gaa/Aaa	4/10	0.602740744798269	3	FACETS	0.917	0.846	0.99	0.458	0.423	0.495	CLONAL	1	TRUE	1	0.602740744798269	3		433	843	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561504	9561504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542553062	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	167	411	0	ENST00000353224.5:c.278C>T	p.Ser93Leu	p.S93L	ENST00000353224	NM_177990.2	93	tCg/tTg	4/10	0.602740744798269	3	FACETS	0.865	0.795	0.937	0.432	0.397	0.469	CLONAL	1	TRUE	1	0.602740744798269	3		411	834	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306721	41306721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	187	416	0	ENST00000373198.4:c.938C>T	p.Ser313Phe	p.S313F	ENST00000373198	NM_133170.3	313	tCc/tTc	7/32	0.412435691821156	3	FACETS	1	0.968	1	0.54	0.5	0.581	CLONAL	1	TRUE	1	0.602740744798269	3		416	748	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578191	7578192	+	missense_variant	Missense_Mutation	DNP	AG	AG	TA	novel	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	345	515	0	ENST00000269305.4:c.657_658delinsTA	p.Tyr220Asn	p.Y220N	ENST00000269305	NM_001126112.2	219	ccCTat/ccTAat	6/11	0.533663058525488	2	FACETS	0.869	0.83	0.907	0.869	0.83	0.907	CLONAL	2	TRUE	0	0.602740744798269	2		515	659	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142939	7142940	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0002504-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	113	471	0	ENST00000302850.5:c.2429_2430delinsTT	p.Ser810Phe	p.S810F	ENST00000302850	NM_000208.2	810	tCC/tTT	12/22	NA	2	FACETS	0.595	0.537	0.657			1	INDETERMINATE	1	TRUE	NA	0.602740744798269	2		471	630	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002510-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	41	422	0				ENST00000310581	NM_198253.2	-/1132			0.32061498616842	4	FACETS	0.915	0.779	1	0.915	0.779	1	CLONAL	2	TRUE	2	0.502517679602398	4		422	134	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544688	65544696	+	inframe_deletion	In_Frame_Del	DEL	TGTGGTTTT	TGTGGTTTT	-	novel	NA	P-0002510-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	20	433	0	ENST00000358664.4:c.230_238del	p.Lys77_His79del	p.K77_H79del	ENST00000358664	NM_002382.4	77	aAAAACCACAca/aca	4/5	0.416784520239169	2	FACETS	0.246	0.187	0.314	0.123	0.093	0.157	SUBCLONAL	1	TRUE	0	0.502517679602398	2		433	324	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002539-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	43	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.573003059350882	2		422	140	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0002539-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	124	652	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.573003059350882	2		652	371	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002539-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	106	668	0	ENST00000263967.3:c.3132T>A	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaA	21/21	1	2	FACETS	0.958	0.867	1	0.958	0.867	1	CLONAL	1	TRUE	1	0.573003059350882	2		668	386	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37081761	37081761	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002539-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	94	579	0	ENST00000231790.2:c.1643A>T	p.Tyr548Phe	p.Y548F	ENST00000231790	NM_000249.3	548	tAc/tTc	14/19	1	2	FACETS	0.873	0.783	0.967	0.873	0.783	0.967	CLONAL	1	TRUE	1	0.573003059350882	2		579	376	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964152	28964152	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002539-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	27	667	0	ENST00000282397.4:c.1750T>C	p.Tyr584His	p.Y584H	ENST00000282397	NM_002019.4	584	Tac/Cac	13/30	1	2	FACETS	0.251	0.2	0.31	0.251	0.2	0.31	SUBCLONAL	1	TRUE	1	0.573003059350882	2		667	375	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881504	48881504	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002539-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	76	629	0	ENST00000267163.4:c.227del	p.Leu76Ter	p.L76*	ENST00000267163	NM_000321.2	76	Tta/ta	2/27	0.573003059350882	1	FACETS	0.823	0.733	0.916	0.823	0.733	0.916	CLONAL	1	TRUE	0	0.573003059350882	1		629	230	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574030	7574030	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002539-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	107	603	0	ENST00000269305.4:c.997del	p.Arg333ValfsTer12	p.R333Vfs*12	ENST00000269305	NM_001126112.2	333	Cgt/gt	10/11	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.573003059350882	2		603	368	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0002540-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	19	65	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.248	0.187	0.32	0.248	0.187	0.32	SUBCLONAL	1	TRUE	1	0.18	2		65	852	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0002540-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1228	105	535	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.875	0.781	0.975	0.875	0.781	0.975	CLONAL	1	TRUE	1	0.18	2		536	1333	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0002540-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	41	139	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.834	1	1	0.834	1	CLONAL	1	TRUE	1	0.18	2		139	455	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0002540-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	76	472	1	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	1	2	FACETS	0.738	0.645	0.838	0.738	0.645	0.838	SUBCLONAL	1	TRUE	1	0.18	2		473	1145	SUCCESS
APC	324	MSKCC	GRCh37	5	112174086	112174086	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs878853432	NA	P-0002540-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	83	459	0	ENST00000257430.4:c.2795C>G	p.Ser932Ter	p.S932*	ENST00000257430	NM_000038.5	932	tCa/tGa	16/16	1	2	FACETS	0.852	0.749	0.962	0.852	0.749	0.962	CLONAL	1	TRUE	1	0.18	2		459	1083	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463301	463301	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002540-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1358	76	658	0	ENST00000399788.2:c.970A>T	p.Ile324Phe	p.I324F	ENST00000399788	NM_001042603.1	324	Att/Ttt	8/28	0.3	2	FACETS	0.589	0.514	0.67			1	SUBCLONAL	1	TRUE	NA	0.18	2		658	1434	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969417	44969417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370298215	NA	P-0002540-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	118	317	0	ENST00000377967.4:c.4099G>A	p.Gly1367Arg	p.G1367R	ENST00000377967	NM_021140.2	1367	Gga/Aga	28/29	1	1	FACETS	0.782	0.706	0.862	1	0.985	1	SUBCLONAL	2	TRUE	0	0.18	1		317	763	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120252	70120252	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002540-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	104	522	1	ENST00000245479.2:c.1254del	p.Ile418MetfsTer52	p.I418Mfs*52	ENST00000245479	NM_000346.3	418	atC/at	3/3	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.18	2		523	1132	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002546-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	25	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.282761112741991	2		422	146	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610484	81610484	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002546-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	55	484	0	ENST00000298171.2:c.2082C>G	p.Ser694Arg	p.S694R	ENST00000298171	NM_000369.2	694	agC/agG	10/10	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.282761112741991	2		484	344	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546721	9546721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002546-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	46	199	0	ENST00000353224.5:c.1301C>T	p.Ala434Val	p.A434V	ENST00000353224	NM_177990.2	434	gCg/gTg	5/10	0.24409884730206	3	FACETS	1	0.958	1	0.709	0.601	0.825	CLONAL	1	TRUE	1	0.282761112741991	3		199	262	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412045	+	splice_donor_variant	Splice_Site	INS	-	-	A	novel	NA	P-0002546-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	89	327	0	ENST00000397752.3:c.3028+1_3028+2insA		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.263338690948879	2	FACETS	0.853	0.769	0.94	1	0.975	1	CLONAL	3	TRUE	0	0.282761112741991	2		327	246	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002546-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	233	422	0				ENST00000310581	NM_198253.2	-/1132			0.476220582431363	4	FACETS	0.908	0.85	0.967	0.908	0.85	0.967	CLONAL	2	TRUE	2	0.524134540240733	4		422	746	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610484	81610484	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002546-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	364	484	0	ENST00000298171.2:c.2082C>G	p.Ser694Arg	p.S694R	ENST00000298171	NM_000369.2	694	agC/agG	10/10	0.524991679808999	3	FACETS	0.96	0.914	1	0.96	0.914	1	CLONAL	2	TRUE	1	0.524134540240733	3		484	913	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546721	9546721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002546-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	152	199	0	ENST00000353224.5:c.1301C>T	p.Ala434Val	p.A434V	ENST00000353224	NM_177990.2	434	gCg/gTg	5/10	0.318945029833588	6	FACETS	0.977	0.897	1			1	CLONAL	2	TRUE	NA	0.524134540240733	6		199	608	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295353	1295353	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0002546-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	152	366	0				ENST00000310581	NM_198253.2	-/1132			0.476220582431363	4	FACETS	1	0.961	1	0.542	0.496	0.591	CLONAL	1	TRUE	2	0.524134540240733	4		366	815	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13978741	13978741	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0002546-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1291	255	608	0	ENST00000405192.2:c.365+1G>T		p.X122_splice	ENST00000405192	NM_001163147.1	122			0.524134540240733	5	FACETS	1	0.98	1	0.375	0.349	0.401	CLONAL	1	TRUE	2	0.524134540240733	5		608	1546	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412045	116412046	+	splice_donor_variant,intron_variant	Splice_Site	INS	TA	TA	ATG	novel	NA	P-0002546-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	919	875	0	ENST00000397752.3:c.3028+2_3028+3delinsATG		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.512784656338122	3	FACETS	0.944	0.92	0.968	0.944	0.92	0.968	CLONAL	3	TRUE	0	0.524134540240733	3		875	1563	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002572-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	40	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.952	1			1	INDETERMINATE	1	TRUE	NA	0.660796855259256	2		422	94	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0002572-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	289	143	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.978	0.923	1	0.978	0.923	1	CLONAL	1	TRUE	1	0.660796855259256	2		143	894	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0002572-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	189	327	1	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	0.883	0.82	0.948	0.883	0.82	0.948	CLONAL	1	TRUE	1	0.660796855259256	2		328	648	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002575-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	18	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.797	0.638	0.957			1	INDETERMINATE	2	FALSE	NA	0.594550692239331	2		422	38	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095851	178095851	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002575-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	30	583	2	ENST00000397062.3:c.1480C>A	p.Gln494Lys	p.Q494K	ENST00000397062	NM_006164.4	494	Caa/Aaa	5/5	1	2	FACETS	0.682	0.557	0.819	0.682	0.557	0.819	SUBCLONAL	1	FALSE	1	0.594550692239331	2		585	148	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456701	138456701	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002575-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	13	531	0	ENST00000289153.2:c.649A>T	p.Asn217Tyr	p.N217Y	ENST00000289153	NM_006219.2	217	Aat/Tat	4/22	0.603074566432543	3	FACETS	0.502	0.361	0.67	0.251	0.18	0.335	SUBCLONAL	1	FALSE	1	0.594550692239331	3		531	113	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685261	86685261	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002575-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	13	567	1	ENST00000274376.6:c.2977C>G	p.Arg993Gly	p.R993G	ENST00000274376	NM_002890.2	993	Cgt/Ggt	24/25	0.527997765849505	4	FACETS	0.664	0.479	0.885			1	SUBCLONAL	1	FALSE	NA	0.594550692239331	4		568	105	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350094	81350094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1315332617	NA	P-0002575-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	26	626	0	ENST00000222390.5:c.1238C>T	p.Ser413Leu	p.S413L	ENST00000222390	NM_000601.4	413	tCa/tTa	10/18	0.228473359955092	2	FACETS	0.767	0.619	0.93	0.384	0.309	0.465	INDETERMINATE	1	FALSE	0	0.594550692239331	2		626	114	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164543	36164543	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002575-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	112	334	3	ENST00000300305.3:c.1332del	p.Ser445AlafsTer149	p.S445Afs*149	ENST00000300305		444	ccC/cc	8/8	0.594550692239331	8	FACETS	0.988	0.919	1			1	CLONAL	6	FALSE	NA	0.594550692239331	8		337	177	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038563	47038563	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002575-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	11	320	1	ENST00000377604.3:c.724+1G>A		p.X242_splice	ENST00000377604	NM_001204468.1	242			0.138888148547835	2	FACETS	0.881	0.631	1			1	INDETERMINATE	1	FALSE	NA	0.594550692239331	2		321	42	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	104	422	0				ENST00000310581	NM_198253.2	-/1132			0.274981050729473	3	FACETS	0.9	0.81	0.995	0.9	0.81	0.995	CLONAL	2	TRUE	1	0.274981050729473	3		422	478	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660627	190660627	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1426079795	NA	P-0002582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	102	323	0	ENST00000441310.2:c.265A>G	p.Thr89Ala	p.T89A	ENST00000441310	NM_000534.4	89	Act/Gct	3/13	1	2	FACETS	0.756	0.675	0.843	0.756	0.675	0.843	SUBCLONAL	1	TRUE	1	0.274981050729473	2		323	981	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401775	401775	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1380305124	NA	P-0002582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	97	297	0	ENST00000380956.4:c.1097C>T	p.Ser366Leu	p.S366L	ENST00000380956	NM_001195286.1	366	tCa/tTa	7/9	1	2	FACETS	0.836	0.744	0.933	0.836	0.744	0.933	CLONAL	1	TRUE	1	0.274981050729473	2		297	844	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786146	3786146	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1380	178	722	0	ENST00000262367.5:c.4619T>C	p.Phe1540Ser	p.F1540S	ENST00000262367	NM_004380.2	1540	tTt/tCt	28/31	1	2	FACETS	0.831	0.763	0.902	0.831	0.763	0.902	CLONAL	1	TRUE	1	0.274981050729473	2		722	1558	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069315	30069315	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	129	411	2	ENST00000338641.4:c.1180G>T	p.Glu394Ter	p.E394*	ENST00000338641	NM_000268.3	394	Gag/Tag	12/16	0.226858714892225	1	FACETS	0.923	0.836	1	0.923	0.836	1	CLONAL	1	TRUE	0	0.274981050729473	1		413	877	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069345	30069345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	140	417	0	ENST00000338641.4:c.1210G>A	p.Glu404Lys	p.E404K	ENST00000338641	NM_000268.3	404	Gag/Aag	12/16	0.226858714892225	1	FACETS	0.969	0.882	1	0.969	0.882	1	CLONAL	1	TRUE	0	0.274981050729473	1		417	906	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033760	48033762	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs587779300	NA	P-0002582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	53	427	0	ENST00000234420.5:c.3974_3976del	p.Lys1325del	p.K1325del	ENST00000234420	NM_000179.2	1324	gAGAag/gag	9/10	1	2	FACETS	0.421	0.358	0.491	0.421	0.358	0.491	SUBCLONAL	1	TRUE	1	0.274981050729473	2		427	915	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994176	21994194	+	frameshift_variant	Frame_Shift_Del	DEL	CTCCTCAGTAGCATCAGCA	CTCCTCAGTAGCATCAGCA	-	novel	NA	P-0002582-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	122	510	0	ENST00000579755.1:c.137_155del	p.Val46AlafsTer4	p.V46Afs*4	ENST00000579755		46	gTGCTGATGCTACTGAGGAGc/gc	1/3	1		FACETS		0.841	1				CLONAL	1	TRUE	1	0.274981050729473	2		510	953	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002584-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	562	422	0				ENST00000310581	NM_198253.2	-/1132			0.519097999442889	6	FACETS	0.976	0.95	1	1	0.996	1	CLONAL	6	TRUE	1	0.519097999442889	6		422	754	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468236	50468236	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002584-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	126	388	0	ENST00000331340.3:c.1471G>C	p.Glu491Gln	p.E491Q	ENST00000331340	NM_006060.4	491	Gag/Cag	8/8	0.1964325474184	5	FACETS	0.802	0.725	0.884			1	INDETERMINATE	1	TRUE	NA	0.519097999442889	5		388	1076	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380662	118380662	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs782242103	NA	P-0002584-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	223	481	0	ENST00000534358.1:c.10901-1G>C		p.X3634_splice	ENST00000534358	NM_005933.3	3634			1	2	FACETS	0.985	0.919	1	0.985	0.919	1	CLONAL	1	TRUE	1	0.519097999442889	2		481	872	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947585	48947585	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002584-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	358	621	0	ENST00000267163.4:c.1172C>A	p.Ser391Ter	p.S391*	ENST00000267163	NM_000321.2	391	tCa/tAa	12/27	0.298223535279865	1	FACETS	1	0.995	1	1	0.995	1	INDETERMINATE	1	TRUE	0	0.519097999442889	1		621	738	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916574	39916574	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002584-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	34	244	0	ENST00000378444.4:c.4429G>C	p.Glu1477Gln	p.E1477Q	ENST00000378444	NM_001123385.1	1477	Gaa/Caa	11/15	1	1	FACETS	0.181	0.148	0.219	0.181	0.148	0.219	SUBCLONAL	1	TRUE	0	0.519097999442889	1		244	535	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040620	47040620	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002584-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	310	259	0	ENST00000377604.3:c.1255C>T	p.Gln419Ter	p.Q419*	ENST00000377604	NM_001204468.1	419	Caa/Taa	13/24	1	1	FACETS	0.935	0.897	0.972	1	0.996	1	CLONAL	2	TRUE	0	0.519097999442889	1		259	473	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107147	27107154	+	frameshift_variant	Frame_Shift_Del	DEL	TGTACGAA	TGTACGAA	-	novel	NA	P-0002584-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	222	281	0	ENST00000324856.7:c.6759_6766del	p.Tyr2254ThrfsTer21	p.Y2254Tfs*21	ENST00000324856	NM_006015.4	2253	cTGTACGAA/c	20/20	0.212401683145081	1	FACETS	1	0.941	1	1	0.941	1	INDETERMINATE	1	TRUE	0	0.519097999442889	1		281	630	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579408	7579460	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTG	CAGGGGCCAGGAGGGGGCTGGTGCAGGGGCCGCCGGTGTAGGAGCTGCTGGTG	-	rs1555526610	NA	P-0002584-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	477	399	0	ENST00000269305.4:c.227_279del	p.Ala76ValfsTer55	p.A76Vfs*55	ENST00000269305	NM_001126112.2	76	gCACCAGCAGCTCCTACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTG/g	4/11	0.519097999442889	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.519097999442889	2		399	870	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002585-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	12	422	0				ENST00000310581	NM_198253.2	-/1132			0.598710369569053	1	FACETS	0.511	0.375	0.662	0.511	0.375	0.662	SUBCLONAL	1	TRUE	0	0.763553865805697	1		422	38	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876658468	NA	P-0002585-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	107	562	0	ENST00000269305.4:c.577C>A	p.His193Asn	p.H193N	ENST00000269305	NM_001126112.2	193	Cat/Aat	6/11	0.744272337093311	2	FACETS	0.922	0.863	0.978	0.922	0.863	0.978	CLONAL	2	TRUE	0	0.763553865805697	2		562	152	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753987	57753988	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0002585-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	74	444	0	ENST00000274289.3:c.636dup	p.Ile213TyrfsTer2	p.I213Yfs*2	ENST00000274289	NM_006622.3	212	-/T	5/14	NA	2	FACETS	0.71	0.629	0.795			1	INDETERMINATE	1	TRUE	NA	0.763553865805697	2		444	273	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002586-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	379	422	0				ENST00000310581	NM_198253.2	-/1132			0.675364029437314	6	FACETS	1	0.976	1	1	0.976	1	CLONAL	4	TRUE	2	0.675364029437314	6		422	645	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0002586-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	415	295	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.539002413748123	6	FACETS	0.968	0.93	1	1	0.995	1	CLONAL	4	TRUE	3	0.675364029437314	6		295	746	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868193	37868193	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002586-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	905	438	0	ENST00000269571.5:c.914C>G	p.Ser305Cys	p.S305C	ENST00000269571		305	tCt/tGt	8/27	0.63732856624561	5	FACETS	1	0.991	1			1	CLONAL	3	TRUE	NA	0.675364029437314	5		438	1726	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0002586-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	725	536	0	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.675364029437314	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.675364029437314	2		536	967	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934801	9934801	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002586-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	364	621	1	ENST00000330684.3:c.1489A>T	p.Ile497Phe	p.I497F	ENST00000330684	NM_001134407.1	497	Atc/Ttc	6/13	1	2	FACETS	0.981	0.931	1	0.981	0.931	1	CLONAL	1	TRUE	1	0.675364029437314	2		622	1099	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650748	67650748	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002586-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	370	483	0	ENST00000264010.4:c.1053C>G	p.Phe351Leu	p.F351L	ENST00000264010	NM_006565.3	351	ttC/ttG	5/12	0.675364029437314	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.675364029437314	1		483	635	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701051	29701051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002586-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	659	368	0	ENST00000356175.3:c.8335G>A	p.Glu2779Lys	p.E2779K	ENST00000356175	NM_000267.3	2779	Gaa/Aaa	57/57	0.675364029437314	4	FACETS	0.834	0.807	0.862			1	CLONAL	3	TRUE	NA	0.675364029437314	4		368	1306	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224510	123224511	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0002586-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	622	352	2	ENST00000218089.9:c.3364dup	p.Thr1122AsnfsTer14	p.T1122Nfs*14	ENST00000218089	NM_001042749.1	1121	-/A	31/35	0.57403258556421	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.675364029437314	2		354	795	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002602-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	40	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.902	1			1	INDETERMINATE	4	TRUE	NA	0.2100969581401	2		422	90	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0002602-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	187	318	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.146185752512059	4	FACETS	1	0.974	1	1	0.992	1	CLONAL	3	TRUE	2	0.2100969581401	4		318	649	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044475	47044476	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGGCC	novel	NA	P-0002602-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	158	285	0	ENST00000377604.3:c.1973_1977dup	p.Arg660GlyfsTer46	p.R660Gfs*46	ENST00000377604	NM_001204468.1	658	tgg/tGGGCCgg	18/24	1	2	FACETS	1	0.943	1	1	0.994	1	CLONAL	3	TRUE	1	0.2100969581401	2		285	489	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002606-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	39	422	0				ENST00000310581	NM_198253.2	-/1132			0.17167923206432	3	FACETS	1	0.906	1			1	INDETERMINATE	1	TRUE	NA	0.673497189879519	3		422	140	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644467	18644467	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002606-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	91	273	0	ENST00000266497.5:c.2645T>C	p.Leu882Pro	p.L882P	ENST00000266497		882	cTa/cCa	18/31	0.11630752147996	1	FACETS	0.396	0.353	0.441	0.396	0.353	0.441	INDETERMINATE	1	TRUE	0	0.673497189879519	1		273	453	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579356	7579356	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002606-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	128	208	1	ENST00000269305.4:c.331C>A	p.Leu111Met	p.L111M	ENST00000269305	NM_001126112.2	111	Ctg/Atg	4/11	0.673497189879519	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.673497189879519	1		209	219	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117932	70117932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002606-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	140	122	0	ENST00000245479.2:c.400G>A	p.Glu134Lys	p.E134K	ENST00000245479	NM_000346.3	134	Gag/Aag	1/3	0.503453307967552	3	FACETS	0.992	0.922	1	0.992	0.922	1	CLONAL	2	TRUE	1	0.673497189879519	3		122	280	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165077	47165078	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0002606-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	270	248	0	ENST00000409792.3:c.1048_1049del	p.Asp350PhefsTer2	p.D350Ffs*2	ENST00000409792	NM_014159.6	350	GAt/t	3/21	0.442625223540297	4	FACETS	0.87	0.82	0.921	0.87	0.82	0.921	CLONAL	2	TRUE	2	0.673497189879519	4		248	771	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720654	89720654	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002606-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	66	51	0	ENST00000371953.3:c.808del	p.Met270CysfsTer6	p.M270Cfs*6	ENST00000371953	NM_000314.4	269	Aaa/aa	8/9	0.673497189879519	2	FACETS	1	0.977	1	0.715	0.641	0.79	CLONAL	1	TRUE	0	0.673497189879519	2		51	137	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934151	48934152	+	splice_acceptor_variant	Splice_Site	INS	-	-	G	novel	NA	P-0002606-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	193	173	0	ENST00000267163.4:c.610dup		p.X204_splice	ENST00000267163	NM_000321.2	204			0.673497189879519	2	FACETS	0.907	0.858	0.955	0.907	0.858	0.955	CLONAL	2	TRUE	0	0.673497189879519	2		173	316	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002607-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	111	422	0				ENST00000310581	NM_198253.2	-/1132			0.421421661987922	4	FACETS	1	0.946	1	1	0.946	1	CLONAL	3	TRUE	1	0.421421661987922	4		422	240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577085	+	missense_variant	Missense_Mutation	ONP	CCTC	CCTC	TCTT	novel	NA	P-0002607-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	301	318	0	ENST00000269305.4:c.853_856delinsAAGA	p.Glu285_Glu286delinsLysLys	p.E285_E286delinsKK	ENST00000269305	NM_001126112.2	285	GAGGaa/AAGAaa	8/11	0.335317976962407	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.421421661987922	2		318	661	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162688915	162688915	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002607-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	208	251	1	ENST00000367921.3:c.62C>T	p.Ala21Val	p.A21V	ENST00000367921	NM_006182.2	21	gCa/gTa	3/18	0.334639782453198	3	FACETS	0.813	0.757	0.87	0.813	0.757	0.87	CLONAL	2	TRUE	1	0.421421661987922	3		252	735	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947603	48947603	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002607-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	148	265	0	ENST00000267163.4:c.1190C>A	p.Ser397Ter	p.S397*	ENST00000267163	NM_000321.2	397	tCa/tAa	12/27	0.421421661987922	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.421421661987922	1		265	522	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947618	48947618	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002607-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	134	254	0	ENST00000267163.4:c.1205C>A	p.Ser402Tyr	p.S402Y	ENST00000267163	NM_000321.2	402	tCc/tAc	12/27	0.421421661987922	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.421421661987922	1		254	479	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846065	68846065	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002607-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	154	370	0	ENST00000261769.5:c.1036C>T	p.Gln346Ter	p.Q346*	ENST00000261769	NM_004360.3	346	Caa/Taa	8/16	0.421421661987922	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.421421661987922	1		370	535	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846080	68846080	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555515726	NA	P-0002607-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	158	364	0	ENST00000261769.5:c.1051C>T	p.Gln351Ter	p.Q351*	ENST00000261769	NM_004360.3	351	Caa/Taa	8/16	0.421421661987922	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.421421661987922	1		364	529	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846146	68846146	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002607-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	151	278	0	ENST00000261769.5:c.1117C>G	p.Pro373Ala	p.P373A	ENST00000261769	NM_004360.3	373	Ccg/Gcg	8/16	0.421421661987922	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.421421661987922	1		278	472	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002610-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	107	422	0				ENST00000310581	NM_198253.2	-/1132			0.406527373972903	5	FACETS	0.999	0.919	1	0.999	0.919	1	CLONAL	4	TRUE	1	0.406527373972903	5		422	212	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143260	24143260	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002610-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	106	481	0	ENST00000263121.7:c.496del	p.Leu166PhefsTer10	p.L166Ffs*10	ENST00000263121	NM_003073.3	164	ttC/tt	4/9	0.371129871729677	1	FACETS	0.784	0.705	0.867	0.784	0.705	0.867	SUBCLONAL	1	TRUE	0	0.406527373972903	1		481	530	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204513805	204513805	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002610-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	62	189	0	ENST00000367182.3:c.815A>T	p.Asp272Val	p.D272V	ENST00000367182	NM_001278516.1	272	gAc/gTc	9/11	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.406527373972903	2		189	296	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168537	56168537	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002610-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	135	240	0	ENST00000399503.3:c.1493A>G	p.His498Arg	p.H498R	ENST00000399503	NM_005921.1	498	cAt/cGt	8/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.406527373972903	2		240	631	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045997	47045997	+	stop_lost	Nonstop_Mutation	SNP	G	G	T	novel	NA	P-0002610-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	78	109	0	ENST00000377604.3:c.2792G>T	p.Ter931LeuextTer43	p.*931Lext*43	ENST00000377604	NM_001204468.1	931	tGa/tTa	24/24	1	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.406527373972903	1		109	210	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002613-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	19	422	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		422	184	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002638-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	119	422	0				ENST00000310581	NM_198253.2	-/1132			0.300912220224177	1	FACETS	0.433	0.396	0.471	0.433	0.396	0.471	INDETERMINATE	1	FALSE	0	0.907399396276596	1		422	331	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0002638-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	371	462	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.951	0.907	0.995	0.951	0.907	0.995	CLONAL	1	FALSE	1	0.907399396276596	2		462	860	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030479	49030479	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0002638-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	773	286	0	ENST00000267163.4:c.1954A>T	p.Lys652Ter	p.K652*	ENST00000267163	NM_000321.2	652	Aaa/Taa	19/27	0.906709329161698	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	FALSE	0	0.907399396276596	2		286	838	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3828011	3828011	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0002638-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	89	319	0	ENST00000262367.5:c.2113+1G>C		p.X705_splice	ENST00000262367	NM_004380.2	705			1	2	FACETS	0.209	0.185	0.235	0.209	0.185	0.235	SUBCLONAL	1	FALSE	1	0.907399396276596	2		319	938	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717730	89717731	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002638-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	425	272	0	ENST00000371953.3:c.756dup	p.Ile253TyrfsTer45	p.I253Yfs*45	ENST00000371953	NM_000314.4	252	gat/gaTt	7/9	0.907399396276596	1	FACETS	0.958	0.932	0.983	0.958	0.932	0.983	CLONAL	1	FALSE	0	0.907399396276596	1		272	534	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438317	110438322	+	inframe_deletion	In_Frame_Del	DEL	GTTGTT	GTTGTT	-	rs532810290	NA	P-0002638-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	137	48	0	ENST00000375856.3:c.79_84del	p.Asn27_Asn28del	p.N27_N28del	ENST00000375856	NM_003749.2	27	AACAAC/-	1/2	0.906709329161698	2	FACETS	1	0.99	1	0.716	0.672	0.758	CLONAL	1	FALSE	0	0.907399396276596	2		48	211	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576925	7576926	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	GCTA	novel	NA	P-0002638-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	356	265	0	ENST00000269305.4:c.920-3_920dup	p.Leu308SerfsTer30	p.L308Sfs*30	ENST00000269305	NM_001126112.2	307	gca/gcTAGCa	9/11	1	2	FACETS	0.87	0.827	0.913	0.87	0.827	0.913	CLONAL	1	FALSE	1	0.907399396276596	2		265	902	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002642-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	53	422	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	0.619	0.542	0.698	0.619	0.542	0.698	INDETERMINATE	1	TRUE	0	0.78	1		422	134	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0002642-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	151	142	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.78	2		142	386	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0002642-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	299	305	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	0.934	0.883	0.985	0.934	0.883	0.985	CLONAL	1	TRUE	1	0.78	2		305	821	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692851	89692851	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121909230	NA	P-0002642-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	87	101	0	ENST00000371953.3:c.335T>C	p.Leu112Pro	p.L112P	ENST00000371953	NM_000314.4	112	cTa/cCa	5/9	1	2	FACETS	0.978	0.882	1	0.978	0.882	1	CLONAL	1	TRUE	1	0.78	2		101	228	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002647-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	126	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.890647644894649	2		422	276	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584663	187584663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002647-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	430	494	0	ENST00000441802.2:c.3370G>A	p.Glu1124Lys	p.E1124K	ENST00000441802	NM_005245.3	1124	Gag/Aag	3/27	0.885898268361803	1	FACETS	0.538	0.514	0.561	0.538	0.514	0.561	SUBCLONAL	1	TRUE	0	0.890647644894649	1		494	996	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0002647-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2101	12808	392	3	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.890647644894649	32	FACETS	0.989	0.985	0.994			1	CLONAL	28	TRUE	NA	0.890647644894649	32		395	14909	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720802	89720802	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002647-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	113	128	0	ENST00000371953.3:c.953T>C	p.Leu318Pro	p.L318P	ENST00000371953	NM_000314.4	318	cTt/cCt	8/9	0.890647644894649	1	FACETS	0.945	0.891	0.994	0.945	0.891	0.994	CLONAL	1	TRUE	0	0.890647644894649	1		128	149	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	15	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.732	1	1	0.732	1	CLONAL	1	FALSE	1	0.110957727256736	2		422	270	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0002659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	41	295	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.867	1	1	0.97	1	CLONAL	2	FALSE	1	0.110957727256736	2		295	354	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0002659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	89	400	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.110957727256736	2	FACETS	0.976	0.864	1	0.976	0.864	1	CLONAL	2	FALSE	0	0.110957727256736	2		400	822	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11168326	11168326	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	29	287	0	ENST00000361445.4:c.7546G>A	p.Asp2516Asn	p.D2516N	ENST00000361445	NM_004958.3	2516	Gat/Aat	57/58	1	2	FACETS	0.956	0.765	1	0.956	0.765	1	CLONAL	1	FALSE	1	0.110957727256736	2		287	547	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645469	215645469	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	45	414	0	ENST00000260947.4:c.1129G>C	p.Gly377Arg	p.G377R	ENST00000260947	NM_000465.2	377	Ggg/Cgg	4/11	1	2	FACETS	1	0.842	1	1	0.842	1	CLONAL	1	FALSE	1	0.110957727256736	2		414	807	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620683	52620683	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	23	190	0	ENST00000394830.3:c.3070G>C	p.Glu1024Gln	p.E1024Q	ENST00000394830	NM_018313.4	1024	Gaa/Caa	21/30	0.0876984303462967	1	FACETS	0.866	0.674	1	0.866	0.674	1	CLONAL	1	FALSE	0	0.110957727256736	1		190	452	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938804	178938804	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	18	102	0	ENST00000263967.3:c.2046G>C	p.Gln682His	p.Q682H	ENST00000263967	NM_006218.2	682	caG/caC	14/21	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	FALSE	1	0.110957727256736	2		102	219	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230801	66230801	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	62	376	0	ENST00000273854.3:c.2170G>A	p.Glu724Lys	p.E724K	ENST00000273854	NM_004439.5	724	Gaa/Aaa	12/18	0.0876984303462967	1	FACETS	0.791	0.683	0.909	1	0.972	1	CLONAL	2	FALSE	0	0.110957727256736	1		376	667	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709505	176709505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	56	379	0	ENST00000439151.2:c.5932G>A	p.Glu1978Lys	p.E1978K	ENST00000439151	NM_022455.4	1978	Gaa/Aaa	19/23	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	FALSE	1	0.110957727256736	2		379	925	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974227	2974227	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	46	312	0	ENST00000396946.4:c.1378C>G	p.Gln460Glu	p.Q460E	ENST00000396946	NM_032415.4	460	Cag/Gag	10/25	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	FALSE	1	0.110957727256736	2		312	667	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467780	50467780	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760454379	NA	P-0002659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	30	288	0	ENST00000331340.3:c.1015G>A	p.Glu339Lys	p.E339K	ENST00000331340	NM_006060.4	339	Gag/Aag	8/8	1	2	FACETS	0.945	0.76	1	0.945	0.76	1	CLONAL	1	FALSE	1	0.110957727256736	2		288	572	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224268	55224268	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	61	389	0	ENST00000275493.2:c.1049C>G	p.Ser350Cys	p.S350C	ENST00000275493	NM_005228.3	350	tCc/tGc	9/28	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.110957727256736	2		389	817	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737576	145737576	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	35	323	0	ENST00000428558.2:c.3187G>C	p.Glu1063Gln	p.E1063Q	ENST00000428558	NM_004260.3	1063	Gag/Cag	19/22	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	FALSE	1	0.110957727256736	2		323	580	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124579	108124579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	58	318	0	ENST00000278616.4:c.1937C>T	p.Ser646Leu	p.S646L	ENST00000278616	NM_000051.3	646	tCa/tTa	13/63	0.0726641300033111	4	FACETS	0.775	0.665	0.896	0.775	0.665	0.896	SUBCLONAL	2	FALSE	2	0.110957727256736	4		318	749	SUCCESS
CBL	867	MSKCC	GRCh37	11	119167702	119167702	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	71	422	0	ENST00000264033.4:c.2111C>G	p.Ser704Cys	p.S704C	ENST00000264033	NM_005188.3	704	tCt/tGt	13/16	0.0726641300033111	4	FACETS	0.751	0.654	0.857	0.751	0.654	0.857	SUBCLONAL	2	FALSE	2	0.110957727256736	4		422	946	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435484	18435484	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs773899061	NA	P-0002659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	38	314	0	ENST00000266497.5:c.469G>C	p.Glu157Gln	p.E157Q	ENST00000266497		157	Gag/Cag	1/31	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	FALSE	1	0.110957727256736	2		314	632	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26928012	26928012	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	67	234	0	ENST00000381527.3:c.451G>C	p.Asp151His	p.D151H	ENST00000381527	NM_001260.1	151	Gat/Cat	4/13	0.110957727256736	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	2	FALSE	0	0.110957727256736	2		234	598	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039161	49039161	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	78	209	0	ENST00000267163.4:c.2239G>T	p.Glu747Ter	p.E747*	ENST00000267163	NM_000321.2	747	Gag/Tag	22/27	0.110957727256736	2	FACETS	0.876	0.771	0.988	1	0.968	1	CLONAL	3	FALSE	0	0.110957727256736	2		209	535	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213924	2213924	+	start_lost	Translation_Start_Site	SNP	G	G	A	rs373677359	NA	P-0002659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	47	317	0	ENST00000326181.6:c.3G>A	p.Met1?	p.M1?	ENST00000326181	NM_032271.2	1	atG/atA	2/21	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	FALSE	1	0.110957727256736	2		317	696	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973811	15973811	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0002659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	70	248	0	ENST00000268712.3:c.4181C>G	p.Ser1394Ter	p.S1394*	ENST00000268712	NM_006311.3	1394	tCa/tGa	31/46	0.110957727256736	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	2	FALSE	0	0.110957727256736	2		248	613	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243673	41243673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	89	378	0	ENST00000357654.3:c.3875C>T	p.Ser1292Phe	p.S1292F	ENST00000357654	NM_007294.3	1292	tCt/tTt	10/23	0.0726641300033111	4	FACETS	1	0.918	1	1	0.918	1	CLONAL	2	FALSE	2	0.110957727256736	4		378	852	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59861650	59861650	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs864622208	NA	P-0002659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	58	354	0	ENST00000259008.2:c.1609C>G	p.Leu537Val	p.L537V	ENST00000259008	NM_032043.2	537	Ctt/Gtt	11/20	0.0726641300033111	4	FACETS	1	0.916	1	0.551	0.472	0.638	CLONAL	1	FALSE	2	0.110957727256736	4		354	1054	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113718	11113718	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs781285718	NA	P-0002659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	35	327	0	ENST00000358026.2:c.1826C>G	p.Thr609Ser	p.T609S	ENST00000358026	NM_001128849.1	609	aCc/aGc	12/36	0.0876984303462967	1	FACETS	0.953	0.78	1	0.953	0.78	1	CLONAL	1	FALSE	0	0.110957727256736	1		327	625	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793358	42793358	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	29	290	0	ENST00000575354.2:c.1160C>G	p.Ser387Cys	p.S387C	ENST00000575354	NM_015125.3	387	tCt/tGt	8/20	0.0876984303462967	1	FACETS	0.921	0.738	1	0.921	0.738	1	CLONAL	1	FALSE	0	0.110957727256736	1		290	536	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40709551	40709551	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	44	437	0	ENST00000373198.4:c.4351G>C	p.Glu1451Gln	p.E1451Q	ENST00000373198	NM_133170.3	1451	Gag/Cag	32/32	0.0876984303462967	1	FACETS	0.903	0.755	1	0.903	0.755	1	CLONAL	1	FALSE	0	0.110957727256736	1		437	830	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185061	123185061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002659-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	41	231	0	ENST00000218089.9:c.1108C>T	p.Arg370Trp	p.R370W	ENST00000218089	NM_001042749.1	370	Cgg/Tgg	12/35	1	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	FALSE	0	0.110957727256736	1		231	525	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002668-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	138	422	0				ENST00000310581	NM_198253.2	-/1132			0.752127328821756	4	FACETS	0.845	0.789	0.9	1	0.987	1	CLONAL	3	TRUE	2	0.836421827662831	4		422	239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540652	NA	P-0002668-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	674	305	0	ENST00000269305.4:c.743G>C	p.Arg248Pro	p.R248P	ENST00000269305	NM_001126112.2	248	cGg/cCg	7/11	0.739053542185716	6	FACETS	1	0.995	1			1	CLONAL	6	TRUE	NA	0.836421827662831	6		305	709	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099981	27099981	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002668-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	105	342	0	ENST00000324856.7:c.3860G>C	p.Arg1287Thr	p.R1287T	ENST00000324856	NM_006015.4	1287	aGa/aCa	15/20	0.268202923539918	4	FACETS	1	0.967	1	0.292	0.263	0.322	INDETERMINATE	1	TRUE	0	0.836421827662831	4		342	395	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067192	37067192	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201673334	NA	P-0002668-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	238	342	0	ENST00000231790.2:c.1103C>T	p.Ser368Leu	p.S368L	ENST00000231790	NM_000249.3	368	tCg/tTg	12/19	0.147365710206383	4	FACETS	0.874	0.822	0.926	0.874	0.822	0.926	INDETERMINATE	2	TRUE	2	0.836421827662831	4		342	598	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981514	55981514	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002668-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	164	341	0	ENST00000263923.4:c.423C>G	p.Asn141Lys	p.N141K	ENST00000263923	NM_002253.2	141	aaC/aaG	4/30	0.739601459155275	3	FACETS	0.956	0.882	1	0.478	0.441	0.516	CLONAL	1	TRUE	1	0.836421827662831	3		341	582	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149982921	149982921	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1357303862	NA	P-0002668-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	205	320	0	ENST00000253339.5:c.3337G>A	p.Glu1113Lys	p.E1113K	ENST00000253339		1113	Gaa/Aaa	7/7	0.823329845160279	4	FACETS	1	0.958	1	0.261	0.242	0.28	CLONAL	1	TRUE	0	0.836421827662831	4		320	863	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090868	5090868	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002668-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1434	148	241	0	ENST00000381652.3:c.3016G>C	p.Glu1006Gln	p.E1006Q	ENST00000381652	NM_004972.3	1006	Gaa/Caa	22/25	0.836421827662831	9	FACETS	0.879	0.799	0.962			1	CLONAL	1	TRUE	NA	0.836421827662831	9		241	1582	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426544	49426544	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555188379	NA	P-0002668-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	493	427	0	ENST00000301067.7:c.11944C>T	p.Arg3982Ter	p.R3982*	ENST00000301067	NM_003482.3	3982	Cga/Tga	39/54	0.786778286055902	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	1	0.836421827662831	4		427	712	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941720	48941720	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002668-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	445	215	0	ENST00000267163.4:c.1030C>T	p.Gln344Ter	p.Q344*	ENST00000267163	NM_000321.2	344	Cag/Tag	10/27	0.836421827662831	4	FACETS	0.977	0.958	0.995	0.977	0.958	0.995	CLONAL	4	TRUE	0	0.836421827662831	4		215	500	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831241	3831241	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0002668-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	162	305	0	ENST00000262367.5:c.1640C>G	p.Ser547Ter	p.S547*	ENST00000262367	NM_004380.2	547	tCa/tGa	7/31	0.836421827662831	1	FACETS	0.997	0.946	1	0.997	0.946	1	CLONAL	1	TRUE	0	0.836421827662831	1		305	226	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427975	49427975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	197	428	0	ENST00000301067.7:c.10615C>T	p.Arg3539Trp	p.R3539W	ENST00000301067	NM_003482.3	3539	Cgg/Tgg	38/54	0.576544238622981	3	FACETS	0.939	0.869	1	0.469	0.434	0.505	CLONAL	1	TRUE	1	0.576544238622981	3		428	938	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29552144	29552144	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	182	369	1	ENST00000356175.3:c.1882del	p.Tyr628ThrfsTer3	p.Y628Tfs*3	ENST00000356175	NM_000267.3	626	cTt/ct	17/57	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.576544238622981	2		370	562	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344185	118344186	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs782297546	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	163	406	2	ENST00000534358.1:c.2318dup	p.Ser774ValfsTer12	p.S774Vfs*12	ENST00000534358	NM_005933.3	771	acc/aCcc	3/36	1	2	FACETS	0.916	0.845	0.991	0.916	0.845	0.991	CLONAL	1	TRUE	1	0.576544238622981	2		408	617	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692887	89692887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660535	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	21	197	0	ENST00000371953.3:c.371G>A	p.Cys124Tyr	p.C124Y	ENST00000371953	NM_000314.4	124	tGt/tAt	5/9	1	2	FACETS	0.231	0.177	0.293	0.231	0.177	0.293	SUBCLONAL	1	TRUE	1	0.576544238622981	2		197	316	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407575	407575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748516736	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	228	410	0	ENST00000380956.4:c.1333C>T	p.Arg445Cys	p.R445C	ENST00000380956	NM_001195286.1	445	Cgc/Tgc	9/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.576544238622981	2		410	746	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784393	9784393	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	199	375	0	ENST00000377346.4:c.2778C>A	p.Asn926Lys	p.N926K	ENST00000377346	NM_005026.3	926	aaC/aaA	22/24	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.576544238622981	2		375	640	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843595	156843595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139875058	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	231	461	0	ENST00000524377.1:c.1021G>A	p.Val341Met	p.V341M	ENST00000524377	NM_002529.3	341	Gtg/Atg	8/17	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.576544238622981	2		461	734	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467037	25467037	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	122	326	0	ENST00000264709.3:c.1838A>T	p.His613Leu	p.H613L	ENST00000264709	NM_175629.2	613	cAc/cTc	15/23	1	2	FACETS	0.858	0.78	0.94	0.858	0.78	0.94	CLONAL	1	TRUE	1	0.576544238622981	2		326	493	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022268	26022268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	222	459	1	ENST00000435504.4:c.389G>A	p.Arg130Lys	p.R130K	ENST00000435504		130	aGg/aAg	5/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.576544238622981	2		460	671	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660972	227660972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773580430	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	41	365	0	ENST00000305123.5:c.2483G>A	p.Ser828Asn	p.S828N	ENST00000305123	NM_005544.2	828	aGc/aAc	1/2	1	2	FACETS	0.254	0.211	0.302	0.254	0.211	0.302	SUBCLONAL	1	TRUE	1	0.576544238622981	2		365	559	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412913	49412913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	241	436	0	ENST00000418115.1:c.110C>T	p.Thr37Ile	p.T37I	ENST00000418115	NM_001664.2	37	aCa/aTa	2/5	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.576544238622981	2		436	816	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441246	52441246	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	31	352	1	ENST00000460680.1:c.524C>A	p.Pro175His	p.P175H	ENST00000460680	NM_004656.3	175	cCt/cAt	7/17	1	2	FACETS	0.191	0.153	0.233	0.191	0.153	0.233	SUBCLONAL	1	TRUE	1	0.576544238622981	2		353	564	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259497	89259497	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	175	356	0	ENST00000336596.2:c.641A>G	p.Asp214Gly	p.D214G	ENST00000336596	NM_005233.5	214	gAc/gGc	3/17	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.576544238622981	2		356	485	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161339	185161339	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	161	414	0	ENST00000265026.3:c.766C>A	p.Leu256Ile	p.L256I	ENST00000265026	NM_004721.4	256	Cta/Ata	4/14	1	2	FACETS	0.805	0.74	0.872	0.805	0.74	0.872	CLONAL	1	TRUE	1	0.576544238622981	2		414	694	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151595	55151595	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	194	422	0	ENST00000257290.5:c.2381A>T	p.Asp794Val	p.D794V	ENST00000257290	NM_006206.4	794	gAt/gTt	17/23	1	2	FACETS	0.945	0.878	1	0.945	0.878	1	CLONAL	1	TRUE	1	0.576544238622981	2		422	712	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564731	55564731	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	125	270	0	ENST00000288135.5:c.619G>T	p.Ala207Ser	p.A207S	ENST00000288135	NM_000222.2	207	Gcc/Tcc	3/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.576544238622981	2		270	410	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981203	55981203	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	128	326	0	ENST00000263923.4:c.496C>T	p.Pro166Ser	p.P166S	ENST00000263923	NM_002253.2	166	Cca/Tca	5/30	1	2	FACETS	0.839	0.764	0.917	0.839	0.764	0.917	CLONAL	1	TRUE	1	0.576544238622981	2		326	529	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193857	106193857	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1157107314	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	28	346	0	ENST00000380013.4:c.4319G>A	p.Arg1440Gln	p.R1440Q	ENST00000380013	NM_001127208.2	1440	cGg/cAg	10/11	1	2	FACETS	0.189	0.151	0.234	0.189	0.151	0.234	SUBCLONAL	1	TRUE	1	0.576544238622981	2		346	513	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557879	187557879	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767041778	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	213	469	0	ENST00000441802.2:c.3832G>A	p.Asp1278Asn	p.D1278N	ENST00000441802	NM_005245.3	1278	Gac/Aac	5/27	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.576544238622981	2		469	693	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260664	1260664	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	201	373	0	ENST00000310581.5:c.2895G>T	p.Lys965Asn	p.K965N	ENST00000310581	NM_198253.2	965	aaG/aaT	12/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.576544238622981	2		373	643	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923636	131923636	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	110	288	0	ENST00000265335.6:c.906G>T	p.Glu302Asp	p.E302D	ENST00000265335		302	gaG/gaT	7/25	1	2	FACETS	0.875	0.792	0.962	0.875	0.792	0.962	CLONAL	1	TRUE	1	0.576544238622981	2		288	436	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187516	32187516	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	145	276	0	ENST00000375023.3:c.1363A>C	p.Thr455Pro	p.T455P	ENST00000375023	NM_004557.3	455	Act/Cct	8/30	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.576544238622981	2		276	416	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138608	37138608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	165	384	0	ENST00000373509.5:c.142G>A	p.Gly48Ser	p.G48S	ENST00000373509	NM_002648.3	48	Ggc/Agc	2/6	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.576544238622981	2		384	484	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903728	41903728	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	185	351	0	ENST00000372991.4:c.829G>T	p.Gly277Trp	p.G277W	ENST00000372991	NM_001760.3	277	Ggg/Tgg	5/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.576544238622981	2		351	566	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023045	150023045	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1175780468	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	222	445	0	ENST00000253339.5:c.218C>T	p.Thr73Met	p.T73M	ENST00000253339		73	aCg/aTg	1/7	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.576544238622981	2		445	713	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157222585	157222585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	215	355	0	ENST00000346085.5:c.1852C>T	p.Pro618Ser	p.P618S	ENST00000346085	NM_020732.3	618	Ccg/Tcg	4/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.576544238622981	2		355	620	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367344	50367344	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1264440159	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	156	191	0	ENST00000331340.3:c.151A>G	p.Arg51Gly	p.R51G	ENST00000331340	NM_006060.4	51	Aga/Gga	3/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.576544238622981	2		191	439	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285764	87285764	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759206123	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	200	441	0	ENST00000277120.3:c.101C>T	p.Thr34Met	p.T34M	ENST00000277120		34	aCg/aTg	2/19	1	2	FACETS	0.993	0.923	1	0.993	0.923	1	CLONAL	1	TRUE	1	0.576544238622981	2		441	699	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93607851	93607851	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	138	379	0	ENST00000375746.1:c.553G>T	p.Gly185Ter	p.G185*	ENST00000375746	NM_001174167.1	185	Gga/Tga	3/14	1	2	FACETS	0.88	0.805	0.958	0.88	0.805	0.958	CLONAL	1	TRUE	1	0.576544238622981	2		379	544	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404214	139404214	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	175	277	0	ENST00000277541.6:c.2940T>A	p.Cys980Ter	p.C980*	ENST00000277541	NM_017617.3	980	tgT/tgA	18/34	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.576544238622981	2		277	556	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741576	17741576	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	126	129	3	ENST00000250003.3:c.247G>A	p.Ala83Thr	p.A83T	ENST00000250003	NM_002478.4	83	Gcg/Acg	1/3	1	2	FACETS	0.772	0.712	0.833	1	0.989	1	SUBCLONAL	2	TRUE	1	0.576544238622981	2		132	283	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102098220	102098220	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	161	287	0	ENST00000282441.5:c.1184A>G	p.Asp395Gly	p.D395G	ENST00000282441	NM_001130145.2	395	gAt/gGt	8/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.576544238622981	2		287	510	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343634	118343634	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	146	283	0	ENST00000534358.1:c.1760C>A	p.Pro587His	p.P587H	ENST00000534358	NM_005933.3	587	cCt/cAt	3/36	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.576544238622981	2		283	495	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344619	118344619	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	206	414	0	ENST00000534358.1:c.2745G>T	p.Lys915Asn	p.K915N	ENST00000534358	NM_005933.3	915	aaG/aaT	3/36	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.576544238622981	2		414	616	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025645	1025645	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	139	316	0	ENST00000358495.3:c.730C>A	p.Leu244Met	p.L244M	ENST00000358495	NM_134424.2	244	Ctg/Atg	9/12	0.546844185593125	2	FACETS	1	0.975	1	0.578	0.531	0.626	CLONAL	1	TRUE	0	0.576544238622981	2		316	417	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4383294	4383294	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs778986120	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	42	342	0	ENST00000261254.3:c.88C>A	p.Leu30Met	p.L30M	ENST00000261254	NM_001759.3	30	Ctg/Atg	1/5	0.546844185593125	2	FACETS	0.286	0.239	0.339	0.143	0.119	0.17	SUBCLONAL	1	TRUE	0	0.576544238622981	2		342	509	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438725	49438725	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	341	333	0	ENST00000301067.7:c.4765G>T	p.Gly1589Cys	p.G1589C	ENST00000301067	NM_003482.3	1589	Ggt/Tgt	19/54	0.576544238622981	3	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	1	0.576544238622981	3		333	762	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929168	32929168	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs431825351	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	294	467	0	ENST00000380152.3:c.7178T>C	p.Met2393Thr	p.M2393T	ENST00000380152		2393	aTg/aCg	14/27	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.576544238622981	2		467	808	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	142	391	0	ENST00000330684.3:c.4021A>G	p.Ser1341Gly	p.S1341G	ENST00000330684	NM_001134407.1	1341	Agc/Ggc	13/13	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.576544238622981	2		391	484	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110498	8110498	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	29	284	0	ENST00000585124.1:c.394C>A	p.Leu132Met	p.L132M	ENST00000585124	NM_004217.3	132	Ctg/Atg	5/9	1	2	FACETS	0.24	0.192	0.295	0.24	0.192	0.295	SUBCLONAL	1	TRUE	1	0.576544238622981	2		284	419	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562747	29562747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137854556	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	188	353	0	ENST00000356175.3:c.3827G>A	p.Arg1276Gln	p.R1276Q	ENST00000356175	NM_000267.3	1276	cGa/cAa	28/57	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.576544238622981	2		353	532	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654674	29654674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782220	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	36	386	0	ENST00000356175.3:c.5363C>T	p.Pro1788Leu	p.P1788L	ENST00000356175	NM_000267.3	1788	cCg/cTg	37/57	1	2	FACETS	0.214	0.175	0.257	0.214	0.175	0.257	SUBCLONAL	1	TRUE	1	0.576544238622981	2		386	584	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530035	63530035	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	193	381	0	ENST00000307078.5:c.2400T>A	p.Asn800Lys	p.N800K	ENST00000307078	NM_004655.3	800	aaT/aaA	10/11	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.576544238622981	2		381	668	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1206955	1206955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060499970	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	97	236	0	ENST00000326873.7:c.43G>A	p.Gly15Ser	p.G15S	ENST00000326873	NM_000455.4	15	Ggc/Agc	1/10	1	2	FACETS	0.811	0.728	0.898	0.811	0.728	0.898	CLONAL	1	TRUE	1	0.576544238622981	2		236	415	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119228	3119228	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	175	425	0	ENST00000078429.4:c.760C>A	p.Leu254Met	p.L254M	ENST00000078429	NM_002067.2	254	Ctg/Atg	6/7	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.576544238622981	2		425	593	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105557	11105557	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	186	373	2	ENST00000358026.2:c.1473A>T	p.Arg491Ser	p.R491S	ENST00000358026	NM_001128849.1	491	agA/agT	9/36	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.576544238622981	2		375	589	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152139	11152139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	208	388	4	ENST00000358026.2:c.4423C>T	p.Arg1475Cys	p.R1475C	ENST00000358026	NM_001128849.1	1475	Cgc/Tgc	31/36	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.576544238622981	2		392	671	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744945	39744945	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	36	376	0	ENST00000361337.2:c.1735G>T	p.Asp579Tyr	p.D579Y	ENST00000361337	NM_003286.2	579	Gat/Tat	17/21	1	2	FACETS	0.233	0.191	0.281	0.233	0.191	0.281	SUBCLONAL	1	TRUE	1	0.576544238622981	2		376	535	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480483	57480483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	101	242	0	ENST00000371085.3:c.478C>T	p.Arg160Cys	p.R160C	ENST00000371085	NM_000516.4	160	Cgt/Tgt	6/13	1	2	FACETS	0.859	0.773	0.948	0.859	0.773	0.948	CLONAL	1	TRUE	1	0.576544238622981	2		242	408	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11554273	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	35	380	0	ENST00000371085.3:c.601C>A	p.Arg201Ser	p.R201S	ENST00000371085	NM_000516.4	201	Cgt/Agt	8/13	1	2	FACETS	0.173	0.141	0.21	0.173	0.141	0.21	SUBCLONAL	1	TRUE	1	0.576544238622981	2		380	700	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44921916	44921916	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	218	428	0	ENST00000377967.4:c.1450A>G	p.Arg484Gly	p.R484G	ENST00000377967	NM_021140.2	484	Aga/Gga	15/29	NA	2	FACETS	1	0.962	1			1	INDETERMINATE	1	TRUE	NA	0.576544238622981	2		428	724	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006867	47006867	+	5_prime_UTR_variant	5'UTR	SNP	G	G	T	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	231	423	1	ENST00000377604.3:c.-14G>T		p.*5*	ENST00000377604	NM_001204468.1	-/852		2/24	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.576544238622981	2		424	707	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030585	47030585	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs377667483	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	145	363	2	ENST00000377604.3:c.360T>G	p.Asp120Glu	p.D120E	ENST00000377604	NM_001204468.1	120	gaT/gaG	4/24	NA	2	FACETS	1	0.932	1			1	INDETERMINATE	1	TRUE	NA	0.576544238622981	2		365	495	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446222	29446223	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	188	337	2	ENST00000389048.3:c.3344dup	p.Asn1115LysfsTer18	p.N1115Kfs*18	ENST00000389048	NM_004304.4	1115	aac/aaAc	20/29	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.576544238622981	2		339	637	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268379	142268380	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1559984993	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	156	349	0	ENST00000350721.4:c.3112dup	p.Ser1038PhefsTer11	p.S1038Ffs*11	ENST00000350721	NM_001184.3	1038	tct/tTct	15/47	1	2	FACETS	0.92	0.847	0.996	0.92	0.847	0.996	CLONAL	1	TRUE	1	0.576544238622981	2		349	588	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534473	187534473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	160	271	0	ENST00000441802.2:c.9253del	p.Asp3086IlefsTer30	p.D3086Ifs*30	ENST00000441802	NM_005245.3	3085	Ctt/tt	13/27	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.576544238622981	2		271	469	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259555	55259557	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	122	245	0	ENST00000275493.2:c.2615_2617del	p.Glu872del	p.E872del	ENST00000275493	NM_005228.3	871	gcAGAa/gca	21/28	1	2	FACETS	0.971	0.884	1	0.971	0.884	1	CLONAL	1	TRUE	1	0.576544238622981	2		245	436	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874012	151874013	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	43	459	1	ENST00000262189.6:c.8525dup	p.Asn2842LysfsTer2	p.N2842Kfs*2	ENST00000262189	NM_170606.2	2842	aat/aaAt	38/59	1	2	FACETS	0.211	0.175	0.25	0.211	0.175	0.25	SUBCLONAL	1	TRUE	1	0.576544238622981	2		460	708	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93607816	93607817	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	151	378	0	ENST00000375746.1:c.522_523del	p.Arg175GlyfsTer4	p.R175Gfs*4	ENST00000375746	NM_001174167.1	173	aTC/a	3/14	1	2	FACETS	0.85	0.78	0.923	0.85	0.78	0.923	CLONAL	1	TRUE	1	0.576544238622981	2		378	616	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912207	97912208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	190	344	0	ENST00000289081.3:c.683dup	p.Leu228PhefsTer24	p.L228Ffs*24	ENST00000289081	NM_000136.2	228	ttg/ttTg	7/15	1	2	FACETS	0.999	0.927	1	0.999	0.927	1	CLONAL	1	TRUE	1	0.576544238622981	2		344	660	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274647	123274648	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	138	314	0	ENST00000358487.5:c.1270dup	p.Leu424ProfsTer10	p.L424Pfs*10	ENST00000358487	NM_000141.4	424	ctg/cCtg	9/18	1	2	FACETS	0.864	0.79	0.941	0.864	0.79	0.941	CLONAL	1	TRUE	1	0.576544238622981	2		314	554	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154242	2154242	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755455183	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	167	442	3	ENST00000434045.2:c.686del	p.Pro229GlnfsTer27	p.P229Qfs*27	ENST00000434045	NM_001127598.1	229	cCa/ca	5/5	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.576544238622981	2		445	565	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992227	11992229	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	109	268	0	ENST00000396373.4:c.320_322del	p.Pro107del	p.P107del	ENST00000396373	NM_001987.4	106	tCTCct/tct	3/8	0.546844185593125	2	FACETS	0.829	0.749	0.913	0.415	0.374	0.457	CLONAL	1	TRUE	0	0.576544238622981	2		268	456	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433979	49433979	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	250	266	0	ENST00000301067.7:c.7574del	p.Gly2525ValfsTer18	p.G2525Vfs*18	ENST00000301067	NM_003482.3	2525	gGt/gt	31/54	0.576544238622981	3	FACETS	0.977	0.922	1	0.977	0.922	1	CLONAL	2	TRUE	1	0.576544238622981	3		266	572	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448407	49448408	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs797045661	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	172	386	0	ENST00000301067.7:c.303dup	p.Ser102GlufsTer6	p.S102Efs*6	ENST00000301067	NM_003482.3	101	-/G	3/54	0.576544238622981	3	FACETS	0.98	0.904	1	0.49	0.452	0.53	CLONAL	1	TRUE	1	0.576544238622981	3		386	784	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238183	133238184	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	170	433	0	ENST00000320574.5:c.2793dup	p.Glu932Ter	p.E932*	ENST00000320574	NM_006231.2	931	-/T	24/49	0.576544238622981	3	FACETS	0.956	0.88	1	0.478	0.44	0.517	CLONAL	1	TRUE	1	0.576544238622981	3		433	795	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647483	23647483	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	150	387	1	ENST00000261584.4:c.384del	p.His130ThrfsTer47	p.H130Tfs*47	ENST00000261584	NM_024675.3	128	ttT/tt	4/13	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.576544238622981	2		388	517	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532584	63532585	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267606674	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	159	331	3	ENST00000307078.5:c.1994dup	p.Asn666GlnfsTer41	p.N666Qfs*41	ENST00000307078	NM_004655.3	665	ggc/ggGc	8/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.576544238622981	2		334	511	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39623699	39623700	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1234146599	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	180	331	0	ENST00000262039.4:c.2112dup	p.Arg705Ter	p.R705*	ENST00000262039	NM_002647.2	702	-/T	20/25	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.576544238622981	2		331	613	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727909	41727909	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	206	430	0	ENST00000301178.4:c.538del	p.Leu180TrpfsTer18	p.L180Wfs*18	ENST00000301178	NM_021913.4	178	gtC/gt	4/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.576544238622981	2		430	587	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913179	39913179	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002671-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	218	418	2	ENST00000378444.4:c.4936del	p.Leu1646SerfsTer28	p.L1646Sfs*28	ENST00000378444	NM_001123385.1	1646	Ctc/tc	14/15	NA	2	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.576544238622981	2		420	714	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0002674-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	276	139	0				ENST00000310581	NM_198253.2	-/1132			0.364291510376359	3	FACETS	0.874	0.826	0.923	1	0.992	1	CLONAL	3	TRUE	1	0.364291510376359	3		139	683	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730889	40730889	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002674-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	139	247	0	ENST00000373198.4:c.3646G>T	p.Gly1216Trp	p.G1216W	ENST00000373198	NM_133170.3	1216	Ggg/Tgg	27/32	1	2	FACETS	0.959	0.873	1	0.959	0.873	1	CLONAL	1	TRUE	1	0.364291510376359	2		247	796	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974695	21974695	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1131691187	NA	P-0002674-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	166	280	0	ENST00000304494.5:c.132del	p.Tyr44Ter	p.Y44*	ENST00000304494	NM_000077.4	44	taC/ta	1/3	0.364291510376359	1	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	0	0.364291510376359	1		280	731	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578360	7578373	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGCTGCTCACCAT	CAGCTGCTCACCAT	-	novel	NA	P-0002674-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	142	240	0	ENST00000269305.4:c.557_559+11del		p.X186_splice	ENST00000269305	NM_001126112.2	186		5/11	0.364291510376359	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.364291510376359	1		240	595	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002684-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	38	422	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		422	235	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	78	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.962	0.86	1	0.962	0.86	1	CLONAL	1	TRUE	1	0.730327401755265	2		422	222	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274849	38274849	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779707422	NA	P-0002685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	119	265	0	ENST00000425967.3:c.1731C>A	p.Asn577Lys	p.N577K	ENST00000425967	NM_001174067.1	577	aaC/aaA	13/19	0.409784665694993	1	FACETS	0.398	0.36	0.437	0.398	0.36	0.437	INDETERMINATE	1	TRUE	0	0.730327401755265	1		265	520	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692911	89692911	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	219	174	0	ENST00000371953.3:c.395G>C	p.Gly132Ala	p.G132A	ENST00000371953	NM_000314.4	132	gGt/gCt	5/9	0.725746678240416	2	FACETS	0.914	0.871	0.956	0.914	0.871	0.956	CLONAL	2	TRUE	0	0.730327401755265	2		174	328	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550494	29550497	+	frameshift_variant	Frame_Shift_Del	DEL	TAAC	TAAC	-	rs786202782	NA	P-0002685-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	213	206	0	ENST00000356175.3:c.1756_1759del	p.Thr586ValfsTer18	p.T586Vfs*18	ENST00000356175	NM_000267.3	585	tTAACt/tt	16/57	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.730327401755265	2		206	579	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024032	27024032	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0002689-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	10	26	0	ENST00000324856.7:c.1137+1G>A		p.X379_splice	ENST00000324856	NM_006015.4	379			0.584082667938603	3	FACETS	0.826	0.575	1	0.413	0.287	0.561	CLONAL	1	TRUE	1	0.656363691901012	3		26	49	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097658	27097658	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002689-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	98	311	0	ENST00000324856.7:c.3247G>T	p.Gly1083Cys	p.G1083C	ENST00000324856	NM_006015.4	1083	Ggc/Tgc	12/20	0.584082667938603	3	FACETS	0.901	0.809	0.999	0.451	0.404	0.5	CLONAL	1	TRUE	1	0.656363691901012	3		311	440	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812580	43812580	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002689-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	81	299	0	ENST00000372470.3:c.1283C>G	p.Thr428Arg	p.T428R	ENST00000372470	NM_005373.2	428	aCa/aGa	8/12	0.584082667938603	3	FACETS	0.86	0.763	0.964	0.43	0.381	0.482	CLONAL	1	TRUE	1	0.656363691901012	3		299	381	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175826	176175826	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002689-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	95	115	0	ENST00000367669.3:c.289G>T	p.Ala97Ser	p.A97S	ENST00000367669	NM_022457.5	97	Gcc/Tcc	1/20	0.584082667938603	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.656363691901012	3		115	164	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665045	138665045	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002689-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	32	22	0	ENST00000330315.3:c.520G>A	p.Gly174Ser	p.G174S	ENST00000330315	NM_023067.3	174	Ggc/Agc	1/1	0.504083030427877	4	FACETS	0.928	0.798	1	1	0.956	1	CLONAL	3	TRUE	2	0.656363691901012	4		22	58	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683669	162683669	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002689-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	278	286	0	ENST00000366898.1:c.300G>T	p.Gln100His	p.Q100H	ENST00000366898	NM_004562.2	100	caG/caT	3/12	0.656363691901012	3	FACETS	0.88	0.843	0.917	0.88	0.843	0.917	CLONAL	3	TRUE	0	0.656363691901012	3		286	426	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55269467	55269467	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002689-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	187	294	0	ENST00000275493.2:c.3154A>G	p.Arg1052Gly	p.R1052G	ENST00000275493	NM_005228.3	1052	Aga/Gga	26/28	0.504083030427877	4	FACETS	0.895	0.834	0.958	0.895	0.834	0.958	CLONAL	2	TRUE	2	0.656363691901012	4		294	527	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508619	106508619	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002689-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	128	197	0	ENST00000359195.3:c.613A>G	p.Lys205Glu	p.K205E	ENST00000359195	NM_002649.2	205	Aag/Gag	2/11	0.504083030427877	4	FACETS	0.85	0.779	0.924	0.85	0.779	0.924	CLONAL	2	TRUE	2	0.656363691901012	4		197	380	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685272	89685272	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs748031178	NA	P-0002689-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	111	175	0	ENST00000371953.3:c.167T>G	p.Phe56Cys	p.F56C	ENST00000371953	NM_000314.4	56	tTt/tGt	3/9	0.557269179321203	2	FACETS	0.85	0.786	0.913	0.85	0.786	0.913	CLONAL	2	TRUE	0	0.656363691901012	2		175	199	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256226	133256226	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002689-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	71	241	0	ENST00000320574.5:c.435G>T	p.Leu145Phe	p.L145F	ENST00000320574	NM_006231.2	145	ttG/ttT	6/49	0.358054181526914	3	FACETS	0.807	0.709	0.912			1	INDETERMINATE	1	TRUE	NA	0.656363691901012	3		241	356	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222216	2222216	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs936416390	NA	P-0002689-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	275	374	0	ENST00000326181.6:c.500A>C	p.Lys167Thr	p.K167T	ENST00000326181	NM_032271.2	167	aAa/aCa	8/21	0.512586190807985	4	FACETS	0.86	0.817	0.903	0.86	0.817	0.903	CLONAL	3	TRUE	1	0.656363691901012	4		374	538	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492721	56492721	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002689-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	185	324	2	ENST00000407977.2:c.218C>G	p.Ala73Gly	p.A73G	ENST00000407977		73	gCt/gGt	2/10	0.584082667938603	3	FACETS	0.828	0.773	0.884	0.828	0.773	0.884	CLONAL	2	TRUE	1	0.656363691901012	3		326	452	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306757	41306757	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002689-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	95	196	0	ENST00000373198.4:c.902G>T	p.Gly301Val	p.G301V	ENST00000373198	NM_133170.3	301	gGg/gTg	7/32	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.656363691901012	2		196	230	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317431	1317431	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002689-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	143	235	0	ENST00000400841.2:c.634G>T	p.Gly212Cys	p.G212C	ENST00000400841		212	Ggc/Tgc	5/6	0.656363691901012	2	FACETS	0.939	0.881	0.996			1	CLONAL	2	TRUE	NA	0.656363691901012	2		235	232	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968239	2968239	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002689-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	191	307	0	ENST00000396946.4:c.1747del	p.His583IlefsTer17	p.H583Ifs*17	ENST00000396946	NM_032415.4	583	Cat/at	13/25	0.504083030427877	4	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	2	0.656363691901012	4		307	464	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577091	7577091	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002689-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	200	356	0	ENST00000269305.4:c.847del	p.Arg283AlafsTer62	p.R283Afs*62	ENST00000269305	NM_001126112.2	283	Cgc/gc	8/11	0.557269179321203	2	FACETS	0.817	0.77	0.864	0.817	0.77	0.864	CLONAL	2	TRUE	0	0.656363691901012	2		356	373	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002714-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	73	422	0				ENST00000310581	NM_198253.2	-/1132			0.815531910837364	2	FACETS	0.89	0.794	0.99			1	CLONAL	1	TRUE	NA	0.82	2		422	200	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61720146	61720146	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002714-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	497	673	1	ENST00000401558.2:c.1288G>T	p.Val430Leu	p.V430L	ENST00000401558	NM_003400.3	430	Gta/Tta	13/25	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.82	2		674	1209	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693001	89693001	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002714-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	80	219	0	ENST00000371953.3:c.485A>T	p.Asp162Val	p.D162V	ENST00000371953	NM_000314.4	162	gAc/gTc	5/9	1	2	FACETS	0.384	0.339	0.433	0.384	0.339	0.433	SUBCLONAL	1	TRUE	1	0.82	2		219	508	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118368778	118368778	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002714-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	179	315	0	ENST00000534358.1:c.5792G>T	p.Gly1931Val	p.G1931V	ENST00000534358	NM_005933.3	1931	gGc/gTc	21/36	1	2	FACETS	0.941	0.876	1	0.941	0.876	1	CLONAL	1	TRUE	1	0.82	2		315	464	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0002715-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	61	139	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.2292948370836	2		139	413	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264491	16264491	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747375812	NA	P-0002715-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	97	438	0	ENST00000375759.3:c.10694G>A	p.Arg3565Gln	p.R3565Q	ENST00000375759	NM_015001.2	3565	cGa/cAa	13/15	0.0848052205810221	3	FACETS	1	0.954	1			1	INDETERMINATE	1	TRUE	NA	0.2292948370836	3		438	833	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087558	27087558	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0002715-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	117	576	0	ENST00000324856.7:c.2132C>G	p.Ser711Ter	p.S711*	ENST00000324856	NM_006015.4	711	tCa/tGa	5/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.2292948370836	2		576	905	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461597	138461597	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002715-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	94	532	0	ENST00000289153.2:c.424G>C	p.Asp142His	p.D142H	ENST00000289153	NM_006219.2	142	Gat/Cat	3/22	1	2	FACETS	0.89	0.791	0.997	0.89	0.791	0.997	CLONAL	1	TRUE	1	0.2292948370836	2		532	921	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724314	117724314	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002715-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	104	469	0	ENST00000368508.3:c.565C>G	p.His189Asp	p.H189D	ENST00000368508	NM_002944.2	189	Cat/Gat	6/43	0.2292948370836	1	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	0	0.2292948370836	1		469	802	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884356	151884356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002715-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	76	499	0	ENST00000262189.6:c.4999G>A	p.Glu1667Lys	p.E1667K	ENST00000262189	NM_170606.2	1667	Gaa/Aaa	33/59	1	2	FACETS	0.896	0.785	1	0.896	0.785	1	CLONAL	1	TRUE	1	0.2292948370836	2		499	740	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69456203	69456203	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749614691	NA	P-0002715-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	115	600	0	ENST00000227507.2:c.122C>T	p.Ser41Leu	p.S41L	ENST00000227507	NM_053056.2	41	tCg/tTg	1/5	0.2292948370836	1	FACETS	0.926	0.833	1	0.926	0.833	1	CLONAL	1	TRUE	0	0.2292948370836	1		600	959	SUCCESS
ATM	472	MSKCC	GRCh37	11	108165783	108165783	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060501627	NA	P-0002715-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	84	461	0	ENST00000278616.4:c.4906C>T	p.Gln1636Ter	p.Q1636*	ENST00000278616	NM_000051.3	1636	Cag/Tag	32/63	0.2292948370836	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.2292948370836	1		461	612	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38064117	38064117	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002715-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	64	506	0	ENST00000250448.2:c.61G>C	p.Asp21His	p.D21H	ENST00000250448	NM_004496.3	21	Gac/Cac	1/2	1	2	FACETS	0.663	0.573	0.761	0.663	0.573	0.761	SUBCLONAL	1	TRUE	1	0.2292948370836	2		506	842	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358517	67358517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002715-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	36	361	0	ENST00000327367.4:c.25C>T	p.Pro9Ser	p.P9S	ENST00000327367	NM_005902.3	9	Ccc/Tcc	1/9	1	2	FACETS	0.516	0.423	0.621	0.516	0.423	0.621	SUBCLONAL	1	TRUE	1	0.2292948370836	2		361	608	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786117	3786117	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002715-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	158	817	0	ENST00000262367.5:c.4648G>C	p.Glu1550Gln	p.E1550Q	ENST00000262367	NM_004380.2	1550	Gaa/Caa	28/31	0.2292948370836	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.2292948370836	1		817	1180	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687288	37687288	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002715-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	140	607	0	ENST00000447079.4:c.4192C>T	p.Pro1398Ser	p.P1398S	ENST00000447079	NM_015083.1	1398	Cca/Tca	14/14	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.2292948370836	2		607	1064	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791010	42791010	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs764723800	NA	P-0002715-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	124	509	0	ENST00000575354.2:c.155C>A	p.Ser52Tyr	p.S52Y	ENST00000575354	NM_015125.3	52	tCc/tAc	2/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.2292948370836	2		509	924	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566488	41566488	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002715-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	81	685	0	ENST00000263253.7:c.4365G>C	p.Gln1455His	p.Q1455H	ENST00000263253	NM_001429.3	1455	caG/caC	27/31	1	2	FACETS	0.61	0.535	0.69	0.61	0.535	0.69	SUBCLONAL	1	TRUE	1	0.2292948370836	2		685	1159	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938391	76938391	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002715-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	67	463	0	ENST00000373344.5:c.2357C>T	p.Ser786Phe	p.S786F	ENST00000373344	NM_000489.3	786	tCt/tTt	9/35	0.2292948370836	0	FACETS	0.774	0.673	0.883			1	SUBCLONAL	1	TRUE	NA	0.2292948370836	0		463	582	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002734-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	25	422	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		422	319	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002754-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	117	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.878	0.802	0.956	0.878	0.802	0.956	CLONAL	1	TRUE	1	0.815059909215839	2		422	327	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030479	49030479	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0002754-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	245	298	0	ENST00000267163.4:c.1959del	p.Val654CysfsTer4	p.V654Cfs*4	ENST00000267163	NM_000321.2	652	Aaa/aa	19/27	0.777456832795554	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.815059909215839	1		298	343	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012389	29012389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161996687	NA	P-0002754-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	300	445	0	ENST00000282397.4:c.482C>T	p.Thr161Met	p.T161M	ENST00000282397	NM_002019.4	161	aCg/aTg	4/30	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.815059909215839	2		445	693	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0002758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	53	456	0	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.390281644801321	5	FACETS	0.963	0.836	1	0.642	0.557	0.731	CLONAL	2	TRUE	2	0.595255716638217	5		456	175	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0002758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	43	450	0	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	1	2	FACETS	0.996	0.851	1	0.996	0.851	1	CLONAL	1	TRUE	1	0.595255716638217	2		450	145	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778738	76778738	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	19	296	0	ENST00000373344.5:c.6841G>T	p.Glu2281Ter	p.E2281*	ENST00000373344	NM_000489.3	2281	Gag/Tag	31/35	0.344191919691135	0	FACETS	0.68	0.551	0.809			1	INDETERMINATE	1	TRUE	NA	0.595255716638217	0		296	38	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119789	70119789	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	51	439	0	ENST00000245479.2:c.791G>C	p.Arg264Thr	p.R264T	ENST00000245479	NM_000346.3	264	aGa/aCa	3/3	0.384798832984174	5	FACETS	0.865	0.756	0.976			1	CLONAL	3	TRUE	NA	0.595255716638217	5		439	125	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11308032	11308032	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	63	519	0	ENST00000361445.4:c.960G>T	p.Gln320His	p.Q320H	ENST00000361445	NM_004958.3	320	caG/caT	7/58	0.595255716638217	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.595255716638217	2		519	98	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143132	30143132	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1262491330	NA	P-0002758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	33	444	0	ENST00000389048.3:c.394G>T	p.Val132Leu	p.V132L	ENST00000389048	NM_004304.4	132	Gtg/Ttg	1/29	0.223016481380538	2	FACETS	1	0.874	1	0.528	0.441	0.621	INDETERMINATE	1	TRUE	0	0.595255716638217	2		444	105	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198260781	198260781	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0002758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	46	464	0	ENST00000335508.6:c.3538A>T	p.Arg1180Ter	p.R1180*	ENST00000335508	NM_012433.2	1180	Aga/Tga	23/25	0.595255716638217	3	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	1	0.595255716638217	3		464	87	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691796	30691796	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	28	497	0	ENST00000295754.5:c.298G>T	p.Val100Phe	p.V100F	ENST00000295754	NM_003242.5	100	Gtt/Ttt	3/7	1	2	FACETS	0.896	0.732	1	0.896	0.732	1	CLONAL	1	TRUE	1	0.595255716638217	2		497	105	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259587	89259587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	15	340	0	ENST00000336596.2:c.731G>A	p.Cys244Tyr	p.C244Y	ENST00000336596	NM_005233.5	244	tGc/tAc	3/17	1	2	FACETS	1	0.808	1	1	0.808	1	CLONAL	1	TRUE	1	0.595255716638217	2		340	47	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524922	187524922	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	40	517	0	ENST00000441802.2:c.10758G>C	p.Met3586Ile	p.M3586I	ENST00000441802	NM_005245.3	3586	atG/atC	19/27	0.162755587891189	0	FACETS	0.504	0.43	0.58			1	INDETERMINATE	1	TRUE	0	0.595255716638217	0		517	108	SUCCESS
APC	324	MSKCC	GRCh37	5	112103068	112103068	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	25	396	0	ENST00000257430.4:c.403G>T	p.Glu135Ter	p.E135*	ENST00000257430	NM_000038.5	135	Gaa/Taa	4/16	0.579499552503608	1	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	0	0.595255716638217	1		396	57	SUCCESS
APC	324	MSKCC	GRCh37	5	112173860	112173860	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	29	446	0	ENST00000257430.4:c.2569G>C	p.Gly857Arg	p.G857R	ENST00000257430	NM_000038.5	857	Gga/Cga	16/16	0.579499552503608	1	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	0	0.595255716638217	1		446	65	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335697	81335697	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	14	469	0	ENST00000222390.5:c.1663G>T	p.Gly555Ter	p.G555*	ENST00000222390	NM_000601.4	555	Gga/Tga	15/18	0.51114380634746	1	FACETS	0.501	0.37	0.65	0.501	0.37	0.65	SUBCLONAL	1	TRUE	0	0.595255716638217	1		469	66	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90970984	90970984	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	23	485	0	ENST00000265433.3:c.1093G>C	p.Ala365Pro	p.A365P	ENST00000265433	NM_002485.4	365	Gct/Cct	9/16	1	2	FACETS	0.805	0.641	0.986	0.805	0.641	0.986	CLONAL	1	TRUE	1	0.595255716638217	2		485	96	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738392	145738392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	78	437	0	ENST00000428558.2:c.2593G>A	p.Glu865Lys	p.E865K	ENST00000428558	NM_004260.3	865	Gaa/Aaa	16/22	0.390281644801321	5	FACETS	0.926	0.824	1	0.617	0.549	0.688	CLONAL	2	TRUE	2	0.595255716638217	5		437	268	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249766	110249766	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	53	296	0	ENST00000374672.4:c.909C>A	p.His303Gln	p.H303Q	ENST00000374672	NM_004235.4	303	caC/caA	3/5	0.592188254148605	2	FACETS	0.995	0.863	1	0.497	0.431	0.567	CLONAL	1	TRUE	0	0.595255716638217	2		296	179	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156596	2156596	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0002758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	29	365	0	ENST00000434045.2:c.325+1G>T		p.X109_splice	ENST00000434045	NM_001127598.1	109			0.196810533195256		FACETS		0.291	0.425				INDETERMINATE	1	TRUE	0	0.595255716638217	0		365	111	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715776	18715776	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	30	508	1	ENST00000266497.5:c.3607A>G	p.Arg1203Gly	p.R1203G	ENST00000266497		1203	Agg/Ggg	25/31	0.162755587891189	0	FACETS	0.492	0.409	0.578			1	INDETERMINATE	1	TRUE	0	0.595255716638217	0		509	83	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954316	48954316	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	16	381	0	ENST00000267163.4:c.1437C>G	p.Asp479Glu	p.D479E	ENST00000267163	NM_000321.2	479	gaC/gaG	16/27	0.107153498441415	0	FACETS	0.262	0.197	0.336			1	INDETERMINATE	1	TRUE	0	0.595255716638217	0		381	83	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434986	110434986	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	39	316	0	ENST00000375856.3:c.3415G>T	p.Asp1139Tyr	p.D1139Y	ENST00000375856	NM_003749.2	1139	Gac/Tac	1/2	0.107153498441415	0	FACETS	0.399	0.337	0.464			1	INDETERMINATE	1	TRUE	0	0.595255716638217	0		316	133	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95599651	95599651	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0002758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	23	382	0	ENST00000393063.1:c.144+1G>T		p.X48_splice	ENST00000393063	NM_030621.3	48			0.223016481380538	2	FACETS	1	0.844	1	0.529	0.426	0.641	INDETERMINATE	1	TRUE	0	0.595255716638217	2		382	73	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500550	99500550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	49	371	0	ENST00000268035.6:c.3983G>T	p.Gly1328Val	p.G1328V	ENST00000268035	NM_000875.3	1328	gGc/gTc	21/21	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.595255716638217	2		371	143	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579378	7579378	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	36	444	0	ENST00000269305.4:c.309C>A	p.Tyr103Ter	p.Y103*	ENST00000269305	NM_001126112.2	103	taC/taA	4/11	1	2	FACETS	0.876	0.734	1	0.876	0.734	1	CLONAL	1	TRUE	1	0.595255716638217	2		444	138	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602763	10602763	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs774469695	NA	P-0002758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	140	428	0	ENST00000171111.5:c.815G>C	p.Arg272Pro	p.R272P	ENST00000171111	NM_203500.1	272	cGc/cCc	3/6	0.579655906151361	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.595255716638217	2		428	228	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105651	11105651	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	121	413	0	ENST00000358026.2:c.1567G>T	p.Glu523Ter	p.E523*	ENST00000358026	NM_001128849.1	523	Gag/Tag	9/36	0.579655906151361	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.595255716638217	2		413	180	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271758	15271758	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	30	347	0	ENST00000263388.2:c.6681C>A	p.His2227Gln	p.H2227Q	ENST00000263388	NM_000435.2	2227	caC/caA	33/33	0.579655906151361	2	FACETS	0.586	0.477	0.707	0.293	0.238	0.354	SUBCLONAL	1	TRUE	0	0.595255716638217	2		347	172	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0002758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	46	160	0	ENST00000304494.5:c.172del	p.Arg58GlufsTer88	p.R58Efs*88	ENST00000304494	NM_000077.4	58	Cga/ga	2/3	0.592188254148605	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	0	0.595255716638217	2		160	71	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039826	47039847	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCCAATGAAGGCAGTCGCAT	CCTCCAATGAAGGCAGTCGCAT	-	novel	NA	P-0002758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	44	282	0	ENST00000377604.3:c.1170_1191del	p.Ser391ValfsTer87	p.S391Vfs*87	ENST00000377604	NM_001204468.1	390	gCCTCCAATGAAGGCAGTCGCATc/gc	12/24	0.344191919691135	0	FACETS	0.739	0.649	0.827			1	INDETERMINATE	1	TRUE	NA	0.595255716638217	0		282	81	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039856	47039872	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCTGTGGCCAGCACT	CCTCTGTGGCCAGCACT	-	novel	NA	P-0002758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	49	250	0	ENST00000377604.3:c.1199_1215del	p.Ala400GlyfsTer37	p.A400Gfs*37	ENST00000377604	NM_001204468.1	400	gCCTCTGTGGCCAGCACT/g	12/24	0.344191919691135	0	FACETS	0.766	0.68	0.85			1	INDETERMINATE	1	TRUE	NA	0.595255716638217	0		250	87	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039877	47039884	+	frameshift_variant	Frame_Shift_Del	DEL	TTGCTGCG	TTGCTGCG	C	novel	NA	P-0002758-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	49	213	0	ENST00000377604.3:c.1220_1227delinsC	p.Ile407ThrfsTer76	p.I407Tfs*76	ENST00000377604	NM_001204468.1	407	aTTGCTGCG/aC	12/24	0.344191919691135	0	FACETS	0.793	0.706	0.878			1	INDETERMINATE	1	TRUE	NA	0.595255716638217	0		213	84	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002763-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	33	422	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	FALSE	NA	NA	NA		422	95	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002776-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	31	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.564	0.462	0.676			1	INDETERMINATE	1	TRUE	NA	0.695906130863322	2		422	158	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0002776-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	146	244	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.113013845139145	4	FACETS	0.941	0.87	1	0.941	0.87	1	INDETERMINATE	2	TRUE	2	0.695906130863322	4		244	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577534	7577534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934571	NA	P-0002776-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	308	272	1	ENST00000269305.4:c.747G>T	p.Arg249Ser	p.R249S	ENST00000269305	NM_001126112.2	249	agG/agT	7/11	0.695906130863322	2	FACETS	0.905	0.867	0.942	0.905	0.867	0.942	CLONAL	2	TRUE	0	0.695906130863322	2		273	489	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187860	11187860	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002776-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	128	189	0	ENST00000361445.4:c.6037A>G	p.Ser2013Gly	p.S2013G	ENST00000361445	NM_004958.3	2013	Agc/Ggc	44/58	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	1	TRUE	NA	0.695906130863322	2		189	325	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670025	29670025	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0002776-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	528	299	0	ENST00000356175.3:c.7000-2A>C		p.X2334_splice	ENST00000356175	NM_000267.3	2334			0.695906130863322	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.695906130863322	2		299	715	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077433	30077433	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002776-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	148	164	0	ENST00000338641.4:c.1580A>T	p.Glu527Val	p.E527V	ENST00000338641	NM_000268.3	527	gAa/gTa	15/16	0.385360413949198	1	FACETS	1	0.98	1	1	0.98	1	INDETERMINATE	1	TRUE	0	0.695906130863322	1		164	248	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030345	49030346	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0002776-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	224	266	0	ENST00000267163.4:c.1821_1822del	p.Pro609CysfsTer43	p.P609Cfs*43	ENST00000267163	NM_000321.2	607	cTT/c	19/27	0.462147757771629	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.695906130863322	1		266	414	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339266	70339286	+	inframe_deletion	In_Frame_Del	DEL	AGCCTGCTGTCTCTGGGGATG	AGCCTGCTGTCTCTGGGGATG	-	novel	NA	P-0002776-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	258	471	0	ENST00000374080.3:c.146_166del	p.Pro49_Glu55del	p.P49_E55del	ENST00000374080		48	cAGCCTGCTGTCTCTGGGGATGag/cag	2/45	0.159847594772579	4	FACETS	1	0.988	1	0.616	0.577	0.656	INDETERMINATE	1	TRUE	2	0.695906130863322	4		471	1021	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0002777-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	33	403	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.630865280613357	2	FACETS	0.126	0.102	0.154	0.063	0.051	0.077	SUBCLONAL	1	TRUE	0	0.630865280613357	2		404	828	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002777-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	170	422	0				ENST00000310581	NM_198253.2	-/1132			0.570122285255853	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.630865280613357	4		422	355	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0002777-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	38	531	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.630865280613357	2	FACETS	0.148	0.122	0.178	0.074	0.061	0.089	SUBCLONAL	1	TRUE	0	0.630865280613357	2		531	813	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0002777-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	408	558	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.630865280613357	6	FACETS	1	0.954	1			1	CLONAL	2	TRUE	NA	0.630865280613357	6		558	1457	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764146326	NA	P-0002777-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	641	531	0	ENST00000269305.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000269305	NM_001126112.2	281	Gac/Aac	8/11	0.630865280613357	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.630865280613357	2		531	817	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0002777-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	53	354	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.630865280613357	1	FACETS	0.226	0.193	0.263	0.226	0.193	0.263	SUBCLONAL	1	TRUE	0	0.630865280613357	1		354	508	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356289	66356289	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002777-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	493	447	0	ENST00000273854.3:c.1208G>C	p.Gly403Ala	p.G403A	ENST00000273854	NM_004439.5	403	gGt/gCt	5/18	0.630865280613357	2	FACETS	0.861	0.84	0.881	1	0.997	1	CLONAL	3	TRUE	0	0.630865280613357	2		447	605	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268084	153268084	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002777-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	624	333	0	ENST00000281708.4:c.724C>T	p.Gln242Ter	p.Q242*	ENST00000281708	NM_033632.3	242	Cag/Tag	4/12	0.630865280613357	3	FACETS	0.897	0.881	0.913	1	0.998	1	CLONAL	4	TRUE	0	0.630865280613357	3		333	725	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629902	187629902	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002777-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	55	416	0	ENST00000441802.2:c.1080C>G	p.Phe360Leu	p.F360L	ENST00000441802	NM_005245.3	360	ttC/ttG	2/27	0.630865280613357	2	FACETS	0.21	0.179	0.244	0.105	0.089	0.122	SUBCLONAL	1	TRUE	0	0.630865280613357	2		416	831	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288774	33288774	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002777-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	113	276	0	ENST00000374542.5:c.778C>T	p.Arg260Cys	p.R260C	ENST00000374542	NM_001141970.1	260	Cgt/Tgt	3/8	0.511860534772544	4	FACETS	0.933	0.842	1			1	CLONAL	1	TRUE	NA	0.630865280613357	4		276	626	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725487	117725487	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002777-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	36	396	0	ENST00000368508.3:c.394C>G	p.Gln132Glu	p.Q132E	ENST00000368508	NM_002944.2	132	Cag/Gag	5/43	0.630865280613357	1	FACETS	0.158	0.129	0.19	0.158	0.129	0.19	SUBCLONAL	1	TRUE	0	0.630865280613357	1		396	495	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012290	152012290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002777-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	42	610	0	ENST00000262189.6:c.523G>A	p.Asp175Asn	p.D175N	ENST00000262189	NM_170606.2	175	Gac/Aac	4/59	0.164937499962443	2	FACETS	0.159	0.131	0.189	0.079	0.065	0.095	INDETERMINATE	1	TRUE	0	0.630865280613357	2		610	840	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420049	49420049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002777-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	117	493	0	ENST00000301067.7:c.15700G>A	p.Glu5234Lys	p.E5234K	ENST00000301067	NM_003482.3	5234	Gag/Aag	48/54	0.312244872692535	4	FACETS	0.687	0.619	0.76	0.344	0.309	0.38	INDETERMINATE	1	TRUE	2	0.630865280613357	4		493	880	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030486	49030486	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0002777-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	357	239	0	ENST00000267163.4:c.1960+1G>T		p.X654_splice	ENST00000267163	NM_000321.2	654			0.630865280613357	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	0	0.630865280613357	3		239	460	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41209086	41209086	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs80357432	NA	P-0002777-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	87	581	0	ENST00000357654.3:c.5260G>C	p.Glu1754Gln	p.E1754Q	ENST00000357654	NM_007294.3	1754	Gaa/Caa	19/23	0.630865280613357	3	FACETS	0.312	0.275	0.352	0.156	0.137	0.176	SUBCLONAL	1	TRUE	1	0.630865280613357	3		581	1161	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652121	36652122	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0002777-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	351	347	0	ENST00000244741.5:c.247dup	p.Arg83ProfsTer6	p.R83Pfs*6	ENST00000244741	NM_000389.4	81	-/C	2/3	0.511860534772544	4	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.630865280613357	4		347	788	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0002801-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	155	291	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	2	FALSE	NA	0.3	2		292	470	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172065	99172065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1297649299	NA	P-0002801-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	82	188	1	ENST00000074304.5:c.1631G>A	p.Arg544His	p.R544H	ENST00000074304	NM_001134224.1	544	cGt/cAt	17/26	0.3	3	FACETS	1	0.96	1	0.601	0.531	0.676	CLONAL	1	FALSE	1	0.3	3		189	523	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456904	149456904	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002801-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	136	346	0	ENST00000286301.3:c.824A>G	p.Asn275Ser	p.N275S	ENST00000286301	NM_005211.3	275	aAc/aGc	6/22	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.3	2		346	722	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358978	81358978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374484762	NA	P-0002801-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	117	339	0	ENST00000222390.5:c.983G>A	p.Arg328His	p.R328H	ENST00000222390	NM_000601.4	328	cGt/cAt	8/18	0.3	3	FACETS	0.989	0.891	1	0.494	0.445	0.547	CLONAL	1	FALSE	1	0.3	3		339	907	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971156	21971156	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002801-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	63	69	0	ENST00000304494.5:c.202G>A	p.Ala68Thr	p.A68T	ENST00000304494	NM_000077.4	68	Gcg/Acg	2/3	0.3	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	FALSE	0	0.3	2		69	192	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591892	48591892	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002801-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	134	351	0	ENST00000342988.3:c.1055G>C	p.Gly352Ala	p.G352A	ENST00000342988	NM_005359.5	352	gGa/gCa	9/12	0.3	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	FALSE	0	0.3	1		351	664	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308068	30308068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002801-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2333	438	338	0	ENST00000262643.3:c.205G>A	p.Ala69Thr	p.A69T	ENST00000262643	NM_001238.2	69	Gca/Aca	5/12	0.3	19	FACETS	0.935	0.887	0.985			1	CLONAL	4	FALSE	NA	0.3	19		338	2771	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31379483	31379483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002801-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	331	322	0	ENST00000328111.2:c.890C>T	p.Ser297Phe	p.S297F	ENST00000328111	NM_006892.3	297	tCc/tTc	8/23	0.3	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	FALSE	1	0.3	4		322	915	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002815-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	62	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.759717056201662	2		422	161	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0002815-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	177	314	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.907	0.842	0.973	0.907	0.842	0.973	CLONAL	1	TRUE	1	0.759717056201662	2		314	514	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791758	42791758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1380826096	NA	P-0002815-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	84	579	0	ENST00000575354.2:c.644G>A	p.Arg215Gln	p.R215Q	ENST00000575354	NM_015125.3	215	cGg/cAg	5/20	0.759717056201662	1	FACETS	0.408	0.363	0.455	0.408	0.363	0.455	SUBCLONAL	1	TRUE	0	0.759717056201662	1		579	336	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798385	42798386	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CTGCAGCTCGGAGC	novel	NA	P-0002815-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	52	467	0	ENST00000575354.2:c.4258_4271dup	p.Asn1425AlafsTer34	p.N1425Afs*34	ENST00000575354	NM_015125.3	1419	agc/agCTGCAGCTCGGAGCc	18/20	0.759717056201662	1	FACETS	0.245	0.209	0.284	0.245	0.209	0.284	SUBCLONAL	1	TRUE	0	0.759717056201662	1		467	346	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0002830-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	21	393	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		393	379	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971196	21971198	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	novel	NA	P-0002830-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	14	97	0	ENST00000304494.5:c.160_162del	p.Met54del	p.M54del	ENST00000304494	NM_000077.4	54	ATG/-	2/3	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		97	261	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002836-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	142	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.806393714844479	2		422	322	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588751	29588751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs760703505	NA	P-0002836-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	377	361	0	ENST00000356175.3:c.4537C>T	p.Arg1513Ter	p.R1513*	ENST00000356175	NM_000267.3	1513	Cga/Tga	34/57	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.806393714844479	2		361	920	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439843	52439843	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747079481	NA	P-0002836-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	337	328	0	ENST00000460680.1:c.869A>G	p.Asn290Ser	p.N290S	ENST00000460680	NM_004656.3	290	aAc/aGc	10/17	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.806393714844479	2		328	810	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332875	152332875	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1131692059	NA	P-0002836-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	380	380	2	ENST00000206249.3:c.1181G>A	p.Arg394His	p.R394H	ENST00000206249	NM_000125.3	394	cGc/cAc	5/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.806393714844479	2		382	873	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692916	89692918	+	inframe_deletion	In_Frame_Del	DEL	ATG	ATG	-	rs1554898152	NA	P-0002836-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	249	278	0	ENST00000371953.3:c.402_404del	p.Met134del	p.M134del	ENST00000371953	NM_000314.4	134	ATG/-	5/9	0.806393714844479	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.806393714844479	1		278	358	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002860-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	79	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.776525654122638	2		422	181	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928069	178928086	+	inframe_deletion	In_Frame_Del	DEL	TCATGGATTAGAAGATTT	TCATGGATTAGAAGATTT	-	novel	NA	P-0002860-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	189	327	0	ENST00000263967.3:c.1347_1364del	p.His450_Leu455del	p.H450_L455del	ENST00000263967	NM_006218.2	449	ccTCATGGATTAGAAGATTTg/ccg	8/21	1	2	FACETS	0.77	0.715	0.827	0.77	0.715	0.827	SUBCLONAL	1	TRUE	1	0.776525654122638	2		327	632	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0002862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	37	496	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	0.763432811563105	1	FACETS	0.076	0.062	0.092	0.076	0.062	0.092	SUBCLONAL	1	TRUE	0	0.775313761891995	1		496	765	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	125	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.937	0.859	1	0.937	0.859	1	CLONAL	1	TRUE	1	0.775313761891995	2		422	344	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578493	7578493	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1206165503	NA	P-0002862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	368	392	0	ENST00000269305.4:c.437G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tGg/tAg	5/11	0.763432811563105	1	FACETS	0.894	0.858	0.931	0.894	0.858	0.931	CLONAL	1	TRUE	0	0.775313761891995	1		392	650	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602817	10602817	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs374203165	NA	P-0002862-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	415	435	1	ENST00000171111.5:c.761A>G	p.Lys254Arg	p.K254R	ENST00000171111	NM_203500.1	254	aAg/aGg	3/6	0.775313761891995	3	FACETS	0.959	0.912	1	0.48	0.456	0.504	CLONAL	1	TRUE	1	0.775313761891995	3		436	1549	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002870-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	93	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.985	0.892	1	0.985	0.892	1	CLONAL	1	TRUE	1	0.807166391092273	2		422	234	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692911	89692911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909241	NA	P-0002870-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	147	306	0	ENST00000371953.3:c.395G>A	p.Gly132Asp	p.G132D	ENST00000371953	NM_000314.4	132	gGt/gAt	5/9	0.807166391092273	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.807166391092273	1		306	198	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807140	1807140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002870-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	285	373	0	ENST00000260795.2:c.1471G>A	p.Ala491Thr	p.A491T	ENST00000260795		491	Gcc/Acc	10/17	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.807166391092273	2		373	604	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932492	39932492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002870-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	283	432	0	ENST00000378444.4:c.2107C>T	p.Pro703Ser	p.P703S	ENST00000378444	NM_001123385.1	703	Ccc/Tcc	4/15	0.119554517448435	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.807166391092273	0		432	698	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002875-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	128	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.617745086300552	2		422	328	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0002875-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	147	318	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.617745086300552	2		318	376	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267698	198267698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002875-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	84	266	0	ENST00000335508.6:c.1781G>A	p.Arg594Gln	p.R594Q	ENST00000335508	NM_012433.2	594	cGa/cAa	13/25	1	2	FACETS	0.904	0.807	1	0.904	0.807	1	CLONAL	1	TRUE	1	0.617745086300552	2		266	301	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2588120	2588120	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1017287074	NA	P-0002875-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	17	23	0	ENST00000342085.4:c.7A>G	p.Arg3Gly	p.R3G	ENST00000342085	NM_002613.4	3	Agg/Ggg	1/14	1	2	FACETS	1	0.867	1	1	0.867	1	CLONAL	1	TRUE	1	0.617745086300552	2		23	47	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002888-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	71	422	0				ENST00000310581	NM_198253.2	-/1132			0.481818278124432	3	FACETS	1	0.914	1	0.525	0.462	0.593	CLONAL	1	TRUE	1	0.481818278124432	3		422	348	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202641	108202642	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACTTTGTTTATTATACTGGCCTTAGCAAATGCAA	novel	NA	P-0002888-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	100	389	0	ENST00000278616.4:c.7668_7701dup	p.Arg2568PhefsTer14	p.R2568Ffs*14	ENST00000278616	NM_000051.3	2555	-/ACTTTGTTTATTATACTGGCCTTAGCAAATGCAA	52/63	0.481818278124432	1	FACETS	0.612	0.548	0.679	0.612	0.548	0.679	SUBCLONAL	1	TRUE	0	0.481818278124432	1		389	515	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002891-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	25	422	0				ENST00000310581	NM_198253.2	-/1132			0.232831230941493	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.748269179084879	0		422	81	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0002891-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	175	462	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.514406845850135	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.748269179084879	1		462	253	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030478	49030479	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1566234123	NA	P-0002891-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	100	258	0	ENST00000267163.4:c.1959dup	p.Val654SerfsTer14	p.V654Sfs*14	ENST00000267163	NM_000321.2	651	-/A	19/27	0.741119268410139	1	FACETS	0.747	0.681	0.813	0.747	0.681	0.813	SUBCLONAL	1	TRUE	0	0.748269179084879	1		258	224	SUCCESS
ALK	238	MSKCC	GRCh37	2	29420441	29420441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573049471	NA	P-0002891-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	106	439	0	ENST00000389048.3:c.4040G>A	p.Arg1347Gln	p.R1347Q	ENST00000389048	NM_004304.4	1347	cGg/cAg	27/29	1	2	FACETS	0.874	0.793	0.958	0.874	0.793	0.958	CLONAL	1	TRUE	1	0.748269179084879	2		439	324	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29422330	29422330	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0002891-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	126	309	0	ENST00000356175.3:c.3G>A	p.Met1?	p.M1?	ENST00000356175	NM_000267.3	1	atG/atA	1/57	0.741119268410139	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.748269179084879	1		309	193	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164375	47164378	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	novel	NA	P-0002891-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	158	343	0	ENST00000409792.3:c.1748_1751del	p.Lys583SerfsTer17	p.K583Sfs*17	ENST00000409792	NM_014159.6	583	aAACAg/ag	3/21	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.748269179084879	2		343	422	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720654	89720655	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0002891-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	43	99	0	ENST00000371953.3:c.807_808del	p.Lys269AsnfsTer28	p.K269Nfs*28	ENST00000371953	NM_000314.4	269	AAa/a	8/9	0.546429429460715	1	FACETS	0.719	0.623	0.818	0.719	0.623	0.818	SUBCLONAL	1	TRUE	0	0.748269179084879	1		99	100	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002899-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	140	422	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		422	307	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002906-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	86	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.409400057495624	2		422	373	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638440	176638440	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002906-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	206	1090	0	ENST00000439151.2:c.3040G>T	p.Asp1014Tyr	p.D1014Y	ENST00000439151	NM_022455.4	1014	Gac/Tac	5/23	0.409400057495624	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.409400057495624	1		1090	736	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579533	7579533	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002906-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	151	1058	0	ENST00000269305.4:c.154C>T	p.Gln52Ter	p.Q52*	ENST00000269305	NM_001126112.2	52	Caa/Taa	4/11	0.409400057495624	1	FACETS	0.973	0.893	1	0.973	0.893	1	CLONAL	1	TRUE	0	0.409400057495624	1		1058	603	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12043200	12043200	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002906-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	127	1158	0	ENST00000353533.5:c.1085T>C	p.Leu362Pro	p.L362P	ENST00000353533	NM_003010.3	362	cTg/cCg	10/11	0.409400057495624	1	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	0	0.409400057495624	1		1158	492	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135804181	135804187	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTCAC	CTGTCAC	-	novel	NA	P-0002906-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	152	988	0	ENST00000298552.3:c.73_79del	p.Val25LeufsTer16	p.V25Lfs*16	ENST00000298552	NM_001162426.1	25	GTGACAGct/ct	3/23	0.409400057495624	1	FACETS	0.914	0.839	0.992	0.914	0.839	0.992	CLONAL	1	TRUE	0	0.409400057495624	1		988	646	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002910-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	54	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.344169985543001	2		422	278	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0002910-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	122	310	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.344169985543001	2		310	706	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498019	29498019	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002910-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	218	681	0	ENST00000389048.3:c.1987G>C	p.Glu663Gln	p.E663Q	ENST00000389048	NM_004304.4	663	Gag/Cag	11/29	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.344169985543001	2		681	1247	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020745	112020745	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002910-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	232	757	1	ENST00000368678.4:c.826C>T	p.Gln276Ter	p.Q276*	ENST00000368678		276	Cag/Tag	8/13	0.106569706319844	0	FACETS	0.655	0.61	0.703			1	INDETERMINATE	1	TRUE	0	0.344169985543001	0		758	1349	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871029	12871029	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002910-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	127	283	0	ENST00000228872.4:c.256G>T	p.Glu86Ter	p.E86*	ENST00000228872	NM_004064.3	86	Gag/Tag	1/3	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.344169985543001	2		283	606	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336064	73336064	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002910-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	114	317	0	ENST00000377767.4:c.2339G>C	p.Arg780Thr	p.R780T	ENST00000377767	NM_014953.3	780	aGa/aCa	17/21	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.344169985543001	2		317	616	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95598909	95598909	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002910-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	132	439	0	ENST00000393063.1:c.250C>T	p.Gln84Ter	p.Q84*	ENST00000393063	NM_030621.3	84	Cag/Tag	4/28	1	2	FACETS	0.964	0.875	1	0.964	0.875	1	CLONAL	1	TRUE	1	0.344169985543001	2		439	796	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56865884	56865884	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002910-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	255	729	0	ENST00000308159.5:c.1216G>A	p.Val406Met	p.V406M	ENST00000308159	NM_014669.4	406	Gtg/Atg	11/22	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.344169985543001	2		729	1350	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933311	39933311	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002910-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	176	646	0	ENST00000378444.4:c.1288C>T	p.Gln430Ter	p.Q430*	ENST00000378444	NM_001123385.1	430	Cag/Tag	4/15	1	2	FACETS	0.931	0.857	1	0.931	0.857	1	CLONAL	1	TRUE	1	0.344169985543001	2		646	1098	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002936-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	41	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.946	1			1	INDETERMINATE	1	FALSE	NA	0.631587404636318	2		422	105	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs764146326	NA	P-0002936-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	331	532	0	ENST00000269305.4:c.841G>C	p.Asp281His	p.D281H	ENST00000269305	NM_001126112.2	281	Gac/Cac	8/11	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	FALSE	1	0.631587404636318	2		532	736	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267708	198267708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002936-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	245	377	0	ENST00000335508.6:c.1771G>A	p.Val591Met	p.V591M	ENST00000335508	NM_012433.2	591	Gtg/Atg	13/25	0.102308763074662	4	FACETS	0.965	0.907	1	0.965	0.907	1	INDETERMINATE	2	FALSE	2	0.631587404636318	4		377	656	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923093	48923094	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0002936-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	281	410	1	ENST00000267163.4:c.542dup	p.Ser182IlefsTer3	p.S182Ifs*3	ENST00000267163	NM_000321.2	181	ata/aTta	6/27	0.631587404636318	1	FACETS	0.773	0.743	0.802	1	0.996	1	SUBCLONAL	2	FALSE	0	0.631587404636318	1		411	394	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428384	33428385	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0002936-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	172	406	0	ENST00000345365.6:c.739-1_739insC	p.Val247ArgfsTer80	p.V247Rfs*80	ENST00000345365	NM_002878.3	246	-/C		1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.631587404636318	2		406	417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578402	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	GCTCATGGTGGGGG	GCTCATGGTGGGGG	T	novel	NA	P-0002936-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	9	323	0	ENST00000269305.4:c.528_541delinsA	p.Cys176Ter	p.C176*	ENST00000269305	NM_001126112.2	176	tgCCCCCACCATGAGCgc/tgAgc	5/11	1	2	FACETS	0.072	0.047	0.104	0.072	0.047	0.104	SUBCLONAL	1	FALSE	1	0.631587404636318	2		323	397	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0002953-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	288	291	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.23832228894546	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	3	TRUE	0	0.309447363516674	2		292	570	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002953-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	119	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.841	0.77	0.913	1	0.991	1	CLONAL	3	TRUE	1	0.309447363516674	2		422	305	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0002953-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	99	295	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.309447363516674	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.309447363516674	3		295	320	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031970	26031970	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002953-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	151	223	0	ENST00000244661.2:c.319G>A	p.Asp107Asn	p.D107N	ENST00000244661	NM_003537.3	107	Gac/Aac	1/1	1	2	FACETS	1	0.963	1	1	0.992	1	CLONAL	2	TRUE	1	0.309447363516674	2		223	455	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373178	118373178	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200497972	NA	P-0002953-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	316	518	1	ENST00000534358.1:c.6571C>T	p.Arg2191Ter	p.R2191*	ENST00000534358	NM_005933.3	2191	Cga/Tga	27/36	1	2	FACETS	1	0.982	1	1	0.996	1	CLONAL	2	TRUE	1	0.309447363516674	2		519	939	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087404	27087404	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002953-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	421	489	1	ENST00000324856.7:c.1978G>T	p.Gly660Ter	p.G660*	ENST00000324856	NM_006015.4	660	Gga/Tga	5/20	0.309447363516674	3	FACETS	1	0.982	1	1	0.996	1	CLONAL	3	TRUE	1	0.309447363516674	3		490	997	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440372	52440372	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002953-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	218	227	0	ENST00000460680.1:c.680G>C	p.Arg227Pro	p.R227P	ENST00000460680	NM_004656.3	227	cGc/cCc	9/17	0.309447363516674	3	FACETS	0.91	0.852	0.969	1	0.991	1	CLONAL	3	TRUE	1	0.309447363516674	3		227	596	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440379	52440379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002953-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	236	220	0	ENST00000460680.1:c.673G>A	p.Asp225Asn	p.D225N	ENST00000460680	NM_004656.3	225	Gac/Aac	9/17	0.309447363516674	3	FACETS	1	0.985	1	1	0.994	1	CLONAL	3	TRUE	1	0.309447363516674	3		220	518	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806089	1806089	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913479	NA	P-0002953-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	274	428	2	ENST00000260795.2:c.1108G>T	p.Gly370Cys	p.G370C	ENST00000260795		370	Ggc/Tgc	8/17	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.309447363516674	2		430	752	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721577	176721577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002953-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	278	454	2	ENST00000439151.2:c.7208C>T	p.Ser2403Leu	p.S2403L	ENST00000439151	NM_022455.4	2403	tCa/tTa	23/23	1	2	FACETS	1	0.986	1	1	0.996	1	CLONAL	2	TRUE	1	0.309447363516674	2		456	786	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056283	26056283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1459637809	NA	P-0002953-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	283	477	0	ENST00000343677.2:c.374G>A	p.Gly125Glu	p.G125E	ENST00000343677	NM_005319.3	125	gGa/gAa	1/1	1	2	FACETS	1	0.987	1	1	0.996	1	CLONAL	2	TRUE	1	0.309447363516674	2		477	795	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850987	63850987	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002953-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	30	344	0	ENST00000279873.7:c.1765G>T	p.Glu589Ter	p.E589*	ENST00000279873	NM_032199.2	589	Gaa/Taa	10/10	1	2	FACETS	0.33	0.265	0.405	0.33	0.265	0.405	SUBCLONAL	1	TRUE	1	0.309447363516674	2		344	587	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279606	123279606	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002953-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	90	349	0	ENST00000358487.5:c.826T>A	p.Phe276Ile	p.F276I	ENST00000358487	NM_000141.4	276	Ttt/Att	7/18	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.309447363516674	2		349	577	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264333	30264333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002953-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	18	53	1	ENST00000322652.5:c.68G>A	p.Gly23Asp	p.G23D	ENST00000322652	NM_015355.2	23	gGc/gAc	1/16	0.23832228894546	2	FACETS	1	0.902	1	0.701	0.539	0.883	CLONAL	1	TRUE	0	0.309447363516674	2		54	83	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657668	37657668	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002953-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	175	386	0	ENST00000447079.4:c.2585G>C	p.Cys862Ser	p.C862S	ENST00000447079	NM_015083.1	862	tGt/tCt	6/14	0.23832228894546	2	FACETS	1	0.988	1	0.693	0.639	0.749	CLONAL	1	TRUE	0	0.309447363516674	2		386	816	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872213	45872213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002953-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	274	430	1	ENST00000391945.4:c.221C>T	p.Ser74Leu	p.S74L	ENST00000391945	NM_000400.3	74	tCa/tTa	4/23	0.309447363516674	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.309447363516674	3		431	865	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950067	44950067	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1473353111	NA	P-0002953-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	147	630	0	ENST00000377967.4:c.3836G>A	p.Arg1279Gln	p.R1279Q	ENST00000377967	NM_021140.2	1279	cGa/cAa	26/29	0.309447363516674	5	FACETS	1	0.929	1			1	CLONAL	1	TRUE	NA	0.309447363516674	5		630	1358	SUCCESS
REL	5966	MSKCC	GRCh37	2	61144055	61144077	+	frameshift_variant	Frame_Shift_Del	DEL	TGTGGTGAGACTGTGTTTTCAAG	TGTGGTGAGACTGTGTTTTCAAG	-	novel	NA	P-0002953-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	255	411	0	ENST00000295025.8:c.439_461del	p.Val147PhefsTer4	p.V147Ffs*4	ENST00000295025	NM_002908.2	146	aaTGTGGTGAGACTGTGTTTTCAAGtt/aatt	5/11	1	2	FACETS	1	0.981	1	1	0.995	1	CLONAL	2	TRUE	1	0.309447363516674	2		411	749	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44733136	44733183	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGCGTTAACGAGTAAACTGTGTCTGTCTCCACAGCCGCCTCTTTGGGT	AGCGTTAACGAGTAAACTGTGTCTGTCTCCACAGCCGCCTCTTTGGGT	-	novel	NA	P-0002953-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	312	430	1	ENST00000377967.4:c.162-34_175del		p.X54_splice	ENST00000377967	NM_021140.2	54		2/29	0.309447363516674	5	FACETS	1	0.989	1			1	CLONAL	3	TRUE	NA	0.309447363516674	5		431	846	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577124	7577124	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912657	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	125	412	0	ENST00000269305.4:c.814G>T	p.Val272Leu	p.V272L	ENST00000269305	NM_001126112.2	272	Gtg/Ttg	8/11	0.302085700259894	2	FACETS	0.753	0.686	0.822	0.753	0.686	0.822	SUBCLONAL	2	TRUE	0	0.36641782572784	2		412	453	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099008	27099008	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	113	268	0	ENST00000324856.7:c.3424C>T	p.Gln1142Ter	p.Q1142*	ENST00000324856	NM_006015.4	1142	Cag/Tag	13/20	0.353673530147635	3	FACETS	1	0.931	1	1	0.931	1	CLONAL	2	TRUE	1	0.36641782572784	3		268	355	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43806076	43806076	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1171488184	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	61	371	0	ENST00000372470.3:c.872G>C	p.Cys291Ser	p.C291S	ENST00000372470	NM_005373.2	291	tGc/tCc	6/12	0.353673530147635	3	FACETS	0.749	0.647	0.86	0.374	0.323	0.43	SUBCLONAL	1	TRUE	1	0.36641782572784	3		371	526	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414921	78414921	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	212	319	0	ENST00000370768.2:c.1845G>T	p.Trp615Cys	p.W615C	ENST00000370768	NM_003902.3	615	tgG/tgT	19/20	0.278349834797737	5	FACETS	1	0.987	1	0.83	0.774	0.888	CLONAL	2	TRUE	2	0.36641782572784	5		319	720	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745634	162745634	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	76	278	0	ENST00000367921.3:c.2048+1G>T		p.X683_splice	ENST00000367921	NM_006182.2	683			0.36641782572784	4	FACETS	1	0.934	1	0.547	0.481	0.618	CLONAL	1	TRUE	2	0.36641782572784	4		278	518	SUCCESS
FH	2271	MSKCC	GRCh37	1	241672084	241672084	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	58	200	0	ENST00000366560.3:c.557G>T	p.Ser186Ile	p.S186I	ENST00000366560	NM_000143.3	186	aGc/aTc	5/10	0.36641782572784	3	FACETS	0.881	0.759	1	0.441	0.379	0.507	CLONAL	1	TRUE	1	0.36641782572784	3		200	425	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295717	212295717	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	267	389	0	ENST00000342788.4:c.2596A>T	p.Arg866Ter	p.R866*	ENST00000342788	NM_005235.2	866	Aga/Tga	21/28	0.36641782572784	4	FACETS	0.902	0.85	0.955	0.902	0.85	0.955	CLONAL	3	TRUE	1	0.36641782572784	4		389	736	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660096	227660096	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1205422488	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	138	252	0	ENST00000305123.5:c.3359G>T	p.Gly1120Val	p.G1120V	ENST00000305123	NM_005544.2	1120	gGa/gTa	1/2	0.36641782572784	4	FACETS	1	0.969	1	0.744	0.682	0.808	CLONAL	2	TRUE	1	0.36641782572784	4		252	461	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437686	52437686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141453056	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	83	295	2	ENST00000460680.1:c.1475G>A	p.Ser492Asn	p.S492N	ENST00000460680	NM_004656.3	492	aGt/aAt	13/17	NA	2	FACETS	0.75	0.669	0.835			1	INDETERMINATE	2	TRUE	NA	0.36641782572784	2		297	302	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259454	89259454	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	80	432	0	ENST00000336596.2:c.598A>T	p.Lys200Ter	p.K200*	ENST00000336596	NM_005233.5	200	Aaa/Taa	3/17	0.277167137682878	4	FACETS	0.874	0.769	0.986			1	CLONAL	1	TRUE	NA	0.36641782572784	4		432	683	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176552	142176552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	109	376	0	ENST00000350721.4:c.7549C>T	p.His2517Tyr	p.H2517Y	ENST00000350721	NM_001184.3	2517	Cat/Tat	45/47	0.207612855038404	3	FACETS	1	0.913	1			1	INDETERMINATE	1	TRUE	NA	0.36641782572784	3		376	692	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201656	66201656	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	64	330	0	ENST00000273854.3:c.2846C>A	p.Ser949Tyr	p.S949Y	ENST00000273854	NM_004439.5	949	tCc/tAc	16/18	1	2	FACETS	0.585	0.507	0.67	0.585	0.507	0.67	SUBCLONAL	1	TRUE	1	0.36641782572784	2		330	597	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539602	187539602	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	119	318	0	ENST00000441802.2:c.8138C>A	p.Ser2713Ter	p.S2713*	ENST00000441802	NM_005245.3	2713	tCa/tAa	10/27	0.36641782572784	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.36641782572784	1		318	360	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460518	149460518	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	45	293	0	ENST00000286301.3:c.119T>C	p.Leu40Ser	p.L40S	ENST00000286301	NM_005211.3	40	tTg/tCg	3/22	0.353673530147635	3	FACETS	0.759	0.639	0.89	0.379	0.319	0.445	SUBCLONAL	1	TRUE	1	0.36641782572784	3		293	383	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180958	32180958	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	66	311	0	ENST00000375023.3:c.2392C>A	p.Gln798Lys	p.Q798K	ENST00000375023	NM_004557.3	798	Cag/Aag	15/30	0.36641782572784	2	FACETS	1	0.911	1	0.527	0.46	0.598	CLONAL	1	TRUE	0	0.36641782572784	2		311	342	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332887	152332887	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	49	286	0	ENST00000206249.3:c.1193A>C	p.His398Pro	p.H398P	ENST00000206249	NM_000125.3	398	cAc/cCc	5/8	0.36641782572784	3	FACETS	0.577	0.489	0.675	0.289	0.244	0.338	SUBCLONAL	1	TRUE	1	0.36641782572784	3		286	548	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522520	157522520	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554235993	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	131	434	0	ENST00000346085.5:c.4792C>T	p.Gln1598Ter	p.Q1598*	ENST00000346085	NM_020732.3	1598	Caa/Taa	18/20	0.36641782572784	3	FACETS	1	0.986	1	0.736	0.67	0.804	CLONAL	1	TRUE	1	0.36641782572784	3		434	575	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978390	2978390	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	249	391	0	ENST00000396946.4:c.940G>C	p.Glu314Gln	p.E314Q	ENST00000396946	NM_032415.4	314	Gag/Cag	7/25	0.36641782572784	4	FACETS	0.987	0.93	1	1	0.993	1	CLONAL	3	TRUE	2	0.36641782572784	4		391	627	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367353	50367353	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	76	188	0	ENST00000331340.3:c.160G>A	p.Ala54Thr	p.A54T	ENST00000331340	NM_006060.4	54	Gcc/Acc	3/8	0.36641782572784	6	FACETS	0.808	0.711	0.911	0.404	0.355	0.456	CLONAL	2	TRUE	2	0.36641782572784	6		188	445	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268956	55268956	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	150	341	0	ENST00000275493.2:c.3022G>T	p.Asp1008Tyr	p.D1008Y	ENST00000275493	NM_005228.3	1008	Gac/Tac	25/28	0.36641782572784	6	FACETS	0.873	0.798	0.95	0.436	0.399	0.475	CLONAL	2	TRUE	2	0.36641782572784	6		341	813	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335628	81335628	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	366	323	0	ENST00000222390.5:c.1732G>T	p.Asp578Tyr	p.D578Y	ENST00000222390	NM_000601.4	578	Gat/Tat	15/18	0.36641782572784	6	FACETS	0.966	0.92	1	0.966	0.92	1	CLONAL	4	TRUE	2	0.36641782572784	6		323	896	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878740	151878740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	236	265	0	ENST00000262189.6:c.6205G>A	p.Val2069Ile	p.V2069I	ENST00000262189	NM_170606.2	2069	Gtt/Att	36/59	0.36641782572784	5	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	2	0.36641782572784	5		265	601	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372045	55372045	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	26	193	0	ENST00000297316.4:c.735C>A	p.Cys245Ter	p.C245*	ENST00000297316	NM_022454.3	245	tgC/tgA	2/2	0.251162923440748	4	FACETS	0.74	0.588	0.913	0.37	0.294	0.457	CLONAL	1	TRUE	2	0.36641782572784	4		193	262	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485851	8485851	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	138	395	0	ENST00000356435.5:c.2966C>G	p.Thr989Arg	p.T989R	ENST00000356435		989	aCa/aGa	17/35	0.36641782572784	8	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.36641782572784	8		395	1059	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521463	8521463	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	156	298	0	ENST00000356435.5:c.775G>T	p.Ala259Ser	p.A259S	ENST00000356435		259	Gcc/Tcc	9/35	0.36641782572784	8	FACETS	0.835	0.764	0.91			1	CLONAL	2	TRUE	NA	0.36641782572784	8		298	1070	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971123	21971123	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1554654113	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	77	221	0	ENST00000304494.5:c.235A>C	p.Thr79Pro	p.T79P	ENST00000304494	NM_000077.4	79	Acc/Ccc	2/3	0.213379744309586	4	FACETS	0.932	0.826	1			1	INDETERMINATE	2	TRUE	NA	0.36641782572784	4		221	308	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400096	139400096	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	104	330	0	ENST00000277541.6:c.4252G>T	p.Ala1418Ser	p.A1418S	ENST00000277541	NM_017617.3	1418	Gcc/Tcc	25/34	0.36641782572784	3	FACETS	0.848	0.765	0.934	0.848	0.765	0.934	CLONAL	2	TRUE	1	0.36641782572784	3		330	396	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100740	8100740	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	88	324	0	ENST00000346208.3:c.714C>A	p.Ser238Arg	p.S238R	ENST00000346208		238	agC/agA	3/6	0.257660183934419	5	FACETS	0.846	0.753	0.944	0.564	0.502	0.629	CLONAL	2	TRUE	2	0.36641782572784	5		324	440	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450771	70450771	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	57	293	0	ENST00000373644.4:c.5611G>T	p.Gly1871Trp	p.G1871W	ENST00000373644	NM_030625.2	1871	Ggg/Tgg	12/12	1	2	FACETS	0.609	0.523	0.703	0.609	0.523	0.703	SUBCLONAL	1	TRUE	1	0.36641782572784	2		293	511	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741394	17741394	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	34	353	0	ENST00000250003.3:c.65C>A	p.Ser22Tyr	p.S22Y	ENST00000250003	NM_002478.4	22	tCc/tAc	1/3	0.353673530147635	3	FACETS	0.492	0.402	0.594	0.246	0.201	0.297	SUBCLONAL	1	TRUE	1	0.36641782572784	3		353	446	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741446	17741446	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	30	382	0	ENST00000250003.3:c.117C>A	p.Asp39Glu	p.D39E	ENST00000250003	NM_002478.4	39	gaC/gaA	1/3	0.353673530147635	3	FACETS	0.483	0.389	0.59	0.242	0.194	0.295	SUBCLONAL	1	TRUE	1	0.36641782572784	3		382	401	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450138	32450138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777166391	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	66	257	0	ENST00000332351.3:c.674C>T	p.Thr225Met	p.T225M	ENST00000332351	NM_024426.4	225	aCg/aTg	2/10	0.353673530147635	3	FACETS	1	0.961	1	0.636	0.556	0.722	CLONAL	1	TRUE	1	0.36641782572784	3		257	335	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128684	64128684	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	103	333	0	ENST00000334205.4:c.541G>T	p.Gly181Trp	p.G181W	ENST00000334205	NM_003942.2	181	Ggg/Tgg	5/17	0.353673530147635	3	FACETS	1	0.981	1	0.705	0.634	0.779	CLONAL	1	TRUE	1	0.36641782572784	3		333	472	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514457	125514457	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	67	303	0	ENST00000428830.2:c.1152G>T	p.Leu384Phe	p.L384F	ENST00000428830	NM_001114121.2	384	ttG/ttT	11/14	0.353673530147635	3	FACETS	0.704	0.611	0.803	0.352	0.305	0.402	SUBCLONAL	1	TRUE	1	0.36641782572784	3		303	615	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893598	28893598	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	101	370	0	ENST00000282397.4:c.3248G>T	p.Trp1083Leu	p.W1083L	ENST00000282397	NM_002019.4	1083	tGg/tTg	24/30	0.36641782572784	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.36641782572784	1		370	360	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669565	88669565	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	63	364	0	ENST00000360948.2:c.1333C>A	p.Leu445Met	p.L445M	ENST00000360948	NM_001012338.2	445	Ctg/Atg	12/19	1	2	FACETS	0.917	0.797	1	0.917	0.797	1	CLONAL	1	TRUE	1	0.36641782572784	2		364	375	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031815	10031815	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs397518465	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	31	178	0	ENST00000330684.3:c.1007+1G>A		p.X336_splice	ENST00000330684	NM_001134407.1	336			0.207612855038404	3	FACETS	0.632	0.512	0.766			1	INDETERMINATE	1	TRUE	NA	0.36641782572784	3		178	317	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132624	67132624	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	116	404	0	ENST00000412916.2:c.507A>T	p.Gln169His	p.Q169H	ENST00000412916		169	caA/caT	6/6	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.36641782572784	2		404	465	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556117	29556117	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	69	140	0	ENST00000356175.3:c.2484G>T	p.Leu828Phe	p.L828F	ENST00000356175	NM_000267.3	828	ttG/ttT	21/57	0.198290387089662	4	FACETS	0.83	0.729	0.937	0.83	0.729	0.937	INDETERMINATE	2	TRUE	2	0.36641782572784	4		140	310	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657502	29657502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	52	192	0	ENST00000356175.3:c.5735G>A	p.Gly1912Glu	p.G1912E	ENST00000356175	NM_000267.3	1912	gGa/gAa	38/57	0.198290387089662	4	FACETS	0.944	0.805	1	0.472	0.402	0.547	INDETERMINATE	1	TRUE	2	0.36641782572784	4		192	411	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78831599	78831599	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	64	300	2	ENST00000306801.3:c.1408G>T	p.Val470Phe	p.V470F	ENST00000306801	NM_020761.2	470	Gtc/Ttc	13/34	0.198290387089662	4	FACETS	1	0.937	1	0.567	0.492	0.647	INDETERMINATE	1	TRUE	2	0.36641782572784	4		302	421	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39567820	39567820	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	171	230	0	ENST00000262039.4:c.576G>T	p.Trp192Cys	p.W192C	ENST00000262039	NM_002647.2	192	tgG/tgT	5/25	0.251162923440748	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.36641782572784	4		230	573	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166284	7166284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747464322	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	170	428	0	ENST00000302850.5:c.1742G>A	p.Arg581Gln	p.R581Q	ENST00000302850	NM_000208.2	581	cGg/cAg	8/22	0.36641782572784	2	FACETS	0.955	0.885	1	0.955	0.885	1	CLONAL	2	TRUE	0	0.36641782572784	2		428	486	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602869	10602869	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	210	301	0	ENST00000171111.5:c.709C>A	p.Leu237Met	p.L237M	ENST00000171111	NM_203500.1	237	Ctg/Atg	3/6	0.36641782572784	2	FACETS	0.882	0.831	0.934	1	0.991	1	CLONAL	3	TRUE	0	0.36641782572784	2		301	433	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017166	31017166	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	144	327	0	ENST00000375687.4:c.497G>C	p.Gly166Ala	p.G166A	ENST00000375687	NM_015338.5	166	gGg/gCg	7/13	0.251162923440748	4	FACETS	0.822	0.752	0.896	0.822	0.752	0.896	CLONAL	2	TRUE	2	0.36641782572784	4		327	653	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750646	39750646	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	81	147	2	ENST00000361337.2:c.2046G>T	p.Lys682Asn	p.K682N	ENST00000361337	NM_003286.2	682	aaG/aaT	20/21	0.251162923440748	4	FACETS	0.828	0.734	0.926	0.828	0.734	0.926	CLONAL	2	TRUE	2	0.36641782572784	4		149	365	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339603	70339603	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057524478	NA	P-0002964-T02-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	162	245	0	ENST00000374080.3:c.272G>T	p.Arg91Leu	p.R91L	ENST00000374080		91	cGc/cTc	3/45	0.213379744309586	2	FACETS	0.849	0.792	0.907			1	INDETERMINATE	3	TRUE	NA	0.36641782572784	2		245	347	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002967-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	86	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.961	1	1	0.988	1	CLONAL	2	TRUE	1	0.476345411488207	2		422	164	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645156	67645156	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0002967-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	82	401	0	ENST00000264010.4:c.421G>T	p.Glu141Ter	p.E141*	ENST00000264010	NM_006565.3	141	Gaa/Taa	3/12	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.476345411488207	2		401	232	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004856	16004856	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002967-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	19	416	0	ENST00000268712.3:c.2398C>T	p.Gln800Ter	p.Q800*	ENST00000268712	NM_006311.3	800	Cag/Tag	20/46	0.476345411488207	0	FACETS	0.232	0.177	0.296			1	SUBCLONAL	1	TRUE	0	0.476345411488207	0		416	180	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0002980-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	116	588	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.82	0.737	0.907	0.82	0.737	0.907	CLONAL	1	TRUE	1	0.27	2		588	1048	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456789	32456789	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002980-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	34	240	0	ENST00000332351.3:c.103G>T	p.Asp35Tyr	p.D35Y	ENST00000332351	NM_024426.4	35	Gac/Tac	1/10	1	2	FACETS	0.86	0.705	1	0.86	0.705	1	CLONAL	1	TRUE	1	0.27	2		240	293	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380238	25380238	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs770020203	NA	P-0002980-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	128	612	0	ENST00000311936.3:c.220A>G	p.Thr74Ala	p.T74A	ENST00000311936	NM_004985.3	74	Act/Gct	3/5	1	2	FACETS	0.93	0.841	1	0.93	0.841	1	CLONAL	1	TRUE	1	0.27	2		612	1020	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987085	36987085	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002980-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	37	381	0	ENST00000354822.5:c.604C>G	p.Gln202Glu	p.Q202E	ENST00000354822	NM_001079668.2	202	Cag/Gag	3/3	1	2	FACETS	0.633	0.522	0.757	0.633	0.522	0.757	SUBCLONAL	1	TRUE	1	0.27	2		381	433	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771319	68771319	+	start_lost	Translation_Start_Site	SNP	A	A	T	novel	NA	P-0002980-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	36	240	0	ENST00000261769.5:c.1A>T	p.Met1?	p.M1?	ENST00000261769	NM_004360.3	1	Atg/Ttg	1/16	1	2	FACETS	0.796	0.656	0.952	0.796	0.656	0.952	CLONAL	1	TRUE	1	0.27	2		240	335	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220698	1220698	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs730881975	NA	P-0002980-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	98	536	2	ENST00000326873.7:c.716G>C	p.Trp239Ser	p.W239S	ENST00000326873	NM_000455.4	239	tGg/tCg	5/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.27	2		538	645	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971192	21971192	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0002980-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	13	145	0	ENST00000304494.5:c.166del	p.Ser56AlafsTer90	p.S56Afs*90	ENST00000304494	NM_000077.4	56	Agc/gc	2/3	1	2	FACETS	0.523	0.374	0.705	0.523	0.374	0.705	SUBCLONAL	1	TRUE	1	0.27	2		145	184	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0002991-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	374	422	0				ENST00000310581	NM_198253.2	-/1132			0.486011111080401	6	FACETS	0.981	0.942	1			1	CLONAL	5	FALSE	NA	0.486011111080401	6		422	619	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0002991-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	640	394	2	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.32507105520698	5	FACETS	1	0.986	1			1	CLONAL	5	FALSE	NA	0.486011111080401	5		396	894	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747084	40747084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762809890	NA	P-0002991-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	369	461	2	ENST00000373198.4:c.2998G>A	p.Ala1000Thr	p.A1000T	ENST00000373198	NM_133170.3	1000	Gcc/Acc	22/32	0.456899591477612	5	FACETS	0.98	0.929	1			1	CLONAL	2	FALSE	NA	0.486011111080401	5		463	1339	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106732	27106732	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002991-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	586	497	0	ENST00000324856.7:c.6343C>T	p.Gln2115Ter	p.Q2115*	ENST00000324856	NM_006015.4	2115	Cag/Tag	20/20	0.308829408247442	5	FACETS	0.989	0.956	1	0.791	0.765	0.817	CLONAL	4	FALSE	0	0.486011111080401	5		497	1054	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703616	47703616	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002991-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	120	557	0	ENST00000233146.2:c.2116G>A	p.Asp706Asn	p.D706N	ENST00000233146	NM_000251.2	706	Gac/Aac	13/16	0.466103479719431	4	FACETS	0.793	0.716	0.876	0.397	0.358	0.438	SUBCLONAL	1	FALSE	2	0.486011111080401	4		557	925	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47710037	47710037	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1553370893	NA	P-0002991-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	98	468	0	ENST00000233146.2:c.2754G>T	p.Lys918Asn	p.K918N	ENST00000233146	NM_000251.2	918	aaG/aaT	16/16	0.466103479719431	4	FACETS	0.637	0.567	0.711	0.318	0.283	0.356	SUBCLONAL	1	FALSE	2	0.486011111080401	4		468	941	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159039	143159039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002991-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	56	553	0	ENST00000262992.4:c.814C>T	p.His272Tyr	p.H272Y	ENST00000262992	NM_001101669.1	272	Cac/Tac	10/24	0.262668444351848	3	FACETS	0.508	0.435	0.588	0.254	0.217	0.294	INDETERMINATE	1	FALSE	1	0.486011111080401	3		553	564	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6036981	6036981	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs777286241	NA	P-0002991-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	405	563	0	ENST00000265849.7:c.779C>G	p.Ser260Cys	p.S260C	ENST00000265849	NM_000535.5	260	tCc/tGc	7/15	0.413860530688114	4	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	FALSE	2	0.486011111080401	4		563	1191	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954378	48954378	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0002991-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	447	397	0	ENST00000267163.4:c.1498+1G>T		p.X500_splice	ENST00000267163	NM_000321.2	500			0.246442348961719	5	FACETS	0.929	0.897	0.959			1	INDETERMINATE	5	FALSE	NA	0.486011111080401	5		397	685	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312695	91312695	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002991-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	369	590	0	ENST00000355112.3:c.2434A>G	p.Lys812Glu	p.K812E	ENST00000355112	NM_000057.2	812	Aaa/Gaa	12/22	0.413860530688114	4	FACETS	0.987	0.937	1	0.987	0.937	1	CLONAL	2	FALSE	2	0.486011111080401	4		590	1143	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860398	42860398	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0002991-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	132	525	0	ENST00000398585.3:c.479C>G	p.Ser160Ter	p.S160*	ENST00000398585	NM_001135099.1	160	tCa/tGa	5/14	0.413860530688114	4	FACETS	0.735	0.666	0.808	0.368	0.333	0.404	SUBCLONAL	1	FALSE	2	0.486011111080401	4		525	1098	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210224	123210224	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002991-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	313	296	0	ENST00000218089.9:c.2576A>G	p.His859Arg	p.H859R	ENST00000218089	NM_001042749.1	859	cAc/cGc	26/35	0.406527366061622	2	FACETS	0.902	0.866	0.937			1	CLONAL	3	FALSE	NA	0.486011111080401	2		296	476	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425675	49425680	+	inframe_deletion	In_Frame_Del	DEL	TGTCTG	TGTCTG	-	novel	NA	P-0002991-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	234	392	0	ENST00000301067.7:c.12808_12813del	p.Gln4270_Thr4271del	p.Q4270_T4271del	ENST00000301067	NM_003482.3	4270	CAGACA/-	39/54	0.256490544530459	4	FACETS	0.998	0.935	1	0.998	0.935	1	INDETERMINATE	2	FALSE	2	0.486011111080401	4		392	717	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	126	403	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.345473846837073	2		404	653	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413049	139413049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064795070	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	220	302	0	ENST00000277541.6:c.1093C>T	p.Arg365Cys	p.R365C	ENST00000277541	NM_017617.3	365	Cgc/Tgc	6/34	0.345473846837073	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	3	TRUE	0	0.345473846837073	3		302	474	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	50	139	0				ENST00000310581	NM_198253.2	-/1132			0.345473846837073	4	FACETS	1	0.951	1	0.431	0.368	0.5	CLONAL	1	TRUE	1	0.345473846837073	4		139	301	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300507	11300507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	107	390	0	ENST00000361445.4:c.1639C>T	p.Leu547Phe	p.L547F	ENST00000361445	NM_004958.3	547	Ctt/Ttt	11/58	0.325376917318016	3	FACETS	1	0.926	1	0.519	0.466	0.575	CLONAL	1	TRUE	1	0.345473846837073	3		390	700	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120529649	120529649	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	242	345	1	ENST00000256646.2:c.808C>T	p.Gln270Ter	p.Q270*	ENST00000256646	NM_024408.3	270	Cag/Tag	5/34	0.319834651524803	4	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	2	0.345473846837073	4		346	938	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551502	150551502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	242	400	0	ENST00000369026.2:c.505G>A	p.Glu169Lys	p.E169K	ENST00000369026	NM_021960.4	169	Gag/Aag	1/3	0.319834651524803	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.345473846837073	4		400	877	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849035	156849035	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	143	358	0	ENST00000524377.1:c.1927G>A	p.Gly643Ser	p.G643S	ENST00000524377	NM_002529.3	643	Ggt/Agt	15/17	0.319834651524803	4	FACETS	0.955	0.875	1	0.955	0.875	1	CLONAL	2	TRUE	2	0.345473846837073	4		358	583	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085914	16085914	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143438192	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	59	269	0	ENST00000281043.3:c.1090C>T	p.Pro364Ser	p.P364S	ENST00000281043	NM_005378.4	364	Ccc/Tcc	3/3	0.319834651524803	4	FACETS	0.921	0.793	1	0.46	0.396	0.53	CLONAL	1	TRUE	2	0.345473846837073	4		269	499	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026813	48026813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622153	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	178	335	0	ENST00000234420.5:c.1691C>T	p.Ser564Leu	p.S564L	ENST00000234420	NM_000179.2	564	tCa/tTa	4/10	0.319834651524803	4	FACETS	0.927	0.856	1	0.927	0.856	1	CLONAL	2	TRUE	2	0.345473846837073	4		335	748	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732676	204732676	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	108	325	0	ENST00000302823.3:c.11T>C	p.Leu4Pro	p.L4P	ENST00000302823	NM_005214.4	4	cTt/cCt	1/4	0.345473846837073	2	FACETS	1	0.911	1	0.507	0.455	0.561	CLONAL	1	TRUE	0	0.345473846837073	2		325	617	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280750	41280750	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	71	289	1	ENST00000349496.5:c.2263G>T	p.Asp755Tyr	p.D755Y	ENST00000349496	NM_001904.3	755	Gat/Tat	15/15	0.325376917318016	3	FACETS	0.784	0.684	0.891	0.392	0.342	0.446	SUBCLONAL	1	TRUE	1	0.345473846837073	3		290	615	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163221	47163221	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	207	398	0	ENST00000409792.3:c.2905A>T	p.Ile969Leu	p.I969L	ENST00000409792	NM_014159.6	969	Ata/Tta	3/21	NA	2	FACETS	0.894	0.834	0.956			1	INDETERMINATE	2	TRUE	NA	0.345473846837073	2		398	670	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670816	134670816	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	85	199	0	ENST00000398015.3:c.727G>A	p.Asp243Asn	p.D243N	ENST00000398015	NM_004441.4	243	Gat/Aat	3/16	0.325376917318016	3	FACETS	0.975	0.872	1	0.975	0.872	1	CLONAL	2	TRUE	1	0.345473846837073	3		199	296	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825322	134825322	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1328961585	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	92	342	0	ENST00000398015.3:c.838G>A	p.Glu280Lys	p.E280K	ENST00000398015	NM_004441.4	280	Gaa/Aaa	4/16	0.325376917318016	3	FACETS	0.99	0.881	1	0.495	0.44	0.553	CLONAL	1	TRUE	1	0.345473846837073	3		342	631	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417834	138417834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs912490737	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	136	404	2	ENST00000289153.2:c.1685G>A	p.Arg562Gln	p.R562Q	ENST00000289153	NM_006219.2	562	cGa/cAa	11/22	0.325376917318016	3	FACETS	1	0.963	1	0.556	0.505	0.609	CLONAL	1	TRUE	1	0.345473846837073	3		406	831	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178943827	178943827	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	150	260	0	ENST00000263967.3:c.2494C>T	p.Arg832Ter	p.R832*	ENST00000263967	NM_006218.2	832	Cga/Tga	17/21	0.325376917318016	3	FACETS	0.886	0.813	0.96	0.886	0.813	0.96	CLONAL	2	TRUE	1	0.345473846837073	3		260	575	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167790	185167790	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	116	433	0	ENST00000265026.3:c.1113C>A	p.His371Gln	p.H371Q	ENST00000265026	NM_004721.4	371	caC/caA	6/14	0.325376917318016	3	FACETS	1	0.913	1	0.507	0.457	0.56	CLONAL	1	TRUE	1	0.345473846837073	3		433	777	SUCCESS
FIP1L1	81608	MSKCC	GRCh37	4	54292044	54292044	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	91	233	0	ENST00000358575.5:c.884T>G	p.Leu295Ter	p.L295*	ENST00000358575	NM_001134937.1	295	tTa/tGa	11/18	0.336854520112968	3	FACETS	0.774	0.692	0.861	0.774	0.692	0.861	SUBCLONAL	2	TRUE	1	0.345473846837073	3		233	399	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953837	55953837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	83	369	0	ENST00000263923.4:c.3599C>T	p.Ser1200Phe	p.S1200F	ENST00000263923	NM_002253.2	1200	tCc/tTc	27/30	0.336854520112968	3	FACETS	0.931	0.823	1	0.466	0.411	0.524	CLONAL	1	TRUE	1	0.345473846837073	3		369	605	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467644	66467644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202165566	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	84	324	0	ENST00000273854.3:c.625G>A	p.Gly209Arg	p.G209R	ENST00000273854	NM_004439.5	209	Gga/Aga	3/18	0.336854520112968	3	FACETS	0.947	0.838	1	0.474	0.419	0.532	CLONAL	1	TRUE	1	0.345473846837073	3		324	602	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180039520	180039520	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	80	405	0	ENST00000261937.6:c.3523G>T	p.Gly1175Cys	p.G1175C	ENST00000261937	NM_182925.4	1175	Ggc/Tgc	26/30	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.345473846837073	2		405	392	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554840	106554840	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	90	243	0	ENST00000369096.4:c.1957C>T	p.His653Tyr	p.H653Y	ENST00000369096	NM_001198.3	653	Cat/Tat	7/7	1	2	FACETS	0.898	0.799	1	0.898	0.799	1	CLONAL	1	TRUE	1	0.345473846837073	2		243	580	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137527335	137527335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	146	346	0	ENST00000367739.4:c.311C>T	p.Ala104Val	p.A104V	ENST00000367739	NM_000416.2	104	gCc/gTc	3/7	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.345473846837073	2		346	667	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683653	162683653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	35	345	0	ENST00000366898.1:c.316G>A	p.Asp106Asn	p.D106N	ENST00000366898	NM_004562.2	106	Gac/Aac	3/12	1	2	FACETS	0.375	0.306	0.451	0.375	0.306	0.451	SUBCLONAL	1	TRUE	1	0.345473846837073	2		345	541	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450244	50450244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	142	311	1	ENST00000331340.3:c.428G>A	p.Arg143Gln	p.R143Q	ENST00000331340	NM_006060.4	143	cGg/cAg	5/8	0.319834651524803	4	FACETS	0.853	0.78	0.93	0.853	0.78	0.93	CLONAL	2	TRUE	2	0.345473846837073	4		312	648	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233033	55233033	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	108	302	0	ENST00000275493.2:c.1783T>G	p.Cys595Gly	p.C595G	ENST00000275493	NM_005228.3	595	Tgc/Ggc	15/28	0.319834651524803	4	FACETS	1	0.907	1	0.506	0.454	0.562	CLONAL	1	TRUE	2	0.345473846837073	4		302	831	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381497	81381498	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	106	418	0	ENST00000222390.5:c.563_564delinsAA	p.Trp188Ter	p.W188*	ENST00000222390	NM_000601.4	188	tGG/tAA	5/18	NA	2	FACETS	0.846	0.759	0.939			1	INDETERMINATE	1	TRUE	NA	0.345473846837073	2		418	725	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499755	8499755	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	83	397	0	ENST00000356435.5:c.2214T>A	p.Asn738Lys	p.N738K	ENST00000356435		738	aaT/aaA	14/35	0.345473846837073	5	FACETS	0.714	0.628	0.806	0.143	0.125	0.162	SUBCLONAL	1	TRUE	0	0.345473846837073	5		397	1022	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606404	93606404	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	73	302	0	ENST00000375746.1:c.224C>T	p.Ala75Val	p.A75V	ENST00000375746	NM_001174167.1	75	gCc/gTc	2/14	NA	2	FACETS	0.948	0.832	1			1	INDETERMINATE	1	TRUE	NA	0.345473846837073	2		302	446	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396531	139396532	+	missense_variant	Missense_Mutation	DNP	CT	CT	TA	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	184	292	0	ENST00000277541.6:c.5393_5394delinsTA	p.Lys1798Ile	p.K1798I	ENST00000277541	NM_017617.3	1798	aAG/aTA	29/34	0.345473846837073	3	FACETS	0.994	0.929	1	0.994	0.929	1	CLONAL	3	TRUE	0	0.345473846837073	3		292	419	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70441156	70441156	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	81	339	0	ENST00000373644.4:c.4825G>A	p.Glu1609Lys	p.E1609K	ENST00000373644	NM_030625.2	1609	Gaa/Aaa	9/12	0.336854520112968	3	FACETS	0.748	0.659	0.844	0.374	0.329	0.422	SUBCLONAL	1	TRUE	1	0.345473846837073	3		339	735	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156738	2156738	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	87	329	0	ENST00000434045.2:c.184G>A	p.Gly62Arg	p.G62R	ENST00000434045	NM_001127598.1	62	Ggg/Agg	3/5	0.325376917318016	3	FACETS	1	0.925	1	0.527	0.468	0.591	CLONAL	1	TRUE	1	0.345473846837073	3		329	560	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118367017	118367017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	266	361	2	ENST00000534358.1:c.5599C>T	p.Pro1867Ser	p.P1867S	ENST00000534358	NM_005933.3	1867	Ccc/Tcc	20/36	0.345473846837073	4	FACETS	0.938	0.884	0.993	0.938	0.884	0.993	CLONAL	3	TRUE	1	0.345473846837073	4		363	736	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945063	31945063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	61	204	0	ENST00000340398.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000340398	NM_001013699.2	13	gGt/gAt	1/1	0.345473846837073	3	FACETS	0.986	0.853	1	0.493	0.426	0.565	CLONAL	1	TRUE	1	0.345473846837073	3		204	420	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416638	49416638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	55	213	0	ENST00000301067.7:c.16073C>T	p.Thr5358Ile	p.T5358I	ENST00000301067	NM_003482.3	5358	aCc/aTc	51/54	0.148379046400904	3	FACETS	0.924	0.793	1	0.308	0.264	0.356	INDETERMINATE	1	TRUE	0	0.345473846837073	3		213	404	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425449	49425449	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	109	402	0	ENST00000301067.7:c.13039C>T	p.Gln4347Ter	p.Q4347*	ENST00000301067	NM_003482.3	4347	Cag/Tag	39/54	0.148379046400904	3	FACETS	1	0.959	1	0.377	0.338	0.417	INDETERMINATE	1	TRUE	0	0.345473846837073	3		402	655	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488252	56488252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769847060	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	61	353	0	ENST00000267101.3:c.1771C>T	p.His591Tyr	p.H591Y	ENST00000267101	NM_001982.3	591	Cat/Tat	15/28	0.148379046400904	3	FACETS	0.687	0.592	0.79	0.229	0.197	0.264	INDETERMINATE	1	TRUE	0	0.345473846837073	3		353	603	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69203058	69203058	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1361311287	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	189	324	0	ENST00000462284.1:c.85G>A	p.Glu29Lys	p.E29K	ENST00000462284	NM_002392.5	29	Gaa/Aaa	2/11	0.148379046400904	3	FACETS	0.95	0.882	1	0.634	0.588	0.681	INDETERMINATE	2	TRUE	0	0.345473846837073	3		324	675	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112942555	112942555	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	240	309	0	ENST00000351677.2:c.1769A>G	p.Lys590Arg	p.K590R	ENST00000351677	NM_002834.3	590	aAa/aGa	15/16	0.148379046400904	3	FACETS	1	0.985	1	0.766	0.719	0.814	INDETERMINATE	2	TRUE	0	0.345473846837073	3		309	709	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555605	21555605	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	161	352	0	ENST00000382592.4:c.2665G>T	p.Gly889Trp	p.G889W	ENST00000382592	NM_014572.2	889	Ggg/Tgg	6/8	0.345473846837073	2	FACETS	0.994	0.919	1	0.994	0.919	1	CLONAL	2	TRUE	0	0.345473846837073	2		352	469	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589732	28589732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	166	347	0	ENST00000241453.7:c.2648C>T	p.Ser883Leu	p.S883L	ENST00000241453	NM_004119.2	883	tCa/tTa	21/24	0.345473846837073	2	FACETS	0.924	0.855	0.995	0.924	0.855	0.995	CLONAL	2	TRUE	0	0.345473846837073	2		347	520	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335641	73335641	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	138	282	0	ENST00000377767.4:c.2530G>T	p.Gly844Ter	p.G844*	ENST00000377767	NM_014953.3	844	Gga/Tga	19/21	0.235670158055125	3	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.345473846837073	3		282	658	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435246	110435246	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	55	99	0	ENST00000375856.3:c.3155C>T	p.Thr1052Ile	p.T1052I	ENST00000375856	NM_003749.2	1052	aCc/aTc	1/2	0.345473846837073	2	FACETS	0.91	0.793	1	0.91	0.793	1	CLONAL	2	TRUE	0	0.345473846837073	2		99	175	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574706	95574706	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	100	344	0	ENST00000393063.1:c.2391T>G	p.Asp797Glu	p.D797E	ENST00000393063	NM_030621.3	797	gaT/gaG	16/28	0.318564482761035	4	FACETS	0.927	0.828	1			1	CLONAL	1	TRUE	NA	0.345473846837073	4		344	840	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130270	2130270	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	196	390	0	ENST00000219476.3:c.3502A>T	p.Lys1168Ter	p.K1168*	ENST00000219476	NM_000548.3	1168	Aag/Tag	30/42	0.345473846837073	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.345473846837073	2		390	544	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885956	59885956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28997569	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	99	311	0	ENST00000259008.2:c.790C>T	p.Arg264Trp	p.R264W	ENST00000259008	NM_032043.2	264	Cgg/Tgg	7/20	0.325376917318016	3	FACETS	1	0.924	1	0.521	0.466	0.58	CLONAL	1	TRUE	1	0.345473846837073	3		311	645	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5258104	5258104	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	193	381	0	ENST00000357368.4:c.630C>G	p.Asp210Glu	p.D210E	ENST00000357368	NM_002850.3	210	gaC/gaG	8/38	0.345473846837073	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	0	0.345473846837073	2		381	551	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138521	11138521	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	196	419	1	ENST00000358026.2:c.3277C>T	p.Arg1093Ter	p.R1093*	ENST00000358026	NM_001128849.1	1093	Cga/Tga	24/36	0.345473846837073	2	FACETS	0.903	0.841	0.968	0.903	0.841	0.968	CLONAL	2	TRUE	0	0.345473846837073	2		420	628	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281566	15281566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	242	408	0	ENST00000263388.2:c.4807G>A	p.Asp1603Asn	p.D1603N	ENST00000263388	NM_000435.2	1603	Gat/Aat	26/33	0.345473846837073	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.345473846837073	2		408	627	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031693	36031693	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	191	435	0	ENST00000358208.4:c.1522G>A	p.Glu508Lys	p.E508K	ENST00000358208		508	Gag/Aag	12/12	0.325376917318016	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.345473846837073	3		435	579	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933871	39933871	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs865796679	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	113	182	1	ENST00000378444.4:c.728G>A	p.Arg243His	p.R243H	ENST00000378444	NM_001123385.1	243	cGc/cAc	4/15	0.318564482761035	2	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.345473846837073	2		183	453	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030467	47030467	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	216	203	0	ENST00000377604.3:c.242G>A	p.Arg81Lys	p.R81K	ENST00000377604	NM_001204468.1	81	aGg/aAg	4/24	0.318564482761035	2	FACETS	1	0.969	1			1	CLONAL	3	TRUE	NA	0.345473846837073	2		203	402	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577077	7577082	+	inframe_deletion	In_Frame_Del	DEL	CTCTTC	CTCTTC	-	novel	NA	P-0002998-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	111	382	0	ENST00000269305.4:c.856_861del	p.Glu286_Glu287del	p.E286_E287del	ENST00000269305	NM_001126112.2	286	GAAGAG/-	8/11	1	2	FACETS	0.958	0.862	1	0.958	0.862	1	CLONAL	1	TRUE	1	0.345473846837073	2		382	671	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003000-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	38	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.94	0.779	1	0.94	0.779	1	CLONAL	1	TRUE	1	0.237903283444012	2		422	340	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858085	9858085	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003000-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	105	646	0	ENST00000330684.3:c.3316C>G	p.Leu1106Val	p.L1106V	ENST00000330684	NM_001134407.1	1106	Ctg/Gtg	13/13	1	2	FACETS	0.91	0.814	1	0.91	0.814	1	CLONAL	1	TRUE	1	0.237903283444012	2		646	970	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938565	44938565	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs772184839	NA	P-0003000-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	74	279	0	ENST00000377967.4:c.3113A>G	p.Tyr1038Cys	p.Y1038C	ENST00000377967	NM_021140.2	1038	tAc/tGc	20/29	1	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.237903283444012	1		279	376	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938577	44938577	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0003000-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	73	261	0	ENST00000377967.4:c.3125C>G	p.Ser1042Ter	p.S1042*	ENST00000377967	NM_021140.2	1042	tCa/tGa	20/29	1	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.237903283444012	1		261	362	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023778	27023778	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003000-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	56	390	0	ENST00000324856.7:c.884del	p.Leu295ProfsTer68	p.L295Pfs*68	ENST00000324856	NM_006015.4	295	cTc/cc	1/20	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.237903283444012	2		390	468	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061765	38061766	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0003000-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	56	401	0	ENST00000250448.2:c.223dup	p.Ala75GlyfsTer152	p.A75Gfs*152	ENST00000250448	NM_004496.3	75	gcc/gGcc	2/2	1	2	FACETS	0.798	0.683	0.923	0.798	0.683	0.923	CLONAL	1	TRUE	1	0.237903283444012	2		401	590	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0003008-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	46	393	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.3	3	FACETS	1	0.882	1	1	0.882	1	CLONAL	2	TRUE	1	0.23	3		393	214	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs587781702	NA	P-0003008-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	33	295	0	ENST00000269305.4:c.920-1G>C		p.X307_splice	ENST00000269305	NM_001126112.2	307			1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.23	2		295	237	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432137	121432137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747958319	NA	P-0003008-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	42	369	0	ENST00000257555.6:c.884C>T	p.Pro295Leu	p.P295L	ENST00000257555		295	cCg/cTg	4/10	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.23	2		369	285	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971115	21971133	+	frameshift_variant	Frame_Shift_Del	DEL	GGGTCGGGTGAGAGTGGCG	GGGTCGGGTGAGAGTGGCG	-	rs730881674	NA	P-0003008-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	22	214	0	ENST00000304494.5:c.225_243del	p.Ala76CysfsTer64	p.A76Cfs*64	ENST00000304494	NM_000077.4	75	ccCGCCACTCTCACCCGACCC/cc	2/3	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.23	2		214	144	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003010-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	26	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.988	0.785	1	0.988	0.785	1	CLONAL	1	TRUE	1	0.19	2		422	277	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467699	50467699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003010-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	61	449	0	ENST00000331340.3:c.934G>A	p.Asp312Asn	p.D312N	ENST00000331340	NM_006060.4	312	Gac/Aac	8/8	1	2	FACETS	0.774	0.666	0.891	0.774	0.666	0.891	SUBCLONAL	1	TRUE	1	0.19	2		449	830	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547031	9547031	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003010-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	17	141	0	ENST00000353224.5:c.991G>A	p.Val331Met	p.V331M	ENST00000353224	NM_177990.2	331	Gtg/Atg	5/10	1	2	FACETS	1	0.766	1	1	0.766	1	CLONAL	1	TRUE	1	0.19	2		141	175	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411927	63411927	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003010-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	44	755	0	ENST00000330258.3:c.1240C>A	p.Gln414Lys	p.Q414K	ENST00000330258	NM_152424.3	414	Caa/Aaa	2/2	0.3	1	FACETS	0.586	0.49	0.693	0.586	0.49	0.693	SUBCLONAL	1	TRUE	0	0.19	1		755	715	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729086	66729103	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	AATTCATCTGGAGATCAA	AATTCATCTGGAGATCAA	-	novel	NA	P-0003010-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	114	535	0	ENST00000307102.5:c.295_312del	p.Ile99_Lys104del	p.I99_K104del	ENST00000307102	NM_002755.3	98	ctAATTCATCTGGAGATCAAa/cta	3/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.19	2		535	932	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	12	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.863	1			1	INDETERMINATE	1	TRUE	NA	0.485514564476396	2		422	37	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0003020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	67	462	0	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.421720222193661	3	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	1	0.485514564476396	3		462	162	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970913	21970913	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	11	517	0	ENST00000304494.5:c.445G>T	p.Glu149Ter	p.E149*	ENST00000304494	NM_000077.4	149	Gaa/Taa	2/3	0.423598277462292	2	FACETS	0.292	0.202	0.403	0.146	0.101	0.202	SUBCLONAL	1	TRUE	0	0.485514564476396	2		517	155	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588758	52588758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	18	453	0	ENST00000394830.3:c.4270C>T	p.Pro1424Ser	p.P1424S	ENST00000394830	NM_018313.4	1424	Ccg/Tcg	27/30	0.365663467452775	4	FACETS	0.382	0.288	0.494	0.191	0.144	0.247	SUBCLONAL	1	TRUE	2	0.485514564476396	4		453	288	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952073	178952073	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519937	NA	P-0003020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	103	525	0	ENST00000263967.3:c.3128T>C	p.Met1043Thr	p.M1043T	ENST00000263967	NM_006218.2	1043	aTg/aCg	21/21	0.365663467452775	4	FACETS	0.916	0.828	1	0.916	0.828	1	CLONAL	2	TRUE	2	0.485514564476396	4		525	344	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984024	2984024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	45	666	0	ENST00000396946.4:c.506C>T	p.Thr169Met	p.T169M	ENST00000396946	NM_032415.4	169	aCg/aTg	5/25	0.402773134772552	5	FACETS	1	0.916	1	0.283	0.239	0.331	CLONAL	1	TRUE	1	0.485514564476396	5		666	283	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268819	98268823	+	stop_gained	Nonsense_Mutation	ONP	AAATA	AAATA	TAATT	novel	NA	P-0003020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	52	490	0	ENST00000331920.6:c.260_264delinsAATTA	p.Leu87_Phe88delinsTer	p.L87_F88delins*	ENST00000331920	NM_000264.3	87	tTATTT/tAATTA	2/24	0.164731905589437	4	FACETS	0.78	0.673	0.894	0.78	0.673	0.894	INDETERMINATE	2	TRUE	2	0.485514564476396	4		490	204	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720671	89720671	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587782607	NA	P-0003020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	32	145	0	ENST00000371953.3:c.822G>A	p.Trp274Ter	p.W274*	ENST00000371953	NM_000314.4	274	tgG/tgA	8/9	0.485514564476396	1	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	0	0.485514564476396	1		145	97	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50488224	50488224	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003020-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	14	647	0	ENST00000394963.4:c.1138G>C	p.Asp380His	p.D380H	ENST00000394963	NM_003076.4	380	Gac/Cac	10/13	0.421720222193661	3	FACETS	0.295	0.213	0.394	0.147	0.106	0.197	SUBCLONAL	1	TRUE	1	0.485514564476396	3		647	243	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	67	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.6	2		422	196	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0003024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	213	400	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.413641364600369	5	FACETS	0.941	0.877	1			1	CLONAL	2	TRUE	NA	0.6	5		400	717	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0003024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	207	437	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.919	0.855	0.984	0.919	0.855	0.984	CLONAL	1	TRUE	1	0.6	2		437	751	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188183	11188183	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057524049	NA	P-0003024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	123	137	0	ENST00000361445.4:c.5911G>A	p.Ala1971Thr	p.A1971T	ENST00000361445	NM_004958.3	1971	Gcc/Acc	43/58	0.413641364600369	4	FACETS	1	0.984	1	0.71	0.646	0.776	CLONAL	1	TRUE	2	0.6	4		137	462	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057691	27057691	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	274	319	0	ENST00000324856.7:c.1399C>T	p.Gln467Ter	p.Q467*	ENST00000324856	NM_006015.4	467	Cag/Tag	3/20	0.413641364600369	4	FACETS	0.829	0.78	0.879	0.829	0.78	0.879	CLONAL	2	TRUE	2	0.6	4		319	881	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100291	27100291	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0003024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	186	237	0	ENST00000324856.7:c.4005-2A>G		p.X1335_splice	ENST00000324856	NM_006015.4	1335			0.413641364600369	4	FACETS	1	0.988	1	0.684	0.634	0.736	CLONAL	1	TRUE	2	0.6	4		237	725	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843424	156843424	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0003024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	67	107	0	ENST00000524377.1:c.851-1G>T		p.X284_splice	ENST00000524377	NM_002529.3	284			0.413641364600369	2	FACETS	0.735	0.644	0.831			1	SUBCLONAL	1	TRUE	NA	0.6	2		107	304	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128018834	128018834	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	207	484	1	ENST00000285398.2:c.2034A>T	p.Arg678Ser	p.R678S	ENST00000285398	NM_000122.1	678	agA/agT	13/15	1	2	FACETS	0.943	0.878	1	0.943	0.878	1	CLONAL	1	TRUE	1	0.6	2		485	732	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339027	225339027	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	147	569	0	ENST00000264414.4:c.2242C>T	p.Leu748Phe	p.L748F	ENST00000264414	NM_003590.4	748	Ctt/Ttt	16/16	0.107753359726706	0	FACETS	0.375	0.345	0.407			1	INDETERMINATE	1	TRUE	0	0.6	0		569	522	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661591	227661591	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	220	421	2	ENST00000305123.5:c.1864G>A	p.Val622Met	p.V622M	ENST00000305123	NM_005544.2	622	Gtg/Atg	1/2	0.107753359726706	0	FACETS	0.385	0.36	0.412			1	INDETERMINATE	1	TRUE	0	0.6	0		423	761	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662438	117662438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	134	536	0	ENST00000368508.3:c.4939G>A	p.Glu1647Lys	p.E1647K	ENST00000368508	NM_002944.2	1647	Gag/Aag	30/43	0.413641364600369	1	FACETS	0.695	0.636	0.755	0.695	0.636	0.755	SUBCLONAL	1	TRUE	0	0.6	1		536	450	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6048638	6048638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	209	249	0	ENST00000265849.7:c.13G>A	p.Glu5Lys	p.E5K	ENST00000265849	NM_000535.5	5	Gag/Aag	1/15	1	2	FACETS	0.96	0.894	1	0.96	0.894	1	CLONAL	1	TRUE	1	0.6	2		249	726	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877954	151877954	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	156	264	1	ENST00000262189.6:c.6991G>A	p.Glu2331Lys	p.E2331K	ENST00000262189	NM_170606.2	2331	Gag/Aag	36/59	0.107753359726706	3	FACETS	1	0.98	1	0.6	0.553	0.65	INDETERMINATE	1	TRUE	1	0.6	3		265	563	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967728	90967728	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1060503470	NA	P-0003024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	110	320	0	ENST00000265433.3:c.1180A>G	p.Arg394Gly	p.R394G	ENST00000265433	NM_002485.4	394	Aga/Gga	10/16	1	2	FACETS	0.994	0.901	1	0.994	0.901	1	CLONAL	1	TRUE	1	0.6	2		320	369	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97876927	97876927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	220	478	0	ENST00000289081.3:c.1138G>A	p.Glu380Lys	p.E380K	ENST00000289081	NM_000136.2	380	Gaa/Aaa	12/15	1	2	FACETS	0.988	0.923	1	0.988	0.923	1	CLONAL	1	TRUE	1	0.6	2		478	742	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400009	139400009	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	174	202	0	ENST00000277541.6:c.4339G>A	p.Glu1447Lys	p.E1447K	ENST00000277541	NM_017617.3	1447	Gag/Aag	25/34	0.413641364600369	4	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.6	4		202	632	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405476	70405476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	175	444	0	ENST00000373644.4:c.2990C>T	p.Ser997Leu	p.S997L	ENST00000373644	NM_030625.2	997	tCa/tTa	4/12	1	2	FACETS	0.911	0.843	0.982	0.911	0.843	0.982	CLONAL	1	TRUE	1	0.6	2		444	640	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392067	118392067	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	164	335	0	ENST00000534358.1:c.11578G>A	p.Glu3860Lys	p.E3860K	ENST00000534358	NM_005933.3	3860	Gag/Aag	35/36	0.413641364600369	4	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.6	4		335	669	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448443	49448443	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	169	293	2	ENST00000301067.7:c.268G>A	p.Asp90Asn	p.D90N	ENST00000301067	NM_003482.3	90	Gat/Aat	3/54	0.107753359726706	3	FACETS	1	0.972	1	0.556	0.513	0.601	INDETERMINATE	1	TRUE	1	0.6	3		295	658	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495489	56495489	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	203	264	0	ENST00000267101.3:c.3679G>A	p.Val1227Met	p.V1227M	ENST00000267101	NM_001982.3	1227	Gtg/Atg	28/28	0.107753359726706	3	FACETS	1	0.989	1	0.653	0.608	0.699	INDETERMINATE	1	TRUE	1	0.6	3		264	674	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495511	56495511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	225	261	0	ENST00000267101.3:c.3701C>T	p.Ser1234Phe	p.S1234F	ENST00000267101	NM_001982.3	1234	tCt/tTt	28/28	0.107753359726706	3	FACETS	1	0.991	1	0.705	0.66	0.752	INDETERMINATE	1	TRUE	1	0.6	3		261	691	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219495	133219495	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	172	295	0	ENST00000320574.5:c.4639C>A	p.Pro1547Thr	p.P1547T	ENST00000320574	NM_006231.2	1547	Cca/Aca	36/49	1	2	FACETS	0.935	0.865	1	0.935	0.865	1	CLONAL	1	TRUE	1	0.6	2		295	613	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577599	7577599	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	151	153	0	ENST00000269305.4:c.682G>C	p.Asp228His	p.D228H	ENST00000269305	NM_001126112.2	228	Gac/Cac	7/11	0.413641364600369	5	FACETS	0.925	0.851	1			1	CLONAL	2	TRUE	NA	0.6	5		153	517	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683495	29683495	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	123	235	0	ENST00000356175.3:c.7570G>C	p.Asp2524His	p.D2524H	ENST00000356175	NM_000267.3	2524	Gat/Cat	51/57	0.413641364600369	5	FACETS	0.858	0.781	0.938			1	CLONAL	2	TRUE	NA	0.6	5		235	454	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223325	2223325	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	162	214	0	ENST00000398665.3:c.3436C>G	p.Pro1146Ala	p.P1146A	ENST00000398665	NM_032482.2	1146	Ccg/Gcg	25/28	0.413641364600369	4	FACETS	1	0.988	1	0.721	0.665	0.78	CLONAL	1	TRUE	2	0.6	4		214	599	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872219	45872219	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	187	191	0	ENST00000391945.4:c.215A>G	p.Tyr72Cys	p.Y72C	ENST00000391945	NM_000400.3	72	tAc/tGc	4/23	0.413641364600369	4	FACETS	1	0.99	1	0.74	0.686	0.795	CLONAL	1	TRUE	2	0.6	4		191	674	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877454	40877454	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	134	278	0	ENST00000373198.4:c.2242A>T	p.Thr748Ser	p.T748S	ENST00000373198	NM_133170.3	748	Acc/Tcc	15/32	0.413641364600369	1	FACETS	0.665	0.609	0.724	0.665	0.609	0.724	SUBCLONAL	1	TRUE	0	0.6	1		278	470	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525934	41525934	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	196	317	0	ENST00000263253.7:c.1209G>A	p.Trp403Ter	p.W403*	ENST00000263253	NM_001429.3	403	tgG/tgA	5/31	0.413641364600369	5	FACETS	0.931	0.865	0.998			1	CLONAL	2	TRUE	NA	0.6	5		317	667	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608892	100608892	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	252	332	0	ENST00000308731.7:c.1716C>A	p.Ser572Arg	p.S572R	ENST00000308731	NM_000061.2	572	agC/agA	17/19	1	1	FACETS	0.76	0.726	0.793	1	0.995	1	SUBCLONAL	2	TRUE	0	0.6	1		332	387	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372571	118372575	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGGTA	AGGTA	-	novel	NA	P-0003024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	174	266	0	ENST00000534358.1:c.6505_6505+4del		p.X2169_splice	ENST00000534358	NM_005933.3	2169		26/36	0.413641364600369	4	FACETS	0.768	0.711	0.827			1	SUBCLONAL	2	TRUE	NA	0.6	4		266	604	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481903	56481905	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0003024-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	188	316	0	ENST00000267101.3:c.833_835del	p.Thr278del	p.T278del	ENST00000267101	NM_001982.3	277	caCACc/cac	7/28	0.107753359726706	3	FACETS	1	0.977	1	0.567	0.525	0.609	INDETERMINATE	1	TRUE	1	0.6	3		316	719	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003029-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	56	295	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.281976873289718	3	FACETS	1	0.883	1	0.516	0.443	0.595	CLONAL	1	TRUE	1	0.294305367955537	3		295	423	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0003029-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	75	139	0				ENST00000310581	NM_198253.2	-/1132			0.24915129192968	3	FACETS	0.919	0.813	1			1	CLONAL	2	TRUE	NA	0.294305367955537	3		139	318	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101054	26101054	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003029-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1287	268	760	0	ENST00000435504.4:c.38G>A	p.Trp13Ter	p.W13*	ENST00000435504		13	tGg/tAg	1/13	0.294305367955537	5	FACETS	0.844	0.789	0.901	0.563	0.526	0.601	CLONAL	2	TRUE	2	0.294305367955537	5		760	1555	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488700	212488700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003029-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	140	649	0	ENST00000342788.4:c.2149G>A	p.Glu717Lys	p.E717K	ENST00000342788	NM_005235.2	717	Gag/Aag	18/28	0.294305367955537	3	FACETS	1	0.951	1	0.534	0.485	0.585	CLONAL	1	TRUE	1	0.294305367955537	3		649	1022	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440328	52440328	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003029-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	101	495	0	ENST00000460680.1:c.724G>T	p.Glu242Ter	p.E242*	ENST00000460680	NM_004656.3	242	Gag/Tag	9/17	1	2	FACETS	0.845	0.755	0.941	0.845	0.755	0.941	CLONAL	1	TRUE	1	0.294305367955537	2		495	812	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442078	52442078	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003029-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	89	387	0	ENST00000460680.1:c.271T>C	p.Cys91Arg	p.C91R	ENST00000460680	NM_004656.3	91	Tgt/Cgt	5/17	1	2	FACETS	0.976	0.866	1	0.976	0.866	1	CLONAL	1	TRUE	1	0.294305367955537	2		387	620	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538904	187538904	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003029-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	279	678	0	ENST00000441802.2:c.8836G>A	p.Asp2946Asn	p.D2946N	ENST00000441802	NM_005245.3	2946	Gat/Aat	10/27	0.294305367955537	3	FACETS	0.939	0.882	0.998	0.939	0.882	0.998	CLONAL	2	TRUE	1	0.294305367955537	3		678	1158	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163252	32163252	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003029-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	322	838	0	ENST00000375023.3:c.5974G>C	p.Glu1992Gln	p.E1992Q	ENST00000375023	NM_004557.3	1992	Gaa/Caa	30/30	0.277699604578017	4	FACETS	0.972	0.916	1	0.972	0.916	1	CLONAL	2	TRUE	2	0.294305367955537	4		838	1457	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287254	38287254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55642501	NA	P-0003029-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	230	628	0	ENST00000425967.3:c.403G>A	p.Val135Ile	p.V135I	ENST00000425967	NM_001174067.1	135	Gta/Ata	4/19	0.294305367955537	3	FACETS	0.848	0.79	0.908	0.848	0.79	0.908	CLONAL	2	TRUE	1	0.294305367955537	3		628	1057	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370709	55370709	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003029-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	67	221	0	ENST00000297316.4:c.11C>A	p.Pro4Gln	p.P4Q	ENST00000297316	NM_022454.3	4	cCg/cAg	1/2	0.294305367955537	3	FACETS	1	0.97	1	0.706	0.617	0.801	CLONAL	1	TRUE	1	0.294305367955537	3		221	370	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11552822	NA	P-0003029-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	77	316	0	ENST00000304494.5:c.250G>T	p.Asp84Tyr	p.D84Y	ENST00000304494	NM_000077.4	84	Gac/Tac	2/3	0.294305367955537	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.294305367955537	1		316	406	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039240	49039240	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267603841	NA	P-0003029-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	221	576	0	ENST00000267163.4:c.2318C>T	p.Ser773Phe	p.S773F	ENST00000267163	NM_000321.2	773	tCc/tTc	22/27	0.294305367955537	3	FACETS	0.923	0.86	0.989	0.923	0.86	0.989	CLONAL	2	TRUE	1	0.294305367955537	3		576	933	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039392	49039392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs947540268	NA	P-0003029-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	284	890	0	ENST00000267163.4:c.2377C>T	p.Pro793Ser	p.P793S	ENST00000267163	NM_000321.2	793	Cct/Tct	23/27	0.294305367955537	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	1	0.294305367955537	3		890	1103	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003029-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	280	639	0	ENST00000269305.4:c.811G>C	p.Glu271Gln	p.E271Q	ENST00000269305	NM_001126112.2	271	Gag/Cag	8/11	NA	2	FACETS	0.925	0.869	0.981			1	INDETERMINATE	2	TRUE	NA	0.294305367955537	2		639	1029	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15995180	15995180	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003029-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	267	652	1	ENST00000268712.3:c.3013G>T	p.Glu1005Ter	p.E1005*	ENST00000268712	NM_006311.3	1005	Gaa/Taa	22/46	0.277699604578017	4	FACETS	0.932	0.873	0.993	0.932	0.873	0.993	CLONAL	2	TRUE	2	0.294305367955537	4		653	1260	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39763632	39763632	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003029-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	186	505	0	ENST00000288319.7:c.820C>G	p.Gln274Glu	p.Q274E	ENST00000288319	NM_182918.3	274	Caa/Gaa	8/10	0.294305367955537	2	FACETS	0.956	0.887	1	0.956	0.887	1	CLONAL	2	TRUE	0	0.294305367955537	2		505	661	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0003051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	24	139	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.812	1	1	0.812	1	CLONAL	1	TRUE	1	0.344907657217229	2		139	136	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	77	270	0	ENST00000304494.5:c.322G>C	p.Asp108His	p.D108H	ENST00000304494	NM_000077.4	108	Gat/Cat	2/3	0.222204696021238	3	FACETS	1	0.948	1			1	CLONAL	2	TRUE	NA	0.344907657217229	3		270	236	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519975	NA	P-0003051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	105	344	0	ENST00000269305.4:c.403T>C	p.Cys135Arg	p.C135R	ENST00000269305	NM_001126112.2	135	Tgc/Cgc	5/11	0.305993544620618	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	2	TRUE	0	0.344907657217229	2		344	297	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418394	49418394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1565756106	NA	P-0003051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	136	300	0	ENST00000301067.7:c.16019G>A	p.Arg5340Gln	p.R5340Q	ENST00000301067	NM_003482.3	5340	cGa/cAa	50/54	0.297523648422295	3	FACETS	1	0.97	1			1	CLONAL	2	TRUE	NA	0.344907657217229	3		300	412	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146844	185146844	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	28	182	0	ENST00000265026.3:c.475G>A	p.Asp159Asn	p.D159N	ENST00000265026	NM_004721.4	159	Gat/Aat	2/14	0.200566409662206	3	FACETS	0.915	0.736	1	0.458	0.368	0.558	INDETERMINATE	1	TRUE	1	0.344907657217229	3		182	208	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534507	140534507	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	45	416	0	ENST00000288602.6:c.406T>C	p.Ser136Pro	p.S136P	ENST00000288602	NM_004333.4	136	Tca/Cca	3/18	NA	2	FACETS	0.597	0.502	0.702			1	INDETERMINATE	1	TRUE	NA	0.344907657217229	2		416	437	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575126	64575126	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0003051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	35	344	0	ENST00000312049.6:c.681C>G	p.Tyr227Ter	p.Y227*	ENST00000312049	NM_130799.2	227	taC/taG	4/10	0.344907657217229	3	FACETS	0.534	0.437	0.642	0.267	0.218	0.321	SUBCLONAL	1	TRUE	1	0.344907657217229	3		344	446	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396908	396908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753659585	NA	P-0003051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	137	467	3	ENST00000262320.3:c.118G>A	p.Ala40Thr	p.A40T	ENST00000262320	NM_003502.3	40	Gcc/Acc	2/11	0.338942384087139	2	FACETS	0.831	0.761	0.903	0.831	0.761	0.903	CLONAL	2	TRUE	0	0.344907657217229	2		470	478	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267680	7267680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	81	347	0	ENST00000302850.5:c.328C>T	p.Arg110Trp	p.R110W	ENST00000302850	NM_000208.2	110	Cgg/Tgg	2/22	0.277169162989997	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.344907657217229	1		347	343	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	58	422	0				ENST00000310581	NM_198253.2	-/1132			0.249423101235079	4	FACETS	1	0.895	1	1	0.981	1	CLONAL	4	TRUE	2	0.249423101235079	4		422	143	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480132	20480133	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0003059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	88	320	0	ENST00000346618.3:c.454dup	p.Thr152AsnfsTer15	p.T152Nfs*15	ENST00000346618	NM_001949.4	150	tta/ttAa	2/7	1	2	FACETS	0.832	0.736	0.935	0.832	0.736	0.935	CLONAL	1	TRUE	1	0.249423101235079	2		320	848	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254848	16254853	+	inframe_deletion	In_Frame_Del	DEL	GAACGT	GAACGT	-	novel	NA	P-0003059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	68	307	0	ENST00000375759.3:c.2116_2121del	p.Glu707_Arg708del	p.E707_R708del	ENST00000375759	NM_015001.2	705	GAACGT/-	11/15	1	2	FACETS	0.804	0.699	0.918	0.804	0.699	0.918	CLONAL	1	TRUE	1	0.249423101235079	2		307	678	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0003062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	218	217	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.927	0.868	0.987	0.927	0.868	0.987	CLONAL	1	TRUE	1	0.767453896894358	2		217	613	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0003062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	304	318	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.982	0.929	1	0.982	0.929	1	CLONAL	1	TRUE	1	0.767453896894358	2		318	807	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0003062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	43	139	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.767453896894358	2		139	107	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11291032	11291032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	329	489	0	ENST00000361445.4:c.2729G>A	p.Arg910Gln	p.R910Q	ENST00000361445	NM_004958.3	910	cGg/cAg	18/58	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.767453896894358	2		489	855	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804373	43804373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	190	303	0	ENST00000372470.3:c.373C>T	p.Leu125Phe	p.L125F	ENST00000372470	NM_005373.2	125	Ctc/Ttc	3/12	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.767453896894358	2		303	493	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728809	190728809	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	292	260	0	ENST00000441310.2:c.2197C>T	p.Pro733Ser	p.P733S	ENST00000441310	NM_000534.4	733	Cct/Tct	10/13	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.767453896894358	2		260	678	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12632463	12632463	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	215	329	0	ENST00000251849.4:c.1204C>A	p.His402Asn	p.H402N	ENST00000251849	NM_002880.3	402	Cat/Aat	12/17	1	2	FACETS	0.937	0.877	0.998	0.937	0.877	0.998	CLONAL	1	TRUE	1	0.767453896894358	2		329	598	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47079233	47079233	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	282	358	0	ENST00000409792.3:c.7273C>T	p.Pro2425Ser	p.P2425S	ENST00000409792	NM_014159.6	2425	Cca/Tca	18/21	1	2	FACETS	0.984	0.929	1	0.984	0.929	1	CLONAL	1	TRUE	1	0.767453896894358	2		358	747	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586386	189586386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113993967	NA	P-0003062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	110	158	0	ENST00000264731.3:c.1010G>A	p.Arg337Gln	p.R337Q	ENST00000264731	NM_003722.4	337	cGa/cAa	8/14	1	2	FACETS	0.882	0.802	0.964	0.882	0.802	0.964	CLONAL	1	TRUE	1	0.767453896894358	2		158	325	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149452997	149452997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	243	398	0	ENST00000286301.3:c.949G>A	p.Glu317Lys	p.E317K	ENST00000286301	NM_005211.3	317	Gag/Aag	7/22	1	2	FACETS	0.967	0.909	1	0.967	0.909	1	CLONAL	1	TRUE	1	0.767453896894358	2		398	655	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518079	176518079	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	205	389	0	ENST00000292408.4:c.577G>A	p.Gly193Arg	p.G193R	ENST00000292408	NM_213647.1	193	Ggg/Agg	5/18	1	2	FACETS	0.997	0.932	1	0.997	0.932	1	CLONAL	1	TRUE	1	0.767453896894358	2		389	536	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675456	30675456	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	267	407	0	ENST00000376406.3:c.2900C>T	p.Pro967Leu	p.P967L	ENST00000376406	NM_014641.2	967	cCa/cTa	8/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.767453896894358	2		407	629	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273086	55273086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780967013	NA	P-0003062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	278	483	0	ENST00000275493.2:c.3409G>A	p.Glu1137Lys	p.E1137K	ENST00000275493	NM_005228.3	1137	Gag/Aag	28/28	1	2	FACETS	0.988	0.933	1	0.988	0.933	1	CLONAL	1	TRUE	1	0.767453896894358	2		483	733	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878073	151878073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	183	236	0	ENST00000262189.6:c.6872C>T	p.Ser2291Phe	p.S2291F	ENST00000262189	NM_170606.2	2291	tCc/tTc	36/59	0.767453896894358	3	FACETS	1	0.942	1	0.509	0.472	0.548	CLONAL	1	TRUE	1	0.767453896894358	3		236	648	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0003062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	461	661	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.767453896894358	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.767453896894358	1		661	725	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653814	89653814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587780004	NA	P-0003062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	601	311	0	ENST00000371953.3:c.112C>T	p.Pro38Ser	p.P38S	ENST00000371953	NM_000314.4	38	Cct/Tct	2/9	0.762121102483883	2	FACETS	0.99	0.966	1	0.99	0.966	1	CLONAL	2	TRUE	0	0.767453896894358	2		311	791	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134688	41134688	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1034299550	NA	P-0003062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	357	676	0	ENST00000379561.5:c.940C>T	p.Arg314Cys	p.R314C	ENST00000379561	NM_002015.3	314	Cgc/Tgc	2/3	1	2	FACETS	0.929	0.883	0.977	0.929	0.883	0.977	CLONAL	1	TRUE	1	0.767453896894358	2		676	1001	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829143	72829143	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	269	554	0	ENST00000268489.5:c.7438T>G	p.Leu2480Val	p.L2480V	ENST00000268489	NM_006885.3	2480	Ttg/Gtg	9/10	0.767453896894358	1	FACETS	0.96	0.916	1	0.96	0.916	1	CLONAL	1	TRUE	0	0.767453896894358	1		554	450	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7167992	7167992	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	227	372	0	ENST00000302850.5:c.1597T>C	p.Phe533Leu	p.F533L	ENST00000302850	NM_000208.2	533	Ttc/Ctc	7/22	1	2	FACETS	0.993	0.932	1	0.993	0.932	1	CLONAL	1	TRUE	1	0.767453896894358	2		372	596	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944407	40944407	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0003062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	202	388	0	ENST00000373198.4:c.2095A>T	p.Lys699Ter	p.K699*	ENST00000373198	NM_133170.3	699	Aaa/Taa	12/32	NA	2	FACETS	0.95	0.888	1			1	INDETERMINATE	1	TRUE	NA	0.767453896894358	2		388	554	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356757	70356757	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	345	628	0	ENST00000374080.3:c.5429G>A	p.Gly1810Asp	p.G1810D	ENST00000374080		1810	gGc/gAc	38/45	0.767453896894358	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.767453896894358	1		628	531	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971124	21971125	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0003078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	100	99	0	ENST00000304494.5:c.233_234del	p.Leu78HisfsTer41	p.L78Hfs*41	ENST00000304494	NM_000077.4	78	cTC/c	2/3	0.302683742777632	5	FACETS	1	0.938	1	1	0.983	1	CLONAL	4	TRUE	2	0.337652482757861	5		99	216	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243778438	243778438	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	174	304	0	ENST00000263826.5:c.587A>C	p.Glu196Ala	p.E196A	ENST00000263826	NM_005465.4	196	gAa/gCa	6/13	0.295706899343238	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.337652482757861	4		304	613	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265427	152265427	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	113	202	0	ENST00000206249.3:c.880A>C	p.Ser294Arg	p.S294R	ENST00000206249	NM_000125.3	294	Agc/Cgc	4/8	0.295706899343238	4	FACETS	0.79	0.713	0.87	0.79	0.713	0.87	SUBCLONAL	2	TRUE	2	0.337652482757861	4		202	567	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729892	41729892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762543780	NA	P-0003078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	315	518	0	ENST00000242208.4:c.637G>A	p.Ala213Thr	p.A213T	ENST00000242208	NM_002192.2	213	Gct/Act	3/3	0.337652482757861	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.337652482757861	3		518	1051	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8252018	8252018	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	166	273	0	ENST00000335790.3:c.59A>G	p.Lys20Arg	p.K20R	ENST00000335790	NM_002315.2	20	aAg/aGg	2/4	0.337652482757861	3	FACETS	0.981	0.905	1	0.981	0.905	1	CLONAL	2	TRUE	1	0.337652482757861	3		273	586	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577544	7577544	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587780074	NA	P-0003078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	205	241	0	ENST00000269305.4:c.737T>A	p.Met246Lys	p.M246K	ENST00000269305	NM_001126112.2	246	aTg/aAg	7/11	0.168173971415629	2	FACETS	1	0.987	1	1	0.987	1	INDETERMINATE	2	TRUE	0	0.337652482757861	2		241	499	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221332	1221361	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCTGAAAGGTGGGAGCCTCATCCCTCTGCC	GCTGAAAGGTGGGAGCCTCATCCCTCTGCC	-	novel	NA	P-0003078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	35	214	0	ENST00000326873.7:c.855_862+22del		p.X285_splice	ENST00000326873	NM_000455.4	285		6/10	0.337652482757861	2	FACETS	0.412	0.337	0.496	0.206	0.168	0.248	SUBCLONAL	1	TRUE	0	0.337652482757861	2		214	503	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922789	44922790	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0003078-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	283	179	0	ENST00000377967.4:c.1652dup	p.Ser552Ter	p.S552*	ENST00000377967	NM_021140.2	550	-/C	16/29	0.337652482757861	2	FACETS	1	0.969	1			1	CLONAL	3	TRUE	NA	0.337652482757861	2		179	545	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	26	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.644	0.518	0.784			1	INDETERMINATE	1	TRUE	NA	0.645663894697083	2		422	125	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0003079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	34	305	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	0.645663894697083	1	FACETS	0.232	0.19	0.279	0.232	0.19	0.279	SUBCLONAL	1	TRUE	0	0.645663894697083	1		305	307	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210075	55210075	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1251	18471	385	13	ENST00000275493.2:c.185T>G	p.Leu62Arg	p.L62R	ENST00000275493	NM_005228.3	62	cTt/cGt	2/28	0.645663894697083	36	FACETS	0.993	0.99	0.995			1	CLONAL	35	TRUE	NA	0.645663894697083	36		398	19722	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170313	32170313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201260854	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	70	155	0	ENST00000375023.3:c.3295G>A	p.Gly1099Arg	p.G1099R	ENST00000375023	NM_004557.3	1099	Gga/Aga	21/30	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.369021393779988	2		155	362	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121912651	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	13	197	0	ENST00000269305.4:c.742C>G	p.Arg248Gly	p.R248G	ENST00000269305	NM_001126112.2	248	Cgg/Ggg	7/11	1	2	FACETS	0.125	0.088	0.17	0.125	0.088	0.17	SUBCLONAL	1	TRUE	1	0.369021393779988	2		197	563	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606696	29606696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769910087	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	95	262	0	ENST00000389048.3:c.1184G>A	p.Arg395His	p.R395H	ENST00000389048	NM_004304.4	395	cGt/cAt	5/29	1	2	FACETS	0.946	0.845	1	0.946	0.845	1	CLONAL	1	TRUE	1	0.369021393779988	2		262	544	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578419	7578419	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587781845	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	93	170	0	ENST00000269305.4:c.511G>T	p.Glu171Ter	p.E171*	ENST00000269305	NM_001126112.2	171	Gag/Tag	5/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.369021393779988	2		170	464	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974685	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	88	259	0	ENST00000304494.5:c.142_143delinsTT	p.Pro48Leu	p.P48L	ENST00000304494	NM_000077.4	48	CCg/TTg	1/3	0.369021393779988	1	FACETS	0.866	0.771	0.967	0.866	0.771	0.967	CLONAL	1	TRUE	0	0.369021393779988	1		259	449	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484378	120484378	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	96	229	0	ENST00000256646.2:c.2753-1G>A		p.X918_splice	ENST00000256646	NM_024408.3	918			1	2	FACETS	0.913	0.815	1	0.913	0.815	1	CLONAL	1	TRUE	1	0.369021393779988	2		229	570	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957434	175957434	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	161	326	0	ENST00000367669.3:c.1962T>A	p.Tyr654Ter	p.Y654*	ENST00000367669	NM_022457.5	654	taT/taA	17/20	0.284184786408354	3	FACETS	1	0.956	1	0.532	0.488	0.579	CLONAL	1	TRUE	1	0.369021393779988	3		326	971	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085671	16085671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	100	269	0	ENST00000281043.3:c.847G>A	p.Glu283Lys	p.E283K	ENST00000281043	NM_005378.4	283	Gag/Aag	3/3	1	2	FACETS	0.801	0.716	0.891	0.801	0.716	0.891	CLONAL	1	TRUE	1	0.369021393779988	2		269	677	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182526	99182526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	99	238	0	ENST00000074304.5:c.2329C>T	p.Pro777Ser	p.P777S	ENST00000074304	NM_001134224.1	777	Ccg/Tcg	22/26	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.369021393779988	2		238	529	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149562	202149562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	162	244	0	ENST00000358485.4:c.1003G>A	p.Glu335Lys	p.E335K	ENST00000358485	NM_001080125.1	335	Gag/Aag	8/9	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.369021393779988	2		244	779	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735565	204735565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1325759242	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	75	128	0	ENST00000302823.3:c.366G>A	p.Met122Ile	p.M122I	ENST00000302823	NM_005214.4	122	atG/atA	2/4	1	2	FACETS	0.872	0.767	0.985	0.872	0.767	0.985	CLONAL	1	TRUE	1	0.369021393779988	2		128	466	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732963	30732963	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	193	204	2	ENST00000295754.5:c.1576G>T	p.Glu526Ter	p.E526*	ENST00000295754	NM_003242.5	526	Gag/Tag	7/7	0.369021393779988	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.369021393779988	2		206	502	SUCCESS
ATR	545	MSKCC	GRCh37	3	142168287	142168287	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	130	189	0	ENST00000350721.4:c.7919G>A	p.Trp2640Ter	p.W2640*	ENST00000350721	NM_001184.3	2640	tGg/tAg	47/47	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.369021393779988	2		189	570	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430921	181430921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	121	298	0	ENST00000325404.1:c.773C>T	p.Ser258Phe	p.S258F	ENST00000325404	NM_003106.3	258	tCc/tTc	1/1	1	2	FACETS	0.908	0.821	1	0.908	0.821	1	CLONAL	1	TRUE	1	0.369021393779988	2		298	722	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750440	41750440	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	92	207	0	ENST00000226382.2:c.188G>A	p.Gly63Glu	p.G63E	ENST00000226382	NM_003924.3	63	gGa/gAa	1/3	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.369021393779988	2		207	493	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156546	55156546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	129	256	0	ENST00000257290.5:c.2947G>A	p.Asp983Asn	p.D983N	ENST00000257290	NM_006206.4	983	Gac/Aac	22/23	1	2	FACETS	0.949	0.861	1	0.949	0.861	1	CLONAL	1	TRUE	1	0.369021393779988	2		256	737	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980402	55980402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1357848255	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	133	311	0	ENST00000263923.4:c.689C>T	p.Pro230Leu	p.P230L	ENST00000263923	NM_002253.2	230	cCg/cTg	6/30	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.369021393779988	2		311	613	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231742	66231742	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	117	250	0	ENST00000273854.3:c.1958C>T	p.Pro653Leu	p.P653L	ENST00000273854	NM_004439.5	653	cCa/cTa	11/18	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.369021393779988	2		250	562	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510195	187510195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	112	240	0	ENST00000441802.2:c.13318G>A	p.Glu4440Lys	p.E4440K	ENST00000441802	NM_005245.3	4440	Gaa/Aaa	27/27	1	2	FACETS	0.981	0.884	1	0.981	0.884	1	CLONAL	1	TRUE	1	0.369021393779988	2		240	619	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294346	1294346	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	63	120	0	ENST00000310581.5:c.655C>T	p.Pro219Ser	p.P219S	ENST00000310581	NM_198253.2	219	Ccg/Tcg	2/16	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.369021393779988	2		120	297	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755615	57755615	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	78	188	0	ENST00000274289.3:c.172C>T	p.His58Tyr	p.H58Y	ENST00000274289	NM_006622.3	58	Cac/Tac	1/14	1	2	FACETS	0.946	0.834	1	0.946	0.834	1	CLONAL	1	TRUE	1	0.369021393779988	2		188	447	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86658485	86658485	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	84	143	0	ENST00000274376.6:c.1450A>T	p.Lys484Ter	p.K484*	ENST00000274376	NM_002890.2	484	Aag/Tag	10/25	1	2	FACETS	0.849	0.752	0.953	0.849	0.752	0.953	CLONAL	1	TRUE	1	0.369021393779988	2		143	536	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139054	37139056	+	missense_variant	Missense_Mutation	TNP	TTC	TTC	CTT	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	83	211	0	ENST00000373509.5:c.394_396delinsCTT	p.Phe132Leu	p.F132L	ENST00000373509	NM_002648.3	132	TTC/CTT	4/6	1	2	FACETS	0.98	0.868	1	0.98	0.868	1	CLONAL	1	TRUE	1	0.369021393779988	2		211	459	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041150	112041151	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	147	384	0	ENST00000368678.4:c.104_105delinsTT	p.Thr35Ile	p.T35I	ENST00000368678		35	aCC/aTT	3/13	1	2	FACETS	0.882	0.805	0.963	0.882	0.805	0.963	CLONAL	1	TRUE	1	0.369021393779988	2		384	903	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6031606	6031606	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1461669945	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	66	90	0	ENST00000265849.7:c.986C>T	p.Ser329Leu	p.S329L	ENST00000265849	NM_000535.5	329	tCa/tTa	9/15	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.369021393779988	2		90	327	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233037	55233037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1477025000	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	135	257	0	ENST00000275493.2:c.1787C>T	p.Pro596Leu	p.P596L	ENST00000275493	NM_005228.3	596	cCg/cTg	15/28	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.369021393779988	2		257	689	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877885	151877885	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	122	176	0	ENST00000262189.6:c.7060C>T	p.Gln2354Ter	p.Q2354*	ENST00000262189	NM_170606.2	2354	Caa/Taa	36/59	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.369021393779988	2		176	619	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399183	139399183	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	121	169	0	ENST00000277541.6:c.4960C>T	p.Pro1654Ser	p.P1654S	ENST00000277541	NM_017617.3	1654	Cct/Tct	26/34	0.36675684018177	2	FACETS	0.834	0.761	0.91	0.834	0.761	0.91	CLONAL	2	TRUE	0	0.369021393779988	2		169	393	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401167	139401168	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	152	178	0	ENST00000277541.6:c.3901_3901+1delinsAA		p.X1301_splice	ENST00000277541	NM_017617.3	1301		23/34	0.36675684018177	2	FACETS	0.926	0.854	0.999	0.926	0.854	0.999	CLONAL	2	TRUE	0	0.369021393779988	2		178	445	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597810	43597810	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	158	322	0	ENST00000355710.3:c.358A>T	p.Thr120Ser	p.T120S	ENST00000355710	NM_020975.4	120	Acc/Tcc	3/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.369021393779988	2		322	781	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852261	63852261	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	103	195	0	ENST00000279873.7:c.3039G>T	p.Lys1013Asn	p.K1013N	ENST00000279873	NM_032199.2	1013	aaG/aaT	10/10	1	2	FACETS	0.988	0.887	1	0.988	0.887	1	CLONAL	1	TRUE	1	0.369021393779988	2		195	565	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910762	114910762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	192	466	0	ENST00000543371.1:c.881C>T	p.Pro294Leu	p.P294L	ENST00000543371	NM_001198531.1	294	cCt/cTt	9/14	1	2	FACETS	0.92	0.85	0.993	0.92	0.85	0.993	CLONAL	1	TRUE	1	0.369021393779988	2		466	1131	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533782	533782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	103	291	0	ENST00000451590.1:c.274G>A	p.Asp92Asn	p.D92N	ENST00000451590	NM_001130442.1	92	Gac/Aac	3/5	1	2	FACETS	0.914	0.819	1	0.914	0.819	1	CLONAL	1	TRUE	1	0.369021393779988	2		291	611	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514523	125514523	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	134	219	0	ENST00000428830.2:c.1218A>C	p.Lys406Asn	p.K406N	ENST00000428830	NM_001114121.2	406	aaA/aaC	11/14	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.369021393779988	2		219	665	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425665	49425665	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	69	199	0	ENST00000301067.7:c.12823C>T	p.Gln4275Ter	p.Q4275*	ENST00000301067	NM_003482.3	4275	Cag/Tag	39/54	1	2	FACETS	0.856	0.748	0.971	0.856	0.748	0.971	CLONAL	1	TRUE	1	0.369021393779988	2		199	437	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436362	49436362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	88	260	0	ENST00000301067.7:c.5849C>T	p.Ser1950Phe	p.S1950F	ENST00000301067	NM_003482.3	1950	tCc/tTc	27/54	1	2	FACETS	0.781	0.692	0.875	0.781	0.692	0.875	SUBCLONAL	1	TRUE	1	0.369021393779988	2		260	611	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118758	115118758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	129	282	0	ENST00000257566.3:c.583G>A	p.Glu195Lys	p.E195K	ENST00000257566	NM_016569.3	195	Gaa/Aaa	2/8	1	2	FACETS	0.921	0.836	1	0.921	0.836	1	CLONAL	1	TRUE	1	0.369021393779988	2		282	759	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578275	28578275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	119	247	0	ENST00000241453.7:c.2896C>T	p.Pro966Ser	p.P966S	ENST00000241453	NM_004119.2	966	Cct/Tct	24/24	1	2	FACETS	0.967	0.874	1	0.967	0.874	1	CLONAL	1	TRUE	1	0.369021393779988	2		247	667	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972504	32972504	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	136	272	0	ENST00000380152.3:c.9854C>T	p.Pro3285Leu	p.P3285L	ENST00000380152		3285	cCc/cTc	27/27	1	2	FACETS	0.979	0.891	1	0.979	0.891	1	CLONAL	1	TRUE	1	0.369021393779988	2		272	753	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678460	88678460	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	127	285	0	ENST00000360948.2:c.1076C>T	p.Ser359Phe	p.S359F	ENST00000360948	NM_001012338.2	359	tCc/tTc	9/19	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.369021393779988	2		285	652	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863600	68863600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555517841	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	161	237	0	ENST00000261769.5:c.2339C>T	p.Pro780Leu	p.P780L	ENST00000261769	NM_004360.3	780	cCt/cTt	15/16	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.369021393779988	2		237	801	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821598	72821598	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	26	80	0	ENST00000268489.5:c.10577G>A	p.Gly3526Asp	p.G3526D	ENST00000268489	NM_006885.3	3526	gGc/gAc	10/10	1	2	FACETS	0.946	0.758	1	0.946	0.758	1	CLONAL	1	TRUE	1	0.369021393779988	2		80	149	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882954	89882954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1311396994	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	19	37	0	ENST00000389301.3:c.70G>A	p.Glu24Lys	p.E24K	ENST00000389301	NM_000135.2	24	Gag/Aag	1/43	1	2	FACETS	1	0.771	1	1	0.771	1	CLONAL	1	TRUE	1	0.369021393779988	2		37	103	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579314	7579314	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs1057520003	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	76	170	0	ENST00000269305.4:c.373A>C	p.Thr125Pro	p.T125P	ENST00000269305	NM_001126112.2	125	Acg/Ccg	4/11	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.369021393779988	2		170	411	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974826	15974826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	147	314	0	ENST00000268712.3:c.4049C>T	p.Ser1350Phe	p.S1350F	ENST00000268712	NM_006311.3	1350	tCc/tTc	30/46	1	2	FACETS	0.952	0.869	1	0.952	0.869	1	CLONAL	1	TRUE	1	0.369021393779988	2		314	837	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487505	38487505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	90	287	0	ENST00000254066.5:c.35G>A	p.Gly12Glu	p.G12E	ENST00000254066	NM_000964.3	12	gGg/gAg	2/9	1	2	FACETS	0.893	0.795	0.998	0.893	0.795	0.998	CLONAL	1	TRUE	1	0.369021393779988	2		287	546	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763487	59763487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781964	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	88	183	0	ENST00000259008.2:c.2615C>T	p.Ser872Leu	p.S872L	ENST00000259008	NM_032043.2	872	tCa/tTa	19/20	1	2	FACETS	0.878	0.78	0.983	0.878	0.78	0.983	CLONAL	1	TRUE	1	0.369021393779988	2		183	543	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1620984	1620984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772853413	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	105	307	0	ENST00000344749.5:c.1076C>T	p.Ser359Phe	p.S359F	ENST00000344749	NM_001136139.2	359	tCc/tTc	13/19	0.369021393779988	1	FACETS	0.917	0.825	1	0.917	0.825	1	CLONAL	1	TRUE	0	0.369021393779988	1		307	506	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302667	15302667	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	97	286	0	ENST00000263388.2:c.691C>T	p.Gln231Ter	p.Q231*	ENST00000263388	NM_000435.2	231	Cag/Tag	5/33	0.369021393779988	1	FACETS	0.814	0.728	0.904	0.814	0.728	0.904	CLONAL	1	TRUE	0	0.369021393779988	1		286	527	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792783	33792783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	16	56	0	ENST00000498907.2:c.538C>T	p.Pro180Ser	p.P180S	ENST00000498907	NM_004364.3	180	Cct/Tct	1/1	1	2	FACETS	0.913	0.685	1	0.913	0.685	1	CLONAL	1	TRUE	1	0.369021393779988	2		56	95	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797401	42797401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	75	201	0	ENST00000575354.2:c.3763G>A	p.Glu1255Lys	p.E1255K	ENST00000575354	NM_015125.3	1255	Gag/Aag	15/20	1	2	FACETS	0.907	0.798	1	0.907	0.798	1	CLONAL	1	TRUE	1	0.369021393779988	2		201	448	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016187	31016187	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	146	313	0	ENST00000375687.4:c.433C>G	p.Leu145Val	p.L145V	ENST00000375687	NM_015338.5	145	Ctt/Gtt	6/13	0.369021393779988	3	FACETS	1	0.955	1	0.536	0.489	0.586	CLONAL	1	TRUE	1	0.369021393779988	3		313	874	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021634	31021634	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137920574	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	87	145	0	ENST00000375687.4:c.1633C>T	p.Arg545Cys	p.R545C	ENST00000375687	NM_015338.5	545	Cgt/Tgt	12/13	0.369021393779988	3	FACETS	1	0.9	1	0.508	0.45	0.569	CLONAL	1	TRUE	1	0.369021393779988	3		145	550	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288356	21288357	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	144	333	0	ENST00000354336.3:c.601_602delinsTT	p.Pro201Leu	p.P201L	ENST00000354336	NM_005207.3	201	CCa/TTa	2/3	1	2	FACETS	0.953	0.87	1	0.953	0.87	1	CLONAL	1	TRUE	1	0.369021393779988	2		333	819	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572822	41572822	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	183	316	0	ENST00000263253.7:c.5107C>T	p.His1703Tyr	p.H1703Y	ENST00000263253	NM_001429.3	1703	Cac/Tac	31/31	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.369021393779988	2		316	863	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096521	178096526	+	inframe_deletion	In_Frame_Del	DEL	TGAGTT	TGAGTT	-	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	104	239	0	ENST00000397062.3:c.805_810del	p.Asn269_Ser270del	p.N269_S270del	ENST00000397062	NM_006164.4	269	AACTCA/-	5/5	1	2	FACETS	0.849	0.761	0.942	0.849	0.761	0.942	CLONAL	1	TRUE	1	0.369021393779988	2		239	664	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0003104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	26	73	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.369021393779988	2		73	126	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	50	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.846	0.73	0.969	0.846	0.73	0.969	CLONAL	1	TRUE	1	0.671572301926886	2		422	176	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	75	314	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.671572301926886	2		314	211	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105598	27105598	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758555204	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	91	376	1	ENST00000324856.7:c.5209G>A	p.Gly1737Ser	p.G1737S	ENST00000324856	NM_006015.4	1737	Ggt/Agt	20/20	0.671572301926886	1	FACETS	0.952	0.868	1	0.952	0.868	1	CLONAL	1	TRUE	0	0.671572301926886	1		377	189	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78425868	78425868	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	50	161	0	ENST00000370768.2:c.1576+1G>A		p.X526_splice	ENST00000370768	NM_003902.3	526			0.671572301926886	1	FACETS	0.951	0.837	1	0.951	0.837	1	CLONAL	1	TRUE	0	0.671572301926886	1		161	104	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115251151	115251151	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	64	362	0	ENST00000369535.4:c.*4+1G>A			ENST00000369535	NM_002524.4	-/189			0.671572301926886	1	FACETS	0.911	0.813	1	0.911	0.813	1	CLONAL	1	TRUE	0	0.671572301926886	1		362	139	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570820	226570820	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	99	180	0	ENST00000366794.5:c.1076C>T	p.Pro359Leu	p.P359L	ENST00000366794	NM_001618.3	359	cCa/cTa	8/23	1	2	FACETS	0.855	0.77	0.942	0.855	0.77	0.942	CLONAL	1	TRUE	1	0.671572301926886	2		180	345	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47607019	47607019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	84	336	0	ENST00000263735.4:c.769C>T	p.Pro257Ser	p.P257S	ENST00000263735	NM_002354.2	257	Cct/Tct	7/9	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.671572301926886	2		336	240	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635605	47635605	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63751429	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	81	281	0	ENST00000233146.2:c.277C>T	p.Leu93Phe	p.L93F	ENST00000233146	NM_000251.2	93	Ctt/Ttt	2/16	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.671572301926886	2		281	228	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280762	41280762	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	63	267	0	ENST00000349496.5:c.2275G>A	p.Ala759Thr	p.A759T	ENST00000349496	NM_001904.3	759	Gcc/Acc	15/15	1	2	FACETS	0.83	0.728	0.938	0.83	0.728	0.938	CLONAL	1	TRUE	1	0.671572301926886	2		267	226	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678806	52678806	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	48	210	0	ENST00000394830.3:c.814-1G>A		p.X272_splice	ENST00000394830	NM_018313.4	272			1	2	FACETS	0.851	0.732	0.977	0.851	0.732	0.977	CLONAL	1	TRUE	1	0.671572301926886	2		210	168	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119595313	119595313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771909190	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	70	318	0	ENST00000316626.5:c.856C>T	p.Pro286Ser	p.P286S	ENST00000316626		286	Cca/Tca	8/12	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.671572301926886	2		318	196	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204714	128204714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	109	342	0	ENST00000341105.2:c.727C>T	p.His243Tyr	p.H243Y	ENST00000341105	NM_032638.4	243	Cac/Tac	3/6	1	2	FACETS	0.887	0.804	0.973	0.887	0.804	0.973	CLONAL	1	TRUE	1	0.671572301926886	2		342	366	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146689	185146689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765812365	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	56	201	0	ENST00000265026.3:c.320G>A	p.Gly107Glu	p.G107E	ENST00000265026	NM_004721.4	107	gGa/gAa	2/14	1	2	FACETS	0.683	0.592	0.781	0.683	0.592	0.781	SUBCLONAL	1	TRUE	1	0.671572301926886	2		201	244	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589852	55589852	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	57	316	0	ENST00000288135.5:c.1334G>A	p.Gly445Glu	p.G445E	ENST00000288135	NM_000222.2	445	gGa/gAa	8/21	1	2	FACETS	0.981	0.858	1	0.981	0.858	1	CLONAL	1	TRUE	1	0.671572301926886	2		316	173	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524113	187524113	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	69	339	0	ENST00000441802.2:c.11426C>T	p.Pro3809Leu	p.P3809L	ENST00000441802	NM_005245.3	3809	cCc/cTc	20/27	1	2	FACETS	0.998	0.884	1	0.998	0.884	1	CLONAL	1	TRUE	1	0.671572301926886	2		339	206	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	231023	231023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	144	256	0	ENST00000264932.6:c.803C>T	p.Ser268Phe	p.S268F	ENST00000264932	NM_004168.2	268	tCt/tTt	7/15	1	2	FACETS	0.914	0.84	0.991	0.914	0.84	0.991	CLONAL	1	TRUE	1	0.671572301926886	2		256	469	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177998	56177998	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	53	356	0	ENST00000399503.3:c.2971C>T	p.Pro991Ser	p.P991S	ENST00000399503	NM_005921.1	991	Cca/Tca	14/20	1	2	FACETS	0.793	0.686	0.907	0.793	0.686	0.907	CLONAL	1	TRUE	1	0.671572301926886	2		356	199	SUCCESS
APC	324	MSKCC	GRCh37	5	112178415	112178415	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	54	328	0	ENST00000257430.4:c.7124A>G	p.Gln2375Arg	p.Q2375R	ENST00000257430	NM_000038.5	2375	cAa/cGa	16/16	1	2	FACETS	0.855	0.742	0.975	0.855	0.742	0.975	CLONAL	1	TRUE	1	0.671572301926886	2		328	188	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041154	112041154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	204	430	0	ENST00000368678.4:c.101C>T	p.Pro34Leu	p.P34L	ENST00000368678		34	cCc/cTc	3/13	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.671572301926886	NA		430	560	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005659	150005659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1200168979	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	47	192	1	ENST00000253339.5:c.566G>A	p.Arg189Lys	p.R189K	ENST00000253339		189	aGg/aAg	3/7	1	2	FACETS	0.859	0.738	0.987	0.859	0.738	0.987	CLONAL	1	TRUE	1	0.671572301926886	2		193	163	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739928	41739928	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	97	406	0	ENST00000242208.4:c.45G>A	p.Trp15Ter	p.W15*	ENST00000242208	NM_002192.2	15	tgG/tgA	2/3	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.671572301926886	2		406	286	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859981	151859981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	52	287	0	ENST00000262189.6:c.10681C>T	p.Pro3561Ser	p.P3561S	ENST00000262189	NM_170606.2	3561	Cct/Tct	43/59	1	2	FACETS	0.89	0.771	1	0.89	0.771	1	CLONAL	1	TRUE	1	0.671572301926886	2		287	174	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372023	55372023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	65	152	0	ENST00000297316.4:c.713C>T	p.Ala238Val	p.A238V	ENST00000297316	NM_022454.3	238	gCc/gTc	2/2	0.280551488116463	3	FACETS	1	0.901	1	0.515	0.452	0.582	INDETERMINATE	1	TRUE	1	0.671572301926886	3		152	251	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486134	8486134	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	63	341	0	ENST00000356435.5:c.2683C>T	p.Leu895Phe	p.L895F	ENST00000356435		895	Ctc/Ttc	17/35	1	2	FACETS	0.873	0.766	0.984	0.873	0.766	0.984	CLONAL	1	TRUE	1	0.671572301926886	2		341	215	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851644	63851644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	64	255	0	ENST00000279873.7:c.2422G>A	p.Glu808Lys	p.E808K	ENST00000279873	NM_032199.2	808	Gag/Aag	10/10	0.265898529973852	5	FACETS	0.976	0.86	1			1	INDETERMINATE	2	TRUE	NA	0.671572301926886	5		255	196	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925378	114925378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747779097	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	139	459	0	ENST00000543371.1:c.1456G>A	p.Asp486Asn	p.D486N	ENST00000543371	NM_001198531.1	486	Gat/Aat	14/14	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.671572301926886	2		459	366	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204750	94204750	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147383852	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	39	223	0	ENST00000323929.3:c.835G>A	p.Ala279Thr	p.A279T	ENST00000323929	NM_005591.3	279	Gct/Act	8/20	1	2	FACETS	0.915	0.775	1	0.915	0.775	1	CLONAL	1	TRUE	1	0.671572301926886	2		223	127	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495826	56495826	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	60	121	0	ENST00000267101.3:c.4016C>A	p.Ala1339Asp	p.A1339D	ENST00000267101	NM_001982.3	1339	gCc/gAc	28/28	1	2	FACETS	0.993	0.872	1	0.993	0.872	1	CLONAL	1	TRUE	1	0.671572301926886	2		121	180	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865062	57865062	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	122	502	0	ENST00000228682.2:c.2539C>T	p.Leu847Phe	p.L847F	ENST00000228682	NM_005269.2	847	Ctc/Ttc	12/12	1	2	FACETS	0.929	0.848	1	0.929	0.848	1	CLONAL	1	TRUE	1	0.671572301926886	2		502	391	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953646	32953646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	53	432	0	ENST00000380152.3:c.8947G>A	p.Asp2983Asn	p.D2983N	ENST00000380152		2983	Gat/Aat	22/27	0.18180697807851	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.671572301926886	0		432	177	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820681	3820681	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	123	199	0	ENST00000262367.5:c.2770G>A	p.Ala924Thr	p.A924T	ENST00000262367	NM_004380.2	924	Gcc/Acc	14/31	1	2	FACETS	0.947	0.864	1	0.947	0.864	1	CLONAL	1	TRUE	1	0.671572301926886	2		199	387	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337314	89337314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	106	240	0	ENST00000301030.4:c.7717G>A	p.Asp2573Asn	p.D2573N	ENST00000301030	NM_001256183.1	2573	Gac/Aac	12/13	0.226090932312491	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.671572301926886	0		240	329	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350279	89350279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	151	523	0	ENST00000301030.4:c.2671G>A	p.Asp891Asn	p.D891N	ENST00000301030	NM_001256183.1	891	Gac/Aac	9/13	0.226090932312491	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.671572301926886	0		523	467	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354811	40354811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	117	514	1	ENST00000293328.3:c.2093G>A	p.Gly698Glu	p.G698E	ENST00000293328	NM_012448.3	698	gGa/gAa	17/19	0.671572301926886	3	FACETS	1	0.94	1	0.523	0.475	0.573	CLONAL	1	TRUE	1	0.671572301926886	3		515	445	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774100	56774100	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753912045	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	66	383	0	ENST00000337432.4:c.451G>A	p.Val151Met	p.V151M	ENST00000337432	NM_058216.2	151	Gtg/Atg	3/9	0.671572301926886	3	FACETS	0.847	0.741	0.96	0.423	0.37	0.48	CLONAL	1	TRUE	1	0.671572301926886	3		383	310	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733082	74733082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	239	386	0	ENST00000359995.5:c.161C>T	p.Ser54Phe	p.S54F	ENST00000359995	NM_001195427.1	54	tCc/tTc	1/3	0.55319590257314	4	FACETS	1	0.992	1	0.494	0.463	0.527	CLONAL	1	TRUE	1	0.671572301926886	4		386	802	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78854288	78854288	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1322614757	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	116	270	0	ENST00000306801.3:c.1583C>T	p.Pro528Leu	p.P528L	ENST00000306801	NM_020761.2	528	cCa/cTa	14/34	0.55319590257314	4	FACETS	1	0.972	1	0.399	0.361	0.438	CLONAL	1	TRUE	1	0.671572301926886	4		270	483	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78921106	78921106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	99	246	0	ENST00000306801.3:c.3220G>A	p.Glu1074Lys	p.E1074K	ENST00000306801	NM_020761.2	1074	Gag/Aag	27/34	0.55319590257314	4	FACETS	1	0.973	1	0.414	0.372	0.458	CLONAL	1	TRUE	1	0.671572301926886	4		246	397	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56376726	56376726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	63	466	0	ENST00000348428.3:c.766C>T	p.Pro256Ser	p.P256S	ENST00000348428	NM_006785.3	256	Cct/Tct	5/17	1	2	FACETS	0.798	0.699	0.903	0.798	0.699	0.903	CLONAL	1	TRUE	1	0.671572301926886	2		466	235	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2164190	2164190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	113	193	0	ENST00000398665.3:c.7G>A	p.Glu3Lys	p.E3K	ENST00000398665	NM_032482.2	3	Gag/Aag	1/28	1	2	FACETS	0.919	0.836	1	0.919	0.836	1	CLONAL	1	TRUE	1	0.671572301926886	2		193	366	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105546	11105546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	107	286	0	ENST00000358026.2:c.1462G>A	p.Glu488Lys	p.E488K	ENST00000358026	NM_001128849.1	488	Gaa/Aaa	9/36	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.671572301926886	2		286	314	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366230	15366230	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381188597	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	113	373	0	ENST00000263377.2:c.1925C>T	p.Pro642Leu	p.P642L	ENST00000263377	NM_058243.2	642	cCc/cTc	10/20	1	2	FACETS	0.843	0.765	0.924	0.843	0.765	0.924	CLONAL	1	TRUE	1	0.671572301926886	2		373	399	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376196	15376196	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1296531466	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	115	120	1	ENST00000263377.2:c.818C>T	p.Pro273Leu	p.P273L	ENST00000263377	NM_058243.2	273	cCc/cTc	5/20	1	2	FACETS	0.993	0.905	1	0.993	0.905	1	CLONAL	1	TRUE	1	0.671572301926886	2		121	345	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791806	42791806	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	184	243	0	ENST00000575354.2:c.692G>A	p.Ser231Asn	p.S231N	ENST00000575354	NM_015125.3	231	aGc/aAc	5/20	0.671572301926886	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.671572301926886	1		243	330	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498333	29498333	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	89	318	0	ENST00000389048.3:c.1847del	p.Gly616AspfsTer49	p.G616Dfs*49	ENST00000389048	NM_004304.4	616	gGa/ga	10/29	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.671572301926886	2		318	246	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589620	67589621	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAATATGATAGATTATAT	novel	NA	P-0003120-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	51	215	0	ENST00000274335.5:c.1387_1404dup	p.Tyr463_Glu468dup	p.Y463_E468dup	ENST00000274335		463	-/GAATATGATAGATTATAT	10/15	1	2	FACETS	0.593	0.509	0.684	0.593	0.509	0.684	SUBCLONAL	1	TRUE	1	0.671572301926886	2		215	256	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	183	422	0				ENST00000310581	NM_198253.2	-/1132			0.179106296217703	8	FACETS	1	0.964	1	1	0.986	1	CLONAL	8	TRUE	1	0.179106296217703	8		422	377	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275074	41275074	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	57	275	0	ENST00000349496.5:c.1240A>G	p.Ile414Val	p.I414V	ENST00000349496	NM_001904.3	414	Ata/Gta	9/15	0.179106296217703	3	FACETS	1	0.942	1	0.6	0.514	0.693	CLONAL	1	TRUE	1	0.179106296217703	3		275	578	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967819	93967819	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	52	325	0	ENST00000369303.4:c.2108G>C	p.Arg703Thr	p.R703T	ENST00000369303	NM_004440.3	703	aGa/aCa	11/17	0.179106296217703	1	FACETS	0.753	0.64	0.878	0.753	0.64	0.878	SUBCLONAL	1	TRUE	0	0.179106296217703	1		325	702	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276860	123276860	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	110	300	0	ENST00000358487.5:c.1057C>A	p.His353Asn	p.H353N	ENST00000358487	NM_000141.4	353	Cac/Aac	8/18	0.179106296217703	1	FACETS	0.921	0.83	1	1	0.987	1	CLONAL	2	TRUE	0	0.179106296217703	1		300	607	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981761	101981761	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	145	224	0	ENST00000282441.5:c.182C>G	p.Ser61Trp	p.S61W	ENST00000282441	NM_001130145.2	61	tCg/tGg	1/9	1	2	FACETS	0.85	0.778	0.925	1	0.992	1	CLONAL	3	TRUE	1	0.179106296217703	2		224	635	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877314	28877314	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	49	145	0	ENST00000282397.4:c.4007C>T	p.Pro1336Leu	p.P1336L	ENST00000282397	NM_002019.4	1336	cCa/cTa	30/30	1	2	FACETS	0.791	0.672	0.92	1	0.966	1	CLONAL	2	TRUE	1	0.179106296217703	2		145	346	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37882031	37882031	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1790	214	274	0	ENST00000269571.5:c.2797G>C	p.Asp933His	p.D933H	ENST00000269571		933	Gac/Cac	23/27	0.179106296217703	26	FACETS	0.939	0.869	1			1	CLONAL	4	TRUE	NA	0.179106296217703	26		274	2004	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023646	27023650	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCT	CGCCT	-	novel	NA	P-0003131-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	154	214	0	ENST00000324856.7:c.753_757del	p.Pro252LeufsTer146	p.P252Lfs*146	ENST00000324856	NM_006015.4	251	cCGCCT/c	1/20	0.179106296217703	4	FACETS	0.853	0.782	0.928	1	0.983	1	CLONAL	3	TRUE	2	0.179106296217703	4		214	792	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	84	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.898394647714412	2		422	177	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223564	55223564	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5754	19073	527	4	ENST00000275493.2:c.931T>C	p.Cys311Arg	p.C311R	ENST00000275493	NM_005228.3	311	Tgt/Cgt	8/28	0.898394647714412	24	FACETS	0.98	0.975	0.984			1	CLONAL	19	TRUE	NA	0.898394647714412	24		531	24827	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164648	47164648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757035494	NA	P-0003170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	301	478	0	ENST00000409792.3:c.1478G>A	p.Arg493Gln	p.R493Q	ENST00000409792	NM_014159.6	493	cGg/cAg	3/21	1	2	FACETS	0.902	0.854	0.95	0.902	0.854	0.95	CLONAL	1	TRUE	1	0.898394647714412	2		478	743	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	60	139	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.869	0.764	0.978	0.869	0.764	0.978	CLONAL	1	TRUE	1	0.80287384803467	2		139	172	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	121	180	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.765703094910269	1	FACETS	0.93	0.868	0.991	0.93	0.868	0.991	CLONAL	1	TRUE	0	0.80287384803467	1		180	194	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780693	9780693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767714303	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	112	183	0	ENST00000377346.4:c.1495G>A	p.Glu499Lys	p.E499K	ENST00000377346	NM_005026.3	499	Gag/Aag	12/24	1	2	FACETS	0.986	0.901	1	0.986	0.901	1	CLONAL	1	TRUE	1	0.80287384803467	2		183	283	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259339	11259339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	144	270	1	ENST00000361445.4:c.4229C>T	p.Pro1410Leu	p.P1410L	ENST00000361445	NM_004958.3	1410	cCt/cTt	28/58	1	2	FACETS	0.852	0.785	0.921	0.852	0.785	0.921	CLONAL	1	TRUE	1	0.80287384803467	2		271	421	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242673	16242673	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	180	356	0	ENST00000375759.3:c.1294T>A	p.Phe432Ile	p.F432I	ENST00000375759	NM_015001.2	432	Ttt/Att	6/15	1	2	FACETS	0.934	0.869	1	0.934	0.869	1	CLONAL	1	TRUE	1	0.80287384803467	2		356	480	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261124	16261124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	96	109	0	ENST00000375759.3:c.8389C>T	p.Pro2797Ser	p.P2797S	ENST00000375759	NM_015001.2	2797	Ccg/Tcg	11/15	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.80287384803467	2		109	227	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058631	72058631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	206	407	0	ENST00000357731.5:c.809G>A	p.Gly270Glu	p.G270E	ENST00000357731	NM_173808.2	270	gGa/gAa	6/7	1	2	FACETS	0.938	0.877	1	0.938	0.877	1	CLONAL	1	TRUE	1	0.80287384803467	2		407	547	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497856	120497856	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	104	116	0	ENST00000256646.2:c.2027-1G>A		p.X676_splice	ENST00000256646	NM_024408.3	676			1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.80287384803467	2		116	250	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724427	162724427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	120	196	0	ENST00000367921.3:c.199G>A	p.Glu67Lys	p.E67K	ENST00000367921	NM_006182.2	67	Gaa/Aaa	5/18	1	2	FACETS	0.952	0.872	1	0.952	0.872	1	CLONAL	1	TRUE	1	0.80287384803467	2		196	314	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967305	25967305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766049052	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	147	215	0	ENST00000435504.4:c.1901C>T	p.Ser634Leu	p.S634L	ENST00000435504		634	tCg/tTg	13/13	0.77664095736988	3	FACETS	1	0.924	1	0.503	0.462	0.545	CLONAL	1	TRUE	1	0.80287384803467	3		215	510	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209103936	209103936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	162	194	0	ENST00000345146.2:c.1013G>A	p.Arg338Lys	p.R338K	ENST00000345146	NM_005896.2	338	aGa/aAa	9/10	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.80287384803467	2		194	400	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568895	212568895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	140	257	0	ENST00000342788.4:c.1223C>T	p.Pro408Leu	p.P408L	ENST00000342788	NM_005235.2	408	cCa/cTa	11/28	1	2	FACETS	0.966	0.891	1	0.966	0.891	1	CLONAL	1	TRUE	1	0.80287384803467	2		257	361	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370726	225370726	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	182	243	0	ENST00000264414.4:c.1153C>T	p.Pro385Ser	p.P385S	ENST00000264414	NM_003590.4	385	Cct/Tct	8/16	1	2	FACETS	0.937	0.872	1	0.937	0.872	1	CLONAL	1	TRUE	1	0.80287384803467	2		243	484	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277249	41277249	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	168	235	0	ENST00000349496.5:c.1718G>T	p.Cys573Phe	p.C573F	ENST00000349496	NM_001904.3	573	tGt/tTt	11/15	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.80287384803467	2		235	402	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037153	71037153	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1161489431	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	138	199	0	ENST00000318789.4:c.1138C>T	p.Pro380Ser	p.P380S	ENST00000318789	NM_032682.5	380	Cct/Tct	14/21	NA	2	FACETS	0.922	0.849	0.996			1	INDETERMINATE	1	TRUE	NA	0.80287384803467	2		199	373	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390995	89390995	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	166	298	0	ENST00000336596.2:c.1061G>T	p.Arg354Leu	p.R354L	ENST00000336596	NM_005233.5	354	cGg/cTg	5/17	0.80287384803467	4	FACETS	0.755	0.693	0.819			1	SUBCLONAL	1	TRUE	NA	0.80287384803467	4		298	988	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445106	89445106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301060598	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	103	200	0	ENST00000336596.2:c.1426G>A	p.Glu476Lys	p.E476K	ENST00000336596	NM_005233.5	476	Gaa/Aaa	6/17	0.80287384803467	4	FACETS	0.588	0.526	0.654			1	SUBCLONAL	1	TRUE	NA	0.80287384803467	4		200	787	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448471	89448471	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	129	237	0	ENST00000336596.2:c.1435G>A	p.Glu479Lys	p.E479K	ENST00000336596	NM_005233.5	479	Gaa/Aaa	7/17	0.80287384803467	4	FACETS	0.607	0.549	0.667			1	SUBCLONAL	1	TRUE	NA	0.80287384803467	4		237	955	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480345	89480345	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs774448099	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	146	292	0	ENST00000336596.2:c.2182C>T	p.Arg728Ter	p.R728*	ENST00000336596	NM_005233.5	728	Cga/Tga	13/17	0.80287384803467	4	FACETS	0.623	0.567	0.681			1	SUBCLONAL	1	TRUE	NA	0.80287384803467	4		292	1053	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499514	89499514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141716319	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	106	196	0	ENST00000336596.2:c.2684C>T	p.Ala895Val	p.A895V	ENST00000336596	NM_005233.5	895	gCc/gTc	15/17	0.80287384803467	4	FACETS	0.585	0.524	0.65			1	SUBCLONAL	1	TRUE	NA	0.80287384803467	4		196	814	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582434	119582434	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769830542	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	105	146	0	ENST00000316626.5:c.967C>T	p.Pro323Ser	p.P323S	ENST00000316626		323	Cca/Tca	10/12	1	2	FACETS	0.884	0.803	0.967	0.884	0.803	0.967	CLONAL	1	TRUE	1	0.80287384803467	2		146	296	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960089	134960089	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1224986515	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	133	253	0	ENST00000398015.3:c.2446G>A	p.Glu816Lys	p.E816K	ENST00000398015	NM_004441.4	816	Gaa/Aaa	13/16	1	2	FACETS	0.939	0.863	1	0.939	0.863	1	CLONAL	1	TRUE	1	0.80287384803467	2		253	353	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453514	138453514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	158	285	0	ENST00000289153.2:c.934C>T	p.Pro312Ser	p.P312S	ENST00000289153	NM_006219.2	312	Cct/Tct	5/22	1	2	FACETS	0.892	0.826	0.961	0.892	0.826	0.961	CLONAL	1	TRUE	1	0.80287384803467	2		285	441	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747879	41747879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	125	240	0	ENST00000226382.2:c.890C>T	p.Ser297Leu	p.S297L	ENST00000226382	NM_003924.3	297	tCg/tTg	3/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.80287384803467	2		240	276	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602887	55602887	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	130	199	0	ENST00000288135.5:c.2597G>A	p.Gly866Glu	p.G866E	ENST00000288135	NM_000222.2	866	gGa/gAa	19/21	1	2	FACETS	0.816	0.747	0.886	0.816	0.747	0.886	CLONAL	1	TRUE	1	0.80287384803467	2		199	397	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981161	55981161	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	154	316	0	ENST00000263923.4:c.538G>A	p.Asp180Asn	p.D180N	ENST00000263923	NM_002253.2	180	Gac/Aac	5/30	1	2	FACETS	0.876	0.809	0.944	0.876	0.809	0.944	CLONAL	1	TRUE	1	0.80287384803467	2		316	438	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981570	55981570	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	111	194	0	ENST00000263923.4:c.367T>G	p.Ser123Ala	p.S123A	ENST00000263923	NM_002253.2	123	Tct/Gct	4/30	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.80287384803467	2		194	267	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213917	66213917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	151	241	0	ENST00000273854.3:c.2513G>A	p.Gly838Glu	p.G838E	ENST00000273854	NM_004439.5	838	gGa/gAa	15/18	1	2	FACETS	0.977	0.904	1	0.977	0.904	1	CLONAL	1	TRUE	1	0.80287384803467	2		241	385	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230774	66230774	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	145	300	0	ENST00000273854.3:c.2197C>T	p.His733Tyr	p.H733Y	ENST00000273854	NM_004439.5	733	Cat/Tat	12/18	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.80287384803467	2		300	345	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230825	66230825	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	109	341	2	ENST00000273854.3:c.2146A>G	p.Lys716Glu	p.K716E	ENST00000273854	NM_004439.5	716	Aag/Gag	12/18	1	2	FACETS	0.851	0.774	0.931	0.851	0.774	0.931	CLONAL	1	TRUE	1	0.80287384803467	2		343	319	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280031	66280031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867811974	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	156	236	0	ENST00000273854.3:c.1658G>A	p.Arg553Gln	p.R553Q	ENST00000273854	NM_004439.5	553	cGa/cAa	7/18	1	2	FACETS	0.989	0.917	1	0.989	0.917	1	CLONAL	1	TRUE	1	0.80287384803467	2		236	393	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106197348	106197348	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1053451791	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	161	274	0	ENST00000380013.4:c.5681C>T	p.Pro1894Leu	p.P1894L	ENST00000380013	NM_001127208.2	1894	cCc/cTc	11/11	1	2	FACETS	0.931	0.862	1	0.931	0.862	1	CLONAL	1	TRUE	1	0.80287384803467	2		274	431	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081612	143081612	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	183	282	1	ENST00000262992.4:c.1462C>G	p.Pro488Ala	p.P488A	ENST00000262992	NM_001101669.1	488	Cct/Gct	15/24	1	2	FACETS	0.948	0.883	1	0.948	0.883	1	CLONAL	1	TRUE	1	0.80287384803467	2		283	481	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517879	187517879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	192	301	1	ENST00000441802.2:c.12815C>T	p.Ser4272Phe	p.S4272F	ENST00000441802	NM_005245.3	4272	tCc/tTc	25/27	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.80287384803467	2		302	421	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521286	187521286	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750085546	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	197	419	0	ENST00000441802.2:c.11869C>T	p.Arg3957Cys	p.R3957C	ENST00000441802	NM_005245.3	3957	Cgt/Tgt	22/27	1	2	FACETS	0.922	0.861	0.985	0.922	0.861	0.985	CLONAL	1	TRUE	1	0.80287384803467	2		419	532	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539951	187539951	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs777631605	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	128	222	0	ENST00000441802.2:c.7789C>T	p.Arg2597Ter	p.R2597*	ENST00000441802	NM_005245.3	2597	Cga/Tga	10/27	1	2	FACETS	0.826	0.756	0.898	0.826	0.756	0.898	CLONAL	1	TRUE	1	0.80287384803467	2		222	386	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557298	187557298	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	141	270	0	ENST00000441802.2:c.4064C>T	p.Pro1355Leu	p.P1355L	ENST00000441802	NM_005245.3	1355	cCc/cTc	6/27	1	2	FACETS	0.834	0.767	0.903	0.834	0.767	0.903	CLONAL	1	TRUE	1	0.80287384803467	2		270	421	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562496	176562496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	56	367	0	ENST00000439151.2:c.392C>T	p.Ser131Phe	p.S131F	ENST00000439151	NM_022455.4	131	tCt/tTt	2/23	0.590753693848466	1	FACETS	0.241	0.207	0.278	0.241	0.207	0.278	SUBCLONAL	1	TRUE	0	0.80287384803467	1		367	346	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721012	176721013	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	157	247	0	ENST00000439151.2:c.6643_6644delinsTT	p.Pro2215Phe	p.P2215F	ENST00000439151	NM_022455.4	2215	CCt/TTt	23/23	0.590753693848466	1	FACETS	0.893	0.839	0.947	0.893	0.839	0.947	CLONAL	1	TRUE	0	0.80287384803467	1		247	262	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394999	394999	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	82	136	0	ENST00000380956.4:c.395C>T	p.Ala132Val	p.A132V	ENST00000380956	NM_001195286.1	132	gCc/gTc	3/9	1	2	FACETS	0.982	0.883	1	0.982	0.883	1	CLONAL	1	TRUE	1	0.80287384803467	2		136	208	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032084	26032084	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	209	566	0	ENST00000244661.2:c.205C>T	p.Gln69Ter	p.Q69*	ENST00000244661	NM_003537.3	69	Cag/Tag	1/1	1	2	FACETS	0.995	0.933	1	0.995	0.933	1	CLONAL	1	TRUE	1	0.80287384803467	2		566	523	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93968000	93968000	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	173	411	0	ENST00000369303.4:c.1927G>A	p.Glu643Lys	p.E643K	ENST00000369303	NM_004440.3	643	Gaa/Aaa	11/17	0.590753693848466	1	FACETS	0.592	0.55	0.634	0.592	0.55	0.634	SUBCLONAL	1	TRUE	0	0.80287384803467	1		411	436	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979321	93979321	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	153	474	0	ENST00000369303.4:c.1507A>G	p.Asn503Asp	p.N503D	ENST00000369303	NM_004440.3	503	Aat/Gat	7/17	0.590753693848466	1	FACETS	0.52	0.48	0.561	0.52	0.48	0.561	SUBCLONAL	1	TRUE	0	0.80287384803467	1		474	439	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106543577	106543577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	133	177	0	ENST00000369096.4:c.379C>T	p.Pro127Ser	p.P127S	ENST00000369096	NM_001198.3	127	Cct/Tct	3/7	NA	2	FACETS	0.998	0.919	1			1	INDETERMINATE	1	TRUE	NA	0.80287384803467	2		177	332	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647518	117647518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	217	432	0	ENST00000368508.3:c.5426G>A	p.Gly1809Glu	p.G1809E	ENST00000368508	NM_002944.2	1809	gGa/gAa	33/43	0.69567566658654	1	FACETS	0.599	0.562	0.637	0.599	0.562	0.637	SUBCLONAL	1	TRUE	0	0.80287384803467	1		432	540	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662582	117662582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	122	278	0	ENST00000368508.3:c.4883G>A	p.Gly1628Glu	p.G1628E	ENST00000368508	NM_002944.2	1628	gGa/gAa	29/43	1	2	FACETS	0.847	0.774	0.921	0.847	0.774	0.921	CLONAL	1	TRUE	1	0.80287384803467	2		278	359	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686238	117686238	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs772772410	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	137	222	0	ENST00000368508.3:c.3103C>T	p.Arg1035Ter	p.R1035*	ENST00000368508	NM_002944.2	1035	Cga/Tga	20/43	1	2	FACETS	0.905	0.833	0.979	0.905	0.833	0.979	CLONAL	1	TRUE	1	0.80287384803467	2		222	377	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710935	117710935	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	134	157	0	ENST00000368508.3:c.1337C>T	p.Ala446Val	p.A446V	ENST00000368508	NM_002944.2	446	gCt/gTt	12/43	1	2	FACETS	0.991	0.913	1	0.991	0.913	1	CLONAL	1	TRUE	1	0.80287384803467	2		157	337	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505506	157505506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	136	222	0	ENST00000346085.5:c.3487C>T	p.Pro1163Ser	p.P1163S	ENST00000346085	NM_020732.3	1163	Ccg/Tcg	13/20	1	2	FACETS	0.941	0.866	1	0.941	0.866	1	CLONAL	1	TRUE	1	0.80287384803467	2		222	360	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2984049	2984049	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	159	282	0	ENST00000396946.4:c.481G>A	p.Asp161Asn	p.D161N	ENST00000396946	NM_032415.4	161	Gat/Aat	5/25	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.80287384803467	2		282	384	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339512	81339512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866698564	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	237	378	0	ENST00000222390.5:c.1492G>A	p.Gly498Arg	p.G498R	ENST00000222390	NM_000601.4	498	Ggg/Agg	13/18	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.80287384803467	2		378	588	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508208	106508208	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770811999	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	82	99	0	ENST00000359195.3:c.202G>A	p.Glu68Lys	p.E68K	ENST00000359195	NM_002649.2	68	Gag/Aag	2/11	1	2	FACETS	0.987	0.888	1	0.987	0.888	1	CLONAL	1	TRUE	1	0.80287384803467	2		99	207	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878010	151878010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	118	205	0	ENST00000262189.6:c.6935C>T	p.Ser2312Phe	p.S2312F	ENST00000262189	NM_170606.2	2312	tCt/tTt	36/59	1	2	FACETS	0.862	0.787	0.939	0.862	0.787	0.939	CLONAL	1	TRUE	1	0.80287384803467	2		205	341	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878595	151878595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	121	160	0	ENST00000262189.6:c.6350C>T	p.Ser2117Phe	p.S2117F	ENST00000262189	NM_170606.2	2117	tCc/tTc	36/59	1	2	FACETS	0.942	0.863	1	0.942	0.863	1	CLONAL	1	TRUE	1	0.80287384803467	2		160	320	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539105	23539105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	171	234	0	ENST00000380871.4:c.334G>A	p.Ala112Thr	p.A112T	ENST00000380871	NM_006167.3	112	Gcc/Acc	2/2	0.111547569581667	4	FACETS	0.912	0.849	0.976	0.912	0.849	0.976	INDETERMINATE	2	TRUE	2	0.80287384803467	4		234	421	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958508	90958508	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	108	154	0	ENST00000265433.3:c.1930C>T	p.Gln644Ter	p.Q644*	ENST00000265433	NM_002485.4	644	Cag/Tag	13/16	0.111547569581667	4	FACETS	0.892	0.814	0.971	0.892	0.814	0.971	INDETERMINATE	2	TRUE	2	0.80287384803467	4		154	272	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753011	128753011	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	148	277	0	ENST00000377970.2:c.1172C>T	p.Ala391Val	p.A391V	ENST00000377970	NM_002467.4	391	gCc/gTc	3/3	0.111547569581667	4	FACETS	0.831	0.767	0.896	0.831	0.767	0.896	INDETERMINATE	2	TRUE	2	0.80287384803467	4		277	400	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331736	8331736	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	130	205	0	ENST00000356435.5:c.5380G>A	p.Asp1794Asn	p.D1794N	ENST00000356435		1794	Gac/Aac	33/35	0.750002132472014	1	FACETS	0.974	0.913	1	0.974	0.913	1	CLONAL	1	TRUE	0	0.80287384803467	1		205	199	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499838	8499838	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	159	197	0	ENST00000356435.5:c.2131C>T	p.Pro711Ser	p.P711S	ENST00000356435		711	Cct/Tct	14/35	0.750002132472014	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.80287384803467	1		197	237	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504309	8504309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	155	231	0	ENST00000356435.5:c.1774G>A	p.Gly592Ser	p.G592S	ENST00000356435		592	Ggc/Agc	12/35	0.750002132472014	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.80287384803467	1		231	221	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	125	161	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.750002132472014	1	FACETS	0.997	0.935	1	0.997	0.935	1	CLONAL	1	TRUE	0	0.80287384803467	1		161	187	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209490	98209490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140417636	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	256	183	0	ENST00000331920.6:c.4048C>T	p.Arg1350Trp	p.R1350W	ENST00000331920	NM_000264.3	1350	Cgg/Tgg	23/24	0.80287384803467	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.80287384803467	2		183	313	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98247966	98247966	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	216	167	0	ENST00000331920.6:c.584+1G>A		p.X195_splice	ENST00000331920	NM_000264.3	195			0.80287384803467	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	0	0.80287384803467	2		167	268	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401829	139401829	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	313	260	0	ENST00000277541.6:c.3571C>T	p.Pro1191Ser	p.P1191S	ENST00000277541	NM_017617.3	1191	Ccc/Tcc	22/34	0.80287384803467	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.80287384803467	2		260	387	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742964	17742964	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756275519	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	127	222	0	ENST00000250003.3:c.872G>A	p.Gly291Glu	p.G291E	ENST00000250003	NM_002478.4	291	gGa/gAa	3/3	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.80287384803467	2		222	276	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132897	64132897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs951024884	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	150	330	0	ENST00000334205.4:c.1031C>T	p.Pro344Leu	p.P344L	ENST00000334205	NM_003942.2	344	cCc/cTc	9/17	1	2	FACETS	0.918	0.848	0.989	0.918	0.848	0.989	CLONAL	1	TRUE	1	0.80287384803467	2		330	407	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102207515	102207515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	244	448	0	ENST00000263464.3:c.1604C>T	p.Pro535Leu	p.P535L	ENST00000263464	NM_001165.4	535	cCc/cTc	8/9	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.80287384803467	2		448	607	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380336	25380336	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	125	171	0	ENST00000311936.3:c.122G>A	p.Arg41Lys	p.R41K	ENST00000311936	NM_004985.3	41	aGg/aAg	3/5	1	2	FACETS	0.892	0.817	0.969	0.892	0.817	0.969	CLONAL	1	TRUE	1	0.80287384803467	2		171	349	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46215271	46215271	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	152	211	0	ENST00000334344.6:c.705+1G>A		p.X235_splice	ENST00000334344	NM_152641.2	235			1	2	FACETS	0.912	0.843	0.983	0.912	0.843	0.983	CLONAL	1	TRUE	1	0.80287384803467	2		211	415	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415831	49415831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	161	239	0	ENST00000301067.7:c.16516G>A	p.Glu5506Lys	p.E5506K	ENST00000301067	NM_003482.3	5506	Gag/Aag	53/54	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.80287384803467	2		239	397	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424741	49424741	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783692	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	167	366	0	ENST00000301067.7:c.13606C>T	p.Arg4536Ter	p.R4536*	ENST00000301067	NM_003482.3	4536	Cga/Tga	40/54	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.80287384803467	2		366	412	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431588	49431588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1305161243	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	109	171	0	ENST00000301067.7:c.9551C>T	p.Ser3184Phe	p.S3184F	ENST00000301067	NM_003482.3	3184	tCc/tTc	34/54	1	2	FACETS	0.785	0.712	0.86	0.785	0.712	0.86	SUBCLONAL	1	TRUE	1	0.80287384803467	2		171	346	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433850	49433850	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	135	242	0	ENST00000301067.7:c.7703C>T	p.Pro2568Leu	p.P2568L	ENST00000301067	NM_003482.3	2568	cCc/cTc	31/54	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.80287384803467	2		242	312	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442531	49442531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	114	243	0	ENST00000301067.7:c.4042C>T	p.Pro1348Ser	p.P1348S	ENST00000301067	NM_003482.3	1348	Ccc/Tcc	13/54	1	2	FACETS	0.861	0.784	0.939	0.861	0.784	0.939	CLONAL	1	TRUE	1	0.80287384803467	2		243	330	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233411	69233411	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	171	277	0	ENST00000462284.1:c.1276C>T	p.Gln426Ter	p.Q426*	ENST00000462284	NM_002392.5	426	Caa/Taa	11/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.80287384803467	2		277	398	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434443	121434443	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	180	318	0	ENST00000257555.6:c.1207C>T	p.Leu403Phe	p.L403F	ENST00000257555		403	Ctc/Ttc	6/10	1	2	FACETS	0.988	0.92	1	0.988	0.92	1	CLONAL	1	TRUE	1	0.80287384803467	2		318	454	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220070	133220070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	199	319	0	ENST00000320574.5:c.4367C>T	p.Ser1456Leu	p.S1456L	ENST00000320574	NM_006231.2	1456	tCa/tTa	34/49	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.80287384803467	2		319	451	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515397	103515397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	124	217	0	ENST00000355739.4:c.1898C>T	p.Ser633Phe	p.S633F	ENST00000355739	NM_000123.3	633	tCc/tTc	8/15	0.111547569581667	4	FACETS	0.826	0.757	0.897	0.826	0.757	0.897	INDETERMINATE	2	TRUE	2	0.80287384803467	4		217	337	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052719	42052719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	202	377	0	ENST00000219905.7:c.7390C>T	p.Leu2464Phe	p.L2464F	ENST00000219905	NM_001164273.1	2464	Ctt/Ttt	20/24	0.590753693848466	1	FACETS	0.577	0.539	0.615	0.577	0.539	0.615	SUBCLONAL	1	TRUE	0	0.80287384803467	1		377	522	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996170	73996170	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	127	318	0	ENST00000318443.5:c.904G>A	p.Asp302Asn	p.D302N	ENST00000318443	NM_001024736.1	302	Gac/Aac	5/10	1	2	FACETS	0.86	0.788	0.934	0.86	0.788	0.934	CLONAL	1	TRUE	1	0.80287384803467	2		318	368	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106675	2106675	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	141	292	0	ENST00000219476.3:c.679T>A	p.Cys227Ser	p.C227S	ENST00000219476	NM_000548.3	227	Tgc/Agc	8/42	1	2	FACETS	0.96	0.885	1	0.96	0.885	1	CLONAL	1	TRUE	1	0.80287384803467	2		292	366	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128586	30128586	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	214	374	1	ENST00000263025.4:c.796C>T	p.Gln266Ter	p.Q266*	ENST00000263025	NM_002746.2	266	Cag/Tag	6/9	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.80287384803467	2		375	485	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830756	72830756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1410398135	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	220	465	0	ENST00000268489.5:c.5825G>A	p.Gly1942Glu	p.G1942E	ENST00000268489	NM_006885.3	1942	gGg/gAg	9/10	0.590753693848466	1	FACETS	0.614	0.577	0.652	0.614	0.577	0.652	SUBCLONAL	1	TRUE	0	0.80287384803467	1		465	534	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992390	72992390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	210	538	0	ENST00000268489.5:c.1655C>T	p.Ser552Phe	p.S552F	ENST00000268489	NM_006885.3	552	tCt/tTt	2/10	0.590753693848466	1	FACETS	0.569	0.533	0.606	0.569	0.533	0.606	SUBCLONAL	1	TRUE	0	0.80287384803467	1		538	550	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992784	72992784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	187	402	0	ENST00000268489.5:c.1261G>A	p.Gly421Arg	p.G421R	ENST00000268489	NM_006885.3	421	Ggg/Agg	2/10	0.590753693848466	1	FACETS	0.56	0.522	0.599	0.56	0.522	0.599	SUBCLONAL	1	TRUE	0	0.80287384803467	1		402	498	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576135	29576135	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs868573462	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	173	262	1	ENST00000356175.3:c.4108C>T	p.Gln1370Ter	p.Q1370*	ENST00000356175	NM_000267.3	1370	Cag/Tag	30/57	NA	2	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.80287384803467	2		263	408	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353773	40353773	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1351859924	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	158	458	0	ENST00000293328.3:c.2347C>T	p.Pro783Ser	p.P783S	ENST00000293328	NM_012448.3	783	Ccg/Tcg	19/19	NA	2	FACETS	0.813	0.751	0.877			1	INDETERMINATE	1	TRUE	NA	0.80287384803467	2		458	484	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354388	40354388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	217	563	0	ENST00000293328.3:c.2207C>T	p.Pro736Leu	p.P736L	ENST00000293328	NM_012448.3	736	cCc/cTc	18/19	NA	2	FACETS	0.913	0.855	0.972			1	INDETERMINATE	1	TRUE	NA	0.80287384803467	2		563	592	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78519544	78519544	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	155	233	1	ENST00000306801.3:c.115A>T	p.Ile39Phe	p.I39F	ENST00000306801	NM_020761.2	39	Att/Ttt	1/34	1	2	FACETS	0.988	0.915	1	0.988	0.915	1	CLONAL	1	TRUE	1	0.80287384803467	2		234	391	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39542509	39542509	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	204	323	0	ENST00000262039.4:c.313C>T	p.Gln105Ter	p.Q105*	ENST00000262039	NM_002647.2	105	Caa/Taa	3/25	1	2	FACETS	0.962	0.9	1	0.962	0.9	1	CLONAL	1	TRUE	1	0.80287384803467	2		323	528	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625658	1625658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757102267	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	161	374	0	ENST00000344749.5:c.416C>T	p.Ser139Phe	p.S139F	ENST00000344749	NM_001136139.2	139	tCc/tTc	7/19	1	2	FACETS	0.872	0.807	0.938	0.872	0.807	0.938	CLONAL	1	TRUE	1	0.80287384803467	2		374	460	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223093	5223093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269321557	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	136	214	1	ENST00000357368.4:c.2710C>T	p.Arg904Trp	p.R904W	ENST00000357368	NM_002850.3	904	Cgg/Tgg	18/38	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.80287384803467	2		215	302	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143993	11143993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568509370	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	159	224	0	ENST00000358026.2:c.3574C>T	p.Arg1192Cys	p.R1192C	ENST00000358026	NM_001128849.1	1192	Cgc/Tgc	26/36	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.80287384803467	2		224	378	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271638	15271639	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	169	390	0	ENST00000263388.2:c.6800_6801delinsTT	p.Ser2267Phe	p.S2267F	ENST00000263388	NM_000435.2	2267	tCC/tTT	33/33	1	2	FACETS	0.963	0.895	1	0.963	0.895	1	CLONAL	1	TRUE	1	0.80287384803467	2		390	437	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296140	15296140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	165	266	0	ENST00000263388.2:c.2224C>T	p.Pro742Ser	p.P742S	ENST00000263388	NM_000435.2	742	Ccg/Tcg	14/33	1	2	FACETS	0.949	0.881	1	0.949	0.881	1	CLONAL	1	TRUE	1	0.80287384803467	2		266	433	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17949193	17949193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	139	219	0	ENST00000458235.1:c.1448C>T	p.Ser483Phe	p.S483F	ENST00000458235	NM_000215.3	483	tCc/tTc	11/24	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.80287384803467	2		219	324	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952501	17952502	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	140	251	0	ENST00000458235.1:c.931_932delinsTT	p.Pro311Leu	p.P311L	ENST00000458235	NM_000215.3	311	CCg/TTg	7/24	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.80287384803467	2		251	318	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795043	42795043	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1447243957	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	129	280	0	ENST00000575354.2:c.2123G>A	p.Arg708Lys	p.R708K	ENST00000575354	NM_015125.3	708	aGg/aAg	10/20	1	2	FACETS	0.91	0.836	0.987	0.91	0.836	0.987	CLONAL	1	TRUE	1	0.80287384803467	2		280	353	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912865	50912865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	183	437	0	ENST00000440232.2:c.2096C>T	p.Ser699Phe	p.S699F	ENST00000440232	NM_002691.3	699	tCc/tTc	17/27	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.80287384803467	2		437	456	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944419	40944419	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	171	279	0	ENST00000373198.4:c.2083C>T	p.Leu695Phe	p.L695F	ENST00000373198	NM_133170.3	695	Ctc/Ttc	12/32	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.80287384803467	2		279	396	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46251038	46251038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1348905384	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	228	417	1	ENST00000371998.3:c.47G>A	p.Arg16Gln	p.R16Q	ENST00000371998		16	cGa/cAa	3/23	1	2	FACETS	0.969	0.91	1	0.969	0.91	1	CLONAL	1	TRUE	1	0.80287384803467	2		418	586	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264965	46264965	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	202	468	0	ENST00000371998.3:c.1835C>T	p.Pro612Leu	p.P612L	ENST00000371998		612	cCt/cTt	12/23	0.590753693848466	1	FACETS	0.564	0.527	0.602	0.564	0.527	0.602	SUBCLONAL	1	TRUE	0	0.80287384803467	1		468	534	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961372	54961372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	84	135	0	ENST00000312783.6:c.260C>T	p.Pro87Leu	p.P87L	ENST00000312783	NM_198436.1	87	cCt/cTt	4/10	NA	2	FACETS	0.922	0.829	1			1	INDETERMINATE	1	TRUE	NA	0.80287384803467	2		135	227	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123499665	123499665	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1556620706	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	172	151	0	ENST00000371139.4:c.192G>A	p.Trp64Ter	p.W64*	ENST00000371139	NM_001114937.2	64	tgG/tgA	2/4	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.80287384803467	1		151	219	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023151	27023179	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	GCGGAGCCGGCAGCGGCGGCGGGCCCGGC	-	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	184	23	0	ENST00000324856.7:c.267_295del	p.Ser90ProfsTer11	p.S90Pfs*11	ENST00000324856	NM_006015.4	86	gGCGGAGCCGGCAGCGGCGGCGGGCCCGGC/g	1/20	1	2	FACETS	1	0.992	1	1	0.995	1	CLONAL	2	TRUE	1	0.80287384803467	2		23	208	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530956	187530958	+	frameshift_variant	Frame_Shift_Del	DEL	GTG	GTG	AT	novel	NA	P-0003182-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	136	213	0	ENST00000441802.2:c.10065_10067delinsAT	p.Thr3356TrpfsTer20	p.T3356Wfs*20	ENST00000441802	NM_005245.3	3355	atCACg/atATg	15/27	1	2	FACETS	0.875	0.805	0.948	0.875	0.805	0.948	CLONAL	1	TRUE	1	0.80287384803467	2		213	387	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0003225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	295	318	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.437799924590027	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.461578680340249	3		318	733	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0003225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	165	88	0				ENST00000310581	NM_198253.2	-/1132			0.418124178273539	4	FACETS	1	0.979	1	1	0.992	1	CLONAL	3	TRUE	2	0.461578680340249	4		88	313	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	109	243	0	ENST00000335508.6:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000335508	NM_012433.2	902	Gaa/Aaa	18/25	0.369573310475404	4	FACETS	1	0.983	1			1	CLONAL	1	TRUE	NA	0.461578680340249	4		243	468	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196627	106196627	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	101	292	0	ENST00000380013.4:c.4960C>T	p.Gln1654Ter	p.Q1654*	ENST00000380013	NM_001127208.2	1654	Cag/Tag	11/11	0.437799924590027	3	FACETS	0.889	0.796	0.987	0.444	0.398	0.494	CLONAL	1	TRUE	1	0.461578680340249	3		292	606	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852284	128852284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	271	207	0	ENST00000249373.3:c.2356G>A	p.Asp786Asn	p.D786N	ENST00000249373	NM_005631.4	786	Gac/Aac	12/12	0.437799924590027	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.461578680340249	3		207	602	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28589333	28589333	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	606	277	1	ENST00000241453.7:c.2714G>A	p.Gly905Glu	p.G905E	ENST00000241453	NM_004119.2	905	gGa/gAa	22/24	0.461578680340249	7	FACETS	0.944	0.915	0.972			1	CLONAL	6	TRUE	NA	0.461578680340249	7		278	999	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310143	91310143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs940792839	NA	P-0003225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	122	276	0	ENST00000355112.3:c.2197C>T	p.Pro733Ser	p.P733S	ENST00000355112	NM_000057.2	733	Cca/Tca	10/22	0.300759094979974	5	FACETS	0.83	0.753	0.91			1	CLONAL	2	TRUE	NA	0.461578680340249	5		276	539	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39638005	39638005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	90	194	0	ENST00000262039.4:c.2422C>T	p.His808Tyr	p.H808Y	ENST00000262039	NM_002647.2	808	Cac/Tac	22/25	0.276077781465684	3	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.461578680340249	3		194	416	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044523	47044523	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	207	273	0	ENST00000377604.3:c.2020C>A	p.Gln674Lys	p.Q674K	ENST00000377604	NM_001204468.1	674	Cag/Aag	18/24	0.350307083926509	3	FACETS	1	0.99	1	0.702	0.653	0.753	CLONAL	1	TRUE	1	0.461578680340249	3		273	786	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003238-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	85	422	0				ENST00000310581	NM_198253.2	-/1132			0.167123896244098	1	FACETS	0.611	0.552	0.671	0.611	0.552	0.671	INDETERMINATE	1	TRUE	0	0.825550395745164	1		422	198	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0003238-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	302	155	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	2	TRUE	1	0.825550395745164	2		156	353	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440372	52440372	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003238-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	226	227	0	ENST00000460680.1:c.680G>C	p.Arg227Pro	p.R227P	ENST00000460680	NM_004656.3	227	cGc/cCc	9/17	0.825550395745164	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.825550395745164	1		227	313	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105745	27105745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003238-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	217	262	0	ENST00000324856.7:c.5356G>A	p.Glu1786Lys	p.E1786K	ENST00000324856	NM_006015.4	1786	Gag/Aag	20/20	1	2	FACETS	0.893	0.836	0.95	0.893	0.836	0.95	CLONAL	1	TRUE	1	0.825550395745164	2		262	589	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651338	52651338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1192414131	NA	P-0003238-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	263	408	0	ENST00000394830.3:c.1758G>A	p.Met586Ile	p.M586I	ENST00000394830	NM_018313.4	586	atG/atA	15/30	0.825550395745164	1	FACETS	0.977	0.936	1	0.977	0.936	1	CLONAL	1	TRUE	0	0.825550395745164	1		408	383	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549884	187549884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756351356	NA	P-0003238-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	194	240	0	ENST00000441802.2:c.4357C>T	p.Arg1453Cys	p.R1453C	ENST00000441802	NM_005245.3	1453	Cgt/Tgt	8/27	1	2	FACETS	0.925	0.864	0.988	0.925	0.864	0.988	CLONAL	1	TRUE	1	0.825550395745164	2		240	508	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26971348	26971348	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs755340500	NA	P-0003238-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	154	297	0	ENST00000381527.3:c.919A>G	p.Lys307Glu	p.K307E	ENST00000381527	NM_001260.1	307	Aaa/Gaa	9/13	0.167123896244098	1	FACETS	0.52	0.481	0.561	0.52	0.481	0.561	INDETERMINATE	1	TRUE	0	0.825550395745164	1		297	421	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465606	99465606	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003238-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	238	203	0	ENST00000268035.6:c.2431G>A	p.Glu811Lys	p.E811K	ENST00000268035	NM_000875.3	811	Gag/Aag	11/21	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.825550395745164	2		203	563	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348815	89348815	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003238-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	485	648	0	ENST00000301030.4:c.4135G>C	p.Asp1379His	p.D1379H	ENST00000301030	NM_001256183.1	1379	Gat/Cat	9/13	0.139293775816689	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.825550395745164	0		648	1207	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348926	89348926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003238-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	425	534	0	ENST00000301030.4:c.4024G>A	p.Glu1342Lys	p.E1342K	ENST00000301030	NM_001256183.1	1342	Gag/Aag	9/13	0.139293775816689	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.825550395745164	0		534	1051	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534347	63534347	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003238-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	361	335	0	ENST00000307078.5:c.1174G>C	p.Glu392Gln	p.E392Q	ENST00000307078	NM_004655.3	392	Gag/Cag	5/11	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.825550395745164	2		335	855	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143985	11143985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003238-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	274	262	0	ENST00000358026.2:c.3566G>A	p.Arg1189Gln	p.R1189Q	ENST00000358026	NM_001128849.1	1189	cGa/cAa	26/36	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.825550395745164	2		262	650	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484414	57484414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003238-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	303	310	0	ENST00000371085.3:c.595C>T	p.Arg199Cys	p.R199C	ENST00000371085	NM_000516.4	199	Cgc/Tgc	8/13	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.825550395745164	2		310	722	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485737	57485737	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003238-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	275	274	0	ENST00000371085.3:c.1039-1G>A		p.X347_splice	ENST00000371085	NM_000516.4	347			1	2	FACETS	0.986	0.931	1	0.986	0.931	1	CLONAL	1	TRUE	1	0.825550395745164	2		274	676	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196830	123196830	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003238-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	290	235	0	ENST00000218089.9:c.1717C>T	p.Gln573Ter	p.Q573*	ENST00000218089	NM_001042749.1	573	Cag/Tag	18/35	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.825550395745164	1		235	340	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	73	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.925	1	1	0.984	1	CLONAL	2	TRUE	1	0.258719335036025	2		422	266	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0003257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	236	424	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	1	2	FACETS	1	0.974	1	1	0.995	1	CLONAL	2	TRUE	1	0.258719335036025	2		424	845	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0003257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	311	383	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	0.258719335036025	3	FACETS	0.966	0.913	1	1	0.994	1	CLONAL	3	TRUE	1	0.258719335036025	3		383	937	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098945	178098945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	222	396	0	ENST00000397062.3:c.100C>G	p.Arg34Gly	p.R34G	ENST00000397062	NM_006164.4	34	Cga/Gga	2/5	1	2	FACETS	1	0.957	1	1	0.994	1	CLONAL	2	TRUE	1	0.258719335036025	2		396	829	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097304	178097304	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763097686	NA	P-0003257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	148	279	0	ENST00000397062.3:c.410C>T	p.Ser137Leu	p.S137L	ENST00000397062	NM_006164.4	137	tCg/tTg	4/5	1	2	FACETS	0.921	0.844	1	1	0.991	1	CLONAL	2	TRUE	1	0.258719335036025	2		279	621	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795082	42795082	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	321	478	0	ENST00000575354.2:c.2162C>G	p.Ser721Cys	p.S721C	ENST00000575354	NM_015125.3	721	tCc/tGc	10/20	1	2	FACETS	1	0.987	1	1	0.996	1	CLONAL	2	TRUE	1	0.258719335036025	2		478	1086	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256093	16256093	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	200	395	0	ENST00000375759.3:c.3358G>C	p.Asp1120His	p.D1120H	ENST00000375759	NM_015001.2	1120	Gat/Cat	11/15	1	2	FACETS	1	0.981	1	1	0.994	1	CLONAL	2	TRUE	1	0.258719335036025	2		395	671	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256416	16256416	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1234631776	NA	P-0003257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	261	415	0	ENST00000375759.3:c.3681G>C	p.Lys1227Asn	p.K1227N	ENST00000375759	NM_015001.2	1227	aaG/aaC	11/15	1	2	FACETS	1	0.966	1	1	0.995	1	CLONAL	2	TRUE	1	0.258719335036025	2		415	967	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25459815	25459815	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	294	417	0	ENST00000264709.3:c.2468G>A	p.Arg823Lys	p.R823K	ENST00000264709	NM_175629.2	823	aGg/aAg	21/23	1	2	FACETS	1	0.983	1	1	0.996	1	CLONAL	2	TRUE	1	0.258719335036025	2		417	1022	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146625	185146625	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	198	330	0	ENST00000265026.3:c.256C>T	p.Gln86Ter	p.Q86*	ENST00000265026	NM_004721.4	86	Cag/Tag	2/14	0.258719335036025	3	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	1	0.258719335036025	3		330	857	SUCCESS
APC	324	MSKCC	GRCh37	5	112176306	112176306	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	189	347	1	ENST00000257430.4:c.5015G>T	p.Gly1672Val	p.G1672V	ENST00000257430	NM_000038.5	1672	gGa/gTa	16/16	1	2	FACETS	0.899	0.832	0.968	1	0.992	1	CLONAL	2	TRUE	1	0.258719335036025	2		348	813	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520724	176520724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	261	373	0	ENST00000292408.4:c.1467G>A	p.Met489Ile	p.M489I	ENST00000292408	NM_213647.1	489	atG/atA	11/18	1	2	FACETS	1	0.978	1	1	0.995	1	CLONAL	2	TRUE	1	0.258719335036025	2		373	925	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437700	49437700	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	362	662	0	ENST00000301067.7:c.5270G>C	p.Arg1757Pro	p.R1757P	ENST00000301067	NM_003482.3	1757	cGa/cCa	22/54	1	2	FACETS	1	0.968	1	1	0.996	1	CLONAL	2	TRUE	1	0.258719335036025	2		662	1357	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437731	49437731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	294	562	0	ENST00000301067.7:c.5239G>A	p.Glu1747Lys	p.E1747K	ENST00000301067	NM_003482.3	1747	Gaa/Aaa	22/54	1	2	FACETS	0.997	0.938	1	1	0.995	1	CLONAL	2	TRUE	1	0.258719335036025	2		562	1140	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292688	91292688	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	182	364	0	ENST00000355112.3:c.190G>C	p.Asp64His	p.D64H	ENST00000355112	NM_000057.2	64	Gat/Cat	3/22	1	2	FACETS	0.942	0.871	1	1	0.992	1	CLONAL	2	TRUE	1	0.258719335036025	2		364	747	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292785	91292785	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	169	409	0	ENST00000355112.3:c.287G>T	p.Gly96Val	p.G96V	ENST00000355112	NM_000057.2	96	gGa/gTa	3/22	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.258719335036025	2		409	893	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292800	91292800	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs781707344	NA	P-0003257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	156	399	0	ENST00000355112.3:c.302G>C	p.Arg101Thr	p.R101T	ENST00000355112	NM_000057.2	101	aGa/aCa	3/22	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.258719335036025	2		399	876	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368266	45368266	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	214	455	0	ENST00000262160.6:c.1336C>G	p.Leu446Val	p.L446V	ENST00000262160	NM_005901.5	446	Cta/Gta	11/11	0.236402444540764	0	FACETS	0.91	0.849	0.971			1	CLONAL	2	TRUE	0	0.258719335036025	0		455	674	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795260	42795260	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	199	328	0	ENST00000575354.2:c.2340C>G	p.Phe780Leu	p.F780L	ENST00000575354	NM_015125.3	780	ttC/ttG	10/20	1	2	FACETS	0.952	0.884	1	1	0.993	1	CLONAL	2	TRUE	1	0.258719335036025	2		328	808	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100915	41100915	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	258	343	0	ENST00000373198.4:c.1441G>A	p.Glu481Lys	p.E481K	ENST00000373198	NM_133170.3	481	Gag/Aag	8/32	0.208235504539255	3	FACETS	0.858	0.805	0.912	1	0.99	1	CLONAL	3	TRUE	1	0.258719335036025	3		343	875	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0003266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	177	314	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.982	0.914	1	0.982	0.914	1	CLONAL	1	TRUE	1	0.799300429485604	2		314	451	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791758	42791758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1380826096	NA	P-0003266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	14	579	0	ENST00000575354.2:c.644G>A	p.Arg215Gln	p.R215Q	ENST00000575354	NM_015125.3	215	cGg/cAg	5/20	0.799300429485604	1	FACETS	0.052	0.037	0.07	0.052	0.037	0.07	SUBCLONAL	1	TRUE	0	0.799300429485604	1		579	405	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0003266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	101	139	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.799300429485604	2		139	235	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0003266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	45	321	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	1	2	FACETS	0.287	0.241	0.337	0.287	0.241	0.337	SUBCLONAL	1	TRUE	1	0.799300429485604	2		321	393	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123159713	123159713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	206	537	0	ENST00000218089.9:c.68C>T	p.Ser23Phe	p.S23F	ENST00000218089	NM_001042749.1	23	tCt/tTt	4/35	0.208714172971091	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.799300429485604	0		537	599	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510627	38510627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	46	525	0	ENST00000254066.5:c.881G>A	p.Arg294Gln	p.R294Q	ENST00000254066	NM_000964.3	294	cGg/cAg	7/9	1	2	FACETS	0.137	0.115	0.162	0.137	0.115	0.162	SUBCLONAL	1	TRUE	1	0.799300429485604	2		525	839	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794676	42794676	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0003266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	35	351	0	ENST00000575354.2:c.1756A>T	p.Lys586Ter	p.K586*	ENST00000575354	NM_015125.3	586	Aag/Tag	10/20	0.799300429485604	1	FACETS	0.139	0.113	0.167	0.139	0.113	0.167	SUBCLONAL	1	TRUE	0	0.799300429485604	1		351	379	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795716	42795716	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0003266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	48	477	0	ENST00000575354.2:c.2705C>G	p.Ser902Ter	p.S902*	ENST00000575354	NM_015125.3	902	tCa/tGa	11/20	0.799300429485604	1	FACETS	0.201	0.17	0.235	0.201	0.17	0.235	SUBCLONAL	1	TRUE	0	0.799300429485604	1		477	358	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797980	42797981	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0003266-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	23	485	0	ENST00000575354.2:c.4034_4035del	p.Val1345GlyfsTer16	p.V1345Gfs*16	ENST00000575354	NM_015125.3	1344	tcTGtg/tctg	16/20	0.799300429485604	1	FACETS	0.075	0.058	0.095	0.075	0.058	0.095	SUBCLONAL	1	TRUE	0	0.799300429485604	1		485	459	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0003331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	15	70	0				ENST00000310581	NM_198253.2	-/1132			0.213517698953739	3	FACETS	0.808	0.604	1	0.808	0.604	1	CLONAL	2	TRUE	1	0.286895750017282	3		70	74	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913384	NA	P-0003331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	33	163	0	ENST00000304494.5:c.262G>T	p.Glu88Ter	p.E88*	ENST00000304494	NM_000077.4	88	Gag/Tag	2/3	0.286895750017282	3	FACETS	0.756	0.623	0.902	0.504	0.415	0.602	CLONAL	2	TRUE	0	0.286895750017282	3		163	174	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137412	202137412	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	46	226	1	ENST00000358485.4:c.640G>T	p.Gly214Ter	p.G214*	ENST00000358485	NM_001080125.1	214	Gga/Tga	4/9	1	2	FACETS	0.788	0.665	0.923	0.788	0.665	0.923	CLONAL	1	TRUE	1	0.286895750017282	2		227	407	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403510	138403510	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	43	372	0	ENST00000289153.2:c.2272C>A	p.Leu758Met	p.L758M	ENST00000289153	NM_006219.2	758	Ctg/Atg	15/22	1	2	FACETS	0.617	0.516	0.728	0.617	0.516	0.728	SUBCLONAL	1	TRUE	1	0.286895750017282	2		372	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577093	7577093	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs730882008	NA	P-0003331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	119	418	0	ENST00000269305.4:c.845G>C	p.Arg282Pro	p.R282P	ENST00000269305	NM_001126112.2	282	cGg/cCg	8/11	0.279751017986495	3	FACETS	0.998	0.907	1			1	CLONAL	2	TRUE	NA	0.286895750017282	3		418	475	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687163	37687163	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761089485	NA	P-0003331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	46	272	0	ENST00000447079.4:c.4067G>A	p.Arg1356Gln	p.R1356Q	ENST00000447079	NM_015083.1	1356	cGa/cAa	14/14	1	2	FACETS	0.857	0.724	1	0.857	0.724	1	CLONAL	1	TRUE	1	0.286895750017282	2		272	374	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918736	50918736	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1422842883	NA	P-0003331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	26	293	0	ENST00000440232.2:c.2606C>T	p.Ser869Leu	p.S869L	ENST00000440232	NM_002691.3	869	tCg/tTg	21/27	0.133231644821027	0	FACETS	0.499	0.396	0.616			1	INDETERMINATE	1	TRUE	0	0.286895750017282	0		293	259	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022440	31022440	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1569328496	NA	P-0003331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	29	111	0	ENST00000375687.4:c.1925G>A	p.Gly642Glu	p.G642E	ENST00000375687	NM_015338.5	642	gGa/gAa	13/13	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.286895750017282	2		111	155	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023357	31023357	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	47	206	0	ENST00000375687.4:c.2842G>T	p.Glu948Ter	p.E948*	ENST00000375687	NM_015338.5	948	Gag/Tag	13/13	1	2	FACETS	0.91	0.771	1	0.91	0.771	1	CLONAL	1	TRUE	1	0.286895750017282	2		206	360	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	37	422	0				ENST00000310581	NM_198253.2	-/1132			0.197729221485476	4	FACETS	0.784	0.663	0.911	0.784	0.663	0.911	INDETERMINATE	2	TRUE	2	0.728742911488998	4		422	112	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0003339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	97	314	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.728742911488998	2		314	244	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798132	42798132	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003339-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	14	435	1	ENST00000575354.2:c.4086G>T	p.Leu1362Phe	p.L1362F	ENST00000575354	NM_015125.3	1362	ttG/ttT	17/20	0.728742911488998	1	FACETS	0.145	0.105	0.194	0.145	0.105	0.194	SUBCLONAL	1	TRUE	0	0.728742911488998	1		436	168	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	29	422	0				ENST00000310581	NM_198253.2	-/1132			0.322280204697202	4	FACETS	0.915	0.747	1	0.915	0.747	1	CLONAL	2	TRUE	2	0.322280204697202	4		422	130	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	50	142	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.322280204697202	3	FACETS	1	0.863	1	1	0.863	1	CLONAL	2	TRUE	1	0.322280204697202	3		142	180	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49033844	49033844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853294	NA	P-0003354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	86	455	1	ENST00000267163.4:c.1981C>T	p.Arg661Trp	p.R661W	ENST00000267163	NM_000321.2	661	Cgg/Tgg	20/27	0.249872835439091	1	FACETS	0.914	0.811	1	0.914	0.811	1	CLONAL	1	TRUE	0	0.322280204697202	1		456	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0003354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	242	421	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	TRUE	NA	0.322280204697202	2		421	608	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	92	662	0	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.322280204697202	NA		662	602	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670652	134670652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	95	529	0	ENST00000398015.3:c.563C>T	p.Ser188Phe	p.S188F	ENST00000398015	NM_004441.4	188	tCt/tTt	3/16	0.322280204697202	3	FACETS	1	0.959	1	0.577	0.515	0.643	CLONAL	1	TRUE	1	0.322280204697202	3		529	593	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964866	55964866	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs777472312	NA	P-0003354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	60	336	1	ENST00000263923.4:c.2371C>T	p.Arg791Trp	p.R791W	ENST00000263923	NM_002253.2	791	Cgg/Tgg	16/30	0.305483966151272	2	FACETS	0.777	0.671	0.893	0.389	0.335	0.447	SUBCLONAL	1	TRUE	0	0.322280204697202	2		337	479	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77043802	77043802	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	84	555	0	ENST00000356341.3:c.1524G>C	p.Lys508Asn	p.K508N	ENST00000356341	NM_002576.4	508	aaG/aaC	14/15	0.322280204697202	3	FACETS	0.901	0.796	1	0.45	0.398	0.507	CLONAL	1	TRUE	1	0.322280204697202	3		555	672	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133959	41133959	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	96	701	0	ENST00000379561.5:c.1669C>T	p.Gln557Ter	p.Q557*	ENST00000379561	NM_002015.3	557	Caa/Taa	2/3	0.249872835439091	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.322280204697202	1		701	481	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828782	72828782	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0003354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	99	774	0	ENST00000268489.5:c.7799C>G	p.Ser2600Ter	p.S2600*	ENST00000268489	NM_006885.3	2600	tCa/tGa	9/10	0.322280204697202	1	FACETS	0.798	0.713	0.888	0.798	0.713	0.888	SUBCLONAL	1	TRUE	0	0.322280204697202	1		774	646	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119789	70119789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778047936	NA	P-0003354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	76	433	0	ENST00000245479.2:c.791G>A	p.Arg264Lys	p.R264K	ENST00000245479	NM_000346.3	264	aGa/aAa	3/3	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.322280204697202	2		433	459	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795601	42795601	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	78	441	0	ENST00000575354.2:c.2681C>G	p.Ser894Cys	p.S894C	ENST00000575354	NM_015125.3	894	tCc/tGc	10/20	0.109864059299045	5	FACETS	1	0.96	1	0.305	0.268	0.345	INDETERMINATE	1	TRUE	1	0.322280204697202	5		441	588	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796616	42796616	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0003354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	60	233	0	ENST00000575354.2:c.3173C>G	p.Ser1058Ter	p.S1058*	ENST00000575354	NM_015125.3	1058	tCa/tGa	13/20	0.109864059299045	5	FACETS	1	0.963	1	0.339	0.293	0.389	INDETERMINATE	1	TRUE	1	0.322280204697202	5		233	407	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226052	53226052	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	79	290	0	ENST00000375401.3:c.2797G>A	p.Glu933Lys	p.E933K	ENST00000375401	NM_004187.3	933	Gag/Aag	19/26	0.322280204697202	0	FACETS	0.629	0.561	0.701			1	SUBCLONAL	2	TRUE	NA	0.322280204697202	0		290	264	SUCCESS
AR	367	MSKCC	GRCh37	X	66765924	66765924	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003354-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	80	269	0	ENST00000374690.3:c.936C>G	p.Phe312Leu	p.F312L	ENST00000374690	NM_000044.3	312	ttC/ttG	1/8	1	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.322280204697202	1		269	322	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0003358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	167	217	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.903	0.835	0.973	0.903	0.835	0.973	CLONAL	1	TRUE	1	0.684971743804667	2		217	540	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0003358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	102	139	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.684971743804667	2		139	256	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0003358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	441	270	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.672376754367152	2	FACETS	0.889	0.857	0.921	0.889	0.857	0.921	CLONAL	2	TRUE	0	0.684971743804667	2		270	724	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432459	49432459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	354	250	0	ENST00000301067.7:c.8680C>T	p.Pro2894Ser	p.P2894S	ENST00000301067	NM_003482.3	2894	Ccg/Tcg	34/54	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.684971743804667	2		250	1021	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36931998	36931998	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	935	445	0	ENST00000361632.4:c.2471G>A	p.Gly824Glu	p.G824E	ENST00000361632		824	gGg/gAg	16/16	0.672376754367152	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.684971743804667	2		445	1289	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12653457	12653457	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	334	255	0	ENST00000251849.4:c.312A>C	p.Glu104Asp	p.E104D	ENST00000251849	NM_002880.3	104	gaA/gaC	3/17	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.684971743804667	2		255	905	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587175	189587175	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	117	230	0	ENST00000264731.3:c.1192G>A	p.Asp398Asn	p.D398N	ENST00000264731	NM_003722.4	398	Gat/Aat	9/14	1	2	FACETS	0.63	0.57	0.693	0.63	0.57	0.693	SUBCLONAL	1	TRUE	1	0.684971743804667	2		230	542	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971123	21971123	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	38	94	0	ENST00000304494.5:c.235A>G	p.Thr79Ala	p.T79A	ENST00000304494	NM_000077.4	79	Acc/Gcc	2/3	0.682164954513472	1	FACETS	0.396	0.331	0.467	0.396	0.331	0.467	SUBCLONAL	1	TRUE	0	0.684971743804667	1		94	184	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347168	347168	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	385	390	0	ENST00000262320.3:c.1843G>C	p.Ala615Pro	p.A615P	ENST00000262320	NM_003502.3	615	Gcc/Ccc	7/11	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.684971743804667	2		390	1044	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100461	2100461	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	294	276	0	ENST00000219476.3:c.199G>T	p.Val67Phe	p.V67F	ENST00000219476	NM_000548.3	67	Gtc/Ttc	3/42	1	2	FACETS	0.953	0.899	1	0.953	0.899	1	CLONAL	1	TRUE	1	0.684971743804667	2		276	901	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577610	7577610	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0003358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	196	137	0	ENST00000269305.4:c.673-2A>T		p.X225_splice	ENST00000269305	NM_001126112.2	225			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.684971743804667	2		137	522	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211101	2211101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	301	307	0	ENST00000398665.3:c.1355C>T	p.Ala452Val	p.A452V	ENST00000398665	NM_032482.2	452	gCc/gTc	15/28	1	2	FACETS	0.956	0.903	1	0.956	0.903	1	CLONAL	1	TRUE	1	0.684971743804667	2		307	919	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289974	15289974	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265439284	NA	P-0003358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	338	348	0	ENST00000263388.2:c.3580C>T	p.Pro1194Ser	p.P1194S	ENST00000263388	NM_000435.2	1194	Ccc/Tcc	22/33	1	2	FACETS	0.956	0.906	1	0.956	0.906	1	CLONAL	1	TRUE	1	0.684971743804667	2		348	1032	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796310	42796310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	393	371	0	ENST00000575354.2:c.2959C>T	p.Pro987Ser	p.P987S	ENST00000575354	NM_015125.3	987	Cct/Tct	12/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.684971743804667	2		371	1145	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730823	40730823	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	247	244	0	ENST00000373198.4:c.3712C>T	p.Pro1238Ser	p.P1238S	ENST00000373198	NM_133170.3	1238	Ccc/Tcc	27/32	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.684971743804667	2		244	666	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833931	44833931	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	276	340	0	ENST00000377967.4:c.355T>C	p.Tyr119His	p.Y119H	ENST00000377967	NM_021140.2	119	Tac/Cac	4/29	0.251750639278996	1	FACETS	0.578	0.543	0.613	0.578	0.543	0.613	INDETERMINATE	1	TRUE	0	0.684971743804667	1		340	917	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971106	21971116	+	frameshift_variant	Frame_Shift_Del	DEL	GTCGTGCACGG	GTCGTGCACGG	-	novel	NA	P-0003358-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	36	97	0	ENST00000304494.5:c.242_252del	p.Pro81ArgfsTer35	p.P81Rfs*35	ENST00000304494	NM_000077.4	81	cCCGTGCACGAC/c	2/3	0.682164954513472	1	FACETS	0.368	0.305	0.436	0.368	0.305	0.436	SUBCLONAL	1	TRUE	0	0.684971743804667	1		97	188	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	79	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.824682169370344	2		422	191	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068384	26068384	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	229	366	2	ENST00000435504.4:c.106C>T	p.Gln36Ter	p.Q36*	ENST00000435504		36	Caa/Taa	2/13	1	2	FACETS	0.938	0.881	0.996	0.938	0.881	0.996	CLONAL	1	TRUE	1	0.824682169370344	2		368	592	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508499	106508499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752602335	NA	P-0003362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	53	93	0	ENST00000359195.3:c.493G>A	p.Val165Ile	p.V165I	ENST00000359195	NM_002649.2	165	Gtc/Atc	2/11	1	2	FACETS	0.752	0.653	0.855	0.752	0.653	0.855	SUBCLONAL	1	TRUE	1	0.824682169370344	2		93	171	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0003362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	301	370	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.824682169370344	2		370	629	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226566970	226566970	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	266	346	0	ENST00000366794.5:c.1618G>C	p.Glu540Gln	p.E540Q	ENST00000366794	NM_001618.3	540	Gaa/Caa	12/23	1	2	FACETS	0.93	0.877	0.983	0.93	0.877	0.983	CLONAL	1	TRUE	1	0.824682169370344	2		346	694	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976506	25976506	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	249	328	0	ENST00000435504.4:c.1039G>T	p.Glu347Ter	p.E347*	ENST00000435504		347	Gag/Tag	11/13	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.824682169370344	2		328	579	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098930	178098930	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0003362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	207	358	0	ENST00000397062.3:c.115T>G	p.Phe39Val	p.F39V	ENST00000397062	NM_006164.4	39	Ttc/Gtc	2/5	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.824682169370344	2		358	480	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447772	187447772	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	177	185	0	ENST00000232014.4:c.421G>A	p.Glu141Lys	p.E141K	ENST00000232014	NM_001130845.1	141	Gaa/Aaa	5/10	1	2	FACETS	0.902	0.839	0.966	0.902	0.839	0.966	CLONAL	1	TRUE	1	0.824682169370344	2		185	476	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153250867	153250867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	192	393	0	ENST00000281708.4:c.1193C>T	p.Ser398Phe	p.S398F	ENST00000281708	NM_033632.3	398	tCt/tTt	8/12	1	2	FACETS	0.968	0.904	1	0.968	0.904	1	CLONAL	1	TRUE	1	0.824682169370344	2		393	481	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032138	26032138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	327	458	0	ENST00000244661.2:c.151G>A	p.Glu51Lys	p.E51K	ENST00000244661	NM_003537.3	51	Gag/Aag	1/1	1	2	FACETS	0.865	0.82	0.911	0.865	0.82	0.911	CLONAL	1	TRUE	1	0.824682169370344	2		458	917	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793802	89793802	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	149	260	0	ENST00000336032.3:c.871A>G	p.Ser291Gly	p.S291G	ENST00000336032	NM_006813.2	291	Agt/Ggt	2/2	1	2	FACETS	0.974	0.901	1	0.974	0.901	1	CLONAL	1	TRUE	1	0.824682169370344	2		260	371	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971292	13971292	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772105404	NA	P-0003362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	227	306	0	ENST00000405192.2:c.637C>T	p.Arg213Cys	p.R213C	ENST00000405192	NM_001163147.1	213	Cgc/Tgc	8/12	1	2	FACETS	0.951	0.893	1	0.951	0.893	1	CLONAL	1	TRUE	1	0.824682169370344	2		306	579	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859516	151859516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	227	339	0	ENST00000262189.6:c.11146G>A	p.Glu3716Lys	p.E3716K	ENST00000262189	NM_170606.2	3716	Gaa/Aaa	43/59	1	2	FACETS	0.922	0.865	0.98	0.922	0.865	0.98	CLONAL	1	TRUE	1	0.824682169370344	2		339	597	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751118	128751118	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	260	406	0	ENST00000377970.2:c.655T>G	p.Ser219Ala	p.S219A	ENST00000377970	NM_002467.4	219	Tcg/Gcg	2/3	1	2	FACETS	0.936	0.882	0.99	0.936	0.882	0.99	CLONAL	1	TRUE	1	0.824682169370344	2		406	674	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606461	93606461	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	205	343	1	ENST00000375746.1:c.281A>G	p.Gln94Arg	p.Q94R	ENST00000375746	NM_001174167.1	94	cAg/cGg	2/14	0.112084108946962	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.824682169370344	0		344	601	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431936	49431936	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	263	392	0	ENST00000301067.7:c.9203A>G	p.Glu3068Gly	p.E3068G	ENST00000301067	NM_003482.3	3068	gAg/gGg	34/54	1	2	FACETS	0.971	0.916	1	0.971	0.916	1	CLONAL	1	TRUE	1	0.824682169370344	2		392	657	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885541	111885541	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	489	638	1	ENST00000341259.2:c.1318C>A	p.His440Asn	p.H440N	ENST00000341259	NM_005475.2	440	Cac/Aac	7/8	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.824682169370344	2		639	1154	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114208	115114208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	340	452	0	ENST00000257566.3:c.1009G>A	p.Asp337Asn	p.D337N	ENST00000257566	NM_016569.3	337	Gat/Aat	6/8	1	2	FACETS	0.916	0.87	0.963	0.916	0.87	0.963	CLONAL	1	TRUE	1	0.824682169370344	2		452	900	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075130	16075130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	152	212	0	ENST00000268712.3:c.422C>T	p.Ala141Val	p.A141V	ENST00000268712	NM_006311.3	141	gCa/gTa	4/46	0.610773303724442	1	FACETS	0.802	0.751	0.853	0.802	0.751	0.853	CLONAL	1	TRUE	0	0.824682169370344	1		212	270	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860619	45860619	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	336	439	0	ENST00000391945.4:c.1388C>A	p.Pro463Gln	p.P463Q	ENST00000391945	NM_000400.3	463	cCg/cAg	15/23	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.824682169370344	2		439	755	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252865	36252865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060499616	NA	P-0003362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	209	259	0	ENST00000300305.3:c.497G>A	p.Arg166Gln	p.R166Q	ENST00000300305		166	cGa/cAa	4/8	1	2	FACETS	0.928	0.869	0.989	0.928	0.869	0.989	CLONAL	1	TRUE	1	0.824682169370344	2		259	546	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175874	24175874	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	196	305	0	ENST00000263121.7:c.1102C>T	p.Gln368Ter	p.Q368*	ENST00000263121	NM_003073.3	368	Cag/Tag	8/9	1	2	FACETS	0.909	0.848	0.97	0.909	0.848	0.97	CLONAL	1	TRUE	1	0.824682169370344	2		305	523	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891528	76891528	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	327	232	0	ENST00000373344.5:c.4577C>T	p.Ala1526Val	p.A1526V	ENST00000373344	NM_000489.3	1526	gCt/gTt	16/35	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.824682169370344	1		232	399	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569798	67569847	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GAGCTCCAGCAACCTGGCAGAATTACGACAGCTTCTTGATTGTGGTGAGT	GAGCTCCAGCAACCTGGCAGAATTACGACAGCTTCTTGATTGTGGTGAGT	-	novel	NA	P-0003362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	81	216	0	ENST00000274335.5:c.460_502+7del		p.X154_splice	ENST00000274335		154		3/15	1	2	FACETS	0.702	0.625	0.781	0.702	0.625	0.781	SUBCLONAL	1	TRUE	1	0.824682169370344	2		216	280	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831243	3831246	+	frameshift_variant	Frame_Shift_Del	DEL	AATC	AATC	-	novel	NA	P-0003362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	159	301	0	ENST00000262367.5:c.1635_1638del	p.Leu545PhefsTer16	p.L545Ffs*16	ENST00000262367	NM_004380.2	545	ttGATT/tt	7/31	1	2	FACETS	0.847	0.784	0.913	0.847	0.784	0.913	CLONAL	1	TRUE	1	0.824682169370344	2		301	455	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115972	8115973	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0003362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	46	176	0	ENST00000346208.3:c.1320dup	p.Ala441ArgfsTer66	p.A441Rfs*66	ENST00000346208		440	acc/aCcc	6/6	1	2	FACETS	0.355	0.3	0.415	0.355	0.3	0.415	SUBCLONAL	1	TRUE	1	0.824682169370344	2		176	314	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499412	89499413	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0003362-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	215	357	0	ENST00000336596.2:c.2582_2583delinsCT	p.Trp861Ser	p.W861S	ENST00000336596	NM_005233.5	861	tGG/tCT	15/17	1	2	FACETS	0.858	0.802	0.914	0.858	0.802	0.914	CLONAL	1	TRUE	1	0.824682169370344	2		357	608	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	19	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.17	2		422	176	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0003370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	19	142	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.863	0.656	1	0.863	0.656	1	CLONAL	1	TRUE	1	0.17	2		142	259	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0003370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	10	168	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.35	0.236	0.495	0.35	0.236	0.495	SUBCLONAL	1	TRUE	1	0.17	2		168	336	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982463	25982463	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	42	279	0	ENST00000435504.4:c.827C>G	p.Ser276Cys	p.S276C	ENST00000435504		276	tCc/tGc	9/13	1	2	FACETS	0.748	0.623	0.887	0.748	0.623	0.887	SUBCLONAL	1	TRUE	1	0.17	2		279	661	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462608	40462608	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745972463	NA	P-0003370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	45	399	0	ENST00000345506.4:c.2306G>A	p.Arg769His	p.R769H	ENST00000345506	NM_003152.3	769	cGc/cAc	20/20	1	2	FACETS	0.598	0.501	0.707	0.598	0.501	0.707	SUBCLONAL	1	TRUE	1	0.17	2		399	885	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41197781	41197781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80356942	NA	P-0003370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	74	380	0	ENST00000357654.3:c.5506G>A	p.Glu1836Lys	p.E1836K	ENST00000357654	NM_007294.3	1836	Gag/Aag	23/23	1	2	FACETS	0.977	0.854	1	0.977	0.854	1	CLONAL	1	TRUE	1	0.17	2		380	891	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56376666	56376666	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	74	526	0	ENST00000348428.3:c.706C>T	p.Gln236Ter	p.Q236*	ENST00000348428	NM_006785.3	236	Caa/Taa	5/17	1	2	FACETS	0.835	0.729	0.951	0.835	0.729	0.951	CLONAL	1	TRUE	1	0.17	2		526	1042	SUCCESS
ATM	472	MSKCC	GRCh37	11	108127026	108127029	+	frameshift_variant	Frame_Shift_Ins	INS	GAAG	GAAG	AAAAA	novel	NA	P-0003370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	53	273	0	ENST00000278616.4:c.2209_2212delinsAAAAA	p.Glu737LysfsTer6	p.E737Kfs*6	ENST00000278616	NM_000051.3	737	GAAGag/AAAAAag	14/63	1	2	FACETS	0.916	0.78	1	0.916	0.78	1	CLONAL	1	TRUE	1	0.17	2		273	681	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0003372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	259	310	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.254251803852995	3	FACETS	0.971	0.913	1	1	0.993	1	CLONAL	3	TRUE	1	0.254251803852995	3		310	788	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913385	NA	P-0003372-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	40	155	0	ENST00000304494.5:c.247C>G	p.His83Asp	p.H83D	ENST00000304494	NM_000077.4	83	Cac/Gac	2/3	0.254251803852995	1	FACETS	0.785	0.661	0.918	1	0.961	1	CLONAL	2	TRUE	0	0.254251803852995	1		155	175	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	32	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.888	0.732	1	0.888	0.732	1	CLONAL	1	TRUE	1	0.483486375556167	2		422	149	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0003373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	114	413	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	1	2	FACETS	0.761	0.686	0.839	0.761	0.686	0.839	SUBCLONAL	1	TRUE	1	0.483486375556167	2		413	620	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455075	50455075	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	60	338	0	ENST00000331340.3:c.622C>T	p.Arg208Ter	p.R208*	ENST00000331340	NM_006060.4	208	Cga/Tga	6/8	1	2	FACETS	0.51	0.44	0.586	0.51	0.44	0.586	SUBCLONAL	1	TRUE	1	0.483486375556167	2		338	487	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729636	41729636	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	209	662	0	ENST00000242208.4:c.893G>A	p.Arg298Gln	p.R298Q	ENST00000242208	NM_002192.2	298	cGg/cAg	3/3	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.483486375556167	2		662	740	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647224	23647224	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	55	453	0	ENST00000261584.4:c.643G>C	p.Glu215Gln	p.E215Q	ENST00000261584	NM_024675.3	215	Gaa/Caa	4/13	0.202720649265633	2	FACETS	0.395	0.338	0.458	0.197	0.169	0.229	INDETERMINATE	1	TRUE	0	0.483486375556167	2		453	576	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246271	41246271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	112	476	0	ENST00000357654.3:c.1277C>T	p.Ser426Leu	p.S426L	ENST00000357654	NM_007294.3	426	tCa/tTa	10/23	0.293723841896007	1	FACETS	0.658	0.594	0.725	0.658	0.594	0.725	SUBCLONAL	1	TRUE	0	0.483486375556167	1		476	534	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565601	41565601	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	95	318	1	ENST00000263253.7:c.4267G>T	p.Glu1423Ter	p.E1423*	ENST00000263253	NM_001429.3	1423	Gaa/Taa	26/31	1	2	FACETS	0.826	0.738	0.918	0.826	0.738	0.918	CLONAL	1	TRUE	1	0.483486375556167	2		319	476	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651926	36651926	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	56	221	0	ENST00000244741.5:c.49del	p.Ala17ProfsTer14	p.A17Pfs*14	ENST00000244741	NM_000389.4	16	aaG/aa	2/3	0.48172626889	2	FACETS	0.855	0.739	0.979	0.427	0.369	0.49	CLONAL	1	TRUE	0	0.483486375556167	2		221	271	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	29	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.410236161609185	2		422	109	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0003377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	186	400	0	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.243202320008248	3	FACETS	1	0.981	1	0.593	0.547	0.64	INDETERMINATE	1	TRUE	1	0.410236161609185	3		400	922	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681655	30681655	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	172	286	0	ENST00000376406.3:c.442G>A	p.Glu148Lys	p.E148K	ENST00000376406	NM_014641.2	148	Gaa/Aaa	3/15	0.247551298798011	4	FACETS	1	0.981	1	0.606	0.557	0.657	CLONAL	1	TRUE	2	0.410236161609185	4		286	976	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175855	176175855	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	12	31	0	ENST00000367669.3:c.260C>G	p.Ser87Cys	p.S87C	ENST00000367669	NM_022457.5	87	tCc/tGc	1/20	0.279895088371691	3	FACETS	0.678	0.481	0.915	0.339	0.24	0.458	SUBCLONAL	1	TRUE	1	0.410236161609185	3		31	104	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681483	30681483	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	158	386	0	ENST00000376406.3:c.529G>T	p.Glu177Ter	p.E177*	ENST00000376406	NM_014641.2	177	Gaa/Taa	4/15	0.247551298798011	4	FACETS	1	0.938	1	0.515	0.471	0.561	CLONAL	1	TRUE	2	0.410236161609185	4		386	1055	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001284	150001284	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	68	366	0	ENST00000253339.5:c.2320G>C	p.Asp774His	p.D774H	ENST00000253339		774	Gat/Cat	4/7	0.316647193547395	1	FACETS	0.476	0.414	0.542	0.476	0.414	0.542	SUBCLONAL	1	TRUE	0	0.410236161609185	1		366	554	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341213	8341213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	113	278	0	ENST00000356435.5:c.5003G>A	p.Cys1668Tyr	p.C1668Y	ENST00000356435		1668	tGt/tAt	30/35	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.410236161609185	2		278	454	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343285	118343285	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	57	224	0	ENST00000534358.1:c.1411C>G	p.Gln471Glu	p.Q471E	ENST00000534358	NM_005933.3	471	Caa/Gaa	3/36	1	2	FACETS	0.49	0.42	0.566	0.49	0.42	0.566	SUBCLONAL	1	TRUE	1	0.410236161609185	2		224	567	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343655	118343655	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	59	210	0	ENST00000534358.1:c.1781C>T	p.Ser594Leu	p.S594L	ENST00000534358	NM_005933.3	594	tCa/tTa	3/36	1	2	FACETS	0.571	0.491	0.657	0.571	0.491	0.657	SUBCLONAL	1	TRUE	1	0.410236161609185	2		210	504	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443932	18443932	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	67	229	0	ENST00000266497.5:c.905A>G	p.His302Arg	p.H302R	ENST00000266497		302	cAt/cGt	3/31	1	2	FACETS	0.835	0.729	0.949	0.835	0.729	0.949	CLONAL	1	TRUE	1	0.410236161609185	2		229	391	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3794927	3794927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	80	351	0	ENST00000262367.5:c.3950G>A	p.Arg1317Lys	p.R1317K	ENST00000262367	NM_004380.2	1317	aGa/aAa	23/31	0.365561993225008	1	FACETS	0.502	0.442	0.566	0.502	0.442	0.566	SUBCLONAL	1	TRUE	0	0.410236161609185	1		351	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs786201059	NA	P-0003377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	132	388	0	ENST00000269305.4:c.856G>C	p.Glu286Gln	p.E286Q	ENST00000269305	NM_001126112.2	286	Gaa/Caa	8/11	0.243202320008248	3	FACETS	0.927	0.841	1	0.463	0.42	0.508	INDETERMINATE	1	TRUE	1	0.410236161609185	3		388	837	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554556	29554556	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	48	247	0	ENST00000356175.3:c.2341C>A	p.His781Asn	p.H781N	ENST00000356175	NM_000267.3	781	Cat/Aat	20/57	0.243202320008248	3	FACETS	0.514	0.434	0.602	0.257	0.217	0.301	INDETERMINATE	1	TRUE	1	0.410236161609185	3		247	549	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578257	7578257	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1131691035	NA	P-0003377-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	91	386	0	ENST00000269305.4:c.592del	p.Glu198LysfsTer49	p.E198Kfs*49	ENST00000269305	NM_001126112.2	198	Gaa/aa	6/11	0.243202320008248	3	FACETS	0.608	0.539	0.682	0.304	0.269	0.341	INDETERMINATE	1	TRUE	1	0.410236161609185	3		386	879	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	10	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.7	1			1	INDETERMINATE	2	TRUE	NA	0.18	2		422	55	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0003404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	19	558	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.445	0.337	0.574	0.445	0.337	0.574	SUBCLONAL	1	TRUE	1	0.18	2		558	474	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431635	6431635	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1459952760	NA	P-0003404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	22	246	0	ENST00000356142.4:c.188A>T	p.Asp63Val	p.D63V	ENST00000356142	NM_018890.3	63	gAt/gTt	3/7	1	2	FACETS	0.704	0.546	0.889	0.704	0.546	0.889	SUBCLONAL	1	TRUE	1	0.18	2		246	347	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480320	56480320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	29	360	0	ENST00000267101.3:c.427C>A	p.Leu143Met	p.L143M	ENST00000267101	NM_001982.3	143	Ctg/Atg	4/28	1	2	FACETS	0.742	0.595	0.91	0.742	0.595	0.91	CLONAL	1	TRUE	1	0.18	2		360	434	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288973	11288973	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	22	267	0	ENST00000361445.4:c.2782G>A	p.Asp928Asn	p.D928N	ENST00000361445	NM_004958.3	928	Gac/Aac	19/58	1	2	FACETS	0.757	0.587	0.954	0.757	0.587	0.954	CLONAL	1	TRUE	1	0.18	2		267	323	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257698	16257698	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	32	448	0	ENST00000375759.3:c.4963G>C	p.Glu1655Gln	p.E1655Q	ENST00000375759	NM_015001.2	1655	Gag/Cag	11/15	1	2	FACETS	0.801	0.65	0.972	0.801	0.65	0.972	CLONAL	1	TRUE	1	0.18	2		448	444	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198264988	198264988	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	35	427	0	ENST00000335508.6:c.2889G>C	p.Lys963Asn	p.K963N	ENST00000335508	NM_012433.2	963	aaG/aaC	19/25	1	2	FACETS	0.596	0.487	0.718	0.596	0.487	0.718	SUBCLONAL	1	TRUE	1	0.18	2		427	653	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	40	416	0	ENST00000335508.6:c.2704G>C	p.Glu902Gln	p.E902Q	ENST00000335508	NM_012433.2	902	Gaa/Caa	18/25	1	2	FACETS	0.751	0.623	0.894	0.751	0.623	0.894	SUBCLONAL	1	TRUE	1	0.18	2		416	592	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125716	47125716	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	39	517	0	ENST00000409792.3:c.5554C>T	p.His1852Tyr	p.H1852Y	ENST00000409792	NM_014159.6	1852	Cat/Tat	12/21	NA	2	FACETS	0.754	0.624	0.899			1	INDETERMINATE	1	TRUE	NA	0.18	2		517	575	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518840	187518840	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	27	439	0	ENST00000441802.2:c.12364G>C	p.Glu4122Gln	p.E4122Q	ENST00000441802	NM_005245.3	4122	Gaa/Caa	24/27	1	2	FACETS	0.56	0.444	0.692	0.56	0.444	0.692	SUBCLONAL	1	TRUE	1	0.18	2		439	536	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436602	49436602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	34	470	0	ENST00000301067.7:c.5704G>A	p.Glu1902Lys	p.E1902K	ENST00000301067	NM_003482.3	1902	Gaa/Aaa	26/54	1	2	FACETS	0.735	0.6	0.888	0.735	0.6	0.888	SUBCLONAL	1	TRUE	1	0.18	2		470	514	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091123	29091123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659827	NA	P-0003404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	26	409	0	ENST00000328354.6:c.1367C>T	p.Ser456Leu	p.S456L	ENST00000328354	NM_007194.3	456	tCa/tTa	12/15	1	2	FACETS	0.683	0.54	0.847	0.683	0.54	0.847	SUBCLONAL	1	TRUE	1	0.18	2		409	423	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045494	47045494	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	37	257	0	ENST00000377604.3:c.2461C>T	p.Arg821Cys	p.R821C	ENST00000377604	NM_001204468.1	821	Cgc/Tgc	22/24	1	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.18	1		257	253	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101357	27101385	+	frameshift_variant	Frame_Shift_Del	DEL	TCCCATGGCACACGCCAGCCCCCATATGG	TCCCATGGCACACGCCAGCCCCCATATGG	-	novel	NA	P-0003404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	28	477	0	ENST00000324856.7:c.4643_4671del	p.His1548LeufsTer14	p.H1548Lfs*14	ENST00000324856	NM_006015.4	1547	TCCCATGGCACACGCCAGCCCCCATATGGt/t	18/20	1	2	FACETS	0.59	0.471	0.727	0.59	0.471	0.727	SUBCLONAL	1	TRUE	1	0.18	2		477	527	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003436-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	28	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.931	1			1	INDETERMINATE	1	TRUE	NA	0.737335816238459	2		422	61	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0003436-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	134	558	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.737335816238459	2		558	332	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258277	16258277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003436-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	102	590	0	ENST00000375759.3:c.5542G>A	p.Asp1848Asn	p.D1848N	ENST00000375759	NM_015001.2	1848	Gac/Aac	11/15	1	2	FACETS	0.974	0.884	1	0.974	0.884	1	CLONAL	1	TRUE	1	0.737335816238459	2		590	284	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652044	36652044	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753291170	NA	P-0003436-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	176	434	0	ENST00000244741.5:c.166G>A	p.Glu56Lys	p.E56K	ENST00000244741	NM_000389.4	56	Gag/Aag	2/3	0.553236353887934	3	FACETS	1	0.99	1	0.819	0.775	0.861	CLONAL	2	TRUE	0	0.737335816238459	3		434	266	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683508	29683508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003436-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	129	386	0	ENST00000356175.3:c.7583C>T	p.Ser2528Leu	p.S2528L	ENST00000356175	NM_000267.3	2528	tCa/tTa	51/57	1	2	FACETS	0.909	0.833	0.987	0.909	0.833	0.987	CLONAL	1	TRUE	1	0.737335816238459	2		386	385	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872823	37872823	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1285769371	NA	P-0003436-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	133	522	0	ENST00000269571.5:c.1702C>G	p.Gln568Glu	p.Q568E	ENST00000269571		568	Cag/Gag	14/27	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.737335816238459	2		522	313	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879604	37879604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196929947	NA	P-0003436-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	115	439	0	ENST00000269571.5:c.1979G>A	p.Gly660Asp	p.G660D	ENST00000269571		660	gGc/gAc	17/27	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.737335816238459	2		439	282	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121076	29121076	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555926951	NA	P-0003436-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	129	566	1	ENST00000328354.6:c.481G>C	p.Glu161Gln	p.E161Q	ENST00000328354	NM_007194.3	161	Gaa/Caa	4/15	1	2	FACETS	0.895	0.82	0.972	0.895	0.82	0.972	CLONAL	1	TRUE	1	0.737335816238459	2		567	391	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349924	70349924	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003436-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	119	331	0	ENST00000374080.3:c.3907G>C	p.Asp1303His	p.D1303H	ENST00000374080		1303	Gac/Cac	28/45	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.737335816238459	1		331	176	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	43	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.714	0.604	0.832	0.714	0.604	0.832	SUBCLONAL	1	TRUE	1	0.602320213764317	2		422	200	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0003534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	156	310	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.853	0.785	0.924	0.853	0.785	0.924	CLONAL	1	TRUE	1	0.602320213764317	2		310	607	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	32	422	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.768	0.657	0.879			1	INDETERMINATE	2	FALSE	NA	0.67169885892142	2		422	62	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864869	57864869	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003598-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	63	641	0	ENST00000228682.2:c.2346G>C	p.Glu782Asp	p.E782D	ENST00000228682	NM_005269.2	782	gaG/gaC	12/12	0.430167232433311	3	FACETS	0.469	0.406	0.538			1	SUBCLONAL	1	FALSE	NA	0.67169885892142	3		641	534	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003598-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	241	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.929	0.875	0.984	0.929	0.875	0.984	CLONAL	1	TRUE	1	0.868932171243984	2		422	597	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711936	89711946	+	frameshift_variant	Frame_Shift_Del	DEL	ATCTGGATTAT	ATCTGGATTAT	-	novel	NA	P-0003598-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	23	188	0	ENST00000371953.3:c.555_565del	p.His185GlnfsTer13	p.H185Qfs*13	ENST00000371953	NM_000314.4	185	cATCTGGATTAT/c	6/9	0.868932171243984	1	FACETS	0.101	0.079	0.128	0.101	0.079	0.128	SUBCLONAL	1	TRUE	0	0.868932171243984	1		188	295	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003598-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	68	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.41792591574155	2		422	299	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130180	2130180	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45451497	NA	P-0003598-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	112	536	4	ENST00000219476.3:c.3412C>T	p.Arg1138Ter	p.R1138*	ENST00000219476	NM_000548.3	1138	Cga/Tga	30/42	0.41792591574155	1	FACETS	0.825	0.745	0.908	0.825	0.745	0.908	CLONAL	1	TRUE	0	0.41792591574155	1		540	514	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851966	63851966	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003598-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	67	275	0	ENST00000279873.7:c.2744del	p.His915ProfsTer29	p.H915Pfs*29	ENST00000279873	NM_032199.2	915	cAc/cc	10/10	0.41792591574155	1	FACETS	0.884	0.775	0.999	0.884	0.775	0.999	CLONAL	1	TRUE	0	0.41792591574155	1		275	287	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0003614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	46	314	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.140247646833493	1	FACETS	0.712	0.615	0.814	0.712	0.615	0.814	INDETERMINATE	1	TRUE	0	0.66042813582535	1		314	131	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0003614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	11	139	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.757	0.541	1	0.757	0.541	1	CLONAL	1	TRUE	1	0.66042813582535	2		139	44	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589583	67589584	+	inframe_insertion	In_Frame_Ins	INS	-	-	ACATGAATATAACACTCA	novel	NA	P-0003614-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	29	230	0	ENST00000274335.5:c.1347_1364dup	p.His450_Gln455dup	p.H450_Q455dup	ENST00000274335		450	tta/ttACATGAATATAACACTCAa	10/15	1	2	FACETS	0.751	0.614	0.899	0.751	0.614	0.899	SUBCLONAL	1	TRUE	1	0.66042813582535	2		230	117	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	77	422	0				ENST00000310581	NM_198253.2	-/1132			0.77288533443569	4	FACETS	0.998	0.898	1	0.998	0.898	1	CLONAL	2	TRUE	2	0.77288533443569	4		422	177	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721094	176721094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	173	276	0	ENST00000439151.2:c.6725G>A	p.Gly2242Glu	p.G2242E	ENST00000439151	NM_022455.4	2242	gGa/gAa	23/23	0.77288533443569	4	FACETS	0.884	0.822	0.947	0.884	0.822	0.947	CLONAL	2	TRUE	2	0.77288533443569	4		276	449	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984848	9984848	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	194	406	0	ENST00000330684.3:c.1117G>A	p.Glu373Lys	p.E373K	ENST00000330684	NM_001134407.1	373	Gaa/Aaa	4/13	0.627682912560044	4	FACETS	0.836	0.78	0.894	0.836	0.78	0.894	CLONAL	2	TRUE	2	0.77288533443569	4		406	532	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594221	55594221	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913512	NA	P-0003620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	289	414	0	ENST00000288135.5:c.1924A>G	p.Lys642Glu	p.K642E	ENST00000288135	NM_000222.2	642	Aaa/Gaa	13/21	0.728210579247738	4	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	2	0.77288533443569	4		414	621	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057649	27057649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	231	435	0	ENST00000324856.7:c.1357C>T	p.Pro453Ser	p.P453S	ENST00000324856	NM_006015.4	453	Cct/Tct	3/20	0.728210579247738	4	FACETS	0.956	0.9	1	0.956	0.9	1	CLONAL	2	TRUE	2	0.77288533443569	4		435	554	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837973	156837973	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	239	286	0	ENST00000524377.1:c.506G>A	p.Gly169Glu	p.G169E	ENST00000524377	NM_002529.3	169	gGa/gAa	5/17	0.77288533443569	4	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	2	0.77288533443569	4		286	532	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849110	156849110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	257	377	0	ENST00000524377.1:c.2002G>A	p.Asp668Asn	p.D668N	ENST00000524377	NM_002529.3	668	Gat/Aat	15/17	0.77288533443569	4	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	2	0.77288533443569	4		377	585	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968136	55968136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747362899	NA	P-0003620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	329	521	0	ENST00000263923.4:c.2194G>A	p.Glu732Lys	p.E732K	ENST00000263923	NM_002253.2	732	Gaa/Aaa	15/30	0.728210579247738	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.77288533443569	4		521	720	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542506	187542506	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0003620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	207	504	0	ENST00000441802.2:c.5234T>A	p.Leu1745Ter	p.L1745*	ENST00000441802	NM_005245.3	1745	tTg/tAg	10/27	0.728210579247738	4	FACETS	0.913	0.855	0.972	0.913	0.855	0.972	CLONAL	2	TRUE	2	0.77288533443569	4		504	520	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148515023	148515023	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	254	433	0	ENST00000320356.2:c.1186G>A	p.Glu396Lys	p.E396K	ENST00000320356	NM_004456.4	396	Gag/Aag	10/20	0.627682912560044	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.77288533443569	4		433	537	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015115	37015115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	276	404	0	ENST00000358127.4:c.289G>A	p.Glu97Lys	p.E97K	ENST00000358127	NM_001280556.1	97	Gaa/Aaa	3/10	0.630911303571154	5	FACETS	0.843	0.798	0.888			1	CLONAL	3	TRUE	NA	0.77288533443569	5		404	610	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412642	139412642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	389	275	0	ENST00000277541.6:c.1202C>T	p.Pro401Leu	p.P401L	ENST00000277541	NM_017617.3	401	cCc/cTc	7/34	0.77288533443569	3	FACETS	1	0.994	1			1	CLONAL	3	TRUE	NA	0.77288533443569	3		275	443	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692793	89692793	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	158	245	0	ENST00000371953.3:c.277C>T	p.His93Tyr	p.H93Y	ENST00000371953	NM_000314.4	93	Cat/Tat	5/9	0.77288533443569	2	FACETS	0.988	0.941	1	0.988	0.941	1	CLONAL	2	TRUE	0	0.77288533443569	2		245	207	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575044	64575044	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894268	NA	P-0003620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	241	269	0	ENST00000312049.6:c.763G>A	p.Glu255Lys	p.E255K	ENST00000312049	NM_130799.2	255	Gag/Aag	4/10	0.77288533443569	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.77288533443569	4		269	533	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376322	118376322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	256	518	0	ENST00000534358.1:c.9715C>T	p.Pro3239Ser	p.P3239S	ENST00000534358	NM_005933.3	3239	Ccc/Tcc	27/36	0.77288533443569	4	FACETS	0.926	0.873	0.98	0.926	0.873	0.98	CLONAL	2	TRUE	2	0.77288533443569	4		518	634	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715777	18715777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1203196085	NA	P-0003620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	185	394	0	ENST00000266497.5:c.3608G>A	p.Arg1203Lys	p.R1203K	ENST00000266497		1203	aGg/aAg	25/31	0.77288533443569	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.77288533443569	3		394	314	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145338	58145338	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555201372	NA	P-0003620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	257	336	0	ENST00000257904.6:c.163C>T	p.Arg55Cys	p.R55C	ENST00000257904	NM_000075.3	55	Cgt/Tgt	2/8	0.619851479937763	4	FACETS	1	0.991	1			1	CLONAL	2	TRUE	NA	0.77288533443569	4		336	487	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110584	4110584	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519807	NA	P-0003620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	291	275	0	ENST00000262948.5:c.373T>A	p.Cys125Ser	p.C125S	ENST00000262948	NM_030662.3	125	Tgc/Agc	3/11	0.77288533443569	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.77288533443569	4		275	613	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546620	9546620	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764351685	NA	P-0003620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	222	430	0	ENST00000353224.5:c.1402G>A	p.Glu468Lys	p.E468K	ENST00000353224	NM_177990.2	468	Gag/Aag	5/10	0.77288533443569	4	FACETS	0.909	0.853	0.966	0.909	0.853	0.966	CLONAL	2	TRUE	2	0.77288533443569	4		430	560	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024038	31024038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1569336680	NA	P-0003620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	263	357	0	ENST00000375687.4:c.3523G>A	p.Glu1175Lys	p.E1175K	ENST00000375687	NM_015338.5	1175	Gag/Aag	13/13	0.77288533443569	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.77288533443569	4		357	540	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94211948	94211949	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0003620-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	157	392	0	ENST00000323929.3:c.496_497delinsTT	p.Pro166Leu	p.P166L	ENST00000323929	NM_005591.3	166	CCg/TTg	6/20	0.77288533443569	4	FACETS	0.806	0.745	0.868	0.806	0.745	0.868	CLONAL	2	TRUE	2	0.77288533443569	4		392	447	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	42	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.654000516826454	2		422	99	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913240	NA	P-0003651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	168	472	0	ENST00000311936.3:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000311936	NM_004985.3	61	cAa/cGa	3/5	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.654000516826454	2		472	491	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041618	47041619	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0003651-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	202	263	0	ENST00000377604.3:c.1844dup	p.Tyr615Ter	p.Y615*	ENST00000377604	NM_001204468.1	615	tat/tAat	17/24	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.654000516826454	1		263	319	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	67	422	0				ENST00000310581	NM_198253.2	-/1132			0.121023852005444	2	FACETS	1	0.917	1	1	0.977	1	CLONAL	3	TRUE	0	0.160140115327493	2		422	264	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934578	NA	P-0003664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	65	199	0	ENST00000269305.4:c.524G>T	p.Arg175Leu	p.R175L	ENST00000269305	NM_001126112.2	175	cGc/cTc	5/11	0.160140115327493	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.160140115327493	1		199	504	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003673-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	22	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.843	0.663	1	0.843	0.663	1	CLONAL	1	TRUE	1	0.45	2		422	116	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0003673-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	47	310	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.45	2		310	198	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170814993	170814993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003673-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	45	144	0	ENST00000296930.5:c.41C>T	p.Pro14Leu	p.P14L	ENST00000296930	NM_002520.6	14	cCc/cTc	1/11	1	2	FACETS	0.99	0.842	1	0.99	0.842	1	CLONAL	1	TRUE	1	0.45	2		144	202	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	57	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.633383806494894	2		422	160	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520017	NA	P-0003681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	16	248	0	ENST00000326873.7:c.647C>T	p.Ser216Phe	p.S216F	ENST00000326873	NM_000455.4	216	tCc/tTc	5/10	0.633383806494894	1	FACETS	0.118	0.087	0.155	0.118	0.087	0.155	SUBCLONAL	1	TRUE	0	0.633383806494894	1		248	293	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154760	2154760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143785521	NA	P-0003681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	228	301	0	ENST00000434045.2:c.461C>T	p.Pro154Leu	p.P154L	ENST00000434045	NM_001127598.1	154	cCg/cTg	4/5	0.633383806494894	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.633383806494894	1		301	398	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	43	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.588109402877656	2		422	133	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0003682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	110	168	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	NA	2	FACETS	0.866	0.797	0.934			1	INDETERMINATE	2	TRUE	NA	0.588109402877656	2		168	216	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222163	53222163	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	70	165	0	ENST00000375401.3:c.4669C>T	p.Gln1557Ter	p.Q1557*	ENST00000375401	NM_004187.3	1557	Cag/Tag	26/26	0.198938143441143	1	FACETS	0.67	0.591	0.752	0.67	0.591	0.752	INDETERMINATE	1	TRUE	0	0.588109402877656	1		165	251	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097687	27097687	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	170	338	0	ENST00000324856.7:c.3276G>C	p.Leu1092Phe	p.L1092F	ENST00000324856	NM_006015.4	1092	ttG/ttC	12/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.588109402877656	2		338	505	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845367	151845367	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0003682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	135	265	0	ENST00000262189.6:c.13645C>A	p.Arg4549Ser	p.R4549S	ENST00000262189	NM_170606.2	4549	Cgc/Agc	52/59	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.588109402877656	2		265	441	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807374	3807374	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587783482	NA	P-0003682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	133	273	0	ENST00000262367.5:c.3613G>T	p.Glu1205Ter	p.E1205*	ENST00000262367	NM_004380.2	1205	Gag/Tag	19/31	1	2	FACETS	0.88	0.804	0.959	0.88	0.804	0.959	CLONAL	1	TRUE	1	0.588109402877656	2		273	514	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091821	29091821	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs267606211	NA	P-0003682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	99	182	2	ENST00000328354.6:c.1136C>G	p.Ser379Cys	p.S379C	ENST00000328354	NM_007194.3	379	tCt/tGt	11/15	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.588109402877656	2		184	317	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969371	44969372	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0003682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	164	402	0	ENST00000377967.4:c.4054_4055del	p.Lys1352AspfsTer36	p.K1352Dfs*36	ENST00000377967	NM_021140.2	1351	cgAAag/cgag	28/29	0.198938143441143	1	FACETS	0.732	0.676	0.789	0.732	0.676	0.789	INDETERMINATE	1	TRUE	0	0.588109402877656	1		402	538	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431662	49431662	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0003682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	111	315	0	ENST00000301067.7:c.9477del	p.Ser3159ArgfsTer2	p.S3159Rfs*2	ENST00000301067	NM_003482.3	3159	agC/ag	34/54	1	2	FACETS	0.899	0.814	0.987	0.899	0.814	0.987	CLONAL	1	TRUE	1	0.588109402877656	2		315	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0004121-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	93	498	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.256308390099814	2		498	638	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913351	NA	P-0004121-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	27	359	0	ENST00000288602.6:c.1397G>T	p.Gly466Val	p.G466V	ENST00000288602	NM_004333.4	466	gGa/gTa	11/18	1	2	FACETS	0.602	0.479	0.742	0.602	0.479	0.742	SUBCLONAL	1	TRUE	1	0.256308390099814	2		359	350	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220649	1220649	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060499964	NA	P-0004121-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	127	795	0	ENST00000326873.7:c.667G>A	p.Glu223Lys	p.E223K	ENST00000326873	NM_000455.4	223	Gag/Aag	5/10	0.14835928448804	3	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.256308390099814	3		795	756	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100075	27100075	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004121-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	55	731	0	ENST00000324856.7:c.3871G>T	p.Glu1291Ter	p.E1291*	ENST00000324856	NM_006015.4	1291	Gag/Tag	16/20	1	2	FACETS	0.62	0.53	0.72	0.62	0.53	0.72	SUBCLONAL	1	TRUE	1	0.256308390099814	2		731	692	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435386	18435386	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004121-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	31	299	0	ENST00000266497.5:c.371G>C	p.Cys124Ser	p.C124S	ENST00000266497		124	tGc/tCc	1/31	1	2	FACETS	0.722	0.585	0.877	0.722	0.585	0.877	SUBCLONAL	1	TRUE	1	0.256308390099814	2		299	335	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549372	21549372	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004121-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	31	601	0	ENST00000382592.4:c.2904G>T	p.Lys968Asn	p.K968N	ENST00000382592	NM_014572.2	968	aaG/aaT	8/8	1	2	FACETS	0.414	0.334	0.505	0.414	0.334	0.505	SUBCLONAL	1	TRUE	1	0.256308390099814	2		601	584	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641596	23641596	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004121-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	54	535	0	ENST00000261584.4:c.1879del	p.Val627Ter	p.V627*	ENST00000261584	NM_024675.3	627	Gtg/tg	5/13	1	2	FACETS	0.801	0.684	0.929	0.801	0.684	0.929	CLONAL	1	TRUE	1	0.256308390099814	2		535	526	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828665	72828665	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004121-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	74	604	0	ENST00000268489.5:c.7916A>G	p.Gln2639Arg	p.Q2639R	ENST00000268489	NM_006885.3	2639	cAg/cGg	9/10	1	2	FACETS	0.868	0.76	0.985	0.868	0.76	0.985	CLONAL	1	TRUE	1	0.256308390099814	2		604	665	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849423	89849423	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004121-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	48	729	0	ENST00000389301.3:c.1558G>T	p.Asp520Tyr	p.D520Y	ENST00000389301	NM_000135.2	520	Gac/Tac	16/43	1	2	FACETS	0.565	0.477	0.663	0.565	0.477	0.663	SUBCLONAL	1	TRUE	1	0.256308390099814	2		729	663	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41209133	41209133	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004121-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	106	551	0	ENST00000357654.3:c.5213G>T	p.Gly1738Val	p.G1738V	ENST00000357654	NM_007294.3	1738	gGa/gTa	19/23	0.256308390099814	3	FACETS	1	0.98	1	0.699	0.628	0.775	CLONAL	1	TRUE	1	0.256308390099814	3		551	667	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734144	58734144	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004121-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	67	519	0	ENST00000305921.3:c.1202A>G	p.Tyr401Cys	p.Y401C	ENST00000305921	NM_003620.3	401	tAt/tGt	5/6	0.230465116987038	3	FACETS	0.942	0.819	1	0.471	0.409	0.538	CLONAL	1	TRUE	1	0.256308390099814	3		519	626	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119836	70119836	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0004121-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	43	707	0	ENST00000245479.2:c.838del	p.Ser280AlafsTer103	p.S280Afs*103	ENST00000245479	NM_000346.3	280	Agc/gc	3/3	0.230465116987038	3	FACETS	0.513	0.428	0.608	0.256	0.214	0.304	SUBCLONAL	1	TRUE	1	0.256308390099814	3		707	738	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259178	36259178	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004121-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	45	615	0	ENST00000300305.3:c.313C>A	p.His105Asn	p.H105N	ENST00000300305		105	Cac/Aac	3/8	1	2	FACETS	0.476	0.399	0.562	0.476	0.399	0.562	SUBCLONAL	1	TRUE	1	0.256308390099814	2		615	738	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670286	134670286	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004121-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	56	538	0	ENST00000398015.3:c.197C>A	p.Pro66His	p.P66H	ENST00000398015	NM_004441.4	66	cCc/cAc	3/16	1	2	FACETS	0.848	0.727	0.98	0.848	0.727	0.98	CLONAL	1	TRUE	1	0.256308390099814	2		538	515	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355241	81355241	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004121-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	17	298	0	ENST00000222390.5:c.1133C>A	p.Ser378Tyr	p.S378Y	ENST00000222390	NM_000601.4	378	tCc/tAc	9/18	1	2	FACETS	0.435	0.324	0.567	0.435	0.324	0.567	SUBCLONAL	1	TRUE	1	0.256308390099814	2		298	305	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376014	8376015	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0004121-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	46	375	0	ENST00000356435.5:c.4582_4583delinsAA	p.Pro1528Asn	p.P1528N	ENST00000356435		1528	CCt/AAt	28/35	1	2	FACETS	0.918	0.775	1	0.918	0.775	1	CLONAL	1	TRUE	1	0.256308390099814	2		375	391	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93627334	93627340	+	frameshift_variant	Frame_Shift_Del	DEL	TGTTAAT	TGTTAAT	-	novel	NA	P-0004121-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	21	427	0	ENST00000375746.1:c.802_808del	p.Val268LeufsTer20	p.V268Lfs*20	ENST00000375746	NM_001174167.1	267	aaTGTTAAT/aa	6/14	0.256308390099814	1	FACETS	0.355	0.272	0.451	0.355	0.272	0.451	SUBCLONAL	1	TRUE	0	0.256308390099814	1		427	403	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422678	47422678	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004121-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	69	625	0	ENST00000377045.4:c.150G>C	p.Lys50Asn	p.K50N	ENST00000377045	NM_001654.4	50	aaG/aaC	3/16	1	2	FACETS	0.837	0.729	0.954	0.837	0.729	0.954	CLONAL	1	TRUE	1	0.256308390099814	2		625	643	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435286	110435288	+	missense_variant	Missense_Mutation	TNP	CCG	CCG	ACA	novel	NA	P-0004121-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	32	293	1	ENST00000375856.3:c.3113_3115delinsTGT	p.Pro1038_Gly1039delinsLeuTrp	p.P1038_G1039delinsLW	ENST00000375856	NM_003749.2	1038	cCGGgg/cTGTgg	1/2	NA	2	FACETS	0.773	0.629	0.935			1	INDETERMINATE	1	TRUE	NA	0.256308390099814	2		294	323	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005916-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	56	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.2	2		422	492	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0005916-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	52	668	1	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	1	2	FACETS	0.57	0.483	0.665	0.57	0.483	0.665	SUBCLONAL	1	TRUE	1	0.2	2		669	913	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525099	9525099	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005916-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	32	641	0	ENST00000353224.5:c.1786G>C	p.Glu596Gln	p.E596Q	ENST00000353224	NM_177990.2	596	Gag/Cag	8/10	1	2	FACETS	0.537	0.435	0.653	0.537	0.435	0.653	SUBCLONAL	1	TRUE	1	0.2	2		641	596	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201142	108201142	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005916-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	22	414	0	ENST00000278616.4:c.7509G>C	p.Met2503Ile	p.M2503I	ENST00000278616	NM_000051.3	2503	atG/atC	50/63	1	2	FACETS	0.518	0.4	0.654	0.518	0.4	0.654	SUBCLONAL	1	TRUE	1	0.2	2		414	425	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797300	135797300	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs118203401	NA	P-0005916-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	36	345	0	ENST00000298552.3:c.569del	p.Arg190ProfsTer20	p.R190Pfs*20	ENST00000298552	NM_001162426.1	190	cGc/cc	7/23	1	2	FACETS	0.887	0.729	1	0.887	0.729	1	CLONAL	1	TRUE	1	0.2	2		345	406	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0006660-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	107	143	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.240495387822052	3	FACETS	1	0.982	1	0.73	0.656	0.808	CLONAL	1	TRUE	1	0.265102472737621	3		143	626	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0006660-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	41	148	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	0.240495387822052	3	FACETS	0.562	0.467	0.668	0.281	0.233	0.334	SUBCLONAL	1	TRUE	1	0.265102472737621	3		148	623	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14038623	14038623	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006660-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	124	481	0	ENST00000311895.7:c.1948G>C	p.Asp650His	p.D650H	ENST00000311895	NM_005236.2	650	Gat/Cat	10/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.265102472737621	2		481	703	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020808	26020808	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs377197123	NA	P-0006660-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	47	382	0	ENST00000357647.3:c.91C>G	p.Pro31Ala	p.P31A	ENST00000357647	NM_003529.2	31	Ccg/Gcg	1/1	0.265102472737621	3	FACETS	0.698	0.589	0.82	0.349	0.294	0.41	SUBCLONAL	1	TRUE	1	0.265102472737621	3		382	575	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246670422	246670422	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006660-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	83	756	0	ENST00000388985.4:c.98C>G	p.Ser33Trp	p.S33W	ENST00000388985		33	tCg/tGg	1/12	0.265102472737621	3	FACETS	0.613	0.54	0.693	0.204	0.179	0.231	SUBCLONAL	1	TRUE	0	0.265102472737621	3		756	1156	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305439	65305439	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006660-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	69	583	0	ENST00000342505.4:c.2689G>A	p.Glu897Lys	p.E897K	ENST00000342505	NM_002227.2	897	Gaa/Aaa	20/25	1	2	FACETS	0.723	0.629	0.825	0.723	0.629	0.825	SUBCLONAL	1	TRUE	1	0.265102472737621	2		583	720	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216597	108216597	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782202	NA	P-0006660-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	27	305	1	ENST00000278616.4:c.8546G>A	p.Arg2849Gln	p.R2849Q	ENST00000278616	NM_000051.3	2849	cGa/cAa	58/63	1	2	FACETS	0.423	0.335	0.523	0.423	0.335	0.523	SUBCLONAL	1	TRUE	1	0.265102472737621	2		306	482	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856106	151856106	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs772980746	NA	P-0006660-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	78	517	0	ENST00000262189.6:c.11512C>G	p.Pro3838Ala	p.P3838A	ENST00000262189	NM_170606.2	3838	Cca/Gca	44/59	1	2	FACETS	0.816	0.717	0.923	0.816	0.717	0.923	CLONAL	1	TRUE	1	0.265102472737621	2		517	721	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0007136-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	810	403	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.899161851572668	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.900651816724291	2		404	895	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398282	25398282	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913535	NA	P-0007136-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	229	278	0	ENST00000311936.3:c.37G>T	p.Gly13Cys	p.G13C	ENST00000311936	NM_004985.3	13	Ggc/Tgc	2/5	0.900651816724291	3	FACETS	0.886	0.84	0.933	0.886	0.84	0.933	CLONAL	2	TRUE	1	0.900651816724291	3		278	416	SUCCESS
APC	324	MSKCC	GRCh37	5	112175207	112175207	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs121913462	NA	P-0007136-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	77	145	0	ENST00000257430.4:c.3916G>T	p.Glu1306Ter	p.E1306*	ENST00000257430	NM_000038.5	1306	Gaa/Taa	16/16	0.900651816724291	1	FACETS	0.989	0.928	1	0.989	0.928	1	CLONAL	1	TRUE	0	0.900651816724291	1		145	95	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672519	30672519	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007136-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	589	461	0	ENST00000376406.3:c.4441T>A	p.Ser1481Thr	p.S1481T	ENST00000376406	NM_014641.2	1481	Tcc/Acc	10/15	0.873412570656924	3	FACETS	0.926	0.896	0.956	0.926	0.896	0.956	CLONAL	2	TRUE	1	0.900651816724291	3		461	1024	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981660	101981660	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007136-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	10	67	0	ENST00000282441.5:c.81G>C	p.Gln27His	p.Q27H	ENST00000282441	NM_001130145.2	27	caG/caC	1/9	0.551877889530439	2	FACETS	0.202	0.137	0.282	0.101	0.068	0.141	SUBCLONAL	1	TRUE	0	0.900651816724291	2		67	110	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218347	133218347	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760235113	NA	P-0007136-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	844	627	0	ENST00000320574.5:c.5264G>A	p.Gly1755Glu	p.G1755E	ENST00000320574	NM_006231.2	1755	gGg/gAg	39/49	0.900651816724291	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.900651816724291	3		627	1351	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792869	33792869	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007136-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	262	179	0	ENST00000498907.2:c.452G>C	p.Gly151Ala	p.G151A	ENST00000498907	NM_004364.3	151	gGg/gCg	1/1	0.900651816724291	4	FACETS	0.975	0.923	1	0.975	0.923	1	CLONAL	2	TRUE	2	0.900651816724291	4		179	567	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412109	63412109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157288902	NA	P-0007136-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	775	628	0	ENST00000330258.3:c.1058G>A	p.Arg353Gln	p.R353Q	ENST00000330258	NM_152424.3	353	cGa/cAa	2/2	0.425970846424139	6	FACETS	0.92	0.89	0.949	0.92	0.89	0.949	INDETERMINATE	3	TRUE	3	0.900651816724291	6		628	1747	SUCCESS
AR	367	MSKCC	GRCh37	X	66765176	66765176	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs62636527	NA	P-0007136-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	31	189	2	ENST00000374690.3:c.188A>T	p.Gln63Leu	p.Q63L	ENST00000374690	NM_000044.3	63	cAg/cTg	1/8	0.425970846424139	6	FACETS	0.405	0.327	0.494	0.135	0.109	0.165	INDETERMINATE	1	TRUE	3	0.900651816724291	6		191	476	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911340	32911340	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007136-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	135	334	0	ENST00000380152.3:c.2848G>T	p.Val950Phe	p.V950F	ENST00000380152		950	Gtt/Ttt	11/27	0.900651816724291	5	FACETS	0.746	0.677	0.818	0.186	0.169	0.205	SUBCLONAL	1	TRUE	1	0.900651816724291	5		334	945	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39239288	39239288	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs139859866	NA	P-0007136-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	172	350	0	ENST00000402219.2:c.2369T>C	p.Leu790Ser	p.L790S	ENST00000402219	NM_005633.3	790	tTa/tCa	14/23	0.900651816724291	3	FACETS	0.977	0.904	1	0.488	0.452	0.526	CLONAL	1	TRUE	1	0.900651816724291	3		350	567	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0008878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	77	535	1	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.274183909211436	3	FACETS	0.827	0.732	0.927	0.551	0.488	0.618	CLONAL	2	TRUE	0	0.333128324285497	3		536	326	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999088	100999088	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	145	1019	0	ENST00000325455.5:c.714G>C	p.Lys238Asn	p.K238N	ENST00000325455	NM_001202474.3	238	aaG/aaC	1/8	0.139202648854821	4	FACETS	1	0.922	1	1	0.922	1	INDETERMINATE	2	TRUE	2	0.333128324285497	4		1019	577	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576091	29576091	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	62	685	0	ENST00000356175.3:c.4064C>A	p.Ser1355Ter	p.S1355*	ENST00000356175	NM_000267.3	1355	tCa/tAa	30/57	1	2	FACETS	0.833	0.721	0.953	0.833	0.721	0.953	CLONAL	1	TRUE	1	0.333128324285497	2		685	447	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4123808	4123808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1325938060	NA	P-0008878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	48	655	0	ENST00000262948.5:c.65C>T	p.Pro22Leu	p.P22L	ENST00000262948	NM_030662.3	22	cCa/cTa	1/11	0.108557123345412	5	FACETS	0.967	0.818	1	0.242	0.204	0.283	INDETERMINATE	1	TRUE	1	0.333128324285497	5		655	447	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308405	30308405	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	66	795	0	ENST00000262643.3:c.419T>G	p.Leu140Arg	p.L140R	ENST00000262643	NM_001238.2	140	cTg/cGg	6/12	0.108557123345412	5	FACETS	1	0.87	1	0.251	0.217	0.287	INDETERMINATE	1	TRUE	1	0.333128324285497	5		795	593	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0008878-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	80	860	0	ENST00000269305.4:c.994-1G>T		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.328977433399675	1	FACETS	0.965	0.853	1	0.965	0.853	1	CLONAL	1	TRUE	0	0.333128324285497	1		860	415	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0009261-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	19	558	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.32	0.242	0.413	0.32	0.242	0.413	SUBCLONAL	1	TRUE	1	0.236543928238637	2		558	502	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009261-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	53	927	0	ENST00000269305.4:c.380C>A	p.Ser127Tyr	p.S127Y	ENST00000269305	NM_001126112.2	127	tCc/tAc	5/11	1	2	FACETS	0.85	0.725	0.987	0.85	0.725	0.987	CLONAL	1	TRUE	1	0.236543928238637	2		927	527	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009261-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	26	951	1	ENST00000269571.5:c.829G>T	p.Asp277Tyr	p.D277Y	ENST00000269571		277	Gac/Tac	7/27	1	2	FACETS	0.44	0.347	0.546	0.44	0.347	0.546	SUBCLONAL	1	TRUE	1	0.236543928238637	2		952	500	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224496	224496	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009261-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	21	209	0	ENST00000264932.6:c.172G>C	p.Val58Leu	p.V58L	ENST00000264932	NM_004168.2	58	Gtg/Ctg	3/15	0.23659319614357	3	FACETS	0.834	0.651	1	0.834	0.651	1	CLONAL	2	TRUE	1	0.236543928238637	3		209	119	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162864368	162864368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009261-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	35	618	1	ENST00000366898.1:c.145G>A	p.Glu49Lys	p.E49K	ENST00000366898	NM_004562.2	49	Gag/Aag	2/12	1	2	FACETS	0.729	0.598	0.876	0.729	0.598	0.876	SUBCLONAL	1	TRUE	1	0.236543928238637	2		619	406	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534564	140534564	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009261-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	28	375	0	ENST00000288602.6:c.349A>T	p.Met117Leu	p.M117L	ENST00000288602	NM_004333.4	117	Atg/Ttg	3/18	0.208350948689321	3	FACETS	1	0.857	1			1	CLONAL	1	TRUE	NA	0.236543928238637	3		375	244	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953228	81953228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369760877	NA	P-0009261-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	16	552	1	ENST00000359376.3:c.2194C>T	p.Arg732Cys	p.R732C	ENST00000359376	NM_002661.3	732	Cgc/Tgc	20/33	1	2	FACETS	0.451	0.333	0.592	0.451	0.333	0.592	SUBCLONAL	1	TRUE	1	0.236543928238637	2		553	300	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829847	72829847	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750842718	NA	P-0009261-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	25	906	0	ENST00000268489.5:c.6734C>T	p.Ser2245Leu	p.S2245L	ENST00000268489	NM_006885.3	2245	tCa/tTa	9/10	1	2	FACETS	0.451	0.354	0.562	0.451	0.354	0.562	SUBCLONAL	1	TRUE	1	0.236543928238637	2		906	469	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828381	72828381	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009261-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	19	720	0	ENST00000268489.5:c.8200C>T	p.His2734Tyr	p.H2734Y	ENST00000268489	NM_006885.3	2734	Cac/Tac	9/10	1	2	FACETS	0.439	0.332	0.565	0.439	0.332	0.565	SUBCLONAL	1	TRUE	1	0.236543928238637	2		720	366	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248709	59248709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1363866933	NA	P-0009261-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	40	972	0	ENST00000371222.2:c.34G>A	p.Asp12Asn	p.D12N	ENST00000371222	NM_002228.3	12	Gat/Aat	1/1	1	2	FACETS	0.492	0.407	0.586	0.492	0.407	0.586	SUBCLONAL	1	TRUE	1	0.236543928238637	2		972	688	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967262	38967262	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0009261-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	50	170	0	ENST00000357387.3:c.1218+1G>T		p.X406_splice	ENST00000357387	NM_152756.3	406			0.23659319614357	5	FACETS	1	0.939	1	0.792	0.679	0.914	CLONAL	2	TRUE	2	0.236543928238637	5		170	241	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262289	16262289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs544993359	NA	P-0009261-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	16	424	0	ENST00000375759.3:c.9554G>A	p.Arg3185Gln	p.R3185Q	ENST00000375759	NM_015001.2	3185	cGa/cAa	11/15	1	2	FACETS	0.449	0.332	0.59	0.449	0.332	0.59	SUBCLONAL	1	TRUE	1	0.236543928238637	2		424	301	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361078	70361107	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGCAGCAGCAGCAACAGCAACAGCAGCAGC	AGCAGCAGCAGCAACAGCAACAGCAGCAGC	-	rs773480549	NA	P-0009628-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	15	189	0	ENST00000374080.3:c.6300_6329del		p.X2100_splice	ENST00000374080		2100		43/45	0.0466035126653042	2	FACETS	0.883	0.649	1			1	INDETERMINATE	1	TRUE	NA	0.22355020890878	2		189	152	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852680	63852680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009628-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	55	521	0	ENST00000279873.7:c.3458C>T	p.Ser1153Leu	p.S1153L	ENST00000279873	NM_032199.2	1153	tCa/tTa	10/10	0.0668250711596798	3	FACETS	0.929	0.794	1	0.464	0.397	0.538	INDETERMINATE	1	TRUE	1	0.22355020890878	3		521	589	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435308	18435308	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009628-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	59	342	0	ENST00000266497.5:c.293G>A	p.Trp98Ter	p.W98*	ENST00000266497		98	tGg/tAg	1/31	0.206958963712884	4	FACETS	0.87	0.752	0.998	0.87	0.752	0.998	CLONAL	2	TRUE	2	0.22355020890878	4		342	371	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425584	49425584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009628-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	43	828	0	ENST00000301067.7:c.12904C>T	p.Leu4302Phe	p.L4302F	ENST00000301067	NM_003482.3	4302	Ctt/Ttt	39/54	0.0996962900881142	4	FACETS	0.64	0.534	0.759	0.32	0.267	0.38	INDETERMINATE	1	TRUE	2	0.22355020890878	4		828	735	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41001294	41001294	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009628-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	28	425	0	ENST00000267868.3:c.415A>G	p.Thr139Ala	p.T139A	ENST00000267868	NM_002875.4	139	Acg/Gcg	5/10	0.0668250711596798	3	FACETS	0.56	0.447	0.69	0.28	0.223	0.345	INDETERMINATE	1	TRUE	1	0.22355020890878	3		425	497	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661889	29661889	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009628-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	62	389	0	ENST00000356175.3:c.5783T>G	p.Met1928Arg	p.M1928R	ENST00000356175	NM_000267.3	1928	aTg/aGg	39/57	0.0996962900881142	4	FACETS	1	0.94	1	0.581	0.502	0.667	INDETERMINATE	1	TRUE	2	0.22355020890878	4		389	584	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739389	145739389	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009628-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	53	764	0	ENST00000428558.2:c.1981G>T	p.Glu661Ter	p.E661*	ENST00000428558	NM_004260.3	661	Gag/Tag	12/22	0.0466035126653042	3	FACETS	0.678	0.576	0.789			1	INDETERMINATE	1	TRUE	NA	0.22355020890878	3		764	778	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0010250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	142	531	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.985	0.896	1	0.985	0.896	1	CLONAL	1	TRUE	1	0.23	2		531	1253	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100382	27100382	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010250-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	68	628	0	ENST00000324856.7:c.4094A>T	p.Gln1365Leu	p.Q1365L	ENST00000324856	NM_006015.4	1365	cAa/cTa	17/20	0.260880300528529	1	FACETS	0.581	0.504	0.665	0.581	0.504	0.665	SUBCLONAL	1	TRUE	0	0.23	1		628	900	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0011016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	14	295	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.433373200687135	2	FACETS	0.115	0.082	0.154	0.057	0.041	0.077	SUBCLONAL	1	TRUE	0	0.508587808988708	2		295	480	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577551	7577551	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519989	NA	P-0011016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	287	576	1	ENST00000269305.4:c.730G>T	p.Gly244Cys	p.G244C	ENST00000269305	NM_001126112.2	244	Ggc/Tgc	7/11	0.487985342222632	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.508587808988708	1		577	799	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510329	187510329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs558459409	NA	P-0011016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	123	268	1	ENST00000441802.2:c.13184C>T	p.Pro4395Leu	p.P4395L	ENST00000441802	NM_005245.3	4395	cCg/cTg	27/27	0.504144796214525	1	FACETS	0.888	0.811	0.969	0.888	0.811	0.969	CLONAL	1	TRUE	0	0.508587808988708	1		269	406	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867563	35867563	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	224	255	0	ENST00000303115.3:c.377T>C	p.Ile126Thr	p.I126T	ENST00000303115	NM_002185.3	126	aTa/aCa	3/8	0.287642180857357	4	FACETS	0.969	0.914	1	0.727	0.686	0.768	INDETERMINATE	3	TRUE	0	0.508587808988708	4		255	457	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180050984	180050984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	143	703	1	ENST00000261937.6:c.1499C>T	p.Pro500Leu	p.P500L	ENST00000261937	NM_182925.4	500	cCc/cTc	11/30	0.36593023737575	1	FACETS	0.421	0.384	0.461	0.421	0.384	0.461	SUBCLONAL	1	TRUE	0	0.508587808988708	1		704	995	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963931	2963931	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	503	671	0	ENST00000396946.4:c.1876G>C	p.Glu626Gln	p.E626Q	ENST00000396946	NM_032415.4	626	Gag/Cag	15/25	0.476968482366211	3	FACETS	0.898	0.86	0.936	0.898	0.86	0.936	CLONAL	2	TRUE	1	0.508587808988708	3		671	1382	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434172	121434172	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	237	628	0	ENST00000257555.6:c.1063G>T	p.Gly355Cys	p.G355C	ENST00000257555		355	Ggc/Tgc	5/10	1	2	FACETS	0.9	0.84	0.961	0.9	0.84	0.961	CLONAL	1	TRUE	1	0.508587808988708	2		628	1036	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569794	95569794	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	149	269	1	ENST00000393063.1:c.3939G>T	p.Glu1313Asp	p.E1313D	ENST00000393063	NM_030621.3	1313	gaG/gaT	22/28	0.433373200687135	2	FACETS	1	0.989	1	0.744	0.687	0.801	CLONAL	1	TRUE	0	0.508587808988708	2		270	394	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14021929	14021929	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	61	372	0	ENST00000311895.7:c.629A>T	p.Glu210Val	p.E210V	ENST00000311895	NM_005236.2	210	gAa/gTa	4/11	1	2	FACETS	0.503	0.434	0.577	0.503	0.434	0.577	SUBCLONAL	1	TRUE	1	0.508587808988708	2		372	477	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685517	29685517	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	118	251	1	ENST00000356175.3:c.7927A>G	p.Lys2643Glu	p.K2643E	ENST00000356175	NM_000267.3	2643	Aag/Gag	54/57	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.508587808988708	2		252	365	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942703	44942703	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0011016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	132	285	0	ENST00000377967.4:c.3285-2A>T		p.X1095_splice	ENST00000377967	NM_021140.2	1095			1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.508587808988708	2		285	519	SUCCESS
AR	367	MSKCC	GRCh37	X	66765917	66765917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	258	693	0	ENST00000374690.3:c.929C>T	p.Ser310Phe	p.S310F	ENST00000374690	NM_000044.3	310	tCc/tTc	1/8	1	2	FACETS	0.927	0.868	0.987	0.927	0.868	0.987	CLONAL	1	TRUE	1	0.508587808988708	2		693	1095	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340937	70340937	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	244	566	0	ENST00000374080.3:c.670C>A	p.His224Asn	p.H224N	ENST00000374080		224	Cat/Aat	5/45	1	2	FACETS	0.941	0.879	1	0.941	0.879	1	CLONAL	1	TRUE	1	0.508587808988708	2		566	1020	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953753	48953762	+	frameshift_variant	Frame_Shift_Del	DEL	GTATTACCGA	GTATTACCGA	-	novel	NA	P-0011016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	65	207	0	ENST00000267163.4:c.1359_1368del	p.Tyr453Ter	p.Y453*	ENST00000267163	NM_000321.2	452	ttGTATTACCGA/tt	14/27	0.504144796214525	1	FACETS	0.625	0.546	0.709	0.625	0.546	0.709	SUBCLONAL	1	TRUE	0	0.508587808988708	1		207	305	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643320	38643320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	63	407	0	ENST00000299084.4:c.790C>T	p.Pro264Ser	p.P264S	ENST00000299084	NM_152594.2	264	Cct/Tct	7/7	1	2	FACETS	0.518	0.449	0.593	0.518	0.449	0.593	SUBCLONAL	1	TRUE	1	0.508587808988708	2		407	478	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112128	115112129	+	missense_variant	Missense_Mutation	DNP	CA	CA	AG	novel	NA	P-0011016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	205	535	0	ENST00000257566.3:c.1611_1612delinsCT	p.Gly538Cys	p.G538C	ENST00000257566	NM_016569.3	537	gcTGgc/gcCTgc	7/8	1	2	FACETS	0.911	0.846	0.978	0.911	0.846	0.978	CLONAL	1	TRUE	1	0.508587808988708	2		535	885	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50816329	50816329	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	55	341	0	ENST00000398568.2:c.1769G>T	p.Gly590Val	p.G590V	ENST00000398568	NM_001042412.1	590	gGc/gTc	10/18	0.452630859254529	1	FACETS	0.372	0.319	0.431	0.372	0.319	0.431	SUBCLONAL	1	TRUE	0	0.508587808988708	1		341	433	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492861	8492861	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0011016-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	191	353	0	ENST00000356435.5:c.2467+1G>T		p.X823_splice	ENST00000356435		823			0.352695045752419	1	FACETS	0.836	0.776	0.898	0.836	0.776	0.898	CLONAL	1	TRUE	0	0.508587808988708	1		353	670	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012278-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	94	698	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.205762399795095	4	FACETS	0.915	0.812	1	0.458	0.406	0.513	CLONAL	1	TRUE	2	0.246480293827156	4		698	1039	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572092	64572093	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs767319284	NA	P-0012278-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	85	686	0	ENST00000312049.6:c.1546dup	p.Arg516ProfsTer15	p.R516Pfs*15	ENST00000312049	NM_130799.2	516	cgg/cCgg	10/10	1	2	FACETS	0.682	0.601	0.769	0.682	0.601	0.769	SUBCLONAL	1	TRUE	1	0.246480293827156	2		686	1011	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115967	8115968	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0012278-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	71	438	0	ENST00000346208.3:c.1315dup	p.Val439GlyfsTer68	p.V439Gfs*68	ENST00000346208		438	atg/atGg	6/6	1	2	FACETS	0.768	0.67	0.875	0.768	0.67	0.875	SUBCLONAL	1	TRUE	1	0.246480293827156	2		438	750	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793345	139793345	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012278-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	118	779	0	ENST00000247668.2:c.153C>G	p.His51Gln	p.H51Q	ENST00000247668	NM_021138.3	51	caC/caG	2/11	1	2	FACETS	0.733	0.659	0.811	0.733	0.659	0.811	SUBCLONAL	1	TRUE	1	0.246480293827156	2		779	1307	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429340	47429340	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012278-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	116	858	0	ENST00000377045.4:c.1468T>G	p.Ser490Ala	p.S490A	ENST00000377045	NM_001654.4	490	Tca/Gca	14/16	1	2	FACETS	0.819	0.736	0.907	0.819	0.736	0.907	CLONAL	1	TRUE	1	0.246480293827156	2		858	1149	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658468	NA	P-0013674-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	578	848	0	ENST00000269305.4:c.577C>T	p.His193Tyr	p.H193Y	ENST00000269305	NM_001126112.2	193	Cat/Tat	6/11	0.710966594833319	2	FACETS	0.931	0.906	0.957	0.931	0.906	0.957	CLONAL	2	TRUE	0	0.748583053924645	2		848	829	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169988207	169988207	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0013674-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	170	368	0	ENST00000295797.4:c.451-2A>C		p.X151_splice	ENST00000295797	NM_002740.5	151			0.603680780349609	3	FACETS	0.968	0.894	1	0.484	0.447	0.522	CLONAL	1	TRUE	1	0.748583053924645	3		368	645	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631129	69631129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs281860303	NA	P-0014385-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	284	756	0	ENST00000334134.2:c.283C>T	p.Arg95Trp	p.R95W	ENST00000334134	NM_005247.2	95	Cgg/Tgg	2/3	0.346803679545573	4	FACETS	0.872	0.819	0.926	0.872	0.819	0.926	CLONAL	2	TRUE	2	0.38261593869323	4		756	1177	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443631	29443631	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519784	NA	P-0014385-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	415	850	0	ENST00000389048.3:c.3586C>A	p.Leu1196Met	p.L1196M	ENST00000389048	NM_004304.4	1196	Ctg/Atg	23/29	0.38261593869323	4	FACETS	0.899	0.858	0.941			1	CLONAL	3	TRUE	NA	0.38261593869323	4		850	1112	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457737	149457737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759467764	NA	P-0014385-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	164	816	0	ENST00000286301.3:c.667G>A	p.Val223Met	p.V223M	ENST00000286301	NM_005211.3	223	Gtg/Atg	5/22	0.372206454316377	5	FACETS	1	0.957	1	0.357	0.327	0.389	CLONAL	1	TRUE	2	0.38261593869323	5		816	1260	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242468	55242482	+	inframe_deletion	In_Frame_Del	DEL	ATTAAGAGAAGCAAC	ATTAAGAGAAGCAAC	-	rs121913442	NA	P-0016054-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	125	569	0	ENST00000275493.2:c.2240_2254del	p.Leu747_Thr751del	p.L747_T751del	ENST00000275493	NM_005228.3	746	gaATTAAGAGAAGCAACa/gaa	19/28	0.290185620099015	5	FACETS	0.963	0.874	1	0.642	0.582	0.705	CLONAL	2	TRUE	2	0.290185620099015	5		569	642	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843429	128843429	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs115491500	NA	P-0016054-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	60	700	0	ENST00000249373.3:c.536C>T	p.Thr179Met	p.T179M	ENST00000249373	NM_005631.4	179	aCg/aTg	2/12	0.290185620099015	5	FACETS	0.669	0.575	0.772	0.223	0.191	0.258	SUBCLONAL	1	TRUE	2	0.290185620099015	5		700	887	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30046511	30046511	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs45582934	NA	P-0016054-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	310	744	53	ENST00000331968.5:c.2672A>G	p.His891Arg	p.H891R	ENST00000331968	NM_002742.2	891	cAc/cGc	18/18	0.246769190913406	4	FACETS	1	0.974	1			1	CLONAL	3	TRUE	NA	0.290185620099015	4		797	877	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38272410	38272410	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121909628	NA	P-0016054-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	73	526	0	ENST00000425967.3:c.1957C>T	p.Arg653Ter	p.R653*	ENST00000425967	NM_001174067.1	653	Cga/Tga	15/19	0.286325885731312	2	FACETS	0.85	0.744	0.964	0.425	0.372	0.482	CLONAL	1	TRUE	0	0.290185620099015	2		526	592	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45422926	45422926	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016054-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	76	514	0	ENST00000262160.6:c.202C>T	p.Gln68Ter	p.Q68*	ENST00000262160	NM_005901.5	68	Caa/Taa	2/11	0.190877681013201	3	FACETS	0.84	0.742	0.944	0.56	0.494	0.63	CLONAL	2	TRUE	0	0.290185620099015	3		514	357	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392173	81392173	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016054-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	17	214	0	ENST00000222390.5:c.104G>C	p.Arg35Thr	p.R35T	ENST00000222390	NM_000601.4	35	aGa/aCa	2/18	0.290185620099015	5	FACETS	0.904	0.686	1	0.603	0.457	0.769	CLONAL	2	TRUE	2	0.290185620099015	5		214	93	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226125	53226125	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016054-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	123	889	0	ENST00000375401.3:c.2724del	p.Arg909GlyfsTer26	p.R909Gfs*26	ENST00000375401	NM_004187.3	908	ggG/gg	19/26	1	2	FACETS	0.887	0.801	0.978	0.887	0.801	0.978	CLONAL	1	TRUE	1	0.290185620099015	2		889	956	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783767	50783767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375455772	NA	P-0016054-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	56	764	0	ENST00000398568.2:c.158G>A	p.Arg53His	p.R53H	ENST00000398568	NM_001042412.1	53	cGt/cAt	3/18	0.290185620099015	3	FACETS	0.658	0.563	0.762	0.329	0.281	0.381	SUBCLONAL	1	TRUE	1	0.290185620099015	3		764	672	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180479	38180489	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCCGCGACG	GGGCCGCGACG	-	novel	NA	P-0016054-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	78	853	0	ENST00000396334.3:c.327_337del	p.Gly110ArgfsTer10	p.G110Rfs*10	ENST00000396334	NM_002468.4	109	ctGGGCCGCGACGac/ctac	1/5	0.290185620099015	3	FACETS	0.605	0.53	0.686	0.303	0.265	0.343	SUBCLONAL	1	TRUE	1	0.290185620099015	3		853	1017	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242470	55242487	+	inframe_deletion	In_Frame_Del	DEL	TAAGAGAAGCAACATCTC	TAAGAGAAGCAACATCTC	-	rs121913438	NA	P-0017326-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	44	606	0	ENST00000275493.2:c.2240_2257del	p.Leu747_Pro753delinsSer	p.L747_P753delinsS	ENST00000275493	NM_005228.3	747	tTAAGAGAAGCAACATCTCcg/tcg	19/28	1	2	FACETS	0.444	0.371	0.526	0.444	0.371	0.526	SUBCLONAL	1	TRUE	1	0.25	2		606	792	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032594	47032594	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017326-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	101	868	0	ENST00000377604.3:c.500del	p.Ser167Ter	p.S167*	ENST00000377604	NM_001204468.1	167	tCa/ta	5/24	0.236100110286569	1	FACETS	0.727	0.649	0.811	0.727	0.649	0.811	SUBCLONAL	1	TRUE	0	0.25	1		868	972	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0018410-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	60	479	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.722	0.624	0.828	0.722	0.624	0.828	SUBCLONAL	1	TRUE	1	0.395721257128728	2		480	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0018410-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	133	550	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.379004489312752	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.395721257128728	1		550	519	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971032	21971092	+	frameshift_variant	Frame_Shift_Del	DEL	GCATCGCGCACGTCCAGCCGCGCCCCGGCCCGGTGCAGCACCACCAGCGTGTCCAGGAAGC	GCATCGCGCACGTCCAGCCGCGCCCCGGCCCGGTGCAGCACCACCAGCGTGTCCAGGAAGC	TGG	novel	NA	P-0018410-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	85	495	3	ENST00000304494.5:c.266_326delinsCCA	p.Gly89AlafsTer38	p.G89Afs*38	ENST00000304494	NM_000077.4	89	gGCTTCCTGGACACGCTGGTGGTGCTGCACCGGGCCGGGGCGCGGCTGGACGTGCGCGATGCc/gCCAc	2/3	0.357488806280893	1	FACETS	0.921	0.82	1	0.921	0.82	1	CLONAL	1	TRUE	0	0.395721257128728	1		498	374	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579336	7579351	+	frameshift_variant	Frame_Shift_Del	DEL	CCCAGAATGCAAGAAG	CCCAGAATGCAAGAAG	-	novel	NA	P-0019042-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	621	844	1	ENST00000269305.4:c.336_351del	p.Phe113GlnfsTer5	p.F113Qfs*5	ENST00000269305	NM_001126112.2	112	ggCTTCTTGCATTCTGGG/gg	4/11	0.916127440348408	2	FACETS	0.964	0.949	0.978	0.964	0.949	0.978	CLONAL	2	TRUE	0	0.937524708694625	2		845	687	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30108080	30108080	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1239799730	NA	P-0019042-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	194	627	0	ENST00000331968.5:c.727C>T	p.Arg243Ter	p.R243*	ENST00000331968	NM_002742.2	243	Cga/Tga	5/18	0.323071789785217	5	FACETS	1	0.987	1	0.259	0.24	0.279	INDETERMINATE	1	TRUE	0	0.937524708694625	5		627	769	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502298	157502298	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0019042-T05-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	167	627	1	ENST00000346085.5:c.3331G>A	p.Gly1111Arg	p.G1111R	ENST00000346085	NM_020732.3	1111	Ggg/Agg	12/20	0.700247456066499	3	FACETS	0.619	0.569	0.671	0.309	0.284	0.336	SUBCLONAL	1	TRUE	1	0.937524708694625	3		628	846	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0020770-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	55	65	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.539907194883672	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.539907194883672	1		65	119	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28897002	28897002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554058758	NA	P-0020770-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	73	540	0	ENST00000282397.4:c.2878G>A	p.Val960Ile	p.V960I	ENST00000282397	NM_002019.4	960	Gtc/Atc	21/30	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.539907194883672	2		540	202	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658535	206658535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1281179215	NA	P-0020770-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	38	450	0	ENST00000367120.3:c.1508C>T	p.Ala503Val	p.A503V	ENST00000367120	NM_014002.3	503	gCg/gTg	15/22	0.462564959471357	3	FACETS	0.623	0.517	0.74	0.208	0.172	0.247	SUBCLONAL	1	TRUE	0	0.539907194883672	3		450	287	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060568	38060571	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	AGCT	AGCT	-	novel	NA	P-0020770-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	24	879	0	ENST00000250448.2:c.1418_*2del		p.*473*	ENST00000250448	NM_004496.3	473		2/2	1	2	FACETS	0.729	0.58	0.894	0.729	0.58	0.894	SUBCLONAL	1	TRUE	1	0.539907194883672	2		879	122	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467921	50467921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0020770-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	23	505	1	ENST00000331340.3:c.1156C>T	p.Arg386Cys	p.R386C	ENST00000331340	NM_006060.4	386	Cgc/Tgc	8/8	1	2	FACETS	0.536	0.421	0.665	0.536	0.421	0.665	SUBCLONAL	1	TRUE	1	0.539907194883672	2		506	159	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56882298	56882298	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0020770-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	69	536	0	ENST00000519728.1:c.996G>T	p.Lys332Asn	p.K332N	ENST00000519728	NM_002350.3	332	aaG/aaT	10/13	0.539907194883672	3	FACETS	0.78	0.691	0.873	0.78	0.691	0.873	SUBCLONAL	2	TRUE	1	0.539907194883672	3		536	208	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28586411	28586412	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0021422-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1101	63	441	0	ENST00000253063.3:c.54dup	p.Ala19ArgfsTer41	p.A19Rfs*41	ENST00000253063	NM_031459.4	18	ttc/ttCc	1/10	1	2	FACETS	0.404	0.348	0.465	0.404	0.348	0.465	SUBCLONAL	1	FALSE	1	0.267965255776569	2		441	1164	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022381	26022381	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0021422-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	92	369	0	ENST00000435504.4:c.276del	p.Glu93SerfsTer74	p.E93Sfs*74	ENST00000435504		92	aaA/aa	5/13	1	2	FACETS	0.689	0.611	0.773	0.689	0.611	0.773	SUBCLONAL	1	FALSE	1	0.267965255776569	2		369	996	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147514	47147514	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0021422-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	87	305	0	ENST00000409792.3:c.4812C>A	p.Tyr1604Ter	p.Y1604*	ENST00000409792	NM_014159.6	1604	taC/taA	6/21	0.267965255776569	1	FACETS	0.851	0.754	0.955	0.851	0.754	0.955	CLONAL	1	FALSE	0	0.267965255776569	1		305	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0021747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	178	191	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.387730940756209	1	FACETS	0.899	0.831	0.97	0.899	0.831	0.97	CLONAL	1	TRUE	0	0.431289483937912	1		191	720	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279631	123279866	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGAGGCATTTGCCGGCAGTCCGGCTTGGAGGATGGGCCGGTGAGGCGATCGCTCTGGTGGAGAGAGGGAAGAAAGGAGGAGTGGGGATGGGAGAATGAGAGACCAATAAATAAGCTGTGTTGTCCAGAGGGCTGTCAGTGACCTCATGCCAGAAAAGCCTCAAGCCTGCTGGCTGACACCTTTGAAATAACACTGTGGCCCCATGAATAACAGAAACGACTTCAAAGGAGACTGCC	GGAGGCATTTGCCGGCAGTCCGGCTTGGAGGATGGGCCGGTGAGGCGATCGCTCTGGTGGAGAGAGGGAAGAAAGGAGGAGTGGGGATGGGAGAATGAGAGACCAATAAATAAGCTGTGTTGTCCAGAGGGCTGTCAGTGACCTCATGCCAGAAAAGCCTCAAGCCTGCTGGCTGACACCTTTGAAATAACACTGTGGCCCCATGAATAACAGAAACGACTTCAAAGGAGACTGCC	-	novel	NA	P-0021747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	250	636	0	ENST00000358487.5:c.749-183_801del		p.X250_splice	ENST00000358487	NM_000141.4	250		7/18	0.403525669926204	2	FACETS	0.845	0.795	0.896	0.845	0.795	0.896	CLONAL	2	TRUE	0	0.431289483937912	2		636	686	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5214479	5214479	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0021747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	149	665	0	ENST00000357368.4:c.4507C>T	p.Gln1503Ter	p.Q1503*	ENST00000357368	NM_002850.3	1503	Cag/Tag	30/38	1	2	FACETS	0.823	0.752	0.897	0.823	0.752	0.897	CLONAL	1	TRUE	1	0.431289483937912	2		665	840	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023640	31023640	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0021747-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	225	802	0	ENST00000375687.4:c.3125C>A	p.Pro1042Gln	p.P1042Q	ENST00000375687	NM_015338.5	1042	cCa/cAa	13/13	1	2	FACETS	0.979	0.911	1	0.979	0.911	1	CLONAL	1	TRUE	1	0.431289483937912	2		802	1066	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0024270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	211	403	1	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.773788560439007	1	FACETS	0.995	0.946	1	0.995	0.946	1	CLONAL	1	TRUE	0	0.783787342115729	1		404	329	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0024270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	278	1099	2	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	1	2	FACETS	0.956	0.903	1	0.956	0.903	1	CLONAL	1	TRUE	1	0.783787342115729	2		1101	742	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0024270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	152	425	0	ENST00000349496.5:c.101G>A	p.Gly34Glu	p.G34E	ENST00000349496	NM_001904.3	34	gGa/gAa	3/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.783787342115729	2		425	367	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405948	49405948	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0024270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	233	786	0	ENST00000418115.1:c.190G>A	p.Glu64Lys	p.E64K	ENST00000418115	NM_001664.2	64	Gaa/Aaa	3/5	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.783787342115729	2		786	540	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692983	89692983	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0024270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	195	637	0	ENST00000371953.3:c.467G>T	p.Gly156Val	p.G156V	ENST00000371953	NM_000314.4	156	gGg/gTg	5/9	0.728299170325836	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.783787342115729	1		637	292	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525554	137525554	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	195	719	0	ENST00000367739.4:c.461G>C	p.Gly154Ala	p.G154A	ENST00000367739	NM_000416.2	154	gGa/gCa	4/7	1	2	FACETS	0.955	0.891	1	0.955	0.891	1	CLONAL	1	TRUE	1	0.783787342115729	2		719	521	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30107724	30107724	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	216	661	0	ENST00000331968.5:c.956A>G	p.Asn319Ser	p.N319S	ENST00000331968	NM_002742.2	319	aAc/aGc	6/18	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.783787342115729	2		661	537	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902539	1902539	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0024270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	189	917	0	ENST00000382891.5:c.158T>C	p.Leu53Pro	p.L53P	ENST00000382891	NM_133335.3	53	cTc/cCc	2/22	1	2	FACETS	0.768	0.713	0.824	0.768	0.713	0.824	SUBCLONAL	1	TRUE	1	0.783787342115729	2		917	628	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876454	35876454	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0024270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	168	807	0	ENST00000303115.3:c.1246C>G	p.Pro416Ala	p.P416A	ENST00000303115	NM_002185.3	416	Ccc/Gcc	8/8	1	2	FACETS	0.895	0.83	0.962	0.895	0.83	0.962	CLONAL	1	TRUE	1	0.783787342115729	2		807	479	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922288	39922289	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs886042842	NA	P-0024270-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	132	256	0	ENST00000378444.4:c.3883_3884del	p.Leu1296PhefsTer29	p.L1296Ffs*29	ENST00000378444	NM_001123385.1	1295	AGt/t	9/15	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.783787342115729	1		256	166	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0026136-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	45	357	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.751	0.631	0.884	0.751	0.631	0.884	SUBCLONAL	1	TRUE	1	0.23	2		357	521	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0026136-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	38	656	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	0.681	0.563	0.814	0.681	0.563	0.814	SUBCLONAL	1	TRUE	1	0.23	2		656	485	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122257	2122257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397515241	NA	P-0026136-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	56	529	0	ENST00000219476.3:c.2113G>A	p.Val705Met	p.V705M	ENST00000219476	NM_000548.3	705	Gtg/Atg	20/42	0.3	3	FACETS	0.604	0.516	0.701			1	SUBCLONAL	1	TRUE	NA	0.23	3		529	899	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968200	134968200	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143309901	NA	P-0026136-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	77	593	1	ENST00000398015.3:c.2713C>T	p.Arg905Cys	p.R905C	ENST00000398015	NM_004441.4	905	Cgc/Tgc	15/16	1	2	FACETS	0.988	0.867	1	0.988	0.867	1	CLONAL	1	TRUE	1	0.23	2		594	678	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730904	40730904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770182876	NA	P-0026136-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	43	652	0	ENST00000373198.4:c.3631G>A	p.Glu1211Lys	p.E1211K	ENST00000373198	NM_133170.3	1211	Gag/Aag	27/32	1	2	FACETS	0.504	0.42	0.597	0.504	0.42	0.597	SUBCLONAL	1	TRUE	1	0.23	2		652	742	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2137898	2137898	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45483392	NA	P-0026136-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	181	837	1	ENST00000219476.3:c.5024C>T	p.Pro1675Leu	p.P1675L	ENST00000219476	NM_000548.3	1675	cCg/cTg	39/42	0.3	3	FACETS	0.804	0.741	0.87			1	CLONAL	2	TRUE	NA	0.23	3		838	1091	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65323381	65323381	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0026136-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	95	565	0	ENST00000342505.4:c.1416T>G	p.Phe472Leu	p.F472L	ENST00000342505	NM_002227.2	472	ttT/ttG	10/25	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.23	2		565	739	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920731	96920731	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0026136-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	26	390	0	ENST00000258439.3:c.249C>G	p.Phe83Leu	p.F83L	ENST00000258439	NM_001193304.2	83	ttC/ttG	3/4	1	2	FACETS	0.436	0.344	0.541	0.436	0.344	0.541	SUBCLONAL	1	TRUE	1	0.23	2		390	519	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20402660	20402660	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0026136-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	111	598	0	ENST00000346618.3:c.198del	p.Thr67ProfsTer13	p.T67Pfs*13	ENST00000346618	NM_001949.4	66	tCc/tc	1/7	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.23	2		598	812	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056465	26056465	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0026136-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	30	282	0	ENST00000343677.2:c.192del	p.Ala65ArgfsTer24	p.A65Rfs*24	ENST00000343677	NM_005319.3	64	aaA/aa	1/1	1	2	FACETS	0.659	0.531	0.804	0.659	0.531	0.804	SUBCLONAL	1	TRUE	1	0.23	2		282	396	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0027316-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	164	302	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	0.286207792901387	2	FACETS	0.885	0.818	0.955	0.885	0.818	0.955	CLONAL	2	TRUE	0	0.34	2		302	545	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023289	27023290	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0027316-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	51	200	0	ENST00000324856.7:c.400dup	p.Ala134GlyfsTer266	p.A134Gfs*266	ENST00000324856	NM_006015.4	132	gtg/gtGg	1/20	1	2	FACETS	0.636	0.541	0.74	0.636	0.541	0.74	SUBCLONAL	1	TRUE	1	0.34	2		200	472	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218417	1218417	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0027316-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	125	625	0	ENST00000326873.7:c.292G>T	p.Glu98Ter	p.E98*	ENST00000326873	NM_000455.4	98	Gaa/Taa	2/10	1	2	FACETS	0.641	0.578	0.707	0.641	0.578	0.707	SUBCLONAL	1	TRUE	1	0.34	2		625	1148	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948409	71948409	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0027316-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1453	257	992	0	ENST00000298229.2:c.3121G>C	p.Asp1041His	p.D1041H	ENST00000298229	NM_001567.3	1041	Gat/Cat	26/28	1	2	FACETS	0.884	0.825	0.946	0.884	0.825	0.946	CLONAL	1	TRUE	1	0.34	2		992	1710	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100259	157100260	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1554248082	NA	P-0027316-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	36	127	0	ENST00000346085.5:c.1202dup	p.Phe402LeufsTer133	p.F402Lfs*133	ENST00000346085	NM_020732.3	399	gcg/gcGg	1/20	1	2	FACETS	0.638	0.526	0.763	0.638	0.526	0.763	SUBCLONAL	1	TRUE	1	0.34	2		127	332	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	190	492	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	1	2	FACETS	0.933	0.868	0.999	0.933	0.868	0.999	CLONAL	1	TRUE	1	0.7	2		492	582	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807525	36807525	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778434947	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	329	924	0	ENST00000373129.3:c.1139G>A	p.Arg380His	p.R380H	ENST00000373129	NM_032017.1	380	cGt/cAt	12/12	1	2	FACETS	0.983	0.932	1	0.983	0.932	1	CLONAL	1	TRUE	1	0.7	2		924	956	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023904	27023904	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1232964733	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	24	206	0	ENST00000324856.7:c.1015del	p.Ala339LeufsTer24	p.A339Lfs*24	ENST00000324856	NM_006015.4	337	tGg/tg	1/20	1	2	FACETS	0.396	0.313	0.491	0.396	0.313	0.491	SUBCLONAL	1	TRUE	1	0.7	2		206	173	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7978975	7978975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769562383	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	260	806	0	ENST00000319144.4:c.1592C>T	p.Pro531Leu	p.P531L	ENST00000319144	NM_001139.2	531	cCg/cTg	12/15	1	2	FACETS	0.981	0.923	1	0.981	0.923	1	CLONAL	1	TRUE	1	0.7	2		806	757	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022441	31022442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs750318549	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	148	451	4	ENST00000375687.4:c.1934dup	p.Gly646TrpfsTer12	p.G646Wfs*12	ENST00000375687	NM_015338.5	642	-/G	13/13	1	2	FACETS	0.859	0.791	0.931	0.859	0.791	0.931	CLONAL	1	TRUE	1	0.7	2		455	492	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	300	155	1	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	0.389631019521963	2	FACETS	0.969	0.915	1			1	INDETERMINATE	1	TRUE	NA	0.7	2		156	885	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030479	49030479	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	84	298	0	ENST00000267163.4:c.1959del	p.Val654CysfsTer4	p.V654Cfs*4	ENST00000267163	NM_000321.2	652	Aaa/aa	19/27	1	2	FACETS	0.463	0.41	0.52	0.463	0.41	0.52	SUBCLONAL	1	TRUE	1	0.7	2		298	518	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762959	40762959	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs387906659	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	49	738	0	ENST00000392038.2:c.49G>A	p.Glu17Lys	p.E17K	ENST00000392038	NM_001626.4	17	Gaa/Aaa	3/14	1	2	FACETS	0.177	0.149	0.208	0.177	0.149	0.208	SUBCLONAL	1	TRUE	1	0.7	2		738	791	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129008	64129008	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781669147	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	62	923	0	ENST00000334205.4:c.638C>T	p.Thr213Met	p.T213M	ENST00000334205	NM_003942.2	213	aCg/aTg	6/17	1	2	FACETS	0.189	0.163	0.218	0.189	0.163	0.218	SUBCLONAL	1	TRUE	1	0.7	2		923	936	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16021323	16021323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	150	239	0	ENST00000268712.3:c.1934G>A	p.Arg645His	p.R645H	ENST00000268712	NM_006311.3	645	cGt/cAt	18/46	1	2	FACETS	0.948	0.874	1	0.948	0.874	1	CLONAL	1	TRUE	1	0.7	2		239	452	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7174633	7174633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs72549237	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	294	928	0	ENST00000302850.5:c.1084G>A	p.Val362Ile	p.V362I	ENST00000302850	NM_000208.2	362	Gtc/Atc	4/22	1	2	FACETS	0.9	0.849	0.952	0.9	0.849	0.952	CLONAL	1	TRUE	1	0.7	2		928	933	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100176	27100176	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	119	697	0	ENST00000324856.7:c.3977del	p.Pro1326ArgfsTer155	p.P1326Rfs*155	ENST00000324856	NM_006015.4	1324	taC/ta	16/20	1	2	FACETS	0.454	0.41	0.501	0.454	0.41	0.501	SUBCLONAL	1	TRUE	1	0.7	2		697	749	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351422	70351422	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	316	493	2	ENST00000374080.3:c.4070G>A	p.Arg1357His	p.R1357H	ENST00000374080		1357	cGc/cAc	29/45	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.7	1		495	457	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209357	98209357	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748812637	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	318	920	0	ENST00000331920.6:c.4181G>A	p.Arg1394Gln	p.R1394Q	ENST00000331920	NM_000264.3	1394	cGa/cAa	23/24	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.7	2		920	899	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625159	69625159	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554980306	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	323	1075	2	ENST00000334134.2:c.634C>T	p.Arg212Trp	p.R212W	ENST00000334134	NM_005247.2	212	Cgg/Tgg	3/3	1	2	FACETS	0.948	0.898	1	0.948	0.898	1	CLONAL	1	TRUE	1	0.7	2		1077	973	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881111	37881111	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778267	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	387	1025	0	ENST00000269571.5:c.2440C>T	p.Arg814Cys	p.R814C	ENST00000269571		814	Cgc/Tgc	20/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.7	2		1025	1051	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156729	106156729	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1440692352	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	119	636	1	ENST00000380013.4:c.1630C>T	p.Arg544Ter	p.R544*	ENST00000380013	NM_001127208.2	544	Cga/Tga	3/11	1	2	FACETS	0.491	0.444	0.541	0.491	0.444	0.541	SUBCLONAL	1	TRUE	1	0.7	2		637	692	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944548	38944548	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs925027853	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	179	151	0	ENST00000357387.3:c.4913C>T	p.Thr1638Ile	p.T1638I	ENST00000357387	NM_152756.3	1638	aCa/aTa	36/38	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.7	2		151	470	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432651	49432651	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs727503983	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	357	1074	1	ENST00000301067.7:c.8488C>T	p.Arg2830Ter	p.R2830*	ENST00000301067	NM_003482.3	2830	Cga/Tga	34/54	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.7	2		1075	993	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991697	72991699	+	inframe_deletion	In_Frame_Del	DEL	GCC	GCC	-	rs757316139	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	213	568	7	ENST00000268489.5:c.2346_2348del	p.Ala784del	p.A784del	ENST00000268489	NM_006885.3	782	gcGGCa/gca	2/10	1	2	FACETS	0.958	0.896	1	0.958	0.896	1	CLONAL	1	TRUE	1	0.7	2		575	635	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62294212	62294212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866785110	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	300	902	1	ENST00000360203.5:c.508C>T	p.Arg170Cys	p.R170C	ENST00000360203	NM_001283009.1	170	Cgc/Tgc	6/35	1	2	FACETS	0.94	0.888	0.993	0.94	0.888	0.993	CLONAL	1	TRUE	1	0.7	2		903	912	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41267002	41267002	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	217	600	0	ENST00000349496.5:c.673C>T	p.Arg225Cys	p.R225C	ENST00000349496	NM_001904.3	225	Cgt/Tgt	5/15	1	2	FACETS	0.978	0.915	1	0.978	0.915	1	CLONAL	1	TRUE	1	0.7	2		600	634	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874148	151874148	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs747256476	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	454	262	8	ENST00000262189.6:c.8390del	p.Lys2797ArgfsTer26	p.K2797Rfs*26	ENST00000262189	NM_170606.2	2797	aAg/ag	38/59	1	2	FACETS	0.907	0.876	0.938	1	0.997	1	CLONAL	2	TRUE	1	0.7	2		270	715	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455118	50455118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200163039	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	201	501	1	ENST00000331340.3:c.665G>A	p.Arg222His	p.R222H	ENST00000331340	NM_006060.4	222	cGc/cAc	6/8	1	2	FACETS	0.934	0.87	0.999	0.934	0.87	0.999	CLONAL	1	TRUE	1	0.7	2		502	615	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420607	49420607	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123724	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	352	926	1	ENST00000301067.7:c.15142C>T	p.Arg5048Cys	p.R5048C	ENST00000301067	NM_003482.3	5048	Cgt/Tgt	48/54	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.7	2		927	957	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635695	47635695	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs267607924	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	179	227	0	ENST00000233146.2:c.366+1G>T		p.X122_splice	ENST00000233146	NM_000251.2	122			1	2	FACETS	0.951	0.883	1	0.951	0.883	1	CLONAL	1	TRUE	1	0.7	2		227	538	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721772	176721772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587784217	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	283	695	2	ENST00000439151.2:c.7403G>A	p.Arg2468Gln	p.R2468Q	ENST00000439151	NM_022455.4	2468	cGg/cAg	23/23	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.7	2		697	780	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994778	73994778	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11574476	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	304	986	1	ENST00000318443.5:c.262G>A	p.Ala88Thr	p.A88T	ENST00000318443	NM_001024736.1	88	Gcc/Acc	3/10	1	2	FACETS	0.992	0.937	1	0.992	0.937	1	CLONAL	1	TRUE	1	0.7	2		987	876	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427772	72427772	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	172	454	0	ENST00000477973.2:c.718G>A	p.Val240Met	p.V240M	ENST00000477973	NM_012234.5	240	Gtg/Atg	4/4	1	2	FACETS	0.991	0.919	1	0.991	0.919	1	CLONAL	1	TRUE	1	0.7	2		454	496	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902158	50902158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373637566	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	319	1011	1	ENST00000440232.2:c.50G>A	p.Arg17Gln	p.R17Q	ENST00000440232	NM_002691.3	17	cGg/cAg	2/27	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.7	2		1012	883	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638455	176638455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1460977537	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	335	941	1	ENST00000439151.2:c.3055C>T	p.Arg1019Cys	p.R1019C	ENST00000439151	NM_022455.4	1019	Cgc/Tgc	5/23	1	2	FACETS	0.938	0.889	0.989	0.938	0.889	0.989	CLONAL	1	TRUE	1	0.7	2		942	1020	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3794922	3794922	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555475250	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	196	390	1	ENST00000262367.5:c.3955C>T	p.Arg1319Ter	p.R1319*	ENST00000262367	NM_004380.2	1319	Cga/Tga	23/31	1	2	FACETS	0.903	0.841	0.967	0.903	0.841	0.967	CLONAL	1	TRUE	1	0.7	2		391	620	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572248	64572248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778728934	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	310	874	4	ENST00000312049.6:c.1391C>T	p.Ala464Val	p.A464V	ENST00000312049	NM_130799.2	464	gCg/gTg	10/10	1	2	FACETS	0.979	0.926	1	0.979	0.926	1	CLONAL	1	TRUE	1	0.7	2		878	905	SUCCESS
APC	324	MSKCC	GRCh37	5	112102982	112102982	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201764637	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	173	574	0	ENST00000257430.4:c.317G>A	p.Arg106His	p.R106H	ENST00000257430	NM_000038.5	106	cGt/cAt	4/16	1	2	FACETS	0.809	0.748	0.872	0.809	0.748	0.872	CLONAL	1	TRUE	1	0.7	2		574	611	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466299	120466299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372710038	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	55	651	0	ENST00000256646.2:c.4820G>A	p.Arg1607His	p.R1607H	ENST00000256646	NM_024408.3	1607	cGc/cAc	26/34	1	2	FACETS	0.218	0.186	0.254	0.218	0.186	0.254	SUBCLONAL	1	TRUE	1	0.7	2		651	720	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77090986	77090986	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	192	506	0	ENST00000356341.3:c.244G>C	p.Glu82Gln	p.E82Q	ENST00000356341	NM_002576.4	82	Gaa/Caa	3/15	1	2	FACETS	0.847	0.787	0.908	0.847	0.787	0.908	CLONAL	1	TRUE	1	0.7	2		506	648	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617406	158617406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1366850999	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	210	543	1	ENST00000263640.3:c.1250G>A	p.Arg417Gln	p.R417Q	ENST00000263640	NM_001105.4	417	cGg/cAg	9/11	0.389631019521963	2	FACETS	0.949	0.887	1			1	INDETERMINATE	1	TRUE	NA	0.7	2		544	632	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655382	45655382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749547790	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	348	1097	3	ENST00000407780.3:c.470C>T	p.Thr157Met	p.T157M	ENST00000407780	NM_001283052.1	157	aCg/aTg	4/7	1	2	FACETS	0.925	0.877	0.974	0.925	0.877	0.974	CLONAL	1	TRUE	1	0.7	2		1100	1075	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539471	187539474	+	frameshift_variant	Frame_Shift_Del	DEL	TCTG	TCTG	-	rs1199646858	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	181	471	0	ENST00000441802.2:c.8266_8269del	p.Gln2756AlafsTer4	p.Q2756Afs*4	ENST00000441802	NM_005245.3	2756	CAGAgc/gc	10/27	1	2	FACETS	0.917	0.851	0.984	0.917	0.851	0.984	CLONAL	1	TRUE	1	0.7	2		471	564	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540088	187540092	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGT	AAAGT	-	novel	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	208	494	0	ENST00000441802.2:c.7648_7652del	p.Thr2550GlyfsTer4	p.T2550Gfs*4	ENST00000441802	NM_005245.3	2550	ACTTTg/g	10/27	1	2	FACETS	0.957	0.894	1	0.957	0.894	1	CLONAL	1	TRUE	1	0.7	2		494	621	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505387	157505387	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1240545481	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	271	616	0	ENST00000346085.5:c.3368G>A	p.Arg1123His	p.R1123H	ENST00000346085	NM_020732.3	1123	cGt/cAt	13/20	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.7	2		616	773	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776931	76776934	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	novel	NA	P-0030383-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	199	159	0	ENST00000373344.5:c.7018_7021del	p.Asn2340ValfsTer2	p.N2340Vfs*2	ENST00000373344	NM_000489.3	2340	AACAgt/gt	33/35	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.7	1		159	322	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0030728-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	176	275	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.80927547863355	2	FACETS	1	0.973	1	0.541	0.505	0.578	CLONAL	1	FALSE	0	0.806966325351462	2		275	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577568	7577568	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs730882005	NA	P-0030728-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	737	185	0	ENST00000269305.4:c.713G>T	p.Cys238Phe	p.C238F	ENST00000269305	NM_001126112.2	238	tGt/tTt	7/11	0.806149318597017	3	FACETS	0.972	0.954	0.989	0.972	0.954	0.989	CLONAL	3	FALSE	0	0.806966325351462	3		185	879	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273278	55273278	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369585356	NA	P-0030728-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	228	531	1	ENST00000275493.2:c.3601G>A	p.Ala1201Thr	p.A1201T	ENST00000275493	NM_005228.3	1201	Gcg/Acg	28/28	0.763338110581125	4	FACETS	1	0.94	1			1	CLONAL	1	FALSE	NA	0.806966325351462	4		532	1012	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261243	16261243	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030728-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	276	489	0	ENST00000375759.3:c.8508G>C	p.Gln2836His	p.Q2836H	ENST00000375759	NM_015001.2	2836	caG/caC	11/15	0.80927547863355	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	0	0.806966325351462	1		489	394	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965122	15965122	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0030728-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	166	349	0	ENST00000268712.3:c.5474T>C	p.Val1825Ala	p.V1825A	ENST00000268712	NM_006311.3	1825	gTg/gCg	37/46	0.694597962315989	3	FACETS	0.979	0.904	1			1	CLONAL	1	FALSE	NA	0.806966325351462	3		349	590	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19261517	19261518	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	-	novel	NA	P-0030728-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	254	613	0	ENST00000162023.5:c.27_28del	p.Arg10HisfsTer24	p.R10Hfs*24	ENST00000162023		9	tcCCgc/tcgc	6/13	0.441793361076838	3	FACETS	0.871	0.816	0.928	0.436	0.408	0.464	INDETERMINATE	1	FALSE	1	0.806966325351462	3		613	1014	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460396	149460396	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0030728-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	261	658	0	ENST00000286301.3:c.241A>T	p.Thr81Ser	p.T81S	ENST00000286301	NM_005211.3	81	Acc/Tcc	3/22	0.80927547863355	2	FACETS	0.958	0.904	1	0.479	0.452	0.507	CLONAL	1	FALSE	0	0.806966325351462	2		658	675	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044916	47044916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030728-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1300	362	893	1	ENST00000377604.3:c.2242G>A	p.Glu748Lys	p.E748K	ENST00000377604	NM_001204468.1	748	Gag/Aag	20/24	0.6889885271244	4	FACETS	0.975	0.922	1			1	CLONAL	1	FALSE	NA	0.806966325351462	4		894	1662	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649102	37649102	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030728-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	138	437	1	ENST00000447079.4:c.2207G>A	p.Gly736Glu	p.G736E	ENST00000447079	NM_015083.1	736	gGa/gAa	4/14	0.332679281622345	6	FACETS	0.974	0.886	1	0.325	0.295	0.356	INDETERMINATE	1	FALSE	3	0.806966325351462	6		438	918	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59886060	59886060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0030728-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	221	412	0	ENST00000259008.2:c.686C>T	p.Ser229Leu	p.S229L	ENST00000259008	NM_032043.2	229	tCa/tTa	7/20	0.694597962315989	3	FACETS	0.961	0.897	1			1	CLONAL	1	FALSE	NA	0.806966325351462	3		412	800	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117569	70117569	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0030728-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	287	586	0	ENST00000245479.2:c.37G>C	p.Glu13Gln	p.E13Q	ENST00000245479	NM_000346.3	13	Gag/Cag	1/3	0.80927547863355	4	FACETS	0.974	0.914	1	0.325	0.304	0.345	CLONAL	1	FALSE	1	0.806966325351462	4		586	1320	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374741	118374741	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0030953-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	213	400	0	ENST00000534358.1:c.8134T>C	p.Cys2712Arg	p.C2712R	ENST00000534358	NM_005933.3	2712	Tgt/Cgt	27/36	0.372465557022368	2	FACETS	0.877	0.82	0.935	0.877	0.82	0.935	CLONAL	2	FALSE	0	0.398954992426058	2		400	609	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555632	21555636	+	frameshift_variant	Frame_Shift_Del	DEL	TGTAG	TGTAG	-	novel	NA	P-0030953-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	301	732	0	ENST00000382592.4:c.2634_2638del	p.Tyr879ArgfsTer15	p.Y879Rfs*15	ENST00000382592	NM_014572.2	878	aaCTACAtc/aatc	6/8	0.391280024540498	2	FACETS	0.873	0.825	0.922	0.873	0.825	0.922	CLONAL	2	FALSE	0	0.398954992426058	2		732	864	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89866048	89866048	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0030953-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	83	422	0	ENST00000389301.3:c.793-2A>T		p.X265_splice	ENST00000389301	NM_000135.2	265			0.372465557022368	2	FACETS	0.674	0.596	0.759	0.337	0.298	0.38	SUBCLONAL	1	FALSE	0	0.398954992426058	2		422	617	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573806	41573806	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs199650847	NA	P-0030953-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	605	946	0	ENST00000263253.7:c.6091C>G	p.Pro2031Ala	p.P2031A	ENST00000263253	NM_001429.3	2031	Cca/Gca	31/31	0.380312651257312	3	FACETS	0.935	0.902	0.968	0.935	0.902	0.968	CLONAL	3	FALSE	0	0.398954992426058	3		946	1297	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64126900	64126900	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0030953-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	173	846	0	ENST00000334205.4:c.106C>A	p.Leu36Ile	p.L36I	ENST00000334205	NM_003942.2	36	Ctc/Atc	2/17	0.389736361547317	3	FACETS	0.942	0.866	1	0.471	0.433	0.511	CLONAL	1	FALSE	1	0.398954992426058	3		846	1104	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125507439	125507439	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0030953-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	67	265	0	ENST00000428830.2:c.814+1del		p.G272fs	ENST00000428830	NM_001114121.2	272	Ggg/gg	8/14	0.372465557022368	2	FACETS	0.829	0.724	0.943	0.415	0.362	0.472	CLONAL	1	FALSE	0	0.398954992426058	2		265	405	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517895	8517895	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0030953-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	76	398	0	ENST00000356435.5:c.1496G>C	p.Gly499Ala	p.G499A	ENST00000356435		499	gGa/gCa	10/35	0.372465557022368	2	FACETS	0.834	0.734	0.94	0.417	0.367	0.47	CLONAL	1	FALSE	0	0.398954992426058	2		398	457	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98224203	98224203	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0030953-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	108	415	0	ENST00000331920.6:c.2638G>T	p.Gly880Ter	p.G880*	ENST00000331920	NM_000264.3	880	Gga/Tga	16/24	0.192964796526302	5	FACETS	1	0.949	1			1	INDETERMINATE	1	FALSE	NA	0.398954992426058	5		415	791	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483953	212483953	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0031597-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	71	495	0	ENST00000342788.4:c.2250del	p.Lys751ArgfsTer20	p.K751Rfs*20	ENST00000342788	NM_005235.2	750	atT/at	19/28	1	2	FACETS	0.987	0.86	1	0.987	0.86	1	CLONAL	1	TRUE	1	0.17	2		495	846	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668751	52668751	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0031597-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	38	474	0	ENST00000394830.3:c.1168T>A	p.Tyr390Asn	p.Y390N	ENST00000394830	NM_018313.4	390	Tat/Aat	12/30	1	2	FACETS	0.56	0.461	0.671	0.56	0.461	0.671	SUBCLONAL	1	TRUE	1	0.17	2		474	798	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243870	53243870	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0031597-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	73	347	0	ENST00000375401.3:c.1122+1G>T		p.X374_splice	ENST00000375401	NM_004187.3	374			1	1	FACETS	0.877	0.77	0.992	1	0.98	1	CLONAL	2	TRUE	0	0.17	1		347	448	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0032175-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	236	262	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.546036631669538	5	FACETS	1	0.985	1	0.766	0.719	0.815	CLONAL	2	TRUE	2	0.546036631669538	5		262	684	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0032175-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	187	291	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.546036631669538	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.546036631669538	2		292	311	SUCCESS
APC	324	MSKCC	GRCh37	5	112174096	112174096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs137854575	NA	P-0032175-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	57	342	0	ENST00000257430.4:c.2805C>A	p.Tyr935Ter	p.Y935*	ENST00000257430	NM_000038.5	935	taC/taA	16/16	0.313636855842317	2	FACETS	0.985	0.857	1	0.492	0.428	0.56	INDETERMINATE	1	TRUE	0	0.546036631669538	2		342	212	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913351	NA	P-0032829-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	15	469	0	ENST00000288602.6:c.1397G>A	p.Gly466Glu	p.G466E	ENST00000288602	NM_004333.4	466	gGa/gAa	11/18	1	2	FACETS	0.761	0.562	0.996	0.761	0.562	0.996	CLONAL	1	TRUE	1	0.32305978962009	2		469	122	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41274911	41274911	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs868651538	NA	P-0032829-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	52	467	1	ENST00000349496.5:c.1161T>A	p.Asn387Lys	p.N387K	ENST00000349496	NM_001904.3	387	aaT/aaA	8/15	0.27016066086145	2	FACETS	0.843	0.728	0.964	0.843	0.728	0.964	CLONAL	2	TRUE	0	0.32305978962009	2		468	191	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105581	27105582	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0032829-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	52	740	1	ENST00000324856.7:c.5195dup	p.Glu1733GlyfsTer3	p.E1733Gfs*3	ENST00000324856	NM_006015.4	1731	tta/ttAa	20/20	0.32305978962009	4	FACETS	0.884	0.753	1			1	CLONAL	1	TRUE	NA	0.32305978962009	4		741	482	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971099	21971103	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCA	GGGCA	-	novel	NA	P-0032829-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	73	333	0	ENST00000304494.5:c.255_259del	p.Ala86GlyfsTer32	p.A86Gfs*32	ENST00000304494	NM_000077.4	85	gcTGCCCgg/gcgg	2/3	0.32305978962009	1	FACETS	0.761	0.674	0.851	1	0.978	1	SUBCLONAL	2	TRUE	0	0.32305978962009	1		333	249	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117757	115117757	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0032829-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	20	451	0	ENST00000257566.3:c.678T>A	p.Asp226Glu	p.D226E	ENST00000257566	NM_016569.3	226	gaT/gaA	3/8	1	2	FACETS	0.527	0.404	0.67	0.527	0.404	0.67	SUBCLONAL	1	TRUE	1	0.32305978962009	2		451	235	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593445	48593445	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0032829-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	39	434	0	ENST00000342988.3:c.1196T>A	p.Val399Asp	p.V399D	ENST00000342988	NM_005359.5	399	gTc/gAc	10/12	0.196985795298323	2	FACETS	0.958	0.799	1	0.479	0.399	0.566	CLONAL	1	TRUE	0	0.32305978962009	2		434	252	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577574	7577574	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs730882026	NA	P-0033300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	149	264	2	ENST00000269305.4:c.707A>G	p.Tyr236Cys	p.Y236C	ENST00000269305	NM_001126112.2	236	tAc/tGc	7/11	0.249315699991223	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.249315699991223	1		266	840	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61710176	61710177	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0033300-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	68	360	0	ENST00000401558.2:c.2726_2727dup	p.Ala910LeufsTer22	p.A910Lfs*22	ENST00000401558	NM_003400.3	909	-/CT	22/25	1	2	FACETS	0.828	0.72	0.945	0.828	0.72	0.945	CLONAL	1	TRUE	1	0.249315699991223	2		360	659	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806092	1806092	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913484	NA	P-0033799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	82	795	0	ENST00000260795.2:c.1111A>T	p.Ser371Cys	p.S371C	ENST00000260795		371	Agt/Tgt	8/17	1	2	FACETS	0.521	0.46	0.587	0.521	0.46	0.587	SUBCLONAL	1	TRUE	1	0.558717909751233	2		795	563	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397742	49397742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11552757	NA	P-0033799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	118	439	0	ENST00000418115.1:c.482C>T	p.Ala161Val	p.A161V	ENST00000418115	NM_001664.2	161	gCa/gTa	5/5	1	2	FACETS	0.862	0.782	0.946	0.862	0.782	0.946	CLONAL	1	TRUE	1	0.558717909751233	2		439	490	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521253	187521253	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	140	535	0	ENST00000441802.2:c.11902C>T	p.Gln3968Ter	p.Q3968*	ENST00000441802	NM_005245.3	3968	Caa/Taa	22/27	0.514310225114226	1	FACETS	0.943	0.869	1	0.943	0.869	1	CLONAL	1	TRUE	0	0.558717909751233	1		535	383	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216899	7216899	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0033799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	119	511	1	ENST00000380728.2:c.622C>T	p.Gln208Ter	p.Q208*	ENST00000380728		208	Cag/Tag	7/11	1	2	FACETS	0.962	0.874	1	0.962	0.874	1	CLONAL	1	TRUE	1	0.558717909751233	2		512	443	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056181	27056181	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	210	515	0	ENST00000324856.7:c.1177C>T	p.Gln393Ter	p.Q393*	ENST00000324856	NM_006015.4	393	Cag/Tag	2/20	0.221590975676785	2	FACETS	1	0.992	1	0.724	0.679	0.77	INDETERMINATE	1	TRUE	0	0.558717909751233	2		515	519	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118354897	118354897	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0033799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	93	277	0	ENST00000534358.1:c.4087-1G>A		p.X1363_splice	ENST00000534358	NM_005933.3	1363			0.233271305920693	2	FACETS	0.951	0.853	1	0.476	0.426	0.527	INDETERMINATE	1	TRUE	0	0.558717909751233	2		277	350	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807967	3807967	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	77	475	0	ENST00000262367.5:c.3452G>A	p.Trp1151Ter	p.W1151*	ENST00000262367	NM_004380.2	1151	tGg/tAg	18/31	0.319773019683556	1	FACETS	0.415	0.365	0.468	0.415	0.365	0.468	INDETERMINATE	1	TRUE	0	0.558717909751233	1		475	479	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56401603	56401603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0033799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	41	256	0	ENST00000348428.3:c.1465G>A	p.Gly489Arg	p.G489R	ENST00000348428	NM_006785.3	489	Gga/Aga	12/17	0.308730339535721	1	FACETS	0.366	0.306	0.432	0.366	0.306	0.432	INDETERMINATE	1	TRUE	0	0.558717909751233	1		256	289	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513814	41513814	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	140	448	1	ENST00000263253.7:c.718C>T	p.Gln240Ter	p.Q240*	ENST00000263253	NM_001429.3	240	Cag/Tag	2/31	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.558717909751233	2		449	500	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659164	86659164	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0033799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	14	49	0	ENST00000274376.6:c.1454-1G>A		p.X485_splice	ENST00000274376	NM_002890.2	485			0.295120090029852	1	FACETS	0.573	0.425	0.743	0.573	0.425	0.743	INDETERMINATE	1	TRUE	0	0.558717909751233	1		49	63	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138913	37138913	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0033799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	148	517	0	ENST00000373509.5:c.253C>T	p.Arg85Ter	p.R85*	ENST00000373509	NM_002648.3	85	Cga/Tga	4/6	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.558717909751233	2		517	494	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918645	44918646	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AATGC	novel	NA	P-0033799-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	97	185	0	ENST00000377967.4:c.1131_1135dup	p.Thr379MetfsTer62	p.T379Mfs*62	ENST00000377967	NM_021140.2	376	-/AATGC	12/29	1	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.558717909751233	1		185	230	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061334	38061334	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0034921-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	114	734	0	ENST00000250448.2:c.655C>A	p.Arg219Ser	p.R219S	ENST00000250448	NM_004496.3	219	Cgc/Agc	2/2	1	2	FACETS	0.848	0.762	0.94	0.848	0.762	0.94	CLONAL	1	TRUE	1	0.248860511082899	2		734	1080	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307243	118307243	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555138451	NA	P-0034921-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	30	230	0	ENST00000534358.1:c.16C>T	p.Arg6Trp	p.R6W	ENST00000534358	NM_005933.3	6	Cgg/Tgg	1/36	1	2	FACETS	0.765	0.618	0.932	0.765	0.618	0.932	CLONAL	1	TRUE	1	0.248860511082899	2		230	315	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051240	13051240	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs938433963	NA	P-0034921-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	56	513	0	ENST00000316448.5:c.676G>C	p.Asp226His	p.D226H	ENST00000316448	NM_004343.3	226	Gat/Cat	5/9	1	2	FACETS	0.669	0.572	0.775	0.669	0.572	0.775	SUBCLONAL	1	TRUE	1	0.248860511082899	2		513	673	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0035636-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	102	422	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		422	857	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148875	119148875	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	rs397517076	NA	P-0035890-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	180	289	0	ENST00000264033.4:c.1096-1G>T		p.X366_splice	ENST00000264033	NM_005188.3	366			0.397299053050209	3	FACETS	0.971	0.909	1	0.971	0.909	1	CLONAL	3	TRUE	0	0.405078018394928	3		289	367	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172434	108172434	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs879254135	NA	P-0035890-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	251	473	1	ENST00000278616.4:c.5237G>T	p.Gly1746Val	p.G1746V	ENST00000278616	NM_000051.3	1746	gGa/gTa	35/63	0.397299053050209	3	FACETS	1	0.99	1	0.828	0.781	0.876	CLONAL	2	TRUE	0	0.405078018394928	3		474	600	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17127420	17127420	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035890-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	203	720	0	ENST00000285071.4:c.434A>T	p.Asp145Val	p.D145V	ENST00000285071	NM_144997.5	145	gAt/gTt	6/14	0.405078018394928	3	FACETS	1	0.982	1	0.589	0.545	0.633	CLONAL	1	TRUE	1	0.405078018394928	3		720	1024	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709162	117709162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867987684	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	177	263	0	ENST00000368508.3:c.1795G>A	p.Glu599Lys	p.E599K	ENST00000368508	NM_002944.2	599	Gaa/Aaa	13/43	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	FALSE	1	0.582308072230216	2		263	591	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40743950	40743950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781527200	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	335	433	0	ENST00000392038.2:c.757C>T	p.Arg253Trp	p.R253W	ENST00000392038	NM_001626.4	253	Cgg/Tgg	9/14	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.582308072230216	2		433	1129	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453145	140453145	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913366	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	368	469	0	ENST00000288602.6:c.1790T>G	p.Leu597Arg	p.L597R	ENST00000288602	NM_004333.4	597	cTa/cGa	15/18	0.582308072230216	2	FACETS	0.935	0.896	0.974	0.935	0.896	0.974	CLONAL	2	FALSE	0	0.582308072230216	2		469	676	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578554	7578554	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	rs886039483	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	328	821	0	ENST00000269305.4:c.376T>G	p.Tyr126Asp	p.Y126D	ENST00000269305	NM_001126112.2	126	Tac/Gac	5/11	0.582308072230216	1	FACETS	0.954	0.906	1	0.954	0.906	1	CLONAL	1	FALSE	0	0.582308072230216	1		821	837	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923335	9923335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	260	681	0	ENST00000330684.3:c.1952C>T	p.Ala651Val	p.A651V	ENST00000330684	NM_001134407.1	651	gCc/gTc	9/13	1	2	FACETS	0.996	0.935	1	0.996	0.935	1	CLONAL	1	FALSE	1	0.582308072230216	2		681	897	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285682	46285682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	230	505	0	ENST00000334344.6:c.5042C>T	p.Ser1681Phe	p.S1681F	ENST00000334344	NM_152641.2	1681	tCt/tTt	17/21	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.582308072230216	2		505	771	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962858	2962858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	353	932	0	ENST00000396946.4:c.2050G>A	p.Gly684Arg	p.G684R	ENST00000396946	NM_032415.4	684	Ggg/Agg	16/25	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.582308072230216	2		932	1185	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411267	63411267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866313799	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	330	816	0	ENST00000330258.3:c.1900C>T	p.Arg634Cys	p.R634C	ENST00000330258	NM_152424.3	634	Cgt/Tgt	2/2	0.582308072230216	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	0	0.582308072230216	1		816	794	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312713	91312713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1279814185	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	196	435	0	ENST00000355112.3:c.2452C>T	p.Arg818Cys	p.R818C	ENST00000355112	NM_000057.2	818	Cgc/Tgc	12/22	1	2	FACETS	0.886	0.822	0.951	0.886	0.822	0.951	CLONAL	1	FALSE	1	0.582308072230216	2		435	760	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576880	212576880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	230	490	0	ENST00000342788.4:c.1019G>A	p.Gly340Glu	p.G340E	ENST00000342788	NM_005235.2	340	gGa/gAa	9/28	0.531249513214774	2	FACETS	0.765	0.721	0.81	0.765	0.721	0.81	SUBCLONAL	2	FALSE	0	0.582308072230216	2		490	516	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284946	15284946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	730	920	1	ENST00000263388.2:c.4669C>T	p.Pro1557Ser	p.P1557S	ENST00000263388	NM_000435.2	1557	Cct/Tct	25/33	0.261345051575667	3	FACETS	1	0.981	1			1	INDETERMINATE	2	FALSE	NA	0.582308072230216	3		921	1589	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964429	55964429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747827262	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	178	521	0	ENST00000263923.4:c.2384G>A	p.Gly795Glu	p.G795E	ENST00000263923	NM_002253.2	795	gGg/gAg	17/30	1	2	FACETS	0.776	0.716	0.838	0.776	0.716	0.838	SUBCLONAL	1	FALSE	1	0.582308072230216	2		521	788	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509774	106509774	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	567	667	0	ENST00000359195.3:c.1768C>T	p.Pro590Ser	p.P590S	ENST00000359195	NM_002649.2	590	Cct/Tct	2/11	0.582308072230216	2	FACETS	0.985	0.952	1	0.985	0.952	1	CLONAL	2	FALSE	0	0.582308072230216	2		667	989	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970900	21970900	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	377	905	0	ENST00000304494.5:c.457+1G>A		p.X153_splice	ENST00000304494	NM_000077.4	153			0.582308072230216	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	0	0.582308072230216	1		905	866	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93968002	93968002	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs766856886	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	131	424	0	ENST00000369303.4:c.1925G>A	p.Gly642Glu	p.G642E	ENST00000369303	NM_004440.3	642	gGa/gAa	11/17	1	2	FACETS	0.759	0.691	0.83	0.759	0.691	0.83	SUBCLONAL	1	FALSE	1	0.582308072230216	2		424	593	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964427	55964427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	184	533	0	ENST00000263923.4:c.2386G>A	p.Glu796Lys	p.E796K	ENST00000263923	NM_002253.2	796	Gaa/Aaa	17/30	1	2	FACETS	0.797	0.737	0.859	0.797	0.737	0.859	SUBCLONAL	1	FALSE	1	0.582308072230216	2		533	793	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608604	189608604	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	245	672	1	ENST00000264731.3:c.1679C>T	p.Ser560Leu	p.S560L	ENST00000264731	NM_003722.4	560	tCa/tTa	13/14	0.582308072230216	2	FACETS	0.939	0.879	1	0.47	0.439	0.501	CLONAL	1	FALSE	0	0.582308072230216	2		673	896	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139895	55139895	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	164	404	1	ENST00000257290.5:c.1556C>T	p.Pro519Leu	p.P519L	ENST00000257290	NM_006206.4	519	cCc/cTc	10/23	1	2	FACETS	0.963	0.888	1	0.963	0.888	1	CLONAL	1	FALSE	1	0.582308072230216	2		405	585	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135098	11135098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	352	925	0	ENST00000358026.2:c.3065C>T	p.Ser1022Phe	p.S1022F	ENST00000358026	NM_001128849.1	1022	tCc/tTc	21/36	0.582308072230216	3	FACETS	1	0.962	1	0.511	0.483	0.54	CLONAL	1	FALSE	1	0.582308072230216	3		925	1527	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612211	189612211	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	445	673	1	ENST00000264731.3:c.1963C>T	p.Arg655Ter	p.R655*	ENST00000264731	NM_003722.4	655	Cga/Tga	14/14	0.582308072230216	2	FACETS	0.888	0.853	0.922	0.888	0.853	0.922	CLONAL	2	FALSE	0	0.582308072230216	2		674	861	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685305	89685305	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	88	259	0	ENST00000371953.3:c.200T>A	p.Ile67Lys	p.I67K	ENST00000371953	NM_000314.4	67	aTa/aAa	3/9	NA	2	FACETS	0.746	0.665	0.832			1	INDETERMINATE	1	FALSE	NA	0.582308072230216	2		259	405	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	201	466	0				ENST00000310581	NM_198253.2	-/1132			0.582308072230216	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	0	0.582308072230216	1		466	451	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237728	16237728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	327	651	1	ENST00000375759.3:c.1175C>T	p.Ala392Val	p.A392V	ENST00000375759	NM_015001.2	392	gCc/gTc	5/15	0.582308072230216	3	FACETS	1	0.977	1	0.534	0.504	0.565	CLONAL	1	FALSE	1	0.582308072230216	3		652	1358	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163784	72163784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	159	457	0	ENST00000357731.5:c.574G>A	p.Gly192Arg	p.G192R	ENST00000357731	NM_173808.2	192	Gga/Aga	4/7	1	2	FACETS	0.782	0.719	0.848	0.782	0.719	0.848	SUBCLONAL	1	FALSE	1	0.582308072230216	2		457	698	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615008	43615008	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1372786615	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	245	771	0	ENST00000355710.3:c.2422A>G	p.Lys808Glu	p.K808E	ENST00000355710	NM_020975.4	808	Aaa/Gaa	14/20	0.259304926938149	0	FACETS	0.36	0.337	0.385			1	INDETERMINATE	1	FALSE	0	0.582308072230216	0		771	975	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925340	114925340	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	267	721	0	ENST00000543371.1:c.1418T>C	p.Ile473Thr	p.I473T	ENST00000543371	NM_001198531.1	473	aTa/aCa	14/14	1	2	FACETS	0.959	0.901	1	0.959	0.901	1	CLONAL	1	FALSE	1	0.582308072230216	2		721	956	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998444	100998444	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	194	560	0	ENST00000325455.5:c.1358C>A	p.Ser453Tyr	p.S453Y	ENST00000325455	NM_001202474.3	453	tCc/tAc	1/8	1	2	FACETS	0.907	0.841	0.974	0.907	0.841	0.974	CLONAL	1	FALSE	1	0.582308072230216	2		560	735	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998544	100998544	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	261	738	0	ENST00000325455.5:c.1258G>A	p.Gly420Arg	p.G420R	ENST00000325455	NM_001202474.3	420	Ggg/Agg	1/8	1	2	FACETS	0.965	0.906	1	0.965	0.906	1	CLONAL	1	FALSE	1	0.582308072230216	2		738	929	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376188	118376188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	272	508	0	ENST00000534358.1:c.9581C>T	p.Pro3194Leu	p.P3194L	ENST00000534358	NM_005933.3	3194	cCt/cTt	27/36	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.582308072230216	2		508	875	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420092	420092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760930800	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1275	316	668	2	ENST00000399788.2:c.3175C>T	p.Arg1059Trp	p.R1059W	ENST00000399788	NM_001042603.1	1059	Cgg/Tgg	21/28	0.49748585643254	5	FACETS	1	0.991	1			1	CLONAL	1	FALSE	NA	0.582308072230216	5		670	1591	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446008	49446009	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	382	1098	1	ENST00000301067.7:c.1457_1458delinsTT	p.Ser486Phe	p.S486F	ENST00000301067	NM_003482.3	486	tCC/tTT	10/54	1	2	FACETS	0.935	0.887	0.984	0.935	0.887	0.984	CLONAL	1	FALSE	1	0.582308072230216	2		1099	1403	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121437430	121437430	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1168108747	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	224	612	0	ENST00000257555.6:c.1768G>A	p.Val590Met	p.V590M	ENST00000257555		590	Gtg/Atg	9/10	1	2	FACETS	0.907	0.846	0.97	0.907	0.846	0.97	CLONAL	1	FALSE	1	0.582308072230216	2		612	848	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919626	28919626	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	795	695	0	ENST00000282397.4:c.2311C>T	p.Leu771Phe	p.L771F	ENST00000282397	NM_002019.4	771	Ctc/Ttc	16/30	0.557539321614885	3	FACETS	0.998	0.973	1	0.998	0.973	1	CLONAL	3	FALSE	0	0.582308072230216	3		695	1178	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562313	95562313	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	139	456	0	ENST00000393063.1:c.4944T>A	p.Cys1648Ter	p.C1648*	ENST00000393063	NM_030621.3	1648	tgT/tgA	24/28	0.294644927640714	1	FACETS	0.483	0.44	0.527	0.483	0.44	0.527	INDETERMINATE	1	FALSE	0	0.582308072230216	1		456	701	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020438	14020438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	197	402	0	ENST00000311895.7:c.409C>T	p.His137Tyr	p.H137Y	ENST00000311895	NM_005236.2	137	Cac/Tac	3/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.582308072230216	2		402	634	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511694	66511695	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	AATA	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	251	472	0	ENST00000358598.2:c.155_158dup	p.Tyr53Ter	p.Y53*	ENST00000358598	NM_212471.2	52	gaa/gAATAaa	2/11	0.582308072230216	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	0	0.582308072230216	1		472	602	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101103	4101104	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	347	464	2	ENST00000262948.5:c.618_619delinsAA	p.Glu207Lys	p.E207K	ENST00000262948	NM_030662.3	206	ggGGag/ggAAag	6/11	0.582308072230216	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	FALSE	1	0.582308072230216	3		466	768	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231498	5231498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	292	765	0	ENST00000357368.4:c.1978C>T	p.Pro660Ser	p.P660S	ENST00000357368	NM_002850.3	660	Ccg/Tcg	14/38	0.582308072230216	3	FACETS	0.972	0.913	1	0.486	0.456	0.517	CLONAL	1	FALSE	1	0.582308072230216	3		765	1332	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288748	15288748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	89	185	1	ENST00000263388.2:c.3991C>T	p.Pro1331Ser	p.P1331S	ENST00000263388	NM_000435.2	1331	Ccg/Tcg	24/33	0.261345051575667	3	FACETS	1	0.971	1			1	INDETERMINATE	1	FALSE	NA	0.582308072230216	3		186	317	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366147	15366147	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	309	701	0	ENST00000263377.2:c.2008T>C	p.Tyr670His	p.Y670H	ENST00000263377	NM_058243.2	670	Tat/Cat	10/20	0.261345051575667	3	FACETS	1	0.971	1			1	INDETERMINATE	1	FALSE	NA	0.582308072230216	3		701	1308	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366227	15366227	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868727577	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	714	889	0	ENST00000263377.2:c.1928C>T	p.Ser643Phe	p.S643F	ENST00000263377	NM_058243.2	643	tCc/tTc	10/20	0.261345051575667	3	FACETS	1	0.974	1			1	INDETERMINATE	2	FALSE	NA	0.582308072230216	3		889	1570	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213599	36213599	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754201347	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	355	899	0	ENST00000222270.7:c.2701C>T	p.Arg901Trp	p.R901W	ENST00000222270	NM_014727.1	901	Cgg/Tgg	5/37	1	2	FACETS	0.938	0.888	0.989	0.938	0.888	0.989	CLONAL	1	FALSE	1	0.582308072230216	2		899	1300	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100933	41100933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	246	683	0	ENST00000373198.4:c.1423G>A	p.Glu475Lys	p.E475K	ENST00000373198	NM_133170.3	475	Gag/Aag	8/32	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	1	0.582308072230216	2		683	828	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422928	12422928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765206131	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	309	686	0	ENST00000287820.6:c.418C>T	p.Arg140Cys	p.R140C	ENST00000287820	NM_015869.4	140	Cgt/Tgt	3/7	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.582308072230216	2		686	983	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165786	47165786	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	251	523	0	ENST00000409792.3:c.340C>T	p.Pro114Ser	p.P114S	ENST00000409792	NM_014159.6	114	Cct/Tct	3/21	1	2	FACETS	0.933	0.874	0.993	0.933	0.874	0.993	CLONAL	1	FALSE	1	0.582308072230216	2		523	924	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643668	52643668	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	278	614	0	ENST00000394830.3:c.2228C>T	p.Ser743Phe	p.S743F	ENST00000394830	NM_018313.4	743	tCt/tTt	17/30	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.582308072230216	2		614	912	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916849	178916850	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	438	695	2	ENST00000263967.3:c.236_237delinsAA	p.Arg79Lys	p.R79K	ENST00000263967	NM_006218.2	79	aGG/aAA	2/21	0.582308072230216	3	FACETS	0.843	0.805	0.881			1	CLONAL	2	FALSE	NA	0.582308072230216	3		697	1152	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143181667	143181667	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	257	512	0	ENST00000262992.4:c.666T>A	p.Asp222Glu	p.D222E	ENST00000262992	NM_001101669.1	222	gaT/gaA	9/24	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.582308072230216	2		512	854	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947428	38947428	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	177	393	0	ENST00000357387.3:c.4252T>A	p.Tyr1418Asn	p.Y1418N	ENST00000357387	NM_152756.3	1418	Tat/Aat	32/38	0.582308072230216	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	0	0.582308072230216	1		393	385	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564516	86564516	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	322	655	0	ENST00000274376.6:c.248G>T	p.Gly83Val	p.G83V	ENST00000274376	NM_002890.2	83	gGa/gTa	1/25	0.582308072230216	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	0	0.582308072230216	1		655	728	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057743	180057743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	273	783	0	ENST00000261937.6:c.212G>A	p.Gly71Glu	p.G71E	ENST00000261937	NM_182925.4	71	gGa/gAa	3/30	0.582308072230216	1	FACETS	0.951	0.898	1	0.951	0.898	1	CLONAL	1	FALSE	0	0.582308072230216	1		783	699	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140885	37140885	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	289	702	0	ENST00000373509.5:c.721C>T	p.Pro241Ser	p.P241S	ENST00000373509	NM_002648.3	241	Cct/Tct	5/6	1	2	FACETS	0.931	0.876	0.987	0.931	0.876	0.987	CLONAL	1	FALSE	1	0.582308072230216	2		702	1066	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93973593	93973593	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	129	424	0	ENST00000369303.4:c.1783G>A	p.Glu595Lys	p.E595K	ENST00000369303	NM_004440.3	595	Gag/Aag	9/17	1	2	FACETS	0.897	0.818	0.979	0.897	0.818	0.979	CLONAL	1	FALSE	1	0.582308072230216	2		424	494	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068007	94068008	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	97	367	1	ENST00000369303.4:c.954_955delinsAA	p.Ala319Thr	p.A319T	ENST00000369303	NM_004440.3	318	agGGct/agAAct	4/17	1	2	FACETS	0.668	0.597	0.742	0.668	0.597	0.742	SUBCLONAL	1	FALSE	1	0.582308072230216	2		368	499	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658349	117658349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	281	800	0	ENST00000368508.3:c.5234G>A	p.Ser1745Asn	p.S1745N	ENST00000368508	NM_002944.2	1745	aGc/aAc	31/43	1	2	FACETS	0.917	0.862	0.974	0.917	0.862	0.974	CLONAL	1	FALSE	1	0.582308072230216	2		800	1052	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715366	117715366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	131	389	0	ENST00000368508.3:c.1123G>A	p.Asp375Asn	p.D375N	ENST00000368508	NM_002944.2	375	Gat/Aat	10/43	1	2	FACETS	0.877	0.8	0.957	0.877	0.8	0.957	CLONAL	1	FALSE	1	0.582308072230216	2		389	513	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099340	157099340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1250963206	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	213	407	0	ENST00000346085.5:c.277C>T	p.His93Tyr	p.H93Y	ENST00000346085	NM_020732.3	93	Cac/Tac	1/20	0.359809496337635	3	FACETS	0.767	0.717	0.818			1	SUBCLONAL	2	FALSE	NA	0.582308072230216	3		407	616	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863311	56863311	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	236	596	0	ENST00000519728.1:c.455C>T	p.Ala152Val	p.A152V	ENST00000519728	NM_002350.3	152	gCt/gTt	6/13	1	2	FACETS	0.931	0.87	0.993	0.931	0.87	0.993	CLONAL	1	FALSE	1	0.582308072230216	2		596	871	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934289	68934289	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	233	541	0	ENST00000288368.4:c.355T>C	p.Tyr119His	p.Y119H	ENST00000288368	NM_024870.2	119	Tat/Cat	4/40	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.582308072230216	2		541	752	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626640	100626640	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0035974-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	216	496	0	ENST00000308731.7:c.290G>T	p.Arg97Met	p.R97M	ENST00000308731	NM_000061.2	97	aGg/aTg	4/19	0.434326600578938	0	FACETS	0.575	0.539	0.611			1	SUBCLONAL	1	FALSE	0	0.582308072230216	0		496	539	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577095	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519984	NA	P-0038098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	40	911	0	ENST00000269305.4:c.843C>G	p.Asp281Glu	p.D281E	ENST00000269305	NM_001126112.2	281	gaC/gaG	8/11	1	2	FACETS	0.949	0.79	1	0.949	0.79	1	CLONAL	1	TRUE	1	0.22	2		911	383	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979442	2979442	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	17	841	0	ENST00000396946.4:c.805C>G	p.Leu269Val	p.L269V	ENST00000396946	NM_032415.4	269	Ctg/Gtg	6/25	0.205157365851692	4	FACETS	0.952	0.713	1	0.476	0.356	0.617	CLONAL	1	TRUE	2	0.22	4		841	198	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206665035	206665035	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0038098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	17	745	0	ENST00000367120.3:c.1788C>A	p.Cys596Ter	p.C596*	ENST00000367120	NM_014002.3	596	tgC/tgA	18/22	1	2	FACETS	0.699	0.523	0.908	0.699	0.523	0.908	SUBCLONAL	1	TRUE	1	0.22	2		745	221	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8251878	8251878	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0038098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	44	888	0	ENST00000335790.3:c.199A>T	p.Thr67Ser	p.T67S	ENST00000335790	NM_002315.2	67	Acc/Tcc	2/4	0.0922680230279472	3	FACETS	0.816	0.689	0.955	0.816	0.689	0.955	INDETERMINATE	2	TRUE	1	0.22	3		888	272	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205562	61205562	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	15	664	1	ENST00000301761.2:c.347G>T	p.Trp116Leu	p.W116L	ENST00000301761	NM_017841.2	116	tGg/tTg	3/4	0.0922680230279472	3	FACETS	1	0.892	1	0.749	0.555	0.976	INDETERMINATE	1	TRUE	1	0.22	3		665	101	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11136184	11136184	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	27	838	1	ENST00000358026.2:c.3168G>T	p.Glu1056Asp	p.E1056D	ENST00000358026	NM_001128849.1	1056	gaG/gaT	22/36	1	2	FACETS	0.792	0.631	0.975	0.792	0.631	0.975	CLONAL	1	TRUE	1	0.22	2		839	310	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138577	11138577	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	15	929	0	ENST00000358026.2:c.3333C>G	p.Ile1111Met	p.I1111M	ENST00000358026	NM_001128849.1	1111	atC/atG	24/36	1	2	FACETS	1	0.739	1	1	0.739	1	CLONAL	1	TRUE	1	0.22	2		929	136	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661909	227661909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0038098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	21	1011	1	ENST00000305123.5:c.1546G>T	p.Asp516Tyr	p.D516Y	ENST00000305123	NM_005544.2	516	Gat/Tat	1/2	1	2	FACETS	0.994	0.77	1	0.994	0.77	1	CLONAL	1	TRUE	1	0.22	2		1012	192	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39690115	39690115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0038098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	17	336	0	ENST00000361337.2:c.140C>T	p.Ser47Phe	p.S47F	ENST00000361337	NM_003286.2	47	tCc/tTc	3/21	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.22	2		336	111	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202232	138202232	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	29	768	0	ENST00000237289.4:c.2149G>T	p.Ala717Ser	p.A717S	ENST00000237289	NM_001270507.1	717	Gcc/Tcc	9/9	1	2	FACETS	0.76	0.61	0.929	0.76	0.61	0.929	CLONAL	1	TRUE	1	0.22	2		768	347	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636929	176636929	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	12	781	0	ENST00000439151.2:c.1529G>T	p.Ser510Ile	p.S510I	ENST00000439151	NM_022455.4	510	aGt/aTt	5/23	1	2	FACETS	1	0.801	1	1	0.801	1	CLONAL	1	TRUE	1	0.22	2		781	93	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534815	18534815	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0038098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	12	613	0	ENST00000266497.5:c.1872+1G>T		p.X624_splice	ENST00000266497		624			1	2	FACETS	0.873	0.617	1	0.873	0.617	1	CLONAL	1	TRUE	1	0.22	2		613	125	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562750	29562750	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1555615480	NA	P-0038098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	11	549	0	ENST00000356175.3:c.3830G>T	p.Gly1277Val	p.G1277V	ENST00000356175	NM_000267.3	1277	gGc/gTc	28/57	1	2	FACETS	1	0.818	1	1	0.818	1	CLONAL	1	TRUE	1	0.22	2		549	79	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439987	220439987	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0038098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	20	1122	0	ENST00000243786.2:c.840C>G	p.Ile280Met	p.I280M	ENST00000243786	NM_002191.3	280	atC/atG	2/2	1	2	FACETS	0.784	0.601	0.996	0.784	0.601	0.996	CLONAL	1	TRUE	1	0.22	2		1122	232	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395666	31395666	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038098-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	18	749	0	ENST00000328111.2:c.2519G>T	p.Arg840Leu	p.R840L	ENST00000328111	NM_006892.3	840	cGa/cTa	23/23	1	2	FACETS	0.496	0.373	0.642	0.496	0.373	0.642	SUBCLONAL	1	TRUE	1	0.22	2		749	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0038412-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	457	92	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.809011464579333	1	FACETS	0.975	0.943	1	0.975	0.943	1	CLONAL	1	TRUE	0	0.809011464579333	1		92	690	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913558	32913559	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359479	NA	P-0038412-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	75	434	1	ENST00000380152.3:c.5073dup	p.Trp1692MetfsTer3	p.W1692Mfs*3	ENST00000380152		1689	gca/gcAa	11/27	0.809011464579333	1	FACETS	0.812	0.737	0.886	0.812	0.737	0.886	CLONAL	1	TRUE	0	0.809011464579333	1		435	136	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643216	38643216	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0038412-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	83	324	0	ENST00000299084.4:c.686T>C	p.Val229Ala	p.V229A	ENST00000299084	NM_152594.2	229	gTc/gCc	7/7	1	2	FACETS	0.92	0.827	1	0.92	0.827	1	CLONAL	1	TRUE	1	0.809011464579333	2		324	223	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855593	45855593	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0038412-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	334	852	0	ENST00000391945.4:c.2064C>G	p.Asp688Glu	p.D688E	ENST00000391945	NM_000400.3	688	gaC/gaG	22/23	1	2	FACETS	0.879	0.834	0.926	0.879	0.834	0.926	CLONAL	1	TRUE	1	0.809011464579333	2		852	939	SUCCESS
APC	324	MSKCC	GRCh37	5	112173710	112173710	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0038412-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	43	359	0	ENST00000257430.4:c.2419G>T	p.Asp807Tyr	p.D807Y	ENST00000257430	NM_000038.5	807	Gat/Tat	16/16	1	2	FACETS	0.407	0.343	0.477	0.407	0.343	0.477	SUBCLONAL	1	TRUE	1	0.809011464579333	2		359	261	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189835	66189835	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs55784741	NA	P-0039208-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	65	627	0	ENST00000273854.3:c.3111G>T	p.Leu1037Phe	p.L1037F	ENST00000273854	NM_004439.5	1037	ttG/ttT	18/18	0.260802902485367	1	FACETS	0.402	0.35	0.458	0.402	0.35	0.458	INDETERMINATE	1	TRUE	0	0.574455093431012	1		627	401	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045714	26045714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039208-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	139	358	0	ENST00000540144.1:c.76G>A	p.Ala26Thr	p.A26T	ENST00000540144	NM_003531.2	26	Gcc/Acc	1/1	0.358182664976486	5	FACETS	0.853	0.781	0.928	0.569	0.52	0.619	CLONAL	2	TRUE	2	0.574455093431012	5		358	528	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42026793	42026793	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0039208-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	38	430	0	ENST00000219905.7:c.3916+1G>C		p.X1306_splice	ENST00000219905	NM_001164273.1	1306			0.284249860676022	1	FACETS	0.725	0.612	0.846	0.725	0.612	0.846	INDETERMINATE	1	TRUE	0	0.574455093431012	1		430	130	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563494	87563494	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039208-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	92	695	0	ENST00000277120.3:c.1882C>T	p.Pro628Ser	p.P628S	ENST00000277120		628	Ccc/Tcc	16/19	0.574455093431012	1	FACETS	0.562	0.503	0.625	0.562	0.503	0.625	SUBCLONAL	1	TRUE	0	0.574455093431012	1		695	406	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0039280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	62	422	0				ENST00000310581	NM_198253.2	-/1132			0.874951917721027	6	FACETS	1	0.958	1	0.314	0.273	0.358	CLONAL	1	FALSE	2	0.874951917721027	6		422	310	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0039280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	218	842	0	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	0.812085929555946	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	FALSE	2	0.874951917721027	4		842	446	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0039280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	209	805	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	0.874951917721027	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	FALSE	0	0.874951917721027	2		805	230	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027222	49027223	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATGG	novel	NA	P-0039280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	132	497	0	ENST00000267163.4:c.1790_1791insTGGA	p.Gln597HisfsTer4	p.Q597Hfs*4	ENST00000267163	NM_000321.2	597	cag/cATGGag	18/27	0.862621364709345	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	3	FALSE	0	0.874951917721027	3		497	143	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197835	66197835	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0039280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	21	270	0	ENST00000273854.3:c.2864T>C	p.Leu955Ser	p.L955S	ENST00000273854	NM_004439.5	955	tTa/tCa	17/18	0.674583813676924	4	FACETS	0.648	0.504	0.811	0.324	0.252	0.406	SUBCLONAL	1	FALSE	2	0.874951917721027	4		270	139	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270165	66270165	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1416732153	NA	P-0039280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	127	442	0	ENST00000273854.3:c.1717C>T	p.Pro573Ser	p.P573S	ENST00000273854	NM_004439.5	573	Cct/Tct	8/18	0.674583813676924	4	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	FALSE	2	0.874951917721027	4		442	262	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876377	35876377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0039280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	58	742	0	ENST00000303115.3:c.1169G>A	p.Cys390Tyr	p.C390Y	ENST00000303115	NM_002185.3	390	tGc/tAc	8/8	0.874951917721027	6	FACETS	0.69	0.594	0.796	0.173	0.148	0.199	SUBCLONAL	1	FALSE	2	0.874951917721027	6		742	528	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158530	26158530	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039280-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	72	558	0	ENST00000289316.2:c.133G>T	p.Val45Leu	p.V45L	ENST00000289316	NM_138720.2	45	Gtg/Ttg	1/2	0.679858050298008	4	FACETS	1	0.935	1	0.363	0.321	0.409	CLONAL	1	FALSE	1	0.874951917721027	4		558	283	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0039522-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	60	479	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.412919875321073	3	FACETS	1	0.972	1	0.748	0.652	0.849	CLONAL	1	TRUE	1	0.411531816890981	3		480	235	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0039522-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	251	291	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.411531816890981	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.411531816890981	2		292	561	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55597561	55597561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751005114	NA	P-0039522-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	62	541	3	ENST00000288135.5:c.2209G>A	p.Asp737Asn	p.D737N	ENST00000288135	NM_000222.2	737	Gac/Aac	15/21	0.411531816890981	2	FACETS	1	0.92	1	0.538	0.469	0.612	CLONAL	1	TRUE	0	0.411531816890981	2		544	280	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374103	118374103	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0039522-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	62	515	0	ENST00000534358.1:c.7496G>T	p.Gly2499Val	p.G2499V	ENST00000534358	NM_005933.3	2499	gGa/gTa	27/36	0.11905347930316	6	FACETS	1	0.966	1	0.461	0.4	0.527	INDETERMINATE	1	TRUE	3	0.411531816890981	6		515	397	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0039952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	69	302	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	1	2	FACETS	0.544	0.474	0.619	0.544	0.474	0.619	SUBCLONAL	1	TRUE	1	0.42587138904072	2		302	596	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220489	1220489	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202134	NA	P-0039952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	100	723	0	ENST00000326873.7:c.582C>A	p.Asp194Glu	p.D194E	ENST00000326873	NM_000455.4	194	gaC/gaA	4/10	0.308222893544062	1	FACETS	0.451	0.403	0.503	0.451	0.403	0.503	SUBCLONAL	1	TRUE	0	0.42587138904072	1		723	819	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851295	156851295	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0039952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	159	819	0	ENST00000524377.1:c.2252C>A	p.Ala751Asp	p.A751D	ENST00000524377	NM_002529.3	751	gCc/gAc	17/17	0.421634141312303	3	FACETS	0.848	0.776	0.923	0.424	0.388	0.462	CLONAL	1	TRUE	1	0.42587138904072	3		819	1068	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937624	32937624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398122600	NA	P-0039952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	67	540	0	ENST00000380152.3:c.8285C>T	p.Pro2762Leu	p.P2762L	ENST00000380152		2762	cCt/cTt	18/27	1	2	FACETS	0.452	0.392	0.517	0.452	0.392	0.517	SUBCLONAL	1	TRUE	1	0.42587138904072	2		540	696	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610601	10610602	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0039952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	111	790	0	ENST00000171111.5:c.108dup	p.Glu37Ter	p.E37*	ENST00000171111	NM_203500.1	36	-/T	2/6	0.308222893544062	1	FACETS	0.452	0.405	0.501	0.452	0.405	0.501	SUBCLONAL	1	TRUE	0	0.42587138904072	1		790	908	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	39021230	39021230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0039952-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	43	295	0	ENST00000357387.3:c.106G>A	p.Asp36Asn	p.D36N	ENST00000357387	NM_152756.3	36	Gat/Aat	3/38	1	2	FACETS	0.454	0.38	0.536	0.454	0.38	0.536	SUBCLONAL	1	TRUE	1	0.42587138904072	2		295	445	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100181	27100181	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs912059538	NA	P-0040650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	14	433	0	ENST00000324856.7:c.3977C>T	p.Pro1326Leu	p.P1326L	ENST00000324856	NM_006015.4	1326	cCg/cTg	16/20	0.591621432733073	2	FACETS	0.222	0.16	0.296	0.111	0.08	0.148	SUBCLONAL	1	TRUE	0	0.612763093763943	2		433	206	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578546	7578547	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	271	778	0	ENST00000269305.4:c.383dup	p.Ala129CysfsTer20	p.A129Cfs*20	ENST00000269305	NM_001126112.2	128	cct/ccCt	5/11	0.534895902046345	3	FACETS	0.843	0.804	0.881	0.843	0.804	0.881	CLONAL	3	TRUE	0	0.612763093763943	3		778	457	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163313619	163313619	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0040650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	27	182	0	ENST00000271452.3:c.766G>T	p.Glu256Ter	p.E256*	ENST00000271452	NM_145697.2	256	Gaa/Taa	10/14	0.612763093763943	3	FACETS	0.573	0.459	0.701	0.191	0.153	0.234	SUBCLONAL	1	TRUE	0	0.612763093763943	3		182	201	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48947630	48947630	+	splice_donor_variant	Splice_Site	SNP	T	T	G	rs1060503074	NA	P-0040650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	82	206	0	ENST00000267163.4:c.1215+2T>G		p.X405_splice	ENST00000267163	NM_000321.2	405			0.55034347284578	3	FACETS	0.857	0.785	0.927	0.857	0.785	0.927	CLONAL	3	TRUE	0	0.612763093763943	3		206	136	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755384	39755384	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0040650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	64	497	0	ENST00000288319.7:c.1381T>A	p.Tyr461Asn	p.Y461N	ENST00000288319	NM_182918.3	461	Tac/Aac	10/10	0.612763093763943	1	FACETS	0.485	0.423	0.55	0.485	0.423	0.55	SUBCLONAL	1	TRUE	0	0.612763093763943	1		497	299	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198256	138198256	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0040650-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	22	244	0	ENST00000237289.4:c.849T>G	p.Phe283Leu	p.F283L	ENST00000237289	NM_001270507.1	283	ttT/ttG	6/9	0.55034347284578	3	FACETS	0.502	0.391	0.628	0.167	0.13	0.21	SUBCLONAL	1	TRUE	0	0.612763093763943	3		244	187	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14316397	14316397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782457908	NA	P-0040750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	19	610	0	ENST00000256196.4:c.208G>A	p.Ala70Thr	p.A70T	ENST00000256196		70	Gca/Aca	3/6	0.307539077652237	0	FACETS	0.283	0.215	0.364			1	SUBCLONAL	1	FALSE	0	0.307539077652237	0		610	302	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682652	86682652	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0040750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	52	263	0	ENST00000274376.6:c.2857A>C	p.Met953Leu	p.M953L	ENST00000274376	NM_002890.2	953	Atg/Ctg	23/25	0.307539077652237	16	FACETS	1	0.916	1			1	CLONAL	2	FALSE	NA	0.307539077652237	16		263	479	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932457	39932458	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0040750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	58	1004	0	ENST00000378444.4:c.2141_2142del	p.Val714AspfsTer25	p.V714Dfs*25	ENST00000378444	NM_001123385.1	714	gTG/g	4/15	0.307539077652237	1	FACETS	0.838	0.723	0.962	0.838	0.723	0.962	CLONAL	1	FALSE	0	0.307539077652237	1		1004	381	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933176	39933177	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0040750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	163	916	0	ENST00000378444.4:c.1422dup	p.Val476SerfsTer6	p.V476Sfs*6	ENST00000378444	NM_001123385.1	474	-/C	4/15	0.307539077652237	1	FACETS	0.986	0.913	1	1	0.992	1	CLONAL	2	FALSE	0	0.307539077652237	1		916	455	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918561	44918561	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0040750-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	46	526	0	ENST00000377967.4:c.1045del	p.His349MetfsTer10	p.H349Mfs*10	ENST00000377967	NM_021140.2	348	gaC/ga	12/29	0.307539077652237	1	FACETS	0.858	0.727	1	0.858	0.727	1	CLONAL	1	FALSE	0	0.307539077652237	1		526	295	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0040949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	372	496	0	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.403502814575431	2		496	868	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1219298	1219322	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	GAGCTGTGTGTCCTTAGCGCCCCAC	GAGCTGTGTGTCCTTAGCGCCCCAC	-	novel	NA	P-0040949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	238	531	1	ENST00000326873.7:c.375-24_375del		p.X125_splice	ENST00000326873	NM_000455.4	125			0.405581234888933	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.403502814575431	2		532	587	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346561	81346596	+	inframe_deletion	In_Frame_Del	DEL	GCAATAATCCCAAGGAATGAGTGGATTTCCCGTGTA	GCAATAATCCCAAGGAATGAGTGGATTTCCCGTGTA	-	novel	NA	P-0040949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	103	340	0	ENST00000222390.5:c.1357_1392del	p.Tyr453_Cys464del	p.Y453_C464del	ENST00000222390	NM_000601.4	453	TACACGGGAAATCCACTCATTCCTTGGGATTATTGC/-	11/18	0.371578494454601	4	FACETS	0.896	0.808	0.988	0.597	0.538	0.659	CLONAL	2	TRUE	1	0.403502814575431	4		340	400	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742433	145742433	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0040949-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	220	855	0	ENST00000428558.2:c.354+1G>T		p.X118_splice	ENST00000428558	NM_004260.3	118			0.154259807207253	5	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.403502814575431	5		855	1198	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380276	25380276	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913240	NA	P-0121544-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	70	461	0	ENST00000311936.3:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000311936	NM_004985.3	61	cAa/cTa	3/5	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		461	641	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0041274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	317	143	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.437122273679252	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	4	TRUE	0	0.439478676002761	4		143	490	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521120	187521120	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752997628	NA	P-0041274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	123	464	0	ENST00000441802.2:c.12035C>T	p.Thr4012Met	p.T4012M	ENST00000441802	NM_005245.3	4012	aCg/aTg	22/27	0.364645152904571	5	FACETS	0.864	0.78	0.953	0.288	0.26	0.318	CLONAL	1	TRUE	2	0.439478676002761	5		464	1075	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1940200	1940200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	93	212	0	ENST00000382891.5:c.1697C>T	p.Thr566Met	p.T566M	ENST00000382891	NM_133335.3	566	aCg/aTg	8/22	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.439478676002761	2		212	299	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25458575	25458575	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0041274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	64	253	0	ENST00000264709.3:c.2597+1G>T		p.X866_splice	ENST00000264709	NM_175629.2	866			0.439478676002761	3	FACETS	0.693	0.6	0.792	0.346	0.3	0.396	SUBCLONAL	1	TRUE	1	0.439478676002761	3		253	513	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023720	27023720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0041274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	153	306	0	ENST00000324856.7:c.826G>A	p.Gly276Arg	p.G276R	ENST00000324856	NM_006015.4	276	Gga/Aga	1/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.439478676002761	2		306	609	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555254	226555254	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0041274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	179	470	0	ENST00000366794.5:c.2333T>A	p.Leu778His	p.L778H	ENST00000366794	NM_001618.3	778	cTc/cAc	17/23	0.439478676002761	5	FACETS	1	0.98	1	0.298	0.274	0.324	CLONAL	1	TRUE	1	0.439478676002761	5		470	1132	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828168	243828168	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0041274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	163	90	0	ENST00000263826.5:c.190del	p.Thr64GlnfsTer10	p.T64Qfs*10	ENST00000263826	NM_005465.4	64	Aca/ca	3/13	0.439478676002761	5	FACETS	1	0.983	1	0.607	0.561	0.654	CLONAL	2	TRUE	1	0.439478676002761	5		90	507	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662366	67662366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	163	564	0	ENST00000264010.4:c.1612C>T	p.Leu538Phe	p.L538F	ENST00000264010	NM_006565.3	538	Ctc/Ttc	9/12	0.439478676002761	2	FACETS	0.858	0.787	0.931	0.429	0.393	0.466	CLONAL	1	TRUE	0	0.439478676002761	2		564	865	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732747	204732747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0041274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	126	370	0	ENST00000302823.3:c.82C>T	p.Leu28Phe	p.L28F	ENST00000302823	NM_005214.4	28	Ctt/Ttt	1/4	0.439478676002761	3	FACETS	0.913	0.827	1	0.457	0.413	0.502	CLONAL	1	TRUE	1	0.439478676002761	3		370	766	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68999983	68999985	+	missense_variant	Missense_Mutation	TNP	TGA	TGA	CGT	novel	NA	P-0041274-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	132	351	0	ENST00000288368.4:c.2052_2054delinsCGT	p.Asp685Val	p.D685V	ENST00000288368	NM_024870.2	684	gcTGAt/gcCGTt	19/40	0.439478676002761	6	FACETS	0.944	0.855	1	0.236	0.213	0.26	CLONAL	1	TRUE	2	0.439478676002761	6		351	1196	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0041545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	114	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.852092552477457	2		422	262	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0041545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	92	314	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.968	0.878	1	0.968	0.878	1	CLONAL	1	TRUE	1	0.852092552477457	2		314	223	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791758	42791758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1380826096	NA	P-0041545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	16	579	0	ENST00000575354.2:c.644G>A	p.Arg215Gln	p.R215Q	ENST00000575354	NM_015125.3	215	cGg/cAg	5/20	0.852092552477457	1	FACETS	0.064	0.047	0.085	0.064	0.047	0.085	SUBCLONAL	1	TRUE	0	0.852092552477457	1		579	335	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794440	42794441	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0041545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	107	585	0	ENST00000575354.2:c.1526dup	p.Leu510ThrfsTer4	p.L510Tfs*4	ENST00000575354	NM_015125.3	507	cgc/cgCc	10/20	0.852092552477457	1	FACETS	0.38	0.344	0.418	0.38	0.344	0.418	SUBCLONAL	1	TRUE	0	0.852092552477457	1		585	379	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792033	42792034	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0041545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	68	531	0	ENST00000575354.2:c.839_840del	p.Glu280GlyfsTer34	p.E280Gfs*34	ENST00000575354	NM_015125.3	279	tcAGag/tcag	6/20	0.852092552477457	1	FACETS	0.284	0.249	0.322	0.284	0.249	0.322	SUBCLONAL	1	TRUE	0	0.852092552477457	1		531	322	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412281	139412281	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0041545-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	113	683	1	ENST00000277541.6:c.1364A>G	p.Glu455Gly	p.E455G	ENST00000277541	NM_017617.3	455	gAg/gGg	8/34	1	2	FACETS	0.344	0.309	0.381	0.344	0.309	0.381	SUBCLONAL	1	TRUE	1	0.852092552477457	2		684	771	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562738	29562739	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555615472	NA	P-0041695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	108	431	0	ENST00000356175.3:c.3822_3823del	p.Phe1275ProfsTer8	p.F1275Pfs*8	ENST00000356175	NM_000267.3	1273	aCT/a	28/57	0.903451615549238	3	FACETS	0.506	0.454	0.561	0.253	0.227	0.281	SUBCLONAL	1	TRUE	1	0.903451615549238	3		431	686	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991260	41991260	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0041695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	384	317	1	ENST00000219905.7:c.2093-2A>C		p.X698_splice	ENST00000219905	NM_001164273.1	698			0.903451615549238	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.903451615549238	2		318	422	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81973509	81973510	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CAGCC	novel	NA	P-0041695-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	172	363	0	ENST00000359376.3:c.3328_3332dup	p.Ile1112AlafsTer11	p.I1112Afs*11	ENST00000359376	NM_002661.3	1109	ctc/ctCAGCCc	30/33	0.620099740395329	4	FACETS	0.923	0.851	0.998	0.462	0.425	0.499	CLONAL	1	TRUE	2	0.903451615549238	4		363	785	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0042013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	138	466	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.936	0.864	1	0.936	0.864	1	CLONAL	1	TRUE	1	0.87474033511108	2		466	337	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0042013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	54	314	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.772	0.673	0.875	0.772	0.673	0.875	SUBCLONAL	1	TRUE	1	0.87474033511108	2		314	160	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791758	42791758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1380826096	NA	P-0042013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	174	579	0	ENST00000575354.2:c.644G>A	p.Arg215Gln	p.R215Q	ENST00000575354	NM_015125.3	215	cGg/cAg	5/20	0.87474033511108	1	FACETS	0.713	0.67	0.756	0.713	0.67	0.756	SUBCLONAL	1	TRUE	0	0.87474033511108	1		579	314	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589623	67589634	+	inframe_deletion	In_Frame_Del	DEL	ATATGATAGATT	ATATGATAGATT	-	novel	NA	P-0042013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	52	61	0	ENST00000274335.5:c.1392_1403del	p.Asp464_Tyr467del	p.D464_Y467del	ENST00000274335		462	gaATATGATAGATTa/gaa	10/15	1	2	FACETS	0.831	0.725	0.942	0.831	0.725	0.942	CLONAL	1	TRUE	1	0.87474033511108	2		61	143	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793215	42793218	+	frameshift_variant	Frame_Shift_Del	DEL	CAGT	CAGT	-	novel	NA	P-0042013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	50	920	0	ENST00000575354.2:c.1110_1113del	p.Ser370ArgfsTer6	p.S370Rfs*6	ENST00000575354	NM_015125.3	369	gaCAGT/ga	7/20	0.87474033511108	1	FACETS	0.18	0.153	0.21	0.18	0.153	0.21	SUBCLONAL	1	TRUE	0	0.87474033511108	1		920	357	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8252034	8252034	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536636517	NA	P-0042013-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	84	745	0	ENST00000335790.3:c.43G>A	p.Val15Ile	p.V15I	ENST00000335790	NM_002315.2	15	Gtc/Atc	2/4	1	2	FACETS	0.311	0.274	0.35	0.311	0.274	0.35	SUBCLONAL	1	TRUE	1	0.87474033511108	2		745	618	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295250	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1561215364	NA	P-0042013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	270	466	0				ENST00000310581	NM_198253.2	-/1132			0.644083466710823	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.768419202647069	4		466	572	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0042013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	79	314	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.768419202647069	3	FACETS	0.521	0.459	0.588	0.261	0.229	0.294	SUBCLONAL	1	TRUE	1	0.768419202647069	3		314	546	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791758	42791758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1380826096	NA	P-0042013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	381	579	0	ENST00000575354.2:c.644G>A	p.Arg215Gln	p.R215Q	ENST00000575354	NM_015125.3	215	cGg/cAg	5/20	0.768419202647069	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.768419202647069	2		579	481	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589623	67589634	+	inframe_deletion	In_Frame_Del	DEL	ATATGATAGATT	ATATGATAGATT	-	novel	NA	P-0042013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	94	61	0	ENST00000274335.5:c.1392_1403del	p.Asp464_Tyr467del	p.D464_Y467del	ENST00000274335		462	gaATATGATAGATTa/gaa	10/15	0.768419202647069	2	FACETS	0.868	0.805	0.927	0.868	0.805	0.927	CLONAL	2	TRUE	0	0.768419202647069	2		61	141	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941741	48941741	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0042013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	197	36	0	ENST00000267163.4:c.1049+2T>C		p.X350_splice	ENST00000267163	NM_000321.2	350			0.768419202647069	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	4	TRUE	0	0.768419202647069	4		36	223	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934576	NA	P-0042013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	634	892	0	ENST00000269305.4:c.818G>C	p.Arg273Pro	p.R273P	ENST00000269305	NM_001126112.2	273	cGt/cCt	8/11	0.768419202647069	3	FACETS	0.985	0.964	1	0.985	0.964	1	CLONAL	3	TRUE	0	0.768419202647069	3		892	773	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204732717	204732717	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	138	555	0	ENST00000302823.3:c.52A>T	p.Arg18Trp	p.R18W	ENST00000302823	NM_005214.4	18	Agg/Tgg	1/4	0.768419202647069	3	FACETS	0.94	0.86	1	0.47	0.43	0.512	CLONAL	1	TRUE	1	0.768419202647069	3		555	529	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962393	2962393	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	162	691	0	ENST00000396946.4:c.2144T>A	p.Leu715Gln	p.L715Q	ENST00000396946	NM_032415.4	715	cTa/cAa	17/25	0.490408591927115	4	FACETS	1	0.975	1	0.573	0.527	0.62	CLONAL	1	TRUE	2	0.768419202647069	4		691	651	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080281	5080281	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042013-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	62	160	0	ENST00000381652.3:c.2184A>T	p.Lys728Asn	p.K728N	ENST00000381652	NM_004972.3	728	aaA/aaT	17/25	0.644083466710823	4	FACETS	0.636	0.55	0.728	0.318	0.275	0.364	SUBCLONAL	1	TRUE	2	0.768419202647069	4		160	449	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577547	7577547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912656	NA	P-0042015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	107	309	1	ENST00000269305.4:c.734G>A	p.Gly245Asp	p.G245D	ENST00000269305	NM_001126112.2	245	gGc/gAc	7/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.16	2		310	1213	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720857	89720857	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs786201816	NA	P-0042015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	16	412	0	ENST00000371953.3:c.1008C>G	p.Tyr336Ter	p.Y336*	ENST00000371953	NM_000314.4	336	taC/taG	8/9	1	2	FACETS	0.76	0.562	0.997	0.76	0.562	0.997	CLONAL	1	TRUE	1	0.16	2		412	263	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612677	228612677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545672641	NA	P-0042015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1278	85	939	1	ENST00000366696.1:c.350G>A	p.Arg117Gln	p.R117Q	ENST00000366696	NM_003493.2	117	cGg/cAg	1/1	1	2	FACETS	0.78	0.686	0.88	0.78	0.686	0.88	SUBCLONAL	1	TRUE	1	0.16	2		940	1363	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564667	139564667	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042015-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1465	129	1100	0	ENST00000308874.7:c.456C>A	p.Cys152Ter	p.C152*	ENST00000308874		152	tgC/tgA	7/10	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.16	2		1100	1594	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900209	101900209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	56	180	0	ENST00000374994.4:c.643C>T	p.Arg215Ter	p.R215*	ENST00000374994	NM_004612.2	215	Cga/Tga	4/9	1	2	FACETS	0.856	0.732	0.991	0.856	0.732	0.991	CLONAL	1	TRUE	1	0.19	2		180	689	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891277	101891277	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	76	287	0	ENST00000374994.4:c.238C>T	p.Arg80Ter	p.R80*	ENST00000374994	NM_004612.2	80	Cga/Tga	2/9	1	2	FACETS	0.881	0.771	1	0.881	0.771	1	CLONAL	1	TRUE	1	0.19	2		287	908	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846037	68846037	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0042016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	98	463	0	ENST00000261769.5:c.1009-1G>A		p.X337_splice	ENST00000261769	NM_004360.3	337			1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.19	2		463	985	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056230	27056230	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	160	577	0	ENST00000324856.7:c.1226C>A	p.Ser409Ter	p.S409*	ENST00000324856	NM_006015.4	409	tCa/tAa	2/20	1	2	FACETS	0.857	0.785	0.932	1	0.99	1	CLONAL	2	TRUE	1	0.19	2		577	983	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5207937	5207937	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1414682876	NA	P-0042016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	76	811	0	ENST00000357368.4:c.5774C>A	p.Thr1925Lys	p.T1925K	ENST00000357368	NM_002850.3	1925	aCa/aAa	37/38	0.0998044892838412	0	FACETS	0.661	0.578	0.75			1	INDETERMINATE	1	TRUE	0	0.19	0		811	981	SUCCESS
APC	324	MSKCC	GRCh37	5	112175549	112175549	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042016-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	43	213	0	ENST00000257430.4:c.4258C>T	p.Pro1420Ser	p.P1420S	ENST00000257430	NM_000038.5	1420	Ccc/Tcc	16/16	0.0998044892838412	3	FACETS	0.918	0.768	1	0.459	0.384	0.543	INDETERMINATE	1	TRUE	1	0.19	3		213	540	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696424	47696424	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs193921065	NA	P-0042023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	134	484	0	ENST00000347630.2:c.399C>G	p.Phe133Leu	p.F133L	ENST00000347630	NM_001007230.1	133	ttC/ttG	6/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.33	2		484	652	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629919	187629919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	150	670	0	ENST00000441802.2:c.1063G>A	p.Val355Met	p.V355M	ENST00000441802	NM_005245.3	355	Gtg/Atg	2/27	0.205504701147664	4	FACETS	0.871	0.798	0.947	0.871	0.798	0.947	CLONAL	2	TRUE	2	0.33	4		670	694	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349025	89349025	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042023-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	158	801	0	ENST00000301030.4:c.3925A>G	p.Thr1309Ala	p.T1309A	ENST00000301030	NM_001256183.1	1309	Acg/Gcg	9/13	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.33	2		801	797	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0042024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	511	1099	2	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	0.57408020025662	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.57408020025662	1		1101	1111	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0042024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	153	452	2	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	0.57408020025662	1	FACETS	0.874	0.807	0.942	0.874	0.807	0.942	CLONAL	1	TRUE	0	0.57408020025662	1		454	435	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578266	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0042024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	330	792	0	ENST00000269305.4:c.583dup	p.Ile195AsnfsTer14	p.I195Nfs*14	ENST00000269305	NM_001126112.2	195	atc/aAtc	6/11	0.57408020025662	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.57408020025662	1		792	718	SUCCESS
APC	324	MSKCC	GRCh37	5	112175273	112175273	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs398123121	NA	P-0042024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	135	268	0	ENST00000257430.4:c.3982C>T	p.Gln1328Ter	p.Q1328*	ENST00000257430	NM_000038.5	1328	Cag/Tag	16/16	0.57408020025662	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.57408020025662	1		268	315	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385239	41385239	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377294483	NA	P-0042024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	374	760	0	ENST00000373198.4:c.722G>A	p.Arg241His	p.R241H	ENST00000373198	NM_133170.3	241	cGt/cAt	6/32	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.57408020025662	2		760	1159	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101064	41101064	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	98	732	0	ENST00000373198.4:c.1292A>C	p.Asn431Thr	p.N431T	ENST00000373198	NM_133170.3	431	aAc/aCc	8/32	1	2	FACETS	0.295	0.262	0.331	0.295	0.262	0.331	SUBCLONAL	1	TRUE	1	0.57408020025662	2		732	1156	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070335	37070335	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042024-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	74	429	0	ENST00000231790.2:c.1470G>T	p.Met490Ile	p.M490I	ENST00000231790	NM_000249.3	490	atG/atT	13/19	0.57408020025662	1	FACETS	0.346	0.303	0.392	0.346	0.303	0.392	SUBCLONAL	1	TRUE	0	0.57408020025662	1		429	531	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118942	3118942	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1057519742	NA	P-0042025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	192	672	1	ENST00000078429.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000078429	NM_002067.2	209	cAg/cTg	5/7	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.327437422548387	2		673	1072	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27220064	27220064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780622660	NA	P-0042025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	140	534	0	ENST00000380036.4:c.3121G>A	p.Gly1041Arg	p.G1041R	ENST00000380036	NM_000459.3	1041	Ggg/Agg	21/23	1	2	FACETS	0.987	0.899	1	0.987	0.899	1	CLONAL	1	TRUE	1	0.327437422548387	2		534	866	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	171	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.584039669439188	2		422	503	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191481	10191482	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AAAGAGCGATGCCTCCA	novel	NA	P-0042026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	117	422	0	ENST00000256474.2:c.475_491dup	p.Val165LysfsTer11	p.V165Kfs*11	ENST00000256474	NM_000551.3	158	-/AAAGAGCGATGCCTCCA	3/3	0.584039669439188	1	FACETS	0.771	0.702	0.842	0.771	0.702	0.842	SUBCLONAL	1	TRUE	0	0.584039669439188	1		422	368	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793554	89793554	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	98	301	0	ENST00000336032.3:c.623A>T	p.Gln208Leu	p.Q208L	ENST00000336032	NM_006813.2	208	cAa/cTa	2/2	1	2	FACETS	0.97	0.874	1	0.97	0.874	1	CLONAL	1	TRUE	1	0.584039669439188	2		301	346	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371725	89371728	+	stop_gained	Nonsense_Mutation	ONP	TCTT	TCTT	ACTA	novel	NA	P-0042026-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	63	621	0	ENST00000301030.4:c.112_115delinsTAGT	p.Lys38_Thr39delinsTer	p.K38_T39delins*	ENST00000301030	NM_001256183.1	38	AAGAcc/TAGTcc	4/13	1	2	FACETS	0.296	0.255	0.34	0.296	0.255	0.34	SUBCLONAL	1	TRUE	1	0.584039669439188	2		621	729	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0042028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	409	318	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.923556521130697	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.923556521130697	1		318	455	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974799	21974799	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042028-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	56	160	0	ENST00000304494.5:c.28G>T	p.Glu10Ter	p.E10*	ENST00000304494	NM_000077.4	10	Gag/Tag	1/3	0.923556521130697	1	FACETS	0.531	0.469	0.593	0.531	0.469	0.593	SUBCLONAL	1	TRUE	0	0.923556521130697	1		160	123	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0042030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	33	142	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.862	1	1	0.965	1	CLONAL	2	FALSE	1	0.22492218204811	2		142	140	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413049	139413049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064795070	NA	P-0042030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	65	302	0	ENST00000277541.6:c.1093C>T	p.Arg365Cys	p.R365C	ENST00000277541	NM_017617.3	365	Cgc/Tgc	6/34	0.179582678368052	1	FACETS	0.985	0.855	1	0.985	0.855	1	CLONAL	1	FALSE	0	0.22492218204811	1		302	521	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650364	12650364	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs775781057	NA	P-0042030-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	26	458	0	ENST00000251849.4:c.482A>G	p.Asn161Ser	p.N161S	ENST00000251849	NM_002880.3	161	aAt/aGt	5/17	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	FALSE	1	0.22492218204811	2		458	209	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115928	8115929	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0042031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	144	697	1	ENST00000346208.3:c.1275dup	p.Ser426IlefsTer81	p.S426Ifs*81	ENST00000346208		425	cca/ccAa	6/6	0.0721963855913317	3	FACETS	0.956	0.874	1	0.956	0.874	1	INDETERMINATE	2	TRUE	1	0.248365793979578	3		698	682	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873435	151873435	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	88	582	0	ENST00000262189.6:c.9103C>T	p.Gln3035Ter	p.Q3035*	ENST00000262189	NM_170606.2	3035	Caa/Taa	38/59	0.1272593779612	4	FACETS	0.797	0.708	0.892	0.797	0.708	0.892	INDETERMINATE	2	TRUE	2	0.248365793979578	4		582	555	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432075	49432075	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	143	1050	0	ENST00000301067.7:c.9064G>A	p.Asp3022Asn	p.D3022N	ENST00000301067	NM_003482.3	3022	Gat/Aat	34/54	0.248365793979578	7	FACETS	0.874	0.795	0.956	0.437	0.397	0.478	CLONAL	2	TRUE	3	0.248365793979578	7		1050	1068	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394702	45394702	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	54	292	0	ENST00000262160.6:c.647A>G	p.Tyr216Cys	p.Y216C	ENST00000262160	NM_005901.5	216	tAt/tGt	5/11	0.176437449468741	2	FACETS	1	0.961	1	0.69	0.593	0.795	CLONAL	1	TRUE	0	0.248365793979578	2		292	315	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578213	7578214	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs864309495	NA	P-0042032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	693	864	0	ENST00000269305.4:c.635_636del	p.Phe212SerfsTer3	p.F212Sfs*3	ENST00000269305	NM_001126112.2	212	tTT/t	6/11	0.859047536097485	2	FACETS	0.992	0.976	1	0.992	0.976	1	CLONAL	2	TRUE	0	0.896836078886559	2		864	779	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974777	21974780	+	frameshift_variant	Frame_Shift_Del	DEL	GCCA	GCCA	-	rs587782206	NA	P-0042032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	352	303	0	ENST00000304494.5:c.47_50del	p.Leu16ProfsTer9	p.L16Pfs*9	ENST00000304494	NM_000077.4	16	cTGGCc/cc	1/3	0.859047536097485	2	FACETS	0.896	0.87	0.921	0.896	0.87	0.921	CLONAL	2	TRUE	0	0.896836078886559	2		303	438	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397742	139397742	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	641	920	2	ENST00000277541.6:c.5059C>T	p.Gln1687Ter	p.Q1687*	ENST00000277541	NM_017617.3	1687	Cag/Tag	27/34	0.859047536097485	2	FACETS	0.989	0.972	1	0.989	0.972	1	CLONAL	2	TRUE	0	0.896836078886559	2		922	723	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451554	70451554	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042032-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	549	733	0	ENST00000373644.4:c.6394T>C	p.Tyr2132His	p.Y2132H	ENST00000373644	NM_030625.2	2132	Tat/Cat	12/12	0.896836078886559	3	FACETS	0.955	0.924	0.986	0.955	0.924	0.986	CLONAL	2	TRUE	1	0.896836078886559	3		733	928	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667528	29667528	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042039-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	80	448	0	ENST00000356175.3:c.6864del	p.Pro2289LeufsTer9	p.P2289Lfs*9	ENST00000356175	NM_000267.3	2288	tcG/tc	46/57	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		448	798	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0042047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	160	413	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.287331289733705	3	FACETS	0.831	0.762	0.902	0.831	0.762	0.902	CLONAL	2	TRUE	1	0.26	3		413	837	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2108758	2108758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397515300	NA	P-0042047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	47	660	0	ENST00000219476.3:c.859G>A	p.Glu287Lys	p.E287K	ENST00000219476	NM_000548.3	287	Gag/Aag	10/42	1	2	FACETS	0.462	0.388	0.543	0.462	0.388	0.543	SUBCLONAL	1	TRUE	1	0.26	2		660	783	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645634	12645634	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0042047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	28	228	0	ENST00000251849.4:c.834+1G>T		p.X278_splice	ENST00000251849	NM_002880.3	278			1	2	FACETS	0.865	0.694	1	0.865	0.694	1	CLONAL	1	TRUE	1	0.26	2		228	249	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517856	187517856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042047-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	42	450	0	ENST00000441802.2:c.12838G>A	p.Glu4280Lys	p.E4280K	ENST00000441802	NM_005245.3	4280	Gag/Aag	25/27	1	2	FACETS	0.603	0.503	0.714	0.603	0.503	0.714	SUBCLONAL	1	TRUE	1	0.26	2		450	536	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48919236	48919236	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0042097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	84	29	0	ENST00000267163.4:c.401T>G	p.Leu134Ter	p.L134*	ENST00000267163	NM_000321.2	134	tTa/tGa	4/27	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		29	95	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056331	26056333	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs762045774	NA	P-0042097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	177	308	0	ENST00000343677.2:c.324_326del	p.Asn108del	p.N108del	ENST00000343677	NM_005319.3	108	aaCAAg/aag	1/1	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		308	453	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151174480	151174480	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	96	167	0	ENST00000262187.5:c.214C>G	p.Gln72Glu	p.Q72E	ENST00000262187	NM_005614.3	72	Cag/Gag	4/8	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		167	346	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141568632	141568632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042097-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	616	1043	0	ENST00000220592.5:c.830G>A	p.Arg277Lys	p.R277K	ENST00000220592	NM_012154.3	277	aGg/aAg	7/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		1043	900	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0042098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	183	291	1	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.167200099478325	3	FACETS	0.945	0.873	1	0.945	0.873	1	CLONAL	3	TRUE	0	0.170713874684076	3		292	821	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0042098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	47	119	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.944	0.796	1	0.944	0.796	1	CLONAL	1	TRUE	1	0.170713874684076	2		119	583	SUCCESS
APC	324	MSKCC	GRCh37	5	112174406	112174406	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	34	82	0	ENST00000257430.4:c.3115G>T	p.Gly1039Ter	p.G1039*	ENST00000257430	NM_000038.5	1039	Gga/Tga	16/16	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.170713874684076	2		82	287	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119780	70119781	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0042098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	110	254	0	ENST00000245479.2:c.788dup	p.Arg264GlnfsTer32	p.R264Qfs*32	ENST00000245479	NM_000346.3	261	gag/gaGg	3/3	0.170713874684076	3	FACETS	0.839	0.753	0.929	0.839	0.753	0.929	CLONAL	2	TRUE	1	0.170713874684076	3		254	834	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609331	81609331	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139286618	NA	P-0042098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	55	71	0	ENST00000298171.2:c.929G>A	p.Arg310His	p.R310H	ENST00000298171	NM_000369.2	310	cGc/cAc	10/10	0.170713874684076	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	2	TRUE	0	0.170713874684076	2		71	293	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65300245	65300245	+	stop_lost	Nonstop_Mutation	SNP	T	T	G	novel	NA	P-0042098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	25	70	0	ENST00000342505.4:c.3465A>C	p.Ter1155TyrextTer3	p.*1155Yext*3	ENST00000342505	NM_002227.2	1155	taA/taC	25/25	1	2	FACETS	1	0.805	1	1	0.805	1	CLONAL	1	TRUE	1	0.170713874684076	2		70	287	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720895	119720895	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	29	86	0	ENST00000316626.5:c.280A>G	p.Lys94Glu	p.K94E	ENST00000316626		94	Aag/Gag	2/12	0.170713874684076	3	FACETS	0.848	0.68	1	0.424	0.34	0.52	CLONAL	1	TRUE	1	0.170713874684076	3		86	435	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875028	151875028	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042098-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	26	76	0	ENST00000262189.6:c.7510C>T	p.Gln2504Ter	p.Q2504*	ENST00000262189	NM_170606.2	2504	Caa/Taa	38/59	0.170713874684076	4	FACETS	1	0.903	1	0.63	0.5	0.778	CLONAL	1	TRUE	2	0.170713874684076	4		76	283	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	83	446	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.231918922272932	0	FACETS	0.336	0.297	0.378			1	INDETERMINATE	1	TRUE	0	0.494719677922536	0		446	504	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716323	52716323	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	101	521	1	ENST00000322088.6:c.767C>T	p.Ser256Phe	p.S256F	ENST00000322088	NM_014225.5	256	tCc/tTc	6/15	0.306351299618142	2	FACETS	0.623	0.558	0.693	0.312	0.279	0.347	SUBCLONAL	1	TRUE	0	0.494719677922536	2		522	655	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577129	7577129	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1057519986	NA	P-0042101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	105	538	0	ENST00000269305.4:c.809T>G	p.Phe270Cys	p.F270C	ENST00000269305	NM_001126112.2	270	tTt/tGt	8/11	0.231918922272932	0	FACETS	0.405	0.364	0.448			1	INDETERMINATE	1	TRUE	0	0.494719677922536	0		538	530	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426177	49426177	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	162	580	0	ENST00000301067.7:c.12311A>C	p.Gln4104Pro	p.Q4104P	ENST00000301067	NM_003482.3	4104	cAa/cCa	39/54	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.494719677922536	2		580	629	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951962	178951962	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	142	353	0	ENST00000263967.3:c.3017T>G	p.Leu1006Arg	p.L1006R	ENST00000263967	NM_006218.2	1006	cTt/cGt	21/21	0.264573928212092	3	FACETS	1	0.984	1	0.656	0.601	0.713	INDETERMINATE	1	TRUE	1	0.494719677922536	3		353	546	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416582	49416582	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042101-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	80	413	0	ENST00000301067.7:c.16129A>G	p.Ser5377Gly	p.S5377G	ENST00000301067	NM_003482.3	5377	Agc/Ggc	51/54	1	2	FACETS	0.528	0.465	0.596	0.528	0.465	0.596	SUBCLONAL	1	TRUE	1	0.494719677922536	2		413	612	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591891	48591891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912581	NA	P-0042102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	117	323	0	ENST00000342988.3:c.1054G>A	p.Gly352Arg	p.G352R	ENST00000342988	NM_005359.5	352	Gga/Aga	9/12	0.186656009651256	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.186656009651256	2		323	553	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743939	41743939	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1160421475	NA	P-0042102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	78	709	0	ENST00000301178.4:c.874C>A	p.His292Asn	p.H292N	ENST00000301178	NM_021913.4	292	Cat/Aat	7/20	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.186656009651256	2		709	830	SUCCESS
AR	367	MSKCC	GRCh37	X	66937345	66937345	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042102-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	45	416	0	ENST00000374690.3:c.2199C>A	p.Asp733Glu	p.D733E	ENST00000374690	NM_000044.3	733	gaC/gaA	5/8	1	2	FACETS	0.821	0.69	0.968	0.821	0.69	0.968	CLONAL	1	TRUE	1	0.186656009651256	2		416	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0042105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	102	531	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.23	2		531	830	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368202	45368202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	39	323	0	ENST00000262160.6:c.1400C>T	p.Ser467Leu	p.S467L	ENST00000262160	NM_005901.5	467	tCa/tTa	11/11	1	2	FACETS	0.783	0.649	0.932	0.783	0.649	0.932	CLONAL	1	TRUE	1	0.23	2		323	433	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400934	72400934	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042105-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	31	356	0	ENST00000357731.5:c.237T>G	p.Phe79Leu	p.F79L	ENST00000357731	NM_173808.2	79	ttT/ttG	2/7	1	2	FACETS	0.499	0.403	0.609	0.499	0.403	0.609	SUBCLONAL	1	TRUE	1	0.23	2		356	540	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0042118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	136	143	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.259520671673895	4	FACETS	0.827	0.756	0.9	0.827	0.756	0.9	INDETERMINATE	2	TRUE	2	0.481811755239288	4		143	506	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111433	8111434	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CA	CA	-	rs763236375	NA	P-0042118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	409	742	0	ENST00000346208.3:c.922-3_922-2del		p.X308_splice	ENST00000346208		308			0.331410123753774	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	2	0.481811755239288	4		742	1030	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264404	16264404	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	397	1104	0	ENST00000375759.3:c.10608del	p.Ser3537ProfsTer11	p.S3537Pfs*11	ENST00000375759	NM_015001.2	3536	cGg/cg	13/15	0.383464656337658	6	FACETS	1	0.981	1	0.788	0.752	0.826	CLONAL	3	TRUE	2	0.481811755239288	6		1104	1026	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063321	67063339	+	protein_altering_variant	In_Frame_Del	DEL	TCGTGCCCGACCAGAGAAG	TCGTGCCCGACCAGAGAAG	GGCA	novel	NA	P-0042118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	174	598	2	ENST00000412916.2:c.11_29delinsGGCA	p.Val4_Ser10delinsGlyHis	p.V4_S10delinsGH	ENST00000412916		4	gTCGTGCCCGACCAGAGAAGc/gGGCAc	1/6	0.491707104546088	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.481811755239288	1		600	441	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853420	151853421	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0042118-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	315	507	0	ENST00000262189.6:c.11681dup	p.Leu3894PhefsTer3	p.L3894Ffs*3	ENST00000262189	NM_170606.2	3894	tta/ttTa	45/59	0.458127018991467	4	FACETS	0.999	0.959	1			1	CLONAL	4	TRUE	NA	0.481811755239288	4		507	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0042136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	98	65	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		65	1075	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339566	116339566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35469582	NA	P-0042136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	51	395	0	ENST00000397752.3:c.428G>A	p.Arg143Gln	p.R143Q	ENST00000397752	NM_000245.2	143	cGa/cAa	2/21	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		395	590	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971047	21971063	+	frameshift_variant	Frame_Shift_Del	DEL	AGCCGCGCCCCGGCCCG	AGCCGCGCCCCGGCCCG	-	novel	NA	P-0042136-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	53	665	0	ENST00000304494.5:c.295_311del	p.Arg99GlyfsTer15	p.R99Gfs*15	ENST00000304494	NM_000077.4	99	CGGGCCGGGGCGCGGCTg/g	2/3	0.0856126109576298	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		665	821	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0042158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	88	449	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.314831602428445	1	FACETS	0.804	0.721	0.89	1	0.983	1	CLONAL	2	FALSE	0	0.314831602428445	1		449	293	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0042158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	27	217	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	FALSE	1	0.314831602428445	2		217	159	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100175	27100176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0042158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	45	552	0	ENST00000324856.7:c.3977dup	p.Gln1327AlafsTer11	p.Q1327Afs*11	ENST00000324856	NM_006015.4	1324	tac/taCc	16/20	0.1660817899722	4	FACETS	1	0.948	1	0.657	0.555	0.768	INDETERMINATE	1	FALSE	2	0.314831602428445	4		552	286	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225371674	225371674	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	40	603	0	ENST00000264414.4:c.930G>T	p.Leu310Phe	p.L310F	ENST00000264414	NM_003590.4	310	ttG/ttT	7/16	1	2	FACETS	0.601	0.499	0.713	0.601	0.499	0.713	SUBCLONAL	1	FALSE	1	0.314831602428445	2		603	423	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262372	46262372	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	22	417	0	ENST00000371998.3:c.956A>G	p.Tyr319Cys	p.Y319C	ENST00000371998		319	tAt/tGt	9/23	0.314831602428445	3	FACETS	0.752	0.586	0.944	0.376	0.293	0.472	CLONAL	1	FALSE	1	0.314831602428445	3		417	215	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72842119	72842119	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042158-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	50	293	0	ENST00000325599.8:c.1129A>C	p.Ile377Leu	p.I377L	ENST00000325599	NM_018130.2	377	Ata/Cta	10/11	0.26635709661287	5	FACETS	1	0.946	1	0.812	0.699	0.932	CLONAL	2	FALSE	2	0.314831602428445	5		293	192	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0042158-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	177	449	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.734702365955969	1	FACETS	0.894	0.839	0.949	0.894	0.839	0.949	CLONAL	1	TRUE	0	0.734702365955969	1		449	341	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0042158-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	127	217	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.311554223765923	1	FACETS	0.706	0.649	0.763	0.706	0.649	0.763	INDETERMINATE	1	TRUE	0	0.734702365955969	1		217	310	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100175	27100176	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0042158-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	121	552	0	ENST00000324856.7:c.3977dup	p.Gln1327AlafsTer11	p.Q1327Afs*11	ENST00000324856	NM_006015.4	1324	tac/taCc	16/20	0.371323396211837	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.734702365955969	0		552	508	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72842119	72842119	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042158-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	159	293	0	ENST00000325599.8:c.1129A>C	p.Ile377Leu	p.I377L	ENST00000325599	NM_018130.2	377	Ata/Cta	10/11	0.311554223765923	1	FACETS	0.81	0.755	0.866	0.81	0.755	0.866	INDETERMINATE	1	TRUE	0	0.734702365955969	1		293	338	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980849	40980849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs548511212	NA	P-0042158-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	146	621	0	ENST00000373198.4:c.1637G>A	p.Arg546Gln	p.R546Q	ENST00000373198	NM_133170.3	546	cGg/cAg	10/32	0.701988201065824	1	FACETS	0.34	0.311	0.371	0.34	0.311	0.371	SUBCLONAL	1	TRUE	0	0.734702365955969	1		621	739	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28931589	NA	P-0042158-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	18	311	0	ENST00000349496.5:c.101G>T	p.Gly34Val	p.G34V	ENST00000349496	NM_001904.3	34	gGa/gTa	3/15	0.311554223765923	1	FACETS	0.064	0.048	0.084	0.064	0.048	0.084	INDETERMINATE	1	TRUE	0	0.734702365955969	1		311	483	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467993	50467993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042158-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	160	654	0	ENST00000331340.3:c.1228G>A	p.Gly410Ser	p.G410S	ENST00000331340	NM_006060.4	410	Ggt/Agt	8/8	NA	2	FACETS	0.494	0.453	0.537			1	INDETERMINATE	1	TRUE	NA	0.734702365955969	2		654	881	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211939	36211939	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519283	NA	P-0042158-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1369	142	1022	0	ENST00000222270.7:c.1690C>T	p.Arg564Ter	p.R564*	ENST00000222270	NM_014727.1	564	Cga/Tga	3/37	1	2	FACETS	0.256	0.232	0.281	0.256	0.232	0.281	SUBCLONAL	1	TRUE	1	0.734702365955969	2		1022	1511	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	161	422	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.97	0.906	1	1	0.994	1	CLONAL	3	TRUE	1	0.341610876422952	2		422	324	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519893	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	163	377	1	ENST00000267101.3:c.310G>T	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ttg	3/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.341610876422952	2		378	811	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	63	453	0	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	0.144889093729129	0	FACETS	0.764	0.665	0.869			1	INDETERMINATE	1	TRUE	0	0.341610876422952	0		453	318	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	85	142	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.341610876422952	2		142	346	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	144	467	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.341610876422952	2		467	674	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163297	32163297	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1239036035	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	168	1073	0	ENST00000375023.3:c.5929G>A	p.Glu1977Lys	p.E1977K	ENST00000375023	NM_004557.3	1977	Gag/Aag	30/30	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.341610876422952	2		1073	914	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482537	56482537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	145	368	0	ENST00000267101.3:c.994G>A	p.Glu332Lys	p.E332K	ENST00000267101	NM_001982.3	332	Gag/Aag	9/28	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.341610876422952	2		368	617	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	183	344	0	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	0.341610876422952	2	FACETS	0.928	0.862	0.997	0.928	0.862	0.997	CLONAL	2	TRUE	0	0.341610876422952	2		344	577	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068384	26068384	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	305	366	2	ENST00000435504.4:c.106C>T	p.Gln36Ter	p.Q36*	ENST00000435504		36	Caa/Taa	2/13	0.341610876422952	2	FACETS	1	0.98	1	1	0.997	1	CLONAL	5	TRUE	0	0.341610876422952	2		368	354	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363243	40363243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	156	704	0	ENST00000397332.2:c.986C>T	p.Ser329Leu	p.S329L	ENST00000397332	NM_001033082.2	329	tCg/tTg	3/3	0.230990397902159	4	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.341610876422952	4		704	817	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627774	187627774	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1183516785	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	81	669	0	ENST00000441802.2:c.3208C>T	p.Arg1070Ter	p.R1070*	ENST00000441802	NM_005245.3	1070	Cga/Tga	2/27	1	2	FACETS	0.881	0.778	0.992	0.881	0.778	0.992	CLONAL	1	TRUE	1	0.341610876422952	2		669	538	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55524236	55524236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1490714621	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	86	690	0	ENST00000288135.5:c.55C>T	p.Arg19Cys	p.R19C	ENST00000288135	NM_000222.2	19	Cgc/Tgc	1/21	1	2	FACETS	0.974	0.864	1	0.974	0.864	1	CLONAL	1	TRUE	1	0.341610876422952	2		690	517	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41228557	41228557	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	105	684	0	ENST00000357654.3:c.4432G>C	p.Glu1478Gln	p.E1478Q	ENST00000357654	NM_007294.3	1478	Gag/Cag	13/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.341610876422952	2		684	498	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880998	37880998	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs144434331	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	129	839	0	ENST00000269571.5:c.2327G>T	p.Gly776Val	p.G776V	ENST00000269571		776	gGt/gTt	20/27	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.341610876422952	2		839	707	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774148	56774148	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	197	679	1	ENST00000337432.4:c.499G>A	p.Asp167Asn	p.D167N	ENST00000337432	NM_058216.2	167	Gat/Aat	3/9	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	1	0.341610876422952	2		680	467	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912158	114912158	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	106	715	0	ENST00000543371.1:c.1228C>A	p.His410Asn	p.H410N	ENST00000543371	NM_001198531.1	410	Cat/Aat	11/14	1	2	FACETS	0.979	0.879	1	0.979	0.879	1	CLONAL	1	TRUE	1	0.341610876422952	2		715	634	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477861	140477861	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs397507474	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	79	541	0	ENST00000288602.6:c.1447A>G	p.Lys483Glu	p.K483E	ENST00000288602	NM_004333.4	483	Aaa/Gaa	12/18	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.341610876422952	2		541	447	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608277	100608277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	286	436	0	ENST00000308731.7:c.1813G>A	p.Glu605Lys	p.E605K	ENST00000308731	NM_000061.2	605	Gag/Aag	18/19	1	1	FACETS	1	0.991	1	1	0.997	1	CLONAL	4	TRUE	0	0.341610876422952	1		436	330	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918695	44918695	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746746824	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	161	273	1	ENST00000377967.4:c.1178G>A	p.Arg393Gln	p.R393Q	ENST00000377967	NM_021140.2	393	cGa/cAa	12/29	1	1	FACETS	0.967	0.925	1	1	0.995	1	CLONAL	4	TRUE	0	0.341610876422952	1		274	202	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942153	81942153	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	138	793	1	ENST00000359376.3:c.1690C>T	p.Arg564Trp	p.R564W	ENST00000359376	NM_002661.3	564	Cgg/Tgg	17/33	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.341610876422952	2		794	675	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780289	9780289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201282174	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	181	671	2	ENST00000377346.4:c.1459G>A	p.Ala487Thr	p.A487T	ENST00000377346	NM_005026.3	487	Gcc/Acc	11/24	1	2	FACETS	1	0.975	1	1	0.994	1	CLONAL	2	TRUE	1	0.341610876422952	2		673	481	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495462	56495462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	153	781	1	ENST00000267101.3:c.3652G>A	p.Glu1218Lys	p.E1218K	ENST00000267101	NM_001982.3	1218	Gag/Aag	28/28	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.341610876422952	2		782	675	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976499	18976499	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	168	913	0	ENST00000262803.5:c.3149C>T	p.Ser1050Phe	p.S1050F	ENST00000262803	NM_002911.3	1050	tCt/tTt	22/24	0.341610876422952	2	FACETS	1	0.986	1	0.665	0.613	0.72	CLONAL	1	TRUE	0	0.341610876422952	2		913	739	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135785984	135785984	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	307	817	0	ENST00000298552.3:c.1237C>T	p.Gln413Ter	p.Q413*	ENST00000298552	NM_001162426.1	413	Cag/Tag	12/23	1	2	FACETS	0.88	0.836	0.924	1	0.996	1	CLONAL	3	TRUE	1	0.341610876422952	2		817	681	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157603	106157603	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	51	400	0	ENST00000380013.4:c.2504C>G	p.Ser835Ter	p.S835*	ENST00000380013	NM_001127208.2	835	tCa/tGa	3/11	1	2	FACETS	1	0.876	1	1	0.876	1	CLONAL	1	TRUE	1	0.341610876422952	2		400	291	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374921	149374921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	262	676	0	ENST00000360632.3:c.173C>T	p.Ser58Leu	p.S58L	ENST00000360632	NM_015472.4	58	tCg/tTg	2/7	1	2	FACETS	0.954	0.904	1	1	0.996	1	CLONAL	3	TRUE	1	0.341610876422952	2		676	536	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662301	227662301	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1289819083	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	113	900	2	ENST00000305123.5:c.1154C>T	p.Ser385Leu	p.S385L	ENST00000305123	NM_005544.2	385	tCg/tTg	1/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.341610876422952	2		902	545	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253394	226253394	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	75	212	0	ENST00000366813.1:c.166C>T	p.Gln56Ter	p.Q56*	ENST00000366813		56	Cag/Tag	2/3	0.323086400863214	4	FACETS	1	0.887	1	0.668	0.591	0.749	CLONAL	2	TRUE	1	0.341610876422952	4		212	294	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775794	9775794	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs756298807	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	275	962	0	ENST00000377346.4:c.337A>G	p.Ile113Val	p.I113V	ENST00000377346	NM_005026.3	113	Atc/Gtc	4/24	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.341610876422952	2		962	683	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36823935	36823935	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	107	851	0	ENST00000373129.3:c.247G>C	p.Glu83Gln	p.E83Q	ENST00000373129	NM_032017.1	83	Gag/Cag	5/12	1	2	FACETS	0.943	0.847	1	0.943	0.847	1	CLONAL	1	TRUE	1	0.341610876422952	2		851	664	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508729	148508729	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	154	437	0	ENST00000320356.2:c.1935A>T	p.Glu645Asp	p.E645D	ENST00000320356	NM_004456.4	645	gaA/gaT	16/20	1	2	FACETS	1	0.985	1	1	0.993	1	CLONAL	2	TRUE	1	0.341610876422952	2		437	361	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265468	198265468	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	72	496	0	ENST00000335508.6:c.2689C>T	p.Leu897Phe	p.L897F	ENST00000335508	NM_012433.2	897	Ctt/Ttt	18/25	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.341610876422952	2		496	402	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029427	16029427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	67	305	0	ENST00000268712.3:c.1603G>A	p.Glu535Lys	p.E535K	ENST00000268712	NM_006311.3	535	Gaa/Aaa	15/46	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.341610876422952	2		305	363	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885748	23885748	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	156	821	1	ENST00000374561.5:c.170G>A	p.Gly57Glu	p.G57E	ENST00000374561	NM_002167.4	57	gGa/gAa	1/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.341610876422952	2		822	681	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100112	27100119	+	frameshift_variant	Frame_Shift_Del	DEL	GGGCCCCA	GGGCCCCA	-	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	236	792	0	ENST00000324856.7:c.3908_3915del	p.Gly1303AlafsTer17	p.G1303Afs*17	ENST00000324856	NM_006015.4	1303	gGGGCCCCA/g	16/20	1	2	FACETS	1	0.98	1	1	0.995	1	CLONAL	2	TRUE	1	0.341610876422952	2		792	630	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105761	27105761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	68	573	0	ENST00000324856.7:c.5372C>T	p.Ser1791Leu	p.S1791L	ENST00000324856	NM_006015.4	1791	tCa/tTa	20/20	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.341610876422952	2		573	388	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258691	115258691	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	184	442	0	ENST00000369535.4:c.91G>C	p.Glu31Gln	p.E31Q	ENST00000369535	NM_002524.4	31	Gaa/Caa	2/7	1	2	FACETS	1	0.986	1	1	0.994	1	CLONAL	2	TRUE	1	0.341610876422952	2		442	441	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253406	226253406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	70	140	1	ENST00000366813.1:c.178G>A	p.Glu60Lys	p.E60K	ENST00000366813		60	Gaa/Aaa	2/3	0.323086400863214	4	FACETS	0.881	0.782	0.984	0.881	0.782	0.984	CLONAL	3	TRUE	1	0.341610876422952	4		141	208	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243801039	243801039	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	44	364	0	ENST00000263826.5:c.435G>C	p.Met145Ile	p.M145I	ENST00000263826	NM_005465.4	145	atG/atC	5/13	0.323086400863214	4	FACETS	0.909	0.765	1	0.303	0.255	0.357	CLONAL	1	TRUE	1	0.341610876422952	4		364	380	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759858	63759858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	66	407	0	ENST00000279873.7:c.511G>A	p.Glu171Lys	p.E171K	ENST00000279873	NM_032199.2	171	Gag/Aag	4/10	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.341610876422952	2		407	328	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759861	63759861	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	69	426	0	ENST00000279873.7:c.514G>A	p.Glu172Lys	p.E172K	ENST00000279873	NM_032199.2	172	Gaa/Aaa	4/10	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.341610876422952	2		426	342	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759933	63759933	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	86	467	0	ENST00000279873.7:c.586G>C	p.Asp196His	p.D196H	ENST00000279873	NM_032199.2	196	Gat/Cat	4/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.341610876422952	2		467	371	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457945	69457945	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	3826	1529	651	0	ENST00000227507.2:c.345G>C	p.Glu115Asp	p.E115D	ENST00000227507	NM_053056.2	115	gaG/gaC	2/5	0.341610876422952	41	FACETS	0.985	0.96	1	0.32	0.312	0.329	CLONAL	13	TRUE	1	0.341610876422952	41		651	5355	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911033	94911033	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	118	638	0	ENST00000536441.1:c.1097G>A	p.Arg366Lys	p.R366K	ENST00000536441	NM_144665.3	366	aGa/aAa	8/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.341610876422952	2		638	500	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94924660	94924660	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	161	869	1	ENST00000536441.1:c.250C>T	p.Gln84Ter	p.Q84*	ENST00000536441	NM_144665.3	84	Cag/Tag	3/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.341610876422952	2		870	731	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352679	118352679	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	238	686	0	ENST00000534358.1:c.3884G>A	p.Ser1295Asn	p.S1295N	ENST00000534358	NM_005933.3	1295	aGc/aAc	7/36	1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	1	0.341610876422952	2		686	590	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375357	118375357	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555047328	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	75	459	0	ENST00000534358.1:c.8750C>G	p.Ser2917Cys	p.S2917C	ENST00000534358	NM_005933.3	2917	tCt/tGt	27/36	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.341610876422952	2		459	362	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377021	118377042	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCGTGATCTTGATTCTGCTT	CAGCGTGATCTTGATTCTGCTT	-	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	71	553	0	ENST00000534358.1:c.10417_10438del	p.Arg3473GlyfsTer11	p.R3473Gfs*11	ENST00000534358	NM_005933.3	3472	CAGCGTGATCTTGATTCTGCTTca/ca	27/36	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.341610876422952	2		553	403	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416741	416741	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	165	431	1	ENST00000399788.2:c.3809C>T	p.Ser1270Phe	p.S1270F	ENST00000399788	NM_001042603.1	1270	tCc/tTc	23/28	1	2	FACETS	0.868	0.808	0.928	1	0.994	1	CLONAL	3	TRUE	1	0.341610876422952	2		432	371	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123683	46123683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	84	448	1	ENST00000334344.6:c.64G>A	p.Glu22Lys	p.E22K	ENST00000334344	NM_152641.2	22	Gag/Aag	1/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.341610876422952	2		449	401	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445305	49445305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	290	1036	3	ENST00000301067.7:c.2161G>A	p.Glu721Lys	p.E721K	ENST00000301067	NM_003482.3	721	Gag/Aag	10/54	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.341610876422952	2		1039	708	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490547	56490547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	83	628	0	ENST00000267101.3:c.2191G>A	p.Glu731Lys	p.E731K	ENST00000267101	NM_001982.3	731	Gag/Aag	19/28	1	2	FACETS	0.857	0.758	0.963	0.857	0.758	0.963	CLONAL	1	TRUE	1	0.341610876422952	2		628	567	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145395	58145395	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	91	652	0	ENST00000257904.6:c.106A>T	p.Ser36Cys	p.S36C	ENST00000257904	NM_000075.3	36	Agt/Tgt	2/8	1	2	FACETS	0.927	0.824	1	0.927	0.824	1	CLONAL	1	TRUE	1	0.341610876422952	2		652	575	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28631565	28631565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	69	448	0	ENST00000241453.7:c.403G>A	p.Glu135Lys	p.E135K	ENST00000241453	NM_004119.2	135	Gaa/Aaa	4/24	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.341610876422952	2		448	354	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914937	32914937	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs786202013	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	162	463	0	ENST00000380152.3:c.6445A>G	p.Ile2149Val	p.I2149V	ENST00000380152		2149	Att/Gtt	11/27	1	2	FACETS	0.911	0.849	0.973	1	0.994	1	CLONAL	3	TRUE	1	0.341610876422952	2		463	347	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30047529	30047529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765759559	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	144	499	0	ENST00000331968.5:c.2472G>A	p.Met824Ile	p.M824I	ENST00000331968	NM_002742.2	824	atG/atA	17/18	1	2	FACETS	1	0.972	1	1	0.992	1	CLONAL	2	TRUE	1	0.341610876422952	2		499	378	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871254	35871254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1295773885	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	191	521	0	ENST00000216797.5:c.919G>A	p.Asp307Asn	p.D307N	ENST00000216797	NM_020529.2	307	Gac/Aac	6/6	1	2	FACETS	1	0.95	1	1	0.994	1	CLONAL	2	TRUE	1	0.341610876422952	2		521	546	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061882	38061882	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	128	977	0	ENST00000250448.2:c.107C>G	p.Ser36Ter	p.S36*	ENST00000250448	NM_004496.3	36	tCa/tGa	2/2	1	2	FACETS	0.901	0.816	0.99	0.901	0.816	0.99	CLONAL	1	TRUE	1	0.341610876422952	2		977	832	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43700279	43700279	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	229	692	0	ENST00000382044.4:c.5608C>G	p.Arg1870Gly	p.R1870G	ENST00000382044	NM_001141980.1	1870	Cgt/Ggt	27/28	1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	1	0.341610876422952	2		692	571	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138318	2138318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781630603	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	88	863	1	ENST00000219476.3:c.5251C>T	p.Arg1751Cys	p.R1751C	ENST00000219476	NM_000548.3	1751	Cgc/Tgc	41/42	1	2	FACETS	0.927	0.823	1	0.927	0.823	1	CLONAL	1	TRUE	1	0.341610876422952	2		864	556	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777996	3777996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	152	1082	0	ENST00000262367.5:c.7052C>T	p.Ser2351Phe	p.S2351F	ENST00000262367	NM_004380.2	2351	tCt/tTt	31/31	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.341610876422952	2		1082	830	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89828376	89828376	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	186	658	0	ENST00000389301.3:c.2833G>T	p.Ala945Ser	p.A945S	ENST00000389301	NM_000135.2	945	Gct/Tct	29/43	1	2	FACETS	1	0.978	1	1	0.994	1	CLONAL	2	TRUE	1	0.341610876422952	2		658	487	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618709	37618709	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	94	795	0	ENST00000447079.4:c.385G>A	p.Glu129Lys	p.E129K	ENST00000447079	NM_015083.1	129	Gaa/Aaa	1/14	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.341610876422952	2		795	549	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223095	41223095	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs747688901	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	115	725	0	ENST00000357654.3:c.4836G>C	p.Gln1612His	p.Q1612H	ENST00000357654	NM_007294.3	1612	caG/caC	15/23	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.341610876422952	2		725	615	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245960	41245960	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	88	801	0	ENST00000357654.3:c.1588G>A	p.Glu530Lys	p.E530K	ENST00000357654	NM_007294.3	530	Gaa/Aaa	10/23	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.341610876422952	2		801	493	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267638	7267638	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	476	914	0	ENST00000302850.5:c.370G>C	p.Glu124Gln	p.E124Q	ENST00000302850	NM_000208.2	124	Gag/Cag	2/22	0.341610876422952	2	FACETS	0.883	0.852	0.913	1	0.997	1	CLONAL	4	TRUE	0	0.341610876422952	2		914	789	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276221	15276221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	164	844	0	ENST00000263388.2:c.5773C>T	p.Leu1925Phe	p.L1925F	ENST00000263388	NM_000435.2	1925	Ctc/Ttc	31/33	0.341610876422952	2	FACETS	0.801	0.739	0.866	0.801	0.739	0.866	CLONAL	2	TRUE	0	0.341610876422952	2		844	599	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17382425	17382425	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	152	858	0	ENST00000359435.4:c.305C>G	p.Ser102Ter	p.S102*	ENST00000359435	NM_001033549.1	102	tCa/tGa	3/9	0.341610876422952	2	FACETS	1	0.988	1	0.727	0.667	0.789	CLONAL	1	TRUE	0	0.341610876422952	2		858	612	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18976501	18976501	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	170	904	3	ENST00000262803.5:c.3151C>T	p.Gln1051Ter	p.Q1051*	ENST00000262803	NM_002911.3	1051	Cag/Tag	22/24	0.341610876422952	2	FACETS	1	0.987	1	0.675	0.622	0.73	CLONAL	1	TRUE	0	0.341610876422952	2		907	737	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36217255	36217255	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	151	773	0	ENST00000222270.7:c.4003+1G>T		p.X1335_splice	ENST00000222270	NM_014727.1	1335			0.341610876422952	2	FACETS	1	0.987	1	0.722	0.663	0.784	CLONAL	1	TRUE	0	0.341610876422952	2		773	612	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143029	30143029	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	225	935	0	ENST00000389048.3:c.497T>C	p.Leu166Pro	p.L166P	ENST00000389048	NM_004304.4	166	cTc/cCc	1/29	0.341610876422952	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.341610876422952	2		935	584	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149956	99149956	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	108	678	0	ENST00000074304.5:c.268G>A	p.Glu90Lys	p.E90K	ENST00000074304	NM_001134224.1	90	Gag/Aag	5/26	1	2	FACETS	0.979	0.88	1	0.979	0.88	1	CLONAL	1	TRUE	1	0.341610876422952	2		678	646	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728529	190728529	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	159	491	0	ENST00000441310.2:c.1917T>G	p.Ile639Met	p.I639M	ENST00000441310	NM_000534.4	639	atT/atG	10/13	1	2	FACETS	1	0.976	1	1	0.993	1	CLONAL	2	TRUE	1	0.341610876422952	2		491	413	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274685	198274685	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	117	628	0	ENST00000335508.6:c.713G>C	p.Arg238Pro	p.R238P	ENST00000335508	NM_012433.2	238	cGt/cCt	7/25	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.341610876422952	2		628	515	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661793	227661793	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1328903394	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	233	943	0	ENST00000305123.5:c.1662G>A	p.Met554Ile	p.M554I	ENST00000305123	NM_005544.2	554	atG/atA	1/2	1	2	FACETS	1	0.977	1	1	0.995	1	CLONAL	2	TRUE	1	0.341610876422952	2		943	629	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326798	62326798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	328	1031	0	ENST00000360203.5:c.3617C>T	p.Ser1206Leu	p.S1206L	ENST00000360203	NM_001283009.1	1206	tCa/tTa	34/35	1	2	FACETS	0.865	0.823	0.908	1	0.997	1	CLONAL	3	TRUE	1	0.341610876422952	2		1031	740	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130505	29130505	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs768384031	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	133	759	0	ENST00000328354.6:c.205C>T	p.Gln69Ter	p.Q69*	ENST00000328354	NM_007194.3	69	Cag/Tag	2/15	1	2	FACETS	0.776	0.708	0.845	1	0.988	1	SUBCLONAL	2	TRUE	1	0.341610876422952	2		759	502	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531855	41531855	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	91	701	0	ENST00000263253.7:c.1567C>T	p.Gln523Ter	p.Q523*	ENST00000263253	NM_001429.3	523	Caa/Taa	7/31	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.341610876422952	2		701	521	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620668	52620668	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	72	452	1	ENST00000394830.3:c.3085G>T	p.Glu1029Ter	p.E1029*	ENST00000394830	NM_018313.4	1029	Gag/Tag	21/30	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.341610876422952	2		453	391	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52713612	52713612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	123	587	0	ENST00000394830.3:c.116C>T	p.Ser39Phe	p.S39F	ENST00000394830	NM_018313.4	39	tCc/tTc	2/30	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.341610876422952	2		587	548	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096164	71096164	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	168	511	0	ENST00000318789.4:c.593C>T	p.Ser198Phe	p.S198F	ENST00000318789	NM_032682.5	198	tCt/tTt	10/21	1	2	FACETS	1	0.975	1	1	0.993	1	CLONAL	2	TRUE	1	0.341610876422952	2		511	443	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921533	178921533	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	65	401	0	ENST00000263967.3:c.1015C>G	p.Leu339Val	p.L339V	ENST00000263967	NM_006218.2	339	Ctt/Gtt	5/21	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.341610876422952	2		401	323	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181386	185181386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	73	483	0	ENST00000265026.3:c.1327G>A	p.Glu443Lys	p.E443K	ENST00000265026	NM_004721.4	443	Gaa/Aaa	8/14	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.341610876422952	2		483	425	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186506993	186506993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	64	351	0	ENST00000323963.5:c.1159G>A	p.Asp387Asn	p.D387N	ENST00000323963		387	Gac/Aac	11/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.341610876422952	2		351	286	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595626	55595626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	43	371	0	ENST00000288135.5:c.2116C>T	p.Leu706Phe	p.L706F	ENST00000288135	NM_000222.2	706	Ctt/Ttt	14/21	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.341610876422952	2		371	197	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99850080	99850080	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	134	895	0	ENST00000280892.6:c.44G>T	p.Arg15Met	p.R15M	ENST00000280892	NM_001130678.1	15	aGg/aTg	1/7	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.341610876422952	2		895	620	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106182959	106182959	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1311542921	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	94	403	0	ENST00000380013.4:c.3998T>C	p.Met1333Thr	p.M1333T	ENST00000380013	NM_001127208.2	1333	aTg/aCg	8/11	1	2	FACETS	1	0.973	1	1	0.989	1	CLONAL	2	TRUE	1	0.341610876422952	2		403	229	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557758	187557758	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	67	440	0	ENST00000441802.2:c.3953G>C	p.Gly1318Ala	p.G1318A	ENST00000441802	NM_005245.3	1318	gGa/gCa	5/27	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.341610876422952	2		440	347	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754823	57754823	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	53	321	0	ENST00000274289.3:c.367C>T	p.Gln123Ter	p.Q123*	ENST00000274289	NM_006622.3	123	Caa/Taa	2/14	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.341610876422952	2		321	265	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020917	26020917	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143364138	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	74	477	0	ENST00000357647.3:c.200C>T	p.Pro67Leu	p.P67L	ENST00000357647	NM_003529.2	67	cCt/cTt	1/1	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.341610876422952	2		477	386	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324136	31324136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137854727	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	59	413	0	ENST00000412585.2:c.427G>A	p.Asp143Asn	p.D143N	ENST00000412585	NM_005514.6	143	Gac/Aac	3/8	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.341610876422952	2		413	253	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166219	32166219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	164	866	0	ENST00000375023.3:c.4735G>A	p.Asp1579Asn	p.D1579N	ENST00000375023	NM_004557.3	1579	Gac/Aac	26/30	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.341610876422952	2		866	700	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140795	37140795	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	106	612	0	ENST00000373509.5:c.631G>A	p.Glu211Lys	p.E211K	ENST00000373509	NM_002648.3	211	Gag/Aag	5/6	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.341610876422952	2		612	569	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997455	149997455	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	119	638	0	ENST00000253339.5:c.2824G>C	p.Glu942Gln	p.E942Q	ENST00000253339		942	Gaa/Caa	6/7	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.341610876422952	2		638	523	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742993	145742993	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	108	171	0	ENST00000428558.2:c.111G>C	p.Glu37Asp	p.E37D	ENST00000428558	NM_004260.3	37	gaG/gaC	2/22	0.323086400863214	4	FACETS	0.902	0.827	0.978	1	0.977	1	CLONAL	4	TRUE	1	0.341610876422952	4		171	235	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139407925	139407925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	162	932	0	ENST00000277541.6:c.2272G>A	p.Glu758Lys	p.E758K	ENST00000277541	NM_017617.3	758	Gaa/Aaa	14/34	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.341610876422952	2		932	766	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969345	44969403	+	frameshift_variant	Frame_Shift_Del	DEL	TTTGTCACTAATGAGAGTAATTCACGAAAGACCTACATAGTACATTGCCAAGATTGTGC	TTTGTCACTAATGAGAGTAATTCACGAAAGACCTACATAGTACATTGCCAAGATTGTGC	-	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	127	250	0	ENST00000377967.4:c.4027_4085del	p.Phe1343ThrfsTer26	p.F1343Tfs*26	ENST00000377967	NM_021140.2	1343	TTTGTCACTAATGAGAGTAATTCACGAAAGACCTACATAGTACATTGCCAAGATTGTGCa/a	28/29	1	1	FACETS	1	0.979	1	1	0.994	1	CLONAL	4	TRUE	0	0.341610876422952	1		250	148	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152853853	152853853	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042163-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	53	151	0	ENST00000406277.2:c.711G>C	p.Gln237His	p.Q237H	ENST00000406277	NM_152274.4	237	caG/caC	7/7	1	1	FACETS	1	0.955	1	1	0.982	1	CLONAL	2	TRUE	0	0.341610876422952	1		151	109	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104352380	104352426	+	frameshift_variant	Frame_Shift_Del	DEL	CCTTTGGATAACAGTGAGTCAAGAATTCAGCACATGCTGCTGACAGA	CCTTTGGATAACAGTGAGTCAAGAATTCAGCACATGCTGCTGACAGA	-	novel	NA	P-0042167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	237	723	0	ENST00000369902.3:c.496_542del	p.Pro166GlyfsTer25	p.P166Gfs*25	ENST00000369902	NM_016169.3	166	CCTTTGGATAACAGTGAGTCAAGAATTCAGCACATGCTGCTGACAGAg/g	4/12	0.702826578680461	1	FACETS	0.877	0.828	0.926	0.877	0.828	0.926	CLONAL	1	TRUE	0	0.702826578680461	1		723	499	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441815	49441816	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs756471180	NA	P-0042167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	281	734	2	ENST00000301067.7:c.4168dup	p.Ala1390GlyfsTer42	p.A1390Gfs*42	ENST00000301067	NM_003482.3	1390	gca/gGca	14/54	1	2	FACETS	0.828	0.779	0.878	0.828	0.779	0.878	CLONAL	1	TRUE	1	0.702826578680461	2		736	966	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89371683	89371683	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	409	813	1	ENST00000301030.4:c.157G>T	p.Glu53Ter	p.E53*	ENST00000301030	NM_001256183.1	53	Gag/Tag	4/13	0.424578776705323	1	FACETS	0.874	0.836	0.911	0.874	0.836	0.911	CLONAL	1	TRUE	0	0.702826578680461	1		814	864	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578265	7578265	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760043106	NA	P-0042167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	327	757	0	ENST00000269305.4:c.584T>C	p.Ile195Thr	p.I195T	ENST00000269305	NM_001126112.2	195	aTc/aCc	6/11	1	2	FACETS	0.967	0.916	1	0.967	0.916	1	CLONAL	1	TRUE	1	0.702826578680461	2		757	962	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578446	7578446	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	393	824	0	ENST00000269305.4:c.484A>T	p.Ile162Phe	p.I162F	ENST00000269305	NM_001126112.2	162	Atc/Ttc	5/11	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.702826578680461	2		824	1112	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17116988	17116988	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	137	713	0	ENST00000285071.4:c.1721C>A	p.Ala574Asp	p.A574D	ENST00000285071	NM_144997.5	574	gCc/gAc	14/14	1	2	FACETS	0.392	0.356	0.43	0.392	0.356	0.43	SUBCLONAL	1	TRUE	1	0.702826578680461	2		713	994	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25471001	25471001	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201097136	NA	P-0042167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	383	838	2	ENST00000264709.3:c.760G>A	p.Ala254Thr	p.A254T	ENST00000264709	NM_175629.2	254	Gca/Aca	7/23	0.227152044921053	3	FACETS	1	0.99	1	0.581	0.552	0.611	INDETERMINATE	1	TRUE	1	0.702826578680461	3		840	1267	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724103	61724103	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0042167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	182	421	0	ENST00000401558.2:c.799T>C	p.Cys267Arg	p.C267R	ENST00000401558	NM_003400.3	267	Tgc/Cgc	10/25	0.227152044921053	3	FACETS	1	0.987	1	0.646	0.6	0.693	INDETERMINATE	1	TRUE	1	0.702826578680461	3		421	542	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541001	187541001	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1211646461	NA	P-0042167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	202	465	0	ENST00000441802.2:c.6739C>T	p.His2247Tyr	p.H2247Y	ENST00000441802	NM_005245.3	2247	Cac/Tac	10/27	0.702826578680461	1	FACETS	0.997	0.94	1	0.997	0.94	1	CLONAL	1	TRUE	0	0.702826578680461	1		465	374	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541526	187541526	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1422439427	NA	P-0042167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	235	505	0	ENST00000441802.2:c.6214G>T	p.Glu2072Ter	p.E2072*	ENST00000441802	NM_005245.3	2072	Gaa/Taa	10/27	0.702826578680461	1	FACETS	0.964	0.912	1	0.964	0.912	1	CLONAL	1	TRUE	0	0.702826578680461	1		505	450	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629108	86629108	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	44	366	0	ENST00000274376.6:c.853C>G	p.Arg285Gly	p.R285G	ENST00000274376	NM_002890.2	285	Cga/Gga	4/25	0.189184740973509	1	FACETS	0.254	0.213	0.298	0.254	0.213	0.298	INDETERMINATE	1	TRUE	0	0.702826578680461	1		366	320	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525044	157525049	+	missense_variant	Missense_Mutation	ONP	CTTTTG	CTTTTG	TTTTTT	novel	NA	P-0042167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	174	399	0	ENST00000346085.5:c.4939_4944delinsTTTTTT	p.Leu1647_Leu1648delinsPhePhe	p.L1647_L1648delinsFF	ENST00000346085	NM_020732.3	1647	CTTTTG/TTTTTT	19/20	0.260607307006696	1	FACETS	0.673	0.625	0.722	0.673	0.625	0.722	INDETERMINATE	1	TRUE	0	0.702826578680461	1		399	477	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729798	41729798	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0042167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	129	476	0	ENST00000242208.4:c.731G>T	p.Cys244Phe	p.C244F	ENST00000242208	NM_002192.2	244	tGt/tTt	3/3	0.695737324656217	2	FACETS	0.582	0.529	0.637	0.291	0.264	0.319	SUBCLONAL	1	TRUE	0	0.702826578680461	2		476	631	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971025	21971026	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0042167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	180	469	0	ENST00000304494.5:c.332dup	p.Arg112ProfsTer8	p.R112Pfs*8	ENST00000304494	NM_000077.4	111	ggc/ggGc	2/3	0.702826578680461	1	FACETS	0.818	0.764	0.873	0.818	0.764	0.873	CLONAL	1	TRUE	0	0.702826578680461	1		469	406	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820166	139820166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs540379507	NA	P-0042167-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	155	786	0	ENST00000247668.2:c.1319G>A	p.Arg440Gln	p.R440Q	ENST00000247668	NM_021138.3	440	cGg/cAg	11/11	1	2	FACETS	0.456	0.417	0.497	0.456	0.417	0.497	SUBCLONAL	1	TRUE	1	0.702826578680461	2		786	967	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0042173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	21	413	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	1	2	FACETS	0.097	0.074	0.124	0.097	0.074	0.124	SUBCLONAL	1	TRUE	1	0.53	2		413	820	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912664	NA	P-0042173-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	32	901	1	ENST00000269305.4:c.1010G>A	p.Arg337His	p.R337H	ENST00000269305	NM_001126112.2	337	cGc/cAc	10/11	1	2	FACETS	0.147	0.118	0.179	0.147	0.118	0.179	SUBCLONAL	1	TRUE	1	0.53	2		902	822	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412044	116412044	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs869320707	NA	P-0042203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	160	727	0	ENST00000397752.3:c.3028+1G>T		p.X1010_splice	ENST00000397752	NM_000245.2	1010			0.365253409165307	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.370553761365644	2		727	392	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988348	36988348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs546402304	NA	P-0042203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	70	520	1	ENST00000354822.5:c.305C>T	p.Ala102Val	p.A102V	ENST00000354822	NM_001079668.2	102	gCg/gTg	2/3	1	2	FACETS	0.672	0.587	0.765	0.672	0.587	0.765	SUBCLONAL	1	TRUE	1	0.370553761365644	2		521	562	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944391	40944391	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	107	587	0	ENST00000373198.4:c.2111A>T	p.Tyr704Phe	p.Y704F	ENST00000373198	NM_133170.3	704	tAc/tTc	12/32	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.370553761365644	2		587	498	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526269	31526269	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	117	979	0	ENST00000344624.3:c.771C>A	p.Asp257Glu	p.D257E	ENST00000344624		257	gaC/gaA	2/33	1	2	FACETS	0.68	0.612	0.751	0.68	0.612	0.751	SUBCLONAL	1	TRUE	1	0.370553761365644	2		979	929	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874367	151874367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	12	454	0	ENST00000262189.6:c.8171C>T	p.Thr2724Ile	p.T2724I	ENST00000262189	NM_170606.2	2724	aCa/aTa	38/59	0.370553761365644	3	FACETS	0.417	0.293	0.569	0.209	0.146	0.285	SUBCLONAL	1	TRUE	1	0.370553761365644	3		454	184	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020329	123020329	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0042203-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	48	538	0	ENST00000355640.3:c.819del	p.Thr274HisfsTer19	p.T274Hfs*19	ENST00000355640		273	Ggg/gg	2/7	0.25355666949959	0	FACETS	0.493	0.418	0.574			1	SUBCLONAL	1	TRUE	0	0.370553761365644	0		538	331	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947827	178947827	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	51	194	0	ENST00000263967.3:c.2702G>T	p.Cys901Phe	p.C901F	ENST00000263967	NM_006218.2	901	tGt/tTt	19/21	0.288988827422884	3	FACETS	0.873	0.746	1	0.437	0.373	0.506	CLONAL	1	TRUE	1	0.43	3		194	330	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0042217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	212	458	0	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	0.299680275802366	2	FACETS	1	0.986	1	0.614	0.572	0.658	CLONAL	1	TRUE	0	0.43	2		458	803	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0042217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	85	265	1	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	0.200921807474444	3	FACETS	1	0.939	1	0.543	0.482	0.608	INDETERMINATE	1	TRUE	1	0.43	3		266	442	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651558	206651558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782066241	NA	P-0042217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	70	399	0	ENST00000367120.3:c.868G>A	p.Ala290Thr	p.A290T	ENST00000367120	NM_014002.3	290	Gcc/Acc	9/22	0.300971838887716	7	FACETS	0.561	0.487	0.641			1	SUBCLONAL	1	TRUE	NA	0.43	7		399	1205	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41021011	41021011	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	158	351	0	ENST00000267868.3:c.633G>A	p.Met211Ile	p.M211I	ENST00000267868	NM_002875.4	211	atG/atA	7/10	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.43	2		351	730	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117799	70117800	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0042217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	275	341	0	ENST00000245479.2:c.270dup	p.Met91HisfsTer161	p.M91Hfs*161	ENST00000245479	NM_000346.3	89	-/C	1/3	0.264064759839121	3	FACETS	1	0.976	1	0.709	0.669	0.749	CLONAL	2	TRUE	0	0.43	3		341	731	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	44	479	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.363	0.304	0.429	0.363	0.304	0.429	SUBCLONAL	1	TRUE	1	0.46136266716281	2		480	525	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0042240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	38	234	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.348	0.288	0.416	0.348	0.288	0.416	SUBCLONAL	1	TRUE	1	0.46136266716281	2		234	473	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622240	162622240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	40	268	0	ENST00000366898.1:c.457C>T	p.Pro153Ser	p.P153S	ENST00000366898	NM_004562.2	153	Ccc/Tcc	4/12	1	2	FACETS	0.313	0.259	0.373	0.313	0.259	0.373	SUBCLONAL	1	TRUE	1	0.46136266716281	2		268	554	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28886184	28886184	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0042240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	52	628	0	ENST00000282397.4:c.3438A>T	p.Arg1146Ser	p.R1146S	ENST00000282397	NM_002019.4	1146	agA/agT	26/30	0.382693460526765	1	FACETS	0.292	0.248	0.341	0.292	0.248	0.341	SUBCLONAL	1	TRUE	0	0.46136266716281	1		628	593	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604739	48604764	+	frameshift_variant	Frame_Shift_Del	DEL	ACACCTTGCTGGATTGAAATTCACTT	ACACCTTGCTGGATTGAAATTCACTT	-	novel	NA	P-0042240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	38	499	0	ENST00000342988.3:c.1566_1591del	p.Cys523GlyfsTer45	p.C523Gfs*45	ENST00000342988	NM_005359.5	521	ACACCTTGCTGGATTGAAATTCACTTa/a	12/12	1	2	FACETS	0.381	0.315	0.455	0.381	0.315	0.455	SUBCLONAL	1	TRUE	1	0.46136266716281	2		499	432	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68930097	68930097	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	55	479	0	ENST00000288368.4:c.158T>C	p.Met53Thr	p.M53T	ENST00000288368	NM_024870.2	53	aTg/aCg	2/40	1	2	FACETS	0.486	0.416	0.562	0.486	0.416	0.562	SUBCLONAL	1	TRUE	1	0.46136266716281	2		479	491	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970874	70970874	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0042240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	52	574	0	ENST00000276594.2:c.1386+1G>T		p.X462_splice	ENST00000276594	NM_024504.3	462			1	2	FACETS	0.41	0.349	0.477	0.41	0.349	0.477	SUBCLONAL	1	TRUE	1	0.46136266716281	2		574	550	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020356	123020356	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777303823	NA	P-0042240-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	36	466	1	ENST00000355640.3:c.844G>A	p.Glu282Lys	p.E282K	ENST00000355640		282	Gag/Aag	2/7	1	2	FACETS	0.401	0.33	0.481	0.401	0.33	0.481	SUBCLONAL	1	TRUE	1	0.46136266716281	2		467	389	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938646	76938646	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs797044563	NA	P-0042245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	85	467	0	ENST00000373344.5:c.2102G>T	p.Arg701Leu	p.R701L	ENST00000373344	NM_000489.3	701	cGt/cTt	9/35	0.583754863899384	3	FACETS	0.771	0.684	0.864	0.385	0.342	0.432	SUBCLONAL	1	TRUE	1	0.583754863899384	3		467	488	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624296	89624296	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs786201995	NA	P-0042245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	23	464	0	ENST00000371953.3:c.70G>C	p.Asp24His	p.D24H	ENST00000371953	NM_000314.4	24	Gac/Cac	1/9	0.583754863899384	2	FACETS	0.24	0.187	0.302	0.12	0.093	0.151	SUBCLONAL	1	TRUE	0	0.583754863899384	2		464	328	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121909229	NA	P-0042245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	21	405	0	ENST00000371953.3:c.389G>T	p.Arg130Leu	p.R130L	ENST00000371953	NM_000314.4	130	cGa/cTa	5/9	0.583754863899384	2	FACETS	0.226	0.173	0.286	0.113	0.086	0.143	SUBCLONAL	1	TRUE	0	0.583754863899384	2		405	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578247	7578247	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	309	640	0	ENST00000269305.4:c.602del	p.Leu201CysfsTer46	p.L201Cfs*46	ENST00000269305	NM_001126112.2	201	tTg/tg	6/11	0.583754863899384	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.583754863899384	2		640	510	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916728	178916728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	308	333	0	ENST00000263967.3:c.115G>A	p.Glu39Lys	p.E39K	ENST00000263967	NM_006218.2	39	Gag/Aag	2/21	0.583754863899384	5	FACETS	1	0.984	1	1	0.984	1	CLONAL	4	TRUE	1	0.583754863899384	5		333	472	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435522	110435522	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1387644128	NA	P-0042245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	108	421	0	ENST00000375856.3:c.2879C>T	p.Ser960Leu	p.S960L	ENST00000375856	NM_003749.2	960	tCa/tTa	1/2	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.583754863899384	2		421	361	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790830	89790830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	256	665	0	ENST00000336032.3:c.217C>T	p.Arg73Cys	p.R73C	ENST00000336032	NM_006813.2	73	Cgc/Tgc	1/2	0.48112418907568	3	FACETS	0.777	0.731	0.824	0.518	0.487	0.55	SUBCLONAL	2	TRUE	0	0.583754863899384	3		665	729	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969459	44969459	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0042245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	211	411	0	ENST00000377967.4:c.4141G>T	p.Glu1381Ter	p.E1381*	ENST00000377967	NM_021140.2	1381	Gag/Tag	28/29	0.583754863899384	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.583754863899384	2		411	347	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69631165	69631165	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1381894272	NA	P-0042245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	130	669	0	ENST00000334134.2:c.247G>T	p.Val83Leu	p.V83L	ENST00000334134	NM_005247.2	83	Gtg/Ttg	2/3	0.583754863899384	7	FACETS	0.898	0.812	0.989			1	CLONAL	1	TRUE	NA	0.583754863899384	7		669	1220	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670333	134670333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	91	438	0	ENST00000398015.3:c.244G>A	p.Ala82Thr	p.A82T	ENST00000398015	NM_004441.4	82	Gcc/Acc	3/16	0.583754863899384	5	FACETS	0.978	0.87	1	0.244	0.217	0.274	CLONAL	1	TRUE	1	0.583754863899384	5		438	598	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139438551	139438551	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769046407	NA	P-0042245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	128	656	0	ENST00000277541.6:c.65C>T	p.Pro22Leu	p.P22L	ENST00000277541	NM_017617.3	22	cCg/cTg	2/34	0.583754863899384	2	FACETS	0.921	0.84	1	0.461	0.42	0.503	CLONAL	1	TRUE	0	0.583754863899384	2		656	476	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100523	8100523	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0042245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	160	849	0	ENST00000346208.3:c.497C>G	p.Ser166Trp	p.S166W	ENST00000346208		166	tCg/tGg	3/6	0.583754863899384	6	FACETS	0.947	0.866	1	0.237	0.216	0.258	CLONAL	1	TRUE	2	0.583754863899384	6		849	1255	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994340	25994340	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0042245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	91	296	1	ENST00000435504.4:c.473C>T	p.Ser158Leu	p.S158L	ENST00000435504		158	tCa/tTa	6/13	0.539535890210558	3	FACETS	1	0.898	1	0.502	0.449	0.559	CLONAL	1	TRUE	1	0.583754863899384	3		297	401	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056703	180056703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	134	660	0	ENST00000261937.6:c.809G>A	p.Gly270Glu	p.G270E	ENST00000261937	NM_182925.4	270	gGg/gAg	6/30	0.583754863899384	3	FACETS	0.933	0.85	1	0.466	0.425	0.51	CLONAL	1	TRUE	1	0.583754863899384	3		660	636	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040779	47040779	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0042245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	338	812	1	ENST00000377604.3:c.1414A>T	p.Lys472Ter	p.K472*	ENST00000377604	NM_001204468.1	472	Aaa/Taa	13/24	0.583754863899384	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.583754863899384	2		813	535	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938146	76938146	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0042245-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	296	532	0	ENST00000373344.5:c.2602T>A	p.Leu868Met	p.L868M	ENST00000373344	NM_000489.3	868	Ttg/Atg	9/35	0.583754863899384	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.583754863899384	3		532	579	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0042254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	65	588	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	1	2	FACETS	0.724	0.633	0.821	0.724	0.633	0.821	SUBCLONAL	1	TRUE	1	0.594594772956549	2		588	302	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0042254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	75	357	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.898	0.795	1	0.898	0.795	1	CLONAL	1	TRUE	1	0.594594772956549	2		357	281	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0042254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	81	339	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.844	0.75	0.942	0.844	0.75	0.942	CLONAL	1	TRUE	1	0.594594772956549	2		339	323	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717704	89717704	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0042254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	196	302	0	ENST00000371953.3:c.731del	p.Pro244LeufsTer12	p.P244Lfs*12	ENST00000371953	NM_000314.4	243	ttC/tt	7/9	0.594594772956549	2	FACETS	0.958	0.905	1	0.958	0.905	1	CLONAL	2	TRUE	0	0.594594772956549	2		302	344	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470968	25470968	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1483397095	NA	P-0042254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	159	593	1	ENST00000264709.3:c.793G>A	p.Val265Met	p.V265M	ENST00000264709	NM_175629.2	265	Gtg/Atg	7/23	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.594594772956549	2		594	523	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779667	3779667	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	CATGGC	novel	NA	P-0042254-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	111	531	0	ENST00000262367.5:c.5381delinsGCCATG	p.Ser1794CysfsTer7	p.S1794Cfs*7	ENST00000262367	NM_004380.2	1794	tCc/tGCCATGc	31/31	1	2	FACETS	0.889	0.805	0.976	0.889	0.805	0.976	CLONAL	1	TRUE	1	0.594594772956549	2		531	420	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221711	55221711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760101437	NA	P-0042330-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	8	501	0	ENST00000275493.2:c.755G>A	p.Arg252His	p.R252H	ENST00000275493	NM_005228.3	252	cGc/cAc	7/28	0.125148380519483	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		501	388	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	336	479	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.300378946127568	8	FACETS	1	0.959	1	1	0.959	1	CLONAL	7	TRUE	1	0.34	8		480	570	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577556	7577556	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912655	NA	P-0042345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	264	570	1	ENST00000269305.4:c.725G>T	p.Cys242Phe	p.C242F	ENST00000269305	NM_001126112.2	242	tGc/tTc	7/11	0.233529482870251	3	FACETS	1	0.981	1	0.733	0.689	0.778	CLONAL	2	TRUE	0	0.34	3		571	826	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557201	187557201	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0042345-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	167	442	0	ENST00000441802.2:c.4161A>G	p.Ile1387Met	p.I1387M	ENST00000441802	NM_005245.3	1387	atA/atG	6/27	0.300378946127568	3	FACETS	0.999	0.923	1	0.999	0.923	1	CLONAL	2	TRUE	1	0.34	3		442	575	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114816	108114817	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0042346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	208	403	0	ENST00000278616.4:c.640dup	p.Ser214PhefsTer40	p.S214Ffs*40	ENST00000278616	NM_000051.3	211	-/T	6/63	0.646051741679036	2	FACETS	0.917	0.869	0.965	0.917	0.869	0.965	CLONAL	2	TRUE	0	0.646051741679036	2		403	351	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245077	133245077	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764044031	NA	P-0042346-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	334	652	2	ENST00000320574.5:c.2038C>T	p.Arg680Cys	p.R680C	ENST00000320574	NM_006231.2	680	Cgc/Tgc	19/49	0.546819019887055	2	FACETS	0.95	0.912	0.989	0.95	0.912	0.989	CLONAL	2	TRUE	0	0.646051741679036	2		654	544	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214849	36214849	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0042395-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	70	717	0	ENST00000222270.7:c.3275C>A	p.Ser1092Ter	p.S1092*	ENST00000222270	NM_014727.1	1092	tCg/tAg	8/37	1	2	FACETS	0.206	0.179	0.236	0.206	0.179	0.236	SUBCLONAL	1	TRUE	1	0.641819037228594	2		717	1058	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0042403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	163	479	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.767617031144545	1	FACETS	0.976	0.919	1	0.976	0.919	1	CLONAL	1	TRUE	0	0.767617031144545	1		480	268	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184562	7184562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770690301	NA	P-0042403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	458	148	0	ENST00000302850.5:c.739G>A	p.Asp247Asn	p.D247N	ENST00000302850	NM_000208.2	247	Gac/Aac	3/22	0.548566072097749	5	FACETS	1	0.981	1			1	CLONAL	3	TRUE	NA	0.767617031144545	5		148	830	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039179	49039179	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0042403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	265	449	0	ENST00000267163.4:c.2257del	p.Ile753Ter	p.I753*	ENST00000267163	NM_000321.2	753	Ata/ta	22/27	0.767617031144545	4	FACETS	0.997	0.969	1	0.997	0.969	1	CLONAL	4	TRUE	0	0.767617031144545	4		449	306	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054392	42054392	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0042403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	41	416	0	ENST00000219905.7:c.7576G>T	p.Ala2526Ser	p.A2526S	ENST00000219905	NM_001164273.1	2526	Gca/Tca	22/24	1	2	FACETS	0.815	0.694	0.943	0.815	0.694	0.943	CLONAL	1	TRUE	1	0.767617031144545	2		416	131	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578400	+	inframe_deletion	In_Frame_Del	DEL	GGTGGG	GGTGGG	-	novel	NA	P-0042403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	197	876	1	ENST00000269305.4:c.530_535del	p.Pro177_His178del	p.P177_H178del	ENST00000269305	NM_001126112.2	177	cCCCACCat/cat	5/11	0.767617031144545	1	FACETS	0.979	0.927	1	0.979	0.927	1	CLONAL	1	TRUE	0	0.767617031144545	1		877	323	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630047	187630047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199844927	NA	P-0042403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	168	669	0	ENST00000441802.2:c.935G>A	p.Ser312Asn	p.S312N	ENST00000441802	NM_005245.3	312	aGt/aAt	2/27	0.767617031144545	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.767617031144545	1		669	238	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629124	86629124	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0042403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	47	377	0	ENST00000274376.6:c.869A>C	p.Tyr290Ser	p.Y290S	ENST00000274376	NM_002890.2	290	tAc/tCc	4/25	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.767617031144545	2		377	110	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403359	139403359	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0042403-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	198	861	0	ENST00000277541.6:c.3134G>A	p.Cys1045Tyr	p.C1045Y	ENST00000277541	NM_017617.3	1045	tGc/tAc	19/34	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.767617031144545	2		861	504	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55592178	55592179	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGCCTA	novel	NA	P-0042437-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	207	660	0	ENST00000288135.5:c.1504_1509dup	p.Ala502_Tyr503dup	p.A502_Y503dup	ENST00000288135	NM_000222.2	502	tct/tcTGCCTAt	9/21	1	2	FACETS	0.846	0.789	0.905	0.846	0.789	0.905	CLONAL	1	TRUE	1	0.724583577049051	2		660	675	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	54	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.808732715206728	2		280	122	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375566	118375566	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003699-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	213	313	0	ENST00000534358.1:c.8959A>G	p.Thr2987Ala	p.T2987A	ENST00000534358	NM_005933.3	2987	Act/Gct	27/36	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.808732715206728	2		313	489	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0003777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	414	470	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.532474760404898	4	FACETS	1	0.986	1			1	CLONAL	3	TRUE	NA	0.532474760404898	4		470	752	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692799	89692799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	112	159	0	ENST00000371953.3:c.283C>T	p.Pro95Ser	p.P95S	ENST00000371953	NM_000314.4	95	Cca/Tca	5/9	0.532474760404898	2	FACETS	0.983	0.907	1	0.983	0.907	1	CLONAL	2	TRUE	0	0.532474760404898	2		159	214	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257789	133257789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143626223	NA	P-0003777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	90	491	1	ENST00000320574.5:c.139C>T	p.Arg47Trp	p.R47W	ENST00000320574	NM_006231.2	47	Cgg/Tgg	2/49	1	2	FACETS	0.626	0.557	0.7	0.626	0.557	0.7	SUBCLONAL	1	TRUE	1	0.532474760404898	2		492	540	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619180	37619180	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	133	422	2	ENST00000447079.4:c.856C>T	p.Gln286Ter	p.Q286*	ENST00000447079	NM_015083.1	286	Cag/Tag	1/14	1	2	FACETS	0.978	0.893	1	0.978	0.893	1	CLONAL	1	TRUE	1	0.532474760404898	2		424	511	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	65	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.974	0.869	1	0.974	0.869	1	CLONAL	1	TRUE	1	0.920403789425976	2		280	145	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0003783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11795	622	20966	0	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.920403789425976	24	FACETS	1	0.993	1			1	CLONAL	1	TRUE	NA	0.920403789425976	24		20966	12417	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264712	46264712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773102518	NA	P-0003783-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	430	817	0	ENST00000371998.3:c.1582G>A	p.Ala528Thr	p.A528T	ENST00000371998		528	Gcc/Acc	12/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.920403789425976	2		817	933	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003783-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	110	280	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.763898731675759	2		280	230	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221821	55221821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769696078	NA	P-0003783-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20797	169	20966	0	ENST00000275493.2:c.865G>A	p.Ala289Thr	p.A289T	ENST00000275493	NM_005228.3	289	Gcc/Acc	7/28	0.763898731675759	17	FACETS	0.142	0.129	0.156			1	SUBCLONAL	1	TRUE	NA	0.763898731675759	17		20966	20966	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264712	46264712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773102518	NA	P-0003783-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	540	817	0	ENST00000371998.3:c.1582G>A	p.Ala528Thr	p.A528T	ENST00000371998		528	Gcc/Acc	12/23	NA	2	FACETS	0.948	0.91	0.987			1	INDETERMINATE	1	TRUE	NA	0.763898731675759	2		817	1491	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	74	280	0				ENST00000310581	NM_198253.2	-/1132			0.753690036247669	5	FACETS	1	0.966	1	0.797	0.714	0.881	CLONAL	2	TRUE	2	0.753690036247669	5		280	175	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22160227	22160227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	70	357	0	ENST00000215832.6:c.404G>A	p.Arg135Lys	p.R135K	ENST00000215832	NM_002745.4	135	aGa/aAa	3/9	0.753690036247669	3	FACETS	0.532	0.465	0.604	0.266	0.232	0.302	SUBCLONAL	1	TRUE	1	0.753690036247669	3		357	481	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873425	45873425	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	188	388	0	ENST00000391945.4:c.71A>G	p.Tyr24Cys	p.Y24C	ENST00000391945	NM_000400.3	24	tAc/tGc	2/23	0.753690036247669	3	FACETS	1	0.99	1			1	CLONAL	1	TRUE	NA	0.753690036247669	3		388	491	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265540	198265540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	162	451	0	ENST00000335508.6:c.2617G>A	p.Glu873Lys	p.E873K	ENST00000335508	NM_012433.2	873	Gag/Aag	18/25	0.360205451652825	2	FACETS	1	0.952	1	0.517	0.479	0.555	INDETERMINATE	1	TRUE	0	0.753690036247669	2		451	416	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298001	11298001	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	213	451	0	ENST00000361445.4:c.2107C>G	p.Gln703Glu	p.Q703E	ENST00000361445	NM_004958.3	703	Cag/Gag	13/58	0.37669173964385	4	FACETS	0.908	0.85	0.966	0.908	0.85	0.966	INDETERMINATE	2	TRUE	2	0.753690036247669	4		451	546	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458525	120458525	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs369659944	NA	P-0003788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	30	312	0	ENST00000256646.2:c.6820C>G	p.Pro2274Ala	p.P2274A	ENST00000256646	NM_024408.3	2274	Cca/Gca	34/34	0.369844758015066	6	FACETS	0.409	0.329	0.5	0.136	0.109	0.167	INDETERMINATE	1	TRUE	3	0.753690036247669	6		312	488	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128051636	128051636	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756810937	NA	P-0003788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	55	313	0	ENST00000285398.2:c.22G>A	p.Asp8Asn	p.D8N	ENST00000285398	NM_000122.1	8	Gac/Aac	1/15	0.360205451652825	2	FACETS	0.543	0.468	0.623	0.271	0.234	0.312	INDETERMINATE	1	TRUE	0	0.753690036247669	2		313	269	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578331	212578331	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	40	457	0	ENST00000342788.4:c.926C>G	p.Pro309Arg	p.P309R	ENST00000342788	NM_005235.2	309	cCt/cGt	8/28	0.360205451652825	2	FACETS	0.289	0.241	0.343	0.145	0.12	0.172	INDETERMINATE	1	TRUE	0	0.753690036247669	2		457	367	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540924	187540924	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	103	220	0	ENST00000441802.2:c.6816A>G	p.Ile2272Met	p.I2272M	ENST00000441802	NM_005245.3	2272	atA/atG	10/27	0.685967380657102	3	FACETS	1	0.948	1	0.538	0.486	0.591	CLONAL	1	TRUE	1	0.753690036247669	3		220	350	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670918	30670918	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	132	427	0	ENST00000376406.3:c.5828G>C	p.Arg1943Pro	p.R1943P	ENST00000376406	NM_014641.2	1943	cGg/cCg	12/15	0.504587606834328	4	FACETS	1	0.963	1	0.368	0.336	0.402	CLONAL	1	TRUE	1	0.753690036247669	4		427	556	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92462487	92462487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	63	445	0	ENST00000265734.4:c.151G>A	p.Glu51Lys	p.E51K	ENST00000265734	NM_001259.6	51	Gag/Aag	2/8	0.437432344766891	4	FACETS	0.616	0.534	0.705			1	INDETERMINATE	1	TRUE	NA	0.753690036247669	4		445	476	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545662	106545662	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1262374005	NA	P-0003788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	76	421	0	ENST00000359195.3:c.3139G>A	p.Asp1047Asn	p.D1047N	ENST00000359195	NM_002649.2	1047	Gac/Aac	11/11	0.322936945664968	3	FACETS	0.588	0.517	0.664	0.294	0.258	0.332	INDETERMINATE	1	TRUE	1	0.753690036247669	3		421	472	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027735	152027735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	97	602	0	ENST00000262189.6:c.340G>A	p.Glu114Lys	p.E114K	ENST00000262189	NM_170606.2	114	Gag/Aag	3/59	0.322936945664968	3	FACETS	0.593	0.529	0.66	0.296	0.264	0.33	INDETERMINATE	1	TRUE	1	0.753690036247669	3		602	598	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549103	87549103	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs766917919	NA	P-0003788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	233	331	0	ENST00000277120.3:c.1660A>G	p.Ile554Val	p.I554V	ENST00000277120		554	Att/Gtt	15/19	0.306219129383355	5	FACETS	1	0.987	1	0.779	0.732	0.825	INDETERMINATE	2	TRUE	2	0.753690036247669	5		331	564	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060925	38060925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1388855660	NA	P-0003788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	45	277	0	ENST00000250448.2:c.1064C>T	p.Ser355Leu	p.S355L	ENST00000250448	NM_004496.3	355	tCa/tTa	2/2	0.437432344766891	4	FACETS	0.943	0.801	1			1	INDETERMINATE	1	TRUE	NA	0.753690036247669	4		277	222	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576024	29576024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	54	368	0	ENST00000356175.3:c.3997G>A	p.Glu1333Lys	p.E1333K	ENST00000356175	NM_000267.3	1333	Gag/Aag	30/57	0.753690036247669	4	FACETS	0.319	0.272	0.372	0.106	0.09	0.124	SUBCLONAL	1	TRUE	1	0.753690036247669	4		368	787	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734131	58734131	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	83	717	0	ENST00000305921.3:c.1189G>A	p.Asp397Asn	p.D397N	ENST00000305921	NM_003620.3	397	Gac/Aac	5/6	0.753690036247669	4	FACETS	0.368	0.323	0.416	0.123	0.107	0.139	SUBCLONAL	1	TRUE	1	0.753690036247669	4		717	1050	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980923	40980923	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	17	199	0	ENST00000373198.4:c.1563C>G	p.Ile521Met	p.I521M	ENST00000373198	NM_133170.3	521	atC/atG	10/32	NA	2	FACETS	0.206	0.154	0.268			1	INDETERMINATE	1	TRUE	NA	0.753690036247669	2		199	219	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20153875	20153875	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	90	140	0	ENST00000379607.5:c.185G>A	p.Arg62Lys	p.R62K	ENST00000379607	NM_001412.3	62	aGa/aAa	3/7	0.580706839540215	2	FACETS	0.905	0.815	0.998			1	CLONAL	1	TRUE	NA	0.753690036247669	2		140	264	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913186	39913186	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	30	202	0	ENST00000378444.4:c.4929G>T	p.Glu1643Asp	p.E1643D	ENST00000378444	NM_001123385.1	1643	gaG/gaT	14/15	0.580706839540215	2	FACETS	0.22	0.177	0.269			1	SUBCLONAL	1	TRUE	NA	0.753690036247669	2		202	362	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412848	63412848	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003788-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	21	242	0	ENST00000330258.3:c.319G>A	p.Glu107Lys	p.E107K	ENST00000330258	NM_152424.3	107	Gaa/Aaa	2/2	0.547429526775385	2	FACETS	0.225	0.173	0.285			1	SUBCLONAL	1	TRUE	NA	0.753690036247669	2		242	248	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	10	280	0				ENST00000310581	NM_198253.2	-/1132			0.140930104292903	4	FACETS	1	0.723	1	0.533	0.364	0.742	CLONAL	1	TRUE	2	0.22	4		280	104	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504321	8504321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200847027	NA	P-0003790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	48	265	1	ENST00000356435.5:c.1762C>T	p.Arg588Cys	p.R588C	ENST00000356435		588	Cgc/Tgc	12/35	1	2	FACETS	0.887	0.75	1	0.887	0.75	1	CLONAL	1	TRUE	1	0.22	2		266	492	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023529	27023530	+	frameshift_variant	Frame_Shift_Ins	INS	AC	AC	TGT	novel	NA	P-0003790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	49	271	0	ENST00000324856.7:c.635_636delinsTGT	p.Tyr212LeufsTer2	p.Y212Lfs*2	ENST00000324856	NM_006015.4	212	tAC/tTGT	1/20	0.100319216393735	4	FACETS	1	0.885	1	0.527	0.446	0.615	INDETERMINATE	1	TRUE	2	0.22	4		271	516	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0003792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	160	464	0				ENST00000310581	NM_198253.2	-/1132			0.208336542048173	3	FACETS	0.955	0.889	1	1	0.993	1	CLONAL	5	TRUE	1	0.208336542048173	3		464	355	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0003792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	273	500	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	1	0.969	1	1	0.996	1	CLONAL	3	TRUE	1	0.208336542048173	2		500	836	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184342	7184342	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138528064	NA	P-0003792-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	57	313	1	ENST00000302850.5:c.959C>T	p.Thr320Met	p.T320M	ENST00000302850	NM_000208.2	320	aCg/aTg	3/22	1	2	FACETS	0.611	0.523	0.708	0.611	0.523	0.708	SUBCLONAL	1	TRUE	1	0.208336542048173	2		314	895	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	18	280	0				ENST00000310581	NM_198253.2	-/1132			0.445946513131436	1	FACETS	0.784	0.626	0.947	1	0.93	1	CLONAL	2	TRUE	0	0.445946513131436	1		280	40	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508919	106508919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748229046	NA	P-0003808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	37	105	0	ENST00000359195.3:c.913G>A	p.Val305Met	p.V305M	ENST00000359195	NM_002649.2	305	Gtg/Atg	2/11	0.445946513131436	7	FACETS	1	0.952	1	0.373	0.31	0.443	CLONAL	1	TRUE	3	0.445946513131436	7		105	235	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335803	73335803	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0003808-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	50	192	0	ENST00000377767.4:c.2492C>G	p.Ser831Ter	p.S831*	ENST00000377767	NM_014953.3	831	tCa/tGa	18/21	0.428901793148133	4	FACETS	0.849	0.731	0.974	0.849	0.731	0.974	CLONAL	2	TRUE	2	0.445946513131436	4		192	191	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	82	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.908	0.813	1	0.908	0.813	1	CLONAL	1	TRUE	1	0.716472458376323	2		280	252	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772218	68772218	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	380	402	0	ENST00000261769.5:c.67C>T	p.Gln23Ter	p.Q23*	ENST00000261769	NM_004360.3	23	Cag/Tag	2/16	0.716472458376323	1	FACETS	0.938	0.898	0.977	0.938	0.898	0.977	CLONAL	1	TRUE	0	0.716472458376323	1		402	726	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652126	36652139	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGAGGCCGGGAT	GGCGAGGCCGGGAT	-	novel	NA	P-0003826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	197	198	0	ENST00000244741.5:c.249_262del	p.Arg84ValfsTer40	p.R84Vfs*40	ENST00000244741	NM_000389.4	83	cGGCGAGGCCGGGAT/c	2/3	1	2	FACETS	0.88	0.819	0.942	0.88	0.819	0.942	CLONAL	1	TRUE	1	0.716472458376323	2		198	625	SUCCESS
AR	367	MSKCC	GRCh37	X	66765149	66765151	+	inframe_deletion	In_Frame_Del	DEL	TGC	TGC	-	rs752055010	NA	P-0003826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	18	118	0	ENST00000374690.3:c.170_172del	p.Leu57del	p.L57del	ENST00000374690	NM_000044.3	54	tTGCtg/ttg	1/8	1	1	FACETS	0.165	0.125	0.213	0.165	0.125	0.213	SUBCLONAL	1	TRUE	0	0.716472458376323	1		118	195	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482330	87482330	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	328	322	0	ENST00000277120.3:c.1617G>C	p.Gln539His	p.Q539H	ENST00000277120		539	caG/caC	14/19	1	2	FACETS	0.849	0.803	0.896	0.849	0.803	0.896	CLONAL	1	TRUE	1	0.716472458376323	2		322	1078	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81534600	81534600	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	354	303	0	ENST00000298171.2:c.245A>T	p.Tyr82Phe	p.Y82F	ENST00000298171	NM_000369.2	82	tAc/tTc	3/10	1	2	FACETS	0.934	0.886	0.983	0.934	0.886	0.983	CLONAL	1	TRUE	1	0.716472458376323	2		303	1058	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42848513	42848513	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	372	327	0	ENST00000398585.3:c.829C>G	p.Arg277Gly	p.R277G	ENST00000398585	NM_001135099.1	277	Cgc/Ggc	8/14	1	2	FACETS	0.918	0.872	0.965	0.918	0.872	0.965	CLONAL	1	TRUE	1	0.716472458376323	2		327	1131	SUCCESS
AR	367	MSKCC	GRCh37	X	66765158	66765158	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs78686797	NA	P-0003826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	35	104	0	ENST00000374690.3:c.170T>A	p.Leu57Gln	p.L57Q	ENST00000374690	NM_000044.3	57	cTg/cAg	1/8	1	1	FACETS	0.407	0.338	0.482	0.407	0.338	0.482	SUBCLONAL	1	TRUE	0	0.716472458376323	1		104	154	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249522	153249522	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003826-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	255	186	0	ENST00000281708.4:c.1256del	p.Gly419AspfsTer11	p.G419Dfs*11	ENST00000281708	NM_033632.3	419	gGa/ga	9/12	0.551926096661354	1	FACETS	0.887	0.84	0.934	0.887	0.84	0.934	CLONAL	1	TRUE	0	0.716472458376323	1		186	515	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	24	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.428575783732386	2		280	101	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118378317	118378317	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782393372	NA	P-0003827-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	47	208	0	ENST00000534358.1:c.10828C>T	p.Pro3610Ser	p.P3610S	ENST00000534358	NM_005933.3	3610	Cct/Tct	28/36	0.140393594225583	0	FACETS	0.667	0.57	0.769			1	INDETERMINATE	1	TRUE	0	0.428575783732386	0		208	188	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	10	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.575	0.394	0.798	0.575	0.394	0.798	SUBCLONAL	1	TRUE	1	0.386378029946252	2		280	90	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834196	156834196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	66	236	0	ENST00000524377.1:c.263G>A	p.Arg88Lys	p.R88K	ENST00000524377	NM_002529.3	88	aGg/aAg	2/17	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.386378029946252	2		236	291	SUCCESS
APC	324	MSKCC	GRCh37	5	112178853	112178853	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003836-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	80	310	0	ENST00000257430.4:c.7562G>C	p.Arg2521Thr	p.R2521T	ENST00000257430	NM_000038.5	2521	aGa/aCa	16/16	1	2	FACETS	0.866	0.765	0.974	0.866	0.765	0.974	CLONAL	1	TRUE	1	0.386378029946252	2		310	478	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	66	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.587854905921133	2		280	176	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0003865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	523	331	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	0.587854905921133	4	FACETS	1	0.97	1			1	CLONAL	3	TRUE	NA	0.587854905921133	4		331	937	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622516	158622516	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs387906589	NA	P-0003865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	258	368	0	ENST00000263640.3:c.983G>A	p.Gly328Glu	p.G328E	ENST00000263640	NM_001105.4	328	gGg/gAg	8/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.587854905921133	2		368	824	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955419	48955419	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0003865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	163	165	0	ENST00000267163.4:c.1535T>A	p.Leu512Ter	p.L512*	ENST00000267163	NM_000321.2	512	tTg/tAg	17/27	0.501247050963803	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.587854905921133	1		165	385	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110890	8110890	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	162	233	0	ENST00000585124.1:c.205A>G	p.Thr69Ala	p.T69A	ENST00000585124	NM_004217.3	69	Acg/Gcg	4/9	0.587854905921133	2	FACETS	0.872	0.803	0.943	0.436	0.401	0.472	CLONAL	1	TRUE	0	0.587854905921133	2		233	632	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493432	56493433	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GT	GT	-	novel	NA	P-0003865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	163	198	0	ENST00000267101.3:c.2840_2841del	p.Cys947LeufsTer4	p.C947Lfs*4	ENST00000267101	NM_001982.3	947	tGT/t	24/28	1	2	FACETS	0.985	0.909	1	0.985	0.909	1	CLONAL	1	TRUE	1	0.587854905921133	2		198	563	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579346	7579348	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs764486868	NA	P-0003865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	271	188	1	ENST00000269305.4:c.339_341del	p.Phe113del	p.F113del	ENST00000269305	NM_001126112.2	113	ttCTTg/ttg	4/11	0.587854905921133	2	FACETS	0.968	0.922	1	0.968	0.922	1	CLONAL	2	TRUE	0	0.587854905921133	2		189	476	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249542	153249543	+	splice_acceptor_variant	Splice_Site	DNP	CT	CT	AA	novel	NA	P-0003865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	47	133	0	ENST00000281708.4:c.1237-2_1237-1delinsTT		p.X413_splice	ENST00000281708	NM_033632.3	413			1	2	FACETS	0.377	0.318	0.442	0.377	0.318	0.442	SUBCLONAL	1	TRUE	1	0.587854905921133	2		133	424	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0003868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	67	464	0				ENST00000310581	NM_198253.2	-/1132			0.176895324194641	5	FACETS	1	0.964	1	0.827	0.733	0.925	INDETERMINATE	2	TRUE	2	0.499899189178382	5		464	189	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0003868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	819	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.495669417719425	5	FACETS	1	0.996	1			1	CLONAL	4	TRUE	NA	0.499899189178382	5		490	1286	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0003868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	284	524	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	NA	2	FACETS	0.896	0.849	0.943			1	INDETERMINATE	2	TRUE	NA	0.499899189178382	2		524	634	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719306	190719306	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0003868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	165	285	0	ENST00000441310.2:c.1308T>A	p.Phe436Leu	p.F436L	ENST00000441310	NM_000534.4	436	ttT/ttA	9/13	0.265178309307852	2	FACETS	0.849	0.789	0.908	0.849	0.789	0.908	INDETERMINATE	2	TRUE	0	0.499899189178382	2		285	389	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158225	47158225	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	138	318	0	ENST00000409792.3:c.4474C>T	p.Arg1492Ter	p.R1492*	ENST00000409792	NM_014159.6	1492	Cga/Tga	4/21	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.499899189178382	2		318	528	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547225	106547225	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	208	223	2	ENST00000369096.4:c.462G>C	p.Glu154Asp	p.E154D	ENST00000369096	NM_001198.3	154	gaG/gaC	4/7	0.293001594685101	3	FACETS	0.932	0.872	0.993	0.932	0.872	0.993	INDETERMINATE	2	TRUE	1	0.499899189178382	3		225	558	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455144	50455144	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	184	218	0	ENST00000331340.3:c.691G>A	p.Gly231Ser	p.G231S	ENST00000331340	NM_006060.4	231	Ggc/Agc	6/8	0.499899189178382	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	1	0.499899189178382	3		218	440	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	56	170	0	ENST00000304494.5:c.262G>A	p.Glu88Lys	p.E88K	ENST00000304494	NM_000077.4	88	Gag/Aag	2/3	0.46262789436144	2	FACETS	1	0.947	1	0.59	0.513	0.67	CLONAL	1	TRUE	0	0.499899189178382	2		170	190	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99250980	99250980	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	134	360	0	ENST00000268035.6:c.284G>A	p.Ser95Asn	p.S95N	ENST00000268035	NM_000875.3	95	aGc/aAc	2/21	1	2	FACETS	0.797	0.725	0.871	0.797	0.725	0.871	SUBCLONAL	1	TRUE	1	0.499899189178382	2		360	673	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541520	29541520	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs770201871	NA	P-0003868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	171	274	0	ENST00000356175.3:c.1444A>G	p.Thr482Ala	p.T482A	ENST00000356175	NM_000267.3	482	Aca/Gca	13/57	0.176895324194641	5	FACETS	0.999	0.924	1	0.666	0.616	0.718	INDETERMINATE	2	TRUE	2	0.499899189178382	5		274	599	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543906	41543906	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1256254363	NA	P-0003868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	203	409	0	ENST00000263253.7:c.2197C>T	p.Leu733Phe	p.L733F	ENST00000263253	NM_001429.3	733	Ctt/Ttt	12/31	0.293001594685101	3	FACETS	1	0.982	1	0.585	0.543	0.628	INDETERMINATE	1	TRUE	1	0.499899189178382	3		409	868	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036925	180036926	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0003868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	67	367	0	ENST00000261937.6:c.3786_3787del	p.Thr1263AspfsTer22	p.T1263Dfs*22	ENST00000261937	NM_182925.4	1262	ccAAcg/cccg	28/30	0.499899189178382	1	FACETS	0.448	0.39	0.51	0.448	0.39	0.51	SUBCLONAL	1	TRUE	0	0.499899189178382	1		367	449	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738247	145738247	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0003868-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	39	278	0	ENST00000428558.2:c.2738del	p.Leu913TrpfsTer35	p.L913Wfs*35	ENST00000428558	NM_004260.3	913	tTg/tg	16/22	0.499899189178382	5	FACETS	0.433	0.358	0.517	0.144	0.119	0.173	SUBCLONAL	1	TRUE	2	0.499899189178382	5		278	631	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	188	464	0				ENST00000310581	NM_198253.2	-/1132			0.692885009984587	5	FACETS	1	0.967	1	1	0.967	1	CLONAL	3	TRUE	2	0.692885009984587	5		464	354	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11187712	11187712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	185	301	2	ENST00000361445.4:c.6185C>T	p.Pro2062Leu	p.P2062L	ENST00000361445	NM_004958.3	2062	cCc/cTc	44/58	0.683283776868294	3	FACETS	1	0.932	1	0.504	0.466	0.542	CLONAL	1	TRUE	1	0.692885009984587	3		303	714	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255772	16255772	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776153327	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	126	144	0	ENST00000375759.3:c.3037C>T	p.Arg1013Cys	p.R1013C	ENST00000375759	NM_015001.2	1013	Cgc/Tgc	11/15	0.683283776868294	3	FACETS	0.942	0.857	1	0.471	0.428	0.515	CLONAL	1	TRUE	1	0.692885009984587	3		144	520	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260038	16260038	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	241	190	0	ENST00000375759.3:c.7303C>T	p.Pro2435Ser	p.P2435S	ENST00000375759	NM_015001.2	2435	Ccc/Tcc	11/15	0.683283776868294	3	FACETS	0.982	0.929	1	0.982	0.929	1	CLONAL	2	TRUE	1	0.692885009984587	3		190	477	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932837	36932837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	473	327	0	ENST00000361632.4:c.2034G>A	p.Met678Ile	p.M678I	ENST00000361632		678	atG/atA	15/16	0.676544260758164	4	FACETS	0.924	0.89	0.957	0.924	0.89	0.957	CLONAL	3	TRUE	1	0.692885009984587	4		327	834	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805719	43805719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528834914	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	272	254	0	ENST00000372470.3:c.775G>A	p.Glu259Lys	p.E259K	ENST00000372470	NM_005373.2	259	Gaa/Aaa	5/12	0.676544260758164	4	FACETS	0.979	0.924	1	0.652	0.616	0.689	CLONAL	2	TRUE	1	0.692885009984587	4		254	679	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843739	156843739	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	420	325	0	ENST00000524377.1:c.1165G>A	p.Asp389Asn	p.D389N	ENST00000524377	NM_002529.3	389	Gac/Aac	8/17	0.676544260758164	4	FACETS	0.879	0.844	0.914	0.879	0.844	0.914	CLONAL	3	TRUE	1	0.692885009984587	4		325	778	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872696	136872696	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	76	377	0	ENST00000241393.3:c.802G>A	p.Glu268Lys	p.E268K	ENST00000241393	NM_003467.2	268	Gaa/Aaa	2/2	0.587922027649143	3	FACETS	0.461	0.404	0.522			1	SUBCLONAL	1	TRUE	NA	0.692885009984587	3		377	641	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286826	212286826	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	132	196	0	ENST00000342788.4:c.2870G>A	p.Trp957Ter	p.W957*	ENST00000342788	NM_005235.2	957	tGg/tAg	24/28	0.692885009984587	3	FACETS	0.894	0.815	0.976	0.447	0.407	0.488	CLONAL	1	TRUE	1	0.692885009984587	3		196	574	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295674	212295674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1362156940	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	142	284	0	ENST00000342788.4:c.2639G>A	p.Gly880Glu	p.G880E	ENST00000342788	NM_005235.2	880	gGa/gAa	21/28	0.692885009984587	3	FACETS	0.894	0.818	0.974	0.447	0.409	0.487	CLONAL	1	TRUE	1	0.692885009984587	3		284	617	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543810	212543810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	145	216	0	ENST00000342788.4:c.1589G>A	p.Arg530Lys	p.R530K	ENST00000342788	NM_005235.2	530	aGg/aAg	13/28	0.692885009984587	3	FACETS	0.83	0.759	0.904	0.415	0.379	0.452	CLONAL	1	TRUE	1	0.692885009984587	3		216	679	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12647784	12647784	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	151	270	0	ENST00000251849.4:c.596C>T	p.Ser199Phe	p.S199F	ENST00000251849	NM_002880.3	199	tCc/tTc	6/17	0.692885009984587	4	FACETS	0.977	0.895	1	0.489	0.447	0.532	CLONAL	1	TRUE	2	0.692885009984587	4		270	755	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713315	30713315	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764821003	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	279	187	0	ENST00000295754.5:c.640G>A	p.Glu214Lys	p.E214K	ENST00000295754	NM_003242.5	214	Gag/Aag	4/7	0.692885009984587	4	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	2	0.692885009984587	4		187	682	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067153	37067153	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782467	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	209	148	0	ENST00000231790.2:c.1064C>T	p.Pro355Leu	p.P355L	ENST00000231790	NM_000249.3	355	cCc/cTc	12/19	0.692885009984587	4	FACETS	0.867	0.81	0.925	0.867	0.81	0.925	CLONAL	2	TRUE	2	0.692885009984587	4		148	589	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390982	89390982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	167	290	0	ENST00000336596.2:c.1048G>A	p.Asp350Asn	p.D350N	ENST00000336596	NM_005233.5	350	Gac/Aac	5/17	0.692885009984587	4	FACETS	0.998	0.918	1			1	CLONAL	1	TRUE	NA	0.692885009984587	4		290	818	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480459	89480459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	299	216	0	ENST00000336596.2:c.2296G>A	p.Gly766Arg	p.G766R	ENST00000336596	NM_005233.5	766	Gga/Aga	13/17	0.692885009984587	4	FACETS	0.954	0.903	1			1	CLONAL	2	TRUE	NA	0.692885009984587	4		216	766	SUCCESS
ATR	545	MSKCC	GRCh37	3	142272485	142272485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	333	326	0	ENST00000350721.4:c.2630G>A	p.Gly877Glu	p.G877E	ENST00000350721	NM_001184.3	877	gGa/gAa	12/47	0.683283776868294	3	FACETS	0.93	0.886	0.974	0.93	0.886	0.974	CLONAL	2	TRUE	1	0.692885009984587	3		326	696	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178943776	178943776	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	148	231	0	ENST00000263967.3:c.2443C>T	p.Gln815Ter	p.Q815*	ENST00000263967	NM_006218.2	815	Caa/Taa	17/21	0.683283776868294	3	FACETS	0.902	0.826	0.98	0.451	0.413	0.49	CLONAL	1	TRUE	1	0.692885009984587	3		231	638	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189349307	189349307	+	start_lost	Translation_Start_Site	SNP	G	G	T	rs1028553870	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	113	189	0	ENST00000264731.3:c.3G>T	p.Met1?	p.M1?	ENST00000264731	NM_003722.4	1	atG/atT	1/14	0.683283776868294	3	FACETS	0.838	0.757	0.923	0.419	0.378	0.462	CLONAL	1	TRUE	1	0.692885009984587	3		189	524	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972086	55972086	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	870	204	0	ENST00000263923.4:c.1558C>T	p.Gln520Ter	p.Q520*	ENST00000263923	NM_002253.2	520	Caa/Taa	12/30	0.692885009984587	8	FACETS	1	0.984	1			1	CLONAL	6	TRUE	NA	0.692885009984587	8		204	1276	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280071	66280071	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	314	251	0	ENST00000273854.3:c.1618A>G	p.Ile540Val	p.I540V	ENST00000273854	NM_004439.5	540	Att/Gtt	7/18	0.660097465433644	2	FACETS	0.96	0.922	0.997	0.96	0.922	0.997	CLONAL	2	TRUE	0	0.692885009984587	2		251	472	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264708	1264708	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	220	223	0	ENST00000310581.5:c.2655-1G>A		p.X885_splice	ENST00000310581	NM_198253.2	885			0.692885009984587	5	FACETS	0.904	0.845	0.965	0.603	0.563	0.644	CLONAL	2	TRUE	2	0.692885009984587	5		223	716	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295253	1295253	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1232074117	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	200	336	0				ENST00000310581	NM_198253.2	-/1132			0.692885009984587	5	FACETS	1	0.942	1	1	0.942	1	CLONAL	3	TRUE	2	0.692885009984587	5		336	392	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950622	38950622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748585755	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	634	365	0	ENST00000357387.3:c.3328C>T	p.Arg1110Cys	p.R1110C	ENST00000357387	NM_152756.3	1110	Cgt/Tgt	31/38	0.692885009984587	5	FACETS	0.997	0.964	1	0.997	0.964	1	CLONAL	3	TRUE	2	0.692885009984587	5		365	1248	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177540	56177540	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	311	267	1	ENST00000399503.3:c.2513T>C	p.Leu838Ser	p.L838S	ENST00000399503	NM_005921.1	838	tTa/tCa	14/20	0.192488375049364	3	FACETS	0.841	0.807	0.874			1	INDETERMINATE	3	TRUE	NA	0.692885009984587	3		268	479	SUCCESS
APC	324	MSKCC	GRCh37	5	112175550	112175550	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	254	219	0	ENST00000257430.4:c.4259C>T	p.Pro1420Leu	p.P1420L	ENST00000257430	NM_000038.5	1420	cCc/cTc	16/16	0.692885009984587	3	FACETS	0.877	0.828	0.925	0.877	0.828	0.925	CLONAL	2	TRUE	1	0.692885009984587	3		219	563	SUCCESS
APC	324	MSKCC	GRCh37	5	112176558	112176558	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	116	192	0	ENST00000257430.4:c.5267C>G	p.Ser1756Cys	p.S1756C	ENST00000257430	NM_000038.5	1756	tCt/tGt	16/16	0.692885009984587	3	FACETS	0.823	0.744	0.905	0.411	0.372	0.453	CLONAL	1	TRUE	1	0.692885009984587	3		192	548	SUCCESS
APC	324	MSKCC	GRCh37	5	112179155	112179155	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	214	163	0	ENST00000257430.4:c.7864C>T	p.Pro2622Ser	p.P2622S	ENST00000257430	NM_000038.5	2622	Ccc/Tcc	16/16	0.692885009984587	3	FACETS	0.838	0.787	0.89	0.838	0.787	0.89	CLONAL	2	TRUE	1	0.692885009984587	3		163	496	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197211	26197212	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	347	493	0	ENST00000356476.2:c.267_268delinsAA	p.Val90Met	p.V90M	ENST00000356476		89	gcGGtg/gcAAtg	1/1	0.692885009984587	5	FACETS	0.914	0.866	0.963	0.61	0.577	0.642	CLONAL	2	TRUE	2	0.692885009984587	5		493	1117	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671501	30671501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	164	281	0	ENST00000376406.3:c.5459C>T	p.Ser1820Leu	p.S1820L	ENST00000376406	NM_014641.2	1820	tCa/tTa	10/15	0.692885009984587	5	FACETS	0.97	0.89	1	0.323	0.296	0.352	CLONAL	1	TRUE	2	0.692885009984587	5		281	995	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679714	30679714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	192	820	0	ENST00000376406.3:c.2005C>T	p.Pro669Ser	p.P669S	ENST00000376406	NM_014641.2	669	Ccc/Tcc	5/15	0.692885009984587	5	FACETS	1	0.966	1	0.359	0.332	0.388	CLONAL	1	TRUE	2	0.692885009984587	5		820	1048	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32171977	32171977	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	117	153	0	ENST00000375023.3:c.3055G>A	p.Gly1019Ser	p.G1019S	ENST00000375023	NM_004557.3	1019	Ggc/Agc	19/30	0.692885009984587	5	FACETS	1	0.914	1	0.338	0.305	0.372	CLONAL	1	TRUE	2	0.692885009984587	5		153	680	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967200	93967200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	195	337	0	ENST00000369303.4:c.2152G>A	p.Ala718Thr	p.A718T	ENST00000369303	NM_004440.3	718	Gcc/Acc	12/17	0.431034624425253	4	FACETS	0.971	0.899	1			1	CLONAL	1	TRUE	NA	0.692885009984587	4		337	981	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967960	93967960	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	387	380	0	ENST00000369303.4:c.1967G>A	p.Gly656Glu	p.G656E	ENST00000369303	NM_004440.3	656	gGg/gAg	11/17	0.431034624425253	4	FACETS	0.973	0.927	1			1	CLONAL	2	TRUE	NA	0.692885009984587	4		380	972	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94067995	94067995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	360	309	0	ENST00000369303.4:c.967C>T	p.Pro323Ser	p.P323S	ENST00000369303	NM_004440.3	323	Cca/Tca	4/17	0.431034624425253	4	FACETS	1	0.964	1			1	CLONAL	2	TRUE	NA	0.692885009984587	4		309	867	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106554856	106554856	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	227	177	0	ENST00000369096.4:c.1973C>T	p.Pro658Leu	p.P658L	ENST00000369096	NM_001198.3	658	cCa/cTa	7/7	0.623670831118215	5	FACETS	1	0.976	1			1	CLONAL	2	TRUE	NA	0.692885009984587	5		177	617	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2969703	2969704	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	118	177	0	ENST00000396946.4:c.1575_1576delinsAA	p.Gly526Arg	p.G526R	ENST00000396946	NM_032415.4	525	aaGGgg/aaAAgg	12/25	0.692885009984587	3	FACETS	0.972	0.882	1	0.486	0.441	0.533	CLONAL	1	TRUE	1	0.692885009984587	3		177	472	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729949	41729949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1165688714	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	405	1725	1	ENST00000242208.4:c.580G>A	p.Glu194Lys	p.E194K	ENST00000242208	NM_002192.2	194	Gaa/Aaa	3/3	0.692885009984587	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.692885009984587	3		1726	744	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268944	55268944	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	119	262	0	ENST00000275493.2:c.3010G>A	p.Glu1004Lys	p.E1004K	ENST00000275493	NM_005228.3	1004	Gaa/Aaa	25/28	0.692885009984587	3	FACETS	0.814	0.737	0.895	0.407	0.368	0.448	CLONAL	1	TRUE	1	0.692885009984587	3		262	568	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128848618	128848618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	145	235	0	ENST00000249373.3:c.1283C>T	p.Ser428Phe	p.S428F	ENST00000249373	NM_005631.4	428	tCc/tTc	7/12	0.692885009984587	6	FACETS	0.913	0.831	0.998	0.183	0.166	0.2	CLONAL	1	TRUE	1	0.692885009984587	6		235	1094	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860908	151860908	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	90	106	0	ENST00000262189.6:c.9754C>T	p.Arg3252Cys	p.R3252C	ENST00000262189	NM_170606.2	3252	Cgt/Tgt	43/59	0.692885009984587	9	FACETS	0.814	0.72	0.915	0.102	0.09	0.115	CLONAL	1	TRUE	1	0.692885009984587	9		106	1093	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874644	151874644	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1636	161	214	0	ENST00000262189.6:c.7894C>T	p.Gln2632Ter	p.Q2632*	ENST00000262189	NM_170606.2	2632	Caa/Taa	38/59	0.692885009984587	9	FACETS	0.886	0.809	0.967	0.111	0.101	0.121	CLONAL	1	TRUE	1	0.692885009984587	9		214	1797	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370867	55370867	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749912364	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	101	165	0	ENST00000297316.4:c.169G>A	p.Gly57Arg	p.G57R	ENST00000297316	NM_022454.3	57	Ggg/Agg	1/2	0.676544260758164	4	FACETS	0.96	0.862	1	0.32	0.287	0.355	CLONAL	1	TRUE	1	0.692885009984587	4		165	514	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741839	145741839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758876038	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	193	258	0	ENST00000428558.2:c.664C>T	p.Pro222Ser	p.P222S	ENST00000428558	NM_004260.3	222	Cct/Tct	5/22	0.676544260758164	4	FACETS	1	0.985	1	0.412	0.382	0.443	CLONAL	1	TRUE	1	0.692885009984587	4		258	763	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5044462	5044462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	366	324	0	ENST00000381652.3:c.410C>T	p.Ser137Phe	p.S137F	ENST00000381652	NM_004972.3	137	tCt/tTt	5/25	NA	2	FACETS	0.943	0.908	0.978			1	INDETERMINATE	2	TRUE	NA	0.692885009984587	2		324	560	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484293	8484293	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	304	268	0	ENST00000356435.5:c.3239C>T	p.Ser1080Leu	p.S1080L	ENST00000356435		1080	tCa/tTa	19/35	NA	2	FACETS	0.885	0.847	0.922			1	INDETERMINATE	2	TRUE	NA	0.692885009984587	2		268	496	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	172	354	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	NA	2	FACETS	0.919	0.869	0.969			1	INDETERMINATE	2	TRUE	NA	0.692885009984587	2		354	270	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396479	139396479	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763140976	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	148	298	0	ENST00000277541.6:c.5446G>A	p.Glu1816Lys	p.E1816K	ENST00000277541	NM_017617.3	1816	Gag/Aag	29/34	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.692885009984587	2		298	417	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615107	43615107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	303	282	0	ENST00000355710.3:c.2521C>T	p.Pro841Ser	p.P841S	ENST00000355710	NM_020975.4	841	Ccg/Tcg	14/20	NA	2	FACETS	0.932	0.894	0.97			1	INDETERMINATE	2	TRUE	NA	0.692885009984587	2		282	469	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123246929	123246929	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868564661	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	308	255	0	ENST00000358487.5:c.1996C>T	p.Pro666Ser	p.P666S	ENST00000358487	NM_000141.4	666	Cca/Tca	15/18	0.6718629429285	2	FACETS	0.92	0.882	0.958	0.92	0.882	0.958	CLONAL	2	TRUE	0	0.692885009984587	2		255	483	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156615	2156615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	262	228	0	ENST00000434045.2:c.307G>A	p.Asp103Asn	p.D103N	ENST00000434045	NM_001127598.1	103	Gac/Aac	3/5	0.404382081232167	5	FACETS	1	0.99	1	0.823	0.777	0.869	INDETERMINATE	2	TRUE	2	0.692885009984587	5		228	625	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912737	100912737	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	203	354	0	ENST00000325455.5:c.2585G>A	p.Gly862Glu	p.G862E	ENST00000325455	NM_001202474.3	862	gGa/gAa	7/8	0.692885009984587	3	FACETS	1	0.967	1	0.532	0.495	0.571	CLONAL	1	TRUE	1	0.692885009984587	3		354	741	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195542	102195542	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	205	716	0	ENST00000263464.3:c.302C>T	p.Ser101Phe	p.S101F	ENST00000263464	NM_001165.4	101	tCc/tTc	2/9	0.692885009984587	3	FACETS	0.91	0.845	0.977	0.455	0.422	0.489	CLONAL	1	TRUE	1	0.692885009984587	3		716	876	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344594	118344594	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555036710	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	150	281	0	ENST00000534358.1:c.2720C>T	p.Pro907Leu	p.P907L	ENST00000534358	NM_005933.3	907	cCt/cTt	3/36	0.692885009984587	3	FACETS	0.889	0.815	0.966	0.444	0.407	0.483	CLONAL	1	TRUE	1	0.692885009984587	3		281	656	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573894	18573894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759658584	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	162	259	0	ENST00000266497.5:c.2212C>T	p.Arg738Cys	p.R738C	ENST00000266497		738	Cgt/Tgt	15/31	1	2	FACETS	0.976	0.903	1	0.976	0.903	1	CLONAL	1	TRUE	1	0.692885009984587	2		259	479	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245926	46245926	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	153	199	0	ENST00000334344.6:c.4020C>G	p.Asn1340Lys	p.N1340K	ENST00000334344	NM_152641.2	1340	aaC/aaG	15/21	1	2	FACETS	0.914	0.843	0.988	0.914	0.843	0.988	CLONAL	1	TRUE	1	0.692885009984587	2		199	483	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443961	49443961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	107	170	0	ENST00000301067.7:c.3410C>T	p.Pro1137Leu	p.P1137L	ENST00000301067	NM_003482.3	1137	cCt/cTt	11/54	1	2	FACETS	0.882	0.8	0.968	0.882	0.8	0.968	CLONAL	1	TRUE	1	0.692885009984587	2		170	350	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36989294	36989294	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1286887695	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	111	194	1	ENST00000354822.5:c.41C>T	p.Ala14Val	p.A14V	ENST00000354822	NM_001079668.2	14	gCc/gTc	1/3	0.692885009984587	5	FACETS	0.749	0.673	0.83	0.25	0.224	0.277	SUBCLONAL	1	TRUE	2	0.692885009984587	5		195	872	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352607	68352608	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	154	239	0	ENST00000487270.1:c.474_475delinsTT	p.Arg159Cys	p.R159C	ENST00000487270	NM_133509.3	158	tcCCgt/tcTTgt	6/11	0.692885009984587	5	FACETS	0.821	0.75	0.896	0.274	0.25	0.299	CLONAL	1	TRUE	2	0.692885009984587	5		239	1104	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105241439	105241439	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	121	272	0	ENST00000349310.3:c.541C>T	p.Leu181Phe	p.L181F	ENST00000349310	NM_001014432.1	181	Ctc/Ttc	7/15	0.250806547070038	5	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.692885009984587	5		272	552	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022992	33022992	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	144	346	0	ENST00000300177.4:c.101C>T	p.Pro34Leu	p.P34L	ENST00000300177	NM_001191322.1	34	cCc/cTc	2/2	NA	2	FACETS	0.868	0.797	0.941			1	INDETERMINATE	1	TRUE	NA	0.692885009984587	2		346	479	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023091	33023091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	139	297	0	ENST00000300177.4:c.200C>T	p.Ala67Val	p.A67V	ENST00000300177	NM_001191322.1	67	gCc/gTc	2/2	NA	2	FACETS	0.896	0.822	0.971			1	INDETERMINATE	1	TRUE	NA	0.692885009984587	2		297	448	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121831	2121832	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	77	149	0	ENST00000219476.3:c.1993_1994delinsTT	p.Pro665Phe	p.P665F	ENST00000219476	NM_000548.3	665	CCt/TTt	19/42	0.221165662804474	2	FACETS	0.794	0.705	0.887	0.397	0.352	0.444	INDETERMINATE	1	TRUE	0	0.692885009984587	2		149	280	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819312	3819312	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395652583	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	103	159	2	ENST00000262367.5:c.2923C>T	p.Pro975Ser	p.P975S	ENST00000262367	NM_004380.2	975	Ccc/Tcc	15/31	0.221165662804474	2	FACETS	0.887	0.803	0.975	0.444	0.401	0.488	INDETERMINATE	1	TRUE	0	0.692885009984587	2		161	335	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858390	9858390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	127	185	0	ENST00000330684.3:c.3011C>T	p.Ser1004Phe	p.S1004F	ENST00000330684	NM_001134407.1	1004	tCc/tTc	13/13	0.221165662804474	2	FACETS	0.952	0.871	1	0.476	0.435	0.518	INDETERMINATE	1	TRUE	0	0.692885009984587	2		185	385	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858484	9858484	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	156	248	1	ENST00000330684.3:c.2917G>A	p.Asp973Asn	p.D973N	ENST00000330684	NM_001134407.1	973	Gat/Aat	13/13	0.221165662804474	2	FACETS	0.979	0.904	1	0.489	0.452	0.528	INDETERMINATE	1	TRUE	0	0.692885009984587	2		249	460	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216997	7216998	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	CA	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	485	355	0	ENST00000380728.2:c.523_524delinsTG	p.Pro175Ter	p.P175*	ENST00000380728		175	CCa/TGa	7/11	0.192488375049364	3	FACETS	0.943	0.916	0.97			1	INDETERMINATE	3	TRUE	NA	0.692885009984587	3		355	666	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	291	592	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.192488375049364	3	FACETS	0.922	0.886	0.956			1	INDETERMINATE	3	TRUE	NA	0.692885009984587	3		592	409	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089934	16089934	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	14	215	0	ENST00000268712.3:c.176A>C	p.Gln59Pro	p.Q59P	ENST00000268712	NM_006311.3	59	cAa/cCa	3/46	0.313912827501534	4	FACETS	0.25	0.18	0.334			1	INDETERMINATE	1	TRUE	NA	0.692885009984587	4		215	274	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	578	292	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	0.692885009984587	5	FACETS	0.96	0.939	0.98			1	CLONAL	5	TRUE	NA	0.692885009984587	5		292	709	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58677926	58677926	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1438030849	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	487	204	0	ENST00000305921.3:c.151C>T	p.Pro51Ser	p.P51S	ENST00000305921	NM_003620.3	51	Ccg/Tcg	1/6	0.642259036065474	4	FACETS	0.997	0.973	1			1	CLONAL	4	TRUE	NA	0.692885009984587	4		204	597	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615785	1615785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201250905	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	310	345	0	ENST00000344749.5:c.1486G>A	p.Glu496Lys	p.E496K	ENST00000344749	NM_001136139.2	496	Gag/Aag	17/19	0.692885009984587	3	FACETS	0.988	0.941	1	0.988	0.941	1	CLONAL	2	TRUE	1	0.692885009984587	3		345	610	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272140	15272140	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	48	65	0	ENST00000263388.2:c.6299C>T	p.Ser2100Leu	p.S2100L	ENST00000263388	NM_000435.2	2100	tCg/tTg	33/33	0.692885009984587	3	FACETS	1	0.936	1	0.579	0.499	0.664	CLONAL	1	TRUE	1	0.692885009984587	3		65	161	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276618	15276618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	157	164	0	ENST00000263388.2:c.5647G>A	p.Asp1883Asn	p.D1883N	ENST00000263388	NM_000435.2	1883	Gat/Aat	30/33	0.692885009984587	3	FACETS	1	0.975	1	0.569	0.524	0.615	CLONAL	1	TRUE	1	0.692885009984587	3		164	536	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276770	15276770	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	129	192	0	ENST00000263388.2:c.5495G>A	p.Gly1832Glu	p.G1832E	ENST00000263388	NM_000435.2	1832	gGg/gAg	30/33	0.692885009984587	3	FACETS	0.887	0.808	0.97	0.444	0.404	0.485	CLONAL	1	TRUE	1	0.692885009984587	3		192	565	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289871	15289871	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	95	177	0	ENST00000263388.2:c.3683G>T	p.Gly1228Val	p.G1228V	ENST00000263388	NM_000435.2	1228	gGa/gTa	22/33	0.692885009984587	3	FACETS	0.824	0.738	0.915	0.412	0.369	0.458	CLONAL	1	TRUE	1	0.692885009984587	3		177	448	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354179	15354179	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1393147270	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	70	47	0	ENST00000263377.2:c.2701C>T	p.Pro901Ser	p.P901S	ENST00000263377	NM_058243.2	901	Cca/Tca	14/20	0.692885009984587	3	FACETS	0.866	0.776	0.958	0.866	0.776	0.958	CLONAL	2	TRUE	1	0.692885009984587	3		47	157	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794515	42794515	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	326	311	0	ENST00000575354.2:c.1595C>T	p.Pro532Leu	p.P532L	ENST00000575354	NM_015125.3	532	cCa/cTa	10/20	0.692885009984587	3	FACETS	0.984	0.938	1	0.984	0.938	1	CLONAL	2	TRUE	1	0.692885009984587	3		311	644	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716352	52716352	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	241	186	0	ENST00000322088.6:c.796A>T	p.Lys266Ter	p.K266*	ENST00000322088	NM_014225.5	266	Aag/Tag	6/15	0.692885009984587	3	FACETS	0.954	0.902	1	0.954	0.902	1	CLONAL	2	TRUE	1	0.692885009984587	3		186	491	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543580	9543580	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	183	275	0	ENST00000353224.5:c.1574T>A	p.Phe525Tyr	p.F525Y	ENST00000353224	NM_177990.2	525	tTt/tAt	6/10	0.250806547070038	5	FACETS	0.826	0.766	0.888			1	INDETERMINATE	2	TRUE	NA	0.692885009984587	5		275	652	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561520	9561520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	210	127	0	ENST00000353224.5:c.262G>A	p.Asp88Asn	p.D88N	ENST00000353224	NM_177990.2	88	Gat/Aat	4/10	0.250806547070038	5	FACETS	0.916	0.861	0.971			1	INDETERMINATE	3	TRUE	NA	0.692885009984587	5		127	450	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730877	40730877	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1479203418	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	262	162	0	ENST00000373198.4:c.3658C>T	p.Arg1220Trp	p.R1220W	ENST00000373198	NM_133170.3	1220	Cgg/Tgg	27/32	0.692885009984587	4	FACETS	1	0.976	1			1	CLONAL	2	TRUE	NA	0.692885009984587	4		162	604	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790114	40790114	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	196	150	0	ENST00000373198.4:c.2617G>A	p.Asp873Asn	p.D873N	ENST00000373198	NM_133170.3	873	Gac/Aac	18/32	0.692885009984587	4	FACETS	0.912	0.851	0.974			1	CLONAL	2	TRUE	NA	0.692885009984587	4		150	525	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980844	40980844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	131	387	0	ENST00000373198.4:c.1642G>A	p.Glu548Lys	p.E548K	ENST00000373198	NM_133170.3	548	Gaa/Aaa	10/32	0.692885009984587	4	FACETS	1	0.952	1			1	CLONAL	1	TRUE	NA	0.692885009984587	4		387	598	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419969	41419969	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	315	246	0	ENST00000373198.4:c.352G>A	p.Gly118Arg	p.G118R	ENST00000373198	NM_133170.3	118	Ggg/Agg	3/32	0.692885009984587	4	FACETS	1	0.95	1			1	CLONAL	2	TRUE	NA	0.692885009984587	4		246	769	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420103	41420103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	71	120	0	ENST00000373198.4:c.218C>T	p.Ser73Phe	p.S73F	ENST00000373198	NM_133170.3	73	tCt/tTt	3/32	0.692885009984587	4	FACETS	0.961	0.844	1			1	CLONAL	1	TRUE	NA	0.692885009984587	4		120	361	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231836	36231836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	103	158	0	ENST00000300305.3:c.548C>T	p.Pro183Leu	p.P183L	ENST00000300305		183	cCa/cTa	5/8	0.683283776868294	3	FACETS	0.91	0.819	1	0.455	0.409	0.503	CLONAL	1	TRUE	1	0.692885009984587	3		158	440	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795371	39795371	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	127	264	0	ENST00000288319.7:c.349A>G	p.Asn117Asp	p.N117D	ENST00000288319	NM_182918.3	117	Aac/Gac	3/10	0.683283776868294	3	FACETS	0.94	0.856	1	0.47	0.428	0.514	CLONAL	1	TRUE	1	0.692885009984587	3		264	525	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545939	41545939	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	440	285	0	ENST00000263253.7:c.2554C>T	p.Gln852Ter	p.Q852*	ENST00000263253	NM_001429.3	852	Cag/Tag	14/31	0.623670831118215	5	FACETS	0.969	0.93	1			1	CLONAL	3	TRUE	NA	0.692885009984587	5		285	891	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1331449	1331449	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs764528631	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	148	318	0	ENST00000400841.2:c.79G>A	p.Ala27Thr	p.A27T	ENST00000400841		27	Gca/Aca	1/6	1	1	FACETS	0.642	0.592	0.693	0.642	0.592	0.693	SUBCLONAL	1	TRUE	0	0.692885009984587	1		318	435	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410331	63410331	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	149	153	0	ENST00000330258.3:c.2836C>T	p.Leu946Phe	p.L946F	ENST00000330258	NM_152424.3	946	Ctt/Ttt	2/2	0.51030900481095	2	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.692885009984587	2		153	344	SUCCESS
AR	367	MSKCC	GRCh37	X	66765082	66765082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	125	166	1	ENST00000374690.3:c.94G>A	p.Glu32Lys	p.E32K	ENST00000374690	NM_000044.3	32	Gaa/Aaa	1/8	0.51030900481095	2	FACETS	0.865	0.79	0.943			1	CLONAL	1	TRUE	NA	0.692885009984587	2		167	417	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649643	206649653	+	frameshift_variant	Frame_Shift_Del	DEL	GCTGCCCGGGA	GCTGCCCGGGA	-	novel	NA	P-0003871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	103	134	0	ENST00000367120.3:c.482_492del	p.Ala161GlyfsTer2	p.A161Gfs*2	ENST00000367120	NM_014002.3	160	GCTGCCCGGGAg/g	6/22	0.676544260758164	4	FACETS	0.881	0.791	0.977	0.294	0.263	0.326	CLONAL	1	TRUE	1	0.692885009984587	4		134	571	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	110	280	0				ENST00000310581	NM_198253.2	-/1132			0.733901165834663	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.733901165834663	3		280	178	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0003872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	325	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.35845393265486	5	FACETS	0.887	0.845	0.93	0.887	0.845	0.93	INDETERMINATE	3	TRUE	2	0.733901165834663	5		490	699	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40864896	40864896	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	175	562	0	ENST00000373198.4:c.2372G>A	p.Arg791Lys	p.R791K	ENST00000373198	NM_133170.3	791	aGa/aAa	16/32	0.733901165834663	5	FACETS	0.948	0.872	1	0.316	0.29	0.343	CLONAL	1	TRUE	2	0.733901165834663	5		562	1057	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896585	78896585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	168	496	0	ENST00000306801.3:c.2582C>T	p.Pro861Leu	p.P861L	ENST00000306801	NM_020761.2	861	cCc/cTc	22/34	0.69709879404596	4	FACETS	1	0.954	1	0.525	0.483	0.568	CLONAL	1	TRUE	2	0.733901165834663	4		496	756	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0003872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	191	383	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.733901165834663	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.733901165834663	2		383	254	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067192	37067192	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201673334	NA	P-0003872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	163	507	0	ENST00000231790.2:c.1103C>T	p.Ser368Leu	p.S368L	ENST00000231790	NM_000249.3	368	tCg/tTg	12/19	0.733901165834663	3	FACETS	0.854	0.786	0.925	0.427	0.393	0.463	CLONAL	1	TRUE	1	0.733901165834663	3		507	711	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032098	26032098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773862626	NA	P-0003872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	747	848	3	ENST00000244661.2:c.191G>A	p.Arg64Gln	p.R64Q	ENST00000244661	NM_003537.3	64	cGg/cAg	1/1	0.733901165834663	5	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	2	0.733901165834663	5		851	1360	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681619	30681619	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	374	559	1	ENST00000376406.3:c.478C>T	p.Gln160Ter	p.Q160*	ENST00000376406	NM_014641.2	160	Cag/Tag	3/15	0.733901165834663	5	FACETS	1	0.961	1	0.675	0.641	0.708	CLONAL	2	TRUE	2	0.733901165834663	5		560	1058	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180964	32180964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	141	400	0	ENST00000375023.3:c.2386G>A	p.Gly796Ser	p.G796S	ENST00000375023	NM_004557.3	796	Ggc/Agc	15/30	0.733901165834663	5	FACETS	0.984	0.897	1	0.328	0.299	0.359	CLONAL	1	TRUE	2	0.733901165834663	5		400	820	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332141	70332141	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	195	550	0	ENST00000373644.4:c.46G>A	p.Glu16Lys	p.E16K	ENST00000373644	NM_030625.2	16	Gaa/Aaa	2/12	0.733901165834663	2	FACETS	1	0.96	1	0.519	0.484	0.554	CLONAL	1	TRUE	0	0.733901165834663	2		550	512	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94219136	94219136	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	361	431	0	ENST00000323929.3:c.268C>T	p.Gln90Ter	p.Q90*	ENST00000323929	NM_005591.3	90	Cag/Tag	4/20	0.69739609717486	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.733901165834663	3		431	657	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913257	32913257	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs876660366	NA	P-0003872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	493	757	0	ENST00000380152.3:c.4765C>G	p.Pro1589Ala	p.P1589A	ENST00000380152		1589	Cca/Gca	11/27	0.733901165834663	5	FACETS	0.859	0.821	0.898	0.573	0.547	0.599	CLONAL	2	TRUE	2	0.733901165834663	5		757	1642	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641355	23641355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1363384297	NA	P-0003872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	155	587	1	ENST00000261584.4:c.2120C>T	p.Pro707Leu	p.P707L	ENST00000261584	NM_024675.3	707	cCt/cTt	5/13	0.69739609717486	3	FACETS	0.931	0.856	1	0.466	0.428	0.505	CLONAL	1	TRUE	1	0.733901165834663	3		588	620	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935782	15935782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	137	438	0	ENST00000268712.3:c.7151C>T	p.Pro2384Leu	p.P2384L	ENST00000268712	NM_006311.3	2384	cCt/cTt	46/46	0.69709879404596	4	FACETS	0.963	0.878	1	0.482	0.439	0.526	CLONAL	1	TRUE	2	0.733901165834663	4		438	672	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130318	11130318	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	293	565	0	ENST00000358026.2:c.2557T>C	p.Phe853Leu	p.F853L	ENST00000358026	NM_001128849.1	853	Ttc/Ctc	18/36	0.57884862881472	4	FACETS	0.974	0.922	1	0.974	0.922	1	CLONAL	2	TRUE	2	0.733901165834663	4		565	711	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30312978	30312978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	275	583	0	ENST00000262643.3:c.781G>A	p.Asp261Asn	p.D261N	ENST00000262643	NM_001238.2	261	Gac/Aac	9/12	0.57884862881472	4	FACETS	0.822	0.775	0.87	0.822	0.775	0.87	CLONAL	2	TRUE	2	0.733901165834663	4		583	790	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743912	40743912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	281	422	0	ENST00000373198.4:c.3083G>A	p.Gly1028Glu	p.G1028E	ENST00000373198	NM_133170.3	1028	gGa/gAa	23/32	0.733901165834663	5	FACETS	0.947	0.893	1	0.632	0.595	0.669	CLONAL	2	TRUE	2	0.733901165834663	5		422	849	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225979	53225979	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0003872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	90	621	0	ENST00000375401.3:c.2870G>C	p.Gly957Ala	p.G957A	ENST00000375401	NM_004187.3	957	gGt/gCt	19/26	0.34859581688353	3	FACETS	0.561	0.498	0.627	0.187	0.166	0.209	INDETERMINATE	1	TRUE	0	0.733901165834663	3		621	598	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860076	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0003872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	310	601	0	ENST00000228682.2:c.815_816delinsAA	p.Trp272Ter	p.W272*	ENST00000228682	NM_005269.2	272	tGG/tAA	8/12	0.636677157107544	4	FACETS	0.879	0.832	0.927	0.879	0.832	0.927	CLONAL	2	TRUE	2	0.733901165834663	4		601	833	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68301904	68301905	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0003872-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	122	393	0	ENST00000487270.1:c.306_307delinsTT	p.Leu103Phe	p.L103F	ENST00000487270	NM_133509.3	102	tcCCtc/tcTTtc	4/11	0.733901165834663	3	FACETS	1	0.984	1	0.672	0.615	0.731	CLONAL	1	TRUE	1	0.733901165834663	3		393	338	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	55	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.429641003137225	2		280	237	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0003889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	36	263	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.958	0.797	1	0.958	0.797	1	CLONAL	1	TRUE	1	0.429641003137225	2		263	175	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913381	NA	P-0003889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	107	394	0	ENST00000304494.5:c.322G>T	p.Asp108Tyr	p.D108Y	ENST00000304494	NM_000077.4	108	Gat/Tat	2/3	0.429641003137225	1	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	0	0.429641003137225	1		394	388	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	416	453	0	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	0.134280363243543	5	FACETS	0.857	0.816	0.898			1	INDETERMINATE	3	TRUE	NA	0.429641003137225	5		453	1239	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107258	193107258	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	49	183	0	ENST00000367435.3:c.467G>A	p.Arg156His	p.R156H	ENST00000367435	NM_024529.4	156	cGt/cAt	6/17	1	2	FACETS	0.871	0.743	1	0.871	0.743	1	CLONAL	1	TRUE	1	0.429641003137225	2		183	262	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651292	52651292	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0003889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	173	271	0	ENST00000394830.3:c.1804G>T	p.Glu602Ter	p.E602*	ENST00000394830	NM_018313.4	602	Gag/Tag	15/30	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.429641003137225	2		271	781	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194197	94194197	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	102	417	0	ENST00000323929.3:c.1231G>A	p.Glu411Lys	p.E411K	ENST00000323929	NM_005591.3	411	Gag/Aag	12/20	1	2	FACETS	0.846	0.759	0.939	0.846	0.759	0.939	CLONAL	1	TRUE	1	0.429641003137225	2		417	561	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696713	47696713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	128	259	0	ENST00000347630.2:c.235G>A	p.Glu79Lys	p.E79K	ENST00000347630	NM_001007230.1	79	Gaa/Aaa	5/11	0.289510575200744	3	FACETS	0.954	0.865	1	0.477	0.432	0.524	CLONAL	1	TRUE	1	0.429641003137225	3		259	759	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561457	9561457	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs772596554	NA	P-0003889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	116	187	0	ENST00000353224.5:c.325G>C	p.Asp109His	p.D109H	ENST00000353224	NM_177990.2	109	Gat/Cat	4/10	1	2	FACETS	0.914	0.826	1	0.914	0.826	1	CLONAL	1	TRUE	1	0.429641003137225	2		187	591	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907684	111907687	+	frameshift_variant	Frame_Shift_Del	DEL	GGCG	GGCG	-	novel	NA	P-0003889-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	141	241	0	ENST00000393256.3:c.458_461del	p.Arg153LeufsTer16	p.R153Lfs*16	ENST00000393256	NM_006538.4	153	cGGCGt/ct	3/4	1	2	FACETS	0.844	0.769	0.922	0.844	0.769	0.922	CLONAL	1	TRUE	1	0.429641003137225	2		241	778	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	26	280	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.847	1			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		280	69	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509386	46509386	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	72	214	0	ENST00000262741.5:c.1345G>A	p.Ala449Thr	p.A449T	ENST00000262741	NM_003629.3	449	Gcc/Acc	10/10	NA	2	FACETS	0.579	0.51	0.653			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		214	341	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736307	243736307	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	48	248	0	ENST00000263826.5:c.740G>A	p.Arg247His	p.R247H	ENST00000263826	NM_005465.4	247	cGc/cAc	8/13	0.276599700027762	1	FACETS	0.139	0.117	0.164	0.139	0.117	0.164	INDETERMINATE	1	TRUE	0	0.729046190752756	1		248	601	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363468	40363468	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755352384	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	72	222	0	ENST00000397332.2:c.761C>T	p.Ser254Phe	p.S254F	ENST00000397332	NM_001033082.2	254	tCc/tTc	3/3	NA	2	FACETS	0.558	0.491	0.63			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		222	354	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335667	81335667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	131	304	0	ENST00000222390.5:c.1693C>T	p.Leu565Phe	p.L565F	ENST00000222390	NM_000601.4	565	Ctc/Ttc	15/18	0.729046190752756	3	FACETS	0.492	0.446	0.541	0.246	0.223	0.271	SUBCLONAL	1	TRUE	1	0.729046190752756	3		304	996	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	78	631	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	0.495020052352505	1	FACETS	0.372	0.328	0.417	0.372	0.328	0.417	SUBCLONAL	1	TRUE	0	0.729046190752756	1		631	366	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879409	151879409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61730537	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	79	227	0	ENST00000262189.6:c.5536G>A	p.Val1846Met	p.V1846M	ENST00000262189	NM_170606.2	1846	Gtg/Atg	36/59	0.729046190752756	3	FACETS	0.564	0.497	0.636	0.282	0.248	0.318	SUBCLONAL	1	TRUE	1	0.729046190752756	3		227	524	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119624643	119624643	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	106	279	0	ENST00000316626.5:c.772C>T	p.Pro258Ser	p.P258S	ENST00000316626		258	Cca/Tca	7/12	NA	2	FACETS	0.441	0.395	0.489			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		279	660	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182514	99182514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	65	203	0	ENST00000074304.5:c.2317C>T	p.Pro773Ser	p.P773S	ENST00000074304	NM_001134224.1	773	Cct/Tct	22/26	1	2	FACETS	0.559	0.488	0.635	0.559	0.488	0.635	SUBCLONAL	1	TRUE	1	0.729046190752756	2		203	319	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499732	8499732	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	89	218	0	ENST00000356435.5:c.2237G>A	p.Gly746Glu	p.G746E	ENST00000356435		746	gGa/gAa	14/35	NA	2	FACETS	0.551	0.491	0.615			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		218	443	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494312	2494312	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	43	216	0	ENST00000355716.4:c.703G>A	p.Val235Ile	p.V235I	ENST00000355716	NM_003820.2	235	Gtc/Atc	7/8	NA	2	FACETS	0.539	0.455	0.629			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		216	219	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074456	8074456	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	85	232	1	ENST00000377482.5:c.203G>A	p.Gly68Glu	p.G68E	ENST00000377482	NM_018948.3	68	gGg/gAg	4/4	NA	2	FACETS	0.547	0.486	0.612			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		233	426	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9770652	9770652	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	79	220	0	ENST00000377346.4:c.139C>T	p.Gln47Ter	p.Q47*	ENST00000377346	NM_005026.3	47	Cag/Tag	3/24	NA	2	FACETS	0.625	0.553	0.7			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		220	347	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16248802	16248802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	146	270	0	ENST00000375759.3:c.1808G>A	p.Gly603Asp	p.G603D	ENST00000375759	NM_015001.2	603	gGt/gAt	10/15	NA	2	FACETS	0.578	0.528	0.63			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		270	693	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256354	16256354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	110	204	0	ENST00000375759.3:c.3619C>T	p.Leu1207Phe	p.L1207F	ENST00000375759	NM_015001.2	1207	Ctc/Ttc	11/15	NA	2	FACETS	0.695	0.629	0.765			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		204	434	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264009	16264009	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	101	295	0	ENST00000375759.3:c.10378C>T	p.Pro3460Ser	p.P3460S	ENST00000375759	NM_015001.2	3460	Cca/Tca	12/15	NA	2	FACETS	0.568	0.51	0.629			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		295	488	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087913	27087913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	81	221	0	ENST00000324856.7:c.2200G>A	p.Asp734Asn	p.D734N	ENST00000324856	NM_006015.4	734	Gac/Aac	6/20	NA	2	FACETS	0.586	0.52	0.657			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		221	379	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102131	27102131	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	44	191	0	ENST00000324856.7:c.5057G>A	p.Trp1686Ter	p.W1686*	ENST00000324856	NM_006015.4	1686	tGg/tAg	19/20	NA	2	FACETS	0.349	0.293	0.41			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		191	346	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36808967	36808967	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	87	281	0	ENST00000373129.3:c.1087G>A	p.Glu363Lys	p.E363K	ENST00000373129	NM_032017.1	363	Gag/Aag	11/12	NA	2	FACETS	0.626	0.558	0.698			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		281	381	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36823869	36823869	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	28	183	0	ENST00000373129.3:c.313G>A	p.Gly105Ser	p.G105S	ENST00000373129	NM_032017.1	105	Ggc/Agc	5/12	NA	2	FACETS	0.225	0.18	0.277			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		183	341	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36941250	36941250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1169858333	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	72	258	0	ENST00000361632.4:c.89G>A	p.Ser30Asn	p.S30N	ENST00000361632		30	aGt/aAt	3/16	NA	2	FACETS	0.61	0.537	0.687			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		258	324	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796905	45796905	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	31	166	0	ENST00000450313.1:c.1425G>A	p.Trp475Ter	p.W475*	ENST00000450313	NM_012222.2	475	tgG/tgA	14/16	NA	2	FACETS	0.283	0.23	0.344			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		166	300	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797459	45797459	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	20	179	0	ENST00000450313.1:c.1060G>A	p.Gly354Arg	p.G354R	ENST00000450313	NM_012222.2	354	Gga/Aga	12/16	NA	2	FACETS	0.187	0.143	0.239			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		179	293	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797982	45797982	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1338038953	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	96	203	0	ENST00000450313.1:c.789G>A	p.Trp263Ter	p.W263*	ENST00000450313	NM_012222.2	263	tgG/tgA	10/16	NA	2	FACETS	0.805	0.725	0.889			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		203	327	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532710	46532710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	128	219	0	ENST00000262741.5:c.368G>A	p.Gly123Asp	p.G123D	ENST00000262741	NM_003629.3	123	gGc/gAc	4/10	NA	2	FACETS	0.658	0.599	0.719			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		219	534	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46725638	46725638	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	69	222	0	ENST00000371975.4:c.274C>T	p.Pro92Ser	p.P92S	ENST00000371975	NM_003579.3	92	Cct/Tct	5/18	NA	2	FACETS	0.499	0.437	0.566			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		222	379	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076736	72076736	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769521243	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	116	266	0	ENST00000357731.5:c.761C>T	p.Ala254Val	p.A254V	ENST00000357731	NM_173808.2	254	gCc/gTc	5/7	0.384513979254157	1	FACETS	0.448	0.407	0.492	0.448	0.407	0.492	INDETERMINATE	1	TRUE	0	0.729046190752756	1		266	451	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414961	78414961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	66	152	0	ENST00000370768.2:c.1805G>A	p.Gly602Glu	p.G602E	ENST00000370768	NM_003902.3	602	gGg/gAg	19/20	0.384513979254157	1	FACETS	0.352	0.307	0.399	0.352	0.307	0.399	INDETERMINATE	1	TRUE	0	0.729046190752756	1		152	327	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78426107	78426107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	61	173	0	ENST00000370768.2:c.1418G>A	p.Gly473Glu	p.G473E	ENST00000370768	NM_003902.3	473	gGg/gAg	15/20	0.384513979254157	1	FACETS	0.391	0.34	0.445	0.391	0.34	0.445	INDETERMINATE	1	TRUE	0	0.729046190752756	1		173	272	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429401	78429401	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	107	192	0	ENST00000370768.2:c.1042-1G>A		p.X348_splice	ENST00000370768	NM_003902.3	348			0.384513979254157	1	FACETS	0.441	0.398	0.486	0.441	0.398	0.486	INDETERMINATE	1	TRUE	0	0.729046190752756	1		192	423	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433882	78433882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	34	218	0	ENST00000370768.2:c.217C>T	p.Pro73Ser	p.P73S	ENST00000370768	NM_003902.3	73	Cca/Tca	3/20	0.384513979254157	1	FACETS	0.119	0.097	0.144	0.119	0.097	0.144	INDETERMINATE	1	TRUE	0	0.729046190752756	1		218	499	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120479918	120479918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs940020746	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	86	229	0	ENST00000256646.2:c.3509G>A	p.Gly1170Glu	p.G1170E	ENST00000256646	NM_024408.3	1170	gGa/gAa	21/34	0.384513979254157	1	FACETS	0.399	0.355	0.445	0.399	0.355	0.445	INDETERMINATE	1	TRUE	0	0.729046190752756	1		229	376	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120529606	120529606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	32	222	0	ENST00000256646.2:c.851G>A	p.Cys284Tyr	p.C284Y	ENST00000256646	NM_024408.3	284	tGc/tAc	5/34	0.384513979254157	1	FACETS	0.104	0.084	0.127	0.104	0.084	0.127	INDETERMINATE	1	TRUE	0	0.729046190752756	1		222	535	SUCCESS
INSRR	3645	MSKCC	GRCh37	1	156812039	156812039	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	23	58	0	ENST00000368195.3:c.3262G>A	p.Ala1088Thr	p.A1088T	ENST00000368195	NM_014215.2	1088	Gca/Aca	19/22	0.356421689176725	5	FACETS	1	0.876	1			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	5		58	114	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745931	162745931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs956827605	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	104	185	0	ENST00000367921.3:c.2054C>T	p.Thr685Ile	p.T685I	ENST00000367921	NM_006182.2	685	aCc/aTc	16/18	1	2	FACETS	0.586	0.527	0.648	0.586	0.527	0.648	SUBCLONAL	1	TRUE	1	0.729046190752756	2		185	487	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175914294	175914294	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774985721	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	49	130	0	ENST00000367669.3:c.2191G>A	p.Val731Ile	p.V731I	ENST00000367669	NM_022457.5	731	Gta/Ata	20/20	1	2	FACETS	0.462	0.394	0.536	0.462	0.394	0.536	SUBCLONAL	1	TRUE	1	0.729046190752756	2		130	291	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176105662	176105662	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	105	230	0	ENST00000367669.3:c.853G>A	p.Glu285Lys	p.E285K	ENST00000367669	NM_022457.5	285	Gag/Aag	7/20	1	2	FACETS	0.484	0.435	0.536	0.484	0.435	0.536	SUBCLONAL	1	TRUE	1	0.729046190752756	2		230	595	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193219813	193219813	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	114	191	0	ENST00000367435.3:c.1567G>A	p.Val523Ile	p.V523I	ENST00000367435	NM_024529.4	523	Gta/Ata	17/17	1	2	FACETS	0.618	0.559	0.68	0.618	0.559	0.68	SUBCLONAL	1	TRUE	1	0.729046190752756	2		191	506	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206648319	206648319	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1349445353	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	64	207	0	ENST00000367120.3:c.340G>A	p.Val114Met	p.V114M	ENST00000367120	NM_014002.3	114	Gtg/Atg	5/22	1	2	FACETS	0.556	0.485	0.631	0.556	0.485	0.631	SUBCLONAL	1	TRUE	1	0.729046190752756	2		207	316	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650120	206650120	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553385473	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	57	180	0	ENST00000367120.3:c.640G>A	p.Ala214Thr	p.A214T	ENST00000367120	NM_014002.3	214	Gca/Aca	7/22	1	2	FACETS	0.601	0.521	0.687	0.601	0.521	0.687	SUBCLONAL	1	TRUE	1	0.729046190752756	2		180	260	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226551772	226551772	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	94	135	0	ENST00000366794.5:c.2659-1G>A		p.X887_splice	ENST00000366794	NM_001618.3	887			0.276599700027762	1	FACETS	0.703	0.638	0.77	0.703	0.638	0.77	INDETERMINATE	1	TRUE	0	0.729046190752756	1		135	233	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226579923	226579923	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766857135	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	86	294	0	ENST00000366794.5:c.379G>A	p.Gly127Arg	p.G127R	ENST00000366794	NM_001618.3	127	Ggg/Agg	3/23	0.276599700027762	1	FACETS	0.3	0.266	0.337	0.3	0.266	0.337	INDETERMINATE	1	TRUE	0	0.729046190752756	1		294	499	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243858955	243858955	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	117	255	0	ENST00000263826.5:c.110G>A	p.Gly37Glu	p.G37E	ENST00000263826	NM_005465.4	37	gGa/gAa	2/13	0.276599700027762	1	FACETS	0.338	0.305	0.372	0.338	0.305	0.372	INDETERMINATE	1	TRUE	0	0.729046190752756	1		255	604	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978983	25978983	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	39	238	0	ENST00000435504.4:c.940G>A	p.Val314Ile	p.V314I	ENST00000435504		314	Gtt/Att	10/13	NA	2	FACETS	0.179	0.148	0.214			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		238	597	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982514	25982514	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs372628454	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	92	164	0	ENST00000435504.4:c.776G>A	p.Arg259Lys	p.R259K	ENST00000435504		259	aGa/aAa	9/13	NA	2	FACETS	0.547	0.489	0.61			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		164	461	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26022299	26022299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	125	332	0	ENST00000435504.4:c.358G>A	p.Gly120Ser	p.G120S	ENST00000435504		120	Ggt/Agt	5/13	NA	2	FACETS	0.549	0.498	0.602			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		332	625	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551341	29551341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	54	177	0	ENST00000389048.3:c.1289C>T	p.Ser430Phe	p.S430F	ENST00000389048	NM_004304.4	430	tCc/tTc	6/29	NA	2	FACETS	0.514	0.442	0.592			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		177	288	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142922	30142922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	42	160	0	ENST00000389048.3:c.604G>A	p.Gly202Arg	p.G202R	ENST00000389048	NM_004304.4	202	Gga/Aga	1/29	NA	2	FACETS	0.549	0.463	0.642			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		160	210	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143050	30143050	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	35	258	0	ENST00000389048.3:c.476G>A	p.Gly159Glu	p.G159E	ENST00000389048	NM_004304.4	159	gGg/gAg	1/29	NA	2	FACETS	0.412	0.34	0.492			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		258	233	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47641555	47641555	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1114167845	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	132	122	0	ENST00000233146.2:c.940C>T	p.Gln314Ter	p.Q314*	ENST00000233146	NM_000251.2	314	Cag/Tag	5/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.729046190752756	2		122	332	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672686	47672686	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs267607948	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	189	200	0	ENST00000233146.2:c.1277-1G>A		p.X426_splice	ENST00000233146	NM_000251.2	426			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.729046190752756	2		200	486	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010415	48010415	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	53	182	0	ENST00000234420.5:c.43C>A	p.Pro15Thr	p.P15T	ENST00000234420	NM_000179.2	15	Ccg/Acg	1/10	1	2	FACETS	0.445	0.381	0.514	0.445	0.381	0.514	SUBCLONAL	1	TRUE	1	0.729046190752756	2		182	327	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030789	48030789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	42	128	0	ENST00000234420.5:c.3403C>T	p.Pro1135Ser	p.P1135S	ENST00000234420	NM_000179.2	1135	Cca/Tca	5/10	1	2	FACETS	0.368	0.308	0.434	0.368	0.308	0.434	SUBCLONAL	1	TRUE	1	0.729046190752756	2		128	313	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149144	61149144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1291658597	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	65	260	0	ENST00000295025.8:c.1334C>T	p.Pro445Leu	p.P445L	ENST00000295025	NM_002908.2	445	cCa/cTa	11/11	1	2	FACETS	0.318	0.275	0.364	0.318	0.275	0.364	SUBCLONAL	1	TRUE	1	0.729046190752756	2		260	561	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726887	61726887	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	152	254	0	ENST00000401558.2:c.551G>A	p.Gly184Glu	p.G184E	ENST00000401558	NM_003400.3	184	gGa/gAa	7/25	1	2	FACETS	0.57	0.522	0.62	0.57	0.522	0.62	SUBCLONAL	1	TRUE	1	0.729046190752756	2		254	732	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128016907	128016907	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143140054	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	70	272	0	ENST00000285398.2:c.2182G>A	p.Val728Met	p.V728M	ENST00000285398	NM_000122.1	728	Gtg/Atg	14/15	1	2	FACETS	0.504	0.442	0.571	0.504	0.442	0.571	SUBCLONAL	1	TRUE	1	0.729046190752756	2		272	381	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136875624	136875624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	159	251	0	ENST00000241393.3:c.7G>A	p.Gly3Arg	p.G3R	ENST00000241393	NM_003467.2	3	Ggg/Agg	1/2	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.729046190752756	2		251	435	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158617419	158617419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	131	369	0	ENST00000263640.3:c.1237G>A	p.Glu413Lys	p.E413K	ENST00000263640	NM_001105.4	413	Gaa/Aaa	9/11	1	2	FACETS	0.578	0.526	0.632	0.578	0.526	0.632	SUBCLONAL	1	TRUE	1	0.729046190752756	2		369	622	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719233	190719233	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	76	146	0	ENST00000441310.2:c.1235G>A	p.Ser412Asn	p.S412N	ENST00000441310	NM_000534.4	412	aGt/aAt	9/13	1	2	FACETS	0.478	0.421	0.539	0.478	0.421	0.539	SUBCLONAL	1	TRUE	1	0.729046190752756	2		146	436	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728497	190728497	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219393197	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	87	150	0	ENST00000441310.2:c.1885G>A	p.Glu629Lys	p.E629K	ENST00000441310	NM_000534.4	629	Gaa/Aaa	10/13	1	2	FACETS	0.539	0.479	0.602	0.539	0.479	0.602	SUBCLONAL	1	TRUE	1	0.729046190752756	2		150	443	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728954	190728954	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	57	103	0	ENST00000441310.2:c.2342G>A	p.Ser781Asn	p.S781N	ENST00000441310	NM_000534.4	781	aGt/aAt	10/13	1	2	FACETS	0.44	0.379	0.506	0.44	0.379	0.506	SUBCLONAL	1	TRUE	1	0.729046190752756	2		103	355	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266140	198266140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	102	208	0	ENST00000335508.6:c.2480G>A	p.Arg827Lys	p.R827K	ENST00000335508	NM_012433.2	827	aGa/aAa	17/25	1	2	FACETS	0.535	0.48	0.593	0.535	0.48	0.593	SUBCLONAL	1	TRUE	1	0.729046190752756	2		208	523	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266230	198266230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	27	191	0	ENST00000335508.6:c.2390G>A	p.Gly797Glu	p.G797E	ENST00000335508	NM_012433.2	797	gGg/gAg	17/25	1	2	FACETS	0.141	0.111	0.174	0.141	0.111	0.174	SUBCLONAL	1	TRUE	1	0.729046190752756	2		191	527	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267710	198267710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	104	189	0	ENST00000335508.6:c.1769G>A	p.Arg590Lys	p.R590K	ENST00000335508	NM_012433.2	590	aGa/aAa	13/25	1	2	FACETS	0.495	0.444	0.549	0.495	0.444	0.549	SUBCLONAL	1	TRUE	1	0.729046190752756	2		189	576	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273299	198273299	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	71	174	0	ENST00000335508.6:c.911C>T	p.Pro304Leu	p.P304L	ENST00000335508	NM_012433.2	304	cCt/cTt	8/25	1	2	FACETS	0.492	0.431	0.557	0.492	0.431	0.557	SUBCLONAL	1	TRUE	1	0.729046190752756	2		174	396	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274728	198274728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	65	138	0	ENST00000335508.6:c.670C>T	p.Pro224Ser	p.P224S	ENST00000335508	NM_012433.2	224	Cct/Tct	7/25	1	2	FACETS	0.515	0.449	0.586	0.515	0.449	0.586	SUBCLONAL	1	TRUE	1	0.729046190752756	2		138	346	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149946	202149946	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1280661555	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	68	230	0	ENST00000358485.4:c.1387G>A	p.Ala463Thr	p.A463T	ENST00000358485	NM_001080125.1	463	Gcc/Acc	8/9	1	2	FACETS	0.52	0.455	0.589	0.52	0.455	0.589	SUBCLONAL	1	TRUE	1	0.729046190752756	2		230	359	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209110082	209110082	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148190775	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	92	254	0	ENST00000345146.2:c.481G>A	p.Gly161Arg	p.G161R	ENST00000345146	NM_005896.2	161	Gga/Aga	5/10	1	2	FACETS	0.409	0.364	0.457	0.409	0.364	0.457	SUBCLONAL	1	TRUE	1	0.729046190752756	2		254	617	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293194	212293194	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	90	170	0	ENST00000342788.4:c.2658G>A	p.Trp886Ter	p.W886*	ENST00000342788	NM_005235.2	886	tgG/tgA	22/28	1	2	FACETS	0.461	0.41	0.516	0.461	0.41	0.516	SUBCLONAL	1	TRUE	1	0.729046190752756	2		170	535	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376093	225376093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	126	247	0	ENST00000264414.4:c.861G>A	p.Met287Ile	p.M287I	ENST00000264414	NM_003590.4	287	atG/atA	6/16	1	2	FACETS	0.519	0.471	0.57	0.519	0.471	0.57	SUBCLONAL	1	TRUE	1	0.729046190752756	2		247	666	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661473	227661473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1559159368	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	36	169	0	ENST00000305123.5:c.1982G>A	p.Gly661Asp	p.G661D	ENST00000305123	NM_005544.2	661	gGc/gAc	1/2	1	2	FACETS	0.378	0.313	0.451	0.378	0.313	0.451	SUBCLONAL	1	TRUE	1	0.729046190752756	2		169	261	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661572	227661572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	38	185	0	ENST00000305123.5:c.1883G>A	p.Gly628Asp	p.G628D	ENST00000305123	NM_005544.2	628	gGc/gAc	1/2	1	2	FACETS	0.431	0.358	0.51	0.431	0.358	0.51	SUBCLONAL	1	TRUE	1	0.729046190752756	2		185	242	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641201	12641201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	109	233	0	ENST00000251849.4:c.1097G>A	p.Gly366Asp	p.G366D	ENST00000251849	NM_002880.3	366	gGt/gAt	10/17	1	2	FACETS	0.503	0.452	0.556	0.503	0.452	0.556	SUBCLONAL	1	TRUE	1	0.729046190752756	2		233	595	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713358	30713358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	76	157	0	ENST00000295754.5:c.683G>A	p.Ser228Asn	p.S228N	ENST00000295754	NM_003242.5	228	aGc/aAc	4/7	1	2	FACETS	0.47	0.413	0.53	0.47	0.413	0.53	SUBCLONAL	1	TRUE	1	0.729046190752756	2		157	444	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37059015	37059015	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	92	223	0	ENST00000231790.2:c.809C>T	p.Thr270Ile	p.T270I	ENST00000231790	NM_000249.3	270	aCt/aTt	10/19	1	2	FACETS	0.526	0.469	0.586	0.526	0.469	0.586	SUBCLONAL	1	TRUE	1	0.729046190752756	2		223	480	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067449	37067449	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	73	159	0	ENST00000231790.2:c.1360G>A	p.Gly454Arg	p.G454R	ENST00000231790	NM_000249.3	454	Ggg/Agg	12/19	1	2	FACETS	0.553	0.487	0.624	0.553	0.487	0.624	SUBCLONAL	1	TRUE	1	0.729046190752756	2		159	362	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098642	47098642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	168	219	2	ENST00000409792.3:c.6632G>A	p.Gly2211Glu	p.G2211E	ENST00000409792	NM_014159.6	2211	gGa/gAa	15/21	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.729046190752756	2		221	409	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933167	49933167	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	57	241	0	ENST00000296474.3:c.2943G>A	p.Trp981Ter	p.W981*	ENST00000296474	NM_002447.2	981	tgG/tgA	12/20	NA	2	FACETS	0.46	0.396	0.528			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		241	340	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934803	49934803	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	85	285	0	ENST00000296474.3:c.2093G>T	p.Gly698Val	p.G698V	ENST00000296474	NM_002447.2	698	gGa/gTa	7/20	NA	2	FACETS	0.596	0.53	0.666			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		285	391	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940546	49940546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	94	311	0	ENST00000296474.3:c.497C>T	p.Ala166Val	p.A166V	ENST00000296474	NM_002447.2	166	gCc/gTc	1/20	NA	2	FACETS	0.577	0.516	0.641			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		311	447	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584607	52584607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	78	153	0	ENST00000394830.3:c.4406C>T	p.Pro1469Leu	p.P1469L	ENST00000394830	NM_018313.4	1469	cCc/cTc	29/30	NA	2	FACETS	0.514	0.454	0.579			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		153	416	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	272	514	1	ENST00000394830.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000394830	NM_018313.4	710	Cga/Tga	17/30	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		515	626	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70001022	70001022	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	61	243	0	ENST00000394351.3:c.619G>A	p.Asp207Asn	p.D207N	ENST00000394351	NM_000248.3	207	Gac/Aac	6/9	NA	2	FACETS	0.293	0.252	0.336			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		243	572	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70014277	70014277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	114	362	0	ENST00000394351.3:c.1138G>A	p.Asp380Asn	p.D380N	ENST00000394351	NM_000248.3	380	Gac/Aac	9/9	NA	2	FACETS	0.567	0.512	0.624			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		362	552	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890195	72890195	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	85	204	0	ENST00000325599.8:c.486+1G>A		p.X162_splice	ENST00000325599	NM_018130.2	162			NA	2	FACETS	0.439	0.389	0.493			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		204	531	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890350	72890350	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs141689155	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	85	184	0	ENST00000325599.8:c.332G>A	p.Gly111Asp	p.G111D	ENST00000325599	NM_018130.2	111	gGt/gAt	4/11	NA	2	FACETS	0.503	0.446	0.563			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		184	464	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521695	89521695	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	36	250	0	ENST00000336596.2:c.2772G>A	p.Trp924Ter	p.W924*	ENST00000336596	NM_005233.5	924	tgG/tgA	16/17	NA	2	FACETS	0.179	0.147	0.216			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		250	551	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670858	134670858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	33	66	0	ENST00000398015.3:c.769C>T	p.Pro257Ser	p.P257S	ENST00000398015	NM_004441.4	257	Cct/Tct	3/16	0.48616306975302	1	FACETS	0.449	0.373	0.532	0.449	0.373	0.532	SUBCLONAL	1	TRUE	0	0.729046190752756	1		66	128	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851832	134851832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	70	221	0	ENST00000398015.3:c.1238C>T	p.Ser413Phe	p.S413F	ENST00000398015	NM_004441.4	413	tCc/tTc	5/16	0.48616306975302	1	FACETS	0.416	0.366	0.47	0.416	0.366	0.47	SUBCLONAL	1	TRUE	0	0.729046190752756	1		221	293	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238626	142238626	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	96	195	0	ENST00000350721.4:c.4267G>A	p.Glu1423Lys	p.E1423K	ENST00000350721	NM_001184.3	1423	Gag/Aag	24/47	1	2	FACETS	0.557	0.498	0.619	0.557	0.498	0.619	SUBCLONAL	1	TRUE	1	0.729046190752756	2		195	473	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266703	142266703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	120	238	0	ENST00000350721.4:c.3221G>A	p.Gly1074Glu	p.G1074E	ENST00000350721	NM_001184.3	1074	gGa/gAa	16/47	1	2	FACETS	0.602	0.545	0.661	0.602	0.545	0.661	SUBCLONAL	1	TRUE	1	0.729046190752756	2		238	547	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275345	142275345	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756210333	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	225	215	0	ENST00000350721.4:c.1958C>T	p.Thr653Ile	p.T653I	ENST00000350721	NM_001184.3	653	aCa/aTa	9/47	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.729046190752756	2		215	563	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281130	142281130	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	121	269	0	ENST00000350721.4:c.1114G>A	p.Val372Met	p.V372M	ENST00000350721	NM_001184.3	372	Gtg/Atg	4/47	1	2	FACETS	0.482	0.436	0.531	0.482	0.436	0.531	SUBCLONAL	1	TRUE	1	0.729046190752756	2		269	688	SUCCESS
ATR	545	MSKCC	GRCh37	3	142297510	142297510	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	76	189	1	ENST00000350721.4:c.37C>T	p.Pro13Ser	p.P13S	ENST00000350721	NM_001184.3	13	Ccc/Tcc	1/47	1	2	FACETS	0.586	0.517	0.658	0.586	0.517	0.658	SUBCLONAL	1	TRUE	1	0.729046190752756	2		190	356	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430575	181430575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	69	142	0	ENST00000325404.1:c.427G>A	p.Val143Ile	p.V143I	ENST00000325404	NM_003106.3	143	Gtc/Atc	1/1	1	2	FACETS	0.56	0.491	0.634	0.56	0.491	0.634	SUBCLONAL	1	TRUE	1	0.729046190752756	2		142	338	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184712	185184712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773450302	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	95	304	0	ENST00000265026.3:c.1604G>A	p.Arg535Lys	p.R535K	ENST00000265026	NM_004721.4	535	aGg/aAg	10/14	1	2	FACETS	0.531	0.474	0.59	0.531	0.474	0.59	SUBCLONAL	1	TRUE	1	0.729046190752756	2		304	491	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190821	185190821	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	66	188	0	ENST00000265026.3:c.1702C>T	p.Pro568Ser	p.P568S	ENST00000265026	NM_004721.4	568	Cct/Tct	11/14	1	2	FACETS	0.462	0.403	0.526	0.462	0.403	0.526	SUBCLONAL	1	TRUE	1	0.729046190752756	2		188	392	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447709	187447709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	45	119	0	ENST00000232014.4:c.484G>A	p.Val162Met	p.V162M	ENST00000232014	NM_001130845.1	162	Gtg/Atg	5/10	1	2	FACETS	0.397	0.335	0.465	0.397	0.335	0.465	SUBCLONAL	1	TRUE	1	0.729046190752756	2		119	311	SUCCESS
FIP1L1	81608	MSKCC	GRCh37	4	54266007	54266007	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	85	184	0	ENST00000358575.5:c.770+1G>A		p.X257_splice	ENST00000358575	NM_001134937.1	257			0.315354805250643	1	FACETS	0.335	0.297	0.375	0.335	0.297	0.375	INDETERMINATE	1	TRUE	0	0.729046190752756	1		184	442	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955063	55955063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	83	285	0	ENST00000263923.4:c.3482G>A	p.Gly1161Glu	p.G1161E	ENST00000263923	NM_002253.2	1161	gGa/gAa	26/30	0.315354805250643	1	FACETS	0.354	0.314	0.396	0.354	0.314	0.396	INDETERMINATE	1	TRUE	0	0.729046190752756	1		285	409	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955120	55955120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	73	198	0	ENST00000263923.4:c.3425G>A	p.Cys1142Tyr	p.C1142Y	ENST00000263923	NM_002253.2	1142	tGc/tAc	26/30	0.315354805250643	1	FACETS	0.357	0.314	0.403	0.357	0.314	0.403	INDETERMINATE	1	TRUE	0	0.729046190752756	1		198	356	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968651	55968651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149740758	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	63	196	0	ENST00000263923.4:c.2012G>A	p.Gly671Glu	p.G671E	ENST00000263923	NM_002253.2	671	gGa/gAa	14/30	0.315354805250643	1	FACETS	0.289	0.251	0.33	0.289	0.251	0.33	INDETERMINATE	1	TRUE	0	0.729046190752756	1		196	380	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66189903	66189903	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	112	244	0	ENST00000273854.3:c.3043C>T	p.His1015Tyr	p.H1015Y	ENST00000273854	NM_004439.5	1015	Cac/Tac	18/18	0.315354805250643	1	FACETS	0.383	0.346	0.422	0.383	0.346	0.422	INDETERMINATE	1	TRUE	0	0.729046190752756	1		244	510	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280148	66280148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	48	144	0	ENST00000273854.3:c.1541G>A	p.Ser514Asn	p.S514N	ENST00000273854	NM_004439.5	514	aGc/aAc	7/18	0.315354805250643	1	FACETS	0.262	0.223	0.306	0.262	0.223	0.306	INDETERMINATE	1	TRUE	0	0.729046190752756	1		144	319	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356158	66356158	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	95	210	0	ENST00000273854.3:c.1339G>A	p.Val447Met	p.V447M	ENST00000273854	NM_004439.5	447	Gtg/Atg	5/18	0.315354805250643	1	FACETS	0.366	0.327	0.406	0.366	0.327	0.406	INDETERMINATE	1	TRUE	0	0.729046190752756	1		210	453	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155496	106155496	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	91	203	0	ENST00000380013.4:c.397C>T	p.Pro133Ser	p.P133S	ENST00000380013	NM_001127208.2	133	Cca/Tca	3/11	1	2	FACETS	0.573	0.511	0.638	0.573	0.511	0.638	SUBCLONAL	1	TRUE	1	0.729046190752756	2		203	436	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196426	106196426	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1469293606	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	76	299	1	ENST00000380013.4:c.4759G>A	p.Asp1587Asn	p.D1587N	ENST00000380013	NM_001127208.2	1587	Gat/Aat	11/11	1	2	FACETS	0.351	0.308	0.397	0.351	0.308	0.397	SUBCLONAL	1	TRUE	1	0.729046190752756	2		300	594	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196892	106196892	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	65	220	0	ENST00000380013.4:c.5225C>T	p.Pro1742Leu	p.P1742L	ENST00000380013	NM_001127208.2	1742	cCc/cTc	11/11	1	2	FACETS	0.393	0.341	0.448	0.393	0.341	0.448	SUBCLONAL	1	TRUE	1	0.729046190752756	2		220	454	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067013	143067013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	109	213	0	ENST00000262992.4:c.1700C>T	p.Ala567Val	p.A567V	ENST00000262992	NM_001101669.1	567	gCc/gTc	16/24	1	2	FACETS	0.581	0.523	0.641	0.581	0.523	0.641	SUBCLONAL	1	TRUE	1	0.729046190752756	2		213	515	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143181660	143181660	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	102	312	0	ENST00000262992.4:c.673C>T	p.Pro225Ser	p.P225S	ENST00000262992	NM_001101669.1	225	Cct/Tct	9/24	1	2	FACETS	0.482	0.432	0.535	0.482	0.432	0.535	SUBCLONAL	1	TRUE	1	0.729046190752756	2		312	580	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143181713	143181713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	77	230	0	ENST00000262992.4:c.620C>T	p.Ala207Val	p.A207V	ENST00000262992	NM_001101669.1	207	gCc/gTc	9/24	1	2	FACETS	0.464	0.409	0.523	0.464	0.409	0.523	SUBCLONAL	1	TRUE	1	0.729046190752756	2		230	455	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518143	187518143	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	85	257	0	ENST00000441802.2:c.12551G>A	p.Gly4184Glu	p.G4184E	ENST00000441802	NM_005245.3	4184	gGa/gAa	25/27	NA	2	FACETS	0.555	0.493	0.621			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		257	420	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541778	187541778	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	61	294	0	ENST00000441802.2:c.5962G>A	p.Val1988Met	p.V1988M	ENST00000441802	NM_005245.3	1988	Gtg/Atg	10/27	NA	2	FACETS	0.389	0.336	0.446			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		294	430	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542698	187542698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	105	283	0	ENST00000441802.2:c.5042G>A	p.Ser1681Asn	p.S1681N	ENST00000441802	NM_005245.3	1681	aGc/aAc	10/27	NA	2	FACETS	0.518	0.465	0.574			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		283	556	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629817	187629817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	45	251	1	ENST00000441802.2:c.1165G>A	p.Val389Ile	p.V389I	ENST00000441802	NM_005245.3	389	Gta/Ata	2/27	NA	2	FACETS	0.247	0.207	0.291			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		252	500	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630234	187630234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779324280	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	22	145	0	ENST00000441802.2:c.748G>A	p.Ala250Thr	p.A250T	ENST00000441802	NM_005245.3	250	Gcc/Acc	2/27	NA	2	FACETS	0.181	0.14	0.229			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		145	333	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871157	35871157	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	50	155	0	ENST00000303115.3:c.380-1G>A		p.X127_splice	ENST00000303115	NM_002185.3	127			1	2	FACETS	0.421	0.359	0.488	0.421	0.359	0.488	SUBCLONAL	1	TRUE	1	0.729046190752756	2		155	326	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950117	38950117	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	77	172	0	ENST00000357387.3:c.3833C>T	p.Ser1278Phe	p.S1278F	ENST00000357387	NM_152756.3	1278	tCt/tTt	31/38	1	2	FACETS	0.468	0.413	0.528	0.468	0.413	0.528	SUBCLONAL	1	TRUE	1	0.729046190752756	2		172	451	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38981977	38981977	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	96	155	0	ENST00000357387.3:c.745G>A	p.Glu249Lys	p.E249K	ENST00000357387	NM_152756.3	249	Gaa/Aaa	8/38	1	2	FACETS	0.523	0.467	0.581	0.523	0.467	0.581	SUBCLONAL	1	TRUE	1	0.729046190752756	2		155	504	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56168498	56168498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	133	191	0	ENST00000399503.3:c.1454C>T	p.Pro485Leu	p.P485L	ENST00000399503	NM_005921.1	485	cCt/cTt	8/20	1	2	FACETS	0.573	0.521	0.626	0.573	0.521	0.626	SUBCLONAL	1	TRUE	1	0.729046190752756	2		191	637	SUCCESS
APC	324	MSKCC	GRCh37	5	112174212	112174212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	109	296	0	ENST00000257430.4:c.2921G>A	p.Gly974Asp	p.G974D	ENST00000257430	NM_000038.5	974	gGt/gAt	16/16	1	2	FACETS	0.535	0.482	0.591	0.535	0.482	0.591	SUBCLONAL	1	TRUE	1	0.729046190752756	2		296	559	SUCCESS
APC	324	MSKCC	GRCh37	5	112176062	112176062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	83	216	0	ENST00000257430.4:c.4771G>A	p.Ala1591Thr	p.A1591T	ENST00000257430	NM_000038.5	1591	Gca/Aca	16/16	1	2	FACETS	0.47	0.416	0.528	0.47	0.416	0.528	SUBCLONAL	1	TRUE	1	0.729046190752756	2		216	484	SUCCESS
APC	324	MSKCC	GRCh37	5	112176111	112176111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	117	257	0	ENST00000257430.4:c.4820G>A	p.Arg1607Lys	p.R1607K	ENST00000257430	NM_000038.5	1607	aGg/aAg	16/16	1	2	FACETS	0.553	0.5	0.609	0.553	0.5	0.609	SUBCLONAL	1	TRUE	1	0.729046190752756	2		257	580	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939714	131939714	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786203285	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	120	219	0	ENST00000265335.6:c.2500G>A	p.Glu834Lys	p.E834K	ENST00000265335		834	Gag/Aag	15/25	1	2	FACETS	0.542	0.491	0.596	0.542	0.491	0.596	SUBCLONAL	1	TRUE	1	0.729046190752756	2		219	607	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953761	131953761	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	163	194	0	ENST00000265335.6:c.3165-1G>A		p.X1055_splice	ENST00000265335		1055			1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.729046190752756	2		194	434	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449862	149449862	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554102860	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	56	162	0	ENST00000286301.3:c.1202C>T	p.Pro401Leu	p.P401L	ENST00000286301	NM_005211.3	401	cCc/cTc	9/22	1	2	FACETS	0.433	0.372	0.498	0.433	0.372	0.498	SUBCLONAL	1	TRUE	1	0.729046190752756	2		162	355	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456908	149456908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758675858	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	78	217	0	ENST00000286301.3:c.820G>A	p.Gly274Ser	p.G274S	ENST00000286301	NM_005211.3	274	Ggc/Agc	6/22	1	2	FACETS	0.425	0.374	0.479	0.425	0.374	0.479	SUBCLONAL	1	TRUE	1	0.729046190752756	2		217	504	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456999	149456999	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	55	119	0	ENST00000286301.3:c.730-1G>A		p.X244_splice	ENST00000286301	NM_005211.3	244			1	2	FACETS	0.52	0.448	0.598	0.52	0.448	0.598	SUBCLONAL	1	TRUE	1	0.729046190752756	2		119	290	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460531	149460531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	73	165	0	ENST00000286301.3:c.106G>A	p.Ala36Thr	p.A36T	ENST00000286301	NM_005211.3	36	Gca/Aca	3/22	1	2	FACETS	0.502	0.441	0.567	0.502	0.441	0.567	SUBCLONAL	1	TRUE	1	0.729046190752756	2		165	399	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501521	149501521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	76	234	0	ENST00000261799.4:c.2266G>A	p.Asp756Asn	p.D756N	ENST00000261799	NM_002609.3	756	Gac/Aac	16/23	1	2	FACETS	0.496	0.437	0.559	0.496	0.437	0.559	SUBCLONAL	1	TRUE	1	0.729046190752756	2		234	420	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505065	149505065	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	73	245	0	ENST00000261799.4:c.1750C>T	p.Pro584Ser	p.P584S	ENST00000261799	NM_002609.3	584	Ccc/Tcc	12/23	1	2	FACETS	0.469	0.412	0.53	0.469	0.412	0.53	SUBCLONAL	1	TRUE	1	0.729046190752756	2		245	427	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514384	149514384	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	85	284	0	ENST00000261799.4:c.560G>A	p.Ser187Asn	p.S187N	ENST00000261799	NM_002609.3	187	aGc/aAc	4/23	1	2	FACETS	0.444	0.393	0.498	0.444	0.393	0.498	SUBCLONAL	1	TRUE	1	0.729046190752756	2		284	525	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562268	176562268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	112	247	0	ENST00000439151.2:c.164G>A	p.Gly55Glu	p.G55E	ENST00000439151	NM_022455.4	55	gGa/gAa	2/23	NA	2	FACETS	0.558	0.503	0.615			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		247	551	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562612	176562612	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	67	141	0	ENST00000439151.2:c.508C>T	p.Pro170Ser	p.P170S	ENST00000439151	NM_022455.4	170	Cca/Tca	2/23	NA	2	FACETS	0.489	0.427	0.555			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		141	376	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637130	176637130	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	62	175	0	ENST00000439151.2:c.1730C>T	p.Thr577Ile	p.T577I	ENST00000439151	NM_022455.4	577	aCt/aTt	5/23	NA	2	FACETS	0.389	0.337	0.446			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		175	437	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176700675	176700675	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	97	165	0	ENST00000439151.2:c.5512C>T	p.Leu1838Phe	p.L1838F	ENST00000439151	NM_022455.4	1838	Ctt/Ttt	17/23	NA	2	FACETS	0.548	0.49	0.608			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		165	486	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180049840	180049840	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	10	222	0	ENST00000261937.6:c.1549-1G>A		p.X517_splice	ENST00000261937	NM_182925.4	517			0.729046190752756	1	FACETS	0.092	0.062	0.129	0.092	0.062	0.129	SUBCLONAL	1	TRUE	0	0.729046190752756	1		222	190	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055952	180055952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	37	237	0	ENST00000261937.6:c.1033G>A	p.Ala345Thr	p.A345T	ENST00000261937	NM_182925.4	345	Gcc/Acc	8/30	0.729046190752756	1	FACETS	0.303	0.252	0.359	0.303	0.252	0.359	SUBCLONAL	1	TRUE	0	0.729046190752756	1		237	213	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401556	401556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	46	198	0	ENST00000380956.4:c.878C>T	p.Pro293Leu	p.P293L	ENST00000380956	NM_001195286.1	293	cCc/cTc	7/9	NA	2	FACETS	0.456	0.386	0.531			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		198	277	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032173	26032173	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765944241	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	116	238	0	ENST00000244661.2:c.116C>T	p.Pro39Leu	p.P39L	ENST00000244661	NM_003537.3	39	cCt/cTt	1/1	0.729046190752756	4	FACETS	0.816	0.737	0.9			1	CLONAL	1	TRUE	NA	0.729046190752756	4		238	674	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197375	26197375	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	122	359	0	ENST00000356476.2:c.104G>A	p.Gly35Asp	p.G35D	ENST00000356476		35	gGc/gAc	1/1	0.220743545277769	4	FACETS	0.745	0.673	0.82	0.372	0.336	0.41	INDETERMINATE	1	TRUE	2	0.729046190752756	4		359	777	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673527	30673527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242163611	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	99	266	0	ENST00000376406.3:c.3433G>A	p.Ala1145Thr	p.A1145T	ENST00000376406	NM_014641.2	1145	Gcc/Acc	10/15	0.220743545277769	4	FACETS	0.903	0.809	1	0.452	0.404	0.501	INDETERMINATE	1	TRUE	2	0.729046190752756	4		266	520	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673821	30673821	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	53	99	0	ENST00000376406.3:c.3139G>A	p.Ala1047Thr	p.A1047T	ENST00000376406	NM_014641.2	1047	Gcc/Acc	10/15	0.220743545277769	4	FACETS	0.908	0.78	1	0.454	0.39	0.523	INDETERMINATE	1	TRUE	2	0.729046190752756	4		99	277	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675694	30675694	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	162	383	0	ENST00000376406.3:c.2662G>A	p.Glu888Lys	p.E888K	ENST00000376406	NM_014641.2	888	Gag/Aag	8/15	0.220743545277769	4	FACETS	0.801	0.735	0.871	0.401	0.367	0.436	INDETERMINATE	1	TRUE	2	0.729046190752756	4		383	959	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680427	30680427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	116	230	0	ENST00000376406.3:c.1292C>T	p.Ala431Val	p.A431V	ENST00000376406	NM_014641.2	431	gCa/gTa	5/15	0.220743545277769	4	FACETS	0.778	0.702	0.859	0.389	0.351	0.43	INDETERMINATE	1	TRUE	2	0.729046190752756	4		230	707	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680482	30680482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	115	211	0	ENST00000376406.3:c.1237G>A	p.Ala413Thr	p.A413T	ENST00000376406	NM_014641.2	413	Gcg/Acg	5/15	0.220743545277769	4	FACETS	0.789	0.712	0.871	0.395	0.356	0.436	INDETERMINATE	1	TRUE	2	0.729046190752756	4		211	691	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170054	32170054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	86	248	0	ENST00000375023.3:c.3554G>A	p.Gly1185Glu	p.G1185E	ENST00000375023	NM_004557.3	1185	gGg/gAg	21/30	NA	2	FACETS	0.587	0.522	0.655			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		248	402	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181886	32181886	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	50	183	0	ENST00000375023.3:c.2167+1G>A		p.X723_splice	ENST00000375023	NM_004557.3	723			NA	2	FACETS	0.468	0.4	0.542			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		183	293	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184781	32184781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762081312	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	43	198	0	ENST00000375023.3:c.1802G>A	p.Gly601Glu	p.G601E	ENST00000375023	NM_004557.3	601	gGa/gAa	11/30	NA	2	FACETS	0.362	0.304	0.426			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		198	326	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185775	32185775	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772949126	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	32	384	0	ENST00000375023.3:c.1621C>T	p.Pro541Ser	p.P541S	ENST00000375023	NM_004557.3	541	Cct/Tct	9/30	NA	2	FACETS	0.329	0.268	0.397			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		384	267	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32190494	32190494	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	41	156	0	ENST00000375023.3:c.245C>T	p.Ala82Val	p.A82V	ENST00000375023	NM_004557.3	82	gCc/gTc	3/30	NA	2	FACETS	0.5	0.42	0.587			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		156	225	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287230	33287230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	98	195	0	ENST00000374542.5:c.1867G>A	p.Gly623Arg	p.G623R	ENST00000374542	NM_001141970.1	623	Gga/Aga	6/8	0.197642773091188	5	FACETS	1	0.897	1			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	5		195	561	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662585	117662585	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	91	218	0	ENST00000368508.3:c.4880G>A	p.Gly1627Asp	p.G1627D	ENST00000368508	NM_002944.2	1627	gGt/gAt	29/43	NA	2	FACETS	0.472	0.42	0.527			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		218	529	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708961	117708961	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	89	255	0	ENST00000368508.3:c.1996G>A	p.Gly666Ser	p.G666S	ENST00000368508	NM_002944.2	666	Ggt/Agt	13/43	NA	2	FACETS	0.612	0.546	0.681			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		255	399	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117730744	117730744	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	105	287	0	ENST00000368508.3:c.289+1G>A		p.X97_splice	ENST00000368508	NM_002944.2	97			NA	2	FACETS	0.564	0.507	0.623			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		287	511	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149982884	149982884	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1327531500	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	96	202	0	ENST00000253339.5:c.3374G>A	p.Arg1125His	p.R1125H	ENST00000253339		1125	cGc/cAc	7/7	0.284387228010373	3	FACETS	0.605	0.54	0.674			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	3		202	594	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997399	149997399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1320633717	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	163	256	0	ENST00000253339.5:c.2880G>A	p.Met960Ile	p.M960I	ENST00000253339		960	atG/atA	6/7	0.284387228010373	3	FACETS	0.828	0.761	0.897			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	3		256	737	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505534	157505534	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	40	120	0	ENST00000346085.5:c.3515C>T	p.Thr1172Ile	p.T1172I	ENST00000346085	NM_020732.3	1172	aCc/aTc	13/20	NA	2	FACETS	0.406	0.339	0.48			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		120	270	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511257	157511257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	69	186	0	ENST00000346085.5:c.3775C>T	p.Pro1259Ser	p.P1259S	ENST00000346085	NM_020732.3	1259	Ccc/Tcc	15/20	NA	2	FACETS	0.514	0.45	0.583			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		186	368	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781155	161781155	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	59	237	0	ENST00000366898.1:c.1250C>T	p.Pro417Leu	p.P417L	ENST00000366898	NM_004562.2	417	cCc/cTc	11/12	NA	2	FACETS	0.443	0.383	0.508			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		237	365	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987416	2987416	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	52	225	0	ENST00000396946.4:c.13G>A	p.Gly5Arg	p.G5R	ENST00000396946	NM_032415.4	5	Ggg/Agg	3/25	NA	2	FACETS	0.353	0.301	0.41			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		225	404	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6045540	6045540	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	37	82	0	ENST00000265849.7:c.146C>T	p.Ala49Val	p.A49V	ENST00000265849	NM_000535.5	49	gCt/gTt	2/15	0.729046190752756	3	FACETS	0.47	0.388	0.559	0.235	0.194	0.28	SUBCLONAL	1	TRUE	1	0.729046190752756	3		82	295	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739729	41739729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446232934	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	85	404	3	ENST00000242208.4:c.244G>A	p.Ala82Thr	p.A82T	ENST00000242208	NM_002192.2	82	Gcg/Acg	2/3	0.198494003949131	3	FACETS	0.587	0.52	0.659	0.196	0.173	0.22	INDETERMINATE	1	TRUE	0	0.729046190752756	3		407	542	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50358686	50358686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	43	92	0	ENST00000331340.3:c.29C>T	p.Ser10Phe	p.S10F	ENST00000331340	NM_006060.4	10	tCc/tTc	2/8	0.198494003949131	3	FACETS	0.587	0.495	0.689	0.196	0.165	0.23	INDETERMINATE	1	TRUE	0	0.729046190752756	3		92	274	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334716	81334716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	127	316	0	ENST00000222390.5:c.2000G>A	p.Gly667Glu	p.G667E	ENST00000222390	NM_000601.4	667	gGa/gAa	17/18	0.729046190752756	3	FACETS	0.505	0.457	0.556	0.253	0.228	0.278	SUBCLONAL	1	TRUE	1	0.729046190752756	3		316	941	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334803	81334803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	112	228	0	ENST00000222390.5:c.1913G>A	p.Gly638Glu	p.G638E	ENST00000222390	NM_000601.4	638	gGa/gAa	17/18	0.729046190752756	3	FACETS	0.47	0.422	0.521	0.235	0.211	0.261	SUBCLONAL	1	TRUE	1	0.729046190752756	3		228	892	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508010	106508010	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777512949	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	42	90	0	ENST00000359195.3:c.4G>A	p.Glu2Lys	p.E2K	ENST00000359195	NM_002649.2	2	Gag/Aag	2/11	0.729046190752756	3	FACETS	0.566	0.475	0.665	0.283	0.237	0.333	SUBCLONAL	1	TRUE	1	0.729046190752756	3		90	278	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508374	106508374	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200423506	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	21	40	0	ENST00000359195.3:c.368G>A	p.Arg123His	p.R123H	ENST00000359195	NM_002649.2	123	cGc/cAc	2/11	0.729046190752756	3	FACETS	0.482	0.374	0.606	0.241	0.187	0.303	SUBCLONAL	1	TRUE	1	0.729046190752756	3		40	163	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508446	106508446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	19	36	0	ENST00000359195.3:c.440C>T	p.Ser147Phe	p.S147F	ENST00000359195	NM_002649.2	147	tCc/tTc	2/11	0.729046190752756	3	FACETS	0.477	0.365	0.607	0.239	0.182	0.304	SUBCLONAL	1	TRUE	1	0.729046190752756	3		36	149	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508565	106508565	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	25	86	0	ENST00000359195.3:c.559G>A	p.Glu187Lys	p.E187K	ENST00000359195	NM_002649.2	187	Gag/Aag	2/11	0.729046190752756	3	FACETS	0.377	0.298	0.468	0.189	0.149	0.234	SUBCLONAL	1	TRUE	1	0.729046190752756	3		86	248	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515240	106515240	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs945222564	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	62	141	0	ENST00000359195.3:c.2383G>A	p.Ala795Thr	p.A795T	ENST00000359195	NM_002649.2	795	Gcg/Acg	5/11	0.729046190752756	3	FACETS	0.502	0.435	0.575	0.251	0.217	0.288	SUBCLONAL	1	TRUE	1	0.729046190752756	3		141	462	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412032	116412032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	158	160	0	ENST00000397752.3:c.3017C>T	p.Thr1006Ile	p.T1006I	ENST00000397752	NM_000245.2	1006	aCt/aTt	14/21	0.729046190752756	3	FACETS	0.987	0.909	1	0.494	0.454	0.535	CLONAL	1	TRUE	1	0.729046190752756	3		160	599	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845176	128845176	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1404842660	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	54	194	0	ENST00000249373.3:c.670G>A	p.Glu224Lys	p.E224K	ENST00000249373	NM_005631.4	224	Gag/Aag	3/12	0.729046190752756	3	FACETS	0.384	0.328	0.446	0.192	0.164	0.223	SUBCLONAL	1	TRUE	1	0.729046190752756	3		194	526	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846049	128846049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371993481	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	75	300	1	ENST00000249373.3:c.979G>A	p.Ala327Thr	p.A327T	ENST00000249373	NM_005631.4	327	Gct/Act	5/12	0.729046190752756	3	FACETS	0.433	0.379	0.491	0.217	0.189	0.246	SUBCLONAL	1	TRUE	1	0.729046190752756	3		301	648	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852120	128852120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1168512964	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	61	266	0	ENST00000249373.3:c.2192C>T	p.Thr731Ile	p.T731I	ENST00000249373	NM_005631.4	731	aCc/aTc	12/12	0.729046190752756	3	FACETS	0.491	0.424	0.563	0.246	0.212	0.282	SUBCLONAL	1	TRUE	1	0.729046190752756	3		266	465	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512618	148512618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	69	147	0	ENST00000320356.2:c.1526G>A	p.Arg509Lys	p.R509K	ENST00000320356	NM_004456.4	509	aGa/aAa	13/20	0.729046190752756	3	FACETS	0.415	0.361	0.473	0.208	0.18	0.237	SUBCLONAL	1	TRUE	1	0.729046190752756	3		147	622	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848547	151848547	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	96	221	0	ENST00000262189.6:c.12646G>A	p.Asp4216Asn	p.D4216N	ENST00000262189	NM_170606.2	4216	Gat/Aat	50/59	0.729046190752756	3	FACETS	0.527	0.47	0.588	0.263	0.235	0.294	SUBCLONAL	1	TRUE	1	0.729046190752756	3		221	682	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851460	151851460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1563167589	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	92	260	0	ENST00000262189.6:c.12031G>A	p.Val4011Ile	p.V4011I	ENST00000262189	NM_170606.2	4011	Gtt/Att	47/59	0.729046190752756	3	FACETS	0.541	0.481	0.605	0.271	0.24	0.303	SUBCLONAL	1	TRUE	1	0.729046190752756	3		260	636	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859432	151859432	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	88	229	1	ENST00000262189.6:c.11230G>A	p.Val3744Ile	p.V3744I	ENST00000262189	NM_170606.2	3744	Gta/Ata	43/59	0.729046190752756	3	FACETS	0.52	0.461	0.583	0.26	0.23	0.292	SUBCLONAL	1	TRUE	1	0.729046190752756	3		230	634	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873530	151873530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	88	214	0	ENST00000262189.6:c.9008G>A	p.Ser3003Asn	p.S3003N	ENST00000262189	NM_170606.2	3003	aGt/aAt	38/59	0.729046190752756	3	FACETS	0.469	0.415	0.526	0.234	0.207	0.263	SUBCLONAL	1	TRUE	1	0.729046190752756	3		214	703	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874365	151874365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746319127	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	87	223	0	ENST00000262189.6:c.8173G>A	p.Glu2725Lys	p.E2725K	ENST00000262189	NM_170606.2	2725	Gag/Aag	38/59	0.729046190752756	3	FACETS	0.458	0.405	0.515	0.229	0.202	0.258	SUBCLONAL	1	TRUE	1	0.729046190752756	3		223	711	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874577	151874577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	93	165	0	ENST00000262189.6:c.7961G>A	p.Gly2654Asp	p.G2654D	ENST00000262189	NM_170606.2	2654	gGt/gAt	38/59	0.729046190752756	3	FACETS	0.627	0.559	0.7	0.314	0.279	0.35	SUBCLONAL	1	TRUE	1	0.729046190752756	3		165	555	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874964	151874964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	76	227	0	ENST00000262189.6:c.7574C>T	p.Pro2525Leu	p.P2525L	ENST00000262189	NM_170606.2	2525	cCt/cTt	38/59	0.729046190752756	3	FACETS	0.492	0.432	0.557	0.246	0.216	0.279	SUBCLONAL	1	TRUE	1	0.729046190752756	3		227	578	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878121	151878121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	56	165	1	ENST00000262189.6:c.6824C>T	p.Thr2275Ile	p.T2275I	ENST00000262189	NM_170606.2	2275	aCa/aTa	36/59	0.729046190752756	3	FACETS	0.473	0.406	0.546	0.237	0.203	0.273	SUBCLONAL	1	TRUE	1	0.729046190752756	3		166	443	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884438	151884438	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	210	217	0	ENST00000262189.6:c.4917G>A	p.Trp1639Ter	p.W1639*	ENST00000262189	NM_170606.2	1639	tgG/tgA	33/59	0.729046190752756	3	FACETS	1	0.956	1	0.517	0.481	0.554	CLONAL	1	TRUE	1	0.729046190752756	3		217	760	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949051	151949051	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	107	239	0	ENST00000262189.6:c.1594G>A	p.Glu532Lys	p.E532K	ENST00000262189	NM_170606.2	532	Gaa/Aaa	11/59	0.729046190752756	3	FACETS	0.514	0.461	0.571	0.257	0.23	0.286	SUBCLONAL	1	TRUE	1	0.729046190752756	3		239	779	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012283	152012283	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	114	305	0	ENST00000262189.6:c.530G>A	p.Ser177Asn	p.S177N	ENST00000262189	NM_170606.2	177	aGc/aAc	4/59	0.729046190752756	3	FACETS	0.412	0.37	0.457	0.206	0.185	0.229	SUBCLONAL	1	TRUE	1	0.729046190752756	3		305	1035	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346233	152346233	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1438202364	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	117	374	1	ENST00000359321.1:c.337G>A	p.Gly113Arg	p.G113R	ENST00000359321	NM_005431.1	113	Gga/Aga	3/3	0.729046190752756	3	FACETS	0.593	0.535	0.655	0.297	0.267	0.328	SUBCLONAL	1	TRUE	1	0.729046190752756	3		375	738	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38314892	38314892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	19	145	0	ENST00000425967.3:c.172C>T	p.Pro58Ser	p.P58S	ENST00000425967	NM_001174067.1	58	Ccg/Tcg	3/19	0.276599700027762	1	FACETS	0.122	0.092	0.157	0.122	0.092	0.157	INDETERMINATE	1	TRUE	0	0.729046190752756	1		145	271	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372187	55372187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	21	44	0	ENST00000297316.4:c.877C>T	p.Leu293Phe	p.L293F	ENST00000297316	NM_022454.3	293	Ctt/Ttt	2/2	0.276599700027762	1	FACETS	0.469	0.371	0.577	0.469	0.371	0.577	INDETERMINATE	1	TRUE	0	0.729046190752756	1		44	78	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965860	90965860	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572568222	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	107	220	0	ENST00000265433.3:c.1457C>T	p.Ser486Phe	p.S486F	ENST00000265433	NM_002485.4	486	tCt/tTt	11/16	0.276599700027762	1	FACETS	0.353	0.317	0.39	0.353	0.317	0.39	INDETERMINATE	1	TRUE	0	0.729046190752756	1		220	529	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90982761	90982761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	135	231	0	ENST00000265433.3:c.727G>A	p.Val243Ile	p.V243I	ENST00000265433	NM_002485.4	243	Gtc/Atc	7/16	0.276599700027762	1	FACETS	0.408	0.372	0.445	0.408	0.372	0.445	INDETERMINATE	1	TRUE	0	0.729046190752756	1		231	577	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5055732	5055732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	76	197	0	ENST00000381652.3:c.1000G>A	p.Glu334Lys	p.E334K	ENST00000381652	NM_004972.3	334	Gag/Aag	8/25	NA	2	FACETS	0.356	0.313	0.403			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		197	585	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465651	8465651	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772237001	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	105	228	1	ENST00000356435.5:c.3529C>T	p.Arg1177Cys	p.R1177C	ENST00000356435		1177	Cgc/Tgc	21/35	NA	2	FACETS	0.548	0.492	0.606			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		229	526	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499766	8499766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	85	228	0	ENST00000356435.5:c.2203C>T	p.Pro735Ser	p.P735S	ENST00000356435		735	Ccc/Tcc	14/35	NA	2	FACETS	0.487	0.432	0.545			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		228	479	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020771	37020771	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	49	276	0	ENST00000358127.4:c.74G>A	p.Gly25Glu	p.G25E	ENST00000358127	NM_001280556.1	25	gGg/gAg	2/10	0.147269491219651	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.729046190752756	0		276	334	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87366916	87366916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1251903649	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	98	311	0	ENST00000277120.3:c.1312G>A	p.Val438Met	p.V438M	ENST00000277120		438	Gtg/Atg	12/19	0.147269491219651	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.729046190752756	0		311	470	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563410	87563410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	48	156	0	ENST00000277120.3:c.1798G>A	p.Asp600Asn	p.D600N	ENST00000277120		600	Gac/Aac	16/19	0.147269491219651	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.729046190752756	0		156	322	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570301	87570301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	56	181	0	ENST00000277120.3:c.2041G>A	p.Val681Ile	p.V681I	ENST00000277120		681	Gtc/Atc	17/19	0.147269491219651	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.729046190752756	0		181	273	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635217	87635217	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746097417	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	65	157	0	ENST00000277120.3:c.2269G>A	p.Val757Ile	p.V757I	ENST00000277120		757	Gtc/Atc	18/19	0.147269491219651	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.729046190752756	0		157	349	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239117	98239117	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060502268	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	101	199	0	ENST00000331920.6:c.1526G>A	p.Gly509Asp	p.G509D	ENST00000331920	NM_000264.3	509	gGt/gAt	11/24	NA	2	FACETS	0.628	0.565	0.695			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		199	441	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101895010	101895010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	120	178	0	ENST00000374994.4:c.563G>A	p.Gly188Asp	p.G188D	ENST00000374994	NM_004612.2	188	gGt/gAt	3/9	NA	2	FACETS	0.592	0.537	0.65			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		178	556	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133710861	133710861	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	94	198	0	ENST00000318560.5:c.28G>A	p.Gly10Ser	p.G10S	ENST00000318560	NM_005157.4	10	Ggc/Agc	1/11	NA	2	FACETS	0.578	0.517	0.643			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		198	446	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759554	133759554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253014415	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	65	261	0	ENST00000318560.5:c.1877G>A	p.Gly626Asp	p.G626D	ENST00000318560	NM_005157.4	626	gGc/gAc	11/11	NA	2	FACETS	0.505	0.44	0.574			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		261	353	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759683	133759683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	52	162	0	ENST00000318560.5:c.2006C>T	p.Pro669Leu	p.P669L	ENST00000318560	NM_005157.4	669	cCc/cTc	11/11	NA	2	FACETS	0.61	0.524	0.701			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		162	234	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759716	133759716	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	20	110	0	ENST00000318560.5:c.2039G>A	p.Gly680Asp	p.G680D	ENST00000318560	NM_005157.4	680	gGc/gAc	11/11	NA	2	FACETS	0.337	0.259	0.426			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		110	163	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781043	135781043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	88	343	0	ENST00000298552.3:c.1922C>T	p.Pro641Leu	p.P641L	ENST00000298552	NM_001162426.1	641	cCc/cTc	15/23	NA	2	FACETS	0.463	0.411	0.518			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		343	521	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403377	139403377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	60	181	0	ENST00000277541.6:c.3116G>A	p.Gly1039Asp	p.G1039D	ENST00000277541	NM_017617.3	1039	gGc/gAc	19/34	0.220743545277769	4	FACETS	0.728	0.63	0.834	0.364	0.315	0.417	INDETERMINATE	1	TRUE	2	0.729046190752756	4		181	391	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405113	139405113	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	60	179	0	ENST00000277541.6:c.2732G>A	p.Cys911Tyr	p.C911Y	ENST00000277541	NM_017617.3	911	tGc/tAc	17/34	0.220743545277769	4	FACETS	0.832	0.721	0.952	0.416	0.36	0.476	INDETERMINATE	1	TRUE	2	0.729046190752756	4		179	342	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410432	139410432	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	52	214	0	ENST00000277541.6:c.1669+1G>A		p.X557_splice	ENST00000277541	NM_017617.3	557			0.220743545277769	4	FACETS	0.651	0.556	0.754	0.325	0.278	0.377	INDETERMINATE	1	TRUE	2	0.729046190752756	4		214	379	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411829	139411829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	85	210	0	ENST00000277541.6:c.1450G>A	p.Gly484Ser	p.G484S	ENST00000277541	NM_017617.3	484	Ggt/Agt	9/34	0.220743545277769	4	FACETS	1	0.95	1	0.558	0.497	0.623	INDETERMINATE	1	TRUE	2	0.729046190752756	4		210	361	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139563029	139563029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs950942092	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	68	237	0	ENST00000308874.7:c.101G>A	p.Arg34Gln	p.R34Q	ENST00000308874		34	cGg/cAg	4/10	NA	2	FACETS	0.442	0.386	0.502			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		237	422	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793221	139793221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	92	268	1	ENST00000247668.2:c.29G>A	p.Gly10Asp	p.G10D	ENST00000247668	NM_021138.3	10	gGc/gAc	2/11	NA	2	FACETS	0.479	0.427	0.534			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		269	527	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597964	43597964	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1422505495	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	58	236	0	ENST00000355710.3:c.512G>A	p.Arg171Lys	p.R171K	ENST00000355710	NM_020975.4	171	aGg/aAg	3/20	0.601910670162504	0	FACETS		NA	1			1	NA	1	TRUE	0	0.729046190752756	0		236	168	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609952	43609952	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776164321	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	58	385	1	ENST00000355710.3:c.1904G>A	p.Arg635His	p.R635H	ENST00000355710	NM_020975.4	635	cGc/cAc	11/20	0.601910670162504	0	FACETS		NA	1			1	NA	1	TRUE	0	0.729046190752756	0		386	194	SUCCESS
RET	5979	MSKCC	GRCh37	10	43610093	43610093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1283566936	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	32	272	0	ENST00000355710.3:c.2045C>T	p.Ala682Val	p.A682V	ENST00000355710	NM_020975.4	682	gCc/gTc	11/20	0.601910670162504	0	FACETS		NA	1			1	NA	1	TRUE	0	0.729046190752756	0		272	160	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63829514	63829514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	121	193	0	ENST00000279873.7:c.1157G>A	p.Gly386Glu	p.G386E	ENST00000279873	NM_032199.2	386	gGg/gAg	8/10	NA	2	FACETS	0.767	0.698	0.838			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		193	433	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333858	70333858	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1191715443	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	37	259	0	ENST00000373644.4:c.1763G>A	p.Arg588Lys	p.R588K	ENST00000373644	NM_030625.2	588	aGa/aAa	2/12	0.729046190752756	1	FACETS	0.251	0.208	0.299	0.251	0.208	0.299	SUBCLONAL	1	TRUE	0	0.729046190752756	1		259	257	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88683406	88683406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	56	95	0	ENST00000372037.3:c.1529C>T	p.Ser510Phe	p.S510F	ENST00000372037	NM_004329.2	510	tCc/tTc	13/13	0.729046190752756	1	FACETS	0.603	0.527	0.681	0.603	0.527	0.681	SUBCLONAL	1	TRUE	0	0.729046190752756	1		95	162	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717696	89717696	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1554825207	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	191	191	0	ENST00000371953.3:c.721T>G	p.Phe241Val	p.F241V	ENST00000371953	NM_000314.4	241	Ttt/Gtt	7/9	0.729046190752756	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.729046190752756	1		191	294	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263455	123263455	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	40	102	0	ENST00000358487.5:c.1288G>A	p.Val430Ile	p.V430I	ENST00000358487	NM_000141.4	430	Gtt/Att	10/18	0.729046190752756	1	FACETS	0.601	0.512	0.694	0.601	0.512	0.694	SUBCLONAL	1	TRUE	0	0.729046190752756	1		102	116	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2161369	2161369	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1238531843	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	48	223	0	ENST00000434045.2:c.158T>C	p.Met53Thr	p.M53T	ENST00000434045	NM_001127598.1	53	aTg/aCg	2/5	NA	2	FACETS	0.636	0.544	0.735			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		223	207	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456810	32456810	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1416988433	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	24	65	0	ENST00000332351.3:c.82C>T	p.Pro28Ser	p.P28S	ENST00000332351	NM_024426.4	28	Cca/Tca	1/10	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.729046190752756	NA		65	108	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137063	64137063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	53	147	0	ENST00000334205.4:c.1574G>A	p.Gly525Asp	p.G525D	ENST00000334205	NM_003942.2	525	gGc/gAc	13/17	0.203422412643375	4	FACETS	1	0.903	1	0.53	0.457	0.609	INDETERMINATE	1	TRUE	2	0.729046190752756	4		147	237	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518051	69518051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	38	219	0	ENST00000294312.3:c.314C>T	p.Ala105Val	p.A105V	ENST00000294312	NM_005117.2	105	gCc/gTc	2/3	0.581352152711357	1	FACETS	0.293	0.244	0.347	0.293	0.244	0.347	SUBCLONAL	1	TRUE	0	0.729046190752756	1		219	226	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625438	69625438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	49	194	0	ENST00000334134.2:c.355G>A	p.Glu119Lys	p.E119K	ENST00000334134	NM_005247.2	119	Gag/Aag	3/3	0.581352152711357	1	FACETS	0.357	0.305	0.413	0.357	0.305	0.413	SUBCLONAL	1	TRUE	0	0.729046190752756	1		194	239	SUCCESS
EED	8726	MSKCC	GRCh37	11	85988181	85988181	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	119	226	0	ENST00000263360.6:c.1125+1G>A		p.X375_splice	ENST00000263360	NM_003797.3	375			NA	2	FACETS	0.504	0.455	0.555			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		226	648	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192599	94192599	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61749249	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	40	273	1	ENST00000323929.3:c.1475C>T	p.Ala492Val	p.A492V	ENST00000323929	NM_005591.3	492	gCc/gTc	13/20	NA	2	FACETS	0.165	0.136	0.196			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		274	667	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94209558	94209558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	107	169	0	ENST00000323929.3:c.556G>A	p.Asp186Asn	p.D186N	ENST00000323929	NM_005591.3	186	Gat/Aat	7/20	NA	2	FACETS	0.558	0.502	0.617			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		169	526	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998931	100998931	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	50	281	0	ENST00000325455.5:c.871C>T	p.Pro291Ser	p.P291S	ENST00000325455	NM_001202474.3	291	Ccc/Tcc	1/8	0.665430106325816	1	FACETS	0.312	0.267	0.362	0.312	0.267	0.362	SUBCLONAL	1	TRUE	0	0.729046190752756	1		281	279	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999288	100999288	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	65	305	0	ENST00000325455.5:c.514G>A	p.Val172Ile	p.V172I	ENST00000325455	NM_001202474.3	172	Gtt/Att	1/8	0.665430106325816	1	FACETS	0.338	0.295	0.385	0.338	0.295	0.385	SUBCLONAL	1	TRUE	0	0.729046190752756	1		305	335	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102098205	102098205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1313217696	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	35	192	0	ENST00000282441.5:c.1169C>T	p.Thr390Ile	p.T390I	ENST00000282441	NM_001130145.2	390	aCc/aTc	8/9	1	2	FACETS	0.251	0.205	0.301	0.251	0.205	0.301	SUBCLONAL	1	TRUE	1	0.729046190752756	2		192	383	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115534	108115534	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	102	208	0	ENST00000278616.4:c.682G>A	p.Gly228Ser	p.G228S	ENST00000278616	NM_000051.3	228	Ggt/Agt	7/63	1	2	FACETS	0.506	0.454	0.561	0.506	0.454	0.561	SUBCLONAL	1	TRUE	1	0.729046190752756	2		208	553	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344605	118344605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	102	270	0	ENST00000534358.1:c.2731G>A	p.Val911Ile	p.V911I	ENST00000534358	NM_005933.3	911	Gtt/Att	3/36	1	2	FACETS	0.495	0.444	0.549	0.495	0.444	0.549	SUBCLONAL	1	TRUE	1	0.729046190752756	2		270	565	SUCCESS
CBL	867	MSKCC	GRCh37	11	119145543	119145543	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	51	232	0	ENST00000264033.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000264033	NM_005188.3	250	cCc/cTc	5/16	1	2	FACETS	0.224	0.19	0.262	0.224	0.19	0.262	SUBCLONAL	1	TRUE	1	0.729046190752756	2		232	624	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497501	125497501	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	174	140	0	ENST00000428830.2:c.66-1G>A		p.X22_splice	ENST00000428830	NM_001114121.2	22			1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.729046190752756	2		140	440	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394803	394803	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775874981	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	94	247	0	ENST00000399788.2:c.4892G>A	p.Gly1631Asp	p.G1631D	ENST00000399788	NM_001042603.1	1631	gGc/gAc	28/28	NA	2	FACETS	0.528	0.472	0.588			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		247	488	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420158	420158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	84	205	0	ENST00000399788.2:c.3109C>T	p.Leu1037Phe	p.L1037F	ENST00000399788	NM_001042603.1	1037	Ctt/Ttt	21/28	NA	2	FACETS	0.466	0.413	0.523			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		205	494	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	465661	465661	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	128	279	0	ENST00000399788.2:c.715C>T	p.Leu239Phe	p.L239F	ENST00000399788	NM_001042603.1	239	Ctt/Ttt	6/28	0.220743545277769	4	FACETS	0.847	0.768	0.929	0.423	0.384	0.465	INDETERMINATE	1	TRUE	2	0.729046190752756	4		279	717	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435619	18435619	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1164190418	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	77	201	0	ENST00000266497.5:c.604G>A	p.Glu202Lys	p.E202K	ENST00000266497		202	Gaa/Aaa	1/31	NA	2	FACETS	0.409	0.359	0.461			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		201	517	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123635	46123635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	110	183	1	ENST00000334344.6:c.16G>A	p.Gly6Arg	p.G6R	ENST00000334344	NM_152641.2	6	Ggg/Agg	1/21	NA	2	FACETS	0.567	0.511	0.626			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		184	532	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422670	49422670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	91	195	0	ENST00000301067.7:c.14323G>A	p.Glu4775Lys	p.E4775K	ENST00000301067	NM_003482.3	4775	Gaa/Aaa	45/54	0.381873481585237	4	FACETS	0.756	0.673	0.845			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	4		195	571	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425247	49425247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	93	209	0	ENST00000301067.7:c.13241G>A	p.Ser4414Asn	p.S4414N	ENST00000301067	NM_003482.3	4414	aGc/aAc	39/54	0.381873481585237	4	FACETS	0.925	0.826	1			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	4		209	477	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425593	49425593	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	75	229	0	ENST00000301067.7:c.12895G>A	p.Gly4299Arg	p.G4299R	ENST00000301067	NM_003482.3	4299	Gga/Aga	39/54	0.381873481585237	4	FACETS	0.954	0.841	1			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	4		229	373	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426129	49426129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753017509	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	49	140	0	ENST00000301067.7:c.12359G>A	p.Gly4120Asp	p.G4120D	ENST00000301067	NM_003482.3	4120	gGc/gAc	39/54	0.381873481585237	4	FACETS	0.83	0.708	0.962			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	4		140	280	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433268	49433268	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	68	177	0	ENST00000301067.7:c.8179C>T	p.Pro2727Ser	p.P2727S	ENST00000301067	NM_003482.3	2727	Cct/Tct	32/54	0.381873481585237	4	FACETS	0.851	0.744	0.965			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	4		177	379	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433697	49433697	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	68	187	0	ENST00000301067.7:c.7856C>T	p.Pro2619Leu	p.P2619L	ENST00000301067	NM_003482.3	2619	cCt/cTt	31/54	0.381873481585237	4	FACETS	0.747	0.652	0.848			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	4		187	432	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438297	49438297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	96	129	0	ENST00000301067.7:c.4972G>A	p.Glu1658Lys	p.E1658K	ENST00000301067	NM_003482.3	1658	Gag/Aag	20/54	0.381873481585237	4	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	4		129	388	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447019	49447019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	84	226	0	ENST00000301067.7:c.925G>A	p.Glu309Lys	p.E309K	ENST00000301067	NM_003482.3	309	Gaa/Aaa	7/54	0.381873481585237	4	FACETS	0.706	0.625	0.793			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	4		226	564	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448320	49448320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	100	251	0	ENST00000301067.7:c.391G>A	p.Glu131Lys	p.E131K	ENST00000301067	NM_003482.3	131	Gaa/Aaa	3/54	0.381873481585237	4	FACETS	0.793	0.71	0.881			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	4		251	598	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50479986	50479986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	116	217	0	ENST00000394963.4:c.220C>T	p.Pro74Ser	p.P74S	ENST00000394963	NM_003076.4	74	Cct/Tct	2/13	0.381873481585237	4	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	4		217	498	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482570	56482570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	87	218	0	ENST00000267101.3:c.1027G>A	p.Val343Met	p.V343M	ENST00000267101	NM_001982.3	343	Gtg/Atg	9/28	NA	2	FACETS	0.492	0.437	0.551			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		218	485	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491686	56491686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1565860687	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	77	151	0	ENST00000267101.3:c.2578C>T	p.Pro860Ser	p.P860S	ENST00000267101	NM_001982.3	860	Cct/Tct	21/28	NA	2	FACETS	0.514	0.453	0.579			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		151	411	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495648	56495648	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	50	147	0	ENST00000267101.3:c.3838G>A	p.Gly1280Arg	p.G1280R	ENST00000267101	NM_001982.3	1280	Ggg/Agg	28/28	NA	2	FACETS	0.393	0.335	0.457			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		147	349	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861144	57861144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373249560	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	113	322	0	ENST00000228682.2:c.941G>A	p.Arg314His	p.R314H	ENST00000228682	NM_005269.2	314	cGc/cAc	9/12	NA	2	FACETS	0.507	0.457	0.559			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		322	612	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861999	57861999	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	67	240	0	ENST00000228682.2:c.1300G>A	p.Gly434Ser	p.G434S	ENST00000228682	NM_005269.2	434	Ggt/Agt	10/12	NA	2	FACETS	0.424	0.369	0.482			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		240	434	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865411	57865411	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	89	400	0	ENST00000228682.2:c.2888C>T	p.Ser963Phe	p.S963F	ENST00000228682	NM_005269.2	963	tCc/tTc	12/12	NA	2	FACETS	0.443	0.394	0.496			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		400	551	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222655	69222655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	117	206	0	ENST00000462284.1:c.628G>A	p.Glu210Lys	p.E210K	ENST00000462284	NM_002392.5	210	Gag/Aag	8/11	1	2	FACETS	0.503	0.454	0.554	0.503	0.454	0.554	SUBCLONAL	1	TRUE	1	0.729046190752756	2		206	638	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69229628	69229628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	61	135	0	ENST00000462284.1:c.704G>A	p.Ser235Asn	p.S235N	ENST00000462284	NM_002392.5	235	aGt/aAt	9/11	1	2	FACETS	0.373	0.322	0.427	0.373	0.322	0.427	SUBCLONAL	1	TRUE	1	0.729046190752756	2		135	449	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69229711	69229711	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	79	170	0	ENST00000462284.1:c.787G>A	p.Glu263Lys	p.E263K	ENST00000462284	NM_002392.5	263	Gaa/Aaa	9/11	1	2	FACETS	0.4	0.352	0.451	0.4	0.352	0.451	SUBCLONAL	1	TRUE	1	0.729046190752756	2		170	542	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869578	102869578	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	20	87	1	ENST00000307046.8:c.64-1G>A		p.X22_splice	ENST00000307046	NM_001111285.1	22			1	2	FACETS	0.329	0.253	0.416	0.329	0.253	0.416	SUBCLONAL	1	TRUE	1	0.729046190752756	2		88	167	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856248	111856248	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	22	37	0	ENST00000341259.2:c.299C>T	p.Ala100Val	p.A100V	ENST00000341259	NM_005475.2	100	gCc/gTc	2/8	1	2	FACETS	0.622	0.492	0.767	0.622	0.492	0.767	SUBCLONAL	1	TRUE	1	0.729046190752756	2		37	97	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112884203	112884203	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	69	198	0	ENST00000351677.2:c.137+1G>A		p.X46_splice	ENST00000351677	NM_002834.3	46			0.147269491219651	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.729046190752756	0		198	367	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112892368	112892368	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	100	160	0	ENST00000351677.2:c.526G>A	p.Glu176Lys	p.E176K	ENST00000351677	NM_002834.3	176	Gaa/Aaa	5/16	0.147269491219651	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.729046190752756	0		160	454	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431425	121431425	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	57	161	0	ENST00000257555.6:c.629C>T	p.Ser210Phe	p.S210F	ENST00000257555		210	tCc/tTc	3/10	0.147269491219651	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.729046190752756	0		161	274	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434209	121434209	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	39	164	0	ENST00000257555.6:c.1100C>T	p.Ala367Val	p.A367V	ENST00000257555		367	gCc/gTc	5/10	0.147269491219651	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.729046190752756	0		164	243	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202356	133202356	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	46	148	0	ENST00000320574.5:c.6532G>A	p.Asp2178Asn	p.D2178N	ENST00000320574	NM_006231.2	2178	Gat/Aat	47/49	0.147269491219651	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.729046190752756	0		148	200	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133202732	133202732	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	66	185	0	ENST00000320574.5:c.6502G>A	p.Asp2168Asn	p.D2168N	ENST00000320574	NM_006231.2	2168	Gac/Aac	46/49	0.147269491219651	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.729046190752756	0		185	325	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214691	133214691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780000018	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	66	193	0	ENST00000320574.5:c.5587G>A	p.Val1863Ile	p.V1863I	ENST00000320574	NM_006231.2	1863	Gtc/Atc	41/49	0.147269491219651	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.729046190752756	0		193	352	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219302	133219302	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	113	172	0	ENST00000320574.5:c.4742G>A	p.Gly1581Glu	p.G1581E	ENST00000320574	NM_006231.2	1581	gGg/gAg	37/49	0.147269491219651	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.729046190752756	0		172	274	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226345	133226345	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879255392	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	60	289	0	ENST00000320574.5:c.3713G>A	p.Ser1238Asn	p.S1238N	ENST00000320574	NM_006231.2	1238	aGc/aAc	30/49	0.147269491219651	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.729046190752756	0		289	347	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241888	133241888	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	16	184	0	ENST00000320574.5:c.2468G>A	p.Gly823Glu	p.G823E	ENST00000320574	NM_006231.2	823	gGg/gAg	21/49	0.147269491219651	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.729046190752756	0		184	302	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245464	133245464	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752456199	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	83	224	0	ENST00000320574.5:c.1856G>A	p.Cys619Tyr	p.C619Y	ENST00000320574	NM_006231.2	619	tGt/tAt	17/49	0.147269491219651	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.729046190752756	0		224	352	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254291	133254291	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	59	213	0	ENST00000320574.5:c.593G>A	p.Gly198Asp	p.G198D	ENST00000320574	NM_006231.2	198	gGc/gAc	7/49	0.147269491219651	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.729046190752756	0		213	404	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597507	28597507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	76	693	0	ENST00000241453.7:c.2398G>A	p.Glu800Lys	p.E800K	ENST00000241453	NM_004119.2	800	Gaa/Aaa	19/24	0.729046190752756	1	FACETS	0.417	0.368	0.468	0.417	0.368	0.468	SUBCLONAL	1	TRUE	0	0.729046190752756	1		693	318	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041657	29041657	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	87	221	0	ENST00000282397.4:c.161+1G>A		p.X54_splice	ENST00000282397	NM_002019.4	54			0.729046190752756	1	FACETS	0.499	0.446	0.554	0.499	0.446	0.554	SUBCLONAL	1	TRUE	0	0.729046190752756	1		221	304	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912060	32912060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80358604	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	149	436	2	ENST00000380152.3:c.3568C>T	p.Arg1190Trp	p.R1190W	ENST00000380152		1190	Cgg/Tgg	11/27	0.729046190752756	1	FACETS	0.533	0.491	0.577	0.533	0.491	0.577	SUBCLONAL	1	TRUE	0	0.729046190752756	1		438	487	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912120	32912120	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774392592	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	151	418	0	ENST00000380152.3:c.3628G>A	p.Asp1210Asn	p.D1210N	ENST00000380152		1210	Gat/Aat	11/27	0.729046190752756	1	FACETS	0.516	0.475	0.559	0.516	0.475	0.559	SUBCLONAL	1	TRUE	0	0.729046190752756	1		418	510	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913134	32913134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1566230862	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	173	442	0	ENST00000380152.3:c.4642G>A	p.Glu1548Lys	p.E1548K	ENST00000380152		1548	Gaa/Aaa	11/27	0.729046190752756	1	FACETS	0.622	0.577	0.667	0.622	0.577	0.667	SUBCLONAL	1	TRUE	0	0.729046190752756	1		442	485	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914109	32914109	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	185	407	0	ENST00000380152.3:c.5617G>A	p.Val1873Ile	p.V1873I	ENST00000380152		1873	Gta/Ata	11/27	0.729046190752756	1	FACETS	0.585	0.544	0.628	0.585	0.544	0.628	SUBCLONAL	1	TRUE	0	0.729046190752756	1		407	551	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915232	32915232	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	163	413	0	ENST00000380152.3:c.6740G>A	p.Ser2247Asn	p.S2247N	ENST00000380152		2247	aGt/aAt	11/27	0.729046190752756	1	FACETS	0.536	0.495	0.578	0.536	0.495	0.578	SUBCLONAL	1	TRUE	0	0.729046190752756	1		413	530	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968991	32968991	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	128	306	0	ENST00000380152.3:c.9422G>A	p.Gly3141Glu	p.G3141E	ENST00000380152		3141	gGa/gAa	25/27	0.729046190752756	1	FACETS	0.556	0.509	0.605	0.556	0.509	0.605	SUBCLONAL	1	TRUE	0	0.729046190752756	1		306	401	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335559	73335559	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777105773	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	142	223	0	ENST00000377767.4:c.2612G>A	p.Gly871Glu	p.G871E	ENST00000377767	NM_014953.3	871	gGg/gAg	19/21	0.729046190752756	1	FACETS	0.595	0.548	0.644	0.595	0.548	0.644	SUBCLONAL	1	TRUE	0	0.729046190752756	1		223	416	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514499	103514499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768717246	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	68	147	0	ENST00000355739.4:c.1000G>A	p.Glu334Lys	p.E334K	ENST00000355739	NM_000123.3	334	Gag/Aag	8/15	0.729046190752756	1	FACETS	0.492	0.433	0.553	0.492	0.433	0.553	SUBCLONAL	1	TRUE	0	0.729046190752756	1		147	241	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434473	110434473	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs995801699	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	59	112	0	ENST00000375856.3:c.3928G>A	p.Gly1310Ser	p.G1310S	ENST00000375856	NM_003749.2	1310	Ggt/Agt	1/2	0.729046190752756	1	FACETS	0.527	0.461	0.597	0.527	0.461	0.597	SUBCLONAL	1	TRUE	0	0.729046190752756	1		112	195	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988342	36988342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	12	49	0	ENST00000354822.5:c.311G>A	p.Gly104Glu	p.G104E	ENST00000354822	NM_001079668.2	104	gGg/gAg	2/3	NA	2	FACETS	0.451	0.322	0.603			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		49	73	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061237	38061237	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	44	169	0	ENST00000250448.2:c.752G>A	p.Gly251Asp	p.G251D	ENST00000250448	NM_004496.3	251	gGc/gAc	2/2	NA	2	FACETS	0.447	0.377	0.523			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		169	270	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554356	81554356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1357148448	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	89	279	0	ENST00000298171.2:c.376C>T	p.Pro126Ser	p.P126S	ENST00000298171	NM_000369.2	126	Ccc/Tcc	4/10	NA	2	FACETS	0.483	0.429	0.539			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		279	506	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566196	95566196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	104	201	0	ENST00000393063.1:c.4127C>T	p.Pro1376Leu	p.P1376L	ENST00000393063	NM_030621.3	1376	cCc/cTc	23/28	NA	2	FACETS	0.48	0.431	0.533			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		201	594	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95599662	95599662	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	86	179	0	ENST00000393063.1:c.134G>A	p.Arg45Lys	p.R45K	ENST00000393063	NM_030621.3	45	aGa/aAa	3/28	NA	2	FACETS	0.352	0.311	0.395			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		179	671	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243074	105243074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	64	200	0	ENST00000349310.3:c.209C>T	p.Pro70Leu	p.P70L	ENST00000349310	NM_001014432.1	70	cCc/cTc	5/15	NA	2	FACETS	0.544	0.474	0.618			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		200	323	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021449	42021449	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	114	366	0	ENST00000219905.7:c.3745G>A	p.Glu1249Lys	p.E1249K	ENST00000219905	NM_001164273.1	1249	Gag/Aag	11/24	0.495020052352505	1	FACETS	0.359	0.324	0.396	0.359	0.324	0.396	SUBCLONAL	1	TRUE	0	0.729046190752756	1		366	553	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358518	67358518	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762101727	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	20	124	0	ENST00000327367.4:c.26C>T	p.Pro9Leu	p.P9L	ENST00000327367	NM_005902.3	9	cCc/cTc	1/9	0.495020052352505	1	FACETS	0.181	0.138	0.229	0.181	0.138	0.229	SUBCLONAL	1	TRUE	0	0.729046190752756	1		124	193	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994697	73994697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1183245531	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	50	242	1	ENST00000318443.5:c.181G>A	p.Ala61Thr	p.A61T	ENST00000318443	NM_001024736.1	61	Gca/Aca	3/10	0.495020052352505	1	FACETS	0.386	0.331	0.445	0.386	0.331	0.445	SUBCLONAL	1	TRUE	0	0.729046190752756	1		243	226	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423638	88423638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	35	171	0	ENST00000360948.2:c.2197C>T	p.Pro733Ser	p.P733S	ENST00000360948	NM_001012338.2	733	Ccc/Tcc	18/19	0.495020052352505	1	FACETS	0.307	0.253	0.365	0.307	0.253	0.365	SUBCLONAL	1	TRUE	0	0.729046190752756	1		171	199	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726648	88726648	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	27	169	0	ENST00000360948.2:c.395+1G>A		p.X132_splice	ENST00000360948	NM_001012338.2	132			0.495020052352505	1	FACETS	0.187	0.149	0.23	0.187	0.149	0.23	SUBCLONAL	1	TRUE	0	0.729046190752756	1		169	252	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799305	88799305	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139291499	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	46	249	0	ENST00000360948.2:c.80G>A	p.Gly27Asp	p.G27D	ENST00000360948	NM_001012338.2	27	gGc/gAc	2/19	0.495020052352505	1	FACETS	0.301	0.255	0.352	0.301	0.255	0.352	SUBCLONAL	1	TRUE	0	0.729046190752756	1		249	266	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99440132	99440132	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	68	182	0	ENST00000268035.6:c.1100G>A	p.Gly367Glu	p.G367E	ENST00000268035	NM_000875.3	367	gGg/gAg	4/21	NA	2	FACETS	0.628	0.551	0.71			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		182	297	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127728	2127728	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	38	112	0	ENST00000219476.3:c.2966+1G>A		p.X989_splice	ENST00000219476	NM_000548.3	989			NA	2	FACETS	0.415	0.345	0.492			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		112	251	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222582	2222582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	44	194	0	ENST00000326181.6:c.776G>A	p.Cys259Tyr	p.C259Y	ENST00000326181	NM_032271.2	259	tGc/tAc	9/21	NA	2	FACETS	0.447	0.377	0.523			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		194	270	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778056	3778056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	58	213	0	ENST00000262367.5:c.6992C>T	p.Pro2331Leu	p.P2331L	ENST00000262367	NM_004380.2	2331	cCt/cTt	31/31	NA	2	FACETS	0.512	0.442	0.586			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		213	311	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778464	3778464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	59	170	0	ENST00000262367.5:c.6584G>A	p.Arg2195Lys	p.R2195K	ENST00000262367	NM_004380.2	2195	aGg/aAg	31/31	NA	2	FACETS	0.543	0.471	0.621			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		170	298	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3795278	3795278	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	171	184	0	ENST00000262367.5:c.3914G>A	p.Gly1305Asp	p.G1305D	ENST00000262367	NM_004380.2	1305	gGt/gAt	22/31	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		184	409	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3808895	3808895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	81	200	0	ENST00000262367.5:c.3329C>T	p.Pro1110Leu	p.P1110L	ENST00000262367	NM_004380.2	1110	cCt/cTt	17/31	NA	2	FACETS	0.469	0.414	0.527			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		200	474	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820981	3820981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	69	69	0	ENST00000262367.5:c.2470G>A	p.Val824Met	p.V824M	ENST00000262367	NM_004380.2	824	Gtg/Atg	14/31	NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		69	169	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3830761	3830761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs909245151	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	81	165	0	ENST00000262367.5:c.1795G>A	p.Asp599Asn	p.D599N	ENST00000262367	NM_004380.2	599	Gac/Aac	8/31	NA	2	FACETS	0.516	0.456	0.579			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		165	431	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860777	3860777	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	63	171	0	ENST00000262367.5:c.802G>A	p.Gly268Arg	p.G268R	ENST00000262367	NM_004380.2	268	Gga/Aga	3/31	NA	2	FACETS	0.457	0.397	0.522			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		171	378	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916259	9916259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	37	187	0	ENST00000330684.3:c.2030C>T	p.Ser677Phe	p.S677F	ENST00000330684	NM_001134407.1	677	tCc/tTc	10/13	0.6924381167934	1	FACETS	0.264	0.219	0.314	0.264	0.219	0.314	SUBCLONAL	1	TRUE	0	0.729046190752756	1		187	244	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923383	9923383	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	59	244	0	ENST00000330684.3:c.1904C>T	p.Ala635Val	p.A635V	ENST00000330684	NM_001134407.1	635	gCc/gTc	9/13	0.6924381167934	1	FACETS	0.339	0.294	0.388	0.339	0.294	0.388	SUBCLONAL	1	TRUE	0	0.729046190752756	1		244	303	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934630	9934630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	71	150	0	ENST00000330684.3:c.1525G>A	p.Val509Ile	p.V509I	ENST00000330684	NM_001134407.1	509	Gtt/Att	7/13	0.6924381167934	1	FACETS	0.403	0.355	0.454	0.403	0.355	0.454	SUBCLONAL	1	TRUE	0	0.729046190752756	1		150	307	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032234	10032234	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	40	194	0	ENST00000330684.3:c.589G>A	p.Gly197Ser	p.G197S	ENST00000330684	NM_001134407.1	197	Ggc/Agc	3/13	0.6924381167934	1	FACETS	0.317	0.265	0.373	0.317	0.265	0.373	SUBCLONAL	1	TRUE	0	0.729046190752756	1		194	220	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274039	10274039	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	35	201	0	ENST00000330684.3:c.230C>T	p.Thr77Ile	p.T77I	ENST00000330684	NM_001134407.1	77	aCc/aTc	2/13	0.6924381167934	1	FACETS	0.298	0.246	0.355	0.298	0.246	0.355	SUBCLONAL	1	TRUE	0	0.729046190752756	1		201	205	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274157	10274157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	13	138	0	ENST00000330684.3:c.112G>A	p.Val38Met	p.V38M	ENST00000330684	NM_001134407.1	38	Gtg/Atg	2/13	0.6924381167934	1	FACETS	0.138	0.098	0.186	0.138	0.098	0.186	SUBCLONAL	1	TRUE	0	0.729046190752756	1		138	164	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029396	14029396	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	83	193	0	ENST00000311895.7:c.1607T>C	p.Val536Ala	p.V536A	ENST00000311895	NM_005236.2	536	gTa/gCa	8/11	NA	2	FACETS	0.492	0.435	0.552			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		193	463	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129756	30129756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	122	424	0	ENST00000263025.4:c.457G>A	p.Gly153Ser	p.G153S	ENST00000263025	NM_002746.2	153	Ggc/Agc	3/9	NA	2	FACETS	0.562	0.509	0.617			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		424	596	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645132	67645132	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	102	233	0	ENST00000264010.4:c.397G>A	p.Glu133Lys	p.E133K	ENST00000264010	NM_006565.3	133	Gaa/Aaa	3/12	0.729046190752756	1	FACETS	0.547	0.495	0.601	0.547	0.495	0.601	SUBCLONAL	1	TRUE	0	0.729046190752756	1		233	325	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835768	68835768	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	71	222	0	ENST00000261769.5:c.359G>A	p.Gly120Glu	p.G120E	ENST00000261769	NM_004360.3	120	gGg/gAg	3/16	0.729046190752756	1	FACETS	0.558	0.494	0.624	0.558	0.494	0.624	SUBCLONAL	1	TRUE	0	0.729046190752756	1		222	222	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819641	81819641	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	75	328	0	ENST00000359376.3:c.47G>A	p.Ser16Asn	p.S16N	ENST00000359376	NM_002661.3	16	aGc/aAc	2/33	0.729046190752756	1	FACETS	0.49	0.434	0.548	0.49	0.434	0.548	SUBCLONAL	1	TRUE	0	0.729046190752756	1		328	267	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888091	81888091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	72	317	0	ENST00000359376.3:c.236C>T	p.Ser79Phe	p.S79F	ENST00000359376	NM_002661.3	79	tCc/tTc	3/33	0.729046190752756	1	FACETS	0.453	0.4	0.509	0.453	0.4	0.509	SUBCLONAL	1	TRUE	0	0.729046190752756	1		317	277	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965260	81965260	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	45	228	0	ENST00000359376.3:c.2739+1G>A		p.X913_splice	ENST00000359376	NM_002661.3	913			0.640485440023771	0	FACETS		NA	1			1	NA	1	TRUE	0	0.729046190752756	0		228	139	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89345484	89345484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	115	164	0	ENST00000301030.4:c.7466C>T	p.Pro2489Leu	p.P2489L	ENST00000301030	NM_001256183.1	2489	cCc/cTc	9/13	NA	2	FACETS	1	0.943	1			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		164	303	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346084	89346084	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	11	26	0	ENST00000301030.4:c.6866G>A	p.Gly2289Asp	p.G2289D	ENST00000301030	NM_001256183.1	2289	gGc/gAc	9/13	NA	2	FACETS	0.592	0.42	0.791			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		26	51	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89871700	89871700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	78	195	0	ENST00000389301.3:c.697G>A	p.Ala233Thr	p.A233T	ENST00000389301	NM_000135.2	233	Gcc/Acc	7/43	NA	2	FACETS	0.494	0.436	0.556			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		195	433	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024368	16024368	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	71	148	0	ENST00000268712.3:c.1850C>T	p.Pro617Leu	p.P617L	ENST00000268712	NM_006311.3	617	cCc/cTc	16/46	NA	2	FACETS	0.485	0.425	0.548			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		148	402	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024402	16024402	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	68	158	0	ENST00000268712.3:c.1816G>A	p.Glu606Lys	p.E606K	ENST00000268712	NM_006311.3	606	Gag/Aag	16/46	NA	2	FACETS	0.49	0.428	0.556			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		158	381	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264459	30264459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	60	722	0	ENST00000322652.5:c.194G>A	p.Gly65Glu	p.G65E	ENST00000322652	NM_015355.2	65	gGg/gAg	1/16	1	2	FACETS	0.513	0.445	0.586	0.513	0.445	0.586	SUBCLONAL	1	TRUE	1	0.729046190752756	2		722	321	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33430530	33430530	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765881830	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	102	242	0	ENST00000345365.6:c.610G>A	p.Val204Ile	p.V204I	ENST00000345365	NM_002878.3	204	Gtt/Att	7/10	1	2	FACETS	0.595	0.535	0.659	0.595	0.535	0.659	SUBCLONAL	1	TRUE	1	0.729046190752756	2		242	470	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868640	37868640	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	96	162	0	ENST00000269571.5:c.1087G>A	p.Glu363Lys	p.E363K	ENST00000269571		363	Gag/Aag	9/27	1	2	FACETS	0.714	0.641	0.79	0.714	0.641	0.79	SUBCLONAL	1	TRUE	1	0.729046190752756	2		162	369	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872121	37872121	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370565888	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	68	211	0	ENST00000269571.5:c.1442C>T	p.Pro481Leu	p.P481L	ENST00000269571		481	cCc/cTc	12/27	1	2	FACETS	0.461	0.402	0.523	0.461	0.402	0.523	SUBCLONAL	1	TRUE	1	0.729046190752756	2		211	405	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872836	37872836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	51	186	3	ENST00000269571.5:c.1715G>A	p.Gly572Asp	p.G572D	ENST00000269571		572	gGc/gAc	14/27	1	2	FACETS	0.474	0.406	0.549	0.474	0.406	0.549	SUBCLONAL	1	TRUE	1	0.729046190752756	2		189	295	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881365	37881365	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	61	146	0	ENST00000269571.5:c.2557G>A	p.Val853Ile	p.V853I	ENST00000269571		853	Gtc/Atc	21/27	1	2	FACETS	0.461	0.399	0.527	0.461	0.399	0.527	SUBCLONAL	1	TRUE	1	0.729046190752756	2		146	363	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512374	38512374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	21	160	0	ENST00000254066.5:c.1285G>A	p.Gly429Ser	p.G429S	ENST00000254066	NM_000964.3	429	Ggt/Agt	9/9	1	2	FACETS	0.242	0.187	0.306	0.242	0.187	0.306	SUBCLONAL	1	TRUE	1	0.729046190752756	2		160	238	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481595	40481595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	150	340	0	ENST00000264657.5:c.1210C>T	p.Leu404Phe	p.L404F	ENST00000264657	NM_139276.2	404	Ctc/Ttc	13/24	NA	2	FACETS	0.567	0.519	0.617			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		340	726	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41222971	41222971	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	149	292	0	ENST00000357654.3:c.4960G>A	p.Val1654Met	p.V1654M	ENST00000357654	NM_007294.3	1654	Gtg/Atg	15/23	NA	2	FACETS	0.548	0.501	0.597			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		292	746	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245295	41245295	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	152	276	0	ENST00000357654.3:c.2253G>A	p.Met751Ile	p.M751I	ENST00000357654	NM_007294.3	751	atG/atA	10/23	NA	2	FACETS	0.487	0.445	0.531			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		276	856	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246137	41246137	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1282963652	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	140	287	0	ENST00000357654.3:c.1411C>T	p.Leu471Phe	p.L471F	ENST00000357654	NM_007294.3	471	Ctc/Ttc	10/23	NA	2	FACETS	0.52	0.474	0.568			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		287	739	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804402	46804402	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	40	178	0	ENST00000290295.7:c.605C>T	p.Ser202Phe	p.S202F	ENST00000290295	NM_006361.5	202	tCc/tTc	2/2	0.729046190752756	1	FACETS	0.365	0.307	0.428	0.365	0.307	0.428	SUBCLONAL	1	TRUE	0	0.729046190752756	1		178	191	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440721	56440721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747700626	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	42	235	0	ENST00000407977.2:c.497G>A	p.Gly166Asp	p.G166D	ENST00000407977		166	gGt/gAt	5/10	1	2	FACETS	0.383	0.321	0.451	0.383	0.321	0.451	SUBCLONAL	1	TRUE	1	0.729046190752756	2		235	301	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492700	56492700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	102	272	0	ENST00000407977.2:c.239G>A	p.Gly80Glu	p.G80E	ENST00000407977		80	gGa/gAa	2/10	1	2	FACETS	0.485	0.435	0.538	0.485	0.435	0.538	SUBCLONAL	1	TRUE	1	0.729046190752756	2		272	577	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772321	56772321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	111	214	0	ENST00000337432.4:c.175G>A	p.Glu59Lys	p.E59K	ENST00000337432	NM_058216.2	59	Gaa/Aaa	2/9	1	2	FACETS	0.545	0.491	0.601	0.545	0.491	0.601	SUBCLONAL	1	TRUE	1	0.729046190752756	2		214	559	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554512	63554512	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	20	164	0	ENST00000307078.5:c.227C>T	p.Thr76Ile	p.T76I	ENST00000307078	NM_004655.3	76	aCc/aTc	2/11	1	2	FACETS	0.2	0.152	0.255	0.2	0.152	0.255	SUBCLONAL	1	TRUE	1	0.729046190752756	2		164	275	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120373	70120373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1359136483	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	218	346	0	ENST00000245479.2:c.1375G>A	p.Gly459Ser	p.G459S	ENST00000245479	NM_000346.3	459	Ggc/Agc	3/3	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.729046190752756	2		346	514	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78727898	78727898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	54	195	0	ENST00000306801.3:c.743C>T	p.Ala248Val	p.A248V	ENST00000306801	NM_020761.2	248	gCc/gTc	6/34	1	2	FACETS	0.373	0.319	0.432	0.373	0.319	0.432	SUBCLONAL	1	TRUE	1	0.729046190752756	2		195	397	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866532	78866532	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	48	173	0	ENST00000306801.3:c.2105G>A	p.Gly702Glu	p.G702E	ENST00000306801	NM_020761.2	702	gGa/gAa	19/34	1	2	FACETS	0.41	0.348	0.478	0.41	0.348	0.478	SUBCLONAL	1	TRUE	1	0.729046190752756	2		173	321	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897394	78897394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	66	248	1	ENST00000306801.3:c.2729G>A	p.Gly910Asp	p.G910D	ENST00000306801	NM_020761.2	910	gGc/gAc	23/34	1	2	FACETS	0.517	0.452	0.588	0.517	0.452	0.588	SUBCLONAL	1	TRUE	1	0.729046190752756	2		249	350	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45423039	45423039	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	117	250	0	ENST00000262160.6:c.89G>A	p.Gly30Glu	p.G30E	ENST00000262160	NM_005901.5	30	gGa/gAa	2/11	0.384513979254157	1	FACETS	0.473	0.43	0.519	0.473	0.43	0.519	INDETERMINATE	1	TRUE	0	0.729046190752756	1		250	431	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221965	1221965	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	70	236	0	ENST00000326873.7:c.880C>T	p.Pro294Ser	p.P294S	ENST00000326873	NM_000455.4	294	Ccg/Tcg	7/10	NA	2	FACETS	0.458	0.401	0.52			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		236	419	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621152	1621152	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	79	267	0	ENST00000344749.5:c.994C>T	p.Leu332Phe	p.L332F	ENST00000344749	NM_001136139.2	332	Ctc/Ttc	12/19	NA	2	FACETS	0.636	0.563	0.712			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		267	341	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222130	2222130	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778511604	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	48	268	0	ENST00000398665.3:c.2962C>T	p.Pro988Ser	p.P988S	ENST00000398665	NM_032482.2	988	Ccc/Tcc	24/28	NA	2	FACETS	0.411	0.349	0.479			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		268	320	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3114977	3114977	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	66	213	2	ENST00000078429.4:c.512G>A	p.Gly171Asp	p.G171D	ENST00000078429	NM_002067.2	171	gGc/gAc	4/7	NA	2	FACETS	0.517	0.452	0.588			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		215	350	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099382	4099382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	54	232	0	ENST00000262948.5:c.736G>A	p.Val246Met	p.V246M	ENST00000262948	NM_030662.3	246	Gtg/Atg	7/11	NA	2	FACETS	0.437	0.375	0.504			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		232	339	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267773	7267773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	42	391	0	ENST00000302850.5:c.235C>T	p.Pro79Ser	p.P79S	ENST00000302850	NM_000208.2	79	Ccc/Tcc	2/22	0.193785979223687	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.729046190752756	0		391	265	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249208	10249208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	26	228	0	ENST00000340748.4:c.3974C>T	p.Pro1325Leu	p.P1325L	ENST00000340748		1325	cCt/cTt	34/40	NA	2	FACETS	0.198	0.156	0.245			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		228	361	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10274017	10274017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	95	221	0	ENST00000340748.4:c.863G>A	p.Ser288Asn	p.S288N	ENST00000340748		288	aGt/aAt	11/40	NA	2	FACETS	0.496	0.443	0.553			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		221	525	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291468	10291468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	118	275	0	ENST00000340748.4:c.211G>A	p.Glu71Lys	p.E71K	ENST00000340748		71	Gaa/Aaa	3/40	NA	2	FACETS	0.511	0.461	0.562			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		275	634	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10305527	10305527	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	80	207	0	ENST00000340748.4:c.49G>A	p.Ala17Thr	p.A17T	ENST00000340748		17	Gcc/Acc	1/40	NA	2	FACETS	0.62	0.55	0.694			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		207	354	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107185	11107185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555763975	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	64	204	0	ENST00000358026.2:c.1777G>A	p.Glu593Lys	p.E593K	ENST00000358026	NM_001128849.1	593	Gaa/Aaa	11/36	NA	2	FACETS	0.471	0.409	0.536			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		204	373	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11169486	11169486	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	84	221	0	ENST00000358026.2:c.4652A>G	p.Tyr1551Cys	p.Y1551C	ENST00000358026	NM_001128849.1	1551	tAc/tGc	33/36	NA	2	FACETS	0.531	0.471	0.594			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		221	434	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050325	13050325	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370869315	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	170	322	0	ENST00000316448.5:c.277G>A	p.Val93Met	p.V93M	ENST00000316448	NM_004343.3	93	Gtg/Atg	3/9	0.381873481585237	4	FACETS	0.942	0.867	1			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	4		322	856	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051436	13051436	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	163	344	0	ENST00000316448.5:c.784G>A	p.Glu262Lys	p.E262K	ENST00000316448	NM_004343.3	262	Gaa/Aaa	6/9	0.381873481585237	4	FACETS	0.918	0.843	0.996			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	4		344	842	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271543	15271543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	46	233	0	ENST00000263388.2:c.6896C>T	p.Ser2299Phe	p.S2299F	ENST00000263388	NM_000435.2	2299	tCc/tTc	33/33	0.581352152711357	1	FACETS	0.321	0.272	0.374	0.321	0.272	0.374	SUBCLONAL	1	TRUE	0	0.729046190752756	1		233	250	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295762	15295762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	31	160	0	ENST00000263388.2:c.2365G>A	p.Ala789Thr	p.A789T	ENST00000263388	NM_000435.2	789	Gcc/Acc	15/33	0.581352152711357	1	FACETS	0.245	0.199	0.296	0.245	0.199	0.296	SUBCLONAL	1	TRUE	0	0.729046190752756	1		160	221	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355537	15355537	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	86	229	1	ENST00000263377.2:c.2195G>A	p.Gly732Glu	p.G732E	ENST00000263377	NM_058243.2	732	gGg/gAg	12/20	NA	2	FACETS	0.545	0.484	0.609			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		230	433	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376323	15376323	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1478460919	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	72	185	0	ENST00000263377.2:c.691G>A	p.Asp231Asn	p.D231N	ENST00000263377	NM_058243.2	231	Gac/Aac	5/20	NA	2	FACETS	0.945	0.84	1			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		185	209	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748451	40748451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867449500	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	49	194	0	ENST00000392038.2:c.431G>A	p.Arg144Gln	p.R144Q	ENST00000392038	NM_001626.4	144	cGg/cAg	5/14	NA	2	FACETS	0.464	0.395	0.538			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		194	290	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748455	40748455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	62	233	1	ENST00000392038.2:c.427G>A	p.Ala143Thr	p.A143T	ENST00000392038	NM_001626.4	143	Gca/Aca	5/14	NA	2	FACETS	0.506	0.44	0.577			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		234	336	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758766	41758766	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	56	217	0	ENST00000301178.4:c.1820G>A	p.Gly607Asp	p.G607D	ENST00000301178	NM_021913.4	607	gGt/gAt	16/20	NA	2	FACETS	0.441	0.38	0.508			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		217	348	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758825	41758825	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	78	281	0	ENST00000301178.4:c.1879G>A	p.Asp627Asn	p.D627N	ENST00000301178	NM_021913.4	627	Gac/Aac	16/20	NA	2	FACETS	0.446	0.393	0.502			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		281	480	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42384989	42384989	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	18	275	0	ENST00000221972.3:c.623G>A	p.Gly208Asp	p.G208D	ENST00000221972	NM_021601.3	208	gGc/gAc	5/5	NA	2	FACETS	0.138	0.103	0.178			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		275	359	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42790934	42790934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	55	271	0	ENST00000575354.2:c.79G>A	p.Val27Met	p.V27M	ENST00000575354	NM_015125.3	27	Gtg/Atg	2/20	NA	2	FACETS	0.261	0.223	0.302			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		271	579	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795280	42795280	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	61	168	0	ENST00000575354.2:c.2360G>A	p.Gly787Asp	p.G787D	ENST00000575354	NM_015125.3	787	gGt/gAt	10/20	NA	2	FACETS	0.542	0.47	0.618			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		168	309	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797859	42797859	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1323319406	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	53	198	0	ENST00000575354.2:c.3911G>A	p.Gly1304Asp	p.G1304D	ENST00000575354	NM_015125.3	1304	gGt/gAt	16/20	NA	2	FACETS	0.505	0.433	0.582			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		198	288	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867745	45867745	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	69	224	0	ENST00000391945.4:c.655G>A	p.Asp219Asn	p.D219N	ENST00000391945	NM_000400.3	219	Gac/Aac	8/23	NA	2	FACETS	0.476	0.416	0.539			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		224	398	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525030	9525030	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	90	219	0	ENST00000353224.5:c.1855C>T	p.Pro619Ser	p.P619S	ENST00000353224	NM_177990.2	619	Cct/Tct	8/10	1	2	FACETS	0.667	0.597	0.742	0.667	0.597	0.742	SUBCLONAL	1	TRUE	1	0.729046190752756	2		219	370	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546625	9546625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	46	267	0	ENST00000353224.5:c.1397C>T	p.Ala466Val	p.A466V	ENST00000353224	NM_177990.2	466	gCc/gTc	5/10	1	2	FACETS	0.274	0.23	0.322	0.274	0.23	0.322	SUBCLONAL	1	TRUE	1	0.729046190752756	2		267	461	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309479	30309479	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	118	308	0	ENST00000307677.4:c.543G>A	p.Trp181Ter	p.W181*	ENST00000307677	NM_138578.1	181	tgG/tgA	2/3	1	2	FACETS	0.46	0.415	0.507	0.46	0.415	0.507	SUBCLONAL	1	TRUE	1	0.729046190752756	2		308	704	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309611	30309611	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	124	243	0	ENST00000307677.4:c.411G>A	p.Trp137Ter	p.W137*	ENST00000307677	NM_138578.1	137	tgG/tgA	2/3	1	2	FACETS	0.53	0.48	0.582	0.53	0.48	0.582	SUBCLONAL	1	TRUE	1	0.729046190752756	2		243	642	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021241	31021241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	62	166	0	ENST00000375687.4:c.1240C>T	p.Pro414Ser	p.P414S	ENST00000375687	NM_015338.5	414	Cca/Tca	12/13	1	2	FACETS	0.482	0.418	0.55	0.482	0.418	0.55	SUBCLONAL	1	TRUE	1	0.729046190752756	2		166	353	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022470	31022470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	26	95	0	ENST00000375687.4:c.1955G>A	p.Gly652Asp	p.G652D	ENST00000375687	NM_015338.5	652	gGc/gAc	13/13	1	2	FACETS	0.553	0.444	0.673	0.553	0.444	0.673	SUBCLONAL	1	TRUE	1	0.729046190752756	2		95	129	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022526	31022526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	53	141	0	ENST00000375687.4:c.2011G>A	p.Ala671Thr	p.A671T	ENST00000375687	NM_015338.5	671	Gcc/Acc	13/13	1	2	FACETS	0.67	0.578	0.768	0.67	0.578	0.768	SUBCLONAL	1	TRUE	1	0.729046190752756	2		141	217	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023710	31023710	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	69	182	0	ENST00000375687.4:c.3195G>A	p.Trp1065Ter	p.W1065*	ENST00000375687	NM_015338.5	1065	tgG/tgA	13/13	1	2	FACETS	0.517	0.453	0.586	0.517	0.453	0.586	SUBCLONAL	1	TRUE	1	0.729046190752756	2		182	366	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388687	31388687	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	93	235	0	ENST00000328111.2:c.1952G>A	p.Cys651Tyr	p.C651Y	ENST00000328111	NM_006892.3	651	tGc/tAc	18/23	1	2	FACETS	0.582	0.521	0.648	0.582	0.521	0.648	SUBCLONAL	1	TRUE	1	0.729046190752756	2		235	438	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030910	36030910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	35	154	0	ENST00000358208.4:c.1189G>A	p.Val397Met	p.V397M	ENST00000358208		397	Gtg/Atg	10/12	1	2	FACETS	0.353	0.29	0.422	0.353	0.29	0.422	SUBCLONAL	1	TRUE	1	0.729046190752756	2		154	272	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710658	40710658	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	23	108	0	ENST00000373198.4:c.4194-1G>A		p.X1398_splice	ENST00000373198	NM_133170.3	1398			0.581352152711357	1	FACETS	0.229	0.18	0.285	0.229	0.18	0.285	SUBCLONAL	1	TRUE	0	0.729046190752756	1		108	175	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730831	40730831	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372700928	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	41	163	1	ENST00000373198.4:c.3704G>A	p.Arg1235His	p.R1235H	ENST00000373198	NM_133170.3	1235	cGc/cAc	27/32	0.581352152711357	1	FACETS	0.308	0.258	0.362	0.308	0.258	0.362	SUBCLONAL	1	TRUE	0	0.729046190752756	1		164	232	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743919	40743919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	27	169	0	ENST00000373198.4:c.3076G>A	p.Val1026Ile	p.V1026I	ENST00000373198	NM_133170.3	1026	Gtc/Atc	23/32	0.581352152711357	1	FACETS	0.199	0.159	0.245	0.199	0.159	0.245	SUBCLONAL	1	TRUE	0	0.729046190752756	1		169	236	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747097	40747097	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	59	180	0	ENST00000373198.4:c.2985G>A	p.Trp995Ter	p.W995*	ENST00000373198	NM_133170.3	995	tgG/tgA	22/32	0.581352152711357	1	FACETS	0.356	0.308	0.407	0.356	0.308	0.407	SUBCLONAL	1	TRUE	0	0.729046190752756	1		180	289	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748574	40748574	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	32	178	0	ENST00000373198.4:c.2941+1G>A		p.X981_splice	ENST00000373198	NM_133170.3	981			0.581352152711357	1	FACETS	0.246	0.2	0.296	0.246	0.2	0.296	SUBCLONAL	1	TRUE	0	0.729046190752756	1		178	227	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306706	41306706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	38	177	0	ENST00000373198.4:c.953G>A	p.Gly318Asp	p.G318D	ENST00000373198	NM_133170.3	318	gGc/gAc	7/32	0.581352152711357	1	FACETS	0.296	0.246	0.35	0.296	0.246	0.35	SUBCLONAL	1	TRUE	0	0.729046190752756	1		177	224	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252853	36252853	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	102	182	0	ENST00000300305.3:c.508+1G>A		p.X170_splice	ENST00000300305		170			NA	2	FACETS	0.481	0.431	0.534			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		182	582	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42879927	42879927	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	15	63	0	ENST00000398585.3:c.5C>T	p.Pro2Leu	p.P2L	ENST00000398585	NM_001135099.1	2	cCc/cTc	1/14	0.181232448957033	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.729046190752756	0		63	73	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564777	41564777	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	95	261	0	ENST00000263253.7:c.4078C>T	p.Leu1360Phe	p.L1360F	ENST00000263253	NM_001429.3	1360	Ctc/Ttc	25/31	0.729046190752756	1	FACETS	0.463	0.415	0.512	0.463	0.415	0.512	SUBCLONAL	1	TRUE	0	0.729046190752756	1		261	358	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573669	41573669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	135	195	0	ENST00000263253.7:c.5954G>A	p.Gly1985Glu	p.G1985E	ENST00000263253	NM_001429.3	1985	gGa/gAa	31/31	0.729046190752756	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.729046190752756	1		195	207	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15821878	15821878	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	92	364	0	ENST00000307771.7:c.271G>A	p.Glu91Lys	p.E91K	ENST00000307771	NM_005089.3	91	Gaa/Aaa	4/11	NA	2	FACETS	0.346	0.307	0.387			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		364	730	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15840877	15840877	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	89	226	0	ENST00000307771.7:c.961C>T	p.Pro321Ser	p.P321S	ENST00000307771	NM_005089.3	321	Cca/Tca	11/11	NA	2	FACETS	0.527	0.469	0.589			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		226	463	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930903	39930903	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	57	302	1	ENST00000378444.4:c.3038C>T	p.Ala1013Val	p.A1013V	ENST00000378444	NM_001123385.1	1013	gCt/gTt	5/15	0.729046190752756	1	FACETS	0.215	0.184	0.248	0.215	0.184	0.248	SUBCLONAL	1	TRUE	0	0.729046190752756	1		303	463	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933800	39933800	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	39	197	0	ENST00000378444.4:c.799C>T	p.Leu267Phe	p.L267F	ENST00000378444	NM_001123385.1	267	Ctc/Ttc	4/15	0.729046190752756	1	FACETS	0.356	0.298	0.419	0.356	0.298	0.419	SUBCLONAL	1	TRUE	0	0.729046190752756	1		197	191	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934411	39934411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751977474	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	19	162	0	ENST00000378444.4:c.188G>A	p.Arg63Lys	p.R63K	ENST00000378444	NM_001123385.1	63	aGg/aAg	4/15	0.729046190752756	1	FACETS	0.179	0.136	0.229	0.179	0.136	0.229	SUBCLONAL	1	TRUE	0	0.729046190752756	1		162	185	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030472	47030472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782522553	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	82	270	1	ENST00000377604.3:c.247C>T	p.Arg83Trp	p.R83W	ENST00000377604	NM_001204468.1	83	Cgg/Tgg	4/24	0.48616306975302	1	FACETS	0.436	0.388	0.487	0.436	0.388	0.487	SUBCLONAL	1	TRUE	0	0.729046190752756	1		271	328	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424218	47424218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	113	254	0	ENST00000377045.4:c.223G>A	p.Asp75Asn	p.D75N	ENST00000377045	NM_001654.4	75	Gac/Aac	4/16	0.48616306975302	1	FACETS	0.538	0.489	0.589	0.538	0.489	0.589	SUBCLONAL	1	TRUE	0	0.729046190752756	1		254	366	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428192	47428192	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	92	286	0	ENST00000377045.4:c.1152G>A	p.Trp384Ter	p.W384*	ENST00000377045	NM_001654.4	384	tgG/tgA	11/16	0.48616306975302	1	FACETS	0.427	0.382	0.474	0.427	0.382	0.474	SUBCLONAL	1	TRUE	0	0.729046190752756	1		286	376	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649565	48649565	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	45	314	0	ENST00000376670.3:c.49C>T	p.Gln17Ter	p.Q17*	ENST00000376670	NM_002049.3	17	Cag/Tag	2/6	0.686575280032771	1	FACETS	0.277	0.234	0.324	0.277	0.234	0.324	SUBCLONAL	1	TRUE	0	0.729046190752756	1		314	283	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649686	48649686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	41	297	0	ENST00000376670.3:c.170C>T	p.Ala57Val	p.A57V	ENST00000376670	NM_002049.3	57	gCt/gTt	2/6	0.686575280032771	1	FACETS	0.222	0.185	0.262	0.222	0.185	0.262	SUBCLONAL	1	TRUE	0	0.729046190752756	1		297	322	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226021	53226021	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781785252	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	29	235	0	ENST00000375401.3:c.2828G>A	p.Arg943Gln	p.R943Q	ENST00000375401	NM_004187.3	943	cGa/cAa	19/26	0.686575280032771	1	FACETS	0.183	0.147	0.224	0.183	0.147	0.224	SUBCLONAL	1	TRUE	0	0.729046190752756	1		235	276	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240000	53240000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	92	285	0	ENST00000375401.3:c.1441G>A	p.Val481Met	p.V481M	ENST00000375401	NM_004187.3	481	Gtg/Atg	11/26	0.686575280032771	1	FACETS	0.38	0.339	0.423	0.38	0.339	0.423	SUBCLONAL	1	TRUE	0	0.729046190752756	1		285	422	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410901	63410901	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	51	345	0	ENST00000330258.3:c.2266G>A	p.Glu756Lys	p.E756K	ENST00000330258	NM_152424.3	756	Gaa/Aaa	2/2	0.686575280032771	1	FACETS	0.306	0.261	0.354	0.306	0.261	0.354	SUBCLONAL	1	TRUE	0	0.729046190752756	1		345	291	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411353	63411353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	31	196	0	ENST00000330258.3:c.1814G>A	p.Gly605Asp	p.G605D	ENST00000330258	NM_152424.3	605	gGc/gAc	2/2	0.686575280032771	1	FACETS	0.249	0.202	0.301	0.249	0.202	0.301	SUBCLONAL	1	TRUE	0	0.729046190752756	1		196	217	SUCCESS
AR	367	MSKCC	GRCh37	X	66766426	66766426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	17	74	0	ENST00000374690.3:c.1438C>T	p.Pro480Ser	p.P480S	ENST00000374690	NM_000044.3	480	Ccc/Tcc	1/8	0.686575280032771	1	FACETS	0.353	0.268	0.449	0.353	0.268	0.449	SUBCLONAL	1	TRUE	0	0.729046190752756	1		74	84	SUCCESS
AR	367	MSKCC	GRCh37	X	66931396	66931396	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	86	306	0	ENST00000374690.3:c.2038G>A	p.Ala680Thr	p.A680T	ENST00000374690	NM_000044.3	680	Gcc/Acc	4/8	0.686575280032771	1	FACETS	0.415	0.37	0.463	0.415	0.37	0.463	SUBCLONAL	1	TRUE	0	0.729046190752756	1		306	361	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340021	70340021	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	109	208	0	ENST00000374080.3:c.553+1G>A		p.X185_splice	ENST00000374080		185			0.686575280032771	1	FACETS	0.546	0.495	0.598	0.546	0.495	0.598	SUBCLONAL	1	TRUE	0	0.729046190752756	1		208	348	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937014	76937014	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	54	231	0	ENST00000373344.5:c.3734C>T	p.Ser1245Leu	p.S1245L	ENST00000373344	NM_000489.3	1245	tCa/tTa	9/35	0.686575280032771	1	FACETS	0.218	0.186	0.252	0.218	0.186	0.252	SUBCLONAL	1	TRUE	0	0.729046190752756	1		231	432	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939297	76939297	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	62	269	0	ENST00000373344.5:c.1451G>A	p.Arg484Lys	p.R484K	ENST00000373344	NM_000489.3	484	aGa/aAa	9/35	0.686575280032771	1	FACETS	0.206	0.178	0.237	0.206	0.178	0.237	SUBCLONAL	1	TRUE	0	0.729046190752756	1		269	524	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123019739	123019739	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	54	250	0	ENST00000355640.3:c.227G>A	p.Gly76Glu	p.G76E	ENST00000355640		76	gGa/gAa	2/7	NA	2	FACETS	0.396	0.339	0.458			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		250	374	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171468	123171468	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	53	236	0	ENST00000218089.9:c.380G>A	p.Cys127Tyr	p.C127Y	ENST00000218089	NM_001042749.1	127	tGt/tAt	6/35	NA	2	FACETS	0.339	0.289	0.393			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		236	429	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176421	123176421	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	68	260	0	ENST00000218089.9:c.388G>A	p.Val130Ile	p.V130I	ENST00000218089	NM_001042749.1	130	Gtt/Att	7/35	NA	2	FACETS	0.302	0.263	0.345			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		260	617	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185165	123185165	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	79	228	0	ENST00000218089.9:c.1117G>A	p.Asp373Asn	p.D373N	ENST00000218089	NM_001042749.1	373	Gat/Aat	13/35	NA	2	FACETS	0.353	0.31	0.399			1	INDETERMINATE	1	TRUE	NA	0.729046190752756	2		228	614	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687471	37687472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs760014508	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	27	85	0	ENST00000447079.4:c.4382dup	p.Thr1463AsnfsTer50	p.T1463Nfs*50	ENST00000447079	NM_015083.1	1459	tgg/tGgg	14/14	1	2	FACETS	0.414	0.332	0.506	0.414	0.332	0.506	SUBCLONAL	1	TRUE	1	0.729046190752756	2		85	179	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585394	29585395	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	222	243	0	ENST00000356175.3:c.4145dup	p.Ala1383CysfsTer20	p.A1383Cfs*20	ENST00000356175	NM_000267.3	1381	-/G	31/57	0.729046190752756	1	FACETS	0.987	0.935	1	0.987	0.935	1	CLONAL	1	TRUE	0	0.729046190752756	1		243	392	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811669	102811669	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0003900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	198	304	0	ENST00000307046.8:c.515del	p.Arg172LysfsTer30	p.R172Kfs*30	ENST00000307046	NM_001111285.1	172	aGa/aa	4/4	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.729046190752756	2		304	503	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	31	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.543156500710412	2		280	106	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1057520607	NA	P-0003928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	124	252	0	ENST00000269305.4:c.880G>T	p.Glu294Ter	p.E294*	ENST00000269305	NM_001126112.2	294	Gag/Tag	8/11	0.493498264066719	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.543156500710412	1		252	314	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518072	69518073	+	missense_variant	Missense_Mutation	DNP	AC	AC	GA	novel	NA	P-0003928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	92	327	0	ENST00000294312.3:c.292_293delinsTC	p.Val98Ser	p.V98S	ENST00000294312	NM_005117.2	98	GTg/TCg	2/3	1	2	FACETS	0.818	0.732	0.91	0.818	0.732	0.91	CLONAL	1	TRUE	1	0.543156500710412	2		327	414	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	48	280	0				ENST00000310581	NM_198253.2	-/1132			0.272136317974165	1	FACETS	0.41	0.348	0.477	0.41	0.348	0.477	INDETERMINATE	1	TRUE	0	0.536907718774998	1		280	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578523	7578523	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1567554216	NA	P-0003951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	134	239	0	ENST00000269305.4:c.407A>C	p.Gln136Pro	p.Q136P	ENST00000269305	NM_001126112.2	136	cAa/cCa	5/11	0.257168950175572	1	FACETS	0.748	0.684	0.815	0.748	0.684	0.815	INDETERMINATE	1	TRUE	0	0.536907718774998	1		239	488	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578269	7578269	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780071	NA	P-0003951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	131	487	0	ENST00000269305.4:c.580C>T	p.Leu194Phe	p.L194F	ENST00000269305	NM_001126112.2	194	Ctt/Ttt	6/11	0.257168950175572	1	FACETS	0.373	0.337	0.41	0.373	0.337	0.41	INDETERMINATE	1	TRUE	0	0.536907718774998	1		487	958	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971124	21971125	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0003951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	148	192	0	ENST00000304494.5:c.233_234del	p.Leu78HisfsTer41	p.L78Hfs*41	ENST00000304494	NM_000077.4	78	cTC/c	2/3	0.536907718774998	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.536907718774998	1		192	399	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913233	NA	P-0003951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	723	484	0	ENST00000451590.1:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000451590	NM_001130442.1	61	cAg/cTg	3/5	0.52439931150688	3	FACETS	0.977	0.95	1	0.977	0.95	1	CLONAL	3	TRUE	0	0.536907718774998	3		484	1166	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662151	227662151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1250279823	NA	P-0003951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	339	360	0	ENST00000305123.5:c.1304C>T	p.Pro435Leu	p.P435L	ENST00000305123	NM_005544.2	435	cCc/cTc	1/2	NA	2	FACETS	0.763	0.725	0.801			1	INDETERMINATE	2	TRUE	NA	0.536907718774998	2		360	828	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199342	16199342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	264	705	0	ENST00000375759.3:c.115C>T	p.Pro39Ser	p.P39S	ENST00000375759	NM_015001.2	39	Ccc/Tcc	2/15	0.257168950175572	1	FACETS	0.729	0.684	0.775	0.729	0.684	0.775	INDETERMINATE	1	TRUE	0	0.536907718774998	1		705	987	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089494	27089494	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	155	430	0	ENST00000324856.7:c.2450C>T	p.Ala817Val	p.A817V	ENST00000324856	NM_006015.4	817	gCc/gTc	8/20	1	2	FACETS	0.678	0.621	0.737	0.678	0.621	0.737	SUBCLONAL	1	TRUE	1	0.536907718774998	2		430	852	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52663032	52663032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	405	342	0	ENST00000394830.3:c.1321G>A	p.Glu441Lys	p.E441K	ENST00000394830	NM_018313.4	441	Gaa/Aaa	13/30	0.518930885935082	2	FACETS	0.973	0.933	1	0.973	0.933	1	CLONAL	2	TRUE	0	0.536907718774998	2		342	775	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508905	106508905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755134917	NA	P-0003951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	129	198	0	ENST00000359195.3:c.899G>A	p.Gly300Glu	p.G300E	ENST00000359195	NM_002649.2	300	gGa/gAa	2/11	0.536907718774998	3	FACETS	0.892	0.811	0.978	0.446	0.405	0.489	CLONAL	1	TRUE	1	0.536907718774998	3		198	683	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523609	106523609	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1293996108	NA	P-0003951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	124	187	0	ENST00000359195.3:c.2760+1G>A		p.X920_splice	ENST00000359195	NM_002649.2	920			0.536907718774998	3	FACETS	0.972	0.882	1	0.486	0.441	0.533	CLONAL	1	TRUE	1	0.536907718774998	3		187	603	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38282044	38282044	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0003951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	298	486	0	ENST00000425967.3:c.1012T>C	p.Tyr338His	p.Y338H	ENST00000425967	NM_001174067.1	338	Tat/Cat	8/19	1	2	FACETS	0.947	0.892	1	0.947	0.892	1	CLONAL	1	TRUE	1	0.536907718774998	2		486	1172	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410160	139410160	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1487903012	NA	P-0003951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	110	178	0	ENST00000277541.6:c.1678G>A	p.Gly560Arg	p.G560R	ENST00000277541	NM_017617.3	560	Ggg/Agg	11/34	0.217489358195027	3	FACETS	1	0.938	1	0.526	0.475	0.58	INDETERMINATE	1	TRUE	1	0.536907718774998	3		178	494	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77054969	77054969	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0003951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	531	428	0	ENST00000356341.3:c.893T>A	p.Ile298Asn	p.I298N	ENST00000356341	NM_002576.4	298	aTt/aAt	10/15	0.536907718774998	3	FACETS	0.943	0.906	0.981	0.943	0.906	0.981	CLONAL	2	TRUE	1	0.536907718774998	3		428	1330	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437700	49437700	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0003951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	177	609	0	ENST00000301067.7:c.5270G>A	p.Arg1757Gln	p.R1757Q	ENST00000301067	NM_003482.3	1757	cGa/cAa	22/54	1	2	FACETS	0.548	0.504	0.594	0.548	0.504	0.594	SUBCLONAL	1	TRUE	1	0.536907718774998	2		609	1203	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	360056	360056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	213	545	0	ENST00000262320.3:c.1033C>T	p.Pro345Ser	p.P345S	ENST00000262320	NM_003502.3	345	Cca/Tca	4/11	1	2	FACETS	0.823	0.765	0.883	0.823	0.765	0.883	CLONAL	1	TRUE	1	0.536907718774998	2		545	964	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647605	23647605	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881901	NA	P-0003951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	219	445	0	ENST00000261584.4:c.262C>T	p.Leu88Phe	p.L88F	ENST00000261584	NM_024675.3	88	Ctt/Ttt	4/13	1	2	FACETS	0.824	0.767	0.883	0.824	0.767	0.883	CLONAL	1	TRUE	1	0.536907718774998	2		445	990	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577608	7577608	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs746504075	NA	P-0003951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	41	206	0	ENST00000269305.4:c.673G>A	p.Val225Ile	p.V225I	ENST00000269305	NM_001126112.2	225	Gtt/Att	7/11	0.257168950175572	1	FACETS	0.274	0.228	0.325	0.274	0.228	0.325	INDETERMINATE	1	TRUE	0	0.536907718774998	1		206	408	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021472	31021472	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1335820343	NA	P-0003951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	283	349	0	ENST00000375687.4:c.1471C>T	p.Gln491Ter	p.Q491*	ENST00000375687	NM_015338.5	491	Cag/Tag	12/13	0.297790927888203	3	FACETS	1	0.993	1	0.725	0.683	0.768	INDETERMINATE	1	TRUE	1	0.536907718774998	3		349	922	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944333	76944333	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	340	350	0	ENST00000373344.5:c.572C>T	p.Ser191Leu	p.S191L	ENST00000373344	NM_000489.3	191	tCa/tTa	7/35	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.536907718774998	1		350	688	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804297	43804298	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0003951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	225	401	0	ENST00000372470.3:c.297_298delinsAA	p.Glu100Lys	p.E100K	ENST00000372470	NM_005373.2	99	gaGGaa/gaAAaa	3/12	1	2	FACETS	0.99	0.923	1	0.99	0.923	1	CLONAL	1	TRUE	1	0.536907718774998	2		401	847	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607201	189607202	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0003951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	447	387	0	ENST00000264731.3:c.1580_1581delinsTT	p.Pro527Leu	p.P527L	ENST00000264731	NM_003722.4	527	cCC/cTT	12/14	0.518930885935082	2	FACETS	0.951	0.914	0.989	0.951	0.914	0.989	CLONAL	2	TRUE	0	0.536907718774998	2		387	875	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962280	2962281	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0003951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	202	399	0	ENST00000396946.4:c.2256_2257delinsAA	p.Val753Ile	p.V753I	ENST00000396946	NM_032415.4	752	aaGGtc/aaAAtc	17/25	0.536907718774998	3	FACETS	0.875	0.81	0.942	0.437	0.405	0.471	CLONAL	1	TRUE	1	0.536907718774998	3		399	1091	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436145	110436146	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0003951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	227	443	0	ENST00000375856.3:c.2255_2256delinsTT	p.Ser752Phe	p.S752F	ENST00000375856	NM_003749.2	752	tCC/tTT	1/2	0.257168950175572	1	FACETS	0.713	0.666	0.763	0.713	0.666	0.763	INDETERMINATE	1	TRUE	0	0.536907718774998	1		443	867	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570046	95570047	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0003951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	223	438	0	ENST00000393063.1:c.3686_3687delinsTT	p.Pro1229Leu	p.P1229L	ENST00000393063	NM_030621.3	1229	cCC/cTT	22/28	1	2	FACETS	0.81	0.754	0.868	0.81	0.754	0.868	CLONAL	1	TRUE	1	0.536907718774998	2		438	1026	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022534	12022535	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0003951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	116	494	0	ENST00000396373.4:c.640_641delinsTT	p.Pro214Leu	p.P214L	ENST00000396373	NM_001987.4	214	CCg/TTg	5/8	0.253018882677477	2	FACETS	0.466	0.419	0.515	0.233	0.209	0.258	INDETERMINATE	1	TRUE	0	0.536907718774998	2		494	928	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508280	106508281	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0003951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	125	93	0	ENST00000359195.3:c.274_275delinsAA	p.Gly92Lys	p.G92K	ENST00000359195	NM_002649.2	92	GGa/AAa	2/11	0.536907718774998	3	FACETS	0.914	0.839	0.991	0.914	0.839	0.991	CLONAL	2	TRUE	1	0.536907718774998	3		93	323	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561060	9561061	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0003951-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	195	273	0	ENST00000353224.5:c.721_722delinsAA	p.Gly241Lys	p.G241K	ENST00000353224	NM_177990.2	241	GGg/AAg	4/10	0.297790927888203	3	FACETS	1	0.99	1	0.694	0.645	0.744	INDETERMINATE	1	TRUE	1	0.536907718774998	3		273	664	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003955-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	28	280	0				ENST00000310581	NM_198253.2	-/1132			0.170264988755269	0	FACETS	1	0.822	1			1	INDETERMINATE	1	FALSE	0	0.355689170004629	0		280	101	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879604	37879604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196929947	NA	P-0003955-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	65	308	0	ENST00000269571.5:c.1979G>A	p.Gly660Asp	p.G660D	ENST00000269571		660	gGc/gAc	17/27	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	FALSE	1	0.355689170004629	2		308	345	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240710	55240710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0003955-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	87	559	0	ENST00000275493.2:c.1954G>A	p.Gly652Arg	p.G652R	ENST00000275493	NM_005228.3	652	Ggg/Agg	17/28	0.335952973752699	1	FACETS	0.738	0.655	0.826	0.738	0.655	0.826	SUBCLONAL	1	FALSE	0	0.355689170004629	1		559	545	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59793312	59793312	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs771382903	NA	P-0003955-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	153	476	0	ENST00000259008.2:c.2492G>A	p.Arg831Lys	p.R831K	ENST00000259008	NM_032043.2	831	aGa/aAa	17/20	1	2	FACETS	0.749	0.684	0.817	0.749	0.684	0.817	SUBCLONAL	1	FALSE	1	0.355689170004629	2		476	1149	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372104	45372104	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0003955-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	167	486	0	ENST00000262160.6:c.1065C>G	p.Ile355Met	p.I355M	ENST00000262160	NM_005901.5	355	atC/atG	9/11	1	2	FACETS	0.779	0.714	0.847	0.779	0.714	0.847	SUBCLONAL	1	FALSE	1	0.355689170004629	2		486	1206	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969327	44969327	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0003955-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	213	266	0	ENST00000377967.4:c.4009G>T	p.Glu1337Ter	p.E1337*	ENST00000377967	NM_021140.2	1337	Gag/Tag	28/29	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	0	0.355689170004629	1		266	697	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030637	47030641	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGC	CAGGC	-	novel	NA	P-0003955-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	59	224	0	ENST00000377604.3:c.412_416del	p.Gln138SerfsTer3	p.Q138Sfs*3	ENST00000377604	NM_001204468.1	138	CAGGCa/a	4/24	1	1	FACETS	0.788	0.692	0.889	1	0.975	1	SUBCLONAL	2	FALSE	0	0.355689170004629	1		224	173	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003962-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	40	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.87	0.736	1	0.87	0.736	1	CLONAL	1	TRUE	1	0.634520921000219	2		280	145	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692803	89692803	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554898074	NA	P-0003962-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	86	151	0	ENST00000371953.3:c.287C>T	p.Pro96Leu	p.P96L	ENST00000371953	NM_000314.4	96	cCa/cTa	5/9	0.634520921000219	1	FACETS	0.837	0.755	0.922	0.837	0.755	0.922	CLONAL	1	TRUE	0	0.634520921000219	1		151	221	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0003970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	102	505	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.430554277001386	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.430554277001386	1		506	279	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0003970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	41	67	1				ENST00000310581	NM_198253.2	-/1132			0.289690920767222	3	FACETS	0.761	0.645	0.885	0.761	0.645	0.885	SUBCLONAL	2	TRUE	1	0.430554277001386	3		68	152	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341287	341289	+	stop_gained	Nonsense_Mutation	TNP	CCT	CCT	ACC	novel	NA	P-0003970-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	65	564	2	ENST00000262320.3:c.2195_2197delinsGGT	p.Gln732_Glu733delinsArgTer	p.Q732_E733delinsR*	ENST00000262320	NM_003502.3	732	cAGGag/cGGTag	9/11	NA	2	FACETS	0.738	0.642	0.841			1	INDETERMINATE	1	TRUE	NA	0.430554277001386	2		566	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0003970-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	204	505	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.300321774088815	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.305719128209493	2		506	637	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0003970-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	142	67	1				ENST00000310581	NM_198253.2	-/1132			0.305719128209493	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.305719128209493	3		68	444	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341287	341289	+	stop_gained	Nonsense_Mutation	TNP	CCT	CCT	ACC	novel	NA	P-0003970-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	88	564	2	ENST00000262320.3:c.2195_2197delinsGGT	p.Gln732_Glu733delinsArgTer	p.Q732_E733delinsR*	ENST00000262320	NM_003502.3	732	cAGGag/cGGTag	9/11	NA	2	FACETS	0.717	0.634	0.805			1	INDETERMINATE	1	TRUE	NA	0.305719128209493	2		566	803	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0003990-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	17	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.589	0.441	0.763	0.589	0.441	0.763	SUBCLONAL	1	FALSE	1	0.299181208271535	2		280	193	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170283	119170283	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs144191570	NA	P-0003990-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	64	332	0	ENST00000264033.4:c.2513G>T	p.Gly838Val	p.G838V	ENST00000264033	NM_005188.3	838	gGc/gTc	16/16	0.151843732056122	3	FACETS	1	0.92	1	0.542	0.47	0.619	INDETERMINATE	1	FALSE	1	0.299181208271535	3		332	454	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913530	NA	P-0003990-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	79	400	0	ENST00000311936.3:c.34G>A	p.Gly12Ser	p.G12S	ENST00000311936	NM_004985.3	12	Ggt/Agt	2/5	NA	2	FACETS	0.799	0.703	0.902			1	INDETERMINATE	1	FALSE	NA	0.299181208271535	2		400	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578190	7578190	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121912666	NA	P-0003990-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	36	445	0	ENST00000269305.4:c.659A>G	p.Tyr220Cys	p.Y220C	ENST00000269305	NM_001126112.2	220	tAt/tGt	6/11	0.0927122942110672	3	FACETS	0.494	0.405	0.594			1	INDETERMINATE	1	FALSE	NA	0.299181208271535	3		445	560	SUCCESS
APC	324	MSKCC	GRCh37	5	112175706	112175706	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0003990-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	49	323	0	ENST00000257430.4:c.4415del	p.Val1472GlufsTer35	p.V1472Efs*35	ENST00000257430	NM_000038.5	1472	gTa/ga	16/16	0.279416590310332	3	FACETS	0.956	0.812	1	0.478	0.406	0.557	CLONAL	1	FALSE	1	0.299181208271535	3		323	394	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0004008-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	15	464	0				ENST00000310581	NM_198253.2	-/1132			0.275653335063128	0	FACETS	0.507	0.377	0.657			1	SUBCLONAL	1	TRUE	0	0.41336311037202	0		464	84	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11552761	NA	P-0004008-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	75	726	0	ENST00000418115.1:c.50G>C	p.Gly17Ala	p.G17A	ENST00000418115	NM_001664.2	17	gGa/gCa	2/5	0.268284246642584	4	FACETS	1	0.971	1	0.682	0.601	0.768	CLONAL	1	TRUE	2	0.41336311037202	4		726	376	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787716	135787716	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	rs397514867	NA	P-0004008-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	107	666	0	ENST00000298552.3:c.866C>G	p.Ser289Ter	p.S289*	ENST00000298552	NM_001162426.1	289	tCa/tGa	9/23	0.41336311037202	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.41336311037202	1		666	301	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192044	108192044	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004008-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	100	567	0	ENST00000278616.4:c.6469G>C	p.Glu2157Gln	p.E2157Q	ENST00000278616	NM_000051.3	2157	Gag/Cag	45/63	0.387659806809425	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.41336311037202	1		567	292	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138552	11138552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004008-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	142	684	2	ENST00000358026.2:c.3308G>A	p.Cys1103Tyr	p.C1103Y	ENST00000358026	NM_001128849.1	1103	tGc/tAc	24/36	0.231522665419813	2	FACETS	0.911	0.84	0.983	0.911	0.84	0.983	INDETERMINATE	2	TRUE	0	0.41336311037202	2		686	377	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923027	44923027	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004008-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	167	295	0	ENST00000377967.4:c.1888G>T	p.Glu630Ter	p.E630*	ENST00000377967	NM_021140.2	630	Gag/Tag	16/29	0.133539395345437	2	FACETS	0.872	0.817	0.926			1	INDETERMINATE	3	TRUE	NA	0.41336311037202	2		295	309	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004012-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	25	280	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.921	1			1	INDETERMINATE	1	TRUE	NA	0.220659072219438	2		280	164	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268802	41268802	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004012-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	139	546	0	ENST00000349496.5:c.1040T>C	p.Leu347Pro	p.L347P	ENST00000349496	NM_001904.3	347	cTa/cCa	7/15	0.139131514623004	3	FACETS	1	0.979	1	0.633	0.575	0.694	CLONAL	1	TRUE	1	0.220659072219438	3		546	1105	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004029-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	75	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.32	2		280	320	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0004029-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	64	274	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.405882740824531	3	FACETS	0.827	0.717	0.947	0.414	0.358	0.474	CLONAL	1	TRUE	1	0.32	3		274	561	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0004029-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	85	354	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.32	2		354	432	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004038-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	67	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.954	0.848	1	0.954	0.848	1	CLONAL	1	TRUE	1	0.821810201994667	2		280	171	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70005639	70005639	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763119975	NA	P-0004038-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	89	388	0	ENST00000394351.3:c.668G>A	p.Arg223His	p.R223H	ENST00000394351	NM_000248.3	223	cGc/cAc	7/9	1	2	FACETS	0.37	0.328	0.414	0.37	0.328	0.414	SUBCLONAL	1	TRUE	1	0.821810201994667	2		388	586	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984813	55984813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200544155	NA	P-0004038-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	224	413	2	ENST00000263923.4:c.316C>T	p.Arg106Trp	p.R106W	ENST00000263923	NM_002253.2	106	Cgg/Tgg	3/30	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.821810201994667	2		415	508	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553533	106553533	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004038-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	152	276	0	ENST00000369096.4:c.1498G>A	p.Gly500Arg	p.G500R	ENST00000369096	NM_001198.3	500	Ggg/Agg	5/7	1	2	FACETS	0.887	0.82	0.956	0.887	0.82	0.956	CLONAL	1	TRUE	1	0.821810201994667	2		276	417	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001348	29001348	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004038-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	23	334	0	ENST00000282397.4:c.1384C>A	p.Pro462Thr	p.P462T	ENST00000282397	NM_002019.4	462	Cct/Act	10/30	NA	2	FACETS	0.126	0.098	0.159			1	INDETERMINATE	1	TRUE	NA	0.821810201994667	2		334	443	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357181	70357181	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867804014	NA	P-0004038-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	174	415	0	ENST00000374080.3:c.5696G>A	p.Arg1899Gln	p.R1899Q	ENST00000374080		1899	cGg/cAg	39/45	0.390080567293715	1	FACETS	0.518	0.481	0.555	0.518	0.481	0.555	INDETERMINATE	1	TRUE	0	0.821810201994667	1		415	482	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939373	76939373	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004038-T01-IM3	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	247	544	0	ENST00000373344.5:c.1375A>G	p.Lys459Glu	p.K459E	ENST00000373344	NM_000489.3	459	Aag/Gag	9/35	0.390080567293715	1	FACETS	0.632	0.597	0.668	0.632	0.597	0.668	INDETERMINATE	1	TRUE	0	0.821810201994667	1		544	560	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0004048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	217	558	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.636845126661816	2		558	550	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0004048-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	32	229	0				ENST00000310581	NM_198253.2	-/1132			0.237392284322546	1	FACETS	0.721	0.602	0.847	0.721	0.602	0.847	INDETERMINATE	1	TRUE	0	0.636845126661816	1		229	95	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	51	280	0				ENST00000310581	NM_198253.2	-/1132			0.405631648774189	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	2	TRUE	0	0.428901592850251	2		280	117	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004922	150004922	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	176	377	0	ENST00000253339.5:c.1303C>T	p.Gln435Ter	p.Q435*	ENST00000253339		435	Cag/Tag	3/7	0.245168653681175	4	FACETS	1	0.989	1	0.739	0.682	0.799	INDETERMINATE	1	TRUE	2	0.428901592850251	4		377	793	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468265	120468265	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	93	119	0	ENST00000256646.2:c.4174C>T	p.Gln1392Ter	p.Q1392*	ENST00000256646	NM_024408.3	1392	Cag/Tag	25/34	0.39116121217169	3	FACETS	1	0.973	1	0.644	0.576	0.715	CLONAL	1	TRUE	1	0.428901592850251	3		119	409	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807518	1807518	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	196	266	0	ENST00000260795.2:c.1687C>G	p.Leu563Val	p.L563V	ENST00000260795		563	Ctg/Gtg	12/17	0.229039072311109	1	FACETS	1	0.988	1	1	0.988	1	INDETERMINATE	1	TRUE	0	0.428901592850251	1		266	567	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651883	36651883	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0004056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	308	190	0	ENST00000244741.5:c.5C>G	p.Ser2Ter	p.S2*	ENST00000244741	NM_000389.4	2	tCa/tGa	2/3	0.428901592850251	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	3	TRUE	0	0.428901592850251	3		190	516	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6441986	6441986	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	304	195	0	ENST00000356142.4:c.545G>A	p.Arg182Gln	p.R182Q	ENST00000356142	NM_018890.3	182	cGa/cAa	7/7	0.39116121217169	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.428901592850251	3		195	702	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729970	41729970	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1380653684	NA	P-0004056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	354	523	1	ENST00000242208.4:c.559G>C	p.Asp187His	p.D187H	ENST00000242208	NM_002192.2	187	Gac/Cac	3/3	0.39116121217169	3	FACETS	0.812	0.769	0.856	0.812	0.769	0.856	CLONAL	2	TRUE	1	0.428901592850251	3		524	1234	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456475	32456475	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	57	98	0	ENST00000332351.3:c.417C>A	p.Phe139Leu	p.F139L	ENST00000332351	NM_024426.4	139	ttC/ttA	1/10	0.428901592850251	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.428901592850251	1		98	146	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103400	77103400	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs748471279	NA	P-0004056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	244	566	0	ENST00000356341.3:c.166C>T	p.Arg56Ter	p.R56*	ENST00000356341	NM_002576.4	56	Cga/Tga	2/15	0.428901592850251	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.428901592850251	1		566	676	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907447	32907447	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs80358474	NA	P-0004056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	284	349	0	ENST00000380152.3:c.1832C>G	p.Ser611Ter	p.S611*	ENST00000380152		611	tCa/tGa	10/27	NA	2	FACETS	1	0.975	1			1	INDETERMINATE	2	TRUE	NA	0.428901592850251	2		349	633	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122892	7122892	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	202	352	0	ENST00000302850.5:c.3367G>A	p.Glu1123Lys	p.E1123K	ENST00000302850	NM_000208.2	1123	Gag/Aag	18/22	0.428901592850251	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.428901592850251	1		352	613	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794857	42794857	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	125	189	0	ENST00000575354.2:c.1937G>C	p.Arg646Thr	p.R646T	ENST00000575354	NM_015125.3	646	aGa/aCa	10/20	0.193422409066612	4	FACETS	0.869	0.792	0.95			1	INDETERMINATE	2	TRUE	NA	0.428901592850251	4		189	479	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480495	57480495	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	163	186	0	ENST00000371085.3:c.490G>T	p.Glu164Ter	p.E164*	ENST00000371085	NM_000516.4	164	Gaa/Taa	6/13	0.238417987941957	4	FACETS	0.832	0.766	0.9			1	INDETERMINATE	2	TRUE	NA	0.428901592850251	4		186	653	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175882	24175882	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	150	212	0	ENST00000263121.7:c.1110G>T	p.Arg370Ser	p.R370S	ENST00000263121	NM_003073.3	370	agG/agT	8/9	0.428901592850251	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.428901592850251	1		212	436	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067931	30067965	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGCACTGGTGATTTCTGAGGGGCTGGGGTTCCAGG	AGCACTGGTGATTTCTGAGGGGCTGGGGTTCCAGG	-	novel	NA	P-0004056-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	137	260	0	ENST00000338641.4:c.1118_1122+30del		p.X373_splice	ENST00000338641	NM_000268.3	373		11/16	0.428901592850251	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.428901592850251	1		260	487	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578469	7578469	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762846821	NA	P-0004064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	413	238	1	ENST00000269305.4:c.461G>T	p.Gly154Val	p.G154V	ENST00000269305	NM_001126112.2	154	gGc/gTc	5/11	0.646332261044671	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	4	TRUE	0	0.749367016304637	4		239	482	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	2731	326	0	ENST00000269571.5:c.829G>C	p.Asp277His	p.D277H	ENST00000269571		277	Gac/Cac	7/27	0.749367016304637	18	FACETS	1	0.997	1			1	CLONAL	17	TRUE	NA	0.749367016304637	18		326	2980	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645687	12645687	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs397516828	NA	P-0004064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	163	296	0	ENST00000251849.4:c.782C>G	p.Pro261Arg	p.P261R	ENST00000251849	NM_002880.3	261	cCt/cGt	7/17	0.583129987181263	4	FACETS	0.769	0.711	0.828	0.769	0.711	0.828	SUBCLONAL	2	TRUE	2	0.749367016304637	4		296	495	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782398	9782398	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	138	184	0	ENST00000377346.4:c.2331C>G	p.Ile777Met	p.I777M	ENST00000377346	NM_005026.3	777	atC/atG	18/24	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.749367016304637	2		184	260	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809557	36809557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	66	275	0	ENST00000373129.3:c.908C>T	p.Thr303Ile	p.T303I	ENST00000373129	NM_032017.1	303	aCc/aTc	10/12	0.369365000991477	2	FACETS	0.539	0.471	0.611	0.269	0.235	0.306	INDETERMINATE	1	TRUE	0	0.749367016304637	2		275	327	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945178	32945178	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs80359114	NA	P-0004064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	50	357	0	ENST00000380152.3:c.8573A>G	p.Gln2858Arg	p.Q2858R	ENST00000380152		2858	cAa/cGa	20/27	NA	2	FACETS	0.318	0.27	0.37			1	INDETERMINATE	1	TRUE	NA	0.749367016304637	2		357	420	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490269	29490269	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	146	397	0	ENST00000356175.3:c.354C>A	p.Cys118Ter	p.C118*	ENST00000356175	NM_000267.3	118	tgC/tgA	4/57	0.732141773941817	6	FACETS	1	0.968	1	0.282	0.257	0.308	CLONAL	1	TRUE	2	0.749367016304637	6		397	864	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934162	48934163	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	71	216	0	ENST00000267163.4:c.618dup	p.Gln207ThrfsTer5	p.Q207Tfs*5	ENST00000267163	NM_000321.2	206	tta/ttAa	7/27	0.657186635520387	1	FACETS	0.846	0.763	0.93	0.846	0.763	0.93	CLONAL	1	TRUE	0	0.749367016304637	1		216	140	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295167	1295168	+	upstream_gene_variant	5'Flank	INS	TC	TC	AATG	novel	NA	P-0004064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	71	32	0				ENST00000310581	NM_198253.2	-/1132			0.646332261044671	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	4	TRUE	0	0.749367016304637	4		32	80	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	23	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.164842177204333	2		280	202	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0004093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	47	176	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.164842177204333	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.164842177204333	1		176	382	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778720	NA	P-0004093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	129	603	2	ENST00000269305.4:c.638G>A	p.Arg213Gln	p.R213Q	ENST00000269305	NM_001126112.2	213	cGa/cAa	6/11	1	2	FACETS	0.863	0.782	0.948	1	0.988	1	CLONAL	2	TRUE	1	0.164842177204333	2		605	907	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645699	12645699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80338796	NA	P-0004093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	37	321	0	ENST00000251849.4:c.770C>T	p.Ser257Leu	p.S257L	ENST00000251849	NM_002880.3	257	tCg/tTg	7/17	0.164842177204333	1	FACETS	0.702	0.577	0.841	0.702	0.577	0.841	SUBCLONAL	1	TRUE	0	0.164842177204333	1		321	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577579	7577579	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	57	256	0	ENST00000269305.4:c.702C>A	p.Tyr234Ter	p.Y234*	ENST00000269305	NM_001126112.2	234	taC/taA	7/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.164842177204333	2		256	510	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937555	76937555	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	92	602	0	ENST00000373344.5:c.3193G>T	p.Glu1065Ter	p.E1065*	ENST00000373344	NM_000489.3	1065	Gag/Tag	9/35	0.164842177204333	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.164842177204333	1		602	730	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514540	149514540	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	59	369	0	ENST00000261799.4:c.404T>C	p.Leu135Pro	p.L135P	ENST00000261799	NM_002609.3	135	cTa/cCa	4/23	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.164842177204333	2		369	575	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393696	139393696	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554826746	NA	P-0004093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	116	220	0	ENST00000277541.6:c.5950C>T	p.Arg1984Ter	p.R1984*	ENST00000277541	NM_017617.3	1984	Cga/Tga	32/34	0.164842177204333	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	3	TRUE	0	0.164842177204333	3		220	446	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778911	3778911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753688167	NA	P-0004093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	34	149	0	ENST00000262367.5:c.6137C>T	p.Ala2046Val	p.A2046V	ENST00000262367	NM_004380.2	2046	gCg/gTg	31/31	1	2	FACETS	0.781	0.641	0.937	1	0.951	1	CLONAL	2	TRUE	1	0.164842177204333	2		149	264	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531037	187531047	+	frameshift_variant	Frame_Shift_Del	DEL	TTGATATCTGT	TTGATATCTGT	-	novel	NA	P-0004093-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	116	417	0	ENST00000441802.2:c.9976_9986del	p.Thr3326ArgfsTer2	p.T3326Rfs*2	ENST00000441802	NM_005245.3	3326	ACAGATATCAAc/c	15/27	0.164842177204333	1	FACETS	0.898	0.81	0.991	1	0.987	1	CLONAL	2	TRUE	0	0.164842177204333	1		417	719	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	42	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.919	0.782	1	0.919	0.782	1	CLONAL	1	TRUE	1	0.625853064443809	2		280	146	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645067	86645067	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	216	239	0	ENST00000274376.6:c.1139A>G	p.Asp380Gly	p.D380G	ENST00000274376	NM_002890.2	380	gAt/gGt	8/25	1	2	FACETS	0.87	0.811	0.931	0.87	0.811	0.931	CLONAL	1	TRUE	1	0.625853064443809	2		239	793	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78811778	78811778	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004101-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	140	249	0	ENST00000306801.3:c.1193A>G	p.Glu398Gly	p.E398G	ENST00000306801	NM_020761.2	398	gAg/gGg	10/34	0.625853064443809	3	FACETS	0.891	0.814	0.972	0.446	0.407	0.486	CLONAL	1	TRUE	1	0.625853064443809	3		249	659	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971173	21971173	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	38	84	0	ENST00000304494.5:c.185T>C	p.Leu62Pro	p.L62P	ENST00000304494	NM_000077.4	62	cTg/cCg	2/3	0.269265882325158	3	FACETS	0.953	0.799	1	0.953	0.799	1	CLONAL	2	TRUE	1	0.269265882325158	3		84	168	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732318	74732318	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1358	241	831	0	ENST00000359995.5:c.591G>C	p.Lys197Asn	p.K197N	ENST00000359995	NM_001195427.1	197	aaG/aaC	2/3	0.269265882325158	3	FACETS	1	0.988	1	0.635	0.591	0.681	CLONAL	1	TRUE	1	0.269265882325158	3		831	1599	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128036886	128036886	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	157	422	1	ENST00000285398.2:c.1593C>G	p.Ile531Met	p.I531M	ENST00000285398	NM_000122.1	531	atC/atG	10/15	0.266050299099689	2	FACETS	1	0.985	1	0.673	0.617	0.732	CLONAL	1	TRUE	0	0.269265882325158	2		423	866	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149568	202149568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	166	288	0	ENST00000358485.4:c.1009C>T	p.His337Tyr	p.H337Y	ENST00000358485	NM_001080125.1	337	Cat/Tat	8/9	0.269265882325158	5	FACETS	1	0.954	1			1	CLONAL	2	TRUE	NA	0.269265882325158	5		288	822	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150021	202150021	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	81	163	1	ENST00000358485.4:c.1462C>A	p.Leu488Met	p.L488M	ENST00000358485	NM_001080125.1	488	Ctg/Atg	8/9	0.269265882325158	5	FACETS	0.96	0.849	1			1	CLONAL	2	TRUE	NA	0.269265882325158	5		164	440	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212522478	212522478	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	82	230	0	ENST00000342788.4:c.1946+1G>T		p.X649_splice	ENST00000342788	NM_005235.2	649			0.269265882325158	3	FACETS	0.753	0.666	0.845	0.753	0.666	0.845	SUBCLONAL	2	TRUE	1	0.269265882325158	3		230	459	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439989	220439989	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1438	94	743	1	ENST00000243786.2:c.842T>C	p.Val281Ala	p.V281A	ENST00000243786	NM_002191.3	281	gTg/gCg	2/2	0.269265882325158	3	FACETS	0.517	0.458	0.581	0.259	0.229	0.291	SUBCLONAL	1	TRUE	1	0.269265882325158	3		744	1532	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225370756	225370756	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	64	219	0	ENST00000264414.4:c.1123G>C	p.Glu375Gln	p.E375Q	ENST00000264414	NM_003590.4	375	Gag/Cag	8/16	0.269265882325158	3	FACETS	0.836	0.724	0.958	0.418	0.362	0.479	CLONAL	1	TRUE	1	0.269265882325158	3		219	645	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391067	89391067	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	98	326	1	ENST00000336596.2:c.1133C>A	p.Pro378Gln	p.P378Q	ENST00000336596	NM_005233.5	378	cCa/cAa	5/17	0.269265882325158	9	FACETS	1	0.958	1			1	CLONAL	1	TRUE	NA	0.269265882325158	9		327	1222	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391078	89391078	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	142	337	0	ENST00000336596.2:c.1144T>A	p.Phe382Ile	p.F382I	ENST00000336596	NM_005233.5	382	Ttc/Atc	5/17	0.269265882325158	9	FACETS	0.832	0.756	0.912			1	CLONAL	2	TRUE	NA	0.269265882325158	9		337	1231	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499449	89499449	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1309775529	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	48	289	0	ENST00000336596.2:c.2619G>T	p.Gln873His	p.Q873H	ENST00000336596	NM_005233.5	873	caG/caT	15/17	0.269265882325158	9	FACETS	0.788	0.664	0.925			1	CLONAL	1	TRUE	NA	0.269265882325158	9		289	879	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637265	176637265	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	61	213	0	ENST00000439151.2:c.1865G>C	p.Cys622Ser	p.C622S	ENST00000439151	NM_022455.4	622	tGc/tCc	5/23	0.266050299099689	2	FACETS	0.996	0.861	1	0.498	0.43	0.571	CLONAL	1	TRUE	0	0.269265882325158	2		213	455	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710911	117710911	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	51	199	0	ENST00000368508.3:c.1361C>G	p.Thr454Arg	p.T454R	ENST00000368508	NM_002944.2	454	aCg/aGg	12/43	0.231320675582612	3	FACETS	0.93	0.792	1	0.31	0.264	0.361	CLONAL	1	TRUE	0	0.269265882325158	3		199	462	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878235	151878235	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	122	207	1	ENST00000262189.6:c.6710C>G	p.Ser2237Ter	p.S2237*	ENST00000262189	NM_170606.2	2237	tCa/tGa	36/59	0.202316183254588	4	FACETS	0.909	0.828	0.992			1	CLONAL	3	TRUE	NA	0.269265882325158	4		208	422	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371732	55371732	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	72	205	0	ENST00000297316.4:c.422G>T	p.Arg141Leu	p.R141L	ENST00000297316	NM_022454.3	141	cGg/cTg	2/2	0.269265882325158	5	FACETS	0.797	0.698	0.903	0.399	0.349	0.452	CLONAL	2	TRUE	1	0.269265882325158	5		205	471	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145740421	145740421	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	41	152	0	ENST00000428558.2:c.1519G>T	p.Gly507Cys	p.G507C	ENST00000428558	NM_004260.3	507	Ggc/Tgc	9/22	0.269265882325158	5	FACETS	1	0.9	1	0.278	0.232	0.33	CLONAL	1	TRUE	1	0.269265882325158	5		152	384	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054734	5054734	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	109	263	2	ENST00000381652.3:c.786G>T	p.Gln262His	p.Q262H	ENST00000381652	NM_004972.3	262	caG/caT	7/25	0.269265882325158	3	FACETS	0.819	0.738	0.904	0.819	0.738	0.904	CLONAL	2	TRUE	1	0.269265882325158	3		265	561	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521513	8521513	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	38	212	0	ENST00000356435.5:c.725C>A	p.Pro242His	p.P242H	ENST00000356435		242	cCc/cAc	9/35	0.269265882325158	3	FACETS	0.702	0.58	0.838	0.351	0.29	0.419	SUBCLONAL	1	TRUE	1	0.269265882325158	3		212	456	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607562	43607562	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	48	177	0	ENST00000355710.3:c.1538C>A	p.Ala513Glu	p.A513E	ENST00000355710	NM_020975.4	513	gCg/gAg	8/20	0.257647478098145	4	FACETS	1	0.906	1	0.366	0.31	0.428	CLONAL	1	TRUE	1	0.269265882325158	4		177	412	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615128	43615128	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs794728685	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	152	468	0	ENST00000355710.3:c.2542A>G	p.Met848Val	p.M848V	ENST00000355710	NM_020975.4	848	Atg/Gtg	14/20	0.257647478098145	4	FACETS	1	0.986	1	0.466	0.425	0.509	CLONAL	1	TRUE	1	0.269265882325158	4		468	1025	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114901057	114901057	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	192	731	0	ENST00000543371.1:c.667G>T	p.Asp223Tyr	p.D223Y	ENST00000543371	NM_001198531.1	223	Gac/Tac	6/14	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	1	TRUE	NA	0.269265882325158	2		731	1313	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448329	49448329	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	215	437	0	ENST00000301067.7:c.382C>T	p.His128Tyr	p.H128Y	ENST00000301067	NM_003482.3	128	Cac/Tac	3/54	0.269265882325158	3	FACETS	0.986	0.917	1	0.986	0.917	1	CLONAL	2	TRUE	1	0.269265882325158	3		437	919	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69229702	69229702	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	29	181	0	ENST00000462284.1:c.778C>G	p.Leu260Val	p.L260V	ENST00000462284	NM_002392.5	260	Ctc/Gtc	9/11	0.269265882325158	3	FACETS	0.504	0.404	0.618	0.252	0.202	0.309	SUBCLONAL	1	TRUE	1	0.269265882325158	3		181	485	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112277	115112277	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	60	69	0	ENST00000257566.3:c.1463C>G	p.Ala488Gly	p.A488G	ENST00000257566	NM_016569.3	488	gCg/gGg	7/8	0.269265882325158	5	FACETS	1	0.914	1	1	0.914	1	CLONAL	4	TRUE	1	0.269265882325158	5		69	150	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005460	42005460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1215	207	801	0	ENST00000219905.7:c.3196C>T	p.Arg1066Cys	p.R1066C	ENST00000219905	NM_001164273.1	1066	Cgc/Tgc	9/24	NA	2	FACETS	1	0.968	1			1	INDETERMINATE	1	TRUE	NA	0.269265882325158	2		801	1422	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630687	90630687	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	62	314	0	ENST00000330062.3:c.799C>G	p.Gln267Glu	p.Q267E	ENST00000330062	NM_002168.2	267	Cag/Gag	6/11	0.269265882325158	3	FACETS	0.701	0.605	0.807	0.351	0.302	0.404	SUBCLONAL	1	TRUE	1	0.269265882325158	3		314	745	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273994	10273994	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	79	389	0	ENST00000330684.3:c.275G>T	p.Gly92Val	p.G92V	ENST00000330684	NM_001134407.1	92	gGg/gTg	2/13	1	2	FACETS	0.872	0.767	0.985	0.872	0.767	0.985	CLONAL	1	TRUE	1	0.269265882325158	2		389	673	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984742	72984742	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1337540676	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	89	693	0	ENST00000268489.5:c.2842G>T	p.Ala948Ser	p.A948S	ENST00000268489	NM_006885.3	948	Gcc/Tcc	3/10	1	2	FACETS	0.551	0.487	0.62	0.551	0.487	0.62	SUBCLONAL	1	TRUE	1	0.269265882325158	2		693	1200	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17129588	17129588	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	219	350	0	ENST00000285071.4:c.298A>T	p.Lys100Ter	p.K100*	ENST00000285071	NM_144997.5	100	Aaa/Taa	5/14	0.269265882325158	4	FACETS	0.935	0.873	0.999	0.935	0.873	0.999	CLONAL	3	TRUE	1	0.269265882325158	4		350	736	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440752	56440752	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	109	319	1	ENST00000407977.2:c.466G>T	p.Gly156Trp	p.G156W	ENST00000407977		156	Ggg/Tgg	5/10	0.269265882325158	3	FACETS	1	0.978	1	0.662	0.595	0.733	CLONAL	1	TRUE	1	0.269265882325158	3		320	694	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372040	45372040	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	126	184	0	ENST00000262160.6:c.1129C>T	p.Pro377Ser	p.P377S	ENST00000262160	NM_005901.5	377	Cca/Tca	9/11	0.269265882325158	3	FACETS	0.839	0.766	0.914	1	0.98	1	CLONAL	3	TRUE	1	0.269265882325158	3		184	422	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184585	7184585	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	33	116	0	ENST00000302850.5:c.716G>T	p.Cys239Phe	p.C239F	ENST00000302850	NM_000208.2	239	tGc/tTc	3/22	0.269265882325158	3	FACETS	1	0.879	1	0.366	0.3	0.441	CLONAL	1	TRUE	0	0.269265882325158	3		116	253	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123671	11123671	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	211	275	0	ENST00000358026.2:c.2321A>T	p.Asn774Ile	p.N774I	ENST00000358026	NM_001128849.1	774	aAc/aTc	16/36	0.269265882325158	3	FACETS	0.958	0.895	1	0.958	0.895	1	CLONAL	3	TRUE	0	0.269265882325158	3		275	619	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905546	50905546	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144979965	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	191	725	0	ENST00000440232.2:c.674G>A	p.Arg225His	p.R225H	ENST00000440232	NM_002691.3	225	cGt/cAt	6/27	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.269265882325158	2		725	1208	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905999	50905999	+	splice_donor_variant	Splice_Site	SNP	G	G	T	rs1337231648	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	72	455	0	ENST00000440232.2:c.970+1G>T		p.X324_splice	ENST00000440232	NM_002691.3	324			NA	2	FACETS	0.643	0.56	0.732			1	INDETERMINATE	1	TRUE	NA	0.269265882325158	2		455	832	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52728969	52728969	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	47	255	0	ENST00000322088.6:c.1662-1G>T		p.X554_splice	ENST00000322088	NM_014225.5	554			NA	2	FACETS	0.754	0.637	0.883			1	INDETERMINATE	1	TRUE	NA	0.269265882325158	2		255	463	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817420	39817420	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	120	266	0	ENST00000288319.7:c.143G>T	p.Ser48Ile	p.S48I	ENST00000288319	NM_182918.3	48	aGc/aTc	2/10	0.269265882325158	3	FACETS	1	0.917	1	1	0.917	1	CLONAL	2	TRUE	1	0.269265882325158	3		266	500	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288212	21288212	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1722	165	418	1	ENST00000354336.3:c.457A>G	p.Ile153Val	p.I153V	ENST00000354336	NM_005207.3	153	Ata/Gta	2/3	0.269265882325158	12	FACETS	0.762	0.696	0.831			1	SUBCLONAL	2	TRUE	NA	0.269265882325158	12		419	1887	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24143223	24143223	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	284	426	0	ENST00000263121.7:c.455A>G	p.Asn152Ser	p.N152S	ENST00000263121	NM_003073.3	152	aAc/aGc	4/9	0.269265882325158	6	FACETS	1	0.945	1			1	CLONAL	3	TRUE	NA	0.269265882325158	6		426	1076	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314981	1314981	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	117	302	0	ENST00000400841.2:c.680C>G	p.Pro227Arg	p.P227R	ENST00000400841		227	cCa/cGa	6/6	0.213848010938532	2	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.269265882325158	2		302	638	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044922	47044922	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	87	163	0	ENST00000377604.3:c.2248G>T	p.Glu750Ter	p.E750*	ENST00000377604	NM_001204468.1	750	Gag/Tag	20/24	0.213848010938532	2	FACETS	0.865	0.778	0.955			1	CLONAL	3	TRUE	NA	0.269265882325158	2		163	249	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70351459	70351459	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	40	216	0	ENST00000374080.3:c.4107G>C	p.Gln1369His	p.Q1369H	ENST00000374080		1369	caG/caC	29/45	0.213848010938532	2	FACETS	0.654	0.544	0.777			1	SUBCLONAL	1	TRUE	NA	0.269265882325158	2		216	454	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747067	40747067	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	102	287	0	ENST00000373198.4:c.3015del	p.Thr1006GlnfsTer9	p.T1006Qfs*9	ENST00000373198	NM_133170.3	1005	gtC/gt	22/32	0.269265882325158	4	FACETS	1	0.981	1	0.495	0.443	0.55	CLONAL	1	TRUE	1	0.269265882325158	4		287	648	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288917	212288917	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	59	238	0	ENST00000342788.4:c.2829del	p.Ile944SerfsTer15	p.I944Sfs*15	ENST00000342788	NM_005235.2	943	ccC/cc	23/28	0.269265882325158	3	FACETS	0.875	0.753	1	0.438	0.376	0.504	CLONAL	1	TRUE	1	0.269265882325158	3		238	568	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001410	29001410	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	75	148	0	ENST00000282397.4:c.1322del	p.Pro441ArgfsTer12	p.P441Rfs*12	ENST00000282397	NM_002019.4	441	cCg/cg	10/30	0.266050299099689	2	FACETS	0.827	0.73	0.929	0.827	0.73	0.929	CLONAL	2	TRUE	0	0.269265882325158	2		148	337	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339968	116339969	+	missense_variant	Missense_Mutation	DNP	GA	GA	CT	novel	NA	P-0004114-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	44	300	0	ENST00000397752.3:c.830_831delinsCT	p.Arg277Thr	p.R277T	ENST00000397752	NM_000245.2	277	aGA/aCT	2/21	0.231320675582612	3	FACETS	0.534	0.447	0.632	0.178	0.149	0.211	SUBCLONAL	1	TRUE	0	0.269265882325158	3		300	694	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004119-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	41	280	0				ENST00000310581	NM_198253.2	-/1132			0.273082819429282	4	FACETS	0.975	0.825	1			1	CLONAL	2	TRUE	NA	0.347719619343552	4		280	163	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663336	227663336	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004119-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	53	317	0	ENST00000305123.5:c.119G>T	p.Gly40Val	p.G40V	ENST00000305123	NM_005544.2	40	gGc/gTc	1/2	0.256491026666389	5	FACETS	0.789	0.677	0.909	0.526	0.451	0.606	CLONAL	2	TRUE	2	0.347719619343552	5		317	294	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223610	55223610	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004119-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5889	2679	426	0	ENST00000275493.2:c.977G>A	p.Cys326Tyr	p.C326Y	ENST00000275493	NM_005228.3	326	tGt/tAt	8/28	0.347719619343552	69	FACETS	0.989	0.97	1			1	CLONAL	23	TRUE	NA	0.347719619343552	69		426	8568	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	34	280	0				ENST00000310581	NM_198253.2	-/1132			0.197723624240785	3	FACETS	0.836	0.695	0.988	1	0.93	1	CLONAL	3	TRUE	1	0.219776204364153	3		280	137	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0004137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	51	264	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.146710054024968	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.219776204364153	1		264	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0004137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	78	589	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.146710054024968	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.219776204364153	1		589	546	SUCCESS
APC	324	MSKCC	GRCh37	5	112176601	112176601	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	29	319	0	ENST00000257430.4:c.5310G>C	p.Lys1770Asn	p.K1770N	ENST00000257430	NM_000038.5	1770	aaG/aaC	16/16	1	2	FACETS	0.624	0.5	0.765	0.624	0.5	0.765	SUBCLONAL	1	TRUE	1	0.219776204364153	2		319	423	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141495	11141495	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	47	423	0	ENST00000358026.2:c.3472G>C	p.Ala1158Pro	p.A1158P	ENST00000358026	NM_001128849.1	1158	Gct/Cct	25/36	0.219776204364153	1	FACETS	0.706	0.596	0.828	0.706	0.596	0.828	SUBCLONAL	1	TRUE	0	0.219776204364153	1		423	539	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178948136	178948136	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	31	210	0	ENST00000263967.3:c.2908G>A	p.Glu970Lys	p.E970K	ENST00000263967	NM_006218.2	970	Gaa/Aaa	20/21	1	2	FACETS	0.631	0.51	0.768	0.631	0.51	0.768	SUBCLONAL	1	TRUE	1	0.219776204364153	2		210	447	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363243	40363243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	204	330	0	ENST00000397332.2:c.986C>T	p.Ser329Leu	p.S329L	ENST00000397332	NM_001033082.2	329	tCg/tTg	3/3	0.219776204364153	4	FACETS	0.928	0.866	0.992			1	CLONAL	4	TRUE	NA	0.219776204364153	4		330	610	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551461	150551461	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs752398877	NA	P-0004137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	61	532	0	ENST00000369026.2:c.546C>G	p.Ile182Met	p.I182M	ENST00000369026	NM_021960.4	182	atC/atG	1/3	0.219776204364153	4	FACETS	0.812	0.699	0.935	0.406	0.349	0.468	CLONAL	1	TRUE	2	0.219776204364153	4		532	834	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880464	155880464	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	107	400	0	ENST00000368323.3:c.89G>T	p.Gly30Val	p.G30V	ENST00000368323	NM_006912.5	30	gGt/gTt	2/6	0.219776204364153	4	FACETS	0.998	0.897	1	0.998	0.897	1	CLONAL	2	TRUE	2	0.219776204364153	4		400	595	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663346	227663346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024227751	NA	P-0004137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	23	161	0	ENST00000305123.5:c.109G>A	p.Glu37Lys	p.E37K	ENST00000305123	NM_005544.2	37	Gag/Aag	1/2	0.146710054024968	1	FACETS	0.708	0.553	0.887	0.708	0.553	0.887	SUBCLONAL	1	TRUE	0	0.219776204364153	1		161	263	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582117	189582117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	57	446	0	ENST00000264731.3:c.676C>T	p.Arg226Cys	p.R226C	ENST00000264731	NM_003722.4	226	Cgc/Tgc	5/14	1	2	FACETS	0.829	0.71	0.958	0.829	0.71	0.958	CLONAL	1	TRUE	1	0.219776204364153	2		446	626	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375132	104375132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	83	342	0	ENST00000369902.3:c.1130C>T	p.Ser377Phe	p.S377F	ENST00000369902	NM_016169.3	377	tCc/tTc	9/12	0.146710054024968	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.219776204364153	1		342	489	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577485	64577485	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	31	344	0	ENST00000312049.6:c.97G>T	p.Asp33Tyr	p.D33Y	ENST00000312049	NM_130799.2	33	Gac/Tac	2/10	1	2	FACETS	0.779	0.631	0.947	0.779	0.631	0.947	CLONAL	1	TRUE	1	0.219776204364153	2		344	362	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129664	2129664	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	81	376	0	ENST00000219476.3:c.3391A>T	p.Met1131Leu	p.M1131L	ENST00000219476	NM_000548.3	1131	Atg/Ttg	29/42	0.219776204364153	1	FACETS	0.781	0.692	0.876	1	0.979	1	SUBCLONAL	2	TRUE	0	0.219776204364153	1		376	420	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684368	29684368	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs367858662	NA	P-0004137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	34	369	0	ENST00000356175.3:c.7888C>T	p.Pro2630Ser	p.P2630S	ENST00000356175	NM_000267.3	2630	Ccc/Tcc	53/57	0.146710054024968	1	FACETS	0.618	0.504	0.745	0.618	0.504	0.745	SUBCLONAL	1	TRUE	0	0.219776204364153	1		369	446	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56780586	56780586	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	65	449	0	ENST00000337432.4:c.601C>T	p.Leu201Phe	p.L201F	ENST00000337432	NM_058216.2	201	Ctt/Ttt	4/9	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.219776204364153	2		449	582	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050425	13050425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs536586990	NA	P-0004137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	95	586	0	ENST00000316448.5:c.377C>T	p.Ser126Leu	p.S126L	ENST00000316448	NM_004343.3	126	tCa/tTa	3/9	0.219776204364153	1	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	0	0.219776204364153	1		586	677	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281587	15281587	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	78	552	1	ENST00000263388.2:c.4786G>A	p.Glu1596Lys	p.E1596K	ENST00000263388	NM_000435.2	1596	Gag/Aag	26/33	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.219776204364153	2		553	572	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745204	41745204	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	27	359	0	ENST00000301178.4:c.1270G>A	p.Glu424Lys	p.E424K	ENST00000301178	NM_021913.4	424	Gag/Aag	9/20	0.219776204364153	1	FACETS	0.591	0.47	0.729	0.591	0.47	0.729	SUBCLONAL	1	TRUE	0	0.219776204364153	1		359	370	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872001	45872001	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	80	322	0	ENST00000391945.4:c.247G>A	p.Val83Met	p.V83M	ENST00000391945	NM_000400.3	83	Gtg/Atg	5/23	0.219776204364153	1	FACETS	0.959	0.851	1	1	0.984	1	CLONAL	2	TRUE	0	0.219776204364153	1		322	338	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171718	36171718	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	46	253	0	ENST00000300305.3:c.847C>T	p.Gln283Ter	p.Q283*	ENST00000300305		283	Cag/Tag	7/8	0.146710054024968	1	FACETS	0.936	0.79	1	0.936	0.79	1	CLONAL	1	TRUE	0	0.219776204364153	1		253	398	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15840862	15840862	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	28	203	0	ENST00000307771.7:c.946G>C	p.Glu316Gln	p.E316Q	ENST00000307771	NM_005089.3	316	Gaa/Caa	11/11	0.141783216305892	0	FACETS	0.672	0.538	0.823			1	SUBCLONAL	1	TRUE	NA	0.219776204364153	0		203	296	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942761	44942761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	58	372	0	ENST00000377967.4:c.3341C>T	p.Ser1114Leu	p.S1114L	ENST00000377967	NM_021140.2	1114	tCa/tTa	23/29	0.141783216305892	0	FACETS	1	0.959	1			1	CLONAL	1	TRUE	NA	0.219776204364153	0		372	315	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038792	47038792	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1556777844	NA	P-0004137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	49	132	0	ENST00000377604.3:c.799C>T	p.Gln267Ter	p.Q267*	ENST00000377604	NM_001204468.1	267	Cag/Tag	9/24	0.141783216305892	0	FACETS	0.817	0.7	0.942			1	CLONAL	2	TRUE	NA	0.219776204364153	0		132	213	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577233	64577240	+	frameshift_variant	Frame_Shift_Del	DEL	GCTCACGG	GCTCACGG	-	novel	NA	P-0004137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	55	462	0	ENST00000312049.6:c.342_349del	p.Arg115GlyfsTer62	p.R115Gfs*62	ENST00000312049	NM_130799.2	114	agCCGTGAGCtg/agtg	2/10	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.219776204364153	2		462	441	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061883	38061884	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	51	336	0	ENST00000250448.2:c.105dup	p.Ser36LeufsTer191	p.S36Lfs*191	ENST00000250448	NM_004496.3	35	-/C	2/2	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.219776204364153	2		336	429	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914723	32914741	+	frameshift_variant	Frame_Shift_Del	DEL	GGGAGTGTTAGAGGAATTT	GGGAGTGTTAGAGGAATTT	-	novel	NA	P-0004137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	102	772	0	ENST00000380152.3:c.6232_6250del	p.Gly2078IlefsTer2	p.G2078Ifs*2	ENST00000380152		2077	aaGGGAGTGTTAGAGGAATTT/aa	11/27	0.219776204364153	0	FACETS	0.95	0.85	1			1	CLONAL	1	TRUE	0	0.219776204364153	0		772	762	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	42	280	0				ENST00000310581	NM_198253.2	-/1132			0.20805799459571	2	FACETS	1	0.957	1	0.731	0.617	0.855	CLONAL	1	FALSE	0	0.27605820294809	2		280	208	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188214	10188214	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	155	221	0	ENST00000256474.2:c.357C>A	p.Phe119Leu	p.F119L	ENST00000256474	NM_000551.3	119	ttC/ttA	2/3	0.208765967348258	2	FACETS	0.851	0.781	0.923	0.851	0.781	0.923	CLONAL	2	FALSE	0	0.27605820294809	2		221	660	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367867	15367867	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1454979767	NA	P-0004170-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	149	174	0	ENST00000263377.2:c.1459G>A	p.Asp487Asn	p.D487N	ENST00000263377	NM_058243.2	487	Gac/Aac	8/20	0.20805799459571	2	FACETS	0.942	0.865	1	0.942	0.865	1	CLONAL	2	FALSE	0	0.27605820294809	2		174	573	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	33	280	0				ENST00000310581	NM_198253.2	-/1132			0.145776683308395	3	FACETS	0.872	0.718	1	0.872	0.718	1	CLONAL	2	TRUE	1	0.236311723000412	3		280	179	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0004174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	146	680	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	0.187011099192418	3	FACETS	1	0.981	1	0.825	0.757	0.896	CLONAL	2	TRUE	0	0.236311723000412	3		680	558	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565523	41565523	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	74	299	1	ENST00000263253.7:c.4189T>C	p.Tyr1397His	p.Y1397H	ENST00000263253	NM_001429.3	1397	Tac/Cac	26/31	0.159425678676692	2	FACETS	0.959	0.84	1	0.48	0.42	0.544	CLONAL	1	TRUE	0	0.236311723000412	2		300	653	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	51	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.961	0.83	1	0.961	0.83	1	CLONAL	1	TRUE	1	0.586615331564451	2		280	181	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267698	198267698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	130	428	0	ENST00000335508.6:c.1781G>A	p.Arg594Gln	p.R594Q	ENST00000335508	NM_012433.2	594	cGa/cAa	13/25	1	2	FACETS	0.825	0.752	0.902	0.825	0.752	0.902	CLONAL	1	TRUE	1	0.586615331564451	2		428	537	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	82	660	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.984	0.867	1	0.984	0.867	1	CLONAL	1	TRUE	1	0.213320420357669	2		660	781	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11301616	11301616	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	58	439	0	ENST00000361445.4:c.1535G>C	p.Gly512Ala	p.G512A	ENST00000361445	NM_004958.3	512	gGa/gCa	10/58	0.213320420357669	1	FACETS	0.94	0.808	1	0.94	0.808	1	CLONAL	1	TRUE	0	0.213320420357669	1		439	517	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920325	134920325	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1166499752	NA	P-0004222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	82	580	0	ENST00000398015.3:c.2140G>A	p.Gly714Arg	p.G714R	ENST00000398015	NM_004441.4	714	Ggg/Agg	12/16	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.213320420357669	2		580	720	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603028	48603028	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0004222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	58	307	0	ENST00000342988.3:c.1329T>A	p.Cys443Ter	p.C443*	ENST00000342988	NM_005359.5	443	tgT/tgA	11/12	0.213320420357669	1	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	0	0.213320420357669	1		307	451	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44913201	44913201	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0004222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	102	445	0	ENST00000377967.4:c.875+1G>T		p.X292_splice	ENST00000377967	NM_021140.2	292			0.11634223114905	0	FACETS	0.881	0.793	0.973			1	INDETERMINATE	2	TRUE	NA	0.213320420357669	0		445	427	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578194	7578195	+	inframe_insertion	In_Frame_Ins	INS	-	-	CAC	novel	NA	P-0004222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	96	633	0	ENST00000269305.4:c.652_654dup	p.Val218dup	p.V218dup	ENST00000269305	NM_001126112.2	218	-/GTG	6/11	0.213320420357669	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.213320420357669	1		633	715	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971095	21971096	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004222-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	37	253	0	ENST00000304494.5:c.262dup	p.Glu88GlyfsTer32	p.E88Gfs*32	ENST00000304494	NM_000077.4	88	gag/gGag	2/3	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.213320420357669	2		253	296	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	110	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	FALSE	1	0.901966927726418	2		280	244	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123705	11123705	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	402	439	0	ENST00000358026.2:c.2355G>C	p.Lys785Asn	p.K785N	ENST00000358026	NM_001128849.1	785	aaG/aaC	16/36	1	2	FACETS	0.903	0.862	0.945	0.903	0.862	0.945	CLONAL	1	FALSE	1	0.901966927726418	2		439	987	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0004224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	258	595	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.337673212365704	3	FACETS	1	0.961	1	0.672	0.641	0.702	INDETERMINATE	2	FALSE	0	0.901966927726418	3		595	412	SUCCESS
AR	367	MSKCC	GRCh37	X	66766450	66766450	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	217	140	0	ENST00000374690.3:c.1462C>T	p.Gln488Ter	p.Q488*	ENST00000374690	NM_000044.3	488	Cag/Tag	1/8	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	FALSE	0	0.901966927726418	1		140	230	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0004224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	690	838	1	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.901966927726418	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	FALSE	0	0.901966927726418	1		839	772	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247367	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747241612	NA	P-0004224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	364	261	0	ENST00000281708.4:c.1435C>G	p.Arg479Gly	p.R479G	ENST00000281708	NM_033632.3	479	Cga/Gga	10/12	0.337673212365704	3	FACETS	0.996	0.957	1	0.664	0.638	0.689	INDETERMINATE	2	FALSE	0	0.901966927726418	3		261	588	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135798880	135798880	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0004224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	13	206	0	ENST00000298552.3:c.364-1G>T		p.X122_splice	ENST00000298552	NM_001162426.1	122			0.901966927726418	1	FACETS	0.075	0.053	0.102	0.075	0.053	0.102	SUBCLONAL	1	FALSE	0	0.901966927726418	1		206	210	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911098	32911098	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80358523	NA	P-0004224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	721	944	1	ENST00000380152.3:c.2606C>T	p.Ser869Leu	p.S869L	ENST00000380152		869	tCa/tTa	11/27	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.901966927726418	2		945	1511	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949038	44949038	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004224-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	395	279	0	ENST00000377967.4:c.3599T>G	p.Leu1200Arg	p.L1200R	ENST00000377967	NM_021140.2	1200	cTt/cGt	25/29	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	FALSE	0	0.901966927726418	1		279	432	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	48	280	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.94	1			1	INDETERMINATE	1	TRUE	NA	0.843988439767011	2		280	101	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0004245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	17	560	1	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.201125653878885	4	FACETS	0.094	0.07	0.124	0.047	0.035	0.062	INDETERMINATE	1	TRUE	2	0.843988439767011	4		561	788	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528621	89528621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780470195	NA	P-0004245-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	258	252	0	ENST00000336596.2:c.2921C>T	p.Thr974Met	p.T974M	ENST00000336596	NM_005233.5	974	aCg/aTg	17/17	NA	2	FACETS	0.952	0.898	1			1	INDETERMINATE	1	TRUE	NA	0.843988439767011	2		252	642	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004247-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	34	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.734	0.604	0.878	0.734	0.604	0.878	SUBCLONAL	1	TRUE	1	0.41	2		280	226	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792447	33792447	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1555741996	NA	P-0004247-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	118	458	0	ENST00000498907.2:c.874A>C	p.Asn292His	p.N292H	ENST00000498907	NM_004364.3	292	Aac/Cac	1/1	1	2	FACETS	0.55	0.495	0.609	0.55	0.495	0.609	SUBCLONAL	1	TRUE	1	0.41	2		458	1046	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223610	53223610	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004247-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	72	311	0	ENST00000375401.3:c.3749C>A	p.Ser1250Ter	p.S1250*	ENST00000375401	NM_004187.3	1250	tCa/tAa	23/26	1	2	FACETS	0.508	0.443	0.577	0.508	0.443	0.577	SUBCLONAL	1	TRUE	1	0.41	2		311	692	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	26	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.491373294620248	2		280	79	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0004248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	227	660	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.491373294620248	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.491373294620248	3		660	564	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458423	120458423	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	36	103	0	ENST00000256646.2:c.6922C>G	p.Gln2308Glu	p.Q2308E	ENST00000256646	NM_024408.3	2308	Cag/Gag	34/34	1	2	FACETS	0.97	0.811	1	0.97	0.811	1	CLONAL	1	TRUE	1	0.491373294620248	2		103	151	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266945	41266945	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	102	267	0	ENST00000349496.5:c.616A>T	p.Asn206Tyr	p.N206Y	ENST00000349496	NM_001904.3	206	Aat/Tat	5/15	1	2	FACETS	0.891	0.801	0.985	0.891	0.801	0.985	CLONAL	1	TRUE	1	0.491373294620248	2		267	466	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991455	72991455	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1316526787	NA	P-0004248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	266	386	0	ENST00000268489.5:c.2590T>C	p.Tyr864His	p.Y864H	ENST00000268489	NM_006885.3	864	Tac/Cac	2/10	0.491373294620248	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.491373294620248	3		386	598	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40748476	40748476	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	102	284	0	ENST00000392038.2:c.406A>G	p.Met136Val	p.M136V	ENST00000392038	NM_001626.4	136	Atg/Gtg	5/14	1	2	FACETS	0.996	0.897	1	0.996	0.897	1	CLONAL	1	TRUE	1	0.491373294620248	2		284	417	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023217	27023227	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCTAGGCCC	GCCCTAGGCCC	-	novel	NA	P-0004248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	31	74	0	ENST00000324856.7:c.328_338del	p.Arg110GlufsTer3	p.R110Efs*3	ENST00000324856	NM_006015.4	108	gGCCCTAGGCCC/g	1/20	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.491373294620248	2		74	105	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101127	27101131	+	frameshift_variant	Frame_Shift_Del	DEL	CCAAT	CCAAT	-	novel	NA	P-0004248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	111	284	0	ENST00000324856.7:c.4409_4413del	p.Thr1470SerfsTer19	p.T1470Sfs*19	ENST00000324856	NM_006015.4	1470	aCCAAT/a	18/20	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.491373294620248	2		284	426	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	141	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.854764451003036	2		280	285	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0004257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	270	354	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.854764451003036	1	FACETS	0.965	0.927	1	0.965	0.927	1	CLONAL	1	TRUE	0	0.854764451003036	1		354	375	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0004257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	151	145	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.854764451003036	2		145	341	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0004257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	473	538	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	0.968	0.928	1	0.968	0.928	1	CLONAL	1	TRUE	1	0.854764451003036	2		538	1143	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483868	88483868	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	444	215	1	ENST00000360948.2:c.1702C>T	p.Leu568Phe	p.L568F	ENST00000360948	NM_001012338.2	568	Ctt/Ttt	14/19	1	2	FACETS	0.99	0.948	1	0.99	0.948	1	CLONAL	1	TRUE	1	0.854764451003036	2		216	1049	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223371	2223371	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1469586549	NA	P-0004257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	617	355	0	ENST00000398665.3:c.3482A>G	p.Asp1161Gly	p.D1161G	ENST00000398665	NM_032482.2	1161	gAc/gGc	25/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.854764451003036	2		355	1402	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652036	36652037	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGTCACCGAGAC	novel	NA	P-0004257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	360	243	0	ENST00000244741.5:c.159_170dup	p.Val54_Thr57dup	p.V54_T57dup	ENST00000244741	NM_000389.4	54	ttt/ttTGTCACCGAGACt	2/3	1	2	FACETS	0.749	0.71	0.788	0.749	0.71	0.788	SUBCLONAL	1	TRUE	1	0.854764451003036	2		243	1125	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373157	118373157	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	624	324	0	ENST00000534358.1:c.6551del	p.Pro2184LeufsTer29	p.P2184Lfs*29	ENST00000534358	NM_005933.3	2184	Cct/ct	27/36	1	2	FACETS	0.981	0.946	1	0.981	0.946	1	CLONAL	1	TRUE	1	0.854764451003036	2		324	1488	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929443	44929449	+	frameshift_variant	Frame_Shift_Del	DEL	ACAGTGG	ACAGTGG	-	novel	NA	P-0004257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	678	389	0	ENST00000377967.4:c.2543_2549del	p.His848ArgfsTer17	p.H848Rfs*17	ENST00000377967	NM_021140.2	848	cACAGTGGg/cg	17/29	1	2	FACETS	0.921	0.888	0.954	0.921	0.888	0.954	CLONAL	1	TRUE	1	0.854764451003036	2		389	1722	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004257-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	52	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.911	0.792	1	0.911	0.792	1	CLONAL	1	TRUE	1	0.731928180486766	2		280	156	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0004257-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	135	354	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.731928180486766	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.731928180486766	1		354	223	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0004257-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	140	145	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.981	0.903	1	0.981	0.903	1	CLONAL	1	TRUE	1	0.731928180486766	2		145	390	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0004257-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	199	538	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	1	2	FACETS	0.983	0.918	1	0.983	0.918	1	CLONAL	1	TRUE	1	0.731928180486766	2		538	553	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483868	88483868	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004257-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	241	215	1	ENST00000360948.2:c.1702C>T	p.Leu568Phe	p.L568F	ENST00000360948	NM_001012338.2	568	Ctt/Ttt	14/19	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.731928180486766	2		216	555	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2223371	2223371	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1469586549	NA	P-0004257-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	238	355	0	ENST00000398665.3:c.3482A>G	p.Asp1161Gly	p.D1161G	ENST00000398665	NM_032482.2	1161	gAc/gGc	25/28	1	2	FACETS	0.997	0.937	1	0.997	0.937	1	CLONAL	1	TRUE	1	0.731928180486766	2		355	652	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652036	36652037	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGTCACCGAGAC	novel	NA	P-0004257-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	187	243	0	ENST00000244741.5:c.159_170dup	p.Val54_Thr57dup	p.V54_T57dup	ENST00000244741	NM_000389.4	54	ttt/ttTGTCACCGAGACt	2/3	0.220908070543685	3	FACETS	1	0.982	1	0.588	0.546	0.63	INDETERMINATE	1	TRUE	1	0.731928180486766	3		243	594	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373157	118373157	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004257-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	266	324	0	ENST00000534358.1:c.6551del	p.Pro2184LeufsTer29	p.P2184Lfs*29	ENST00000534358	NM_005933.3	2184	Cct/ct	27/36	1	2	FACETS	0.945	0.89	1	0.945	0.89	1	CLONAL	1	TRUE	1	0.731928180486766	2		324	769	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929443	44929449	+	frameshift_variant	Frame_Shift_Del	DEL	ACAGTGG	ACAGTGG	-	novel	NA	P-0004257-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	344	389	0	ENST00000377967.4:c.2543_2549del	p.His848ArgfsTer17	p.H848Rfs*17	ENST00000377967	NM_021140.2	848	cACAGTGGg/cg	17/29	0.1528966300563	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.731928180486766	0		389	890	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	60	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.811869395291042	2		280	146	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578437	7578437	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882001	NA	P-0004267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	244	202	0	ENST00000269305.4:c.493C>T	p.Gln165Ter	p.Q165*	ENST00000269305	NM_001126112.2	165	Cag/Tag	5/11	NA	2	FACETS	0.948	0.912	0.982			1	INDETERMINATE	2	TRUE	NA	0.811869395291042	2		202	317	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628176	187628176	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004267-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	205	321	0	ENST00000441802.2:c.2806G>A	p.Val936Ile	p.V936I	ENST00000441802	NM_005245.3	936	Gtc/Atc	2/27	1	2	FACETS	0.951	0.89	1	0.951	0.89	1	CLONAL	1	TRUE	1	0.811869395291042	2		321	531	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182152	99182152	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004286-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	45	280	0	ENST00000074304.5:c.2217G>C	p.Leu739Phe	p.L739F	ENST00000074304	NM_001134224.1	739	ttG/ttC	21/26	0.194085971296224	2	FACETS	0.659	0.553	0.776	0.329	0.276	0.388	SUBCLONAL	1	TRUE	0	0.258719361730664	2		280	528	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755620	57755620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004286-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	88	212	1	ENST00000274289.3:c.167C>T	p.Pro56Leu	p.P56L	ENST00000274289	NM_006622.3	56	cCt/cTt	1/14	1	2	FACETS	0.838	0.747	0.934	1	0.983	1	CLONAL	2	TRUE	1	0.258719361730664	2		213	406	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971138	21971138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760640852	NA	P-0004286-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	27	51	0	ENST00000304494.5:c.220G>A	p.Asp74Asn	p.D74N	ENST00000304494	NM_000077.4	74	Gac/Aac	2/3	0.258719361730664	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.258719361730664	1		51	128	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420164	49420164	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004286-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	60	273	0	ENST00000301067.7:c.15585G>C	p.Gln5195His	p.Q5195H	ENST00000301067	NM_003482.3	5195	caG/caC	48/54	1	2	FACETS	0.878	0.757	1	0.878	0.757	1	CLONAL	1	TRUE	1	0.258719361730664	2		273	528	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523581	41523581	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004286-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	116	263	0	ENST00000263253.7:c.997G>C	p.Glu333Gln	p.E333Q	ENST00000263253	NM_001429.3	333	Gag/Cag	4/31	0.179568782098609	3	FACETS	0.759	0.685	0.837	0.506	0.457	0.558	SUBCLONAL	2	TRUE	0	0.258719361730664	3		263	667	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574023	7574023	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004286-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	159	337	0	ENST00000269305.4:c.1004del	p.Arg335LeufsTer10	p.R335Lfs*10	ENST00000269305	NM_001126112.2	335	cGt/ct	10/11	0.246699757894997	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	2	TRUE	0	0.258719361730664	2		337	611	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220377	1220378	+	missense_variant	Missense_Mutation	DNP	TC	TC	AT	novel	NA	P-0004286-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	93	208	0	ENST00000326873.7:c.470_471delinsAT	p.Phe157Tyr	p.F157Y	ENST00000326873	NM_000455.4	157	tTC/tAT	4/10	0.194085971296224	2	FACETS	1	0.98	1	0.734	0.655	0.817	CLONAL	1	TRUE	0	0.258719361730664	2		208	490	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	51	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.6	2		280	128	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952146	178952147	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587776802	NA	P-0004320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	138	242	0	ENST00000263967.3:c.3203dup	p.Asn1068LysfsTer5	p.N1068Kfs*5	ENST00000263967	NM_006218.2	1067	-/A	21/21	1	2	FACETS	0.857	0.784	0.932	0.857	0.784	0.932	CLONAL	1	TRUE	1	0.6	2		242	537	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004329-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	40	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.38980419010507	2		280	175	SUCCESS
APC	324	MSKCC	GRCh37	5	112154721	112154721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745918184	NA	P-0004329-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	80	366	0	ENST00000257430.4:c.992C>T	p.Ser331Leu	p.S331L	ENST00000257430	NM_000038.5	331	tCg/tTg	10/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.38980419010507	2		366	366	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370717	55370717	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004329-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	99	201	0	ENST00000297316.4:c.19G>C	p.Gly7Arg	p.G7R	ENST00000297316	NM_022454.3	7	Gga/Cga	1/2	NA	2	FACETS	1	0.968	1			1	INDETERMINATE	2	TRUE	NA	0.38980419010507	2		201	223	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165761	118165761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	31	348	0	ENST00000369448.3:c.271C>A	p.Leu91Met	p.L91M	ENST00000369448	NM_017709.3	91	Ctg/Atg	2/2	1	2	FACETS	0.482	0.389	0.587	0.482	0.389	0.587	SUBCLONAL	1	TRUE	1	0.31	2		348	415	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225343000	225343000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371342121	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	104	750	0	ENST00000264414.4:c.2092G>A	p.Asp698Asn	p.D698N	ENST00000264414	NM_003590.4	698	Gac/Aac	15/16	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.31	2		750	629	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691872	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs762282124	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	45	393	1	ENST00000295754.5:c.374A>G	p.Glu125Gly	p.E125G	ENST00000295754	NM_003242.5	125	gAa/gGa	3/7	1	2	FACETS	0.51	0.428	0.601	0.51	0.428	0.601	SUBCLONAL	1	TRUE	1	0.31	2		394	569	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164828	47164828	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764693453	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	73	419	0	ENST00000409792.3:c.1298G>A	p.Arg433His	p.R433H	ENST00000409792	NM_014159.6	433	cGc/cAc	3/21	1	2	FACETS	0.869	0.761	0.985	0.869	0.761	0.985	CLONAL	1	TRUE	1	0.31	2		419	542	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651369	52651369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554214396	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	103	640	0	ENST00000394830.3:c.1727G>A	p.Arg576His	p.R576H	ENST00000394830	NM_018313.4	576	cGc/cAc	15/30	1	2	FACETS	0.992	0.889	1	0.992	0.889	1	CLONAL	1	TRUE	1	0.31	2		640	670	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204848	128204848	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745726293	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	91	594	0	ENST00000341105.2:c.593C>T	p.Ala198Val	p.A198V	ENST00000341105	NM_032638.4	198	gCg/gTg	3/6	1	2	FACETS	0.902	0.801	1	0.902	0.801	1	CLONAL	1	TRUE	1	0.31	2		594	651	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916891	178916891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793663	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	94	725	1	ENST00000263967.3:c.278G>A	p.Arg93Gln	p.R93Q	ENST00000263967	NM_006218.2	93	cGg/cAg	2/21	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.31	2		726	592	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921446	178921446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780572147	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	65	599	0	ENST00000263967.3:c.928C>T	p.Arg310Cys	p.R310C	ENST00000263967	NM_006218.2	310	Cgc/Tgc	5/21	1	2	FACETS	0.84	0.73	0.96	0.84	0.73	0.96	CLONAL	1	TRUE	1	0.31	2		599	499	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	45	236	0	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	1	0.858	1	1	0.858	1	CLONAL	1	TRUE	1	0.31	2		236	286	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1805516	1805516	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	114	570	0	ENST00000260795.2:c.1028A>T	p.Asn343Ile	p.N343I	ENST00000260795		343	aAt/aTt	7/17	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.31	2		570	626	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807288	1807288	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs121913112	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	79	467	0	ENST00000260795.2:c.1537G>A	p.Asp513Asn	p.D513N	ENST00000260795		513	Gat/Aat	11/17	1	2	FACETS	0.865	0.762	0.976	0.865	0.762	0.976	CLONAL	1	TRUE	1	0.31	2		467	589	SUCCESS
APC	324	MSKCC	GRCh37	5	112179084	112179084	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	74	384	0	ENST00000257430.4:c.7793C>T	p.Thr2598Ile	p.T2598I	ENST00000257430	NM_000038.5	2598	aCc/aTc	16/16	1	2	FACETS	0.931	0.816	1	0.931	0.816	1	CLONAL	1	TRUE	1	0.31	2		384	513	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638491	176638491	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587784096	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	102	511	0	ENST00000439151.2:c.3091C>T	p.Arg1031Ter	p.R1031*	ENST00000439151	NM_022455.4	1031	Cga/Tga	5/23	0.3	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.31	1		511	528	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	395910	395910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755460615	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	69	484	0	ENST00000380956.4:c.467C>T	p.Thr156Met	p.T156M	ENST00000380956	NM_001195286.1	156	aCg/aTg	4/9	1	2	FACETS	0.823	0.718	0.936	0.823	0.718	0.936	CLONAL	1	TRUE	1	0.31	2		484	541	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748552	43748552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774318829	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	85	624	1	ENST00000523873.1:c.506C>T	p.Ala169Val	p.A169V	ENST00000523873		169	gCc/gTc	6/8	1	2	FACETS	0.809	0.715	0.909	0.809	0.715	0.909	CLONAL	1	TRUE	1	0.31	2		625	678	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420091	152420091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	52	296	0	ENST00000206249.3:c.1778C>T	p.Ala593Val	p.A593V	ENST00000206249	NM_000125.3	593	gCc/gTc	8/8	1	2	FACETS	0.814	0.695	0.944	0.814	0.695	0.944	CLONAL	1	TRUE	1	0.31	2		296	412	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527695	157527695	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	62	382	0	ENST00000346085.5:c.5420G>T	p.Gly1807Val	p.G1807V	ENST00000346085	NM_020732.3	1807	gGg/gTg	20/20	1	2	FACETS	0.784	0.678	0.899	0.784	0.678	0.899	SUBCLONAL	1	TRUE	1	0.31	2		382	510	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148543650	148543650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768812143	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	71	461	0	ENST00000320356.2:c.158C>T	p.Thr53Met	p.T53M	ENST00000320356	NM_004456.4	53	aCg/aTg	3/20	1	2	FACETS	0.896	0.784	1	0.896	0.784	1	CLONAL	1	TRUE	1	0.31	2		461	511	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93657821	93657821	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	79	431	0	ENST00000375746.1:c.1847G>T	p.Arg616Met	p.R616M	ENST00000375746	NM_001174167.1	616	aGg/aTg	14/14	1	2	FACETS	0.951	0.838	1	0.951	0.838	1	CLONAL	1	TRUE	1	0.31	2		431	536	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133730335	133730335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	74	412	1	ENST00000318560.5:c.401G>A	p.Arg134His	p.R134H	ENST00000318560	NM_005157.4	134	cGc/cAc	3/11	1	2	FACETS	0.934	0.82	1	0.934	0.82	1	CLONAL	1	TRUE	1	0.31	2		413	511	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391404	139391404	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770022692	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	73	358	0	ENST00000277541.6:c.6787C>T	p.Arg2263Trp	p.R2263W	ENST00000277541	NM_017617.3	2263	Cgg/Tgg	34/34	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.31	2		358	375	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396253	139396253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754163232	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	96	505	0	ENST00000277541.6:c.5585C>T	p.Pro1862Leu	p.P1862L	ENST00000277541	NM_017617.3	1862	cCg/cTg	30/34	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.31	2		505	572	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404312	139404312	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	89	517	0	ENST00000277541.6:c.2842G>A	p.Glu948Lys	p.E948K	ENST00000277541	NM_017617.3	948	Gag/Aag	18/34	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.31	2		517	561	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139794922	139794922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs551577118	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	127	701	1	ENST00000247668.2:c.316G>A	p.Val106Ile	p.V106I	ENST00000247668	NM_021138.3	106	Gtc/Atc	4/11	0.260876876604428	1	FACETS	0.932	0.845	1	0.932	0.845	1	CLONAL	1	TRUE	0	0.31	1		702	743	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279681	123279681	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	44	187	0	ENST00000358487.5:c.751C>T	p.Arg251Ter	p.R251*	ENST00000358487	NM_000141.4	251	Cga/Tga	7/18	0.209505966728125	1	FACETS	0.995	0.842	1	0.995	0.842	1	CLONAL	1	TRUE	0	0.31	1		187	241	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8252028	8252028	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754674404	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	58	401	0	ENST00000335790.3:c.49C>T	p.Pro17Ser	p.P17S	ENST00000335790	NM_002315.2	17	Ccc/Tcc	2/4	1	2	FACETS	0.974	0.841	1	0.974	0.841	1	CLONAL	1	TRUE	1	0.31	2		401	384	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138825	64138825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1388266879	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	82	412	2	ENST00000334205.4:c.2192G>A	p.Arg731Gln	p.R731Q	ENST00000334205	NM_003942.2	731	cGg/cAg	17/17	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.31	2		414	484	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944913	31944913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	49	320	0	ENST00000340398.3:c.188G>A	p.Arg63Gln	p.R63Q	ENST00000340398	NM_001013699.2	63	cGg/cAg	1/1	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.31	2		320	288	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420688	49420688	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783695	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	68	330	1	ENST00000301067.7:c.15061C>T	p.Arg5021Ter	p.R5021*	ENST00000301067	NM_003482.3	5021	Cga/Tga	48/54	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.31	2		331	438	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436599	49436599	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886041405	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	96	528	0	ENST00000301067.7:c.5707C>T	p.Arg1903Ter	p.R1903*	ENST00000301067	NM_003482.3	1903	Cga/Tga	26/54	1	2	FACETS	0.93	0.829	1	0.93	0.829	1	CLONAL	1	TRUE	1	0.31	2		528	666	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49441822	49441822	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767110613	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	108	503	1	ENST00000301067.7:c.4162C>T	p.Arg1388Trp	p.R1388W	ENST00000301067	NM_003482.3	1388	Cgg/Tgg	14/54	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.31	2		504	649	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	123	960	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.31	2		960	721	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494908	56494908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs551223118	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	82	396	0	ENST00000267101.3:c.3265C>T	p.Arg1089Trp	p.R1089W	ENST00000267101	NM_001982.3	1089	Cgg/Tgg	27/28	1	2	FACETS	0.936	0.827	1	0.936	0.827	1	CLONAL	1	TRUE	1	0.31	2		396	565	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495034	56495034	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150312718	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	91	451	0	ENST00000267101.3:c.3391G>A	p.Ala1131Thr	p.A1131T	ENST00000267101	NM_001982.3	1131	Gcc/Acc	27/28	1	2	FACETS	0.964	0.857	1	0.964	0.857	1	CLONAL	1	TRUE	1	0.31	2		451	609	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924336	112924336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507536	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	99	455	0	ENST00000351677.2:c.1282G>A	p.Val428Met	p.V428M	ENST00000351677	NM_002834.3	428	Gtg/Atg	11/16	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.31	2		455	569	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214706	133214706	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1193081581	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	68	374	0	ENST00000320574.5:c.5572C>T	p.Arg1858Cys	p.R1858C	ENST00000320574	NM_006231.2	1858	Cgc/Tgc	41/49	1	2	FACETS	0.988	0.862	1	0.988	0.862	1	CLONAL	1	TRUE	1	0.31	2		374	444	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133237718	133237718	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	83	536	0	ENST00000320574.5:c.2897C>T	p.Ala966Val	p.A966V	ENST00000320574	NM_006231.2	966	gCt/gTt	25/49	1	2	FACETS	0.903	0.798	1	0.903	0.798	1	CLONAL	1	TRUE	1	0.31	2		536	593	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563294	21563294	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1249786123	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	78	515	0	ENST00000382592.4:c.625C>T	p.Arg209Trp	p.R209W	ENST00000382592	NM_014572.2	209	Cgg/Tgg	4/8	1	2	FACETS	0.987	0.869	1	0.987	0.869	1	CLONAL	1	TRUE	1	0.31	2		515	510	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134142	41134142	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144907712	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	101	669	0	ENST00000379561.5:c.1486G>A	p.Val496Ile	p.V496I	ENST00000379561	NM_002015.3	496	Gtc/Atc	2/3	1	2	FACETS	0.992	0.888	1	0.992	0.888	1	CLONAL	1	TRUE	1	0.31	2		669	657	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437493	110437493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749782460	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	43	325	0	ENST00000375856.3:c.908G>A	p.Arg303His	p.R303H	ENST00000375856	NM_003749.2	303	cGc/cAc	1/2	1	2	FACETS	0.692	0.58	0.815	0.692	0.58	0.815	SUBCLONAL	1	TRUE	1	0.31	2		325	401	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438250	110438250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1345817777	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	15	57	0	ENST00000375856.3:c.151C>T	p.Arg51Cys	p.R51C	ENST00000375856	NM_003749.2	51	Cgc/Tgc	1/2	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.31	2		57	65	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609940	81609940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142814218	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	66	385	1	ENST00000298171.2:c.1538C>T	p.Thr513Met	p.T513M	ENST00000298171	NM_000369.2	513	aCg/aTg	10/10	1	2	FACETS	0.887	0.772	1	0.887	0.772	1	CLONAL	1	TRUE	1	0.31	2		386	480	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221594	2221594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766294780	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	111	501	3	ENST00000326181.6:c.463G>A	p.Ala155Thr	p.A155T	ENST00000326181	NM_032271.2	155	Gcc/Acc	7/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.31	2		504	603	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790455	3790455	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783490	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	100	518	0	ENST00000262367.5:c.4078C>T	p.Arg1360Ter	p.R1360*	ENST00000262367	NM_004380.2	1360	Cga/Tga	24/31	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.31	2		518	621	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843495	3843495	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	107	899	2	ENST00000262367.5:c.1108C>T	p.Arg370Ter	p.R370*	ENST00000262367	NM_004380.2	370	Cga/Tga	4/31	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.31	2		901	600	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662303	67662303	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	74	475	0	ENST00000264010.4:c.1549C>A	p.His517Asn	p.H517N	ENST00000264010	NM_006565.3	517	Cac/Aac	9/12	1	2	FACETS	0.874	0.767	0.99	0.874	0.767	0.99	CLONAL	1	TRUE	1	0.31	2		475	546	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663349	67663349	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	91	446	0	ENST00000264010.4:c.1750G>T	p.Glu584Ter	p.E584*	ENST00000264010	NM_006565.3	584	Gag/Tag	10/12	1	2	FACETS	0.98	0.872	1	0.98	0.872	1	CLONAL	1	TRUE	1	0.31	2		446	599	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993996	72993996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376729347	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	102	641	0	ENST00000268489.5:c.49G>A	p.Gly17Ser	p.G17S	ENST00000268489	NM_006885.3	17	Ggt/Agt	2/10	0.273024401677554	1	FACETS	0.79	0.707	0.878	0.79	0.707	0.878	SUBCLONAL	1	TRUE	0	0.31	1		641	704	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346507	89346507	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	99	680	0	ENST00000301030.4:c.6443C>A	p.Ala2148Asp	p.A2148D	ENST00000301030	NM_001256183.1	2148	gCc/gAc	9/13	0.273024401677554	1	FACETS	0.774	0.692	0.862	0.774	0.692	0.862	SUBCLONAL	1	TRUE	0	0.31	1		680	697	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346820	89346820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372141194	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	60	440	0	ENST00000301030.4:c.6130G>A	p.Val2044Ile	p.V2044I	ENST00000301030	NM_001256183.1	2044	Gtc/Atc	9/13	0.273024401677554	1	FACETS	0.832	0.72	0.954	0.832	0.72	0.954	CLONAL	1	TRUE	0	0.31	1		440	393	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351994	89351994	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745932163	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	115	775	1	ENST00000301030.4:c.956C>T	p.Thr319Met	p.T319M	ENST00000301030	NM_001256183.1	319	aCg/aTg	9/13	0.273024401677554	1	FACETS	0.835	0.752	0.922	0.835	0.752	0.922	CLONAL	1	TRUE	0	0.31	1		776	751	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805074	89805074	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs74977201	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	80	411	2	ENST00000389301.3:c.4303G>A	p.Ala1435Thr	p.A1435T	ENST00000389301	NM_000135.2	1435	Gcc/Acc	43/43	NA	2	FACETS	1	0.896	1			1	INDETERMINATE	1	TRUE	NA	0.31	2		413	508	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7978988	7978988	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199545653	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	100	554	0	ENST00000319144.4:c.1579G>A	p.Val527Met	p.V527M	ENST00000319144	NM_001139.2	527	Gtg/Atg	12/15	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.31	2		554	636	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17120493	17120493	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	50	379	0	ENST00000285071.4:c.1066C>A	p.Leu356Met	p.L356M	ENST00000285071	NM_144997.5	356	Ctg/Atg	10/14	1	2	FACETS	0.717	0.609	0.835	0.717	0.609	0.835	SUBCLONAL	1	TRUE	1	0.31	2		379	450	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487510	38487510	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567751372	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	70	462	0	ENST00000254066.5:c.40G>A	p.Gly14Arg	p.G14R	ENST00000254066	NM_000964.3	14	Ggg/Agg	2/9	1	2	FACETS	0.847	0.74	0.963	0.847	0.74	0.963	CLONAL	1	TRUE	1	0.31	2		462	533	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533844	63533844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	65	418	0	ENST00000307078.5:c.1310C>T	p.Thr437Met	p.T437M	ENST00000307078	NM_004655.3	437	aCg/aTg	6/11	0.294519267922973	3	FACETS	0.939	0.815	1	0.469	0.407	0.536	CLONAL	1	TRUE	1	0.31	3		418	516	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276250	15276250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747223569	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	110	538	2	ENST00000263388.2:c.5744G>A	p.Arg1915His	p.R1915H	ENST00000263388	NM_000435.2	1915	cGc/cAc	31/33	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.31	2		540	627	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281232	15281232	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	88	479	0	ENST00000263388.2:c.5024G>A	p.Trp1675Ter	p.W1675*	ENST00000263388	NM_000435.2	1675	tGg/tAg	27/33	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.31	2		479	531	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272814	18272814	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	137	532	0	ENST00000222254.8:c.854A>G	p.Glu285Gly	p.E285G	ENST00000222254	NM_005027.3	285	gAg/gGg	7/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.31	2		532	672	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944593	40944593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	60	290	0	ENST00000373198.4:c.1909C>T	p.Arg637Trp	p.R637W	ENST00000373198	NM_133170.3	637	Cgg/Tgg	12/32	0.273024401677554	1	FACETS	0.929	0.805	1	0.929	0.805	1	CLONAL	1	TRUE	0	0.31	1		290	352	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121018	29121018	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137853009	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	109	681	2	ENST00000328354.6:c.539G>A	p.Arg180His	p.R180H	ENST00000328354	NM_007194.3	180	cGc/cAc	4/15	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.31	2		683	659	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410102	63410102	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761242587	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	92	291	0	ENST00000330258.3:c.3065G>A	p.Arg1022His	p.R1022H	ENST00000330258	NM_152424.3	1022	cGt/cAt	2/2	1	1	FACETS	0.919	0.828	1	1	0.986	1	CLONAL	2	TRUE	0	0.31	1		291	273	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874315	76874315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	89	356	0	ENST00000373344.5:c.5407C>T	p.Arg1803Cys	p.R1803C	ENST00000373344	NM_000489.3	1803	Cgt/Tgt	21/35	1	1	FACETS	1	0.952	1	1	0.988	1	CLONAL	2	TRUE	0	0.31	1		356	223	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197044	123197044	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	67	315	0	ENST00000218089.9:c.1810C>T	p.Arg604Ter	p.R604*	ENST00000218089	NM_001042749.1	604	Cga/Tga	19/35	1	1	FACETS	0.767	0.676	0.864	1	0.976	1	SUBCLONAL	2	TRUE	0	0.31	1		315	238	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595549	55595550	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004330-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	50	514	0	ENST00000288135.5:c.2045dup	p.Leu682PhefsTer6	p.L682Ffs*6	ENST00000288135	NM_000222.2	680	aat/aaTt	14/21	1	2	FACETS	0.766	0.651	0.892	0.766	0.651	0.892	SUBCLONAL	1	TRUE	1	0.31	2		514	421	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0004348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	49	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.831	0.709	0.963	0.831	0.709	0.963	CLONAL	1	FALSE	1	0.432054369876789	2		464	273	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467675	50467675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759124417	NA	P-0004348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	100	499	0	ENST00000331340.3:c.910G>A	p.Glu304Lys	p.E304K	ENST00000331340	NM_006060.4	304	Gaa/Aaa	8/8	0.384636420346065	4	FACETS	0.984	0.879	1	0.328	0.293	0.365	CLONAL	1	FALSE	1	0.432054369876789	4		499	674	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166421	118166421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775789017	NA	P-0004348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	82	308	0	ENST00000369448.3:c.931C>T	p.Arg311Cys	p.R311C	ENST00000369448	NM_017709.3	311	Cgc/Tgc	2/2	1	2	FACETS	0.928	0.823	1	0.928	0.823	1	CLONAL	1	FALSE	1	0.432054369876789	2		308	409	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484375	120484375	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	55	208	0	ENST00000256646.2:c.2755C>T	p.Pro919Ser	p.P919S	ENST00000256646	NM_024408.3	919	Cct/Tct	18/34	1	2	FACETS	0.675	0.58	0.779	0.675	0.58	0.779	SUBCLONAL	1	FALSE	1	0.432054369876789	2		208	377	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243668576	243668576	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	80	249	0	ENST00000263826.5:c.1415C>T	p.Ser472Phe	p.S472F	ENST00000263826	NM_005465.4	472	tCc/tTc	13/13	1	2	FACETS	0.993	0.88	1	0.993	0.88	1	CLONAL	1	FALSE	1	0.432054369876789	2		249	373	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356251	66356251	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	63	421	1	ENST00000273854.3:c.1246C>T	p.Pro416Ser	p.P416S	ENST00000273854	NM_004439.5	416	Ccc/Tcc	5/18	0.388963552050663	1	FACETS	0.742	0.647	0.844	0.742	0.647	0.844	SUBCLONAL	1	FALSE	0	0.432054369876789	1		422	308	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534467	187534467	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375998390	NA	P-0004348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	67	211	0	ENST00000441802.2:c.9259C>T	p.Arg3087Cys	p.R3087C	ENST00000441802	NM_005245.3	3087	Cgt/Tgt	13/27	1	2	FACETS	0.931	0.815	1	0.931	0.815	1	CLONAL	1	FALSE	1	0.432054369876789	2		211	333	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638974	176638974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	80	272	0	ENST00000439151.2:c.3574C>T	p.Pro1192Ser	p.P1192S	ENST00000439151	NM_022455.4	1192	Cct/Tct	5/23	1	2	FACETS	0.88	0.778	0.987	0.88	0.778	0.987	CLONAL	1	FALSE	1	0.432054369876789	2		272	421	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288278	33288278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	123	311	0	ENST00000374542.5:c.1130C>T	p.Ser377Phe	p.S377F	ENST00000374542	NM_001141970.1	377	tCc/tTc	4/8	0.432054369876789	5	FACETS	1	0.978	1	0.424	0.383	0.466	CLONAL	1	FALSE	2	0.432054369876789	5		311	738	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983093	111983093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771152377	NA	P-0004348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	71	424	0	ENST00000368678.4:c.1454C>T	p.Pro485Leu	p.P485L	ENST00000368678		485	cCg/cTg	13/13	0.279122407432463	0	FACETS	0.396	0.347	0.45			1	SUBCLONAL	1	FALSE	0	0.432054369876789	0		424	471	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386535	81386535	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	60	342	0	ENST00000222390.5:c.452C>T	p.Pro151Leu	p.P151L	ENST00000222390	NM_000601.4	151	cCc/cTc	4/18	0.384636420346065	4	FACETS	0.837	0.723	0.962	0.279	0.241	0.321	CLONAL	1	FALSE	1	0.432054369876789	4		342	475	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453145	140453145	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913366	NA	P-0004348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	207	235	0	ENST00000288602.6:c.1790T>A	p.Leu597Gln	p.L597Q	ENST00000288602	NM_004333.4	597	cTa/cAa	15/18	0.384636420346065	4	FACETS	0.908	0.85	0.965	0.908	0.85	0.965	CLONAL	3	FALSE	1	0.432054369876789	4		235	504	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494149	140494149	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	208	373	0	ENST00000288602.6:c.1099C>T	p.Pro367Ser	p.P367S	ENST00000288602	NM_004333.4	367	Ccc/Tcc	8/18	0.384636420346065	4	FACETS	0.875	0.82	0.932	0.875	0.82	0.932	CLONAL	3	FALSE	1	0.432054369876789	4		373	525	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229649	98229649	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762942660	NA	P-0004348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	66	221	0	ENST00000331920.6:c.2309G>A	p.Arg770Gln	p.R770Q	ENST00000331920	NM_000264.3	770	cGa/cAa	15/24	1	2	FACETS	0.923	0.807	1	0.923	0.807	1	CLONAL	1	FALSE	1	0.432054369876789	2		221	331	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123325105	123325105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	64	374	0	ENST00000358487.5:c.223G>A	p.Asp75Asn	p.D75N	ENST00000358487	NM_000141.4	75	Gat/Aat	3/18	0.388963552050663	1	FACETS	0.685	0.597	0.779	0.685	0.597	0.779	SUBCLONAL	1	FALSE	0	0.432054369876789	1		374	339	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359419	118359419	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	102	266	0	ENST00000534358.1:c.4423T>C	p.Cys1475Arg	p.C1475R	ENST00000534358	NM_005933.3	1475	Tgt/Cgt	11/36	1	2	FACETS	0.912	0.818	1	0.912	0.818	1	CLONAL	1	FALSE	1	0.432054369876789	2		266	518	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793483	18793483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603405	NA	P-0004348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	67	480	0	ENST00000266497.5:c.4180G>A	p.Glu1394Lys	p.E1394K	ENST00000266497		1394	Gaa/Aaa	30/31	0.398035381770758	1	FACETS	0.739	0.647	0.837	0.739	0.647	0.837	SUBCLONAL	1	FALSE	0	0.432054369876789	1		480	329	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23632749	23632749	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	59	296	0	ENST00000261584.4:c.3047T>A	p.Phe1016Tyr	p.F1016Y	ENST00000261584	NM_024675.3	1016	tTt/tAt	10/13	1	2	FACETS	0.607	0.523	0.698	0.607	0.523	0.698	SUBCLONAL	1	FALSE	1	0.432054369876789	2		296	450	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351379	89351379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1040338311	NA	P-0004348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	123	531	0	ENST00000301030.4:c.1571C>T	p.Ser524Leu	p.S524L	ENST00000301030	NM_001256183.1	524	tCg/tTg	9/13	0.250247966934083	0	FACETS	0.651	0.591	0.712			1	INDETERMINATE	1	FALSE	0	0.432054369876789	0		531	497	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118607	17118607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	115	264	0	ENST00000285071.4:c.1324C>T	p.His442Tyr	p.H442Y	ENST00000285071	NM_144997.5	442	Cac/Tac	12/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.432054369876789	2		264	411	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226673	2226673	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761864765	NA	P-0004348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	88	212	0	ENST00000398665.3:c.4153C>T	p.Arg1385Cys	p.R1385C	ENST00000398665	NM_032482.2	1385	Cgc/Tgc	27/28	1	2	FACETS	0.811	0.721	0.907	0.811	0.721	0.907	CLONAL	1	FALSE	1	0.432054369876789	2		212	502	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267673	7267673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	81	174	0	ENST00000302850.5:c.335C>T	p.Ser112Leu	p.S112L	ENST00000302850	NM_000208.2	112	tCa/tTa	2/22	1	2	FACETS	0.966	0.857	1	0.966	0.857	1	CLONAL	1	FALSE	1	0.432054369876789	2		174	388	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47004909	47004909	+	intron_variant	Intron	SNP	G	G	A	novel	NA	P-0004348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	104	275	0	ENST00000377604.3:c.-126+25G>A		p.*42*	ENST00000377604	NM_001204468.1	-/852			0.223898961409293	0	FACETS	0.487	0.437	0.539			1	INDETERMINATE	1	FALSE	0	0.432054369876789	0		275	562	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266093	41266096	+	frameshift_variant	Frame_Shift_Del	DEL	CCTG	CCTG	-	novel	NA	P-0004348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	76	292	0	ENST00000349496.5:c.90_93del	p.Tyr30Ter	p.Y30*	ENST00000349496	NM_001904.3	30	taCCTG/ta	3/15	1	2	FACETS	0.842	0.742	0.948	0.842	0.742	0.948	CLONAL	1	FALSE	1	0.432054369876789	2		292	418	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453131	140453132	+	missense_variant	Missense_Mutation	DNP	AT	AT	TA	novel	NA	P-0004348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	192	258	0	ENST00000288602.6:c.1803_1804delinsTA	p.Lys601_Ser602delinsAsnThr	p.K601_S602delinsNT	ENST00000288602	NM_004333.4	601	aaATct/aaTAct	15/18	0.384636420346065	4	FACETS	1	0.987	1	0.822	0.767	0.879	CLONAL	2	FALSE	1	0.432054369876789	4		258	516	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0004370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	84	464	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.931	1			1	INDETERMINATE	1	TRUE	NA	0.930807371214521	2		464	175	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0004370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	296	511	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.933	0.884	0.981	0.933	0.884	0.981	CLONAL	1	TRUE	1	0.930807371214521	2		512	682	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589581	67589583	+	inframe_deletion	In_Frame_Del	DEL	ATT	ATT	-	novel	NA	P-0004370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	268	315	0	ENST00000274335.5:c.1345_1347del	p.Leu449del	p.L449del	ENST00000274335		448	aaATTa/aaa	10/15	1	2	FACETS	0.614	0.577	0.652	0.614	0.577	0.652	SUBCLONAL	1	TRUE	1	0.930807371214521	2		315	938	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791757	42791757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568504941	NA	P-0004370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	94	671	0	ENST00000575354.2:c.643C>T	p.Arg215Trp	p.R215W	ENST00000575354	NM_015125.3	215	Cgg/Tgg	5/20	0.87888735799012	1	FACETS	0.321	0.288	0.356	0.321	0.288	0.356	SUBCLONAL	1	TRUE	0	0.930807371214521	1		671	336	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469945	25469945	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs767236033	NA	P-0004370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	78	342	0	ENST00000264709.3:c.1097G>T	p.Arg366Leu	p.R366L	ENST00000264709	NM_175629.2	366	cGc/cTc	9/23	1	2	FACETS	0.313	0.275	0.354	0.313	0.275	0.354	SUBCLONAL	1	TRUE	1	0.930807371214521	2		342	535	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426974	70426974	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	167	314	0	ENST00000373644.4:c.4634A>G	p.Asn1545Ser	p.N1545S	ENST00000373644	NM_030625.2	1545	aAt/aGt	7/12	1	2	FACETS	0.598	0.552	0.646	0.598	0.552	0.646	SUBCLONAL	1	TRUE	1	0.930807371214521	2		314	600	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794752	42794753	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0004370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	219	449	0	ENST00000575354.2:c.1833_1834del	p.Pro612ArgfsTer77	p.P612Rfs*77	ENST00000575354	NM_015125.3	611	cCA/c	10/20	0.87888735799012	1	FACETS	0.695	0.659	0.73	0.695	0.659	0.73	SUBCLONAL	1	TRUE	0	0.930807371214521	1		449	362	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430815	78430822	+	frameshift_variant	Frame_Shift_Del	DEL	TCATGATT	TCATGATT	-	novel	NA	P-0004370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	124	398	0	ENST00000370768.2:c.567_574del	p.Glu189AspfsTer4	p.E189Dfs*4	ENST00000370768	NM_003902.3	189	gaAATCATGAtt/gatt	8/20	0.930807371214521	1	FACETS	0.343	0.313	0.375	0.343	0.313	0.375	SUBCLONAL	1	TRUE	0	0.930807371214521	1		398	415	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15935782	15935782	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	205	438	0	ENST00000268712.3:c.7151C>T	p.Pro2384Leu	p.P2384L	ENST00000268712	NM_006311.3	2384	cCt/cTt	46/46	1	2	FACETS	0.992	0.925	1	0.992	0.925	1	CLONAL	1	TRUE	1	0.64	2		438	646	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023076	150023076	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs187759014	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	192	600	0	ENST00000253339.5:c.187C>T	p.Arg63Ter	p.R63*	ENST00000253339		63	Cga/Tga	1/7	1	2	FACETS	0.98	0.912	1	0.98	0.912	1	CLONAL	1	TRUE	1	0.64	2		600	612	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	125	449	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.64	2		449	389	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920469	134920469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	224	553	0	ENST00000398015.3:c.2284G>A	p.Asp762Asn	p.D762N	ENST00000398015	NM_004441.4	762	Gac/Aac	12/16	1	2	FACETS	0.99	0.926	1	0.99	0.926	1	CLONAL	1	TRUE	1	0.64	2		553	707	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170136	32170136	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771019003	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	229	702	0	ENST00000375023.3:c.3472C>T	p.Arg1158Ter	p.R1158*	ENST00000375023	NM_004557.3	1158	Cga/Tga	21/30	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.64	2		702	676	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120487	2120487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1800729	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	503	656	2	ENST00000219476.3:c.1747G>A	p.Ala583Thr	p.A583T	ENST00000219476	NM_000548.3	583	Gcc/Acc	17/42	1	2	FACETS	1	0.983	1	1	0.998	1	CLONAL	2	TRUE	1	0.64	2		658	768	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342421	70342421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771266719	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	238	489	0	ENST00000374080.3:c.1312C>T	p.Arg438Cys	p.R438C	ENST00000374080		438	Cgc/Tgc	9/45	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.64	2		489	736	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231539	5231539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760884281	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	163	511	2	ENST00000357368.4:c.1937C>T	p.Thr646Met	p.T646M	ENST00000357368	NM_002850.3	646	aCg/aTg	14/38	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.64	2		513	501	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	65	166	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.64	2		166	172	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566507	41566507	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	265	622	2	ENST00000263253.7:c.4384C>T	p.Arg1462Ter	p.R1462*	ENST00000263253	NM_001429.3	1462	Cga/Tga	27/31	1	2	FACETS	0.978	0.919	1	0.978	0.919	1	CLONAL	1	TRUE	1	0.64	2		624	847	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119485	193119485	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	203	547	1	ENST00000367435.3:c.880G>A	p.Asp294Asn	p.D294N	ENST00000367435	NM_024529.4	294	Gat/Aat	9/17	1	2	FACETS	0.948	0.883	1	0.948	0.883	1	CLONAL	1	TRUE	1	0.64	2		548	669	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149251	119149251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267606708	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	261	438	0	ENST00000264033.4:c.1259G>A	p.Arg420Gln	p.R420Q	ENST00000264033	NM_005188.3	420	cGa/cAa	9/16	1	2	FACETS	0.998	0.938	1	0.998	0.938	1	CLONAL	1	TRUE	1	0.64	2		438	817	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	242	508	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.93	0.871	0.99	0.93	0.871	0.99	CLONAL	1	TRUE	1	0.64	2		508	813	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518099	8518099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764400127	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	226	469	1	ENST00000356435.5:c.1292C>T	p.Ser431Leu	p.S431L	ENST00000356435		431	tCg/tTg	10/35	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.64	2		470	698	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845243	151845243	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1323051494	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	207	418	0	ENST00000262189.6:c.13769G>A	p.Arg4590His	p.R4590H	ENST00000262189	NM_170606.2	4590	cGc/cAc	52/59	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.64	2		418	587	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500303	99500303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61740868	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	216	565	1	ENST00000268035.6:c.3736C>T	p.Arg1246Cys	p.R1246C	ENST00000268035	NM_000875.3	1246	Cgc/Tgc	21/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.64	2		566	646	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490382	29490382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754096545	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	185	413	0	ENST00000356175.3:c.467G>A	p.Arg156His	p.R156H	ENST00000356175	NM_000267.3	156	cGc/cAc	4/57	1	2	FACETS	0.906	0.841	0.974	0.906	0.841	0.974	CLONAL	1	TRUE	1	0.64	2		413	638	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900288	101900288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111854391	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	143	279	2	ENST00000374994.4:c.722C>T	p.Ser241Leu	p.S241L	ENST00000374994	NM_004612.2	241	tCg/tTg	4/9	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.64	2		281	419	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137522064	137522064	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	344	370	0	ENST00000367739.4:c.815A>C	p.Lys272Thr	p.K272T	ENST00000367739	NM_000416.2	272	aAa/aCa	6/7	1	2	FACETS	0.986	0.947	1	1	0.997	1	CLONAL	2	TRUE	1	0.64	2		370	545	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982356	25982356	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	149	397	0	ENST00000435504.4:c.934C>T	p.Arg312Ter	p.R312*	ENST00000435504		312	Cga/Tga	9/13	1	2	FACETS	0.836	0.768	0.907	0.836	0.768	0.907	CLONAL	1	TRUE	1	0.64	2		397	557	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	187	459	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	1	2	FACETS	0.968	0.899	1	0.968	0.899	1	CLONAL	1	TRUE	1	0.64	2		459	604	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037474	12037474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	200	322	1	ENST00000396373.4:c.1105C>T	p.Arg369Trp	p.R369W	ENST00000396373	NM_001987.4	369	Cgg/Tgg	6/8	1	2	FACETS	0.977	0.91	1	0.977	0.91	1	CLONAL	1	TRUE	1	0.64	2		323	640	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	144	413	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	1	2	FACETS	0.9	0.826	0.976	0.9	0.826	0.976	CLONAL	1	TRUE	1	0.64	2		413	500	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200387	138200387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760531232	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	152	305	0	ENST00000237289.4:c.1805C>T	p.Thr602Met	p.T602M	ENST00000237289	NM_001270507.1	602	aCg/aTg	7/9	1	2	FACETS	0.956	0.88	1	0.956	0.88	1	CLONAL	1	TRUE	1	0.64	2		305	497	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845086	128845086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761395599	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	243	686	0	ENST00000249373.3:c.580G>A	p.Glu194Lys	p.E194K	ENST00000249373	NM_005631.4	194	Gaa/Aaa	3/12	1	2	FACETS	0.995	0.933	1	0.995	0.933	1	CLONAL	1	TRUE	1	0.64	2		686	763	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58142372	58142372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	219	467	0	ENST00000257904.6:c.848G>A	p.Arg283Gln	p.R283Q	ENST00000257904	NM_000075.3	283	cGa/cAa	8/8	1	2	FACETS	0.979	0.915	1	0.979	0.915	1	CLONAL	1	TRUE	1	0.64	2		467	699	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	213	351	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.64	2		351	626	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573563	48573564	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs786203560	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	129	419	1	ENST00000342988.3:c.153dup	p.Asp52ArgfsTer2	p.D52Rfs*2	ENST00000342988	NM_005359.5	49	-/A	2/12	1	2	FACETS	0.871	0.795	0.949	0.871	0.795	0.949	CLONAL	1	TRUE	1	0.64	2		420	463	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480483	57480483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	193	279	0	ENST00000371085.3:c.478C>T	p.Arg160Cys	p.R160C	ENST00000371085	NM_000516.4	160	Cgt/Tgt	6/13	1	2	FACETS	0.973	0.905	1	0.973	0.905	1	CLONAL	1	TRUE	1	0.64	2		279	620	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119631622	119631622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	109	597	0	ENST00000316626.5:c.644C>T	p.Ser215Leu	p.S215L	ENST00000316626		215	tCg/tTg	6/12	1	2	FACETS	0.852	0.771	0.936	0.852	0.771	0.936	CLONAL	1	TRUE	1	0.64	2		597	400	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512376	149512376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746410632	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	188	531	1	ENST00000261799.4:c.1064G>A	p.Arg355His	p.R355H	ENST00000261799	NM_002609.3	355	cGc/cAc	7/23	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.64	2		532	584	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554008	63554008	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199798353	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	291	460	0	ENST00000307078.5:c.731C>T	p.Ser244Leu	p.S244L	ENST00000307078	NM_004655.3	244	tCg/tTg	2/11	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.64	2		460	825	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003745	45003745	+	start_lost	Translation_Start_Site	SNP	A	A	T	rs1023835002	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	237	438	0	ENST00000558401.1:c.1A>T	p.Met1?	p.M1?	ENST00000558401	NM_004048.2	1	Atg/Ttg	1/4	1	2	FACETS	0.907	0.848	0.966	0.907	0.848	0.966	CLONAL	1	TRUE	1	0.64	2		438	817	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060694	38060694	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	251	855	0	ENST00000250448.2:c.1295C>T	p.Thr432Met	p.T432M	ENST00000250448	NM_004496.3	432	aCg/aTg	2/2	1	2	FACETS	0.953	0.894	1	0.953	0.894	1	CLONAL	1	TRUE	1	0.64	2		855	823	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2491363	2491363	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376398200	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	171	462	0	ENST00000355716.4:c.406G>A	p.Ala136Thr	p.A136T	ENST00000355716	NM_003820.2	136	Gcc/Acc	4/8	1	2	FACETS	0.894	0.826	0.963	0.894	0.826	0.963	CLONAL	1	TRUE	1	0.64	2		462	598	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782144	9782144	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	186	455	1	ENST00000377346.4:c.2167G>A	p.Ala723Thr	p.A723T	ENST00000377346	NM_005026.3	723	Gcc/Acc	17/24	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.64	2		456	580	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298671	11298671	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	151	405	0	ENST00000361445.4:c.1790A>G	p.His597Arg	p.H597R	ENST00000361445	NM_004958.3	597	cAc/cGc	12/58	1	2	FACETS	0.936	0.862	1	0.936	0.862	1	CLONAL	1	TRUE	1	0.64	2		405	504	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237761	16237761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	164	351	0	ENST00000375759.3:c.1208G>A	p.Gly403Asp	p.G403D	ENST00000375759	NM_015001.2	403	gGc/gAc	5/15	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.64	2		351	492	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254594	16254594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758979720	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	198	690	0	ENST00000375759.3:c.1859G>A	p.Arg620Gln	p.R620Q	ENST00000375759	NM_015001.2	620	cGa/cAa	11/15	1	2	FACETS	0.861	0.8	0.923	0.861	0.8	0.923	CLONAL	1	TRUE	1	0.64	2		690	719	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256105	16256105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	249	561	0	ENST00000375759.3:c.3370C>T	p.Pro1124Ser	p.P1124S	ENST00000375759	NM_015001.2	1124	Cca/Tca	11/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.64	2		561	747	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257116	16257116	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	197	553	0	ENST00000375759.3:c.4381A>C	p.Asn1461His	p.N1461H	ENST00000375759	NM_015001.2	1461	Aat/Cat	11/15	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.64	2		553	614	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27093043	27093043	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	206	276	0	ENST00000324856.7:c.2974G>T	p.Glu992Ter	p.E992*	ENST00000324856	NM_006015.4	992	Gaa/Taa	10/20	1	2	FACETS	0.909	0.847	0.973	0.909	0.847	0.973	CLONAL	1	TRUE	1	0.64	2		276	708	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102139	27102139	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	279	482	0	ENST00000324856.7:c.5065G>T	p.Asp1689Tyr	p.D1689Y	ENST00000324856	NM_006015.4	1689	Gat/Tat	19/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.64	2		482	763	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36934852	36934852	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	261	618	0	ENST00000361632.4:c.1481T>C	p.Ile494Thr	p.I494T	ENST00000361632		494	aTc/aCc	11/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.64	2		618	782	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43817921	43817921	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	268	585	0	ENST00000372470.3:c.1600G>T	p.Asp534Tyr	p.D534Y	ENST00000372470	NM_005373.2	534	Gac/Tac	11/12	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.64	2		585	825	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46724361	46724361	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	270	554	0	ENST00000371975.4:c.214G>T	p.Ala72Ser	p.A72S	ENST00000371975	NM_003579.3	72	Gca/Tca	4/18	1	2	FACETS	0.959	0.902	1	0.959	0.902	1	CLONAL	1	TRUE	1	0.64	2		554	880	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46733226	46733226	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	261	682	0	ENST00000371975.4:c.987G>T	p.Gln329His	p.Q329H	ENST00000371975	NM_003579.3	329	caG/caT	9/18	1	2	FACETS	0.953	0.895	1	0.953	0.895	1	CLONAL	1	TRUE	1	0.64	2		682	856	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65305346	65305346	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	290	696	0	ENST00000342505.4:c.2782A>T	p.Ile928Phe	p.I928F	ENST00000342505	NM_002227.2	928	Atc/Ttc	20/25	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.64	2		696	897	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307158	65307158	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	219	351	0	ENST00000342505.4:c.2530G>T	p.Asp844Tyr	p.D844Y	ENST00000342505	NM_002227.2	844	Gac/Tac	18/25	1	2	FACETS	0.884	0.825	0.945	0.884	0.825	0.945	CLONAL	1	TRUE	1	0.64	2		351	774	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332628	65332628	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748142963	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	221	642	0	ENST00000342505.4:c.911C>T	p.Ser304Leu	p.S304L	ENST00000342505	NM_002227.2	304	tCg/tTg	7/25	1	2	FACETS	0.973	0.909	1	0.973	0.909	1	CLONAL	1	TRUE	1	0.64	2		642	710	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748011	72748011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151324323	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	289	534	0	ENST00000357731.5:c.167C>T	p.Ala56Val	p.A56V	ENST00000357731	NM_173808.2	56	gCg/gTg	1/7	1	2	FACETS	0.995	0.938	1	0.995	0.938	1	CLONAL	1	TRUE	1	0.64	2		534	908	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748038	72748038	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	285	770	0	ENST00000357731.5:c.140A>G	p.Asn47Ser	p.N47S	ENST00000357731	NM_173808.2	47	aAc/aGc	1/7	1	2	FACETS	0.966	0.91	1	0.966	0.91	1	CLONAL	1	TRUE	1	0.64	2		770	922	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428511	78428511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408536007	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	148	536	0	ENST00000370768.2:c.1288C>T	p.Arg430Cys	p.R430C	ENST00000370768	NM_003902.3	430	Cgt/Tgt	14/20	1	2	FACETS	0.995	0.916	1	0.995	0.916	1	CLONAL	1	TRUE	1	0.64	2		536	465	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120467936	120467936	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	260	576	1	ENST00000256646.2:c.4503G>T	p.Lys1501Asn	p.K1501N	ENST00000256646	NM_024408.3	1501	aaG/aaT	25/34	1	2	FACETS	0.968	0.91	1	0.968	0.91	1	CLONAL	1	TRUE	1	0.64	2		577	839	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846217	156846217	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	216	602	0	ENST00000524377.1:c.1658C>A	p.Ala553Asp	p.A553D	ENST00000524377	NM_002529.3	553	gCt/gAt	14/17	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.64	2		602	632	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162735830	162735830	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	229	627	0	ENST00000367921.3:c.1139C>A	p.Ser380Tyr	p.S380Y	ENST00000367921	NM_006182.2	380	tCt/tAt	10/18	1	2	FACETS	0.943	0.882	1	0.943	0.882	1	CLONAL	1	TRUE	1	0.64	2		627	759	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743362	162743362	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372362070	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	170	298	2	ENST00000367921.3:c.1832G>A	p.Arg611Gln	p.R611Q	ENST00000367921	NM_006182.2	611	cGa/cAa	14/18	1	2	FACETS	0.9	0.832	0.971	0.9	0.832	0.971	CLONAL	1	TRUE	1	0.64	2		300	590	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743387	162743387	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	157	366	2	ENST00000367921.3:c.1856+1G>A		p.X619_splice	ENST00000367921	NM_006182.2	619			1	2	FACETS	0.949	0.875	1	0.949	0.875	1	CLONAL	1	TRUE	1	0.64	2		368	517	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945619	206945619	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	252	488	0	ENST00000423557.1:c.162C>A	p.Phe54Leu	p.F54L	ENST00000423557	NM_000572.2	54	ttC/ttA	1/5	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.64	2		488	769	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578214	226578214	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	238	488	1	ENST00000366794.5:c.514T>G	p.Phe172Val	p.F172V	ENST00000366794	NM_001618.3	172	Ttc/Gtc	4/23	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.64	2		489	735	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716138	243716138	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	163	496	1	ENST00000263826.5:c.1056G>T	p.Glu352Asp	p.E352D	ENST00000263826	NM_005465.4	352	gaG/gaT	10/13	1	2	FACETS	0.924	0.854	0.998	0.924	0.854	0.998	CLONAL	1	TRUE	1	0.64	2		497	551	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736287	243736287	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	180	313	0	ENST00000263826.5:c.760G>T	p.Glu254Ter	p.E254*	ENST00000263826	NM_005465.4	254	Gaa/Taa	8/13	1	2	FACETS	0.953	0.884	1	0.953	0.884	1	CLONAL	1	TRUE	1	0.64	2		313	590	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828116	243828116	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	206	547	0	ENST00000263826.5:c.242C>T	p.Thr81Ile	p.T81I	ENST00000263826	NM_005465.4	81	aCt/aTt	3/13	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.64	2		547	644	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25466788	25466788	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	232	545	0	ENST00000264709.3:c.1915C>A	p.Leu639Ile	p.L639I	ENST00000264709	NM_175629.2	639	Ctc/Atc	16/23	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.64	2		545	721	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25498407	25498407	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	228	452	0	ENST00000264709.3:c.454G>A	p.Glu152Lys	p.E152K	ENST00000264709	NM_175629.2	152	Gaa/Aaa	5/23	1	2	FACETS	0.983	0.92	1	0.983	0.92	1	CLONAL	1	TRUE	1	0.64	2		452	725	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25964963	25964963	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368569134	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	266	478	2	ENST00000435504.4:c.4243G>A	p.Ala1415Thr	p.A1415T	ENST00000435504		1415	Gct/Act	13/13	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.64	2		480	794	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519761	29519761	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	182	406	0	ENST00000389048.3:c.1810T>C	p.Ser604Pro	p.S604P	ENST00000389048	NM_004304.4	604	Tct/Cct	9/29	1	2	FACETS	0.943	0.875	1	0.943	0.875	1	CLONAL	1	TRUE	1	0.64	2		406	603	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47601060	47601060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149274310	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	225	472	0	ENST00000263735.4:c.298G>A	p.Asp100Asn	p.D100N	ENST00000263735	NM_002354.2	100	Gat/Aat	3/9	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.64	2		472	680	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702266	47702266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759263820	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	194	431	1	ENST00000233146.2:c.1862G>A	p.Arg621Gln	p.R621Q	ENST00000233146	NM_000251.2	621	cGa/cAa	12/16	1	2	FACETS	0.881	0.819	0.946	0.881	0.819	0.946	CLONAL	1	TRUE	1	0.64	2		432	688	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010582	48010582	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	158	491	0	ENST00000234420.5:c.210G>T	p.Lys70Asn	p.K70N	ENST00000234420	NM_000179.2	70	aaG/aaT	1/10	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.64	2		491	469	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023108	48023108	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786204186	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	317	319	0	ENST00000234420.5:c.533G>A	p.Arg178His	p.R178H	ENST00000234420	NM_000179.2	178	cGt/cAt	3/10	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.64	2		319	986	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026763	48026763	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	169	398	0	ENST00000234420.5:c.1641A>C	p.Glu547Asp	p.E547D	ENST00000234420	NM_000179.2	547	gaA/gaC	4/10	1	2	FACETS	0.991	0.917	1	0.991	0.917	1	CLONAL	1	TRUE	1	0.64	2		398	533	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027751	48027751	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	201	343	0	ENST00000234420.5:c.2629G>T	p.Glu877Ter	p.E877*	ENST00000234420	NM_000179.2	877	Gaa/Taa	4/10	1	2	FACETS	0.92	0.856	0.985	0.92	0.856	0.985	CLONAL	1	TRUE	1	0.64	2		343	683	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634746	158634746	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373187352	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	303	304	0	ENST00000263640.3:c.440G>A	p.Arg147Gln	p.R147Q	ENST00000263640	NM_001105.4	147	cGa/cAa	5/11	1	2	FACETS	0.993	0.937	1	0.993	0.937	1	CLONAL	1	TRUE	1	0.64	2		304	954	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095836	178095836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1328262363	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	208	152	0	ENST00000397062.3:c.1495C>T	p.Arg499Trp	p.R499W	ENST00000397062	NM_006164.4	499	Cgg/Tgg	5/5	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.64	2		152	585	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190670399	190670399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	181	384	1	ENST00000441310.2:c.337G>A	p.Ala113Thr	p.A113T	ENST00000441310	NM_000534.4	113	Gct/Act	4/13	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.64	2		385	565	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266573	198266573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	184	367	0	ENST00000335508.6:c.2263C>T	p.Pro755Ser	p.P755S	ENST00000335508	NM_012433.2	755	Cct/Tct	16/25	1	2	FACETS	0.944	0.876	1	0.944	0.876	1	CLONAL	1	TRUE	1	0.64	2		367	609	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736118	204736118	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	226	394	1	ENST00000302823.3:c.475G>T	p.Asp159Tyr	p.D159Y	ENST00000302823	NM_005214.4	159	Gat/Tat	3/4	1	2	FACETS	0.951	0.889	1	0.951	0.889	1	CLONAL	1	TRUE	1	0.64	2		395	743	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248498	212248498	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	255	455	0	ENST00000342788.4:c.3769G>T	p.Asp1257Tyr	p.D1257Y	ENST00000342788	NM_005235.2	1257	Gac/Tac	28/28	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.64	2		455	771	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593560	215593560	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1559372078	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	245	449	0	ENST00000260947.4:c.2174G>T	p.Arg725Ile	p.R725I	ENST00000260947	NM_000465.2	725	aGa/aTa	11/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.64	2		449	686	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657048	215657048	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	164	507	0	ENST00000260947.4:c.337A>C	p.Asn113His	p.N113H	ENST00000260947	NM_000465.2	113	Aat/Cat	3/11	1	2	FACETS	0.939	0.867	1	0.939	0.867	1	CLONAL	1	TRUE	1	0.64	2		507	546	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657051	215657051	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs758972589	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	175	393	0	ENST00000260947.4:c.334C>T	p.Arg112Ter	p.R112*	ENST00000260947	NM_000465.2	112	Cga/Tga	3/11	1	2	FACETS	0.996	0.923	1	0.996	0.923	1	CLONAL	1	TRUE	1	0.64	2		393	549	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439482	220439482	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	284	596	0	ENST00000243786.2:c.335G>T	p.Arg112Ile	p.R112I	ENST00000243786	NM_002191.3	112	aGa/aTa	2/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.64	2		596	809	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242800986	242800986	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	210	533	0	ENST00000334409.5:c.5A>G	p.Gln2Arg	p.Q2R	ENST00000334409	NM_005018.2	2	cAg/cGg	1/5	1	2	FACETS	0.928	0.865	0.993	0.928	0.865	0.993	CLONAL	1	TRUE	1	0.64	2		533	707	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626689	12626689	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	247	409	0	ENST00000251849.4:c.1600T>G	p.Tyr534Asp	p.Y534D	ENST00000251849	NM_002880.3	534	Tat/Gat	15/17	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.64	2		409	756	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30733088	30733088	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	181	227	0	ENST00000295754.5:c.1701A>C	p.Lys567Asn	p.K567N	ENST00000295754	NM_003242.5	567	aaA/aaC	7/7	1	2	FACETS	0.977	0.906	1	0.977	0.906	1	CLONAL	1	TRUE	1	0.64	2		227	579	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38180402	38180402	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	224	508	0	ENST00000396334.3:c.250A>G	p.Thr84Ala	p.T84A	ENST00000396334	NM_002468.4	84	Act/Gct	1/5	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.64	2		508	699	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182283	38182283	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	248	483	0	ENST00000396334.3:c.719A>G	p.Tyr240Cys	p.Y240C	ENST00000396334	NM_002468.4	240	tAc/tGc	4/5	1	2	FACETS	0.975	0.915	1	0.975	0.915	1	CLONAL	1	TRUE	1	0.64	2		483	795	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266527	41266527	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	228	392	0	ENST00000349496.5:c.324G>T	p.Gln108His	p.Q108H	ENST00000349496	NM_001904.3	108	caG/caT	4/15	1	2	FACETS	0.938	0.877	1	0.938	0.877	1	CLONAL	1	TRUE	1	0.64	2		392	760	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47079168	47079168	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	263	494	0	ENST00000409792.3:c.7338A>C	p.Glu2446Asp	p.E2446D	ENST00000409792	NM_014159.6	2446	gaA/gaC	18/21	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.64	2		494	819	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098912	47098912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	226	503	1	ENST00000409792.3:c.6362G>A	p.Arg2121His	p.R2121H	ENST00000409792	NM_014159.6	2121	cGc/cAc	15/21	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.64	2		504	705	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164133	47164133	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	129	349	0	ENST00000409792.3:c.1993A>C	p.Ser665Arg	p.S665R	ENST00000409792	NM_014159.6	665	Agt/Cgt	3/21	1	2	FACETS	0.854	0.78	0.931	0.854	0.78	0.931	CLONAL	1	TRUE	1	0.64	2		349	472	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165174	47165174	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	215	307	0	ENST00000409792.3:c.952T>G	p.Phe318Val	p.F318V	ENST00000409792	NM_014159.6	318	Ttt/Gtt	3/21	1	2	FACETS	0.965	0.901	1	0.965	0.901	1	CLONAL	1	TRUE	1	0.64	2		307	696	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405966	49405966	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	287	414	0	ENST00000418115.1:c.172T>C	p.Trp58Arg	p.W58R	ENST00000418115	NM_001664.2	58	Tgg/Cgg	3/5	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.64	2		414	879	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721541	49721541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772223669	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	147	489	0	ENST00000449682.2:c.2098G>A	p.Ala700Thr	p.A700T	ENST00000449682	NM_020998.3	700	Gca/Aca	18/18	1	2	FACETS	0.875	0.804	0.949	0.875	0.804	0.949	CLONAL	1	TRUE	1	0.64	2		489	525	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721854	49721854	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	68	148	0	ENST00000449682.2:c.1909T>G	p.Leu637Val	p.L637V	ENST00000449682	NM_020998.3	637	Ttg/Gtg	17/18	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.64	2		148	202	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725191	49725191	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	106	234	1	ENST00000449682.2:c.234G>T	p.Met78Ile	p.M78I	ENST00000449682	NM_020998.3	78	atG/atT	2/18	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.64	2		235	286	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936370	49936370	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	329	525	0	ENST00000296474.3:c.1478A>G	p.Asp493Gly	p.D493G	ENST00000296474	NM_002447.2	493	gAc/gGc	3/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.64	2		525	989	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940813	49940813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	318	641	1	ENST00000296474.3:c.230G>A	p.Arg77His	p.R77H	ENST00000296474	NM_002447.2	77	cGc/cAc	1/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.64	2		642	907	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439281	52439281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143891879	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	154	344	0	ENST00000460680.1:c.961G>A	p.Ala321Thr	p.A321T	ENST00000460680	NM_004656.3	321	Gca/Aca	11/17	1	2	FACETS	0.974	0.898	1	0.974	0.898	1	CLONAL	1	TRUE	1	0.64	2		344	494	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52584803	52584803	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1406912189	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	291	711	0	ENST00000394830.3:c.4319T>C	p.Val1440Ala	p.V1440A	ENST00000394830	NM_018313.4	1440	gTa/gCa	28/30	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.64	2		711	830	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620542	52620542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	306	487	0	ENST00000394830.3:c.3211C>T	p.Arg1071Cys	p.R1071C	ENST00000394830	NM_018313.4	1071	Cgc/Tgc	21/30	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.64	2		487	853	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643843	52643843	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	208	472	0	ENST00000394830.3:c.2053C>A	p.Leu685Met	p.L685M	ENST00000394830	NM_018313.4	685	Ctg/Atg	17/30	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.64	2		472	593	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987025	69987025	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750608171	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	296	402	0	ENST00000394351.3:c.86G>A	p.Arg29Gln	p.R29Q	ENST00000394351	NM_000248.3	29	cGg/cAg	2/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.64	2		402	891	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990453	69990453	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	175	378	0	ENST00000394351.3:c.412A>G	p.Met138Val	p.M138V	ENST00000394351	NM_000248.3	138	Atg/Gtg	4/9	1	2	FACETS	0.971	0.9	1	0.971	0.9	1	CLONAL	1	TRUE	1	0.64	2		378	563	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71019954	71019954	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	187	389	0	ENST00000318789.4:c.1655A>G	p.Asn552Ser	p.N552S	ENST00000318789	NM_032682.5	552	aAc/aGc	19/21	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.64	2		389	583	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021809	71021809	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	170	217	0	ENST00000318789.4:c.1549C>A	p.Leu517Ile	p.L517I	ENST00000318789	NM_032682.5	517	Ctt/Att	18/21	1	2	FACETS	0.869	0.803	0.938	0.869	0.803	0.938	CLONAL	1	TRUE	1	0.64	2		217	611	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026112	71026112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs797045585	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	186	347	0	ENST00000318789.4:c.1510C>T	p.Arg504Cys	p.R504C	ENST00000318789	NM_032682.5	504	Cgc/Tgc	17/21	1	2	FACETS	0.855	0.792	0.919	0.855	0.792	0.919	CLONAL	1	TRUE	1	0.64	2		347	680	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096171	71096171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1176882078	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	205	225	0	ENST00000318789.4:c.586C>T	p.Leu196Phe	p.L196F	ENST00000318789	NM_032682.5	196	Ctc/Ttc	10/21	1	2	FACETS	0.924	0.861	0.99	0.924	0.861	0.99	CLONAL	1	TRUE	1	0.64	2		225	693	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71161721	71161721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	278	401	0	ENST00000318789.4:c.248C>T	p.Ser83Phe	p.S83F	ENST00000318789	NM_032682.5	83	tCt/tTt	7/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.64	2		401	782	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259135	89259135	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	176	293	0	ENST00000336596.2:c.279G>T	p.Gln93His	p.Q93H	ENST00000336596	NM_005233.5	93	caG/caT	3/17	1	2	FACETS	0.873	0.808	0.94	0.873	0.808	0.94	CLONAL	1	TRUE	1	0.64	2		293	630	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259223	89259223	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	176	466	0	ENST00000336596.2:c.367T>C	p.Tyr123His	p.Y123H	ENST00000336596	NM_005233.5	123	Tac/Cac	3/17	1	2	FACETS	0.927	0.859	0.998	0.927	0.859	0.998	CLONAL	1	TRUE	1	0.64	2		466	593	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259538	89259538	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	141	462	0	ENST00000336596.2:c.682G>T	p.Gly228Trp	p.G228W	ENST00000336596	NM_005233.5	228	Ggg/Tgg	3/17	1	2	FACETS	0.876	0.803	0.951	0.876	0.803	0.951	CLONAL	1	TRUE	1	0.64	2		462	503	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391154	89391154	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	188	467	0	ENST00000336596.2:c.1220T>G	p.Phe407Cys	p.F407C	ENST00000336596	NM_005233.5	407	tTt/tGt	5/17	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.64	2		467	576	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457231	89457231	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	91	365	0	ENST00000336596.2:c.1712A>C	p.Lys571Thr	p.K571T	ENST00000336596	NM_005233.5	571	aAg/aCg	9/17	1	2	FACETS	0.942	0.846	1	0.942	0.846	1	CLONAL	1	TRUE	1	0.64	2		365	302	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670219	134670219	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	226	450	0	ENST00000398015.3:c.130G>T	p.Glu44Ter	p.E44*	ENST00000398015	NM_004441.4	44	Gaa/Taa	3/16	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.64	2		450	631	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670615	134670615	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781004053	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	241	671	0	ENST00000398015.3:c.526G>A	p.Ala176Thr	p.A176T	ENST00000398015	NM_004441.4	176	Gct/Act	3/16	1	2	FACETS	0.939	0.88	1	0.939	0.88	1	CLONAL	1	TRUE	1	0.64	2		671	802	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670844	134670844	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773800250	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	95	203	1	ENST00000398015.3:c.755G>A	p.Arg252Gln	p.R252Q	ENST00000398015	NM_004441.4	252	cGa/cAa	3/16	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.64	2		204	292	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884813	134884813	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	168	373	0	ENST00000398015.3:c.1589A>G	p.Asp530Gly	p.D530G	ENST00000398015	NM_004441.4	530	gAt/gGt	8/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.64	2		373	509	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898789	134898789	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	194	554	0	ENST00000398015.3:c.1847T>C	p.Val616Ala	p.V616A	ENST00000398015	NM_004441.4	616	gTa/gCa	10/16	1	2	FACETS	0.906	0.842	0.972	0.906	0.842	0.972	CLONAL	1	TRUE	1	0.64	2		554	669	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967270	134967270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374549505	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	233	488	0	ENST00000398015.3:c.2609G>A	p.Arg870Gln	p.R870Q	ENST00000398015	NM_004441.4	870	cGg/cAg	14/16	1	2	FACETS	0.968	0.906	1	0.968	0.906	1	CLONAL	1	TRUE	1	0.64	2		488	752	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138382870	138382870	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	187	494	0	ENST00000289153.2:c.2674G>T	p.Asp892Tyr	p.D892Y	ENST00000289153	NM_006219.2	892	Gat/Tat	19/22	1	2	FACETS	0.929	0.862	0.998	0.929	0.862	0.998	CLONAL	1	TRUE	1	0.64	2		494	629	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417853	138417853	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	216	571	0	ENST00000289153.2:c.1666G>T	p.Asp556Tyr	p.D556Y	ENST00000289153	NM_006219.2	556	Gat/Tat	11/22	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.64	2		571	667	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138431116	138431116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	217	342	0	ENST00000289153.2:c.1333G>A	p.Val445Ile	p.V445I	ENST00000289153	NM_006219.2	445	Gtt/Att	8/22	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.64	2		342	661	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138452213	138452213	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	232	550	0	ENST00000289153.2:c.1040A>G	p.Glu347Gly	p.E347G	ENST00000289153	NM_006219.2	347	gAa/gGa	6/22	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.64	2		550	674	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188288	142188288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1470834016	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	178	342	0	ENST00000350721.4:c.6443G>A	p.Arg2148Gln	p.R2148Q	ENST00000350721	NM_001184.3	2148	cGa/cAa	38/47	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.64	2		342	498	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188945	142188945	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	163	580	0	ENST00000350721.4:c.6302C>A	p.Ala2101Glu	p.A2101E	ENST00000350721	NM_001184.3	2101	gCa/gAa	37/47	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.64	2		580	490	SUCCESS
ATR	545	MSKCC	GRCh37	3	142259767	142259767	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs762440684	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	143	476	0	ENST00000350721.4:c.3560A>G	p.Asp1187Gly	p.D1187G	ENST00000350721	NM_001184.3	1187	gAt/gGt	18/47	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.64	2		476	447	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586472	189586472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	156	312	0	ENST00000264731.3:c.1096G>A	p.Asp366Asn	p.D366N	ENST00000264731	NM_003722.4	366	Gac/Aac	8/14	1	2	FACETS	0.932	0.859	1	0.932	0.859	1	CLONAL	1	TRUE	1	0.64	2		312	523	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612028	189612028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs900140738	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	211	405	0	ENST00000264731.3:c.1780C>T	p.Arg594Ter	p.R594*	ENST00000264731	NM_003722.4	594	Cga/Tga	14/14	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.64	2		405	642	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133483	55133483	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	255	595	0	ENST00000257290.5:c.787G>T	p.Glu263Ter	p.E263*	ENST00000257290	NM_006206.4	263	Gaa/Taa	6/23	1	2	FACETS	0.985	0.925	1	0.985	0.925	1	CLONAL	1	TRUE	1	0.64	2		595	809	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138572	55138572	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	208	471	0	ENST00000257290.5:c.1249A>G	p.Ile417Val	p.I417V	ENST00000257290	NM_006206.4	417	Att/Gtt	9/23	1	2	FACETS	0.957	0.893	1	0.957	0.893	1	CLONAL	1	TRUE	1	0.64	2		471	679	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156535	55156535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778598	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	239	422	0	ENST00000257290.5:c.2936G>A	p.Arg979His	p.R979H	ENST00000257290	NM_006206.4	979	cGc/cAc	22/23	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.64	2		422	731	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55597538	55597538	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	149	544	0	ENST00000288135.5:c.2186C>A	p.Ser729Tyr	p.S729Y	ENST00000288135	NM_000222.2	729	tCt/tAt	15/21	1	2	FACETS	0.827	0.759	0.897	0.827	0.759	0.897	CLONAL	1	TRUE	1	0.64	2		544	563	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602667	55602667	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1330182390	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	157	446	0	ENST00000288135.5:c.2488C>T	p.Arg830Ter	p.R830*	ENST00000288135	NM_000222.2	830	Cga/Tga	18/21	1	2	FACETS	0.87	0.801	0.941	0.87	0.801	0.941	CLONAL	1	TRUE	1	0.64	2		446	564	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970834	55970834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747693621	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	243	600	0	ENST00000263923.4:c.1963G>A	p.Val655Met	p.V655M	ENST00000263923	NM_002253.2	655	Gtg/Atg	13/30	1	2	FACETS	0.942	0.883	1	0.942	0.883	1	CLONAL	1	TRUE	1	0.64	2		600	806	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980368	55980368	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	179	378	0	ENST00000263923.4:c.723G>T	p.Lys241Asn	p.K241N	ENST00000263923	NM_002253.2	241	aaG/aaT	6/30	1	2	FACETS	0.995	0.923	1	0.995	0.923	1	CLONAL	1	TRUE	1	0.64	2		378	562	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197717	66197717	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	134	355	0	ENST00000273854.3:c.2982G>T	p.Met994Ile	p.M994I	ENST00000273854	NM_004439.5	994	atG/atT	17/18	1	2	FACETS	0.928	0.85	1	0.928	0.85	1	CLONAL	1	TRUE	1	0.64	2		355	451	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201756	66201756	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	239	447	0	ENST00000273854.3:c.2746C>G	p.Gln916Glu	p.Q916E	ENST00000273854	NM_004439.5	916	Cag/Gag	16/18	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.64	2		447	726	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213915	66213915	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	136	293	0	ENST00000273854.3:c.2515A>G	p.Lys839Glu	p.K839E	ENST00000273854	NM_004439.5	839	Aaa/Gaa	15/18	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.64	2		293	421	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467716	66467716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	193	341	0	ENST00000273854.3:c.553G>A	p.Glu185Lys	p.E185K	ENST00000273854	NM_004439.5	185	Gaa/Aaa	3/18	1	2	FACETS	0.984	0.915	1	0.984	0.915	1	CLONAL	1	TRUE	1	0.64	2		341	613	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155850	106155850	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	206	325	0	ENST00000380013.4:c.751G>C	p.Ala251Pro	p.A251P	ENST00000380013	NM_001127208.2	251	Gcc/Ccc	3/11	1	2	FACETS	0.921	0.858	0.986	0.921	0.858	0.986	CLONAL	1	TRUE	1	0.64	2		325	699	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156424	106156424	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	251	639	0	ENST00000380013.4:c.1325A>G	p.Asn442Ser	p.N442S	ENST00000380013	NM_001127208.2	442	aAc/aGc	3/11	1	2	FACETS	0.946	0.888	1	0.946	0.888	1	CLONAL	1	TRUE	1	0.64	2		639	829	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180832	106180832	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	182	289	0	ENST00000380013.4:c.3860T>G	p.Phe1287Cys	p.F1287C	ENST00000380013	NM_001127208.2	1287	tTt/tGt	7/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.64	2		289	515	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159104	143159104	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1405228238	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	127	371	0	ENST00000262992.4:c.749G>A	p.Arg250Gln	p.R250Q	ENST00000262992	NM_001101669.1	250	cGa/cAa	10/24	1	2	FACETS	0.929	0.849	1	0.929	0.849	1	CLONAL	1	TRUE	1	0.64	2		371	427	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268182	153268182	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	189	491	0	ENST00000281708.4:c.626T>G	p.Phe209Cys	p.F209C	ENST00000281708	NM_033632.3	209	tTt/tGt	4/12	1	2	FACETS	0.894	0.829	0.96	0.894	0.829	0.96	CLONAL	1	TRUE	1	0.64	2		491	661	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332915	153332915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200698994	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	172	376	0	ENST00000281708.4:c.41G>A	p.Arg14Gln	p.R14Q	ENST00000281708	NM_033632.3	14	cGa/cAa	2/12	1	2	FACETS	0.933	0.864	1	0.933	0.864	1	CLONAL	1	TRUE	1	0.64	2		376	576	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517921	187517921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	213	446	3	ENST00000441802.2:c.12773C>T	p.Pro4258Leu	p.P4258L	ENST00000441802	NM_005245.3	4258	cCg/cTg	25/27	1	2	FACETS	0.921	0.859	0.984	0.921	0.859	0.984	CLONAL	1	TRUE	1	0.64	2		449	723	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187522466	187522466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781093382	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	219	807	0	ENST00000441802.2:c.11597C>T	p.Ala3866Val	p.A3866V	ENST00000441802	NM_005245.3	3866	gCg/gTg	21/27	1	2	FACETS	0.978	0.913	1	0.978	0.913	1	CLONAL	1	TRUE	1	0.64	2		807	700	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549912	187549912	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	153	317	0	ENST00000441802.2:c.4329C>A	p.Phe1443Leu	p.F1443L	ENST00000441802	NM_005245.3	1443	ttC/ttA	8/27	1	2	FACETS	0.951	0.876	1	0.951	0.876	1	CLONAL	1	TRUE	1	0.64	2		317	503	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628637	187628637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199928348	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	229	554	0	ENST00000441802.2:c.2345G>A	p.Arg782His	p.R782H	ENST00000441802	NM_005245.3	782	cGt/cAt	2/27	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.64	2		554	673	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630661	187630661	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	219	641	0	ENST00000441802.2:c.321T>G	p.Ile107Met	p.I107M	ENST00000441802	NM_005245.3	107	atT/atG	2/27	1	2	FACETS	0.922	0.861	0.985	0.922	0.861	0.985	CLONAL	1	TRUE	1	0.64	2		641	742	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224478	224478	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	63	56	0	ENST00000264932.6:c.154T>C	p.Ser52Pro	p.S52P	ENST00000264932	NM_004168.2	52	Tct/Cct	3/15	1	2	FACETS	1	0.977	1	1	0.987	1	CLONAL	2	TRUE	1	0.64	2		56	82	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1278815	1278815	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1388515349	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	181	510	1	ENST00000310581.5:c.2227C>T	p.Arg743Trp	p.R743W	ENST00000310581	NM_198253.2	743	Cgg/Tgg	6/16	1	2	FACETS	0.927	0.86	0.997	0.927	0.86	0.997	CLONAL	1	TRUE	1	0.64	2		511	610	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295298	1295298	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	125	489	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.64	2		490	360	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56161265	56161265	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	163	411	0	ENST00000399503.3:c.1134A>C	p.Lys378Asn	p.K378N	ENST00000399503	NM_005921.1	378	aaA/aaC	5/20	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.64	2		411	473	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179422	56179422	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	229	561	0	ENST00000399503.3:c.3735A>C	p.Lys1245Asn	p.K1245N	ENST00000399503	NM_005921.1	1245	aaA/aaC	15/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.64	2		561	712	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750594	57750594	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	159	363	0	ENST00000274289.3:c.1874T>C	p.Phe625Ser	p.F625S	ENST00000274289	NM_006622.3	625	tTc/tCc	14/14	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.64	2		363	485	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753015	57753015	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	185	293	0	ENST00000274289.3:c.1001T>G	p.Phe334Cys	p.F334C	ENST00000274289	NM_006622.3	334	tTt/tGt	7/14	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.64	2		293	521	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576407	67576407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201598843	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	178	559	0	ENST00000274335.5:c.686C>T	p.Ser229Leu	p.S229L	ENST00000274335		229	tCg/tTg	5/15	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.64	2		559	531	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589558	67589558	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	121	160	0	ENST00000274335.5:c.1321A>C	p.Asn441His	p.N441H	ENST00000274335		441	Aat/Cat	10/15	1	2	FACETS	0.977	0.891	1	0.977	0.891	1	CLONAL	1	TRUE	1	0.64	2		160	387	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665697	86665697	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	127	341	0	ENST00000274376.6:c.1678G>T	p.Glu560Ter	p.E560*	ENST00000274376	NM_002890.2	560	Gaa/Taa	12/25	1	2	FACETS	0.914	0.835	0.997	0.914	0.835	0.997	CLONAL	1	TRUE	1	0.64	2		341	434	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670690	86670690	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	144	214	0	ENST00000274376.6:c.1968A>G	p.Ile656Met	p.I656M	ENST00000274376	NM_002890.2	656	atA/atG	15/25	1	2	FACETS	0.882	0.81	0.957	0.882	0.81	0.957	CLONAL	1	TRUE	1	0.64	2		214	510	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685209	86685209	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	203	466	0	ENST00000274376.6:c.2926-1G>T		p.X976_splice	ENST00000274376	NM_002890.2	976			1	2	FACETS	0.958	0.893	1	0.958	0.893	1	CLONAL	1	TRUE	1	0.64	2		466	662	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267600319	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	212	333	0	ENST00000257430.4:c.4199C>T	p.Ser1400Leu	p.S1400L	ENST00000257430	NM_000038.5	1400	tCg/tTg	16/16	1	2	FACETS	0.98	0.915	1	0.98	0.915	1	CLONAL	1	TRUE	1	0.64	2		333	676	SUCCESS
APC	324	MSKCC	GRCh37	5	112176828	112176828	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	180	400	0	ENST00000257430.4:c.5537A>G	p.Tyr1846Cys	p.Y1846C	ENST00000257430	NM_000038.5	1846	tAc/tGc	16/16	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.64	2		400	554	SUCCESS
APC	324	MSKCC	GRCh37	5	112178682	112178682	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs766473931	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	245	614	0	ENST00000257430.4:c.7391C>A	p.Ser2464Tyr	p.S2464Y	ENST00000257430	NM_000038.5	2464	tCt/tAt	16/16	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.64	2		614	730	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925404	131925404	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	135	336	0	ENST00000265335.6:c.1327A>C	p.Ile443Leu	p.I443L	ENST00000265335		443	Att/Ctt	9/25	1	2	FACETS	0.95	0.871	1	0.95	0.871	1	CLONAL	1	TRUE	1	0.64	2		336	444	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944865	131944865	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	150	183	0	ENST00000265335.6:c.2886G>T	p.Glu962Asp	p.E962D	ENST00000265335		962	gaG/gaT	18/25	1	2	FACETS	0.888	0.816	0.962	0.888	0.816	0.962	CLONAL	1	TRUE	1	0.64	2		183	528	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456995	149456995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41338945	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	141	324	1	ENST00000286301.3:c.733G>A	p.Ala245Thr	p.A245T	ENST00000286301	NM_005211.3	245	Gca/Aca	6/22	1	2	FACETS	0.956	0.878	1	0.956	0.878	1	CLONAL	1	TRUE	1	0.64	2		325	461	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509442	149509442	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	225	727	0	ENST00000261799.4:c.1457A>G	p.Glu486Gly	p.E486G	ENST00000261799	NM_002609.3	486	gAg/gGg	10/23	1	2	FACETS	0.905	0.845	0.966	0.905	0.845	0.966	CLONAL	1	TRUE	1	0.64	2		727	777	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638875	176638875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137888392	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	310	486	0	ENST00000439151.2:c.3475C>T	p.Arg1159Trp	p.R1159W	ENST00000439151	NM_022455.4	1159	Cgg/Tgg	5/23	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.64	2		486	893	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056376	180056376	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	244	555	0	ENST00000261937.6:c.868G>T	p.Glu290Ter	p.E290*	ENST00000261937	NM_182925.4	290	Gaa/Taa	7/30	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.64	2		555	639	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158491	26158491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	209	359	0	ENST00000289316.2:c.94C>T	p.Arg32Cys	p.R32C	ENST00000289316	NM_138720.2	32	Cgc/Tgc	1/2	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.64	2		359	644	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858261	27858261	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	298	484	0	ENST00000359303.2:c.310C>A	p.Leu104Ile	p.L104I	ENST00000359303	NM_003535.2	104	Ctc/Atc	1/1	1	2	FACETS	0.929	0.876	0.984	0.929	0.876	0.984	CLONAL	1	TRUE	1	0.64	2		484	1002	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858492	27858492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	280	332	0	ENST00000359303.2:c.79C>T	p.Arg27Cys	p.R27C	ENST00000359303	NM_003535.2	27	Cgc/Tgc	1/1	1	2	FACETS	0.973	0.917	1	0.973	0.917	1	CLONAL	1	TRUE	1	0.64	2		332	899	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681476	30681476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756890775	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	206	451	0	ENST00000376406.3:c.536G>A	p.Arg179His	p.R179H	ENST00000376406	NM_014641.2	179	cGt/cAt	4/15	1	2	FACETS	0.926	0.863	0.991	0.926	0.863	0.991	CLONAL	1	TRUE	1	0.64	2		451	695	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163530	32163530	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	179	478	0	ENST00000375023.3:c.5696G>T	p.Ser1899Ile	p.S1899I	ENST00000375023	NM_004557.3	1899	aGc/aTc	30/30	1	2	FACETS	0.823	0.761	0.886	0.823	0.761	0.886	CLONAL	1	TRUE	1	0.64	2		478	680	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138919	37138919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	193	386	0	ENST00000373509.5:c.259C>T	p.Pro87Ser	p.P87S	ENST00000373509	NM_002648.3	87	Ccc/Tcc	4/6	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.64	2		386	567	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903835	41903835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767328984	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	142	452	0	ENST00000372991.4:c.722G>A	p.Arg241Gln	p.R241Q	ENST00000372991	NM_001760.3	241	cGg/cAg	5/5	1	2	FACETS	0.934	0.858	1	0.934	0.858	1	CLONAL	1	TRUE	1	0.64	2		452	475	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745233	43745233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1267535717	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	322	790	5	ENST00000523873.1:c.146G>A	p.Arg49His	p.R49H	ENST00000523873		49	cGc/cAc	3/8	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.64	2		795	974	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43746655	43746655	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs766541343	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	322	461	0	ENST00000523873.1:c.422A>G	p.Lys141Arg	p.K141R	ENST00000523873		141	aAa/aGa	5/8	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.64	2		461	995	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120557	94120557	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	316	384	0	ENST00000369303.4:c.494T>C	p.Met165Thr	p.M165T	ENST00000369303	NM_004440.3	165	aTg/aCg	3/17	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.64	2		384	981	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017478	112017478	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	231	300	0	ENST00000368678.4:c.1033+2T>C		p.X345_splice	ENST00000368678		345			1	2	FACETS	0.966	0.904	1	0.966	0.904	1	CLONAL	1	TRUE	1	0.64	2		300	747	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017660	112017660	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	260	382	0	ENST00000368678.4:c.854-1G>A		p.X285_splice	ENST00000368678		285			1	2	FACETS	0.993	0.934	1	0.993	0.934	1	CLONAL	1	TRUE	1	0.64	2		382	818	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117717414	117717414	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1562361642	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	205	590	0	ENST00000368508.3:c.793G>A	p.Ala265Thr	p.A265T	ENST00000368508	NM_002944.2	265	Gca/Aca	8/43	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.64	2		590	635	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001477	150001477	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	146	473	1	ENST00000253339.5:c.2127G>T	p.Lys709Asn	p.K709N	ENST00000253339		709	aaG/aaT	4/7	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.64	2		474	417	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976790	2976790	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1053219257	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	267	764	1	ENST00000396946.4:c.1222C>T	p.Arg408Cys	p.R408C	ENST00000396946	NM_032415.4	408	Cgc/Tgc	9/25	1	2	FACETS	0.971	0.913	1	0.971	0.913	1	CLONAL	1	TRUE	1	0.64	2		765	859	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026391	6026391	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	rs1554297049	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	151	268	0	ENST00000265849.7:c.2005A>C	p.Ser669Arg	p.S669R	ENST00000265849	NM_000535.5	669	Agt/Cgt	11/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.64	2		268	435	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043355	6043355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188006077	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	74	182	0	ENST00000265849.7:c.319C>T	p.Arg107Trp	p.R107W	ENST00000265849	NM_000535.5	107	Cgg/Tgg	4/15	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.64	2		182	221	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450336	50450336	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	221	490	0	ENST00000331340.3:c.520A>G	p.Lys174Glu	p.K174E	ENST00000331340	NM_006060.4	174	Aaa/Gaa	5/8	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.64	2		490	657	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227930	55227930	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	224	363	0	ENST00000275493.2:c.1397A>C	p.Asn466Thr	p.N466T	ENST00000275493	NM_005228.3	466	aAc/aCc	12/28	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.64	2		363	677	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392146	81392146	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	134	570	0	ENST00000222390.5:c.131A>C	p.Lys44Thr	p.K44T	ENST00000222390	NM_000601.4	44	aAa/aCa	2/18	1	2	FACETS	0.935	0.856	1	0.935	0.856	1	CLONAL	1	TRUE	1	0.64	2		570	448	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508768	106508768	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	227	381	1	ENST00000359195.3:c.762G>T	p.Lys254Asn	p.K254N	ENST00000359195	NM_002649.2	254	aaG/aaT	2/11	1	2	FACETS	0.963	0.9	1	0.963	0.9	1	CLONAL	1	TRUE	1	0.64	2		382	737	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526650	106526650	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	208	556	1	ENST00000359195.3:c.2943G>T	p.Glu981Asp	p.E981D	ENST00000359195	NM_002649.2	981	gaG/gaT	10/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.64	2		557	633	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435767	116435767	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	234	571	0	ENST00000397752.3:c.3857A>G	p.Asp1286Gly	p.D1286G	ENST00000397752	NM_000245.2	1286	gAc/gGc	20/21	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.64	2		571	717	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436176	116436176	+	stop_lost	Nonstop_Mutation	SNP	T	T	C	rs1249739995	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	150	275	0	ENST00000397752.3:c.4171T>C	p.Ter1391GlnextTer2	p.*1391Qext*2	ENST00000397752	NM_000245.2	1391	Tag/Cag	21/21	1	2	FACETS	0.928	0.854	1	0.928	0.854	1	CLONAL	1	TRUE	1	0.64	2		275	505	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850335	128850335	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	218	491	0	ENST00000249373.3:c.1598G>T	p.Ser533Ile	p.S533I	ENST00000249373	NM_005631.4	533	aGc/aTc	9/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.64	2		491	647	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525868	148525868	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	219	375	0	ENST00000320356.2:c.589G>T	p.Glu197Ter	p.E197*	ENST00000320356	NM_004456.4	197	Gaa/Taa	6/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.64	2		375	623	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148526829	148526829	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1488870104	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	143	645	1	ENST00000320356.2:c.475G>A	p.Gly159Arg	p.G159R	ENST00000320356	NM_004456.4	159	Ggg/Agg	5/20	1	2	FACETS	0.85	0.779	0.923	0.85	0.779	0.923	CLONAL	1	TRUE	1	0.64	2		646	526	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151167701	151167701	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	180	539	0	ENST00000262187.5:c.418T>C	p.Ser140Pro	p.S140P	ENST00000262187	NM_005614.3	140	Tct/Cct	7/8	1	2	FACETS	0.852	0.789	0.918	0.852	0.789	0.918	CLONAL	1	TRUE	1	0.64	2		539	660	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859338	151859338	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	237	517	0	ENST00000262189.6:c.11324A>C	p.Glu3775Ala	p.E3775A	ENST00000262189	NM_170606.2	3775	gAa/gCa	43/59	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.64	2		517	678	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860599	151860599	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	246	475	0	ENST00000262189.6:c.10063A>C	p.Ile3355Leu	p.I3355L	ENST00000262189	NM_170606.2	3355	Att/Ctt	43/59	1	2	FACETS	0.953	0.893	1	0.953	0.893	1	CLONAL	1	TRUE	1	0.64	2		475	807	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874251	151874251	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	172	540	0	ENST00000262189.6:c.8287G>T	p.Glu2763Ter	p.E2763*	ENST00000262189	NM_170606.2	2763	Gaa/Taa	38/59	1	2	FACETS	0.919	0.85	0.99	0.919	0.85	0.99	CLONAL	1	TRUE	1	0.64	2		540	585	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874709	151874709	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139770288	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	228	454	2	ENST00000262189.6:c.7829G>A	p.Arg2610Gln	p.R2610Q	ENST00000262189	NM_170606.2	2610	cGa/cAa	38/59	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.64	2		456	673	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879228	151879228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200152380	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	223	422	0	ENST00000262189.6:c.5717G>A	p.Arg1906Gln	p.R1906Q	ENST00000262189	NM_170606.2	1906	cGa/cAa	36/59	1	2	FACETS	0.956	0.893	1	0.956	0.893	1	CLONAL	1	TRUE	1	0.64	2		422	729	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151948016	151948016	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1277470476	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	208	441	0	ENST00000262189.6:c.1657G>T	p.Asp553Tyr	p.D553Y	ENST00000262189	NM_170606.2	553	Gat/Tat	12/59	1	2	FACETS	0.979	0.913	1	0.979	0.913	1	CLONAL	1	TRUE	1	0.64	2		441	664	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345963	152345963	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	346	454	0	ENST00000359321.1:c.607T>G	p.Ser203Ala	p.S203A	ENST00000359321	NM_005431.1	203	Tcg/Gcg	3/3	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.64	2		454	939	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090520	5090520	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	148	227	0	ENST00000381652.3:c.2836G>T	p.Glu946Ter	p.E946*	ENST00000381652	NM_004972.3	946	Gaa/Taa	21/25	1	2	FACETS	0.841	0.772	0.912	0.841	0.772	0.912	CLONAL	1	TRUE	1	0.64	2		227	550	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5467842	5467842	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	238	336	0	ENST00000381577.3:c.853A>G	p.Thr285Ala	p.T285A	ENST00000381577	NM_014143.3	285	Aca/Gca	7/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.64	2		336	688	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484349	8484349	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	185	556	0	ENST00000356435.5:c.3183A>C	p.Glu1061Asp	p.E1061D	ENST00000356435		1061	gaA/gaC	19/35	1	2	FACETS	0.851	0.789	0.916	0.851	0.789	0.916	CLONAL	1	TRUE	1	0.64	2		556	679	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499694	8499694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1202079054	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	211	536	0	ENST00000356435.5:c.2275C>T	p.Pro759Ser	p.P759S	ENST00000356435		759	Ccc/Tcc	14/35	1	2	FACETS	0.967	0.902	1	0.967	0.902	1	CLONAL	1	TRUE	1	0.64	2		536	682	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500788	8500788	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	210	425	0	ENST00000356435.5:c.2094G>T	p.Glu698Asp	p.E698D	ENST00000356435		698	gaG/gaT	13/35	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.64	2		425	634	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507432	8507432	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	107	374	0	ENST00000356435.5:c.1546C>T	p.Pro516Ser	p.P516S	ENST00000356435		516	Cca/Tca	11/35	1	2	FACETS	0.914	0.827	1	0.914	0.827	1	CLONAL	1	TRUE	1	0.64	2		374	366	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528596	8528596	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	235	599	1	ENST00000356435.5:c.536G>A	p.Arg179Gln	p.R179Q	ENST00000356435		179	cGa/cAa	4/35	1	2	FACETS	0.968	0.906	1	0.968	0.906	1	CLONAL	1	TRUE	1	0.64	2		600	759	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633358	8633358	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	166	682	0	ENST00000356435.5:c.311T>C	p.Val104Ala	p.V104A	ENST00000356435		104	gTg/gCg	3/35	1	2	FACETS	0.899	0.83	0.97	0.899	0.83	0.97	CLONAL	1	TRUE	1	0.64	2		682	577	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002659	37002659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1385943435	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	159	405	0	ENST00000358127.4:c.590G>A	p.Arg197His	p.R197H	ENST00000358127	NM_001280556.1	197	cGc/cAc	5/10	1	2	FACETS	0.954	0.88	1	0.954	0.88	1	CLONAL	1	TRUE	1	0.64	2		405	521	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015022	37015022	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	213	429	0	ENST00000358127.4:c.382A>G	p.Thr128Ala	p.T128A	ENST00000358127	NM_001280556.1	128	Acc/Gcc	3/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.64	2		429	618	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285847	87285847	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	245	486	0	ENST00000277120.3:c.184A>C	p.Ser62Arg	p.S62R	ENST00000277120		62	Agt/Cgt	2/19	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.64	2		486	747	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87325682	87325682	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	159	570	0	ENST00000277120.3:c.559G>A	p.Ala187Thr	p.A187T	ENST00000277120		187	Gca/Aca	6/19	1	2	FACETS	0.867	0.799	0.938	0.867	0.799	0.938	CLONAL	1	TRUE	1	0.64	2		570	573	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482309	87482309	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	267	663	0	ENST00000277120.3:c.1596C>A	p.Tyr532Ter	p.Y532*	ENST00000277120		532	taC/taA	14/19	1	2	FACETS	0.979	0.921	1	0.979	0.921	1	CLONAL	1	TRUE	1	0.64	2		663	852	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570282	87570282	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	184	436	0	ENST00000277120.3:c.2022G>T	p.Gln674His	p.Q674H	ENST00000277120		674	caG/caT	17/19	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.64	2		436	556	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636204	87636204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs532184896	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	198	391	0	ENST00000277120.3:c.2369G>A	p.Arg790Gln	p.R790Q	ENST00000277120		790	cGa/cAa	19/19	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.64	2		391	611	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97897776	97897776	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	151	446	0	ENST00000289081.3:c.695T>G	p.Ile232Ser	p.I232S	ENST00000289081	NM_000136.2	232	aTt/aGt	8/15	1	2	FACETS	0.906	0.833	0.98	0.906	0.833	0.98	CLONAL	1	TRUE	1	0.64	2		446	521	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912218	97912218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374176091	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	254	412	0	ENST00000289081.3:c.673G>A	p.Glu225Lys	p.E225K	ENST00000289081	NM_000136.2	225	Gag/Aag	7/15	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.64	2		412	741	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229475	98229475	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	265	665	0	ENST00000331920.6:c.2483A>G	p.Asn828Ser	p.N828S	ENST00000331920	NM_000264.3	828	aAc/aGc	15/24	1	2	FACETS	0.979	0.92	1	0.979	0.92	1	CLONAL	1	TRUE	1	0.64	2		665	846	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894916	101894916	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060502040	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	261	340	0	ENST00000374994.4:c.469C>T	p.Arg157Ter	p.R157*	ENST00000374994	NM_004612.2	157	Cga/Tga	3/9	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.64	2		340	800	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915943	127915943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781486938	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	261	472	0	ENST00000373547.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000373547	NM_002721.4	180	Gaa/Aaa	6/7	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.64	2		472	796	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781234	135781234	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	329	837	0	ENST00000298552.3:c.1731G>T	p.Glu577Asp	p.E577D	ENST00000298552	NM_001162426.1	577	gaG/gaT	15/23	1	2	FACETS	0.979	0.927	1	0.979	0.927	1	CLONAL	1	TRUE	1	0.64	2		837	1050	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797298	135797298	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	190	210	0	ENST00000298552.3:c.571C>T	p.Leu191Phe	p.L191F	ENST00000298552	NM_001162426.1	191	Ctt/Ttt	7/23	1	2	FACETS	0.911	0.846	0.978	0.911	0.846	0.978	CLONAL	1	TRUE	1	0.64	2		210	652	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797313	135797313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1279777367	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	162	198	2	ENST00000298552.3:c.556G>A	p.Ala186Thr	p.A186T	ENST00000298552	NM_001162426.1	186	Gca/Aca	7/23	1	2	FACETS	0.891	0.822	0.963	0.891	0.822	0.963	CLONAL	1	TRUE	1	0.64	2		200	568	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566734	139566734	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144969763	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	223	660	0	ENST00000308874.7:c.818C>T	p.Ser273Leu	p.S273L	ENST00000308874		273	tCg/tTg	10/10	1	2	FACETS	0.975	0.911	1	0.975	0.911	1	CLONAL	1	TRUE	1	0.64	2		660	715	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814824	139814824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755691522	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	295	663	0	ENST00000247668.2:c.817G>A	p.Glu273Lys	p.E273K	ENST00000247668	NM_021138.3	273	Gag/Aag	8/11	1	2	FACETS	0.973	0.918	1	0.973	0.918	1	CLONAL	1	TRUE	1	0.64	2		663	947	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814912	139814912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767867108	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	284	574	0	ENST00000247668.2:c.905C>T	p.Ala302Val	p.A302V	ENST00000247668	NM_021138.3	302	gCc/gTc	8/11	1	2	FACETS	0.972	0.916	1	0.972	0.916	1	CLONAL	1	TRUE	1	0.64	2		574	913	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100573	8100573	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	198	475	0	ENST00000346208.3:c.547T>C	p.Cys183Arg	p.C183R	ENST00000346208		183	Tgc/Cgc	3/6	1	2	FACETS	0.956	0.89	1	0.956	0.89	1	CLONAL	1	TRUE	1	0.64	2		475	647	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100768	8100768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370055470	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	162	476	0	ENST00000346208.3:c.742G>A	p.Gly248Arg	p.G248R	ENST00000346208		248	Gga/Aga	3/6	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.64	2		476	476	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106013	8106013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	189	369	0	ENST00000346208.3:c.833G>A	p.Gly278Asp	p.G278D	ENST00000346208		278	gGc/gAc	4/6	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.64	2		369	558	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845621	63845621	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	125	186	0	ENST00000279873.7:c.1360G>T	p.Glu454Ter	p.E454*	ENST00000279873	NM_032199.2	454	Gaa/Taa	9/10	1	2	FACETS	0.93	0.849	1	0.93	0.849	1	CLONAL	1	TRUE	1	0.64	2		186	420	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332272	70332272	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	297	299	0	ENST00000373644.4:c.177G>T	p.Lys59Asn	p.K59N	ENST00000373644	NM_030625.2	59	aaG/aaT	2/12	1	2	FACETS	0.963	0.908	1	0.963	0.908	1	CLONAL	1	TRUE	1	0.64	2		299	964	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406042	70406042	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	168	572	0	ENST00000373644.4:c.3556A>C	p.Ile1186Leu	p.I1186L	ENST00000373644	NM_030625.2	1186	Ata/Cta	4/12	1	2	FACETS	0.885	0.818	0.955	0.885	0.818	0.955	CLONAL	1	TRUE	1	0.64	2		572	593	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406089	70406089	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	160	583	0	ENST00000373644.4:c.3603T>G	p.Phe1201Leu	p.F1201L	ENST00000373644	NM_030625.2	1201	ttT/ttG	4/12	1	2	FACETS	0.973	0.898	1	0.973	0.898	1	CLONAL	1	TRUE	1	0.64	2		583	514	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534248	534248	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	274	694	0	ENST00000451590.1:c.75G>T	p.Gln25His	p.Q25H	ENST00000451590	NM_001130442.1	25	caG/caT	2/5	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.64	2		694	784	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514124	69514124	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	252	570	0	ENST00000294312.3:c.557A>G	p.Asp186Gly	p.D186G	ENST00000294312	NM_005117.2	186	gAc/gGc	3/3	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.64	2		570	761	SUCCESS
EED	8726	MSKCC	GRCh37	11	85968618	85968618	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	178	291	0	ENST00000263360.6:c.614T>G	p.Leu205Arg	p.L205R	ENST00000263360	NM_003797.3	205	cTt/cGt	6/12	1	2	FACETS	0.897	0.831	0.965	0.897	0.831	0.965	CLONAL	1	TRUE	1	0.64	2		291	620	SUCCESS
EED	8726	MSKCC	GRCh37	11	85975226	85975226	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	91	430	0	ENST00000263360.6:c.647G>A	p.Arg216Gln	p.R216Q	ENST00000263360	NM_003797.3	216	cGa/cAa	7/12	1	2	FACETS	0.75	0.671	0.833	0.75	0.671	0.833	SUBCLONAL	1	TRUE	1	0.64	2		430	379	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977189	85977189	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	136	350	0	ENST00000263360.6:c.791G>T	p.Arg264Met	p.R264M	ENST00000263360	NM_003797.3	264	aGg/aTg	8/12	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.64	2		350	412	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195662	102195662	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	309	371	1	ENST00000263464.3:c.422C>A	p.Ser141Tyr	p.S141Y	ENST00000263464	NM_001165.4	141	tCt/tAt	2/9	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.64	2		372	921	SUCCESS
ATM	472	MSKCC	GRCh37	11	108099982	108099982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	133	249	0	ENST00000278616.4:c.263C>T	p.Ala88Val	p.A88V	ENST00000278616	NM_000051.3	88	gCc/gTc	4/63	1	2	FACETS	0.99	0.907	1	0.99	0.907	1	CLONAL	1	TRUE	1	0.64	2		249	420	SUCCESS
ATM	472	MSKCC	GRCh37	11	108126964	108126964	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs864622294	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	198	490	0	ENST00000278616.4:c.2147T>C	p.Val716Ala	p.V716A	ENST00000278616	NM_000051.3	716	gTc/gCc	14/63	1	2	FACETS	0.939	0.874	1	0.939	0.874	1	CLONAL	1	TRUE	1	0.64	2		490	659	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141873	108141873	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs538105098	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	214	293	0	ENST00000278616.4:c.2921C>T	p.Ser974Phe	p.S974F	ENST00000278616	NM_000051.3	974	tCc/tTc	19/63	1	2	FACETS	0.958	0.894	1	0.958	0.894	1	CLONAL	1	TRUE	1	0.64	2		293	698	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141989	108141989	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	149	360	0	ENST00000278616.4:c.2933C>A	p.Ser978Tyr	p.S978Y	ENST00000278616	NM_000051.3	978	tCt/tAt	20/63	1	2	FACETS	0.997	0.918	1	0.997	0.918	1	CLONAL	1	TRUE	1	0.64	2		360	467	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153564	108153564	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	183	346	0	ENST00000278616.4:c.3704C>A	p.Pro1235His	p.P1235H	ENST00000278616	NM_000051.3	1235	cCt/cAt	25/63	1	2	FACETS	0.948	0.88	1	0.948	0.88	1	CLONAL	1	TRUE	1	0.64	2		346	603	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196874	108196874	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	147	482	0	ENST00000278616.4:c.6897C>A	p.Phe2299Leu	p.F2299L	ENST00000278616	NM_000051.3	2299	ttC/ttA	47/63	1	2	FACETS	0.984	0.905	1	0.984	0.905	1	CLONAL	1	TRUE	1	0.64	2		482	467	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118368660	118368660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555044474	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	178	357	0	ENST00000534358.1:c.5674C>T	p.Arg1892Cys	p.R1892C	ENST00000534358	NM_005933.3	1892	Cgt/Tgt	21/36	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.64	2		357	526	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371736	118371736	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	202	446	1	ENST00000534358.1:c.6193C>T	p.Arg2065Cys	p.R2065C	ENST00000534358	NM_005933.3	2065	Cgc/Tgc	25/36	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.64	2		447	599	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390362	118390362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	249	546	0	ENST00000534358.1:c.11176C>T	p.Leu3726Phe	p.L3726F	ENST00000534358	NM_005933.3	3726	Ctc/Ttc	32/36	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.64	2		546	760	SUCCESS
CBL	867	MSKCC	GRCh37	11	119077282	119077282	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	263	576	0	ENST00000264033.4:c.155A>C	p.Asp52Ala	p.D52A	ENST00000264033	NM_005188.3	52	gAc/gCc	1/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.64	2		576	800	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497662	125497662	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	142	432	0	ENST00000428830.2:c.226G>T	p.Glu76Ter	p.E76*	ENST00000428830	NM_001114121.2	76	Gaa/Taa	3/14	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.64	2		432	412	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422237	422237	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	233	510	0	ENST00000399788.2:c.3021A>C	p.Lys1007Asn	p.K1007N	ENST00000399788	NM_001042603.1	1007	aaA/aaC	20/28	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.64	2		510	687	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435061	18435061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603400	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	91	258	0	ENST00000266497.5:c.46G>A	p.Glu16Lys	p.E16K	ENST00000266497		16	Gaa/Aaa	1/31	0.3	1	FACETS	0.591	0.53	0.655	0.591	0.53	0.655	INDETERMINATE	1	TRUE	0	0.64	1		258	327	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25368397	25368397	+	intron_variant	Intron	SNP	A	A	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	158	302	0	ENST00000311936.3:c.451-5552T>A		p.*151*	ENST00000311936	NM_004985.3	183/189			1	2	FACETS	0.874	0.805	0.945	0.874	0.805	0.945	CLONAL	1	TRUE	1	0.64	2		302	565	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46240651	46240651	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	100	378	0	ENST00000334344.6:c.1511T>C	p.Val504Ala	p.V504A	ENST00000334344	NM_152641.2	504	gTt/gCt	12/21	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.64	2		378	281	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243909	46243909	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	187	592	0	ENST00000334344.6:c.2003C>A	p.Ser668Tyr	p.S668Y	ENST00000334344	NM_152641.2	668	tCt/tAt	15/21	1	2	FACETS	0.982	0.913	1	0.982	0.913	1	CLONAL	1	TRUE	1	0.64	2		592	595	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246235	46246235	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	216	585	0	ENST00000334344.6:c.4329T>G	p.Ser1443Arg	p.S1443R	ENST00000334344	NM_152641.2	1443	agT/agG	15/21	1	2	FACETS	0.918	0.857	0.981	0.918	0.857	0.981	CLONAL	1	TRUE	1	0.64	2		585	735	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285869	46285869	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	133	442	0	ENST00000334344.6:c.5137T>C	p.Ser1713Pro	p.S1713P	ENST00000334344	NM_152641.2	1713	Tct/Cct	18/21	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.64	2		442	382	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416447	49416447	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	230	577	0	ENST00000301067.7:c.16264A>C	p.Met5422Leu	p.M5422L	ENST00000301067	NM_003482.3	5422	Atg/Ctg	51/54	1	2	FACETS	0.901	0.842	0.961	0.901	0.842	0.961	CLONAL	1	TRUE	1	0.64	2		577	798	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426001	49426001	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	270	590	0	ENST00000301067.7:c.12487C>A	p.Pro4163Thr	p.P4163T	ENST00000301067	NM_003482.3	4163	Ccc/Acc	39/54	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.64	2		590	806	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426648	49426648	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	142	398	0	ENST00000301067.7:c.11840A>C	p.Gln3947Pro	p.Q3947P	ENST00000301067	NM_003482.3	3947	cAg/cCg	39/54	1	2	FACETS	0.991	0.91	1	0.991	0.91	1	CLONAL	1	TRUE	1	0.64	2		398	448	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427503	49427503	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1011790338	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	195	544	0	ENST00000301067.7:c.10985T>C	p.Met3662Thr	p.M3662T	ENST00000301067	NM_003482.3	3662	aTg/aCg	39/54	1	2	FACETS	0.9	0.837	0.966	0.9	0.837	0.966	CLONAL	1	TRUE	1	0.64	2		544	677	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446445	49446445	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	171	377	0	ENST00000301067.7:c.1160C>A	p.Ala387Asp	p.A387D	ENST00000301067	NM_003482.3	387	gCt/gAt	9/54	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.64	2		377	520	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446735	49446735	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	192	443	2	ENST00000301067.7:c.1075C>A	p.Arg359Ser	p.R359S	ENST00000301067	NM_003482.3	359	Cgc/Agc	8/54	1	2	FACETS	0.93	0.864	0.998	0.93	0.864	0.998	CLONAL	1	TRUE	1	0.64	2		445	645	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49449076	49449076	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	267	592	0	ENST00000301067.7:c.32A>G	p.Lys11Arg	p.K11R	ENST00000301067	NM_003482.3	11	aAa/aGa	1/54	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.64	2		592	808	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69210629	69210629	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1385829631	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	200	577	0	ENST00000462284.1:c.212G>A	p.Arg71Gln	p.R71Q	ENST00000462284	NM_002392.5	71	cGa/cAa	4/11	1	2	FACETS	0.833	0.774	0.894	0.833	0.774	0.894	CLONAL	1	TRUE	1	0.64	2		577	750	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69233440	69233440	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1376586613	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	202	535	1	ENST00000462284.1:c.1305T>G	p.Ser435Arg	p.S435R	ENST00000462284	NM_002392.5	435	agT/agG	11/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.64	2		536	589	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885212	111885212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	268	757	0	ENST00000341259.2:c.1100G>A	p.Gly367Asp	p.G367D	ENST00000341259	NM_005475.2	367	gGc/gAc	6/8	1	2	FACETS	0.939	0.883	0.997	0.939	0.883	0.997	CLONAL	1	TRUE	1	0.64	2		757	892	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114125	115114125	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	175	502	0	ENST00000257566.3:c.1092C>A	p.Asn364Lys	p.N364K	ENST00000257566	NM_016569.3	364	aaC/aaA	6/8	1	2	FACETS	0.864	0.799	0.931	0.864	0.799	0.931	CLONAL	1	TRUE	1	0.64	2		502	633	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219113	133219113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771896231	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	210	635	0	ENST00000320574.5:c.4931C>T	p.Ser1644Leu	p.S1644L	ENST00000320574	NM_006231.2	1644	tCg/tTg	37/49	1	2	FACETS	0.958	0.894	1	0.958	0.894	1	CLONAL	1	TRUE	1	0.64	2		635	685	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133236037	133236037	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	224	518	0	ENST00000320574.5:c.3119C>A	p.Ser1040Tyr	p.S1040Y	ENST00000320574	NM_006231.2	1040	tCt/tAt	26/49	1	2	FACETS	0.997	0.933	1	0.997	0.933	1	CLONAL	1	TRUE	1	0.64	2		518	702	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	228	593	1	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.64	2		594	686	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588592	28588592	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	211	614	0	ENST00000241453.7:c.2856A>T	p.Glu952Asp	p.E952D	ENST00000241453	NM_004119.2	952	gaA/gaT	23/24	1	2	FACETS	0.922	0.86	0.986	0.922	0.86	0.986	CLONAL	1	TRUE	1	0.64	2		614	715	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601376	28601376	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	157	453	0	ENST00000241453.7:c.2056C>T	p.Pro686Ser	p.P686S	ENST00000241453	NM_004119.2	686	Cca/Tca	17/24	1	2	FACETS	0.914	0.842	0.987	0.914	0.842	0.987	CLONAL	1	TRUE	1	0.64	2		453	537	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622581	28622581	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	82	279	0	ENST00000241453.7:c.1037-1G>T		p.X346_splice	ENST00000241453	NM_004119.2	346			1	2	FACETS	0.902	0.805	1	0.902	0.805	1	CLONAL	1	TRUE	1	0.64	2		279	284	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001410	29001410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771714708	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	154	353	0	ENST00000282397.4:c.1322C>T	p.Pro441Leu	p.P441L	ENST00000282397	NM_002019.4	441	cCg/cTg	10/30	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.64	2		353	460	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906796	32906796	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	144	592	0	ENST00000380152.3:c.1181A>G	p.Glu394Gly	p.E394G	ENST00000380152		394	gAa/gGa	10/27	0.3	0	FACETS	0.32	0.293	0.347			1	INDETERMINATE	1	TRUE	0	0.64	0		592	507	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912606	32912606	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	167	887	0	ENST00000380152.3:c.4114T>G	p.Phe1372Val	p.F1372V	ENST00000380152		1372	Ttt/Gtt	11/27	0.3	0	FACETS	0.358	0.331	0.386			1	INDETERMINATE	1	TRUE	0	0.64	0		887	525	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951156	48951156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060503078	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	124	331	0	ENST00000267163.4:c.1318G>A	p.Glu440Lys	p.E440K	ENST00000267163	NM_000321.2	440	Gaa/Aaa	13/27	1	2	FACETS	0.95	0.867	1	0.95	0.867	1	CLONAL	1	TRUE	1	0.64	2		331	408	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953748	48953748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759079385	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	229	222	0	ENST00000267163.4:c.1351C>T	p.Arg451Cys	p.R451C	ENST00000267163	NM_000321.2	451	Cgc/Tgc	14/27	1	2	FACETS	0.959	0.897	1	0.959	0.897	1	CLONAL	1	TRUE	1	0.64	2		222	746	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030456	49030456	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	137	408	0	ENST00000267163.4:c.1931C>A	p.Ser644Tyr	p.S644Y	ENST00000267163	NM_000321.2	644	tCt/tAt	19/27	1	2	FACETS	0.896	0.82	0.973	0.896	0.82	0.973	CLONAL	1	TRUE	1	0.64	2		408	478	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030483	49030483	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	151	261	0	ENST00000267163.4:c.1958A>C	p.Lys653Thr	p.K653T	ENST00000267163	NM_000321.2	653	aAa/aCa	19/27	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.64	2		261	394	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345058	73345058	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	145	370	0	ENST00000377767.4:c.1739G>T	p.Ser580Ile	p.S580I	ENST00000377767	NM_014953.3	580	aGt/aTt	13/21	1	2	FACETS	0.966	0.888	1	0.966	0.888	1	CLONAL	1	TRUE	1	0.64	2		370	469	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514697	103514697	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	154	280	0	ENST00000355739.4:c.1198G>T	p.Asp400Tyr	p.D400Y	ENST00000355739	NM_000123.3	400	Gat/Tat	8/15	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.64	2		280	464	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515141	103515141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770246574	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	203	284	0	ENST00000355739.4:c.1642G>A	p.Glu548Lys	p.E548K	ENST00000355739	NM_000123.3	548	Gaa/Aaa	8/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.64	2		284	605	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434991	110434991	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	117	296	1	ENST00000375856.3:c.3410G>A	p.Arg1137His	p.R1137H	ENST00000375856	NM_003749.2	1137	cGc/cAc	1/2	1	2	FACETS	0.858	0.78	0.94	0.858	0.78	0.94	CLONAL	1	TRUE	1	0.64	2		297	426	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436187	110436187	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	144	596	1	ENST00000375856.3:c.2214G>T	p.Glu738Asp	p.E738D	ENST00000375856	NM_003749.2	738	gaG/gaT	1/2	1	2	FACETS	0.962	0.884	1	0.962	0.884	1	CLONAL	1	TRUE	1	0.64	2		597	468	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436492	110436492	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	197	851	0	ENST00000375856.3:c.1909A>C	p.Ile637Leu	p.I637L	ENST00000375856	NM_003749.2	637	Atc/Ctc	1/2	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.64	2		851	596	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061256	38061256	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	202	684	0	ENST00000250448.2:c.733A>G	p.Thr245Ala	p.T245A	ENST00000250448	NM_004496.3	245	Acg/Gcg	2/2	1	2	FACETS	0.991	0.923	1	0.991	0.923	1	CLONAL	1	TRUE	1	0.64	2		684	637	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610234	81610234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370450995	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	224	385	0	ENST00000298171.2:c.1832C>T	p.Pro611Leu	p.P611L	ENST00000298171	NM_000369.2	611	cCg/cTg	10/10	1	2	FACETS	0.97	0.906	1	0.97	0.906	1	CLONAL	1	TRUE	1	0.64	2		385	722	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95556920	95556920	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	219	454	0	ENST00000393063.1:c.5684G>A	p.Arg1895Gln	p.R1895Q	ENST00000393063	NM_030621.3	1895	cGa/cAa	28/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.64	2		454	631	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557540	95557540	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	222	622	0	ENST00000393063.1:c.5527G>T	p.Glu1843Ter	p.E1843*	ENST00000393063	NM_030621.3	1843	Gaa/Taa	26/28	1	2	FACETS	0.936	0.875	0.999	0.936	0.875	0.999	CLONAL	1	TRUE	1	0.64	2		622	741	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570433	95570433	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1417728231	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	128	255	0	ENST00000393063.1:c.3300A>C	p.Lys1100Asn	p.K1100N	ENST00000393063	NM_030621.3	1100	aaA/aaC	22/28	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.64	2		255	359	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590627	95590627	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	271	806	0	ENST00000393063.1:c.1282G>T	p.Glu428Ter	p.E428*	ENST00000393063	NM_030621.3	428	Gag/Tag	9/28	1	2	FACETS	0.981	0.923	1	0.981	0.923	1	CLONAL	1	TRUE	1	0.64	2		806	863	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105236731	105236731	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745803788	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	234	589	2	ENST00000349310.3:c.1390G>A	p.Glu464Lys	p.E464K	ENST00000349310	NM_001014432.1	464	Gag/Aag	15/15	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.64	2		591	689	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003323	42003323	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	301	490	0	ENST00000219905.7:c.2860T>G	p.Phe954Val	p.F954V	ENST00000219905	NM_001164273.1	954	Ttt/Gtt	8/24	1	2	FACETS	0.919	0.866	0.972	0.919	0.866	0.972	CLONAL	1	TRUE	1	0.64	2		490	1024	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005410	42005410	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	322	845	0	ENST00000219905.7:c.3146A>C	p.Asn1049Thr	p.N1049T	ENST00000219905	NM_001164273.1	1049	aAt/aCt	9/24	1	2	FACETS	0.943	0.891	0.996	0.943	0.891	0.996	CLONAL	1	TRUE	1	0.64	2		845	1067	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042485	42042485	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	242	465	0	ENST00000219905.7:c.6680A>C	p.Lys2227Thr	p.K2227T	ENST00000219905	NM_001164273.1	2227	aAa/aCa	17/24	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.64	2		465	685	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052578	42052578	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	297	363	0	ENST00000219905.7:c.7249G>T	p.Glu2417Ter	p.E2417*	ENST00000219905	NM_001164273.1	2417	Gaa/Taa	20/24	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.64	2		363	904	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007794	45007794	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	197	440	0	ENST00000558401.1:c.241T>C	p.Ser81Pro	p.S81P	ENST00000558401	NM_004048.2	81	Tct/Cct	2/4	1	2	FACETS	0.985	0.917	1	0.985	0.917	1	CLONAL	1	TRUE	1	0.64	2		440	625	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727487	88727487	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1352987249	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	197	511	0	ENST00000360948.2:c.292G>T	p.Asp98Tyr	p.D98Y	ENST00000360948	NM_001012338.2	98	Gac/Tac	3/19	1	2	FACETS	0.957	0.891	1	0.957	0.891	1	CLONAL	1	TRUE	1	0.64	2		511	643	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292798	91292798	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	182	621	1	ENST00000355112.3:c.300G>T	p.Gln100His	p.Q100H	ENST00000355112	NM_000057.2	100	caG/caT	3/22	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.64	2		622	547	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293253	91293253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	105	290	1	ENST00000355112.3:c.755C>T	p.Ala252Val	p.A252V	ENST00000355112	NM_000057.2	252	gCt/gTt	3/22	1	2	FACETS	0.959	0.869	1	0.959	0.869	1	CLONAL	1	TRUE	1	0.64	2		291	342	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99192862	99192862	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	213	375	0	ENST00000268035.6:c.52T>C	p.Phe18Leu	p.F18L	ENST00000268035	NM_000875.3	18	Ttt/Ctt	1/21	1	2	FACETS	0.939	0.876	1	0.939	0.876	1	CLONAL	1	TRUE	1	0.64	2		375	709	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442819	99442819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1365982598	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	217	442	0	ENST00000268035.6:c.1216C>T	p.Arg406Cys	p.R406C	ENST00000268035	NM_000875.3	406	Cgc/Tgc	5/21	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.64	2		442	657	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99456289	99456289	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	172	424	1	ENST00000268035.6:c.1606A>G	p.Thr536Ala	p.T536A	ENST00000268035	NM_000875.3	536	Aca/Gca	8/21	1	2	FACETS	0.922	0.853	0.993	0.922	0.853	0.993	CLONAL	1	TRUE	1	0.64	2		425	583	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486151	99486151	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	183	386	1	ENST00000268035.6:c.3458-1G>T		p.X1153_splice	ENST00000268035	NM_000875.3	1153			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.64	2		387	553	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343685	343685	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs750092964	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	269	670	0	ENST00000262320.3:c.1989G>T	p.Glu663Asp	p.E663D	ENST00000262320	NM_003502.3	663	gaG/gaT	8/11	1	2	FACETS	0.997	0.938	1	0.997	0.938	1	CLONAL	1	TRUE	1	0.64	2		670	843	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098712	2098712	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	252	513	0	ENST00000219476.3:c.96G>T	p.Glu32Asp	p.E32D	ENST00000219476	NM_000548.3	32	gaG/gaT	2/42	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.64	2		513	743	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2100479	2100479	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	213	498	0	ENST00000219476.3:c.217T>A	p.Phe73Ile	p.F73I	ENST00000219476	NM_000548.3	73	Ttt/Att	3/42	1	2	FACETS	0.947	0.883	1	0.947	0.883	1	CLONAL	1	TRUE	1	0.64	2		498	703	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121909	2121909	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760489473	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	184	760	1	ENST00000219476.3:c.2071C>T	p.Arg691Cys	p.R691C	ENST00000219476	NM_000548.3	691	Cgc/Tgc	19/42	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.64	2		761	564	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789684	3789684	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	258	610	0	ENST00000262367.5:c.4175G>A	p.Arg1392Gln	p.R1392Q	ENST00000262367	NM_004380.2	1392	cGa/cAa	25/31	1	2	FACETS	0.999	0.939	1	0.999	0.939	1	CLONAL	1	TRUE	1	0.64	2		610	807	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832822	3832822	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	248	510	1	ENST00000262367.5:c.1436G>T	p.Ser479Ile	p.S479I	ENST00000262367	NM_004380.2	479	aGc/aTc	6/31	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.64	2		511	747	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857464	9857464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	209	473	0	ENST00000330684.3:c.3937C>T	p.Leu1313Phe	p.L1313F	ENST00000330684	NM_001134407.1	1313	Ctc/Ttc	13/13	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.64	2		473	644	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024573	14024573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373570729	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	160	305	1	ENST00000311895.7:c.799C>T	p.Arg267Cys	p.R267C	ENST00000311895	NM_005236.2	267	Cgc/Tgc	5/11	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.64	2		306	498	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029576	14029576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751782722	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	126	205	0	ENST00000311895.7:c.1787C>T	p.Ala596Val	p.A596V	ENST00000311895	NM_005236.2	596	gCg/gTg	8/11	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.64	2		205	375	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649442	23649442	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	204	601	0	ENST00000261584.4:c.57G>T	p.Glu19Asp	p.E19D	ENST00000261584	NM_024675.3	19	gaG/gaT	2/13	1	2	FACETS	0.935	0.871	1	0.935	0.871	1	CLONAL	1	TRUE	1	0.64	2		601	682	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67132671	67132671	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	235	609	0	ENST00000412916.2:c.554A>C	p.Lys185Thr	p.K185T	ENST00000412916		185	aAa/aCa	6/6	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.64	2		609	673	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650710	67650710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243010179	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	276	546	1	ENST00000264010.4:c.1015C>T	p.Arg339Trp	p.R339W	ENST00000264010	NM_006565.3	339	Cgg/Tgg	5/12	1	2	FACETS	0.968	0.911	1	0.968	0.911	1	CLONAL	1	TRUE	1	0.64	2		547	891	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842445	68842445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	169	555	0	ENST00000261769.5:c.506G>A	p.Gly169Asp	p.G169D	ENST00000261769	NM_004360.3	169	gGc/gAc	4/16	1	2	FACETS	0.838	0.774	0.905	0.838	0.774	0.905	CLONAL	1	TRUE	1	0.64	2		555	630	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863571	68863571	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	262	508	0	ENST00000261769.5:c.2310C>A	p.Ser770Arg	p.S770R	ENST00000261769	NM_004360.3	770	agC/agA	15/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.64	2		508	739	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821909	72821909	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	210	549	0	ENST00000268489.5:c.10266A>C	p.Glu3422Asp	p.E3422D	ENST00000268489	NM_006885.3	3422	gaA/gaC	10/10	0.124176010467909	0	FACETS	0.332	0.309	0.355			1	INDETERMINATE	1	TRUE	0	0.64	0		549	712	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827964	72827964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768307205	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	330	998	1	ENST00000268489.5:c.8617G>A	p.Glu2873Lys	p.E2873K	ENST00000268489	NM_006885.3	2873	Gaa/Aaa	9/10	0.124176010467909	0	FACETS	0.343	0.325	0.363			1	INDETERMINATE	1	TRUE	0	0.64	0		999	1081	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828699	72828699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762362472	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	315	874	2	ENST00000268489.5:c.7882G>A	p.Glu2628Lys	p.E2628K	ENST00000268489	NM_006885.3	2628	Gaa/Aaa	9/10	0.124176010467909	0	FACETS	0.337	0.318	0.356			1	INDETERMINATE	1	TRUE	0	0.64	0		876	1052	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832615	72832615	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	210	495	0	ENST00000268489.5:c.3968-2A>G		p.X1323_splice	ENST00000268489	NM_006885.3	1323			0.124176010467909	0	FACETS	0.382	0.356	0.408			1	INDETERMINATE	1	TRUE	0	0.64	0		495	619	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993579	72993579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769010742	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	304	475	1	ENST00000268489.5:c.466G>A	p.Ala156Thr	p.A156T	ENST00000268489	NM_006885.3	156	Gcc/Acc	2/10	0.124176010467909	0	FACETS	0.407	0.384	0.429			1	INDETERMINATE	1	TRUE	0	0.64	0		476	841	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81888121	81888121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762900860	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	309	734	0	ENST00000359376.3:c.266G>A	p.Arg89His	p.R89H	ENST00000359376	NM_002661.3	89	cGc/cAc	3/33	0.124176010467909	0	FACETS	0.381	0.36	0.402			1	INDETERMINATE	1	TRUE	0	0.64	0		734	913	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944259	81944259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	278	544	1	ENST00000359376.3:c.1868G>A	p.Arg623His	p.R623H	ENST00000359376	NM_002661.3	623	cGc/cAc	18/33	0.124176010467909	0	FACETS	0.351	0.33	0.372			1	INDETERMINATE	1	TRUE	0	0.64	0		545	891	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953133	81953133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs566611968	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	301	312	1	ENST00000359376.3:c.2099G>A	p.Arg700Gln	p.R700Q	ENST00000359376	NM_002661.3	700	cGg/cAg	20/33	0.124176010467909	0	FACETS	0.356	0.336	0.377			1	INDETERMINATE	1	TRUE	0	0.64	0		313	951	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969848	81969848	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568724894	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	304	736	1	ENST00000359376.3:c.2917G>A	p.Asp973Asn	p.D973N	ENST00000359376	NM_002661.3	973	Gac/Aac	27/33	0.124176010467909	0	FACETS	0.375	0.354	0.397			1	INDETERMINATE	1	TRUE	0	0.64	0		737	911	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346993	89346993	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs758181637	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	217	535	0	ENST00000301030.4:c.5957G>T	p.Arg1986Ile	p.R1986I	ENST00000301030	NM_001256183.1	1986	aGa/aTa	9/13	0.124176010467909	0	FACETS	0.362	0.338	0.386			1	INDETERMINATE	1	TRUE	0	0.64	0		535	675	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348665	89348665	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	339	831	1	ENST00000301030.4:c.4285G>T	p.Asp1429Tyr	p.D1429Y	ENST00000301030	NM_001256183.1	1429	Gat/Tat	9/13	0.124176010467909	0	FACETS	0.347	0.329	0.366			1	INDETERMINATE	1	TRUE	0	0.64	0		832	1098	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349450	89349450	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	355	894	1	ENST00000301030.4:c.3500C>A	p.Ser1167Tyr	p.S1167Y	ENST00000301030	NM_001256183.1	1167	tCt/tAt	9/13	0.124176010467909	0	FACETS	0.38	0.36	0.4			1	INDETERMINATE	1	TRUE	0	0.64	0		895	1051	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979495	7979495	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	226	414	0	ENST00000319144.4:c.1530G>T	p.Glu510Asp	p.E510D	ENST00000319144	NM_001139.2	510	gaG/gaT	11/15	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.64	2		414	703	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108653	8108653	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749454960	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	270	551	0	ENST00000585124.1:c.742C>T	p.Arg248Cys	p.R248C	ENST00000585124	NM_004217.3	248	Cgc/Tgc	8/9	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.64	2		551	815	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8109883	8109883	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs146905713	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	278	579	0	ENST00000585124.1:c.612A>C	p.Glu204Asp	p.E204D	ENST00000585124	NM_004217.3	204	gaA/gaC	7/9	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.64	2		579	793	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013730	12013730	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	168	299	0	ENST00000353533.5:c.672A>C	p.Lys224Asn	p.K224N	ENST00000353533	NM_003010.3	224	aaA/aaC	6/11	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.64	2		299	495	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15938151	15938151	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	271	399	0	ENST00000268712.3:c.7063T>C	p.Ser2355Pro	p.S2355P	ENST00000268712	NM_006311.3	2355	Tct/Cct	45/46	1	2	FACETS	0.969	0.912	1	0.969	0.912	1	CLONAL	1	TRUE	1	0.64	2		399	874	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961900	15961900	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs770977157	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	207	398	0	ENST00000268712.3:c.5895G>T	p.Arg1965Ser	p.R1965S	ENST00000268712	NM_006311.3	1965	agG/agT	38/46	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.64	2		398	618	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971393	15971393	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759642635	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	234	484	0	ENST00000268712.3:c.4556C>T	p.Ser1519Leu	p.S1519L	ENST00000268712	NM_006311.3	1519	tCg/tTg	32/46	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.64	2		484	688	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15973567	15973567	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	240	469	0	ENST00000268712.3:c.4425T>G	p.Ile1475Met	p.I1475M	ENST00000268712	NM_006311.3	1475	atT/atG	31/46	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.64	2		469	690	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024364	16024364	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	197	261	0	ENST00000268712.3:c.1852+2T>C		p.X618_splice	ENST00000268712	NM_006311.3	618			1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.64	2		261	595	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528141	29528141	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	157	713	0	ENST00000356175.3:c.1149C>A	p.Cys383Ter	p.C383*	ENST00000356175	NM_000267.3	383	tgC/tgA	10/57	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.64	2		713	485	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528490	29528490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343309278	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	170	432	0	ENST00000356175.3:c.1247G>A	p.Arg416Gln	p.R416Q	ENST00000356175	NM_000267.3	416	cGa/cAa	11/57	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.64	2		432	516	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560198	29560198	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	138	334	0	ENST00000356175.3:c.3675G>T	p.Met1225Ile	p.M1225I	ENST00000356175	NM_000267.3	1225	atG/atT	27/57	1	2	FACETS	0.9	0.825	0.978	0.9	0.825	0.978	CLONAL	1	TRUE	1	0.64	2		334	479	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586102	29586102	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370852681	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	107	464	0	ENST00000356175.3:c.4322G>A	p.Arg1441Gln	p.R1441Q	ENST00000356175	NM_000267.3	1441	cGg/cAg	32/57	1	2	FACETS	0.942	0.853	1	0.942	0.853	1	CLONAL	1	TRUE	1	0.64	2		464	355	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370280	40370280	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143171571	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	265	558	1	ENST00000293328.3:c.1058G>A	p.Arg353His	p.R353H	ENST00000293328	NM_012448.3	353	cGc/cAc	9/19	0.3	2	FACETS	0.955	0.898	1			1	INDETERMINATE	1	TRUE	NA	0.64	2		559	867	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40460196	40460196	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs758514352	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	250	378	0	ENST00000345506.4:c.1907C>T	p.Pro636Leu	p.P636L	ENST00000345506	NM_003152.3	636	cCg/cTg	17/20	0.3	2	FACETS	0.936	0.878	0.995			1	INDETERMINATE	1	TRUE	NA	0.64	2		378	835	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481655	40481655	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	339	470	0	ENST00000264657.5:c.1150T>G	p.Phe384Val	p.F384V	ENST00000264657	NM_139276.2	384	Ttt/Gtt	13/24	0.3	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.64	2		470	991	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246754	41246754	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	185	569	0	ENST00000357654.3:c.794C>A	p.Ser265Tyr	p.S265Y	ENST00000357654	NM_007294.3	265	tCt/tAt	10/23	0.3	2	FACETS	0.926	0.86	0.995			1	INDETERMINATE	1	TRUE	NA	0.64	2		569	624	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435452	56435452	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs766948615	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	167	602	0	ENST00000407977.2:c.1685T>G	p.Phe562Cys	p.F562C	ENST00000407977		562	tTc/tGc	9/10	1	2	FACETS	0.945	0.874	1	0.945	0.874	1	CLONAL	1	TRUE	1	0.64	2		602	552	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533932	63533932	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749846538	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	116	389	0	ENST00000307078.5:c.1222G>A	p.Glu408Lys	p.E408K	ENST00000307078	NM_004655.3	408	Gag/Aag	6/11	1	2	FACETS	0.882	0.801	0.966	0.882	0.801	0.966	CLONAL	1	TRUE	1	0.64	2		389	411	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743329	743329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	201	443	0	ENST00000314574.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000314574	NM_005433.3	271	Gaa/Aaa	7/12	1	2	FACETS	0.882	0.821	0.946	0.882	0.821	0.946	CLONAL	1	TRUE	1	0.64	2		443	712	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745711	745711	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs530952013	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	136	438	0	ENST00000314574.4:c.721A>G	p.Thr241Ala	p.T241A	ENST00000314574	NM_005433.3	241	Aca/Gca	6/12	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.64	2		438	383	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39575929	39575929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	108	260	0	ENST00000262039.4:c.862C>T	p.Pro288Ser	p.P288S	ENST00000262039	NM_002647.2	288	Ccc/Tcc	8/25	1	2	FACETS	0.805	0.728	0.886	0.805	0.728	0.886	CLONAL	1	TRUE	1	0.64	2		260	419	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45391501	45391501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	113	277	1	ENST00000262160.6:c.659C>T	p.Thr220Met	p.T220M	ENST00000262160	NM_005901.5	220	aCg/aTg	6/11	1	2	FACETS	0.91	0.826	0.997	0.91	0.826	0.997	CLONAL	1	TRUE	1	0.64	2		278	388	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48573650	48573650	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	79	261	1	ENST00000342988.3:c.234G>T	p.Leu78Phe	p.L78F	ENST00000342988	NM_005359.5	78	ttG/ttT	2/12	1	2	FACETS	0.939	0.836	1	0.939	0.836	1	CLONAL	1	TRUE	1	0.64	2		262	263	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56412904	56412904	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	189	545	1	ENST00000348428.3:c.1918G>T	p.Asp640Tyr	p.D640Y	ENST00000348428	NM_006785.3	640	Gat/Tat	16/17	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.64	2		546	571	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414797	56414797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	301	540	0	ENST00000348428.3:c.2198C>T	p.Ser733Phe	p.S733F	ENST00000348428	NM_006785.3	733	tCt/tTt	17/17	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.64	2		540	884	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60795873	60795873	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	221	518	0	ENST00000333681.4:c.705T>G	p.Tyr235Ter	p.Y235*	ENST00000333681		235	taT/taG	3/3	1	2	FACETS	0.884	0.825	0.945	0.884	0.825	0.945	CLONAL	1	TRUE	1	0.64	2		518	781	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632366	1632366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202212254	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	274	717	0	ENST00000344749.5:c.184G>A	p.Gly62Ser	p.G62S	ENST00000344749	NM_001136139.2	62	Ggc/Agc	4/19	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.64	2		717	774	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222493	2222493	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	108	273	0	ENST00000398665.3:c.3325G>T	p.Ala1109Ser	p.A1109S	ENST00000398665	NM_032482.2	1109	Gcc/Tcc	24/28	1	2	FACETS	0.837	0.758	0.921	0.837	0.758	0.921	CLONAL	1	TRUE	1	0.64	2		273	403	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226775	2226775	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1440793289	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	166	430	0	ENST00000398665.3:c.4255G>A	p.Asp1419Asn	p.D1419N	ENST00000398665	NM_032482.2	1419	Gac/Aac	27/28	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.64	2		430	495	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3094690	3094690	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	82	336	0	ENST00000078429.4:c.41A>C	p.Glu14Ala	p.E14A	ENST00000078429	NM_002067.2	14	gAg/gCg	1/7	1	2	FACETS	0.743	0.66	0.83	0.743	0.66	0.83	SUBCLONAL	1	TRUE	1	0.64	2		336	345	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142931	7142931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754190685	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	269	556	2	ENST00000302850.5:c.2438G>A	p.Arg813Gln	p.R813Q	ENST00000302850	NM_000208.2	813	cGa/cAa	12/22	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.64	2		558	798	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291166	10291166	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	247	669	0	ENST00000340748.4:c.305A>G	p.Glu102Gly	p.E102G	ENST00000340748		102	gAa/gGa	4/40	1	2	FACETS	0.879	0.824	0.936	0.879	0.824	0.936	CLONAL	1	TRUE	1	0.64	2		669	878	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107179	11107179	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	225	456	0	ENST00000358026.2:c.1771A>C	p.Asn591His	p.N591H	ENST00000358026	NM_001128849.1	591	Aat/Cat	11/36	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.64	2		456	676	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132552	11132552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	228	646	1	ENST00000358026.2:c.2768C>T	p.Ala923Val	p.A923V	ENST00000358026	NM_001128849.1	923	gCg/gTg	19/36	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.64	2		647	712	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132617	11132617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1445478818	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	248	687	0	ENST00000358026.2:c.2833G>A	p.Ala945Thr	p.A945T	ENST00000358026	NM_001128849.1	945	Gca/Aca	19/36	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.64	2		687	707	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054624	13054624	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	344	758	0	ENST00000316448.5:c.1151A>G	p.Asp384Gly	p.D384G	ENST00000316448	NM_004343.3	384	gAc/gGc	9/9	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.64	2		758	983	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298770	15298770	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	192	710	0	ENST00000263388.2:c.1528G>A	p.Glu510Lys	p.E510K	ENST00000263388	NM_000435.2	510	Gaa/Aaa	10/33	1	2	FACETS	0.98	0.912	1	0.98	0.912	1	CLONAL	1	TRUE	1	0.64	2		710	612	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955206	17955206	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	200	648	0	ENST00000458235.1:c.21G>T	p.Glu7Asp	p.E7D	ENST00000458235	NM_000215.3	7	gaG/gaT	2/24	1	2	FACETS	0.984	0.917	1	0.984	0.917	1	CLONAL	1	TRUE	1	0.64	2		648	635	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260201	19260201	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	191	471	0	ENST00000162023.5:c.92A>C	p.Lys31Thr	p.K31T	ENST00000162023		31	aAg/aCg	7/13	1	2	FACETS	0.971	0.902	1	0.971	0.902	1	CLONAL	1	TRUE	1	0.64	2		471	615	SUCCESS
AXL	558	MSKCC	GRCh37	19	41736905	41736905	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	215	582	0	ENST00000301178.4:c.620C>T	p.Ala207Val	p.A207V	ENST00000301178	NM_021913.4	207	gCc/gTc	5/20	1	2	FACETS	0.896	0.835	0.958	0.896	0.835	0.958	CLONAL	1	TRUE	1	0.64	2		582	750	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754717	41754717	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749923407	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	203	570	1	ENST00000301178.4:c.1703C>T	p.Thr568Met	p.T568M	ENST00000301178	NM_021913.4	568	aCg/aTg	14/20	1	2	FACETS	0.874	0.813	0.936	0.874	0.813	0.936	CLONAL	1	TRUE	1	0.64	2		571	726	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793550	42793550	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	215	773	0	ENST00000575354.2:c.1352A>C	p.Asp451Ala	p.D451A	ENST00000575354	NM_015125.3	451	gAt/gCt	8/20	1	2	FACETS	0.963	0.899	1	0.963	0.899	1	CLONAL	1	TRUE	1	0.64	2		773	698	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794015	42794015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	237	580	1	ENST00000575354.2:c.1376G>A	p.Gly459Asp	p.G459D	ENST00000575354	NM_015125.3	459	gGc/gAc	9/20	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.64	2		581	707	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796574	42796574	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	159	701	0	ENST00000575354.2:c.3131C>T	p.Ser1044Leu	p.S1044L	ENST00000575354	NM_015125.3	1044	tCg/tTg	13/20	1	2	FACETS	0.98	0.905	1	0.98	0.905	1	CLONAL	1	TRUE	1	0.64	2		701	507	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860924	45860924	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	223	546	0	ENST00000391945.4:c.1271G>T	p.Arg424Ile	p.R424I	ENST00000391945	NM_000400.3	424	aGa/aTa	13/23	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.64	2		546	697	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906366	50906366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762494977	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	226	712	0	ENST00000440232.2:c.1027C>T	p.Arg343Cys	p.R343C	ENST00000440232	NM_002691.3	343	Cgc/Tgc	9/27	1	2	FACETS	0.97	0.907	1	0.97	0.907	1	CLONAL	1	TRUE	1	0.64	2		712	728	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52716335	52716335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	200	485	0	ENST00000322088.6:c.779G>A	p.Arg260His	p.R260H	ENST00000322088	NM_014225.5	260	cGc/cAc	6/15	1	2	FACETS	0.986	0.918	1	0.986	0.918	1	CLONAL	1	TRUE	1	0.64	2		485	634	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52729023	52729023	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	231	488	0	ENST00000322088.6:c.1715A>G	p.Asp572Gly	p.D572G	ENST00000322088	NM_014225.5	572	gAt/gGt	14/15	1	2	FACETS	0.986	0.923	1	0.986	0.923	1	CLONAL	1	TRUE	1	0.64	2		488	732	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019139	31019139	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	263	361	0	ENST00000375687.4:c.734A>G	p.Asn245Ser	p.N245S	ENST00000375687	NM_015338.5	245	aAc/aGc	9/13	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.64	2		361	775	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022418	31022418	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	114	200	0	ENST00000375687.4:c.1903G>T	p.Glu635Ter	p.E635*	ENST00000375687	NM_015338.5	635	Gag/Tag	13/13	1	2	FACETS	0.942	0.857	1	0.942	0.857	1	CLONAL	1	TRUE	1	0.64	2		200	378	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31025100	31025100	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	184	383	0	ENST00000375687.4:c.4585G>T	p.Gly1529Ter	p.G1529*	ENST00000375687	NM_015338.5	1529	Gga/Tga	13/13	1	2	FACETS	0.958	0.89	1	0.958	0.89	1	CLONAL	1	TRUE	1	0.64	2		383	600	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389213	31389213	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	199	353	0	ENST00000328111.2:c.2126A>G	p.Asp709Gly	p.D709G	ENST00000328111	NM_006892.3	709	gAc/gGc	19/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.64	2		353	547	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944415	40944415	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	193	493	1	ENST00000373198.4:c.2087C>A	p.Ser696Tyr	p.S696Y	ENST00000373198	NM_133170.3	696	tCt/tAt	12/32	1	2	FACETS	0.853	0.792	0.916	0.853	0.792	0.916	CLONAL	1	TRUE	1	0.64	2		494	707	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306602	41306602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1419824411	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	244	612	0	ENST00000373198.4:c.1057G>A	p.Asp353Asn	p.D353N	ENST00000373198	NM_133170.3	353	Gat/Aat	7/32	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.64	2		612	719	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514513	41514513	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	218	508	0	ENST00000373198.4:c.148A>G	p.Asn50Asp	p.N50D	ENST00000373198	NM_133170.3	50	Aat/Gat	2/32	1	2	FACETS	0.936	0.874	1	0.936	0.874	1	CLONAL	1	TRUE	1	0.64	2		508	728	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54963246	54963246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745894289	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	219	267	0	ENST00000312783.6:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000312783	NM_198436.1	3	cGa/cAa	3/10	1	2	FACETS	0.965	0.902	1	0.965	0.902	1	CLONAL	1	TRUE	1	0.64	2		267	709	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484406	57484406	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	237	603	0	ENST00000371085.3:c.587A>G	p.Asp196Gly	p.D196G	ENST00000371085	NM_000516.4	196	gAc/gGc	8/13	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.64	2		603	727	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164440	36164440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	57	135	0	ENST00000300305.3:c.1435C>T	p.Pro479Ser	p.P479S	ENST00000300305		479	Ccc/Tcc	8/8	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.64	2		135	151	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21304014	21304014	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	212	530	0	ENST00000354336.3:c.793A>G	p.Lys265Glu	p.K265E	ENST00000354336	NM_005207.3	265	Aaa/Gaa	3/3	1	2	FACETS	0.998	0.931	1	0.998	0.931	1	CLONAL	1	TRUE	1	0.64	2		530	664	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092906	29092906	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	236	709	0	ENST00000328354.6:c.1078G>T	p.Glu360Ter	p.E360*	ENST00000328354	NM_007194.3	360	Gag/Tag	10/15	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.64	2		709	725	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30090776	30090776	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	260	525	0	ENST00000338641.4:c.1773C>A	p.Phe591Leu	p.F591L	ENST00000338641	NM_000268.3	591	ttC/ttA	16/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.64	2		525	763	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317422	1317422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759127718	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	243	762	0	ENST00000400841.2:c.643C>T	p.Arg215Trp	p.R215W	ENST00000400841		215	Cgg/Tgg	5/6	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.64	2		762	717	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15827398	15827398	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	181	461	0	ENST00000307771.7:c.514T>A	p.Cys172Ser	p.C172S	ENST00000307771	NM_005089.3	172	Tgt/Agt	7/11	1	2	FACETS	0.946	0.877	1	0.946	0.877	1	CLONAL	1	TRUE	1	0.64	2		461	598	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841040	15841040	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	302	863	0	ENST00000307771.7:c.1124G>T	p.Ser375Ile	p.S375I	ENST00000307771	NM_005089.3	375	aGc/aTc	11/11	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.64	2		863	942	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841178	15841178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753128407	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	195	602	0	ENST00000307771.7:c.1262G>A	p.Arg421Gln	p.R421Q	ENST00000307771	NM_005089.3	421	cGa/cAa	11/11	1	2	FACETS	0.951	0.884	1	0.951	0.884	1	CLONAL	1	TRUE	1	0.64	2		602	641	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923726	39923726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775087931	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	301	692	0	ENST00000378444.4:c.3365C>T	p.Ser1122Leu	p.S1122L	ENST00000378444	NM_001123385.1	1122	tCg/tTg	7/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.64	2		692	876	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932139	39932139	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	267	740	1	ENST00000378444.4:c.2460C>A	p.Asn820Lys	p.N820K	ENST00000378444	NM_001123385.1	820	aaC/aaA	4/15	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.64	2		741	754	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933673	39933673	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	186	583	0	ENST00000378444.4:c.926A>G	p.Asn309Ser	p.N309S	ENST00000378444	NM_001123385.1	309	aAc/aGc	4/15	1	2	FACETS	0.9	0.835	0.967	0.9	0.835	0.967	CLONAL	1	TRUE	1	0.64	2		583	646	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937104	39937104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	222	616	1	ENST00000378444.4:c.79G>A	p.Glu27Lys	p.E27K	ENST00000378444	NM_001123385.1	27	Gaa/Aaa	2/15	1	2	FACETS	0.935	0.873	0.998	0.935	0.873	0.998	CLONAL	1	TRUE	1	0.64	2		617	742	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938548	44938548	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	190	488	0	ENST00000377967.4:c.3096T>G	p.Ile1032Met	p.I1032M	ENST00000377967	NM_021140.2	1032	atT/atG	20/29	1	2	FACETS	0.792	0.734	0.852	0.792	0.734	0.852	SUBCLONAL	1	TRUE	1	0.64	2		488	750	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942809	44942809	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1236403360	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	244	814	0	ENST00000377967.4:c.3389A>G	p.Asn1130Ser	p.N1130S	ENST00000377967	NM_021140.2	1130	aAc/aGc	23/29	1	2	FACETS	0.947	0.888	1	0.947	0.888	1	CLONAL	1	TRUE	1	0.64	2		814	805	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038745	47038745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556777782	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	161	650	1	ENST00000377604.3:c.752C>T	p.Thr251Met	p.T251M	ENST00000377604	NM_001204468.1	251	aCg/aTg	9/24	1	2	FACETS	0.988	0.913	1	0.988	0.913	1	CLONAL	1	TRUE	1	0.64	2		651	509	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53241016	53241016	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	312	759	1	ENST00000375401.3:c.1195G>A	p.Glu399Lys	p.E399K	ENST00000375401	NM_004187.3	399	Gag/Aag	9/26	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.64	2		760	950	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246390	53246390	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	307	647	0	ENST00000375401.3:c.592C>T	p.Arg198Ter	p.R198*	ENST00000375401	NM_004187.3	198	Cga/Tga	5/26	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.64	2		647	944	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63409914	63409914	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	277	686	1	ENST00000330258.3:c.3253C>A	p.Pro1085Thr	p.P1085T	ENST00000330258	NM_152424.3	1085	Cct/Act	2/2	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.64	2		687	829	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410481	63410481	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	280	633	0	ENST00000330258.3:c.2686C>A	p.Leu896Ile	p.L896I	ENST00000330258	NM_152424.3	896	Ctc/Atc	2/2	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.64	2		633	821	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411603	63411603	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	271	732	0	ENST00000330258.3:c.1564G>T	p.Asp522Tyr	p.D522Y	ENST00000330258	NM_152424.3	522	Gat/Tat	2/2	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.64	2		732	840	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411759	63411759	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	278	728	0	ENST00000330258.3:c.1408G>T	p.Gly470Cys	p.G470C	ENST00000330258	NM_152424.3	470	Ggt/Tgt	2/2	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.64	2		728	860	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412430	63412430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	293	864	1	ENST00000330258.3:c.737C>T	p.Ser246Phe	p.S246F	ENST00000330258	NM_152424.3	246	tCt/tTt	2/2	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.64	2		865	910	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412964	63412964	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	275	758	0	ENST00000330258.3:c.203C>A	p.Thr68Asn	p.T68N	ENST00000330258	NM_152424.3	68	aCt/aAt	2/2	1	2	FACETS	0.96	0.904	1	0.96	0.904	1	CLONAL	1	TRUE	1	0.64	2		758	895	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413051	63413051	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	318	784	1	ENST00000330258.3:c.116G>A	p.Gly39Glu	p.G39E	ENST00000330258	NM_152424.3	39	gGa/gAa	2/2	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.64	2		785	941	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345972	70345972	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	271	470	0	ENST00000374080.3:c.2509T>C	p.Ser837Pro	p.S837P	ENST00000374080		837	Tca/Cca	18/45	1	2	FACETS	0.966	0.908	1	0.966	0.908	1	CLONAL	1	TRUE	1	0.64	2		470	877	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357481	70357481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	230	719	0	ENST00000374080.3:c.5822C>T	p.Ser1941Phe	p.S1941F	ENST00000374080		1941	tCc/tTc	40/45	1	2	FACETS	0.89	0.831	0.949	0.89	0.831	0.949	CLONAL	1	TRUE	1	0.64	2		719	808	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360668	70360668	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	56	179	0	ENST00000374080.3:c.6228G>T	p.Gln2076His	p.Q2076H	ENST00000374080		2076	caG/caT	42/45	1	2	FACETS	0.871	0.757	0.99	0.871	0.757	0.99	CLONAL	1	TRUE	1	0.64	2		179	201	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76855205	76855205	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	166	749	0	ENST00000373344.5:c.5782A>G	p.Thr1928Ala	p.T1928A	ENST00000373344	NM_000489.3	1928	Aca/Gca	24/35	0.3	0	FACETS	0.355	0.328	0.383			1	INDETERMINATE	1	TRUE	0	0.64	0		749	526	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888698	76888698	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	127	609	0	ENST00000373344.5:c.5131C>A	p.Pro1711Thr	p.P1711T	ENST00000373344	NM_000489.3	1711	Cca/Aca	19/35	0.3	0	FACETS	0.313	0.286	0.342			1	INDETERMINATE	1	TRUE	0	0.64	0		609	456	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937828	76937828	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	145	628	0	ENST00000373344.5:c.2920A>G	p.Ser974Gly	p.S974G	ENST00000373344	NM_000489.3	974	Agc/Ggc	9/35	0.3	0	FACETS	0.379	0.349	0.41			1	INDETERMINATE	1	TRUE	0	0.64	0		628	430	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937891	76937891	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	127	618	0	ENST00000373344.5:c.2857A>G	p.Thr953Ala	p.T953A	ENST00000373344	NM_000489.3	953	Aca/Gca	9/35	0.3	0	FACETS	0.368	0.337	0.401			1	INDETERMINATE	1	TRUE	0	0.64	0		618	388	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938330	76938330	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	137	589	0	ENST00000373344.5:c.2418G>T	p.Lys806Asn	p.K806N	ENST00000373344	NM_000489.3	806	aaG/aaT	9/35	0.3	0	FACETS	0.399	0.367	0.432			1	INDETERMINATE	1	TRUE	0	0.64	0		589	386	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938710	76938710	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	122	634	0	ENST00000373344.5:c.2038G>T	p.Glu680Ter	p.E680*	ENST00000373344	NM_000489.3	680	Gaa/Taa	9/35	0.3	0	FACETS	0.335	0.305	0.366			1	INDETERMINATE	1	TRUE	0	0.64	0		634	410	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76954080	76954080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	174	768	0	ENST00000373344.5:c.171G>A	p.Met57Ile	p.M57I	ENST00000373344	NM_000489.3	57	atG/atA	3/35	0.3	2	FACETS	0.851	0.787	0.917			1	INDETERMINATE	1	TRUE	NA	0.64	2		768	639	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123156522	123156522	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	193	663	0	ENST00000218089.9:c.44+1G>T		p.X15_splice	ENST00000218089	NM_001042749.1	15			0.3	2	FACETS	0.91	0.845	0.976			1	INDETERMINATE	1	TRUE	NA	0.64	2		663	663	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179058	123179058	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	127	672	1	ENST00000218089.9:c.507G>T	p.Lys169Asn	p.K169N	ENST00000218089	NM_001042749.1	169	aaG/aaT	8/35	0.3	2	FACETS	0.947	0.866	1			1	INDETERMINATE	1	TRUE	NA	0.64	2		673	419	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195187	123195187	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	147	560	0	ENST00000218089.9:c.1530G>T	p.Glu510Asp	p.E510D	ENST00000218089	NM_001042749.1	510	gaG/gaT	16/35	0.3	2	FACETS	0.921	0.846	0.997			1	INDETERMINATE	1	TRUE	NA	0.64	2		560	499	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195719	123195719	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	152	656	0	ENST00000218089.9:c.1633A>C	p.Lys545Gln	p.K545Q	ENST00000218089	NM_001042749.1	545	Aaa/Caa	17/35	0.3	2	FACETS	0.941	0.866	1			1	INDETERMINATE	1	TRUE	NA	0.64	2		656	505	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210314	123210314	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	153	521	0	ENST00000218089.9:c.2666A>G	p.Tyr889Cys	p.Y889C	ENST00000218089	NM_001042749.1	889	tAt/tGt	26/35	0.3	2	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.64	2		521	442	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217381	123217381	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	204	421	0	ENST00000218089.9:c.3035G>A	p.Arg1012Gln	p.R1012Q	ENST00000218089	NM_001042749.1	1012	cGa/cAa	29/35	0.3	2	FACETS	1	0.961	1			1	INDETERMINATE	1	TRUE	NA	0.64	2		421	611	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224443	123224443	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	248	684	5	ENST00000218089.9:c.3296G>T	p.Ser1099Ile	p.S1099I	ENST00000218089	NM_001042749.1	1099	aGt/aTt	31/35	0.3	2	FACETS	0.99	0.929	1			1	INDETERMINATE	1	TRUE	NA	0.64	2		689	783	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229241	123229241	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1569521908	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	270	270	0	ENST00000218089.9:c.3725G>A	p.Arg1242Gln	p.R1242Q	ENST00000218089	NM_001042749.1	1242	cGa/cAa	34/35	0.3	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.64	2		270	769	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480521	123480521	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	210	435	0	ENST00000371139.4:c.29A>C	p.Lys10Thr	p.K10T	ENST00000371139	NM_001114937.2	10	aAa/aCa	1/4	0.3	2	FACETS	0.972	0.907	1			1	INDETERMINATE	1	TRUE	NA	0.64	2		435	675	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771860	135771861	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	247	598	0	ENST00000298552.3:c.3256dup	p.Ser1086LysfsTer13	p.S1086Kfs*13	ENST00000298552	NM_001162426.1	1086	agc/aAgc	23/23	1	2	FACETS	0.886	0.83	0.944	0.886	0.83	0.944	CLONAL	1	TRUE	1	0.64	2		598	871	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158364	106158365	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	229	610	0	ENST00000380013.4:c.3269dup	p.Thr1091AspfsTer13	p.T1091Dfs*13	ENST00000380013	NM_001127208.2	1089	gaa/gAaa	3/11	1	2	FACETS	0.952	0.89	1	0.952	0.89	1	CLONAL	1	TRUE	1	0.64	2		610	752	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218483	1218486	+	stop_gained	Nonsense_Mutation	ONP	GAAG	GAAG	AAAT	novel	NA	P-0004379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	189	511	0	ENST00000326873.7:c.358_361delinsAAAT	p.Glu120_Glu121delinsLysTer	p.E120_E121delinsK*	ENST00000326873	NM_000455.4	120	GAAGag/AAATag	2/10	1	2	FACETS	0.878	0.814	0.943	0.878	0.814	0.943	CLONAL	1	TRUE	1	0.64	2		511	673	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023076	150023076	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs187759014	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	48	600	0	ENST00000253339.5:c.187C>T	p.Arg63Ter	p.R63*	ENST00000253339		63	Cga/Tga	1/7	0.213688332421629	3	FACETS	0.941	0.799	1	0.471	0.399	0.549	CLONAL	1	TRUE	1	0.34	3		600	351	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	25	449	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.34	2		449	106	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920469	134920469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	111	553	0	ENST00000398015.3:c.2284G>A	p.Asp762Asn	p.D762N	ENST00000398015	NM_004441.4	762	Gac/Aac	12/16	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.34	2		553	575	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170136	32170136	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771019003	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	153	702	0	ENST00000375023.3:c.3472C>T	p.Arg1158Ter	p.R1158*	ENST00000375023	NM_004557.3	1158	Cga/Tga	21/30	0.213688332421629	3	FACETS	0.83	0.762	0.901	0.83	0.762	0.901	CLONAL	2	TRUE	1	0.34	3		702	634	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120487	2120487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1800729	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	161	656	2	ENST00000219476.3:c.1747G>A	p.Ala583Thr	p.A583T	ENST00000219476	NM_000548.3	583	Gcc/Acc	17/42	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.34	2		658	717	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231539	5231539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760884281	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	113	511	2	ENST00000357368.4:c.1937C>T	p.Thr646Met	p.T646M	ENST00000357368	NM_002850.3	646	aCg/aTg	14/38	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.34	2		513	644	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	33	166	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.114195292829279	3	FACETS	0.916	0.761	1	0.916	0.761	1	INDETERMINATE	2	TRUE	1	0.34	3		166	124	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119485	193119485	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	45	547	1	ENST00000367435.3:c.880G>A	p.Asp294Asn	p.D294N	ENST00000367435	NM_024529.4	294	Gat/Aat	9/17	1	2	FACETS	0.802	0.686	0.926	1	0.967	1	CLONAL	2	TRUE	1	0.34	2		548	165	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149251	119149251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267606708	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	58	438	0	ENST00000264033.4:c.1259G>A	p.Arg420Gln	p.R420Q	ENST00000264033	NM_005188.3	420	cGa/cAa	9/16	1	2	FACETS	0.992	0.857	1	0.992	0.857	1	CLONAL	1	TRUE	1	0.34	2		438	344	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500303	99500303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61740868	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	90	565	1	ENST00000268035.6:c.3736C>T	p.Arg1246Cys	p.R1246C	ENST00000268035	NM_000875.3	1246	Cgc/Tgc	21/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.34	2		566	462	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490382	29490382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754096545	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	39	413	0	ENST00000356175.3:c.467G>A	p.Arg156His	p.R156H	ENST00000356175	NM_000267.3	156	cGc/cAc	4/57	1	2	FACETS	0.989	0.826	1	0.989	0.826	1	CLONAL	1	TRUE	1	0.34	2		413	232	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900288	101900288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111854391	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	34	279	2	ENST00000374994.4:c.722C>T	p.Ser241Leu	p.S241L	ENST00000374994	NM_004612.2	241	tCg/tTg	4/9	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.34	2		281	185	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711900	89711900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913294	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	49	459	0	ENST00000371953.3:c.518G>A	p.Arg173His	p.R173H	ENST00000371953	NM_000314.4	173	cGc/cAc	6/9	0.114195292829279	3	FACETS	1	0.964	1	0.74	0.633	0.854	INDETERMINATE	1	TRUE	1	0.34	3		459	228	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037474	12037474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	29	322	1	ENST00000396373.4:c.1105C>T	p.Arg369Trp	p.R369W	ENST00000396373	NM_001987.4	369	Cgg/Tgg	6/8	0.114195292829279	3	FACETS	1	0.937	1	0.713	0.58	0.858	INDETERMINATE	1	TRUE	1	0.34	3		323	140	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	42	413	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.114195292829279	3	FACETS	1	0.953	1	0.698	0.589	0.816	INDETERMINATE	1	TRUE	1	0.34	3		413	207	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845086	128845086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761395599	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	110	686	0	ENST00000249373.3:c.580G>A	p.Glu194Lys	p.E194K	ENST00000249373	NM_005631.4	194	Gaa/Aaa	3/12	0.114195292829279	3	FACETS	1	0.971	1	0.605	0.544	0.668	INDETERMINATE	1	TRUE	1	0.34	3		686	626	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	94	351	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.34	2		351	404	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57480483	57480483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	61	279	0	ENST00000371085.3:c.478C>T	p.Arg160Cys	p.R160C	ENST00000371085	NM_000516.4	160	Cgt/Tgt	6/13	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.34	2		279	338	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512376	149512376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746410632	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	146	531	1	ENST00000261799.4:c.1064G>A	p.Arg355His	p.R355H	ENST00000261799	NM_002609.3	355	cGc/cAc	7/23	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.34	2		532	674	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060694	38060694	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	181	855	0	ENST00000250448.2:c.1295C>T	p.Thr432Met	p.T432M	ENST00000250448	NM_004496.3	432	aCg/aTg	2/2	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.34	2		855	860	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298671	11298671	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	60	405	0	ENST00000361445.4:c.1790A>G	p.His597Arg	p.H597R	ENST00000361445	NM_004958.3	597	cAc/cGc	12/58	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.34	2		405	283	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237761	16237761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	33	351	0	ENST00000375759.3:c.1208G>A	p.Gly403Asp	p.G403D	ENST00000375759	NM_015001.2	403	gGc/gAc	5/15	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.34	2		351	140	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27093043	27093043	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	31	276	0	ENST00000324856.7:c.2974G>T	p.Glu992Ter	p.E992*	ENST00000324856	NM_006015.4	992	Gaa/Taa	10/20	1	2	FACETS	1	0.844	1	1	0.844	1	CLONAL	1	TRUE	1	0.34	2		276	176	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27102139	27102139	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	60	482	0	ENST00000324856.7:c.5065G>T	p.Asp1689Tyr	p.D1689Y	ENST00000324856	NM_006015.4	1689	Gat/Tat	19/20	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.34	2		482	334	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46724361	46724361	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	41	554	0	ENST00000371975.4:c.214G>T	p.Ala72Ser	p.A72S	ENST00000371975	NM_003579.3	72	Gca/Tca	4/18	1	2	FACETS	0.738	0.616	0.871	0.738	0.616	0.871	SUBCLONAL	1	TRUE	1	0.34	2		554	327	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65307158	65307158	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	58	351	0	ENST00000342505.4:c.2530G>T	p.Asp844Tyr	p.D844Y	ENST00000342505	NM_002227.2	844	Gac/Tac	18/25	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.34	2		351	272	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748011	72748011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs151324323	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	93	534	0	ENST00000357731.5:c.167C>T	p.Ala56Val	p.A56V	ENST00000357731	NM_173808.2	56	gCg/gTg	1/7	1	2	FACETS	0.98	0.874	1	0.98	0.874	1	CLONAL	1	TRUE	1	0.34	2		534	558	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428511	78428511	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1408536007	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	52	536	0	ENST00000370768.2:c.1288C>T	p.Arg430Cys	p.R430C	ENST00000370768	NM_003902.3	430	Cgt/Tgt	14/20	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.34	2		536	283	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846217	156846217	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	115	602	0	ENST00000524377.1:c.1658C>A	p.Ala553Asp	p.A553D	ENST00000524377	NM_002529.3	553	gCt/gAt	14/17	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.34	2		602	564	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162743362	162743362	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372362070	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	44	298	2	ENST00000367921.3:c.1832G>A	p.Arg611Gln	p.R611Q	ENST00000367921	NM_006182.2	611	cGa/cAa	14/18	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.34	2		300	229	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578214	226578214	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	90	488	1	ENST00000366794.5:c.514T>G	p.Phe172Val	p.F172V	ENST00000366794	NM_001618.3	172	Ttc/Gtc	4/23	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.34	2		489	514	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716138	243716138	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	12	496	1	ENST00000263826.5:c.1056G>T	p.Glu352Asp	p.E352D	ENST00000263826	NM_005465.4	352	gaG/gaT	10/13	1	2	FACETS	0.304	0.213	0.416	0.304	0.213	0.416	SUBCLONAL	1	TRUE	1	0.34	2		497	232	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736287	243736287	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	35	313	0	ENST00000263826.5:c.760G>T	p.Glu254Ter	p.E254*	ENST00000263826	NM_005465.4	254	Gaa/Taa	8/13	1	2	FACETS	0.915	0.756	1	0.915	0.756	1	CLONAL	1	TRUE	1	0.34	2		313	225	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25498407	25498407	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	49	452	0	ENST00000264709.3:c.454G>A	p.Glu152Lys	p.E152K	ENST00000264709	NM_175629.2	152	Gaa/Aaa	5/23	1	2	FACETS	0.954	0.813	1	0.954	0.813	1	CLONAL	1	TRUE	1	0.34	2		452	302	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519761	29519761	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	70	406	0	ENST00000389048.3:c.1810T>C	p.Ser604Pro	p.S604P	ENST00000389048	NM_004304.4	604	Tct/Cct	9/29	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.34	2		406	329	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47601060	47601060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149274310	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	83	472	0	ENST00000263735.4:c.298G>A	p.Asp100Asn	p.D100N	ENST00000263735	NM_002354.2	100	Gat/Aat	3/9	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.34	2		472	362	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702266	47702266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759263820	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	43	431	1	ENST00000233146.2:c.1862G>A	p.Arg621Gln	p.R621Q	ENST00000233146	NM_000251.2	621	cGa/cAa	12/16	1	2	FACETS	0.996	0.84	1	0.996	0.84	1	CLONAL	1	TRUE	1	0.34	2		432	254	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48010582	48010582	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	75	491	0	ENST00000234420.5:c.210G>T	p.Lys70Asn	p.K70N	ENST00000234420	NM_000179.2	70	aaG/aaT	1/10	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.34	2		491	386	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48023108	48023108	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786204186	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	30	319	0	ENST00000234420.5:c.533G>A	p.Arg178His	p.R178H	ENST00000234420	NM_000179.2	178	cGt/cAt	3/10	1	2	FACETS	1	0.834	1	1	0.834	1	CLONAL	1	TRUE	1	0.34	2		319	172	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026763	48026763	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	30	398	0	ENST00000234420.5:c.1641A>C	p.Glu547Asp	p.E547D	ENST00000234420	NM_000179.2	547	gaA/gaC	4/10	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.34	2		398	148	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027751	48027751	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	24	343	0	ENST00000234420.5:c.2629G>T	p.Glu877Ter	p.E877*	ENST00000234420	NM_000179.2	877	Gaa/Taa	4/10	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.34	2		343	120	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634746	158634746	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373187352	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	60	304	0	ENST00000263640.3:c.440G>A	p.Arg147Gln	p.R147Q	ENST00000263640	NM_001105.4	147	cGa/cAa	5/11	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.34	2		304	245	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095836	178095836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1328262363	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	56	152	0	ENST00000397062.3:c.1495C>T	p.Arg499Trp	p.R499W	ENST00000397062	NM_006164.4	499	Cgg/Tgg	5/5	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.34	2		152	238	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190670399	190670399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	20	384	1	ENST00000441310.2:c.337G>A	p.Ala113Thr	p.A113T	ENST00000441310	NM_000534.4	113	Gct/Act	4/13	1	2	FACETS	0.665	0.511	0.842	0.665	0.511	0.842	SUBCLONAL	1	TRUE	1	0.34	2		385	177	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266573	198266573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	25	367	0	ENST00000335508.6:c.2263C>T	p.Pro755Ser	p.P755S	ENST00000335508	NM_012433.2	755	Cct/Tct	16/25	1	2	FACETS	0.967	0.771	1	0.967	0.771	1	CLONAL	1	TRUE	1	0.34	2		367	152	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736118	204736118	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	48	394	1	ENST00000302823.3:c.475G>T	p.Asp159Tyr	p.D159Y	ENST00000302823	NM_005214.4	159	Gat/Tat	3/4	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.34	2		395	266	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248498	212248498	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	23	455	0	ENST00000342788.4:c.3769G>T	p.Asp1257Tyr	p.D1257Y	ENST00000342788	NM_005235.2	1257	Gac/Tac	28/28	1	2	FACETS	0.297	0.231	0.374	0.297	0.231	0.374	SUBCLONAL	1	TRUE	1	0.34	2		455	456	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657051	215657051	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs758972589	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	38	393	0	ENST00000260947.4:c.334C>T	p.Arg112Ter	p.R112*	ENST00000260947	NM_000465.2	112	Cga/Tga	3/11	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.34	2		393	218	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242800986	242800986	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	65	533	0	ENST00000334409.5:c.5A>G	p.Gln2Arg	p.Q2R	ENST00000334409	NM_005018.2	2	cAg/cGg	1/5	1	2	FACETS	0.812	0.705	0.926	0.812	0.705	0.926	CLONAL	1	TRUE	1	0.34	2		533	471	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626689	12626689	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	72	409	0	ENST00000251849.4:c.1600T>G	p.Tyr534Asp	p.Y534D	ENST00000251849	NM_002880.3	534	Tat/Gat	15/17	1	2	FACETS	0.827	0.732	0.927	1	0.98	1	CLONAL	2	TRUE	1	0.34	2		409	256	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30733088	30733088	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	57	227	0	ENST00000295754.5:c.1701A>C	p.Lys567Asn	p.K567N	ENST00000295754	NM_003242.5	567	aaA/aaC	7/7	1	2	FACETS	0.822	0.716	0.934	1	0.974	1	CLONAL	2	TRUE	1	0.34	2		227	204	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182283	38182283	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	123	483	0	ENST00000396334.3:c.719A>G	p.Tyr240Cys	p.Y240C	ENST00000396334	NM_002468.4	240	tAc/tGc	4/5	1	2	FACETS	0.78	0.71	0.852	1	0.987	1	SUBCLONAL	2	TRUE	1	0.34	2		483	464	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266527	41266527	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	32	392	0	ENST00000349496.5:c.324G>T	p.Gln108His	p.Q108H	ENST00000349496	NM_001904.3	108	caG/caT	4/15	1	2	FACETS	0.844	0.69	1	0.844	0.69	1	CLONAL	1	TRUE	1	0.34	2		392	223	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47079168	47079168	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	66	494	0	ENST00000409792.3:c.7338A>C	p.Glu2446Asp	p.E2446D	ENST00000409792	NM_014159.6	2446	gaA/gaC	18/21	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.34	2		494	295	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164133	47164133	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	31	349	0	ENST00000409792.3:c.1993A>C	p.Ser665Arg	p.S665R	ENST00000409792	NM_014159.6	665	Agt/Cgt	3/21	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.34	2		349	126	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165174	47165174	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	22	307	0	ENST00000409792.3:c.952T>G	p.Phe318Val	p.F318V	ENST00000409792	NM_014159.6	318	Ttt/Gtt	3/21	1	2	FACETS	1	0.855	1	1	0.855	1	CLONAL	1	TRUE	1	0.34	2		307	116	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405966	49405966	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	20	414	0	ENST00000418115.1:c.172T>C	p.Trp58Arg	p.W58R	ENST00000418115	NM_001664.2	58	Tgg/Cgg	3/5	1	2	FACETS	0.325	0.248	0.415	0.325	0.248	0.415	SUBCLONAL	1	TRUE	1	0.34	2		414	362	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721854	49721854	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	22	148	0	ENST00000449682.2:c.1909T>G	p.Leu637Val	p.L637V	ENST00000449682	NM_020998.3	637	Ttg/Gtg	17/18	1	2	FACETS	0.799	0.635	0.977	1	0.935	1	CLONAL	2	TRUE	1	0.34	2		148	81	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936370	49936370	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	96	525	0	ENST00000296474.3:c.1478A>G	p.Asp493Gly	p.D493G	ENST00000296474	NM_002447.2	493	gAc/gGc	3/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.34	2		525	414	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940813	49940813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	67	641	1	ENST00000296474.3:c.230G>A	p.Arg77His	p.R77H	ENST00000296474	NM_002447.2	77	cGc/cAc	1/20	1	2	FACETS	0.78	0.679	0.889	0.78	0.679	0.889	SUBCLONAL	1	TRUE	1	0.34	2		642	505	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620542	52620542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	138	487	0	ENST00000394830.3:c.3211C>T	p.Arg1071Cys	p.R1071C	ENST00000394830	NM_018313.4	1071	Cgc/Tgc	21/30	1	2	FACETS	0.802	0.734	0.872	1	0.989	1	CLONAL	2	TRUE	1	0.34	2		487	506	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643843	52643843	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	44	472	0	ENST00000394830.3:c.2053C>A	p.Leu685Met	p.L685M	ENST00000394830	NM_018313.4	685	Ctg/Atg	17/30	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.34	2		472	184	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987025	69987025	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750608171	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	108	402	0	ENST00000394351.3:c.86G>A	p.Arg29Gln	p.R29Q	ENST00000394351	NM_000248.3	29	cGg/cAg	2/9	1	2	FACETS	0.786	0.711	0.865	1	0.985	1	SUBCLONAL	2	TRUE	1	0.34	2		402	404	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990453	69990453	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	38	378	0	ENST00000394351.3:c.412A>G	p.Met138Val	p.M138V	ENST00000394351	NM_000248.3	138	Atg/Gtg	4/9	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.34	2		378	192	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021809	71021809	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	21	217	0	ENST00000318789.4:c.1549C>A	p.Leu517Ile	p.L517I	ENST00000318789	NM_032682.5	517	Ctt/Att	18/21	1	2	FACETS	1	0.894	1	1	0.894	1	CLONAL	1	TRUE	1	0.34	2		217	98	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026112	71026112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs797045585	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	31	347	0	ENST00000318789.4:c.1510C>T	p.Arg504Cys	p.R504C	ENST00000318789	NM_032682.5	504	Cgc/Tgc	17/21	1	2	FACETS	0.608	0.493	0.737	0.608	0.493	0.737	SUBCLONAL	1	TRUE	1	0.34	2		347	300	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096171	71096171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1176882078	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	74	225	0	ENST00000318789.4:c.586C>T	p.Leu196Phe	p.L196F	ENST00000318789	NM_032682.5	196	Ctc/Ttc	10/21	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.34	2		225	314	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71161721	71161721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	16	401	0	ENST00000318789.4:c.248C>T	p.Ser83Phe	p.S83F	ENST00000318789	NM_032682.5	83	tCt/tTt	7/21	1	2	FACETS	0.384	0.284	0.504	0.384	0.284	0.504	SUBCLONAL	1	TRUE	1	0.34	2		401	245	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259135	89259135	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	32	293	0	ENST00000336596.2:c.279G>T	p.Gln93His	p.Q93H	ENST00000336596	NM_005233.5	93	caG/caT	3/17	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.34	2		293	128	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89457231	89457231	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	23	365	0	ENST00000336596.2:c.1712A>C	p.Lys571Thr	p.K571T	ENST00000336596	NM_005233.5	571	aAg/aCg	9/17	1	2	FACETS	0.801	0.629	0.995	0.801	0.629	0.995	CLONAL	1	TRUE	1	0.34	2		365	169	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967270	134967270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374549505	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	72	488	0	ENST00000398015.3:c.2609G>A	p.Arg870Gln	p.R870Q	ENST00000398015	NM_004441.4	870	cGg/cAg	14/16	1	2	FACETS	0.821	0.718	0.931	0.821	0.718	0.931	CLONAL	1	TRUE	1	0.34	2		488	516	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138431116	138431116	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	23	342	0	ENST00000289153.2:c.1333G>A	p.Val445Ile	p.V445I	ENST00000289153	NM_006219.2	445	Gtt/Att	8/22	1	2	FACETS	0.825	0.649	1	0.825	0.649	1	CLONAL	1	TRUE	1	0.34	2		342	164	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188288	142188288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1470834016	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	21	342	0	ENST00000350721.4:c.6443G>A	p.Arg2148Gln	p.R2148Q	ENST00000350721	NM_001184.3	2148	cGa/cAa	38/47	1	2	FACETS	0.895	0.697	1	0.895	0.697	1	CLONAL	1	TRUE	1	0.34	2		342	138	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612028	189612028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs900140738	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	95	405	0	ENST00000264731.3:c.1780C>T	p.Arg594Ter	p.R594*	ENST00000264731	NM_003722.4	594	Cga/Tga	14/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.34	2		405	388	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156535	55156535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778598	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	39	422	0	ENST00000257290.5:c.2936G>A	p.Arg979His	p.R979H	ENST00000257290	NM_006206.4	979	cGc/cAc	22/23	1	2	FACETS	0.691	0.574	0.82	0.691	0.574	0.82	SUBCLONAL	1	TRUE	1	0.34	2		422	332	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980368	55980368	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	44	378	0	ENST00000263923.4:c.723G>T	p.Lys241Asn	p.K241N	ENST00000263923	NM_002253.2	241	aaG/aaT	6/30	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.34	2		378	196	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197717	66197717	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	36	355	0	ENST00000273854.3:c.2982G>T	p.Met994Ile	p.M994I	ENST00000273854	NM_004439.5	994	atG/atT	17/18	1	2	FACETS	1	0.871	1	1	0.871	1	CLONAL	1	TRUE	1	0.34	2		355	200	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66201756	66201756	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	61	447	0	ENST00000273854.3:c.2746C>G	p.Gln916Glu	p.Q916E	ENST00000273854	NM_004439.5	916	Cag/Gag	16/18	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.34	2		447	309	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213915	66213915	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	22	293	0	ENST00000273854.3:c.2515A>G	p.Lys839Glu	p.K839E	ENST00000273854	NM_004439.5	839	Aaa/Gaa	15/18	1	2	FACETS	1	0.832	1	1	0.832	1	CLONAL	1	TRUE	1	0.34	2		293	121	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467716	66467716	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	37	341	0	ENST00000273854.3:c.553G>A	p.Glu185Lys	p.E185K	ENST00000273854	NM_004439.5	185	Gaa/Aaa	3/18	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.34	2		341	173	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155850	106155850	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	33	325	0	ENST00000380013.4:c.751G>C	p.Ala251Pro	p.A251P	ENST00000380013	NM_001127208.2	251	Gcc/Ccc	3/11	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.34	2		325	182	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180832	106180832	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	31	289	0	ENST00000380013.4:c.3860T>G	p.Phe1287Cys	p.F1287C	ENST00000380013	NM_001127208.2	1287	tTt/tGt	7/11	1	2	FACETS	0.94	0.767	1	0.94	0.767	1	CLONAL	1	TRUE	1	0.34	2		289	194	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143159104	143159104	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1405228238	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	39	371	0	ENST00000262992.4:c.749G>A	p.Arg250Gln	p.R250Q	ENST00000262992	NM_001101669.1	250	cGa/cAa	10/24	1	2	FACETS	0.972	0.812	1	0.972	0.812	1	CLONAL	1	TRUE	1	0.34	2		371	236	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332915	153332915	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200698994	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	48	376	0	ENST00000281708.4:c.41G>A	p.Arg14Gln	p.R14Q	ENST00000281708	NM_033632.3	14	cGa/cAa	2/12	1	2	FACETS	0.914	0.777	1	0.914	0.777	1	CLONAL	1	TRUE	1	0.34	2		376	309	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517921	187517921	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	36	446	3	ENST00000441802.2:c.12773C>T	p.Pro4258Leu	p.P4258L	ENST00000441802	NM_005245.3	4258	cCg/cTg	25/27	1	2	FACETS	0.886	0.733	1	0.886	0.733	1	CLONAL	1	TRUE	1	0.34	2		449	239	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549912	187549912	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	35	317	0	ENST00000441802.2:c.4329C>A	p.Phe1443Leu	p.F1443L	ENST00000441802	NM_005245.3	1443	ttC/ttA	8/27	1	2	FACETS	0.88	0.738	1	1	0.963	1	CLONAL	2	TRUE	1	0.34	2		317	117	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295298	1295298	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	28	489	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.297	0.236	0.366	0.297	0.236	0.366	SUBCLONAL	1	TRUE	1	0.34	2		490	555	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750594	57750594	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	21	363	0	ENST00000274289.3:c.1874T>C	p.Phe625Ser	p.F625S	ENST00000274289	NM_006622.3	625	tTc/tCc	14/14	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.34	2		363	105	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753015	57753015	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	22	293	0	ENST00000274289.3:c.1001T>G	p.Phe334Cys	p.F334C	ENST00000274289	NM_006622.3	334	tTt/tGt	7/14	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.34	2		293	110	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589558	67589558	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	17	160	0	ENST00000274335.5:c.1321A>C	p.Asn441His	p.N441H	ENST00000274335		441	Aat/Cat	10/15	1	2	FACETS	0.847	0.654	1	1	0.924	1	CLONAL	2	TRUE	1	0.34	2		160	59	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665697	86665697	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	25	341	0	ENST00000274376.6:c.1678G>T	p.Glu560Ter	p.E560*	ENST00000274376	NM_002890.2	560	Gaa/Taa	12/25	1	2	FACETS	0.919	0.732	1	0.919	0.732	1	CLONAL	1	TRUE	1	0.34	2		341	160	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670690	86670690	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	27	214	0	ENST00000274376.6:c.1968A>G	p.Ile656Met	p.I656M	ENST00000274376	NM_002890.2	656	atA/atG	15/25	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.34	2		214	122	SUCCESS
APC	324	MSKCC	GRCh37	5	112175490	112175490	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267600319	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	45	333	0	ENST00000257430.4:c.4199C>T	p.Ser1400Leu	p.S1400L	ENST00000257430	NM_000038.5	1400	tCg/tTg	16/16	1	2	FACETS	0.765	0.653	0.885	1	0.964	1	SUBCLONAL	2	TRUE	1	0.34	2		333	173	SUCCESS
APC	324	MSKCC	GRCh37	5	112176828	112176828	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	22	400	0	ENST00000257430.4:c.5537A>G	p.Tyr1846Cys	p.Y1846C	ENST00000257430	NM_000038.5	1846	tAc/tGc	16/16	1	2	FACETS	0.628	0.489	0.788	0.628	0.489	0.788	SUBCLONAL	1	TRUE	1	0.34	2		400	206	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944865	131944865	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	19	183	0	ENST00000265335.6:c.2886G>T	p.Glu962Asp	p.E962D	ENST00000265335		962	gaG/gaT	18/25	1	2	FACETS	0.787	0.614	0.978	1	0.924	1	CLONAL	2	TRUE	1	0.34	2		183	71	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509442	149509442	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	140	727	0	ENST00000261799.4:c.1457A>G	p.Glu486Gly	p.E486G	ENST00000261799	NM_002609.3	486	gAg/gGg	10/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.34	2		727	664	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638875	176638875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137888392	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	49	486	0	ENST00000439151.2:c.3475C>T	p.Arg1159Trp	p.R1159W	ENST00000439151	NM_022455.4	1159	Cgg/Tgg	5/23	1	2	FACETS	0.819	0.696	0.953	0.819	0.696	0.953	CLONAL	1	TRUE	1	0.34	2		486	352	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858261	27858261	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	89	484	0	ENST00000359303.2:c.310C>A	p.Leu104Ile	p.L104I	ENST00000359303	NM_003535.2	104	Ctc/Atc	1/1	0.213688332421629	3	FACETS	1	0.979	1	0.729	0.65	0.813	CLONAL	1	TRUE	1	0.34	3		484	420	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858492	27858492	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	65	332	0	ENST00000359303.2:c.79C>T	p.Arg27Cys	p.R27C	ENST00000359303	NM_003535.2	27	Cgc/Tgc	1/1	0.213688332421629	3	FACETS	0.835	0.731	0.944	0.835	0.731	0.944	CLONAL	2	TRUE	1	0.34	3		332	268	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681476	30681476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756890775	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	23	451	0	ENST00000376406.3:c.536G>A	p.Arg179His	p.R179H	ENST00000376406	NM_014641.2	179	cGt/cAt	4/15	0.213688332421629	3	FACETS	0.937	0.736	1	0.468	0.368	0.582	CLONAL	1	TRUE	1	0.34	3		451	169	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903835	41903835	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767328984	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	82	452	0	ENST00000372991.4:c.722G>A	p.Arg241Gln	p.R241Q	ENST00000372991	NM_001760.3	241	cGg/cAg	5/5	0.213688332421629	3	FACETS	1	0.976	1	0.705	0.626	0.79	CLONAL	1	TRUE	1	0.34	3		452	400	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43746655	43746655	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs766541343	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	77	461	0	ENST00000523873.1:c.422A>G	p.Lys141Arg	p.K141R	ENST00000523873		141	aAa/aGa	5/8	0.213688332421629	3	FACETS	0.818	0.724	0.917	0.818	0.724	0.917	CLONAL	2	TRUE	1	0.34	3		461	324	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120557	94120557	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	27	384	0	ENST00000369303.4:c.494T>C	p.Met165Thr	p.M165T	ENST00000369303	NM_004440.3	165	aTg/aCg	3/17	0.213688332421629	3	FACETS	1	0.881	1	0.57	0.458	0.695	CLONAL	1	TRUE	1	0.34	3		384	163	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017478	112017478	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	49	300	0	ENST00000368678.4:c.1033+2T>C		p.X345_splice	ENST00000368678		345			0.213688332421629	3	FACETS	0.823	0.706	0.948	0.823	0.706	0.948	CLONAL	2	TRUE	1	0.34	3		300	205	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017660	112017660	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	47	382	0	ENST00000368678.4:c.854-1G>A		p.X285_splice	ENST00000368678		285			0.213688332421629	3	FACETS	1	0.959	1	0.703	0.599	0.815	CLONAL	1	TRUE	1	0.34	3		382	230	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6043355	6043355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188006077	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	17	182	0	ENST00000265849.7:c.319C>T	p.Arg107Trp	p.R107W	ENST00000265849	NM_000535.5	107	Cgg/Tgg	4/15	0.114195292829279	3	FACETS	0.791	0.604	1	0.791	0.604	1	INDETERMINATE	2	TRUE	1	0.34	3		182	74	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227930	55227930	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	31	363	0	ENST00000275493.2:c.1397A>C	p.Asn466Thr	p.N466T	ENST00000275493	NM_005228.3	466	aAc/aCc	12/28	0.114195292829279	3	FACETS	1	0.925	1	0.639	0.523	0.767	INDETERMINATE	1	TRUE	1	0.34	3		363	167	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508768	106508768	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	63	381	1	ENST00000359195.3:c.762G>T	p.Lys254Asn	p.K254N	ENST00000359195	NM_002649.2	254	aaG/aaT	2/11	0.114195292829279	3	FACETS	1	0.959	1	0.634	0.551	0.722	INDETERMINATE	1	TRUE	1	0.34	3		382	342	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436176	116436176	+	stop_lost	Nonstop_Mutation	SNP	T	T	C	rs1249739995	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	42	275	0	ENST00000397752.3:c.4171T>C	p.Ter1391GlnextTer2	p.*1391Qext*2	ENST00000397752	NM_000245.2	1391	Tag/Cag	21/21	0.114195292829279	3	FACETS	1	0.945	1	1	0.945	1	INDETERMINATE	2	TRUE	1	0.34	3		275	117	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525868	148525868	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	31	375	0	ENST00000320356.2:c.589G>T	p.Glu197Ter	p.E197*	ENST00000320356	NM_004456.4	197	Gaa/Taa	6/20	0.114195292829279	3	FACETS	0.94	0.765	1	0.47	0.382	0.568	INDETERMINATE	1	TRUE	1	0.34	3		375	227	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860599	151860599	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	35	475	0	ENST00000262189.6:c.10063A>C	p.Ile3355Leu	p.I3355L	ENST00000262189	NM_170606.2	3355	Att/Ctt	43/59	0.114195292829279	3	FACETS	0.803	0.66	0.962	0.401	0.33	0.481	INDETERMINATE	1	TRUE	1	0.34	3		475	300	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879228	151879228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200152380	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	43	422	0	ENST00000262189.6:c.5717G>A	p.Arg1906Gln	p.R1906Q	ENST00000262189	NM_170606.2	1906	cGa/cAa	36/59	0.114195292829279	3	FACETS	1	0.935	1	0.611	0.516	0.716	INDETERMINATE	1	TRUE	1	0.34	3		422	242	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151948016	151948016	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1277470476	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	51	441	0	ENST00000262189.6:c.1657G>T	p.Asp553Tyr	p.D553Y	ENST00000262189	NM_170606.2	553	Gat/Tat	12/59	0.114195292829279	3	FACETS	0.78	0.67	0.897	0.78	0.67	0.897	INDETERMINATE	2	TRUE	1	0.34	3		441	225	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345963	152345963	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	67	454	0	ENST00000359321.1:c.607T>G	p.Ser203Ala	p.S203A	ENST00000359321	NM_005431.1	203	Tcg/Gcg	3/3	0.114195292829279	3	FACETS	0.776	0.681	0.878	0.776	0.681	0.878	INDETERMINATE	2	TRUE	1	0.34	3		454	297	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090520	5090520	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	30	227	0	ENST00000381652.3:c.2836G>T	p.Glu946Ter	p.E946*	ENST00000381652	NM_004972.3	946	Gaa/Taa	21/25	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.34	2		227	119	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5467842	5467842	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	35	336	0	ENST00000381577.3:c.853A>G	p.Thr285Ala	p.T285A	ENST00000381577	NM_014143.3	285	Aca/Gca	7/7	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.34	2		336	153	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285847	87285847	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	77	486	0	ENST00000277120.3:c.184A>C	p.Ser62Arg	p.S62R	ENST00000277120		62	Agt/Cgt	2/19	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.34	2		486	379	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570282	87570282	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	70	436	0	ENST00000277120.3:c.2022G>T	p.Gln674His	p.Q674H	ENST00000277120		674	caG/caT	17/19	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.34	2		436	344	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636204	87636204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs532184896	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	63	391	0	ENST00000277120.3:c.2369G>A	p.Arg790Gln	p.R790Q	ENST00000277120		790	cGa/cAa	19/19	1	2	FACETS	0.908	0.789	1	0.908	0.789	1	CLONAL	1	TRUE	1	0.34	2		391	408	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912218	97912218	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374176091	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	50	412	0	ENST00000289081.3:c.673G>A	p.Glu225Lys	p.E225K	ENST00000289081	NM_000136.2	225	Gag/Aag	7/15	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.34	2		412	275	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894916	101894916	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1060502040	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	44	340	0	ENST00000374994.4:c.469C>T	p.Arg157Ter	p.R157*	ENST00000374994	NM_004612.2	157	Cga/Tga	3/9	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.34	2		340	205	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915943	127915943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781486938	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	51	472	0	ENST00000373547.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000373547	NM_002721.4	180	Gaa/Aaa	6/7	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.34	2		472	262	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797298	135797298	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	31	210	0	ENST00000298552.3:c.571C>T	p.Leu191Phe	p.L191F	ENST00000298552	NM_001162426.1	191	Ctt/Ttt	7/23	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.34	2		210	151	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797313	135797313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1279777367	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	33	198	2	ENST00000298552.3:c.556G>A	p.Ala186Thr	p.A186T	ENST00000298552	NM_001162426.1	186	Gca/Aca	7/23	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.34	2		200	176	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139566734	139566734	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144969763	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	154	660	0	ENST00000308874.7:c.818C>T	p.Ser273Leu	p.S273L	ENST00000308874		273	tCg/tTg	10/10	1	2	FACETS	0.751	0.69	0.814	1	0.988	1	SUBCLONAL	2	TRUE	1	0.34	2		660	603	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814824	139814824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755691522	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	118	663	0	ENST00000247668.2:c.817G>A	p.Glu273Lys	p.E273K	ENST00000247668	NM_021138.3	273	Gag/Aag	8/11	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.34	2		663	674	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814912	139814912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767867108	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	161	574	0	ENST00000247668.2:c.905C>T	p.Ala302Val	p.A302V	ENST00000247668	NM_021138.3	302	gCc/gTc	8/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.34	2		574	662	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100768	8100768	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370055470	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	88	476	0	ENST00000346208.3:c.742G>A	p.Gly248Arg	p.G248R	ENST00000346208		248	Gga/Aga	3/6	0.114195292829279	3	FACETS	1	0.968	1	0.626	0.556	0.699	INDETERMINATE	1	TRUE	1	0.34	3		476	484	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845621	63845621	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	25	186	0	ENST00000279873.7:c.1360G>T	p.Glu454Ter	p.E454*	ENST00000279873	NM_032199.2	454	Gaa/Taa	9/10	0.114195292829279	3	FACETS	0.887	0.715	1	0.887	0.715	1	INDETERMINATE	2	TRUE	1	0.34	3		186	97	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332272	70332272	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	24	299	0	ENST00000373644.4:c.177G>T	p.Lys59Asn	p.K59N	ENST00000373644	NM_030625.2	59	aaG/aaT	2/12	0.114195292829279	3	FACETS	1	0.912	1	0.655	0.521	0.805	INDETERMINATE	1	TRUE	1	0.34	3		299	126	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406042	70406042	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	26	572	0	ENST00000373644.4:c.3556A>C	p.Ile1186Leu	p.I1186L	ENST00000373644	NM_030625.2	1186	Ata/Cta	4/12	0.114195292829279	3	FACETS	0.828	0.66	1	0.414	0.33	0.51	INDETERMINATE	1	TRUE	1	0.34	3		572	216	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406089	70406089	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	45	583	0	ENST00000373644.4:c.3603T>G	p.Phe1201Leu	p.F1201L	ENST00000373644	NM_030625.2	1201	ttT/ttG	4/12	0.114195292829279	3	FACETS	1	0.952	1	0.667	0.566	0.777	INDETERMINATE	1	TRUE	1	0.34	3		583	232	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534248	534248	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	95	694	0	ENST00000451590.1:c.75G>T	p.Gln25His	p.Q25H	ENST00000451590	NM_001130442.1	25	caG/caT	2/5	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.34	2		694	557	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514124	69514124	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	34	570	0	ENST00000294312.3:c.557A>G	p.Asp186Gly	p.D186G	ENST00000294312	NM_005117.2	186	gAc/gGc	3/3	1	2	FACETS	0.427	0.349	0.516	0.427	0.349	0.516	SUBCLONAL	1	TRUE	1	0.34	2		570	468	SUCCESS
EED	8726	MSKCC	GRCh37	11	85968618	85968618	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	10	291	0	ENST00000263360.6:c.614T>G	p.Leu205Arg	p.L205R	ENST00000263360	NM_003797.3	205	cTt/cGt	6/12	1	2	FACETS	0.363	0.246	0.509	0.363	0.246	0.509	SUBCLONAL	1	TRUE	1	0.34	2		291	162	SUCCESS
EED	8726	MSKCC	GRCh37	11	85977189	85977189	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	20	350	0	ENST00000263360.6:c.791G>T	p.Arg264Met	p.R264M	ENST00000263360	NM_003797.3	264	aGg/aTg	8/12	1	2	FACETS	0.613	0.471	0.777	0.613	0.471	0.777	SUBCLONAL	1	TRUE	1	0.34	2		350	192	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195662	102195662	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	31	371	1	ENST00000263464.3:c.422C>A	p.Ser141Tyr	p.S141Y	ENST00000263464	NM_001165.4	141	tCt/tAt	2/9	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.34	2		372	164	SUCCESS
ATM	472	MSKCC	GRCh37	11	108099982	108099982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	31	249	0	ENST00000278616.4:c.263C>T	p.Ala88Val	p.A88V	ENST00000278616	NM_000051.3	88	gCc/gTc	4/63	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.34	2		249	144	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141873	108141873	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs538105098	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	19	293	0	ENST00000278616.4:c.2921C>T	p.Ser974Phe	p.S974F	ENST00000278616	NM_000051.3	974	tCc/tTc	19/63	1	2	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	1	0.34	2		293	89	SUCCESS
ATM	472	MSKCC	GRCh37	11	108141989	108141989	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	41	360	0	ENST00000278616.4:c.2933C>A	p.Ser978Tyr	p.S978Y	ENST00000278616	NM_000051.3	978	tCt/tAt	20/63	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.34	2		360	187	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153564	108153564	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	21	346	0	ENST00000278616.4:c.3704C>A	p.Pro1235His	p.P1235H	ENST00000278616	NM_000051.3	1235	cCt/cAt	25/63	1	2	FACETS	0.864	0.672	1	0.864	0.672	1	CLONAL	1	TRUE	1	0.34	2		346	143	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118368660	118368660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555044474	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	38	357	0	ENST00000534358.1:c.5674C>T	p.Arg1892Cys	p.R1892C	ENST00000534358	NM_005933.3	1892	Cgt/Tgt	21/36	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.34	2		357	153	SUCCESS
CBL	867	MSKCC	GRCh37	11	119077282	119077282	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	116	576	0	ENST00000264033.4:c.155A>C	p.Asp52Ala	p.D52A	ENST00000264033	NM_005188.3	52	gAc/gCc	1/16	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.34	2		576	608	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422237	422237	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	56	510	0	ENST00000399788.2:c.3021A>C	p.Lys1007Asn	p.K1007N	ENST00000399788	NM_001042603.1	1007	aaA/aaC	20/28	0.114195292829279	3	FACETS	1	0.968	1	0.741	0.641	0.848	INDETERMINATE	1	TRUE	1	0.34	3		510	260	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435061	18435061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603400	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	38	258	0	ENST00000266497.5:c.46G>A	p.Glu16Lys	p.E16K	ENST00000266497		16	Gaa/Aaa	1/31	0.114195292829279	3	FACETS	1	0.942	1	1	0.942	1	INDETERMINATE	2	TRUE	1	0.34	3		258	105	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25368397	25368397	+	intron_variant	Intron	SNP	A	A	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	30	302	0	ENST00000311936.3:c.451-5552T>A		p.*151*	ENST00000311936	NM_004985.3	183/189			0.114195292829279	3	FACETS	1	0.93	1	0.666	0.543	0.801	INDETERMINATE	1	TRUE	1	0.34	3		302	155	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416447	49416447	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	112	577	0	ENST00000301067.7:c.16264A>C	p.Met5422Leu	p.M5422L	ENST00000301067	NM_003482.3	5422	Atg/Ctg	51/54	0.114195292829279	3	FACETS	0.762	0.688	0.839	0.762	0.688	0.839	INDETERMINATE	2	TRUE	1	0.34	3		577	506	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426648	49426648	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	65	398	0	ENST00000301067.7:c.11840A>C	p.Gln3947Pro	p.Q3947P	ENST00000301067	NM_003482.3	3947	cAg/cCg	39/54	0.114195292829279	3	FACETS	0.788	0.689	0.892	0.788	0.689	0.892	INDETERMINATE	2	TRUE	1	0.34	3		398	284	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427503	49427503	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1011790338	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	67	544	0	ENST00000301067.7:c.10985T>C	p.Met3662Thr	p.M3662T	ENST00000301067	NM_003482.3	3662	aTg/aCg	39/54	0.114195292829279	3	FACETS	1	0.953	1	0.599	0.523	0.68	INDETERMINATE	1	TRUE	1	0.34	3		544	385	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219113	133219113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771896231	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	80	635	0	ENST00000320574.5:c.4931C>T	p.Ser1644Leu	p.S1644L	ENST00000320574	NM_006231.2	1644	tCg/tTg	37/49	0.114195292829279	3	FACETS	1	0.951	1	0.575	0.507	0.646	INDETERMINATE	1	TRUE	1	0.34	3		635	479	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	74	593	1	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	0.114195292829279	3	FACETS	0.806	0.712	0.905	0.806	0.712	0.905	INDETERMINATE	2	TRUE	1	0.34	3		594	316	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906796	32906796	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	33	592	0	ENST00000380152.3:c.1181A>G	p.Glu394Gly	p.E394G	ENST00000380152		394	gAa/gGa	10/27	0.114195292829279	3	FACETS	0.958	0.785	1	0.479	0.392	0.576	INDETERMINATE	1	TRUE	1	0.34	3		592	237	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951156	48951156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060503078	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	28	331	0	ENST00000267163.4:c.1318G>A	p.Glu440Lys	p.E440K	ENST00000267163	NM_000321.2	440	Gaa/Aaa	13/27	0.114195292829279	3	FACETS	1	0.869	1	0.551	0.444	0.669	INDETERMINATE	1	TRUE	1	0.34	3		331	175	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48953748	48953748	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759079385	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	12	222	0	ENST00000267163.4:c.1351C>T	p.Arg451Cys	p.R451C	ENST00000267163	NM_000321.2	451	Cgc/Tgc	14/27	0.114195292829279	3	FACETS	0.467	0.328	0.636	0.233	0.164	0.318	INDETERMINATE	1	TRUE	1	0.34	3		222	177	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030483	49030483	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	16	261	0	ENST00000267163.4:c.1958A>C	p.Lys653Thr	p.K653T	ENST00000267163	NM_000321.2	653	aAa/aCa	19/27	0.114195292829279	3	FACETS	0.958	0.716	1	0.479	0.358	0.62	INDETERMINATE	1	TRUE	1	0.34	3		261	115	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345058	73345058	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	28	370	0	ENST00000377767.4:c.1739G>T	p.Ser580Ile	p.S580I	ENST00000377767	NM_014953.3	580	aGt/aTt	13/21	0.114195292829279	3	FACETS	1	0.907	1	0.61	0.493	0.74	INDETERMINATE	1	TRUE	1	0.34	3		370	158	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514697	103514697	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	39	280	0	ENST00000355739.4:c.1198G>T	p.Asp400Tyr	p.D400Y	ENST00000355739	NM_000123.3	400	Gat/Tat	8/15	0.114195292829279	3	FACETS	1	0.94	1	0.645	0.54	0.76	INDETERMINATE	1	TRUE	1	0.34	3		280	208	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515141	103515141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770246574	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	15	284	0	ENST00000355739.4:c.1642G>A	p.Glu548Lys	p.E548K	ENST00000355739	NM_000123.3	548	Gaa/Aaa	8/15	0.114195292829279	3	FACETS	1	0.828	1	0.58	0.431	0.753	INDETERMINATE	1	TRUE	1	0.34	3		284	89	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436187	110436187	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	44	596	1	ENST00000375856.3:c.2214G>T	p.Glu738Asp	p.E738D	ENST00000375856	NM_003749.2	738	gaG/gaT	1/2	0.114195292829279	3	FACETS	0.443	0.371	0.524	0.222	0.185	0.262	INDETERMINATE	1	TRUE	1	0.34	3		597	683	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436492	110436492	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	152	851	0	ENST00000375856.3:c.1909A>C	p.Ile637Leu	p.I637L	ENST00000375856	NM_003749.2	637	Atc/Ctc	1/2	0.114195292829279	3	FACETS	1	0.983	1	0.643	0.588	0.7	INDETERMINATE	1	TRUE	1	0.34	3		851	814	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061256	38061256	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	152	684	0	ENST00000250448.2:c.733A>G	p.Thr245Ala	p.T245A	ENST00000250448	NM_004496.3	245	Acg/Gcg	2/2	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.34	2		684	629	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610234	81610234	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370450995	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	38	385	0	ENST00000298171.2:c.1832C>T	p.Pro611Leu	p.P611L	ENST00000298171	NM_000369.2	611	cCg/cTg	10/10	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.34	2		385	192	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95556920	95556920	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	72	454	0	ENST00000393063.1:c.5684G>A	p.Arg1895Gln	p.R1895Q	ENST00000393063	NM_030621.3	1895	cGa/cAa	28/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.34	2		454	303	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003323	42003323	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	55	490	0	ENST00000219905.7:c.2860T>G	p.Phe954Val	p.F954V	ENST00000219905	NM_001164273.1	954	Ttt/Gtt	8/24	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.34	2		490	276	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042485	42042485	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	18	465	0	ENST00000219905.7:c.6680A>C	p.Lys2227Thr	p.K2227T	ENST00000219905	NM_001164273.1	2227	aAa/aCa	17/24	1	2	FACETS	0.464	0.35	0.599	0.464	0.35	0.599	SUBCLONAL	1	TRUE	1	0.34	2		465	228	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052578	42052578	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	55	363	0	ENST00000219905.7:c.7249G>T	p.Glu2417Ter	p.E2417*	ENST00000219905	NM_001164273.1	2417	Gaa/Taa	20/24	1	2	FACETS	0.957	0.823	1	0.957	0.823	1	CLONAL	1	TRUE	1	0.34	2		363	338	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99192862	99192862	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	77	375	0	ENST00000268035.6:c.52T>C	p.Phe18Leu	p.F18L	ENST00000268035	NM_000875.3	18	Ttt/Ctt	1/21	1	2	FACETS	0.876	0.771	0.989	0.876	0.771	0.989	CLONAL	1	TRUE	1	0.34	2		375	517	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442819	99442819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1365982598	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	80	442	0	ENST00000268035.6:c.1216C>T	p.Arg406Cys	p.R406C	ENST00000268035	NM_000875.3	406	Cgc/Tgc	5/21	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.34	2		442	326	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486151	99486151	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	41	386	1	ENST00000268035.6:c.3458-1G>T		p.X1153_splice	ENST00000268035	NM_000875.3	1153			1	2	FACETS	0.846	0.709	0.997	0.846	0.709	0.997	CLONAL	1	TRUE	1	0.34	2		387	285	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121909	2121909	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760489473	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	183	760	1	ENST00000219476.3:c.2071C>T	p.Arg691Cys	p.R691C	ENST00000219476	NM_000548.3	691	Cgc/Tgc	19/42	1	2	FACETS	0.759	0.703	0.817	1	0.99	1	SUBCLONAL	2	TRUE	1	0.34	2		761	709	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832822	3832822	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	111	510	1	ENST00000262367.5:c.1436G>T	p.Ser479Ile	p.S479I	ENST00000262367	NM_004380.2	479	aGc/aTc	6/31	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.34	2		511	503	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024573	14024573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373570729	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	39	305	1	ENST00000311895.7:c.799C>T	p.Arg267Cys	p.R267C	ENST00000311895	NM_005236.2	267	Cgc/Tgc	5/11	1	2	FACETS	0.797	0.672	0.929	1	0.962	1	CLONAL	2	TRUE	1	0.34	2		306	144	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029576	14029576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751782722	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	22	205	0	ENST00000311895.7:c.1787C>T	p.Ala596Val	p.A596V	ENST00000311895	NM_005236.2	596	gCg/gTg	8/11	1	2	FACETS	0.899	0.704	1	0.899	0.704	1	CLONAL	1	TRUE	1	0.34	2		205	144	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650710	67650710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243010179	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	140	546	1	ENST00000264010.4:c.1015C>T	p.Arg339Trp	p.R339W	ENST00000264010	NM_006565.3	339	Cgg/Tgg	5/12	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.34	2		547	577	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68863571	68863571	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	185	508	0	ENST00000261769.5:c.2310C>A	p.Ser770Arg	p.S770R	ENST00000261769	NM_004360.3	770	agC/agA	15/16	1	2	FACETS	0.754	0.698	0.811	1	0.99	1	SUBCLONAL	2	TRUE	1	0.34	2		508	722	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993579	72993579	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769010742	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	83	475	1	ENST00000268489.5:c.466G>A	p.Ala156Thr	p.A156T	ENST00000268489	NM_006885.3	156	Gcc/Acc	2/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.34	2		476	343	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944259	81944259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	167	544	1	ENST00000359376.3:c.1868G>A	p.Arg623His	p.R623H	ENST00000359376	NM_002661.3	623	cGc/cAc	18/33	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.34	2		545	720	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953133	81953133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs566611968	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	72	312	1	ENST00000359376.3:c.2099G>A	p.Arg700Gln	p.R700Q	ENST00000359376	NM_002661.3	700	cGg/cAg	20/33	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.34	2		313	352	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348665	89348665	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	81	831	1	ENST00000301030.4:c.4285G>T	p.Asp1429Tyr	p.D1429Y	ENST00000301030	NM_001256183.1	1429	Gat/Tat	9/13	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.34	2		832	396	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979495	7979495	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	70	414	0	ENST00000319144.4:c.1530G>T	p.Glu510Asp	p.E510D	ENST00000319144	NM_001139.2	510	gaG/gaT	11/15	1	2	FACETS	0.911	0.797	1	0.911	0.797	1	CLONAL	1	TRUE	1	0.34	2		414	452	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8109883	8109883	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs146905713	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	117	579	0	ENST00000585124.1:c.612A>C	p.Glu204Asp	p.E204D	ENST00000585124	NM_004217.3	204	gaA/gaC	7/9	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.34	2		579	496	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013730	12013730	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	32	299	0	ENST00000353533.5:c.672A>C	p.Lys224Asn	p.K224N	ENST00000353533	NM_003010.3	224	aaA/aaC	6/11	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.34	2		299	155	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15938151	15938151	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	63	399	0	ENST00000268712.3:c.7063T>C	p.Ser2355Pro	p.S2355P	ENST00000268712	NM_006311.3	2355	Tct/Cct	45/46	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.34	2		399	289	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024364	16024364	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	87	261	0	ENST00000268712.3:c.1852+2T>C		p.X618_splice	ENST00000268712	NM_006311.3	618			1	2	FACETS	0.833	0.746	0.925	1	0.983	1	CLONAL	2	TRUE	1	0.34	2		261	307	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528490	29528490	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343309278	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	19	432	0	ENST00000356175.3:c.1247G>A	p.Arg416Gln	p.R416Q	ENST00000356175	NM_000267.3	416	cGa/cAa	11/57	1	2	FACETS	0.604	0.461	0.771	0.604	0.461	0.771	SUBCLONAL	1	TRUE	1	0.34	2		432	185	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370280	40370280	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143171571	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	155	558	1	ENST00000293328.3:c.1058G>A	p.Arg353His	p.R353H	ENST00000293328	NM_012448.3	353	cGc/cAc	9/19	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.34	2		559	667	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40460196	40460196	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs758514352	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	21	378	0	ENST00000345506.4:c.1907C>T	p.Pro636Leu	p.P636L	ENST00000345506	NM_003152.3	636	cCg/cTg	17/20	1	2	FACETS	0.354	0.272	0.45	0.354	0.272	0.45	SUBCLONAL	1	TRUE	1	0.34	2		378	349	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481655	40481655	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	57	470	0	ENST00000264657.5:c.1150T>G	p.Phe384Val	p.F384V	ENST00000264657	NM_139276.2	384	Ttt/Gtt	13/24	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.34	2		470	253	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246754	41246754	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	56	569	0	ENST00000357654.3:c.794C>A	p.Ser265Tyr	p.S265Y	ENST00000357654	NM_007294.3	265	tCt/tAt	10/23	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.34	2		569	278	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435452	56435452	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs766948615	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	111	602	0	ENST00000407977.2:c.1685T>G	p.Phe562Cys	p.F562C	ENST00000407977		562	tTc/tGc	9/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.34	2		602	514	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533932	63533932	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749846538	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	83	389	0	ENST00000307078.5:c.1222G>A	p.Glu408Lys	p.E408K	ENST00000307078	NM_004655.3	408	Gag/Aag	6/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.34	2		389	348	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743329	743329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	53	443	0	ENST00000314574.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000314574	NM_005433.3	271	Gaa/Aaa	7/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.34	2		443	241	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39575929	39575929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	35	260	0	ENST00000262039.4:c.862C>T	p.Pro288Ser	p.P288S	ENST00000262039	NM_002647.2	288	Ccc/Tcc	8/25	1	2	FACETS	0.927	0.766	1	0.927	0.766	1	CLONAL	1	TRUE	1	0.34	2		260	222	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45391501	45391501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	41	277	1	ENST00000262160.6:c.659C>T	p.Thr220Met	p.T220M	ENST00000262160	NM_005901.5	220	aCg/aTg	6/11	1	2	FACETS	0.82	0.696	0.953	1	0.965	1	CLONAL	2	TRUE	1	0.34	2		278	147	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56414797	56414797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	53	540	0	ENST00000348428.3:c.2198C>T	p.Ser733Phe	p.S733F	ENST00000348428	NM_006785.3	733	tCt/tTt	17/17	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.34	2		540	285	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632366	1632366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202212254	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	65	717	0	ENST00000344749.5:c.184G>A	p.Gly62Ser	p.G62S	ENST00000344749	NM_001136139.2	62	Ggc/Agc	4/19	1	2	FACETS	0.474	0.41	0.544	0.474	0.41	0.544	SUBCLONAL	1	TRUE	1	0.34	2		717	806	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291166	10291166	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	135	669	0	ENST00000340748.4:c.305A>G	p.Glu102Gly	p.E102G	ENST00000340748		102	gAa/gGa	4/40	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.34	2		669	531	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107179	11107179	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	30	456	0	ENST00000358026.2:c.1771A>C	p.Asn591His	p.N591H	ENST00000358026	NM_001128849.1	591	Aat/Cat	11/36	1	2	FACETS	0.346	0.278	0.423	0.346	0.278	0.423	SUBCLONAL	1	TRUE	1	0.34	2		456	510	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132552	11132552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	160	646	1	ENST00000358026.2:c.2768C>T	p.Ala923Val	p.A923V	ENST00000358026	NM_001128849.1	923	gCg/gTg	19/36	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.34	2		647	698	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132617	11132617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1445478818	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	49	687	0	ENST00000358026.2:c.2833G>A	p.Ala945Thr	p.A945T	ENST00000358026	NM_001128849.1	945	Gca/Aca	19/36	1	2	FACETS	0.379	0.32	0.445	0.379	0.32	0.445	SUBCLONAL	1	TRUE	1	0.34	2		687	760	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298770	15298770	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	212	710	0	ENST00000263388.2:c.1528G>A	p.Glu510Lys	p.E510K	ENST00000263388	NM_000435.2	510	Gaa/Aaa	10/33	1	2	FACETS	0.822	0.765	0.879	1	0.993	1	CLONAL	2	TRUE	1	0.34	2		710	759	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955206	17955206	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	132	648	0	ENST00000458235.1:c.21G>T	p.Glu7Asp	p.E7D	ENST00000458235	NM_000215.3	7	gaG/gaT	2/24	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.34	2		648	664	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793550	42793550	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	117	773	0	ENST00000575354.2:c.1352A>C	p.Asp451Ala	p.D451A	ENST00000575354	NM_015125.3	451	gAt/gCt	8/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.34	2		773	622	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794015	42794015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	109	580	1	ENST00000575354.2:c.1376G>A	p.Gly459Asp	p.G459D	ENST00000575354	NM_015125.3	459	gGc/gAc	9/20	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.34	2		581	634	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796574	42796574	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	89	701	0	ENST00000575354.2:c.3131C>T	p.Ser1044Leu	p.S1044L	ENST00000575354	NM_015125.3	1044	tCg/tTg	13/20	1	2	FACETS	0.932	0.828	1	0.932	0.828	1	CLONAL	1	TRUE	1	0.34	2		701	562	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906366	50906366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762494977	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	140	712	0	ENST00000440232.2:c.1027C>T	p.Arg343Cys	p.R343C	ENST00000440232	NM_002691.3	343	Cgc/Tgc	9/27	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.34	2		712	723	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019139	31019139	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	50	361	0	ENST00000375687.4:c.734A>G	p.Asn245Ser	p.N245S	ENST00000375687	NM_015338.5	245	aAc/aGc	9/13	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.34	2		361	249	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022418	31022418	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	14	200	0	ENST00000375687.4:c.1903G>T	p.Glu635Ter	p.E635*	ENST00000375687	NM_015338.5	635	Gag/Tag	13/13	1	2	FACETS	0.895	0.656	1	0.895	0.656	1	CLONAL	1	TRUE	1	0.34	2		200	92	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944415	40944415	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	21	493	1	ENST00000373198.4:c.2087C>A	p.Ser696Tyr	p.S696Y	ENST00000373198	NM_133170.3	696	tCt/tAt	12/32	1	2	FACETS	0.398	0.307	0.505	0.398	0.307	0.505	SUBCLONAL	1	TRUE	1	0.34	2		494	310	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306602	41306602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1419824411	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	83	612	0	ENST00000373198.4:c.1057G>A	p.Asp353Asn	p.D353N	ENST00000373198	NM_133170.3	353	Gat/Aat	7/32	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.34	2		612	452	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514513	41514513	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	66	508	0	ENST00000373198.4:c.148A>G	p.Asn50Asp	p.N50D	ENST00000373198	NM_133170.3	50	Aat/Gat	2/32	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.34	2		508	336	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54963246	54963246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745894289	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	17	267	0	ENST00000312783.6:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000312783	NM_198436.1	3	cGa/cAa	3/10	1	2	FACETS	0.943	0.714	1	0.943	0.714	1	CLONAL	1	TRUE	1	0.34	2		267	106	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30090776	30090776	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	139	525	0	ENST00000338641.4:c.1773C>A	p.Phe591Leu	p.F591L	ENST00000338641	NM_000268.3	591	ttC/ttA	16/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.34	2		525	628	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317422	1317422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759127718	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	101	762	0	ENST00000400841.2:c.643C>T	p.Arg215Trp	p.R215W	ENST00000400841		215	Cgg/Tgg	5/6	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.34	2		762	521	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923726	39923726	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775087931	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	147	692	0	ENST00000378444.4:c.3365C>T	p.Ser1122Leu	p.S1122L	ENST00000378444	NM_001123385.1	1122	tCg/tTg	7/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.34	2		692	713	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932139	39932139	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	133	740	1	ENST00000378444.4:c.2460C>A	p.Asn820Lys	p.N820K	ENST00000378444	NM_001123385.1	820	aaC/aaA	4/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.34	2		741	638	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937104	39937104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	151	616	1	ENST00000378444.4:c.79G>A	p.Glu27Lys	p.E27K	ENST00000378444	NM_001123385.1	27	Gaa/Aaa	2/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.34	2		617	803	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938548	44938548	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	42	488	0	ENST00000377967.4:c.3096T>G	p.Ile1032Met	p.I1032M	ENST00000377967	NM_021140.2	1032	atT/atG	20/29	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.34	2		488	227	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038745	47038745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556777782	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	28	650	1	ENST00000377604.3:c.752C>T	p.Thr251Met	p.T251M	ENST00000377604	NM_001204468.1	251	aCg/aTg	9/24	1	2	FACETS	0.301	0.24	0.371	0.301	0.24	0.371	SUBCLONAL	1	TRUE	1	0.34	2		651	547	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246390	53246390	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	123	647	0	ENST00000375401.3:c.592C>T	p.Arg198Ter	p.R198*	ENST00000375401	NM_004187.3	198	Cga/Tga	5/26	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.34	2		647	655	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412430	63412430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	96	864	1	ENST00000330258.3:c.737C>T	p.Ser246Phe	p.S246F	ENST00000330258	NM_152424.3	246	tCt/tTt	2/2	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.34	2		865	488	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345972	70345972	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	29	470	0	ENST00000374080.3:c.2509T>C	p.Ser837Pro	p.S837P	ENST00000374080		837	Tca/Cca	18/45	1	2	FACETS	0.339	0.271	0.416	0.339	0.271	0.416	SUBCLONAL	1	TRUE	1	0.34	2		470	503	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357481	70357481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	63	719	0	ENST00000374080.3:c.5822C>T	p.Ser1941Phe	p.S1941F	ENST00000374080		1941	tCc/tTc	40/45	1	2	FACETS	0.868	0.753	0.992	0.868	0.753	0.992	CLONAL	1	TRUE	1	0.34	2		719	427	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70360668	70360668	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	29	179	0	ENST00000374080.3:c.6228G>T	p.Gln2076His	p.Q2076H	ENST00000374080		2076	caG/caT	42/45	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.34	2		179	116	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937828	76937828	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	20	628	0	ENST00000373344.5:c.2920A>G	p.Ser974Gly	p.S974G	ENST00000373344	NM_000489.3	974	Agc/Ggc	9/35	1	2	FACETS	0.383	0.293	0.489	0.383	0.293	0.489	SUBCLONAL	1	TRUE	1	0.34	2		628	307	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938330	76938330	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	64	589	0	ENST00000373344.5:c.2418G>T	p.Lys806Asn	p.K806N	ENST00000373344	NM_000489.3	806	aaG/aaT	9/35	1	2	FACETS	0.753	0.66	0.852	1	0.974	1	SUBCLONAL	2	TRUE	1	0.34	2		589	250	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938710	76938710	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	49	634	0	ENST00000373344.5:c.2038G>T	p.Glu680Ter	p.E680*	ENST00000373344	NM_000489.3	680	Gaa/Taa	9/35	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.34	2		634	229	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179058	123179058	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	59	672	1	ENST00000218089.9:c.507G>T	p.Lys169Asn	p.K169N	ENST00000218089	NM_001042749.1	169	aaG/aaT	8/35	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.34	2		673	276	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217381	123217381	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	38	421	0	ENST00000218089.9:c.3035G>A	p.Arg1012Gln	p.R1012Q	ENST00000218089	NM_001042749.1	1012	cGa/cAa	29/35	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.34	2		421	192	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229241	123229241	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1569521908	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	30	270	0	ENST00000218089.9:c.3725G>A	p.Arg1242Gln	p.R1242Q	ENST00000218089	NM_001042749.1	1242	cGa/cAa	34/35	1	2	FACETS	0.896	0.728	1	0.896	0.728	1	CLONAL	1	TRUE	1	0.34	2		270	197	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123480521	123480521	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	102	435	0	ENST00000371139.4:c.29A>C	p.Lys10Thr	p.K10T	ENST00000371139	NM_001114937.2	10	aAa/aCa	1/4	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.34	2		435	504	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	90	476	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.806	0.715	0.902	0.806	0.715	0.902	CLONAL	1	TRUE	1	0.34	2		477	657	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453486	138453486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1451809865	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	19	342	0	ENST00000289153.2:c.962G>A	p.Arg321Gln	p.R321Q	ENST00000289153	NM_006219.2	321	cGa/cAa	5/22	1	2	FACETS	0.716	0.548	0.911	0.716	0.548	0.911	CLONAL	1	TRUE	1	0.34	2		342	156	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178136	142178136	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	12	294	0	ENST00000350721.4:c.7282C>A	p.Leu2428Ile	p.L2428I	ENST00000350721	NM_001184.3	2428	Ctc/Atc	43/47	1	2	FACETS	0.487	0.343	0.661	0.487	0.343	0.661	SUBCLONAL	1	TRUE	1	0.34	2		294	145	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	10	1089	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.175	0.118	0.248	0.175	0.118	0.248	SUBCLONAL	1	TRUE	1	0.34	2		1090	336	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742123	145742123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs550470182	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	27	541	1	ENST00000428558.2:c.380C>T	p.Pro127Leu	p.P127L	ENST00000428558	NM_004260.3	127	cCg/cTg	5/22	1	2	FACETS	0.321	0.255	0.397	0.321	0.255	0.397	SUBCLONAL	1	TRUE	1	0.34	2		542	495	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381502	81381502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	37	290	0	ENST00000222390.5:c.559C>T	p.Pro187Ser	p.P187S	ENST00000222390	NM_000601.4	187	Ccc/Tcc	5/18	0.114195292829279	3	FACETS	1	0.886	1	0.544	0.452	0.646	INDETERMINATE	1	TRUE	1	0.34	3		290	234	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156858	106156858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	16	546	1	ENST00000380013.4:c.1759C>T	p.Pro587Ser	p.P587S	ENST00000380013	NM_001127208.2	587	Cca/Tca	3/11	1	2	FACETS	0.55	0.409	0.718	0.55	0.409	0.718	SUBCLONAL	1	TRUE	1	0.34	2		547	171	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539884	187539884	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	17	370	0	ENST00000441802.2:c.7856T>G	p.Leu2619Arg	p.L2619R	ENST00000441802	NM_005245.3	2619	cTt/cGt	10/27	1	2	FACETS	0.402	0.3	0.522	0.402	0.3	0.522	SUBCLONAL	1	TRUE	1	0.34	2		370	249	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401074	139401074	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746910989	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	38	405	1	ENST00000277541.6:c.3919G>A	p.Val1307Ile	p.V1307I	ENST00000277541	NM_017617.3	1307	Gtc/Atc	24/34	1	2	FACETS	0.373	0.307	0.446	0.373	0.307	0.446	SUBCLONAL	1	TRUE	1	0.34	2		406	600	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120671	115120671	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	111	810	0	ENST00000257566.3:c.335T>G	p.Leu112Arg	p.L112R	ENST00000257566	NM_016569.3	112	cTt/cGt	1/8	0.114195292829279	3	FACETS	1	0.945	1	0.538	0.484	0.595	INDETERMINATE	1	TRUE	1	0.34	3		810	710	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211110	55211110	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	15	400	0	ENST00000275493.2:c.353C>T	p.Ala118Val	p.A118V	ENST00000275493	NM_005228.3	118	gCc/gTc	3/28	0.114195292829279	3	FACETS	0.574	0.421	0.756	0.287	0.21	0.378	INDETERMINATE	1	TRUE	1	0.34	3		400	180	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748510	43748510	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774265827	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	49	323	0	ENST00000523873.1:c.464G>A	p.Arg155His	p.R155H	ENST00000523873		155	cGc/cAc	6/8	0.213688332421629	3	FACETS	0.986	0.839	1	0.493	0.419	0.574	CLONAL	1	TRUE	1	0.34	3		323	342	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231558	5231558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868011195	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	68	388	2	ENST00000357368.4:c.1918C>T	p.Arg640Cys	p.R640C	ENST00000357368	NM_002850.3	640	Cgc/Tgc	14/38	1	2	FACETS	0.75	0.654	0.855	0.75	0.654	0.855	SUBCLONAL	1	TRUE	1	0.34	2		390	533	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856469	111856469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	64	335	0	ENST00000341259.2:c.520G>A	p.Ala174Thr	p.A174T	ENST00000341259	NM_005475.2	174	Gcc/Acc	2/8	0.114195292829279	3	FACETS	0.916	0.795	1	0.458	0.397	0.524	INDETERMINATE	1	TRUE	1	0.34	3		335	481	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468285	50468285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	23	454	0	ENST00000331340.3:c.1520C>T	p.Ser507Leu	p.S507L	ENST00000331340	NM_006060.4	507	tCg/tTg	8/8	0.114195292829279	3	FACETS	0.352	0.273	0.443	0.176	0.136	0.222	INDETERMINATE	1	TRUE	1	0.34	3		454	450	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726957	61726957	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	16	499	0	ENST00000401558.2:c.481G>A	p.Glu161Lys	p.E161K	ENST00000401558	NM_003400.3	161	Gaa/Aaa	7/25	1	2	FACETS	0.424	0.314	0.555	0.424	0.314	0.555	SUBCLONAL	1	TRUE	1	0.34	2		499	222	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971024	21971024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	42	494	0	ENST00000304494.5:c.334C>T	p.Arg112Cys	p.R112C	ENST00000304494	NM_000077.4	112	Cgt/Tgt	2/3	1	2	FACETS	0.514	0.429	0.608	0.514	0.429	0.608	SUBCLONAL	1	TRUE	1	0.34	2		494	481	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191118	185191118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564401067	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	23	475	2	ENST00000265026.3:c.1999G>A	p.Ala667Thr	p.A667T	ENST00000265026	NM_004721.4	667	Gcc/Acc	11/14	1	2	FACETS	0.359	0.279	0.451	0.359	0.279	0.451	SUBCLONAL	1	TRUE	1	0.34	2		477	377	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197187	26197187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	32	407	0	ENST00000356476.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000356476		98	Gag/Aag	1/1	0.213688332421629	3	FACETS	0.665	0.541	0.805	0.333	0.27	0.403	SUBCLONAL	1	TRUE	1	0.34	3		407	331	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546787	9546787	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	30	288	0	ENST00000353224.5:c.1235C>T	p.Pro412Leu	p.P412L	ENST00000353224	NM_177990.2	412	cCg/cTg	5/10	1	2	FACETS	0.825	0.669	0.998	0.825	0.669	0.998	CLONAL	1	TRUE	1	0.34	2		288	214	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001305	150001305	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568586257	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	18	559	0	ENST00000253339.5:c.2299C>T	p.Arg767Cys	p.R767C	ENST00000253339		767	Cgt/Tgt	4/7	0.213688332421629	3	FACETS	0.568	0.429	0.732	0.284	0.214	0.366	SUBCLONAL	1	TRUE	1	0.34	3		559	218	SUCCESS
AR	367	MSKCC	GRCh37	X	66765719	66765719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	118	875	0	ENST00000374690.3:c.731C>T	p.Ser244Leu	p.S244L	ENST00000374690	NM_000044.3	244	tCg/tTg	1/8	1	2	FACETS	0.802	0.723	0.885	0.802	0.723	0.885	CLONAL	1	TRUE	1	0.34	2		875	866	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050943	49050943	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767232453	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	20	265	0	ENST00000267163.4:c.2627G>A	p.Arg876His	p.R876H	ENST00000267163	NM_000321.2	876	cGc/cAc	25/27	0.114195292829279	3	FACETS	0.949	0.733	1	0.475	0.366	0.599	INDETERMINATE	1	TRUE	1	0.34	3		265	145	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212587117	212587117	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	13	365	0	ENST00000342788.4:c.883+1G>A		p.X295_splice	ENST00000342788	NM_005235.2	295			1	2	FACETS	0.597	0.429	0.8	0.597	0.429	0.8	SUBCLONAL	1	TRUE	1	0.34	2		365	128	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206943236	206943236	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs766492258	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	34	303	1	ENST00000423557.1:c.382C>T	p.Arg128Ter	p.R128*	ENST00000423557	NM_000572.2	128	Cga/Tga	4/5	1	2	FACETS	0.862	0.709	1	0.862	0.709	1	CLONAL	1	TRUE	1	0.34	2		304	232	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617189	100617189	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	35	529	1	ENST00000308731.7:c.560C>A	p.Pro187His	p.P187H	ENST00000308731	NM_000061.2	187	cCt/cAt	7/19	1	2	FACETS	0.493	0.404	0.592	0.493	0.404	0.592	SUBCLONAL	1	TRUE	1	0.34	2		530	418	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515335	103515335	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	11	228	0	ENST00000355739.4:c.1836G>T	p.Glu612Asp	p.E612D	ENST00000355739	NM_000123.3	612	gaG/gaT	8/15	0.114195292829279	3	FACETS	0.67	0.466	0.919	0.335	0.233	0.46	INDETERMINATE	1	TRUE	1	0.34	3		228	113	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46512281	46512281	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	33	387	1	ENST00000262741.5:c.958G>T	p.Gly320Ter	p.G320*	ENST00000262741	NM_003629.3	320	Gga/Tga	8/10	1	2	FACETS	0.679	0.555	0.817	0.679	0.555	0.817	SUBCLONAL	1	TRUE	1	0.34	2		388	286	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228800	36228800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1393734909	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	104	730	2	ENST00000222270.7:c.7699C>T	p.Arg2567Cys	p.R2567C	ENST00000222270	NM_014727.1	2567	Cgt/Tgt	35/37	1	2	FACETS	0.837	0.75	0.93	0.837	0.75	0.93	CLONAL	1	TRUE	1	0.34	2		732	731	SUCCESS
APC	324	MSKCC	GRCh37	5	112175486	112175486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424719678	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	10	327	0	ENST00000257430.4:c.4195C>T	p.Arg1399Cys	p.R1399C	ENST00000257430	NM_000038.5	1399	Cgt/Tgt	16/16	1	2	FACETS	0.336	0.228	0.472	0.336	0.228	0.472	SUBCLONAL	1	TRUE	1	0.34	2		327	175	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694712	176694712	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	21	286	0	ENST00000439151.2:c.5296C>T	p.Arg1766Ter	p.R1766*	ENST00000439151	NM_022455.4	1766	Cga/Tga	15/23	1	2	FACETS	0.722	0.56	0.909	0.722	0.56	0.909	CLONAL	1	TRUE	1	0.34	2		286	171	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32900639	32900639	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41293469	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	14	337	0	ENST00000380152.3:c.520C>T	p.Arg174Cys	p.R174C	ENST00000380152		174	Cgt/Tgt	7/27	0.114195292829279	3	FACETS	0.688	0.5	0.912	0.344	0.25	0.456	INDETERMINATE	1	TRUE	1	0.34	3		337	140	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143370	30143370	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	75	642	0	ENST00000389048.3:c.156G>T	p.Lys52Asn	p.K52N	ENST00000389048	NM_004304.4	52	aaG/aaT	1/29	1	2	FACETS	0.812	0.713	0.919	0.812	0.713	0.919	CLONAL	1	TRUE	1	0.34	2		642	543	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276614	115276614	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	28	514	0	ENST00000438362.2:c.845G>T	p.Arg282Ile	p.R282I	ENST00000438362	NM_001242891.1	282	aGa/aTa	8/20	1	2	FACETS	0.692	0.556	0.846	0.692	0.556	0.846	SUBCLONAL	1	TRUE	1	0.34	2		514	238	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46574157	46574157	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	157	614	2	ENST00000263734.3:c.172C>T	p.Arg58Ter	p.R58*	ENST00000263734	NM_001430.4	58	Cga/Tga	2/16	1	2	FACETS	0.771	0.709	0.835	1	0.989	1	SUBCLONAL	2	TRUE	1	0.34	2		616	599	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054752	5054752	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	12	257	0	ENST00000381652.3:c.804G>T	p.Glu268Asp	p.E268D	ENST00000381652	NM_004972.3	268	gaG/gaT	7/25	1	2	FACETS	0.685	0.486	0.925	0.685	0.486	0.925	SUBCLONAL	1	TRUE	1	0.34	2		257	103	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31423030	31423030	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	33	448	0	ENST00000344624.3:c.3283C>T	p.Arg1095Ter	p.R1095*	ENST00000344624		1095	Cga/Tga	26/33	1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.34	2		448	184	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346188	152346188	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	18	468	0	ENST00000359321.1:c.382C>A	p.Leu128Ile	p.L128I	ENST00000359321	NM_005431.1	128	Ctt/Att	3/3	0.114195292829279	3	FACETS	0.616	0.466	0.793	0.308	0.233	0.397	INDETERMINATE	1	TRUE	1	0.34	3		468	201	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65332758	65332758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	20	400	0	ENST00000342505.4:c.781G>A	p.Val261Met	p.V261M	ENST00000342505	NM_002227.2	261	Gtg/Atg	7/25	1	2	FACETS	0.717	0.553	0.907	0.717	0.553	0.907	CLONAL	1	TRUE	1	0.34	2		400	164	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11270917	11270917	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750592225	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	24	367	3	ENST00000361445.4:c.3608G>A	p.Arg1203Gln	p.R1203Q	ENST00000361445	NM_004958.3	1203	cGa/cAa	24/58	1	2	FACETS	0.616	0.485	0.766	0.616	0.485	0.766	SUBCLONAL	1	TRUE	1	0.34	2		370	229	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322564	39322564	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	38	361	0	ENST00000373001.3:c.428T>C	p.Val143Ala	p.V143A	ENST00000373001	NM_022157.3	143	gTc/gCc	2/7	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.34	2		361	160	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363258	40363258	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199701756	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	82	530	0	ENST00000397332.2:c.971G>A	p.Arg324Gln	p.R324Q	ENST00000397332	NM_001033082.2	324	cGg/cAg	3/3	1	2	FACETS	0.944	0.835	1	0.944	0.835	1	CLONAL	1	TRUE	1	0.34	2		530	511	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65300310	65300310	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	24	288	0	ENST00000342505.4:c.3400T>G	p.Phe1134Val	p.F1134V	ENST00000342505	NM_002227.2	1134	Ttc/Gtc	25/25	1	2	FACETS	0.784	0.62	0.971	0.784	0.62	0.971	CLONAL	1	TRUE	1	0.34	2		288	180	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115276716	115276716	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	30	364	0	ENST00000438362.2:c.743G>T	p.Arg248Ile	p.R248I	ENST00000438362	NM_001242891.1	248	aGa/aTa	8/20	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.34	2		364	130	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874530	155874530	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs869025191	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	25	498	0	ENST00000368323.3:c.229G>T	p.Ala77Ser	p.A77S	ENST00000368323	NM_006912.5	77	Gct/Tct	4/6	1	2	FACETS	0.561	0.443	0.696	0.561	0.443	0.696	SUBCLONAL	1	TRUE	1	0.34	2		498	262	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570799	226570799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1407958928	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	47	470	0	ENST00000366794.5:c.1097C>T	p.Ala366Val	p.A366V	ENST00000366794	NM_001618.3	366	gCg/gTg	8/23	1	2	FACETS	0.394	0.332	0.464	0.394	0.332	0.464	SUBCLONAL	1	TRUE	1	0.34	2		470	701	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669314	241669314	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	25	364	0	ENST00000366560.3:c.893C>T	p.Ala298Val	p.A298V	ENST00000366560	NM_000143.3	298	gCt/gTt	6/10	1	2	FACETS	0.697	0.552	0.861	0.697	0.552	0.861	SUBCLONAL	1	TRUE	1	0.34	2		364	211	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850704	63850704	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1460795394	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	16	263	0	ENST00000279873.7:c.1482G>T	p.Lys494Asn	p.K494N	ENST00000279873	NM_032199.2	494	aaG/aaT	10/10	0.114195292829279	3	FACETS	0.729	0.542	0.949	0.365	0.271	0.475	INDETERMINATE	1	TRUE	1	0.34	3		263	151	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127947	64127947	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	28	540	0	ENST00000334205.4:c.347-2A>G		p.X116_splice	ENST00000334205	NM_003942.2	116			1	2	FACETS	0.382	0.305	0.47	0.382	0.305	0.47	SUBCLONAL	1	TRUE	1	0.34	2		540	431	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137339	64137339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	71	621	0	ENST00000334205.4:c.1771G>A	p.Asp591Asn	p.D591N	ENST00000334205	NM_003942.2	591	Gac/Aac	14/17	1	2	FACETS	0.714	0.623	0.811	0.714	0.623	0.811	SUBCLONAL	1	TRUE	1	0.34	2		621	585	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94917629	94917629	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	33	488	1	ENST00000536441.1:c.892C>A	p.Leu298Ile	p.L298I	ENST00000536441	NM_144665.3	298	Ctt/Att	6/10	1	2	FACETS	0.616	0.503	0.743	0.616	0.503	0.743	SUBCLONAL	1	TRUE	1	0.34	2		489	315	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102196290	102196290	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	27	249	0	ENST00000263464.3:c.947T>C	p.Phe316Ser	p.F316S	ENST00000263464	NM_001165.4	316	tTt/tCt	3/9	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.34	2		249	132	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344621	118344621	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	16	402	0	ENST00000534358.1:c.2747T>G	p.Val916Gly	p.V916G	ENST00000534358	NM_005933.3	916	gTt/gGt	3/36	1	2	FACETS	0.49	0.363	0.641	0.49	0.363	0.641	SUBCLONAL	1	TRUE	1	0.34	2		402	192	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246419	46246419	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	22	255	0	ENST00000334344.6:c.4513T>C	p.Ser1505Pro	p.S1505P	ENST00000334344	NM_152641.2	1505	Tct/Cct	15/21	0.114195292829279	3	FACETS	1	0.805	1	0.515	0.403	0.642	INDETERMINATE	1	TRUE	1	0.34	3		255	147	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478826	56478826	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	69	552	0	ENST00000267101.3:c.282C>A	p.Phe94Leu	p.F94L	ENST00000267101	NM_001982.3	94	ttC/ttA	3/28	0.114195292829279	3	FACETS	0.857	0.747	0.976	0.429	0.373	0.488	INDETERMINATE	1	TRUE	1	0.34	3		552	554	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913436	28913436	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	14	340	0	ENST00000282397.4:c.2357C>A	p.Ser786Tyr	p.S786Y	ENST00000282397	NM_002019.4	786	tCt/tAt	17/30	0.114195292829279	3	FACETS	0.817	0.596	1	0.408	0.298	0.539	INDETERMINATE	1	TRUE	1	0.34	3		340	118	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438168	110438168	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766745986	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	63	309	0	ENST00000375856.3:c.233G>A	p.Ser78Asn	p.S78N	ENST00000375856	NM_003749.2	78	aGc/aAc	1/2	0.114195292829279	3	FACETS	0.97	0.841	1	0.485	0.42	0.555	INDETERMINATE	1	TRUE	1	0.34	3		309	447	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105579	30105579	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1036795627	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	33	670	0	ENST00000331968.5:c.1107G>T	p.Glu369Asp	p.E369D	ENST00000331968	NM_002742.2	369	gaG/gaT	7/18	1	2	FACETS	0.307	0.249	0.372	0.307	0.249	0.372	SUBCLONAL	1	TRUE	1	0.34	2		670	633	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557649	95557649	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	20	487	0	ENST00000393063.1:c.5418G>T	p.Lys1806Asn	p.K1806N	ENST00000393063	NM_030621.3	1806	aaG/aaT	26/28	1	2	FACETS	0.404	0.309	0.516	0.404	0.309	0.516	SUBCLONAL	1	TRUE	1	0.34	2		487	291	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023000	33023000	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	46	336	0	ENST00000300177.4:c.109G>T	p.Asp37Tyr	p.D37Y	ENST00000300177	NM_001191322.1	37	Gac/Tac	2/2	1	2	FACETS	0.896	0.759	1	0.896	0.759	1	CLONAL	1	TRUE	1	0.34	2		336	302	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38631954	38631954	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	21	476	0	ENST00000299084.4:c.440C>A	p.Ser147Tyr	p.S147Y	ENST00000299084	NM_152594.2	147	tCt/tAt	5/7	1	2	FACETS	0.615	0.475	0.775	0.615	0.475	0.775	SUBCLONAL	1	TRUE	1	0.34	2		476	201	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38641689	38641689	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	50	344	0	ENST00000299084.4:c.649T>C	p.Ser217Pro	p.S217P	ENST00000299084	NM_152594.2	217	Tcc/Ccc	6/7	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.34	2		344	218	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643299	38643299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1404721092	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	37	375	0	ENST00000299084.4:c.769C>T	p.Arg257Cys	p.R257C	ENST00000299084	NM_152594.2	257	Cgc/Tgc	7/7	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.34	2		375	151	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701242	43701242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368366606	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	31	416	2	ENST00000382044.4:c.5453G>A	p.Arg1818Gln	p.R1818Q	ENST00000382044	NM_001141980.1	1818	cGg/cAg	26/28	1	2	FACETS	0.635	0.515	0.77	0.635	0.515	0.77	SUBCLONAL	1	TRUE	1	0.34	2		418	287	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748574	43748574	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	73	829	2	ENST00000382044.4:c.2232A>T	p.Glu744Asp	p.E744D	ENST00000382044	NM_001141980.1	744	gaA/gaT	12/28	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.34	2		831	354	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748952	43748952	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	133	848	0	ENST00000382044.4:c.1854A>C	p.Glu618Asp	p.E618D	ENST00000382044	NM_001141980.1	618	gaA/gaC	12/28	1	2	FACETS	0.758	0.692	0.827	1	0.987	1	SUBCLONAL	2	TRUE	1	0.34	2		848	516	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43773135	43773135	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	26	620	0	ENST00000382044.4:c.457G>T	p.Glu153Ter	p.E153*	ENST00000382044	NM_001141980.1	153	Gaa/Taa	5/28	1	2	FACETS	0.358	0.283	0.444	0.358	0.283	0.444	SUBCLONAL	1	TRUE	1	0.34	2		620	427	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007795	45007795	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	18	385	0	ENST00000558401.1:c.242C>A	p.Ser81Tyr	p.S81Y	ENST00000558401	NM_004048.2	81	tCt/tAt	2/4	1	2	FACETS	0.662	0.501	0.848	0.662	0.501	0.848	SUBCLONAL	1	TRUE	1	0.34	2		385	160	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347492	91347492	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	29	418	0	ENST00000355112.3:c.3654T>G	p.Cys1218Trp	p.C1218W	ENST00000355112	NM_000057.2	1218	tgT/tgG	19/22	1	2	FACETS	0.594	0.478	0.726	0.594	0.478	0.726	SUBCLONAL	1	TRUE	1	0.34	2		418	287	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642751	3642751	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	37	610	1	ENST00000294008.3:c.2276A>G	p.Asp759Gly	p.D759G	ENST00000294008	NM_032444.2	759	gAc/gGc	11/15	1	2	FACETS	0.317	0.261	0.381	0.317	0.261	0.381	SUBCLONAL	1	TRUE	1	0.34	2		611	686	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3645643	3645643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372150541	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	97	667	3	ENST00000294008.3:c.1976C>T	p.Ser659Leu	p.S659L	ENST00000294008	NM_032444.2	659	tCg/tTg	9/15	1	2	FACETS	0.748	0.666	0.834	0.748	0.666	0.834	SUBCLONAL	1	TRUE	1	0.34	2		670	763	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3658691	3658691	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	111	843	1	ENST00000294008.3:c.275G>T	p.Arg92Met	p.R92M	ENST00000294008	NM_032444.2	92	aGg/aTg	2/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.34	2		844	511	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134444	30134444	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	34	569	0	ENST00000263025.4:c.87G>T	p.Glu29Asp	p.E29D	ENST00000263025	NM_002746.2	29	gaG/gaT	1/9	1	2	FACETS	0.328	0.267	0.397	0.328	0.267	0.397	SUBCLONAL	1	TRUE	1	0.34	2		569	610	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50828333	50828333	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	58	367	0	ENST00000398568.2:c.2671C>T	p.Arg891Trp	p.R891W	ENST00000398568	NM_001042412.1	891	Cgg/Tgg	17/18	1	2	FACETS	0.967	0.835	1	0.967	0.835	1	CLONAL	1	TRUE	1	0.34	2		367	353	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992613	72992613	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	34	468	0	ENST00000268489.5:c.1432G>T	p.Glu478Ter	p.E478*	ENST00000268489	NM_006885.3	478	Gaa/Taa	2/10	1	2	FACETS	0.778	0.639	0.933	0.778	0.639	0.933	CLONAL	1	TRUE	1	0.34	2		468	257	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838142	89838142	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	87	549	0	ENST00000389301.3:c.2095A>C	p.Ile699Leu	p.I699L	ENST00000389301	NM_000135.2	699	Ata/Cta	23/43	1	2	FACETS	0.838	0.742	0.939	0.838	0.742	0.939	CLONAL	1	TRUE	1	0.34	2		549	611	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428038	33428038	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	19	496	0	ENST00000345365.6:c.921G>T	p.Glu307Asp	p.E307D	ENST00000345365	NM_002878.3	307	gaG/gaT	10/10	1	2	FACETS	0.384	0.291	0.493	0.384	0.291	0.493	SUBCLONAL	1	TRUE	1	0.34	2		496	291	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40880898	40880898	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	55	599	0	ENST00000428826.2:c.62C>A	p.Ser21Tyr	p.S21Y	ENST00000428826		21	tCt/tAt	3/21	1	2	FACETS	0.825	0.708	0.952	0.825	0.708	0.952	CLONAL	1	TRUE	1	0.34	2		599	392	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244466	41244466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357049	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	20	609	0	ENST00000357654.3:c.3082C>T	p.Arg1028Cys	p.R1028C	ENST00000357654	NM_007294.3	1028	Cgt/Tgt	10/23	1	2	FACETS	0.488	0.374	0.621	0.488	0.374	0.621	SUBCLONAL	1	TRUE	1	0.34	2		609	241	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55334886	55334886	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	24	496	0	ENST00000284073.2:c.163G>T	p.Asp55Tyr	p.D55Y	ENST00000284073	NM_138962.2	55	Gat/Tat	3/14	1	2	FACETS	0.562	0.442	0.7	0.562	0.442	0.7	SUBCLONAL	1	TRUE	1	0.34	2		496	251	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007134	62007134	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	58	506	0	ENST00000392795.3:c.548A>G	p.Asp183Gly	p.D183G	ENST00000392795	NM_001039933.1	183	gAc/gGc	4/6	1	2	FACETS	0.849	0.732	0.975	0.849	0.732	0.975	CLONAL	1	TRUE	1	0.34	2		506	402	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119809	70119809	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771635102	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	71	615	0	ENST00000245479.2:c.811C>T	p.Arg271Cys	p.R271C	ENST00000245479	NM_000346.3	271	Cgc/Tgc	3/3	1	2	FACETS	0.771	0.673	0.875	0.771	0.673	0.875	SUBCLONAL	1	TRUE	1	0.34	2		615	542	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211736	5211736	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	100	705	1	ENST00000357368.4:c.5099C>T	p.Ala1700Val	p.A1700V	ENST00000357368	NM_002850.3	1700	gCc/gTc	33/38	1	2	FACETS	0.854	0.763	0.95	0.854	0.763	0.95	CLONAL	1	TRUE	1	0.34	2		706	689	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295237	15295237	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	119	755	0	ENST00000263388.2:c.2435A>G	p.Asp812Gly	p.D812G	ENST00000263388	NM_000435.2	812	gAc/gGc	16/33	1	2	FACETS	0.799	0.721	0.882	0.799	0.721	0.882	SUBCLONAL	1	TRUE	1	0.34	2		755	876	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211427	36211427	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	43	787	0	ENST00000222270.7:c.1178C>A	p.Ala393Asp	p.A393D	ENST00000222270	NM_014727.1	393	gCt/gAt	3/37	1	2	FACETS	0.33	0.275	0.391	0.33	0.275	0.391	SUBCLONAL	1	TRUE	1	0.34	2		787	766	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229343	36229343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	32	552	0	ENST00000222270.7:c.8033G>A	p.Arg2678His	p.R2678H	ENST00000222270	NM_014727.1	2678	cGc/cAc	37/37	1	2	FACETS	0.388	0.314	0.472	0.388	0.314	0.472	SUBCLONAL	1	TRUE	1	0.34	2		552	485	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50143258	50143258	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	29	373	0	ENST00000246792.3:c.98T>C	p.Val33Ala	p.V33A	ENST00000246792	NM_006270.3	33	gTg/gCg	1/6	1	2	FACETS	0.391	0.313	0.48	0.391	0.313	0.48	SUBCLONAL	1	TRUE	1	0.34	2		373	436	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467035	25467035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	68	505	2	ENST00000264709.3:c.1840G>A	p.Asp614Asn	p.D614N	ENST00000264709	NM_175629.2	614	Gac/Aac	15/23	1	2	FACETS	0.828	0.722	0.942	0.828	0.722	0.942	CLONAL	1	TRUE	1	0.34	2		507	483	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443668	29443668	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	34	574	0	ENST00000389048.3:c.3549T>G	p.Ile1183Met	p.I1183M	ENST00000389048	NM_004304.4	1183	atT/atG	23/29	1	2	FACETS	0.351	0.286	0.425	0.351	0.286	0.425	SUBCLONAL	1	TRUE	1	0.34	2		574	569	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46605087	46605087	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1174585697	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	42	747	0	ENST00000263734.3:c.1304G>A	p.Ser435Asn	p.S435N	ENST00000263734	NM_001430.4	435	aGc/aAc	10/16	1	2	FACETS	0.301	0.25	0.358	0.301	0.25	0.358	SUBCLONAL	1	TRUE	1	0.34	2		747	820	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172193	99172193	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	62	531	0	ENST00000074304.5:c.1759G>T	p.Asp587Tyr	p.D587Y	ENST00000074304	NM_001134224.1	587	Gac/Tac	17/26	1	2	FACETS	0.715	0.618	0.82	0.715	0.618	0.82	SUBCLONAL	1	TRUE	1	0.34	2		531	510	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044328	128044328	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	73	504	0	ENST00000285398.2:c.1293G>T	p.Lys431Asn	p.K431N	ENST00000285398	NM_000122.1	431	aaG/aaT	8/15	1	2	FACETS	0.931	0.817	1	0.931	0.817	1	CLONAL	1	TRUE	1	0.34	2		504	461	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158637024	158637024	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	60	464	0	ENST00000263640.3:c.156G>T	p.Gln52His	p.Q52H	ENST00000263640	NM_001105.4	52	caG/caT	4/11	1	2	FACETS	0.704	0.608	0.81	0.704	0.608	0.81	SUBCLONAL	1	TRUE	1	0.34	2		464	501	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31390266	31390266	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	23	347	0	ENST00000328111.2:c.2221G>T	p.Gly741Trp	p.G741W	ENST00000328111	NM_006892.3	741	Ggg/Tgg	20/23	1	2	FACETS	0.425	0.332	0.534	0.425	0.332	0.534	SUBCLONAL	1	TRUE	1	0.34	2		347	318	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326261	62326261	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767674666	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	145	791	1	ENST00000360203.5:c.3277G>A	p.Asp1093Asn	p.D1093N	ENST00000360203	NM_001283009.1	1093	Gac/Aac	32/35	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.34	2		792	718	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62326810	62326810	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	147	779	0	ENST00000360203.5:c.3629A>C	p.His1210Pro	p.H1210P	ENST00000360203	NM_001283009.1	1210	cAc/cCc	34/35	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.34	2		779	635	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12393123	12393123	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	48	482	0	ENST00000287820.6:c.32A>G	p.Asp11Gly	p.D11G	ENST00000287820	NM_015869.4	11	gAc/gGc	1/7	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.34	2		482	224	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458264	12458264	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	56	524	0	ENST00000287820.6:c.881A>G	p.His294Arg	p.H294R	ENST00000287820	NM_015869.4	294	cAc/cGc	6/7	1	2	FACETS	0.874	0.752	1	0.874	0.752	1	CLONAL	1	TRUE	1	0.34	2		524	377	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71161761	71161761	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	13	341	1	ENST00000318789.4:c.208C>A	p.Leu70Ile	p.L70I	ENST00000318789	NM_032682.5	70	Ctt/Att	7/21	1	2	FACETS	0.375	0.267	0.505	0.375	0.267	0.505	SUBCLONAL	1	TRUE	1	0.34	2		342	204	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259155	89259155	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	23	312	0	ENST00000336596.2:c.299A>G	p.Lys100Arg	p.K100R	ENST00000336596	NM_005233.5	100	aAg/aGg	3/17	1	2	FACETS	1	0.803	1	1	0.803	1	CLONAL	1	TRUE	1	0.34	2		312	133	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134885803	134885803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	30	397	0	ENST00000398015.3:c.1714G>A	p.Glu572Lys	p.E572K	ENST00000398015	NM_004441.4	572	Gag/Aag	9/16	1	2	FACETS	0.532	0.429	0.648	0.532	0.429	0.648	SUBCLONAL	1	TRUE	1	0.34	2		397	332	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461530	138461530	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	46	491	0	ENST00000289153.2:c.491T>C	p.Val164Ala	p.V164A	ENST00000289153	NM_006219.2	164	gTg/gCg	3/22	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.34	2		491	240	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149238693	149238693	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	56	622	0	ENST00000360632.3:c.1102A>C	p.Asn368His	p.N368H	ENST00000360632	NM_015472.4	368	Aac/Cac	7/7	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.34	2		622	287	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169988215	169988215	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	12	253	0	ENST00000295797.4:c.457C>A	p.His153Asn	p.H153N	ENST00000295797	NM_002740.5	153	Cac/Aac	6/18	1	2	FACETS	0.48	0.339	0.653	0.48	0.339	0.653	SUBCLONAL	1	TRUE	1	0.34	2		253	147	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917643	178917643	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	10	261	0	ENST00000263967.3:c.518C>A	p.Ser173Tyr	p.S173Y	ENST00000263967	NM_006218.2	173	tCt/tAt	3/21	1	2	FACETS	0.474	0.323	0.663	0.474	0.323	0.663	SUBCLONAL	1	TRUE	1	0.34	2		261	124	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136887	55136887	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	24	426	0	ENST00000257290.5:c.1209G>T	p.Lys403Asn	p.K403N	ENST00000257290	NM_006206.4	403	aaG/aaT	8/23	1	2	FACETS	0.567	0.446	0.706	0.567	0.446	0.706	SUBCLONAL	1	TRUE	1	0.34	2		426	249	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155183	55155183	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	25	422	0	ENST00000257290.5:c.2782A>C	p.Ile928Leu	p.I928L	ENST00000257290	NM_006206.4	928	Atc/Ctc	21/23	1	2	FACETS	0.457	0.36	0.568	0.457	0.36	0.568	SUBCLONAL	1	TRUE	1	0.34	2		422	322	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602935	55602935	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	28	309	0	ENST00000288135.5:c.2645T>G	p.Met882Arg	p.M882R	ENST00000288135	NM_000222.2	882	aTg/aGg	19/21	1	2	FACETS	0.726	0.583	0.886	0.726	0.583	0.886	SUBCLONAL	1	TRUE	1	0.34	2		309	227	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953824	55953824	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	25	477	0	ENST00000263923.4:c.3612G>T	p.Glu1204Asp	p.E1204D	ENST00000263923	NM_002253.2	1204	gaG/gaT	27/30	1	2	FACETS	0.618	0.489	0.765	0.618	0.489	0.765	SUBCLONAL	1	TRUE	1	0.34	2		477	238	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980349	55980349	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	28	429	0	ENST00000263923.4:c.742G>T	p.Ala248Ser	p.A248S	ENST00000263923	NM_002253.2	248	Gca/Tca	6/30	1	2	FACETS	0.766	0.616	0.935	0.766	0.616	0.935	CLONAL	1	TRUE	1	0.34	2		429	215	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143130150	143130150	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	28	454	0	ENST00000262992.4:c.866T>G	p.Leu289Arg	p.L289R	ENST00000262992	NM_001101669.1	289	cTt/cGt	11/24	1	2	FACETS	0.633	0.508	0.775	0.633	0.508	0.775	SUBCLONAL	1	TRUE	1	0.34	2		454	260	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143326426	143326426	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	37	374	0	ENST00000262992.4:c.188T>C	p.Val63Ala	p.V63A	ENST00000262992	NM_001101669.1	63	gTg/gCg	4/24	1	2	FACETS	0.603	0.498	0.72	0.603	0.498	0.72	SUBCLONAL	1	TRUE	1	0.34	2		374	361	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143352366	143352366	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	73	540	0	ENST00000262992.4:c.47T>G	p.Leu16Arg	p.L16R	ENST00000262992	NM_001101669.1	16	cTt/cGt	2/24	1	2	FACETS	0.938	0.823	1	0.938	0.823	1	CLONAL	1	TRUE	1	0.34	2		540	458	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541170	187541170	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	18	294	0	ENST00000441802.2:c.6570G>T	p.Glu2190Asp	p.E2190D	ENST00000441802	NM_005245.3	2190	gaG/gaT	10/27	1	2	FACETS	0.605	0.458	0.777	0.605	0.458	0.777	SUBCLONAL	1	TRUE	1	0.34	2		294	175	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549514	187549514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1040319596	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	26	317	0	ENST00000441802.2:c.4604G>A	p.Arg1535Gln	p.R1535Q	ENST00000441802	NM_005245.3	1535	cGa/cAa	9/27	1	2	FACETS	0.732	0.583	0.9	0.732	0.583	0.9	SUBCLONAL	1	TRUE	1	0.34	2		317	209	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293769	1293769	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1262077490	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	61	809	1	ENST00000310581.5:c.1232C>T	p.Thr411Met	p.T411M	ENST00000310581	NM_198253.2	411	aCg/aTg	2/16	1	2	FACETS	0.465	0.4	0.536	0.465	0.4	0.536	SUBCLONAL	1	TRUE	1	0.34	2		810	772	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31424569	31424569	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	96	560	0	ENST00000344624.3:c.3226del	p.Glu1076LysfsTer41	p.E1076Kfs*41	ENST00000344624		1076	Gaa/aa	25/33	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.34	2		560	418	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31472304	31472304	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	32	579	0	ENST00000344624.3:c.2107C>A	p.Leu703Ile	p.L703I	ENST00000344624		703	Ctc/Atc	14/33	1	2	FACETS	0.499	0.405	0.605	0.499	0.405	0.605	SUBCLONAL	1	TRUE	1	0.34	2		579	377	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950470	38950470	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	12	360	0	ENST00000357387.3:c.3480G>T	p.Glu1160Asp	p.E1160D	ENST00000357387	NM_152756.3	1160	gaG/gaT	31/38	1	2	FACETS	0.523	0.369	0.709	0.523	0.369	0.709	SUBCLONAL	1	TRUE	1	0.34	2		360	135	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80083395	80083395	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	71	550	0	ENST00000265081.6:c.2447A>G	p.Glu816Gly	p.E816G	ENST00000265081	NM_002439.4	816	gAa/gGa	18/24	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.34	2		550	300	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523327	176523327	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1490727566	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	99	648	0	ENST00000292408.4:c.1984T>C	p.Phe662Leu	p.F662L	ENST00000292408	NM_213647.1	662	Ttt/Ctt	15/18	1	2	FACETS	0.771	0.688	0.86	0.771	0.688	0.86	SUBCLONAL	1	TRUE	1	0.34	2		648	755	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405042	405042	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	45	296	0	ENST00000380956.4:c.1124G>T	p.Gly375Val	p.G375V	ENST00000380956	NM_001195286.1	375	gGc/gTc	8/9	0.213688332421629	3	FACETS	0.663	0.558	0.78	0.332	0.279	0.39	SUBCLONAL	1	TRUE	1	0.34	3		296	467	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407514	407514	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs760504688	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	15	330	0	ENST00000380956.4:c.1272C>A	p.Phe424Leu	p.F424L	ENST00000380956	NM_001195286.1	424	ttC/ttA	9/9	0.213688332421629	3	FACETS	0.555	0.407	0.732	0.278	0.203	0.366	SUBCLONAL	1	TRUE	1	0.34	3		330	186	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948236	31948236	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	71	541	0	ENST00000375333.2:c.824T>C	p.Val275Ala	p.V275A	ENST00000375333	NM_032454.1	275	gTg/gCg	6/8	0.213688332421629	3	FACETS	0.964	0.843	1	0.482	0.421	0.547	CLONAL	1	TRUE	1	0.34	3		541	507	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818098	32818098	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	64	489	0	ENST00000354258.4:c.1427G>A	p.Ser476Asn	p.S476N	ENST00000354258	NM_000593.5	476	aGt/aAt	5/11	0.213688332421629	3	FACETS	1	0.945	1	0.583	0.507	0.664	CLONAL	1	TRUE	1	0.34	3		489	378	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109309796	109309796	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	40	519	0	ENST00000436639.2:c.1519A>G	p.Thr507Ala	p.T507A	ENST00000436639	NM_014454.2	507	Acc/Gcc	9/10	0.213688332421629	3	FACETS	1	0.894	1	0.546	0.457	0.644	CLONAL	1	TRUE	1	0.34	3		519	252	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117629960	117629960	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	10	262	0	ENST00000368508.3:c.6566A>C	p.Asp2189Ala	p.D2189A	ENST00000368508	NM_002944.2	2189	gAt/gCt	41/43	0.213688332421629	3	FACETS	0.459	0.311	0.643	0.229	0.155	0.322	SUBCLONAL	1	TRUE	1	0.34	3		262	150	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117737471	117737471	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	14	316	0	ENST00000368508.3:c.178G>T	p.Gly60Ter	p.G60*	ENST00000368508	NM_002944.2	60	Gga/Tga	3/43	0.213688332421629	3	FACETS	0.518	0.375	0.69	0.259	0.187	0.345	SUBCLONAL	1	TRUE	1	0.34	3		316	186	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099317	157099317	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1042976677	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	49	369	0	ENST00000346085.5:c.254A>G	p.His85Arg	p.H85R	ENST00000346085	NM_020732.3	85	cAc/cGc	1/20	0.213688332421629	3	FACETS	1	0.938	1	0.598	0.51	0.693	CLONAL	1	TRUE	1	0.34	3		369	282	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935659	13935659	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	29	343	0	ENST00000405192.2:c.1197C>A	p.Phe399Leu	p.F399L	ENST00000405192	NM_001163147.1	399	ttC/ttA	12/12	0.114195292829279	3	FACETS	0.795	0.641	0.969	0.398	0.32	0.485	INDETERMINATE	1	TRUE	1	0.34	3		343	251	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729763	41729763	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	41	336	1	ENST00000242208.4:c.766C>A	p.Leu256Ile	p.L256I	ENST00000242208	NM_002192.2	256	Ctc/Atc	3/3	0.114195292829279	3	FACETS	1	0.9	1	0.551	0.462	0.649	INDETERMINATE	1	TRUE	1	0.34	3		337	256	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444375	50444375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776572250	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	41	304	1	ENST00000331340.3:c.305C>T	p.Ser102Leu	p.S102L	ENST00000331340	NM_006060.4	102	tCg/tTg	4/8	0.114195292829279	3	FACETS	0.966	0.809	1	0.483	0.404	0.57	INDETERMINATE	1	TRUE	1	0.34	3		305	292	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151835916	151835916	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	21	420	0	ENST00000262189.6:c.14608A>G	p.Ile4870Val	p.I4870V	ENST00000262189	NM_170606.2	4870	Atc/Gtc	58/59	0.114195292829279	3	FACETS	0.682	0.527	0.86	0.341	0.263	0.43	INDETERMINATE	1	TRUE	1	0.34	3		420	212	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873942	151873942	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	13	463	0	ENST00000262189.6:c.8596G>T	p.Glu2866Ter	p.E2866*	ENST00000262189	NM_170606.2	2866	Gaa/Taa	38/59	0.114195292829279	3	FACETS	0.367	0.261	0.495	0.183	0.13	0.248	INDETERMINATE	1	TRUE	1	0.34	3		463	244	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007101	152007101	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	32	354	0	ENST00000262189.6:c.799G>T	p.Glu267Ter	p.E267*	ENST00000262189	NM_170606.2	267	Gaa/Taa	6/59	0.114195292829279	3	FACETS	0.888	0.725	1	0.444	0.362	0.535	INDETERMINATE	1	TRUE	1	0.34	3		354	248	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205181	38205181	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	55	663	1	ENST00000317025.8:c.509C>A	p.Ser170Tyr	p.S170Y	ENST00000317025	NM_023034.1	170	tCt/tAt	2/24	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.34	2		664	317	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205497	38205497	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	19	782	0	ENST00000317025.8:c.193G>T	p.Asp65Tyr	p.D65Y	ENST00000317025	NM_023034.1	65	Gat/Tat	2/24	1	2	FACETS	0.307	0.232	0.395	0.307	0.232	0.395	SUBCLONAL	1	TRUE	1	0.34	2		782	364	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863325	56863325	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	40	346	0	ENST00000519728.1:c.469G>T	p.Glu157Ter	p.E157*	ENST00000519728	NM_002350.3	157	Gaa/Taa	6/13	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.34	2		346	200	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005880	69005880	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	43	458	0	ENST00000288368.4:c.2291C>A	p.Ala764Asp	p.A764D	ENST00000288368	NM_024870.2	764	gCt/gAt	21/40	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.34	2		458	215	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70981431	70981431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	155	751	2	ENST00000276594.2:c.665C>T	p.Ala222Val	p.A222V	ENST00000276594	NM_024504.3	222	gCg/gTg	2/8	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.34	2		753	701	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5078429	5078429	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	10	328	0	ENST00000381652.3:c.2116G>A	p.Val706Ile	p.V706I	ENST00000381652	NM_004972.3	706	Gtt/Att	16/25	1	2	FACETS	0.348	0.236	0.489	0.348	0.236	0.489	SUBCLONAL	1	TRUE	1	0.34	2		328	169	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518097	8518097	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	22	424	0	ENST00000356435.5:c.1294A>G	p.Thr432Ala	p.T432A	ENST00000356435		432	Acc/Gcc	10/35	1	2	FACETS	0.411	0.318	0.518	0.411	0.318	0.518	SUBCLONAL	1	TRUE	1	0.34	2		424	315	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215830	98215830	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	63	509	0	ENST00000331920.6:c.3379C>A	p.Leu1127Met	p.L1127M	ENST00000331920	NM_000264.3	1127	Ctg/Atg	20/24	1	2	FACETS	0.631	0.546	0.724	0.631	0.546	0.724	SUBCLONAL	1	TRUE	1	0.34	2		509	587	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128434643	128434643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371524490	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	61	493	0	ENST00000265960.3:c.211G>A	p.Asp71Asn	p.D71N	ENST00000265960	NM_001006617.1	71	Gat/Aat	2/12	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.34	2		493	258	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133710859	133710859	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	69	490	0	ENST00000318560.5:c.26T>C	p.Val9Ala	p.V9A	ENST00000318560	NM_005157.4	9	gTg/gCg	1/11	1	2	FACETS	0.89	0.778	1	0.89	0.778	1	CLONAL	1	TRUE	1	0.34	2		490	456	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133729586	133729586	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	20	492	0	ENST00000318560.5:c.215T>G	p.Phe72Cys	p.F72C	ENST00000318560	NM_005157.4	72	tTt/tGt	2/11	1	2	FACETS	0.315	0.24	0.402	0.315	0.24	0.402	SUBCLONAL	1	TRUE	1	0.34	2		492	374	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137300061	137300061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754761323	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	89	676	0	ENST00000481739.1:c.346G>A	p.Val116Ile	p.V116I	ENST00000481739	NM_002957.4	116	Gtc/Atc	3/10	1	2	FACETS	0.734	0.651	0.823	0.734	0.651	0.823	SUBCLONAL	1	TRUE	1	0.34	2		676	713	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938534	44938534	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	29	458	0	ENST00000377967.4:c.3082T>C	p.Ser1028Pro	p.S1028P	ENST00000377967	NM_021140.2	1028	Tct/Cct	20/29	1	2	FACETS	0.797	0.644	0.969	0.797	0.644	0.969	CLONAL	1	TRUE	1	0.34	2		458	214	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650432	48650432	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	98	778	0	ENST00000376670.3:c.402G>T	p.Glu134Asp	p.E134D	ENST00000376670	NM_002049.3	134	gaG/gaT	3/6	1	2	FACETS	0.924	0.825	1	0.924	0.825	1	CLONAL	1	TRUE	1	0.34	2		778	624	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412713	63412713	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	35	544	0	ENST00000330258.3:c.454G>T	p.Glu152Ter	p.E152*	ENST00000330258	NM_152424.3	152	Gag/Tag	2/2	1	2	FACETS	0.777	0.64	0.929	0.777	0.64	0.929	CLONAL	1	TRUE	1	0.34	2		544	265	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352313	70352313	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	25	492	2	ENST00000374080.3:c.4340C>A	p.Ala1447Asp	p.A1447D	ENST00000374080		1447	gCt/gAt	31/45	1	2	FACETS	0.327	0.257	0.407	0.327	0.257	0.407	SUBCLONAL	1	TRUE	1	0.34	2		494	450	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357586	70357586	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	27	735	0	ENST00000374080.3:c.5837C>A	p.Pro1946His	p.P1946H	ENST00000374080		1946	cCt/cAt	41/45	1	2	FACETS	0.311	0.246	0.385	0.311	0.246	0.385	SUBCLONAL	1	TRUE	1	0.34	2		735	511	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357595	70357595	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	79	761	0	ENST00000374080.3:c.5846C>A	p.Ser1949Tyr	p.S1949Y	ENST00000374080		1949	tCt/tAt	41/45	1	2	FACETS	0.831	0.732	0.937	0.831	0.732	0.937	CLONAL	1	TRUE	1	0.34	2		761	559	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937349	76937349	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	19	468	0	ENST00000373344.5:c.3399A>C	p.Glu1133Asp	p.E1133D	ENST00000373344	NM_000489.3	1133	gaA/gaC	9/35	1	2	FACETS	0.594	0.453	0.759	0.594	0.453	0.759	SUBCLONAL	1	TRUE	1	0.34	2		468	188	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937979	76937979	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	38	573	1	ENST00000373344.5:c.2769G>T	p.Lys923Asn	p.K923N	ENST00000373344	NM_000489.3	923	aaG/aaT	9/35	1	2	FACETS	0.955	0.796	1	0.955	0.796	1	CLONAL	1	TRUE	1	0.34	2		574	234	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608974	100608974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	25	410	0	ENST00000308731.7:c.1634A>G	p.Tyr545Cys	p.Y545C	ENST00000308731	NM_000061.2	545	tAt/tGt	17/19	1	2	FACETS	0.639	0.506	0.791	0.639	0.506	0.791	SUBCLONAL	1	TRUE	1	0.34	2		410	230	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210212	123210212	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	30	482	0	ENST00000218089.9:c.2564T>A	p.Ile855Asn	p.I855N	ENST00000218089	NM_001042749.1	855	aTt/aAt	26/35	1	2	FACETS	0.633	0.511	0.769	0.633	0.511	0.769	SUBCLONAL	1	TRUE	1	0.34	2		482	279	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152853897	152853897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004379-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	38	367	0	ENST00000406277.2:c.667C>T	p.Leu223Phe	p.L223F	ENST00000406277	NM_152274.4	223	Ctt/Ttt	7/7	1	2	FACETS	0.998	0.832	1	0.998	0.832	1	CLONAL	1	TRUE	1	0.34	2		367	224	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	24	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.845	1	1	0.956	1	CLONAL	2	TRUE	1	0.399892092278478	2		280	58	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057835	27057835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	61	616	1	ENST00000324856.7:c.1543C>T	p.Gln515Ter	p.Q515*	ENST00000324856	NM_006015.4	515	Cag/Tag	3/20	0.279690848049227	2	FACETS	0.877	0.785	0.968	1	0.972	1	CLONAL	3	TRUE	0	0.399892092278478	2		617	116	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652117	36652118	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0004387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	33	283	0	ENST00000244741.5:c.243dup	p.Pro82AlafsTer7	p.P82Afs*7	ENST00000244741	NM_000389.4	80	acg/acGg	2/3	0.282998920938322	4	FACETS	1	0.904	1	0.748	0.625	0.878	CLONAL	2	TRUE	1	0.399892092278478	4		283	103	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	138	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.828173564439712	2		280	296	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0004404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	203	511	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.967	0.905	1	0.967	0.905	1	CLONAL	1	TRUE	1	0.828173564439712	2		511	507	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446429	49446432	+	frameshift_variant	Frame_Shift_Del	DEL	GCAT	GCAT	-	novel	NA	P-0004404-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	257	286	0	ENST00000301067.7:c.1173_1176del	p.Cys392LysfsTer9	p.C392Kfs*9	ENST00000301067	NM_003482.3	391	gcATGC/gc	9/54	1	2	FACETS	0.902	0.85	0.955	0.902	0.85	0.955	CLONAL	1	TRUE	1	0.828173564439712	2		286	688	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	40	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.825	0.713	0.94	1	0.969	1	CLONAL	2	TRUE	1	0.550728436383752	2		280	88	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0004419-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	41	595	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.550728436383752	2		595	120	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0004437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	13	464	0				ENST00000310581	NM_198253.2	-/1132			0.386853459502652	1	FACETS	0.638	0.462	0.845	0.638	0.462	0.845	SUBCLONAL	1	FALSE	0	0.386853459502652	1		464	85	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295674	212295674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1362156940	NA	P-0004437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	59	284	0	ENST00000342788.4:c.2639G>A	p.Gly880Glu	p.G880E	ENST00000342788	NM_005235.2	880	gGa/gAa	21/28	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	FALSE	1	0.386853459502652	2		284	302	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955063	55955063	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	92	285	0	ENST00000263923.4:c.3482G>A	p.Gly1161Glu	p.G1161E	ENST00000263923	NM_002253.2	1161	gGa/gAa	26/30	0.240982133211485	1	FACETS	0.986	0.883	1	0.986	0.883	1	CLONAL	1	FALSE	0	0.386853459502652	1		285	389	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0004437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	89	511	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.143200345177253	4	FACETS	0.818	0.73	0.911	0.818	0.73	0.911	INDETERMINATE	2	FALSE	2	0.386853459502652	4		511	390	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198262733	198262733	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	73	218	0	ENST00000335508.6:c.3242T>C	p.Phe1081Ser	p.F1081S	ENST00000335508	NM_012433.2	1081	tTt/tCt	22/25	1	2	FACETS	0.826	0.725	0.934	0.826	0.725	0.934	CLONAL	1	FALSE	1	0.386853459502652	2		218	457	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682361	52682361	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	76	267	0	ENST00000394830.3:c.812A>G	p.Lys271Arg	p.K271R	ENST00000394830	NM_018313.4	271	aAg/aGg	8/30	0.386853459502652	1	FACETS	0.938	0.829	1	0.938	0.829	1	CLONAL	1	FALSE	0	0.386853459502652	1		267	338	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138384011	138384011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759151757	NA	P-0004437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	93	308	2	ENST00000289153.2:c.2539C>T	p.Arg847Cys	p.R847C	ENST00000289153	NM_006219.2	847	Cgc/Tgc	18/22	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	FALSE	1	0.386853459502652	2		310	406	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217214	66217214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	80	318	0	ENST00000273854.3:c.2401C>T	p.Leu801Phe	p.L801F	ENST00000273854	NM_004439.5	801	Ctt/Ttt	14/18	0.240982133211485	1	FACETS	0.814	0.72	0.913	0.814	0.72	0.913	CLONAL	1	FALSE	0	0.386853459502652	1		318	410	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295254	1295254	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0004437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	12	138	0				ENST00000310581	NM_198253.2	-/1132			0.386853459502652	1	FACETS	0.596	0.424	0.8	0.596	0.424	0.8	SUBCLONAL	1	FALSE	0	0.386853459502652	1		138	84	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671931	30671931	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	48	285	0	ENST00000376406.3:c.5029C>T	p.Gln1677Ter	p.Q1677*	ENST00000376406	NM_014641.2	1677	Cag/Tag	10/15	0.283046407694773	3	FACETS	0.911	0.774	1	0.304	0.258	0.354	CLONAL	1	FALSE	0	0.386853459502652	3		285	325	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692891	89692891	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	37	119	0	ENST00000371953.3:c.375A>C	p.Lys125Asn	p.K125N	ENST00000371953	NM_000314.4	125	aaA/aaC	5/9	0.263319154997421	2	FACETS	0.843	0.7	0.999	0.421	0.35	0.5	CLONAL	1	FALSE	0	0.386853459502652	2		119	227	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248601	8248601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	36	263	0	ENST00000335790.3:c.286C>T	p.Pro96Ser	p.P96S	ENST00000335790	NM_002315.2	96	Cca/Tca	3/4	1	2	FACETS	0.785	0.65	0.935	0.785	0.65	0.935	CLONAL	1	FALSE	1	0.386853459502652	2		263	237	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998537	100998537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1005434284	NA	P-0004437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	27	255	0	ENST00000325455.5:c.1265C>T	p.Pro422Leu	p.P422L	ENST00000325455	NM_001202474.3	422	cCg/cTg	1/8	0.386853459502652	1	FACETS	0.651	0.523	0.794	0.651	0.523	0.794	SUBCLONAL	1	FALSE	0	0.386853459502652	1		255	173	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527895	103527895	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	65	223	1	ENST00000355739.4:c.3203C>T	p.Ser1068Leu	p.S1068L	ENST00000355739	NM_000123.3	1068	tCa/tTa	15/15	0.143200345177253	4	FACETS	1	0.97	1	0.706	0.616	0.802	INDETERMINATE	1	FALSE	2	0.386853459502652	4		224	330	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570311	95570311	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780815020	NA	P-0004437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	46	186	0	ENST00000393063.1:c.3422C>T	p.Ser1141Phe	p.S1141F	ENST00000393063	NM_030621.3	1141	tCc/tTc	22/28	1	2	FACETS	0.894	0.758	1	0.894	0.758	1	CLONAL	1	FALSE	1	0.386853459502652	2		186	266	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624936	9624936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760501160	NA	P-0004437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	54	577	0	ENST00000353224.5:c.41C>T	p.Pro14Leu	p.P14L	ENST00000353224	NM_177990.2	14	cCg/cTg	3/10	1	2	FACETS	0.875	0.752	1	0.875	0.752	1	CLONAL	1	FALSE	1	0.386853459502652	2		577	319	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	130	683	1	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	0.352101898893351	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.353099825834488	2		684	342	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582127	189582127	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	99	593	0	ENST00000264731.3:c.686C>A	p.Pro229His	p.P229H	ENST00000264731	NM_003722.4	229	cCt/cAt	5/14	0.353099825834488	3	FACETS	0.914	0.823	1	0.914	0.823	1	CLONAL	2	TRUE	1	0.353099825834488	3		593	361	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058748	180058748	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	10	416	2	ENST00000261937.6:c.89del	p.Pro30ArgfsTer3	p.P30Rfs*3	ENST00000261937	NM_182925.4	30	cCg/cg	2/30	1	2	FACETS	0.373	0.253	0.522	0.373	0.253	0.522	SUBCLONAL	1	TRUE	1	0.353099825834488	2		418	152	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089777	27089777	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	23	150	0	ENST00000324856.7:c.2732+1G>T		p.X911_splice	ENST00000324856	NM_006015.4	911			0.193376680807022	3	FACETS	0.824	0.657	1	0.549	0.438	0.672	INDETERMINATE	2	TRUE	0	0.353099825834488	3		150	93	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471797	120471797	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1217252161	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	113	595	0	ENST00000256646.2:c.3694G>T	p.Gly1232Cys	p.G1232C	ENST00000256646	NM_024408.3	1232	Ggt/Tgt	23/34	0.353099825834488	3	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	1	0.353099825834488	3		595	364	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162475	47162475	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs761799105	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	115	591	1	ENST00000409792.3:c.3651G>T	p.Trp1217Cys	p.W1217C	ENST00000409792	NM_014159.6	1217	tgG/tgT	3/21	0.353099825834488	3	FACETS	0.953	0.866	1	0.953	0.866	1	CLONAL	2	TRUE	1	0.353099825834488	3		592	402	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987154	69987154	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	38	459	0	ENST00000394351.3:c.215A>T	p.Asn72Ile	p.N72I	ENST00000394351	NM_000248.3	72	aAc/aTc	2/9	0.353099825834488	3	FACETS	0.978	0.813	1	0.489	0.406	0.58	CLONAL	1	TRUE	1	0.353099825834488	3		459	259	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71064805	71064805	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	52	419	0	ENST00000318789.4:c.870-1G>A		p.X290_splice	ENST00000318789	NM_032682.5	290			0.353099825834488	3	FACETS	1	0.957	1	0.661	0.568	0.762	CLONAL	1	TRUE	1	0.353099825834488	3		419	262	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133830	55133830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	120	560	0	ENST00000257290.5:c.1043C>T	p.Ser348Phe	p.S348F	ENST00000257290	NM_006206.4	348	tCc/tTc	7/23	0.193376680807022	3	FACETS	1	0.96	1	0.726	0.663	0.792	INDETERMINATE	2	TRUE	0	0.353099825834488	3		560	367	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149499098	149499098	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	40	456	0	ENST00000261799.4:c.2730C>A	p.Asn910Lys	p.N910K	ENST00000261799	NM_002609.3	910	aaC/aaA	20/23	1	2	FACETS	0.998	0.837	1	0.998	0.837	1	CLONAL	1	TRUE	1	0.353099825834488	2		456	227	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517564	176517564	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	39	563	1	ENST00000292408.4:c.265G>T	p.Ala89Ser	p.A89S	ENST00000292408	NM_213647.1	89	Gcc/Tcc	3/18	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.353099825834488	2		564	216	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394849	394849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1377317453	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	30	374	0	ENST00000380956.4:c.245G>A	p.Arg82Gln	p.R82Q	ENST00000380956	NM_001195286.1	82	cGa/cAa	3/9	0.224147112821955	5	FACETS	1	0.861	1	0.36	0.291	0.436	CLONAL	1	TRUE	2	0.353099825834488	5		374	241	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185804	32185804	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	73	532	1	ENST00000375023.3:c.1592T>A	p.Leu531Gln	p.L531Q	ENST00000375023	NM_004557.3	531	cTg/cAg	9/30	0.224147112821955	5	FACETS	1	0.927	1	0.712	0.629	0.8	CLONAL	2	TRUE	2	0.353099825834488	5		533	296	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969077	93969077	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	109	802	0	ENST00000369303.4:c.1919G>A	p.Gly640Asp	p.G640D	ENST00000369303	NM_004440.3	640	gGt/gAt	10/17	0.353099825834488	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.353099825834488	1		802	345	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979365	93979365	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	137	723	2	ENST00000369303.4:c.1463G>T	p.Arg488Leu	p.R488L	ENST00000369303	NM_004440.3	488	cGg/cTg	7/17	0.353099825834488	1	FACETS	0.828	0.761	0.896	1	0.99	1	CLONAL	2	TRUE	0	0.353099825834488	1		725	386	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946330	2946330	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	95	664	0	ENST00000396946.4:c.3407A>G	p.Lys1136Arg	p.K1136R	ENST00000396946	NM_032415.4	1136	aAg/aGg	25/25	0.353099825834488	7	FACETS	1	0.913	1	0.512	0.457	0.569	CLONAL	2	TRUE	3	0.353099825834488	7		664	495	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739826	41739826	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	173	875	0	ENST00000242208.4:c.147C>G	p.Asn49Lys	p.N49K	ENST00000242208	NM_002192.2	49	aaC/aaG	2/3	0.353099825834488	5	FACETS	0.957	0.887	1	0.957	0.887	1	CLONAL	3	TRUE	2	0.353099825834488	5		875	522	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248995	55248995	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	73	433	0	ENST00000275493.2:c.2293G>T	p.Val765Leu	p.V765L	ENST00000275493	NM_005228.3	765	Gtg/Ttg	20/28	0.353099825834488	5	FACETS	1	0.908	1	0.689	0.608	0.775	CLONAL	2	TRUE	2	0.353099825834488	5		433	306	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508361	106508361	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	50	185	0	ENST00000359195.3:c.355C>A	p.Leu119Met	p.L119M	ENST00000359195	NM_002649.2	119	Ctg/Atg	2/11	0.353099825834488	5	FACETS	0.908	0.786	1	0.908	0.786	1	CLONAL	3	TRUE	2	0.353099825834488	5		185	159	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507423	8507423	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	40	419	0	ENST00000356435.5:c.1555C>A	p.Pro519Thr	p.P519T	ENST00000356435		519	Cca/Aca	11/35	1	2	FACETS	0.903	0.755	1	0.903	0.755	1	CLONAL	1	TRUE	1	0.353099825834488	2		419	251	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998708	100998708	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	70	905	0	ENST00000325455.5:c.1094C>A	p.Pro365His	p.P365H	ENST00000325455	NM_001202474.3	365	cCc/cAc	1/8	0.353099825834488	3	FACETS	1	0.936	1	0.555	0.486	0.63	CLONAL	1	TRUE	1	0.353099825834488	3		905	420	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	465691	465691	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	30	543	0	ENST00000399788.2:c.685G>C	p.Asp229His	p.D229H	ENST00000399788	NM_001042603.1	229	Gat/Cat	6/28	NA	2	FACETS	0.488	0.394	0.595			1	INDETERMINATE	1	TRUE	NA	0.353099825834488	2		543	348	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	472265	472265	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	85	417	0	ENST00000399788.2:c.538-2A>T		p.X180_splice	ENST00000399788	NM_001042603.1	180			NA	2	FACETS	0.905	0.811	1			1	INDETERMINATE	2	TRUE	NA	0.353099825834488	2		417	266	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432333	49432333	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	102	585	0	ENST00000301067.7:c.8806G>A	p.Ala2936Thr	p.A2936T	ENST00000301067	NM_003482.3	2936	Gcc/Acc	34/54	0.352101898893351	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.353099825834488	2		585	263	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582900	95582900	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	75	586	0	ENST00000393063.1:c.1642C>T	p.Gln548Ter	p.Q548*	ENST00000393063	NM_030621.3	548	Caa/Taa	11/28	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.353099825834488	2		586	354	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989148	41989148	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	94	871	0	ENST00000219905.7:c.1940G>T	p.Gly647Val	p.G647V	ENST00000219905	NM_001164273.1	647	gGg/gTg	3/24	0.302567179458126	1	FACETS	0.929	0.83	1	0.929	0.83	1	CLONAL	1	TRUE	0	0.353099825834488	1		871	472	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119764	70119764	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	57	586	0	ENST00000245479.2:c.766G>T	p.Gly256Trp	p.G256W	ENST00000245479	NM_000346.3	256	Ggg/Tgg	3/3	0.353099825834488	3	FACETS	1	0.938	1	0.579	0.5	0.665	CLONAL	1	TRUE	1	0.353099825834488	3		586	328	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223048	1223048	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	81	543	0	ENST00000326873.7:c.985A>T	p.Lys329Ter	p.K329*	ENST00000326873	NM_000455.4	329	Aag/Tag	8/10	0.353099825834488	2	FACETS	0.859	0.767	0.955	0.859	0.767	0.955	CLONAL	2	TRUE	0	0.353099825834488	2		543	267	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7126655	7126655	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866953305	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	32	422	0	ENST00000302850.5:c.2953G>T	p.Asp985Tyr	p.D985Y	ENST00000302850	NM_000208.2	985	Gat/Tat	16/22	0.353099825834488	2	FACETS	0.859	0.703	1	0.43	0.351	0.517	CLONAL	1	TRUE	0	0.353099825834488	2		422	211	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039347	47039347	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	83	442	1	ENST00000377604.3:c.970G>T	p.Ala324Ser	p.A324S	ENST00000377604	NM_001204468.1	324	Gcg/Tcg	10/24	1	1	FACETS	1	0.919	1	1	0.987	1	CLONAL	2	TRUE	0	0.353099825834488	1		443	190	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504136	123504136	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	50	272	0	ENST00000371139.4:c.312del	p.Lys105SerfsTer13	p.K105Sfs*13	ENST00000371139	NM_001114937.2	104	aaG/aa	3/4	1	1	FACETS	0.799	0.693	0.909	1	0.971	1	CLONAL	2	TRUE	0	0.353099825834488	1		272	146	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519850	29519851	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	62	608	0	ENST00000389048.3:c.1720_1721delinsAT	p.Gly574Met	p.G574M	ENST00000389048	NM_004304.4	574	GGg/ATg	9/29	0.250374697709936	3	FACETS	1	0.961	1	0.646	0.561	0.736	CLONAL	1	TRUE	1	0.353099825834488	3		608	320	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661835	227661836	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	A	novel	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	31	278	0	ENST00000305123.5:c.1619_1620delinsT	p.Pro540LeufsTer15	p.P540Lfs*15	ENST00000305123	NM_005544.2	540	cCG/cT	1/2	0.250374697709936	3	FACETS	1	0.918	1	0.619	0.506	0.743	CLONAL	1	TRUE	1	0.353099825834488	3		278	167	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7128878	7128879	+	stop_gained	Nonsense_Mutation	DNP	AG	AG	TA	novel	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	30	559	0	ENST00000302850.5:c.2929_2930delinsTA	p.Leu977Ter	p.L977*	ENST00000302850	NM_000208.2	977	CTa/TAa	15/22	0.353099825834488	2	FACETS	0.603	0.487	0.733	0.301	0.243	0.367	SUBCLONAL	1	TRUE	0	0.353099825834488	2		559	282	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231413	46231413	+	frameshift_variant	Frame_Shift_Ins	INS	C	C	GGTGCTAT	novel	NA	P-0004442-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	92	461	0	ENST00000334344.6:c.1253delinsGGTGCTAT	p.Thr418ArgfsTer45	p.T418Rfs*45	ENST00000334344	NM_152641.2	418	aCa/aGGTGCTATa	10/21	0.352101898893351	2	FACETS	0.969	0.873	1	0.969	0.873	1	CLONAL	2	TRUE	0	0.353099825834488	2		461	269	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	103	229	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.933890204469561	2		229	199	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645693	12645693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397516827	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	259	357	0	ENST00000251849.4:c.776C>T	p.Ser259Phe	p.S259F	ENST00000251849	NM_002880.3	259	tCc/tTc	7/17	1	2	FACETS	0.971	0.919	1	0.971	0.919	1	CLONAL	1	TRUE	1	0.933890204469561	2		357	571	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230641	46230641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	318	508	0	ENST00000334344.6:c.890C>T	p.Ser297Phe	p.S297F	ENST00000334344	NM_152641.2	297	tCc/tTc	8/21	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.933890204469561	2		508	667	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972949	55972949	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	284	486	0	ENST00000263923.4:c.1441C>T	p.Pro481Ser	p.P481S	ENST00000263923	NM_002253.2	481	Cct/Tct	11/30	1	2	FACETS	0.944	0.895	0.994	0.944	0.895	0.994	CLONAL	1	TRUE	1	0.933890204469561	2		486	644	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741760	145741760	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759352592	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	254	418	0	ENST00000428558.2:c.743G>A	p.Arg248His	p.R248H	ENST00000428558	NM_004260.3	248	cGt/cAt	5/22	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.933890204469561	2		418	518	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450324	50450324	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	250	413	0	ENST00000331340.3:c.508G>A	p.Glu170Lys	p.E170K	ENST00000331340	NM_006060.4	170	Gag/Aag	5/8	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.933890204469561	2		413	533	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935438	36935438	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	326	601	0	ENST00000361632.4:c.1289C>T	p.Pro430Leu	p.P430L	ENST00000361632		430	cCa/cTa	10/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.933890204469561	2		601	669	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913255	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	329	402	0	ENST00000369535.4:c.183A>C	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caC	3/7	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.933890204469561	2		402	681	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142996	30142996	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	326	441	1	ENST00000389048.3:c.530G>A	p.Trp177Ter	p.W177*	ENST00000389048	NM_004304.4	177	tGg/tAg	1/29	1	2	FACETS	0.995	0.947	1	0.995	0.947	1	CLONAL	1	TRUE	1	0.933890204469561	2		442	702	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439964	220439964	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	366	694	0	ENST00000243786.2:c.817G>A	p.Glu273Lys	p.E273K	ENST00000243786	NM_002191.3	273	Gag/Aag	2/2	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.933890204469561	2		694	771	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050356	37050356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	271	506	0	ENST00000231790.2:c.505C>T	p.Pro169Ser	p.P169S	ENST00000231790	NM_000249.3	169	Cca/Tca	6/19	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.933890204469561	2		506	579	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437704	52437704	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	340	626	0	ENST00000460680.1:c.1457C>T	p.Pro486Leu	p.P486L	ENST00000460680	NM_004656.3	486	cCc/cTc	13/17	1	2	FACETS	0.983	0.936	1	0.983	0.936	1	CLONAL	1	TRUE	1	0.933890204469561	2		626	741	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528644	89528644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147992008	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	273	233	0	ENST00000336596.2:c.2944C>T	p.Pro982Ser	p.P982S	ENST00000336596	NM_005233.5	982	Ccc/Tcc	17/17	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.933890204469561	2		233	539	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143044547	143044547	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	269	433	0	ENST00000262992.4:c.1915T>C	p.Phe639Leu	p.F639L	ENST00000262992	NM_001101669.1	639	Ttt/Ctt	18/24	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.933890204469561	2		433	533	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541302	187541302	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	334	583	0	ENST00000441802.2:c.6438A>T	p.Leu2146Phe	p.L2146F	ENST00000441802	NM_005245.3	2146	ttA/ttT	10/27	1	2	FACETS	0.977	0.93	1	0.977	0.93	1	CLONAL	1	TRUE	1	0.933890204469561	2		583	732	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294766	1294766	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	23	35	0	ENST00000310581.5:c.235G>A	p.Glu79Lys	p.E79K	ENST00000310581	NM_198253.2	79	Gag/Aag	2/16	1	2	FACETS	0.849	0.691	1	0.849	0.691	1	CLONAL	1	TRUE	1	0.933890204469561	2		35	58	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056167	26056167	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375244851	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	289	382	0	ENST00000343677.2:c.490G>A	p.Ala164Thr	p.A164T	ENST00000343677	NM_005319.3	164	Gcc/Acc	1/1	0.933890204469561	4	FACETS	1	0.983	1	0.373	0.35	0.395	CLONAL	1	TRUE	1	0.933890204469561	4		382	1071	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099762	157099762	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	138	194	0	ENST00000346085.5:c.699C>G	p.Tyr233Ter	p.Y233*	ENST00000346085	NM_020732.3	233	taC/taG	1/20	1	2	FACETS	0.988	0.916	1	0.988	0.916	1	CLONAL	1	TRUE	1	0.933890204469561	2		194	299	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367317	50367317	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	273	295	0	ENST00000331340.3:c.124G>A	p.Gly42Arg	p.G42R	ENST00000331340	NM_006060.4	42	Gga/Aga	3/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.933890204469561	2		295	519	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339856	116339856	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	353	489	0	ENST00000397752.3:c.718G>A	p.Glu240Lys	p.E240K	ENST00000397752	NM_000245.2	240	Gag/Aag	2/21	1	2	FACETS	0.957	0.912	1	0.957	0.912	1	CLONAL	1	TRUE	1	0.933890204469561	2		489	790	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340007	116340007	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	333	381	0	ENST00000397752.3:c.869C>T	p.Ser290Phe	p.S290F	ENST00000397752	NM_000245.2	290	tCc/tTc	2/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.933890204469561	2		381	690	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453125	140453125	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	239	400	0	ENST00000288602.6:c.1810T>G	p.Trp604Gly	p.W604G	ENST00000288602	NM_004333.4	604	Tgg/Ggg	15/18	1	2	FACETS	0.958	0.904	1	0.958	0.904	1	CLONAL	1	TRUE	1	0.933890204469561	2		400	534	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879469	151879469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	257	404	0	ENST00000262189.6:c.5476C>T	p.His1826Tyr	p.H1826Y	ENST00000262189	NM_170606.2	1826	Cat/Tat	36/59	1	2	FACETS	0.927	0.875	0.979	0.927	0.875	0.979	CLONAL	1	TRUE	1	0.933890204469561	2		404	594	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050778	5050778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	277	395	0	ENST00000381652.3:c.561G>A	p.Met187Ile	p.M187I	ENST00000381652	NM_004972.3	187	atG/atA	6/25	NA	2	FACETS	0.976	0.924	1			1	INDETERMINATE	1	TRUE	NA	0.933890204469561	2		395	608	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390650	139390650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1564567473	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	276	462	0	ENST00000277541.6:c.7541C>T	p.Pro2514Leu	p.P2514L	ENST00000277541	NM_017617.3	2514	cCt/cTt	34/34	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.933890204469561	2		462	585	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12043937	12043937	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	296	366	0	ENST00000396373.4:c.1316C>T	p.Ser439Phe	p.S439F	ENST00000396373	NM_001987.4	439	tCc/tTc	8/8	1	2	FACETS	0.994	0.943	1	0.994	0.943	1	CLONAL	1	TRUE	1	0.933890204469561	2		366	638	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435673	18435673	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	147	271	0	ENST00000266497.5:c.658A>T	p.Thr220Ser	p.T220S	ENST00000266497		220	Aca/Tca	1/31	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.933890204469561	2		271	307	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793468	18793468	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	245	490	0	ENST00000266497.5:c.4165G>A	p.Asp1389Asn	p.D1389N	ENST00000266497		1389	Gac/Aac	30/31	1	2	FACETS	0.99	0.935	1	0.99	0.935	1	CLONAL	1	TRUE	1	0.933890204469561	2		490	530	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856364	111856364	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	56	78	0	ENST00000341259.2:c.415C>T	p.Arg139Cys	p.R139C	ENST00000341259	NM_005475.2	139	Cgc/Tgc	2/8	1	2	FACETS	0.93	0.82	1	0.93	0.82	1	CLONAL	1	TRUE	1	0.933890204469561	2		78	129	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608264	28608264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1312380044	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	630	574	0	ENST00000241453.7:c.1792G>A	p.Glu598Lys	p.E598K	ENST00000241453	NM_004119.2	598	Gaa/Aaa	14/24	0.736019259583211	3	FACETS	1	0.974	1			1	CLONAL	2	TRUE	NA	0.933890204469561	3		574	986	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610098	28610098	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	316	530	0	ENST00000241453.7:c.1392G>A	p.Trp464Ter	p.W464*	ENST00000241453	NM_004119.2	464	tgG/tgA	11/24	0.736019259583211	3	FACETS	1	0.947	1			1	CLONAL	1	TRUE	NA	0.933890204469561	3		530	991	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95578533	95578533	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	271	522	0	ENST00000393063.1:c.2092T>G	p.Cys698Gly	p.C698G	ENST00000393063	NM_030621.3	698	Tgc/Ggc	14/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.933890204469561	2		522	555	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020582	14020582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	238	449	0	ENST00000311895.7:c.553C>T	p.Leu185Phe	p.L185F	ENST00000311895	NM_005236.2	185	Ctt/Ttt	3/11	1	2	FACETS	0.932	0.878	0.986	0.932	0.878	0.986	CLONAL	1	TRUE	1	0.933890204469561	2		449	547	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68855909	68855909	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767636524	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	248	405	0	ENST00000261769.5:c.1717C>T	p.Pro573Ser	p.P573S	ENST00000261769	NM_004360.3	573	Cca/Tca	12/16	0.11026265761656	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.933890204469561	0		405	546	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348929	89348929	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	320	709	0	ENST00000301030.4:c.4021C>T	p.Pro1341Ser	p.P1341S	ENST00000301030	NM_001256183.1	1341	Cct/Tct	9/13	NA	2	FACETS	0.944	0.897	0.991			1	INDETERMINATE	1	TRUE	NA	0.933890204469561	2		709	726	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436175	56436175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444015068	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	388	342	1	ENST00000407977.2:c.962C>T	p.Ser321Leu	p.S321L	ENST00000407977		321	tCa/tTa	9/10	0.904460306860251	3	FACETS	0.977	0.94	1	0.977	0.94	1	CLONAL	2	TRUE	1	0.933890204469561	3		343	624	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554645	63554645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1173490917	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	193	227	0	ENST00000307078.5:c.94G>A	p.Glu32Lys	p.E32K	ENST00000307078	NM_004655.3	32	Gag/Aag	2/11	0.904460306860251	3	FACETS	0.975	0.907	1	0.487	0.453	0.523	CLONAL	1	TRUE	1	0.933890204469561	3		227	622	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78857768	78857768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	164	319	0	ENST00000306801.3:c.1838C>T	p.Pro613Leu	p.P613L	ENST00000306801	NM_020761.2	613	cCc/cTc	16/34	0.904460306860251	3	FACETS	0.881	0.813	0.951	0.44	0.406	0.476	CLONAL	1	TRUE	1	0.933890204469561	3		319	585	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395781	45395781	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	183	368	0	ENST00000262160.6:c.353C>T	p.Ser118Phe	p.S118F	ENST00000262160	NM_005901.5	118	tCc/tTc	4/11	1	2	FACETS	0.968	0.905	1	0.968	0.905	1	CLONAL	1	TRUE	1	0.933890204469561	2		368	405	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42842607	42842607	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004457-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	288	472	0	ENST00000398585.3:c.1250G>A	p.Trp417Ter	p.W417*	ENST00000398585	NM_001135099.1	417	tGg/tAg	11/14	1	2	FACETS	0.959	0.909	1	0.959	0.909	1	CLONAL	1	TRUE	1	0.933890204469561	2		472	643	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0004518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	20	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.817	1	1	0.817	1	CLONAL	1	TRUE	1	0.28	2		464	134	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0004518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	80	558	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.121119700430131	3	FACETS	1	0.949	1	0.57	0.503	0.643	INDETERMINATE	1	TRUE	1	0.28	3		558	571	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557629	95557629	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	85	562	2	ENST00000393063.1:c.5438A>G	p.Glu1813Gly	p.E1813G	ENST00000393063	NM_030621.3	1813	gAg/gGg	26/28	1	2	FACETS	0.994	0.879	1	0.994	0.879	1	CLONAL	1	TRUE	1	0.28	2		564	611	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561263	9561263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769939031	NA	P-0004518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	49	291	0	ENST00000353224.5:c.519G>A	p.Met173Ile	p.M173I	ENST00000353224	NM_177990.2	173	atG/atA	4/10	1	2	FACETS	0.97	0.824	1	0.97	0.824	1	CLONAL	1	TRUE	1	0.28	2		291	361	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642495	117642495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs9489124	NA	P-0004518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	103	911	2	ENST00000368508.3:c.5704G>A	p.Glu1902Lys	p.E1902K	ENST00000368508	NM_002944.2	1902	Gaa/Aaa	35/43	0.3	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.28	1		913	612	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965706	93965706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	108	807	0	ENST00000369303.4:c.2222G>A	p.Gly741Glu	p.G741E	ENST00000369303	NM_004440.3	741	gGa/gAa	13/17	0.3	1	FACETS	0.872	0.782	0.966	0.872	0.782	0.966	CLONAL	1	TRUE	0	0.28	1		807	761	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509388	46509388	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	78	511	0	ENST00000262741.5:c.1343T>C	p.Leu448Pro	p.L448P	ENST00000262741	NM_003629.3	448	cTt/cCt	10/10	0.3	1	FACETS	0.982	0.865	1	0.982	0.865	1	CLONAL	1	TRUE	0	0.28	1		511	488	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443613	29443613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519783	NA	P-0004518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	44	385	0	ENST00000389048.3:c.3604G>A	p.Gly1202Arg	p.G1202R	ENST00000389048	NM_004304.4	1202	Gga/Aga	23/29	1	2	FACETS	0.97	0.817	1	0.97	0.817	1	CLONAL	1	TRUE	1	0.28	2		385	324	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455170	29455170	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	77	472	0	ENST00000389048.3:c.2632G>A	p.Gly878Ser	p.G878S	ENST00000389048	NM_004304.4	878	Ggt/Agt	15/29	1	2	FACETS	0.806	0.713	0.905	1	0.98	1	CLONAL	2	TRUE	1	0.28	2		472	341	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167794	185167794	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	56	563	0	ENST00000265026.3:c.1117C>T	p.Pro373Ser	p.P373S	ENST00000265026	NM_004721.4	373	Cca/Tca	6/14	0.3	1	FACETS	0.735	0.631	0.849	0.735	0.631	0.849	SUBCLONAL	1	TRUE	0	0.28	1		563	468	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447336	187447336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760940345	NA	P-0004518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	46	299	0	ENST00000232014.4:c.857C>T	p.Pro286Leu	p.P286L	ENST00000232014	NM_001130845.1	286	cCc/cTc	5/10	0.3	3	FACETS	1	0.932	1			1	CLONAL	1	TRUE	NA	0.28	3		299	314	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449577	149449577	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	47	453	0	ENST00000286301.3:c.1369G>T	p.Val457Phe	p.V457F	ENST00000286301	NM_005211.3	457	Gtc/Ttc	10/22	0.3	2	FACETS	0.848	0.717	0.991			1	CLONAL	1	TRUE	NA	0.28	2		453	396	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722087	176722087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	46	345	0	ENST00000439151.2:c.7718C>T	p.Ser2573Phe	p.S2573F	ENST00000439151	NM_022455.4	2573	tCc/tTc	23/23	0.3	2	FACETS	0.91	0.769	1			1	CLONAL	1	TRUE	NA	0.28	2		345	361	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920529	127920529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	87	738	1	ENST00000373547.4:c.370G>A	p.Gly124Arg	p.G124R	ENST00000373547	NM_002721.4	124	Gga/Aga	4/7	0.294077843929073	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.28	1		739	450	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333233	70333233	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	70	549	0	ENST00000373644.4:c.1138G>A	p.Gly380Ser	p.G380S	ENST00000373644	NM_030625.2	380	Ggt/Agt	2/12	0.3	1	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	0	0.28	1		549	424	SUCCESS
ATM	472	MSKCC	GRCh37	11	108124735	108124735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	69	405	0	ENST00000278616.4:c.2093C>T	p.Ser698Leu	p.S698L	ENST00000278616	NM_000051.3	698	tCa/tTa	13/63	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.28	2		405	471	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344107	118344107	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs727503777	NA	P-0004518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	55	342	0	ENST00000534358.1:c.2233C>T	p.Arg745Ter	p.R745*	ENST00000534358	NM_005933.3	745	Cga/Tga	3/36	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.28	2		342	386	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445991	49445991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265398099	NA	P-0004518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	58	508	1	ENST00000301067.7:c.1475C>T	p.Ser492Leu	p.S492L	ENST00000301067	NM_003482.3	492	tCg/tTg	10/54	1	2	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	1	0.28	2		509	399	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891705	28891705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750234866	NA	P-0004518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	54	612	1	ENST00000282397.4:c.3316G>A	p.Asp1106Asn	p.D1106N	ENST00000282397	NM_002019.4	1106	Gat/Aat	25/30	0.121119700430131	0	FACETS	0.652	0.558	0.754			1	INDETERMINATE	1	TRUE	0	0.28	0		613	426	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553573	29553573	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	46	224	0	ENST00000356175.3:c.2122T>G	p.Ser708Ala	p.S708A	ENST00000356175	NM_000267.3	708	Tcc/Gcc	18/57	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.28	2		224	298	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561396	9561396	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1262495622	NA	P-0004518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	38	321	0	ENST00000353224.5:c.386C>T	p.Ser129Phe	p.S129F	ENST00000353224	NM_177990.2	129	tCc/tTc	4/10	1	2	FACETS	0.93	0.772	1	0.93	0.772	1	CLONAL	1	TRUE	1	0.28	2		321	292	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024546	31024546	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	40	392	0	ENST00000375687.4:c.4031C>T	p.Ser1344Phe	p.S1344F	ENST00000375687	NM_015338.5	1344	tCc/tTc	13/13	1	2	FACETS	0.729	0.607	0.865	0.729	0.607	0.865	SUBCLONAL	1	TRUE	1	0.28	2		392	392	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770581	40770581	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	47	404	0	ENST00000373198.4:c.2801A>G	p.Lys934Arg	p.K934R	ENST00000373198	NM_133170.3	934	aAg/aGg	19/32	0.3	1	FACETS	0.818	0.693	0.955	0.818	0.693	0.955	CLONAL	1	TRUE	0	0.28	1		404	353	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939417	76939417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781932965	NA	P-0004518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	84	751	0	ENST00000373344.5:c.1331G>A	p.Arg444Gln	p.R444Q	ENST00000373344	NM_000489.3	444	cGa/cAa	9/35	0.294077843929073	1	FACETS	0.738	0.652	0.831	0.738	0.652	0.831	SUBCLONAL	1	TRUE	0	0.28	1		751	699	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266122	41266136	+	inframe_deletion	In_Frame_Del	DEL	CTACCACAGCTCCTT	CTACCACAGCTCCTT	-	novel	NA	P-0004518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	91	463	0	ENST00000349496.5:c.121_135del	p.Thr41_Ser45del	p.T41_S45del	ENST00000349496	NM_001904.3	40	aCTACCACAGCTCCTTct/act	3/15	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.28	2		463	558	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131094	55131095	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0004518-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	59	459	0	ENST00000257290.5:c.637_638delinsAT	p.Glu213Met	p.E213M	ENST00000257290	NM_006206.4	213	GAg/ATg	5/23	0.121119700430131	0	FACETS	0.717	0.619	0.824			1	INDETERMINATE	1	TRUE	0	0.28	0		459	423	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0004578-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	58	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.974	0.859	1	0.974	0.859	1	CLONAL	1	TRUE	1	0.821269580019599	2		464	145	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0004578-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	265	511	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.821269580019599	2		512	597	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791797	42791797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004578-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	255	354	0	ENST00000575354.2:c.683G>A	p.Arg228Gln	p.R228Q	ENST00000575354	NM_015125.3	228	cGg/cAg	5/20	0.821269580019599	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.821269580019599	1		354	361	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176012345	176012345	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	53	228	0	ENST00000367669.3:c.1589C>G	p.Ala530Gly	p.A530G	ENST00000367669	NM_022457.5	530	gCt/gGt	14/20	0.404389502373007	3	FACETS	0.389	0.333	0.451	0.195	0.166	0.226	INDETERMINATE	1	TRUE	1	0.929315814084817	3		228	429	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965227	25965227	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	42	190	1	ENST00000435504.4:c.3979T>C	p.Tyr1327His	p.Y1327H	ENST00000435504		1327	Tat/Cat	13/13	0.48993120308862	1	FACETS	0.329	0.28	0.382	0.329	0.28	0.382	INDETERMINATE	1	TRUE	0	0.929315814084817	1		191	147	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707900	47707900	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	58	225	0	ENST00000233146.2:c.2524G>C	p.Glu842Gln	p.E842Q	ENST00000233146	NM_000251.2	842	Gag/Cag	15/16	1	2	FACETS	0.501	0.435	0.572	0.501	0.435	0.572	SUBCLONAL	1	TRUE	1	0.929315814084817	2		225	249	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440387	187440387	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	59	118	0	ENST00000232014.4:c.1980T>G	p.Cys660Trp	p.C660W	ENST00000232014	NM_001130845.1	660	tgT/tgG	10/10	NA	2	FACETS	0.51	0.443	0.581			1	INDETERMINATE	1	TRUE	NA	0.929315814084817	2		118	249	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149453024	149453024	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	85	169	0	ENST00000286301.3:c.922A>G	p.Asn308Asp	p.N308D	ENST00000286301	NM_005211.3	308	Aac/Gac	7/22	1	2	FACETS	0.989	0.896	1	0.989	0.896	1	CLONAL	1	TRUE	1	0.929315814084817	2		169	185	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334966	81334966	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	65	209	0	ENST00000222390.5:c.1861G>T	p.Gly621Ter	p.G621*	ENST00000222390	NM_000601.4	621	Gga/Tga	16/18	1	2	FACETS	0.522	0.457	0.591	0.522	0.457	0.591	SUBCLONAL	1	TRUE	1	0.929315814084817	2		209	268	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97897771	97897771	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	65	193	0	ENST00000289081.3:c.700C>A	p.Leu234Ile	p.L234I	ENST00000289081	NM_000136.2	234	Ctc/Atc	8/15	0.404389502373007	3	FACETS	0.667	0.583	0.757	0.334	0.291	0.379	INDETERMINATE	1	TRUE	1	0.929315814084817	3		193	307	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67459192	67459192	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0004593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	53	203	0	ENST00000327367.4:c.607+1G>C		p.X203_splice	ENST00000327367	NM_005902.3	203			0.926317824044098	1	FACETS	0.47	0.412	0.529	0.47	0.412	0.529	SUBCLONAL	1	TRUE	0	0.929315814084817	1		203	130	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41267759	41267759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879255290	NA	P-0004593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	85	258	0	ENST00000357654.3:c.118G>A	p.Asp40Asn	p.D40N	ENST00000357654	NM_007294.3	40	Gac/Aac	3/23	0.270693836879692	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.929315814084817	0		258	223	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922195	39922329	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCTTTAATTTTCTGCTGTTTGGCAGGCGGCCTGGAGGCTGGTGCGCAGCTTGGCTGAGCCTGCTTTTTGCCGCCTGCACTGGTGGATGAAAGACTCTTCATGGGCGGAGAGCCGGAGAACACAGGCAAGCCTAAA	TCTTTAATTTTCTGCTGTTTGGCAGGCGGCCTGGAGGCTGGTGCGCAGCTTGGCTGAGCCTGCTTTTTGCCGCCTGCACTGGTGGATGAAAGACTCTTCATGGGCGGAGAGCCGGAGAACACAGGCAAGCCTAAA	-	novel	NA	P-0004593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	58	132	0	ENST00000378444.4:c.3848-5_3977del		p.X1283_splice	ENST00000378444	NM_001123385.1	1283		9/15	1	1	FACETS	0.514	0.455	0.574	0.514	0.455	0.574	SUBCLONAL	1	TRUE	0	0.929315814084817	1		132	130	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7573982	7573982	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1567541975	NA	P-0004617-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	595	543	0	ENST00000269305.4:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000269305	NM_001126112.2	349	Gaa/Taa	10/11	0.652174151167143	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.652174151167143	2		543	891	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965415	25965415	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004617-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	229	391	1	ENST00000435504.4:c.3791A>G	p.Asp1264Gly	p.D1264G	ENST00000435504		1264	gAt/gGt	13/13	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.652174151167143	2		392	666	SUCCESS
APC	324	MSKCC	GRCh37	5	112174529	112174529	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004617-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	211	332	0	ENST00000257430.4:c.3238G>T	p.Glu1080Ter	p.E1080*	ENST00000257430	NM_000038.5	1080	Gag/Tag	16/16	0.652174151167143	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.652174151167143	1		332	418	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971105	21971105	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004617-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	133	174	0	ENST00000304494.5:c.253G>C	p.Ala85Pro	p.A85P	ENST00000304494	NM_000077.4	85	Gct/Cct	2/3	0.652174151167143	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.652174151167143	1		174	258	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134434	2134434	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004617-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	294	459	0	ENST00000219476.3:c.4211A>C	p.Lys1404Thr	p.K1404T	ENST00000219476	NM_000548.3	1404	aAg/aCg	34/42	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.652174151167143	2		459	879	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39629498	39629498	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004617-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	519	357	0	ENST00000262039.4:c.2192G>A	p.Gly731Glu	p.G731E	ENST00000262039	NM_002647.2	731	gGa/gAa	21/25	0.608940548919453	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.652174151167143	3		357	1049	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227945	123227945	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004617-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	230	225	1	ENST00000218089.9:c.3656T>C	p.Ile1219Thr	p.I1219T	ENST00000218089	NM_001042749.1	1219	aTt/aCt	33/35	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.652174151167143	1		226	361	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021808	71021828	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGATTATGACGCACTGCATTC	AGATTATGACGCACTGCATTC	-	novel	NA	P-0004617-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	202	349	0	ENST00000318789.4:c.1531-1_1550del		p.X511_splice	ENST00000318789	NM_032682.5	511		18/21	0.652174151167143	1	FACETS	0.913	0.857	0.971	0.913	0.857	0.971	CLONAL	1	TRUE	0	0.652174151167143	1		349	457	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004618-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	126	280	0				ENST00000310581	NM_198253.2	-/1132			0.392137523349678	3	FACETS	0.894	0.818	0.973	0.894	0.818	0.973	CLONAL	2	TRUE	1	0.456547885330736	3		280	379	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074183	8074183	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004618-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1337	220	680	0	ENST00000377482.5:c.476C>G	p.Ser159Cys	p.S159C	ENST00000377482	NM_018948.3	159	tCt/tGt	4/4	1	2	FACETS	0.619	0.574	0.666	0.619	0.574	0.666	SUBCLONAL	1	TRUE	1	0.456547885330736	2		680	1557	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105761	27105761	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004618-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	331	450	0	ENST00000324856.7:c.5372C>A	p.Ser1791Ter	p.S1791*	ENST00000324856	NM_006015.4	1791	tCa/tAa	20/20	1	2	FACETS	0.991	0.935	1	0.991	0.935	1	CLONAL	1	TRUE	1	0.456547885330736	2		450	1463	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107204	27107204	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004618-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	270	283	0	ENST00000324856.7:c.6815C>A	p.Ser2272Ter	p.S2272*	ENST00000324856	NM_006015.4	2272	tCa/tAa	20/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.456547885330736	2		283	1038	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0004618-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	120	445	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.587	0.53	0.648	0.587	0.53	0.648	SUBCLONAL	1	TRUE	1	0.456547885330736	2		445	895	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215252	142215252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004618-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	394	374	0	ENST00000350721.4:c.5849C>T	p.Ser1950Leu	p.S1950L	ENST00000350721	NM_001184.3	1950	tCa/tTa	34/47	0.392137523349678	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.456547885330736	3		374	1029	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401246	139401246	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004618-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1289	423	457	0	ENST00000277541.6:c.3823C>A	p.Pro1275Thr	p.P1275T	ENST00000277541	NM_017617.3	1275	Ccc/Acc	23/34	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.456547885330736	2		457	1712	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118362022	118362022	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0004618-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	172	323	0	ENST00000534358.1:c.4808C>G	p.Ser1603Ter	p.S1603*	ENST00000534358	NM_005933.3	1603	tCa/tGa	14/36	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.456547885330736	2		323	646	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431919	49431919	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004618-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	257	308	0	ENST00000301067.7:c.9220G>C	p.Glu3074Gln	p.E3074Q	ENST00000301067	NM_003482.3	3074	Gaa/Caa	34/54	1	2	FACETS	0.982	0.919	1	0.982	0.919	1	CLONAL	1	TRUE	1	0.456547885330736	2		308	1147	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432408	49432408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004618-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	283	264	0	ENST00000301067.7:c.8731G>A	p.Glu2911Lys	p.E2911K	ENST00000301067	NM_003482.3	2911	Gag/Aag	34/54	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.456547885330736	2		264	1061	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432473	49432473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004618-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	419	423	1	ENST00000301067.7:c.8666G>A	p.Gly2889Glu	p.G2889E	ENST00000301067	NM_003482.3	2889	gGa/gAa	34/54	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.456547885330736	2		424	1598	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440476	49440476	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004618-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	342	341	0	ENST00000301067.7:c.4334G>C	p.Cys1445Ser	p.C1445S	ENST00000301067	NM_003482.3	1445	tGt/tCt	15/54	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.456547885330736	2		341	1283	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004618-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	324	496	0	ENST00000267101.3:c.273G>A	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atA	3/28	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.456547885330736	2		496	1409	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115114163	115114163	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004618-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	494	487	0	ENST00000257566.3:c.1054G>A	p.Ala352Thr	p.A352T	ENST00000257566	NM_016569.3	352	Gct/Act	6/8	0.267349714740464	3	FACETS	0.892	0.853	0.931	0.892	0.853	0.931	INDETERMINATE	2	TRUE	1	0.456547885330736	3		487	1490	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39620703	39620703	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004618-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	229	392	0	ENST00000262039.4:c.2101C>G	p.Gln701Glu	p.Q701E	ENST00000262039	NM_002647.2	701	Cag/Gag	19/25	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.456547885330736	2		392	899	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101829	11101829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004618-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	337	460	0	ENST00000358026.2:c.1249C>T	p.Arg417Cys	p.R417C	ENST00000358026	NM_001128849.1	417	Cgc/Tgc	8/36	0.456547885330736	2	FACETS	1	0.986	1	0.56	0.529	0.592	CLONAL	1	TRUE	0	0.456547885330736	2		460	1317	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52722950	52722950	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004618-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	285	383	0	ENST00000322088.6:c.1135G>A	p.Glu379Lys	p.E379K	ENST00000322088	NM_014225.5	379	Gag/Aag	10/15	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.456547885330736	2		383	1190	SUCCESS
BTK	695	MSKCC	GRCh37	X	100613313	100613313	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004618-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	295	520	0	ENST00000308731.7:c.1087C>G	p.Gln363Glu	p.Q363E	ENST00000308731	NM_000061.2	363	Cag/Gag	12/19	0.41176506748141	1	FACETS	0.902	0.849	0.956	0.902	0.849	0.956	CLONAL	1	TRUE	0	0.456547885330736	1		520	1106	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651987	36651988	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0004618-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	348	447	0	ENST00000244741.5:c.110dup	p.Met38AsnfsTer10	p.M38Nfs*10	ENST00000244741	NM_000389.4	37	cta/cTta	2/3	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.456547885330736	2		447	1488	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060774	38060775	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004618-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1636	558	610	0	ENST00000250448.2:c.1214dup	p.Met406HisfsTer9	p.M406Hfs*9	ENST00000250448	NM_004496.3	405	ctc/ctTc	2/2	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.456547885330736	2		610	2194	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	18	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.903	0.689	1	0.903	0.689	1	CLONAL	1	TRUE	1	0.349556888397267	2		280	114	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0004622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	46	595	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.895	0.77	1	1	0.972	1	CLONAL	2	TRUE	1	0.349556888397267	2		595	147	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978935	25978935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	69	465	0	ENST00000435504.4:c.988G>A	p.Glu330Lys	p.E330K	ENST00000435504		330	Gaa/Aaa	10/13	1	2	FACETS	0.961	0.84	1	0.961	0.84	1	CLONAL	1	TRUE	1	0.349556888397267	2		465	411	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593651	215593651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111367604	NA	P-0004622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	60	395	0	ENST00000260947.4:c.2083G>A	p.Val695Ile	p.V695I	ENST00000260947	NM_000465.2	695	Gtc/Atc	11/11	0.349556888397267	1	FACETS	0.905	0.785	1	0.905	0.785	1	CLONAL	1	TRUE	0	0.349556888397267	1		395	313	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942761	44942761	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0004622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	70	557	0	ENST00000377967.4:c.3341C>G	p.Ser1114Ter	p.S1114*	ENST00000377967	NM_021140.2	1114	tCa/tGa	23/29	0.155402447921206	0	FACETS	0.612	0.535	0.693			1	INDETERMINATE	1	TRUE	0	0.349556888397267	0		557	426	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106141	27106171	+	frameshift_variant	Frame_Shift_Del	DEL	CGGTCTAGCACCTTGACCGAGGATGGAGCTA	CGGTCTAGCACCTTGACCGAGGATGGAGCTA	-	novel	NA	P-0004622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	102	357	0	ENST00000324856.7:c.5752_5782del	p.Ser1919ValfsTer27	p.S1919Vfs*27	ENST00000324856	NM_006015.4	1918	CGGTCTAGCACCTTGACCGAGGATGGAGCTAag/ag	20/20	0.124556290086595	3	FACETS	1	0.925	1			1	INDETERMINATE	2	TRUE	NA	0.349556888397267	3		357	334	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651963	36651966	+	frameshift_variant	Frame_Shift_Del	DEL	CAGC	CAGC	-	novel	NA	P-0004622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	55	293	0	ENST00000244741.5:c.85_88del	p.Gln29Ter	p.Q29*	ENST00000244741	NM_000389.4	29	CAGCtg/tg	2/3	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.349556888397267	2		293	272	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797313	135797313	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004622-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	61	335	0	ENST00000298552.3:c.556del	p.Ala186HisfsTer24	p.A186Hfs*24	ENST00000298552	NM_001162426.1	186	Gca/ca	7/23	0.349556888397267	1	FACETS	0.941	0.818	1	0.941	0.818	1	CLONAL	1	TRUE	0	0.349556888397267	1		335	306	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004622-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	89	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.883	0.795	0.975	0.883	0.795	0.975	CLONAL	1	TRUE	1	0.760342070719984	2		280	265	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0004622-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	248	595	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.987	1	1	0.996	1	CLONAL	2	TRUE	1	0.760342070719984	2		595	310	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978935	25978935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004622-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	299	465	0	ENST00000435504.4:c.988G>A	p.Glu330Lys	p.E330K	ENST00000435504		330	Gaa/Aaa	10/13	1	2	FACETS	0.918	0.867	0.969	0.918	0.867	0.969	CLONAL	1	TRUE	1	0.760342070719984	2		465	857	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593651	215593651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs111367604	NA	P-0004622-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	262	395	0	ENST00000260947.4:c.2083G>A	p.Val695Ile	p.V695I	ENST00000260947	NM_000465.2	695	Gtc/Atc	11/11	1	2	FACETS	0.99	0.933	1	0.99	0.933	1	CLONAL	1	TRUE	1	0.760342070719984	2		395	696	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942761	44942761	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0004622-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	367	557	0	ENST00000377967.4:c.3341C>G	p.Ser1114Ter	p.S1114*	ENST00000377967	NM_021140.2	1114	tCa/tGa	23/29	1	2	FACETS	0.935	0.888	0.981	0.935	0.888	0.981	CLONAL	1	TRUE	1	0.760342070719984	2		557	1033	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106141	27106171	+	frameshift_variant	Frame_Shift_Del	DEL	CGGTCTAGCACCTTGACCGAGGATGGAGCTA	CGGTCTAGCACCTTGACCGAGGATGGAGCTA	-	novel	NA	P-0004622-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	268	357	0	ENST00000324856.7:c.5752_5782del	p.Ser1919ValfsTer27	p.S1919Vfs*27	ENST00000324856	NM_006015.4	1918	CGGTCTAGCACCTTGACCGAGGATGGAGCTAag/ag	20/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.760342070719984	2		357	660	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651963	36651966	+	frameshift_variant	Frame_Shift_Del	DEL	CAGC	CAGC	-	novel	NA	P-0004622-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	193	293	0	ENST00000244741.5:c.85_88del	p.Gln29Ter	p.Q29*	ENST00000244741	NM_000389.4	29	CAGCtg/tg	2/3	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.760342070719984	2		293	495	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797313	135797313	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004622-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	246	335	0	ENST00000298552.3:c.556del	p.Ala186HisfsTer24	p.A186Hfs*24	ENST00000298552	NM_001162426.1	186	Gca/ca	7/23	0.760342070719984	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.760342070719984	1		335	390	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63829469	63829469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1206856276	NA	P-0004622-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	213	313	1	ENST00000279873.7:c.1112G>A	p.Arg371His	p.R371H	ENST00000279873	NM_032199.2	371	cGc/cAc	8/10	1	2	FACETS	0.91	0.85	0.97	0.91	0.85	0.97	CLONAL	1	TRUE	1	0.760342070719984	2		314	616	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	33	280	0				ENST00000310581	NM_198253.2	-/1132			0.451021285255616	1	FACETS	0.846	0.717	0.979	0.846	0.717	0.979	CLONAL	1	FALSE	0	0.67246038149075	1		280	77	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0004630-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	208	511	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	FALSE	1	0.67246038149075	2		512	615	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004633-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	51	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.32	2		280	306	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0004633-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	113	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.96	0.864	1	0.96	0.864	1	CLONAL	1	TRUE	1	0.32	2		490	736	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469540	25469540	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004633-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	46	489	0	ENST00000264709.3:c.1228G>T	p.Ala410Ser	p.A410S	ENST00000264709	NM_175629.2	410	Gcc/Tcc	10/23	1	2	FACETS	0.351	0.294	0.414	0.351	0.294	0.414	SUBCLONAL	1	TRUE	1	0.32	2		489	819	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	47	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.864	0.737	1	0.864	0.737	1	CLONAL	1	TRUE	1	0.488017154164374	2		280	223	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0004660-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	113	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.926	0.838	1	0.926	0.838	1	CLONAL	1	TRUE	1	0.488017154164374	2		490	500	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	39	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.225444057747589	2		280	251	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0004661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	161	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.225444057747589	4	FACETS	1	0.971	1			1	CLONAL	2	TRUE	NA	0.225444057747589	4		490	778	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953864	55953864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	38	327	0	ENST00000263923.4:c.3572G>A	p.Gly1191Glu	p.G1191E	ENST00000263923	NM_002253.2	1191	gGa/gAa	27/30	1	2	FACETS	0.451	0.371	0.54	0.451	0.371	0.54	SUBCLONAL	1	TRUE	1	0.225444057747589	2		327	748	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527313	157527313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	50	261	0	ENST00000346085.5:c.5038C>T	p.Leu1680Phe	p.L1680F	ENST00000346085	NM_020732.3	1680	Ctc/Ttc	20/20	NA	2	FACETS	0.971	0.825	1			1	INDETERMINATE	1	TRUE	NA	0.225444057747589	2		261	457	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468230	50468230	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	147	235	0	ENST00000331340.3:c.1465C>T	p.Pro489Ser	p.P489S	ENST00000331340	NM_006060.4	489	Cct/Tct	8/8	0.225444057747589	4	FACETS	1	0.965	1	0.736	0.673	0.801	CLONAL	2	TRUE	1	0.225444057747589	4		235	724	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145431	58145431	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs11547328	NA	P-0004661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	74	330	0	ENST00000257904.6:c.70C>A	p.Arg24Ser	p.R24S	ENST00000257904	NM_000075.3	24	Cgt/Agt	2/8	1	2	FACETS	0.849	0.743	0.965	0.849	0.743	0.965	CLONAL	1	TRUE	1	0.225444057747589	2		330	773	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576102	29576102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	84	448	0	ENST00000356175.3:c.4075C>T	p.Pro1359Ser	p.P1359S	ENST00000356175	NM_000267.3	1359	Cct/Tct	30/57	1	2	FACETS	0.8	0.705	0.902	0.8	0.705	0.902	CLONAL	1	TRUE	1	0.225444057747589	2		448	932	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394696	45394696	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004661-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	29	224	0	ENST00000262160.6:c.653C>T	p.Pro218Leu	p.P218L	ENST00000262160	NM_005901.5	218	cCa/cTa	5/11	0.173151353328918	3	FACETS	0.625	0.501	0.767	0.313	0.25	0.384	SUBCLONAL	1	TRUE	1	0.225444057747589	3		224	458	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	100	280	0				ENST00000310581	NM_198253.2	-/1132			0.568585502035476	3	FACETS	0.955	0.87	1	0.955	0.87	1	CLONAL	2	TRUE	1	0.570259625817024	3		280	236	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982093	38982093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768369548	NA	P-0004663-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	143	311	0	ENST00000357387.3:c.629C>T	p.Thr210Ile	p.T210I	ENST00000357387	NM_152756.3	210	aCc/aTc	8/38	0.568585502035476	3	FACETS	0.955	0.873	1	0.477	0.436	0.521	CLONAL	1	TRUE	1	0.570259625817024	3		311	675	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971175	21971175	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004664-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	182	103	0	ENST00000304494.5:c.183del	p.Glu61AspfsTer85	p.E61Dfs*85	ENST00000304494	NM_000077.4	61	gaG/ga	2/3	0.3	2	FACETS	1	0.992	1	1	0.992	1	INDETERMINATE	2	TRUE	0	0.75	2		103	213	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004667-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	57	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.919	0.807	1	0.919	0.807	1	CLONAL	1	TRUE	1	0.8	2		280	155	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653808	89653808	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004667-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	220	295	0	ENST00000371953.3:c.106G>A	p.Gly36Arg	p.G36R	ENST00000371953	NM_000314.4	36	Gga/Aga	2/9	1	2	FACETS	0.914	0.856	0.972	0.914	0.856	0.972	CLONAL	1	TRUE	1	0.8	2		295	602	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952227	17952227	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004667-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	155	342	0	ENST00000458235.1:c.1113A>C	p.Glu371Asp	p.E371D	ENST00000458235	NM_000215.3	371	gaA/gaC	8/24	1	2	FACETS	0.947	0.877	1	0.947	0.877	1	CLONAL	1	TRUE	1	0.8	2		342	409	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	79	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.886	0.797	0.977	0.886	0.797	0.977	CLONAL	1	TRUE	1	0.94358300828959	2		280	189	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0004674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	232	511	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.987	0.931	1	0.987	0.931	1	CLONAL	1	TRUE	1	0.94358300828959	2		512	498	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131976410	131976410	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	363	458	0	ENST00000265335.6:c.3665G>C	p.Cys1222Ser	p.C1222S	ENST00000265335		1222	tGc/tCc	24/25	1	2	FACETS	0.992	0.946	1	0.992	0.946	1	CLONAL	1	TRUE	1	0.94358300828959	2		458	776	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412240	139412240	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	53	527	0	ENST00000277541.6:c.1405G>A	p.Asp469Asn	p.D469N	ENST00000277541	NM_017617.3	469	Gac/Aac	8/34	1	2	FACETS	0.135	0.114	0.157	0.135	0.114	0.157	SUBCLONAL	1	TRUE	1	0.94358300828959	2		527	834	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412649	139412649	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs762886963	NA	P-0004674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	292	416	0	ENST00000277541.6:c.1195A>G	p.Thr399Ala	p.T399A	ENST00000277541	NM_017617.3	399	Acc/Gcc	7/34	1	2	FACETS	0.955	0.906	1	0.955	0.906	1	CLONAL	1	TRUE	1	0.94358300828959	2		416	648	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412741	139412741	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	111	310	0	ENST00000277541.6:c.1103T>A	p.Leu368Gln	p.L368Q	ENST00000277541	NM_017617.3	368	cTg/cAg	7/34	1	2	FACETS	0.449	0.405	0.495	0.449	0.405	0.495	SUBCLONAL	1	TRUE	1	0.94358300828959	2		310	524	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123693	11123693	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	375	526	0	ENST00000358026.2:c.2343G>A	p.Met781Ile	p.M781I	ENST00000358026	NM_001128849.1	781	atG/atA	16/36	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.94358300828959	2		526	775	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399416	139399417	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	36	449	0	ENST00000277541.6:c.4726dup	p.Val1576GlyfsTer34	p.V1576Gfs*34	ENST00000277541	NM_017617.3	1576	gtg/gGtg	26/34	1	2	FACETS	0.119	0.097	0.144	0.119	0.097	0.144	SUBCLONAL	1	TRUE	1	0.94358300828959	2		449	640	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410452	139410453	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs864622059	NA	P-0004674-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	68	407	0	ENST00000277541.6:c.1649dup	p.Tyr550Ter	p.Y550*	ENST00000277541	NM_017617.3	550	tac/taAc	10/34	1	2	FACETS	0.174	0.151	0.199	0.174	0.151	0.199	SUBCLONAL	1	TRUE	1	0.94358300828959	2		407	829	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	80	280	0				ENST00000310581	NM_198253.2	-/1132			0.718755916036551	4	FACETS	0.96	0.865	1			1	CLONAL	2	TRUE	NA	0.803656453684087	4		280	187	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0004683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	317	511	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.803656453684087	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.803656453684087	3		512	550	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591106	67591106	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	174	240	0	ENST00000274335.5:c.1699A>G	p.Lys567Glu	p.K567E	ENST00000274335		567	Aaa/Gaa	12/15	0.803656453684087	4	FACETS	1	0.93	1	0.505	0.465	0.545	CLONAL	1	TRUE	2	0.803656453684087	4		240	774	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057949	27057949	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	289	317	0	ENST00000324856.7:c.1657C>T	p.Gln553Ter	p.Q553*	ENST00000324856	NM_006015.4	553	Cag/Tag	3/20	0.803656453684087	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.803656453684087	2		317	343	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469540	25469540	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764880874	NA	P-0004683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	166	383	0	ENST00000264709.3:c.1228G>A	p.Ala410Thr	p.A410T	ENST00000264709	NM_175629.2	410	Gcc/Acc	10/23	0.311735280019031	5	FACETS	0.772	0.713	0.833			1	INDETERMINATE	2	TRUE	NA	0.803656453684087	5		383	590	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273101	198273101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	319	349	0	ENST00000335508.6:c.1109C>T	p.Pro370Leu	p.P370L	ENST00000335508	NM_012433.2	370	cCt/cTt	8/25	0.803656453684087	3	FACETS	0.976	0.933	1	0.976	0.933	1	CLONAL	2	TRUE	1	0.803656453684087	3		349	570	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012371	152012371	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	418	370	0	ENST00000262189.6:c.442G>A	p.Gly148Arg	p.G148R	ENST00000262189	NM_170606.2	148	Gga/Aga	4/59	0.791873315899738	4	FACETS	0.998	0.955	1	0.998	0.955	1	CLONAL	2	TRUE	2	0.803656453684087	4		370	940	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971109	21971109	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs34968276	NA	P-0004683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	140	164	0	ENST00000304494.5:c.249C>G	p.His83Gln	p.H83Q	ENST00000304494	NM_000077.4	83	caC/caG	2/3	0.803656453684087	2	FACETS	0.979	0.931	1	0.979	0.931	1	CLONAL	2	TRUE	0	0.803656453684087	2		164	178	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678560	88678560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758189455	NA	P-0004683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	200	205	0	ENST00000360948.2:c.976C>T	p.Arg326Cys	p.R326C	ENST00000360948	NM_001012338.2	326	Cgt/Tgt	9/19	0.791873315899738	4	FACETS	0.949	0.889	1	0.949	0.889	1	CLONAL	2	TRUE	2	0.803656453684087	4		205	473	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794601	42794601	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004683-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	311	366	0	ENST00000575354.2:c.1681G>T	p.Glu561Ter	p.E561*	ENST00000575354	NM_015125.3	561	Gag/Tag	10/20	0.803656453684087	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.803656453684087	2		366	374	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0004687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	197	506	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.230152618387569	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.230152618387569	3		506	880	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444358	49444358	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	49	275	0	ENST00000301067.7:c.3013C>T	p.Pro1005Ser	p.P1005S	ENST00000301067	NM_003482.3	1005	Cca/Tca	11/54	0.230152618387569	3	FACETS	1	0.962	1	0.737	0.627	0.857	CLONAL	1	TRUE	1	0.230152618387569	3		275	322	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692841	89692841	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	38	139	0	ENST00000371953.3:c.325G>T	p.Asp109Tyr	p.D109Y	ENST00000371953	NM_000314.4	109	Gac/Tac	5/9	0.229211700766172	3	FACETS	0.894	0.746	1			1	CLONAL	2	TRUE	NA	0.230152618387569	3		139	206	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105550	27105550	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	37	543	0	ENST00000324856.7:c.5161C>T	p.Arg1721Ter	p.R1721*	ENST00000324856	NM_006015.4	1721	Cga/Tga	20/20	1	2	FACETS	0.566	0.466	0.679	0.566	0.466	0.679	SUBCLONAL	1	TRUE	1	0.230152618387569	2		543	568	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176105633	176105633	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	49	537	0	ENST00000367669.3:c.882G>C	p.Lys294Asn	p.K294N	ENST00000367669	NM_022457.5	294	aaG/aaC	7/20	0.230152618387569	4	FACETS	0.613	0.518	0.719	0.204	0.172	0.24	SUBCLONAL	1	TRUE	1	0.230152618387569	4		537	854	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259406	89259406	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	81	517	1	ENST00000336596.2:c.550C>T	p.Gln184Ter	p.Q184*	ENST00000336596	NM_005233.5	184	Caa/Taa	3/17	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.230152618387569	2		518	640	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390213	89390213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	41	391	0	ENST00000336596.2:c.962C>T	p.Ala321Val	p.A321V	ENST00000336596	NM_005233.5	321	gCt/gTt	4/17	1	2	FACETS	0.758	0.631	0.899	0.758	0.631	0.899	SUBCLONAL	1	TRUE	1	0.230152618387569	2		391	470	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538226	187538226	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	31	512	0	ENST00000441802.2:c.9008T>A	p.Phe3003Tyr	p.F3003Y	ENST00000441802	NM_005245.3	3003	tTc/tAc	11/27	0.230152618387569	1	FACETS	0.441	0.356	0.538	0.441	0.356	0.538	SUBCLONAL	1	TRUE	0	0.230152618387569	1		512	540	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295321	1295321	+	upstream_gene_variant	5'Flank	SNP	C	C	A	novel	NA	P-0004687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	23	320	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.709	0.553	0.888	0.709	0.553	0.888	SUBCLONAL	1	TRUE	1	0.230152618387569	2		320	282	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394981	394981	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	20	268	0	ENST00000380956.4:c.377G>C	p.Arg126Thr	p.R126T	ENST00000380956	NM_001195286.1	126	aGg/aCg	3/9	0.229211700766172	3	FACETS	0.486	0.371	0.621			1	SUBCLONAL	1	TRUE	NA	0.230152618387569	3		268	399	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032045	26032045	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	67	718	0	ENST00000244661.2:c.244G>C	p.Asp82His	p.D82H	ENST00000244661	NM_003537.3	82	Gat/Cat	1/1	0.230152618387569	8	FACETS	0.848	0.734	0.972	0.212	0.183	0.243	CLONAL	1	TRUE	4	0.230152618387569	8		718	1161	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129208	152129208	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	41	475	0	ENST00000206249.3:c.161A>G	p.Tyr54Cys	p.Y54C	ENST00000206249	NM_000125.3	54	tAc/tGc	1/8	NA	2	FACETS	0.75	0.625	0.889			1	INDETERMINATE	1	TRUE	NA	0.230152618387569	2		475	475	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575444	64575444	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	28	519	0	ENST00000312049.6:c.573G>T	p.Glu191Asp	p.E191D	ENST00000312049	NM_130799.2	191	gaG/gaT	3/10	0.230152618387569	6	FACETS	0.704	0.561	0.867			1	SUBCLONAL	1	TRUE	NA	0.230152618387569	6		519	505	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180417	94180417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565212475	NA	P-0004687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	51	509	0	ENST00000323929.3:c.1751C>T	p.Ser584Leu	p.S584L	ENST00000323929	NM_005591.3	584	tCa/tTa	15/20	0.175247270497734	3	FACETS	0.852	0.724	0.993			1	CLONAL	1	TRUE	NA	0.230152618387569	3		509	580	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359450	118359450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	32	459	0	ENST00000534358.1:c.4454G>A	p.Cys1485Tyr	p.C1485Y	ENST00000534358	NM_005933.3	1485	tGt/tAt	11/36	1	2	FACETS	0.532	0.431	0.646	0.532	0.431	0.646	SUBCLONAL	1	TRUE	1	0.230152618387569	2		459	523	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402137	402137	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	91	634	0	ENST00000399788.2:c.4654G>T	p.Ala1552Ser	p.A1552S	ENST00000399788	NM_001042603.1	1552	Gcc/Tcc	27/28	NA	2	FACETS	1	0.907	1			1	INDETERMINATE	1	TRUE	NA	0.230152618387569	2		634	772	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	438026	438026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769454180	NA	P-0004687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	74	426	0	ENST00000399788.2:c.1943G>A	p.Arg648Gln	p.R648Q	ENST00000399788	NM_001042603.1	648	cGa/cAa	14/28	NA	2	FACETS	1	0.923	1			1	INDETERMINATE	1	TRUE	NA	0.230152618387569	2		426	599	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562826	21562826	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	22	227	0	ENST00000382592.4:c.1093A>T	p.Thr365Ser	p.T365S	ENST00000382592	NM_014572.2	365	Acc/Tcc	4/8	0.230152618387569	1	FACETS	0.769	0.598	0.965	0.769	0.598	0.965	CLONAL	1	TRUE	0	0.230152618387569	1		227	220	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240171	41240171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1291996842	NA	P-0004687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	15	93	0	ENST00000379561.5:c.179C>T	p.Ser60Leu	p.S60L	ENST00000379561	NM_002015.3	60	tCg/tTg	1/3	0.230152618387569	3	FACETS	1	0.841	1	0.606	0.447	0.792	CLONAL	1	TRUE	1	0.230152618387569	3		93	120	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987117	36987117	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	63	256	0	ENST00000354822.5:c.572G>C	p.Arg191Pro	p.R191P	ENST00000354822	NM_001079668.2	191	cGc/cCc	3/3	0.230152618387569	3	FACETS	1	0.925	1	1	0.925	1	CLONAL	2	TRUE	1	0.230152618387569	3		256	281	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67473783	67473783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	48	364	0	ENST00000327367.4:c.863G>A	p.Arg288Lys	p.R288K	ENST00000327367	NM_005902.3	288	aGa/aAa	6/9	0.220231147042232	1	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	0	0.230152618387569	1		364	327	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576096	88576096	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	36	418	1	ENST00000360948.2:c.1577C>A	p.Pro526Gln	p.P526Q	ENST00000360948	NM_001012338.2	526	cCg/cAg	13/19	0.220231147042232	1	FACETS	0.756	0.623	0.906	0.756	0.623	0.906	CLONAL	1	TRUE	0	0.230152618387569	1		419	366	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347067	347067	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	28	508	0	ENST00000262320.3:c.1944G>C	p.Arg648Ser	p.R648S	ENST00000262320	NM_003502.3	648	agG/agC	7/11	0.230152618387569	1	FACETS	0.656	0.525	0.806	0.656	0.525	0.806	SUBCLONAL	1	TRUE	0	0.230152618387569	1		508	328	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024521	16024521	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	34	514	0	ENST00000268712.3:c.1697A>T	p.Gln566Leu	p.Q566L	ENST00000268712	NM_006311.3	566	cAa/cTa	16/46	0.220231147042232	1	FACETS	0.468	0.381	0.565	0.468	0.381	0.565	SUBCLONAL	1	TRUE	0	0.230152618387569	1		514	559	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2180733	2180733	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	57	444	0	ENST00000398665.3:c.103C>T	p.His35Tyr	p.H35Y	ENST00000398665	NM_032482.2	35	Cat/Tat	2/28	0.193918340795029	0	FACETS	0.98	0.844	1			1	CLONAL	1	TRUE	0	0.230152618387569	0		444	389	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117203	7117203	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	53	500	0	ENST00000302850.5:c.4013A>G	p.Glu1338Gly	p.E1338G	ENST00000302850	NM_000208.2	1338	gAg/gGg	22/22	0.230152618387569	0	FACETS	0.916	0.784	1			1	CLONAL	1	TRUE	0	0.230152618387569	0		500	387	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705255	52705255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	69	488	0	ENST00000322088.6:c.137G>A	p.Arg46Lys	p.R46K	ENST00000322088	NM_014225.5	46	aGg/aAg	2/15	0.193918340795029	0	FACETS	0.844	0.736	0.96			1	CLONAL	1	TRUE	0	0.230152618387569	0		488	547	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827958	40827958	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs200990749	NA	P-0004687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	23	385	0	ENST00000373198.4:c.2470G>T	p.Asp824Tyr	p.D824Y	ENST00000373198	NM_133170.3	824	Gac/Tac	17/32	1	2	FACETS	0.609	0.475	0.765	0.609	0.475	0.765	SUBCLONAL	1	TRUE	1	0.230152618387569	2		385	328	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980906	40980906	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	22	272	0	ENST00000373198.4:c.1580G>T	p.Gly527Val	p.G527V	ENST00000373198	NM_133170.3	527	gGc/gTc	10/32	1	2	FACETS	0.711	0.552	0.895	0.711	0.552	0.895	SUBCLONAL	1	TRUE	1	0.230152618387569	2		272	269	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755416	39755416	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	22	373	0	ENST00000288319.7:c.1349A>T	p.Asn450Ile	p.N450I	ENST00000288319	NM_182918.3	450	aAc/aTc	10/10	0.209887662526842	4	FACETS	0.543	0.42	0.687			1	SUBCLONAL	1	TRUE	NA	0.230152618387569	4		373	433	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1315012	1315012	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	26	394	0	ENST00000400841.2:c.649G>T	p.Ala217Ser	p.A217S	ENST00000400841		217	Gcc/Tcc	6/6	0.230152618387569	1	FACETS	0.61	0.483	0.754	0.61	0.483	0.754	SUBCLONAL	1	TRUE	0	0.230152618387569	1		394	328	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938272	76938272	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0004687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	92	558	0	ENST00000373344.5:c.2476A>T	p.Lys826Ter	p.K826*	ENST00000373344	NM_000489.3	826	Aag/Tag	9/35	0.230152618387569	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.230152618387569	1		558	671	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950424	17950438	+	inframe_deletion	In_Frame_Del	DEL	TGGGGCTGCGCCGGA	TGGGGCTGCGCCGGA	-	novel	NA	P-0004687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	26	329	0	ENST00000458235.1:c.1289_1303del	p.Ile430_Pro434del	p.I430_P434del	ENST00000458235	NM_000215.3	430	aTCCGGCGCAGCCCCAca/aca	10/24	0.230152618387569	3	FACETS	0.656	0.519	0.813	0.328	0.259	0.407	SUBCLONAL	1	TRUE	1	0.230152618387569	3		329	384	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103400	77103400	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs748471279	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	132	566	0	ENST00000356341.3:c.166C>T	p.Arg56Ter	p.R56*	ENST00000356341	NM_002576.4	56	Cga/Tga	2/15	1	2	FACETS	0.812	0.735	0.893	0.812	0.735	0.893	CLONAL	1	TRUE	1	0.28	2		566	1161	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	75	236	0	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	0.981	0.861	1	0.981	0.861	1	CLONAL	1	TRUE	1	0.28	2		236	546	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156858	106156858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	151	546	1	ENST00000380013.4:c.1759C>T	p.Pro587Ser	p.P587S	ENST00000380013	NM_001127208.2	587	Cca/Tca	3/11	1	2	FACETS	0.916	0.835	1	0.916	0.835	1	CLONAL	1	TRUE	1	0.28	2		547	1178	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783259	9783259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	61	468	0	ENST00000377346.4:c.2503G>A	p.Ala835Thr	p.A835T	ENST00000377346	NM_005026.3	835	Gcc/Acc	20/24	1	2	FACETS	0.394	0.339	0.455	0.394	0.339	0.455	SUBCLONAL	1	TRUE	1	0.28	2		468	1105	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784985	9784985	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	77	337	0	ENST00000377346.4:c.2988G>T	p.Gln996His	p.Q996H	ENST00000377346	NM_005026.3	996	caG/caT	23/24	1	2	FACETS	0.744	0.653	0.843	0.744	0.653	0.843	SUBCLONAL	1	TRUE	1	0.28	2		337	739	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190834	11190834	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	49	144	0	ENST00000361445.4:c.5365G>A	p.Ala1789Thr	p.A1789T	ENST00000361445	NM_004958.3	1789	Gcc/Acc	39/58	1	2	FACETS	0.795	0.675	0.928	0.795	0.675	0.928	CLONAL	1	TRUE	1	0.28	2		144	440	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298078	11298078	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776106629	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	41	349	1	ENST00000361445.4:c.2030C>T	p.Ala677Val	p.A677V	ENST00000361445	NM_004958.3	677	gCg/gTg	13/58	1	2	FACETS	0.365	0.303	0.435	0.365	0.303	0.435	SUBCLONAL	1	TRUE	1	0.28	2		350	802	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11313967	11313967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	63	608	0	ENST00000361445.4:c.769C>T	p.Arg257Trp	p.R257W	ENST00000361445	NM_004958.3	257	Cgg/Tgg	6/58	1	2	FACETS	0.377	0.324	0.434	0.377	0.324	0.434	SUBCLONAL	1	TRUE	1	0.28	2		608	1195	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11318574	11318574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	55	512	1	ENST00000361445.4:c.239C>T	p.Ala80Val	p.A80V	ENST00000361445	NM_004958.3	80	gCc/gTc	3/58	1	2	FACETS	0.385	0.328	0.448	0.385	0.328	0.448	SUBCLONAL	1	TRUE	1	0.28	2		513	1020	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11318628	11318628	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375240279	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	123	450	1	ENST00000361445.4:c.185G>A	p.Arg62His	p.R62H	ENST00000361445	NM_004958.3	62	cGc/cAc	3/58	1	2	FACETS	0.978	0.884	1	0.978	0.884	1	CLONAL	1	TRUE	1	0.28	2		451	898	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202788	16202788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs988492642	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	50	505	0	ENST00000375759.3:c.496G>A	p.Asp166Asn	p.D166N	ENST00000375759	NM_015001.2	166	Gat/Aat	3/15	1	2	FACETS	0.382	0.323	0.448	0.382	0.323	0.448	SUBCLONAL	1	TRUE	1	0.28	2		505	934	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16203034	16203034	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	116	320	0	ENST00000375759.3:c.742T>C	p.Ser248Pro	p.S248P	ENST00000375759	NM_015001.2	248	Tcc/Ccc	3/15	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.28	2		320	804	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255718	16255718	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	85	311	1	ENST00000375759.3:c.2983G>T	p.Ala995Ser	p.A995S	ENST00000375759	NM_015001.2	995	Gca/Tca	11/15	1	2	FACETS	0.8	0.707	0.9	0.8	0.707	0.9	SUBCLONAL	1	TRUE	1	0.28	2		312	759	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264452	16264452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	49	470	0	ENST00000375759.3:c.10655G>A	p.Arg3552Lys	p.R3552K	ENST00000375759	NM_015001.2	3552	aGg/aAg	13/15	1	2	FACETS	0.36	0.303	0.422	0.36	0.303	0.422	SUBCLONAL	1	TRUE	1	0.28	2		470	973	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264470	16264470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs565813781	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	117	412	0	ENST00000375759.3:c.10673C>T	p.Thr3558Met	p.T3558M	ENST00000375759	NM_015001.2	3558	aCg/aTg	13/15	1	2	FACETS	0.927	0.835	1	0.927	0.835	1	CLONAL	1	TRUE	1	0.28	2		412	902	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056166	27056166	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	138	395	0	ENST00000324856.7:c.1162G>A	p.Gly388Ser	p.G388S	ENST00000324856	NM_006015.4	388	Ggc/Agc	2/20	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.28	2		395	947	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087503	27087503	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	109	393	1	ENST00000324856.7:c.2077C>T	p.Arg693Ter	p.R693*	ENST00000324856	NM_006015.4	693	Cga/Tga	5/20	1	2	FACETS	0.847	0.76	0.94	0.847	0.76	0.94	CLONAL	1	TRUE	1	0.28	2		394	919	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087877	27087877	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	151	398	0	ENST00000324856.7:c.2164A>G	p.Asn722Asp	p.N722D	ENST00000324856	NM_006015.4	722	Aac/Gac	6/20	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.28	2		398	912	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088672	27088672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	146	518	0	ENST00000324856.7:c.2281C>T	p.Gln761Ter	p.Q761*	ENST00000324856	NM_006015.4	761	Cag/Tag	7/20	1	2	FACETS	0.984	0.897	1	0.984	0.897	1	CLONAL	1	TRUE	1	0.28	2		518	1060	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	47	334	1	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	0.394	0.331	0.463	0.394	0.331	0.463	SUBCLONAL	1	TRUE	1	0.28	2		335	853	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807378	36807378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780818464	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	82	377	0	ENST00000373129.3:c.1286C>T	p.Ala429Val	p.A429V	ENST00000373129	NM_032017.1	429	gCg/gTg	12/12	1	2	FACETS	0.757	0.667	0.854	0.757	0.667	0.854	SUBCLONAL	1	TRUE	1	0.28	2		377	774	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363385	40363385	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	112	370	0	ENST00000397332.2:c.844G>A	p.Glu282Lys	p.E282K	ENST00000397332	NM_001033082.2	282	Gaa/Aaa	3/3	1	2	FACETS	0.967	0.87	1	0.967	0.87	1	CLONAL	1	TRUE	1	0.28	2		370	827	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803903	43803903	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs142565191	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	70	279	0	ENST00000372470.3:c.212+1G>A		p.X71_splice	ENST00000372470	NM_005373.2	71			1	2	FACETS	0.774	0.675	0.881	0.774	0.675	0.881	SUBCLONAL	1	TRUE	1	0.28	2		279	646	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46543206	46543206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	129	552	0	ENST00000262741.5:c.295G>A	p.Asp99Asn	p.D99N	ENST00000262741	NM_003629.3	99	Gat/Aat	3/10	1	2	FACETS	0.982	0.89	1	0.982	0.89	1	CLONAL	1	TRUE	1	0.28	2		552	938	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46736354	46736354	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	96	471	1	ENST00000371975.4:c.1066C>T	p.His356Tyr	p.H356Y	ENST00000371975	NM_003579.3	356	Cat/Tat	10/18	1	2	FACETS	0.685	0.609	0.766	0.685	0.609	0.766	SUBCLONAL	1	TRUE	1	0.28	2		472	1001	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439637	51439637	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs781400938	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	135	382	1	ENST00000262662.1:c.202C>T	p.Arg68Ter	p.R68*	ENST00000262662		68	Cga/Tga	4/4	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.28	2		383	919	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301830	65301830	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	106	421	0	ENST00000342505.4:c.3209C>A	p.Thr1070Asn	p.T1070N	ENST00000342505	NM_002227.2	1070	aCt/aAt	23/25	1	2	FACETS	0.879	0.788	0.977	0.879	0.788	0.977	CLONAL	1	TRUE	1	0.28	2		421	861	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78422373	78422373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766248444	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	59	253	1	ENST00000370768.2:c.1589C>T	p.Thr530Met	p.T530M	ENST00000370768	NM_003902.3	530	aCg/aTg	17/20	1	2	FACETS	0.702	0.604	0.81	0.702	0.604	0.81	SUBCLONAL	1	TRUE	1	0.28	2		254	600	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115252306	115252306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730880968	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	157	555	0	ENST00000369535.4:c.334G>A	p.Val112Met	p.V112M	ENST00000369535	NM_002524.4	112	Gtg/Atg	4/7	1	2	FACETS	0.986	0.902	1	0.986	0.902	1	CLONAL	1	TRUE	1	0.28	2		555	1137	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464896	120464896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	89	326	1	ENST00000256646.2:c.5176C>T	p.Arg1726Cys	p.R1726C	ENST00000256646	NM_024408.3	1726	Cgt/Tgt	28/34	1	2	FACETS	0.897	0.795	1	0.897	0.795	1	CLONAL	1	TRUE	1	0.28	2		327	709	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466595	120466595	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	43	390	2	ENST00000256646.2:c.4524C>A	p.Tyr1508Ter	p.Y1508*	ENST00000256646	NM_024408.3	1508	taC/taA	26/34	1	2	FACETS	0.37	0.308	0.439	0.37	0.308	0.439	SUBCLONAL	1	TRUE	1	0.28	2		392	830	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843623	156843623	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	125	563	0	ENST00000524377.1:c.1049A>G	p.Gln350Arg	p.Q350R	ENST00000524377	NM_002529.3	350	cAg/cGg	8/17	1	2	FACETS	0.791	0.714	0.872	0.791	0.714	0.872	SUBCLONAL	1	TRUE	1	0.28	2		563	1129	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849054	156849054	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786205449	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	122	416	0	ENST00000524377.1:c.1946G>A	p.Arg649Gln	p.R649Q	ENST00000524377	NM_002529.3	649	cGg/cAg	15/17	1	2	FACETS	0.967	0.874	1	0.967	0.874	1	CLONAL	1	TRUE	1	0.28	2		416	901	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162722971	162722971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	151	521	1	ENST00000367921.3:c.169G>A	p.Ala57Thr	p.A57T	ENST00000367921	NM_006182.2	57	Gct/Act	4/18	1	2	FACETS	0.992	0.906	1	0.992	0.906	1	CLONAL	1	TRUE	1	0.28	2		522	1087	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724990	162724990	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	153	519	0	ENST00000367921.3:c.462C>A	p.Asp154Glu	p.D154E	ENST00000367921	NM_006182.2	154	gaC/gaA	6/18	1	2	FACETS	0.971	0.886	1	0.971	0.886	1	CLONAL	1	TRUE	1	0.28	2		519	1126	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737052	162737052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765973930	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	154	543	1	ENST00000367921.3:c.1196G>A	p.Arg399Gln	p.R399Q	ENST00000367921	NM_006182.2	399	cGg/cAg	11/18	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.28	2		544	1067	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518580	204518580	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	108	379	0	ENST00000367182.3:c.1243G>A	p.Asp415Asn	p.D415N	ENST00000367182	NM_001278516.1	415	Gat/Aat	11/11	1	2	FACETS	0.918	0.824	1	0.918	0.824	1	CLONAL	1	TRUE	1	0.28	2		379	840	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666635	206666635	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1430127416	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	153	479	0	ENST00000367120.3:c.1969C>T	p.Arg657Ter	p.R657*	ENST00000367120	NM_014002.3	657	Cga/Tga	20/22	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.28	2		479	1065	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612777	228612777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758908744	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1444	77	840	1	ENST00000366696.1:c.250C>T	p.Arg84Cys	p.R84C	ENST00000366696	NM_003493.2	84	Cgc/Tgc	1/1	1	2	FACETS	0.362	0.316	0.411	0.362	0.316	0.411	SUBCLONAL	1	TRUE	1	0.28	2		841	1521	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243859016	243859016	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	47	292	0	ENST00000263826.5:c.49G>T	p.Glu17Ter	p.E17*	ENST00000263826	NM_005465.4	17	Gaa/Taa	2/13	1	2	FACETS	0.825	0.697	0.965	0.825	0.697	0.965	CLONAL	1	TRUE	1	0.28	2		292	407	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469038	25469038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775263815	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	49	440	0	ENST00000264709.3:c.1420C>T	p.Arg474Cys	p.R474C	ENST00000264709	NM_175629.2	474	Cgc/Tgc	11/23	1	2	FACETS	0.383	0.323	0.45	0.383	0.323	0.45	SUBCLONAL	1	TRUE	1	0.28	2		440	913	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469533	25469533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	57	518	0	ENST00000264709.3:c.1235G>A	p.Gly412Glu	p.G412E	ENST00000264709	NM_175629.2	412	gGg/gAg	10/23	1	2	FACETS	0.375	0.32	0.435	0.375	0.32	0.435	SUBCLONAL	1	TRUE	1	0.28	2		518	1086	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973193	25973193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369212828	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	123	261	0	ENST00000435504.4:c.1232C>T	p.Ser411Phe	p.S411F	ENST00000435504		411	tCc/tTc	12/13	1	2	FACETS	0.986	0.891	1	0.986	0.891	1	CLONAL	1	TRUE	1	0.28	2		261	891	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462691	29462691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368581969	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	46	353	0	ENST00000389048.3:c.2210C>T	p.Ser737Leu	p.S737L	ENST00000389048	NM_004304.4	737	tCg/tTg	13/29	1	2	FACETS	0.389	0.327	0.459	0.389	0.327	0.459	SUBCLONAL	1	TRUE	1	0.28	2		353	844	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47602435	47602435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146044104	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	160	476	0	ENST00000263735.4:c.488G>A	p.Arg163Gln	p.R163Q	ENST00000263735	NM_002354.2	163	cGg/cAg	4/9	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.28	2		476	1125	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47657061	47657061	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	83	358	0	ENST00000233146.2:c.1257G>T	p.Gln419His	p.Q419H	ENST00000233146	NM_000251.2	419	caG/caT	7/16	1	2	FACETS	0.676	0.595	0.763	0.676	0.595	0.763	SUBCLONAL	1	TRUE	1	0.28	2		358	877	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026962	48026962	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	111	464	0	ENST00000234420.5:c.1840T>C	p.Ser614Pro	p.S614P	ENST00000234420	NM_000179.2	614	Tcc/Ccc	4/10	1	2	FACETS	0.842	0.756	0.933	0.842	0.756	0.933	CLONAL	1	TRUE	1	0.28	2		464	942	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027552	48027552	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	42	268	1	ENST00000234420.5:c.2430G>T	p.Glu810Asp	p.E810D	ENST00000234420	NM_000179.2	810	gaG/gaT	4/10	1	2	FACETS	0.621	0.518	0.735	0.621	0.518	0.735	SUBCLONAL	1	TRUE	1	0.28	2		269	483	SUCCESS
REL	5966	MSKCC	GRCh37	2	61118870	61118870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	99	450	0	ENST00000295025.8:c.63G>A	p.Met21Ile	p.M21I	ENST00000295025	NM_002908.2	21	atG/atA	2/11	1	2	FACETS	0.835	0.745	0.931	0.835	0.745	0.931	CLONAL	1	TRUE	1	0.28	2		450	847	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149242	61149242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	120	334	0	ENST00000295025.8:c.1432C>T	p.Pro478Ser	p.P478S	ENST00000295025	NM_002908.2	478	Cca/Tca	11/11	1	2	FACETS	0.993	0.896	1	0.993	0.896	1	CLONAL	1	TRUE	1	0.28	2		334	863	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149251	61149251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395570590	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	119	326	0	ENST00000295025.8:c.1441G>A	p.Asp481Asn	p.D481N	ENST00000295025	NM_002908.2	481	Gat/Aat	11/11	1	2	FACETS	0.991	0.894	1	0.991	0.894	1	CLONAL	1	TRUE	1	0.28	2		326	858	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99163079	99163079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1403218618	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	111	379	0	ENST00000074304.5:c.1085C>T	p.Ala362Val	p.A362V	ENST00000074304	NM_001134224.1	362	gCg/gTg	13/26	1	2	FACETS	0.885	0.795	0.981	0.885	0.795	0.981	CLONAL	1	TRUE	1	0.28	2		379	896	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172124	99172124	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	98	381	0	ENST00000074304.5:c.1690C>A	p.Pro564Thr	p.P564T	ENST00000074304	NM_001134224.1	564	Ccc/Acc	17/26	1	2	FACETS	0.83	0.74	0.927	0.83	0.74	0.927	CLONAL	1	TRUE	1	0.28	2		381	843	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182538	99182538	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767204088	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	101	337	0	ENST00000074304.5:c.2341G>A	p.Ala781Thr	p.A781T	ENST00000074304	NM_001134224.1	781	Gcc/Acc	22/26	1	2	FACETS	0.891	0.796	0.992	0.891	0.796	0.992	CLONAL	1	TRUE	1	0.28	2		337	810	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921764	111921764	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	123	386	0	ENST00000393256.3:c.553C>T	p.Arg185Ter	p.R185*	ENST00000393256	NM_006538.4	185	Cga/Tga	4/4	1	2	FACETS	0.857	0.774	0.945	0.857	0.774	0.945	CLONAL	1	TRUE	1	0.28	2		386	1025	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921765	111921765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572257286	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	147	379	0	ENST00000393256.3:c.554G>A	p.Arg185Gln	p.R185Q	ENST00000393256	NM_006538.4	185	cGa/cAa	4/4	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.28	2		379	1019	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044465	128044465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374264195	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	128	449	1	ENST00000285398.2:c.1156G>A	p.Asp386Asn	p.D386N	ENST00000285398	NM_000122.1	386	Gac/Aac	8/15	1	2	FACETS	0.846	0.765	0.931	0.846	0.765	0.931	CLONAL	1	TRUE	1	0.28	2		450	1081	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046290	128046290	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs368191279	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	62	438	1	ENST00000285398.2:c.973C>T	p.Arg325Ter	p.R325*	ENST00000285398	NM_000122.1	325	Cga/Tga	7/15	1	2	FACETS	0.43	0.37	0.495	0.43	0.37	0.495	SUBCLONAL	1	TRUE	1	0.28	2		439	1031	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128047329	128047329	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748503195	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	157	451	0	ENST00000285398.2:c.593G>A	p.Arg198His	p.R198H	ENST00000285398	NM_000122.1	198	cGc/cAc	5/15	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.28	2		451	1054	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872812	136872812	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1360	79	686	0	ENST00000241393.3:c.686C>T	p.Ser229Phe	p.S229F	ENST00000241393	NM_003467.2	229	tCc/tTc	2/2	1	2	FACETS	0.392	0.343	0.445	0.392	0.343	0.445	SUBCLONAL	1	TRUE	1	0.28	2		686	1439	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634770	158634770	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1159	179	660	0	ENST00000263640.3:c.416C>T	p.Ala139Val	p.A139V	ENST00000263640	NM_001105.4	139	gCc/gTc	5/11	1	2	FACETS	0.956	0.879	1	0.956	0.879	1	CLONAL	1	TRUE	1	0.28	2		660	1338	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273294	198273294	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	83	328	1	ENST00000335508.6:c.916C>T	p.His306Tyr	p.H306Y	ENST00000335508	NM_012433.2	306	Cat/Tat	8/25	1	2	FACETS	0.718	0.632	0.809	0.718	0.632	0.809	SUBCLONAL	1	TRUE	1	0.28	2		329	826	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285173	198285173	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	43	420	0	ENST00000335508.6:c.394C>T	p.Arg132Cys	p.R132C	ENST00000335508	NM_012433.2	132	Cgt/Tgt	4/25	1	2	FACETS	0.422	0.352	0.501	0.422	0.352	0.501	SUBCLONAL	1	TRUE	1	0.28	2		420	727	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141631	202141631	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs17860424	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	131	450	0	ENST00000358485.4:c.919C>T	p.Arg307Trp	p.R307W	ENST00000358485	NM_001080125.1	307	Cgg/Tgg	7/9	1	2	FACETS	0.908	0.822	0.998	0.908	0.822	0.998	CLONAL	1	TRUE	1	0.28	2		450	1031	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735317	204735317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553657378	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	27	189	0	ENST00000302823.3:c.118G>A	p.Val40Met	p.V40M	ENST00000302823	NM_005214.4	40	Gtg/Atg	2/4	1	2	FACETS	0.454	0.361	0.561	0.454	0.361	0.561	SUBCLONAL	1	TRUE	1	0.28	2		189	425	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989546	212989546	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	171	462	0	ENST00000342788.4:c.165C>A	p.Asn55Lys	p.N55K	ENST00000342788	NM_005235.2	55	aaC/aaA	2/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.28	2		462	1064	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342921	225342921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766952042	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	90	485	0	ENST00000264414.4:c.2171C>T	p.Ala724Val	p.A724V	ENST00000264414	NM_003590.4	724	gCg/gTg	15/16	1	2	FACETS	0.849	0.753	0.952	0.849	0.753	0.952	CLONAL	1	TRUE	1	0.28	2		485	757	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422491	225422491	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	119	512	0	ENST00000264414.4:c.149G>T	p.Ser50Ile	p.S50I	ENST00000264414	NM_003590.4	50	aGt/aTt	2/16	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.28	2		512	821	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422574	225422574	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	49	261	0	ENST00000264414.4:c.67-1G>T		p.X23_splice	ENST00000264414	NM_003590.4	23			1	2	FACETS	0.831	0.705	0.969	0.831	0.705	0.969	CLONAL	1	TRUE	1	0.28	2		261	421	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713834	30713834	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35766612	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	103	348	0	ENST00000295754.5:c.1159G>A	p.Val387Met	p.V387M	ENST00000295754	NM_003242.5	387	Gtg/Atg	4/7	1	2	FACETS	0.93	0.832	1	0.93	0.832	1	CLONAL	1	TRUE	1	0.28	2		348	791	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070390	37070390	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	66	413	0	ENST00000231790.2:c.1525C>A	p.Leu509Ile	p.L509I	ENST00000231790	NM_000249.3	509	Ctc/Atc	13/19	1	2	FACETS	0.557	0.482	0.638	0.557	0.482	0.638	SUBCLONAL	1	TRUE	1	0.28	2		413	847	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090431	37090431	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	124	422	0	ENST00000231790.2:c.2026C>T	p.Leu676Phe	p.L676F	ENST00000231790	NM_000249.3	676	Ctc/Ttc	18/19	1	2	FACETS	0.94	0.85	1	0.94	0.85	1	CLONAL	1	TRUE	1	0.28	2		422	942	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125211	47125211	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs573687627	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	110	384	0	ENST00000409792.3:c.6059A>G	p.Lys2020Arg	p.K2020R	ENST00000409792	NM_014159.6	2020	aAg/aGg	12/21	1	2	FACETS	0.985	0.884	1	0.985	0.884	1	CLONAL	1	TRUE	1	0.28	2		384	798	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163010	47163010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	136	544	0	ENST00000409792.3:c.3116C>T	p.Ser1039Phe	p.S1039F	ENST00000409792	NM_014159.6	1039	tCt/tTt	3/21	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.28	2		544	906	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164328	47164328	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	61	430	0	ENST00000409792.3:c.1798T>A	p.Leu600Ile	p.L600I	ENST00000409792	NM_014159.6	600	Tta/Ata	3/21	1	2	FACETS	0.508	0.437	0.586	0.508	0.437	0.586	SUBCLONAL	1	TRUE	1	0.28	2		430	857	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442575	52442575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	96	263	0	ENST00000460680.1:c.170G>A	p.Arg57Gln	p.R57Q	ENST00000460680	NM_004656.3	57	cGg/cAg	4/17	1	2	FACETS	0.978	0.872	1	0.978	0.872	1	CLONAL	1	TRUE	1	0.28	2		263	701	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52582108	52582108	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775162970	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	75	444	0	ENST00000394830.3:c.4720C>T	p.Arg1574Cys	p.R1574C	ENST00000394830	NM_018313.4	1574	Cgc/Tgc	30/30	1	2	FACETS	0.591	0.516	0.671	0.591	0.516	0.671	SUBCLONAL	1	TRUE	1	0.28	2		444	907	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52696207	52696207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1223	183	674	1	ENST00000394830.3:c.470C>T	p.Ala157Val	p.A157V	ENST00000394830	NM_018313.4	157	gCa/gTa	5/30	1	2	FACETS	0.93	0.855	1	0.93	0.855	1	CLONAL	1	TRUE	1	0.28	2		675	1406	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008521	70008521	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876657699	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	104	375	0	ENST00000394351.3:c.808C>T	p.Arg270Ter	p.R270*	ENST00000394351	NM_000248.3	270	Cga/Tga	8/9	1	2	FACETS	0.768	0.687	0.855	0.768	0.687	0.855	SUBCLONAL	1	TRUE	1	0.28	2		375	967	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026105	71026105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	104	399	0	ENST00000318789.4:c.1517C>T	p.Ala506Val	p.A506V	ENST00000318789	NM_032682.5	506	gCg/gTg	17/21	1	2	FACETS	0.932	0.834	1	0.932	0.834	1	CLONAL	1	TRUE	1	0.28	2		399	797	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71064716	71064716	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	98	338	0	ENST00000318789.4:c.958T>G	p.Phe320Val	p.F320V	ENST00000318789	NM_032682.5	320	Ttc/Gtc	12/21	1	2	FACETS	0.919	0.819	1	0.919	0.819	1	CLONAL	1	TRUE	1	0.28	2		338	762	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096170	71096170	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	107	341	1	ENST00000318789.4:c.587T>C	p.Leu196Pro	p.L196P	ENST00000318789	NM_032682.5	196	cTc/cCc	10/21	1	2	FACETS	0.918	0.822	1	0.918	0.822	1	CLONAL	1	TRUE	1	0.28	2		342	833	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71096192	71096192	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	93	334	0	ENST00000318789.4:c.565C>T	p.Gln189Ter	p.Q189*	ENST00000318789	NM_032682.5	189	Cag/Tag	10/21	1	2	FACETS	0.801	0.712	0.897	0.801	0.712	0.897	CLONAL	1	TRUE	1	0.28	2		334	829	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247519	71247519	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	92	346	0	ENST00000318789.4:c.14C>A	p.Ser5Tyr	p.S5Y	ENST00000318789	NM_032682.5	5	tCt/tAt	6/21	1	2	FACETS	0.879	0.78	0.983	0.879	0.78	0.983	CLONAL	1	TRUE	1	0.28	2		346	748	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72861878	72861878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201983708	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	120	460	2	ENST00000325599.8:c.1004G>A	p.Arg335His	p.R335H	ENST00000325599	NM_018130.2	335	cGc/cAc	9/11	1	2	FACETS	0.952	0.859	1	0.952	0.859	1	CLONAL	1	TRUE	1	0.28	2		462	900	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259111	89259111	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	79	411	0	ENST00000336596.2:c.255C>A	p.Asn85Lys	p.N85K	ENST00000336596	NM_005233.5	85	aaC/aaA	3/17	1	2	FACETS	0.931	0.82	1	0.931	0.82	1	CLONAL	1	TRUE	1	0.28	2		411	606	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259184	89259184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	83	356	0	ENST00000336596.2:c.328C>T	p.Pro110Ser	p.P110S	ENST00000336596	NM_005233.5	110	Cca/Tca	3/17	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.28	2		356	570	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391214	89391214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs530556931	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	32	193	0	ENST00000336596.2:c.1280C>T	p.Ala427Val	p.A427V	ENST00000336596	NM_005233.5	427	gCg/gTg	5/17	1	2	FACETS	0.427	0.346	0.519	0.427	0.346	0.519	SUBCLONAL	1	TRUE	1	0.28	2		193	535	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499405	89499405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	132	432	0	ENST00000336596.2:c.2575G>A	p.Asp859Asn	p.D859N	ENST00000336596	NM_005233.5	859	Gac/Aac	15/17	1	2	FACETS	0.972	0.881	1	0.972	0.881	1	CLONAL	1	TRUE	1	0.28	2		432	970	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521666	89521666	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs748629890	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	122	466	0	ENST00000336596.2:c.2743A>G	p.Thr915Ala	p.T915A	ENST00000336596	NM_005233.5	915	Aca/Gca	16/17	1	2	FACETS	0.993	0.897	1	0.993	0.897	1	CLONAL	1	TRUE	1	0.28	2		466	878	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880859	134880859	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	58	420	1	ENST00000398015.3:c.1423-1G>T		p.X475_splice	ENST00000398015	NM_004441.4	475			1	2	FACETS	0.438	0.375	0.508	0.438	0.375	0.508	SUBCLONAL	1	TRUE	1	0.28	2		421	945	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134911520	134911520	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756316035	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	42	281	0	ENST00000398015.3:c.1985G>A	p.Arg662His	p.R662H	ENST00000398015	NM_004441.4	662	cGt/cAt	11/16	1	2	FACETS	0.421	0.35	0.5	0.421	0.35	0.5	SUBCLONAL	1	TRUE	1	0.28	2		281	713	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967308	134967308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201143675	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	185	412	0	ENST00000398015.3:c.2647C>T	p.Arg883Trp	p.R883W	ENST00000398015	NM_004441.4	883	Cgg/Tgg	14/16	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.28	2		412	998	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417933	138417933	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776210981	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	104	315	0	ENST00000289153.2:c.1586G>A	p.Arg529Gln	p.R529Q	ENST00000289153	NM_006219.2	529	cGa/cAa	11/22	1	2	FACETS	0.989	0.886	1	0.989	0.886	1	CLONAL	1	TRUE	1	0.28	2		315	751	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916936	178916936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886042002	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	38	701	0	ENST00000263967.3:c.323G>A	p.Arg108His	p.R108H	ENST00000263967	NM_006218.2	108	cGt/cAt	2/21	1	2	FACETS	0.276	0.227	0.331	0.276	0.227	0.331	SUBCLONAL	1	TRUE	1	0.28	2		701	983	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921483	178921483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	148	514	1	ENST00000263967.3:c.965C>T	p.Thr322Ile	p.T322I	ENST00000263967	NM_006218.2	322	aCa/aTa	5/21	1	2	FACETS	0.892	0.813	0.975	0.892	0.813	0.975	CLONAL	1	TRUE	1	0.28	2		515	1185	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951965	178951965	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	96	479	0	ENST00000263967.3:c.3020G>A	p.Gly1007Asp	p.G1007D	ENST00000263967	NM_006218.2	1007	gGc/gAc	21/21	1	2	FACETS	0.902	0.804	1	0.902	0.804	1	CLONAL	1	TRUE	1	0.28	2		479	760	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183540	185183540	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	143	415	0	ENST00000265026.3:c.1394C>T	p.Ala465Val	p.A465V	ENST00000265026	NM_004721.4	465	gCg/gTg	9/14	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.28	2		415	891	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184657	185184657	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs56408536	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	179	605	0	ENST00000265026.3:c.1549C>T	p.Arg517Ter	p.R517*	ENST00000265026	NM_004721.4	517	Cga/Tga	10/14	1	2	FACETS	0.978	0.9	1	0.978	0.9	1	CLONAL	1	TRUE	1	0.28	2		605	1307	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198306	185198306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs528512189	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	77	248	0	ENST00000265026.3:c.2788C>T	p.Arg930Cys	p.R930C	ENST00000265026	NM_004721.4	930	Cgt/Tgt	13/14	1	2	FACETS	0.837	0.735	0.947	0.837	0.735	0.947	CLONAL	1	TRUE	1	0.28	2		248	657	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586503	189586503	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs143591434	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	62	179	0	ENST00000264731.3:c.1127G>A	p.Arg376His	p.R376H	ENST00000264731	NM_003722.4	376	cGc/cAc	8/14	1	2	FACETS	0.952	0.825	1	0.952	0.825	1	CLONAL	1	TRUE	1	0.28	2		179	465	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1795672	1795672	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	22	89	0	ENST00000260795.2:c.11C>A	p.Pro4His	p.P4H	ENST00000260795		4	cCt/cAt	1/17	1	2	FACETS	1	0.883	1	1	0.883	1	CLONAL	1	TRUE	1	0.28	2		89	130	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803121	1803121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745863884	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	42	690	1	ENST00000260795.2:c.473G>A	p.Arg158Gln	p.R158Q	ENST00000260795		158	cGg/cAg	4/17	1	2	FACETS	0.365	0.303	0.433	0.365	0.303	0.433	SUBCLONAL	1	TRUE	1	0.28	2		691	823	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806119	1806119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931614	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	49	477	0	ENST00000260795.2:c.1138G>A	p.Gly380Arg	p.G380R	ENST00000260795		380	Ggg/Agg	8/17	1	2	FACETS	0.358	0.302	0.421	0.358	0.302	0.421	SUBCLONAL	1	TRUE	1	0.28	2		477	977	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806228	1806228	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868356240	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	107	381	3	ENST00000260795.2:c.1247G>A	p.Arg416His	p.R416H	ENST00000260795		416	cGc/cAc	8/17	1	2	FACETS	0.904	0.811	1	0.904	0.811	1	CLONAL	1	TRUE	1	0.28	2		384	845	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133759	55133759	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	158	622	0	ENST00000257290.5:c.972G>T	p.Leu324Phe	p.L324F	ENST00000257290	NM_006206.4	324	ttG/ttT	7/23	1	2	FACETS	0.941	0.861	1	0.941	0.861	1	CLONAL	1	TRUE	1	0.28	2		622	1199	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594182	55594182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	98	347	0	ENST00000288135.5:c.1885G>A	p.Ala629Thr	p.A629T	ENST00000288135	NM_000222.2	629	Gcc/Acc	13/21	1	2	FACETS	0.879	0.784	0.981	0.879	0.784	0.981	CLONAL	1	TRUE	1	0.28	2		347	796	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213873	66213873	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1383933498	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	136	599	0	ENST00000273854.3:c.2557C>T	p.Arg853Ter	p.R853*	ENST00000273854	NM_004439.5	853	Cga/Tga	15/18	1	2	FACETS	0.948	0.861	1	0.948	0.861	1	CLONAL	1	TRUE	1	0.28	2		599	1025	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467490	66467490	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	196	414	0	ENST00000273854.3:c.779G>A	p.Gly260Asp	p.G260D	ENST00000273854	NM_004439.5	260	gGc/gAc	3/18	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.28	2		414	1027	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391500	84391500	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553936765	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	20	194	0	ENST00000321945.7:c.332C>T	p.Thr111Met	p.T111M	ENST00000321945	NM_139076.2	111	aCg/aTg	5/9	1	2	FACETS	0.406	0.31	0.518	0.406	0.31	0.518	SUBCLONAL	1	TRUE	1	0.28	2		194	352	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190905	106190905	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1164864545	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	38	237	0	ENST00000380013.4:c.4182+1G>A		p.X1394_splice	ENST00000380013	NM_001127208.2	1394			1	2	FACETS	0.441	0.364	0.528	0.441	0.364	0.528	SUBCLONAL	1	TRUE	1	0.28	2		237	615	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196648	106196648	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	127	466	0	ENST00000380013.4:c.4981T>G	p.Tyr1661Asp	p.Y1661D	ENST00000380013	NM_001127208.2	1661	Tat/Gat	11/11	1	2	FACETS	0.853	0.772	0.94	0.853	0.772	0.94	CLONAL	1	TRUE	1	0.28	2		466	1063	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045844	143045844	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777966937	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	101	336	0	ENST00000262992.4:c.1790G>A	p.Arg597Gln	p.R597Q	ENST00000262992	NM_001101669.1	597	cGa/cAa	17/24	1	2	FACETS	0.842	0.752	0.938	0.842	0.752	0.938	CLONAL	1	TRUE	1	0.28	2		336	857	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247373	153247373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	55	306	0	ENST00000281708.4:c.1429G>A	p.Gly477Ser	p.G477S	ENST00000281708	NM_033632.3	477	Ggt/Agt	10/12	1	2	FACETS	0.893	0.765	1	0.893	0.765	1	CLONAL	1	TRUE	1	0.28	2		306	440	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187531056	187531056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1163461363	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	121	455	1	ENST00000441802.2:c.9967G>A	p.Val3323Ile	p.V3323I	ENST00000441802	NM_005245.3	3323	Gtt/Att	15/27	1	2	FACETS	0.808	0.728	0.892	0.808	0.728	0.892	CLONAL	1	TRUE	1	0.28	2		456	1070	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532552	187532552	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs748152388	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	175	422	0	ENST00000441802.2:c.9841G>T	p.Asp3281Tyr	p.D3281Y	ENST00000441802	NM_005245.3	3281	Gat/Tat	14/27	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.28	2		422	925	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539195	187539195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	140	524	0	ENST00000441802.2:c.8545G>A	p.Asp2849Asn	p.D2849N	ENST00000441802	NM_005245.3	2849	Gat/Aat	10/27	1	2	FACETS	0.932	0.847	1	0.932	0.847	1	CLONAL	1	TRUE	1	0.28	2		524	1073	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541475	187541477	+	missense_variant	Missense_Mutation	TNP	CGG	CGG	TGA	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	129	492	0	ENST00000441802.2:c.6263_6265delinsTCA	p.Ala2088_Val2089delinsValIle	p.A2088_V2089delinsVI	ENST00000441802	NM_005245.3	2088	gCCGtt/gTCAtt	10/27	1	2	FACETS	0.88	0.797	0.968	0.88	0.797	0.968	CLONAL	1	TRUE	1	0.28	2		492	1047	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549323	187549323	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs556046628	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	126	464	0	ENST00000441802.2:c.4795T>C	p.Tyr1599His	p.Y1599H	ENST00000441802	NM_005245.3	1599	Tac/Cac	9/27	1	2	FACETS	0.848	0.767	0.935	0.848	0.767	0.935	CLONAL	1	TRUE	1	0.28	2		464	1061	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549707	187549707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377067763	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	184	346	0	ENST00000441802.2:c.4534G>A	p.Gly1512Ser	p.G1512S	ENST00000441802	NM_005245.3	1512	Ggc/Agc	8/27	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.28	2		346	898	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187560875	187560875	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	125	422	0	ENST00000441802.2:c.3642+1G>T		p.X1214_splice	ENST00000441802	NM_005245.3	1214			1	2	FACETS	0.94	0.85	1	0.94	0.85	1	CLONAL	1	TRUE	1	0.28	2		422	950	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627774	187627774	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1183516785	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	170	536	1	ENST00000441802.2:c.3208C>T	p.Arg1070Ter	p.R1070*	ENST00000441802	NM_005245.3	1070	Cga/Tga	2/27	1	2	FACETS	0.948	0.87	1	0.948	0.87	1	CLONAL	1	TRUE	1	0.28	2		537	1281	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225663	225663	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375576259	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	52	255	0	ENST00000264932.6:c.442G>A	p.Ala148Thr	p.A148T	ENST00000264932	NM_004168.2	148	Gcc/Acc	4/15	1	2	FACETS	0.609	0.518	0.709	0.609	0.518	0.709	SUBCLONAL	1	TRUE	1	0.28	2		255	610	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279510	1279510	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1295347738	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	46	398	1	ENST00000310581.5:c.2026C>A	p.Leu676Met	p.L676M	ENST00000310581	NM_198253.2	676	Ctg/Atg	5/16	1	2	FACETS	0.39	0.327	0.46	0.39	0.327	0.46	SUBCLONAL	1	TRUE	1	0.28	2		399	843	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294463	1294463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	44	168	0	ENST00000310581.5:c.538G>A	p.Ala180Thr	p.A180T	ENST00000310581	NM_198253.2	180	Gct/Act	2/16	1	2	FACETS	0.802	0.674	0.943	0.802	0.674	0.943	CLONAL	1	TRUE	1	0.28	2		168	392	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873627	35873627	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	126	379	0	ENST00000303115.3:c.583C>A	p.Leu195Ile	p.L195I	ENST00000303115	NM_002185.3	195	Ctc/Atc	5/8	1	2	FACETS	0.945	0.855	1	0.945	0.855	1	CLONAL	1	TRUE	1	0.28	2		379	952	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38944623	38944623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	69	447	0	ENST00000357387.3:c.4838G>A	p.Arg1613His	p.R1613H	ENST00000357387	NM_152756.3	1613	cGc/cAc	36/38	1	2	FACETS	0.527	0.458	0.603	0.527	0.458	0.603	SUBCLONAL	1	TRUE	1	0.28	2		447	935	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38952450	38952450	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	78	388	0	ENST00000357387.3:c.2975C>A	p.Ala992Asp	p.A992D	ENST00000357387	NM_152756.3	992	gCt/gAt	30/38	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.28	2		388	527	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38958911	38958911	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	99	269	0	ENST00000357387.3:c.2201A>C	p.Lys734Thr	p.K734T	ENST00000357387	NM_152756.3	734	aAa/aCa	23/38	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.28	2		269	698	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967451	38967451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200672374	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	50	420	1	ENST00000357387.3:c.1139G>A	p.Arg380His	p.R380H	ENST00000357387	NM_152756.3	380	cGt/cAt	13/38	1	2	FACETS	0.377	0.318	0.441	0.377	0.318	0.441	SUBCLONAL	1	TRUE	1	0.28	2		421	948	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56155603	56155603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	121	332	0	ENST00000399503.3:c.695C>T	p.Ser232Phe	p.S232F	ENST00000399503	NM_005921.1	232	tCt/tTt	3/20	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.28	2		332	859	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184159	56184159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	96	401	0	ENST00000399503.3:c.4364C>T	p.Ser1455Phe	p.S1455F	ENST00000399503	NM_005921.1	1455	tCc/tTc	19/20	1	2	FACETS	0.809	0.72	0.904	0.809	0.72	0.904	CLONAL	1	TRUE	1	0.28	2		401	848	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750420	57750420	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	129	446	0	ENST00000274289.3:c.2048G>T	p.Arg683Ile	p.R683I	ENST00000274289	NM_006622.3	683	aGa/aTa	14/14	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.28	2		446	752	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569243	67569243	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	98	362	1	ENST00000274335.5:c.360G>T	p.Glu120Asp	p.E120D	ENST00000274335		120	gaG/gaT	2/15	1	2	FACETS	0.897	0.8	1	0.897	0.8	1	CLONAL	1	TRUE	1	0.28	2		363	780	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86648982	86648982	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1333866018	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	67	315	0	ENST00000274376.6:c.1262A>G	p.Asp421Gly	p.D421G	ENST00000274376	NM_002890.2	421	gAc/gGc	9/25	1	2	FACETS	0.983	0.856	1	0.983	0.856	1	CLONAL	1	TRUE	1	0.28	2		315	487	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497347	149497347	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140261309	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	90	389	0	ENST00000261799.4:c.2971C>T	p.Arg991Cys	p.R991C	ENST00000261799	NM_002609.3	991	Cgc/Tgc	22/23	1	2	FACETS	0.838	0.743	0.94	0.838	0.743	0.94	CLONAL	1	TRUE	1	0.28	2		389	767	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562478	176562478	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761430959	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	162	535	0	ENST00000439151.2:c.374C>T	p.Ala125Val	p.A125V	ENST00000439151	NM_022455.4	125	gCt/gTt	2/23	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.28	2		535	1072	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637762	176637762	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057520339	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	110	469	0	ENST00000439151.2:c.2362C>T	p.Arg788Ter	p.R788*	ENST00000439151	NM_022455.4	788	Cga/Tga	5/23	1	2	FACETS	0.884	0.793	0.98	0.884	0.793	0.98	CLONAL	1	TRUE	1	0.28	2		469	889	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675313	176675313	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	106	325	0	ENST00000439151.2:c.4629G>T	p.Glu1543Asp	p.E1543D	ENST00000439151	NM_022455.4	1543	gaG/gaT	11/23	1	2	FACETS	0.922	0.826	1	0.922	0.826	1	CLONAL	1	TRUE	1	0.28	2		325	821	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707683	176707683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587784154	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	135	392	0	ENST00000439151.2:c.5740C>T	p.Arg1914Cys	p.R1914C	ENST00000439151	NM_022455.4	1914	Cgc/Tgc	18/23	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.28	2		392	962	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721049	176721049	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748597598	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	92	352	0	ENST00000439151.2:c.6680C>T	p.Pro2227Leu	p.P2227L	ENST00000439151	NM_022455.4	2227	cCg/cTg	23/23	1	2	FACETS	0.792	0.703	0.887	0.792	0.703	0.887	SUBCLONAL	1	TRUE	1	0.28	2		352	830	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721130	176721130	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	101	266	0	ENST00000439151.2:c.6761C>A	p.Pro2254His	p.P2254H	ENST00000439151	NM_022455.4	2254	cCt/cAt	23/23	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.28	2		266	706	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394888	394888	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	38	320	0	ENST00000380956.4:c.284C>T	p.Thr95Met	p.T95M	ENST00000380956	NM_001195286.1	95	aCg/aTg	3/9	1	2	FACETS	0.383	0.316	0.459	0.383	0.316	0.459	SUBCLONAL	1	TRUE	1	0.28	2		320	708	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672428	30672428	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	113	380	0	ENST00000376406.3:c.4532C>T	p.Thr1511Ile	p.T1511I	ENST00000376406	NM_014641.2	1511	aCa/aTa	10/15	1	2	FACETS	0.935	0.841	1	0.935	0.841	1	CLONAL	1	TRUE	1	0.28	2		380	863	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188203	32188203	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	113	363	0	ENST00000375023.3:c.1138C>A	p.Leu380Ile	p.L380I	ENST00000375023	NM_004557.3	380	Ctc/Atc	6/30	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.28	2		363	802	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652078	36652078	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45548832	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	121	412	1	ENST00000244741.5:c.200G>A	p.Arg67His	p.R67H	ENST00000244741	NM_000389.4	67	cGt/cAt	2/3	1	2	FACETS	0.95	0.857	1	0.95	0.857	1	CLONAL	1	TRUE	1	0.28	2		413	910	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974378	93974378	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	88	653	1	ENST00000369303.4:c.1676C>A	p.Ala559Asp	p.A559D	ENST00000369303	NM_004440.3	559	gCt/gAt	8/17	1	2	FACETS	0.804	0.712	0.903	0.804	0.712	0.903	CLONAL	1	TRUE	1	0.28	2		654	782	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120861	94120861	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	166	670	0	ENST00000369303.4:c.190A>C	p.Asn64His	p.N64H	ENST00000369303	NM_004440.3	64	Aac/Cac	3/17	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.28	2		670	1177	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94129031	94129031	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	146	663	0	ENST00000369303.4:c.29G>A	p.Trp10Ter	p.W10*	ENST00000369303	NM_004440.3	10	tGg/tAg	1/17	1	2	FACETS	0.88	0.801	0.963	0.88	0.801	0.963	CLONAL	1	TRUE	1	0.28	2		663	1185	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111995759	111995759	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	188	643	0	ENST00000368678.4:c.1339T>C	p.Trp447Arg	p.W447R	ENST00000368678		447	Tgg/Cgg	12/13	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.28	2		643	1319	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708958	117708958	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	47	409	0	ENST00000368508.3:c.1999A>G	p.Thr667Ala	p.T667A	ENST00000368508	NM_002944.2	667	Act/Gct	13/43	1	2	FACETS	0.368	0.309	0.433	0.368	0.309	0.433	SUBCLONAL	1	TRUE	1	0.28	2		409	913	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525060	157525060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1215965074	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	178	520	2	ENST00000346085.5:c.4955C>T	p.Thr1652Met	p.T1652M	ENST00000346085	NM_020732.3	1652	aCg/aTg	19/20	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.28	2		522	1003	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528608	157528608	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	175	368	0	ENST00000346085.5:c.6333C>A	p.Phe2111Leu	p.F2111L	ENST00000346085	NM_020732.3	2111	ttC/ttA	20/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.28	2		368	915	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683697	162683697	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528661586	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	127	454	0	ENST00000366898.1:c.272C>T	p.Ala91Val	p.A91V	ENST00000366898	NM_004562.2	91	gCg/gTg	3/12	1	2	FACETS	0.968	0.876	1	0.968	0.876	1	CLONAL	1	TRUE	1	0.28	2		454	937	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739938	41739938	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	68	620	0	ENST00000242208.4:c.35C>T	p.Ala12Val	p.A12V	ENST00000242208	NM_002192.2	12	gCa/gTa	2/3	1	2	FACETS	0.392	0.34	0.45	0.392	0.34	0.45	SUBCLONAL	1	TRUE	1	0.28	2		620	1238	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450315	50450315	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	112	419	0	ENST00000331340.3:c.499C>T	p.His167Tyr	p.H167Y	ENST00000331340	NM_006060.4	167	Cat/Tat	5/8	1	2	FACETS	0.965	0.868	1	0.965	0.868	1	CLONAL	1	TRUE	1	0.28	2		419	829	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467738	50467738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1261826984	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	119	414	0	ENST00000331340.3:c.973G>A	p.Glu325Lys	p.E325K	ENST00000331340	NM_006060.4	325	Gag/Aag	8/8	1	2	FACETS	0.96	0.866	1	0.96	0.866	1	CLONAL	1	TRUE	1	0.28	2		414	885	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55087046	55087046	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	26	209	0	ENST00000275493.2:c.76G>A	p.Glu26Lys	p.E26K	ENST00000275493	NM_005228.3	26	Gag/Aag	1/28	1	2	FACETS	0.429	0.339	0.532	0.429	0.339	0.532	SUBCLONAL	1	TRUE	1	0.28	2		209	433	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266502	55266502	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1223694747	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	186	441	0	ENST00000275493.2:c.2794C>T	p.Arg932Cys	p.R932C	ENST00000275493	NM_005228.3	932	Cgc/Tgc	23/28	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.28	2		441	967	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335067	81335067	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	42	314	0	ENST00000222390.5:c.1760C>T	p.Pro587Leu	p.P587L	ENST00000222390	NM_000601.4	587	cCt/cTt	16/18	1	2	FACETS	0.664	0.554	0.785	0.664	0.554	0.785	SUBCLONAL	1	TRUE	1	0.28	2		314	452	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81359020	81359020	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	59	532	0	ENST00000222390.5:c.941G>A	p.Arg314Lys	p.R314K	ENST00000222390	NM_000601.4	314	aGg/aAg	8/18	1	2	FACETS	0.376	0.322	0.435	0.376	0.322	0.435	SUBCLONAL	1	TRUE	1	0.28	2		532	1121	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372695	81372695	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	117	489	0	ENST00000222390.5:c.839G>A	p.Trp280Ter	p.W280*	ENST00000222390	NM_000601.4	280	tGg/tAg	7/18	1	2	FACETS	0.813	0.732	0.899	0.813	0.732	0.899	CLONAL	1	TRUE	1	0.28	2		489	1028	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392036	81392036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	87	468	0	ENST00000222390.5:c.241C>T	p.Pro81Ser	p.P81S	ENST00000222390	NM_000601.4	81	Cca/Tca	2/18	1	2	FACETS	0.722	0.638	0.812	0.722	0.638	0.812	SUBCLONAL	1	TRUE	1	0.28	2		468	861	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81399269	81399269	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	82	258	0	ENST00000222390.5:c.19C>A	p.Leu7Met	p.L7M	ENST00000222390	NM_000601.4	7	Ctg/Atg	1/18	1	2	FACETS	0.877	0.773	0.988	0.877	0.773	0.988	CLONAL	1	TRUE	1	0.28	2		258	668	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411699	116411699	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	67	336	0	ENST00000397752.3:c.2878C>T	p.Gln960Ter	p.Q960*	ENST00000397752	NM_000245.2	960	Caa/Taa	13/21	1	2	FACETS	0.818	0.711	0.934	0.818	0.711	0.934	CLONAL	1	TRUE	1	0.28	2		336	585	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845415	151845415	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	56	408	1	ENST00000262189.6:c.13597C>T	p.Arg4533Ter	p.R4533*	ENST00000262189	NM_170606.2	4533	Cga/Tga	52/59	1	2	FACETS	0.411	0.351	0.477	0.411	0.351	0.477	SUBCLONAL	1	TRUE	1	0.28	2		409	973	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849994	151849994	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	117	311	0	ENST00000262189.6:c.12322C>T	p.Arg4108Ter	p.R4108*	ENST00000262189	NM_170606.2	4108	Cga/Tga	49/59	1	2	FACETS	0.982	0.885	1	0.982	0.885	1	CLONAL	1	TRUE	1	0.28	2		311	851	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151875048	151875048	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531219111	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	83	326	0	ENST00000262189.6:c.7490G>A	p.Arg2497His	p.R2497H	ENST00000262189	NM_170606.2	2497	cGc/cAc	38/59	1	2	FACETS	0.972	0.859	1	0.972	0.859	1	CLONAL	1	TRUE	1	0.28	2		326	610	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945085	151945085	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	21	174	0	ENST00000262189.6:c.2434A>G	p.Met812Val	p.M812V	ENST00000262189	NM_170606.2	812	Atg/Gtg	14/59	1	2	FACETS	0.521	0.401	0.66	0.521	0.401	0.66	SUBCLONAL	1	TRUE	1	0.28	2		174	288	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346419	152346419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	164	658	0	ENST00000359321.1:c.151G>A	p.Gly51Arg	p.G51R	ENST00000359321	NM_005431.1	51	Gga/Aga	3/3	1	2	FACETS	0.876	0.802	0.954	0.876	0.802	0.954	CLONAL	1	TRUE	1	0.28	2		658	1337	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38274856	38274856	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	120	466	0	ENST00000425967.3:c.1724T>C	p.Ile575Thr	p.I575T	ENST00000425967	NM_001174067.1	575	aTc/aCc	13/19	1	2	FACETS	0.868	0.783	0.959	0.868	0.783	0.959	CLONAL	1	TRUE	1	0.28	2		466	987	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38283643	38283643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs186746130	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	169	504	0	ENST00000425967.3:c.835G>A	p.Val279Met	p.V279M	ENST00000425967	NM_001174067.1	279	Gtg/Atg	7/19	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.28	2		504	1039	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285882	38285882	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs773225979	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	57	509	0	ENST00000425967.3:c.529A>G	p.Thr177Ala	p.T177A	ENST00000425967	NM_001174067.1	177	Acc/Gcc	5/19	1	2	FACETS	0.36	0.307	0.417	0.36	0.307	0.417	SUBCLONAL	1	TRUE	1	0.28	2		509	1132	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370933	55370933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	39	357	0	ENST00000297316.4:c.235G>A	p.Ala79Thr	p.A79T	ENST00000297316	NM_022454.3	79	Gct/Act	1/2	1	2	FACETS	0.372	0.307	0.445	0.372	0.307	0.445	SUBCLONAL	1	TRUE	1	0.28	2		357	749	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90994984	90994984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	44	384	0	ENST00000265433.3:c.137C>T	p.Ala46Val	p.A46V	ENST00000265433	NM_002485.4	46	gCt/gTt	2/16	1	2	FACETS	0.397	0.332	0.469	0.397	0.332	0.469	SUBCLONAL	1	TRUE	1	0.28	2		384	792	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737090	145737090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	47	352	0	ENST00000428558.2:c.3476C>T	p.Ala1159Val	p.A1159V	ENST00000428558	NM_004260.3	1159	gCt/gTt	21/22	1	2	FACETS	0.429	0.361	0.504	0.429	0.361	0.504	SUBCLONAL	1	TRUE	1	0.28	2		352	783	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739479	145739479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748941688	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	79	282	3	ENST00000428558.2:c.1891C>T	p.Arg631Cys	p.R631C	ENST00000428558	NM_004260.3	631	Cgc/Tgc	12/22	1	2	FACETS	0.916	0.806	1	0.916	0.806	1	CLONAL	1	TRUE	1	0.28	2		285	616	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5055753	5055753	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1294030432	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	89	457	0	ENST00000381652.3:c.1021G>A	p.Val341Ile	p.V341I	ENST00000381652	NM_004972.3	341	Gtt/Att	8/25	1	2	FACETS	0.934	0.828	1	0.934	0.828	1	CLONAL	1	TRUE	1	0.28	2		457	681	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069110	5069110	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	114	470	4	ENST00000381652.3:c.1415G>T	p.Ser472Ile	p.S472I	ENST00000381652	NM_004972.3	472	aGc/aTc	11/25	1	2	FACETS	0.897	0.807	0.992	0.897	0.807	0.992	CLONAL	1	TRUE	1	0.28	2		474	908	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8338983	8338983	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	124	515	2	ENST00000356435.5:c.5318C>T	p.Pro1773Leu	p.P1773L	ENST00000356435		1773	cCc/cTc	32/35	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.28	2		517	765	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8339013	8339013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	43	473	0	ENST00000356435.5:c.5288C>T	p.Ser1763Phe	p.S1763F	ENST00000356435		1763	tCt/tTt	32/35	1	2	FACETS	0.46	0.384	0.545	0.46	0.384	0.545	SUBCLONAL	1	TRUE	1	0.28	2		473	667	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971037	21971037	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs772527888	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	99	277	0	ENST00000579755.1:c.364C>T	p.Arg122Ter	p.R122*	ENST00000579755		122	Cga/Tga	2/3	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.28	2		277	554	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966674	36966674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	89	303	0	ENST00000358127.4:c.652G>A	p.Asp218Asn	p.D218N	ENST00000358127	NM_001280556.1	218	Gac/Aac	6/10	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.28	2		303	595	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336391	80336391	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	93	267	0	ENST00000286548.4:c.928C>A	p.Leu310Met	p.L310M	ENST00000286548	NM_002072.3	310	Ctg/Atg	7/7	1	2	FACETS	0.933	0.83	1	0.933	0.83	1	CLONAL	1	TRUE	1	0.28	2		267	712	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87475991	87475991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1052936605	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	104	473	0	ENST00000277120.3:c.1433G>A	p.Arg478Lys	p.R478K	ENST00000277120		478	aGa/aAa	13/19	1	2	FACETS	0.898	0.804	0.999	0.898	0.804	0.999	CLONAL	1	TRUE	1	0.28	2		473	827	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570254	87570254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747525829	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	86	197	0	ENST00000277120.3:c.1994C>T	p.Thr665Met	p.T665M	ENST00000277120		665	aCg/aTg	17/19	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.28	2		197	576	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606409	93606409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748600980	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	37	346	0	ENST00000375746.1:c.229G>A	p.Ala77Thr	p.A77T	ENST00000375746	NM_001174167.1	77	Gcc/Acc	2/14	1	2	FACETS	0.369	0.303	0.443	0.369	0.303	0.443	SUBCLONAL	1	TRUE	1	0.28	2		346	716	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639972	93639972	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	45	365	1	ENST00000375746.1:c.1301G>A	p.Arg434Gln	p.R434Q	ENST00000375746	NM_001174167.1	434	cGg/cAg	10/14	1	2	FACETS	0.432	0.362	0.51	0.432	0.362	0.51	SUBCLONAL	1	TRUE	1	0.28	2		366	744	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93657854	93657854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	113	358	0	ENST00000375746.1:c.1880G>A	p.Arg627His	p.R627H	ENST00000375746	NM_001174167.1	627	cGc/cAc	14/14	1	2	FACETS	0.951	0.855	1	0.951	0.855	1	CLONAL	1	TRUE	1	0.28	2		358	849	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97897683	97897683	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	129	515	3	ENST00000289081.3:c.788C>A	p.Ser263Tyr	p.S263Y	ENST00000289081	NM_000136.2	263	tCc/tAc	8/15	1	2	FACETS	0.856	0.774	0.942	0.856	0.774	0.942	CLONAL	1	TRUE	1	0.28	2		518	1077	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220314	98220314	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1420175816	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	83	301	1	ENST00000331920.6:c.3149C>T	p.Pro1050Leu	p.P1050L	ENST00000331920	NM_000264.3	1050	cCc/cTc	18/24	1	2	FACETS	0.871	0.768	0.98	0.871	0.768	0.98	CLONAL	1	TRUE	1	0.28	2		302	681	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229429	98229429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	161	598	0	ENST00000331920.6:c.2529G>A	p.Met843Ile	p.M843I	ENST00000331920	NM_000264.3	843	atG/atA	15/24	1	2	FACETS	0.971	0.889	1	0.971	0.889	1	CLONAL	1	TRUE	1	0.28	2		598	1184	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127911992	127911992	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1401828703	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	134	613	0	ENST00000373547.4:c.878G>A	p.Arg293His	p.R293H	ENST00000373547	NM_002721.4	293	cGt/cAt	7/7	1	2	FACETS	0.898	0.814	0.986	0.898	0.814	0.986	CLONAL	1	TRUE	1	0.28	2		613	1066	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393635	139393635	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	46	391	0	ENST00000277541.6:c.6011G>A	p.Arg2004His	p.R2004H	ENST00000277541	NM_017617.3	2004	cGc/cAc	32/34	1	2	FACETS	0.402	0.337	0.474	0.402	0.337	0.474	SUBCLONAL	1	TRUE	1	0.28	2		391	817	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396275	139396275	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	116	537	0	ENST00000277541.6:c.5563A>G	p.Met1855Val	p.M1855V	ENST00000277541	NM_017617.3	1855	Atg/Gtg	30/34	1	2	FACETS	0.883	0.795	0.977	0.883	0.795	0.977	CLONAL	1	TRUE	1	0.28	2		537	938	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397682	139397682	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1216073441	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	82	354	0	ENST00000277541.6:c.5119G>A	p.Ala1707Thr	p.A1707T	ENST00000277541	NM_017617.3	1707	Gcc/Acc	27/34	1	2	FACETS	0.901	0.795	1	0.901	0.795	1	CLONAL	1	TRUE	1	0.28	2		354	650	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410064	139410064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1472690723	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	113	379	0	ENST00000277541.6:c.1774C>T	p.Arg592Cys	p.R592C	ENST00000277541	NM_017617.3	592	Cgc/Tgc	11/34	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.28	2		379	799	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411813	139411813	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	119	492	0	ENST00000277541.6:c.1466T>C	p.Val489Ala	p.V489A	ENST00000277541	NM_017617.3	489	gTc/gCc	9/34	1	2	FACETS	0.974	0.878	1	0.974	0.878	1	CLONAL	1	TRUE	1	0.28	2		492	873	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601893	43601893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057521089	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	93	430	0	ENST00000355710.3:c.937C>T	p.Arg313Trp	p.R313W	ENST00000355710	NM_020975.4	313	Cgg/Tgg	5/20	1	2	FACETS	0.746	0.662	0.835	0.746	0.662	0.835	SUBCLONAL	1	TRUE	1	0.28	2		430	891	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606814	43606814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746512075	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	97	342	0	ENST00000355710.3:c.1423C>T	p.Arg475Trp	p.R475W	ENST00000355710	NM_020975.4	475	Cgg/Tgg	7/20	1	2	FACETS	0.944	0.842	1	0.944	0.842	1	CLONAL	1	TRUE	1	0.28	2		342	734	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852457	63852457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	111	392	0	ENST00000279873.7:c.3235C>T	p.Pro1079Ser	p.P1079S	ENST00000279873	NM_032199.2	1079	Cca/Tca	10/10	1	2	FACETS	0.852	0.765	0.944	0.852	0.765	0.944	CLONAL	1	TRUE	1	0.28	2		392	931	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70411641	70411641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	70	484	0	ENST00000373644.4:c.4315C>T	p.His1439Tyr	p.H1439Y	ENST00000373644	NM_030625.2	1439	Cac/Tac	5/12	1	2	FACETS	0.482	0.418	0.55	0.482	0.418	0.55	SUBCLONAL	1	TRUE	1	0.28	2		484	1038	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681434	88681434	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782496	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	86	277	0	ENST00000372037.3:c.1324C>T	p.Arg442Cys	p.R442C	ENST00000372037	NM_004329.2	442	Cgt/Tgt	11/13	1	2	FACETS	0.924	0.818	1	0.924	0.818	1	CLONAL	1	TRUE	1	0.28	2		277	665	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910824	114910824	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1319	188	774	1	ENST00000543371.1:c.943G>T	p.Val315Phe	p.V315F	ENST00000543371	NM_001198531.1	315	Gtc/Ttc	9/14	1	2	FACETS	0.891	0.821	0.965	0.891	0.821	0.965	CLONAL	1	TRUE	1	0.28	2		775	1507	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123260450	123260450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	42	360	0	ENST00000358487.5:c.1451G>A	p.Gly484Asp	p.G484D	ENST00000358487	NM_000141.4	484	gGc/gAc	11/18	1	2	FACETS	0.363	0.302	0.432	0.363	0.302	0.432	SUBCLONAL	1	TRUE	1	0.28	2		360	826	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533838	533838	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	139	471	0	ENST00000451590.1:c.218G>A	p.Arg73His	p.R73H	ENST00000451590	NM_001130442.1	73	cGc/cAc	3/5	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.28	2		471	991	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894230	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	17	218	0	ENST00000451590.1:c.35G>A	p.Gly12Asp	p.G12D	ENST00000451590	NM_001130442.1	12	gGc/gAc	2/5	1	2	FACETS	0.152	0.113	0.2	0.152	0.113	0.2	SUBCLONAL	1	TRUE	1	0.28	2		218	798	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8248580	8248580	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772724227	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	117	463	0	ENST00000335790.3:c.307C>T	p.Arg103Trp	p.R103W	ENST00000335790	NM_002315.2	103	Cgg/Tgg	3/4	1	2	FACETS	0.916	0.825	1	0.916	0.825	1	CLONAL	1	TRUE	1	0.28	2		463	912	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741577	17741577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758659312	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	26	205	1	ENST00000250003.3:c.248C>T	p.Ala83Val	p.A83V	ENST00000250003	NM_002478.4	83	gCg/gTg	1/3	1	2	FACETS	0.416	0.329	0.517	0.416	0.329	0.517	SUBCLONAL	1	TRUE	1	0.28	2		206	446	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456425	32456425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1201988298	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	32	312	0	ENST00000332351.3:c.467G>A	p.Cys156Tyr	p.C156Y	ENST00000332351	NM_024426.4	156	tGc/tAc	1/10	1	2	FACETS	0.375	0.303	0.456	0.375	0.303	0.456	SUBCLONAL	1	TRUE	1	0.28	2		312	610	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136070	64136070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	26	200	0	ENST00000334205.4:c.1331G>A	p.Arg444His	p.R444H	ENST00000334205	NM_003942.2	444	cGc/cAc	11/17	1	2	FACETS	0.366	0.289	0.455	0.366	0.289	0.455	SUBCLONAL	1	TRUE	1	0.28	2		200	507	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571919	64571919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1280	202	735	0	ENST00000312049.6:c.1720G>A	p.Ala574Thr	p.A574T	ENST00000312049	NM_130799.2	574	Gcc/Acc	10/10	1	2	FACETS	0.974	0.9	1	0.974	0.9	1	CLONAL	1	TRUE	1	0.28	2		735	1482	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998235	100998235	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	84	327	0	ENST00000325455.5:c.1567C>A	p.Leu523Ile	p.L523I	ENST00000325455	NM_001202474.3	523	Ctc/Atc	1/8	1	2	FACETS	0.974	0.861	1	0.974	0.861	1	CLONAL	1	TRUE	1	0.28	2		327	616	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201802	102201802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1222	68	655	0	ENST00000263464.3:c.1154C>T	p.Ala385Val	p.A385V	ENST00000263464	NM_001165.4	385	gCc/gTc	6/9	1	2	FACETS	0.377	0.326	0.432	0.377	0.326	0.432	SUBCLONAL	1	TRUE	1	0.28	2		655	1290	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206865	102206865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138752976	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1391	207	792	1	ENST00000263464.3:c.1493C>T	p.Thr498Met	p.T498M	ENST00000263464	NM_001165.4	498	aCg/aTg	7/9	1	2	FACETS	0.925	0.856	0.998	0.925	0.856	0.998	CLONAL	1	TRUE	1	0.28	2		793	1598	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170456	108170456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555104518	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	111	407	0	ENST00000278616.4:c.5021G>A	p.Cys1674Tyr	p.C1674Y	ENST00000278616	NM_000051.3	1674	tGc/tAc	34/63	1	2	FACETS	0.872	0.783	0.967	0.872	0.783	0.967	CLONAL	1	TRUE	1	0.28	2		407	909	SUCCESS
ATM	472	MSKCC	GRCh37	11	108180936	108180936	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	100	458	0	ENST00000278616.4:c.5812T>C	p.Tyr1938His	p.Y1938H	ENST00000278616	NM_000051.3	1938	Tat/Cat	39/63	1	2	FACETS	0.849	0.758	0.947	0.849	0.758	0.947	CLONAL	1	TRUE	1	0.28	2		458	841	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198407	108198407	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs878853536	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	129	394	0	ENST00000278616.4:c.7011T>G	p.Cys2337Trp	p.C2337W	ENST00000278616	NM_000051.3	2337	tgT/tgG	48/63	1	2	FACETS	0.99	0.897	1	0.99	0.897	1	CLONAL	1	TRUE	1	0.28	2		394	931	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111959611	111959611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1199609768	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	102	319	0	ENST00000375549.3:c.190C>T	p.Leu64Phe	p.L64F	ENST00000375549	NM_003002.3	64	Ctc/Ttc	3/4	1	2	FACETS	0.959	0.857	1	0.959	0.857	1	CLONAL	1	TRUE	1	0.28	2		319	760	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118369112	118369112	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	101	361	0	ENST00000534358.1:c.5830G>A	p.Ala1944Thr	p.A1944T	ENST00000534358	NM_005933.3	1944	Gcc/Acc	22/36	1	2	FACETS	0.98	0.876	1	0.98	0.876	1	CLONAL	1	TRUE	1	0.28	2		361	736	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552618	18552618	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	135	427	0	ENST00000266497.5:c.2029T>G	p.Leu677Val	p.L677V	ENST00000266497		677	Tta/Gta	14/31	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.28	2		427	955	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650629	18650629	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	66	402	0	ENST00000266497.5:c.2840G>A	p.Gly947Asp	p.G947D	ENST00000266497		947	gGc/gAc	20/31	1	2	FACETS	0.802	0.696	0.916	0.802	0.696	0.916	CLONAL	1	TRUE	1	0.28	2		402	588	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398207	25398207	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	89	449	0	ENST00000311936.3:c.111+1G>A		p.X37_splice	ENST00000311936	NM_004985.3	37			1	2	FACETS	0.854	0.757	0.958	0.854	0.757	0.958	CLONAL	1	TRUE	1	0.28	2		449	744	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944829	31944829	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	162	644	1	ENST00000340398.3:c.272C>T	p.Ala91Val	p.A91V	ENST00000340398	NM_001013699.2	91	gCg/gTg	1/1	1	2	FACETS	0.887	0.811	0.966	0.887	0.811	0.966	CLONAL	1	TRUE	1	0.28	2		645	1305	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418699	49418699	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	87	353	0	ENST00000301067.7:c.15815C>G	p.Ala5272Gly	p.A5272G	ENST00000301067	NM_003482.3	5272	gCt/gGt	49/54	1	2	FACETS	0.858	0.76	0.964	0.858	0.76	0.964	CLONAL	1	TRUE	1	0.28	2		353	724	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420108	49420108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123729	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	131	516	1	ENST00000301067.7:c.15641G>A	p.Arg5214His	p.R5214H	ENST00000301067	NM_003482.3	5214	cGc/cAc	48/54	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.28	2		517	935	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425124	49425124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372839823	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	146	513	0	ENST00000301067.7:c.13364G>A	p.Arg4455His	p.R4455H	ENST00000301067	NM_003482.3	4455	cGc/cAc	39/54	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.28	2		513	1031	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433319	49433319	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	116	279	0	ENST00000301067.7:c.8128G>A	p.Ala2710Thr	p.A2710T	ENST00000301067	NM_003482.3	2710	Gct/Act	32/54	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.28	2		279	648	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434444	49434444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373234419	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	64	225	0	ENST00000301067.7:c.7109G>A	p.Arg2370His	p.R2370H	ENST00000301067	NM_003482.3	2370	cGc/cAc	31/54	1	2	FACETS	0.83	0.719	0.95	0.83	0.719	0.95	CLONAL	1	TRUE	1	0.28	2		225	551	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437701	49437701	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555194045	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	235	591	2	ENST00000301067.7:c.5269C>T	p.Arg1757Ter	p.R1757*	ENST00000301067	NM_003482.3	1757	Cga/Tga	22/54	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.28	2		593	1236	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443758	49443758	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748757592	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	50	450	0	ENST00000301067.7:c.3613G>A	p.Val1205Ile	p.V1205I	ENST00000301067	NM_003482.3	1205	Gtt/Att	11/54	1	2	FACETS	0.357	0.302	0.419	0.357	0.302	0.419	SUBCLONAL	1	TRUE	1	0.28	2		450	1000	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448200	49448200	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	137	425	0	ENST00000301067.7:c.401-1G>T		p.X134_splice	ENST00000301067	NM_003482.3	134			1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.28	2		425	960	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448713	49448713	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	132	426	3	ENST00000301067.7:c.146C>A	p.Pro49His	p.P49H	ENST00000301067	NM_003482.3	49	cCc/cAc	2/54	1	2	FACETS	0.957	0.868	1	0.957	0.868	1	CLONAL	1	TRUE	1	0.28	2		429	985	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480110	50480110	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376164103	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	103	322	0	ENST00000394963.4:c.344C>T	p.Ala115Val	p.A115V	ENST00000394963	NM_003076.4	115	gCg/gTg	2/13	1	2	FACETS	0.973	0.871	1	0.973	0.871	1	CLONAL	1	TRUE	1	0.28	2		322	756	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50482386	50482386	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	125	449	0	ENST00000394963.4:c.737A>G	p.Lys246Arg	p.K246R	ENST00000394963	NM_003076.4	246	aAa/aGa	6/13	1	2	FACETS	0.945	0.854	1	0.945	0.854	1	CLONAL	1	TRUE	1	0.28	2		449	945	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489541	56489541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772747085	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	94	411	0	ENST00000267101.3:c.2006G>A	p.Arg669His	p.R669H	ENST00000267101	NM_001982.3	669	cGc/cAc	17/28	1	2	FACETS	0.832	0.74	0.931	0.832	0.74	0.931	CLONAL	1	TRUE	1	0.28	2		411	807	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861940	57861940	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775972834	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	71	614	0	ENST00000228682.2:c.1241C>T	p.Pro414Leu	p.P414L	ENST00000228682	NM_005269.2	414	cCc/cTc	10/12	1	2	FACETS	0.419	0.365	0.479	0.419	0.365	0.479	SUBCLONAL	1	TRUE	1	0.28	2		614	1209	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864622	57864622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1242	189	623	1	ENST00000228682.2:c.2099C>T	p.Ala700Val	p.A700V	ENST00000228682	NM_005269.2	700	gCt/gTt	12/12	1	2	FACETS	0.943	0.869	1	0.943	0.869	1	CLONAL	1	TRUE	1	0.28	2		624	1431	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143000	58143000	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	101	392	0	ENST00000257904.6:c.784C>T	p.Pro262Ser	p.P262S	ENST00000257904	NM_000075.3	262	Cct/Tct	7/8	1	2	FACETS	0.918	0.82	1	0.918	0.82	1	CLONAL	1	TRUE	1	0.28	2		392	786	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416800	121416800	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770695671	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	108	525	0	ENST00000257555.6:c.229G>A	p.Asp77Asn	p.D77N	ENST00000257555		77	Gat/Aat	1/10	1	2	FACETS	0.808	0.724	0.897	0.808	0.724	0.897	CLONAL	1	TRUE	1	0.28	2		525	955	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214643	133214643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767012802	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	92	376	0	ENST00000320574.5:c.5635C>T	p.Arg1879Cys	p.R1879C	ENST00000320574	NM_006231.2	1879	Cgt/Tgt	41/49	1	2	FACETS	0.818	0.727	0.917	0.818	0.727	0.917	CLONAL	1	TRUE	1	0.28	2		376	803	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133214646	133214646	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199979862	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	136	381	1	ENST00000320574.5:c.5632C>T	p.Arg1878Cys	p.R1878C	ENST00000320574	NM_006231.2	1878	Cgc/Tgc	41/49	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.28	2		382	809	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226041	133226041	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373170535	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	113	346	0	ENST00000320574.5:c.3856C>T	p.Arg1286Cys	p.R1286C	ENST00000320574	NM_006231.2	1286	Cgc/Tgc	31/49	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.28	2		346	770	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248860	133248860	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs116260568	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	196	429	0	ENST00000320574.5:c.1735C>T	p.Arg579Cys	p.R579C	ENST00000320574	NM_006231.2	579	Cgc/Tgc	16/49	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.28	2		429	995	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250213	133250213	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	183	491	1	ENST00000320574.5:c.1307C>A	p.Pro436His	p.P436H	ENST00000320574	NM_006231.2	436	cCc/cAc	13/49	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.28	2		492	987	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133256623	133256623	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555230189	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	118	519	1	ENST00000320574.5:c.340C>T	p.Arg114Ter	p.R114*	ENST00000320574	NM_006231.2	114	Cga/Tga	5/49	1	2	FACETS	0.835	0.752	0.923	0.835	0.752	0.923	CLONAL	1	TRUE	1	0.28	2		520	1010	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562477	21562477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757658067	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	26	54	0	ENST00000382592.4:c.1442C>T	p.Ala481Val	p.A481V	ENST00000382592	NM_014572.2	481	gCg/gTg	4/8	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.28	2		54	161	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967513	26967513	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	105	452	0	ENST00000381527.3:c.656C>A	p.Ala219Asp	p.A219D	ENST00000381527	NM_001260.1	219	gCt/gAt	7/13	1	2	FACETS	0.9	0.806	1	0.9	0.806	1	CLONAL	1	TRUE	1	0.28	2		452	833	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592707	28592707	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	115	416	0	ENST00000241453.7:c.2438C>T	p.Ala813Val	p.A813V	ENST00000241453	NM_004119.2	813	gCc/gTc	20/24	1	2	FACETS	0.983	0.885	1	0.983	0.885	1	CLONAL	1	TRUE	1	0.28	2		416	836	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896980	28896980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371199947	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	111	493	1	ENST00000282397.4:c.2900C>T	p.Ala967Val	p.A967V	ENST00000282397	NM_002019.4	967	gCg/gTg	21/30	1	2	FACETS	0.825	0.74	0.915	0.825	0.74	0.915	CLONAL	1	TRUE	1	0.28	2		494	961	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28931793	28931793	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	111	443	0	ENST00000282397.4:c.2146C>A	p.Leu716Met	p.L716M	ENST00000282397	NM_002019.4	716	Ctg/Atg	15/30	1	2	FACETS	0.817	0.733	0.906	0.817	0.733	0.906	CLONAL	1	TRUE	1	0.28	2		443	971	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906958	32906958	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358423	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	40	297	0	ENST00000380152.3:c.1343G>A	p.Arg448His	p.R448H	ENST00000380152		448	cGt/cAt	10/27	1	2	FACETS	0.432	0.358	0.515	0.432	0.358	0.515	SUBCLONAL	1	TRUE	1	0.28	2		297	661	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911711	32911711	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	138	821	2	ENST00000380152.3:c.3219G>T	p.Gln1073His	p.Q1073H	ENST00000380152		1073	caG/caT	11/27	1	2	FACETS	0.867	0.787	0.951	0.867	0.787	0.951	CLONAL	1	TRUE	1	0.28	2		823	1137	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913023	32913023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376338226	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	131	807	1	ENST00000380152.3:c.4531G>A	p.Glu1511Lys	p.E1511K	ENST00000380152		1511	Gaa/Aaa	11/27	1	2	FACETS	0.912	0.826	1	0.912	0.826	1	CLONAL	1	TRUE	1	0.28	2		808	1026	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134123	41134123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751383976	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	263	632	0	ENST00000379561.5:c.1505C>T	p.Ser502Leu	p.S502L	ENST00000379561	NM_002015.3	502	tCg/tTg	2/3	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.28	2		632	1354	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73349479	73349479	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	90	420	0	ENST00000377767.4:c.857C>A	p.Ala286Asp	p.A286D	ENST00000377767	NM_014953.3	286	gCt/gAt	6/21	1	2	FACETS	0.976	0.866	1	0.976	0.866	1	CLONAL	1	TRUE	1	0.28	2		420	659	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103498677	103498677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	103	457	0	ENST00000355739.4:c.61G>A	p.Ala21Thr	p.A21T	ENST00000355739	NM_000123.3	21	Gcg/Acg	1/15	1	2	FACETS	0.756	0.675	0.842	0.756	0.675	0.842	SUBCLONAL	1	TRUE	1	0.28	2		457	973	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504571	103504571	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	116	563	0	ENST00000355739.4:c.192A>C	p.Lys64Asn	p.K64N	ENST00000355739	NM_000123.3	64	aaA/aaC	2/15	1	2	FACETS	0.792	0.712	0.877	0.792	0.712	0.877	SUBCLONAL	1	TRUE	1	0.28	2		563	1046	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103508412	103508412	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	96	293	0	ENST00000355739.4:c.478G>A	p.Glu160Lys	p.E160K	ENST00000355739	NM_000123.3	160	Gaa/Aaa	5/15	1	2	FACETS	0.982	0.876	1	0.982	0.876	1	CLONAL	1	TRUE	1	0.28	2		293	698	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436706	110436706	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	98	334	0	ENST00000375856.3:c.1695G>T	p.Gln565His	p.Q565H	ENST00000375856	NM_003749.2	565	caG/caT	1/2	1	2	FACETS	0.896	0.799	1	0.896	0.799	1	CLONAL	1	TRUE	1	0.28	2		334	781	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438184	110438184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	27	153	0	ENST00000375856.3:c.217C>T	p.Leu73Phe	p.L73F	ENST00000375856	NM_003749.2	73	Ctc/Ttc	1/2	1	2	FACETS	0.745	0.595	0.915	0.745	0.595	0.915	CLONAL	1	TRUE	1	0.28	2		153	259	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872524	35872524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377380656	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	247	605	2	ENST00000216797.5:c.379G>A	p.Ala127Thr	p.A127T	ENST00000216797	NM_020529.2	127	Gct/Act	3/6	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.28	2		607	1286	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986503	36986503	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	45	449	0	ENST00000354822.5:c.1186C>A	p.Leu396Ile	p.L396I	ENST00000354822	NM_001079668.2	396	Cta/Ata	3/3	1	2	FACETS	0.392	0.329	0.464	0.392	0.329	0.464	SUBCLONAL	1	TRUE	1	0.28	2		449	819	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987144	36987144	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	31	216	0	ENST00000354822.5:c.545A>G	p.Asn182Ser	p.N182S	ENST00000354822	NM_001079668.2	182	aAc/aGc	3/3	1	2	FACETS	0.403	0.325	0.491	0.403	0.325	0.491	SUBCLONAL	1	TRUE	1	0.28	2		216	550	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569756	95569756	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	45	410	1	ENST00000393063.1:c.3977C>T	p.Ala1326Val	p.A1326V	ENST00000393063	NM_030621.3	1326	gCc/gTc	22/28	1	2	FACETS	0.361	0.302	0.426	0.361	0.302	0.426	SUBCLONAL	1	TRUE	1	0.28	2		411	891	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570213	95570213	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	123	438	0	ENST00000393063.1:c.3520G>T	p.Ala1174Ser	p.A1174S	ENST00000393063	NM_030621.3	1174	Gca/Tca	22/28	1	2	FACETS	0.928	0.838	1	0.928	0.838	1	CLONAL	1	TRUE	1	0.28	2		438	947	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574771	95574771	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	130	468	0	ENST00000393063.1:c.2326G>A	p.Val776Ile	p.V776I	ENST00000393063	NM_030621.3	776	Gtt/Att	16/28	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.28	2		468	918	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246427	105246427	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	131	436	1	ENST00000349310.3:c.173C>T	p.Ala58Val	p.A58V	ENST00000349310	NM_001014432.1	58	gCg/gTg	4/15	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.28	2		437	911	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022941	33022941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1188	164	675	0	ENST00000300177.4:c.50C>T	p.Thr17Ile	p.T17I	ENST00000300177	NM_001191322.1	17	aCc/aTc	2/2	1	2	FACETS	0.866	0.793	0.943	0.866	0.793	0.943	CLONAL	1	TRUE	1	0.28	2		675	1352	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961108	41961108	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	153	586	0	ENST00000219905.7:c.16C>T	p.Gln6Ter	p.Q6*	ENST00000219905	NM_001164273.1	6	Cag/Tag	2/24	1	2	FACETS	0.973	0.889	1	0.973	0.889	1	CLONAL	1	TRUE	1	0.28	2		586	1123	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991139	41991139	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	163	549	0	ENST00000219905.7:c.2092G>T	p.Gly698Cys	p.G698C	ENST00000219905	NM_001164273.1	698	Ggt/Tgt	4/24	1	2	FACETS	0.92	0.843	1	0.92	0.843	1	CLONAL	1	TRUE	1	0.28	2		549	1265	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007743	45007743	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	113	426	1	ENST00000558401.1:c.190G>T	p.Glu64Ter	p.E64*	ENST00000558401	NM_004048.2	64	Gag/Tag	2/4	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.28	2		427	714	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66777400	66777400	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	142	478	0	ENST00000307102.5:c.766A>C	p.Met256Leu	p.M256L	ENST00000307102	NM_002755.3	256	Atg/Ctg	7/11	1	2	FACETS	0.972	0.884	1	0.972	0.884	1	CLONAL	1	TRUE	1	0.28	2		478	1044	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423587	88423587	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1366437707	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	124	480	0	ENST00000360948.2:c.2248G>A	p.Glu750Lys	p.E750K	ENST00000360948	NM_001012338.2	750	Gag/Aag	18/19	1	2	FACETS	0.873	0.788	0.962	0.873	0.788	0.962	CLONAL	1	TRUE	1	0.28	2		480	1015	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354465	91354465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	95	319	0	ENST00000355112.3:c.3905C>T	p.Ser1302Phe	p.S1302F	ENST00000355112	NM_000057.2	1302	tCc/tTc	21/22	1	2	FACETS	0.898	0.799	1	0.898	0.799	1	CLONAL	1	TRUE	1	0.28	2		319	756	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434791	99434791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	42	397	0	ENST00000268035.6:c.878C>T	p.Ser293Phe	p.S293F	ENST00000268035	NM_000875.3	293	tCc/tTc	3/21	1	2	FACETS	0.375	0.312	0.446	0.375	0.312	0.446	SUBCLONAL	1	TRUE	1	0.28	2		397	800	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442709	99442709	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1567185393	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	113	355	0	ENST00000268035.6:c.1106A>G	p.Asn369Ser	p.N369S	ENST00000268035	NM_000875.3	369	aAc/aGc	5/21	1	2	FACETS	0.96	0.863	1	0.96	0.863	1	CLONAL	1	TRUE	1	0.28	2		355	841	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478173	99478173	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	114	390	0	ENST00000268035.6:c.3077C>A	p.Pro1026His	p.P1026H	ENST00000268035	NM_000875.3	1026	cCt/cAt	16/21	1	2	FACETS	0.956	0.86	1	0.956	0.86	1	CLONAL	1	TRUE	1	0.28	2		390	852	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478237	99478237	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	101	259	0	ENST00000268035.6:c.3141T>G	p.Phe1047Leu	p.F1047L	ENST00000268035	NM_000875.3	1047	ttT/ttG	16/21	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.28	2		259	586	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2213953	2213953	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759408599	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	119	520	1	ENST00000326181.6:c.32G>A	p.Arg11His	p.R11H	ENST00000326181	NM_032271.2	11	cGc/cAc	2/21	1	2	FACETS	0.826	0.744	0.913	0.826	0.744	0.913	CLONAL	1	TRUE	1	0.28	2		521	1029	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221579	2221579	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	115	449	0	ENST00000326181.6:c.448T>C	p.Phe150Leu	p.F150L	ENST00000326181	NM_032271.2	150	Ttc/Ctc	7/21	1	2	FACETS	0.828	0.745	0.917	0.828	0.745	0.917	CLONAL	1	TRUE	1	0.28	2		449	992	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222281	2222281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1268399486	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	54	490	0	ENST00000326181.6:c.565C>T	p.Arg189Trp	p.R189W	ENST00000326181	NM_032271.2	189	Cgg/Tgg	8/21	1	2	FACETS	0.407	0.346	0.474	0.407	0.346	0.474	SUBCLONAL	1	TRUE	1	0.28	2		490	948	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778852	3778852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479729612	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	94	281	0	ENST00000262367.5:c.6196G>A	p.Ala2066Thr	p.A2066T	ENST00000262367	NM_004380.2	2066	Gct/Act	31/31	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.28	2		281	659	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788668	3788668	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	95	437	0	ENST00000262367.5:c.4286T>C	p.Val1429Ala	p.V1429A	ENST00000262367	NM_004380.2	1429	gTg/gCg	26/31	1	2	FACETS	0.737	0.655	0.824	0.737	0.655	0.824	SUBCLONAL	1	TRUE	1	0.28	2		437	921	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823855	3823855	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs117910358	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	107	404	0	ENST00000262367.5:c.2360C>T	p.Ala787Val	p.A787V	ENST00000262367	NM_004380.2	787	gCg/gTg	13/31	1	2	FACETS	0.808	0.724	0.898	0.808	0.724	0.898	CLONAL	1	TRUE	1	0.28	2		404	946	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024666	14024666	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	204	532	0	ENST00000311895.7:c.892C>A	p.Leu298Ile	p.L298I	ENST00000311895	NM_005236.2	298	Ctc/Atc	5/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.28	2		532	1016	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647440	23647440	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	140	509	1	ENST00000261584.4:c.427C>A	p.Leu143Met	p.L143M	ENST00000261584	NM_024675.3	143	Ctg/Atg	4/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.28	2		510	888	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133204	30133204	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	176	578	0	ENST00000263025.4:c.294G>T	p.Glu98Asp	p.E98D	ENST00000263025	NM_002746.2	98	gaG/gaT	2/9	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.28	2		578	1209	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645069	67645069	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	142	446	0	ENST00000264010.4:c.334G>T	p.Glu112Ter	p.E112*	ENST00000264010	NM_006565.3	112	Gaa/Taa	3/12	1	2	FACETS	0.852	0.775	0.934	0.852	0.775	0.934	CLONAL	1	TRUE	1	0.28	2		446	1190	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663385	67663385	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377088539	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	125	437	0	ENST00000264010.4:c.1786C>T	p.Arg596Cys	p.R596C	ENST00000264010	NM_006565.3	596	Cgt/Tgt	10/12	1	2	FACETS	0.866	0.782	0.954	0.866	0.782	0.954	CLONAL	1	TRUE	1	0.28	2		437	1031	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821772	72821772	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754322025	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	70	582	0	ENST00000268489.5:c.10403G>A	p.Arg3468His	p.R3468H	ENST00000268489	NM_006885.3	3468	cGc/cAc	10/10	1	2	FACETS	0.446	0.388	0.51	0.446	0.388	0.51	SUBCLONAL	1	TRUE	1	0.28	2		582	1120	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829973	72829973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200698025	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	241	670	1	ENST00000268489.5:c.6608G>A	p.Arg2203His	p.R2203H	ENST00000268489	NM_006885.3	2203	cGt/cAt	9/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.28	2		671	1394	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830695	72830695	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1266	215	818	0	ENST00000268489.5:c.5886G>T	p.Glu1962Asp	p.E1962D	ENST00000268489	NM_006885.3	1962	gaG/gaT	9/10	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.28	2		818	1481	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831701	72831701	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	177	691	0	ENST00000268489.5:c.4880C>T	p.Ala1627Val	p.A1627V	ENST00000268489	NM_006885.3	1627	gCc/gTc	9/10	1	2	FACETS	0.937	0.861	1	0.937	0.861	1	CLONAL	1	TRUE	1	0.28	2		691	1349	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831764	72831764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1282	187	783	0	ENST00000268489.5:c.4817G>A	p.Ser1606Asn	p.S1606N	ENST00000268489	NM_006885.3	1606	aGc/aAc	9/10	1	2	FACETS	0.909	0.837	0.985	0.909	0.837	0.985	CLONAL	1	TRUE	1	0.28	2		783	1469	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993849	72993849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758323451	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	86	407	0	ENST00000268489.5:c.196G>A	p.Ala66Thr	p.A66T	ENST00000268489	NM_006885.3	66	Gcg/Acg	2/10	1	2	FACETS	0.751	0.663	0.845	0.751	0.663	0.845	SUBCLONAL	1	TRUE	1	0.28	2		407	818	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81972509	81972509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755617580	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	172	624	1	ENST00000359376.3:c.3302C>T	p.Thr1101Met	p.T1101M	ENST00000359376	NM_002661.3	1101	aCg/aTg	29/33	1	2	FACETS	0.956	0.878	1	0.956	0.878	1	CLONAL	1	TRUE	1	0.28	2		625	1285	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346153	89346153	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748996527	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	63	252	0	ENST00000301030.4:c.6797C>T	p.Ala2266Val	p.A2266V	ENST00000301030	NM_001256183.1	2266	gCg/gTg	9/13	1	2	FACETS	0.907	0.786	1	0.907	0.786	1	CLONAL	1	TRUE	1	0.28	2		252	496	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572957	7572957	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	148	533	0	ENST00000269305.4:c.1152G>A	p.Met384Ile	p.M384I	ENST00000269305	NM_001126112.2	384	atG/atA	11/11	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.28	2		533	977	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979661	7979661	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1053727821	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	66	283	0	ENST00000319144.4:c.1364G>A	p.Gly455Asp	p.G455D	ENST00000319144	NM_001139.2	455	gGc/gAc	11/15	1	2	FACETS	0.74	0.642	0.846	0.74	0.642	0.846	SUBCLONAL	1	TRUE	1	0.28	2		283	637	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979663	7979663	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	118	284	0	ENST00000319144.4:c.1363-1G>T		p.X455_splice	ENST00000319144	NM_001139.2	455			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.28	2		284	628	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110098	8110098	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	114	265	0	ENST00000585124.1:c.507C>A	p.Ser169Arg	p.S169R	ENST00000585124	NM_004217.3	169	agC/agA	6/9	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.28	2		265	685	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028632	12028632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753665559	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	217	624	1	ENST00000353533.5:c.835G>A	p.Ala279Thr	p.A279T	ENST00000353533	NM_003010.3	279	Gca/Aca	8/11	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.28	2		625	1038	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983936	15983936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	91	393	0	ENST00000268712.3:c.3283G>A	p.Glu1095Lys	p.E1095K	ENST00000268712	NM_006311.3	1095	Gaa/Aaa	24/46	1	2	FACETS	0.876	0.778	0.981	0.876	0.778	0.981	CLONAL	1	TRUE	1	0.28	2		393	742	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131277	17131277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778275358	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	149	522	1	ENST00000285071.4:c.175C>T	p.Arg59Cys	p.R59C	ENST00000285071	NM_144997.5	59	Cgt/Tgt	4/14	1	2	FACETS	0.898	0.819	0.982	0.898	0.819	0.982	CLONAL	1	TRUE	1	0.28	2		523	1185	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586148	29586148	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs773151680	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	27	281	0	ENST00000356175.3:c.4367+1G>A		p.X1456_splice	ENST00000356175	NM_000267.3	1456			1	2	FACETS	0.433	0.344	0.536	0.433	0.344	0.536	SUBCLONAL	1	TRUE	1	0.28	2		281	445	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654636	29654636	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	141	495	0	ENST00000356175.3:c.5325G>T	p.Glu1775Asp	p.E1775D	ENST00000356175	NM_000267.3	1775	gaG/gaT	37/57	1	2	FACETS	0.898	0.816	0.984	0.898	0.816	0.984	CLONAL	1	TRUE	1	0.28	2		495	1122	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663821	29663821	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755791578	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	115	534	0	ENST00000356175.3:c.6253G>A	p.Val2085Ile	p.V2085I	ENST00000356175	NM_000267.3	2085	Gtt/Att	41/57	1	2	FACETS	0.883	0.795	0.977	0.883	0.795	0.977	CLONAL	1	TRUE	1	0.28	2		534	930	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677303	29677303	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	105	499	0	ENST00000356175.3:c.7361C>A	p.Thr2454Lys	p.T2454K	ENST00000356175	NM_000267.3	2454	aCa/aAa	49/57	1	2	FACETS	0.924	0.827	1	0.924	0.827	1	CLONAL	1	TRUE	1	0.28	2		499	812	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33430286	33430286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	168	565	0	ENST00000345365.6:c.725G>A	p.Gly242Asp	p.G242D	ENST00000345365	NM_002878.3	242	gGc/gAc	8/10	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.28	2		565	1195	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37673787	37673787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1300041019	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	96	362	0	ENST00000447079.4:c.2941C>T	p.Arg981Cys	p.R981C	ENST00000447079	NM_015083.1	981	Cgt/Tgt	10/14	1	2	FACETS	0.832	0.741	0.93	0.832	0.741	0.93	CLONAL	1	TRUE	1	0.28	2		362	824	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37873620	37873620	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	143	522	2	ENST00000269571.5:c.1785C>A	p.Phe595Leu	p.F595L	ENST00000269571		595	ttC/ttA	15/27	1	2	FACETS	0.922	0.839	1	0.922	0.839	1	CLONAL	1	TRUE	1	0.28	2		524	1108	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879858	37879858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	108	362	1	ENST00000269571.5:c.2153C>T	p.Thr718Met	p.T718M	ENST00000269571		718	aCg/aTg	18/27	1	2	FACETS	0.949	0.851	1	0.949	0.851	1	CLONAL	1	TRUE	1	0.28	2		363	813	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512383	38512383	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1188389540	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	55	246	2	ENST00000254066.5:c.1294C>T	p.Arg432Trp	p.R432W	ENST00000254066	NM_000964.3	432	Cgg/Tgg	9/9	1	2	FACETS	0.764	0.654	0.885	0.764	0.654	0.885	SUBCLONAL	1	TRUE	1	0.28	2		248	514	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362303	40362303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	157	596	0	ENST00000293328.3:c.1792G>A	p.Val598Ile	p.V598I	ENST00000293328	NM_012448.3	598	Gta/Ata	15/19	1	2	FACETS	0.837	0.764	0.913	0.837	0.764	0.913	CLONAL	1	TRUE	1	0.28	2		596	1340	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40375543	40375543	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1357	79	727	0	ENST00000293328.3:c.407C>T	p.Ala136Val	p.A136V	ENST00000293328	NM_012448.3	136	gCc/gTc	5/19	1	2	FACETS	0.393	0.344	0.446	0.393	0.344	0.446	SUBCLONAL	1	TRUE	1	0.28	2		727	1436	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40461470	40461470	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1231	190	682	0	ENST00000345506.4:c.2190C>A	p.Cys730Ter	p.C730*	ENST00000345506	NM_003152.3	730	tgC/tgA	19/20	1	2	FACETS	0.955	0.88	1	0.955	0.88	1	CLONAL	1	TRUE	1	0.28	2		682	1421	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475607	40475607	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1304	73	645	0	ENST00000264657.5:c.1637G>A	p.Trp546Ter	p.W546*	ENST00000264657	NM_139276.2	546	tGg/tAg	18/24	1	2	FACETS	0.379	0.33	0.432	0.379	0.33	0.432	SUBCLONAL	1	TRUE	1	0.28	2		645	1377	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223109	41223109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567775064	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	142	531	1	ENST00000357654.3:c.4822G>A	p.Ala1608Thr	p.A1608T	ENST00000357654	NM_007294.3	1608	Gca/Aca	15/23	1	2	FACETS	0.921	0.838	1	0.921	0.838	1	CLONAL	1	TRUE	1	0.28	2		532	1101	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245027	41245027	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1800709	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	115	546	1	ENST00000357654.3:c.2521C>T	p.Arg841Trp	p.R841W	ENST00000357654	NM_007294.3	841	Cgg/Tgg	10/23	1	2	FACETS	0.983	0.885	1	0.983	0.885	1	CLONAL	1	TRUE	1	0.28	2		547	836	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256241	41256241	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	131	422	0	ENST00000357654.3:c.339C>A	p.Asn113Lys	p.N113K	ENST00000357654	NM_007294.3	113	aaC/aaA	6/23	1	2	FACETS	0.953	0.864	1	0.953	0.864	1	CLONAL	1	TRUE	1	0.28	2		422	982	SUCCESS
MAP3K14	9020	MSKCC	GRCh37	17	43364731	43364731	+	splice_acceptor_variant,non_coding_transcript_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	160	587	1	ENST00000344686.2:n.436-1G>T		p.X146_splice	ENST00000344686		146			1	2	FACETS	0.994	0.91	1	0.994	0.91	1	CLONAL	1	TRUE	1	0.28	2		588	1150	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677876	47677876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	123	304	1	ENST00000347630.2:c.989C>T	p.Ser330Leu	p.S330L	ENST00000347630	NM_001007230.1	330	tCg/tTg	11/11	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.28	2		305	725	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56434959	56434959	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	59	450	0	ENST00000407977.2:c.2178G>T	p.Trp726Cys	p.W726C	ENST00000407977		726	tgG/tgT	9/10	1	2	FACETS	0.439	0.376	0.508	0.439	0.376	0.508	SUBCLONAL	1	TRUE	1	0.28	2		450	960	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772411	56772411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876658197	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	156	536	0	ENST00000337432.4:c.265G>A	p.Glu89Lys	p.E89K	ENST00000337432	NM_058216.2	89	Gaa/Aaa	2/9	1	2	FACETS	0.952	0.87	1	0.952	0.87	1	CLONAL	1	TRUE	1	0.28	2		536	1171	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63530136	63530136	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	158	523	0	ENST00000307078.5:c.2299A>G	p.Thr767Ala	p.T767A	ENST00000307078	NM_004655.3	767	Act/Gct	10/11	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.28	2		523	1123	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534394	63534394	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772908702	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	52	404	0	ENST00000307078.5:c.1127C>T	p.Ser376Leu	p.S376L	ENST00000307078	NM_004655.3	376	tCg/tTg	5/11	1	2	FACETS	0.45	0.382	0.525	0.45	0.382	0.525	SUBCLONAL	1	TRUE	1	0.28	2		404	826	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66519051	66519051	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	89	334	0	ENST00000358598.2:c.332C>T	p.Ala111Val	p.A111V	ENST00000358598	NM_212471.2	111	gCa/gTa	3/11	1	2	FACETS	0.77	0.682	0.864	0.77	0.682	0.864	SUBCLONAL	1	TRUE	1	0.28	2		334	826	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119903	70119903	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	119	344	0	ENST00000245479.2:c.905G>A	p.Gly302Asp	p.G302D	ENST00000245479	NM_000346.3	302	gGc/gAc	3/3	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.28	2		344	737	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78599593	78599593	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs772240053	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	31	241	0	ENST00000306801.3:c.265G>A	p.Asp89Asn	p.D89N	ENST00000306801	NM_020761.2	89	Gat/Aat	2/34	1	2	FACETS	0.36	0.29	0.44	0.36	0.29	0.44	SUBCLONAL	1	TRUE	1	0.28	2		241	615	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681708	78681708	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767783333	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	65	418	1	ENST00000306801.3:c.416G>A	p.Arg139His	p.R139H	ENST00000306801	NM_020761.2	139	cGc/cAc	4/34	1	2	FACETS	0.461	0.398	0.53	0.461	0.398	0.53	SUBCLONAL	1	TRUE	1	0.28	2		419	1007	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575689	48575689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750355699	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	103	353	0	ENST00000342988.3:c.449G>A	p.Ser150Asn	p.S150N	ENST00000342988	NM_005359.5	150	aGt/aAt	4/12	1	2	FACETS	0.884	0.791	0.984	0.884	0.791	0.984	CLONAL	1	TRUE	1	0.28	2		353	832	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581204	48581204	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	128	517	0	ENST00000342988.3:c.508C>G	p.Pro170Ala	p.P170A	ENST00000342988	NM_005359.5	170	Cca/Gca	5/12	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.28	2		517	901	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591919	48591919	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767347	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	139	421	0	ENST00000342988.3:c.1082G>A	p.Arg361His	p.R361H	ENST00000342988	NM_005359.5	361	cGc/cAc	9/12	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.28	2		421	926	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593519	48593519	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	37	307	0	ENST00000342988.3:c.1270G>T	p.Asp424Tyr	p.D424Y	ENST00000342988	NM_005359.5	424	Gat/Tat	10/12	1	2	FACETS	0.384	0.316	0.461	0.384	0.316	0.461	SUBCLONAL	1	TRUE	1	0.28	2		307	688	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210837	2210837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753115153	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	63	242	0	ENST00000398665.3:c.1334C>T	p.Ala445Val	p.A445V	ENST00000398665	NM_032482.2	445	gCg/gTg	14/28	1	2	FACETS	0.856	0.741	0.98	0.856	0.741	0.98	CLONAL	1	TRUE	1	0.28	2		242	526	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226346	2226346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759369415	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	138	455	0	ENST00000398665.3:c.3826C>T	p.Arg1276Trp	p.R1276W	ENST00000398665	NM_032482.2	1276	Cgg/Tgg	27/28	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.28	2		455	921	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226637	2226637	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	114	354	1	ENST00000398665.3:c.4117C>A	p.Leu1373Met	p.L1373M	ENST00000398665	NM_032482.2	1373	Ctg/Atg	27/28	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.28	2		355	791	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208010	5208010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	125	548	0	ENST00000357368.4:c.5701C>T	p.Arg1901Trp	p.R1901W	ENST00000357368	NM_002850.3	1901	Cgg/Tgg	37/38	1	2	FACETS	0.831	0.75	0.916	0.831	0.75	0.916	CLONAL	1	TRUE	1	0.28	2		548	1075	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208016	5208016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1042776388	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	119	517	0	ENST00000357368.4:c.5695C>T	p.Arg1899Trp	p.R1899W	ENST00000357368	NM_002850.3	1899	Cgg/Tgg	37/38	1	2	FACETS	0.821	0.74	0.908	0.821	0.74	0.908	CLONAL	1	TRUE	1	0.28	2		517	1035	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208051	5208051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1477222866	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	109	429	1	ENST00000357368.4:c.5660C>T	p.Thr1887Met	p.T1887M	ENST00000357368	NM_002850.3	1887	aCg/aTg	37/38	1	2	FACETS	0.877	0.786	0.973	0.877	0.786	0.973	CLONAL	1	TRUE	1	0.28	2		430	888	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5218798	5218798	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	130	405	0	ENST00000357368.4:c.3935G>T	p.Ser1312Ile	p.S1312I	ENST00000357368	NM_002850.3	1312	aGt/aTt	24/38	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.28	2		405	902	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222993	5222993	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762510209	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	71	262	0	ENST00000357368.4:c.2810C>T	p.Ala937Val	p.A937V	ENST00000357368	NM_002850.3	937	gCg/gTg	18/38	1	2	FACETS	0.855	0.747	0.972	0.855	0.747	0.972	CLONAL	1	TRUE	1	0.28	2		262	593	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244342	5244342	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	134	498	0	ENST00000357368.4:c.1140G>T	p.Glu380Asp	p.E380D	ENST00000357368	NM_002850.3	380	gaG/gaT	11/38	1	2	FACETS	0.931	0.845	1	0.931	0.845	1	CLONAL	1	TRUE	1	0.28	2		498	1028	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274277	5274277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1327116960	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	61	458	0	ENST00000357368.4:c.170C>T	p.Thr57Met	p.T57M	ENST00000357368	NM_002850.3	57	aCg/aTg	3/38	1	2	FACETS	0.481	0.414	0.555	0.481	0.414	0.555	SUBCLONAL	1	TRUE	1	0.28	2		458	906	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5286129	5286129	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	193	456	0	ENST00000357368.4:c.23G>T	p.Gly8Val	p.G8V	ENST00000357368	NM_002850.3	8	gGc/gTc	2/38	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.28	2		456	958	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267389	7267389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767658477	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	115	428	0	ENST00000302850.5:c.619G>A	p.Glu207Lys	p.E207K	ENST00000302850	NM_000208.2	207	Gaa/Aaa	2/22	1	2	FACETS	0.93	0.837	1	0.93	0.837	1	CLONAL	1	TRUE	1	0.28	2		428	883	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267410	7267410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	139	422	1	ENST00000302850.5:c.598G>A	p.Val200Ile	p.V200I	ENST00000302850	NM_000208.2	200	Gtc/Atc	2/22	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.28	2		423	980	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10247805	10247805	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770535972	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	121	552	1	ENST00000340748.4:c.4397G>A	p.Arg1466His	p.R1466H	ENST00000340748		1466	cGc/cAc	36/40	1	2	FACETS	0.887	0.801	0.979	0.887	0.801	0.979	CLONAL	1	TRUE	1	0.28	2		553	974	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10284582	10284582	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	126	452	0	ENST00000340748.4:c.601-1G>T		p.X201_splice	ENST00000340748		201			1	2	FACETS	0.89	0.805	0.981	0.89	0.805	0.981	CLONAL	1	TRUE	1	0.28	2		452	1011	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602281	10602281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	110	344	0	ENST00000171111.5:c.1297G>A	p.Gly433Ser	p.G433S	ENST00000171111	NM_203500.1	433	Ggc/Agc	3/6	1	2	FACETS	0.95	0.853	1	0.95	0.853	1	CLONAL	1	TRUE	1	0.28	2		344	827	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134234	11134234	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1085307769	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	152	450	1	ENST00000358026.2:c.2900G>A	p.Arg967His	p.R967H	ENST00000358026	NM_001128849.1	967	cGt/cAt	20/36	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.28	2		451	939	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138521	11138521	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	212	494	0	ENST00000358026.2:c.3277C>T	p.Arg1093Ter	p.R1093*	ENST00000358026	NM_001128849.1	1093	Cga/Tga	24/36	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.28	2		494	1146	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14628978	14628978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	65	543	0	ENST00000254322.2:c.184G>A	p.Glu62Lys	p.E62K	ENST00000254322	NM_006145.1	62	Gag/Aag	1/3	1	2	FACETS	0.434	0.375	0.499	0.434	0.375	0.499	SUBCLONAL	1	TRUE	1	0.28	2		543	1070	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297751	15297751	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1014927149	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	144	540	0	ENST00000263388.2:c.1889C>T	p.Thr630Ile	p.T630I	ENST00000263388	NM_000435.2	630	aCc/aTc	12/33	1	2	FACETS	0.946	0.862	1	0.946	0.862	1	CLONAL	1	TRUE	1	0.28	2		540	1087	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349666	15349666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200976853	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	56	201	1	ENST00000263377.2:c.3908C>T	p.Ala1303Val	p.A1303V	ENST00000263377	NM_058243.2	1303	gCg/gTg	19/20	1	2	FACETS	0.768	0.658	0.887	0.768	0.658	0.887	SUBCLONAL	1	TRUE	1	0.28	2		202	521	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15379802	15379802	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	178	517	0	ENST00000263377.2:c.337C>T	p.Arg113Cys	p.R113C	ENST00000263377	NM_058243.2	113	Cgc/Tgc	3/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.28	2		517	1110	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17937659	17937659	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144968714	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	117	377	0	ENST00000458235.1:c.3268G>A	p.Ala1090Thr	p.A1090T	ENST00000458235	NM_000215.3	1090	Gcc/Acc	24/24	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.28	2		377	758	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17943711	17943711	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	105	260	0	ENST00000458235.1:c.2378C>A	p.Pro793His	p.P793H	ENST00000458235	NM_000215.3	793	cCt/cAt	18/24	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.28	2		260	678	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945948	17945948	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373027121	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	162	464	1	ENST00000458235.1:c.1991C>T	p.Pro664Leu	p.P664L	ENST00000458235	NM_000215.3	664	cCg/cTg	15/24	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.28	2		465	1112	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945969	17945969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758959409	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	47	439	0	ENST00000458235.1:c.1970G>A	p.Arg657Gln	p.R657Q	ENST00000458235	NM_000215.3	657	cGg/cAg	15/24	1	2	FACETS	0.32	0.269	0.377	0.32	0.269	0.377	SUBCLONAL	1	TRUE	1	0.28	2		439	1048	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266888	18266888	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	56	256	0	ENST00000222254.8:c.199C>T	p.Arg67Ter	p.R67*	ENST00000222254	NM_005027.3	67	Cga/Tga	2/16	1	2	FACETS	0.759	0.651	0.877	0.759	0.651	0.877	SUBCLONAL	1	TRUE	1	0.28	2		256	527	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278050	18278050	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	103	407	0	ENST00000222254.8:c.1670A>G	p.Asp557Gly	p.D557G	ENST00000222254	NM_005027.3	557	gAc/gGc	13/16	1	2	FACETS	0.913	0.816	1	0.913	0.816	1	CLONAL	1	TRUE	1	0.28	2		407	806	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279682	18279682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1431128842	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	68	199	0	ENST00000222254.8:c.1955G>A	p.Arg652Gln	p.R652Q	ENST00000222254	NM_005027.3	652	cGg/cAg	15/16	1	2	FACETS	0.898	0.782	1	0.898	0.782	1	CLONAL	1	TRUE	1	0.28	2		199	541	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257985	19257985	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	85	331	0	ENST00000162023.5:c.401C>A	p.Ala134Asp	p.A134D	ENST00000162023		134	gCt/gAt	9/13	1	2	FACETS	0.79	0.697	0.888	0.79	0.697	0.888	SUBCLONAL	1	TRUE	1	0.28	2		331	769	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42788884	42788884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	40	346	0	ENST00000575354.2:c.28C>T	p.Pro10Ser	p.P10S	ENST00000575354	NM_015125.3	10	Ccc/Tcc	1/20	1	2	FACETS	0.433	0.359	0.516	0.433	0.359	0.516	SUBCLONAL	1	TRUE	1	0.28	2		346	660	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795838	42795838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1422422589	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	64	431	0	ENST00000575354.2:c.2827C>T	p.Pro943Ser	p.P943S	ENST00000575354	NM_015125.3	943	Cca/Tca	11/20	1	2	FACETS	0.454	0.391	0.521	0.454	0.391	0.521	SUBCLONAL	1	TRUE	1	0.28	2		431	1008	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795858	42795858	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	133	436	0	ENST00000575354.2:c.2847C>A	p.Phe949Leu	p.F949L	ENST00000575354	NM_015125.3	949	ttC/ttA	11/20	1	2	FACETS	0.928	0.841	1	0.928	0.841	1	CLONAL	1	TRUE	1	0.28	2		436	1024	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50902658	50902658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750825686	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	183	588	1	ENST00000440232.2:c.233G>A	p.Arg78His	p.R78H	ENST00000440232	NM_002691.3	78	cGc/cAc	3/27	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.28	2		589	1303	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905516	50905516	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs993539085	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	67	618	1	ENST00000440232.2:c.644C>T	p.Ala215Val	p.A215V	ENST00000440232	NM_002691.3	215	gCg/gTg	6/27	1	2	FACETS	0.415	0.359	0.476	0.415	0.359	0.476	SUBCLONAL	1	TRUE	1	0.28	2		619	1153	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906421	50906421	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756138051	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	157	492	0	ENST00000440232.2:c.1082C>T	p.Ala361Val	p.A361V	ENST00000440232	NM_002691.3	361	gCc/gTc	9/27	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.28	2		492	1112	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910662	50910662	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	132	555	1	ENST00000440232.2:c.1765C>T	p.Pro589Ser	p.P589S	ENST00000440232	NM_002691.3	589	Ccc/Tcc	14/27	1	2	FACETS	0.889	0.805	0.977	0.889	0.805	0.977	CLONAL	1	TRUE	1	0.28	2		556	1061	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918111	50918111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760358465	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	59	611	0	ENST00000440232.2:c.2428G>A	p.Ala810Thr	p.A810T	ENST00000440232	NM_002691.3	810	Gcg/Acg	20/27	1	2	FACETS	0.393	0.337	0.455	0.393	0.337	0.455	SUBCLONAL	1	TRUE	1	0.28	2		611	1071	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918759	50918759	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555793039	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	56	538	0	ENST00000440232.2:c.2629G>A	p.Asp877Asn	p.D877N	ENST00000440232	NM_002691.3	877	Gat/Aat	21/27	1	2	FACETS	0.359	0.306	0.417	0.359	0.306	0.417	SUBCLONAL	1	TRUE	1	0.28	2		538	1114	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624942	9624942	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	50	430	1	ENST00000353224.5:c.35C>T	p.Ser12Phe	p.S12F	ENST00000353224	NM_177990.2	12	tCt/tTt	3/10	1	2	FACETS	0.395	0.333	0.462	0.395	0.333	0.462	SUBCLONAL	1	TRUE	1	0.28	2		431	905	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017813	31017813	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	130	427	0	ENST00000375687.4:c.675G>T	p.Gln225His	p.Q225H	ENST00000375687	NM_015338.5	225	caG/caT	8/13	1	2	FACETS	0.981	0.889	1	0.981	0.889	1	CLONAL	1	TRUE	1	0.28	2		427	947	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023964	31023964	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773823004	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	151	442	0	ENST00000375687.4:c.3449G>A	p.Gly1150Glu	p.G1150E	ENST00000375687	NM_015338.5	1150	gGa/gAa	13/13	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.28	2		442	1013	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31372580	31372580	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	101	378	0	ENST00000328111.2:c.221G>A	p.Gly74Asp	p.G74D	ENST00000328111	NM_006892.3	74	gGc/gAc	4/23	1	2	FACETS	0.777	0.693	0.866	0.777	0.693	0.866	SUBCLONAL	1	TRUE	1	0.28	2		378	929	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389203	31389203	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs996239307	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	78	305	1	ENST00000328111.2:c.2116G>A	p.Asp706Asn	p.D706N	ENST00000328111	NM_006892.3	706	Gac/Aac	19/23	1	2	FACETS	0.78	0.685	0.883	0.78	0.685	0.883	SUBCLONAL	1	TRUE	1	0.28	2		306	714	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790093	40790093	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	76	299	2	ENST00000373198.4:c.2638C>A	p.Pro880Thr	p.P880T	ENST00000373198	NM_133170.3	880	Ccc/Acc	18/32	1	2	FACETS	0.839	0.736	0.95	0.839	0.736	0.95	CLONAL	1	TRUE	1	0.28	2		301	647	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256699	46256699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749607074	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	176	663	2	ENST00000371998.3:c.755G>A	p.Arg252His	p.R252H	ENST00000371998		252	cGc/cAc	8/23	1	2	FACETS	0.983	0.903	1	0.983	0.903	1	CLONAL	1	TRUE	1	0.28	2		665	1279	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268699	46268699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	188	624	0	ENST00000371998.3:c.2984C>T	p.Ala995Val	p.A995V	ENST00000371998		995	gCt/gTt	16/23	1	2	FACETS	0.963	0.887	1	0.963	0.887	1	CLONAL	1	TRUE	1	0.28	2		624	1395	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268767	46268767	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1340282435	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1309	76	631	0	ENST00000371998.3:c.3052G>A	p.Glu1018Lys	p.E1018K	ENST00000371998		1018	Gaa/Aaa	16/23	1	2	FACETS	0.392	0.342	0.446	0.392	0.342	0.446	SUBCLONAL	1	TRUE	1	0.28	2		631	1385	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945623	54945623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	55	161	0	ENST00000312783.6:c.947G>A	p.Gly316Glu	p.G316E	ENST00000312783	NM_198436.1	316	gGa/gAa	9/10	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.28	2		161	381	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485816	57485816	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759578554	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	51	426	0	ENST00000371085.3:c.1117C>T	p.Arg373Cys	p.R373C	ENST00000371085	NM_000516.4	373	Cgc/Tgc	13/13	1	2	FACETS	0.383	0.325	0.449	0.383	0.325	0.449	SUBCLONAL	1	TRUE	1	0.28	2		426	950	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485819	57485819	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	127	426	0	ENST00000371085.3:c.1120C>T	p.Arg374Cys	p.R374C	ENST00000371085	NM_000516.4	374	Cgt/Tgt	13/13	1	2	FACETS	0.957	0.866	1	0.957	0.866	1	CLONAL	1	TRUE	1	0.28	2		426	948	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39762950	39762950	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	59	434	0	ENST00000288319.7:c.886C>T	p.Leu296Phe	p.L296F	ENST00000288319	NM_182918.3	296	Ctt/Ttt	9/10	1	2	FACETS	0.393	0.337	0.455	0.393	0.337	0.455	SUBCLONAL	1	TRUE	1	0.28	2		434	1071	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42842584	42842584	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147233451	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	144	451	1	ENST00000398585.3:c.1273G>A	p.Glu425Lys	p.E425K	ENST00000398585	NM_001135099.1	425	Gag/Aag	11/14	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.28	2		452	978	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852526	42852526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779200981	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	59	504	0	ENST00000398585.3:c.560G>A	p.Arg187His	p.R187H	ENST00000398585	NM_001135099.1	187	cGc/cAc	6/14	1	2	FACETS	0.371	0.318	0.43	0.371	0.318	0.43	SUBCLONAL	1	TRUE	1	0.28	2		504	1135	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221630	22221630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	21	193	0	ENST00000215832.6:c.101G>A	p.Gly34Asp	p.G34D	ENST00000215832	NM_002745.4	34	gGc/gAc	1/9	1	2	FACETS	0.463	0.356	0.587	0.463	0.356	0.587	SUBCLONAL	1	TRUE	1	0.28	2		193	324	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167557	24167557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	67	230	0	ENST00000263121.7:c.941G>A	p.Ser314Asn	p.S314N	ENST00000263121	NM_003073.3	314	aGc/aAc	7/9	1	2	FACETS	0.831	0.722	0.948	0.831	0.722	0.948	CLONAL	1	TRUE	1	0.28	2		230	576	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130561	29130561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	52	384	0	ENST00000328354.6:c.149G>A	p.Ser50Asn	p.S50N	ENST00000328354	NM_007194.3	50	aGc/aAc	2/15	1	2	FACETS	0.393	0.333	0.459	0.393	0.333	0.459	SUBCLONAL	1	TRUE	1	0.28	2		384	945	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513733	41513733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	57	437	0	ENST00000263253.7:c.637G>A	p.Gly213Arg	p.G213R	ENST00000263253	NM_001429.3	213	Gga/Aga	2/31	1	2	FACETS	0.421	0.36	0.489	0.421	0.36	0.489	SUBCLONAL	1	TRUE	1	0.28	2		437	966	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314919	1314919	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	173	511	0	ENST00000400841.2:c.742C>A	p.Leu248Ile	p.L248I	ENST00000400841		248	Ctt/Att	6/6	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.28	2		511	1120	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921573	39921573	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	58	541	1	ENST00000378444.4:c.4247C>T	p.Pro1416Leu	p.P1416L	ENST00000378444	NM_001123385.1	1416	cCa/cTa	10/15	1	2	FACETS	0.372	0.318	0.431	0.372	0.318	0.431	SUBCLONAL	1	TRUE	1	0.28	2		542	1114	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930896	39930896	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	64	645	0	ENST00000378444.4:c.3045C>A	p.Tyr1015Ter	p.Y1015*	ENST00000378444	NM_001123385.1	1015	taC/taA	5/15	1	2	FACETS	0.387	0.333	0.445	0.387	0.333	0.445	SUBCLONAL	1	TRUE	1	0.28	2		645	1182	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933007	39933007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	140	484	1	ENST00000378444.4:c.1592C>T	p.Ala531Val	p.A531V	ENST00000378444	NM_001123385.1	531	gCa/gTa	4/15	1	2	FACETS	0.867	0.788	0.951	0.867	0.788	0.951	CLONAL	1	TRUE	1	0.28	2		485	1153	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732929	44732929	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	76	314	0	ENST00000377967.4:c.132G>T	p.Glu44Asp	p.E44D	ENST00000377967	NM_021140.2	44	gaG/gaT	1/29	1	2	FACETS	0.855	0.75	0.968	0.855	0.75	0.968	CLONAL	1	TRUE	1	0.28	2		314	635	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820622	44820622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1201454112	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	110	582	1	ENST00000377967.4:c.319G>A	p.Glu107Lys	p.E107K	ENST00000377967	NM_021140.2	107	Gaa/Aaa	3/29	1	2	FACETS	0.888	0.797	0.984	0.888	0.797	0.984	CLONAL	1	TRUE	1	0.28	2		583	885	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922920	44922920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1204	213	621	1	ENST00000377967.4:c.1781G>A	p.Gly594Asp	p.G594D	ENST00000377967	NM_021140.2	594	gGc/gAc	16/29	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.28	2		622	1417	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966766	44966766	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	136	547	0	ENST00000377967.4:c.3990C>A	p.Tyr1330Ter	p.Y1330*	ENST00000377967	NM_021140.2	1330	taC/taA	27/29	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.28	2		547	930	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040710	47040710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	137	553	0	ENST00000377604.3:c.1345G>A	p.Gly449Ser	p.G449S	ENST00000377604	NM_001204468.1	449	Ggc/Agc	13/24	1	2	FACETS	0.841	0.764	0.924	0.841	0.764	0.924	CLONAL	1	TRUE	1	0.28	2		553	1163	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428232	47428232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1462354021	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	197	525	0	ENST00000377045.4:c.1192G>A	p.Asp398Asn	p.D398N	ENST00000377045	NM_001654.4	398	Gac/Aac	11/16	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.28	2		525	1120	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429307	47429307	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	58	536	0	ENST00000377045.4:c.1435C>T	p.Arg479Cys	p.R479C	ENST00000377045	NM_001654.4	479	Cgt/Tgt	14/16	1	2	FACETS	0.371	0.317	0.43	0.371	0.317	0.43	SUBCLONAL	1	TRUE	1	0.28	2		536	1116	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650858	48650858	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782632688	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	158	547	1	ENST00000376670.3:c.727C>T	p.Arg243Trp	p.R243W	ENST00000376670	NM_002049.3	243	Cgg/Tgg	4/6	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.28	2		548	1067	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246405	53246405	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	162	555	3	ENST00000375401.3:c.577C>A	p.His193Asn	p.H193N	ENST00000375401	NM_004187.3	193	Cac/Aac	5/26	1	2	FACETS	0.96	0.879	1	0.96	0.879	1	CLONAL	1	TRUE	1	0.28	2		558	1205	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345277	70345277	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	149	467	2	ENST00000374080.3:c.2303G>A	p.Arg768His	p.R768H	ENST00000374080		768	cGc/cAc	16/45	1	2	FACETS	0.974	0.888	1	0.974	0.888	1	CLONAL	1	TRUE	1	0.28	2		469	1093	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348181	70348181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	156	517	0	ENST00000374080.3:c.3245C>T	p.Thr1082Ile	p.T1082I	ENST00000374080		1082	aCc/aTc	23/45	1	2	FACETS	0.982	0.897	1	0.982	0.897	1	CLONAL	1	TRUE	1	0.28	2		517	1135	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70357220	70357220	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767294730	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	98	347	3	ENST00000374080.3:c.5735G>A	p.Arg1912His	p.R1912H	ENST00000374080		1912	cGc/cAc	39/45	1	2	FACETS	0.856	0.763	0.955	0.856	0.763	0.955	CLONAL	1	TRUE	1	0.28	2		350	818	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76854981	76854981	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	137	790	0	ENST00000373344.5:c.5855T>C	p.Val1952Ala	p.V1952A	ENST00000373344	NM_000489.3	1952	gTt/gCt	25/35	1	2	FACETS	0.969	0.88	1	0.969	0.88	1	CLONAL	1	TRUE	1	0.28	2		790	1010	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611252	100611252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	110	322	0	ENST00000308731.7:c.1354C>T	p.Leu452Phe	p.L452F	ENST00000308731	NM_000061.2	452	Ctt/Ttt	15/19	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.28	2		322	749	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123025113	123025113	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	167	588	2	ENST00000355640.3:c.1003G>T	p.Gly335Ter	p.G335*	ENST00000355640		335	Gga/Tga	4/7	1	2	FACETS	0.921	0.844	1	0.921	0.844	1	CLONAL	1	TRUE	1	0.28	2		590	1295	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123034385	123034385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1308142786	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	124	533	0	ENST00000355640.3:c.1142G>A	p.Arg381Gln	p.R381Q	ENST00000355640		381	cGa/cAa	6/7	1	2	FACETS	0.907	0.82	1	0.907	0.82	1	CLONAL	1	TRUE	1	0.28	2		533	976	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026278	48026278	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	114	310	0	ENST00000234420.5:c.1157del	p.Pro386LeufsTer25	p.P386Lfs*25	ENST00000234420	NM_000179.2	386	Cct/ct	4/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.28	2		310	711	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911321	32911322	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359356	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	149	783	0	ENST00000380152.3:c.2835dup	p.Asp946ArgfsTer13	p.D946Rfs*13	ENST00000380152		943	-/A	11/27	1	2	FACETS	0.886	0.808	0.969	0.886	0.808	0.969	CLONAL	1	TRUE	1	0.28	2		783	1201	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922695	44922695	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004688-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	227	515	1	ENST00000377967.4:c.1556del	p.Arg519HisfsTer29	p.R519Hfs*29	ENST00000377967	NM_021140.2	519	cGa/ca	16/29	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.28	2		516	1171	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0004700-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	495	511	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.363944073825649	3	FACETS	0.967	0.929	1	0.967	0.929	1	CLONAL	3	TRUE	0	0.392156296764565	3		511	1041	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0004700-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	156	300	0				ENST00000310581	NM_198253.2	-/1132			0.383816896713459	4	FACETS	0.931	0.856	1			1	CLONAL	2	TRUE	NA	0.392156296764565	4		300	595	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295201	1295201	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0004700-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	123	127	0				ENST00000310581	NM_198253.2	-/1132			0.383816896713459	4	FACETS	0.97	0.884	1			1	CLONAL	2	TRUE	NA	0.392156296764565	4		127	450	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385271	41385271	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004700-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	222	299	0	ENST00000373198.4:c.690G>A	p.Trp230Ter	p.W230*	ENST00000373198	NM_133170.3	230	tgG/tgA	6/32	0.387897107235412	3	FACETS	0.846	0.79	0.904	0.846	0.79	0.904	CLONAL	2	TRUE	1	0.392156296764565	3		299	800	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260581	16260581	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004700-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	416	496	0	ENST00000375759.3:c.7846C>T	p.Pro2616Ser	p.P2616S	ENST00000375759	NM_015001.2	2616	Ccc/Tcc	11/15	0.363944073825649	3	FACETS	0.92	0.881	0.96	0.92	0.881	0.96	CLONAL	3	TRUE	0	0.392156296764565	3		496	919	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0004742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	38	176	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	1	2	FACETS	0.893	0.738	1	0.893	0.738	1	CLONAL	1	TRUE	1	0.18	2		176	473	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61712950	61712950	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	66	560	0	ENST00000401558.2:c.2461C>G	p.Gln821Glu	p.Q821E	ENST00000401558	NM_003400.3	821	Caa/Gaa	20/25	0.179202546103319	3	FACETS	0.735	0.636	0.844	0.368	0.318	0.422	SUBCLONAL	1	TRUE	1	0.18	3		560	1087	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519920	NA	P-0004742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	29	320	0	ENST00000397062.3:c.85G>C	p.Asp29His	p.D29H	ENST00000397062	NM_006164.4	29	Gat/Cat	2/5	0.179202546103319	3	FACETS	0.826	0.663	1	0.413	0.331	0.507	CLONAL	1	TRUE	1	0.18	3		320	425	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750684	128750684	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1294281543	NA	P-0004742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	62	440	0	ENST00000377970.2:c.221C>T	p.Pro74Leu	p.P74L	ENST00000377970	NM_002467.4	74	cCg/cTg	2/3	1	2	FACETS	0.887	0.764	1	0.887	0.764	1	CLONAL	1	TRUE	1	0.18	2		440	777	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829423	72829423	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	91	645	0	ENST00000268489.5:c.7158G>A	p.Met2386Ile	p.M2386I	ENST00000268489	NM_006885.3	2386	atG/atA	9/10	1	2	FACETS	0.856	0.758	0.962	0.856	0.758	0.962	CLONAL	1	TRUE	1	0.18	2		645	1181	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0004742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	88	769	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.18	2		769	900	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925484	114925486	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0004742-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	90	622	0	ENST00000543371.1:c.1562_1564del	p.Leu521_Lys522delinsGln	p.L521_K522delinsQ	ENST00000543371	NM_001198531.1	521	cTGAag/cag	14/14	1	2	FACETS	0.988	0.875	1	0.988	0.875	1	CLONAL	1	TRUE	1	0.18	2		622	1012	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	135	280	0				ENST00000310581	NM_198253.2	-/1132			0.330810914447178	4	FACETS	1	0.972	1	1	0.972	1	INDETERMINATE	2	TRUE	2	0.855524496011137	4		280	267	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913381	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	304	394	0	ENST00000304494.5:c.322G>T	p.Asp108Tyr	p.D108Y	ENST00000304494	NM_000077.4	108	Gat/Tat	2/3	0.855524496011137	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.855524496011137	1		394	332	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	846	589	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.546678852588835	3	FACETS	1	0.997	1			1	CLONAL	3	TRUE	NA	0.855524496011137	3		589	903	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519893	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	426	680	2	ENST00000267101.3:c.310G>T	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ttg	3/28	0.491593488541348	4	FACETS	0.966	0.925	1			1	INDETERMINATE	2	TRUE	NA	0.855524496011137	4		682	956	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	483	333	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	0.85490611226827	4	FACETS	1	0.994	1	0.773	0.745	0.802	CLONAL	2	TRUE	1	0.855524496011137	4		333	903	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032069	26032069	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	455	1034	0	ENST00000244661.2:c.220G>C	p.Glu74Gln	p.E74Q	ENST00000244661	NM_003537.3	74	Gaa/Caa	1/1	0.172641187057942	3	FACETS	0.927	0.892	0.962	0.618	0.595	0.641	INDETERMINATE	2	TRUE	0	0.855524496011137	3		1034	819	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974792	21974792	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs141798398	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	112	175	0	ENST00000304494.5:c.35C>A	p.Ser12Ter	p.S12*	ENST00000304494	NM_000077.4	12	tCg/tAg	1/3	0.855524496011137	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.855524496011137	1		175	134	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552758	106552758	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	225	757	2	ENST00000369096.4:c.723G>C	p.Lys241Asn	p.K241N	ENST00000369096	NM_001198.3	241	aaG/aaC	5/7	0.259262409530467	2	FACETS	0.627	0.585	0.67	0.313	0.292	0.335	INDETERMINATE	1	TRUE	0	0.855524496011137	2		759	839	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974787	21974787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1563892848	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	115	191	0	ENST00000304494.5:c.40G>A	p.Asp14Asn	p.D14N	ENST00000304494	NM_000077.4	14	Gac/Aac	1/3	0.855524496011137	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.855524496011137	1		191	136	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074169	8074169	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs535537176	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	492	923	0	ENST00000377482.5:c.490C>G	p.Leu164Val	p.L164V	ENST00000377482	NM_018948.3	164	Ctg/Gtg	4/4	0.255036667542896	4	FACETS	1	0.994	1	1	0.994	1	INDETERMINATE	2	TRUE	2	0.855524496011137	4		923	934	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259760	16259760	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747967254	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	369	598	0	ENST00000375759.3:c.7025G>A	p.Arg2342Gln	p.R2342Q	ENST00000375759	NM_015001.2	2342	cGa/cAa	11/15	0.255036667542896	4	FACETS	0.899	0.857	0.942	0.899	0.857	0.942	INDETERMINATE	2	TRUE	2	0.855524496011137	4		598	890	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36808989	36808989	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	118	636	0	ENST00000373129.3:c.1065G>C	p.Met355Ile	p.M355I	ENST00000373129	NM_032017.1	355	atG/atC	11/12	0.255036667542896	4	FACETS	0.651	0.587	0.719	0.326	0.293	0.36	INDETERMINATE	1	TRUE	2	0.855524496011137	4		636	786	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248409	59248409	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1184098204	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	92	399	1	ENST00000371222.2:c.334G>C	p.Glu112Gln	p.E112Q	ENST00000371222	NM_002228.3	112	Gag/Cag	1/1	0.255036667542896	4	FACETS	1	0.93	1	0.525	0.47	0.583	INDETERMINATE	1	TRUE	2	0.855524496011137	4		400	380	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965437	25965437	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	384	605	0	ENST00000435504.4:c.3769G>C	p.Asp1257His	p.D1257H	ENST00000435504		1257	Gat/Cat	13/13	0.172641187057942	3	FACETS	0.938	0.9	0.976	0.626	0.6	0.651	INDETERMINATE	2	TRUE	0	0.855524496011137	3		605	683	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965581	25965581	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	302	502	0	ENST00000435504.4:c.3625G>A	p.Asp1209Asn	p.D1209N	ENST00000435504		1209	Gac/Aac	13/13	0.172641187057942	3	FACETS	0.894	0.852	0.935	0.596	0.568	0.624	INDETERMINATE	2	TRUE	0	0.855524496011137	3		502	564	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966396	25966396	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1336667691	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	443	671	1	ENST00000435504.4:c.2810G>A	p.Gly937Glu	p.G937E	ENST00000435504		937	gGa/gAa	13/13	0.172641187057942	3	FACETS	0.891	0.856	0.925	0.594	0.571	0.617	INDETERMINATE	2	TRUE	0	0.855524496011137	3		672	830	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966716	25966716	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	307	522	0	ENST00000435504.4:c.2490G>C	p.Glu830Asp	p.E830D	ENST00000435504		830	gaG/gaC	13/13	0.172641187057942	3	FACETS	0.861	0.82	0.902	0.574	0.547	0.601	INDETERMINATE	2	TRUE	0	0.855524496011137	3		522	595	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646225	215646225	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	176	227	0	ENST00000260947.4:c.373G>C	p.Glu125Gln	p.E125Q	ENST00000260947	NM_000465.2	125	Gaa/Caa	4/11	0.172641187057942	3	FACETS	1	0.954	1	0.675	0.637	0.713	INDETERMINATE	2	TRUE	0	0.855524496011137	3		227	290	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405945	49405945	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	186	709	0	ENST00000418115.1:c.193G>T	p.Asp65Tyr	p.D65Y	ENST00000418115	NM_001664.2	65	Gat/Tat	3/5	0.313602240391772	1	FACETS	0.444	0.412	0.476	0.444	0.412	0.476	INDETERMINATE	1	TRUE	0	0.855524496011137	1		709	561	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940753	49940753	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	191	802	0	ENST00000296474.3:c.290G>C	p.Gly97Ala	p.G97A	ENST00000296474	NM_002447.2	97	gGa/gCa	1/20	0.249705058325656	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.855524496011137	0		802	461	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623143	52623143	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	227	594	0	ENST00000394830.3:c.2908G>A	p.Glu970Lys	p.E970K	ENST00000394830	NM_018313.4	970	Gag/Aag	19/30	0.249705058325656	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.855524496011137	0		594	605	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623266	52623266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749924765	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	153	394	1	ENST00000394830.3:c.2785G>A	p.Glu929Lys	p.E929K	ENST00000394830	NM_018313.4	929	Gaa/Aaa	19/30	0.249705058325656	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.855524496011137	0		395	352	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72890267	72890267	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	207	626	0	ENST00000325599.8:c.415G>C	p.Glu139Gln	p.E139Q	ENST00000325599	NM_018130.2	139	Gaa/Caa	4/11	0.249705058325656	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.855524496011137	0		626	447	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269119	142269119	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	420	447	0	ENST00000350721.4:c.2831G>C	p.Ser944Thr	p.S944T	ENST00000350721	NM_001184.3	944	aGt/aCt	14/47	0.855524496011137	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.855524496011137	3		447	657	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84388672	84388672	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	297	526	0	ENST00000321945.7:c.616G>C	p.Asp206His	p.D206H	ENST00000321945	NM_139076.2	206	Gat/Cat	7/9	0.255036667542896	4	FACETS	0.874	0.828	0.921	0.874	0.828	0.921	INDETERMINATE	2	TRUE	2	0.855524496011137	4		526	737	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520273	176520273	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759709290	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	70	271	1	ENST00000292408.4:c.1192C>T	p.Arg398Trp	p.R398W	ENST00000292408	NM_213647.1	398	Cgg/Tgg	9/18	0.259262409530467	2	FACETS	0.74	0.656	0.829	0.37	0.328	0.415	INDETERMINATE	1	TRUE	0	0.855524496011137	2		272	221	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176662842	176662842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779028625	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	313	517	0	ENST00000439151.2:c.3817C>T	p.Arg1273Cys	p.R1273C	ENST00000439151	NM_022455.4	1273	Cgc/Tgc	6/23	0.259262409530467	2	FACETS	1	0.994	1	0.643	0.614	0.672	INDETERMINATE	1	TRUE	0	0.855524496011137	2		517	569	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189097	32189097	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	127	411	2	ENST00000375023.3:c.457C>T	p.Gln153Ter	p.Q153*	ENST00000375023	NM_004557.3	153	Cag/Tag	4/30	0.172641187057942	3	FACETS	1	0.958	1	0.36	0.329	0.391	INDETERMINATE	1	TRUE	0	0.855524496011137	3		413	393	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971307	13971307	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	173	545	0	ENST00000405192.2:c.622C>A	p.Arg208Ser	p.R208S	ENST00000405192	NM_001163147.1	208	Cgt/Agt	8/12	0.259262409530467	2	FACETS	0.723	0.67	0.779	0.362	0.335	0.39	INDETERMINATE	1	TRUE	0	0.855524496011137	2		545	559	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81399283	81399283	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	133	554	0	ENST00000222390.5:c.5G>C	p.Trp2Ser	p.W2S	ENST00000222390	NM_000601.4	2	tGg/tCg	1/18	0.491593488541348	4	FACETS	0.737	0.669	0.808			1	INDETERMINATE	1	TRUE	NA	0.855524496011137	4		554	783	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787841	135787841	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	288	421	0	ENST00000298552.3:c.741G>A	p.Trp247Ter	p.W247*	ENST00000298552	NM_001162426.1	247	tgG/tgA	9/23	0.855524496011137	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.855524496011137	1		421	340	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911614	114911614	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	230	721	0	ENST00000543371.1:c.1132G>A	p.Ala378Thr	p.A378T	ENST00000543371	NM_001198531.1	378	Gcg/Acg	10/14	0.307130173807757	2	FACETS	0.722	0.675	0.769	0.361	0.337	0.385	INDETERMINATE	1	TRUE	0	0.855524496011137	2		721	745	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155060	108155060	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	240	459	0	ENST00000278616.4:c.3853G>C	p.Asp1285His	p.D1285H	ENST00000278616	NM_000051.3	1285	Gac/Cac	26/63	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.855524496011137	2		459	519	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4387980	4387980	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	160	613	0	ENST00000261254.3:c.466C>G	p.Pro156Ala	p.P156A	ENST00000261254	NM_001759.3	156	Cct/Gct	3/5	0.255036667542896	4	FACETS	1	0.947	1	0.519	0.478	0.563	INDETERMINATE	1	TRUE	2	0.855524496011137	4		613	668	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992190	11992190	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	342	512	0	ENST00000396373.4:c.280C>T	p.Leu94Phe	p.L94F	ENST00000396373	NM_001987.4	94	Ctc/Ttc	3/8	0.255036667542896	4	FACETS	1	0.982	1	1	0.982	1	INDETERMINATE	2	TRUE	2	0.855524496011137	4		512	703	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434181	49434181	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	196	686	0	ENST00000301067.7:c.7372C>T	p.Gln2458Ter	p.Q2458*	ENST00000301067	NM_003482.3	2458	Cag/Tag	31/54	0.491593488541348	4	FACETS	0.938	0.869	1			1	INDETERMINATE	1	TRUE	NA	0.855524496011137	4		686	906	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73334699	73334699	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	330	467	0	ENST00000377767.4:c.2761C>T	p.Gln921Ter	p.Q921*	ENST00000377767	NM_014953.3	921	Cag/Tag	20/21	0.427623653102724	4	FACETS	0.889	0.845	0.934			1	INDETERMINATE	2	TRUE	NA	0.855524496011137	4		467	805	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95570392	95570392	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1278843875	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	113	356	0	ENST00000393063.1:c.3341C>G	p.Ser1114Cys	p.S1114C	ENST00000393063	NM_030621.3	1114	tCt/tGt	22/28	0.191166108653212	2	FACETS	0.757	0.689	0.827	0.378	0.344	0.414	INDETERMINATE	1	TRUE	0	0.855524496011137	2		356	349	SUCCESS
BLM	641	MSKCC	GRCh37	15	91341444	91341444	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs771055974	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	414	693	0	ENST00000355112.3:c.3235G>C	p.Asp1079His	p.D1079H	ENST00000355112	NM_000057.2	1079	Gac/Cac	17/22	0.330810914447178	4	FACETS	0.914	0.874	0.955	0.914	0.874	0.955	INDETERMINATE	2	TRUE	2	0.855524496011137	4		693	982	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99482565	99482565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769418210	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	111	546	1	ENST00000268035.6:c.3433G>A	p.Glu1145Lys	p.E1145K	ENST00000268035	NM_000875.3	1145	Gaa/Aaa	18/21	0.330810914447178	4	FACETS	0.745	0.671	0.824	0.373	0.335	0.412	INDETERMINATE	1	TRUE	2	0.855524496011137	4		547	646	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786769	3786769	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	250	660	0	ENST00000262367.5:c.4442A>G	p.Asp1481Gly	p.D1481G	ENST00000262367	NM_004380.2	1481	gAt/gGt	27/31	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.855524496011137	2		660	563	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842388	68842388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	262	684	0	ENST00000261769.5:c.449G>A	p.Arg150Lys	p.R150K	ENST00000261769	NM_004360.3	150	aGa/aAa	4/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.855524496011137	2		684	586	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627206	37627206	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	373	560	0	ENST00000447079.4:c.1121G>A	p.Arg374Lys	p.R374K	ENST00000447079	NM_015083.1	374	aGa/aAa	2/14	0.427623653102724	4	FACETS	0.982	0.937	1			1	INDETERMINATE	2	TRUE	NA	0.855524496011137	4		560	824	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462551	40462551	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	353	670	2	ENST00000345506.4:c.2249G>A	p.Gly750Glu	p.G750E	ENST00000345506	NM_003152.3	750	gGa/gAa	20/20	0.232092671364403	5	FACETS	1	0.989	1	0.748	0.712	0.784	INDETERMINATE	2	TRUE	2	0.855524496011137	5		672	840	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604685	48604685	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	58	432	0	ENST00000342988.3:c.1507A>T	p.Met503Leu	p.M503L	ENST00000342988	NM_005359.5	503	Atg/Ttg	12/12	0.307130173807757	2	FACETS	0.25	0.214	0.288	0.125	0.107	0.144	INDETERMINATE	1	TRUE	0	0.855524496011137	2		432	543	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10244905	10244905	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	299	654	0	ENST00000340748.4:c.4804G>C	p.Glu1602Gln	p.E1602Q	ENST00000340748		1602	Gag/Cag	39/40	0.255036667542896	4	FACETS	0.924	0.876	0.972	0.924	0.876	0.972	INDETERMINATE	2	TRUE	2	0.855524496011137	4		654	702	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602754	10602754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	404	686	0	ENST00000171111.5:c.824C>T	p.Ser275Leu	p.S275L	ENST00000171111	NM_203500.1	275	tCg/tTg	3/6	0.255036667542896	4	FACETS	1	0.979	1	1	0.979	1	INDETERMINATE	2	TRUE	2	0.855524496011137	4		686	845	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573521	41573521	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	344	575	1	ENST00000263253.7:c.5806G>A	p.Ala1936Thr	p.A1936T	ENST00000263253	NM_001429.3	1936	Gcg/Acg	31/31	0.427623653102724	4	FACETS	1	0.976	1			1	INDETERMINATE	2	TRUE	NA	0.855524496011137	4		576	721	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938423	44938423	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	518	393	0	ENST00000377967.4:c.2971G>T	p.Glu991Ter	p.E991*	ENST00000377967	NM_021140.2	991	Gaa/Taa	20/29	0.663917842053361	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.855524496011137	2		393	568	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164952	123164952	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	451	345	0	ENST00000218089.9:c.265A>T	p.Lys89Ter	p.K89*	ENST00000218089	NM_001042749.1	89	Aaa/Taa	5/35	0.663917842053361	2	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.855524496011137	2		345	513	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3819280	3819281	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0004755-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	186	513	0	ENST00000262367.5:c.2954_2955delinsAA	p.Ser985Ter	p.S985*	ENST00000262367	NM_004380.2	985	tCC/tAA	15/31	1	2	FACETS	0.843	0.785	0.902	0.843	0.785	0.902	CLONAL	1	TRUE	1	0.855524496011137	2		513	516	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	258	280	0				ENST00000310581	NM_198253.2	-/1132			0.639751389051059	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.652698657145985	3		280	499	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0004765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	312	176	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	2	TRUE	NA	0.652698657145985	2		176	470	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0004765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	422	595	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.652698657145985	3	FACETS	0.979	0.948	1	0.979	0.948	1	CLONAL	3	TRUE	0	0.652698657145985	3		595	584	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107125	27107125	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	150	176	0	ENST00000324856.7:c.6736G>T	p.Glu2246Ter	p.E2246*	ENST00000324856	NM_006015.4	2246	Gag/Tag	20/20	0.639751389051059	3	FACETS	1	0.937	1	0.512	0.47	0.556	CLONAL	1	TRUE	1	0.652698657145985	3		176	595	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226576430	226576430	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	143	284	0	ENST00000366794.5:c.644G>C	p.Gly215Ala	p.G215A	ENST00000366794	NM_001618.3	215	gGa/gCa	5/23	0.639751389051059	3	FACETS	0.988	0.905	1	0.494	0.452	0.538	CLONAL	1	TRUE	1	0.652698657145985	3		284	588	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71050155	71050155	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	167	251	0	ENST00000318789.4:c.1030C>T	p.Gln344Ter	p.Q344*	ENST00000318789	NM_032682.5	344	Caa/Taa	13/21	0.461181570738715	5	FACETS	1	0.981	1	0.778	0.722	0.834	CLONAL	2	TRUE	2	0.652698657145985	5		251	434	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16062127	16062127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751755424	NA	P-0004765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	237	302	0	ENST00000268712.3:c.679C>T	p.Pro227Ser	p.P227S	ENST00000268712	NM_006311.3	227	Cct/Tct	6/46	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.652698657145985	2		302	629	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59857624	59857624	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	170	240	0	ENST00000259008.2:c.1933C>T	p.Gln645Ter	p.Q645*	ENST00000259008	NM_032043.2	645	Cag/Tag	13/20	0.519384313752803	6	FACETS	1	0.988	1			1	CLONAL	1	TRUE	NA	0.652698657145985	6		240	836	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797356	135797356	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	219	207	0	ENST00000298552.3:c.513del	p.His171GlnfsTer39	p.H171Qfs*39	ENST00000298552	NM_001162426.1	171	caC/ca	7/23	0.652698657145985	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	3	TRUE	0	0.652698657145985	3		207	269	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651970	36651971	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0004765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	644	277	0	ENST00000244741.5:c.94dup	p.Arg32ProfsTer4	p.R32Pfs*4	ENST00000244741	NM_000389.4	31	agc/agCc	2/3	0.652698657145985	3	FACETS	0.999	0.975	1	0.999	0.975	1	CLONAL	3	TRUE	0	0.652698657145985	3		277	873	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004766-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	18	280	0				ENST00000310581	NM_198253.2	-/1132			0.3	0	FACETS	0.97	0.735	1			1	CLONAL	1	TRUE	0	0.18	0		280	169	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533552	533552	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004766-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	37	395	0	ENST00000451590.1:c.351G>C	p.Lys117Asn	p.K117N	ENST00000451590	NM_001130442.1	117	aaG/aaC	4/5	1	2	FACETS	0.78	0.642	0.935	0.78	0.642	0.935	CLONAL	1	TRUE	1	0.18	2		395	527	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004800-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	178	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.976	1	1	0.994	1	CLONAL	2	TRUE	1	0.378113112949517	2		280	427	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0004800-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	216	558	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.378113112949517	1	FACETS	0.796	0.745	0.847	1	0.993	1	SUBCLONAL	2	TRUE	0	0.378113112949517	1		558	582	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148727	20148727	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0004800-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	204	233	0	ENST00000379607.5:c.338-2A>T		p.X113_splice	ENST00000379607	NM_001412.3	113			1	1	FACETS	0.923	0.877	0.968	1	0.995	1	CLONAL	3	TRUE	0	0.378113112949517	1		233	316	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	147	354	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.429845860249012	3	FACETS	1	0.977	1	0.594	0.543	0.646	CLONAL	1	TRUE	1	0.429845860249012	3		354	700	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	57	505	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	1	2	FACETS	0.344	0.295	0.399	0.344	0.295	0.399	SUBCLONAL	1	TRUE	1	0.429845860249012	2		506	770	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	172	300	0				ENST00000310581	NM_198253.2	-/1132			0.429845860249012	3	FACETS	1	0.989	1	0.741	0.684	0.8	CLONAL	1	TRUE	1	0.429845860249012	3		300	656	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851693	134851693	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1042789	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	55	400	0	ENST00000398015.3:c.1099C>T	p.Arg367Cys	p.R367C	ENST00000398015	NM_004441.4	367	Cgc/Tgc	5/16	1	2	FACETS	0.337	0.287	0.391	0.337	0.287	0.391	SUBCLONAL	1	TRUE	1	0.429845860249012	2		400	760	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928226	178928226	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519872	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	49	346	0	ENST00000263967.3:c.1412C>T	p.Pro471Leu	p.P471L	ENST00000263967	NM_006218.2	471	cCa/cTa	9/21	1	2	FACETS	0.296	0.25	0.348	0.296	0.25	0.348	SUBCLONAL	1	TRUE	1	0.429845860249012	2		346	769	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672738	86672738	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	61	378	0	ENST00000274376.6:c.2225C>T	p.Ser742Leu	p.S742L	ENST00000274376	NM_002890.2	742	tCa/tTa	17/25	0.19330034092065	3	FACETS	0.411	0.353	0.474	0.205	0.176	0.237	INDETERMINATE	1	TRUE	1	0.429845860249012	3		378	839	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407526	407526	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	87	419	0	ENST00000380956.4:c.1284C>G	p.Tyr428Ter	p.Y428*	ENST00000380956	NM_001195286.1	428	taC/taG	9/9	1	2	FACETS	0.393	0.347	0.443	0.393	0.347	0.443	SUBCLONAL	1	TRUE	1	0.429845860249012	2		419	1030	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045678	26045679	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1274	91	693	0	ENST00000540144.1:c.40_41delinsAA	p.Gly14Asn	p.G14N	ENST00000540144	NM_003531.2	14	GGc/AAc	1/1	1	2	FACETS	0.31	0.274	0.349	0.31	0.274	0.349	SUBCLONAL	1	TRUE	1	0.429845860249012	2		693	1365	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680835	30680835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	68	518	0	ENST00000376406.3:c.884C>T	p.Pro295Leu	p.P295L	ENST00000376406	NM_014641.2	295	cCt/cTt	5/15	1	2	FACETS	0.305	0.265	0.35	0.305	0.265	0.35	SUBCLONAL	1	TRUE	1	0.429845860249012	2		518	1036	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120563	94120563	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1320	80	610	0	ENST00000369303.4:c.488G>A	p.Arg163Lys	p.R163K	ENST00000369303	NM_004440.3	163	aGa/aAa	3/17	1	2	FACETS	0.266	0.233	0.302	0.266	0.233	0.302	SUBCLONAL	1	TRUE	1	0.429845860249012	2		610	1400	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553404	106553404	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1166070164	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	49	213	1	ENST00000369096.4:c.1369C>T	p.Pro457Ser	p.P457S	ENST00000369096	NM_001198.3	457	Ccc/Tcc	5/7	1	2	FACETS	0.453	0.384	0.53	0.453	0.384	0.53	SUBCLONAL	1	TRUE	1	0.429845860249012	2		214	503	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374403	81374403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372600489	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	60	452	0	ENST00000222390.5:c.659G>A	p.Arg220Gln	p.R220Q	ENST00000222390	NM_000601.4	220	cGa/cAa	6/18	1	2	FACETS	0.27	0.231	0.312	0.27	0.231	0.312	SUBCLONAL	1	TRUE	1	0.429845860249012	2		452	1034	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849913	151849913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1053970999	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	64	395	0	ENST00000262189.6:c.12403G>A	p.Gly4135Ser	p.G4135S	ENST00000262189	NM_170606.2	4135	Ggt/Agt	49/59	1	2	FACETS	0.326	0.281	0.375	0.326	0.281	0.375	SUBCLONAL	1	TRUE	1	0.429845860249012	2		395	913	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372004	55372004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	97	272	0	ENST00000297316.4:c.694C>T	p.Pro232Ser	p.P232S	ENST00000297316	NM_022454.3	232	Ccc/Tcc	2/2	0.137903160367343	4	FACETS	0.996	0.889	1	0.498	0.444	0.555	INDETERMINATE	1	TRUE	2	0.429845860249012	4		272	648	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741464	145741464	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs534507419	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	121	538	1	ENST00000428558.2:c.1039C>T	p.Arg347Cys	p.R347C	ENST00000428558	NM_004260.3	347	Cgc/Tgc	5/22	0.137903160367343	4	FACETS	0.686	0.618	0.758	0.343	0.309	0.379	INDETERMINATE	1	TRUE	2	0.429845860249012	4		539	1173	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126433	5126433	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	170	318	0	ENST00000381652.3:c.3278G>A	p.Gly1093Glu	p.G1093E	ENST00000381652	NM_004972.3	1093	gGa/gAa	24/25	0.429845860249012	3	FACETS	1	0.985	1	0.641	0.59	0.693	CLONAL	1	TRUE	1	0.429845860249012	3		318	750	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332242	70332242	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	66	680	0	ENST00000373644.4:c.147A>C	p.Leu49Phe	p.L49F	ENST00000373644	NM_030625.2	49	ttA/ttC	2/12	1	2	FACETS	0.278	0.24	0.319	0.278	0.24	0.319	SUBCLONAL	1	TRUE	1	0.429845860249012	2		680	1105	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243226	123243226	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	68	600	0	ENST00000358487.5:c.2287C>G	p.Leu763Val	p.L763V	ENST00000358487	NM_000141.4	763	Ctc/Gtc	17/18	1	2	FACETS	0.265	0.23	0.304	0.265	0.23	0.304	SUBCLONAL	1	TRUE	1	0.429845860249012	2		600	1192	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414302	32414302	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	52	289	0	ENST00000332351.3:c.1250-1G>T		p.X417_splice	ENST00000332351	NM_024426.4	417			1	2	FACETS	0.362	0.308	0.422	0.362	0.308	0.422	SUBCLONAL	1	TRUE	1	0.429845860249012	2		289	668	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856050	111856051	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	41	340	0	ENST00000341259.2:c.101_102delinsTT	p.Ala34Val	p.A34V	ENST00000341259	NM_005475.2	34	gCC/gTT	2/8	1	2	FACETS	0.3	0.249	0.357	0.3	0.249	0.357	SUBCLONAL	1	TRUE	1	0.429845860249012	2		340	635	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434498	121434498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	76	450	0	ENST00000257555.6:c.1262C>T	p.Ser421Phe	p.S421F	ENST00000257555		421	tCc/tTc	6/10	1	2	FACETS	0.37	0.323	0.42	0.37	0.323	0.42	SUBCLONAL	1	TRUE	1	0.429845860249012	2		450	956	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936983	48936983	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131690863	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	56	457	0	ENST00000267163.4:c.751C>T	p.Arg251Ter	p.R251*	ENST00000267163	NM_000321.2	251	Cga/Tga	8/27	1	2	FACETS	0.26	0.222	0.302	0.26	0.222	0.302	SUBCLONAL	1	TRUE	1	0.429845860249012	2		457	1002	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478614	99478614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1277066179	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	68	404	0	ENST00000268035.6:c.3256G>A	p.Asp1086Asn	p.D1086N	ENST00000268035	NM_000875.3	1086	Gat/Aat	17/21	1	2	FACETS	0.351	0.304	0.401	0.351	0.304	0.401	SUBCLONAL	1	TRUE	1	0.429845860249012	2		404	902	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346822	89346822	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253174351	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	54	467	0	ENST00000301030.4:c.6128C>T	p.Ala2043Val	p.A2043V	ENST00000301030	NM_001256183.1	2043	gCc/gTc	9/13	1	2	FACETS	0.319	0.272	0.371	0.319	0.272	0.371	SUBCLONAL	1	TRUE	1	0.429845860249012	2		467	787	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	65	524	0	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	1	2	FACETS	0.348	0.301	0.4	0.348	0.301	0.4	SUBCLONAL	1	TRUE	1	0.429845860249012	2		524	868	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579442	7579442	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs534447939	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	40	396	0	ENST00000269305.4:c.245C>T	p.Pro82Leu	p.P82L	ENST00000269305	NM_001126112.2	82	cCg/cTg	4/11	1	2	FACETS	0.271	0.225	0.324	0.271	0.225	0.324	SUBCLONAL	1	TRUE	1	0.429845860249012	2		396	686	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579580	7579580	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781866	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	52	320	0	ENST00000269305.4:c.107C>T	p.Pro36Leu	p.P36L	ENST00000269305	NM_001126112.2	36	cCg/cTg	4/11	1	2	FACETS	0.39	0.331	0.454	0.39	0.331	0.454	SUBCLONAL	1	TRUE	1	0.429845860249012	2		320	621	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960910	15960910	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776220711	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	56	409	0	ENST00000268712.3:c.6310G>A	p.Glu2104Lys	p.E2104K	ENST00000268712	NM_006311.3	2104	Gaa/Aaa	40/46	1	2	FACETS	0.329	0.281	0.381	0.329	0.281	0.381	SUBCLONAL	1	TRUE	1	0.429845860249012	2		409	793	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29483080	29483080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	46	501	0	ENST00000356175.3:c.140C>T	p.Ser47Phe	p.S47F	ENST00000356175	NM_000267.3	47	tCc/tTc	2/57	1	2	FACETS	0.233	0.195	0.275	0.233	0.195	0.275	SUBCLONAL	1	TRUE	1	0.429845860249012	2		501	919	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794470	42794471	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	82	490	1	ENST00000575354.2:c.1550_1551delinsTT	p.Pro517Leu	p.P517L	ENST00000575354	NM_015125.3	517	cCC/cTT	10/20	1	2	FACETS	0.343	0.301	0.388	0.343	0.301	0.388	SUBCLONAL	1	TRUE	1	0.429845860249012	2		491	1113	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	30946621	30946621	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	44	196	0	ENST00000375687.4:c.43G>C	p.Glu15Gln	p.E15Q	ENST00000375687	NM_015338.5	15	Gag/Cag	1/13	1	2	FACETS	0.421	0.353	0.497	0.421	0.353	0.497	SUBCLONAL	1	TRUE	1	0.429845860249012	2		196	486	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748610	40748610	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	70	452	0	ENST00000373198.4:c.2906G>A	p.Gly969Glu	p.G969E	ENST00000373198	NM_133170.3	969	gGa/gAa	21/32	1	2	FACETS	0.319	0.277	0.365	0.319	0.277	0.365	SUBCLONAL	1	TRUE	1	0.429845860249012	2		452	1021	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164717	36164718	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	116	414	0	ENST00000300305.3:c.1157_1158delinsTT	p.Pro386Leu	p.P386L	ENST00000300305		386	cCC/cTT	8/8	1	2	FACETS	0.58	0.522	0.642	0.58	0.522	0.642	SUBCLONAL	1	TRUE	1	0.429845860249012	2		414	930	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314925	1314925	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004831-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	50	542	0	ENST00000400841.2:c.736C>T	p.Leu246Phe	p.L246F	ENST00000400841		246	Ctc/Ttc	6/6	1	1	FACETS	0.216	0.182	0.253	0.216	0.182	0.253	SUBCLONAL	1	TRUE	0	0.429845860249012	1		542	845	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	94	145	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.948	0.851	1	0.948	0.851	1	CLONAL	1	FALSE	1	0.535770638482003	2		145	370	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073427	8073427	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1187045234	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	394	1358	0	ENST00000377482.5:c.1232T>G	p.Phe411Cys	p.F411C	ENST00000377482	NM_018948.3	411	tTt/tGt	4/4	1	2	FACETS	0.97	0.921	1	0.97	0.921	1	CLONAL	1	FALSE	1	0.535770638482003	2		1358	1516	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073435	8073435	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1365672479	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	417	1354	0	ENST00000377482.5:c.1224A>C	p.Glu408Asp	p.E408D	ENST00000377482	NM_018948.3	408	gaA/gaC	4/4	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	FALSE	1	0.535770638482003	2		1354	1538	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074126	8074126	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	401	1252	2	ENST00000377482.5:c.533A>G	p.Asp178Gly	p.D178G	ENST00000377482	NM_018948.3	178	gAt/gGt	4/4	1	2	FACETS	0.999	0.948	1	0.999	0.948	1	CLONAL	1	FALSE	1	0.535770638482003	2		1254	1499	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9782177	9782177	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	143	521	0	ENST00000377346.4:c.2200C>A	p.Pro734Thr	p.P734T	ENST00000377346	NM_005026.3	734	Cca/Aca	17/24	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	1	0.535770638482003	2		521	518	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307888	11307888	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	297	896	0	ENST00000361445.4:c.1104G>T	p.Glu368Asp	p.E368D	ENST00000361445	NM_004958.3	368	gaG/gaT	7/58	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.535770638482003	2		896	1029	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259962	16259962	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	262	920	3	ENST00000375759.3:c.7227G>T	p.Glu2409Asp	p.E2409D	ENST00000375759	NM_015001.2	2409	gaG/gaT	11/15	1	2	FACETS	0.977	0.916	1	0.977	0.916	1	CLONAL	1	FALSE	1	0.535770638482003	2		923	1001	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363069	40363069	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	197	600	0	ENST00000397332.2:c.1160G>T	p.Arg387Ile	p.R387I	ENST00000397332	NM_001033082.2	387	aGa/aTa	3/3	1	2	FACETS	0.93	0.863	0.999	0.93	0.863	0.999	CLONAL	1	FALSE	1	0.535770638482003	2		600	791	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521530	46521530	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs747237909	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	277	871	1	ENST00000262741.5:c.878A>C	p.Lys293Thr	p.K293T	ENST00000262741	NM_003629.3	293	aAa/aCa	7/10	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.535770638482003	2		872	1011	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46733260	46733260	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	246	759	0	ENST00000371975.4:c.1021T>G	p.Phe341Val	p.F341V	ENST00000371975	NM_003579.3	341	Ttt/Gtt	9/18	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	FALSE	1	0.535770638482003	2		759	889	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733503	85733503	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	309	1203	1	ENST00000370580.1:c.509C>A	p.Ser170Tyr	p.S170Y	ENST00000370580	NM_003921.4	170	tCt/tAt	3/3	1	2	FACETS	0.978	0.921	1	0.978	0.921	1	CLONAL	1	FALSE	1	0.535770638482003	2		1204	1180	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851255	156851255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1480681042	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	251	500	2	ENST00000524377.1:c.2212G>A	p.Asp738Asn	p.D738N	ENST00000524377	NM_002529.3	738	Gac/Aac	17/17	1	2	FACETS	0.995	0.932	1	0.995	0.932	1	CLONAL	1	FALSE	1	0.535770638482003	2		502	942	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099338	193099338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	151	459	0	ENST00000367435.3:c.272G>A	p.Arg91Gln	p.R91Q	ENST00000367435	NM_024529.4	91	cGa/cAa	3/17	1	2	FACETS	0.906	0.832	0.984	0.906	0.832	0.984	CLONAL	1	FALSE	1	0.535770638482003	2		459	622	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104720	193104720	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1131691732	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	142	504	0	ENST00000367435.3:c.423+1G>A		p.X141_splice	ENST00000367435	NM_024529.4	141			1	2	FACETS	0.821	0.75	0.894	0.821	0.75	0.894	CLONAL	1	FALSE	1	0.535770638482003	2		504	646	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111048	193111048	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	156	611	1	ENST00000367435.3:c.581G>T	p.Arg194Ile	p.R194I	ENST00000367435	NM_024529.4	194	aGa/aTa	7/17	1	2	FACETS	0.917	0.843	0.994	0.917	0.843	0.994	CLONAL	1	FALSE	1	0.535770638482003	2		612	635	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111186	193111186	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	133	593	1	ENST00000367435.3:c.719G>A	p.Ser240Asn	p.S240N	ENST00000367435	NM_024529.4	240	aGc/aAc	7/17	1	2	FACETS	0.796	0.725	0.87	0.796	0.725	0.87	SUBCLONAL	1	FALSE	1	0.535770638482003	2		594	624	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716043	243716043	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1376625347	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	140	520	0	ENST00000263826.5:c.1151A>G	p.Asp384Gly	p.D384G	ENST00000263826	NM_005465.4	384	gAt/gGt	10/13	1	2	FACETS	0.814	0.743	0.888	0.814	0.743	0.888	CLONAL	1	FALSE	1	0.535770638482003	2		520	642	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727102	243727102	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	144	582	0	ENST00000263826.5:c.868T>G	p.Phe290Val	p.F290V	ENST00000263826	NM_005465.4	290	Ttt/Gtt	9/13	1	2	FACETS	0.836	0.765	0.91	0.836	0.765	0.91	CLONAL	1	FALSE	1	0.535770638482003	2		582	643	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243778426	243778426	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	145	540	0	ENST00000263826.5:c.599T>G	p.Leu200Ter	p.L200*	ENST00000263826	NM_005465.4	200	tTa/tGa	6/13	1	2	FACETS	0.907	0.831	0.986	0.907	0.831	0.986	CLONAL	1	FALSE	1	0.535770638482003	2		540	597	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085942	16085942	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	176	511	2	ENST00000281043.3:c.1118G>A	p.Arg373Gln	p.R373Q	ENST00000281043	NM_005378.4	373	cGa/cAa	3/3	1	2	FACETS	0.965	0.892	1	0.965	0.892	1	CLONAL	1	FALSE	1	0.535770638482003	2		513	681	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068357	26068357	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	151	574	0	ENST00000435504.4:c.133G>T	p.Glu45Ter	p.E45*	ENST00000435504		45	Gaa/Taa	2/13	1	2	FACETS	0.794	0.727	0.863	0.794	0.727	0.863	SUBCLONAL	1	FALSE	1	0.535770638482003	2		574	710	SUCCESS
ALK	238	MSKCC	GRCh37	2	29430047	29430047	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1553390742	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	228	803	0	ENST00000389048.3:c.3928A>G	p.Thr1310Ala	p.T1310A	ENST00000389048	NM_004304.4	1310	Aca/Gca	26/29	1	2	FACETS	0.927	0.865	0.991	0.927	0.865	0.991	CLONAL	1	FALSE	1	0.535770638482003	2		803	918	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455275	29455275	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748379491	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	213	601	0	ENST00000389048.3:c.2527G>A	p.Gly843Arg	p.G843R	ENST00000389048	NM_004304.4	843	Gga/Aga	15/29	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.535770638482003	2		601	733	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940455	29940455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138686378	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	167	791	5	ENST00000389048.3:c.776G>A	p.Arg259His	p.R259H	ENST00000389048	NM_004304.4	259	cGc/cAc	2/29	1	2	FACETS	0.833	0.767	0.902	0.833	0.767	0.902	CLONAL	1	FALSE	1	0.535770638482003	2		796	748	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47690242	47690242	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1558508227	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	196	737	0	ENST00000233146.2:c.1459G>T	p.Asp487Tyr	p.D487Y	ENST00000233146	NM_000251.2	487	Gac/Tac	9/16	1	2	FACETS	0.823	0.763	0.886	0.823	0.763	0.886	CLONAL	1	FALSE	1	0.535770638482003	2		737	889	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61720080	61720080	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	149	507	0	ENST00000401558.2:c.1354A>C	p.Asn452His	p.N452H	ENST00000401558	NM_003400.3	452	Aat/Cat	13/25	1	2	FACETS	0.845	0.775	0.919	0.845	0.775	0.919	CLONAL	1	FALSE	1	0.535770638482003	2		507	658	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645665	215645665	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1060501297	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	169	531	0	ENST00000260947.4:c.933G>T	p.Lys311Asn	p.K311N	ENST00000260947	NM_000465.2	311	aaG/aaT	4/11	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.535770638482003	2		531	573	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183595	10183595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	306	912	0	ENST00000256474.2:c.64G>A	p.Glu22Lys	p.E22K	ENST00000256474	NM_000551.3	22	Gag/Aag	1/3	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.535770638482003	2		912	1046	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37050324	37050324	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	195	724	0	ENST00000231790.2:c.473A>G	p.Asn158Ser	p.N158S	ENST00000231790	NM_000249.3	158	aAc/aGc	6/19	1	2	FACETS	0.907	0.841	0.975	0.907	0.841	0.975	CLONAL	1	FALSE	1	0.535770638482003	2		724	803	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41268762	41268762	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1245266458	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	207	714	1	ENST00000349496.5:c.1000G>A	p.Glu334Lys	p.E334K	ENST00000349496	NM_001904.3	334	Gaa/Aaa	7/15	1	2	FACETS	0.884	0.821	0.949	0.884	0.821	0.949	CLONAL	1	FALSE	1	0.535770638482003	2		715	874	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163233	47163233	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	171	687	0	ENST00000409792.3:c.2893G>T	p.Glu965Ter	p.E965*	ENST00000409792	NM_014159.6	965	Gaa/Taa	3/21	1	2	FACETS	0.882	0.813	0.953	0.882	0.813	0.953	CLONAL	1	FALSE	1	0.535770638482003	2		687	724	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49724685	49724685	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	163	620	0	ENST00000449682.2:c.504G>T	p.Glu168Asp	p.E168D	ENST00000449682	NM_020998.3	168	gaG/gaT	5/18	NA	2	FACETS	0.967	0.891	1			1	INDETERMINATE	1	FALSE	NA	0.535770638482003	2		620	629	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026984	71026984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763413735	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	133	390	0	ENST00000318789.4:c.1343C>T	p.Ser448Leu	p.S448L	ENST00000318789	NM_032682.5	448	tCg/tTg	15/21	1	2	FACETS	0.918	0.838	1	0.918	0.838	1	CLONAL	1	FALSE	1	0.535770638482003	2		390	541	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71050190	71050190	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs971116457	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	150	392	1	ENST00000318789.4:c.995C>T	p.Ala332Val	p.A332V	ENST00000318789	NM_032682.5	332	gCg/gTg	13/21	1	2	FACETS	0.857	0.786	0.932	0.857	0.786	0.932	CLONAL	1	FALSE	1	0.535770638482003	2		393	653	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72891469	72891469	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	187	515	0	ENST00000325599.8:c.293G>T	p.Arg98Ile	p.R98I	ENST00000325599	NM_018130.2	98	aGa/aTa	3/11	1	2	FACETS	0.866	0.801	0.933	0.866	0.801	0.933	CLONAL	1	FALSE	1	0.535770638482003	2		515	806	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664792	138664792	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	16	46	0	ENST00000330315.3:c.773A>G	p.Tyr258Cys	p.Y258C	ENST00000330315	NM_023067.3	258	tAc/tGc	1/1	1	2	FACETS	0.766	0.578	0.979	0.766	0.578	0.979	CLONAL	1	FALSE	1	0.535770638482003	2		46	78	SUCCESS
ATR	545	MSKCC	GRCh37	3	142224146	142224146	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	139	473	0	ENST00000350721.4:c.5032-1G>T		p.X1678_splice	ENST00000350721	NM_001184.3	1678			1	2	FACETS	0.933	0.854	1	0.933	0.854	1	CLONAL	1	FALSE	1	0.535770638482003	2		473	556	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269003	142269003	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537845660	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	212	723	0	ENST00000350721.4:c.2947G>A	p.Asp983Asn	p.D983N	ENST00000350721	NM_001184.3	983	Gac/Aac	14/47	1	2	FACETS	0.885	0.823	0.949	0.885	0.823	0.949	CLONAL	1	FALSE	1	0.535770638482003	2		723	894	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281484	142281484	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	202	633	0	ENST00000350721.4:c.760G>T	p.Glu254Ter	p.E254*	ENST00000350721	NM_001184.3	254	Gaa/Taa	4/47	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	1	0.535770638482003	2		633	754	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281952	142281952	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	50	128	0	ENST00000350721.4:c.293-1G>T		p.X98_splice	ENST00000350721	NM_001184.3	98			1	2	FACETS	0.648	0.553	0.751	0.648	0.553	0.751	SUBCLONAL	1	FALSE	1	0.535770638482003	2		128	288	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916946	178916946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	243	973	1	ENST00000263967.3:c.333G>T	p.Lys111Asn	p.K111N	ENST00000263967	NM_006218.2	111	aaG/aaT	2/21	1	2	FACETS	0.834	0.779	0.891	0.834	0.779	0.891	CLONAL	1	FALSE	1	0.535770638482003	2		974	1088	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584500	189584500	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	192	652	2	ENST00000264731.3:c.796C>T	p.Arg266Ter	p.R266*	ENST00000264731	NM_003722.4	266	Cga/Tga	6/14	1	2	FACETS	0.922	0.855	0.992	0.922	0.855	0.992	CLONAL	1	FALSE	1	0.535770638482003	2		654	777	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131106	55131106	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	263	691	1	ENST00000257290.5:c.649G>T	p.Glu217Ter	p.E217*	ENST00000257290	NM_006206.4	217	Gaa/Taa	5/23	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	1	0.535770638482003	2		692	976	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968610	55968610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374980446	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	230	692	0	ENST00000263923.4:c.2053G>A	p.Glu685Lys	p.E685K	ENST00000263923	NM_002253.2	685	Gaa/Aaa	14/30	1	2	FACETS	0.975	0.91	1	0.975	0.91	1	CLONAL	1	FALSE	1	0.535770638482003	2		692	881	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230870	66230870	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765807043	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	147	574	0	ENST00000273854.3:c.2101G>A	p.Glu701Lys	p.E701K	ENST00000273854	NM_004439.5	701	Gaa/Aaa	12/18	1	2	FACETS	0.853	0.782	0.928	0.853	0.782	0.928	CLONAL	1	FALSE	1	0.535770638482003	2		574	643	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84393430	84393430	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	144	482	0	ENST00000321945.7:c.227C>A	p.Ser76Tyr	p.S76Y	ENST00000321945	NM_139076.2	76	tCt/tAt	4/9	1	2	FACETS	0.875	0.801	0.953	0.875	0.801	0.953	CLONAL	1	FALSE	1	0.535770638482003	2		482	614	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106162525	106162525	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	131	494	1	ENST00000380013.4:c.3439T>G	p.Phe1147Val	p.F1147V	ENST00000380013	NM_001127208.2	1147	Ttt/Gtt	4/11	1	2	FACETS	0.825	0.751	0.902	0.825	0.751	0.902	CLONAL	1	FALSE	1	0.535770638482003	2		495	593	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332718	153332718	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	179	530	0	ENST00000281708.4:c.238A>C	p.Asn80His	p.N80H	ENST00000281708	NM_033632.3	80	Aac/Cac	2/12	1	2	FACETS	0.97	0.897	1	0.97	0.897	1	CLONAL	1	FALSE	1	0.535770638482003	2		530	689	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557284	187557284	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	243	705	1	ENST00000441802.2:c.4078G>T	p.Glu1360Ter	p.E1360*	ENST00000441802	NM_005245.3	1360	Gaa/Taa	6/27	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.535770638482003	2		706	879	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584696	187584696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144526682	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	290	834	4	ENST00000441802.2:c.3337G>A	p.Asp1113Asn	p.D1113N	ENST00000441802	NM_005245.3	1113	Gat/Aat	3/27	1	2	FACETS	0.992	0.934	1	0.992	0.934	1	CLONAL	1	FALSE	1	0.535770638482003	2		838	1091	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873734	35873734	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	160	553	0	ENST00000303115.3:c.690G>T	p.Glu230Asp	p.E230D	ENST00000303115	NM_002185.3	230	gaG/gaT	5/8	1	2	FACETS	0.953	0.877	1	0.953	0.877	1	CLONAL	1	FALSE	1	0.535770638482003	2		553	627	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875685	35875685	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	198	671	0	ENST00000303115.3:c.872G>T	p.Arg291Ile	p.R291I	ENST00000303115	NM_002185.3	291	aGa/aTa	7/8	1	2	FACETS	0.902	0.837	0.97	0.902	0.837	0.97	CLONAL	1	FALSE	1	0.535770638482003	2		671	819	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950600	38950600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	217	869	0	ENST00000357387.3:c.3350G>A	p.Gly1117Glu	p.G1117E	ENST00000357387	NM_152756.3	1117	gGa/gAa	31/38	1	2	FACETS	0.796	0.74	0.854	0.796	0.74	0.854	SUBCLONAL	1	FALSE	1	0.535770638482003	2		869	1018	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56152491	56152491	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561183082	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	193	622	0	ENST00000399503.3:c.547C>T	p.Arg183Ter	p.R183*	ENST00000399503	NM_005921.1	183	Cga/Tga	2/20	1	2	FACETS	0.902	0.836	0.97	0.902	0.836	0.97	CLONAL	1	FALSE	1	0.535770638482003	2		622	799	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184180	56184180	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	138	446	0	ENST00000399503.3:c.4385T>G	p.Phe1462Cys	p.F1462C	ENST00000399503	NM_005921.1	1462	tTt/tGt	19/20	1	2	FACETS	0.788	0.719	0.86	0.788	0.719	0.86	SUBCLONAL	1	FALSE	1	0.535770638482003	2		446	654	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57752839	57752839	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	131	475	2	ENST00000274289.3:c.1089C>A	p.Phe363Leu	p.F363L	ENST00000274289	NM_006622.3	363	ttC/ttA	8/14	1	2	FACETS	0.886	0.807	0.968	0.886	0.807	0.968	CLONAL	1	FALSE	1	0.535770638482003	2		477	552	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575550	67575550	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	148	403	0	ENST00000274335.5:c.623C>A	p.Ser208Tyr	p.S208Y	ENST00000274335		208	tCt/tAt	4/15	1	2	FACETS	0.88	0.806	0.956	0.88	0.806	0.956	CLONAL	1	FALSE	1	0.535770638482003	2		403	628	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86629147	86629147	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	165	495	0	ENST00000274376.6:c.892G>T	p.Glu298Ter	p.E298*	ENST00000274376	NM_002890.2	298	Gaa/Taa	4/25	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	FALSE	1	0.535770638482003	2		495	616	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645121	86645121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	160	445	0	ENST00000274376.6:c.1193G>A	p.Arg398Gln	p.R398Q	ENST00000274376	NM_002890.2	398	cGa/cAa	8/25	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.535770638482003	2		445	564	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86649000	86649000	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755634472	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	155	519	0	ENST00000274376.6:c.1280G>A	p.Arg427Gln	p.R427Q	ENST00000274376	NM_002890.2	427	cGa/cAa	9/25	1	2	FACETS	0.905	0.832	0.982	0.905	0.832	0.982	CLONAL	1	FALSE	1	0.535770638482003	2		519	639	SUCCESS
APC	324	MSKCC	GRCh37	5	112175876	112175876	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554085992	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	196	542	0	ENST00000257430.4:c.4585C>T	p.Gln1529Ter	p.Q1529*	ENST00000257430	NM_000038.5	1529	Cag/Tag	16/16	1	2	FACETS	0.923	0.856	0.992	0.923	0.856	0.992	CLONAL	1	FALSE	1	0.535770638482003	2		542	793	SUCCESS
APC	324	MSKCC	GRCh37	5	112177788	112177788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752091655	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	153	504	0	ENST00000257430.4:c.6497G>A	p.Arg2166Gln	p.R2166Q	ENST00000257430	NM_000038.5	2166	cGa/cAa	16/16	1	2	FACETS	0.828	0.759	0.899	0.828	0.759	0.899	CLONAL	1	FALSE	1	0.535770638482003	2		504	690	SUCCESS
APC	324	MSKCC	GRCh37	5	112177901	112177901	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs752654519	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	180	445	1	ENST00000257430.4:c.6610C>T	p.Arg2204Ter	p.R2204*	ENST00000257430	NM_000038.5	2204	Cga/Tga	16/16	1	2	FACETS	0.991	0.917	1	0.991	0.917	1	CLONAL	1	FALSE	1	0.535770638482003	2		446	678	SUCCESS
APC	324	MSKCC	GRCh37	5	112178000	112178000	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768922431	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	203	679	1	ENST00000257430.4:c.6709C>T	p.Arg2237Ter	p.R2237*	ENST00000257430	NM_000038.5	2237	Cga/Tga	16/16	1	2	FACETS	0.936	0.869	1	0.936	0.869	1	CLONAL	1	FALSE	1	0.535770638482003	2		680	810	SUCCESS
APC	324	MSKCC	GRCh37	5	112178541	112178541	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	165	540	0	ENST00000257430.4:c.7250C>A	p.Ser2417Tyr	p.S2417Y	ENST00000257430	NM_000038.5	2417	tCt/tAt	16/16	1	2	FACETS	0.923	0.851	0.999	0.923	0.851	0.999	CLONAL	1	FALSE	1	0.535770638482003	2		540	667	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176666761	176666761	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	214	672	0	ENST00000439151.2:c.4197T>G	p.Asn1399Lys	p.N1399K	ENST00000439151	NM_022455.4	1399	aaT/aaG	8/23	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	1	0.535770638482003	2		672	799	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673782	176673782	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	209	680	0	ENST00000439151.2:c.4482G>T	p.Glu1494Asp	p.E1494D	ENST00000439151	NM_022455.4	1494	gaG/gaT	10/23	1	2	FACETS	0.91	0.846	0.976	0.91	0.846	0.976	CLONAL	1	FALSE	1	0.535770638482003	2		680	857	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401711	401711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753680565	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	237	640	0	ENST00000380956.4:c.1033G>A	p.Asp345Asn	p.D345N	ENST00000380956	NM_001195286.1	345	Gac/Aac	7/9	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.535770638482003	2		640	858	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	405111	405111	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	222	731	0	ENST00000380956.4:c.1193G>T	p.Arg398Ile	p.R398I	ENST00000380956	NM_001195286.1	398	aGa/aTa	8/9	1	2	FACETS	0.926	0.863	0.991	0.926	0.863	0.991	CLONAL	1	FALSE	1	0.535770638482003	2		731	895	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967895	93967895	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	269	1016	0	ENST00000369303.4:c.2032G>T	p.Asp678Tyr	p.D678Y	ENST00000369303	NM_004440.3	678	Gac/Tac	11/17	1	2	FACETS	0.883	0.828	0.94	0.883	0.828	0.94	CLONAL	1	FALSE	1	0.535770638482003	2		1016	1137	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979246	93979246	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	261	1047	0	ENST00000369303.4:c.1582C>T	p.Pro528Ser	p.P528S	ENST00000369303	NM_004440.3	528	Ccc/Tcc	7/17	1	2	FACETS	0.877	0.821	0.934	0.877	0.821	0.934	CLONAL	1	FALSE	1	0.535770638482003	2		1047	1111	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715366	117715366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	151	538	0	ENST00000368508.3:c.1123G>T	p.Asp375Tyr	p.D375Y	ENST00000368508	NM_002944.2	375	Gat/Tat	10/43	1	2	FACETS	0.833	0.763	0.905	0.833	0.763	0.905	CLONAL	1	FALSE	1	0.535770638482003	2		538	677	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202210	138202210	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	228	596	0	ENST00000237289.4:c.2127A>C	p.Gln709His	p.Q709H	ENST00000237289	NM_001270507.1	709	caA/caC	9/9	1	2	FACETS	0.999	0.933	1	0.999	0.933	1	CLONAL	1	FALSE	1	0.535770638482003	2		596	852	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265319	152265319	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	176	614	0	ENST00000206249.3:c.772G>T	p.Asp258Tyr	p.D258Y	ENST00000206249	NM_000125.3	258	Gac/Tac	4/8	1	2	FACETS	0.784	0.723	0.848	0.784	0.723	0.848	SUBCLONAL	1	FALSE	1	0.535770638482003	2		614	838	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157525044	157525044	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	241	773	0	ENST00000346085.5:c.4939C>A	p.Leu1647Ile	p.L1647I	ENST00000346085	NM_020732.3	1647	Ctt/Att	19/20	1	2	FACETS	0.963	0.901	1	0.963	0.901	1	CLONAL	1	FALSE	1	0.535770638482003	2		773	934	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729604	41729604	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	305	1065	2	ENST00000242208.4:c.925C>T	p.Arg309Trp	p.R309W	ENST00000242208	NM_002192.2	309	Cgg/Tgg	3/3	1	2	FACETS	0.868	0.817	0.92	0.868	0.817	0.92	CLONAL	1	FALSE	1	0.535770638482003	2		1067	1312	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444401	50444401	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	170	205	0	ENST00000331340.3:c.331C>T	p.Arg111Ter	p.R111*	ENST00000331340	NM_006060.4	111	Cga/Tga	4/8	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	FALSE	1	0.535770638482003	2		205	626	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509539	106509539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	235	615	1	ENST00000359195.3:c.1533G>T	p.Glu511Asp	p.E511D	ENST00000359195	NM_002649.2	511	gaG/gaT	2/11	1	2	FACETS	0.999	0.934	1	0.999	0.934	1	CLONAL	1	FALSE	1	0.535770638482003	2		616	878	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027816	152027816	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	202	565	0	ENST00000262189.6:c.259G>T	p.Glu87Ter	p.E87*	ENST00000262189	NM_170606.2	87	Gaa/Taa	3/59	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	FALSE	1	0.535770638482003	2		565	752	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152346008	152346008	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139219364	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	336	1152	0	ENST00000359321.1:c.562C>T	p.Arg188Cys	p.R188C	ENST00000359321	NM_005431.1	188	Cgc/Tgc	3/3	1	2	FACETS	0.972	0.919	1	0.972	0.919	1	CLONAL	1	FALSE	1	0.535770638482003	2		1152	1290	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050761	5050761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	153	534	0	ENST00000381652.3:c.544G>A	p.Ala182Thr	p.A182T	ENST00000381652	NM_004972.3	182	Gca/Aca	6/25	1	2	FACETS	0.86	0.789	0.934	0.86	0.789	0.934	CLONAL	1	FALSE	1	0.535770638482003	2		534	664	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449814	8449814	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	150	458	1	ENST00000356435.5:c.3899G>T	p.Arg1300Ile	p.R1300I	ENST00000356435		1300	aGa/aTa	23/35	1	2	FACETS	0.913	0.838	0.992	0.913	0.838	0.992	CLONAL	1	FALSE	1	0.535770638482003	2		459	613	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484149	8484149	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	194	681	0	ENST00000356435.5:c.3383T>G	p.Leu1128Arg	p.L1128R	ENST00000356435		1128	cTg/cGg	19/35	1	2	FACETS	0.894	0.829	0.962	0.894	0.829	0.962	CLONAL	1	FALSE	1	0.535770638482003	2		681	810	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504401	8504401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757922864	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	129	419	1	ENST00000356435.5:c.1682G>A	p.Arg561Gln	p.R561Q	ENST00000356435		561	cGa/cAa	12/35	1	2	FACETS	0.893	0.814	0.976	0.893	0.814	0.976	CLONAL	1	FALSE	1	0.535770638482003	2		420	539	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633380	8633380	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	160	722	1	ENST00000356435.5:c.289G>T	p.Glu97Ter	p.E97*	ENST00000356435		97	Gaa/Taa	3/35	1	2	FACETS	0.841	0.773	0.912	0.841	0.773	0.912	CLONAL	1	FALSE	1	0.535770638482003	2		723	710	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974825	21974825	+	start_lost	Translation_Start_Site	SNP	A	A	G	rs759871071	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	31	109	0	ENST00000304494.5:c.2T>C	p.Met1?	p.M1?	ENST00000304494	NM_000077.4	1	aTg/aCg	1/3	1	2	FACETS	0.723	0.592	0.867	0.723	0.592	0.867	SUBCLONAL	1	FALSE	1	0.535770638482003	2		109	160	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342596	87342596	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	153	564	2	ENST00000277120.3:c.881C>A	p.Ser294Tyr	p.S294Y	ENST00000277120		294	tCt/tAt	9/19	1	2	FACETS	0.84	0.77	0.912	0.84	0.77	0.912	CLONAL	1	FALSE	1	0.535770638482003	2		566	680	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570366	87570366	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	284	613	1	ENST00000277120.3:c.2106G>T	p.Glu702Asp	p.E702D	ENST00000277120		702	gaG/gaT	17/19	1	2	FACETS	0.885	0.831	0.94	0.885	0.831	0.94	CLONAL	1	FALSE	1	0.535770638482003	2		614	1198	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98011564	98011564	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	169	524	0	ENST00000289081.3:c.10G>T	p.Asp4Tyr	p.D4Y	ENST00000289081	NM_000136.2	4	Gat/Tat	2/15	1	2	FACETS	0.9	0.83	0.973	0.9	0.83	0.973	CLONAL	1	FALSE	1	0.535770638482003	2		524	701	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232138	98232138	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs863224650	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	184	577	0	ENST00000331920.6:c.1804C>T	p.Arg602Ter	p.R602*	ENST00000331920	NM_000264.3	602	Cga/Tga	13/24	1	2	FACETS	0.853	0.789	0.92	0.853	0.789	0.92	CLONAL	1	FALSE	1	0.535770638482003	2		577	805	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333850	70333850	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs762232511	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	210	664	2	ENST00000373644.4:c.1755G>T	p.Lys585Asn	p.K585N	ENST00000373644	NM_030625.2	585	aaG/aaT	2/12	1	2	FACETS	0.976	0.909	1	0.976	0.909	1	CLONAL	1	FALSE	1	0.535770638482003	2		666	803	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88672037	88672037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1053423400	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	87	340	1	ENST00000372037.3:c.571C>T	p.Arg191Cys	p.R191C	ENST00000372037	NM_004329.2	191	Cgt/Tgt	8/13	1	2	FACETS	0.875	0.781	0.975	0.875	0.781	0.975	CLONAL	1	FALSE	1	0.535770638482003	2		341	371	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104377097	104377097	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	245	969	0	ENST00000369902.3:c.1208A>G	p.Asp403Gly	p.D403G	ENST00000369902	NM_016169.3	403	gAc/gGc	10/12	1	2	FACETS	0.89	0.832	0.949	0.89	0.832	0.949	CLONAL	1	FALSE	1	0.535770638482003	2		969	1028	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589651	69589651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	93	288	0	ENST00000168712.1:c.202G>A	p.Ala68Thr	p.A68T	ENST00000168712	NM_002007.2	68	Gcc/Acc	1/3	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.535770638482003	2		288	312	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102198863	102198863	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	264	944	0	ENST00000263464.3:c.1032+2T>C		p.X344_splice	ENST00000263464	NM_001165.4	344			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.535770638482003	2		944	966	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115673	108115673	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	149	447	0	ENST00000278616.4:c.821C>A	p.Ser274Tyr	p.S274Y	ENST00000278616	NM_000051.3	274	tCt/tAt	7/63	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	FALSE	1	0.535770638482003	2		447	551	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115717	108115717	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555067259	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	119	387	0	ENST00000278616.4:c.865A>C	p.Ile289Leu	p.I289L	ENST00000278616	NM_000051.3	289	Atc/Ctc	7/63	1	2	FACETS	0.941	0.855	1	0.941	0.855	1	CLONAL	1	FALSE	1	0.535770638482003	2		387	472	SUCCESS
ATM	472	MSKCC	GRCh37	11	108153581	108153581	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	95	450	0	ENST00000278616.4:c.3721T>G	p.Tyr1241Asp	p.Y1241D	ENST00000278616	NM_000051.3	1241	Tac/Gac	25/63	1	2	FACETS	0.829	0.742	0.92	0.829	0.742	0.92	CLONAL	1	FALSE	1	0.535770638482003	2		450	428	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344036	118344036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	167	488	0	ENST00000534358.1:c.2162G>A	p.Arg721Gln	p.R721Q	ENST00000534358	NM_005933.3	721	cGa/cAa	3/36	1	2	FACETS	0.971	0.896	1	0.971	0.896	1	CLONAL	1	FALSE	1	0.535770638482003	2		488	642	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	420091	420091	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs545445538	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	243	697	0	ENST00000399788.2:c.3176G>A	p.Arg1059Gln	p.R1059Q	ENST00000399788	NM_001042603.1	1059	cGg/cAg	21/28	1	2	FACETS	0.84	0.784	0.897	0.84	0.784	0.897	CLONAL	1	FALSE	1	0.535770638482003	2		697	1080	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446950	18446950	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	99	431	0	ENST00000266497.5:c.1034+1G>T		p.X345_splice	ENST00000266497		345			1	2	FACETS	0.823	0.739	0.912	0.823	0.739	0.912	CLONAL	1	FALSE	1	0.535770638482003	2		431	449	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499648	18499648	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	230	728	0	ENST00000266497.5:c.1503T>G	p.Phe501Leu	p.F501L	ENST00000266497		501	ttT/ttG	10/31	1	2	FACETS	0.935	0.873	1	0.935	0.873	1	CLONAL	1	FALSE	1	0.535770638482003	2		728	918	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285685	46285685	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	119	459	0	ENST00000334344.6:c.5045T>G	p.Phe1682Cys	p.F1682C	ENST00000334344	NM_152641.2	1682	tTt/tGt	17/21	1	2	FACETS	0.812	0.736	0.892	0.812	0.736	0.892	CLONAL	1	FALSE	1	0.535770638482003	2		459	547	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418670	49418670	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783698	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	262	789	0	ENST00000301067.7:c.15844C>T	p.Arg5282Ter	p.R5282*	ENST00000301067	NM_003482.3	5282	Cga/Tga	49/54	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.535770638482003	2		789	927	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859665	57859665	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	360	1277	0	ENST00000228682.2:c.719A>G	p.Asp240Gly	p.D240G	ENST00000228682	NM_005269.2	240	gAt/gGt	7/12	1	2	FACETS	0.973	0.921	1	0.973	0.921	1	CLONAL	1	FALSE	1	0.535770638482003	2		1277	1381	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861838	57861838	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381253752	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	437	1338	0	ENST00000228682.2:c.1139G>A	p.Arg380Gln	p.R380Q	ENST00000228682	NM_005269.2	380	cGa/cAa	10/12	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.535770638482003	2		1338	1510	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115392	115115392	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	237	772	0	ENST00000257566.3:c.934G>T	p.Glu312Ter	p.E312*	ENST00000257566	NM_016569.3	312	Gaa/Taa	5/8	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.535770638482003	2		772	851	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536873	120536873	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	308	1240	0	ENST00000229340.5:c.313G>T	p.Glu105Ter	p.E105*	ENST00000229340	NM_006861.6	105	Gaa/Taa	4/6	1	2	FACETS	0.866	0.815	0.918	0.866	0.815	0.918	CLONAL	1	FALSE	1	0.535770638482003	2		1240	1328	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253184	133253184	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519943	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	287	797	0	ENST00000320574.5:c.857C>G	p.Pro286Arg	p.P286R	ENST00000320574	NM_006231.2	286	cCt/cGt	9/49	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	FALSE	1	0.535770638482003	2		797	1007	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21553895	21553895	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	363	903	1	ENST00000382592.4:c.2707C>A	p.Leu903Ile	p.L903I	ENST00000382592	NM_014572.2	903	Ctc/Atc	7/8	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	FALSE	NA	0.535770638482003	2		904	1237	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134988	41134988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	359	1073	1	ENST00000379561.5:c.640C>T	p.Arg214Cys	p.R214C	ENST00000379561	NM_002015.3	214	Cgt/Tgt	2/3	1	2	FACETS	0.976	0.924	1	0.976	0.924	1	CLONAL	1	FALSE	1	0.535770638482003	2		1074	1373	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881438	48881438	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	112	481	0	ENST00000267163.4:c.160G>T	p.Glu54Ter	p.E54*	ENST00000267163	NM_000321.2	54	Gaa/Taa	2/27	1	2	FACETS	0.66	0.595	0.729	0.66	0.595	0.729	SUBCLONAL	1	FALSE	1	0.535770638482003	2		481	633	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916843	48916843	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	99	402	0	ENST00000267163.4:c.373G>T	p.Glu125Ter	p.E125*	ENST00000267163	NM_000321.2	125	Gaa/Taa	3/27	1	2	FACETS	0.741	0.664	0.822	0.741	0.664	0.822	SUBCLONAL	1	FALSE	1	0.535770638482003	2		402	499	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955481	48955481	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237070816	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	176	604	0	ENST00000267163.4:c.1597G>A	p.Glu533Lys	p.E533K	ENST00000267163	NM_000321.2	533	Gaa/Aaa	17/27	1	2	FACETS	0.878	0.811	0.948	0.878	0.811	0.948	CLONAL	1	FALSE	1	0.535770638482003	2		604	748	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566237	95566237	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	136	512	0	ENST00000393063.1:c.4086G>T	p.Lys1362Asn	p.K1362N	ENST00000393063	NM_030621.3	1362	aaG/aaT	23/28	1	2	FACETS	0.838	0.764	0.914	0.838	0.764	0.914	CLONAL	1	FALSE	1	0.535770638482003	2		512	606	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729175	66729175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908596	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	273	316	0	ENST00000307102.5:c.383G>A	p.Gly128Asp	p.G128D	ENST00000307102	NM_002755.3	128	gGc/gAc	3/11	1	2	FACETS	0.993	0.933	1	0.993	0.933	1	CLONAL	1	FALSE	1	0.535770638482003	2		316	1026	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476262	88476262	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	171	637	0	ENST00000360948.2:c.1870G>T	p.Asp624Tyr	p.D624Y	ENST00000360948	NM_001012338.2	624	Gac/Tac	15/19	1	2	FACETS	0.933	0.861	1	0.933	0.861	1	CLONAL	1	FALSE	1	0.535770638482003	2		637	684	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680780	88680780	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	201	669	0	ENST00000360948.2:c.477G>T	p.Gln159His	p.Q159H	ENST00000360948	NM_001012338.2	159	caG/caT	6/19	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	FALSE	1	0.535770638482003	2		669	747	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434589	99434589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752189789	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	203	572	0	ENST00000268035.6:c.676G>A	p.Glu226Lys	p.E226K	ENST00000268035	NM_000875.3	226	Gag/Aag	3/21	1	2	FACETS	0.993	0.923	1	0.993	0.923	1	CLONAL	1	FALSE	1	0.535770638482003	2		572	763	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134992	2134992	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774441486	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	301	1051	1	ENST00000219476.3:c.4534G>A	p.Asp1512Asn	p.D1512N	ENST00000219476	NM_000548.3	1512	Gac/Aac	35/42	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.535770638482003	2		1052	1048	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857401	9857401	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	162	656	0	ENST00000330684.3:c.4000A>G	p.Ser1334Gly	p.S1334G	ENST00000330684	NM_001134407.1	1334	Agc/Ggc	13/13	NA	2	FACETS	0.801	0.736	0.868			1	INDETERMINATE	1	FALSE	NA	0.535770638482003	2		656	755	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858276	9858276	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	198	657	0	ENST00000330684.3:c.3125G>T	p.Arg1042Met	p.R1042M	ENST00000330684	NM_001134407.1	1042	aGg/aTg	13/13	NA	2	FACETS	0.91	0.845	0.978			1	INDETERMINATE	1	FALSE	NA	0.535770638482003	2		657	812	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858544	9858544	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1555482851	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	250	772	0	ENST00000330684.3:c.2857G>T	p.Glu953Ter	p.E953*	ENST00000330684	NM_001134407.1	953	Gag/Tag	13/13	NA	2	FACETS	1	0.968	1			1	INDETERMINATE	1	FALSE	NA	0.535770638482003	2		772	887	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923465	9923465	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	236	718	0	ENST00000330684.3:c.1822C>A	p.Leu608Ile	p.L608I	ENST00000330684	NM_001134407.1	608	Ctt/Att	9/13	1	2	FACETS	0.961	0.898	1	0.961	0.898	1	CLONAL	1	FALSE	1	0.535770638482003	2		718	917	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857307	68857307	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs971882211	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	182	510	1	ENST00000261769.5:c.1942G>T	p.Glu648Ter	p.E648*	ENST00000261769	NM_004360.3	648	Gaa/Taa	13/16	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	FALSE	1	0.535770638482003	2		511	660	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822178	72822178	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	365	1196	0	ENST00000268489.5:c.9997C>A	p.Gln3333Lys	p.Q3333K	ENST00000268489	NM_006885.3	3333	Cag/Aag	10/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.535770638482003	2		1196	1338	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832339	72832339	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	356	1227	0	ENST00000268489.5:c.4242A>C	p.Glu1414Asp	p.E1414D	ENST00000268489	NM_006885.3	1414	gaA/gaC	9/10	1	2	FACETS	0.97	0.918	1	0.97	0.918	1	CLONAL	1	FALSE	1	0.535770638482003	2		1227	1370	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350710	89350710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138898373	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	425	1537	3	ENST00000301030.4:c.2240C>T	p.Ser747Leu	p.S747L	ENST00000301030	NM_001256183.1	747	tCg/tTg	9/13	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.535770638482003	2		1540	1572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	653	465	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.535770638482003	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	FALSE	0	0.535770638482003	2		467	1183	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040679	16040679	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	197	648	0	ENST00000268712.3:c.1455G>T	p.Glu485Asp	p.E485D	ENST00000268712	NM_006311.3	485	gaG/gaT	14/46	1	2	FACETS	0.877	0.813	0.942	0.877	0.813	0.942	CLONAL	1	FALSE	1	0.535770638482003	2		648	839	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006623	62006623	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	206	775	0	ENST00000392795.3:c.656T>G	p.Val219Gly	p.V219G	ENST00000392795	NM_001039933.1	219	gTg/gGg	6/6	1	2	FACETS	0.992	0.923	1	0.992	0.923	1	CLONAL	1	FALSE	1	0.535770638482003	2		775	775	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554264	63554264	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs753036084	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	257	798	0	ENST00000307078.5:c.475G>T	p.Asp159Tyr	p.D159Y	ENST00000307078	NM_004655.3	159	Gat/Tat	2/11	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	1	0.535770638482003	2		798	957	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554343	63554343	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	271	824	0	ENST00000307078.5:c.396A>C	p.Lys132Asn	p.K132N	ENST00000307078	NM_004655.3	132	aaA/aaC	2/11	1	2	FACETS	0.958	0.899	1	0.958	0.899	1	CLONAL	1	FALSE	1	0.535770638482003	2		824	1056	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593465	48593465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs794726995	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	188	573	2	ENST00000342988.3:c.1216G>A	p.Ala406Thr	p.A406T	ENST00000342988	NM_005359.5	406	Gcg/Acg	10/12	1	2	FACETS	0.892	0.826	0.96	0.892	0.826	0.96	CLONAL	1	FALSE	1	0.535770638482003	2		575	787	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604736	48604736	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	253	598	0	ENST00000342988.3:c.1558G>T	p.Glu520Ter	p.E520*	ENST00000342988	NM_005359.5	520	Gaa/Taa	12/12	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.535770638482003	2		598	890	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60795942	60795942	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	271	763	3	ENST00000333681.4:c.636C>A	p.Phe212Leu	p.F212L	ENST00000333681		212	ttC/ttA	3/3	1	2	FACETS	0.891	0.836	0.948	0.891	0.836	0.948	CLONAL	1	FALSE	1	0.535770638482003	2		766	1135	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626925	14626925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374296355	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	338	1228	0	ENST00000254322.2:c.850G>A	p.Val284Ile	p.V284I	ENST00000254322	NM_006145.1	284	Gta/Ata	3/3	1	2	FACETS	0.906	0.856	0.958	0.906	0.856	0.958	CLONAL	1	FALSE	1	0.535770638482003	2		1228	1392	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726544	41726544	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs891614619	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	201	662	0	ENST00000301178.4:c.89C>T	p.Thr30Met	p.T30M	ENST00000301178	NM_021913.4	30	aCg/aTg	2/20	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	1	0.535770638482003	2		662	735	SUCCESS
AXL	558	MSKCC	GRCh37	19	41748909	41748909	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	228	847	1	ENST00000301178.4:c.1434G>T	p.Glu478Asp	p.E478D	ENST00000301178	NM_021913.4	478	gaG/gaT	11/20	1	2	FACETS	0.873	0.814	0.934	0.873	0.814	0.934	CLONAL	1	FALSE	1	0.535770638482003	2		848	975	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023264	31023264	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	257	868	0	ENST00000375687.4:c.2749G>T	p.Glu917Ter	p.E917*	ENST00000375687	NM_015338.5	917	Gaa/Taa	13/13	1	2	FACETS	0.951	0.891	1	0.951	0.891	1	CLONAL	1	FALSE	1	0.535770638482003	2		868	1009	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39725906	39725906	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	161	482	0	ENST00000361337.2:c.777C>A	p.Phe259Leu	p.F259L	ENST00000361337	NM_003286.2	259	ttC/ttA	10/21	1	2	FACETS	0.866	0.796	0.938	0.866	0.796	0.938	CLONAL	1	FALSE	1	0.535770638482003	2		482	694	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1327744	1327744	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	299	835	0	ENST00000400841.2:c.137G>A	p.Trp46Ter	p.W46*	ENST00000400841		46	tGg/tAg	2/6	1	1	FACETS	0.749	0.706	0.793	0.749	0.706	0.793	SUBCLONAL	1	FALSE	0	0.535770638482003	1		835	1091	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411783	63411783	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	336	630	0	ENST00000330258.3:c.1384G>T	p.Glu462Ter	p.E462*	ENST00000330258	NM_152424.3	462	Gaa/Taa	2/2	1	1	FACETS	0.77	0.737	0.803	1	0.996	1	SUBCLONAL	2	FALSE	0	0.535770638482003	1		630	596	SUCCESS
AR	367	MSKCC	GRCh37	X	66765820	66765820	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1250886649	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	267	435	2	ENST00000374690.3:c.832G>A	p.Ala278Thr	p.A278T	ENST00000374690	NM_000044.3	278	Gct/Act	1/8	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	FALSE	0	0.535770638482003	1		437	536	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348535	70348535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	326	499	1	ENST00000374080.3:c.3442C>T	p.Arg1148Cys	p.R1148C	ENST00000374080		1148	Cgc/Tgc	24/45	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	FALSE	0	0.535770638482003	1		500	624	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617205	100617205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	284	435	0	ENST00000308731.7:c.544C>T	p.Arg182Trp	p.R182W	ENST00000308731	NM_000061.2	182	Cgg/Tgg	7/19	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	FALSE	0	0.535770638482003	1		435	549	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94226073	94226073	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0004865-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	31	102	0	ENST00000323929.3:c.-105-1G>T		p.X35_splice	ENST00000323929	NM_005591.3	35			1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	FALSE	1	0.535770638482003	2		102	96	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004876-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	35	280	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.945	1			1	INDETERMINATE	1	TRUE	NA	0.243498231352821	2		280	204	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865272	57865272	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004876-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	101	592	0	ENST00000228682.2:c.2749G>T	p.Asp917Tyr	p.D917Y	ENST00000228682	NM_005269.2	917	Gat/Tat	12/12	1	2	FACETS	0.775	0.695	0.86	1	0.983	1	SUBCLONAL	2	TRUE	1	0.243498231352821	2		592	535	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73335818	73335818	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs904553704	NA	P-0004876-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	68	335	0	ENST00000377767.4:c.2477A>G	p.Tyr826Cys	p.Y826C	ENST00000377767	NM_014953.3	826	tAt/tGt	18/21	0.243498231352821	3	FACETS	0.849	0.743	0.962	0.849	0.743	0.962	CLONAL	2	TRUE	1	0.243498231352821	3		335	369	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2103416	2103416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375824753	NA	P-0004876-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	49	347	1	ENST00000219476.3:c.299C>T	p.Ala100Val	p.A100V	ENST00000219476	NM_000548.3	100	gCg/gTg	4/42	0.243498231352821	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.243498231352821	1		348	293	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733170	74733170	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0004876-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	108	444	0	ENST00000359995.5:c.73A>T	p.Thr25Ser	p.T25S	ENST00000359995	NM_001195427.1	25	Acc/Tcc	1/3	0.203494354471256	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.243498231352821	1		444	541	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092967	27092980	+	frameshift_variant	Frame_Shift_Del	DEL	GATGATGGGCCTTG	GATGATGGGCCTTG	-	novel	NA	P-0004876-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	81	423	0	ENST00000324856.7:c.2899_2912del	p.Met967GlyfsTer35	p.M967Gfs*35	ENST00000324856	NM_006015.4	966	gaGATGATGGGCCTTGgg/gagg	10/20	1	2	FACETS	0.794	0.703	0.89	1	0.98	1	SUBCLONAL	2	TRUE	1	0.243498231352821	2		423	419	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162335	47162342	+	frameshift_variant	Frame_Shift_Del	DEL	TGAGAGAA	TGAGAGAA	-	novel	NA	P-0004876-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	52	274	0	ENST00000409792.3:c.3784_3791del	p.Phe1262ArgfsTer11	p.F1262Rfs*11	ENST00000409792	NM_014159.6	1262	TTCTCTCAa/a	3/21	1	2	FACETS	0.768	0.659	0.886	1	0.967	1	SUBCLONAL	2	TRUE	1	0.243498231352821	2		274	278	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266129	41266130	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCTCCT	novel	NA	P-0004876-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	81	367	0	ENST00000349496.5:c.127_132dup	p.Ala43_Pro44dup	p.A43_P44dup	ENST00000349496	NM_001904.3	43	-/GCTCCT	3/15	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.243498231352821	2		367	467	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004917-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	168	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.977	0.911	1	0.977	0.911	1	CLONAL	1	TRUE	1	0.929367564943233	2		280	370	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0004917-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	283	354	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.929367564943233	2		354	572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0004921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	175	550	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.371960621024718	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.371960621024718	1		550	724	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0004921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	204	654	1	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	0.371960621024718	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.371960621024718	1		655	816	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851645	134851645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395878132	NA	P-0004921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	125	425	2	ENST00000398015.3:c.1051C>T	p.Arg351Trp	p.R351W	ENST00000398015	NM_004441.4	351	Cgg/Tgg	5/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.371960621024718	2		427	592	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295386	1295386	+	upstream_gene_variant	5'Flank	SNP	G	G	C	novel	NA	P-0004921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	10	142	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.392	0.267	0.549			1	INDETERMINATE	1	TRUE	NA	0.371960621024718	2		142	137	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553611	106553611	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0004921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	56	150	0	ENST00000369096.4:c.1576G>C	p.Glu526Gln	p.E526Q	ENST00000369096	NM_001198.3	526	Gaa/Caa	5/7	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.371960621024718	2		150	283	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511656	38511656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775118101	NA	P-0004921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1808	123	430	0	ENST00000254066.5:c.1154G>A	p.Arg385Gln	p.R385Q	ENST00000254066	NM_000964.3	385	cGa/cAa	8/9	0.371960621024718	11	FACETS	0.916	0.824	1			1	CLONAL	1	TRUE	NA	0.371960621024718	11		430	1931	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101911542	101911542	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	139	444	0	ENST00000374994.4:c.1467del	p.Thr491HisfsTer56	p.T491Hfs*56	ENST00000374994	NM_004612.2	489	aaG/aa	9/9	0.339389320362435	3	FACETS	0.871	0.792	0.954	0.435	0.396	0.477	CLONAL	1	TRUE	1	0.371960621024718	3		444	1018	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56171029	56171030	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0004921-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	101	320	0	ENST00000399503.3:c.1858dup	p.Ser620LysfsTer26	p.S620Kfs*26	ENST00000399503	NM_005921.1	619	-/A	10/20	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.371960621024718	2		320	522	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0004933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	96	263	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.662329009835762	3	FACETS	0.789	0.706	0.877	0.395	0.353	0.439	SUBCLONAL	1	TRUE	1	0.662329009835762	3		263	489	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0004933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	162	300	0				ENST00000310581	NM_198253.2	-/1132			0.306223263424415	3	FACETS	1	0.958	1			1	INDETERMINATE	2	TRUE	NA	0.662329009835762	3		300	315	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0004933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	156	157	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.535157922437778	3	FACETS	0.977	0.927	1	0.977	0.927	1	CLONAL	3	TRUE	0	0.662329009835762	3		157	214	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55972013	55972013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	320	383	0	ENST00000263923.4:c.1631C>T	p.Ser544Phe	p.S544F	ENST00000263923	NM_002253.2	544	tCc/tTc	12/30	0.616940572626159	4	FACETS	0.94	0.891	0.99	0.94	0.891	0.99	CLONAL	2	TRUE	2	0.662329009835762	4		383	854	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673628	30673628	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0004933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1249	239	726	0	ENST00000376406.3:c.3332A>C	p.Lys1111Thr	p.K1111T	ENST00000376406	NM_014641.2	1111	aAg/aCg	10/15	0.662329009835762	5	FACETS	0.967	0.9	1	0.322	0.3	0.346	CLONAL	1	TRUE	2	0.662329009835762	5		726	1488	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609907	117609907	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761470868	NA	P-0004933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	571	553	0	ENST00000368508.3:c.6792G>A	p.Met2264Ile	p.M2264I	ENST00000368508	NM_002944.2	2264	atG/atA	43/43	0.662329009835762	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.662329009835762	4		553	1397	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140501361	140501361	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0004933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	403	257	0	ENST00000288602.6:c.712-1G>A		p.X238_splice	ENST00000288602	NM_004333.4	238			0.662329009835762	6	FACETS	0.981	0.942	1	0.981	0.942	1	CLONAL	4	TRUE	2	0.662329009835762	6		257	721	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841940	151841940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0004933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	324	449	0	ENST00000262189.6:c.14201C>T	p.Thr4734Ile	p.T4734I	ENST00000262189	NM_170606.2	4734	aCc/aTc	55/59	0.662329009835762	6	FACETS	0.925	0.873	0.978	0.463	0.436	0.489	CLONAL	2	TRUE	2	0.662329009835762	6		449	1229	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911604	114911604	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	592	812	2	ENST00000543371.1:c.1122G>T	p.Leu374Phe	p.L374F	ENST00000543371	NM_001198531.1	374	ttG/ttT	10/14	0.662329009835762	2	FACETS	0.995	0.966	1	0.995	0.966	1	CLONAL	2	TRUE	0	0.662329009835762	2		814	898	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202531	67202531	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	278	366	0	ENST00000312629.5:c.1340T>C	p.Leu447Pro	p.L447P	ENST00000312629	NM_003952.2	447	cTa/cCa	15/15	0.616940572626159	4	FACETS	0.983	0.928	1	0.983	0.928	1	CLONAL	2	TRUE	2	0.662329009835762	4		366	710	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110618	8110618	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0004933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	178	422	0	ENST00000585124.1:c.274T>G	p.Tyr92Asp	p.Y92D	ENST00000585124	NM_004217.3	92	Tac/Gac	5/9	0.550187710702625	3	FACETS	0.975	0.901	1	0.487	0.45	0.526	CLONAL	1	TRUE	1	0.662329009835762	3		422	734	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439993	56439993	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0004933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	385	552	1	ENST00000407977.2:c.599G>A	p.Trp200Ter	p.W200*	ENST00000407977		200	tGg/tAg	6/10	0.662329009835762	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.662329009835762	3		553	758	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653807	89653807	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0004933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	361	373	0	ENST00000371953.3:c.107del	p.Gly36AspfsTer18	p.G36Dfs*18	ENST00000371953	NM_000314.4	35	atG/at	2/9	0.662329009835762	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.662329009835762	2		373	515	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009090	27009092	+	missense_variant	Missense_Mutation	TNP	AGC	AGC	TAT	novel	NA	P-0004933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	68	141	1	ENST00000335756.4:c.26_28delinsTAT	p.Lys9_Pro10delinsIleSer	p.K9_P10delinsIS	ENST00000335756	NM_001809.3	9	aAGCcc/aTATcc	1/5	0.662329009835762	3	FACETS	1	0.904	1			1	CLONAL	1	TRUE	NA	0.662329009835762	3		142	265	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453145	140453146	+	missense_variant	Missense_Mutation	DNP	AG	AG	GA	rs121913368	NA	P-0004933-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	603	457	0	ENST00000288602.6:c.1789_1790delinsTC	p.Leu597Ser	p.L597S	ENST00000288602	NM_004333.4	597	CTa/TCa	15/18	0.662329009835762	6	FACETS	0.941	0.909	0.972	0.941	0.909	0.972	CLONAL	4	TRUE	2	0.662329009835762	6		457	1125	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0004953-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	42	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.17	2		280	484	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425644	49425644	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1057517992	NA	P-0004953-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	37	357	1	ENST00000301067.7:c.12844C>T	p.Arg4282Ter	p.R4282*	ENST00000301067	NM_003482.3	4282	Cga/Tga	39/54	1	2	FACETS	0.594	0.488	0.713	0.594	0.488	0.713	SUBCLONAL	1	TRUE	1	0.17	2		358	733	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420634	49420636	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	novel	NA	P-0004953-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	47	297	0	ENST00000301067.7:c.15113_15115del	p.Glu5038del	p.E5038del	ENST00000301067	NM_003482.3	5038	gAGGgt/ggt	48/54	1	2	FACETS	0.718	0.604	0.844	0.718	0.604	0.844	SUBCLONAL	1	TRUE	1	0.17	2		297	770	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0004997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	86	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.64	2		464	255	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0004997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	77	595	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.3	2	FACETS	0.821	0.729	0.919			1	INDETERMINATE	1	TRUE	NA	0.64	2		595	293	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412940	49412940	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0004997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	210	413	0	ENST00000418115.1:c.83A>G	p.Asp28Gly	p.D28G	ENST00000418115	NM_001664.2	28	gAc/gGc	2/5	1	2	FACETS	0.919	0.857	0.983	0.919	0.857	0.983	CLONAL	1	TRUE	1	0.64	2		413	714	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860608	151860608	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	155	334	0	ENST00000262189.6:c.10054C>T	p.Gln3352Ter	p.Q3352*	ENST00000262189	NM_170606.2	3352	Cag/Tag	43/59	1	2	FACETS	0.871	0.802	0.943	0.871	0.802	0.943	CLONAL	1	TRUE	1	0.64	2		334	556	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427240	49427240	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0004997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	138	254	0	ENST00000301067.7:c.11248C>A	p.Gln3750Lys	p.Q3750K	ENST00000301067	NM_003482.3	3750	Cag/Aag	39/54	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.64	2		254	430	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431175	49431175	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0004997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	162	418	0	ENST00000301067.7:c.9964C>T	p.Gln3322Ter	p.Q3322*	ENST00000301067	NM_003482.3	3322	Cag/Tag	34/54	1	2	FACETS	0.938	0.866	1	0.938	0.866	1	CLONAL	1	TRUE	1	0.64	2		418	540	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431790	49431790	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0004997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	128	272	0	ENST00000301067.7:c.9349G>T	p.Glu3117Ter	p.E3117*	ENST00000301067	NM_003482.3	3117	Gag/Tag	34/54	1	2	FACETS	0.966	0.884	1	0.966	0.884	1	CLONAL	1	TRUE	1	0.64	2		272	414	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937715	44937715	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0004997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	116	154	0	ENST00000377967.4:c.2903C>G	p.Thr968Arg	p.T968R	ENST00000377967	NM_021140.2	968	aCa/aGa	19/29	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.64	1		154	201	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	182	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.715347517955945	2		280	497	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220274	55220274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005051-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4483	114	433	0	ENST00000275493.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000275493	NM_005228.3	222	Cgc/Tgc	6/28	0.715347517955945	23	FACETS	0.59	0.528	0.657			1	SUBCLONAL	1	TRUE	NA	0.715347517955945	23		433	4597	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	43	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.882	1	1	0.973	1	CLONAL	2	TRUE	1	0.213511120456489	2		280	192	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023307	27023307	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0005076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	47	78	0	ENST00000324856.7:c.413C>G	p.Ser138Ter	p.S138*	ENST00000324856	NM_006015.4	138	tCa/tGa	1/20	0.213511120456489	2	FACETS	1	0.923	1	1	0.971	1	CLONAL	3	TRUE	0	0.213511120456489	2		78	133	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0005076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	223	599	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.213511120456489	4	FACETS	0.946	0.889	1			1	CLONAL	5	TRUE	NA	0.213511120456489	4		599	536	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073487	8073487	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	209	598	0	ENST00000377482.5:c.1172C>A	p.Ser391Ter	p.S391*	ENST00000377482	NM_018948.3	391	tCa/tAa	4/4	0.213511120456489	2	FACETS	0.928	0.874	0.982	1	0.995	1	CLONAL	5	TRUE	0	0.213511120456489	2		598	422	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097266	178097266	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	77	402	0	ENST00000397062.3:c.448C>T	p.His150Tyr	p.H150Y	ENST00000397062	NM_006164.4	150	Cac/Tac	4/5	0.213511120456489	1	FACETS	0.956	0.846	1	1	0.983	1	CLONAL	2	TRUE	0	0.213511120456489	1		402	337	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242436	55242436	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	106	307	0	ENST00000275493.2:c.2206G>A	p.Glu736Lys	p.E736K	ENST00000275493	NM_005228.3	736	Gag/Aag	19/28	0.193670393225784	3	FACETS	0.866	0.782	0.954	1	0.978	1	CLONAL	3	TRUE	1	0.213511120456489	3		307	423	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55260483	55260483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	121	435	0	ENST00000275493.2:c.2650G>A	p.Glu884Lys	p.E884K	ENST00000275493	NM_005228.3	884	Gaa/Aaa	22/28	0.193670393225784	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.213511120456489	3		435	542	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42053981	42053981	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	103	536	0	ENST00000219905.7:c.7443G>C	p.Leu2481Phe	p.L2481F	ENST00000219905	NM_001164273.1	2481	ttG/ttC	21/24	0.191644113254429	0	FACETS	0.973	0.878	1			1	CLONAL	2	TRUE	0	0.213511120456489	0		536	390	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843558	3843558	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005076-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	104	363	0	ENST00000262367.5:c.1045G>T	p.Glu349Ter	p.E349*	ENST00000262367	NM_004380.2	349	Gaa/Taa	4/31	0.121638420807795	1	FACETS	1	0.946	1	1	0.989	1	INDETERMINATE	2	TRUE	0	0.213511120456489	1		363	406	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	65	280	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.989	0.871	1			1	INDETERMINATE	1	TRUE	NA	0.626134097868368	2		280	210	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692799	89692799	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	135	159	0	ENST00000371953.3:c.283C>T	p.Pro95Ser	p.P95S	ENST00000371953	NM_000314.4	95	Cca/Tca	5/9	0.626134097868368	1	FACETS	0.887	0.818	0.957	0.887	0.818	0.957	CLONAL	1	TRUE	0	0.626134097868368	1		159	334	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667635	29667638	+	frameshift_variant	Frame_Shift_Del	DEL	TAGA	TAGA	-	novel	NA	P-0005128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	40	368	0	ENST00000356175.3:c.6974_6977del	p.Asp2325ValfsTer49	p.D2325Vfs*49	ENST00000356175	NM_000267.3	2324	tTAGAt/tt	46/57	0.546240059720821	0	FACETS	0.115	0.095	0.137			1	SUBCLONAL	1	TRUE	0	0.626134097868368	0		368	415	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464916	120464916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587737953	NA	P-0005128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	220	302	0	ENST00000256646.2:c.5156G>A	p.Arg1719Gln	p.R1719Q	ENST00000256646	NM_024408.3	1719	cGa/cAa	28/34	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.626134097868368	2		302	645	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117645500	117645500	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	483	561	1	ENST00000368508.3:c.5636C>T	p.Thr1879Ile	p.T1879I	ENST00000368508	NM_002944.2	1879	aCc/aTc	34/43	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.626134097868368	2		562	1462	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467725	50467725	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	140	299	1	ENST00000331340.3:c.960C>A	p.Asn320Lys	p.N320K	ENST00000331340	NM_006060.4	320	aaC/aaA	8/8	0.626134097868368	3	FACETS	0.486	0.442	0.534	0.243	0.221	0.267	SUBCLONAL	1	TRUE	1	0.626134097868368	3		300	1207	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755347	39755347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	254	292	0	ENST00000288319.7:c.1418C>T	p.Ser473Phe	p.S473F	ENST00000288319	NM_182918.3	473	tCt/tTt	10/10	1	2	FACETS	0.948	0.889	1	0.948	0.889	1	CLONAL	1	TRUE	1	0.626134097868368	2		292	856	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971012	21971013	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0005128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	15	178	0	ENST00000304494.5:c.345_346del	p.Asp116ProfsTer3	p.D116Pfs*3	ENST00000304494	NM_000077.4	115	gtGGac/gtac	2/3	0.514679150575245	0	FACETS	0.072	0.052	0.096			1	SUBCLONAL	1	TRUE	0	0.626134097868368	0		178	248	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	149	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.875	0.808	0.944	0.875	0.808	0.944	CLONAL	1	TRUE	1	0.832663773871112	2		280	409	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589138	67589138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519757	NA	P-0005141-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	331	371	0	ENST00000274335.5:c.1126G>A	p.Gly376Arg	p.G376R	ENST00000274335		376	Gga/Aga	9/15	1	2	FACETS	0.964	0.915	1	0.964	0.915	1	CLONAL	1	TRUE	1	0.832663773871112	2		371	825	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	123	280	0				ENST00000310581	NM_198253.2	-/1132			0.3	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.87	0		280	245	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0005143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	145	595	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.896	0.828	0.966	0.896	0.828	0.966	CLONAL	1	TRUE	1	0.87	2		595	372	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097631	27097631	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	250	515	0	ENST00000324856.7:c.3220C>T	p.Arg1074Trp	p.R1074W	ENST00000324856	NM_006015.4	1074	Cgg/Tgg	12/20	1	2	FACETS	0.986	0.93	1	0.986	0.93	1	CLONAL	1	TRUE	1	0.87	2		515	583	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165020	47165020	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	226	413	0	ENST00000409792.3:c.1106C>A	p.Ser369Tyr	p.S369Y	ENST00000409792	NM_014159.6	369	tCt/tAt	3/21	1	2	FACETS	0.923	0.867	0.98	0.923	0.867	0.98	CLONAL	1	TRUE	1	0.87	2		413	563	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786956	135786956	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0005143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	160	388	0	ENST00000298552.3:c.914-1G>A		p.X305_splice	ENST00000298552	NM_001162426.1	305			0.868319643606798	1	FACETS	0.962	0.915	1	0.962	0.915	1	CLONAL	1	TRUE	0	0.87	1		388	216	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40770626	40770626	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	119	429	0	ENST00000373198.4:c.2756A>G	p.Gln919Arg	p.Q919R	ENST00000373198	NM_133170.3	919	cAg/cGg	19/32	0.3	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.87	0		429	297	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123176461	123176465	+	frameshift_variant	Frame_Shift_Del	DEL	AGATA	AGATA	-	novel	NA	P-0005143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	313	301	0	ENST00000218089.9:c.429_433del	p.Glu143AspfsTer6	p.E143Dfs*6	ENST00000218089	NM_001042749.1	143	gAGATA/g	7/35	1	1	FACETS	0.963	0.93	0.996	0.963	0.93	0.996	CLONAL	1	TRUE	0	0.87	1		301	422	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3820754	3820775	+	frameshift_variant	Frame_Shift_Del	DEL	GGGAGTCTGCCCGGAAGACGAC	GGGAGTCTGCCCGGAAGACGAC	-	novel	NA	P-0005143-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	164	605	0	ENST00000262367.5:c.2676_2697del	p.Ser893ProfsTer27	p.S893Pfs*27	ENST00000262367	NM_004380.2	892	gtGTCGTCTTCCGGGCAGACTCCC/gt	14/31	0.1294349554839	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.87	0		605	518	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255210	16255210	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	101	545	0	ENST00000375759.3:c.2475A>T	p.Lys825Asn	p.K825N	ENST00000375759	NM_015001.2	825	aaA/aaT	11/15	0.258737400342235	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.258737400342235	1		545	551	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248766	212248766	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs549128376	NA	P-0005160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	37	245	1	ENST00000342788.4:c.3501G>T	p.Glu1167Asp	p.E1167D	ENST00000342788	NM_005235.2	1167	gaG/gaT	28/28	0.258737400342235	1	FACETS	1	0.869	1	1	0.869	1	CLONAL	1	TRUE	0	0.258737400342235	1		246	236	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405948	49405948	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	58	490	0	ENST00000418115.1:c.190G>A	p.Glu64Lys	p.E64K	ENST00000418115	NM_001664.2	64	Gaa/Aaa	3/5	0.258737400342235	1	FACETS	0.735	0.632	0.847	0.735	0.632	0.847	SUBCLONAL	1	TRUE	0	0.258737400342235	1		490	531	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971057	21971057	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894094	NA	P-0005160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	286	292	0	ENST00000304494.5:c.301G>T	p.Gly101Trp	p.G101W	ENST00000304494	NM_000077.4	101	Ggg/Tgg	2/3	0.258737400342235	3	FACETS	1	0.961	1	1	0.994	1	CLONAL	3	TRUE	1	0.258737400342235	3		292	814	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650633	18650633	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	83	403	0	ENST00000266497.5:c.2844G>T	p.Leu948Phe	p.L948F	ENST00000266497		948	ttG/ttT	20/31	0.192944181335259	2	FACETS	0.782	0.694	0.876	0.782	0.694	0.876	SUBCLONAL	2	TRUE	0	0.258737400342235	2		403	410	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440047	49440047	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	129	445	0	ENST00000301067.7:c.4579G>T	p.Glu1527Ter	p.E1527*	ENST00000301067	NM_003482.3	1527	Gaa/Taa	16/54	0.192944181335259	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.258737400342235	2		445	472	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201552	133201552	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	229	391	0	ENST00000320574.5:c.6686A>C	p.Glu2229Ala	p.E2229A	ENST00000320574	NM_006231.2	2229	gAg/gCg	48/49	0.250939024219095	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	0	0.258737400342235	2		391	866	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039195	49039195	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	65	444	0	ENST00000267163.4:c.2273C>A	p.Ser758Ter	p.S758*	ENST00000267163	NM_000321.2	758	tCg/tAg	22/27	0.258737400342235	1	FACETS	0.913	0.794	1	0.913	0.794	1	CLONAL	1	TRUE	0	0.258737400342235	1		444	479	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679729	88679729	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	30	476	0	ENST00000360948.2:c.734T>G	p.Val245Gly	p.V245G	ENST00000360948	NM_001012338.2	245	gTc/gGc	7/19	0.253027927783639	3	FACETS	0.571	0.459	0.697	0.19	0.153	0.233	SUBCLONAL	1	TRUE	0	0.258737400342235	3		476	459	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993506	72993506	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	179	540	0	ENST00000268489.5:c.539A>T	p.Lys180Met	p.K180M	ENST00000268489	NM_006885.3	180	aAg/aTg	2/10	0.258737400342235	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.258737400342235	1		540	913	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0005160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	83	378	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.258737400342235	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.258737400342235	1		378	454	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59820466	59820466	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	83	405	0	ENST00000259008.2:c.2287G>T	p.Gly763Cys	p.G763C	ENST00000259008	NM_032043.2	763	Ggt/Tgt	16/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.258737400342235	2		405	467	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560934	9560934	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs369268475	NA	P-0005160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	26	416	0	ENST00000353224.5:c.848G>T	p.Arg283Leu	p.R283L	ENST00000353224	NM_177990.2	283	cGg/cTg	4/10	0.170620290425836	3	FACETS	0.559	0.442	0.693	0.28	0.221	0.347	SUBCLONAL	1	TRUE	1	0.258737400342235	3		416	406	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	55	660	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.568	0.485	0.659	0.568	0.485	0.659	SUBCLONAL	1	FALSE	1	0.264648740249638	2		660	732	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420108	49420108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398123729	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	80	516	1	ENST00000301067.7:c.15641G>A	p.Arg5214His	p.R5214H	ENST00000301067	NM_003482.3	5214	cGc/cAc	48/54	1	2	FACETS	0.635	0.558	0.719	0.635	0.558	0.719	SUBCLONAL	1	FALSE	1	0.264648740249638	2		517	952	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	70	469	0	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	0.694	0.604	0.792	0.694	0.604	0.792	SUBCLONAL	1	FALSE	1	0.264648740249638	2		469	762	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433847	78433848	+	splice_donor_variant	Splice_Site	DEL	AC	AC	-	rs1477051807	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	70	418	0	ENST00000370768.2:c.250+1_250+2del		p.X84_splice	ENST00000370768	NM_003902.3	84			1	2	FACETS	0.672	0.585	0.767	0.672	0.585	0.767	SUBCLONAL	1	FALSE	1	0.264648740249638	2		418	787	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	38	257	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	FALSE	1	0.264648740249638	2		260	214	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977554	2977554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs992263343	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	142	374	0	ENST00000396946.4:c.1130G>A	p.Arg377Gln	p.R377Q	ENST00000396946	NM_032415.4	377	cGg/cAg	8/25	0.15170510666157	3	FACETS	1	0.984	1	0.678	0.618	0.742	INDETERMINATE	1	FALSE	1	0.264648740249638	3		374	896	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448298	56448298	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	40	294	0	ENST00000407977.2:c.349del	p.Arg117AlafsTer41	p.R117Afs*41	ENST00000407977		117	Cgc/gc	3/10	1	2	FACETS	0.573	0.475	0.681	0.573	0.475	0.681	SUBCLONAL	1	FALSE	1	0.264648740249638	2		294	528	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	44	358	2	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	0.553	0.463	0.653	0.553	0.463	0.653	SUBCLONAL	1	FALSE	1	0.264648740249638	2		360	601	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680655	88680655	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142726068	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	74	539	1	ENST00000360948.2:c.602G>A	p.Arg201His	p.R201H	ENST00000360948	NM_001012338.2	201	cGc/cAc	6/19	1	2	FACETS	0.637	0.556	0.724	0.637	0.556	0.724	SUBCLONAL	1	FALSE	1	0.264648740249638	2		540	878	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803616	1803616	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779284979	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	49	291	1	ENST00000260795.2:c.794C>T	p.Ala265Val	p.A265V	ENST00000260795		265	gCg/gTg	6/17	1	2	FACETS	0.569	0.481	0.666	0.569	0.481	0.666	SUBCLONAL	1	FALSE	1	0.264648740249638	2		292	651	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434745	110434745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	47	289	0	ENST00000375856.3:c.3656C>T	p.Pro1219Leu	p.P1219L	ENST00000375856	NM_003749.2	1219	cCg/cTg	1/2	1	2	FACETS	0.563	0.474	0.661	0.563	0.474	0.661	SUBCLONAL	1	FALSE	1	0.264648740249638	2		289	631	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937914	36937914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs606231473	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	90	606	0	ENST00000361632.4:c.922C>T	p.Arg308Cys	p.R308C	ENST00000361632		308	Cgc/Tgc	7/16	1	2	FACETS	0.696	0.616	0.782	0.696	0.616	0.782	SUBCLONAL	1	FALSE	1	0.264648740249638	2		606	977	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652386	206652386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781784265	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	87	473	0	ENST00000367120.3:c.1093G>A	p.Val365Ile	p.V365I	ENST00000367120	NM_014002.3	365	Gtc/Atc	10/22	1	2	FACETS	0.778	0.688	0.875	0.778	0.688	0.875	SUBCLONAL	1	FALSE	1	0.264648740249638	2		473	845	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828079	243828079	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	67	441	0	ENST00000263826.5:c.279G>T	p.Glu93Asp	p.E93D	ENST00000263826	NM_005465.4	93	gaG/gaT	3/13	1	2	FACETS	0.687	0.596	0.786	0.687	0.596	0.786	SUBCLONAL	1	FALSE	1	0.264648740249638	2		441	737	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630499	47630499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267607913	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	48	340	0	ENST00000233146.2:c.169G>A	p.Val57Met	p.V57M	ENST00000233146	NM_000251.2	57	Gtg/Atg	1/16	1	2	FACETS	0.528	0.445	0.619	0.528	0.445	0.619	SUBCLONAL	1	FALSE	1	0.264648740249638	2		340	687	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038196	128038196	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs150954655	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	72	481	2	ENST00000285398.2:c.1354C>T	p.Arg452Ter	p.R452*	ENST00000285398	NM_000122.1	452	Cga/Tga	9/15	1	2	FACETS	0.681	0.594	0.775	0.681	0.594	0.775	SUBCLONAL	1	FALSE	1	0.264648740249638	2		483	799	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270162	198270162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	75	439	0	ENST00000335508.6:c.1274G>A	p.Arg425Gln	p.R425Q	ENST00000335508	NM_012433.2	425	cGa/cAa	10/25	1	2	FACETS	0.738	0.646	0.837	0.738	0.646	0.837	SUBCLONAL	1	FALSE	1	0.264648740249638	2		439	768	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212652872	212652872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	45	396	0	ENST00000342788.4:c.434G>A	p.Gly145Asp	p.G145D	ENST00000342788	NM_005235.2	145	gGt/gAt	4/28	1	2	FACETS	0.563	0.472	0.664	0.563	0.472	0.664	SUBCLONAL	1	FALSE	1	0.264648740249638	2		396	604	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439724	220439724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201577506	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	84	589	2	ENST00000243786.2:c.577G>A	p.Val193Ile	p.V193I	ENST00000243786	NM_002191.3	193	Gtc/Atc	2/2	1	2	FACETS	0.583	0.513	0.658	0.583	0.513	0.658	SUBCLONAL	1	FALSE	1	0.264648740249638	2		591	1089	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528572	89528572	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762601076	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	64	448	4	ENST00000336596.2:c.2872G>A	p.Val958Met	p.V958M	ENST00000336596	NM_005233.5	958	Gtg/Atg	17/17	1	2	FACETS	0.691	0.598	0.792	0.691	0.598	0.792	SUBCLONAL	1	FALSE	1	0.264648740249638	2		452	700	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924382	131924382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757836195	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	56	314	0	ENST00000265335.6:c.1055G>A	p.Arg352His	p.R352H	ENST00000265335		352	cGt/cAt	8/25	1	2	FACETS	0.82	0.703	0.948	0.82	0.703	0.948	CLONAL	1	FALSE	1	0.264648740249638	2		314	516	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271533	26271533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1368	145	914	1	ENST00000305910.3:c.80G>A	p.Arg27Gln	p.R27Q	ENST00000305910	NM_003534.2	27	cGg/cAg	1/1	1	2	FACETS	0.724	0.658	0.794	0.724	0.658	0.794	SUBCLONAL	1	FALSE	1	0.264648740249638	2		915	1513	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129373	152129373	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	60	315	0	ENST00000206249.3:c.326T>C	p.Met109Thr	p.M109T	ENST00000206249	NM_000125.3	109	aTg/aCg	1/8	1	2	FACETS	0.711	0.612	0.818	0.711	0.612	0.818	SUBCLONAL	1	FALSE	1	0.264648740249638	2		315	638	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2951852	2951852	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770667388	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	66	433	0	ENST00000396946.4:c.3098C>T	p.Ala1033Val	p.A1033V	ENST00000396946	NM_032415.4	1033	gCg/gTg	23/25	0.15170510666157	3	FACETS	0.606	0.524	0.695	0.303	0.262	0.348	INDETERMINATE	1	FALSE	1	0.264648740249638	3		433	932	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730040	41730040	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	188	711	1	ENST00000242208.4:c.489G>T	p.Lys163Asn	p.K163N	ENST00000242208	NM_002192.2	163	aaG/aaT	3/3	0.15170510666157	3	FACETS	1	0.988	1	0.694	0.64	0.75	INDETERMINATE	1	FALSE	1	0.264648740249638	3		712	1159	SUCCESS
MET	4233	MSKCC	GRCh37	7	116415000	116415000	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	66	524	0	ENST00000397752.3:c.3094T>C	p.Ser1032Pro	p.S1032P	ENST00000397752	NM_000245.2	1032	Tcc/Ccc	15/21	0.15170510666157	3	FACETS	0.747	0.647	0.855	0.374	0.323	0.428	INDETERMINATE	1	FALSE	1	0.264648740249638	3		524	756	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860343	151860343	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	48	529	0	ENST00000262189.6:c.10319A>C	p.Glu3440Ala	p.E3440A	ENST00000262189	NM_170606.2	3440	gAg/gCg	43/59	0.15170510666157	3	FACETS	0.507	0.427	0.595	0.254	0.213	0.298	INDETERMINATE	1	FALSE	1	0.264648740249638	3		529	810	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100420	8100420	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs991194737	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	78	444	0	ENST00000346208.3:c.394G>A	p.Val132Ile	p.V132I	ENST00000346208		132	Gtc/Atc	3/6	1	2	FACETS	0.759	0.666	0.859	0.759	0.666	0.859	SUBCLONAL	1	FALSE	1	0.264648740249638	2		444	777	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742934	17742934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	57	267	0	ENST00000250003.3:c.842G>A	p.Arg281His	p.R281H	ENST00000250003	NM_002478.4	281	cGc/cAc	3/3	1	2	FACETS	0.814	0.699	0.94	0.814	0.699	0.94	CLONAL	1	FALSE	1	0.264648740249638	2		267	529	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94170371	94170371	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745614941	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	48	413	0	ENST00000323929.3:c.1898G>A	p.Arg633Gln	p.R633Q	ENST00000323929	NM_005591.3	633	cGa/cAa	17/20	1	2	FACETS	0.482	0.407	0.566	0.482	0.407	0.566	SUBCLONAL	1	FALSE	1	0.264648740249638	2		413	752	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998199	100998199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	56	347	0	ENST00000325455.5:c.1603C>T	p.Pro535Ser	p.P535S	ENST00000325455	NM_001202474.3	535	Ccg/Tcg	1/8	1	2	FACETS	0.599	0.513	0.695	0.599	0.513	0.695	SUBCLONAL	1	FALSE	1	0.264648740249638	2		347	706	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111886063	111886063	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770527337	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	184	611	1	ENST00000341259.2:c.1685G>A	p.Arg562Gln	p.R562Q	ENST00000341259	NM_005475.2	562	cGg/cAg	8/8	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.264648740249638	2		612	1167	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220437	133220437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775072147	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	56	355	1	ENST00000320574.5:c.4276G>A	p.Val1426Ile	p.V1426I	ENST00000320574	NM_006231.2	1426	Gta/Ata	33/49	1	2	FACETS	0.534	0.456	0.619	0.534	0.456	0.619	SUBCLONAL	1	FALSE	1	0.264648740249638	2		356	793	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257858	133257858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	158	485	0	ENST00000320574.5:c.70G>A	p.Gly24Ser	p.G24S	ENST00000320574	NM_006231.2	24	Ggc/Agc	2/49	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.264648740249638	2		485	894	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347237	89347237	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	89	496	0	ENST00000301030.4:c.5713G>T	p.Gly1905Trp	p.G1905W	ENST00000301030	NM_001256183.1	1905	Ggg/Tgg	9/13	1	2	FACETS	0.773	0.684	0.868	0.773	0.684	0.868	SUBCLONAL	1	FALSE	1	0.264648740249638	2		496	870	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533316	29533316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1466678870	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	86	466	1	ENST00000356175.3:c.1319G>A	p.Arg440Gln	p.R440Q	ENST00000356175	NM_000267.3	440	cGa/cAa	12/57	1	2	FACETS	0.821	0.725	0.923	0.821	0.725	0.923	CLONAL	1	FALSE	1	0.264648740249638	2		467	792	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370307	40370307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1255	105	885	0	ENST00000293328.3:c.1031C>T	p.Thr344Ile	p.T344I	ENST00000293328	NM_012448.3	344	aCc/aTc	9/19	1	2	FACETS	0.583	0.521	0.651	0.583	0.521	0.651	SUBCLONAL	1	FALSE	1	0.264648740249638	2		885	1360	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40486062	40486062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	109	631	0	ENST00000264657.5:c.803C>T	p.Thr268Met	p.T268M	ENST00000264657	NM_139276.2	268	aCg/aTg	9/24	1	2	FACETS	0.833	0.747	0.925	0.833	0.747	0.925	CLONAL	1	FALSE	1	0.264648740249638	2		631	989	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120253	70120253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1374439151	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	105	557	0	ENST00000245479.2:c.1255G>A	p.Ala419Thr	p.A419T	ENST00000245479	NM_000346.3	419	Gcc/Acc	3/3	1	2	FACETS	0.834	0.746	0.928	0.834	0.746	0.928	CLONAL	1	FALSE	1	0.264648740249638	2		557	951	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121145	3121145	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	94	437	0	ENST00000078429.4:c.1048C>T	p.Gln350Ter	p.Q350*	ENST00000078429	NM_002067.2	350	Cag/Tag	7/7	1	2	FACETS	0.708	0.629	0.793	0.708	0.629	0.793	SUBCLONAL	1	FALSE	1	0.264648740249638	2		437	1003	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244223	5244223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199851847	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	67	349	0	ENST00000357368.4:c.1259G>A	p.Arg420His	p.R420H	ENST00000357368	NM_002850.3	420	cGc/cAc	11/38	1	2	FACETS	0.694	0.602	0.793	0.694	0.602	0.793	SUBCLONAL	1	FALSE	1	0.264648740249638	2		349	730	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602571	10602571	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1352112075	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	79	416	0	ENST00000171111.5:c.1007G>A	p.Arg336Gln	p.R336Q	ENST00000171111	NM_203500.1	336	cGa/cAa	3/6	1	2	FACETS	0.629	0.552	0.712	0.629	0.552	0.712	SUBCLONAL	1	FALSE	1	0.264648740249638	2		416	949	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40739787	40739787	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	84	427	0	ENST00000392038.2:c.1438C>A	p.Arg480Ser	p.R480S	ENST00000392038	NM_001626.4	480	Cgc/Agc	14/14	1	2	FACETS	0.777	0.685	0.875	0.777	0.685	0.875	SUBCLONAL	1	FALSE	1	0.264648740249638	2		427	817	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547019	9547019	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	45	175	0	ENST00000353224.5:c.1003C>T	p.Arg335Ter	p.R335*	ENST00000353224	NM_177990.2	335	Cga/Tga	5/10	0.15170510666157	3	FACETS	1	0.955	1	0.7	0.592	0.818	INDETERMINATE	1	FALSE	1	0.264648740249638	3		175	275	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220401	123220401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	110	253	0	ENST00000218089.9:c.3058G>A	p.Val1020Ile	p.V1020I	ENST00000218089	NM_001042749.1	1020	Gtt/Att	30/35	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	0	0.264648740249638	1		253	490	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346158	89346158	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs878855327	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	20	140	0	ENST00000301030.4:c.6792del	p.Ala2265ProfsTer72	p.A2265Pfs*72	ENST00000301030	NM_001256183.1	2264	ccC/cc	9/13	1	2	FACETS	0.488	0.373	0.622	0.488	0.373	0.622	SUBCLONAL	1	FALSE	1	0.264648740249638	2		140	310	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049853	16049853	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	49	393	0	ENST00000268712.3:c.919del	p.Ile307SerfsTer19	p.I307Sfs*19	ENST00000268712	NM_006311.3	307	Atc/tc	10/46	1	2	FACETS	0.548	0.463	0.641	0.548	0.463	0.641	SUBCLONAL	1	FALSE	1	0.264648740249638	2		393	676	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934243	49934243	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1407832113	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	85	602	1	ENST00000296474.3:c.2264del	p.Gly755ValfsTer19	p.G755Vfs*19	ENST00000296474	NM_002447.2	755	gGt/gt	8/20	1	2	FACETS	0.699	0.617	0.788	0.699	0.617	0.788	SUBCLONAL	1	FALSE	1	0.264648740249638	2		603	919	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910590	29910590	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	54	241	0	ENST00000376809.5:c.133del	p.Arg45AlafsTer32	p.R45Afs*32	ENST00000376809	NM_002116.7	44	Ccc/cc	2/8	1	2	FACETS	0.986	0.844	1	0.986	0.844	1	CLONAL	1	FALSE	1	0.264648740249638	2		241	414	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21553861	21553861	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	63	543	3	ENST00000382592.4:c.2741del	p.Leu914TrpfsTer10	p.L914Wfs*10	ENST00000382592	NM_014572.2	914	tTg/tg	7/8	1	2	FACETS	0.525	0.453	0.604	0.525	0.453	0.604	SUBCLONAL	1	FALSE	1	0.264648740249638	2		546	907	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096044	11096044	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	62	415	0	ENST00000358026.2:c.321del	p.Pro109ArgfsTer194	p.P109Rfs*194	ENST00000358026	NM_001128849.1	106	atG/at	3/36	1	2	FACETS	0.774	0.669	0.889	0.774	0.669	0.889	SUBCLONAL	1	FALSE	1	0.264648740249638	2		415	605	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874990	151874992	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs766092762	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	92	446	0	ENST00000262189.6:c.7546_7548del	p.Arg2516del	p.R2516del	ENST00000262189	NM_170606.2	2516	AGA/-	38/59	0.15170510666157	3	FACETS	1	0.927	1	0.529	0.47	0.592	INDETERMINATE	1	FALSE	1	0.264648740249638	3		446	744	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347484	91347484	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	82	595	4	ENST00000355112.3:c.3651del	p.Lys1217AsnfsTer62	p.K1217Nfs*62	ENST00000355112	NM_000057.2	1216	Aaa/aa	19/22	1	2	FACETS	0.573	0.504	0.648	0.573	0.504	0.648	SUBCLONAL	1	FALSE	1	0.264648740249638	2		599	1081	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448304	56448304	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	62	271	0	ENST00000407977.2:c.343del	p.Ala115ProfsTer43	p.A115Pfs*43	ENST00000407977		115	Gcc/cc	3/10	1	2	FACETS	0.974	0.843	1	0.974	0.843	1	CLONAL	1	FALSE	1	0.264648740249638	2		271	481	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430901	181430901	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	72	582	1	ENST00000325404.1:c.758del	p.Pro253LeufsTer21	p.P253Lfs*21	ENST00000325404	NM_003106.3	251	agC/ag	1/1	1	2	FACETS	0.562	0.49	0.641	0.562	0.49	0.641	SUBCLONAL	1	FALSE	1	0.264648740249638	2		583	968	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446270	187446270	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	38	293	0	ENST00000232014.4:c.1418del	p.Pro473ArgfsTer117	p.P473Rfs*117	ENST00000232014	NM_001130845.1	473	cCg/cg	6/10	1	2	FACETS	0.603	0.498	0.721	0.603	0.498	0.721	SUBCLONAL	1	FALSE	1	0.264648740249638	2		293	476	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44732910	44732910	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	43	225	0	ENST00000377967.4:c.117del	p.Ser40AlafsTer2	p.S40Afs*2	ENST00000377967	NM_021140.2	38	tCc/tc	1/29	1	1	FACETS	0.799	0.67	0.94	0.799	0.67	0.94	CLONAL	1	FALSE	0	0.264648740249638	1		225	353	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151856099	151856100	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	64	542	0	ENST00000262189.6:c.11518dup	p.Thr3840AsnfsTer6	p.T3840Nfs*6	ENST00000262189	NM_170606.2	3840	aca/aAca	44/59	0.15170510666157	3	FACETS	0.631	0.545	0.725	0.315	0.272	0.363	INDETERMINATE	1	FALSE	1	0.264648740249638	3		542	868	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021441	42021442	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	62	757	2	ENST00000219905.7:c.3744dup	p.Glu1249ArgfsTer25	p.E1249Rfs*25	ENST00000219905	NM_001164273.1	1246	cga/cgAa	11/24	1	2	FACETS	0.438	0.377	0.505	0.438	0.377	0.505	SUBCLONAL	1	FALSE	1	0.264648740249638	2		759	1069	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145358	58145360	+	inframe_deletion	In_Frame_Del	DEL	CCT	CCT	-	rs1555201374	NA	P-0005197-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	90	444	1	ENST00000257904.6:c.141_143del	p.Gly48del	p.G48del	ENST00000257904	NM_000075.3	47	ggAGGc/ggc	2/8	1	2	FACETS	0.839	0.743	0.941	0.839	0.743	0.941	CLONAL	1	FALSE	1	0.264648740249638	2		445	811	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	64	464	0				ENST00000310581	NM_198253.2	-/1132			0.120227869231113	4	FACETS	1	0.967	1	0.678	0.593	0.769	INDETERMINATE	1	TRUE	2	0.505558789036259	4		464	281	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	129	354	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.330159172547719	1	FACETS	0.893	0.817	0.972	0.893	0.817	0.972	CLONAL	1	TRUE	0	0.505558789036259	1		354	427	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195542	102195542	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	51	716	0	ENST00000263464.3:c.302C>T	p.Ser101Phe	p.S101F	ENST00000263464	NM_001165.4	101	tCc/tTc	2/9	0.42890761913357	0	FACETS	0.333	0.284	0.385			1	SUBCLONAL	1	TRUE	0	0.505558789036259	0		716	300	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340007	116340007	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	46	381	0	ENST00000397752.3:c.869C>T	p.Ser290Phe	p.S290F	ENST00000397752	NM_000245.2	290	tCc/tTc	2/21	1	2	FACETS	0.788	0.67	0.915	0.788	0.67	0.915	CLONAL	1	TRUE	1	0.505558789036259	2		381	231	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610098	28610098	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	91	530	0	ENST00000241453.7:c.1392G>A	p.Trp464Ter	p.W464*	ENST00000241453	NM_004119.2	464	tgG/tgA	11/24	1	2	FACETS	0.911	0.815	1	0.911	0.815	1	CLONAL	1	TRUE	1	0.505558789036259	2		530	395	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255734	16255734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	138	453	1	ENST00000375759.3:c.2999C>T	p.Pro1000Leu	p.P1000L	ENST00000375759	NM_015001.2	1000	cCa/cTa	11/15	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.505558789036259	2		454	543	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36823931	36823931	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747619342	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	206	560	0	ENST00000373129.3:c.251G>A	p.Arg84Gln	p.R84Q	ENST00000373129	NM_032017.1	84	cGg/cAg	5/12	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.505558789036259	2		560	713	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166268	118166268	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	34	440	0	ENST00000369448.3:c.778C>T	p.Gln260Ter	p.Q260*	ENST00000369448	NM_017709.3	260	Cag/Tag	2/2	1	2	FACETS	0.243	0.198	0.294	0.243	0.198	0.294	SUBCLONAL	1	TRUE	1	0.505558789036259	2		440	553	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945747	206945747	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	125	399	0	ENST00000423557.1:c.34C>T	p.Leu12Phe	p.L12F	ENST00000423557	NM_000572.2	12	Ctc/Ttc	1/5	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.505558789036259	2		399	484	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667525	241667525	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368849989	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	91	386	0	ENST00000366560.3:c.925C>T	p.Pro309Ser	p.P309S	ENST00000366560	NM_000143.3	309	Ccg/Tcg	7/10	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.505558789036259	2		386	349	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143167	30143167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	136	304	0	ENST00000389048.3:c.359C>T	p.Ala120Val	p.A120V	ENST00000389048	NM_004304.4	120	gCc/gTc	1/29	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.505558789036259	2		304	506	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606125	47606125	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	81	459	0	ENST00000263735.4:c.589C>T	p.Gln197Ter	p.Q197*	ENST00000263735	NM_002354.2	197	Caa/Taa	6/9	1	2	FACETS	0.945	0.84	1	0.945	0.84	1	CLONAL	1	TRUE	1	0.505558789036259	2		459	339	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881333	111881333	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	165	459	1	ENST00000393256.3:c.11A>C	p.Gln4Pro	p.Q4P	ENST00000393256	NM_006538.4	4	cAa/cCa	2/4	0.207564148321572	4	FACETS	1	0.984	1	0.638	0.587	0.691	INDETERMINATE	1	TRUE	2	0.505558789036259	4		460	770	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050212	128050212	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	137	476	0	ENST00000285398.2:c.445C>T	p.Pro149Ser	p.P149S	ENST00000285398	NM_000122.1	149	Cct/Tct	3/15	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.505558789036259	2		476	505	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645501	215645501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553622247	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	93	512	0	ENST00000260947.4:c.1097C>T	p.Pro366Leu	p.P366L	ENST00000260947	NM_000465.2	366	cCt/cTt	4/11	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.505558789036259	2		512	348	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178199	142178199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746049210	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	43	319	0	ENST00000350721.4:c.7219C>T	p.Arg2407Cys	p.R2407C	ENST00000350721	NM_001184.3	2407	Cgc/Tgc	43/47	1	2	FACETS	0.749	0.633	0.876	0.749	0.633	0.876	SUBCLONAL	1	TRUE	1	0.505558789036259	2		319	227	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167812	185167812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	110	484	0	ENST00000265026.3:c.1135C>T	p.Pro379Ser	p.P379S	ENST00000265026	NM_004721.4	379	Cct/Tct	6/14	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.505558789036259	2		484	403	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526280	189526280	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	75	347	0	ENST00000264731.3:c.544C>T	p.Gln182Ter	p.Q182*	ENST00000264731	NM_003722.4	182	Cag/Tag	4/14	1	2	FACETS	0.817	0.721	0.92	0.817	0.721	0.92	CLONAL	1	TRUE	1	0.505558789036259	2		347	363	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803097	1803097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	166	422	0	ENST00000260795.2:c.449C>T	p.Ala150Val	p.A150V	ENST00000260795		150	gCc/gTc	4/17	1	2	FACETS	0.911	0.839	0.986	0.911	0.839	0.986	CLONAL	1	TRUE	1	0.505558789036259	2		422	721	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138618	55138618	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750809787	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	100	451	0	ENST00000257290.5:c.1295C>T	p.Thr432Met	p.T432M	ENST00000257290	NM_006206.4	432	aCg/aTg	9/23	1	2	FACETS	0.745	0.668	0.827	0.745	0.668	0.827	SUBCLONAL	1	TRUE	1	0.505558789036259	2		451	531	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554978	187554978	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	73	392	2	ENST00000441802.2:c.4184-1G>T		p.X1395_splice	ENST00000441802	NM_005245.3	1395			1	2	FACETS	0.905	0.798	1	0.905	0.798	1	CLONAL	1	TRUE	1	0.505558789036259	2		394	319	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1280367	1280367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	207	434	0	ENST00000310581.5:c.1856C>T	p.Ser619Phe	p.S619F	ENST00000310581	NM_198253.2	619	tCc/tTc	4/16	0.120227869231113	4	FACETS	0.813	0.757	0.871	0.813	0.757	0.871	INDETERMINATE	2	TRUE	2	0.505558789036259	4		434	758	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282608	1282608	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	198	475	0	ENST00000310581.5:c.1705C>T	p.Gln569Ter	p.Q569*	ENST00000310581	NM_198253.2	569	Caa/Taa	3/16	0.120227869231113	4	FACETS	1	0.989	1	0.68	0.63	0.731	INDETERMINATE	1	TRUE	2	0.505558789036259	4		475	867	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871205	35871205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372676633	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	95	433	0	ENST00000303115.3:c.427G>A	p.Ala143Thr	p.A143T	ENST00000303115	NM_002185.3	143	Gcc/Acc	4/8	1	2	FACETS	0.933	0.836	1	0.933	0.836	1	CLONAL	1	TRUE	1	0.505558789036259	2		433	403	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876347	35876347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	77	427	0	ENST00000303115.3:c.1139C>T	p.Pro380Leu	p.P380L	ENST00000303115	NM_002185.3	380	cCt/cTt	8/8	1	2	FACETS	0.923	0.817	1	0.923	0.817	1	CLONAL	1	TRUE	1	0.505558789036259	2		427	330	SUCCESS
APC	324	MSKCC	GRCh37	5	112178211	112178211	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs901983934	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	81	462	1	ENST00000257430.4:c.6920C>T	p.Ser2307Leu	p.S2307L	ENST00000257430	NM_000038.5	2307	tCg/tTg	16/16	1	2	FACETS	0.822	0.728	0.92	0.822	0.728	0.92	CLONAL	1	TRUE	1	0.505558789036259	2		463	390	SUCCESS
APC	324	MSKCC	GRCh37	5	112178502	112178503	+	missense_variant	Missense_Mutation	DNP	TG	TG	GA	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	78	443	0	ENST00000257430.4:c.7211_7212delinsGA	p.Met2404Arg	p.M2404R	ENST00000257430	NM_000038.5	2404	aTG/aGA	16/16	1	2	FACETS	0.905	0.801	1	0.905	0.801	1	CLONAL	1	TRUE	1	0.505558789036259	2		443	341	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170818714	170818715	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	78	334	0	ENST00000296930.5:c.263_264delinsTT	p.Ser88Phe	p.S88F	ENST00000296930	NM_002520.6	88	tCC/tTT	4/11	1	2	FACETS	0.872	0.772	0.978	0.872	0.772	0.978	CLONAL	1	TRUE	1	0.505558789036259	2		334	354	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393183	393183	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	164	325	0	ENST00000380956.4:c.31G>A	p.Glu11Lys	p.E11K	ENST00000380956	NM_001195286.1	11	Gag/Aag	2/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.505558789036259	NA		325	606	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979257	93979257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	94	687	0	ENST00000369303.4:c.1571G>A	p.Gly524Glu	p.G524E	ENST00000369303	NM_004440.3	524	gGa/gAa	7/17	0.418320114090194	0	FACETS	0.611	0.55	0.674			1	SUBCLONAL	1	TRUE	0	0.505558789036259	0		687	301	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100465	157100465	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	33	17	23	0	ENST00000346085.5:c.1402C>T	p.Gln468Ter	p.Q468*	ENST00000346085	NM_020732.3	468	Cag/Tag	1/20	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.505558789036259	2		23	50	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522149	157522149	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	91	380	0	ENST00000346085.5:c.4421C>T	p.Pro1474Leu	p.P1474L	ENST00000346085	NM_020732.3	1474	cCc/cTc	18/20	1	2	FACETS	0.976	0.873	1	0.976	0.873	1	CLONAL	1	TRUE	1	0.505558789036259	2		380	369	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6045628	6045628	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs573374779	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	39	123	0	ENST00000265849.7:c.58C>T	p.Arg20Trp	p.R20W	ENST00000265849	NM_000535.5	20	Cgg/Tgg	2/15	1	2	FACETS	1	0.865	1	1	0.865	1	CLONAL	1	TRUE	1	0.505558789036259	2		123	150	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273131	55273131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368892932	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	124	478	1	ENST00000275493.2:c.3454G>A	p.Asp1152Asn	p.D1152N	ENST00000275493	NM_005228.3	1152	Gac/Aac	28/28	1	2	FACETS	0.926	0.841	1	0.926	0.841	1	CLONAL	1	TRUE	1	0.505558789036259	2		479	530	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335633	81335633	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	58	411	0	ENST00000222390.5:c.1727G>A	p.Gly576Glu	p.G576E	ENST00000222390	NM_000601.4	576	gGa/gAa	15/18	1	2	FACETS	0.914	0.794	1	0.914	0.794	1	CLONAL	1	TRUE	1	0.505558789036259	2		411	251	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140500213	140500213	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757803696	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	146	457	0	ENST00000288602.6:c.929C>T	p.Thr310Ile	p.T310I	ENST00000288602	NM_004333.4	310	aCt/aTt	7/18	0.416760861378068	3	FACETS	0.94	0.868	1	0.94	0.868	1	CLONAL	2	TRUE	1	0.505558789036259	3		457	385	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874754	151874754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775427298	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	186	368	0	ENST00000262189.6:c.7784C>T	p.Pro2595Leu	p.P2595L	ENST00000262189	NM_170606.2	2595	cCc/cTc	38/59	0.416760861378068	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.505558789036259	3		368	422	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877914	151877914	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773409339	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	84	402	0	ENST00000262189.6:c.7031C>T	p.Ser2344Phe	p.S2344F	ENST00000262189	NM_170606.2	2344	tCc/tTc	36/59	0.416760861378068	3	FACETS	0.833	0.738	0.934	0.416	0.369	0.467	CLONAL	1	TRUE	1	0.505558789036259	3		402	500	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151944989	151944989	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs745861231	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	20	137	0	ENST00000262189.6:c.2530C>G	p.Gln844Glu	p.Q844E	ENST00000262189	NM_170606.2	844	Cag/Gag	14/59	0.416760861378068	3	FACETS	0.774	0.599	0.974	0.387	0.299	0.487	CLONAL	1	TRUE	1	0.505558789036259	3		137	128	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742016	145742016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	180	363	0	ENST00000428558.2:c.487C>T	p.Pro163Ser	p.P163S	ENST00000428558	NM_004260.3	163	Cct/Tct	5/22	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.505558789036259	2		363	679	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319890	8319890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	55	456	0	ENST00000356435.5:c.5611G>A	p.Asp1871Asn	p.D1871N	ENST00000356435		1871	Gat/Aat	34/35	0.330159172547719	1	FACETS	0.669	0.578	0.766	0.669	0.578	0.766	SUBCLONAL	1	TRUE	0	0.505558789036259	1		456	243	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375972	8375972	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	74	592	0	ENST00000356435.5:c.4625A>G	p.Asn1542Ser	p.N1542S	ENST00000356435		1542	aAc/aGc	28/35	0.330159172547719	1	FACETS	0.591	0.521	0.666	0.591	0.521	0.666	SUBCLONAL	1	TRUE	0	0.505558789036259	1		592	370	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485905	8485905	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	80	553	0	ENST00000356435.5:c.2912T>C	p.Leu971Pro	p.L971P	ENST00000356435		971	cTt/cCt	17/35	0.330159172547719	1	FACETS	0.842	0.75	0.938	0.842	0.75	0.938	CLONAL	1	TRUE	0	0.505558789036259	1		553	281	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500757	8500757	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	92	311	0	ENST00000356435.5:c.2125G>A	p.Asp709Asn	p.D709N	ENST00000356435		709	Gat/Aat	13/35	0.330159172547719	1	FACETS	0.735	0.658	0.816	0.735	0.658	0.816	SUBCLONAL	1	TRUE	0	0.505558789036259	1		311	370	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359899	87359899	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	23	481	0	ENST00000277120.3:c.1207G>C	p.Ala403Pro	p.A403P	ENST00000277120		403	Gca/Cca	11/19	0.505558789036259	1	FACETS	0.229	0.178	0.287	0.229	0.178	0.287	SUBCLONAL	1	TRUE	0	0.505558789036259	1		481	297	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209264	98209264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778630	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	182	505	0	ENST00000331920.6:c.4274C>T	p.Ser1425Leu	p.S1425L	ENST00000331920	NM_000264.3	1425	tCg/tTg	23/24	0.505558789036259	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.505558789036259	1		505	487	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615101	43615101	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	167	528	0	ENST00000355710.3:c.2515G>A	p.Asp839Asn	p.D839N	ENST00000355710	NM_020975.4	839	Gac/Aac	14/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.505558789036259	2		528	600	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404804	70404804	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	84	406	1	ENST00000373644.4:c.2318C>T	p.Ser773Leu	p.S773L	ENST00000373644	NM_030625.2	773	tCa/tTa	4/12	1	2	FACETS	0.831	0.738	0.929	0.831	0.738	0.929	CLONAL	1	TRUE	1	0.505558789036259	2		407	400	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451522	70451522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	99	534	0	ENST00000373644.4:c.6362C>T	p.Ser2121Phe	p.S2121F	ENST00000373644	NM_030625.2	2121	tCc/tTc	12/12	1	2	FACETS	0.888	0.797	0.983	0.888	0.797	0.983	CLONAL	1	TRUE	1	0.505558789036259	2		534	441	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104352359	104352359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	130	491	0	ENST00000369902.3:c.475G>A	p.Asp159Asn	p.D159N	ENST00000369902	NM_016169.3	159	Gac/Aac	4/12	1	2	FACETS	0.922	0.84	1	0.922	0.84	1	CLONAL	1	TRUE	1	0.505558789036259	2		491	558	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925598	114925598	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755806253	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	178	712	2	ENST00000543371.1:c.1676C>T	p.Pro559Leu	p.P559L	ENST00000543371	NM_001198531.1	559	cCc/cTc	14/14	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.505558789036259	2		714	632	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243282	123243282	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375719482	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	103	487	0	ENST00000358487.5:c.2231C>T	p.Pro744Leu	p.P744L	ENST00000358487	NM_000141.4	744	cCc/cTc	17/18	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.505558789036259	2		487	382	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922195	100922195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	48	659	0	ENST00000325455.5:c.2317G>A	p.Gly773Arg	p.G773R	ENST00000325455	NM_001202474.3	773	Ggg/Agg	5/8	0.42890761913357	0	FACETS	0.467	0.4	0.539			1	SUBCLONAL	1	TRUE	0	0.505558789036259	0		659	201	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352592	118352592	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	73	571	0	ENST00000534358.1:c.3797C>T	p.Pro1266Leu	p.P1266L	ENST00000534358	NM_005933.3	1266	cCc/cTc	7/36	0.419818203219755	1	FACETS	0.484	0.424	0.547	0.484	0.424	0.547	SUBCLONAL	1	TRUE	0	0.505558789036259	1		571	446	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402232	402232	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1255186042	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	125	564	0	ENST00000399788.2:c.4559G>A	p.Gly1520Glu	p.G1520E	ENST00000399788	NM_001042603.1	1520	gGa/gAa	27/28	NA	2	FACETS	0.926	0.842	1			1	INDETERMINATE	1	TRUE	NA	0.505558789036259	2		564	534	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037487	12037487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	130	336	0	ENST00000396373.4:c.1118C>T	p.Pro373Leu	p.P373L	ENST00000396373	NM_001987.4	373	cCc/cTc	6/8	0.344123474327492	4	FACETS	0.771	0.704	0.842			1	SUBCLONAL	2	TRUE	NA	0.505558789036259	4		336	502	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18644429	18644429	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	56	467	0	ENST00000266497.5:c.2607A>C	p.Gln869His	p.Q869H	ENST00000266497		869	caA/caC	18/31	NA	2	FACETS	0.8	0.691	0.916			1	INDETERMINATE	1	TRUE	NA	0.505558789036259	2		467	277	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18699293	18699293	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	63	507	0	ENST00000266497.5:c.3394C>T	p.Gln1132Ter	p.Q1132*	ENST00000266497		1132	Caa/Taa	24/31	NA	2	FACETS	0.884	0.771	1			1	INDETERMINATE	1	TRUE	NA	0.505558789036259	2		507	282	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793399	18793399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	77	513	0	ENST00000266497.5:c.4096G>A	p.Glu1366Lys	p.E1366K	ENST00000266497		1366	Gaa/Aaa	30/31	NA	2	FACETS	1	0.891	1			1	INDETERMINATE	1	TRUE	NA	0.505558789036259	2		513	303	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424958105	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	76	525	0	ENST00000334344.6:c.940C>T	p.Arg314Cys	p.R314C	ENST00000334344	NM_152641.2	314	Cgt/Tgt	8/21	NA	2	FACETS	0.964	0.853	1			1	INDETERMINATE	1	TRUE	NA	0.505558789036259	2		525	312	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433358	49433358	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	111	266	0	ENST00000301067.7:c.8089C>G	p.Arg2697Gly	p.R2697G	ENST00000301067	NM_003482.3	2697	Cgc/Ggc	32/54	1	2	FACETS	0.998	0.903	1	0.998	0.903	1	CLONAL	1	TRUE	1	0.505558789036259	2		266	440	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438254	49438254	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	160	444	0	ENST00000301067.7:c.5015C>T	p.Pro1672Leu	p.P1672L	ENST00000301067	NM_003482.3	1672	cCt/cTt	20/54	1	2	FACETS	0.904	0.831	0.98	0.904	0.831	0.98	CLONAL	1	TRUE	1	0.505558789036259	2		444	700	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443710	49443710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	177	510	0	ENST00000301067.7:c.3661C>T	p.Pro1221Ser	p.P1221S	ENST00000301067	NM_003482.3	1221	Cct/Tct	11/54	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.505558789036259	2		510	693	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416767	121416767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	154	447	0	ENST00000257555.6:c.196G>A	p.Glu66Lys	p.E66K	ENST00000257555		66	Gag/Aag	1/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.505558789036259	2		447	525	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001922	29001922	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	56	530	0	ENST00000282397.4:c.1243T>C	p.Phe415Leu	p.F415L	ENST00000282397	NM_002019.4	415	Ttt/Ctt	9/30	1	2	FACETS	0.661	0.57	0.76	0.661	0.57	0.76	SUBCLONAL	1	TRUE	1	0.505558789036259	2		530	335	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81558939	81558939	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1230091225	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	66	387	1	ENST00000298171.2:c.532G>A	p.Glu178Lys	p.E178K	ENST00000298171	NM_000369.2	178	Gaa/Aaa	6/10	1	2	FACETS	0.766	0.669	0.869	0.766	0.669	0.869	SUBCLONAL	1	TRUE	1	0.505558789036259	2		388	341	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572480	95572480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	69	458	1	ENST00000393063.1:c.2885C>T	p.Ser962Phe	p.S962F	ENST00000393063	NM_030621.3	962	tCc/tTc	19/28	1	2	FACETS	0.935	0.822	1	0.935	0.822	1	CLONAL	1	TRUE	1	0.505558789036259	2		459	292	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058306	42058306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1171419846	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	106	668	0	ENST00000219905.7:c.8026C>T	p.Pro2676Ser	p.P2676S	ENST00000219905	NM_001164273.1	2676	Cct/Tct	24/24	0.505558789036259	1	FACETS	0.734	0.662	0.809	0.734	0.662	0.809	SUBCLONAL	1	TRUE	0	0.505558789036259	1		668	427	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858615	9858615	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767268773	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	121	607	1	ENST00000330684.3:c.2786C>T	p.Ser929Phe	p.S929F	ENST00000330684	NM_001134407.1	929	tCc/tTc	13/13	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.505558789036259	2		608	453	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031882	10031882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	62	567	0	ENST00000330684.3:c.941C>T	p.Pro314Leu	p.P314L	ENST00000330684	NM_001134407.1	314	cCc/cTc	3/13	1	2	FACETS	0.837	0.729	0.952	0.837	0.729	0.952	CLONAL	1	TRUE	1	0.505558789036259	2		567	293	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346411	89346411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	234	576	2	ENST00000301030.4:c.6539C>T	p.Ser2180Phe	p.S2180F	ENST00000301030	NM_001256183.1	2180	tCc/tTc	9/13	0.120649375823615	3	FACETS	1	0.99	1	0.654	0.611	0.698	INDETERMINATE	1	TRUE	1	0.505558789036259	3		578	887	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351259	89351259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	213	719	0	ENST00000301030.4:c.1691C>T	p.Ser564Phe	p.S564F	ENST00000301030	NM_001256183.1	564	tCt/tTt	9/13	0.120649375823615	3	FACETS	1	0.986	1	0.612	0.569	0.656	INDETERMINATE	1	TRUE	1	0.505558789036259	3		719	863	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352506	89352506	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	204	606	1	ENST00000301030.4:c.833C>A	p.Thr278Lys	p.T278K	ENST00000301030	NM_001256183.1	278	aCg/aAg	8/13	0.120649375823615	3	FACETS	1	0.986	1	0.623	0.579	0.669	INDETERMINATE	1	TRUE	1	0.505558789036259	3		607	811	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357487	89357487	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	211	644	0	ENST00000301030.4:c.331C>T	p.Leu111Phe	p.L111F	ENST00000301030	NM_001256183.1	111	Ctc/Ttc	5/13	0.120649375823615	3	FACETS	0.76	0.709	0.812	0.76	0.709	0.812	INDETERMINATE	2	TRUE	1	0.505558789036259	3		644	688	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29541468	29541468	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1131691131	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	20	106	0	ENST00000356175.3:c.1393-1G>A		p.X465_splice	ENST00000356175	NM_000267.3	465			1	2	FACETS	0.965	0.756	1	0.965	0.756	1	CLONAL	1	TRUE	1	0.505558789036259	2		106	82	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562628	29562628	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs1555615431	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	93	475	0	ENST00000356175.3:c.3709-1G>A		p.X1237_splice	ENST00000356175	NM_000267.3	1237			1	2	FACETS	0.8	0.714	0.89	0.8	0.714	0.89	SUBCLONAL	1	TRUE	1	0.505558789036259	2		475	460	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37646923	37646923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	151	578	2	ENST00000447079.4:c.2045C>T	p.Pro682Leu	p.P682L	ENST00000447079	NM_015083.1	682	cCc/cTc	3/14	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.505558789036259	2		580	568	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481442	40481442	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	154	644	0	ENST00000264657.5:c.1267C>G	p.Arg423Gly	p.R423G	ENST00000264657	NM_139276.2	423	Cga/Gga	14/24	0.505558789036259	1	FACETS	0.784	0.72	0.849	0.784	0.72	0.849	SUBCLONAL	1	TRUE	0	0.505558789036259	1		644	581	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740467	58740467	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs773389405	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	106	656	0	ENST00000305921.3:c.1372C>T	p.Arg458Ter	p.R458*	ENST00000305921	NM_003620.3	458	Cga/Tga	6/6	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.505558789036259	2		656	395	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511674	66511674	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	86	457	0	ENST00000358598.2:c.134G>C	p.Arg45Thr	p.R45T	ENST00000358598	NM_212471.2	45	aGa/aCa	2/11	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.505558789036259	2		457	332	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622407	1622407	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	174	342	0	ENST00000344749.5:c.557C>T	p.Pro186Leu	p.P186L	ENST00000344749	NM_001136139.2	186	cCa/cTa	9/19	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.505558789036259	2		342	639	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222278	2222278	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1185838025	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	251	524	0	ENST00000398665.3:c.3110C>T	p.Pro1037Leu	p.P1037L	ENST00000398665	NM_032482.2	1037	cCt/cTt	24/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.505558789036259	2		524	882	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7174716	7174716	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373995681	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	139	396	0	ENST00000302850.5:c.1001C>T	p.Pro334Leu	p.P334L	ENST00000302850	NM_000208.2	334	cCc/cTc	4/22	1	2	FACETS	0.968	0.885	1	0.968	0.885	1	CLONAL	1	TRUE	1	0.505558789036259	2		396	568	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184355	7184355	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	175	554	0	ENST00000302850.5:c.946C>T	p.Pro316Ser	p.P316S	ENST00000302850	NM_000208.2	316	Ccc/Tcc	3/22	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.505558789036259	2		554	648	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281144	15281144	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	164	500	2	ENST00000263388.2:c.5112G>A	p.Met1704Ile	p.M1704I	ENST00000263388	NM_000435.2	1704	atG/atA	27/33	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.505558789036259	2		502	631	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281203	15281203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	192	518	2	ENST00000263388.2:c.5053G>A	p.Asp1685Asn	p.D1685N	ENST00000263388	NM_000435.2	1685	Gac/Aac	27/33	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.505558789036259	2		520	721	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523352	9523352	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	64	450	0	ENST00000353224.5:c.1885C>T	p.Leu629Phe	p.L629F	ENST00000353224	NM_177990.2	629	Ctc/Ttc	9/10	1	2	FACETS	0.858	0.75	0.974	0.858	0.75	0.974	CLONAL	1	TRUE	1	0.505558789036259	2		450	295	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546826	9546826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	62	333	0	ENST00000353224.5:c.1196C>T	p.Ser399Phe	p.S399F	ENST00000353224	NM_177990.2	399	tCc/tTc	5/10	1	2	FACETS	0.864	0.753	0.982	0.864	0.753	0.982	CLONAL	1	TRUE	1	0.505558789036259	2		333	284	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39721218	39721218	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	90	382	0	ENST00000361337.2:c.721T>C	p.Tyr241His	p.Y241H	ENST00000361337	NM_003286.2	241	Tat/Cat	9/21	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.505558789036259	2		382	353	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747117	40747117	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	115	477	0	ENST00000373198.4:c.2965G>A	p.Asp989Asn	p.D989N	ENST00000373198	NM_133170.3	989	Gac/Aac	22/32	0.419818203219755	1	FACETS	0.716	0.648	0.786	0.716	0.648	0.786	SUBCLONAL	1	TRUE	0	0.505558789036259	1		477	475	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420032	41420032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	112	535	0	ENST00000373198.4:c.289G>A	p.Glu97Lys	p.E97K	ENST00000373198	NM_133170.3	97	Gag/Aag	3/32	0.419818203219755	1	FACETS	0.892	0.81	0.977	0.892	0.81	0.977	CLONAL	1	TRUE	0	0.505558789036259	1		535	371	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54958207	54958207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	118	381	0	ENST00000312783.6:c.400G>A	p.Glu134Lys	p.E134K	ENST00000312783	NM_198436.1	134	Gaa/Aaa	6/10	NA	2	FACETS	0.912	0.827	1			1	INDETERMINATE	1	TRUE	NA	0.505558789036259	2		381	512	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46231156	46231228	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTACAAAATGTCTAATGTCAAGGGATAGATTTTTAAAGATGAGAGGTGAGTTTTCACTGAAGTATTTACTTTC	TTACAAAATGTCTAATGTCAAGGGATAGATTTTTAAAGATGAGAGGTGAGTTTTCACTGAAGTATTTACTTTC	-	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	67	417	1	ENST00000334344.6:c.1077_1120+29del		p.X359_splice	ENST00000334344	NM_152641.2	359		9/21	NA	2	FACETS	0.937	0.822	1			1	INDETERMINATE	1	TRUE	NA	0.505558789036259	2		418	283	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273568	5273569	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	T	novel	NA	P-0005228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	161	399	0	ENST00000357368.4:c.263_264delinsA	p.Gly88GlufsTer4	p.G88Efs*4	ENST00000357368	NM_002850.3	88	gGG/gA	4/38	1	2	FACETS	0.926	0.852	1	0.926	0.852	1	CLONAL	1	TRUE	1	0.505558789036259	2		399	688	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0005232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	67	464	0				ENST00000310581	NM_198253.2	-/1132			0.182254784862821	3	FACETS	0.817	0.734	0.901	0.817	0.734	0.901	INDETERMINATE	2	TRUE	1	0.872075437752656	3		464	135	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0005232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	158	236	0	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.872075437752656	2		236	249	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790690	89790690	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1221702643	NA	P-0005232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	225	419	0	ENST00000336032.3:c.77G>A	p.Arg26Gln	p.R26Q	ENST00000336032	NM_006813.2	26	cGa/cAa	1/2	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.872075437752656	2		419	504	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367318	50367318	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	163	302	2	ENST00000331340.3:c.125G>T	p.Gly42Val	p.G42V	ENST00000331340	NM_006060.4	42	gGa/gTa	3/8	1	2	FACETS	0.949	0.882	1	0.949	0.882	1	CLONAL	1	TRUE	1	0.872075437752656	2		304	394	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961225	41961225	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	224	557	1	ENST00000219905.7:c.133C>T	p.Gln45Ter	p.Q45*	ENST00000219905	NM_001164273.1	45	Cag/Tag	2/24	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.872075437752656	2		558	491	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961591	41961591	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	229	574	0	ENST00000219905.7:c.499C>G	p.His167Asp	p.H167D	ENST00000219905	NM_001164273.1	167	Cat/Gat	2/24	NA	2	FACETS	1	0.943	1			1	INDETERMINATE	1	TRUE	NA	0.872075437752656	2		574	524	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663425	67663425	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	171	401	0	ENST00000264010.4:c.1826C>T	p.Ser609Phe	p.S609F	ENST00000264010	NM_006565.3	609	tCc/tTc	10/12	0.161812278213363	1	FACETS	0.556	0.518	0.594	0.556	0.518	0.594	INDETERMINATE	1	TRUE	0	0.872075437752656	1		401	398	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630479	187630480	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0005232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	155	443	1	ENST00000441802.2:c.502_503del	p.Ile168ArgfsTer21	p.I168Rfs*21	ENST00000441802	NM_005245.3	168	ATc/c	2/27	0.344239903281913	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.872075437752656	0		444	354	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005254-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	65	280	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.947	1			1	INDETERMINATE	1	TRUE	NA	0.81702829882889	2		280	144	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654857	29654857	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786202112	NA	P-0005254-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	224	373	0	ENST00000356175.3:c.5546G>A	p.Arg1849Gln	p.R1849Q	ENST00000356175	NM_000267.3	1849	cGg/cAg	37/57	0.81702829882889	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.81702829882889	1		373	305	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0005260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	77	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.159404985424446	4	FACETS	1	0.972	1	0.675	0.598	0.757	INDETERMINATE	1	TRUE	2	0.548509791876579	4		490	322	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0005260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	13	229	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.649	0.472	0.856			1	INDETERMINATE	1	TRUE	NA	0.548509791876579	2		229	73	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566827	212566827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202247795	NA	P-0005260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	92	345	0	ENST00000342788.4:c.1354G>A	p.Glu452Lys	p.E452K	ENST00000342788	NM_005235.2	452	Gaa/Aaa	12/28	0.244924964463208	4	FACETS	1	0.978	1	0.698	0.625	0.775	INDETERMINATE	1	TRUE	2	0.548509791876579	4		345	372	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120360	94120360	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs749418654	NA	P-0005260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	118	661	0	ENST00000369303.4:c.691C>T	p.Arg231Ter	p.R231*	ENST00000369303	NM_004440.3	231	Cga/Tga	3/17	0.370057356482568	4	FACETS	0.755	0.686	0.827	0.755	0.686	0.827	SUBCLONAL	2	TRUE	2	0.548509791876579	4		661	441	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553653	106553653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	49	432	4	ENST00000369096.4:c.1618G>A	p.Ala540Thr	p.A540T	ENST00000369096	NM_001198.3	540	Gcc/Acc	5/7	0.370057356482568	4	FACETS	0.881	0.75	1	0.441	0.375	0.512	CLONAL	1	TRUE	2	0.548509791876579	4		436	314	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541715	120541715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1261521534	NA	P-0005260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	32	662	1	ENST00000229340.5:c.142C>T	p.Arg48Trp	p.R48W	ENST00000229340	NM_006861.6	48	Cgg/Tgg	3/6	NA	2	FACETS	0.384	0.312	0.464			1	INDETERMINATE	1	TRUE	NA	0.548509791876579	2		663	304	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989448	7989448	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	24	465	0	ENST00000319144.4:c.238G>A	p.Asp80Asn	p.D80N	ENST00000319144	NM_001139.2	80	Gac/Aac	2/15	1	2	FACETS	0.512	0.404	0.633	0.512	0.404	0.633	SUBCLONAL	1	TRUE	1	0.548509791876579	2		465	171	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733280	40733280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370508724	NA	P-0005260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	51	445	0	ENST00000373198.4:c.3526C>T	p.Arg1176Cys	p.R1176C	ENST00000373198	NM_133170.3	1176	Cgt/Tgt	26/32	1	2	FACETS	0.795	0.683	0.915	0.795	0.683	0.915	CLONAL	1	TRUE	1	0.548509791876579	2		445	234	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815572	139815573	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0005260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	28	662	0	ENST00000247668.2:c.1043_1044del	p.Ser348TyrfsTer71	p.S348Yfs*71	ENST00000247668	NM_021138.3	348	tCC/t	9/11	NA	2	FACETS	0.442	0.355	0.54			1	INDETERMINATE	1	TRUE	NA	0.548509791876579	2		662	231	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711875	89711899	+	stop_gained,frameshift_variant,splice_region_variant	Nonsense_Mutation	DEL	GGAGTAACTATTCCCAGTCAGAGGC	GGAGTAACTATTCCCAGTCAGAGGC	TA	novel	NA	P-0005260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	59	371	0	ENST00000371953.3:c.493_517delinsTA	p.Gly165Ter	p.G165*	ENST00000371953	NM_000314.4	165	GGAGTAACTATTCCCAGTCAGAGGCgc/TAgc	6/9	0.293016278954249	4	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.548509791876579	4		371	226	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971188	21971190	+	frameshift_variant	Frame_Shift_Del	DEL	GCG	GCG	AA	novel	NA	P-0005260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	59	186	0	ENST00000304494.5:c.168_170delinsTT	p.Ala57SerfsTer89	p.A57Sfs*89	ENST00000304494	NM_000077.4	56	agCGCc/agTTc	2/3	0.159404985424446	4	FACETS	1	0.901	1	1	0.901	1	INDETERMINATE	2	TRUE	2	0.548509791876579	4		186	162	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692902	89692902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909218	NA	P-0005263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	28	253	0	ENST00000371953.3:c.386G>A	p.Gly129Glu	p.G129E	ENST00000371953	NM_000314.4	129	gGa/gAa	5/9	0.278831337687261	1	FACETS	0.507	0.405	0.622	0.507	0.405	0.622	SUBCLONAL	1	TRUE	0	0.278831337687261	1		253	341	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190804	11190804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225264	NA	P-0005263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	49	208	0	ENST00000361445.4:c.5395G>A	p.Glu1799Lys	p.E1799K	ENST00000361445	NM_004958.3	1799	Gaa/Aaa	39/58	1	2	FACETS	0.648	0.549	0.758	0.648	0.549	0.758	SUBCLONAL	1	TRUE	1	0.278831337687261	2		208	542	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162737119	162737119	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	45	434	0	ENST00000367921.3:c.1263G>C	p.Trp421Cys	p.W421C	ENST00000367921	NM_006182.2	421	tgG/tgC	11/18	0.278831337687261	3	FACETS	0.452	0.378	0.534	0.226	0.189	0.267	SUBCLONAL	1	TRUE	1	0.278831337687261	3		434	814	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52675997	52675997	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	56	433	0	ENST00000394830.3:c.1060G>C	p.Glu354Gln	p.E354Q	ENST00000394830	NM_018313.4	354	Gaa/Caa	11/30	0.278831337687261	1	FACETS	0.568	0.486	0.657	0.568	0.486	0.657	SUBCLONAL	1	TRUE	0	0.278831337687261	1		433	609	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243010	105243010	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	67	374	0	ENST00000349310.3:c.273G>C	p.Glu91Asp	p.E91D	ENST00000349310	NM_001014432.1	91	gaG/gaC	5/15	1	2	FACETS	0.513	0.445	0.588	0.513	0.445	0.588	SUBCLONAL	1	TRUE	1	0.278831337687261	2		374	936	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105243094	105243094	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1566818959	NA	P-0005263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	46	363	0	ENST00000349310.3:c.189G>A	p.Met63Ile	p.M63I	ENST00000349310	NM_001014432.1	63	atG/atA	5/15	1	2	FACETS	0.424	0.356	0.5	0.424	0.356	0.5	SUBCLONAL	1	TRUE	1	0.278831337687261	2		363	778	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057961	27057962	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	78	284	0	ENST00000324856.7:c.1670dup	p.Ser558ValfsTer65	p.S558Vfs*65	ENST00000324856	NM_006015.4	557	cag/cAag	3/20	0.278831337687261	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.278831337687261	1		284	362	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006805	47006806	+	5_prime_UTR_variant	5'UTR	INS	-	-	G	novel	NA	P-0005263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	88	435	0	ENST00000377604.3:c.-71dup		p.*24*	ENST00000377604	NM_001204468.1	-/852		2/24	1	2	FACETS	0.942	0.835	1	0.942	0.835	1	CLONAL	1	TRUE	1	0.278831337687261	2		435	670	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	33	280	0				ENST00000310581	NM_198253.2	-/1132			0.339082206488124	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.33	1		280	116	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0005293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	211	558	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	1	0.33	2		558	531	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148727	20148727	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0005293-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	163	233	0	ENST00000379607.5:c.338-2A>T		p.X113_splice	ENST00000379607	NM_001412.3	113			1	2	FACETS	0.984	0.91	1	1	0.992	1	CLONAL	2	TRUE	1	0.33	2		233	502	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0005311-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	108	521	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.251656583129873	2		522	851	SUCCESS
APC	324	MSKCC	GRCh37	5	112175676	112175677	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs387906234	NA	P-0005311-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	170	343	0	ENST00000257430.4:c.4393_4394del	p.Ser1465TrpfsTer3	p.S1465Wfs*3	ENST00000257430	NM_000038.5	1462	aAG/a	16/16	0.251656583129873	2	FACETS	1	0.988	1	0.725	0.666	0.786	CLONAL	1	TRUE	0	0.251656583129873	2		343	932	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713812	30713812	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005311-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	167	302	0	ENST00000295754.5:c.1137C>A	p.Asp379Glu	p.D379E	ENST00000295754	NM_003242.5	379	gaC/gaA	4/7	0.251656583129873	2	FACETS	0.88	0.81	0.953	0.88	0.81	0.953	CLONAL	2	TRUE	0	0.251656583129873	2		302	754	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739909	41739909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005311-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	107	414	0	ENST00000242208.4:c.64C>T	p.Pro22Ser	p.P22S	ENST00000242208	NM_002192.2	22	Ccc/Tcc	2/3	1	2	FACETS	0.732	0.655	0.815	0.732	0.655	0.815	SUBCLONAL	1	TRUE	1	0.251656583129873	2		414	1161	SUCCESS
CDK6	1021	MSKCC	GRCh37	7	92354984	92354984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005311-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	85	340	0	ENST00000265734.4:c.493G>A	p.Gly165Ser	p.G165S	ENST00000265734	NM_001259.6	165	Ggc/Agc	4/8	1	2	FACETS	0.679	0.599	0.765	0.679	0.599	0.765	SUBCLONAL	1	TRUE	1	0.251656583129873	2		340	995	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206650052	206650053	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0005311-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	115	323	1	ENST00000367120.3:c.575dup	p.Pro193AlafsTer112	p.P193Afs*112	ENST00000367120	NM_014002.3	191	cga/cgAa	7/22	1	2	FACETS	0.944	0.849	1	0.944	0.849	1	CLONAL	1	TRUE	1	0.251656583129873	2		324	968	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120115	70120115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005311-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	60	61	0	ENST00000245479.2:c.1121del	p.Pro374ArgfsTer9	p.P374Rfs*9	ENST00000245479	NM_000346.3	373	Ccc/cc	3/3	0.251656583129873	2	FACETS	0.958	0.843	1	1	0.972	1	CLONAL	3	TRUE	0	0.251656583129873	2		61	166	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33290670	33290670	+	5_prime_UTR_variant	5'UTR	SNP	C	C	T	rs766488565	NA	P-0005311-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	57	309	1	ENST00000374542.5:c.-84G>A		p.*28*	ENST00000374542	NM_001141970.1	-/740		1/8	1	2	FACETS	0.473	0.405	0.549	0.473	0.405	0.549	SUBCLONAL	1	TRUE	1	0.251656583129873	2		310	957	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	17	280	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	0.527	0.397	0.678	0.527	0.397	0.678	SUBCLONAL	1	TRUE	0	0.4	1		280	129	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0005350-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	75	463	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.220166047526648	4	FACETS	0.526	0.46	0.598	0.263	0.23	0.299	INDETERMINATE	1	TRUE	2	0.4	4		463	998	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	71	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.843	0.757	0.929	1	0.983	1	CLONAL	2	TRUE	1	0.561817587446079	2		464	150	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	12	500	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	0.078	0.054	0.108	0.078	0.054	0.108	SUBCLONAL	1	TRUE	1	0.561817587446079	2		500	546	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	52	263	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.561817587446079	2		263	161	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	18	660	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.228	0.171	0.295	0.228	0.171	0.295	SUBCLONAL	1	TRUE	1	0.561817587446079	2		660	281	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258034	123258034	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs121913476	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	110	550	0	ENST00000358487.5:c.1647T>G	p.Asn549Lys	p.N549K	ENST00000358487	NM_000141.4	549	aaT/aaG	12/18	0.561817587446079	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.561817587446079	1		550	214	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923035	44923035	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	149	202	0	ENST00000377967.4:c.1896G>A	p.Trp632Ter	p.W632*	ENST00000377967	NM_021140.2	632	tgG/tgA	16/29	1	1	FACETS	0.935	0.886	0.981	1	0.993	1	CLONAL	2	TRUE	0	0.561817587446079	1		202	204	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175957470	175957470	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	126	506	0	ENST00000367669.3:c.1926A>C	p.Glu642Asp	p.E642D	ENST00000367669	NM_022457.5	642	gaA/gaC	17/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.561817587446079	2		506	418	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131303	202131303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	93	463	1	ENST00000358485.4:c.271C>T	p.Gln91Ter	p.Q91*	ENST00000358485	NM_001080125.1	91	Caa/Taa	2/9	1	2	FACETS	0.828	0.754	0.902	1	0.986	1	CLONAL	2	TRUE	1	0.561817587446079	2		464	200	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662172	227662172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770740222	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	187	515	0	ENST00000305123.5:c.1283C>T	p.Ser428Leu	p.S428L	ENST00000305123	NM_005544.2	428	tCg/tTg	1/2	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.561817587446079	2		515	474	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231104	142231104	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	91	278	0	ENST00000350721.4:c.4850T>A	p.Met1617Lys	p.M1617K	ENST00000350721	NM_001184.3	1617	aTg/aAg	27/47	1	2	FACETS	0.79	0.717	0.864	1	0.985	1	SUBCLONAL	2	TRUE	1	0.561817587446079	2		278	205	SUCCESS
ATR	545	MSKCC	GRCh37	3	142241574	142241574	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	70	337	0	ENST00000350721.4:c.4262T>G	p.Ile1421Ser	p.I1421S	ENST00000350721	NM_001184.3	1421	aTt/aGt	23/47	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.561817587446079	2		337	228	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55602775	55602775	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	47	351	1	ENST00000288135.5:c.2596G>C	p.Gly866Arg	p.G866R	ENST00000288135	NM_000222.2	866	Gga/Cga	18/21	0.265875930434804	0	FACETS	0.531	0.459	0.607			1	INDETERMINATE	1	TRUE	0	0.561817587446079	0		352	138	SUCCESS
APC	324	MSKCC	GRCh37	5	112178680	112178680	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	88	435	0	ENST00000257430.4:c.7389A>T	p.Glu2463Asp	p.E2463D	ENST00000257430	NM_000038.5	2463	gaA/gaT	16/16	0.108723828655497	3	FACETS	0.757	0.68	0.837	0.757	0.68	0.837	INDETERMINATE	2	TRUE	1	0.561817587446079	3		435	265	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056316	180056316	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	132	645	2	ENST00000261937.6:c.928T>C	p.Cys310Arg	p.C310R	ENST00000261937	NM_182925.4	310	Tgc/Cgc	7/30	0.351391228918003	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.561817587446079	1		647	298	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651906	36651906	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	135	389	0	ENST00000244741.5:c.28C>T	p.Gln10Ter	p.Q10*	ENST00000244741	NM_000389.4	10	Cag/Tag	2/3	0.188052556999988	5	FACETS	1	0.945	1	0.693	0.635	0.752	INDETERMINATE	2	TRUE	2	0.561817587446079	5		389	426	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453139	140453139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913375	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	107	377	1	ENST00000288602.6:c.1796C>T	p.Thr599Ile	p.T599I	ENST00000288602	NM_004333.4	599	aCa/aTa	15/18	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.561817587446079	2		378	273	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117875482	117875482	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	25	675	0	ENST00000297338.2:c.161G>T	p.Arg54Leu	p.R54L	ENST00000297338	NM_006265.2	54	cGg/cTg	3/14	1	2	FACETS	0.253	0.199	0.315	0.253	0.199	0.315	SUBCLONAL	1	TRUE	1	0.561817587446079	2		675	352	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80646099	80646099	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	13	33	0	ENST00000286548.4:c.53C>G	p.Ala18Gly	p.A18G	ENST00000286548	NM_002072.3	18	gCc/gGc	1/7	1	2	FACETS	1	0.849	1	1	0.849	1	CLONAL	1	TRUE	1	0.561817587446079	2		33	38	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589794	69589794	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	12	64	0	ENST00000168712.1:c.59T>C	p.Leu20Pro	p.L20P	ENST00000168712	NM_002007.2	20	cTg/cCg	1/3	1	2	FACETS	0.7	0.504	0.929	0.7	0.504	0.929	SUBCLONAL	1	TRUE	1	0.561817587446079	2		64	61	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243430	46243430	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	99	509	0	ENST00000334344.6:c.1783C>T	p.His595Tyr	p.H595Y	ENST00000334344	NM_152641.2	595	Cat/Tat	14/21	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.561817587446079	2		509	334	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118949	115118949	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	68	231	0	ENST00000257566.3:c.392G>A	p.Arg131Gln	p.R131Q	ENST00000257566	NM_016569.3	131	cGa/cAa	2/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.561817587446079	2		231	176	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060652	38060652	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	253	645	0	ENST00000250448.2:c.1337C>T	p.Thr446Ile	p.T446I	ENST00000250448	NM_004496.3	446	aCc/aTc	2/2	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.561817587446079	2		645	641	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641282	23641282	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	73	424	0	ENST00000261584.4:c.2193A>C	p.Leu731Phe	p.L731F	ENST00000261584	NM_024675.3	731	ttA/ttC	5/13	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.561817587446079	2		424	259	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81971404	81971404	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	172	545	0	ENST00000359376.3:c.3094G>C	p.Gly1032Arg	p.G1032R	ENST00000359376	NM_002661.3	1032	Ggg/Cgg	28/33	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.561817587446079	2		545	504	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15960988	15960988	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	129	521	0	ENST00000268712.3:c.6232A>C	p.Thr2078Pro	p.T2078P	ENST00000268712	NM_006311.3	2078	Act/Cct	40/46	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.561817587446079	2		521	327	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864639	37864639	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	183	511	0	ENST00000269571.5:c.291G>C	p.Gln97His	p.Q97H	ENST00000269571		97	caG/caC	3/27	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.561817587446079	2		511	482	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492784	56492784	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	110	438	0	ENST00000407977.2:c.155C>T	p.Pro52Leu	p.P52L	ENST00000407977		52	cCc/cTc	2/10	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.561817587446079	2		438	343	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533036	63533036	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	31	512	0	ENST00000307078.5:c.1858T>C	p.Trp620Arg	p.W620R	ENST00000307078	NM_004655.3	620	Tgg/Cgg	7/11	1	2	FACETS	0.242	0.195	0.295	0.242	0.195	0.295	SUBCLONAL	1	TRUE	1	0.561817587446079	2		512	456	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207153	1207153	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	115	440	0	ENST00000326873.7:c.241A>C	p.Lys81Gln	p.K81Q	ENST00000326873	NM_000455.4	81	Aag/Cag	1/10	1	2	FACETS	0.922	0.836	1	0.922	0.836	1	CLONAL	1	TRUE	1	0.561817587446079	2		440	444	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207159	1207159	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	116	423	0	ENST00000326873.7:c.247A>G	p.Lys83Glu	p.K83E	ENST00000326873	NM_000455.4	83	Aag/Gag	1/10	1	2	FACETS	0.92	0.834	1	0.92	0.834	1	CLONAL	1	TRUE	1	0.561817587446079	2		423	449	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856356	45856356	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	199	514	0	ENST00000391945.4:c.1816G>C	p.Glu606Gln	p.E606Q	ENST00000391945	NM_000400.3	606	Gag/Cag	19/23	1	2	FACETS	0.8	0.75	0.85	1	0.993	1	SUBCLONAL	2	TRUE	1	0.561817587446079	2		514	443	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523292	9523292	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	136	482	0	ENST00000353224.5:c.1945C>G	p.Leu649Val	p.L649V	ENST00000353224	NM_177990.2	649	Ctc/Gtc	9/10	1	2	FACETS	0.786	0.727	0.846	1	0.99	1	SUBCLONAL	2	TRUE	1	0.561817587446079	2		482	308	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272281	21272281	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	124	348	0	ENST00000354336.3:c.59C>T	p.Ser20Phe	p.S20F	ENST00000354336	NM_005207.3	20	tCt/tTt	1/3	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.561817587446079	2		348	351	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937891	76937891	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	72	240	0	ENST00000373344.5:c.2857A>C	p.Thr953Pro	p.T953P	ENST00000373344	NM_000489.3	953	Aca/Cca	9/35	1	1	FACETS	0.823	0.753	0.89	1	0.985	1	CLONAL	2	TRUE	0	0.561817587446079	1		240	112	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005513	42005535	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAAGAAAAGTTGTACTTGTTA	GAAAAGAAAAGTTGTACTTGTTA	-	novel	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	151	765	3	ENST00000219905.7:c.3249_3271del	p.Lys1084ArgfsTer6	p.K1084Rfs*6	ENST00000219905	NM_001164273.1	1083	ttGAAAAGAAAAGTTGTACTTGTTAaa/ttaa	9/24	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.561817587446079	2		768	435	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230670	46230671	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	118	535	0	ENST00000334344.6:c.920dup	p.Ala308SerfsTer2	p.A308Sfs*2	ENST00000334344	NM_152641.2	307	gca/gCca	8/21	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.561817587446079	2		535	322	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100727	8100728	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs771019738	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	121	282	2	ENST00000346208.3:c.708dup	p.Ser237GlnfsTer66	p.S237Qfs*66	ENST00000346208		234	ttc/ttCc	3/6	0.351391228918003	1	FACETS	0.842	0.769	0.917	0.842	0.769	0.917	CLONAL	1	TRUE	0	0.561817587446079	1		284	368	SUCCESS
CALR	811	MSKCC	GRCh37	19	13050410	13050425	+	frameshift_variant	Frame_Shift_Del	DEL	ACATGCACGGAGACTC	ACATGCACGGAGACTC	-	novel	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	45	695	0	ENST00000316448.5:c.363_378del	p.Asp121GlufsTer31	p.D121Efs*31	ENST00000316448	NM_004343.3	121	gACATGCACGGAGACTCa/ga	3/9	1	2	FACETS	0.24	0.201	0.283	0.24	0.201	0.283	SUBCLONAL	1	TRUE	1	0.561817587446079	2		695	668	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42000019	42000020	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	124	722	0	ENST00000219905.7:c.2287dup	p.Trp763LeufsTer12	p.W763Lfs*12	ENST00000219905	NM_001164273.1	761	cct/ccTt	6/24	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.561817587446079	2		722	387	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385045	31385046	+	missense_variant	Missense_Mutation	DNP	AC	AC	TG	novel	NA	P-0005359-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	166	469	0	ENST00000328111.2:c.1430_1431delinsTG	p.Tyr477Leu	p.Y477L	ENST00000328111	NM_006892.3	477	tAC/tTG	14/23	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.561817587446079	2		469	419	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005361-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	63	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.854	0.741	0.975	0.854	0.741	0.975	CLONAL	1	TRUE	1	0.357338502208831	2		280	413	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653807	89653807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554893782	NA	P-0005361-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	36	444	0	ENST00000371953.3:c.105G>A	p.Met35Ile	p.M35I	ENST00000371953	NM_000314.4	35	atG/atA	2/9	0.319424707014067	1	FACETS	0.432	0.355	0.518	0.432	0.355	0.518	SUBCLONAL	1	TRUE	0	0.357338502208831	1		444	383	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572404	41572404	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs139310551	NA	P-0005361-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	121	514	0	ENST00000263253.7:c.4933C>T	p.Arg1645Ter	p.R1645*	ENST00000263253	NM_001429.3	1645	Cga/Tga	30/31	0.265079177859951	1	FACETS	0.853	0.772	0.938	0.853	0.772	0.938	CLONAL	1	TRUE	0	0.357338502208831	1		514	652	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	139	464	0				ENST00000310581	NM_198253.2	-/1132			0.544908716979505	3	FACETS	1	0.959	1			1	CLONAL	2	TRUE	NA	0.60696277253767	3		464	285	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729949	41729949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1165688714	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	590	1725	1	ENST00000242208.4:c.580G>A	p.Glu194Lys	p.E194K	ENST00000242208	NM_002192.2	194	Gaa/Aaa	3/3	0.586964253614487	5	FACETS	0.955	0.921	0.99	0.955	0.921	0.99	CLONAL	3	TRUE	2	0.60696277253767	5		1726	1296	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199342	16199342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	346	705	0	ENST00000375759.3:c.115C>T	p.Pro39Ser	p.P39S	ENST00000375759	NM_015001.2	39	Ccc/Tcc	2/15	0.589901388437336	4	FACETS	0.997	0.947	1	0.997	0.947	1	CLONAL	2	TRUE	2	0.60696277253767	4		705	919	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	218	333	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	0.586964253614487	5	FACETS	0.904	0.844	0.966	0.603	0.562	0.644	CLONAL	2	TRUE	2	0.60696277253767	5		333	759	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504401	8504401	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757922864	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	218	419	1	ENST00000356435.5:c.1682G>A	p.Arg561Gln	p.R561Q	ENST00000356435		561	cGa/cAa	12/35	0.60696277253767	2	FACETS	0.984	0.933	1	0.984	0.933	1	CLONAL	2	TRUE	0	0.60696277253767	2		420	365	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	393	465	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.589718066014586	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.60696277253767	2		467	592	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	269	599	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.60696277253767	4	FACETS	0.885	0.833	0.938	0.59	0.555	0.625	CLONAL	2	TRUE	1	0.60696277253767	4		599	805	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171657	36171657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	264	558	0	ENST00000300305.3:c.908C>T	p.Ser303Leu	p.S303L	ENST00000300305		303	tCa/tTa	7/8	0.57884627984158	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.60696277253767	3		558	556	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95583017	95583017	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886037672	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	77	274	0	ENST00000393063.1:c.1525C>T	p.Arg509Ter	p.R509*	ENST00000393063	NM_030621.3	509	Cga/Tga	11/28	0.577698637884601	4	FACETS	0.971	0.856	1	0.324	0.285	0.365	CLONAL	1	TRUE	1	0.60696277253767	4		274	420	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860254	151860254	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	319	709	0	ENST00000262189.6:c.10408C>T	p.Gln3470Ter	p.Q3470*	ENST00000262189	NM_170606.2	3470	Cag/Tag	43/59	0.586964253614487	5	FACETS	0.919	0.868	0.971	0.612	0.578	0.647	CLONAL	2	TRUE	2	0.60696277253767	5		709	1093	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592251	29592251	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs797044942	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	116	433	1	ENST00000356175.3:c.4666C>T	p.Gln1556Ter	p.Q1556*	ENST00000356175	NM_000267.3	1556	Cag/Tag	35/57	0.60696277253767	4	FACETS	0.964	0.871	1	0.321	0.29	0.355	CLONAL	1	TRUE	1	0.60696277253767	4		434	637	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244872	46244872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766470086	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	316	686	0	ENST00000334344.6:c.2966C>T	p.Ser989Leu	p.S989L	ENST00000334344	NM_152641.2	989	tCg/tTg	15/21	0.589901388437336	4	FACETS	0.958	0.908	1	0.958	0.908	1	CLONAL	2	TRUE	2	0.60696277253767	4		686	873	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592680	28592680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	115	618	2	ENST00000241453.7:c.2465G>A	p.Gly822Glu	p.G822E	ENST00000241453	NM_004119.2	822	gGg/gAg	20/24	1	2	FACETS	0.837	0.758	0.918	0.837	0.758	0.918	CLONAL	1	TRUE	1	0.60696277253767	2		620	453	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344210	118344210	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201960342	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	192	341	0	ENST00000534358.1:c.2336C>T	p.Ser779Leu	p.S779L	ENST00000534358	NM_005933.3	779	tCg/tTg	3/36	0.60696277253767	2	FACETS	0.947	0.894	1	0.947	0.894	1	CLONAL	2	TRUE	0	0.60696277253767	2		341	334	SUCCESS
ATM	472	MSKCC	GRCh37	11	108168019	108168019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	217	356	0	ENST00000278616.4:c.4915C>T	p.Pro1639Ser	p.P1639S	ENST00000278616	NM_000051.3	1639	Ccg/Tcg	33/63	0.60696277253767	2	FACETS	0.982	0.931	1	0.982	0.931	1	CLONAL	2	TRUE	0	0.60696277253767	2		356	364	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509235	106509235	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	524	629	0	ENST00000359195.3:c.1229G>A	p.Trp410Ter	p.W410*	ENST00000359195	NM_002649.2	410	tGg/tAg	2/11	0.586964253614487	5	FACETS	1	0.964	1	1	0.964	1	CLONAL	3	TRUE	2	0.60696277253767	5		629	1098	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341196	8341196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	148	576	1	ENST00000356435.5:c.5020C>T	p.Arg1674Cys	p.R1674C	ENST00000356435		1674	Cgc/Tgc	30/35	0.60696277253767	2	FACETS	0.966	0.888	1	0.483	0.444	0.523	CLONAL	1	TRUE	0	0.60696277253767	2		577	505	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747879	41747879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	129	490	0	ENST00000226382.2:c.890C>T	p.Ser297Leu	p.S297L	ENST00000226382	NM_003924.3	297	tCg/tTg	3/3	0.589901388437336	4	FACETS	1	0.973	1	0.588	0.535	0.643	CLONAL	1	TRUE	2	0.60696277253767	4		490	581	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321372	1321372	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1319865856	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	253	549	0	ENST00000400841.2:c.383C>T	p.Ser128Leu	p.S128L	ENST00000400841		128	tCg/tTg	4/6	0.532515005101736	2	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.60696277253767	2		549	737	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38508290	38508290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	124	609	0	ENST00000254066.5:c.598C>T	p.Pro200Ser	p.P200S	ENST00000254066	NM_000964.3	200	Cct/Tct	5/9	0.60696277253767	4	FACETS	0.881	0.798	0.969	0.294	0.266	0.323	CLONAL	1	TRUE	1	0.60696277253767	4		609	745	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16247393	16247393	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747220001	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	205	530	0	ENST00000375759.3:c.1664C>T	p.Ala555Val	p.A555V	ENST00000375759	NM_015001.2	555	gCc/gTc	9/15	0.589901388437336	4	FACETS	0.812	0.757	0.869	0.812	0.757	0.869	CLONAL	2	TRUE	2	0.60696277253767	4		530	668	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107174	27107174	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375849292	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	215	353	0	ENST00000324856.7:c.6785C>T	p.Ser2262Leu	p.S2262L	ENST00000324856	NM_006015.4	2262	tCg/tTg	20/20	0.589901388437336	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.60696277253767	4		353	539	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937211	36937211	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	217	826	0	ENST00000361632.4:c.1108G>A	p.Gly370Ser	p.G370S	ENST00000361632		370	Ggt/Agt	9/16	0.589901388437336	4	FACETS	1	0.938	1	0.505	0.469	0.543	CLONAL	1	TRUE	2	0.60696277253767	4		826	1137	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797519	45797519	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	133	549	0	ENST00000450313.1:c.1000C>T	p.Pro334Ser	p.P334S	ENST00000450313	NM_012222.2	334	Ccc/Tcc	12/16	0.589901388437336	4	FACETS	1	0.918	1	0.504	0.459	0.552	CLONAL	1	TRUE	2	0.60696277253767	4		549	698	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076796	72076796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	300	619	2	ENST00000357731.5:c.701C>T	p.Thr234Ile	p.T234I	ENST00000357731	NM_173808.2	234	aCc/aTc	5/7	0.589901388437336	4	FACETS	0.955	0.903	1	0.955	0.903	1	CLONAL	2	TRUE	2	0.60696277253767	4		621	832	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471724	120471724	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	269	570	0	ENST00000256646.2:c.3767T>A	p.Phe1256Tyr	p.F1256Y	ENST00000256646	NM_024408.3	1256	tTt/tAt	23/34	0.589901388437336	4	FACETS	0.97	0.915	1	0.97	0.915	1	CLONAL	2	TRUE	2	0.60696277253767	4		570	734	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120484374	120484374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	196	416	0	ENST00000256646.2:c.2756C>T	p.Pro919Leu	p.P919L	ENST00000256646	NM_024408.3	919	cCt/cTt	18/34	0.589901388437336	4	FACETS	0.834	0.776	0.894	0.834	0.776	0.894	CLONAL	2	TRUE	2	0.60696277253767	4		416	622	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843734	156843734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	307	721	2	ENST00000524377.1:c.1160C>T	p.Pro387Leu	p.P387L	ENST00000524377	NM_002529.3	387	cCc/cTc	8/17	0.586964253614487	5	FACETS	0.946	0.893	1	0.631	0.595	0.667	CLONAL	2	TRUE	2	0.60696277253767	5		723	1021	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740290	162740290	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	196	332	1	ENST00000367921.3:c.1492G>T	p.Glu498Ter	p.E498*	ENST00000367921	NM_006182.2	498	Gag/Tag	12/18	0.586964253614487	5	FACETS	1	0.946	1	0.679	0.632	0.727	CLONAL	2	TRUE	2	0.60696277253767	5		333	606	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193099331	193099331	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	226	450	0	ENST00000367435.3:c.265C>T	p.Pro89Ser	p.P89S	ENST00000367435	NM_024529.4	89	Cct/Tct	3/17	0.586964253614487	5	FACETS	0.837	0.781	0.894	0.558	0.521	0.596	CLONAL	2	TRUE	2	0.60696277253767	5		450	850	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666444	206666444	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	342	401	0	ENST00000367120.3:c.1924C>T	p.Leu642Phe	p.L642F	ENST00000367120	NM_014002.3	642	Ctc/Ttc	19/22	0.586964253614487	5	FACETS	1	0.965	1	1	0.965	1	CLONAL	3	TRUE	2	0.60696277253767	5		401	708	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206666674	206666674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553391211	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	376	522	0	ENST00000367120.3:c.2008C>T	p.Pro670Ser	p.P670S	ENST00000367120	NM_014002.3	670	Cct/Tct	20/22	0.586964253614487	5	FACETS	0.898	0.856	0.939	0.898	0.856	0.939	CLONAL	3	TRUE	2	0.60696277253767	5		522	879	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462610	29462610	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	147	639	0	ENST00000389048.3:c.2291A>G	p.Asn764Ser	p.N764S	ENST00000389048	NM_004304.4	764	aAc/aGc	13/29	0.60696277253767	4	FACETS	0.915	0.835	0.998	0.457	0.417	0.499	CLONAL	1	TRUE	2	0.60696277253767	4		639	851	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570052	212570052	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	223	471	0	ENST00000342788.4:c.1189G>A	p.Glu397Lys	p.E397K	ENST00000342788	NM_005235.2	397	Gag/Aag	10/28	0.27535718094008	5	FACETS	1	0.975	1	0.721	0.675	0.768	INDETERMINATE	2	TRUE	2	0.60696277253767	5		471	649	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570054	212570054	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368876919	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	202	478	0	ENST00000342788.4:c.1187G>A	p.Arg396Lys	p.R396K	ENST00000342788	NM_005235.2	396	aGa/aAa	10/28	0.27535718094008	5	FACETS	0.981	0.914	1	0.654	0.609	0.7	INDETERMINATE	2	TRUE	2	0.60696277253767	5		478	648	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812235	212812235	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767277487	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	242	502	2	ENST00000342788.4:c.341G>A	p.Arg114Gln	p.R114Q	ENST00000342788	NM_005235.2	114	cGa/cAa	3/28	0.27535718094008	5	FACETS	1	0.964	1	0.693	0.65	0.737	INDETERMINATE	2	TRUE	2	0.60696277253767	5		504	733	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812335	212812335	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	189	387	1	ENST00000342788.4:c.241C>T	p.Arg81Ter	p.R81*	ENST00000342788	NM_005235.2	81	Cga/Tga	3/28	0.27535718094008	5	FACETS	1	0.981	1	0.766	0.713	0.819	INDETERMINATE	2	TRUE	2	0.60696277253767	5		388	518	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713514	30713514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	231	480	0	ENST00000295754.5:c.839C>T	p.Pro280Leu	p.P280L	ENST00000295754	NM_003242.5	280	cCc/cTc	4/7	0.589901388437336	4	FACETS	0.931	0.873	0.99	0.931	0.873	0.99	CLONAL	2	TRUE	2	0.60696277253767	4		480	657	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164832	47164832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1017636782	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	244	351	0	ENST00000409792.3:c.1294C>T	p.Arg432Cys	p.R432C	ENST00000409792	NM_014159.6	432	Cgt/Tgt	3/21	0.589901388437336	4	FACETS	0.963	0.905	1	0.963	0.905	1	CLONAL	2	TRUE	2	0.60696277253767	4		351	671	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164873	47164873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867368102	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	231	489	2	ENST00000409792.3:c.1253C>T	p.Ser418Phe	p.S418F	ENST00000409792	NM_014159.6	418	tCc/tTc	3/21	0.589901388437336	4	FACETS	0.921	0.864	0.98	0.921	0.864	0.98	CLONAL	2	TRUE	2	0.60696277253767	4		491	664	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165057	47165057	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775499197	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	227	418	1	ENST00000409792.3:c.1069C>T	p.Pro357Ser	p.P357S	ENST00000409792	NM_014159.6	357	Cct/Tct	3/21	0.589901388437336	4	FACETS	0.992	0.93	1	0.992	0.93	1	CLONAL	2	TRUE	2	0.60696277253767	4		419	606	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498375	89498375	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	203	305	0	ENST00000336596.2:c.2347G>A	p.Gly783Arg	p.G783R	ENST00000336596	NM_005233.5	783	Gga/Aga	14/17	0.589901388437336	4	FACETS	0.961	0.898	1	0.961	0.898	1	CLONAL	2	TRUE	2	0.60696277253767	4		305	559	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134960038	134960038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1346978629	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	258	585	2	ENST00000398015.3:c.2395C>T	p.Arg799Cys	p.R799C	ENST00000398015	NM_004441.4	799	Cgc/Tgc	13/16	0.59161759618259	3	FACETS	0.981	0.927	1	0.981	0.927	1	CLONAL	2	TRUE	1	0.60696277253767	3		587	565	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138453507	138453507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	157	612	1	ENST00000289153.2:c.941C>T	p.Pro314Leu	p.P314L	ENST00000289153	NM_006219.2	314	cCa/cTa	5/22	0.59161759618259	3	FACETS	0.969	0.89	1	0.484	0.445	0.526	CLONAL	1	TRUE	1	0.60696277253767	3		613	696	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281895	142281895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	184	371	1	ENST00000350721.4:c.349C>T	p.His117Tyr	p.H117Y	ENST00000350721	NM_001184.3	117	Cat/Tat	4/47	0.59161759618259	3	FACETS	0.966	0.904	1	0.966	0.904	1	CLONAL	2	TRUE	1	0.60696277253767	3		372	409	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928318	178928318	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	226	451	0	ENST00000263967.3:c.1504C>T	p.Arg502Ter	p.R502*	ENST00000263967	NM_006218.2	502	Cga/Tga	9/21	0.59161759618259	3	FACETS	0.84	0.788	0.892	0.84	0.788	0.892	CLONAL	2	TRUE	1	0.60696277253767	3		451	578	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146487	185146487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	139	512	0	ENST00000265026.3:c.118C>T	p.Pro40Ser	p.P40S	ENST00000265026	NM_004721.4	40	Ccc/Tcc	2/14	0.59161759618259	3	FACETS	0.976	0.891	1	0.488	0.445	0.532	CLONAL	1	TRUE	1	0.60696277253767	3		512	612	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187449654	187449654	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	174	581	2	ENST00000232014.4:c.226C>T	p.Pro76Ser	p.P76S	ENST00000232014	NM_001130845.1	76	Cct/Tct	4/10	0.59161759618259	3	FACETS	1	0.943	1	0.513	0.474	0.554	CLONAL	1	TRUE	1	0.60696277253767	3		583	728	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586442	189586442	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	227	538	1	ENST00000264731.3:c.1066G>A	p.Glu356Lys	p.E356K	ENST00000264731	NM_003722.4	356	Gaa/Aaa	8/14	0.59161759618259	3	FACETS	0.987	0.93	1	0.987	0.93	1	CLONAL	2	TRUE	1	0.60696277253767	3		539	494	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1795723	1795723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	99	308	0	ENST00000260795.2:c.62C>T	p.Ser21Phe	p.S21F	ENST00000260795		21	tCc/tTc	1/17	0.589901388437336	4	FACETS	1	0.961	1	0.575	0.516	0.637	CLONAL	1	TRUE	2	0.60696277253767	4		308	456	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151558	55151558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	275	540	1	ENST00000257290.5:c.2344C>T	p.Leu782Phe	p.L782F	ENST00000257290	NM_006206.4	782	Ctt/Ttt	17/23	0.589901388437336	4	FACETS	1	0.947	1	1	0.947	1	CLONAL	2	TRUE	2	0.60696277253767	4		541	726	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152108	55152108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377487797	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	313	588	0	ENST00000257290.5:c.2540C>T	p.Ser847Leu	p.S847L	ENST00000257290	NM_006206.4	847	tCg/tTg	18/23	0.589901388437336	4	FACETS	0.998	0.946	1	0.998	0.946	1	CLONAL	2	TRUE	2	0.60696277253767	4		588	830	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976861	55976861	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	300	547	0	ENST00000263923.4:c.1051C>T	p.Pro351Ser	p.P351S	ENST00000263923	NM_002253.2	351	Cct/Tct	8/30	0.589901388437336	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	2	0.60696277253767	4		547	776	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332853	153332853	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751626529	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	228	457	0	ENST00000281708.4:c.103C>T	p.Arg35Cys	p.R35C	ENST00000281708	NM_033632.3	35	Cgt/Tgt	2/12	0.589901388437336	4	FACETS	0.943	0.884	1	0.943	0.884	1	CLONAL	2	TRUE	2	0.60696277253767	4		457	640	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542804	187542804	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	298	609	1	ENST00000441802.2:c.4936C>T	p.Pro1646Ser	p.P1646S	ENST00000441802	NM_005245.3	1646	Cca/Tca	10/27	0.589901388437336	4	FACETS	0.986	0.933	1	0.986	0.933	1	CLONAL	2	TRUE	2	0.60696277253767	4		610	800	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628110	187628110	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	306	629	3	ENST00000441802.2:c.2872C>T	p.Gln958Ter	p.Q958*	ENST00000441802	NM_005245.3	958	Cag/Tag	2/27	0.589901388437336	4	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	2	0.60696277253767	4		632	782	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35861023	35861023	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138482569	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	318	546	0	ENST00000303115.3:c.152C>T	p.Ser51Leu	p.S51L	ENST00000303115	NM_002185.3	51	tCg/tTg	2/8	0.544908716979505	3	FACETS	1	0.983	1			1	CLONAL	2	TRUE	NA	0.60696277253767	3		546	641	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945785	38945785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	187	443	0	ENST00000357387.3:c.4441C>T	p.His1481Tyr	p.H1481Y	ENST00000357387	NM_152756.3	1481	Cac/Tac	34/38	0.544908716979505	3	FACETS	0.851	0.794	0.909			1	CLONAL	2	TRUE	NA	0.60696277253767	3		443	472	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519328	176519328	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	148	299	0	ENST00000292408.4:c.734C>T	p.Ser245Phe	p.S245F	ENST00000292408	NM_213647.1	245	tCc/tTc	7/18	0.494085382708029	4	FACETS	1	0.924	1	1	0.924	1	CLONAL	2	TRUE	2	0.60696277253767	4		299	392	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056287	180056287	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	324	627	0	ENST00000261937.6:c.957T>G	p.Phe319Leu	p.F319L	ENST00000261937	NM_182925.4	319	ttT/ttG	7/30	0.297138401720585	4	FACETS	1	0.972	1			1	INDETERMINATE	2	TRUE	NA	0.60696277253767	4		627	828	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401508	401508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	127	490	0	ENST00000380956.4:c.830C>T	p.Ser277Phe	p.S277F	ENST00000380956	NM_001195286.1	277	tCc/tTc	7/9	0.60696277253767	6	FACETS	0.968	0.876	1	0.194	0.175	0.213	CLONAL	1	TRUE	1	0.60696277253767	6		490	957	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20480133	20480133	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	169	653	0	ENST00000346618.3:c.450A>T	p.Leu150Phe	p.L150F	ENST00000346618	NM_001949.4	150	ttA/ttT	2/7	0.60696277253767	6	FACETS	1	0.937	1	0.205	0.188	0.223	CLONAL	1	TRUE	1	0.60696277253767	6		653	1202	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673130	30673130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	190	332	0	ENST00000376406.3:c.3830C>T	p.Ser1277Phe	p.S1277F	ENST00000376406	NM_014641.2	1277	tCt/tTt	10/15	0.60696277253767	6	FACETS	1	0.981	1	0.461	0.429	0.495	CLONAL	2	TRUE	1	0.60696277253767	6		332	601	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163318	32163318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs969543760	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	235	718	0	ENST00000375023.3:c.5908C>T	p.Pro1970Ser	p.P1970S	ENST00000375023	NM_004557.3	1970	Cct/Tct	30/30	0.60696277253767	6	FACETS	1	0.987	1	0.249	0.231	0.267	CLONAL	1	TRUE	1	0.60696277253767	6		718	1378	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955086	93955086	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	181	773	1	ENST00000369303.4:c.2812G>A	p.Glu938Lys	p.E938K	ENST00000369303	NM_004440.3	938	Gaa/Aaa	16/17	0.510762889333622	3	FACETS	0.965	0.891	1	0.482	0.445	0.521	CLONAL	1	TRUE	1	0.60696277253767	3		774	806	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066501	94066501	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	202	890	2	ENST00000369303.4:c.1258G>A	p.Gly420Arg	p.G420R	ENST00000369303	NM_004440.3	420	Gga/Aga	5/17	0.510762889333622	3	FACETS	0.957	0.887	1	0.478	0.443	0.514	CLONAL	1	TRUE	1	0.60696277253767	3		892	907	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120326	94120326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370195460	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	176	690	4	ENST00000369303.4:c.725C>T	p.Ala242Val	p.A242V	ENST00000369303	NM_004440.3	242	gCg/gTg	3/17	0.510762889333622	3	FACETS	1	0.953	1	0.521	0.481	0.563	CLONAL	1	TRUE	1	0.60696277253767	3		694	725	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120845	94120845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465346253	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	412	1499	1	ENST00000369303.4:c.206G>A	p.Arg69Gln	p.R69Q	ENST00000369303	NM_004440.3	69	cGa/cAa	3/17	0.510762889333622	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	1	0.60696277253767	3		1500	832	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662342	117662342	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764212412	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	266	488	0	ENST00000368508.3:c.5035C>T	p.Pro1679Ser	p.P1679S	ENST00000368508	NM_002944.2	1679	Cca/Tca	30/43	0.589718066014586	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.60696277253767	2		488	412	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468168	50468168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	227	486	0	ENST00000331340.3:c.1403G>A	p.Arg468Gln	p.R468Q	ENST00000331340	NM_006060.4	468	cGg/cAg	8/8	0.586964253614487	5	FACETS	1	0.955	1	0.683	0.64	0.728	CLONAL	2	TRUE	2	0.60696277253767	5		486	697	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494214	140494214	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	344	709	0	ENST00000288602.6:c.1034C>T	p.Pro345Leu	p.P345L	ENST00000288602	NM_004333.4	345	cCc/cTc	8/18	0.586964253614487	5	FACETS	0.937	0.887	0.987	0.624	0.591	0.658	CLONAL	2	TRUE	2	0.60696277253767	5		709	1156	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878271	151878271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778818239	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	429	569	0	ENST00000262189.6:c.6674C>T	p.Pro2225Leu	p.P2225L	ENST00000262189	NM_170606.2	2225	cCa/cTa	36/59	0.586964253614487	5	FACETS	1	0.964	1	1	0.964	1	CLONAL	3	TRUE	2	0.60696277253767	5		569	895	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372497	55372497	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	286	518	0	ENST00000297316.4:c.1187C>T	p.Ser396Phe	p.S396F	ENST00000297316	NM_022454.3	396	tCc/tTc	2/2	0.60696277253767	4	FACETS	0.973	0.919	1	0.973	0.919	1	CLONAL	2	TRUE	2	0.60696277253767	4		518	778	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341914	8341914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	246	739	1	ENST00000356435.5:c.4726G>A	p.Glu1576Lys	p.E1576K	ENST00000356435		1576	Gaa/Aaa	29/35	0.60696277253767	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.60696277253767	2		740	395	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375935	8375935	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	211	470	1	ENST00000356435.5:c.4661+1G>A		p.X1554_splice	ENST00000356435		1554			0.60696277253767	2	FACETS	0.901	0.851	0.95	0.901	0.851	0.95	CLONAL	2	TRUE	0	0.60696277253767	2		471	386	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375967	8375967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	269	587	1	ENST00000356435.5:c.4630C>T	p.Pro1544Ser	p.P1544S	ENST00000356435		1544	Ccc/Tcc	28/35	0.60696277253767	2	FACETS	0.895	0.851	0.939	0.895	0.851	0.939	CLONAL	2	TRUE	0	0.60696277253767	2		588	495	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518034	8518034	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	255	636	1	ENST00000356435.5:c.1357G>A	p.Val453Ile	p.V453I	ENST00000356435		453	Gtt/Att	10/35	0.60696277253767	2	FACETS	0.982	0.935	1	0.982	0.935	1	CLONAL	2	TRUE	0	0.60696277253767	2		637	428	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8527351	8527351	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	240	427	0	ENST00000356435.5:c.544T>G	p.Ser182Ala	p.S182A	ENST00000356435		182	Tct/Gct	5/35	0.60696277253767	2	FACETS	0.967	0.919	1	0.967	0.919	1	CLONAL	2	TRUE	0	0.60696277253767	2		427	409	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971018	21971018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104894104	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	282	389	1	ENST00000304494.5:c.340C>T	p.Pro114Ser	p.P114S	ENST00000304494	NM_000077.4	114	Ccc/Tcc	2/3	0.60696277253767	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.60696277253767	2		390	406	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231296	98231296	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	116	412	0	ENST00000331920.6:c.1987C>T	p.Gln663Ter	p.Q663*	ENST00000331920	NM_000264.3	663	Cag/Tag	14/24	0.60696277253767	2	FACETS	1	0.961	1	0.549	0.5	0.599	CLONAL	1	TRUE	0	0.60696277253767	2		412	348	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100426	8100426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	310	573	0	ENST00000346208.3:c.400C>T	p.Pro134Ser	p.P134S	ENST00000346208		134	Ccc/Tcc	3/6	0.532515005101736	4	FACETS	1	0.955	1			1	CLONAL	2	TRUE	NA	0.60696277253767	4		573	813	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63816982	63816982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	207	490	0	ENST00000279873.7:c.953G>A	p.Arg318Lys	p.R318K	ENST00000279873	NM_032199.2	318	aGg/aAg	6/10	0.589901388437336	4	FACETS	0.842	0.785	0.9	0.842	0.785	0.9	CLONAL	2	TRUE	2	0.60696277253767	4		490	651	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852319	63852319	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1340574832	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	275	480	0	ENST00000279873.7:c.3097C>T	p.Pro1033Ser	p.P1033S	ENST00000279873	NM_032199.2	1033	Ccc/Tcc	10/10	0.589901388437336	4	FACETS	0.948	0.894	1	0.948	0.894	1	CLONAL	2	TRUE	2	0.60696277253767	4		480	768	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711993	89711993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	159	217	0	ENST00000371953.3:c.611C>T	p.Pro204Leu	p.P204L	ENST00000371953	NM_000314.4	204	cCa/cTa	6/9	0.589901388437336	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.60696277253767	4		217	355	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256067	123256067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	321	709	0	ENST00000358487.5:c.1842G>A	p.Met614Ile	p.M614I	ENST00000358487	NM_000141.4	614	atG/atA	13/18	0.589901388437336	4	FACETS	0.922	0.873	0.972	0.922	0.873	0.972	CLONAL	2	TRUE	2	0.60696277253767	4		709	922	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276902	123276902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	304	758	0	ENST00000358487.5:c.1015G>A	p.Glu339Lys	p.E339K	ENST00000358487	NM_000141.4	339	Gaa/Aaa	8/18	0.589901388437336	4	FACETS	0.962	0.91	1	0.962	0.91	1	CLONAL	2	TRUE	2	0.60696277253767	4		758	837	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909854	100909854	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	169	382	0	ENST00000325455.5:c.2795A>G	p.Lys932Arg	p.K932R	ENST00000325455	NM_001202474.3	932	aAa/aGa	8/8	0.60696277253767	2	FACETS	0.96	0.903	1	0.96	0.903	1	CLONAL	2	TRUE	0	0.60696277253767	2		382	290	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100920685	100920685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	377	706	0	ENST00000325455.5:c.2463G>A	p.Met821Ile	p.M821I	ENST00000325455	NM_001202474.3	821	atG/atA	6/8	0.60696277253767	2	FACETS	0.994	0.955	1	0.994	0.955	1	CLONAL	2	TRUE	0	0.60696277253767	2		706	625	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922293	100922293	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149186732	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	336	601	0	ENST00000325455.5:c.2219G>A	p.Arg740Gln	p.R740Q	ENST00000325455	NM_001202474.3	740	cGa/cAa	5/8	0.60696277253767	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.60696277253767	2		601	529	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170460	119170460	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	181	383	2	ENST00000264033.4:c.2690C>T	p.Ser897Phe	p.S897F	ENST00000264033	NM_005188.3	897	tCc/tTc	16/16	0.60696277253767	2	FACETS	0.997	0.942	1	0.997	0.942	1	CLONAL	2	TRUE	0	0.60696277253767	2		385	299	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992110	11992110	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	215	435	1	ENST00000396373.4:c.200C>T	p.Ala67Val	p.A67V	ENST00000396373	NM_001987.4	67	gCc/gTc	3/8	0.589901388437336	4	FACETS	0.953	0.892	1	0.953	0.892	1	CLONAL	2	TRUE	2	0.60696277253767	4		436	597	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435469	18435469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	190	454	0	ENST00000266497.5:c.454G>A	p.Asp152Asn	p.D152N	ENST00000266497		152	Gat/Aat	1/31	0.589901388437336	4	FACETS	0.863	0.803	0.925	0.863	0.803	0.925	CLONAL	2	TRUE	2	0.60696277253767	4		454	583	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18473956	18473956	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	92	465	0	ENST00000266497.5:c.1198A>T	p.Lys400Ter	p.K400*	ENST00000266497		400	Aaa/Taa	6/31	0.589901388437336	4	FACETS	0.728	0.647	0.814	0.364	0.323	0.407	SUBCLONAL	1	TRUE	2	0.60696277253767	4		465	669	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691178	18691178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	208	536	0	ENST00000266497.5:c.3289G>A	p.Glu1097Lys	p.E1097K	ENST00000266497		1097	Gaa/Aaa	23/31	0.589901388437336	4	FACETS	0.938	0.877	1	0.938	0.877	1	CLONAL	2	TRUE	2	0.60696277253767	4		536	587	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800915	18800915	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	251	596	0	ENST00000266497.5:c.4291C>T	p.Pro1431Ser	p.P1431S	ENST00000266497		1431	Cca/Tca	31/31	0.589901388437336	4	FACETS	0.888	0.835	0.943	0.888	0.835	0.943	CLONAL	2	TRUE	2	0.60696277253767	4		596	748	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945093	31945093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	218	503	0	ENST00000340398.3:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000340398	NM_001013699.2	3	cGa/cAa	1/1	0.589901388437336	4	FACETS	0.946	0.886	1	0.946	0.886	1	CLONAL	2	TRUE	2	0.60696277253767	4		503	610	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46254648	46254648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	376	679	0	ENST00000334344.6:c.4838C>T	p.Ser1613Phe	p.S1613F	ENST00000334344	NM_152641.2	1613	tCt/tTt	16/21	0.589901388437336	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.60696277253767	4		679	938	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857533	57857533	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199861974	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	468	624	1	ENST00000228682.2:c.59G>A	p.Arg20Gln	p.R20Q	ENST00000228682	NM_005269.2	20	cGg/cAg	2/12	0.60696277253767	4	FACETS	0.836	0.803	0.87	1	0.995	1	CLONAL	3	TRUE	2	0.60696277253767	4		625	988	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57857808	57857808	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	503	730	0	ENST00000228682.2:c.127C>T	p.Gln43Ter	p.Q43*	ENST00000228682	NM_005269.2	43	Caa/Taa	3/12	0.60696277253767	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	2	0.60696277253767	4		730	1123	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864555	57864555	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	537	804	0	ENST00000228682.2:c.2032C>T	p.Pro678Ser	p.P678S	ENST00000228682	NM_005269.2	678	Cct/Tct	12/12	0.60696277253767	4	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	2	0.60696277253767	4		804	1166	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115111971	115111971	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	76	275	0	ENST00000257566.3:c.1769A>C	p.Gln590Pro	p.Q590P	ENST00000257566	NM_016569.3	590	cAg/cCg	7/8	0.304132634232441	4	FACETS	1	0.935	1	0.545	0.481	0.613	INDETERMINATE	1	TRUE	2	0.60696277253767	4		275	369	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434154	121434154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1378349542	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	225	568	0	ENST00000257555.6:c.1045C>T	p.His349Tyr	p.H349Y	ENST00000257555		349	Cac/Tac	5/10	0.304132634232441	4	FACETS	0.867	0.811	0.924	0.867	0.811	0.924	INDETERMINATE	2	TRUE	2	0.60696277253767	4		568	687	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434164	121434164	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	199	553	0	ENST00000257555.6:c.1055C>T	p.Ser352Phe	p.S352F	ENST00000257555		352	tCc/tTc	5/10	0.304132634232441	4	FACETS	0.843	0.785	0.902	0.843	0.785	0.902	INDETERMINATE	2	TRUE	2	0.60696277253767	4		553	625	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209315	133209315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	229	593	0	ENST00000320574.5:c.6071C>T	p.Pro2024Leu	p.P2024L	ENST00000320574	NM_006231.2	2024	cCc/cTc	44/49	0.304132634232441	4	FACETS	0.854	0.799	0.91	0.854	0.799	0.91	INDETERMINATE	2	TRUE	2	0.60696277253767	4		593	710	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240618	133240618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555226423	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	296	623	1	ENST00000320574.5:c.2678C>T	p.Pro893Leu	p.P893L	ENST00000320574	NM_006231.2	893	cCa/cTa	23/49	0.304132634232441	4	FACETS	0.998	0.944	1	0.998	0.944	1	INDETERMINATE	2	TRUE	2	0.60696277253767	4		624	785	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245062	133245062	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs116326665	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	169	356	0	ENST00000320574.5:c.2053C>T	p.Arg685Trp	p.R685W	ENST00000320574	NM_006231.2	685	Cgg/Tgg	19/49	0.304132634232441	4	FACETS	1	0.98	1	1	0.98	1	INDETERMINATE	2	TRUE	2	0.60696277253767	4		356	394	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28963953	28963953	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	120	626	1	ENST00000282397.4:c.1949A>T	p.Lys650Met	p.K650M	ENST00000282397	NM_002019.4	650	aAg/aTg	13/30	1	2	FACETS	0.824	0.748	0.902	0.824	0.748	0.902	CLONAL	1	TRUE	1	0.60696277253767	2		627	480	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914949	32914949	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	230	892	0	ENST00000380152.3:c.6457C>T	p.Pro2153Ser	p.P2153S	ENST00000380152		2153	Cca/Tca	11/27	1	2	FACETS	0.926	0.866	0.989	0.926	0.866	0.989	CLONAL	1	TRUE	1	0.60696277253767	2		892	818	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73351584	73351584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	139	571	0	ENST00000377767.4:c.628C>T	p.Arg210Cys	p.R210C	ENST00000377767	NM_014953.3	210	Cgt/Tgt	4/21	1	2	FACETS	0.946	0.867	1	0.946	0.867	1	CLONAL	1	TRUE	1	0.60696277253767	2		571	484	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554350	81554350	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	460	613	0	ENST00000298171.2:c.370G>A	p.Glu124Lys	p.E124K	ENST00000298171	NM_000369.2	124	Gag/Aag	4/10	0.577698637884601	4	FACETS	0.955	0.919	0.991	0.955	0.919	0.991	CLONAL	3	TRUE	1	0.60696277253767	4		613	850	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574813	95574813	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	120	479	1	ENST00000393063.1:c.2284C>T	p.Pro762Ser	p.P762S	ENST00000393063	NM_030621.3	762	Ccc/Tcc	16/28	0.577698637884601	4	FACETS	0.943	0.853	1	0.314	0.284	0.346	CLONAL	1	TRUE	1	0.60696277253767	4		480	674	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988752	41988752	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	484	892	0	ENST00000219905.7:c.1544C>T	p.Ser515Phe	p.S515F	ENST00000219905	NM_001164273.1	515	tCc/tTc	3/24	0.545162051540017	4	FACETS	0.975	0.933	1	0.975	0.933	1	CLONAL	2	TRUE	2	0.60696277253767	4		892	1314	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41991076	41991076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	322	608	0	ENST00000219905.7:c.2029C>T	p.His677Tyr	p.H677Y	ENST00000219905	NM_001164273.1	677	Cat/Tat	4/24	0.545162051540017	4	FACETS	0.963	0.913	1	0.963	0.913	1	CLONAL	2	TRUE	2	0.60696277253767	4		608	885	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028529	42028529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	502	909	3	ENST00000219905.7:c.4067C>T	p.Ser1356Phe	p.S1356F	ENST00000219905	NM_001164273.1	1356	tCc/tTc	13/24	0.545162051540017	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.60696277253767	4		912	1227	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88428945	88428945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	256	481	0	ENST00000360948.2:c.2155G>A	p.Asp719Asn	p.D719N	ENST00000360948	NM_001012338.2	719	Gat/Aat	17/19	0.545162051540017	4	FACETS	0.935	0.88	0.991	0.935	0.88	0.991	CLONAL	2	TRUE	2	0.60696277253767	4		481	725	SUCCESS
BLM	641	MSKCC	GRCh37	15	91337538	91337538	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	148	458	0	ENST00000355112.3:c.3161T>A	p.Phe1054Tyr	p.F1054Y	ENST00000355112	NM_000057.2	1054	tTt/tAt	16/22	0.545162051540017	4	FACETS	1	0.961	1	0.543	0.497	0.592	CLONAL	1	TRUE	2	0.60696277253767	4		458	721	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779191	3779191	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	113	239	0	ENST00000262367.5:c.5857C>T	p.Pro1953Ser	p.P1953S	ENST00000262367	NM_004380.2	1953	Cct/Tct	31/31	0.57884627984158	3	FACETS	0.967	0.887	1	0.967	0.887	1	CLONAL	2	TRUE	1	0.60696277253767	3		239	251	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786758	3786758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	366	699	0	ENST00000262367.5:c.4453C>T	p.His1485Tyr	p.H1485Y	ENST00000262367	NM_004380.2	1485	Cat/Tat	27/31	0.57884627984158	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.60696277253767	3		699	765	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900356	3900356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	343	561	2	ENST00000262367.5:c.740C>T	p.Ser247Phe	p.S247F	ENST00000262367	NM_004380.2	247	tCc/tTc	2/31	0.57884627984158	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.60696277253767	3		563	695	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7978979	7978979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	291	623	0	ENST00000319144.4:c.1588G>A	p.Asp530Asn	p.D530N	ENST00000319144	NM_001139.2	530	Gat/Aat	12/15	0.589718066014586	2	FACETS	0.984	0.941	1	0.984	0.941	1	CLONAL	2	TRUE	0	0.60696277253767	2		623	487	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687306	37687306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1172789499	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	149	558	0	ENST00000447079.4:c.4210C>T	p.Arg1404Cys	p.R1404C	ENST00000447079	NM_015083.1	1404	Cgt/Tgt	14/14	0.60696277253767	4	FACETS	0.969	0.886	1	0.323	0.295	0.352	CLONAL	1	TRUE	1	0.60696277253767	4		558	814	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881024	37881024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	517	569	0	ENST00000269571.5:c.2353C>T	p.Leu785Phe	p.L785F	ENST00000269571		785	Ctt/Ttt	20/27	0.60696277253767	4	FACETS	0.978	0.944	1	0.978	0.944	1	CLONAL	3	TRUE	1	0.60696277253767	4		569	933	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369273	40369273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	216	848	3	ENST00000293328.3:c.1285C>T	p.Arg429Cys	p.R429C	ENST00000293328	NM_012448.3	429	Cgt/Tgt	11/19	0.60696277253767	4	FACETS	1	0.954	1	0.345	0.32	0.371	CLONAL	1	TRUE	1	0.60696277253767	4		851	1105	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40376844	40376844	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775502922	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1214	295	1122	1	ENST00000293328.3:c.328C>T	p.Arg110Cys	p.R110C	ENST00000293328	NM_012448.3	110	Cgc/Tgc	4/19	0.60696277253767	4	FACETS	1	0.963	1	0.345	0.324	0.367	CLONAL	1	TRUE	1	0.60696277253767	4		1123	1509	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58701074	58701074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	824	1079	1	ENST00000305921.3:c.665C>T	p.Pro222Leu	p.P222L	ENST00000305921	NM_003620.3	222	cCc/cTc	2/6	0.595653011956005	4	FACETS	1	0.993	1			1	CLONAL	3	TRUE	NA	0.60696277253767	4		1080	1383	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70120026	70120026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1258787580	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	13	46	0	ENST00000245479.2:c.1028C>T	p.Pro343Leu	p.P343L	ENST00000245479	NM_000346.3	343	cCg/cTg	3/3	0.60696277253767	6	FACETS	1	0.829	1	0.243	0.176	0.322	CLONAL	1	TRUE	1	0.60696277253767	6		46	78	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936290	78936290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	171	674	1	ENST00000306801.3:c.3722C>T	p.Pro1241Leu	p.P1241L	ENST00000306801	NM_020761.2	1241	cCc/cTc	32/34	0.60696277253767	6	FACETS	0.987	0.906	1	0.197	0.181	0.215	CLONAL	1	TRUE	1	0.60696277253767	6		675	1264	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098480	11098480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	153	277	1	ENST00000358026.2:c.998C>T	p.Pro333Leu	p.P333L	ENST00000358026	NM_001128849.1	333	cCc/cTc	6/36	0.57884627984158	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	1	0.60696277253767	3		278	307	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296353	15296353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	234	539	0	ENST00000263388.2:c.2089C>T	p.His697Tyr	p.H697Y	ENST00000263388	NM_000435.2	697	Cat/Tat	13/33	0.57884627984158	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.60696277253767	3		539	494	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273857	18273857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	335	693	0	ENST00000222254.8:c.1190C>T	p.Ser397Phe	p.S397F	ENST00000222254	NM_005027.3	397	tCc/tTc	10/16	0.57884627984158	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.60696277253767	3		693	699	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765783	41765783	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	123	242	0	ENST00000301178.4:c.2659G>A	p.Ala887Thr	p.A887T	ENST00000301178	NM_021913.4	887	Gcc/Acc	20/20	0.57884627984158	3	FACETS	0.961	0.885	1	0.961	0.885	1	CLONAL	2	TRUE	1	0.60696277253767	3		242	275	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799020	42799020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1025458986	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	285	484	0	ENST00000575354.2:c.4504C>T	p.Pro1502Ser	p.P1502S	ENST00000575354	NM_015125.3	1502	Ccc/Tcc	20/20	0.57884627984158	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.60696277253767	3		484	587	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45873796	45873796	+	start_lost,splice_region_variant	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	94	362	0	ENST00000391945.4:c.3G>A	p.Met1?	p.M1?	ENST00000391945	NM_000400.3	1	atG/atA	1/23	0.57884627984158	3	FACETS	0.973	0.871	1	0.486	0.435	0.54	CLONAL	1	TRUE	1	0.60696277253767	3		362	415	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560791	9560791	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	104	392	0	ENST00000353224.5:c.990+1G>A		p.X330_splice	ENST00000353224	NM_177990.2	330			0.57884627984158	3	FACETS	1	0.958	1	0.557	0.502	0.614	CLONAL	1	TRUE	1	0.60696277253767	3		392	401	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36028577	36028577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	343	653	0	ENST00000358208.4:c.919C>T	p.Pro307Ser	p.P307S	ENST00000358208		307	Cca/Tca	8/12	0.57884627984158	3	FACETS	0.972	0.926	1	0.972	0.926	1	CLONAL	2	TRUE	1	0.60696277253767	3		653	758	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39725977	39725977	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	157	314	0	ENST00000361337.2:c.848G>A	p.Arg283Lys	p.R283K	ENST00000361337	NM_003286.2	283	aGa/aAa	10/21	0.57884627984158	3	FACETS	0.906	0.842	0.972	0.906	0.842	0.972	CLONAL	2	TRUE	1	0.60696277253767	3		314	372	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728792	39728792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	105	480	0	ENST00000361337.2:c.1072C>T	p.Pro358Ser	p.P358S	ENST00000361337	NM_003286.2	358	Cct/Tct	12/21	0.57884627984158	3	FACETS	0.968	0.872	1	0.484	0.436	0.534	CLONAL	1	TRUE	1	0.60696277253767	3		480	466	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713475	40713475	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	214	467	0	ENST00000373198.4:c.4040G>C	p.Gly1347Ala	p.G1347A	ENST00000373198	NM_133170.3	1347	gGt/gCt	30/32	0.57884627984158	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.60696277253767	3		467	450	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733359	40733359	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	87	305	0	ENST00000373198.4:c.3448-1G>A		p.X1150_splice	ENST00000373198	NM_133170.3	1150			0.57884627984158	3	FACETS	1	0.905	1	0.508	0.453	0.566	CLONAL	1	TRUE	1	0.60696277253767	3		305	368	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076954	41076954	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	222	585	0	ENST00000373198.4:c.1466C>T	p.Pro489Leu	p.P489L	ENST00000373198	NM_133170.3	489	cCt/cTt	9/32	0.57884627984158	3	FACETS	0.814	0.763	0.865	0.814	0.763	0.865	CLONAL	2	TRUE	1	0.60696277253767	3		585	586	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101134	41101134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	204	408	0	ENST00000373198.4:c.1222G>A	p.Glu408Lys	p.E408K	ENST00000373198	NM_133170.3	408	Gag/Aag	8/32	0.57884627984158	3	FACETS	0.996	0.935	1	0.996	0.935	1	CLONAL	2	TRUE	1	0.60696277253767	3		408	440	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408867	41408867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	176	677	0	ENST00000373198.4:c.559C>T	p.His187Tyr	p.H187Y	ENST00000373198	NM_133170.3	187	Cat/Tat	4/32	0.57884627984158	3	FACETS	1	0.942	1	0.512	0.473	0.553	CLONAL	1	TRUE	1	0.60696277253767	3		677	738	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171685	36171685	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	152	634	1	ENST00000300305.3:c.880C>T	p.Pro294Ser	p.P294S	ENST00000300305		294	Cct/Tct	7/8	0.57884627984158	3	FACETS	0.954	0.875	1	0.477	0.437	0.519	CLONAL	1	TRUE	1	0.60696277253767	3		635	684	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573257	41573257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	208	414	0	ENST00000263253.7:c.5542C>T	p.Pro1848Ser	p.P1848S	ENST00000263253	NM_001429.3	1848	Cct/Tct	31/31	0.545162051540017	4	FACETS	0.973	0.91	1	0.973	0.91	1	CLONAL	2	TRUE	2	0.60696277253767	4		414	566	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317548	1317548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	245	563	0	ENST00000400841.2:c.517G>A	p.Glu173Lys	p.E173K	ENST00000400841		173	Gaa/Aaa	5/6	0.532515005101736	2	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.60696277253767	2		563	707	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123040927	123040927	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	78	112	0	ENST00000355640.3:c.1390C>T	p.Pro464Ser	p.P464S	ENST00000355640		464	Cct/Tct	7/7	0.595653011956005	2	FACETS	1	0.981	1			1	CLONAL	1	TRUE	NA	0.60696277253767	2		112	174	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094261	193094262	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	115	539	0	ENST00000367435.3:c.151_152delinsTT	p.Pro51Phe	p.P51F	ENST00000367435	NM_024529.4	51	CCc/TTc	2/17	0.586964253614487	5	FACETS	0.761	0.685	0.842	0.254	0.228	0.281	SUBCLONAL	1	TRUE	2	0.60696277253767	5		539	951	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411630	116411631	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	263	590	0	ENST00000397752.3:c.2809_2810delinsAA	p.Gly937Asn	p.G937N	ENST00000397752	NM_000245.2	937	GGt/AAt	13/21	0.586964253614487	5	FACETS	0.932	0.876	0.99	0.621	0.584	0.66	CLONAL	2	TRUE	2	0.60696277253767	5		590	888	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30050704	30050706	+	missense_variant	Missense_Mutation	TNP	TTC	TTC	CTA	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	200	425	0	ENST00000338641.4:c.506_508delinsCTA	p.Leu169_Pro170delinsProThr	p.L169_P170delinsPT	ENST00000338641	NM_000268.3	169	cTTCca/cCTAca	5/16	0.545162051540017	4	FACETS	0.908	0.847	0.971	0.908	0.847	0.971	CLONAL	2	TRUE	2	0.60696277253767	4		425	583	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043899	180043900	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TA	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	243	660	1	ENST00000261937.6:c.3096_3096+1delinsTA		p.X1032_splice	ENST00000261937	NM_182925.4	1032		22/30	0.297138401720585	4	FACETS	0.906	0.851	0.963			1	INDETERMINATE	2	TRUE	NA	0.60696277253767	4		661	710	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420909	49420910	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	209	254	0	ENST00000301067.7:c.14839_14840delinsTT	p.Pro4947Phe	p.P4947F	ENST00000301067	NM_003482.3	4947	CCc/TTc	48/54	0.589901388437336	4	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	2	0.60696277253767	4		254	464	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652837	29652838	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0005366-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	283	395	0	ENST00000356175.3:c.4773-1_4773delinsAA		p.X1591_splice	ENST00000356175	NM_000267.3	1591		36/57	0.60696277253767	4	FACETS	0.873	0.829	0.917	0.873	0.829	0.917	CLONAL	3	TRUE	1	0.60696277253767	4		395	572	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0005370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	369	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.517864165772593	3	FACETS	0.97	0.923	1	0.97	0.923	1	CLONAL	2	TRUE	1	0.517864165772593	3		490	925	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0005370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	58	229	0				ENST00000310581	NM_198253.2	-/1132			0.280345248713655	1	FACETS	0.641	0.556	0.731	0.641	0.556	0.731	INDETERMINATE	1	TRUE	0	0.517864165772593	1		229	259	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430402	78430402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372081866	NA	P-0005370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	243	442	1	ENST00000370768.2:c.766C>T	p.Arg256Cys	p.R256C	ENST00000370768	NM_003902.3	256	Cgt/Tgt	10/20	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.517864165772593	2		443	900	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251821	212251821	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	148	398	1	ENST00000342788.4:c.3238C>T	p.Pro1080Ser	p.P1080S	ENST00000342788	NM_005235.2	1080	Ccc/Tcc	27/28	1	2	FACETS	0.853	0.781	0.928	0.853	0.781	0.928	CLONAL	1	TRUE	1	0.517864165772593	2		399	670	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72891539	72891539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755870786	NA	P-0005370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	190	348	1	ENST00000325599.8:c.223C>T	p.Arg75Cys	p.R75C	ENST00000325599	NM_018130.2	75	Cgc/Tgc	3/11	1	2	FACETS	0.937	0.868	1	0.937	0.868	1	CLONAL	1	TRUE	1	0.517864165772593	2		349	783	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259301	89259301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	228	491	0	ENST00000336596.2:c.445G>A	p.Asp149Asn	p.D149N	ENST00000336596	NM_005233.5	149	Gat/Aat	3/17	1	2	FACETS	0.929	0.866	0.993	0.929	0.866	0.993	CLONAL	1	TRUE	1	0.517864165772593	2		491	948	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55219001	55219001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	258	507	0	ENST00000275493.2:c.574C>T	p.Pro192Ser	p.P192S	ENST00000275493	NM_005228.3	192	Cca/Tca	5/28	0.517864165772593	3	FACETS	1	0.964	1	0.522	0.488	0.557	CLONAL	1	TRUE	1	0.517864165772593	3		507	1201	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499793	8499793	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	249	449	0	ENST00000356435.5:c.2176A>T	p.Thr726Ser	p.T726S	ENST00000356435		726	Aca/Tca	14/35	0.517864165772593	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.517864165772593	1		449	658	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850622	63850622	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	193	310	0	ENST00000279873.7:c.1400T>A	p.Val467Asp	p.V467D	ENST00000279873	NM_032199.2	467	gTt/gAt	10/10	0.517864165772593	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.517864165772593	1		310	513	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410723	32410723	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	200	362	0	ENST00000332351.3:c.1435G>A	p.Glu479Lys	p.E479K	ENST00000332351	NM_024426.4	479	Gaa/Aaa	10/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.517864165772593	2		362	721	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216484	108216484	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	226	435	0	ENST00000278616.4:c.8433G>T	p.Lys2811Asn	p.K2811N	ENST00000278616	NM_000051.3	2811	aaG/aaT	58/63	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.517864165772593	2		435	815	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254658	10254658	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	125	272	0	ENST00000340748.4:c.2852A>G	p.Lys951Arg	p.K951R	ENST00000340748		951	aAg/aGg	28/40	1	2	FACETS	0.814	0.739	0.892	0.814	0.739	0.892	CLONAL	1	TRUE	1	0.517864165772593	2		272	593	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795751	42795751	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	209	375	0	ENST00000575354.2:c.2740T>G	p.Ser914Ala	p.S914A	ENST00000575354	NM_015125.3	914	Tca/Gca	11/20	1	2	FACETS	0.933	0.868	1	0.933	0.868	1	CLONAL	1	TRUE	1	0.517864165772593	2		375	865	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755678	39755678	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005370-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	220	456	0	ENST00000288319.7:c.1087G>A	p.Asp363Asn	p.D363N	ENST00000288319	NM_182918.3	363	Gat/Aat	10/10	1	2	FACETS	0.932	0.868	0.998	0.932	0.868	0.998	CLONAL	1	TRUE	1	0.517864165772593	2		456	912	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	39	280	0				ENST00000310581	NM_198253.2	-/1132			0.193456409757398	1	FACETS	1	0.834	1	1	0.834	1	CLONAL	1	TRUE	0	0.247517484475171	1		280	276	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0005373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	251	538	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	0.240681971339405	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.247517484475171	2		538	868	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0005373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	123	463	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.169898832985868	2	FACETS	0.875	0.794	0.959	0.875	0.794	0.959	CLONAL	2	TRUE	0	0.247517484475171	2		463	568	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578235	7578235	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057520007	NA	P-0005373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	126	1461	0	ENST00000269305.4:c.614A>G	p.Tyr205Cys	p.Y205C	ENST00000269305	NM_001126112.2	205	tAt/tGt	6/11	0.247517484475171	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.247517484475171	1		1461	633	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447088	187447088	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	170	787	1	ENST00000232014.4:c.1105G>T	p.Asp369Tyr	p.D369Y	ENST00000232014	NM_001130845.1	369	Gac/Tac	5/10	0.169898832985868	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.247517484475171	2		788	591	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372343	55372343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	145	775	2	ENST00000297316.4:c.1033G>A	p.Gly345Ser	p.G345S	ENST00000297316	NM_022454.3	345	Ggc/Agc	2/2	0.145210514200564	3	FACETS	0.978	0.895	1	0.978	0.895	1	INDETERMINATE	2	TRUE	1	0.247517484475171	3		777	673	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427012	49427012	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	43	870	1	ENST00000301067.7:c.11476C>T	p.Gln3826Ter	p.Q3826*	ENST00000301067	NM_003482.3	3826	Cag/Tag	39/54	1	2	FACETS	0.664	0.556	0.785	0.664	0.556	0.785	SUBCLONAL	1	TRUE	1	0.247517484475171	2		871	523	SUCCESS
AR	367	MSKCC	GRCh37	X	66765496	66765496	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	166	613	2	ENST00000374690.3:c.508A>G	p.Thr170Ala	p.T170A	ENST00000374690	NM_000044.3	170	Act/Gct	1/8	1	1	FACETS	1	0.984	1	1	0.993	1	CLONAL	2	TRUE	0	0.247517484475171	1		615	477	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942739	44942739	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005373-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	143	782	2	ENST00000377967.4:c.3320del	p.Pro1107LeufsTer13	p.P1107Lfs*13	ENST00000377967	NM_021140.2	1107	Cct/ct	23/29	0.193995164961906	2	FACETS	0.978	0.901	1			1	CLONAL	3	TRUE	NA	0.247517484475171	2		784	394	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0005383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	86	464	0				ENST00000310581	NM_198253.2	-/1132			0.271720565160464	4	FACETS	0.794	0.709	0.883			1	INDETERMINATE	2	FALSE	NA	0.484340529375067	4		464	332	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	221	170	0	ENST00000304494.5:c.262G>A	p.Glu88Lys	p.E88K	ENST00000304494	NM_000077.4	88	Gag/Aag	2/3	0.464865595703294	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	FALSE	0	0.484340529375067	2		170	444	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894230	NA	P-0005383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	4441	218	0	ENST00000451590.1:c.35G>A	p.Gly12Asp	p.G12D	ENST00000451590	NM_001130442.1	12	gGc/gAc	2/5	NA	2	FACETS	0.935	0.93	0.941			1	INDETERMINATE	4	FALSE	NA	0.484340529375067	2		218	4902	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984762	72984762	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1224592041	NA	P-0005383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	197	387	0	ENST00000268489.5:c.2822C>T	p.Ser941Leu	p.S941L	ENST00000268489	NM_006885.3	941	tCg/tTg	3/10	0.149045424704509	2	FACETS	0.829	0.768	0.893	0.415	0.384	0.447	INDETERMINATE	1	FALSE	0	0.484340529375067	2		387	981	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074066	8074066	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1437	238	448	0	ENST00000377482.5:c.593G>A	p.Arg198Lys	p.R198K	ENST00000377482	NM_018948.3	198	aGg/aAg	4/4	0.400163694282027	4	FACETS	0.871	0.81	0.934	0.435	0.405	0.467	CLONAL	1	FALSE	2	0.484340529375067	4		448	1675	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267360	198267360	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs374250186	NA	P-0005383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	192	283	1	ENST00000335508.6:c.1997A>T	p.Lys666Met	p.K666M	ENST00000335508	NM_012433.2	666	aAg/aTg	14/25	0.485141318545307	3	FACETS	0.954	0.882	1	0.477	0.441	0.515	CLONAL	1	FALSE	1	0.484340529375067	3		284	1032	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643951	52643951	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	151	151	0	ENST00000394830.3:c.1945C>T	p.Pro649Ser	p.P649S	ENST00000394830	NM_018313.4	649	Cct/Tct	17/30	0.397036823388222	3	FACETS	0.884	0.816	0.954			1	CLONAL	2	FALSE	NA	0.484340529375067	3		151	438	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235435	235435	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	182	224	0	ENST00000264932.6:c.1241C>T	p.Pro414Leu	p.P414L	ENST00000264932	NM_004168.2	414	cCc/cTc	9/15	0.271720565160464	4	FACETS	0.852	0.789	0.916			1	INDETERMINATE	2	FALSE	NA	0.484340529375067	4		224	655	SUCCESS
APC	324	MSKCC	GRCh37	5	112176515	112176515	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876658835	NA	P-0005383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	209	203	0	ENST00000257430.4:c.5224C>T	p.Arg1742Cys	p.R1742C	ENST00000257430	NM_000038.5	1742	Cgt/Tgt	16/16	0.27817559619499	4	FACETS	0.841	0.783	0.9	0.841	0.783	0.9	INDETERMINATE	2	FALSE	2	0.484340529375067	4		203	762	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778008	27778008	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1361	600	490	1	ENST00000369163.2:c.157C>T	p.Arg53Cys	p.R53C	ENST00000369163	NM_003536.2	53	Cgc/Tgc	1/1	0.485141318545307	4	FACETS	0.938	0.9	0.976	0.938	0.9	0.976	CLONAL	2	FALSE	2	0.484340529375067	4		491	1961	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729934	41729934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146325702	NA	P-0005383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	434	407	0	ENST00000242208.4:c.595G>A	p.Gly199Arg	p.G199R	ENST00000242208	NM_002192.2	199	Ggg/Agg	3/3	0.400163694282027	4	FACETS	0.846	0.805	0.888	0.846	0.805	0.888	CLONAL	2	FALSE	2	0.484340529375067	4		407	1572	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514334	69514334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765440889	NA	P-0005383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	225	212	1	ENST00000294312.3:c.347C>T	p.Ser116Leu	p.S116L	ENST00000294312	NM_005117.2	116	tCg/tTg	3/3	0.27817559619499	4	FACETS	0.851	0.8	0.903	1	0.99	1	INDETERMINATE	3	FALSE	2	0.484340529375067	4		213	540	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625194	69625194	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554980316	NA	P-0005383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	284	254	0	ENST00000334134.2:c.599G>A	p.Arg200Lys	p.R200K	ENST00000334134	NM_005247.2	200	aGa/aAa	3/3	0.27817559619499	4	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	2	FALSE	2	0.484340529375067	4		254	814	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047261	77047261	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	413	338	0	ENST00000356341.3:c.1283C>T	p.Pro428Leu	p.P428L	ENST00000356341	NM_002576.4	428	cCa/cTa	13/15	0.31431736213697	5	FACETS	1	0.993	1			1	CLONAL	2	FALSE	NA	0.484340529375067	5		338	1187	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245237	46245237	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1404927149	NA	P-0005383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	303	205	0	ENST00000334344.6:c.3331G>A	p.Val1111Met	p.V1111M	ENST00000334344	NM_152641.2	1111	Gtg/Atg	15/21	0.485141318545307	3	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	FALSE	1	0.484340529375067	3		205	748	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331727	68331727	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	206	147	0	ENST00000487270.1:c.323G>A	p.Gly108Asp	p.G108D	ENST00000487270	NM_133509.3	108	gGt/gAt	5/11	0.445158691953056	3	FACETS	0.957	0.904	1	0.957	0.904	1	CLONAL	3	FALSE	0	0.484340529375067	3		147	368	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777966	3777966	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	127	281	0	ENST00000262367.5:c.7082C>T	p.Ser2361Phe	p.S2361F	ENST00000262367	NM_004380.2	2361	tCc/tTc	31/31	1	2	FACETS	0.757	0.687	0.83	0.757	0.687	0.83	SUBCLONAL	1	FALSE	1	0.484340529375067	2		281	693	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532589	63532589	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	170	169	0	ENST00000307078.5:c.1990G>A	p.Gly664Arg	p.G664R	ENST00000307078	NM_004655.3	664	Ggg/Agg	8/11	0.38253272085209	5	FACETS	1	0.977	1	0.759	0.703	0.817	CLONAL	2	FALSE	2	0.484340529375067	5		169	532	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258397	16258406	+	frameshift_variant	Frame_Shift_Del	DEL	GAACATCCCG	GAACATCCCG	TACATCCCA	novel	NA	P-0005383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	328	283	0	ENST00000375759.3:c.5662_5671delinsTACATCCCA	p.Glu1888TyrfsTer17	p.E1888Yfs*17	ENST00000375759	NM_015001.2	1888	GAACATCCCGaa/TACATCCCAaa	11/15	0.400163694282027	4	FACETS	0.958	0.907	1	0.958	0.907	1	CLONAL	2	FALSE	2	0.484340529375067	4		283	1049	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629514	187629515	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0005383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	238	245	0	ENST00000441802.2:c.1467_1468delinsTT	p.Pro490Ser	p.P490S	ENST00000441802	NM_005245.3	489	gaCCct/gaTTct	2/27	0.271720565160464	4	FACETS	0.991	0.929	1			1	INDETERMINATE	2	FALSE	NA	0.484340529375067	4		245	736	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250857	10250858	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0005383-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	207	214	0	ENST00000340748.4:c.3622_3623delinsAA	p.Gly1208Asn	p.G1208N	ENST00000340748		1208	GGc/AAc	32/40	0.18500164063542	4	FACETS	0.882	0.822	0.945	0.882	0.822	0.945	INDETERMINATE	2	FALSE	2	0.484340529375067	4		214	719	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	84	280	0				ENST00000310581	NM_198253.2	-/1132			0.170635131408119	2	FACETS	0.779	0.697	0.863	0.779	0.697	0.863	INDETERMINATE	2	FALSE	0	0.407103218922581	2		280	265	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94194197	94194197	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	110	417	0	ENST00000323929.3:c.1231G>A	p.Glu411Lys	p.E411K	ENST00000323929	NM_005591.3	411	Gag/Aag	12/20	1	2	FACETS	0.847	0.762	0.936	0.847	0.762	0.936	CLONAL	1	FALSE	1	0.407103218922581	2		417	638	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0005385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	30	595	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.348	0.28	0.426	0.348	0.28	0.426	SUBCLONAL	1	FALSE	1	0.407103218922581	2		595	423	SUCCESS
ATM	472	MSKCC	GRCh37	11	108178641	108178641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775036118	NA	P-0005385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	99	255	0	ENST00000278616.4:c.5692C>T	p.Arg1898Ter	p.R1898*	ENST00000278616	NM_000051.3	1898	Cga/Tga	38/63	1	2	FACETS	0.948	0.85	1	0.948	0.85	1	CLONAL	1	FALSE	1	0.407103218922581	2		255	513	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367486	40367486	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	19	50	0	ENST00000397332.2:c.75G>A	p.Trp25Ter	p.W25*	ENST00000397332	NM_001033082.2	25	tgG/tgA	1/3	1	2	FACETS	0.972	0.751	1	0.972	0.751	1	CLONAL	1	FALSE	1	0.407103218922581	2		50	96	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140764	55140764	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	142	461	0	ENST00000257290.5:c.1625T>A	p.Leu542His	p.L542H	ENST00000257290	NM_006206.4	542	cTt/cAt	11/23	1	2	FACETS	0.791	0.721	0.865	0.791	0.721	0.865	SUBCLONAL	1	FALSE	1	0.407103218922581	2		461	882	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652015	36652015	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	299	406	0	ENST00000244741.5:c.137G>C	p.Arg46Pro	p.R46P	ENST00000244741	NM_000389.4	46	cGt/cCt	2/3	0.194056932644915	2	FACETS	0.986	0.934	1	0.986	0.934	1	INDETERMINATE	2	FALSE	0	0.407103218922581	2		406	745	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066519	94066519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	110	744	0	ENST00000369303.4:c.1240G>A	p.Glu414Lys	p.E414K	ENST00000369303	NM_004440.3	414	Gaa/Aaa	5/17	0.154996501351297	0	FACETS	0.306	0.274	0.34			1	INDETERMINATE	1	FALSE	0	0.407103218922581	0		744	1047	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787737	135787737	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0005385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	282	525	0	ENST00000298552.3:c.845C>G	p.Ser282Ter	p.S282*	ENST00000298552	NM_001162426.1	282	tCa/tGa	9/23	0.407103218922581	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	0	0.407103218922581	1		525	887	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851261	63851261	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	167	352	0	ENST00000279873.7:c.2039C>G	p.Ser680Cys	p.S680C	ENST00000279873	NM_032199.2	680	tCt/tGt	10/10	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	1	FALSE	NA	0.407103218922581	2		352	731	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544129	18544129	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	141	547	0	ENST00000266497.5:c.1946C>G	p.Pro649Arg	p.P649R	ENST00000266497		649	cCa/cGa	13/31	1	2	FACETS	0.771	0.702	0.843	0.771	0.702	0.843	SUBCLONAL	1	FALSE	1	0.407103218922581	2		547	899	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434997	49434997	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	27	112	0	ENST00000301067.7:c.6556G>T	p.Glu2186Ter	p.E2186*	ENST00000301067	NM_003482.3	2186	Gag/Tag	31/54	1	2	FACETS	0.845	0.68	1	0.845	0.68	1	CLONAL	1	FALSE	1	0.407103218922581	2		112	157	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26828820	26828820	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	168	441	0	ENST00000381527.3:c.42G>T	p.Glu14Asp	p.E14D	ENST00000381527	NM_001260.1	14	gaG/gaT	1/13	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.407103218922581	2		441	740	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129448	30129448	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	195	570	0	ENST00000263025.4:c.580G>C	p.Glu194Gln	p.E194Q	ENST00000263025	NM_002746.2	194	Gag/Cag	4/9	1	2	FACETS	0.926	0.856	0.998	0.926	0.856	0.998	CLONAL	1	FALSE	1	0.407103218922581	2		570	1035	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56867273	56867273	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	51	605	0	ENST00000308159.5:c.1492G>C	p.Glu498Gln	p.E498Q	ENST00000308159	NM_014669.4	498	Gag/Cag	13/22	NA	2	FACETS	0.26	0.22	0.305			1	INDETERMINATE	1	FALSE	NA	0.407103218922581	2		605	963	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245601	41245601	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	143	517	0	ENST00000357654.3:c.1947G>T	p.Glu649Asp	p.E649D	ENST00000357654	NM_007294.3	649	gaG/gaT	10/23	1	2	FACETS	0.865	0.789	0.945	0.865	0.789	0.945	CLONAL	1	FALSE	1	0.407103218922581	2		517	812	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245606	41245606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	140	516	1	ENST00000357654.3:c.1942G>A	p.Glu648Lys	p.E648K	ENST00000357654	NM_007294.3	648	Gaa/Aaa	10/23	1	2	FACETS	0.854	0.778	0.934	0.854	0.778	0.934	CLONAL	1	FALSE	1	0.407103218922581	2		517	805	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246800	41246800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567802220	NA	P-0005385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	153	495	0	ENST00000357654.3:c.748G>A	p.Glu250Lys	p.E250K	ENST00000357654	NM_007294.3	250	Gag/Aag	10/23	1	2	FACETS	0.902	0.826	0.982	0.902	0.826	0.982	CLONAL	1	FALSE	1	0.407103218922581	2		495	833	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231092	53231092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	44	338	0	ENST00000375401.3:c.1810G>A	p.Gly604Ser	p.G604S	ENST00000375401	NM_004187.3	604	Ggc/Agc	13/26	1	1	FACETS	0.353	0.296	0.416	0.353	0.296	0.416	SUBCLONAL	1	FALSE	0	0.407103218922581	1		338	488	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185004	123185004	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005385-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	170	256	0	ENST00000218089.9:c.1051C>G	p.Leu351Val	p.L351V	ENST00000218089	NM_001042749.1	351	Cta/Gta	12/35	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	0	0.407103218922581	1		256	501	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	22	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.878	0.686	1	1	0.953	1	CLONAL	3	TRUE	1	0.1	2		280	167	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0005427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	26	599	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.58	0.457	0.723	0.58	0.457	0.723	SUBCLONAL	1	TRUE	1	0.1	2		599	896	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209110083	209110083	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	39	258	0	ENST00000345146.2:c.480C>G	p.Asp160Glu	p.D160E	ENST00000345146	NM_005896.2	160	gaC/gaG	5/10	1	2	FACETS	0.806	0.668	0.96	1	0.957	1	CLONAL	2	TRUE	1	0.1	2		258	484	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187443346	187443346	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	23	204	0	ENST00000232014.4:c.1780C>G	p.Arg594Gly	p.R594G	ENST00000232014	NM_001130845.1	594	Cga/Gga	8/10	1	2	FACETS	0.601	0.467	0.759	0.601	0.467	0.759	SUBCLONAL	1	TRUE	1	0.1	2		204	765	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732535	74732535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	29	172	0	ENST00000359995.5:c.374G>A	p.Arg125His	p.R125H	ENST00000359995	NM_001195427.1	125	cGt/cAt	2/3	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.1	2		172	434	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143462	30143462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	10	77	0	ENST00000389048.3:c.64G>A	p.Gly22Arg	p.G22R	ENST00000389048	NM_004304.4	22	Ggg/Agg	1/29	1	2	FACETS	0.847	0.577	1	1	0.863	1	CLONAL	2	TRUE	1	0.1	2		77	118	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97887428	97887428	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	157	253	0	ENST00000289081.3:c.936A>G	p.Ile312Met	p.I312M	ENST00000289081	NM_000136.2	312	atA/atG	10/15	1	2	FACETS	0.95	0.873	1	1	0.994	1	CLONAL	5	TRUE	1	0.1	2		253	661	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106937	27106937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1470694207	NA	P-0005427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	38	197	1	ENST00000324856.7:c.6548G>A	p.Arg2183His	p.R2183H	ENST00000324856	NM_006015.4	2183	cGt/cAt	20/20	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.1	2		198	567	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026344	48026344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553412644	NA	P-0005427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	28	196	0	ENST00000234420.5:c.1222C>T	p.Pro408Ser	p.P408S	ENST00000234420	NM_000179.2	408	Cct/Tct	4/10	1	2	FACETS	0.765	0.612	0.94	1	0.937	1	CLONAL	2	TRUE	1	0.1	2		196	366	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157519989	157519989	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1554234983	NA	P-0005427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	72	292	1	ENST00000346085.5:c.4058C>A	p.Ser1353Ter	p.S1353*	ENST00000346085	NM_020732.3	1353	tCg/tAg	17/20	1	2	FACETS	0.911	0.795	1	1	0.98	1	CLONAL	2	TRUE	1	0.1	2		293	790	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468236	50468236	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	28	201	0	ENST00000331340.3:c.1471G>A	p.Glu491Lys	p.E491K	ENST00000331340	NM_006060.4	491	Gag/Aag	8/8	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.1	2		201	444	SUCCESS
ATM	472	MSKCC	GRCh37	11	108216608	108216608	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	23	184	0	ENST00000278616.4:c.8557A>G	p.Thr2853Ala	p.T2853A	ENST00000278616	NM_000051.3	2853	Acg/Gcg	58/63	1	2	FACETS	0.878	0.686	1	1	0.938	1	CLONAL	2	TRUE	1	0.1	2		184	262	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	495065	495065	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	47	264	0	ENST00000399788.2:c.241G>A	p.Glu81Lys	p.E81K	ENST00000399788	NM_001042603.1	81	Gag/Aag	2/28	1	2	FACETS	0.794	0.669	0.932	1	0.963	1	CLONAL	2	TRUE	1	0.1	2		264	592	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866359	37866359	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	50	185	0	ENST00000269571.5:c.664G>T	p.Gly222Cys	p.G222C	ENST00000269571		222	Ggt/Tgt	6/27	1	2	FACETS	0.835	0.708	0.975	1	0.968	1	CLONAL	2	TRUE	1	0.1	2		185	599	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774771	73774771	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	60	385	2	ENST00000254810.4:c.316G>A	p.Glu106Lys	p.E106K	ENST00000254810	NM_005324.3	106	Gaa/Aaa	4/4	1	2	FACETS	0.988	0.851	1	1	0.978	1	CLONAL	2	TRUE	1	0.1	2		387	607	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129670	11129670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057524313	NA	P-0005427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	79	267	1	ENST00000358026.2:c.2476G>A	p.Ala826Thr	p.A826T	ENST00000358026	NM_001128849.1	826	Gcc/Acc	17/36	1	2	FACETS	0.817	0.717	0.925	1	0.979	1	CLONAL	2	TRUE	1	0.1	2		268	967	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923060	44923060	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	20	351	0	ENST00000377967.4:c.1921C>T	p.Gln641Ter	p.Q641*	ENST00000377967	NM_021140.2	641	Cag/Tag	16/29	0.0523784330341122	2	FACETS	0.766	0.587	0.976			1	INDETERMINATE	2	TRUE	NA	0.1	2		351	261	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030637	47030637	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	69	144	0	ENST00000377604.3:c.412C>T	p.Gln138Ter	p.Q138*	ENST00000377604	NM_001204468.1	138	Cag/Tag	4/24	0.0523784330341122	2	FACETS	0.842	0.735	0.959			1	INDETERMINATE	3	TRUE	NA	0.1	2		144	546	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789656	3789714	+	frameshift_variant	Frame_Shift_Del	DEL	TTCCTCAAAAGCAAACAGAGCTTTGGTTCGATATGGGAAAGATTCAGACATTTCCCCAG	TTCCTCAAAAGCAAACAGAGCTTTGGTTCGATATGGGAAAGATTCAGACATTTCCCCAG	-	novel	NA	P-0005427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	44	302	0	ENST00000262367.5:c.4145_4203del	p.Ser1382TyrfsTer2	p.S1382Yfs*2	ENST00000262367	NM_004380.2	1382	tCTGGGGAAATGTCTGAATCTTTCCCATATCGAACCAAAGCTCTGTTTGCTTTTGAGGAA/t	25/31	0.3	3	FACETS	1	0.93	1	0.609	0.51	0.721	CLONAL	1	TRUE	1	0.1	3		302	758	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225360616	225360616	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	32	278	0	ENST00000264414.4:c.1775del	p.Leu592CysfsTer8	p.L592Cfs*8	ENST00000264414	NM_003590.4	592	tTg/tg	13/16	1	2	FACETS	0.755	0.612	0.916	1	0.943	1	CLONAL	2	TRUE	1	0.1	2		278	424	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953322	17953336	+	inframe_deletion	In_Frame_Del	DEL	GCAGGGCTCTGCGCA	GCAGGGCTCTGCGCA	-	novel	NA	P-0005427-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	38	270	0	ENST00000458235.1:c.650_664del	p.Val217_Arg222delinsGly	p.V217_R222delinsG	ENST00000458235	NM_000215.3	217	gTGCGCAGAGCCCTGCgc/ggc	6/24	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.1	2		270	625	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0005473-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	157	659	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.131905073810261	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.138708725463629	2		660	990	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49026177	49026875	+	intron_variant	Intron	DEL	AATTTTTTCAAAAAATAAGCTCCTGGATTCATTGATTTTTTAAGGGTTTTTTGTGTCTCTGTCTCCTTCAGTTCTGCTCTGATCTTGGTTATTTTTTGTCTTCTGCTAGCTTTGGGGTTTGTTTGCTCTTTGAACTGGTTTTAGTATCAATATTGTACTAGCTTCATAAAATGAGATGAGGAATGTTTCTAGTTTTTCCATTCCAGGAAGAAAATCTGAGTAAAAGTGGAATTATCTGTCCCTTGAATGTTTGGTAGAATTTACTGGTAAAACCAAATGAGCTTGATGTTTTATTTATGGGAAGATTTTAAATTATTGATTCAAATTATTTAATAGTTGCAGGACTATGTAAGTTATTTTATTTCTTTTTTATTGAGTTTTGGTAATTTGTATTTTTGTAGTAATTTTCCACTTGGTCTACGTTTTCCAATTTATTGATATAAAATTATTCATAATAATTCCCTATTATCTTTTTAATCTTTGTGATTTTGTCCCATTTTTCATACCTAATACTGCCTATCTATCTCTTTTCTTTATCTTGATCAATCTGACTGGAGATTTGTTAGTTATTTCAAAGAATCCATTTTTGGCTTTGTTGACCAAACTGTGTTTTATCTTTGTTTTCAGTTTCATTAAGTTCTGCTCATGTCTTCATTTCTTTCTCTCCACTTTCTTCGTTTTTTTTCTGTCTTTCCTCCT	AATTTTTTCAAAAAATAAGCTCCTGGATTCATTGATTTTTTAAGGGTTTTTTGTGTCTCTGTCTCCTTCAGTTCTGCTCTGATCTTGGTTATTTTTTGTCTTCTGCTAGCTTTGGGGTTTGTTTGCTCTTTGAACTGGTTTTAGTATCAATATTGTACTAGCTTCATAAAATGAGATGAGGAATGTTTCTAGTTTTTCCATTCCAGGAAGAAAATCTGAGTAAAAGTGGAATTATCTGTCCCTTGAATGTTTGGTAGAATTTACTGGTAAAACCAAATGAGCTTGATGTTTTATTTATGGGAAGATTTTAAATTATTGATTCAAATTATTTAATAGTTGCAGGACTATGTAAGTTATTTTATTTCTTTTTTATTGAGTTTTGGTAATTTGTATTTTTGTAGTAATTTTCCACTTGGTCTACGTTTTCCAATTTATTGATATAAAATTATTCATAATAATTCCCTATTATCTTTTTAATCTTTGTGATTTTGTCCCATTTTTCATACCTAATACTGCCTATCTATCTCTTTTCTTTATCTTGATCAATCTGACTGGAGATTTGTTAGTTATTTCAAAGAATCCATTTTTGGCTTTGTTGACCAAACTGTGTTTTATCTTTGTTTTCAGTTTCATTAAGTTCTGCTCATGTCTTCATTTCTTTCTCTCCACTTTCTTCGTTTTTTTTCTGTCTTTCCTCCT	-	novel	NA	P-0005473-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	0	88	1	0	ENST00000267163.4:c.1696-950_1696-252del		p.*566*	ENST00000267163	NM_000321.2	-/928			0.138708725463629	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	16	TRUE	1	0.138708725463629	4		1	88	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0005493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	433	464	0				ENST00000310581	NM_198253.2	-/1132			0.380536731501157	2	FACETS	1	0.992	1	0.592	0.564	0.621	CLONAL	1	TRUE	0	0.491138314286811	2		464	1489	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0005493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	308	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.270373412276153	5	FACETS	1	0.974	1	0.703	0.663	0.743	INDETERMINATE	2	TRUE	2	0.491138314286811	5		490	1033	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576851	7576851	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0005493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	703	379	0	ENST00000269305.4:c.993+2T>G		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.416536693020866	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.491138314286811	2		379	1334	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331980	81331980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1383506132	NA	P-0005493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	457	451	0	ENST00000222390.5:c.2104C>T	p.Arg702Cys	p.R702C	ENST00000222390	NM_000601.4	702	Cgt/Tgt	18/18	0.270373412276153	5	FACETS	1	0.984	1	0.713	0.68	0.746	INDETERMINATE	2	TRUE	2	0.491138314286811	5		451	1512	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800948	18800948	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	49	350	0	ENST00000266497.5:c.4324A>T	p.Asn1442Tyr	p.N1442Y	ENST00000266497		1442	Aac/Tac	31/31	NA	2	FACETS	0.415	0.351	0.485			1	INDETERMINATE	1	TRUE	NA	0.491138314286811	2		350	481	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17117084	17117084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	476	401	0	ENST00000285071.4:c.1625C>T	p.Ser542Phe	p.S542F	ENST00000285071	NM_144997.5	542	tCc/tTc	14/14	0.416536693020866	2	FACETS	0.852	0.817	0.888	0.852	0.817	0.888	CLONAL	2	TRUE	0	0.491138314286811	2		401	1137	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560913	9560913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559720359	NA	P-0005493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	609	498	2	ENST00000353224.5:c.869C>T	p.Ser290Leu	p.S290L	ENST00000353224	NM_177990.2	290	tCg/tTg	4/10	0.225216741261068	3	FACETS	0.984	0.947	1	0.656	0.631	0.681	INDETERMINATE	2	TRUE	0	0.491138314286811	3		500	1570	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039373	49039374	+	stop_gained	Nonsense_Mutation	DNP	TC	TC	AT	novel	NA	P-0005493-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	237	484	0	ENST00000267163.4:c.2358_2359delinsAT	p.Arg787Ter	p.R787*	ENST00000267163	NM_000321.2	786	ccTCga/ccATga	23/27	0.424114790370275	1	FACETS	0.769	0.718	0.821	0.769	0.718	0.821	SUBCLONAL	1	TRUE	0	0.491138314286811	1		484	947	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	33	280	0				ENST00000310581	NM_198253.2	-/1132			0.178849715384749	0	FACETS	0.912	0.747	1			1	CLONAL	1	FALSE	0	0.23093957229412	0		280	241	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107180	27107180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1308037041	NA	P-0005497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	39	285	0	ENST00000324856.7:c.6791C>T	p.Ser2264Leu	p.S2264L	ENST00000324856	NM_006015.4	2264	tCa/tTa	20/20	0.224717001542314	4	FACETS	0.807	0.669	0.962			1	CLONAL	1	FALSE	NA	0.23093957229412	4		285	515	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577118	7577118	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057520005	NA	P-0005497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	108	571	0	ENST00000269305.4:c.820G>T	p.Val274Phe	p.V274F	ENST00000269305	NM_001126112.2	274	Gtt/Ttt	8/11	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.23093957229412	2		571	712	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	109	596	0	ENST00000269305.4:c.811G>C	p.Glu271Gln	p.E271Q	ENST00000269305	NM_001126112.2	271	Gag/Cag	8/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.23093957229412	2		596	691	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107135	27107135	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0005497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	45	234	0	ENST00000324856.7:c.6746C>G	p.Ser2249Ter	p.S2249*	ENST00000324856	NM_006015.4	2249	tCa/tGa	20/20	0.224717001542314	4	FACETS	1	0.901	1			1	CLONAL	1	FALSE	NA	0.23093957229412	4		234	437	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8492922	8492922	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	48	557	0	ENST00000356435.5:c.2407T>G	p.Tyr803Asp	p.Y803D	ENST00000356435		803	Tac/Gac	16/35	1	2	FACETS	0.614	0.518	0.72	0.614	0.518	0.72	SUBCLONAL	1	FALSE	1	0.23093957229412	2		557	677	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65569028	65569028	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	62	507	0	ENST00000358664.4:c.30G>C	p.Glu10Asp	p.E10D	ENST00000358664	NM_002382.4	10	gaG/gaC	1/5	1	2	FACETS	0.489	0.421	0.564	0.489	0.421	0.564	SUBCLONAL	1	FALSE	1	0.23093957229412	2		507	1098	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216076	7216076	+	stop_lost	Nonstop_Mutation	SNP	C	C	G	novel	NA	P-0005497-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1424	168	760	0	ENST00000380728.2:c.983G>C	p.Ter328SerextTer?	p.*328Sext*?	ENST00000380728		328	tGa/tCa	11/11	1	2	FACETS	0.914	0.837	0.995	0.914	0.837	0.995	CLONAL	1	FALSE	1	0.23093957229412	2		760	1592	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	192	280	0				ENST00000310581	NM_198253.2	-/1132			0.254923290571406	3	FACETS	1	0.935	1	1	0.935	1	CLONAL	3	TRUE	0	0.254923290571406	3		280	564	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	281	505	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.254923290571406	3	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	1	0.254923290571406	3		506	1198	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356251	66356251	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	139	421	1	ENST00000273854.3:c.1246C>T	p.Pro416Ser	p.P416S	ENST00000273854	NM_004439.5	416	Ccc/Tcc	5/18	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.254923290571406	2		422	852	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462108	120462108	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	193	567	0	ENST00000256646.2:c.5608C>T	p.Gln1870Ter	p.Q1870*	ENST00000256646	NM_024408.3	1870	Cag/Tag	31/34	0.254440068571952	3	FACETS	1	0.989	1	0.719	0.663	0.776	CLONAL	1	TRUE	1	0.254923290571406	3		567	1188	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543748	29543748	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	237	421	0	ENST00000389048.3:c.1415G>A	p.Arg472Gln	p.R472Q	ENST00000389048	NM_004304.4	472	cGg/cAg	7/29	0.254923290571406	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	1	0.254923290571406	3		421	850	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178917531	178917531	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	251	394	1	ENST00000263967.3:c.406G>A	p.Val136Ile	p.V136I	ENST00000263967	NM_006218.2	136	Gta/Ata	3/21	0.254923290571406	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	1	0.254923290571406	4		395	740	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806185	1806185	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	76	656	0	ENST00000260795.2:c.1204C>T	p.Pro402Ser	p.P402S	ENST00000260795		402	Ccc/Tcc	8/17	0.197579022420501	3	FACETS	0.568	0.496	0.645			1	SUBCLONAL	1	TRUE	NA	0.254923290571406	3		656	1184	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55963934	55963934	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	67	332	0	ENST00000263923.4:c.2510-1G>A		p.X837_splice	ENST00000263923	NM_002253.2	837			1	2	FACETS	0.792	0.688	0.904	0.792	0.688	0.904	CLONAL	1	TRUE	1	0.254923290571406	2		332	664	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980297	55980297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs539911006	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	83	405	0	ENST00000263923.4:c.794C>T	p.Ser265Leu	p.S265L	ENST00000263923	NM_002253.2	265	tCg/tTg	6/30	1	2	FACETS	0.872	0.769	0.982	0.872	0.769	0.982	CLONAL	1	TRUE	1	0.254923290571406	2		405	747	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467434	66467434	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	50	390	0	ENST00000273854.3:c.835G>T	p.Glu279Ter	p.E279*	ENST00000273854	NM_004439.5	279	Gaa/Taa	3/18	1	2	FACETS	0.569	0.481	0.665	0.569	0.481	0.665	SUBCLONAL	1	TRUE	1	0.254923290571406	2		390	690	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539090	187539090	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	85	487	0	ENST00000441802.2:c.8650C>T	p.Gln2884Ter	p.Q2884*	ENST00000441802	NM_005245.3	2884	Cag/Tag	10/27	1	2	FACETS	0.758	0.669	0.854	0.758	0.669	0.854	SUBCLONAL	1	TRUE	1	0.254923290571406	2		487	880	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630411	187630411	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	159	492	2	ENST00000441802.2:c.571C>T	p.Arg191Ter	p.R191*	ENST00000441802	NM_005245.3	191	Cga/Tga	2/27	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.254923290571406	2		494	986	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295230	1295230	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs796516131	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	51	310	0				ENST00000310581	NM_198253.2	-/1132			0.254923290571406	3	FACETS	0.776	0.659	0.905	0.259	0.219	0.302	CLONAL	1	TRUE	0	0.254923290571406	3		310	581	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876184	35876184	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	313	502	0	ENST00000303115.3:c.976G>A	p.Asp326Asn	p.D326N	ENST00000303115	NM_002185.3	326	Gat/Aat	8/8	0.254923290571406	3	FACETS	0.932	0.881	0.984	0.932	0.881	0.984	CLONAL	3	TRUE	0	0.254923290571406	3		502	990	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962591	38962591	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	154	367	0	ENST00000357387.3:c.1664T>G	p.Leu555Arg	p.L555R	ENST00000357387	NM_152756.3	555	cTt/cGt	18/38	0.254923290571406	3	FACETS	0.835	0.768	0.903	0.835	0.768	0.903	CLONAL	3	TRUE	0	0.254923290571406	3		367	544	SUCCESS
APC	324	MSKCC	GRCh37	5	112177485	112177485	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112487226	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	82	422	0	ENST00000257430.4:c.6194C>T	p.Pro2065Leu	p.P2065L	ENST00000257430	NM_000038.5	2065	cCc/cTc	16/16	0.254923290571406	3	FACETS	0.763	0.671	0.862	0.254	0.223	0.288	SUBCLONAL	1	TRUE	0	0.254923290571406	3		422	951	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501478	149501478	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	406	661	0	ENST00000261799.4:c.2309A>G	p.Asn770Ser	p.N770S	ENST00000261799	NM_002609.3	770	aAc/aGc	16/23	0.254923290571406	3	FACETS	0.942	0.896	0.988	0.942	0.896	0.988	CLONAL	3	TRUE	0	0.254923290571406	3		661	1271	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271483	26271483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755365560	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1588	719	1325	1	ENST00000305910.3:c.130C>T	p.Pro44Ser	p.P44S	ENST00000305910	NM_003534.2	44	Ccc/Tcc	1/1	0.243935613848673	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	1	0.254923290571406	4		1326	2307	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678023	117678023	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	198	542	0	ENST00000368508.3:c.3910A>C	p.Ile1304Leu	p.I1304L	ENST00000368508	NM_002944.2	1304	Att/Ctt	25/43	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.254923290571406	2		542	1094	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517317	157517317	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	197	549	0	ENST00000346085.5:c.3881C>T	p.Pro1294Leu	p.P1294L	ENST00000346085	NM_020732.3	1294	cCc/cTc	16/20	1	2	FACETS	0.813	0.753	0.876	1	0.992	1	CLONAL	2	TRUE	1	0.254923290571406	2		549	950	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2957001	2957001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	151	347	0	ENST00000396946.4:c.2626G>A	p.Glu876Lys	p.E876K	ENST00000396946	NM_032415.4	876	Gaa/Aaa	20/25	0.168953718657827	5	FACETS	0.93	0.851	1	0.62	0.567	0.676	CLONAL	2	TRUE	2	0.254923290571406	5		347	880	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873725	151873726	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	134	332	0	ENST00000262189.6:c.8812_8813delinsTT	p.Pro2938Leu	p.P2938L	ENST00000262189	NM_170606.2	2938	CCa/TTa	38/59	0.168953718657827	5	FACETS	0.954	0.867	1	0.636	0.578	0.696	CLONAL	2	TRUE	2	0.254923290571406	5		332	762	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128752773	128752773	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	167	294	0	ENST00000377970.2:c.934C>T	p.Leu312Phe	p.L312F	ENST00000377970	NM_002467.4	312	Ctc/Ttc	3/3	0.254923290571406	5	FACETS	1	0.97	1	0.74	0.68	0.802	CLONAL	2	TRUE	2	0.254923290571406	5		294	816	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080255	5080256	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	113	418	0	ENST00000381652.3:c.2158_2159delinsTT	p.Pro720Leu	p.P720L	ENST00000381652	NM_004972.3	720	CCa/TTa	17/25	0.254923290571406	2	FACETS	1	0.982	1	0.706	0.636	0.779	CLONAL	1	TRUE	0	0.254923290571406	2		418	628	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971187	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AT	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	81	153	1	ENST00000304494.5:c.171_172delinsAT	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	57	gcCCga/gcATga	2/3	0.254923290571406	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	TRUE	0	0.254923290571406	2		154	268	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971187	21971187	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	81	152	0	ENST00000579755.1:c.214C>A	p.Pro72Thr	p.P72T	ENST00000579755		72	Ccg/Acg	2/3	0.254923290571406	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	0	0.254923290571406	2		152	270	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606259	93606259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	215	629	1	ENST00000375746.1:c.79G>A	p.Asp27Asn	p.D27N	ENST00000375746	NM_001174167.1	27	Gat/Aat	2/14	0.168953718657827	5	FACETS	0.946	0.877	1	0.63	0.585	0.678	CLONAL	2	TRUE	2	0.254923290571406	5		630	1233	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209556	98209556	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	134	328	1	ENST00000331920.6:c.3982G>A	p.Glu1328Lys	p.E1328K	ENST00000331920	NM_000264.3	1328	Gaa/Aaa	23/24	0.168953718657827	5	FACETS	1	0.974	1	0.785	0.716	0.858	CLONAL	2	TRUE	2	0.254923290571406	5		329	617	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101909953	101909953	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	120	316	0	ENST00000374994.4:c.1273C>T	p.Gln425Ter	p.Q425*	ENST00000374994	NM_004612.2	425	Caa/Taa	8/9	0.168953718657827	5	FACETS	0.968	0.876	1	0.646	0.584	0.711	CLONAL	2	TRUE	2	0.254923290571406	5		316	672	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400334	139400334	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	25	95	0	ENST00000277541.6:c.4015-1G>A		p.X1339_splice	ENST00000277541	NM_017617.3	1339			0.254440068571952	3	FACETS	1	0.879	1	0.582	0.462	0.718	CLONAL	1	TRUE	1	0.254923290571406	3		95	190	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412375	139412375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1341448592	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	186	378	0	ENST00000277541.6:c.1270G>A	p.Glu424Lys	p.E424K	ENST00000277541	NM_017617.3	424	Gag/Aag	8/34	0.254440068571952	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.254923290571406	3		378	739	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104309758	104309758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	290	638	1	ENST00000369902.3:c.349G>A	p.Gly117Ser	p.G117S	ENST00000369902	NM_016169.3	117	Ggc/Agc	3/12	0.254440068571952	3	FACETS	0.97	0.911	1	0.97	0.911	1	CLONAL	2	TRUE	1	0.254923290571406	3		639	1322	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047156	77047157	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	200	665	0	ENST00000356341.3:c.1387_1388delinsTT	p.Pro463Leu	p.P463L	ENST00000356341	NM_002576.4	463	CCa/TTa	13/15	0.254923290571406	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.254923290571406	1		665	1065	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922258	100922258	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	186	861	0	ENST00000325455.5:c.2254C>T	p.Gln752Ter	p.Q752*	ENST00000325455	NM_001202474.3	752	Cag/Tag	5/8	0.254923290571406	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.254923290571406	1		861	1095	SUCCESS
ATM	472	MSKCC	GRCh37	11	108213988	108213988	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs749737164	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	146	369	0	ENST00000278616.4:c.8308T>G	p.Cys2770Gly	p.C2770G	ENST00000278616	NM_000051.3	2770	Tgc/Ggc	57/63	0.254923290571406	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.254923290571406	1		369	697	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022624	12022624	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	130	495	0	ENST00000396373.4:c.730C>T	p.His244Tyr	p.H244Y	ENST00000396373	NM_001987.4	244	Cac/Tac	5/8	0.177167615828365	3	FACETS	1	0.982	1	0.676	0.613	0.743	CLONAL	1	TRUE	1	0.254923290571406	3		495	850	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910809	32910809	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	965	998	5	ENST00000380152.3:c.2317C>T	p.Pro773Ser	p.P773S	ENST00000380152		773	Cct/Tct	11/27	0.243935613848673	4	FACETS	0.933	0.907	0.959	1	0.998	1	CLONAL	5	TRUE	1	0.254923290571406	4		1003	2036	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061733	38061733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	49	314	0	ENST00000250448.2:c.256C>T	p.Pro86Ser	p.P86S	ENST00000250448	NM_004496.3	86	Ccg/Tcg	2/2	0.254440068571952	3	FACETS	0.794	0.672	0.928	0.397	0.336	0.464	CLONAL	1	TRUE	1	0.254923290571406	3		314	546	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41011031	41011031	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1424	148	883	0	ENST00000267868.3:c.464G>A	p.Gly155Glu	p.G155E	ENST00000267868	NM_002875.4	155	gGa/gAa	6/10	0.104262415004764	0	FACETS	0.55	0.501	0.603			1	INDETERMINATE	1	TRUE	0	0.254923290571406	0		883	1572	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42002918	42002918	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	118	814	3	ENST00000219905.7:c.2455C>T	p.Arg819Cys	p.R819C	ENST00000219905	NM_001164273.1	819	Cgt/Tgt	8/24	0.104262415004764	0	FACETS	0.527	0.474	0.584			1	INDETERMINATE	1	TRUE	0	0.254923290571406	0		817	1308	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041699	42041699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1361	166	911	0	ENST00000219905.7:c.5894C>T	p.Ser1965Phe	p.S1965F	ENST00000219905	NM_001164273.1	1965	tCc/tTc	17/24	0.104262415004764	0	FACETS	0.635	0.582	0.692			1	INDETERMINATE	1	TRUE	0	0.254923290571406	0		911	1527	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679778	88679778	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	79	682	0	ENST00000360948.2:c.685A>G	p.Ile229Val	p.I229V	ENST00000360948	NM_001012338.2	229	Atc/Gtc	7/19	0.104262415004764	0	FACETS	0.464	0.407	0.526			1	INDETERMINATE	1	TRUE	0	0.254923290571406	0		682	995	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858007	9858007	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	69	481	1	ENST00000330684.3:c.3394C>T	p.Pro1132Ser	p.P1132S	ENST00000330684	NM_001134407.1	1132	Cca/Tca	13/13	0.254440068571952	3	FACETS	0.593	0.514	0.678	0.296	0.257	0.339	SUBCLONAL	1	TRUE	1	0.254923290571406	3		482	1030	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858306	9858306	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	113	349	0	ENST00000330684.3:c.3095C>T	p.Ser1032Phe	p.S1032F	ENST00000330684	NM_001134407.1	1032	tCc/tTc	13/13	0.254440068571952	3	FACETS	0.783	0.706	0.865	0.783	0.706	0.865	SUBCLONAL	2	TRUE	1	0.254923290571406	3		349	638	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992907	72992907	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1401	357	1022	1	ENST00000268489.5:c.1138C>T	p.Pro380Ser	p.P380S	ENST00000268489	NM_006885.3	380	Cca/Tca	2/10	0.254440068571952	3	FACETS	0.898	0.848	0.949	0.898	0.848	0.949	CLONAL	2	TRUE	1	0.254923290571406	3		1023	1758	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836429	89836429	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	72	336	0	ENST00000389301.3:c.2320C>T	p.Pro774Ser	p.P774S	ENST00000389301	NM_000135.2	774	Ccg/Tcg	26/43	0.254440068571952	3	FACETS	1	0.96	1	0.621	0.543	0.704	CLONAL	1	TRUE	1	0.254923290571406	3		336	513	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574018	7574018	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1315	138	681	1	ENST00000269305.4:c.1009C>A	p.Arg337Ser	p.R337S	ENST00000269305	NM_001126112.2	337	Cgc/Agc	10/11	0.254923290571406	3	FACETS	0.84	0.762	0.923	0.42	0.381	0.462	CLONAL	1	TRUE	1	0.254923290571406	3		682	1453	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30315429	30315429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758186567	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	277	618	0	ENST00000322652.5:c.1114C>T	p.Pro372Ser	p.P372S	ENST00000322652	NM_015355.2	372	Cct/Tct	10/16	0.254923290571406	3	FACETS	0.993	0.931	1	0.993	0.931	1	CLONAL	2	TRUE	1	0.254923290571406	3		618	1234	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40371841	40371842	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	346	870	0	ENST00000293328.3:c.569_570delinsTT	p.Ala190Val	p.A190V	ENST00000293328	NM_012448.3	190	gCC/gTT	6/19	NA	2	FACETS	0.986	0.933	1			1	INDETERMINATE	2	TRUE	NA	0.254923290571406	2		870	1376	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119306	3119306	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1409264282	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	241	724	1	ENST00000078429.4:c.838G>A	p.Glu280Lys	p.E280K	ENST00000078429	NM_002067.2	280	Gag/Aag	6/7	1	2	FACETS	0.794	0.741	0.85	1	0.993	1	SUBCLONAL	2	TRUE	1	0.254923290571406	2		725	1190	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121094	3121094	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	112	684	0	ENST00000078429.4:c.997G>T	p.Asp333Tyr	p.D333Y	ENST00000078429	NM_002067.2	333	Gac/Tac	7/7	1	2	FACETS	0.795	0.713	0.882	0.795	0.713	0.882	SUBCLONAL	1	TRUE	1	0.254923290571406	2		684	1105	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10266565	10266565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	236	619	0	ENST00000340748.4:c.1408G>A	p.Asp470Asn	p.D470N	ENST00000340748		470	Gat/Aat	18/40	1	2	FACETS	0.842	0.785	0.9	1	0.993	1	CLONAL	2	TRUE	1	0.254923290571406	2		619	1100	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791313	42791313	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1243568637	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	70	538	0	ENST00000575354.2:c.373C>T	p.Pro125Ser	p.P125S	ENST00000575354	NM_015125.3	125	Ccc/Tcc	3/20	1	2	FACETS	0.695	0.605	0.793	0.695	0.605	0.793	SUBCLONAL	1	TRUE	1	0.254923290571406	2		538	790	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729947	47729947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	95	332	0	ENST00000449228.1:c.442G>A	p.Gly148Ser	p.G148S	ENST00000449228	NM_001127240.2	148	Ggc/Agc	3/4	1	2	FACETS	0.775	0.693	0.861	1	0.982	1	SUBCLONAL	2	TRUE	1	0.254923290571406	2		332	481	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520176	9520176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	90	557	0	ENST00000353224.5:c.2093C>T	p.Pro698Leu	p.P698L	ENST00000353224	NM_177990.2	698	cCa/cTa	10/10	0.254440068571952	3	FACETS	0.663	0.587	0.746	0.332	0.293	0.373	SUBCLONAL	1	TRUE	1	0.254923290571406	3		557	1200	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306532	41306532	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	141	371	0	ENST00000373198.4:c.1127C>T	p.Pro376Leu	p.P376L	ENST00000373198	NM_133170.3	376	cCc/cTc	7/32	0.254440068571952	3	FACETS	0.81	0.739	0.885	0.81	0.739	0.885	CLONAL	2	TRUE	1	0.254923290571406	3		371	770	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21272275	21272275	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138882903	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	185	400	1	ENST00000354336.3:c.53C>T	p.Pro18Leu	p.P18L	ENST00000354336	NM_005207.3	18	cCg/cTg	1/3	0.254440068571952	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.254923290571406	3		401	676	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29090022	29090022	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs876659250	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	21	167	0	ENST00000328354.6:c.1459C>T	p.Gln487Ter	p.Q487*	ENST00000328354	NM_007194.3	487	Cag/Tag	13/15	0.254440068571952	3	FACETS	0.561	0.432	0.712	0.281	0.216	0.356	SUBCLONAL	1	TRUE	1	0.254923290571406	3		167	331	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569631	41569632	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	188	392	0	ENST00000263253.7:c.4622_4623delinsTT	p.Thr1541Ile	p.T1541I	ENST00000263253	NM_001429.3	1541	aCC/aTT	29/31	0.254440068571952	3	FACETS	0.996	0.921	1	0.996	0.921	1	CLONAL	2	TRUE	1	0.254923290571406	3		392	835	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573483	41573483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	211	494	0	ENST00000263253.7:c.5768C>T	p.Pro1923Leu	p.P1923L	ENST00000263253	NM_001429.3	1923	cCt/cTt	31/31	0.254440068571952	3	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	1	0.254923290571406	3		494	928	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911441	39911441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	114	416	0	ENST00000378444.4:c.5189C>T	p.Thr1730Met	p.T1730M	ENST00000378444	NM_001123385.1	1730	aCg/aTg	15/15	0.0922238338785779	2	FACETS	1	0.952	1			1	INDETERMINATE	1	TRUE	NA	0.254923290571406	2		416	815	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412803	63412803	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	194	365	0	ENST00000330258.3:c.364G>A	p.Glu122Lys	p.E122K	ENST00000330258	NM_152424.3	122	Gag/Aag	2/2	0.0922238338785779	2	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.254923290571406	2		365	643	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412823	63412823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	162	325	0	ENST00000330258.3:c.344G>A	p.Gly115Asp	p.G115D	ENST00000330258	NM_152424.3	115	gGc/gAc	2/2	0.0922238338785779	2	FACETS	1	0.967	1			1	INDETERMINATE	2	TRUE	NA	0.254923290571406	2		325	583	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467342	66467421	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGGAGGCAAACTCTTACCTTGACAGGTGCCATTTTTCTCTTCATATCCTGCCTTGCACATGCATTTCCCGATGGGCACCA	TGGAGGCAAACTCTTACCTTGACAGGTGCCATTTTTCTCTTCATATCCTGCCTTGCACATGCATTTCCCGATGGGCACCA	AG	novel	NA	P-0005509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	39	230	0	ENST00000273854.3:c.848_910+17delinsCT		p.X283_splice	ENST00000273854	NM_004439.5	283		3/18	1	2	FACETS	0.736	0.61	0.875	0.736	0.61	0.875	SUBCLONAL	1	TRUE	1	0.254923290571406	2		230	416	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	211	280	0				ENST00000310581	NM_198253.2	-/1132			0.258554897068449	7	FACETS	1	0.977	1	0.45	0.417	0.485	CLONAL	2	TRUE	2	0.258554897068449	7		280	1193	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0005511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1718	220	683	1	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	0.206913042046567	3	FACETS	0.992	0.919	1	0.496	0.459	0.534	CLONAL	1	TRUE	1	0.258554897068449	3		684	1938	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301800	65301800	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	921	555	0	ENST00000342505.4:c.3239C>T	p.Ser1080Leu	p.S1080L	ENST00000342505	NM_002227.2	1080	tCa/tTa	23/25	0.258554897068449	10	FACETS	0.98	0.952	1			1	CLONAL	8	TRUE	NA	0.258554897068449	10		555	1849	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091386	193091386	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1256	105	575	0	ENST00000367435.3:c.56T>C	p.Val19Ala	p.V19A	ENST00000367435	NM_024529.4	19	gTg/gCg	1/17	0.258554897068449	3	FACETS	0.674	0.602	0.751	0.225	0.2	0.251	SUBCLONAL	1	TRUE	0	0.258554897068449	3		575	1361	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151199	202151199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	293	569	0	ENST00000358485.4:c.1499C>T	p.Thr500Ile	p.T500I	ENST00000358485	NM_001080125.1	500	aCc/aTc	9/9	0.206913042046567	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.258554897068449	3		569	1202	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1266579	1266579	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1725	121	517	2	ENST00000310581.5:c.2654G>A	p.Arg885Lys	p.R885K	ENST00000310581	NM_198253.2	885	aGg/aAg	10/16	0.258554897068449	7	FACETS	0.835	0.751	0.924	0.167	0.15	0.185	CLONAL	1	TRUE	2	0.258554897068449	7		519	1846	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295270	1295270	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs796093488	NA	P-0005511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1614	305	462	0				ENST00000310581	NM_198253.2	-/1132			0.258554897068449	7	FACETS	1	0.949	1	0.405	0.38	0.431	CLONAL	2	TRUE	2	0.258554897068449	7		462	1919	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522644	176522644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1338	132	624	0	ENST00000292408.4:c.1741G>A	p.Glu581Lys	p.E581K	ENST00000292408	NM_213647.1	581	Gag/Aag	13/18	0.206595368463569	2	FACETS	0.695	0.628	0.765	0.347	0.314	0.383	SUBCLONAL	1	TRUE	0	0.258554897068449	2		624	1470	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444266	50444266	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	96	516	0	ENST00000331340.3:c.196G>A	p.Glu66Lys	p.E66K	ENST00000331340	NM_006060.4	66	Gag/Aag	4/8	0.206913042046567	3	FACETS	0.806	0.716	0.901	0.403	0.358	0.451	CLONAL	1	TRUE	1	0.258554897068449	3		516	1041	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249056	55249056	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	197	547	0	ENST00000275493.2:c.2354C>G	p.Thr785Ser	p.T785S	ENST00000275493	NM_005228.3	785	aCc/aGc	20/28	0.206913042046567	3	FACETS	1	0.988	1	0.672	0.62	0.725	CLONAL	1	TRUE	1	0.258554897068449	3		547	1281	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80343465	80343465	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	120	450	1	ENST00000286548.4:c.854A>G	p.Tyr285Cys	p.Y285C	ENST00000286548	NM_002072.3	285	tAt/tGt	6/7	0.206913042046567	3	FACETS	1	0.984	1	0.734	0.663	0.808	CLONAL	1	TRUE	1	0.258554897068449	3		451	714	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891163	101891163	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	51	495	0	ENST00000374994.4:c.124A>G	p.Thr42Ala	p.T42A	ENST00000374994	NM_004612.2	42	Aca/Gca	2/9	0.206913042046567	3	FACETS	0.598	0.507	0.698	0.299	0.253	0.349	SUBCLONAL	1	TRUE	1	0.258554897068449	3		495	745	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250047	110250047	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	35	387	0	ENST00000374672.4:c.628C>G	p.Pro210Ala	p.P210A	ENST00000374672	NM_004235.4	210	Ccg/Gcg	3/5	0.206913042046567	3	FACETS	0.52	0.425	0.627	0.26	0.212	0.314	SUBCLONAL	1	TRUE	1	0.258554897068449	3		387	588	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870988	12870988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1280938448	NA	P-0005511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	437	469	0	ENST00000228872.4:c.215G>A	p.Gly72Asp	p.G72D	ENST00000228872	NM_004064.3	72	gGc/gAc	1/3	0.258554897068449	6	FACETS	0.905	0.862	0.948	0.905	0.862	0.948	CLONAL	4	TRUE	2	0.258554897068449	6		469	1417	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240597	133240597	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	218	588	0	ENST00000320574.5:c.2699T>C	p.Met900Thr	p.M900T	ENST00000320574	NM_006231.2	900	aTg/aCg	23/49	0.206913042046567	3	FACETS	1	0.989	1	0.685	0.635	0.737	CLONAL	1	TRUE	1	0.258554897068449	3		588	1390	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047494	49047494	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0005511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	82	449	0	ENST00000267163.4:c.2490-2A>G		p.X830_splice	ENST00000267163	NM_000321.2	830			0.206913042046567	3	FACETS	0.807	0.714	0.905	0.807	0.714	0.905	CLONAL	2	TRUE	1	0.258554897068449	3		449	444	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436469	110436469	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1392	124	647	0	ENST00000375856.3:c.1932C>A	p.Ser644Arg	p.S644R	ENST00000375856	NM_003749.2	644	agC/agA	1/2	0.206913042046567	3	FACETS	0.714	0.644	0.79	0.357	0.322	0.395	SUBCLONAL	1	TRUE	1	0.258554897068449	3		647	1516	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348160	89348160	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2200	260	839	0	ENST00000301030.4:c.4790G>T	p.Arg1597Leu	p.R1597L	ENST00000301030	NM_001256183.1	1597	cGc/cTc	9/13	0.206595368463569	2	FACETS	0.818	0.762	0.876	0.409	0.381	0.438	CLONAL	1	TRUE	0	0.258554897068449	2		839	2460	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0005511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1445	329	506	1	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.206913042046567	3	FACETS	0.81	0.763	0.859	0.81	0.763	0.859	CLONAL	2	TRUE	1	0.258554897068449	3		507	1774	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990655	7990655	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1389	151	600	0	ENST00000319144.4:c.106C>T	p.Gln36Ter	p.Q36*	ENST00000319144	NM_001139.2	36	Cag/Tag	1/15	0.206913042046567	3	FACETS	0.857	0.78	0.937	0.428	0.39	0.469	CLONAL	1	TRUE	1	0.258554897068449	3		600	1540	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33446593	33446593	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1610	162	1059	0	ENST00000345365.6:c.40G>C	p.Glu14Gln	p.E14Q	ENST00000345365	NM_002878.3	14	Gag/Cag	1/10	0.206913042046567	3	FACETS	0.799	0.73	0.871	0.399	0.365	0.436	SUBCLONAL	1	TRUE	1	0.258554897068449	3		1059	1772	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676207	37676207	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0005511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1162	130	588	0	ENST00000447079.4:c.2964-2A>T		p.X988_splice	ENST00000447079	NM_015083.1	988			0.206913042046567	3	FACETS	0.879	0.795	0.968	0.439	0.397	0.484	CLONAL	1	TRUE	1	0.258554897068449	3		588	1292	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41228521	41228521	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	68	649	0	ENST00000357654.3:c.4468G>C	p.Glu1490Gln	p.E1490Q	ENST00000357654	NM_007294.3	1490	Gaa/Caa	13/23	0.206913042046567	3	FACETS	0.79	0.686	0.902	0.395	0.343	0.451	CLONAL	1	TRUE	1	0.258554897068449	3		649	752	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7141810	7141810	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1337	315	669	0	ENST00000302850.5:c.2560G>T	p.Val854Phe	p.V854F	ENST00000302850	NM_000208.2	854	Gtt/Ttt	13/22	0.238170734988382	3	FACETS	0.833	0.783	0.884	0.833	0.783	0.884	CLONAL	2	TRUE	1	0.258554897068449	3		669	1652	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765555	41765555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1191232462	NA	P-0005511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1336	309	597	0	ENST00000301178.4:c.2431C>T	p.Pro811Ser	p.P811S	ENST00000301178	NM_021913.4	811	Cct/Tct	20/20	0.238170734988382	3	FACETS	0.82	0.771	0.871	0.82	0.771	0.871	CLONAL	2	TRUE	1	0.258554897068449	3		597	1645	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1238	112	540	0	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	0.238170734988382	3	FACETS	0.725	0.649	0.805	0.362	0.324	0.403	SUBCLONAL	1	TRUE	1	0.258554897068449	3		540	1350	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031762	36031762	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	433	526	0	ENST00000358208.4:c.1591C>A	p.Gln531Lys	p.Q531K	ENST00000358208		531	Cag/Aag	12/12	0.238170734988382	3	FACETS	0.869	0.828	0.911	1	0.994	1	CLONAL	3	TRUE	1	0.258554897068449	3		526	1451	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514453	41514453	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	331	543	1	ENST00000373198.4:c.208C>G	p.Pro70Ala	p.P70A	ENST00000373198	NM_133170.3	70	Ccc/Gcc	2/32	0.238170734988382	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.258554897068449	3		544	1328	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037952	49037982	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCCTCATGCTGTTCAGGAGGTAGGTAATTT	TTCCTCATGCTGTTCAGGAGGTAGGTAATTT	-	novel	NA	P-0005511-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	43	701	0	ENST00000267163.4:c.2193_2211+12del		p.X731_splice	ENST00000267163	NM_000321.2	731		21/27	0.206913042046567	3	FACETS	0.529	0.441	0.627	0.265	0.22	0.314	SUBCLONAL	1	TRUE	1	0.258554897068449	3		701	710	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	169	280	0				ENST00000310581	NM_198253.2	-/1132			0.412149544649687	5	FACETS	1	0.975	1	0.289	0.265	0.314	CLONAL	1	TRUE	1	0.412149544649687	5		280	1148	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578211	7578211	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587778720	NA	P-0005511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1356	236	683	1	ENST00000269305.4:c.638G>T	p.Arg213Leu	p.R213L	ENST00000269305	NM_001126112.2	213	cGa/cTa	6/11	1	2	FACETS	0.719	0.669	0.772	0.719	0.669	0.772	SUBCLONAL	1	TRUE	1	0.412149544649687	2		684	1592	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301800	65301800	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	677	555	0	ENST00000342505.4:c.3239C>T	p.Ser1080Leu	p.S1080L	ENST00000342505	NM_002227.2	1080	tCa/tTa	23/25	0.412149544649687	6	FACETS	0.923	0.89	0.955			1	CLONAL	4	TRUE	NA	0.412149544649687	6		555	1624	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091386	193091386	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	214	575	0	ENST00000367435.3:c.56T>C	p.Val19Ala	p.V19A	ENST00000367435	NM_024529.4	19	gTg/gCg	1/17	0.412149544649687	2	FACETS	0.789	0.731	0.848	0.394	0.365	0.424	SUBCLONAL	1	TRUE	0	0.412149544649687	2		575	1317	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151199	202151199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	332	569	0	ENST00000358485.4:c.1499C>T	p.Thr500Ile	p.T500I	ENST00000358485	NM_001080125.1	500	aCc/aTc	9/9	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.412149544649687	2		569	1147	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1266579	1266579	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1829	137	517	2	ENST00000310581.5:c.2654G>A	p.Arg885Lys	p.R885K	ENST00000310581	NM_198253.2	885	aGg/aAg	10/16	0.412149544649687	5	FACETS	0.547	0.495	0.602	0.137	0.123	0.151	SUBCLONAL	1	TRUE	1	0.412149544649687	5		519	1966	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295270	1295270	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs796093488	NA	P-0005511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1345	215	462	0				ENST00000310581	NM_198253.2	-/1132			0.412149544649687	5	FACETS	1	0.969	1	0.271	0.25	0.292	CLONAL	1	TRUE	1	0.412149544649687	5		462	1560	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522644	176522644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	184	624	0	ENST00000292408.4:c.1741G>A	p.Glu581Lys	p.E581K	ENST00000292408	NM_213647.1	581	Gag/Aag	13/18	0.235319041977137	2	FACETS	0.678	0.625	0.735	0.339	0.312	0.368	INDETERMINATE	1	TRUE	0	0.412149544649687	2		624	1316	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444266	50444266	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	71	516	0	ENST00000331340.3:c.196G>A	p.Glu66Lys	p.E66K	ENST00000331340	NM_006060.4	66	Gag/Aag	4/8	1	2	FACETS	0.305	0.265	0.349	0.305	0.265	0.349	SUBCLONAL	1	TRUE	1	0.412149544649687	2		516	1129	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249056	55249056	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	199	547	0	ENST00000275493.2:c.2354C>G	p.Thr785Ser	p.T785S	ENST00000275493	NM_005228.3	785	aCc/aGc	20/28	1	2	FACETS	0.805	0.744	0.868	0.805	0.744	0.868	CLONAL	1	TRUE	1	0.412149544649687	2		547	1200	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80343465	80343465	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	168	450	1	ENST00000286548.4:c.854A>G	p.Tyr285Cys	p.Y285C	ENST00000286548	NM_002072.3	285	tAt/tGt	6/7	1	2	FACETS	0.861	0.791	0.934	0.861	0.791	0.934	CLONAL	1	TRUE	1	0.412149544649687	2		451	947	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891163	101891163	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	84	495	0	ENST00000374994.4:c.124A>G	p.Thr42Ala	p.T42A	ENST00000374994	NM_004612.2	42	Aca/Gca	2/9	1	2	FACETS	0.623	0.551	0.701	0.623	0.551	0.701	SUBCLONAL	1	TRUE	1	0.412149544649687	2		495	654	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250047	110250047	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	56	387	0	ENST00000374672.4:c.628C>G	p.Pro210Ala	p.P210A	ENST00000374672	NM_004235.4	210	Ccg/Gcg	3/5	1	2	FACETS	0.368	0.315	0.427	0.368	0.315	0.427	SUBCLONAL	1	TRUE	1	0.412149544649687	2		387	738	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870988	12870988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1280938448	NA	P-0005511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	489	469	0	ENST00000228872.4:c.215G>A	p.Gly72Asp	p.G72D	ENST00000228872	NM_004064.3	72	gGc/gAc	1/3	0.412149544649687	3	FACETS	0.958	0.916	1	0.958	0.916	1	CLONAL	2	TRUE	1	0.412149544649687	3		469	1493	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240597	133240597	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	242	588	0	ENST00000320574.5:c.2699T>C	p.Met900Thr	p.M900T	ENST00000320574	NM_006231.2	900	aTg/aCg	23/49	0.277311864196332	3	FACETS	1	0.975	1	0.546	0.509	0.585	CLONAL	1	TRUE	1	0.412149544649687	3		588	1296	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047494	49047494	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0005511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	188	449	0	ENST00000267163.4:c.2490-2A>G		p.X830_splice	ENST00000267163	NM_000321.2	830			0.303672731104484	3	FACETS	1	0.989	1	0.693	0.641	0.746	CLONAL	1	TRUE	1	0.412149544649687	3		449	794	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436469	110436469	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0005511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	246	647	0	ENST00000375856.3:c.1932C>A	p.Ser644Arg	p.S644R	ENST00000375856	NM_003749.2	644	agC/agA	1/2	0.303672731104484	3	FACETS	1	0.933	1	0.5	0.466	0.536	CLONAL	1	TRUE	1	0.412149544649687	3		647	1439	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348160	89348160	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1294	176	839	0	ENST00000301030.4:c.4790G>T	p.Arg1597Leu	p.R1597L	ENST00000301030	NM_001256183.1	1597	cGc/cTc	9/13	0.412149544649687	1	FACETS	0.461	0.423	0.501	0.461	0.423	0.501	SUBCLONAL	1	TRUE	0	0.412149544649687	1		839	1470	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0005511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1174	376	506	1	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.412149544649687	2		507	1550	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990655	7990655	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	230	600	0	ENST00000319144.4:c.106C>T	p.Gln36Ter	p.Q36*	ENST00000319144	NM_001139.2	36	Cag/Tag	1/15	1	2	FACETS	0.83	0.772	0.89	0.83	0.772	0.89	CLONAL	1	TRUE	1	0.412149544649687	2		600	1345	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676207	37676207	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0005511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	155	588	0	ENST00000447079.4:c.2964-2A>T		p.X988_splice	ENST00000447079	NM_015083.1	988			1	2	FACETS	0.655	0.598	0.715	0.655	0.598	0.715	SUBCLONAL	1	TRUE	1	0.412149544649687	2		588	1148	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41228521	41228521	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0005511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	140	649	0	ENST00000357654.3:c.4468G>C	p.Glu1490Gln	p.E1490Q	ENST00000357654	NM_007294.3	1490	Gaa/Caa	13/23	0.403231578185706	1	FACETS	0.505	0.458	0.553	0.505	0.458	0.553	SUBCLONAL	1	TRUE	0	0.412149544649687	1		649	1069	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7141810	7141810	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	358	669	0	ENST00000302850.5:c.2560G>T	p.Val854Phe	p.V854F	ENST00000302850	NM_000208.2	854	Gtt/Ttt	13/22	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.412149544649687	2		669	1390	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765555	41765555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1191232462	NA	P-0005511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	337	597	0	ENST00000301178.4:c.2431C>T	p.Pro811Ser	p.P811S	ENST00000301178	NM_021913.4	811	Cct/Tct	20/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.412149544649687	2		597	1379	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	203	540	0	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	1	2	FACETS	0.807	0.747	0.87	0.807	0.747	0.87	CLONAL	1	TRUE	1	0.412149544649687	2		540	1220	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031762	36031762	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0005511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	433	526	0	ENST00000358208.4:c.1591C>A	p.Gln531Lys	p.Q531K	ENST00000358208		531	Cag/Aag	12/12	0.277311864196332	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.412149544649687	3		526	1111	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514453	41514453	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0005511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	329	543	1	ENST00000373198.4:c.208C>G	p.Pro70Ala	p.P70A	ENST00000373198	NM_133170.3	70	Ccc/Gcc	2/32	0.277311864196332	3	FACETS	0.92	0.871	0.971	0.92	0.871	0.971	CLONAL	2	TRUE	1	0.412149544649687	3		544	1046	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037952	49037982	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTCCTCATGCTGTTCAGGAGGTAGGTAATTT	TTCCTCATGCTGTTCAGGAGGTAGGTAATTT	-	novel	NA	P-0005511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	67	701	0	ENST00000267163.4:c.2193_2211+12del		p.X731_splice	ENST00000267163	NM_000321.2	731		21/27	0.303672731104484	3	FACETS	0.468	0.406	0.536	0.234	0.203	0.268	SUBCLONAL	1	TRUE	1	0.412149544649687	3		701	838	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138452279	138452279	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	58	335	0	ENST00000289153.2:c.974A>T	p.His325Leu	p.H325L	ENST00000289153	NM_006219.2	325	cAt/cTt	6/22	0.198196400286673	5	FACETS	0.519	0.445	0.601	0.173	0.148	0.201	INDETERMINATE	1	TRUE	2	0.412149544649687	5		335	877	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755587	39755587	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005511-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	72	524	0	ENST00000288319.7:c.1178A>G	p.His393Arg	p.H393R	ENST00000288319	NM_182918.3	393	cAc/cGc	10/10	0.218353813417896	2	FACETS	0.315	0.274	0.359	0.157	0.137	0.18	INDETERMINATE	1	TRUE	0	0.412149544649687	2		524	1110	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	97	280	0				ENST00000310581	NM_198253.2	-/1132			0.105071086985832	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.691334149746184	0		280	323	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28903806	28903806	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	237	507	0	ENST00000282397.4:c.2653A>T	p.Ile885Phe	p.I885F	ENST00000282397	NM_002019.4	885	Att/Ttt	19/30	NA	2	FACETS	0.879	0.823	0.936			1	INDETERMINATE	1	TRUE	NA	0.691334149746184	2		507	780	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611258	100611258	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0005539-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	139	317	0	ENST00000308731.7:c.1350-2A>T		p.X450_splice	ENST00000308731	NM_000061.2	450			0.369218659641309	1	FACETS	0.581	0.533	0.63	0.581	0.533	0.63	INDETERMINATE	1	TRUE	0	0.691334149746184	1		317	453	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	211	280	0				ENST00000310581	NM_198253.2	-/1132			0.266865736845691	4	FACETS	0.999	0.932	1	0.999	0.932	1	CLONAL	3	TRUE	1	0.277790407395933	4		280	648	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15978896	15978896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	113	487	0	ENST00000268712.3:c.3622G>A	p.Gly1208Ser	p.G1208S	ENST00000268712	NM_006311.3	1208	Ggc/Agc	27/46	0.269600452590887	3	FACETS	0.943	0.847	1	0.471	0.423	0.522	CLONAL	1	TRUE	1	0.277790407395933	3		487	983	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59934586	59934586	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779629295	NA	P-0005540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	50	402	0	ENST00000259008.2:c.212C>T	p.Pro71Leu	p.P71L	ENST00000259008	NM_032043.2	71	cCa/cTa	4/20	0.254169368695218	4	FACETS	0.832	0.706	0.971	0.416	0.353	0.486	CLONAL	1	TRUE	2	0.277790407395933	4		402	553	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0005542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	115	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.915	0.827	1	0.915	0.827	1	CLONAL	1	TRUE	1	0.451274380035761	2		464	557	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0005542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	502	505	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.398770571997262	2	FACETS	0.944	0.906	0.982	0.944	0.906	0.982	CLONAL	2	TRUE	0	0.451274380035761	2		506	1179	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720659	89720660	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0005542-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	24	107	0	ENST00000371953.3:c.813dup	p.His272SerfsTer26	p.H272Sfs*26	ENST00000371953	NM_000314.4	270	-/T	8/9	0.451274380035761	1	FACETS	0.564	0.447	0.696	0.564	0.447	0.696	SUBCLONAL	1	TRUE	0	0.451274380035761	1		107	146	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005547-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	159	280	0				ENST00000310581	NM_198253.2	-/1132			0.565483411073812	6	FACETS	0.843	0.782	0.905	0.843	0.782	0.905	CLONAL	3	FALSE	3	0.847241111095508	6		280	400	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420014	41420014	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs200831045	NA	P-0005547-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	422	576	0	ENST00000373198.4:c.307A>G	p.Ile103Val	p.I103V	ENST00000373198	NM_133170.3	103	Atc/Gtc	3/32	0.605154668311616	5	FACETS	1	0.966	1	0.676	0.645	0.707	CLONAL	2	FALSE	2	0.847241111095508	5		576	1116	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624267	89624268	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GA	rs1057524874	NA	P-0005547-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	263	150	0	ENST00000371953.3:c.44_45dup	p.Tyr16AspfsTer9	p.Y16Dfs*9	ENST00000371953	NM_000314.4	14	agg/agGAg	1/9	0.78233388603905	3	FACETS	0.963	0.935	0.988	0.963	0.935	0.988	CLONAL	3	FALSE	0	0.847241111095508	3		150	306	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	72	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.35	2		280	408	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0005574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	88	558	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.958	0.851	1	0.958	0.851	1	CLONAL	1	TRUE	1	0.35	2		558	525	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041043	47041043	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1556779625	NA	P-0005574-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	155	430	0	ENST00000377604.3:c.1573C>T	p.Gln525Ter	p.Q525*	ENST00000377604	NM_001204468.1	525	Cag/Tag	14/24	1	2	FACETS	0.954	0.873	1	0.954	0.873	1	CLONAL	1	TRUE	1	0.35	2		430	928	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579377	7579377	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555934	NA	P-0005588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	314	464	1	ENST00000269305.4:c.310C>T	p.Gln104Ter	p.Q104*	ENST00000269305	NM_001126112.2	104	Cag/Tag	4/11	0.557159508629929	4	FACETS	1	0.988	1			1	CLONAL	4	FALSE	NA	0.688787072751814	4		465	373	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162735790	162735790	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0005588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	129	437	0	ENST00000367921.3:c.1100-1G>A		p.X367_splice	ENST00000367921	NM_006182.2	367			0.688787072751814	10	FACETS	0.832	0.754	0.914	0.277	0.251	0.305	CLONAL	2	FALSE	4	0.688787072751814	10		437	845	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55569976	55569976	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	107	408	0	ENST00000288135.5:c.843A>C	p.Arg281Ser	p.R281S	ENST00000288135	NM_000222.2	281	agA/agC	5/21	0.638493409875083	3	FACETS	1	0.975	1	0.614	0.557	0.674	CLONAL	1	FALSE	1	0.688787072751814	3		408	340	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920502	50920502	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	69	560	0	ENST00000440232.2:c.3194T>G	p.Leu1065Arg	p.L1065R	ENST00000440232	NM_002691.3	1065	cTg/cGg	26/27	NA	2	FACETS	1	0.933	1			1	INDETERMINATE	1	FALSE	NA	0.688787072751814	2		560	187	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653772	89653781	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	AAGTACTCAG	AAGTACTCAG	-	novel	NA	P-0005588-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	34	143	243	0	ENST00000371953.3:c.80-9_80del		p.X27_splice	ENST00000371953	NM_000314.4	27			0.688787072751814	6	FACETS	0.93	0.887	0.968			1	CLONAL	6	FALSE	NA	0.688787072751814	6		243	177	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0005609-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	210	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.613744522967813	2		464	641	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481402	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913355	NA	P-0005609-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	124	704	0	ENST00000288602.6:c.1406G>C	p.Gly469Ala	p.G469A	ENST00000288602	NM_004333.4	469	gGa/gCa	11/18	1	2	FACETS	0.397	0.358	0.437	0.397	0.358	0.437	SUBCLONAL	1	TRUE	1	0.613744522967813	2		704	1019	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0005609-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	294	471	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	0.947	0.892	1	0.947	0.892	1	CLONAL	1	TRUE	1	0.613744522967813	2		471	1012	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005616-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	24	280	0				ENST00000310581	NM_198253.2	-/1132			0.614418101741179	1	FACETS	0.637	0.512	0.772	0.637	0.512	0.772	SUBCLONAL	1	TRUE	0	0.614418101741179	1		280	85	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0005616-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	103	558	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.614418101741179	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.614418101741179	1		558	208	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0005616-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	110	471	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	0.298374898658149	4	FACETS	0.957	0.872	1	0.957	0.872	1	INDETERMINATE	2	TRUE	2	0.614418101741179	4		471	302	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	266	280	0				ENST00000310581	NM_198253.2	-/1132			0.382473753933813	5	FACETS	1	0.987	1			1	CLONAL	2	TRUE	NA	0.382473753933813	5		280	932	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247525	71247525	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005641-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	112	245	1	ENST00000318789.4:c.8A>T	p.Gln3Leu	p.Q3L	ENST00000318789	NM_032682.5	3	cAa/cTa	6/21	0.317939109065213	3	FACETS	1	0.979	1	0.658	0.594	0.725	CLONAL	1	TRUE	1	0.382473753933813	3		246	530	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0005678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	157	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.794	0.731	0.859	0.794	0.731	0.859	SUBCLONAL	1	TRUE	1	0.69	2		464	573	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0005678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	244	354	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.69	2		354	660	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0005687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	310	464	0				ENST00000310581	NM_198253.2	-/1132			0.468749483656307	6	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	3	TRUE	3	0.84556680525359	6		464	628	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0005687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1973	191	449	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	0.84556680525359	13	FACETS	1	0.979	1			1	CLONAL	1	TRUE	NA	0.84556680525359	13		449	2164	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395110	139395110	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005687-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	228	611	0	ENST00000277541.6:c.5828C>T	p.Ala1943Val	p.A1943V	ENST00000277541	NM_017617.3	1943	gCc/gTc	31/34	0.84556680525359	2	FACETS	0.963	0.905	1	0.482	0.452	0.511	CLONAL	1	TRUE	0	0.84556680525359	2		611	560	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874395	151874395	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	167	425	0	ENST00000262189.6:c.8143G>T	p.Glu2715Ter	p.E2715*	ENST00000262189	NM_170606.2	2715	Gaa/Taa	38/59	1	2	FACETS	0.897	0.826	0.971	0.897	0.826	0.971	CLONAL	1	TRUE	1	0.50046706540833	2		425	744	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699383	47699383	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	227	489	0	ENST00000347630.2:c.125G>A	p.Ser42Asn	p.S42N	ENST00000347630	NM_001007230.1	42	aGc/aAc	4/11	1	2	FACETS	0.938	0.875	1	0.938	0.875	1	CLONAL	1	TRUE	1	0.50046706540833	2		489	967	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793265	33793265	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1315626965	NA	P-0005692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	112	269	0	ENST00000498907.2:c.56T>A	p.Leu19Gln	p.L19Q	ENST00000498907	NM_004364.3	19	cTg/cAg	1/1	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.50046706540833	2		269	447	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27009121	27009133	+	frameshift_variant	Frame_Shift_Del	DEL	CCCGACCCCGACC	CCCGACCCCGACC	-	novel	NA	P-0005692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	53	259	0	ENST00000335756.4:c.61_73del	p.Thr21AlafsTer9	p.T21Afs*9	ENST00000335756	NM_001809.3	19	agCCCGACCCCGACC/ag	1/5	1	2	FACETS	0.603	0.517	0.697	0.603	0.517	0.697	SUBCLONAL	1	TRUE	1	0.50046706540833	2		259	351	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061137	38061197	+	protein_altering_variant	In_Frame_Del	DEL	GCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGC	GCCCCCGCTTCCGCTCCCGCCCCCGCCGCCGGCCCCCGGCTGCTTCTCGCACTTGAAGCGC	T	novel	NA	P-0005692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	201	112	0	ENST00000250448.2:c.792_852delinsA	p.Arg265_Gly284del	p.R265_G284del	ENST00000250448	NM_004496.3	264	aaGCGCTTCAAGTGCGAGAAGCAGCCGGGGGCCGGCGGCGGGGGCGGGAGCGGAAGCGGGGGC/aaA	2/2	1	2	FACETS	0.861	0.817	0.903	1	0.995	1	CLONAL	3	TRUE	1	0.50046706540833	2		112	311	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925318	131925324	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTAGAA	TTTAGAA	-	novel	NA	P-0005692-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	97	248	0	ENST00000265335.6:c.1246-4_1248del		p.X416_splice	ENST00000265335		416		9/25	1	2	FACETS	0.827	0.74	0.917	0.827	0.74	0.917	CLONAL	1	TRUE	1	0.50046706540833	2		248	469	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	119	280	0				ENST00000310581	NM_198253.2	-/1132			0.143350658785342	4	FACETS	0.99	0.9	1	0.99	0.9	1	INDETERMINATE	2	TRUE	2	0.356853103630072	4		280	457	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729949	41729949	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1165688714	NA	P-0005725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	287	1725	1	ENST00000242208.4:c.580G>A	p.Glu194Lys	p.E194K	ENST00000242208	NM_002192.2	194	Gaa/Aaa	3/3	0.356853103630072	6	FACETS	1	0.952	1	0.508	0.477	0.541	CLONAL	2	TRUE	2	0.356853103630072	6		1726	1356	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120845	94120845	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1465346253	NA	P-0005725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	192	1499	1	ENST00000369303.4:c.206G>A	p.Arg69Gln	p.R69Q	ENST00000369303	NM_004440.3	69	cGa/cAa	3/17	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.356853103630072	2		1500	769	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841505	156841505	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145222195	NA	P-0005725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	242	1289	1	ENST00000524377.1:c.808G>A	p.Asp270Asn	p.D270N	ENST00000524377	NM_002529.3	270	Gat/Aat	7/17	0.326680289479371	4	FACETS	0.818	0.763	0.874	0.818	0.763	0.874	CLONAL	2	TRUE	2	0.356853103630072	4		1290	1125	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508728	148508728	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs267601395	NA	P-0005725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	412	454	0	ENST00000320356.2:c.1936T>A	p.Tyr646Asn	p.Y646N	ENST00000320356	NM_004456.4	646	Tac/Aac	16/20	0.356853103630072	6	FACETS	1	0.98	1	0.789	0.751	0.827	CLONAL	3	TRUE	2	0.356853103630072	6		454	1254	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556193	29556193	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555614261	NA	P-0005725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	157	461	2	ENST00000356175.3:c.2560C>T	p.Gln854Ter	p.Q854*	ENST00000356175	NM_000267.3	854	Cag/Tag	21/57	0.263741048167138	5	FACETS	0.938	0.872	1	0.751	0.697	0.804	CLONAL	4	TRUE	0	0.356853103630072	5		463	360	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416634	29416634	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	253	926	0	ENST00000389048.3:c.4319C>T	p.Ala1440Val	p.A1440V	ENST00000389048	NM_004304.4	1440	gCc/gTc	29/29	0.356853103630072	3	FACETS	0.79	0.74	0.843	0.79	0.74	0.843	SUBCLONAL	2	TRUE	1	0.356853103630072	3		926	1057	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641217	12641217	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	251	1331	3	ENST00000251849.4:c.1081G>A	p.Gly361Arg	p.G361R	ENST00000251849	NM_002880.3	361	Gga/Aga	10/17	0.345033950581199	4	FACETS	0.865	0.809	0.923	0.865	0.809	0.923	CLONAL	2	TRUE	2	0.356853103630072	4		1334	1103	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623250	52623250	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	194	820	0	ENST00000394830.3:c.2801C>T	p.Ser934Phe	p.S934F	ENST00000394830	NM_018313.4	934	tCc/tTc	19/30	0.345033950581199	4	FACETS	0.921	0.854	0.99	0.921	0.854	0.99	CLONAL	2	TRUE	2	0.356853103630072	4		820	801	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238564	142238564	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	271	966	0	ENST00000350721.4:c.4329G>A	p.Trp1443Ter	p.W1443*	ENST00000350721	NM_001184.3	1443	tgG/tgA	24/47	0.345033950581199	4	FACETS	0.912	0.855	0.97	0.912	0.855	0.97	CLONAL	2	TRUE	2	0.356853103630072	4		966	1130	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191374	185191374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	225	980	0	ENST00000265026.3:c.2255G>A	p.Gly752Glu	p.G752E	ENST00000265026	NM_004721.4	752	gGg/gAg	11/14	0.345033950581199	4	FACETS	0.984	0.918	1	0.984	0.918	1	CLONAL	2	TRUE	2	0.356853103630072	4		980	869	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607225	189607225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	170	1257	0	ENST00000264731.3:c.1604C>T	p.Ser535Phe	p.S535F	ENST00000264731	NM_003722.4	535	tCc/tTc	12/14	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.356853103630072	2		1257	857	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607257	189607257	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	150	1140	0	ENST00000264731.3:c.1636G>A	p.Asp546Asn	p.D546N	ENST00000264731	NM_003722.4	546	Gat/Aat	12/14	NA	2	FACETS	1	0.955	1			1	INDETERMINATE	1	TRUE	NA	0.356853103630072	2		1140	787	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873724	35873724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148165103	NA	P-0005725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	148	1038	3	ENST00000303115.3:c.680G>A	p.Arg227Lys	p.R227K	ENST00000303115	NM_002185.3	227	aGa/aAa	5/8	0.143350658785342	4	FACETS	0.834	0.763	0.907	0.834	0.763	0.907	INDETERMINATE	2	TRUE	2	0.356853103630072	4		1041	675	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721964	176721964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	229	853	0	ENST00000439151.2:c.7595C>T	p.Ser2532Leu	p.S2532L	ENST00000439151	NM_022455.4	2532	tCa/tTa	23/23	0.326680289479371	4	FACETS	0.955	0.891	1	0.955	0.891	1	CLONAL	2	TRUE	2	0.356853103630072	4		853	912	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056608	26056608	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	126	388	0	ENST00000343677.2:c.49A>G	p.Lys17Glu	p.K17E	ENST00000343677	NM_005319.3	17	Aag/Gag	1/1	0.356853103630072	8	FACETS	0.867	0.788	0.95			1	CLONAL	3	TRUE	NA	0.356853103630072	8		388	562	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708106	117708106	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0005725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	174	1161	0	ENST00000368508.3:c.2071T>A	p.Leu691Ile	p.L691I	ENST00000368508	NM_002944.2	691	Tta/Ata	14/43	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.356853103630072	2		1161	713	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975505	13975505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	133	547	0	ENST00000405192.2:c.382C>T	p.Pro128Ser	p.P128S	ENST00000405192	NM_001163147.1	128	Cca/Tca	7/12	0.356853103630072	6	FACETS	1	0.942	1	0.523	0.476	0.571	CLONAL	2	TRUE	2	0.356853103630072	6		547	611	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211055	55211055	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866460345	NA	P-0005725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	356	1231	0	ENST00000275493.2:c.298C>T	p.Pro100Ser	p.P100S	ENST00000275493	NM_005228.3	100	Cct/Tct	3/28	0.166060916319952	5	FACETS	0.897	0.854	0.94	0.897	0.854	0.94	INDETERMINATE	4	TRUE	1	0.356853103630072	5		1231	854	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374393	81374393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	125	1141	2	ENST00000222390.5:c.669G>A	p.Met223Ile	p.M223I	ENST00000222390	NM_000601.4	223	atG/atA	6/18	0.356853103630072	5	FACETS	1	0.984	1	0.481	0.436	0.529	CLONAL	1	TRUE	2	0.356853103630072	5		1143	745	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500963	8500963	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141920894	NA	P-0005725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	131	1146	2	ENST00000356435.5:c.1919G>A	p.Gly640Asp	p.G640D	ENST00000356435		640	gGc/gAc	13/35	0.356853103630072	0	FACETS	0.984	0.899	1			1	CLONAL	1	TRUE	0	0.356853103630072	0		1148	480	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94201013	94201013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	186	1098	0	ENST00000323929.3:c.1064C>T	p.Ser355Phe	p.S355F	ENST00000323929	NM_005591.3	355	tCt/tTt	10/20	0.262083871430155	4	FACETS	0.757	0.699	0.817	0.757	0.699	0.817	SUBCLONAL	2	TRUE	2	0.356853103630072	4		1098	934	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343285	118343285	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	139	843	0	ENST00000534358.1:c.1411C>T	p.Gln471Ter	p.Q471*	ENST00000534358	NM_005933.3	471	Caa/Taa	3/36	0.266478716796499	3	FACETS	0.922	0.844	1	0.614	0.563	0.668	CLONAL	2	TRUE	0	0.356853103630072	3		843	498	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95566145	95566145	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	167	692	0	ENST00000393063.1:c.4178A>G	p.Asn1393Ser	p.N1393S	ENST00000393063	NM_030621.3	1393	aAc/aGc	23/28	0.262083871430155	4	FACETS	0.962	0.887	1	0.962	0.887	1	CLONAL	2	TRUE	2	0.356853103630072	4		692	660	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996135	73996135	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs548667844	NA	P-0005725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	307	1163	0	ENST00000318443.5:c.869C>T	p.Thr290Ile	p.T290I	ENST00000318443	NM_001024736.1	290	aCc/aTc	5/10	0.262083871430155	4	FACETS	0.972	0.916	1	0.972	0.916	1	CLONAL	2	TRUE	2	0.356853103630072	4		1163	1201	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139637	202139637	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0005725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	233	1197	0	ENST00000358485.4:c.799del	p.Ile267SerfsTer21	p.I267Sfs*21	ENST00000358485	NM_001080125.1	266	acA/ac	6/9	0.160263386253561	3	FACETS	0.923	0.862	0.984			1	INDETERMINATE	2	TRUE	NA	0.356853103630072	3		1197	834	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393567	139393567	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0005725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	243	968	1	ENST00000277541.6:c.6079del	p.Leu2027TrpfsTer12	p.L2027Wfs*12	ENST00000277541	NM_017617.3	2027	Ctg/tg	32/34	0.324260711917209	2	FACETS	0.789	0.739	0.841	0.789	0.739	0.841	SUBCLONAL	2	TRUE	0	0.356853103630072	2		969	863	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	140	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.944	0.875	1	1	0.994	1	CLONAL	6	TRUE	1	0.162055013062198	2		280	305	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs786201057	NA	P-0005748-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	9	518	2	ENST00000269305.4:c.374C>T	p.Thr125Met	p.T125M	ENST00000269305	NM_001126112.2	125	aCg/aTg	4/11	1	2	FACETS	0.319	0.21	0.459	0.319	0.21	0.459	SUBCLONAL	1	TRUE	1	0.162055013062198	2		520	348	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005776-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	38	280	0				ENST00000310581	NM_198253.2	-/1132			0.360500771176566	3	FACETS	0.862	0.718	1	0.431	0.359	0.51	CLONAL	1	TRUE	1	0.452448599944534	3		280	239	SUCCESS
APC	324	MSKCC	GRCh37	5	112175752	112175752	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1114167577	NA	P-0005776-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	99	335	0	ENST00000257430.4:c.4463del	p.Leu1488TyrfsTer19	p.L1488Yfs*19	ENST00000257430	NM_000038.5	1487	acT/ac	16/16	0.231958338843857	4	FACETS	0.96	0.866	1	0.96	0.866	1	INDETERMINATE	2	TRUE	2	0.452448599944534	4		335	331	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs17851045	NA	P-0005776-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	148	439	0	ENST00000311936.3:c.183A>C	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caC	3/5	0.413276187942095	3	FACETS	0.893	0.823	0.966	0.893	0.823	0.966	CLONAL	2	TRUE	1	0.452448599944534	3		439	449	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170135	32170135	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542331250	NA	P-0005776-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	50	481	0	ENST00000375023.3:c.3473G>A	p.Arg1158Gln	p.R1158Q	ENST00000375023	NM_004557.3	1158	cGa/cAa	21/30	0.452448599944534	4	FACETS	0.677	0.575	0.789	0.226	0.191	0.263	SUBCLONAL	1	TRUE	1	0.452448599944534	4		481	474	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907098	101907098	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1554701911	NA	P-0005776-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	133	468	1	ENST00000374994.4:c.1058G>T	p.Gly353Val	p.G353V	ENST00000374994	NM_004612.2	353	gGa/gTa	6/9	0.360500771176566	3	FACETS	1	0.986	1	0.727	0.664	0.792	CLONAL	1	TRUE	1	0.452448599944534	3		469	496	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727077	40727077	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005776-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	38	500	0	ENST00000373198.4:c.3887A>T	p.Glu1296Val	p.E1296V	ENST00000373198	NM_133170.3	1296	gAg/gTg	28/32	0.452448599944534	6	FACETS	0.453	0.373	0.543	0.113	0.093	0.136	SUBCLONAL	1	TRUE	2	0.452448599944534	6		500	706	SUCCESS
APC	324	MSKCC	GRCh37	5	112173765	112173781	+	frameshift_variant	Frame_Shift_Del	DEL	ATTTGAATACTACAGTG	ATTTGAATACTACAGTG	-	novel	NA	P-0005776-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	62	406	0	ENST00000257430.4:c.2474_2490del	p.Tyr825PhefsTer13	p.Y825Ffs*13	ENST00000257430	NM_000038.5	825	tATTTGAATACTACAGTG/t	16/16	0.231958338843857	4	FACETS	1	0.878	1	0.506	0.439	0.579	INDETERMINATE	1	TRUE	2	0.452448599944534	4		406	393	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023137	150023141	+	frameshift_variant	Frame_Shift_Del	DEL	AGATA	AGATA	-	novel	NA	P-0005776-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	102	567	0	ENST00000253339.5:c.122_126del	p.Leu41Ter	p.L41*	ENST00000253339		41	tTATCT/t	1/7	0.452448599944534	4	FACETS	1	0.947	1	0.364	0.326	0.404	CLONAL	1	TRUE	1	0.452448599944534	4		567	600	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005852-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	83	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.793	0.706	0.885	0.793	0.706	0.885	SUBCLONAL	1	TRUE	1	0.63211880803249	2		280	331	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0005852-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1424	3509	910	2	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.63211880803249	10	FACETS	0.993	0.981	1			1	CLONAL	8	TRUE	NA	0.63211880803249	10		912	4933	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439798	51439798	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0005852-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	140	143	1	ENST00000262662.1:c.364del	p.Leu122TrpfsTer2	p.L122Wfs*2	ENST00000262662		121	ttC/tt	4/4	1	2	FACETS	0.955	0.876	1	0.955	0.876	1	CLONAL	1	TRUE	1	0.63211880803249	2		144	464	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589535	67589535	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	rs1403833564	NA	P-0005852-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	150	213	0	ENST00000274335.5:c.1300-2A>G		p.X434_splice	ENST00000274335		434			1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.63211880803249	2		213	463	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1271271	1271271	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199422301	NA	P-0005852-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	158	232	0	ENST00000310581.5:c.2431C>T	p.Arg811Cys	p.R811C	ENST00000310581	NM_198253.2	811	Cgc/Tgc	8/16	1	2	FACETS	0.863	0.795	0.934	0.863	0.795	0.934	CLONAL	1	TRUE	1	0.63211880803249	2		232	579	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923266	131923266	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs774666779	NA	P-0005852-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	97	166	0	ENST00000265335.6:c.769G>T	p.Glu257Ter	p.E257*	ENST00000265335		257	Gaa/Taa	6/25	1	2	FACETS	0.905	0.815	0.999	0.905	0.815	0.999	CLONAL	1	TRUE	1	0.63211880803249	2		166	339	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89712018	89712018	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0005852-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	32	99	0	ENST00000371953.3:c.634+2T>A		p.X212_splice	ENST00000371953	NM_000314.4	212			0.63211880803249	1	FACETS	0.721	0.602	0.847	0.721	0.602	0.847	SUBCLONAL	1	TRUE	0	0.63211880803249	1		99	96	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280037	18280037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772782368	NA	P-0005852-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	79	99	0	ENST00000222254.8:c.2120C>T	p.Ala707Val	p.A707V	ENST00000222254	NM_005027.3	707	gCg/gTg	16/16	0.63211880803249	3	FACETS	1	0.932	1	0.534	0.474	0.597	CLONAL	1	TRUE	1	0.63211880803249	3		99	308	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054593	13054595	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs761039756	NA	P-0005852-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2653	526	713	2	ENST00000316448.5:c.1122_1124del	p.Lys375del	p.K375del	ENST00000316448	NM_004343.3	374	AAG/-	9/9	0.63211880803249	3	FACETS	0.689	0.657	0.722	0.344	0.328	0.361	SUBCLONAL	1	TRUE	1	0.63211880803249	3		715	3179	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	162	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.983	1	1	0.993	1	CLONAL	2	TRUE	1	0.22	2		280	590	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0005866-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	165	500	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	0.231137310497542	1	FACETS	1	0.978	1	1	0.994	1	CLONAL	3	TRUE	0	0.22	1		500	394	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005870-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	112	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.444203780785751	2		280	430	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059200	47059201	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTCA	novel	NA	P-0005870-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	209	382	0	ENST00000409792.3:c.7457_7460dup	p.Pro2488GlufsTer7	p.P2488Efs*7	ENST00000409792	NM_014159.6	2487	aac/aaTGAAc	20/21	1	2	FACETS	0.974	0.905	1	0.974	0.905	1	CLONAL	1	TRUE	1	0.444203780785751	2		382	966	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005877-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	105	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.851	0.766	0.941	0.851	0.766	0.941	CLONAL	1	TRUE	1	0.490345315561547	2		280	503	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638917	176638917	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749199217	NA	P-0005877-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	229	417	1	ENST00000439151.2:c.3517C>T	p.Arg1173Cys	p.R1173C	ENST00000439151	NM_022455.4	1173	Cgc/Tgc	5/23	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.490345315561547	2		418	856	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	115	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.734817441600827	2		280	296	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0005882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	329	550	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.72107151576023	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.734817441600827	1		550	528	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435728	116435728	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005882-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	93	318	0	ENST00000397752.3:c.3818T>C	p.Leu1273Pro	p.L1273P	ENST00000397752	NM_000245.2	1273	cTc/cCc	20/21	0.734817441600827	3	FACETS	0.481	0.428	0.538	0.241	0.214	0.27	SUBCLONAL	1	TRUE	1	0.734817441600827	3		318	719	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	46	280	0				ENST00000310581	NM_198253.2	-/1132			0.212020697479522	1	FACETS	0.604	0.516	0.699	0.604	0.516	0.699	INDETERMINATE	1	TRUE	0	0.576405048445725	1		280	188	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245843	46245843	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	190	421	1	ENST00000334344.6:c.3937C>T	p.Gln1313Ter	p.Q1313*	ENST00000334344	NM_152641.2	1313	Caa/Taa	15/21	0.178716202223061	4	FACETS	1	0.988	1	0.66	0.611	0.711	INDETERMINATE	1	TRUE	2	0.576405048445725	4		422	787	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528489	29528489	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764079291	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	218	637	0	ENST00000356175.3:c.1246C>T	p.Arg416Ter	p.R416*	ENST00000356175	NM_000267.3	416	Cga/Tga	11/57	0.247826890931603	3	FACETS	0.998	0.929	1	0.499	0.464	0.535	INDETERMINATE	1	TRUE	1	0.576405048445725	3		637	976	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339680	116339680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	293	288	0	ENST00000397752.3:c.542G>A	p.Gly181Glu	p.G181E	ENST00000397752	NM_000245.2	181	gGa/gAa	2/21	0.576405048445725	3	FACETS	0.976	0.925	1	0.976	0.925	1	CLONAL	2	TRUE	1	0.576405048445725	3		288	671	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032215	26032215	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs984289609	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	284	435	0	ENST00000244661.2:c.74C>T	p.Ala25Val	p.A25V	ENST00000244661	NM_003537.3	25	gCt/gTt	1/1	0.373192694263023	6	FACETS	1	0.98	1	0.544	0.512	0.577	CLONAL	2	TRUE	2	0.576405048445725	6		435	975	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076812	72076812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	144	462	0	ENST00000357731.5:c.685G>A	p.Glu229Lys	p.E229K	ENST00000357731	NM_173808.2	229	Gaa/Aaa	5/7	0.187150157440751	3	FACETS	1	0.951	1	0.528	0.483	0.574	INDETERMINATE	1	TRUE	1	0.576405048445725	3		462	610	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939048	36939048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	208	629	1	ENST00000361632.4:c.661C>T	p.Pro221Ser	p.P221S	ENST00000361632		221	Ccc/Tcc	5/16	0.187150157440751	3	FACETS	1	0.988	1	0.636	0.592	0.681	INDETERMINATE	1	TRUE	1	0.576405048445725	3		630	731	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313277	65313277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	214	503	2	ENST00000342505.4:c.1837G>A	p.Glu613Lys	p.E613K	ENST00000342505	NM_002227.2	613	Gaa/Aaa	13/25	0.187150157440751	3	FACETS	1	0.977	1	0.556	0.517	0.596	INDETERMINATE	1	TRUE	1	0.576405048445725	3		505	860	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841545	156841545	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	131	332	0	ENST00000524377.1:c.848C>T	p.Ser283Phe	p.S283F	ENST00000524377	NM_002529.3	283	tCc/tTc	7/17	0.576405048445725	3	FACETS	0.911	0.828	0.997	0.455	0.414	0.499	CLONAL	1	TRUE	1	0.576405048445725	3		332	643	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086130	16086130	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs984467548	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	126	345	3	ENST00000281043.3:c.1306G>A	p.Glu436Lys	p.E436K	ENST00000281043	NM_005378.4	436	Gag/Aag	3/3	NA	2	FACETS	0.838	0.762	0.916			1	INDETERMINATE	1	TRUE	NA	0.576405048445725	2		348	522	SUCCESS
ALK	238	MSKCC	GRCh37	2	29497971	29497971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	147	407	0	ENST00000389048.3:c.2035C>T	p.Pro679Ser	p.P679S	ENST00000389048	NM_004304.4	679	Cct/Tct	11/29	1	2	FACETS	0.876	0.804	0.952	0.876	0.804	0.952	CLONAL	1	TRUE	1	0.576405048445725	2		407	582	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705547	47705547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553369748	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	245	471	0	ENST00000233146.2:c.2347C>T	p.His783Tyr	p.H783Y	ENST00000233146	NM_000251.2	783	Cat/Tat	14/16	0.247826890931603	3	FACETS	1	0.99	1	0.64	0.6	0.682	INDETERMINATE	1	TRUE	1	0.576405048445725	3		471	855	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248683	212248683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	137	374	0	ENST00000342788.4:c.3584C>T	p.Pro1195Leu	p.P1195L	ENST00000342788	NM_005235.2	1195	cCa/cTa	28/28	0.247826890931603	3	FACETS	0.891	0.812	0.974	0.446	0.406	0.487	INDETERMINATE	1	TRUE	1	0.576405048445725	3		374	687	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537981	212537981	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs535202189	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	243	331	0	ENST00000342788.4:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000342788	NM_005235.2	542	Gaa/Aaa	14/28	0.247826890931603	3	FACETS	0.809	0.76	0.859	0.809	0.76	0.859	INDETERMINATE	2	TRUE	1	0.576405048445725	3		331	671	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259389	89259389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	205	639	1	ENST00000336596.2:c.533G>A	p.Gly178Glu	p.G178E	ENST00000336596	NM_005233.5	178	gGa/gAa	3/17	0.516326676428998	3	FACETS	0.762	0.706	0.821	0.381	0.353	0.411	SUBCLONAL	1	TRUE	1	0.576405048445725	3		640	1202	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445074	89445074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	164	426	0	ENST00000336596.2:c.1394G>A	p.Gly465Glu	p.G465E	ENST00000336596	NM_005233.5	465	gGg/gAg	6/17	0.516326676428998	3	FACETS	0.956	0.879	1	0.478	0.439	0.518	CLONAL	1	TRUE	1	0.576405048445725	3		426	767	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528606	89528606	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	164	368	0	ENST00000336596.2:c.2906T>A	p.Ile969Asn	p.I969N	ENST00000336596	NM_005233.5	969	aTt/aAt	17/17	0.516326676428998	3	FACETS	1	0.947	1	0.518	0.477	0.561	CLONAL	1	TRUE	1	0.576405048445725	3		368	707	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749400	41749400	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1302196737	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	65	286	0	ENST00000226382.2:c.395C>T	p.Ala132Val	p.A132V	ENST00000226382	NM_003924.3	132	gCc/gTc	2/3	0.18116474644766	2	FACETS	0.656	0.572	0.745	0.328	0.286	0.373	INDETERMINATE	1	TRUE	0	0.576405048445725	2		286	344	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155629	106155629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	136	327	0	ENST00000380013.4:c.530C>T	p.Pro177Leu	p.P177L	ENST00000380013	NM_001127208.2	177	cCa/cTa	3/11	0.187150157440751	3	FACETS	1	0.977	1	0.597	0.546	0.65	INDETERMINATE	1	TRUE	1	0.576405048445725	3		327	509	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908113	41908113	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	233	388	0	ENST00000372991.4:c.409T>G	p.Leu137Val	p.L137V	ENST00000372991	NM_001760.3	137	Ttg/Gtg	2/5	0.576405048445725	3	FACETS	0.824	0.773	0.875	0.824	0.773	0.875	CLONAL	2	TRUE	1	0.576405048445725	3		388	632	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793766	89793766	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	160	265	0	ENST00000336032.3:c.835T>C	p.Tyr279His	p.Y279H	ENST00000336032	NM_006813.2	279	Tat/Cat	2/2	0.576405048445725	3	FACETS	0.852	0.782	0.926	0.426	0.391	0.463	CLONAL	1	TRUE	1	0.576405048445725	3		265	839	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677869	117677869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	154	352	2	ENST00000368508.3:c.4064C>T	p.Ala1355Val	p.A1355V	ENST00000368508	NM_002944.2	1355	gCc/gTc	25/43	0.576405048445725	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.576405048445725	1		354	380	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641194	93641194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	142	361	1	ENST00000375746.1:c.1540G>A	p.Gly514Arg	p.G514R	ENST00000375746	NM_001174167.1	514	Gga/Aga	11/14	1	2	FACETS	0.792	0.724	0.863	0.792	0.724	0.863	SUBCLONAL	1	TRUE	1	0.576405048445725	2		362	622	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650908	93650908	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs761206068	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	100	278	0	ENST00000375746.1:c.1834G>A	p.Asp612Asn	p.D612N	ENST00000375746	NM_001174167.1	612	Gat/Aat	13/14	1	2	FACETS	0.805	0.724	0.891	0.805	0.724	0.891	CLONAL	1	TRUE	1	0.576405048445725	2		278	431	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70441204	70441204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	169	409	0	ENST00000373644.4:c.4873C>T	p.Pro1625Ser	p.P1625S	ENST00000373644	NM_030625.2	1625	Cca/Tca	9/12	1	2	FACETS	0.819	0.755	0.885	0.819	0.755	0.885	CLONAL	1	TRUE	1	0.576405048445725	2		409	716	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135691	64135691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151034403	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	119	409	0	ENST00000334205.4:c.1159C>T	p.Arg387Trp	p.R387W	ENST00000334205	NM_003942.2	387	Cgg/Tgg	10/17	0.539038942192467	3	FACETS	0.847	0.766	0.932	0.423	0.383	0.466	CLONAL	1	TRUE	1	0.576405048445725	3		409	628	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200421	67200421	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	236	294	0	ENST00000312629.5:c.617-2A>C		p.X206_splice	ENST00000312629	NM_003952.2	206			0.539038942192467	3	FACETS	0.819	0.769	0.87	0.819	0.769	0.87	CLONAL	2	TRUE	1	0.576405048445725	3		294	644	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111957636	111957636	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1440670464	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	219	536	0	ENST00000375549.3:c.5C>T	p.Ala2Val	p.A2V	ENST00000375549	NM_003002.3	2	gCg/gTg	1/4	0.497298805796352	1	FACETS	0.783	0.731	0.835	0.783	0.731	0.835	SUBCLONAL	1	TRUE	0	0.576405048445725	1		536	691	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219243	133219243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147467247	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	116	439	1	ENST00000320574.5:c.4801C>T	p.Pro1601Ser	p.P1601S	ENST00000320574	NM_006231.2	1601	Cct/Tct	37/49	1	2	FACETS	0.975	0.885	1	0.975	0.885	1	CLONAL	1	TRUE	1	0.576405048445725	2		440	413	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008066	29008066	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	152	367	0	ENST00000282397.4:c.703A>G	p.Ser235Gly	p.S235G	ENST00000282397	NM_002019.4	235	Agc/Ggc	6/30	NA	2	FACETS	0.707	0.648	0.769			1	INDETERMINATE	1	TRUE	NA	0.576405048445725	2		367	746	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95577779	95577779	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	248	441	0	ENST00000393063.1:c.2131C>T	p.His711Tyr	p.H711Y	ENST00000393063	NM_030621.3	711	Cat/Tat	15/28	1	2	FACETS	0.872	0.816	0.93	0.872	0.816	0.93	CLONAL	1	TRUE	1	0.576405048445725	2		441	987	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423581	88423581	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	320	476	0	ENST00000360948.2:c.2254G>A	p.Asp752Asn	p.D752N	ENST00000360948	NM_001012338.2	752	Gat/Aat	18/19	0.576405048445725	3	FACETS	0.915	0.868	0.962	0.915	0.868	0.962	CLONAL	2	TRUE	1	0.576405048445725	3		476	782	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30134458	30134458	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1044163469	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	115	404	0	ENST00000263025.4:c.73C>T	p.Pro25Ser	p.P25S	ENST00000263025	NM_002746.2	25	Ccg/Tcg	1/9	1	2	FACETS	0.694	0.627	0.764	0.694	0.627	0.764	SUBCLONAL	1	TRUE	1	0.576405048445725	2		404	575	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827750	72827750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	202	573	1	ENST00000268489.5:c.8831C>T	p.Pro2944Leu	p.P2944L	ENST00000268489	NM_006885.3	2944	cCt/cTt	9/10	1	2	FACETS	0.893	0.83	0.958	0.893	0.83	0.958	CLONAL	1	TRUE	1	0.576405048445725	2		574	785	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980052	7980052	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	109	397	0	ENST00000319144.4:c.1285C>T	p.Pro429Ser	p.P429S	ENST00000319144	NM_001139.2	429	Ccc/Tcc	10/15	0.247826890931603	3	FACETS	1	0.924	1	0.514	0.464	0.566	INDETERMINATE	1	TRUE	1	0.576405048445725	3		397	474	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62008701	62008701	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	359	431	0	ENST00000392795.3:c.115C>T	p.Pro39Ser	p.P39S	ENST00000392795	NM_001039933.1	39	Ccc/Tcc	2/6	0.576405048445725	4	FACETS	1	0.991	1	0.774	0.737	0.811	CLONAL	2	TRUE	1	0.576405048445725	4		431	846	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244295	5244295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1054047470	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	174	443	1	ENST00000357368.4:c.1187C>T	p.Ser396Leu	p.S396L	ENST00000357368	NM_002850.3	396	tCg/tTg	11/38	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.576405048445725	2		444	567	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166264	7166264	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	186	501	2	ENST00000302850.5:c.1762C>T	p.Gln588Ter	p.Q588*	ENST00000302850	NM_000208.2	588	Cag/Tag	8/22	1	2	FACETS	0.994	0.922	1	0.994	0.922	1	CLONAL	1	TRUE	1	0.576405048445725	2		503	649	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10266562	10266562	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	189	481	0	ENST00000340748.4:c.1411G>T	p.Gly471Ter	p.G471*	ENST00000340748		471	Gga/Tga	18/40	1	2	FACETS	0.879	0.815	0.946	0.879	0.815	0.946	CLONAL	1	TRUE	1	0.576405048445725	2		481	746	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292483	15292483	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	152	480	1	ENST00000263388.2:c.2696G>A	p.Gly899Asp	p.G899D	ENST00000263388	NM_000435.2	899	gGc/gAc	17/33	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.576405048445725	2		481	520	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17947943	17947943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	78	387	1	ENST00000458235.1:c.1781G>A	p.Gly594Glu	p.G594E	ENST00000458235	NM_000215.3	594	gGa/gAa	13/24	1	2	FACETS	0.728	0.643	0.817	0.728	0.643	0.817	SUBCLONAL	1	TRUE	1	0.576405048445725	2		388	372	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47729959	47729959	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	92	171	0	ENST00000449228.1:c.430C>T	p.Gln144Ter	p.Q144*	ENST00000449228	NM_001127240.2	144	Cag/Tag	3/4	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.576405048445725	2		171	280	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546886	9546886	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	130	440	0	ENST00000353224.5:c.1136A>C	p.Lys379Thr	p.K379T	ENST00000353224	NM_177990.2	379	aAa/aCa	5/10	1	2	FACETS	0.956	0.873	1	0.956	0.873	1	CLONAL	1	TRUE	1	0.576405048445725	2		440	472	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39728736	39728736	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	125	246	0	ENST00000361337.2:c.1016G>A	p.Gly339Glu	p.G339E	ENST00000361337	NM_003286.2	339	gGa/gAa	12/21	1	2	FACETS	0.786	0.714	0.861	0.786	0.714	0.861	SUBCLONAL	1	TRUE	1	0.576405048445725	2		246	552	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980850	40980850	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752620539	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	106	415	0	ENST00000373198.4:c.1636C>T	p.Arg546Trp	p.R546W	ENST00000373198	NM_133170.3	546	Cgg/Tgg	10/32	0.544395137442589	1	FACETS	0.596	0.538	0.658	0.596	0.538	0.658	SUBCLONAL	1	TRUE	0	0.576405048445725	1		415	439	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527607	41527607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	164	432	0	ENST00000263253.7:c.1498C>T	p.Pro500Ser	p.P500S	ENST00000263253	NM_001429.3	500	Ccc/Tcc	6/31	0.576405048445725	3	FACETS	0.928	0.853	1	0.464	0.426	0.503	CLONAL	1	TRUE	1	0.576405048445725	3		432	790	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971174	21971187	+	frameshift_variant	Frame_Shift_Del	DEL	GCTCCGCCACTCGG	GCTCCGCCACTCGG	-	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	94	120	129	0	ENST00000304494.5:c.171_184del	p.Arg58AlafsTer57	p.R58Afs*57	ENST00000304494	NM_000077.4	57	gcCCGAGTGGCGGAGCtg/gctg	2/3	NA	2	FACETS	0.973	0.903	1			1	INDETERMINATE	2	TRUE	NA	0.576405048445725	2		129	214	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287463	46287472	+	frameshift_variant	Frame_Shift_Del	DEL	AATATTAAAA	AATATTAAAA	-	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	150	328	0	ENST00000334344.6:c.5328_5337del	p.Lys1777ValfsTer11	p.K1777Vfs*11	ENST00000334344	NM_152641.2	1774	ttAATATTAAAA/tt	20/21	0.178716202223061	4	FACETS	1	0.96	1	0.54	0.494	0.589	INDETERMINATE	1	TRUE	2	0.576405048445725	4		328	759	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585361	29585362	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	130	334	0	ENST00000356175.3:c.4111-1_4111delinsAA		p.X1371_splice	ENST00000356175	NM_000267.3	1371		31/57	0.247826890931603	3	FACETS	0.962	0.876	1	0.481	0.438	0.526	INDETERMINATE	1	TRUE	1	0.576405048445725	3		334	604	SUCCESS
APC	324	MSKCC	GRCh37	5	112178261	112178262	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	184	383	0	ENST00000257430.4:c.6970_6971delinsTT	p.Pro2324Phe	p.P2324F	ENST00000257430	NM_000038.5	2324	CCt/TTt	16/16	0.178716202223061	4	FACETS	1	0.984	1	0.623	0.576	0.672	INDETERMINATE	1	TRUE	2	0.576405048445725	4		383	808	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534285	534286	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0005918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	180	351	0	ENST00000451590.1:c.37_38delinsAA	p.Gly13Asn	p.G13N	ENST00000451590	NM_001130442.1	13	GGt/AAt	2/5	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.576405048445725	2		351	508	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	111	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.896	0.812	0.984	0.896	0.812	0.984	CLONAL	1	TRUE	1	0.602663497712535	2		280	411	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0005951-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	202	511	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.947	0.881	1	0.947	0.881	1	CLONAL	1	TRUE	1	0.602663497712535	2		512	708	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005963-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	265	280	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.929009408527198	2		280	558	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579313	7579313	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs786201057	NA	P-0005963-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	478	703	0	ENST00000269305.4:c.374C>G	p.Thr125Arg	p.T125R	ENST00000269305	NM_001126112.2	125	aCg/aGg	4/11	0.929009408527198	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.929009408527198	1		703	518	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923601	39923601	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0005963-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	737	381	1	ENST00000378444.4:c.3490C>T	p.Arg1164Ter	p.R1164*	ENST00000378444	NM_001123385.1	1164	Cga/Tga	7/15	0.929009408527198	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.929009408527198	2		382	775	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0005969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	95	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.983	0.881	1	0.983	0.881	1	CLONAL	1	TRUE	1	0.461360292586287	2		280	419	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913499	NA	P-0005969-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	182	294	0	ENST00000345146.2:c.394C>G	p.Arg132Gly	p.R132G	ENST00000345146	NM_005896.2	132	Cgt/Ggt	4/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.461360292586287	2		294	740	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794359	242794359	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0005970-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	572	480	0	ENST00000334409.5:c.583G>A	p.Ala195Thr	p.A195T	ENST00000334409	NM_005018.2	195	Gcc/Acc	3/5	0.789508021878784	3	FACETS	1	0.989	1			1	CLONAL	2	TRUE	NA	0.789508021878784	3		480	963	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478803	57478803	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0005970-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	271	340	0	ENST00000371085.3:c.389A>G	p.Tyr130Cys	p.Y130C	ENST00000371085	NM_000516.4	130	tAc/tGc	5/13	0.382730405049774	6	FACETS	0.771	0.723	0.821	0.514	0.482	0.547	INDETERMINATE	2	TRUE	3	0.789508021878784	6		340	1148	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650870	48650870	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782126313	NA	P-0005970-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	351	265	0	ENST00000376670.3:c.739C>T	p.Arg247Cys	p.R247C	ENST00000376670	NM_002049.3	247	Cgc/Tgc	4/6	0.789508021878784	3	FACETS	1	0.978	1			1	CLONAL	1	TRUE	NA	0.789508021878784	3		265	1171	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220632	1220632	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782146	NA	P-0005970-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	299	414	1	ENST00000326873.7:c.650C>T	p.Pro217Leu	p.P217L	ENST00000326873	NM_000455.4	217	cCg/cTg	5/10	0.789508021878784	3	FACETS	1	0.969	1	0.52	0.49	0.55	CLONAL	1	TRUE	1	0.789508021878784	3		415	1016	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244890	41244891	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs397508990	NA	P-0005970-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	82	364	1	ENST00000357654.3:c.2657_2658del	p.Ser886CysfsTer16	p.S886Cfs*16	ENST00000357654	NM_007294.3	886	tCT/t	10/23	0.427758329994057	5	FACETS	0.483	0.424	0.545	0.161	0.141	0.182	INDETERMINATE	1	TRUE	2	0.789508021878784	5		365	940	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557001	95557370	+	splice_acceptor_variant,splice_donor_variant,intron_variant	Splice_Site	DEL	CTGTAAAAAATCCAAACAGCTTGAATTAGAAGTCAGAAGTATTTATTATCATTGTCAATCAGCATTTAGTGTGCACTCTCAGGCCAGGAGTCCCATGTATAAGCTGACACCACACAAAGGAAACACGCGTTACGACTTACTGCAATTGCATACCCCCGACAGACAGGGCTGCCGTCTAGTCTTTATTACAGCATTATTTCATAAAAACAGAAGGAAAAAAGAGAAGTCAATCAGATTACAAACAGAAATCTGACAACAGCACACCACAGTGTAAATATTTTTCAGAATCATTAGTTTACAATATCTTTGTGAACTTTTCCCCTTTGATGTTTTTAAGTTAATGTTTTTTCCATGTACATTTTTTGCTTAC	CTGTAAAAAATCCAAACAGCTTGAATTAGAAGTCAGAAGTATTTATTATCATTGTCAATCAGCATTTAGTGTGCACTCTCAGGCCAGGAGTCCCATGTATAAGCTGACACCACACAAAGGAAACACGCGTTACGACTTACTGCAATTGCATACCCCCGACAGACAGGGCTGCCGTCTAGTCTTTATTACAGCATTATTTCATAAAAACAGAAGGAAAAAAGAGAAGTCAATCAGATTACAAACAGAAATCTGACAACAGCACACCACAGTGTAAATATTTTTCAGAATCATTAGTTTACAATATCTTTGTGAACTTTTCCCCTTTGATGTTTTTAAGTTAATGTTTTTTCCATGTACATTTTTTGCTTAC	-	novel	NA	P-0005970-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	108	258	0	ENST00000393063.1:c.5603+1_5604-1del		p.X1868_splice	ENST00000393063	NM_030621.3	1868			0.789508021878784	3	FACETS	0.476	0.427	0.528	0.238	0.213	0.264	SUBCLONAL	1	TRUE	1	0.789508021878784	3		258	802	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95557447	95557539	+	splice_acceptor_variant,splice_donor_variant,intron_variant	Splice_Site	DEL	CTGCAATCAAAATGAAAGAATAATATGAATAATATCTCTGAAGTTGTTTTTAATTTTGTGGGTTTTTTTCTTTCTAAAGGGAGCCAACAATAC	CTGCAATCAAAATGAAAGAATAATATGAATAATATCTCTGAAGTTGTTTTTAATTTTGTGGGTTTTTTTCTTTCTAAAGGGAGCCAACAATAC	-	novel	NA	P-0005970-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	138	228	1	ENST00000393063.1:c.5527+1_5528-1del		p.X1843_splice	ENST00000393063	NM_030621.3	1843			0.789508021878784	3	FACETS	0.583	0.531	0.638	0.292	0.265	0.319	SUBCLONAL	1	TRUE	1	0.789508021878784	3		229	836	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	130	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.894	0.823	0.967	0.894	0.823	0.967	CLONAL	1	TRUE	1	0.886295165825839	2		280	328	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888199	112888199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121918454	NA	P-0006022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	316	504	0	ENST00000351677.2:c.215C>T	p.Ala72Val	p.A72V	ENST00000351677	NM_002834.3	72	gCc/gTc	3/16	1	2	FACETS	0.93	0.882	0.978	0.93	0.882	0.978	CLONAL	1	TRUE	1	0.886295165825839	2		504	767	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103828	47103828	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs976581260	NA	P-0006022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	298	439	1	ENST00000409792.3:c.6118C>T	p.Arg2040Ter	p.R2040*	ENST00000409792	NM_014159.6	2040	Cga/Tga	14/21	1	2	FACETS	0.995	0.944	1	0.995	0.944	1	CLONAL	1	TRUE	1	0.886295165825839	2		440	676	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461101	120461101	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs312262796	NA	P-0006022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	64	416	0	ENST00000256646.2:c.5857C>T	p.Arg1953Cys	p.R1953C	ENST00000256646	NM_024408.3	1953	Cgc/Tgc	32/34	1	2	FACETS	0.206	0.178	0.237	0.206	0.178	0.237	SUBCLONAL	1	TRUE	1	0.886295165825839	2		416	700	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653827	89653827	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	241	350	0	ENST00000371953.3:c.125T>A	p.Leu42His	p.L42H	ENST00000371953	NM_000314.4	42	cTt/cAt	2/9	0.886295165825839	1	FACETS	0.98	0.944	1	0.98	0.944	1	CLONAL	1	TRUE	0	0.886295165825839	1		350	309	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556867	29556868	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1555614418	NA	P-0006022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	178	262	0	ENST00000356175.3:c.2866dup	p.Thr956AsnfsTer19	p.T956Nfs*19	ENST00000356175	NM_000267.3	955	-/A	22/57	1	2	FACETS	0.915	0.853	0.978	0.915	0.853	0.978	CLONAL	1	TRUE	1	0.886295165825839	2		262	439	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684361	29684362	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0006022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	308	452	0	ENST00000356175.3:c.7884_7885del	p.Phe2629SerfsTer9	p.F2629Sfs*9	ENST00000356175	NM_000267.3	2627	gtTGtg/gttg	53/57	1	2	FACETS	0.921	0.873	0.969	0.921	0.873	0.969	CLONAL	1	TRUE	1	0.886295165825839	2		452	755	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123205158	123205162	+	frameshift_variant	Frame_Shift_Del	DEL	GATAA	GATAA	TAT	novel	NA	P-0006022-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	274	268	0	ENST00000218089.9:c.2518_2522delinsTAT	p.Asp840TyrfsTer2	p.D840Yfs*2	ENST00000218089	NM_001042749.1	840	GATAAt/TATt	25/35	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.886295165825839	1		268	331	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891705	28891705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750234866	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	130	612	1	ENST00000282397.4:c.3316G>A	p.Asp1106Asn	p.D1106N	ENST00000282397	NM_002019.4	1106	Gat/Aat	25/30	0.320753127705352	1	FACETS	0.367	0.333	0.403	0.367	0.333	0.403	INDETERMINATE	1	TRUE	0	0.655592403881242	1		613	726	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	82	300	0				ENST00000310581	NM_198253.2	-/1132			0.320753127705352	1	FACETS	0.345	0.305	0.387	0.345	0.305	0.387	INDETERMINATE	1	TRUE	0	0.655592403881242	1		300	488	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770132	56770132	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766958594	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	365	459	1	ENST00000337432.4:c.128C>T	p.Pro43Leu	p.P43L	ENST00000337432	NM_058216.2	43	cCc/cTc	1/9	0.305118394796165	1	FACETS	0.791	0.753	0.83	0.791	0.753	0.83	INDETERMINATE	1	TRUE	0	0.655592403881242	1		460	946	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610608	52610609	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	211	561	0	ENST00000394830.3:c.3564dup	p.Glu1189ArgfsTer6	p.E1189Rfs*6	ENST00000394830	NM_018313.4	1188	-/A	23/30	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.655592403881242	2		561	630	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	236	382	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	0.903	0.845	0.963	0.903	0.845	0.963	CLONAL	1	TRUE	1	0.655592403881242	2		382	797	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317572	1317572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	216	332	0	ENST00000400841.2:c.493G>A	p.Glu165Lys	p.E165K	ENST00000400841		165	Gaa/Aaa	5/6	1	1	FACETS	0.792	0.743	0.843	0.792	0.743	0.843	SUBCLONAL	1	TRUE	0	0.655592403881242	1		332	559	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39762961	39762961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	182	501	0	ENST00000288319.7:c.875C>T	p.Pro292Leu	p.P292L	ENST00000288319	NM_182918.3	292	cCt/cTt	9/10	1	2	FACETS	0.862	0.799	0.927	0.862	0.799	0.927	CLONAL	1	TRUE	1	0.655592403881242	2		501	644	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076902	41076902	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	210	572	1	ENST00000373198.4:c.1518G>A	p.Trp506Ter	p.W506*	ENST00000373198	NM_133170.3	506	tgG/tgA	9/32	1	2	FACETS	0.9	0.839	0.962	0.9	0.839	0.962	CLONAL	1	TRUE	1	0.655592403881242	2		573	712	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199343	16199343	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	289	591	1	ENST00000375759.3:c.116C>T	p.Pro39Leu	p.P39L	ENST00000375759	NM_015001.2	39	cCc/cTc	2/15	1	2	FACETS	0.976	0.921	1	0.976	0.921	1	CLONAL	1	TRUE	1	0.655592403881242	2		592	903	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256144	16256144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138355680	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	282	640	0	ENST00000375759.3:c.3409C>T	p.Arg1137Cys	p.R1137C	ENST00000375759	NM_015001.2	1137	Cgt/Tgt	11/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.655592403881242	2		640	839	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259577	16259577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	216	415	0	ENST00000375759.3:c.6842C>T	p.Ser2281Phe	p.S2281F	ENST00000375759	NM_015001.2	2281	tCt/tTt	11/15	1	2	FACETS	0.928	0.866	0.991	0.928	0.866	0.991	CLONAL	1	TRUE	1	0.655592403881242	2		415	710	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261878	16261878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763414538	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	167	266	0	ENST00000375759.3:c.9143C>T	p.Thr3048Met	p.T3048M	ENST00000375759	NM_015001.2	3048	aCg/aTg	11/15	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.655592403881242	2		266	491	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965601	25965601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	140	478	1	ENST00000435504.4:c.3605C>T	p.Ser1202Phe	p.S1202F	ENST00000435504		1202	tCc/tTc	13/13	0.320753127705352	1	FACETS	0.474	0.433	0.516	0.474	0.433	0.516	INDETERMINATE	1	TRUE	0	0.655592403881242	1		479	606	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672740	47672740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	136	603	1	ENST00000233146.2:c.1330C>T	p.Arg444Cys	p.R444C	ENST00000233146	NM_000251.2	444	Cgt/Tgt	8/16	0.320753127705352	1	FACETS	0.52	0.475	0.567	0.52	0.475	0.567	INDETERMINATE	1	TRUE	0	0.655592403881242	1		604	536	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295786	212295786	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751446160	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	164	505	0	ENST00000342788.4:c.2527G>A	p.Asp843Asn	p.D843N	ENST00000342788	NM_005235.2	843	Gat/Aat	21/28	0.307207148572837	1	FACETS	0.814	0.756	0.873	0.814	0.756	0.873	INDETERMINATE	1	TRUE	0	0.655592403881242	1		505	413	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52692265	52692265	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	263	652	0	ENST00000394830.3:c.595C>T	p.Pro199Ser	p.P199S	ENST00000394830	NM_018313.4	199	Cca/Tca	6/30	1	2	FACETS	0.96	0.902	1	0.96	0.902	1	CLONAL	1	TRUE	1	0.655592403881242	2		652	836	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522586	176522586	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	374	492	0	ENST00000292408.4:c.1683C>G	p.Phe561Leu	p.F561L	ENST00000292408	NM_213647.1	561	ttC/ttG	13/18	0.320753127705352	1	FACETS	0.89	0.849	0.931	0.89	0.849	0.931	INDETERMINATE	1	TRUE	0	0.655592403881242	1		492	862	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636877	176636877	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	207	468	0	ENST00000439151.2:c.1477C>T	p.Pro493Ser	p.P493S	ENST00000439151	NM_022455.4	493	Cct/Tct	5/23	0.320753127705352	1	FACETS	0.851	0.797	0.905	0.851	0.797	0.905	INDETERMINATE	1	TRUE	0	0.655592403881242	1		468	499	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665396	176665396	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	127	535	0	ENST00000439151.2:c.4080A>T	p.Glu1360Asp	p.E1360D	ENST00000439151	NM_022455.4	1360	gaA/gaT	7/23	0.320753127705352	1	FACETS	0.305	0.276	0.336	0.305	0.276	0.336	INDETERMINATE	1	TRUE	0	0.655592403881242	1		535	854	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965719	93965719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	223	748	1	ENST00000369303.4:c.2209G>A	p.Gly737Arg	p.G737R	ENST00000369303	NM_004440.3	737	Gga/Aga	13/17	1	2	FACETS	0.929	0.869	0.992	0.929	0.869	0.992	CLONAL	1	TRUE	1	0.655592403881242	2		749	732	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50455063	50455063	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	192	519	0	ENST00000331340.3:c.610G>A	p.Gly204Arg	p.G204R	ENST00000331340	NM_006060.4	204	Gga/Aga	6/8	0.655592403881242	4	FACETS	0.821	0.758	0.887	0.274	0.252	0.296	CLONAL	1	TRUE	1	0.655592403881242	4		519	1181	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509625	106509625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	374	568	1	ENST00000359195.3:c.1619G>A	p.Gly540Glu	p.G540E	ENST00000359195	NM_002649.2	540	gGg/gAg	2/11	1	2	FACETS	0.998	0.948	1	0.998	0.948	1	CLONAL	1	TRUE	1	0.655592403881242	2		569	1143	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549095	87549095	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	225	522	0	ENST00000277120.3:c.1652G>A	p.Arg551Gln	p.R551Q	ENST00000277120		551	cGa/cAa	15/19	0.655592403881242	1	FACETS	0.959	0.904	1	0.959	0.904	1	CLONAL	1	TRUE	0	0.655592403881242	1		522	481	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231374	98231374	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1564034151	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	222	422	0	ENST00000331920.6:c.1909A>G	p.Thr637Ala	p.T637A	ENST00000331920	NM_000264.3	637	Acc/Gcc	14/24	0.655592403881242	1	FACETS	0.946	0.891	1	0.946	0.891	1	CLONAL	1	TRUE	0	0.655592403881242	1		422	481	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115729	8115729	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	306	640	0	ENST00000346208.3:c.1075G>A	p.Glu359Lys	p.E359K	ENST00000346208		359	Gaa/Aaa	6/6	0.655592403881242	1	FACETS	0.951	0.904	0.998	0.951	0.904	0.998	CLONAL	1	TRUE	0	0.655592403881242	1		640	660	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851569	63851569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	168	285	0	ENST00000279873.7:c.2347C>T	p.Pro783Ser	p.P783S	ENST00000279873	NM_032199.2	783	Ccc/Tcc	10/10	0.655592403881242	1	FACETS	0.857	0.798	0.917	0.857	0.798	0.917	CLONAL	1	TRUE	0	0.655592403881242	1		285	402	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514163	69514163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	338	600	0	ENST00000294312.3:c.518C>T	p.Pro173Leu	p.P173L	ENST00000294312	NM_005117.2	173	cCa/cTa	3/3	1	2	FACETS	0.954	0.903	1	0.954	0.903	1	CLONAL	1	TRUE	1	0.655592403881242	2		600	1081	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425385	49425385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	310	676	0	ENST00000301067.7:c.13103C>T	p.Thr4368Ile	p.T4368I	ENST00000301067	NM_003482.3	4368	aCc/aTc	39/54	1	2	FACETS	0.981	0.927	1	0.981	0.927	1	CLONAL	1	TRUE	1	0.655592403881242	2		676	964	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433727	49433727	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	374	648	0	ENST00000301067.7:c.7826C>T	p.Pro2609Leu	p.P2609L	ENST00000301067	NM_003482.3	2609	cCa/cTa	31/54	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.655592403881242	2		648	1113	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434853	49434853	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	322	581	0	ENST00000301067.7:c.6700C>T	p.Pro2234Ser	p.P2234S	ENST00000301067	NM_003482.3	2234	Ccc/Tcc	31/54	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.655592403881242	2		581	919	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929332	32929332	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	301	844	0	ENST00000380152.3:c.7342A>G	p.Lys2448Glu	p.K2448E	ENST00000380152		2448	Aag/Gag	14/27	0.320753127705352	1	FACETS	0.827	0.784	0.872	0.827	0.784	0.872	INDETERMINATE	1	TRUE	0	0.655592403881242	1		844	746	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336181	73336181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	91	593	0	ENST00000377767.4:c.2222G>A	p.Arg741Lys	p.R741K	ENST00000377767	NM_014953.3	741	aGa/aAa	17/21	0.320753127705352	1	FACETS	0.361	0.321	0.403	0.361	0.321	0.403	INDETERMINATE	1	TRUE	0	0.655592403881242	1		593	517	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528253	103528253	+	stop_lost	Nonstop_Mutation	SNP	A	A	T	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	17	88	0	ENST00000355739.4:c.3561A>T	p.Ter1187TyrextTer8	p.*1187Yext*8	ENST00000355739	NM_000123.3	1187	taA/taT	15/15	0.320753127705352	1	FACETS	0.309	0.233	0.396	0.309	0.233	0.396	INDETERMINATE	1	TRUE	0	0.655592403881242	1		88	113	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569706	95569706	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	191	371	0	ENST00000393063.1:c.4027C>T	p.Leu1343Phe	p.L1343F	ENST00000393063	NM_030621.3	1343	Ctt/Ttt	22/28	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.655592403881242	2		371	560	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117779	70117779	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	473	639	0	ENST00000245479.2:c.247G>A	p.Gly83Ser	p.G83S	ENST00000245479	NM_000346.3	83	Ggc/Agc	1/3	0.454266724812479	3	FACETS	1	0.994	1	0.62	0.592	0.649	CLONAL	1	TRUE	1	0.655592403881242	3		639	1544	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145743	11145743	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199962502	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	462	642	1	ENST00000358026.2:c.4105C>T	p.Arg1369Cys	p.R1369C	ENST00000358026	NM_001128849.1	1369	Cgt/Tgt	29/36	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.655592403881242	2		643	1237	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560985	9560985	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	265	470	1	ENST00000353224.5:c.797G>A	p.Arg266Lys	p.R266K	ENST00000353224	NM_177990.2	266	aGg/aAg	4/10	1	2	FACETS	0.924	0.868	0.981	0.924	0.868	0.981	CLONAL	1	TRUE	1	0.655592403881242	2		471	875	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419857	41419857	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1425481575	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	284	530	0	ENST00000373198.4:c.464C>T	p.Thr155Ile	p.T155I	ENST00000373198	NM_133170.3	155	aCt/aTt	3/32	1	2	FACETS	0.921	0.867	0.976	0.921	0.867	0.976	CLONAL	1	TRUE	1	0.655592403881242	2		530	941	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281191	46281191	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	364	791	0	ENST00000371998.3:c.3988A>G	p.Ser1330Gly	p.S1330G	ENST00000371998		1330	Agt/Ggt	21/23	1	2	FACETS	0.991	0.941	1	0.991	0.941	1	CLONAL	1	TRUE	1	0.655592403881242	2		791	1120	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410907	63410907	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	245	333	0	ENST00000330258.3:c.2260C>T	p.Pro754Ser	p.P754S	ENST00000330258	NM_152424.3	754	Cca/Tca	2/2	1	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.655592403881242	1		333	421	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702537	52702538	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	171	469	0	ENST00000394830.3:c.360dup	p.Asn121Ter	p.N121*	ENST00000394830	NM_018313.4	120	-/T	4/30	1	2	FACETS	0.901	0.833	0.971	0.901	0.833	0.971	CLONAL	1	TRUE	1	0.655592403881242	2		469	579	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256561	115256562	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	146	477	0	ENST00000369535.4:c.149_150delinsTT	p.Thr50Ile	p.T50I	ENST00000369535	NM_002524.4	50	aCC/aTT	3/7	1	2	FACETS	0.916	0.842	0.993	0.916	0.842	0.993	CLONAL	1	TRUE	1	0.655592403881242	2		477	486	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514219	69514220	+	missense_variant	Missense_Mutation	DNP	GT	GT	AA	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	328	633	0	ENST00000294312.3:c.461_462delinsTT	p.Tyr154Phe	p.Y154F	ENST00000294312	NM_005117.2	154	tAC/tTT	3/3	1	2	FACETS	0.937	0.886	0.989	0.937	0.886	0.989	CLONAL	1	TRUE	1	0.655592403881242	2		633	1068	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420213	88420214	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	220	557	1	ENST00000360948.2:c.2472_2473delinsTT	p.His825Tyr	p.H825Y	ENST00000360948	NM_001012338.2	824	ctCCat/ctTTat	19/19	NA	2	FACETS	1	0.957	1			1	INDETERMINATE	1	TRUE	NA	0.655592403881242	2		558	652	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041539	14041540	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	247	534	0	ENST00000311895.7:c.2086_2087delinsTT	p.Pro696Leu	p.P696L	ENST00000311895	NM_005236.2	696	CCa/TTa	11/11	1	2	FACETS	0.957	0.898	1	0.957	0.898	1	CLONAL	1	TRUE	1	0.655592403881242	2		534	787	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877399	89877400	+	missense_variant	Missense_Mutation	DNP	CC	CC	TA	novel	NA	P-0006034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	303	507	0	ENST00000389301.3:c.363_364delinsTA	p.Gly122Arg	p.G122R	ENST00000389301	NM_000135.2	121	gtGGga/gtTAga	4/43	1	2	FACETS	0.95	0.897	1	0.95	0.897	1	CLONAL	1	TRUE	1	0.655592403881242	2		507	973	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	168	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.941	0.875	1	0.941	0.875	1	CLONAL	1	TRUE	1	0.836099756776841	2		280	427	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076751	72076751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	349	567	1	ENST00000357731.5:c.746G>A	p.Gly249Asp	p.G249D	ENST00000357731	NM_173808.2	249	gGt/gAt	5/7	1	2	FACETS	0.958	0.911	1	0.958	0.911	1	CLONAL	1	TRUE	1	0.836099756776841	2		568	871	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627440	14627442	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0006045-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	450	611	1	ENST00000254322.2:c.628_630del	p.Lys210del	p.K210del	ENST00000254322	NM_006145.1	210	AAG/-	2/3	0.836741762563204	3	FACETS	1	0.978	1	0.521	0.497	0.546	CLONAL	1	TRUE	1	0.836099756776841	3		612	1465	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006045-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	77	280	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.965	1			1	INDETERMINATE	1	TRUE	NA	0.613660235399998	2		280	210	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076751	72076751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006045-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	364	567	1	ENST00000357731.5:c.746G>A	p.Gly249Asp	p.G249D	ENST00000357731	NM_173808.2	249	gGt/gAt	5/7	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.613660235399998	2		568	1140	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627440	14627442	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0006045-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	315	611	1	ENST00000254322.2:c.628_630del	p.Lys210del	p.K210del	ENST00000254322	NM_006145.1	210	AAG/-	2/3	0.613660235399998	3	FACETS	0.954	0.898	1	0.477	0.449	0.506	CLONAL	1	TRUE	1	0.613660235399998	3		612	1407	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0006049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	262	464	0				ENST00000310581	NM_198253.2	-/1132			0.836038302116765	3	FACETS	0.883	0.828	0.939			1	CLONAL	1	TRUE	NA	0.888434685154869	3		464	965	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0006049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	1231	506	1	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	NA	2	FACETS	1	0.998	1			1	INDETERMINATE	2	TRUE	NA	0.888434685154869	2		507	1332	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17947943	17947943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	445	387	1	ENST00000458235.1:c.1781G>A	p.Gly594Glu	p.G594E	ENST00000458235	NM_000215.3	594	gGa/gAa	13/24	1	2	FACETS	0.992	0.95	1	0.992	0.95	1	CLONAL	1	TRUE	1	0.888434685154869	2		388	1010	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097683	27097683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1314	528	567	0	ENST00000324856.7:c.3272C>T	p.Ser1091Phe	p.S1091F	ENST00000324856	NM_006015.4	1091	tCc/tTc	12/20	0.875854314384673	3	FACETS	0.932	0.891	0.973	0.466	0.445	0.487	CLONAL	1	TRUE	1	0.888434685154869	3		567	1842	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804242	43804242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	1019	519	1	ENST00000372470.3:c.242C>T	p.Ser81Phe	p.S81F	ENST00000372470	NM_005373.2	81	tCc/tTc	3/12	0.875854314384673	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.888434685154869	3		520	1623	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466411	120466411	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	556	473	0	ENST00000256646.2:c.4708G>A	p.Gly1570Ser	p.G1570S	ENST00000256646	NM_024408.3	1570	Ggt/Agt	26/34	0.888376592632151	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.888434685154869	1		473	665	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745987	162745987	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	816	441	1	ENST00000367921.3:c.2110C>T	p.Leu704Phe	p.L704F	ENST00000367921	NM_006182.2	704	Ctt/Ttt	16/18	0.875854314384673	3	FACETS	0.997	0.97	1	0.997	0.97	1	CLONAL	2	TRUE	1	0.888434685154869	3		442	1331	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445053	89445053	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	371	560	0	ENST00000336596.2:c.1373A>T	p.Gln458Leu	p.Q458L	ENST00000336596	NM_005233.5	458	cAa/cTa	6/17	1	2	FACETS	0.98	0.935	1	0.98	0.935	1	CLONAL	1	TRUE	1	0.888434685154869	2		560	852	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467824	66467824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	358	594	0	ENST00000273854.3:c.445G>A	p.Glu149Lys	p.E149K	ENST00000273854	NM_004439.5	149	Gaa/Aaa	3/18	1	2	FACETS	0.977	0.931	1	0.977	0.931	1	CLONAL	1	TRUE	1	0.888434685154869	2		594	825	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748489	43748489	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	669	621	0	ENST00000523873.1:c.443G>A	p.Gly148Glu	p.G148E	ENST00000523873		148	gGa/gAa	6/8	1	2	FACETS	0.97	0.936	1	0.97	0.936	1	CLONAL	1	TRUE	1	0.888434685154869	2		621	1553	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127911957	127911957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	1190	720	0	ENST00000373547.4:c.913C>T	p.Leu305Phe	p.L305F	ENST00000373547	NM_002721.4	305	Ctt/Ttt	7/7	0.875854314384673	3	FACETS	0.957	0.936	0.979	0.957	0.936	0.979	CLONAL	2	TRUE	1	0.888434685154869	3		720	2021	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412675	139412675	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	451	517	0	ENST00000277541.6:c.1169A>G	p.Asn390Ser	p.N390S	ENST00000277541	NM_017617.3	390	aAc/aGc	7/34	0.875854314384673	3	FACETS	0.968	0.923	1	0.484	0.461	0.507	CLONAL	1	TRUE	1	0.888434685154869	3		517	1515	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413165	139413165	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	1060	493	0	ENST00000277541.6:c.977G>A	p.Gly326Asp	p.G326D	ENST00000277541	NM_017617.3	326	gGc/gAc	6/34	0.875854314384673	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.888434685154869	3		493	1656	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955432	48955432	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	295	368	0	ENST00000267163.4:c.1548G>A	p.Trp516Ter	p.W516*	ENST00000267163	NM_000321.2	516	tgG/tgA	17/27	0.888376592632151	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.888434685154869	1		368	369	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436041	110436041	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1337039748	NA	P-0006049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	394	455	1	ENST00000375856.3:c.2360C>T	p.Ala787Val	p.A787V	ENST00000375856	NM_003749.2	787	gCc/gTc	1/2	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.888434685154869	2		456	875	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804219	46804219	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1575	682	697	1	ENST00000290295.7:c.788G>A	p.Trp263Ter	p.W263*	ENST00000290295	NM_006361.5	263	tGg/tAg	2/2	0.875854314384673	3	FACETS	0.982	0.945	1	0.491	0.472	0.51	CLONAL	1	TRUE	1	0.888434685154869	3		698	2257	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897435	78897435	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	495	572	0	ENST00000306801.3:c.2770C>A	p.Pro924Thr	p.P924T	ENST00000306801	NM_020761.2	924	Ccc/Acc	23/34	0.875854314384673	3	FACETS	1	0.973	1	0.512	0.489	0.535	CLONAL	1	TRUE	1	0.888434685154869	3		572	1573	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39725892	39725892	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	358	423	0	ENST00000361337.2:c.763G>A	p.Glu255Lys	p.E255K	ENST00000361337	NM_003286.2	255	Gaa/Aaa	10/21	1	2	FACETS	0.928	0.884	0.973	0.928	0.884	0.973	CLONAL	1	TRUE	1	0.888434685154869	2		423	868	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922871	44922871	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	676	616	0	ENST00000377967.4:c.1732C>T	p.Pro578Ser	p.P578S	ENST00000377967	NM_021140.2	578	Ccc/Tcc	16/29	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.888434685154869	2		616	1468	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70341551	70341551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006049-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	810	603	3	ENST00000374080.3:c.986C>T	p.Pro329Leu	p.P329L	ENST00000374080		329	cCc/cTc	7/45	0.888434685154869	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.888434685154869	1		606	958	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	193	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.833715354177939	2		280	450	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0006054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21648	5601	910	2	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.833715354177939	22	FACETS	0.921	0.907	0.934			1	CLONAL	5	TRUE	NA	0.833715354177939	22		912	27249	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023069	33023069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006054-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	391	573	2	ENST00000300177.4:c.178C>T	p.Arg60Trp	p.R60W	ENST00000300177	NM_001191322.1	60	Cgg/Tgg	2/2	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.833715354177939	2		575	923	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	226	280	0				ENST00000310581	NM_198253.2	-/1132			0.751293063566148	3	FACETS	1	0.991	1	0.671	0.629	0.713	CLONAL	1	TRUE	1	0.751293063566148	3		280	617	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0006064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	151	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.511	0.468	0.557	0.511	0.468	0.557	SUBCLONAL	1	TRUE	1	0.751293063566148	2		490	786	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845466	128845466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006064-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	233	412	0	ENST00000249373.3:c.763G>A	p.Asp255Asn	p.D255N	ENST00000249373	NM_005631.4	255	Gac/Aac	4/12	1	2	FACETS	0.617	0.576	0.66	0.617	0.576	0.66	SUBCLONAL	1	TRUE	1	0.751293063566148	2		412	1005	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	91	280	0				ENST00000310581	NM_198253.2	-/1132			0.352082133911696	0	FACETS	0.863	0.786	0.941			1	CLONAL	3	TRUE	0	0.27	0		280	190	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0006082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	182	490	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.352082133911696	3	FACETS	0.89	0.831	0.949	1	0.993	1	CLONAL	4	TRUE	1	0.27	3		490	430	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266709	198266709	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	135	389	0	ENST00000335508.6:c.2223G>T	p.Lys741Asn	p.K741N	ENST00000335508	NM_012433.2	741	aaG/aaT	15/25	0.148694632860952	3	FACETS	1	0.972	1	1	0.99	1	INDETERMINATE	3	TRUE	1	0.27	3		389	337	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	64	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.751	0.655	0.853	0.751	0.655	0.853	SUBCLONAL	1	TRUE	1	0.553511288652896	2		280	308	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0006097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	66	595	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.664	0.58	0.755	0.664	0.58	0.755	SUBCLONAL	1	TRUE	1	0.553511288652896	2		595	359	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916929	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519931	NA	P-0006097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	409	970	0	ENST00000263967.3:c.316G>C	p.Gly106Arg	p.G106R	ENST00000263967	NM_006218.2	106	Ggc/Cgc	2/21	1	2	FACETS	0.998	0.948	1	0.998	0.948	1	CLONAL	1	TRUE	1	0.553511288652896	2		970	1481	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	191	540	0	ENST00000335508.6:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000335508	NM_012433.2	902	Gaa/Aaa	18/25	1	2	FACETS	0.961	0.892	1	0.961	0.892	1	CLONAL	1	TRUE	1	0.553511288652896	2		540	718	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900371	101900371	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1564162124	NA	P-0006097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	247	331	0	ENST00000374994.4:c.805G>A	p.Asp269Asn	p.D269N	ENST00000374994	NM_004612.2	269	Gac/Aac	4/9	0.553511288652896	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	0	0.553511288652896	2		331	421	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44941858	44941858	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0006097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	419	429	0	ENST00000377967.4:c.3182C>G	p.Ser1061Ter	p.S1061*	ENST00000377967	NM_021140.2	1061	tCa/tGa	21/29	1	1	FACETS	0.792	0.763	0.821	1	0.997	1	SUBCLONAL	2	TRUE	0	0.553511288652896	1		429	691	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123202503	123202504	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	360	314	0	ENST00000218089.9:c.2356dup	p.Gln786ProfsTer8	p.Q786Pfs*8	ENST00000218089	NM_001042749.1	785	-/C	24/35	1	1	FACETS	0.834	0.802	0.865	1	0.997	1	CLONAL	2	TRUE	0	0.553511288652896	1		314	564	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923425	9923426	+	missense_variant	Missense_Mutation	DNP	TT	TT	AA	novel	NA	P-0006097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	127	770	0	ENST00000330684.3:c.1861_1862inv	p.Asn621Phe	p.N621F	ENST00000330684	NM_001134407.1	621	AAt/TTt	9/13	1	2	FACETS	0.665	0.603	0.73	0.665	0.603	0.73	SUBCLONAL	1	TRUE	1	0.553511288652896	2		770	690	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	146	280	0				ENST00000310581	NM_198253.2	-/1132			0.279464907303655	4	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	FALSE	2	0.340236501883174	4		280	477	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923060	44923060	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	74	351	0	ENST00000377967.4:c.1921C>T	p.Gln641Ter	p.Q641*	ENST00000377967	NM_021140.2	641	Cag/Tag	16/29	1	1	FACETS	0.755	0.671	0.843	1	0.978	1	SUBCLONAL	2	FALSE	0	0.340236501883174	1		351	239	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501191	NA	P-0006129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	152	432	2	ENST00000269305.4:c.811G>A	p.Glu271Lys	p.E271K	ENST00000269305	NM_001126112.2	271	Gag/Aag	8/11	0.23286076425271	3	FACETS	1	0.963	1	0.549	0.501	0.598	CLONAL	1	FALSE	1	0.340236501883174	3		434	953	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0006129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	166	384	1	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.23286076425271	3	FACETS	0.75	0.69	0.812	0.75	0.69	0.812	SUBCLONAL	2	FALSE	1	0.340236501883174	3		385	761	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65300340	65300340	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	42	203	0	ENST00000342505.4:c.3370G>A	p.Val1124Ile	p.V1124I	ENST00000342505	NM_002227.2	1124	Gtt/Att	25/25	0.293617483893464	2	FACETS	0.815	0.683	0.959	0.407	0.341	0.48	CLONAL	1	FALSE	0	0.340236501883174	2		203	303	SUCCESS
APC	324	MSKCC	GRCh37	5	112174040	112174040	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1561579402	NA	P-0006129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	123	367	0	ENST00000257430.4:c.2749G>A	p.Asp917Asn	p.D917N	ENST00000257430	NM_000038.5	917	Gat/Aat	16/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	FALSE	1	0.340236501883174	2		367	575	SUCCESS
BLM	641	MSKCC	GRCh37	15	91292929	91292929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	95	296	0	ENST00000355112.3:c.431C>T	p.Ser144Leu	p.S144L	ENST00000355112	NM_000057.2	144	tCa/tTa	3/22	1	2	FACETS	0.911	0.812	1	0.911	0.812	1	CLONAL	1	FALSE	1	0.340236501883174	2		296	613	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857394	68857394	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006129-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	149	430	1	ENST00000261769.5:c.2029C>T	p.Gln677Ter	p.Q677*	ENST00000261769	NM_004360.3	677	Caa/Taa	13/16	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	FALSE	1	0.340236501883174	2		431	649	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0006142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	247	229	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.745427405754936	2		229	538	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0006142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	213	595	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.745427405754936	2		595	544	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603032	48603032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs377767360	NA	P-0006142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	48	291	0	ENST00000342988.3:c.1333C>T	p.Arg445Ter	p.R445*	ENST00000342988	NM_005359.5	445	Cga/Tga	11/12	0.745427405754936	1	FACETS	0.173	0.146	0.203	0.173	0.146	0.203	SUBCLONAL	1	TRUE	0	0.745427405754936	1		291	466	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151960145	151960145	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	202	443	2	ENST00000262189.6:c.1255C>T	p.Gln419Ter	p.Q419*	ENST00000262189	NM_170606.2	419	Caa/Taa	9/59	0.745427405754936	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.745427405754936	1		445	263	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095680	178095680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	307	531	1	ENST00000397062.3:c.1651C>T	p.His551Tyr	p.H551Y	ENST00000397062	NM_006164.4	551	Cac/Tac	5/5	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.745427405754936	2		532	750	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121544	108121544	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs554805703	NA	P-0006142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	100	428	0	ENST00000278616.4:c.1352G>A	p.Arg451His	p.R451H	ENST00000278616	NM_000051.3	451	cGt/cAt	10/63	1	2	FACETS	0.511	0.458	0.567	0.511	0.458	0.567	SUBCLONAL	1	TRUE	1	0.745427405754936	2		428	525	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48603120	48603120	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	49	370	0	ENST00000342988.3:c.1421C>T	p.Ser474Leu	p.S474L	ENST00000342988	NM_005359.5	474	tCa/tTa	11/12	0.745427405754936	1	FACETS	0.162	0.137	0.19	0.162	0.137	0.19	SUBCLONAL	1	TRUE	0	0.745427405754936	1		370	509	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023664	27023673	+	frameshift_variant	Frame_Shift_Del	DEL	CCTCCGCCTC	CCTCCGCCTC	-	novel	NA	P-0006142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	261	344	0	ENST00000324856.7:c.771_780del	p.Ser258ArgfsTer102	p.S258Rfs*102	ENST00000324856	NM_006015.4	257	gCCTCCGCCTCc/gc	1/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.745427405754936	2		344	633	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446027	49446027	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	648	586	0	ENST00000301067.7:c.1439del	p.Pro480LeufsTer450	p.P480Lfs*450	ENST00000301067	NM_003482.3	480	cCt/ct	10/54	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.745427405754936	2		586	1415	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	94	280	0				ENST00000310581	NM_198253.2	-/1132			0.294096932017505	4	FACETS	1	0.962	1			1	CLONAL	3	FALSE	NA	0.453859996061135	4		280	183	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319334	11319334	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	78	462	0	ENST00000361445.4:c.133C>T	p.Gln45Ter	p.Q45*	ENST00000361445	NM_004958.3	45	Cag/Tag	2/58	0.305660618583482	4	FACETS	1	0.97	1	0.661	0.584	0.742	CLONAL	1	FALSE	2	0.453859996061135	4		462	378	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745569	162745569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	95	485	1	ENST00000367921.3:c.1984C>T	p.Leu662Phe	p.L662F	ENST00000367921	NM_006182.2	662	Ctc/Ttc	15/18	0.305660618583482	4	FACETS	0.88	0.791	0.972	0.88	0.791	0.972	CLONAL	2	FALSE	2	0.453859996061135	4		486	346	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085957	16085957	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	53	491	1	ENST00000281043.3:c.1133A>G	p.Glu378Gly	p.E378G	ENST00000281043	NM_005378.4	378	gAg/gGg	3/3	0.413537735953815	3	FACETS	1	0.958	1	0.657	0.567	0.753	CLONAL	1	FALSE	1	0.453859996061135	3		492	218	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498327	29498327	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766821017	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	22	346	1	ENST00000389048.3:c.1853G>A	p.Gly618Glu	p.G618E	ENST00000389048	NM_004304.4	618	gGa/gAa	10/29	NA	2	FACETS	0.422	0.328	0.53			1	INDETERMINATE	1	FALSE	NA	0.453859996061135	2		347	230	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940471	29940471	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774815140	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	32	680	0	ENST00000389048.3:c.760C>T	p.Pro254Ser	p.P254S	ENST00000389048	NM_004304.4	254	Cct/Tct	2/29	NA	2	FACETS	0.448	0.364	0.542			1	INDETERMINATE	1	FALSE	NA	0.453859996061135	2		680	315	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630407	47630407	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	68	592	0	ENST00000233146.2:c.77T>C	p.Met26Thr	p.M26T	ENST00000233146	NM_000251.2	26	aTg/aCg	1/16	0.294531148847814	3	FACETS	1	0.963	1	0.632	0.555	0.713	CLONAL	1	FALSE	1	0.453859996061135	3		592	291	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637434	47637434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	96	599	0	ENST00000233146.2:c.568C>T	p.Leu190Phe	p.L190F	ENST00000233146	NM_000251.2	190	Ctc/Ttc	3/16	0.294531148847814	3	FACETS	0.763	0.687	0.843	0.763	0.687	0.843	SUBCLONAL	2	FALSE	1	0.453859996061135	3		599	340	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686266	30686266	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	84	487	0	ENST00000295754.5:c.122A>T	p.Asn41Ile	p.N41I	ENST00000295754	NM_003242.5	41	aAc/aTc	2/7	0.290758222391497	5	FACETS	1	0.972	1	0.443	0.393	0.497	CLONAL	1	FALSE	2	0.453859996061135	5		487	468	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713513	30713513	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	78	432	4	ENST00000295754.5:c.838C>T	p.Pro280Ser	p.P280S	ENST00000295754	NM_003242.5	280	Ccc/Tcc	4/7	0.290758222391497	5	FACETS	0.862	0.764	0.966	0.575	0.509	0.644	CLONAL	2	FALSE	2	0.453859996061135	5		436	335	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713519	30713519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	76	432	1	ENST00000295754.5:c.844G>A	p.Glu282Lys	p.E282K	ENST00000295754	NM_003242.5	282	Gag/Aag	4/7	0.290758222391497	5	FACETS	0.835	0.738	0.938	0.557	0.492	0.625	CLONAL	2	FALSE	2	0.453859996061135	5		433	337	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713601	30713601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202168735	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	87	396	0	ENST00000295754.5:c.926C>T	p.Thr309Met	p.T309M	ENST00000295754	NM_003242.5	309	aCg/aTg	4/7	0.290758222391497	5	FACETS	0.841	0.75	0.937	0.561	0.5	0.625	CLONAL	2	FALSE	2	0.453859996061135	5		396	383	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437777	52437777	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	117	894	0	ENST00000460680.1:c.1384C>T	p.Pro462Ser	p.P462S	ENST00000460680	NM_004656.3	462	Cct/Tct	13/17	0.240240237271623	5	FACETS	0.897	0.813	0.984	0.598	0.542	0.656	INDETERMINATE	2	FALSE	2	0.453859996061135	5		894	483	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403565	138403565	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	85	674	0	ENST00000289153.2:c.2217G>T	p.Lys739Asn	p.K739N	ENST00000289153	NM_006219.2	739	aaG/aaT	15/22	NA	2	FACETS	0.888	0.789	0.992			1	INDETERMINATE	1	FALSE	NA	0.453859996061135	2		674	422	SUCCESS
ATR	545	MSKCC	GRCh37	3	142222283	142222283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	83	380	0	ENST00000350721.4:c.5209C>T	p.His1737Tyr	p.H1737Y	ENST00000350721	NM_001184.3	1737	Cat/Tat	30/47	0.240240237271623	5	FACETS	0.992	0.884	1	0.661	0.589	0.736	INDETERMINATE	2	FALSE	2	0.453859996061135	5		380	310	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916642	178916642	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	161	862	0	ENST00000263967.3:c.29T>G	p.Leu10Arg	p.L10R	ENST00000263967	NM_006218.2	10	cTg/cGg	2/21	0.240240237271623	5	FACETS	1	0.962	1	0.712	0.657	0.769	INDETERMINATE	2	FALSE	2	0.453859996061135	5		862	558	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612184	189612184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	68	604	0	ENST00000264731.3:c.1936C>T	p.Leu646Phe	p.L646F	ENST00000264731	NM_003722.4	646	Ctc/Ttc	14/14	0.240240237271623	5	FACETS	1	0.969	1	0.461	0.403	0.523	INDETERMINATE	1	FALSE	2	0.453859996061135	5		604	364	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55971017	55971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	32	666	0	ENST00000263923.4:c.1780C>T	p.His594Tyr	p.H594Y	ENST00000263923	NM_002253.2	594	Cat/Tat	13/30	0.413537735953815	3	FACETS	0.466	0.379	0.565	0.233	0.189	0.283	SUBCLONAL	1	FALSE	1	0.453859996061135	3		666	371	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294057	1294057	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369958224	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	27	765	1	ENST00000310581.5:c.944G>A	p.Arg315His	p.R315H	ENST00000310581	NM_198253.2	315	cGt/cAt	2/16	0.294096932017505	4	FACETS	0.437	0.347	0.539			1	SUBCLONAL	1	FALSE	NA	0.453859996061135	4		766	396	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873660	35873660	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs201559094	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	161	408	0	ENST00000303115.3:c.616C>T	p.Arg206Ter	p.R206*	ENST00000303115	NM_002185.3	206	Cga/Tga	5/8	0.453859996061135	5	FACETS	0.895	0.829	0.963	0.895	0.829	0.963	CLONAL	3	FALSE	2	0.453859996061135	5		408	444	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495375	149495375	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	83	504	0	ENST00000261799.4:c.3272A>G	p.Asp1091Gly	p.D1091G	ENST00000261799	NM_002609.3	1091	gAt/gGt	23/23	0.305660618583482	4	FACETS	0.88	0.785	0.98	0.88	0.785	0.98	CLONAL	2	FALSE	2	0.453859996061135	4		504	302	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166244	32166245	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	89	702	0	ENST00000375023.3:c.4709_4710delinsTT	p.Pro1570Leu	p.P1570L	ENST00000375023	NM_004557.3	1570	cCC/cTT	26/30	NA	2	FACETS	1	0.919	1			1	INDETERMINATE	1	FALSE	NA	0.453859996061135	2		702	379	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181896	32181896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	61	708	0	ENST00000375023.3:c.2158G>A	p.Gly720Ser	p.G720S	ENST00000375023	NM_004557.3	720	Ggc/Agc	13/30	NA	2	FACETS	0.864	0.751	0.986			1	INDETERMINATE	1	FALSE	NA	0.453859996061135	2		708	311	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641054	117641054	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1216964547	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	77	573	0	ENST00000368508.3:c.5917G>A	p.Gly1973Arg	p.G1973R	ENST00000368508	NM_002944.2	1973	Gga/Aga	36/43	0.288394973718652	3	FACETS	1	0.957	1	0.588	0.52	0.66	CLONAL	1	FALSE	1	0.453859996061135	3		573	354	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004308	150004308	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	123	671	1	ENST00000253339.5:c.1917T>A	p.Phe639Leu	p.F639L	ENST00000253339		639	ttT/ttA	3/7	0.290758222391497	5	FACETS	0.963	0.876	1	0.642	0.584	0.702	CLONAL	2	FALSE	2	0.453859996061135	5		672	473	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162622218	162622218	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	95	550	0	ENST00000366898.1:c.479G>A	p.Gly160Glu	p.G160E	ENST00000366898	NM_004562.2	160	gGa/gAa	4/12	0.290758222391497	5	FACETS	0.969	0.87	1	0.646	0.58	0.715	CLONAL	2	FALSE	2	0.453859996061135	5		550	363	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985560	2985561	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	114	402	0	ENST00000396946.4:c.250_251delinsAA	p.Gly84Lys	p.G84K	ENST00000396946	NM_032415.4	84	GGg/AAg	4/25	0.453859996061135	5	FACETS	1	0.966	1	0.753	0.684	0.823	CLONAL	2	FALSE	2	0.453859996061135	5		402	374	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50358670	50358670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	65	238	1	ENST00000331340.3:c.13G>A	p.Glu5Lys	p.E5K	ENST00000331340	NM_006060.4	5	Gag/Aag	2/8	0.453859996061135	5	FACETS	0.86	0.753	0.973	0.573	0.502	0.649	CLONAL	2	FALSE	2	0.453859996061135	5		239	280	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55269017	55269018	+	missense_variant	Missense_Mutation	DNP	CC	CC	TG	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	100	438	0	ENST00000275493.2:c.3083_3084delinsTG	p.Ser1028Leu	p.S1028L	ENST00000275493	NM_005228.3	1028	tCC/tTG	25/28	0.453859996061135	5	FACETS	1	0.969	1	0.786	0.711	0.864	CLONAL	2	FALSE	2	0.453859996061135	5		438	314	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851484	151851484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	173	581	0	ENST00000262189.6:c.12007C>T	p.Pro4003Ser	p.P4003S	ENST00000262189	NM_170606.2	4003	Ccc/Tcc	47/59	0.453859996061135	3	FACETS	1	0.987	1	0.823	0.768	0.878	CLONAL	2	FALSE	0	0.453859996061135	3		581	379	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317921	8317921	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150063446	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	49	628	0	ENST00000356435.5:c.5692C>T	p.Arg1898Cys	p.R1898C	ENST00000356435		1898	Cgt/Tgt	35/35	NA	2	FACETS	0.679	0.578	0.789			1	INDETERMINATE	1	FALSE	NA	0.453859996061135	2		628	318	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341941	8341941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	44	385	0	ENST00000356435.5:c.4699G>A	p.Asp1567Asn	p.D1567N	ENST00000356435		1567	Gat/Aat	29/35	NA	2	FACETS	0.68	0.574	0.797			1	INDETERMINATE	1	FALSE	NA	0.453859996061135	2		385	285	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485926	8485926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770180884	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	70	684	1	ENST00000356435.5:c.2891C>T	p.Pro964Leu	p.P964L	ENST00000356435		964	cCc/cTc	17/35	NA	2	FACETS	0.881	0.773	0.996			1	INDETERMINATE	1	FALSE	NA	0.453859996061135	2		685	350	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485962	8485962	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	74	720	0	ENST00000356435.5:c.2855C>T	p.Thr952Ile	p.T952I	ENST00000356435		952	aCc/aTc	17/35	NA	2	FACETS	0.901	0.794	1			1	INDETERMINATE	1	FALSE	NA	0.453859996061135	2		720	362	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570260	87570260	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777251032	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	56	410	0	ENST00000277120.3:c.2000C>T	p.Ser667Leu	p.S667L	ENST00000277120		667	tCg/tTg	17/19	0.298738546148155	3	FACETS	1	0.969	1			1	CLONAL	1	FALSE	NA	0.453859996061135	3		410	208	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399994	139399994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	67	569	1	ENST00000277541.6:c.4354C>T	p.Pro1452Ser	p.P1452S	ENST00000277541	NM_017617.3	1452	Ccc/Tcc	25/34	0.305660618583482	4	FACETS	1	0.962	1	0.635	0.555	0.72	CLONAL	1	FALSE	2	0.453859996061135	4		570	338	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137784	64137784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	134	757	1	ENST00000334205.4:c.1885C>T	p.Arg629Cys	p.R629C	ENST00000334205	NM_003942.2	629	Cgc/Tgc	15/17	0.424031319521274	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	FALSE	2	0.453859996061135	4		758	373	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514026	125514026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775909758	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	66	622	0	ENST00000428830.2:c.964C>T	p.Arg322Cys	p.R322C	ENST00000428830	NM_001114121.2	322	Cgc/Tgc	10/14	0.291325412013915	1	FACETS	0.596	0.52	0.678	0.596	0.52	0.678	SUBCLONAL	1	FALSE	0	0.453859996061135	1		622	377	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1039289	1039289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs11571421	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	156	595	0	ENST00000358495.3:c.208C>T	p.Arg70Trp	p.R70W	ENST00000358495	NM_134424.2	70	Cgg/Tgg	4/12	0.453859996061135	5	FACETS	0.949	0.879	1	0.949	0.879	1	CLONAL	3	FALSE	2	0.453859996061135	5		595	406	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435169	18435169	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	87	648	0	ENST00000266497.5:c.154C>T	p.Pro52Ser	p.P52S	ENST00000266497		52	Cca/Tca	1/31	0.290758222391497	5	FACETS	1	0.966	1	0.411	0.364	0.46	CLONAL	1	FALSE	2	0.453859996061135	5		648	523	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434663	49434663	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778904794	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	52	567	0	ENST00000301067.7:c.6890C>T	p.Pro2297Leu	p.P2297L	ENST00000301067	NM_003482.3	2297	cCt/cTt	31/54	0.290758222391497	5	FACETS	1	0.952	1	0.428	0.366	0.494	CLONAL	1	FALSE	2	0.453859996061135	5		567	300	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444788	49444789	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	66	665	0	ENST00000301067.7:c.2677_2678delinsTT	p.Pro893Phe	p.P893F	ENST00000301067	NM_003482.3	893	CCc/TTc	10/54	0.290758222391497	5	FACETS	1	0.971	1	0.484	0.422	0.549	CLONAL	1	FALSE	2	0.453859996061135	5		665	337	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444797	49444797	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	59	657	0	ENST00000301067.7:c.2669C>T	p.Ser890Phe	p.S890F	ENST00000301067	NM_003482.3	890	tCc/tTc	10/54	0.290758222391497	5	FACETS	1	0.963	1	0.45	0.389	0.515	CLONAL	1	FALSE	2	0.453859996061135	5		657	324	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145425	58145425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	114	499	0	ENST00000257904.6:c.76C>T	p.Pro26Ser	p.P26S	ENST00000257904	NM_000075.3	26	Ccc/Tcc	2/8	0.290758222391497	5	FACETS	0.918	0.831	1	0.612	0.554	0.672	CLONAL	2	FALSE	2	0.453859996061135	5		499	460	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622502	28622502	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	37	497	0	ENST00000241453.7:c.1115G>A	p.Arg372Lys	p.R372K	ENST00000241453	NM_004119.2	372	aGg/aAg	9/24	1	2	FACETS	0.57	0.472	0.679	0.57	0.472	0.679	SUBCLONAL	1	FALSE	1	0.453859996061135	2		497	286	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626813	28626813	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	18	422	0	ENST00000241453.7:c.485-2A>G		p.X162_splice	ENST00000241453	NM_004119.2	162			1	2	FACETS	0.431	0.326	0.554	0.431	0.326	0.554	SUBCLONAL	1	FALSE	1	0.453859996061135	2		422	184	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912123	32912123	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	117	1133	0	ENST00000380152.3:c.3631G>A	p.Glu1211Lys	p.E1211K	ENST00000380152		1211	Gaa/Aaa	11/27	1	2	FACETS	0.937	0.849	1	0.937	0.849	1	CLONAL	1	FALSE	1	0.453859996061135	2		1133	550	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105238774	105238775	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	59	580	0	ENST00000349310.3:c.1187_1188delinsTT	p.Ser396Phe	p.S396F	ENST00000349310	NM_001014432.1	396	tCC/tTT	13/15	0.24334873760441	5	FACETS	0.857	0.745	0.976	0.343	0.298	0.391	INDETERMINATE	2	FALSE	0	0.453859996061135	5		580	255	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42052689	42052689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	125	875	0	ENST00000219905.7:c.7360C>T	p.His2454Tyr	p.H2454Y	ENST00000219905	NM_001164273.1	2454	Cat/Tat	20/24	0.291325412013915	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	0	0.453859996061135	1		875	402	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670452	88670452	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143617169	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	57	590	0	ENST00000360948.2:c.1234G>A	p.Glu412Lys	p.E412K	ENST00000360948	NM_001012338.2	412	Gaa/Aaa	11/19	0.305660618583482	4	FACETS	1	0.948	1	0.607	0.524	0.695	CLONAL	1	FALSE	2	0.453859996061135	4		590	301	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467827	99467827	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	162	668	0	ENST00000268035.6:c.2696G>A	p.Gly899Glu	p.G899E	ENST00000268035	NM_000875.3	899	gGg/gAg	13/21	0.453859996061135	5	FACETS	0.985	0.915	1			1	CLONAL	3	FALSE	NA	0.453859996061135	5		668	406	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500550	99500550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1368444933	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	142	523	1	ENST00000268035.6:c.3983G>A	p.Gly1328Asp	p.G1328D	ENST00000268035	NM_000875.3	1328	gGc/gAc	21/21	0.453859996061135	5	FACETS	0.993	0.917	1			1	CLONAL	3	FALSE	NA	0.453859996061135	5		524	353	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354414	354414	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201609463	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	61	663	1	ENST00000262320.3:c.1144C>T	p.Arg382Cys	p.R382C	ENST00000262320	NM_003502.3	382	Cgc/Tgc	5/11	NA	2	FACETS	0.914	0.795	1			1	INDETERMINATE	1	FALSE	NA	0.453859996061135	2		664	294	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857524	9857524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778230379	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	44	363	2	ENST00000330684.3:c.3877G>A	p.Asp1293Asn	p.D1293N	ENST00000330684	NM_001134407.1	1293	Gat/Aat	13/13	NA	2	FACETS	1	0.906	1			1	INDETERMINATE	1	FALSE	NA	0.453859996061135	2		365	178	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032279	10032279	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	41	448	0	ENST00000330684.3:c.544G>A	p.Glu182Lys	p.E182K	ENST00000330684	NM_001134407.1	182	Gaa/Aaa	3/13	NA	2	FACETS	0.789	0.663	0.926			1	INDETERMINATE	1	FALSE	NA	0.453859996061135	2		448	229	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579717	7579717	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs922736614	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	72	591	0	ENST00000269305.4:c.79C>T	p.Pro27Ser	p.P27S	ENST00000269305	NM_001126112.2	27	Cct/Tct	3/11	0.28005259128465	2	FACETS	0.785	0.699	0.875	0.785	0.699	0.875	SUBCLONAL	2	FALSE	0	0.453859996061135	2		591	202	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701036	29701036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1475978079	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	12	330	0	ENST00000356175.3:c.8320G>A	p.Asp2774Asn	p.D2774N	ENST00000356175	NM_000267.3	2774	Gac/Aac	57/57	NA	2	FACETS	0.258	0.181	0.352			1	INDETERMINATE	1	FALSE	NA	0.453859996061135	2		330	205	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369299	40369299	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	105	825	0	ENST00000293328.3:c.1259C>T	p.Ser420Phe	p.S420F	ENST00000293328	NM_012448.3	420	tCc/tTc	11/19	0.453859996061135	3	FACETS	1	0.979	1	0.448	0.404	0.495	CLONAL	1	FALSE	0	0.453859996061135	3		825	422	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745842	745842	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	65	418	1	ENST00000314574.4:c.590C>T	p.Ser197Phe	p.S197F	ENST00000314574	NM_005433.3	197	tCt/tTt	6/12	0.413537735953815	3	FACETS	1	0.914	1	0.531	0.463	0.603	CLONAL	1	FALSE	1	0.453859996061135	3		419	331	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118990	3118990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	31	677	0	ENST00000078429.4:c.674C>T	p.Ser225Phe	p.S225F	ENST00000078429	NM_002067.2	225	tCc/tTc	5/7	0.288394973718652	3	FACETS	0.684	0.556	0.827	0.342	0.278	0.414	SUBCLONAL	1	FALSE	1	0.453859996061135	3		677	245	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222924	5222925	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	29	453	0	ENST00000357368.4:c.2878_2879delinsAA	p.Gly960Lys	p.G960K	ENST00000357368	NM_002850.3	960	GGg/AAg	18/38	0.288394973718652	3	FACETS	0.733	0.592	0.89	0.366	0.296	0.445	SUBCLONAL	1	FALSE	1	0.453859996061135	3		453	214	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240214	5240214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770776322	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	53	505	0	ENST00000357368.4:c.1700G>A	p.Arg567Gln	p.R567Q	ENST00000357368	NM_002850.3	567	cGg/cAg	12/38	0.288394973718652	3	FACETS	0.75	0.65	0.856	0.75	0.65	0.856	SUBCLONAL	2	FALSE	1	0.453859996061135	3		505	191	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249209	10249209	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	42	630	0	ENST00000340748.4:c.3973C>T	p.Pro1325Ser	p.P1325S	ENST00000340748		1325	Cct/Tct	34/40	0.288394973718652	3	FACETS	0.725	0.608	0.854	0.363	0.304	0.427	SUBCLONAL	1	FALSE	1	0.453859996061135	3		630	313	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10279006	10279007	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	69	612	0	ENST00000340748.4:c.754_755delinsTT	p.Pro252Leu	p.P252L	ENST00000340748		252	CCa/TTa	9/40	0.288394973718652	3	FACETS	1	0.915	1	0.528	0.463	0.598	CLONAL	1	FALSE	1	0.453859996061135	3		612	353	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257552	19257552	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	127	64	433	0	ENST00000162023.5:c.674C>T	p.Ser225Phe	p.S225F	ENST00000162023		225	tCc/tTc	10/13	0.294096932017505	4	FACETS	1	0.928	1			1	CLONAL	2	FALSE	NA	0.453859996061135	4		433	191	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383635	42383636	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	62	825	0	ENST00000221972.3:c.410_411delinsAA	p.Gly137Glu	p.G137E	ENST00000221972	NM_021601.3	137	gGG/gAA	3/5	0.453859996061135	4	FACETS	0.895	0.775	1			1	CLONAL	1	FALSE	NA	0.453859996061135	4		825	444	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523348	9523348	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	51	582	1	ENST00000353224.5:c.1889G>A	p.Gly630Glu	p.G630E	ENST00000353224	NM_177990.2	630	gGg/gAg	9/10	0.305660618583482	4	FACETS	1	0.856	1	0.501	0.428	0.581	CLONAL	1	FALSE	2	0.453859996061135	4		583	326	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023853	31023853	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	61	534	0	ENST00000375687.4:c.3338A>G	p.Gln1113Arg	p.Q1113R	ENST00000375687	NM_015338.5	1113	cAg/cGg	13/13	0.305660618583482	4	FACETS	1	0.924	1	0.549	0.476	0.627	CLONAL	1	FALSE	2	0.453859996061135	4		534	356	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40899090	40899090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1044332813	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	56	810	0	ENST00000373198.4:c.2180C>T	p.Pro727Leu	p.P727L	ENST00000373198	NM_133170.3	727	cCa/cTa	14/32	1	2	FACETS	0.834	0.719	0.956	0.834	0.719	0.956	CLONAL	1	FALSE	1	0.453859996061135	2		810	296	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514563	41514563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	44	304	0	ENST00000373198.4:c.98C>T	p.Ser33Phe	p.S33F	ENST00000373198	NM_133170.3	33	tCc/tTc	2/32	1	2	FACETS	0.729	0.615	0.853	0.729	0.615	0.853	SUBCLONAL	1	FALSE	1	0.453859996061135	2		304	266	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314906	1314906	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	67	665	0	ENST00000400841.2:c.755G>A	p.Trp252Ter	p.W252*	ENST00000400841		252	tGg/tAg	6/6	0.298738546148155	2	FACETS	1	0.929	1			1	CLONAL	1	FALSE	NA	0.453859996061135	2		665	272	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930342	39930342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	60	323	0	ENST00000378444.4:c.3122C>T	p.Ser1041Phe	p.S1041F	ENST00000378444	NM_001123385.1	1041	tCc/tTc	6/15	0.298738546148155	2	FACETS	0.837	0.738	0.939			1	CLONAL	2	FALSE	NA	0.453859996061135	2		323	158	SUCCESS
AR	367	MSKCC	GRCh37	X	66766249	66766249	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	33	231	0	ENST00000374690.3:c.1261G>A	p.Gly421Arg	p.G421R	ENST00000374690	NM_000044.3	421	Gga/Aga	1/8	0.291625682093708	0	FACETS	0.902	0.759	1			1	CLONAL	1	FALSE	NA	0.453859996061135	0		231	88	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025629	1025660	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACGGCGGATGAGCTCAGGCTTCTGCATGAGAG	ACGGCGGATGAGCTCAGGCTTCTGCATGAGAG	-	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	125	526	0	ENST00000358495.3:c.726-11_746del		p.X242_splice	ENST00000358495	NM_134424.2	242		9/12	0.453859996061135	5	FACETS	0.958	0.88	1	0.958	0.88	1	CLONAL	3	FALSE	2	0.453859996061135	5		526	322	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404595	70404614	+	frameshift_variant	Frame_Shift_Del	DEL	AGGCATCGAGGTGGAGAAGT	AGGCATCGAGGTGGAGAAGT	G	novel	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	98	723	0	ENST00000373644.4:c.2109_2128delinsG	p.Ile705HisfsTer8	p.I705Hfs*8	ENST00000373644	NM_030625.2	703	acAGGCATCGAGGTGGAGAAGTgg/acGgg	4/12	0.282589573010645	4	FACETS	0.756	0.679	0.837			1	SUBCLONAL	2	FALSE	NA	0.453859996061135	4		723	415	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574678	41574679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs754418509	NA	P-0006155-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	46	758	1	ENST00000263253.7:c.6970dup	p.His2324ProfsTer55	p.H2324Pfs*55	ENST00000263253	NM_001429.3	2321	-/C	31/31	0.240240237271623	5	FACETS	0.869	0.734	1	0.29	0.244	0.34	INDETERMINATE	1	FALSE	2	0.453859996061135	5		759	392	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006164-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	164	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.77	0.709	0.833	0.77	0.709	0.833	SUBCLONAL	1	TRUE	1	0.648485127106058	2		280	657	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0006164-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	159	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.96	0.886	1	0.96	0.886	1	CLONAL	1	TRUE	1	0.648485127106058	2		490	511	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5463007	5463007	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006164-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	145	422	0	ENST00000381577.3:c.568C>G	p.Leu190Val	p.L190V	ENST00000381577	NM_014143.3	190	Ctt/Gtt	4/7	1	2	FACETS	0.884	0.812	0.958	0.884	0.812	0.958	CLONAL	1	TRUE	1	0.648485127106058	2		422	506	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0006192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	182	229	0				ENST00000310581	NM_198253.2	-/1132			0.642654295980143	1	FACETS	0.561	0.525	0.598	0.561	0.525	0.598	SUBCLONAL	1	TRUE	0	0.895355678656054	1		229	400	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202896	16202896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	645	593	0	ENST00000375759.3:c.604G>A	p.Glu202Lys	p.E202K	ENST00000375759	NM_015001.2	202	Gaa/Aaa	3/15	0.491327508822291	1	FACETS	0.732	0.71	0.754	0.732	0.71	0.754	INDETERMINATE	1	TRUE	0	0.895355678656054	1		593	1087	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248773	212248773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	330	253	0	ENST00000342788.4:c.3494C>T	p.Pro1165Leu	p.P1165L	ENST00000342788	NM_005235.2	1165	cCa/cTa	28/28	0.440812797498311	1	FACETS	0.68	0.65	0.71	0.68	0.65	0.71	INDETERMINATE	1	TRUE	0	0.895355678656054	1		253	599	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566709	212566709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	563	360	2	ENST00000342788.4:c.1472G>A	p.Arg491Lys	p.R491K	ENST00000342788	NM_005235.2	491	aGa/aAa	12/28	0.440812797498311	1	FACETS	0.73	0.707	0.754	0.73	0.707	0.754	INDETERMINATE	1	TRUE	0	0.895355678656054	1		362	951	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549439	187549439	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs374571513	NA	P-0006192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	1160	490	0	ENST00000441802.2:c.4679C>G	p.Pro1560Arg	p.P1560R	ENST00000441802	NM_005245.3	1560	cCg/cGg	9/27	0.888031687556828	3	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	1	0.895355678656054	3		490	1820	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933397	100933397	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	837	721	0	ENST00000325455.5:c.1993G>A	p.Glu665Lys	p.E665K	ENST00000325455	NM_001202474.3	665	Gaa/Aaa	4/8	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.895355678656054	2		721	1825	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15989718	15989718	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	547	386	0	ENST00000268712.3:c.3055C>T	p.Pro1019Ser	p.P1019S	ENST00000268712	NM_006311.3	1019	Cct/Tct	23/46	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.895355678656054	2		386	1203	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210675	2210675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747494025	NA	P-0006192-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	335	549	0	ENST00000398665.3:c.1172C>T	p.Pro391Leu	p.P391L	ENST00000398665	NM_032482.2	391	cCc/cTc	14/28	0.240726758526115	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.895355678656054	0		549	820	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0006194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	890	464	0				ENST00000310581	NM_198253.2	-/1132			0.851083122200141	8	FACETS	1	0.982	1	1	0.982	1	CLONAL	6	TRUE	2	0.851083122200141	8		464	1233	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0006194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	431	251	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.851083122200141	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.851083122200141	2		251	485	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097233	178097233	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	151	638	0	ENST00000397062.3:c.481C>G	p.Gln161Glu	p.Q161E	ENST00000397062	NM_006164.4	161	Cag/Gag	4/5	0.668097019461724	4	FACETS	1	0.933	1	0.51	0.468	0.554	CLONAL	1	TRUE	2	0.851083122200141	4		638	644	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346669	225346669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	284	571	0	ENST00000264414.4:c.1969C>T	p.His657Tyr	p.H657Y	ENST00000264414	NM_003590.4	657	Cat/Tat	14/16	0.668097019461724	4	FACETS	0.936	0.886	0.986	0.936	0.886	0.986	CLONAL	2	TRUE	2	0.851083122200141	4		571	660	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843416	3843416	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	166	438	1	ENST00000262367.5:c.1187C>A	p.Thr396Lys	p.T396K	ENST00000262367	NM_004380.2	396	aCg/aAg	4/31	0.707143096239723	3	FACETS	0.988	0.913	1	0.494	0.456	0.533	CLONAL	1	TRUE	1	0.851083122200141	3		439	563	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490346	29490346	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	151	538	0	ENST00000356175.3:c.431C>G	p.Ser144Cys	p.S144C	ENST00000356175	NM_000267.3	144	tCt/tGt	4/57	0.851083122200141	4	FACETS	1	0.968	1	0.555	0.509	0.602	CLONAL	1	TRUE	2	0.851083122200141	4		538	592	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076933	41076933	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs554343349	NA	P-0006194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	151	571	0	ENST00000373198.4:c.1487G>T	p.Gly496Val	p.G496V	ENST00000373198	NM_133170.3	496	gGg/gTg	9/32	0.773503953527277	4	FACETS	1	0.933	1	0.51	0.468	0.554	CLONAL	1	TRUE	2	0.851083122200141	4		571	644	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135797271	135797272	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0006194-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	504	597	0	ENST00000298552.3:c.597dup	p.Val200ArgfsTer18	p.V200Rfs*18	ENST00000298552	NM_001162426.1	199	-/C	7/23	0.851083122200141	3	FACETS	0.957	0.937	0.976	0.957	0.937	0.976	CLONAL	3	TRUE	0	0.851083122200141	3		597	588	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006199-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	101	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.497060250523124	2		280	312	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913407	NA	P-0006199-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	360	333	0	ENST00000349496.5:c.133T>G	p.Ser45Ala	p.S45A	ENST00000349496	NM_001904.3	45	Tct/Gct	3/15	0.497060250523124	3	FACETS	0.847	0.809	0.884	1	0.994	1	CLONAL	3	TRUE	1	0.497060250523124	3		333	712	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582277	119582277	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006199-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	290	259	0	ENST00000316626.5:c.1124T>G	p.Phe375Cys	p.F375C	ENST00000316626		375	tTc/tGc	10/12	0.379421535543258	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.497060250523124	2		259	468	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166739	32166739	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1157907497	NA	P-0006199-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	223	410	0	ENST00000375023.3:c.4499G>A	p.Arg1500His	p.R1500H	ENST00000375023	NM_004557.3	1500	cGc/cAc	24/30	0.172652465657328	5	FACETS	0.969	0.905	1			1	INDETERMINATE	2	TRUE	NA	0.497060250523124	5		410	808	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878466	151878466	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006199-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	198	425	0	ENST00000262189.6:c.6479C>G	p.Ser2160Cys	p.S2160C	ENST00000262189	NM_170606.2	2160	tCt/tGt	36/59	0.411401770794766	3	FACETS	0.814	0.758	0.871	0.814	0.758	0.871	CLONAL	2	TRUE	1	0.497060250523124	3		425	611	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448170	49448170	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006199-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	295	419	1	ENST00000301067.7:c.430G>T	p.Ala144Ser	p.A144S	ENST00000301067	NM_003482.3	144	Gca/Tca	4/54	0.497060250523124	3	FACETS	0.92	0.87	0.972	0.92	0.87	0.972	CLONAL	2	TRUE	1	0.497060250523124	3		420	805	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987186	36987186	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006199-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	61	231	0	ENST00000354822.5:c.503G>T	p.Ser168Ile	p.S168I	ENST00000354822	NM_001079668.2	168	aGc/aTc	3/3	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.497060250523124	2		231	202	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687492	37687507	+	frameshift_variant	Frame_Shift_Del	DEL	TCTGCTTATGGAAAAC	TCTGCTTATGGAAAAC	-	novel	NA	P-0006199-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	141	240	0	ENST00000447079.4:c.4399_4414del	p.Ala1467IlefsTer27	p.A1467Ifs*27	ENST00000447079	NM_015083.1	1466	TCTGCTTATGGAAAACtc/tc	14/14	0.411401770794766	3	FACETS	1	0.934	1	1	0.934	1	CLONAL	2	TRUE	1	0.497060250523124	3		240	350	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006204-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	40	280	0				ENST00000310581	NM_198253.2	-/1132			0.320985381911269	2	FACETS	0.715	0.598	0.844	0.358	0.299	0.422	SUBCLONAL	1	TRUE	0	0.420452154203537	2		280	266	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244257	5244257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006204-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	126	508	1	ENST00000357368.4:c.1225G>A	p.Gly409Ser	p.G409S	ENST00000357368	NM_002850.3	409	Ggc/Agc	11/38	0.190668820986042	0	FACETS	0.705	0.642	0.77			1	INDETERMINATE	1	TRUE	0	0.420452154203537	0		509	493	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410343	63410343	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1404477878	NA	P-0006204-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	44	346	1	ENST00000330258.3:c.2824C>T	p.Arg942Ter	p.R942*	ENST00000330258	NM_152424.3	942	Cga/Tga	2/2	1	1	FACETS	0.471	0.396	0.553	0.471	0.396	0.553	SUBCLONAL	1	TRUE	0	0.420452154203537	1		347	351	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0006209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	379	464	0				ENST00000310581	NM_198253.2	-/1132			0.367584356603011	3	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	1	0.410776726680425	3		464	1026	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913233	NA	P-0006209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	292	484	0	ENST00000451590.1:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000451590	NM_001130442.1	61	cAg/cTg	3/5	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.410776726680425	2		484	1295	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247367	153247367	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs747241612	NA	P-0006209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	94	261	0	ENST00000281708.4:c.1435C>G	p.Arg479Gly	p.R479G	ENST00000281708	NM_033632.3	479	Cga/Gga	10/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.410776726680425	2		261	406	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856356	45856356	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	287	514	0	ENST00000391945.4:c.1816G>C	p.Glu606Gln	p.E606Q	ENST00000391945	NM_000400.3	606	Gag/Cag	19/23	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.410776726680425	2		514	1307	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941653	48941653	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0006209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	112	301	0	ENST00000267163.4:c.963C>G	p.Tyr321Ter	p.Y321*	ENST00000267163	NM_000321.2	321	taC/taG	10/27	1	2	FACETS	0.887	0.799	0.979	0.887	0.799	0.979	CLONAL	1	TRUE	1	0.410776726680425	2		301	615	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856640	111856640	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs899111445	NA	P-0006209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	180	286	0	ENST00000341259.2:c.691G>A	p.Asp231Asn	p.D231N	ENST00000341259	NM_005475.2	231	Gat/Aat	2/8	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.410776726680425	2		286	657	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432598	78432598	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs960308225	NA	P-0006209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	158	264	0	ENST00000370768.2:c.385G>C	p.Glu129Gln	p.E129Q	ENST00000370768	NM_003902.3	129	Gaa/Caa	6/20	0.354987329858592	2	FACETS	0.934	0.865	1	0.934	0.865	1	CLONAL	2	TRUE	0	0.410776726680425	2		264	412	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874261	155874261	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs483352822	NA	P-0006209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	265	347	3	ENST00000368323.3:c.270G>T	p.Met90Ile	p.M90I	ENST00000368323	NM_006912.5	90	atG/atT	5/6	0.402619658694719	4	FACETS	0.898	0.842	0.955	0.898	0.842	0.955	CLONAL	2	TRUE	2	0.410776726680425	4		350	1014	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183659	10183659	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	271	512	1	ENST00000256474.2:c.128C>T	p.Ser43Phe	p.S43F	ENST00000256474	NM_000551.3	43	tCc/tTc	1/3	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.410776726680425	2		513	1265	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946214	55946214	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	227	495	0	ENST00000263923.4:c.3965A>C	p.Glu1322Ala	p.E1322A	ENST00000263923	NM_002253.2	1322	gAg/gCg	30/30	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.410776726680425	2		495	1068	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285798	87285798	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	260	477	0	ENST00000277120.3:c.135C>A	p.Cys45Ter	p.C45*	ENST00000277120		45	tgC/tgA	2/19	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.410776726680425	2		477	1235	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442781	442781	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	153	319	0	ENST00000399788.2:c.1525C>T	p.His509Tyr	p.H509Y	ENST00000399788	NM_001042603.1	509	Cat/Tat	12/28	1	2	FACETS	0.936	0.857	1	0.936	0.857	1	CLONAL	1	TRUE	1	0.410776726680425	2		319	796	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298815	46298815	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	133	360	0	ENST00000334344.6:c.5462C>A	p.Thr1821Lys	p.T1821K	ENST00000334344	NM_152641.2	1821	aCa/aAa	21/21	1	2	FACETS	0.925	0.842	1	0.925	0.842	1	CLONAL	1	TRUE	1	0.410776726680425	2		360	700	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490296	56490296	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	129	335	0	ENST00000267101.3:c.2065C>T	p.Pro689Ser	p.P689S	ENST00000267101	NM_001982.3	689	Cct/Tct	18/28	1	2	FACETS	0.869	0.789	0.953	0.869	0.789	0.953	CLONAL	1	TRUE	1	0.410776726680425	2		335	723	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49037866	49037866	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs587778860	NA	P-0006209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	74	322	0	ENST00000267163.4:c.2107-1G>A		p.X703_splice	ENST00000267163	NM_000321.2	703			1	2	FACETS	0.854	0.751	0.964	0.854	0.751	0.964	CLONAL	1	TRUE	1	0.410776726680425	2		322	422	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465586	99465586	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	142	297	0	ENST00000268035.6:c.2411A>G	p.His804Arg	p.H804R	ENST00000268035	NM_000875.3	804	cAc/cGc	11/21	1	2	FACETS	0.851	0.776	0.93	0.851	0.776	0.93	CLONAL	1	TRUE	1	0.410776726680425	2		297	812	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788662	3788662	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	395	426	0	ENST00000262367.5:c.4292T>G	p.Ile1431Ser	p.I1431S	ENST00000262367	NM_004380.2	1431	aTt/aGt	26/31	0.354987329858592	2	FACETS	0.943	0.899	0.987	0.943	0.899	0.987	CLONAL	2	TRUE	0	0.410776726680425	2		426	1020	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991796	72991796	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1357	298	599	0	ENST00000268489.5:c.2249A>G	p.His750Arg	p.H750R	ENST00000268489	NM_006885.3	750	cAt/cGt	2/10	1	2	FACETS	0.877	0.823	0.932	0.877	0.823	0.932	CLONAL	1	TRUE	1	0.410776726680425	2		599	1655	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490318	29490318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775191883	NA	P-0006209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	116	411	0	ENST00000356175.3:c.403C>T	p.Arg135Trp	p.R135W	ENST00000356175	NM_000267.3	135	Cgg/Tgg	4/57	1	2	FACETS	0.771	0.695	0.85	0.771	0.695	0.85	SUBCLONAL	1	TRUE	1	0.410776726680425	2		411	733	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866707	37866707	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	233	396	0	ENST00000269571.5:c.874G>C	p.Gly292Arg	p.G292R	ENST00000269571		292	Ggc/Cgc	7/27	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.410776726680425	2		396	1079	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1327792	1327792	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	203	367	0	ENST00000400841.2:c.89T>A	p.Val30Glu	p.V30E	ENST00000400841		30	gTa/gAa	2/6	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.410776726680425	2		367	869	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833957	44833957	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	169	645	1	ENST00000377967.4:c.381G>A	p.Trp127Ter	p.W127*	ENST00000377967	NM_021140.2	127	tgG/tgA	4/29	1	2	FACETS	0.953	0.877	1	0.953	0.877	1	CLONAL	1	TRUE	1	0.410776726680425	2		646	863	SUCCESS
AR	367	MSKCC	GRCh37	X	66766040	66766040	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	247	502	1	ENST00000374690.3:c.1052G>A	p.Gly351Glu	p.G351E	ENST00000374690	NM_000044.3	351	gGa/gAa	1/8	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.410776726680425	2		503	1163	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427029	49427040	+	inframe_deletion	In_Frame_Del	DEL	GGGCCCAAAGCT	GGGCCCAAAGCT	-	novel	NA	P-0006209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	155	322	0	ENST00000301067.7:c.11448_11459del	p.Ala3817_Pro3820del	p.A3817_P3820del	ENST00000301067	NM_003482.3	3816	ggAGCTTTGGGCCCc/ggc	39/54	1	2	FACETS	0.937	0.859	1	0.937	0.859	1	CLONAL	1	TRUE	1	0.410776726680425	2		322	805	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023753	27023753	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1383675220	NA	P-0006209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	616	453	0	ENST00000324856.7:c.862del	p.Gln288SerfsTer75	p.Q288Sfs*75	ENST00000324856	NM_006015.4	287	Ccc/cc	1/20	0.354987329858592	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.410776726680425	2		453	1260	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023728	27023749	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCTCCGCGGCCGGCGGGGGA	CCCCTCCGCGGCCGGCGGGGGA	-	novel	NA	P-0006209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	600	453	0	ENST00000324856.7:c.834_855del	p.Pro279LeufsTer77	p.P279Lfs*77	ENST00000324856	NM_006015.4	278	ggCCCCTCCGCGGCCGGCGGGGGA/gg	1/20	0.354987329858592	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.410776726680425	2		453	1299	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118363844	118363845	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ATCCACCAGTTCTTACTGAGGTC	novel	NA	P-0006209-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	121	480	0	ENST00000534358.1:c.5079_5101dup	p.Ser1701IlefsTer17	p.S1701Ifs*17	ENST00000534358	NM_005933.3	1693	gat/gATCCACCAGTTCTTACTGAGGTCat	16/36	0.410776726680425	1	FACETS	0.554	0.5	0.611	0.554	0.5	0.611	SUBCLONAL	1	TRUE	0	0.410776726680425	1		480	845	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	49	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.882	0.768	1	0.882	0.768	1	CLONAL	1	TRUE	1	0.881778950849768	2		280	126	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0006218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	70	595	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.986	0.882	1	0.986	0.882	1	CLONAL	1	TRUE	1	0.881778950849768	2		595	161	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225306	2225306	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	62	541	1	ENST00000326181.6:c.1391G>A	p.Trp464Ter	p.W464*	ENST00000326181	NM_032271.2	464	tGg/tAg	16/21	1	2	FACETS	0.997	0.886	1	0.997	0.886	1	CLONAL	1	TRUE	1	0.881778950849768	2		542	141	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	66	468	0	ENST00000269305.4:c.775G>A	p.Asp259Asn	p.D259N	ENST00000269305	NM_001126112.2	259	Gac/Aac	7/11	1	2	FACETS	0.985	0.878	1	0.985	0.878	1	CLONAL	1	TRUE	1	0.881778950849768	2		468	152	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44833923	44833924	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0006218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	67	335	0	ENST00000377967.4:c.349dup	p.Gln117ProfsTer9	p.Q117Pfs*9	ENST00000377967	NM_021140.2	116	tac/taCc	4/29	1	1	FACETS	0.988	0.917	1	0.988	0.917	1	CLONAL	1	TRUE	0	0.881778950849768	1		335	86	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224554	123224555	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	25	402	0	ENST00000218089.9:c.3408dup	p.Ser1137Ter	p.S1137*	ENST00000218089	NM_001042749.1	1136	gat/gaTt	31/35	1	1	FACETS	0.311	0.25	0.378	0.311	0.25	0.378	SUBCLONAL	1	TRUE	0	0.881778950849768	1		402	102	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105635	27105636	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0006218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	32	659	0	ENST00000324856.7:c.5247_5248dup	p.Phe1750CysfsTer21	p.F1750Cfs*21	ENST00000324856	NM_006015.4	1749	agg/agGTg	20/20	1	2	FACETS	0.38	0.311	0.456	0.38	0.311	0.456	SUBCLONAL	1	TRUE	1	0.881778950849768	2		659	191	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039668	47039668	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20	94	381	0	ENST00000377604.3:c.1121del	p.Gly374AlafsTer111	p.G374Afs*111	ENST00000377604	NM_001204468.1	374	Ggc/gc	11/24	1	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.881778950849768	1		381	114	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0006233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	65	464	0				ENST00000310581	NM_198253.2	-/1132			0.154360556592769	1	FACETS	0.791	0.688	0.902	0.791	0.688	0.902	INDETERMINATE	1	TRUE	0	0.308259370732694	1		464	451	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0006233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	46	599	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.299933411407259	2	FACETS	0.338	0.284	0.399	0.169	0.142	0.2	SUBCLONAL	1	TRUE	0	0.308259370732694	2		599	882	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29090022	29090022	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs876659250	NA	P-0006233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	14	167	0	ENST00000328354.6:c.1459C>T	p.Gln487Ter	p.Q487*	ENST00000328354	NM_007194.3	487	Cag/Tag	13/15	1	2	FACETS	0.571	0.415	0.759	0.571	0.415	0.759	SUBCLONAL	1	TRUE	1	0.308259370732694	2		167	159	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0006233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	20	497	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	0.202	0.154	0.259	0.202	0.154	0.259	SUBCLONAL	1	TRUE	1	0.308259370732694	2		497	642	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48584560	48584560	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	43	683	0	ENST00000342988.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000342988	NM_005359.5	245	Cag/Tag	6/12	1	2	FACETS	0.494	0.413	0.584	0.494	0.413	0.584	SUBCLONAL	1	TRUE	1	0.308259370732694	2		683	565	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255721	16255721	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	62	565	1	ENST00000375759.3:c.2986G>A	p.Glu996Lys	p.E996K	ENST00000375759	NM_015001.2	996	Gaa/Aaa	11/15	1	2	FACETS	0.769	0.665	0.882	0.769	0.665	0.882	SUBCLONAL	1	TRUE	1	0.308259370732694	2		566	523	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733534	85733534	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1258904674	NA	P-0006233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	144	1166	0	ENST00000370580.1:c.478T>A	p.Ser160Thr	p.S160T	ENST00000370580	NM_003921.4	160	Tcc/Acc	3/3	1	2	FACETS	0.999	0.911	1	0.999	0.911	1	CLONAL	1	TRUE	1	0.308259370732694	2		1166	935	SUCCESS
ATR	545	MSKCC	GRCh37	3	142242909	142242909	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	80	738	1	ENST00000350721.4:c.4078G>C	p.Glu1360Gln	p.E1360Q	ENST00000350721	NM_001184.3	1360	Gaa/Caa	22/47	1	2	FACETS	0.752	0.662	0.849	0.752	0.662	0.849	SUBCLONAL	1	TRUE	1	0.308259370732694	2		739	690	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295193	1295193	+	upstream_gene_variant	5'Flank	SNP	G	G	C	novel	NA	P-0006233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	40	384	0				ENST00000310581	NM_198253.2	-/1132			0.154360556592769	1	FACETS	0.722	0.603	0.854	0.722	0.603	0.854	INDETERMINATE	1	TRUE	0	0.308259370732694	1		384	304	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675515	30675515	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	126	874	0	ENST00000376406.3:c.2841G>C	p.Gln947His	p.Q947H	ENST00000376406	NM_014641.2	947	caG/caC	8/15	1	2	FACETS	0.894	0.809	0.984	0.894	0.809	0.984	CLONAL	1	TRUE	1	0.308259370732694	2		874	914	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675551	30675551	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	152	1100	0	ENST00000376406.3:c.2805G>C	p.Glu935Asp	p.E935D	ENST00000376406	NM_014641.2	935	gaG/gaC	8/15	1	2	FACETS	0.88	0.803	0.96	0.88	0.803	0.96	CLONAL	1	TRUE	1	0.308259370732694	2		1100	1121	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075194	16075194	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	114	315	0	ENST00000268712.3:c.358C>T	p.Gln120Ter	p.Q120*	ENST00000268712	NM_006311.3	120	Cag/Tag	4/46	0.191216093035592	2	FACETS	1	0.982	1	0.694	0.627	0.764	CLONAL	1	TRUE	0	0.308259370732694	2		315	533	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586058	29586058	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876660206	NA	P-0006233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	99	452	0	ENST00000356175.3:c.4278G>C	p.Gln1426His	p.Q1426H	ENST00000356175	NM_000267.3	1426	caG/caC	32/57	0.308259370732694	3	FACETS	1	0.914	1			1	CLONAL	2	TRUE	NA	0.308259370732694	3		452	365	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56409177	56409177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258933374	NA	P-0006233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	52	1015	3	ENST00000348428.3:c.1684G>A	p.Asp562Asn	p.D562N	ENST00000348428	NM_006785.3	562	Gat/Aat	14/17	1	2	FACETS	0.396	0.336	0.463	0.396	0.336	0.463	SUBCLONAL	1	TRUE	1	0.308259370732694	2		1018	851	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743882	41743882	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	52	876	0	ENST00000301178.4:c.817G>C	p.Ala273Pro	p.A273P	ENST00000301178	NM_021913.4	273	Gcg/Ccg	7/20	1	2	FACETS	0.368	0.312	0.43	0.368	0.312	0.43	SUBCLONAL	1	TRUE	1	0.308259370732694	2		876	917	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551100	41551100	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	110	781	1	ENST00000263253.7:c.3244C>T	p.Gln1082Ter	p.Q1082*	ENST00000263253	NM_001429.3	1082	Cag/Tag	17/31	1	2	FACETS	0.852	0.765	0.944	0.852	0.765	0.944	CLONAL	1	TRUE	1	0.308259370732694	2		782	838	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574304	41574304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	151	902	4	ENST00000263253.7:c.6589G>A	p.Ala2197Thr	p.A2197T	ENST00000263253	NM_001429.3	2197	Gca/Aca	31/31	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.308259370732694	2		906	960	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089465	27089468	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	TGGC	TGGC	-	novel	NA	P-0006233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	88	538	0	ENST00000324856.7:c.2422_2425del	p.Gly808ThrfsTer24	p.G808Tfs*24	ENST00000324856	NM_006015.4	807	ggTGGC/gg	8/20	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.308259370732694	2		538	553	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137403	202137413	+	frameshift_variant	Frame_Shift_Del	DEL	CTGGGAGAAGG	CTGGGAGAAGG	-	novel	NA	P-0006233-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	86	533	0	ENST00000358485.4:c.631_641del	p.Leu211LysfsTer24	p.L211Kfs*24	ENST00000358485	NM_001080125.1	211	CTGGGAGAAGGa/a	4/9	1	2	FACETS	0.873	0.773	0.98	0.873	0.773	0.98	CLONAL	1	TRUE	1	0.308259370732694	2		533	639	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	192	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.923	0.859	0.989	0.923	0.859	0.989	CLONAL	1	TRUE	1	0.699079544977987	2		280	595	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0006259-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	246	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.955	0.897	1	0.955	0.897	1	CLONAL	1	TRUE	1	0.699079544977987	2		490	737	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0006312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	12	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.985	0.702	1	0.985	0.702	1	CLONAL	1	TRUE	1	0.28	2		464	87	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006312-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	24	258	1	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	1	2	FACETS	1	0.819	1	1	0.819	1	CLONAL	1	TRUE	1	0.28	2		259	165	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0006312-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	244	464	0				ENST00000310581	NM_198253.2	-/1132			0.345503681009189	4	FACETS	1	0.951	1	1	0.951	1	CLONAL	3	TRUE	1	0.36212903284808	4		464	605	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577558	7577558	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006312-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	253	258	1	ENST00000269305.4:c.723del	p.Cys242AlafsTer5	p.C242Afs*5	ENST00000269305	NM_001126112.2	241	tcC/tc	7/11	0.36212903284808	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.36212903284808	2		259	666	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913288	32913288	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs149759218	NA	P-0006312-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	441	597	0	ENST00000380152.3:c.4796A>G	p.Asn1599Ser	p.N1599S	ENST00000380152		1599	aAt/aGt	11/27	0.36212903284808	2	FACETS	0.913	0.871	0.956	0.913	0.871	0.956	CLONAL	2	TRUE	0	0.36212903284808	2		597	1334	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554837	187554837	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs780613153	NA	P-0006312-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	122	266	0	ENST00000441802.2:c.4323+1G>A		p.X1441_splice	ENST00000441802	NM_005245.3	1441			0.343022394690673	4	FACETS	1	0.92	1	0.51	0.461	0.563	CLONAL	1	TRUE	2	0.36212903284808	4		266	899	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118599	11118599	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006312-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	96	244	1	ENST00000358026.2:c.2023C>T	p.Gln675Ter	p.Q675*	ENST00000358026	NM_001128849.1	675	Cag/Tag	14/36	1	2	FACETS	0.881	0.786	0.981	0.881	0.786	0.981	CLONAL	1	TRUE	1	0.36212903284808	2		245	602	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971155	21971694	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCTGCCCATCATCATGACCTGCCAGAGAGAACAGAATGGTCAGAGCCAGGGTGGGGGCCGGCATGACGGAAAGGAAGCTTGTGTAGAGCCCCCTCACCGCCAAGCAGACCCCCACACAAGCCCCAGGTGTCTAATTACCCCTACATTTGCTTCCAGTTTCCAATTTCCTTCTTGAGTTCTCTATCCATTCTTCAGTACACAATGAATTCCATTATATCCTCCGAACTTCTGCGGAGCTGTCGTCACAGGCAGAGAGCACTGTGAGGCACGGGCAAAATAGCAAAGGGGCAGGGACAGACTGACTTTTACTCCAGGCTAACTTCCTGTATTTCCCCTGAGATACAACTACTGAAATTTCTTCCTGAAATTATGTTAGGCCTGGAGATTTTTTTTTTTTTTTTTGTTCACTGCTGTATATCCAAGCGCAGAATGTGGTAATTGTTAAAAAGAGAAAACTTGTTTGTTTGTTAAAACAAATTCTCACAAAACTTTTAAGTTACACTTA	GCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCTGCCCATCATCATGACCTGCCAGAGAGAACAGAATGGTCAGAGCCAGGGTGGGGGCCGGCATGACGGAAAGGAAGCTTGTGTAGAGCCCCCTCACCGCCAAGCAGACCCCCACACAAGCCCCAGGTGTCTAATTACCCCTACATTTGCTTCCAGTTTCCAATTTCCTTCTTGAGTTCTCTATCCATTCTTCAGTACACAATGAATTCCATTATATCCTCCGAACTTCTGCGGAGCTGTCGTCACAGGCAGAGAGCACTGTGAGGCACGGGCAAAATAGCAAAGGGGCAGGGACAGACTGACTTTTACTCCAGGCTAACTTCCTGTATTTCCCCTGAGATACAACTACTGAAATTTCTTCCTGAAATTATGTTAGGCCTGGAGATTTTTTTTTTTTTTTTTGTTCACTGCTGTATATCCAAGCGCAGAATGTGGTAATTGTTAAAAAGAGAAAACTTGTTTGTTTGTTAAAACAAATTCTCACAAAACTTTTAAGTTACACTTA	-	novel	NA	P-0006312-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	86	51	0	ENST00000304494.5:c.151-487_203del		p.X51_splice	ENST00000304494	NM_000077.4	51		2/3	0.353011830609069	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	0	0.36212903284808	3		51	163	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0006361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	140	464	0				ENST00000310581	NM_198253.2	-/1132			0.440838608392026	1	FACETS	0.482	0.441	0.525	0.482	0.441	0.525	SUBCLONAL	1	TRUE	0	0.685425840630758	1		464	557	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145401	61145401	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006361-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	73	784	3	ENST00000295025.8:c.611T>A	p.Ile204Lys	p.I204K	ENST00000295025	NM_002908.2	204	aTa/aAa	6/11	0.440838608392026	1	FACETS	0.385	0.338	0.434	0.385	0.338	0.434	SUBCLONAL	1	TRUE	0	0.685425840630758	1		787	364	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401074	139401074	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746910989	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	319	405	1	ENST00000277541.6:c.3919G>A	p.Val1307Ile	p.V1307I	ENST00000277541	NM_017617.3	1307	Gtc/Atc	24/34	0.461252318758451	1	FACETS	0.96	0.907	1	0.96	0.907	1	CLONAL	1	TRUE	0	0.461252318758451	1		406	1108	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332337	70332337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761821309	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	355	513	2	ENST00000373644.4:c.242G>A	p.Arg81His	p.R81H	ENST00000373644	NM_030625.2	81	cGc/cAc	2/12	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.461252318758451	2		515	1484	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105930	27105931	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs758608743	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	302	325	0	ENST00000324856.7:c.5548dup	p.Asp1850GlyfsTer4	p.D1850Gfs*4	ENST00000324856	NM_006015.4	1847	-/G	20/20	1	2	FACETS	0.927	0.871	0.984	0.927	0.871	0.984	CLONAL	1	TRUE	1	0.461252318758451	2		325	1413	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308383	15308383	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1235	373	356	0	ENST00000263388.2:c.125del	p.Pro42LeufsTer194	p.P42Lfs*194	ENST00000263388	NM_000435.2	42	cCt/ct	2/33	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.461252318758451	2		356	1608	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126730	5126730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1437629509	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	276	406	0	ENST00000381652.3:c.3338G>A	p.Arg1113His	p.R1113H	ENST00000381652	NM_004972.3	1113	cGc/cAc	25/25	0.461252318758451	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.461252318758451	1		406	841	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434352	49434352	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748969699	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1302	382	411	0	ENST00000301067.7:c.7201C>T	p.Arg2401Cys	p.R2401C	ENST00000301067	NM_003482.3	2401	Cgc/Tgc	31/54	1	2	FACETS	0.984	0.932	1	0.984	0.932	1	CLONAL	1	TRUE	1	0.461252318758451	2		411	1684	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375045	31375045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745506485	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	309	302	0	ENST00000328111.2:c.442C>T	p.Arg148Trp	p.R148W	ENST00000328111	NM_006892.3	148	Cgg/Tgg	6/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.461252318758451	2		302	1293	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481411	140481411	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913351	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	357	325	0	ENST00000288602.6:c.1397G>A	p.Gly466Glu	p.G466E	ENST00000288602	NM_004333.4	466	gGa/gAa	11/18	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	1	TRUE	NA	0.461252318758451	2		325	1216	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578493	7578493	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1206165503	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	426	416	0	ENST00000269305.4:c.437G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tGg/tAg	5/11	0.461252318758451	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.461252318758451	1		416	1398	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44911017	44911017	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	422	263	0	ENST00000377967.4:c.718C>T	p.Gln240Ter	p.Q240*	ENST00000377967	NM_021140.2	240	Caa/Taa	9/29	1	1	FACETS	0.765	0.732	0.798	1	0.996	1	SUBCLONAL	2	TRUE	0	0.461252318758451	1		263	920	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225365174	225365174	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	298	345	1	ENST00000264414.4:c.1516C>T	p.Arg506Trp	p.R506W	ENST00000264414	NM_003590.4	506	Cgg/Tgg	11/16	1	2	FACETS	0.978	0.92	1	0.978	0.92	1	CLONAL	1	TRUE	1	0.461252318758451	2		346	1321	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262742	16262742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769028117	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	147	153	1	ENST00000375759.3:c.10007G>A	p.Arg3336Gln	p.R3336Q	ENST00000375759	NM_015001.2	3336	cGg/cAg	11/15	1	2	FACETS	0.877	0.802	0.955	0.877	0.802	0.955	CLONAL	1	TRUE	1	0.461252318758451	2		154	727	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844744	156844744	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1226	997	586	0	ENST00000524377.1:c.1298C>A	p.Ser433Tyr	p.S433Y	ENST00000524377	NM_002529.3	433	tCt/tAt	11/17	0.454931482790584	2	FACETS	0.972	0.945	1	0.972	0.945	1	CLONAL	2	TRUE	0	0.461252318758451	2		586	2223	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703506	47703506	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs63751640	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	257	431	0	ENST00000233146.2:c.2006G>A	p.Gly669Asp	p.G669D	ENST00000233146	NM_000251.2	669	gGc/gAc	13/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.461252318758451	2		431	1084	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248666	212248666	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770116535	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	197	456	0	ENST00000342788.4:c.3601G>A	p.Glu1201Lys	p.E1201K	ENST00000342788	NM_005235.2	1201	Gag/Aag	28/28	1	2	FACETS	0.858	0.794	0.924	0.858	0.794	0.924	CLONAL	1	TRUE	1	0.461252318758451	2		456	996	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225362541	225362541	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs767240461	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	271	362	0	ENST00000264414.4:c.1636C>T	p.Arg546Ter	p.R546*	ENST00000264414	NM_003590.4	546	Cga/Tga	12/16	1	2	FACETS	0.997	0.935	1	0.997	0.935	1	CLONAL	1	TRUE	1	0.461252318758451	2		362	1179	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178937446	178937446	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	194	227	0	ENST00000263967.3:c.1834C>T	p.Arg612Ter	p.R612*	ENST00000263967	NM_006218.2	612	Cga/Tga	12/21	0.337578317326454	4	FACETS	0.75	0.695	0.807	0.5	0.463	0.538	SUBCLONAL	2	TRUE	1	0.461252318758451	4		227	819	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447244	187447244	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542190544	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1451	314	321	1	ENST00000232014.4:c.949G>A	p.Glu317Lys	p.E317K	ENST00000232014	NM_001130845.1	317	Gag/Aag	5/10	0.337578317326454	4	FACETS	1	0.984	1	0.376	0.353	0.399	CLONAL	1	TRUE	1	0.461252318758451	4		322	1765	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586436	189586436	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	208	340	0	ENST00000264731.3:c.1060G>T	p.Ala354Ser	p.A354S	ENST00000264731	NM_003722.4	354	Gcg/Tcg	8/14	0.337578317326454	4	FACETS	1	0.968	1	0.359	0.333	0.387	CLONAL	1	TRUE	1	0.461252318758451	4		340	1222	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139725	55139725	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	312	378	0	ENST00000257290.5:c.1386G>T	p.Trp462Cys	p.W462C	ENST00000257290	NM_006206.4	462	tgG/tgT	10/23	1	2	FACETS	0.987	0.93	1	0.987	0.93	1	CLONAL	1	TRUE	1	0.461252318758451	2		378	1370	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155196	55155196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1116	331	398	0	ENST00000257290.5:c.2795G>A	p.Cys932Tyr	p.C932Y	ENST00000257290	NM_006206.4	932	tGc/tAc	21/23	1	2	FACETS	0.992	0.936	1	0.992	0.936	1	CLONAL	1	TRUE	1	0.461252318758451	2		398	1447	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143043366	143043366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199940140	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	202	327	2	ENST00000262992.4:c.2050G>A	p.Val684Ile	p.V684I	ENST00000262992	NM_001101669.1	684	Gtt/Att	19/24	1	2	FACETS	0.972	0.902	1	0.972	0.902	1	CLONAL	1	TRUE	1	0.461252318758451	2		329	901	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143067150	143067150	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	184	267	0	ENST00000262992.4:c.1564-1G>C		p.X522_splice	ENST00000262992	NM_001101669.1	522			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.461252318758451	2		267	779	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540125	187540125	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1239739775	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	287	435	0	ENST00000441802.2:c.7615A>G	p.Arg2539Gly	p.R2539G	ENST00000441802	NM_005245.3	2539	Aga/Gga	10/27	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.461252318758451	2		435	1124	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295220	1295220	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	262	177	0				ENST00000310581	NM_198253.2	-/1132			0.253028388660667	3	FACETS	0.917	0.863	0.972	0.917	0.863	0.972	INDETERMINATE	2	TRUE	1	0.461252318758451	3		177	762	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642456	117642456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759091073	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	283	448	0	ENST00000368508.3:c.5743G>A	p.Gly1915Arg	p.G1915R	ENST00000368508	NM_002944.2	1915	Gga/Aga	35/43	0.180299652640397	1	FACETS	0.77	0.723	0.818	0.77	0.723	0.818	INDETERMINATE	1	TRUE	0	0.461252318758451	1		448	1226	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528886	157528886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	326	405	0	ENST00000346085.5:c.6611C>T	p.Ala2204Val	p.A2204V	ENST00000346085	NM_020732.3	2204	gCc/gTc	20/20	0.461252318758451	1	FACETS	0.971	0.918	1	0.971	0.918	1	CLONAL	1	TRUE	0	0.461252318758451	1		405	1120	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6038867	6038867	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1275	344	409	0	ENST00000265849.7:c.577A>G	p.Ile193Val	p.I193V	ENST00000265849	NM_000535.5	193	Atc/Gtc	6/15	NA	2	FACETS	0.921	0.87	0.974			1	INDETERMINATE	1	TRUE	NA	0.461252318758451	2		409	1619	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224321	55224321	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1253	370	376	1	ENST00000275493.2:c.1102G>T	p.Asp368Tyr	p.D368Y	ENST00000275493	NM_005228.3	368	Gat/Tat	9/28	NA	2	FACETS	0.988	0.936	1			1	INDETERMINATE	1	TRUE	NA	0.461252318758451	2		377	1623	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412020	116412020	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	211	332	0	ENST00000397752.3:c.3005A>G	p.Asp1002Gly	p.D1002G	ENST00000397752	NM_000245.2	1002	gAc/gGc	14/21	1	2	FACETS	0.963	0.895	1	0.963	0.895	1	CLONAL	1	TRUE	1	0.461252318758451	2		332	950	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240375	98240375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1293146883	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	139	366	0	ENST00000331920.6:c.1309G>A	p.Val437Ile	p.V437I	ENST00000331920	NM_000264.3	437	Gtc/Atc	9/24	0.461252318758451	1	FACETS	0.423	0.384	0.464	0.423	0.384	0.464	SUBCLONAL	1	TRUE	0	0.461252318758451	1		366	1096	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759955	133759955	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	449	542	0	ENST00000318560.5:c.2278C>T	p.Pro760Ser	p.P760S	ENST00000318560	NM_005157.4	760	Ccg/Tcg	11/11	0.461252318758451	1	FACETS	0.966	0.92	1	0.966	0.92	1	CLONAL	1	TRUE	0	0.461252318758451	1		542	1551	SUCCESS
RET	5979	MSKCC	GRCh37	10	43617418	43617418	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1584	202	456	0	ENST00000355710.3:c.2755G>T	p.Ala919Ser	p.A919S	ENST00000355710	NM_020975.4	919	Gca/Tca	16/20	1	2	FACETS	0.49	0.453	0.53	0.49	0.453	0.53	SUBCLONAL	1	TRUE	1	0.461252318758451	2		456	1786	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202585	67202585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374915842	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	329	353	1	ENST00000312629.5:c.1394G>A	p.Arg465His	p.R465H	ENST00000312629	NM_003952.2	465	cGt/cAt	15/15	1	2	FACETS	0.966	0.911	1	0.966	0.911	1	CLONAL	1	TRUE	1	0.461252318758451	2		354	1477	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425793	49425793	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	296	321	0	ENST00000301067.7:c.12695A>G	p.Gln4232Arg	p.Q4232R	ENST00000301067	NM_003482.3	4232	cAg/cGg	39/54	1	2	FACETS	0.915	0.86	0.972	0.915	0.86	0.972	CLONAL	1	TRUE	1	0.461252318758451	2		321	1402	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813361	102813361	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1280732914	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1218	411	425	0	ENST00000307046.8:c.328G>A	p.Ala110Thr	p.A110T	ENST00000307046	NM_001111285.1	110	Gca/Aca	3/4	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.461252318758451	2		425	1629	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2114301	2114301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45517176	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	381	429	0	ENST00000219476.3:c.1472C>T	p.Ser491Leu	p.S491L	ENST00000219476	NM_000548.3	491	tCg/tTg	15/42	0.461252318758451	1	FACETS	0.961	0.912	1	0.961	0.912	1	CLONAL	1	TRUE	0	0.461252318758451	1		429	1323	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779158	3779158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1278592398	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	243	259	1	ENST00000262367.5:c.5890C>T	p.Arg1964Cys	p.R1964C	ENST00000262367	NM_004380.2	1964	Cgt/Tgt	31/31	0.461252318758451	1	FACETS	0.963	0.902	1	0.963	0.902	1	CLONAL	1	TRUE	0	0.461252318758451	1		260	842	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892162	9892162	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	230	465	2	ENST00000330684.3:c.2328C>A	p.Asp776Glu	p.D776E	ENST00000330684	NM_001134407.1	776	gaC/gaA	11/13	0.461252318758451	1	FACETS	0.84	0.784	0.898	0.84	0.784	0.898	CLONAL	1	TRUE	0	0.461252318758451	1		467	913	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646702	23646702	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555461427	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	295	408	0	ENST00000261584.4:c.1165C>T	p.Leu389Phe	p.L389F	ENST00000261584	NM_024675.3	389	Ctt/Ttt	4/13	0.461252318758451	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.461252318758451	1		408	935	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830751	72830751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761415382	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1470	558	554	0	ENST00000268489.5:c.5830G>A	p.Ala1944Thr	p.A1944T	ENST00000268489	NM_006885.3	1944	Gcc/Acc	9/10	0.257991364896638	1	FACETS	0.918	0.879	0.958	0.918	0.879	0.958	INDETERMINATE	1	TRUE	0	0.461252318758451	1		554	2028	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110536	4110536	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	351	369	0	ENST00000262948.5:c.421G>A	p.Gly141Arg	p.G141R	ENST00000262948	NM_030662.3	141	Ggg/Agg	3/11	1	2	FACETS	0.99	0.935	1	0.99	0.935	1	CLONAL	1	TRUE	1	0.461252318758451	2		369	1538	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231350	5231350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370338775	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	317	311	0	ENST00000357368.4:c.2126C>T	p.Ser709Leu	p.S709L	ENST00000357368	NM_002850.3	709	tCg/tTg	14/38	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.461252318758451	2		311	1362	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602692	10602692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1278385562	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1693	415	387	0	ENST00000171111.5:c.886C>T	p.Arg296Cys	p.R296C	ENST00000171111	NM_203500.1	296	Cgc/Tgc	3/6	0.461252318758451	3	FACETS	1	0.977	1			1	CLONAL	1	TRUE	NA	0.461252318758451	3		387	2108	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602748	10602748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1308	770	399	0	ENST00000171111.5:c.830C>T	p.Thr277Met	p.T277M	ENST00000171111	NM_203500.1	277	aCg/aTg	3/6	0.461252318758451	3	FACETS	0.989	0.955	1			1	CLONAL	2	TRUE	NA	0.461252318758451	3		399	2078	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15311597	15311597	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	118	120	0	ENST00000263388.2:c.118+2T>C		p.X40_splice	ENST00000263388	NM_000435.2	40			1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.461252318758451	2		120	493	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279287	18279287	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	338	350	0	ENST00000222254.8:c.1739G>T	p.Trp580Leu	p.W580L	ENST00000222254	NM_005027.3	580	tGg/tTg	14/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.461252318758451	2		350	1371	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727073	41727073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs949895144	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2794	451	509	1	ENST00000301178.4:c.331G>A	p.Asp111Asn	p.D111N	ENST00000301178	NM_021913.4	111	Gac/Aac	3/20	0.461252318758451	5	FACETS	1	0.964	1	0.255	0.241	0.269	CLONAL	1	TRUE	1	0.461252318758451	5		510	3245	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383113	42383113	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2896	380	556	0	ENST00000221972.3:c.133A>G	p.Ser45Gly	p.S45G	ENST00000221972	NM_021601.3	45	Agc/Ggc	2/5	0.461252318758451	5	FACETS	0.851	0.803	0.901	0.213	0.2	0.226	CLONAL	1	TRUE	1	0.461252318758451	5		556	3276	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022656	31022656	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1338	372	478	0	ENST00000375687.4:c.2141C>A	p.Ser714Tyr	p.S714Y	ENST00000375687	NM_015338.5	714	tCc/tAc	13/13	1	2	FACETS	0.943	0.893	0.995	0.943	0.893	0.995	CLONAL	1	TRUE	1	0.461252318758451	2		478	1710	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031750	36031750	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879255268	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	365	410	0	ENST00000358208.4:c.1579G>A	p.Glu527Lys	p.E527K	ENST00000358208		527	Gag/Aag	12/12	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.461252318758451	2		410	1520	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39916463	39916463	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	211	262	1	ENST00000378444.4:c.4540C>T	p.Arg1514Ter	p.R1514*	ENST00000378444	NM_001123385.1	1514	Cga/Tga	11/15	1	1	FACETS	0.744	0.691	0.799	0.744	0.691	0.799	SUBCLONAL	1	TRUE	0	0.461252318758451	1		263	946	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410336	63410336	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	241	268	1	ENST00000330258.3:c.2831G>T	p.Ser944Ile	p.S944I	ENST00000330258	NM_152424.3	944	aGt/aTt	2/2	0.180299652640397	0	FACETS	0.532	0.497	0.569			1	INDETERMINATE	1	TRUE	NA	0.461252318758451	0		269	1058	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410585	63410585	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	484	285	0	ENST00000330258.3:c.2582G>C	p.Gly861Ala	p.G861A	ENST00000330258	NM_152424.3	861	gGc/gCc	2/2	0.180299652640397	0	FACETS	0.538	0.517	0.56			1	INDETERMINATE	2	TRUE	NA	0.461252318758451	0		285	1050	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411699	63411699	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1464297548	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	403	240	0	ENST00000330258.3:c.1468G>C	p.Val490Leu	p.V490L	ENST00000330258	NM_152424.3	490	Gtc/Ctc	2/2	0.180299652640397	0	FACETS	1	0.979	1			1	INDETERMINATE	1	TRUE	NA	0.461252318758451	0		240	905	SUCCESS
AR	367	MSKCC	GRCh37	X	66766312	66766314	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	160	115	0	ENST00000374690.3:c.1328_1330del	p.Glu443del	p.E443del	ENST00000374690	NM_000044.3	442	GAA/-	1/8	0.180299652640397	0	FACETS	0.921	0.854	0.988			1	INDETERMINATE	1	TRUE	NA	0.461252318758451	0		115	406	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029445	16029446	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	299	442	13	ENST00000268712.3:c.1584dup	p.Glu529ArgfsTer7	p.E529Rfs*7	ENST00000268712	NM_006311.3	528	-/A	15/46	0.461252318758451	1	FACETS	0.82	0.771	0.869	0.82	0.771	0.869	CLONAL	1	TRUE	0	0.461252318758451	1		455	1217	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564408	86564408	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	338	377	0	ENST00000274376.6:c.144del	p.Tyr49IlefsTer24	p.Y49Ifs*24	ENST00000274376	NM_002890.2	47	gCc/gc	1/25	0.461252318758451	1	FACETS	0.917	0.868	0.969	0.917	0.868	0.969	CLONAL	1	TRUE	0	0.461252318758451	1		377	1229	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541344	187541345	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	202	399	0	ENST00000441802.2:c.6395dup	p.Leu2132PhefsTer3	p.L2132Ffs*3	ENST00000441802	NM_005245.3	2132	ttg/ttTg	10/27	1	2	FACETS	0.848	0.786	0.913	0.848	0.786	0.913	CLONAL	1	TRUE	1	0.461252318758451	2		399	1033	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584580	187584581	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1307	340	456	0	ENST00000441802.2:c.3452dup	p.Asn1151LysfsTer4	p.N1151Kfs*4	ENST00000441802	NM_005245.3	1151	aat/aaAt	3/27	1	2	FACETS	0.895	0.844	0.947	0.895	0.844	0.947	CLONAL	1	TRUE	1	0.461252318758451	2		456	1647	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430251	181430251	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1462	91	254	0	ENST00000325404.1:c.107del	p.Asn36ThrfsTer10	p.N36Tfs*10	ENST00000325404	NM_003106.3	35	Aaa/aa	1/1	0.337578317326454	4	FACETS	0.371	0.328	0.418	0.124	0.109	0.14	SUBCLONAL	1	TRUE	1	0.461252318758451	4		254	1553	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204706	128204706	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2446	221	565	0	ENST00000341105.2:c.735del	p.Ile246SerfsTer80	p.I246Sfs*80	ENST00000341105	NM_032638.4	245	ccC/cc	3/6	0.337578317326454	4	FACETS	0.525	0.486	0.566	0.175	0.162	0.189	SUBCLONAL	1	TRUE	1	0.461252318758451	4		565	2667	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47707974	47707975	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TT	novel	NA	P-0006368-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1300	306	438	2	ENST00000233146.2:c.2598_2599delinsTT	p.Met866_Glu867delinsIleTer	p.M866_E867delinsI*	ENST00000233146	NM_000251.2	866	atGGaa/atTTaa	15/16	1	2	FACETS	0.826	0.776	0.877	0.826	0.776	0.877	CLONAL	1	TRUE	1	0.461252318758451	2		440	1606	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	179	464	0				ENST00000310581	NM_198253.2	-/1132			0.48440484785338	4	FACETS	1	0.967	1	0.364	0.335	0.394	CLONAL	1	TRUE	1	0.48440484785338	4		464	1004	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30679714	30679714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1339	348	820	0	ENST00000376406.3:c.2005C>T	p.Pro669Ser	p.P669S	ENST00000376406	NM_014641.2	669	Ccc/Tcc	5/15	0.48440484785338	3	FACETS	1	0.975	1	0.529	0.499	0.56	CLONAL	1	TRUE	1	0.48440484785338	3		820	1687	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317422	1317422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759127718	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	258	762	0	ENST00000400841.2:c.643C>T	p.Arg215Trp	p.R215W	ENST00000400841		215	Cgg/Tgg	5/6	1	1	FACETS	0.676	0.632	0.721	0.676	0.632	0.721	SUBCLONAL	1	TRUE	0	0.48440484785338	1		762	1195	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	216	251	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	1	2	FACETS	0.942	0.876	1	0.942	0.876	1	CLONAL	1	TRUE	1	0.48440484785338	2		251	947	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367321	50367321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	218	512	1	ENST00000331340.3:c.128G>A	p.Gly43Glu	p.G43E	ENST00000331340	NM_006060.4	43	gGa/gAa	3/8	1	2	FACETS	0.937	0.872	1	0.937	0.872	1	CLONAL	1	TRUE	1	0.48440484785338	2		513	961	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459558	50459558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	188	456	0	ENST00000331340.3:c.847C>T	p.Leu283Phe	p.L283F	ENST00000331340	NM_006060.4	283	Ctt/Ttt	7/8	1	2	FACETS	0.944	0.874	1	0.944	0.874	1	CLONAL	1	TRUE	1	0.48440484785338	2		456	822	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509639	29509639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	169	790	2	ENST00000356175.3:c.844C>T	p.Gln282Ter	p.Q282*	ENST00000356175	NM_000267.3	282	Cag/Tag	8/57	0.48440484785338	1	FACETS	0.944	0.873	1	0.944	0.873	1	CLONAL	1	TRUE	0	0.48440484785338	1		792	560	SUCCESS
ALK	238	MSKCC	GRCh37	2	29473981	29473981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768366852	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	299	664	2	ENST00000389048.3:c.2194G>A	p.Asp732Asn	p.D732N	ENST00000389048	NM_004304.4	732	Gac/Aac	12/29	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.48440484785338	2		666	1079	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534285	534285	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894226	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	231	651	0	ENST00000451590.1:c.38G>A	p.Gly13Asp	p.G13D	ENST00000451590	NM_001130442.1	13	gGt/gAt	2/5	0.205012669426902	1	FACETS	0.763	0.712	0.816	0.763	0.712	0.816	INDETERMINATE	1	TRUE	0	0.48440484785338	1		651	947	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937219	36937219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140159756	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	388	1146	3	ENST00000361632.4:c.1100G>A	p.Arg367Gln	p.R367Q	ENST00000361632		367	cGg/cAg	9/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.48440484785338	2		1149	1531	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274554	198274554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	324	767	1	ENST00000335508.6:c.844G>A	p.Gly282Arg	p.G282R	ENST00000335508	NM_012433.2	282	Gga/Aga	7/25	0.48440484785338	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.48440484785338	1		768	963	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165695	47165695	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	296	785	0	ENST00000409792.3:c.431T>C	p.Phe144Ser	p.F144S	ENST00000409792	NM_014159.6	144	tTt/tCt	3/21	1	2	FACETS	0.986	0.927	1	0.986	0.927	1	CLONAL	1	TRUE	1	0.48440484785338	2		785	1240	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723339	49723339	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	85	271	1	ENST00000449682.2:c.1204G>A	p.Gly402Ser	p.G402S	ENST00000449682	NM_020998.3	402	Ggt/Agt	10/18	1	2	FACETS	0.907	0.807	1	0.907	0.807	1	CLONAL	1	TRUE	1	0.48440484785338	2		272	387	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133740	55133740	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	238	850	0	ENST00000257290.5:c.953A>G	p.Lys318Arg	p.K318R	ENST00000257290	NM_006206.4	318	aAa/aGa	7/23	0.48440484785338	1	FACETS	0.898	0.841	0.957	0.898	0.841	0.957	CLONAL	1	TRUE	0	0.48440484785338	1		850	829	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193899	106193899	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	185	750	0	ENST00000380013.4:c.4361T>G	p.Val1454Gly	p.V1454G	ENST00000380013	NM_001127208.2	1454	gTc/gGc	10/11	0.48440484785338	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.48440484785338	1		750	519	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517828	187517828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	244	690	1	ENST00000441802.2:c.12866C>T	p.Pro4289Leu	p.P4289L	ENST00000441802	NM_005245.3	4289	cCc/cTc	25/27	0.48440484785338	1	FACETS	0.96	0.9	1	0.96	0.9	1	CLONAL	1	TRUE	0	0.48440484785338	1		691	795	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629322	187629322	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	300	538	0	ENST00000441802.2:c.1660C>T	p.Leu554Phe	p.L554F	ENST00000441802	NM_005245.3	554	Ctt/Ttt	2/27	0.48440484785338	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.48440484785338	1		538	881	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294061	1294061	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1577	277	834	3	ENST00000310581.5:c.940C>T	p.Pro314Ser	p.P314S	ENST00000310581	NM_198253.2	314	Cca/Tca	2/16	0.48440484785338	4	FACETS	0.916	0.857	0.977	0.305	0.285	0.326	CLONAL	1	TRUE	1	0.48440484785338	4		837	1854	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671591	30671591	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1325	322	952	0	ENST00000376406.3:c.5369A>T	p.Lys1790Met	p.K1790M	ENST00000376406	NM_014641.2	1790	aAg/aTg	10/15	0.48440484785338	3	FACETS	1	0.944	1	0.501	0.472	0.532	CLONAL	1	TRUE	1	0.48440484785338	3		952	1647	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166330	32166330	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1313	305	789	0	ENST00000375023.3:c.4624G>A	p.Glu1542Lys	p.E1542K	ENST00000375023	NM_004557.3	1542	Gaa/Aaa	26/30	0.48440484785338	3	FACETS	0.967	0.909	1	0.483	0.454	0.514	CLONAL	1	TRUE	1	0.48440484785338	3		789	1618	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959064	2959064	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	230	684	0	ENST00000396946.4:c.2452C>T	p.Arg818Trp	p.R818W	ENST00000396946	NM_032415.4	818	Cgg/Tgg	18/25	1	2	FACETS	0.872	0.812	0.934	0.872	0.812	0.934	CLONAL	1	TRUE	1	0.48440484785338	2		684	1089	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849988	151849988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	250	704	0	ENST00000262189.6:c.12328C>T	p.Pro4110Ser	p.P4110S	ENST00000262189	NM_170606.2	4110	Cct/Tct	49/59	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.48440484785338	2		704	1000	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152007097	152007097	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	275	718	0	ENST00000262189.6:c.803C>T	p.Pro268Leu	p.P268L	ENST00000262189	NM_170606.2	268	cCa/cTa	6/59	1	2	FACETS	0.953	0.894	1	0.953	0.894	1	CLONAL	1	TRUE	1	0.48440484785338	2		718	1191	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404342	139404342	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs554142958	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	312	904	2	ENST00000277541.6:c.2812C>T	p.Arg938Trp	p.R938W	ENST00000277541	NM_017617.3	938	Cgg/Tgg	18/34	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.48440484785338	2		906	1152	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416803	121416803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	367	1081	0	ENST00000257555.6:c.232G>A	p.Gly78Arg	p.G78R	ENST00000257555		78	Ggg/Agg	1/10	0.48440484785338	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.48440484785338	1		1081	1133	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133245005	133245005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	291	768	2	ENST00000320574.5:c.2110G>A	p.Ala704Thr	p.A704T	ENST00000320574	NM_006231.2	704	Gct/Act	19/49	0.48440484785338	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.48440484785338	1		770	885	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28610104	28610104	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	227	901	1	ENST00000241453.7:c.1386G>A	p.Trp462Ter	p.W462*	ENST00000241453	NM_004119.2	462	tgG/tgA	11/24	1	2	FACETS	0.885	0.824	0.948	0.885	0.824	0.948	CLONAL	1	TRUE	1	0.48440484785338	2		902	1059	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001422	29001422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752383804	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	94	563	3	ENST00000282397.4:c.1310C>T	p.Ser437Leu	p.S437L	ENST00000282397	NM_002019.4	437	tCg/tTg	10/30	1	2	FACETS	0.951	0.852	1	0.951	0.852	1	CLONAL	1	TRUE	1	0.48440484785338	2		566	408	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039185	49039185	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	177	698	0	ENST00000267163.4:c.2263T>A	p.Phe755Ile	p.F755I	ENST00000267163	NM_000321.2	755	Ttc/Atc	22/27	1	2	FACETS	0.784	0.722	0.848	0.784	0.722	0.848	SUBCLONAL	1	TRUE	1	0.48440484785338	2		698	932	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81558899	81558899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	145	657	1	ENST00000298171.2:c.492G>A	p.Met164Ile	p.M164I	ENST00000298171	NM_000369.2	164	atG/atA	6/10	1	2	FACETS	0.918	0.84	0.999	0.918	0.84	0.999	CLONAL	1	TRUE	1	0.48440484785338	2		658	652	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849430	68849430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	233	673	1	ENST00000261769.5:c.1333G>A	p.Glu445Lys	p.E445K	ENST00000261769	NM_004360.3	445	Gag/Aag	10/16	0.48440484785338	1	FACETS	0.891	0.833	0.951	0.891	0.833	0.951	CLONAL	1	TRUE	0	0.48440484785338	1		674	818	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942171	81942171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	393	992	1	ENST00000359376.3:c.1708C>T	p.Pro570Ser	p.P570S	ENST00000359376	NM_002661.3	570	Ccc/Tcc	17/33	0.48440484785338	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.48440484785338	1		993	1184	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574035	7574035	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	236	788	1	ENST00000269305.4:c.994-2A>T		p.X332_splice	ENST00000269305	NM_001126112.2	332			1	2	FACETS	0.879	0.82	0.941	0.879	0.82	0.941	CLONAL	1	TRUE	1	0.48440484785338	2		789	1108	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866579	78866579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	204	351	0	ENST00000306801.3:c.2152C>T	p.Arg718Cys	p.R718C	ENST00000306801	NM_020761.2	718	Cgt/Tgt	19/34	1	2	FACETS	0.839	0.778	0.902	0.839	0.778	0.902	CLONAL	1	TRUE	1	0.48440484785338	2		351	1004	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246822	10246822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	202	673	0	ENST00000340748.4:c.4583C>T	p.Thr1528Ile	p.T1528I	ENST00000340748		1528	aCc/aTc	37/40	0.205012669426902	1	FACETS	0.8	0.743	0.859	0.8	0.743	0.859	INDETERMINATE	1	TRUE	0	0.48440484785338	1		673	790	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353866	15353866	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	81	534	0	ENST00000263377.2:c.3014C>T	p.Ser1005Phe	p.S1005F	ENST00000263377	NM_058243.2	1005	tCc/tTc	14/20	0.205012669426902	1	FACETS	0.374	0.33	0.422	0.374	0.33	0.422	INDETERMINATE	1	TRUE	0	0.48440484785338	1		534	677	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713347	40713347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	204	648	0	ENST00000373198.4:c.4168G>A	p.Glu1390Lys	p.E1390K	ENST00000373198	NM_133170.3	1390	Gag/Aag	30/32	1	2	FACETS	0.833	0.772	0.896	0.833	0.772	0.896	CLONAL	1	TRUE	1	0.48440484785338	2		648	1011	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156695	20156695	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	313	384	1	ENST00000379607.5:c.62C>T	p.Ser21Phe	p.S21F	ENST00000379607	NM_001412.3	21	tCt/tTt	2/7	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.48440484785338	1		385	668	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932638	39932638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	412	566	0	ENST00000378444.4:c.1961C>T	p.Pro654Leu	p.P654L	ENST00000378444	NM_001123385.1	654	cCc/cTc	4/15	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.48440484785338	1		566	861	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344134	70344134	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	350	463	0	ENST00000374080.3:c.1870C>T	p.Leu624Phe	p.L624F	ENST00000374080		624	Ctt/Ttt	13/45	1	1	FACETS	0.764	0.729	0.799	1	0.996	1	SUBCLONAL	2	TRUE	0	0.48440484785338	1		463	717	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405712	139405737	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CACACGTGGCACCTGCGGGAAGGAGA	CACACGTGGCACCTGCGGGAAGGAGA	-	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	196	603	0	ENST00000277541.6:c.2468-14_2479del		p.X823_splice	ENST00000277541	NM_017617.3	823		16/34	1	2	FACETS	0.854	0.79	0.919	0.854	0.79	0.919	CLONAL	1	TRUE	1	0.48440484785338	2		603	948	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955494	48955555	+	frameshift_variant	Frame_Shift_Del	DEL	AAGCAGAAGGCAACTTGACAAGAGAAATGATAAAACATTTAGAACGATGTGAACATCGAATC	AAGCAGAAGGCAACTTGACAAGAGAAATGATAAAACATTTAGAACGATGTGAACATCGAATC	-	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	60	825	0	ENST00000267163.4:c.1611_1672del	p.Lys537AsnfsTer14	p.K537Nfs*14	ENST00000267163	NM_000321.2	537	aAAGCAGAAGGCAACTTGACAAGAGAAATGATAAAACATTTAGAACGATGTGAACATCGAATC/a	17/27	1	2	FACETS	0.396	0.34	0.456	0.396	0.34	0.456	SUBCLONAL	1	TRUE	1	0.48440484785338	2		825	626	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8501047	8501048	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0006407-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	105	424	0	ENST00000356435.5:c.1834_1835delinsTT	p.Pro612Phe	p.P612F	ENST00000356435		612	CCt/TTt	13/35	0.183992509206378	0	FACETS	0.461	0.415	0.509			1	INDETERMINATE	1	TRUE	0	0.48440484785338	0		424	485	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0006416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	159	464	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.610421334095976	2		464	465	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624274	89624274	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs587782187	NA	P-0006416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	33	226	0	ENST00000371953.3:c.48T>A	p.Tyr16Ter	p.Y16*	ENST00000371953	NM_000314.4	16	taT/taA	1/9	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.610421334095976	NA		226	267	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845625	68845625	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660645	NA	P-0006416-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	43	600	1	ENST00000261769.5:c.871G>A	p.Asp291Asn	p.D291N	ENST00000261769	NM_004360.3	291	Gat/Aat	7/16	0.207435918515103	1	FACETS	0.146	0.122	0.173	0.146	0.122	0.173	INDETERMINATE	1	TRUE	0	0.610421334095976	1		601	670	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0006416-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	130	464	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.642550438044154	2		464	360	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222583	2222583	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006416-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	67	367	0	ENST00000326181.6:c.777C>G	p.Cys259Trp	p.C259W	ENST00000326181	NM_032271.2	259	tgC/tgG	9/21	0.179565215362122	1	FACETS	0.249	0.216	0.284	0.249	0.216	0.284	INDETERMINATE	1	TRUE	0	0.642550438044154	1		367	569	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	37	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.928	0.779	1	1	0.966	1	CLONAL	2	FALSE	1	0.288967563962723	2		280	138	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0006428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	83	491	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	1	0.919	1	1	0.989	1	CLONAL	3	FALSE	1	0.288967563962723	2		491	188	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89341317	89341317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555523386	NA	P-0006428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	41	220	0	ENST00000301030.4:c.7618C>T	p.Arg2540Trp	p.R2540W	ENST00000301030	NM_001256183.1	2540	Cgg/Tgg	11/13	0.123595179020741	0	FACETS	0.664	0.563	0.772			1	INDETERMINATE	2	FALSE	0	0.288967563962723	0		220	152	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29652868	29652912	+	inframe_deletion	In_Frame_Del	DEL	GCTGATATACCATGTCTTACTGACTTTAAAGCCATATTATGCAAA	GCTGATATACCATGTCTTACTGACTTTAAAGCCATATTATGCAAA	-	novel	NA	P-0006428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	12	348	0	ENST00000356175.3:c.4805_4849del	p.Leu1602_Lys1616del	p.L1602_K1616del	ENST00000356175	NM_000267.3	1601	ttGCTGATATACCATGTCTTACTGACTTTAAAGCCATATTATGCAAAg/ttg	36/57	1	2	FACETS	0.546	0.385	0.743	0.546	0.385	0.743	SUBCLONAL	1	FALSE	1	0.288967563962723	2		348	152	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412627	139412627	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	94	392	0	ENST00000277541.6:c.1217del	p.Gly406AlafsTer225	p.G406Afs*225	ENST00000277541	NM_017617.3	406	gGc/gc	7/34	1	2	FACETS	0.791	0.709	0.878	1	0.983	1	SUBCLONAL	2	FALSE	1	0.288967563962723	2		392	411	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393672	139393673	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GCGG	novel	NA	P-0006428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	54	428	0	ENST00000277541.6:c.5970_5973dup	p.Met1992ProfsTer4	p.M1992Pfs*4	ENST00000277541	NM_017617.3	1991	-/CCGC	32/34	1	2	FACETS	0.997	0.855	1	0.997	0.855	1	CLONAL	1	FALSE	1	0.288967563962723	2		428	375	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930234	39930241	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTCGTT	CTTTCGTT	-	novel	NA	P-0006428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	47	663	0	ENST00000378444.4:c.3223_3230del	p.Asn1075Ter	p.N1075*	ENST00000378444	NM_001123385.1	1075	AACGAAAGt/t	6/15	0.238197745980565	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	0	0.288967563962723	1		663	203	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148504767	148504784	+	inframe_deletion	In_Frame_Del	DEL	CGACATACTTCAGGGCAT	CGACATACTTCAGGGCAT	-	novel	NA	P-0006428-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	24	365	0	ENST00000320356.2:c.2210_2227del	p.Asp737_Val742del	p.D737_V742del	ENST00000320356	NM_004456.4	737	gATGCCCTGAAGTATGTCGgc/ggc	20/20	1	2	FACETS	0.923	0.729	1	0.923	0.729	1	CLONAL	1	FALSE	1	0.288967563962723	2		365	180	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	176	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.946	0.874	1	0.946	0.874	1	CLONAL	1	TRUE	1	0.544826260952184	2		464	683	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843734	156843734	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	553	721	2	ENST00000524377.1:c.1160C>T	p.Pro387Leu	p.P387L	ENST00000524377	NM_002529.3	387	cCc/cTc	8/17	0.369781269806983	4	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	2	0.544826260952184	4		723	1529	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467824	66467824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	147	594	0	ENST00000273854.3:c.445G>A	p.Glu149Lys	p.E149K	ENST00000273854	NM_004439.5	149	Gaa/Aaa	3/18	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.544826260952184	2		594	522	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189843	11189843	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	312	600	0	ENST00000361445.4:c.5666T>A	p.Phe1889Tyr	p.F1889Y	ENST00000361445	NM_004958.3	1889	tTc/tAc	40/58	0.463152305702441	3	FACETS	0.925	0.877	0.973	0.925	0.877	0.973	CLONAL	2	TRUE	1	0.544826260952184	3		600	788	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260216	16260216	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375082858	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	124	225	0	ENST00000375759.3:c.7481C>T	p.Pro2494Leu	p.P2494L	ENST00000375759	NM_015001.2	2494	cCc/cTc	11/15	0.463152305702441	3	FACETS	0.928	0.852	1	0.928	0.852	1	CLONAL	2	TRUE	1	0.544826260952184	3		225	312	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163809	72163809	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	161	610	0	ENST00000357731.5:c.549A>T	p.Glu183Asp	p.E183D	ENST00000357731	NM_173808.2	183	gaA/gaT	4/7	0.463152305702441	3	FACETS	0.941	0.864	1	0.471	0.432	0.511	CLONAL	1	TRUE	1	0.544826260952184	3		610	799	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844740	156844740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1550	349	826	0	ENST00000524377.1:c.1294C>T	p.Leu432Phe	p.L432F	ENST00000524377	NM_002529.3	432	Ctt/Ttt	11/17	0.369781269806983	4	FACETS	1	0.97	1	0.521	0.491	0.552	CLONAL	1	TRUE	2	0.544826260952184	4		826	1899	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849152	156849152	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs768180688	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	237	541	0	ENST00000524377.1:c.2044C>T	p.Arg682Cys	p.R682C	ENST00000524377	NM_002529.3	682	Cgt/Tgt	15/17	0.369781269806983	4	FACETS	1	0.979	1	0.56	0.522	0.6	CLONAL	1	TRUE	2	0.544826260952184	4		541	1199	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851429	156851429	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	419	265	0	ENST00000524377.1:c.2386G>A	p.Gly796Ser	p.G796S	ENST00000524377	NM_002529.3	796	Ggc/Agc	17/17	0.369781269806983	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.544826260952184	4		265	1121	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226574035	226574035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	340	623	0	ENST00000366794.5:c.826G>A	p.Glu276Lys	p.E276K	ENST00000366794	NM_001618.3	276	Gag/Aag	6/23	0.544826260952184	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.544826260952184	2		623	623	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436869	29436869	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	170	698	1	ENST00000389048.3:c.3724G>A	p.Glu1242Lys	p.E1242K	ENST00000389048	NM_004304.4	1242	Gaa/Aaa	24/29	1	2	FACETS	0.817	0.753	0.884	0.817	0.753	0.884	CLONAL	1	TRUE	1	0.544826260952184	2		699	764	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719275	190719275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	97	376	0	ENST00000441310.2:c.1277C>T	p.Ser426Phe	p.S426F	ENST00000441310	NM_000534.4	426	tCt/tTt	9/13	1	2	FACETS	0.94	0.844	1	0.94	0.844	1	CLONAL	1	TRUE	1	0.544826260952184	2		376	379	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149917	202149917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	132	527	3	ENST00000358485.4:c.1358C>T	p.Pro453Leu	p.P453L	ENST00000358485	NM_001080125.1	453	cCg/cTg	8/9	1	2	FACETS	0.868	0.792	0.948	0.868	0.792	0.948	CLONAL	1	TRUE	1	0.544826260952184	2		530	558	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251785	212251785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	168	534	0	ENST00000342788.4:c.3274C>T	p.Pro1092Ser	p.P1092S	ENST00000342788	NM_005235.2	1092	Cct/Tct	27/28	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.544826260952184	2		534	552	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812260	212812260	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751175543	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	151	552	0	ENST00000342788.4:c.316C>T	p.Arg106Cys	p.R106C	ENST00000342788	NM_005235.2	106	Cgt/Tgt	3/28	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.544826260952184	2		552	552	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439722	220439723	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	336	700	2	ENST00000243786.2:c.575_576delinsTT	p.Pro192Leu	p.P192L	ENST00000243786	NM_002191.3	192	cCC/cTT	2/2	1	2	FACETS	0.871	0.822	0.921	0.871	0.822	0.921	CLONAL	1	TRUE	1	0.544826260952184	2		702	1416	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225360680	225360680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	139	458	0	ENST00000264414.4:c.1711G>A	p.Asp571Asn	p.D571N	ENST00000264414	NM_003590.4	571	Gat/Aat	13/16	1	2	FACETS	0.991	0.907	1	0.991	0.907	1	CLONAL	1	TRUE	1	0.544826260952184	2		458	515	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161702	47161702	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	127	555	1	ENST00000409792.3:c.4424T>C	p.Leu1475Pro	p.L1475P	ENST00000409792	NM_014159.6	1475	cTt/cCt	3/21	1	2	FACETS	0.782	0.711	0.857	0.782	0.711	0.857	SUBCLONAL	1	TRUE	1	0.544826260952184	2		556	596	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49400036	49400036	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	203	619	0	ENST00000418115.1:c.301C>T	p.Pro101Ser	p.P101S	ENST00000418115	NM_001664.2	101	Cca/Tca	4/5	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.544826260952184	2		619	743	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468436	89468436	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	137	446	0	ENST00000336596.2:c.1970T>C	p.Val657Ala	p.V657A	ENST00000336596	NM_005233.5	657	gTt/gCt	11/17	1	2	FACETS	0.913	0.834	0.994	0.913	0.834	0.994	CLONAL	1	TRUE	1	0.544826260952184	2		446	551	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119720961	119720961	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	175	667	1	ENST00000316626.5:c.214C>T	p.Gln72Ter	p.Q72*	ENST00000316626		72	Caa/Taa	2/12	1	2	FACETS	0.932	0.861	1	0.932	0.861	1	CLONAL	1	TRUE	1	0.544826260952184	2		668	689	SUCCESS
ATR	545	MSKCC	GRCh37	3	142185191	142185191	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	167	619	0	ENST00000350721.4:c.6872C>T	p.Ala2291Val	p.A2291V	ENST00000350721	NM_001184.3	2291	gCc/gTc	40/47	1	2	FACETS	0.862	0.794	0.933	0.862	0.794	0.933	CLONAL	1	TRUE	1	0.544826260952184	2		619	711	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55594051	55594051	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	177	600	0	ENST00000288135.5:c.1837A>C	p.Lys613Gln	p.K613Q	ENST00000288135	NM_000222.2	613	Aag/Cag	12/21	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.544826260952184	2		600	621	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946137	55946137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	225	538	0	ENST00000263923.4:c.4042G>A	p.Gly1348Arg	p.G1348R	ENST00000263923	NM_002253.2	1348	Ggg/Agg	30/30	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.544826260952184	2		538	751	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946257	55946257	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761896566	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	154	534	1	ENST00000263923.4:c.3922G>A	p.Gly1308Arg	p.G1308R	ENST00000263923	NM_002253.2	1308	Gga/Aga	30/30	1	2	FACETS	0.985	0.906	1	0.985	0.906	1	CLONAL	1	TRUE	1	0.544826260952184	2		535	574	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961104	55961104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371148535	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	167	548	0	ENST00000263923.4:c.2836C>T	p.Arg946Cys	p.R946C	ENST00000263923	NM_002253.2	946	Cgt/Tgt	21/30	1	2	FACETS	0.976	0.901	1	0.976	0.901	1	CLONAL	1	TRUE	1	0.544826260952184	2		548	628	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213917	66213917	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	133	475	0	ENST00000273854.3:c.2513G>A	p.Gly838Glu	p.G838E	ENST00000273854	NM_004439.5	838	gGa/gAa	15/18	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.544826260952184	2		475	444	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584486	187584486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1035563944	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	123	490	1	ENST00000441802.2:c.3547C>T	p.Pro1183Ser	p.P1183S	ENST00000441802	NM_005245.3	1183	Cca/Tca	3/27	1	2	FACETS	0.957	0.871	1	0.957	0.871	1	CLONAL	1	TRUE	1	0.544826260952184	2		491	472	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254614	1254614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201330213	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	203	465	1	ENST00000310581.5:c.3164C>T	p.Ser1055Leu	p.S1055L	ENST00000310581	NM_198253.2	1055	tCg/tTg	15/16	1	2	FACETS	0.927	0.861	0.995	0.927	0.861	0.995	CLONAL	1	TRUE	1	0.544826260952184	2		466	804	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	134	75	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.544826260952184	2		75	491	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754889	57754889	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	55	431	2	ENST00000274289.3:c.301G>T	p.Asp101Tyr	p.D101Y	ENST00000274289	NM_006622.3	101	Gat/Tat	2/14	1	2	FACETS	0.35	0.299	0.406	0.35	0.299	0.406	SUBCLONAL	1	TRUE	1	0.544826260952184	2		433	577	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86681160	86681160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	139	486	0	ENST00000274376.6:c.2801C>T	p.Ala934Val	p.A934V	ENST00000274376	NM_002890.2	934	gCt/gTt	22/25	1	2	FACETS	0.985	0.902	1	0.985	0.902	1	CLONAL	1	TRUE	1	0.544826260952184	2		486	518	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523645	176523645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	299	768	1	ENST00000292408.4:c.2056G>A	p.Gly686Arg	p.G686R	ENST00000292408	NM_213647.1	686	Ggg/Agg	16/18	1	2	FACETS	0.953	0.897	1	0.953	0.897	1	CLONAL	1	TRUE	1	0.544826260952184	2		769	1152	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665379	176665380	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	136	560	0	ENST00000439151.2:c.4063_4064delinsTT	p.Pro1355Phe	p.P1355F	ENST00000439151	NM_022455.4	1355	CCc/TTc	7/23	1	2	FACETS	0.865	0.79	0.944	0.865	0.79	0.944	CLONAL	1	TRUE	1	0.544826260952184	2		560	577	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721703	176721703	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	140	497	0	ENST00000439151.2:c.7334A>T	p.Asn2445Ile	p.N2445I	ENST00000439151	NM_022455.4	2445	aAt/aTt	23/23	1	2	FACETS	0.946	0.866	1	0.946	0.866	1	CLONAL	1	TRUE	1	0.544826260952184	2		497	543	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26046038	26046038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867056701	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	247	812	0	ENST00000540144.1:c.400G>A	p.Glu134Lys	p.E134K	ENST00000540144	NM_003531.2	134	Gaa/Aaa	1/1	0.537072478661901	3	FACETS	0.892	0.833	0.954	0.446	0.416	0.477	CLONAL	1	TRUE	1	0.544826260952184	3		812	1293	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30668382	30668382	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	250	798	0	ENST00000376406.3:c.6130C>G	p.Gln2044Glu	p.Q2044E	ENST00000376406	NM_014641.2	2044	Cag/Gag	15/15	0.537072478661901	3	FACETS	1	0.969	1	0.53	0.495	0.566	CLONAL	1	TRUE	1	0.544826260952184	3		798	1102	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32165239	32165239	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	232	522	0	ENST00000375023.3:c.4889C>T	p.Thr1630Ile	p.T1630I	ENST00000375023	NM_004557.3	1630	aCc/aTc	27/30	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.544826260952184	2		522	763	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965671	93965672	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	205	775	0	ENST00000369303.4:c.2256_2257delinsAA	p.Met752_Gly753delinsIleArg	p.M752_G753delinsIR	ENST00000369303	NM_004440.3	752	atGGga/atAAga	13/17	1	2	FACETS	0.894	0.83	0.959	0.894	0.83	0.959	CLONAL	1	TRUE	1	0.544826260952184	2		775	842	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120442	94120442	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	253	880	0	ENST00000369303.4:c.609G>C	p.Lys203Asn	p.K203N	ENST00000369303	NM_004440.3	203	aaG/aaC	3/17	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.544826260952184	2		880	921	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985473	2985473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	412	568	2	ENST00000396946.4:c.338G>A	p.Arg113Gln	p.R113Q	ENST00000396946	NM_032415.4	113	cGg/cAg	4/25	0.544826260952184	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.544826260952184	3		570	943	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13949269	13949269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	360	613	1	ENST00000405192.2:c.859G>A	p.Glu287Lys	p.E287K	ENST00000405192	NM_001163147.1	287	Gaa/Aaa	9/12	0.544826260952184	3	FACETS	0.943	0.897	0.988	0.943	0.897	0.988	CLONAL	2	TRUE	1	0.544826260952184	3		614	892	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971175	13971175	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	157	562	0	ENST00000405192.2:c.754C>T	p.Pro252Ser	p.P252S	ENST00000405192	NM_001163147.1	252	Cct/Tct	8/12	0.544826260952184	3	FACETS	1	0.958	1	0.534	0.49	0.579	CLONAL	1	TRUE	1	0.544826260952184	3		562	687	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211050	55211050	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17289589	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	181	453	0	ENST00000275493.2:c.293G>A	p.Arg98Gln	p.R98Q	ENST00000275493	NM_005228.3	98	cGa/cAa	3/28	0.544826260952184	3	FACETS	1	0.953	1	0.522	0.482	0.563	CLONAL	1	TRUE	1	0.544826260952184	3		453	810	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339556	81339556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	125	538	0	ENST00000222390.5:c.1448C>T	p.Pro483Leu	p.P483L	ENST00000222390	NM_000601.4	483	cCc/cTc	13/18	0.544826260952184	3	FACETS	1	0.908	1	0.5	0.454	0.548	CLONAL	1	TRUE	1	0.544826260952184	3		538	584	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388076	81388076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	176	496	0	ENST00000222390.5:c.299C>T	p.Pro100Leu	p.P100L	ENST00000222390	NM_000601.4	100	cCc/cTc	3/18	0.544826260952184	3	FACETS	1	0.954	1	0.524	0.483	0.566	CLONAL	1	TRUE	1	0.544826260952184	3		496	785	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106519995	106519995	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	306	610	0	ENST00000359195.3:c.2423A>T	p.Lys808Ile	p.K808I	ENST00000359195	NM_002649.2	808	aAa/aTa	6/11	0.535034032760229	2	FACETS	0.941	0.896	0.985	0.941	0.896	0.985	CLONAL	2	TRUE	0	0.544826260952184	2		610	597	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851531	151851531	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	242	312	0	ENST00000262189.6:c.11961-1G>A		p.X3987_splice	ENST00000262189	NM_170606.2	3987			0.535034032760229	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.544826260952184	2		312	408	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873564	151873564	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141611378	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	267	487	0	ENST00000262189.6:c.8974G>A	p.Gly2992Arg	p.G2992R	ENST00000262189	NM_170606.2	2992	Ggg/Agg	38/59	0.535034032760229	2	FACETS	0.928	0.881	0.976	0.928	0.881	0.976	CLONAL	2	TRUE	0	0.544826260952184	2		487	528	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277228	38277228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1404194266	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	41	660	2	ENST00000425967.3:c.1200G>A	p.Met400Ile	p.M400I	ENST00000425967	NM_001174067.1	400	atG/atA	10/19	1	2	FACETS	0.202	0.167	0.24	0.202	0.167	0.24	SUBCLONAL	1	TRUE	1	0.544826260952184	2		662	746	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331660	8331660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	184	581	0	ENST00000356435.5:c.5456G>A	p.Gly1819Glu	p.G1819E	ENST00000356435		1819	gGa/gAa	33/35	1	2	FACETS	0.972	0.9	1	0.972	0.9	1	CLONAL	1	TRUE	1	0.544826260952184	2		581	695	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133729454	133729455	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	96	348	0	ENST00000318560.5:c.83_84delinsTT	p.Ala28Val	p.A28V	ENST00000318560	NM_005157.4	28	gCC/gTT	2/11	1	2	FACETS	0.874	0.785	0.969	0.874	0.785	0.969	CLONAL	1	TRUE	1	0.544826260952184	2		348	403	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135804237	135804237	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	150	446	0	ENST00000298552.3:c.23G>A	p.Gly8Glu	p.G8E	ENST00000298552	NM_001162426.1	8	gGg/gAg	3/23	1	2	FACETS	0.999	0.918	1	0.999	0.918	1	CLONAL	1	TRUE	1	0.544826260952184	2		446	551	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403354	139403354	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	241	541	0	ENST00000277541.6:c.3139T>G	p.Cys1047Gly	p.C1047G	ENST00000277541	NM_017617.3	1047	Tgc/Ggc	19/34	1	2	FACETS	0.97	0.907	1	0.97	0.907	1	CLONAL	1	TRUE	1	0.544826260952184	2		541	912	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412303	139412303	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs869025494	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	286	586	0	ENST00000277541.6:c.1342C>T	p.Arg448Ter	p.R448*	ENST00000277541	NM_017617.3	448	Cga/Tga	8/34	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.544826260952184	2		586	960	SUCCESS
ATM	472	MSKCC	GRCh37	11	108173601	108173601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	80	272	0	ENST00000278616.4:c.5341G>A	p.Asp1781Asn	p.D1781N	ENST00000278616	NM_000051.3	1781	Gac/Aac	36/63	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.544826260952184	2		272	268	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198453	108198453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	142	498	0	ENST00000278616.4:c.7057C>T	p.Pro2353Ser	p.P2353S	ENST00000278616	NM_000051.3	2353	Cct/Tct	48/63	1	2	FACETS	0.89	0.814	0.968	0.89	0.814	0.968	CLONAL	1	TRUE	1	0.544826260952184	2		498	586	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201099	108201099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759728261	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	117	420	2	ENST00000278616.4:c.7466C>T	p.Ser2489Phe	p.S2489F	ENST00000278616	NM_000051.3	2489	tCc/tTc	50/63	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.544826260952184	2		422	426	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307529	118307529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	236	483	1	ENST00000534358.1:c.302C>T	p.Ser101Leu	p.S101L	ENST00000534358	NM_005933.3	101	tCa/tTa	1/36	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.544826260952184	2		484	804	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375059	118375059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	125	462	0	ENST00000534358.1:c.8452C>T	p.Pro2818Ser	p.P2818S	ENST00000534358	NM_005933.3	2818	Ccc/Tcc	27/36	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.544826260952184	2		462	445	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376796	118376796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	136	506	0	ENST00000534358.1:c.10189G>A	p.Asp3397Asn	p.D3397N	ENST00000534358	NM_005933.3	3397	Gac/Aac	27/36	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.544826260952184	2		506	484	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	430192	430193	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	192	658	1	ENST00000399788.2:c.2509_2510delinsTT	p.Pro837Leu	p.P837L	ENST00000399788	NM_001042603.1	837	CCg/TTg	18/28	NA	2	FACETS	0.964	0.894	1			1	INDETERMINATE	1	TRUE	NA	0.544826260952184	2		659	731	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524146	18524146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	168	613	1	ENST00000266497.5:c.1658C>T	p.Pro553Leu	p.P553L	ENST00000266497		553	cCa/cTa	11/31	0.279476637930684	1	FACETS	0.706	0.651	0.762	0.706	0.651	0.762	INDETERMINATE	1	TRUE	0	0.544826260952184	1		614	636	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865069	57865069	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1198368567	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	280	918	1	ENST00000228682.2:c.2546C>T	p.Ser849Phe	p.S849F	ENST00000228682	NM_005269.2	849	tCc/tTc	12/12	0.279476637930684	1	FACETS	0.742	0.698	0.787	0.742	0.698	0.787	INDETERMINATE	1	TRUE	0	0.544826260952184	1		919	1008	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811693	102811693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	202	626	1	ENST00000307046.8:c.491G>A	p.Gly164Glu	p.G164E	ENST00000307046	NM_001111285.1	164	gGg/gAg	4/4	0.318449543867684	2	FACETS	0.964	0.896	1	0.482	0.448	0.517	INDETERMINATE	1	TRUE	0	0.544826260952184	2		627	769	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609590	81609590	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377272347	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	179	709	0	ENST00000298171.2:c.1188G>A	p.Met396Ile	p.M396I	ENST00000298171	NM_000369.2	396	atG/atA	10/10	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.544826260952184	2		709	645	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2121831	2121831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	152	340	0	ENST00000219476.3:c.1993C>T	p.Pro665Ser	p.P665S	ENST00000219476	NM_000548.3	665	Cct/Tct	19/42	1	2	FACETS	0.984	0.905	1	0.984	0.905	1	CLONAL	1	TRUE	1	0.544826260952184	2		340	567	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831220	3831220	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1168098333	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	211	567	1	ENST00000262367.5:c.1661C>T	p.Ser554Phe	p.S554F	ENST00000262367	NM_004380.2	554	tCc/tTc	7/31	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.544826260952184	2		568	712	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3929832	3929832	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	276	484	1	ENST00000262367.5:c.85+1G>A		p.X29_splice	ENST00000262367	NM_004380.2	29			1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.544826260952184	2		485	716	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858184	9858184	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	227	659	0	ENST00000330684.3:c.3217G>A	p.Glu1073Lys	p.E1073K	ENST00000330684	NM_001134407.1	1073	Gaa/Aaa	13/13	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.544826260952184	2		659	720	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923469	9923469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs775819322	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	181	638	1	ENST00000330684.3:c.1818G>A	p.Trp606Ter	p.W606*	ENST00000330684	NM_001134407.1	606	tgG/tgA	9/13	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.544826260952184	2		639	655	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614901	23614901	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	219	713	1	ENST00000261584.4:c.3440G>T	p.Cys1147Phe	p.C1147F	ENST00000261584	NM_024675.3	1147	tGt/tTt	13/13	1	2	FACETS	0.997	0.93	1	0.997	0.93	1	CLONAL	1	TRUE	1	0.544826260952184	2		714	806	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68847400	68847400	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	145	532	0	ENST00000261769.5:c.1320+2T>C		p.X440_splice	ENST00000261769	NM_004360.3	440			1	2	FACETS	0.919	0.842	0.999	0.919	0.842	0.999	CLONAL	1	TRUE	1	0.544826260952184	2		532	579	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347138	89347138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1225667881	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	355	688	2	ENST00000301030.4:c.5812C>T	p.Pro1938Ser	p.P1938S	ENST00000301030	NM_001256183.1	1938	Ccc/Tcc	9/13	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.544826260952184	2		690	1289	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836263	89836263	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1320172669	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	324	788	0	ENST00000389301.3:c.2486C>T	p.Ser829Phe	p.S829F	ENST00000389301	NM_000135.2	829	tCc/tTc	26/43	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.544826260952184	2		788	1138	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782329	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	286	426	0	ENST00000269305.4:c.746G>C	p.Arg249Thr	p.R249T	ENST00000269305	NM_001126112.2	249	aGg/aCg	7/11	0.544826260952184	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.544826260952184	1		426	679	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15967405	15967405	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	222	570	1	ENST00000268712.3:c.5198C>A	p.Ser1733Tyr	p.S1733Y	ENST00000268712	NM_006311.3	1733	tCc/tAc	35/46	0.544826260952184	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.544826260952184	1		571	583	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40500519	40500519	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	232	641	0	ENST00000264657.5:c.16C>G	p.Gln6Glu	p.Q6E	ENST00000264657	NM_139276.2	6	Cag/Gag	2/24	0.544826260952184	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.544826260952184	1		641	588	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534430	63534431	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	163	463	1	ENST00000307078.5:c.1090_1091delinsTT	p.Pro364Phe	p.P364F	ENST00000307078	NM_004655.3	364	CCc/TTc	5/11	0.544826260952184	1	FACETS	0.888	0.822	0.957	0.888	0.822	0.957	CLONAL	1	TRUE	0	0.544826260952184	1		464	490	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78919535	78919535	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	233	559	0	ENST00000306801.3:c.3094C>T	p.His1032Tyr	p.H1032Y	ENST00000306801	NM_020761.2	1032	Cac/Tac	26/34	0.544826260952184	1	FACETS	0.982	0.921	1	0.982	0.921	1	CLONAL	1	TRUE	0	0.544826260952184	1		559	634	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619437	1619437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	274	609	1	ENST00000344749.5:c.1204C>T	p.His402Tyr	p.H402Y	ENST00000344749	NM_001136139.2	402	Cac/Tac	15/19	1	2	FACETS	0.893	0.838	0.95	0.893	0.838	0.95	CLONAL	1	TRUE	1	0.544826260952184	2		610	1126	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220074	5220074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	298	582	0	ENST00000357368.4:c.3641C>T	p.Ser1214Phe	p.S1214F	ENST00000357368	NM_002850.3	1214	tCt/tTt	22/38	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.544826260952184	2		582	1059	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5220081	5220081	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542361035	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	296	574	0	ENST00000357368.4:c.3634C>T	p.Arg1212Cys	p.R1212C	ENST00000357368	NM_002850.3	1212	Cgc/Tgc	22/38	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.544826260952184	2		574	1059	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291020	15291020	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	209	675	0	ENST00000263388.2:c.3190G>T	p.Glu1064Ter	p.E1064*	ENST00000263388	NM_000435.2	1064	Gaa/Taa	20/33	1	2	FACETS	0.829	0.771	0.89	0.829	0.771	0.89	CLONAL	1	TRUE	1	0.544826260952184	2		675	925	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354235	15354235	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	230	472	0	ENST00000263377.2:c.2645C>T	p.Pro882Leu	p.P882L	ENST00000263377	NM_058243.2	882	cCc/cTc	14/20	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.544826260952184	2		472	843	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726632	41726632	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	258	677	0	ENST00000301178.4:c.177G>T	p.Gln59His	p.Q59H	ENST00000301178	NM_021913.4	59	caG/caT	2/20	1	2	FACETS	0.981	0.92	1	0.981	0.92	1	CLONAL	1	TRUE	1	0.544826260952184	2		677	965	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560883	9560883	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	215	712	0	ENST00000353224.5:c.899G>A	p.Gly300Glu	p.G300E	ENST00000353224	NM_177990.2	300	gGa/gAa	4/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.544826260952184	2		712	718	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39713167	39713167	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	189	555	0	ENST00000361337.2:c.573G>C	p.Lys191Asn	p.K191N	ENST00000361337	NM_003286.2	191	aaG/aaC	8/21	0.463152305702441	3	FACETS	0.92	0.85	0.992	0.46	0.425	0.496	CLONAL	1	TRUE	1	0.544826260952184	3		555	960	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747054	40747054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	157	544	0	ENST00000373198.4:c.3028G>A	p.Glu1010Lys	p.E1010K	ENST00000373198	NM_133170.3	1010	Gaa/Aaa	22/32	0.463152305702441	3	FACETS	1	0.965	1	0.545	0.5	0.591	CLONAL	1	TRUE	1	0.544826260952184	3		544	673	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877329	40877330	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	214	408	0	ENST00000373198.4:c.2366_2367delinsAA	p.Arg789Lys	p.R789K	ENST00000373198	NM_133170.3	789	aGG/aAA	15/32	0.463152305702441	3	FACETS	1	0.939	1	1	0.939	1	CLONAL	2	TRUE	1	0.544826260952184	3		408	500	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513343	44513343	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1405742986	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	242	471	0	ENST00000291552.4:c.592C>T	p.Arg198Ter	p.R198*	ENST00000291552	NM_006758.2	198	Cga/Tga	8/8	1	2	FACETS	0.991	0.928	1	0.991	0.928	1	CLONAL	1	TRUE	1	0.544826260952184	2		471	896	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656878	45656878	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	245	518	0	ENST00000407780.3:c.278G>C	p.Arg93Pro	p.R93P	ENST00000407780	NM_001283052.1	93	cGg/cCg	3/7	1	2	FACETS	0.984	0.921	1	0.984	0.921	1	CLONAL	1	TRUE	1	0.544826260952184	2		518	914	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074269	30074269	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	139	586	0	ENST00000338641.4:c.1531G>C	p.Asp511His	p.D511H	ENST00000338641	NM_000268.3	511	Gat/Cat	14/16	1	2	FACETS	0.88	0.804	0.958	0.88	0.804	0.958	CLONAL	1	TRUE	1	0.544826260952184	2		586	580	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30074298	30074298	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	106	435	0	ENST00000338641.4:c.1560G>C	p.Glu520Asp	p.E520D	ENST00000338641	NM_000268.3	520	gaG/gaC	14/16	1	2	FACETS	0.926	0.836	1	0.926	0.836	1	CLONAL	1	TRUE	1	0.544826260952184	2		435	420	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426072	47426072	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	323	359	0	ENST00000377045.4:c.592C>T	p.Pro198Ser	p.P198S	ENST00000377045	NM_001654.4	198	Ccc/Tcc	7/16	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.544826260952184	1		359	576	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430406	47430406	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	210	311	0	ENST00000377045.4:c.1681C>T	p.Pro561Ser	p.P561S	ENST00000377045	NM_001654.4	561	Ccc/Tcc	15/16	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.544826260952184	1		311	417	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650334	48650334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	177	355	0	ENST00000376670.3:c.304G>A	p.Gly102Arg	p.G102R	ENST00000376670	NM_002049.3	102	Ggg/Agg	3/6	1	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.544826260952184	1		355	408	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030397	49030412	+	frameshift_variant	Frame_Shift_Del	DEL	TACTGCAAATGCAGAG	TACTGCAAATGCAGAG	CAGAA	novel	NA	P-0006437-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	135	370	0	ENST00000267163.4:c.1872_1887delinsCAGAA	p.Thr625ArgfsTer24	p.T625Rfs*24	ENST00000267163	NM_000321.2	624	tcTACTGCAAATGCAGAG/tcCAGAA	19/27	1	2	FACETS	0.977	0.894	1	0.977	0.894	1	CLONAL	1	TRUE	1	0.544826260952184	2		370	507	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006496-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	19	280	0				ENST00000310581	NM_198253.2	-/1132			0.341262642618904	0	FACETS	0.54	0.414	0.685			1	SUBCLONAL	1	FALSE	0	0.341056043748938	0		280	136	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0006496-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	84	315	0	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	0.341056043748938	5	FACETS	1	0.883	1	0.334	0.294	0.376	CLONAL	1	FALSE	2	0.341056043748938	5		315	744	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	73	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.968	0.85	1	0.968	0.85	1	CLONAL	1	TRUE	1	0.35	2		280	431	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0006509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	175	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.35	2		490	935	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0006543-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	316	176	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.861629166217482	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.879836888474489	1		176	362	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469669	NA	P-0006543-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	547	283	0	ENST00000374080.3:c.130G>A	p.Gly44Ser	p.G44S	ENST00000374080		44	Ggt/Agt	2/45	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.879836888474489	2		283	1157	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578195	7578197	+	inframe_deletion	In_Frame_Del	DEL	CAC	CAC	-	novel	NA	P-0006543-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	1015	704	4	ENST00000269305.4:c.652_654del	p.Val218del	p.V218del	ENST00000269305	NM_001126112.2	218	GTG/-	6/11	0.879836888474489	2	FACETS	0.97	0.956	0.984	0.97	0.956	0.984	CLONAL	2	TRUE	0	0.879836888474489	2		708	1189	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426847	70426847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006543-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	320	488	2	ENST00000373644.4:c.4507C>T	p.Arg1503Trp	p.R1503W	ENST00000373644	NM_030625.2	1503	Cgg/Tgg	7/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.879836888474489	2		490	712	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428435	49428436	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	rs1555189455	NA	P-0006543-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	323	558	0	ENST00000301067.7:c.10369_10370del	p.Leu3457AlafsTer10	p.L3457Afs*10	ENST00000301067	NM_003482.3	3457	CTg/g	36/54	1	2	FACETS	0.995	0.946	1	0.995	0.946	1	CLONAL	1	TRUE	1	0.879836888474489	2		558	738	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001374	150001376	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	rs753305883	NA	P-0006543-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	42	555	0	ENST00000253339.5:c.2228_2230del	p.Leu743del	p.L743del	ENST00000253339		743	cTTCga/cga	4/7	1	2	FACETS	0.115	0.095	0.137	0.115	0.095	0.137	SUBCLONAL	1	TRUE	1	0.879836888474489	2		555	832	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446070	49446081	+	frameshift_variant	Frame_Shift_Del	DEL	GTGATGCCTCAG	GTGATGCCTCAG	A	novel	NA	P-0006543-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	507	839	3	ENST00000301067.7:c.1385_1396delinsT	p.Pro462LeufsTer7	p.P462Lfs*7	ENST00000301067	NM_003482.3	462	cCTGAGGCATCACgc/cTgc	10/54	1	2	FACETS	0.882	0.846	0.919	0.882	0.846	0.919	CLONAL	1	TRUE	1	0.879836888474489	2		842	1306	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	188	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.963	1	1	0.993	1	CLONAL	2	TRUE	1	0.204082524523221	2		464	865	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	188	383	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	1	2	FACETS	1	0.927	1	1	0.993	1	CLONAL	2	TRUE	1	0.204082524523221	2		383	919	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578479	7578479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934874	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1213	232	680	0	ENST00000269305.4:c.451C>T	p.Pro151Ser	p.P151S	ENST00000269305	NM_001126112.2	151	Ccc/Tcc	5/11	1	2	FACETS	0.787	0.732	0.844	1	0.992	1	SUBCLONAL	2	TRUE	1	0.204082524523221	2		680	1445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	206	476	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.204082524523221	2		477	1346	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245843	46245843	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	118	421	1	ENST00000334344.6:c.3937C>T	p.Gln1313Ter	p.Q1313*	ENST00000334344	NM_152641.2	1313	Caa/Taa	15/21	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.204082524523221	2		422	1028	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16247377	16247377	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748683309	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	140	357	1	ENST00000375759.3:c.1648C>T	p.Arg550Cys	p.R550C	ENST00000375759	NM_015001.2	550	Cgc/Tgc	9/15	0.204082524523221	2	FACETS	0.954	0.87	1	0.954	0.87	1	CLONAL	2	TRUE	0	0.204082524523221	2		358	719	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36826837	36826837	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	241	798	0	ENST00000373129.3:c.97G>T	p.Gly33Ter	p.G33*	ENST00000373129	NM_032017.1	33	Gga/Tga	3/12	0.204082524523221	2	FACETS	0.978	0.913	1	0.978	0.913	1	CLONAL	2	TRUE	0	0.204082524523221	2		798	1207	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459307	120459307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	69	190	0	ENST00000256646.2:c.6038C>T	p.Pro2013Leu	p.P2013L	ENST00000256646	NM_024408.3	2013	cCt/cTt	34/34	0.204082524523221	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	2	TRUE	0	0.204082524523221	2		190	312	SUCCESS
H3C13	653604	MSKCC	GRCh37	1	149784830	149784830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	147	635	0	ENST00000331491.1:c.407C>T	p.Ala136Val	p.A136V	ENST00000331491	NM_001123375.2	136	gCc/gTc	1/1	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.204082524523221	2		635	1148	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085635	16085635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	105	597	0	ENST00000281043.3:c.811G>A	p.Glu271Lys	p.E271K	ENST00000281043	NM_005378.4	271	Gaa/Aaa	3/3	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.204082524523221	2		597	952	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125767	47125767	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	68	416	0	ENST00000409792.3:c.5503C>T	p.Pro1835Ser	p.P1835S	ENST00000409792	NM_014159.6	1835	Cct/Tct	12/21	1	2	FACETS	0.999	0.869	1	0.999	0.869	1	CLONAL	1	TRUE	1	0.204082524523221	2		416	667	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668786	52668786	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	102	563	0	ENST00000394830.3:c.1133C>T	p.Ser378Phe	p.S378F	ENST00000394830	NM_018313.4	378	tCc/tTc	12/30	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.204082524523221	2		563	891	SUCCESS
ATR	545	MSKCC	GRCh37	3	142241581	142241581	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	113	534	0	ENST00000350721.4:c.4255T>C	p.Tyr1419His	p.Y1419H	ENST00000350721	NM_001184.3	1419	Tat/Cat	23/47	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.204082524523221	2		534	862	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952025	178952025	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	86	613	0	ENST00000263967.3:c.3080C>T	p.Ala1027Val	p.A1027V	ENST00000263967	NM_006218.2	1027	gCc/gTc	21/21	1	2	FACETS	0.91	0.804	1	0.91	0.804	1	CLONAL	1	TRUE	1	0.204082524523221	2		613	926	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55151632	55151633	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	108	647	0	ENST00000257290.5:c.2418_2419delinsAA	p.Met806_Glu807delinsIleLys	p.M806_E807delinsIK	ENST00000257290	NM_006206.4	806	atGGag/atAAag	17/23	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.204082524523221	2		647	1003	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630459	187630459	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	140	821	0	ENST00000441802.2:c.523G>T	p.Asp175Tyr	p.D175Y	ENST00000441802	NM_005245.3	175	Gat/Tat	2/27	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.204082524523221	2		821	1185	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497196	149497196	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	130	473	0	ENST00000261799.4:c.3122C>T	p.Ser1041Phe	p.S1041F	ENST00000261799	NM_002609.3	1041	tCc/tTc	22/23	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.204082524523221	2		473	897	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553236	106553236	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	144	494	0	ENST00000369096.4:c.1201G>C	p.Ala401Pro	p.A401P	ENST00000369096	NM_001198.3	401	Gct/Cct	5/7	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.204082524523221	2		494	1035	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641177	117641177	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773843792	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1503	240	1139	1	ENST00000368508.3:c.5794G>A	p.Glu1932Lys	p.E1932K	ENST00000368508	NM_002944.2	1932	Gag/Aag	36/43	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.204082524523221	2		1140	1743	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642516	117642516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1272	230	1010	0	ENST00000368508.3:c.5683G>A	p.Gly1895Arg	p.G1895R	ENST00000368508	NM_002944.2	1895	Ggg/Agg	35/43	1	2	FACETS	0.75	0.697	0.805	1	0.991	1	SUBCLONAL	2	TRUE	1	0.204082524523221	2		1010	1502	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004247	150004247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	118	656	0	ENST00000253339.5:c.1978C>T	p.Arg660Cys	p.R660C	ENST00000253339		660	Cgt/Tgt	3/7	0.171717718954131	3	FACETS	1	0.965	1	0.578	0.52	0.64	CLONAL	1	TRUE	1	0.204082524523221	3		656	1102	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850250	128850250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	137	776	3	ENST00000249373.3:c.1513C>T	p.Pro505Ser	p.P505S	ENST00000249373	NM_005631.4	505	Cct/Tct	9/12	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.204082524523221	2		779	1247	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852355	63852355	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	134	638	2	ENST00000279873.7:c.3133A>T	p.Lys1045Ter	p.K1045*	ENST00000279873	NM_032199.2	1045	Aag/Tag	10/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.204082524523221	2		640	1081	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132833	64132833	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1447050686	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	159	830	1	ENST00000334205.4:c.967C>T	p.Arg323Cys	p.R323C	ENST00000334205	NM_003942.2	323	Cgc/Tgc	9/17	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.204082524523221	2		831	1277	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192621	94192621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	108	606	1	ENST00000323929.3:c.1453C>T	p.Leu485Phe	p.L485F	ENST00000323929	NM_005591.3	485	Ctt/Ttt	13/20	1	2	FACETS	0.931	0.833	1	0.931	0.833	1	CLONAL	1	TRUE	1	0.204082524523221	2		607	1137	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111958656	111958656	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	52	392	0	ENST00000375549.3:c.128G>A	p.Trp43Ter	p.W43*	ENST00000375549	NM_003002.3	43	tGg/tAg	2/4	1	2	FACETS	0.873	0.742	1	0.873	0.742	1	CLONAL	1	TRUE	1	0.204082524523221	2		392	584	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344839	118344839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139989306	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	147	740	2	ENST00000534358.1:c.2965C>T	p.Leu989Phe	p.L989F	ENST00000534358	NM_005933.3	989	Ctc/Ttc	3/36	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.204082524523221	2		742	1116	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373333	118373333	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	130	780	0	ENST00000534358.1:c.6726T>G	p.Ser2242Arg	p.S2242R	ENST00000534358	NM_005933.3	2242	agT/agG	27/36	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.204082524523221	2		780	1160	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376479	118376479	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	68	556	0	ENST00000534358.1:c.9872G>A	p.Arg3291Lys	p.R3291K	ENST00000534358	NM_005933.3	3291	aGa/aAa	27/36	1	2	FACETS	0.762	0.661	0.871	0.762	0.661	0.871	SUBCLONAL	1	TRUE	1	0.204082524523221	2		556	875	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025614	1025614	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	196	616	0	ENST00000358495.3:c.761C>G	p.Thr254Arg	p.T254R	ENST00000358495	NM_134424.2	254	aCg/aGg	9/12	1	2	FACETS	0.827	0.765	0.892	1	0.992	1	CLONAL	2	TRUE	1	0.204082524523221	2		616	1161	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885338	111885338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	142	617	1	ENST00000341259.2:c.1226G>A	p.Gly409Glu	p.G409E	ENST00000341259	NM_005475.2	409	gGg/gAg	6/8	NA	2	FACETS	1	0.981	1			1	INDETERMINATE	1	TRUE	NA	0.204082524523221	2		618	1066	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112892443	112892443	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	111	637	0	ENST00000351677.2:c.601C>T	p.Pro201Ser	p.P201S	ENST00000351677	NM_002834.3	201	Cct/Tct	5/16	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.204082524523221	2		637	926	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609785	28609785	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	49	460	0	ENST00000241453.7:c.1444G>T	p.Val482Phe	p.V482F	ENST00000241453	NM_004119.2	482	Gtc/Ttc	12/24	1	2	FACETS	0.697	0.589	0.816	0.697	0.589	0.816	SUBCLONAL	1	TRUE	1	0.204082524523221	2		460	689	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034753	42034753	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	114	842	0	ENST00000219905.7:c.4595C>T	p.Pro1532Leu	p.P1532L	ENST00000219905	NM_001164273.1	1532	cCc/cTc	15/24	1	2	FACETS	0.906	0.813	1	0.906	0.813	1	CLONAL	1	TRUE	1	0.204082524523221	2		842	1233	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215384	41215384	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	140	627	1	ENST00000357654.3:c.5159C>T	p.Thr1720Ile	p.T1720I	ENST00000357654	NM_007294.3	1720	aCc/aTc	18/23	NA	2	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.204082524523221	2		628	973	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213939	2213939	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	159	591	0	ENST00000398665.3:c.1751A>C	p.Gln584Pro	p.Q584P	ENST00000398665	NM_032482.2	584	cAg/cCg	18/28	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.204082524523221	2		591	1050	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300201	15300201	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	192	892	0	ENST00000263388.2:c.1075C>T	p.Pro359Ser	p.P359S	ENST00000263388	NM_000435.2	359	Ccc/Tcc	7/33	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.204082524523221	2		892	1343	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741806	40741806	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	142	518	0	ENST00000392038.2:c.1166C>T	p.Pro389Leu	p.P389L	ENST00000392038	NM_001626.4	389	cCc/cTc	11/14	1	2	FACETS	0.8	0.729	0.874	1	0.988	1	SUBCLONAL	2	TRUE	1	0.204082524523221	2		518	870	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749535	41749535	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773912722	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	154	769	0	ENST00000301178.4:c.1460C>T	p.Pro487Leu	p.P487L	ENST00000301178	NM_021913.4	487	cCa/cTa	12/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.204082524523221	2		769	1332	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023394	31023395	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	66	471	1	ENST00000375687.4:c.2879_2880delinsAA	p.Trp960Ter	p.W960*	ENST00000375687	NM_015338.5	960	tGG/tAA	13/13	1	2	FACETS	0.965	0.837	1	0.965	0.837	1	CLONAL	1	TRUE	1	0.204082524523221	2		472	670	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484610	57484610	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	73	404	0	ENST00000371085.3:c.694C>T	p.Arg232Cys	p.R232C	ENST00000371085	NM_000516.4	232	Cgc/Tgc	9/13	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.204082524523221	2		404	654	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30032742	30032742	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	45	531	0	ENST00000338641.4:c.117G>A	p.Met39Ile	p.M39I	ENST00000338641	NM_000268.3	39	atG/atA	2/16	1	2	FACETS	0.521	0.436	0.615	0.521	0.436	0.615	SUBCLONAL	1	TRUE	1	0.204082524523221	2		531	847	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317580	1317580	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006571-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	66	360	0	ENST00000400841.2:c.485C>T	p.Ser162Phe	p.S162F	ENST00000400841		162	tCc/tTc	5/6	1	1	FACETS	0.859	0.745	0.983	0.859	0.745	0.983	CLONAL	1	TRUE	0	0.204082524523221	1		360	676	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	179	464	0				ENST00000310581	NM_198253.2	-/1132			0.814876413535148	4	FACETS	0.919	0.857	0.981	0.919	0.857	0.981	CLONAL	2	TRUE	2	0.814876413535148	4		464	434	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913255	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	789	402	0	ENST00000369535.4:c.183A>C	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caC	3/7	0.372776851510428	6	FACETS	1	0.994	1	1	0.998	1	INDETERMINATE	4	TRUE	3	0.814876413535148	6		402	1197	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142996	30142996	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	265	441	1	ENST00000389048.3:c.530G>A	p.Trp177Ter	p.W177*	ENST00000389048	NM_004304.4	177	tGg/tAg	1/29	0.371160584087131	5	FACETS	0.986	0.929	1	0.657	0.619	0.696	INDETERMINATE	2	TRUE	2	0.814876413535148	5		442	733	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260569	16260569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	489	417	0	ENST00000375759.3:c.7834C>T	p.Pro2612Ser	p.P2612S	ENST00000375759	NM_015001.2	2612	Cca/Tca	11/15	0.814876413535148	3	FACETS	0.998	0.963	1	0.998	0.963	1	CLONAL	2	TRUE	1	0.814876413535148	3		417	846	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099897	27099897	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	207	429	1	ENST00000324856.7:c.3776C>T	p.Pro1259Leu	p.P1259L	ENST00000324856	NM_006015.4	1259	cCc/cTc	15/20	0.814876413535148	3	FACETS	0.851	0.791	0.913	0.426	0.395	0.457	CLONAL	1	TRUE	1	0.814876413535148	3		430	840	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162746023	162746023	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	301	459	0	ENST00000367921.3:c.2146T>G	p.Cys716Gly	p.C716G	ENST00000367921	NM_006182.2	716	Tgt/Ggt	16/18	0.814876413535148	4	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.814876413535148	4		459	1129	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652458	206652458	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	196	296	0	ENST00000367120.3:c.1165G>A	p.Gly389Arg	p.G389R	ENST00000367120	NM_014002.3	389	Ggg/Agg	10/22	0.323027634153671	6	FACETS	1	0.955	1	0.689	0.641	0.738	INDETERMINATE	2	TRUE	3	0.814876413535148	6		296	612	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47606908	47606908	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1257057505	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	251	342	0	ENST00000263735.4:c.658G>A	p.Val220Ile	p.V220I	ENST00000263735	NM_002354.2	220	Gtt/Att	7/9	0.371160584087131	5	FACETS	0.97	0.912	1	0.646	0.608	0.686	INDETERMINATE	2	TRUE	2	0.814876413535148	5		342	706	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026182	48026182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	256	457	0	ENST00000234420.5:c.1060G>A	p.Gly354Arg	p.G354R	ENST00000234420	NM_000179.2	354	Gga/Aga	4/10	0.371160584087131	5	FACETS	1	0.992	1	0.484	0.453	0.515	INDETERMINATE	1	TRUE	2	0.814876413535148	5		457	962	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182556	99182556	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	325	380	0	ENST00000074304.5:c.2359C>T	p.Gln787Ter	p.Q787*	ENST00000074304	NM_001134224.1	787	Cag/Tag	22/26	0.814876413535148	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.814876413535148	4		380	715	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543810	212543810	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	192	347	0	ENST00000342788.4:c.1589G>T	p.Arg530Met	p.R530M	ENST00000342788	NM_005235.2	530	aGg/aTg	13/28	0.372776851510428	6	FACETS	1	0.988	1	0.444	0.411	0.479	INDETERMINATE	1	TRUE	3	0.814876413535148	6		347	930	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570064	212570064	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55671017	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	229	403	0	ENST00000342788.4:c.1177C>T	p.Arg393Trp	p.R393W	ENST00000342788	NM_005235.2	393	Cgg/Tgg	10/28	0.372776851510428	6	FACETS	0.754	0.703	0.807	0.503	0.469	0.538	INDETERMINATE	2	TRUE	3	0.814876413535148	6		403	980	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30686341	30686341	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	186	351	0	ENST00000295754.5:c.197C>T	p.Ser66Phe	p.S66F	ENST00000295754	NM_003242.5	66	tCc/tTc	2/7	0.814876413535148	4	FACETS	0.975	0.901	1	0.487	0.45	0.526	CLONAL	1	TRUE	2	0.814876413535148	4		351	850	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713823	30713823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	371	377	0	ENST00000295754.5:c.1148C>T	p.Ser383Phe	p.S383F	ENST00000295754	NM_003242.5	383	tCc/tTc	4/7	0.814876413535148	4	FACETS	0.943	0.899	0.988	0.943	0.899	0.988	CLONAL	2	TRUE	2	0.814876413535148	4		377	876	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37038192	37038193	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	462	442	0	ENST00000231790.2:c.199_200delinsAA	p.Gly67Lys	p.G67K	ENST00000231790	NM_000249.3	67	GGg/AAg	2/19	0.814876413535148	4	FACETS	0.909	0.87	0.948	0.909	0.87	0.948	CLONAL	2	TRUE	2	0.814876413535148	4		442	1132	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439835	52439835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	241	455	0	ENST00000460680.1:c.877C>T	p.Pro293Ser	p.P293S	ENST00000460680	NM_004656.3	293	Ccg/Tcg	10/17	0.486635006551458	4	FACETS	1	0.99	1	0.431	0.403	0.459	INDETERMINATE	1	TRUE	1	0.814876413535148	4		455	831	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643834	52643834	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	215	368	2	ENST00000394830.3:c.2062C>T	p.Pro688Ser	p.P688S	ENST00000394830	NM_018313.4	688	Ccc/Tcc	17/30	0.486635006551458	4	FACETS	1	0.991	1	0.464	0.433	0.496	INDETERMINATE	1	TRUE	1	0.814876413535148	4		370	688	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259557	89259557	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	152	317	0	ENST00000336596.2:c.701C>T	p.Ser234Phe	p.S234F	ENST00000336596	NM_005233.5	234	tCt/tTt	3/17	0.814876413535148	3	FACETS	0.898	0.825	0.973	0.449	0.412	0.487	CLONAL	1	TRUE	1	0.814876413535148	3		317	585	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898705	134898705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	387	408	2	ENST00000398015.3:c.1763C>T	p.Ser588Phe	p.S588F	ENST00000398015	NM_004441.4	588	tCc/tTc	10/16	0.814876413535148	3	FACETS	0.977	0.938	1	0.977	0.938	1	CLONAL	2	TRUE	1	0.814876413535148	3		410	684	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161405	185161405	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	234	497	0	ENST00000265026.3:c.832C>T	p.Arg278Cys	p.R278C	ENST00000265026	NM_004721.4	278	Cgt/Tgt	4/14	0.814876413535148	3	FACETS	0.988	0.924	1	0.494	0.462	0.527	CLONAL	1	TRUE	1	0.814876413535148	3		497	818	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143324207	143324208	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	517	247	0	ENST00000262992.4:c.256-1_256delinsAA		p.X86_splice	ENST00000262992	NM_001101669.1	86		5/24	0.814876413535148	4	FACETS	0.977	0.946	1			1	CLONAL	3	TRUE	NA	0.814876413535148	4		247	786	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35860953	35860953	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs200803157	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	156	322	1	ENST00000303115.3:c.83-1G>A		p.X28_splice	ENST00000303115	NM_002185.3	28			0.814876413535148	4	FACETS	0.99	0.909	1	0.495	0.454	0.537	CLONAL	1	TRUE	2	0.814876413535148	4		323	702	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874635	35874635	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs752967041	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	438	479	1	ENST00000303115.3:c.791G>A	p.Trp264Ter	p.W264*	ENST00000303115	NM_002185.3	264	tGg/tAg	6/8	0.814876413535148	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.814876413535148	4		480	974	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950105	38950105	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	184	407	1	ENST00000357387.3:c.3845C>A	p.Ser1282Ter	p.S1282*	ENST00000357387	NM_152756.3	1282	tCa/tAa	31/38	0.814876413535148	4	FACETS	0.906	0.836	0.978	0.453	0.418	0.489	CLONAL	1	TRUE	2	0.814876413535148	4		408	905	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460362	149460362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	177	420	0	ENST00000286301.3:c.275G>A	p.Gly92Glu	p.G92E	ENST00000286301	NM_005211.3	92	gGa/gAa	3/22	1	2	FACETS	0.896	0.833	0.96	0.896	0.833	0.96	CLONAL	1	TRUE	1	0.814876413535148	2		420	485	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030251	180030251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781063816	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	152	448	1	ENST00000261937.6:c.4033G>A	p.Glu1345Lys	p.E1345K	ENST00000261937	NM_182925.4	1345	Gag/Aag	30/30	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.814876413535148	NA		449	569	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169935	32169935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142477287	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	811	469	0	ENST00000375023.3:c.3673C>T	p.Arg1225Trp	p.R1225W	ENST00000375023	NM_004557.3	1225	Cgg/Tgg	21/30	0.575032969286696	6	FACETS	0.938	0.912	0.964	0.938	0.912	0.964	CLONAL	4	TRUE	2	0.814876413535148	6		469	1395	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185817	32185817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	224	463	0	ENST00000375023.3:c.1579G>A	p.Asp527Asn	p.D527N	ENST00000375023	NM_004557.3	527	Gat/Aat	9/30	0.575032969286696	6	FACETS	1	0.987	1	0.313	0.29	0.336	CLONAL	1	TRUE	2	0.814876413535148	6		463	1156	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965756	93965756	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	221	469	0	ENST00000369303.4:c.2173-1G>A		p.X725_splice	ENST00000369303	NM_004440.3	725			1	2	FACETS	0.957	0.897	1	0.957	0.897	1	CLONAL	1	TRUE	1	0.814876413535148	2		469	567	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630035	117630035	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	249	462	0	ENST00000368508.3:c.6491C>T	p.Ala2164Val	p.A2164V	ENST00000368508	NM_002944.2	2164	gCt/gTt	41/43	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.814876413535148	2		462	596	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781195	161781195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	183	515	0	ENST00000366898.1:c.1210G>A	p.Glu404Lys	p.E404K	ENST00000366898	NM_004562.2	404	Gaa/Aaa	11/12	1	2	FACETS	0.948	0.883	1	0.948	0.883	1	CLONAL	1	TRUE	1	0.814876413535148	2		515	474	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2972204	2972204	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	392	353	0	ENST00000396946.4:c.1535C>T	p.Ser512Phe	p.S512F	ENST00000396946	NM_032415.4	512	tCc/tTc	11/25	0.752088618893554	4	FACETS	0.898	0.857	0.94			1	CLONAL	2	TRUE	NA	0.814876413535148	4		353	972	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388017	81388017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	439	436	0	ENST00000222390.5:c.358G>A	p.Glu120Lys	p.E120K	ENST00000222390	NM_000601.4	120	Gaa/Aaa	3/18	0.814876413535148	4	FACETS	0.907	0.867	0.947	0.907	0.867	0.947	CLONAL	2	TRUE	2	0.814876413535148	4		436	1078	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508025	106508025	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	342	370	0	ENST00000359195.3:c.19A>G	p.Lys7Glu	p.K7E	ENST00000359195	NM_002649.2	7	Aaa/Gaa	2/11	0.814876413535148	4	FACETS	0.922	0.877	0.968	0.922	0.877	0.968	CLONAL	2	TRUE	2	0.814876413535148	4		370	826	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508721	106508721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754275924	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	493	378	0	ENST00000359195.3:c.715G>A	p.Asp239Asn	p.D239N	ENST00000359195	NM_002649.2	239	Gac/Aac	2/11	0.814876413535148	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	2	0.814876413535148	4		378	1008	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370927	55370927	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	308	367	0	ENST00000297316.4:c.229G>A	p.Val77Met	p.V77M	ENST00000297316	NM_022454.3	77	Gtg/Atg	1/2	0.610982861012133	4	FACETS	0.981	0.932	1			1	CLONAL	2	TRUE	NA	0.814876413535148	4		367	699	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126751	5126751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	207	449	0	ENST00000381652.3:c.3359C>T	p.Ala1120Val	p.A1120V	ENST00000381652	NM_004972.3	1120	gCt/gTt	25/25	0.770833000393152	3	FACETS	0.961	0.895	1			1	CLONAL	1	TRUE	NA	0.814876413535148	3		449	744	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376681	8376681	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	162	410	0	ENST00000356435.5:c.4432G>T	p.Gly1478Ter	p.G1478*	ENST00000356435		1478	Gga/Tga	27/35	0.221459106316062	3	FACETS	0.908	0.837	0.982			1	INDETERMINATE	1	TRUE	NA	0.814876413535148	3		410	616	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518183	8518184	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	128	344	0	ENST00000356435.5:c.1207_1208delinsTT	p.Pro403Phe	p.P403F	ENST00000356435		403	CCt/TTt	10/35	0.221459106316062	3	FACETS	0.859	0.782	0.938			1	INDETERMINATE	1	TRUE	NA	0.814876413535148	3		344	515	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93636974	93636974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	187	333	1	ENST00000375746.1:c.1024C>T	p.Pro342Ser	p.P342S	ENST00000375746	NM_001174167.1	342	Ccc/Tcc	9/14	0.814876413535148	2	FACETS	1	0.975	1	0.541	0.506	0.577	CLONAL	1	TRUE	0	0.814876413535148	2		334	424	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601881	43601881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	284	435	1	ENST00000355710.3:c.925G>A	p.Glu309Lys	p.E309K	ENST00000355710	NM_020975.4	309	Gag/Aag	5/20	0.323027634153671	6	FACETS	1	0.99	1	0.815	0.77	0.86	INDETERMINATE	2	TRUE	3	0.814876413535148	6		436	750	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63845508	63845508	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	433	404	0	ENST00000279873.7:c.1247C>T	p.Pro416Leu	p.P416L	ENST00000279873	NM_032199.2	416	cCc/cTc	9/10	0.323027634153671	6	FACETS	0.902	0.863	0.941	0.902	0.863	0.941	INDETERMINATE	3	TRUE	3	0.814876413535148	6		404	1033	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244981	123244981	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	406	511	1	ENST00000358487.5:c.2123C>T	p.Pro708Leu	p.P708L	ENST00000358487	NM_000141.4	708	cCc/cTc	16/18	0.657124889113953	3	FACETS	0.989	0.951	1	0.989	0.951	1	CLONAL	2	TRUE	1	0.814876413535148	3		512	709	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298174	123298174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	199	493	0	ENST00000358487.5:c.680G>A	p.Gly227Glu	p.G227E	ENST00000358487	NM_000141.4	227	gGa/gAa	6/18	0.657124889113953	3	FACETS	1	0.949	1	0.512	0.476	0.549	CLONAL	1	TRUE	1	0.814876413535148	3		493	671	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573229	64573229	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863224807	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	181	470	3	ENST00000312049.6:c.1063C>T	p.Arg355Trp	p.R355W	ENST00000312049	NM_130799.2	355	Cgg/Tgg	8/10	0.770833000393152	3	FACETS	0.902	0.835	0.972			1	CLONAL	1	TRUE	NA	0.814876413535148	3		473	693	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999411	100999411	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1335446824	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	381	549	0	ENST00000325455.5:c.391C>T	p.Pro131Ser	p.P131S	ENST00000325455	NM_001202474.3	131	Cct/Tct	1/8	0.812136707485408	2	FACETS	0.986	0.959	1	0.986	0.959	1	CLONAL	2	TRUE	0	0.814876413535148	2		549	474	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206738	102206738	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	655	634	0	ENST00000263464.3:c.1366C>T	p.Gln456Ter	p.Q456*	ENST00000263464	NM_001165.4	456	Caa/Taa	7/9	0.812136707485408	2	FACETS	0.98	0.959	1	0.98	0.959	1	CLONAL	2	TRUE	0	0.814876413535148	2		634	820	SUCCESS
CBL	867	MSKCC	GRCh37	11	119169209	119169209	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778158	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	293	314	0	ENST00000264033.4:c.2393C>T	p.Ser798Phe	p.S798F	ENST00000264033	NM_005188.3	798	tCc/tTc	15/16	0.812136707485408	2	FACETS	0.991	0.959	1	0.991	0.959	1	CLONAL	2	TRUE	0	0.814876413535148	2		314	363	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425268	49425268	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	398	367	0	ENST00000301067.7:c.13220T>G	p.Val4407Gly	p.V4407G	ENST00000301067	NM_003482.3	4407	gTg/gGg	39/54	0.814876413535148	3	FACETS	0.991	0.952	1	0.991	0.952	1	CLONAL	2	TRUE	1	0.814876413535148	3		367	694	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445935	49445935	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750950395	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	536	611	1	ENST00000301067.7:c.1531C>T	p.Pro511Ser	p.P511S	ENST00000301067	NM_003482.3	511	Cct/Tct	10/54	0.814876413535148	3	FACETS	0.941	0.908	0.974	0.941	0.908	0.974	CLONAL	2	TRUE	1	0.814876413535148	3		612	984	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218392	69218392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	480	486	0	ENST00000462284.1:c.484C>T	p.Pro162Ser	p.P162S	ENST00000462284	NM_002392.5	162	Cca/Tca	7/11	0.814876413535148	3	FACETS	0.912	0.878	0.946	0.912	0.878	0.946	CLONAL	2	TRUE	1	0.814876413535148	3		486	909	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906409	32906409	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1325120431	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	397	384	0	ENST00000380152.3:c.794G>A	p.Gly265Glu	p.G265E	ENST00000380152		265	gGa/gAa	10/27	0.811524057963825	2	FACETS	0.944	0.916	0.971	0.944	0.916	0.971	CLONAL	2	TRUE	0	0.814876413535148	2		384	516	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467875	99467875	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1469290616	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	34	438	0	ENST00000268035.6:c.2744C>T	p.Ser915Leu	p.S915L	ENST00000268035	NM_000875.3	915	tCg/tTg	13/21	0.689459235734497	2	FACETS	0.167	0.136	0.202	0.083	0.068	0.101	SUBCLONAL	1	TRUE	0	0.814876413535148	2		438	500	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862896	9862896	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1198247451	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	195	424	2	ENST00000330684.3:c.2407G>A	p.Glu803Lys	p.E803K	ENST00000330684	NM_001134407.1	803	Gag/Aag	12/13	0.109007128346747	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.814876413535148	0		426	507	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916172	9916172	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1423127538	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	163	401	0	ENST00000330684.3:c.2117C>T	p.Thr706Ile	p.T706I	ENST00000330684	NM_001134407.1	706	aCc/aTc	10/13	0.109007128346747	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.814876413535148	0		401	431	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934811	9934811	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555494770	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	259	592	0	ENST00000330684.3:c.1479G>A	p.Trp493Ter	p.W493*	ENST00000330684	NM_001134407.1	493	tgG/tgA	6/13	0.109007128346747	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.814876413535148	0		592	734	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992916	72992916	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	265	657	0	ENST00000268489.5:c.1129G>A	p.Glu377Lys	p.E377K	ENST00000268489	NM_006885.3	377	Gaa/Aaa	2/10	0.371160584087131	5	FACETS	1	0.987	1	0.402	0.376	0.429	INDETERMINATE	1	TRUE	2	0.814876413535148	5		657	1198	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346129	89346129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1325611711	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	189	242	0	ENST00000301030.4:c.6821C>T	p.Pro2274Leu	p.P2274L	ENST00000301030	NM_001256183.1	2274	cCc/cTc	9/13	0.371160584087131	5	FACETS	0.9	0.844	0.955	0.9	0.844	0.955	INDETERMINATE	3	TRUE	2	0.814876413535148	5		242	382	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346532	89346532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	144	575	0	ENST00000301030.4:c.6418G>A	p.Glu2140Lys	p.E2140K	ENST00000301030	NM_001256183.1	2140	Gag/Aag	9/13	0.371160584087131	5	FACETS	1	0.947	1	0.35	0.319	0.382	INDETERMINATE	1	TRUE	2	0.814876413535148	5		575	748	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	403	455	1	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.812136707485408	2	FACETS	0.997	0.971	1	0.997	0.971	1	CLONAL	2	TRUE	0	0.814876413535148	2		456	496	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108545	8108545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140224531	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	458	365	0	ENST00000585124.1:c.850C>T	p.Arg284Cys	p.R284C	ENST00000585124	NM_004217.3	284	Cgc/Tgc	8/9	0.812136707485408	2	FACETS	0.967	0.942	0.992	0.967	0.942	0.992	CLONAL	2	TRUE	0	0.814876413535148	2		365	581	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576045	29576045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876658268	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	293	496	0	ENST00000356175.3:c.4018C>T	p.Leu1340Phe	p.L1340F	ENST00000356175	NM_000267.3	1340	Ctt/Ttt	30/57	0.221459106316062	3	FACETS	1	0.994	1			1	INDETERMINATE	1	TRUE	NA	0.814876413535148	3		496	706	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760691	59760691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs929857537	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	239	470	0	ENST00000259008.2:c.3716C>T	p.Ser1239Phe	p.S1239F	ENST00000259008	NM_032043.2	1239	tCc/tTc	20/20	0.814876413535148	3	FACETS	0.823	0.769	0.879	0.274	0.256	0.293	CLONAL	1	TRUE	0	0.814876413535148	3		470	1003	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210737	2210737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	241	493	0	ENST00000398665.3:c.1234G>A	p.Gly412Arg	p.G412R	ENST00000398665	NM_032482.2	412	Ggg/Agg	14/28	0.249255250053771	5	FACETS	1	0.992	1	0.495	0.462	0.527	INDETERMINATE	1	TRUE	2	0.814876413535148	5		493	886	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10283839	10283839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758190156	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	189	427	0	ENST00000340748.4:c.647C>T	p.Pro216Leu	p.P216L	ENST00000340748		216	cCg/cTg	8/40	0.372776851510428	6	FACETS	1	0.978	1	0.386	0.356	0.417	INDETERMINATE	1	TRUE	3	0.814876413535148	6		427	1054	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18280025	18280025	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	150	224	0	ENST00000222254.8:c.2108A>G	p.Gln703Arg	p.Q703R	ENST00000222254	NM_005027.3	703	cAg/cGg	16/16	0.67444237222413	3	FACETS	1	0.99	1			1	CLONAL	1	TRUE	NA	0.814876413535148	3		224	350	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798235	42798235	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	249	353	0	ENST00000575354.2:c.4189T>A	p.Ser1397Thr	p.S1397T	ENST00000575354	NM_015125.3	1397	Tcc/Acc	17/20	0.378269165379453	5	FACETS	1	0.941	1			1	INDETERMINATE	2	TRUE	NA	0.814876413535148	5		353	679	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546683	9546683	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	584	463	1	ENST00000353224.5:c.1339G>A	p.Glu447Lys	p.E447K	ENST00000353224	NM_177990.2	447	Gaa/Aaa	5/10	0.657631369034581	6	FACETS	1	0.979	1	1	0.979	1	CLONAL	3	TRUE	3	0.814876413535148	6		464	1230	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561450	9561450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	208	446	0	ENST00000353224.5:c.332G>A	p.Gly111Glu	p.G111E	ENST00000353224	NM_177990.2	111	gGa/gAa	4/10	0.657631369034581	6	FACETS	1	0.977	1	0.375	0.348	0.404	CLONAL	1	TRUE	3	0.814876413535148	6		446	1192	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561477	9561477	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	190	377	1	ENST00000353224.5:c.305A>T	p.Lys102Ile	p.K102I	ENST00000353224	NM_177990.2	102	aAa/aTa	4/10	0.657631369034581	6	FACETS	1	0.976	1	0.377	0.348	0.408	CLONAL	1	TRUE	3	0.814876413535148	6		378	1083	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40738999	40738999	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	151	373	0	ENST00000373198.4:c.3285A>C	p.Glu1095Asp	p.E1095D	ENST00000373198	NM_133170.3	1095	gaA/gaC	24/32	0.752088618893554	4	FACETS	0.817	0.748	0.89			1	CLONAL	1	TRUE	NA	0.814876413535148	4		373	823	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419992	41419992	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	192	503	0	ENST00000373198.4:c.329C>G	p.Ser110Cys	p.S110C	ENST00000373198	NM_133170.3	110	tCc/tGc	3/32	0.752088618893554	4	FACETS	0.799	0.738	0.862			1	SUBCLONAL	1	TRUE	NA	0.814876413535148	4		503	1071	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420005	41420005	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	193	503	0	ENST00000373198.4:c.316C>T	p.His106Tyr	p.H106Y	ENST00000373198	NM_133170.3	106	Cat/Tat	3/32	0.752088618893554	4	FACETS	0.787	0.727	0.849			1	SUBCLONAL	1	TRUE	NA	0.814876413535148	4		503	1093	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484260	57484261	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	650	345	0	ENST00000371085.3:c.574_575delinsTT	p.Pro192Leu	p.P192L	ENST00000371085	NM_000516.4	192	CCg/TTg	7/13	0.814876413535148	5	FACETS	0.936	0.911	0.96	0.936	0.911	0.96	CLONAL	4	TRUE	1	0.814876413535148	5		345	947	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795396	39795396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	199	458	0	ENST00000288319.7:c.324G>A	p.Met108Ile	p.M108I	ENST00000288319	NM_182918.3	108	atG/atA	3/10	0.371160584087131	5	FACETS	1	0.985	1	0.41	0.38	0.441	INDETERMINATE	1	TRUE	2	0.814876413535148	5		458	883	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918292	44918292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	243	226	0	ENST00000377967.4:c.917C>T	p.Ser306Phe	p.S306F	ENST00000377967	NM_021140.2	306	tCt/tTt	11/29	0.752088618893554	2	FACETS	1	0.96	1			1	CLONAL	1	TRUE	NA	0.814876413535148	2		226	583	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044578	128044585	+	frameshift_variant	Frame_Shift_Del	DEL	AGGGACTT	AGGGACTT	-	novel	NA	P-0006621-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	391	417	0	ENST00000285398.2:c.1036_1043del	p.Lys346GlyfsTer37	p.K346Gfs*37	ENST00000285398	NM_000122.1	346	AAGTCCCTg/g	8/15	0.606412261612904	4	FACETS	0.951	0.908	0.994	0.951	0.908	0.994	CLONAL	2	TRUE	2	0.814876413535148	4		417	916	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	213	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.52	2		464	730	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774771	73774771	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	202	385	2	ENST00000254810.4:c.316G>A	p.Glu106Lys	p.E106K	ENST00000254810	NM_005324.3	106	Gaa/Aaa	4/4	1	2	FACETS	0.933	0.866	1	0.933	0.866	1	CLONAL	1	TRUE	1	0.52	2		387	833	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971199	21971199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894095	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	21	191	0	ENST00000304494.5:c.159G>A	p.Met53Ile	p.M53I	ENST00000304494	NM_000077.4	53	atG/atA	2/3	0.3	0	FACETS	0.175	0.135	0.221			1	INDETERMINATE	1	TRUE	0	0.52	0		191	222	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	32	240	1	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.191	0.154	0.233	0.191	0.154	0.233	SUBCLONAL	1	TRUE	1	0.52	2		241	645	SUCCESS
ATM	472	MSKCC	GRCh37	11	108160488	108160488	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730881369	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	201	482	0	ENST00000278616.4:c.4396C>T	p.Arg1466Ter	p.R1466*	ENST00000278616	NM_000051.3	1466	Cga/Tga	29/63	1	2	FACETS	0.857	0.795	0.921	0.857	0.795	0.921	CLONAL	1	TRUE	1	0.52	2		482	902	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568590	41568590	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	198	545	0	ENST00000263253.7:c.4540G>A	p.Glu1514Lys	p.E1514K	ENST00000263253	NM_001429.3	1514	Gaa/Aaa	28/31	1	2	FACETS	0.87	0.807	0.936	0.87	0.807	0.936	CLONAL	1	TRUE	1	0.52	2		545	875	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272398	11272398	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	229	368	0	ENST00000361445.4:c.3532T>C	p.Ser1178Pro	p.S1178P	ENST00000361445	NM_004958.3	1178	Tct/Cct	23/58	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.52	2		368	822	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245993	16245993	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751262776	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	189	502	1	ENST00000375759.3:c.1616G>A	p.Arg539Gln	p.R539Q	ENST00000375759	NM_015001.2	539	cGa/cAa	8/15	1	2	FACETS	0.754	0.697	0.814	0.754	0.697	0.814	SUBCLONAL	1	TRUE	1	0.52	2		503	964	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36934832	36934832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1380783424	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	363	670	0	ENST00000361632.4:c.1501G>A	p.Glu501Lys	p.E501K	ENST00000361632		501	Gag/Aag	11/16	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.52	2		670	1380	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113380	209113380	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	141	286	0	ENST00000345146.2:c.127G>A	p.Asp43Asn	p.D43N	ENST00000345146	NM_005896.2	43	Gat/Aat	4/10	1	2	FACETS	0.907	0.829	0.988	0.907	0.829	0.988	CLONAL	1	TRUE	1	0.52	2		286	598	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49721992	49721992	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	11	122	0	ENST00000449682.2:c.1867G>A	p.Glu623Lys	p.E623K	ENST00000449682	NM_020998.3	623	Gag/Aag	16/18	1	2	FACETS	0.205	0.142	0.285	0.205	0.142	0.285	SUBCLONAL	1	TRUE	1	0.52	2		122	206	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89156901	89156901	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	218	398	0	ENST00000336596.2:c.3G>A	p.Met1?	p.M1?	ENST00000336596	NM_005233.5	1	atG/atA	1/17	1	2	FACETS	0.907	0.845	0.972	0.907	0.845	0.972	CLONAL	1	TRUE	1	0.52	2		398	924	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266619	142266619	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	37	520	1	ENST00000350721.4:c.3305C>T	p.Ser1102Phe	p.S1102F	ENST00000350721	NM_001184.3	1102	tCc/tTc	16/47	1	2	FACETS	0.218	0.179	0.262	0.218	0.179	0.262	SUBCLONAL	1	TRUE	1	0.52	2		521	653	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191307	185191307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	150	300	1	ENST00000265026.3:c.2188G>A	p.Asp730Asn	p.D730N	ENST00000265026	NM_004721.4	730	Gac/Aac	11/14	1	2	FACETS	0.836	0.766	0.909	0.836	0.766	0.909	CLONAL	1	TRUE	1	0.52	2		301	690	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193757	106193757	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	124	299	0	ENST00000380013.4:c.4219G>T	p.Gly1407Ter	p.G1407*	ENST00000380013	NM_001127208.2	1407	Gga/Tga	10/11	1	2	FACETS	0.766	0.694	0.84	0.766	0.694	0.84	SUBCLONAL	1	TRUE	1	0.52	2		299	623	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629533	187629533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	50	426	0	ENST00000441802.2:c.1449G>A	p.Met483Ile	p.M483I	ENST00000441802	NM_005245.3	483	atG/atA	2/27	1	2	FACETS	0.195	0.165	0.229	0.195	0.165	0.229	SUBCLONAL	1	TRUE	1	0.52	2		426	986	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67592024	67592024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	219	410	1	ENST00000274335.5:c.1840G>A	p.Glu614Lys	p.E614K	ENST00000274335		614	Gaa/Aaa	14/15	1	2	FACETS	0.874	0.813	0.936	0.874	0.813	0.936	CLONAL	1	TRUE	1	0.52	2		411	964	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045930	26045930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1385	386	1223	1	ENST00000540144.1:c.292G>A	p.Glu98Lys	p.E98K	ENST00000540144	NM_003531.2	98	Gag/Aag	1/1	1	2	FACETS	0.838	0.794	0.884	0.838	0.794	0.884	CLONAL	1	TRUE	1	0.52	2		1224	1771	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527754	157527754	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	212	336	0	ENST00000346085.5:c.5479A>C	p.Thr1827Pro	p.T1827P	ENST00000346085	NM_020732.3	1827	Acc/Ccc	20/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.52	2		336	792	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334798	81334798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	87	420	0	ENST00000222390.5:c.1918G>A	p.Glu640Lys	p.E640K	ENST00000222390	NM_000601.4	640	Gag/Aag	17/18	1	2	FACETS	0.927	0.827	1	0.927	0.827	1	CLONAL	1	TRUE	1	0.52	2		420	361	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089800	5089800	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	179	464	0	ENST00000381652.3:c.2698G>A	p.Glu900Lys	p.E900K	ENST00000381652	NM_004972.3	900	Gaa/Aaa	20/25	0.3	2	FACETS	0.793	0.732	0.857			1	INDETERMINATE	1	TRUE	NA	0.52	2		464	868	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400012	139400012	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1198437870	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	221	459	0	ENST00000277541.6:c.4336G>A	p.Glu1446Lys	p.E1446K	ENST00000277541	NM_017617.3	1446	Gag/Aag	25/34	1	2	FACETS	0.893	0.831	0.956	0.893	0.831	0.956	CLONAL	1	TRUE	1	0.52	2		459	952	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244999	123244999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150015885	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	185	465	1	ENST00000358487.5:c.2105C>T	p.Ser702Leu	p.S702L	ENST00000358487	NM_000141.4	702	tCg/tTg	16/18	1	2	FACETS	0.674	0.621	0.728	0.674	0.621	0.728	SUBCLONAL	1	TRUE	1	0.52	2		466	1056	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123246893	123246893	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	276	603	0	ENST00000358487.5:c.2032A>G	p.Arg678Gly	p.R678G	ENST00000358487	NM_000141.4	678	Aga/Gga	15/18	1	2	FACETS	0.994	0.934	1	0.994	0.934	1	CLONAL	1	TRUE	1	0.52	2		603	1068	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123258035	123258035	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	248	630	0	ENST00000358487.5:c.1646A>C	p.Asn549Thr	p.N549T	ENST00000358487	NM_000141.4	549	aAt/aCt	12/18	1	2	FACETS	0.864	0.808	0.922	0.864	0.808	0.922	CLONAL	1	TRUE	1	0.52	2		630	1104	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111957432	111957432	+	upstream_gene_variant	5'Flank	SNP	C	C	T	rs1352755224	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	20	47	0				ENST00000375549	NM_003002.3	21/98			1	2	FACETS	0.726	0.564	0.908	0.726	0.564	0.908	CLONAL	1	TRUE	1	0.52	2		47	106	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433560	49433560	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	311	549	0	ENST00000301067.7:c.7993C>T	p.Gln2665Ter	p.Q2665*	ENST00000301067	NM_003482.3	2665	Cag/Tag	31/54	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.52	2		549	1153	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872475	35872475	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757053022	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	344	573	0	ENST00000216797.5:c.428G>A	p.Arg143Gln	p.R143Q	ENST00000216797	NM_020529.2	143	cGa/cAa	3/6	1	2	FACETS	0.969	0.916	1	0.969	0.916	1	CLONAL	1	TRUE	1	0.52	2		573	1365	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988466	41988466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	255	790	0	ENST00000219905.7:c.1258G>A	p.Asp420Asn	p.D420N	ENST00000219905	NM_001164273.1	420	Gat/Aat	3/24	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.52	2		790	971	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619165	37619165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	258	505	1	ENST00000447079.4:c.841G>A	p.Glu281Lys	p.E281K	ENST00000447079	NM_015083.1	281	Gag/Aag	1/14	1	2	FACETS	0.941	0.882	1	0.941	0.882	1	CLONAL	1	TRUE	1	0.52	2		506	1054	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56492817	56492817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	254	369	1	ENST00000407977.2:c.122C>T	p.Ser41Leu	p.S41L	ENST00000407977		41	tCa/tTa	2/10	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.52	2		370	954	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629035	14629035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764010316	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	188	405	0	ENST00000254322.2:c.127G>A	p.Glu43Lys	p.E43K	ENST00000254322	NM_006145.1	43	Gag/Aag	1/3	1	2	FACETS	0.87	0.805	0.938	0.87	0.805	0.938	CLONAL	1	TRUE	1	0.52	2		405	831	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355117	15355117	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1326616087	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	230	544	1	ENST00000263377.2:c.2506C>T	p.Pro836Ser	p.P836S	ENST00000263377	NM_058243.2	836	Ccc/Tcc	13/20	1	2	FACETS	0.833	0.776	0.892	0.833	0.776	0.892	CLONAL	1	TRUE	1	0.52	2		545	1062	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872374	45872374	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	256	512	0	ENST00000391945.4:c.137C>G	p.Thr46Ser	p.T46S	ENST00000391945	NM_000400.3	46	aCc/aGc	3/23	1	2	FACETS	0.975	0.913	1	0.975	0.913	1	CLONAL	1	TRUE	1	0.52	2		512	1010	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933338	39933338	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	174	649	0	ENST00000378444.4:c.1261G>C	p.Gly421Arg	p.G421R	ENST00000378444	NM_001123385.1	421	Ggc/Cgc	4/15	1	2	FACETS	0.518	0.475	0.562	0.518	0.475	0.562	SUBCLONAL	1	TRUE	1	0.52	2		649	1292	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44820527	44820527	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	92	415	0	ENST00000377967.4:c.226-2A>T		p.X76_splice	ENST00000377967	NM_021140.2	76			1	2	FACETS	0.857	0.766	0.952	0.857	0.766	0.952	CLONAL	1	TRUE	1	0.52	2		415	413	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44937684	44937684	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	99	480	0	ENST00000377967.4:c.2872C>T	p.Gln958Ter	p.Q958*	ENST00000377967	NM_021140.2	958	Caa/Taa	19/29	1	2	FACETS	0.782	0.701	0.867	0.782	0.701	0.867	SUBCLONAL	1	TRUE	1	0.52	2		480	487	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259041	153259044	+	frameshift_variant	Frame_Shift_Del	DEL	ATCA	ATCA	-	novel	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	97	434	0	ENST00000281708.4:c.771_774del	p.Asp258ValfsTer7	p.D258Vfs*7	ENST00000281708	NM_033632.3	257	atTGAT/at	5/12	1	2	FACETS	0.794	0.711	0.881	0.794	0.711	0.881	SUBCLONAL	1	TRUE	1	0.52	2		434	470	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100393	8100402	+	frameshift_variant	Frame_Shift_Del	DEL	CACCACGGCT	CACCACGGCT	-	novel	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	153	626	0	ENST00000346208.3:c.368_377del	p.His123ProfsTer69	p.H123Pfs*69	ENST00000346208		123	CACCACGGCTcc/cc	3/6	0.220035238620107	2	FACETS	0.489	0.446	0.534	0.245	0.223	0.267	INDETERMINATE	1	TRUE	0	0.52	2		626	1203	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253806	153253808	+	frameshift_variant	Frame_Shift_Del	DEL	GCG	GCG	C	novel	NA	P-0006645-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	100	413	0	ENST00000281708.4:c.925_927delinsG	p.Arg309ValfsTer7	p.R309Vfs*7	ENST00000281708	NM_033632.3	309	CGC/G	6/12	1	2	FACETS	0.853	0.766	0.944	0.853	0.766	0.944	CLONAL	1	TRUE	1	0.52	2		413	451	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006662-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	182	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.963	0.899	1	0.963	0.899	1	CLONAL	1	TRUE	1	0.857130129991267	2		280	441	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266103	41266103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913399	NA	P-0006662-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	480	433	0	ENST00000349496.5:c.100G>A	p.Gly34Arg	p.G34R	ENST00000349496	NM_001904.3	34	Gga/Aga	3/15	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.857130129991267	2		433	1078	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577469	64577469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs794728616	NA	P-0006662-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	849	379	0	ENST00000312049.6:c.113C>T	p.Ser38Phe	p.S38F	ENST00000312049	NM_130799.2	38	tCc/tTc	2/10	0.850179976251854	2	FACETS	0.992	0.976	1	0.992	0.976	1	CLONAL	2	TRUE	0	0.857130129991267	2		379	998	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098815	178098815	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0006662-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	495	466	0	ENST00000397062.3:c.230A>T	p.Asp77Val	p.D77V	ENST00000397062	NM_006164.4	77	gAt/gTt	2/5	1	2	FACETS	0.974	0.934	1	0.974	0.934	1	CLONAL	1	TRUE	1	0.857130129991267	2		466	1186	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55987291	55987291	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006662-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	314	360	0	ENST00000263923.4:c.134C>A	p.Ala45Asp	p.A45D	ENST00000263923	NM_002253.2	45	gCt/gAt	2/30	1	2	FACETS	0.954	0.905	1	0.954	0.905	1	CLONAL	1	TRUE	1	0.857130129991267	2		360	768	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	236645	236645	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs567820710	NA	P-0006662-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	333	368	0	ENST00000264932.6:c.1363A>C	p.Asn455His	p.N455H	ENST00000264932	NM_004168.2	455	Aac/Cac	10/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.857130129991267	2		368	735	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342935	118342935	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006662-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	895	423	0	ENST00000534358.1:c.1061G>C	p.Arg354Thr	p.R354T	ENST00000534358	NM_005933.3	354	aGg/aCg	3/36	0.850179976251854	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.857130129991267	2		423	1033	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89335037	89335037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006662-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	109	253	0	ENST00000301030.4:c.7841C>T	p.Ala2614Val	p.A2614V	ENST00000301030	NM_001256183.1	2614	gCg/gTg	13/13	1	2	FACETS	0.512	0.461	0.564	0.512	0.461	0.564	SUBCLONAL	1	TRUE	1	0.857130129991267	2		253	497	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	138	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.658744018288979	2		280	394	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0006665-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	193	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.97	0.903	1	0.97	0.903	1	CLONAL	1	TRUE	1	0.658744018288979	2		490	604	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	34	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.972	0.799	1	0.972	0.799	1	CLONAL	1	TRUE	1	0.27	2		280	259	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44923060	44923060	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	68	351	0	ENST00000377967.4:c.1921C>T	p.Gln641Ter	p.Q641*	ENST00000377967	NM_021140.2	641	Cag/Tag	16/29	0.3	2	FACETS	1	0.959	1			1	CLONAL	1	TRUE	NA	0.27	2		351	403	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577090	7577090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371409680	NA	P-0006705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	17	509	0	ENST00000269305.4:c.848G>A	p.Arg283His	p.R283H	ENST00000269305	NM_001126112.2	283	cGc/cAc	8/11	1	2	FACETS	0.17	0.126	0.223	0.17	0.126	0.223	SUBCLONAL	1	TRUE	1	0.27	2		509	742	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100928	27100928	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	60	414	0	ENST00000324856.7:c.4210C>T	p.Gln1404Ter	p.Q1404*	ENST00000324856	NM_006015.4	1404	Cag/Tag	18/20	0.3	2	FACETS	0.633	0.545	0.73			1	SUBCLONAL	1	TRUE	NA	0.27	2		414	702	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662339	67662339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201123106	NA	P-0006705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	63	456	0	ENST00000264010.4:c.1585G>A	p.Asp529Asn	p.D529N	ENST00000264010	NM_006565.3	529	Gat/Aat	9/12	0.154690695127324	3	FACETS	0.634	0.547	0.728	0.317	0.273	0.364	INDETERMINATE	1	TRUE	1	0.27	3		456	836	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216753	7216753	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	101	700	0	ENST00000380728.2:c.670C>G	p.Gln224Glu	p.Q224E	ENST00000380728		224	Cag/Gag	8/11	1	2	FACETS	0.996	0.89	1	0.996	0.89	1	CLONAL	1	TRUE	1	0.27	2		700	751	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216947	7216947	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	77	613	0	ENST00000380728.2:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000380728		192	Cag/Tag	7/11	1	2	FACETS	0.78	0.684	0.883	0.78	0.684	0.883	SUBCLONAL	1	TRUE	1	0.27	2		613	731	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578239	7578240	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AG	rs1567551718	NA	P-0006705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	84	524	0	ENST00000269305.4:c.609_610delinsCT	p.Glu204Ter	p.E204*	ENST00000269305	NM_001126112.2	203	gtGGag/gtCTag	6/11	1	2	FACETS	0.916	0.809	1	0.916	0.809	1	CLONAL	1	TRUE	1	0.27	2		524	679	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	188	280	0				ENST00000310581	NM_198253.2	-/1132			0.264813735898493	3	FACETS	0.899	0.837	0.963	1	0.989	1	CLONAL	3	TRUE	1	0.291909857664468	3		280	547	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060925	38060925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1388855660	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	254	277	0	ENST00000250448.2:c.1064C>T	p.Ser355Leu	p.S355L	ENST00000250448	NM_004496.3	355	tCa/tTa	2/2	0.291909857664468	1	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	0	0.291909857664468	1		277	625	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8075675	8075675	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	167	586	1	ENST00000377482.5:c.5C>T	p.Ser2Leu	p.S2L	ENST00000377482	NM_018948.3	2	tCa/tTa	2/4	1	2	FACETS	0.818	0.754	0.885	1	0.99	1	CLONAL	2	TRUE	1	0.291909857664468	2		587	699	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257733	16257734	+	missense_variant	Missense_Mutation	DNP	TT	TT	CA	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	248	500	0	ENST00000375759.3:c.4998_4999delinsCA	p.Leu1667Met	p.L1667M	ENST00000375759	NM_015001.2	1666	ccTTtg/ccCAtg	11/15	0.147811162576929	3	FACETS	0.844	0.792	0.897	1	0.99	1	INDETERMINATE	3	TRUE	1	0.291909857664468	3		500	769	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263838	16263838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs183490080	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	499	677	0	ENST00000375759.3:c.10207C>T	p.Arg3403Cys	p.R3403C	ENST00000375759	NM_015001.2	3403	Cgc/Tgc	12/15	0.147811162576929	3	FACETS	0.957	0.916	0.998	1	0.996	1	INDETERMINATE	3	TRUE	1	0.291909857664468	3		677	1365	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27024029	27024029	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	69	139	0	ENST00000324856.7:c.1135C>T	p.Gln379Ter	p.Q379*	ENST00000324856	NM_006015.4	379	Cag/Tag	1/20	0.147811162576929	3	FACETS	0.89	0.789	0.994	1	0.971	1	INDETERMINATE	3	TRUE	1	0.291909857664468	3		139	203	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551844	150551844	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	148	122	0	ENST00000369026.2:c.163G>T	p.Ala55Ser	p.A55S	ENST00000369026	NM_021960.4	55	Gcg/Tcg	1/3	1	2	FACETS	1	0.956	1	1	0.994	1	CLONAL	3	TRUE	1	0.291909857664468	2		122	325	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253416	226253416	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	84	95	0	ENST00000366813.1:c.188T>G	p.Ile63Ser	p.I63S	ENST00000366813		63	aTt/aGt	2/3	1	2	FACETS	0.95	0.857	1	1	0.989	1	CLONAL	3	TRUE	1	0.291909857664468	2		95	202	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470597	25470597	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	335	520	0	ENST00000264709.3:c.877G>C	p.Gly293Arg	p.G293R	ENST00000264709	NM_175629.2	293	Ggg/Cgg	8/23	1	2	FACETS	1	0.991	1	1	0.997	1	CLONAL	2	TRUE	1	0.291909857664468	2		520	945	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729940	30729940	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752444160	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	309	479	1	ENST00000295754.5:c.1461G>A	p.Met487Ile	p.M487I	ENST00000295754	NM_003242.5	487	atG/atA	6/7	0.236906716837228	4	FACETS	1	0.99	1	0.809	0.763	0.856	CLONAL	2	TRUE	1	0.291909857664468	4		480	1127	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940061	49940061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1440811627	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	546	782	2	ENST00000296474.3:c.982C>T	p.Pro328Ser	p.P328S	ENST00000296474	NM_002447.2	328	Cca/Tca	1/20	1	2	FACETS	1	0.995	1	1	0.998	1	CLONAL	2	TRUE	1	0.291909857664468	2		784	1520	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204825	128204825	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	423	719	1	ENST00000341105.2:c.616G>A	p.Glu206Lys	p.E206K	ENST00000341105	NM_032638.4	206	Gag/Aag	3/6	1	2	FACETS	1	0.988	1	1	0.997	1	CLONAL	2	TRUE	1	0.291909857664468	2		720	1315	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664804	138664804	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	43	52	0	ENST00000330315.3:c.761C>T	p.Ser254Leu	p.S254L	ENST00000330315	NM_023067.3	254	tCg/tTg	1/1	1	2	FACETS	1	0.925	1	1	0.975	1	CLONAL	2	TRUE	1	0.291909857664468	2		52	130	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279171	142279171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	246	641	2	ENST00000350721.4:c.1475G>A	p.Gly492Glu	p.G492E	ENST00000350721	NM_001184.3	492	gGa/gAa	6/47	1	2	FACETS	0.951	0.891	1	1	0.994	1	CLONAL	2	TRUE	1	0.291909857664468	2		643	886	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430962	181430962	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	248	584	0	ENST00000325404.1:c.814G>A	p.Asp272Asn	p.D272N	ENST00000325404	NM_003106.3	272	Gac/Aac	1/1	0.166260611662204	0	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	0	0.291909857664468	0		584	1014	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138567	55138567	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	54	418	0	ENST00000257290.5:c.1244C>T	p.Ser415Leu	p.S415L	ENST00000257290	NM_006206.4	415	tCa/tTa	9/23	1	2	FACETS	0.436	0.371	0.508	0.436	0.371	0.508	SUBCLONAL	1	TRUE	1	0.291909857664468	2		418	848	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564512	55564512	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	260	413	1	ENST00000288135.5:c.400G>A	p.Val134Ile	p.V134I	ENST00000288135	NM_000222.2	134	Gtc/Atc	3/21	1	2	FACETS	1	0.954	1	1	0.995	1	CLONAL	2	TRUE	1	0.291909857664468	2		414	874	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247165	153247165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	82	261	0	ENST00000281708.4:c.1637C>T	p.Ser546Leu	p.S546L	ENST00000281708	NM_033632.3	546	tCa/tTa	10/12	0.291909857664468	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.291909857664468	1		261	393	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247328	153247328	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	161	513	0	ENST00000281708.4:c.1474C>T	p.Gln492Ter	p.Q492*	ENST00000281708	NM_033632.3	492	Cag/Tag	10/12	0.291909857664468	1	FACETS	1	0.955	1	1	0.993	1	CLONAL	2	TRUE	0	0.291909857664468	1		513	451	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524519	187524519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	186	598	0	ENST00000441802.2:c.11161G>A	p.Asp3721Asn	p.D3721N	ENST00000441802	NM_005245.3	3721	Gac/Aac	19/27	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.291909857664468	2		598	920	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197189	26197189	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1444	747	1185	0	ENST00000356476.2:c.290G>A	p.Cys97Tyr	p.C97Y	ENST00000356476		97	tGc/tAc	1/1	1	2	FACETS	1	0.995	1	1	0.998	1	CLONAL	2	TRUE	1	0.291909857664468	2		1185	2191	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197472	26197472	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1214166794	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	575	891	1	ENST00000356476.2:c.7C>T	p.Arg3Cys	p.R3C	ENST00000356476		3	Cgt/Tgt	1/1	1	2	FACETS	1	0.994	1	1	0.998	1	CLONAL	2	TRUE	1	0.291909857664468	2		892	1687	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41904302	41904302	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	187	357	0	ENST00000372991.4:c.706G>A	p.Glu236Lys	p.E236K	ENST00000372991	NM_001760.3	236	Gaa/Aaa	4/5	1	2	FACETS	0.975	0.905	1	1	0.993	1	CLONAL	2	TRUE	1	0.291909857664468	2		357	657	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662438	117662438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	179	594	0	ENST00000368508.3:c.4939G>A	p.Glu1647Lys	p.E1647K	ENST00000368508	NM_002944.2	1647	Gag/Aag	30/43	0.229318129133286	1	FACETS	0.999	0.928	1	1	0.993	1	CLONAL	2	TRUE	0	0.291909857664468	1		594	524	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117709171	117709171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	150	454	0	ENST00000368508.3:c.1786G>A	p.Glu596Lys	p.E596K	ENST00000368508	NM_002944.2	596	Gaa/Aaa	13/43	0.229318129133286	1	FACETS	0.808	0.743	0.876	1	0.99	1	CLONAL	2	TRUE	0	0.291909857664468	1		454	543	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502191	157502191	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs940353111	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	282	478	4	ENST00000346085.5:c.3224G>A	p.Arg1075Gln	p.R1075Q	ENST00000346085	NM_020732.3	1075	cGa/cAa	12/20	1	2	FACETS	1	0.962	1	1	0.995	1	CLONAL	2	TRUE	1	0.291909857664468	2		482	939	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2974182	2974182	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763473945	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	445	696	0	ENST00000396946.4:c.1423G>A	p.Asp475Asn	p.D475N	ENST00000396946	NM_032415.4	475	Gac/Aac	10/25	1	2	FACETS	1	0.991	1	1	0.997	1	CLONAL	2	TRUE	1	0.291909857664468	2		696	1340	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6439797	6439797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	311	515	0	ENST00000356142.4:c.323C>T	p.Ser108Leu	p.S108L	ENST00000356142	NM_018890.3	108	tCa/tTa	5/7	1	2	FACETS	1	0.966	1	1	0.996	1	CLONAL	2	TRUE	1	0.291909857664468	2		515	1033	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730093	41730093	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs979257752	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	528	985	0	ENST00000242208.4:c.436G>A	p.Asp146Asn	p.D146N	ENST00000242208	NM_002192.2	146	Gac/Aac	3/3	1	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	2	TRUE	1	0.291909857664468	2		985	1650	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55260462	55260462	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	364	624	0	ENST00000275493.2:c.2629C>G	p.Pro877Ala	p.P877A	ENST00000275493	NM_005228.3	877	Cct/Gct	22/28	1	2	FACETS	1	0.986	1	1	0.997	1	CLONAL	2	TRUE	1	0.291909857664468	2		624	1127	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476832	140476832	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs869025340	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	86	675	0	ENST00000288602.6:c.1574T>C	p.Leu525Pro	p.L525P	ENST00000288602	NM_004333.4	525	cTg/cCg	13/18	1	2	FACETS	0.941	0.833	1	0.941	0.833	1	CLONAL	1	TRUE	1	0.291909857664468	2		675	626	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151188058	151188058	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	60	901	0	ENST00000262187.5:c.95T>C	p.Val32Ala	p.V32A	ENST00000262187	NM_005614.3	32	gTg/gCg	2/8	1	2	FACETS	0.368	0.316	0.426	0.368	0.316	0.426	SUBCLONAL	1	TRUE	1	0.291909857664468	2		901	1116	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859555	151859555	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	92	581	0	ENST00000262189.6:c.11107G>C	p.Glu3703Gln	p.E3703Q	ENST00000262189	NM_170606.2	3703	Gaa/Caa	43/59	1	2	FACETS	0.574	0.508	0.644	0.574	0.508	0.644	SUBCLONAL	1	TRUE	1	0.291909857664468	2		581	1099	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287247	38287247	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752855457	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	404	697	0	ENST00000425967.3:c.410G>A	p.Ser137Asn	p.S137N	ENST00000425967	NM_001174067.1	137	aGc/aAc	4/19	0.291909857664468	1	FACETS	1	0.99	1	1	0.997	1	CLONAL	2	TRUE	0	0.291909857664468	1		697	1048	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868953	117868953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	245	683	0	ENST00000297338.2:c.746C>T	p.Ser249Phe	p.S249F	ENST00000297338	NM_006265.2	249	tCt/tTt	7/14	0.236906716837228	4	FACETS	1	0.977	1	0.731	0.683	0.78	CLONAL	2	TRUE	1	0.291909857664468	4		683	989	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994138	21994138	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	355	572	0	ENST00000579755.1:c.193G>A	p.Gly65Ser	p.G65S	ENST00000579755		65	Ggt/Agt	1/3	1		FACETS		0.988	1				CLONAL	2	TRUE	1	0.291909857664468	2		572	1078	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97887418	97887418	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs776529713	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	289	613	0	ENST00000289081.3:c.946C>T	p.Gln316Ter	p.Q316*	ENST00000289081	NM_000136.2	316	Cag/Tag	10/15	1	2	FACETS	1	0.983	1	1	0.996	1	CLONAL	2	TRUE	1	0.291909857664468	2		613	899	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101909944	101909944	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	154	396	0	ENST00000374994.4:c.1264G>A	p.Glu422Lys	p.E422K	ENST00000374994	NM_004612.2	422	Gaa/Aaa	8/9	1	2	FACETS	0.845	0.782	0.91	1	0.993	1	CLONAL	3	TRUE	1	0.291909857664468	2		396	416	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64136035	64136035	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	170	391	0	ENST00000334205.4:c.1296G>C	p.Gln432His	p.Q432H	ENST00000334205	NM_003942.2	432	caG/caC	11/17	0.166260611662204	0	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	0	0.291909857664468	0		391	699	SUCCESS
EED	8726	MSKCC	GRCh37	11	85975286	85975286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	236	660	1	ENST00000263360.6:c.707G>A	p.Arg236Lys	p.R236K	ENST00000263360	NM_003797.3	236	aGa/aAa	7/12	0.166260611662204	0	FACETS	0.804	0.754	0.855			1	INDETERMINATE	2	TRUE	0	0.291909857664468	0		661	712	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	493286	493286	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	325	609	2	ENST00000399788.2:c.277C>T	p.Gln93Ter	p.Q93*	ENST00000399788	NM_001042603.1	93	Caa/Taa	3/28	1	2	FACETS	1	0.984	1	1	0.996	1	CLONAL	2	TRUE	1	0.291909857664468	2		611	1012	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215820	133215820	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	381	626	0	ENST00000320574.5:c.5443G>A	p.Asp1815Asn	p.D1815N	ENST00000320574	NM_006231.2	1815	Gac/Aac	40/49	1	2	FACETS	1	0.987	1	1	0.997	1	CLONAL	2	TRUE	1	0.291909857664468	2		626	1178	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32953937	32953937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80359152	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	179	474	0	ENST00000380152.3:c.9004G>A	p.Glu3002Lys	p.E3002K	ENST00000380152		3002	Gaa/Aaa	23/27	1	2	FACETS	0.836	0.778	0.896	1	0.994	1	CLONAL	3	TRUE	1	0.291909857664468	2		474	489	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240137	41240137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	65	136	0	ENST00000379561.5:c.213G>A	p.Met71Ile	p.M71I	ENST00000379561	NM_002015.3	71	atG/atA	1/3	1	2	FACETS	0.902	0.791	1	1	0.979	1	CLONAL	2	TRUE	1	0.291909857664468	2		136	247	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68301827	68301827	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767643278	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	139	609	0	ENST00000487270.1:c.229G>A	p.Asp77Asn	p.D77N	ENST00000487270	NM_133509.3	77	Gat/Aat	4/11	0.291909857664468	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.291909857664468	1		609	600	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242030	105242030	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1319030326	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	428	675	1	ENST00000349310.3:c.394G>A	p.Glu132Lys	p.E132K	ENST00000349310	NM_001014432.1	132	Gaa/Aaa	6/15	0.291909857664468	1	FACETS	1	0.991	1	1	0.997	1	CLONAL	2	TRUE	0	0.291909857664468	1		676	1106	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33023126	33023126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	424	806	0	ENST00000300177.4:c.235G>A	p.Glu79Lys	p.E79K	ENST00000300177	NM_001191322.1	79	Gag/Aag	2/2	0.229318129133286	1	FACETS	0.843	0.803	0.885	1	0.996	1	CLONAL	2	TRUE	0	0.291909857664468	1		806	1471	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304419	91304419	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	140	484	0	ENST00000355112.3:c.1816G>A	p.Asp606Asn	p.D606N	ENST00000355112	NM_000057.2	606	Gac/Aac	7/22	0.229318129133286	1	FACETS	0.962	0.884	1	1	0.991	1	CLONAL	2	TRUE	0	0.291909857664468	1		484	426	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3843447	3843447	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587783461	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	449	561	1	ENST00000262367.5:c.1156C>T	p.Arg386Ter	p.R386*	ENST00000262367	NM_004380.2	386	Cga/Tga	4/31	0.187886180456488	2	FACETS	0.949	0.909	0.99	1	0.996	1	CLONAL	3	TRUE	0	0.291909857664468	2		562	1080	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614877	23614877	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs755609496	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	90	668	0	ENST00000261584.4:c.3464C>G	p.Ser1155Cys	p.S1155C	ENST00000261584	NM_024675.3	1155	tCt/tGt	13/13	0.187886180456488	2	FACETS	0.599	0.53	0.673	0.3	0.265	0.337	SUBCLONAL	1	TRUE	0	0.291909857664468	2		668	1029	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346067	89346067	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1173462781	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	50	78	0	ENST00000301030.4:c.6883G>A	p.Glu2295Lys	p.E2295K	ENST00000301030	NM_001256183.1	2295	Gag/Aag	9/13	1	2	FACETS	0.968	0.847	1	1	0.982	1	CLONAL	3	TRUE	1	0.291909857664468	2		78	118	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346466	89346466	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1164	129	727	3	ENST00000301030.4:c.6484C>A	p.Pro2162Thr	p.P2162T	ENST00000301030	NM_001256183.1	2162	Cct/Act	9/13	1	2	FACETS	0.684	0.618	0.753	0.684	0.618	0.753	SUBCLONAL	1	TRUE	1	0.291909857664468	2		730	1293	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89882362	89882362	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	371	522	0	ENST00000389301.3:c.112G>A	p.Glu38Lys	p.E38K	ENST00000389301	NM_000135.2	38	Gaa/Aaa	2/43	1	2	FACETS	1	0.993	1	1	0.997	1	CLONAL	2	TRUE	1	0.291909857664468	2		522	1022	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512450	38512450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	300	432	1	ENST00000254066.5:c.1361G>A	p.Arg454Lys	p.R454K	ENST00000254066	NM_000964.3	454	aGa/aAa	9/9	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.291909857664468	2		433	875	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40456623	40456623	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	538	801	0	ENST00000345506.4:c.1333G>A	p.Glu445Lys	p.E445K	ENST00000345506	NM_003152.3	445	Gag/Aag	12/20	1	2	FACETS	1	0.993	1	1	0.998	1	CLONAL	2	TRUE	1	0.291909857664468	2		801	1584	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10599926	10599926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	132	599	1	ENST00000171111.5:c.1650G>A	p.Met550Ile	p.M550I	ENST00000171111	NM_203500.1	550	atG/atA	5/6	0.229318129133286	1	FACETS	0.709	0.642	0.779	0.709	0.642	0.779	SUBCLONAL	1	TRUE	0	0.291909857664468	1		600	1090	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367789	15367789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	315	490	1	ENST00000263377.2:c.1537G>A	p.Glu513Lys	p.E513K	ENST00000263377	NM_058243.2	513	Gag/Aag	8/20	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.291909857664468	2		491	923	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860556	45860556	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	449	684	0	ENST00000391945.4:c.1451C>T	p.Thr484Met	p.T484M	ENST00000391945	NM_000400.3	484	aCg/aTg	15/23	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	2	TRUE	NA	0.291909857664468	2		684	1279	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735428	40735428	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1351	98	624	0	ENST00000373198.4:c.3445G>A	p.Glu1149Lys	p.E1149K	ENST00000373198	NM_133170.3	1149	Gag/Aag	25/32	0.236906716837228	4	FACETS	0.599	0.532	0.67	0.2	0.177	0.224	SUBCLONAL	1	TRUE	1	0.291909857664468	4		624	1449	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866486	42866486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28532009	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	566	767	0	ENST00000398585.3:c.146G>A	p.Gly49Glu	p.G49E	ENST00000398585	NM_001135099.1	49	gGa/gAa	3/14	1	2	FACETS	1	0.995	1	1	0.998	1	CLONAL	2	TRUE	1	0.291909857664468	2		767	1597	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127164	22127164	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1057519911	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	337	640	0	ENST00000215832.6:c.964G>A	p.Glu322Lys	p.E322K	ENST00000215832	NM_002745.4	322	Gag/Aag	7/9	1	2	FACETS	1	0.986	1	1	0.996	1	CLONAL	2	TRUE	1	0.291909857664468	2		640	1042	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872191	45872199	+	frameshift_variant	Frame_Shift_Del	DEL	CTCAATCTC	CTCAATCTC	GCCTT	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	291	570	0	ENST00000391945.4:c.235_243delinsAAGGC	p.Glu79LysfsTer4	p.E79Kfs*4	ENST00000391945	NM_000400.3	79	GAGATTGAG/AAGGC	4/23	NA	2	FACETS	0.991	0.933	1			1	INDETERMINATE	2	TRUE	NA	0.291909857664468	2		570	1006	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100937	27100955	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGCCCAGCCCCAGCCTG	CCAGCCCAGCCCCAGCCTG	-	novel	NA	P-0006714-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	404	543	2	ENST00000324856.7:c.4225_4243del	p.Gln1409SerfsTer66	p.Q1409Sfs*66	ENST00000324856	NM_006015.4	1407	CCAGCCCAGCCCCAGCCTGcc/cc	18/20	0.147811162576929	3	FACETS	0.938	0.894	0.983	1	0.995	1	INDETERMINATE	3	TRUE	1	0.291909857664468	3		545	1127	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	161	280	0				ENST00000310581	NM_198253.2	-/1132			0.459598431993822	1	FACETS	0.609	0.566	0.653	0.609	0.566	0.653	INDETERMINATE	1	TRUE	0	0.806623765286268	1		280	391	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	369	528	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.687780023341805	3	FACETS	0.856	0.818	0.894	0.856	0.818	0.894	CLONAL	2	TRUE	1	0.806623765286268	3		528	750	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	196	472	1	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	0.806623765286268	1	FACETS	0.479	0.445	0.512	0.479	0.445	0.512	SUBCLONAL	1	TRUE	0	0.806623765286268	1		473	606	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654535	29654535	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	399	459	0	ENST00000356175.3:c.5224C>T	p.Gln1742Ter	p.Q1742*	ENST00000356175	NM_000267.3	1742	Caa/Taa	37/57	1	2	FACETS	0.94	0.897	0.985	0.94	0.897	0.985	CLONAL	1	TRUE	1	0.806623765286268	2		459	1052	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560464	95560464	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	188	276	0	ENST00000393063.1:c.5125G>A	p.Asp1709Asn	p.D1709N	ENST00000393063	NM_030621.3	1709	Gat/Aat	25/28	1	2	FACETS	0.829	0.772	0.889	0.829	0.772	0.889	CLONAL	1	TRUE	1	0.806623765286268	2		276	562	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015003	37015003	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	516	332	0	ENST00000358127.4:c.401C>T	p.Ser134Phe	p.S134F	ENST00000358127	NM_001280556.1	134	tCc/tTc	3/10	0.766294420081875	2	FACETS	0.928	0.903	0.953	0.928	0.903	0.953	CLONAL	2	TRUE	0	0.806623765286268	2		332	689	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933744	49933744	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs750582514	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	616	676	0	ENST00000296474.3:c.2533C>T	p.Arg845Ter	p.R845*	ENST00000296474	NM_002447.2	845	Cga/Tga	10/20	1	2	FACETS	0.964	0.928	1	0.964	0.928	1	CLONAL	1	TRUE	1	0.806623765286268	2		676	1585	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226846	142226846	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	249	515	0	ENST00000350721.4:c.4958G>A	p.Arg1653Gln	p.R1653Q	ENST00000350721	NM_001184.3	1653	cGa/cAa	28/47	0.386166862565935	1	FACETS	0.732	0.693	0.772	0.732	0.693	0.772	INDETERMINATE	1	TRUE	0	0.806623765286268	1		515	503	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713742	30713742	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs727504292	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	329	379	0	ENST00000295754.5:c.1067G>C	p.Arg356Pro	p.R356P	ENST00000295754	NM_003242.5	356	cGg/cCg	4/7	1	2	FACETS	0.957	0.909	1	0.957	0.909	1	CLONAL	1	TRUE	1	0.806623765286268	2		379	852	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935006	49935006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	730	747	0	ENST00000296474.3:c.1993G>A	p.Gly665Ser	p.G665S	ENST00000296474	NM_002447.2	665	Ggc/Agc	6/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.806623765286268	2		747	1763	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251912	153251912	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	236	560	0	ENST00000281708.4:c.1094G>A	p.Trp365Ter	p.W365*	ENST00000281708	NM_033632.3	365	tGg/tAg	7/12	0.459598431993822	1	FACETS	0.718	0.679	0.758	0.718	0.679	0.758	INDETERMINATE	1	TRUE	0	0.806623765286268	1		560	486	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707785	176707785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886041941	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	217	491	0	ENST00000439151.2:c.5842C>T	p.Arg1948Cys	p.R1948C	ENST00000439151	NM_022455.4	1948	Cgc/Tgc	18/23	0.459598431993822	1	FACETS	0.334	0.31	0.358	0.334	0.31	0.358	INDETERMINATE	1	TRUE	0	0.806623765286268	1		491	961	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198257	138198257	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	254	394	0	ENST00000237289.4:c.850G>T	p.Glu284Ter	p.E284*	ENST00000237289	NM_001270507.1	284	Gaa/Taa	6/9	0.794643686406182	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.806623765286268	1		394	369	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467680	50467680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867719866	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	415	518	1	ENST00000331340.3:c.915G>A	p.Met305Ile	p.M305I	ENST00000331340	NM_006060.4	305	atG/atA	8/8	1	2	FACETS	0.963	0.92	1	0.963	0.92	1	CLONAL	1	TRUE	1	0.806623765286268	2		519	1068	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151873738	151873738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770069367	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	277	391	0	ENST00000262189.6:c.8800C>T	p.Pro2934Ser	p.P2934S	ENST00000262189	NM_170606.2	2934	Cca/Tca	38/59	1	2	FACETS	0.885	0.835	0.936	0.885	0.835	0.936	CLONAL	1	TRUE	1	0.806623765286268	2		391	776	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275887	38275887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	422	459	0	ENST00000425967.3:c.1382C>T	p.Ser461Phe	p.S461F	ENST00000425967	NM_001174067.1	461	tCt/tTt	11/19	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.806623765286268	2		459	1027	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8338945	8338945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	373	576	0	ENST00000356435.5:c.5356G>A	p.Glu1786Lys	p.E1786K	ENST00000356435		1786	Gaa/Aaa	32/35	0.766294420081875	2	FACETS	0.923	0.894	0.951	0.923	0.894	0.951	CLONAL	2	TRUE	0	0.806623765286268	2		576	501	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720876	89720876	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	88	222	0	ENST00000371953.3:c.1026+1G>T		p.X342_splice	ENST00000371953	NM_000314.4	342			0.806623765286268	1	FACETS	0.824	0.754	0.893	0.824	0.754	0.893	CLONAL	1	TRUE	0	0.806623765286268	1		222	158	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298166	123298166	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	398	492	0	ENST00000358487.5:c.688A>G	p.Thr230Ala	p.T230A	ENST00000358487	NM_000141.4	230	Acc/Gcc	6/18	0.806623765286268	1	FACETS	0.874	0.84	0.907	0.874	0.84	0.907	CLONAL	1	TRUE	0	0.806623765286268	1		492	674	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243840	46243840	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	132	321	0	ENST00000334344.6:c.1934C>T	p.Thr645Ile	p.T645I	ENST00000334344	NM_152641.2	645	aCc/aTc	15/21	1	2	FACETS	0.822	0.754	0.893	0.822	0.754	0.893	CLONAL	1	TRUE	1	0.806623765286268	2		321	398	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495421	56495421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	583	630	0	ENST00000267101.3:c.3611G>A	p.Arg1204Lys	p.R1204K	ENST00000267101	NM_001982.3	1204	aGa/aAa	28/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.806623765286268	2		630	1400	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95595842	95595842	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	149	402	0	ENST00000393063.1:c.701C>T	p.Ala234Val	p.A234V	ENST00000393063	NM_030621.3	234	gCt/gTt	7/28	1	2	FACETS	0.897	0.828	0.967	0.897	0.828	0.967	CLONAL	1	TRUE	1	0.806623765286268	2		402	412	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868132	56868132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	454	704	0	ENST00000308159.5:c.1630C>T	p.Pro544Ser	p.P544S	ENST00000308159	NM_014669.4	544	Cca/Tca	14/22	0.195903721564228	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.806623765286268	0		704	1253	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655455	67655455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	240	549	0	ENST00000264010.4:c.1318C>T	p.Pro440Ser	p.P440S	ENST00000264010	NM_006565.3	440	Ccc/Tcc	7/12	0.195903721564228	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.806623765286268	0		549	714	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993437	72993437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	539	754	0	ENST00000268489.5:c.608C>T	p.Ser203Phe	p.S203F	ENST00000268489	NM_006885.3	203	tCc/tTc	2/10	0.195903721564228	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.806623765286268	0		754	1481	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929463	81929463	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	508	617	1	ENST00000359376.3:c.1124C>G	p.Thr375Arg	p.T375R	ENST00000359376	NM_002661.3	375	aCg/aGg	13/33	0.195903721564228	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.806623765286268	0		618	1413	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866435	37866435	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	468	459	0	ENST00000269571.5:c.740C>T	p.Pro247Leu	p.P247L	ENST00000269571		247	cCc/cTc	6/27	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.806623765286268	2		459	1156	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775203	73775203	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	475	565	1	ENST00000254810.4:c.53G>T	p.Arg18Leu	p.R18L	ENST00000254810	NM_005324.3	18	cGc/cTc	2/4	1	2	FACETS	0.948	0.907	0.988	0.948	0.907	0.988	CLONAL	1	TRUE	1	0.806623765286268	2		566	1243	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274344	5274344	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	152	332	0	ENST00000357368.4:c.103T>C	p.Phe35Leu	p.F35L	ENST00000357368	NM_002850.3	35	Ttt/Ctt	3/38	1	2	FACETS	0.484	0.443	0.527	0.484	0.443	0.527	SUBCLONAL	1	TRUE	1	0.806623765286268	2		332	778	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794781	42794781	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1284125732	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	489	473	1	ENST00000575354.2:c.1861C>T	p.Pro621Ser	p.P621S	ENST00000575354	NM_015125.3	621	Ccc/Tcc	10/20	0.459598431993822	1	FACETS	0.759	0.73	0.788	0.759	0.73	0.788	INDETERMINATE	1	TRUE	0	0.806623765286268	1		474	953	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101130	41101130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	340	407	0	ENST00000373198.4:c.1226C>T	p.Pro409Leu	p.P409L	ENST00000373198	NM_133170.3	409	cCc/cTc	8/32	0.410714447793843	3	FACETS	1	0.989	1	0.581	0.551	0.612	INDETERMINATE	1	TRUE	1	0.806623765286268	3		407	1018	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028803	47028803	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	309	544	0	ENST00000377604.3:c.107A>G	p.Tyr36Cys	p.Y36C	ENST00000377604	NM_001204468.1	36	tAc/tGc	3/24	1	2	FACETS	0.532	0.5	0.564	0.532	0.5	0.564	SUBCLONAL	1	TRUE	1	0.806623765286268	2		544	1441	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76872111	76872111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1557097008	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	145	703	0	ENST00000373344.5:c.5536C>T	p.Leu1846Phe	p.L1846F	ENST00000373344	NM_000489.3	1846	Ctc/Ttc	22/35	1	2	FACETS	0.414	0.378	0.453	0.414	0.378	0.453	SUBCLONAL	1	TRUE	1	0.806623765286268	2		703	868	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181291	123181291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	310	684	1	ENST00000218089.9:c.755G>A	p.Arg252Gln	p.R252Q	ENST00000218089	NM_001042749.1	252	cGg/cAg	9/35	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.806623765286268	2		685	767	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169149	32169150	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	364	446	0	ENST00000375023.3:c.3883_3884delinsTT	p.Pro1295Phe	p.P1295F	ENST00000375023	NM_004557.3	1295	CCc/TTc	22/30	1	2	FACETS	0.904	0.86	0.95	0.904	0.86	0.95	CLONAL	1	TRUE	1	0.806623765286268	2		446	998	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411383	63411384	+	missense_variant	Missense_Mutation	DNP	GC	GC	CA	novel	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	238	510	0	ENST00000330258.3:c.1783_1784delinsTG	p.Ala595Cys	p.A595C	ENST00000330258	NM_152424.3	595	GCc/TGc	2/2	1	2	FACETS	0.477	0.445	0.511	0.477	0.445	0.511	SUBCLONAL	1	TRUE	1	0.806623765286268	2		510	1236	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028800	47028803	+	missense_variant	Missense_Mutation	ONP	ACTA	ACTA	GCTG	novel	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	308	560	0	ENST00000377604.3:c.104_107delinsGCTG	p.Asp35_Tyr36delinsGlyCys	p.D35_Y36delinsGC	ENST00000377604	NM_001204468.1	35	gACTAc/gGCTGc	3/24	1	2	FACETS	0.525	0.494	0.557	0.525	0.494	0.557	SUBCLONAL	1	TRUE	1	0.806623765286268	2		560	1454	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971093	21971094	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0006719-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	360	233	0	ENST00000304494.5:c.264_265delinsAA	p.Gly89Ser	p.G89S	ENST00000304494	NM_000077.4	88	gaGGgc/gaAAgc	2/3	0.766294420081875	2	FACETS	0.952	0.922	0.98	0.952	0.922	0.98	CLONAL	2	TRUE	0	0.806623765286268	2		233	469	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006800-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	154	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.612854124918233	2		280	341	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730916	40730916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765075213	NA	P-0006800-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	93	450	1	ENST00000373198.4:c.3619C>T	p.Arg1207Cys	p.R1207C	ENST00000373198	NM_133170.3	1207	Cgt/Tgt	27/32	0.612854124918233	3	FACETS	0.633	0.564	0.707	0.317	0.282	0.354	SUBCLONAL	1	TRUE	1	0.612854124918233	3		451	626	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106658	27106658	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0006800-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	486	552	0	ENST00000324856.7:c.6269A>C	p.His2090Pro	p.H2090P	ENST00000324856	NM_006015.4	2090	cAc/cCc	20/20	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.612854124918233	2		552	704	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528611	8528611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201846121	NA	P-0006800-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	105	862	2	ENST00000356435.5:c.521G>A	p.Arg174His	p.R174H	ENST00000356435		174	cGt/cAt	4/35	0.346222142570993	1	FACETS	0.438	0.394	0.485	0.438	0.394	0.485	INDETERMINATE	1	TRUE	0	0.612854124918233	1		864	542	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285754	87285754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370304899	NA	P-0006800-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	117	793	3	ENST00000277120.3:c.91G>A	p.Ala31Thr	p.A31T	ENST00000277120		31	Gcc/Acc	2/19	1	2	FACETS	0.529	0.477	0.583	0.529	0.477	0.583	SUBCLONAL	1	TRUE	1	0.612854124918233	2		796	722	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786817	3786817	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0006800-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	169	498	0	ENST00000262367.5:c.4395-1G>T		p.X1465_splice	ENST00000262367	NM_004380.2	1465			0.346029853157151	1	FACETS	0.947	0.881	1	0.947	0.881	1	INDETERMINATE	1	TRUE	0	0.612854124918233	1		498	404	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562982	29562982	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1306237220	NA	P-0006800-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	133	817	2	ENST00000356175.3:c.3917G>A	p.Arg1306Gln	p.R1306Q	ENST00000356175	NM_000267.3	1306	cGa/cAa	29/57	0.471206948894173	3	FACETS	0.621	0.564	0.682	0.311	0.281	0.341	SUBCLONAL	1	TRUE	1	0.612854124918233	3		819	913	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302381	15302381	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006800-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	144	842	0	ENST00000263388.2:c.890G>C	p.Gly297Ala	p.G297A	ENST00000263388	NM_000435.2	297	gGc/gCc	6/33	NA	2	FACETS	0.61	0.557	0.666			1	INDETERMINATE	1	TRUE	NA	0.612854124918233	2		842	770	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877433	40877433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006800-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	82	651	1	ENST00000373198.4:c.2263G>A	p.Glu755Lys	p.E755K	ENST00000373198	NM_133170.3	755	Gag/Aag	15/32	0.612854124918233	3	FACETS	0.453	0.399	0.511	0.226	0.199	0.256	SUBCLONAL	1	TRUE	1	0.612854124918233	3		652	772	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578535	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519996	NA	P-0006829-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	24	1003	0	ENST00000269305.4:c.395A>G	p.Lys132Arg	p.K132R	ENST00000269305	NM_001126112.2	132	aAg/aGg	5/11	0.608804066662759	1	FACETS	0.058	0.045	0.074	0.058	0.045	0.074	SUBCLONAL	1	TRUE	0	0.608804066662759	1		1003	941	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239419	105239419	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006829-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	276	736	0	ENST00000349310.3:c.968A>G	p.Asp323Gly	p.D323G	ENST00000349310	NM_001014432.1	323	gAc/gGc	12/15	0.516758357073301	3	FACETS	1	0.952	1			1	CLONAL	1	TRUE	NA	0.608804066662759	3		736	1163	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662927	227662930	+	frameshift_variant	Frame_Shift_Del	DEL	TGTC	TGTC	-	novel	NA	P-0006829-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	288	829	0	ENST00000305123.5:c.525_528del	p.Thr176ArgfsTer3	p.T176Rfs*3	ENST00000305123	NM_005544.2	175	caGACA/ca	1/2	1	2	FACETS	0.923	0.869	0.978	0.923	0.869	0.978	CLONAL	1	TRUE	1	0.608804066662759	2		829	1025	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	613	334	1	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	0.997	0.977	1	1	0.998	1	CLONAL	2	TRUE	1	0.84113407884892	2		335	731	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266097	41266097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931588	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	297	315	0	ENST00000349496.5:c.94G>A	p.Asp32Asn	p.D32N	ENST00000349496	NM_001904.3	32	Gac/Aac	3/15	1	2	FACETS	0.992	0.94	1	0.992	0.94	1	CLONAL	1	TRUE	1	0.84113407884892	2		315	712	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	384	401	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.84113407884892	2		402	698	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	57	274	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	0.757	0.662	0.857	0.757	0.662	0.857	SUBCLONAL	1	TRUE	1	0.84113407884892	2		275	179	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921553	178921553	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913284	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	182	267	0	ENST00000263967.3:c.1035T>A	p.Asn345Lys	p.N345K	ENST00000263967	NM_006218.2	345	aaT/aaA	5/21	1	2	FACETS	0.824	0.766	0.884	0.824	0.766	0.884	CLONAL	1	TRUE	1	0.84113407884892	2		267	525	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	135	368	7	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.461	0.42	0.505	0.461	0.42	0.505	SUBCLONAL	1	TRUE	1	0.84113407884892	2		375	696	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	17	486	4	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	0.063	0.046	0.083	0.063	0.046	0.083	SUBCLONAL	1	TRUE	1	0.84113407884892	2		490	643	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37070349	37070349	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs63750855	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	298	402	1	ENST00000231790.2:c.1489del	p.Arg497GlyfsTer11	p.R497Gfs*11	ENST00000231790	NM_000249.3	495	aCc/ac	13/19	1	2	FACETS	0.836	0.79	0.882	0.836	0.79	0.882	CLONAL	1	TRUE	1	0.84113407884892	2		403	848	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466019	69466019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	284	329	1	ENST00000227507.2:c.857C>T	p.Thr286Ile	p.T286I	ENST00000227507	NM_053056.2	286	aCa/aTa	5/5	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.84113407884892	2		330	650	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457303	67457303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs768713596	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	36	315	0	ENST00000327367.4:c.277C>T	p.Arg93Ter	p.R93*	ENST00000327367	NM_005902.3	93	Cga/Tga	2/9	1	2	FACETS	0.137	0.112	0.165	0.137	0.112	0.165	SUBCLONAL	1	TRUE	1	0.84113407884892	2		315	625	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	174	361	2	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	1	2	FACETS	0.732	0.678	0.788	0.732	0.678	0.788	SUBCLONAL	1	TRUE	1	0.84113407884892	2		363	565	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690846	89690846	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	134	202	0	ENST00000371953.3:c.253G>T	p.Val85Phe	p.V85F	ENST00000371953	NM_000314.4	85	Gtt/Ttt	4/9	1	2	FACETS	0.793	0.727	0.86	0.793	0.727	0.86	SUBCLONAL	1	TRUE	1	0.84113407884892	2		202	402	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47034435	47034435	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	40	394	0	ENST00000377604.3:c.520G>A	p.Ala174Thr	p.A174T	ENST00000377604	NM_001204468.1	174	Gcc/Acc	6/24	NA	2	FACETS	0.124	0.102	0.148			1	INDETERMINATE	1	TRUE	NA	0.84113407884892	2		394	767	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319387	11319387	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	45	342	0	ENST00000361445.4:c.80G>A	p.Ser27Asn	p.S27N	ENST00000361445	NM_004958.3	27	aGt/aAt	2/58	0.810966657754385	2	FACETS	0.159	0.133	0.188	0.08	0.066	0.094	SUBCLONAL	1	TRUE	0	0.84113407884892	2		342	672	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193094325	193094325	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	222	287	0	ENST00000367435.3:c.215C>A	p.Pro72His	p.P72H	ENST00000367435	NM_024529.4	72	cCt/cAt	2/17	1	2	FACETS	0.829	0.776	0.883	0.829	0.776	0.883	CLONAL	1	TRUE	1	0.84113407884892	2		287	637	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660565	190660565	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	30	252	0	ENST00000441310.2:c.203T>C	p.Val68Ala	p.V68A	ENST00000441310	NM_000534.4	68	gTa/gCa	3/13	1	2	FACETS	0.127	0.102	0.156	0.127	0.102	0.156	SUBCLONAL	1	TRUE	1	0.84113407884892	2		252	562	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391136	89391136	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753359922	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	152	296	0	ENST00000336596.2:c.1202C>T	p.Ala401Val	p.A401V	ENST00000336596	NM_005233.5	401	gCa/gTa	5/17	1	2	FACETS	0.644	0.592	0.698	0.644	0.592	0.698	SUBCLONAL	1	TRUE	1	0.84113407884892	2		296	561	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637120	176637120	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	150	280	0	ENST00000439151.2:c.1720G>T	p.Gly574Ter	p.G574*	ENST00000439151	NM_022455.4	574	Gga/Tga	5/23	1	2	FACETS	0.903	0.835	0.972	0.903	0.835	0.972	CLONAL	1	TRUE	1	0.84113407884892	2		280	395	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151868386	151868386	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	234	325	0	ENST00000262189.6:c.9416G>A	p.Ser3139Asn	p.S3139N	ENST00000262189	NM_170606.2	3139	aGt/aAt	40/59	1	2	FACETS	0.953	0.896	1	0.953	0.896	1	CLONAL	1	TRUE	1	0.84113407884892	2		325	584	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425776	49425776	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398123714	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	193	276	1	ENST00000301067.7:c.12712C>T	p.Arg4238Cys	p.R4238C	ENST00000301067	NM_003482.3	4238	Cgc/Tgc	39/54	1	2	FACETS	0.976	0.913	1	0.976	0.913	1	CLONAL	1	TRUE	1	0.84113407884892	2		277	470	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478813	56478813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	327	397	1	ENST00000267101.3:c.269C>T	p.Ala90Val	p.A90V	ENST00000267101	NM_001982.3	90	gCc/gTc	3/28	1	2	FACETS	0.973	0.924	1	0.973	0.924	1	CLONAL	1	TRUE	1	0.84113407884892	2		398	799	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112919935	112919935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748162361	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	101	165	3	ENST00000351677.2:c.1150C>T	p.Arg384Cys	p.R384C	ENST00000351677	NM_002834.3	384	Cgt/Tgt	10/16	1	2	FACETS	0.934	0.85	1	0.934	0.85	1	CLONAL	1	TRUE	1	0.84113407884892	2		168	257	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913150	32913150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80358697	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	307	554	1	ENST00000380152.3:c.4658C>T	p.Thr1553Ile	p.T1553I	ENST00000380152		1553	aCt/aTt	11/27	1	2	FACETS	0.699	0.659	0.739	0.699	0.659	0.739	SUBCLONAL	1	TRUE	1	0.84113407884892	2		555	1045	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3860620	3860620	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1449645780	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	234	401	1	ENST00000262367.5:c.959C>T	p.Thr320Ile	p.T320I	ENST00000262367	NM_004380.2	320	aCc/aTc	3/31	1	2	FACETS	0.929	0.873	0.986	0.929	0.873	0.986	CLONAL	1	TRUE	1	0.84113407884892	2		402	599	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950391	15950391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1200358570	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	53	394	1	ENST00000268712.3:c.6553C>T	p.Pro2185Ser	p.P2185S	ENST00000268712	NM_006311.3	2185	Cca/Tca	42/46	1	2	FACETS	0.214	0.182	0.249	0.214	0.182	0.249	SUBCLONAL	1	TRUE	1	0.84113407884892	2		395	589	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560127	29560127	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	268	360	0	ENST00000356175.3:c.3604G>A	p.Ala1202Thr	p.A1202T	ENST00000356175	NM_000267.3	1202	Gct/Act	27/57	1	2	FACETS	0.989	0.935	1	0.989	0.935	1	CLONAL	1	TRUE	1	0.84113407884892	2		360	644	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37863295	37863295	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	329	412	0	ENST00000269571.5:c.126C>G	p.His42Gln	p.H42Q	ENST00000269571		42	caC/caG	2/27	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.84113407884892	2		412	762	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11113759	11113759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	328	397	0	ENST00000358026.2:c.1867G>A	p.Glu623Lys	p.E623K	ENST00000358026	NM_001128849.1	623	Gag/Aag	12/36	1	2	FACETS	0.968	0.919	1	0.968	0.919	1	CLONAL	1	TRUE	1	0.84113407884892	2		397	806	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289952	15289952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778635935	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	58	321	2	ENST00000263388.2:c.3602G>A	p.Arg1201His	p.R1201H	ENST00000263388	NM_000435.2	1201	cGc/cAc	22/33	1	2	FACETS	0.219	0.188	0.253	0.219	0.188	0.253	SUBCLONAL	1	TRUE	1	0.84113407884892	2		323	629	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039844	47039844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	41	264	0	ENST00000377604.3:c.1187G>A	p.Arg396His	p.R396H	ENST00000377604	NM_001204468.1	396	cGc/cAc	12/24	NA	2	FACETS	0.13	0.108	0.155			1	INDETERMINATE	1	TRUE	NA	0.84113407884892	2		264	750	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223614	53223614	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	32	316	1	ENST00000375401.3:c.3745C>T	p.Arg1249Cys	p.R1249C	ENST00000375401	NM_004187.3	1249	Cgc/Tgc	23/26	NA	2	FACETS	0.136	0.11	0.166			1	INDETERMINATE	1	TRUE	NA	0.84113407884892	2		317	559	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67655348	67655348	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	208	298	0	ENST00000264010.4:c.1214del	p.Lys405SerfsTer18	p.K405Sfs*18	ENST00000264010	NM_006565.3	404	gAa/ga	7/12	1	2	FACETS	0.93	0.87	0.99	0.93	0.87	0.99	CLONAL	1	TRUE	1	0.84113407884892	2		298	532	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933400	39933400	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	80	487	0	ENST00000378444.4:c.1199del	p.Gly400AlafsTer42	p.G400Afs*42	ENST00000378444	NM_001123385.1	400	gGc/gc	4/15	NA	2	FACETS	0.236	0.207	0.267			1	INDETERMINATE	1	TRUE	NA	0.84113407884892	2		487	807	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538269	187538269	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs748652484	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	283	400	2	ENST00000441802.2:c.8965del	p.Arg2989GlyfsTer20	p.R2989Gfs*20	ENST00000441802	NM_005245.3	2989	Agg/gg	11/27	1	2	FACETS	0.801	0.755	0.848	0.801	0.755	0.848	CLONAL	1	TRUE	1	0.84113407884892	2		402	840	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169116	32169116	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1263727065	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	202	298	0	ENST00000375023.3:c.3917del	p.Pro1306GlnfsTer3	p.P1306Qfs*3	ENST00000375023	NM_004557.3	1306	cCa/ca	22/30	1	2	FACETS	0.925	0.866	0.986	0.925	0.866	0.986	CLONAL	1	TRUE	1	0.84113407884892	2		298	519	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493628	56493629	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0006849-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	68	347	1	ENST00000267101.3:c.2944_2945del	p.Ser982TrpfsTer57	p.S982Wfs*57	ENST00000267101	NM_001982.3	982	AGt/t	25/28	1	2	FACETS	0.225	0.195	0.257	0.225	0.195	0.257	SUBCLONAL	1	TRUE	1	0.84113407884892	2		348	719	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006870-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	36	280	0				ENST00000310581	NM_198253.2	-/1132			0.3	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		280	183	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0006870-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	113	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		490	486	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	92	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.95	0.846	1	0.95	0.846	1	CLONAL	1	TRUE	1	0.33	2		280	587	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220274	55220274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1581	4961	433	0	ENST00000275493.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000275493	NM_005228.3	222	Cgc/Tgc	6/28	0.3	28	FACETS	1	0.997	1			1	CLONAL	24	TRUE	NA	0.33	28		433	6542	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	86	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.786	0.702	0.873	0.786	0.702	0.873	SUBCLONAL	1	TRUE	1	0.688445565892111	2		280	318	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251748	212251748	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0006879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	165	344	0	ENST00000342788.4:c.3311A>G	p.Asp1104Gly	p.D1104G	ENST00000342788	NM_005235.2	1104	gAc/gGc	27/28	0.688445565892111	1	FACETS	0.908	0.848	0.969	0.908	0.848	0.969	CLONAL	1	TRUE	0	0.688445565892111	1		344	346	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94209506	94209506	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0006879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	304	355	0	ENST00000323929.3:c.608C>A	p.Pro203Gln	p.P203Q	ENST00000323929	NM_005591.3	203	cCa/cAa	7/20	1	2	FACETS	0.986	0.932	1	0.986	0.932	1	CLONAL	1	TRUE	1	0.688445565892111	2		355	896	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888189	112888189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507511	NA	P-0006879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	211	741	0	ENST00000351677.2:c.205G>A	p.Glu69Lys	p.E69K	ENST00000351677	NM_002834.3	69	Gag/Aag	3/16	1	2	FACETS	0.918	0.856	0.98	0.918	0.856	0.98	CLONAL	1	TRUE	1	0.688445565892111	2		741	668	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941694	48941694	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0006879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	214	246	0	ENST00000267163.4:c.1004T>A	p.Leu335Ter	p.L335*	ENST00000267163	NM_000321.2	335	tTa/tAa	10/27	0.688445565892111	1	FACETS	0.957	0.902	1	0.957	0.902	1	CLONAL	1	TRUE	0	0.688445565892111	1		246	426	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789636	3789636	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	261	447	0	ENST00000262367.5:c.4223G>A	p.Cys1408Tyr	p.C1408Y	ENST00000262367	NM_004380.2	1408	tGc/tAc	25/31	1	2	FACETS	0.947	0.89	1	0.947	0.89	1	CLONAL	1	TRUE	1	0.688445565892111	2		447	801	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577095	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519984	NA	P-0006879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	33	424	0	ENST00000269305.4:c.843C>G	p.Asp281Glu	p.D281E	ENST00000269305	NM_001126112.2	281	gaC/gaG	8/11	1	2	FACETS	0.12	0.097	0.146	0.12	0.097	0.146	SUBCLONAL	1	TRUE	1	0.688445565892111	2		424	797	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562687	29562687	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1555615457	NA	P-0006879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	227	441	0	ENST00000356175.3:c.3767T>G	p.Leu1256Arg	p.L1256R	ENST00000356175	NM_000267.3	1256	cTg/cGg	28/57	1	2	FACETS	0.928	0.868	0.988	0.928	0.868	0.988	CLONAL	1	TRUE	1	0.688445565892111	2		441	711	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661970	29661970	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0006879-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	224	334	0	ENST00000356175.3:c.5864del	p.Asp1955AlafsTer3	p.D1955Afs*3	ENST00000356175	NM_000267.3	1955	gAc/gc	39/57	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.688445565892111	2		334	602	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	23	280	0				ENST00000310581	NM_198253.2	-/1132			0.298602412452231	0	FACETS	1	0.832	1			1	CLONAL	1	FALSE	0	0.308400317539905	0		280	98	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0006891-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	463	354	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	0.308400317539905	6	FACETS	1	0.966	1			1	CLONAL	5	FALSE	NA	0.308400317539905	6		354	964	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0006902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	156	464	0				ENST00000310581	NM_198253.2	-/1132			0.216947109779211	1	FACETS	1	0.958	1	1	0.958	1	INDETERMINATE	1	TRUE	0	0.617252696935425	1		464	336	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0006902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	168	595	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.778	0.726	0.829	1	0.992	1	SUBCLONAL	2	TRUE	1	0.617252696935425	2		595	350	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0006902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	341	463	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.617252696935425	2		463	816	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65569036	65569036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	330	426	2	ENST00000358664.4:c.22G>A	p.Glu8Lys	p.E8K	ENST00000358664	NM_002382.4	8	Gag/Aag	1/5	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.617252696935425	2		428	758	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806555	1806555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1189213092	NA	P-0006902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	195	315	0	ENST00000260795.2:c.1271C>T	p.Ser424Phe	p.S424F	ENST00000260795		424	tCc/tTc	9/17	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.617252696935425	2		315	443	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937918	36937918	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs370712007	NA	P-0006902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	358	535	0	ENST00000361632.4:c.918G>C	p.Gln306His	p.Q306H	ENST00000361632		306	caG/caC	7/16	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.617252696935425	2		535	813	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678626	88678626	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs751051788	NA	P-0006902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	87	163	0	ENST00000360948.2:c.910C>A	p.Pro304Thr	p.P304T	ENST00000360948	NM_001012338.2	304	Ccc/Acc	9/19	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.617252696935425	2		163	267	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197026	123197026	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	337	255	1	ENST00000218089.9:c.1792G>T	p.Glu598Ter	p.E598*	ENST00000218089	NM_001042749.1	598	Gaa/Taa	19/35	1	1	FACETS	0.946	0.921	0.97	1	0.997	1	CLONAL	2	TRUE	0	0.617252696935425	1		256	399	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900369	3900369	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006902-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	245	445	0	ENST00000262367.5:c.727del	p.Leu243Ter	p.L243*	ENST00000262367	NM_004380.2	243	Cta/ta	2/31	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.617252696935425	2		445	685	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006922-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	59	280	0				ENST00000310581	NM_198253.2	-/1132			0.3	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		280	116	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0006922-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	283	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		490	610	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0006952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	177	280	0				ENST00000310581	NM_198253.2	-/1132			0.3	2	FACETS	0.947	0.879	1			1	CLONAL	5	TRUE	NA	0.14	2		280	534	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0006952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	34	599	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.431	0.351	0.523	0.431	0.351	0.523	SUBCLONAL	1	TRUE	1	0.14	2		599	1126	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574004	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0006952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1305	91	749	1	ENST00000269305.4:c.1023_1024delinsTT	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	341	ttCCga/ttTTga	10/11	1	2	FACETS	0.931	0.824	1	0.931	0.824	1	CLONAL	1	TRUE	1	0.14	2		750	1396	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435258	110435258	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	19	130	0	ENST00000375856.3:c.3143C>T	p.Ser1048Leu	p.S1048L	ENST00000375856	NM_003749.2	1048	tCg/tTg	1/2	1	2	FACETS	1	0.825	1	1	0.825	1	CLONAL	1	TRUE	1	0.14	2		130	245	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212145	98212145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1223	86	729	0	ENST00000331920.6:c.3527C>T	p.Ser1176Phe	p.S1176F	ENST00000331920	NM_000264.3	1176	tCt/tTt	21/24	1	2	FACETS	0.939	0.827	1	0.939	0.827	1	CLONAL	1	TRUE	1	0.14	2		729	1309	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488718	212488718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267599191	NA	P-0006952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	40	625	0	ENST00000342788.4:c.2131C>T	p.Arg711Cys	p.R711C	ENST00000342788	NM_005235.2	711	Cgt/Tgt	18/28	1	2	FACETS	0.486	0.402	0.581	0.486	0.402	0.581	SUBCLONAL	1	TRUE	1	0.14	2		625	1176	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851588	134851588	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0006952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	59	561	0	ENST00000398015.3:c.994A>T	p.Ile332Phe	p.I332F	ENST00000398015	NM_004441.4	332	Atc/Ttc	5/16	0.3	2	FACETS	0.867	0.744	1			1	CLONAL	1	TRUE	NA	0.14	2		561	972	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268985	142268985	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs911751877	NA	P-0006952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1365	75	693	1	ENST00000350721.4:c.2965C>T	p.Arg989Cys	p.R989C	ENST00000350721	NM_001184.3	989	Cgt/Tgt	14/47	1	2	FACETS	0.744	0.649	0.847	0.744	0.649	0.847	SUBCLONAL	1	TRUE	1	0.14	2		694	1440	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235387	235387	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1553999477	NA	P-0006952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	532	501	0	ENST00000264932.6:c.1193A>T	p.Glu398Val	p.E398V	ENST00000264932	NM_004168.2	398	gAg/gTg	9/15	0.3	5	FACETS	0.971	0.932	1			1	CLONAL	7	TRUE	NA	0.14	5		501	1353	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295255	1295255	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs796338008	NA	P-0006952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	209	379	2				ENST00000310581	NM_198253.2	-/1132			0.3	2	FACETS	0.909	0.848	0.971			1	CLONAL	5	TRUE	NA	0.14	2		381	657	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6029582	6029582	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0006952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	52	509	0	ENST00000265849.7:c.993C>G	p.Cys331Trp	p.C331W	ENST00000265849	NM_000535.5	331	tgC/tgG	10/15	1	2	FACETS	0.782	0.663	0.913	0.782	0.663	0.913	CLONAL	1	TRUE	1	0.14	2		509	950	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259427	55259427	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0006952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	57	468	0	ENST00000275493.2:c.2485G>T	p.Glu829Ter	p.E829*	ENST00000275493	NM_005228.3	829	Gag/Tag	21/28	1	2	FACETS	0.854	0.731	0.99	0.854	0.731	0.99	CLONAL	1	TRUE	1	0.14	2		468	953	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069154	5069154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764423560	NA	P-0006952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	71	428	1	ENST00000381652.3:c.1459C>T	p.Arg487Cys	p.R487C	ENST00000381652	NM_004972.3	487	Cgc/Tgc	11/25	0.3	2	FACETS	0.829	0.721	0.946			1	CLONAL	1	TRUE	NA	0.14	2		429	1224	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652281	48652281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0006952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	66	494	4	ENST00000376670.3:c.952G>A	p.Gly318Ser	p.G318S	ENST00000376670	NM_002049.3	318	Ggc/Agc	6/6	1	1	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	0	0.14	1		498	778	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894985	101894985	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0006952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1331	79	552	0	ENST00000374994.4:c.539del	p.Leu180Ter	p.L180*	ENST00000374994	NM_004612.2	180	Tta/ta	3/9	1	2	FACETS	0.8	0.701	0.908	0.8	0.701	0.908	CLONAL	1	TRUE	1	0.14	2		552	1410	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235403	235404	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0006952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	462	495	0	ENST00000264932.6:c.1209_1210delinsTT	p.Pro404Ser	p.P404S	ENST00000264932	NM_004168.2	403	ctCCcc/ctTTcc	9/15	0.3	5	FACETS	1	0.978	1			1	CLONAL	6	TRUE	NA	0.14	5		495	1284	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55225404	55225405	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0006952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	61	574	3	ENST00000275493.2:c.1256_1257delinsTT	p.Ala419Val	p.A419V	ENST00000275493	NM_005228.3	419	gCC/gTT	11/28	1	2	FACETS	0.858	0.738	0.989	0.858	0.738	0.989	CLONAL	1	TRUE	1	0.14	2		577	1016	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971016	21971017	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0006952-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	95	223	0	ENST00000304494.5:c.341_342delinsTT	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCC/cTT	2/3	1	2	FACETS	0.919	0.819	1	1	0.985	1	CLONAL	2	TRUE	1	0.14	2		223	738	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0006953-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	313	521	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.313459713309062	4	FACETS	0.886	0.837	0.936	0.886	0.837	0.936	CLONAL	3	TRUE	1	0.313459713309062	4		522	987	SUCCESS
CCND2	894	MSKCC	GRCh37	12	4388008	4388008	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759672856	NA	P-0006953-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	130	415	1	ENST00000261254.3:c.494G>A	p.Arg165His	p.R165H	ENST00000261254	NM_001759.3	165	cGc/cAc	3/5	0.313459713309062	3	FACETS	1	0.923	1			1	CLONAL	1	TRUE	NA	0.313459713309062	3		416	940	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428626	49428626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0006953-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	167	500	1	ENST00000301067.7:c.10324G>A	p.Gly3442Ser	p.G3442S	ENST00000301067	NM_003482.3	3442	Ggc/Agc	35/54	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.313459713309062	2		501	1024	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948464	54948464	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0006953-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	111	378	2	ENST00000312783.6:c.854G>T	p.Arg285Met	p.R285M	ENST00000312783	NM_198436.1	285	aGg/aTg	8/10	1	2	FACETS	0.885	0.796	0.98	0.885	0.796	0.98	CLONAL	1	TRUE	1	0.313459713309062	2		380	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572928	7572929	+	frameshift_variant,stop_lost	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0006953-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	154	470	0	ENST00000269305.4:c.1180_1181del	p.Ter394ThrfsTer76	p.*394Tfs*76	ENST00000269305	NM_001126112.2	394	TGa/a	11/11	0.312006934083684	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.313459713309062	1		470	820	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121434595	NA	P-0006983-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	294	310	0	ENST00000369535.4:c.37G>C	p.Gly13Arg	p.G13R	ENST00000369535	NM_002524.4	13	Ggt/Cgt	2/7	0.613431940754534	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.613431940754534	1		310	610	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347843	89347843	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767704252	NA	P-0006983-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	440	551	0	ENST00000301030.4:c.5107G>A	p.Val1703Met	p.V1703M	ENST00000301030	NM_001256183.1	1703	Gtg/Atg	9/13	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.613431940754534	2		551	1323	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350485	15350485	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200957651	NA	P-0006983-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	127	240	1	ENST00000263377.2:c.3430G>A	p.Val1144Ile	p.V1144I	ENST00000263377	NM_058243.2	1144	Gtc/Atc	16/20	0.316220282905678	1	FACETS	0.56	0.509	0.612	0.56	0.509	0.612	INDETERMINATE	1	TRUE	0	0.613431940754534	1		241	513	SUCCESS
APC	324	MSKCC	GRCh37	5	112175232	112175232	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0006983-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	335	305	0	ENST00000257430.4:c.3942del	p.Arg1314SerfsTer7	p.R1314Sfs*7	ENST00000257430	NM_000038.5	1314	aGg/ag	16/16	0.567796897100839	2	FACETS	0.848	0.81	0.886	0.848	0.81	0.886	CLONAL	2	TRUE	0	0.613431940754534	2		305	644	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4101279	4101280	+	splice_acceptor_variant	Splice_Site	DEL	CT	CT	-	novel	NA	P-0006983-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	128	402	0	ENST00000262948.5:c.529-2_529-1del		p.X177_splice	ENST00000262948	NM_030662.3	177			0.316220282905678	1	FACETS	0.373	0.338	0.41	0.373	0.338	0.41	INDETERMINATE	1	TRUE	0	0.613431940754534	1		402	776	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	205	280	0				ENST00000310581	NM_198253.2	-/1132			0.534054396023129	4	FACETS	1	0.94	1	1	0.94	1	CLONAL	2	TRUE	2	0.534054396023129	4		280	585	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0007002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	517	599	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.534054396023129	5	FACETS	1	0.979	1			1	CLONAL	3	TRUE	NA	0.534054396023129	5		599	1133	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056286	27056286	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	352	329	0	ENST00000324856.7:c.1282C>T	p.Gln428Ter	p.Q428*	ENST00000324856	NM_006015.4	428	Cag/Tag	2/20	0.534054396023129	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	2	0.534054396023129	4		329	839	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447377	187447377	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	39	235	0	ENST00000232014.4:c.816T>A	p.Asp272Glu	p.D272E	ENST00000232014	NM_001130845.1	272	gaT/gaA	5/10	0.534054396023129	4	FACETS	0.335	0.277	0.4	0.167	0.138	0.2	SUBCLONAL	1	TRUE	2	0.534054396023129	4		235	669	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786425	135786425	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	298	505	0	ENST00000298552.3:c.1105C>G	p.Leu369Val	p.L369V	ENST00000298552	NM_001162426.1	369	Ctg/Gtg	11/23	0.236133605149359	3	FACETS	1	0.993	1	0.701	0.661	0.742	INDETERMINATE	1	TRUE	1	0.534054396023129	3		505	1008	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786931	135786931	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	254	403	0	ENST00000298552.3:c.938C>G	p.Ser313Cys	p.S313C	ENST00000298552	NM_001162426.1	313	tCc/tGc	10/23	0.236133605149359	3	FACETS	0.791	0.743	0.839	0.791	0.743	0.839	INDETERMINATE	2	TRUE	1	0.534054396023129	3		403	762	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651992	36652012	+	inframe_deletion	In_Frame_Del	DEL	GGCGGGCTGCATCCAGGAGGC	GGCGGGCTGCATCCAGGAGGC	-	novel	NA	P-0007002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	338	351	2	ENST00000244741.5:c.114_134del	p.Met38_Ala45delinsIle	p.M38_A45delinsI	ENST00000244741	NM_000389.4	38	atGGCGGGCTGCATCCAGGAGGCc/atc	2/3	0.534054396023129	5	FACETS	1	0.991	1	0.802	0.76	0.844	CLONAL	2	TRUE	2	0.534054396023129	5		353	948	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651943	36651944	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CGGCA	novel	NA	P-0007002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	315	286	0	ENST00000244741.5:c.69_70insACGGC	p.Pro24ThrfsTer9	p.P24Tfs*9	ENST00000244741	NM_000389.4	22	ttc/ttCGGCAc	2/3	0.534054396023129	5	FACETS	0.873	0.828	0.919	0.873	0.828	0.919	CLONAL	3	TRUE	2	0.534054396023129	5		286	811	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026638	48026642	+	missense_variant	Missense_Mutation	ONP	GATAG	GATAG	CATAA	novel	NA	P-0007002-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	70	298	0	ENST00000234420.5:c.1516_1520delinsCATAA	p.Asp506_Arg507delinsHisLys	p.D506_R507delinsHK	ENST00000234420	NM_000179.2	506	GATAGa/CATAAa	4/10	0.346299949061107	4	FACETS	0.616	0.537	0.701	0.308	0.268	0.351	SUBCLONAL	1	TRUE	2	0.534054396023129	4		298	653	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	317	280	0				ENST00000310581	NM_198253.2	-/1132			0.208618417586674	3	FACETS	1	0.994	1	0.714	0.677	0.751	INDETERMINATE	1	TRUE	1	0.773300444561962	3		280	796	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0007017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	536	769	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.773300444561962	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.773300444561962	1		769	772	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047495	49047495	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs587778838	NA	P-0007017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	121	149	0	ENST00000267163.4:c.2490-1G>A		p.X830_splice	ENST00000267163	NM_000321.2	830			0.208618417586674	3	FACETS	1	0.92	1	0.506	0.46	0.553	INDETERMINATE	1	TRUE	1	0.773300444561962	3		149	429	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253367	226253367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	144	146	0	ENST00000366813.1:c.139G>A	p.Val47Met	p.V47M	ENST00000366813		47	Gtg/Atg	2/3	1	2	FACETS	0.782	0.719	0.848	0.782	0.719	0.848	SUBCLONAL	1	TRUE	1	0.773300444561962	2		146	476	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948174	55948174	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0007017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	262	327	0	ENST00000263923.4:c.3797C>G	p.Ser1266Ter	p.S1266*	ENST00000263923	NM_002253.2	1266	tCa/tGa	29/30	1	2	FACETS	0.814	0.765	0.864	0.814	0.765	0.864	CLONAL	1	TRUE	1	0.773300444561962	2		327	832	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955568	55955568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	435	432	0	ENST00000263923.4:c.3377G>A	p.Arg1126Lys	p.R1126K	ENST00000263923	NM_002253.2	1126	aGg/aAg	25/30	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.773300444561962	2		432	1021	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941685	48941694	+	frameshift_variant	Frame_Shift_Del	DEL	ATGCAAGATT	ATGCAAGATT	-	novel	NA	P-0007017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	152	168	0	ENST00000267163.4:c.997_1006del	p.Ala333PhefsTer13	p.A333Ffs*13	ENST00000267163	NM_000321.2	332	gATGCAAGATTa/ga	10/27	0.208618417586674	3	FACETS	1	0.984	1	0.628	0.58	0.677	INDETERMINATE	1	TRUE	1	0.773300444561962	3		168	434	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105637	27105638	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0007017-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	544	462	0	ENST00000324856.7:c.5248_5249del	p.Phe1750GlnfsTer5	p.F1750Qfs*5	ENST00000324856	NM_006015.4	1750	TTc/c	20/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.773300444561962	2		462	1342	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0007018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	71	464	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.894	1			1	INDETERMINATE	1	TRUE	NA	0.583126976089546	2		464	241	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971000	21971000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	123	342	0	ENST00000304494.5:c.358G>T	p.Glu120Ter	p.E120*	ENST00000304494	NM_000077.4	120	Gag/Tag	2/3	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.583126976089546	2		342	397	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223543	55223543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	281	545	0	ENST00000275493.2:c.910C>T	p.His304Tyr	p.H304Y	ENST00000275493	NM_005228.3	304	Cac/Tac	8/28	0.511919154136179	4	FACETS	0.926	0.873	0.98	0.617	0.582	0.653	CLONAL	2	TRUE	1	0.583126976089546	4		545	824	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888165	112888165	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs397507510	NA	P-0007018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	25	338	0	ENST00000351677.2:c.181G>T	p.Asp61Tyr	p.D61Y	ENST00000351677	NM_002834.3	61	Gat/Tat	3/16	1	2	FACETS	0.253	0.199	0.315	0.253	0.199	0.315	SUBCLONAL	1	TRUE	1	0.583126976089546	2		338	339	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578536	7578536	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs747342068	NA	P-0007018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	59	362	0	ENST00000269305.4:c.394A>G	p.Lys132Glu	p.K132E	ENST00000269305	NM_001126112.2	132	Aag/Gag	5/11	0.22251143972541	2	FACETS	0.632	0.548	0.723	0.316	0.274	0.362	INDETERMINATE	1	TRUE	0	0.583126976089546	2		362	320	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856617	111856617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1364785726	NA	P-0007018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	98	403	1	ENST00000341259.2:c.668C>T	p.Ala223Val	p.A223V	ENST00000341259	NM_005475.2	223	gCg/gTg	2/8	1	2	FACETS	0.983	0.886	1	0.983	0.886	1	CLONAL	1	TRUE	1	0.583126976089546	2		404	342	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920486	50920486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777018011	NA	P-0007018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	116	551	2	ENST00000440232.2:c.3178C>T	p.Arg1060Cys	p.R1060C	ENST00000440232	NM_002691.3	1060	Cgc/Tgc	26/27	NA	2	FACETS	0.774	0.701	0.851			1	INDETERMINATE	1	TRUE	NA	0.583126976089546	2		553	514	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589608	67589609	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAAAAAAGTCGAGAATAT	novel	NA	P-0007018-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	32	525	0	ENST00000274335.5:c.1374_1391dup	p.Glu458_Tyr463dup	p.E458_Y463dup	ENST00000274335		458	-/GAAAAAAGTCGAGAATAT	10/15	1	2	FACETS	0.584	0.478	0.7	0.584	0.478	0.7	SUBCLONAL	1	TRUE	1	0.583126976089546	2		525	188	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0007018-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	75	464	0				ENST00000310581	NM_198253.2	-/1132			0.357340554964774	0	FACETS	0.605	0.532	0.683			1	SUBCLONAL	1	FALSE	0	0.357340554964774	0		464	446	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856617	111856617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1364785726	NA	P-0007018-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	124	403	1	ENST00000341259.2:c.668C>T	p.Ala223Val	p.A223V	ENST00000341259	NM_005475.2	223	gCg/gTg	2/8	1	2	FACETS	0.764	0.696	0.835	1	0.986	1	SUBCLONAL	2	FALSE	1	0.357340554964774	2		404	454	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589608	67589609	+	inframe_insertion	In_Frame_Ins	INS	-	-	GAAAAAAGTCGAGAATAT	novel	NA	P-0007018-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	65	525	0	ENST00000274335.5:c.1374_1391dup	p.Glu458_Tyr463dup	p.E458_Y463dup	ENST00000274335		458	-/GAAAAAAGTCGAGAATAT	10/15	1	2	FACETS	0.494	0.428	0.567	0.494	0.428	0.567	SUBCLONAL	1	FALSE	1	0.357340554964774	2		525	736	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0007018-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	286	424	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	0.357340554964774	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	FALSE	0	0.357340554964774	2		424	716	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047959	180047959	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs933223149	NA	P-0007018-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	90	1087	2	ENST00000261937.6:c.2216G>A	p.Arg739His	p.R739H	ENST00000261937	NM_182925.4	739	cGc/cAc	15/30	0.357340554964774	0	FACETS	0.591	0.525	0.66			1	SUBCLONAL	1	FALSE	0	0.357340554964774	0		1089	548	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211008	55211008	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007018-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	121	721	0	ENST00000275493.2:c.251A>T	p.Glu84Val	p.E84V	ENST00000275493	NM_005228.3	84	gAg/gTg	3/28	0.190751392650328	2	FACETS	0.928	0.839	1	0.464	0.419	0.511	INDETERMINATE	1	FALSE	0	0.357340554964774	2		721	730	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161850	47161851	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0007018-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	136	735	0	ENST00000409792.3:c.4275_4276del	p.Lys1426SerfsTer2	p.K1426Sfs*2	ENST00000409792	NM_014159.6	1425	aaGAaa/aaaa	3/21	1	2	FACETS	0.89	0.809	0.975	0.89	0.809	0.975	CLONAL	1	FALSE	1	0.357340554964774	2		735	855	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490332	56490332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007018-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	94	649	1	ENST00000267101.3:c.2101G>A	p.Ala701Thr	p.A701T	ENST00000267101	NM_001982.3	701	Gcc/Acc	18/28	1	2	FACETS	0.855	0.762	0.954	0.855	0.762	0.954	CLONAL	1	FALSE	1	0.357340554964774	2		650	615	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799735	72799735	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007018-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	155	910	0	ENST00000325599.8:c.1434T>G	p.Asp478Glu	p.D478E	ENST00000325599	NM_018130.2	478	gaT/gaG	11/11	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	1	0.357340554964774	2		910	826	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007024-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	53	280	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.823	0.705	0.95			1	INDETERMINATE	1	TRUE	NA	0.386795916842939	2		280	333	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0007024-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1191	674	910	2	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.386795916842939	5	FACETS	0.984	0.948	1			1	CLONAL	3	TRUE	NA	0.386795916842939	5		912	1865	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117678076	117678076	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs373090808	NA	P-0007024-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	91	279	0	ENST00000368508.3:c.3857G>A	p.Arg1286His	p.R1286H	ENST00000368508	NM_002944.2	1286	cGc/cAc	25/43	1	2	FACETS	0.989	0.881	1	0.989	0.881	1	CLONAL	1	TRUE	1	0.386795916842939	2		279	476	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224337	55224337	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007024-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	98	359	0	ENST00000275493.2:c.1118C>T	p.Pro373Leu	p.P373L	ENST00000275493	NM_005228.3	373	cCg/cTg	9/28	0.386795916842939	5	FACETS	0.665	0.591	0.744			1	SUBCLONAL	1	TRUE	NA	0.386795916842939	5		359	1204	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511185	148511185	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007024-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	140	471	0	ENST00000320356.2:c.1717A>G	p.Thr573Ala	p.T573A	ENST00000320356	NM_004456.4	573	Acc/Gcc	15/20	0.292216620823631	3	FACETS	0.983	0.895	1	0.491	0.447	0.538	CLONAL	1	TRUE	1	0.386795916842939	3		471	879	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711891	89711891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007024-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	120	276	0	ENST00000371953.3:c.509G>A	p.Ser170Asn	p.S170N	ENST00000371953	NM_000314.4	170	aGt/aAt	6/9	0.386795916842939	1	FACETS	0.864	0.783	0.95	0.864	0.783	0.95	CLONAL	1	TRUE	0	0.386795916842939	1		276	579	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061268	38061268	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007024-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	132	547	1	ENST00000250448.2:c.721G>T	p.Gly241Cys	p.G241C	ENST00000250448	NM_004496.3	241	Ggc/Tgc	2/2	0.386795916842939	1	FACETS	0.903	0.822	0.987	0.903	0.822	0.987	CLONAL	1	TRUE	0	0.386795916842939	1		548	610	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829734	76829734	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007024-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1288	139	598	0	ENST00000373344.5:c.6307A>T	p.Asn2103Tyr	p.N2103Y	ENST00000373344	NM_000489.3	2103	Aat/Tat	28/35	1	2	FACETS	0.504	0.457	0.553	0.504	0.457	0.553	SUBCLONAL	1	TRUE	1	0.386795916842939	2		598	1427	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	117	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.920184739730746	2		280	235	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0007034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	51	331	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	1	2	FACETS	0.187	0.158	0.218	0.187	0.158	0.218	SUBCLONAL	1	TRUE	1	0.920184739730746	2		331	594	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0007034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	293	511	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.884	0.837	0.932	0.884	0.837	0.932	CLONAL	1	TRUE	1	0.920184739730746	2		512	720	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161843	47161846	+	frameshift_variant	Frame_Shift_Del	DEL	CTAA	CTAA	-	novel	NA	P-0007034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	342	465	0	ENST00000409792.3:c.4280_4283del	p.Val1427GlufsTer4	p.V1427Efs*4	ENST00000409792	NM_014159.6	1427	gTTAGa/ga	3/21	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.920184739730746	2		465	730	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106670	27106670	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	22	204	382	0	ENST00000324856.7:c.6281G>A	p.Cys2094Tyr	p.C2094Y	ENST00000324856	NM_006015.4	2094	tGc/tAc	20/20	0.920184739730746	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.920184739730746	1		382	226	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791974	42791974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	61	655	1	ENST00000575354.2:c.778C>T	p.His260Tyr	p.H260Y	ENST00000575354	NM_015125.3	260	Cac/Tac	6/20	0.920184739730746	1	FACETS	0.149	0.128	0.171	0.149	0.128	0.171	SUBCLONAL	1	TRUE	0	0.920184739730746	1		656	480	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799059	42799059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	73	205	373	1	ENST00000575354.2:c.4543C>T	p.Arg1515Cys	p.R1515C	ENST00000575354	NM_015125.3	1515	Cgc/Tgc	20/20	0.920184739730746	1	FACETS	0.865	0.827	0.901	0.865	0.827	0.901	CLONAL	1	TRUE	0	0.920184739730746	1		374	278	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502260	157502260	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	231	368	0	ENST00000346085.5:c.3293del	p.Leu1098ArgfsTer32	p.L1098Rfs*32	ENST00000346085	NM_020732.3	1098	cTg/cg	12/20	1	2	FACETS	0.91	0.856	0.964	0.91	0.856	0.964	CLONAL	1	TRUE	1	0.920184739730746	2		368	552	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0007044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	155	506	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.196740139794927	5	FACETS	0.839	0.769	0.912	0.629	0.576	0.684	CLONAL	3	TRUE	1	0.200195787961488	5		506	800	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574034	7574034	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0007044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	86	525	0	ENST00000269305.4:c.994-1G>T		p.X332_splice	ENST00000269305	NM_001126112.2	332			0.158169790637346	1	FACETS	0.883	0.78	0.993	0.883	0.78	0.993	CLONAL	1	TRUE	0	0.200195787961488	1		525	876	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979391	2979391	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs563898269	NA	P-0007044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	231	377	0	ENST00000396946.4:c.856A>G	p.Ile286Val	p.I286V	ENST00000396946	NM_032415.4	286	Atc/Gtc	6/25	0.196740139794927	5	FACETS	0.889	0.83	0.949	0.889	0.83	0.949	CLONAL	4	TRUE	1	0.200195787961488	5		377	844	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620429	43620429	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	113	482	0	ENST00000355710.3:c.3038G>A	p.Arg1013Lys	p.R1013K	ENST00000355710	NM_020975.4	1013	aGa/aAa	18/20	0.139164127844084	3	FACETS	1	0.983	1	0.736	0.662	0.814	CLONAL	1	TRUE	1	0.200195787961488	3		482	844	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104357048	104357048	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	103	387	0	ENST00000369902.3:c.908A>C	p.Lys303Thr	p.K303T	ENST00000369902	NM_016169.3	303	aAa/aCa	7/12	0.139164127844084	3	FACETS	0.771	0.69	0.857	0.771	0.69	0.857	SUBCLONAL	2	TRUE	1	0.200195787961488	3		387	734	SUCCESS
ATM	472	MSKCC	GRCh37	11	108128226	108128226	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	102	464	2	ENST00000278616.4:c.2269G>T	p.Gly757Ter	p.G757*	ENST00000278616	NM_000051.3	757	Gga/Tga	15/63	0.156938388661583	4	FACETS	1	0.979	1	0.701	0.626	0.781	CLONAL	1	TRUE	2	0.200195787961488	4		466	872	SUCCESS
ATM	472	MSKCC	GRCh37	11	108201096	108201096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774281788	NA	P-0007044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	96	329	0	ENST00000278616.4:c.7463G>A	p.Cys2488Tyr	p.C2488Y	ENST00000278616	NM_000051.3	2488	tGt/tAt	50/63	0.156938388661583	4	FACETS	0.808	0.72	0.902	0.808	0.72	0.902	CLONAL	2	TRUE	2	0.200195787961488	4		329	712	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030470	47030470	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	158	557	2	ENST00000377604.3:c.245G>T	p.Arg82Leu	p.R82L	ENST00000377604	NM_001204468.1	82	cGg/cTg	4/24	0.167468533735134	2	FACETS	0.752	0.688	0.819	0.752	0.688	0.819	SUBCLONAL	2	TRUE	0	0.200195787961488	2		559	1050	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007073-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	58	280	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	0	0.34	1		280	261	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164563	36164563	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1340631548	NA	P-0007073-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	74	231	0	ENST00000300305.3:c.1312G>A	p.Gly438Ser	p.G438S	ENST00000300305		438	Ggc/Agc	8/8	0.0761604268034322	0	FACETS	0.651	0.572	0.736			1	INDETERMINATE	1	TRUE	0	0.34	0		231	441	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	198	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.982	1	1	0.994	1	CLONAL	2	TRUE	1	0.383291803973944	2		280	458	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0007130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	259	354	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	1	2	FACETS	1	0.986	1	1	0.996	1	CLONAL	2	TRUE	1	0.383291803973944	2		354	597	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345562	70345562	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	510	529	0	ENST00000374080.3:c.2421A>T	p.Leu807Phe	p.L807F	ENST00000374080		807	ttA/ttT	17/45	1	2	FACETS	0.862	0.83	0.894	1	0.998	1	CLONAL	3	TRUE	1	0.383291803973944	2		529	1029	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	19	166	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	1	2	FACETS	0.312	0.237	0.399	0.312	0.237	0.399	SUBCLONAL	1	TRUE	1	0.53	2		166	230	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	231	1089	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	0.762	0.71	0.816	0.762	0.71	0.816	SUBCLONAL	1	TRUE	1	0.53	2		1090	1144	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851255	156851255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1480681042	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	49	500	2	ENST00000524377.1:c.2212G>A	p.Asp738Asn	p.D738N	ENST00000524377	NM_002529.3	738	Gac/Aac	17/17	1	2	FACETS	0.304	0.257	0.355	0.304	0.257	0.355	SUBCLONAL	1	TRUE	1	0.53	2		502	609	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	137	257	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.53	2		260	486	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532585	63532585	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267606674	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	160	358	2	ENST00000307078.5:c.1994del	p.Gly665AlafsTer24	p.G665Afs*24	ENST00000307078	NM_004655.3	665	gGc/gc	8/11	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.53	2		360	604	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430901	181430901	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	192	582	1	ENST00000325404.1:c.758del	p.Pro253LeufsTer21	p.P253Lfs*21	ENST00000325404	NM_003106.3	251	agC/ag	1/1	1	2	FACETS	0.978	0.907	1	0.978	0.907	1	CLONAL	1	TRUE	1	0.53	2		583	741	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	173	463	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.808	0.745	0.874	0.808	0.745	0.874	CLONAL	1	TRUE	1	0.53	2		463	808	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	169	401	1	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.987	0.911	1	0.987	0.911	1	CLONAL	1	TRUE	1	0.53	2		402	646	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	183	368	7	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.53	2		375	664	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933400	39933400	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	168	487	0	ENST00000378444.4:c.1199del	p.Gly400AlafsTer42	p.G400Afs*42	ENST00000378444	NM_001123385.1	400	gGc/gc	4/15	1	2	FACETS	0.906	0.835	0.979	0.906	0.835	0.979	CLONAL	1	TRUE	1	0.53	2		487	700	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426860	6426860	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554263326	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	131	456	0	ENST00000356142.4:c.53G>A	p.Cys18Tyr	p.C18Y	ENST00000356142	NM_018890.3	18	tGc/tAc	2/7	1	2	FACETS	0.756	0.687	0.827	0.756	0.687	0.827	SUBCLONAL	1	TRUE	1	0.53	2		456	654	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550422	39550423	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	rs772354291	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	71	279	1	ENST00000262039.4:c.531+9dup		p.X177_splice	ENST00000262039	NM_002647.2	177			1	2	FACETS	0.55	0.481	0.624	0.55	0.481	0.624	SUBCLONAL	1	TRUE	1	0.53	2		280	487	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344186	118344186	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs782297546	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	139	305	0	ENST00000534358.1:c.2318del	p.Pro773ArgfsTer8	p.P773Rfs*8	ENST00000534358	NM_005933.3	771	aCc/ac	3/36	1	2	FACETS	0.87	0.795	0.948	0.87	0.795	0.948	CLONAL	1	TRUE	1	0.53	2		305	603	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760106	133760106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2229071	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	27	422	0	ENST00000318560.5:c.2429C>T	p.Pro810Leu	p.P810L	ENST00000318560	NM_005157.4	810	cCg/cTg	11/11	1	2	FACETS	0.214	0.17	0.265	0.214	0.17	0.265	SUBCLONAL	1	TRUE	1	0.53	2		422	476	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332272	70332273	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1446158817	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	169	684	1	ENST00000373644.4:c.184dup	p.Thr62AsnfsTer4	p.T62Nfs*4	ENST00000373644	NM_030625.2	59	-/A	2/12	1	2	FACETS	0.76	0.699	0.823	0.76	0.699	0.823	SUBCLONAL	1	TRUE	1	0.53	2		685	839	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	178	581	1	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.53	2		582	579	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271190	38271190	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs775166971	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	101	263	0	ENST00000425967.3:c.2518C>T	p.Arg840Ter	p.R840*	ENST00000425967	NM_001174067.1	840	Cga/Tga	19/19	0.3	3	FACETS	1	0.935	1			1	INDETERMINATE	1	TRUE	NA	0.53	3		263	457	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	62	380	0	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	1	2	FACETS	0.493	0.426	0.564	0.493	0.426	0.564	SUBCLONAL	1	TRUE	1	0.53	2		380	475	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795016	42795016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150818299	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	192	411	0	ENST00000575354.2:c.2096C>T	p.Ala699Val	p.A699V	ENST00000575354	NM_015125.3	699	gCg/gTg	10/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.53	2		411	584	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440943	56440943	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786205215	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	230	415	3	ENST00000407977.2:c.394C>T	p.Arg132Ter	p.R132*	ENST00000407977		132	Cga/Tga	4/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.53	2		418	732	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443613	52443613	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	212	390	0	ENST00000460680.1:c.79del	p.Val27CysfsTer45	p.V27Cfs*45	ENST00000460680	NM_004656.3	27	Gtg/tg	3/17	1	2	FACETS	0.942	0.877	1	0.942	0.877	1	CLONAL	1	TRUE	1	0.53	2		390	849	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671655	67671655	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1400980130	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	45	511	0	ENST00000264010.4:c.2070del	p.Glu691SerfsTer30	p.E691Sfs*30	ENST00000264010	NM_006565.3	688	gtA/gt	12/12	1	2	FACETS	0.244	0.204	0.288	0.244	0.204	0.288	SUBCLONAL	1	TRUE	1	0.53	2		511	696	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533905	63533905	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	115	264	0	ENST00000307078.5:c.1249del	p.Ala417ArgfsTer41	p.A417Rfs*41	ENST00000307078	NM_004655.3	417	Gcg/cg	6/11	1	2	FACETS	0.939	0.851	1	0.939	0.851	1	CLONAL	1	TRUE	1	0.53	2		264	462	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	88	240	0	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	0.776	0.691	0.866	0.776	0.691	0.866	SUBCLONAL	1	TRUE	1	0.53	2		240	428	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578397	7578398	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	131	309	0	ENST00000269305.4:c.532dup	p.His178ProfsTer3	p.H178Pfs*3	ENST00000269305	NM_001126112.2	178	cac/cCac	5/11	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.53	2		309	475	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231611	5231611	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755108907	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	95	34	80	0	ENST00000357368.4:c.1865del	p.Pro622LeufsTer16	p.P622Lfs*16	ENST00000357368	NM_002850.3	622	cCt/ct	14/38	1	2	FACETS	0.995	0.829	1	0.995	0.829	1	CLONAL	1	TRUE	1	0.53	2		80	129	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	189	455	5	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.53	2		460	640	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	134	544	7	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.53	2		551	479	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795104	242795104	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	37	448	2	ENST00000334409.5:c.105del	p.Thr36ProfsTer9	p.T36Pfs*9	ENST00000334409	NM_005018.2	35	ccC/cc	2/5	1	2	FACETS	0.258	0.212	0.309	0.258	0.212	0.309	SUBCLONAL	1	TRUE	1	0.53	2		450	542	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740439	58740439	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs758630849	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	253	726	1	ENST00000305921.3:c.1349del	p.Leu450Ter	p.L450*	ENST00000305921	NM_003620.3	448	aaT/aa	6/6	1	2	FACETS	0.893	0.836	0.952	0.893	0.836	0.952	CLONAL	1	TRUE	1	0.53	2		727	1069	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136799	2136799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137854153	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	101	568	0	ENST00000219476.3:c.4916G>A	p.Arg1639His	p.R1639H	ENST00000219476	NM_000548.3	1639	cGc/cAc	38/42	1	2	FACETS	0.537	0.48	0.597	0.537	0.48	0.597	SUBCLONAL	1	TRUE	1	0.53	2		568	710	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753012	57753012	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs772701630	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	191	457	5	ENST00000274289.3:c.1004del	p.Leu335CysfsTer68	p.L335Cfs*68	ENST00000274289	NM_006622.3	335	tTg/tg	7/14	0.185365905163266	3	FACETS	1	0.94	1	0.509	0.471	0.548	INDETERMINATE	1	TRUE	1	0.53	3		462	896	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41223240	41223240	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs56119278	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	142	320	0	ENST00000357654.3:c.4691T>C	p.Leu1564Pro	p.L1564P	ENST00000357654	NM_007294.3	1564	cTg/cCg	15/23	0.185365905163266	0	FACETS	0.433	0.396	0.471			1	INDETERMINATE	1	TRUE	0	0.53	0		320	582	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	245	520	3	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	0.995	0.931	1	0.995	0.931	1	CLONAL	1	TRUE	1	0.53	2		523	929	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935323	36935323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs747437399	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	263	593	6	ENST00000361632.4:c.1404del	p.Ser469AlafsTer22	p.S469Afs*22	ENST00000361632		468	ccC/cc	10/16	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.53	2		599	831	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347983	347983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760961378	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	152	405	3	ENST00000262320.3:c.1523del	p.Gly508ValfsTer197	p.G508Vfs*197	ENST00000262320	NM_003502.3	508	gGt/gt	6/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.53	2		408	537	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202139625	202139626	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	213	456	2	ENST00000358485.4:c.790dup	p.Val264GlyfsTer13	p.V264Gfs*13	ENST00000358485	NM_001080125.1	262	-/G	6/9	1	2	FACETS	0.975	0.908	1	0.975	0.908	1	CLONAL	1	TRUE	1	0.53	2		458	824	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383610	42383610	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	183	461	6	ENST00000221972.3:c.390del	p.Arg131GlyfsTer61	p.R131Gfs*61	ENST00000221972	NM_021601.3	129	Ccc/cc	3/5	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.53	2		467	662	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463298	25463300	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs761103716	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	26	328	0	ENST00000264709.3:c.2193_2195del	p.Phe732del	p.F732del	ENST00000264709	NM_175629.2	731	ttCTTt/ttt	19/23	1	2	FACETS	0.19	0.15	0.236	0.19	0.15	0.236	SUBCLONAL	1	TRUE	1	0.53	2		328	517	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514608	103514608	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370885325	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	171	368	1	ENST00000355739.4:c.1109G>A	p.Arg370His	p.R370H	ENST00000355739	NM_000123.3	370	cGt/cAt	8/15	1	2	FACETS	0.891	0.822	0.963	0.891	0.822	0.963	CLONAL	1	TRUE	1	0.53	2		369	724	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931471	131931471	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753002904	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	129	292	2	ENST00000265335.6:c.2176C>T	p.Arg726Cys	p.R726C	ENST00000265335		726	Cgt/Tgt	13/25	1	2	FACETS	0.856	0.779	0.936	0.856	0.779	0.936	CLONAL	1	TRUE	1	0.53	2		294	569	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484261	57484261	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	138	288	6	ENST00000371085.3:c.575C>T	p.Pro192Leu	p.P192L	ENST00000371085	NM_000516.4	192	cCg/cTg	7/13	1	2	FACETS	0.821	0.75	0.896	0.821	0.75	0.896	CLONAL	1	TRUE	1	0.53	2		294	634	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285913	38285914	+	inframe_insertion	In_Frame_Ins	INS	-	-	TCA	rs138489552	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	200	516	2	ENST00000425967.3:c.495_497dup	p.Asp166dup	p.D166dup	ENST00000425967	NM_001174067.1	166	gac/gaTGAc	5/19	0.3	3	FACETS	1	0.967	1			1	INDETERMINATE	1	TRUE	NA	0.53	3		518	889	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204736165	204736166	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	157	536	0	ENST00000302823.3:c.529dup	p.Tyr177LeufsTer2	p.Y177Lfs*2	ENST00000302823	NM_005214.4	174	-/T	3/4	1	2	FACETS	0.643	0.588	0.699	0.643	0.588	0.699	SUBCLONAL	1	TRUE	1	0.53	2		536	922	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533938	63533939	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	92	195	0	ENST00000307078.5:c.1214_1215dup	p.Gly406ArgfsTer53	p.G406Rfs*53	ENST00000307078	NM_004655.3	405	-/AG	6/11	1	2	FACETS	0.989	0.887	1	0.989	0.887	1	CLONAL	1	TRUE	1	0.53	2		195	351	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494651	2494651	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	242	492	2	ENST00000355716.4:c.791T>C	p.Val264Ala	p.V264A	ENST00000355716	NM_003820.2	264	gTc/gCc	8/8	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.53	2		494	817	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777114	9777114	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs765061150	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	198	472	2	ENST00000377346.4:c.878C>A	p.Ala293Asp	p.A293D	ENST00000377346	NM_005026.3	293	gCc/gAc	7/24	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.53	2		474	674	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259672	11259672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	221	472	0	ENST00000361445.4:c.4033C>T	p.Leu1345Phe	p.L1345F	ENST00000361445	NM_004958.3	1345	Ctc/Ttc	27/58	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.53	2		472	766	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258016	16258016	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	149	374	0	ENST00000375759.3:c.5281A>G	p.Lys1761Glu	p.K1761E	ENST00000375759	NM_015001.2	1761	Aaa/Gaa	11/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.53	2		374	525	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089512	27089512	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1379582665	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	103	498	0	ENST00000324856.7:c.2468A>G	p.Tyr823Cys	p.Y823C	ENST00000324856	NM_006015.4	823	tAc/tGc	8/20	1	2	FACETS	0.523	0.468	0.582	0.523	0.468	0.582	SUBCLONAL	1	TRUE	1	0.53	2		498	743	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094396	27094396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	194	367	2	ENST00000324856.7:c.3104C>T	p.Ala1035Val	p.A1035V	ENST00000324856	NM_006015.4	1035	gCc/gTc	11/20	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.53	2		369	656	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106327	27106327	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780084398	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	197	391	2	ENST00000324856.7:c.5938C>T	p.Arg1980Cys	p.R1980C	ENST00000324856	NM_006015.4	1980	Cgc/Tgc	20/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.53	2		393	721	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107132	27107132	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	136	200	0	ENST00000324856.7:c.6743A>T	p.His2248Leu	p.H2248L	ENST00000324856	NM_006015.4	2248	cAc/cTc	20/20	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.53	2		200	477	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803817	43803817	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs148434485	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	157	599	0	ENST00000372470.3:c.127C>T	p.Arg43Ter	p.R43*	ENST00000372470	NM_005373.2	43	Cga/Tga	2/12	1	2	FACETS	0.91	0.836	0.986	0.91	0.836	0.986	CLONAL	1	TRUE	1	0.53	2		599	651	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799143	45799143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755653922	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	217	511	1	ENST00000450313.1:c.290G>A	p.Arg97Gln	p.R97Q	ENST00000450313	NM_012222.2	97	cGa/cAa	3/16	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.53	2		512	757	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78421008	78421008	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	173	314	0	ENST00000370768.2:c.1712A>G	p.Gln571Arg	p.Q571R	ENST00000370768	NM_003902.3	571	cAg/cGg	18/20	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.53	2		314	634	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564969	226564969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776941221	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	163	428	2	ENST00000366794.5:c.1781C>T	p.Thr594Met	p.T594M	ENST00000366794	NM_001618.3	594	aCg/aTg	13/23	1	2	FACETS	0.868	0.798	0.94	0.868	0.798	0.94	CLONAL	1	TRUE	1	0.53	2		430	709	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028226	48028226	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881801	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	202	522	0	ENST00000234420.5:c.3104G>A	p.Arg1035Gln	p.R1035Q	ENST00000234420	NM_000179.2	1035	cGa/cAa	4/10	1	2	FACETS	0.878	0.815	0.943	0.878	0.815	0.943	CLONAL	1	TRUE	1	0.53	2		522	868	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030679	48030679	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660564	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	152	451	0	ENST00000234420.5:c.3293G>A	p.Cys1098Tyr	p.C1098Y	ENST00000234420	NM_000179.2	1098	tGc/tAc	5/10	1	2	FACETS	0.748	0.685	0.814	0.748	0.685	0.814	SUBCLONAL	1	TRUE	1	0.53	2		451	767	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907671	111907671	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1047792118	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	207	521	1	ENST00000393256.3:c.445G>A	p.Ala149Thr	p.A149T	ENST00000393256	NM_006538.4	149	Gcc/Acc	3/4	1	2	FACETS	0.821	0.762	0.882	0.821	0.762	0.882	CLONAL	1	TRUE	1	0.53	2		522	951	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128038136	128038136	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1225262521	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	229	419	2	ENST00000285398.2:c.1414C>T	p.Arg472Cys	p.R472C	ENST00000285398	NM_000122.1	472	Cgc/Tgc	9/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.53	2		421	776	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270084	198270084	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777705664	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	196	433	0	ENST00000335508.6:c.1352G>A	p.Arg451Gln	p.R451Q	ENST00000335508	NM_012433.2	451	cGa/cAa	10/25	1	2	FACETS	0.881	0.816	0.947	0.881	0.816	0.947	CLONAL	1	TRUE	1	0.53	2		433	840	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285851	198285851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1360783408	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	138	368	0	ENST00000335508.6:c.202G>A	p.Asp68Asn	p.D68N	ENST00000335508	NM_012433.2	68	Gat/Aat	3/25	1	2	FACETS	0.65	0.592	0.711	0.65	0.592	0.711	SUBCLONAL	1	TRUE	1	0.53	2		368	801	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12650368	12650368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	171	396	1	ENST00000251849.4:c.478C>T	p.Leu160Phe	p.L160F	ENST00000251849	NM_002880.3	160	Ctc/Ttc	5/17	1	2	FACETS	0.83	0.765	0.898	0.83	0.765	0.898	CLONAL	1	TRUE	1	0.53	2		397	777	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162920	47162920	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1302035546	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	169	452	2	ENST00000409792.3:c.3206T>C	p.Val1069Ala	p.V1069A	ENST00000409792	NM_014159.6	1069	gTt/gCt	3/21	1	2	FACETS	0.857	0.79	0.927	0.857	0.79	0.927	CLONAL	1	TRUE	1	0.53	2		454	744	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940819	49940819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1489965247	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	419	706	4	ENST00000296474.3:c.224G>A	p.Arg75His	p.R75H	ENST00000296474	NM_002447.2	75	cGc/cAc	1/20	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.53	2		710	1217	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52682380	52682380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	99	501	1	ENST00000394830.3:c.793C>T	p.Pro265Ser	p.P265S	ENST00000394830	NM_018313.4	265	Cct/Tct	8/30	1	2	FACETS	0.6	0.536	0.667	0.6	0.536	0.667	SUBCLONAL	1	TRUE	1	0.53	2		502	623	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417882	138417882	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	168	349	3	ENST00000289153.2:c.1637C>A	p.Pro546His	p.P546H	ENST00000289153	NM_006219.2	546	cCc/cAc	11/22	1	2	FACETS	0.796	0.733	0.862	0.796	0.733	0.862	SUBCLONAL	1	TRUE	1	0.53	2		352	796	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190762	185190762	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	125	288	0	ENST00000265026.3:c.1644-1G>T		p.X548_splice	ENST00000265026	NM_004721.4	548			1	2	FACETS	0.907	0.825	0.993	0.907	0.825	0.993	CLONAL	1	TRUE	1	0.53	2		288	520	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801241	1801241	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199740841	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	121	353	3	ENST00000260795.2:c.370C>T	p.Arg124Trp	p.R124W	ENST00000260795		124	Cgg/Tgg	2/17	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.53	2		356	409	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55524239	55524239	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	140	487	4	ENST00000288135.5:c.58G>A	p.Val20Ile	p.V20I	ENST00000288135	NM_000222.2	20	Gtc/Atc	1/21	1	2	FACETS	0.925	0.846	1	0.925	0.846	1	CLONAL	1	TRUE	1	0.53	2		491	571	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968100	55968100	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	177	427	0	ENST00000263923.4:c.2230G>T	p.Gly744Cys	p.G744C	ENST00000263923	NM_002253.2	744	Ggc/Tgc	15/30	1	2	FACETS	0.85	0.784	0.918	0.85	0.784	0.918	CLONAL	1	TRUE	1	0.53	2		427	786	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218785	66218785	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs746836106	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	95	497	0	ENST00000273854.3:c.2273A>G	p.Asn758Ser	p.N758S	ENST00000273854	NM_004439.5	758	aAt/aGt	13/18	0.185365905163266	3	FACETS	0.718	0.64	0.8	0.359	0.32	0.4	INDETERMINATE	1	TRUE	1	0.53	3		497	632	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467842	66467842	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	185	425	0	ENST00000273854.3:c.427G>T	p.Gly143Ter	p.G143*	ENST00000273854	NM_004439.5	143	Gga/Tga	3/18	0.185365905163266	3	FACETS	1	0.968	1	0.543	0.502	0.586	INDETERMINATE	1	TRUE	1	0.53	3		425	813	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384712	84384712	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	96	343	0	ENST00000321945.7:c.731T>C	p.Val244Ala	p.V244A	ENST00000321945	NM_139076.2	244	gTa/gCa	8/9	0.185365905163266	3	FACETS	0.953	0.853	1	0.476	0.426	0.529	INDETERMINATE	1	TRUE	1	0.53	3		343	481	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391501	84391501	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	33	145	0	ENST00000321945.7:c.331A>G	p.Thr111Ala	p.T111A	ENST00000321945	NM_139076.2	111	Acg/Gcg	5/9	0.185365905163266	3	FACETS	0.474	0.387	0.573	0.237	0.193	0.287	INDETERMINATE	1	TRUE	1	0.53	3		145	332	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187538277	187538277	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	119	407	1	ENST00000441802.2:c.8957G>T	p.Arg2986Met	p.R2986M	ENST00000441802	NM_005245.3	2986	aGg/aTg	11/27	0.185365905163266	3	FACETS	0.978	0.885	1	0.489	0.442	0.538	INDETERMINATE	1	TRUE	1	0.53	3		408	581	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38953624	38953624	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199645898	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	81	299	0	ENST00000357387.3:c.2729G>A	p.Arg910His	p.R910H	ENST00000357387	NM_152756.3	910	cGt/cAt	28/38	0.185365905163266	3	FACETS	0.841	0.743	0.944	0.42	0.371	0.472	INDETERMINATE	1	TRUE	1	0.53	3		299	460	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672801	86672801	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	164	353	0	ENST00000274376.6:c.2288A>G	p.Glu763Gly	p.E763G	ENST00000274376	NM_002890.2	763	gAa/gGa	17/25	0.185365905163266	3	FACETS	0.982	0.903	1	0.491	0.451	0.533	INDETERMINATE	1	TRUE	1	0.53	3		353	797	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672859	86672859	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	62	229	1	ENST00000274376.6:c.2344+2T>C		p.X782_splice	ENST00000274376	NM_002890.2	782			0.185365905163266	3	FACETS	0.722	0.626	0.826	0.361	0.313	0.413	INDETERMINATE	1	TRUE	1	0.53	3		230	410	SUCCESS
APC	324	MSKCC	GRCh37	5	112151246	112151246	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876660572	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	242	509	0	ENST00000257430.4:c.889A>G	p.Thr297Ala	p.T297A	ENST00000257430	NM_000038.5	297	Aca/Gca	9/16	1	2	FACETS	0.923	0.863	0.985	0.923	0.863	0.985	CLONAL	1	TRUE	1	0.53	2		509	989	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149459822	149459822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	160	438	0	ENST00000286301.3:c.385C>T	p.Leu129Phe	p.L129F	ENST00000286301	NM_005211.3	129	Ctc/Ttc	4/22	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.53	2		438	586	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509421	149509421	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	92	529	2	ENST00000261799.4:c.1478G>A	p.Ser493Asn	p.S493N	ENST00000261799	NM_002609.3	493	aGc/aAc	10/23	1	2	FACETS	0.561	0.499	0.627	0.561	0.499	0.627	SUBCLONAL	1	TRUE	1	0.53	2		531	619	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057276	180057276	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	134	470	2	ENST00000261937.6:c.462G>A	p.Met154Ile	p.M154I	ENST00000261937	NM_182925.4	154	atG/atA	4/30	1	2	FACETS	0.908	0.829	0.99	0.908	0.829	0.99	CLONAL	1	TRUE	1	0.53	2		472	557	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250754	26250754	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1231	322	895	2	ENST00000446824.2:c.80G>A	p.Arg27His	p.R27H	ENST00000446824	NM_021018.2	27	cGc/cAc	1/1	0.3	6	FACETS	0.806	0.759	0.854			1	INDETERMINATE	2	TRUE	NA	0.53	6		897	1553	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30668387	30668387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779653282	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	221	630	2	ENST00000376406.3:c.6125G>A	p.Cys2042Tyr	p.C2042Y	ENST00000376406	NM_014641.2	2042	tGc/tAc	15/15	0.185365905163266	3	FACETS	1	0.939	1	0.505	0.47	0.542	INDETERMINATE	1	TRUE	1	0.53	3		632	1044	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288846	33288846	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	149	228	2	ENST00000374542.5:c.706T>G	p.Phe236Val	p.F236V	ENST00000374542	NM_001141970.1	236	Ttt/Gtt	3/8	0.3	6	FACETS	1	0.946	1			1	INDETERMINATE	2	TRUE	NA	0.53	6		230	557	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068015	94068015	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	228	676	3	ENST00000369303.4:c.947A>G	p.Tyr316Cys	p.Y316C	ENST00000369303	NM_004440.3	316	tAt/tGt	4/17	0.185365905163266	3	FACETS	0.95	0.884	1	0.475	0.442	0.509	INDETERMINATE	1	TRUE	1	0.53	3		679	1146	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687384	117687384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1476549252	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	178	419	3	ENST00000368508.3:c.2667G>A	p.Met889Ile	p.M889I	ENST00000368508	NM_002944.2	889	atG/atA	18/43	0.0978863208689058	0	FACETS	0.43	0.397	0.464			1	INDETERMINATE	1	TRUE	0	0.53	0		422	734	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971366	13971366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568607536	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	41	369	0	ENST00000405192.2:c.563G>A	p.Arg188His	p.R188H	ENST00000405192	NM_001163147.1	188	cGc/cAc	8/12	1	2	FACETS	0.221	0.184	0.264	0.221	0.184	0.264	SUBCLONAL	1	TRUE	1	0.53	2		369	699	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468059	50468059	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	114	309	1	ENST00000331340.3:c.1294C>T	p.His432Tyr	p.H432Y	ENST00000331340	NM_006060.4	432	Cac/Tac	8/8	1	2	FACETS	0.909	0.824	0.999	0.909	0.824	0.999	CLONAL	1	TRUE	1	0.53	2		310	473	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852243	128852243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149170801	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	45	444	1	ENST00000249373.3:c.2315G>A	p.Arg772His	p.R772H	ENST00000249373	NM_005631.4	772	cGc/cAc	12/12	1	2	FACETS	0.273	0.228	0.322	0.273	0.228	0.322	SUBCLONAL	1	TRUE	1	0.53	2		445	623	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845414	151845414	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769432614	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	200	361	0	ENST00000262189.6:c.13598G>A	p.Arg4533Gln	p.R4533Q	ENST00000262189	NM_170606.2	4533	cGa/cAa	52/59	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.53	2		361	746	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737414	145737414	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	115	276	1	ENST00000428558.2:c.3273G>T	p.Gln1091His	p.Q1091H	ENST00000428558	NM_004260.3	1091	caG/caT	20/22	0.500725622212027	3	FACETS	1	0.964	1	0.565	0.511	0.621	CLONAL	1	TRUE	1	0.53	3		277	486	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739038	145739038	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	227	420	1	ENST00000428558.2:c.2117A>G	p.Tyr706Cys	p.Y706C	ENST00000428558	NM_004260.3	706	tAc/tGc	13/22	0.500725622212027	3	FACETS	1	0.979	1	0.56	0.522	0.6	CLONAL	1	TRUE	1	0.53	3		421	967	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87359921	87359921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	42	485	1	ENST00000277120.3:c.1229C>T	p.Thr410Ile	p.T410I	ENST00000277120		410	aCc/aTc	11/19	1	2	FACETS	0.209	0.173	0.248	0.209	0.173	0.248	SUBCLONAL	1	TRUE	1	0.53	2		486	760	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760739	133760739	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370992010	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	191	518	0	ENST00000318560.5:c.3062G>A	p.Arg1021Gln	p.R1021Q	ENST00000318560	NM_005157.4	1021	cGg/cAg	11/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.53	2		518	639	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391913	139391913	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	241	578	1	ENST00000277541.6:c.6278T>C	p.Met2093Thr	p.M2093T	ENST00000277541	NM_017617.3	2093	aTg/aCg	34/34	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.53	2		579	806	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395287	139395287	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs545259523	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	107	216	2	ENST00000277541.6:c.5651C>T	p.Pro1884Leu	p.P1884L	ENST00000277541	NM_017617.3	1884	cCg/cTg	31/34	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.53	2		218	352	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137232	64137232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	232	518	1	ENST00000334205.4:c.1664C>T	p.Ala555Val	p.A555V	ENST00000334205	NM_003942.2	555	gCg/gTg	14/17	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.53	2		519	779	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69633614	69633614	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	30	67	1	ENST00000334134.2:c.88G>T	p.Gly30Cys	p.G30C	ENST00000334134	NM_005247.2	30	Ggc/Tgc	1/3	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.53	2		68	88	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94180576	94180576	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	134	523	0	ENST00000323929.3:c.1592C>A	p.Ser531Tyr	p.S531Y	ENST00000323929	NM_005591.3	531	tCt/tAt	15/20	1	2	FACETS	0.553	0.502	0.607	0.553	0.502	0.607	SUBCLONAL	1	TRUE	1	0.53	2		523	914	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102196012	102196012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	391	688	1	ENST00000263464.3:c.772C>T	p.Arg258Cys	p.R258C	ENST00000263464	NM_001165.4	258	Cgc/Tgc	2/9	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.53	2		689	1400	SUCCESS
ATM	472	MSKCC	GRCh37	11	108100001	108100001	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	96	306	0	ENST00000278616.4:c.282G>A	p.Met94Ile	p.M94I	ENST00000278616	NM_000051.3	94	atG/atA	4/63	1	2	FACETS	0.705	0.63	0.784	0.705	0.63	0.784	SUBCLONAL	1	TRUE	1	0.53	2		306	514	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	493279	493279	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	136	454	0	ENST00000399788.2:c.284C>A	p.Ala95Glu	p.A95E	ENST00000399788	NM_001042603.1	95	gCa/gAa	3/28	1	2	FACETS	0.829	0.756	0.905	0.829	0.756	0.905	CLONAL	1	TRUE	1	0.53	2		454	619	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398228	25398228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	155	370	1	ENST00000311936.3:c.91G>A	p.Glu31Lys	p.E31K	ENST00000311936	NM_004985.3	31	Gaa/Aaa	2/5	1	2	FACETS	0.725	0.664	0.788	0.725	0.664	0.788	SUBCLONAL	1	TRUE	1	0.53	2		371	807	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420871	49420871	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555185969	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	179	421	0	ENST00000301067.7:c.14878C>T	p.Arg4960Ter	p.R4960*	ENST00000301067	NM_003482.3	4960	Cga/Tga	48/54	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.53	2		421	656	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492501	50492501	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	173	404	0	ENST00000394963.4:c.1397T>C	p.Met466Thr	p.M466T	ENST00000394963	NM_003076.4	466	aTg/aCg	12/13	1	2	FACETS	0.974	0.9	1	0.974	0.9	1	CLONAL	1	TRUE	1	0.53	2		404	670	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435424	121435424	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs769492388	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	95	481	0	ENST00000257555.6:c.1457A>G	p.Gln486Arg	p.Q486R	ENST00000257555		486	cAg/cGg	7/10	0.3	2	FACETS	0.704	0.629	0.784			1	INDETERMINATE	1	TRUE	NA	0.53	2		481	509	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608473	28608473	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	73	475	1	ENST00000241453.7:c.1669G>T	p.Val557Phe	p.V557F	ENST00000241453	NM_004119.2	557	Gtt/Ttt	13/24	1	2	FACETS	0.509	0.446	0.577	0.509	0.446	0.577	SUBCLONAL	1	TRUE	1	0.53	2		476	541	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636175	28636175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764656426	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	196	468	1	ENST00000241453.7:c.197C>T	p.Ala66Val	p.A66V	ENST00000241453	NM_004119.2	66	gCg/gTg	3/24	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.53	2		469	691	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32910543	32910543	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	132	700	0	ENST00000380152.3:c.2051A>G	p.Gln684Arg	p.Q684R	ENST00000380152		684	cAg/cGg	11/27	1	2	FACETS	0.646	0.587	0.708	0.646	0.587	0.708	SUBCLONAL	1	TRUE	1	0.53	2		700	771	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972653	32972653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	110	330	1	ENST00000380152.3:c.10003G>A	p.Glu3335Lys	p.E3335K	ENST00000380152		3335	Gaa/Aaa	27/27	1	2	FACETS	0.783	0.706	0.864	0.783	0.706	0.864	SUBCLONAL	1	TRUE	1	0.53	2		331	530	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134151	41134151	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1421986524	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	238	688	2	ENST00000379561.5:c.1477G>T	p.Gly493Cys	p.G493C	ENST00000379561	NM_002015.3	493	Ggc/Tgc	2/3	1	2	FACETS	0.866	0.808	0.925	0.866	0.808	0.925	CLONAL	1	TRUE	1	0.53	2		690	1037	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239857	41239857	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	201	515	1	ENST00000379561.5:c.493T>C	p.Tyr165His	p.Y165H	ENST00000379561	NM_002015.3	165	Tac/Cac	1/3	1	2	FACETS	0.965	0.896	1	0.965	0.896	1	CLONAL	1	TRUE	1	0.53	2		516	786	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73345226	73345226	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1162786323	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	146	453	2	ENST00000377767.4:c.1663G>A	p.Val555Met	p.V555M	ENST00000377767	NM_014953.3	555	Gtg/Atg	12/21	1	2	FACETS	0.705	0.644	0.769	0.705	0.644	0.769	SUBCLONAL	1	TRUE	1	0.53	2		455	781	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524735	103524735	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	133	350	1	ENST00000355739.4:c.2866G>A	p.Asp956Asn	p.D956N	ENST00000355739	NM_000123.3	956	Gac/Aac	13/15	1	2	FACETS	0.7	0.637	0.766	0.7	0.637	0.766	SUBCLONAL	1	TRUE	1	0.53	2		351	717	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435138	110435138	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746947070	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	183	342	0	ENST00000375856.3:c.3263C>T	p.Ala1088Val	p.A1088V	ENST00000375856	NM_003749.2	1088	gCg/gTg	1/2	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.53	2		342	596	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986922	36986922	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	35	296	0	ENST00000354822.5:c.767A>G	p.Gln256Arg	p.Q256R	ENST00000354822	NM_001079668.2	256	cAg/cGg	3/3	1	2	FACETS	0.329	0.27	0.396	0.329	0.27	0.396	SUBCLONAL	1	TRUE	1	0.53	2		296	401	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95596439	95596439	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	171	363	0	ENST00000393063.1:c.529T>C	p.Cys177Arg	p.C177R	ENST00000393063	NM_030621.3	177	Tgt/Cgt	6/28	1	2	FACETS	0.935	0.863	1	0.935	0.863	1	CLONAL	1	TRUE	1	0.53	2		363	690	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99482542	99482542	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	196	516	1	ENST00000268035.6:c.3410C>T	p.Ala1137Val	p.A1137V	ENST00000268035	NM_000875.3	1137	gCt/gTt	18/21	1	2	FACETS	0.982	0.912	1	0.982	0.912	1	CLONAL	1	TRUE	1	0.53	2		517	753	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120493	2120493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370324876	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	220	512	2	ENST00000219476.3:c.1753C>T	p.Arg585Cys	p.R585C	ENST00000219476	NM_000548.3	585	Cgt/Tgt	17/42	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.53	2		514	714	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225955	2225955	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs756230613	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	123	375	0	ENST00000326181.6:c.1746+1G>A		p.X582_splice	ENST00000326181	NM_032271.2	582			1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.53	2		375	408	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778516	3778516	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	157	701	1	ENST00000262367.5:c.6532C>T	p.His2178Tyr	p.H2178Y	ENST00000262367	NM_004380.2	2178	Cac/Tac	31/31	1	2	FACETS	0.869	0.798	0.942	0.869	0.798	0.942	CLONAL	1	TRUE	1	0.53	2		702	682	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779017	3779017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	67	284	0	ENST00000262367.5:c.6031C>T	p.Pro2011Ser	p.P2011S	ENST00000262367	NM_004380.2	2011	Ccc/Tcc	31/31	1	2	FACETS	0.637	0.556	0.724	0.637	0.556	0.724	SUBCLONAL	1	TRUE	1	0.53	2		284	397	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788590	3788590	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	140	497	0	ENST00000262367.5:c.4364T>A	p.Ile1455Asn	p.I1455N	ENST00000262367	NM_004380.2	1455	aTt/aAt	26/31	1	2	FACETS	0.948	0.868	1	0.948	0.868	1	CLONAL	1	TRUE	1	0.53	2		497	557	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858775	9858775	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1399604502	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	110	295	0	ENST00000330684.3:c.2626A>G	p.Ile876Val	p.I876V	ENST00000330684	NM_001134407.1	876	Att/Gtt	13/13	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.53	2		295	402	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836327	89836327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	239	537	1	ENST00000389301.3:c.2422C>T	p.Pro808Ser	p.P808S	ENST00000389301	NM_000135.2	808	Cct/Tct	26/43	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.53	2		538	814	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858392	89858392	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	211	487	1	ENST00000389301.3:c.1168C>A	p.Leu390Ile	p.L390I	ENST00000389301	NM_000135.2	390	Ctc/Atc	13/43	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.53	2		488	725	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17117001	17117001	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752161850	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	180	481	1	ENST00000285071.4:c.1708C>T	p.Arg570Cys	p.R570C	ENST00000285071	NM_144997.5	570	Cgc/Tgc	14/14	1	2	FACETS	0.946	0.875	1	0.946	0.875	1	CLONAL	1	TRUE	1	0.53	2		482	718	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528119	29528119	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	134	363	0	ENST00000356175.3:c.1127T>C	p.Met376Thr	p.M376T	ENST00000356175	NM_000267.3	376	aTg/aCg	10/57	1	2	FACETS	0.793	0.722	0.866	0.793	0.722	0.866	SUBCLONAL	1	TRUE	1	0.53	2		363	638	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804180	46804180	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	258	621	0	ENST00000290295.7:c.827C>T	p.Ala276Val	p.A276V	ENST00000290295	NM_006361.5	276	gCc/gTc	2/2	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.53	2		621	873	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134201	11134201	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	49	401	0	ENST00000358026.2:c.2867T>C	p.Leu956Pro	p.L956P	ENST00000358026	NM_001128849.1	956	cTg/cCg	20/36	1	2	FACETS	0.304	0.257	0.355	0.304	0.257	0.355	SUBCLONAL	1	TRUE	1	0.53	2		401	609	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145789	11145789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	173	521	1	ENST00000358026.2:c.4151C>T	p.Thr1384Met	p.T1384M	ENST00000358026	NM_001128849.1	1384	aCg/aTg	29/36	1	2	FACETS	0.986	0.911	1	0.986	0.911	1	CLONAL	1	TRUE	1	0.53	2		522	662	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289660	15289660	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	213	622	2	ENST00000263388.2:c.3811C>A	p.Leu1271Met	p.L1271M	ENST00000263388	NM_000435.2	1271	Ctg/Atg	23/33	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.53	2		624	789	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349600	15349600	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	154	370	2	ENST00000263377.2:c.3974G>T	p.Arg1325Met	p.R1325M	ENST00000263377	NM_058243.2	1325	aGg/aTg	19/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.53	2		372	517	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18276988	18276988	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	206	405	2	ENST00000222254.8:c.1435A>G	p.Thr479Ala	p.T479A	ENST00000222254	NM_005027.3	479	Act/Gct	12/16	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.53	2		407	769	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867091	45867091	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1260632618	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	148	306	0	ENST00000391945.4:c.1028G>A	p.Arg343Gln	p.R343Q	ENST00000391945	NM_000400.3	343	cGg/cAg	11/23	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.53	2		306	410	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867145	45867145	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs530045760	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	97	338	0	ENST00000391945.4:c.974C>T	p.Thr325Met	p.T325M	ENST00000391945	NM_000400.3	325	aCg/aTg	11/23	1	2	FACETS	0.893	0.801	0.989	0.893	0.801	0.989	CLONAL	1	TRUE	1	0.53	2		338	410	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867491	45867491	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	71	379	1	ENST00000391945.4:c.815+2T>C		p.X272_splice	ENST00000391945	NM_000400.3	272			1	2	FACETS	0.492	0.429	0.559	0.492	0.429	0.559	SUBCLONAL	1	TRUE	1	0.53	2		380	545	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385069	31385069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867242533	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	192	498	3	ENST00000328111.2:c.1454G>A	p.Arg485Gln	p.R485Q	ENST00000328111	NM_006892.3	485	cGa/cAa	14/23	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.53	2		501	697	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46275913	46275913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	203	739	1	ENST00000371998.3:c.3349G>A	p.Ala1117Thr	p.A1117T	ENST00000371998		1117	Gca/Aca	18/23	1	2	FACETS	0.826	0.767	0.888	0.826	0.767	0.888	CLONAL	1	TRUE	1	0.53	2		740	927	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42843873	42843873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748528218	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	71	445	0	ENST00000398585.3:c.1046C>T	p.Ala349Val	p.A349V	ENST00000398585	NM_001135099.1	349	gCg/gTg	10/14	0.185365905163266	3	FACETS	0.407	0.354	0.464	0.203	0.177	0.232	INDETERMINATE	1	TRUE	1	0.53	3		445	833	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30070869	30070869	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373650983	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	212	511	0	ENST00000338641.4:c.1385G>A	p.Arg462His	p.R462H	ENST00000338641	NM_000268.3	462	cGc/cAc	13/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.53	2		511	723	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222384	53222384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556832434	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	154	529	5	ENST00000375401.3:c.4448G>A	p.Arg1483Gln	p.R1483Q	ENST00000375401	NM_004187.3	1483	cGg/cAg	26/26	0.185365905163266	0	FACETS	0.406	0.372	0.441			1	INDETERMINATE	1	TRUE	0	0.53	0		534	673	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53227807	53227807	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	213	527	2	ENST00000375401.3:c.2381T>C	p.Leu794Pro	p.L794P	ENST00000375401	NM_004187.3	794	cTg/cCg	17/26	0.185365905163266	0	FACETS	0.456	0.425	0.489			1	INDETERMINATE	1	TRUE	0	0.53	0		529	828	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245008	53245008	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	91	635	2	ENST00000375401.3:c.932G>A	p.Arg311Lys	p.R311K	ENST00000375401	NM_004187.3	311	aGg/aAg	7/26	0.185365905163266	0	FACETS	0.182	0.161	0.204			1	INDETERMINATE	1	TRUE	0	0.53	0		637	889	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53246988	53246988	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	180	570	0	ENST00000375401.3:c.512C>T	p.Ala171Val	p.A171V	ENST00000375401	NM_004187.3	171	gCc/gTc	4/26	0.185365905163266	0	FACETS	0.41	0.378	0.442			1	INDETERMINATE	1	TRUE	0	0.53	0		570	779	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412806	63412806	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	157	544	1	ENST00000330258.3:c.361C>T	p.Pro121Ser	p.P121S	ENST00000330258	NM_152424.3	121	Cct/Tct	2/2	0.185365905163266	0	FACETS	0.481	0.443	0.521			1	INDETERMINATE	1	TRUE	0	0.53	0		545	579	SUCCESS
AR	367	MSKCC	GRCh37	X	66766208	66766208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	100	272	2	ENST00000374690.3:c.1220G>A	p.Arg407His	p.R407H	ENST00000374690	NM_000044.3	407	cGc/cAc	1/8	0.185365905163266	0	FACETS	0.529	0.478	0.583			1	INDETERMINATE	1	TRUE	0	0.53	0		274	335	SUCCESS
AR	367	MSKCC	GRCh37	X	66766426	66766426	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	38	176	0	ENST00000374690.3:c.1438C>A	p.Pro480Thr	p.P480T	ENST00000374690	NM_000044.3	480	Ccc/Acc	1/8	0.185365905163266	0	FACETS	0.401	0.336	0.472			1	INDETERMINATE	1	TRUE	0	0.53	0		176	168	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938174	76938174	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	49	531	0	ENST00000373344.5:c.2574del	p.Gly859GlufsTer10	p.G859Efs*10	ENST00000373344	NM_000489.3	858	aaA/aa	9/35	0.185365905163266	0	FACETS	0.145	0.123	0.17			1	INDETERMINATE	1	TRUE	0	0.53	0		531	598	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698141	47698145	+	frameshift_variant	Frame_Shift_Del	DEL	AAAAC	AAAAC	-	rs63750474	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	70	460	1	ENST00000233146.2:c.1700_1704del	p.Lys567ArgfsTer3	p.K567Rfs*3	ENST00000233146	NM_000251.2	567	AAAACa/a	11/16	0.185365905163266	0	FACETS	0.312	0.273	0.354			1	INDETERMINATE	1	TRUE	0	0.53	0		461	398	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775476	39775477	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	147	395	0	ENST00000288319.7:c.543dup	p.Ser182GlnfsTer26	p.S182Qfs*26	ENST00000288319	NM_182918.3	181	-/C	4/10	0.185365905163266	3	FACETS	0.98	0.897	1	0.49	0.448	0.534	INDETERMINATE	1	TRUE	1	0.53	3		395	716	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436011	110436011	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	71	316	2	ENST00000375856.3:c.2390del	p.Gly797AlafsTer30	p.G797Afs*30	ENST00000375856	NM_003749.2	797	gGc/gc	1/2	1	2	FACETS	0.5	0.437	0.568	0.5	0.437	0.568	SUBCLONAL	1	TRUE	1	0.53	2		318	536	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588798	52588798	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1559827261	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	178	458	4	ENST00000394830.3:c.4230del	p.Pro1411LeufsTer21	p.P1411Lfs*21	ENST00000394830	NM_018313.4	1410	ggG/gg	27/30	1	2	FACETS	0.909	0.84	0.981	0.909	0.84	0.981	CLONAL	1	TRUE	1	0.53	2		462	739	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295203	1295204	+	upstream_gene_variant	5'Flank	INS	-	-	G	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	72	246	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.927	0.818	1	0.927	0.818	1	CLONAL	1	TRUE	1	0.53	2		246	293	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531806	46531807	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	149	502	0	ENST00000262741.5:c.540dup	p.Leu181ThrfsTer13	p.L181Tfs*13	ENST00000262741	NM_003629.3	180	-/A	5/10	1	2	FACETS	0.795	0.728	0.865	0.795	0.728	0.865	SUBCLONAL	1	TRUE	1	0.53	2		502	707	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420988	49420989	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	85	442	0	ENST00000301067.7:c.14760dup	p.Ala4922GlyfsTer10	p.A4922Gfs*10	ENST00000301067	NM_003482.3	4920	-/C	48/54	1	2	FACETS	0.54	0.478	0.606	0.54	0.478	0.606	SUBCLONAL	1	TRUE	1	0.53	2		442	594	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630605	187630605	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	158	406	0	ENST00000441802.2:c.377del	p.Asn126IlefsTer20	p.N126Ifs*20	ENST00000441802	NM_005245.3	126	aAt/at	2/27	0.185365905163266	3	FACETS	1	0.938	1	0.513	0.471	0.557	INDETERMINATE	1	TRUE	1	0.53	3		406	735	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771987	135771988	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs2234980	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	34	148	1	ENST00000298552.3:c.3127_3129dup	p.Ser1043dup	p.S1043dup	ENST00000298552	NM_001162426.1	1043	-/AGC	23/23	1	2	FACETS	0.528	0.434	0.632	0.528	0.434	0.632	SUBCLONAL	1	TRUE	1	0.53	2		149	243	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116262	209116263	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs754375602	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	84	327	0	ENST00000345146.2:c.13dup	p.Ile5AsnfsTer13	p.I5Nfs*13	ENST00000345146	NM_005896.2	5	atc/aAtc	3/10	1	2	FACETS	0.585	0.518	0.657	0.585	0.518	0.657	SUBCLONAL	1	TRUE	1	0.53	2		327	542	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5216758	5216758	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	48	479	0	ENST00000357368.4:c.4069del	p.Leu1357SerfsTer59	p.L1357Sfs*59	ENST00000357368	NM_002850.3	1357	Ctc/tc	26/38	1	2	FACETS	0.268	0.226	0.315	0.268	0.226	0.315	SUBCLONAL	1	TRUE	1	0.53	2		479	676	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23635362	23635363	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	36	451	0	ENST00000261584.4:c.2800_2801dup	p.Ala935Ter	p.A935*	ENST00000261584	NM_024675.3	934	gta/gtGTa	8/13	1	2	FACETS	0.295	0.242	0.355	0.295	0.242	0.355	SUBCLONAL	1	TRUE	1	0.53	2		451	460	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828228	72828228	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	193	792	1	ENST00000268489.5:c.8353del	p.Leu2785SerfsTer4	p.L2785Sfs*4	ENST00000268489	NM_006885.3	2785	Ctc/tc	9/10	1	2	FACETS	0.773	0.715	0.833	0.773	0.715	0.833	SUBCLONAL	1	TRUE	1	0.53	2		793	942	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443668	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	184	457	0	ENST00000301067.7:c.3703_3704del	p.Gly1235TrpfsTer14	p.G1235Wfs*14	ENST00000301067	NM_003482.3	1235	GGt/t	11/54	1	2	FACETS	0.963	0.892	1	0.963	0.892	1	CLONAL	1	TRUE	1	0.53	2		457	721	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41247906	41247907	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	142	500	0	ENST00000357654.3:c.626dup	p.Gln210SerfsTer6	p.Q210Sfs*6	ENST00000357654	NM_007294.3	209	cct/ccCt	9/23	0.185365905163266	0	FACETS	0.383	0.349	0.417			1	INDETERMINATE	1	TRUE	0	0.53	0		500	658	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11273523	11273524	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	181	494	2	ENST00000361445.4:c.3217dup	p.Gln1073ProfsTer13	p.Q1073Pfs*13	ENST00000361445	NM_004958.3	1073	cag/cCag	21/58	1	2	FACETS	0.852	0.787	0.919	0.852	0.787	0.919	CLONAL	1	TRUE	1	0.53	2		496	802	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058747	180058748	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755445139	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	128	419	0	ENST00000261937.6:c.89dup	p.Thr31AspfsTer15	p.T31Dfs*15	ENST00000261937	NM_182925.4	30	ccg/ccCg	2/30	1	2	FACETS	0.881	0.802	0.964	0.881	0.802	0.964	CLONAL	1	TRUE	1	0.53	2		419	548	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020764	37020764	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	148	531	1	ENST00000358127.4:c.81del	p.Phe27LeufsTer2	p.F27Lfs*2	ENST00000358127	NM_001280556.1	27	ttT/tt	2/10	1	2	FACETS	0.653	0.597	0.713	0.653	0.597	0.713	SUBCLONAL	1	TRUE	1	0.53	2		532	855	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287213	33287213	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	218	316	1	ENST00000374542.5:c.1884del	p.Cys629AlafsTer16	p.C629Afs*16	ENST00000374542	NM_001141970.1	628	ccC/cc	6/8	0.3	6	FACETS	1	0.958	1			1	INDETERMINATE	2	TRUE	NA	0.53	6		317	816	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426786	49426788	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	83	245	0	ENST00000301067.7:c.11700_11702del	p.Gln3905del	p.Q3905del	ENST00000301067	NM_003482.3	3900	ctTCAg/ctg	39/54	1	2	FACETS	0.903	0.803	1	0.903	0.803	1	CLONAL	1	TRUE	1	0.53	2		245	347	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528592	157528594	+	inframe_deletion	In_Frame_Del	DEL	GTC	GTC	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	138	328	0	ENST00000346085.5:c.6320_6322del	p.Arg2107del	p.R2107del	ENST00000346085	NM_020732.3	2106	aGTCgt/agt	20/20	1	2	FACETS	0.903	0.825	0.983	0.903	0.825	0.983	CLONAL	1	TRUE	1	0.53	2		328	577	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383944	84383944	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	87	371	0	ENST00000321945.7:c.908del	p.Asn303IlefsTer17	p.N303Ifs*17	ENST00000321945	NM_139076.2	303	aAt/at	9/9	0.185365905163266	3	FACETS	0.794	0.705	0.889	0.397	0.352	0.445	INDETERMINATE	1	TRUE	1	0.53	3		371	523	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945008	31945008	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	75	646	0	ENST00000340398.3:c.93del	p.Ser32LeufsTer5	p.S32Lfs*5	ENST00000340398	NM_001013699.2	31	ccC/cc	1/1	1	2	FACETS	0.274	0.239	0.312	0.274	0.239	0.312	SUBCLONAL	1	TRUE	1	0.53	2		646	1032	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660807	227660808	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCT	rs747646240	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	74	331	1	ENST00000305123.5:c.2645_2647dup	p.Gln882dup	p.Q882dup	ENST00000305123	NM_005544.2	882	ccc/cAGCcc	1/2	1	2	FACETS	0.55	0.482	0.622	0.55	0.482	0.622	SUBCLONAL	1	TRUE	1	0.53	2		332	508	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18272109	18272123	+	inframe_deletion	In_Frame_Del	DEL	CCGGCGCTGGAGCCA	CCGGCGCTGGAGCCA	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	26	33	0	ENST00000222254.8:c.622_636del	p.Ala208_Pro212del	p.A208_P212del	ENST00000222254	NM_005027.3	207	CCGGCGCTGGAGCCA/-	6/16	1	2	FACETS	0.846	0.682	1	0.846	0.682	1	CLONAL	1	TRUE	1	0.53	2		33	116	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247894	59247894	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1218	493	563	1	ENST00000371222.2:c.849del	p.Val284Ter	p.V284*	ENST00000371222	NM_002228.3	283	aaA/aa	1/1	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.53	2		564	1711	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630434	187630435	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	223	570	3	ENST00000441802.2:c.547dup	p.Glu183GlyfsTer7	p.E183Gfs*7	ENST00000441802	NM_005245.3	183	gaa/gGaa	2/27	0.185365905163266	3	FACETS	1	0.976	1	0.55	0.512	0.59	INDETERMINATE	1	TRUE	1	0.53	3		573	967	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133737	41133738	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	216	738	0	ENST00000379561.5:c.1890dup	p.Asn631Ter	p.N631*	ENST00000379561	NM_002015.3	630	-/T	2/3	1	2	FACETS	0.756	0.702	0.812	0.756	0.702	0.812	SUBCLONAL	1	TRUE	1	0.53	2		738	1078	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56170949	56170949	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	78	368	0	ENST00000399503.3:c.1780del	p.Ala594ProfsTer62	p.A594Pfs*62	ENST00000399503	NM_005921.1	593	Ggg/gg	10/20	0.185365905163266	3	FACETS	0.494	0.433	0.559	0.247	0.216	0.28	INDETERMINATE	1	TRUE	1	0.53	3		368	754	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190819	185190819	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	84	460	0	ENST00000265026.3:c.1703del	p.Pro568LeufsTer39	p.P568Lfs*39	ENST00000265026	NM_004721.4	567	tCc/tc	11/14	1	2	FACETS	0.428	0.377	0.482	0.428	0.377	0.482	SUBCLONAL	1	TRUE	1	0.53	2		460	741	SUCCESS
AR	367	MSKCC	GRCh37	X	66765489	66765489	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	64	448	1	ENST00000374690.3:c.503del	p.Gly168AlafsTer7	p.G168Afs*7	ENST00000374690	NM_000044.3	167	ctG/ct	1/8	0.185365905163266	0	FACETS	0.227	0.196	0.259			1	INDETERMINATE	1	TRUE	0	0.53	0		449	501	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18524120	18524120	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	76	380	1	ENST00000266497.5:c.1635del	p.Glu548LysfsTer2	p.E548Kfs*2	ENST00000266497		544	aaT/aa	11/31	0.3	2	FACETS	0.523	0.46	0.592			1	INDETERMINATE	1	TRUE	NA	0.53	2		381	548	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641388	18641389	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1229278001	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	72	239	0	ENST00000266497.5:c.2393dup	p.Asn798LysfsTer5	p.N798Kfs*5	ENST00000266497		796	cta/ctAa	17/31	0.3	2	FACETS	0.719	0.631	0.812			1	INDETERMINATE	1	TRUE	NA	0.53	2		239	378	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7119460	7119461	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	AG	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	136	437	0	ENST00000302850.5:c.3793_3794insCT	p.Val1265AlafsTer16	p.V1265Afs*16	ENST00000302850	NM_000208.2	1265	gtc/gCTtc	21/22	1	2	FACETS	0.794	0.724	0.868	0.794	0.724	0.868	SUBCLONAL	1	TRUE	1	0.53	2		437	646	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243444	46243444	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	200	609	0	ENST00000334344.6:c.1800del	p.Lys600AsnfsTer47	p.K600Nfs*47	ENST00000334344	NM_152641.2	599	gtA/gt	14/21	1	2	FACETS	0.818	0.758	0.879	0.818	0.758	0.879	CLONAL	1	TRUE	1	0.53	2		609	923	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928976	44928976	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	303	695	2	ENST00000377967.4:c.2080del	p.Ala694LeufsTer21	p.A694Lfs*21	ENST00000377967	NM_021140.2	692	caG/ca	17/29	1	2	FACETS	0.819	0.77	0.869	0.819	0.77	0.869	CLONAL	1	TRUE	1	0.53	2		697	1396	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103513936	103513936	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	170	536	0	ENST00000355739.4:c.755del	p.Lys252ArgfsTer3	p.K252Rfs*3	ENST00000355739	NM_000123.3	251	cAa/ca	7/15	1	2	FACETS	0.827	0.762	0.894	0.827	0.762	0.894	CLONAL	1	TRUE	1	0.53	2		536	776	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499363	89499363	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1317589623	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	157	385	1	ENST00000336596.2:c.2538del	p.Met847TrpfsTer10	p.M847Wfs*10	ENST00000336596	NM_005233.5	845	Ccc/cc	15/17	1	2	FACETS	0.837	0.768	0.908	0.837	0.768	0.908	CLONAL	1	TRUE	1	0.53	2		386	708	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024636	31024637	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs1555912897	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	155	518	0	ENST00000375687.4:c.4127dup	p.Pro1377SerfsTer3	p.P1377Sfs*3	ENST00000375687	NM_015338.5	1374	gtg/gtGg	13/13	1	2	FACETS	0.886	0.814	0.961	0.886	0.814	0.961	CLONAL	1	TRUE	1	0.53	2		518	660	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271331	18271331	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	221	480	0	ENST00000222254.8:c.377del	p.Pro126LeufsTer4	p.P126Lfs*4	ENST00000222254	NM_005027.3	125	Ccc/cc	3/16	1	2	FACETS	0.961	0.896	1	0.961	0.896	1	CLONAL	1	TRUE	1	0.53	2		480	868	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797204	42797205	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	29	359	0	ENST00000575354.2:c.3570dup	p.Ser1191ValfsTer3	p.S1191Vfs*3	ENST00000575354	NM_015125.3	1189	gtg/gtGg	15/20	1	2	FACETS	0.222	0.177	0.272	0.222	0.177	0.272	SUBCLONAL	1	TRUE	1	0.53	2		359	494	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2191141	2191141	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	223	521	3	ENST00000398665.3:c.399del	p.Glu134ArgfsTer14	p.E134Rfs*14	ENST00000398665	NM_032482.2	132	tCc/tc	5/28	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.53	2		524	781	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627306	37627307	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGC	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	187	481	0	ENST00000447079.4:c.1221_1222insTGC	p.Ala407_Ala408insCys	p.A407_A408insC	ENST00000447079	NM_015083.1	407	-/TGC	2/14	1	2	FACETS	0.865	0.8	0.932	0.865	0.8	0.932	CLONAL	1	TRUE	1	0.53	2		481	816	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202148	67202148	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1265076720	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	146	379	4	ENST00000312629.5:c.1255del	p.Arg419GlyfsTer75	p.R419Gfs*75	ENST00000312629	NM_003952.2	417	agC/ag	14/15	1	2	FACETS	0.96	0.88	1	0.96	0.88	1	CLONAL	1	TRUE	1	0.53	2		383	574	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380758	118380758	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	183	495	1	ENST00000534358.1:c.11001del	p.Lys3667AsnfsTer30	p.K3667Nfs*30	ENST00000534358	NM_005933.3	3666	Aaa/aa	30/36	1	2	FACETS	0.847	0.783	0.914	0.847	0.783	0.914	CLONAL	1	TRUE	1	0.53	2		496	815	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852611	63852611	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	174	320	1	ENST00000279873.7:c.3393del	p.Phe1131LeufsTer20	p.F1131Lfs*20	ENST00000279873	NM_032199.2	1130	aTt/at	10/10	0.3	6	FACETS	0.893	0.824	0.965			1	INDETERMINATE	2	TRUE	NA	0.53	6		321	757	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527651	157527652	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	207	428	2	ENST00000346085.5:c.5381dup	p.Asn1795GlufsTer7	p.N1795Efs*7	ENST00000346085	NM_020732.3	1792	-/A	20/20	1	2	FACETS	0.967	0.899	1	0.967	0.899	1	CLONAL	1	TRUE	1	0.53	2		430	808	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027151	71027152	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TC	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	221	384	0	ENST00000318789.4:c.1175_1176insGA	p.Lys393ThrfsTer23	p.K393Tfs*23	ENST00000318789	NM_032682.5	392	tcc/tcGAc	15/21	0.3	1	FACETS	0.847	0.791	0.904	0.847	0.791	0.904	INDETERMINATE	1	TRUE	0	0.53	1		384	724	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085825	16085825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	52	444	0	ENST00000281043.3:c.1005del	p.Ser336LeufsTer15	p.S336Lfs*15	ENST00000281043	NM_005378.4	334	gCc/gc	3/3	1	2	FACETS	0.27	0.229	0.315	0.27	0.229	0.315	SUBCLONAL	1	TRUE	1	0.53	2		444	727	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523008	25523009	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	GG	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	198	541	1	ENST00000264709.3:c.175_176dup	p.Val60ArgfsTer13	p.V60Rfs*13	ENST00000264709	NM_175629.2	59	ccg/ccCCg	3/23	1	2	FACETS	0.984	0.914	1	0.984	0.914	1	CLONAL	1	TRUE	1	0.53	2		542	759	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2488147	2488147	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	237	435	4	ENST00000355716.4:c.48del	p.Thr18ProfsTer4	p.T18Pfs*4	ENST00000355716	NM_003820.2	15	aCc/ac	1/8	1	2	FACETS	0.935	0.873	0.998	0.935	0.873	0.998	CLONAL	1	TRUE	1	0.53	2		439	957	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98211549	98211550	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	A	novel	NA	P-0007147-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	169	390	8	ENST00000331920.6:c.3605_3606delinsT	p.Pro1202LeufsTer53	p.P1202Lfs*53	ENST00000331920	NM_000264.3	1202	cCC/cT	22/24	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.53	2		398	614	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0007238-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	324	464	0				ENST00000310581	NM_198253.2	-/1132			0.777533491742037	2	FACETS	0.965	0.932	0.996	0.965	0.932	0.996	CLONAL	2	TRUE	0	0.777533491742037	2		464	432	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0007238-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	435	511	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.777533491742037	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.777533491742037	2		511	542	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342959	225342959	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007238-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	278	424	0	ENST00000264414.4:c.2133G>A	p.Met711Ile	p.M711I	ENST00000264414	NM_003590.4	711	atG/atA	15/16	0.340950890552386	2	FACETS	1	0.994	1	0.68	0.646	0.713	INDETERMINATE	1	TRUE	0	0.777533491742037	2		424	526	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	50	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.32	2		464	281	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295253	1295253	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1232074117	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	43	336	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.924	0.777	1	0.924	0.777	1	CLONAL	1	TRUE	1	0.32	2		336	291	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663346	227663346	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1024227751	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	31	161	0	ENST00000305123.5:c.109G>A	p.Glu37Lys	p.E37K	ENST00000305123	NM_005544.2	37	Gag/Aag	1/2	0.3	4	FACETS	0.951	0.772	1			1	CLONAL	1	TRUE	NA	0.32	4		161	269	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498327	29498327	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766821017	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	95	346	1	ENST00000389048.3:c.1853G>A	p.Gly618Glu	p.G618E	ENST00000389048	NM_004304.4	618	gGa/gAa	10/29	0.274329565665983	1	FACETS	0.752	0.67	0.839	0.752	0.67	0.839	SUBCLONAL	1	TRUE	0	0.32	1		347	663	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1763	292	774	2	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	0.181730484012322	4	FACETS	1	0.986	1	0.586	0.549	0.625	INDETERMINATE	1	TRUE	2	0.32	4		776	2055	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	153	616	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	0.3	3	FACETS	1	0.931	1			1	CLONAL	1	TRUE	NA	0.32	3		616	1086	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578518	7578518	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934875	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	86	333	0	ENST00000269305.4:c.412G>C	p.Ala138Pro	p.A138P	ENST00000269305	NM_001126112.2	138	Gcc/Ccc	5/11	0.3	3	FACETS	0.812	0.718	0.913			1	CLONAL	1	TRUE	NA	0.32	3		333	768	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682533	37682533	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	107	354	1	ENST00000447079.4:c.3724C>T	p.Arg1242Ter	p.R1242*	ENST00000447079	NM_015083.1	1242	Cga/Tga	13/14	0.264004410364283	3	FACETS	0.921	0.826	1	0.461	0.413	0.512	CLONAL	1	TRUE	1	0.32	3		355	842	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413214	139413214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	42	348	0	ENST00000277541.6:c.928G>A	p.Gly310Arg	p.G310R	ENST00000277541	NM_017617.3	310	Ggg/Agg	6/34	0.137631185388048	3	FACETS	0.418	0.348	0.497	0.209	0.174	0.249	INDETERMINATE	1	TRUE	1	0.32	3		348	728	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056413	26056413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs967486148	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	89	200	0	ENST00000343677.2:c.244C>T	p.Leu82Phe	p.L82F	ENST00000343677	NM_005319.3	82	Ctt/Ttt	1/1	0.3	8	FACETS	1	0.97	1			1	CLONAL	1	TRUE	NA	0.32	8		200	839	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133979	41133979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149675484	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1476	378	700	0	ENST00000379561.5:c.1649C>T	p.Ser550Leu	p.S550L	ENST00000379561	NM_002015.3	550	tCg/tTg	2/3	0.271279649106807	4	FACETS	0.841	0.796	0.888	0.561	0.53	0.592	CLONAL	2	TRUE	1	0.32	4		700	1854	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514302	69514302	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1255340343	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	81	346	0	ENST00000294312.3:c.379C>T	p.Arg127Cys	p.R127C	ENST00000294312	NM_005117.2	127	Cgc/Tgc	3/3	NA	2	FACETS	0.806	0.711	0.908			1	INDETERMINATE	1	TRUE	NA	0.32	2		346	628	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257873	16257873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	54	122	0	ENST00000375759.3:c.5138C>T	p.Ala1713Val	p.A1713V	ENST00000375759	NM_015001.2	1713	gCc/gTc	11/15	0.3	4	FACETS	1	0.934	1			1	CLONAL	1	TRUE	NA	0.32	4		122	383	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800912	243800912	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	90	471	1	ENST00000263826.5:c.561+1G>A		p.X187_splice	ENST00000263826	NM_005465.4	187			0.264004410364283	3	FACETS	0.587	0.519	0.66	0.294	0.259	0.33	SUBCLONAL	1	TRUE	1	0.32	3		472	1111	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182196	99182196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751224706	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	92	379	0	ENST00000074304.5:c.2261C>T	p.Ser754Phe	p.S754F	ENST00000074304	NM_001134224.1	754	tCc/tTc	21/26	0.24911345568156	4	FACETS	0.893	0.792	1			1	CLONAL	1	TRUE	NA	0.32	4		379	850	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881600	111881600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1258929049	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	145	403	0	ENST00000393256.3:c.278C>T	p.Ser93Phe	p.S93F	ENST00000393256	NM_006538.4	93	tCc/tTc	2/4	0.24911345568156	4	FACETS	1	0.967	1			1	CLONAL	1	TRUE	NA	0.32	4		403	1059	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270079	198270079	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1086	101	394	0	ENST00000335508.6:c.1357A>G	p.Met453Val	p.M453V	ENST00000335508	NM_012433.2	453	Atg/Gtg	10/25	0.3	5	FACETS	0.787	0.701	0.879	0.262	0.233	0.293	SUBCLONAL	1	TRUE	2	0.32	5		394	1187	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447207	187447207	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	50	295	0	ENST00000232014.4:c.986T>C	p.Val329Ala	p.V329A	ENST00000232014	NM_001130845.1	329	gTt/gCt	5/10	0.181730484012322	4	FACETS	0.575	0.487	0.673	0.288	0.243	0.337	INDETERMINATE	1	TRUE	2	0.32	4		295	717	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153703	55153703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	108	417	0	ENST00000257290.5:c.2669C>T	p.Ser890Phe	p.S890F	ENST00000257290	NM_006206.4	890	tCc/tTc	19/23	1	2	FACETS	0.761	0.682	0.845	0.761	0.682	0.845	SUBCLONAL	1	TRUE	1	0.32	2		417	887	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955640	55955640	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	100	426	0	ENST00000263923.4:c.3305G>A	p.Gly1102Asp	p.G1102D	ENST00000263923	NM_002253.2	1102	gGt/gAt	25/30	1	2	FACETS	0.764	0.682	0.851	0.764	0.682	0.851	SUBCLONAL	1	TRUE	1	0.32	2		426	818	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260701	1260701	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	82	325	0	ENST00000310581.5:c.2858C>T	p.Ser953Phe	p.S953F	ENST00000310581	NM_198253.2	953	tCc/tTc	12/16	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.32	2		325	486	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591262	67591262	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	121	341	0	ENST00000274335.5:c.1760A>T	p.Lys587Ile	p.K587I	ENST00000274335		587	aAa/aTa	13/15	0.253826108263386	4	FACETS	0.983	0.887	1	0.492	0.443	0.543	CLONAL	1	TRUE	2	0.32	4		341	1015	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149437127	149437127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	102	413	0	ENST00000286301.3:c.2161G>A	p.Asp721Asn	p.D721N	ENST00000286301	NM_005211.3	721	Gac/Aac	16/22	0.264004410364283	3	FACETS	1	0.899	1	0.502	0.449	0.559	CLONAL	1	TRUE	1	0.32	3		413	736	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099499	157099499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	104	276	1	ENST00000346085.5:c.436G>A	p.Gly146Ser	p.G146S	ENST00000346085	NM_020732.3	146	Ggc/Agc	1/20	0.3	4	FACETS	1	0.965	1			1	CLONAL	1	TRUE	NA	0.32	4		277	728	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836345	151836345	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	98	208	0	ENST00000262189.6:c.14461-1G>A		p.X4821_splice	ENST00000262189	NM_170606.2	4821			0.181730484012322	4	FACETS	1	0.978	1	0.688	0.615	0.765	INDETERMINATE	1	TRUE	2	0.32	4		208	588	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151882713	151882713	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs745593306	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	55	113	0	ENST00000262189.6:c.5012G>A	p.Trp1671Ter	p.W1671*	ENST00000262189	NM_170606.2	1671	tGg/tAg	34/59	0.181730484012322	4	FACETS	1	0.96	1	0.675	0.581	0.778	INDETERMINATE	1	TRUE	2	0.32	4		113	336	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884347	151884347	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	91	334	1	ENST00000262189.6:c.5008G>A	p.Asp1670Asn	p.D1670N	ENST00000262189	NM_170606.2	1670	Gat/Aat	33/59	0.181730484012322	4	FACETS	0.927	0.822	1	0.463	0.411	0.52	INDETERMINATE	1	TRUE	2	0.32	4		335	810	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74858992	74858992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	30	86	0	ENST00000284811.8:c.212C>T	p.Ser71Leu	p.S71L	ENST00000284811		71	tCg/tTg	4/4	0.3	5	FACETS	0.851	0.687	1	0.284	0.229	0.346	CLONAL	1	TRUE	2	0.32	5		86	326	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518163	8518163	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	125	397	0	ENST00000356435.5:c.1228A>G	p.Thr410Ala	p.T410A	ENST00000356435		410	Aca/Gca	10/35	NA	2	FACETS	0.893	0.808	0.983			1	INDETERMINATE	1	TRUE	NA	0.32	2		397	875	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528722	8528722	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	135	395	0	ENST00000356435.5:c.410T>C	p.Val137Ala	p.V137A	ENST00000356435		137	gTt/gCt	4/35	NA	2	FACETS	0.944	0.857	1			1	INDETERMINATE	1	TRUE	NA	0.32	2		395	894	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606539	93606539	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	91	293	0	ENST00000375746.1:c.359T>C	p.Phe120Ser	p.F120S	ENST00000375746	NM_001174167.1	120	tTt/tCt	2/14	0.137631185388048	3	FACETS	1	0.937	1	0.54	0.48	0.604	INDETERMINATE	1	TRUE	1	0.32	3		293	611	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395134	139395134	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374787627	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	69	371	0	ENST00000277541.6:c.5804C>T	p.Ala1935Val	p.A1935V	ENST00000277541	NM_017617.3	1935	gCc/gTc	31/34	0.137631185388048	3	FACETS	0.759	0.661	0.865	0.38	0.33	0.433	INDETERMINATE	1	TRUE	1	0.32	3		371	659	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154784	2154784	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	125	522	0	ENST00000434045.2:c.437C>T	p.Ser146Phe	p.S146F	ENST00000434045	NM_001127598.1	146	tCc/tTc	4/5	0.137631185388048	3	FACETS	1	0.978	1	0.638	0.578	0.701	INDETERMINATE	1	TRUE	1	0.32	3		522	710	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196887	108196887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	88	350	0	ENST00000278616.4:c.6910G>A	p.Glu2304Lys	p.E2304K	ENST00000278616	NM_000051.3	2304	Gag/Aag	47/63	0.181730484012322	4	FACETS	0.772	0.682	0.868	0.386	0.341	0.434	INDETERMINATE	1	TRUE	2	0.32	4		350	941	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342518	118342518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1211	141	507	0	ENST00000534358.1:c.644C>T	p.Ser215Phe	p.S215F	ENST00000534358	NM_005933.3	215	tCt/tTt	3/36	0.181730484012322	4	FACETS	0.86	0.781	0.944	0.43	0.39	0.472	INDETERMINATE	1	TRUE	2	0.32	4		507	1352	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420493	49420493	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs727503979	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	62	265	0	ENST00000301067.7:c.15256C>T	p.Arg5086Ter	p.R5086*	ENST00000301067	NM_003482.3	5086	Cga/Tga	48/54	0.3	5	FACETS	0.808	0.697	0.929	0.269	0.232	0.31	CLONAL	1	TRUE	2	0.32	5		265	710	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102813350	102813350	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	99	416	0	ENST00000307046.8:c.339G>T	p.Lys113Asn	p.K113N	ENST00000307046	NM_001111285.1	113	aaG/aaT	3/4	0.3	5	FACETS	1	0.909	1	0.341	0.303	0.38	CLONAL	1	TRUE	2	0.32	5		416	896	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226445	133226445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	110	337	1	ENST00000320574.5:c.3613C>T	p.Pro1205Ser	p.P1205S	ENST00000320574	NM_006231.2	1205	Ccg/Tcg	30/49	1	2	FACETS	0.967	0.869	1	0.967	0.869	1	CLONAL	1	TRUE	1	0.32	2		338	711	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347954	347954	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867582108	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	71	429	0	ENST00000262320.3:c.1552C>T	p.Pro518Ser	p.P518S	ENST00000262320	NM_003502.3	518	Ccc/Tcc	6/11	0.137631185388048	3	FACETS	0.736	0.642	0.838	0.368	0.321	0.419	INDETERMINATE	1	TRUE	1	0.32	3		429	699	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020568	14020568	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	84	412	1	ENST00000311895.7:c.539G>A	p.Arg180Lys	p.R180K	ENST00000311895	NM_005236.2	180	aGa/aAa	3/11	0.137631185388048	3	FACETS	0.607	0.534	0.684	0.303	0.267	0.342	INDETERMINATE	1	TRUE	1	0.32	3		413	1004	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983140	7983140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	150	399	0	ENST00000319144.4:c.874G>A	p.Asp292Asn	p.D292N	ENST00000319144	NM_001139.2	292	Gac/Aac	7/15	0.3	3	FACETS	1	0.984	1			1	CLONAL	1	TRUE	NA	0.32	3		399	808	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37872772	37872772	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	88	313	0	ENST00000269571.5:c.1651C>T	p.Pro551Ser	p.P551S	ENST00000269571		551	Ccc/Tcc	14/27	0.264004410364283	3	FACETS	0.906	0.803	1	0.453	0.401	0.509	CLONAL	1	TRUE	1	0.32	3		313	704	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740453	58740453	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs765346414	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1225	145	698	0	ENST00000305921.3:c.1358C>G	p.Ser453Ter	p.S453*	ENST00000305921	NM_003620.3	453	tCa/tGa	6/6	0.264004410364283	3	FACETS	0.767	0.698	0.841	0.384	0.349	0.421	SUBCLONAL	1	TRUE	1	0.32	3		698	1370	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632393	1632393	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770897713	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	70	376	1	ENST00000344749.5:c.157C>T	p.Arg53Trp	p.R53W	ENST00000344749	NM_001136139.2	53	Cgg/Tgg	4/19	NA	2	FACETS	0.683	0.595	0.777			1	INDETERMINATE	1	TRUE	NA	0.32	2		377	641	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2185874	2185874	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1378442482	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	119	527	2	ENST00000398665.3:c.146C>T	p.Pro49Leu	p.P49L	ENST00000398665	NM_032482.2	49	cCg/cTg	3/28	NA	2	FACETS	0.703	0.633	0.777			1	INDETERMINATE	1	TRUE	NA	0.32	2		529	1058	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600434	10600434	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867169234	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	68	459	3	ENST00000171111.5:c.1421C>T	p.Ala474Val	p.A474V	ENST00000171111	NM_203500.1	474	gCc/gTc	4/6	1	2	FACETS	0.487	0.422	0.557	0.487	0.422	0.557	SUBCLONAL	1	TRUE	1	0.32	2		462	873	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077558	30077558	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	62	372	0	ENST00000338641.4:c.1705G>A	p.Gly569Ser	p.G569S	ENST00000338641	NM_000268.3	569	Ggt/Agt	15/16	0.264004410364283	3	FACETS	0.646	0.557	0.742	0.323	0.278	0.371	SUBCLONAL	1	TRUE	1	0.32	3		372	696	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568555	41568555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555911573	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1007	148	466	0	ENST00000263253.7:c.4505C>T	p.Pro1502Leu	p.P1502L	ENST00000263253	NM_001429.3	1502	cCt/cTt	28/31	0.264004410364283	3	FACETS	0.929	0.847	1	0.465	0.423	0.508	CLONAL	1	TRUE	1	0.32	3		466	1155	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468040	120468042	+	inframe_deletion	In_Frame_Del	DEL	AGC	AGC	-	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	151	490	0	ENST00000256646.2:c.4397_4399del	p.Cys1466del	p.C1466del	ENST00000256646	NM_024408.3	1466	tGCTcc/tcc	25/34	0.181730484012322	4	FACETS	1	0.98	1	0.623	0.569	0.68	INDETERMINATE	1	TRUE	2	0.32	4		490	1000	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49442494	49442494	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	128	394	0	ENST00000301067.7:c.4079del	p.Met1360SerfsTer16	p.M1360Sfs*16	ENST00000301067	NM_003482.3	1360	aTg/ag	13/54	0.3	5	FACETS	1	0.946	1	0.356	0.321	0.392	CLONAL	1	TRUE	2	0.32	5		394	1110	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400312	139400313	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	CA	CA	-	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	19	72	0	ENST00000277541.6:c.4035_4036del	p.Cys1345Ter	p.C1345*	ENST00000277541	NM_017617.3	1345	tgTGag/tgag	25/34	0.137631185388048	3	FACETS	1	0.908	1	0.71	0.548	0.893	INDETERMINATE	1	TRUE	1	0.32	3		72	97	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965188	25965189	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	74	318	0	ENST00000435504.4:c.4017_4018delinsAA	p.Met1339_Asp1340delinsIleAsn	p.M1339_D1340delinsIN	ENST00000435504		1339	atGGac/atAAac	13/13	0.273762625962692	3	FACETS	0.712	0.623	0.809			1	SUBCLONAL	1	TRUE	NA	0.32	3		318	753	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198288569	198288570	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1280	82	456	0	ENST00000335508.6:c.157_158delinsAA	p.Gly53Lys	p.G53K	ENST00000335508	NM_012433.2	53	GGa/AAa	2/25	0.3	5	FACETS	0.557	0.489	0.63	0.186	0.163	0.21	SUBCLONAL	1	TRUE	2	0.32	5		456	1362	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195699	123195700	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0007277-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	250	326	1	ENST00000218089.9:c.1613_1614delinsAT	p.Pro538His	p.P538H	ENST00000218089	NM_001042749.1	538	cCC/cAT	17/35	0.24911345568156	2	FACETS	0.826	0.773	0.88			1	CLONAL	2	TRUE	NA	0.32	2		327	946	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0007280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	94	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.62	2		464	298	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0007280-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	192	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.933	0.866	1	0.933	0.866	1	CLONAL	1	TRUE	1	0.62	2		490	664	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	132	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.880105318269981	2		280	265	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803564	1803564	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121913482	NA	P-0007285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	179	236	0	ENST00000260795.2:c.742C>T	p.Arg248Cys	p.R248C	ENST00000260795		248	Cgc/Tgc	6/17	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.880105318269981	2		236	360	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482437	56482437	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	240	389	1	ENST00000267101.3:c.985A>G	p.Lys329Glu	p.K329E	ENST00000267101	NM_001982.3	329	Aaa/Gaa	8/28	1	2	FACETS	0.896	0.842	0.949	0.896	0.842	0.949	CLONAL	1	TRUE	1	0.880105318269981	2		390	609	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114911593	114911593	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	620	980	0	ENST00000543371.1:c.1111G>C	p.Glu371Gln	p.E371Q	ENST00000543371	NM_001198531.1	371	Gag/Cag	10/14	1	2	FACETS	0.987	0.951	1	0.987	0.951	1	CLONAL	1	TRUE	1	0.880105318269981	2		980	1428	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77043802	77043802	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	407	664	0	ENST00000356341.3:c.1524G>C	p.Lys508Asn	p.K508N	ENST00000356341	NM_002576.4	508	aaG/aaC	14/15	1	2	FACETS	0.975	0.931	1	0.975	0.931	1	CLONAL	1	TRUE	1	0.880105318269981	2		664	949	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779811	135779811	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs118203621	NA	P-0007285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	360	445	0	ENST00000298552.3:c.2028G>A	p.Trp676Ter	p.W676*	ENST00000298552	NM_001162426.1	676	tgG/tgA	16/23	0.880105318269981	1	FACETS	0.975	0.944	1	0.975	0.944	1	CLONAL	1	TRUE	0	0.880105318269981	1		445	470	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894839	101894840	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TGGA	novel	NA	P-0007285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	218	392	0	ENST00000374994.4:c.393_396dup	p.Pro133TrpfsTer30	p.P133Wfs*30	ENST00000374994	NM_004612.2	131	gct/gcTGGAt	3/9	0.880105318269981	1	FACETS	0.922	0.882	0.96	0.922	0.882	0.96	CLONAL	1	TRUE	0	0.880105318269981	1		392	301	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373832	118373833	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TA	novel	NA	P-0007285-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	234	323	0	ENST00000534358.1:c.7225_7226delinsTA	p.Gly2409Ter	p.G2409*	ENST00000534358	NM_005933.3	2409	GGa/TAa	27/36	1	2	FACETS	0.974	0.917	1	0.974	0.917	1	CLONAL	1	TRUE	1	0.880105318269981	2		323	546	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	30	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.991	0.802	1	0.991	0.802	1	CLONAL	1	TRUE	1	0.229229945246401	2		280	264	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374293	138374293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	72	508	0	ENST00000289153.2:c.3151G>A	p.Glu1051Lys	p.E1051K	ENST00000289153	NM_006219.2	1051	Gaa/Aaa	22/22	1	2	FACETS	0.918	0.802	1	0.918	0.802	1	CLONAL	1	TRUE	1	0.229229945246401	2		508	684	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10188252	10188252	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1559428134	NA	P-0007347-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	92	603	0	ENST00000256474.2:c.397del	p.Thr133LeufsTer26	p.T133Lfs*26	ENST00000256474	NM_000551.3	132	cAa/ca	2/3	0.229229945246401	1	FACETS	0.994	0.883	1	0.994	0.883	1	CLONAL	1	TRUE	0	0.229229945246401	1		603	715	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	45	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.829	0.705	0.964	0.829	0.705	0.964	CLONAL	1	TRUE	1	0.5	2		280	217	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0007382-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	83	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	1	0.5	2		490	332	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	120	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.926	0.847	1	0.926	0.847	1	CLONAL	1	TRUE	1	0.77381674054153	2		280	335	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220274	55220274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9241	1406	433	0	ENST00000275493.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000275493	NM_005228.3	222	Cgc/Tgc	6/28	0.77381674054153	21	FACETS	0.95	0.922	0.979			1	CLONAL	3	TRUE	NA	0.77381674054153	21		433	10647	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915455	112915455	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121918463	NA	P-0007504-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	453	412	0	ENST00000351677.2:c.854T>C	p.Phe285Ser	p.F285S	ENST00000351677	NM_002834.3	285	tTt/tCt	8/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.77381674054153	2		412	1134	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007504-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	120	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.965	0.884	1	0.965	0.884	1	CLONAL	1	TRUE	1	0.79714680193675	2		280	312	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0007504-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6854	5189	387	0	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.79714680193675	27	FACETS	0.988	0.975	1			1	CLONAL	12	TRUE	NA	0.79714680193675	27		387	12043	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007516-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	61	280	0				ENST00000310581	NM_198253.2	-/1132			0.523547757767118	3	FACETS	0.994	0.865	1	0.497	0.432	0.566	CLONAL	1	TRUE	1	0.523022434775	3		280	296	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509483	149509483	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007516-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	188	357	0	ENST00000261799.4:c.1416G>C	p.Glu472Asp	p.E472D	ENST00000261799	NM_002609.3	472	gaG/gaC	10/23	0.523547757767118	3	FACETS	1	0.987	1	0.64	0.594	0.689	CLONAL	1	TRUE	1	0.523022434775	3		357	708	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	194	280	0				ENST00000310581	NM_198253.2	-/1132			0.356414995756178	6	FACETS	1	0.983	1	0.78	0.727	0.835	INDETERMINATE	2	TRUE	3	0.680937972796943	6		280	575	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0007517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	1035	511	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.680937972796943	7	FACETS	1	0.995	1			1	CLONAL	5	TRUE	NA	0.680937972796943	7		511	1547	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7128865	7128865	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs1038787462	NA	P-0007517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	216	420	0	ENST00000302850.5:c.2943G>C	p.Lys981Asn	p.K981N	ENST00000302850	NM_000208.2	981	aaG/aaC	15/22	0.680937972796943	3	FACETS	1	0.947	1	0.51	0.475	0.546	CLONAL	1	TRUE	1	0.680937972796943	3		420	834	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426015	49426015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	480	425	0	ENST00000301067.7:c.12473C>T	p.Pro4158Leu	p.P4158L	ENST00000301067	NM_003482.3	4158	cCc/cTc	39/54	0.680937972796943	3	FACETS	0.968	0.931	1	0.968	0.931	1	CLONAL	2	TRUE	1	0.680937972796943	3		425	976	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346771	89346771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	474	368	0	ENST00000301030.4:c.6179C>T	p.Ser2060Phe	p.S2060F	ENST00000301030	NM_001256183.1	2060	tCc/tTc	9/13	0.371828930603292	5	FACETS	0.914	0.878	0.951	0.914	0.878	0.951	INDETERMINATE	3	TRUE	2	0.680937972796943	5		368	1026	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243029	41243029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	515	535	0	ENST00000357654.3:c.4117G>A	p.Glu1373Lys	p.E1373K	ENST00000357654	NM_007294.3	1373	Gag/Aag	11/23	0.680937972796943	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.680937972796943	3		535	1001	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123566	108123567	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0007517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	186	460	0	ENST00000278616.4:c.1827_1828del	p.Lys610AsnfsTer11	p.K610Nfs*11	ENST00000278616	NM_000051.3	609	GAg/g	12/63	0.680937972796943	2	FACETS	0.911	0.861	0.959	0.911	0.861	0.959	CLONAL	2	TRUE	0	0.680937972796943	2		460	300	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158372	108158374	+	inframe_deletion	In_Frame_Del	DEL	TTA	TTA	-	novel	NA	P-0007517-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	270	465	0	ENST00000278616.4:c.4041_4043del	p.Leu1348del	p.L1348del	ENST00000278616	NM_000051.3	1347	TTA/-	27/63	0.680937972796943	2	FACETS	0.962	0.921	1	0.962	0.921	1	CLONAL	2	TRUE	0	0.680937972796943	2		465	412	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0007525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	97	263	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.186357853767564	3	FACETS	0.78	0.697	0.869	0.78	0.697	0.869	SUBCLONAL	2	TRUE	1	0.223625070569182	3		263	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578253	7578253	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555525857	NA	P-0007525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	57	313	1	ENST00000269305.4:c.596G>A	p.Gly199Glu	p.G199E	ENST00000269305	NM_001126112.2	199	gGa/gAa	6/11	0.186357853767564	3	FACETS	1	0.949	1	0.617	0.531	0.712	CLONAL	1	TRUE	1	0.223625070569182	3		314	459	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060594	38060618	+	frameshift_variant	Frame_Shift_Del	DEL	GGAATACACACCTTGGTAGTACGCC	GGAATACACACCTTGGTAGTACGCC	-	novel	NA	P-0007525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	44	378	0	ENST00000250448.2:c.1371_1395del	p.Ala458AspfsTer4	p.A458Dfs*4	ENST00000250448	NM_004496.3	457	ccGGCGTACTACCAAGGTGTGTATTCC/cc	2/2	0.177811374900009	3	FACETS	0.955	0.802	1	0.478	0.401	0.563	CLONAL	1	TRUE	1	0.223625070569182	3		378	458	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597494	52597497	+	frameshift_variant	Frame_Shift_Del	DEL	AGGA	AGGA	-	novel	NA	P-0007525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	16	234	0	ENST00000394830.3:c.3813_3816del	p.Pro1272ArgfsTer15	p.P1272Rfs*15	ENST00000394830	NM_018313.4	1271	gtTCCT/gt	25/30	0.177811374900009	3	FACETS	0.497	0.367	0.653	0.249	0.183	0.327	SUBCLONAL	1	TRUE	1	0.223625070569182	3		234	320	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52595775	52595781	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CTATTTA	CTATTTA	-	novel	NA	P-0007525-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	30	303	0	ENST00000394830.3:c.4132+2_4132+8del		p.X1378_splice	ENST00000394830	NM_018313.4	1378			0.177811374900009	3	FACETS	0.831	0.67	1	0.415	0.335	0.507	CLONAL	1	TRUE	1	0.223625070569182	3		303	359	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	68	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.74	2		280	183	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0007528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	144	511	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.197879311319546	3	FACETS	1	0.936	1	0.512	0.469	0.556	INDETERMINATE	1	TRUE	1	0.74	3		511	521	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223427	53223427	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	140	575	0	ENST00000375401.3:c.3932T>G	p.Leu1311Arg	p.L1311R	ENST00000375401	NM_004187.3	1311	cTc/cGc	23/26	1	2	FACETS	0.821	0.753	0.89	0.821	0.753	0.89	CLONAL	1	TRUE	1	0.74	2		575	461	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	52	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.268756637246289	2		280	298	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980844	40980844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	119	387	0	ENST00000373198.4:c.1642G>A	p.Glu548Lys	p.E548K	ENST00000373198	NM_133170.3	548	Gaa/Aaa	10/32	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.268756637246289	2		387	843	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	500	659	1	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.268756637246289	3	FACETS	1	0.984	1			1	CLONAL	3	TRUE	NA	0.268756637246289	3		660	1334	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11319334	11319334	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	176	462	0	ENST00000361445.4:c.133C>T	p.Gln45Ter	p.Q45*	ENST00000361445	NM_004958.3	45	Cag/Tag	2/58	1	2	FACETS	0.765	0.705	0.827	1	0.99	1	SUBCLONAL	2	TRUE	1	0.268756637246289	2		462	856	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514563	41514563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	97	304	0	ENST00000373198.4:c.98C>T	p.Ser33Phe	p.S33F	ENST00000373198	NM_133170.3	33	tCc/tTc	2/32	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.268756637246289	2		304	696	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857284	9857284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	147	493	0	ENST00000330684.3:c.4117G>A	p.Asp1373Asn	p.D1373N	ENST00000330684	NM_001134407.1	1373	Gat/Aat	13/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.268756637246289	2		493	880	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970901	21970901	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs45476696	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	146	407	0	ENST00000304494.5:c.457G>A	p.Asp153Asn	p.D153N	ENST00000304494	NM_000077.4	153	Gac/Aac	2/3	0.268756637246289	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.268756637246289	1		407	728	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3789685	3789685	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	148	487	0	ENST00000262367.5:c.4174C>T	p.Arg1392Ter	p.R1392*	ENST00000262367	NM_004380.2	1392	Cga/Tga	25/31	1	2	FACETS	0.984	0.897	1	0.984	0.897	1	CLONAL	1	TRUE	1	0.268756637246289	2		487	1119	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166500	118166500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	137	384	0	ENST00000369448.3:c.1010C>T	p.Ala337Val	p.A337V	ENST00000369448	NM_017709.3	337	gCc/gTc	2/2	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.268756637246289	2		384	884	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458828	120458828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	129	405	0	ENST00000256646.2:c.6517C>T	p.Pro2173Ser	p.P2173S	ENST00000256646	NM_024408.3	2173	Cct/Tct	34/34	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.268756637246289	2		405	769	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120509023	120509023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782444829	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	169	449	0	ENST00000256646.2:c.1543C>T	p.Arg515Cys	p.R515C	ENST00000256646	NM_024408.3	515	Cgt/Tgt	9/34	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.268756637246289	2		449	1161	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982427	25982427	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	159	504	0	ENST00000435504.4:c.863A>G	p.Asn288Ser	p.N288S	ENST00000435504		288	aAc/aGc	9/13	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.268756637246289	2		504	1094	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266711	198266711	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	128	387	0	ENST00000335508.6:c.2221A>T	p.Lys741Ter	p.K741*	ENST00000335508	NM_012433.2	741	Aag/Tag	15/25	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.268756637246289	2		387	807	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939998	49939998	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1359	216	794	1	ENST00000296474.3:c.1045G>A	p.Val349Ile	p.V349I	ENST00000296474	NM_002447.2	349	Gtc/Atc	1/20	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.268756637246289	2		795	1575	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670282	134670282	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748807854	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	126	438	0	ENST00000398015.3:c.193G>A	p.Glu65Lys	p.E65K	ENST00000398015	NM_004441.4	65	Gag/Aag	3/16	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.268756637246289	2		438	689	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526316	189526316	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	40	202	0	ENST00000264731.3:c.579+1G>A		p.X193_splice	ENST00000264731	NM_003722.4	193			1	2	FACETS	0.843	0.702	0.999	0.843	0.702	0.999	CLONAL	1	TRUE	1	0.268756637246289	2		202	353	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607246	189607246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1374623968	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	55	511	0	ENST00000264731.3:c.1625C>T	p.Pro542Leu	p.P542L	ENST00000264731	NM_003722.4	542	cCg/cTg	12/14	1	2	FACETS	0.456	0.389	0.53	0.456	0.389	0.53	SUBCLONAL	1	TRUE	1	0.268756637246289	2		511	897	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144683	55144683	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	52	350	1	ENST00000257290.5:c.2156+1G>A		p.X719_splice	ENST00000257290	NM_006206.4	719			0.223146282376153	1	FACETS	0.488	0.414	0.568	0.488	0.414	0.568	SUBCLONAL	1	TRUE	0	0.268756637246289	1		351	687	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293431	1293431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	77	239	0	ENST00000310581.5:c.1570C>T	p.Pro524Ser	p.P524S	ENST00000310581	NM_198253.2	524	Cca/Tca	2/16	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.268756637246289	2		239	451	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38966798	38966798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768191069	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	138	453	0	ENST00000357387.3:c.1244G>A	p.Ser415Asn	p.S415N	ENST00000357387	NM_152756.3	415	aGt/aAt	15/38	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.268756637246289	2		453	970	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86658378	86658378	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	52	364	0	ENST00000274376.6:c.1343A>G	p.Gln448Arg	p.Q448R	ENST00000274376	NM_002890.2	448	cAa/cGa	10/25	1	2	FACETS	0.619	0.526	0.721	0.619	0.526	0.721	SUBCLONAL	1	TRUE	1	0.268756637246289	2		364	625	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674234	86674234	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	104	328	0	ENST00000274376.6:c.2366G>C	p.Arg789Pro	p.R789P	ENST00000274376	NM_002890.2	789	cGa/cCa	18/25	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.268756637246289	2		328	707	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651937	36651937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375050346	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	80	286	1	ENST00000244741.5:c.59G>A	p.Arg20His	p.R20H	ENST00000244741	NM_000389.4	20	cGc/cAc	2/3	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.268756637246289	2		287	531	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946448	2946448	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	117	458	0	ENST00000396946.4:c.3289G>A	p.Glu1097Lys	p.E1097K	ENST00000396946	NM_032415.4	1097	Gag/Aag	25/25	1	2	FACETS	0.977	0.88	1	0.977	0.88	1	CLONAL	1	TRUE	1	0.268756637246289	2		458	891	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397737	116397737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	147	591	0	ENST00000397752.3:c.2011G>A	p.Gly671Ser	p.G671S	ENST00000397752	NM_000245.2	671	Ggt/Agt	8/21	1	2	FACETS	0.969	0.883	1	0.969	0.883	1	CLONAL	1	TRUE	1	0.268756637246289	2		591	1129	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524338	148524338	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771139896	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	139	373	0	ENST00000320356.2:c.646C>T	p.Arg216Trp	p.R216W	ENST00000320356	NM_004456.4	216	Cgg/Tgg	7/20	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.268756637246289	2		373	906	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737690	145737690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	60	337	0	ENST00000428558.2:c.3073G>A	p.Gly1025Arg	p.G1025R	ENST00000428558	NM_004260.3	1025	Ggg/Agg	19/22	0.223146282376153	1	FACETS	0.689	0.594	0.793	0.689	0.594	0.793	SUBCLONAL	1	TRUE	0	0.268756637246289	1		337	561	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485252	8485252	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	247	539	0	ENST00000356435.5:c.3128A>G	p.Asn1043Ser	p.N1043S	ENST00000356435		1043	aAt/aGt	18/35	0.268756637246289	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.268756637246289	1		539	1136	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244913	123244913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1224606327	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	138	452	1	ENST00000358487.5:c.2191G>A	p.Glu731Lys	p.E731K	ENST00000358487	NM_000141.4	731	Gaa/Aaa	16/18	0.223146282376153	1	FACETS	0.903	0.821	0.99	0.903	0.821	0.99	CLONAL	1	TRUE	0	0.268756637246289	1		453	984	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201933	102201933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1526	1726	865	2	ENST00000263464.3:c.1285G>A	p.Glu429Lys	p.E429K	ENST00000263464	NM_001165.4	429	Gaa/Aaa	6/9	0.268756637246289	8	FACETS	1	0.991	1			1	CLONAL	7	TRUE	NA	0.268756637246289	8		867	3252	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374387	118374387	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	133	433	0	ENST00000534358.1:c.7780C>T	p.Leu2594Phe	p.L2594F	ENST00000534358	NM_005933.3	2594	Ctt/Ttt	27/36	0.268756637246289	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.268756637246289	1		433	716	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864682	57864682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	391	865	0	ENST00000228682.2:c.2159C>T	p.Pro720Leu	p.P720L	ENST00000228682	NM_005269.2	720	cCc/cTc	12/12	0.268756637246289	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	0	0.268756637246289	2		865	1420	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111855978	111855978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1484288251	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	312	584	0	ENST00000341259.2:c.29C>T	p.Ser10Leu	p.S10L	ENST00000341259	NM_005475.2	10	tCg/tTg	2/8	0.268756637246289	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.268756637246289	2		584	1083	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924327	112924327	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	241	566	0	ENST00000351677.2:c.1273G>A	p.Asp425Asn	p.D425N	ENST00000351677	NM_002834.3	425	Gac/Aac	11/16	0.268756637246289	2	FACETS	0.973	0.91	1	0.973	0.91	1	CLONAL	2	TRUE	0	0.268756637246289	2		566	922	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549055	21549055	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs905177711	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	95	300	0	ENST00000382592.4:c.3221C>T	p.Ser1074Phe	p.S1074F	ENST00000382592	NM_014572.2	1074	tCt/tTt	8/8	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.268756637246289	2		300	624	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527880	103527880	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	75	451	0	ENST00000355739.4:c.3188C>T	p.Thr1063Ile	p.T1063I	ENST00000355739	NM_000123.3	1063	aCc/aTc	15/15	1	2	FACETS	0.539	0.471	0.613	0.539	0.471	0.613	SUBCLONAL	1	TRUE	1	0.268756637246289	2		451	1036	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437740	110437740	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	146	531	2	ENST00000375856.3:c.661C>A	p.Leu221Met	p.L221M	ENST00000375856	NM_003749.2	221	Ctg/Atg	1/2	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.268756637246289	2		533	1012	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988838	41988838	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1623	340	1035	0	ENST00000219905.7:c.1630C>T	p.Pro544Ser	p.P544S	ENST00000219905	NM_001164273.1	544	Ccc/Tcc	3/24	0.223146282376153	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.268756637246289	1		1035	1963	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003035	42003035	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1657	171	1011	0	ENST00000219905.7:c.2572C>T	p.Pro858Ser	p.P858S	ENST00000219905	NM_001164273.1	858	Ccc/Tcc	8/24	0.223146282376153	1	FACETS	0.603	0.552	0.656	0.603	0.552	0.656	SUBCLONAL	1	TRUE	0	0.268756637246289	1		1011	1828	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003036	42003036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1664	173	1011	0	ENST00000219905.7:c.2573C>T	p.Pro858Leu	p.P858L	ENST00000219905	NM_001164273.1	858	cCc/cTc	8/24	0.223146282376153	1	FACETS	0.607	0.556	0.66	0.607	0.556	0.66	SUBCLONAL	1	TRUE	0	0.268756637246289	1		1011	1837	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003340	42003340	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1454	304	863	0	ENST00000219905.7:c.2877G>T	p.Leu959Phe	p.L959F	ENST00000219905	NM_001164273.1	959	ttG/ttT	8/24	0.223146282376153	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.268756637246289	1		863	1758	SUCCESS
BLM	641	MSKCC	GRCh37	15	91328178	91328178	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	100	469	0	ENST00000355112.3:c.2690C>T	p.Ser897Phe	p.S897F	ENST00000355112	NM_000057.2	897	tCc/tTc	14/22	0.223146282376153	1	FACETS	0.63	0.561	0.703	0.63	0.561	0.703	SUBCLONAL	1	TRUE	0	0.268756637246289	1		469	1023	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831253	3831253	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	114	443	0	ENST00000262367.5:c.1628C>T	p.Pro543Leu	p.P543L	ENST00000262367	NM_004380.2	543	cCa/cTa	7/31	1	2	FACETS	0.843	0.758	0.934	0.843	0.758	0.934	CLONAL	1	TRUE	1	0.268756637246289	2		443	1006	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934887	9934887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	167	591	2	ENST00000330684.3:c.1403C>T	p.Ser468Phe	p.S468F	ENST00000330684	NM_001134407.1	468	tCc/tTc	6/13	1	2	FACETS	0.999	0.916	1	0.999	0.916	1	CLONAL	1	TRUE	1	0.268756637246289	2		593	1244	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72845640	72845640	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148354034	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1337	165	845	0	ENST00000268489.5:c.3700G>A	p.Asp1234Asn	p.D1234N	ENST00000268489	NM_006885.3	1234	Gat/Aat	7/10	1	2	FACETS	0.817	0.748	0.89	0.817	0.748	0.89	CLONAL	1	TRUE	1	0.268756637246289	2		845	1502	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554566	29554566	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	136	416	0	ENST00000356175.3:c.2351G>A	p.Trp784Ter	p.W784*	ENST00000356175	NM_000267.3	784	tGg/tAg	20/57	0.268756637246289	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.268756637246289	1		416	772	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439925	56439925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755478993	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	79	230	0	ENST00000407977.2:c.667C>T	p.Arg223Cys	p.R223C	ENST00000407977		223	Cgc/Tgc	6/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.268756637246289	2		230	469	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678020	58678020	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	98	365	1	ENST00000305921.3:c.245C>T	p.Ala82Val	p.A82V	ENST00000305921	NM_003620.3	82	gCc/gTc	1/6	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.268756637246289	2		366	668	SUCCESS
YES1	7525	MSKCC	GRCh37	18	751751	751751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	128	400	0	ENST00000314574.4:c.325G>A	p.Asp109Asn	p.D109N	ENST00000314574	NM_005433.3	109	Gac/Aac	3/12	0.223146282376153	1	FACETS	0.983	0.891	1	0.983	0.891	1	CLONAL	1	TRUE	0	0.268756637246289	1		400	839	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799135	42799135	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1411966235	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	73	334	0	ENST00000575354.2:c.4619C>T	p.Pro1540Leu	p.P1540L	ENST00000575354	NM_015125.3	1540	cCc/cTc	20/20	0.223146282376153	1	FACETS	0.924	0.81	1	0.924	0.81	1	CLONAL	1	TRUE	0	0.268756637246289	1		334	509	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50920463	50920463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1005672452	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	120	518	0	ENST00000440232.2:c.3155C>T	p.Ser1052Leu	p.S1052L	ENST00000440232	NM_002691.3	1052	tCg/tTg	26/27	0.223146282376153	1	FACETS	0.94	0.849	1	0.94	0.849	1	CLONAL	1	TRUE	0	0.268756637246289	1		518	822	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624810	9624810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	83	349	0	ENST00000353224.5:c.167C>T	p.Pro56Leu	p.P56L	ENST00000353224	NM_177990.2	56	cCt/cTt	3/10	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.268756637246289	2		349	588	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624811	9624811	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	83	353	1	ENST00000353224.5:c.166C>A	p.Pro56Thr	p.P56T	ENST00000353224	NM_177990.2	56	Cct/Act	3/10	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.268756637246289	2		354	590	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39690106	39690106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	134	286	1	ENST00000361337.2:c.131G>A	p.Arg44Gln	p.R44Q	ENST00000361337	NM_003286.2	44	cGg/cAg	3/21	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.268756637246289	2		287	743	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279780	46279780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	93	406	0	ENST00000371998.3:c.3706C>T	p.His1236Tyr	p.H1236Y	ENST00000371998		1236	Cat/Tat	20/23	1	2	FACETS	0.82	0.728	0.918	0.82	0.728	0.918	CLONAL	1	TRUE	1	0.268756637246289	2		406	844	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545060	41545060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	193	520	0	ENST00000263253.7:c.2260C>T	p.Arg754Cys	p.R754C	ENST00000263253	NM_001429.3	754	Cgt/Tgt	13/31	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.268756637246289	2		520	1087	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756613	756614	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0007544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	93	521	1	ENST00000314574.4:c.214_215delinsAA	p.Gly72Lys	p.G72K	ENST00000314574	NM_005433.3	72	GGa/AAa	2/12	0.223146282376153	1	FACETS	0.526	0.466	0.59	0.526	0.466	0.59	SUBCLONAL	1	TRUE	0	0.268756637246289	1		522	1139	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0007561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	142	464	0				ENST00000310581	NM_198253.2	-/1132			0.138621759285735	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.950837699860184	0		464	317	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0007561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	800	500	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	1	0.950837699860184	2		500	1269	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0007561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	376	292	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	0.950837699860184	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.950837699860184	1		292	395	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254623	16254623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749814808	NA	P-0007561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	487	402	0	ENST00000375759.3:c.1888C>T	p.Arg630Cys	p.R630C	ENST00000375759	NM_015001.2	630	Cgt/Tgt	11/15	0.919808086599417	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.950837699860184	1		402	526	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65311195	65311195	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0007561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	330	264	0	ENST00000342505.4:c.2115+1G>T		p.X705_splice	ENST00000342505	NM_002227.2	705			0.941432543024449	1	FACETS	0.998	0.976	1	0.998	0.976	1	CLONAL	1	TRUE	0	0.950837699860184	1		264	365	SUCCESS
ALK	238	MSKCC	GRCh37	2	29443616	29443616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	350	266	0	ENST00000389048.3:c.3601G>A	p.Gly1201Arg	p.G1201R	ENST00000389048	NM_004304.4	1201	Ggg/Agg	23/29	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.950837699860184	2		266	633	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119582446	119582446	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs768552900	NA	P-0007561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	136	107	0	ENST00000316626.5:c.955C>T	p.Arg319Ter	p.R319*	ENST00000316626		319	Cga/Tga	10/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.950837699860184	2		107	267	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178211	142178211	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	205	184	0	ENST00000350721.4:c.7207G>A	p.Gly2403Arg	p.G2403R	ENST00000350721	NM_001184.3	2403	Gga/Aga	43/47	1	2	FACETS	0.931	0.874	0.989	0.931	0.874	0.989	CLONAL	1	TRUE	1	0.950837699860184	2		184	463	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455608	189455608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	355	287	1	ENST00000264731.3:c.142G>A	p.Glu48Lys	p.E48K	ENST00000264731	NM_003722.4	48	Gaa/Aaa	2/14	1	2	FACETS	0.923	0.879	0.967	0.923	0.879	0.967	CLONAL	1	TRUE	1	0.950837699860184	2		288	809	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66468018	66468018	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	149	139	0	ENST00000273854.3:c.251A>G	p.Glu84Gly	p.E84G	ENST00000273854	NM_004439.5	84	gAa/gGa	3/18	0.950837699860184	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.950837699860184	1		139	164	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156829	106156829	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	316	257	0	ENST00000380013.4:c.1730C>T	p.Ser577Phe	p.S577F	ENST00000380013	NM_001127208.2	577	tCc/tTc	3/11	0.950837699860184	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.950837699860184	1		257	344	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244235	153244235	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	338	295	1	ENST00000281708.4:c.1922C>T	p.Ser641Leu	p.S641L	ENST00000281708	NM_033632.3	641	tCa/tTa	12/12	0.950837699860184	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.950837699860184	1		296	357	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510243	187510243	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1238824270	NA	P-0007561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	224	297	0	ENST00000441802.2:c.13270T>A	p.Tyr4424Asn	p.Y4424N	ENST00000441802	NM_005245.3	4424	Tat/Aat	27/27	0.950837699860184	1	FACETS	0.993	0.966	1	0.993	0.966	1	CLONAL	1	TRUE	0	0.950837699860184	1		297	249	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180050945	180050945	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	405	270	0	ENST00000261937.6:c.1538G>T	p.Gly513Val	p.G513V	ENST00000261937	NM_182925.4	513	gGa/gTa	11/30	0.138621759285735	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.950837699860184	0		270	873	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725456	117725456	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	323	310	0	ENST00000368508.3:c.425G>A	p.Trp142Ter	p.W142*	ENST00000368508	NM_002944.2	142	tGg/tAg	5/43	0.950837699860184	1	FACETS	0.979	0.956	1	0.979	0.956	1	CLONAL	1	TRUE	0	0.950837699860184	1		310	364	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355222	81355222	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	269	245	0	ENST00000222390.5:c.1152T>A	p.Asp384Glu	p.D384E	ENST00000222390	NM_000601.4	384	gaT/gaA	9/18	0.950837699860184	3	FACETS	0.914	0.859	0.971	0.457	0.429	0.486	CLONAL	1	TRUE	1	0.950837699860184	3		245	913	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596032	43596032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749390385	NA	P-0007561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	23	293	255	0	ENST00000355710.3:c.199C>T	p.Arg67Cys	p.R67C	ENST00000355710	NM_020975.4	67	Cgc/Tgc	2/20	0.919808086599417	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.950837699860184	1		255	316	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653814	89653815	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0007561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	29	321	212	0	ENST00000371953.3:c.112_113delinsTT	p.Pro38Phe	p.P38F	ENST00000371953	NM_000314.4	38	CCt/TTt	2/9	0.919808086599417	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.950837699860184	1		212	350	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432121	121432121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18	593	276	0	ENST00000257555.6:c.868C>T	p.Pro290Ser	p.P290S	ENST00000257555		290	Ccc/Tcc	4/10	0.949173027566865	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.950837699860184	2		276	611	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68934907	68934907	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs548011714	NA	P-0007561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	448	315	0	ENST00000487270.1:c.976C>T	p.Pro326Ser	p.P326S	ENST00000487270	NM_133509.3	326	Cct/Tct	10/11	1	2	FACETS	0.991	0.95	1	0.991	0.95	1	CLONAL	1	TRUE	1	0.950837699860184	2		315	951	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827217	72827217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	535	547	2	ENST00000268489.5:c.9364C>T	p.Pro3122Ser	p.P3122S	ENST00000268489	NM_006885.3	3122	Cct/Tct	9/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.950837699860184	2		549	1070	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993798	72993798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1283557059	NA	P-0007561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	403	449	4	ENST00000268489.5:c.247G>A	p.Glu83Lys	p.E83K	ENST00000268489	NM_006885.3	83	Gaa/Aaa	2/10	1	2	FACETS	0.901	0.861	0.941	0.901	0.861	0.941	CLONAL	1	TRUE	1	0.950837699860184	2		453	941	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032480	12032480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	188	208	0	ENST00000353533.5:c.916C>T	p.Pro306Ser	p.P306S	ENST00000353533	NM_003010.3	306	Cct/Tct	9/11	1	2	FACETS	0.926	0.866	0.986	0.926	0.866	0.986	CLONAL	1	TRUE	1	0.950837699860184	2		208	427	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354156	15354157	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0007561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	161	80	0	ENST00000263377.2:c.2723_2724delinsTT	p.Pro908Leu	p.P908L	ENST00000263377	NM_058243.2	908	cCC/cTT	14/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.950837699860184	2		80	273	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366366	15366366	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	194	167	0	ENST00000263377.2:c.1789C>T	p.Pro597Ser	p.P597S	ENST00000263377	NM_058243.2	597	Ccc/Tcc	10/20	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.950837699860184	2		167	408	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741870	40741870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144444132	NA	P-0007561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	319	270	0	ENST00000392038.2:c.1102C>T	p.Arg368Cys	p.R368C	ENST00000392038	NM_001626.4	368	Cgc/Tgc	11/14	1	2	FACETS	0.938	0.892	0.985	0.938	0.892	0.985	CLONAL	1	TRUE	1	0.950837699860184	2		270	715	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538374	9538374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868564987	NA	P-0007561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	252	195	0	ENST00000353224.5:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000353224	NM_177990.2	542	Gaa/Aaa	7/10	0.950837699860184	3	FACETS	1	0.957	1	0.511	0.48	0.543	CLONAL	1	TRUE	1	0.950837699860184	3		195	765	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023493	31023493	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1226960123	NA	P-0007561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	593	238	0	ENST00000375687.4:c.2978G>A	p.Ser993Asn	p.S993N	ENST00000375687	NM_015338.5	993	aGt/aAt	13/13	0.950837699860184	3	FACETS	0.993	0.963	1	0.993	0.963	1	CLONAL	2	TRUE	1	0.950837699860184	3		238	927	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408912	41408912	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	320	278	0	ENST00000373198.4:c.514G>A	p.Gly172Ser	p.G172S	ENST00000373198	NM_133170.3	172	Ggt/Agt	4/32	0.950837699860184	3	FACETS	1	0.964	1	0.512	0.484	0.54	CLONAL	1	TRUE	1	0.950837699860184	3		278	970	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961474	54961474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	180	147	0	ENST00000312783.6:c.158C>T	p.Ser53Phe	p.S53F	ENST00000312783	NM_198436.1	53	tCt/tTt	4/10	0.950837699860184	3	FACETS	0.98	0.909	1	0.49	0.454	0.527	CLONAL	1	TRUE	1	0.950837699860184	3		147	570	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776936	76776936	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	481	496	0	ENST00000373344.5:c.7016C>A	p.Thr2339Lys	p.T2339K	ENST00000373344	NM_000489.3	2339	aCa/aAa	33/35	0.138621759285735	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.950837699860184	0		496	1079	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907828	76907828	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	205	200	0	ENST00000373344.5:c.4333G>A	p.Glu1445Lys	p.E1445K	ENST00000373344	NM_000489.3	1445	Gaa/Aaa	15/35	0.138621759285735	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.950837699860184	0		200	473	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971135	21971226	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTCGGCGCAGTTGGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCTGCCCATCATCATGACCTGCCAGAGAGAACAGAAT	GGTCGGCGCAGTTGGGCTCCGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGGCGCTGCCCATCATCATGACCTGCCAGAGAGAACAGAAT	-	novel	NA	P-0007561-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	54	82	0	ENST00000304494.5:c.151-19_223del		p.X51_splice	ENST00000304494	NM_000077.4	51		2/3	0.950837699860184	1	FACETS	0.655	0.587	0.721	0.655	0.587	0.721	SUBCLONAL	1	TRUE	0	0.950837699860184	1		82	91	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	103	280	0				ENST00000310581	NM_198253.2	-/1132			0.117966197711305	5	FACETS	1	0.976	1			1	INDETERMINATE	2	TRUE	NA	0.564716410827588	5		280	274	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56482341	56482341	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519891	NA	P-0007656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	470	453	0	ENST00000267101.3:c.889G>T	p.Asp297Tyr	p.D297Y	ENST00000267101	NM_001982.3	297	Gat/Tat	8/28	0.526270448163502	3	FACETS	0.971	0.938	1	0.971	0.938	1	CLONAL	3	TRUE	0	0.564716410827588	3		453	733	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151270	202151270	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	87	620	0	ENST00000358485.4:c.1570C>T	p.Gln524Ter	p.Q524*	ENST00000358485	NM_001080125.1	524	Cag/Tag	9/9	NA	2	FACETS	0.319	0.281	0.359			1	INDETERMINATE	1	TRUE	NA	0.564716410827588	2		620	966	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519502	137519502	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	328	355	0	ENST00000367739.4:c.1136C>T	p.Ser379Phe	p.S379F	ENST00000367739	NM_000416.2	379	tCt/tTt	7/7	0.333376669819216	3	FACETS	1	0.99	1	0.763	0.727	0.798	INDETERMINATE	2	TRUE	0	0.564716410827588	3		355	651	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486121	8486121	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	260	471	0	ENST00000356435.5:c.2696A>C	p.Asn899Thr	p.N899T	ENST00000356435		899	aAc/aCc	17/35	0.191853892077032	5	FACETS	0.984	0.924	1	0.656	0.616	0.697	INDETERMINATE	2	TRUE	2	0.564716410827588	5		471	864	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778060	135778060	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	343	487	0	ENST00000298552.3:c.2323C>A	p.Leu775Ile	p.L775I	ENST00000298552	NM_001162426.1	775	Ctc/Atc	18/23	0.191853892077032	5	FACETS	1	0.984	1	0.726	0.688	0.765	INDETERMINATE	2	TRUE	2	0.564716410827588	5		487	1030	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343460	118343460	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	216	294	0	ENST00000534358.1:c.1586G>C	p.Arg529Thr	p.R529T	ENST00000534358	NM_005933.3	529	aGa/aCa	3/36	0.564716410827588	2	FACETS	0.915	0.864	0.966	0.915	0.864	0.966	CLONAL	2	TRUE	0	0.564716410827588	2		294	418	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343477	118343477	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs782485631	NA	P-0007656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	218	292	0	ENST00000534358.1:c.1603G>C	p.Glu535Gln	p.E535Q	ENST00000534358	NM_005933.3	535	Gag/Cag	3/36	0.564716410827588	2	FACETS	0.935	0.883	0.986	0.935	0.883	0.986	CLONAL	2	TRUE	0	0.564716410827588	2		292	413	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343586	118343586	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	228	304	0	ENST00000534358.1:c.1712C>A	p.Pro571Gln	p.P571Q	ENST00000534358	NM_005933.3	571	cCa/cAa	3/36	0.564716410827588	2	FACETS	0.924	0.874	0.974	0.924	0.874	0.974	CLONAL	2	TRUE	0	0.564716410827588	2		304	437	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344204	118344204	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	259	313	0	ENST00000534358.1:c.2330C>G	p.Ser777Cys	p.S777C	ENST00000534358	NM_005933.3	777	tCt/tGt	3/36	0.564716410827588	2	FACETS	0.908	0.861	0.955	0.908	0.861	0.955	CLONAL	2	TRUE	0	0.564716410827588	2		313	505	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344230	118344230	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	197	258	0	ENST00000534358.1:c.2356C>A	p.Pro786Thr	p.P786T	ENST00000534358	NM_005933.3	786	Cct/Act	3/36	0.564716410827588	2	FACETS	0.883	0.83	0.936	0.883	0.83	0.936	CLONAL	2	TRUE	0	0.564716410827588	2		258	395	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881414	48881414	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0007656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	211	258	0	ENST00000267163.4:c.138-2A>G		p.X46_splice	ENST00000267163	NM_000321.2	46			0.564716410827588	2	FACETS	0.936	0.884	0.989	0.936	0.884	0.989	CLONAL	2	TRUE	0	0.564716410827588	2		258	399	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786766	3786766	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587783496	NA	P-0007656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	351	483	0	ENST00000262367.5:c.4445A>G	p.Tyr1482Cys	p.Y1482C	ENST00000262367	NM_004380.2	1482	tAc/tGc	27/31	0.563284518763556	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.564716410827588	2		483	595	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369458	40369458	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	210	873	0	ENST00000293328.3:c.1194C>G	p.Asn398Lys	p.N398K	ENST00000293328	NM_012448.3	398	aaC/aaG	10/19	NA	2	FACETS	0.676	0.627	0.726			1	INDETERMINATE	1	TRUE	NA	0.564716410827588	2		873	1101	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149808	202149812	+	stop_gained	Nonsense_Mutation	ONP	CAGGC	CAGGC	TAGGT	novel	NA	P-0007656-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	42	380	0	ENST00000358485.4:c.1249_1253delinsTAGGT	p.Gln417_Ala418delinsTer	p.Q417_A418delins*	ENST00000358485	NM_001080125.1	417	CAGGCt/TAGGTt	8/9	NA	2	FACETS	0.25	0.208	0.296			1	INDETERMINATE	1	TRUE	NA	0.564716410827588	2		380	596	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	212	280	0				ENST00000310581	NM_198253.2	-/1132			0.651212416924157	5	FACETS	0.826	0.77	0.884	0.551	0.513	0.589	CLONAL	2	FALSE	2	0.728816018935622	5		280	737	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0007658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	451	550	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.63651389073334	2	FACETS	0.837	0.808	0.867	0.837	0.808	0.867	CLONAL	2	FALSE	0	0.728816018935622	2		550	739	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0007658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	398	491	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	0.393418700441801	3	FACETS	0.78	0.745	0.816	0.78	0.745	0.816	INDETERMINATE	2	FALSE	1	0.728816018935622	3		491	955	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0007658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	849	421	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.728816018935622	4	FACETS	0.943	0.918	0.967			1	CLONAL	3	FALSE	NA	0.728816018935622	4		421	1424	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485397	57485397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	145	327	1	ENST00000371085.3:c.979G>A	p.Glu327Lys	p.E327K	ENST00000371085	NM_000516.4	327	Gag/Aag	12/13	0.651212416924157	5	FACETS	0.763	0.695	0.835	0.254	0.231	0.279	SUBCLONAL	1	FALSE	2	0.728816018935622	5		328	1091	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261577	16261577	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	338	318	0	ENST00000375759.3:c.8842G>T	p.Val2948Phe	p.V2948F	ENST00000375759	NM_015001.2	2948	Gtc/Ttc	11/15	0.313451054562466	5	FACETS	1	0.989	1	0.758	0.72	0.796	INDETERMINATE	2	FALSE	2	0.728816018935622	5		318	854	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330586	65330586	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs561562970	NA	P-0007658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	221	623	0	ENST00000342505.4:c.1060G>A	p.Glu354Lys	p.E354K	ENST00000342505	NM_002227.2	354	Gag/Aag	8/25	0.313451054562466	5	FACETS	1	0.955	1	0.345	0.321	0.371	INDETERMINATE	1	FALSE	2	0.728816018935622	5		623	1225	SUCCESS
ATR	545	MSKCC	GRCh37	3	142241667	142241667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	155	380	0	ENST00000350721.4:c.4169C>T	p.Ser1390Leu	p.S1390L	ENST00000350721	NM_001184.3	1390	tCa/tTa	23/47	0.616244876253923	5	FACETS	0.809	0.739	0.882	0.27	0.246	0.294	CLONAL	1	FALSE	2	0.728816018935622	5		380	1101	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046343	180046343	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	95	282	0	ENST00000261937.6:c.2671C>A	p.Arg891Ser	p.R891S	ENST00000261937	NM_182925.4	891	Cgc/Agc	19/30	0.573060647614706	4	FACETS	0.555	0.494	0.621	0.278	0.247	0.311	SUBCLONAL	1	FALSE	2	0.728816018935622	4		282	812	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6029578	6029578	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	286	480	0	ENST00000265849.7:c.997G>A	p.Asp333Asn	p.D333N	ENST00000265849	NM_000535.5	333	Gat/Aat	10/15	0.24799590295121	5	FACETS	0.877	0.826	0.929	0.584	0.55	0.619	INDETERMINATE	2	FALSE	2	0.728816018935622	5		480	937	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069037	5069037	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	171	391	0	ENST00000381652.3:c.1342G>A	p.Glu448Lys	p.E448K	ENST00000381652	NM_004972.3	448	Gaa/Aaa	11/25	0.63651389073334	2	FACETS	0.825	0.763	0.888	0.412	0.381	0.444	CLONAL	1	FALSE	0	0.728816018935622	2		391	569	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571883	64571883	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1354	647	891	2	ENST00000312049.6:c.1756C>T	p.Gln586Ter	p.Q586*	ENST00000312049	NM_130799.2	586	Cag/Tag	10/10	0.183813498854729	5	FACETS	0.929	0.893	0.965	0.619	0.595	0.643	INDETERMINATE	2	FALSE	2	0.728816018935622	5		893	2001	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202594	67202594	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0007658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	302	463	1	ENST00000312629.5:c.1403C>G	p.Ser468Ter	p.S468*	ENST00000312629	NM_003952.2	468	tCa/tGa	15/15	0.183813498854729	5	FACETS	0.862	0.813	0.912	0.575	0.542	0.608	INDETERMINATE	2	FALSE	2	0.728816018935622	5		464	1006	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574226	95574226	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	326	363	1	ENST00000393063.1:c.2641C>A	p.Leu881Ile	p.L881I	ENST00000393063	NM_030621.3	881	Ctt/Att	17/28	0.573060647614706	4	FACETS	1	0.963	1	1	0.963	1	CLONAL	2	FALSE	2	0.728816018935622	4		364	761	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138300	2138300	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760413281	NA	P-0007658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	412	413	1	ENST00000219476.3:c.5233C>T	p.Arg1745Cys	p.R1745C	ENST00000219476	NM_000548.3	1745	Cgc/Tgc	41/42	0.313451054562466	5	FACETS	1	0.98	1	0.699	0.667	0.732	INDETERMINATE	2	FALSE	2	0.728816018935622	5		414	1128	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868636	37868636	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	930	434	0	ENST00000269571.5:c.1083C>G	p.Ile361Met	p.I361M	ENST00000269571		361	atC/atG	9/27	0.728816018935622	4	FACETS	0.958	0.934	0.982			1	CLONAL	3	FALSE	NA	0.728816018935622	4		434	1535	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369481	40369481	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1307918431	NA	P-0007658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	1267	664	0	ENST00000293328.3:c.1171G>A	p.Asp391Asn	p.D391N	ENST00000293328	NM_012448.3	391	Gat/Aat	10/19	0.728816018935622	4	FACETS	0.974	0.954	0.994			1	CLONAL	3	FALSE	NA	0.728816018935622	4		664	2057	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52719895	52719895	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	809	456	0	ENST00000322088.6:c.1107C>A	p.Phe369Leu	p.F369L	ENST00000322088	NM_014225.5	369	ttC/ttA	9/15	0.600644301756304	6	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	FALSE	3	0.728816018935622	6		456	1666	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568656	41568656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	288	352	1	ENST00000263253.7:c.4606G>A	p.Glu1536Lys	p.E1536K	ENST00000263253	NM_001429.3	1536	Gaa/Aaa	28/31	0.573060647614706	4	FACETS	0.797	0.752	0.843	0.797	0.752	0.843	SUBCLONAL	2	FALSE	2	0.728816018935622	4		353	857	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568668	41568668	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0007658-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	230	291	0	ENST00000263253.7:c.4617+1G>C		p.X1539_splice	ENST00000263253	NM_001429.3	1539			0.573060647614706	4	FACETS	0.763	0.714	0.813	0.763	0.714	0.813	SUBCLONAL	2	FALSE	2	0.728816018935622	4		291	715	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	29	280	0				ENST00000310581	NM_198253.2	-/1132			0.389234500482972	1	FACETS	0.153	0.123	0.187	0.153	0.123	0.187	INDETERMINATE	1	TRUE	0	0.78254759855681	1		280	295	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0007682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	373	538	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	0.389234500482972	1	FACETS	0.759	0.725	0.792	0.759	0.725	0.792	INDETERMINATE	1	TRUE	0	0.78254759855681	1		538	765	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0007682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	536	1211	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	0.389234500482972	1	FACETS	0.714	0.687	0.741	0.714	0.687	0.741	INDETERMINATE	1	TRUE	0	0.78254759855681	1		1211	1168	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117759	115117759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	360	504	0	ENST00000257566.3:c.676G>A	p.Asp226Asn	p.D226N	ENST00000257566	NM_016569.3	226	Gat/Aat	3/8	0.389234500482972	1	FACETS	0.735	0.701	0.769	0.735	0.701	0.769	INDETERMINATE	1	TRUE	0	0.78254759855681	1		504	762	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390342	118390342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	304	439	0	ENST00000534358.1:c.11156G>A	p.Gly3719Asp	p.G3719D	ENST00000534358	NM_005933.3	3719	gGt/gAt	32/36	0.389234500482972	1	FACETS	0.765	0.728	0.803	0.765	0.728	0.803	INDETERMINATE	1	TRUE	0	0.78254759855681	1		439	618	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118812	115118812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	367	468	0	ENST00000257566.3:c.529G>A	p.Asp177Asn	p.D177N	ENST00000257566	NM_016569.3	177	Gac/Aac	2/8	0.389234500482972	1	FACETS	0.739	0.705	0.772	0.739	0.705	0.772	INDETERMINATE	1	TRUE	0	0.78254759855681	1		468	773	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437385	110437385	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0007682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	32	76	0	ENST00000375856.3:c.1016T>G	p.Val339Gly	p.V339G	ENST00000375856	NM_003749.2	339	gTg/gGg	1/2	0.403412545759713	3	FACETS	0.488	0.399	0.588	0.244	0.199	0.294	INDETERMINATE	1	TRUE	1	0.78254759855681	3		76	233	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949967	44949967	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0007682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	328	242	0	ENST00000377967.4:c.3737-1G>T		p.X1246_splice	ENST00000377967	NM_021140.2	1246			1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.78254759855681	1		242	404	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	INS	-	-	GGGGCTGGGCTGGGAGGGCCCGGAA	novel	NA	P-0007682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	33	232	0				ENST00000310581	NM_198253.2	-/1132			0.389234500482972	1	FACETS	0.162	0.132	0.196	0.162	0.132	0.196	INDETERMINATE	1	TRUE	0	0.78254759855681	1		232	317	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33792738	33792739	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0007682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	80	65	0	ENST00000498907.2:c.582dup	p.His195AlafsTer126	p.H195Afs*126	ENST00000498907	NM_004364.3	194	-/G	1/1	0.403412545759713	3	FACETS	0.857	0.775	0.939	0.857	0.775	0.939	INDETERMINATE	2	TRUE	1	0.78254759855681	3		65	166	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3794941	3794944	+	frameshift_variant	Frame_Shift_Del	DEL	CAAG	CAAG	-	novel	NA	P-0007682-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	328	488	0	ENST00000262367.5:c.3933_3936del	p.Cys1311Ter	p.C1311*	ENST00000262367	NM_004380.2	1311	tgCTTG/tg	23/31	0.389234500482972	1	FACETS	0.661	0.628	0.694	0.661	0.628	0.694	INDETERMINATE	1	TRUE	0	0.78254759855681	1		488	772	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0007741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	59	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.226990901896335	3	FACETS	0.981	0.844	1	0.491	0.422	0.565	CLONAL	1	TRUE	1	0.226990901896335	3		490	590	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0007741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	19	263	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.764	0.582	0.978	0.764	0.582	0.978	CLONAL	1	TRUE	1	0.226990901896335	2		263	219	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061250	38061250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1459219194	NA	P-0007741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	88	513	2	ENST00000250448.2:c.739C>T	p.His247Tyr	p.H247Y	ENST00000250448	NM_004496.3	247	Cac/Tac	2/2	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.226990901896335	2		515	639	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105892	27105892	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	99	323	0	ENST00000324856.7:c.5503C>T	p.Gln1835Ter	p.Q1835*	ENST00000324856	NM_006015.4	1835	Cag/Tag	20/20	0.196931614850692	2	FACETS	1	0.972	1	0.638	0.569	0.71	CLONAL	1	TRUE	0	0.226990901896335	2		323	684	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820971	36820971	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766507697	NA	P-0007741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	94	501	0	ENST00000373129.3:c.406C>T	p.Arg136Cys	p.R136C	ENST00000373129	NM_032017.1	136	Cgc/Tgc	6/12	0.196931614850692	2	FACETS	1	0.948	1	0.556	0.494	0.621	CLONAL	1	TRUE	0	0.226990901896335	2		501	745	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845584	68845586	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	CAG	CAG	-	novel	NA	P-0007741-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	67	287	0	ENST00000261769.5:c.833-3_833-1del		p.X278_splice	ENST00000261769	NM_004360.3	278			0.226990901896335	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.226990901896335	1		287	478	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	118	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.695019942843924	2		280	285	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955538	48955538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913303	NA	P-0007751-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	138	484	0	ENST00000267163.4:c.1654C>T	p.Arg552Ter	p.R552*	ENST00000267163	NM_000321.2	552	Cga/Tga	17/27	0.677259602264187	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.695019942843924	1		484	249	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007755-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	101	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.330777684152606	2		280	463	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0007755-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	38	595	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.286	0.235	0.343	0.286	0.235	0.343	SUBCLONAL	1	TRUE	1	0.330777684152606	2		595	804	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867687	45867687	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007755-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	235	540	0	ENST00000391945.4:c.713A>G	p.Asn238Ser	p.N238S	ENST00000391945	NM_000400.3	238	aAc/aGc	8/23	0.282836540331884	3	FACETS	0.822	0.767	0.879			1	CLONAL	2	TRUE	NA	0.330777684152606	3		540	1007	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577565	7577565	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519999	NA	P-0007755-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	142	461	0	ENST00000269305.4:c.716A>G	p.Asn239Ser	p.N239S	ENST00000269305	NM_001126112.2	239	aAc/aGc	7/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.330777684152606	2		461	801	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100081	157100092	+	inframe_deletion	In_Frame_Del	DEL	GCGGCGGCGGCC	GCGGCGGCGGCC	-	rs763063242	NA	P-0007755-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	21	41	0	ENST00000346085.5:c.1029_1040del	p.Ala347_Ala350del	p.A347_A350del	ENST00000346085	NM_020732.3	340	GCGGCGGCGGCC/-	1/20	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.330777684152606	2		41	92	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681461	30681461	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007755-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	142	458	0	ENST00000376406.3:c.551C>T	p.Ser184Leu	p.S184L	ENST00000376406	NM_014641.2	184	tCa/tTa	4/15	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.330777684152606	2		458	829	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527328	157527328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007755-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	67	329	0	ENST00000346085.5:c.5053G>A	p.Glu1685Lys	p.E1685K	ENST00000346085	NM_020732.3	1685	Gag/Aag	20/20	1	2	FACETS	0.739	0.643	0.843	0.739	0.643	0.843	SUBCLONAL	1	TRUE	1	0.330777684152606	2		329	548	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41547874	41547874	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0007755-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	55	464	0	ENST00000263253.7:c.2855C>G	p.Ser952Ter	p.S952*	ENST00000263253	NM_001429.3	952	tCa/tGa	15/31	NA	2	FACETS	0.359	0.306	0.418			1	INDETERMINATE	1	TRUE	NA	0.330777684152606	2		464	926	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907194	32907194	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007755-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	69	430	0	ENST00000380152.3:c.1579C>G	p.Pro527Ala	p.P527A	ENST00000380152		527	Cca/Gca	10/27	1	2	FACETS	0.455	0.395	0.52	0.455	0.395	0.52	SUBCLONAL	1	TRUE	1	0.330777684152606	2		430	917	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247369	153247369	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007755-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	111	231	0	ENST00000281708.4:c.1433C>T	p.Ser478Phe	p.S478F	ENST00000281708	NM_033632.3	478	tCt/tTt	10/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.330777684152606	2		231	573	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428532	72428532	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007755-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	115	398	0	ENST00000477973.2:c.472C>T	p.Gln158Ter	p.Q158*	ENST00000477973	NM_012234.5	158	Cag/Tag	2/4	NA	2	FACETS	0.879	0.792	0.971			1	INDETERMINATE	1	TRUE	NA	0.330777684152606	2		398	791	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151919142	151919142	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007755-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	109	325	0	ENST00000262189.6:c.3443C>A	p.Ser1148Ter	p.S1148*	ENST00000262189	NM_170606.2	1148	tCa/tAa	22/59	NA	2	FACETS	1	0.948	1			1	INDETERMINATE	1	TRUE	NA	0.330777684152606	2		325	608	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482185	87482185	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007755-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	114	451	0	ENST00000277120.3:c.1472A>G	p.Asp491Gly	p.D491G	ENST00000277120		491	gAt/gGt	14/19	0.314907419867972	1	FACETS	0.814	0.733	0.899	0.814	0.733	0.899	CLONAL	1	TRUE	0	0.330777684152606	1		451	707	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900894	3900894	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0007755-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	171	564	0	ENST00000262367.5:c.202A>T	p.Lys68Ter	p.K68*	ENST00000262367	NM_004380.2	68	Aaa/Taa	2/31	0.330777684152606	1	FACETS	0.991	0.912	1	0.991	0.912	1	CLONAL	1	TRUE	0	0.330777684152606	1		564	871	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39637883	39637883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007755-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	137	387	0	ENST00000262039.4:c.2300G>A	p.Gly767Asp	p.G767D	ENST00000262039	NM_002647.2	767	gGt/gAt	22/25	0.314907419867972	1	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	0	0.330777684152606	1		387	683	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368262	31368262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007755-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	127	333	0	ENST00000328111.2:c.133G>A	p.Glu45Lys	p.E45K	ENST00000328111	NM_006892.3	45	Gag/Aag	2/23	NA	2	FACETS	1	0.969	1			1	INDETERMINATE	1	TRUE	NA	0.330777684152606	2		333	665	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565505	41565505	+	splice_acceptor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0007755-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	156	347	0	ENST00000263253.7:c.4173-2A>G		p.X1391_splice	ENST00000263253	NM_001429.3	1391			NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	TRUE	NA	0.330777684152606	2		347	725	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533500	63533526	+	inframe_deletion	In_Frame_Del	DEL	AGCAGTAATACTCGCTGCCCCCAGGGC	AGCAGTAATACTCGCTGCCCCCAGGGC	-	novel	NA	P-0007755-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	124	475	1	ENST00000307078.5:c.1628_1654del	p.Cys543_Cys551del	p.C543_C551del	ENST00000307078	NM_004655.3	543	tGCCCTGGGGGCAGCGAGTATTACTGCTac/tac	6/11	0.109168023174057	0	FACETS	0.626	0.566	0.689			1	INDETERMINATE	1	TRUE	0	0.330777684152606	0		476	802	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27092709	27092721	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAGGCCGCCAGGC	TAGGCCGCCAGGC	-	novel	NA	P-0007755-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	123	367	0	ENST00000324856.7:c.2733-1_2744del		p.X911_splice	ENST00000324856	NM_006015.4	911		9/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.330777684152606	2		367	688	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852148	63852148	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0007755-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	54	326	0	ENST00000279873.7:c.2927del	p.Gly976GlufsTer6	p.G976Efs*6	ENST00000279873	NM_032199.2	976	Gga/ga	10/10	0.155419965486474	0	FACETS	0.33	0.281	0.383			1	INDETERMINATE	1	TRUE	0	0.330777684152606	0		326	663	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436408	49436408	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1426177890	NA	P-0007755-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	47	439	0	ENST00000301067.7:c.5803C>G	p.Leu1935Val	p.L1935V	ENST00000301067	NM_003482.3	1935	Ctg/Gtg	27/54	1	2	FACETS	0.323	0.271	0.38	0.323	0.271	0.38	SUBCLONAL	1	TRUE	1	0.330777684152606	2		439	880	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578556	7578556	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	rs786202799	NA	P-0007755-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	63	312	1	ENST00000269305.4:c.376-2A>T		p.X126_splice	ENST00000269305	NM_001126112.2	126			1	2	FACETS	0.633	0.547	0.726	0.633	0.547	0.726	SUBCLONAL	1	TRUE	1	0.330777684152606	2		313	602	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095846	29095846	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs768973809	NA	P-0007755-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	76	556	0	ENST00000328354.6:c.988C>T	p.Gln330Ter	p.Q330*	ENST00000328354	NM_007194.3	330	Cag/Tag	9/15	0.213271678604299	1	FACETS	0.423	0.37	0.48	0.423	0.37	0.48	SUBCLONAL	1	TRUE	0	0.330777684152606	1		556	907	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976584	55976584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007755-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	79	528	0	ENST00000263923.4:c.1241C>T	p.Ser414Phe	p.S414F	ENST00000263923	NM_002253.2	414	tCt/tTt	9/30	1	2	FACETS	0.529	0.464	0.599	0.529	0.464	0.599	SUBCLONAL	1	TRUE	1	0.330777684152606	2		528	903	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244227	153244227	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007755-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	98	475	0	ENST00000281708.4:c.1930G>T	p.Gly644Ter	p.G644*	ENST00000281708	NM_033632.3	644	Gga/Tga	12/12	1	2	FACETS	0.634	0.564	0.708	0.634	0.564	0.708	SUBCLONAL	1	TRUE	1	0.330777684152606	2		475	935	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399456	139399456	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007755-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	70	461	0	ENST00000277541.6:c.4687G>C	p.Glu1563Gln	p.E1563Q	ENST00000277541	NM_017617.3	1563	Gag/Cag	26/34	0.314907419867972	1	FACETS	0.433	0.377	0.494	0.433	0.377	0.494	SUBCLONAL	1	TRUE	0	0.330777684152606	1		461	816	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0007777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	203	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.781026688444649	2		464	491	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038526	47038526	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	435	639	2	ENST00000377604.3:c.688C>T	p.Arg230Ter	p.R230*	ENST00000377604	NM_001204468.1	230	Cga/Tga	8/24	1	2	FACETS	0.971	0.928	1	0.971	0.928	1	CLONAL	1	TRUE	1	0.781026688444649	2		641	1147	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67588170	67588183	+	frameshift_variant	Frame_Shift_Del	DEL	TACTGGGGAGATAT	TACTGGGGAGATAT	G	novel	NA	P-0007777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	33	272	0	ENST00000274335.5:c.1000_1013delinsG	p.Tyr334AlafsTer6	p.Y334Afs*6	ENST00000274335		334	TACTGGGGAGATATc/Gc	7/15	1	2	FACETS	0.133	0.108	0.162	0.133	0.108	0.162	SUBCLONAL	1	TRUE	1	0.781026688444649	2		272	634	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	59	280	0				ENST00000310581	NM_198253.2	-/1132			0.193917358295834	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.809296343948628	0		280	136	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755390	39755390	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	166	396	0	ENST00000288319.7:c.1375G>T	p.Gly459Cys	p.G459C	ENST00000288319	NM_182918.3	459	Ggt/Tgt	10/10	0.193917358295834	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.809296343948628	0		396	443	SUCCESS
APC	324	MSKCC	GRCh37	5	112178647	112178649	+	inframe_deletion	In_Frame_Del	DEL	AAG	AAG	-	rs1291144227	NA	P-0007835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	276	363	0	ENST00000257430.4:c.7361_7363del	p.Arg2454del	p.R2454del	ENST00000257430	NM_000038.5	2452	ttAAGa/tta	16/16	0.184954226230182	4	FACETS	0.861	0.813	0.909	0.861	0.813	0.909	INDETERMINATE	2	FALSE	2	0.809296343948628	4		363	717	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007844-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	59	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.999	0.878	1	0.999	0.878	1	CLONAL	1	TRUE	1	0.702881137081343	2		280	168	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245538	16245538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1362193717	NA	P-0007844-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	161	351	0	ENST00000375759.3:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000375759	NM_015001.2	505	Cgc/Tgc	7/15	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.702881137081343	2		351	426	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720876	89720876	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs786201041	NA	P-0007844-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	157	216	0	ENST00000371953.3:c.1026+1G>A		p.X342_splice	ENST00000371953	NM_000314.4	342			0.685230678181413	2	FACETS	0.975	0.923	1	0.975	0.923	1	CLONAL	2	TRUE	0	0.702881137081343	2		216	229	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	32	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.857	1	1	0.965	1	CLONAL	2	FALSE	1	0.307267502215077	2		280	101	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0007913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	153	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.955	1	1	0.992	1	CLONAL	2	FALSE	1	0.307267502215077	2		490	474	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450939	70450939	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0007913-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	109	256	5	ENST00000373644.4:c.5779T>G	p.Ser1927Ala	p.S1927A	ENST00000373644	NM_030625.2	1927	Tcc/Gcc	12/12	1	2	FACETS	1	0.97	1	1	0.99	1	CLONAL	2	FALSE	1	0.307267502215077	2		261	307	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	145	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.914	0.842	0.988	1	0.994	1	CLONAL	5	TRUE	1	0.15	2		280	423	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	90	157	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.3	0	FACETS	0.862	0.788	0.935			1	CLONAL	7	TRUE	0	0.15	0		157	169	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257552	19257552	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	264	433	0	ENST00000162023.5:c.674C>T	p.Ser225Phe	p.S225F	ENST00000162023		225	tCc/tTc	10/13	1	2	FACETS	0.906	0.853	0.96	1	0.996	1	CLONAL	5	TRUE	1	0.15	2		433	777	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629322	187629322	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	314	538	0	ENST00000441802.2:c.1660C>T	p.Leu554Phe	p.L554F	ENST00000441802	NM_005245.3	554	Ctt/Ttt	2/27	1	2	FACETS	1	0.965	1	1	0.997	1	CLONAL	4	TRUE	1	0.15	2		538	1018	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6439797	6439797	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	392	515	0	ENST00000356142.4:c.323C>T	p.Ser108Leu	p.S108L	ENST00000356142	NM_018890.3	108	tCa/tTa	5/7	1	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	4	TRUE	1	0.15	2		515	1163	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413709	138413710	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs751821336	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	256	361	2	ENST00000289153.2:c.1810dup	p.Arg604ProfsTer29	p.R604Pfs*29	ENST00000289153	NM_006219.2	604	cgg/cCgg	12/22	1	2	FACETS	1	0.974	1	1	0.996	1	CLONAL	4	TRUE	1	0.15	2		363	800	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9787030	9787030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397518423	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	391	524	0	ENST00000377346.4:c.3061G>A	p.Glu1021Lys	p.E1021K	ENST00000377346	NM_005026.3	1021	Gaa/Aaa	24/24	1	2	FACETS	1	0.975	1	1	0.997	1	CLONAL	5	TRUE	1	0.15	2		524	1008	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551831	150551831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	96	139	0	ENST00000369026.2:c.176G>A	p.Gly59Glu	p.G59E	ENST00000369026	NM_021960.4	59	gGa/gAa	1/3	0.651826718060119	3	FACETS	0.961	0.864	1	1	0.987	1	CLONAL	4	TRUE	1	0.15	3		139	358	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972819	25972819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	382	613	0	ENST00000435504.4:c.1606C>T	p.Pro536Ser	p.P536S	ENST00000435504		536	Cca/Tca	12/13	1	2	FACETS	1	0.989	1	1	0.997	1	CLONAL	4	TRUE	1	0.15	2		613	1132	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149642	61149642	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	127	140	0	ENST00000295025.8:c.1832C>T	p.Ser611Phe	p.S611F	ENST00000295025	NM_002908.2	611	tCc/tTc	11/11	1	2	FACETS	1	0.952	1	1	0.993	1	CLONAL	4	TRUE	1	0.15	2		140	399	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726011	61726011	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	380	411	0	ENST00000401558.2:c.628C>T	p.Gln210Ter	p.Q210*	ENST00000401558	NM_003400.3	210	Cag/Tag	8/25	1	2	FACETS	0.925	0.88	0.971	1	0.997	1	CLONAL	5	TRUE	1	0.15	2		411	1095	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99136602	99136602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	229	352	0	ENST00000074304.5:c.91G>A	p.Gly31Ser	p.G31S	ENST00000074304	NM_001134224.1	31	Ggc/Agc	3/26	1	2	FACETS	1	0.975	1	1	0.996	1	CLONAL	4	TRUE	1	0.15	2		352	707	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248527	212248527	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	360	668	0	ENST00000342788.4:c.3740T>C	p.Leu1247Pro	p.L1247P	ENST00000342788	NM_005235.2	1247	cTg/cCg	28/28	1	2	FACETS	1	0.97	1	1	0.997	1	CLONAL	4	TRUE	1	0.15	2		668	1163	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285309	212285309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	295	446	0	ENST00000342788.4:c.2992C>T	p.Pro998Ser	p.P998S	ENST00000342788	NM_005235.2	998	Cca/Tca	25/28	1	2	FACETS	1	0.972	1	1	0.997	1	CLONAL	4	TRUE	1	0.15	2		446	937	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266124	41266124	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913412	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	334	437	1	ENST00000349496.5:c.121A>G	p.Thr41Ala	p.T41A	ENST00000349496	NM_001904.3	41	Acc/Gcc	3/15	1	2	FACETS	1	0.982	1	1	0.997	1	CLONAL	4	TRUE	1	0.15	2		438	1028	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412884	49412884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	517	655	1	ENST00000418115.1:c.139G>A	p.Glu47Lys	p.E47K	ENST00000418115	NM_001664.2	47	Gag/Aag	2/5	1	2	FACETS	0.955	0.916	0.996	1	0.998	1	CLONAL	5	TRUE	1	0.15	2		656	1443	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437161	52437161	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	320	476	0	ENST00000460680.1:c.1883C>A	p.Ser628Ter	p.S628*	ENST00000460680	NM_004656.3	628	tCa/tAa	14/17	1	2	FACETS	1	0.948	1	1	0.997	1	CLONAL	5	TRUE	1	0.15	2		476	853	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873104	134873104	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202048188	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	252	358	0	ENST00000398015.3:c.1408C>T	p.Arg470Trp	p.R470W	ENST00000398015	NM_004441.4	470	Cgg/Tgg	6/16	1	2	FACETS	0.919	0.864	0.975	1	0.996	1	CLONAL	5	TRUE	1	0.15	2		358	731	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612146	189612146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	348	493	0	ENST00000264731.3:c.1898C>T	p.Thr633Ile	p.T633I	ENST00000264731	NM_003722.4	633	aCc/aTc	14/14	1	2	FACETS	0.916	0.869	0.964	1	0.997	1	CLONAL	5	TRUE	1	0.15	2		493	1013	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	124	454	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	1	2	FACETS	0.788	0.712	0.869	1	0.986	1	SUBCLONAL	2	TRUE	1	0.15	2		454	1049	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956220	55956220	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1190050670	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	322	510	0	ENST00000263923.4:c.3095G>A	p.Arg1032Gln	p.R1032Q	ENST00000263923	NM_002253.2	1032	cGa/cAa	23/30	1	2	FACETS	1	0.986	1	1	0.997	1	CLONAL	4	TRUE	1	0.15	2		510	963	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249511	153249511	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	298	373	0	ENST00000281708.4:c.1267G>T	p.Gly423Ter	p.G423*	ENST00000281708	NM_033632.3	423	Gga/Tga	9/12	1	2	FACETS	1	0.982	1	1	0.997	1	CLONAL	4	TRUE	1	0.15	2		373	911	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512361	149512361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	231	386	0	ENST00000261799.4:c.1079C>T	p.Ser360Phe	p.S360F	ENST00000261799	NM_002609.3	360	tCc/tTc	7/23	1	2	FACETS	1	0.963	1	1	0.996	1	CLONAL	4	TRUE	1	0.15	2		386	739	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517504	176517504	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	295	462	0	ENST00000292408.4:c.205G>A	p.Glu69Lys	p.E69K	ENST00000292408	NM_213647.1	69	Gag/Aag	3/18	1	2	FACETS	0.935	0.884	0.988	1	0.997	1	CLONAL	5	TRUE	1	0.15	2		462	841	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673571	30673571	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756557914	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	543	874	0	ENST00000376406.3:c.3389C>T	p.Ser1130Phe	p.S1130F	ENST00000376406	NM_014641.2	1130	tCc/tTc	10/15	1	2	FACETS	1	0.971	1	1	0.998	1	CLONAL	5	TRUE	1	0.15	2		874	1427	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188182	32188182	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	157	269	0	ENST00000375023.3:c.1159G>A	p.Gly387Arg	p.G387R	ENST00000375023	NM_004557.3	387	Gga/Aga	6/30	1	2	FACETS	0.94	0.865	1	1	0.994	1	CLONAL	4	TRUE	1	0.15	2		269	557	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903789	41903790	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	211	427	0	ENST00000372991.4:c.767_768delinsAA	p.Arg256Lys	p.R256K	ENST00000372991	NM_001760.3	256	aGG/aAA	5/5	1	2	FACETS	0.943	0.879	1	1	0.995	1	CLONAL	4	TRUE	1	0.15	2		427	746	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120633	94120633	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	454	956	1	ENST00000369303.4:c.418G>A	p.Glu140Lys	p.E140K	ENST00000369303	NM_004440.3	140	Gaa/Aaa	3/17	0.138177374663276	0	FACETS	0.828	0.789	0.867			1	CLONAL	4	TRUE	0	0.15	0		957	1554	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515213	106515213	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267601224	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	320	421	0	ENST00000359195.3:c.2356C>T	p.Pro786Ser	p.P786S	ENST00000359195	NM_002649.2	786	Cca/Tca	5/11	1	2	FACETS	1	0.95	1	1	0.997	1	CLONAL	5	TRUE	1	0.15	2		421	851	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481403	140481403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913357	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	325	439	2	ENST00000288602.6:c.1405G>A	p.Gly469Arg	p.G469R	ENST00000288602	NM_004333.4	469	Gga/Aga	11/18	1	2	FACETS	0.966	0.916	1	1	0.997	1	CLONAL	5	TRUE	1	0.15	2		441	897	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860668	151860668	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	345	553	1	ENST00000262189.6:c.9994T>A	p.Leu3332Ile	p.L3332I	ENST00000262189	NM_170606.2	3332	Tta/Ata	43/59	1	2	FACETS	1	0.985	1	1	0.997	1	CLONAL	4	TRUE	1	0.15	2		554	1046	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869692	117869692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1337189031	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	495	692	1	ENST00000297338.2:c.502C>T	p.Arg168Cys	p.R168C	ENST00000297338	NM_006265.2	168	Cgt/Tgt	6/14	1	2	FACETS	0.917	0.878	0.957	1	0.998	1	CLONAL	5	TRUE	1	0.15	2		693	1439	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341925	8341925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	278	458	0	ENST00000356435.5:c.4715G>A	p.Arg1572Lys	p.R1572K	ENST00000356435		1572	aGa/aAa	29/35	1	2	FACETS	1	0.974	1	1	0.996	1	CLONAL	4	TRUE	1	0.15	2		458	876	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971187	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	89	164	0	ENST00000304494.5:c.171_172delinsTT	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	57	gcCCga/gcTTga	2/3	0.3	0	FACETS	0.863	0.789	0.936			1	CLONAL	7	TRUE	0	0.15	0		164	167	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759397	133759397	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	464	732	1	ENST00000318560.5:c.1720C>T	p.Arg574Ter	p.R574*	ENST00000318560	NM_005157.4	574	Cga/Tga	11/11	1	2	FACETS	0.932	0.891	0.974	1	0.998	1	CLONAL	5	TRUE	1	0.15	2		733	1327	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390617	139390617	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs567323027	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	388	649	1	ENST00000277541.6:c.7574C>T	p.Pro2525Leu	p.P2525L	ENST00000277541	NM_017617.3	2525	cCg/cTg	34/34	1	2	FACETS	1	0.976	1	1	0.997	1	CLONAL	4	TRUE	1	0.15	2		650	1238	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391370	139391370	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	251	417	1	ENST00000277541.6:c.6821C>T	p.Ser2274Phe	p.S2274F	ENST00000277541	NM_017617.3	2274	tCc/tTc	34/34	1	2	FACETS	0.927	0.871	0.984	1	0.996	1	CLONAL	5	TRUE	1	0.15	2		418	722	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396743	139396743	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	200	312	0	ENST00000277541.6:c.5365G>C	p.Glu1789Gln	p.E1789Q	ENST00000277541	NM_017617.3	1789	Gag/Cag	28/34	1	2	FACETS	1	0.962	1	1	0.995	1	CLONAL	4	TRUE	1	0.15	2		312	636	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88672067	88672068	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	71	159	0	ENST00000372037.3:c.601_602delinsTT	p.Pro201Leu	p.P201L	ENST00000372037	NM_004329.2	201	CCa/TTa	8/13	0.138177374663276	1	FACETS	0.979	0.863	1	1	0.986	1	CLONAL	3	TRUE	0	0.15	1		159	298	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375057	104375057	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	230	419	1	ENST00000369902.3:c.1055C>T	p.Ser352Phe	p.S352F	ENST00000369902	NM_016169.3	352	tCc/tTc	9/12	0.138177374663276	1	FACETS	0.938	0.878	1	1	0.996	1	CLONAL	4	TRUE	0	0.15	1		420	756	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158421	108158421	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	239	271	0	ENST00000278616.4:c.4088C>T	p.Thr1363Ile	p.T1363I	ENST00000278616	NM_000051.3	1363	aCt/aTt	27/63	0.138177374663276	1	FACETS	1	0.979	1	1	0.996	1	CLONAL	4	TRUE	0	0.15	1		271	673	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344314	118344314	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	146	184	1	ENST00000534358.1:c.2440C>T	p.Gln814Ter	p.Q814*	ENST00000534358	NM_005933.3	814	Cag/Tag	3/36	0.138177374663276	1	FACETS	1	0.972	1	1	0.994	1	CLONAL	4	TRUE	0	0.15	1		185	403	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109942	115109942	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	180	298	0	ENST00000257566.3:c.1936C>T	p.Pro646Ser	p.P646S	ENST00000257566	NM_016569.3	646	Ccg/Tcg	8/8	1	2	FACETS	0.914	0.85	0.981	1	0.995	1	CLONAL	5	TRUE	1	0.15	2		298	525	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26974660	26974660	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	331	450	0	ENST00000381527.3:c.1004T>C	p.Phe335Ser	p.F335S	ENST00000381527	NM_001260.1	335	tTc/tCc	10/13	1	2	FACETS	0.913	0.865	0.962	1	0.997	1	CLONAL	5	TRUE	1	0.15	2		450	967	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436941	110436941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	54	108	0	ENST00000375856.3:c.1460C>T	p.Ser487Phe	p.S487F	ENST00000375856	NM_003749.2	487	tCc/tTc	1/2	1	2	FACETS	0.986	0.863	1	1	0.985	1	CLONAL	5	TRUE	1	0.15	2		108	146	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858754	9858754	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	225	337	0	ENST00000330684.3:c.2647C>T	p.Pro883Ser	p.P883S	ENST00000330684	NM_001134407.1	883	Cca/Tca	13/13	1	2	FACETS	1	0.981	1	1	0.996	1	CLONAL	4	TRUE	1	0.15	2		337	669	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821176	72821176	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	492	886	0	ENST00000268489.5:c.10999G>A	p.Asp3667Asn	p.D3667N	ENST00000268489	NM_006885.3	3667	Gat/Aat	10/10	0.3	1	FACETS	1	0.957	1	1	0.998	1	CLONAL	4	TRUE	0	0.15	1		886	1515	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929529	81929529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	467	806	0	ENST00000359376.3:c.1190C>T	p.Ser397Leu	p.S397L	ENST00000359376	NM_002661.3	397	tCg/tTg	13/33	1	2	FACETS	0.959	0.917	1	1	0.998	1	CLONAL	5	TRUE	1	0.15	2		806	1298	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553539	29553540	+	stop_gained	Nonsense_Mutation	DNP	GA	GA	AC	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	182	307	2	ENST00000356175.3:c.2088_2089delinsAC	p.Trp696_Asn697delinsTer	p.W696_N697delins*	ENST00000356175	NM_000267.3	696	tgGAac/tgACac	18/57	1	2	FACETS	1	0.954	1	1	0.995	1	CLONAL	4	TRUE	1	0.15	2		309	585	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562641	29562641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854562	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	488	567	1	ENST00000356175.3:c.3721C>T	p.Arg1241Ter	p.R1241*	ENST00000356175	NM_000267.3	1241	Cga/Tga	28/57	1	2	FACETS	0.953	0.912	0.995	1	0.998	1	CLONAL	5	TRUE	1	0.15	2		568	1365	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511566	38511566	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	314	459	0	ENST00000254066.5:c.1064T>A	p.Leu355Gln	p.L355Q	ENST00000254066	NM_000964.3	355	cTg/cAg	8/9	1	2	FACETS	0.983	0.931	1	1	0.997	1	CLONAL	5	TRUE	1	0.15	2		459	852	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243973	41243974	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	315	435	0	ENST00000357654.3:c.3574_3575delinsTT	p.Pro1192Phe	p.P1192F	ENST00000357654	NM_007294.3	1192	CCt/TTt	10/23	1	2	FACETS	1	0.961	1	1	0.997	1	CLONAL	4	TRUE	1	0.15	2		435	1029	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73775182	73775182	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1284930716	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	499	722	0	ENST00000254810.4:c.74C>T	p.Ala25Val	p.A25V	ENST00000254810	NM_005324.3	25	gCc/gTc	2/4	0.212946005096498	3	FACETS	0.942	0.901	0.983	1	0.997	1	CLONAL	5	TRUE	1	0.15	3		722	1519	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219368	5219369	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	317	471	3	ENST00000357368.4:c.3875_3876delinsTT	p.Ala1292Val	p.A1292V	ENST00000357368	NM_002850.3	1292	gCC/gTT	23/38	1	2	FACETS	1	0.982	1	1	0.997	1	CLONAL	4	TRUE	1	0.15	2		474	973	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573672	41573672	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144626200	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	327	461	3	ENST00000263253.7:c.5957C>T	p.Pro1986Leu	p.P1986L	ENST00000263253	NM_001429.3	1986	cCg/cTg	31/31	1	2	FACETS	1	0.98	1	1	0.997	1	CLONAL	5	TRUE	1	0.15	2		464	821	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440923	52440950	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCTAGTGGAGACCAAGACAAGGAATCAG	CCTAGTGGAGACCAAGACAAGGAATCAG	-	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	192	390	0	ENST00000460680.1:c.581-27_581del		p.X194_splice	ENST00000460680	NM_004656.3	194		8/17	1	2	FACETS	1	0.98	1	1	0.995	1	CLONAL	3	TRUE	1	0.15	2		390	741	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352351	73352351	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0007918-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	367	667	0	ENST00000377767.4:c.554del	p.Ile185LysfsTer14	p.I185Kfs*14	ENST00000377767	NM_014953.3	185	aTa/aa	3/21	1	2	FACETS	0.98	0.93	1	1	0.997	1	CLONAL	4	TRUE	1	0.15	2		667	1248	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56855455	56855455	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0007920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	158	735	2	ENST00000308159.5:c.604C>T	p.Gln202Ter	p.Q202*	ENST00000308159	NM_014669.4	202	Cag/Tag	7/22	0.397786358971346	3	FACETS	0.899	0.823	0.979	0.449	0.411	0.49	CLONAL	1	TRUE	1	0.404928098841969	3		737	1044	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133228	41133926	+	splice_donor_variant,coding_sequence_variant,3_prime_UTR_variant,intron_variant	Splice_Site	DEL	CAAATTAAAATCAATTCAACTTAACATGTTAAGAGTGACAGACATACTTAGGGGCAAAAAGCTAGAGCTTTCTCAAACAGCTCTAAAATCATTCAATGGGGAAAATTCTACTTTACAAAAAACCCTTCAGCATTTGATTTATATCAAATGTATTCATTTATTGAAGAGCTACTAAAAAGATGCAGCCATCGAACTGTCAAAAAGAAATCTTTAAAGCAGTTAAAGGAAGCTTCCTTCTGTGTAAGCTCAGAAGGAAAACTGTAAGCTGCAAAAAGGACAGAGAATGAATGATAAAAGATCCCTCTCTGCAAGGGACAGTCAGTTGACATCAAAGATGTGCTAACCATGGCAAGTTACTGTGTTCCTCGCTTTTAAGTTCTATTTTTCAAAAGGTCTTTTGATATTGGGGTGAACTTACCTGCTCACTAACCCTCAGCCTGACACCCAGCTATGTGTCGTTGTCTTGACACTGTGTGGGAAGCTTTGGTTGGGCAACACATTGTCAAAGTTAAAATCCAATGTATCTCCATCCATGAGGTCATTCCGAATGATGGATTCCATGTCACAGTCTAAGCGCTCAATGAACATGCCATCCAAGTCACTTGGGAGCTTCTCCTGGTGGAGAAGGCCCATTCTGCCATAGCCATTGCAGCTGCTCACGGAGGAGTAGCCCCCCAGGGCACTCATCTGCATGGGGTG	CAAATTAAAATCAATTCAACTTAACATGTTAAGAGTGACAGACATACTTAGGGGCAAAAAGCTAGAGCTTTCTCAAACAGCTCTAAAATCATTCAATGGGGAAAATTCTACTTTACAAAAAACCCTTCAGCATTTGATTTATATCAAATGTATTCATTTATTGAAGAGCTACTAAAAAGATGCAGCCATCGAACTGTCAAAAAGAAATCTTTAAAGCAGTTAAAGGAAGCTTCCTTCTGTGTAAGCTCAGAAGGAAAACTGTAAGCTGCAAAAAGGACAGAGAATGAATGATAAAAGATCCCTCTCTGCAAGGGACAGTCAGTTGACATCAAAGATGTGCTAACCATGGCAAGTTACTGTGTTCCTCGCTTTTAAGTTCTATTTTTCAAAAGGTCTTTTGATATTGGGGTGAACTTACCTGCTCACTAACCCTCAGCCTGACACCCAGCTATGTGTCGTTGTCTTGACACTGTGTGGGAAGCTTTGGTTGGGCAACACATTGTCAAAGTTAAAATCCAATGTATCTCCATCCATGAGGTCATTCCGAATGATGGATTCCATGTCACAGTCTAAGCGCTCAATGAACATGCCATCCAAGTCACTTGGGAGCTTCTCCTGGTGGAGAAGGCCCATTCTGCCATAGCCATTGCAGCTGCTCACGGAGGAGTAGCCCCCCAGGGCACTCATCTGCATGGGGTG	-	novel	NA	P-0007920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1	124	2	0	ENST00000379561.5:c.1702_*15-57del		p.X568_splice	ENST00000379561	NM_002015.3	568		2/3	0.404928098841969	2	FACETS		NA	1	1	0.994	1	NA	5	TRUE	0	0.404928098841969	2		2	125	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007983-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	121	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.668175767517907	2		280	278	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0007983-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	502	511	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.54796680939106	4	FACETS	0.857	0.825	0.889			1	CLONAL	3	TRUE	NA	0.668175767517907	4		511	975	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0007983-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	161	424	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.668175767517907	2		424	408	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913384	NA	P-0007983-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	95	238	1	ENST00000304494.5:c.262G>T	p.Glu88Ter	p.E88*	ENST00000304494	NM_000077.4	88	Gag/Tag	2/3	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.668175767517907	2		239	250	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120467939	120467939	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0007983-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	59	401	0	ENST00000256646.2:c.4500C>G	p.Ser1500Arg	p.S1500R	ENST00000256646	NM_024408.3	1500	agC/agG	25/34	0.54796680939106	4	FACETS	0.256	0.219	0.297			1	SUBCLONAL	1	TRUE	NA	0.668175767517907	4		401	1149	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113154	209113154	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458009455	NA	P-0007983-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	236	372	0	ENST00000345146.2:c.353C>T	p.Pro118Leu	p.P118L	ENST00000345146	NM_005896.2	118	cCc/cTc	4/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.668175767517907	2		372	658	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713796	30713796	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057524399	NA	P-0007983-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	165	228	0	ENST00000295754.5:c.1121C>T	p.Pro374Leu	p.P374L	ENST00000295754	NM_003242.5	374	cCc/cTc	4/7	1	2	FACETS	0.95	0.878	1	0.95	0.878	1	CLONAL	1	TRUE	1	0.668175767517907	2		228	520	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561705	55561705	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007983-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	177	215	0	ENST00000288135.5:c.95G>A	p.Gly32Glu	p.G32E	ENST00000288135	NM_000222.2	32	gGg/gAg	2/21	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.668175767517907	2		215	499	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865269	57865269	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007983-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	321	447	0	ENST00000228682.2:c.2746G>A	p.Glu916Lys	p.E916K	ENST00000228682	NM_005269.2	916	Gaa/Aaa	12/12	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.668175767517907	2		447	928	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005401	29005401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0007983-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	94	350	0	ENST00000282397.4:c.860C>T	p.Ser287Phe	p.S287F	ENST00000282397	NM_002019.4	287	tCc/tTc	7/30	0.108165787204827	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.668175767517907	0		350	352	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281346	15281346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781302445	NA	P-0007983-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	109	192	0	ENST00000263388.2:c.4910C>T	p.Pro1637Leu	p.P1637L	ENST00000263388	NM_000435.2	1637	cCa/cTa	27/33	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.668175767517907	2		192	313	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0007994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	140	280	0				ENST00000310581	NM_198253.2	-/1132			0.454000371469447	3	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	1	0.454000371469447	3		280	316	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577117	7577117	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057520006	NA	P-0007994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	403	560	2	ENST00000269305.4:c.821T>C	p.Val274Ala	p.V274A	ENST00000269305	NM_001126112.2	274	gTt/gCt	8/11	0.454000371469447	4	FACETS	0.977	0.929	1	0.977	0.929	1	CLONAL	2	TRUE	2	0.454000371469447	4		562	1321	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578272	7578272	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs876658468	NA	P-0007994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	332	449	0	ENST00000269305.4:c.577C>A	p.His193Asn	p.H193N	ENST00000269305	NM_001126112.2	193	Cat/Aat	6/11	0.454000371469447	4	FACETS	0.962	0.91	1	0.962	0.91	1	CLONAL	2	TRUE	2	0.454000371469447	4		449	1105	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651893	36651894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0007994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	231	248	0	ENST00000244741.5:c.19dup	p.Asp7GlyfsTer29	p.D7Gfs*29	ENST00000244741	NM_000389.4	5	-/G	2/3	0.454000371469447	5	FACETS	1	0.964	1	0.698	0.652	0.745	CLONAL	2	TRUE	2	0.454000371469447	5		248	817	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928858	49928858	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0007994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	203	725	0	ENST00000296474.3:c.3508C>A	p.Leu1170Ile	p.L1170I	ENST00000296474	NM_002447.2	1170	Ctc/Atc	16/20	0.454000371469447	3	FACETS	0.883	0.817	0.951	0.441	0.408	0.476	CLONAL	1	TRUE	1	0.454000371469447	3		725	1243	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211137	55211137	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	94	421	0	ENST00000275493.2:c.380C>A	p.Ala127Glu	p.A127E	ENST00000275493	NM_005228.3	127	gCa/gAa	3/28	0.454000371469447	4	FACETS	0.596	0.529	0.667	0.298	0.264	0.334	SUBCLONAL	1	TRUE	2	0.454000371469447	4		421	1011	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2227045	2227045	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0007994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	125	121	0	ENST00000398665.3:c.4525C>A	p.His1509Asn	p.H1509N	ENST00000398665	NM_032482.2	1509	Cac/Aac	27/28	0.454000371469447	4	FACETS	0.847	0.778	0.918	1	0.982	1	CLONAL	3	TRUE	2	0.454000371469447	4		121	315	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31395599	31395599	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908940	NA	P-0007994-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1835	154	429	3	ENST00000328111.2:c.2452G>A	p.Val818Met	p.V818M	ENST00000328111	NM_006892.3	818	Gtg/Atg	23/23	0.454000371469447	10	FACETS	0.96	0.875	1			1	CLONAL	1	TRUE	NA	0.454000371469447	10		432	1989	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0121553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	77	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.851	0.754	0.954	0.851	0.754	0.954	CLONAL	1	NA	1	0.548238700344109	2		464	330	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533875	533875	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28933406	NA	P-0121553-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	213	242	0	ENST00000451590.1:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000451590	NM_001130442.1	61	Cag/Aag	3/5	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	NA	1	0.548238700344109	2		242	714	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	63	257	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.28	2		260	308	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225955	2225955	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs756230613	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	85	375	0	ENST00000326181.6:c.1746+1G>A		p.X582_splice	ENST00000326181	NM_032271.2	582			1	2	FACETS	0.867	0.773	0.967	1	0.983	1	CLONAL	2	TRUE	1	0.28	2		375	350	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097751	27097751	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	97	474	0	ENST00000324856.7:c.3344del	p.Pro1115GlnfsTer46	p.P1115Qfs*46	ENST00000324856	NM_006015.4	1114	Ccc/cc	12/20	0.3	3	FACETS	1	0.965	1			1	CLONAL	1	TRUE	NA	0.28	3		474	658	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484420	57484420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11554273	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	49	489	2	ENST00000371085.3:c.601C>T	p.Arg201Cys	p.R201C	ENST00000371085	NM_000516.4	201	Cgt/Tgt	8/13	0.3	2	FACETS	0.785	0.666	0.916			1	CLONAL	1	TRUE	NA	0.28	2		491	446	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273784	18273784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587776934	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	67	501	0	ENST00000222254.8:c.1117G>A	p.Gly373Arg	p.G373R	ENST00000222254	NM_005027.3	373	Ggg/Agg	10/16	0.0816069511940174	0	FACETS	0.538	0.468	0.615			1	INDETERMINATE	1	TRUE	0	0.28	0		501	640	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884011	37884011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150680317	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	66	485	0	ENST00000269571.5:c.3482G>A	p.Arg1161Gln	p.R1161Q	ENST00000269571		1161	cGa/cAa	27/27	0.3	3	FACETS	1	0.952	1			1	CLONAL	1	TRUE	NA	0.28	3		485	447	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260214	16260214	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	25	181	0	ENST00000375759.3:c.7484del	p.Pro2495LeufsTer4	p.P2495Lfs*4	ENST00000375759	NM_015001.2	2493	agC/ag	11/15	0.3	3	FACETS	1	0.825	1			1	CLONAL	1	TRUE	NA	0.28	3		181	195	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19261529	19261529	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	86	612	0	ENST00000162023.5:c.16del	p.Ile6SerfsTer14	p.I6Sfs*14	ENST00000162023		6	Atc/tc	6/13	0.0816069511940174	0	FACETS	0.723	0.64	0.811			1	INDETERMINATE	1	TRUE	0	0.28	0		612	612	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418718	49418718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760369709	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	30	241	0	ENST00000301067.7:c.15796C>T	p.Arg5266Cys	p.R5266C	ENST00000301067	NM_003482.3	5266	Cgc/Tgc	49/54	0.0816069511940174	3	FACETS	0.825	0.667	1	0.413	0.333	0.502	INDETERMINATE	1	TRUE	1	0.28	3		241	296	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412898	49412898	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1057519954	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	79	744	0	ENST00000418115.1:c.125A>G	p.Tyr42Cys	p.Y42C	ENST00000418115	NM_001664.2	42	tAt/tGt	2/5	1	2	FACETS	0.731	0.642	0.827	0.731	0.642	0.827	SUBCLONAL	1	TRUE	1	0.28	2		744	772	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630542	187630542	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	105	728	2	ENST00000441802.2:c.440C>T	p.Pro147Leu	p.P147L	ENST00000441802	NM_005245.3	147	cCg/cTg	2/27	0.0816069511940174	3	FACETS	1	0.902	1	0.504	0.451	0.561	INDETERMINATE	1	TRUE	1	0.28	3		730	848	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128046958	128046958	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs772883177	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	75	608	5	ENST00000285398.2:c.777A>T	p.Glu259Asp	p.E259D	ENST00000285398	NM_000122.1	259	gaA/gaT	6/15	0.3	2	FACETS	0.946	0.83	1			1	CLONAL	1	TRUE	NA	0.28	2		613	566	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286237	66286238	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	66	679	0	ENST00000273854.3:c.1448dup	p.Asn483LysfsTer21	p.N483Kfs*21	ENST00000273854	NM_004439.5	483	aac/aaAc	6/18	0.0816069511940174	3	FACETS	0.715	0.619	0.818	0.357	0.309	0.409	INDETERMINATE	1	TRUE	1	0.28	3		679	752	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439700	220439701	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CT	novel	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	59	831	0	ENST00000243786.2:c.562_563dup	p.Leu189CysfsTer2	p.L189Cfs*2	ENST00000243786	NM_002191.3	185	gct/gCTct	2/2	1	2	FACETS	0.722	0.621	0.831	0.722	0.621	0.831	SUBCLONAL	1	TRUE	1	0.28	2		831	584	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783293	9783293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	59	492	0	ENST00000377346.4:c.2537C>T	p.Ala846Val	p.A846V	ENST00000377346	NM_005026.3	846	gCc/gTc	20/24	0.3	1	FACETS	0.753	0.649	0.867	0.753	0.649	0.867	SUBCLONAL	1	TRUE	0	0.28	1		492	481	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294598	1294598	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200843534	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	15	172	0	ENST00000310581.5:c.403G>A	p.Gly135Arg	p.G135R	ENST00000310581	NM_198253.2	135	Ggg/Agg	2/16	0.3	0	FACETS	0.555	0.409	0.728			1	SUBCLONAL	1	TRUE	0	0.28	0		172	139	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590380	67590380	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	47	422	0	ENST00000274335.5:c.1442G>T	p.Arg481Met	p.R481M	ENST00000274335		481	aGg/aTg	11/15	0.0816069511940174	3	FACETS	0.607	0.511	0.712	0.303	0.255	0.356	INDETERMINATE	1	TRUE	1	0.28	3		422	631	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27777861	27777861	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	105	851	0	ENST00000369163.2:c.10A>G	p.Thr4Ala	p.T4A	ENST00000369163	NM_003536.2	4	Acg/Gcg	1/1	0.3	7	FACETS	1	0.947	1			1	CLONAL	1	TRUE	NA	0.28	7		851	1163	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27840056	27840056	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1229	132	1060	0	ENST00000328488.2:c.38G>C	p.Gly13Ala	p.G13A	ENST00000328488	NM_003533.2	13	gGc/gCc	1/1	0.3	4	FACETS	0.887	0.802	0.976			1	CLONAL	1	TRUE	NA	0.28	4		1060	1361	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277065	38277065	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369096310	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	33	317	1	ENST00000425967.3:c.1363C>T	p.Arg455Cys	p.R455C	ENST00000425967	NM_001174067.1	455	Cgc/Tgc	10/19	0.22992093216898	3	FACETS	0.822	0.671	0.991	0.411	0.335	0.496	CLONAL	1	TRUE	1	0.28	3		318	327	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8524992	8524992	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	92	558	0	ENST00000356435.5:c.612A>T	p.Lys204Asn	p.K204N	ENST00000356435		204	aaA/aaT	7/35	1	2	FACETS	0.939	0.834	1	0.939	0.834	1	CLONAL	1	TRUE	1	0.28	2		558	700	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908873	101908873	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200595614	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	36	555	0	ENST00000374994.4:c.1237C>T	p.Arg413Ter	p.R413*	ENST00000374994	NM_004612.2	413	Cga/Tga	7/9	1	2	FACETS	0.472	0.387	0.567	0.472	0.387	0.567	SUBCLONAL	1	TRUE	1	0.28	2		555	545	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597879	43597879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	65	736	0	ENST00000355710.3:c.427G>A	p.Ala143Thr	p.A143T	ENST00000355710	NM_020975.4	143	Gcc/Acc	3/20	0.3	1	FACETS	0.67	0.581	0.766	0.67	0.581	0.766	SUBCLONAL	1	TRUE	0	0.28	1		736	596	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456375	32456375	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	29	425	0	ENST00000332351.3:c.517G>A	p.Gly173Arg	p.G173R	ENST00000332351	NM_024426.4	173	Gga/Aga	1/10	0.0816069511940174	0	FACETS	0.492	0.396	0.601			1	INDETERMINATE	1	TRUE	0	0.28	0		425	303	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999077	100999077	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	89	718	0	ENST00000325455.5:c.725G>A	p.Arg242Gln	p.R242Q	ENST00000325455	NM_001202474.3	242	cGg/cAg	1/8	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.28	2		718	560	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156091	119156091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	66	608	1	ENST00000264033.4:c.1756C>T	p.Leu586Phe	p.L586F	ENST00000264033	NM_005188.3	586	Ctt/Ttt	11/16	1	2	FACETS	0.718	0.622	0.821	0.718	0.622	0.821	SUBCLONAL	1	TRUE	1	0.28	2		609	657	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562652	21562652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748829851	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	22	170	3	ENST00000382592.4:c.1267G>A	p.Glu423Lys	p.E423K	ENST00000382592	NM_014572.2	423	Gag/Aag	4/8	0.3	1	FACETS	1	0.828	1	1	0.828	1	CLONAL	1	TRUE	0	0.28	1		173	127	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027205	49027205	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	80	565	1	ENST00000267163.4:c.1772C>A	p.Pro591His	p.P591H	ENST00000267163	NM_000321.2	591	cCt/cAt	18/27	0.0816069511940174	3	FACETS	0.821	0.722	0.928	0.411	0.361	0.464	INDETERMINATE	1	TRUE	1	0.28	3		566	793	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420299	88420299	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	44	379	4	ENST00000360948.2:c.2387C>A	p.Pro796His	p.P796H	ENST00000360948	NM_001012338.2	796	cCc/cAc	19/19	1	2	FACETS	0.906	0.762	1	0.906	0.762	1	CLONAL	1	TRUE	1	0.28	2		383	347	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124200	2124200	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs45481704	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	44	347	0	ENST00000219476.3:c.2356-1G>A		p.X786_splice	ENST00000219476	NM_000548.3	786			1	2	FACETS	1	0.861	1	1	0.861	1	CLONAL	1	TRUE	1	0.28	2		347	307	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226308	2226308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	59	471	1	ENST00000326181.6:c.1921C>T	p.Arg641Cys	p.R641C	ENST00000326181	NM_032271.2	641	Cgt/Tgt	20/21	1	2	FACETS	0.941	0.811	1	0.941	0.811	1	CLONAL	1	TRUE	1	0.28	2		472	448	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801749	3801749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	71	488	0	ENST00000262367.5:c.3757G>A	p.Asp1253Asn	p.D1253N	ENST00000262367	NM_004380.2	1253	Gac/Aac	20/31	1	2	FACETS	0.904	0.79	1	0.904	0.79	1	CLONAL	1	TRUE	1	0.28	2		488	561	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979514	7979514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141010860	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	47	529	3	ENST00000319144.4:c.1511C>T	p.Ala504Val	p.A504V	ENST00000319144	NM_001139.2	504	gCg/gTg	11/15	0.3	2	FACETS	0.714	0.603	0.837			1	SUBCLONAL	1	TRUE	NA	0.28	2		532	470	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017210	31017210	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	72	522	0	ENST00000375687.4:c.541G>A	p.Gly181Arg	p.G181R	ENST00000375687	NM_015338.5	181	Ggg/Agg	7/13	0.0816069511940174	0	FACETS	0.668	0.585	0.759			1	INDETERMINATE	1	TRUE	0	0.28	0		522	554	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44949994	44949994	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1450363794	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	66	376	1	ENST00000377967.4:c.3763C>T	p.Arg1255Trp	p.R1255W	ENST00000377967	NM_021140.2	1255	Cgg/Tgg	26/29	1	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.28	1		377	340	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006828	47006828	+	5_prime_UTR_variant	5'UTR	SNP	G	G	A	rs781795179	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	91	284	0	ENST00000377604.3:c.-53G>A		p.*18*	ENST00000377604	NM_001204468.1	-/852		2/24	1	1	FACETS	0.913	0.82	1	1	0.986	1	CLONAL	2	TRUE	0	0.28	1		284	306	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161969983	161969983	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	90	532	0	ENST00000366898.1:c.986del	p.Gly329AlafsTer106	p.G329Afs*106	ENST00000366898	NM_004562.2	329	gGc/gc	9/12	0.0816069511940174	3	FACETS	1	0.967	1	0.618	0.549	0.691	INDETERMINATE	1	TRUE	1	0.28	3		532	593	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202351	138202351	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	35	321	0	ENST00000237289.4:c.2274del	p.Lys759SerfsTer57	p.K759Sfs*57	ENST00000237289	NM_001270507.1	756	gaC/ga	9/9	0.0816069511940174	3	FACETS	0.651	0.533	0.783	0.325	0.266	0.392	INDETERMINATE	1	TRUE	1	0.28	3		321	438	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564706	86564706	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008034-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	59	465	0	ENST00000274376.6:c.442del	p.Ala148ArgfsTer26	p.A148Rfs*26	ENST00000274376	NM_002890.2	146	ttG/tt	1/25	0.0816069511940174	3	FACETS	0.984	0.848	1	0.492	0.424	0.566	INDETERMINATE	1	TRUE	1	0.28	3		465	488	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	11	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.538	0.372	0.743	0.538	0.372	0.743	SUBCLONAL	1	TRUE	1	0.228592616964608	2		280	179	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101118	41101118	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751886972	NA	P-0008062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	34	344	1	ENST00000373198.4:c.1238C>T	p.Ala413Val	p.A413V	ENST00000373198	NM_133170.3	413	gCg/gTg	8/32	1	2	FACETS	0.676	0.552	0.815	0.676	0.552	0.815	SUBCLONAL	1	TRUE	1	0.228592616964608	2		345	440	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257776	16257776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	30	267	0	ENST00000375759.3:c.5041G>A	p.Glu1681Lys	p.E1681K	ENST00000375759	NM_015001.2	1681	Gaa/Aaa	11/15	1	2	FACETS	0.583	0.469	0.713	0.583	0.469	0.713	SUBCLONAL	1	TRUE	1	0.228592616964608	2		267	450	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106158116	106158116	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	44	482	0	ENST00000380013.4:c.3017T>C	p.Val1006Ala	p.V1006A	ENST00000380013	NM_001127208.2	1006	gTa/gCa	3/11	1	2	FACETS	0.515	0.43	0.609	0.515	0.43	0.609	SUBCLONAL	1	TRUE	1	0.228592616964608	2		482	748	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434090	49434090	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	32	255	1	ENST00000301067.7:c.7463C>A	p.Ser2488Ter	p.S2488*	ENST00000301067	NM_003482.3	2488	tCg/tAg	31/54	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.228592616964608	2		256	264	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942757	44942758	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	373	702	0	ENST00000377967.4:c.3338dup	p.Ser1114IlefsTer37	p.S1114Ifs*37	ENST00000377967	NM_021140.2	1113	gta/gTta	23/29	0.175501153869057	2	FACETS	0.841	0.798	0.886	1	0.993	1	CLONAL	3	TRUE	0	0.228592616964608	2		702	1293	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577569	7577569	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	117	434	0	ENST00000269305.4:c.712del	p.Cys238ValfsTer9	p.C238Vfs*9	ENST00000269305	NM_001126112.2	238	Tgt/gt	7/11	0.175501153869057	2	FACETS	0.893	0.808	0.983	0.893	0.808	0.983	CLONAL	2	TRUE	0	0.228592616964608	2		434	573	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185170	123185170	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008062-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	75	508	0	ENST00000218089.9:c.1123del	p.Ile375LeufsTer4	p.I375Lfs*4	ENST00000218089	NM_001042749.1	374	agA/ag	13/35	0.228592616964608	1	FACETS	0.879	0.77	0.996	0.879	0.77	0.996	CLONAL	1	TRUE	0	0.228592616964608	1		508	661	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0008073-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	178	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.982	0.911	1	0.982	0.911	1	CLONAL	1	TRUE	1	0.675217058356072	2		464	537	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0008073-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	330	263	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.675217058356072	4	FACETS	1	0.974	1	0.692	0.657	0.727	CLONAL	2	TRUE	1	0.675217058356072	4		263	789	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309884	65309884	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008073-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	234	369	0	ENST00000342505.4:c.2266A>T	p.Ile756Phe	p.I756F	ENST00000342505	NM_002227.2	756	Atc/Ttc	17/25	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.675217058356072	2		369	652	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149441140	149441140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008073-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	313	531	0	ENST00000286301.3:c.1772G>A	p.Gly591Glu	p.G591E	ENST00000286301	NM_005211.3	591	gGa/gAa	13/22	1	2	FACETS	0.965	0.912	1	0.965	0.912	1	CLONAL	1	TRUE	1	0.675217058356072	2		531	961	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425421	49425421	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008073-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	328	524	0	ENST00000301067.7:c.13067G>A	p.Gly4356Glu	p.G4356E	ENST00000301067	NM_003482.3	4356	gGg/gAg	39/54	1	2	FACETS	0.981	0.929	1	0.981	0.929	1	CLONAL	1	TRUE	1	0.675217058356072	2		524	990	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873698	35873698	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008073-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	357	502	0	ENST00000216797.5:c.153G>C	p.Glu51Asp	p.E51D	ENST00000216797	NM_020529.2	51	gaG/gaC	1/6	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.675217058356072	2		502	1028	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873756	35873756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28933100	NA	P-0008073-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	342	481	1	ENST00000216797.5:c.95G>A	p.Ser32Asn	p.S32N	ENST00000216797	NM_020529.2	32	aGc/aAc	1/6	1	2	FACETS	0.968	0.917	1	0.968	0.917	1	CLONAL	1	TRUE	1	0.675217058356072	2		482	1047	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878364	151878380	+	frameshift_variant	Frame_Shift_Del	DEL	ACAGGTGTAACAAACAA	ACAGGTGTAACAAACAA	-	novel	NA	P-0008073-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	341	451	0	ENST00000262189.6:c.6565_6581del	p.Leu2189AsnfsTer7	p.L2189Nfs*7	ENST00000262189	NM_170606.2	2189	TTGTTTGTTACACCTGTa/a	36/59	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.675217058356072	2		451	930	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	192	280	0				ENST00000310581	NM_198253.2	-/1132			0.286097099791331	1	FACETS	0.814	0.753	0.877	0.814	0.753	0.877	CLONAL	1	TRUE	0	0.411503754320994	1		280	911	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793483	18793483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603405	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	78	480	0	ENST00000266497.5:c.4180G>A	p.Glu1394Lys	p.E1394K	ENST00000266497		1394	Gaa/Aaa	30/31	0.253427304498535	1	FACETS	0.858	0.759	0.962	0.858	0.759	0.962	CLONAL	1	TRUE	0	0.411503754320994	1		480	351	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295230	1295230	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs796516131	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	190	310	0				ENST00000310581	NM_198253.2	-/1132			0.286097099791331	1	FACETS	0.793	0.733	0.855	0.793	0.733	0.855	SUBCLONAL	1	TRUE	0	0.411503754320994	1		310	925	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	273	384	1	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.286097099791331	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.411503754320994	1		385	803	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779715	3779715	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1220965943	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	139	307	0	ENST00000262367.5:c.5333C>T	p.Ser1778Leu	p.S1778L	ENST00000262367	NM_004380.2	1778	tCg/tTg	31/31	0.253427304498535	1	FACETS	0.878	0.802	0.957	0.878	0.802	0.957	CLONAL	1	TRUE	0	0.411503754320994	1		307	611	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262001	16262001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	63	208	0	ENST00000375759.3:c.9266C>T	p.Ser3089Phe	p.S3089F	ENST00000375759	NM_015001.2	3089	tCc/tTc	11/15	0.286097099791331	1	FACETS	0.545	0.473	0.624	0.545	0.473	0.624	SUBCLONAL	1	TRUE	0	0.411503754320994	1		208	446	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363635	40363635	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	109	261	0	ENST00000397332.2:c.594A>C	p.Glu198Asp	p.E198D	ENST00000397332	NM_001033082.2	198	gaA/gaC	3/3	0.411503754320994	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.411503754320994	1		261	329	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578130	226578130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	228	351	0	ENST00000366794.5:c.598C>T	p.Pro200Ser	p.P200S	ENST00000366794	NM_001618.3	200	Cca/Tca	4/23	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.411503754320994	2		351	868	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667351	241667351	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	181	788	0	ENST00000366560.3:c.1099A>T	p.Ile367Phe	p.I367F	ENST00000366560	NM_000143.3	367	Atc/Ttc	7/10	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.411503754320994	2		788	822	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660801	227660801	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	167	339	0	ENST00000305123.5:c.2654T>A	p.Leu885Gln	p.L885Q	ENST00000305123	NM_005544.2	885	cTg/cAg	1/2	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.411503754320994	2		339	793	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691947	30691947	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	59	288	0	ENST00000295754.5:c.449C>T	p.Ser150Leu	p.S150L	ENST00000295754	NM_003242.5	150	tCa/tTa	3/7	0.213287179637751	2	FACETS	0.831	0.719	0.952	0.416	0.359	0.476	INDETERMINATE	1	TRUE	0	0.411503754320994	2		288	345	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947223	178947223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	125	382	0	ENST00000263967.3:c.2659G>A	p.Gly887Arg	p.G887R	ENST00000263967	NM_006218.2	887	Gga/Aga	18/21	0.389858494705754	1	FACETS	0.752	0.69	0.815	1	0.987	1	SUBCLONAL	2	TRUE	0	0.411503754320994	1		382	321	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127391	55127391	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	68	592	0	ENST00000257290.5:c.179C>T	p.Pro60Leu	p.P60L	ENST00000257290	NM_006206.4	60	cCc/cTc	3/23	1	2	FACETS	0.456	0.396	0.522	0.456	0.396	0.522	SUBCLONAL	1	TRUE	1	0.411503754320994	2		592	724	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532819	187532819	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1307123924	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	104	627	0	ENST00000441802.2:c.9574C>T	p.Gln3192Ter	p.Q3192*	ENST00000441802	NM_005245.3	3192	Cag/Tag	14/27	0.389858494705754	1	FACETS	0.723	0.65	0.801	0.723	0.65	0.801	SUBCLONAL	1	TRUE	0	0.411503754320994	1		627	555	SUCCESS
APC	324	MSKCC	GRCh37	5	112111328	112111328	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	15	242	0	ENST00000257430.4:c.425C>G	p.Ser142Ter	p.S142*	ENST00000257430	NM_000038.5	142	tCa/tGa	5/16	0.286097099791331	1	FACETS	0.508	0.375	0.664	0.508	0.375	0.664	SUBCLONAL	1	TRUE	0	0.411503754320994	1		242	114	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977973	131977973	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	57	447	0	ENST00000265335.6:c.3856T>C	p.Phe1286Leu	p.F1286L	ENST00000265335		1286	Ttc/Ctc	25/25	0.286097099791331	1	FACETS	0.661	0.57	0.759	0.661	0.57	0.759	SUBCLONAL	1	TRUE	0	0.411503754320994	1		447	333	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394923	394923	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	143	362	1	ENST00000380956.4:c.319T>A	p.Phe107Ile	p.F107I	ENST00000380956	NM_001195286.1	107	Ttt/Att	3/9	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.411503754320994	2		363	692	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964515	93964515	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	75	581	0	ENST00000369303.4:c.2383-1G>A		p.X795_splice	ENST00000369303	NM_004440.3	795			0.389858494705754	1	FACETS	0.834	0.736	0.938	0.834	0.736	0.938	CLONAL	1	TRUE	0	0.411503754320994	1		581	347	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066482	94066482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542602078	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	200	826	2	ENST00000369303.4:c.1277G>A	p.Arg426Gln	p.R426Q	ENST00000369303	NM_004440.3	426	cGa/cAa	5/17	0.389858494705754	1	FACETS	0.99	0.919	1	0.99	0.919	1	CLONAL	1	TRUE	0	0.411503754320994	1		828	780	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954934	2954934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	311	602	0	ENST00000396946.4:c.2776C>T	p.Pro926Ser	p.P926S	ENST00000396946	NM_032415.4	926	Ccg/Tcg	21/25	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.411503754320994	2		602	1436	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81346574	81346574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	102	594	0	ENST00000222390.5:c.1379C>T	p.Pro460Leu	p.P460L	ENST00000222390	NM_000601.4	460	cCt/cTt	11/18	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.411503754320994	2		594	487	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8331661	8331661	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	240	749	0	ENST00000356435.5:c.5455G>A	p.Gly1819Arg	p.G1819R	ENST00000356435		1819	Gga/Aga	33/35	0.286097099791331	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.411503754320994	1		749	857	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409487	80409487	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	9	349	0	ENST00000286548.4:c.627A>C	p.Gln209His	p.Q209H	ENST00000286548	NM_002072.3	209	caA/caC	5/7	0.286097099791331	1	FACETS	0.166	0.11	0.238	0.166	0.11	0.238	SUBCLONAL	1	TRUE	0	0.411503754320994	1		349	209	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742814	17742814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	384	448	0	ENST00000250003.3:c.722G>A	p.Gly241Glu	p.G241E	ENST00000250003	NM_002478.4	241	gGg/gAg	3/3	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.411503754320994	2		448	1521	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998991	100998991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1270021730	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	388	601	0	ENST00000325455.5:c.811G>A	p.Glu271Lys	p.E271K	ENST00000325455	NM_001202474.3	271	Gaa/Aaa	1/8	0.411503754320994	1	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	0	0.411503754320994	1		601	1425	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195282	102195282	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	141	987	1	ENST00000263464.3:c.42G>A	p.Met14Ile	p.M14I	ENST00000263464	NM_001165.4	14	atG/atA	2/9	0.411503754320994	1	FACETS	0.782	0.714	0.853	0.782	0.714	0.853	SUBCLONAL	1	TRUE	0	0.411503754320994	1		988	696	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245343	46245343	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	157	479	1	ENST00000334344.6:c.3437C>T	p.Ser1146Leu	p.S1146L	ENST00000334344	NM_152641.2	1146	tCg/tTg	15/21	0.253427304498535	1	FACETS	0.878	0.807	0.953	0.878	0.807	0.953	CLONAL	1	TRUE	0	0.411503754320994	1		480	690	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435233	49435233	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1418940802	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	183	250	0	ENST00000301067.7:c.6320C>T	p.Pro2107Leu	p.P2107L	ENST00000301067	NM_003482.3	2107	cCc/cTc	31/54	0.253427304498535	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.411503754320994	1		250	629	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864423	57864423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1359000505	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	322	776	1	ENST00000228682.2:c.1900G>A	p.Gly634Arg	p.G634R	ENST00000228682	NM_005269.2	634	Ggg/Agg	12/12	0.253427304498535	1	FACETS	0.846	0.797	0.896	0.846	0.797	0.896	CLONAL	1	TRUE	0	0.411503754320994	1		777	1470	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563270	21563270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	324	486	2	ENST00000382592.4:c.649C>T	p.Pro217Ser	p.P217S	ENST00000382592	NM_014572.2	217	Ccc/Tcc	4/8	0.253427304498535	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.411503754320994	1		488	1181	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906780	32906780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	28	771	0	ENST00000380152.3:c.1165C>T	p.Pro389Ser	p.P389S	ENST00000380152		389	Ccg/Tcg	10/27	0.253427304498535	1	FACETS	0.285	0.228	0.351	0.285	0.228	0.351	SUBCLONAL	1	TRUE	0	0.411503754320994	1		771	379	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913830	32913830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	49	997	0	ENST00000380152.3:c.5338G>A	p.Glu1780Lys	p.E1780K	ENST00000380152		1780	Gaa/Aaa	11/27	0.253427304498535	1	FACETS	0.337	0.285	0.394	0.337	0.285	0.394	SUBCLONAL	1	TRUE	0	0.411503754320994	1		997	561	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007620	45007620	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	27	275	0	ENST00000558401.1:c.68-1G>A		p.X23_splice	ENST00000558401	NM_004048.2	23			0.411503754320994	1	FACETS	0.617	0.495	0.752	0.617	0.495	0.752	SUBCLONAL	1	TRUE	0	0.411503754320994	1		275	169	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472600	88472600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	225	449	0	ENST00000360948.2:c.1955G>A	p.Gly652Glu	p.G652E	ENST00000360948	NM_001012338.2	652	gGg/gAg	16/19	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.411503754320994	2		449	1046	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934585	9934585	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	195	636	0	ENST00000330684.3:c.1570T>G	p.Phe524Val	p.F524V	ENST00000330684	NM_001134407.1	524	Ttc/Gtc	7/13	0.253427304498535	1	FACETS	0.786	0.727	0.846	0.786	0.727	0.846	SUBCLONAL	1	TRUE	0	0.411503754320994	1		636	958	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351541	89351541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1288	425	1023	0	ENST00000301030.4:c.1409G>A	p.Gly470Glu	p.G470E	ENST00000301030	NM_001256183.1	470	gGa/gAa	9/13	0.253427304498535	1	FACETS	0.958	0.91	1	0.958	0.91	1	CLONAL	1	TRUE	0	0.411503754320994	1		1023	1713	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351737	89351737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1385566000	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1256	366	1170	1	ENST00000301030.4:c.1213C>T	p.Arg405Cys	p.R405C	ENST00000301030	NM_001256183.1	405	Cgt/Tgt	9/13	0.253427304498535	1	FACETS	0.871	0.824	0.919	0.871	0.824	0.919	CLONAL	1	TRUE	0	0.411503754320994	1		1171	1622	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40709551	40709551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568484928	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1197	216	863	0	ENST00000373198.4:c.4351G>A	p.Glu1451Lys	p.E1451K	ENST00000373198	NM_133170.3	1451	Gag/Aag	32/32	0.411503754320994	3	FACETS	0.896	0.831	0.964	0.448	0.415	0.482	CLONAL	1	TRUE	1	0.411503754320994	3		863	1413	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164451	36164451	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	74	149	0	ENST00000300305.3:c.1424C>T	p.Ala475Val	p.A475V	ENST00000300305		475	gCc/gTc	8/8	1	2	FACETS	0.696	0.61	0.787	0.696	0.61	0.787	SUBCLONAL	1	TRUE	1	0.411503754320994	2		149	517	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608325	100608325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	67	375	0	ENST00000308731.7:c.1765G>A	p.Glu589Lys	p.E589K	ENST00000308731	NM_000061.2	589	Gaa/Aaa	18/19	1	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.411503754320994	1		375	188	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201492	67201493	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	317	538	0	ENST00000312629.5:c.934dup	p.Ile312AsnfsTer10	p.I312Nfs*10	ENST00000312629	NM_003952.2	311	-/A	11/15	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.411503754320994	2		538	1440	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556122	29556123	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	49	185	0	ENST00000356175.3:c.2492_2493del	p.Thr831ArgfsTer33	p.T831Rfs*33	ENST00000356175	NM_000267.3	830	gAC/g	21/57	0.286097099791331	1	FACETS	0.923	0.792	1	0.923	0.792	1	CLONAL	1	TRUE	0	0.411503754320994	1		185	205	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971097	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	271	273	0	ENST00000304494.5:c.261_262delinsAA	p.Glu88Lys	p.E88K	ENST00000304494	NM_000077.4	87	cgGGag/cgAAag	2/3	0.286097099791331	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.411503754320994	1		273	764	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71161718	71161719	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	105	628	0	ENST00000318789.4:c.250_251delinsTT	p.Pro84Phe	p.P84F	ENST00000318789	NM_032682.5	84	CCc/TTc	7/21	0.287755268348081	5	FACETS	1	0.965	1			1	CLONAL	1	TRUE	NA	0.411503754320994	5		628	702	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631826	90631827	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	187	437	0	ENST00000330062.3:c.526_527delinsAA	p.Gly176Asn	p.G176N	ENST00000330062	NM_002168.2	176	GGc/AAc	4/11	1	2	FACETS	0.917	0.847	0.99	0.917	0.847	0.99	CLONAL	1	TRUE	1	0.411503754320994	2		437	991	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427428	49427429	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	180	595	0	ENST00000301067.7:c.11059_11060delinsAA	p.Gly3687Asn	p.G3687N	ENST00000301067	NM_003482.3	3687	GGt/AAt	39/54	0.253427304498535	1	FACETS	0.75	0.691	0.81	0.75	0.691	0.81	SUBCLONAL	1	TRUE	0	0.411503754320994	1		595	927	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450712	70450713	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	97	485	0	ENST00000373644.4:c.5552_5553delinsTT	p.Ser1851Phe	p.S1851F	ENST00000373644	NM_030625.2	1851	tCC/tTT	12/12	0.253427304498535	1	FACETS	0.435	0.387	0.486	0.435	0.387	0.486	SUBCLONAL	1	TRUE	0	0.411503754320994	1		485	861	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225530	133225531	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	novel	NA	P-0008080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	225	519	0	ENST00000320574.5:c.4133_4134delinsAA	p.Gly1378Glu	p.G1378E	ENST00000320574	NM_006231.2	1378	gGT/gAA	32/49	0.253427304498535	1	FACETS	0.912	0.85	0.976	0.912	0.85	0.976	CLONAL	1	TRUE	0	0.411503754320994	1		519	952	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	25	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.976	0.769	1	0.976	0.769	1	CLONAL	1	TRUE	1	0.14	2		280	366	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0008097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	35	414	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	1	2	FACETS	0.805	0.658	0.971	0.805	0.658	0.971	CLONAL	1	TRUE	1	0.14	2		414	621	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705256	52705256	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008097-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	53	472	0	ENST00000322088.6:c.138G>T	p.Arg46Ser	p.R46S	ENST00000322088	NM_014225.5	46	agG/agT	2/15	0.3	2	FACETS	0.722	0.614	0.843			1	SUBCLONAL	1	TRUE	NA	0.14	2		472	1048	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	213	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.747244957914516	2		280	545	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0008103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	368	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.939	0.892	0.986	0.939	0.892	0.986	CLONAL	1	TRUE	1	0.747244957914516	2		490	1049	SUCCESS
ATM	472	MSKCC	GRCh37	11	108170575	108170576	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	-	novel	NA	P-0008103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	458	445	0	ENST00000278616.4:c.5140_5141del	p.Met1714AlafsTer6	p.M1714Afs*6	ENST00000278616	NM_000051.3	1714	ATg/g	34/63	NA	2	FACETS	0.947	0.905	0.989			1	INDETERMINATE	1	TRUE	NA	0.747244957914516	2		445	1295	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	38	280	0				ENST00000310581	NM_198253.2	-/1132			0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		280	522	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577082	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs786201059	NA	P-0008106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	109	560	0	ENST00000269305.4:c.856G>T	p.Glu286Ter	p.E286*	ENST00000269305	NM_001126112.2	286	Gaa/Taa	8/11	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		560	1276	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	189	280	0				ENST00000310581	NM_198253.2	-/1132			0.917882572101807	5	FACETS	0.957	0.901	1	0.957	0.901	1	CLONAL	3	TRUE	2	0.917882572101807	5		280	341	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0008149-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	32	670	505	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.902970711367934	4	FACETS	0.997	0.986	1	0.997	0.986	1	CLONAL	4	TRUE	0	0.917882572101807	4		506	702	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	204	476	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	1	2	FACETS	0.875	0.811	0.943	0.875	0.811	0.943	CLONAL	1	TRUE	1	0.390325945205502	2		477	1194	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	193	486	4	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.390325945205502	2		490	968	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443613	52443613	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	91	390	0	ENST00000460680.1:c.79del	p.Val27CysfsTer45	p.V27Cfs*45	ENST00000460680	NM_004656.3	27	Gtg/tg	3/17	1	2	FACETS	0.586	0.52	0.657	0.586	0.52	0.657	SUBCLONAL	1	TRUE	1	0.390325945205502	2		390	796	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	107	341	0	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	0.853	0.766	0.944	0.853	0.766	0.944	CLONAL	1	TRUE	1	0.390325945205502	2		341	643	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263754	16263754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747098120	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	138	394	0	ENST00000375759.3:c.10123G>A	p.Gly3375Ser	p.G3375S	ENST00000375759	NM_015001.2	3375	Ggt/Agt	12/15	1	2	FACETS	0.876	0.798	0.959	0.876	0.798	0.959	CLONAL	1	TRUE	1	0.390325945205502	2		394	807	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662352	227662352	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	66	264	1	ENST00000305123.5:c.1103del	p.Pro368ArgfsTer95	p.P368Rfs*95	ENST00000305123	NM_005544.2	368	cCg/cg	1/2	1	2	FACETS	0.694	0.604	0.792	0.694	0.604	0.792	SUBCLONAL	1	TRUE	1	0.390325945205502	2		265	487	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	38	330	3	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.331	0.272	0.396	0.331	0.272	0.396	SUBCLONAL	1	TRUE	1	0.390325945205502	2		333	589	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026115	14026116	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs769120755	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	112	586	0	ENST00000311895.7:c.1081dup	p.Met361AsnfsTer4	p.M361Nfs*4	ENST00000311895	NM_005236.2	359	gaa/gAaa	6/11	1	2	FACETS	0.796	0.716	0.88	0.796	0.716	0.88	SUBCLONAL	1	TRUE	1	0.390325945205502	2		586	721	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914070	32914070	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs397507790	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	148	930	0	ENST00000380152.3:c.5583del	p.Val1862Ter	p.V1862*	ENST00000380152		1860	Aaa/aa	11/27	1	2	FACETS	0.817	0.746	0.892	0.817	0.746	0.892	CLONAL	1	TRUE	1	0.390325945205502	2		930	928	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771923	135771923	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753388676	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	110	323	0	ENST00000298552.3:c.3194C>T	p.Thr1065Met	p.T1065M	ENST00000298552	NM_001162426.1	1065	aCg/aTg	23/23	1	2	FACETS	0.83	0.747	0.918	0.83	0.747	0.918	CLONAL	1	TRUE	1	0.390325945205502	2		323	679	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	51	549	0	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	0.39	0.331	0.455	0.39	0.331	0.455	SUBCLONAL	1	TRUE	1	0.390325945205502	2		549	670	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737107	145737109	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs780986647	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	142	490	0	ENST00000428558.2:c.3457_3459del	p.Glu1153del	p.E1153del	ENST00000428558	NM_004260.3	1153	GAG/-	21/22	1	2	FACETS	0.832	0.758	0.909	0.832	0.758	0.909	CLONAL	1	TRUE	1	0.390325945205502	2		490	875	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70008501	70008501	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147148433	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	146	400	1	ENST00000394351.3:c.788G>A	p.Arg263His	p.R263H	ENST00000394351	NM_000248.3	263	cGc/cAc	8/9	1	2	FACETS	0.887	0.81	0.968	0.887	0.81	0.968	CLONAL	1	TRUE	1	0.390325945205502	2		401	843	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007825	45007825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	136	385	0	ENST00000558401.1:c.276del	p.Thr93LeufsTer10	p.T93Lfs*10	ENST00000558401	NM_004048.2	91	aCc/ac	2/4	1	2	FACETS	0.975	0.888	1	0.975	0.888	1	CLONAL	1	TRUE	1	0.390325945205502	2		385	715	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444378	49444378	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	111	334	1	ENST00000301067.7:c.2993del	p.Pro998LeufsTer2	p.P998Lfs*2	ENST00000301067	NM_003482.3	998	cCt/ct	11/54	1	2	FACETS	0.982	0.886	1	0.982	0.886	1	CLONAL	1	TRUE	1	0.390325945205502	2		335	579	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615698	1615698	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1412	100	899	0	ENST00000344749.5:c.1573del	p.Arg525GlyfsTer18	p.R525Gfs*18	ENST00000344749	NM_001136139.2	525	Cgg/gg	17/19	1	2	FACETS	0.339	0.301	0.379	0.339	0.301	0.379	SUBCLONAL	1	TRUE	1	0.390325945205502	2		899	1512	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114842	108114842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145355104	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	80	442	1	ENST00000278616.4:c.659C>T	p.Ala220Val	p.A220V	ENST00000278616	NM_000051.3	220	gCg/gTg	6/63	1	2	FACETS	0.722	0.636	0.813	0.722	0.636	0.813	SUBCLONAL	1	TRUE	1	0.390325945205502	2		443	568	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572093	64572093	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs767319284	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	202	575	4	ENST00000312049.6:c.1546del	p.Arg516GlyfsTer43	p.R516Gfs*43	ENST00000312049	NM_130799.2	516	Cgg/gg	10/10	1	2	FACETS	0.914	0.846	0.984	0.914	0.846	0.984	CLONAL	1	TRUE	1	0.390325945205502	2		579	1133	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339093	65339093	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	177	536	0	ENST00000342505.4:c.443C>A	p.Pro148His	p.P148H	ENST00000342505	NM_002227.2	148	cCt/cAt	5/25	1	2	FACETS	0.82	0.754	0.888	0.82	0.754	0.888	CLONAL	1	TRUE	1	0.390325945205502	2		536	1106	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430832	78430832	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	168	454	0	ENST00000370768.2:c.557C>T	p.Ala186Val	p.A186V	ENST00000370768	NM_003902.3	186	gCa/gTa	8/20	1	2	FACETS	0.991	0.911	1	0.991	0.911	1	CLONAL	1	TRUE	1	0.390325945205502	2		454	869	SUCCESS
ALK	238	MSKCC	GRCh37	2	29450539	29450539	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	47	419	0	ENST00000389048.3:c.2816-1G>T		p.X939_splice	ENST00000389048	NM_004304.4	939			1	2	FACETS	0.338	0.284	0.398	0.338	0.284	0.398	SUBCLONAL	1	TRUE	1	0.390325945205502	2		419	712	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646041	215646041	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	48	485	0	ENST00000260947.4:c.557G>C	p.Ser186Thr	p.S186T	ENST00000260947	NM_000465.2	186	aGt/aCt	4/11	1	2	FACETS	0.311	0.262	0.366	0.311	0.262	0.366	SUBCLONAL	1	TRUE	1	0.390325945205502	2		485	790	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37081727	37081727	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs63751277	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	203	480	0	ENST00000231790.2:c.1609C>T	p.Gln537Ter	p.Q537*	ENST00000231790	NM_000249.3	537	Cag/Tag	14/19	1	2	FACETS	0.953	0.882	1	0.953	0.882	1	CLONAL	1	TRUE	1	0.390325945205502	2		480	1092	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934752	49934752	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs777611015	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	215	593	1	ENST00000296474.3:c.2144G>T	p.Arg715Leu	p.R715L	ENST00000296474	NM_002447.2	715	cGg/cTg	7/20	1	2	FACETS	0.95	0.882	1	0.95	0.882	1	CLONAL	1	TRUE	1	0.390325945205502	2		594	1160	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49939835	49939835	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371024286	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	241	773	0	ENST00000296474.3:c.1208C>T	p.Ser403Leu	p.S403L	ENST00000296474	NM_002447.2	403	tCg/tTg	1/20	1	2	FACETS	0.863	0.804	0.924	0.863	0.804	0.924	CLONAL	1	TRUE	1	0.390325945205502	2		773	1431	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55595603	55595603	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	78	393	0	ENST00000288135.5:c.2093C>A	p.Ala698Glu	p.A698E	ENST00000288135	NM_000222.2	698	gCa/gAa	14/21	1	2	FACETS	0.803	0.707	0.905	0.803	0.707	0.905	CLONAL	1	TRUE	1	0.390325945205502	2		393	498	SUCCESS
APC	324	MSKCC	GRCh37	5	112178790	112178790	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1561616049	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	56	540	0	ENST00000257430.4:c.7499A>G	p.Gln2500Arg	p.Q2500R	ENST00000257430	NM_000038.5	2500	cAg/cGg	16/16	1	2	FACETS	0.317	0.271	0.368	0.317	0.271	0.368	SUBCLONAL	1	TRUE	1	0.390325945205502	2		540	905	SUCCESS
APC	324	MSKCC	GRCh37	5	112178936	112178936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199539353	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	108	419	0	ENST00000257430.4:c.7645C>T	p.Arg2549Cys	p.R2549C	ENST00000257430	NM_000038.5	2549	Cgt/Tgt	16/16	1	2	FACETS	0.816	0.733	0.904	0.816	0.733	0.904	CLONAL	1	TRUE	1	0.390325945205502	2		419	678	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149509322	149509322	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	33	307	0	ENST00000261799.4:c.1577A>G	p.His526Arg	p.H526R	ENST00000261799	NM_002609.3	526	cAc/cGc	10/23	1	2	FACETS	0.304	0.247	0.369	0.304	0.247	0.369	SUBCLONAL	1	TRUE	1	0.390325945205502	2		307	556	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170827167	170827167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	48	556	0	ENST00000296930.5:c.535G>A	p.Asp179Asn	p.D179N	ENST00000296930	NM_002520.6	179	Gat/Aat	7/11	1	2	FACETS	0.341	0.287	0.4	0.341	0.287	0.4	SUBCLONAL	1	TRUE	1	0.390325945205502	2		556	722	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741800	145741800	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	196	434	1	ENST00000428558.2:c.703C>T	p.Gln235Ter	p.Q235*	ENST00000428558	NM_004260.3	235	Cag/Tag	5/22	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.390325945205502	2		435	917	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900201	101900201	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	128	638	2	ENST00000374994.4:c.635G>A	p.Gly212Asp	p.G212D	ENST00000374994	NM_004612.2	212	gGc/gAc	4/9	1	2	FACETS	0.649	0.587	0.714	0.649	0.587	0.714	SUBCLONAL	1	TRUE	1	0.390325945205502	2		640	1011	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133729594	133729594	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	178	576	0	ENST00000318560.5:c.223A>G	p.Ser75Gly	p.S75G	ENST00000318560	NM_005157.4	75	Agt/Ggt	2/11	1	2	FACETS	0.823	0.758	0.892	0.823	0.758	0.892	CLONAL	1	TRUE	1	0.390325945205502	2		576	1108	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601873	43601873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	159	422	0	ENST00000355710.3:c.917C>T	p.Ala306Val	p.A306V	ENST00000355710	NM_020975.4	306	gCa/gTa	5/20	1	2	FACETS	0.973	0.893	1	0.973	0.893	1	CLONAL	1	TRUE	1	0.390325945205502	2		422	837	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63759873	63759873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141049493	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	53	474	0	ENST00000279873.7:c.526G>A	p.Val176Met	p.V176M	ENST00000279873	NM_032199.2	176	Gtg/Atg	4/10	1	2	FACETS	0.261	0.222	0.305	0.261	0.222	0.305	SUBCLONAL	1	TRUE	1	0.390325945205502	2		474	1039	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123246907	123246907	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	170	630	0	ENST00000358487.5:c.2018A>G	p.Glu673Gly	p.E673G	ENST00000358487	NM_000141.4	673	gAa/gGa	15/18	1	2	FACETS	0.96	0.883	1	0.96	0.883	1	CLONAL	1	TRUE	1	0.390325945205502	2		630	907	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375594	118375594	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs191446381	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	48	326	0	ENST00000534358.1:c.8987A>G	p.His2996Arg	p.H2996R	ENST00000534358	NM_005933.3	2996	cAt/cGt	27/36	1	2	FACETS	0.373	0.315	0.438	0.373	0.315	0.438	SUBCLONAL	1	TRUE	1	0.390325945205502	2		326	659	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484069	50484069	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	163	518	1	ENST00000394963.4:c.919A>T	p.Ile307Phe	p.I307F	ENST00000394963	NM_003076.4	307	Atc/Ttc	8/13	1	2	FACETS	0.859	0.788	0.934	0.859	0.788	0.934	CLONAL	1	TRUE	1	0.390325945205502	2		519	972	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56489085	56489085	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	54	504	0	ENST00000267101.3:c.1904T>A	p.Val635Glu	p.V635E	ENST00000267101	NM_001982.3	635	gTg/gAg	16/28	1	2	FACETS	0.282	0.24	0.329	0.282	0.24	0.329	SUBCLONAL	1	TRUE	1	0.390325945205502	2		504	981	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856019	111856019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs984848263	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	58	393	0	ENST00000341259.2:c.70C>T	p.Arg24Trp	p.R24W	ENST00000341259	NM_005475.2	24	Cgg/Tgg	2/8	1	2	FACETS	0.335	0.287	0.388	0.335	0.287	0.388	SUBCLONAL	1	TRUE	1	0.390325945205502	2		393	887	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856116	111856116	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1314581870	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	173	401	0	ENST00000341259.2:c.167C>T	p.Ala56Val	p.A56V	ENST00000341259	NM_005475.2	56	gCg/gTg	2/8	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.390325945205502	2		401	875	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562282	21562282	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs543513326	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	45	469	0	ENST00000382592.4:c.1637C>T	p.Ala546Val	p.A546V	ENST00000382592	NM_014572.2	546	gCg/gTg	4/8	1	2	FACETS	0.27	0.226	0.319	0.27	0.226	0.319	SUBCLONAL	1	TRUE	1	0.390325945205502	2		469	855	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563444	21563444	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	188	543	0	ENST00000382592.4:c.476-1G>T		p.X159_splice	ENST00000382592	NM_014572.2	159			1	2	FACETS	0.977	0.903	1	0.977	0.903	1	CLONAL	1	TRUE	1	0.390325945205502	2		543	986	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48878068	48878068	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564059250	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	50	135	0	ENST00000267163.4:c.20G>A	p.Arg7Gln	p.R7Q	ENST00000267163	NM_000321.2	7	cGa/cAa	1/27	1	2	FACETS	0.893	0.763	1	0.893	0.763	1	CLONAL	1	TRUE	1	0.390325945205502	2		135	287	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40993338	40993338	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145617142	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	151	565	0	ENST00000267868.3:c.164C>T	p.Ala55Val	p.A55V	ENST00000267868	NM_002875.4	55	gCg/gTg	3/10	1	2	FACETS	0.939	0.859	1	0.939	0.859	1	CLONAL	1	TRUE	1	0.390325945205502	2		565	824	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99472849	99472849	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	174	512	1	ENST00000268035.6:c.2845G>A	p.Gly949Arg	p.G949R	ENST00000268035	NM_000875.3	949	Gga/Aga	14/21	1	2	FACETS	0.8	0.735	0.867	0.8	0.735	0.867	SUBCLONAL	1	TRUE	1	0.390325945205502	2		513	1115	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112583	2112583	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs397515206	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	290	435	0	ENST00000219476.3:c.1343T>C	p.Leu448Pro	p.L448P	ENST00000219476	NM_000548.3	448	cTg/cCg	13/42	NA	2	FACETS	0.866	0.817	0.916			1	INDETERMINATE	2	TRUE	NA	0.390325945205502	2		435	858	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857151	9857151	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1346618506	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	165	602	0	ENST00000330684.3:c.4250G>A	p.Arg1417Gln	p.R1417Q	ENST00000330684	NM_001134407.1	1417	cGg/cAg	13/13	1	2	FACETS	0.795	0.729	0.864	0.795	0.729	0.864	SUBCLONAL	1	TRUE	1	0.390325945205502	2		602	1063	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662450	67662450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	199	594	0	ENST00000264010.4:c.1696C>T	p.Arg566Cys	p.R566C	ENST00000264010	NM_006565.3	566	Cgt/Tgt	9/12	1	2	FACETS	0.902	0.835	0.973	0.902	0.835	0.973	CLONAL	1	TRUE	1	0.390325945205502	2		594	1130	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842703	68842703	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	170	615	1	ENST00000261769.5:c.639G>A	p.Trp213Ter	p.W213*	ENST00000261769	NM_004360.3	213	tgG/tgA	5/16	1	2	FACETS	0.787	0.722	0.854	0.787	0.722	0.854	SUBCLONAL	1	TRUE	1	0.390325945205502	2		616	1107	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805956	89805956	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	106	329	1	ENST00000389301.3:c.3940A>G	p.Arg1314Gly	p.R1314G	ENST00000389301	NM_000135.2	1314	Agg/Ggg	40/43	1	2	FACETS	0.766	0.687	0.85	0.766	0.687	0.85	SUBCLONAL	1	TRUE	1	0.390325945205502	2		330	709	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428245	33428245	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769732230	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	127	454	1	ENST00000345365.6:c.878C>T	p.Ala293Val	p.A293V	ENST00000345365	NM_002878.3	293	gCg/gTg	9/10	1	2	FACETS	0.814	0.738	0.895	0.814	0.738	0.895	CLONAL	1	TRUE	1	0.390325945205502	2		455	799	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37863341	37863341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	181	596	0	ENST00000269571.5:c.172G>A	p.Gly58Arg	p.G58R	ENST00000269571		58	Gga/Aga	2/27	1	2	FACETS	0.953	0.879	1	0.953	0.879	1	CLONAL	1	TRUE	1	0.390325945205502	2		596	973	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40354428	40354428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs929910807	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	224	946	0	ENST00000293328.3:c.2167G>A	p.Ala723Thr	p.A723T	ENST00000293328	NM_012448.3	723	Gcc/Acc	18/19	NA	2	FACETS	0.891	0.828	0.957			1	INDETERMINATE	1	TRUE	NA	0.390325945205502	2		946	1288	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437606	56437606	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886926322	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	101	361	3	ENST00000407977.2:c.856C>T	p.Arg286Trp	p.R286W	ENST00000407977		286	Cgg/Tgg	8/10	NA	2	FACETS	0.779	0.697	0.866			1	INDETERMINATE	1	TRUE	NA	0.390325945205502	2		364	664	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439930	56439930	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs2285990	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	92	254	0	ENST00000407977.2:c.662G>A	p.Arg221Gln	p.R221Q	ENST00000407977		221	cGg/cAg	6/10	NA	2	FACETS	0.749	0.667	0.838			1	INDETERMINATE	1	TRUE	NA	0.390325945205502	2		254	629	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78935208	78935208	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	42	449	1	ENST00000306801.3:c.3620A>G	p.Tyr1207Cys	p.Y1207C	ENST00000306801	NM_020761.2	1207	tAc/tGc	31/34	1	2	FACETS	0.263	0.218	0.312	0.263	0.218	0.312	SUBCLONAL	1	TRUE	1	0.390325945205502	2		450	819	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281256	15281256	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752437137	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	134	289	0	ENST00000263388.2:c.5000G>A	p.Arg1667His	p.R1667H	ENST00000263388	NM_000435.2	1667	cGc/cAc	27/33	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.390325945205502	2		289	630	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15379824	15379824	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	62	576	1	ENST00000263377.2:c.315G>T	p.Met105Ile	p.M105I	ENST00000263377	NM_058243.2	105	atG/atT	3/20	1	2	FACETS	0.367	0.316	0.423	0.367	0.316	0.423	SUBCLONAL	1	TRUE	1	0.390325945205502	2		577	865	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918720	50918720	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765437818	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	141	374	1	ENST00000440232.2:c.2590G>A	p.Ala864Thr	p.A864T	ENST00000440232	NM_002691.3	864	Gca/Aca	21/27	1	2	FACETS	0.936	0.853	1	0.936	0.853	1	CLONAL	1	TRUE	1	0.390325945205502	2		375	772	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543608	9543608	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776769814	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	188	560	1	ENST00000353224.5:c.1546G>A	p.Gly516Ser	p.G516S	ENST00000353224	NM_177990.2	516	Ggc/Agc	6/10	1	2	FACETS	0.885	0.817	0.956	0.885	0.817	0.956	CLONAL	1	TRUE	1	0.390325945205502	2		561	1088	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30309666	30309666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	54	432	0	ENST00000307677.4:c.356C>T	p.Ala119Val	p.A119V	ENST00000307677	NM_138578.1	119	gCa/gTa	2/3	1	2	FACETS	0.307	0.261	0.358	0.307	0.261	0.358	SUBCLONAL	1	TRUE	1	0.390325945205502	2		432	901	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923083	39923083	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	64	410	0	ENST00000378444.4:c.3625C>T	p.Arg1209Cys	p.R1209C	ENST00000378444	NM_001123385.1	1209	Cgc/Tgc	8/15	1	1	FACETS	0.369	0.319	0.424	0.369	0.319	0.424	SUBCLONAL	1	TRUE	0	0.390325945205502	1		410	715	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030463	47030463	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781862400	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	236	315	0	ENST00000377604.3:c.238C>T	p.Arg80Cys	p.R80C	ENST00000377604	NM_001204468.1	80	Cgt/Tgt	4/24	1	1	FACETS	0.811	0.762	0.86	1	0.994	1	CLONAL	2	TRUE	0	0.390325945205502	1		315	600	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163711	47163712	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	34	466	0	ENST00000409792.3:c.2414_2415del	p.Cys805Ter	p.C805*	ENST00000409792	NM_014159.6	805	tGT/t	3/21	1	2	FACETS	0.284	0.231	0.344	0.284	0.231	0.344	SUBCLONAL	1	TRUE	1	0.390325945205502	2		466	613	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448295	56448296	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	103	232	0	ENST00000407977.2:c.351_352insAC	p.Pro118ThrfsTer41	p.P118Tfs*41	ENST00000407977		117	-/AC	3/10	NA	2	FACETS	0.818	0.733	0.908			1	INDETERMINATE	1	TRUE	NA	0.390325945205502	2		232	645	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983227	149983228	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	112	507	0	ENST00000253339.5:c.3030dup	p.Lys1011Ter	p.K1011*	ENST00000253339		1010	-/T	7/7	1	2	FACETS	0.787	0.708	0.871	0.787	0.708	0.871	SUBCLONAL	1	TRUE	1	0.390325945205502	2		507	729	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63553979	63553980	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	185	524	0	ENST00000307078.5:c.759_760del	p.Lys253AsnfsTer15	p.K253Nfs*15	ENST00000307078	NM_004655.3	253	aaAAct/aact	2/11	1	2	FACETS	0.907	0.837	0.98	0.907	0.837	0.98	CLONAL	1	TRUE	1	0.390325945205502	2		524	1045	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500894	8500894	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	115	464	0	ENST00000356435.5:c.1988del	p.Leu663TrpfsTer25	p.L663Wfs*25	ENST00000356435		663	tTg/tg	13/35	1	2	FACETS	0.709	0.638	0.784	0.709	0.638	0.784	SUBCLONAL	1	TRUE	1	0.390325945205502	2		464	831	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848015	151848017	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	114	469	0	ENST00000262189.6:c.12742_12744del	p.Ser4248del	p.S4248del	ENST00000262189	NM_170606.2	4248	TCA/-	51/59	1	2	FACETS	0.884	0.797	0.975	0.884	0.797	0.975	CLONAL	1	TRUE	1	0.390325945205502	2		469	661	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199761	138199763	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	161	564	0	ENST00000237289.4:c.1183_1185del	p.Phe395del	p.F395del	ENST00000237289	NM_001270507.1	393	ccCTTc/ccc	7/9	1	2	FACETS	0.72	0.659	0.784	0.72	0.659	0.784	SUBCLONAL	1	TRUE	1	0.390325945205502	2		564	1145	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128984	64128984	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	197	490	0	ENST00000334205.4:c.618del	p.Glu207LysfsTer26	p.E207Kfs*26	ENST00000334205	NM_003942.2	205	gCc/gc	6/17	1	2	FACETS	0.936	0.865	1	0.936	0.865	1	CLONAL	1	TRUE	1	0.390325945205502	2		490	1079	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533685	41533689	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTC	CCCTC	-	novel	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	162	543	0	ENST00000263253.7:c.1653_1657del	p.Ser552GlyfsTer63	p.S552Gfs*63	ENST00000263253	NM_001429.3	551	CCCTCc/c	8/31	1	2	FACETS	0.866	0.795	0.942	0.866	0.795	0.942	CLONAL	1	TRUE	1	0.390325945205502	2		543	958	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41489075	41489076	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555902247	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	124	400	0	ENST00000263253.7:c.70_71del	p.Ser24GlyfsTer14	p.S24Gfs*14	ENST00000263253	NM_001429.3	23	CTc/c	1/31	1	2	FACETS	0.777	0.703	0.855	0.777	0.703	0.855	SUBCLONAL	1	TRUE	1	0.390325945205502	2		400	818	SUCCESS
BLM	641	MSKCC	GRCh37	15	91310207	91310208	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs747341586	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	97	715	0	ENST00000355112.3:c.2268dup	p.Asp757ArgfsTer18	p.D757Rfs*18	ENST00000355112	NM_000057.2	754	tca/tcAa	10/22	1	2	FACETS	0.664	0.592	0.741	0.664	0.592	0.741	SUBCLONAL	1	TRUE	1	0.390325945205502	2		715	748	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95569765	95569765	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs35252236	NA	P-0008180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	124	416	2	ENST00000393063.1:c.3968del	p.Leu1323Ter	p.L1323*	ENST00000393063	NM_030621.3	1323	tTa/ta	22/28	1	2	FACETS	0.832	0.753	0.915	0.832	0.753	0.915	CLONAL	1	TRUE	1	0.390325945205502	2		418	764	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	50	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.381817263066017	2		280	225	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0008214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	150	560	1	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.364519261870889	1	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	0	0.381817263066017	1		561	611	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs149680468	NA	P-0008214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	168	491	0	ENST00000281708.4:c.1513C>G	p.Arg505Gly	p.R505G	ENST00000281708	NM_033632.3	505	Cgc/Ggc	10/12	1	2	FACETS	0.984	0.905	1	0.984	0.905	1	CLONAL	1	TRUE	1	0.381817263066017	2		491	894	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971000	21971000	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	226	342	0	ENST00000304494.5:c.358G>T	p.Glu120Ter	p.E120*	ENST00000304494	NM_000077.4	120	Gag/Tag	2/3	0.381817263066017	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.381817263066017	2		342	517	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098810	178098810	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519922	NA	P-0008214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	245	604	0	ENST00000397062.3:c.235G>A	p.Glu79Lys	p.E79K	ENST00000397062	NM_006164.4	79	Gag/Aag	2/5	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.381817263066017	2		604	1058	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202150030	202150030	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs931648756	NA	P-0008214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	127	327	1	ENST00000358485.4:c.1471C>T	p.Arg491Ter	p.R491*	ENST00000358485	NM_001080125.1	491	Cga/Tga	8/9	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.381817263066017	2		328	627	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539648	187539648	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	136	621	0	ENST00000441802.2:c.8092del	p.Met2698CysfsTer25	p.M2698Cfs*25	ENST00000441802	NM_005245.3	2698	Atg/tg	10/27	0.133998516689145	1	FACETS	0.725	0.66	0.794	0.725	0.66	0.794	INDETERMINATE	1	TRUE	0	0.381817263066017	1		621	795	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584734	187584735	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CA	novel	NA	P-0008214-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	117	482	0	ENST00000441802.2:c.3297_3298dup	p.Glu1100ValfsTer9	p.E1100Vfs*9	ENST00000441802	NM_005245.3	1100	gaa/gTGaa	3/27	0.133998516689145	1	FACETS	0.692	0.624	0.763	0.692	0.624	0.763	INDETERMINATE	1	TRUE	0	0.381817263066017	1		482	717	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	69	464	0				ENST00000310581	NM_198253.2	-/1132			0.601482585191907	4	FACETS	0.998	0.888	1	0.998	0.888	1	CLONAL	2	TRUE	2	0.601482585191907	4		464	184	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980844	40980844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	302	387	0	ENST00000373198.4:c.1642G>A	p.Glu548Lys	p.E548K	ENST00000373198	NM_133170.3	548	Gaa/Aaa	10/32	0.45095808712654	5	FACETS	0.952	0.904	1			1	CLONAL	3	TRUE	NA	0.601482585191907	5		387	669	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436175	56436175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1444015068	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	195	342	1	ENST00000407977.2:c.962C>T	p.Ser321Leu	p.S321L	ENST00000407977		321	tCa/tTa	9/10	0.601482585191907	3	FACETS	0.931	0.872	0.991	0.931	0.872	0.991	CLONAL	2	TRUE	1	0.601482585191907	3		343	453	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164832	47164832	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1017636782	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	100	351	0	ENST00000409792.3:c.1294C>T	p.Arg432Cys	p.R432C	ENST00000409792	NM_014159.6	432	Cgt/Tgt	3/21	0.601482585191907	3	FACETS	0.89	0.799	0.986	0.445	0.399	0.493	CLONAL	1	TRUE	1	0.601482585191907	3		351	486	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	181	251	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.591094655964768	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.601482585191907	2		251	282	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043938	180043938	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	105	567	0	ENST00000261937.6:c.3058C>T	p.Gln1020Ter	p.Q1020*	ENST00000261937	NM_182925.4	1020	Cag/Tag	22/30	0.601482585191907	3	FACETS	0.757	0.68	0.839	0.378	0.34	0.42	SUBCLONAL	1	TRUE	1	0.601482585191907	3		567	600	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760520	133760520	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1240583398	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	98	513	0	ENST00000318560.5:c.2843C>T	p.Pro948Leu	p.P948L	ENST00000318560	NM_005157.4	948	cCc/cTc	11/11	0.601482585191907	3	FACETS	0.858	0.769	0.952	0.429	0.384	0.476	CLONAL	1	TRUE	1	0.601482585191907	3		513	494	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450891	70450891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	155	264	0	ENST00000373644.4:c.5731C>T	p.Pro1911Ser	p.P1911S	ENST00000373644	NM_030625.2	1911	Ccc/Tcc	12/12	0.598102564933515	4	FACETS	0.994	0.92	1	0.994	0.92	1	CLONAL	2	TRUE	2	0.601482585191907	4		264	415	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658412	117658412	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	99	466	0	ENST00000368508.3:c.5171C>T	p.Ser1724Leu	p.S1724L	ENST00000368508	NM_002944.2	1724	tCa/tTa	31/43	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.601482585191907	2		466	312	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059246	27059246	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs927444249	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	380	518	0	ENST00000324856.7:c.1883T>C	p.Met628Thr	p.M628T	ENST00000324856	NM_006015.4	628	aTg/aCg	4/20	0.601482585191907	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.601482585191907	4		518	952	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837991	156837991	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	216	389	0	ENST00000524377.1:c.524T>G	p.Leu175Arg	p.L175R	ENST00000524377	NM_002529.3	175	cTg/cGg	5/17	0.601482585191907	5	FACETS	0.916	0.854	0.979	0.61	0.569	0.653	CLONAL	2	TRUE	2	0.601482585191907	5		389	746	SUCCESS
SDHC	6391	MSKCC	GRCh37	1	161310389	161310389	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1558174466	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	399	607	0	ENST00000367975.2:c.185C>G	p.Ser62Cys	p.S62C	ENST00000367975	NM_003001.3	62	tCt/tGt	4/6	0.601482585191907	5	FACETS	0.942	0.896	0.99	0.628	0.597	0.66	CLONAL	2	TRUE	2	0.601482585191907	5		607	1339	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162725511	162725511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	508	423	0	ENST00000367921.3:c.623C>T	p.Ser208Phe	p.S208F	ENST00000367921	NM_006182.2	208	tCc/tTc	7/18	0.601482585191907	5	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	2	0.601482585191907	5		423	941	SUCCESS
ALK	238	MSKCC	GRCh37	2	29543641	29543641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	97	405	0	ENST00000389048.3:c.1522G>A	p.Asp508Asn	p.D508N	ENST00000389048	NM_004304.4	508	Gat/Aat	7/29	0.601482585191907	3	FACETS	0.761	0.681	0.847	0.381	0.34	0.424	SUBCLONAL	1	TRUE	1	0.601482585191907	3		405	551	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735386	204735386	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	97	238	0	ENST00000302823.3:c.187C>T	p.Pro63Ser	p.P63S	ENST00000302823	NM_005214.4	63	Cca/Tca	2/4	0.358332983611044	3	FACETS	1	0.966	1	0.586	0.527	0.647	INDETERMINATE	1	TRUE	1	0.601482585191907	3		238	358	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141026	55141026	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765680542	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	105	410	3	ENST00000257290.5:c.1672C>T	p.Arg558Cys	p.R558C	ENST00000257290	NM_006206.4	558	Cgc/Tgc	12/23	0.547076424469462	3	FACETS	0.938	0.845	1	0.469	0.422	0.518	CLONAL	1	TRUE	1	0.601482585191907	3		413	484	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155962	106155962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	105	237	1	ENST00000380013.4:c.863C>T	p.Pro288Leu	p.P288L	ENST00000380013	NM_001127208.2	288	cCa/cTa	3/11	0.547076424469462	3	FACETS	1	0.953	1	0.547	0.494	0.603	CLONAL	1	TRUE	1	0.601482585191907	3		238	415	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35860954	35860954	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	186	243	0	ENST00000303115.3:c.83G>A	p.Gly28Glu	p.G28E	ENST00000303115	NM_002185.3	28	gGa/gAa	2/8	0.601482585191907	4	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	2	0.601482585191907	4		243	489	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178656	32178656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	255	379	0	ENST00000375023.3:c.2738C>T	p.Ser913Phe	p.S913F	ENST00000375023	NM_004557.3	913	tCc/tTc	18/30	0.601482585191907	5	FACETS	1	0.978	1	0.723	0.679	0.767	CLONAL	2	TRUE	2	0.601482585191907	5		379	744	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068121	94068121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149408123	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	163	630	1	ENST00000369303.4:c.841C>T	p.Arg281Cys	p.R281C	ENST00000369303	NM_004440.3	281	Cgt/Tgt	4/17	1	2	FACETS	0.887	0.818	0.959	0.887	0.818	0.959	CLONAL	1	TRUE	1	0.601482585191907	2		631	611	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94128987	94128987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370009055	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	156	596	1	ENST00000369303.4:c.73G>A	p.Gly25Arg	p.G25R	ENST00000369303	NM_004440.3	25	Ggg/Agg	1/17	1	2	FACETS	0.878	0.807	0.95	0.878	0.807	0.95	CLONAL	1	TRUE	1	0.601482585191907	2		597	591	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681028	117681028	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	105	392	0	ENST00000368508.3:c.3592T>C	p.Tyr1198His	p.Y1198H	ENST00000368508	NM_002944.2	1198	Tat/Cat	23/43	1	2	FACETS	0.981	0.887	1	0.981	0.887	1	CLONAL	1	TRUE	1	0.601482585191907	2		392	356	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729961	41729961	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867739441	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1809	422	945	0	ENST00000242208.4:c.568G>A	p.Glu190Lys	p.E190K	ENST00000242208	NM_002192.2	190	Gaa/Aaa	3/3	0.601482585191907	7	FACETS	0.787	0.747	0.829			1	SUBCLONAL	2	TRUE	NA	0.601482585191907	7		945	2231	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386512	81386512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	108	378	1	ENST00000222390.5:c.475G>A	p.Glu159Lys	p.E159K	ENST00000222390	NM_000601.4	159	Gaa/Aaa	4/18	0.601482585191907	3	FACETS	0.867	0.781	0.957	0.433	0.39	0.479	CLONAL	1	TRUE	1	0.601482585191907	3		379	539	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340334	116340334	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	80	168	0	ENST00000397752.3:c.1196A>T	p.Asn399Ile	p.N399I	ENST00000397752	NM_000245.2	399	aAt/aTt	2/21	0.601482585191907	3	FACETS	1	0.963	1	0.599	0.533	0.668	CLONAL	1	TRUE	1	0.601482585191907	3		168	289	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878983	151878983	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	239	340	0	ENST00000262189.6:c.5962C>T	p.Pro1988Ser	p.P1988S	ENST00000262189	NM_170606.2	1988	Cct/Tct	36/59	0.299256338103957	4	FACETS	1	0.977	1			1	INDETERMINATE	2	TRUE	NA	0.601482585191907	4		340	592	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340437	8340437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	265	403	0	ENST00000356435.5:c.5159C>T	p.Pro1720Leu	p.P1720L	ENST00000356435		1720	cCc/cTc	31/35	0.601482585191907	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.601482585191907	3		403	541	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484355	8484355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1290617956	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	61	350	0	ENST00000356435.5:c.3177G>A	p.Met1059Ile	p.M1059I	ENST00000356435		1059	atG/atA	19/35	0.601482585191907	3	FACETS	0.64	0.554	0.733	0.32	0.277	0.367	SUBCLONAL	1	TRUE	1	0.601482585191907	3		350	412	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771963	135771963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	127	182	0	ENST00000298552.3:c.3154C>T	p.Pro1052Ser	p.P1052S	ENST00000298552	NM_001162426.1	1052	Cca/Tca	23/23	0.601482585191907	3	FACETS	1	0.925	1	1	0.925	1	CLONAL	2	TRUE	1	0.601482585191907	3		182	274	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374147	118374147	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782437914	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	239	428	0	ENST00000534358.1:c.7540G>A	p.Glu2514Lys	p.E2514K	ENST00000534358	NM_005933.3	2514	Gaa/Aaa	27/36	0.591094655964768	2	FACETS	0.926	0.879	0.973	0.926	0.879	0.973	CLONAL	2	TRUE	0	0.601482585191907	2		428	429	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375983	118375983	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	259	440	0	ENST00000534358.1:c.9376G>T	p.Gly3126Ter	p.G3126*	ENST00000534358	NM_005933.3	3126	Gga/Tga	27/36	0.591094655964768	2	FACETS	0.948	0.902	0.994	0.948	0.902	0.994	CLONAL	2	TRUE	0	0.601482585191907	2		440	454	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392816	118392816	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	297	445	0	ENST00000534358.1:c.11848C>T	p.Pro3950Ser	p.P3950S	ENST00000534358	NM_005933.3	3950	Ccc/Tcc	36/36	0.591094655964768	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.601482585191907	2		445	472	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793369	18793369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531443561	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	87	459	0	ENST00000266497.5:c.4066C>T	p.Pro1356Ser	p.P1356S	ENST00000266497		1356	Cca/Tca	30/31	1	2	FACETS	0.72	0.641	0.803	0.72	0.641	0.803	SUBCLONAL	1	TRUE	1	0.601482585191907	2		459	402	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488276	56488276	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	195	437	1	ENST00000267101.3:c.1795C>T	p.Pro599Ser	p.P599S	ENST00000267101	NM_001982.3	599	Cca/Tca	15/28	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.601482585191907	2		438	570	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937088	48937088	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	143	297	0	ENST00000267163.4:c.856G>A	p.Asp286Asn	p.D286N	ENST00000267163	NM_000321.2	286	Gat/Aat	8/27	0.598102564933515	4	FACETS	0.826	0.759	0.895	0.826	0.759	0.895	CLONAL	2	TRUE	2	0.601482585191907	4		297	461	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349954	89349954	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780895582	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	356	915	0	ENST00000301030.4:c.2996C>T	p.Pro999Leu	p.P999L	ENST00000301030	NM_001256183.1	999	cCg/cTg	9/13	0.235830232031084	1	FACETS	0.969	0.923	1	0.969	0.923	1	INDETERMINATE	1	TRUE	0	0.601482585191907	1		915	854	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663800	29663800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060500382	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	285	411	1	ENST00000356175.3:c.6232C>T	p.His2078Tyr	p.H2078Y	ENST00000356175	NM_000267.3	2078	Cat/Tat	41/57	0.591094655964768	2	FACETS	0.983	0.938	1	0.983	0.938	1	CLONAL	2	TRUE	0	0.601482585191907	2		412	482	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880225	37880225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	127	640	1	ENST00000269571.5:c.2269G>A	p.Glu757Lys	p.E757K	ENST00000269571		757	Gaa/Aaa	19/27	0.591094655964768	2	FACETS	0.871	0.794	0.951	0.435	0.397	0.476	CLONAL	1	TRUE	0	0.601482585191907	2		641	485	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012614	36012614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	270	311	0	ENST00000358208.4:c.58C>T	p.Pro20Ser	p.P20S	ENST00000358208		20	Ccc/Tcc	2/12	0.601482585191907	5	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	2	0.601482585191907	5		311	547	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306800	41306800	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	170	145	0	ENST00000373198.4:c.860-1G>A		p.X287_splice	ENST00000373198	NM_133170.3	287			0.45095808712654	5	FACETS	0.893	0.839	0.946			1	CLONAL	4	TRUE	NA	0.601482585191907	5		145	301	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41420050	41420050	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	303	330	0	ENST00000373198.4:c.271C>T	p.Leu91Phe	p.L91F	ENST00000373198	NM_133170.3	91	Ctc/Ttc	3/32	0.45095808712654	5	FACETS	1	0.975	1			1	CLONAL	3	TRUE	NA	0.601482585191907	5		330	615	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961315	54961315	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	215	303	0	ENST00000312783.6:c.317C>T	p.Pro106Leu	p.P106L	ENST00000312783	NM_198436.1	106	cCt/cTt	4/10	0.601482585191907	5	FACETS	0.963	0.899	1			1	CLONAL	2	TRUE	NA	0.601482585191907	5		303	706	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130427	29130427	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587781269	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	210	382	0	ENST00000328354.6:c.283C>T	p.Arg95Ter	p.R95*	ENST00000328354	NM_007194.3	95	Cga/Tga	2/15	0.299256338103957	4	FACETS	1	0.987	1			1	INDETERMINATE	2	TRUE	NA	0.601482585191907	4		382	467	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987421	2987422	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	783	320	0	ENST00000396946.4:c.8-1_8delinsAA		p.X3_splice	ENST00000396946	NM_032415.4	3		3/25	0.601482585191907	10	FACETS	1	0.978	1			1	CLONAL	8	TRUE	NA	0.601482585191907	10		320	1107	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546674	9546675	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0008228-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	190	414	0	ENST00000353224.5:c.1347_1348delinsAA	p.Ala450Thr	p.A450T	ENST00000353224	NM_177990.2	449	ttGGcc/ttAAcc	5/10	0.601482585191907	5	FACETS	0.816	0.757	0.878	0.544	0.504	0.585	CLONAL	2	TRUE	2	0.601482585191907	5		414	736	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	49	280	0				ENST00000310581	NM_198253.2	-/1132			0.492517626364141	1	FACETS	0.69	0.597	0.787	0.69	0.597	0.787	SUBCLONAL	1	FALSE	0	0.648468744544785	1		280	148	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0008240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	39	595	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.72	0.606	0.844	0.72	0.606	0.844	SUBCLONAL	1	FALSE	1	0.648468744544785	2		595	167	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845367	151845367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	155	318	1	ENST00000262189.6:c.13645C>T	p.Arg4549Cys	p.R4549C	ENST00000262189	NM_170606.2	4549	Cgc/Tgc	52/59	1	2	FACETS	0.982	0.906	1	0.982	0.906	1	CLONAL	1	FALSE	1	0.648468744544785	2		319	487	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81336625	81336625	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs527951814	NA	P-0008240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	227	583	0	ENST00000222390.5:c.1597C>T	p.Arg533Ter	p.R533*	ENST00000222390	NM_000601.4	533	Cga/Tga	14/18	1	2	FACETS	0.906	0.847	0.966	0.906	0.847	0.966	CLONAL	1	FALSE	1	0.648468744544785	2		583	773	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152012370	152012370	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	236	552	2	ENST00000262189.6:c.443G>T	p.Gly148Val	p.G148V	ENST00000262189	NM_170606.2	148	gGa/gTa	4/59	NA	2	FACETS	0.938	0.878	0.999			1	INDETERMINATE	1	FALSE	NA	0.648468744544785	2		554	776	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49440398	49440398	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	114	369	1	ENST00000301067.7:c.4412G>A	p.Cys1471Tyr	p.C1471Y	ENST00000301067	NM_003482.3	1471	tGc/tAc	15/54	1	2	FACETS	0.913	0.83	1	0.913	0.83	1	CLONAL	1	FALSE	1	0.648468744544785	2		370	385	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135079	11135079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770969438	NA	P-0008240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	48	358	0	ENST00000358026.2:c.3046G>A	p.Val1016Met	p.V1016M	ENST00000358026	NM_001128849.1	1016	Gtg/Atg	21/36	0.202832426335562	0	FACETS	0.198	0.168	0.23			1	INDETERMINATE	1	FALSE	0	0.648468744544785	0		358	263	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39774536	39774536	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	196	578	0	ENST00000288319.7:c.616G>C	p.Asp206His	p.D206H	ENST00000288319	NM_182918.3	206	Gat/Cat	5/10	1	2	FACETS	0.952	0.886	1	0.952	0.886	1	CLONAL	1	FALSE	1	0.648468744544785	2		578	635	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842090	3842090	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008240-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	140	387	0	ENST00000262367.5:c.1222del	p.His408IlefsTer26	p.H408Ifs*26	ENST00000262367	NM_004380.2	408	Cat/at	5/31	0.331724352902692	0	FACETS	0.361	0.331	0.391			1	INDETERMINATE	1	FALSE	0	0.648468744544785	0		387	421	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	136	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.937	0.864	1	0.937	0.864	1	CLONAL	1	TRUE	1	0.861754191519118	2		280	337	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0008244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	186	511	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.874	0.814	0.934	0.874	0.814	0.934	CLONAL	1	TRUE	1	0.861754191519118	2		512	494	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799050	42799050	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008244-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	286	323	1	ENST00000575354.2:c.4534C>T	p.Arg1512Cys	p.R1512C	ENST00000575354	NM_015125.3	1512	Cgt/Tgt	20/20	0.861754191519118	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.861754191519118	1		324	368	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	418	464	0				ENST00000310581	NM_198253.2	-/1132			0.312120744492428	4	FACETS	1	0.978	1	1	0.978	1	INDETERMINATE	2	TRUE	2	0.706275281927346	4		464	974	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185775	32185775	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772949126	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	295	384	0	ENST00000375023.3:c.1621C>T	p.Pro541Ser	p.P541S	ENST00000375023	NM_004557.3	541	Cct/Tct	9/30	0.274726981548179	6	FACETS	1	0.993	1	0.366	0.343	0.389	INDETERMINATE	1	TRUE	2	0.706275281927346	6		384	1377	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230641	46230641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	671	508	0	ENST00000334344.6:c.890C>T	p.Ser297Phe	p.S297F	ENST00000334344	NM_152641.2	297	tCc/tTc	8/21	0.657048287188815	2	FACETS	0.887	0.862	0.912	0.887	0.862	0.912	CLONAL	2	TRUE	0	0.706275281927346	2		508	1071	SUCCESS
APC	324	MSKCC	GRCh37	5	112177901	112177901	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs752654519	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	445	445	1	ENST00000257430.4:c.6610C>T	p.Arg2204Ter	p.R2204*	ENST00000257430	NM_000038.5	2204	Cga/Tga	16/16	0.218171002950698	4	FACETS	0.847	0.808	0.885	0.847	0.808	0.885	INDETERMINATE	2	TRUE	2	0.706275281927346	4		446	1270	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873660	35873660	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs201559094	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	528	408	0	ENST00000303115.3:c.616C>T	p.Arg206Ter	p.R206*	ENST00000303115	NM_002185.3	206	Cga/Tga	5/8	0.312120744492428	4	FACETS	0.904	0.867	0.941	0.904	0.867	0.941	INDETERMINATE	2	TRUE	2	0.706275281927346	4		408	1411	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866579	78866579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	270	351	0	ENST00000306801.3:c.2152C>T	p.Arg718Cys	p.R718C	ENST00000306801	NM_020761.2	718	Cgt/Tgt	19/34	0.7010625950409	2	FACETS	0.773	0.726	0.821	0.387	0.363	0.411	SUBCLONAL	1	TRUE	0	0.706275281927346	2		351	989	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	322	572	1	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.218171002950698	4	FACETS	1	0.985	1	0.56	0.528	0.593	INDETERMINATE	1	TRUE	2	0.706275281927346	4		573	1389	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578534	7578534	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs866775781	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	709	335	0	ENST00000269305.4:c.396G>T	p.Lys132Asn	p.K132N	ENST00000269305	NM_001126112.2	132	aaG/aaT	5/11	0.7010625950409	2	FACETS	0.988	0.963	1	0.988	0.963	1	CLONAL	2	TRUE	0	0.706275281927346	2		335	1016	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547022	9547022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs58486349	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	260	150	0	ENST00000353224.5:c.1000G>A	p.Asp334Asn	p.D334N	ENST00000353224	NM_177990.2	334	Gat/Aat	5/10	0.312120744492428	4	FACETS	0.947	0.902	0.992	1	0.994	1	INDETERMINATE	3	TRUE	2	0.706275281927346	4		150	442	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498004	29498004	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1208550472	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	643	576	0	ENST00000389048.3:c.2002G>A	p.Glu668Lys	p.E668K	ENST00000389048	NM_004304.4	668	Gaa/Aaa	11/29	0.179042028281231	2	FACETS	1	0.996	1	0.62	0.598	0.642	INDETERMINATE	1	TRUE	0	0.706275281927346	2		576	1469	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456447	189456447	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	329	418	0	ENST00000264731.3:c.208C>T	p.Gln70Ter	p.Q70*	ENST00000264731	NM_003722.4	70	Cag/Tag	3/14	0.706275281927346	3	FACETS	0.962	0.908	1	0.481	0.454	0.509	CLONAL	1	TRUE	1	0.706275281927346	3		418	1311	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	798	765	2	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.149275143210428	2	FACETS	1	0.997	1	0.637	0.617	0.657	INDETERMINATE	1	TRUE	0	0.706275281927346	2		767	1774	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94203678	94203678	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	381	411	0	ENST00000323929.3:c.976C>T	p.Pro326Ser	p.P326S	ENST00000323929	NM_005591.3	326	Cct/Tct	9/20	0.372493782456111	1	FACETS	0.844	0.806	0.882	0.844	0.806	0.882	INDETERMINATE	1	TRUE	0	0.706275281927346	1		411	827	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469086	25469086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1420356837	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	302	460	0	ENST00000264709.3:c.1372C>T	p.Arg458Trp	p.R458W	ENST00000264709	NM_175629.2	458	Cgg/Tgg	11/23	0.179042028281231	2	FACETS	0.741	0.698	0.785	0.371	0.349	0.393	INDETERMINATE	1	TRUE	0	0.706275281927346	2		460	1154	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073598	8073598	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1162	460	676	0	ENST00000377482.5:c.1061C>T	p.Pro354Leu	p.P354L	ENST00000377482	NM_018948.3	354	cCt/cTt	4/4	0.179042028281231	2	FACETS	0.803	0.766	0.841	0.402	0.383	0.421	INDETERMINATE	1	TRUE	0	0.706275281927346	2		676	1622	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs984459719	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	326	506	1	ENST00000324856.7:c.2291C>T	p.Ser764Phe	p.S764F	ENST00000324856	NM_006015.4	764	tCc/tTc	7/20	0.152739728007226	1	FACETS	0.508	0.479	0.537	0.508	0.479	0.537	INDETERMINATE	1	TRUE	0	0.706275281927346	1		507	1176	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106805	27106805	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	110	325	0	ENST00000324856.7:c.6416C>T	p.Pro2139Leu	p.P2139L	ENST00000324856	NM_006015.4	2139	cCc/cTc	20/20	0.152739728007226	1	FACETS	0.245	0.22	0.272	0.245	0.22	0.272	INDETERMINATE	1	TRUE	0	0.706275281927346	1		325	823	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649701	206649701	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	154	184	0	ENST00000367120.3:c.536A>T	p.Tyr179Phe	p.Y179F	ENST00000367120	NM_014002.3	179	tAc/tTc	6/22	0.149275143210428	2	FACETS	0.656	0.602	0.712	0.328	0.301	0.356	INDETERMINATE	1	TRUE	0	0.706275281927346	2		184	665	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965761	25965761	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377352572	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	287	359	0	ENST00000435504.4:c.3445C>T	p.Arg1149Cys	p.R1149C	ENST00000435504		1149	Cgt/Tgt	13/13	0.179042028281231	2	FACETS	0.75	0.705	0.795	0.375	0.352	0.398	INDETERMINATE	1	TRUE	0	0.706275281927346	2		359	1084	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416469	29416469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1255053275	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	331	553	0	ENST00000389048.3:c.4484C>T	p.Ser1495Phe	p.S1495F	ENST00000389048	NM_004304.4	1495	tCc/tTc	29/29	0.179042028281231	2	FACETS	0.729	0.688	0.77	0.364	0.344	0.385	INDETERMINATE	1	TRUE	0	0.706275281927346	2		553	1286	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474031	29474031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763862465	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	605	472	0	ENST00000389048.3:c.2144G>A	p.Gly715Glu	p.G715E	ENST00000389048	NM_004304.4	715	gGg/gAg	12/29	0.179042028281231	2	FACETS	1	0.996	1	0.648	0.625	0.672	INDETERMINATE	1	TRUE	0	0.706275281927346	2		472	1321	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754827	29754827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373120394	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	400	344	0	ENST00000389048.3:c.1108G>A	p.Glu370Lys	p.E370K	ENST00000389048	NM_004304.4	370	Gag/Aag	4/29	0.179042028281231	2	FACETS	1	0.993	1	0.599	0.572	0.627	INDETERMINATE	1	TRUE	0	0.706275281927346	2		344	945	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286791	212286791	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	440	422	0	ENST00000342788.4:c.2905G>A	p.Glu969Lys	p.E969K	ENST00000342788	NM_005235.2	969	Gaa/Aaa	24/28	0.179042028281231	2	FACETS	1	0.995	1	0.641	0.614	0.668	INDETERMINATE	1	TRUE	0	0.706275281927346	2		422	972	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288993	212288993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867944951	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	304	552	0	ENST00000342788.4:c.2753G>A	p.Gly918Glu	p.G918E	ENST00000342788	NM_005235.2	918	gGa/gAa	23/28	0.179042028281231	2	FACETS	0.723	0.681	0.766	0.361	0.34	0.383	INDETERMINATE	1	TRUE	0	0.706275281927346	2		552	1191	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812181	212812181	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	280	418	0	ENST00000342788.4:c.395A>T	p.Gln132Leu	p.Q132L	ENST00000342788	NM_005235.2	132	cAa/cTa	3/28	0.179042028281231	2	FACETS	0.738	0.693	0.783	0.369	0.346	0.392	INDETERMINATE	1	TRUE	0	0.706275281927346	2		418	1075	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468357	89468357	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs867931903	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	119	225	0	ENST00000336596.2:c.1891G>A	p.Glu631Lys	p.E631K	ENST00000336596	NM_005233.5	631	Gaa/Aaa	11/17	0.218171002950698	4	FACETS	0.812	0.734	0.895	0.406	0.367	0.448	INDETERMINATE	1	TRUE	2	0.706275281927346	4		225	708	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468522	89468522	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	206	360	0	ENST00000336596.2:c.2056G>A	p.Glu686Lys	p.E686K	ENST00000336596	NM_005233.5	686	Gaa/Aaa	11/17	0.218171002950698	4	FACETS	0.872	0.808	0.938	0.436	0.404	0.469	INDETERMINATE	1	TRUE	2	0.706275281927346	4		360	1142	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413734	138413734	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	175	265	0	ENST00000289153.2:c.1786C>T	p.Gln596Ter	p.Q596*	ENST00000289153	NM_006219.2	596	Cag/Tag	12/22	0.149275143210428	2	FACETS	0.686	0.634	0.741	0.343	0.317	0.371	INDETERMINATE	1	TRUE	0	0.706275281927346	2		265	722	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277609	142277609	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs983647070	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	272	257	0	ENST00000350721.4:c.1742C>T	p.Ser581Leu	p.S581L	ENST00000350721	NM_001184.3	581	tCa/tTa	8/47	0.149275143210428	2	FACETS	1	0.987	1	0.573	0.541	0.605	INDETERMINATE	1	TRUE	0	0.706275281927346	2		257	672	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182681705	182681705	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	300	364	2	ENST00000292782.4:c.353C>T	p.Ser118Phe	p.S118F	ENST00000292782	NM_020640.2	118	tCc/tTc	3/7	0.706275281927346	3	FACETS	0.968	0.911	1	0.484	0.455	0.513	CLONAL	1	TRUE	1	0.706275281927346	3		366	1188	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189456474	189456474	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1484040098	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	497	416	0	ENST00000264731.3:c.235G>A	p.Glu79Lys	p.E79K	ENST00000264731	NM_003722.4	79	Gaa/Aaa	3/14	0.706275281927346	3	FACETS	1	0.996	1	0.689	0.66	0.719	CLONAL	1	TRUE	1	0.706275281927346	3		416	1381	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607164	189607164	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	694	445	0	ENST00000264731.3:c.1543G>A	p.Asp515Asn	p.D515N	ENST00000264731	NM_003722.4	515	Gac/Aac	12/14	0.706275281927346	3	FACETS	0.962	0.931	0.993	0.962	0.931	0.993	CLONAL	2	TRUE	1	0.706275281927346	3		445	1382	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749412	41749412	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	235	272	0	ENST00000226382.2:c.383G>T	p.Arg128Leu	p.R128L	ENST00000226382	NM_003924.3	128	cGg/cTg	2/3	NA	2	FACETS	0.784	0.733	0.836			1	INDETERMINATE	1	TRUE	NA	0.706275281927346	2		272	849	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518864	187518864	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	260	483	0	ENST00000441802.2:c.12340C>T	p.Gln4114Ter	p.Q4114*	ENST00000441802	NM_005245.3	4114	Cag/Tag	24/27	0.706275281927346	1	FACETS	0.497	0.466	0.529	0.497	0.466	0.529	SUBCLONAL	1	TRUE	0	0.706275281927346	1		483	958	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295252	1295252	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	202	350	0				ENST00000310581	NM_198253.2	-/1132			0.312120744492428	4	FACETS	0.93	0.861	1	0.465	0.43	0.501	INDETERMINATE	1	TRUE	2	0.706275281927346	4		350	1050	SUCCESS
APC	324	MSKCC	GRCh37	5	112177697	112177697	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	166	274	0	ENST00000257430.4:c.6406C>T	p.Leu2136Phe	p.L2136F	ENST00000257430	NM_000038.5	2136	Ctt/Ttt	16/16	0.218171002950698	4	FACETS	0.895	0.822	0.971	0.448	0.411	0.486	INDETERMINATE	1	TRUE	2	0.706275281927346	4		274	896	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523630	176523630	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	707	568	1	ENST00000292408.4:c.2041G>A	p.Glu681Lys	p.E681K	ENST00000292408	NM_213647.1	681	Gag/Aag	16/18	0.218171002950698	4	FACETS	1	0.983	1	1	0.983	1	INDETERMINATE	2	TRUE	2	0.706275281927346	4		569	1663	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180030334	180030334	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1251	318	489	1	ENST00000261937.6:c.3950G>A	p.Gly1317Glu	p.G1317E	ENST00000261937	NM_182925.4	1317	gGg/gAg	30/30	0.218171002950698	4	FACETS	0.979	0.922	1	0.49	0.461	0.519	INDETERMINATE	1	TRUE	2	0.706275281927346	4		490	1569	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048115	180048115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	219	327	0	ENST00000261937.6:c.2158G>A	p.Glu720Lys	p.E720K	ENST00000261937	NM_182925.4	720	Gaa/Aaa	14/30	0.218171002950698	4	FACETS	0.939	0.873	1	0.469	0.436	0.504	INDETERMINATE	1	TRUE	2	0.706275281927346	4		327	1127	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052916	180052916	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	516	335	0	ENST00000261937.6:c.1374G>A	p.Trp458Ter	p.W458*	ENST00000261937	NM_182925.4	458	tgG/tgA	10/30	0.218171002950698	4	FACETS	0.947	0.909	0.986	0.947	0.909	0.986	INDETERMINATE	2	TRUE	2	0.706275281927346	4		335	1316	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671595	30671595	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1300	531	442	1	ENST00000376406.3:c.5365C>T	p.Gln1789Ter	p.Q1789*	ENST00000376406	NM_014641.2	1789	Caa/Taa	10/15	0.274726981548179	6	FACETS	0.991	0.948	1	0.495	0.474	0.517	INDETERMINATE	2	TRUE	2	0.706275281927346	6		443	1831	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673796	30673796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1269	92	294	0	ENST00000376406.3:c.3164C>T	p.Ser1055Phe	p.S1055F	ENST00000376406	NM_014641.2	1055	tCt/tTt	10/15	0.274726981548179	6	FACETS	0.462	0.409	0.519	0.115	0.102	0.13	INDETERMINATE	1	TRUE	2	0.706275281927346	6		294	1361	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187435	32187435	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1499	285	424	0	ENST00000375023.3:c.1444C>T	p.Gln482Ter	p.Q482*	ENST00000375023	NM_004557.3	482	Cag/Tag	8/30	0.274726981548179	6	FACETS	1	0.978	1	0.273	0.255	0.291	INDETERMINATE	1	TRUE	2	0.706275281927346	6		424	1784	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662618	117662618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	644	538	0	ENST00000368508.3:c.4847G>A	p.Gly1616Glu	p.G1616E	ENST00000368508	NM_002944.2	1616	gGa/gAa	29/43	0.706275281927346	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.706275281927346	1		538	978	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2953091	2953091	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	368	249	1	ENST00000396946.4:c.2849C>T	p.Pro950Leu	p.P950L	ENST00000396946	NM_032415.4	950	cCt/cTt	22/25	0.218171002950698	4	FACETS	0.993	0.946	1	0.993	0.946	1	INDETERMINATE	2	TRUE	2	0.706275281927346	4		250	895	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977561	2977561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	303	396	0	ENST00000396946.4:c.1123G>A	p.Val375Met	p.V375M	ENST00000396946	NM_032415.4	375	Gtg/Atg	8/25	0.218171002950698	4	FACETS	1	0.985	1	0.569	0.536	0.604	INDETERMINATE	1	TRUE	2	0.706275281927346	4		396	1286	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459447	50459447	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	171	303	0	ENST00000331340.3:c.736C>T	p.His246Tyr	p.H246Y	ENST00000331340	NM_006060.4	246	Cac/Tac	7/8	0.218171002950698	4	FACETS	0.831	0.764	0.901	0.416	0.382	0.451	INDETERMINATE	1	TRUE	2	0.706275281927346	4		303	994	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55240686	55240686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	265	424	0	ENST00000275493.2:c.1930C>T	p.Pro644Ser	p.P644S	ENST00000275493	NM_005228.3	644	Ccg/Tcg	17/28	0.218171002950698	4	FACETS	0.869	0.812	0.927	0.434	0.406	0.464	INDETERMINATE	1	TRUE	2	0.706275281927346	4		424	1474	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436150	116436150	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752694306	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	150	274	0	ENST00000397752.3:c.4145G>A	p.Arg1382Gln	p.R1382Q	ENST00000397752	NM_000245.2	1382	cGa/cAa	21/21	0.218171002950698	4	FACETS	0.765	0.698	0.834	0.382	0.349	0.417	INDETERMINATE	1	TRUE	2	0.706275281927346	4		274	948	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494160	140494160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1340	310	498	1	ENST00000288602.6:c.1088C>T	p.Ser363Phe	p.S363F	ENST00000288602	NM_004333.4	363	tCc/tTc	8/18	0.218171002950698	4	FACETS	0.908	0.853	0.964	0.454	0.426	0.482	INDETERMINATE	1	TRUE	2	0.706275281927346	4		499	1650	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874661	151874661	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	215	384	2	ENST00000262189.6:c.7877A>G	p.Glu2626Gly	p.E2626G	ENST00000262189	NM_170606.2	2626	gAa/gGa	38/59	0.218171002950698	4	FACETS	0.828	0.768	0.89	0.414	0.384	0.445	INDETERMINATE	1	TRUE	2	0.706275281927346	4		386	1255	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877824	151877824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	226	429	1	ENST00000262189.6:c.7121C>T	p.Ala2374Val	p.A2374V	ENST00000262189	NM_170606.2	2374	gCc/gTc	36/59	0.218171002950698	4	FACETS	0.822	0.764	0.882	0.411	0.382	0.441	INDETERMINATE	1	TRUE	2	0.706275281927346	4		430	1329	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635173	87635173	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	340	312	0	ENST00000277120.3:c.2225T>C	p.Met742Thr	p.M742T	ENST00000277120		742	aTg/aCg	18/19	0.149275143210428	2	FACETS	1	0.991	1	0.591	0.562	0.62	INDETERMINATE	1	TRUE	0	0.706275281927346	2		312	815	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597873	43597873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749190212	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1218	87	552	0	ENST00000355710.3:c.421G>A	p.Gly141Ser	p.G141S	ENST00000355710	NM_020975.4	141	Ggc/Agc	3/20	0.372237885404924	1	FACETS	0.122	0.107	0.138	0.122	0.107	0.138	INDETERMINATE	1	TRUE	0	0.706275281927346	1		552	1305	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375003	118375003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	171	322	1	ENST00000534358.1:c.8396C>T	p.Ser2799Phe	p.S2799F	ENST00000534358	NM_005933.3	2799	tCc/tTc	27/36	0.372493782456111	1	FACETS	0.401	0.369	0.434	0.401	0.369	0.434	INDETERMINATE	1	TRUE	0	0.706275281927346	1		323	781	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656259	18656259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201569993	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	286	396	0	ENST00000266497.5:c.2938C>T	p.His980Tyr	p.H980Y	ENST00000266497		980	Cat/Tat	21/31	0.657048287188815	2	FACETS	0.907	0.855	0.96	0.453	0.427	0.48	CLONAL	1	TRUE	0	0.706275281927346	2		396	893	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56491687	56491687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	438	300	0	ENST00000267101.3:c.2579C>T	p.Pro860Leu	p.P860L	ENST00000267101	NM_001982.3	860	cCt/cTt	21/28	0.657048287188815	2	FACETS	0.858	0.827	0.888	0.858	0.827	0.888	CLONAL	2	TRUE	0	0.706275281927346	2		300	723	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519190	103519190	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	147	316	0	ENST00000355739.4:c.2528A>G	p.Gln843Arg	p.Q843R	ENST00000355739	NM_000123.3	843	cAa/cGa	11/15	1	2	FACETS	0.458	0.418	0.501	0.458	0.418	0.501	SUBCLONAL	1	TRUE	1	0.706275281927346	2		316	908	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68292234	68292234	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	221	431	0	ENST00000487270.1:c.138T>G	p.Tyr46Ter	p.Y46*	ENST00000487270	NM_133509.3	46	taT/taG	3/11	0.372493782456111	1	FACETS	0.352	0.327	0.378	0.352	0.327	0.378	INDETERMINATE	1	TRUE	0	0.706275281927346	1		431	1150	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021422	42021422	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1710	423	631	0	ENST00000219905.7:c.3718C>T	p.Arg1240Ter	p.R1240*	ENST00000219905	NM_001164273.1	1240	Cga/Tga	11/24	NA	2	FACETS	0.562	0.533	0.591			1	INDETERMINATE	1	TRUE	NA	0.706275281927346	2		631	2133	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304071	91304071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567041087	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1411	315	534	0	ENST00000355112.3:c.1468C>T	p.Pro490Ser	p.P490S	ENST00000355112	NM_000057.2	490	Cct/Tct	7/22	0.273174147072861	4	FACETS	0.882	0.829	0.936	0.441	0.414	0.468	INDETERMINATE	1	TRUE	2	0.706275281927346	4		534	1726	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467191	99467191	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773555066	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1415	308	516	0	ENST00000268035.6:c.2572C>T	p.Pro858Ser	p.P858S	ENST00000268035	NM_000875.3	858	Ccc/Tcc	12/21	0.273174147072861	4	FACETS	0.864	0.812	0.918	0.432	0.406	0.459	INDETERMINATE	1	TRUE	2	0.706275281927346	4		516	1723	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857703	9857703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	207	408	1	ENST00000330684.3:c.3698C>T	p.Pro1233Leu	p.P1233L	ENST00000330684	NM_001134407.1	1233	cCc/cTc	13/13	0.26059281277692	2	FACETS	0.614	0.57	0.66	0.307	0.285	0.33	INDETERMINATE	1	TRUE	0	0.706275281927346	2		409	955	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346223	89346223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	201	323	0	ENST00000301030.4:c.6727C>T	p.Pro2243Ser	p.P2243S	ENST00000301030	NM_001256183.1	2243	Ccc/Tcc	9/13	0.372237885404924	1	FACETS	0.469	0.435	0.504	0.469	0.435	0.504	INDETERMINATE	1	TRUE	0	0.706275281927346	1		323	785	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346733	89346733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1466198155	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	399	462	0	ENST00000301030.4:c.6217C>T	p.Pro2073Ser	p.P2073S	ENST00000301030	NM_001256183.1	2073	Ccg/Tcg	9/13	0.372237885404924	1	FACETS	0.72	0.687	0.754	0.72	0.687	0.754	INDETERMINATE	1	TRUE	0	0.706275281927346	1		462	1015	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29665053	29665053	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691093	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	398	210	0	ENST00000356175.3:c.6652C>T	p.Gln2218Ter	p.Q2218*	ENST00000356175	NM_000267.3	2218	Caa/Taa	44/57	0.703910307294294	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.706275281927346	2		210	548	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207178	1207178	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	184	366	0	ENST00000326873.7:c.266C>T	p.Pro89Leu	p.P89L	ENST00000326873	NM_000455.4	89	cCc/cTc	1/10	NA	2	FACETS	0.607	0.561	0.655			1	INDETERMINATE	1	TRUE	NA	0.706275281927346	2		366	858	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220485	1220485	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	265	408	0	ENST00000326873.7:c.578C>T	p.Ser193Phe	p.S193F	ENST00000326873	NM_000455.4	193	tCc/tTc	4/10	NA	2	FACETS	0.809	0.759	0.859			1	INDETERMINATE	1	TRUE	NA	0.706275281927346	2		408	928	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355048	15355048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	136	190	0	ENST00000263377.2:c.2575C>T	p.Pro859Ser	p.P859S	ENST00000263377	NM_058243.2	859	Cct/Tct	13/20	0.180124169612	2	FACETS	0.592	0.539	0.646	0.296	0.269	0.323	INDETERMINATE	1	TRUE	0	0.706275281927346	2		190	651	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278032	18278032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756172410	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	316	346	0	ENST00000222254.8:c.1652C>T	p.Ser551Leu	p.S551L	ENST00000222254	NM_005027.3	551	tCg/tTg	13/16	0.180124169612	2	FACETS	1	0.99	1	0.59	0.56	0.621	INDETERMINATE	1	TRUE	0	0.706275281927346	2		346	758	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31387068	31387068	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	602	336	0	ENST00000328111.2:c.1693C>T	p.Pro565Ser	p.P565S	ENST00000328111	NM_006892.3	565	Cct/Tct	16/23	0.312120744492428	4	FACETS	0.986	0.949	1	0.986	0.949	1	INDETERMINATE	2	TRUE	2	0.706275281927346	4		336	1475	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264737	46264737	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1773	459	625	0	ENST00000371998.3:c.1607C>T	p.Ser536Phe	p.S536F	ENST00000371998		536	tCc/tTc	12/23	0.312120744492428	4	FACETS	0.994	0.945	1	0.497	0.472	0.522	INDETERMINATE	1	TRUE	2	0.706275281927346	4		625	2232	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167590	24167590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1244451002	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	260	170	0	ENST00000263121.7:c.974C>T	p.Thr325Ile	p.T325I	ENST00000263121	NM_003073.3	325	aCc/aTc	7/9	0.706275281927346	5	FACETS	0.925	0.869	0.981	0.616	0.579	0.654	CLONAL	2	TRUE	2	0.706275281927346	5		170	820	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573068	41573068	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	434	339	2	ENST00000263253.7:c.5353C>T	p.Leu1785Phe	p.L1785F	ENST00000263253	NM_001429.3	1785	Ctc/Ttc	31/31	0.403359286315373	4	FACETS	0.76	0.724	0.796			1	INDETERMINATE	2	TRUE	NA	0.706275281927346	4		341	1380	SUCCESS
AR	367	MSKCC	GRCh37	X	66937368	66937368	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	357	585	0	ENST00000374690.3:c.2222C>T	p.Ser741Phe	p.S741F	ENST00000374690	NM_000044.3	741	tCc/tTc	5/8	0.706275281927346	1	FACETS	0.597	0.566	0.629	0.597	0.566	0.629	SUBCLONAL	1	TRUE	0	0.706275281927346	1		585	1095	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95577759	95577802	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTCCCAACTGGCATCAAATGGTCATCCAGTTCGCCTAACAAAT	TTTCCCAACTGGCATCAAATGGTCATCCAGTTCGCCTAACAAAT	-	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	164	574	0	ENST00000393063.1:c.2117-9_2151del		p.X706_splice	ENST00000393063	NM_030621.3	706		15/28	0.372493782456111	1	FACETS	0.252	0.231	0.275	0.252	0.231	0.275	INDETERMINATE	1	TRUE	0	0.706275281927346	1		574	1190	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180939	32180940	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1271	122	327	1	ENST00000375023.3:c.2410_2411delinsAA	p.Gly804Lys	p.G804K	ENST00000375023	NM_004557.3	804	GGa/AAa	15/30	0.274726981548179	6	FACETS	0.598	0.539	0.662	0.15	0.134	0.166	INDETERMINATE	1	TRUE	2	0.706275281927346	6		328	1393	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93639903	93639904	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	41	331	0	ENST00000375746.1:c.1232_1233delinsTT	p.Pro411Leu	p.P411L	ENST00000375746	NM_001174167.1	411	cCC/cTT	10/14	0.149275143210428	2	FACETS	0.143	0.119	0.171	0.072	0.059	0.086	INDETERMINATE	1	TRUE	0	0.706275281927346	2		331	810	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101027	41101028	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	212	340	0	ENST00000373198.4:c.1328_1329delinsTT	p.Thr443Ile	p.T443I	ENST00000373198	NM_133170.3	443	aCC/aTT	8/32	0.312120744492428	4	FACETS	0.838	0.777	0.902	0.419	0.388	0.451	INDETERMINATE	1	TRUE	2	0.706275281927346	4		340	1222	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246816	10246817	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0008246-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	175	275	0	ENST00000340748.4:c.4588_4589delinsTT	p.Pro1530Phe	p.P1530F	ENST00000340748		1530	CCc/TTc	37/40	0.180124169612	2	FACETS	0.61	0.563	0.66	0.305	0.281	0.33	INDETERMINATE	1	TRUE	0	0.706275281927346	2		275	812	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	215	280	0				ENST00000310581	NM_198253.2	-/1132			0.429628002214646	4	FACETS	0.983	0.924	1	0.983	0.924	1	CLONAL	3	TRUE	1	0.429628002214646	4		280	485	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0008248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	231	476	1	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.402828521810548	1	FACETS	0.997	0.931	1	0.997	0.931	1	CLONAL	1	TRUE	0	0.429628002214646	1		477	847	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0008248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	220	424	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	0.421496363738665	2	FACETS	0.974	0.914	1	0.974	0.914	1	CLONAL	2	TRUE	0	0.429628002214646	2		424	526	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215646042	215646042	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs16852741	NA	P-0008248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	141	481	1	ENST00000260947.4:c.556A>G	p.Ser186Gly	p.S186G	ENST00000260947	NM_000465.2	186	Agt/Ggt	4/11	1	2	FACETS	0.78	0.711	0.853	0.78	0.711	0.853	SUBCLONAL	1	TRUE	1	0.429628002214646	2		482	841	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628521	187628521	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	328	594	0	ENST00000441802.2:c.2461G>T	p.Glu821Ter	p.E821*	ENST00000441802	NM_005245.3	821	Gag/Tag	2/27	NA	2	FACETS	0.761	0.72	0.803			1	INDETERMINATE	2	TRUE	NA	0.429628002214646	2		594	1003	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671702	30671702	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0008248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	133	479	0	ENST00000376406.3:c.5258C>G	p.Ser1753Ter	p.S1753*	ENST00000376406	NM_014641.2	1753	tCa/tGa	10/15	1	2	FACETS	0.791	0.719	0.867	0.791	0.719	0.867	SUBCLONAL	1	TRUE	1	0.429628002214646	2		479	783	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979549	7979549	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	188	508	0	ENST00000319144.4:c.1476C>A	p.Asp492Glu	p.D492E	ENST00000319144	NM_001139.2	492	gaC/gaA	11/15	0.402828521810548	1	FACETS	0.984	0.913	1	0.984	0.913	1	CLONAL	1	TRUE	0	0.429628002214646	1		508	698	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16040688	16040688	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	168	533	0	ENST00000268712.3:c.1446G>C	p.Lys482Asn	p.K482N	ENST00000268712	NM_006311.3	482	aaG/aaC	14/46	1	2	FACETS	0.802	0.737	0.87	0.802	0.737	0.87	CLONAL	1	TRUE	1	0.429628002214646	2		533	975	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022583	31022583	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	189	460	0	ENST00000375687.4:c.2068G>C	p.Asp690His	p.D690H	ENST00000375687	NM_015338.5	690	Gat/Cat	13/13	0.223561958275622	5	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.429628002214646	5		460	1185	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28913374	28913374	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	206	607	0	ENST00000282397.4:c.2419del	p.Asp807MetfsTer54	p.D807Mfs*54	ENST00000282397	NM_002019.4	807	Gat/at	17/30	1	2	FACETS	0.891	0.826	0.959	0.891	0.826	0.959	CLONAL	1	TRUE	1	0.429628002214646	2		607	1076	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397656	139397656	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	266	368	0	ENST00000277541.6:c.5145del	p.Tyr1716ThrfsTer82	p.Y1716Tfs*82	ENST00000277541	NM_017617.3	1715	ccC/cc	27/34	0.421496363738665	2	FACETS	0.972	0.918	1	0.972	0.918	1	CLONAL	2	TRUE	0	0.429628002214646	2		368	637	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	113	280	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.954	1			1	INDETERMINATE	1	TRUE	NA	0.81690365645129	2		280	261	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195628	123195631	+	frameshift_variant	Frame_Shift_Del	DEL	AGAT	AGAT	-	novel	NA	P-0008257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	183	141	0	ENST00000218089.9:c.1544_1547del	p.Asp515GlyfsTer6	p.D515Gfs*6	ENST00000218089	NM_001042749.1	514	acAGAT/ac	17/35	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.81690365645129	1		141	244	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692911	89692911	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	246	258	0	ENST00000371953.3:c.395G>C	p.Gly132Ala	p.G132A	ENST00000371953	NM_000314.4	132	gGt/gCt	5/9	0.81690365645129	1	FACETS	0.933	0.89	0.974	0.933	0.89	0.974	CLONAL	1	TRUE	0	0.81690365645129	1		258	382	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221830	55221830	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	14661	502	4	ENST00000275493.2:c.874G>T	p.Val292Leu	p.V292L	ENST00000275493	NM_005228.3	292	Gtg/Ttg	7/28	0.81690365645129	26	FACETS	0.993	0.99	0.996			1	CLONAL	25	TRUE	NA	0.81690365645129	26		506	15616	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946355	2946355	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372251654	NA	P-0008257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	242	395	0	ENST00000396946.4:c.3382G>A	p.Val1128Ile	p.V1128I	ENST00000396946	NM_032415.4	1128	Gta/Ata	25/25	0.326035979343214	3	FACETS	1	0.939	1			1	INDETERMINATE	1	TRUE	NA	0.81690365645129	3		395	832	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289908	15289908	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1257835251	NA	P-0008257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	203	358	1	ENST00000263388.2:c.3646G>A	p.Ala1216Thr	p.A1216T	ENST00000263388	NM_000435.2	1216	Gcg/Acg	22/33	0.81690365645129	3	FACETS	1	0.942	1	0.507	0.471	0.543	CLONAL	1	TRUE	1	0.81690365645129	3		359	691	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171666	36171666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758682659	NA	P-0008257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	214	264	0	ENST00000300305.3:c.899C>T	p.Thr300Met	p.T300M	ENST00000300305		300	aCg/aTg	7/8	0.81690365645129	3	FACETS	0.971	0.905	1	0.485	0.452	0.52	CLONAL	1	TRUE	1	0.81690365645129	3		264	760	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55248990	55248991	+	inframe_insertion	In_Frame_Ins	INS	-	-	CTACGTGATGGCCAGCGTGGA	novel	NA	P-0008257-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9127	550	286	0	ENST00000275493.2:c.2290_2310dup	p.Tyr764_Asp770dup	p.Y764_D770dup	ENST00000275493	NM_005228.3	764	gcc/gcCTACGTGATGGCCAGCGTGGAc	20/28	0.81690365645129	26	FACETS	0.752	0.715	0.789			1	SUBCLONAL	2	TRUE	NA	0.81690365645129	26		286	9677	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	54	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.51	0.436	0.591	0.51	0.436	0.591	SUBCLONAL	1	TRUE	1	0.436818528108076	2		280	485	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0008290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	299	500	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.436818528108076	2		500	1242	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651893	36651894	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0008290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	45	248	0	ENST00000244741.5:c.19dup	p.Asp7GlyfsTer29	p.D7Gfs*29	ENST00000244741	NM_000389.4	5	-/G	2/3	1	2	FACETS	0.284	0.238	0.335	0.284	0.238	0.335	SUBCLONAL	1	TRUE	1	0.436818528108076	2		248	726	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6414399	6414399	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	112	241	0	ENST00000356142.4:c.33C>A	p.Asp11Glu	p.D11E	ENST00000356142	NM_018890.3	11	gaC/gaA	1/7	0.436818528108076	3	FACETS	1	0.926	1	0.516	0.465	0.57	CLONAL	1	TRUE	1	0.436818528108076	3		241	605	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11552822	NA	P-0008290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	46	161	0	ENST00000304494.5:c.250G>T	p.Asp84Tyr	p.D84Y	ENST00000304494	NM_000077.4	84	Gac/Tac	2/3	1	2	FACETS	0.392	0.33	0.461	0.392	0.33	0.461	SUBCLONAL	1	TRUE	1	0.436818528108076	2		161	537	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927016	131927016	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1060501974	NA	P-0008290-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	44	463	0	ENST00000265335.6:c.1553T>A	p.Leu518Gln	p.L518Q	ENST00000265335		518	cTg/cAg	10/25	1	2	FACETS	0.232	0.194	0.275	0.232	0.194	0.275	SUBCLONAL	1	TRUE	1	0.436818528108076	2		463	867	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	103	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.848	0.762	0.938	0.848	0.762	0.938	CLONAL	1	TRUE	1	0.503130352894075	2		280	483	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589574	67589582	+	inframe_deletion	In_Frame_Del	DEL	GGAAAAAAT	GGAAAAAAT	-	novel	NA	P-0008306-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	145	399	1	ENST00000274335.5:c.1337_1345del	p.Gly446_Leu449delinsVal	p.G446_L449delinsV	ENST00000274335		446	gGGAAAAAATta/gta	10/15	1	2	FACETS	0.711	0.649	0.776	0.711	0.649	0.776	SUBCLONAL	1	TRUE	1	0.503130352894075	2		400	811	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	62	280	0				ENST00000310581	NM_198253.2	-/1132			0.430882508365569	3	FACETS	1	0.902	1	1	0.979	1	CLONAL	3	TRUE	1	0.430882508365569	3		280	116	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651906	36651906	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	67	389	0	ENST00000244741.5:c.28C>T	p.Gln10Ter	p.Q10*	ENST00000244741	NM_000389.4	10	Cag/Tag	2/3	0.220442260813538	6	FACETS	0.946	0.829	1	0.631	0.553	0.714	INDETERMINATE	2	TRUE	3	0.430882508365569	6		389	306	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039844	47039844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	10	264	0	ENST00000377604.3:c.1187G>A	p.Arg396His	p.R396H	ENST00000377604	NM_001204468.1	396	cGc/cAc	12/24	0.400655410709601	2	FACETS	0.24	0.163	0.338			1	SUBCLONAL	1	TRUE	NA	0.430882508365569	2		264	193	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936094	178936094	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913286	NA	P-0008311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	48	323	0	ENST00000263967.3:c.1636C>A	p.Gln546Lys	p.Q546K	ENST00000263967	NM_006218.2	546	Cag/Aag	10/21	0.144310424048077	6	FACETS	1	0.942	1	0.799	0.687	0.918	INDETERMINATE	2	TRUE	3	0.430882508365569	6		323	173	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089676	27089676	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	39	500	0	ENST00000324856.7:c.2632C>T	p.Gln878Ter	p.Q878*	ENST00000324856	NM_006015.4	878	Cag/Tag	8/20	0.149343249121748	3	FACETS	0.996	0.833	1	0.498	0.416	0.587	INDETERMINATE	1	TRUE	1	0.430882508365569	3		500	221	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164103	47164103	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	23	439	0	ENST00000409792.3:c.2023G>A	p.Gly675Arg	p.G675R	ENST00000409792	NM_014159.6	675	Gga/Aga	3/21	0.430882508365569	3	FACETS	0.519	0.406	0.649	0.26	0.203	0.325	SUBCLONAL	1	TRUE	1	0.430882508365569	3		439	250	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131944830	131944830	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	10	403	2	ENST00000265335.6:c.2851G>T	p.Val951Phe	p.V951F	ENST00000265335		951	Gtt/Ttt	18/25	0.149343249121748	3	FACETS	0.355	0.241	0.498	0.177	0.12	0.249	INDETERMINATE	1	TRUE	1	0.430882508365569	3		405	159	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406298	406298	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	52	650	0	ENST00000399788.2:c.4143C>G	p.Ile1381Met	p.I1381M	ENST00000399788	NM_001042603.1	1381	atC/atG	25/28	0.426038627911311	0	FACETS	0.704	0.609	0.806			1	SUBCLONAL	1	TRUE	0	0.430882508365569	0		650	195	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41011093	41011093	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	62	676	0	ENST00000267868.3:c.526G>C	p.Glu176Gln	p.E176Q	ENST00000267868	NM_002875.4	176	Gag/Cag	6/10	0.237397133983811	5	FACETS	0.79	0.688	0.899	0.526	0.458	0.599	INDETERMINATE	2	TRUE	2	0.430882508365569	5		676	300	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0008333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	95	464	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.813829476226817	2		464	188	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0008333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	176	511	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.246772520730021	4	FACETS	1	0.959	1	1	0.959	1	INDETERMINATE	2	TRUE	2	0.813829476226817	4		512	379	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794102	42794102	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	18	294	0	ENST00000575354.2:c.1463A>G	p.Lys488Arg	p.K488R	ENST00000575354	NM_015125.3	488	aAg/aGg	9/20	0.813829476226817	1	FACETS	0.243	0.185	0.309	0.243	0.185	0.309	SUBCLONAL	1	TRUE	0	0.813829476226817	1		294	108	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	92	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.944	0.848	1	0.944	0.848	1	CLONAL	1	TRUE	1	0.614978559118719	2		280	317	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0008380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	318	505	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.614978559118719	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.614978559118719	1		506	599	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720670	89720670	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs786204875	NA	P-0008380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	30	90	0	ENST00000371953.3:c.821G>A	p.Trp274Ter	p.W274*	ENST00000371953	NM_000314.4	274	tGg/tAg	8/9	0.614978559118719	1	FACETS	0.866	0.723	1	0.866	0.723	1	CLONAL	1	TRUE	0	0.614978559118719	1		90	78	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554008	63554008	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199798353	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	364	460	0	ENST00000307078.5:c.731C>T	p.Ser244Leu	p.S244L	ENST00000307078	NM_004655.3	244	tCg/tTg	2/11	0.29719298035217	2	FACETS	0.991	0.941	1	0.991	0.941	1	CLONAL	2	TRUE	0	0.33	2		460	1113	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	55	300	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.838	0.719	0.966	0.838	0.719	0.966	CLONAL	1	TRUE	1	0.33	2		300	398	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	325	550	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.29719298035217	2	FACETS	0.99	0.937	1	0.99	0.937	1	CLONAL	2	TRUE	0	0.33	2		550	995	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259389	89259389	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	221	639	1	ENST00000336596.2:c.533G>A	p.Gly178Glu	p.G178E	ENST00000336596	NM_005233.5	178	gGa/gAa	3/17	0.284401815971821	3	FACETS	1	0.991	1			1	CLONAL	1	TRUE	NA	0.33	3		640	1099	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258747	115258747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913237	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	120	382	0	ENST00000369535.4:c.35G>A	p.Gly12Asp	p.G12D	ENST00000369535	NM_002524.4	12	gGt/gAt	2/7	1	2	FACETS	0.959	0.867	1	0.959	0.867	1	CLONAL	1	TRUE	1	0.33	2		382	758	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	78	240	1	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	0.228888757438699	1	FACETS	0.556	0.488	0.629	0.556	0.488	0.629	SUBCLONAL	1	TRUE	0	0.33	1		241	710	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012474	29012474	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	131	340	1	ENST00000282397.4:c.397A>T	p.Arg133Ter	p.R133*	ENST00000282397	NM_002019.4	133	Aga/Tga	4/30	0.275836141533885	3	FACETS	0.914	0.834	0.997	0.914	0.834	0.997	CLONAL	2	TRUE	1	0.33	3		341	506	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149778	202149778	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242650624	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	117	506	0	ENST00000358485.4:c.1219C>T	p.Leu407Phe	p.L407F	ENST00000358485	NM_001080125.1	407	Ctt/Ttt	8/9	1	2	FACETS	0.833	0.751	0.92	0.833	0.751	0.92	CLONAL	1	TRUE	1	0.33	2		506	851	SUCCESS
APC	324	MSKCC	GRCh37	5	112116491	112116491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	88	266	0	ENST00000257430.4:c.536C>T	p.Ser179Phe	p.S179F	ENST00000257430	NM_000038.5	179	tCc/tTc	6/16	1	2	FACETS	0.961	0.853	1	0.961	0.853	1	CLONAL	1	TRUE	1	0.33	2		266	555	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272521	11272521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	107	322	0	ENST00000361445.4:c.3409G>A	p.Glu1137Lys	p.E1137K	ENST00000361445	NM_004958.3	1137	Gag/Aag	23/58	1	2	FACETS	0.886	0.795	0.982	0.886	0.795	0.982	CLONAL	1	TRUE	1	0.33	2		322	732	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432421	78432421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	122	533	0	ENST00000370768.2:c.430C>T	p.Pro144Ser	p.P144S	ENST00000370768	NM_003902.3	144	Cca/Tca	7/20	1	2	FACETS	0.867	0.783	0.955	0.867	0.783	0.955	CLONAL	1	TRUE	1	0.33	2		533	853	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243708900	243708900	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs12083401	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	58	370	0	ENST00000263826.5:c.1164-1G>A		p.X388_splice	ENST00000263826	NM_005465.4	388			1	2	FACETS	0.62	0.533	0.715	0.62	0.533	0.715	SUBCLONAL	1	TRUE	1	0.33	2		370	567	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151208	202151208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	120	485	0	ENST00000358485.4:c.1508C>T	p.Thr503Ile	p.T503I	ENST00000358485	NM_001080125.1	503	aCt/aTt	9/9	1	2	FACETS	0.864	0.78	0.953	0.864	0.78	0.953	CLONAL	1	TRUE	1	0.33	2		485	842	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259488	89259488	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	169	469	0	ENST00000336596.2:c.632T>A	p.Met211Lys	p.M211K	ENST00000336596	NM_005233.5	211	aTg/aAg	3/17	0.284401815971821	3	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.33	3		469	854	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808989	1808989	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	rs121913103	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	50	206	0	ENST00000260795.2:c.2421A>G	p.Ter807TrpextTer101	p.*807Wext*101	ENST00000260795		807	tgA/tgG	17/17	1	2	FACETS	0.739	0.628	0.86	0.739	0.628	0.86	SUBCLONAL	1	TRUE	1	0.33	2		206	410	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213822	66213822	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	111	625	0	ENST00000273854.3:c.2608G>A	p.Glu870Lys	p.E870K	ENST00000273854	NM_004439.5	870	Gaa/Aaa	15/18	1	2	FACETS	0.876	0.788	0.97	0.876	0.788	0.97	CLONAL	1	TRUE	1	0.33	2		625	768	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964429	93964429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	123	602	0	ENST00000369303.4:c.2468G>A	p.Gly823Glu	p.G823E	ENST00000369303	NM_004440.3	823	gGa/gAa	14/17	1	2	FACETS	0.782	0.706	0.862	0.782	0.706	0.862	SUBCLONAL	1	TRUE	1	0.33	2		602	953	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81358987	81358987	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381615839	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	111	537	1	ENST00000222390.5:c.974C>T	p.Pro325Leu	p.P325L	ENST00000222390	NM_000601.4	325	cCa/cTa	8/18	1	2	FACETS	0.93	0.837	1	0.93	0.837	1	CLONAL	1	TRUE	1	0.33	2		538	723	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508316	106508316	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	48	133	0	ENST00000359195.3:c.310G>A	p.Gly104Arg	p.G104R	ENST00000359195	NM_002649.2	104	Ggg/Agg	2/11	1	2	FACETS	0.924	0.785	1	0.924	0.785	1	CLONAL	1	TRUE	1	0.33	2		133	315	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545750	106545750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	114	503	0	ENST00000359195.3:c.3227G>A	p.Arg1076Lys	p.R1076K	ENST00000359195	NM_002649.2	1076	aGa/aAa	11/11	1	2	FACETS	0.897	0.808	0.992	0.897	0.808	0.992	CLONAL	1	TRUE	1	0.33	2		503	770	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846173	128846173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	178	516	0	ENST00000249373.3:c.1103C>T	p.Pro368Leu	p.P368L	ENST00000249373	NM_005631.4	368	cCc/cTc	5/12	1	2	FACETS	0.863	0.794	0.936	0.863	0.794	0.936	CLONAL	1	TRUE	1	0.33	2		516	1250	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151855959	151855959	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	123	455	0	ENST00000262189.6:c.11659C>T	p.His3887Tyr	p.H3887Y	ENST00000262189	NM_170606.2	3887	Cac/Tac	44/59	1	2	FACETS	0.867	0.783	0.955	0.867	0.783	0.955	CLONAL	1	TRUE	1	0.33	2		455	860	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341168	8341168	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	265	541	0	ENST00000356435.5:c.5048C>T	p.Ser1683Phe	p.S1683F	ENST00000356435		1683	tCc/tTc	30/35	0.300313460167867	4	FACETS	0.848	0.797	0.899	0.848	0.797	0.899	CLONAL	3	TRUE	1	0.33	4		541	840	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504347	8504347	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	77	409	0	ENST00000356435.5:c.1736G>A	p.Ser579Asn	p.S579N	ENST00000356435		579	aGc/aAc	12/35	0.300313460167867	4	FACETS	0.782	0.685	0.886	0.261	0.228	0.296	SUBCLONAL	1	TRUE	1	0.33	4		409	794	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518130	8518130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	276	362	1	ENST00000356435.5:c.1261C>T	p.Pro421Ser	p.P421S	ENST00000356435		421	Ccg/Tcg	10/35	0.300313460167867	4	FACETS	1	0.99	1	0.831	0.782	0.881	CLONAL	2	TRUE	1	0.33	4		363	892	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908883	101908883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1256701693	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	293	429	0	ENST00000374994.4:c.1247C>T	p.Ser416Phe	p.S416F	ENST00000374994	NM_004612.2	416	tCc/tTc	7/9	0.300313460167867	4	FACETS	0.846	0.797	0.895	0.846	0.797	0.895	CLONAL	3	TRUE	1	0.33	4		429	931	SUCCESS
RET	5979	MSKCC	GRCh37	10	43607664	43607664	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	105	406	0	ENST00000355710.3:c.1640A>G	p.Asp547Gly	p.D547G	ENST00000355710	NM_020975.4	547	gAt/gGt	8/20	1	2	FACETS	0.798	0.715	0.887	0.798	0.715	0.887	SUBCLONAL	1	TRUE	1	0.33	2		406	797	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243279	123243279	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	136	523	1	ENST00000358487.5:c.2234C>T	p.Ser745Phe	p.S745F	ENST00000358487	NM_000141.4	745	tCc/tTc	17/18	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.33	2		524	813	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118359373	118359373	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	119	444	0	ENST00000534358.1:c.4377T>G	p.Cys1459Trp	p.C1459W	ENST00000534358	NM_005933.3	1459	tgT/tgG	11/36	0.228888757438699	1	FACETS	0.736	0.664	0.812	0.736	0.664	0.812	SUBCLONAL	1	TRUE	0	0.33	1		444	818	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1036339	1036339	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	210	493	2	ENST00000358495.3:c.439G>A	p.Val147Met	p.V147M	ENST00000358495	NM_134424.2	147	Gtg/Atg	6/12	1	2	FACETS	0.978	0.906	1	0.978	0.906	1	CLONAL	1	TRUE	1	0.33	2		495	1301	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906615	32906615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	88	455	1	ENST00000380152.3:c.1000C>T	p.His334Tyr	p.H334Y	ENST00000380152		334	Cat/Tat	10/27	0.275836141533885	3	FACETS	0.84	0.744	0.942	0.42	0.372	0.471	CLONAL	1	TRUE	1	0.33	3		456	740	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515276	103515276	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	78	430	1	ENST00000355739.4:c.1777C>T	p.Pro593Ser	p.P593S	ENST00000355739	NM_000123.3	593	Cct/Tct	8/15	0.275836141533885	3	FACETS	0.697	0.612	0.789	0.349	0.306	0.395	SUBCLONAL	1	TRUE	1	0.33	3		431	790	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058340	42058340	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	72	693	0	ENST00000219905.7:c.8060C>T	p.Thr2687Ile	p.T2687I	ENST00000219905	NM_001164273.1	2687	aCc/aTc	24/24	0.228888757438699	1	FACETS	0.382	0.333	0.436	0.382	0.333	0.436	SUBCLONAL	1	TRUE	0	0.33	1		693	953	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819709	81819709	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1201	245	644	4	ENST00000359376.3:c.115G>T	p.Glu39Ter	p.E39*	ENST00000359376	NM_002661.3	39	Gag/Tag	2/33	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.33	2		648	1446	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512473	38512473	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	256	338	0	ENST00000254066.5:c.1384C>T	p.Pro462Ser	p.P462S	ENST00000254066	NM_000964.3	462	Ccg/Tcg	9/9	0.29719298035217	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.33	2		338	708	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980867	40980867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	190	422	0	ENST00000373198.4:c.1619G>A	p.Gly540Glu	p.G540E	ENST00000373198	NM_133170.3	540	gGg/gAg	10/32	0.226400585490125	2	FACETS	0.856	0.794	0.919	0.856	0.794	0.919	CLONAL	2	TRUE	0	0.33	2		422	673	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980879	40980879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs192708116	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	201	387	1	ENST00000373198.4:c.1607C>T	p.Ser536Leu	p.S536L	ENST00000373198	NM_133170.3	536	tCg/tTg	10/32	0.226400585490125	2	FACETS	0.894	0.832	0.958	0.894	0.832	0.958	CLONAL	2	TRUE	0	0.33	2		388	681	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262806	46262806	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780175917	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	257	714	1	ENST00000371998.3:c.979C>T	p.His327Tyr	p.H327Y	ENST00000371998		327	Cat/Tat	10/23	0.226400585490125	2	FACETS	1	0.993	1	0.735	0.688	0.783	CLONAL	1	TRUE	0	0.33	2		715	1060	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45651307	45651307	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	163	633	0	ENST00000407780.3:c.718G>A	p.Asp240Asn	p.D240N	ENST00000407780	NM_001283052.1	240	Gac/Aac	5/7	1	2	FACETS	0.754	0.69	0.821	0.754	0.69	0.821	SUBCLONAL	1	TRUE	1	0.33	2		633	1311	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413049	139413050	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	457	395	1	ENST00000277541.6:c.1092_1093delinsTT	p.Arg365Cys	p.R365C	ENST00000277541	NM_017617.3	364	ggCCgc/ggTTgc	6/34	0.300313460167867	4	FACETS	0.934	0.896	0.972	0.934	0.896	0.972	CLONAL	4	TRUE	0	0.33	4		396	986	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376145	118376147	+	missense_variant	Missense_Mutation	TNP	ATC	ATC	TTT	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	51	351	0	ENST00000534358.1:c.9538_9540delinsTTT	p.Ile3180Phe	p.I3180F	ENST00000534358	NM_005933.3	3180	ATC/TTT	27/36	0.228888757438699	1	FACETS	0.365	0.309	0.426	0.365	0.309	0.426	SUBCLONAL	1	TRUE	0	0.33	1		351	708	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230693	+	frameshift_variant	Frame_Shift_Del	DEL	CGT	CGT	TG	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	119	618	0	ENST00000334344.6:c.940_942delinsTG	p.Arg314CysfsTer14	p.R314Cfs*14	ENST00000334344	NM_152641.2	314	CGT/TG	8/21	1	2	FACETS	0.786	0.709	0.868	0.786	0.709	0.868	SUBCLONAL	1	TRUE	1	0.33	2		618	917	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562742	29562743	+	missense_variant	Missense_Mutation	DNP	CT	CT	TA	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	183	486	1	ENST00000356175.3:c.3822_3823delinsTA	p.Phe1275Ile	p.F1275I	ENST00000356175	NM_000267.3	1274	ctCTtc/ctTAtc	28/57	0.29719298035217	2	FACETS	0.886	0.821	0.952	0.886	0.821	0.952	CLONAL	2	TRUE	0	0.33	2		487	626	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554001	63554002	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	319	459	0	ENST00000307078.5:c.737_738delinsTT	p.Thr246Ile	p.T246I	ENST00000307078	NM_004655.3	246	aCC/aTT	2/11	0.29719298035217	2	FACETS	0.903	0.854	0.954	0.903	0.854	0.954	CLONAL	2	TRUE	0	0.33	2		459	1070	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220608	1220609	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0008401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	147	478	0	ENST00000326873.7:c.626_627delinsTT	p.Thr209Ile	p.T209I	ENST00000326873	NM_000455.4	209	aCC/aTT	5/10	1	2	FACETS	0.998	0.911	1	0.998	0.911	1	CLONAL	1	TRUE	1	0.33	2		478	893	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	207	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.8123784254346	2		280	485	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0008402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	204	511	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.8123784254346	2		512	465	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413070	139413072	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0008402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	76	555	0	ENST00000277541.6:c.1070_1072del	p.Phe357del	p.F357del	ENST00000277541	NM_017617.3	357	tTCTac/tac	6/34	1	2	FACETS	0.186	0.162	0.212	0.186	0.162	0.212	SUBCLONAL	1	FALSE	1	0.8123784254346	2		555	1006	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430654	78430654	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0008402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	200	374	0	ENST00000370768.2:c.637-1G>A		p.X213_splice	ENST00000370768	NM_003902.3	213			0.8123784254346	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	0	0.8123784254346	1		374	276	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295195	1295195	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0008402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	175	210	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	FALSE	1	0.8123784254346	2		210	416	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27022917	27022939	+	frameshift_variant	Frame_Shift_Del	DEL	CCGCCGCCAGCAGCCTGGGCAAC	CCGCCGCCAGCAGCCTGGGCAAC	-	novel	NA	P-0008402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	24	88	0	ENST00000324856.7:c.31_53del	p.Ser11AlafsTer92	p.S11Afs*92	ENST00000324856	NM_006015.4	8	gCCGCCGCCAGCAGCCTGGGCAAC/g	1/20	0.8123784254346	1	FACETS	0.308	0.245	0.377	0.308	0.245	0.377	SUBCLONAL	1	FALSE	0	0.8123784254346	1		88	114	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023958	27023959	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0008402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	29	170	0	ENST00000324856.7:c.1065_1066del	p.Arg356GlufsTer43	p.R356Efs*43	ENST00000324856	NM_006015.4	355	cAA/c	1/20	0.8123784254346	1	FACETS	0.174	0.14	0.212	0.174	0.14	0.212	SUBCLONAL	1	FALSE	0	0.8123784254346	1		170	244	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798165	42798169	+	frameshift_variant	Frame_Shift_Del	DEL	CCCCA	CCCCA	-	novel	NA	P-0008402-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	491	472	0	ENST00000575354.2:c.4122_4126del	p.Thr1375AlafsTer64	p.T1375Afs*64	ENST00000575354	NM_015125.3	1373	tcCCCCAcc/tccc	17/20	0.8123784254346	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	FALSE	0	0.8123784254346	1		472	656	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0008417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	35	616	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.992	0.812	1	0.992	0.812	1	CLONAL	1	TRUE	1	0.13	2		616	543	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27097632	27097632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	29	498	0	ENST00000324856.7:c.3221G>A	p.Arg1074Gln	p.R1074Q	ENST00000324856	NM_006015.4	1074	cGg/cAg	12/20	1	2	FACETS	0.779	0.623	0.956	0.779	0.623	0.956	CLONAL	1	TRUE	1	0.13	2		498	573	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522062	157522062	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	21	383	0	ENST00000346085.5:c.4334C>A	p.Pro1445His	p.P1445H	ENST00000346085	NM_020732.3	1445	cCt/cAt	18/20	0.3	2	FACETS	0.985	0.758	1			1	CLONAL	1	TRUE	NA	0.13	2		383	328	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135779085	135779085	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763357144	NA	P-0008417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	22	359	0	ENST00000298552.3:c.2161C>T	p.Arg721Cys	p.R721C	ENST00000298552	NM_001162426.1	721	Cgc/Tgc	17/23	1	2	FACETS	0.94	0.728	1	0.94	0.728	1	CLONAL	1	TRUE	1	0.13	2		359	360	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437625	110437625	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	23	311	0	ENST00000375856.3:c.776T>C	p.Val259Ala	p.V259A	ENST00000375856	NM_003749.2	259	gTg/gCg	1/2	0.3	2	FACETS	1	0.886	1			1	CLONAL	1	TRUE	NA	0.13	2		311	287	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33430520	33430520	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370228071	NA	P-0008417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	29	637	1	ENST00000345365.6:c.620C>T	p.Ser207Leu	p.S207L	ENST00000345365	NM_002878.3	207	tCg/tTg	7/10	1	2	FACETS	0.996	0.799	1	0.996	0.799	1	CLONAL	1	TRUE	1	0.13	2		638	448	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119852	70119852	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	21	428	0	ENST00000245479.2:c.854A>G	p.Asn285Ser	p.N285S	ENST00000245479	NM_000346.3	285	aAc/aGc	3/3	0.176049193964322	3	FACETS	0.852	0.655	1	0.426	0.327	0.541	CLONAL	1	TRUE	1	0.13	3		428	404	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794871	42794872	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	21	289	0	ENST00000575354.2:c.1951_1952insT	p.Pro651LeufsTer39	p.P651Lfs*39	ENST00000575354	NM_015125.3	651	ccc/cTcc	10/20	0.135821604426614	1	FACETS	1	0.8	1	1	0.8	1	CLONAL	1	TRUE	0	0.13	1		289	290	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004238	150004239	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	22	554	0	ENST00000253339.5:c.1986dup	p.Gln663ThrfsTer5	p.Q663Tfs*5	ENST00000253339		662	-/A	3/7	0.3	2	FACETS	0.81	0.626	1			1	CLONAL	1	TRUE	NA	0.13	2		554	418	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36206896	36206910	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTCCTATTGTGGGGA	GTCCTATTGTGGGGA	-	novel	NA	P-0008417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	20	232	0	ENST00000300305.3:c.614-12_616del		p.X205_splice	ENST00000300305		205		6/8	1	2	FACETS	1	0.795	1	1	0.795	1	CLONAL	1	TRUE	1	0.13	2		232	295	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0008433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	69	506	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.363294729478671	4	FACETS	1	0.939	1			1	CLONAL	3	TRUE	NA	0.523132497948491	4		506	127	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863224683	NA	P-0008433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	46	577	0	ENST00000269305.4:c.388C>T	p.Leu130Phe	p.L130F	ENST00000269305	NM_001126112.2	130	Ctc/Ttc	5/11	0.318032508547078	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.523132497948491	1		577	109	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10270693	10270693	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0008433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	56	487	1	ENST00000340748.4:c.1041+1G>T		p.X347_splice	ENST00000340748		347			0.467415941480286	3	FACETS	1	0.944	1	0.587	0.509	0.67	CLONAL	1	TRUE	1	0.523132497948491	3		488	230	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914933	32914934	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs80359589	NA	P-0008433-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	104	660	0	ENST00000380152.3:c.6443_6444del	p.Ser2148TyrfsTer2	p.S2148Yfs*2	ENST00000380152		2147	caCTct/cact	11/27	NA	2	FACETS	0.889	0.831	0.945			1	INDETERMINATE	3	TRUE	NA	0.523132497948491	2		660	149	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0008439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	33	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.2	2		464	278	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0008439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	61	463	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.302033779041827	3	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	1	0.2	3		463	305	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532627	63532627	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs74006838	NA	P-0008439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	65	341	1	ENST00000307078.5:c.1952C>T	p.Ser651Leu	p.S651L	ENST00000307078	NM_004655.3	651	tCg/tTg	8/11	1	2	FACETS	0.934	0.815	1	1	0.979	1	CLONAL	2	TRUE	1	0.2	2		342	348	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782705	NA	P-0008439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	58	494	0	ENST00000269305.4:c.455C>T	p.Pro152Leu	p.P152L	ENST00000269305	NM_001126112.2	152	cCg/cTg	5/11	0.301953346944003	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.2	1		494	392	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719635	190719635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs531239757	NA	P-0008439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	19	426	0	ENST00000441310.2:c.1637G>A	p.Cys546Tyr	p.C546Y	ENST00000441310	NM_000534.4	546	tGt/tAt	9/13	1	2	FACETS	1	0.859	1	1	0.859	1	CLONAL	1	TRUE	1	0.2	2		426	160	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663157	227663157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs570775459	NA	P-0008439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	76	530	0	ENST00000305123.5:c.298G>A	p.Glu100Lys	p.E100K	ENST00000305123	NM_005544.2	100	Gag/Aag	1/2	1	2	FACETS	0.797	0.701	0.899	1	0.978	1	SUBCLONAL	2	TRUE	1	0.2	2		530	477	SUCCESS
APC	324	MSKCC	GRCh37	5	112111384	112111384	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658325	NA	P-0008439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	20	510	1	ENST00000257430.4:c.481C>T	p.Gln161Ter	p.Q161*	ENST00000257430	NM_000038.5	161	Caa/Taa	5/16	0.301953346944003	1	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	0	0.2	1		511	136	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637822	176637822	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	49	590	1	ENST00000439151.2:c.2422G>A	p.Glu808Lys	p.E808K	ENST00000439151	NM_022455.4	808	Gag/Aag	5/23	1	2	FACETS	0.803	0.684	0.933	1	0.967	1	CLONAL	2	TRUE	1	0.2	2		591	305	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913197	32913197	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	59	858	0	ENST00000380152.3:c.4705T>A	p.Tyr1569Asn	p.Y1569N	ENST00000380152		1569	Tac/Aac	11/27	0.199426869046327	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.2	1		858	389	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346892	89346892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755603365	NA	P-0008439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	48	363	0	ENST00000301030.4:c.6058G>A	p.Ala2020Thr	p.A2020T	ENST00000301030	NM_001256183.1	2020	Gcc/Acc	9/13	1	2	FACETS	0.851	0.724	0.989	1	0.969	1	CLONAL	2	TRUE	1	0.2	2		363	282	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30057288	30057288	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	68	500	0	ENST00000338641.4:c.770C>A	p.Pro257Gln	p.P257Q	ENST00000338641	NM_000268.3	257	cCg/cAg	8/16	1	2	FACETS	0.892	0.78	1	1	0.979	1	CLONAL	2	TRUE	1	0.2	2		500	381	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060409	38061028	+	stop_lost,3_prime_UTR_variant	Nonstop_Mutation	DEL	TTGCACTGGGGGAAAGGTTGTGCATGAAAAATGAAATAAAAATAGTTGTTGGGATTTTATTATGCTGTTGACGGTTTGGTTTGTGTGGTTTTGTTTGCTGTTGATTTTTTCTCTCTTGCTACCAGCATGGCTATGCCAGACAAACCCCCCAGTCCCGGGAGCTAGGAAGTGTTTAGGACGGGTCTGGAATACACACCTTGGTAGTACGCCGGCTCCAGGGCTGAGGGCTCGATGGGGCTCCTGGTGGTCACCGAGGCGCTGCCTAGAGGCAGGCTGGCGGGCAACGTAGAGCCGTAAGGCGAGTATTGCAGTGCCTGTTCGTATGCCTTGAAGTCCAGCTTATGCTGCTGCTCCGAGGAGGACATGAGGTTGTTGATGGAGAACGGGTGGTTGAAGGAGTAGTGGGGGTCCCCTTTCAGGTGCAGCTGGGACTCGTGGGGTGCCAAGCCGTGTGCCGGGTGAGAGGCGGGCACAGAGGCCAGCGCCCCGGGCCCGGAGCTTATGGGGGGCGCAGTTGAGGAGGCTGGAGTCTTCAACTCCGAGGCGCCCCCTGTCGCCGTCGCCCCACTGTGGTCCAGAGTCTGGGGGCTGGCGGCGGGCCCGGGGGCCGGCGCGCCCTC	TTGCACTGGGGGAAAGGTTGTGCATGAAAAATGAAATAAAAATAGTTGTTGGGATTTTATTATGCTGTTGACGGTTTGGTTTGTGTGGTTTTGTTTGCTGTTGATTTTTTCTCTCTTGCTACCAGCATGGCTATGCCAGACAAACCCCCCAGTCCCGGGAGCTAGGAAGTGTTTAGGACGGGTCTGGAATACACACCTTGGTAGTACGCCGGCTCCAGGGCTGAGGGCTCGATGGGGCTCCTGGTGGTCACCGAGGCGCTGCCTAGAGGCAGGCTGGCGGGCAACGTAGAGCCGTAAGGCGAGTATTGCAGTGCCTGTTCGTATGCCTTGAAGTCCAGCTTATGCTGCTGCTCCGAGGAGGACATGAGGTTGTTGATGGAGAACGGGTGGTTGAAGGAGTAGTGGGGGTCCCCTTTCAGGTGCAGCTGGGACTCGTGGGGTGCCAAGCCGTGTGCCGGGTGAGAGGCGGGCACAGAGGCCAGCGCCCCGGGCCCGGAGCTTATGGGGGGCGCAGTTGAGGAGGCTGGAGTCTTCAACTCCGAGGCGCCCCCTGTCGCCGTCGCCCCACTGTGGTCCAGAGTCTGGGGGCTGGCGGCGGGCCCGGGGGCCGGCGCGCCCTC	-	novel	NA	P-0008439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	19	59	0	ENST00000250448.2:c.961_*161del		p.*321*	ENST00000250448	NM_004496.3	321		2/2	1	2	FACETS	1	0.87	1	1	0.955	1	CLONAL	3	TRUE	1	0.2	2		59	55	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694589	176694593	+	frameshift_variant	Frame_Shift_Del	DEL	TGCCC	TGCCC	-	novel	NA	P-0008439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	36	553	0	ENST00000439151.2:c.5176_5180del	p.Pro1726CysfsTer5	p.P1726Cfs*5	ENST00000439151	NM_022455.4	1725	TGCCCt/t	15/23	1	2	FACETS	0.928	0.764	1	0.928	0.764	1	CLONAL	1	TRUE	1	0.2	2		553	388	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023270	27023274	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGG	GGCGG	-	novel	NA	P-0008439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	53	290	0	ENST00000324856.7:c.376_380del	p.Gly126GlnfsTer272	p.G126Qfs*272	ENST00000324856	NM_006015.4	126	GGCGGc/c	1/20	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.2	2		290	376	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244510	41244511	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs397507208	NA	P-0008439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	27	646	0	ENST00000357654.3:c.3037_3038del	p.Glu1013AsnfsTer4	p.E1013Nfs*4	ENST00000357654	NM_007294.3	1013	GAa/a	10/23	0.302033779041827	1	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	0	0.2	1		646	216	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441312	52441328	+	frameshift_variant	Frame_Shift_Del	DEL	GGGAGGTGGCGTGGCTC	GGGAGGTGGCGTGGCTC	-	novel	NA	P-0008439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	74	549	0	ENST00000460680.1:c.442_458del	p.Glu148Ter	p.E148*	ENST00000460680	NM_004656.3	148	GAGCCACGCCACCTCCCt/t	7/17	0.234599369215526	3	FACETS	1	0.968	1	0.667	0.584	0.756	CLONAL	1	TRUE	1	0.2	3		549	610	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440884	52440885	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0008439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	129	529	0	ENST00000460680.1:c.619dup	p.Arg207ProfsTer36	p.R207Pfs*36	ENST00000460680	NM_004656.3	207	cgg/cCgg	8/17	0.234599369215526	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.2	3		529	576	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256687	19256688	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0008439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	65	518	0	ENST00000162023.5:c.1025dup	p.Leu343ProfsTer?	p.L343Pfs*?	ENST00000162023		342	ctc/ctTc	13/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.2	2		518	469	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696608	176696619	+	frameshift_variant	Frame_Shift_Del	DEL	GGCCAGCTGAGA	GGCCAGCTGAGA	C	novel	NA	P-0008439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	35	411	0	ENST00000439151.2:c.5309_5320delinsC	p.Trp1770SerfsTer12	p.W1770Sfs*12	ENST00000439151	NM_022455.4	1770	tGGCCAGCTGAGAtc/tCtc	16/23	1	2	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	1	0.2	2		411	338	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867570	45867571	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0008439-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	55	469	0	ENST00000391945.4:c.737_738delinsTT	p.Ser246Phe	p.S246F	ENST00000391945	NM_000400.3	246	tCC/tTT	9/23	0.232034698035908	3	FACETS	1	0.958	1	0.674	0.577	0.779	CLONAL	1	TRUE	1	0.2	3		469	449	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008457-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	132	280	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.996	0.914	1			1	INDETERMINATE	1	TRUE	NA	0.664095390784169	2		280	399	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72897419	72897419	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs758930353	NA	P-0008457-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	310	447	0	ENST00000325599.8:c.73C>G	p.Arg25Gly	p.R25G	ENST00000325599	NM_018130.2	25	Cgg/Ggg	1/11	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.664095390784169	2		447	932	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1406	444	524	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.35659370557169	7	FACETS	0.849	0.807	0.891	0.424	0.403	0.446	CLONAL	3	FALSE	1	0.35659370557169	7		524	1850	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498375	89498375	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	193	305	0	ENST00000336596.2:c.2347G>A	p.Gly783Arg	p.G783R	ENST00000336596	NM_005233.5	783	Gga/Aga	14/17	1	2	FACETS	1	0.982	1	1	0.994	1	CLONAL	2	FALSE	1	0.35659370557169	2		305	474	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346771	89346771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	300	368	0	ENST00000301030.4:c.6179C>T	p.Ser2060Phe	p.S2060F	ENST00000301030	NM_001256183.1	2060	tCc/tTc	9/13	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	2	FALSE	NA	0.35659370557169	2		368	707	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258251	16258251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1428730712	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	739	409	0	ENST00000375759.3:c.5516C>T	p.Pro1839Leu	p.P1839L	ENST00000375759	NM_015001.2	1839	cCc/cTc	11/15	0.35659370557169	7	FACETS	0.946	0.915	0.977	1	0.996	1	CLONAL	5	FALSE	3	0.35659370557169	7		409	1658	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101387	27101387	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	655	358	0	ENST00000324856.7:c.4669C>T	p.Pro1557Ser	p.P1557S	ENST00000324856	NM_006015.4	1557	Ccc/Tcc	18/20	0.35659370557169	7	FACETS	1	0.967	1	1	0.996	1	CLONAL	5	FALSE	3	0.35659370557169	7		358	1388	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206941988	206941988	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376415487	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	189	341	0	ENST00000423557.1:c.530G>A	p.Arg177Gln	p.R177Q	ENST00000423557	NM_000572.2	177	cGa/cAa	5/5	0.35659370557169	4	FACETS	0.982	0.91	1	0.655	0.607	0.704	CLONAL	2	FALSE	1	0.35659370557169	4		341	732	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47607086	47607086	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	828	479	0	ENST00000263735.4:c.836T>C	p.Val279Ala	p.V279A	ENST00000263735	NM_002354.2	279	gTt/gCt	7/9	0.35659370557169	4	FACETS	1	0.996	1	1	0.998	1	CLONAL	4	FALSE	1	0.35659370557169	4		479	1401	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61717817	61717818	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	822	471	0	ENST00000401558.2:c.1981_1982delinsTT	p.Pro661Phe	p.P661F	ENST00000401558	NM_003400.3	661	CCt/TTt	17/25	0.35659370557169	4	FACETS	1	0.993	1	1	0.998	1	CLONAL	4	FALSE	1	0.35659370557169	4		471	1478	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637656	52637656	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	474	485	0	ENST00000394830.3:c.2660T>C	p.Leu887Pro	p.L887P	ENST00000394830	NM_018313.4	887	cTt/cCt	18/30	0.35323172240403	3	FACETS	0.96	0.92	0.999			1	CLONAL	3	FALSE	NA	0.35659370557169	3		485	1088	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390946	89390946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	236	414	0	ENST00000336596.2:c.1012G>A	p.Glu338Lys	p.E338K	ENST00000336596	NM_005233.5	338	Gag/Aag	5/17	1	2	FACETS	1	0.966	1	1	0.995	1	CLONAL	2	FALSE	1	0.35659370557169	2		414	635	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295229	1295229	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	164	190	0				ENST00000310581	NM_198253.2	-/1132			0.35659370557169	9	FACETS	0.951	0.875	1			1	CLONAL	3	FALSE	NA	0.35659370557169	9		190	725	SUCCESS
APC	324	MSKCC	GRCh37	5	112178217	112178217	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060503329	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	402	471	0	ENST00000257430.4:c.6926C>T	p.Pro2309Leu	p.P2309L	ENST00000257430	NM_000038.5	2309	cCt/cTt	16/16	0.35659370557169	1	FACETS	1	0.994	1	1	0.997	1	CLONAL	2	FALSE	0	0.35659370557169	1		471	755	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131927030	131927030	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	236	559	0	ENST00000265335.6:c.1567C>T	p.Gln523Ter	p.Q523*	ENST00000265335		523	Cag/Tag	10/25	0.35659370557169	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	0	0.35659370557169	1		559	957	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512446	149512446	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1291265658	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	118	310	0	ENST00000261799.4:c.994C>T	p.Arg332Trp	p.R332W	ENST00000261799	NM_002609.3	332	Cgg/Tgg	7/23	0.35659370557169	0	FACETS	1	0.949	1			1	CLONAL	1	FALSE	0	0.35659370557169	0		310	401	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672359	30672359	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	428	399	0	ENST00000376406.3:c.4601C>T	p.Ala1534Val	p.A1534V	ENST00000376406	NM_014641.2	1534	gCc/gTc	10/15	0.304686171355504	4	FACETS	1	0.981	1			1	CLONAL	3	FALSE	NA	0.35659370557169	4		399	1037	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163552	32163552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1428549201	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	231	277	0	ENST00000375023.3:c.5674G>A	p.Gly1892Arg	p.G1892R	ENST00000375023	NM_004557.3	1892	Ggg/Agg	30/30	0.144973404749714	0	FACETS	0.763	0.718	0.809			1	INDETERMINATE	2	FALSE	0	0.35659370557169	0		277	546	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117639351	117639351	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	219	444	0	ENST00000368508.3:c.6005G>A	p.Ser2002Asn	p.S2002N	ENST00000368508	NM_002944.2	2002	aGc/aAc	37/43	0.288529820763116	0	FACETS	0.743	0.697	0.789			1	SUBCLONAL	2	FALSE	0	0.35659370557169	0		444	532	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658353	117658353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	260	573	0	ENST00000368508.3:c.5230G>A	p.Glu1744Lys	p.E1744K	ENST00000368508	NM_002944.2	1744	Gaa/Aaa	31/43	0.288529820763116	0	FACETS	0.671	0.632	0.711			1	SUBCLONAL	2	FALSE	0	0.35659370557169	0		573	699	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527955	157527955	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774509236	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	247	210	0	ENST00000346085.5:c.5680C>T	p.Pro1894Ser	p.P1894S	ENST00000346085	NM_020732.3	1894	Cct/Tct	20/20	0.35323172240403	3	FACETS	0.886	0.835	0.938			1	CLONAL	3	FALSE	NA	0.35659370557169	3		210	614	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332024	81332024	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	379	485	0	ENST00000222390.5:c.2060T>C	p.Val687Ala	p.V687A	ENST00000222390	NM_000601.4	687	gTt/gCt	18/18	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	FALSE	1	0.35659370557169	2		485	897	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81386620	81386620	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	181	270	1	ENST00000222390.5:c.368-1G>A		p.X123_splice	ENST00000222390	NM_000601.4	123			1	2	FACETS	1	0.966	1	1	0.994	1	CLONAL	2	FALSE	1	0.35659370557169	2		271	478	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508281	106508281	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778832310	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	71	130	0	ENST00000359195.3:c.275G>A	p.Gly92Glu	p.G92E	ENST00000359195	NM_002649.2	92	gGa/gAa	2/11	1	2	FACETS	1	0.944	1	1	0.985	1	CLONAL	2	FALSE	1	0.35659370557169	2		130	182	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132735	152132735	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs867190035	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	258	225	1	ENST00000262189.6:c.137C>A	p.Ser46Tyr	p.S46Y	ENST00000262189	NM_170606.2	46	tCc/tAc	1/59	0.158312848168782	4	FACETS	1	0.988	1	1	0.995	1	INDETERMINATE	3	FALSE	2	0.35659370557169	4		226	568	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089699	5089699	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	211	399	0	ENST00000381652.3:c.2597G>T	p.Cys866Phe	p.C866F	ENST00000381652	NM_004972.3	866	tGc/tTc	20/25	0.35659370557169	1	FACETS	0.817	0.764	0.871	1	0.993	1	CLONAL	2	FALSE	0	0.35659370557169	1		399	595	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499711	8499711	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	343	354	0	ENST00000356435.5:c.2258G>A	p.Arg753Lys	p.R753K	ENST00000356435		753	aGg/aAg	14/35	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	FALSE	1	0.35659370557169	2		354	806	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250326	110250326	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	289	398	0	ENST00000374672.4:c.349C>T	p.Pro117Ser	p.P117S	ENST00000374672	NM_004235.4	117	Ccg/Tcg	3/5	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	FALSE	1	0.35659370557169	2		398	680	SUCCESS
RET	5979	MSKCC	GRCh37	10	43623668	43623669	+	missense_variant	Missense_Mutation	DNP	GG	GG	AC	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	232	417	0	ENST00000355710.3:c.3296_3297delinsAC	p.Trp1099Tyr	p.W1099Y	ENST00000355710	NM_020975.4	1099	tGG/tAC	20/20	0.352255523392608	0	FACETS	0.637	0.597	0.678			1	SUBCLONAL	2	FALSE	0	0.35659370557169	0		417	657	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405605	70405605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	274	317	0	ENST00000373644.4:c.3119C>T	p.Pro1040Leu	p.P1040L	ENST00000373644	NM_030625.2	1040	cCa/cTa	4/12	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	FALSE	1	0.35659370557169	2		317	650	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114799874	114799874	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1305520561	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	419	457	1	ENST00000543371.1:c.541G>A	p.Ala181Thr	p.A181T	ENST00000543371	NM_001198531.1	181	Gca/Aca	5/14	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	FALSE	1	0.35659370557169	2		458	1004	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114912146	114912146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	482	566	0	ENST00000543371.1:c.1216G>A	p.Glu406Lys	p.E406K	ENST00000543371	NM_001198531.1	406	Gag/Aag	11/14	1	2	FACETS	1	0.99	1	1	0.997	1	CLONAL	2	FALSE	1	0.35659370557169	2		566	1220	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111958649	111958649	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764006625	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	259	240	0	ENST00000375549.3:c.121C>T	p.Pro41Ser	p.P41S	ENST00000375549	NM_003002.3	41	Cca/Tca	2/4	0.195237632230673	3	FACETS	0.987	0.933	1			1	INDETERMINATE	3	FALSE	NA	0.35659370557169	3		240	578	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144588	119144588	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	353	323	0	ENST00000264033.4:c.601C>T	p.Pro201Ser	p.P201S	ENST00000264033	NM_005188.3	201	Cct/Tct	4/16	0.195237632230673	3	FACETS	0.986	0.939	1			1	INDETERMINATE	3	FALSE	NA	0.35659370557169	3		323	789	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125503130	125503130	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	434	518	0	ENST00000428830.2:c.497A>C	p.Lys166Thr	p.K166T	ENST00000428830	NM_001114121.2	166	aAg/aCg	6/14	0.195237632230673	3	FACETS	0.926	0.886	0.967			1	INDETERMINATE	3	FALSE	NA	0.35659370557169	3		518	1032	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431793	49431793	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765227366	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	197	229	0	ENST00000301067.7:c.9346C>T	p.Pro3116Ser	p.P3116S	ENST00000301067	NM_003482.3	3116	Cct/Tct	34/54	0.158312848168782	4	FACETS	1	0.977	1	1	0.993	1	INDETERMINATE	3	FALSE	2	0.35659370557169	4		229	457	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864571	57864571	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	474	560	0	ENST00000228682.2:c.2048C>T	p.Ser683Phe	p.S683F	ENST00000228682	NM_005269.2	683	tCt/tTt	12/12	0.158312848168782	4	FACETS	1	0.963	1	1	0.996	1	INDETERMINATE	3	FALSE	2	0.35659370557169	4		560	1195	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041212	29041212	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	293	432	0	ENST00000282397.4:c.216A>T	p.Glu72Asp	p.E72D	ENST00000282397	NM_002019.4	72	gaA/gaT	3/30	0.35659370557169	1	FACETS	0.851	0.805	0.899	1	0.995	1	CLONAL	2	FALSE	0	0.35659370557169	1		432	793	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918694	32918695	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	242	326	0	ENST00000380152.3:c.6842-1_6842delinsAA		p.X2281_splice	ENST00000380152		2281		12/27	1	2	FACETS	1	0.975	1	1	0.995	1	CLONAL	2	FALSE	1	0.35659370557169	2		326	635	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48951106	48951110	+	stop_gained	Nonsense_Mutation	ONP	GATAC	GATAC	AATAA	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	276	420	0	ENST00000267163.4:c.1268_1272delinsAATAA	p.Gly423_Tyr424delinsGluTer	p.G423_Y424delinsE*	ENST00000267163	NM_000321.2	423	gGATAC/gAATAA	13/27	1	2	FACETS	1	0.977	1	1	0.996	1	CLONAL	2	FALSE	1	0.35659370557169	2		420	728	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73340182	73340182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	351	392	1	ENST00000377767.4:c.1898C>T	p.Ser633Phe	p.S633F	ENST00000377767	NM_014953.3	633	tCc/tTc	15/21	1	2	FACETS	1	0.991	1	1	0.997	1	CLONAL	2	FALSE	1	0.35659370557169	2		393	843	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021524	42021524	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	574	662	1	ENST00000219905.7:c.3820C>T	p.Pro1274Ser	p.P1274S	ENST00000219905	NM_001164273.1	1274	Cct/Tct	11/24	1	2	FACETS	1	0.992	1	1	0.998	1	CLONAL	2	FALSE	1	0.35659370557169	2		663	1440	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032318	42032318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	540	582	0	ENST00000219905.7:c.4502C>T	p.Ser1501Phe	p.S1501F	ENST00000219905	NM_001164273.1	1501	tCc/tTc	14/24	1	2	FACETS	1	0.994	1	1	0.998	1	CLONAL	2	FALSE	1	0.35659370557169	2		582	1273	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669510	88669510	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	426	416	0	ENST00000360948.2:c.1388G>A	p.Gly463Glu	p.G463E	ENST00000360948	NM_001012338.2	463	gGa/gAa	12/19	1	2	FACETS	1	0.994	1	1	0.997	1	CLONAL	2	FALSE	1	0.35659370557169	2		416	976	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669600	88669600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	279	278	0	ENST00000360948.2:c.1298C>T	p.Ser433Phe	p.S433F	ENST00000360948	NM_001012338.2	433	tCc/tTc	12/19	1	2	FACETS	0.854	0.809	0.899	1	0.996	1	CLONAL	3	FALSE	1	0.35659370557169	2		278	611	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347087	347087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	425	455	0	ENST00000262320.3:c.1924G>A	p.Glu642Lys	p.E642K	ENST00000262320	NM_003502.3	642	Gag/Aag	7/11	0.35659370557169	3	FACETS	0.973	0.931	1			1	CLONAL	3	FALSE	NA	0.35659370557169	3		455	962	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2138280	2138280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	403	398	0	ENST00000219476.3:c.5213C>T	p.Ser1738Phe	p.S1738F	ENST00000219476	NM_000548.3	1738	tCc/tTc	41/42	0.35659370557169	3	FACETS	0.967	0.924	1			1	CLONAL	3	FALSE	NA	0.35659370557169	3		398	918	SUCCESS
PDPK1	5170	MSKCC	GRCh37	16	2647218	2647218	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	396	399	1	ENST00000342085.4:c.1496C>T	p.Pro499Leu	p.P499L	ENST00000342085	NM_002613.4	499	cCt/cTt	13/14	0.35659370557169	3	FACETS	0.931	0.889	0.973			1	CLONAL	3	FALSE	NA	0.35659370557169	3		400	937	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646515	23646515	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	279	311	0	ENST00000261584.4:c.1352T>A	p.Leu451Ter	p.L451*	ENST00000261584	NM_024675.3	451	tTa/tAa	4/13	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	2	FALSE	NA	0.35659370557169	2		311	712	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829920	72829920	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	334	640	1	ENST00000268489.5:c.6661G>A	p.Glu2221Lys	p.E2221K	ENST00000268489	NM_006885.3	2221	Gag/Aag	9/10	0.35659370557169	1	FACETS	1	0.96	1	1	0.996	1	CLONAL	2	FALSE	0	0.35659370557169	1		641	762	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592258	29592258	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	335	332	2	ENST00000356175.3:c.4673A>T	p.His1558Leu	p.H1558L	ENST00000356175	NM_000267.3	1558	cAt/cTt	35/57	0.35659370557169	5	FACETS	0.931	0.881	0.981			1	CLONAL	3	FALSE	NA	0.35659370557169	5		334	1033	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677242	29677242	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	737	410	0	ENST00000356175.3:c.7300C>A	p.Leu2434Ile	p.L2434I	ENST00000356175	NM_000267.3	2434	Cta/Ata	49/57	0.35659370557169	5	FACETS	1	0.977	1			1	CLONAL	5	FALSE	NA	0.35659370557169	5		410	1261	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627499	37627499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757042254	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	438	545	0	ENST00000447079.4:c.1414G>A	p.Val472Ile	p.V472I	ENST00000447079	NM_015083.1	472	Gta/Ata	2/14	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	2	FALSE	NA	0.35659370557169	2		545	1112	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676337	37676337	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756065405	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	324	393	1	ENST00000447079.4:c.3092C>T	p.Pro1031Leu	p.P1031L	ENST00000447079	NM_015083.1	1031	cCa/cTa	11/14	NA	2	FACETS	1	0.976	1			1	INDETERMINATE	2	FALSE	NA	0.35659370557169	2		394	867	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246492	41246492	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	478	584	0	ENST00000357654.3:c.1056A>T	p.Glu352Asp	p.E352D	ENST00000357654	NM_007294.3	352	gaA/gaT	10/23	0.35659370557169	0	FACETS	0.865	0.839	0.889			1	CLONAL	3	FALSE	0	0.35659370557169	0		584	665	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119258	3119258	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	455	447	0	ENST00000078429.4:c.790T>C	p.Phe264Leu	p.F264L	ENST00000078429	NM_002067.2	264	Ttc/Ctc	6/7	0.179925431149586	3	FACETS	0.955	0.915	0.996	1	0.996	1	INDETERMINATE	3	FALSE	1	0.35659370557169	3		447	1049	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145653	11145653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	245	268	0	ENST00000358026.2:c.4015G>A	p.Glu1339Lys	p.E1339K	ENST00000358026	NM_001128849.1	1339	Gag/Aag	29/36	0.179925431149586	3	FACETS	0.849	0.798	0.899	1	0.99	1	INDETERMINATE	3	FALSE	1	0.35659370557169	3		268	636	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289973	15289974	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	226	408	0	ENST00000263388.2:c.3580_3581delinsTT	p.Pro1194Phe	p.P1194F	ENST00000263388	NM_000435.2	1194	CCc/TTc	22/33	0.353482813580893	1	FACETS	0.816	0.765	0.869	1	0.993	1	CLONAL	2	FALSE	0	0.35659370557169	1		408	638	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354044	15354044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	56	82	0	ENST00000263377.2:c.2836C>T	p.Pro946Ser	p.P946S	ENST00000263377	NM_058243.2	946	Cct/Tct	14/20	0.353482813580893	1	FACETS	0.817	0.715	0.922	1	0.975	1	CLONAL	2	FALSE	0	0.35659370557169	1		82	158	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749613	41749613	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	258	421	0	ENST00000301178.4:c.1537+1G>A		p.X513_splice	ENST00000301178	NM_021913.4	513			0.353482813580893	1	FACETS	0.834	0.785	0.884	1	0.994	1	CLONAL	2	FALSE	0	0.35659370557169	1		421	713	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561060	9561060	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	154	285	0	ENST00000353224.5:c.722G>A	p.Gly241Glu	p.G241E	ENST00000353224	NM_177990.2	241	gGg/gAg	4/10	0.35659370557169	1	FACETS	0.931	0.863	1	1	0.992	1	CLONAL	2	FALSE	0	0.35659370557169	1		285	381	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565564	41565564	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	435	494	0	ENST00000263253.7:c.4230G>T	p.Arg1410Ser	p.R1410S	ENST00000263253	NM_001429.3	1410	agG/agT	26/31	NA	2	FACETS	1	0.993	1			1	INDETERMINATE	2	FALSE	NA	0.35659370557169	2		494	1032	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652227	48652227	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	368	263	0	ENST00000376670.3:c.898G>A	p.Asp300Asn	p.D300N	ENST00000376670	NM_002049.3	300	Gat/Aat	6/6	0.221905479791832	0	FACETS		NA	1			1	NA	4	FALSE	NA	0.35659370557169	0		263	428	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576898	7576899	+	frameshift_variant	Frame_Shift_Del	DEL	GG	GG	A	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	989	404	0	ENST00000269305.4:c.947_948delinsT	p.Pro316LeufsTer29	p.P316Lfs*29	ENST00000269305	NM_001126112.2	316	cCC/cT	9/11	0.35659370557169	7	FACETS	0.967	0.945	0.989	1	0.997	1	CLONAL	7	FALSE	1	0.35659370557169	7		404	1550	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378666	25378669	+	frameshift_variant	Frame_Shift_Del	DEL	ATAG	ATAG	TAA	novel	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	246	361	0	ENST00000311936.3:c.329_332delinsTTA	p.Pro110LeufsTer4	p.P110Lfs*4	ENST00000311936	NM_004985.3	110	cCTATg/cTTAg	4/5	0.144973404749714	0	FACETS	0.755	0.711	0.799			1	INDETERMINATE	2	FALSE	0	0.35659370557169	0		361	588	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955572	48955572	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587778863	NA	P-0008466-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	215	297	0	ENST00000267163.4:c.1688G>A	p.Trp563Ter	p.W563*	ENST00000267163	NM_000321.2	563	tGg/tAg	17/27	1	2	FACETS	1	0.977	1	1	0.995	1	CLONAL	2	FALSE	1	0.35659370557169	2		297	553	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874261	151874261	+	stop_gained	Nonsense_Mutation	SNP	A	A	C	novel	NA	P-0008470-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	289	310	0	ENST00000262189.6:c.8277T>G	p.Tyr2759Ter	p.Y2759*	ENST00000262189	NM_170606.2	2759	taT/taG	38/59	0.446786949602069	7	FACETS	0.981	0.929	1	0.981	0.929	1	CLONAL	4	TRUE	3	0.446786949602069	7		310	698	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410657	32410657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008470-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	138	442	0	ENST00000332351.3:c.1501C>T	p.Arg501Cys	p.R501C	ENST00000332351	NM_024426.4	501	Cgc/Tgc	10/10	0.154006366222065	1	FACETS	0.808	0.748	0.868	1	0.99	1	INDETERMINATE	2	TRUE	0	0.446786949602069	1		442	297	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221703	22221703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008470-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	51	128	0	ENST00000215832.6:c.28G>A	p.Gly10Ser	p.G10S	ENST00000215832	NM_002745.4	10	Ggc/Agc	1/9	0.176829217592934	4	FACETS	1	0.889	1	1	0.973	1	INDETERMINATE	3	TRUE	2	0.446786949602069	4		128	109	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495642	72495662	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	AGTACCTGGTGGAGGTGCCTT	AGTACCTGGTGGAGGTGCCTT	-	novel	NA	P-0008470-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	52	247	0	ENST00000477973.2:c.408_423+5del		p.X136_splice	ENST00000477973	NM_012234.5	136		1/4	0.306407984114213	4	FACETS	1	0.948	1	0.619	0.531	0.714	CLONAL	1	TRUE	2	0.446786949602069	4		247	272	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	44	464	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.912	1			1	INDETERMINATE	1	TRUE	NA	0.542785539930114	2		464	148	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267773	7267773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	67	391	0	ENST00000302850.5:c.235C>T	p.Pro79Ser	p.P79S	ENST00000302850	NM_000208.2	79	Ccc/Tcc	2/22	0.234173320713437	0	FACETS	0.426	0.374	0.481			1	INDETERMINATE	1	TRUE	0	0.542785539930114	0		391	265	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193119485	193119485	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	211	547	1	ENST00000367435.3:c.880G>A	p.Asp294Asn	p.D294N	ENST00000367435	NM_024529.4	294	Gat/Aat	9/17	0.150552844779125	4	FACETS	0.848	0.791	0.907	0.848	0.791	0.907	INDETERMINATE	2	TRUE	2	0.542785539930114	4		548	707	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642495	117642495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs9489124	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	284	911	2	ENST00000368508.3:c.5704G>A	p.Glu1902Lys	p.E1902K	ENST00000368508	NM_002944.2	1902	Gaa/Aaa	35/43	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.542785539930114	2		913	989	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11259672	11259672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	81	472	0	ENST00000361445.4:c.4033C>T	p.Leu1345Phe	p.L1345F	ENST00000361445	NM_004958.3	1345	Ctc/Ttc	27/58	0.273220766761911	1	FACETS	0.574	0.509	0.643	0.574	0.509	0.643	INDETERMINATE	1	TRUE	0	0.542785539930114	1		472	379	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188989	11188989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	82	702	0	ENST00000361445.4:c.5734G>A	p.Asp1912Asn	p.D1912N	ENST00000361445	NM_004958.3	1912	Gat/Aat	41/58	0.273220766761911	1	FACETS	0.57	0.506	0.638	0.57	0.506	0.638	INDETERMINATE	1	TRUE	0	0.542785539930114	1		702	386	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245520	16245520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	234	584	0	ENST00000375759.3:c.1495G>A	p.Glu499Lys	p.E499K	ENST00000375759	NM_015001.2	499	Gaa/Aaa	7/15	0.308900746490073	4	FACETS	0.924	0.866	0.983			1	INDETERMINATE	2	TRUE	NA	0.542785539930114	4		584	720	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255809	16255809	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	180	437	0	ENST00000375759.3:c.3074G>A	p.Arg1025Lys	p.R1025K	ENST00000375759	NM_015001.2	1025	aGa/aAa	11/15	0.308900746490073	4	FACETS	0.942	0.875	1			1	INDETERMINATE	2	TRUE	NA	0.542785539930114	4		437	543	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933511	36933512	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	161	925	1	ENST00000361632.4:c.1775_1776delinsTT	p.Pro592Leu	p.P592L	ENST00000361632		592	cCC/cTT	13/16	NA	2	FACETS	0.994	0.916	1			1	INDETERMINATE	1	TRUE	NA	0.542785539930114	2		926	597	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937232	36937232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	158	916	2	ENST00000361632.4:c.1087G>A	p.Glu363Lys	p.E363K	ENST00000361632		363	Gaa/Aaa	9/16	NA	2	FACETS	1	0.949	1			1	INDETERMINATE	1	TRUE	NA	0.542785539930114	2		918	560	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937938	36937938	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	130	926	1	ENST00000361632.4:c.898G>A	p.Ala300Thr	p.A300T	ENST00000361632		300	Gcc/Acc	7/16	NA	2	FACETS	1	0.919	1			1	INDETERMINATE	1	TRUE	NA	0.542785539930114	2		927	476	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78435633	78435633	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	206	644	1	ENST00000370768.2:c.187C>A	p.Gln63Lys	p.Q63K	ENST00000370768	NM_003902.3	63	Caa/Aaa	2/20	0.327721349251471	4	FACETS	0.766	0.713	0.821	0.766	0.713	0.821	SUBCLONAL	2	TRUE	2	0.542785539930114	4		645	764	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166491	118166491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	147	488	0	ENST00000369448.3:c.1001C>T	p.Ser334Phe	p.S334F	ENST00000369448	NM_017709.3	334	tCc/tTc	2/2	0.327721349251471	4	FACETS	1	0.988	1	0.74	0.678	0.803	CLONAL	1	TRUE	2	0.542785539930114	4		488	565	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468429	120468429	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	104	262	0	ENST00000256646.2:c.4010T>A	p.Phe1337Tyr	p.F1337Y	ENST00000256646	NM_024408.3	1337	tTt/tAt	25/34	0.327721349251471	4	FACETS	0.954	0.865	1	0.954	0.865	1	CLONAL	2	TRUE	2	0.542785539930114	4		262	310	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471703	120471704	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	189	493	1	ENST00000256646.2:c.3787_3788delinsAA	p.Gly1263Lys	p.G1263K	ENST00000256646	NM_024408.3	1263	GGa/AAa	23/34	0.327721349251471	4	FACETS	0.857	0.796	0.919	0.857	0.796	0.919	CLONAL	2	TRUE	2	0.542785539930114	4		494	627	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510184	120510184	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	217	517	0	ENST00000256646.2:c.1325G>C	p.Cys442Ser	p.C442S	ENST00000256646	NM_024408.3	442	tGt/tCt	8/34	0.327721349251471	4	FACETS	0.848	0.792	0.906	0.848	0.792	0.906	CLONAL	2	TRUE	2	0.542785539930114	4		517	727	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740171	162740171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs189206909	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	227	587	0	ENST00000367921.3:c.1373G>A	p.Arg458His	p.R458H	ENST00000367921	NM_006182.2	458	cGc/cAc	12/18	0.150552844779125	4	FACETS	0.785	0.733	0.838	0.785	0.733	0.838	INDETERMINATE	2	TRUE	2	0.542785539930114	4		587	822	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226566868	226566868	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	147	654	1	ENST00000366794.5:c.1720C>T	p.Leu574Phe	p.L574F	ENST00000366794	NM_001618.3	574	Ctt/Ttt	12/23	0.150552844779125	4	FACETS	0.885	0.814	0.958	0.885	0.814	0.958	INDETERMINATE	2	TRUE	2	0.542785539930114	4		655	472	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243708891	243708891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	147	458	0	ENST00000263826.5:c.1172G>A	p.Gly391Glu	p.G391E	ENST00000263826	NM_005465.4	391	gGa/gAa	11/13	0.150552844779125	4	FACETS	0.846	0.778	0.916	0.846	0.778	0.916	INDETERMINATE	2	TRUE	2	0.542785539930114	4		458	494	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243777040	243777040	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	135	457	1	ENST00000263826.5:c.629C>T	p.Ser210Phe	p.S210F	ENST00000263826	NM_005465.4	210	tCc/tTc	7/13	0.150552844779125	4	FACETS	0.804	0.736	0.875	0.804	0.736	0.875	INDETERMINATE	2	TRUE	2	0.542785539930114	4		458	477	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99160452	99160452	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777449349	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	113	503	0	ENST00000074304.5:c.931G>A	p.Asp311Asn	p.D311N	ENST00000074304	NM_001134224.1	311	Gac/Aac	11/26	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.542785539930114	2		503	356	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198273304	198273304	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	102	386	0	ENST00000335508.6:c.906T>G	p.Asp302Glu	p.D302E	ENST00000335508	NM_012433.2	302	gaT/gaG	8/25	0.16986813723307	4	FACETS	1	0.983	1	0.749	0.675	0.826	INDETERMINATE	1	TRUE	2	0.542785539930114	4		386	387	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285794	198285794	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs537380381	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	171	417	0	ENST00000335508.6:c.259C>T	p.Pro87Ser	p.P87S	ENST00000335508	NM_012433.2	87	Cct/Tct	3/25	0.16986813723307	4	FACETS	0.94	0.871	1	0.94	0.871	1	INDETERMINATE	2	TRUE	2	0.542785539930114	4		417	517	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251614	212251614	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781436663	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	249	489	0	ENST00000342788.4:c.3445G>A	p.Gly1149Ser	p.G1149S	ENST00000342788	NM_005235.2	1149	Ggt/Agt	27/28	0.16986813723307	4	FACETS	0.897	0.842	0.953	0.897	0.842	0.953	INDETERMINATE	2	TRUE	2	0.542785539930114	4		489	789	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215609815	215609815	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	288	699	0	ENST00000260947.4:c.1879G>T	p.Gly627Ter	p.G627*	ENST00000260947	NM_000465.2	627	Gga/Tga	9/11	0.16986813723307	4	FACETS	0.907	0.855	0.959	0.907	0.855	0.959	INDETERMINATE	2	TRUE	2	0.542785539930114	4		699	903	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47084111	47084111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	153	559	1	ENST00000409792.3:c.7178C>T	p.Pro2393Leu	p.P2393L	ENST00000409792	NM_014159.6	2393	cCc/cTc	17/21	0.542785539930114	1	FACETS	0.919	0.848	0.991	0.919	0.848	0.991	CLONAL	1	TRUE	0	0.542785539930114	1		560	447	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588782	52588782	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1304065662	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	162	523	0	ENST00000394830.3:c.4246C>T	p.Leu1416Phe	p.L1416F	ENST00000394830	NM_018313.4	1416	Ctt/Ttt	27/30	0.542785539930114	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.542785539930114	1		523	346	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52637657	52637657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	178	728	0	ENST00000394830.3:c.2659C>T	p.Leu887Phe	p.L887F	ENST00000394830	NM_018313.4	887	Ctt/Ttt	18/30	0.542785539930114	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.542785539930114	1		728	423	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480383	89480383	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	211	538	0	ENST00000336596.2:c.2220G>A	p.Met740Ile	p.M740I	ENST00000336596	NM_005233.5	740	atG/atA	13/17	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.542785539930114	2		538	581	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498507	89498507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	216	496	0	ENST00000336596.2:c.2479G>A	p.Glu827Lys	p.E827K	ENST00000336596	NM_005233.5	827	Gag/Aag	14/17	NA	2	FACETS	0.79	0.742	0.838			1	INDETERMINATE	2	TRUE	NA	0.542785539930114	2		496	504	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499335	89499336	+	missense_variant	Missense_Mutation	DNP	AG	AG	GA	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	164	482	0	ENST00000336596.2:c.2505_2506delinsGA	p.Ala836Thr	p.A836T	ENST00000336596	NM_005233.5	835	aaAGct/aaGAct	15/17	NA	2	FACETS	0.755	0.702	0.81			1	INDETERMINATE	2	TRUE	NA	0.542785539930114	2		482	400	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880912	134880912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	228	603	0	ENST00000398015.3:c.1475G>A	p.Arg492Lys	p.R492K	ENST00000398015	NM_004441.4	492	aGg/aAg	7/16	0.308900746490073	4	FACETS	0.85	0.801	0.9			1	INDETERMINATE	3	TRUE	NA	0.542785539930114	4		603	508	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138426012	138426012	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	279	591	0	ENST00000289153.2:c.1519C>T	p.Pro507Ser	p.P507S	ENST00000289153	NM_006219.2	507	Ccc/Tcc	9/22	0.308900746490073	4	FACETS	0.847	0.803	0.892			1	INDETERMINATE	3	TRUE	NA	0.542785539930114	4		591	624	SUCCESS
ATR	545	MSKCC	GRCh37	3	142279217	142279217	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	174	607	0	ENST00000350721.4:c.1429C>T	p.Leu477Phe	p.L477F	ENST00000350721	NM_001184.3	477	Ctt/Ttt	6/47	0.542785539930114	5	FACETS	1	0.981	1	0.403	0.37	0.436	CLONAL	1	TRUE	2	0.542785539930114	5		607	963	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561794	55561794	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	145	512	0	ENST00000288135.5:c.184G>A	p.Gly62Ser	p.G62S	ENST00000288135	NM_000222.2	62	Ggc/Agc	2/21	NA	2	FACETS	0.942	0.864	1			1	INDETERMINATE	1	TRUE	NA	0.542785539930114	2		512	567	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955556	55955556	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	174	847	0	ENST00000263923.4:c.3389A>C	p.Tyr1130Ser	p.Y1130S	ENST00000263923	NM_002253.2	1130	tAt/tCt	25/30	NA	2	FACETS	0.944	0.872	1			1	INDETERMINATE	1	TRUE	NA	0.542785539930114	2		847	679	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984833	55984833	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	158	681	1	ENST00000263923.4:c.296G>T	p.Gly99Val	p.G99V	ENST00000263923	NM_002253.2	99	gGa/gTa	3/30	NA	2	FACETS	0.91	0.837	0.985			1	INDETERMINATE	1	TRUE	NA	0.542785539930114	2		682	640	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66213909	66213909	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	192	580	0	ENST00000273854.3:c.2521C>T	p.Pro841Ser	p.P841S	ENST00000273854	NM_004439.5	841	Cca/Tca	15/18	0.358172079389071	4	FACETS	0.783	0.727	0.841			1	SUBCLONAL	2	TRUE	NA	0.542785539930114	4		580	697	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231698	66231698	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	238	614	0	ENST00000273854.3:c.2002A>C	p.Lys668Gln	p.K668Q	ENST00000273854	NM_004439.5	668	Aag/Cag	11/18	0.358172079389071	4	FACETS	0.858	0.804	0.914			1	CLONAL	2	TRUE	NA	0.542785539930114	4		614	788	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66231707	66231707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1211795184	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	191	609	0	ENST00000273854.3:c.1993G>A	p.Glu665Lys	p.E665K	ENST00000273854	NM_004439.5	665	Gaa/Aaa	11/18	0.358172079389071	4	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.542785539930114	4		609	770	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196229	106196229	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	175	435	0	ENST00000380013.4:c.4562T>A	p.Val1521Asp	p.V1521D	ENST00000380013	NM_001127208.2	1521	gTc/gAc	11/11	0.419104002597929	2	FACETS	0.775	0.722	0.828	0.775	0.722	0.828	SUBCLONAL	2	TRUE	0	0.542785539930114	2		435	416	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524771	187524771	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	197	498	0	ENST00000441802.2:c.10909G>T	p.Glu3637Ter	p.E3637*	ENST00000441802	NM_005245.3	3637	Gag/Tag	19/27	0.542785539930114	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.542785539930114	1		498	374	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177752	56177752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	165	460	0	ENST00000399503.3:c.2725G>A	p.Glu909Lys	p.E909K	ENST00000399503	NM_005921.1	909	Gag/Aag	14/20	0.542785539930114	5	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.542785539930114	5		460	820	SUCCESS
APC	324	MSKCC	GRCh37	5	112177491	112177491	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	148	487	0	ENST00000257430.4:c.6200A>T	p.Asn2067Ile	p.N2067I	ENST00000257430	NM_000038.5	2067	aAt/aTt	16/16	0.273220766761911	1	FACETS	1	0.973	1	1	0.973	1	INDETERMINATE	1	TRUE	0	0.542785539930114	1		487	358	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149436936	149436936	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	106	587	0	ENST00000286301.3:c.2233G>A	p.Glu745Lys	p.E745K	ENST00000286301	NM_005211.3	745	Gag/Aag	17/22	1	2	FACETS	0.917	0.828	1	0.917	0.828	1	CLONAL	1	TRUE	1	0.542785539930114	2		587	426	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158404	26158404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	166	414	0	ENST00000289316.2:c.7G>A	p.Glu3Lys	p.E3K	ENST00000289316	NM_138720.2	3	Gaa/Aaa	1/2	0.484810871911244	4	FACETS	1	0.987	1	0.344	0.317	0.373	CLONAL	1	TRUE	0	0.542785539930114	4		414	685	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168916	32168916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs919103129	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	154	777	0	ENST00000375023.3:c.4117G>A	p.Glu1373Lys	p.E1373K	ENST00000375023	NM_004557.3	1373	Gag/Aag	22/30	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	1	TRUE	NA	0.542785539930114	2		777	506	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172106	32172106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	295	741	0	ENST00000375023.3:c.2926C>T	p.Pro976Ser	p.P976S	ENST00000375023	NM_004557.3	976	Ccc/Tcc	19/30	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	2	TRUE	NA	0.542785539930114	2		741	493	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112029210	112029210	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	174	786	0	ENST00000368678.4:c.358T>A	p.Trp120Arg	p.W120R	ENST00000368678		120	Tgg/Agg	5/13	NA	2	FACETS	0.903	0.834	0.975			1	INDETERMINATE	1	TRUE	NA	0.542785539930114	2		786	710	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609658	117609658	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	128	430	0	ENST00000368508.3:c.7041T>A	p.Asp2347Glu	p.D2347E	ENST00000368508	NM_002944.2	2347	gaT/gaA	43/43	NA	2	FACETS	0.997	0.91	1			1	INDETERMINATE	1	TRUE	NA	0.542785539930114	2		430	473	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662757	117662757	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs192730088	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	144	331	0	ENST00000368508.3:c.4708T>A	p.Ser1570Thr	p.S1570T	ENST00000368508	NM_002944.2	1570	Tca/Aca	29/43	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.542785539930114	2		331	476	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117683798	117683798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	168	455	1	ENST00000368508.3:c.3349G>A	p.Gly1117Ser	p.G1117S	ENST00000368508	NM_002944.2	1117	Ggc/Agc	21/43	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.542785539930114	2		456	563	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710582	117710582	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	216	468	0	ENST00000368508.3:c.1690C>T	p.Leu564Phe	p.L564F	ENST00000368508	NM_002944.2	564	Ctt/Ttt	12/43	0.455593944512684	4	FACETS	0.979	0.916	1	0.979	0.916	1	CLONAL	2	TRUE	2	0.542785539930114	4		468	627	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005321	150005321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	187	773	0	ENST00000253339.5:c.904C>T	p.Pro302Ser	p.P302S	ENST00000253339		302	Cca/Tca	3/7	0.150552844779125	4	FACETS	0.787	0.73	0.846	0.787	0.73	0.846	INDETERMINATE	2	TRUE	2	0.542785539930114	4		773	675	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979406	2979406	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	1261	568	0	ENST00000396946.4:c.841C>T	p.Gln281Ter	p.Q281*	ENST00000396946	NM_032415.4	281	Cag/Tag	6/25	0.542785539930114	10	FACETS	0.969	0.955	0.982			1	CLONAL	10	TRUE	NA	0.542785539930114	10		568	1521	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971172	13971172	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	2171	442	0	ENST00000405192.2:c.757C>T	p.Pro253Ser	p.P253S	ENST00000405192	NM_001163147.1	253	Cct/Tct	8/12	0.542785539930114	21	FACETS	0.977	0.967	0.986			1	CLONAL	20	TRUE	NA	0.542785539930114	21		442	2521	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520000	106520000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	134	608	0	ENST00000359195.3:c.2428C>T	p.Pro810Ser	p.P810S	ENST00000359195	NM_002649.2	810	Cca/Tca	6/11	0.307554720721095	4	FACETS	1	0.982	1	0.653	0.596	0.713	INDETERMINATE	1	TRUE	2	0.542785539930114	4		608	583	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845452	128845452	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	102	495	0	ENST00000249373.3:c.749C>T	p.Ala250Val	p.A250V	ENST00000249373	NM_005631.4	250	gCc/gTc	4/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.542785539930114	2		495	290	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511121	148511121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	116	447	0	ENST00000320356.2:c.1781G>A	p.Gly594Glu	p.G594E	ENST00000320356	NM_004456.4	594	gGa/gAa	15/20	1	2	FACETS	0.867	0.785	0.952	0.867	0.785	0.952	CLONAL	1	TRUE	1	0.542785539930114	2		447	493	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738652	145738653	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	62	312	0	ENST00000428558.2:c.2411_2412delinsAA	p.Arg804Gln	p.R804Q	ENST00000428558	NM_004260.3	804	cGG/cAA	15/22	0.3872304234912	6	FACETS	0.854	0.744	0.97	0.427	0.372	0.485	CLONAL	2	TRUE	2	0.542785539930114	6		312	279	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974679	21974679	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs864622636	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	229	420	1	ENST00000304494.5:c.148C>T	p.Gln50Ter	p.Q50*	ENST00000304494	NM_000077.4	50	Cag/Tag	1/3	0.273220766761911	1	FACETS	1	0.991	1	1	0.991	1	INDETERMINATE	1	TRUE	0	0.542785539930114	1		421	483	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391189	139391190	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	59	371	0	ENST00000277541.6:c.7001_7002delinsTT	p.Pro2334Leu	p.P2334L	ENST00000277541	NM_017617.3	2334	cCC/cTT	34/34	0.514261663145782	3	FACETS	1	0.931	1	0.555	0.483	0.632	CLONAL	1	TRUE	1	0.542785539930114	3		371	249	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396940	139396940	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1264629893	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	14	177	0	ENST00000277541.6:c.5168G>A	p.Ser1723Asn	p.S1723N	ENST00000277541	NM_017617.3	1723	aGt/aAt	28/34	0.514261663145782	3	FACETS	0.669	0.49	0.88	0.335	0.245	0.44	SUBCLONAL	1	TRUE	1	0.542785539930114	3		177	98	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396941	139396941	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	14	175	0	ENST00000277541.6:c.5168-1G>A		p.X1723_splice	ENST00000277541	NM_017617.3	1723			0.514261663145782	3	FACETS	0.676	0.495	0.889	0.338	0.247	0.445	SUBCLONAL	1	TRUE	1	0.542785539930114	3		175	97	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409853	139409853	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	101	371	0	ENST00000277541.6:c.1904-1G>A		p.X635_splice	ENST00000277541	NM_017617.3	635			0.514261663145782	3	FACETS	0.982	0.894	1	0.982	0.894	1	CLONAL	2	TRUE	1	0.542785539930114	3		371	241	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802672	139802672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	62	554	1	ENST00000247668.2:c.517G>A	p.Ala173Thr	p.A173T	ENST00000247668	NM_021138.3	173	Gca/Aca	5/11	NA	2	FACETS	0.742	0.645	0.845			1	INDETERMINATE	1	TRUE	NA	0.542785539930114	2		555	308	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106076	8106076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	96	343	0	ENST00000346208.3:c.896C>T	p.Pro299Leu	p.P299L	ENST00000346208		299	cCc/cTc	4/6	0.542785539930114	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.542785539930114	1		343	228	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850891	63850891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	177	432	0	ENST00000279873.7:c.1669C>T	p.Pro557Ser	p.P557S	ENST00000279873	NM_032199.2	557	Cct/Tct	10/10	0.542785539930114	4	FACETS	0.915	0.848	0.983			1	CLONAL	2	TRUE	NA	0.542785539930114	4		432	550	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451027	70451027	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	109	380	0	ENST00000373644.4:c.5867C>T	p.Pro1956Leu	p.P1956L	ENST00000373644	NM_030625.2	1956	cCa/cTa	12/12	0.273220766761911	1	FACETS	0.719	0.651	0.79	0.719	0.651	0.79	INDETERMINATE	1	TRUE	0	0.542785539930114	1		380	407	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77047156	77047157	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	199	676	0	ENST00000356341.3:c.1387_1388delinsAT	p.Pro463Ile	p.P463I	ENST00000356341	NM_002576.4	463	CCa/ATa	13/15	0.308900746490073	4	FACETS	0.76	0.706	0.816			1	INDETERMINATE	2	TRUE	NA	0.542785539930114	4		676	744	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909900	100909901	+	missense_variant	Missense_Mutation	DNP	AT	AT	GA	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	175	742	0	ENST00000325455.5:c.2748_2749delinsTC	p.Gln916His	p.Q916H	ENST00000325455	NM_001202474.3	916	caATta/caTCta	8/8	0.542785539930114	1	FACETS	0.902	0.837	0.968	0.902	0.837	0.968	CLONAL	1	TRUE	0	0.542785539930114	1		742	521	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998271	100998271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	93	338	0	ENST00000325455.5:c.1531C>T	p.Leu511Phe	p.L511F	ENST00000325455	NM_001202474.3	511	Ctc/Ttc	1/8	0.542785539930114	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.542785539930114	1		338	174	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118366590	118366590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs551537456	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	150	477	1	ENST00000534358.1:c.5539C>T	p.Pro1847Ser	p.P1847S	ENST00000534358	NM_005933.3	1847	Cct/Tct	19/36	0.542785539930114	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.542785539930114	1		478	370	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373911	118373911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	178	696	0	ENST00000534358.1:c.7304C>T	p.Ser2435Phe	p.S2435F	ENST00000534358	NM_005933.3	2435	tCc/tTc	27/36	0.542785539930114	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.542785539930114	1		696	361	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793456	18793456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1357943621	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	194	670	2	ENST00000266497.5:c.4153C>T	p.Pro1385Ser	p.P1385S	ENST00000266497		1385	Cca/Tca	30/31	0.273220766761911	1	FACETS	1	0.943	1	1	0.943	1	INDETERMINATE	1	TRUE	0	0.542785539930114	1		672	515	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944944	31944944	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144139961	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	94	479	0	ENST00000340398.3:c.157C>T	p.Arg53Cys	p.R53C	ENST00000340398	NM_001013699.2	53	Cgt/Tgt	1/1	0.273220766761911	1	FACETS	0.762	0.685	0.843	0.762	0.685	0.843	INDETERMINATE	1	TRUE	0	0.542785539930114	1		479	331	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230439	46230440	+	splice_donor_variant	Splice_Site	DNP	GT	GT	AC	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	183	480	1	ENST00000334344.6:c.772+1_772+2inv		p.X258_splice	ENST00000334344	NM_152641.2	258			0.300713191452035	5	FACETS	1	0.939	1			1	INDETERMINATE	2	TRUE	NA	0.542785539930114	5		481	604	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427920	49427920	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	198	743	1	ENST00000301067.7:c.10670C>T	p.Pro3557Leu	p.P3557L	ENST00000301067	NM_003482.3	3557	cCa/cTa	38/54	0.251412900589708	4	FACETS	1	0.946	1	1	0.946	1	INDETERMINATE	2	TRUE	2	0.542785539930114	4		744	554	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493718	56493718	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	200	664	0	ENST00000267101.3:c.3034G>A	p.Asp1012Asn	p.D1012N	ENST00000267101	NM_001982.3	1012	Gac/Aac	25/28	0.251412900589708	4	FACETS	0.921	0.859	0.986	0.921	0.859	0.986	INDETERMINATE	2	TRUE	2	0.542785539930114	4		664	617	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495026	56495026	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	144	469	0	ENST00000267101.3:c.3383G>A	p.Gly1128Glu	p.G1128E	ENST00000267101	NM_001982.3	1128	gGa/gAa	27/28	0.542785539930114	4	FACETS	0.786	0.721	0.853			1	SUBCLONAL	2	TRUE	NA	0.542785539930114	4		469	521	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563128	21563128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	96	508	0	ENST00000382592.4:c.791C>T	p.Pro264Leu	p.P264L	ENST00000382592	NM_014572.2	264	cCc/cTc	4/8	0.542785539930114	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.542785539930114	1		508	206	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134835	41134835	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	285	989	2	ENST00000379561.5:c.793A>G	p.Lys265Glu	p.K265E	ENST00000379561	NM_002015.3	265	Aag/Gag	2/3	0.478399819670783	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.542785539930114	1		991	638	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251244	99251244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	200	585	1	ENST00000268035.6:c.548C>T	p.Pro183Leu	p.P183L	ENST00000268035	NM_000875.3	183	cCa/cTa	2/21	0.308900746490073	4	FACETS	1	0.942	1			1	INDETERMINATE	2	TRUE	NA	0.542785539930114	4		586	563	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2106705	2106705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555498859	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	144	702	0	ENST00000219476.3:c.709C>T	p.Pro237Ser	p.P237S	ENST00000219476	NM_000548.3	237	Ccg/Tcg	8/42	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.542785539930114	2		702	354	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807367	3807367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	111	443	0	ENST00000262367.5:c.3620C>T	p.Ser1207Phe	p.S1207F	ENST00000262367	NM_004380.2	1207	tCc/tTc	19/31	NA	2	FACETS	0.936	0.847	1			1	INDETERMINATE	1	TRUE	NA	0.542785539930114	2		443	437	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858003	9858003	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	154	648	0	ENST00000330684.3:c.3398C>T	p.Pro1133Leu	p.P1133L	ENST00000330684	NM_001134407.1	1133	cCc/cTc	13/13	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.542785539930114	2		648	520	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100651	67100651	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	199	747	2	ENST00000412916.2:c.349C>T	p.Gln117Ter	p.Q117*	ENST00000412916		117	Caa/Taa	4/6	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	1	TRUE	NA	0.542785539930114	2		749	688	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992399	72992399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747830670	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	153	1111	0	ENST00000268489.5:c.1646C>T	p.Ser549Phe	p.S549F	ENST00000268489	NM_006885.3	549	tCt/tTt	2/10	0.226582285452241	0	FACETS	0.509	0.469	0.551			1	INDETERMINATE	1	TRUE	0	0.542785539930114	0		1111	506	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81957138	81957138	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	196	775	1	ENST00000359376.3:c.2356G>A	p.Asp786Asn	p.D786N	ENST00000359376	NM_002661.3	786	Gat/Aat	22/33	0.226582285452241	0	FACETS	0.563	0.524	0.602			1	INDETERMINATE	1	TRUE	0	0.542785539930114	0		776	587	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577085	+	missense_variant	Missense_Mutation	ONP	CCTC	CCTC	TCTT	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	278	416	0	ENST00000269305.4:c.853_856delinsAAGA	p.Glu285_Glu286delinsLysLys	p.E285_E286delinsKK	ENST00000269305	NM_001126112.2	285	GAGGaa/AAGAaa	8/11	0.533702963496476	3	FACETS	1	0.963	1	1	0.963	1	CLONAL	3	TRUE	0	0.542785539930114	3		416	431	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579418	7579418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526625	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	78	660	0	ENST00000269305.4:c.269C>T	p.Ser90Phe	p.S90F	ENST00000269305	NM_001126112.2	90	tCc/tTc	4/11	0.533702963496476	3	FACETS	1	0.978	1	0.485	0.432	0.54	CLONAL	1	TRUE	0	0.542785539930114	3		660	251	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38487485	38487485	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	84	476	0	ENST00000254066.5:c.15C>G	p.Ser5Arg	p.S5R	ENST00000254066	NM_000964.3	5	agC/agG	2/9	NA	2	FACETS	0.812	0.722	0.907			1	INDETERMINATE	1	TRUE	NA	0.542785539930114	2		476	381	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1223169	1223169	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1230130092	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	84	410	0	ENST00000326873.7:c.1106C>T	p.Pro369Leu	p.P369L	ENST00000326873	NM_000455.4	369	cCc/cTc	8/10	0.105442671373317	0	FACETS	0.557	0.499	0.617			1	INDETERMINATE	1	TRUE	0	0.542785539930114	0		410	254	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210743	5210743	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	90	583	0	ENST00000357368.4:c.5308G>A	p.Glu1770Lys	p.E1770K	ENST00000357368	NM_002850.3	1770	Gag/Aag	34/38	0.234173320713437	0	FACETS	0.461	0.413	0.511			1	INDETERMINATE	1	TRUE	0	0.542785539930114	0		583	329	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281227	15281227	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	83	627	0	ENST00000263388.2:c.5029C>T	p.Pro1677Ser	p.P1677S	ENST00000263388	NM_000435.2	1677	Cct/Tct	27/33	0.105442671373317	0	FACETS	0.448	0.399	0.499			1	INDETERMINATE	1	TRUE	0	0.542785539930114	0		627	312	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289677	15289677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138092938	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	92	674	1	ENST00000263388.2:c.3794C>T	p.Pro1265Leu	p.P1265L	ENST00000263388	NM_000435.2	1265	cCg/cTg	23/33	0.105442671373317	0	FACETS	0.508	0.457	0.562			1	INDETERMINATE	1	TRUE	0	0.542785539930114	0		675	305	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296150	15296150	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	63	562	0	ENST00000263388.2:c.2214T>A	p.Cys738Ter	p.C738*	ENST00000263388	NM_000435.2	738	tgT/tgA	14/33	0.105442671373317	0	FACETS	0.421	0.368	0.477			1	INDETERMINATE	1	TRUE	0	0.542785539930114	0		562	252	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796963	42796963	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	139	613	0	ENST00000575354.2:c.3421C>T	p.Pro1141Ser	p.P1141S	ENST00000575354	NM_015125.3	1141	Cct/Tct	14/20	0.460623702117381	3	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.542785539930114	3		613	443	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799311	42799311	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	15	151	0	ENST00000575354.2:c.4795C>T	p.Pro1599Ser	p.P1599S	ENST00000575354	NM_015125.3	1599	Cca/Tca	20/20	0.460623702117381	3	FACETS	0.889	0.663	1			1	CLONAL	1	TRUE	NA	0.542785539930114	3		151	79	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867755	45867756	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	148	666	0	ENST00000391945.4:c.644_645delinsTT	p.Pro215Leu	p.P215L	ENST00000391945	NM_000400.3	215	cCC/cTT	8/23	0.460623702117381	3	FACETS	0.816	0.752	0.881			1	CLONAL	2	TRUE	NA	0.542785539930114	3		666	425	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560894	9560894	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	190	447	0	ENST00000353224.5:c.888G>A	p.Met296Ile	p.M296I	ENST00000353224	NM_177990.2	296	atG/atA	4/10	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.542785539930114	2		447	657	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560902	9560902	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	171	640	1	ENST00000353224.5:c.880G>T	p.Glu294Ter	p.E294*	ENST00000353224	NM_177990.2	294	Gaa/Taa	4/10	NA	2	FACETS	1	0.947	1			1	INDETERMINATE	1	TRUE	NA	0.542785539930114	2		641	611	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023751	31023751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	103	488	0	ENST00000375687.4:c.3236C>T	p.Ser1079Phe	p.S1079F	ENST00000375687	NM_015338.5	1079	tCc/tTc	13/13	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	TRUE	NA	0.542785539930114	2		488	320	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523617	41523617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	162	609	0	ENST00000263253.7:c.1033C>T	p.Leu345Phe	p.L345F	ENST00000263253	NM_001429.3	345	Ctt/Ttt	4/31	NA	2	FACETS	0.916	0.843	0.991			1	INDETERMINATE	1	TRUE	NA	0.542785539930114	2		609	652	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574622	41574622	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144787962	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	175	842	0	ENST00000263253.7:c.6907C>T	p.Leu2303Phe	p.L2303F	ENST00000263253	NM_001429.3	2303	Ctc/Ttc	31/31	0.300713191452035	5	FACETS	0.761	0.702	0.822			1	INDETERMINATE	2	TRUE	NA	0.542785539930114	5		842	769	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932524	39932524	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	102	325	0	ENST00000378444.4:c.2075T>G	p.Phe692Cys	p.F692C	ENST00000378444	NM_001123385.1	692	tTt/tGt	4/15	1	1	FACETS	0.845	0.784	0.905	1	0.989	1	CLONAL	2	TRUE	0	0.542785539930114	1		325	162	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465387	120465397	+	frameshift_variant	Frame_Shift_Del	DEL	AGAAAGACTTT	AGAAAGACTTT	-	novel	NA	P-0008480-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	126	383	0	ENST00000256646.2:c.4864_4874del	p.Lys1622GlyfsTer3	p.K1622Gfs*3	ENST00000256646	NM_024408.3	1622	AAAGTCTTTCTg/g	27/34	0.327721349251471	4	FACETS	0.785	0.716	0.857	0.785	0.716	0.857	SUBCLONAL	2	TRUE	2	0.542785539930114	4		383	456	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008484-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	108	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.541842679349897	2		280	331	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0008484-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	393	511	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.541842679349897	2		511	1169	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209630	98209630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779365332	NA	P-0008484-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	120	201	1	ENST00000331920.6:c.3908G>A	p.Arg1303His	p.R1303H	ENST00000331920	NM_000264.3	1303	cGc/cAc	23/24	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.541842679349897	2		202	345	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0008528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	210	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.560601688177326	2		464	622	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0008528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	87	263	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.560603286721674	3	FACETS	0.891	0.793	0.995	0.445	0.396	0.498	CLONAL	1	TRUE	1	0.560601688177326	3		263	446	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220437	133220437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775072147	NA	P-0008528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	207	355	1	ENST00000320574.5:c.4276G>A	p.Val1426Ile	p.V1426I	ENST00000320574	NM_006231.2	1426	Gta/Ata	33/49	1	2	FACETS	0.986	0.918	1	0.986	0.918	1	CLONAL	1	TRUE	1	0.560601688177326	2		356	749	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs866987936	NA	P-0008528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	128	281	0	ENST00000281708.4:c.1436G>C	p.Arg479Pro	p.R479P	ENST00000281708	NM_033632.3	479	cGa/cCa	10/12	1	2	FACETS	0.89	0.811	0.972	0.89	0.811	0.972	CLONAL	1	TRUE	1	0.560601688177326	2		281	513	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631294	176631294	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0008528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	224	522	1	ENST00000439151.2:c.1236+1G>T		p.X412_splice	ENST00000439151	NM_022455.4	412			0.560603286721674	3	FACETS	0.79	0.734	0.848	0.395	0.367	0.424	SUBCLONAL	1	TRUE	1	0.560601688177326	3		523	1295	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435896	49435896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	367	595	0	ENST00000301067.7:c.6085C>T	p.Pro2029Ser	p.P2029S	ENST00000301067	NM_003482.3	2029	Cct/Tct	28/54	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.560601688177326	2		595	1307	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480404	56480404	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	221	390	0	ENST00000267101.3:c.511G>A	p.Asp171Asn	p.D171N	ENST00000267101	NM_001982.3	171	Gat/Aat	4/28	1	2	FACETS	0.862	0.803	0.923	0.862	0.803	0.923	CLONAL	1	TRUE	1	0.560601688177326	2		390	915	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480410	56480410	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	212	388	0	ENST00000267101.3:c.517G>A	p.Glu173Lys	p.E173K	ENST00000267101	NM_001982.3	173	Gag/Aag	4/28	1	2	FACETS	0.878	0.817	0.942	0.878	0.817	0.942	CLONAL	1	TRUE	1	0.560601688177326	2		388	861	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777933	3777933	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008528-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2045	445	734	0	ENST00000262367.5:c.7115C>G	p.Ser2372Trp	p.S2372W	ENST00000262367	NM_004380.2	2372	tCg/tGg	31/31	0.538274106194886	4	FACETS	0.995	0.945	1	0.498	0.472	0.524	CLONAL	1	TRUE	2	0.560601688177326	4		734	2490	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	67	280	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.741	0.646	0.843			1	INDETERMINATE	1	TRUE	NA	0.415520840254035	2		280	435	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467675	50467675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759124417	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	116	499	0	ENST00000331340.3:c.910G>A	p.Glu304Lys	p.E304K	ENST00000331340	NM_006060.4	304	Gaa/Aaa	8/8	1	2	FACETS	0.74	0.667	0.816	0.74	0.667	0.816	SUBCLONAL	1	TRUE	1	0.415520840254035	2		499	755	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	192	572	1	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	1	2	FACETS	0.86	0.794	0.928	0.86	0.794	0.928	CLONAL	1	TRUE	1	0.415520840254035	2		573	1075	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560894	9560894	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	159	447	0	ENST00000353224.5:c.888G>A	p.Met296Ile	p.M296I	ENST00000353224	NM_177990.2	296	atG/atA	4/10	1	2	FACETS	0.764	0.699	0.831	0.764	0.699	0.831	SUBCLONAL	1	TRUE	1	0.415520840254035	2		447	1002	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023598	31023598	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200702600	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	189	545	0	ENST00000375687.4:c.3083C>T	p.Ser1028Leu	p.S1028L	ENST00000375687	NM_015338.5	1028	tCg/tTg	13/13	1	2	FACETS	0.937	0.866	1	0.937	0.866	1	CLONAL	1	TRUE	1	0.415520840254035	2		545	971	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143018	7143018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753688285	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	100	291	0	ENST00000302850.5:c.2351C>T	p.Ser784Phe	p.S784F	ENST00000302850	NM_000208.2	784	tCc/tTc	12/22	1	2	FACETS	0.806	0.722	0.896	0.806	0.722	0.896	CLONAL	1	TRUE	1	0.415520840254035	2		291	597	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606679	29606679	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs865931787	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	357	598	1	ENST00000389048.3:c.1201C>T	p.Arg401Ter	p.R401*	ENST00000389048	NM_004304.4	401	Cga/Tga	5/29	0.354705765481627	3	FACETS	0.937	0.888	0.985	0.937	0.888	0.985	CLONAL	2	TRUE	1	0.415520840254035	3		599	1108	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651115	206651115	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781821296	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	168	482	1	ENST00000367120.3:c.725C>T	p.Pro242Leu	p.P242L	ENST00000367120	NM_014002.3	242	cCg/cTg	8/22	1	2	FACETS	0.823	0.756	0.893	0.823	0.756	0.893	CLONAL	1	TRUE	1	0.415520840254035	2		483	983	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117718277	117718277	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1298952570	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	154	235	0	ENST00000368508.3:c.580C>T	p.Pro194Ser	p.P194S	ENST00000368508	NM_002944.2	194	Cct/Tct	7/43	0.353219057837302	2	FACETS	1	0.989	1	0.737	0.679	0.796	CLONAL	1	TRUE	0	0.415520840254035	2		235	503	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971170	21971170	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	42	136	0	ENST00000304494.5:c.188T>A	p.Leu63Gln	p.L63Q	ENST00000304494	NM_000077.4	63	cTg/cAg	2/3	1	2	FACETS	0.857	0.721	1	0.857	0.721	1	CLONAL	1	TRUE	1	0.415520840254035	2		136	236	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146527	185146527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35961174	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	148	355	1	ENST00000265026.3:c.158G>A	p.Arg53Gln	p.R53Q	ENST00000265026	NM_004721.4	53	cGa/cAa	2/14	1	2	FACETS	0.935	0.855	1	0.935	0.855	1	CLONAL	1	TRUE	1	0.415520840254035	2		356	762	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809757	36809757	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	314	335	0	ENST00000373129.3:c.848T>C	p.Phe283Ser	p.F283S	ENST00000373129	NM_032017.1	283	tTc/tCc	9/12	0.354705765481627	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.415520840254035	3		335	853	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804262	43804262	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	399	428	0	ENST00000372470.3:c.262G>A	p.Gly88Arg	p.G88R	ENST00000372470	NM_005373.2	88	Gga/Aga	3/12	0.354705765481627	3	FACETS	0.984	0.937	1	0.984	0.937	1	CLONAL	2	TRUE	1	0.415520840254035	3		428	1178	SUCCESS
FH	2271	MSKCC	GRCh37	1	241665789	241665789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	326	437	0	ENST00000366560.3:c.1190G>A	p.Gly397Glu	p.G397E	ENST00000366560	NM_000143.3	397	gGa/gAa	8/10	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.415520840254035	2		437	1239	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881467	111881467	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1431222585	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	127	328	1	ENST00000393256.3:c.145G>A	p.Gly49Arg	p.G49R	ENST00000393256	NM_006538.4	49	Gga/Aga	2/4	0.354705765481627	3	FACETS	0.892	0.808	0.98	0.446	0.404	0.49	CLONAL	1	TRUE	1	0.415520840254035	3		329	828	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873426	136873426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1317	584	807	0	ENST00000241393.3:c.72G>A	p.Met24Ile	p.M24I	ENST00000241393	NM_003467.2	24	atG/atA	2/2	0.354705765481627	3	FACETS	0.893	0.856	0.93	0.893	0.856	0.93	CLONAL	2	TRUE	1	0.415520840254035	3		807	1901	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662133	227662133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762160657	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	148	450	0	ENST00000305123.5:c.1322C>T	p.Ser441Phe	p.S441F	ENST00000305123	NM_005544.2	441	tCc/tTc	1/2	0.354705765481627	3	FACETS	1	0.925	1	0.507	0.463	0.553	CLONAL	1	TRUE	1	0.415520840254035	3		450	849	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52662960	52662960	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	185	376	0	ENST00000394830.3:c.1393C>T	p.Pro465Ser	p.P465S	ENST00000394830	NM_018313.4	465	Ccc/Tcc	13/30	1	2	FACETS	0.85	0.784	0.918	0.85	0.784	0.918	CLONAL	1	TRUE	1	0.415520840254035	2		376	1048	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71015158	71015158	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1364685833	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	142	359	0	ENST00000318789.4:c.1772G>A	p.Gly591Glu	p.G591E	ENST00000318789	NM_032682.5	591	gGa/gAa	20/21	1	2	FACETS	0.804	0.733	0.879	0.804	0.733	0.879	CLONAL	1	TRUE	1	0.415520840254035	2		359	850	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163765	32163765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1412061983	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	129	310	0	ENST00000375023.3:c.5461G>A	p.Gly1821Arg	p.G1821R	ENST00000375023	NM_004557.3	1821	Ggg/Agg	30/30	0.164046719299408	4	FACETS	1	0.98	1	0.645	0.586	0.707	INDETERMINATE	1	TRUE	2	0.415520840254035	4		310	681	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724395	117724395	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	243	367	0	ENST00000368508.3:c.484A>C	p.Thr162Pro	p.T162P	ENST00000368508	NM_002944.2	162	Act/Cct	6/43	0.353219057837302	2	FACETS	0.761	0.714	0.81	0.761	0.714	0.81	SUBCLONAL	2	TRUE	0	0.415520840254035	2		367	768	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397761	116397761	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	184	517	0	ENST00000397752.3:c.2035G>A	p.Gly679Arg	p.G679R	ENST00000397752	NM_000245.2	679	Gga/Aga	8/21	1	2	FACETS	0.835	0.77	0.902	0.835	0.77	0.902	CLONAL	1	TRUE	1	0.415520840254035	2		517	1061	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152027719	152027719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	235	602	1	ENST00000262189.6:c.356C>T	p.Ser119Phe	p.S119F	ENST00000262189	NM_170606.2	119	tCc/tTc	3/59	1	2	FACETS	0.882	0.821	0.944	0.882	0.821	0.944	CLONAL	1	TRUE	1	0.415520840254035	2		603	1283	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922301	100922301	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	185	464	0	ENST00000325455.5:c.2213-2A>G		p.X738_splice	ENST00000325455	NM_001202474.3	738			1	2	FACETS	0.843	0.778	0.911	0.843	0.778	0.911	CLONAL	1	TRUE	1	0.415520840254035	2		464	1056	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102199653	102199653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	101	338	0	ENST00000263464.3:c.1058G>A	p.Gly353Glu	p.G353E	ENST00000263464	NM_001165.4	353	gGa/gAa	5/9	1	2	FACETS	0.664	0.594	0.739	0.664	0.594	0.739	SUBCLONAL	1	TRUE	1	0.415520840254035	2		338	732	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149260	119149260	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs868103494	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	240	503	0	ENST00000264033.4:c.1268T>A	p.Ile423Asn	p.I423N	ENST00000264033	NM_005188.3	423	aTt/aAt	9/16	1	2	FACETS	0.887	0.827	0.95	0.887	0.827	0.95	CLONAL	1	TRUE	1	0.415520840254035	2		503	1302	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658340	18658340	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	106	375	0	ENST00000266497.5:c.3145C>T	p.His1049Tyr	p.H1049Y	ENST00000266497		1049	Cat/Tat	22/31	1	2	FACETS	0.712	0.638	0.789	0.712	0.638	0.789	SUBCLONAL	1	TRUE	1	0.415520840254035	2		375	717	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431337	121431337	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565885498	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	77	245	0	ENST00000257555.6:c.541G>A	p.Gly181Arg	p.G181R	ENST00000257555		181	Ggg/Agg	3/10	NA	2	FACETS	0.722	0.636	0.815			1	INDETERMINATE	1	TRUE	NA	0.415520840254035	2		245	513	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549277	21549277	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	251	641	1	ENST00000382592.4:c.2999C>A	p.Ser1000Ter	p.S1000*	ENST00000382592	NM_014572.2	1000	tCg/tAg	8/8	1	2	FACETS	0.917	0.856	0.979	0.917	0.856	0.979	CLONAL	1	TRUE	1	0.415520840254035	2		642	1318	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41240226	41240226	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs931846569	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	64	138	1	ENST00000379561.5:c.124C>T	p.Pro42Ser	p.P42S	ENST00000379561	NM_002015.3	42	Ccg/Tcg	1/3	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.415520840254035	2		139	273	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955446	48955446	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	161	327	0	ENST00000267163.4:c.1562T>C	p.Leu521Pro	p.L521P	ENST00000267163	NM_000321.2	521	cTt/cCt	17/27	1	2	FACETS	0.933	0.856	1	0.933	0.856	1	CLONAL	1	TRUE	1	0.415520840254035	2		327	831	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779076	3779076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776500881	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	100	273	1	ENST00000262367.5:c.5972C>T	p.Pro1991Leu	p.P1991L	ENST00000262367	NM_004380.2	1991	cCg/cTg	31/31	1	2	FACETS	0.994	0.892	1	0.994	0.892	1	CLONAL	1	TRUE	1	0.415520840254035	2		274	484	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347176	89347176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	176	568	0	ENST00000301030.4:c.5774C>T	p.Pro1925Leu	p.P1925L	ENST00000301030	NM_001256183.1	1925	cCc/cTc	9/13	1	2	FACETS	0.908	0.836	0.983	0.908	0.836	0.983	CLONAL	1	TRUE	1	0.415520840254035	2		568	933	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657450	29657450	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs62070718	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	366	360	0	ENST00000356175.3:c.5683G>A	p.Ala1895Thr	p.A1895T	ENST00000356175	NM_000267.3	1895	Gca/Aca	38/57	0.415520840254035	3	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	1	0.415520840254035	3		360	1032	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33428227	33428227	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1379526157	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	116	395	0	ENST00000345365.6:c.896C>T	p.Ser299Phe	p.S299F	ENST00000345365	NM_002878.3	299	tCc/tTc	9/10	0.415520840254035	3	FACETS	0.678	0.61	0.751	0.339	0.305	0.376	SUBCLONAL	1	TRUE	1	0.415520840254035	3		395	994	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627971	37627971	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868596372	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	416	501	0	ENST00000447079.4:c.1886C>T	p.Pro629Leu	p.P629L	ENST00000447079	NM_015083.1	629	cCt/cTt	2/14	0.415520840254035	3	FACETS	0.971	0.925	1	0.971	0.925	1	CLONAL	2	TRUE	1	0.415520840254035	3		501	1245	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45871950	45871950	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs964247601	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	187	420	0	ENST00000391945.4:c.298G>A	p.Glu100Lys	p.E100K	ENST00000391945	NM_000400.3	100	Gag/Aag	5/23	1	2	FACETS	0.926	0.855	1	0.926	0.855	1	CLONAL	1	TRUE	1	0.415520840254035	2		420	972	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561130	9561130	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	125	338	0	ENST00000353224.5:c.652G>A	p.Glu218Lys	p.E218K	ENST00000353224	NM_177990.2	218	Gag/Aag	4/10	1	2	FACETS	0.878	0.796	0.964	0.878	0.796	0.964	CLONAL	1	TRUE	1	0.415520840254035	2		338	685	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39817402	39817402	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	178	334	0	ENST00000288319.7:c.161A>C	p.Gln54Pro	p.Q54P	ENST00000288319	NM_182918.3	54	cAg/cCg	2/10	1	2	FACETS	0.932	0.859	1	0.932	0.859	1	CLONAL	1	TRUE	1	0.415520840254035	2		334	919	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911535	39911535	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140145812	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	228	586	0	ENST00000378444.4:c.5095C>T	p.Arg1699Trp	p.R1699W	ENST00000378444	NM_001123385.1	1699	Cgg/Tgg	15/15	1	2	FACETS	0.914	0.85	0.98	0.914	0.85	0.98	CLONAL	1	TRUE	1	0.415520840254035	2		586	1201	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044701	47044701	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	205	561	2	ENST00000377604.3:c.2101G>A	p.Gly701Arg	p.G701R	ENST00000377604	NM_001204468.1	701	Gga/Aga	19/24	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.415520840254035	2		563	953	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649619	48649619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557020030	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	208	669	0	ENST00000376670.3:c.103C>T	p.Pro35Ser	p.P35S	ENST00000376670	NM_002049.3	35	Ccc/Tcc	2/6	1	2	FACETS	0.92	0.853	0.989	0.92	0.853	0.989	CLONAL	1	TRUE	1	0.415520840254035	2		669	1088	SUCCESS
AR	367	MSKCC	GRCh37	X	66765835	66765835	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	166	553	1	ENST00000374690.3:c.847C>T	p.Pro283Ser	p.P283S	ENST00000374690	NM_000044.3	283	Cct/Tct	1/8	1	2	FACETS	0.807	0.741	0.876	0.807	0.741	0.876	CLONAL	1	TRUE	1	0.415520840254035	2		554	990	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912128	76912128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	209	539	0	ENST00000373344.5:c.4136C>T	p.Ser1379Leu	p.S1379L	ENST00000373344	NM_000489.3	1379	tCa/tTa	13/35	1	2	FACETS	0.901	0.835	0.968	0.901	0.835	0.968	CLONAL	1	TRUE	1	0.415520840254035	2		539	1117	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938172	76938172	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	195	630	1	ENST00000373344.5:c.2576G>A	p.Gly859Glu	p.G859E	ENST00000373344	NM_000489.3	859	gGa/gAa	9/35	1	2	FACETS	0.758	0.7	0.819	0.758	0.7	0.819	SUBCLONAL	1	TRUE	1	0.415520840254035	2		631	1238	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087539	27087540	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	157	416	0	ENST00000324856.7:c.2116_2117dup	p.Ala707LeufsTer36	p.A707Lfs*36	ENST00000324856	NM_006015.4	705	agt/aGTgt	5/20	0.354705765481627	3	FACETS	0.84	0.768	0.915	0.42	0.384	0.458	CLONAL	1	TRUE	1	0.415520840254035	3		416	1087	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911609	32911609	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	212	730	0	ENST00000380152.3:c.3117del	p.Thr1040LeufsTer3	p.T1040Lfs*3	ENST00000380152		1039	ccT/cc	11/27	1	2	FACETS	0.719	0.666	0.774	0.719	0.666	0.774	SUBCLONAL	1	TRUE	1	0.415520840254035	2		730	1419	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5216745	5216746	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	171	554	0	ENST00000357368.4:c.4081_4082delinsAA	p.Gly1361Lys	p.G1361K	ENST00000357368	NM_002850.3	1361	GGg/AAg	26/38	1	2	FACETS	0.832	0.765	0.902	0.832	0.765	0.902	CLONAL	1	TRUE	1	0.415520840254035	2		554	989	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272104	15272105	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	31	132	1	ENST00000263388.2:c.6334_6335delinsAA	p.Gly2112Asn	p.G2112N	ENST00000263388	NM_000435.2	2112	GGt/AAt	33/33	1	2	FACETS	0.714	0.582	0.861	0.714	0.582	0.861	SUBCLONAL	1	TRUE	1	0.415520840254035	2		133	209	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796544	42796545	+	missense_variant	Missense_Mutation	DNP	CC	CC	GT	novel	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	99	296	0	ENST00000575354.2:c.3101_3102delinsGT	p.Pro1034Arg	p.P1034R	ENST00000575354	NM_015125.3	1034	cCC/cGT	13/20	1	2	FACETS	0.762	0.682	0.848	0.762	0.682	0.848	SUBCLONAL	1	TRUE	1	0.415520840254035	2		296	625	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760807	59760808	+	missense_variant	Missense_Mutation	DNP	AT	AT	GA	novel	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	469	532	0	ENST00000259008.2:c.3599_3600delinsTC	p.His1200Leu	p.H1200L	ENST00000259008	NM_032043.2	1200	cAT/cTC	20/20	0.415520840254035	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.415520840254035	3		532	1293	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586097	29586100	+	frameshift_variant	Frame_Shift_Del	DEL	TATG	TATG	ACT	novel	NA	P-0008557-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	267	324	0	ENST00000356175.3:c.4317_4320delinsACT	p.His1439GlnfsTer9	p.H1439Qfs*9	ENST00000356175	NM_000267.3	1439	caTATG/caACT	32/57	0.415520840254035	3	FACETS	0.902	0.849	0.957	0.902	0.849	0.957	CLONAL	2	TRUE	1	0.415520840254035	3		324	860	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008575-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	218	280	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.81966152071048	2		280	478	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008575-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	557	585	0	ENST00000267101.3:c.310G>C	p.Val104Leu	p.V104L	ENST00000267101	NM_001982.3	104	Gtg/Ctg	3/28	1	2	FACETS	0.973	0.935	1	0.973	0.935	1	CLONAL	1	TRUE	1	0.81966152071048	2		585	1397	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135787845	135787845	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1564490210	NA	P-0008575-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	275	209	0	ENST00000298552.3:c.738-1G>A		p.X246_splice	ENST00000298552	NM_001162426.1	246			0.81966152071048	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.81966152071048	1		209	356	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008672-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	59	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.341057395549195	2		280	290	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0008672-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	86	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.904	0.801	1	0.904	0.801	1	CLONAL	1	TRUE	1	0.341057395549195	2		490	558	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577330	64577333	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	rs587776841	NA	P-0008672-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	92	676	0	ENST00000312049.6:c.249_252del	p.Ile85SerfsTer33	p.I85Sfs*33	ENST00000312049	NM_130799.2	83	ctGTCT/ct	2/10	0.341057395549195	1	FACETS	0.725	0.645	0.81	0.725	0.645	0.81	SUBCLONAL	1	TRUE	0	0.341057395549195	1		676	617	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008672-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	117	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.814395426020459	2		280	262	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0008672-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	192	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA	2	FACETS	0.972	0.908	1			1	INDETERMINATE	1	TRUE	NA	0.814395426020459	2		490	485	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0008672-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	142	157	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.814395426020459	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.814395426020459	1		157	205	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577330	64577333	+	frameshift_variant	Frame_Shift_Del	DEL	AGAC	AGAC	-	rs587776841	NA	P-0008672-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	157	676	0	ENST00000312049.6:c.249_252del	p.Ile85SerfsTer33	p.I85Sfs*33	ENST00000312049	NM_130799.2	83	ctGTCT/ct	2/10	0.814395426020459	1	FACETS	0.788	0.737	0.839	0.788	0.737	0.839	SUBCLONAL	1	TRUE	0	0.814395426020459	1		676	290	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249071	55249071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434569	NA	P-0008705-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	209	551	0	ENST00000275493.2:c.2369C>T	p.Thr790Met	p.T790M	ENST00000275493	NM_005228.3	790	aCg/aTg	20/28	0.719274604324158	3	FACETS	1	0.943	1	0.507	0.472	0.543	CLONAL	1	TRUE	1	0.719274604324158	3		551	779	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0008705-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	499	265	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.719274604324158	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.719274604324158	3		265	926	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670404	88670404	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008705-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	135	374	0	ENST00000360948.2:c.1282G>C	p.Asp428His	p.D428H	ENST00000360948	NM_001012338.2	428	Gac/Cac	11/19	0.719274604324158	2	FACETS	0.922	0.847	1	0.461	0.423	0.5	CLONAL	1	TRUE	0	0.719274604324158	2		374	407	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81960701	81960701	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008705-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	220	568	0	ENST00000359376.3:c.2432A>G	p.Tyr811Cys	p.Y811C	ENST00000359376	NM_002661.3	811	tAt/tGt	23/33	0.719274604324158	2	FACETS	1	0.955	1	0.511	0.479	0.545	CLONAL	1	TRUE	0	0.719274604324158	2		568	598	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69011990	69011990	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008705-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	267	728	0	ENST00000288368.4:c.2627T>G	p.Val876Gly	p.V876G	ENST00000288368	NM_024870.2	876	gTg/gGg	23/40	0.243992367073222	5	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.719274604324158	5		728	1088	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150549855	150549855	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1270654728	NA	P-0008715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	64	338	0	ENST00000369026.2:c.1049G>A	p.Arg350Lys	p.R350K	ENST00000369026	NM_021960.4	350	aGa/aAa	3/3	0.421121811058905	5	FACETS	0.635	0.549	0.729	0.159	0.137	0.183	SUBCLONAL	1	TRUE	1	0.495532242579164	5		338	709	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940459	29940459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	53	457	0	ENST00000389048.3:c.772C>T	p.His258Tyr	p.H258Y	ENST00000389048	NM_004304.4	258	Cat/Tat	2/29	0.394601664055157	4	FACETS	0.485	0.413	0.565	0.162	0.137	0.189	SUBCLONAL	1	TRUE	1	0.495532242579164	4		457	659	SUCCESS
ALK	238	MSKCC	GRCh37	2	29940515	29940515	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	75	662	0	ENST00000389048.3:c.716A>G	p.Asp239Gly	p.D239G	ENST00000389048	NM_004304.4	239	gAt/gGt	2/29	0.394601664055157	4	FACETS	0.542	0.474	0.615	0.181	0.157	0.205	SUBCLONAL	1	TRUE	1	0.495532242579164	4		662	836	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178097161	178097161	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	40	356	0	ENST00000397062.3:c.553G>C	p.Glu185Gln	p.E185Q	ENST00000397062	NM_006164.4	185	Gag/Cag	4/5	0.411326667137813	3	FACETS	0.353	0.292	0.42	0.176	0.146	0.21	SUBCLONAL	1	TRUE	1	0.495532242579164	3		356	571	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342959	225342959	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	188	654	0	ENST00000264414.4:c.2133G>C	p.Met711Ile	p.M711I	ENST00000264414	NM_003590.4	711	atG/atC	15/16	0.411326667137813	3	FACETS	1	0.976	1	0.564	0.521	0.607	CLONAL	1	TRUE	1	0.495532242579164	3		654	840	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403538	138403538	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	323	612	0	ENST00000289153.2:c.2244G>C	p.Gln748His	p.Q748H	ENST00000289153	NM_006219.2	748	caG/caC	15/22	0.495532242579164	3	FACETS	0.883	0.836	0.931	0.589	0.557	0.621	CLONAL	2	TRUE	0	0.495532242579164	3		612	921	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968287	2968287	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	130	422	1	ENST00000396946.4:c.1699C>T	p.Pro567Ser	p.P567S	ENST00000396946	NM_032415.4	567	Ccc/Tcc	13/25	0.394601664055157	4	FACETS	1	0.947	1	0.354	0.321	0.388	CLONAL	1	TRUE	1	0.495532242579164	4		423	739	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339198	116339198	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	235	449	0	ENST00000397752.3:c.60G>C	p.Gln20His	p.Q20H	ENST00000397752	NM_000245.2	20	caG/caC	2/21	0.388120264750813	3	FACETS	0.905	0.849	0.961	0.603	0.566	0.641	CLONAL	2	TRUE	0	0.495532242579164	3		449	654	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528720	8528720	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	29	446	0	ENST00000356435.5:c.412G>C	p.Glu138Gln	p.E138Q	ENST00000356435		138	Gag/Cag	4/35	0.495532242579164	1	FACETS	0.217	0.174	0.266	0.217	0.174	0.266	SUBCLONAL	1	TRUE	0	0.495532242579164	1		446	406	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93636499	93636499	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	165	604	0	ENST00000375746.1:c.929A>T	p.Gln310Leu	p.Q310L	ENST00000375746	NM_001174167.1	310	cAa/cTa	8/14	0.183124772624853	3	FACETS	1	0.979	1	0.593	0.546	0.642	INDETERMINATE	1	TRUE	1	0.495532242579164	3		604	701	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332811	70332811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	177	490	0	ENST00000373644.4:c.716C>T	p.Ser239Phe	p.S239F	ENST00000373644	NM_030625.2	239	tCc/tTc	2/12	0.394601664055157	4	FACETS	1	0.99	1	0.494	0.456	0.533	CLONAL	1	TRUE	1	0.495532242579164	4		490	721	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426919	70426919	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	117	450	0	ENST00000373644.4:c.4579C>T	p.Leu1527Phe	p.L1527F	ENST00000373644	NM_030625.2	1527	Ctt/Ttt	7/12	0.394601664055157	4	FACETS	1	0.955	1	0.366	0.33	0.404	CLONAL	1	TRUE	1	0.495532242579164	4		450	643	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435987	110435987	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	31	218	0	ENST00000375856.3:c.2414C>G	p.Ser805Cys	p.S805C	ENST00000375856	NM_003749.2	805	tCc/tGc	1/2	0.495532242579164	4	FACETS	0.611	0.496	0.742	0.153	0.124	0.186	SUBCLONAL	1	TRUE	0	0.495532242579164	4		218	306	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577112	7577112	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	390	622	0	ENST00000269305.4:c.826G>T	p.Ala276Ser	p.A276S	ENST00000269305	NM_001126112.2	276	Gcc/Tcc	8/11	0.388120264750813	3	FACETS	0.874	0.837	0.911	0.874	0.837	0.911	CLONAL	3	TRUE	0	0.495532242579164	3		622	749	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370320	40370320	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs760876362	NA	P-0008715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	110	1004	0	ENST00000293328.3:c.1018C>G	p.Gln340Glu	p.Q340E	ENST00000293328	NM_012448.3	340	Cag/Gag	9/19	0.486999004156255	2	FACETS	0.486	0.436	0.54	0.243	0.218	0.27	SUBCLONAL	1	TRUE	0	0.495532242579164	2		1004	913	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4094487	4094487	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	218	396	0	ENST00000262948.5:c.1056G>T	p.Lys352Asn	p.K352N	ENST00000262948	NM_030662.3	352	aaG/aaT	10/11	0.458271103892501	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.495532242579164	2		396	435	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549427	187549461	+	frameshift_variant	Frame_Shift_Del	DEL	GCGGTGAACCACGGGGCGTGGTCATTCGTGTCGCT	GCGGTGAACCACGGGGCGTGGTCATTCGTGTCGCT	-	novel	NA	P-0008715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	207	415	0	ENST00000441802.2:c.4657_4691del	p.Ser1553PhefsTer9	p.S1553Ffs*9	ENST00000441802	NM_005245.3	1553	AGCGACACGAATGACCACGCCCCGTGGTTCACCGCt/t	9/27	0.458271103892501	2	FACETS	0.939	0.882	0.996	0.939	0.882	0.996	CLONAL	2	TRUE	0	0.495532242579164	2		415	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577101	7577101	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	374	611	1	ENST00000269305.4:c.837del	p.Arg280GlufsTer65	p.R280Efs*65	ENST00000269305	NM_001126112.2	279	ggG/gg	8/11	0.388120264750813	3	FACETS	0.851	0.814	0.888	0.851	0.814	0.888	CLONAL	3	TRUE	0	0.495532242579164	3		612	738	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295162	1295164	+	5_prime_UTR_variant	5'UTR	TNP	GAA	GAA	TAT	novel	NA	P-0008715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	31	149	0				ENST00000310581	NM_198253.2	-/1132		1/16	0.395091856210177	6	FACETS	0.874	0.709	1	0.219	0.177	0.265	CLONAL	1	TRUE	2	0.495532242579164	6		149	285	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435525	110435526	+	frameshift_variant	Frame_Shift_Del	DEL	CC	CC	A	novel	NA	P-0008715-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	25	113	0	ENST00000375856.3:c.2875_2876delinsT	p.Gly959SerfsTer21	p.G959Sfs*21	ENST00000375856	NM_003749.2	959	GGc/Tc	1/2	0.495532242579164	4	FACETS	0.662	0.524	0.819	0.165	0.131	0.205	SUBCLONAL	1	TRUE	0	0.495532242579164	4		113	228	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	174	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.865	0.801	0.932	0.865	0.801	0.932	CLONAL	1	TRUE	1	0.669216487234642	2		280	601	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0008725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	269	511	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.669216487234642	2		512	716	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164856	47164856	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1278528667	NA	P-0008725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	121	373	1	ENST00000409792.3:c.1270C>T	p.Arg424Ter	p.R424*	ENST00000409792	NM_014159.6	424	Cga/Tga	3/21	1	2	FACETS	0.451	0.407	0.497	0.451	0.407	0.497	SUBCLONAL	1	TRUE	1	0.669216487234642	2		374	802	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11143999	11143999	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1171822727	NA	P-0008725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	74	346	0	ENST00000358026.2:c.3580G>A	p.Gly1194Arg	p.G1194R	ENST00000358026	NM_001128849.1	1194	Ggg/Agg	26/36	1	2	FACETS	0.289	0.252	0.329	0.289	0.252	0.329	SUBCLONAL	1	TRUE	1	0.669216487234642	2		346	765	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78428616	78428616	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0008725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	49	335	0	ENST00000370768.2:c.1184-1G>A		p.X395_splice	ENST00000370768	NM_003902.3	395			0.669216487234642	1	FACETS	0.366	0.312	0.425	0.366	0.312	0.425	SUBCLONAL	1	TRUE	0	0.669216487234642	1		335	266	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47098949	47098949	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	141	440	0	ENST00000409792.3:c.6325C>T	p.Arg2109Ter	p.R2109*	ENST00000409792	NM_014159.6	2109	Cga/Tga	15/21	1	2	FACETS	0.474	0.431	0.519	0.474	0.431	0.519	SUBCLONAL	1	TRUE	1	0.669216487234642	2		440	889	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73352466	73352466	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	57	581	0	ENST00000377767.4:c.439A>G	p.Arg147Gly	p.R147G	ENST00000377767	NM_014953.3	147	Aga/Gga	3/21	0.406480366790769	1	FACETS	0.161	0.138	0.187	0.161	0.138	0.187	SUBCLONAL	1	TRUE	0	0.669216487234642	1		581	702	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791022	42791023	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0008725-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	81	452	0	ENST00000575354.2:c.168dup	p.Glu57ArgfsTer20	p.E57Rfs*20	ENST00000575354	NM_015125.3	56	agc/agCc	2/20	0.669216487234642	1	FACETS	0.27	0.238	0.305	0.27	0.238	0.305	SUBCLONAL	1	TRUE	0	0.669216487234642	1		452	596	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	56	280	0				ENST00000310581	NM_198253.2	-/1132			0.162384224023957	4	FACETS	0.842	0.73	0.961	0.842	0.73	0.961	INDETERMINATE	2	TRUE	2	0.414359655996016	4		280	227	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	78	354	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.357138290203415	2	FACETS	0.888	0.795	0.984	0.888	0.795	0.984	CLONAL	2	TRUE	0	0.414359655996016	2		354	212	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624936	9624936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760501160	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	58	577	0	ENST00000353224.5:c.41C>T	p.Pro14Leu	p.P14L	ENST00000353224	NM_177990.2	14	cCg/cTg	3/10	0.33553702039352	4	FACETS	1	0.908	1	0.534	0.46	0.613	CLONAL	1	TRUE	2	0.414359655996016	4		577	371	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	100	465	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.103691165397725	4	FACETS	0.778	0.699	0.86	0.778	0.699	0.86	INDETERMINATE	2	TRUE	2	0.414359655996016	4		467	439	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210675	2210675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747494025	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	79	549	0	ENST00000398665.3:c.1172C>T	p.Pro391Leu	p.P391L	ENST00000398665	NM_032482.2	391	cCc/cTc	14/28	0.103691165397725	4	FACETS	1	0.972	1	0.674	0.596	0.757	INDETERMINATE	1	TRUE	2	0.414359655996016	4		549	400	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867535	35867535	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	58	394	0	ENST00000303115.3:c.349A>G	p.Thr117Ala	p.T117A	ENST00000303115	NM_002185.3	117	Acc/Gcc	3/8	0.162384224023957	4	FACETS	0.884	0.769	1	0.884	0.769	1	INDETERMINATE	2	TRUE	2	0.414359655996016	4		394	224	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28877480	28877480	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	70	258	0	ENST00000282397.4:c.3841G>A	p.Glu1281Lys	p.E1281K	ENST00000282397	NM_002019.4	1281	Gag/Aag	30/30	NA	2	FACETS	1	0.961	1			1	INDETERMINATE	1	TRUE	NA	0.414359655996016	2		258	276	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857500	9857500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	36	346	0	ENST00000330684.3:c.3901G>A	p.Glu1301Lys	p.E1301K	ENST00000330684	NM_001134407.1	1301	Gag/Aag	13/13	1	2	FACETS	0.597	0.493	0.713	0.597	0.493	0.713	SUBCLONAL	1	TRUE	1	0.414359655996016	2		346	291	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433373	49433373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771966959	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	42	224	0	ENST00000301067.7:c.8074C>T	p.Arg2692Trp	p.R2692W	ENST00000301067	NM_003482.3	2692	Cgg/Tgg	32/54	0.264417691393132	4	FACETS	0.783	0.663	0.913			1	CLONAL	2	TRUE	NA	0.414359655996016	4		224	183	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254813	16254813	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	86	557	0	ENST00000375759.3:c.2078G>A	p.Arg693Lys	p.R693K	ENST00000375759	NM_015001.2	693	aGg/aAg	11/15	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.414359655996016	2		557	353	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932010	36932010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	62	899	1	ENST00000361632.4:c.2459C>T	p.Pro820Leu	p.P820L	ENST00000361632		820	cCc/cTc	16/16	0.414359655996016	1	FACETS	0.503	0.435	0.576	0.503	0.435	0.576	SUBCLONAL	1	TRUE	0	0.414359655996016	1		900	472	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165951	118165951	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	47	272	0	ENST00000369448.3:c.461T>G	p.Leu154Arg	p.L154R	ENST00000369448	NM_017709.3	154	cTg/cGg	2/2	1	2	FACETS	0.869	0.739	1	0.869	0.739	1	CLONAL	1	TRUE	1	0.414359655996016	2		272	261	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193205417	193205417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1386267118	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	133	404	0	ENST00000367435.3:c.1348C>T	p.Pro450Ser	p.P450S	ENST00000367435	NM_024529.4	450	Cct/Tct	15/17	0.307848415449346	5	FACETS	1	0.969	1	0.751	0.687	0.817	CLONAL	2	TRUE	2	0.414359655996016	5		404	462	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61709653	61709653	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	154	382	0	ENST00000401558.2:c.2834T>G	p.Ile945Ser	p.I945S	ENST00000401558	NM_003400.3	945	aTt/aGt	23/25	0.414359655996016	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	3	TRUE	0	0.414359655996016	3		382	296	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47059223	47059223	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	72	297	0	ENST00000409792.3:c.7438C>T	p.Gln2480Ter	p.Q2480*	ENST00000409792	NM_014159.6	2480	Cag/Tag	20/21	0.414359655996016	3	FACETS	1	0.972	1	0.692	0.61	0.779	CLONAL	1	TRUE	1	0.414359655996016	3		297	303	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49933972	49933972	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	135	603	3	ENST00000296474.3:c.2439+1G>A		p.X813_splice	ENST00000296474	NM_002447.2	813			NA	2	FACETS	0.797	0.731	0.864			1	INDETERMINATE	2	TRUE	NA	0.414359655996016	2		606	409	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455560	189455560	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	30	455	0	ENST00000264731.3:c.94A>T	p.Lys32Ter	p.K32*	ENST00000264731	NM_003722.4	32	Aaa/Taa	2/14	0.162384224023957	4	FACETS	0.721	0.583	0.877	0.361	0.291	0.439	INDETERMINATE	1	TRUE	2	0.414359655996016	4		455	284	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955873	55955873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	87	480	0	ENST00000263923.4:c.3289G>A	p.Glu1097Lys	p.E1097K	ENST00000263923	NM_002253.2	1097	Gaa/Aaa	24/30	0.414359655996016	3	FACETS	0.773	0.691	0.859	0.773	0.691	0.859	SUBCLONAL	2	TRUE	1	0.414359655996016	3		480	328	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961109	55961109	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374755237	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	81	432	0	ENST00000263923.4:c.2831G>A	p.Arg944Gln	p.R944Q	ENST00000263923	NM_002253.2	944	cGa/cAa	21/30	0.414359655996016	3	FACETS	1	0.972	1	0.665	0.59	0.744	CLONAL	1	TRUE	1	0.414359655996016	3		432	355	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549794	187549794	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	89	427	0	ENST00000441802.2:c.4447C>T	p.Gln1483Ter	p.Q1483*	ENST00000441802	NM_005245.3	1483	Cag/Tag	8/27	0.414359655996016	3	FACETS	0.853	0.765	0.945	0.853	0.765	0.945	CLONAL	2	TRUE	1	0.414359655996016	3		427	304	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950762	38950762	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1184965562	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	35	341	0	ENST00000357387.3:c.3188A>G	p.Asp1063Gly	p.D1063G	ENST00000357387	NM_152756.3	1063	gAt/gGt	31/38	0.162384224023957	4	FACETS	1	0.935	1	0.649	0.538	0.771	INDETERMINATE	1	TRUE	2	0.414359655996016	4		341	184	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057684	180057684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	69	662	0	ENST00000261937.6:c.271C>T	p.Pro91Ser	p.P91S	ENST00000261937	NM_182925.4	91	Ccc/Tcc	3/30	0.162384224023957	4	FACETS	1	0.923	1	0.539	0.471	0.612	INDETERMINATE	1	TRUE	2	0.414359655996016	4		662	437	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2972169	2972169	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs901997929	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	217	476	0	ENST00000396946.4:c.1570G>A	p.Ala524Thr	p.A524T	ENST00000396946	NM_032415.4	524	Gcc/Acc	11/25	0.414359655996016	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	1	0.414359655996016	4		476	472	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397806	116397806	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	137	735	0	ENST00000397752.3:c.2080G>A	p.Gly694Arg	p.G694R	ENST00000397752	NM_000245.2	694	Gga/Aga	8/21	0.414359655996016	4	FACETS	0.871	0.802	0.941	0.871	0.802	0.941	CLONAL	3	TRUE	1	0.414359655996016	4		735	358	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38275836	38275836	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	118	374	0	ENST00000425967.3:c.1433C>T	p.Ser478Leu	p.S478L	ENST00000425967	NM_001174067.1	478	tCa/tTa	11/19	NA	2	FACETS	0.863	0.789	0.939			1	INDETERMINATE	2	TRUE	NA	0.414359655996016	2		374	330	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317936	8317936	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	76	374	0	ENST00000356435.5:c.5677T>A	p.Tyr1893Asn	p.Y1893N	ENST00000356435		1893	Tat/Aat	35/35	0.357138290203415	2	FACETS	0.861	0.769	0.956	0.861	0.769	0.956	CLONAL	2	TRUE	0	0.414359655996016	2		374	213	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319913	8319913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	116	448	0	ENST00000356435.5:c.5588G>A	p.Arg1863Lys	p.R1863K	ENST00000356435		1863	aGa/aAa	34/35	0.357138290203415	2	FACETS	0.823	0.751	0.898	0.823	0.751	0.898	CLONAL	2	TRUE	0	0.414359655996016	2		448	340	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206810	102206810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	125	954	1	ENST00000263464.3:c.1438G>A	p.Asp480Asn	p.D480N	ENST00000263464	NM_001165.4	480	Gat/Aat	7/9	0.414359655996016	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.414359655996016	1		955	374	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285682	46285682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	66	403	0	ENST00000334344.6:c.5042C>T	p.Ser1681Phe	p.S1681F	ENST00000334344	NM_152641.2	1681	tCt/tTt	17/21	0.264417691393132	4	FACETS	1	0.886	1			1	CLONAL	2	TRUE	NA	0.414359655996016	4		403	224	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428045	49428045	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	41	236	0	ENST00000301067.7:c.10545C>A	p.Phe3515Leu	p.F3515L	ENST00000301067	NM_003482.3	3515	ttC/ttA	38/54	0.264417691393132	4	FACETS	1	0.935	1			1	CLONAL	1	TRUE	NA	0.414359655996016	4		236	226	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592630	28592630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	65	670	0	ENST00000241453.7:c.2515G>A	p.Asp839Asn	p.D839N	ENST00000241453	NM_004119.2	839	Gat/Aat	20/24	NA	2	FACETS	0.839	0.731	0.955			1	INDETERMINATE	1	TRUE	NA	0.414359655996016	2		670	374	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472598	88472598	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1186552712	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	92	436	0	ENST00000360948.2:c.1957C>T	p.Leu653Phe	p.L653F	ENST00000360948	NM_001012338.2	653	Ctc/Ttc	16/19	0.33553702039352	4	FACETS	1	0.977	1	0.689	0.615	0.767	CLONAL	1	TRUE	2	0.414359655996016	4		436	456	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81960694	81960694	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	137	782	0	ENST00000359376.3:c.2425G>A	p.Gly809Arg	p.G809R	ENST00000359376	NM_002661.3	809	Gga/Aga	23/33	0.335967108379861	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.414359655996016	1		782	445	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8111154	8111154	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	51	379	1	ENST00000585124.1:c.53C>T	p.Pro18Leu	p.P18L	ENST00000585124	NM_004217.3	18	cCa/cTa	3/9	0.103691165397725	4	FACETS	1	0.947	1	0.622	0.532	0.718	INDETERMINATE	1	TRUE	2	0.414359655996016	4		380	280	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29553597	29553597	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	55	288	0	ENST00000356175.3:c.2146G>T	p.Glu716Ter	p.E716*	ENST00000356175	NM_000267.3	716	Gaa/Taa	18/57	0.103691165397725	4	FACETS	1	0.966	1	0.719	0.621	0.825	INDETERMINATE	1	TRUE	2	0.414359655996016	4		288	261	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29585404	29585404	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	49	446	2	ENST00000356175.3:c.4153G>T	p.Gly1385Ter	p.G1385*	ENST00000356175	NM_000267.3	1385	Gga/Tga	31/57	0.103691165397725	4	FACETS	1	0.952	1	0.651	0.556	0.753	INDETERMINATE	1	TRUE	2	0.414359655996016	4		448	257	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362461	40362461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	90	891	0	ENST00000293328.3:c.1735G>A	p.Glu579Lys	p.E579K	ENST00000293328	NM_012448.3	579	Gaa/Aaa	14/19	0.18654005573121	0	FACETS	0.613	0.547	0.683			1	INDETERMINATE	1	TRUE	0	0.414359655996016	0		891	415	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39644793	39644793	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	64	355	0	ENST00000262039.4:c.2522A>C	p.Lys841Thr	p.K841T	ENST00000262039	NM_002647.2	841	aAg/aCg	23/25	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.414359655996016	2		355	246	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223146	5223146	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	89	505	0	ENST00000357368.4:c.2657C>T	p.Ser886Phe	p.S886F	ENST00000357368	NM_002850.3	886	tCc/tTc	18/38	0.103691165397725	4	FACETS	0.87	0.778	0.967	0.87	0.778	0.967	INDETERMINATE	2	TRUE	2	0.414359655996016	4		505	349	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624930	9624930	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	60	623	1	ENST00000353224.5:c.47A>T	p.Asn16Ile	p.N16I	ENST00000353224	NM_177990.2	16	aAc/aTc	3/10	0.33553702039352	4	FACETS	1	0.893	1	0.518	0.448	0.594	CLONAL	1	TRUE	2	0.414359655996016	4		624	395	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019446	31019446	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	80	321	0	ENST00000375687.4:c.943C>T	p.His315Tyr	p.H315Y	ENST00000375687	NM_015338.5	315	Cat/Tat	10/13	0.33553702039352	4	FACETS	1	0.971	1	0.66	0.583	0.74	CLONAL	1	TRUE	2	0.414359655996016	4		321	414	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039826	47039826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	83	726	0	ENST00000377604.3:c.1169C>T	p.Ala390Val	p.A390V	ENST00000377604	NM_001204468.1	390	gCc/gTc	12/24	0.414359655996016	1	FACETS	0.977	0.871	1	0.977	0.871	1	CLONAL	1	TRUE	0	0.414359655996016	1		726	325	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165282	47165283	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	32	473	0	ENST00000409792.3:c.843dup	p.Glu282ArgfsTer9	p.E282Rfs*9	ENST00000409792	NM_014159.6	281	-/A	3/21	NA	2	FACETS	0.534	0.435	0.646			1	INDETERMINATE	1	TRUE	NA	0.414359655996016	2		473	289	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690574	88690576	+	missense_variant	Missense_Mutation	TNP	AAG	AAG	GAA	novel	NA	P-0008728-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	96	335	0	ENST00000360948.2:c.454_456delinsTTC	p.Leu152Phe	p.L152F	ENST00000360948	NM_001012338.2	152	CTT/TTC	5/19	0.33553702039352	4	FACETS	0.867	0.779	0.959	0.867	0.779	0.959	CLONAL	2	TRUE	2	0.414359655996016	4		335	378	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0008733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	249	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.664191656392077	2		464	587	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0008733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	257	511	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.664191656392077	2		511	726	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106771	27106771	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	246	485	0	ENST00000324856.7:c.6382C>T	p.Gln2128Ter	p.Q2128*	ENST00000324856	NM_006015.4	2128	Cag/Tag	20/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.664191656392077	2		485	739	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289244	33289244	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	504	455	0	ENST00000374542.5:c.308C>G	p.Ala103Gly	p.A103G	ENST00000374542	NM_001141970.1	103	gCg/gGg	3/8	0.664191656392077	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.664191656392077	3		455	948	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453987	140453987	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs180177040	NA	P-0008733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	142	453	0	ENST00000288602.6:c.1741A>G	p.Asn581Asp	p.N581D	ENST00000288602	NM_004333.4	581	Aat/Gat	14/18	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.664191656392077	2		453	412	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852320	63852320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	281	445	0	ENST00000279873.7:c.3098C>T	p.Pro1033Leu	p.P1033L	ENST00000279873	NM_032199.2	1033	cCc/cTc	10/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.664191656392077	2		445	687	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499730	18499730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	154	333	0	ENST00000266497.5:c.1585G>A	p.Val529Met	p.V529M	ENST00000266497		529	Gtg/Atg	10/31	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.664191656392077	2		333	406	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948844	17948844	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	379	672	0	ENST00000458235.1:c.1598C>T	p.Thr533Ile	p.T533I	ENST00000458235	NM_000215.3	533	aCc/aTc	12/24	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.664191656392077	2		672	997	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737824	145737825	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0008733-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	179	423	0	ENST00000428558.2:c.3005_3006del	p.Ser1002CysfsTer30	p.S1002Cfs*30	ENST00000428558	NM_004260.3	1002	tCT/t	18/22	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.664191656392077	2		423	478	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008770-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	97	280	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	FALSE	NA	0.877136117697625	2		280	193	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578225	7578225	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008770-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	469	448	1	ENST00000269305.4:c.624C>A	p.Asp208Glu	p.D208E	ENST00000269305	NM_001126112.2	208	gaC/gaA	6/11	1	2	FACETS	0.999	0.958	1	0.999	0.958	1	CLONAL	1	FALSE	1	0.877136117697625	2		449	1070	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690824	89690825	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0008770-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	174	175	0	ENST00000371953.3:c.232dup	p.Thr78AsnfsTer5	p.T78Nfs*5	ENST00000371953	NM_000314.4	77	-/A	4/9	0.873517343151935	1	FACETS	0.87	0.825	0.914	0.87	0.825	0.914	CLONAL	1	FALSE	0	0.877136117697625	1		175	256	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008773-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	68	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.952	0.831	1	0.952	0.831	1	CLONAL	1	TRUE	1	0.33	2		280	433	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0008773-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	67	354	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.33	2		354	273	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519920	NA	P-0008773-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	60	320	0	ENST00000397062.3:c.85G>C	p.Asp29His	p.D29H	ENST00000397062	NM_006164.4	29	Gat/Cat	2/5	1	2	FACETS	0.712	0.614	0.818	0.712	0.614	0.818	SUBCLONAL	1	TRUE	1	0.33	2		320	511	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526298	189526298	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008773-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	354	223	0	ENST00000264731.3:c.562A>C	p.Lys188Gln	p.K188Q	ENST00000264731	NM_003722.4	188	Aag/Cag	4/14	0.3	5	FACETS	1	0.976	1	1	0.976	1	CLONAL	4	TRUE	1	0.33	5		223	773	SUCCESS
AR	367	MSKCC	GRCh37	X	66765072	66765072	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008773-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	343	593	0	ENST00000374690.3:c.84G>C	p.Gln28His	p.Q28H	ENST00000374690	NM_000044.3	28	caG/caC	1/8	0.292996347697576	2	FACETS	0.985	0.934	1	0.985	0.934	1	CLONAL	2	TRUE	0	0.33	2		593	1055	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	89	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.864	0.775	0.957	0.864	0.775	0.957	CLONAL	1	TRUE	1	0.698156029341041	2		280	295	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220274	55220274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1630	7341	433	0	ENST00000275493.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000275493	NM_005228.3	222	Cgc/Tgc	6/28	0.698156029341041	24	FACETS	1	0.998	1			1	CLONAL	20	TRUE	NA	0.698156029341041	24		433	8971	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678781	52678781	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008777-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	239	454	0	ENST00000394830.3:c.838T>C	p.Phe280Leu	p.F280L	ENST00000394830	NM_018313.4	280	Ttt/Ctt	9/30	1	2	FACETS	0.86	0.806	0.916	0.86	0.806	0.916	CLONAL	1	TRUE	1	0.698156029341041	2		454	796	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0008780-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	60	20	176	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	FALSE	1	0.351402683787931	2		176	80	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0008780-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	22	660	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.711	0.555	0.89	0.711	0.555	0.89	SUBCLONAL	1	FALSE	1	0.351402683787931	2		660	176	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579408	7579430	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGGGCCAGGAGGGGGCTGGTG	CAGGGGCCAGGAGGGGGCTGGTG	-	rs886041861	NA	P-0008780-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	23	427	0	ENST00000269305.4:c.257_279del	p.Ala86ValfsTer55	p.A86Vfs*55	ENST00000269305	NM_001126112.2	86	gCACCAGCCCCCTCCTGGCCCCTG/g	4/11	0.351402683787931	1	FACETS	1	0.846	1	1	0.846	1	CLONAL	1	FALSE	0	0.351402683787931	1		427	100	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026531	48026531	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0008780-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	35	574	0	ENST00000234420.5:c.1409C>G	p.Ser470Ter	p.S470*	ENST00000234420	NM_000179.2	470	tCa/tGa	4/10	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	FALSE	1	0.351402683787931	2		574	155	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048728	180048728	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008780-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	16	472	1	ENST00000261937.6:c.1834A>T	p.Asn612Tyr	p.N612Y	ENST00000261937	NM_182925.4	612	Aac/Tac	13/30	0.351402683787931	1	FACETS	1	0.804	1	1	0.804	1	CLONAL	1	FALSE	0	0.351402683787931	1		473	70	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342496	118342496	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008780-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	33	639	0	ENST00000534358.1:c.622G>C	p.Asp208His	p.D208H	ENST00000534358	NM_005933.3	208	Gat/Cat	3/36	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	FALSE	1	0.351402683787931	2		639	158	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911684	32911687	+	frameshift_variant	Frame_Shift_Del	DEL	AATT	AATT	-	rs80359375	NA	P-0008780-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	31	936	1	ENST00000380152.3:c.3195_3198del	p.Asn1066LeufsTer10	p.N1066Lfs*10	ENST00000380152		1064	tcAATT/tc	11/27	0.230060503697827	1	FACETS	0.724	0.59	0.872	0.724	0.59	0.872	SUBCLONAL	1	FALSE	0	0.351402683787931	1		937	201	SUCCESS
REL	5966	MSKCC	GRCh37	2	61147615	61147615	+	splice_donor_variant	Splice_Site	SNP	T	T	C	rs1453496462	NA	P-0008784-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	47	207	0	ENST00000295025.8:c.1018+2T>C		p.X340_splice	ENST00000295025	NM_002908.2	340			1	2	FACETS	0.762	0.643	0.894	0.762	0.643	0.894	SUBCLONAL	1	TRUE	1	0.239842709532471	2		207	514	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170817081	170817081	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008784-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	35	440	0	ENST00000296930.5:c.85T>G	p.Tyr29Asp	p.Y29D	ENST00000296930	NM_002520.6	29	Tat/Gat	2/11	1	2	FACETS	0.813	0.667	0.976	0.813	0.667	0.976	CLONAL	1	TRUE	1	0.239842709532471	2		440	359	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151181846	151181846	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008784-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	12	645	0	ENST00000262187.5:c.169C>T	p.Gln57Ter	p.Q57*	ENST00000262187	NM_005614.3	57	Caa/Taa	3/8	1	2	FACETS	0.437	0.307	0.597	0.437	0.307	0.597	SUBCLONAL	1	TRUE	1	0.239842709532471	2		645	229	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409488	80409488	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913492	NA	P-0008784-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	13	264	0	ENST00000286548.4:c.626A>T	p.Gln209Leu	p.Q209L	ENST00000286548	NM_002072.3	209	cAa/cTa	5/7	0.216997614331782	1	FACETS	0.852	0.613	1	0.852	0.613	1	CLONAL	1	TRUE	0	0.239842709532471	1		264	112	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778455	3778455	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008784-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	22	438	0	ENST00000262367.5:c.6593T>A	p.Leu2198Gln	p.L2198Q	ENST00000262367	NM_004380.2	2198	cTg/cAg	31/31	0.239842709532471	1	FACETS	0.398	0.307	0.503	0.398	0.307	0.503	SUBCLONAL	1	TRUE	0	0.239842709532471	1		438	406	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750375	39750375	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008784-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	11	371	0	ENST00000361337.2:c.1990G>A	p.Asp664Asn	p.D664N	ENST00000361337	NM_003286.2	664	Gac/Aac	19/21	1	2	FACETS	0.559	0.387	0.772	0.559	0.387	0.772	SUBCLONAL	1	TRUE	1	0.239842709532471	2		371	164	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030585	47030585	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs377667483	NA	P-0008784-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	109	515	1	ENST00000377604.3:c.360T>G	p.Asp120Glu	p.D120E	ENST00000377604	NM_001204468.1	120	gaT/gaG	4/24	1	2	FACETS	0.967	0.867	1	0.967	0.867	1	CLONAL	1	TRUE	1	0.239842709532471	2		516	940	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030585	47030585	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008784-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	50	516	0	ENST00000377604.3:c.360T>A	p.Asp120Glu	p.D120E	ENST00000377604	NM_001204468.1	120	gaT/gaA	4/24	1	2	FACETS	0.444	0.375	0.52	0.444	0.375	0.52	SUBCLONAL	1	TRUE	1	0.239842709532471	2		516	940	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441322	52441339	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTGGCTCGGGCCTGGGGA	GTGGCTCGGGCCTGGGGA	C	novel	NA	P-0008784-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	51	506	0	ENST00000460680.1:c.438-7_448delinsG		p.X146_splice	ENST00000460680	NM_004656.3	146		7/17	0.239842709532471	1	FACETS	1	0.884	1	1	0.884	1	CLONAL	1	TRUE	0	0.239842709532471	1		506	359	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0008789-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	86	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.881	0.783	0.987	0.881	0.783	0.987	CLONAL	1	TRUE	1	0.39985648699274	2		464	488	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720823	89720823	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1114167654	NA	P-0008789-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	89	169	0	ENST00000371953.3:c.974T>G	p.Leu325Arg	p.L325R	ENST00000371953	NM_000314.4	325	cTt/cGt	8/9	0.39985648699274	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.39985648699274	1		169	265	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0008834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	182	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.670630251107863	2		464	475	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0008834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	55	263	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.837	0.727	0.953	0.837	0.727	0.953	CLONAL	1	TRUE	1	0.670630251107863	2		263	196	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0008834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	171	595	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.670630251107863	2		595	408	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716156	243716156	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	141	410	0	ENST00000263826.5:c.1038C>G	p.Phe346Leu	p.F346L	ENST00000263826	NM_005465.4	346	ttC/ttG	10/13	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.670630251107863	2		410	417	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440359	52440359	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	132	208	1	ENST00000460680.1:c.693G>T	p.Met231Ile	p.M231I	ENST00000460680	NM_004656.3	231	atG/atT	9/17	1	2	FACETS	0.739	0.674	0.806	0.739	0.674	0.806	SUBCLONAL	1	TRUE	1	0.670630251107863	2		209	533	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441262	52441262	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	302	320	0	ENST00000460680.1:c.508T>C	p.Phe170Leu	p.F170L	ENST00000460680	NM_004656.3	170	Ttt/Ctt	7/17	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.670630251107863	2		320	785	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017552	112017552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373817482	NA	P-0008834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	101	492	1	ENST00000368678.4:c.961G>A	p.Asp321Asn	p.D321N	ENST00000368678		321	Gac/Aac	9/13	1	2	FACETS	0.309	0.276	0.345	0.309	0.276	0.345	SUBCLONAL	1	TRUE	1	0.670630251107863	2		493	974	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151866283	151866283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	31	290	0	ENST00000262189.6:c.9505C>T	p.Pro3169Ser	p.P3169S	ENST00000262189	NM_170606.2	3169	Cca/Tca	41/59	1	2	FACETS	0.26	0.21	0.316	0.26	0.21	0.316	SUBCLONAL	1	TRUE	1	0.670630251107863	2		290	356	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336422	80336422	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs374303316	NA	P-0008834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	44	198	0	ENST00000286548.4:c.897G>C	p.Gln299His	p.Q299H	ENST00000286548	NM_002072.3	299	caG/caC	7/7	0.670630251107863	1	FACETS	0.328	0.277	0.384	0.328	0.277	0.384	SUBCLONAL	1	TRUE	0	0.670630251107863	1		198	266	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139268	108139268	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55723361	NA	P-0008834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	144	332	1	ENST00000278616.4:c.2770C>T	p.Arg924Trp	p.R924W	ENST00000278616	NM_000051.3	924	Cgg/Tgg	18/63	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.670630251107863	2		333	412	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3823915	3823915	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	223	279	0	ENST00000262367.5:c.2300C>A	p.Ser767Tyr	p.S767Y	ENST00000262367	NM_004380.2	767	tCc/tAc	13/31	0.181890589542939	1	FACETS	0.681	0.638	0.726	0.681	0.638	0.726	INDETERMINATE	1	TRUE	0	0.670630251107863	1		279	649	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578270	7578270	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	262	301	0	ENST00000269305.4:c.579T>A	p.His193Gln	p.H193Q	ENST00000269305	NM_001126112.2	193	caT/caA	6/11	0.670630251107863	1	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	0	0.670630251107863	1		301	499	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245465	41245465	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28897681	NA	P-0008834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	47	492	1	ENST00000357654.3:c.2083G>A	p.Asp695Asn	p.D695N	ENST00000357654	NM_007294.3	695	Gat/Aat	10/23	1	2	FACETS	0.236	0.198	0.277	0.236	0.198	0.277	SUBCLONAL	1	TRUE	1	0.670630251107863	2		493	595	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs371769427	NA	P-0008834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	113	329	1	ENST00000291552.4:c.101C>A	p.Ser34Tyr	p.S34Y	ENST00000291552	NM_006758.2	34	tCt/tAt	2/8	1	2	FACETS	0.731	0.662	0.803	0.731	0.662	0.803	SUBCLONAL	1	TRUE	1	0.670630251107863	2		330	461	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574216	41574216	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	234	351	0	ENST00000263253.7:c.6501G>C	p.Gln2167His	p.Q2167H	ENST00000263253	NM_001429.3	2167	caG/caC	31/31	1	2	FACETS	0.973	0.912	1	0.973	0.912	1	CLONAL	1	TRUE	1	0.670630251107863	2		351	717	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412773	63412773	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	261	204	0	ENST00000330258.3:c.394A>G	p.Ser132Gly	p.S132G	ENST00000330258	NM_152424.3	132	Agt/Ggt	2/2	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.670630251107863	1		204	382	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929322	44929325	+	frameshift_variant	Frame_Shift_Del	DEL	CATA	CATA	-	novel	NA	P-0008834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	247	233	0	ENST00000377967.4:c.2424_2427del	p.His808GlnfsTer58	p.H808Qfs*58	ENST00000377967	NM_021140.2	808	CATAca/ca	17/29	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.670630251107863	1		233	363	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045540	47045540	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	238	165	0	ENST00000377604.3:c.2508del	p.Lys837SerfsTer10	p.K837Sfs*10	ENST00000377604	NM_001204468.1	836	aGg/ag	22/24	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.670630251107863	1		165	352	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652043	36652044	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGACACCACTGGAGG	novel	NA	P-0008834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	96	246	0	ENST00000244741.5:c.167_182dup	p.Phe63ThrfsTer5	p.F63Tfs*5	ENST00000244741	NM_000389.4	55	-/GAGACACCACTGGAGG	2/3	0.165652202933803	2	FACETS	0.388	0.345	0.433	0.194	0.172	0.217	INDETERMINATE	1	TRUE	0	0.670630251107863	2		246	738	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588173	69588173	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008834-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	641	441	0	ENST00000168712.1:c.525del	p.Gly176AlafsTer6	p.G176Afs*6	ENST00000168712	NM_002007.2	175	ccC/cc	3/3	0.398889144199498	3	FACETS	0.95	0.918	0.983	0.95	0.918	0.983	INDETERMINATE	2	TRUE	1	0.670630251107863	3		441	1343	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	129	464	0				ENST00000310581	NM_198253.2	-/1132			0.76946618519604	3	FACETS	1	0.958	1	0.539	0.493	0.587	CLONAL	1	TRUE	1	0.778438552284457	3		464	427	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245843	46245843	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	245	421	1	ENST00000334344.6:c.3937C>T	p.Gln1313Ter	p.Q1313*	ENST00000334344	NM_152641.2	1313	Caa/Taa	15/21	NA	2	FACETS	0.985	0.927	1			1	INDETERMINATE	1	TRUE	NA	0.778438552284457	2		422	639	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295786	212295786	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751446160	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	186	505	0	ENST00000342788.4:c.2527G>A	p.Asp843Asn	p.D843N	ENST00000342788	NM_005235.2	843	Gat/Aat	21/28	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.778438552284457	2		505	433	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38942984	38942984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs77464125	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	319	464	1	ENST00000357387.3:c.5003C>T	p.Pro1668Leu	p.P1668L	ENST00000357387	NM_152756.3	1668	cCg/cTg	37/38	0.76946618519604	3	FACETS	1	0.979	1	0.536	0.506	0.566	CLONAL	1	TRUE	1	0.778438552284457	3		465	1062	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913255	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	206	452	0	ENST00000369535.4:c.183A>T	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caT	3/7	1	2	FACETS	0.933	0.872	0.996	0.933	0.872	0.996	CLONAL	1	TRUE	1	0.778438552284457	2		452	567	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662582	117662582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	138	521	0	ENST00000368508.3:c.4883G>A	p.Gly1628Glu	p.G1628E	ENST00000368508	NM_002944.2	1628	gGa/gAa	29/43	1	2	FACETS	0.926	0.852	1	0.926	0.852	1	CLONAL	1	TRUE	1	0.778438552284457	2		521	383	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753194	128753194	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	394	284	0	ENST00000377970.2:c.1355C>T	p.Ser452Phe	p.S452F	ENST00000377970	NM_002467.4	452	tCt/tTt	3/3	0.608111403833687	3	FACETS	1	0.979	1			1	CLONAL	2	TRUE	NA	0.778438552284457	3		284	684	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601310	28601310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	349	569	0	ENST00000241453.7:c.2122G>A	p.Glu708Lys	p.E708K	ENST00000241453	NM_004119.2	708	Gaa/Aaa	17/24	0.76946618519604	3	FACETS	1	0.974	1	0.523	0.495	0.552	CLONAL	1	TRUE	1	0.778438552284457	3		569	1190	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298225	123298225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	211	305	0	ENST00000358487.5:c.629G>A	p.Arg210Gln	p.R210Q	ENST00000358487	NM_000141.4	210	cGa/cAa	6/18	1	2	FACETS	0.97	0.908	1	0.97	0.908	1	CLONAL	1	TRUE	1	0.778438552284457	2		305	559	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975495	13975495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1003578447	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	167	268	0	ENST00000405192.2:c.392G>A	p.Gly131Glu	p.G131E	ENST00000405192	NM_001163147.1	131	gGa/gAa	7/12	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.778438552284457	2		268	420	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008201	29008201	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	379	412	1	ENST00000282397.4:c.670C>T	p.Arg224Ter	p.R224*	ENST00000282397	NM_002019.4	224	Cga/Tga	5/30	0.76946618519604	3	FACETS	0.986	0.945	1	0.986	0.945	1	CLONAL	2	TRUE	1	0.778438552284457	3		413	686	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543829	212543829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771154734	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	304	347	0	ENST00000342788.4:c.1570C>T	p.Arg524Cys	p.R524C	ENST00000342788	NM_005235.2	524	Cgc/Tgc	13/28	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.778438552284457	2		347	757	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027385	48027385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	159	409	1	ENST00000234420.5:c.2263G>A	p.Glu755Lys	p.E755K	ENST00000234420	NM_000179.2	755	Gaa/Aaa	4/10	1	2	FACETS	0.92	0.852	0.99	0.92	0.852	0.99	CLONAL	1	TRUE	1	0.778438552284457	2		410	444	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61753575	61753575	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	370	579	0	ENST00000401558.2:c.208T>C	p.Ser70Pro	p.S70P	ENST00000401558	NM_003400.3	70	Tct/Cct	3/25	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.778438552284457	2		579	828	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627263	12627263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	361	533	0	ENST00000251849.4:c.1453G>A	p.Gly485Arg	p.G485R	ENST00000251849	NM_002880.3	485	Gga/Aga	14/17	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.778438552284457	2		533	893	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277237	41277237	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	180	423	0	ENST00000349496.5:c.1706T>C	p.Ile569Thr	p.I569T	ENST00000349496	NM_001904.3	569	aTa/aCa	11/15	1	2	FACETS	0.936	0.871	1	0.936	0.871	1	CLONAL	1	TRUE	1	0.778438552284457	2		423	494	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940148	49940148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	417	552	2	ENST00000296474.3:c.895G>A	p.Asp299Asn	p.D299N	ENST00000296474	NM_002447.2	299	Gac/Aac	1/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.778438552284457	2		554	993	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428194	72428194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	250	528	0	ENST00000477973.2:c.698C>T	p.Ser233Leu	p.S233L	ENST00000477973	NM_012234.5	233	tCa/tTa	3/4	1	2	FACETS	0.926	0.87	0.982	0.926	0.87	0.982	CLONAL	1	TRUE	1	0.778438552284457	2		528	694	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140786	55140786	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs747156883	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	303	454	1	ENST00000257290.5:c.1647G>A	p.Trp549Ter	p.W549*	ENST00000257290	NM_006206.4	549	tgG/tgA	11/23	1	2	FACETS	0.918	0.868	0.969	0.918	0.868	0.969	CLONAL	1	TRUE	1	0.778438552284457	2		455	848	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874636	35874636	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	239	530	2	ENST00000303115.3:c.792G>A	p.Trp264Ter	p.W264*	ENST00000303115	NM_002185.3	264	tgG/tgA	6/8	0.76946618519604	3	FACETS	1	0.95	1	0.508	0.476	0.542	CLONAL	1	TRUE	1	0.778438552284457	3		532	839	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633834	86633834	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	605	585	0	ENST00000274376.6:c.943G>A	p.Asp315Asn	p.D315N	ENST00000274376	NM_002890.2	315	Gat/Aat	5/25	0.76946618519604	3	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	1	0.778438552284457	3		585	1077	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674329	117674329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	220	403	0	ENST00000368508.3:c.4145G>A	p.Gly1382Glu	p.G1382E	ENST00000368508	NM_002944.2	1382	gGa/gAa	26/43	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.778438552284457	2		403	540	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985534	2985534	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	310	645	1	ENST00000396946.4:c.277G>A	p.Glu93Lys	p.E93K	ENST00000396946	NM_032415.4	93	Gag/Aag	4/25	1	2	FACETS	0.941	0.891	0.992	0.941	0.891	0.992	CLONAL	1	TRUE	1	0.778438552284457	2		646	846	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741225	145741225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	694	545	1	ENST00000428558.2:c.1181G>A	p.Gly394Asp	p.G394D	ENST00000428558	NM_004260.3	394	gGt/gAt	6/22	0.608111403833687	3	FACETS	0.968	0.939	0.998			1	CLONAL	2	TRUE	NA	0.778438552284457	3		546	1279	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449832	8449832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	126	289	0	ENST00000356435.5:c.3881G>A	p.Arg1294Lys	p.R1294K	ENST00000356435		1294	aGg/aAg	23/35	1	2	FACETS	0.996	0.915	1	0.996	0.915	1	CLONAL	1	TRUE	1	0.778438552284457	2		289	325	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518342	8518342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	176	308	0	ENST00000356435.5:c.1049C>T	p.Pro350Leu	p.P350L	ENST00000356435		350	cCt/cTt	10/35	1	2	FACETS	0.977	0.909	1	0.977	0.909	1	CLONAL	1	TRUE	1	0.778438552284457	2		308	463	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298199	123298199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	276	365	0	ENST00000358487.5:c.655G>A	p.Glu219Lys	p.E219K	ENST00000358487	NM_000141.4	219	Gaa/Aaa	6/18	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.778438552284457	2		365	709	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999512	100999512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	408	607	0	ENST00000325455.5:c.290G>A	p.Gly97Glu	p.G97E	ENST00000325455	NM_001202474.3	97	gGa/gAa	1/8	1	2	FACETS	0.979	0.934	1	0.979	0.934	1	CLONAL	1	TRUE	1	0.778438552284457	2		607	1071	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434077	121434077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	351	447	0	ENST00000257555.6:c.968G>A	p.Gly323Glu	p.G323E	ENST00000257555		323	gGa/gAa	5/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.778438552284457	2		447	868	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240616	133240616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	396	479	0	ENST00000320574.5:c.2680G>A	p.Gly894Ser	p.G894S	ENST00000320574	NM_006231.2	894	Ggc/Agc	23/49	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.778438552284457	2		479	919	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472522	88472522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55890138	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	381	455	2	ENST00000360948.2:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000360948	NM_001012338.2	678	cGa/cAa	16/19	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.778438552284457	2		457	838	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476382	88476382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	215	315	0	ENST00000360948.2:c.1750G>A	p.Asp584Asn	p.D584N	ENST00000360948	NM_001012338.2	584	Gat/Aat	15/19	1	2	FACETS	0.938	0.878	0.999	0.938	0.878	0.999	CLONAL	1	TRUE	1	0.778438552284457	2		315	589	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454591	99454591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768988732	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	366	484	1	ENST00000268035.6:c.1510C>T	p.Arg504Cys	p.R504C	ENST00000268035	NM_000875.3	504	Cgc/Tgc	7/21	1	2	FACETS	0.992	0.944	1	0.992	0.944	1	CLONAL	1	TRUE	1	0.778438552284457	2		485	948	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222317	2222317	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	520	411	0	ENST00000326181.6:c.601C>T	p.Pro201Ser	p.P201S	ENST00000326181	NM_032271.2	201	Ccc/Tcc	8/21	0.76946618519604	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.778438552284457	3		411	912	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81914540	81914540	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770601419	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	514	775	1	ENST00000359376.3:c.674C>T	p.Ser225Leu	p.S225L	ENST00000359376	NM_002661.3	225	tCg/tTg	8/33	0.778438552284457	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.778438552284457	1		776	755	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528054	29528054	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	122	69	0	ENST00000356175.3:c.1063-1G>A		p.X355_splice	ENST00000356175	NM_000267.3	355			0.778438552284457	3	FACETS	1	0.988	1	1	0.988	1	CLONAL	3	TRUE	0	0.778438552284457	3		69	134	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868193	37868193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	585	407	1	ENST00000269571.5:c.914C>T	p.Ser305Phe	p.S305F	ENST00000269571		305	tCt/tTt	8/27	0.778438552284457	3	FACETS	1	0.984	1	0.685	0.663	0.707	CLONAL	2	TRUE	0	0.778438552284457	3		408	1016	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581232	48581232	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	274	439	0	ENST00000342988.3:c.536T>G	p.Ile179Ser	p.I179S	ENST00000342988	NM_005359.5	179	aTt/aGt	5/12	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.778438552284457	2		439	694	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355272	15355272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1357419013	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	56	96	0	ENST00000263377.2:c.2351C>T	p.Ser784Phe	p.S784F	ENST00000263377	NM_058243.2	784	tCc/tTc	13/20	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.778438552284457	2		96	140	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794445	42794445	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	449	571	0	ENST00000575354.2:c.1525C>T	p.Pro509Ser	p.P509S	ENST00000575354	NM_015125.3	509	Cca/Tca	10/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.778438552284457	2		571	1133	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024077	31024077	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	310	411	1	ENST00000375687.4:c.3562C>T	p.Leu1188Phe	p.L1188F	ENST00000375687	NM_015338.5	1188	Ctt/Ttt	13/13	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.778438552284457	2		412	721	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790090	40790090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1201649058	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	211	344	0	ENST00000373198.4:c.2641C>T	p.Arg881Trp	p.R881W	ENST00000373198	NM_133170.3	881	Cgg/Tgg	18/32	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.778438552284457	2		344	526	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514518	41514518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	311	464	2	ENST00000373198.4:c.143G>A	p.Gly48Glu	p.G48E	ENST00000373198	NM_133170.3	48	gGg/gAg	2/32	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.778438552284457	2		466	735	SUCCESS
AR	367	MSKCC	GRCh37	X	66863224	66863224	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	250	544	0	ENST00000374690.3:c.1743G>C	p.Lys581Asn	p.K581N	ENST00000374690	NM_000044.3	581	aaG/aaC	2/8	1	2	FACETS	0.912	0.858	0.968	0.912	0.858	0.968	CLONAL	1	TRUE	1	0.778438552284457	2		544	704	SUCCESS
AR	367	MSKCC	GRCh37	X	66942680	66942680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	487	701	2	ENST00000374690.3:c.2461G>A	p.Gly821Arg	p.G821R	ENST00000374690	NM_000044.3	821	Ggg/Agg	7/8	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.778438552284457	2		703	1125	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349933	70349933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	386	540	0	ENST00000374080.3:c.3916G>A	p.Asp1306Asn	p.D1306N	ENST00000374080		1306	Gac/Aac	28/45	1	2	FACETS	0.977	0.931	1	0.977	0.931	1	CLONAL	1	TRUE	1	0.778438552284457	2		540	1015	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76953090	76953090	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	232	639	0	ENST00000373344.5:c.223G>A	p.Gly75Arg	p.G75R	ENST00000373344	NM_000489.3	75	Gga/Aga	4/35	NA	2	FACETS	0.963	0.904	1			1	INDETERMINATE	1	TRUE	NA	0.778438552284457	2		639	619	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224587	123224587	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	268	620	0	ENST00000218089.9:c.3440A>T	p.Glu1147Val	p.E1147V	ENST00000218089	NM_001042749.1	1147	gAa/gTa	31/35	NA	2	FACETS	0.978	0.923	1			1	INDETERMINATE	1	TRUE	NA	0.778438552284457	2		620	704	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342972	225342972	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	305	708	0	ENST00000264414.4:c.2120del	p.Ile707LysfsTer4	p.I707Kfs*4	ENST00000264414	NM_003590.4	707	aTa/aa	15/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.778438552284457	2		708	717	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2972201	2972202	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	244	413	1	ENST00000396946.4:c.1537_1538delinsTT	p.Pro513Phe	p.P513F	ENST00000396946	NM_032415.4	513	CCc/TTc	11/25	1	2	FACETS	0.973	0.916	1	0.973	0.916	1	CLONAL	1	TRUE	1	0.778438552284457	2		414	644	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511039	148511103	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTGTTGCTCACCTTTTTGGAGCCCCGCTGAATACTGCAGTTCTTGCAGGACACATTTTTACTGT	CTTGTTGCTCACCTTTTTGGAGCCCCGCTGAATACTGCAGTTCTTGCAGGACACATTTTTACTGT	G	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	162	278	0	ENST00000320356.2:c.1799_1851+12delinsC		p.X600_splice	ENST00000320356	NM_004456.4	600		15/20	1	2	FACETS	0.915	0.847	0.984	0.915	0.847	0.984	CLONAL	1	TRUE	1	0.778438552284457	2		278	455	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705250	52705251	+	stop_gained	Nonsense_Mutation	DNP	TG	TG	GT	novel	NA	P-0008857-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	345	534	1	ENST00000322088.6:c.132_133delinsGT	p.Glu45Ter	p.E45*	ENST00000322088	NM_014225.5	44	gtTGaa/gtGTaa	2/15	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.778438552284457	2		535	872	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	65	464	0				ENST00000310581	NM_198253.2	-/1132			0.384389944577967	3	FACETS	0.702	0.61	0.802	0.351	0.305	0.401	SUBCLONAL	1	TRUE	1	0.459141340266227	3		464	496	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245843	46245843	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	166	421	1	ENST00000334344.6:c.3937C>T	p.Gln1313Ter	p.Q1313*	ENST00000334344	NM_152641.2	1313	Caa/Taa	15/21	1	2	FACETS	0.718	0.659	0.78	0.718	0.659	0.78	SUBCLONAL	1	TRUE	1	0.459141340266227	2		422	1007	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295786	212295786	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751446160	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	189	505	0	ENST00000342788.4:c.2527G>A	p.Asp843Asn	p.D843N	ENST00000342788	NM_005235.2	843	Gat/Aat	21/28	1	2	FACETS	0.809	0.747	0.873	0.809	0.747	0.873	CLONAL	1	TRUE	1	0.459141340266227	2		505	1018	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38942984	38942984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs77464125	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	199	464	1	ENST00000357387.3:c.5003C>T	p.Pro1668Leu	p.P1668L	ENST00000357387	NM_152756.3	1668	cCg/cTg	37/38	0.384389944577967	3	FACETS	0.835	0.771	0.9	0.417	0.385	0.45	CLONAL	1	TRUE	1	0.459141340266227	3		465	1277	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs121913255	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	204	452	0	ENST00000369535.4:c.183A>T	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caT	3/7	1	2	FACETS	0.762	0.706	0.821	0.762	0.706	0.821	SUBCLONAL	1	TRUE	1	0.459141340266227	2		452	1166	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662582	117662582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	177	521	0	ENST00000368508.3:c.4883G>A	p.Gly1628Glu	p.G1628E	ENST00000368508	NM_002944.2	1628	gGa/gAa	29/43	1	2	FACETS	0.751	0.692	0.814	0.751	0.692	0.814	SUBCLONAL	1	TRUE	1	0.459141340266227	2		521	1026	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753194	128753194	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	291	284	0	ENST00000377970.2:c.1355C>T	p.Ser452Phe	p.S452F	ENST00000377970	NM_002467.4	452	tCt/tTt	3/3	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.459141340266227	2		284	926	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601310	28601310	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1197	184	569	0	ENST00000241453.7:c.2122G>A	p.Glu708Lys	p.E708K	ENST00000241453	NM_004119.2	708	Gaa/Aaa	17/24	0.384389944577967	3	FACETS	0.714	0.657	0.773	0.357	0.328	0.387	SUBCLONAL	1	TRUE	1	0.459141340266227	3		569	1381	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298225	123298225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	103	305	0	ENST00000358487.5:c.629G>A	p.Arg210Gln	p.R210Q	ENST00000358487	NM_000141.4	210	cGa/cAa	6/18	1	2	FACETS	0.662	0.593	0.735	0.662	0.593	0.735	SUBCLONAL	1	TRUE	1	0.459141340266227	2		305	678	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975495	13975495	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1003578447	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	137	268	0	ENST00000405192.2:c.392G>A	p.Gly131Glu	p.G131E	ENST00000405192	NM_001163147.1	131	gGa/gAa	7/12	1	2	FACETS	0.95	0.867	1	0.95	0.867	1	CLONAL	1	TRUE	1	0.459141340266227	2		268	628	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29008201	29008201	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	311	412	1	ENST00000282397.4:c.670C>T	p.Arg224Ter	p.R224*	ENST00000282397	NM_002019.4	224	Cga/Tga	5/30	0.384389944577967	3	FACETS	0.762	0.719	0.806	0.762	0.719	0.806	SUBCLONAL	2	TRUE	1	0.459141340266227	3		413	1093	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543829	212543829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771154734	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	180	347	0	ENST00000342788.4:c.1570C>T	p.Arg524Cys	p.R524C	ENST00000342788	NM_005235.2	524	Cgc/Tgc	13/28	1	2	FACETS	0.839	0.774	0.907	0.839	0.774	0.907	CLONAL	1	TRUE	1	0.459141340266227	2		347	934	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027385	48027385	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	174	409	1	ENST00000234420.5:c.2263G>A	p.Glu755Lys	p.E755K	ENST00000234420	NM_000179.2	755	Gaa/Aaa	4/10	1	2	FACETS	0.785	0.722	0.85	0.785	0.722	0.85	SUBCLONAL	1	TRUE	1	0.459141340266227	2		410	966	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61753575	61753575	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	211	579	0	ENST00000401558.2:c.208T>C	p.Ser70Pro	p.S70P	ENST00000401558	NM_003400.3	70	Tct/Cct	3/25	1	2	FACETS	0.734	0.68	0.79	0.734	0.68	0.79	SUBCLONAL	1	TRUE	1	0.459141340266227	2		579	1252	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627263	12627263	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	210	533	0	ENST00000251849.4:c.1453G>A	p.Gly485Arg	p.G485R	ENST00000251849	NM_002880.3	485	Gga/Aga	14/17	1	2	FACETS	0.71	0.658	0.765	0.71	0.658	0.765	SUBCLONAL	1	TRUE	1	0.459141340266227	2		533	1288	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277237	41277237	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	215	423	0	ENST00000349496.5:c.1706T>C	p.Ile569Thr	p.I569T	ENST00000349496	NM_001904.3	569	aTa/aCa	11/15	1	2	FACETS	0.849	0.789	0.912	0.849	0.789	0.912	CLONAL	1	TRUE	1	0.459141340266227	2		423	1103	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940148	49940148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	262	552	2	ENST00000296474.3:c.895G>A	p.Asp299Asn	p.D299N	ENST00000296474	NM_002447.2	299	Gac/Aac	1/20	1	2	FACETS	0.992	0.929	1	0.992	0.929	1	CLONAL	1	TRUE	1	0.459141340266227	2		554	1151	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72428194	72428194	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	299	528	0	ENST00000477973.2:c.698C>T	p.Ser233Leu	p.S233L	ENST00000477973	NM_012234.5	233	tCa/tTa	3/4	1	2	FACETS	0.882	0.829	0.937	0.882	0.829	0.937	CLONAL	1	TRUE	1	0.459141340266227	2		528	1477	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140786	55140786	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs747156883	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	181	454	1	ENST00000257290.5:c.1647G>A	p.Trp549Ter	p.W549*	ENST00000257290	NM_006206.4	549	tgG/tgA	11/23	1	2	FACETS	0.771	0.71	0.834	0.771	0.71	0.834	SUBCLONAL	1	TRUE	1	0.459141340266227	2		455	1023	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874636	35874636	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1243	207	530	2	ENST00000303115.3:c.792G>A	p.Trp264Ter	p.W264*	ENST00000303115	NM_002185.3	264	tgG/tgA	6/8	0.384389944577967	3	FACETS	0.765	0.707	0.824	0.382	0.353	0.412	SUBCLONAL	1	TRUE	1	0.459141340266227	3		532	1450	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633834	86633834	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	432	585	0	ENST00000274376.6:c.943G>A	p.Asp315Asn	p.D315N	ENST00000274376	NM_002890.2	315	Gat/Aat	5/25	0.384389944577967	3	FACETS	0.811	0.772	0.85	0.811	0.772	0.85	CLONAL	2	TRUE	1	0.459141340266227	3		585	1427	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674329	117674329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	164	403	0	ENST00000368508.3:c.4145G>A	p.Gly1382Glu	p.G1382E	ENST00000368508	NM_002944.2	1382	gGa/gAa	26/43	1	2	FACETS	0.727	0.667	0.79	0.727	0.667	0.79	SUBCLONAL	1	TRUE	1	0.459141340266227	2		403	982	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985534	2985534	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	215	645	1	ENST00000396946.4:c.277G>A	p.Glu93Lys	p.E93K	ENST00000396946	NM_032415.4	93	Gag/Aag	4/25	1	2	FACETS	0.813	0.755	0.873	0.813	0.755	0.873	CLONAL	1	TRUE	1	0.459141340266227	2		646	1152	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741225	145741225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	435	545	1	ENST00000428558.2:c.1181G>A	p.Gly394Asp	p.G394D	ENST00000428558	NM_004260.3	394	gGt/gAt	6/22	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	1	0.459141340266227	2		546	1387	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8449832	8449832	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	111	289	0	ENST00000356435.5:c.3881G>A	p.Arg1294Lys	p.R1294K	ENST00000356435		1294	aGg/aAg	23/35	1	2	FACETS	0.671	0.603	0.742	0.671	0.603	0.742	SUBCLONAL	1	TRUE	1	0.459141340266227	2		289	721	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518342	8518342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	133	308	0	ENST00000356435.5:c.1049C>T	p.Pro350Leu	p.P350L	ENST00000356435		350	cCt/cTt	10/35	1	2	FACETS	0.793	0.721	0.868	0.793	0.721	0.868	SUBCLONAL	1	TRUE	1	0.459141340266227	2		308	731	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298199	123298199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	141	365	0	ENST00000358487.5:c.655G>A	p.Glu219Lys	p.E219K	ENST00000358487	NM_000141.4	219	Gaa/Aaa	6/18	1	2	FACETS	0.681	0.62	0.745	0.681	0.62	0.745	SUBCLONAL	1	TRUE	1	0.459141340266227	2		365	902	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999512	100999512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	228	607	0	ENST00000325455.5:c.290G>A	p.Gly97Glu	p.G97E	ENST00000325455	NM_001202474.3	97	gGa/gAa	1/8	1	2	FACETS	0.779	0.724	0.835	0.779	0.724	0.835	SUBCLONAL	1	TRUE	1	0.459141340266227	2		607	1275	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121434077	121434077	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	171	447	0	ENST00000257555.6:c.968G>A	p.Gly323Glu	p.G323E	ENST00000257555		323	gGa/gAa	5/10	1	2	FACETS	0.733	0.674	0.795	0.733	0.674	0.795	SUBCLONAL	1	TRUE	1	0.459141340266227	2		447	1016	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240616	133240616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	182	479	0	ENST00000320574.5:c.2680G>A	p.Gly894Ser	p.G894S	ENST00000320574	NM_006231.2	894	Ggc/Agc	23/49	1	2	FACETS	0.742	0.684	0.803	0.742	0.684	0.803	SUBCLONAL	1	TRUE	1	0.459141340266227	2		479	1068	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472522	88472522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55890138	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	186	455	2	ENST00000360948.2:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000360948	NM_001012338.2	678	cGa/cAa	16/19	1	2	FACETS	0.805	0.743	0.869	0.805	0.743	0.869	CLONAL	1	TRUE	1	0.459141340266227	2		457	1007	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476382	88476382	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	131	315	0	ENST00000360948.2:c.1750G>A	p.Asp584Asn	p.D584N	ENST00000360948	NM_001012338.2	584	Gat/Aat	15/19	1	2	FACETS	0.775	0.704	0.85	0.775	0.704	0.85	SUBCLONAL	1	TRUE	1	0.459141340266227	2		315	736	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99454591	99454591	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768988732	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	195	484	1	ENST00000268035.6:c.1510C>T	p.Arg504Cys	p.R504C	ENST00000268035	NM_000875.3	504	Cgc/Tgc	7/21	1	2	FACETS	0.707	0.653	0.763	0.707	0.653	0.763	SUBCLONAL	1	TRUE	1	0.459141340266227	2		485	1201	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222317	2222317	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	296	411	0	ENST00000326181.6:c.601C>T	p.Pro201Ser	p.P201S	ENST00000326181	NM_032271.2	201	Ccc/Tcc	8/21	0.384389944577967	3	FACETS	0.826	0.779	0.874	0.826	0.779	0.874	CLONAL	2	TRUE	1	0.459141340266227	3		411	960	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81914540	81914540	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770601419	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	288	775	1	ENST00000359376.3:c.674C>T	p.Ser225Leu	p.S225L	ENST00000359376	NM_002661.3	225	tCg/tTg	8/33	0.459141340266227	1	FACETS	0.755	0.709	0.802	0.755	0.709	0.802	SUBCLONAL	1	TRUE	0	0.459141340266227	1		776	1280	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528054	29528054	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	97	69	0	ENST00000356175.3:c.1063-1G>A		p.X355_splice	ENST00000356175	NM_000267.3	355			0.379580859766035	3	FACETS	0.931	0.854	1	0.931	0.854	1	CLONAL	3	TRUE	0	0.459141340266227	3		69	186	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868193	37868193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	320	407	1	ENST00000269571.5:c.914C>T	p.Ser305Phe	p.S305F	ENST00000269571		305	tCt/tTt	8/27	0.379580859766035	3	FACETS	0.758	0.715	0.801	0.505	0.477	0.534	SUBCLONAL	2	TRUE	0	0.459141340266227	3		408	1131	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581232	48581232	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	211	439	0	ENST00000342988.3:c.536T>G	p.Ile179Ser	p.I179S	ENST00000342988	NM_005359.5	179	aTt/aGt	5/12	1	2	FACETS	0.81	0.751	0.871	0.81	0.751	0.871	CLONAL	1	TRUE	1	0.459141340266227	2		439	1135	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355272	15355272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1357419013	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	33	96	0	ENST00000263377.2:c.2351C>T	p.Ser784Phe	p.S784F	ENST00000263377	NM_058243.2	784	tCc/tTc	13/20	1	2	FACETS	0.745	0.612	0.891	0.745	0.612	0.891	SUBCLONAL	1	TRUE	1	0.459141340266227	2		96	193	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794445	42794445	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	277	571	0	ENST00000575354.2:c.1525C>T	p.Pro509Ser	p.P509S	ENST00000575354	NM_015125.3	509	Cca/Tca	10/20	1	2	FACETS	0.964	0.904	1	0.964	0.904	1	CLONAL	1	TRUE	1	0.459141340266227	2		571	1252	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024077	31024077	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	183	411	1	ENST00000375687.4:c.3562C>T	p.Leu1188Phe	p.L1188F	ENST00000375687	NM_015338.5	1188	Ctt/Ttt	13/13	1	2	FACETS	0.9	0.831	0.971	0.9	0.831	0.971	CLONAL	1	TRUE	1	0.459141340266227	2		412	886	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790090	40790090	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1201649058	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	114	344	0	ENST00000373198.4:c.2641C>T	p.Arg881Trp	p.R881W	ENST00000373198	NM_133170.3	881	Cgg/Tgg	18/32	1	2	FACETS	0.645	0.581	0.713	0.645	0.581	0.713	SUBCLONAL	1	TRUE	1	0.459141340266227	2		344	770	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514518	41514518	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	217	464	2	ENST00000373198.4:c.143G>A	p.Gly48Glu	p.G48E	ENST00000373198	NM_133170.3	48	gGg/gAg	2/32	1	2	FACETS	0.866	0.804	0.929	0.866	0.804	0.929	CLONAL	1	TRUE	1	0.459141340266227	2		466	1092	SUCCESS
AR	367	MSKCC	GRCh37	X	66863224	66863224	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	209	544	0	ENST00000374690.3:c.1743G>C	p.Lys581Asn	p.K581N	ENST00000374690	NM_000044.3	581	aaG/aaC	2/8	1	2	FACETS	0.832	0.772	0.895	0.832	0.772	0.895	CLONAL	1	TRUE	1	0.459141340266227	2		544	1094	SUCCESS
AR	367	MSKCC	GRCh37	X	66942680	66942680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1126	283	701	2	ENST00000374690.3:c.2461G>A	p.Gly821Arg	p.G821R	ENST00000374690	NM_000044.3	821	Ggg/Agg	7/8	1	2	FACETS	0.875	0.821	0.931	0.875	0.821	0.931	CLONAL	1	TRUE	1	0.459141340266227	2		703	1409	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349933	70349933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	185	540	0	ENST00000374080.3:c.3916G>A	p.Asp1306Asn	p.D1306N	ENST00000374080		1306	Gac/Aac	28/45	1	2	FACETS	0.688	0.634	0.744	0.688	0.634	0.744	SUBCLONAL	1	TRUE	1	0.459141340266227	2		540	1172	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76953090	76953090	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	224	639	0	ENST00000373344.5:c.223G>A	p.Gly75Arg	p.G75R	ENST00000373344	NM_000489.3	75	Gga/Aga	4/35	1	2	FACETS	0.722	0.67	0.775	0.722	0.67	0.775	SUBCLONAL	1	TRUE	1	0.459141340266227	2		639	1352	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224587	123224587	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1203	229	620	0	ENST00000218089.9:c.3440A>T	p.Glu1147Val	p.E1147V	ENST00000218089	NM_001042749.1	1147	gAa/gTa	31/35	1	2	FACETS	0.697	0.647	0.748	0.697	0.647	0.748	SUBCLONAL	1	TRUE	1	0.459141340266227	2		620	1432	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342972	225342972	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1325	260	708	0	ENST00000264414.4:c.2120del	p.Ile707LysfsTer4	p.I707Kfs*4	ENST00000264414	NM_003590.4	707	aTa/aa	15/16	1	2	FACETS	0.715	0.667	0.764	0.715	0.667	0.764	SUBCLONAL	1	TRUE	1	0.459141340266227	2		708	1585	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2972201	2972202	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	135	413	1	ENST00000396946.4:c.1537_1538delinsTT	p.Pro513Phe	p.P513F	ENST00000396946	NM_032415.4	513	CCc/TTc	11/25	1	2	FACETS	0.652	0.592	0.715	0.652	0.592	0.715	SUBCLONAL	1	TRUE	1	0.459141340266227	2		414	902	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511039	148511103	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTTGTTGCTCACCTTTTTGGAGCCCCGCTGAATACTGCAGTTCTTGCAGGACACATTTTTACTGT	CTTGTTGCTCACCTTTTTGGAGCCCCGCTGAATACTGCAGTTCTTGCAGGACACATTTTTACTGT	G	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	103	278	0	ENST00000320356.2:c.1799_1851+12delinsC		p.X600_splice	ENST00000320356	NM_004456.4	600		15/20	1	2	FACETS	0.671	0.601	0.745	0.671	0.601	0.745	SUBCLONAL	1	TRUE	1	0.459141340266227	2		278	669	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705251	52705251	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0008857-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	169	463	0	ENST00000322088.6:c.133G>T	p.Glu45Ter	p.E45*	ENST00000322088	NM_014225.5	45	Gaa/Taa	2/15	1	2	FACETS	0.631	0.579	0.685	0.631	0.579	0.685	SUBCLONAL	1	TRUE	1	0.459141340266227	2		463	1167	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	50	280	0				ENST00000310581	NM_198253.2	-/1132			0.342430536843853	6	FACETS	0.785	0.665	0.917	0.157	0.133	0.184	CLONAL	1	TRUE	1	0.342430536843853	6		280	627	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0008871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	165	506	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.342430536843853	3	FACETS	0.885	0.815	0.956	0.885	0.815	0.956	CLONAL	2	TRUE	1	0.342430536843853	3		506	638	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259265	89259265	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	71	355	0	ENST00000336596.2:c.409G>C	p.Glu137Gln	p.E137Q	ENST00000336596	NM_005233.5	137	Gag/Cag	3/17	0.342430536843853	3	FACETS	0.858	0.75	0.975	0.286	0.25	0.325	CLONAL	1	TRUE	0	0.342430536843853	3		355	566	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541502	187541502	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	163	549	1	ENST00000441802.2:c.6238G>T	p.Val2080Leu	p.V2080L	ENST00000441802	NM_005245.3	2080	Gtg/Ttg	10/27	NA	2	FACETS	1	0.95	1			1	INDETERMINATE	1	TRUE	NA	0.342430536843853	2		550	909	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180055895	180055895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	403	464	0	ENST00000261937.6:c.1090C>T	p.Pro364Ser	p.P364S	ENST00000261937	NM_182925.4	364	Ccc/Tcc	8/30	0.342430536843853	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	3	TRUE	0	0.342430536843853	3		464	876	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522329	157522329	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1244601527	NA	P-0008871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	137	416	1	ENST00000346085.5:c.4601G>A	p.Arg1534His	p.R1534H	ENST00000346085	NM_020732.3	1534	cGc/cAc	18/20	0.330482297192856	2	FACETS	1	0.959	1	0.546	0.497	0.597	CLONAL	1	TRUE	0	0.342430536843853	2		417	733	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404954	404954	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	82	361	0	ENST00000399788.2:c.4240A>G	p.Ser1414Gly	p.S1414G	ENST00000399788	NM_001042603.1	1414	Agc/Ggc	26/28	0.342430536843853	3	FACETS	0.897	0.792	1	0.449	0.396	0.505	CLONAL	1	TRUE	1	0.342430536843853	3		361	625	SUCCESS
AR	367	MSKCC	GRCh37	X	66765710	66765710	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	325	543	0	ENST00000374690.3:c.722A>G	p.Lys241Arg	p.K241R	ENST00000374690	NM_000044.3	241	aAg/aGg	1/8	NA	2	FACETS	0.917	0.867	0.968			1	INDETERMINATE	2	TRUE	NA	0.342430536843853	2		543	1035	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76763896	76763896	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	191	511	0	ENST00000373344.5:c.7412C>G	p.Pro2471Arg	p.P2471R	ENST00000373344	NM_000489.3	2471	cCa/cGa	35/35	0.322137946951749	3	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	1	0.342430536843853	3		511	637	SUCCESS
BTK	695	MSKCC	GRCh37	X	100625036	100625036	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs868960790	NA	P-0008871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	218	538	0	ENST00000308731.7:c.341T>C	p.Phe114Ser	p.F114S	ENST00000308731	NM_000061.2	114	tTc/tCc	5/19	0.322137946951749	3	FACETS	0.915	0.853	0.979	0.915	0.853	0.979	CLONAL	2	TRUE	1	0.342430536843853	3		538	815	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447317	187447317	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0008871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	230	254	0	ENST00000232014.4:c.876del	p.Tyr293ThrfsTer31	p.Y293Tfs*31	ENST00000232014	NM_001130845.1	292	ccC/cc	5/10	0.342430536843853	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	3	TRUE	0	0.342430536843853	3		254	496	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098964	178098966	+	inframe_deletion	In_Frame_Del	DEL	ATC	ATC	-	novel	NA	P-0008871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	160	296	0	ENST00000397062.3:c.79_81del	p.Asp27del	p.D27del	ENST00000397062	NM_006164.4	27	GAT/-	2/5	0.330482297192856	2	FACETS	0.988	0.914	1	0.988	0.914	1	CLONAL	2	TRUE	0	0.342430536843853	2		296	473	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786055	135786055	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs397514832	NA	P-0008871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	99	389	0	ENST00000298552.3:c.1166del	p.Gly389GlufsTer51	p.G389Efs*51	ENST00000298552	NM_001162426.1	389	gGa/ga	12/23	1	2	FACETS	0.967	0.865	1	0.967	0.865	1	CLONAL	1	TRUE	1	0.342430536843853	2		389	598	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220659	1220660	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0008871-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	447	445	0	ENST00000326873.7:c.677_678del	p.Asn226ArgfsTer39	p.N226Rfs*39	ENST00000326873	NM_000455.4	226	aAC/a	5/10	0.303777957487935	3	FACETS	1	0.98	1			1	CLONAL	3	TRUE	NA	0.342430536843853	3		445	982	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032271	26032271	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1278314228	NA	P-0008873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	266	331	0	ENST00000244661.2:c.18G>C	p.Gln6His	p.Q6H	ENST00000244661	NM_003537.3	6	caG/caC	1/1	0.196592166533518	3	FACETS	1	0.99	1	0.623	0.585	0.662	INDETERMINATE	1	TRUE	1	0.605153290061507	3		331	919	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577498	7577498	+	splice_donor_variant	Splice_Site	SNP	C	C	A	rs1555525429	NA	P-0008873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	299	338	0	ENST00000269305.4:c.782+1G>T		p.X261_splice	ENST00000269305	NM_001126112.2	261			0.545547725751631	1	FACETS	0.899	0.851	0.947	0.899	0.851	0.947	CLONAL	1	TRUE	0	0.605153290061507	1		338	767	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552670	18552670	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	192	543	0	ENST00000266497.5:c.2081T>C	p.Val694Ala	p.V694A	ENST00000266497		694	gTc/gCc	14/31	0.605153290061507	1	FACETS	0.882	0.823	0.941	0.882	0.823	0.941	CLONAL	1	TRUE	0	0.605153290061507	1		543	502	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86564366	86564412	+	frameshift_variant	Frame_Shift_Del	DEL	TGTGTCGGGTGAAGATACCCGCGGCCCTGCCTGTGGCAGCCGCCCCC	TGTGTCGGGTGAAGATACCCGCGGCCCTGCCTGTGGCAGCCGCCCCC	-	novel	NA	P-0008873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	279	326	0	ENST00000274376.6:c.99_145del	p.Cys34SerfsTer62	p.C34Sfs*62	ENST00000274376	NM_002890.2	33	gTGTGTCGGGTGAAGATACCCGCGGCCCTGCCTGTGGCAGCCGCCCCC/g	1/25	0.605153290061507	1	FACETS	0.88	0.831	0.929	0.88	0.831	0.929	CLONAL	1	TRUE	0	0.605153290061507	1		326	731	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0008912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	397	464	0				ENST00000310581	NM_198253.2	-/1132			0.926812255011818	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.926812255011818	2		464	410	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0008912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	470	558	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.872100571475214	4	FACETS	0.952	0.914	0.991	0.952	0.914	0.991	CLONAL	2	TRUE	2	0.926812255011818	4		558	1026	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913384	NA	P-0008912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	9	300	238	1	ENST00000304494.5:c.262G>T	p.Glu88Ter	p.E88*	ENST00000304494	NM_000077.4	88	Gag/Tag	2/3	0.926812255011818	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.926812255011818	2		239	309	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968287	2968287	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	613	422	1	ENST00000396946.4:c.1699C>T	p.Pro567Ser	p.P567S	ENST00000396946	NM_032415.4	567	Ccc/Tcc	13/25	0.872100571475214	4	FACETS	0.926	0.893	0.96	0.926	0.893	0.96	CLONAL	2	TRUE	2	0.926812255011818	4		423	1376	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699367	117699367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	652	430	0	ENST00000369458.3:c.274G>A	p.Glu92Lys	p.E92K	ENST00000369458	NM_024626.3	92	Gag/Aag	3/6	0.872100571475214	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.926812255011818	4		430	1291	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668691	52668691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	397	493	0	ENST00000394830.3:c.1228C>T	p.His410Tyr	p.H410Y	ENST00000394830	NM_018313.4	410	Cat/Tat	12/30	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.926812255011818	2		493	844	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586431	189586431	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779097193	NA	P-0008912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	11	364	220	0	ENST00000264731.3:c.1055G>A	p.Arg352Lys	p.R352K	ENST00000264731	NM_003722.4	352	aGg/aAg	8/14	0.926812255011818	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.926812255011818	2		220	375	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968633	55968633	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200338299	NA	P-0008912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	424	380	0	ENST00000263923.4:c.2030C>T	p.Thr677Met	p.T677M	ENST00000263923	NM_002253.2	677	aCg/aTg	14/30	0.787718489581908	4	FACETS	0.895	0.856	0.934	0.895	0.856	0.934	CLONAL	2	TRUE	2	0.926812255011818	4		380	985	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188974	32188974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	995	528	0	ENST00000375023.3:c.580G>A	p.Asp194Asn	p.D194N	ENST00000375023	NM_004557.3	194	Gat/Aat	4/30	0.900893765398272	5	FACETS	0.987	0.962	1	0.987	0.962	1	CLONAL	3	TRUE	2	0.926812255011818	5		528	1734	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390999	139390999	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	546	358	2	ENST00000277541.6:c.7192C>T	p.Gln2398Ter	p.Q2398*	ENST00000277541	NM_017617.3	2398	Cag/Tag	34/34	0.926812255011818	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.926812255011818	2		360	558	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373404	118373404	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	6	437	323	0	ENST00000534358.1:c.6797C>T	p.Ser2266Phe	p.S2266F	ENST00000534358	NM_005933.3	2266	tCt/tTt	27/36	0.926812255011818	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.926812255011818	2		323	443	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626698	28626698	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs565606567	NA	P-0008912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	482	346	1	ENST00000241453.7:c.598G>A	p.Asp200Asn	p.D200N	ENST00000241453	NM_004119.2	200	Gat/Aat	5/24	0.872100571475214	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	2	0.926812255011818	4		347	937	SUCCESS
AR	367	MSKCC	GRCh37	X	66931393	66931393	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343361020	NA	P-0008912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	740	621	0	ENST00000374690.3:c.2035G>A	p.Glu679Lys	p.E679K	ENST00000374690	NM_000044.3	679	Gaa/Aaa	4/8	0.926812255011818	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.926812255011818	2		621	761	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692815	89692815	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7	251	162	0	ENST00000371953.3:c.300del	p.Ile101SerfsTer12	p.I101Sfs*12	ENST00000371953	NM_000314.4	100	cTt/ct	5/9	0.926812255011818	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.926812255011818	2		162	258	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579357	7579359	+	frameshift_variant	Frame_Shift_Del	DEL	ACG	ACG	CA	novel	NA	P-0008912-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	510	376	0	ENST00000269305.4:c.328_330delinsTG	p.Arg110CysfsTer13	p.R110Cfs*13	ENST00000269305	NM_001126112.2	110	CGT/TG	4/11	NA	2	FACETS	1	0.995	1			1	INDETERMINATE	2	TRUE	NA	0.926812255011818	2		376	540	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210741	2210741	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	227	657	5	ENST00000398665.3:c.1238G>A	p.Arg413His	p.R413H	ENST00000398665	NM_032482.2	413	cGc/cAc	14/28	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	1	0.311285426749776	2		662	1413	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661658	227661658	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	73	389	2	ENST00000305123.5:c.1797C>A	p.His599Gln	p.H599Q	ENST00000305123	NM_005544.2	599	caC/caA	1/2	NA	2	FACETS	0.525	0.458	0.598			1	INDETERMINATE	1	FALSE	NA	0.311285426749776	2		391	893	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911075	29911075	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1445	106	657	1	ENST00000376809.5:c.374G>A	p.Cys125Tyr	p.C125Y	ENST00000376809	NM_002116.7	125	tGc/tAc	3/8	1	2	FACETS	0.439	0.392	0.49	0.439	0.392	0.49	SUBCLONAL	1	FALSE	1	0.311285426749776	2		658	1551	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37671998	37671999	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATACACAAAGAT	novel	NA	P-0008928-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	113	688	0	ENST00000447079.4:c.2784_2785insTACACAAAGATA	p.Glu928_Leu929insTyrThrLysIle	p.E928_L929insYTKI	ENST00000447079	NM_015083.1	928	gaa/gaATACACAAAGATa	9/14	1	2	FACETS	0.601	0.539	0.667	0.601	0.539	0.667	SUBCLONAL	1	FALSE	1	0.311285426749776	2		688	1208	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	80	75	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.927	0.829	1	0.927	0.829	1	CLONAL	1	TRUE	1	0.728321361613113	2		75	237	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562641	29562641	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854562	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	429	567	1	ENST00000356175.3:c.3721C>T	p.Arg1241Ter	p.R1241*	ENST00000356175	NM_000267.3	1241	Cga/Tga	28/57	NA	2	FACETS	0.987	0.956	1			1	INDETERMINATE	2	TRUE	NA	0.728321361613113	2		568	597	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641144	117641144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866970127	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	415	750	1	ENST00000368508.3:c.5827G>A	p.Glu1943Lys	p.E1943K	ENST00000368508	NM_002944.2	1943	Gaa/Aaa	36/43	0.487498335846702	4	FACETS	1	0.982	1			1	CLONAL	2	TRUE	NA	0.728321361613113	4		751	937	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956205	55956205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148668147	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	150	518	4	ENST00000263923.4:c.3110C>T	p.Ser1037Leu	p.S1037L	ENST00000263923	NM_002253.2	1037	tCg/tTg	23/30	0.728321361613113	3	FACETS	0.915	0.84	0.994	0.458	0.42	0.497	CLONAL	1	TRUE	1	0.728321361613113	3		522	614	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663590	117663590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	248	588	1	ENST00000368508.3:c.4642G>A	p.Glu1548Lys	p.E1548K	ENST00000368508	NM_002944.2	1548	Gag/Aag	28/43	0.487498335846702	4	FACETS	0.886	0.834	0.94			1	CLONAL	2	TRUE	NA	0.728321361613113	4		589	664	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434595	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	438	403	0	ENST00000369535.4:c.37G>A	p.Gly13Ser	p.G13S	ENST00000369535	NM_002524.4	13	Ggt/Agt	2/7	0.728321361613113	3	FACETS	0.989	0.963	1	0.989	0.963	1	CLONAL	3	TRUE	0	0.728321361613113	3		403	553	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873223	136873223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	658	784	0	ENST00000241393.3:c.275C>T	p.Pro92Leu	p.P92L	ENST00000241393	NM_003467.2	92	cCc/cTc	2/2	0.728321361613113	3	FACETS	0.985	0.954	1	0.985	0.954	1	CLONAL	2	TRUE	1	0.728321361613113	3		784	1251	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626993	158626993	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1401182199	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	204	730	0	ENST00000263640.3:c.677G>A	p.Ser226Asn	p.S226N	ENST00000263640	NM_001105.4	226	aGc/aAc	7/11	0.728321361613113	3	FACETS	0.889	0.825	0.954	0.444	0.412	0.477	CLONAL	1	TRUE	1	0.728321361613113	3		730	860	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582195	189582195	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	385	340	0	ENST00000264731.3:c.754G>A	p.Glu252Lys	p.E252K	ENST00000264731	NM_003722.4	252	Gaa/Aaa	5/14	0.728321361613113	4	FACETS	1	0.992	1			1	CLONAL	2	TRUE	NA	0.728321361613113	4		340	786	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518291	187518291	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	96	94	0	ENST00000441802.2:c.12403C>T	p.Pro4135Ser	p.P4135S	ENST00000441802	NM_005245.3	4135	Cct/Tct	25/27	0.728321361613113	3	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	1	0.728321361613113	3		94	176	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120545	94120545	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	431	881	0	ENST00000369303.4:c.506C>G	p.Thr169Ser	p.T169S	ENST00000369303	NM_004440.3	169	aCt/aGt	3/17	0.487498335846702	4	FACETS	0.91	0.869	0.951			1	CLONAL	2	TRUE	NA	0.728321361613113	4		881	1124	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522454	157522454	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	350	517	0	ENST00000346085.5:c.4726C>T	p.Pro1576Ser	p.P1576S	ENST00000346085	NM_020732.3	1576	Ccg/Tcg	18/20	0.717416383857243	4	FACETS	0.888	0.844	0.933	0.888	0.844	0.933	CLONAL	2	TRUE	2	0.728321361613113	4		517	935	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509849	106509849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426277818	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	437	580	0	ENST00000359195.3:c.1843G>A	p.Glu615Lys	p.E615K	ENST00000359195	NM_002649.2	615	Gaa/Aaa	2/11	0.717416383857243	4	FACETS	0.99	0.947	1	0.99	0.947	1	CLONAL	2	TRUE	2	0.728321361613113	4		580	1048	SUCCESS
MET	4233	MSKCC	GRCh37	7	116409720	116409720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	164	322	0	ENST00000397752.3:c.2605G>A	p.Ala869Thr	p.A869T	ENST00000397752	NM_000245.2	869	Gca/Aca	12/21	0.717416383857243	4	FACETS	0.94	0.873	1	0.94	0.873	1	CLONAL	2	TRUE	2	0.728321361613113	4		322	414	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411950	116411950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	198	425	0	ENST00000397752.3:c.2935C>T	p.His979Tyr	p.H979Y	ENST00000397752	NM_000245.2	979	Cat/Tat	14/21	0.717416383857243	4	FACETS	0.925	0.864	0.986	0.925	0.864	0.986	CLONAL	2	TRUE	2	0.728321361613113	4		425	508	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878329	151878329	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	416	501	1	ENST00000262189.6:c.6616C>T	p.Pro2206Ser	p.P2206S	ENST00000262189	NM_170606.2	2206	Cct/Tct	36/59	0.717416383857243	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.728321361613113	4		502	941	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375969	8375969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1242333397	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	239	465	0	ENST00000356435.5:c.4628C>T	p.Pro1543Leu	p.P1543L	ENST00000356435		1543	cCt/cTt	28/35	0.408453739948812	4	FACETS	0.886	0.833	0.941	0.886	0.833	0.941	INDETERMINATE	2	TRUE	2	0.728321361613113	4		465	640	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402567	139402567	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	235	344	0	ENST00000277541.6:c.3350A>C	p.Gln1117Pro	p.Q1117P	ENST00000277541	NM_017617.3	1117	cAg/cCg	21/34	0.518689923572397	4	FACETS	0.91	0.855	0.965	0.91	0.855	0.965	CLONAL	2	TRUE	2	0.728321361613113	4		344	613	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572643	64572643	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs864622615	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	234	330	0	ENST00000312049.6:c.1213C>T	p.Gln405Ter	p.Q405*	ENST00000312049	NM_130799.2	405	Cag/Tag	9/10	0.680681991687703	2	FACETS	0.832	0.791	0.873	0.832	0.791	0.873	CLONAL	2	TRUE	0	0.728321361613113	2		330	386	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148890	119148890	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs754168206	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	352	291	0	ENST00000264033.4:c.1110A>C	p.Leu370Phe	p.L370F	ENST00000264033	NM_005188.3	370	ttA/ttC	8/16	0.728321361613113	3	FACETS	0.99	0.96	1	0.99	0.96	1	CLONAL	3	TRUE	0	0.728321361613113	3		291	444	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865602	57865602	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	295	765	2	ENST00000228682.2:c.3079C>T	p.Pro1027Ser	p.P1027S	ENST00000228682	NM_005269.2	1027	Cct/Tct	12/12	0.728321361613113	3	FACETS	0.94	0.885	0.998	0.47	0.442	0.499	CLONAL	1	TRUE	1	0.728321361613113	3		767	1175	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133225576	133225576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1399456425	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	193	434	0	ENST00000320574.5:c.4088C>T	p.Pro1363Leu	p.P1363L	ENST00000320574	NM_006231.2	1363	cCc/cTc	32/49	0.728321361613113	3	FACETS	1	0.965	1	0.532	0.494	0.571	CLONAL	1	TRUE	1	0.728321361613113	3		434	680	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031816	10031816	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs757262372	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	157	244	0	ENST00000330684.3:c.1007C>T	p.Pro336Leu	p.P336L	ENST00000330684	NM_001134407.1	336	cCa/cTa	3/13	0.717416383857243	4	FACETS	0.955	0.886	1	0.955	0.886	1	CLONAL	2	TRUE	2	0.728321361613113	4		244	390	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618635	37618635	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	376	391	1	ENST00000447079.4:c.311G>T	p.Arg104Leu	p.R104L	ENST00000447079	NM_015083.1	104	cGg/cTg	1/14	0.728321361613113	3	FACETS	0.961	0.92	1	0.961	0.92	1	CLONAL	2	TRUE	1	0.728321361613113	3		392	733	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435498	56435498	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769254736	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	175	481	0	ENST00000407977.2:c.1639C>T	p.His547Tyr	p.H547Y	ENST00000407977		547	Cat/Tat	9/10	0.728321361613113	3	FACETS	0.88	0.812	0.95	0.44	0.406	0.475	CLONAL	1	TRUE	1	0.728321361613113	3		481	745	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48581238	48581238	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	163	510	0	ENST00000342988.3:c.542C>T	p.Thr181Ile	p.T181I	ENST00000342988	NM_005359.5	181	aCc/aTc	5/12	0.728321361613113	3	FACETS	0.998	0.92	1	0.499	0.46	0.539	CLONAL	1	TRUE	1	0.728321361613113	3		510	612	SUCCESS
AXL	558	MSKCC	GRCh37	19	41759589	41759589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1345126131	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	463	568	1	ENST00000301178.4:c.2012G>A	p.Arg671Gln	p.R671Q	ENST00000301178	NM_021913.4	671	cGg/cAg	17/20	0.728321361613113	3	FACETS	0.957	0.92	0.994	0.957	0.92	0.994	CLONAL	2	TRUE	1	0.728321361613113	3		569	906	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374369	31374369	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767930436	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	429	545	0	ENST00000328111.2:c.368C>T	p.Ser123Phe	p.S123F	ENST00000328111	NM_006892.3	123	tCc/tTc	5/23	0.717416383857243	4	FACETS	0.945	0.903	0.988	0.945	0.903	0.988	CLONAL	2	TRUE	2	0.728321361613113	4		545	1077	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46267787	46267787	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	664	863	0	ENST00000371998.3:c.2548C>T	p.Pro850Ser	p.P850S	ENST00000371998		850	Cct/Tct	14/23	0.717416383857243	4	FACETS	0.989	0.954	1	0.989	0.954	1	CLONAL	2	TRUE	2	0.728321361613113	4		863	1593	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961460	54961460	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	132	259	0	ENST00000312783.6:c.172C>T	p.Pro58Ser	p.P58S	ENST00000312783	NM_198436.1	58	Cct/Tct	4/10	0.717416383857243	4	FACETS	1	0.983	1	0.665	0.608	0.724	CLONAL	1	TRUE	2	0.728321361613113	4		259	471	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543879	41543879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	608	563	2	ENST00000263253.7:c.2170C>T	p.Pro724Ser	p.P724S	ENST00000263253	NM_001429.3	724	Cct/Tct	12/31	0.400474667477042	4	FACETS	0.915	0.894	0.936			1	INDETERMINATE	4	TRUE	NA	0.728321361613113	4		565	788	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649608	48649608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	564	336	0	ENST00000376670.3:c.92G>A	p.Gly31Glu	p.G31E	ENST00000376670	NM_002049.3	31	gGg/gAg	2/6	0.690070847503241	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.728321361613113	2		336	700	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412094	63412094	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374751715	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	773	485	0	ENST00000330258.3:c.1073G>A	p.Arg358Gln	p.R358Q	ENST00000330258	NM_152424.3	358	cGa/cAa	2/2	0.690070847503241	2	FACETS	1	0.998	1			1	CLONAL	2	TRUE	NA	0.728321361613113	2		485	916	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742111	145742112	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	69	196	0	ENST00000428558.2:c.391_392delinsAA	p.Gly131Lys	p.G131K	ENST00000428558	NM_004260.3	131	GGa/AAa	5/22	0.728321361613113	3	FACETS	0.808	0.709	0.913	0.404	0.354	0.457	CLONAL	1	TRUE	1	0.728321361613113	3		196	320	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918761	32918762	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	236	569	1	ENST00000380152.3:c.6908_6909delinsTT	p.Ser2303Phe	p.S2303F	ENST00000380152		2303	tCC/tTT	12/27	0.717416383857243	4	FACETS	0.816	0.766	0.868	0.816	0.766	0.868	CLONAL	2	TRUE	2	0.728321361613113	4		570	686	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295253	+	upstream_gene_variant	5'Flank	ONP	GAGG	GAGG	AAGA	novel	NA	P-0008942-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	135	309	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.946	0.869	1	0.946	0.869	1	CLONAL	1	TRUE	1	0.728321361613113	2		309	392	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008963-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	86	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.972	0.876	1	0.972	0.876	1	CLONAL	1	TRUE	1	0.789738452941279	2		280	224	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0008963-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	154	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.789738452941279	2		490	386	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0008963-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	12	558	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.064	0.044	0.089	0.064	0.044	0.089	SUBCLONAL	1	TRUE	1	0.789738452941279	2		558	474	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729175	66729175	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908596	NA	P-0008963-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	25	316	0	ENST00000307102.5:c.383G>A	p.Gly128Asp	p.G128D	ENST00000307102	NM_002755.3	128	gGc/gAc	3/11	1	2	FACETS	0.13	0.102	0.162	0.13	0.102	0.162	SUBCLONAL	1	TRUE	1	0.789738452941279	2		316	488	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974679	21974679	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs864622636	NA	P-0008963-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	145	420	1	ENST00000304494.5:c.148C>T	p.Gln50Ter	p.Q50*	ENST00000304494	NM_000077.4	50	Cag/Tag	1/3	0.789738452941279	1	FACETS	0.751	0.698	0.804	0.751	0.698	0.804	SUBCLONAL	1	TRUE	0	0.789738452941279	1		421	296	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578318	212578318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008963-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	206	420	1	ENST00000342788.4:c.939G>A	p.Met313Ile	p.M313I	ENST00000342788	NM_005235.2	313	atG/atA	8/28	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.789738452941279	2		421	499	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514980	148514980	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008963-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	242	544	0	ENST00000320356.2:c.1229C>T	p.Ser410Leu	p.S410L	ENST00000320356	NM_004456.4	410	tCg/tTg	10/20	1	2	FACETS	0.889	0.835	0.945	0.889	0.835	0.945	CLONAL	1	TRUE	1	0.789738452941279	2		544	689	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218623	98218623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778629	NA	P-0008963-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	105	282	0	ENST00000331920.6:c.3241G>A	p.Val1081Met	p.V1081M	ENST00000331920	NM_000264.3	1081	Gtg/Atg	19/24	0.789738452941279	1	FACETS	0.583	0.53	0.637	0.583	0.53	0.637	SUBCLONAL	1	TRUE	0	0.789738452941279	1		282	276	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944419	40944419	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008963-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	210	569	0	ENST00000373198.4:c.2083C>T	p.Leu695Phe	p.L695F	ENST00000373198	NM_133170.3	695	Ctc/Ttc	12/32	0.783767839387855	3	FACETS	0.965	0.898	1	0.482	0.449	0.517	CLONAL	1	TRUE	1	0.789738452941279	3		569	769	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	72	280	0				ENST00000310581	NM_198253.2	-/1132			0.474366460131488	3	FACETS	1	0.932	1	0.544	0.479	0.614	CLONAL	1	TRUE	1	0.474366460131488	3		280	345	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66727441	66727441	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519728	NA	P-0008964-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	167	330	0	ENST00000307102.5:c.157T>G	p.Phe53Val	p.F53V	ENST00000307102	NM_002755.3	53	Ttt/Gtt	2/11	1	2	FACETS	0.896	0.824	0.97	0.896	0.824	0.97	CLONAL	1	TRUE	1	0.474366460131488	2		330	786	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0008968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	265	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.964	0.912	1	0.964	0.912	1	CLONAL	1	TRUE	1	0.921104665880175	2		464	597	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0008968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	394	595	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.921104665880175	3	FACETS	0.998	0.961	1			1	CLONAL	2	TRUE	NA	0.921104665880175	3		595	626	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942017	44942017	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0008968-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	46	317	313	0	ENST00000377967.4:c.3268del	p.Leu1090TyrfsTer14	p.L1090Yfs*14	ENST00000377967	NM_021140.2	1089	gaC/ga	22/29	1	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.921104665880175	1		313	363	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0008972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	119	464	0				ENST00000310581	NM_198253.2	-/1132			0.3	3	FACETS	0.879	0.794	0.968	1	0.979	1	CLONAL	3	TRUE	1	0.14	3		464	690	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0008972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	67	75	0				ENST00000310581	NM_198253.2	-/1132			0.3	3	FACETS	1	0.894	1	1	0.894	1	CLONAL	2	TRUE	1	0.14	3		75	497	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577581	7577581	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs864622237	NA	P-0008972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	21	333	0	ENST00000269305.4:c.700T>A	p.Tyr234Asn	p.Y234N	ENST00000269305	NM_001126112.2	234	Tac/Aac	7/11	1	2	FACETS	0.403	0.308	0.514	0.403	0.308	0.514	SUBCLONAL	1	TRUE	1	0.14	2		333	745	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577575	7577575	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs587782289	NA	P-0008972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	32	336	0	ENST00000269305.4:c.706T>C	p.Tyr236His	p.Y236H	ENST00000269305	NM_001126112.2	236	Tac/Cac	7/11	1	2	FACETS	0.604	0.488	0.735	0.604	0.488	0.735	SUBCLONAL	1	TRUE	1	0.14	2		336	757	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552812	226552812	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	48	401	0	ENST00000366794.5:c.2549C>T	p.Pro850Leu	p.P850L	ENST00000366794	NM_001618.3	850	cCc/cTc	19/23	1	2	FACETS	0.741	0.624	0.871	0.741	0.624	0.871	SUBCLONAL	1	TRUE	1	0.14	2		401	925	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399396	139399396	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	59	264	0	ENST00000277541.6:c.4747G>T	p.Glu1583Ter	p.E1583*	ENST00000277541	NM_017617.3	1583	Gag/Tag	26/34	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.14	2		264	687	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304487	91304487	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0008972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	28	220	0	ENST00000355112.3:c.1882+2T>G		p.X628_splice	ENST00000355112	NM_000057.2	628			1	2	FACETS	0.789	0.629	0.972	0.789	0.629	0.972	CLONAL	1	TRUE	1	0.14	2		220	507	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349993	70349993	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008972-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	40	219	0	ENST00000374080.3:c.3976T>C	p.Tyr1326His	p.Y1326H	ENST00000374080		1326	Tat/Cat	28/45	1	1	FACETS	0.942	0.782	1	0.942	0.782	1	CLONAL	1	TRUE	0	0.14	1		219	564	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	259	464	0				ENST00000310581	NM_198253.2	-/1132			0.756667642154779	2	FACETS	0.989	0.953	1	0.989	0.953	1	CLONAL	2	TRUE	0	0.774735825630773	2		464	338	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs397516896	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	147	333	0	ENST00000288602.6:c.1780G>A	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	594	Gat/Aat	15/18	1	2	FACETS	0.942	0.869	1	0.942	0.869	1	CLONAL	1	TRUE	1	0.774735825630773	2		333	403	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374403	81374403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372600489	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	174	452	0	ENST00000222390.5:c.659G>A	p.Arg220Gln	p.R220Q	ENST00000222390	NM_000601.4	220	cGa/cAa	6/18	1	2	FACETS	0.888	0.824	0.953	0.888	0.824	0.953	CLONAL	1	TRUE	1	0.774735825630773	2		452	506	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148508728	148508728	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs267601395	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	310	454	0	ENST00000320356.2:c.1936T>A	p.Tyr646Asn	p.Y646N	ENST00000320356	NM_004456.4	646	Tac/Aac	16/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.774735825630773	2		454	771	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528489	29528489	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764079291	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	497	637	0	ENST00000356175.3:c.1246C>T	p.Arg416Ter	p.R416*	ENST00000356175	NM_000267.3	416	Cga/Tga	11/57	0.769158516011398	3	FACETS	0.947	0.912	0.982	0.947	0.912	0.982	CLONAL	2	TRUE	1	0.774735825630773	3		637	940	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11129655	11129655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	219	512	3	ENST00000358026.2:c.2461G>A	p.Glu821Lys	p.E821K	ENST00000358026	NM_001128849.1	821	Gag/Aag	17/36	0.226739420780223	1	FACETS	0.602	0.564	0.641	0.602	0.564	0.641	INDETERMINATE	1	TRUE	0	0.774735825630773	1		515	575	SUCCESS
AR	367	MSKCC	GRCh37	X	66766427	66766427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	100	89	0	ENST00000374690.3:c.1439C>T	p.Pro480Leu	p.P480L	ENST00000374690	NM_000044.3	480	cCc/cTc	1/8	1	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.774735825630773	1		89	130	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36931984	36931984	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	428	687	0	ENST00000361632.4:c.2485G>A	p.Gly829Arg	p.G829R	ENST00000361632		829	Ggg/Agg	16/16	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.774735825630773	2		687	1065	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721087	61721087	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs572708816	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	168	382	0	ENST00000401558.2:c.1187G>A	p.Gly396Glu	p.G396E	ENST00000401558	NM_003400.3	396	gGa/gAa	12/25	0.774735825630773	3	FACETS	0.87	0.802	0.94	0.435	0.401	0.47	CLONAL	1	TRUE	1	0.774735825630773	3		382	692	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247418	71247418	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752297898	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	282	383	0	ENST00000318789.4:c.115G>A	p.Gly39Arg	p.G39R	ENST00000318789	NM_032682.5	39	Gga/Aga	6/21	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.774735825630773	2		383	616	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427729	72427729	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs764695313	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	225	329	0	ENST00000477973.2:c.761A>G	p.Asn254Ser	p.N254S	ENST00000477973	NM_012234.5	254	aAc/aGc	4/4	1	2	FACETS	0.965	0.905	1	0.965	0.905	1	CLONAL	1	TRUE	1	0.774735825630773	2		329	602	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584536	189584536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	161	496	0	ENST00000264731.3:c.832G>A	p.Asp278Asn	p.D278N	ENST00000264731	NM_003722.4	278	Gat/Aat	6/14	0.226739420780223	1	FACETS	0.45	0.415	0.486	0.45	0.415	0.486	INDETERMINATE	1	TRUE	0	0.774735825630773	1		496	566	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156790	106156790	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	234	413	1	ENST00000380013.4:c.1691G>T	p.Trp564Leu	p.W564L	ENST00000380013	NM_001127208.2	564	tGg/tTg	3/11	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.774735825630773	2		414	584	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143191904	143191904	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	284	471	0	ENST00000262992.4:c.527T>C	p.Val176Ala	p.V176A	ENST00000262992	NM_001101669.1	176	gTt/gCt	8/24	1	2	FACETS	0.948	0.896	1	0.948	0.896	1	CLONAL	1	TRUE	1	0.774735825630773	2		471	773	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295204	1295204	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs2735943	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	86	156	0				ENST00000310581	NM_198253.2	-/1132			0.756667642154779	2	FACETS	1	0.957	1	0.552	0.499	0.606	CLONAL	1	TRUE	0	0.774735825630773	2		156	201	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721147	176721147	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1377562220	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	249	184	0	ENST00000439151.2:c.6778C>T	p.Gln2260Ter	p.Q2260*	ENST00000439151	NM_022455.4	2260	Cag/Tag	23/23	0.770558457368805	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.774735825630773	2		184	313	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178597	32178597	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	235	404	0	ENST00000375023.3:c.2797C>T	p.Pro933Ser	p.P933S	ENST00000375023	NM_004557.3	933	Cca/Tca	18/30	1	2	FACETS	0.98	0.921	1	0.98	0.921	1	CLONAL	1	TRUE	1	0.774735825630773	2		404	619	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287449	33287449	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	176	303	0	ENST00000374542.5:c.1648G>T	p.Glu550Ter	p.E550*	ENST00000374542	NM_001141970.1	550	Gaa/Taa	6/8	1	2	FACETS	0.869	0.806	0.933	0.869	0.806	0.933	CLONAL	1	TRUE	1	0.774735825630773	2		303	523	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511234	157511234	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754960836	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	244	397	1	ENST00000346085.5:c.3752G>A	p.Arg1251Gln	p.R1251Q	ENST00000346085	NM_020732.3	1251	cGg/cAg	15/20	0.769711235008934	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.774735825630773	1		398	377	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814845	139814845	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	411	684	2	ENST00000247668.2:c.838G>A	p.Ala280Thr	p.A280T	ENST00000247668	NM_021138.3	280	Gcc/Acc	8/11	0.774735825630773	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.774735825630773	1		686	603	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505344	125505344	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	304	494	0	ENST00000428830.2:c.634A>T	p.Ser212Cys	p.S212C	ENST00000428830	NM_001114121.2	212	Agt/Tgt	7/14	0.761700541379388	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.774735825630773	1		494	461	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233836	133233836	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	275	502	0	ENST00000320574.5:c.3468C>G	p.Asn1156Lys	p.N1156K	ENST00000320574	NM_006231.2	1156	aaC/aaG	29/49	0.226739420780223	1	FACETS	0.546	0.514	0.578	0.546	0.514	0.578	INDETERMINATE	1	TRUE	0	0.774735825630773	1		502	797	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961522	41961522	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	424	821	1	ENST00000219905.7:c.430C>T	p.Pro144Ser	p.P144S	ENST00000219905	NM_001164273.1	144	Cct/Tct	2/24	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.774735825630773	2		822	1087	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857436	9857436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	249	539	0	ENST00000330684.3:c.3965G>A	p.Gly1322Glu	p.G1322E	ENST00000330684	NM_001134407.1	1322	gGa/gAa	13/13	NA	2	FACETS	0.94	0.884	0.997			1	INDETERMINATE	1	TRUE	NA	0.774735825630773	2		539	684	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831953	72831953	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	385	830	0	ENST00000268489.5:c.4628G>C	p.Arg1543Pro	p.R1543P	ENST00000268489	NM_006885.3	1543	cGc/cCc	9/10	0.774735825630773	1	FACETS	0.937	0.9	0.973	0.937	0.9	0.973	CLONAL	1	TRUE	0	0.774735825630773	1		830	650	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41215370	41215370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	266	530	0	ENST00000357654.3:c.5173G>A	p.Glu1725Lys	p.E1725K	ENST00000357654	NM_007294.3	1725	Gaa/Aaa	18/23	0.769158516011398	3	FACETS	0.966	0.907	1	0.483	0.453	0.514	CLONAL	1	TRUE	1	0.774735825630773	3		530	986	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677874	47677874	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	172	317	0	ENST00000347630.2:c.991G>A	p.Asp331Asn	p.D331N	ENST00000347630	NM_001007230.1	331	Gat/Aat	11/11	0.769158516011398	3	FACETS	0.96	0.887	1	0.48	0.443	0.518	CLONAL	1	TRUE	1	0.774735825630773	3		317	642	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953411	17953411	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	129	325	0	ENST00000458235.1:c.575C>T	p.Ala192Val	p.A192V	ENST00000458235	NM_000215.3	192	gCc/gTc	6/24	0.226739420780223	1	FACETS	0.524	0.48	0.57	0.524	0.48	0.57	INDETERMINATE	1	TRUE	0	0.774735825630773	1		325	389	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560970	9560970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781706438	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	239	416	0	ENST00000353224.5:c.812C>T	p.Ser271Leu	p.S271L	ENST00000353224	NM_177990.2	271	tCg/tTg	4/10	1	2	FACETS	0.97	0.912	1	0.97	0.912	1	CLONAL	1	TRUE	1	0.774735825630773	2		416	636	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023295	31023295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	246	456	0	ENST00000375687.4:c.2780G>A	p.Gly927Glu	p.G927E	ENST00000375687	NM_015338.5	927	gGa/gAa	13/13	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.774735825630773	2		456	583	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024491	31024491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	223	387	0	ENST00000375687.4:c.3976C>T	p.Pro1326Ser	p.P1326S	ENST00000375687	NM_015338.5	1326	Cct/Tct	13/13	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.774735825630773	2		387	547	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39706268	39706268	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	255	412	0	ENST00000361337.2:c.326G>T	p.Gly109Val	p.G109V	ENST00000361337	NM_003286.2	109	gGc/gTc	5/21	1	2	FACETS	0.994	0.937	1	0.994	0.937	1	CLONAL	1	TRUE	1	0.774735825630773	2		412	662	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755557	39755557	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753079929	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	252	418	0	ENST00000288319.7:c.1208C>T	p.Pro403Leu	p.P403L	ENST00000288319	NM_182918.3	403	cCc/cTc	10/10	0.226739420780223	1	FACETS	0.614	0.578	0.65	0.614	0.578	0.65	INDETERMINATE	1	TRUE	0	0.774735825630773	1		418	649	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504147	123504147	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1343327378	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	208	243	0	ENST00000371139.4:c.323C>T	p.Ala108Val	p.A108V	ENST00000371139	NM_001114937.2	108	gCt/gTt	3/4	1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.774735825630773	1		243	274	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528461	29528462	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	novel	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	265	555	1	ENST00000356175.3:c.1218_1219del	p.Phe406LeufsTer22	p.F406Lfs*22	ENST00000356175	NM_000267.3	406	ttTCac/ttac	11/57	0.769158516011398	3	FACETS	1	0.979	1	0.545	0.512	0.579	CLONAL	1	TRUE	1	0.774735825630773	3		556	871	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247516	71247517	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	221	350	0	ENST00000318789.4:c.16_17delinsAA	p.Gly6Lys	p.G6K	ENST00000318789	NM_032682.5	6	GGg/AAg	6/21	1	2	FACETS	0.937	0.878	0.997	0.937	0.878	0.997	CLONAL	1	TRUE	1	0.774735825630773	2		350	609	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147519	47147519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	205	412	0	ENST00000409792.3:c.4807C>T	p.His1603Tyr	p.H1603Y	ENST00000409792	NM_014159.6	1603	Cat/Tat	6/21	1	2	FACETS	0.879	0.821	0.939	0.879	0.821	0.939	CLONAL	1	TRUE	1	0.774735825630773	2		412	602	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	179	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.939	0.876	1	0.939	0.876	1	CLONAL	1	TRUE	1	0.854403574314958	2		280	446	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0008975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	314	511	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.957	0.908	1	0.957	0.908	1	CLONAL	1	TRUE	1	0.854403574314958	2		511	768	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148727	20148727	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0008975-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	277	233	0	ENST00000379607.5:c.338-2A>T		p.X113_splice	ENST00000379607	NM_001412.3	113			1	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.854403574314958	1		233	340	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	250	280	0				ENST00000310581	NM_198253.2	-/1132			0.611069064063412	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.615154369724907	3		280	522	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445991	49445991	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1265398099	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	336	508	1	ENST00000301067.7:c.1475C>T	p.Ser492Leu	p.S492L	ENST00000301067	NM_003482.3	492	tCg/tTg	10/54	1	2	FACETS	0.927	0.876	0.978	0.927	0.876	0.978	CLONAL	1	TRUE	1	0.615154369724907	2		509	1179	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295201	1295201	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	78	127	0				ENST00000310581	NM_198253.2	-/1132			0.611069064063412	3	FACETS	0.877	0.776	0.985	0.439	0.388	0.493	CLONAL	1	TRUE	1	0.615154369724907	3		127	378	SUCCESS
APC	324	MSKCC	GRCh37	5	112116491	112116491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	181	266	0	ENST00000257430.4:c.536C>T	p.Ser179Phe	p.S179F	ENST00000257430	NM_000038.5	179	tCc/tTc	6/16	0.611069064063412	3	FACETS	0.882	0.815	0.953	0.441	0.407	0.477	CLONAL	1	TRUE	1	0.615154369724907	3		266	872	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101358	27101358	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	605	438	1	ENST00000324856.7:c.4640C>T	p.Ser1547Phe	p.S1547F	ENST00000324856	NM_006015.4	1547	tCc/tTc	18/20	0.611069064063412	3	FACETS	0.922	0.888	0.956	0.922	0.888	0.956	CLONAL	2	TRUE	1	0.615154369724907	3		439	1395	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812246	43812246	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	635	447	0	ENST00000372470.3:c.1111G>A	p.Ala371Thr	p.A371T	ENST00000372470	NM_005373.2	371	Gcc/Acc	7/12	0.611069064063412	3	FACETS	0.913	0.881	0.946	0.913	0.881	0.946	CLONAL	2	TRUE	1	0.615154369724907	3		447	1478	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43817888	43817888	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	rs1190279641	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	267	405	0	ENST00000372470.3:c.1567A>G	p.Arg523Gly	p.R523G	ENST00000372470	NM_005373.2	523	Aga/Gga	11/12	0.611069064063412	3	FACETS	0.854	0.799	0.91	0.427	0.399	0.455	CLONAL	1	TRUE	1	0.615154369724907	3		405	1329	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25459872	25459872	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs750597155	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	335	399	1	ENST00000264709.3:c.2411C>T	p.Pro804Leu	p.P804L	ENST00000264709	NM_175629.2	804	cCg/cTg	21/23	0.611069064063412	3	FACETS	1	0.964	1	0.513	0.485	0.543	CLONAL	1	TRUE	1	0.615154369724907	3		400	1387	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446322	29446322	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1615	378	652	0	ENST00000389048.3:c.3245A>G	p.Lys1082Arg	p.K1082R	ENST00000389048	NM_004304.4	1082	aAg/aGg	20/29	0.611069064063412	3	FACETS	0.806	0.762	0.851	0.403	0.381	0.426	CLONAL	1	TRUE	1	0.615154369724907	3		652	1993	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99136555	99136555	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1058	263	404	0	ENST00000074304.5:c.44G>T	p.Arg15Leu	p.R15L	ENST00000074304	NM_001134224.1	15	cGt/cTt	3/26	0.611069064063412	3	FACETS	0.846	0.792	0.903	0.423	0.396	0.452	CLONAL	1	TRUE	1	0.615154369724907	3		404	1321	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537918	212537918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146197533	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	510	693	1	ENST00000342788.4:c.1687G>A	p.Glu563Lys	p.E563K	ENST00000342788	NM_005235.2	563	Gaa/Aaa	14/28	0.611069064063412	3	FACETS	0.935	0.898	0.972	0.935	0.898	0.972	CLONAL	2	TRUE	1	0.615154369724907	3		694	1159	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125764	47125764	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775677070	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	267	354	0	ENST00000409792.3:c.5506C>T	p.Pro1836Ser	p.P1836S	ENST00000409792	NM_014159.6	1836	Ccg/Tcg	12/21	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.615154369724907	2		354	864	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155370	47155370	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	147	523	0	ENST00000409792.3:c.4711C>T	p.Pro1571Ser	p.P1571S	ENST00000409792	NM_014159.6	1571	Cct/Tct	5/21	1	2	FACETS	0.396	0.361	0.434	0.396	0.361	0.434	SUBCLONAL	1	TRUE	1	0.615154369724907	2		523	1206	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49929248	49929248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763498892	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	460	581	2	ENST00000296474.3:c.3295G>A	p.Gly1099Arg	p.G1099R	ENST00000296474	NM_002447.2	1099	Gga/Aga	15/20	1	2	FACETS	0.994	0.949	1	0.994	0.949	1	CLONAL	1	TRUE	1	0.615154369724907	2		583	1504	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430309	181430309	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	175	221	0	ENST00000325404.1:c.161G>A	p.Gly54Glu	p.G54E	ENST00000325404	NM_003106.3	54	gGg/gAg	1/1	1	2	FACETS	0.964	0.893	1	0.964	0.893	1	CLONAL	1	TRUE	1	0.615154369724907	2		221	590	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189584548	189584548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	389	477	0	ENST00000264731.3:c.844G>A	p.Gly282Arg	p.G282R	ENST00000264731	NM_003722.4	282	Gga/Aga	6/14	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.615154369724907	2		477	1241	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961101	55961101	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	303	479	0	ENST00000263923.4:c.2839C>T	p.Gln947Ter	p.Q947*	ENST00000263923	NM_002253.2	947	Caa/Taa	21/30	0.568382127801871	1	FACETS	0.774	0.732	0.818	0.774	0.732	0.818	SUBCLONAL	1	TRUE	0	0.615154369724907	1		479	881	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55962398	55962398	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	67	413	0	ENST00000263923.4:c.2726G>A	p.Gly909Glu	p.G909E	ENST00000263923	NM_002253.2	909	gGa/gAa	19/30	0.568382127801871	1	FACETS	0.176	0.153	0.202	0.176	0.153	0.202	SUBCLONAL	1	TRUE	0	0.615154369724907	1		413	855	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968583	55968583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	98	467	0	ENST00000263923.4:c.2080C>T	p.Pro694Ser	p.P694S	ENST00000263923	NM_002253.2	694	Ccc/Tcc	14/30	0.568382127801871	1	FACETS	0.219	0.195	0.245	0.219	0.195	0.245	SUBCLONAL	1	TRUE	0	0.615154369724907	1		467	1006	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155778	106155778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	256	358	0	ENST00000380013.4:c.679G>A	p.Glu227Lys	p.E227K	ENST00000380013	NM_001127208.2	227	Gaa/Aaa	3/11	0.568382127801871	1	FACETS	0.91	0.859	0.963	0.91	0.859	0.963	CLONAL	1	TRUE	0	0.615154369724907	1		358	633	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630059	187630059	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866303516	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	298	430	0	ENST00000441802.2:c.923C>T	p.Ser308Phe	p.S308F	ENST00000441802	NM_005245.3	308	tCc/tTc	2/27	1	2	FACETS	0.926	0.873	0.981	0.926	0.873	0.981	CLONAL	1	TRUE	1	0.615154369724907	2		430	1046	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630386	187630386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	326	499	0	ENST00000441802.2:c.596C>T	p.Pro199Leu	p.P199L	ENST00000441802	NM_005245.3	199	cCa/cTa	2/27	1	2	FACETS	0.883	0.834	0.933	0.883	0.834	0.933	CLONAL	1	TRUE	1	0.615154369724907	2		499	1200	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264601	1264601	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	309	480	0	ENST00000310581.5:c.2761C>T	p.Gln921Ter	p.Q921*	ENST00000310581	NM_198253.2	921	Cag/Tag	11/16	0.611069064063412	3	FACETS	0.91	0.857	0.966	0.455	0.428	0.483	CLONAL	1	TRUE	1	0.615154369724907	3		480	1443	SUCCESS
APC	324	MSKCC	GRCh37	5	112170771	112170771	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	715	529	0	ENST00000257430.4:c.1867C>G	p.Arg623Gly	p.R623G	ENST00000257430	NM_000038.5	623	Cgg/Ggg	15/16	0.611069064063412	3	FACETS	0.918	0.887	0.949	0.918	0.887	0.949	CLONAL	2	TRUE	1	0.615154369724907	3		529	1656	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170079	32170079	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1311098727	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	237	431	0	ENST00000375023.3:c.3529G>A	p.Gly1177Arg	p.G1177R	ENST00000375023	NM_004557.3	1177	Ggg/Agg	21/30	0.611069064063412	3	FACETS	0.784	0.73	0.84	0.392	0.365	0.42	SUBCLONAL	1	TRUE	1	0.615154369724907	3		431	1285	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066678	94066678	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1631	483	621	0	ENST00000369303.4:c.1081A>T	p.Asn361Tyr	p.N361Y	ENST00000369303	NM_004440.3	361	Aac/Tac	5/17	0.611069064063412	3	FACETS	0.971	0.926	1	0.486	0.463	0.509	CLONAL	1	TRUE	1	0.615154369724907	3		621	2114	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609759	117609759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1548	336	491	0	ENST00000368508.3:c.6940G>A	p.Asp2314Asn	p.D2314N	ENST00000368508	NM_002944.2	2314	Gat/Aat	43/43	0.526684808434016	4	FACETS	0.937	0.882	0.992			1	CLONAL	1	TRUE	NA	0.615154369724907	4		491	1884	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662627	117662627	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1603	301	469	0	ENST00000368508.3:c.4838T>A	p.Phe1613Tyr	p.F1613Y	ENST00000368508	NM_002944.2	1613	tTt/tAt	29/43	0.526684808434016	4	FACETS	0.83	0.779	0.883			1	CLONAL	1	TRUE	NA	0.615154369724907	4		469	1904	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687430	117687430	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	462	375	1	ENST00000368508.3:c.2621A>T	p.Glu874Val	p.E874V	ENST00000368508	NM_002944.2	874	gAa/gTa	18/43	0.526684808434016	4	FACETS	0.871	0.832	0.911			1	CLONAL	2	TRUE	NA	0.615154369724907	4		376	1393	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202299	138202299	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	479	277	0	ENST00000237289.4:c.2216C>T	p.Pro739Leu	p.P739L	ENST00000237289	NM_001270507.1	739	cCc/cTc	9/9	0.604916072885338	3	FACETS	0.986	0.946	1	0.986	0.946	1	CLONAL	2	TRUE	1	0.615154369724907	3		277	1033	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522556	157522556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1265377330	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1262	308	431	2	ENST00000346085.5:c.4828C>T	p.Pro1610Ser	p.P1610S	ENST00000346085	NM_020732.3	1610	Cct/Tct	18/20	0.604916072885338	3	FACETS	0.834	0.784	0.885	0.417	0.392	0.443	CLONAL	1	TRUE	1	0.615154369724907	3		433	1570	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527357	157527357	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	633	431	0	ENST00000346085.5:c.5082T>G	p.Ile1694Met	p.I1694M	ENST00000346085	NM_020732.3	1694	atT/atG	20/20	0.604916072885338	3	FACETS	0.945	0.912	0.978	0.945	0.912	0.978	CLONAL	2	TRUE	1	0.615154369724907	3		431	1424	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81392179	81392179	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	204	357	0	ENST00000222390.5:c.98G>T	p.Arg33Met	p.R33M	ENST00000222390	NM_000601.4	33	aGg/aTg	2/18	0.611069064063412	3	FACETS	0.952	0.884	1	0.476	0.442	0.512	CLONAL	1	TRUE	1	0.615154369724907	3		357	911	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486281	8486281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	213	333	0	ENST00000356435.5:c.2536C>T	p.Pro846Ser	p.P846S	ENST00000356435		846	Ccg/Tcg	17/35	0.586966395429714	2	FACETS	0.861	0.802	0.922	0.431	0.401	0.461	CLONAL	1	TRUE	0	0.615154369724907	2		333	804	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966611	36966611	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs984035588	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	503	452	1	ENST00000358127.4:c.715C>T	p.Arg239Cys	p.R239C	ENST00000358127	NM_001280556.1	239	Cgc/Tgc	6/10	0.586966395429714	2	FACETS	0.869	0.837	0.901	0.869	0.837	0.901	CLONAL	2	TRUE	0	0.615154369724907	2		453	941	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101894928	101894928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	698	514	0	ENST00000374994.4:c.481G>A	p.Glu161Lys	p.E161K	ENST00000374994	NM_004612.2	161	Gaa/Aaa	3/9	0.611069064063412	3	FACETS	0.933	0.902	0.965	0.933	0.902	0.965	CLONAL	2	TRUE	1	0.615154369724907	3		514	1590	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615538	43615538	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	215	341	0	ENST00000355710.3:c.2617C>T	p.Arg873Trp	p.R873W	ENST00000355710	NM_020975.4	873	Cgg/Tgg	15/20	0.313586991972003	3	FACETS	0.933	0.867	1	0.466	0.433	0.5	INDETERMINATE	1	TRUE	1	0.615154369724907	3		341	980	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851953	63851953	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	179	259	0	ENST00000279873.7:c.2731C>T	p.Pro911Ser	p.P911S	ENST00000279873	NM_032199.2	911	Ccc/Tcc	10/10	0.313586991972003	3	FACETS	0.983	0.908	1	0.492	0.454	0.531	INDETERMINATE	1	TRUE	1	0.615154369724907	3		259	774	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446314	70446314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868773920	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1222	402	580	0	ENST00000373644.4:c.5254C>T	p.Pro1752Ser	p.P1752S	ENST00000373644	NM_030625.2	1752	Ccc/Tcc	11/12	0.313586991972003	3	FACETS	1	0.978	1	0.526	0.499	0.554	INDETERMINATE	1	TRUE	1	0.615154369724907	3		580	1624	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201807	102201807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	366	628	0	ENST00000263464.3:c.1159G>A	p.Glu387Lys	p.E387K	ENST00000263464	NM_001165.4	387	Gaa/Aaa	6/9	0.615154369724907	1	FACETS	0.894	0.851	0.937	0.894	0.851	0.937	CLONAL	1	TRUE	0	0.615154369724907	1		628	922	SUCCESS
CBL	867	MSKCC	GRCh37	11	119167741	119167741	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	264	375	0	ENST00000264033.4:c.2150C>T	p.Ser717Leu	p.S717L	ENST00000264033	NM_005188.3	717	tCa/tTa	13/16	0.615154369724907	1	FACETS	0.814	0.767	0.862	0.814	0.767	0.862	CLONAL	1	TRUE	0	0.615154369724907	1		375	730	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18443862	18443862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	224	529	0	ENST00000266497.5:c.835C>T	p.Pro279Ser	p.P279S	ENST00000266497		279	Ccg/Tcg	3/31	1	2	FACETS	0.956	0.893	1	0.956	0.893	1	CLONAL	1	TRUE	1	0.615154369724907	2		529	762	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18691098	18691098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	196	369	0	ENST00000266497.5:c.3209C>T	p.Ala1070Val	p.A1070V	ENST00000266497		1070	gCt/gTt	23/31	1	2	FACETS	0.729	0.676	0.785	0.729	0.676	0.785	SUBCLONAL	1	TRUE	1	0.615154369724907	2		369	874	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432452	49432452	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	336	530	0	ENST00000301067.7:c.8687C>T	p.Pro2896Leu	p.P2896L	ENST00000301067	NM_003482.3	2896	cCt/cTt	34/54	1	2	FACETS	0.931	0.88	0.982	0.931	0.88	0.982	CLONAL	1	TRUE	1	0.615154369724907	2		530	1174	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434469	49434469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1449737126	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	212	280	2	ENST00000301067.7:c.7084C>T	p.Pro2362Ser	p.P2362S	ENST00000301067	NM_003482.3	2362	Cct/Tct	31/54	1	2	FACETS	0.865	0.805	0.926	0.865	0.805	0.926	CLONAL	1	TRUE	1	0.615154369724907	2		282	797	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434936	49434936	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1007923504	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	152	224	0	ENST00000301067.7:c.6617C>T	p.Pro2206Leu	p.P2206L	ENST00000301067	NM_003482.3	2206	cCt/cTt	31/54	1	2	FACETS	0.879	0.808	0.953	0.879	0.808	0.953	CLONAL	1	TRUE	1	0.615154369724907	2		224	562	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445394	49445394	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	181	223	0	ENST00000301067.7:c.2072C>T	p.Pro691Leu	p.P691L	ENST00000301067	NM_003482.3	691	cCa/cTa	10/54	1	2	FACETS	0.885	0.819	0.952	0.885	0.819	0.952	CLONAL	1	TRUE	1	0.615154369724907	2		223	665	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863272	57863272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1305707895	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1091	409	603	2	ENST00000228682.2:c.1367G>A	p.Gly456Glu	p.G456E	ENST00000228682	NM_005269.2	456	gGg/gAg	11/12	1	2	FACETS	0.886	0.842	0.931	0.886	0.842	0.931	CLONAL	1	TRUE	1	0.615154369724907	2		605	1500	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416809	121416809	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs76845985	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	358	521	4	ENST00000257555.6:c.238G>T	p.Asp80Tyr	p.D80Y	ENST00000257555		80	Gac/Tac	1/10	1	2	FACETS	0.977	0.926	1	0.977	0.926	1	CLONAL	1	TRUE	1	0.615154369724907	2		525	1191	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636143	28636143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371663652	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	287	446	0	ENST00000241453.7:c.229G>A	p.Glu77Lys	p.E77K	ENST00000241453	NM_004119.2	77	Gaa/Aaa	3/24	0.615154369724907	3	FACETS	0.936	0.879	0.994	0.468	0.439	0.497	CLONAL	1	TRUE	1	0.615154369724907	3		446	1304	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28885782	28885782	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	275	492	0	ENST00000282397.4:c.3580T>G	p.Phe1194Val	p.F1194V	ENST00000282397	NM_002019.4	1194	Ttc/Gtc	27/30	0.615154369724907	3	FACETS	0.871	0.816	0.928	0.436	0.408	0.464	CLONAL	1	TRUE	1	0.615154369724907	3		492	1342	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893575	28893575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	536	442	0	ENST00000282397.4:c.3271G>A	p.Glu1091Lys	p.E1091K	ENST00000282397	NM_002019.4	1091	Gaa/Aaa	24/30	0.615154369724907	3	FACETS	0.893	0.858	0.928	0.893	0.858	0.928	CLONAL	2	TRUE	1	0.615154369724907	3		442	1276	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857900	9857900	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	284	383	0	ENST00000330684.3:c.3501G>A	p.Met1167Ile	p.M1167I	ENST00000330684	NM_001134407.1	1167	atG/atA	13/13	1	2	FACETS	0.909	0.855	0.964	0.909	0.855	0.964	CLONAL	1	TRUE	1	0.615154369724907	2		383	1016	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857935	9857935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	290	362	0	ENST00000330684.3:c.3466G>A	p.Glu1156Lys	p.E1156K	ENST00000330684	NM_001134407.1	1156	Gaa/Aaa	13/13	1	2	FACETS	0.971	0.915	1	0.971	0.915	1	CLONAL	1	TRUE	1	0.615154369724907	2		362	971	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	567	408	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.565698387342017	2	FACETS	0.908	0.878	0.938	0.908	0.878	0.938	CLONAL	2	TRUE	0	0.615154369724907	2		408	1015	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271682	15271682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1316	293	510	0	ENST00000263388.2:c.6757G>A	p.Glu2253Lys	p.E2253K	ENST00000263388	NM_000435.2	2253	Gag/Aag	33/33	0.615154369724907	3	FACETS	0.774	0.726	0.824	0.387	0.363	0.412	SUBCLONAL	1	TRUE	1	0.615154369724907	3		510	1609	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272089	15272089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	197	134	1	ENST00000263388.2:c.6350C>T	p.Ser2117Phe	p.S2117F	ENST00000263388	NM_000435.2	2117	tCc/tTc	33/33	0.615154369724907	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.615154369724907	3		135	409	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727079	41727079	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1210	820	525	0	ENST00000301178.4:c.337G>A	p.Gly113Arg	p.G113R	ENST00000301178	NM_021913.4	113	Gga/Aga	3/20	0.225976038236588	5	FACETS	0.842	0.815	0.869	0.842	0.815	0.869	INDETERMINATE	3	TRUE	2	0.615154369724907	5		525	2030	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546725	9546725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210292896	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	447	314	0	ENST00000353224.5:c.1297C>T	p.Arg433Trp	p.R433W	ENST00000353224	NM_177990.2	433	Cgg/Tgg	5/10	0.615154369724907	3	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	1	0.615154369724907	3		314	925	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827909	40827909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778174338	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	360	441	1	ENST00000373198.4:c.2519C>T	p.Ser840Phe	p.S840F	ENST00000373198	NM_133170.3	840	tCt/tTt	17/32	0.615154369724907	3	FACETS	1	0.96	1	0.509	0.481	0.538	CLONAL	1	TRUE	1	0.615154369724907	3		442	1503	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944591	40944592	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	122	273	0	ENST00000373198.4:c.1910_1911delinsAA	p.Arg637Gln	p.R637Q	ENST00000373198	NM_133170.3	637	cGG/cAA	12/32	0.615154369724907	3	FACETS	0.668	0.604	0.736	0.334	0.302	0.368	SUBCLONAL	1	TRUE	1	0.615154369724907	3		273	776	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306689	41306689	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868376470	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	260	368	0	ENST00000373198.4:c.970G>A	p.Glu324Lys	p.E324K	ENST00000373198	NM_133170.3	324	Gaa/Aaa	7/32	0.615154369724907	3	FACETS	0.909	0.851	0.969	0.454	0.425	0.485	CLONAL	1	TRUE	1	0.615154369724907	3		368	1216	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46268728	46268728	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1627	393	658	0	ENST00000371998.3:c.3013A>T	p.Asn1005Tyr	p.N1005Y	ENST00000371998		1005	Aac/Tac	16/23	0.615154369724907	3	FACETS	0.827	0.783	0.872	0.414	0.391	0.436	CLONAL	1	TRUE	1	0.615154369724907	3		658	2020	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39763629	39763629	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542821839	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	80	364	0	ENST00000288319.7:c.823C>T	p.Pro275Ser	p.P275S	ENST00000288319	NM_182918.3	275	Cca/Tca	8/10	0.442100079194278	2	FACETS	0.301	0.265	0.341	0.151	0.132	0.171	SUBCLONAL	1	TRUE	0	0.615154369724907	2		364	863	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617194	100617194	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	789	569	1	ENST00000308731.7:c.555A>T	p.Lys185Asn	p.K185N	ENST00000308731	NM_000061.2	185	aaA/aaT	7/19	0.586966395429714	2	FACETS	0.907	0.881	0.933	0.907	0.881	0.933	CLONAL	2	TRUE	0	0.615154369724907	2		570	1414	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504128	123504128	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	289	478	0	ENST00000371139.4:c.304G>T	p.Val102Phe	p.V102F	ENST00000371139	NM_001114937.2	102	Gtt/Ttt	3/4	0.586966395429714	2	FACETS	0.901	0.848	0.955	0.45	0.424	0.478	CLONAL	1	TRUE	0	0.615154369724907	2		478	1043	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29496919	29496919	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0008997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	520	363	0	ENST00000356175.3:c.491del	p.Leu164Ter	p.L164*	ENST00000356175	NM_000267.3	164	Tta/ta	5/57	0.565698387342017	2	FACETS	0.93	0.898	0.962	0.93	0.898	0.962	CLONAL	2	TRUE	0	0.615154369724907	2		363	909	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0009119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	49	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.851	1	1	0.851	1	CLONAL	1	TRUE	1	0.23	2		464	425	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0009119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	27	145	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.72	0.574	0.887	0.72	0.574	0.887	SUBCLONAL	1	TRUE	1	0.23	2		145	326	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164723	32164723	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1458	165	461	2	ENST00000375023.3:c.5179G>A	p.Val1727Met	p.V1727M	ENST00000375023	NM_004557.3	1727	Gtg/Atg	28/30	0.179465508018644	4	FACETS	1	0.961	1	0.544	0.497	0.593	CLONAL	1	TRUE	2	0.23	4		463	1623	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983361	149983361	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1202209521	NA	P-0009119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	46	155	0	ENST00000253339.5:c.2897A>G	p.Gln966Arg	p.Q966R	ENST00000253339		966	cAa/cGa	7/7	1	2	FACETS	0.891	0.751	1	0.891	0.751	1	CLONAL	1	TRUE	1	0.23	2		155	449	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372254	55372254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1358462345	NA	P-0009119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	16	86	1	ENST00000297316.4:c.944C>T	p.Pro315Leu	p.P315L	ENST00000297316	NM_022454.3	315	cCg/cTg	2/2	1	2	FACETS	0.495	0.366	0.65	0.495	0.366	0.65	SUBCLONAL	1	TRUE	1	0.23	2		87	281	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272201	15272201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113178142	NA	P-0009119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	12	81	0	ENST00000263388.2:c.6238C>T	p.Arg2080Trp	p.R2080W	ENST00000263388	NM_000435.2	2080	Cgg/Tgg	33/33	1	2	FACETS	0.458	0.321	0.625	0.458	0.321	0.625	SUBCLONAL	1	TRUE	1	0.23	2		81	228	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578282	+	frameshift_variant	Frame_Shift_Del	DEL	GGATAAGATGCTGAGGAGGG	GGATAAGATGCTGAGGAGGG	-	novel	NA	P-0009119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	124	401	0	ENST00000269305.4:c.567_586del	p.Pro190SerfsTer12	p.P190Sfs*12	ENST00000269305	NM_001126112.2	189	gcCCCTCCTCAGCATCTTATCCga/gcga	6/11	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.23	2		401	1042	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653202	29653203	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0009119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	68	193	0	ENST00000356175.3:c.5138_5139dup	p.Glu1714LysfsTer4	p.E1714Kfs*4	ENST00000356175	NM_000267.3	1713	gaa/gAAaa	36/57	1	2	FACETS	0.917	0.797	1	0.917	0.797	1	CLONAL	1	TRUE	1	0.23	2		193	645	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0009148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	89	117	464	0				ENST00000310581	NM_198253.2	-/1132			0.650557869268897	1	FACETS	0.634	0.587	0.679	0.634	0.587	0.679	SUBCLONAL	1	TRUE	0	0.945378280322812	1		464	206	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0009148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	516	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.356285604015001	4	FACETS	0.985	0.957	1	0.738	0.717	0.759	INDETERMINATE	3	TRUE	0	0.945378280322812	4		490	719	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0009148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	157	631	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	1	2	FACETS	0.574	0.528	0.621	0.574	0.528	0.621	SUBCLONAL	1	TRUE	1	0.945378280322812	2		631	579	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964429	93964429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	235	602	0	ENST00000369303.4:c.2468G>A	p.Gly823Glu	p.G823E	ENST00000369303	NM_004440.3	823	gGa/gAa	14/17	0.309792687152544	2	FACETS	0.618	0.578	0.659	0.309	0.289	0.33	INDETERMINATE	1	TRUE	0	0.945378280322812	2		602	804	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874551	35874551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs201084372	NA	P-0009148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	276	435	0	ENST00000303115.3:c.707G>A	p.Gly236Glu	p.G236E	ENST00000303115	NM_002185.3	236	gGg/gAg	6/8	0.309792687152544	2	FACETS	1	0.994	1	0.646	0.617	0.675	INDETERMINATE	1	TRUE	0	0.945378280322812	2		435	452	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89693002	89693003	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0009148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	239	212	0	ENST00000371953.3:c.491dup	p.Val166SerfsTer14	p.V166Sfs*14	ENST00000371953	NM_000314.4	162	-/A	5/9	0.945378280322812	1	FACETS	0.966	0.937	0.992	0.966	0.937	0.992	CLONAL	1	TRUE	0	0.945378280322812	1		212	276	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32182001	32182001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	369	437	0	ENST00000375023.3:c.2053G>A	p.Gly685Arg	p.G685R	ENST00000375023	NM_004557.3	685	Ggg/Agg	13/30	0.494574250702443	1	FACETS	0.765	0.738	0.792	0.765	0.738	0.792	INDETERMINATE	1	TRUE	0	0.945378280322812	1		437	538	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587161	189587161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173679499	NA	P-0009148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	392	353	0	ENST00000264731.3:c.1178G>A	p.Arg393Gln	p.R393Q	ENST00000264731	NM_003722.4	393	cGa/cAa	9/14	0.317112168137274	4	FACETS	1	0.978	1	0.76	0.736	0.783	INDETERMINATE	3	TRUE	0	0.945378280322812	4		353	531	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016292	150016292	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	483	500	0	ENST00000253339.5:c.414T>G	p.Ile138Met	p.I138M	ENST00000253339		138	atT/atG	2/7	NA	2	FACETS	1	0.996	1			1	INDETERMINATE	1	TRUE	NA	0.945378280322812	2		500	778	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970939	21970939	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554653893	NA	P-0009148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	16	11	400	0	ENST00000304494.5:c.419G>A	p.Ser140Asn	p.S140N	ENST00000304494	NM_000077.4	140	aGt/aAt	2/3	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.945378280322812	NA		400	27	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549125	87549125	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1075108	NA	P-0009148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	163	394	0	ENST00000277120.3:c.1682G>A	p.Gly561Asp	p.G561D	ENST00000277120		561	gGc/gAc	15/19	NA	2	FACETS	0.584	0.539	0.632			1	INDETERMINATE	1	TRUE	NA	0.945378280322812	2		394	590	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576198	88576198	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768882070	NA	P-0009148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	133	220	0	ENST00000360948.2:c.1475C>T	p.Ser492Leu	p.S492L	ENST00000360948	NM_001012338.2	492	tCg/tTg	13/19	0.272467326566298	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.945378280322812	0		220	270	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858091	45858091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	158	408	0	ENST00000391945.4:c.1562G>A	p.Gly521Glu	p.G521E	ENST00000391945	NM_000400.3	521	gGg/gAg	17/23	0.258627640822102	3	FACETS	1	0.933	1			1	INDETERMINATE	1	TRUE	NA	0.945378280322812	3		408	487	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069340	30069340	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	372	321	0	ENST00000338641.4:c.1205C>T	p.Ala402Val	p.A402V	ENST00000338641	NM_000268.3	402	gCc/gTc	12/16	0.372369621371218	4	FACETS	1	0.994	1			1	INDETERMINATE	2	TRUE	NA	0.945378280322812	4		321	621	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56772495	56772495	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	328	330	0	ENST00000337432.4:c.350del	p.Leu117Ter	p.L117*	ENST00000337432	NM_058216.2	117	Tta/ta	2/9	0.309792687152544	2	FACETS	1	0.996	1	0.704	0.676	0.73	INDETERMINATE	1	TRUE	0	0.945378280322812	2		330	493	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	185	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.698090682453856	2		280	474	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211585	46211585	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0009174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	333	459	0	ENST00000334344.6:c.551C>G	p.Ser184Ter	p.S184*	ENST00000334344	NM_152641.2	184	tCa/tGa	5/21	1	2	FACETS	0.859	0.813	0.907	0.859	0.813	0.907	CLONAL	1	TRUE	1	0.698090682453856	2		459	1110	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921440	39921462	+	frameshift_variant	Frame_Shift_Del	DEL	CTTATTGACAATAAGTCTCCGTG	CTTATTGACAATAAGTCTCCGTG	-	novel	NA	P-0009174-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	302	255	0	ENST00000378444.4:c.4358_4380del	p.Ala1453GlufsTer16	p.A1453Efs*16	ENST00000378444	NM_001123385.1	1453	gCACGGAGACTTATTGTCAATAAG/g	10/15	1	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.698090682453856	1		255	504	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0009177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	262	558	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.229528531396471	3	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	1	0.229528531396471	3		558	1270	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0009177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	170	229	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.848	0.784	0.914			1	INDETERMINATE	3	TRUE	NA	0.229528531396471	2		229	582	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0009177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	138	75	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.921	0.846	0.999			1	INDETERMINATE	3	TRUE	NA	0.229528531396471	2		75	435	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630630	158630630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1591	167	774	1	ENST00000263640.3:c.613G>A	p.Ala205Thr	p.A205T	ENST00000263640	NM_001105.4	205	Gct/Act	6/11	0.229528531396471	3	FACETS	0.923	0.844	1	0.461	0.422	0.503	CLONAL	1	TRUE	1	0.229528531396471	3		775	1758	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097608	11097608	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1489647083	NA	P-0009177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1381	338	636	0	ENST00000358026.2:c.788C>T	p.Pro263Leu	p.P263L	ENST00000358026	NM_001128849.1	263	cCa/cTa	5/36	0.229528531396471	4	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	2	0.229528531396471	4		636	1719	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40757428	40757428	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763638227	NA	P-0009177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	224	488	0	ENST00000373198.4:c.2870C>T	p.Pro957Leu	p.P957L	ENST00000373198	NM_133170.3	957	cCg/cTg	20/32	0.229528531396471	3	FACETS	0.877	0.816	0.941	0.877	0.816	0.941	CLONAL	2	TRUE	1	0.229528531396471	3		488	1240	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579314	7579315	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GC	novel	NA	P-0009177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	194	357	0	ENST00000269305.4:c.371_372dup	p.Thr125AlafsTer46	p.T125Afs*46	ENST00000269305	NM_001126112.2	124	-/GC	4/11	0.222650112345374	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.229528531396471	2		357	766	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64571838	64571839	+	frameshift_variant	Frame_Shift_Del	DEL	AC	AC	-	novel	NA	P-0009177-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1505	483	852	0	ENST00000312049.6:c.1800_1801del	p.Ser601PhefsTer77	p.S601Ffs*77	ENST00000312049	NM_130799.2	600	ctGTct/ctct	10/10	0.229528531396471	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.229528531396471	3		852	1988	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	59	589	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.352211567841782	2		589	310	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095836	178095836	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1328262363	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	50	152	0	ENST00000397062.3:c.1495C>T	p.Arg499Trp	p.R499W	ENST00000397062	NM_006164.4	499	Cgg/Tgg	5/5	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.352211567841782	2		152	256	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	41	300	0				ENST00000310581	NM_198253.2	-/1132			0.352211567841782	3	FACETS	1	0.956	1	0.721	0.608	0.843	CLONAL	1	TRUE	1	0.352211567841782	3		300	190	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	19	157	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.352211567841782	1	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	0	0.352211567841782	1		157	68	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138944	64138944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	36	147	0	ENST00000334205.4:c.2311C>T	p.Pro771Ser	p.P771S	ENST00000334205	NM_003942.2	771	Ccc/Tcc	17/17	0.352211567841782	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	0	0.352211567841782	1		147	150	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578289	7578289	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1064795841	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	44	164	0	ENST00000269305.4:c.560G>A	p.Gly187Asp	p.G187D	ENST00000269305	NM_001126112.2	187	gGt/gAt	6/11	1	2	FACETS	1	0.881	1	1	0.881	1	CLONAL	1	TRUE	1	0.352211567841782	2		164	238	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292570	15292570	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	33	155	1	ENST00000263388.2:c.2609C>T	p.Ser870Phe	p.S870F	ENST00000263388	NM_000435.2	870	tCc/tTc	17/33	0.352211567841782	1	FACETS	0.936	0.772	1	0.936	0.772	1	CLONAL	1	TRUE	0	0.352211567841782	1		156	165	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416417	49416417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565753611	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	21	357	0	ENST00000301067.7:c.16294C>T	p.Arg5432Trp	p.R5432W	ENST00000301067	NM_003482.3	5432	Cgg/Tgg	51/54	1	2	FACETS	0.523	0.404	0.661	0.523	0.404	0.661	SUBCLONAL	1	TRUE	1	0.352211567841782	2		357	228	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590732	189590732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	66	209	0	ENST00000264731.3:c.1297G>A	p.Glu433Lys	p.E433K	ENST00000264731	NM_003722.4	433	Gaa/Aaa	10/14	0.239502128427104	3	FACETS	1	0.97	1	0.7	0.612	0.793	CLONAL	1	TRUE	1	0.352211567841782	3		209	315	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031973	26031973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	85	351	0	ENST00000244661.2:c.316G>A	p.Glu106Lys	p.E106K	ENST00000244661	NM_003537.3	106	Gag/Aag	1/1	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.352211567841782	2		351	460	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458612	120458612	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	52	134	0	ENST00000256646.2:c.6733C>T	p.His2245Tyr	p.H2245Y	ENST00000256646	NM_024408.3	2245	Cat/Tat	34/34	0.25095940065696	3	FACETS	0.827	0.713	0.948	0.827	0.713	0.948	CLONAL	2	TRUE	1	0.352211567841782	3		134	210	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880249	155880249	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	45	163	0	ENST00000368323.3:c.155C>T	p.Pro52Leu	p.P52L	ENST00000368323	NM_006912.5	52	cCc/cTc	3/6	1	2	FACETS	0.994	0.842	1	0.994	0.842	1	CLONAL	1	TRUE	1	0.352211567841782	2		163	257	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846241	156846241	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	45	170	0	ENST00000524377.1:c.1682C>T	p.Ala561Val	p.A561V	ENST00000524377	NM_002529.3	561	gCt/gTt	14/17	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.352211567841782	2		170	234	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26029123	26029123	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	132	224	0	ENST00000435504.4:c.227G>A	p.Gly76Asp	p.G76D	ENST00000435504		76	gGt/gAt	4/13	0.352211567841782	3	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	1	0.352211567841782	3		224	422	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426738	212426738	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	21	487	0	ENST00000342788.4:c.2377C>T	p.Gln793Ter	p.Q793*	ENST00000342788	NM_005235.2	793	Cag/Tag	20/28	1	2	FACETS	0.53	0.409	0.67	0.53	0.409	0.67	SUBCLONAL	1	TRUE	1	0.352211567841782	2		487	225	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259578	89259578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	22	89	0	ENST00000336596.2:c.722G>A	p.Arg241Lys	p.R241K	ENST00000336596	NM_005233.5	241	aGg/aAg	3/17	1	2	FACETS	0.801	0.626	0.999	0.801	0.626	0.999	CLONAL	1	TRUE	1	0.352211567841782	2		89	156	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480430	89480430	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	32	209	0	ENST00000336596.2:c.2267G>A	p.Ser756Asn	p.S756N	ENST00000336596	NM_005233.5	756	aGt/aAt	13/17	1	2	FACETS	0.702	0.572	0.846	0.702	0.572	0.846	SUBCLONAL	1	TRUE	1	0.352211567841782	2		209	259	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461594	138461594	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	43	164	0	ENST00000289153.2:c.427C>T	p.Pro143Ser	p.P143S	ENST00000289153	NM_006219.2	143	Cct/Tct	3/22	0.15318553106441	1	FACETS	0.89	0.752	1	0.89	0.752	1	INDETERMINATE	1	TRUE	0	0.352211567841782	1		164	226	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215886	142215886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	65	177	1	ENST00000350721.4:c.5707C>T	p.Leu1903Phe	p.L1903F	ENST00000350721	NM_001184.3	1903	Ctc/Ttc	33/47	0.239502128427104	3	FACETS	0.851	0.746	0.962	0.851	0.746	0.962	CLONAL	2	TRUE	1	0.352211567841782	3		178	255	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916813	178916813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	122	364	1	ENST00000263967.3:c.200C>T	p.Ser67Phe	p.S67F	ENST00000263967	NM_006218.2	67	tCt/tTt	2/21	0.239502128427104	3	FACETS	0.842	0.765	0.921	0.842	0.765	0.921	CLONAL	2	TRUE	1	0.352211567841782	3		365	484	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927441	178927441	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	85	189	0	ENST00000263967.3:c.1204C>T	p.Leu402Phe	p.L402F	ENST00000263967	NM_006218.2	402	Ctt/Ttt	7/21	0.239502128427104	3	FACETS	0.835	0.744	0.93	0.835	0.744	0.93	CLONAL	2	TRUE	1	0.352211567841782	3		189	340	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55984966	55984966	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	45	141	0	ENST00000263923.4:c.163G>A	p.Gly55Arg	p.G55R	ENST00000263923	NM_002253.2	55	Gga/Aga	3/30	0.224244281916503	1	FACETS	0.993	0.844	1	0.993	0.844	1	CLONAL	1	TRUE	0	0.352211567841782	1		141	212	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286274	66286274	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143584300	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	43	153	0	ENST00000273854.3:c.1412C>T	p.Pro471Leu	p.P471L	ENST00000273854	NM_004439.5	471	cCa/cTa	6/18	0.224244281916503	1	FACETS	0.845	0.713	0.989	0.845	0.713	0.989	CLONAL	1	TRUE	0	0.352211567841782	1		153	238	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467448	66467448	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	21	123	0	ENST00000273854.3:c.821T>A	p.Met274Lys	p.M274K	ENST00000273854	NM_004439.5	274	aTg/aAg	3/18	0.224244281916503	1	FACETS	0.54	0.418	0.68	0.54	0.418	0.68	SUBCLONAL	1	TRUE	0	0.352211567841782	1		123	182	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157597	106157597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	48	229	0	ENST00000380013.4:c.2498C>T	p.Ser833Phe	p.S833F	ENST00000380013	NM_001127208.2	833	tCt/tTt	3/11	0.224244281916503	1	FACETS	0.829	0.706	0.962	0.829	0.706	0.962	CLONAL	1	TRUE	0	0.352211567841782	1		229	271	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541040	187541040	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	18	117	1	ENST00000441802.2:c.6700G>A	p.Gly2234Arg	p.G2234R	ENST00000441802	NM_005245.3	2234	Gga/Aga	10/27	0.224244281916503	1	FACETS	0.602	0.457	0.769	0.602	0.457	0.769	SUBCLONAL	1	TRUE	0	0.352211567841782	1		118	140	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962607	38962607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	50	182	0	ENST00000357387.3:c.1648C>T	p.Leu550Phe	p.L550F	ENST00000357387	NM_152756.3	550	Ctt/Ttt	18/38	0.352211567841782	3	FACETS	1	0.92	1	0.56	0.478	0.649	CLONAL	1	TRUE	1	0.352211567841782	3		182	298	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176696688	176696688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	33	192	0	ENST00000439151.2:c.5389C>T	p.Leu1797Phe	p.L1797F	ENST00000439151	NM_022455.4	1797	Ctc/Ttc	16/23	1	2	FACETS	0.884	0.726	1	0.884	0.726	1	CLONAL	1	TRUE	1	0.352211567841782	2		192	212	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681552	117681552	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	66	243	0	ENST00000368508.3:c.3398C>A	p.Ser1133Tyr	p.S1133Y	ENST00000368508	NM_002944.2	1133	tCt/tAt	22/43	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.352211567841782	2		243	268	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508037	106508037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747163273	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	11	89	0	ENST00000359195.3:c.31G>A	p.Val11Met	p.V11M	ENST00000359195	NM_002649.2	11	Gtg/Atg	2/11	1	2	FACETS	0.48	0.333	0.661	0.48	0.333	0.661	SUBCLONAL	1	TRUE	1	0.352211567841782	2		89	130	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482208	87482208	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	52	199	0	ENST00000277120.3:c.1495C>T	p.His499Tyr	p.H499Y	ENST00000277120		499	Cac/Tac	14/19	0.352211567841782	2	FACETS	1	0.889	1	0.522	0.447	0.602	CLONAL	1	TRUE	0	0.352211567841782	2		199	283	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98011453	98011453	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	66	201	0	ENST00000289081.3:c.121T>C	p.Phe41Leu	p.F41L	ENST00000289081	NM_000136.2	41	Ttc/Ctc	2/15	0.352211567841782	2	FACETS	1	0.957	1	0.612	0.536	0.694	CLONAL	1	TRUE	0	0.352211567841782	2		201	306	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802585	139802585	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs956492484	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	81	259	0	ENST00000247668.2:c.430C>T	p.Arg144Cys	p.R144C	ENST00000247668	NM_021138.3	144	Cgc/Tgc	5/11	0.352211567841782	1	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	0	0.352211567841782	1		259	263	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104268951	104268951	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	71	255	0	ENST00000369902.3:c.208T>C	p.Tyr70His	p.Y70H	ENST00000369902	NM_016169.3	70	Tat/Cat	2/12	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.352211567841782	2		255	353	SUCCESS
CBL	867	MSKCC	GRCh37	11	119077306	119077306	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	72	223	0	ENST00000264033.4:c.179G>A	p.Trp60Ter	p.W60*	ENST00000264033	NM_005188.3	60	tGg/tAg	1/16	0.352211567841782	1	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	0	0.352211567841782	1		223	284	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12006438	12006438	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	28	253	1	ENST00000396373.4:c.406C>T	p.Pro136Ser	p.P136S	ENST00000396373	NM_001987.4	136	Cct/Tct	4/8	1	2	FACETS	0.439	0.351	0.54	0.439	0.351	0.54	SUBCLONAL	1	TRUE	1	0.352211567841782	2		254	362	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856415	111856415	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	46	132	0	ENST00000341259.2:c.466G>A	p.Ala156Thr	p.A156T	ENST00000341259	NM_005475.2	156	Gcg/Acg	2/8	1	2	FACETS	0.773	0.662	0.891	1	0.966	1	SUBCLONAL	2	TRUE	1	0.352211567841782	2		132	169	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906773	32906773	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	63	252	0	ENST00000380152.3:c.1158A>C	p.Glu386Asp	p.E386D	ENST00000380152		386	gaA/gaC	10/27	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.352211567841782	2		252	351	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81606063	81606063	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs189506473	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	53	205	0	ENST00000298171.2:c.733G>A	p.Gly245Ser	p.G245S	ENST00000298171	NM_000369.2	245	Ggc/Agc	9/10	0.352211567841782	2	FACETS	0.909	0.779	1	0.455	0.389	0.525	CLONAL	1	TRUE	0	0.352211567841782	2		205	331	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610464	81610464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	44	209	0	ENST00000298171.2:c.2062G>A	p.Asp688Asn	p.D688N	ENST00000298171	NM_000369.2	688	Gat/Aat	10/10	0.352211567841782	2	FACETS	0.922	0.778	1	0.461	0.389	0.54	CLONAL	1	TRUE	0	0.352211567841782	2		209	271	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476286	88476286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	50	164	0	ENST00000360948.2:c.1846G>A	p.Val616Ile	p.V616I	ENST00000360948	NM_001012338.2	616	Gtc/Atc	15/19	0.224244281916503	1	FACETS	0.943	0.808	1	0.943	0.808	1	CLONAL	1	TRUE	0	0.352211567841782	1		164	248	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	359974	359974	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	51	270	0	ENST00000262320.3:c.1115C>T	p.Pro372Leu	p.P372L	ENST00000262320	NM_003502.3	372	cCc/cTc	4/11	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.352211567841782	2		270	262	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857076	9857076	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	44	190	0	ENST00000330684.3:c.4325C>T	p.Pro1442Leu	p.P1442L	ENST00000330684	NM_001134407.1	1442	cCc/cTc	13/13	1	2	FACETS	0.915	0.773	1	0.915	0.773	1	CLONAL	1	TRUE	1	0.352211567841782	2		190	273	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821158	72821158	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	57	301	0	ENST00000268489.5:c.11017G>C	p.Asp3673His	p.D3673H	ENST00000268489	NM_006885.3	3673	Gac/Cac	10/10	1	2	FACETS	0.767	0.66	0.883	0.767	0.66	0.883	SUBCLONAL	1	TRUE	1	0.352211567841782	2		301	422	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322710	30322710	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761306912	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	52	208	0	ENST00000322652.5:c.1723C>T	p.Arg575Cys	p.R575C	ENST00000322652	NM_015355.2	575	Cgt/Tgt	14/16	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.352211567841782	2		208	265	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60795940	60795940	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	31	152	0	ENST00000333681.4:c.638C>T	p.Ser213Phe	p.S213F	ENST00000333681		213	tCc/tTc	3/3	1	2	FACETS	0.743	0.604	0.898	0.743	0.604	0.898	SUBCLONAL	1	TRUE	1	0.352211567841782	2		152	237	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211121	2211121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	19	197	0	ENST00000398665.3:c.1375C>T	p.Pro459Ser	p.P459S	ENST00000398665	NM_032482.2	459	Ccg/Tcg	15/28	0.352211567841782	1	FACETS	0.324	0.246	0.416	0.324	0.246	0.416	SUBCLONAL	1	TRUE	0	0.352211567841782	1		197	274	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296139	15296139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780152379	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	38	178	0	ENST00000263388.2:c.2225C>T	p.Pro742Leu	p.P742L	ENST00000263388	NM_000435.2	742	cCg/cTg	14/33	0.352211567841782	1	FACETS	0.993	0.832	1	0.993	0.832	1	CLONAL	1	TRUE	0	0.352211567841782	1		178	179	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257880	19257880	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1266163850	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	47	236	0	ENST00000162023.5:c.506C>T	p.Pro169Leu	p.P169L	ENST00000162023		169	cCc/cTc	9/13	0.352211567841782	1	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	0	0.352211567841782	1		236	203	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725025	47725025	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199804290	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	21	231	0	ENST00000449228.1:c.719C>T	p.Ser240Leu	p.S240L	ENST00000449228	NM_001127240.2	240	tCg/tTg	4/4	0.352211567841782	1	FACETS	0.404	0.312	0.511	0.404	0.312	0.511	SUBCLONAL	1	TRUE	0	0.352211567841782	1		231	243	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523329	9523329	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867092977	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	40	221	0	ENST00000353224.5:c.1908G>A	p.Met636Ile	p.M636I	ENST00000353224	NM_177990.2	636	atG/atA	9/10	1	2	FACETS	0.805	0.673	0.951	0.805	0.673	0.951	CLONAL	1	TRUE	1	0.352211567841782	2		221	282	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023214	31023214	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	49	212	0	ENST00000375687.4:c.2699C>T	p.Pro900Leu	p.P900L	ENST00000375687	NM_015338.5	900	cCc/cTc	13/13	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.352211567841782	2		212	278	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46252712	46252712	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	73	320	0	ENST00000371998.3:c.141A>C	p.Glu47Asp	p.E47D	ENST00000371998		47	gaA/gaC	4/23	1	2	FACETS	0.849	0.745	0.962	0.849	0.745	0.962	CLONAL	1	TRUE	1	0.352211567841782	2		320	488	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913268	39913268	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	72	102	0	ENST00000378444.4:c.4847T>C	p.Val1616Ala	p.V1616A	ENST00000378444	NM_001123385.1	1616	gTt/gCt	14/15	0.165693117159374	2	FACETS	1	0.964	1			1	INDETERMINATE	2	TRUE	NA	0.352211567841782	2		102	172	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76778858	76778858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	103	165	0	ENST00000373344.5:c.6721C>T	p.Leu2241Phe	p.L2241F	ENST00000373344	NM_000489.3	2241	Ctt/Ttt	31/35	0.165693117159374	2	FACETS	0.903	0.827	0.979			1	INDETERMINATE	3	TRUE	NA	0.352211567841782	2		165	216	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579351	7579351	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	31	138	0	ENST00000269305.4:c.336del	p.Phe113SerfsTer10	p.F113Sfs*10	ENST00000269305	NM_001126112.2	112	ggC/gg	4/11	1	2	FACETS	0.863	0.703	1	0.863	0.703	1	CLONAL	1	TRUE	1	0.352211567841782	2		138	204	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227659924	227659924	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	58	276	0	ENST00000305123.5:c.3531del	p.Asn1178ThrfsTer3	p.N1178Tfs*3	ENST00000305123	NM_005544.2	1177	ctT/ct	1/2	0.240768113815212	3	FACETS	1	0.925	1			1	CLONAL	1	TRUE	NA	0.352211567841782	3		276	349	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056220	27056221	+	missense_variant	Missense_Mutation	DNP	GG	GG	AC	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	73	170	0	ENST00000324856.7:c.1216_1217delinsAC	p.Gly406Thr	p.G406T	ENST00000324856	NM_006015.4	406	GGa/ACa	2/20	0.25095940065696	3	FACETS	0.883	0.781	0.991	0.883	0.781	0.991	CLONAL	2	TRUE	1	0.352211567841782	3		170	276	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570780	226570781	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	28	107	0	ENST00000366794.5:c.1115_1116delinsTT	p.Ser372Phe	p.S372F	ENST00000366794	NM_001618.3	372	tCC/tTT	8/23	1	2	FACETS	0.981	0.793	1	0.981	0.793	1	CLONAL	1	TRUE	1	0.352211567841782	2		107	162	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405868	157405869	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	52	143	0	ENST00000346085.5:c.2110_2111delinsAA	p.Gly704Lys	p.G704K	ENST00000346085	NM_020732.3	704	GGg/AAg	6/20	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.352211567841782	2		143	230	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345844	152345845	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	133	324	0	ENST00000359321.1:c.725_726delinsTT	p.Ser242Phe	p.S242F	ENST00000359321	NM_005431.1	242	tCC/tTT	3/3	1	2	FACETS	0.874	0.801	0.95	1	0.99	1	CLONAL	2	TRUE	1	0.352211567841782	2		324	432	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128008	30128009	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	48	251	0	ENST00000263025.4:c.1120_1121delinsAA	p.Gly374Lys	p.G374K	ENST00000263025	NM_002746.2	374	GGa/AAa	8/9	1	2	FACETS	0.831	0.706	0.968	0.831	0.706	0.968	CLONAL	1	TRUE	1	0.352211567841782	2		251	328	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007607	62007608	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	26	173	0	ENST00000392795.3:c.259_260delinsTT	p.Pro87Phe	p.P87F	ENST00000392795	NM_001039933.1	87	CCc/TTc	3/6	0.352211567841782	3	FACETS	0.736	0.585	0.907	0.368	0.292	0.454	CLONAL	1	TRUE	1	0.352211567841782	3		173	236	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296139	15296140	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	40	173	2	ENST00000263388.2:c.2224_2225delinsTT	p.Pro742Leu	p.P742L	ENST00000263388	NM_000435.2	742	CCg/TTg	14/33	0.352211567841782	1	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	0	0.352211567841782	1		175	174	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144036	11144037	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	14	160	0	ENST00000358026.2:c.3617_3618delinsTT	p.Thr1206Ile	p.T1206I	ENST00000358026	NM_001128849.1	1206	aCC/aTT	26/36	0.352211567841782	1	FACETS	0.264	0.191	0.353	0.264	0.191	0.353	SUBCLONAL	1	TRUE	0	0.352211567841782	1		160	248	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375495	15375496	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	52	234	0	ENST00000263377.2:c.931_932delinsTT	p.Pro311Leu	p.P311L	ENST00000263377	NM_058243.2	311	CCg/TTg	6/20	0.352211567841782	1	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	0	0.352211567841782	1		234	216	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793058	42793059	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0009189-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	10	140	0	ENST00000575354.2:c.950_951delinsTT	p.Ser317Phe	p.S317F	ENST00000575354	NM_015125.3	317	tCC/tTT	7/20	0.352211567841782	1	FACETS	0.267	0.181	0.376	0.267	0.181	0.376	SUBCLONAL	1	TRUE	0	0.352211567841782	1		140	175	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	41	280	0				ENST00000310581	NM_198253.2	-/1132			0.234027094551364	3	FACETS	0.908	0.76	1	0.454	0.38	0.536	CLONAL	1	TRUE	1	0.350017987660897	3		280	303	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971177	21971177	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913382	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	70	117	0	ENST00000304494.5:c.181G>T	p.Glu61Ter	p.E61*	ENST00000304494	NM_000077.4	61	Gag/Tag	2/3	0.229107890759681	2	FACETS	0.752	0.663	0.845	0.752	0.663	0.845	SUBCLONAL	2	TRUE	0	0.350017987660897	2		117	266	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579529	7579529	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876658483	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	161	377	3	ENST00000269305.4:c.158G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tGg/tAg	4/11	0.234027094551364	3	FACETS	1	0.985	1	0.661	0.606	0.717	CLONAL	1	TRUE	1	0.350017987660897	3		380	818	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795103	242795104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768249210	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	76	349	0	ENST00000334409.5:c.105dup	p.Thr36HisfsTer70	p.T36Hfs*70	ENST00000334409	NM_005018.2	35	-/C	2/5	0.250576890140754	3	FACETS	0.683	0.598	0.774	0.228	0.199	0.258	SUBCLONAL	1	TRUE	0	0.350017987660897	3		349	747	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064794618	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	88	375	0	ENST00000269305.4:c.159G>A	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tgG/tgA	4/11	0.234027094551364	3	FACETS	0.728	0.644	0.817	0.364	0.322	0.409	SUBCLONAL	1	TRUE	1	0.350017987660897	3		375	812	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209617	98209617	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	71	185	0	ENST00000331920.6:c.3921del	p.Arg1308GlufsTer64	p.R1308Efs*64	ENST00000331920	NM_000264.3	1307	ccC/cc	23/24	0.350017987660897	3	FACETS	0.889	0.777	1	0.296	0.259	0.337	CLONAL	1	TRUE	0	0.350017987660897	3		185	536	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845524	151845524	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	101	333	0	ENST00000262189.6:c.13488del	p.Phe4496LeufsTer21	p.F4496Lfs*21	ENST00000262189	NM_170606.2	4496	ttT/tt	52/59	0.243820289844256	4	FACETS	0.751	0.67	0.838	0.376	0.335	0.419	SUBCLONAL	1	TRUE	2	0.350017987660897	4		333	1037	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647028	23647028	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1555461597	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	65	453	0	ENST00000261584.4:c.839del	p.Asn280ThrfsTer8	p.N280Tfs*8	ENST00000261584	NM_024675.3	280	aAc/ac	4/13	0.234027094551364	3	FACETS	0.379	0.327	0.435	0.189	0.163	0.218	SUBCLONAL	1	TRUE	1	0.350017987660897	3		453	1152	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55268045	55268045	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144496976	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	124	471	1	ENST00000275493.2:c.2885G>A	p.Arg962His	p.R962H	ENST00000275493	NM_005228.3	962	cGt/cAt	24/28	0.243820289844256	4	FACETS	0.782	0.706	0.863	0.391	0.353	0.432	SUBCLONAL	1	TRUE	2	0.350017987660897	4		472	1223	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27107200	27107200	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1266828809	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	78	296	0	ENST00000324856.7:c.6811G>A	p.Val2271Ile	p.V2271I	ENST00000324856	NM_006015.4	2271	Gtt/Att	20/20	0.264826699660272	4	FACETS	0.659	0.578	0.747	0.22	0.192	0.249	SUBCLONAL	1	TRUE	1	0.350017987660897	4		296	913	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120508181	120508181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	328	342	0	ENST00000256646.2:c.1576G>A	p.Gly526Arg	p.G526R	ENST00000256646	NM_024408.3	526	Ggg/Agg	10/34	0.350017987660897	3	FACETS	1	0.991	1	0.808	0.765	0.85	CLONAL	2	TRUE	0	0.350017987660897	3		342	909	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845922	156845922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	262	509	2	ENST00000524377.1:c.1552G>A	p.Glu518Lys	p.E518K	ENST00000524377	NM_002529.3	518	Gag/Aag	13/17	0.250576890140754	3	FACETS	0.793	0.743	0.845	0.529	0.495	0.563	SUBCLONAL	2	TRUE	0	0.350017987660897	3		511	1109	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967246	25967246	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	105	313	0	ENST00000435504.4:c.1960G>A	p.Ala654Thr	p.A654T	ENST00000435504		654	Gcc/Acc	13/13	0.250576890140754	3	FACETS	0.818	0.732	0.909	0.273	0.244	0.303	CLONAL	1	TRUE	0	0.350017987660897	3		313	862	SUCCESS
ALK	238	MSKCC	GRCh37	2	29519805	29519805	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769505453	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	204	350	0	ENST00000389048.3:c.1766G>A	p.Gly589Asp	p.G589D	ENST00000389048	NM_004304.4	589	gGc/gAc	9/29	0.250576890140754	3	FACETS	0.778	0.722	0.836	0.519	0.481	0.557	SUBCLONAL	2	TRUE	0	0.350017987660897	3		350	880	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478026	138478026	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	112	448	0	ENST00000289153.2:c.160T>A	p.Tyr54Asn	p.Y54N	ENST00000289153	NM_006219.2	54	Tat/Aat	1/22	0.234027094551364	3	FACETS	0.816	0.733	0.905	0.408	0.366	0.453	CLONAL	1	TRUE	1	0.350017987660897	3		448	921	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153705	55153705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759510574	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	80	403	0	ENST00000257290.5:c.2671C>T	p.Leu891Phe	p.L891F	ENST00000257290	NM_006206.4	891	Ctt/Ttt	19/23	0.250576890140754	3	FACETS	0.585	0.514	0.662	0.195	0.171	0.221	SUBCLONAL	1	TRUE	0	0.350017987660897	3		403	918	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518900	187518900	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745695748	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	76	421	1	ENST00000441802.2:c.12304G>A	p.Gly4102Arg	p.G4102R	ENST00000441802	NM_005245.3	4102	Gga/Aga	24/27	0.250576890140754	3	FACETS	0.434	0.379	0.494	0.145	0.126	0.165	SUBCLONAL	1	TRUE	0	0.350017987660897	3		422	1175	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056748	180056748	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	904	93	505	0	ENST00000261937.6:c.764G>A	p.Trp255Ter	p.W255*	ENST00000261937	NM_182925.4	255	tGg/tAg	6/30	0.234027094551364	3	FACETS	0.626	0.556	0.702	0.313	0.278	0.351	SUBCLONAL	1	TRUE	1	0.350017987660897	3		505	997	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120779	94120779	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	483	611	0	ENST00000369303.4:c.272C>T	p.Ser91Phe	p.S91F	ENST00000369303	NM_004440.3	91	tCc/tTc	3/17	0.250576890140754	3	FACETS	1	0.982	1	0.7	0.668	0.731	CLONAL	2	TRUE	0	0.350017987660897	3		611	1545	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630029	117630029	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs976517290	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	272	408	0	ENST00000368508.3:c.6497C>T	p.Ser2166Phe	p.S2166F	ENST00000368508	NM_002944.2	2166	tCc/tTc	41/43	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.350017987660897	2		408	1110	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265520	152265520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	133	242	0	ENST00000206249.3:c.973C>T	p.Pro325Ser	p.P325S	ENST00000206249	NM_000125.3	325	Ccg/Tcg	4/8	0.250576890140754	3	FACETS	1	0.985	1	0.474	0.431	0.518	CLONAL	1	TRUE	0	0.350017987660897	3		242	628	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431653	6431653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	51	274	0	ENST00000356142.4:c.206C>T	p.Pro69Leu	p.P69L	ENST00000356142	NM_018890.3	69	cCc/cTc	3/7	0.243820289844256	4	FACETS	0.591	0.501	0.689	0.295	0.25	0.345	SUBCLONAL	1	TRUE	2	0.350017987660897	4		274	666	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273083	55273083	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	226	325	0	ENST00000275493.2:c.3406C>G	p.Pro1136Ala	p.P1136A	ENST00000275493	NM_005228.3	1136	Ccc/Gcc	28/28	0.243820289844256	4	FACETS	0.818	0.762	0.877	0.818	0.762	0.877	CLONAL	2	TRUE	2	0.350017987660897	4		325	1065	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829225	128829225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	92	308	0	ENST00000249373.3:c.233G>A	p.Cys78Tyr	p.C78Y	ENST00000249373	NM_005631.4	78	tGc/tAc	1/12	0.243820289844256	4	FACETS	0.911	0.809	1	0.456	0.404	0.51	CLONAL	1	TRUE	2	0.350017987660897	4		308	779	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879120	151879120	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772288933	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	84	363	0	ENST00000262189.6:c.5825C>T	p.Thr1942Ile	p.T1942I	ENST00000262189	NM_170606.2	1942	aCa/aTa	36/59	0.243820289844256	4	FACETS	0.635	0.56	0.717	0.318	0.28	0.359	SUBCLONAL	1	TRUE	2	0.350017987660897	4		363	1020	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485972	8485972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	133	479	0	ENST00000356435.5:c.2845G>A	p.Gly949Ser	p.G949S	ENST00000356435		949	Ggc/Agc	17/35	0.229107890759681	2	FACETS	0.74	0.671	0.813	0.37	0.335	0.407	SUBCLONAL	1	TRUE	0	0.350017987660897	2		479	1027	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537195	80537195	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	58	182	0	ENST00000286548.4:c.203C>T	p.Ser68Phe	p.S68F	ENST00000286548	NM_002072.3	68	tCt/tTt	2/7	0.350017987660897	3	FACETS	0.764	0.657	0.88	0.255	0.219	0.294	SUBCLONAL	1	TRUE	0	0.350017987660897	3		182	510	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760096	133760096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	335	324	0	ENST00000318560.5:c.2419G>A	p.Gly807Ser	p.G807S	ENST00000318560	NM_005157.4	807	Ggc/Agc	11/11	0.350017987660897	3	FACETS	0.884	0.84	0.929	0.884	0.84	0.929	CLONAL	3	TRUE	0	0.350017987660897	3		324	848	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100909932	100909932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	391	523	1	ENST00000325455.5:c.2717C>T	p.Pro906Leu	p.P906L	ENST00000325455	NM_001202474.3	906	cCa/cTa	8/8	0.350017987660897	3	FACETS	0.897	0.851	0.944	0.897	0.851	0.944	CLONAL	2	TRUE	1	0.350017987660897	3		524	1463	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426835	121426835	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs754728827	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	73	266	0	ENST00000257555.6:c.526C>T	p.Gln176Ter	p.Q176*	ENST00000257555		176	Cag/Tag	2/10	0.234027094551364	3	FACETS	0.683	0.596	0.776	0.341	0.298	0.388	SUBCLONAL	1	TRUE	1	0.350017987660897	3		266	718	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563266	21563266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1320375890	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	106	368	0	ENST00000382592.4:c.653G>A	p.Gly218Glu	p.G218E	ENST00000382592	NM_014572.2	218	gGa/gAa	4/8	0.33017979960751	3	FACETS	0.897	0.804	0.996	0.449	0.402	0.498	CLONAL	1	TRUE	1	0.350017987660897	3		368	793	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913641	32913641	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs893978143	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	133	559	0	ENST00000380152.3:c.5149G>A	p.Glu1717Lys	p.E1717K	ENST00000380152		1717	Gaa/Aaa	11/27	0.33017979960751	3	FACETS	0.768	0.696	0.844	0.384	0.348	0.422	SUBCLONAL	1	TRUE	1	0.350017987660897	3		559	1163	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059287	42059287	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1457	117	535	1	ENST00000219905.7:c.9007G>T	p.Ala3003Ser	p.A3003S	ENST00000219905	NM_001164273.1	3003	Gca/Tca	24/24	0.350017987660897	4	FACETS	0.573	0.515	0.636	0.191	0.171	0.212	SUBCLONAL	1	TRUE	1	0.350017987660897	4		536	1574	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994617	73994617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	76	282	0	ENST00000318443.5:c.101C>T	p.Pro34Leu	p.P34L	ENST00000318443	NM_001024736.1	34	cCt/cTt	3/10	0.350017987660897	4	FACETS	0.688	0.602	0.781	0.229	0.2	0.261	SUBCLONAL	1	TRUE	1	0.350017987660897	4		282	852	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129372	30129372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	96	426	0	ENST00000263025.4:c.656C>T	p.Ser219Phe	p.S219F	ENST00000263025	NM_002746.2	219	tCc/tTc	4/9	0.234027094551364	3	FACETS	0.627	0.557	0.702	0.313	0.278	0.351	SUBCLONAL	1	TRUE	1	0.350017987660897	3		426	1028	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11094856	11094856	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	123	476	0	ENST00000358026.2:c.29G>A	p.Gly10Glu	p.G10E	ENST00000358026	NM_001128849.1	10	gGa/gAa	2/36	0.234027094551364	3	FACETS	0.758	0.684	0.836	0.379	0.342	0.418	SUBCLONAL	1	TRUE	1	0.350017987660897	3		476	1090	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525018	9525018	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	92	296	0	ENST00000353224.5:c.1867G>A	p.Glu623Lys	p.E623K	ENST00000353224	NM_177990.2	623	Gag/Aag	8/10	0.332478191214278	4	FACETS	0.718	0.637	0.806	0.359	0.318	0.403	SUBCLONAL	1	TRUE	2	0.350017987660897	4		296	988	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561223	9561223	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	82	364	1	ENST00000353224.5:c.559C>T	p.Pro187Ser	p.P187S	ENST00000353224	NM_177990.2	187	Cct/Tct	4/10	0.332478191214278	4	FACETS	0.558	0.491	0.631	0.279	0.245	0.316	SUBCLONAL	1	TRUE	2	0.350017987660897	4		365	1133	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650406	48650406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	127	290	1	ENST00000376670.3:c.376G>A	p.Gly126Arg	p.G126R	ENST00000376670	NM_002049.3	126	Gga/Aga	3/6	0.350017987660897	2	FACETS	1	0.954	1			1	CLONAL	1	TRUE	NA	0.350017987660897	2		291	670	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8108230	8108231	+	frameshift_variant	Frame_Shift_Del	DEL	GA	GA	-	novel	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	101	357	0	ENST00000585124.1:c.993_994del	p.Arg332GlufsTer31	p.R332Efs*31	ENST00000585124	NM_004217.3	331	tcTCgg/tcgg	9/9	0.234027094551364	3	FACETS	0.731	0.652	0.815	0.365	0.326	0.408	SUBCLONAL	1	TRUE	1	0.350017987660897	3		357	928	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401813	139401813	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	137	412	0	ENST00000277541.6:c.3587del	p.Gly1196AlafsTer249	p.G1196Afs*249	ENST00000277541	NM_017617.3	1196	gGc/gc	22/34	0.350017987660897	3	FACETS	0.869	0.789	0.954	0.29	0.263	0.318	CLONAL	1	TRUE	0	0.350017987660897	3		412	1058	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955112	17955112	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755706305	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	85	324	3	ENST00000458235.1:c.115del	p.Gln39SerfsTer108	p.Q39Sfs*108	ENST00000458235	NM_000215.3	39	Cag/ag	2/24	0.234027094551364	3	FACETS	0.671	0.592	0.755	0.335	0.296	0.378	SUBCLONAL	1	TRUE	1	0.350017987660897	3		327	851	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843498	156843514	+	frameshift_variant	Frame_Shift_Del	DEL	GCCGGCACCGTCTCTGC	GCCGGCACCGTCTCTGC	-	novel	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	208	363	0	ENST00000524377.1:c.926_942del	p.Pro309LeufsTer10	p.P309Lfs*10	ENST00000524377	NM_002529.3	308	caGCCGGCACCGTCTCTGCgc/cagc	8/17	0.250576890140754	3	FACETS	0.983	0.916	1	0.656	0.611	0.702	CLONAL	2	TRUE	0	0.350017987660897	3		363	710	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47698102	47698119	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	AGCAAATTGACTTCTTTA	AGCAAATTGACTTCTTTA	-	novel	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	131	319	0	ENST00000233146.2:c.1662-1_1678del		p.X554_splice	ENST00000233146	NM_000251.2	554		11/16	0.250576890140754	3	FACETS	0.792	0.722	0.866	0.528	0.481	0.577	SUBCLONAL	2	TRUE	0	0.350017987660897	3		319	555	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412380	139412381	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	211	200	0	ENST00000277541.6:c.1264_1265delinsTT	p.Pro422Phe	p.P422F	ENST00000277541	NM_017617.3	422	CCc/TTc	8/34	0.350017987660897	3	FACETS	0.843	0.789	0.898	0.843	0.789	0.898	CLONAL	3	TRUE	0	0.350017987660897	3		200	560	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524144	187524147	+	frameshift_variant	Frame_Shift_Del	DEL	ACGG	ACGG	CAA	novel	NA	P-0009258-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	277	358	0	ENST00000441802.2:c.11392_11395delinsTTG	p.Pro3798LeufsTer35	p.P3798Lfs*35	ENST00000441802	NM_005245.3	3798	CCGTgc/TTGgc	20/27	0.250576890140754	3	FACETS	0.947	0.89	1	0.631	0.593	0.67	CLONAL	2	TRUE	0	0.350017987660897	3		358	982	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	93	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.957	1	1	0.988	1	CLONAL	2	TRUE	1	0.209536289621136	2		280	391	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0009263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	37	595	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.467	0.384	0.561	0.467	0.384	0.561	SUBCLONAL	1	TRUE	1	0.209536289621136	2		595	756	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0009263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	93	145	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.957	0.855	1	1	0.986	1	CLONAL	2	TRUE	1	0.209536289621136	2		145	464	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949758	151949758	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	408	452	0	ENST00000262189.6:c.1342C>T	p.Gln448Ter	p.Q448*	ENST00000262189	NM_170606.2	448	Cag/Tag	10/59	0.209536289621136	4	FACETS	0.922	0.878	0.967	1	0.993	1	CLONAL	4	TRUE	1	0.209536289621136	4		452	1277	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098966	178098966	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	76	318	0	ENST00000397062.3:c.79G>T	p.Asp27Tyr	p.D27Y	ENST00000397062	NM_006164.4	27	Gat/Tat	2/5	1	2	FACETS	0.855	0.749	0.97	0.855	0.749	0.97	CLONAL	1	TRUE	1	0.209536289621136	2		318	848	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518173	187518173	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1046322764	NA	P-0009263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	237	412	3	ENST00000441802.2:c.12521C>T	p.Pro4174Leu	p.P4174L	ENST00000441802	NM_005245.3	4174	cCg/cTg	25/27	1	2	FACETS	0.995	0.928	1	1	0.994	1	CLONAL	2	TRUE	1	0.209536289621136	2		415	1137	SUCCESS
APC	324	MSKCC	GRCh37	5	112175555	112175555	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	249	466	0	ENST00000257430.4:c.4264G>A	p.Asp1422Asn	p.D1422N	ENST00000257430	NM_000038.5	1422	Gat/Aat	16/16	1	2	FACETS	0.985	0.92	1	1	0.994	1	CLONAL	2	TRUE	1	0.209536289621136	2		466	1206	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168740	32168740	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1367	154	488	0	ENST00000375023.3:c.4183G>A	p.Asp1395Asn	p.D1395N	ENST00000375023	NM_004557.3	1395	Gac/Aac	23/30	0.209536289621136	3	FACETS	1	0.953	1	0.534	0.487	0.584	CLONAL	1	TRUE	1	0.209536289621136	3		488	1521	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674222	117674222	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777817381	NA	P-0009263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1066	132	594	1	ENST00000368508.3:c.4252G>A	p.Val1418Ile	p.V1418I	ENST00000368508	NM_002944.2	1418	Gtt/Att	26/43	0.209536289621136	1	FACETS	0.942	0.853	1	0.942	0.853	1	CLONAL	1	TRUE	0	0.209536289621136	1		595	1198	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117866632	117866632	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1518	551	763	0	ENST00000297338.2:c.1013G>C	p.Arg338Thr	p.R338T	ENST00000297338	NM_006265.2	338	aGa/aCa	9/14	0.209536289621136	3	FACETS	0.936	0.896	0.977	1	0.996	1	CLONAL	3	TRUE	1	0.209536289621136	3		763	2069	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402720	139402720	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	107	382	0	ENST00000277541.6:c.3289C>T	p.Pro1097Ser	p.P1097S	ENST00000277541	NM_017617.3	1097	Ccc/Tcc	20/34	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.209536289621136	2		382	985	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413085	139413085	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1300110216	NA	P-0009263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	260	470	0	ENST00000277541.6:c.1057C>T	p.Arg353Cys	p.R353C	ENST00000277541	NM_017617.3	353	Cgt/Tgt	6/34	1	2	FACETS	1	0.955	1	1	0.995	1	CLONAL	2	TRUE	1	0.209536289621136	2		470	1211	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434240	49434240	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0009263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1398	299	686	0	ENST00000301067.7:c.7313C>G	p.Ser2438Ter	p.S2438*	ENST00000301067	NM_003482.3	2438	tCa/tGa	31/54	1	2	FACETS	0.841	0.789	0.894	1	0.994	1	CLONAL	2	TRUE	1	0.209536289621136	2		686	1697	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865540	57865540	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1295636010	NA	P-0009263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1524	173	678	0	ENST00000228682.2:c.3017G>A	p.Gly1006Asp	p.G1006D	ENST00000228682	NM_005269.2	1006	gGc/gAc	12/12	1	2	FACETS	0.973	0.892	1	0.973	0.892	1	CLONAL	1	TRUE	1	0.209536289621136	2		678	1697	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95597845	95597845	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0009263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	88	410	0	ENST00000393063.1:c.438+1G>T		p.X146_splice	ENST00000393063	NM_030621.3	146			1	2	FACETS	0.739	0.652	0.832	0.739	0.652	0.832	SUBCLONAL	1	TRUE	1	0.209536289621136	2		410	1137	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003787	45003787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1329285364	NA	P-0009263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	200	476	0	ENST00000558401.1:c.43C>T	p.Leu15Phe	p.L15F	ENST00000558401	NM_004048.2	15	Ctt/Ttt	1/4	1	2	FACETS	0.842	0.78	0.908	1	0.992	1	CLONAL	2	TRUE	1	0.209536289621136	2		476	1133	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99472879	99472879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	109	458	0	ENST00000268035.6:c.2875C>T	p.His959Tyr	p.H959Y	ENST00000268035	NM_000875.3	959	Cat/Tat	14/21	1	2	FACETS	0.853	0.764	0.949	0.853	0.764	0.949	CLONAL	1	TRUE	1	0.209536289621136	2		458	1219	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475330	40475330	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1375	717	729	0	ENST00000264657.5:c.1696G>C	p.Asp566His	p.D566H	ENST00000264657	NM_139276.2	566	Gac/Cac	19/24	0.209536289621136	4	FACETS	0.989	0.954	1	1	0.997	1	CLONAL	4	TRUE	1	0.209536289621136	4		729	2092	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221634	22221634	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	116	266	0	ENST00000215832.6:c.97G>C	p.Glu33Gln	p.E33Q	ENST00000215832	NM_002745.4	33	Gag/Cag	1/9	1	2	FACETS	0.938	0.848	1	1	0.988	1	CLONAL	2	TRUE	1	0.209536289621136	2		266	590	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971154	21971188	+	frameshift_variant	Frame_Shift_Del	DEL	CGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGG	CGCGCCGTGGAGCAGCAGCAGCTCCGCCACTCGGG	-	novel	NA	P-0009263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	100	169	0	ENST00000304494.5:c.170_204del	p.Ala57GlyfsTer51	p.A57Gfs*51	ENST00000304494	NM_000077.4	57	gCCCGAGTGGCGGAGCTGCTGCTGCTCCACGGCGCG/g	2/3	0.209536289621136	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	0	0.209536289621136	2		169	425	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412496	139412716	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CTGGGCACCCCCTGAAGCCAGAATCGACTTCTCATCGGTTCTGGGGCCAGGCTGCCACCCCCACCTGGCCGCACCCCCTGTGCTGGCACCTACCCAGCGAGCACTCATCCACGTCCTGGCTGCAGGCCGGGCCCGTGTACCCCGAGGGGCAGGTGCAGATGGCCTTGCCATTGACAGGGTTGGTGTCGCAGTTGGAGCCCTCGTTACAGGGGTTGCTGATG	CTGGGCACCCCCTGAAGCCAGAATCGACTTCTCATCGGTTCTGGGGCCAGGCTGCCACCCCCACCTGGCCGCACCCCCTGTGCTGGCACCTACCCAGCGAGCACTCATCCACGTCCTGGCTGCAGGCCGGGCCCGTGTACCCCGAGGGGCAGGTGCAGATGGCCTTGCCATTGACAGGGTTGGTGTCGCAGTTGGAGCCCTCGTTACAGGGGTTGCTGATG	-	novel	NA	P-0009263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	64	115	0	ENST00000277541.6:c.1128_1255+93del		p.X376_splice	ENST00000277541	NM_017617.3	376		7/34	1	2	FACETS	1	0.877	1	1	0.981	1	CLONAL	2	TRUE	1	0.209536289621136	2		115	304	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881608	111881609	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	A	novel	NA	P-0009263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	216	448	0	ENST00000393256.3:c.287dup	p.Tyr96Ter	p.Y96*	ENST00000393256	NM_006538.4	96	tat/tAat	2/4	1	2	FACETS	0.916	0.851	0.984	1	0.993	1	CLONAL	2	TRUE	1	0.209536289621136	2		448	1125	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851469	151851469	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009263-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1275	281	489	0	ENST00000262189.6:c.12022del	p.Glu4008ArgfsTer6	p.E4008Rfs*6	ENST00000262189	NM_170606.2	4008	Gag/ag	47/59	0.209536289621136	4	FACETS	1	0.965	1	0.695	0.651	0.74	CLONAL	2	TRUE	1	0.209536289621136	4		489	1556	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0009292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	663	464	0				ENST00000310581	NM_198253.2	-/1132			0.525669305398731	7	FACETS	0.996	0.966	1	0.996	0.966	1	CLONAL	5	TRUE	2	0.525669305398731	7		464	1172	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0009292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	530	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.514690157073235	5	FACETS	0.978	0.94	1	0.978	0.94	1	CLONAL	3	TRUE	2	0.525669305398731	5		490	1229	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748206	41748206	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	104	491	0	ENST00000226382.2:c.563A>C	p.Lys188Thr	p.K188T	ENST00000226382	NM_003924.3	188	aAg/aCg	3/3	0.525669305398731	3	FACETS	0.432	0.386	0.482	0.216	0.193	0.241	SUBCLONAL	1	TRUE	1	0.525669305398731	3		491	1156	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460581	149460581	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	188	206	0	ENST00000286301.3:c.56G>C	p.Gly19Ala	p.G19A	ENST00000286301	NM_005211.3	19	gGa/gCa	3/22	0.443277982831753	2	FACETS	0.797	0.744	0.849	0.797	0.744	0.849	SUBCLONAL	2	TRUE	0	0.525669305398731	2		206	449	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915886	127915886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	427	639	2	ENST00000373547.4:c.595C>T	p.Pro199Ser	p.P199S	ENST00000373547	NM_002721.4	199	Cct/Tct	6/7	0.12141899632377	3	FACETS	1	0.995	1	0.717	0.682	0.752	INDETERMINATE	1	TRUE	1	0.525669305398731	3		641	1431	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414232	32414232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	549	494	0	ENST00000332351.3:c.1319G>A	p.Arg440Lys	p.R440K	ENST00000332351	NM_024426.4	440	aGa/aAa	8/10	0.429787642485441	3	FACETS	1	0.995	1	0.791	0.762	0.819	CLONAL	2	TRUE	0	0.525669305398731	3		494	1112	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993158	72993158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1332687082	NA	P-0009292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	300	742	0	ENST00000268489.5:c.887C>T	p.Ser296Leu	p.S296L	ENST00000268489	NM_006885.3	296	tCg/tTg	2/10	1	2	FACETS	0.881	0.828	0.934	0.881	0.828	0.934	CLONAL	1	TRUE	1	0.525669305398731	2		742	1296	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030442	49030443	+	stop_gained	Nonsense_Mutation	DNP	GA	GA	AT	novel	NA	P-0009292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	734	243	0	ENST00000267163.4:c.1917_1918delinsAT	p.Lys640Ter	p.K640*	ENST00000267163	NM_000321.2	639	caGAag/caATag	19/27	0.525669305398731	5	FACETS	0.983	0.96	1	0.983	0.96	1	CLONAL	5	TRUE	0	0.525669305398731	5		243	1016	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579472	7579475	+	frameshift_variant	Frame_Shift_Del	DEL	GGGG	GGGG	CGA	novel	NA	P-0009292-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	351	261	0	ENST00000269305.4:c.212_215delinsTCG	p.Pro71LeufsTer52	p.P71Lfs*52	ENST00000269305	NM_001126112.2	71	cCCCCc/cTCGc	4/11	0.464729614043834	3	FACETS	1	0.994	1	0.825	0.789	0.862	CLONAL	2	TRUE	0	0.525669305398731	3		261	681	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0009297-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	55	176	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.205275628938025	4	FACETS	0.842	0.723	0.971	0.561	0.482	0.647	CLONAL	2	TRUE	1	0.212955964213781	4		176	372	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578527	7578527	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009297-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	119	321	0	ENST00000269305.4:c.403del	p.Cys135AlafsTer35	p.C135Afs*35	ENST00000269305	NM_001126112.2	135	Tgc/gc	5/11	0.162512668760954	5	FACETS	0.85	0.77	0.935	0.638	0.577	0.701	CLONAL	3	TRUE	1	0.212955964213781	5		321	578	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468382	89468382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs570346631	NA	P-0009297-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	72	231	1	ENST00000336596.2:c.1916G>A	p.Arg639His	p.R639H	ENST00000336596	NM_005233.5	639	cGc/cAc	11/17	0.212955964213781	5	FACETS	1	0.97	1	0.464	0.405	0.527	CLONAL	1	TRUE	2	0.212955964213781	5		232	641	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243675729	243675729	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0009297-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	86	231	0	ENST00000263826.5:c.1252-1G>A		p.X418_splice	ENST00000263826	NM_005465.4	418			0.212955964213781	8	FACETS	1	0.955	1	0.464	0.411	0.52	CLONAL	2	TRUE	3	0.212955964213781	8		231	571	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391076	89391076	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009297-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	173	439	0	ENST00000336596.2:c.1142G>C	p.Arg381Pro	p.R381P	ENST00000336596	NM_005233.5	381	cGc/cCc	5/17	0.212955964213781	5	FACETS	1	0.979	1	0.788	0.725	0.853	CLONAL	2	TRUE	2	0.212955964213781	5		439	907	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751576	57751576	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009297-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	78	281	0	ENST00000274289.3:c.1415C>A	p.Ala472Glu	p.A472E	ENST00000274289	NM_006622.3	472	gCa/gAa	11/14	0.162512668760954	5	FACETS	0.835	0.734	0.942	0.417	0.367	0.471	CLONAL	2	TRUE	1	0.212955964213781	5		281	579	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464372	120464387	+	frameshift_variant	Frame_Shift_Del	DEL	CCAGTGTTCACTTGTT	CCAGTGTTCACTTGTT	-	novel	NA	P-0009297-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	58	352	2	ENST00000256646.2:c.5259_5274del	p.Thr1754SerfsTer11	p.T1754Sfs*11	ENST00000256646	NM_024408.3	1753	ggAACAAGTGAACACTGG/gg	29/34	0.212955964213781	5	FACETS	0.875	0.75	1	0.292	0.25	0.338	CLONAL	1	TRUE	2	0.212955964213781	5		354	821	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0009308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	165	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.98	0.903	1	1	0.992	1	CLONAL	2	TRUE	1	0.25177681760266	2		464	669	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0009308-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	300	558	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.247822959946569	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.25177681760266	2		558	1138	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0009311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	216	464	0				ENST00000310581	NM_198253.2	-/1132			0.644376440672656	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.644376440672656	1		464	340	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0009311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	161	176	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.644376440672656	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.644376440672656	1		176	265	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0009311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	323	528	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.242764177573094	2	FACETS	1	0.994	1	0.68	0.646	0.714	INDETERMINATE	1	TRUE	0	0.644376440672656	2		528	737	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0009311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	504	572	1	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.644376440672656	3	FACETS	0.94	0.903	0.977	0.94	0.903	0.977	CLONAL	2	TRUE	1	0.644376440672656	3		573	1100	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874636	35874636	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	352	530	2	ENST00000303115.3:c.792G>A	p.Trp264Ter	p.W264*	ENST00000303115	NM_002185.3	264	tgG/tgA	6/8	0.644376440672656	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.644376440672656	1		532	666	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867546	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs11466445	NA	P-0009311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	12	7	0	ENST00000374994.4:c.70_78del	p.Ala24_Ala26del	p.A24_A26del	ENST00000374994	NM_004612.2	17	ctGGCGGCGGCg/ctg	1/9	0.171323083058217	4	FACETS	1	0.876	1	0.729	0.533	0.949	INDETERMINATE	1	TRUE	2	0.644376440672656	4		7	42	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266104	41266104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28931589	NA	P-0009311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	372	496	0	ENST00000349496.5:c.101G>A	p.Gly34Glu	p.G34E	ENST00000349496	NM_001904.3	34	gGa/gAa	3/15	0.171323083058217	4	FACETS	0.902	0.858	0.947	0.902	0.858	0.947	INDETERMINATE	2	TRUE	2	0.644376440672656	4		496	1052	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312725	91312725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	457	456	1	ENST00000355112.3:c.2464C>T	p.Pro822Ser	p.P822S	ENST00000355112	NM_000057.2	822	Cct/Tct	12/22	0.171323083058217	4	FACETS	0.937	0.895	0.979	0.937	0.895	0.979	INDETERMINATE	2	TRUE	2	0.644376440672656	4		457	1245	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245996	16245996	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	401	484	0	ENST00000375759.3:c.1619A>G	p.Tyr540Cys	p.Y540C	ENST00000375759	NM_015001.2	540	tAt/tGt	8/15	0.242764177573094	2	FACETS	1	0.996	1	0.736	0.705	0.768	INDETERMINATE	1	TRUE	0	0.644376440672656	2		484	845	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259481	16259481	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1241804668	NA	P-0009311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	115	254	0	ENST00000375759.3:c.6746C>T	p.Pro2249Leu	p.P2249L	ENST00000375759	NM_015001.2	2249	cCc/cTc	11/15	0.242764177573094	2	FACETS	0.771	0.699	0.846	0.385	0.349	0.423	INDETERMINATE	1	TRUE	0	0.644376440672656	2		254	463	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405872	49405872	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	501	600	0	ENST00000418115.1:c.266C>T	p.Pro89Leu	p.P89L	ENST00000418115	NM_001664.2	89	cCt/cTt	3/5	0.171323083058217	4	FACETS	0.879	0.842	0.917	0.879	0.842	0.917	INDETERMINATE	2	TRUE	2	0.644376440672656	4		600	1454	SUCCESS
APC	324	MSKCC	GRCh37	5	112176150	112176150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	213	519	0	ENST00000257430.4:c.4859C>T	p.Ser1620Leu	p.S1620L	ENST00000257430	NM_000038.5	1620	tCa/tTa	16/16	0.198357997346488	2	FACETS	0.724	0.673	0.777	0.362	0.336	0.389	INDETERMINATE	1	TRUE	0	0.644376440672656	2		519	913	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55266434	55266434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	357	542	1	ENST00000275493.2:c.2726C>T	p.Thr909Ile	p.T909I	ENST00000275493	NM_005228.3	909	aCc/aTc	23/28	0.644376440672656	3	FACETS	1	0.985	1	0.553	0.523	0.583	CLONAL	1	TRUE	1	0.644376440672656	3		543	1325	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515196	106515196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	303	426	0	ENST00000359195.3:c.2339C>T	p.Pro780Leu	p.P780L	ENST00000359195	NM_002649.2	780	cCc/cTc	5/11	0.644376440672656	3	FACETS	1	0.989	1	0.595	0.561	0.63	CLONAL	1	TRUE	1	0.644376440672656	3		426	1045	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69462881	69462881	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4827	499	514	0	ENST00000227507.2:c.694T>C	p.Phe232Leu	p.F232L	ENST00000227507	NM_053056.2	232	Ttc/Ctc	4/5	0.644376440672656	13	FACETS	1	0.994	1			1	CLONAL	1	TRUE	NA	0.644376440672656	13		514	5326	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118353140	118353140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	417	675	1	ENST00000534358.1:c.4016C>T	p.Pro1339Leu	p.P1339L	ENST00000534358	NM_005933.3	1339	cCa/cTa	8/36	0.644376440672656	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.644376440672656	1		676	781	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499655	18499655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	357	614	0	ENST00000266497.5:c.1510G>A	p.Asp504Asn	p.D504N	ENST00000266497		504	Gat/Aat	10/31	0.171323083058217	4	FACETS	0.808	0.766	0.85	0.808	0.766	0.85	INDETERMINATE	2	TRUE	2	0.644376440672656	4		614	1128	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245288	46245288	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	252	311	0	ENST00000334344.6:c.3382C>T	p.Gln1128Ter	p.Q1128*	ENST00000334344	NM_152641.2	1128	Cag/Tag	15/21	0.171323083058217	4	FACETS	0.836	0.785	0.888	0.836	0.785	0.888	INDETERMINATE	2	TRUE	2	0.644376440672656	4		311	769	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811762	102811762	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	336	494	0	ENST00000307046.8:c.422A>G	p.Asn141Ser	p.N141S	ENST00000307046	NM_001111285.1	141	aAc/aGc	4/4	0.171323083058217	4	FACETS	0.791	0.749	0.834	0.791	0.749	0.834	INDETERMINATE	2	TRUE	2	0.644376440672656	4		494	1084	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590938	95590938	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	207	327	0	ENST00000393063.1:c.971T>G	p.Met324Arg	p.M324R	ENST00000393063	NM_030621.3	324	aTg/aGg	9/28	0.171323083058217	4	FACETS	0.852	0.795	0.91	0.852	0.795	0.91	INDETERMINATE	2	TRUE	2	0.644376440672656	4		327	620	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66777374	66777374	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	453	599	0	ENST00000307102.5:c.740G>A	p.Trp247Ter	p.W247*	ENST00000307102	NM_002755.3	247	tGg/tAg	7/11	0.171323083058217	4	FACETS	0.869	0.83	0.909	0.869	0.83	0.909	INDETERMINATE	2	TRUE	2	0.644376440672656	4		599	1330	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853794	59853794	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	421	619	1	ENST00000259008.2:c.2065C>T	p.Gln689Ter	p.Q689*	ENST00000259008	NM_032043.2	689	Caa/Taa	14/20	0.235248828455244	5	FACETS	0.974	0.928	1	0.649	0.618	0.681	INDETERMINATE	2	TRUE	2	0.644376440672656	5		620	1319	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59937198	59937198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	368	568	0	ENST00000259008.2:c.164C>T	p.Ala55Val	p.A55V	ENST00000259008	NM_032043.2	55	gCc/gTc	3/20	0.235248828455244	5	FACETS	1	0.992	1	0.804	0.766	0.843	INDETERMINATE	2	TRUE	2	0.644376440672656	5		568	931	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3120989	3120989	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	141	228	0	ENST00000078429.4:c.892C>T	p.Pro298Ser	p.P298S	ENST00000078429	NM_002067.2	298	Ccc/Tcc	7/7	1	2	FACETS	0.925	0.849	1	0.925	0.849	1	CLONAL	1	TRUE	1	0.644376440672656	2		228	473	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303241	15303241	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	269	487	1	ENST00000263388.2:c.287C>T	p.Ser96Leu	p.S96L	ENST00000263388	NM_000435.2	96	tCa/tTa	3/33	1	2	FACETS	0.885	0.832	0.94	0.885	0.832	0.94	CLONAL	1	TRUE	1	0.644376440672656	2		488	943	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349616	15349616	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	150	357	0	ENST00000263377.2:c.3958A>T	p.Met1320Leu	p.M1320L	ENST00000263377	NM_058243.2	1320	Atg/Ttg	19/20	1	2	FACETS	0.717	0.658	0.779	0.717	0.658	0.779	SUBCLONAL	1	TRUE	1	0.644376440672656	2		357	649	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953858	17953858	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777195283	NA	P-0009311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	299	392	0	ENST00000458235.1:c.544G>A	p.Gly182Arg	p.G182R	ENST00000458235	NM_000215.3	182	Gga/Aga	5/24	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.644376440672656	2		392	778	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39746874	39746874	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	168	216	0	ENST00000361337.2:c.1888T>C	p.Cys630Arg	p.C630R	ENST00000361337	NM_003286.2	630	Tgt/Cgt	18/21	0.539654346012932	4	FACETS	1	0.986	1	0.44	0.406	0.476	CLONAL	1	TRUE	1	0.644376440672656	4		216	649	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41521893	41521893	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	321	548	0	ENST00000263253.7:c.755C>T	p.Pro252Leu	p.P252L	ENST00000263253	NM_001429.3	252	cCt/cTt	3/31	0.305545218236285	4	FACETS	0.753	0.711	0.795	0.753	0.711	0.795	INDETERMINATE	2	TRUE	2	0.644376440672656	4		548	1088	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66736993	66736994	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0009311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	264	338	0	ENST00000307102.5:c.517-1_517delinsAA		p.X173_splice	ENST00000307102	NM_002755.3	173		5/11	0.171323083058217	4	FACETS	0.919	0.866	0.973	0.919	0.866	0.973	INDETERMINATE	2	TRUE	2	0.644376440672656	4		338	733	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29422354	29422355	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009311-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	370	462	0	ENST00000356175.3:c.27_28delinsAA	p.Trp9_Val10delinsTer	p.W9_V10delins*	ENST00000356175	NM_000267.3	9	tgGGtc/tgAAtc	1/57	0.171323083058217	4	FACETS	0.862	0.819	0.906	0.862	0.819	0.906	INDETERMINATE	2	TRUE	2	0.644376440672656	4		462	1095	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	35	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	TRUE	1	0.270278555687874	2		280	245	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578503	7578503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782620	NA	P-0009331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	100	376	0	ENST00000269305.4:c.427G>A	p.Val143Met	p.V143M	ENST00000269305	NM_001126112.2	143	Gtg/Atg	5/11	0.270278555687874	1	FACETS	0.938	0.839	1	0.938	0.839	1	CLONAL	1	TRUE	0	0.270278555687874	1		376	682	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914037	32914037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555284257	NA	P-0009331-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1194	192	941	1	ENST00000380152.3:c.5545G>A	p.Gly1849Ser	p.G1849S	ENST00000380152		1849	Ggt/Agt	11/27	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.270278555687874	2		942	1386	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	97	521	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.873	0.776	0.977	0.873	0.776	0.977	CLONAL	1	TRUE	1	0.195981377262828	2		522	1134	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602619	10602619	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1239985410	NA	P-0009379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	116	382	0	ENST00000171111.5:c.959G>T	p.Arg320Leu	p.R320L	ENST00000171111	NM_203500.1	320	cGg/cTg	3/6	0.195981377262828	1	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	0	0.195981377262828	1		382	988	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971180	21971180	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	41	126	0	ENST00000304494.5:c.178del	p.Ala60ArgfsTer86	p.A60Rfs*86	ENST00000304494	NM_000077.4	60	Gcg/cg	2/3	0.180590141870979	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.195981377262828	1		126	323	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17354353	17354353	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	94	385	0	ENST00000375499.3:c.431G>T	p.Ser144Ile	p.S144I	ENST00000375499	NM_003000.2	144	aGc/aTc	5/8	0.180590141870979	1	FACETS	0.912	0.81	1	0.912	0.81	1	CLONAL	1	TRUE	0	0.195981377262828	1		385	949	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001915	29001915	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	77	481	0	ENST00000282397.4:c.1250A>C	p.Asn417Thr	p.N417T	ENST00000282397	NM_002019.4	417	aAc/aCc	9/30	0.180590141870979	1	FACETS	0.566	0.495	0.643	0.566	0.495	0.643	SUBCLONAL	1	TRUE	0	0.195981377262828	1		481	1252	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207009	1207009	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	89	304	0	ENST00000326873.7:c.97G>T	p.Glu33Ter	p.E33*	ENST00000326873	NM_000455.4	33	Gag/Tag	1/10	0.195981377262828	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.195981377262828	1		304	757	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130288	11130309	+	frameshift_variant	Frame_Shift_Del	DEL	GCCTTTGTCCCCCAGCTCCGGA	GCCTTTGTCCCCCAGCTCCGGA	-	novel	NA	P-0009379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	101	422	0	ENST00000358026.2:c.2528_2549del	p.Ala843ValfsTer8	p.A843Vfs*8	ENST00000358026	NM_001128849.1	843	GCCTTTGTCCCCCAGCTCCGGAgt/gt	18/36	0.195981377262828	1	FACETS	0.891	0.794	0.993	0.891	0.794	0.993	CLONAL	1	TRUE	0	0.195981377262828	1		422	1044	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039434	47039443	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATCGTGGTGA	ATCGTGGTGA	-	novel	NA	P-0009379-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	111	194	0	ENST00000377604.3:c.1057_1062+4del		p.X353_splice	ENST00000377604	NM_001204468.1	353		10/24	1	1	FACETS	0.859	0.774	0.948	1	0.986	1	CLONAL	2	TRUE	0	0.195981377262828	1		194	595	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0009403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	45	274	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	1	2	FACETS	0.631	0.529	0.744	0.631	0.529	0.744	SUBCLONAL	1	TRUE	1	0.19	2		274	751	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0009403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	58	506	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.855	0.734	0.988	0.855	0.734	0.988	CLONAL	1	TRUE	1	0.19	2		506	714	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056210	26056210	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	66	411	0	ENST00000343677.2:c.447G>C	p.Lys149Asn	p.K149N	ENST00000343677	NM_005319.3	149	aaG/aaC	1/1	1	2	FACETS	0.708	0.613	0.812	0.708	0.613	0.812	SUBCLONAL	1	TRUE	1	0.19	2		411	981	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028835	47028835	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	102	454	0	ENST00000377604.3:c.139G>T	p.Glu47Ter	p.E47*	ENST00000377604	NM_001204468.1	47	Gag/Tag	3/24	0.134045126365613	1	FACETS	0.884	0.789	0.986	0.884	0.789	0.986	CLONAL	1	TRUE	0	0.19	1		454	1099	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77103588	77103588	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0009403-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	31	181	0	ENST00000356341.3:c.-21-2A>T		p.X7_splice	ENST00000356341	NM_002576.4	7			1	2	FACETS	0.814	0.658	0.99	0.814	0.658	0.99	CLONAL	1	TRUE	1	0.19	2		181	401	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	74	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.938	0.839	1	0.938	0.839	1	CLONAL	1	TRUE	1	0.8626505216089	2		280	183	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	253	511	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.917	0.864	0.97	0.917	0.864	0.97	CLONAL	1	TRUE	1	0.8626505216089	2		512	640	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139410452	139410453	+	stop_gained,frameshift_variant	Nonsense_Mutation	INS	-	-	T	rs864622059	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	315	407	0	ENST00000277541.6:c.1649dup	p.Tyr550Ter	p.Y550*	ENST00000277541	NM_017617.3	550	tac/taAc	10/34	1	2	FACETS	0.906	0.859	0.954	0.906	0.859	0.954	CLONAL	1	TRUE	1	0.8626505216089	2		407	806	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78422373	78422373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766248444	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	17	253	1	ENST00000370768.2:c.1589C>T	p.Thr530Met	p.T530M	ENST00000370768	NM_003902.3	530	aCg/aTg	17/20	0.8626505216089	1	FACETS	0.066	0.049	0.086	0.066	0.049	0.086	SUBCLONAL	1	TRUE	0	0.8626505216089	1		254	340	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743993	41743993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	40	529	0	ENST00000301178.4:c.928G>A	p.Ala310Thr	p.A310T	ENST00000301178	NM_021913.4	310	Gca/Aca	7/20	0.8626505216089	1	FACETS	0.097	0.08	0.116	0.097	0.08	0.116	SUBCLONAL	1	TRUE	0	0.8626505216089	1		529	544	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591097	67591097	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519841	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	263	275	0	ENST00000274335.5:c.1690A>G	p.Asn564Asp	p.N564D	ENST00000274335		564	Aac/Gac	12/15	1	2	FACETS	0.969	0.916	1	0.969	0.916	1	CLONAL	1	TRUE	1	0.8626505216089	2		275	629	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	936	71	719	0	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	1	2	FACETS	0.163	0.142	0.187	0.163	0.142	0.187	SUBCLONAL	1	TRUE	1	0.8626505216089	2		719	1007	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168731	32168731	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1245029988	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	50	449	3	ENST00000375023.3:c.4192G>A	p.Ala1398Thr	p.A1398T	ENST00000375023	NM_004557.3	1398	Gca/Aca	23/30	1	2	FACETS	0.125	0.105	0.147	0.125	0.105	0.147	SUBCLONAL	1	TRUE	1	0.8626505216089	2		452	929	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577550	7577550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs985033810	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	21	351	0	ENST00000269305.4:c.731G>A	p.Gly244Asp	p.G244D	ENST00000269305	NM_001126112.2	244	gGc/gAc	7/11	1	2	FACETS	0.062	0.047	0.079	0.062	0.047	0.079	SUBCLONAL	1	TRUE	1	0.8626505216089	2		351	790	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142851	7142851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139912396	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	47	279	0	ENST00000302850.5:c.2518G>A	p.Val840Ile	p.V840I	ENST00000302850	NM_000208.2	840	Gtc/Atc	12/22	1	2	FACETS	0.2	0.169	0.235	0.2	0.169	0.235	SUBCLONAL	1	TRUE	1	0.8626505216089	2		279	544	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796882	42796883	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs761345552	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	293	412	0	ENST00000575354.2:c.3347dup	p.Ser1117LysfsTer34	p.S1117Kfs*34	ENST00000575354	NM_015125.3	1114	gcc/gCcc	14/20	0.8626505216089	1	FACETS	0.824	0.788	0.859	0.824	0.788	0.859	CLONAL	1	TRUE	0	0.8626505216089	1		412	469	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24176330	24176330	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1057517825	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	283	416	1	ENST00000263121.7:c.1121G>A	p.Arg374Gln	p.R374Q	ENST00000263121	NM_003073.3	374	cGg/cAg	9/9	1	2	FACETS	0.906	0.857	0.957	0.906	0.857	0.957	CLONAL	1	TRUE	1	0.8626505216089	2		417	724	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054254	30054254	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1555994854	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	350	434	0	ENST00000338641.4:c.675+1G>A		p.X225_splice	ENST00000338641	NM_000268.3	225			1	2	FACETS	0.9	0.855	0.945	0.9	0.855	0.945	CLONAL	1	TRUE	1	0.8626505216089	2		434	902	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807574	36807574	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs770162943	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	13	186	0	ENST00000373129.3:c.1090G>A	p.Ala364Thr	p.A364T	ENST00000373129	NM_032017.1	364	Gcg/Acg	12/12	0.8626505216089	1	FACETS	0.067	0.048	0.092	0.067	0.048	0.092	SUBCLONAL	1	TRUE	0	0.8626505216089	1		186	254	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72748152	72748152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	66	498	0	ENST00000357731.5:c.26G>A	p.Gly9Asp	p.G9D	ENST00000357731	NM_173808.2	9	gGt/gAt	1/7	0.8626505216089	1	FACETS	0.142	0.123	0.162	0.142	0.123	0.162	SUBCLONAL	1	TRUE	0	0.8626505216089	1		498	614	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551469	150551469	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	58	637	0	ENST00000369026.2:c.538G>A	p.Glu180Lys	p.E180K	ENST00000369026	NM_021960.4	180	Gag/Aag	1/3	1	2	FACETS	0.132	0.113	0.153	0.132	0.113	0.153	SUBCLONAL	1	TRUE	1	0.8626505216089	2		637	1018	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456465	29456465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	551	597	0	ENST00000389048.3:c.2453G>A	p.Gly818Glu	p.G818E	ENST00000389048	NM_004304.4	818	gGa/gAa	14/29	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.8626505216089	2		597	1251	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703517	47703517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1558519543	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	319	366	0	ENST00000233146.2:c.2017G>A	p.Gly673Arg	p.G673R	ENST00000233146	NM_000251.2	673	Gga/Aga	13/16	1	2	FACETS	0.99	0.94	1	0.99	0.94	1	CLONAL	1	TRUE	1	0.8626505216089	2		366	747	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026465	48026465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553412772	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	344	463	0	ENST00000234420.5:c.1343G>A	p.Gly448Glu	p.G448E	ENST00000234420	NM_000179.2	448	gGg/gAg	4/10	1	2	FACETS	0.901	0.856	0.947	0.901	0.856	0.947	CLONAL	1	TRUE	1	0.8626505216089	2		463	885	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164348	47164348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	247	286	0	ENST00000409792.3:c.1778C>T	p.Pro593Leu	p.P593L	ENST00000409792	NM_014159.6	593	cCt/cTt	3/21	1	2	FACETS	0.892	0.839	0.945	0.892	0.839	0.945	CLONAL	1	TRUE	1	0.8626505216089	2		286	642	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498452	89498452	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	59	388	0	ENST00000336596.2:c.2424G>A	p.Trp808Ter	p.W808*	ENST00000336596	NM_005233.5	808	tgG/tgA	14/17	1	2	FACETS	0.16	0.137	0.186	0.16	0.137	0.186	SUBCLONAL	1	TRUE	1	0.8626505216089	2		388	853	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564587	55564587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	259	350	0	ENST00000288135.5:c.475G>A	p.Asp159Asn	p.D159N	ENST00000288135	NM_000222.2	159	Gac/Aac	3/21	1	2	FACETS	0.918	0.866	0.971	0.918	0.866	0.971	CLONAL	1	TRUE	1	0.8626505216089	2		350	654	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534263	187534263	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	21	203	0	ENST00000441802.2:c.9463G>A	p.Gly3155Arg	p.G3155R	ENST00000441802	NM_005245.3	3155	Gga/Aga	13/27	1	2	FACETS	0.131	0.1	0.167	0.131	0.1	0.167	SUBCLONAL	1	TRUE	1	0.8626505216089	2		203	372	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584624	187584624	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	381	511	0	ENST00000441802.2:c.3409C>T	p.Pro1137Ser	p.P1137S	ENST00000441802	NM_005245.3	1137	Cca/Tca	3/27	1	2	FACETS	0.944	0.9	0.988	0.944	0.9	0.988	CLONAL	1	TRUE	1	0.8626505216089	2		511	936	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178083	56178083	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	217	199	0	ENST00000399503.3:c.3056C>T	p.Pro1019Leu	p.P1019L	ENST00000399503	NM_005921.1	1019	cCt/cTt	14/20	1	2	FACETS	0.988	0.928	1	0.988	0.928	1	CLONAL	1	TRUE	1	0.8626505216089	2		199	509	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576766	67576766	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	103	175	0	ENST00000274335.5:c.848C>T	p.Thr283Ile	p.T283I	ENST00000274335		283	aCt/aTt	6/15	1	2	FACETS	0.702	0.635	0.772	0.702	0.635	0.772	SUBCLONAL	1	TRUE	1	0.8626505216089	2		175	340	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37138800	37138800	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	137	217	0	ENST00000373509.5:c.233G>A	p.Gly78Glu	p.G78E	ENST00000373509	NM_002648.3	78	gGa/gAa	3/6	1	2	FACETS	0.861	0.792	0.931	0.861	0.792	0.931	CLONAL	1	TRUE	1	0.8626505216089	2		217	369	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681127	117681127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	48	372	0	ENST00000368508.3:c.3493G>A	p.Val1165Ile	p.V1165I	ENST00000368508	NM_002944.2	1165	Gtt/Att	23/43	1	2	FACETS	0.141	0.118	0.166	0.141	0.118	0.166	SUBCLONAL	1	TRUE	1	0.8626505216089	2		372	790	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200221	138200221	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	33	237	0	ENST00000237289.4:c.1639G>A	p.Ala547Thr	p.A547T	ENST00000237289	NM_001270507.1	547	Gcc/Acc	7/9	1	2	FACETS	0.124	0.1	0.151	0.124	0.1	0.151	SUBCLONAL	1	TRUE	1	0.8626505216089	2		237	617	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148524341	148524341	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	30	286	0	ENST00000320356.2:c.643C>T	p.Pro215Ser	p.P215S	ENST00000320356	NM_004456.4	215	Cct/Tct	7/20	1	2	FACETS	0.126	0.101	0.155	0.126	0.101	0.155	SUBCLONAL	1	TRUE	1	0.8626505216089	2		286	551	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98011468	98011468	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	57	418	0	ENST00000289081.3:c.106C>T	p.Leu36Phe	p.L36F	ENST00000289081	NM_000136.2	36	Ctt/Ttt	2/15	1	2	FACETS	0.131	0.111	0.152	0.131	0.111	0.152	SUBCLONAL	1	TRUE	1	0.8626505216089	2		418	1010	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413100	139413100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201236538	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	75	392	1	ENST00000277541.6:c.1042G>A	p.Ala348Thr	p.A348T	ENST00000277541	NM_017617.3	348	Gcc/Acc	6/34	1	2	FACETS	0.227	0.198	0.258	0.227	0.198	0.258	SUBCLONAL	1	TRUE	1	0.8626505216089	2		393	766	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67201497	67201497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	52	316	0	ENST00000312629.5:c.938G>A	p.Gly313Glu	p.G313E	ENST00000312629	NM_003952.2	313	gGg/gAg	11/15	1	2	FACETS	0.172	0.146	0.201	0.172	0.146	0.201	SUBCLONAL	1	TRUE	1	0.8626505216089	2		316	701	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497657	125497657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	51	331	0	ENST00000428830.2:c.221G>A	p.Arg74Lys	p.R74K	ENST00000428830	NM_001114121.2	74	aGg/aAg	3/14	1	2	FACETS	0.177	0.15	0.207	0.177	0.15	0.207	SUBCLONAL	1	TRUE	1	0.8626505216089	2		331	667	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230712	46230712	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	354	463	0	ENST00000334344.6:c.961C>T	p.His321Tyr	p.H321Y	ENST00000334344	NM_152641.2	321	Cat/Tat	8/21	1	2	FACETS	0.903	0.859	0.948	0.903	0.859	0.948	CLONAL	1	TRUE	1	0.8626505216089	2		463	909	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433569	49433569	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	81	577	1	ENST00000301067.7:c.7984C>T	p.Pro2662Ser	p.P2662S	ENST00000301067	NM_003482.3	2662	Cca/Tca	31/54	1	2	FACETS	0.199	0.175	0.226	0.199	0.175	0.226	SUBCLONAL	1	TRUE	1	0.8626505216089	2		578	942	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438231	49438231	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372347705	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	54	522	0	ENST00000301067.7:c.5038G>A	p.Glu1680Lys	p.E1680K	ENST00000301067	NM_003482.3	1680	Gag/Aag	20/54	1	2	FACETS	0.116	0.098	0.136	0.116	0.098	0.136	SUBCLONAL	1	TRUE	1	0.8626505216089	2		522	1079	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480062	50480062	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs936279527	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	37	328	0	ENST00000394963.4:c.296C>T	p.Ser99Phe	p.S99F	ENST00000394963	NM_003076.4	99	tCc/tTc	2/13	1	2	FACETS	0.131	0.108	0.158	0.131	0.108	0.158	SUBCLONAL	1	TRUE	1	0.8626505216089	2		328	653	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112433	115112433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	35	286	0	ENST00000257566.3:c.1307G>A	p.Arg436His	p.R436H	ENST00000257566	NM_016569.3	436	cGc/cAc	7/8	1	2	FACETS	0.148	0.121	0.179	0.148	0.121	0.179	SUBCLONAL	1	TRUE	1	0.8626505216089	2		286	547	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435346	110435346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1468014834	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	15	84	0	ENST00000375856.3:c.3055C>T	p.Pro1019Ser	p.P1019S	ENST00000375856	NM_003749.2	1019	Ccg/Tcg	1/2	1	2	FACETS	0.163	0.119	0.216	0.163	0.119	0.216	SUBCLONAL	1	TRUE	1	0.8626505216089	2		84	213	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610167	81610167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	51	304	0	ENST00000298171.2:c.1765C>T	p.Leu589Phe	p.L589F	ENST00000298171	NM_000369.2	589	Ctc/Ttc	10/10	0.8626505216089	1	FACETS	0.181	0.154	0.211	0.181	0.154	0.211	SUBCLONAL	1	TRUE	0	0.8626505216089	1		304	371	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989208	41989208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1212052861	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	463	559	0	ENST00000219905.7:c.2000C>T	p.Ser667Phe	p.S667F	ENST00000219905	NM_001164273.1	667	tCc/tTc	3/24	1	2	FACETS	0.905	0.866	0.944	0.905	0.866	0.944	CLONAL	1	TRUE	1	0.8626505216089	2		559	1186	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66779572	66779572	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	261	300	0	ENST00000307102.5:c.902G>A	p.Gly301Glu	p.G301E	ENST00000307102	NM_002755.3	301	gGa/gAa	8/11	1	2	FACETS	0.826	0.777	0.875	0.826	0.777	0.875	CLONAL	1	TRUE	1	0.8626505216089	2		300	733	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73994622	73994622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	142	280	0	ENST00000318443.5:c.106G>A	p.Asp36Asn	p.D36N	ENST00000318443	NM_001024736.1	36	Gac/Aac	3/10	1	2	FACETS	0.869	0.801	0.938	0.869	0.801	0.938	CLONAL	1	TRUE	1	0.8626505216089	2		280	379	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223975	2223975	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	377	488	0	ENST00000326181.6:c.1189G>A	p.Gly397Ser	p.G397S	ENST00000326181	NM_032271.2	397	Ggc/Agc	13/21	1	2	FACETS	0.973	0.928	1	0.973	0.928	1	CLONAL	1	TRUE	1	0.8626505216089	2		488	898	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858373	9858373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753651908	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	213	311	0	ENST00000330684.3:c.3028C>T	p.Pro1010Ser	p.P1010S	ENST00000330684	NM_001134407.1	1010	Ccc/Tcc	13/13	1	2	FACETS	0.965	0.905	1	0.965	0.905	1	CLONAL	1	TRUE	1	0.8626505216089	2		311	512	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11348810	11348810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	10	74	0	ENST00000332029.2:c.526G>A	p.Glu176Lys	p.E176K	ENST00000332029	NM_003745.1	176	Gag/Aag	2/2	1	2	FACETS	0.142	0.096	0.2	0.142	0.096	0.2	SUBCLONAL	1	TRUE	1	0.8626505216089	2		74	163	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041843	14041843	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1354794475	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	232	371	1	ENST00000311895.7:c.2390G>A	p.Arg797Lys	p.R797K	ENST00000311895	NM_005236.2	797	aGa/aAa	11/11	1	2	FACETS	0.781	0.732	0.831	0.781	0.732	0.831	SUBCLONAL	1	TRUE	1	0.8626505216089	2		372	689	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827427	72827427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	574	760	0	ENST00000268489.5:c.9154G>A	p.Val3052Ile	p.V3052I	ENST00000268489	NM_006885.3	3052	Gtt/Att	9/10	1	2	FACETS	0.927	0.892	0.963	0.927	0.892	0.963	CLONAL	1	TRUE	1	0.8626505216089	2		760	1435	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991365	72991365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754686167	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1229	86	691	0	ENST00000268489.5:c.2680G>A	p.Asp894Asn	p.D894N	ENST00000268489	NM_006885.3	894	Gat/Aat	2/10	1	2	FACETS	0.152	0.133	0.171	0.152	0.133	0.171	SUBCLONAL	1	TRUE	1	0.8626505216089	2		691	1315	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968931	15968931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	319	385	0	ENST00000268712.3:c.4819G>A	p.Glu1607Lys	p.E1607K	ENST00000268712	NM_006311.3	1607	Gag/Aag	33/46	1	2	FACETS	0.879	0.834	0.926	0.879	0.834	0.926	CLONAL	1	TRUE	1	0.8626505216089	2		385	841	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63531745	63531745	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs183475174	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	51	474	0	ENST00000307078.5:c.2236G>A	p.Asp746Asn	p.D746N	ENST00000307078	NM_004655.3	746	Gat/Aat	9/11	1	2	FACETS	0.121	0.102	0.142	0.121	0.102	0.142	SUBCLONAL	1	TRUE	1	0.8626505216089	2		474	978	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575664	48575664	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs61751987	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	122	224	0	ENST00000342988.3:c.425-1G>A		p.X142_splice	ENST00000342988	NM_005359.5	142			1	2	FACETS	0.673	0.614	0.735	0.673	0.614	0.735	SUBCLONAL	1	TRUE	1	0.8626505216089	2		224	420	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215574	5215574	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1226089200	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	293	379	1	ENST00000357368.4:c.4129G>A	p.Asp1377Asn	p.D1377N	ENST00000357368	NM_002850.3	1377	Gac/Aac	27/38	1	2	FACETS	0.942	0.892	0.993	0.942	0.892	0.993	CLONAL	1	TRUE	1	0.8626505216089	2		380	721	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10249227	10249227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	239	352	0	ENST00000340748.4:c.3955G>A	p.Ala1319Thr	p.A1319T	ENST00000340748		1319	Gcc/Acc	34/40	1	2	FACETS	0.892	0.839	0.946	0.892	0.839	0.946	CLONAL	1	TRUE	1	0.8626505216089	2		352	621	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375538	15375538	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	289	287	0	ENST00000263377.2:c.889C>T	p.Pro297Ser	p.P297S	ENST00000263377	NM_058243.2	297	Ccc/Tcc	6/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.8626505216089	2		287	620	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921426	39921426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	58	399	0	ENST00000378444.4:c.4394C>T	p.Thr1465Ile	p.T1465I	ENST00000378444	NM_001123385.1	1465	aCc/aTc	10/15	1	2	FACETS	0.161	0.138	0.187	0.161	0.138	0.187	SUBCLONAL	1	TRUE	1	0.8626505216089	2		399	835	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922918	39922918	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	57	503	0	ENST00000378444.4:c.3790G>A	p.Ala1264Thr	p.A1264T	ENST00000378444	NM_001123385.1	1264	Gcc/Acc	8/15	1	2	FACETS	0.124	0.106	0.145	0.124	0.106	0.145	SUBCLONAL	1	TRUE	1	0.8626505216089	2		503	1062	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47422632	47422632	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	105	524	0	ENST00000377045.4:c.104T>A	p.Val35Asp	p.V35D	ENST00000377045	NM_001654.4	35	gTc/gAc	3/16	1	2	FACETS	0.222	0.198	0.247	0.222	0.198	0.247	SUBCLONAL	1	TRUE	1	0.8626505216089	2		524	1097	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339590	70339590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	70	667	0	ENST00000374080.3:c.259C>T	p.Pro87Ser	p.P87S	ENST00000374080		87	Cct/Tct	3/45	1	2	FACETS	0.133	0.115	0.152	0.133	0.115	0.152	SUBCLONAL	1	TRUE	1	0.8626505216089	2		667	1221	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938689	76938689	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	403	469	0	ENST00000373344.5:c.2059G>A	p.Glu687Lys	p.E687K	ENST00000373344	NM_000489.3	687	Gag/Aag	9/35	1	2	FACETS	0.941	0.898	0.984	0.941	0.898	0.984	CLONAL	1	TRUE	1	0.8626505216089	2		469	993	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972711	76972711	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	349	511	0	ENST00000373344.5:c.30G>C	p.Lys10Asn	p.K10N	ENST00000373344	NM_000489.3	10	aaG/aaC	2/35	1	2	FACETS	0.816	0.775	0.859	0.816	0.775	0.859	CLONAL	1	TRUE	1	0.8626505216089	2		511	991	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728574	190728574	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	314	395	0	ENST00000441310.2:c.1965del	p.Lys655AsnfsTer14	p.K655Nfs*14	ENST00000441310	NM_000534.4	654	atA/at	10/13	1	2	FACETS	0.889	0.842	0.936	0.889	0.842	0.936	CLONAL	1	TRUE	1	0.8626505216089	2		395	819	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120491682	120491683	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	novel	NA	P-0009411-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	45	374	0	ENST00000256646.2:c.2546_2547del	p.Lys849ArgfsTer6	p.K849Rfs*6	ENST00000256646	NM_024408.3	849	aAA/a	16/34	0.8626505216089	1	FACETS	0.115	0.096	0.136	0.115	0.096	0.136	SUBCLONAL	1	TRUE	0	0.8626505216089	1		374	516	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0009412-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	357	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.964	0.915	1	0.964	0.915	1	CLONAL	1	FALSE	1	0.674245224592387	2		464	1098	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0009412-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	959	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.267119344703309	3	FACETS	0.94	0.914	0.967			1	INDETERMINATE	2	FALSE	NA	0.674245224592387	3		490	2023	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606679	29606679	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs865931787	NA	P-0009412-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1361	664	598	1	ENST00000389048.3:c.1201C>T	p.Arg401Ter	p.R401*	ENST00000389048	NM_004304.4	401	Cga/Tga	5/29	1	2	FACETS	0.973	0.936	1	0.973	0.936	1	CLONAL	1	FALSE	1	0.674245224592387	2		599	2025	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857436	9857436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009412-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1250	510	539	0	ENST00000330684.3:c.3965G>A	p.Gly1322Glu	p.G1322E	ENST00000330684	NM_001134407.1	1322	gGa/gAa	13/13	1	2	FACETS	0.86	0.822	0.898	0.86	0.822	0.898	CLONAL	1	FALSE	1	0.674245224592387	2		539	1760	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0009412-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	574	467	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.674245224592387	2		467	1664	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251593	212251593	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009412-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	550	453	0	ENST00000342788.4:c.3466G>A	p.Asp1156Asn	p.D1156N	ENST00000342788	NM_005235.2	1156	Gac/Aac	27/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.674245224592387	2		453	1571	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940189	49940189	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009412-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1455	761	740	0	ENST00000296474.3:c.854C>T	p.Ala285Val	p.A285V	ENST00000296474	NM_002447.2	285	gCc/gTc	1/20	NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	FALSE	NA	0.674245224592387	2		740	2216	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860422	151860422	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009412-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1376	1130	613	1	ENST00000262189.6:c.10240C>T	p.Gln3414Ter	p.Q3414*	ENST00000262189	NM_170606.2	3414	Caa/Taa	43/59	0.267119344703309	3	FACETS	0.894	0.871	0.918			1	INDETERMINATE	2	FALSE	NA	0.674245224592387	3		614	2506	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741608	145741608	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1319378486	NA	P-0009412-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1217	587	625	2	ENST00000428558.2:c.895C>T	p.Pro299Ser	p.P299S	ENST00000428558	NM_004260.3	299	Cca/Tca	5/22	0.291629635658737	3	FACETS	1	0.996	1	0.645	0.619	0.672	INDETERMINATE	1	FALSE	1	0.674245224592387	3		627	1804	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87285668	87285668	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1181805012	NA	P-0009412-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	388	394	1	ENST00000277120.3:c.5C>T	p.Ser2Leu	p.S2L	ENST00000277120		2	tCg/tTg	2/19	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	FALSE	1	0.674245224592387	2		395	1137	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609111	43609111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767402	NA	P-0009412-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	487	844	0	ENST00000355710.3:c.1867G>A	p.Glu623Lys	p.E623K	ENST00000355710	NM_020975.4	623	Gaa/Aaa	10/20	0.238433898405046	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.674245224592387	0		844	1517	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244942	123244942	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009412-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	390	664	2	ENST00000358487.5:c.2162G>A	p.Arg721Lys	p.R721K	ENST00000358487	NM_000141.4	721	aGa/aAa	16/18	0.238433898405046	0	FACETS		NA	1			1	INDETERMINATE	1	FALSE	0	0.674245224592387	0		666	1530	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115392	115115392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009412-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1380	736	603	0	ENST00000257566.3:c.934G>A	p.Glu312Lys	p.E312K	ENST00000257566	NM_016569.3	312	Gaa/Aaa	5/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.674245224592387	2		603	2116	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28980009	28980009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866351272	NA	P-0009412-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	447	458	0	ENST00000282397.4:c.1459G>A	p.Glu487Lys	p.E487K	ENST00000282397	NM_002019.4	487	Gaa/Aaa	11/30	NA	2	FACETS	0.866	0.825	0.908			1	INDETERMINATE	1	FALSE	NA	0.674245224592387	2		458	1531	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220617	1220617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555738389	NA	P-0009412-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	563	548	0	ENST00000326873.7:c.635C>T	p.Thr212Ile	p.T212I	ENST00000326873	NM_000455.4	212	aCc/aTc	5/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.674245224592387	2		548	1608	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221023	5221023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009412-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	411	443	0	ENST00000357368.4:c.3443C>T	p.Pro1148Leu	p.P1148L	ENST00000357368	NM_002850.3	1148	cCc/cTc	20/38	1	2	FACETS	0.938	0.893	0.984	0.938	0.893	0.984	CLONAL	1	FALSE	1	0.674245224592387	2		443	1300	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855834	45855834	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009412-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	565	594	0	ENST00000391945.4:c.1976A>T	p.His659Leu	p.H659L	ENST00000391945	NM_000400.3	659	cAc/cTc	21/23	1	2	FACETS	0.99	0.95	1	0.99	0.95	1	CLONAL	1	FALSE	1	0.674245224592387	2		594	1693	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024689	31024689	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009412-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1293	707	642	0	ENST00000375687.4:c.4174C>A	p.Pro1392Thr	p.P1392T	ENST00000375687	NM_015338.5	1392	Ccc/Acc	13/13	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.674245224592387	2		642	2000	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727111	40727111	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779663880	NA	P-0009412-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	573	576	0	ENST00000373198.4:c.3853G>A	p.Asp1285Asn	p.D1285N	ENST00000373198	NM_133170.3	1285	Gat/Aat	28/32	1	2	FACETS	0.974	0.935	1	0.974	0.935	1	CLONAL	1	FALSE	1	0.674245224592387	2		576	1745	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933211	39933211	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009412-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	756	407	0	ENST00000378444.4:c.1388C>T	p.Pro463Leu	p.P463L	ENST00000378444	NM_001123385.1	463	cCc/cTc	4/15	1	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	FALSE	0	0.674245224592387	1		407	1140	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	42	280	0				ENST00000310581	NM_198253.2	-/1132			0.256351937527585	3	FACETS	1	0.923	1	0.588	0.494	0.692	CLONAL	1	TRUE	1	0.290928525369083	3		280	281	SUCCESS
APC	324	MSKCC	GRCh37	5	112164586	112164586	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854573	NA	P-0009418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	46	277	0	ENST00000257430.4:c.1660C>T	p.Arg554Ter	p.R554*	ENST00000257430	NM_000038.5	554	Cga/Tga	14/16	0.256351937527585	3	FACETS	0.702	0.591	0.825	0.351	0.295	0.413	SUBCLONAL	1	TRUE	1	0.290928525369083	3		277	516	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0009418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	349	447	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.24515035044569	4	FACETS	0.956	0.91	1	1	0.993	1	CLONAL	4	TRUE	1	0.290928525369083	4		447	810	SUCCESS
APC	324	MSKCC	GRCh37	5	112175760	112175761	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs398123122	NA	P-0009418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	86	344	0	ENST00000257430.4:c.4473dup	p.Ala1492CysfsTer22	p.A1492Cfs*22	ENST00000257430	NM_000038.5	1490	cat/caTt	16/16	0.256351937527585	3	FACETS	1	0.978	1	0.736	0.654	0.823	CLONAL	1	TRUE	1	0.290928525369083	3		344	460	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480469	89480469	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	83	411	1	ENST00000336596.2:c.2306G>A	p.Arg769His	p.R769H	ENST00000336596	NM_005233.5	769	cGt/cAt	13/17	0.256351937527585	3	FACETS	0.905	0.799	1	0.453	0.399	0.51	CLONAL	1	TRUE	1	0.290928525369083	3		412	722	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462683	29462683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766541301	NA	P-0009418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	86	375	0	ENST00000389048.3:c.2218G>A	p.Gly740Arg	p.G740R	ENST00000389048	NM_004304.4	740	Gga/Aga	13/29	0.256351937527585	3	FACETS	1	0.91	1	0.516	0.457	0.58	CLONAL	1	TRUE	1	0.290928525369083	3		375	656	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562787	21562787	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1381086646	NA	P-0009418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	73	167	3	ENST00000382592.4:c.1132C>T	p.Arg378Trp	p.R378W	ENST00000382592	NM_014572.2	378	Cgg/Tgg	4/8	0.290928525369083	5	FACETS	1	0.921	1	0.707	0.623	0.796	CLONAL	2	TRUE	2	0.290928525369083	5		170	340	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792096	42792096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009418-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	41	251	0	ENST00000575354.2:c.900G>A	p.Met300Ile	p.M300I	ENST00000575354	NM_015125.3	300	atG/atA	6/20	0.290928525369083	3	FACETS	0.889	0.743	1	0.296	0.247	0.351	CLONAL	1	TRUE	0	0.290928525369083	3		251	363	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0009468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	266	157	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.497006415771317	4	FACETS	1	0.968	1			1	CLONAL	2	TRUE	NA	0.496702445567253	4		157	770	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0009468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1303	654	506	1	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.43115355477943	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.496702445567253	4		507	1957	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416417	49416417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1565753611	NA	P-0009468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	206	357	0	ENST00000301067.7:c.16294C>T	p.Arg5432Trp	p.R5432W	ENST00000301067	NM_003482.3	5432	Cgg/Tgg	51/54	0.446819537230986	3	FACETS	0.873	0.809	0.94	0.437	0.404	0.47	CLONAL	1	TRUE	1	0.496702445567253	3		357	1186	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100207	27100207	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs387906846	NA	P-0009468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	345	308	0	ENST00000324856.7:c.4003C>T	p.Arg1335Ter	p.R1335*	ENST00000324856	NM_006015.4	1335	Cga/Tga	16/20	0.471455545641587	2	FACETS	0.962	0.918	1	0.962	0.918	1	CLONAL	2	TRUE	0	0.496702445567253	2		308	722	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96920640	96920640	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1303	246	392	0	ENST00000258439.3:c.340G>C	p.Asp114His	p.D114H	ENST00000258439	NM_001193304.2	114	Gat/Cat	3/4	0.444423005836486	4	FACETS	0.957	0.892	1			1	CLONAL	1	TRUE	NA	0.496702445567253	4		392	1549	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156116	99156116	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	153	260	0	ENST00000074304.5:c.796C>G	p.Leu266Val	p.L266V	ENST00000074304	NM_001134224.1	266	Cta/Gta	10/26	0.444423005836486	4	FACETS	0.872	0.796	0.951			1	CLONAL	1	TRUE	NA	0.496702445567253	4		260	1058	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157488319	157488319	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	244	163	0	ENST00000346085.5:c.3025G>T	p.Ala1009Ser	p.A1009S	ENST00000346085	NM_020732.3	1009	Gca/Tca	10/20	0.497006415771317	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.496702445567253	3		163	559	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729633	41729633	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1261	887	611	1	ENST00000242208.4:c.896A>T	p.Gln299Leu	p.Q299L	ENST00000242208	NM_002192.2	299	cAg/cTg	3/3	0.497006415771317	5	FACETS	0.967	0.937	0.997	0.967	0.937	0.997	CLONAL	3	TRUE	2	0.496702445567253	5		612	2148	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5029838	5029838	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1196610367	NA	P-0009468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	108	443	0	ENST00000381652.3:c.282C>G	p.Ile94Met	p.I94M	ENST00000381652	NM_004972.3	94	atC/atG	4/25	0.424682703887365	3	FACETS	0.757	0.68	0.839			1	SUBCLONAL	1	TRUE	NA	0.496702445567253	3		443	717	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772709	135772709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	629	504	0	ENST00000298552.3:c.2837G>A	p.Ser946Asn	p.S946N	ENST00000298552	NM_001162426.1	946	aGc/aAc	22/23	0.446819537230986	3	FACETS	0.989	0.953	1	0.989	0.953	1	CLONAL	2	TRUE	1	0.496702445567253	3		504	1598	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998747	100998747	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	670	532	1	ENST00000325455.5:c.1055C>A	p.Pro352Gln	p.P352Q	ENST00000325455	NM_001202474.3	352	cCg/cAg	1/8	0.496702445567253	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.496702445567253	2		533	1224	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001417	29001417	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	80	256	0	ENST00000282397.4:c.1315C>A	p.Pro439Thr	p.P439T	ENST00000282397	NM_002019.4	439	Cca/Aca	10/30	0.433666581021605	3	FACETS	0.433	0.38	0.49	0.144	0.126	0.164	SUBCLONAL	1	TRUE	0	0.496702445567253	3		256	929	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577138	7577138	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587780075	NA	P-0009468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1188	627	502	0	ENST00000269305.4:c.800G>C	p.Arg267Pro	p.R267P	ENST00000269305	NM_001126112.2	267	cGg/cCg	8/11	0.43115355477943	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.496702445567253	4		502	1815	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032487	12032487	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	239	265	0	ENST00000353533.5:c.923C>T	p.Pro308Leu	p.P308L	ENST00000353533	NM_003010.3	308	cCa/cTa	9/11	0.43115355477943	4	FACETS	0.866	0.81	0.922	0.866	0.81	0.922	CLONAL	2	TRUE	2	0.496702445567253	4		265	832	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743332	743332	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	536	442	0	ENST00000314574.4:c.808T>A	p.Trp270Arg	p.W270R	ENST00000314574	NM_005433.3	270	Tgg/Agg	7/12	0.43115355477943	4	FACETS	0.93	0.891	0.971	0.93	0.891	0.971	CLONAL	2	TRUE	2	0.496702445567253	4		442	1736	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611065	100611065	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	150	276	1	ENST00000308731.7:c.1541C>A	p.Ser514Ter	p.S514*	ENST00000308731	NM_000061.2	514	tCa/tAa	15/19	0.444423005836486	2	FACETS	0.572	0.522	0.625			1	SUBCLONAL	1	TRUE	NA	0.496702445567253	2		277	1055	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181269	123181269	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	396	267	0	ENST00000218089.9:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000218089	NM_001042749.1	245	Caa/Taa	9/35	0.444423005836486	2	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.496702445567253	2		267	671	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971207	21971207	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	245	139	0	ENST00000304494.5:c.151del	p.Val51SerfsTer2	p.V51Sfs*2	ENST00000304494	NM_000077.4	51	Gtc/tc	2/3	0.497006415771317	4	FACETS	1	0.985	1			1	CLONAL	2	TRUE	NA	0.496702445567253	4		139	644	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662629	117662649	+	inframe_deletion	In_Frame_Del	DEL	TTCACTTTGTCTTAGAGGAGT	TTCACTTTGTCTTAGAGGAGT	-	novel	NA	P-0009468-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	63	425	0	ENST00000368508.3:c.4816_4836del	p.Thr1606_Glu1612del	p.T1606_E1612del	ENST00000368508	NM_002944.2	1606	ACTCCTCTAAGACAAAGTGAA/-	29/43	0.314300066399519	3	FACETS	0.304	0.262	0.351	0.152	0.131	0.176	SUBCLONAL	1	TRUE	1	0.496702445567253	3		425	1040	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0009473-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	181	589	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.319618886669099	2		589	843	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0009473-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	394	506	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.110389711009109	3	FACETS	1	0.985	1			1	INDETERMINATE	3	TRUE	NA	0.319618886669099	3		506	893	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458724	120458724	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009473-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	63	312	0	ENST00000256646.2:c.6621G>A	p.Met2207Ile	p.M2207I	ENST00000256646	NM_024408.3	2207	atG/atA	34/34	1	2	FACETS	0.91	0.79	1	0.91	0.79	1	CLONAL	1	TRUE	1	0.319618886669099	2		312	433	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186503787	186503787	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs142804104	NA	P-0009473-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	163	634	0	ENST00000323963.5:c.464T>C	p.Ile155Thr	p.I155T	ENST00000323963		155	aTt/aCt	5/11	1	2	FACETS	0.834	0.764	0.908	0.834	0.764	0.908	CLONAL	1	TRUE	1	0.319618886669099	2		634	1223	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295179	1295179	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0009473-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	19	167	0				ENST00000310581	NM_198253.2	-/1132			0.2494404500468	3	FACETS	0.369	0.279	0.474	0.184	0.139	0.237	SUBCLONAL	1	TRUE	1	0.319618886669099	3		167	374	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974703	21974703	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0009473-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	149	424	0	ENST00000304494.5:c.124A>C	p.Asn42His	p.N42H	ENST00000304494	NM_000077.4	42	Aat/Cat	1/3	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.319618886669099	2		424	669	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922294	100922294	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1315135533	NA	P-0009473-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	98	464	1	ENST00000325455.5:c.2218C>T	p.Arg740Ter	p.R740*	ENST00000325455	NM_001202474.3	740	Cga/Tga	5/8	1	2	FACETS	0.797	0.711	0.889	0.797	0.711	0.889	SUBCLONAL	1	TRUE	1	0.319618886669099	2		465	769	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999795	100999795	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009473-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	70	579	0	ENST00000325455.5:c.7G>A	p.Glu3Lys	p.E3K	ENST00000325455	NM_001202474.3	3	Gag/Aag	1/8	1	2	FACETS	0.624	0.543	0.711	0.624	0.543	0.711	SUBCLONAL	1	TRUE	1	0.319618886669099	2		579	702	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202285	108202285	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1565532703	NA	P-0009473-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	68	284	1	ENST00000278616.4:c.7629+1G>A		p.X2543_splice	ENST00000278616	NM_000051.3	2543			1	2	FACETS	0.965	0.842	1	0.965	0.842	1	CLONAL	1	TRUE	1	0.319618886669099	2		285	441	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578427	7578427	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867114783	NA	P-0009475-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	264	271	0	ENST00000269305.4:c.503A>G	p.His168Arg	p.H168R	ENST00000269305	NM_001126112.2	168	cAc/cGc	5/11	0.878150465616273	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.887480693082502	1		271	314	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48923091	48923091	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0009475-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	291	332	0	ENST00000267163.4:c.540-1G>A		p.X180_splice	ENST00000267163	NM_000321.2	180			0.887480693082502	1	FACETS	0.973	0.94	1	0.973	0.94	1	CLONAL	1	TRUE	0	0.887480693082502	1		332	375	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295192	1295193	+	upstream_gene_variant	5'Flank	INS	-	-	GCGGAAAGGAAGGGGAGGGGCT	novel	NA	P-0009475-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	59	175	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.449	0.389	0.513	0.449	0.389	0.513	SUBCLONAL	1	TRUE	1	0.887480693082502	2		175	296	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0009476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	470	506	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.257229785730933	6	FACETS	1	0.986	1	1	0.986	1	CLONAL	6	TRUE	0	0.257229785730933	6		506	879	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579475	7579475	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	128	218	0	ENST00000269305.4:c.212C>T	p.Pro71Leu	p.P71L	ENST00000269305	NM_001126112.2	71	cCc/cTc	4/11	0.257229785730933	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.257229785730933	3		218	478	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474022	29474022	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	166	311	0	ENST00000389048.3:c.2153G>C	p.Gly718Ala	p.G718A	ENST00000389048	NM_004304.4	718	gGc/gCc	12/29	0.222048327615117	4	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	2	0.257229785730933	4		311	785	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120831	115120831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	144	209	1	ENST00000257566.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000257566	NM_016569.3	59	Gcc/Acc	1/8	0.257229785730933	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	3	TRUE	1	0.257229785730933	4		210	429	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030574	47030574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	94	263	0	ENST00000377604.3:c.349G>A	p.Glu117Lys	p.E117K	ENST00000377604	NM_001204468.1	117	Gag/Aag	4/24	0.252316795417453	3	FACETS	0.751	0.67	0.837	0.751	0.67	0.837	SUBCLONAL	2	TRUE	1	0.257229785730933	3		263	549	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652238	48652239	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0009476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	136	420	0	ENST00000376670.3:c.909_910insT	p.Thr304TyrfsTer40	p.T304Yfs*40	ENST00000376670	NM_002049.3	303	-/T	6/6	0.252316795417453	3	FACETS	1	0.983	1	0.68	0.618	0.746	CLONAL	1	TRUE	1	0.257229785730933	3		420	877	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230388	46230388	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	205	298	0	ENST00000334344.6:c.723del	p.Asp242MetfsTer50	p.D242Mfs*50	ENST00000334344	NM_152641.2	241	gTt/gt	7/21	0.126858054185127	3	FACETS	1	0.953	1			1	INDETERMINATE	3	TRUE	NA	0.257229785730933	3		298	585	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579469	7579470	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CG	novel	NA	P-0009476-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	100	219	0	ENST00000269305.4:c.216_217dup	p.Val73AlafsTer51	p.V73Afs*51	ENST00000269305	NM_001126112.2	73	gtg/gCGtg	4/11	0.257229785730933	3	FACETS	0.975	0.876	1	0.975	0.876	1	CLONAL	2	TRUE	1	0.257229785730933	3		219	450	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	35	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.22	2		280	272	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266112	41266112	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913228	NA	P-0009500-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	18	417	0	ENST00000349496.5:c.109T>C	p.Ser37Pro	p.S37P	ENST00000349496	NM_001904.3	37	Tct/Cct	3/15	1	2	FACETS	0.219	0.164	0.285	0.219	0.164	0.285	SUBCLONAL	1	TRUE	1	0.22	2		417	747	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	155	280	0				ENST00000310581	NM_198253.2	-/1132			0.474457942648102	3	FACETS	1	0.943	1	1	0.943	1	CLONAL	2	TRUE	1	0.474457942648102	3		280	396	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0009506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	575	511	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.262999624547607	4	FACETS	0.907	0.878	0.936			1	INDETERMINATE	4	TRUE	NA	0.474457942648102	4		511	985	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577543	7577543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	242	355	0	ENST00000269305.4:c.738G>T	p.Met246Ile	p.M246I	ENST00000269305	NM_001126112.2	246	atG/atT	7/11	NA	2	FACETS	0.872	0.821	0.923			1	INDETERMINATE	2	TRUE	NA	0.474457942648102	2		355	585	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	34	280	0				ENST00000310581	NM_198253.2	-/1132			0.386377462282987	3	FACETS	0.957	0.804	1	0.957	0.804	1	CLONAL	2	FALSE	1	0.437366894223935	3		280	99	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0009509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	609	354	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	0.437366894223935	3	FACETS	0.988	0.971	1	1	0.998	1	CLONAL	5	FALSE	0	0.437366894223935	3		354	687	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352673	118352673	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	269	568	0	ENST00000534358.1:c.3878A>C	p.Lys1293Thr	p.K1293T	ENST00000534358	NM_005933.3	1293	aAg/aCg	7/36	0.386377462282987	3	FACETS	0.986	0.929	1	0.986	0.929	1	CLONAL	2	FALSE	1	0.437366894223935	3		568	760	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390506	118390506	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	150	408	0	ENST00000534358.1:c.11320A>T	p.Arg3774Trp	p.R3774W	ENST00000534358	NM_005933.3	3774	Agg/Tgg	32/36	0.386377462282987	3	FACETS	0.97	0.895	1	0.97	0.895	1	CLONAL	2	FALSE	1	0.437366894223935	3		408	431	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457597	67457597	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	79	433	0	ENST00000327367.4:c.407C>G	p.Pro136Arg	p.P136R	ENST00000327367	NM_005902.3	136	cCt/cGt	3/9	0.437366894223935	3	FACETS	0.774	0.681	0.873	0.387	0.34	0.437	SUBCLONAL	1	FALSE	1	0.437366894223935	3		433	569	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138147	64138147	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	139	413	0	ENST00000334205.4:c.2070del	p.Leu691SerfsTer29	p.L691Sfs*29	ENST00000334205	NM_003942.2	690	gtG/gt	16/17	0.386377462282987	3	FACETS	0.947	0.871	1	0.947	0.871	1	CLONAL	2	FALSE	1	0.437366894223935	3		413	409	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444073	49444073	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	194	513	0	ENST00000301067.7:c.3298del	p.Asp1100ThrfsTer19	p.D1100Tfs*19	ENST00000301067	NM_003482.3	1100	Gac/ac	11/54	1	2	FACETS	0.814	0.759	0.87	1	0.992	1	CLONAL	2	FALSE	1	0.437366894223935	2		513	545	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457602	67457602	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009509-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	39	454	2	ENST00000327367.4:c.412G>T	p.Val138Leu	p.V138L	ENST00000327367	NM_005902.3	138	Gtg/Ttg	3/9	0.437366894223935	3	FACETS	0.356	0.294	0.425	0.178	0.147	0.213	SUBCLONAL	1	FALSE	1	0.437366894223935	3		456	611	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	27	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.813	1	1	0.813	1	CLONAL	1	TRUE	1	0.2	2		280	265	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0009510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	61	511	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.526	0.452	0.608	0.526	0.452	0.608	SUBCLONAL	1	TRUE	1	0.2	2		511	1159	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469144	25469144	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009510-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	246	565	5	ENST00000264709.3:c.1314del	p.Asp438GlufsTer213	p.D438Efs*213	ENST00000264709	NM_175629.2	438	gaC/ga	11/23	1	2	FACETS	1	0.945	1	1	0.995	1	CLONAL	2	TRUE	1	0.2	2		570	1214	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0009527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	235	464	0				ENST00000310581	NM_198253.2	-/1132			0.686577979921987	3	FACETS	0.96	0.907	1	0.96	0.907	1	CLONAL	2	TRUE	1	0.686577979921987	3		464	479	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0009527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	480	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.686577979921987	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.686577979921987	4		490	1174	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518532	204518532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	551	336	0	ENST00000367182.3:c.1195C>T	p.His399Tyr	p.H399Y	ENST00000367182	NM_001278516.1	399	Cac/Tac	11/11	0.686577979921987	6	FACETS	1	0.968	1	0.755	0.726	0.784	CLONAL	3	TRUE	2	0.686577979921987	6		336	1261	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259231	89259231	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	404	357	0	ENST00000336596.2:c.375G>A	p.Met125Ile	p.M125I	ENST00000336596	NM_005233.5	125	atG/atA	3/17	0.686577979921987	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.686577979921987	2		357	563	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874641	35874641	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	660	610	0	ENST00000303115.3:c.797A>T	p.Lys266Ile	p.K266I	ENST00000303115	NM_002185.3	266	aAa/aTa	6/8	0.686577979921987	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.686577979921987	3		610	1260	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724370	117724370	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	519	459	1	ENST00000368508.3:c.509G>T	p.Trp170Leu	p.W170L	ENST00000368508	NM_002944.2	170	tGg/tTg	6/43	0.686577979921987	2	FACETS	0.972	0.942	1	0.972	0.942	1	CLONAL	2	TRUE	0	0.686577979921987	2		460	778	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205220	61205220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	454	473	2	ENST00000301761.2:c.160C>T	p.Pro54Ser	p.P54S	ENST00000301761	NM_017841.2	54	Cca/Tca	2/4	0.686577979921987	3	FACETS	0.95	0.912	0.988	0.95	0.912	0.988	CLONAL	2	TRUE	1	0.686577979921987	3		475	935	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212489	133212489	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	256	526	0	ENST00000320574.5:c.5800C>T	p.His1934Tyr	p.H1934Y	ENST00000320574	NM_006231.2	1934	Cac/Tac	42/49	0.686577979921987	3	FACETS	1	0.969	1	0.527	0.493	0.561	CLONAL	1	TRUE	1	0.686577979921987	3		526	951	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003234	42003234	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1294	887	804	2	ENST00000219905.7:c.2771C>A	p.Ser924Ter	p.S924*	ENST00000219905	NM_001164273.1	924	tCa/tAa	8/24	0.559931178990855	4	FACETS	0.999	0.968	1	0.999	0.968	1	CLONAL	2	TRUE	2	0.686577979921987	4		806	2181	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81973616	81973616	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1205	812	725	0	ENST00000359376.3:c.3433C>T	p.Pro1145Ser	p.P1145S	ENST00000359376	NM_002661.3	1145	Ccc/Tcc	30/33	0.559931178990855	4	FACETS	0.989	0.957	1	0.989	0.957	1	CLONAL	2	TRUE	2	0.686577979921987	4		725	2017	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980462	7980462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	478	456	2	ENST00000319144.4:c.1121C>T	p.Ser374Phe	p.S374F	ENST00000319144	NM_001139.2	374	tCt/tTt	9/15	0.559931178990855	4	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	2	0.686577979921987	4		458	1150	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231792	36231792	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	547	535	1	ENST00000300305.3:c.592G>A	p.Asp198Asn	p.D198N	ENST00000300305		198	Gat/Aat	5/8	0.559931178990855	4	FACETS	0.965	0.927	1	0.965	0.927	1	CLONAL	2	TRUE	2	0.686577979921987	4		536	1392	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211110	55211111	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0009527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	650	505	0	ENST00000275493.2:c.353_354delinsTT	p.Ala118Val	p.A118V	ENST00000275493	NM_005228.3	118	gCC/gTT	3/28	0.686577979921987	5	FACETS	0.952	0.92	0.984	0.952	0.92	0.984	CLONAL	3	TRUE	2	0.686577979921987	5		505	1346	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097628	11097629	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0009527-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	450	596	0	ENST00000358026.2:c.808_809delinsTT	p.Pro270Phe	p.P270F	ENST00000358026	NM_001128849.1	270	CCc/TTc	5/36	0.686577979921987	3	FACETS	0.901	0.864	0.938	0.901	0.864	0.938	CLONAL	2	TRUE	1	0.686577979921987	3		596	977	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	69	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.571838981051751	2		280	230	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0009538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	560	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.571838981051751	4	FACETS	0.877	0.85	0.903	0.877	0.85	0.903	CLONAL	4	TRUE	0	0.571838981051751	4		490	878	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878538	151878538	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	582	328	0	ENST00000262189.6:c.6407G>A	p.Gly2136Glu	p.G2136E	ENST00000262189	NM_170606.2	2136	gGa/gAa	36/59	0.472992521958033	4	FACETS	0.919	0.887	0.952	1	0.997	1	CLONAL	3	TRUE	2	0.571838981051751	4		328	1160	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759841	133759841	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372281632	NA	P-0009538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	149	302	0	ENST00000318560.5:c.2164G>A	p.Val722Ile	p.V722I	ENST00000318560	NM_005157.4	722	Gtt/Att	11/11	0.571838981051751	3	FACETS	0.798	0.729	0.87	0.399	0.364	0.435	SUBCLONAL	1	TRUE	1	0.571838981051751	3		302	840	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858202	9858202	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	180	517	0	ENST00000330684.3:c.3199C>T	p.Arg1067Trp	p.R1067W	ENST00000330684	NM_001134407.1	1067	Cgg/Tgg	13/13	1	2	FACETS	0.714	0.658	0.771	0.714	0.658	0.771	SUBCLONAL	1	TRUE	1	0.571838981051751	2		517	882	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578389	7578389	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587782596	NA	P-0009538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	360	242	0	ENST00000269305.4:c.541C>T	p.Arg181Cys	p.R181C	ENST00000269305	NM_001126112.2	181	Cgc/Tgc	5/11	0.346036956632977	3	FACETS	1	0.994	1	0.815	0.781	0.85	CLONAL	2	TRUE	0	0.571838981051751	3		242	662	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024497	16024497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	494	496	0	ENST00000268712.3:c.1721C>T	p.Thr574Ile	p.T574I	ENST00000268712	NM_006311.3	574	aCt/aTt	16/46	0.346036956632977	3	FACETS	1	0.994	1	0.773	0.744	0.802	CLONAL	2	TRUE	0	0.571838981051751	3		496	958	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302860	15302860	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	195	371	0	ENST00000263388.2:c.590C>T	p.Pro197Leu	p.P197L	ENST00000263388	NM_000435.2	197	cCc/cTc	4/33	0.571838981051751	3	FACETS	0.915	0.846	0.985	0.457	0.423	0.493	CLONAL	1	TRUE	1	0.571838981051751	3		371	959	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217305	123217305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009538-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	401	231	0	ENST00000218089.9:c.2959C>T	p.Pro987Ser	p.P987S	ENST00000218089	NM_001042749.1	987	Ccg/Tcg	29/35	0.402060325311916	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.571838981051751	2		231	576	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	76	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.527326914285672	2		280	249	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266137	41266137	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913409	NA	P-0009540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	163	397	0	ENST00000349496.5:c.134C>T	p.Ser45Phe	p.S45F	ENST00000349496	NM_001904.3	45	tCt/tTt	3/15	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.527326914285672	2		397	602	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578271	7578271	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786201838	NA	P-0009540-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	241	441	0	ENST00000269305.4:c.578A>G	p.His193Arg	p.H193R	ENST00000269305	NM_001126112.2	193	cAt/cGt	6/11	0.527326914285672	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.527326914285672	1		441	543	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0009563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	89	145	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.931	0.834	1	0.931	0.834	1	CLONAL	1	TRUE	1	0.593446735875528	2		145	322	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11552822	NA	P-0009563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	138	161	0	ENST00000304494.5:c.250G>T	p.Asp84Tyr	p.D84Y	ENST00000304494	NM_000077.4	84	Gac/Tac	2/3	0.542353947525773	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.593446735875528	1		161	279	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057520000	NA	P-0009563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	540	574	3	ENST00000269305.4:c.452C>A	p.Pro151His	p.P151H	ENST00000269305	NM_001126112.2	151	cCc/cAc	5/11	0.588306052760442	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.593446735875528	2		577	879	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5286147	5286147	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs202019323	NA	P-0009563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	193	495	1	ENST00000357368.4:c.5C>T	p.Ala2Val	p.A2V	ENST00000357368	NM_002850.3	2	gCg/gTg	2/38	0.591424880066315	1	FACETS	0.953	0.891	1	0.953	0.891	1	CLONAL	1	TRUE	0	0.593446735875528	1		496	480	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095918	29095918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587783051	NA	P-0009563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	285	608	0	ENST00000328354.6:c.916G>A	p.Gly306Arg	p.G306R	ENST00000328354	NM_007194.3	306	Ggg/Agg	9/15	0.593446735875528	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.593446735875528	1		608	661	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343531	343531	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	298	809	1	ENST00000262320.3:c.2143G>T	p.Glu715Ter	p.E715*	ENST00000262320	NM_003502.3	715	Gag/Tag	8/11	0.591424880066315	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.593446735875528	1		810	700	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256236	41256236	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659528	NA	P-0009563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	246	657	0	ENST00000357654.3:c.344C>T	p.Pro115Leu	p.P115L	ENST00000357654	NM_007294.3	115	cCt/cTt	6/23	0.588306052760442	2	FACETS	1	0.943	1	0.503	0.471	0.536	CLONAL	1	TRUE	0	0.593446735875528	2		657	824	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971122	21971123	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0009589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	86	122	0	ENST00000304494.5:c.235dup	p.Thr79AsnfsTer41	p.T79Nfs*41	ENST00000304494	NM_000077.4	79	acc/aAcc	2/3	0.519661438540581	1	FACETS	0.939	0.842	1	0.939	0.842	1	CLONAL	1	TRUE	0	0.519661438540581	1		122	261	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858982	57858982	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009589-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	442	725	0	ENST00000228682.2:c.478G>T	p.Ala160Ser	p.A160S	ENST00000228682	NM_005269.2	160	Gcc/Tcc	5/12	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.519661438540581	2		725	1548	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009605-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	79	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.919	1	1	0.985	1	CLONAL	2	TRUE	1	0.24935912781353	2		280	304	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533262	533462	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TCCCGGGAGACTTACAGCGCGAGGGGCCGCTGGGTCACATGGGTCCCGGGGGGTCCCAGAGGGTCCCGGAGCTGGAGCTAGAGCCAGAGCGGCTGCCCTGTGTCAAGGGAGAGGGTCAGTGAGTGCTGCTCCCTGGCTGGGGCGGGGCGGGGCGGGTCCCTGGCTAGCTGTGGGGTGGAGAGCTGCCTCACCTGCCGGGTC	TCCCGGGAGACTTACAGCGCGAGGGGCCGCTGGGTCACATGGGTCCCGGGGGGTCCCAGAGGGTCCCGGAGCTGGAGCTAGAGCCAGAGCGGCTGCCCTGTGTCAAGGGAGAGGGTCAGTGAGTGCTGCTCCCTGGCTGGGGCGGGGCGGGGCGGGTCCCTGGCTAGCTGTGGGGTGGAGAGCTGCCTCACCTGCCGGGTC	-	novel	NA	P-0009605-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	162	227	0	ENST00000451590.1:c.441_450+191del		p.X147_splice	ENST00000451590	NM_001130442.1	147		4/5	1	2	FACETS	1	0.979	1	1	0.993	1	CLONAL	2	TRUE	1	0.24935912781353	2		227	552	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057947	27057948	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0009605-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	260	324	0	ENST00000324856.7:c.1656dup	p.Gln553ThrfsTer70	p.Q553Tfs*70	ENST00000324856	NM_006015.4	552	tca/tcAa	3/20	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.24935912781353	2		324	913	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009618-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	25	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.816	1	1	0.816	1	CLONAL	1	TRUE	1	0.17	2		280	284	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0009618-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1142	90	838	1	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	1	2	FACETS	0.859	0.76	0.966	0.859	0.76	0.966	CLONAL	1	TRUE	1	0.17	2		839	1232	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322731	30322731	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009618-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	68	685	0	ENST00000322652.5:c.1744G>C	p.Asp582His	p.D582H	ENST00000322652	NM_015355.2	582	Gat/Cat	14/16	1	2	FACETS	0.884	0.767	1	0.884	0.767	1	CLONAL	1	TRUE	1	0.17	2		685	905	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	224	521	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.485569842941763	3	FACETS	0.928	0.863	0.996	0.464	0.431	0.498	CLONAL	1	TRUE	1	0.485569842941763	3		522	1235	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0009647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	303	567	0	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.476738742316561	2	FACETS	0.981	0.933	1	0.981	0.933	1	CLONAL	2	TRUE	0	0.485569842941763	2		567	636	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48593525	48593525	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	180	274	0	ENST00000342988.3:c.1276G>T	p.Val426Phe	p.V426F	ENST00000342988	NM_005359.5	426	Gtt/Ttt	10/12	0.485569842941763	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.485569842941763	1		274	550	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912582	32912583	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0009647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1263	659	653	0	ENST00000380152.3:c.4091dup	p.Cys1365MetfsTer3	p.C1365Mfs*3	ENST00000380152		1364	ata/aTta	11/27	NA	2	FACETS	1	0.997	1			1	INDETERMINATE	1	TRUE	NA	0.485569842941763	2		653	1922	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89685257	89685269	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	GTTTTGTTTTAAG	GTTTTGTTTTAAG	-	novel	NA	P-0009647-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	155	185	0	ENST00000371953.3:c.165-8_169del		p.X55_splice	ENST00000371953	NM_000314.4	55			0.420405614385678	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.485569842941763	1		185	464	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009685-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	21	280	0				ENST00000310581	NM_198253.2	-/1132			0.582619452820202	1	FACETS	0.762	0.615	0.916	0.762	0.615	0.916	CLONAL	1	TRUE	0	0.692505767171905	1		280	52	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0009685-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	152	511	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.272809978226137	5	FACETS	1	0.972	1	0.738	0.683	0.795	INDETERMINATE	2	TRUE	2	0.692505767171905	5		512	404	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796871	42796871	+	frameshift_variant	Frame_Shift_Ins	INS	A	A	TGCCATCCCCTCAGCACCCCTGGCCC	novel	NA	P-0009685-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	270	714	0	ENST00000575354.2:c.3329delinsTGCCATCCCCTCAGCACCCCTGGCCC	p.Gln1110LeufsTer49	p.Q1110Lfs*49	ENST00000575354	NM_015125.3	1110	cAg/cTGCCATCCCCTCAGCACCCCTGGCCCg	14/20	0.707371225175791	4	FACETS	1	0.992	1			1	CLONAL	4	TRUE	NA	0.692505767171905	4		714	309	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	36	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.951	0.805	1	1	0.974	1	CLONAL	3	FALSE	1	0.2524693078831	2		280	100	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286247	66286247	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	14	684	0	ENST00000273854.3:c.1439T>C	p.Ile480Thr	p.I480T	ENST00000273854	NM_004439.5	480	aTt/aCt	6/18	0.2524693078831	0	FACETS	0.921	0.676	1			1	CLONAL	1	FALSE	0	0.2524693078831	0		684	90	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56488201	56488201	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	26	473	0	ENST00000267101.3:c.1720G>A	p.Ala574Thr	p.A574T	ENST00000267101	NM_001982.3	574	Gct/Act	15/28	0.248934688154039	3	FACETS	1	0.834	1	0.527	0.42	0.649	CLONAL	1	FALSE	1	0.2524693078831	3		473	220	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009737-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	94	280	0				ENST00000310581	NM_198253.2	-/1132			0.299899379199952	3	FACETS	0.901	0.808	0.999	0.901	0.808	0.999	CLONAL	2	TRUE	1	0.32	3		280	378	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0009737-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	534	521	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.3	6	FACETS	1	0.991	1	1	0.997	1	CLONAL	7	TRUE	0	0.32	6		522	746	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356152	66356152	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009737-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	72	350	0	ENST00000273854.3:c.1345G>C	p.Asp449His	p.D449H	ENST00000273854	NM_004439.5	449	Gac/Cac	5/18	1	2	FACETS	0.687	0.6	0.781	0.687	0.6	0.781	SUBCLONAL	1	TRUE	1	0.32	2		350	655	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406210	406210	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009737-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	51	367	0	ENST00000399788.2:c.4231C>T	p.Gln1411Ter	p.Q1411*	ENST00000399788	NM_001042603.1	1411	Caa/Taa	25/28	0.3	6	FACETS	0.922	0.783	1	0.154	0.13	0.179	CLONAL	1	TRUE	0	0.32	6		367	567	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346339	73346339	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009737-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	90	378	0	ENST00000377767.4:c.1461C>G	p.Asp487Glu	p.D487E	ENST00000377767	NM_014953.3	487	gaC/gaG	10/21	1	2	FACETS	0.907	0.814	1	1	0.985	1	CLONAL	2	TRUE	1	0.32	2		378	310	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570469	39570469	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1380208670	NA	P-0009737-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	63	462	1	ENST00000262039.4:c.665G>T	p.Arg222Leu	p.R222L	ENST00000262039	NM_002647.2	222	cGa/cTa	6/25	0.299899379199952	3	FACETS	0.958	0.83	1	0.479	0.415	0.548	CLONAL	1	TRUE	1	0.32	3		463	477	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933893	39933893	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009737-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	110	563	0	ENST00000378444.4:c.706C>A	p.Pro236Thr	p.P236T	ENST00000378444	NM_001123385.1	236	Cca/Aca	4/15	0.163884190689219	3	FACETS	0.752	0.674	0.835	0.376	0.337	0.418	INDETERMINATE	1	TRUE	1	0.32	3		563	1061	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006816	47006816	+	5_prime_UTR_variant	5'UTR	DEL	G	G	-	novel	NA	P-0009737-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	213	433	0	ENST00000377604.3:c.-63del		p.*21*	ENST00000377604	NM_001204468.1	-/852		2/24	0.163884190689219	3	FACETS	0.822	0.764	0.882	0.822	0.764	0.882	INDETERMINATE	2	TRUE	1	0.32	3		433	939	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0009744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	126	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.422366565730789	2		464	482	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0009744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	266	558	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.422366565730789	2		558	1200	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314906	1314906	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	222	665	0	ENST00000400841.2:c.755G>A	p.Trp252Ter	p.W252*	ENST00000400841		252	tGg/tAg	6/6	0.422366565730789	0	FACETS	0.681	0.634	0.729			1	SUBCLONAL	1	TRUE	NA	0.422366565730789	0		665	892	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612073	189612073	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142762485	NA	P-0009744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	176	472	1	ENST00000264731.3:c.1825G>A	p.Glu609Lys	p.E609K	ENST00000264731	NM_003722.4	609	Gaa/Aaa	14/14	1	2	FACETS	0.952	0.878	1	0.952	0.878	1	CLONAL	1	TRUE	1	0.422366565730789	2		473	875	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586386	189586386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs113993967	NA	P-0009744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	99	258	2	ENST00000264731.3:c.1010G>A	p.Arg337Gln	p.R337Q	ENST00000264731	NM_003722.4	337	cGa/cAa	8/14	1	2	FACETS	0.951	0.853	1	0.951	0.853	1	CLONAL	1	TRUE	1	0.422366565730789	2		260	493	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187419	32187419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	206	576	0	ENST00000375023.3:c.1460G>A	p.Gly487Glu	p.G487E	ENST00000375023	NM_004557.3	487	gGa/gAa	8/30	1	2	FACETS	0.982	0.911	1	0.982	0.911	1	CLONAL	1	TRUE	1	0.422366565730789	2		576	993	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166104	118166104	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	237	582	0	ENST00000369448.3:c.614A>C	p.His205Pro	p.H205P	ENST00000369448	NM_017709.3	205	cAc/cCc	2/2	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.422366565730789	2		582	1016	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610700	52610700	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	191	508	0	ENST00000394830.3:c.3473G>A	p.Trp1158Ter	p.W1158*	ENST00000394830	NM_018313.4	1158	tGg/tAg	23/30	0.422366565730789	1	FACETS	0.916	0.849	0.985	0.916	0.849	0.985	CLONAL	1	TRUE	0	0.422366565730789	1		508	779	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134873054	134873054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	202	557	1	ENST00000398015.3:c.1358C>T	p.Ser453Leu	p.S453L	ENST00000398015	NM_004441.4	453	tCa/tTa	6/16	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.422366565730789	2		558	945	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168988	32168988	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	319	867	3	ENST00000375023.3:c.4045G>A	p.Glu1349Lys	p.E1349K	ENST00000375023	NM_004557.3	1349	Gaa/Aaa	22/30	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.422366565730789	2		870	1397	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518406	8518406	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	60	208	0	ENST00000356435.5:c.985C>T	p.Pro329Ser	p.P329S	ENST00000356435		329	Cct/Tct	10/35	0.422366565730789	1	FACETS	0.762	0.662	0.87	0.762	0.662	0.87	SUBCLONAL	1	TRUE	0	0.422366565730789	1		208	294	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961379	41961379	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1371	360	1194	1	ENST00000219905.7:c.287T>A	p.Ile96Asn	p.I96N	ENST00000219905	NM_001164273.1	96	aTt/aAt	2/24	NA	2	FACETS	0.985	0.931	1			1	INDETERMINATE	1	TRUE	NA	0.422366565730789	2		1195	1731	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15943778	15943778	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	220	588	0	ENST00000268712.3:c.6710A>T	p.Asn2237Ile	p.N2237I	ENST00000268712	NM_006311.3	2237	aAt/aTt	43/46	1	2	FACETS	0.931	0.865	0.999	0.931	0.865	0.999	CLONAL	1	TRUE	1	0.422366565730789	2		588	1119	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56402553	56402553	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	171	507	1	ENST00000348428.3:c.1595T>C	p.Val532Ala	p.V532A	ENST00000348428	NM_006785.3	532	gTt/gCt	13/17	1	2	FACETS	0.88	0.81	0.954	0.88	0.81	0.954	CLONAL	1	TRUE	1	0.422366565730789	2		508	920	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5229512	5229512	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	37	121	0	ENST00000357368.4:c.2339C>T	p.Ala780Val	p.A780V	ENST00000357368	NM_002850.3	780	gCc/gTc	15/38	1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.422366565730789	2		121	161	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31389138	31389138	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	227	599	0	ENST00000328111.2:c.2051C>T	p.Pro684Leu	p.P684L	ENST00000328111	NM_006892.3	684	cCc/cTc	19/23	0.415370028707807	3	FACETS	1	0.937	1	0.504	0.469	0.541	CLONAL	1	TRUE	1	0.422366565730789	3		599	1291	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5090825	5090827	+	inframe_deletion	In_Frame_Del	DEL	AAT	AAT	-	novel	NA	P-0009744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	180	646	1	ENST00000381652.3:c.2973_2975del	p.Lys991_Ile992delinsAsn	p.K991_I992delinsN	ENST00000381652	NM_004972.3	991	aaAATt/aat	22/25	0.422366565730789	1	FACETS	0.828	0.765	0.894	0.828	0.765	0.894	CLONAL	1	TRUE	0	0.422366565730789	1		647	812	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350488	15350489	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	156	273	0	ENST00000263377.2:c.3426_3427delinsTT	p.Pro1143Ser	p.P1143S	ENST00000263377	NM_058243.2	1142	gcCCcc/gcTTcc	16/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.422366565730789	2		273	506	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165922	118165923	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009744-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	154	435	0	ENST00000369448.3:c.432_433delinsAA	p.Val145Ile	p.V145I	ENST00000369448	NM_017709.3	144	aaGGtt/aaAAtt	2/2	1	2	FACETS	0.952	0.872	1	0.952	0.872	1	CLONAL	1	TRUE	1	0.422366565730789	2		435	766	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0009747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	69	229	0				ENST00000310581	NM_198253.2	-/1132			0.127391211345028	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.14	3		229	426	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298225	123298225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	42	305	0	ENST00000358487.5:c.629G>A	p.Arg210Gln	p.R210Q	ENST00000358487	NM_000141.4	210	cGa/cAa	6/18	1	2	FACETS	0.926	0.772	1	0.926	0.772	1	CLONAL	1	TRUE	1	0.14	2		305	648	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196463	106196463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	99	629	0	ENST00000380013.4:c.4796C>T	p.Ser1599Phe	p.S1599F	ENST00000380013	NM_001127208.2	1599	tCc/tTc	11/11	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.14	2		629	1307	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246137	46246137	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	57	421	0	ENST00000334344.6:c.4231C>T	p.Gln1411Ter	p.Q1411*	ENST00000334344	NM_152641.2	1411	Caa/Taa	15/21	1	2	FACETS	0.985	0.843	1	0.985	0.843	1	CLONAL	1	TRUE	1	0.14	2		421	827	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892266	9892266	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868291959	NA	P-0009747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	58	426	0	ENST00000330684.3:c.2224G>A	p.Asp742Asn	p.D742N	ENST00000330684	NM_001134407.1	742	Gat/Aat	11/13	1	2	FACETS	0.909	0.778	1	0.909	0.778	1	CLONAL	1	TRUE	1	0.14	2		426	912	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515250	149515250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	59	570	0	ENST00000261799.4:c.232G>A	p.Asp78Asn	p.D78N	ENST00000261799	NM_002609.3	78	Gat/Aat	3/23	1	2	FACETS	0.851	0.729	0.983	0.851	0.729	0.983	CLONAL	1	TRUE	1	0.14	2		570	991	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518111	8518111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	59	393	1	ENST00000356435.5:c.1280G>A	p.Arg427Gln	p.R427Q	ENST00000356435		427	cGa/cAa	10/35	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.14	2		394	786	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81904539	81904539	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs201294738	NA	P-0009747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1277	85	605	1	ENST00000359376.3:c.647C>T	p.Ser216Leu	p.S216L	ENST00000359376	NM_002661.3	216	tCg/tTg	7/33	1	2	FACETS	0.892	0.785	1	0.892	0.785	1	CLONAL	1	TRUE	1	0.14	2		606	1362	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480488	120480488	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	56	429	2	ENST00000256646.2:c.3329C>T	p.Ser1110Phe	p.S1110F	ENST00000256646	NM_024408.3	1110	tCc/tTc	20/34	1	2	FACETS	0.804	0.686	0.933	0.804	0.686	0.933	CLONAL	1	TRUE	1	0.14	2		431	995	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149497215	149497215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748918501	NA	P-0009747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	44	370	0	ENST00000261799.4:c.3103G>A	p.Glu1035Lys	p.E1035K	ENST00000261799	NM_002609.3	1035	Gag/Aag	22/23	1	2	FACETS	0.806	0.674	0.953	0.806	0.674	0.953	CLONAL	1	TRUE	1	0.14	2		370	780	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677858	117677858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	53	404	0	ENST00000368508.3:c.4075G>A	p.Glu1359Lys	p.E1359K	ENST00000368508	NM_002944.2	1359	Gag/Aag	25/43	1	2	FACETS	0.934	0.794	1	0.934	0.794	1	CLONAL	1	TRUE	1	0.14	2		404	811	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537213	80537213	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	34	203	0	ENST00000286548.4:c.185T>A	p.Ile62Asn	p.I62N	ENST00000286548	NM_002072.3	62	aTc/aAc	2/7	1	2	FACETS	0.973	0.795	1	0.973	0.795	1	CLONAL	1	TRUE	1	0.14	2		203	499	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606289	93606289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	70	570	0	ENST00000375746.1:c.109G>A	p.Gly37Arg	p.G37R	ENST00000375746	NM_001174167.1	37	Ggg/Agg	2/14	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.14	2		570	997	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274803	123274803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	68	435	1	ENST00000358487.5:c.1115C>T	p.Ser372Phe	p.S372F	ENST00000358487	NM_000141.4	372	tCc/tTc	9/18	1	2	FACETS	0.984	0.854	1	0.984	0.854	1	CLONAL	1	TRUE	1	0.14	2		436	987	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410666	32410666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	114	628	0	ENST00000332351.3:c.1492G>A	p.Glu498Lys	p.E498K	ENST00000332351	NM_024426.4	498	Gaa/Aaa	10/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.14	2		628	1229	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025621	1025621	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763842232	NA	P-0009747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	48	532	0	ENST00000358495.3:c.754G>A	p.Glu252Lys	p.E252K	ENST00000358495	NM_134424.2	252	Gag/Aag	9/12	1	2	FACETS	0.771	0.65	0.906	0.771	0.65	0.906	CLONAL	1	TRUE	1	0.14	2		532	889	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491450	18491450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	63	443	0	ENST00000266497.5:c.1363G>A	p.Glu455Lys	p.E455K	ENST00000266497		455	Gaa/Aaa	8/31	1	2	FACETS	0.865	0.745	0.995	0.865	0.745	0.995	CLONAL	1	TRUE	1	0.14	2		443	1041	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134015	41134015	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752387735	NA	P-0009747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1685	117	1023	0	ENST00000379561.5:c.1613C>T	p.Pro538Leu	p.P538L	ENST00000379561	NM_002015.3	538	cCc/cTc	2/3	1	2	FACETS	0.928	0.833	1	0.928	0.833	1	CLONAL	1	TRUE	1	0.14	2		1023	1802	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004636	16004636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	97	565	0	ENST00000268712.3:c.2618C>T	p.Pro873Leu	p.P873L	ENST00000268712	NM_006311.3	873	cCc/cTc	20/46	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.14	2		565	1170	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0009747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1184	75	546	0	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	1	2	FACETS	0.851	0.743	0.968	0.851	0.743	0.968	CLONAL	1	TRUE	1	0.14	2		546	1259	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584423	39584423	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	83	526	0	ENST00000262039.4:c.1088C>T	p.Ser363Phe	p.S363F	ENST00000262039	NM_002647.2	363	tCc/tTc	10/25	1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.14	2		526	1156	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743942	40743942	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868489194	NA	P-0009747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	45	337	0	ENST00000373198.4:c.3053G>A	p.Arg1018Gln	p.R1018Q	ENST00000373198	NM_133170.3	1018	cGa/cAa	23/32	1	2	FACETS	0.9	0.755	1	0.9	0.755	1	CLONAL	1	TRUE	1	0.14	2		337	714	SUCCESS
AR	367	MSKCC	GRCh37	X	66863144	66863144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	112	419	0	ENST00000374690.3:c.1663C>T	p.Pro555Ser	p.P555S	ENST00000374690	NM_000044.3	555	Cca/Tca	2/8	1	1	FACETS	0.9	0.809	0.996	1	0.987	1	CLONAL	2	TRUE	0	0.14	1		419	827	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429355	78429356	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AC	novel	NA	P-0009747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1198	85	542	1	ENST00000370768.2:c.1085_1086dup	p.Arg363ValfsTer29	p.R363Vfs*29	ENST00000370768	NM_003902.3	362	-/GT	13/20	1	2	FACETS	0.946	0.834	1	0.946	0.834	1	CLONAL	1	TRUE	1	0.14	2		543	1283	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344727	65344728	+	missense_variant	Missense_Mutation	DNP	GG	GG	AC	novel	NA	P-0009747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	52	395	0	ENST00000342505.4:c.309_310delinsGT	p.Arg104Trp	p.R104W	ENST00000342505	NM_002227.2	103	ctCCgg/ctGTgg	4/25	1	2	FACETS	0.89	0.755	1	0.89	0.755	1	CLONAL	1	TRUE	1	0.14	2		395	835	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888303	112888304	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0009747-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	45	353	0	ENST00000351677.2:c.319_320delinsTT	p.Pro107Phe	p.P107F	ENST00000351677	NM_002834.3	107	CCt/TTt	3/16	1	2	FACETS	0.721	0.604	0.851	0.721	0.604	0.851	SUBCLONAL	1	TRUE	1	0.14	2		353	892	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0009749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	102	464	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	FALSE	NA	0.863015564358475	2		464	209	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0009749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	371	511	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.863015564358475	2		512	817	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849663	68849663	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587780113	NA	P-0009749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	107	478	1	ENST00000261769.5:c.1565+1G>A		p.X522_splice	ENST00000261769	NM_004360.3	522			0.281303669697406	1	FACETS	0.282	0.254	0.312	0.282	0.254	0.312	INDETERMINATE	1	FALSE	0	0.863015564358475	1		479	500	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505463	157505463	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0009749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	40	589	0	ENST00000346085.5:c.3444C>G	p.Tyr1148Ter	p.Y1148*	ENST00000346085	NM_020732.3	1148	taC/taG	13/20	NA	2	FACETS	0.164	0.136	0.195			1	INDETERMINATE	1	FALSE	NA	0.863015564358475	2		589	566	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850359	128850359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1162853719	NA	P-0009749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	70	502	0	ENST00000249373.3:c.1622C>T	p.Thr541Met	p.T541M	ENST00000249373	NM_005631.4	541	aCg/aTg	9/12	0.863015564358475	3	FACETS	0.342	0.297	0.389	0.171	0.148	0.195	SUBCLONAL	1	FALSE	1	0.863015564358475	3		502	680	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70406046	70406046	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	134	709	0	ENST00000373644.4:c.3560G>A	p.Cys1187Tyr	p.C1187Y	ENST00000373644	NM_030625.2	1187	tGc/tAc	4/12	NA	2	FACETS	0.371	0.337	0.407			1	INDETERMINATE	1	FALSE	NA	0.863015564358475	2		709	836	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939109	36939123	+	inframe_deletion	In_Frame_Del	DEL	GCCCATATTCTGGTA	GCCCATATTCTGGTA	-	novel	NA	P-0009749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	33	1020	2	ENST00000361632.4:c.586_600del	p.Tyr196_Gly200del	p.Y196_G200del	ENST00000361632		196	TACCAGAATATGGGC/-	5/16	0.863015564358475	1	FACETS	0.079	0.064	0.096	0.079	0.064	0.096	SUBCLONAL	1	FALSE	0	0.863015564358475	1		1022	550	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795273	42795274	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0009749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	84	488	0	ENST00000575354.2:c.2357dup	p.Gly787TrpfsTer144	p.G787Wfs*144	ENST00000575354	NM_015125.3	785	gcc/gCcc	10/20	0.610872003897744	1	FACETS	0.414	0.371	0.46	0.414	0.371	0.46	SUBCLONAL	1	FALSE	0	0.863015564358475	1		488	267	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268810	98268811	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0009749-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	43	706	0	ENST00000331920.6:c.272dup	p.Cys92LeufsTer48	p.C92Lfs*48	ENST00000331920	NM_000264.3	91	ggt/ggGt	2/24	0.281303669697406	1	FACETS	0.066	0.055	0.079	0.066	0.055	0.079	INDETERMINATE	1	FALSE	0	0.863015564358475	1		706	859	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	65	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.29289692738634	2		280	409	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	214	560	1	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.29289692738634	2		561	1188	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561263	9561263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769939031	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	75	291	0	ENST00000353224.5:c.519G>A	p.Met173Ile	p.M173I	ENST00000353224	NM_177990.2	173	atG/atA	4/10	1	2	FACETS	0.637	0.557	0.723	0.637	0.557	0.723	SUBCLONAL	1	TRUE	1	0.29289692738634	2		291	804	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385271	41385271	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	106	299	0	ENST00000373198.4:c.690G>A	p.Trp230Ter	p.W230*	ENST00000373198	NM_133170.3	230	tgG/tgA	6/32	1	2	FACETS	0.901	0.808	1	0.901	0.808	1	CLONAL	1	TRUE	1	0.29289692738634	2		299	803	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444401	50444401	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	68	205	0	ENST00000331340.3:c.331C>T	p.Arg111Ter	p.R111*	ENST00000331340	NM_006060.4	111	Cga/Tga	4/8	0.238001352105468	3	FACETS	0.732	0.636	0.836	0.366	0.318	0.418	SUBCLONAL	1	TRUE	1	0.29289692738634	3		205	727	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566827	212566827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202247795	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	144	345	0	ENST00000342788.4:c.1354G>A	p.Glu452Lys	p.E452K	ENST00000342788	NM_005235.2	452	Gaa/Aaa	12/28	0.112971670451897	4	FACETS	1	0.984	1	0.689	0.628	0.753	INDETERMINATE	1	TRUE	2	0.29289692738634	4		345	923	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514563	41514563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	117	304	0	ENST00000373198.4:c.98C>T	p.Ser33Phe	p.S33F	ENST00000373198	NM_133170.3	33	tCc/tTc	2/32	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.29289692738634	2		304	732	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156851429	156851429	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	34	265	0	ENST00000524377.1:c.2386G>A	p.Gly796Ser	p.G796S	ENST00000524377	NM_002529.3	796	Ggc/Agc	17/17	1	2	FACETS	0.341	0.278	0.413	0.341	0.278	0.413	SUBCLONAL	1	TRUE	1	0.29289692738634	2		265	680	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965756	93965756	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	149	469	0	ENST00000369303.4:c.2173-1G>A		p.X725_splice	ENST00000369303	NM_004440.3	725			0.167090912625486	4	FACETS	1	0.981	1	0.641	0.585	0.7	INDETERMINATE	1	TRUE	2	0.29289692738634	4		469	1026	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244913	123244913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1224606327	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	102	452	1	ENST00000358487.5:c.2191G>A	p.Glu731Lys	p.E731K	ENST00000358487	NM_000141.4	731	Gaa/Aaa	16/18	1	2	FACETS	0.643	0.574	0.717	0.643	0.574	0.717	SUBCLONAL	1	TRUE	1	0.29289692738634	2		453	1083	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005401	29005401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	74	350	0	ENST00000282397.4:c.860C>T	p.Ser287Phe	p.S287F	ENST00000282397	NM_002019.4	287	tCc/tTc	7/30	0.29289692738634	3	FACETS	0.782	0.684	0.888	0.391	0.342	0.444	SUBCLONAL	1	TRUE	1	0.29289692738634	3		350	741	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845367	151845367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	53	318	1	ENST00000262189.6:c.13645C>T	p.Arg4549Cys	p.R4549C	ENST00000262189	NM_170606.2	4549	Cgc/Tgc	52/59	0.238001352105468	3	FACETS	0.532	0.452	0.619	0.266	0.226	0.31	SUBCLONAL	1	TRUE	1	0.29289692738634	3		319	780	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347176	89347176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	123	568	0	ENST00000301030.4:c.5774C>T	p.Pro1925Leu	p.P1925L	ENST00000301030	NM_001256183.1	1925	cCc/cTc	9/13	1	2	FACETS	0.667	0.601	0.736	0.667	0.601	0.736	SUBCLONAL	1	TRUE	1	0.29289692738634	2		568	1260	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472522	88472522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55890138	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	106	455	2	ENST00000360948.2:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000360948	NM_001012338.2	678	cGa/cAa	16/19	1	2	FACETS	0.66	0.59	0.735	0.66	0.59	0.735	SUBCLONAL	1	TRUE	1	0.29289692738634	2		457	1096	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295204	1295204	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs2735943	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	18	156	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.376	0.282	0.486	0.376	0.282	0.486	SUBCLONAL	1	TRUE	1	0.29289692738634	2		156	327	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587161	189587161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173679499	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	75	353	0	ENST00000264731.3:c.1178G>A	p.Arg393Gln	p.R393Q	ENST00000264731	NM_003722.4	393	cGa/cAa	9/14	1	2	FACETS	0.672	0.588	0.763	0.672	0.588	0.763	SUBCLONAL	1	TRUE	1	0.29289692738634	2		353	762	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312725	91312725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	128	456	1	ENST00000355112.3:c.2464C>T	p.Pro822Ser	p.P822S	ENST00000355112	NM_000057.2	822	Cct/Tct	12/22	1	2	FACETS	0.777	0.702	0.856	0.777	0.702	0.856	SUBCLONAL	1	TRUE	1	0.29289692738634	2		457	1125	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11273601	11273601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	64	207	0	ENST00000361445.4:c.3140C>T	p.Ser1047Leu	p.S1047L	ENST00000361445	NM_004958.3	1047	tCa/tTa	21/58	1	2	FACETS	0.737	0.638	0.844	0.737	0.638	0.844	SUBCLONAL	1	TRUE	1	0.29289692738634	2		207	593	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11298094	11298094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	64	211	0	ENST00000361445.4:c.2014C>T	p.Arg672Cys	p.R672C	ENST00000361445	NM_004958.3	672	Cgc/Tgc	13/58	1	2	FACETS	0.744	0.645	0.853	0.744	0.645	0.853	SUBCLONAL	1	TRUE	1	0.29289692738634	2		211	587	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259967	16259967	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	158	474	0	ENST00000375759.3:c.7232C>T	p.Ser2411Leu	p.S2411L	ENST00000375759	NM_015001.2	2411	tCg/tTg	11/15	1	2	FACETS	0.906	0.828	0.987	0.906	0.828	0.987	CLONAL	1	TRUE	1	0.29289692738634	2		474	1191	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262078	16262078	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	32	118	0	ENST00000375759.3:c.9343G>A	p.Glu3115Lys	p.E3115K	ENST00000375759	NM_015001.2	3115	Gaa/Aaa	11/15	1	2	FACETS	0.674	0.548	0.816	0.674	0.548	0.816	SUBCLONAL	1	TRUE	1	0.29289692738634	2		118	324	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17350563	17350563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1557740003	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	63	295	1	ENST00000375499.3:c.547C>T	p.Leu183Phe	p.L183F	ENST00000375499	NM_003000.2	183	Ctc/Ttc	6/8	1	2	FACETS	0.651	0.562	0.747	0.651	0.562	0.747	SUBCLONAL	1	TRUE	1	0.29289692738634	2		296	661	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932851	36932851	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1349	160	569	0	ENST00000361632.4:c.2020G>A	p.Val674Met	p.V674M	ENST00000361632		674	Gtg/Atg	15/16	1	2	FACETS	0.724	0.661	0.79	0.724	0.661	0.79	SUBCLONAL	1	TRUE	1	0.29289692738634	2		569	1509	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433860	78433860	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	84	422	0	ENST00000370768.2:c.239C>T	p.Pro80Leu	p.P80L	ENST00000370768	NM_003902.3	80	cCt/cTt	3/20	0.238001352105468	3	FACETS	0.946	0.836	1	0.473	0.418	0.533	CLONAL	1	TRUE	1	0.29289692738634	3		422	695	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115252203	115252203	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1035	121	405	0	ENST00000369535.4:c.437C>T	p.Ala146Val	p.A146V	ENST00000369535	NM_002524.4	146	gCc/gTc	4/7	0.238001352105468	3	FACETS	0.819	0.738	0.905	0.41	0.369	0.453	CLONAL	1	TRUE	1	0.29289692738634	3		405	1156	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695728	117695728	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057433609	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	86	326	0	ENST00000369458.3:c.709G>A	p.Asp237Asn	p.D237N	ENST00000369458	NM_024626.3	237	Gat/Aat	4/6	0.238001352105468	3	FACETS	0.687	0.606	0.774	0.343	0.303	0.387	SUBCLONAL	1	TRUE	1	0.29289692738634	3		326	980	SUCCESS
INSRR	3645	MSKCC	GRCh37	1	156812021	156812021	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	25	148	0	ENST00000368195.3:c.3280C>T	p.Gln1094Ter	p.Q1094*	ENST00000368195	NM_014215.2	1094	Caa/Taa	19/22	1	2	FACETS	0.473	0.372	0.588	0.473	0.372	0.588	SUBCLONAL	1	TRUE	1	0.29289692738634	2		148	361	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838333	156838333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148324672	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	101	440	0	ENST00000524377.1:c.611C>T	p.Ser204Leu	p.S204L	ENST00000524377	NM_002529.3	204	tCg/tTg	6/17	1	2	FACETS	0.659	0.587	0.735	0.659	0.587	0.735	SUBCLONAL	1	TRUE	1	0.29289692738634	2		440	1047	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846306	156846306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371344688	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	199	471	1	ENST00000524377.1:c.1747C>T	p.Arg583Cys	p.R583C	ENST00000524377	NM_002529.3	583	Cgc/Tgc	14/17	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.29289692738634	2		472	1280	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965154	25965154	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777510322	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	90	325	0	ENST00000435504.4:c.4052C>T	p.Ser1351Phe	p.S1351F	ENST00000435504		1351	tCt/tTt	13/13	1	2	FACETS	0.667	0.59	0.748	0.667	0.59	0.748	SUBCLONAL	1	TRUE	1	0.29289692738634	2		325	922	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966913	25966913	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	114	479	0	ENST00000435504.4:c.2293C>T	p.Pro765Ser	p.P765S	ENST00000435504		765	Cct/Tct	13/13	1	2	FACETS	0.683	0.614	0.758	0.683	0.614	0.758	SUBCLONAL	1	TRUE	1	0.29289692738634	2		479	1139	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991701	25991701	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	109	347	0	ENST00000435504.4:c.541C>T	p.Gln181Ter	p.Q181*	ENST00000435504		181	Caa/Taa	7/13	1	2	FACETS	0.767	0.688	0.852	0.767	0.688	0.852	SUBCLONAL	1	TRUE	1	0.29289692738634	2		347	970	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455223	29455223	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	133	486	0	ENST00000389048.3:c.2579G>A	p.Arg860Lys	p.R860K	ENST00000389048	NM_004304.4	860	aGa/aAa	15/29	1	2	FACETS	0.782	0.708	0.859	0.782	0.708	0.859	SUBCLONAL	1	TRUE	1	0.29289692738634	2		486	1162	SUCCESS
ALK	238	MSKCC	GRCh37	2	29473989	29473989	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	106	460	0	ENST00000389048.3:c.2186C>T	p.Pro729Leu	p.P729L	ENST00000389048	NM_004304.4	729	cCa/cTa	12/29	1	2	FACETS	0.699	0.625	0.777	0.699	0.625	0.777	SUBCLONAL	1	TRUE	1	0.29289692738634	2		460	1036	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639666	47639666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060502021	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	74	322	0	ENST00000233146.2:c.759G>A	p.Met253Ile	p.M253I	ENST00000233146	NM_000251.2	253	atG/atA	4/16	1	2	FACETS	0.64	0.56	0.728	0.64	0.56	0.728	SUBCLONAL	1	TRUE	1	0.29289692738634	2		322	789	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158622475	158622475	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1438	199	613	1	ENST00000263640.3:c.1024A>T	p.Ile342Phe	p.I342F	ENST00000263640	NM_001105.4	342	Att/Ttt	8/11	0.112971670451897	4	FACETS	1	0.964	1	0.537	0.495	0.58	INDETERMINATE	1	TRUE	2	0.29289692738634	4		614	1637	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096626	178096626	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754094243	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	66	270	0	ENST00000397062.3:c.705G>A	p.Met235Ile	p.M235I	ENST00000397062	NM_006164.4	235	atG/atA	5/5	0.112971670451897	4	FACETS	0.793	0.687	0.907	0.396	0.343	0.454	INDETERMINATE	1	TRUE	2	0.29289692738634	4		270	735	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113095	209113095	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	71	289	0	ENST00000345146.2:c.412C>T	p.Gln138Ter	p.Q138*	ENST00000345146	NM_005896.2	138	Caa/Taa	4/10	0.112971670451897	4	FACETS	0.808	0.704	0.92	0.404	0.352	0.46	INDETERMINATE	1	TRUE	2	0.29289692738634	4		289	776	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248420	212248420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868458258	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	91	351	0	ENST00000342788.4:c.3847G>A	p.Glu1283Lys	p.E1283K	ENST00000342788	NM_005235.2	1283	Gaa/Aaa	28/28	0.112971670451897	4	FACETS	0.874	0.775	0.981	0.437	0.387	0.491	INDETERMINATE	1	TRUE	2	0.29289692738634	4		351	919	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537975	212537975	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267599192	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	114	307	0	ENST00000342788.4:c.1630C>T	p.Arg544Trp	p.R544W	ENST00000342788	NM_005235.2	544	Cgg/Tgg	14/28	0.112971670451897	4	FACETS	1	0.975	1	0.63	0.567	0.696	INDETERMINATE	1	TRUE	2	0.29289692738634	4		307	799	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215632279	215632279	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	126	442	0	ENST00000260947.4:c.1495C>T	p.His499Tyr	p.H499Y	ENST00000260947	NM_000465.2	499	Cac/Tac	6/11	0.112971670451897	4	FACETS	0.899	0.812	0.992	0.45	0.406	0.496	INDETERMINATE	1	TRUE	2	0.29289692738634	4		442	1237	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439812	220439812	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1172410247	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1365	141	648	1	ENST00000243786.2:c.665G>A	p.Arg222Lys	p.R222K	ENST00000243786	NM_002191.3	222	aGa/aAa	2/2	0.112971670451897	4	FACETS	0.827	0.75	0.907	0.413	0.375	0.454	INDETERMINATE	1	TRUE	2	0.29289692738634	4		649	1506	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067242	37067242	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750760	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	166	405	0	ENST00000231790.2:c.1153C>T	p.Arg385Cys	p.R385C	ENST00000231790	NM_000249.3	385	Cgt/Tgt	12/19	0.112971670451897	4	FACETS	1	0.985	1	0.667	0.611	0.725	INDETERMINATE	1	TRUE	2	0.29289692738634	4		405	1099	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936406	49936406	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1572	279	660	0	ENST00000296474.3:c.1442A>G	p.Asn481Ser	p.N481S	ENST00000296474	NM_002447.2	481	aAc/aGc	3/20	0.112971670451897	4	FACETS	1	0.991	1	0.665	0.622	0.71	INDETERMINATE	1	TRUE	2	0.29289692738634	4		660	1851	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613080	52613080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	104	273	0	ENST00000394830.3:c.3448C>T	p.Arg1150Cys	p.R1150C	ENST00000394830	NM_018313.4	1150	Cgt/Tgt	22/30	0.112971670451897	4	FACETS	1	0.958	1	0.569	0.509	0.633	INDETERMINATE	1	TRUE	2	0.29289692738634	4		273	807	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52677351	52677351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	43	265	0	ENST00000394830.3:c.908C>T	p.Ser303Phe	p.S303F	ENST00000394830	NM_018313.4	303	tCc/tTc	10/30	0.112971670451897	4	FACETS	0.498	0.415	0.59	0.249	0.207	0.295	INDETERMINATE	1	TRUE	2	0.29289692738634	4		265	763	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259197	89259197	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	110	304	0	ENST00000336596.2:c.341G>A	p.Gly114Glu	p.G114E	ENST00000336596	NM_005233.5	114	gGa/gAa	3/17	0.112971670451897	4	FACETS	1	0.967	1	0.594	0.533	0.658	INDETERMINATE	1	TRUE	2	0.29289692738634	4		304	818	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259244	89259244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	110	312	0	ENST00000336596.2:c.388G>A	p.Asp130Asn	p.D130N	ENST00000336596	NM_005233.5	130	Gat/Aat	3/17	0.112971670451897	4	FACETS	1	0.96	1	0.568	0.51	0.63	INDETERMINATE	1	TRUE	2	0.29289692738634	4		312	855	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259262	89259262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770780950	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	116	441	1	ENST00000336596.2:c.406C>T	p.Arg136Ter	p.R136*	ENST00000336596	NM_005233.5	136	Cga/Tga	3/17	0.112971670451897	4	FACETS	1	0.967	1	0.588	0.529	0.65	INDETERMINATE	1	TRUE	2	0.29289692738634	4		442	871	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259388	89259388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1392	142	516	0	ENST00000336596.2:c.532G>A	p.Gly178Arg	p.G178R	ENST00000336596	NM_005233.5	178	Gga/Aga	3/17	0.112971670451897	4	FACETS	0.817	0.742	0.897	0.409	0.371	0.449	INDETERMINATE	1	TRUE	2	0.29289692738634	4		516	1534	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259629	89259629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	48	142	0	ENST00000336596.2:c.773C>T	p.Ser258Phe	p.S258F	ENST00000336596	NM_005233.5	258	tCc/tTc	3/17	0.112971670451897	4	FACETS	1	0.931	1	0.589	0.499	0.686	INDETERMINATE	1	TRUE	2	0.29289692738634	4		142	360	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390157	89390157	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	95	391	0	ENST00000336596.2:c.906G>A	p.Met302Ile	p.M302I	ENST00000336596	NM_005233.5	302	atG/atA	4/17	0.112971670451897	4	FACETS	0.758	0.673	0.849	0.379	0.336	0.425	INDETERMINATE	1	TRUE	2	0.29289692738634	4		391	1107	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445067	89445067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	142	354	0	ENST00000336596.2:c.1387C>T	p.Pro463Ser	p.P463S	ENST00000336596	NM_005233.5	463	Cct/Tct	6/17	0.112971670451897	4	FACETS	1	0.979	1	0.626	0.569	0.685	INDETERMINATE	1	TRUE	2	0.29289692738634	4		354	1002	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499372	89499372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	157	327	0	ENST00000336596.2:c.2542G>A	p.Asp848Asn	p.D848N	ENST00000336596	NM_005233.5	848	Gac/Aac	15/17	0.112971670451897	4	FACETS	1	0.988	1	0.747	0.684	0.813	INDETERMINATE	1	TRUE	2	0.29289692738634	4		327	928	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119642331	119642331	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	52	192	0	ENST00000316626.5:c.367-1G>A		p.X123_splice	ENST00000316626		123			1	2	FACETS	0.944	0.807	1	0.944	0.807	1	CLONAL	1	TRUE	1	0.29289692738634	2		192	376	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670531	134670531	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	111	401	0	ENST00000398015.3:c.442C>T	p.Gln148Ter	p.Q148*	ENST00000398015	NM_004441.4	148	Cag/Tag	3/16	1	2	FACETS	0.779	0.699	0.864	0.779	0.699	0.864	SUBCLONAL	1	TRUE	1	0.29289692738634	2		401	973	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134885807	134885807	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	89	317	0	ENST00000398015.3:c.1718C>T	p.Ala573Val	p.A573V	ENST00000398015	NM_004441.4	573	gCt/gTt	9/16	1	2	FACETS	0.808	0.716	0.907	0.808	0.716	0.907	CLONAL	1	TRUE	1	0.29289692738634	2		317	752	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968274	134968275	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	83	454	0	ENST00000398015.3:c.2787_2788delinsAA	p.Asp930Asn	p.D930N	ENST00000398015	NM_004441.4	929	agGGac/agAAac	15/16	1	2	FACETS	0.558	0.491	0.63	0.558	0.491	0.63	SUBCLONAL	1	TRUE	1	0.29289692738634	2		454	1016	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176561	142176561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	72	436	1	ENST00000350721.4:c.7540C>T	p.Arg2514Cys	p.R2514C	ENST00000350721	NM_001184.3	2514	Cgc/Tgc	45/47	1	2	FACETS	0.603	0.526	0.687	0.603	0.526	0.687	SUBCLONAL	1	TRUE	1	0.29289692738634	2		437	815	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916653	178916653	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	121	599	0	ENST00000263967.3:c.40C>T	p.His14Tyr	p.H14Y	ENST00000263967	NM_006218.2	14	Cac/Tac	2/21	1	2	FACETS	0.767	0.692	0.847	0.767	0.692	0.847	SUBCLONAL	1	TRUE	1	0.29289692738634	2		599	1077	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921495	178921496	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	81	335	0	ENST00000263967.3:c.977_978delinsTT	p.Ser326Phe	p.S326F	ENST00000263967	NM_006218.2	326	tCC/tTT	5/21	1	2	FACETS	0.769	0.677	0.868	0.769	0.677	0.868	SUBCLONAL	1	TRUE	1	0.29289692738634	2		335	719	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190956	185190956	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1724	211	725	0	ENST00000265026.3:c.1837G>A	p.Glu613Lys	p.E613K	ENST00000265026	NM_004721.4	613	Gaa/Aaa	11/14	1	2	FACETS	0.745	0.688	0.803	0.745	0.688	0.803	SUBCLONAL	1	TRUE	1	0.29289692738634	2		725	1935	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446273	187446273	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1466913399	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	71	396	0	ENST00000232014.4:c.1415C>T	p.Pro472Leu	p.P472L	ENST00000232014	NM_001130845.1	472	cCc/cTc	6/10	1	2	FACETS	0.763	0.666	0.868	0.763	0.666	0.868	SUBCLONAL	1	TRUE	1	0.29289692738634	2		396	635	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189604245	189604245	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756980788	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1151	143	416	0	ENST00000264731.3:c.1412G>A	p.Ser471Asn	p.S471N	ENST00000264731	NM_003722.4	471	aGc/aAc	11/14	1	2	FACETS	0.755	0.686	0.827	0.755	0.686	0.827	SUBCLONAL	1	TRUE	1	0.29289692738634	2		416	1294	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803732	1803732	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	105	376	0	ENST00000260795.2:c.910C>T	p.Pro304Ser	p.P304S	ENST00000260795		304	Ccc/Tcc	6/17	1	2	FACETS	0.779	0.697	0.867	0.779	0.697	0.867	SUBCLONAL	1	TRUE	1	0.29289692738634	2		376	920	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127262	55127262	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	66	233	0	ENST00000257290.5:c.50G>A	p.Gly17Glu	p.G17E	ENST00000257290	NM_006206.4	17	gGg/gAg	3/23	1	2	FACETS	0.781	0.678	0.892	0.781	0.678	0.892	SUBCLONAL	1	TRUE	1	0.29289692738634	2		233	577	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55130014	55130014	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	109	430	2	ENST00000257290.5:c.548C>T	p.Thr183Ile	p.T183I	ENST00000257290	NM_006206.4	183	aCt/aTt	4/23	1	2	FACETS	0.649	0.581	0.721	0.649	0.581	0.721	SUBCLONAL	1	TRUE	1	0.29289692738634	2		432	1147	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55138563	55138563	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	83	276	0	ENST00000257290.5:c.1240C>T	p.Pro414Ser	p.P414S	ENST00000257290	NM_006206.4	414	Cct/Tct	9/23	1	2	FACETS	0.747	0.658	0.842	0.747	0.658	0.842	SUBCLONAL	1	TRUE	1	0.29289692738634	2		276	759	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564552	55564552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	105	360	0	ENST00000288135.5:c.440C>T	p.Ser147Phe	p.S147F	ENST00000288135	NM_000222.2	147	tCc/tTc	3/21	1	2	FACETS	0.855	0.765	0.95	0.855	0.765	0.95	CLONAL	1	TRUE	1	0.29289692738634	2		360	839	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955863	55955863	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868047715	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	92	389	0	ENST00000263923.4:c.3299C>T	p.Ser1100Phe	p.S1100F	ENST00000263923	NM_002253.2	1100	tCc/tTc	24/30	1	2	FACETS	0.714	0.633	0.8	0.714	0.633	0.8	SUBCLONAL	1	TRUE	1	0.29289692738634	2		389	880	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956127	55956127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763517390	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	92	421	1	ENST00000263923.4:c.3188G>A	p.Gly1063Glu	p.G1063E	ENST00000263923	NM_002253.2	1063	gGa/gAa	23/30	1	2	FACETS	0.637	0.565	0.715	0.637	0.565	0.715	SUBCLONAL	1	TRUE	1	0.29289692738634	2		422	986	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007403	143007403	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	71	254	0	ENST00000262992.4:c.2381C>T	p.Ser794Leu	p.S794L	ENST00000262992	NM_001101669.1	794	tCa/tTa	22/24	1	2	FACETS	0.766	0.668	0.871	0.766	0.668	0.871	SUBCLONAL	1	TRUE	1	0.29289692738634	2		254	633	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557368	187557368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754907142	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	77	244	2	ENST00000441802.2:c.3994C>T	p.Arg1332Cys	p.R1332C	ENST00000441802	NM_005245.3	1332	Cgc/Tgc	6/27	1	2	FACETS	0.78	0.685	0.883	0.78	0.685	0.883	SUBCLONAL	1	TRUE	1	0.29289692738634	2		246	674	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1268645	1268645	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1322978833	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	164	444	2	ENST00000310581.5:c.2572C>T	p.Arg858Trp	p.R858W	ENST00000310581	NM_198253.2	858	Cgg/Tgg	9/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.29289692738634	2		446	1004	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295334	1295334	+	upstream_gene_variant	5'Flank	SNP	C	C	T	rs894008518	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	34	306	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.345	0.281	0.418	0.345	0.281	0.418	SUBCLONAL	1	TRUE	1	0.29289692738634	2		306	673	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867411	35867412	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	36	233	0	ENST00000303115.3:c.225_226delinsAA	p.Ala76Thr	p.A76T	ENST00000303115	NM_002185.3	75	ggGGcc/ggAAcc	3/8	1	2	FACETS	0.564	0.463	0.676	0.564	0.463	0.676	SUBCLONAL	1	TRUE	1	0.29289692738634	2		233	436	SUCCESS
APC	324	MSKCC	GRCh37	5	112154777	112154777	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	154	324	0	ENST00000257430.4:c.1048T>A	p.Ser350Thr	p.S350T	ENST00000257430	NM_000038.5	350	Tct/Act	10/16	0.229865262641387	2	FACETS	1	0.984	1	0.652	0.597	0.709	CLONAL	1	TRUE	0	0.29289692738634	2		324	807	SUCCESS
APC	324	MSKCC	GRCh37	5	112154847	112154847	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	91	363	1	ENST00000257430.4:c.1118C>T	p.Ser373Phe	p.S373F	ENST00000257430	NM_000038.5	373	tCc/tTc	10/16	0.229865262641387	2	FACETS	0.69	0.612	0.775	0.345	0.306	0.388	SUBCLONAL	1	TRUE	0	0.29289692738634	2		364	900	SUCCESS
APC	324	MSKCC	GRCh37	5	112179365	112179365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	235	404	0	ENST00000257430.4:c.8074C>T	p.Pro2692Ser	p.P2692S	ENST00000257430	NM_000038.5	2692	Cca/Tca	16/16	0.229865262641387	2	FACETS	0.78	0.728	0.834	0.78	0.728	0.834	SUBCLONAL	2	TRUE	0	0.29289692738634	2		404	1028	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149452904	149452904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779489294	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1250	150	577	0	ENST00000286301.3:c.1042G>A	p.Glu348Lys	p.E348K	ENST00000286301	NM_005211.3	348	Gag/Aag	7/22	0.229865262641387	2	FACETS	0.732	0.666	0.8	0.366	0.333	0.4	SUBCLONAL	1	TRUE	0	0.29289692738634	2		577	1400	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520680	176520680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1039989029	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	92	406	0	ENST00000292408.4:c.1423G>A	p.Glu475Lys	p.E475K	ENST00000292408	NM_213647.1	475	Gag/Aag	11/18	0.229865262641387	2	FACETS	0.648	0.574	0.726	0.324	0.287	0.363	SUBCLONAL	1	TRUE	0	0.29289692738634	2		406	970	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056973	180056973	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	142	530	0	ENST00000261937.6:c.646C>T	p.Leu216Phe	p.L216F	ENST00000261937	NM_182925.4	216	Ctt/Ttt	5/30	0.229865262641387	2	FACETS	0.773	0.702	0.847	0.386	0.351	0.424	SUBCLONAL	1	TRUE	0	0.29289692738634	2		530	1255	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057702	180057702	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202063909	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	135	462	1	ENST00000261937.6:c.253G>A	p.Glu85Lys	p.E85K	ENST00000261937	NM_182925.4	85	Gag/Aag	3/30	0.229865262641387	2	FACETS	0.804	0.729	0.884	0.402	0.364	0.442	CLONAL	1	TRUE	0	0.29289692738634	2		463	1146	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170141	32170141	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	95	358	0	ENST00000375023.3:c.3467G>A	p.Gly1156Asp	p.G1156D	ENST00000375023	NM_004557.3	1156	gGc/gAc	21/30	0.167090912625486	4	FACETS	0.835	0.742	0.935	0.418	0.371	0.468	INDETERMINATE	1	TRUE	2	0.29289692738634	4		358	1004	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170292	32170293	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	137	265	0	ENST00000375023.3:c.3315_3316delinsTT	p.Pro1106Ser	p.P1106S	ENST00000375023	NM_004557.3	1105	tcCCct/tcTTct	21/30	0.167090912625486	4	FACETS	0.757	0.689	0.828	0.757	0.689	0.828	INDETERMINATE	2	TRUE	2	0.29289692738634	4		265	799	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170328	32170328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	109	316	0	ENST00000375023.3:c.3280C>T	p.His1094Tyr	p.H1094Y	ENST00000375023	NM_004557.3	1094	Cat/Tat	21/30	0.167090912625486	4	FACETS	1	0.962	1	0.576	0.517	0.639	INDETERMINATE	1	TRUE	2	0.29289692738634	4		316	835	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32181950	32181950	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1275	109	435	0	ENST00000375023.3:c.2104C>T	p.His702Tyr	p.H702Y	ENST00000375023	NM_004557.3	702	Cat/Tat	13/30	0.167090912625486	4	FACETS	0.695	0.622	0.774	0.348	0.311	0.387	INDETERMINATE	1	TRUE	2	0.29289692738634	4		435	1384	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188244	32188244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs996553122	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	132	437	0	ENST00000375023.3:c.1097C>T	p.Pro366Leu	p.P366L	ENST00000375023	NM_004557.3	366	cCg/cTg	6/30	0.167090912625486	4	FACETS	0.9	0.814	0.99	0.45	0.407	0.495	INDETERMINATE	1	TRUE	2	0.29289692738634	4		437	1295	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43742121	43742121	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1705	174	684	0	ENST00000523873.1:c.110A>G	p.His37Arg	p.H37R	ENST00000523873		37	cAt/cGt	2/8	0.167090912625486	4	FACETS	0.818	0.749	0.889	0.409	0.374	0.445	INDETERMINATE	1	TRUE	2	0.29289692738634	4		684	1879	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955046	93955046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs141581954	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	156	476	0	ENST00000369303.4:c.2852C>T	p.Ser951Phe	p.S951F	ENST00000369303	NM_004440.3	951	tCc/tTc	16/17	0.167090912625486	4	FACETS	1	0.984	1	0.66	0.603	0.719	INDETERMINATE	1	TRUE	2	0.29289692738634	4		476	1044	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955074	93955074	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	115	564	0	ENST00000369303.4:c.2824G>A	p.Asp942Asn	p.D942N	ENST00000369303	NM_004440.3	942	Gat/Aat	16/17	0.167090912625486	4	FACETS	0.83	0.746	0.92	0.415	0.373	0.46	INDETERMINATE	1	TRUE	2	0.29289692738634	4		564	1223	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967228	93967228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1247358846	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	94	420	0	ENST00000369303.4:c.2124G>A	p.Met708Ile	p.M708I	ENST00000369303	NM_004440.3	708	atG/atA	12/17	0.167090912625486	4	FACETS	1	0.931	1	0.532	0.473	0.595	INDETERMINATE	1	TRUE	2	0.29289692738634	4		420	780	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068105	94068105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1373	281	616	0	ENST00000369303.4:c.857C>T	p.Ser286Phe	p.S286F	ENST00000369303	NM_004440.3	286	tCt/tTt	4/17	0.167090912625486	4	FACETS	1	0.993	1	0.75	0.702	0.799	INDETERMINATE	1	TRUE	2	0.29289692738634	4		616	1654	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117680982	117680982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	99	255	0	ENST00000368508.3:c.3638C>T	p.Ser1213Phe	p.S1213F	ENST00000368508	NM_002944.2	1213	tCt/tTt	23/43	0.167090912625486	4	FACETS	1	0.979	1	0.7	0.626	0.779	INDETERMINATE	1	TRUE	2	0.29289692738634	4		255	624	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681547	117681547	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151330473	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	113	451	0	ENST00000368508.3:c.3403G>A	p.Gly1135Arg	p.G1135R	ENST00000368508	NM_002944.2	1135	Ggg/Agg	22/43	0.167090912625486	4	FACETS	1	0.967	1	0.591	0.531	0.654	INDETERMINATE	1	TRUE	2	0.29289692738634	4		451	844	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686895	117686895	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	132	355	0	ENST00000368508.3:c.2822C>T	p.Ser941Phe	p.S941F	ENST00000368508	NM_002944.2	941	tCc/tTc	19/43	0.167090912625486	4	FACETS	1	0.978	1	0.633	0.574	0.695	INDETERMINATE	1	TRUE	2	0.29289692738634	4		355	920	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687290	117687290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1064	120	442	0	ENST00000368508.3:c.2761G>A	p.Ala921Thr	p.A921T	ENST00000368508	NM_002944.2	921	Gcc/Acc	18/43	0.167090912625486	4	FACETS	0.895	0.806	0.989	0.447	0.403	0.495	INDETERMINATE	1	TRUE	2	0.29289692738634	4		442	1184	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117714396	117714396	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	169	378	0	ENST00000368508.3:c.1253C>T	p.Ser418Leu	p.S418L	ENST00000368508	NM_002944.2	418	tCa/tTa	11/43	0.167090912625486	4	FACETS	0.888	0.817	0.962	0.888	0.817	0.962	INDETERMINATE	2	TRUE	2	0.29289692738634	4		378	840	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724328	117724328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	174	776	0	ENST00000368508.3:c.551C>T	p.Pro184Leu	p.P184L	ENST00000368508	NM_002944.2	184	cCc/cTc	6/43	0.167090912625486	4	FACETS	1	0.987	1	0.693	0.637	0.752	INDETERMINATE	1	TRUE	2	0.29289692738634	4		776	1108	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196933	138196933	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	80	298	0	ENST00000237289.4:c.595C>T	p.Leu199Phe	p.L199F	ENST00000237289	NM_001270507.1	199	Ctt/Ttt	4/9	0.167090912625486	4	FACETS	0.752	0.661	0.851	0.376	0.33	0.426	INDETERMINATE	1	TRUE	2	0.29289692738634	4		298	939	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152201873	152201873	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779180038	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	78	291	0	ENST00000206249.3:c.727C>T	p.Arg243Cys	p.R243C	ENST00000206249	NM_000125.3	243	Cgt/Tgt	3/8	0.167090912625486	4	FACETS	0.829	0.727	0.938	0.414	0.363	0.469	INDETERMINATE	1	TRUE	2	0.29289692738634	4		291	831	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265635	152265635	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367647625	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	34	136	0	ENST00000206249.3:c.1088G>A	p.Arg363Lys	p.R363K	ENST00000206249	NM_000125.3	363	aGg/aAg	4/8	0.167090912625486	4	FACETS	0.776	0.634	0.934	0.388	0.317	0.467	INDETERMINATE	1	TRUE	2	0.29289692738634	4		136	387	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415558	152415558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770516501	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1162	260	495	0	ENST00000206249.3:c.1408G>A	p.Glu470Lys	p.E470K	ENST00000206249	NM_000125.3	470	Gaa/Aaa	7/8	0.167090912625486	4	FACETS	0.807	0.754	0.862	0.807	0.754	0.862	INDETERMINATE	2	TRUE	2	0.29289692738634	4		495	1422	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206855	162206855	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1285127997	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	139	335	0	ENST00000366898.1:c.820G>A	p.Asp274Asn	p.D274N	ENST00000366898	NM_004562.2	274	Gat/Aat	7/12	0.167090912625486	4	FACETS	1	0.979	1	0.633	0.576	0.694	INDETERMINATE	1	TRUE	2	0.29289692738634	4		335	969	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946316	2946316	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759870621	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	186	373	0	ENST00000396946.4:c.3421G>A	p.Glu1141Lys	p.E1141K	ENST00000396946	NM_032415.4	1141	Gag/Aag	25/25	0.238001352105468	3	FACETS	1	0.987	1	0.665	0.613	0.719	CLONAL	1	TRUE	1	0.29289692738634	3		373	1095	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962857	2962858	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	124	382	1	ENST00000396946.4:c.2050_2051delinsAA	p.Gly684Lys	p.G684K	ENST00000396946	NM_032415.4	684	GGg/AAg	16/25	0.238001352105468	3	FACETS	0.95	0.858	1	0.475	0.429	0.524	CLONAL	1	TRUE	1	0.29289692738634	3		383	1022	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963866	2963866	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	211	451	0	ENST00000396946.4:c.1940+1G>A		p.X647_splice	ENST00000396946	NM_032415.4	647			0.238001352105468	3	FACETS	1	0.99	1	0.714	0.662	0.768	CLONAL	1	TRUE	1	0.29289692738634	3		451	1157	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968280	2968280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	113	416	1	ENST00000396946.4:c.1706G>A	p.Gly569Glu	p.G569E	ENST00000396946	NM_032415.4	569	gGa/gAa	13/25	0.238001352105468	3	FACETS	0.7	0.628	0.777	0.35	0.314	0.389	SUBCLONAL	1	TRUE	1	0.29289692738634	3		417	1263	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987272	2987272	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	99	341	0	ENST00000396946.4:c.157G>A	p.Asp53Asn	p.D53N	ENST00000396946	NM_032415.4	53	Gat/Aat	3/25	0.238001352105468	3	FACETS	0.747	0.665	0.834	0.373	0.332	0.417	SUBCLONAL	1	TRUE	1	0.29289692738634	3		341	1038	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450267	50450267	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	92	327	0	ENST00000331340.3:c.451G>A	p.Gly151Arg	p.G151R	ENST00000331340	NM_006060.4	151	Ggg/Agg	5/8	0.238001352105468	3	FACETS	0.75	0.665	0.841	0.375	0.332	0.421	SUBCLONAL	1	TRUE	1	0.29289692738634	3		327	960	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450292	50450292	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs374333820	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	199	373	0	ENST00000331340.3:c.476A>G	p.Asn159Ser	p.N159S	ENST00000331340	NM_006060.4	159	aAc/aGc	5/8	0.238001352105468	3	FACETS	0.758	0.702	0.817	0.758	0.702	0.817	SUBCLONAL	2	TRUE	1	0.29289692738634	3		373	1027	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55210078	55210078	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	258	483	0	ENST00000275493.2:c.188G>A	p.Gly63Glu	p.G63E	ENST00000275493	NM_005228.3	63	gGg/gAg	2/28	0.238001352105468	3	FACETS	0.759	0.709	0.81	0.759	0.709	0.81	SUBCLONAL	2	TRUE	1	0.29289692738634	3		483	1331	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211097	55211097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1219568637	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	197	418	0	ENST00000275493.2:c.340G>A	p.Glu114Lys	p.E114K	ENST00000275493	NM_005228.3	114	Gaa/Aaa	3/28	0.238001352105468	3	FACETS	1	0.989	1	0.705	0.652	0.76	CLONAL	1	TRUE	1	0.29289692738634	3		418	1094	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224495	55224495	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	131	424	2	ENST00000275493.2:c.1177G>A	p.Asp393Asn	p.D393N	ENST00000275493	NM_005228.3	393	Gat/Aat	10/28	0.238001352105468	3	FACETS	0.85	0.769	0.935	0.425	0.384	0.468	CLONAL	1	TRUE	1	0.29289692738634	3		426	1207	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273092	55273092	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1473630143	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	102	375	0	ENST00000275493.2:c.3415C>T	p.Leu1139Phe	p.L1139F	ENST00000275493	NM_005228.3	1139	Ctc/Ttc	28/28	0.238001352105468	3	FACETS	0.789	0.704	0.88	0.395	0.352	0.44	SUBCLONAL	1	TRUE	1	0.29289692738634	3		375	1012	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508922	106508922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769688408	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	53	184	0	ENST00000359195.3:c.916G>A	p.Val306Ile	p.V306I	ENST00000359195	NM_002649.2	306	Gta/Ata	2/11	0.238001352105468	3	FACETS	0.792	0.675	0.919	0.396	0.337	0.46	CLONAL	1	TRUE	1	0.29289692738634	3		184	524	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509747	106509747	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761655879	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	109	344	0	ENST00000359195.3:c.1741G>A	p.Glu581Lys	p.E581K	ENST00000359195	NM_002649.2	581	Gaa/Aaa	2/11	0.238001352105468	3	FACETS	0.863	0.773	0.958	0.431	0.386	0.479	CLONAL	1	TRUE	1	0.29289692738634	3		344	989	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106526694	106526694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772274649	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	181	312	0	ENST00000359195.3:c.2987G>A	p.Gly996Glu	p.G996E	ENST00000359195	NM_002649.2	996	gGa/gAa	10/11	0.238001352105468	3	FACETS	0.79	0.729	0.853	0.79	0.729	0.853	SUBCLONAL	2	TRUE	1	0.29289692738634	3		312	897	SUCCESS
MET	4233	MSKCC	GRCh37	7	116380130	116380130	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1000	91	458	0	ENST00000397752.3:c.1519G>A	p.Gly507Arg	p.G507R	ENST00000397752	NM_000245.2	507	Ggg/Agg	4/21	0.238001352105468	3	FACETS	0.653	0.578	0.733	0.326	0.289	0.367	SUBCLONAL	1	TRUE	1	0.29289692738634	3		458	1091	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846127	128846127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1484	187	574	1	ENST00000249373.3:c.1057C>T	p.Leu353Phe	p.L353F	ENST00000249373	NM_005631.4	353	Ctc/Ttc	5/12	0.238001352105468	3	FACETS	0.876	0.806	0.949	0.438	0.403	0.475	CLONAL	1	TRUE	1	0.29289692738634	3		575	1671	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860446	151860446	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057518278	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1107	197	468	0	ENST00000262189.6:c.10216G>A	p.Glu3406Lys	p.E3406K	ENST00000262189	NM_170606.2	3406	Gaa/Aaa	43/59	0.238001352105468	3	FACETS	1	0.981	1	0.591	0.546	0.638	CLONAL	1	TRUE	1	0.29289692738634	3		468	1304	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372314	55372314	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	69	230	0	ENST00000297316.4:c.1004C>T	p.Pro335Leu	p.P335L	ENST00000297316	NM_022454.3	335	cCc/cTc	2/2	1	2	FACETS	0.962	0.839	1	0.962	0.839	1	CLONAL	1	TRUE	1	0.29289692738634	2		230	490	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74859038	74859038	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	23	72	0	ENST00000284811.8:c.166G>A	p.Glu56Lys	p.E56K	ENST00000284811		56	Gaa/Aaa	4/4	1	2	FACETS	0.969	0.763	1	0.969	0.763	1	CLONAL	1	TRUE	1	0.29289692738634	2		72	162	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457240	5457240	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	251	285	0	ENST00000381577.3:c.214G>A	p.Glu72Lys	p.E72K	ENST00000381577	NM_014143.3	72	Gaa/Aaa	3/7	0.24052876418788	3	FACETS	1	0.983	1	0.755	0.707	0.803	CLONAL	2	TRUE	0	0.29289692738634	3		285	868	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8375966	8375966	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	323	421	0	ENST00000356435.5:c.4631C>T	p.Pro1544Leu	p.P1544L	ENST00000356435		1544	cCc/cTc	28/35	0.24052876418788	3	FACETS	1	0.976	1	0.708	0.668	0.748	CLONAL	2	TRUE	0	0.29289692738634	3		421	1191	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8471007	8471007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764232627	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	101	430	0	ENST00000356435.5:c.3492G>A	p.Met1164Ile	p.M1164I	ENST00000356435		1164	atG/atA	20/35	0.24052876418788	3	FACETS	0.804	0.718	0.897	0.268	0.239	0.299	CLONAL	1	TRUE	0	0.29289692738634	3		430	983	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37006508	37006508	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	103	405	0	ENST00000358127.4:c.437C>T	p.Pro146Leu	p.P146L	ENST00000358127	NM_001280556.1	146	cCa/cTa	4/10	0.24052876418788	3	FACETS	0.714	0.637	0.796	0.238	0.212	0.266	SUBCLONAL	1	TRUE	0	0.29289692738634	3		405	1130	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87549127	87549127	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	318	424	1	ENST00000277120.3:c.1684G>A	p.Glu562Lys	p.E562K	ENST00000277120		562	Gaa/Aaa	15/19	0.24052876418788	3	FACETS	1	0.987	1	0.757	0.715	0.8	CLONAL	2	TRUE	0	0.29289692738634	3		425	1096	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93629443	93629443	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	105	368	0	ENST00000375746.1:c.877A>C	p.Ile293Leu	p.I293L	ENST00000375746	NM_001174167.1	293	Atc/Ctc	7/14	0.24052876418788	3	FACETS	0.796	0.712	0.887	0.265	0.237	0.296	SUBCLONAL	1	TRUE	0	0.29289692738634	3		368	1032	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242835	98242835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	301	394	0	ENST00000331920.6:c.782C>T	p.Pro261Leu	p.P261L	ENST00000331920	NM_000264.3	261	cCt/cTt	6/24	0.24052876418788	3	FACETS	1	0.981	1	0.726	0.684	0.769	CLONAL	2	TRUE	0	0.29289692738634	3		394	1082	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133755949	133755949	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	291	363	0	ENST00000318560.5:c.1576C>T	p.Pro526Ser	p.P526S	ENST00000318560	NM_005157.4	526	Cca/Tca	10/11	0.24052876418788	3	FACETS	1	0.988	1	0.784	0.739	0.831	CLONAL	2	TRUE	0	0.29289692738634	3		363	968	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760025	133760025	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1221027936	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	381	493	0	ENST00000318560.5:c.2348C>T	p.Pro783Leu	p.P783L	ENST00000318560	NM_005157.4	783	cCc/cTc	11/11	0.24052876418788	3	FACETS	1	0.992	1	0.812	0.771	0.854	CLONAL	2	TRUE	0	0.29289692738634	3		493	1224	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596017	43596017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	74	352	0	ENST00000355710.3:c.184G>A	p.Glu62Lys	p.E62K	ENST00000355710	NM_020975.4	62	Gag/Aag	2/20	1	2	FACETS	0.594	0.519	0.675	0.594	0.519	0.675	SUBCLONAL	1	TRUE	1	0.29289692738634	2		352	851	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604664	43604664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1478152005	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	81	290	0	ENST00000355710.3:c.1249C>T	p.Arg417Cys	p.R417C	ENST00000355710	NM_020975.4	417	Cgc/Tgc	6/20	1	2	FACETS	0.805	0.709	0.908	0.805	0.709	0.908	CLONAL	1	TRUE	1	0.29289692738634	2		290	687	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333410	70333410	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	109	472	0	ENST00000373644.4:c.1315C>T	p.Pro439Ser	p.P439S	ENST00000373644	NM_030625.2	439	Cca/Tca	2/12	1	2	FACETS	0.675	0.605	0.75	0.675	0.605	0.75	SUBCLONAL	1	TRUE	1	0.29289692738634	2		472	1102	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244982	123244982	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	128	464	1	ENST00000358487.5:c.2122C>T	p.Pro708Ser	p.P708S	ENST00000358487	NM_000141.4	708	Ccc/Tcc	16/18	1	2	FACETS	0.759	0.686	0.836	0.759	0.686	0.836	SUBCLONAL	1	TRUE	1	0.29289692738634	2		465	1152	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276865	123276865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	119	402	0	ENST00000358487.5:c.1052C>T	p.Ser351Phe	p.S351F	ENST00000358487	NM_000141.4	351	tCc/tTc	8/18	1	2	FACETS	0.779	0.702	0.861	0.779	0.702	0.861	SUBCLONAL	1	TRUE	1	0.29289692738634	2		402	1043	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533476	533476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs909222512	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	143	378	0	ENST00000451590.1:c.427G>A	p.Glu143Lys	p.E143K	ENST00000451590	NM_001130442.1	143	Gag/Aag	4/5	0.238001352105468	3	FACETS	0.941	0.856	1	0.47	0.428	0.515	CLONAL	1	TRUE	1	0.29289692738634	3		378	1190	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518524	69518524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	117	174	0	ENST00000294312.3:c.121C>T	p.Pro41Ser	p.P41S	ENST00000294312	NM_005117.2	41	Ccc/Tcc	1/3	0.238001352105468	3	FACETS	0.866	0.784	0.951	0.866	0.784	0.951	CLONAL	2	TRUE	1	0.29289692738634	3		174	529	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77043867	77043867	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1323	310	574	0	ENST00000356341.3:c.1459C>T	p.Pro487Ser	p.P487S	ENST00000356341	NM_002576.4	487	Cca/Tca	14/15	0.238001352105468	3	FACETS	1	0.994	1	0.743	0.699	0.789	CLONAL	1	TRUE	1	0.29289692738634	3		574	1633	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912815	100912815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1000609240	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	232	492	0	ENST00000325455.5:c.2507G>A	p.Arg836Gln	p.R836Q	ENST00000325455	NM_001202474.3	836	cGa/cAa	7/8	0.238001352105468	3	FACETS	1	0.991	1	0.711	0.662	0.762	CLONAL	1	TRUE	1	0.29289692738634	3		492	1277	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962530	100962530	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752817186	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1312	140	499	0	ENST00000325455.5:c.1867C>T	p.Arg623Cys	p.R623C	ENST00000325455	NM_001202474.3	623	Cgc/Tgc	3/8	0.238001352105468	3	FACETS	0.755	0.685	0.829	0.377	0.342	0.415	SUBCLONAL	1	TRUE	1	0.29289692738634	3		499	1452	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195301	102195301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1573	173	675	0	ENST00000263464.3:c.61G>A	p.Glu21Lys	p.E21K	ENST00000263464	NM_001165.4	21	Gaa/Aaa	2/9	0.238001352105468	3	FACETS	0.776	0.711	0.844	0.388	0.355	0.422	SUBCLONAL	1	TRUE	1	0.29289692738634	3		675	1746	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102196078	102196078	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	137	525	0	ENST00000263464.3:c.838G>A	p.Gly280Ser	p.G280S	ENST00000263464	NM_001165.4	280	Ggt/Agt	2/9	0.238001352105468	3	FACETS	0.814	0.738	0.895	0.407	0.369	0.448	CLONAL	1	TRUE	1	0.29289692738634	3		525	1317	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343772	118343772	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	109	449	0	ENST00000534358.1:c.1898C>T	p.Ser633Phe	p.S633F	ENST00000534358	NM_005933.3	633	tCc/tTc	3/36	0.238001352105468	3	FACETS	0.78	0.699	0.867	0.39	0.349	0.434	SUBCLONAL	1	TRUE	1	0.29289692738634	3		449	1094	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373238	118373238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782789725	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	250	464	0	ENST00000534358.1:c.6631C>T	p.Arg2211Trp	p.R2211W	ENST00000534358	NM_005933.3	2211	Cgg/Tgg	27/36	0.238001352105468	3	FACETS	0.805	0.752	0.859	0.805	0.752	0.859	CLONAL	2	TRUE	1	0.29289692738634	3		464	1216	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394804	394804	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760277077	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	112	322	0	ENST00000399788.2:c.4891G>A	p.Gly1631Ser	p.G1631S	ENST00000399788	NM_001042603.1	1631	Ggc/Agc	28/28	1	2	FACETS	0.87	0.782	0.964	0.87	0.782	0.964	CLONAL	1	TRUE	1	0.29289692738634	2		322	879	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432886	432886	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	56	345	0	ENST00000399788.2:c.2030C>T	p.Ser677Leu	p.S677L	ENST00000399788	NM_001042603.1	677	tCa/tTa	15/28	1	2	FACETS	0.403	0.344	0.468	0.403	0.344	0.468	SUBCLONAL	1	TRUE	1	0.29289692738634	2		345	948	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022532	12022532	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	102	433	1	ENST00000396373.4:c.638C>T	p.Ser213Phe	p.S213F	ENST00000396373	NM_001987.4	213	tCc/tTc	5/8	1	2	FACETS	0.598	0.533	0.668	0.598	0.533	0.668	SUBCLONAL	1	TRUE	1	0.29289692738634	2		434	1164	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18719980	18719980	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs889775181	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	66	310	0	ENST00000266497.5:c.3877G>A	p.Glu1293Lys	p.E1293K	ENST00000266497		1293	Gaa/Aaa	27/31	1	2	FACETS	0.667	0.578	0.763	0.667	0.578	0.763	SUBCLONAL	1	TRUE	1	0.29289692738634	2		310	676	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431588	49431588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1305161243	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	84	304	0	ENST00000301067.7:c.9551C>T	p.Ser3184Phe	p.S3184F	ENST00000301067	NM_003482.3	3184	tCc/tTc	34/54	1	2	FACETS	0.731	0.645	0.823	0.731	0.645	0.823	SUBCLONAL	1	TRUE	1	0.29289692738634	2		304	785	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433782	49433782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	141	468	1	ENST00000301067.7:c.7771G>A	p.Gly2591Ser	p.G2591S	ENST00000301067	NM_003482.3	2591	Ggc/Agc	31/54	1	2	FACETS	0.834	0.758	0.914	0.834	0.758	0.914	CLONAL	1	TRUE	1	0.29289692738634	2		469	1155	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438191	49438191	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	316	512	0	ENST00000301067.7:c.5078G>T	p.Arg1693Leu	p.R1693L	ENST00000301067	NM_003482.3	1693	cGg/cTg	20/54	1	2	FACETS	0.791	0.745	0.838	1	0.994	1	SUBCLONAL	2	TRUE	1	0.29289692738634	2		512	1364	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858941	57858941	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754019701	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1395	395	744	1	ENST00000228682.2:c.437C>T	p.Ser146Leu	p.S146L	ENST00000228682	NM_005269.2	146	tCg/tTg	5/12	0.229865262641387	2	FACETS	0.753	0.714	0.794	0.753	0.714	0.794	SUBCLONAL	2	TRUE	0	0.29289692738634	2		745	1790	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811603	102811603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	288	577	0	ENST00000307046.8:c.581G>A	p.Gly194Glu	p.G194E	ENST00000307046	NM_001111285.1	194	gGa/gAa	4/4	0.229865262641387	2	FACETS	1	0.993	1	0.729	0.684	0.775	CLONAL	1	TRUE	0	0.29289692738634	2		577	1349	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811643	102811643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	334	614	0	ENST00000307046.8:c.541G>A	p.Glu181Lys	p.E181K	ENST00000307046	NM_001111285.1	181	Gag/Aag	4/4	0.229865262641387	2	FACETS	0.782	0.737	0.827	0.782	0.737	0.827	SUBCLONAL	2	TRUE	0	0.29289692738634	2		614	1459	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111855975	111855975	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	234	475	0	ENST00000341259.2:c.26C>T	p.Ser9Phe	p.S9F	ENST00000341259	NM_005475.2	9	tCc/tTc	2/8	0.229865262641387	2	FACETS	1	0.99	1	0.675	0.629	0.723	CLONAL	1	TRUE	0	0.29289692738634	2		475	1184	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856031	111856031	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	113	414	0	ENST00000341259.2:c.82G>A	p.Glu28Lys	p.E28K	ENST00000341259	NM_005475.2	28	Gag/Aag	2/8	0.229865262641387	2	FACETS	0.785	0.705	0.87	0.392	0.352	0.435	SUBCLONAL	1	TRUE	0	0.29289692738634	2		414	983	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856444	111856445	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	59	179	0	ENST00000341259.2:c.495_496delinsTT	p.Pro166Ser	p.P166S	ENST00000341259	NM_005475.2	165	acCCcc/acTTcc	2/8	0.229865262641387	2	FACETS	0.848	0.731	0.975	0.424	0.365	0.488	CLONAL	1	TRUE	0	0.29289692738634	2		179	475	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117387	115117387	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	84	454	0	ENST00000257566.3:c.787C>T	p.Leu263Phe	p.L263F	ENST00000257566	NM_016569.3	263	Ctc/Ttc	4/8	0.229865262641387	2	FACETS	0.576	0.508	0.65	0.288	0.254	0.325	SUBCLONAL	1	TRUE	0	0.29289692738634	2		454	995	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120753	115120753	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	196	425	0	ENST00000257566.3:c.253G>A	p.Ala85Thr	p.A85T	ENST00000257566	NM_016569.3	85	Gcg/Acg	1/8	0.229865262641387	2	FACETS	1	0.989	1	0.704	0.651	0.758	CLONAL	1	TRUE	0	0.29289692738634	2		425	951	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120761	115120762	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	168	398	0	ENST00000257566.3:c.244_245delinsAA	p.Gly82Lys	p.G82K	ENST00000257566	NM_016569.3	82	GGg/AAg	1/8	0.229865262641387	2	FACETS	1	0.984	1	0.641	0.589	0.695	CLONAL	1	TRUE	0	0.29289692738634	2		398	895	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233952	133233952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	104	349	0	ENST00000320574.5:c.3442C>T	p.Pro1148Ser	p.P1148S	ENST00000320574	NM_006231.2	1148	Cct/Tct	28/49	0.229865262641387	2	FACETS	0.742	0.663	0.826	0.371	0.331	0.413	SUBCLONAL	1	TRUE	0	0.29289692738634	2		349	957	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895622	28895622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	101	482	0	ENST00000282397.4:c.3152C>T	p.Pro1051Leu	p.P1051L	ENST00000282397	NM_002019.4	1051	cCc/cTc	23/30	0.29289692738634	3	FACETS	0.659	0.588	0.736	0.33	0.294	0.368	SUBCLONAL	1	TRUE	1	0.29289692738634	3		482	1199	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001416	29001416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	68	244	0	ENST00000282397.4:c.1316C>T	p.Pro439Leu	p.P439L	ENST00000282397	NM_002019.4	439	cCa/cTa	10/30	0.29289692738634	3	FACETS	0.763	0.663	0.871	0.381	0.331	0.436	SUBCLONAL	1	TRUE	1	0.29289692738634	3		244	698	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041237	29041237	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	113	344	0	ENST00000282397.4:c.191C>T	p.Pro64Leu	p.P64L	ENST00000282397	NM_002019.4	64	cCt/cTt	3/30	0.29289692738634	3	FACETS	0.826	0.742	0.916	0.413	0.371	0.458	CLONAL	1	TRUE	1	0.29289692738634	3		344	1071	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041243	29041243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	217	313	0	ENST00000282397.4:c.185C>T	p.Ser62Phe	p.S62F	ENST00000282397	NM_002019.4	62	tCt/tTt	3/30	0.29289692738634	3	FACETS	0.813	0.755	0.872	0.813	0.755	0.872	CLONAL	2	TRUE	1	0.29289692738634	3		313	1045	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041725	29041725	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	198	344	0	ENST00000282397.4:c.94C>T	p.Pro32Ser	p.P32S	ENST00000282397	NM_002019.4	32	Cct/Tct	2/30	0.29289692738634	3	FACETS	0.767	0.71	0.826	0.767	0.71	0.826	SUBCLONAL	2	TRUE	1	0.29289692738634	3		344	1010	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911404	32911404	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1393	123	722	0	ENST00000380152.3:c.2912T>C	p.Leu971Ser	p.L971S	ENST00000380152		971	tTa/tCa	11/27	0.29289692738634	3	FACETS	0.635	0.572	0.702	0.318	0.286	0.351	SUBCLONAL	1	TRUE	1	0.29289692738634	3		722	1516	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914707	32914707	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80358862	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1188	150	731	1	ENST00000380152.3:c.6215C>T	p.Ser2072Phe	p.S2072F	ENST00000380152		2072	tCc/tTc	11/27	0.29289692738634	3	FACETS	0.878	0.8	0.96	0.439	0.4	0.48	CLONAL	1	TRUE	1	0.29289692738634	3		732	1338	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937323	32937323	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1566245207	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	70	271	0	ENST00000380152.3:c.7984A>G	p.Thr2662Ala	p.T2662A	ENST00000380152		2662	Acg/Gcg	18/27	0.29289692738634	3	FACETS	0.714	0.622	0.815	0.357	0.311	0.408	SUBCLONAL	1	TRUE	1	0.29289692738634	3		271	767	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133889	41133889	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1374	136	559	0	ENST00000379561.5:c.1739C>T	p.Ser580Phe	p.S580F	ENST00000379561	NM_002015.3	580	tCc/tTc	2/3	0.29289692738634	3	FACETS	0.705	0.639	0.775	0.353	0.319	0.388	SUBCLONAL	1	TRUE	1	0.29289692738634	3		559	1510	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36988507	36988508	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	199	408	0	ENST00000354822.5:c.145_146delinsTT	p.Pro49Phe	p.P49F	ENST00000354822	NM_001079668.2	49	CCc/TTc	2/3	0.229865262641387	2	FACETS	1	0.989	1	0.705	0.653	0.759	CLONAL	1	TRUE	0	0.29289692738634	2		408	964	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609525	81609525	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	211	381	0	ENST00000298171.2:c.1123G>A	p.Glu375Lys	p.E375K	ENST00000298171	NM_000369.2	375	Gaa/Aaa	10/10	0.229865262641387	2	FACETS	1	0.991	1	0.724	0.672	0.778	CLONAL	1	TRUE	0	0.29289692738634	2		381	995	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961408	41961408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1446	208	690	0	ENST00000219905.7:c.316C>T	p.Pro106Ser	p.P106S	ENST00000219905	NM_001164273.1	106	Cct/Tct	2/24	1	2	FACETS	0.859	0.794	0.926	0.859	0.794	0.926	CLONAL	1	TRUE	1	0.29289692738634	2		690	1654	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41962143	41962143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	147	543	1	ENST00000219905.7:c.1051G>A	p.Glu351Lys	p.E351K	ENST00000219905	NM_001164273.1	351	Gag/Aag	2/24	1	2	FACETS	0.813	0.741	0.89	0.813	0.741	0.89	CLONAL	1	TRUE	1	0.29289692738634	2		544	1234	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989031	41989031	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1422	144	720	1	ENST00000219905.7:c.1823C>T	p.Pro608Leu	p.P608L	ENST00000219905	NM_001164273.1	608	cCa/cTa	3/24	1	2	FACETS	0.628	0.57	0.689	0.628	0.57	0.689	SUBCLONAL	1	TRUE	1	0.29289692738634	2		721	1566	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034965	42034965	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1487	158	646	0	ENST00000219905.7:c.4807C>T	p.Gln1603Ter	p.Q1603*	ENST00000219905	NM_001164273.1	1603	Caa/Taa	15/24	1	2	FACETS	0.656	0.598	0.716	0.656	0.598	0.716	SUBCLONAL	1	TRUE	1	0.29289692738634	2		646	1645	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73995367	73995367	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	38	154	0	ENST00000318443.5:c.673C>T	p.Pro225Ser	p.P225S	ENST00000318443	NM_001024736.1	225	Ccc/Tcc	4/10	1	2	FACETS	0.777	0.644	0.924	0.777	0.644	0.924	CLONAL	1	TRUE	1	0.29289692738634	2		154	334	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476298	88476298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373273419	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	93	376	0	ENST00000360948.2:c.1834C>T	p.Pro612Ser	p.P612S	ENST00000360948	NM_001012338.2	612	Ccc/Tcc	15/19	1	2	FACETS	0.673	0.597	0.754	0.673	0.597	0.754	SUBCLONAL	1	TRUE	1	0.29289692738634	2		376	944	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88576273	88576273	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	52	133	1	ENST00000360948.2:c.1400C>T	p.Pro467Leu	p.P467L	ENST00000360948	NM_001012338.2	467	cCc/cTc	13/19	1	2	FACETS	0.913	0.78	1	0.913	0.78	1	CLONAL	1	TRUE	1	0.29289692738634	2		134	389	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680722	88680722	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	99	415	0	ENST00000360948.2:c.535G>A	p.Glu179Lys	p.E179K	ENST00000360948	NM_001012338.2	179	Gag/Aag	6/19	1	2	FACETS	0.669	0.596	0.748	0.669	0.596	0.748	SUBCLONAL	1	TRUE	1	0.29289692738634	2		415	1010	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88726680	88726680	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866711936	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	101	375	0	ENST00000360948.2:c.364G>A	p.Ala122Thr	p.A122T	ENST00000360948	NM_001012338.2	122	Gcc/Acc	4/19	1	2	FACETS	0.718	0.641	0.801	0.718	0.641	0.801	SUBCLONAL	1	TRUE	1	0.29289692738634	2		375	960	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500417	99500417	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777816523	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	108	435	0	ENST00000268035.6:c.3850G>A	p.Glu1284Lys	p.E1284K	ENST00000268035	NM_000875.3	1284	Gag/Aag	21/21	1	2	FACETS	0.727	0.651	0.807	0.727	0.651	0.807	SUBCLONAL	1	TRUE	1	0.29289692738634	2		435	1015	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343579	343580	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1302	165	597	0	ENST00000262320.3:c.2094_2095delinsTT	p.Pro699Ser	p.P699S	ENST00000262320	NM_003502.3	698	caCCca/caTTca	8/11	1	2	FACETS	0.768	0.703	0.836	0.768	0.703	0.836	SUBCLONAL	1	TRUE	1	0.29289692738634	2		597	1467	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129399	2129399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45517287	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	89	382	1	ENST00000219476.3:c.3254C>T	p.Ser1085Leu	p.S1085L	ENST00000219476	NM_000548.3	1085	tCg/tTg	28/42	1	2	FACETS	0.775	0.687	0.87	0.775	0.687	0.87	SUBCLONAL	1	TRUE	1	0.29289692738634	2		383	784	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2131787	2131787	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1020561347	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	126	376	0	ENST00000219476.3:c.3802C>T	p.Arg1268Cys	p.R1268C	ENST00000219476	NM_000548.3	1268	Cgc/Tgc	31/42	1	2	FACETS	0.954	0.863	1	0.954	0.863	1	CLONAL	1	TRUE	1	0.29289692738634	2		376	902	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857481	9857481	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	88	280	0	ENST00000330684.3:c.3920C>T	p.Pro1307Leu	p.P1307L	ENST00000330684	NM_001134407.1	1307	cCc/cTc	13/13	1	2	FACETS	0.801	0.709	0.899	0.801	0.709	0.899	CLONAL	1	TRUE	1	0.29289692738634	2		280	750	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857805	9857805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1304	145	563	2	ENST00000330684.3:c.3596C>T	p.Pro1199Leu	p.P1199L	ENST00000330684	NM_001134407.1	1199	cCg/cTg	13/13	1	2	FACETS	0.683	0.621	0.749	0.683	0.621	0.749	SUBCLONAL	1	TRUE	1	0.29289692738634	2		565	1449	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892182	9892182	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	123	500	0	ENST00000330684.3:c.2308C>T	p.Pro770Ser	p.P770S	ENST00000330684	NM_001134407.1	770	Cct/Tct	11/13	1	2	FACETS	0.673	0.607	0.743	0.673	0.607	0.743	SUBCLONAL	1	TRUE	1	0.29289692738634	2		500	1248	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923318	9923318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867335598	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	81	340	0	ENST00000330684.3:c.1969G>A	p.Glu657Lys	p.E657K	ENST00000330684	NM_001134407.1	657	Gaa/Aaa	9/13	1	2	FACETS	0.643	0.566	0.727	0.643	0.566	0.727	SUBCLONAL	1	TRUE	1	0.29289692738634	2		340	860	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9928010	9928010	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	114	423	1	ENST00000330684.3:c.1729G>A	p.Glu577Lys	p.E577K	ENST00000330684	NM_001134407.1	577	Gaa/Aaa	8/13	1	2	FACETS	0.77	0.692	0.853	0.77	0.692	0.853	SUBCLONAL	1	TRUE	1	0.29289692738634	2		424	1011	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032087	10032087	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	130	435	0	ENST00000330684.3:c.736C>T	p.Leu246Phe	p.L246F	ENST00000330684	NM_001134407.1	246	Ctt/Ttt	3/13	1	2	FACETS	0.836	0.757	0.919	0.836	0.757	0.919	CLONAL	1	TRUE	1	0.29289692738634	2		435	1062	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273979	10273979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1085307680	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	120	478	0	ENST00000330684.3:c.290G>A	p.Gly97Asp	p.G97D	ENST00000330684	NM_001134407.1	97	gGc/gAc	2/13	1	2	FACETS	0.702	0.632	0.776	0.702	0.632	0.776	SUBCLONAL	1	TRUE	1	0.29289692738634	2		478	1167	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041554	14041554	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs772728961	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	97	337	0	ENST00000311895.7:c.2101C>G	p.Arg701Gly	p.R701G	ENST00000311895	NM_005236.2	701	Cgt/Ggt	11/11	1	2	FACETS	0.754	0.671	0.842	0.754	0.671	0.842	SUBCLONAL	1	TRUE	1	0.29289692738634	2		337	879	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68849500	68849501	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	106	415	0	ENST00000261769.5:c.1403_1404delinsTT	p.Thr468Ile	p.T468I	ENST00000261769	NM_004360.3	468	aCC/aTT	10/16	1	2	FACETS	0.626	0.559	0.696	0.626	0.559	0.696	SUBCLONAL	1	TRUE	1	0.29289692738634	2		415	1157	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821349	72821349	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567505140	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	124	476	0	ENST00000268489.5:c.10826C>T	p.Ser3609Phe	p.S3609F	ENST00000268489	NM_006885.3	3609	tCc/tTc	10/10	1	2	FACETS	0.785	0.709	0.866	0.785	0.709	0.866	SUBCLONAL	1	TRUE	1	0.29289692738634	2		476	1078	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821433	72821433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764472267	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1544	146	831	0	ENST00000268489.5:c.10742C>T	p.Pro3581Leu	p.P3581L	ENST00000268489	NM_006885.3	3581	cCt/cTt	10/10	1	2	FACETS	0.59	0.536	0.647	0.59	0.536	0.647	SUBCLONAL	1	TRUE	1	0.29289692738634	2		831	1690	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992148	72992148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1255	169	579	0	ENST00000268489.5:c.1897G>A	p.Glu633Lys	p.E633K	ENST00000268489	NM_006885.3	633	Gag/Aag	2/10	1	2	FACETS	0.81	0.743	0.881	0.81	0.743	0.881	CLONAL	1	TRUE	1	0.29289692738634	2		579	1424	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993718	72993718	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	130	504	0	ENST00000268489.5:c.327A>T	p.Arg109Ser	p.R109S	ENST00000268489	NM_006885.3	109	agA/agT	2/10	1	2	FACETS	0.688	0.622	0.757	0.688	0.622	0.757	SUBCLONAL	1	TRUE	1	0.29289692738634	2		504	1291	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942197	81942197	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1185	129	463	1	ENST00000359376.3:c.1733+1G>A		p.X578_splice	ENST00000359376	NM_002661.3	578			1	2	FACETS	0.67	0.606	0.739	0.67	0.606	0.739	SUBCLONAL	1	TRUE	1	0.29289692738634	2		464	1314	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357215	89357215	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1351	180	628	0	ENST00000301030.4:c.419C>T	p.Pro140Leu	p.P140L	ENST00000301030	NM_001256183.1	140	cCc/cTc	6/13	1	2	FACETS	0.803	0.738	0.871	0.803	0.738	0.871	CLONAL	1	TRUE	1	0.29289692738634	2		628	1531	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16005024	16005024	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs760547329	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	76	276	0	ENST00000268712.3:c.2230C>T	p.Arg744Ter	p.R744*	ENST00000268712	NM_006311.3	744	Cga/Tga	20/46	1	2	FACETS	0.748	0.656	0.847	0.748	0.656	0.847	SUBCLONAL	1	TRUE	1	0.29289692738634	2		276	694	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556367	29556367	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	252	341	0	ENST00000356175.3:c.2734C>T	p.Gln912Ter	p.Q912*	ENST00000356175	NM_000267.3	912	Caa/Taa	21/57	0.29289692738634	2	FACETS	0.997	0.935	1	0.997	0.935	1	CLONAL	2	TRUE	0	0.29289692738634	2		341	863	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649017	37649017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	195	291	0	ENST00000447079.4:c.2122C>T	p.Arg708Cys	p.R708C	ENST00000447079	NM_015083.1	708	Cgt/Tgt	4/14	0.29289692738634	2	FACETS	0.832	0.772	0.895	0.832	0.772	0.895	CLONAL	2	TRUE	0	0.29289692738634	2		291	800	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696356	47696356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	75	348	0	ENST00000347630.2:c.467C>T	p.Thr156Ile	p.T156I	ENST00000347630	NM_001007230.1	156	aCc/aTc	6/11	0.29289692738634	2	FACETS	0.639	0.559	0.726	0.32	0.279	0.363	SUBCLONAL	1	TRUE	0	0.29289692738634	2		348	801	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436016	56436016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	153	266	0	ENST00000407977.2:c.1121C>T	p.Pro374Leu	p.P374L	ENST00000407977		374	cCc/cTc	9/10	0.29289692738634	2	FACETS	0.888	0.816	0.963	0.888	0.816	0.963	CLONAL	2	TRUE	0	0.29289692738634	2		266	588	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56439904	56439904	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	75	278	0	ENST00000407977.2:c.687+1G>A		p.X229_splice	ENST00000407977		229			0.29289692738634	2	FACETS	0.706	0.618	0.801	0.353	0.309	0.401	SUBCLONAL	1	TRUE	0	0.29289692738634	2		278	725	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740416	58740416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777279856	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1224	242	612	0	ENST00000305921.3:c.1321C>T	p.Arg441Cys	p.R441C	ENST00000305921	NM_003620.3	441	Cgt/Tgt	6/6	0.29289692738634	2	FACETS	1	0.98	1	0.564	0.525	0.604	CLONAL	1	TRUE	0	0.29289692738634	2		612	1466	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78914311	78914311	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	244	351	0	ENST00000306801.3:c.2935G>A	p.Asp979Asn	p.D979N	ENST00000306801	NM_020761.2	979	Gac/Aac	25/34	0.29289692738634	2	FACETS	0.881	0.824	0.939	0.881	0.824	0.939	CLONAL	2	TRUE	0	0.29289692738634	2		351	946	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743272	743272	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs188857712	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	111	582	2	ENST00000314574.4:c.868G>A	p.Glu290Lys	p.E290K	ENST00000314574	NM_005433.3	290	Gaa/Aaa	7/12	0.238001352105468	3	FACETS	0.674	0.604	0.749	0.337	0.302	0.375	SUBCLONAL	1	TRUE	1	0.29289692738634	3		584	1289	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39570433	39570433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747825815	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	39	305	0	ENST00000262039.4:c.629G>A	p.Arg210Gln	p.R210Q	ENST00000262039	NM_002647.2	210	cGa/cAa	6/25	0.238001352105468	3	FACETS	0.501	0.415	0.598	0.251	0.207	0.299	SUBCLONAL	1	TRUE	1	0.29289692738634	3		305	609	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39573250	39573250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	75	409	0	ENST00000262039.4:c.731C>T	p.Ser244Phe	p.S244F	ENST00000262039	NM_002647.2	244	tCt/tTt	7/25	0.238001352105468	3	FACETS	0.776	0.679	0.88	0.388	0.339	0.44	SUBCLONAL	1	TRUE	1	0.29289692738634	3		409	757	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117201	7117201	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374120246	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	123	482	1	ENST00000302850.5:c.4015G>A	p.Glu1339Lys	p.E1339K	ENST00000302850	NM_000208.2	1339	Gag/Aag	22/22	0.29289692738634	3	FACETS	0.811	0.731	0.895	0.405	0.365	0.448	CLONAL	1	TRUE	1	0.29289692738634	3		483	1188	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144531	11144531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	91	385	0	ENST00000358026.2:c.3863C>T	p.Pro1288Leu	p.P1288L	ENST00000358026	NM_001128849.1	1288	cCa/cTa	27/36	0.29289692738634	3	FACETS	0.659	0.583	0.74	0.33	0.291	0.37	SUBCLONAL	1	TRUE	1	0.29289692738634	3		385	1081	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272266	15272266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1363323415	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	115	243	0	ENST00000263388.2:c.6173C>T	p.Ser2058Leu	p.S2058L	ENST00000263388	NM_000435.2	2058	tCg/tTg	33/33	0.29289692738634	3	FACETS	1	0.983	1	0.73	0.659	0.804	CLONAL	1	TRUE	1	0.29289692738634	3		243	617	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272332	15272332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1428027646	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	148	279	0	ENST00000263388.2:c.6107C>T	p.Pro2036Leu	p.P2036L	ENST00000263388	NM_000435.2	2036	cCc/cTc	33/33	0.29289692738634	3	FACETS	0.854	0.782	0.93	0.854	0.782	0.93	CLONAL	2	TRUE	1	0.29289692738634	3		279	678	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281353	15281353	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	47	179	0	ENST00000263388.2:c.4903G>A	p.Glu1635Lys	p.E1635K	ENST00000263388	NM_000435.2	1635	Gag/Aag	27/33	0.29289692738634	3	FACETS	0.878	0.742	1	0.439	0.371	0.514	CLONAL	1	TRUE	1	0.29289692738634	3		179	419	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355342	15355342	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749297547	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	16	84	0	ENST00000263377.2:c.2281C>T	p.Pro761Ser	p.P761S	ENST00000263377	NM_058243.2	761	Ccc/Tcc	13/20	0.29289692738634	3	FACETS	0.464	0.343	0.609	0.232	0.171	0.305	SUBCLONAL	1	TRUE	1	0.29289692738634	3		84	270	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945795	17945795	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	104	355	0	ENST00000458235.1:c.2065C>T	p.Pro689Ser	p.P689S	ENST00000458235	NM_000215.3	689	Ccc/Tcc	16/24	0.112971670451897	4	FACETS	0.88	0.786	0.98	0.44	0.393	0.49	INDETERMINATE	1	TRUE	2	0.29289692738634	4		355	1043	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946779	17946779	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs773308335	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	238	419	0	ENST00000458235.1:c.1868G>A	p.Trp623Ter	p.W623*	ENST00000458235	NM_000215.3	623	tGg/tAg	14/24	0.112971670451897	4	FACETS	0.973	0.908	1	0.973	0.908	1	INDETERMINATE	2	TRUE	2	0.29289692738634	4		419	1080	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17952561	17952561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759001177	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	64	285	0	ENST00000458235.1:c.872C>T	p.Pro291Leu	p.P291L	ENST00000458235	NM_000215.3	291	cCc/cTc	7/24	0.112971670451897	4	FACETS	0.764	0.66	0.876	0.382	0.33	0.438	INDETERMINATE	1	TRUE	2	0.29289692738634	4		285	740	SUCCESS
CEBPA	1050	MSKCC	GRCh37	19	33793175	33793175	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	66	192	0	ENST00000498907.2:c.146C>T	p.Pro49Leu	p.P49L	ENST00000498907	NM_004364.3	49	cCg/cTg	1/1	0.112971670451897	4	FACETS	1	0.938	1	0.569	0.495	0.649	INDETERMINATE	1	TRUE	2	0.29289692738634	4		192	512	SUCCESS
AXL	558	MSKCC	GRCh37	19	41736932	41736933	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	108	370	0	ENST00000301178.4:c.647_648delinsTT	p.Ser216Phe	p.S216F	ENST00000301178	NM_021913.4	216	tCC/tTT	5/20	0.112971670451897	4	FACETS	0.806	0.721	0.896	0.403	0.36	0.448	INDETERMINATE	1	TRUE	2	0.29289692738634	4		370	1183	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867256	45867256	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780129241	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	44	186	0	ENST00000391945.4:c.937G>A	p.Glu313Lys	p.E313K	ENST00000391945	NM_000400.3	313	Gaa/Aaa	10/23	0.112971670451897	4	FACETS	0.867	0.728	1	0.434	0.364	0.511	INDETERMINATE	1	TRUE	2	0.29289692738634	4		186	448	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910288	50910288	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1169141963	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1602	158	684	0	ENST00000440232.2:c.1543G>A	p.Asp515Asn	p.D515N	ENST00000440232	NM_002691.3	515	Gat/Aat	13/27	0.112971670451897	4	FACETS	0.793	0.723	0.866	0.396	0.361	0.433	INDETERMINATE	1	TRUE	2	0.29289692738634	4		684	1760	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9523292	9523292	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	127	474	0	ENST00000353224.5:c.1945C>T	p.Leu649Phe	p.L649F	ENST00000353224	NM_177990.2	649	Ctc/Ttc	9/10	1	2	FACETS	0.701	0.633	0.773	0.701	0.633	0.773	SUBCLONAL	1	TRUE	1	0.29289692738634	2		474	1237	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538263	9538263	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748547848	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	113	411	0	ENST00000353224.5:c.1735G>A	p.Asp579Asn	p.D579N	ENST00000353224	NM_177990.2	579	Gat/Aat	7/10	1	2	FACETS	0.772	0.693	0.855	0.772	0.693	0.855	SUBCLONAL	1	TRUE	1	0.29289692738634	2		411	1000	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561090	9561090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	71	268	0	ENST00000353224.5:c.692C>T	p.Ser231Leu	p.S231L	ENST00000353224	NM_177990.2	231	tCa/tTa	4/10	1	2	FACETS	0.731	0.638	0.832	0.731	0.638	0.832	SUBCLONAL	1	TRUE	1	0.29289692738634	2		268	663	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561257	9561257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	74	295	0	ENST00000353224.5:c.525G>A	p.Met175Ile	p.M175I	ENST00000353224	NM_177990.2	175	atG/atA	4/10	1	2	FACETS	0.611	0.534	0.694	0.611	0.534	0.694	SUBCLONAL	1	TRUE	1	0.29289692738634	2		295	827	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624949	9624949	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	64	305	0	ENST00000353224.5:c.28G>A	p.Glu10Lys	p.E10K	ENST00000353224	NM_177990.2	10	Gaa/Aaa	3/10	1	2	FACETS	0.539	0.466	0.619	0.539	0.466	0.619	SUBCLONAL	1	TRUE	1	0.29289692738634	2		305	811	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017196	31017196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	186	519	0	ENST00000375687.4:c.527C>T	p.Pro176Leu	p.P176L	ENST00000375687	NM_015338.5	176	cCt/cTt	7/13	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.29289692738634	2		519	1170	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386282	31386282	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	95	406	0	ENST00000328111.2:c.1507T>A	p.Cys503Ser	p.C503S	ENST00000328111	NM_006892.3	503	Tgc/Agc	15/23	1	2	FACETS	0.576	0.511	0.646	0.576	0.511	0.646	SUBCLONAL	1	TRUE	1	0.29289692738634	2		406	1126	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40864884	40864884	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs951863604	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	149	455	0	ENST00000373198.4:c.2384C>T	p.Ser795Phe	p.S795F	ENST00000373198	NM_133170.3	795	tCc/tTc	16/32	1	2	FACETS	0.925	0.844	1	0.925	0.844	1	CLONAL	1	TRUE	1	0.29289692738634	2		455	1100	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076934	41076934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759824186	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	163	391	0	ENST00000373198.4:c.1486G>A	p.Gly496Arg	p.G496R	ENST00000373198	NM_133170.3	496	Ggg/Agg	9/32	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.29289692738634	2		391	1057	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264412	46264412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746670862	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1629	189	644	0	ENST00000371998.3:c.1459C>T	p.Arg487Cys	p.R487C	ENST00000371998		487	Cgt/Tgt	11/23	1	2	FACETS	0.71	0.653	0.769	0.71	0.653	0.769	SUBCLONAL	1	TRUE	1	0.29289692738634	2		644	1818	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44515829	44515829	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	61	406	0	ENST00000291552.4:c.224A>G	p.Gln75Arg	p.Q75R	ENST00000291552	NM_006758.2	75	cAg/cGg	4/8	0.112971670451897	4	FACETS	0.452	0.388	0.522	0.226	0.194	0.261	INDETERMINATE	1	TRUE	2	0.29289692738634	4		406	1191	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655368	45655368	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	268	433	0	ENST00000407780.3:c.484A>G	p.Asn162Asp	p.N162D	ENST00000407780	NM_001283052.1	162	Aac/Gac	4/7	0.112971670451897	4	FACETS	0.9	0.842	0.959	0.9	0.842	0.959	INDETERMINATE	2	TRUE	2	0.29289692738634	4		433	1315	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121013	29121013	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786203973	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	238	442	1	ENST00000328354.6:c.544C>T	p.Pro182Ser	p.P182S	ENST00000328354	NM_007194.3	182	Cct/Tct	4/15	0.226163626534795	4	FACETS	0.775	0.722	0.83	0.775	0.722	0.83	SUBCLONAL	2	TRUE	2	0.29289692738634	4		443	1356	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546183	41546183	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	54	99	0	ENST00000263253.7:c.2798C>T	p.Pro933Leu	p.P933L	ENST00000263253	NM_001429.3	933	cCt/cTt	14/31	0.226163626534795	4	FACETS	0.762	0.654	0.877	0.762	0.654	0.877	SUBCLONAL	2	TRUE	2	0.29289692738634	4		99	313	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314897	1314897	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1015	104	411	0	ENST00000400841.2:c.764G>A	p.Trp255Ter	p.W255*	ENST00000400841		255	tGg/tAg	6/6	1	1	FACETS	0.542	0.484	0.604	0.542	0.484	0.604	SUBCLONAL	1	TRUE	0	0.29289692738634	1		411	1119	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325361	1325361	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	121	422	2	ENST00000400841.2:c.314C>T	p.Pro105Leu	p.P105L	ENST00000400841		105	cCc/cTc	3/6	1	1	FACETS	0.572	0.515	0.633	0.572	0.515	0.633	SUBCLONAL	1	TRUE	0	0.29289692738634	1		424	1232	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44970630	44970630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	146	269	0	ENST00000377967.4:c.4180C>T	p.Pro1394Ser	p.P1394S	ENST00000377967	NM_021140.2	1394	Cct/Tct	29/29	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.29289692738634	1		269	626	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410525	63410525	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372769953	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	73	311	0	ENST00000330258.3:c.2642G>A	p.Arg881Gln	p.R881Q	ENST00000330258	NM_152424.3	881	cGa/cAa	2/2	1	1	FACETS	0.523	0.456	0.595	0.523	0.456	0.595	SUBCLONAL	1	TRUE	0	0.29289692738634	1		311	814	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413030	63413030	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	287	354	0	ENST00000330258.3:c.137C>T	p.Ser46Leu	p.S46L	ENST00000330258	NM_152424.3	46	tCa/tTa	2/2	1	1	FACETS	0.895	0.843	0.947	1	0.995	1	CLONAL	2	TRUE	0	0.29289692738634	1		354	935	SUCCESS
AR	367	MSKCC	GRCh37	X	66863246	66863246	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	91	169	0	ENST00000374690.3:c.1765G>A	p.Glu589Lys	p.E589K	ENST00000374690	NM_000044.3	589	Gaa/Aaa	2/8	1	1	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	0	0.29289692738634	1		169	438	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974743	21974747	+	frameshift_variant	Frame_Shift_Del	DEL	CACCT	CACCT	GTG	novel	NA	P-0009752-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	95	244	0	ENST00000304494.5:c.80_84delinsCAC	p.Glu27AlafsTer16	p.E27Afs*16	ENST00000304494	NM_000077.4	27	gAGGTG/gCAC	1/3	0.24052876418788	3	FACETS	1	0.962	1	0.392	0.349	0.437	CLONAL	1	TRUE	0	0.29289692738634	3		244	633	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	114	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.725015519036109	2		280	314	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624305	89624305	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	rs746128825	NA	P-0009790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	184	247	0	ENST00000371953.3:c.79T>A	p.Tyr27Asn	p.Y27N	ENST00000371953	NM_000314.4	27	Tat/Aat	1/9	0.725015519036109	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.725015519036109	1		247	317	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511204	157511719	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CAGATGTGAGTGATTCATCCTTCCCGAAACGGAACTCCATGACTCCAAACGCCCCCTACCAGCAGGGCATGAGCATGCCCGATGTGATGGGCAGGATGCCCTATGAGCCCAACAAGGACCCCTTTGGGGGAATGAGAAAAGGTACGTGTAGAGGGGCCTCCACCCGGCCATGGACCAGTGGGCATTCTACTCTCTGCCGTTCCACAACAGTTCACCTTTCACTCAGAACACCTCTGAGCCCATGCTGCATCGGTGTGGGTCCCAGGTCCCCATCCTACTCCACTTGTGGCCTTGGGAAAAGCAGTTAGCCTCTTTGTGCCCTCATCCTGTCCCCGGCTGGCCTCAGTGCCCTCAGCCTGTTCCCTGGCACATGCTCCCTGTTTCCGGATACCTGCCACCTCCTTACACGTGCCAAGTTACGTTCCTCATCTAGAAATTGGGAAAATAATAGGACCCGCTTCCAAAGGCATGGCGAGGATTAAGTTCCTGCAACAGAGCTCAGAGAAGAGTGGCTGG	CAGATGTGAGTGATTCATCCTTCCCGAAACGGAACTCCATGACTCCAAACGCCCCCTACCAGCAGGGCATGAGCATGCCCGATGTGATGGGCAGGATGCCCTATGAGCCCAACAAGGACCCCTTTGGGGGAATGAGAAAAGGTACGTGTAGAGGGGCCTCCACCCGGCCATGGACCAGTGGGCATTCTACTCTCTGCCGTTCCACAACAGTTCACCTTTCACTCAGAACACCTCTGAGCCCATGCTGCATCGGTGTGGGTCCCAGGTCCCCATCCTACTCCACTTGTGGCCTTGGGAAAAGCAGTTAGCCTCTTTGTGCCCTCATCCTGTCCCCGGCTGGCCTCAGTGCCCTCAGCCTGTTCCCTGGCACATGCTCCCTGTTTCCGGATACCTGCCACCTCCTTACACGTGCCAAGTTACGTTCCTCATCTAGAAATTGGGAAAATAATAGGACCCGCTTCCAAAGGCATGGCGAGGATTAAGTTCCTGCAACAGAGCTCAGAGAAGAGTGGCTGG	-	novel	NA	P-0009790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	65	422	0	ENST00000346085.5:c.3725_3862+378del		p.X1242_splice	ENST00000346085	NM_020732.3	1242		15/20	1	2	FACETS	0.281	0.243	0.322	0.281	0.243	0.322	SUBCLONAL	1	TRUE	1	0.725015519036109	2		422	638	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0009795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	582	464	0				ENST00000310581	NM_198253.2	-/1132			0.679987786962433	4	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	1	0.679987786962433	4		464	898	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0009795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	107	157	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.67827496488993	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.679987786962433	1		157	182	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577085	+	missense_variant	Missense_Mutation	ONP	CCTC	CCTC	TCTT	novel	NA	P-0009795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	619	416	0	ENST00000269305.4:c.853_856delinsAAGA	p.Glu285_Glu286delinsLysLys	p.E285_E286delinsKK	ENST00000269305	NM_001126112.2	285	GAGGaa/AAGAaa	8/11	0.579742116024454	3	FACETS	0.901	0.869	0.933			1	CLONAL	2	TRUE	NA	0.679987786962433	3		416	1354	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570788	226570788	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	208	312	0	ENST00000366794.5:c.1108C>T	p.Pro370Ser	p.P370S	ENST00000366794	NM_001618.3	370	Ccg/Tcg	8/23	0.568461539123869	3	FACETS	1	0.951	1	0.514	0.478	0.551	CLONAL	1	TRUE	1	0.679987786962433	3		312	798	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295699	212295699	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776347334	NA	P-0009795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	131	422	0	ENST00000342788.4:c.2614G>A	p.Glu872Lys	p.E872K	ENST00000342788	NM_005235.2	872	Gaa/Aaa	21/28	0.308047708362151	1	FACETS	0.604	0.553	0.657	0.604	0.553	0.657	INDETERMINATE	1	TRUE	0	0.679987786962433	1		422	421	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916924	178916924	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs863225060	NA	P-0009795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	735	699	0	ENST00000263967.3:c.311C>T	p.Pro104Leu	p.P104L	ENST00000263967	NM_006218.2	104	cCa/cTa	2/21	0.679987786962433	3	FACETS	0.937	0.915	0.96	0.937	0.915	0.96	CLONAL	3	TRUE	0	0.679987786962433	3		699	1030	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807901	1807901	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0009795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	259	388	2	ENST00000260795.2:c.1959+1G>A		p.X653_splice	ENST00000260795		653			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.679987786962433	2		390	735	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486346	8486346	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	65	117	1	ENST00000356435.5:c.2471C>T	p.Pro824Leu	p.P824L	ENST00000356435		824	cCa/cTa	17/35	0.67827496488993	1	FACETS	0.921	0.824	1	0.921	0.824	1	CLONAL	1	TRUE	0	0.679987786962433	1		118	137	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391527	139391527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	592	524	1	ENST00000277541.6:c.6664C>T	p.Pro2222Ser	p.P2222S	ENST00000277541	NM_017617.3	2222	Ccg/Tcg	34/34	0.671486866064357	4	FACETS	0.976	0.939	1	0.65	0.626	0.676	CLONAL	2	TRUE	1	0.679987786962433	4		525	1499	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401377	139401377	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	793	317	0	ENST00000277541.6:c.3692C>T	p.Pro1231Leu	p.P1231L	ENST00000277541	NM_017617.3	1231	cCc/cTc	23/34	0.671486866064357	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	1	0.679987786962433	4		317	1223	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615064	43615064	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0009795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	298	502	1	ENST00000355710.3:c.2478C>A	p.Tyr826Ter	p.Y826*	ENST00000355710	NM_020975.4	826	taC/taA	14/20	1	2	FACETS	0.994	0.939	1	0.994	0.939	1	CLONAL	1	TRUE	1	0.679987786962433	2		503	882	SUCCESS
ATM	472	MSKCC	GRCh37	11	108183205	108183205	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	119	408	0	ENST00000278616.4:c.5986G>A	p.Glu1996Lys	p.E1996K	ENST00000278616	NM_000051.3	1996	Gaa/Aaa	40/63	1	2	FACETS	0.814	0.74	0.891	0.814	0.74	0.891	CLONAL	1	TRUE	1	0.679987786962433	2		408	430	SUCCESS
CBL	867	MSKCC	GRCh37	11	119156031	119156032	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0009795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	321	559	1	ENST00000264033.4:c.1696_1697delinsTT	p.Pro566Phe	p.P566F	ENST00000264033	NM_005188.3	566	CCt/TTt	11/16	1	2	FACETS	0.858	0.81	0.906	0.858	0.81	0.906	CLONAL	1	TRUE	1	0.679987786962433	2		560	1101	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945066	31945066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	318	536	0	ENST00000340398.3:c.35C>T	p.Thr12Ile	p.T12I	ENST00000340398	NM_001013699.2	12	aCc/aTc	1/1	1	2	FACETS	0.879	0.83	0.929	0.879	0.83	0.929	CLONAL	1	TRUE	1	0.679987786962433	2		536	1064	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49449105	49449105	+	start_lost	Translation_Start_Site	SNP	C	C	T	novel	NA	P-0009795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	203	396	0	ENST00000301067.7:c.3G>A	p.Met1?	p.M1?	ENST00000301067	NM_003482.3	1	atG/atA	1/54	1	2	FACETS	0.86	0.801	0.921	0.86	0.801	0.921	CLONAL	1	TRUE	1	0.679987786962433	2		396	694	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32890664	32890664	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs397507881	NA	P-0009795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	168	317	0	ENST00000380152.3:c.67G>A	p.Asp23Asn	p.D23N	ENST00000380152		23	Gat/Aat	2/27	1	2	FACETS	0.939	0.869	1	0.939	0.869	1	CLONAL	1	TRUE	1	0.679987786962433	2		317	526	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347716	89347717	+	missense_variant	Missense_Mutation	DNP	GA	GA	AC	novel	NA	P-0009795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	346	710	1	ENST00000301030.4:c.5233_5234delinsGT	p.Ser1745Val	p.S1745V	ENST00000301030	NM_001256183.1	1745	TCc/GTc	9/13	1	2	FACETS	0.834	0.789	0.88	0.834	0.789	0.88	CLONAL	1	TRUE	1	0.679987786962433	2		711	1220	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0009795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	244	370	0	ENST00000269305.4:c.920-2A>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.579742116024454	3	FACETS	1	0.982	1			1	CLONAL	1	TRUE	NA	0.679987786962433	3		370	853	SUCCESS
AXL	558	MSKCC	GRCh37	19	41745133	41745133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	306	605	2	ENST00000301178.4:c.1199C>T	p.Ser400Phe	p.S400F	ENST00000301178	NM_021913.4	400	tCc/tTc	9/20	1	2	FACETS	0.83	0.782	0.878	0.83	0.782	0.878	CLONAL	1	TRUE	1	0.679987786962433	2		607	1085	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41527520	41527520	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	279	416	0	ENST00000263253.7:c.1411C>T	p.Leu471Phe	p.L471F	ENST00000263253	NM_001429.3	471	Ctt/Ttt	6/31	1	2	FACETS	0.975	0.918	1	0.975	0.918	1	CLONAL	1	TRUE	1	0.679987786962433	2		416	842	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540491	187540523	+	inframe_deletion	In_Frame_Del	DEL	CATCATAGGCTTTTACACAGGTCACGAAATGCC	CATCATAGGCTTTTACACAGGTCACGAAATGCC	-	novel	NA	P-0009795-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	33	252	0	ENST00000441802.2:c.7217_7249del	p.Gly2406_Asp2416del	p.G2406_D2416del	ENST00000441802	NM_005245.3	2406	gGGCATTTCGTGACCTGTGTAAAAGCCTATGATGca/gca	10/27	0.587368239330404	1	FACETS	0.231	0.189	0.279	0.231	0.189	0.279	SUBCLONAL	1	TRUE	0	0.679987786962433	1		252	277	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	108	354	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.254767305765342	5	FACETS	0.948	0.872	1	1	0.982	1	INDETERMINATE	4	FALSE	2	0.450332324340588	5		354	212	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	24	67	1				ENST00000310581	NM_198253.2	-/1132			0.450332324340588	4	FACETS	1	0.927	1			1	CLONAL	1	FALSE	NA	0.450332324340588	4		68	108	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	55	660	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.348115430751236	3	FACETS	1	0.966	1	0.709	0.615	0.809	CLONAL	1	FALSE	1	0.450332324340588	3		660	211	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	42	511	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	0.217130243536121	3	FACETS	0.762	0.648	0.883	0.762	0.648	0.883	INDETERMINATE	2	FALSE	1	0.450332324340588	3		512	150	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	58	257	3	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	0.217130243536121	3	FACETS	1	0.944	1	0.587	0.509	0.67	INDETERMINATE	1	FALSE	1	0.450332324340588	3		260	269	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31379479	31379479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145632647	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	53	525	0	ENST00000328111.2:c.886G>A	p.Val296Ile	p.V296I	ENST00000328111	NM_006892.3	296	Gtc/Atc	8/23	0.213151024448518	4	FACETS	0.809	0.699	0.926	0.809	0.699	0.926	INDETERMINATE	2	FALSE	2	0.450332324340588	4		525	211	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	36	272	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.111043113008998	5	FACETS	0.875	0.731	1			1	INDETERMINATE	2	FALSE	NA	0.450332324340588	5		272	153	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101267	27101268	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	47	478	1	ENST00000324856.7:c.4555dup	p.Gln1519ProfsTer13	p.Q1519Pfs*13	ENST00000324856	NM_006015.4	1517	gcc/gCcc	18/20	1	2	FACETS	0.654	0.555	0.763	0.654	0.555	0.763	SUBCLONAL	1	FALSE	1	0.450332324340588	2		479	319	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088787	27088788	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	42	374	0	ENST00000324856.7:c.2402dup	p.Gln802SerfsTer15	p.Q802Sfs*15	ENST00000324856	NM_006015.4	799	cag/caGg	7/20	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	FALSE	1	0.450332324340588	2		374	142	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78935196	78935196	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs752994517	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	63	412	0	ENST00000306801.3:c.3608G>A	p.Arg1203His	p.R1203H	ENST00000306801	NM_020761.2	1203	cGc/cAc	31/34	0.286920126919432	5	FACETS	1	0.963	1	0.44	0.383	0.502	CLONAL	1	FALSE	2	0.450332324340588	5		412	355	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125499299	125499299	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	29	424	2	ENST00000428830.2:c.368G>T	p.Gly123Val	p.G123V	ENST00000428830	NM_001114121.2	123	gGt/gTt	5/14	0.286920126919432	5	FACETS	1	0.93	1	0.452	0.367	0.547	CLONAL	1	FALSE	2	0.450332324340588	5		426	159	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	43	365	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	0.348115430751236	3	FACETS	1	0.937	1	0.609	0.516	0.71	CLONAL	1	FALSE	1	0.450332324340588	3		365	192	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680656	88680656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761690006	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	35	481	0	ENST00000360948.2:c.601C>T	p.Arg201Cys	p.R201C	ENST00000360948	NM_001012338.2	201	Cgc/Tgc	6/19	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	FALSE	1	0.450332324340588	2		481	149	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225603	2225603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	83	354	2	ENST00000326181.6:c.1606G>A	p.Gly536Ser	p.G536S	ENST00000326181	NM_032271.2	536	Ggc/Agc	17/21	0.263797359086374	4	FACETS	0.825	0.735	0.92	0.825	0.735	0.92	INDETERMINATE	2	FALSE	2	0.450332324340588	4		356	324	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864656	37864656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs950730453	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	51	574	0	ENST00000269571.5:c.308G>A	p.Arg103Gln	p.R103Q	ENST00000269571		103	cGa/cAa	3/27	NA	2	FACETS	0.94	0.807	1			1	INDETERMINATE	1	FALSE	NA	0.450332324340588	2		574	241	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862749	9862749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150316865	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	17	454	0	ENST00000330684.3:c.2554G>A	p.Val852Met	p.V852M	ENST00000330684	NM_001134407.1	852	Gtg/Atg	12/13	0.450332324340588	0	FACETS	0.61	0.468	0.769			1	SUBCLONAL	1	FALSE	0	0.450332324340588	0		454	68	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687472	37687472	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	19	226	2	ENST00000447079.4:c.4382del	p.Gly1461AlafsTer38	p.G1461Afs*38	ENST00000447079	NM_015083.1	1459	tGg/tg	14/14	NA	2	FACETS	0.4	0.304	0.511			1	INDETERMINATE	1	FALSE	NA	0.450332324340588	2		228	211	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436026	56436026	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771831816	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	54	290	0	ENST00000407977.2:c.1111C>T	p.Arg371Ter	p.R371*	ENST00000407977		371	Cga/Tga	9/10	0.217130243536121	3	FACETS	0.888	0.762	1	0.444	0.381	0.512	INDETERMINATE	1	FALSE	1	0.450332324340588	3		290	331	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780062	9780062	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	77	415	0	ENST00000377346.4:c.1326G>A	p.Trp442Ter	p.W442*	ENST00000377346	NM_005026.3	442	tgG/tgA	10/24	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	1	0.450332324340588	2		415	320	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459254	120459254	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	44	263	0	ENST00000256646.2:c.6091G>T	p.Asp2031Tyr	p.D2031Y	ENST00000256646	NM_024408.3	2031	Gac/Tac	34/34	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	FALSE	1	0.450332324340588	2		263	142	SUCCESS
ALK	238	MSKCC	GRCh37	2	29446220	29446220	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	30	485	1	ENST00000389048.3:c.3347T>C	p.Ile1116Thr	p.I1116T	ENST00000389048	NM_004304.4	1116	aTc/aCc	20/29	0.449180744969464	0	FACETS	0.542	0.444	0.65			1	SUBCLONAL	1	FALSE	0	0.450332324340588	0		486	135	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149221	61149221	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761644483	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	14	333	0	ENST00000295025.8:c.1411G>A	p.Gly471Arg	p.G471R	ENST00000295025	NM_002908.2	471	Gga/Aga	11/11	0.254767305765342	5	FACETS	0.965	0.72	1	0.643	0.48	0.827	INDETERMINATE	2	FALSE	2	0.450332324340588	5		333	54	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663429	227663429	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	39	122	0	ENST00000305123.5:c.26G>A	p.Gly9Asp	p.G9D	ENST00000305123	NM_005544.2	9	gGc/gAc	1/2	0.217130243536121	3	FACETS	0.996	0.834	1	0.498	0.417	0.587	INDETERMINATE	1	FALSE	1	0.450332324340588	3		122	213	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184670	185184670	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs188669013	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	29	634	1	ENST00000265026.3:c.1562G>A	p.Arg521His	p.R521H	ENST00000265026	NM_004721.4	521	cGt/cAt	10/14	0.217130243536121	3	FACETS	1	0.938	1	0.704	0.577	0.843	INDETERMINATE	1	FALSE	1	0.450332324340588	3		635	112	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149435832	149435832	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1209791630	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	42	492	0	ENST00000286301.3:c.2392G>A	p.Gly798Arg	p.G798R	ENST00000286301	NM_005211.3	798	Ggg/Agg	18/22	0.450332324340588	0	FACETS	0.513	0.433	0.599			1	SUBCLONAL	1	FALSE	0	0.450332324340588	0		492	200	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910553	29910553	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	16	118	0	ENST00000376809.5:c.93T>A	p.Tyr31Ter	p.Y31*	ENST00000376809	NM_002116.7	31	taT/taA	2/8	0.450332324340588	6	FACETS	1	0.86	1	0.417	0.312	0.539	CLONAL	1	FALSE	3	0.450332324340588	6		118	108	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41730074	41730074	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377167564	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	24	958	1	ENST00000242208.4:c.455G>A	p.Arg152His	p.R152H	ENST00000242208	NM_002192.2	152	cGt/cAt	3/3	0.286920126919432	5	FACETS	0.911	0.73	1	0.607	0.486	0.74	CLONAL	2	FALSE	2	0.450332324340588	5		959	98	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836804	151836804	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	28	532	0	ENST00000262189.6:c.14416C>T	p.Arg4806Ter	p.R4806*	ENST00000262189	NM_170606.2	4806	Cga/Tga	56/59	0.263797359086374	4	FACETS	1	0.899	1	0.593	0.48	0.719	INDETERMINATE	1	FALSE	2	0.450332324340588	4		532	152	SUCCESS
RET	5979	MSKCC	GRCh37	10	43600600	43600600	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139213499	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	94	455	2	ENST00000355710.3:c.826G>A	p.Val276Ile	p.V276I	ENST00000355710	NM_020975.4	276	Gtc/Atc	4/20	0.254767305765342	5	FACETS	0.892	0.8	0.989	0.595	0.533	0.66	INDETERMINATE	2	FALSE	2	0.450332324340588	5		457	392	SUCCESS
ATM	472	MSKCC	GRCh37	11	108129731	108129731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	18	471	0	ENST00000278616.4:c.2395G>A	p.Ala799Thr	p.A799T	ENST00000278616	NM_000051.3	799	Gca/Aca	16/63	0.432154853882169	1	FACETS	0.319	0.241	0.411	0.319	0.241	0.411	SUBCLONAL	1	FALSE	0	0.450332324340588	1		471	194	SUCCESS
CBL	867	MSKCC	GRCh37	11	119145624	119145624	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	40	487	0	ENST00000264033.4:c.830T>C	p.Val277Ala	p.V277A	ENST00000264033	NM_005188.3	277	gTg/gCg	5/16	0.286920126919432	5	FACETS	0.948	0.801	1	0.632	0.534	0.737	CLONAL	2	FALSE	2	0.450332324340588	5		487	157	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	443551	443551	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	21	411	1	ENST00000399788.2:c.1346C>A	p.Pro449His	p.P449H	ENST00000399788	NM_001042603.1	449	cCt/cAt	11/28	0.267725233362869	4	FACETS	1	0.91	1			1	INDETERMINATE	1	FALSE	NA	0.450332324340588	4		412	99	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445808	49445808	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	72	715	1	ENST00000301067.7:c.1658C>A	p.Pro553His	p.P553H	ENST00000301067	NM_003482.3	553	cCt/cAt	10/54	0.323755212136207	4	FACETS	1	0.972	1			1	CLONAL	1	FALSE	NA	0.450332324340588	4		716	334	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549019	21549019	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	41	209	0	ENST00000382592.4:c.3257T>C	p.Val1086Ala	p.V1086A	ENST00000382592	NM_014572.2	1086	gTg/gCg	8/8	0.217130243536121	3	FACETS	1	0.943	1	0.637	0.538	0.744	INDETERMINATE	1	FALSE	1	0.450332324340588	3		209	175	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030384	49030384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs554834063	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	49	332	0	ENST00000267163.4:c.1859C>T	p.Thr620Met	p.T620M	ENST00000267163	NM_000321.2	620	aCg/aTg	19/27	0.450332324340588	7	FACETS	1	0.917	1			1	CLONAL	2	FALSE	NA	0.450332324340588	7		332	210	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36987207	36987207	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	40	157	0	ENST00000354822.5:c.482C>T	p.Pro161Leu	p.P161L	ENST00000354822	NM_001079668.2	161	cCg/cTg	3/3	0.348115430751236	3	FACETS	0.95	0.796	1	0.475	0.398	0.56	CLONAL	1	FALSE	1	0.450332324340588	3		157	229	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988445	41988445	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777496210	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	26	847	1	ENST00000219905.7:c.1237G>A	p.Val413Ile	p.V413I	ENST00000219905	NM_001164273.1	413	Gta/Ata	3/24	1	2	FACETS	0.675	0.54	0.828	0.675	0.54	0.828	SUBCLONAL	1	FALSE	1	0.450332324340588	2		848	171	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347568	91347568	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1249106324	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	22	435	0	ENST00000355112.3:c.3730G>A	p.Val1244Ile	p.V1244I	ENST00000355112	NM_000057.2	1244	Gtc/Atc	19/22	1	2	FACETS	1	0.864	1	1	0.864	1	CLONAL	1	FALSE	1	0.450332324340588	2		435	87	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	348061	348061	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	76	306	0	ENST00000262320.3:c.1445C>A	p.Pro482His	p.P482H	ENST00000262320	NM_003502.3	482	cCt/cAt	6/11	0.263797359086374	4	FACETS	1	0.974	1	0.707	0.625	0.795	INDETERMINATE	1	FALSE	2	0.450332324340588	4		306	346	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133798	2133798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45517323	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	62	337	0	ENST00000219476.3:c.3986G>A	p.Arg1329His	p.R1329H	ENST00000219476	NM_000548.3	1329	cGc/cAc	33/42	0.263797359086374	4	FACETS	1	0.959	1	0.636	0.553	0.724	INDETERMINATE	1	FALSE	2	0.450332324340588	4		337	314	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984685	72984685	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776123634	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	62	735	1	ENST00000268489.5:c.2899G>A	p.Val967Met	p.V967M	ENST00000268489	NM_006885.3	967	Gtg/Atg	3/10	0.209192026546562	1	FACETS	0.645	0.56	0.735	0.645	0.56	0.735	INDETERMINATE	1	FALSE	0	0.450332324340588	1		736	331	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534326	63534326	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1157452251	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	91	484	0	ENST00000307078.5:c.1195C>T	p.Arg399Ter	p.R399*	ENST00000307078	NM_004655.3	399	Cga/Tga	5/11	0.286920126919432	5	FACETS	0.954	0.854	1	0.636	0.569	0.706	CLONAL	2	FALSE	2	0.450332324340588	5		484	355	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222056	2222056	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373291232	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	84	502	0	ENST00000398665.3:c.2888C>T	p.Ala963Val	p.A963V	ENST00000398665	NM_032482.2	963	gCc/gTc	24/28	0.213151024448518	4	FACETS	1	0.976	1	0.694	0.616	0.775	INDETERMINATE	1	FALSE	2	0.450332324340588	4		502	390	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7120688	7120688	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913156	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	12	634	3	ENST00000302850.5:c.3602G>A	p.Arg1201Gln	p.R1201Q	ENST00000302850	NM_000208.2	1201	cGg/cAg	20/22	0.213151024448518	4	FACETS	0.394	0.277	0.538	0.197	0.138	0.269	INDETERMINATE	1	FALSE	2	0.450332324340588	4		637	196	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7163043	7163043	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	25	431	0	ENST00000302850.5:c.2029G>A	p.Gly677Arg	p.G677R	ENST00000302850	NM_000208.2	677	Ggg/Agg	9/22	0.213151024448518	4	FACETS	1	0.882	1	0.579	0.462	0.71	INDETERMINATE	1	FALSE	2	0.450332324340588	4		431	139	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291588	15291588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1333396423	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	82	534	1	ENST00000263388.2:c.3046G>A	p.Val1016Ile	p.V1016I	ENST00000263388	NM_000435.2	1016	Gtc/Atc	19/33	0.213151024448518	4	FACETS	0.757	0.672	0.845	0.757	0.672	0.845	INDETERMINATE	2	FALSE	2	0.450332324340588	4		535	349	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912399	50912399	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	91	652	0	ENST00000440232.2:c.1913T>C	p.Ile638Thr	p.I638T	ENST00000440232	NM_002691.3	638	aTc/aCc	16/27	0.213151024448518	4	FACETS	0.801	0.717	0.889	0.801	0.717	0.889	INDETERMINATE	2	FALSE	2	0.450332324340588	4		652	366	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024474	31024474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760162421	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	43	433	1	ENST00000375687.4:c.3959C>T	p.Ala1320Val	p.A1320V	ENST00000375687	NM_015338.5	1320	gCg/gTg	13/13	0.213151024448518	4	FACETS	1	0.956	1	0.707	0.598	0.823	INDETERMINATE	1	FALSE	2	0.450332324340588	4		434	196	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877385	40877385	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	13	337	1	ENST00000373198.4:c.2311G>A	p.Ala771Thr	p.A771T	ENST00000373198	NM_133170.3	771	Gct/Act	15/32	0.330650790386545	0	FACETS	0.567	0.416	0.739			1	SUBCLONAL	1	FALSE	0	0.450332324340588	0		338	56	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573156	41573156	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765425263	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	62	318	0	ENST00000263253.7:c.5441G>A	p.Arg1814Gln	p.R1814Q	ENST00000263253	NM_001429.3	1814	cGg/cAg	31/31	0.286920126919432	5	FACETS	0.812	0.708	0.923	0.541	0.472	0.616	CLONAL	2	FALSE	2	0.450332324340588	5		318	284	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028820	47028820	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370571712	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	84	299	3	ENST00000377604.3:c.124C>T	p.Arg42Cys	p.R42C	ENST00000377604	NM_001204468.1	42	Cgt/Tgt	3/24	1	1	FACETS	0.86	0.782	0.939	1	0.986	1	CLONAL	2	FALSE	0	0.450332324340588	1		302	168	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410553	63410553	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	61	372	0	ENST00000330258.3:c.2614T>C	p.Tyr872His	p.Y872H	ENST00000330258	NM_152424.3	872	Tac/Cac	2/2	0.377752876293064	0	FACETS	0.586	0.522	0.65			1	SUBCLONAL	2	FALSE	NA	0.450332324340588	0		372	127	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17941419	17941420	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	25	291	0	ENST00000458235.1:c.2988dup	p.Glu997ArgfsTer45	p.E997Rfs*45	ENST00000458235	NM_000215.3	996	-/C	22/24	0.213151024448518	4	FACETS	0.546	0.431	0.678	0.273	0.215	0.339	INDETERMINATE	1	FALSE	2	0.450332324340588	4		291	295	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165283	47165283	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	23	482	2	ENST00000409792.3:c.843del	p.Glu282LysfsTer19	p.E282Kfs*19	ENST00000409792	NM_014159.6	281	aaA/aa	3/21	0.446498440689105	1	FACETS	0.768	0.611	0.943	0.768	0.611	0.943	CLONAL	1	FALSE	0	0.450332324340588	1		484	103	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913558	32913559	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359479	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	39	823	0	ENST00000380152.3:c.5073dup	p.Trp1692MetfsTer3	p.W1692Mfs*3	ENST00000380152		1689	gca/gcAa	11/27	0.217130243536121	3	FACETS	0.931	0.778	1	0.465	0.389	0.549	INDETERMINATE	1	FALSE	1	0.450332324340588	3		823	228	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878069	151878070	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	13	338	0	ENST00000262189.6:c.6875dup	p.Ser2293IlefsTer5	p.S2293Ifs*5	ENST00000262189	NM_170606.2	2292	cca/ccCa	36/59	0.432154853882169	1	FACETS	0.932	0.688	1	0.932	0.688	1	CLONAL	1	FALSE	0	0.450332324340588	1		338	48	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932110	39932111	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	rs1555918014	NA	P-0009858-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	42	258	0	ENST00000378444.4:c.2488_2489del	p.Ser830CysfsTer6	p.S830Cfs*6	ENST00000378444	NM_001123385.1	830	AGt/t	4/15	1	1	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	FALSE	0	0.450332324340588	1		258	128	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0009859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	97	145	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.448599092005644	2		145	425	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48954210	48954210	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1354030520	NA	P-0009859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	139	366	0	ENST00000267163.4:c.1411C>T	p.Gln471Ter	p.Q471*	ENST00000267163	NM_000321.2	471	Caa/Taa	15/27	1	2	FACETS	0.644	0.586	0.706	0.644	0.586	0.706	SUBCLONAL	1	TRUE	1	0.448599092005644	2		366	962	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38991102	38991102	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	198	388	0	ENST00000357387.3:c.532C>T	p.Gln178Ter	p.Q178*	ENST00000357387	NM_152756.3	178	Caa/Taa	7/38	1	2	FACETS	0.979	0.907	1	0.979	0.907	1	CLONAL	1	TRUE	1	0.448599092005644	2		388	902	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021828	71021828	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0009859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	40	300	0	ENST00000318789.4:c.1531-1G>A		p.X511_splice	ENST00000318789	NM_032682.5	511			1	2	FACETS	0.234	0.194	0.279	0.234	0.194	0.279	SUBCLONAL	1	TRUE	1	0.448599092005644	2		300	762	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966275	25966275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	223	395	1	ENST00000435504.4:c.2931G>A	p.Met977Ile	p.M977I	ENST00000435504		977	atG/atA	13/13	1	2	FACETS	0.956	0.89	1	0.956	0.89	1	CLONAL	1	TRUE	1	0.448599092005644	2		396	1040	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795073	242795073	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1429395114	NA	P-0009859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	201	491	0	ENST00000334409.5:c.136G>A	p.Glu46Lys	p.E46K	ENST00000334409	NM_005018.2	46	Gaa/Aaa	2/5	1	2	FACETS	0.841	0.778	0.905	0.841	0.778	0.905	CLONAL	1	TRUE	1	0.448599092005644	2		491	1066	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1808865	1808865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763774428	NA	P-0009859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	314	584	0	ENST00000260795.2:c.2297C>T	p.Pro766Leu	p.P766L	ENST00000260795		766	cCt/cTt	17/17	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.448599092005644	2		584	1388	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510225	187510225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	59	426	0	ENST00000441802.2:c.13288G>A	p.Asp4430Asn	p.D4430N	ENST00000441802	NM_005245.3	4430	Gac/Aac	27/27	1	2	FACETS	0.268	0.23	0.311	0.268	0.23	0.311	SUBCLONAL	1	TRUE	1	0.448599092005644	2		426	980	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056443	26056443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1252419231	NA	P-0009859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	85	154	0	ENST00000343677.2:c.214G>A	p.Asp72Asn	p.D72N	ENST00000343677	NM_005319.3	72	Gat/Aat	1/1	1	2	FACETS	0.764	0.677	0.856	0.764	0.677	0.856	SUBCLONAL	1	TRUE	1	0.448599092005644	2		154	496	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112024200	112024200	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	356	633	0	ENST00000368678.4:c.585G>A	p.Met195Ile	p.M195I	ENST00000368678		195	atG/atA	7/13	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.448599092005644	2		633	1511	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525611	137525611	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	170	409	0	ENST00000367739.4:c.404G>A	p.Arg135Lys	p.R135K	ENST00000367739	NM_000416.2	135	aGa/aAa	4/7	1	2	FACETS	0.815	0.749	0.883	0.815	0.749	0.883	CLONAL	1	TRUE	1	0.448599092005644	2		409	930	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388032	81388032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	258	476	0	ENST00000222390.5:c.343G>A	p.Glu115Lys	p.E115K	ENST00000222390	NM_000601.4	115	Gaa/Aaa	3/18	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.448599092005644	2		476	1124	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852057	128852057	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	234	409	0	ENST00000249373.3:c.2129A>T	p.Gln710Leu	p.Q710L	ENST00000249373	NM_005631.4	710	cAg/cTg	12/12	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.448599092005644	2		409	1032	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135796814	135796814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs572899352	NA	P-0009859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	229	427	0	ENST00000298552.3:c.673G>A	p.Glu225Lys	p.E225K	ENST00000298552	NM_001162426.1	225	Gag/Aag	8/23	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.448599092005644	2		427	1006	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70432753	70432753	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301412005	NA	P-0009859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	284	475	0	ENST00000373644.4:c.4775G>A	p.Arg1592Lys	p.R1592K	ENST00000373644	NM_030625.2	1592	aGa/aAa	8/12	1	2	FACETS	0.952	0.893	1	0.952	0.893	1	CLONAL	1	TRUE	1	0.448599092005644	2		475	1330	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15938102	15938102	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	225	428	0	ENST00000268712.3:c.7112G>A	p.Trp2371Ter	p.W2371*	ENST00000268712	NM_006311.3	2371	tGg/tAg	45/46	1	2	FACETS	0.866	0.805	0.928	0.866	0.805	0.928	CLONAL	1	TRUE	1	0.448599092005644	2		428	1159	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968195	15968195	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	292	458	5	ENST00000268712.3:c.5090C>A	p.Ser1697Tyr	p.S1697Y	ENST00000268712	NM_006311.3	1697	tCc/tAc	34/46	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.448599092005644	2		463	1219	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16004687	16004687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	333	583	1	ENST00000268712.3:c.2567G>A	p.Arg856Lys	p.R856K	ENST00000268712	NM_006311.3	856	aGa/aAa	20/46	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.448599092005644	2		584	1379	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012190	16012190	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0009859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	188	425	0	ENST00000268712.3:c.2092C>T	p.Gln698Ter	p.Q698*	ENST00000268712	NM_006311.3	698	Caa/Taa	19/46	1	2	FACETS	0.832	0.768	0.898	0.832	0.768	0.898	CLONAL	1	TRUE	1	0.448599092005644	2		425	1008	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29120995	29120995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	303	490	0	ENST00000328354.6:c.562G>A	p.Glu188Lys	p.E188K	ENST00000328354	NM_007194.3	188	Gaa/Aaa	4/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.448599092005644	2		490	1253	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29130673	29130673	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0009859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	129	277	0	ENST00000328354.6:c.37C>A	p.His13Asn	p.H13N	ENST00000328354	NM_007194.3	13	Cat/Aat	2/15	1	2	FACETS	0.907	0.825	0.993	0.907	0.825	0.993	CLONAL	1	TRUE	1	0.448599092005644	2		277	634	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039859	47039859	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	216	426	0	ENST00000377604.3:c.1202C>T	p.Ser401Phe	p.S401F	ENST00000377604	NM_001204468.1	401	tCt/tTt	12/24	1	2	FACETS	0.848	0.787	0.91	0.848	0.787	0.91	CLONAL	1	TRUE	1	0.448599092005644	2		426	1136	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123229252	123229252	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	319	514	1	ENST00000218089.9:c.3736G>A	p.Glu1246Lys	p.E1246K	ENST00000218089	NM_001042749.1	1246	Gaa/Aaa	34/35	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.448599092005644	2		515	1261	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	133	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.756707865803987	2		280	322	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0009873-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10973	12601	910	2	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.756707865803987	22	FACETS	1	0.997	1			1	CLONAL	12	TRUE	NA	0.756707865803987	22		912	23574	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	90	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.936	0.837	1	0.936	0.837	1	CLONAL	1	TRUE	1	0.52701614744818	2		280	365	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0009876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	323	538	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	0.52701614744818	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.52701614744818	1		538	826	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs104886003	NA	P-0009876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	93	195	0	ENST00000263967.3:c.1633G>C	p.Glu545Gln	p.E545Q	ENST00000263967	NM_006218.2	545	Gag/Cag	10/21	1	2	FACETS	0.949	0.85	1	0.949	0.85	1	CLONAL	1	TRUE	1	0.52701614744818	2		195	372	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651946	36651947	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0009876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	271	310	0	ENST00000244741.5:c.71dup	p.Val25SerfsTer11	p.V25Sfs*11	ENST00000244741	NM_000389.4	23	ggc/ggCc	2/3	0.523811741443663	2	FACETS	0.869	0.823	0.915	0.869	0.823	0.915	CLONAL	2	TRUE	0	0.52701614744818	2		310	592	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246638	46246638	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	87	206	0	ENST00000334344.6:c.4732C>T	p.Gln1578Ter	p.Q1578*	ENST00000334344	NM_152641.2	1578	Caa/Taa	15/21	1	2	FACETS	0.892	0.796	0.994	0.892	0.796	0.994	CLONAL	1	TRUE	1	0.52701614744818	2		206	370	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427932	49427932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	302	553	0	ENST00000301067.7:c.10658G>A	p.Gly3553Asp	p.G3553D	ENST00000301067	NM_003482.3	3553	gGc/gAc	38/54	1	2	FACETS	0.969	0.912	1	0.969	0.912	1	CLONAL	1	TRUE	1	0.52701614744818	2		553	1183	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226387	41226387	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28897691	NA	P-0009876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	225	600	0	ENST00000357654.3:c.4636G>T	p.Asp1546Tyr	p.D1546Y	ENST00000357654	NM_007294.3	1546	Gat/Tat	14/23	1	2	FACETS	0.809	0.753	0.867	0.809	0.753	0.867	CLONAL	1	TRUE	1	0.52701614744818	2		600	1055	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115947	8115948	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	CC	novel	NA	P-0009876-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	109	216	0	ENST00000346208.3:c.1294_1295dup	p.His434ThrfsTer42	p.H434Tfs*42	ENST00000346208		431	-/CC	6/6	NA	2	FACETS	0.797	0.719	0.879			1	INDETERMINATE	1	TRUE	NA	0.52701614744818	2		216	519	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009877-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	249	280	0				ENST00000310581	NM_198253.2	-/1132			0.391569048794332	1	FACETS	0.708	0.668	0.748	0.708	0.668	0.748	INDETERMINATE	1	TRUE	0	0.764689694149432	1		280	568	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32937542	32937542	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs397507396	NA	P-0009877-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	209	641	2	ENST00000380152.3:c.8206del	p.Leu2736SerfsTer2	p.L2736Sfs*2	ENST00000380152		2735	Ccc/cc	18/27	0.391569048794332	1	FACETS	0.345	0.32	0.371	0.345	0.32	0.371	INDETERMINATE	1	TRUE	0	0.764689694149432	1		643	979	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0009878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	305	654	1	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	1	2	FACETS	0.486	0.457	0.515	0.486	0.457	0.515	SUBCLONAL	1	TRUE	1	0.986944872377878	2		655	1272	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0009878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	197	463	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.547	0.508	0.587	0.547	0.508	0.587	SUBCLONAL	1	TRUE	1	0.986944872377878	2		463	730	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68771360	68771360	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0009878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	177	206	0	ENST00000261769.5:c.42del	p.Leu15CysfsTer41	p.L15Cfs*41	ENST00000261769	NM_004360.3	14	ctG/ct	1/16	0.538558921759176	1	FACETS	0.412	0.384	0.441	0.412	0.384	0.441	INDETERMINATE	1	TRUE	0	0.986944872377878	1		206	441	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8115809	8115809	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0009878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1478	454	719	0	ENST00000346208.3:c.1158del	p.Lys387ArgfsTer17	p.K387Rfs*17	ENST00000346208		385	ttC/tt	6/6	1	2	FACETS	0.476	0.453	0.5	0.476	0.453	0.5	SUBCLONAL	1	TRUE	1	0.986944872377878	2		719	1932	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063717	67063718	+	splice_donor_variant	Splice_Site	DEL	GT	GT	-	novel	NA	P-0009878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	106	198	2	ENST00000412916.2:c.165+1_165+2del		p.X55_splice	ENST00000412916		55			0.538558921759176	1	FACETS	0.305	0.276	0.335	0.305	0.276	0.335	INDETERMINATE	1	TRUE	0	0.986944872377878	1		200	357	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419923	152419924	+	missense_variant	Missense_Mutation	DNP	AT	AT	CA	novel	NA	P-0009878-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	205	347	0	ENST00000206249.3:c.1610_1611delinsCA	p.Tyr537Ser	p.Y537S	ENST00000206249	NM_000125.3	537	tAT/tCA	8/8	1	2	FACETS	0.505	0.469	0.542	0.505	0.469	0.542	SUBCLONAL	1	TRUE	1	0.986944872377878	2		347	823	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009898-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	123	280	0				ENST00000310581	NM_198253.2	-/1132			0.318848464643224	6	FACETS	0.966	0.881	1	0.483	0.44	0.528	INDETERMINATE	2	FALSE	2	0.717293250338492	6		280	432	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0009898-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	251	263	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.717293250338492	6	FACETS	1	0.974	1	0.534	0.501	0.568	CLONAL	2	FALSE	2	0.717293250338492	6		263	797	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186815	108186815	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0009898-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	399	656	0	ENST00000278616.4:c.6173C>G	p.Ser2058Ter	p.S2058*	ENST00000278616	NM_000051.3	2058	tCa/tGa	42/63	0.717293250338492	3	FACETS	0.923	0.883	0.962	0.923	0.883	0.962	CLONAL	2	FALSE	1	0.717293250338492	3		656	819	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	142950023	142950023	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs745719080	NA	P-0009898-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	401	594	0	ENST00000262992.4:c.2687G>C	p.Arg896Thr	p.R896T	ENST00000262992	NM_001101669.1	896	aGa/aCa	24/24	0.618097545467837	4	FACETS	0.977	0.932	1	0.977	0.932	1	CLONAL	2	FALSE	2	0.717293250338492	4		594	983	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139392001	139392001	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1294066789	NA	P-0009898-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	169	415	1	ENST00000277541.6:c.6190C>T	p.Pro2064Ser	p.P2064S	ENST00000277541	NM_017617.3	2064	Ccc/Tcc	34/34	0.687007325934767	3	FACETS	1	0.988	1	0.456	0.423	0.49	CLONAL	1	FALSE	0	0.717293250338492	3		416	468	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42035343	42035343	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009898-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1384	77	809	0	ENST00000219905.7:c.5185G>C	p.Gly1729Arg	p.G1729R	ENST00000219905	NM_001164273.1	1729	Ggg/Cgg	15/24	0.421230006695434	4	FACETS	0.252	0.22	0.287	0.126	0.11	0.144	INDETERMINATE	1	FALSE	2	0.717293250338492	4		809	1461	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56402549	56402549	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009898-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	107	571	0	ENST00000348428.3:c.1591G>A	p.Glu531Lys	p.E531K	ENST00000348428	NM_006785.3	531	Gaa/Aaa	13/17	0.717293250338492	3	FACETS	0.375	0.336	0.418	0.188	0.168	0.209	SUBCLONAL	1	FALSE	1	0.717293250338492	3		571	1080	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138491	11138491	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009898-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	331	545	1	ENST00000358026.2:c.3247G>T	p.Glu1083Ter	p.E1083*	ENST00000358026	NM_001128849.1	1083	Gag/Tag	24/36	0.332207928534381	5	FACETS	0.969	0.917	1	0.646	0.611	0.681	INDETERMINATE	2	FALSE	2	0.717293250338492	5		546	989	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53241016	53241016	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009898-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	135	416	0	ENST00000375401.3:c.1195G>C	p.Glu399Gln	p.E399Q	ENST00000375401	NM_004187.3	399	Gag/Cag	9/26	0.717293250338492	2	FACETS	0.389	0.353	0.427			1	SUBCLONAL	1	FALSE	NA	0.717293250338492	2		416	968	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	143	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.855956034043043	2		280	297	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	441	507	0	ENST00000335508.6:c.2704G>C	p.Glu902Gln	p.E902Q	ENST00000335508	NM_012433.2	902	Gaa/Caa	18/25	0.855956034043043	1	FACETS	0.996	0.966	1	0.996	0.966	1	CLONAL	1	TRUE	0	0.855956034043043	1		507	592	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183559	10183559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519261	NA	P-0009910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	216	403	0	ENST00000256474.2:c.28G>A	p.Glu10Lys	p.E10K	ENST00000256474	NM_000551.3	10	Gag/Aag	1/3	0.416185934667223	2	FACETS	0.569	0.529	0.61	0.284	0.264	0.305	INDETERMINATE	1	TRUE	0	0.855956034043043	2		403	887	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783211	9783211	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	488	429	1	ENST00000377346.4:c.2455G>A	p.Gly819Arg	p.G819R	ENST00000377346	NM_005026.3	819	Ggg/Agg	20/24	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.855956034043043	2		430	1130	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057862	27057862	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	686	668	0	ENST00000324856.7:c.1570C>T	p.Gln524Ter	p.Q524*	ENST00000324856	NM_006015.4	524	Cag/Tag	3/20	0.855545972667666	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.855956034043043	1		668	884	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057868	27057868	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	629	650	0	ENST00000324856.7:c.1576C>T	p.Pro526Ser	p.P526S	ENST00000324856	NM_006015.4	526	Cca/Tca	3/20	0.855545972667666	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.855956034043043	1		650	815	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36808977	36808977	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0009910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	66	596	0	ENST00000373129.3:c.1077T>A	p.Asp359Glu	p.D359E	ENST00000373129	NM_032017.1	359	gaT/gaA	11/12	NA	2	FACETS	0.141	0.121	0.162			1	INDETERMINATE	1	TRUE	NA	0.855956034043043	2		596	1095	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37067161	37067161	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0009910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	538	403	0	ENST00000231790.2:c.1072G>T	p.Glu358Ter	p.E358*	ENST00000231790	NM_000249.3	358	Gag/Tag	12/19	0.416185934667223	2	FACETS	1	0.997	1	0.718	0.695	0.741	INDETERMINATE	1	TRUE	0	0.855956034043043	2		403	875	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149440521	149440521	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	227	379	0	ENST00000286301.3:c.1873G>C	p.Asp625His	p.D625H	ENST00000286301	NM_005211.3	625	Gat/Cat	14/22	0.449582127061383	1	FACETS	0.392	0.367	0.419	0.392	0.367	0.419	INDETERMINATE	1	TRUE	0	0.855956034043043	1		379	773	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523692	148523692	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	43	449	0	ENST00000320356.2:c.761G>C	p.Gly254Ala	p.G254A	ENST00000320356	NM_004456.4	254	gGc/gCc	8/20	1	2	FACETS	0.118	0.098	0.14	0.118	0.098	0.14	SUBCLONAL	1	TRUE	1	0.855956034043043	2		449	852	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152008922	152008922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	389	489	0	ENST00000262189.6:c.700C>T	p.Pro234Ser	p.P234S	ENST00000262189	NM_170606.2	234	Cca/Tca	5/59	1	2	FACETS	0.937	0.893	0.981	0.937	0.893	0.981	CLONAL	1	TRUE	1	0.855956034043043	2		489	970	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807919	3807919	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587783481	NA	P-0009910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	253	436	0	ENST00000262367.5:c.3500A>G	p.Tyr1167Cys	p.Y1167C	ENST00000262367	NM_004380.2	1167	tAt/tGt	18/31	0.440802019545206	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.855956034043043	0		436	580	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821110	72821110	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0009910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	400	826	0	ENST00000268489.5:c.11065A>T	p.Lys3689Ter	p.K3689*	ENST00000268489	NM_006885.3	3689	Aag/Tag	10/10	0.449582127061383	1	FACETS	0.351	0.333	0.369	0.351	0.333	0.369	INDETERMINATE	1	TRUE	0	0.855956034043043	1		826	1524	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881111	37881111	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778267	NA	P-0009910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	956	249	558	1	ENST00000269571.5:c.2440C>T	p.Arg814Cys	p.R814C	ENST00000269571		814	Cgc/Tgc	20/27	NA	2	FACETS	0.483	0.451	0.516			1	INDETERMINATE	1	TRUE	NA	0.855956034043043	2		559	1205	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939241	76939241	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1340830235	NA	P-0009910-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	624	675	0	ENST00000373344.5:c.1507C>G	p.Gln503Glu	p.Q503E	ENST00000373344	NM_000489.3	503	Caa/Gaa	9/35	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.855956034043043	2		675	1375	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0009940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	175	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.474975450565221	2		464	606	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467675	50467675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759124417	NA	P-0009940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	198	499	0	ENST00000331340.3:c.910G>A	p.Glu304Lys	p.E304K	ENST00000331340	NM_006060.4	304	Gaa/Aaa	8/8	1	2	FACETS	0.868	0.804	0.935	0.868	0.804	0.935	CLONAL	1	TRUE	1	0.474975450565221	2		499	960	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0009940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	381	765	2	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.474975450565221	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.474975450565221	1		767	1206	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262298	16262298	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	61	124	0	ENST00000375759.3:c.9563C>T	p.Pro3188Leu	p.P3188L	ENST00000375759	NM_015001.2	3188	cCc/cTc	11/15	1	2	FACETS	0.818	0.711	0.933	0.818	0.711	0.933	CLONAL	1	TRUE	1	0.474975450565221	2		124	314	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807399	36807399	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	286	389	0	ENST00000373129.3:c.1265C>T	p.Ser422Phe	p.S422F	ENST00000373129	NM_032017.1	422	tCc/tTc	12/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.474975450565221	2		389	1088	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468348	120468348	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	152	189	0	ENST00000256646.2:c.4091C>T	p.Pro1364Leu	p.P1364L	ENST00000256646	NM_024408.3	1364	cCc/cTc	25/34	1	2	FACETS	0.976	0.895	1	0.976	0.895	1	CLONAL	1	TRUE	1	0.474975450565221	2		189	656	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645876	215645876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	314	665	0	ENST00000260947.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000260947	NM_000465.2	241	tCc/tTc	4/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.474975450565221	2		665	1221	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275254	41275254	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1553631860	NA	P-0009940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	192	276	0	ENST00000349496.5:c.1420C>T	p.Arg474Ter	p.R474*	ENST00000349496	NM_001904.3	474	Cga/Tga	9/15	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.474975450565221	2		276	780	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153271243	153271243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1207004877	NA	P-0009940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	195	430	0	ENST00000281708.4:c.535C>T	p.Arg179Cys	p.R179C	ENST00000281708	NM_033632.3	179	Cgc/Tgc	3/12	0.170206553489186	1	FACETS	0.84	0.78	0.903	0.84	0.78	0.903	INDETERMINATE	1	TRUE	0	0.474975450565221	1		430	745	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575535	67575535	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0009940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	221	346	0	ENST00000274335.5:c.608A>G	p.Tyr203Cys	p.Y203C	ENST00000274335		203	tAc/tGc	4/15	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.474975450565221	2		346	912	SUCCESS
APC	324	MSKCC	GRCh37	5	112174658	112174658	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0009940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	322	536	3	ENST00000257430.4:c.3367C>T	p.Gln1123Ter	p.Q1123*	ENST00000257430	NM_000038.5	1123	Caa/Taa	16/16	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.474975450565221	2		539	1299	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515291	149515291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1244128395	NA	P-0009940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	244	385	2	ENST00000261799.4:c.191G>A	p.Arg64Gln	p.R64Q	ENST00000261799	NM_002609.3	64	cGg/cAg	3/23	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.474975450565221	2		387	993	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463298	463298	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	317	552	2	ENST00000399788.2:c.973C>T	p.Pro325Ser	p.P325S	ENST00000399788	NM_001042603.1	325	Cct/Tct	8/28	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.474975450565221	2		554	1208	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025596	1025596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770234586	NA	P-0009940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	282	424	1	ENST00000358495.3:c.779G>A	p.Arg260Gln	p.R260Q	ENST00000358495	NM_134424.2	260	cGg/cAg	9/12	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.474975450565221	2		425	1012	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2221265	2221265	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	260	461	0	ENST00000326181.6:c.349G>A	p.Glu117Lys	p.E117K	ENST00000326181	NM_032271.2	117	Gag/Aag	6/21	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.474975450565221	2		461	1086	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788618	3788619	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	224	510	0	ENST00000262367.5:c.4335_4336delinsTT	p.Arg1446Cys	p.R1446C	ENST00000262367	NM_004380.2	1445	ctCCgc/ctTTgc	26/31	1	2	FACETS	0.838	0.78	0.899	0.838	0.78	0.899	CLONAL	1	TRUE	1	0.474975450565221	2		510	1125	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59870968	59870968	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0009940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	194	545	1	ENST00000259008.2:c.1463C>T	p.Pro488Leu	p.P488L	ENST00000259008	NM_032043.2	488	cCc/cTc	10/20	1	2	FACETS	0.888	0.822	0.956	0.888	0.822	0.956	CLONAL	1	TRUE	1	0.474975450565221	2		546	920	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226023	53226024	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0009940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	362	323	0	ENST00000375401.3:c.2825_2826delinsTT	p.Ala942Val	p.A942V	ENST00000375401	NM_004187.3	942	gCC/gTT	19/26	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.474975450565221	1		323	827	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626668	100626668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	342	282	0	ENST00000308731.7:c.262G>A	p.Glu88Lys	p.E88K	ENST00000308731	NM_000061.2	88	Gaa/Aaa	4/19	1	1	FACETS	0.787	0.75	0.823	1	0.996	1	SUBCLONAL	2	TRUE	0	0.474975450565221	1		282	698	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151935825	151935825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1297640475	NA	P-0009940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	13	10	13	0	ENST00000262189.6:c.2619del	p.Gln873HisfsTer40	p.Q873Hfs*40	ENST00000262189	NM_170606.2	873	caG/ca	15/59	1	2	FACETS	0.915	0.668	1	1	0.894	1	CLONAL	2	TRUE	1	0.474975450565221	2		13	23	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232189	98232190	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0009940-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	234	399	0	ENST00000331920.6:c.1752_1753insA	p.Phe585IlefsTer42	p.F585Ifs*42	ENST00000331920	NM_000264.3	584	-/A	13/24	0.474975450565221	1	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	0	0.474975450565221	1		399	749	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0009941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	345	463	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.956	0.906	1	0.956	0.906	1	CLONAL	1	TRUE	1	0.700754298843608	2		463	1030	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36252994	36252995	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0009941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	172	239	0	ENST00000300305.3:c.367dup	p.Asp123GlyfsTer15	p.D123Gfs*15	ENST00000300305		123	gat/gGat	4/8	1	2	FACETS	0.825	0.763	0.889	0.825	0.763	0.889	CLONAL	1	TRUE	1	0.700754298843608	2		239	595	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649565	206649565	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	46	268	1	ENST00000367120.3:c.400C>T	p.Arg134Cys	p.R134C	ENST00000367120	NM_014002.3	134	Cgc/Tgc	6/22	0.700754298843608	3	FACETS	0.209	0.175	0.246	0.104	0.087	0.123	SUBCLONAL	1	TRUE	1	0.700754298843608	3		269	850	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206943231	206943231	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0009941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	302	352	0	ENST00000423557.1:c.387T>G	p.Phe129Leu	p.F129L	ENST00000423557	NM_000572.2	129	ttT/ttG	4/5	0.700754298843608	3	FACETS	1	0.967	1	0.518	0.488	0.549	CLONAL	1	TRUE	1	0.700754298843608	3		352	1123	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275369	142275369	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	250	309	0	ENST00000350721.4:c.1934G>C	p.Arg645Thr	p.R645T	ENST00000350721	NM_001184.3	645	aGa/aCa	9/47	1	2	FACETS	0.954	0.896	1	0.954	0.896	1	CLONAL	1	TRUE	1	0.700754298843608	2		309	748	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983804	15983804	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0009941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	355	398	0	ENST00000268712.3:c.3318G>T	p.Lys1106Asn	p.K1106N	ENST00000268712	NM_006311.3	1106	aaG/aaT	25/46	1	2	FACETS	0.945	0.897	0.994	0.945	0.897	0.994	CLONAL	1	TRUE	1	0.700754298843608	2		398	1072	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853857	59853857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0009941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	358	613	0	ENST00000259008.2:c.2002G>A	p.Glu668Lys	p.E668K	ENST00000259008	NM_032043.2	668	Gaa/Aaa	14/20	1	2	FACETS	0.781	0.739	0.823	0.781	0.739	0.823	SUBCLONAL	1	TRUE	1	0.700754298843608	2		613	1309	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41531841	41531841	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0009941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	461	539	0	ENST00000263253.7:c.1553G>C	p.Gly518Ala	p.G518A	ENST00000263253	NM_001429.3	518	gGa/gCa	7/31	1	2	FACETS	0.896	0.855	0.937	0.896	0.855	0.937	CLONAL	1	TRUE	1	0.700754298843608	2		539	1469	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317539	1317539	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0009941-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	409	564	0	ENST00000400841.2:c.526G>C	p.Asp176His	p.D176H	ENST00000400841		176	Gat/Cat	5/6	NA	2	FACETS	0.983	0.937	1			1	INDETERMINATE	1	TRUE	NA	0.700754298843608	2		564	1187	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0009992-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	92	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.979	0.889	1	0.979	0.889	1	CLONAL	1	TRUE	1	0.88223115439792	2		280	213	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0009992-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	154	511	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.814	0.752	0.877	0.814	0.752	0.877	CLONAL	1	TRUE	1	0.88223115439792	2		511	429	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	75	280	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.948	1			1	INDETERMINATE	1	TRUE	NA	0.466295045075498	2		280	286	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0010003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	226	511	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.954	0.889	1	0.954	0.889	1	CLONAL	1	TRUE	1	0.466295045075498	2		512	1016	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554464	63554464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010003-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	70	440	0	ENST00000307078.5:c.275C>T	p.Ala92Val	p.A92V	ENST00000307078	NM_004655.3	92	gCt/gTt	2/11	1	2	FACETS	0.323	0.28	0.369	0.323	0.28	0.369	SUBCLONAL	1	TRUE	1	0.466295045075498	2		440	930	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	99	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.972	0.883	1	1	0.99	1	CLONAL	3	FALSE	1	0.266166202610563	2		280	255	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0010033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	135	595	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.839	0.77	0.91	1	0.992	1	CLONAL	3	FALSE	1	0.266166202610563	2		595	403	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420871	49420871	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555185969	NA	P-0010033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	283	421	0	ENST00000301067.7:c.14878C>T	p.Arg4960Ter	p.R4960*	ENST00000301067	NM_003482.3	4960	Cga/Tga	48/54	1	2	FACETS	0.872	0.823	0.922	1	0.996	1	CLONAL	3	FALSE	1	0.266166202610563	2		421	813	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612735	228612735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	923	1195	1	ENST00000366696.1:c.292G>A	p.Glu98Lys	p.E98K	ENST00000366696	NM_003493.2	98	Gag/Aag	1/1	0.225481658513106	4	FACETS	0.958	0.931	0.984	1	0.998	1	CLONAL	5	FALSE	1	0.266166202610563	4		1196	1834	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631279	176631279	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	39	572	1	ENST00000439151.2:c.1222G>T	p.Gly408Ter	p.G408*	ENST00000439151	NM_022455.4	408	Gga/Tga	4/23	0.266166202610563	0	FACETS	0.322	0.266	0.385			1	SUBCLONAL	1	FALSE	0	0.266166202610563	0		573	668	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481581	20481581	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	70	466	1	ENST00000346618.3:c.650G>T	p.Arg217Met	p.R217M	ENST00000346618	NM_001949.4	217	aGg/aTg	3/7	1	2	FACETS	0.501	0.436	0.573	0.501	0.436	0.573	SUBCLONAL	1	FALSE	1	0.266166202610563	2		467	1049	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673189	30673189	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1389563539	NA	P-0010033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	251	398	0	ENST00000376406.3:c.3771C>G	p.Asp1257Glu	p.D1257E	ENST00000376406	NM_014641.2	1257	gaC/gaG	10/15	1	2	FACETS	0.872	0.82	0.925	1	0.996	1	CLONAL	3	FALSE	1	0.266166202610563	2		398	721	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891591	151891591	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs587777073	NA	P-0010033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	216	446	0	ENST00000262189.6:c.4441C>T	p.Arg1481Ter	p.R1481*	ENST00000262189	NM_170606.2	1481	Cga/Tga	29/59	1	2	FACETS	0.834	0.779	0.889	1	0.995	1	CLONAL	3	FALSE	1	0.266166202610563	2		446	649	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432174	49432174	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	286	445	0	ENST00000301067.7:c.8965G>T	p.Glu2989Ter	p.E2989*	ENST00000301067	NM_003482.3	2989	Gag/Tag	34/54	1	2	FACETS	0.908	0.857	0.959	1	0.996	1	CLONAL	3	FALSE	1	0.266166202610563	2		445	789	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0010059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	49	464	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	0	0.34	1		464	223	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0010059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	179	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.137791293651515	3	FACETS	0.829	0.766	0.894	0.829	0.766	0.894	INDETERMINATE	2	TRUE	1	0.34	3		490	743	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11217299	11217299	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519779	NA	P-0010059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	99	673	0	ENST00000361445.4:c.4379T>C	p.Leu1460Pro	p.L1460P	ENST00000361445	NM_004958.3	1460	cTt/cCt	30/58	0.3	1	FACETS	0.951	0.853	1	0.951	0.853	1	CLONAL	1	TRUE	0	0.34	1		673	508	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	313	280	0				ENST00000310581	NM_198253.2	-/1132			0.26005078503057	4	FACETS	0.973	0.92	1			1	CLONAL	3	TRUE	NA	0.28	4		280	980	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0010061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	321	506	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	1	2	FACETS	0.985	0.93	1	1	0.996	1	CLONAL	2	TRUE	1	0.28	2		506	1164	SUCCESS
RET	5979	MSKCC	GRCh37	10	43620407	43620407	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	69	442	0	ENST00000355710.3:c.3016G>T	p.Glu1006Ter	p.E1006*	ENST00000355710	NM_020975.4	1006	Gag/Tag	18/20	1	2	FACETS	0.487	0.423	0.557	0.487	0.423	0.557	SUBCLONAL	1	TRUE	1	0.28	2		442	1012	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578392	7578392	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs879253911	NA	P-0010061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	110	313	1	ENST00000269305.4:c.538G>A	p.Glu180Lys	p.E180K	ENST00000269305	NM_001126112.2	180	Gag/Aag	5/11	0.261735382516287	1	FACETS	0.922	0.829	1	0.922	0.829	1	CLONAL	1	TRUE	0	0.28	1		314	733	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127412	55127412	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1237	189	577	1	ENST00000257290.5:c.200C>A	p.Ser67Tyr	p.S67Y	ENST00000257290	NM_006206.4	67	tCc/tAc	3/23	1	2	FACETS	0.947	0.872	1	0.947	0.872	1	CLONAL	1	TRUE	1	0.28	2		578	1426	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55154983	55154983	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1332	242	581	4	ENST00000257290.5:c.2692G>T	p.Gly898Cys	p.G898C	ENST00000257290	NM_006206.4	898	Ggc/Tgc	20/23	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.28	2		585	1574	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280049	66280049	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs754344980	NA	P-0010061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	117	514	0	ENST00000273854.3:c.1640G>C	p.Gly547Ala	p.G547A	ENST00000273854	NM_004439.5	547	gGc/gCc	7/18	1	2	FACETS	0.842	0.758	0.932	0.842	0.758	0.932	CLONAL	1	TRUE	1	0.28	2		514	992	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20488477	20488477	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	182	553	0	ENST00000346618.3:c.1133A>T	p.Lys378Ile	p.K378I	ENST00000346618	NM_001949.4	378	aAa/aTa	6/7	1	2	FACETS	0.943	0.868	1	0.943	0.868	1	CLONAL	1	TRUE	1	0.28	2		553	1378	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151871304	151871304	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	241	441	0	ENST00000262189.6:c.9286A>G	p.Ile3096Val	p.I3096V	ENST00000262189	NM_170606.2	3096	Ata/Gta	39/59	0.154768255697934	3	FACETS	0.785	0.732	0.84	0.785	0.732	0.84	INDETERMINATE	2	TRUE	1	0.28	3		441	1250	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332297	70332297	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780528931	NA	P-0010061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1520	106	786	3	ENST00000373644.4:c.202G>A	p.Val68Met	p.V68M	ENST00000373644	NM_030625.2	68	Gtg/Atg	2/12	1	2	FACETS	0.466	0.415	0.519	0.466	0.415	0.519	SUBCLONAL	1	TRUE	1	0.28	2		789	1626	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514155	69514155	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs776116676	NA	P-0010061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1229	144	559	0	ENST00000294312.3:c.526C>A	p.Pro176Thr	p.P176T	ENST00000294312	NM_005117.2	176	Cct/Act	3/3	1	2	FACETS	0.749	0.681	0.821	0.749	0.681	0.821	SUBCLONAL	1	TRUE	1	0.28	2		559	1373	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28578234	28578234	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1179	76	519	0	ENST00000241453.7:c.2937G>T	p.Met979Ile	p.M979I	ENST00000241453	NM_004119.2	979	atG/atT	24/24	1	2	FACETS	0.433	0.378	0.492	0.433	0.378	0.492	SUBCLONAL	1	TRUE	1	0.28	2		519	1255	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10291041	10291041	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765353997	NA	P-0010061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	59	370	0	ENST00000340748.4:c.430G>A	p.Asp144Asn	p.D144N	ENST00000340748		144	Gat/Aat	4/40	1	2	FACETS	0.448	0.384	0.518	0.448	0.384	0.518	SUBCLONAL	1	TRUE	1	0.28	2		370	941	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795743	42795743	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs535815082	NA	P-0010061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1272	377	604	1	ENST00000575354.2:c.2732C>T	p.Pro911Leu	p.P911L	ENST00000575354	NM_015125.3	911	cCg/cTg	11/20	0.218504744719781	3	FACETS	0.931	0.881	0.982			1	CLONAL	2	TRUE	NA	0.28	3		605	1649	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795818	42795818	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1398	161	584	1	ENST00000575354.2:c.2807G>T	p.Gly936Val	p.G936V	ENST00000575354	NM_015125.3	936	gGa/gTa	11/20	0.218504744719781	3	FACETS	0.841	0.768	0.917			1	CLONAL	1	TRUE	NA	0.28	3		585	1559	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922208	39922208	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1410	97	667	1	ENST00000378444.4:c.3964C>A	p.Gln1322Lys	p.Q1322K	ENST00000378444	NM_001123385.1	1322	Cag/Aag	9/15	1	2	FACETS	0.46	0.408	0.515	0.46	0.408	0.515	SUBCLONAL	1	TRUE	1	0.28	2		668	1507	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928873	44928873	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1371	99	559	0	ENST00000377967.4:c.1973G>T	p.Arg658Leu	p.R658L	ENST00000377967	NM_021140.2	658	cGa/cTa	17/29	1	2	FACETS	0.481	0.428	0.538	0.481	0.428	0.538	SUBCLONAL	1	TRUE	1	0.28	2		559	1470	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47004891	47004891	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	T	novel	NA	P-0010061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	176	594	0	ENST00000377604.3:c.-126+7G>T		p.X42_splice	ENST00000377604	NM_001204468.1	42			1	2	FACETS	0.967	0.889	1	0.967	0.889	1	CLONAL	1	TRUE	1	0.28	2		594	1300	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044853	47044853	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	142	409	1	ENST00000377604.3:c.2179G>T	p.Gly727Ter	p.G727*	ENST00000377604	NM_001204468.1	727	Gga/Tga	20/24	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.28	2		410	1008	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47429367	47429367	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1626	119	745	0	ENST00000377045.4:c.1495C>A	p.Leu499Ile	p.L499I	ENST00000377045	NM_001654.4	499	Ctc/Atc	14/16	1	2	FACETS	0.487	0.437	0.54	0.487	0.437	0.54	SUBCLONAL	1	TRUE	1	0.28	2		745	1745	SUCCESS
BTK	695	MSKCC	GRCh37	X	100626628	100626628	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1313	170	738	1	ENST00000308731.7:c.302C>A	p.Pro101His	p.P101H	ENST00000308731	NM_000061.2	101	cCc/cAc	4/19	1	2	FACETS	0.819	0.75	0.891	0.819	0.75	0.891	CLONAL	1	TRUE	1	0.28	2		739	1483	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469580	25469580	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1360	222	642	0	ENST00000264709.3:c.1188del	p.Lys397ArgfsTer10	p.K397Rfs*10	ENST00000264709	NM_175629.2	396	gcC/gc	10/23	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.28	2		642	1582	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923360	9923361	+	missense_variant	Missense_Mutation	DNP	CC	CC	GT	novel	NA	P-0010061-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	153	591	0	ENST00000330684.3:c.1926_1927delinsAC	p.Ala643Pro	p.A643P	ENST00000330684	NM_001134407.1	642	ctGGct/ctACct	9/13	0.3	1	FACETS	0.742	0.677	0.81	0.742	0.677	0.81	SUBCLONAL	1	TRUE	0	0.28	1		591	1267	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	246	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.998	0.941	1	0.998	0.941	1	CLONAL	1	TRUE	1	0.85	2		280	580	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0010103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	239	595	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	0.3	2	FACETS	0.833	0.782	0.885			1	INDETERMINATE	1	TRUE	NA	0.85	2		595	675	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461152	120461152	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	329	315	0	ENST00000256646.2:c.5806G>T	p.Asp1936Tyr	p.D1936Y	ENST00000256646	NM_024408.3	1936	Gat/Tat	32/34	1	2	FACETS	0.819	0.776	0.863	0.819	0.776	0.863	CLONAL	1	TRUE	1	0.85	2		315	945	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151900075	151900075	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0010103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	74	494	0	ENST00000262189.6:c.4036A>T	p.Lys1346Ter	p.K1346*	ENST00000262189	NM_170606.2	1346	Aag/Tag	26/59	1	2	FACETS	0.139	0.121	0.159	0.139	0.121	0.159	SUBCLONAL	1	TRUE	1	0.85	2		494	1254	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786797	3786797	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	405	406	0	ENST00000262367.5:c.4414T>C	p.Trp1472Arg	p.W1472R	ENST00000262367	NM_004380.2	1472	Tgg/Cgg	27/31	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.85	2		406	946	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427439	49427482	+	frameshift_variant	Frame_Shift_Del	DEL	CTGTTGCTGCTGTTGGGCCAGAGCTGTATTAAGGAAGGGGCCAC	CTGTTGCTGCTGTTGGGCCAGAGCTGTATTAAGGAAGGGGCCAC	-	novel	NA	P-0010103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	319	512	0	ENST00000301067.7:c.11006_11049del	p.Gly3669AlafsTer29	p.G3669Afs*29	ENST00000301067	NM_003482.3	3669	gGTGGCCCCTTCCTTAATACAGCTCTGGCCCAACAGCAGCAACAG/g	39/54	1	2	FACETS	0.798	0.756	0.842	0.798	0.756	0.842	SUBCLONAL	1	TRUE	1	0.85	2		512	940	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874712	151874712	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	311	417	0	ENST00000262189.6:c.7826del	p.Arg2609HisfsTer38	p.R2609Hfs*38	ENST00000262189	NM_170606.2	2609	cGa/ca	38/59	1	2	FACETS	0.704	0.664	0.744	0.704	0.664	0.744	SUBCLONAL	1	TRUE	1	0.85	2		417	1040	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652088	36652098	+	frameshift_variant	Frame_Shift_Del	DEL	CCTTGGCCTGC	CCTTGGCCTGC	-	novel	NA	P-0010103-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	384	431	0	ENST00000244741.5:c.212_222del	p.Leu71GlnfsTer14	p.L71Qfs*14	ENST00000244741	NM_000389.4	70	ggCCTTGGCCTGCcc/ggcc	2/3	1	2	FACETS	0.909	0.866	0.953	0.909	0.866	0.953	CLONAL	1	TRUE	1	0.85	2		431	994	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	60	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.5	2		280	238	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0010108-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	140	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.897	0.82	0.978	0.897	0.82	0.978	CLONAL	1	TRUE	1	0.5	2		490	624	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439696	51439696	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	113	430	0	ENST00000262662.1:c.261G>C	p.Gln87His	p.Q87H	ENST00000262662		87	caG/caC	4/4	0.672844535480026	3	FACETS	0.747	0.674	0.824	0.373	0.337	0.412	SUBCLONAL	1	TRUE	1	0.672844535480026	3		430	601	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33290691	33290691	+	5_prime_UTR_variant	5'UTR	SNP	T	T	A	novel	NA	P-0010111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	191	522	0	ENST00000374542.5:c.-105A>T		p.*35*	ENST00000374542	NM_001141970.1	-/740		1/8	0.672844535480026	4	FACETS	0.973	0.9	1	0.487	0.45	0.525	CLONAL	1	TRUE	2	0.672844535480026	4		522	976	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272335	15272335	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771337440	NA	P-0010111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	34	340	0	ENST00000263388.2:c.6104G>A	p.Gly2035Asp	p.G2035D	ENST00000263388	NM_000435.2	2035	gGt/gAt	33/33	0.590331924798771	4	FACETS	0.268	0.218	0.325	0.134	0.109	0.163	SUBCLONAL	1	TRUE	2	0.672844535480026	4		340	630	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0010130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	64	660	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.342	0.296	0.393	0.342	0.296	0.393	SUBCLONAL	1	TRUE	1	0.555785185714983	2		660	673	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211050	55211050	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17289589	NA	P-0010130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	46	453	0	ENST00000275493.2:c.293G>A	p.Arg98Gln	p.R98Q	ENST00000275493	NM_005228.3	98	cGa/cAa	3/28	1	2	FACETS	0.19	0.16	0.225	0.19	0.16	0.225	SUBCLONAL	1	TRUE	1	0.555785185714983	2		453	869	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0010130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	139	485	1	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.535711514578288	1	FACETS	0.297	0.269	0.326	0.297	0.269	0.326	SUBCLONAL	1	TRUE	0	0.555785185714983	1		486	1216	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145430	58145430	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894340	NA	P-0010130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	115	573	0	ENST00000257904.6:c.71G>T	p.Arg24Leu	p.R24L	ENST00000257904	NM_000075.3	24	cGt/cTt	2/8	1	2	FACETS	0.389	0.349	0.431	0.389	0.349	0.431	SUBCLONAL	1	TRUE	1	0.555785185714983	2		573	1065	SUCCESS
ALK	238	MSKCC	GRCh37	2	29430080	29430080	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	57	508	0	ENST00000389048.3:c.3895G>C	p.Glu1299Gln	p.E1299Q	ENST00000389048	NM_004304.4	1299	Gag/Cag	26/29	1	2	FACETS	0.208	0.177	0.241	0.208	0.177	0.241	SUBCLONAL	1	TRUE	1	0.555785185714983	2		508	987	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162747	47162747	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	28	289	0	ENST00000409792.3:c.3379C>G	p.Gln1127Glu	p.Q1127E	ENST00000409792	NM_014159.6	1127	Caa/Gaa	3/21	0.535711514578288	1	FACETS	0.185	0.147	0.227	0.185	0.147	0.227	SUBCLONAL	1	TRUE	0	0.555785185714983	1		289	394	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72842091	72842091	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	64	256	0	ENST00000325599.8:c.1157A>G	p.Tyr386Cys	p.Y386C	ENST00000325599	NM_018130.2	386	tAc/tGc	10/11	NA	2	FACETS	0.29	0.25	0.333			1	INDETERMINATE	1	TRUE	NA	0.555785185714983	2		256	795	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187629939	187629939	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	58	330	0	ENST00000441802.2:c.1043C>G	p.Ser348Cys	p.S348C	ENST00000441802	NM_005245.3	348	tCt/tGt	2/27	0.125285524625805	3	FACETS	0.299	0.256	0.346	0.15	0.128	0.173	INDETERMINATE	1	TRUE	1	0.555785185714983	3		330	892	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168743	32168743	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1299	670	553	0	ENST00000375023.3:c.4180C>A	p.Pro1394Thr	p.P1394T	ENST00000375023	NM_004557.3	1394	Cct/Act	23/30	0.555785185714983	5	FACETS	1	0.993	1	0.449	0.432	0.466	CLONAL	2	TRUE	0	0.555785185714983	5		553	1969	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469983	157469983	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	96	303	0	ENST00000346085.5:c.2777A>T	p.Gln926Leu	p.Q926L	ENST00000346085	NM_020732.3	926	cAg/cTg	9/20	0.125285524625805	3	FACETS	0.509	0.453	0.569	0.255	0.226	0.285	INDETERMINATE	1	TRUE	1	0.555785185714983	3		303	867	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860679	151860679	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1219	87	454	0	ENST00000262189.6:c.9983G>C	p.Arg3328Thr	p.R3328T	ENST00000262189	NM_170606.2	3328	aGa/aCa	43/59	0.125285524625805	3	FACETS	0.306	0.27	0.346	0.153	0.135	0.173	INDETERMINATE	1	TRUE	1	0.555785185714983	3		454	1306	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456696	32456696	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1392405207	NA	P-0010130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	42	172	0	ENST00000332351.3:c.196C>A	p.Pro66Thr	p.P66T	ENST00000332351	NM_024426.4	66	Ccg/Acg	1/10	1	2	FACETS	0.24	0.2	0.285	0.24	0.2	0.285	SUBCLONAL	1	TRUE	1	0.555785185714983	2		172	630	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95590642	95590642	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1196	63	594	0	ENST00000393063.1:c.1267G>C	p.Glu423Gln	p.E423Q	ENST00000393063	NM_030621.3	423	Gaa/Caa	9/28	1	2	FACETS	0.18	0.155	0.208	0.18	0.155	0.208	SUBCLONAL	1	TRUE	1	0.555785185714983	2		594	1259	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67662454	67662454	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	108	405	0	ENST00000264010.4:c.1700G>C	p.Arg567Pro	p.R567P	ENST00000264010	NM_006565.3	567	cGg/cCg	9/12	0.125285524625805	3	FACETS	0.404	0.361	0.45	0.202	0.18	0.225	INDETERMINATE	1	TRUE	1	0.555785185714983	3		405	1229	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991365	72991365	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1689	213	797	1	ENST00000268489.5:c.2680G>T	p.Asp894Tyr	p.D894Y	ENST00000268489	NM_006885.3	894	Gat/Tat	2/10	1	2	FACETS	0.403	0.373	0.435	0.403	0.373	0.435	SUBCLONAL	1	TRUE	1	0.555785185714983	2		798	1902	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38511517	38511517	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1416311365	NA	P-0010130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	96	286	0	ENST00000254066.5:c.1015C>T	p.Arg339Cys	p.R339C	ENST00000254066	NM_000964.3	339	Cgc/Tgc	8/9	1	2	FACETS	0.405	0.36	0.453	0.405	0.36	0.453	SUBCLONAL	1	TRUE	1	0.555785185714983	2		286	853	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2214500	2214500	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	122	444	0	ENST00000398665.3:c.1828G>T	p.Asp610Tyr	p.D610Y	ENST00000398665	NM_032482.2	610	Gac/Tac	19/28	1	2	FACETS	0.386	0.348	0.427	0.386	0.348	0.427	SUBCLONAL	1	TRUE	1	0.555785185714983	2		444	1136	SUCCESS
AR	367	MSKCC	GRCh37	X	66766439	66766439	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	73	245	0	ENST00000374690.3:c.1451C>A	p.Thr484Asn	p.T484N	ENST00000374690	NM_000044.3	484	aCt/aAt	1/8	0.384136440757541	1	FACETS	0.288	0.252	0.328	0.288	0.252	0.328	SUBCLONAL	1	TRUE	0	0.555785185714983	1		245	658	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76777855	76777855	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	29	409	0	ENST00000373344.5:c.6861G>T	p.Met2287Ile	p.M2287I	ENST00000373344	NM_000489.3	2287	atG/atT	32/35	0.384136440757541	1	FACETS	0.148	0.118	0.182	0.148	0.118	0.182	SUBCLONAL	1	TRUE	0	0.555785185714983	1		409	509	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35872017	35872019	+	inframe_deletion	In_Frame_Del	DEL	ACG	ACG	-	novel	NA	P-0010130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1922	171	741	0	ENST00000216797.5:c.594_596del	p.Ile198_Val199delinsMet	p.I198_V199delinsM	ENST00000216797	NM_020529.2	198	atCGTg/atg	4/6	1	2	FACETS	0.294	0.269	0.321	0.294	0.269	0.321	SUBCLONAL	1	TRUE	1	0.555785185714983	2		741	2093	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030513	47030513	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010130-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1593	158	615	0	ENST00000377604.3:c.292del	p.Arg98GlufsTer36	p.R98Efs*36	ENST00000377604	NM_001204468.1	96	ttC/tt	4/24	1	2	FACETS	0.325	0.296	0.355	0.325	0.296	0.355	SUBCLONAL	1	TRUE	1	0.555785185714983	2		615	1751	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	171	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.76	2		280	448	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0010142-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	287	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.978	0.924	1	0.978	0.924	1	CLONAL	1	TRUE	1	0.76	2		490	772	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	327	280	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		280	551	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579692	7579719	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GTCCTTACCAGAACGTTGTTTTCAGGAA	GTCCTTACCAGAACGTTGTTTTCAGGAA	-	novel	NA	P-0010148-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	107	801	540	0	ENST00000269305.4:c.77_96+8del		p.X26_splice	ENST00000269305	NM_001126112.2	26		3/11	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		540	908	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	53	60	280	0				ENST00000310581	NM_198253.2	-/1132			0.342902682393707	0	FACETS	0.681	0.61	0.752			1	SUBCLONAL	3	FALSE	0	0.341854374471151	0		280	113	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0010158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	243	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.341854374471151	5	FACETS	0.881	0.83	0.934	1	0.987	1	CLONAL	4	FALSE	2	0.341854374471151	5		490	610	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463237	25463237	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs760959622	NA	P-0010158-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	36	481	0	ENST00000264709.3:c.2256C>G	p.Phe752Leu	p.F752L	ENST00000264709	NM_175629.2	752	ttC/ttG	19/23	0.341854374471151	5	FACETS	0.649	0.533	0.779	0.216	0.177	0.26	SUBCLONAL	1	FALSE	2	0.341854374471151	5		481	491	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0010220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	106	176	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.201570984622434	3	FACETS	1	0.947	1			1	INDETERMINATE	3	TRUE	NA	0.37650912850006	3		176	214	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161781201	161781201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55830907	NA	P-0010220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	51	502	0	ENST00000366898.1:c.1204C>T	p.Arg402Cys	p.R402C	ENST00000366898	NM_004562.2	402	Cgt/Tgt	11/12	0.253785042283722	1	FACETS	0.398	0.338	0.464	0.398	0.338	0.464	SUBCLONAL	1	TRUE	0	0.37650912850006	1		502	552	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0010220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	283	417	1	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.381127214139462	3	FACETS	0.917	0.869	0.966			1	CLONAL	3	TRUE	NA	0.37650912850006	3		418	649	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158636926	158636926	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1329223493	NA	P-0010220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	346	681	3	ENST00000263640.3:c.254C>T	p.Pro85Leu	p.P85L	ENST00000263640	NM_001105.4	85	cCg/cTg	4/11	0.253785042283722	1	FACETS	1	0.958	1	1	0.996	1	CLONAL	2	TRUE	0	0.37650912850006	1		684	742	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412279	139412279	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	51	558	0	ENST00000277541.6:c.1366T>C	p.Cys456Arg	p.C456R	ENST00000277541	NM_017617.3	456	Tgc/Cgc	8/34	0.381127214139462	3	FACETS	0.444	0.376	0.519			1	SUBCLONAL	1	TRUE	NA	0.37650912850006	3		558	725	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592318	29592318	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1555619407	NA	P-0010220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	300	495	0	ENST00000356175.3:c.4733C>G	p.Ser1578Cys	p.S1578C	ENST00000356175	NM_000267.3	1578	tCc/tGc	35/57	0.37650912850006	6	FACETS	1	0.988	1	0.785	0.739	0.832	CLONAL	2	TRUE	3	0.37650912850006	6		495	1186	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266861	18266861	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010220-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	21	189	0	ENST00000222254.8:c.172C>A	p.Pro58Thr	p.P58T	ENST00000222254	NM_005027.3	58	Ccc/Acc	2/16	0.381127214139462	4	FACETS	0.394	0.302	0.5			1	SUBCLONAL	1	TRUE	NA	0.37650912850006	4		189	390	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	208	280	0				ENST00000310581	NM_198253.2	-/1132			0.701208755879243	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.701208755879243	1		280	342	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0010232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1279	462	558	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.701208755879243	3	FACETS	1	0.969	1	0.511	0.487	0.536	CLONAL	1	TRUE	1	0.701208755879243	3		558	1741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577535	7577535	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782329	NA	P-0010232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	368	426	0	ENST00000269305.4:c.746G>C	p.Arg249Thr	p.R249T	ENST00000269305	NM_001126112.2	249	aGg/aCg	7/11	0.701208755879243	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.701208755879243	1		426	672	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609673	28609673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	360	460	0	ENST00000241453.7:c.1556C>T	p.Ser519Phe	p.S519F	ENST00000241453	NM_004119.2	519	tCc/tTc	12/24	0.701208755879243	1	FACETS	0.946	0.904	0.987	0.946	0.904	0.987	CLONAL	1	TRUE	0	0.701208755879243	1		460	705	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702588	52702588	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	497	416	1	ENST00000394830.3:c.310G>T	p.Glu104Ter	p.E104*	ENST00000394830	NM_018313.4	104	Gaa/Taa	4/30	0.701208755879243	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.701208755879243	1		417	869	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99169254	99169254	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	373	549	0	ENST00000074304.5:c.1184C>T	p.Ser395Leu	p.S395L	ENST00000074304	NM_001134224.1	395	tCa/tTa	15/26	1	2	FACETS	0.932	0.886	0.98	0.932	0.886	0.98	CLONAL	1	TRUE	1	0.701208755879243	2		549	1141	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89391126	89391126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	400	394	1	ENST00000336596.2:c.1192G>A	p.Asp398Asn	p.D398N	ENST00000336596	NM_005233.5	398	Gac/Aac	5/17	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.701208755879243	2		395	1091	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131973805	131973805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507179	NA	P-0010232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	419	387	0	ENST00000265335.6:c.3508G>A	p.Asp1170Asn	p.D1170N	ENST00000265335		1170	Gat/Aat	23/25	0.701208755879243	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.701208755879243	1		387	720	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135786061	135786061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764150061	NA	P-0010232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	345	409	0	ENST00000298552.3:c.1160C>T	p.Pro387Leu	p.P387L	ENST00000298552	NM_001162426.1	387	cCt/cTt	12/23	0.701208755879243	1	FACETS	0.967	0.924	1	0.967	0.924	1	CLONAL	1	TRUE	0	0.701208755879243	1		409	661	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200309	67200309	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0010232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	243	341	0	ENST00000312629.5:c.616+1G>T		p.X206_splice	ENST00000312629	NM_003952.2	206			0.701208755879243	1	FACETS	0.958	0.907	1	0.958	0.907	1	CLONAL	1	TRUE	0	0.701208755879243	1		341	470	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495016	56495016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776728303	NA	P-0010232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	175	415	0	ENST00000267101.3:c.3373C>T	p.Arg1125Trp	p.R1125W	ENST00000267101	NM_001982.3	1125	Cgg/Tgg	27/28	1	2	FACETS	0.453	0.416	0.491	0.453	0.416	0.491	SUBCLONAL	1	TRUE	1	0.701208755879243	2		415	1102	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058975	42058975	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1122	571	651	1	ENST00000219905.7:c.8695C>T	p.Pro2899Ser	p.P2899S	ENST00000219905	NM_001164273.1	2899	Ccc/Tcc	24/24	1	2	FACETS	0.962	0.923	1	0.962	0.923	1	CLONAL	1	TRUE	1	0.701208755879243	2		652	1693	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128249	30128249	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	573	698	0	ENST00000263025.4:c.983C>T	p.Pro328Leu	p.P328L	ENST00000263025	NM_002746.2	328	cCc/cTc	7/9	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.701208755879243	2		698	1559	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352280	70352280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	605	330	0	ENST00000374080.3:c.4307C>T	p.Pro1436Leu	p.P1436L	ENST00000374080		1436	cCc/cTc	31/45	1	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.701208755879243	1		330	826	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158401	26158402	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0010232-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	318	339	0	ENST00000289316.2:c.4_5delinsTT	p.Pro2Phe	p.P2F	ENST00000289316	NM_138720.2	2	CCt/TTt	1/2	1	2	FACETS	0.916	0.866	0.967	0.916	0.866	0.967	CLONAL	1	TRUE	1	0.701208755879243	2		339	990	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	122	280	0				ENST00000310581	NM_198253.2	-/1132			0.575794376328602	2	FACETS	0.936	0.88	0.989	0.936	0.88	0.989	CLONAL	2	TRUE	0	0.753781476554006	2		280	173	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528489	29528489	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764079291	NA	P-0010249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	289	637	0	ENST00000356175.3:c.1246C>T	p.Arg416Ter	p.R416*	ENST00000356175	NM_000267.3	416	Cga/Tga	11/57	0.363571978453942	4	FACETS	1	0.979	1	0.544	0.511	0.577	INDETERMINATE	1	TRUE	2	0.753781476554006	4		637	1237	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0010249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	199	467	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.47916435840621	3	FACETS	1	0.968	1	0.535	0.498	0.574	CLONAL	1	TRUE	1	0.753781476554006	3		467	679	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258745	115258745	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121434595	NA	P-0010249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	681	370	0	ENST00000369535.4:c.37G>T	p.Gly13Cys	p.G13C	ENST00000369535	NM_002524.4	13	Ggt/Tgt	2/7	0.753781476554006	4	FACETS	0.997	0.969	1	0.997	0.969	1	CLONAL	3	TRUE	1	0.753781476554006	4		370	1060	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295672	212295672	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0010249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	334	467	0	ENST00000342788.4:c.2641A>T	p.Lys881Ter	p.K881*	ENST00000342788	NM_005235.2	881	Aag/Tag	21/28	0.47916435840621	3	FACETS	0.803	0.764	0.842	0.803	0.764	0.842	CLONAL	2	TRUE	1	0.753781476554006	3		467	760	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266098	41266098	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913396	NA	P-0010249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	290	489	0	ENST00000349496.5:c.95A>T	p.Asp32Val	p.D32V	ENST00000349496	NM_001904.3	32	gAc/gTc	3/15	0.718594152537741	3	FACETS	1	0.98	1	0.543	0.511	0.575	CLONAL	1	TRUE	1	0.753781476554006	3		489	976	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119545685	119545685	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	372	320	0	ENST00000316626.5:c.1252C>A	p.Arg418Ser	p.R418S	ENST00000316626		418	Cgt/Agt	12/12	0.718594152537741	3	FACETS	0.905	0.865	0.945	0.905	0.865	0.945	CLONAL	2	TRUE	1	0.753781476554006	3		320	751	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876293	35876293	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	48	392	0	ENST00000303115.3:c.1085G>A	p.Gly362Glu	p.G362E	ENST00000303115	NM_002185.3	362	gGa/gAa	8/8	0.575794376328602	2	FACETS	0.239	0.202	0.281	0.12	0.101	0.141	SUBCLONAL	1	TRUE	0	0.753781476554006	2		392	532	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964510	93964510	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1435219791	NA	P-0010249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	62	560	0	ENST00000369303.4:c.2387G>A	p.Gly796Glu	p.G796E	ENST00000369303	NM_004440.3	796	gGa/gAa	14/17	0.484812075417306	3	FACETS	0.279	0.24	0.321	0.093	0.08	0.107	SUBCLONAL	1	TRUE	0	0.753781476554006	3		560	813	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974338	93974338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	707	663	1	ENST00000369303.4:c.1716G>A	p.Met572Ile	p.M572I	ENST00000369303	NM_004440.3	572	atG/atA	8/17	0.484812075417306	3	FACETS	1	0.997	1	0.829	0.808	0.85	CLONAL	2	TRUE	0	0.753781476554006	3		664	1038	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152420081	152420081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	61	401	0	ENST00000206249.3:c.1768G>A	p.Gly590Ser	p.G590S	ENST00000206249	NM_000125.3	590	Ggt/Agt	8/8	0.484812075417306	3	FACETS	0.365	0.314	0.42	0.122	0.104	0.14	SUBCLONAL	1	TRUE	0	0.753781476554006	3		401	611	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971207	21971208	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0010249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	79	108	0	ENST00000304494.5:c.151-1_151delinsAA		p.X51_splice	ENST00000304494	NM_000077.4	51		2/3	0.753781476554006	2	FACETS	0.866	0.797	0.933	0.866	0.797	0.933	CLONAL	2	TRUE	0	0.753781476554006	2		108	121	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610581	81610581	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764711377	NA	P-0010249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	316	491	1	ENST00000298171.2:c.2179G>A	p.Glu727Lys	p.E727K	ENST00000298171	NM_000369.2	727	Gag/Aag	10/10	1	2	FACETS	0.992	0.94	1	0.992	0.94	1	CLONAL	1	TRUE	1	0.753781476554006	2		492	845	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88428957	88428957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	249	553	0	ENST00000360948.2:c.2143C>T	p.Pro715Ser	p.P715S	ENST00000360948	NM_001012338.2	715	Cca/Tca	17/19	0.750781858202759	3	FACETS	1	0.978	1	0.547	0.512	0.582	CLONAL	1	TRUE	1	0.753781476554006	3		553	832	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312713	91312713	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1279814185	NA	P-0010249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	666	583	0	ENST00000355112.3:c.2452C>T	p.Arg818Cys	p.R818C	ENST00000355112	NM_000057.2	818	Cgc/Tgc	12/22	0.750781858202759	3	FACETS	0.979	0.948	1	0.979	0.948	1	CLONAL	2	TRUE	1	0.753781476554006	3		583	1243	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663730	29663730	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1555534677	NA	P-0010249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	585	547	0	ENST00000356175.3:c.6162G>A	p.Trp2054Ter	p.W2054*	ENST00000356175	NM_000267.3	2054	tgG/tgA	41/57	0.363571978453942	4	FACETS	0.838	0.81	0.866	1	0.996	1	INDETERMINATE	3	TRUE	2	0.753781476554006	4		547	1083	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234556	41234556	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs80356989	NA	P-0010249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	530	515	0	ENST00000357654.3:c.4222C>T	p.Gln1408Ter	p.Q1408*	ENST00000357654	NM_007294.3	1408	Cag/Tag	12/23	0.598702812809421	3	FACETS	0.983	0.948	1			1	CLONAL	2	TRUE	NA	0.753781476554006	3		515	985	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827922	40827922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	263	503	1	ENST00000373198.4:c.2506G>A	p.Asp836Asn	p.D836N	ENST00000373198	NM_133170.3	836	Gat/Aat	17/32	0.750781858202759	3	FACETS	0.839	0.786	0.894	0.42	0.393	0.447	CLONAL	1	TRUE	1	0.753781476554006	3		504	1145	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891508	76891508	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1557107880	NA	P-0010249-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	445	365	0	ENST00000373344.5:c.4597A>G	p.Ile1533Val	p.I1533V	ENST00000373344	NM_000489.3	1533	Ata/Gta	16/35	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.753781476554006	1		365	573	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0010348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	125	414	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.638039050169703	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.638039050169703	1		414	240	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128200058	128200058	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	274	582	2	ENST00000341105.2:c.1247A>T	p.Glu416Val	p.E416V	ENST00000341105	NM_032638.4	416	gAg/gTg	6/6	1	2	FACETS	0.975	0.917	1	0.975	0.917	1	CLONAL	1	TRUE	1	0.638039050169703	2		584	881	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656330	18656330	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	118	425	0	ENST00000266497.5:c.3009C>G	p.His1003Gln	p.H1003Q	ENST00000266497		1003	caC/caG	21/31	0.211350925989794	3	FACETS	1	0.941	1	0.525	0.476	0.575	INDETERMINATE	1	TRUE	1	0.638039050169703	3		425	465	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855833	45855833	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	87	527	0	ENST00000391945.4:c.1977C>G	p.His659Gln	p.H659Q	ENST00000391945	NM_000400.3	659	caC/caG	21/23	0.638039050169703	1	FACETS	0.339	0.3	0.38	0.339	0.3	0.38	SUBCLONAL	1	TRUE	0	0.638039050169703	1		527	548	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165737	185165794	+	splice_donor_variant,intron_variant	Splice_Site	DEL	TGAGTGGCGCCACCAGTTGTGCCAACTAAAAAGCCTTTTCCCACTTTCGCCCTATTAG	TGAGTGGCGCCACCAGTTGTGCCAACTAAAAAGCCTTTTCCCACTTTCGCCCTATTAG	GC	novel	NA	P-0010348-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	147	324	0	ENST00000265026.3:c.1010+2_1010+59delinsGC		p.X337_splice	ENST00000265026	NM_004721.4	337			0.638039050169703	3	FACETS	1	0.98	1	0.607	0.557	0.657	CLONAL	1	TRUE	1	0.638039050169703	3		324	501	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	83	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.998	0.882	1	0.998	0.882	1	CLONAL	1	TRUE	1	0.283423194569449	2		280	587	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0010374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	110	413	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.283423194569449	1	FACETS	0.909	0.817	1	0.909	0.817	1	CLONAL	1	TRUE	0	0.283423194569449	1		413	733	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393656	139393656	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196509879	NA	P-0010374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	109	333	0	ENST00000277541.6:c.5990C>T	p.Thr1997Met	p.T1997M	ENST00000277541	NM_017617.3	1997	aCg/aTg	32/34	1	2	FACETS	0.984	0.883	1	0.984	0.883	1	CLONAL	1	TRUE	1	0.283423194569449	2		333	782	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876397	35876397	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	85	281	0	ENST00000303115.3:c.1189G>A	p.Gly397Arg	p.G397R	ENST00000303115	NM_002185.3	397	Ggg/Agg	8/8	1	2	FACETS	0.983	0.87	1	0.983	0.87	1	CLONAL	1	TRUE	1	0.283423194569449	2		281	610	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961116	55961116	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748637684	NA	P-0010374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	128	412	0	ENST00000263923.4:c.2824G>A	p.Gly942Arg	p.G942R	ENST00000263923	NM_002253.2	942	Ggg/Agg	21/30	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.283423194569449	2		412	807	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955452	48955452	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0010374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	120	397	0	ENST00000267163.4:c.1568T>A	p.Leu523Ter	p.L523*	ENST00000267163	NM_000321.2	523	tTa/tAa	17/27	0.283423194569449	1	FACETS	0.917	0.828	1	0.917	0.828	1	CLONAL	1	TRUE	0	0.283423194569449	1		397	793	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556955	29556955	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555614455	NA	P-0010374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	27	130	0	ENST00000356175.3:c.2953C>T	p.Gln985Ter	p.Q985*	ENST00000356175	NM_000267.3	985	Caa/Taa	22/57	0.283423194569449	1	FACETS	0.592	0.473	0.729	0.592	0.473	0.729	SUBCLONAL	1	TRUE	0	0.283423194569449	1		130	276	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191755	123191759	+	frameshift_variant	Frame_Shift_Del	DEL	GAAAA	GAAAA	-	novel	NA	P-0010374-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1716	275	854	0	ENST00000218089.9:c.1347_1351del	p.Arg451LysfsTer10	p.R451Kfs*10	ENST00000218089	NM_001042749.1	448	atGAAAAga/atga	15/35	1	2	FACETS	0.975	0.911	1	0.975	0.911	1	CLONAL	1	TRUE	1	0.283423194569449	2		854	1991	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0010380-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	115	464	0				ENST00000310581	NM_198253.2	-/1132			0.184506291381363	3	FACETS	1	0.981	1	0.669	0.607	0.733	INDETERMINATE	1	TRUE	1	0.52749013294196	3		464	412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121912651	NA	P-0010380-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	317	505	1	ENST00000269305.4:c.742C>T	p.Arg248Trp	p.R248W	ENST00000269305	NM_001126112.2	248	Cgg/Tgg	7/11	0.52749013294196	2	FACETS	0.995	0.949	1	0.995	0.949	1	CLONAL	2	TRUE	0	0.52749013294196	2		506	604	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717756	89717756	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs730882131	NA	P-0010380-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	186	198	0	ENST00000371953.3:c.781C>T	p.Gln261Ter	p.Q261*	ENST00000371953	NM_000314.4	261	Cag/Tag	7/9	0.509676392339261	2	FACETS	0.909	0.852	0.966	0.909	0.852	0.966	CLONAL	2	TRUE	0	0.52749013294196	2		198	388	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161747	47161747	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010380-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	200	669	0	ENST00000409792.3:c.4379G>C	p.Trp1460Ser	p.W1460S	ENST00000409792	NM_014159.6	1460	tGg/tCg	3/21	0.13488673614624	3	FACETS	0.995	0.922	1	0.498	0.461	0.536	INDETERMINATE	1	TRUE	1	0.52749013294196	3		669	963	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940402	49940402	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760399844	NA	P-0010380-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	273	947	0	ENST00000296474.3:c.641G>A	p.Arg214His	p.R214H	ENST00000296474	NM_002447.2	214	cGc/cAc	1/20	0.13488673614624	3	FACETS	1	0.987	1	0.592	0.555	0.629	INDETERMINATE	1	TRUE	1	0.52749013294196	3		947	1105	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039505	49039505	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs764754259	NA	P-0010380-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	258	384	0	ENST00000267163.4:c.2489+1G>A		p.X830_splice	ENST00000267163	NM_000321.2	830			0.509676392339261	2	FACETS	0.806	0.761	0.851	0.806	0.761	0.851	CLONAL	2	TRUE	0	0.52749013294196	2		384	607	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874358	76874358	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010380-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	653	411	0	ENST00000373344.5:c.5364G>T	p.Gln1788His	p.Q1788H	ENST00000373344	NM_000489.3	1788	caG/caT	21/35	0.490920100980451	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.52749013294196	2		411	1042	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950636	38950636	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010380-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1197	139	783	0	ENST00000357387.3:c.3314C>G	p.Pro1105Arg	p.P1105R	ENST00000357387	NM_152756.3	1105	cCt/cGt	31/38	0.184506291381363	3	FACETS	0.499	0.452	0.547	0.249	0.226	0.274	INDETERMINATE	1	TRUE	1	0.52749013294196	3		783	1336	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	41	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.191413041524803	2		280	402	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374921	118374921	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	40	899	0	ENST00000534358.1:c.8314A>G	p.Lys2772Glu	p.K2772E	ENST00000534358	NM_005933.3	2772	Aag/Gag	27/36	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.191413041524803	2		899	295	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45374979	45374980	+	stop_gained,inframe_insertion	Nonsense_Mutation	INS	-	-	TAC	novel	NA	P-0010388-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	12	605	0	ENST00000262160.6:c.863_864insGTA	p.Glu288_Thr289insTer	p.E288_T289ins*	ENST00000262160	NM_005901.5	288	gaa/gaGTAa	8/11	1	2	FACETS	0.609	0.428	0.831	0.609	0.428	0.831	SUBCLONAL	1	TRUE	1	0.191413041524803	2		605	206	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	72	163	280	0				ENST00000310581	NM_198253.2	-/1132			0.749305410692942	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.749305410692942	1		280	235	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138665163	138665163	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519865	NA	P-0010401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	416	354	0	ENST00000330315.3:c.402C>G	p.Cys134Trp	p.C134W	ENST00000330315	NM_023067.3	134	tgC/tgG	1/1	0.746582248612108	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.749305410692942	2		354	553	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965716	25965717	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0010401-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	281	425	0	ENST00000435504.4:c.3489dup	p.Thr1164TyrfsTer4	p.T1164Yfs*4	ENST00000435504		1163	-/T	13/13	1	2	FACETS	0.828	0.78	0.877	0.828	0.78	0.877	CLONAL	1	TRUE	1	0.749305410692942	2		425	906	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	128	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.595990145009712	2		280	407	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	110	354	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.595990145009712	2		354	295	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	66	157	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.595990145009712	2		157	216	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069154	5069154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764423560	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	138	428	1	ENST00000381652.3:c.1459C>T	p.Arg487Cys	p.R487C	ENST00000381652	NM_004972.3	487	Cgc/Tgc	11/25	1	2	FACETS	0.936	0.857	1	0.936	0.857	1	CLONAL	1	TRUE	1	0.595990145009712	2		429	495	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	188	544	7	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.595990145009712	2		551	630	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445525	49445526	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs770315135	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	100	310	0	ENST00000301067.7:c.1940dup	p.Pro648ThrfsTer2	p.P648Tfs*2	ENST00000301067	NM_003482.3	647	cca/ccCa	10/54	1	2	FACETS	0.594	0.532	0.66	0.594	0.532	0.66	SUBCLONAL	1	TRUE	1	0.595990145009712	2		310	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	295	417	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.595990145009712	2		417	859	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807889	1807889	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs78311289	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	215	370	0	ENST00000260795.2:c.1948A>G	p.Lys650Glu	p.K650E	ENST00000260795		650	Aag/Gag	13/17	1	2	FACETS	0.995	0.929	1	0.995	0.929	1	CLONAL	1	TRUE	1	0.595990145009712	2		370	725	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	324	589	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	0.365987755059793	3	FACETS	0.909	0.864	0.955	0.909	0.864	0.955	CLONAL	2	TRUE	1	0.595990145009712	3		589	776	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298764	15298764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	273	361	1	ENST00000263388.2:c.1534G>A	p.Ala512Thr	p.A512T	ENST00000263388	NM_000435.2	512	Gcc/Acc	10/33	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.595990145009712	2		362	779	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416497	49416497	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs566674356	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	321	406	0	ENST00000301067.7:c.16214G>A	p.Arg5405His	p.R5405H	ENST00000301067	NM_003482.3	5405	cGt/cAt	51/54	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.595990145009712	2		406	836	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475061	40475063	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	448	772	0	ENST00000264657.5:c.1847_1849del	p.Glu616del	p.E616del	ENST00000264657	NM_139276.2	616	gAAGga/gga	20/24	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.595990145009712	2		772	1453	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636818	8636818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146973770	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	291	443	0	ENST00000356435.5:c.91G>A	p.Val31Ile	p.V31I	ENST00000356435		31	Gtt/Att	2/35	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.595990145009712	2		443	889	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348566	89348568	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs753054998	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1448	592	1109	4	ENST00000301030.4:c.4382_4384del	p.Lys1461del	p.K1461del	ENST00000301030	NM_001256183.1	1461	aAGAga/aga	9/13	1	2	FACETS	0.974	0.934	1	0.974	0.934	1	CLONAL	1	TRUE	1	0.595990145009712	2		1113	2040	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132861	64132861	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751393577	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	211	593	3	ENST00000334205.4:c.995C>T	p.Ala332Val	p.A332V	ENST00000334205	NM_003942.2	332	gCg/gTg	9/17	1	2	FACETS	0.632	0.586	0.68	0.632	0.586	0.68	SUBCLONAL	1	TRUE	1	0.595990145009712	2		596	1120	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494650	2494650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762829374	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	237	426	1	ENST00000355716.4:c.790G>A	p.Val264Ile	p.V264I	ENST00000355716	NM_003820.2	264	Gtc/Atc	8/8	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.595990145009712	2		427	754	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346157	89346158	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs878855327	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	79	262	0	ENST00000301030.4:c.6792dup	p.Ala2265ArgfsTer8	p.A2265Rfs*8	ENST00000301030	NM_001256183.1	2264	-/C	9/13	1	2	FACETS	0.548	0.483	0.617	0.548	0.483	0.617	SUBCLONAL	1	TRUE	1	0.595990145009712	2		262	484	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693919	47693919	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	160	603	0	ENST00000233146.2:c.1633C>T	p.Gln545Ter	p.Q545*	ENST00000233146	NM_000251.2	545	Cag/Tag	10/16	1	2	FACETS	0.787	0.724	0.853	0.787	0.724	0.853	SUBCLONAL	1	TRUE	1	0.595990145009712	2		603	682	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363490	40363490	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	308	415	0	ENST00000397332.2:c.739C>G	p.Arg247Gly	p.R247G	ENST00000397332	NM_001033082.2	247	Cgt/Ggt	3/3	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.595990145009712	2		415	913	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796900	45796900	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs767747402	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	241	404	0	ENST00000450313.1:c.1430C>T	p.Thr477Met	p.T477M	ENST00000450313	NM_012222.2	477	aCg/aTg	14/16	1	2	FACETS	0.914	0.855	0.974	0.914	0.855	0.974	CLONAL	1	TRUE	1	0.595990145009712	2		404	885	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78426104	78426104	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	155	442	0	ENST00000370768.2:c.1421C>A	p.Pro474His	p.P474H	ENST00000370768	NM_003902.3	474	cCt/cAt	15/20	1	2	FACETS	0.662	0.606	0.72	0.662	0.606	0.72	SUBCLONAL	1	TRUE	1	0.595990145009712	2		442	786	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461130	120461130	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	178	306	0	ENST00000256646.2:c.5828A>G	p.Asp1943Gly	p.D1943G	ENST00000256646	NM_024408.3	1943	gAt/gGt	32/34	1	2	FACETS	0.878	0.812	0.947	0.878	0.812	0.947	CLONAL	1	TRUE	1	0.595990145009712	2		306	680	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849917	156849917	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	208	384	0	ENST00000524377.1:c.2173A>G	p.Lys725Glu	p.K725E	ENST00000524377	NM_002529.3	725	Aag/Gag	16/17	1	2	FACETS	0.864	0.804	0.926	0.864	0.804	0.926	CLONAL	1	TRUE	1	0.595990145009712	2		384	808	SUCCESS
COP1	64326	MSKCC	GRCh37	1	175958588	175958588	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1352317190	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	180	429	0	ENST00000367669.3:c.1757G>A	p.Arg586His	p.R586H	ENST00000367669	NM_022457.5	586	cGt/cAt	16/20	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.595990145009712	2		429	599	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612818	228612818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143639671	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	663	848	0	ENST00000366696.1:c.209G>A	p.Arg70Gln	p.R70Q	ENST00000366696	NM_003493.2	70	cGg/cAg	1/1	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.595990145009712	2		848	1694	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693913	47693913	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	175	606	0	ENST00000233146.2:c.1627G>T	p.Asp543Tyr	p.D543Y	ENST00000233146	NM_000251.2	543	Gat/Tat	10/16	1	2	FACETS	0.826	0.763	0.891	0.826	0.763	0.891	CLONAL	1	TRUE	1	0.595990145009712	2		606	711	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198260807	198260807	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	97	367	0	ENST00000335508.6:c.3512C>T	p.Pro1171Leu	p.P1171L	ENST00000335508	NM_012433.2	1171	cCg/cTg	23/25	1	2	FACETS	0.782	0.702	0.867	0.782	0.702	0.867	SUBCLONAL	1	TRUE	1	0.595990145009712	2		367	416	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47155453	47155453	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752011468	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	204	447	0	ENST00000409792.3:c.4628G>A	p.Arg1543Gln	p.R1543Q	ENST00000409792	NM_014159.6	1543	cGg/cAg	5/21	1	2	FACETS	0.896	0.833	0.961	0.896	0.833	0.961	CLONAL	1	TRUE	1	0.595990145009712	2		447	764	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138375112	138375112	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138462760	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	294	281	0	ENST00000289153.2:c.2947C>T	p.Arg983Cys	p.R983C	ENST00000289153	NM_006219.2	983	Cgc/Tgc	21/22	0.365987755059793	3	FACETS	0.967	0.917	1	0.967	0.917	1	CLONAL	2	TRUE	1	0.595990145009712	3		281	662	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539177	187539177	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	225	441	0	ENST00000441802.2:c.8563G>T	p.Glu2855Ter	p.E2855*	ENST00000441802	NM_005245.3	2855	Gaa/Taa	10/27	1	2	FACETS	0.997	0.932	1	0.997	0.932	1	CLONAL	1	TRUE	1	0.595990145009712	2		441	757	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542357	187542357	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs769432838	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	158	393	0	ENST00000441802.2:c.5383C>T	p.Arg1795Ter	p.R1795*	ENST00000441802	NM_005245.3	1795	Cga/Tga	10/27	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.595990145009712	2		393	514	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953827	131953827	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104895051	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	161	406	0	ENST00000265335.6:c.3230G>A	p.Arg1077Gln	p.R1077Q	ENST00000265335		1077	cGa/cAa	21/25	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.595990145009712	2		406	524	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457730	149457730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	241	411	0	ENST00000286301.3:c.674C>T	p.Ser225Leu	p.S225L	ENST00000286301	NM_005211.3	225	tCa/tTa	5/22	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.595990145009712	2		411	742	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149516594	149516594	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150173975	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	275	340	1	ENST00000261799.4:c.17C>T	p.Ala6Val	p.A6V	ENST00000261799	NM_002609.3	6	gCg/gTg	2/23	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.595990145009712	2		341	776	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839952	27839952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777522650	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1296	298	1053	2	ENST00000328488.2:c.142G>A	p.Ala48Thr	p.A48T	ENST00000328488	NM_003533.2	48	Gcc/Acc	1/1	1	2	FACETS	0.627	0.589	0.667	0.627	0.589	0.667	SUBCLONAL	1	TRUE	1	0.595990145009712	2		1055	1594	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839979	27839979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	263	924	0	ENST00000328488.2:c.115C>T	p.Pro39Ser	p.P39S	ENST00000328488	NM_003533.2	39	Ccc/Tcc	1/1	1	2	FACETS	0.603	0.564	0.644	0.603	0.564	0.644	SUBCLONAL	1	TRUE	1	0.595990145009712	2		924	1463	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004255	150004255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1314146200	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	258	690	0	ENST00000253339.5:c.1970G>A	p.Arg657His	p.R657H	ENST00000253339		657	cGt/cAt	3/7	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.595990145009712	2		690	754	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004463	150004463	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	182	587	0	ENST00000253339.5:c.1762C>T	p.Pro588Ser	p.P588S	ENST00000253339		588	Ccc/Tcc	3/7	1	2	FACETS	0.581	0.535	0.629	0.581	0.535	0.629	SUBCLONAL	1	TRUE	1	0.595990145009712	2		587	1051	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753187	128753187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779123478	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	143	221	1	ENST00000377970.2:c.1348C>T	p.Arg450Trp	p.R450W	ENST00000377970	NM_002467.4	450	Cgg/Tgg	3/3	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.595990145009712	2		222	437	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742477	145742477	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	80	336	0	ENST00000428558.2:c.311A>T	p.Asp104Val	p.D104V	ENST00000428558	NM_004260.3	104	gAc/gTc	4/22	1	2	FACETS	0.402	0.354	0.454	0.402	0.354	0.454	SUBCLONAL	1	TRUE	1	0.595990145009712	2		336	667	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139393659	139393659	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773137647	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	227	340	1	ENST00000277541.6:c.5987C>T	p.Thr1996Met	p.T1996M	ENST00000277541	NM_017617.3	1996	aCg/aTg	32/34	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.595990145009712	2		341	717	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395129	139395129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	384	527	0	ENST00000277541.6:c.5809C>T	p.Arg1937Cys	p.R1937C	ENST00000277541	NM_017617.3	1937	Cgc/Tgc	31/34	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.595990145009712	2		527	1154	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139814803	139814803	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1253	290	782	0	ENST00000247668.2:c.796T>C	p.Ser266Pro	p.S266P	ENST00000247668	NM_021138.3	266	Tca/Cca	8/11	1	2	FACETS	0.631	0.592	0.671	0.631	0.592	0.671	SUBCLONAL	1	TRUE	1	0.595990145009712	2		782	1543	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88635834	88635834	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759014147	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	165	524	0	ENST00000372037.3:c.59G>A	p.Arg20His	p.R20H	ENST00000372037	NM_004329.2	20	cGt/cAt	3/13	1	2	FACETS	0.926	0.854	1	0.926	0.854	1	CLONAL	1	TRUE	1	0.595990145009712	2		524	598	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417913	32417913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147241955	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	137	371	0	ENST00000332351.3:c.1139G>A	p.Arg380Gln	p.R380Q	ENST00000332351	NM_024426.4	380	cGg/cAg	7/10	1	2	FACETS	0.589	0.536	0.644	0.589	0.536	0.644	SUBCLONAL	1	TRUE	1	0.595990145009712	2		371	781	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446070	49446070	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201512665	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	406	607	3	ENST00000301067.7:c.1396C>T	p.Arg466Cys	p.R466C	ENST00000301067	NM_003482.3	466	Cgc/Tgc	10/54	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.595990145009712	2		610	1224	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50481161	50481161	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	300	484	1	ENST00000394963.4:c.547C>T	p.Arg183Ter	p.R183*	ENST00000394963	NM_003076.4	183	Cga/Tga	5/13	1	2	FACETS	0.985	0.929	1	0.985	0.929	1	CLONAL	1	TRUE	1	0.595990145009712	2		485	1022	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856400	111856400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	59	124	2	ENST00000341259.2:c.451G>A	p.Ala151Thr	p.A151T	ENST00000341259	NM_005475.2	151	Gcc/Acc	2/8	1	2	FACETS	0.629	0.544	0.719	0.629	0.544	0.719	SUBCLONAL	1	TRUE	1	0.595990145009712	2		126	315	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112536	115112536	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	227	367	0	ENST00000257566.3:c.1204G>A	p.Glu402Lys	p.E402K	ENST00000257566	NM_016569.3	402	Gag/Aag	7/8	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.595990145009712	2		367	759	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41021807	41021807	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555429623	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	424	561	2	ENST00000267868.3:c.749G>A	p.Arg250Gln	p.R250Q	ENST00000267868	NM_002875.4	250	cGg/cAg	8/10	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.595990145009712	2		563	1236	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457330	67457330	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	244	516	0	ENST00000327367.4:c.304G>A	p.Glu102Lys	p.E102K	ENST00000327367	NM_005902.3	102	Gag/Aag	2/9	1	2	FACETS	0.861	0.805	0.918	0.861	0.805	0.918	CLONAL	1	TRUE	1	0.595990145009712	2		516	951	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90634846	90634846	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	280	333	0	ENST00000330062.3:c.146C>T	p.Pro49Leu	p.P49L	ENST00000330062	NM_002168.2	49	cCc/cTc	2/11	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.595990145009712	2		333	776	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68842747	68842747	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	261	511	0	ENST00000261769.5:c.683A>G	p.Tyr228Cys	p.Y228C	ENST00000261769	NM_004360.3	228	tAc/tGc	5/16	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.595990145009712	2		511	823	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984651	72984651	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750714180	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	534	790	1	ENST00000268489.5:c.2933C>T	p.Ala978Val	p.A978V	ENST00000268489	NM_006885.3	978	gCg/gTg	3/10	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.595990145009712	2		791	1560	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271870	15271870	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528151296	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	93	168	1	ENST00000263388.2:c.6569C>T	p.Ala2190Val	p.A2190V	ENST00000263388	NM_000435.2	2190	gCg/gTg	33/33	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.595990145009712	2		169	296	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45855529	45855529	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141808167	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	366	539	0	ENST00000391945.4:c.2128G>A	p.Val710Met	p.V710M	ENST00000391945	NM_000400.3	710	Gtg/Atg	22/23	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.595990145009712	2		539	1105	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906838	50906838	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749611798	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	404	678	2	ENST00000440232.2:c.1226G>A	p.Arg409Gln	p.R409Q	ENST00000440232	NM_002691.3	409	cGg/cAg	10/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.595990145009712	2		680	1293	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919915	50919915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	362	566	2	ENST00000440232.2:c.3002G>A	p.Gly1001Asp	p.G1001D	ENST00000440232	NM_002691.3	1001	gGc/gAc	24/27	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.595990145009712	2		568	1127	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022377	31022377	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	99	237	0	ENST00000375687.4:c.1862C>T	p.Ala621Val	p.A621V	ENST00000375687	NM_015338.5	621	gCt/gTt	13/13	0.595990145009712	3	FACETS	0.876	0.786	0.972	0.438	0.393	0.486	CLONAL	1	TRUE	1	0.595990145009712	3		237	492	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023343	31023343	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	172	303	0	ENST00000375687.4:c.2828A>T	p.Asp943Val	p.D943V	ENST00000375687	NM_015338.5	943	gAt/gTt	13/13	0.595990145009712	3	FACETS	1	0.968	1	0.546	0.504	0.59	CLONAL	1	TRUE	1	0.595990145009712	3		303	686	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574866	41574866	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	200	364	0	ENST00000263253.7:c.7151A>G	p.Asn2384Ser	p.N2384S	ENST00000263253	NM_001429.3	2384	aAc/aGc	31/31	1	2	FACETS	0.913	0.849	0.979	0.913	0.849	0.979	CLONAL	1	TRUE	1	0.595990145009712	2		364	735	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030479	47030479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139829599	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	349	527	2	ENST00000377604.3:c.254G>A	p.Arg85Gln	p.R85Q	ENST00000377604	NM_001204468.1	85	cGg/cAg	4/24	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.595990145009712	2		529	1069	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045133	47045133	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	275	570	0	ENST00000377604.3:c.2374C>T	p.Arg792Trp	p.R792W	ENST00000377604	NM_001204468.1	792	Cgg/Tgg	21/24	1	2	FACETS	0.96	0.903	1	0.96	0.903	1	CLONAL	1	TRUE	1	0.595990145009712	2		570	961	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76764047	76764047	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	365	719	1	ENST00000373344.5:c.7261C>T	p.Gln2421Ter	p.Q2421*	ENST00000373344	NM_000489.3	2421	Cag/Tag	35/35	1	2	FACETS	0.92	0.871	0.969	0.92	0.871	0.969	CLONAL	1	TRUE	1	0.595990145009712	2		720	1332	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196255	108196256	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	130	302	0	ENST00000278616.4:c.6794dup	p.Lys2266GlnfsTer7	p.K2266Qfs*7	ENST00000278616	NM_000051.3	2264	act/acTt	46/63	1	2	FACETS	0.991	0.907	1	0.991	0.907	1	CLONAL	1	TRUE	1	0.595990145009712	2		302	440	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40362447	40362447	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	368	745	2	ENST00000293328.3:c.1749del	p.Lys583AsnfsTer16	p.K583Nfs*16	ENST00000293328	NM_012448.3	583	aaA/aa	14/19	1	2	FACETS	0.932	0.883	0.982	0.932	0.883	0.982	CLONAL	1	TRUE	1	0.595990145009712	2		747	1325	SUCCESS
YES1	7525	MSKCC	GRCh37	18	745962	745963	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	46	404	0	ENST00000314574.4:c.559_560del	p.Ser187Ter	p.S187*	ENST00000314574	NM_005433.3	187	AGt/t	5/12	0.419958812387178	1	FACETS	0.287	0.242	0.336	0.287	0.242	0.336	SUBCLONAL	1	TRUE	0	0.595990145009712	1		404	378	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572991	7572991	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	367	667	2	ENST00000269305.4:c.1118del	p.Lys373ArgfsTer49	p.K373Rfs*49	ENST00000269305	NM_001126112.2	373	aAg/ag	11/11	1	2	FACETS	0.965	0.915	1	0.965	0.915	1	CLONAL	1	TRUE	1	0.595990145009712	2		669	1276	SUCCESS
APC	324	MSKCC	GRCh37	5	112174413	112174414	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	rs1554084712	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	89	294	0	ENST00000257430.4:c.3123_3124del	p.Pro1043PhefsTer4	p.P1043Ffs*4	ENST00000257430	NM_000038.5	1041	cAA/c	16/16	1	2	FACETS	0.856	0.765	0.951	0.856	0.765	0.951	CLONAL	1	TRUE	1	0.595990145009712	2		294	349	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401764	139401765	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	290	430	0	ENST00000277541.6:c.3635dup	p.Thr1213HisfsTer7	p.T1213Hfs*7	ENST00000277541	NM_017617.3	1212	ggc/ggGc	22/34	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.595990145009712	2		430	900	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47672796	47672796	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	139	460	0	ENST00000233146.2:c.1386+1del		p.Q462fs	ENST00000233146	NM_000251.2	462	caG/ca	8/16	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.595990145009712	2		460	455	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620706	52620707	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	G	rs1236693676	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	58	170	0	ENST00000394830.3:c.3049-3dup		p.X1017_splice	ENST00000394830	NM_018313.4	1017			1	2	FACETS	0.708	0.613	0.809	0.708	0.613	0.809	SUBCLONAL	1	TRUE	1	0.595990145009712	2		170	275	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53224522	53224523	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0010420-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	417	735	0	ENST00000375401.3:c.3190_3191delinsAA	p.Gly1064Lys	p.G1064K	ENST00000375401	NM_004187.3	1064	GGg/AAg	21/26	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.595990145009712	2		735	1347	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	80	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.888	1	1	0.888	1	CLONAL	1	TRUE	1	0.4	2		280	399	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0010441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	117	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.93	0.841	1	0.93	0.841	1	CLONAL	1	TRUE	1	0.4	2		490	629	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14015913	14015913	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1555467298	NA	P-0010441-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	93	244	0	ENST00000311895.7:c.233T>C	p.Ile78Thr	p.I78T	ENST00000311895	NM_005236.2	78	aTa/aCa	2/11	1	2	FACETS	0.864	0.771	0.964	0.864	0.771	0.964	CLONAL	1	TRUE	1	0.4	2		244	538	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	62	280	0				ENST00000310581	NM_198253.2	-/1132			0.280254379498346	3	FACETS	1	0.948	1			1	CLONAL	1	TRUE	NA	0.441668346969993	3		280	291	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0010483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	81	263	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.813	0.719	0.913	0.813	0.719	0.913	CLONAL	1	TRUE	1	0.441668346969993	2		263	451	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259098	89259098	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010483-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	138	291	1	ENST00000336596.2:c.242G>T	p.Trp81Leu	p.W81L	ENST00000336596	NM_005233.5	81	tGg/tTg	3/17	1	2	FACETS	0.9	0.821	0.984	0.9	0.821	0.984	CLONAL	1	TRUE	1	0.441668346969993	2		292	694	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	51	280	0				ENST00000310581	NM_198253.2	-/1132			0.462911006469083	0	FACETS	0.65	0.57	0.731			1	SUBCLONAL	1	FALSE	0	0.574882490412981	0		280	116	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075194	16075194	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	85	315	0	ENST00000268712.3:c.358C>T	p.Gln120Ter	p.Q120*	ENST00000268712	NM_006311.3	120	Cag/Tag	4/46	NA	2	FACETS	0.665	0.59	0.744			1	INDETERMINATE	1	FALSE	NA	0.574882490412981	2		315	445	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0010491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	126	417	1	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.280457568606894	3	FACETS	0.788	0.722	0.856	0.525	0.481	0.571	INDETERMINATE	2	FALSE	0	0.574882490412981	3		418	358	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123220428	123220428	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	259	360	1	ENST00000218089.9:c.3085C>T	p.Gln1029Ter	p.Q1029*	ENST00000218089	NM_001042749.1	1029	Cag/Tag	30/35	0.366722399887847	2	FACETS	1	0.987	1			1	CLONAL	1	FALSE	NA	0.574882490412981	2		361	770	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0010491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	129	96	0	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	0.574882490412981	8	FACETS	0.941	0.871	1			1	CLONAL	5	FALSE	NA	0.574882490412981	8		96	260	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265579	198265579	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	255	463	0	ENST00000335508.6:c.2578G>A	p.Glu860Lys	p.E860K	ENST00000335508	NM_012433.2	860	Gaa/Aaa	18/25	0.423454726465171	5	FACETS	0.936	0.878	0.995			1	CLONAL	2	FALSE	NA	0.574882490412981	5		463	883	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226589926	226589926	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	68	200	0	ENST00000366794.5:c.275G>A	p.Gly92Glu	p.G92E	ENST00000366794	NM_001618.3	92	gGa/gAa	2/23	0.349626281816056	5	FACETS	1	0.963	1			1	CLONAL	1	FALSE	NA	0.574882490412981	5		200	345	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40500444	40500444	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1039	125	671	3	ENST00000264657.5:c.91C>T	p.Arg31Trp	p.R31W	ENST00000264657	NM_139276.2	31	Cgg/Tgg	2/24	0.423454726465171	5	FACETS	0.696	0.628	0.768			1	SUBCLONAL	1	FALSE	NA	0.574882490412981	5		674	1164	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918553	44918553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	306	310	0	ENST00000377967.4:c.1036C>T	p.Gln346Ter	p.Q346*	ENST00000377967	NM_021140.2	346	Caa/Taa	12/29	0.398655961250009	2	FACETS	1	0.993	1			1	CLONAL	1	FALSE	NA	0.574882490412981	2		310	782	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46724370	46724370	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs138566817	NA	P-0010491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	159	778	0	ENST00000371975.4:c.223C>T	p.Arg75Ter	p.R75*	ENST00000371975	NM_003579.3	75	Cga/Tga	4/18	0.382319497376936	4	FACETS	1	0.98	1			1	CLONAL	1	FALSE	NA	0.574882490412981	4		778	716	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944335	206944335	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	97	464	0	ENST00000423557.1:c.295G>T	p.Glu99Ter	p.E99*	ENST00000423557	NM_000572.2	99	Gag/Tag	3/5	0.399070735562112	5	FACETS	0.819	0.73	0.914	0.273	0.243	0.305	CLONAL	1	FALSE	2	0.574882490412981	5		464	767	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143185	30143185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1190182265	NA	P-0010491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	72	149	0	ENST00000389048.3:c.341C>T	p.Ser114Leu	p.S114L	ENST00000389048	NM_004304.4	114	tCa/tTa	1/29	0.566518709491389	2	FACETS	0.956	0.866	1	0.956	0.866	1	CLONAL	2	FALSE	0	0.574882490412981	2		149	131	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183655	10183655	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	78	505	0	ENST00000256474.2:c.124G>A	p.Glu42Lys	p.E42K	ENST00000256474	NM_000551.3	42	Gag/Aag	1/3	0.509884417440995	4	FACETS	0.518	0.454	0.587	0.259	0.227	0.294	SUBCLONAL	1	FALSE	2	0.574882490412981	4		505	825	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935554	49935554	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	264	973	0	ENST00000296474.3:c.1810G>A	p.Glu604Lys	p.E604K	ENST00000296474	NM_002447.2	604	Gag/Aag	5/20	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	FALSE	NA	0.574882490412981	2		973	821	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799631	72799631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763555835	NA	P-0010491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	220	483	0	ENST00000325599.8:c.1538C>T	p.Thr513Ile	p.T513I	ENST00000325599	NM_018130.2	513	aCa/aTa	11/11	0.582881230359764	4	FACETS	0.751	0.701	0.803	0.751	0.701	0.803	SUBCLONAL	2	FALSE	2	0.574882490412981	4		483	802	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540140	187540140	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	94	581	0	ENST00000441802.2:c.7600G>C	p.Asp2534His	p.D2534H	ENST00000441802	NM_005245.3	2534	Gac/Cac	10/27	0.501610488759954	3	FACETS	0.59	0.525	0.659	0.295	0.262	0.33	SUBCLONAL	1	FALSE	1	0.574882490412981	3		581	714	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28891642	28891642	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	127	476	0	ENST00000282397.4:c.3379C>T	p.Pro1127Ser	p.P1127S	ENST00000282397	NM_002019.4	1127	Cct/Tct	25/30	NA	2	FACETS	0.754	0.685	0.826			1	INDETERMINATE	1	FALSE	NA	0.574882490412981	2		476	586	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560130	29560130	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555615051	NA	P-0010491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	88	389	0	ENST00000356175.3:c.3607G>A	p.Asp1203Asn	p.D1203N	ENST00000356175	NM_000267.3	1203	Gat/Aat	27/57	0.398655961250009	4	FACETS	0.733	0.649	0.822			1	SUBCLONAL	1	FALSE	NA	0.574882490412981	4		389	658	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40497663	40497663	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	102	622	0	ENST00000264657.5:c.286G>C	p.Glu96Gln	p.E96Q	ENST00000264657	NM_139276.2	96	Gag/Cag	4/24	0.423454726465171	5	FACETS	0.551	0.491	0.615			1	SUBCLONAL	1	FALSE	NA	0.574882490412981	5		622	1200	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40497671	40497671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	95	594	0	ENST00000264657.5:c.278G>A	p.Arg93Lys	p.R93K	ENST00000264657	NM_139276.2	93	aGg/aAg	4/24	0.423454726465171	5	FACETS	0.552	0.49	0.619			1	SUBCLONAL	1	FALSE	NA	0.574882490412981	5		594	1115	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858949	45858949	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1311061603	NA	P-0010491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	45	400	0	ENST00000391945.4:c.1517C>T	p.Ser506Phe	p.S506F	ENST00000391945	NM_000400.3	506	tCc/tTc	16/23	NA	2	FACETS	0.417	0.352	0.49			1	INDETERMINATE	1	FALSE	NA	0.574882490412981	2		400	375	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867698	45867698	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	119	502	0	ENST00000391945.4:c.702C>A	p.Asp234Glu	p.D234E	ENST00000391945	NM_000400.3	234	gaC/gaA	8/23	NA	2	FACETS	1	0.933	1			1	INDETERMINATE	1	FALSE	NA	0.574882490412981	2		502	402	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44879955	44879955	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269736703	NA	P-0010491-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	225	377	0	ENST00000377967.4:c.544G>A	p.Asp182Asn	p.D182N	ENST00000377967	NM_021140.2	182	Gac/Aac	6/29	0.398655961250009	2	FACETS	1	0.99	1			1	CLONAL	1	FALSE	NA	0.574882490412981	2		377	609	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76919028	76919029	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010496-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	208	367	0	ENST00000373344.5:c.3962dup	p.Asn1321LysfsTer3	p.N1321Kfs*3	ENST00000373344	NM_000489.3	1321	aat/aaAt	12/35	0.76378395344754	1	FACETS	0.879	0.83	0.928	0.879	0.83	0.928	CLONAL	1	TRUE	0	0.76378395344754	1		367	383	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295253	1295253	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1232074117	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	84	336	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.944	0.836	1	0.944	0.836	1	CLONAL	1	TRUE	1	0.32	2		336	556	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	106	351	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.938	0.842	1	0.938	0.842	1	CLONAL	1	TRUE	1	0.32	2		351	706	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103515141	103515141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770246574	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	125	284	0	ENST00000355739.4:c.1642G>A	p.Glu548Lys	p.E548K	ENST00000355739	NM_000123.3	548	Gaa/Aaa	8/15	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.32	2		284	745	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442819	99442819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1365982598	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	121	442	0	ENST00000268035.6:c.1216C>T	p.Arg406Cys	p.R406C	ENST00000268035	NM_000875.3	406	Cgc/Tgc	5/21	1	2	FACETS	0.776	0.7	0.857	0.776	0.7	0.857	SUBCLONAL	1	TRUE	1	0.32	2		442	974	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281952	142281952	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	58	128	0	ENST00000350721.4:c.293-1G>T		p.X98_splice	ENST00000350721	NM_001184.3	98			1	2	FACETS	0.972	0.839	1	0.972	0.839	1	CLONAL	1	TRUE	1	0.32	2		128	373	SUCCESS
ATR	545	MSKCC	GRCh37	3	142178199	142178199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746049210	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	95	319	0	ENST00000350721.4:c.7219C>T	p.Arg2407Cys	p.R2407C	ENST00000350721	NM_001184.3	2407	Cgc/Tgc	43/47	1	2	FACETS	0.792	0.705	0.884	0.792	0.705	0.884	SUBCLONAL	1	TRUE	1	0.32	2		319	750	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945093	31945093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	154	503	0	ENST00000340398.3:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000340398	NM_001013699.2	3	cGa/cAa	1/1	0.3	2	FACETS	0.833	0.761	0.909			1	CLONAL	1	TRUE	NA	0.32	2		503	1155	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545585	106545585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376453517	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	122	287	0	ENST00000359195.3:c.3062G>A	p.Arg1021His	p.R1021H	ENST00000359195	NM_002649.2	1021	cGt/cAt	11/11	1	2	FACETS	0.952	0.861	1	0.952	0.861	1	CLONAL	1	TRUE	1	0.32	2		287	801	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	152	374	2	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	0.0784930142965313	3	FACETS	1	0.98	1	0.623	0.569	0.678	INDETERMINATE	1	TRUE	1	0.32	3		376	885	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	97	243	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.861	0.768	0.96	0.861	0.768	0.96	CLONAL	1	TRUE	1	0.32	2		243	704	SUCCESS
APC	324	MSKCC	GRCh37	5	112174631	112174631	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913331	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	170	496	0	ENST00000257430.4:c.3340C>T	p.Arg1114Ter	p.R1114*	ENST00000257430	NM_000038.5	1114	Cga/Tga	16/16	1	2	FACETS	0.891	0.818	0.968	0.891	0.818	0.968	CLONAL	1	TRUE	1	0.32	2		496	1192	SUCCESS
APC	324	MSKCC	GRCh37	5	112177049	112177049	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	131	418	0	ENST00000257430.4:c.5758C>T	p.Arg1920Ter	p.R1920*	ENST00000257430	NM_000038.5	1920	Cga/Tga	16/16	1	2	FACETS	0.738	0.668	0.811	0.738	0.668	0.811	SUBCLONAL	1	TRUE	1	0.32	2		418	1110	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748309	41748309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs894529129	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	101	319	0	ENST00000226382.2:c.460C>T	p.Arg154Cys	p.R154C	ENST00000226382	NM_003924.3	154	Cgc/Tgc	3/3	0.3	2	FACETS	1	0.91	1			1	CLONAL	1	TRUE	NA	0.32	2		319	620	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027541	48027541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587779923	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	115	246	0	ENST00000234420.5:c.2419G>A	p.Glu807Lys	p.E807K	ENST00000234420	NM_000179.2	807	Gaa/Aaa	4/10	0.3	3	FACETS	1	0.974	1			1	CLONAL	1	TRUE	NA	0.32	3		246	677	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281802	142281802	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	155	346	0	ENST00000350721.4:c.442G>T	p.Glu148Ter	p.E148*	ENST00000350721	NM_001184.3	148	Gaa/Taa	4/47	1	2	FACETS	0.998	0.913	1	0.998	0.913	1	CLONAL	1	TRUE	1	0.32	2		346	971	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20483060	20483060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750169257	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	117	300	0	ENST00000346618.3:c.793G>A	p.Glu265Lys	p.E265K	ENST00000346618	NM_001949.4	265	Gag/Aag	4/7	1	2	FACETS	0.795	0.716	0.878	0.795	0.716	0.878	SUBCLONAL	1	TRUE	1	0.32	2		300	920	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149129	61149129	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144119768	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	84	406	0	ENST00000295025.8:c.1319C>T	p.Ser440Leu	p.S440L	ENST00000295025	NM_002908.2	440	tCg/tTg	11/11	0.3	3	FACETS	0.607	0.534	0.684			1	SUBCLONAL	1	TRUE	NA	0.32	3		406	1004	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772842	135772842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	195	513	0	ENST00000298552.3:c.2781G>T	p.Lys927Asn	p.K927N	ENST00000298552	NM_001162426.1	927	aaG/aaT	21/23	1	2	FACETS	0.932	0.86	1	0.932	0.86	1	CLONAL	1	TRUE	1	0.32	2		513	1308	SUCCESS
YES1	7525	MSKCC	GRCh37	18	751726	751726	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1010928891	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	109	340	0	ENST00000314574.4:c.350G>T	p.Arg117Ile	p.R117I	ENST00000314574	NM_005433.3	117	aGa/aTa	3/12	1	2	FACETS	0.803	0.721	0.891	0.803	0.721	0.891	CLONAL	1	TRUE	1	0.32	2		340	848	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187517847	187517847	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202133523	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	171	459	1	ENST00000441802.2:c.12847G>A	p.Glu4283Lys	p.E4283K	ENST00000441802	NM_005245.3	4283	Gaa/Aaa	25/27	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.32	2		460	1069	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28893668	28893668	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs374452662	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	71	207	0	ENST00000282397.4:c.3178C>T	p.Arg1060Ter	p.R1060*	ENST00000282397	NM_002019.4	1060	Cga/Tga	24/30	1	2	FACETS	0.826	0.722	0.938	0.826	0.722	0.938	CLONAL	1	TRUE	1	0.32	2		207	537	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417901	138417901	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	122	287	0	ENST00000289153.2:c.1618G>T	p.Glu540Ter	p.E540*	ENST00000289153	NM_006219.2	540	Gaa/Taa	11/22	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.32	2		287	760	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380289	25380289	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	124	297	0	ENST00000311936.3:c.169G>A	p.Asp57Asn	p.D57N	ENST00000311936	NM_004985.3	57	Gac/Aac	3/5	0.3	2	FACETS	0.863	0.78	0.951			1	CLONAL	1	TRUE	NA	0.32	2		297	898	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952077	178952077	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	107	348	0	ENST00000263967.3:c.3132T>G	p.Asn1044Lys	p.N1044K	ENST00000263967	NM_006218.2	1044	aaT/aaG	21/21	1	2	FACETS	0.858	0.77	0.952	0.858	0.77	0.952	CLONAL	1	TRUE	1	0.32	2		348	779	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950648	38950648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776074870	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1188	178	553	3	ENST00000357387.3:c.3302C>T	p.Ser1101Leu	p.S1101L	ENST00000357387	NM_152756.3	1101	tCg/tTg	31/38	1	2	FACETS	0.814	0.748	0.884	0.814	0.748	0.884	CLONAL	1	TRUE	1	0.32	2		556	1366	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36231773	36231773	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1569061762	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	200	465	1	ENST00000300305.3:c.611G>A	p.Arg204Gln	p.R204Q	ENST00000300305		204	cGa/cAa	5/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.32	2		466	1183	SUCCESS
ATM	472	MSKCC	GRCh37	11	108198396	108198396	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	106	298	0	ENST00000278616.4:c.7000T>G	p.Tyr2334Asp	p.Y2334D	ENST00000278616	NM_000051.3	2334	Tac/Gac	48/63	1	2	FACETS	0.865	0.775	0.96	0.865	0.775	0.96	CLONAL	1	TRUE	1	0.32	2		298	766	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812205	43812205	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866559375	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	159	436	1	ENST00000372470.3:c.1070G>A	p.Arg357Gln	p.R357Q	ENST00000372470	NM_005373.2	357	cGa/cAa	7/12	1	2	FACETS	0.978	0.896	1	0.978	0.896	1	CLONAL	1	TRUE	1	0.32	2		437	1016	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812585	43812585	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	127	323	1	ENST00000372470.3:c.1288G>A	p.Glu430Lys	p.E430K	ENST00000372470	NM_005373.2	430	Gaa/Aaa	8/12	1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.32	2		324	777	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120459064	120459064	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	80	373	0	ENST00000256646.2:c.6281T>G	p.Leu2094Arg	p.L2094R	ENST00000256646	NM_024408.3	2094	cTg/cGg	34/34	1	2	FACETS	0.501	0.44	0.567	0.501	0.44	0.567	SUBCLONAL	1	TRUE	1	0.32	2		373	998	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156843506	156843506	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1434897221	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	43	365	0	ENST00000524377.1:c.932C>T	p.Pro311Leu	p.P311L	ENST00000524377	NM_002529.3	311	cCg/cTg	8/17	1	2	FACETS	0.375	0.313	0.444	0.375	0.313	0.444	SUBCLONAL	1	TRUE	1	0.32	2		365	717	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945644	206945644	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs769965755	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	153	448	0	ENST00000423557.1:c.137A>G	p.Asp46Gly	p.D46G	ENST00000423557	NM_000572.2	46	gAt/gGt	1/5	1	2	FACETS	0.911	0.832	0.993	0.911	0.832	0.993	CLONAL	1	TRUE	1	0.32	2		448	1050	SUCCESS
H3-3A	3021	MSKCC	GRCh37	1	226253490	226253490	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	223	404	0	ENST00000366813.1:c.262G>A	p.Ala88Thr	p.A88T	ENST00000366813		88	Gca/Aca	2/3	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.32	2		404	1157	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967281	25967281	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	71	470	0	ENST00000435504.4:c.1925T>G	p.Phe642Cys	p.F642C	ENST00000435504		642	tTt/tGt	13/13	0.3	2	FACETS	0.421	0.366	0.481			1	SUBCLONAL	1	TRUE	NA	0.32	2		470	1054	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967318	25967318	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	152	456	1	ENST00000435504.4:c.1888C>T	p.Pro630Ser	p.P630S	ENST00000435504		630	Ccg/Tcg	13/13	0.3	2	FACETS	0.923	0.843	1			1	CLONAL	1	TRUE	NA	0.32	2		457	1029	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630671	158630671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1363	91	570	0	ENST00000263640.3:c.572G>A	p.Gly191Glu	p.G191E	ENST00000263640	NM_001105.4	191	gGa/gAa	6/11	1	2	FACETS	0.391	0.346	0.44	0.391	0.346	0.44	SUBCLONAL	1	TRUE	1	0.32	2		570	1454	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190719551	190719551	+	stop_gained	Nonsense_Mutation	SNP	T	T	G	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	113	312	0	ENST00000441310.2:c.1553T>G	p.Leu518Ter	p.L518*	ENST00000441310	NM_000534.4	518	tTa/tGa	9/13	1	2	FACETS	0.869	0.781	0.961	0.869	0.781	0.961	CLONAL	1	TRUE	1	0.32	2		312	813	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190742037	190742037	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	132	300	0	ENST00000441310.2:c.2674T>G	p.Leu892Val	p.L892V	ENST00000441310	NM_000534.4	892	Tta/Gta	13/13	1	2	FACETS	0.964	0.875	1	0.964	0.875	1	CLONAL	1	TRUE	1	0.32	2		300	856	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191638	10191638	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	103	268	0	ENST00000256474.2:c.631A>G	p.Met211Val	p.M211V	ENST00000256474	NM_000551.3	211	Atg/Gtg	3/3	1	2	FACETS	0.887	0.794	0.985	0.887	0.794	0.985	CLONAL	1	TRUE	1	0.32	2		268	726	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37090474	37090474	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	82	285	0	ENST00000231790.2:c.2069A>G	p.Tyr690Cys	p.Y690C	ENST00000231790	NM_000249.3	690	tAc/tGc	18/19	1	2	FACETS	0.672	0.592	0.758	0.672	0.592	0.758	SUBCLONAL	1	TRUE	1	0.32	2		285	763	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125569	47125569	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	176	457	0	ENST00000409792.3:c.5701G>T	p.Glu1901Ter	p.E1901*	ENST00000409792	NM_014159.6	1901	Gaa/Taa	12/21	1	2	FACETS	0.916	0.842	0.993	0.916	0.842	0.993	CLONAL	1	TRUE	1	0.32	2		457	1201	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163588	47163588	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	87	261	0	ENST00000409792.3:c.2538A>C	p.Lys846Asn	p.K846N	ENST00000409792	NM_014159.6	846	aaA/aaC	3/21	1	2	FACETS	0.884	0.784	0.991	0.884	0.784	0.991	CLONAL	1	TRUE	1	0.32	2		261	615	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702662	52702662	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	67	193	0	ENST00000394830.3:c.237-1G>T		p.X79_splice	ENST00000394830	NM_018313.4	79			1	2	FACETS	0.655	0.569	0.749	0.655	0.569	0.749	SUBCLONAL	1	TRUE	1	0.32	2		193	639	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202732	128202732	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	92	350	1	ENST00000341105.2:c.988C>T	p.Arg330Ter	p.R330*	ENST00000341105	NM_032638.4	330	Cga/Tga	4/6	0.3	2	FACETS	0.747	0.663	0.836			1	SUBCLONAL	1	TRUE	NA	0.32	2		351	770	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138433485	138433485	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	105	311	0	ENST00000289153.2:c.1127A>C	p.Lys376Thr	p.K376T	ENST00000289153	NM_006219.2	376	aAa/aCa	7/22	1	2	FACETS	0.83	0.743	0.922	0.83	0.743	0.922	CLONAL	1	TRUE	1	0.32	2		311	791	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261519	142261519	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	115	258	0	ENST00000350721.4:c.3438A>C	p.Glu1146Asp	p.E1146D	ENST00000350721	NM_001184.3	1146	gaA/gaC	17/47	1	2	FACETS	0.867	0.781	0.958	0.867	0.781	0.958	CLONAL	1	TRUE	1	0.32	2		258	829	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55140704	55140704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765271720	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	122	359	0	ENST00000257290.5:c.1565G>A	p.Arg522His	p.R522H	ENST00000257290	NM_006206.4	522	cGt/cAt	11/23	0.3	1	FACETS	0.732	0.661	0.807	0.732	0.661	0.807	SUBCLONAL	1	TRUE	0	0.32	1		359	875	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156491	55156491	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	104	346	0	ENST00000257290.5:c.2892A>C	p.Lys964Asn	p.K964N	ENST00000257290	NM_006206.4	964	aaA/aaC	22/23	0.3	1	FACETS	0.709	0.635	0.788	0.709	0.635	0.788	SUBCLONAL	1	TRUE	0	0.32	1		346	770	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55956184	55956184	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	124	427	0	ENST00000263923.4:c.3131T>C	p.Ile1044Thr	p.I1044T	ENST00000263923	NM_002253.2	1044	aTc/aCc	23/30	0.3	1	FACETS	0.698	0.63	0.769	0.698	0.63	0.769	SUBCLONAL	1	TRUE	0	0.32	1		427	933	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467866	66467866	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56375573	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	95	373	3	ENST00000273854.3:c.403C>T	p.Arg135Trp	p.R135W	ENST00000273854	NM_004439.5	135	Cgg/Tgg	3/18	0.3	1	FACETS	0.606	0.539	0.678	0.606	0.539	0.678	SUBCLONAL	1	TRUE	0	0.32	1		376	823	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196497	106196497	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	129	366	0	ENST00000380013.4:c.4830T>G	p.Asn1610Lys	p.N1610K	ENST00000380013	NM_001127208.2	1610	aaT/aaG	11/11	1	2	FACETS	0.898	0.814	0.987	0.898	0.814	0.987	CLONAL	1	TRUE	1	0.32	2		366	898	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143094843	143094843	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	78	482	0	ENST00000262992.4:c.1301C>A	p.Ser434Tyr	p.S434Y	ENST00000262992	NM_001101669.1	434	tCt/tAt	14/24	1	2	FACETS	0.448	0.392	0.508	0.448	0.392	0.508	SUBCLONAL	1	TRUE	1	0.32	2		482	1088	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143129648	143129648	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs768272420	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	143	397	0	ENST00000262992.4:c.1002G>T	p.Glu334Asp	p.E334D	ENST00000262992	NM_001101669.1	334	gaG/gaT	12/24	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.32	2		397	852	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153253762	153253762	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	40	236	0	ENST00000281708.4:c.971A>C	p.Lys324Thr	p.K324T	ENST00000281708	NM_033632.3	324	aAa/aCa	6/12	1	2	FACETS	0.352	0.291	0.419	0.352	0.291	0.419	SUBCLONAL	1	TRUE	1	0.32	2		236	711	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187541982	187541982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759008415	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	132	350	0	ENST00000441802.2:c.5758G>A	p.Glu1920Lys	p.E1920K	ENST00000441802	NM_005245.3	1920	Gaa/Aaa	10/27	1	2	FACETS	0.917	0.832	1	0.917	0.832	1	CLONAL	1	TRUE	1	0.32	2		350	900	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542896	187542896	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	127	296	0	ENST00000441802.2:c.4844T>C	p.Val1615Ala	p.V1615A	ENST00000441802	NM_005245.3	1615	gTc/gCc	10/27	1	2	FACETS	0.902	0.817	0.992	0.902	0.817	0.992	CLONAL	1	TRUE	1	0.32	2		296	880	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187627960	187627960	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	176	436	0	ENST00000441802.2:c.3022A>C	p.Lys1008Gln	p.K1008Q	ENST00000441802	NM_005245.3	1008	Aag/Cag	2/27	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.32	2		436	1063	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	226103	226103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs553257776	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	84	252	1	ENST00000264932.6:c.562C>T	p.Arg188Trp	p.R188W	ENST00000264932	NM_004168.2	188	Cgg/Tgg	5/15	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	TRUE	1	0.32	2		253	518	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576462	67576462	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	172	375	0	ENST00000274335.5:c.741C>A	p.Phe247Leu	p.F247L	ENST00000274335		247	ttC/ttA	5/15	1	2	FACETS	0.995	0.915	1	0.995	0.915	1	CLONAL	1	TRUE	1	0.32	2		375	1080	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589618	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519838	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	96	260	0	ENST00000274335.5:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000274335		461	Cga/Tga	10/15	1	2	FACETS	0.946	0.844	1	0.946	0.844	1	CLONAL	1	TRUE	1	0.32	2		260	634	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670009	86670009	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	77	280	0	ENST00000274376.6:c.1806A>C	p.Glu602Asp	p.E602D	ENST00000274376	NM_002890.2	602	gaA/gaC	14/25	1	2	FACETS	0.757	0.664	0.856	0.757	0.664	0.856	SUBCLONAL	1	TRUE	1	0.32	2		280	636	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672759	86672759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	125	331	0	ENST00000274376.6:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000274376	NM_002890.2	749	cGa/cAa	17/25	1	2	FACETS	0.904	0.818	0.995	0.904	0.818	0.995	CLONAL	1	TRUE	1	0.32	2		331	864	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685312	86685312	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	90	163	0	ENST00000274376.6:c.3028C>T	p.Arg1010Ter	p.R1010*	ENST00000274376	NM_002890.2	1010	Cga/Tga	24/25	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.32	2		163	503	SUCCESS
APC	324	MSKCC	GRCh37	5	112174878	112174878	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	120	288	0	ENST00000257430.4:c.3587C>A	p.Ser1196Ter	p.S1196*	ENST00000257430	NM_000038.5	1196	tCa/tAa	16/16	1	2	FACETS	0.952	0.86	1	0.952	0.86	1	CLONAL	1	TRUE	1	0.32	2		288	788	SUCCESS
APC	324	MSKCC	GRCh37	5	112176843	112176843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	100	473	1	ENST00000257430.4:c.5552G>A	p.Gly1851Glu	p.G1851E	ENST00000257430	NM_000038.5	1851	gGa/gAa	16/16	1	2	FACETS	0.554	0.493	0.618	0.554	0.493	0.618	SUBCLONAL	1	TRUE	1	0.32	2		474	1129	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131931456	131931456	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	108	289	0	ENST00000265335.6:c.2161A>C	p.Lys721Gln	p.K721Q	ENST00000265335		721	Aaa/Caa	13/25	1	2	FACETS	0.98	0.88	1	0.98	0.88	1	CLONAL	1	TRUE	1	0.32	2		289	689	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977992	131977992	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	134	365	0	ENST00000265335.6:c.3875A>G	p.Asn1292Ser	p.N1292S	ENST00000265335		1292	aAc/aGc	25/25	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.32	2		365	837	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149434869	149434869	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	155	460	0	ENST00000286301.3:c.2585A>G	p.Asn862Ser	p.N862S	ENST00000286301	NM_005211.3	862	aAc/aGc	20/22	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.32	2		460	969	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495496	149495496	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	198	631	1	ENST00000261799.4:c.3151G>T	p.Glu1051Ter	p.E1051*	ENST00000261799	NM_002609.3	1051	Gaa/Taa	23/23	1	2	FACETS	0.966	0.893	1	0.966	0.893	1	CLONAL	1	TRUE	1	0.32	2		632	1281	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180038451	180038451	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370304760	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	125	395	0	ENST00000261937.6:c.3566G>A	p.Arg1189His	p.R1189H	ENST00000261937	NM_182925.4	1189	cGc/cAc	27/30	0.3	1	FACETS	0.939	0.851	1	0.939	0.851	1	CLONAL	1	TRUE	0	0.32	1		395	699	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048632	180048632	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	74	241	0	ENST00000261937.6:c.1930G>A	p.Ala644Thr	p.A644T	ENST00000261937	NM_182925.4	644	Gcg/Acg	13/30	0.3	1	FACETS	0.839	0.737	0.948	0.839	0.737	0.948	CLONAL	1	TRUE	0	0.32	1		241	463	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29911140	29911140	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	130	337	0	ENST00000376809.5:c.439T>G	p.Tyr147Asp	p.Y147D	ENST00000376809	NM_002116.7	147	Tac/Gac	3/8	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.32	2		337	704	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93955110	93955110	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1167	158	648	1	ENST00000369303.4:c.2788G>T	p.Glu930Ter	p.E930*	ENST00000369303	NM_004440.3	930	Gaa/Taa	16/17	1	2	FACETS	0.745	0.681	0.813	0.745	0.681	0.813	SUBCLONAL	1	TRUE	1	0.32	2		649	1325	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017629	112017629	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1339	234	695	0	ENST00000368678.4:c.884T>C	p.Ile295Thr	p.I295T	ENST00000368678		295	aTa/aCa	9/13	1	2	FACETS	0.93	0.865	0.998	0.93	0.865	0.998	CLONAL	1	TRUE	1	0.32	2		695	1573	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677889	117677889	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	143	457	0	ENST00000368508.3:c.4044G>T	p.Glu1348Asp	p.E1348D	ENST00000368508	NM_002944.2	1348	gaG/gaT	25/43	1	2	FACETS	0.921	0.839	1	0.921	0.839	1	CLONAL	1	TRUE	1	0.32	2		457	970	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138197159	138197159	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	130	393	0	ENST00000237289.4:c.661G>T	p.Gly221Cys	p.G221C	ENST00000237289	NM_001270507.1	221	Ggt/Tgt	5/9	1	2	FACETS	0.856	0.776	0.941	0.856	0.776	0.941	CLONAL	1	TRUE	1	0.32	2		393	949	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163911	152163911	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	124	398	0	ENST00000206249.3:c.632G>T	p.Arg211Ile	p.R211I	ENST00000206249	NM_000125.3	211	aGa/aTa	2/8	1	2	FACETS	0.85	0.768	0.936	0.85	0.768	0.936	CLONAL	1	TRUE	1	0.32	2		398	912	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100550	157100550	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	98	339	2	ENST00000346085.5:c.1487G>T	p.Arg496Met	p.R496M	ENST00000346085	NM_020732.3	496	aGg/aTg	1/20	1	2	FACETS	0.884	0.789	0.985	0.884	0.789	0.985	CLONAL	1	TRUE	1	0.32	2		341	693	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771199	161771199	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	46	218	0	ENST00000366898.1:c.1330G>A	p.Glu444Lys	p.E444K	ENST00000366898	NM_004562.2	444	Gag/Aag	12/12	1	2	FACETS	0.614	0.518	0.721	0.614	0.518	0.721	SUBCLONAL	1	TRUE	1	0.32	2		218	468	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206867	162206867	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	53	329	0	ENST00000366898.1:c.808A>G	p.Thr270Ala	p.T270A	ENST00000366898	NM_004562.2	270	Aca/Gca	7/12	1	2	FACETS	0.463	0.394	0.539	0.463	0.394	0.539	SUBCLONAL	1	TRUE	1	0.32	2		329	715	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206879	162206879	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	52	312	0	ENST00000366898.1:c.796T>G	p.Leu266Val	p.L266V	ENST00000366898	NM_004562.2	266	Tta/Gta	7/12	1	2	FACETS	0.473	0.402	0.551	0.473	0.402	0.551	SUBCLONAL	1	TRUE	1	0.32	2		312	687	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729551	41729551	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1356119994	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1236	217	757	0	ENST00000242208.4:c.978C>A	p.Phe326Leu	p.F326L	ENST00000242208	NM_002192.2	326	ttC/ttA	3/3	1	2	FACETS	0.933	0.866	1	0.933	0.866	1	CLONAL	1	TRUE	1	0.32	2		757	1453	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50459493	50459493	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	114	302	0	ENST00000331340.3:c.782C>A	p.Ser261Tyr	p.S261Y	ENST00000331340	NM_006060.4	261	tCt/tAt	7/8	1	2	FACETS	0.933	0.84	1	0.933	0.84	1	CLONAL	1	TRUE	1	0.32	2		302	764	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273279	55273279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201717672	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	111	209	0	ENST00000275493.2:c.3602C>T	p.Ala1201Val	p.A1201V	ENST00000275493	NM_005228.3	1201	gCg/gTg	28/28	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.32	2		209	629	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350062	81350062	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs759145490	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	111	339	1	ENST00000222390.5:c.1270C>T	p.Arg424Cys	p.R424C	ENST00000222390	NM_000601.4	424	Cgt/Tgt	10/18	1	2	FACETS	0.822	0.738	0.911	0.822	0.738	0.911	CLONAL	1	TRUE	1	0.32	2		340	844	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388115	81388115	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	71	324	0	ENST00000222390.5:c.260T>G	p.Phe87Cys	p.F87C	ENST00000222390	NM_000601.4	87	tTt/tGt	3/18	1	2	FACETS	0.751	0.656	0.853	0.751	0.656	0.853	SUBCLONAL	1	TRUE	1	0.32	2		324	591	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508631	106508631	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	44	377	0	ENST00000359195.3:c.625G>A	p.Glu209Lys	p.E209K	ENST00000359195	NM_002649.2	209	Gag/Aag	2/11	1	2	FACETS	0.611	0.513	0.72	0.611	0.513	0.72	SUBCLONAL	1	TRUE	1	0.32	2		377	450	SUCCESS
MET	4233	MSKCC	GRCh37	7	116340177	116340177	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200074800	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	123	316	1	ENST00000397752.3:c.1039G>A	p.Ala347Thr	p.A347T	ENST00000397752	NM_000245.2	347	Gca/Aca	2/21	1	2	FACETS	0.978	0.885	1	0.978	0.885	1	CLONAL	1	TRUE	1	0.32	2		317	786	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403290	116403290	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	178	458	0	ENST00000397752.3:c.2551T>C	p.Ser851Pro	p.S851P	ENST00000397752	NM_000245.2	851	Tca/Cca	11/21	1	2	FACETS	0.975	0.897	1	0.975	0.897	1	CLONAL	1	TRUE	1	0.32	2		458	1141	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148511095	148511095	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	89	197	0	ENST00000320356.2:c.1807A>C	p.Asn603His	p.N603H	ENST00000320356	NM_004456.4	603	Aat/Cat	15/20	1	2	FACETS	0.952	0.846	1	0.952	0.846	1	CLONAL	1	TRUE	1	0.32	2		197	584	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132852	152132852	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1317128032	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	84	279	0	ENST00000262189.6:c.20A>G	p.Lys7Arg	p.K7R	ENST00000262189	NM_170606.2	7	aAg/aGg	1/59	0.3	2	FACETS	0.756	0.668	0.851			1	SUBCLONAL	1	TRUE	NA	0.32	2		279	694	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372550	55372550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759208720	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	70	172	0	ENST00000297316.4:c.1240G>A	p.Val414Met	p.V414M	ENST00000297316	NM_022454.3	414	Gtg/Atg	2/2	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.32	2		172	382	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739866	145739866	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755425093	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	128	464	2	ENST00000428558.2:c.1664C>T	p.Ser555Leu	p.S555L	ENST00000428558	NM_004260.3	555	tCg/tTg	10/22	1	2	FACETS	0.86	0.779	0.946	0.86	0.779	0.946	CLONAL	1	TRUE	1	0.32	2		466	930	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5080561	5080561	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs755639338	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	128	386	0	ENST00000381652.3:c.2312A>G	p.Gln771Arg	p.Q771R	ENST00000381652	NM_004972.3	771	cAg/cGg	18/25	1	2	FACETS	0.865	0.783	0.951	0.865	0.783	0.951	CLONAL	1	TRUE	1	0.32	2		386	925	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212216	98212216	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	77	200	2	ENST00000331920.6:c.3456C>A	p.Phe1152Leu	p.F1152L	ENST00000331920	NM_000264.3	1152	ttC/ttA	21/24	1	2	FACETS	0.931	0.819	1	0.931	0.819	1	CLONAL	1	TRUE	1	0.32	2		202	517	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229458	98229458	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	157	517	0	ENST00000331920.6:c.2500T>G	p.Leu834Val	p.L834V	ENST00000331920	NM_000264.3	834	Ttg/Gtg	15/24	1	2	FACETS	0.812	0.742	0.886	0.812	0.742	0.886	CLONAL	1	TRUE	1	0.32	2		517	1208	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98229682	98229682	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	55	179	0	ENST00000331920.6:c.2276G>A	p.Gly759Asp	p.G759D	ENST00000331920	NM_000264.3	759	gGc/gAc	15/24	1	2	FACETS	0.721	0.617	0.833	0.721	0.617	0.833	SUBCLONAL	1	TRUE	1	0.32	2		179	477	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101907037	101907037	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	90	244	0	ENST00000374994.4:c.997G>T	p.Asp333Tyr	p.D333Y	ENST00000374994	NM_004612.2	333	Gat/Tat	6/9	1	2	FACETS	0.774	0.686	0.867	0.774	0.686	0.867	SUBCLONAL	1	TRUE	1	0.32	2		244	727	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781510	135781510	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1455	260	758	0	ENST00000298552.3:c.1455A>C	p.Glu485Asp	p.E485D	ENST00000298552	NM_001162426.1	485	gaA/gaC	15/23	1	2	FACETS	0.948	0.884	1	0.948	0.884	1	CLONAL	1	TRUE	1	0.32	2		758	1715	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624245	89624245	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554890335	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	39	99	0	ENST00000371953.3:c.19G>T	p.Glu7Ter	p.E7*	ENST00000371953	NM_000314.4	7	Gag/Tag	1/9	1	2	FACETS	0.979	0.817	1	0.979	0.817	1	CLONAL	1	TRUE	1	0.32	2		99	249	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274782	123274782	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	155	383	1	ENST00000358487.5:c.1136C>A	p.Ala379Asp	p.A379D	ENST00000358487	NM_000141.4	379	gCc/gAc	9/18	1	2	FACETS	0.932	0.853	1	0.932	0.853	1	CLONAL	1	TRUE	1	0.32	2		384	1039	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989557	85989557	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	145	400	0	ENST00000263360.6:c.1316G>A	p.Arg439Gln	p.R439Q	ENST00000263360	NM_003797.3	439	cGa/cAa	12/12	1	2	FACETS	0.877	0.799	0.959	0.877	0.799	0.959	CLONAL	1	TRUE	1	0.32	2		400	1033	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989563	85989563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1363668348	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	137	373	2	ENST00000263360.6:c.1322G>A	p.Arg441Gln	p.R441Q	ENST00000263360	NM_003797.3	441	cGa/cAa	12/12	1	2	FACETS	0.882	0.801	0.967	0.882	0.801	0.967	CLONAL	1	TRUE	1	0.32	2		375	971	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201872	102201872	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs749826929	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1463	234	728	1	ENST00000263464.3:c.1224G>T	p.Glu408Asp	p.E408D	ENST00000263464	NM_001165.4	408	gaG/gaT	6/9	1	2	FACETS	0.862	0.801	0.925	0.862	0.801	0.925	CLONAL	1	TRUE	1	0.32	2		729	1697	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106523	108106523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	120	284	0	ENST00000278616.4:c.458G>A	p.Arg153Lys	p.R153K	ENST00000278616	NM_000051.3	153	aGa/aAa	5/63	1	2	FACETS	0.982	0.887	1	0.982	0.887	1	CLONAL	1	TRUE	1	0.32	2		284	764	SUCCESS
ATM	472	MSKCC	GRCh37	11	108121669	108121669	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750280306	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	173	542	1	ENST00000278616.4:c.1477C>T	p.Arg493Cys	p.R493C	ENST00000278616	NM_000051.3	493	Cgt/Tgt	10/63	1	2	FACETS	0.829	0.761	0.9	0.829	0.761	0.9	CLONAL	1	TRUE	1	0.32	2		543	1305	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155088	108155088	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	127	321	0	ENST00000278616.4:c.3881T>G	p.Ile1294Ser	p.I1294S	ENST00000278616	NM_000051.3	1294	aTt/aGt	26/63	1	2	FACETS	0.992	0.899	1	0.992	0.899	1	CLONAL	1	TRUE	1	0.32	2		321	800	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202198	108202198	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	90	278	0	ENST00000278616.4:c.7543A>C	p.Lys2515Gln	p.K2515Q	ENST00000278616	NM_000051.3	2515	Aaa/Caa	51/63	1	2	FACETS	0.857	0.761	0.96	0.857	0.761	0.96	CLONAL	1	TRUE	1	0.32	2		278	656	SUCCESS
ATM	472	MSKCC	GRCh37	11	108202688	108202688	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	67	308	0	ENST00000278616.4:c.7712T>G	p.Phe2571Cys	p.F2571C	ENST00000278616	NM_000051.3	2571	tTt/tGt	52/63	1	2	FACETS	0.491	0.426	0.563	0.491	0.426	0.563	SUBCLONAL	1	TRUE	1	0.32	2		308	852	SUCCESS
CBL	867	MSKCC	GRCh37	11	119142539	119142539	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	157	399	1	ENST00000264033.4:c.538C>T	p.Arg180Trp	p.R180W	ENST00000264033	NM_005188.3	180	Cgg/Tgg	3/16	1	2	FACETS	0.867	0.793	0.945	0.867	0.793	0.945	CLONAL	1	TRUE	1	0.32	2		400	1132	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170272	119170272	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	119	333	0	ENST00000264033.4:c.2502A>C	p.Glu834Asp	p.E834D	ENST00000264033	NM_005188.3	834	gaA/gaC	16/16	1	2	FACETS	0.844	0.761	0.932	0.844	0.761	0.932	CLONAL	1	TRUE	1	0.32	2		333	881	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406326	406326	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	153	399	0	ENST00000399788.2:c.4115A>C	p.Asn1372Thr	p.N1372T	ENST00000399788	NM_001042603.1	1372	aAt/aCt	25/28	0.3	2	FACETS	0.87	0.795	0.949			1	CLONAL	1	TRUE	NA	0.32	2		399	1099	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419031	419031	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	56	320	1	ENST00000399788.2:c.3316G>A	p.Asp1106Asn	p.D1106N	ENST00000399788	NM_001042603.1	1106	Gac/Aac	22/28	0.3	2	FACETS	0.381	0.325	0.442			1	SUBCLONAL	1	TRUE	NA	0.32	2		321	919	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18496264	18496264	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	72	288	0	ENST00000266497.5:c.1399T>G	p.Phe467Val	p.F467V	ENST00000266497		467	Ttt/Gtt	9/31	0.3	2	FACETS	0.594	0.519	0.676			1	SUBCLONAL	1	TRUE	NA	0.32	2		288	757	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552634	18552634	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1308146539	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	143	511	0	ENST00000266497.5:c.2045T>C	p.Phe682Ser	p.F682S	ENST00000266497		682	tTc/tCc	14/31	0.3	2	FACETS	0.769	0.7	0.842			1	SUBCLONAL	1	TRUE	NA	0.32	2		511	1162	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230399	46230399	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	130	397	0	ENST00000334344.6:c.733G>T	p.Glu245Ter	p.E245*	ENST00000334344	NM_152641.2	245	Gaa/Taa	7/21	0.0784930142965313	3	FACETS	0.825	0.746	0.908	0.412	0.373	0.454	INDETERMINATE	1	TRUE	1	0.32	3		397	1143	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46298771	46298771	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	135	380	0	ENST00000334344.6:c.5418A>C	p.Glu1806Asp	p.E1806D	ENST00000334344	NM_152641.2	1806	gaA/gaC	21/21	0.0784930142965313	3	FACETS	0.959	0.87	1	0.479	0.435	0.526	INDETERMINATE	1	TRUE	1	0.32	3		380	1021	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435768	49435768	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1256251134	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	153	357	0	ENST00000301067.7:c.6115T>C	p.Ser2039Pro	p.S2039P	ENST00000301067	NM_003482.3	2039	Tca/Cca	29/54	0.0784930142965313	3	FACETS	1	0.961	1	0.544	0.497	0.594	INDETERMINATE	1	TRUE	1	0.32	3		357	1019	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865135	57865135	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1516	313	763	0	ENST00000228682.2:c.2612A>G	p.Asp871Gly	p.D871G	ENST00000228682	NM_005269.2	871	gAt/gGt	12/12	0.0784930142965313	3	FACETS	1	0.99	1	0.62	0.583	0.659	INDETERMINATE	1	TRUE	1	0.32	3		763	1829	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865767	57865767	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1226	238	657	0	ENST00000228682.2:c.3244A>G	p.Asn1082Asp	p.N1082D	ENST00000228682	NM_005269.2	1082	Aac/Gac	12/12	0.0784930142965313	3	FACETS	1	0.984	1	0.589	0.548	0.632	INDETERMINATE	1	TRUE	1	0.32	3		657	1464	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112915793	112915793	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	50	306	0	ENST00000351677.2:c.1066A>G	p.Thr356Ala	p.T356A	ENST00000351677	NM_002834.3	356	Aca/Gca	9/16	0.3	2	FACETS	0.397	0.336	0.465			1	SUBCLONAL	1	TRUE	NA	0.32	2		306	787	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	121	412	0	ENST00000320574.5:c.1231G>C	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ctg	13/49	0.3	2	FACETS	0.822	0.742	0.907			1	CLONAL	1	TRUE	NA	0.32	2		412	920	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26974624	26974624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs933264029	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	107	314	0	ENST00000381527.3:c.968G>A	p.Arg323Gln	p.R323Q	ENST00000381527	NM_001260.1	323	cGa/cAa	10/13	1	2	FACETS	0.806	0.722	0.894	0.806	0.722	0.894	CLONAL	1	TRUE	1	0.32	2		314	830	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964163	28964163	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	115	387	0	ENST00000282397.4:c.1739A>G	p.Asn580Ser	p.N580S	ENST00000282397	NM_002019.4	580	aAc/aGc	13/30	1	2	FACETS	0.851	0.766	0.94	0.851	0.766	0.94	CLONAL	1	TRUE	1	0.32	2		387	845	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913081	32913081	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1560	239	716	0	ENST00000380152.3:c.4589A>C	p.Lys1530Thr	p.K1530T	ENST00000380152		1530	aAa/aCa	11/27	1	2	FACETS	0.83	0.772	0.891	0.83	0.772	0.891	CLONAL	1	TRUE	1	0.32	2		716	1799	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95578514	95578514	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	90	248	0	ENST00000393063.1:c.2111A>C	p.Lys704Thr	p.K704T	ENST00000393063	NM_030621.3	704	aAa/aCa	14/28	1	2	FACETS	0.841	0.746	0.942	0.841	0.746	0.942	CLONAL	1	TRUE	1	0.32	2		248	669	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961914	41961914	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs374032826	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1411	249	674	0	ENST00000219905.7:c.822G>T	p.Lys274Asn	p.K274N	ENST00000219905	NM_001164273.1	274	aaG/aaT	2/24	1	2	FACETS	0.938	0.874	1	0.938	0.874	1	CLONAL	1	TRUE	1	0.32	2		674	1660	SUCCESS
BLM	641	MSKCC	GRCh37	15	91308604	91308604	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1181	141	475	0	ENST00000355112.3:c.2153C>A	p.Ser718Ter	p.S718*	ENST00000355112	NM_000057.2	718	tCa/tAa	9/22	1	2	FACETS	0.667	0.605	0.731	0.667	0.605	0.731	SUBCLONAL	1	TRUE	1	0.32	2		475	1322	SUCCESS
BLM	641	MSKCC	GRCh37	15	91337508	91337508	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs747571272	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	150	385	0	ENST00000355112.3:c.3131A>G	p.Tyr1044Cys	p.Y1044C	ENST00000355112	NM_000057.2	1044	tAc/tGc	16/22	1	2	FACETS	0.912	0.832	0.995	0.912	0.832	0.995	CLONAL	1	TRUE	1	0.32	2		385	1028	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3831292	3831292	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	121	319	0	ENST00000262367.5:c.1589A>G	p.Asn530Ser	p.N530S	ENST00000262367	NM_004380.2	530	aAc/aGc	7/31	1	2	FACETS	0.92	0.831	1	0.92	0.831	1	CLONAL	1	TRUE	1	0.32	2		319	822	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822708	72822708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1449	267	815	1	ENST00000268489.5:c.9467G>A	p.Ser3156Asn	p.S3156N	ENST00000268489	NM_006885.3	3156	aGc/aAc	10/10	0.0784930142965313	0	FACETS	0.661	0.618	0.706			1	INDETERMINATE	1	TRUE	0	0.32	0		816	1716	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350096	89350096	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1286	229	738	0	ENST00000301030.4:c.2854A>C	p.Lys952Gln	p.K952Q	ENST00000301030	NM_001256183.1	952	Aag/Cag	9/13	0.0784930142965313	0	FACETS	0.642	0.597	0.69			1	INDETERMINATE	1	TRUE	0	0.32	0		738	1515	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351286	89351286	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1488	275	768	0	ENST00000301030.4:c.1664C>A	p.Ser555Tyr	p.S555Y	ENST00000301030	NM_001256183.1	555	tCt/tAt	9/13	0.0784930142965313	0	FACETS	0.663	0.62	0.707			1	INDETERMINATE	1	TRUE	0	0.32	0		768	1763	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89354962	89354962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1390	243	727	3	ENST00000301030.4:c.718G>A	p.Asp240Asn	p.D240N	ENST00000301030	NM_001256183.1	240	Gac/Aac	7/13	0.0784930142965313	0	FACETS	0.632	0.589	0.678			1	INDETERMINATE	1	TRUE	0	0.32	0		730	1633	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15961052	15961052	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	109	240	0	ENST00000268712.3:c.6169-1G>A		p.X2057_splice	ENST00000268712	NM_006311.3	2057			1	2	FACETS	0.945	0.849	1	0.945	0.849	1	CLONAL	1	TRUE	1	0.32	2		240	721	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983990	15983990	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	164	341	0	ENST00000268712.3:c.3229G>T	p.Glu1077Ter	p.E1077*	ENST00000268712	NM_006311.3	1077	Gaa/Taa	24/46	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.32	2		341	957	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012219	16012219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	114	254	0	ENST00000268712.3:c.2063G>A	p.Arg688Gln	p.R688Q	ENST00000268712	NM_006311.3	688	cGa/cAa	19/46	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.32	2		254	676	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556062	29556062	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	89	199	0	ENST00000356175.3:c.2429A>G	p.Lys810Arg	p.K810R	ENST00000356175	NM_000267.3	810	aAg/aGg	21/57	1	2	FACETS	0.862	0.765	0.966	0.862	0.765	0.966	CLONAL	1	TRUE	1	0.32	2		199	645	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29701150	29701150	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	76	301	0	ENST00000356175.3:c.8434A>G	p.Asn2812Asp	p.N2812D	ENST00000356175	NM_000267.3	2812	Aat/Gat	57/57	1	2	FACETS	0.691	0.606	0.783	0.691	0.606	0.783	SUBCLONAL	1	TRUE	1	0.32	2		301	687	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866710	37866710	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1258412021	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	112	302	0	ENST00000269571.5:c.877G>A	p.Ala293Thr	p.A293T	ENST00000269571		293	Gcc/Acc	7/27	1	2	FACETS	0.84	0.755	0.93	0.84	0.755	0.93	CLONAL	1	TRUE	1	0.32	2		302	833	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866640	78866640	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	84	237	0	ENST00000306801.3:c.2213C>A	p.Ser738Tyr	p.S738Y	ENST00000306801	NM_020761.2	738	tCt/tAt	19/34	1	2	FACETS	0.829	0.733	0.932	0.829	0.733	0.932	CLONAL	1	TRUE	1	0.32	2		237	633	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39575856	39575856	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs140660681	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	63	213	2	ENST00000262039.4:c.789G>T	p.Glu263Asp	p.E263D	ENST00000262039	NM_002647.2	263	gaG/gaT	8/25	1	2	FACETS	0.661	0.571	0.758	0.661	0.571	0.758	SUBCLONAL	1	TRUE	1	0.32	2		215	596	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4117512	4117512	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1457644550	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	35	164	1	ENST00000262948.5:c.208G>A	p.Asp70Asn	p.D70N	ENST00000262948	NM_030662.3	70	Gat/Aat	2/11	1	2	FACETS	0.671	0.551	0.805	0.671	0.551	0.805	SUBCLONAL	1	TRUE	1	0.32	2		165	326	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208357	5208357	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867742806	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	121	402	0	ENST00000357368.4:c.5533C>T	p.Pro1845Ser	p.P1845S	ENST00000357368	NM_002850.3	1845	Ccg/Tcg	36/38	1	2	FACETS	0.904	0.816	0.996	0.904	0.816	0.996	CLONAL	1	TRUE	1	0.32	2		402	837	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7172404	7172404	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	125	391	0	ENST00000302850.5:c.1165G>T	p.Glu389Ter	p.E389*	ENST00000302850	NM_000208.2	389	Gaa/Taa	5/22	1	2	FACETS	0.869	0.786	0.957	0.869	0.786	0.957	CLONAL	1	TRUE	1	0.32	2		391	899	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375108	31375108	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375097618	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	76	267	0	ENST00000328111.2:c.505G>A	p.Asp169Asn	p.D169N	ENST00000328111	NM_006892.3	169	Gac/Aac	6/23	1	2	FACETS	0.901	0.792	1	0.901	0.792	1	CLONAL	1	TRUE	1	0.32	2		267	527	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31394046	31394046	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	92	266	0	ENST00000328111.2:c.2333C>T	p.Ser778Leu	p.S778L	ENST00000328111	NM_006892.3	778	tCg/tTg	22/23	1	2	FACETS	0.766	0.68	0.857	0.766	0.68	0.857	SUBCLONAL	1	TRUE	1	0.32	2		266	751	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39725922	39725922	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762751843	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	66	226	0	ENST00000361337.2:c.793G>A	p.Asp265Asn	p.D265N	ENST00000361337	NM_003286.2	265	Gac/Aac	10/21	1	2	FACETS	0.513	0.444	0.588	0.513	0.444	0.588	SUBCLONAL	1	TRUE	1	0.32	2		226	804	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40747132	40747132	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	94	268	1	ENST00000373198.4:c.2950C>T	p.Gln984Ter	p.Q984*	ENST00000373198	NM_133170.3	984	Cag/Tag	22/32	0.168221216125718	1	FACETS	0.772	0.688	0.862	0.772	0.688	0.862	INDETERMINATE	1	TRUE	0	0.32	1		269	639	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944523	40944523	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	103	369	0	ENST00000373198.4:c.1979C>A	p.Ser660Tyr	p.S660Y	ENST00000373198	NM_133170.3	660	tCt/tAt	12/32	0.168221216125718	1	FACETS	0.648	0.58	0.721	0.648	0.58	0.721	INDETERMINATE	1	TRUE	0	0.32	1		369	834	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44515623	44515623	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	64	374	0	ENST00000291552.4:c.273G>T	p.Glu91Asp	p.E91D	ENST00000291552	NM_006758.2	91	gaG/gaT	5/8	1	2	FACETS	0.481	0.416	0.553	0.481	0.416	0.553	SUBCLONAL	1	TRUE	1	0.32	2		374	831	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565543	41565543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	189	461	0	ENST00000263253.7:c.4209C>A	p.Phe1403Leu	p.F1403L	ENST00000263253	NM_001429.3	1403	ttC/ttA	26/31	0.0784930142965313	3	FACETS	1	0.975	1	0.564	0.52	0.61	INDETERMINATE	1	TRUE	1	0.32	3		461	1214	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39921639	39921639	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1324090329	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	150	172	0	ENST00000378444.4:c.4181T>C	p.Val1394Ala	p.V1394A	ENST00000378444	NM_001123385.1	1394	gTc/gCc	10/15	1	1	FACETS	0.783	0.72	0.847	1	0.989	1	SUBCLONAL	2	TRUE	0	0.32	1		172	503	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39935784	39935784	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	207	250	0	ENST00000378444.4:c.88A>G	p.Lys30Glu	p.K30E	ENST00000378444	NM_001123385.1	30	Aaa/Gaa	3/15	1	1	FACETS	0.797	0.743	0.852	1	0.992	1	SUBCLONAL	2	TRUE	0	0.32	1		250	682	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875925	76875925	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	176	269	2	ENST00000373344.5:c.5210C>A	p.Ser1737Tyr	p.S1737Y	ENST00000373344	NM_000489.3	1737	tCt/tAt	20/35	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.32	1		271	688	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906535	32906536	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs886038058	NA	P-0010499-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	114	423	0	ENST00000380152.3:c.925dup	p.Ser309PhefsTer6	p.S309Ffs*6	ENST00000380152		307	agt/agTt	10/27	1	2	FACETS	0.718	0.645	0.795	0.718	0.645	0.795	SUBCLONAL	1	TRUE	1	0.32	2		423	992	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	87	280	0				ENST00000310581	NM_198253.2	-/1132			0.242901523872077	1	FACETS	0.67	0.597	0.747	0.67	0.597	0.747	INDETERMINATE	1	TRUE	0	0.486528992977981	1		280	404	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060925	38060925	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1388855660	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	51	277	0	ENST00000250448.2:c.1064C>T	p.Ser355Leu	p.S355L	ENST00000250448	NM_004496.3	355	tCa/tTa	2/2	0.283988075348408	1	FACETS	0.421	0.359	0.489	0.421	0.359	0.489	INDETERMINATE	1	TRUE	0	0.486528992977981	1		277	377	SUCCESS
H3C13	653604	MSKCC	GRCh37	1	149784830	149784830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	566	635	0	ENST00000331491.1:c.407C>T	p.Ala136Val	p.A136V	ENST00000331491	NM_001123375.2	136	gCc/gTc	1/1	0.195399627600849	3	FACETS	1	0.992	1			1	INDETERMINATE	2	TRUE	NA	0.486528992977981	3		635	1307	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045930	26045930	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	1127	1223	1	ENST00000540144.1:c.292G>A	p.Glu98Lys	p.E98K	ENST00000540144	NM_003531.2	98	Gag/Aag	1/1	0.485283447845994	3	FACETS	0.858	0.837	0.88	0.858	0.837	0.88	CLONAL	3	TRUE	0	0.486528992977981	3		1224	2237	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378562	25378562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913527	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	121	491	2	ENST00000311936.3:c.436G>A	p.Ala146Thr	p.A146T	ENST00000311936	NM_004985.3	146	Gca/Aca	4/5	1	2	FACETS	0.925	0.839	1	0.925	0.839	1	CLONAL	1	TRUE	1	0.486528992977981	2		493	538	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	112	438	1	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.965	0.873	1	0.965	0.873	1	CLONAL	1	TRUE	1	0.486528992977981	2		439	477	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703632	47703632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138465383	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	110	597	0	ENST00000233146.2:c.2132G>A	p.Arg711Gln	p.R711Q	ENST00000233146	NM_000251.2	711	cGa/cAa	13/16	0.242901523872077	1	FACETS	0.465	0.418	0.515	0.465	0.418	0.515	INDETERMINATE	1	TRUE	0	0.486528992977981	1		597	736	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441477	52441477	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	149	350	0	ENST00000460680.1:c.376-1G>A		p.X126_splice	ENST00000460680	NM_004656.3	126			0.242901523872077	1	FACETS	0.829	0.761	0.899	0.829	0.761	0.899	INDETERMINATE	1	TRUE	0	0.486528992977981	1		350	559	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101186	27101186	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	140	349	0	ENST00000324856.7:c.4468G>A	p.Glu1490Lys	p.E1490K	ENST00000324856	NM_006015.4	1490	Gag/Aag	18/20	0.242901523872077	1	FACETS	0.746	0.682	0.812	0.746	0.682	0.812	INDETERMINATE	1	TRUE	0	0.486528992977981	1		349	584	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685536	29685536	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1131691074	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	118	391	0	ENST00000356175.3:c.7946C>A	p.Ser2649Ter	p.S2649*	ENST00000356175	NM_000267.3	2649	tCa/tAa	54/57	1	2	FACETS	0.998	0.906	1	0.998	0.906	1	CLONAL	1	TRUE	1	0.486528992977981	2		391	486	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100384	27100384	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	175	397	0	ENST00000324856.7:c.4096C>T	p.Gln1366Ter	p.Q1366*	ENST00000324856	NM_006015.4	1366	Cag/Tag	17/20	0.242901523872077	1	FACETS	0.872	0.807	0.94	0.872	0.807	0.94	INDETERMINATE	1	TRUE	0	0.486528992977981	1		397	624	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101181	27101181	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	137	341	0	ENST00000324856.7:c.4463C>T	p.Ser1488Leu	p.S1488L	ENST00000324856	NM_006015.4	1488	tCa/tTa	18/20	0.242901523872077	1	FACETS	0.754	0.689	0.822	0.754	0.689	0.822	INDETERMINATE	1	TRUE	0	0.486528992977981	1		341	565	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550857	150550857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	219	249	0	ENST00000369026.2:c.799C>T	p.Leu267Phe	p.L267F	ENST00000369026	NM_021960.4	267	Ctc/Ttc	2/3	0.195399627600849	3	FACETS	1	0.98	1			1	INDETERMINATE	2	TRUE	NA	0.486528992977981	3		249	510	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463248	25463248	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754613602	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	161	458	0	ENST00000264709.3:c.2245C>T	p.Arg749Cys	p.R749C	ENST00000264709	NM_175629.2	749	Cgc/Tgc	19/23	0.242901523872077	1	FACETS	0.817	0.753	0.884	0.817	0.753	0.884	INDETERMINATE	1	TRUE	0	0.486528992977981	1		458	613	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265468	198265468	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	220	531	0	ENST00000335508.6:c.2689C>G	p.Leu897Val	p.L897V	ENST00000335508	NM_012433.2	897	Ctt/Gtt	18/25	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.486528992977981	2		531	661	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55987340	55987340	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	99	354	0	ENST00000263923.4:c.85C>G	p.Leu29Val	p.L29V	ENST00000263923	NM_002253.2	29	Ctt/Gtt	2/30	0.283988075348408	1	FACETS	0.858	0.773	0.946	0.858	0.773	0.946	INDETERMINATE	1	TRUE	0	0.486528992977981	1		354	359	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495394	149495394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	180	435	0	ENST00000261799.4:c.3253G>A	p.Glu1085Lys	p.E1085K	ENST00000261799	NM_002609.3	1085	Gag/Aag	23/23	1	2	FACETS	0.83	0.765	0.896	0.83	0.765	0.896	CLONAL	1	TRUE	1	0.486528992977981	2		435	892	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401013	139401013	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs751874720	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	145	578	0	ENST00000277541.6:c.3980A>G	p.Asn1327Ser	p.N1327S	ENST00000277541	NM_017617.3	1327	aAc/aGc	24/34	0.486528992977981	2	FACETS	0.476	0.433	0.522	0.238	0.216	0.261	SUBCLONAL	1	TRUE	0	0.486528992977981	2		578	1251	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999192	100999192	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	238	605	1	ENST00000325455.5:c.610C>A	p.His204Asn	p.H204N	ENST00000325455	NM_001202474.3	204	Cac/Aac	1/8	0.445247277752717	2	FACETS	0.973	0.908	1	0.486	0.454	0.52	CLONAL	1	TRUE	0	0.486528992977981	2		606	1006	SUCCESS
ATM	472	MSKCC	GRCh37	11	108199839	108199839	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	244	432	0	ENST00000278616.4:c.7181C>G	p.Ser2394Ter	p.S2394*	ENST00000278616	NM_000051.3	2394	tCa/tGa	49/63	0.445247277752717	2	FACETS	0.885	0.834	0.936	0.885	0.834	0.936	CLONAL	2	TRUE	0	0.486528992977981	2		432	567	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133253212	133253212	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	159	425	0	ENST00000320574.5:c.829G>C	p.Glu277Gln	p.E277Q	ENST00000320574	NM_006231.2	277	Gag/Cag	9/49	1	2	FACETS	0.945	0.868	1	0.945	0.868	1	CLONAL	1	TRUE	1	0.486528992977981	2		425	692	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518174	103518174	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	75	337	0	ENST00000355739.4:c.2112C>A	p.Asn704Lys	p.N704K	ENST00000355739	NM_000123.3	704	aaC/aaA	9/15	1	2	FACETS	0.445	0.389	0.505	0.445	0.389	0.505	SUBCLONAL	1	TRUE	1	0.486528992977981	2		337	693	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422137	81422137	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	117	375	0	ENST00000298171.2:c.113G>C	p.Arg38Thr	p.R38T	ENST00000298171	NM_000369.2	38	aGa/aCa	1/10	0.283988075348408	1	FACETS	0.519	0.468	0.573	0.519	0.468	0.573	INDETERMINATE	1	TRUE	0	0.486528992977981	1		375	701	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988785	41988785	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	157	1085	0	ENST00000219905.7:c.1577C>G	p.Ser526Ter	p.S526*	ENST00000219905	NM_001164273.1	526	tCa/tGa	3/24	0.283988075348408	1	FACETS	0.476	0.435	0.518	0.476	0.435	0.518	INDETERMINATE	1	TRUE	0	0.486528992977981	1		1085	1027	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99473513	99473513	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	148	305	0	ENST00000268035.6:c.2935G>C	p.Glu979Gln	p.E979Q	ENST00000268035	NM_000875.3	979	Gag/Cag	15/21	0.283988075348408	1	FACETS	0.919	0.845	0.995	0.919	0.845	0.995	INDETERMINATE	1	TRUE	0	0.486528992977981	1		305	501	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226298	2226298	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	319	406	0	ENST00000326181.6:c.1911G>C	p.Gln637His	p.Q637H	ENST00000326181	NM_032271.2	637	caG/caC	20/21	0.486678021432416	2	FACETS	0.868	0.825	0.913	0.868	0.825	0.913	CLONAL	2	TRUE	0	0.486528992977981	2		406	755	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650719	67650719	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1131691283	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	466	523	0	ENST00000264010.4:c.1024C>T	p.Arg342Cys	p.R342C	ENST00000264010	NM_006565.3	342	Cgt/Tgt	5/12	0.486678021432416	2	FACETS	0.962	0.923	1	0.962	0.923	1	CLONAL	2	TRUE	0	0.486528992977981	2		523	996	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828191	72828191	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1403	193	1226	2	ENST00000268489.5:c.8390G>T	p.Arg2797Ile	p.R2797I	ENST00000268489	NM_006885.3	2797	aGa/aTa	9/10	0.486678021432416	2	FACETS	0.497	0.458	0.538	0.249	0.229	0.269	SUBCLONAL	1	TRUE	0	0.486528992977981	2		1228	1596	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829005	72829005	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	1032	1326	1	ENST00000268489.5:c.7576C>T	p.Gln2526Ter	p.Q2526*	ENST00000268489	NM_006885.3	2526	Cag/Tag	9/10	0.486678021432416	2	FACETS	0.98	0.954	1	0.98	0.954	1	CLONAL	2	TRUE	0	0.486528992977981	2		1327	2164	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831165	72831165	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	848	994	0	ENST00000268489.5:c.5416G>C	p.Glu1806Gln	p.E1806Q	ENST00000268489	NM_006885.3	1806	Gag/Cag	9/10	0.486678021432416	2	FACETS	0.998	0.969	1	0.998	0.969	1	CLONAL	2	TRUE	0	0.486528992977981	2		994	1746	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831659	72831659	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	690	947	0	ENST00000268489.5:c.4922A>G	p.Asn1641Ser	p.N1641S	ENST00000268489	NM_006885.3	1641	aAc/aGc	9/10	0.486678021432416	2	FACETS	0.951	0.919	0.983	0.951	0.919	0.983	CLONAL	2	TRUE	0	0.486528992977981	2		947	1491	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350674	89350674	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1018	1083	1558	0	ENST00000301030.4:c.2276G>A	p.Arg759Lys	p.R759K	ENST00000301030	NM_001256183.1	759	aGa/aAa	9/13	0.486678021432416	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.486528992977981	2		1558	2101	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89869695	89869695	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	529	705	0	ENST00000389301.3:c.764G>A	p.Arg255Lys	p.R255K	ENST00000389301	NM_000135.2	255	aGa/aAa	8/43	0.486678021432416	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.486528992977981	2		705	996	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761214	59761214	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1490736110	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	212	738	1	ENST00000259008.2:c.3193G>A	p.Gly1065Arg	p.G1065R	ENST00000259008	NM_032043.2	1065	Gga/Aga	20/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.486528992977981	2		739	770	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213956	2213956	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371142941	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	89	209	0	ENST00000398665.3:c.1768C>T	p.Arg590Cys	p.R590C	ENST00000398665	NM_032482.2	590	Cgc/Tgc	18/28	1	2	FACETS	0.859	0.766	0.957	0.859	0.766	0.957	CLONAL	1	TRUE	1	0.486528992977981	2		209	426	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274178	18274178	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	146	313	0	ENST00000222254.8:c.1396G>C	p.Glu466Gln	p.E466Q	ENST00000222254	NM_005027.3	466	Gag/Cag	11/16	1	2	FACETS	0.987	0.904	1	0.987	0.904	1	CLONAL	1	TRUE	1	0.486528992977981	2		313	608	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44894227	44894227	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	167	625	1	ENST00000377967.4:c.616G>T	p.Glu206Ter	p.E206*	ENST00000377967	NM_021140.2	206	Gaa/Taa	7/29	0.242901523872077	1	FACETS	0.856	0.79	0.924	0.856	0.79	0.924	INDETERMINATE	1	TRUE	0	0.486528992977981	1		626	607	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410467	63410467	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	137	673	0	ENST00000330258.3:c.2700G>T	p.Glu900Asp	p.E900D	ENST00000330258	NM_152424.3	900	gaG/gaT	2/2	0.242901523872077	1	FACETS	0.402	0.364	0.441	0.402	0.364	0.441	INDETERMINATE	1	TRUE	0	0.486528992977981	1		673	1061	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776973	76776973	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	57	628	0	ENST00000373344.5:c.6979C>G	p.Leu2327Val	p.L2327V	ENST00000373344	NM_000489.3	2327	Ctc/Gtc	33/35	0.242901523872077	1	FACETS	0.267	0.228	0.309	0.267	0.228	0.309	INDETERMINATE	1	TRUE	0	0.486528992977981	1		628	665	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276289	15276301	+	frameshift_variant	Frame_Shift_Del	DEL	CGGGCATCCAAGT	CGGGCATCCAAGT	-	novel	NA	P-0010531-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	138	362	0	ENST00000263388.2:c.5693_5705del	p.Asp1898AlafsTer9	p.D1898Afs*9	ENST00000263388	NM_000435.2	1898	gACTTGGATGCCCGc/gc	31/33	1	2	FACETS	0.847	0.772	0.924	0.847	0.772	0.924	CLONAL	1	TRUE	1	0.486528992977981	2		362	670	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	101	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.597334673338913	2		280	322	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872953	136872953	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1646	332	1136	0	ENST00000241393.3:c.545A>G	p.Asp182Gly	p.D182G	ENST00000241393	NM_003467.2	182	gAc/gGc	2/2	0.27503997933988	1	FACETS	0.394	0.371	0.418	0.394	0.371	0.418	INDETERMINATE	1	TRUE	0	0.597334673338913	1		1136	1978	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589591	67589592	+	inframe_insertion	In_Frame_Ins	INS	-	-	ATAACACTCAGTTTCAAGAAAAAAGTCGAGAATATG	novel	NA	P-0010534-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	107	421	0	ENST00000274335.5:c.1358_1393dup	p.Asn453_Asp464dup	p.N453_D464dup	ENST00000274335		453	tat/tATAACACTCAGTTTCAAGAAAAAAGTCGAGAATATGat	10/15	1	2	FACETS	0.498	0.447	0.553	0.498	0.447	0.553	SUBCLONAL	1	TRUE	1	0.597334673338913	2		421	719	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	256	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.71611968133298	2		280	698	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942761	44942761	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	409	372	0	ENST00000377967.4:c.3341C>T	p.Ser1114Leu	p.S1114L	ENST00000377967	NM_021140.2	1114	tCa/tTa	23/29	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.71611968133298	1		372	585	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0010582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	275	595	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	0.905	0.852	0.958	0.905	0.852	0.958	CLONAL	1	TRUE	1	0.71611968133298	2		595	849	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265453	198265453	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	217	540	0	ENST00000335508.6:c.2704G>A	p.Glu902Lys	p.E902K	ENST00000335508	NM_012433.2	902	Gaa/Aaa	18/25	1	2	FACETS	0.91	0.85	0.971	0.91	0.85	0.971	CLONAL	1	TRUE	1	0.71611968133298	2		540	666	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339253	70339253	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199469669	NA	P-0010582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	351	283	0	ENST00000374080.3:c.130G>A	p.Gly44Ser	p.G44S	ENST00000374080		44	Ggt/Agt	2/45	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.71611968133298	1		283	494	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247165	153247165	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	148	261	0	ENST00000281708.4:c.1637C>T	p.Ser546Leu	p.S546L	ENST00000281708	NM_033632.3	546	tCa/tTa	10/12	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.71611968133298	2		261	399	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65310517	65310517	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	310	509	1	ENST00000342505.4:c.2171G>A	p.Arg724His	p.R724H	ENST00000342505	NM_002227.2	724	cGt/cAt	16/25	1	2	FACETS	0.987	0.934	1	0.987	0.934	1	CLONAL	1	TRUE	1	0.71611968133298	2		510	877	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43814652	43814652	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1476959650	NA	P-0010582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	217	446	0	ENST00000372470.3:c.1447G>A	p.Val483Met	p.V483M	ENST00000372470	NM_005373.2	483	Gtg/Atg	9/12	1	2	FACETS	0.937	0.876	0.999	0.937	0.876	0.999	CLONAL	1	TRUE	1	0.71611968133298	2		446	647	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47637326	47637326	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs759712763	NA	P-0010582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	496	899	0	ENST00000233146.2:c.460G>T	p.Ala154Ser	p.A154S	ENST00000233146	NM_000251.2	154	Gca/Tca	3/16	1	2	FACETS	0.929	0.889	0.97	0.929	0.889	0.97	CLONAL	1	TRUE	1	0.71611968133298	2		899	1491	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799658	72799658	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	347	775	0	ENST00000325599.8:c.1511T>G	p.Ile504Ser	p.I504S	ENST00000325599	NM_018130.2	504	aTt/aGt	11/11	1	2	FACETS	0.858	0.813	0.904	0.858	0.813	0.904	CLONAL	1	TRUE	1	0.71611968133298	2		775	1129	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100533	157100533	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	196	267	0	ENST00000346085.5:c.1470G>A	p.Trp490Ter	p.W490*	ENST00000346085	NM_020732.3	490	tgG/tgA	1/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.71611968133298	2		267	508	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827454	72827454	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	468	874	0	ENST00000268489.5:c.9127A>G	p.Ile3043Val	p.I3043V	ENST00000268489	NM_006885.3	3043	Atc/Gtc	9/10	1	2	FACETS	0.997	0.953	1	0.997	0.953	1	CLONAL	1	TRUE	1	0.71611968133298	2		874	1311	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089932	16089932	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0010582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	262	426	0	ENST00000268712.3:c.178C>T	p.Gln60Ter	p.Q60*	ENST00000268712	NM_006311.3	60	Cag/Tag	3/46	1	2	FACETS	0.9	0.846	0.955	0.9	0.846	0.955	CLONAL	1	TRUE	1	0.71611968133298	2		426	813	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7119490	7119490	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	406	754	1	ENST00000302850.5:c.3764T>C	p.Leu1255Pro	p.L1255P	ENST00000302850	NM_000208.2	1255	cTg/cCg	21/22	1	2	FACETS	0.929	0.885	0.975	0.929	0.885	0.975	CLONAL	1	TRUE	1	0.71611968133298	2		755	1220	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856345	45856345	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	382	757	0	ENST00000391945.4:c.1827C>G	p.Asp609Glu	p.D609E	ENST00000391945	NM_000400.3	609	gaC/gaG	19/23	1	2	FACETS	0.954	0.907	1	0.954	0.907	1	CLONAL	1	TRUE	1	0.71611968133298	2		757	1118	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123227924	123227924	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	115	279	240	0	ENST00000218089.9:c.3635T>C	p.Met1212Thr	p.M1212T	ENST00000218089	NM_001042749.1	1212	aTg/aCg	33/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.71611968133298	1		240	394	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68772230	68772236	+	frameshift_variant	Frame_Shift_Del	DEL	CCCTGCC	CCCTGCC	-	novel	NA	P-0010582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	361	908	0	ENST00000261769.5:c.79_85del	p.Pro27ThrfsTer27	p.P27Tfs*27	ENST00000261769	NM_004360.3	27	CCCTGCCac/ac	2/16	1	2	FACETS	0.837	0.793	0.881	0.837	0.793	0.881	CLONAL	1	TRUE	1	0.71611968133298	2		908	1205	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56774175	56774190	+	protein_altering_variant	In_Frame_Del	DEL	TGCATTCAGCACCTTC	TGCATTCAGCACCTTC	A	novel	NA	P-0010582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	263	461	0	ENST00000337432.4:c.526_541delinsA	p.Cys176_Gln181delinsLys	p.C176_Q181delinsK	ENST00000337432	NM_058216.2	176	TGCATTCAGCACCTTCag/Aag	3/9	1	2	FACETS	0.875	0.823	0.929	0.875	0.823	0.929	CLONAL	1	TRUE	1	0.71611968133298	2		461	839	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73096300	73096368	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ACATGGTATTATATATTTTTTAATTTTTTGCTTATAGGATTCAGTGGTCCCAATTTAAAGGCTATTTTA	ACATGGTATTATATATTTTTTAATTTTTTGCTTATAGGATTCAGTGGTCCCAATTTAAAGGCTATTTTA	-	novel	NA	P-0010582-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	19	66	0	ENST00000356692.5:c.117-37_148del		p.X39_splice	ENST00000356692		39		3/9	1	2	FACETS	0.884	0.695	1	0.884	0.695	1	CLONAL	1	TRUE	1	0.71611968133298	2		66	60	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	100	280	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.961	1			1	INDETERMINATE	1	TRUE	NA	0.354191240935628	2		280	493	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499657	8499657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010584-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	143	410	0	ENST00000356435.5:c.2312C>T	p.Ala771Val	p.A771V	ENST00000356435		771	gCt/gTt	14/35	0.290305737103939	1	FACETS	0.777	0.709	0.849	0.777	0.709	0.849	SUBCLONAL	1	TRUE	0	0.354191240935628	1		410	855	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0010713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	202	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.997	0.928	1	0.997	0.928	1	CLONAL	1	TRUE	1	0.563460516045653	2		464	719	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717672	89717672	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909219	NA	P-0010713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	253	413	0	ENST00000371953.3:c.697C>T	p.Arg233Ter	p.R233*	ENST00000371953	NM_000314.4	233	Cga/Tga	7/9	0.563460516045653	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.563460516045653	1		413	637	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47612339	47612339	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0010713-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	257	528	0	ENST00000263735.4:c.893A>C	p.Glu298Ala	p.E298A	ENST00000263735	NM_002354.2	298	gAg/gCg	8/9	1	2	FACETS	0.923	0.865	0.983	0.923	0.865	0.983	CLONAL	1	TRUE	1	0.563460516045653	2		528	988	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010743-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	141	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.978	0.903	1	0.978	0.903	1	CLONAL	1	TRUE	1	0.807460119401783	2		280	357	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692895	89692895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781255	NA	P-0010743-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	216	252	0	ENST00000371953.3:c.379G>A	p.Gly127Arg	p.G127R	ENST00000371953	NM_000314.4	127	Gga/Aga	5/9	0.807460119401783	1	FACETS	0.97	0.923	1	0.97	0.923	1	CLONAL	1	TRUE	0	0.807460119401783	1		252	329	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813023	89813023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142833057	NA	P-0010743-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	344	532	0	ENST00000389301.3:c.3482C>T	p.Thr1161Met	p.T1161M	ENST00000389301	NM_000135.2	1161	aCg/aTg	35/43	1	2	FACETS	0.92	0.874	0.967	0.92	0.874	0.967	CLONAL	1	TRUE	1	0.807460119401783	2		532	926	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198266834	198266834	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs559063155	NA	P-0010754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	159	473	0	ENST00000335508.6:c.2098A>G	p.Lys700Glu	p.K700E	ENST00000335508	NM_012433.2	700	Aaa/Gaa	15/25	0.268003244072299	3	FACETS	1	0.987	1	0.683	0.629	0.738	INDETERMINATE	1	TRUE	1	0.529911570750506	3		473	556	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106822	27106822	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0010754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	192	443	1	ENST00000324856.7:c.6433G>T	p.Glu2145Ter	p.E2145*	ENST00000324856	NM_006015.4	2145	Gag/Tag	20/20	0.213093021732947	5	FACETS	0.822	0.762	0.884	0.548	0.508	0.59	INDETERMINATE	2	TRUE	2	0.529911570750506	5		444	791	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056584	26056584	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770343058	NA	P-0010754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	134	197	0	ENST00000343677.2:c.73G>A	p.Ala25Thr	p.A25T	ENST00000343677	NM_005319.3	25	Gcc/Acc	1/1	0.41528999678379	4	FACETS	1	0.954	1	0.539	0.49	0.59	CLONAL	1	TRUE	2	0.529911570750506	4		197	718	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55260477	55260477	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	43	572	1	ENST00000275493.2:c.2644G>A	p.Ala882Thr	p.A882T	ENST00000275493	NM_005228.3	882	Gca/Aca	22/28	0.219833249892402	4	FACETS	1	0.955	1	0.694	0.589	0.806	INDETERMINATE	1	TRUE	2	0.529911570750506	4		573	179	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258800	115258800	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0010754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	23	292	0	ENST00000369535.4:c.-17-2A>G		p.X6_splice	ENST00000369535	NM_002524.4	6			0.213093021732947	5	FACETS	0.875	0.687	1	0.292	0.229	0.363	INDETERMINATE	1	TRUE	2	0.529911570750506	5		292	178	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111503	8111509	+	frameshift_variant	Frame_Shift_Del	DEL	GGAATGC	GGAATGC	TG	novel	NA	P-0010754-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	410	571	0	ENST00000346208.3:c.989_995delinsTG	p.Arg330MetfsTer20	p.R330Mfs*20	ENST00000346208		330	aGGAATGCc/aTGc	5/6	0.350759311630328	3	FACETS	0.758	0.722	0.795	0.758	0.722	0.795	SUBCLONAL	2	TRUE	1	0.529911570750506	3		571	1291	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010762-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	69	280	0				ENST00000310581	NM_198253.2	-/1132			0.480233337528049	5	FACETS	1	0.974	1	0.489	0.43	0.55	CLONAL	1	TRUE	2	0.754225444431734	5		280	266	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609916	81609916	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908876	NA	P-0010762-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	46	410	0	ENST00000298171.2:c.1514G>A	p.Ser505Asn	p.S505N	ENST00000298171	NM_000369.2	505	aGc/aAc	10/10	0.754225444431734	3	FACETS	0.836	0.713	0.968	0.418	0.356	0.484	CLONAL	1	TRUE	1	0.754225444431734	3		410	201	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40733210	40733210	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010762-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	42	413	0	ENST00000373198.4:c.3596A>G	p.Gln1199Arg	p.Q1199R	ENST00000373198	NM_133170.3	1199	cAg/cGg	26/32	0.754225444431734	3	FACETS	1	0.946	1	0.623	0.533	0.718	CLONAL	1	TRUE	1	0.754225444431734	3		413	123	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010802-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	82	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.84	2		280	190	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51439692	51439692	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1363868066	NA	P-0010802-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	261	273	0	ENST00000262662.1:c.257T>C	p.Leu86Ser	p.L86S	ENST00000262662		86	tTa/tCa	4/4	0.81924889663678	1	FACETS	0.951	0.911	0.99	0.951	0.911	0.99	CLONAL	1	TRUE	0	0.84	1		273	379	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0010805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	94	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.805	0.723	0.89	1	0.984	1	CLONAL	2	TRUE	1	0.350781984703368	2		464	333	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0010805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	412	528	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	0.350781984703368	3	FACETS	0.902	0.862	0.943	0.902	0.862	0.943	CLONAL	3	TRUE	0	0.350781984703368	3		528	1020	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056291	180056291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199942873	NA	P-0010805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	259	487	0	ENST00000261937.6:c.953G>A	p.Arg318Gln	p.R318Q	ENST00000261937	NM_182925.4	318	cGa/cAa	7/30	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.350781984703368	2		487	1010	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100312	27100312	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	503	466	0	ENST00000324856.7:c.4024C>T	p.Gln1342Ter	p.Q1342*	ENST00000324856	NM_006015.4	1342	Cag/Tag	17/20	0.350781984703368	3	FACETS	0.954	0.916	0.992	0.954	0.916	0.992	CLONAL	3	TRUE	0	0.350781984703368	3		466	1178	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497738	120497738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782796803	NA	P-0010805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	165	310	0	ENST00000256646.2:c.2144C>T	p.Pro715Leu	p.P715L	ENST00000256646	NM_024408.3	715	cCc/cTc	13/34	0.192797559077571	4	FACETS	0.819	0.753	0.887	0.819	0.753	0.887	INDETERMINATE	2	TRUE	2	0.350781984703368	4		310	776	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12629107	12629107	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	206	275	0	ENST00000251849.4:c.1400G>A	p.Arg467Lys	p.R467K	ENST00000251849	NM_002880.3	467	aGa/aAa	13/17	0.350781984703368	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.350781984703368	4		275	708	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266486	41266486	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	207	340	0	ENST00000349496.5:c.283C>G	p.Arg95Gly	p.R95G	ENST00000349496	NM_001904.3	95	Cga/Gga	4/15	0.335809521865635	4	FACETS	0.792	0.734	0.851	0.792	0.734	0.851	SUBCLONAL	2	TRUE	2	0.350781984703368	4		340	1007	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739837	41739837	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	238	549	0	ENST00000242208.4:c.136G>A	p.Asp46Asn	p.D46N	ENST00000242208	NM_002192.2	46	Gat/Aat	2/3	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.350781984703368	2		549	1083	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846172	128846172	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374812951	NA	P-0010805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	255	514	0	ENST00000249373.3:c.1102C>T	p.Pro368Ser	p.P368S	ENST00000249373	NM_005631.4	368	Ccc/Tcc	5/12	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.350781984703368	2		514	1080	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101910005	101910005	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	106	358	0	ENST00000374994.4:c.1325G>A	p.Arg442Lys	p.R442K	ENST00000374994	NM_004612.2	442	aGa/aAa	8/9	0.268517308427508	2	FACETS	0.738	0.661	0.82	0.369	0.33	0.41	SUBCLONAL	1	TRUE	0	0.350781984703368	2		358	819	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572171	64572171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	177	361	0	ENST00000312049.6:c.1468G>A	p.Glu490Lys	p.E490K	ENST00000312049	NM_130799.2	490	Gag/Aag	10/10	0.268517308427508	2	FACETS	0.851	0.788	0.915	0.851	0.788	0.915	CLONAL	2	TRUE	0	0.350781984703368	2		361	593	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69457939	69457939	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	274	496	0	ENST00000227507.2:c.339G>A	p.Met113Ile	p.M113I	ENST00000227507	NM_053056.2	113	atG/atA	2/5	0.268517308427508	2	FACETS	0.811	0.762	0.861	0.811	0.762	0.861	CLONAL	2	TRUE	0	0.350781984703368	2		496	963	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514308	69514308	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142959398	NA	P-0010805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	179	386	0	ENST00000294312.3:c.373G>A	p.Glu125Lys	p.E125K	ENST00000294312	NM_005117.2	125	Gag/Aag	3/3	0.268517308427508	2	FACETS	0.752	0.695	0.81	0.752	0.695	0.81	SUBCLONAL	2	TRUE	0	0.350781984703368	2		386	679	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518531	69518531	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	58	127	0	ENST00000294312.3:c.114G>A	p.Trp38Ter	p.W38*	ENST00000294312	NM_005117.2	38	tgG/tgA	1/3	0.268517308427508	2	FACETS	0.819	0.714	0.928	0.819	0.714	0.928	CLONAL	2	TRUE	0	0.350781984703368	2		127	202	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378633	25378633	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	94	366	0	ENST00000311936.3:c.365C>T	p.Ser122Phe	p.S122F	ENST00000311936	NM_004985.3	122	tCt/tTt	4/5	1	2	FACETS	0.699	0.621	0.781	0.699	0.621	0.781	SUBCLONAL	1	TRUE	1	0.350781984703368	2		366	767	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422997	49422997	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369583907	NA	P-0010805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	143	416	0	ENST00000301067.7:c.14098G>A	p.Asp4700Asn	p.D4700N	ENST00000301067	NM_003482.3	4700	Gat/Aat	44/54	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.350781984703368	2		416	740	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493661	56493661	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	130	346	0	ENST00000267101.3:c.2977C>T	p.His993Tyr	p.H993Y	ENST00000267101	NM_001982.3	993	Cat/Tat	25/28	1	2	FACETS	0.877	0.796	0.963	0.877	0.796	0.963	CLONAL	1	TRUE	1	0.350781984703368	2		346	845	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912750	32912750	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1195	159	616	0	ENST00000380152.3:c.4258G>A	p.Asp1420Asn	p.D1420N	ENST00000380152		1420	Gat/Aat	11/27	0.268517308427508	2	FACETS	0.67	0.612	0.73	0.335	0.306	0.365	SUBCLONAL	1	TRUE	0	0.350781984703368	2		616	1354	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744443	41744443	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	238	546	0	ENST00000301178.4:c.1063G>A	p.Glu355Lys	p.E355K	ENST00000301178	NM_021913.4	355	Gag/Aag	8/20	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.350781984703368	2		546	1100	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860910	45860910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010805-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	85	506	1	ENST00000391945.4:c.1285G>A	p.Ala429Thr	p.A429T	ENST00000391945	NM_000400.3	429	Gcc/Acc	13/23	1	2	FACETS	0.454	0.4	0.512	0.454	0.4	0.512	SUBCLONAL	1	TRUE	1	0.350781984703368	2		507	1067	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566453	41566453	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010841-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	81	491	0	ENST00000263253.7:c.4330G>A	p.Asp1444Asn	p.D1444N	ENST00000263253	NM_001429.3	1444	Gat/Aat	27/31	1	2	FACETS	0.293	0.257	0.331	0.293	0.257	0.331	SUBCLONAL	1	TRUE	1	0.52	2		491	1065	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47004912	47004912	+	intron_variant	Intron	SNP	G	G	T	novel	NA	P-0010841-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	53	329	0	ENST00000377604.3:c.-126+28G>T		p.*42*	ENST00000377604	NM_001204468.1	-/852			1	2	FACETS	0.292	0.248	0.34	0.292	0.248	0.34	SUBCLONAL	1	TRUE	1	0.52	2		329	698	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880998	37880998	+	protein_altering_variant	In_Frame_Ins	INS	G	G	TTGT	novel	NA	P-0010841-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	134	451	0	ENST00000269571.5:c.2327delinsTTGT	p.Gly776delinsValVal	p.G776delinsVV	ENST00000269571		776	gGt/gTTGTt	20/27	0.140090540784689	3	FACETS	0.614	0.557	0.675	0.307	0.278	0.338	INDETERMINATE	1	TRUE	1	0.52	3		451	1057	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	39	280	0				ENST00000310581	NM_198253.2	-/1132			0.3	0	FACETS	0.518	0.438	0.604			1	INDETERMINATE	1	TRUE	0	0.52	0		280	139	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0010859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	210	511	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.52	2		512	636	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444274	49444274	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0010859-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	59	655	0	ENST00000301067.7:c.3097del	p.Val1033PhefsTer23	p.V1033Ffs*23	ENST00000301067	NM_003482.3	1033	Gtt/tt	11/54	0.2542183940555	4	FACETS	0.446	0.383	0.515	0.223	0.191	0.258	INDETERMINATE	1	TRUE	2	0.52	4		655	773	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	15	27	280	0				ENST00000310581	NM_198253.2	-/1132			0.407156372944734	0	FACETS		NA	1			1	NA	NA	FALSE	0	NA	0		280	42	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0010900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	141	500	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	0.173214964553131	2	FACETS		NA	1			1	NA	NA	FALSE	0	NA	2		500	335	SUCCESS
FH	2271	MSKCC	GRCh37	1	241671997	241671999	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0010900-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	122	417	0	ENST00000366560.3:c.642_644del	p.Leu214_His215delinsPhe	p.L214_H215delinsF	ENST00000366560	NM_000143.3	214	ttACAt/ttt	5/10	0.250100438958096	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		417	268	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0010915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	166	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.571417571726987	2		464	492	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547022	9547022	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs58486349	NA	P-0010915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	74	150	0	ENST00000353224.5:c.1000G>A	p.Asp334Asn	p.D334N	ENST00000353224	NM_177990.2	334	Gat/Aat	5/10	1	2	FACETS	0.896	0.793	1	0.896	0.793	1	CLONAL	1	TRUE	1	0.571417571726987	2		150	289	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612735	228612735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	577	1195	1	ENST00000366696.1:c.292G>A	p.Glu98Lys	p.E98K	ENST00000366696	NM_003493.2	98	Gag/Aag	1/1	0.555898147132432	1	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	0	0.571417571726987	1		1196	1389	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920412	134920412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746798014	NA	P-0010915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	341	628	0	ENST00000398015.3:c.2227C>T	p.Arg743Trp	p.R743W	ENST00000398015	NM_004441.4	743	Cgg/Tgg	12/16	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.571417571726987	2		628	1165	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413577	32413577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1037084691	NA	P-0010915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	223	422	0	ENST00000332351.3:c.1373G>A	p.Arg458Gln	p.R458Q	ENST00000332351	NM_024426.4	458	cGa/cAa	9/10	1	2	FACETS	0.964	0.899	1	0.964	0.899	1	CLONAL	1	TRUE	1	0.571417571726987	2		422	810	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248786	212248786	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0010915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	59	216	0	ENST00000342788.4:c.3482-1G>A		p.X1161_splice	ENST00000342788	NM_005235.2	1161			1	2	FACETS	0.746	0.647	0.851	0.746	0.647	0.851	SUBCLONAL	1	TRUE	1	0.571417571726987	2		216	277	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439974	220439974	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	470	951	0	ENST00000243786.2:c.827G>C	p.Trp276Ser	p.W276S	ENST00000243786	NM_002191.3	276	tGg/tCg	2/2	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.571417571726987	2		951	1610	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280013	66280013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	170	405	0	ENST00000273854.3:c.1676C>T	p.Thr559Ile	p.T559I	ENST00000273854	NM_004439.5	559	aCc/aTc	7/18	1	2	FACETS	0.872	0.805	0.942	0.872	0.805	0.942	CLONAL	1	TRUE	1	0.571417571726987	2		405	682	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140487372	140487372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	221	945	0	ENST00000288602.6:c.1153G>A	p.Asp385Asn	p.D385N	ENST00000288602	NM_004333.4	385	Gac/Aac	9/18	0.571417571726987	3	FACETS	0.787	0.731	0.845	0.393	0.365	0.423	SUBCLONAL	1	TRUE	1	0.571417571726987	3		945	1264	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435626	18435626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	75	395	0	ENST00000266497.5:c.611C>T	p.Ser204Phe	p.S204F	ENST00000266497		204	tCt/tTt	1/31	1	2	FACETS	0.693	0.61	0.78	0.693	0.61	0.78	SUBCLONAL	1	TRUE	1	0.571417571726987	2		395	379	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435633	18435633	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0010915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	74	382	0	ENST00000266497.5:c.618G>T	p.Met206Ile	p.M206I	ENST00000266497		206	atG/atT	1/31	1	2	FACETS	0.717	0.632	0.808	0.717	0.632	0.808	SUBCLONAL	1	TRUE	1	0.571417571726987	2		382	361	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28908165	28908165	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0010915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	261	564	0	ENST00000282397.4:c.2590A>G	p.Lys864Glu	p.K864E	ENST00000282397	NM_002019.4	864	Aaa/Gaa	18/30	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.571417571726987	2		564	881	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28963948	28963948	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0010915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	163	617	0	ENST00000282397.4:c.1954G>T	p.Glu652Ter	p.E652*	ENST00000282397	NM_002019.4	652	Gaa/Taa	13/30	1	2	FACETS	0.748	0.687	0.811	0.748	0.687	0.811	SUBCLONAL	1	TRUE	1	0.571417571726987	2		617	763	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347919	73347919	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	84	381	0	ENST00000377767.4:c.1142C>T	p.Pro381Leu	p.P381L	ENST00000377767	NM_014953.3	381	cCt/cTt	8/21	1	2	FACETS	0.71	0.631	0.794	0.71	0.631	0.794	SUBCLONAL	1	TRUE	1	0.571417571726987	2		381	414	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479765	67479765	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	328	587	1	ENST00000327367.4:c.1072C>T	p.Gln358Ter	p.Q358*	ENST00000327367	NM_005902.3	358	Cag/Tag	8/9	1	2	FACETS	0.978	0.924	1	0.978	0.924	1	CLONAL	1	TRUE	1	0.571417571726987	2		588	1174	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374408	31374408	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs762297902	NA	P-0010915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	394	691	0	ENST00000328111.2:c.407C>A	p.Ser136Tyr	p.S136Y	ENST00000328111	NM_006892.3	136	tCc/tAc	5/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.571417571726987	2		691	1260	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866465	42866465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	422	915	1	ENST00000398585.3:c.167G>A	p.Gly56Glu	p.G56E	ENST00000398585	NM_001135099.1	56	gGa/gAa	3/14	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.571417571726987	2		916	1452	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776960	76776960	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	157	728	0	ENST00000373344.5:c.6992G>A	p.Gly2331Glu	p.G2331E	ENST00000373344	NM_000489.3	2331	gGa/gAa	33/35	NA	2	FACETS	0.868	0.798	0.941			1	INDETERMINATE	1	TRUE	NA	0.571417571726987	2		728	633	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78435620	78435620	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0010915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	272	631	0	ENST00000370768.2:c.200del	p.Leu67Ter	p.L67*	ENST00000370768	NM_003902.3	67	tTa/ta	2/20	0.571417571726987	3	FACETS	0.864	0.816	0.914	0.864	0.816	0.914	CLONAL	2	TRUE	1	0.571417571726987	3		631	708	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481402	140481403	+	missense_variant	Missense_Mutation	DNP	CC	CC	GA	rs1057519720	NA	P-0010915-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	241	530	0	ENST00000288602.6:c.1405_1406delinsTC	p.Gly469Ser	p.G469S	ENST00000288602	NM_004333.4	469	GGa/TCa	11/18	0.571417571726987	3	FACETS	0.82	0.771	0.871	0.82	0.771	0.871	CLONAL	2	TRUE	1	0.571417571726987	3		530	661	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010926-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	69	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.871	0.769	0.977	0.871	0.769	0.977	CLONAL	1	TRUE	1	0.677405139930441	2		280	234	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0010926-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	310	614	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.677405139930441	2		614	763	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579350	7579350	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs587781642	NA	P-0010938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	190	439	0	ENST00000269305.4:c.337T>G	p.Phe113Val	p.F113V	ENST00000269305	NM_001126112.2	113	Ttc/Gtc	4/11	0.39692647775364	2	FACETS	1	0.991	1	0.738	0.687	0.79	CLONAL	1	TRUE	0	0.458149967123937	2		439	562	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133248872	133248872	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0010938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	53	389	0	ENST00000320574.5:c.1723G>A	p.Glu575Lys	p.E575K	ENST00000320574	NM_006231.2	575	Gag/Aag	16/49	0.441256879151432	3	FACETS	0.407	0.346	0.474	0.136	0.115	0.158	SUBCLONAL	1	TRUE	0	0.458149967123937	3		389	699	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215634032	215634032	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753446928	NA	P-0010938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	133	384	0	ENST00000260947.4:c.1319A>G	p.Asp440Gly	p.D440G	ENST00000260947	NM_000465.2	440	gAc/gGc	5/11	0.39692647775364	2	FACETS	0.829	0.755	0.908	0.415	0.377	0.454	CLONAL	1	TRUE	0	0.458149967123937	2		384	700	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441252	52441252	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	215	428	0	ENST00000460680.1:c.518A>C	p.Tyr173Ser	p.Y173S	ENST00000460680	NM_004656.3	173	tAt/tCt	7/17	0.39692647775364	2	FACETS	0.856	0.803	0.911	0.856	0.803	0.911	CLONAL	2	TRUE	0	0.458149967123937	2		428	548	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190800	185190800	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	155	444	0	ENST00000265026.3:c.1681G>C	p.Glu561Gln	p.E561Q	ENST00000265026	NM_004721.4	561	Gaa/Caa	11/14	0.458149967123937	3	FACETS	0.956	0.875	1	0.478	0.437	0.52	CLONAL	1	TRUE	1	0.458149967123937	3		444	870	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38991061	38991061	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	121	291	0	ENST00000357387.3:c.573C>G	p.Ile191Met	p.I191M	ENST00000357387	NM_152756.3	191	atC/atG	7/38	1	2	FACETS	0.886	0.803	0.973	0.886	0.803	0.973	CLONAL	1	TRUE	1	0.458149967123937	2		291	596	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636777	176636777	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	141	382	0	ENST00000439151.2:c.1377C>G	p.Asp459Glu	p.D459E	ENST00000439151	NM_022455.4	459	gaC/gaG	5/23	0.131982767548425	6	FACETS	1	0.95	1			1	INDETERMINATE	1	TRUE	NA	0.458149967123937	6		382	1106	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249386	110249386	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0010938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	373	645	0	ENST00000374672.4:c.1187A>T	p.His396Leu	p.H396L	ENST00000374672	NM_004235.4	396	cAc/cTc	4/5	NA	2	FACETS	0.914	0.871	0.957			1	INDETERMINATE	2	TRUE	NA	0.458149967123937	2		645	891	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127703	64127703	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	45	312	0	ENST00000334205.4:c.196G>C	p.Val66Leu	p.V66L	ENST00000334205	NM_003942.2	66	Gtg/Ctg	3/17	0.155713145050297	2	FACETS	0.471	0.396	0.553	0.236	0.198	0.277	INDETERMINATE	1	TRUE	0	0.458149967123937	2		312	417	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999597	100999597	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0010938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	166	648	0	ENST00000325455.5:c.205C>G	p.Pro69Ala	p.P69A	ENST00000325455	NM_001202474.3	69	Ccc/Gcc	1/8	0.251393947732859	5	FACETS	1	0.97	1	0.374	0.343	0.407	INDETERMINATE	1	TRUE	2	0.458149967123937	5		648	1090	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344419	118344419	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0010938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	43	238	0	ENST00000534358.1:c.2545A>T	p.Arg849Ter	p.R849*	ENST00000534358	NM_005933.3	849	Aga/Tga	3/36	0.37148545353307	3	FACETS	0.483	0.404	0.57	0.161	0.134	0.19	SUBCLONAL	1	TRUE	0	0.458149967123937	3		238	478	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28602348	28602348	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0010938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	185	476	0	ENST00000241453.7:c.2020A>C	p.Ile674Leu	p.I674L	ENST00000241453	NM_004119.2	674	Att/Ctt	16/24	0.199820263571232	4	FACETS	1	0.974	1			1	INDETERMINATE	1	TRUE	NA	0.458149967123937	4		476	1044	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2135234	2135234	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45517352	NA	P-0010938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	116	369	0	ENST00000219476.3:c.4573C>T	p.Gln1525Ter	p.Q1525*	ENST00000219476	NM_000548.3	1525	Cag/Tag	36/42	0.380604017210964	1	FACETS	0.919	0.834	1	0.919	0.834	1	CLONAL	1	TRUE	0	0.458149967123937	1		369	425	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032264	10032264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751692867	NA	P-0010938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	90	292	1	ENST00000330684.3:c.559G>A	p.Val187Ile	p.V187I	ENST00000330684	NM_001134407.1	187	Gtc/Atc	3/13	0.445608855590122	2	FACETS	0.85	0.758	0.948	0.425	0.379	0.474	CLONAL	1	TRUE	0	0.458149967123937	2		293	462	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775440	39775440	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0010938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	89	385	0	ENST00000288319.7:c.580T>C	p.Tyr194His	p.Y194H	ENST00000288319	NM_182918.3	194	Tac/Cac	4/10	1	2	FACETS	0.799	0.711	0.893	0.799	0.711	0.893	SUBCLONAL	1	TRUE	1	0.458149967123937	2		385	486	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929448	44929449	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0010938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	232	518	0	ENST00000377967.4:c.2548_2549insT	p.Gly850ValfsTer6	p.G850Vfs*6	ENST00000377967	NM_021140.2	850	ggg/gTgg	17/29	0.458149967123937	1	FACETS	0.786	0.733	0.841	0.786	0.733	0.841	SUBCLONAL	1	TRUE	0	0.458149967123937	1		518	993	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201973	102201987	+	splice_donor_variant,intron_variant	Splice_Site	DEL	GTATGTAGATTTATT	GTATGTAGATTTATT	-	novel	NA	P-0010938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	66	524	0	ENST00000263464.3:c.1324+1_1324+15del		p.X442_splice	ENST00000263464	NM_001165.4	442			0.251393947732859	5	FACETS	0.419	0.362	0.481	0.14	0.12	0.161	INDETERMINATE	1	TRUE	2	0.458149967123937	5		524	1161	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201966	102201967	+	protein_altering_variant	In_Frame_Ins	INS	GA	GA	TCCTTATTTCATATAGG	novel	NA	P-0010938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1261	90	557	0	ENST00000263464.3:c.1318_1319delinsTCCTTATTTCATATAGG	p.Glu440delinsSerLeuPheHisIleGly	p.E440delinsSLFHIG	ENST00000263464	NM_001165.4	440	GAa/TCCTTATTTCATATAGGa	6/9	0.251393947732859	5	FACETS	0.491	0.434	0.552	0.164	0.144	0.184	INDETERMINATE	1	TRUE	2	0.458149967123937	5		557	1351	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	112	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.66	2		280	337	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0010962-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	148	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.938	0.863	1	0.938	0.863	1	CLONAL	1	TRUE	1	0.66	2		490	478	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0010974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	195	280	0				ENST00000310581	NM_198253.2	-/1132			0.308965678888482	4	FACETS	0.919	0.856	0.984	0.919	0.856	0.984	CLONAL	3	TRUE	1	0.308965678888482	4		280	599	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0010974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	51	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.752	0.64	0.874	0.752	0.64	0.874	SUBCLONAL	1	TRUE	1	0.308965678888482	2		490	439	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245858	46245858	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	76	390	1	ENST00000334344.6:c.3952C>T	p.Gln1318Ter	p.Q1318*	ENST00000334344	NM_152641.2	1318	Cag/Tag	15/21	1	2	FACETS	0.946	0.832	1	0.946	0.832	1	CLONAL	1	TRUE	1	0.308965678888482	2		391	520	SUCCESS
APC	324	MSKCC	GRCh37	5	112103020	112103020	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	203	375	0	ENST00000257430.4:c.355C>G	p.Pro119Ala	p.P119A	ENST00000257430	NM_000038.5	119	Cca/Gca	4/16	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.308965678888482	2		375	934	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197187	26197187	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0010974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1977	295	1056	0	ENST00000356476.2:c.292G>C	p.Glu98Gln	p.E98Q	ENST00000356476		98	Gag/Cag	1/1	1	2	FACETS	0.84	0.787	0.896	0.84	0.787	0.896	CLONAL	1	TRUE	1	0.308965678888482	2		1056	2272	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30680695	30680695	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	144	544	0	ENST00000376406.3:c.1024C>T	p.Pro342Ser	p.P342S	ENST00000376406	NM_014641.2	342	Cca/Tca	5/15	1	2	FACETS	0.866	0.789	0.948	0.866	0.789	0.948	CLONAL	1	TRUE	1	0.308965678888482	2		544	1076	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246290	46246290	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0010974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	105	335	1	ENST00000334344.6:c.4384C>T	p.Gln1462Ter	p.Q1462*	ENST00000334344	NM_152641.2	1462	Cag/Tag	15/21	1	2	FACETS	0.89	0.797	0.988	0.89	0.797	0.988	CLONAL	1	TRUE	1	0.308965678888482	2		336	764	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610074	81610074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0010974-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	103	450	0	ENST00000298171.2:c.1672G>A	p.Val558Met	p.V558M	ENST00000298171	NM_000369.2	558	Gtg/Atg	10/10	1	2	FACETS	0.855	0.765	0.95	0.855	0.765	0.95	CLONAL	1	TRUE	1	0.308965678888482	2		450	780	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011001-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	157	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.685156228750489	2		280	345	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631838	90631838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913503	NA	P-0011001-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	249	471	0	ENST00000330062.3:c.515G>A	p.Arg172Lys	p.R172K	ENST00000330062	NM_002168.2	172	aGg/aAg	4/11	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.685156228750489	2		471	571	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413070	139413072	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	novel	NA	P-0011001-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	70	555	0	ENST00000277541.6:c.1070_1072del	p.Phe357del	p.F357del	ENST00000277541	NM_017617.3	357	tTCTac/tac	6/34	1	2	FACETS	0.281	0.244	0.321	0.281	0.244	0.321	SUBCLONAL	1	TRUE	1	0.685156228750489	2		555	727	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0011001-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	11	263	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.297	0.207	0.408	0.297	0.207	0.408	SUBCLONAL	1	TRUE	1	0.685156228750489	2		263	108	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799063	42799065	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs751580245	NA	P-0011001-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	36	450	0	ENST00000575354.2:c.4550_4552del	p.Lys1517del	p.K1517del	ENST00000575354	NM_015125.3	1516	cAGAag/cag	20/20	0.685156228750489	1	FACETS	0.215	0.177	0.257	0.215	0.177	0.257	SUBCLONAL	1	TRUE	0	0.685156228750489	1		450	322	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42799060	42799060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011001-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	56	456	1	ENST00000575354.2:c.4544G>A	p.Arg1515His	p.R1515H	ENST00000575354	NM_015125.3	1515	cGc/cAc	20/20	0.685156228750489	1	FACETS	0.33	0.284	0.379	0.33	0.284	0.379	SUBCLONAL	1	TRUE	0	0.685156228750489	1		457	326	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413099	139413099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011001-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	79	610	0	ENST00000277541.6:c.1043C>T	p.Ala348Val	p.A348V	ENST00000277541	NM_017617.3	348	gCc/gTc	6/34	1	2	FACETS	0.241	0.211	0.273	0.241	0.211	0.273	SUBCLONAL	1	TRUE	1	0.685156228750489	2		610	957	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796905	42796906	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0011001-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	141	653	0	ENST00000575354.2:c.3365_3366del	p.Val1122GlyfsTer28	p.V1122Gfs*28	ENST00000575354	NM_015125.3	1121	acTGtg/actg	14/20	0.685156228750489	1	FACETS	0.517	0.474	0.562	0.517	0.474	0.562	SUBCLONAL	1	TRUE	0	0.685156228750489	1		653	523	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0011011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	128	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.346630651117955	2		464	612	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533874	533874	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913233	NA	P-0011011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	223	500	0	ENST00000451590.1:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000451590	NM_001130442.1	61	cAg/cGg	3/5	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.346630651117955	2		500	1045	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412884	49412884	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011011-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1393	80	655	1	ENST00000418115.1:c.139G>A	p.Glu47Lys	p.E47K	ENST00000418115	NM_001664.2	47	Gag/Aag	2/5	1	2	FACETS	0.313	0.274	0.356	0.313	0.274	0.356	SUBCLONAL	1	TRUE	1	0.346630651117955	2		656	1473	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	527	280	0				ENST00000310581	NM_198253.2	-/1132			0.582446402801978	6	FACETS	1	0.994	1	1	0.994	1	CLONAL	5	TRUE	1	0.582446402801978	6		280	721	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881001	37881002	+	inframe_insertion	In_Frame_Ins	INS	-	-	GGGCTCCCC	rs397516981	NA	P-0011033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	799	565	0	ENST00000269571.5:c.2331_2339dup	p.Gly778_Pro780dup	p.G778_P780dup	ENST00000269571		778	gtg/gtGGGCTCCCCg	20/27	0.582446402801978	6	FACETS	1	0.985	1			1	CLONAL	3	TRUE	NA	0.582446402801978	6		565	1923	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47044502	47044502	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011033-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	200	528	0	ENST00000377604.3:c.1999G>C	p.Glu667Gln	p.E667Q	ENST00000377604	NM_001204468.1	667	Gaa/Caa	18/24	0.363730788763722	3	FACETS	0.977	0.906	1			1	CLONAL	1	TRUE	NA	0.582446402801978	3		528	908	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	126	280	0				ENST00000310581	NM_198253.2	-/1132			0.107051830055181	5	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.500499851470964	5		280	592	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112335	115112335	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	55	259	0	ENST00000257566.3:c.1405G>C	p.Glu469Gln	p.E469Q	ENST00000257566	NM_016569.3	469	Gag/Cag	7/8	0.500499851470964	3	FACETS	0.811	0.697	0.933	0.405	0.348	0.467	CLONAL	1	TRUE	1	0.500499851470964	3		259	339	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020046	123020046	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011079-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	123	391	0	ENST00000355640.3:c.534C>A	p.His178Gln	p.H178Q	ENST00000355640		178	caC/caA	2/7	0.420702166788672	3	FACETS	0.931	0.844	1			1	CLONAL	1	TRUE	NA	0.500499851470964	3		391	660	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0011080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	170	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.658	0.604	0.714	0.658	0.604	0.714	SUBCLONAL	1	TRUE	1	0.521062035946531	2		464	992	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0011080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	303	354	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.521062035946531	2		354	906	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119634931	119634931	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	83	222	0	ENST00000316626.5:c.568G>A	p.Asp190Asn	p.D190N	ENST00000316626		190	Gat/Aat	5/12	1	2	FACETS	0.552	0.488	0.621	0.552	0.488	0.621	SUBCLONAL	1	TRUE	1	0.521062035946531	2		222	577	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123181255	123181255	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	117	242	0	ENST00000218089.9:c.719A>T	p.Asn240Ile	p.N240I	ENST00000218089	NM_001042749.1	240	aAt/aTt	9/35	1	2	FACETS	0.745	0.673	0.82	0.745	0.673	0.82	SUBCLONAL	1	TRUE	1	0.521062035946531	2		242	603	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195635	123195635	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	275	610	1	ENST00000218089.9:c.1549C>T	p.Gln517Ter	p.Q517*	ENST00000218089	NM_001042749.1	517	Caa/Taa	17/35	1	2	FACETS	0.956	0.898	1	0.956	0.898	1	CLONAL	1	TRUE	1	0.521062035946531	2		611	1104	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717735	89717739	+	frameshift_variant	Frame_Shift_Del	DEL	AAAGT	AAAGT	-	rs606231169	NA	P-0011080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	99	189	0	ENST00000371953.3:c.761_765del	p.Lys254ArgfsTer42	p.K254Rfs*42	ENST00000371953	NM_000314.4	254	AAAGTa/a	7/9	0.521062035946531	1	FACETS	0.959	0.868	1	0.959	0.868	1	CLONAL	1	TRUE	0	0.521062035946531	1		189	293	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011081-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	366	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.838103273117204	2		280	806	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0011081-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	366	558	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.838103273117204	3	FACETS	0.896	0.857	0.934	0.896	0.857	0.934	CLONAL	2	TRUE	1	0.838103273117204	3		558	692	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803121	1803121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745863884	NA	P-0011081-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	474	690	1	ENST00000260795.2:c.473G>A	p.Arg158Gln	p.R158Q	ENST00000260795		158	cGg/cAg	4/17	1	2	FACETS	0.922	0.883	0.962	0.922	0.883	0.962	CLONAL	1	TRUE	1	0.838103273117204	2		691	1227	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0011081-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	19	463	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.099	0.075	0.128	0.099	0.075	0.128	SUBCLONAL	1	TRUE	1	0.838103273117204	2		463	456	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432743	29432743	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011081-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	326	538	1	ENST00000389048.3:c.3745G>A	p.Asp1249Asn	p.D1249N	ENST00000389048	NM_004304.4	1249	Gac/Aac	25/29	1	2	FACETS	0.885	0.839	0.932	0.885	0.839	0.932	CLONAL	1	TRUE	1	0.838103273117204	2		539	879	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024849	31024849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs3171366	NA	P-0011081-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	587	478	0	ENST00000375687.4:c.4334C>T	p.Ser1445Phe	p.S1445F	ENST00000375687	NM_015338.5	1445	tCt/tTt	13/13	0.838103273117204	3	FACETS	0.83	0.8	0.859	0.83	0.8	0.859	CLONAL	2	TRUE	1	0.838103273117204	3		478	1198	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266049	41266050	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0011081-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	218	380	0	ENST00000349496.5:c.46_47delinsTT	p.Pro16Leu	p.P16L	ENST00000349496	NM_001904.3	16	CCa/TTa	3/15	1	2	FACETS	0.768	0.718	0.82	0.768	0.718	0.82	SUBCLONAL	1	TRUE	1	0.838103273117204	2		380	677	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030439	49030440	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0011081-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	276	165	0	ENST00000267163.4:c.1914_1915delinsTT	p.Gln639Ter	p.Q639*	ENST00000267163	NM_000321.2	638	acCCag/acTTag	19/27	0.806748964222138	4	FACETS	0.855	0.815	0.894	0.855	0.815	0.894	CLONAL	3	TRUE	1	0.838103273117204	4		165	472	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579473	7579474	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0011081-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	292	544	0	ENST00000269305.4:c.213_214delinsTT	p.Pro72Ser	p.P72S	ENST00000269305	NM_001126112.2	71	ccCCcc/ccTTcc	4/11	1	2	FACETS	0.822	0.776	0.868	0.822	0.776	0.868	CLONAL	1	TRUE	1	0.838103273117204	2		544	848	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0011083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	32	660	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.150485877623347	3	FACETS	0.683	0.552	0.831	0.341	0.276	0.416	SUBCLONAL	1	TRUE	1	0.15	3		660	672	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0011083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	77	550	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	1	2	FACETS	0.932	0.816	1	0.932	0.816	1	CLONAL	1	TRUE	1	0.15	2		550	1101	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577139	7577139	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs55832599	NA	P-0011083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	30	719	0	ENST00000269305.4:c.799C>T	p.Arg267Trp	p.R267W	ENST00000269305	NM_001126112.2	267	Cgg/Tgg	8/11	1	2	FACETS	0.347	0.278	0.426	0.347	0.278	0.426	SUBCLONAL	1	TRUE	1	0.15	2		719	1153	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0011083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	59	272	0	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	0.3	3	FACETS	1	0.929	1			1	CLONAL	1	TRUE	NA	0.15	3		272	746	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87635188	87635188	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	53	470	1	ENST00000277120.3:c.2240C>T	p.Thr747Met	p.T747M	ENST00000277120		747	aCg/aTg	18/19	1	2	FACETS	0.881	0.75	1	0.881	0.75	1	CLONAL	1	TRUE	1	0.15	2		471	802	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295247	1295247	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0011083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	45	646	1				ENST00000310581	NM_198253.2	-/1132			0.150485877623347	3	FACETS	0.858	0.719	1	0.429	0.359	0.506	CLONAL	1	TRUE	1	0.15	3		647	752	SUCCESS
APC	324	MSKCC	GRCh37	5	112179290	112179290	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	36	255	0	ENST00000257430.4:c.7999A>G	p.Asn2667Asp	p.N2667D	ENST00000257430	NM_000038.5	2667	Aac/Gac	16/16	0.150485877623347	3	FACETS	0.928	0.762	1	0.464	0.381	0.558	CLONAL	1	TRUE	1	0.15	3		255	556	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112924414	112924414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	46	507	0	ENST00000351677.2:c.1360C>T	p.Pro454Ser	p.P454S	ENST00000351677	NM_002834.3	454	Ccg/Tcg	11/16	1	2	FACETS	0.821	0.69	0.967	0.821	0.69	0.967	CLONAL	1	TRUE	1	0.15	2		507	747	SUCCESS
SH2D1A	4068	MSKCC	GRCh37	X	123504070	123504070	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011083-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	22	171	1	ENST00000371139.4:c.246T>A	p.Asn82Lys	p.N82K	ENST00000371139	NM_001114937.2	82	aaT/aaA	3/4	0.3	1	FACETS	0.81	0.628	1	0.81	0.628	1	CLONAL	1	TRUE	0	0.15	1		172	335	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65323411	65323411	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011095-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	77	608	0	ENST00000342505.4:c.1386G>A	p.Met462Ile	p.M462I	ENST00000342505	NM_002227.2	462	atG/atA	10/25	1	2	FACETS	0.844	0.741	0.954	0.844	0.741	0.954	CLONAL	1	TRUE	1	0.28085742448464	2		608	650	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191532	10191532	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011095-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	72	455	0	ENST00000256474.2:c.525C>A	p.Tyr175Ter	p.Y175*	ENST00000256474	NM_000551.3	175	taC/taA	3/3	0.28085742448464	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	0	0.28085742448464	1		455	409	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47058705	47058706	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0011095-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	26	507	0	ENST00000409792.3:c.7572dup	p.Lys2525Ter	p.K2525*	ENST00000409792	NM_014159.6	2524	-/T	21/21	0.28085742448464	1	FACETS	0.607	0.482	0.75	0.607	0.482	0.75	SUBCLONAL	1	TRUE	0	0.28085742448464	1		507	262	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38978754	38978757	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TATT	TATT	-	novel	NA	P-0011095-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	14	319	0	ENST00000357387.3:c.754-5_754-2del		p.X252_splice	ENST00000357387	NM_152756.3	252			1	2	FACETS	0.597	0.433	0.794	0.597	0.433	0.794	SUBCLONAL	1	TRUE	1	0.28085742448464	2		319	167	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	70	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.614	0.542	0.69	0.614	0.542	0.69	SUBCLONAL	1	TRUE	1	0.922845876589767	2		280	247	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0011106-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	168	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.593	0.547	0.64	0.593	0.547	0.64	SUBCLONAL	1	TRUE	1	0.922845876589767	2		490	614	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	124	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.6244289090884	2		280	358	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771933	135771933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs118203745	NA	P-0011119-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	186	456	0	ENST00000298552.3:c.3184C>T	p.Arg1062Trp	p.R1062W	ENST00000298552	NM_001162426.1	1062	Cgg/Tgg	23/23	1	2	FACETS	0.996	0.925	1	0.996	0.925	1	CLONAL	1	TRUE	1	0.6244289090884	2		456	598	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011119-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	128	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.814	0.74	0.892	0.814	0.74	0.892	CLONAL	1	TRUE	1	0.523035685524542	2		280	601	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135771933	135771933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs118203745	NA	P-0011119-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	156	456	0	ENST00000298552.3:c.3184C>T	p.Arg1062Trp	p.R1062W	ENST00000298552	NM_001162426.1	1062	Cgg/Tgg	23/23	1	2	FACETS	0.932	0.857	1	0.932	0.857	1	CLONAL	1	TRUE	1	0.523035685524542	2		456	640	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	191	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.919	0.857	0.981	1	0.995	1	CLONAL	3	TRUE	1	0.282318465024452	2		280	491	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578542	7578542	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs863224683	NA	P-0011128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	47	577	0	ENST00000269305.4:c.388C>T	p.Leu130Phe	p.L130F	ENST00000269305	NM_001126112.2	130	Ctc/Ttc	5/11	0.282318465024452	0	FACETS	0.398	0.335	0.468			1	SUBCLONAL	1	TRUE	0	0.282318465024452	0		577	600	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913400	NA	P-0011128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	23	577	0	ENST00000349496.5:c.98C>T	p.Ser33Phe	p.S33F	ENST00000349496	NM_001904.3	33	tCt/tTt	3/15	1	2	FACETS	0.167	0.129	0.211	0.167	0.129	0.211	SUBCLONAL	1	TRUE	1	0.282318465024452	2		577	976	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934575	NA	P-0011128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	383	558	0	ENST00000269305.4:c.733G>C	p.Gly245Arg	p.G245R	ENST00000269305	NM_001126112.2	245	Ggc/Cgc	7/11	0.282318465024452	0	FACETS	0.96	0.922	0.999			1	CLONAL	3	TRUE	0	0.282318465024452	0		558	676	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755713	57755713	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	63	457	0	ENST00000274289.3:c.74G>T	p.Gly25Val	p.G25V	ENST00000274289	NM_006622.3	25	gGt/gTt	1/14	1	2	FACETS	0.533	0.459	0.612	0.533	0.459	0.612	SUBCLONAL	1	TRUE	1	0.282318465024452	2		457	838	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753169	128753169	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370767192	NA	P-0011128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	200	329	0	ENST00000377970.2:c.1330C>T	p.His444Tyr	p.H444Y	ENST00000377970	NM_002467.4	444	Cac/Tac	3/3	1	2	FACETS	0.947	0.88	1	1	0.993	1	CLONAL	2	TRUE	1	0.282318465024452	2		329	748	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061700	38061702	+	inframe_deletion	In_Frame_Del	DEL	TCA	TCA	-	novel	NA	P-0011128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	16	175	0	ENST00000250448.2:c.287_289del	p.Met96del	p.M96del	ENST00000250448	NM_004496.3	96	aTGAct/act	2/2	1	2	FACETS	0.38	0.281	0.5	0.38	0.281	0.5	SUBCLONAL	1	TRUE	1	0.282318465024452	2		175	298	SUCCESS
ATM	472	MSKCC	GRCh37	11	108100043	108100050	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	AAACAGAA	AAACAGAA	-	novel	NA	P-0011128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	22	245	0	ENST00000278616.4:c.324_331del	p.Asn109SerfsTer3	p.N109Sfs*3	ENST00000278616	NM_000051.3	108	gcAAACAGAAga/gcga	4/63	1	2	FACETS	0.359	0.277	0.454	0.359	0.277	0.454	SUBCLONAL	1	TRUE	1	0.282318465024452	2		245	434	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78414907	78414914	+	frameshift_variant	Frame_Shift_Del	DEL	CTATAATA	CTATAATA	-	novel	NA	P-0011128-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	298	521	0	ENST00000370768.2:c.1852_1859del	p.Tyr618ThrfsTer62	p.Y618Tfs*62	ENST00000370768	NM_003902.3	618	TATTATAGa/a	19/20	1	2	FACETS	0.867	0.819	0.914	1	0.996	1	CLONAL	3	TRUE	1	0.282318465024452	2		521	812	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011141-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	45	280	0				ENST00000310581	NM_198253.2	-/1132			0.106658261387234	0	FACETS	0.972	0.823	1			1	INDETERMINATE	1	FALSE	0	0.274349688812182	0		280	245	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0011141-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	18	145	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.353	0.265	0.457	0.353	0.265	0.457	SUBCLONAL	1	FALSE	1	0.274349688812182	2		145	372	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349964	15349964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1411701353	NA	P-0011141-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	33	395	0	ENST00000263377.2:c.3688G>A	p.Ala1230Thr	p.A1230T	ENST00000263377	NM_058243.2	1230	Gcc/Acc	18/20	0.274349688812182	1	FACETS	0.424	0.345	0.514	0.424	0.345	0.514	SUBCLONAL	1	FALSE	0	0.274349688812182	1		395	489	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	125	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.922	1	1	0.993	1	CLONAL	4	TRUE	1	0.202307444424388	2		280	308	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307492	118307492	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555138701	NA	P-0011159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	280	326	0	ENST00000534358.1:c.265G>A	p.Ala89Thr	p.A89T	ENST00000534358	NM_005933.3	89	Gcc/Acc	1/36	0.202307444424388	4	FACETS	0.99	0.937	1			1	CLONAL	5	TRUE	NA	0.202307444424388	4		326	672	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20148726	20148726	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0011159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	240	410	0	ENST00000379607.5:c.338-1G>C		p.X113_splice	ENST00000379607	NM_001412.3	113			0.202307444424388	1	FACETS	1	0.979	1	1	0.996	1	CLONAL	4	TRUE	0	0.202307444424388	1		410	497	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453141	140453142	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCTAGACCAAAATCACCTATT	novel	NA	P-0011159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	119	352	0	ENST00000288602.6:c.1773_1793dup	p.Ile592_Ala598dup	p.I592_A598dup	ENST00000288602	NM_004333.4	592	gct/gcAATAGGTGATTTTGGTCTAGCt	15/18	0.202307444424388	3	FACETS	0.96	0.868	1	0.96	0.868	1	CLONAL	2	TRUE	1	0.202307444424388	3		352	675	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139409854	139409861	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TGAAGGGG	TGAAGGGG	-	novel	NA	P-0011159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	236	286	0	ENST00000277541.6:c.1904-9_1904-2del		p.X635_splice	ENST00000277541	NM_017617.3	635			1	2	FACETS	0.929	0.873	0.986	1	0.996	1	CLONAL	4	TRUE	1	0.202307444424388	2		286	628	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900293	3900297	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CTTAC	CTTAC	-	novel	NA	P-0011159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	344	520	0	ENST00000262367.5:c.798+1_798+5del		p.X266_splice	ENST00000262367	NM_004380.2	266			0.202307444424388	3	FACETS	0.98	0.93	1	1	0.996	1	CLONAL	4	TRUE	1	0.202307444424388	3		520	955	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	223	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.948	1	1	0.996	1	CLONAL	3	TRUE	1	0.276302810003159	2		280	533	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0011160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	312	558	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	1	0.981	1	1	0.997	1	CLONAL	3	TRUE	1	0.276302810003159	2		558	706	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958459	90958459	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs201781110	NA	P-0011160-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	93	416	1	ENST00000265433.3:c.1979G>T	p.Arg660Ile	p.R660I	ENST00000265433	NM_002485.4	660	aGa/aTa	13/16	1	2	FACETS	1	0.969	1	1	0.989	1	CLONAL	2	TRUE	1	0.276302810003159	2		417	281	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0011199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	110	464	0				ENST00000310581	NM_198253.2	-/1132			0.639309608974238	2	FACETS	0.988	0.897	1			1	CLONAL	1	TRUE	NA	0.64	2		464	348	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0011199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	190	353	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.639309608974238	1	FACETS	0.957	0.896	1	0.957	0.896	1	CLONAL	1	TRUE	0	0.64	1		354	422	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057722	180057722	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200878617	NA	P-0011199-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	190	810	3	ENST00000261937.6:c.233C>T	p.Thr78Met	p.T78M	ENST00000261937	NM_182925.4	78	aCg/aTg	3/30	1	2	FACETS	0.858	0.796	0.922	0.858	0.796	0.922	CLONAL	1	TRUE	1	0.64	2		813	692	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	104	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.928	0.836	1	0.928	0.836	1	CLONAL	1	TRUE	1	0.518996259086971	2		280	432	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239940	53239940	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	328	417	0	ENST00000375401.3:c.1501T>C	p.Trp501Arg	p.W501R	ENST00000375401	NM_004187.3	501	Tgg/Cgg	11/26	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.518996259086971	1		417	665	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011202-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	115	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.995	0.903	1	0.995	0.903	1	CLONAL	1	TRUE	1	0.524069058718077	2		280	441	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53239940	53239940	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011202-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	266	417	0	ENST00000375401.3:c.1501T>C	p.Trp501Arg	p.W501R	ENST00000375401	NM_004187.3	501	Tgg/Cgg	11/26	0.292466634691215	0	FACETS	0.834	0.79	0.879			1	INDETERMINATE	1	TRUE	NA	0.524069058718077	0		417	579	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	96	34	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.394542014387524	2		280	130	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720811	89720812	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs121913291	NA	P-0011207-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	29	166	0	ENST00000371953.3:c.968dup	p.Asn323LysfsTer2	p.N323Kfs*2	ENST00000371953	NM_000314.4	321	aca/acAa	8/9	0.394542014387524	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.394542014387524	1		166	94	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0011210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	149	464	0				ENST00000310581	NM_198253.2	-/1132			0.454850878840749	3	FACETS	1	0.986	1			1	CLONAL	1	TRUE	NA	0.454850878840749	3		464	576	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447865	49447865	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	207	396	0	ENST00000301067.7:c.569C>G	p.Pro190Arg	p.P190R	ENST00000301067	NM_003482.3	190	cCa/cGa	5/54	0.388496324660552	4	FACETS	0.79	0.734	0.848	0.79	0.734	0.848	SUBCLONAL	2	TRUE	2	0.454850878840749	4		396	838	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132435	11132446	+	inframe_deletion	In_Frame_Del	DEL	ACCGCATGAAGA	ACCGCATGAAGA	-	novel	NA	P-0011210-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	162	603	0	ENST00000358026.2:c.2654_2665del	p.Arg885_Asn888del	p.R885_N888del	ENST00000358026	NM_001128849.1	884	cACCGCATGAAGAac/cac	19/36	0.376535196182058	3	FACETS	0.881	0.808	0.958	0.441	0.404	0.479	CLONAL	1	TRUE	1	0.454850878840749	3		603	992	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	24	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.578	0.453	0.721	0.578	0.453	0.721	SUBCLONAL	1	TRUE	1	0.260474614094287	2		464	319	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973193	25973193	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369212828	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	56	261	0	ENST00000435504.4:c.1232C>T	p.Ser411Phe	p.S411F	ENST00000435504		411	tCc/tTc	12/13	1	2	FACETS	0.862	0.739	0.995	0.862	0.739	0.995	CLONAL	1	TRUE	1	0.260474614094287	2		261	499	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	71	465	2	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.666	0.58	0.759	0.666	0.58	0.759	SUBCLONAL	1	TRUE	1	0.260474614094287	2		467	819	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117798	108117798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138398778	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	41	240	1	ENST00000278616.4:c.1009C>T	p.Arg337Cys	p.R337C	ENST00000278616	NM_000051.3	337	Cgt/Tgt	8/63	1	2	FACETS	0.783	0.653	0.927	0.783	0.653	0.927	CLONAL	1	TRUE	1	0.260474614094287	2		241	402	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971016	21971017	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	24	223	0	ENST00000304494.5:c.341_342delinsTT	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCC/cTT	2/3	0.205316422532692	1	FACETS	0.621	0.488	0.774	0.621	0.488	0.774	SUBCLONAL	1	TRUE	0	0.260474614094287	1		223	258	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577082	7577085	+	missense_variant	Missense_Mutation	ONP	CCTC	CCTC	TCTT	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	57	416	0	ENST00000269305.4:c.853_856delinsAAGA	p.Glu285_Glu286delinsLysLys	p.E285_E286delinsKK	ENST00000269305	NM_001126112.2	285	GAGGaa/AAGAaa	8/11	1	2	FACETS	0.705	0.604	0.815	0.705	0.604	0.815	SUBCLONAL	1	TRUE	1	0.260474614094287	2		416	621	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	34	408	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	1	2	FACETS	0.495	0.404	0.599	0.495	0.404	0.599	SUBCLONAL	1	TRUE	1	0.260474614094287	2		408	527	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131514	202131514	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	32	154	0	ENST00000358485.4:c.482G>A	p.Arg161Lys	p.R161K	ENST00000358485	NM_001080125.1	161	aGg/aAg	2/9	1	2	FACETS	0.917	0.747	1	0.917	0.747	1	CLONAL	1	TRUE	1	0.260474614094287	2		154	268	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295217	1295217	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs796849347	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	17	177	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.588	0.44	0.763	0.588	0.44	0.763	SUBCLONAL	1	TRUE	1	0.260474614094287	2		177	222	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412203	139412203	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	87	317	0	ENST00000277541.6:c.1441+1G>A		p.X481_splice	ENST00000277541	NM_017617.3	481			1	2	FACETS	0.786	0.699	0.877	1	0.981	1	SUBCLONAL	2	TRUE	1	0.260474614094287	2		317	425	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78865601	78865601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	57	334	0	ENST00000306801.3:c.2065G>A	p.Glu689Lys	p.E689K	ENST00000306801	NM_020761.2	689	Gaa/Aaa	18/34	1	2	FACETS	0.737	0.632	0.851	0.737	0.632	0.851	SUBCLONAL	1	TRUE	1	0.260474614094287	2		334	594	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971016	21971016	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878853648	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	25	220	2	ENST00000579755.1:c.385C>T	p.Arg129Cys	p.R129C	ENST00000579755		129	Cgt/Tgt	2/3	0.205316422532692	1	FACETS	0.64	0.506	0.793	0.64	0.506	0.793	SUBCLONAL	1	TRUE	0	0.260474614094287	1		222	261	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25469633	25469633	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754459010	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	47	320	0	ENST00000264709.3:c.1135C>T	p.Arg379Cys	p.R379C	ENST00000264709	NM_175629.2	379	Cgc/Tgc	10/23	1	2	FACETS	0.743	0.627	0.87	0.743	0.627	0.87	SUBCLONAL	1	TRUE	1	0.260474614094287	2		320	486	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363091	40363091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142406322	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	53	347	2	ENST00000397332.2:c.1138C>T	p.Arg380Trp	p.R380W	ENST00000397332	NM_001033082.2	380	Cgg/Tgg	3/3	1	2	FACETS	0.725	0.618	0.843	0.725	0.618	0.843	SUBCLONAL	1	TRUE	1	0.260474614094287	2		349	561	SUCCESS
FH	2271	MSKCC	GRCh37	1	241683018	241683018	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	18	228	0	ENST00000366560.3:c.5A>C	p.Tyr2Ser	p.Y2S	ENST00000366560	NM_000143.3	2	tAc/tCc	1/10	1	2	FACETS	0.501	0.377	0.647	0.501	0.377	0.647	SUBCLONAL	1	TRUE	1	0.260474614094287	2		228	276	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99155426	99155426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	47	322	1	ENST00000074304.5:c.652G>A	p.Asp218Asn	p.D218N	ENST00000074304	NM_001134224.1	218	Gac/Aac	9/26	1	2	FACETS	0.627	0.528	0.735	0.627	0.528	0.735	SUBCLONAL	1	TRUE	1	0.260474614094287	2		323	576	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99163120	99163120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779717943	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	60	386	0	ENST00000074304.5:c.1126C>T	p.Arg376Cys	p.R376C	ENST00000074304	NM_001134224.1	376	Cgc/Tgc	13/26	1	2	FACETS	0.747	0.643	0.86	0.747	0.643	0.86	SUBCLONAL	1	TRUE	1	0.260474614094287	2		386	617	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735551	204735551	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	33	229	0	ENST00000302823.3:c.352G>A	p.Gly118Arg	p.G118R	ENST00000302823	NM_005214.4	118	Gga/Aga	2/4	1	2	FACETS	0.627	0.511	0.758	0.627	0.511	0.758	SUBCLONAL	1	TRUE	1	0.260474614094287	2		229	404	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662374	227662374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1473770836	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	23	245	0	ENST00000305123.5:c.1081G>A	p.Gly361Ser	p.G361S	ENST00000305123	NM_005544.2	361	Ggc/Agc	1/2	1	2	FACETS	0.524	0.408	0.658	0.524	0.408	0.658	SUBCLONAL	1	TRUE	1	0.260474614094287	2		245	337	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164080	47164080	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	60	277	0	ENST00000409792.3:c.2046T>A	p.Asp682Glu	p.D682E	ENST00000409792	NM_014159.6	682	gaT/gaA	3/21	1	2	FACETS	0.982	0.848	1	0.982	0.848	1	CLONAL	1	TRUE	1	0.260474614094287	2		277	469	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52598223	52598223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1389353528	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	46	255	0	ENST00000394830.3:c.3643G>A	p.Asp1215Asn	p.D1215N	ENST00000394830	NM_018313.4	1215	Gac/Aac	24/30	0.128982414254686	3	FACETS	0.755	0.635	0.887	0.377	0.317	0.444	INDETERMINATE	1	TRUE	1	0.260474614094287	3		255	529	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52677355	52677355	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	57	246	0	ENST00000394830.3:c.904C>T	p.Pro302Ser	p.P302S	ENST00000394830	NM_018313.4	302	Cca/Tca	10/30	0.128982414254686	3	FACETS	1	0.883	1	0.515	0.443	0.594	INDETERMINATE	1	TRUE	1	0.260474614094287	3		246	480	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498378	89498378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	44	212	0	ENST00000336596.2:c.2350G>A	p.Gly784Arg	p.G784R	ENST00000336596	NM_005233.5	784	Ggg/Agg	14/17	0.128982414254686	3	FACETS	1	0.884	1	0.532	0.447	0.625	INDETERMINATE	1	TRUE	1	0.260474614094287	3		212	359	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281472	142281472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	43	307	0	ENST00000350721.4:c.772C>T	p.Leu258Phe	p.L258F	ENST00000350721	NM_001184.3	258	Ctt/Ttt	4/47	0.128982414254686	3	FACETS	0.591	0.494	0.7	0.296	0.247	0.35	INDETERMINATE	1	TRUE	1	0.260474614094287	3		307	631	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279524	1279524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774381540	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	58	386	0	ENST00000310581.5:c.2012G>A	p.Arg671Gln	p.R671Q	ENST00000310581	NM_198253.2	671	cGg/cAg	5/16	1	2	FACETS	0.903	0.777	1	0.903	0.777	1	CLONAL	1	TRUE	1	0.260474614094287	2		386	493	SUCCESS
APC	324	MSKCC	GRCh37	5	112177484	112177484	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	30	257	0	ENST00000257430.4:c.6193C>T	p.Pro2065Ser	p.P2065S	ENST00000257430	NM_000038.5	2065	Ccc/Tcc	16/16	1	2	FACETS	0.499	0.401	0.609	0.499	0.401	0.609	SUBCLONAL	1	TRUE	1	0.260474614094287	2		257	462	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522617	176522617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	48	390	1	ENST00000292408.4:c.1714C>T	p.Leu572Phe	p.L572F	ENST00000292408	NM_213647.1	572	Ctc/Ttc	13/18	1	2	FACETS	0.684	0.578	0.801	0.684	0.578	0.801	SUBCLONAL	1	TRUE	1	0.260474614094287	2		391	539	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665259	176665259	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	37	280	0	ENST00000439151.2:c.3943G>A	p.Glu1315Lys	p.E1315K	ENST00000439151	NM_022455.4	1315	Gaa/Aaa	7/23	1	2	FACETS	0.592	0.488	0.709	0.592	0.488	0.709	SUBCLONAL	1	TRUE	1	0.260474614094287	2		280	480	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056560	26056560	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766992808	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	32	135	0	ENST00000343677.2:c.97C>T	p.Arg33Cys	p.R33C	ENST00000343677	NM_005319.3	33	Cgt/Tgt	1/1	1	2	FACETS	1	0.868	1	1	0.868	1	CLONAL	1	TRUE	1	0.260474614094287	2		135	228	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672069	30672069	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	43	414	0	ENST00000376406.3:c.4891C>T	p.Pro1631Ser	p.P1631S	ENST00000376406	NM_014641.2	1631	Ccc/Tcc	10/15	1	2	FACETS	0.532	0.444	0.629	0.532	0.444	0.629	SUBCLONAL	1	TRUE	1	0.260474614094287	2		414	621	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111995749	111995749	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	57	569	1	ENST00000368678.4:c.1349G>A	p.Gly450Glu	p.G450E	ENST00000368678		450	gGa/gAa	12/13	1	2	FACETS	0.499	0.427	0.578	0.499	0.427	0.578	SUBCLONAL	1	TRUE	1	0.260474614094287	2		570	877	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403491	139403491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	116	419	0	ENST00000277541.6:c.3002G>A	p.Gly1001Asp	p.G1001D	ENST00000277541	NM_017617.3	1001	gGc/gAc	19/34	1	2	FACETS	0.797	0.721	0.877	1	0.986	1	SUBCLONAL	2	TRUE	1	0.260474614094287	2		419	559	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601824	43601824	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	29	250	0	ENST00000355710.3:c.868G>A	p.Asp290Asn	p.D290N	ENST00000355710	NM_020975.4	290	Gac/Aac	5/20	1	2	FACETS	0.692	0.556	0.845	0.692	0.556	0.845	SUBCLONAL	1	TRUE	1	0.260474614094287	2		250	322	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198920	67198920	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	55	341	0	ENST00000312629.5:c.391A>T	p.Ile131Phe	p.I131F	ENST00000312629	NM_003952.2	131	Att/Ttt	5/15	1	2	FACETS	0.666	0.569	0.772	0.666	0.569	0.772	SUBCLONAL	1	TRUE	1	0.260474614094287	2		341	634	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125505398	125505398	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	41	342	0	ENST00000428830.2:c.688C>T	p.Pro230Ser	p.P230S	ENST00000428830	NM_001114121.2	230	Cct/Tct	7/14	1	2	FACETS	0.481	0.4	0.572	0.481	0.4	0.572	SUBCLONAL	1	TRUE	1	0.260474614094287	2		342	654	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435665	18435665	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	24	217	1	ENST00000266497.5:c.650G>A	p.Trp217Ter	p.W217*	ENST00000266497		217	tGg/tAg	1/31	1	2	FACETS	0.572	0.449	0.714	0.572	0.449	0.714	SUBCLONAL	1	TRUE	1	0.260474614094287	2		218	322	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911104	32911104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	84	544	1	ENST00000380152.3:c.2612C>T	p.Ser871Leu	p.S871L	ENST00000380152		871	tCa/tTa	11/27	1	2	FACETS	0.607	0.535	0.686	0.607	0.535	0.686	SUBCLONAL	1	TRUE	1	0.260474614094287	2		545	1062	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914661	32914661	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	69	611	0	ENST00000380152.3:c.6169G>A	p.Gly2057Arg	p.G2057R	ENST00000380152		2057	Gga/Aga	11/27	1	2	FACETS	0.493	0.428	0.564	0.493	0.428	0.564	SUBCLONAL	1	TRUE	1	0.260474614094287	2		611	1074	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435283	110435283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs997942200	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	17	65	0	ENST00000375856.3:c.3118G>A	p.Glu1040Lys	p.E1040K	ENST00000375856	NM_003749.2	1040	Gag/Aag	1/2	1	2	FACETS	1	0.827	1	1	0.827	1	CLONAL	1	TRUE	1	0.260474614094287	2		65	116	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239281	105239281	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	39	369	1	ENST00000349310.3:c.1106C>T	p.Pro369Leu	p.P369L	ENST00000349310	NM_001014432.1	369	cCg/cTg	12/15	1	2	FACETS	0.547	0.453	0.653	0.547	0.453	0.653	SUBCLONAL	1	TRUE	1	0.260474614094287	2		370	547	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641790	23641790	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	32	217	0	ENST00000261584.4:c.1685G>A	p.Gly562Glu	p.G562E	ENST00000261584	NM_024675.3	562	gGg/gAg	5/13	1	2	FACETS	0.645	0.524	0.782	0.645	0.524	0.782	SUBCLONAL	1	TRUE	1	0.260474614094287	2		217	381	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40353797	40353797	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1490632558	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	102	516	1	ENST00000293328.3:c.2323C>T	p.Arg775Trp	p.R775W	ENST00000293328	NM_012448.3	775	Cgg/Tgg	19/19	1	2	FACETS	0.905	0.809	1	0.905	0.809	1	CLONAL	1	TRUE	1	0.260474614094287	2		517	865	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7152788	7152788	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	62	417	0	ENST00000302850.5:c.2180C>T	p.Ser727Leu	p.S727L	ENST00000302850	NM_000208.2	727	tCg/tTg	10/22	1	2	FACETS	0.704	0.608	0.809	0.704	0.608	0.809	SUBCLONAL	1	TRUE	1	0.260474614094287	2		417	676	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100943	41100943	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	52	265	0	ENST00000373198.4:c.1413G>A	p.Met471Ile	p.M471I	ENST00000373198	NM_133170.3	471	atG/atA	8/32	1	2	FACETS	0.772	0.658	0.898	0.772	0.658	0.898	SUBCLONAL	1	TRUE	1	0.260474614094287	2		265	517	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30069300	30069300	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	50	290	2	ENST00000338641.4:c.1165C>T	p.Gln389Ter	p.Q389*	ENST00000338641	NM_000268.3	389	Cag/Tag	12/16	1	2	FACETS	0.849	0.722	0.989	0.849	0.722	0.989	CLONAL	1	TRUE	1	0.260474614094287	2		292	452	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41564510	41564510	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	59	262	0	ENST00000263253.7:c.3932G>A	p.Arg1311Lys	p.R1311K	ENST00000263253	NM_001429.3	1311	aGg/aAg	24/31	1	2	FACETS	0.902	0.777	1	0.902	0.777	1	CLONAL	1	TRUE	1	0.260474614094287	2		262	502	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262075	16262076	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	12	110	0	ENST00000375759.3:c.9340_9341delinsTT	p.Pro3114Leu	p.P3114L	ENST00000375759	NM_015001.2	3114	CCa/TTa	11/15	1	2	FACETS	0.458	0.322	0.626	0.458	0.322	0.626	SUBCLONAL	1	TRUE	1	0.260474614094287	2		110	201	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429378	78429379	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	54	382	0	ENST00000370768.2:c.1063_1064delinsAA	p.Gly355Lys	p.G355K	ENST00000370768	NM_003902.3	355	GGa/AAa	13/20	1	2	FACETS	0.697	0.595	0.809	0.697	0.595	0.809	SUBCLONAL	1	TRUE	1	0.260474614094287	2		382	595	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430338	181430339	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	33	272	0	ENST00000325404.1:c.190_191delinsTT	p.Pro64Phe	p.P64F	ENST00000325404	NM_003106.3	64	CCc/TTc	1/1	0.128982414254686	3	FACETS	0.828	0.675	0.999	0.414	0.337	0.5	INDETERMINATE	1	TRUE	1	0.260474614094287	3		272	346	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612101	189612102	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	79	404	0	ENST00000264731.3:c.1853_1854delinsAA	p.Arg618Gln	p.R618Q	ENST00000264731	NM_003722.4	618	cGG/cAA	14/14	0.128982414254686	3	FACETS	1	0.954	1	0.588	0.518	0.663	INDETERMINATE	1	TRUE	1	0.260474614094287	3		404	583	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405556	70405557	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	21	215	0	ENST00000373644.4:c.3070_3071delinsAA	p.Gly1024Lys	p.G1024K	ENST00000373644	NM_030625.2	1024	GGg/AAg	4/12	1	2	FACETS	0.53	0.408	0.672	0.53	0.408	0.672	SUBCLONAL	1	TRUE	1	0.260474614094287	2		215	304	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202159	67202160	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	35	289	0	ENST00000312629.5:c.1262_1263delinsTT	p.Pro421Leu	p.P421L	ENST00000312629	NM_003952.2	421	cCC/cTT	14/15	1	2	FACETS	0.684	0.561	0.822	0.684	0.561	0.822	SUBCLONAL	1	TRUE	1	0.260474614094287	2		289	393	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373941	118373942	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	41	264	0	ENST00000534358.1:c.7334_7335delinsTT	p.Ser2445Phe	p.S2445F	ENST00000534358	NM_005933.3	2445	tCC/tTT	27/36	1	2	FACETS	0.594	0.494	0.705	0.594	0.494	0.705	SUBCLONAL	1	TRUE	1	0.260474614094287	2		264	530	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061140	38061141	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	15	49	0	ENST00000250448.2:c.848_849delinsAA	p.Gly283Glu	p.G283E	ENST00000250448	NM_004496.3	283	gGG/gAA	2/2	1	2	FACETS	0.8	0.598	1	1	0.904	1	CLONAL	2	TRUE	1	0.260474614094287	2		49	72	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88423551	88423552	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	55	401	0	ENST00000360948.2:c.2283_2284delinsAA	p.Trp761_Glu762delinsTer	p.W761_E762delins*	ENST00000360948	NM_001012338.2	761	tgGGag/tgAAag	18/19	1	2	FACETS	0.719	0.615	0.834	0.719	0.615	0.834	SUBCLONAL	1	TRUE	1	0.260474614094287	2		401	587	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097020	11097021	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	59	466	0	ENST00000358026.2:c.511_512delinsTT	p.Pro171Leu	p.P171L	ENST00000358026	NM_001128849.1	171	CCa/TTa	4/36	1	2	FACETS	0.856	0.737	0.986	0.856	0.737	0.986	CLONAL	1	TRUE	1	0.260474614094287	2		466	529	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15300083	15300084	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	41	341	0	ENST00000263388.2:c.1192_1192+1delinsAA		p.X398_splice	ENST00000263388	NM_000435.2	398		7/33	1	2	FACETS	0.755	0.629	0.894	0.755	0.629	0.894	SUBCLONAL	1	TRUE	1	0.260474614094287	2		341	417	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164877	123164878	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0011211-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	99	294	0	ENST00000218089.9:c.190_191delinsTT	p.Pro64Phe	p.P64F	ENST00000218089	NM_001042749.1	64	CCt/TTt	5/35	1	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.260474614094287	1		294	501	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	272	280	0				ENST00000310581	NM_198253.2	-/1132			0.250302562241161	5	FACETS	0.858	0.809	0.907	0.858	0.809	0.907	INDETERMINATE	3	TRUE	2	0.526251903599629	5		280	719	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0011216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	449	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.526251903599629	5	FACETS	1	0.973	1	1	0.973	1	CLONAL	3	TRUE	2	0.526251903599629	5		490	998	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913384	NA	P-0011216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	265	238	1	ENST00000304494.5:c.262G>T	p.Glu88Ter	p.E88*	ENST00000304494	NM_000077.4	88	Gag/Tag	2/3	0.526251903599629	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.526251903599629	2		239	459	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577559	7577559	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934573	NA	P-0011216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	437	417	1	ENST00000269305.4:c.722C>T	p.Ser241Phe	p.S241F	ENST00000269305	NM_001126112.2	241	tCc/tTc	7/11	0.101748665343434	3	FACETS	0.859	0.826	0.892			1	INDETERMINATE	3	TRUE	NA	0.526251903599629	3		418	814	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117868419	117868419	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1206	409	480	0	ENST00000297338.2:c.923C>T	p.Pro308Leu	p.P308L	ENST00000297338	NM_006265.2	308	cCt/cTt	8/14	0.526251903599629	6	FACETS	0.988	0.938	1	0.494	0.469	0.519	CLONAL	2	TRUE	2	0.526251903599629	6		480	1615	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005419	29005419	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55687105	NA	P-0011216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	232	317	0	ENST00000282397.4:c.842G>A	p.Arg281Gln	p.R281Q	ENST00000282397	NM_002019.4	281	cGa/cAa	7/30	0.455586092328439	4	FACETS	0.867	0.811	0.924	0.867	0.811	0.924	CLONAL	2	TRUE	2	0.526251903599629	4		317	776	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451861	29451861	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	404	572	0	ENST00000389048.3:c.2704G>T	p.Gly902Ter	p.G902*	ENST00000389048	NM_004304.4	902	Gga/Tga	16/29	0.472769161692316	3	FACETS	0.759	0.722	0.797	0.759	0.722	0.797	SUBCLONAL	2	TRUE	1	0.526251903599629	3		572	1277	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932979	49932979	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1138	548	569	1	ENST00000296474.3:c.2965C>T	p.Leu989Phe	p.L989F	ENST00000296474	NM_002447.2	989	Ctt/Ttt	13/20	0.513360603647523	4	FACETS	0.943	0.903	0.982	0.943	0.903	0.982	CLONAL	2	TRUE	2	0.526251903599629	4		570	1686	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390203	89390203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	419	441	0	ENST00000336596.2:c.952C>T	p.Pro318Ser	p.P318S	ENST00000336596	NM_005233.5	318	Cca/Tca	4/17	0.513360603647523	4	FACETS	0.986	0.939	1	0.986	0.939	1	CLONAL	2	TRUE	2	0.526251903599629	4		441	1233	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407552	407552	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1011269643	NA	P-0011216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	385	419	0	ENST00000380956.4:c.1310C>T	p.Pro437Leu	p.P437L	ENST00000380956	NM_001195286.1	437	cCa/cTa	9/9	0.526251903599629	3	FACETS	0.936	0.892	0.981	0.936	0.892	0.981	CLONAL	2	TRUE	1	0.526251903599629	3		419	987	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499706	8499706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	352	375	0	ENST00000356435.5:c.2263G>A	p.Glu755Lys	p.E755K	ENST00000356435		755	Gaa/Aaa	14/35	0.526251903599629	2	FACETS	0.949	0.906	0.991	0.949	0.906	0.991	CLONAL	2	TRUE	0	0.526251903599629	2		375	705	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528069	103528069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	289	229	0	ENST00000355739.4:c.3377C>T	p.Ala1126Val	p.A1126V	ENST00000355739	NM_000123.3	1126	gCt/gTt	15/15	0.455586092328439	4	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	2	0.526251903599629	4		229	786	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988652	41988652	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	622	576	0	ENST00000219905.7:c.1444A>C	p.Lys482Gln	p.K482Q	ENST00000219905	NM_001164273.1	482	Aag/Cag	3/24	0.300752616701975	4	FACETS	1	0.995	1	1	0.995	1	INDETERMINATE	2	TRUE	2	0.526251903599629	4		576	1484	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339286	70339286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	358	518	0	ENST00000374080.3:c.163G>A	p.Glu55Lys	p.E55K	ENST00000374080		55	Gag/Aag	2/45	0.300752616701975	4	FACETS	0.801	0.758	0.844	0.801	0.758	0.844	INDETERMINATE	2	TRUE	2	0.526251903599629	4		518	1297	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345548	70345548	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	502	609	1	ENST00000374080.3:c.2407G>A	p.Asp803Asn	p.D803N	ENST00000374080		803	Gac/Aac	17/45	0.300752616701975	4	FACETS	0.88	0.841	0.919	0.88	0.841	0.919	INDETERMINATE	2	TRUE	2	0.526251903599629	4		610	1655	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198274507	198274508	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0011216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	262	434	0	ENST00000335508.6:c.890_891delinsTT	p.Pro297Leu	p.P297L	ENST00000335508	NM_012433.2	297	cCC/cTT	7/25	0.472769161692316	3	FACETS	1	0.982	1	0.561	0.526	0.598	CLONAL	1	TRUE	1	0.526251903599629	3		434	1120	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397762	116397763	+	missense_variant	Missense_Mutation	DNP	GA	GA	AG	novel	NA	P-0011216-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	654	483	1	ENST00000397752.3:c.2036_2037delinsAG	p.Gly679Glu	p.G679E	ENST00000397752	NM_000245.2	679	gGA/gAG	8/21	0.526251903599629	5	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	2	0.526251903599629	5		484	1432	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	72	145	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.818	0.718	0.925	0.818	0.718	0.925	CLONAL	1	TRUE	1	0.44	2		145	400	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	181	581	1	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.44	2		582	778	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	200	544	7	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	1	2	FACETS	0.991	0.919	1	0.991	0.919	1	CLONAL	1	TRUE	1	0.44	2		551	917	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128852004	128852004	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	199	737	3	ENST00000249373.3:c.2081del	p.Pro694LeufsTer82	p.P694Lfs*82	ENST00000249373	NM_005631.4	692	caC/ca	12/12	1	2	FACETS	0.933	0.865	1	0.933	0.865	1	CLONAL	1	TRUE	1	0.44	2		740	969	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717769	89717770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	93	286	0	ENST00000371953.3:c.800dup	p.Asp268GlyfsTer30	p.D268Gfs*30	ENST00000371953	NM_000314.4	265	cta/ctAa	7/9	1	2	FACETS	0.933	0.834	1	0.933	0.834	1	CLONAL	1	TRUE	1	0.44	2		286	453	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	260	703	2	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.906	0.847	0.966	0.906	0.847	0.966	CLONAL	1	TRUE	1	0.44	2		705	1305	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330630	65330630	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1181132297	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	237	638	0	ENST00000342505.4:c.1016del	p.Asn339IlefsTer3	p.N339Ifs*3	ENST00000342505	NM_002227.2	339	aAt/at	8/25	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.44	2		638	894	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577532	7577532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064794311	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	247	762	0	ENST00000269305.4:c.749C>T	p.Pro250Leu	p.P250L	ENST00000269305	NM_001126112.2	250	cCc/cTc	7/11	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.44	2		762	1061	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2956964	2956964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395288944	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	181	581	1	ENST00000396946.4:c.2663G>A	p.Arg888His	p.R888H	ENST00000396946	NM_032415.4	888	cGt/cAt	20/25	1	2	FACETS	0.925	0.854	1	0.925	0.854	1	CLONAL	1	TRUE	1	0.44	2		582	889	SUCCESS
APC	324	MSKCC	GRCh37	5	112173917	112173917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913333	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	167	530	0	ENST00000257430.4:c.2626C>T	p.Arg876Ter	p.R876*	ENST00000257430	NM_000038.5	876	Cga/Tga	16/16	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.44	2		530	690	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380283	25380283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913528	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	195	682	1	ENST00000311936.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000311936	NM_004985.3	59	Gca/Aca	3/5	1	2	FACETS	0.919	0.851	0.99	0.919	0.851	0.99	CLONAL	1	TRUE	1	0.44	2		683	964	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830903	72830904	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1461	408	1315	8	ENST00000268489.5:c.5677_5678del	p.Arg1893GlyfsTer35	p.R1893Gfs*35	ENST00000268489	NM_006885.3	1893	AGg/g	9/10	1	2	FACETS	0.992	0.941	1	0.992	0.941	1	CLONAL	1	TRUE	1	0.44	2		1323	1869	SUCCESS
APC	324	MSKCC	GRCh37	5	112164611	112164611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587783034	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	131	464	2	ENST00000257430.4:c.1685C>T	p.Thr562Met	p.T562M	ENST00000257430	NM_000038.5	562	aCg/aTg	14/16	1	2	FACETS	0.975	0.887	1	0.975	0.887	1	CLONAL	1	TRUE	1	0.44	2		466	611	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923087	39923087	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	296	599	0	ENST00000378444.4:c.3621del	p.Lys1207AsnfsTer31	p.K1207Nfs*31	ENST00000378444	NM_001123385.1	1207	aaA/aa	8/15	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.44	1		599	766	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351359	89351359	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756332789	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1392	403	1287	4	ENST00000301030.4:c.1591G>A	p.Ala531Thr	p.A531T	ENST00000301030	NM_001256183.1	531	Gcc/Acc	9/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.44	2		1291	1795	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524834	187524834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771664786	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	247	721	0	ENST00000441802.2:c.10846G>A	p.Val3616Ile	p.V3616I	ENST00000441802	NM_005245.3	3616	Gta/Ata	19/27	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.44	2		721	1066	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98270530	98270530	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs751977093	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	32	402	1	ENST00000331920.6:c.114del	p.Leu39CysfsTer41	p.L39Cfs*41	ENST00000331920	NM_000264.3	38	ggG/gg	1/24	1	2	FACETS	0.247	0.2	0.301	0.247	0.2	0.301	SUBCLONAL	1	TRUE	1	0.44	2		403	588	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140891	37140891	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	232	799	0	ENST00000373509.5:c.727G>A	p.Glu243Lys	p.E243K	ENST00000373509	NM_002648.3	243	Gag/Aag	5/6	1	2	FACETS	0.921	0.858	0.986	0.921	0.858	0.986	CLONAL	1	TRUE	1	0.44	2		799	1145	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57474036	57474036	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750429818	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	96	338	0	ENST00000371085.3:c.253G>A	p.Asp85Asn	p.D85N	ENST00000371085	NM_000516.4	85	Gat/Aat	3/13	0.3	2	FACETS	0.737	0.658	0.821			1	SUBCLONAL	1	TRUE	NA	0.44	2		338	592	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367798	15367798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144627512	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	202	660	0	ENST00000263377.2:c.1528C>T	p.Arg510Trp	p.R510W	ENST00000263377	NM_058243.2	510	Cgg/Tgg	8/20	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.44	2		660	862	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37020769	37020769	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	238	791	0	ENST00000358127.4:c.76del	p.Val26PhefsTer3	p.V26Ffs*3	ENST00000358127	NM_001280556.1	26	Gtt/tt	2/10	1	2	FACETS	0.845	0.787	0.904	0.845	0.787	0.904	CLONAL	1	TRUE	1	0.44	2		791	1281	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341244	341244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773933232	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	275	764	2	ENST00000262320.3:c.2240C>T	p.Ala747Val	p.A747V	ENST00000262320	NM_003502.3	747	gCg/gTg	9/11	1	2	FACETS	0.982	0.921	1	0.982	0.921	1	CLONAL	1	TRUE	1	0.44	2		766	1273	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444809	49444809	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	101	749	0	ENST00000301067.7:c.2657del	p.Pro886LeufsTer44	p.P886Lfs*44	ENST00000301067	NM_003482.3	886	cCt/ct	10/54	1	2	FACETS	0.468	0.418	0.523	0.468	0.418	0.523	SUBCLONAL	1	TRUE	1	0.44	2		749	980	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463266	25463266	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1433353413	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	187	586	0	ENST00000264709.3:c.2227C>T	p.Pro743Ser	p.P743S	ENST00000264709	NM_175629.2	743	Ccc/Tcc	19/23	1	2	FACETS	0.912	0.843	0.984	0.912	0.843	0.984	CLONAL	1	TRUE	1	0.44	2		586	932	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057761	27057761	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1390	420	1254	1	ENST00000324856.7:c.1469C>A	p.Pro490Gln	p.P490Q	ENST00000324856	NM_006015.4	490	cCg/cAg	3/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.44	2		1255	1810	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303750	65303750	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1340186470	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	275	733	0	ENST00000342505.4:c.3005G>A	p.Arg1002Gln	p.R1002Q	ENST00000342505	NM_002227.2	1002	cGg/cAg	22/25	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.44	2		733	1162	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466468	120466468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	176	853	2	ENST00000256646.2:c.4651G>A	p.Val1551Ile	p.V1551I	ENST00000256646	NM_024408.3	1551	Gta/Ata	26/34	1	2	FACETS	0.663	0.609	0.719	0.663	0.609	0.719	SUBCLONAL	1	TRUE	1	0.44	2		855	1207	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61729157	61729157	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	179	767	0	ENST00000401558.2:c.382G>A	p.Gly128Arg	p.G128R	ENST00000401558	NM_003400.3	128	Gga/Aga	6/25	1	2	FACETS	0.896	0.826	0.969	0.896	0.826	0.969	CLONAL	1	TRUE	1	0.44	2		767	908	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162236	47162236	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370953553	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	62	733	0	ENST00000409792.3:c.3890G>A	p.Arg1297His	p.R1297H	ENST00000409792	NM_014159.6	1297	cGt/cAt	3/21	1	2	FACETS	0.246	0.211	0.284	0.246	0.211	0.284	SUBCLONAL	1	TRUE	1	0.44	2		733	1147	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026838	71026838	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138415721	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	129	588	2	ENST00000318789.4:c.1384G>A	p.Ala462Thr	p.A462T	ENST00000318789	NM_032682.5	462	Gca/Aca	16/21	1	2	FACETS	0.763	0.693	0.838	0.763	0.693	0.838	SUBCLONAL	1	TRUE	1	0.44	2		590	768	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185184673	185184673	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1265	91	1029	1	ENST00000265026.3:c.1565C>T	p.Pro522Leu	p.P522L	ENST00000265026	NM_004721.4	522	cCt/cTt	10/14	1	2	FACETS	0.305	0.27	0.343	0.305	0.27	0.343	SUBCLONAL	1	TRUE	1	0.44	2		1030	1356	SUCCESS
FIP1L1	81608	MSKCC	GRCh37	4	54292106	54292106	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	114	457	0	ENST00000358575.5:c.946C>T	p.Arg316Trp	p.R316W	ENST00000358575	NM_001134937.1	316	Cgg/Tgg	11/18	1	2	FACETS	0.74	0.667	0.817	0.74	0.667	0.817	SUBCLONAL	1	TRUE	1	0.44	2		457	700	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247195	153247195	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	221	779	0	ENST00000281708.4:c.1607C>T	p.Thr536Met	p.T536M	ENST00000281708	NM_033632.3	536	aCg/aTg	10/12	1	2	FACETS	0.933	0.868	1	0.933	0.868	1	CLONAL	1	TRUE	1	0.44	2		779	1077	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295339	1295339	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	125	508	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.875	0.794	0.961	0.875	0.794	0.961	CLONAL	1	TRUE	1	0.44	2		510	649	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149440532	149440532	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746302520	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	180	571	3	ENST00000286301.3:c.1862C>T	p.Thr621Met	p.T621M	ENST00000286301	NM_005211.3	621	aCg/aTg	14/22	1	2	FACETS	0.944	0.871	1	0.944	0.871	1	CLONAL	1	TRUE	1	0.44	2		574	867	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721031	176721031	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1433952610	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	71	699	0	ENST00000439151.2:c.6662A>G	p.Tyr2221Cys	p.Y2221C	ENST00000439151	NM_022455.4	2221	tAt/tGt	23/23	1	2	FACETS	0.383	0.334	0.437	0.383	0.334	0.437	SUBCLONAL	1	TRUE	1	0.44	2		699	842	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29910533	29910533	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	50	451	0	ENST00000376809.5:c.74-1G>A		p.X25_splice	ENST00000376809	NM_002116.7	25			1	2	FACETS	0.319	0.27	0.373	0.319	0.27	0.373	SUBCLONAL	1	TRUE	1	0.44	2		451	712	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180969	32180969	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	235	745	0	ENST00000375023.3:c.2381C>T	p.Ala794Val	p.A794V	ENST00000375023	NM_004557.3	794	gCc/gTc	15/30	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.44	2		745	1032	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198219	138198219	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763827898	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	84	376	0	ENST00000237289.4:c.812G>A	p.Arg271Gln	p.R271Q	ENST00000237289	NM_001270507.1	271	cGa/cAa	6/9	1	2	FACETS	0.778	0.689	0.872	0.778	0.689	0.872	SUBCLONAL	1	TRUE	1	0.44	2		376	491	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55229303	55229303	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	164	857	0	ENST00000275493.2:c.1610A>T	p.Asp537Val	p.D537V	ENST00000275493	NM_005228.3	537	gAc/gTc	13/28	1	2	FACETS	0.648	0.594	0.705	0.648	0.594	0.705	SUBCLONAL	1	TRUE	1	0.44	2		857	1150	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859816	117859816	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1212	301	1018	0	ENST00000297338.2:c.1819C>T	p.Gln607Ter	p.Q607*	ENST00000297338	NM_006265.2	607	Caa/Taa	14/14	1	2	FACETS	0.904	0.85	0.961	0.904	0.85	0.961	CLONAL	1	TRUE	1	0.44	2		1018	1513	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1036341	1036341	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775265125	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	245	877	2	ENST00000358495.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000358495	NM_134424.2	146	gCg/gTg	6/12	1	2	FACETS	0.867	0.809	0.927	0.867	0.809	0.927	CLONAL	1	TRUE	1	0.44	2		879	1285	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037451	12037451	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	261	721	0	ENST00000396373.4:c.1082A>G	p.Glu361Gly	p.E361G	ENST00000396373	NM_001987.4	361	gAg/gGg	6/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.44	2		721	1100	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103528104	103528104	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140930348	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	167	443	1	ENST00000355739.4:c.3412G>A	p.Val1138Met	p.V1138M	ENST00000355739	NM_000123.3	1138	Gtg/Atg	15/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.44	2		444	654	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435750	110435750	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1219457876	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	40	140	0	ENST00000375856.3:c.2651G>A	p.Arg884His	p.R884H	ENST00000375856	NM_003749.2	884	cGc/cAc	1/2	1	2	FACETS	0.719	0.601	0.847	0.719	0.601	0.847	SUBCLONAL	1	TRUE	1	0.44	2		140	253	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058345	42058345	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	340	1128	0	ENST00000219905.7:c.8065A>G	p.Arg2689Gly	p.R2689G	ENST00000219905	NM_001164273.1	2689	Agg/Ggg	24/24	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.44	2		1128	1454	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774216	66774216	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1473690179	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	210	730	0	ENST00000307102.5:c.692C>T	p.Ser231Leu	p.S231L	ENST00000307102	NM_002755.3	231	tCg/tTg	6/11	1	2	FACETS	0.932	0.865	1	0.932	0.865	1	CLONAL	1	TRUE	1	0.44	2		730	1024	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779382	3779382	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143180774	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	235	686	0	ENST00000262367.5:c.5666C>T	p.Pro1889Leu	p.P1889L	ENST00000262367	NM_004380.2	1889	cCg/cTg	31/31	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.44	2		686	979	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827613	72827613	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757947521	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1180	335	1159	2	ENST00000268489.5:c.8968G>A	p.Val2990Ile	p.V2990I	ENST00000268489	NM_006885.3	2990	Gtt/Att	9/10	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.44	2		1161	1515	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17131232	17131232	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	312	902	1	ENST00000285071.4:c.220C>A	p.Pro74Thr	p.P74T	ENST00000285071	NM_144997.5	74	Ccg/Acg	4/14	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.44	2		903	1344	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264354	30264354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1284405136	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	129	228	4	ENST00000322652.5:c.89C>T	p.Ala30Val	p.A30V	ENST00000322652	NM_015355.2	30	gCg/gTg	1/16	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.44	2		232	412	SUCCESS
MAP3K14	9020	MSKCC	GRCh37	17	43344772	43344772	+	splice_donor_variant,non_coding_transcript_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	312	781	0	ENST00000344686.2:n.2432+1G>A		p.X811_splice	ENST00000344686		811			1		FACETS		0.989	1				CLONAL	1	TRUE	1	0.44	2		781	1182	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985358	60985358	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	129	865	0	ENST00000333681.4:c.542T>C	p.Leu181Pro	p.L181P	ENST00000333681		181	cTg/cCg	2/3	1	2	FACETS	0.431	0.39	0.476	0.431	0.39	0.476	SUBCLONAL	1	TRUE	1	0.44	2		865	1359	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222225	5222225	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	184	670	1	ENST00000357368.4:c.3110C>T	p.Pro1037Leu	p.P1037L	ENST00000357368	NM_002850.3	1037	cCc/cTc	19/38	1	2	FACETS	0.936	0.864	1	0.936	0.864	1	CLONAL	1	TRUE	1	0.44	2		671	894	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5273473	5273473	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	296	838	0	ENST00000357368.4:c.359C>T	p.Ala120Val	p.A120V	ENST00000357368	NM_002850.3	120	gCc/gTc	4/38	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.44	2		838	1142	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250425	10250425	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748262646	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	218	713	2	ENST00000340748.4:c.3827G>A	p.Arg1276His	p.R1276H	ENST00000340748		1276	cGc/cAc	33/40	1	2	FACETS	0.927	0.862	0.995	0.927	0.862	0.995	CLONAL	1	TRUE	1	0.44	2		715	1069	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11144026	11144026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	234	723	0	ENST00000358026.2:c.3607C>T	p.Arg1203Cys	p.R1203C	ENST00000358026	NM_001128849.1	1203	Cgc/Tgc	26/36	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.44	2		723	1035	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288835	15288835	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	121	246	3	ENST00000263388.2:c.3904G>A	p.Val1302Ile	p.V1302I	ENST00000263388	NM_000435.2	1302	Gtc/Atc	24/33	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.44	2		249	467	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15299808	15299808	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	202	701	1	ENST00000263388.2:c.1370G>A	p.Cys457Tyr	p.C457Y	ENST00000263388	NM_000435.2	457	tGt/tAt	8/33	1	2	FACETS	0.939	0.87	1	0.939	0.87	1	CLONAL	1	TRUE	1	0.44	2		702	978	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271908	18271908	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	57	548	0	ENST00000222254.8:c.511G>T	p.Ala171Ser	p.A171S	ENST00000222254	NM_005027.3	171	Gct/Tct	5/16	1	2	FACETS	0.305	0.261	0.353	0.305	0.261	0.353	SUBCLONAL	1	TRUE	1	0.44	2		548	850	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755574	39755574	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	235	623	0	ENST00000288319.7:c.1191G>T	p.Gln397His	p.Q397H	ENST00000288319	NM_182918.3	397	caG/caT	10/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.44	2		623	969	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230805	53230805	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1255690543	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	327	459	1	ENST00000375401.3:c.1988C>T	p.Ala663Val	p.A663V	ENST00000375401	NM_004187.3	663	gCg/gTg	14/26	1	1	FACETS	0.865	0.824	0.906	1	0.996	1	CLONAL	2	TRUE	0	0.44	1		460	670	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095848	29095849	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1029	275	799	0	ENST00000328354.6:c.985dup	p.Tyr329LeufsTer12	p.Y329Lfs*12	ENST00000328354	NM_007194.3	329	tac/tTac	9/15	1	2	FACETS	0.959	0.899	1	0.959	0.899	1	CLONAL	1	TRUE	1	0.44	2		799	1304	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828285	72828286	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	351	1213	0	ENST00000268489.5:c.8295dup	p.Asp2766Ter	p.D2766*	ENST00000268489	NM_006885.3	2765	-/T	9/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.44	2		1213	1526	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433903	49433903	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	205	683	0	ENST00000301067.7:c.7650del	p.Val2551SerfsTer32	p.V2551Sfs*32	ENST00000301067	NM_003482.3	2550	ccT/cc	31/54	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.44	2		683	887	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495765	72495765	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	193	679	0	ENST00000477973.2:c.305del	p.Arg103AspfsTer33	p.R103Dfs*33	ENST00000477973	NM_012234.5	103	Aga/ga	1/4	1	2	FACETS	0.856	0.791	0.923	0.856	0.791	0.923	CLONAL	1	TRUE	1	0.44	2		679	1025	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965348	25965348	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	211	648	0	ENST00000435504.4:c.3858del	p.Glu1287SerfsTer37	p.E1287Sfs*37	ENST00000435504		1286	ccC/cc	13/13	1	2	FACETS	0.919	0.853	0.987	0.919	0.853	0.987	CLONAL	1	TRUE	1	0.44	2		648	1044	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692825	89692826	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	61	197	0	ENST00000371953.3:c.313dup	p.Cys105LeufsTer2	p.C105Lfs*2	ENST00000371953	NM_000314.4	103	-/T	5/9	1	2	FACETS	0.95	0.826	1	0.95	0.826	1	CLONAL	1	TRUE	1	0.44	2		197	292	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945961	17945961	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	70	919	0	ENST00000458235.1:c.1978del	p.Ala660LeufsTer10	p.A660Lfs*10	ENST00000458235	NM_000215.3	660	Gct/ct	15/24	1	2	FACETS	0.28	0.243	0.321	0.28	0.243	0.321	SUBCLONAL	1	TRUE	1	0.44	2		919	1135	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966176	25966179	+	frameshift_variant	Frame_Shift_Del	DEL	TCTC	TCTC	-	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	213	849	0	ENST00000435504.4:c.3027_3030del	p.Glu1009AspfsTer35	p.E1009Dfs*35	ENST00000435504		1009	gaGAGA/ga	13/13	1	2	FACETS	0.822	0.763	0.884	0.822	0.763	0.884	CLONAL	1	TRUE	1	0.44	2		849	1178	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722906	49722906	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	rs747477010	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	29	190	0	ENST00000449682.2:c.1421del	p.Pro474GlnfsTer52	p.P474Qfs*52	ENST00000449682	NM_020998.3	474	cCa/ca	12/18	1	2	FACETS	0.505	0.407	0.616	0.505	0.407	0.616	SUBCLONAL	1	TRUE	1	0.44	2		190	261	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119794	70119794	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	257	746	0	ENST00000245479.2:c.800del	p.Pro267LeufsTer12	p.P267Lfs*12	ENST00000245479	NM_000346.3	266	Ccc/cc	3/3	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.44	2		746	1142	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151164251	151164252	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	150	409	0	ENST00000262187.5:c.508dup	p.Met170AsnfsTer31	p.M170Nfs*31	ENST00000262187	NM_005614.3	170	atg/aAtg	8/8	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.44	2		409	660	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639608	47639608	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	143	590	0	ENST00000233146.2:c.701del	p.Thr234LysfsTer12	p.T234Kfs*12	ENST00000233146	NM_000251.2	234	aCa/aa	4/16	1	2	FACETS	0.808	0.737	0.883	0.808	0.737	0.883	CLONAL	1	TRUE	1	0.44	2		590	804	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905324	50905324	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1191	323	1152	0	ENST00000440232.2:c.537del	p.Arg180GlyfsTer3	p.R180Gfs*3	ENST00000440232	NM_002691.3	178	Ggg/gg	5/27	1	2	FACETS	0.97	0.914	1	0.97	0.914	1	CLONAL	1	TRUE	1	0.44	2		1152	1514	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47630471	47630473	+	frameshift_variant	Frame_Shift_Del	DEL	CGA	CGA	TT	novel	NA	P-0011226-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	254	599	0	ENST00000233146.2:c.141_143delinsTT	p.Glu48TrpfsTer16	p.E48Wfs*16	ENST00000233146	NM_000251.2	47	ggCGAg/ggTTg	1/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.44	2		599	1009	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	38	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.29	2		280	175	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111029	193111029	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	83	224	0	ENST00000367435.3:c.562A>G	p.Lys188Glu	p.K188E	ENST00000367435	NM_024529.4	188	Aaa/Gaa	7/17	0.213674902782933	5	FACETS	1	0.959	1	0.399	0.352	0.45	CLONAL	1	TRUE	2	0.29	5		224	686	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652331	48652331	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	318	476	0	ENST00000376670.3:c.1002T>A	p.Phe334Leu	p.F334L	ENST00000376670	NM_002049.3	334	ttT/ttA	6/6	0.3	2	FACETS	1	0.989	1			1	CLONAL	3	TRUE	NA	0.29	2		476	646	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	333	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.630367689911654	2		280	985	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0011248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	442	511	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.630367689911654	2		512	1340	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791757	42791757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568504941	NA	P-0011248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	164	671	0	ENST00000575354.2:c.643C>T	p.Arg215Trp	p.R215W	ENST00000575354	NM_015125.3	215	Cgg/Tgg	5/20	0.630367689911654	1	FACETS	0.32	0.293	0.348	0.32	0.293	0.348	SUBCLONAL	1	TRUE	0	0.630367689911654	1		671	1114	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952072	178952072	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519936	NA	P-0011248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	435	436	0	ENST00000263967.3:c.3127A>G	p.Met1043Val	p.M1043V	ENST00000263967	NM_006218.2	1043	Atg/Gtg	21/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.630367689911654	2		436	1310	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791718	42791718	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1344635105	NA	P-0011248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	324	495	0	ENST00000575354.2:c.604C>T	p.Arg202Trp	p.R202W	ENST00000575354	NM_015125.3	202	Cgg/Tgg	5/20	0.630367689911654	1	FACETS	0.652	0.617	0.689	0.652	0.617	0.689	SUBCLONAL	1	TRUE	0	0.630367689911654	1		495	1079	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78435700	78435700	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0011248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	237	232	0	ENST00000370768.2:c.121-1G>C		p.X41_splice	ENST00000370768	NM_003902.3	41			0.630367689911654	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.630367689911654	1		232	512	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106182950	106182950	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	290	543	0	ENST00000380013.4:c.3989C>T	p.Ser1330Phe	p.S1330F	ENST00000380013	NM_001127208.2	1330	tCc/tTc	8/11	1	2	FACETS	0.646	0.606	0.687	0.646	0.606	0.687	SUBCLONAL	1	TRUE	1	0.630367689911654	2		543	1425	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022978	31022979	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs1221361018	NA	P-0011248-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1341	279	605	0	ENST00000375687.4:c.2464dup	p.Thr822AsnfsTer11	p.T822Nfs*11	ENST00000375687	NM_015338.5	821	-/A	13/13	1	2	FACETS	0.546	0.511	0.583	0.546	0.511	0.583	SUBCLONAL	1	TRUE	1	0.630367689911654	2		605	1620	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	82	280	0				ENST00000310581	NM_198253.2	-/1132			0.554068914842444	3	FACETS	0.733	0.648	0.823	0.366	0.324	0.412	SUBCLONAL	1	TRUE	1	0.614490370814354	3		280	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577538	7577538	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11540652	NA	P-0011282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	255	550	0	ENST00000269305.4:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000269305	NM_001126112.2	248	cGg/cAg	7/11	0.614490370814354	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.614490370814354	1		550	533	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971028	21971028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913389	NA	P-0011282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	172	424	0	ENST00000304494.5:c.330G>A	p.Trp110Ter	p.W110*	ENST00000304494	NM_000077.4	110	tgG/tgA	2/3	1	2	FACETS	0.859	0.805	0.912	1	0.993	1	CLONAL	2	TRUE	1	0.614490370814354	2		424	326	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23619258	23619258	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	270	595	0	ENST00000261584.4:c.3277A>G	p.Ile1093Val	p.I1093V	ENST00000261584	NM_024675.3	1093	Att/Gtt	12/13	1	2	FACETS	0.972	0.914	1	0.972	0.914	1	CLONAL	1	TRUE	1	0.614490370814354	2		595	904	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105503	11105503	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0011282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	182	446	0	ENST00000358026.2:c.1420-1G>A		p.X474_splice	ENST00000358026	NM_001128849.1	474			0.614490370814354	1	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	0	0.614490370814354	1		446	390	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127456	55127456	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	276	567	0	ENST00000257290.5:c.244G>T	p.Val82Leu	p.V82L	ENST00000257290	NM_006206.4	82	Gtg/Ttg	3/23	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.614490370814354	2		567	847	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539355	187539365	+	frameshift_variant	Frame_Shift_Del	DEL	AACATCTACAG	AACATCTACAG	-	novel	NA	P-0011282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	149	370	0	ENST00000441802.2:c.8375_8385del	p.Ser2792Ter	p.S2792*	ENST00000441802	NM_005245.3	2792	tCTGTAGATGTT/t	10/27	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.614490370814354	2		370	427	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521391	8521391	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011282-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	205	553	0	ENST00000356435.5:c.847C>G	p.Pro283Ala	p.P283A	ENST00000356435		283	Cca/Gca	9/35	1	2	FACETS	0.908	0.845	0.973	0.908	0.845	0.973	CLONAL	1	TRUE	1	0.614490370814354	2		553	735	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	34	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.988	0.826	1	0.988	0.826	1	CLONAL	1	TRUE	1	0.598627675172476	2		280	115	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0011320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	25	511	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.852	1	1	0.852	1	CLONAL	1	TRUE	1	0.598627675172476	2		512	79	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830556	72830556	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011320-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	38	807	0	ENST00000268489.5:c.6025T>C	p.Tyr2009His	p.Y2009H	ENST00000268489	NM_006885.3	2009	Tac/Cac	9/10	1	2	FACETS	0.721	0.604	0.849	0.721	0.604	0.849	SUBCLONAL	1	TRUE	1	0.598627675172476	2		807	176	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	47	280	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.905	1			1	INDETERMINATE	2	TRUE	NA	0.245944631508975	2		280	178	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0011387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	128	631	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	0.168429279482831	1	FACETS	0.827	0.753	0.904	1	0.988	1	CLONAL	2	TRUE	0	0.245944631508975	1		631	552	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0011387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	142	511	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.779	0.711	0.85	1	0.988	1	SUBCLONAL	2	TRUE	1	0.245944631508975	2		511	741	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150001390	150001390	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	155	555	0	ENST00000253339.5:c.2214G>C	p.Lys738Asn	p.K738N	ENST00000253339		738	aaG/aaC	4/7	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.245944631508975	2		555	895	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518106	103518106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759972289	NA	P-0011387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	115	356	1	ENST00000355739.4:c.2044G>A	p.Glu682Lys	p.E682K	ENST00000355739	NM_000123.3	682	Gaa/Aaa	9/15	0.219463496838125	3	FACETS	0.923	0.834	1	0.923	0.834	1	CLONAL	2	TRUE	1	0.245944631508975	3		357	569	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293213	91293213	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs200756519	NA	P-0011387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	56	247	0	ENST00000355112.3:c.715G>C	p.Asp239His	p.D239H	ENST00000355112	NM_000057.2	239	Gat/Cat	3/22	0.168429279482831	1	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	0	0.245944631508975	1		247	364	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788662	3788662	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	111	402	0	ENST00000262367.5:c.4292T>A	p.Ile1431Asn	p.I1431N	ENST00000262367	NM_004380.2	1431	aTt/aAt	26/31	0.168429279482831	1	FACETS	0.77	0.695	0.849	1	0.984	1	SUBCLONAL	2	TRUE	0	0.245944631508975	1		402	514	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27098992	27098992	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0011387-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	98	366	0	ENST00000324856.7:c.3410del	p.Gly1137AspfsTer24	p.G1137Dfs*24	ENST00000324856	NM_006015.4	1136	gcG/gc	13/20	1	2	FACETS	0.855	0.767	0.948	1	0.985	1	CLONAL	2	TRUE	1	0.245944631508975	2		366	466	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462414	89462414	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011395-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	161	201	0	ENST00000336596.2:c.1886C>A	p.Ala629Glu	p.A629E	ENST00000336596	NM_005233.5	629	gCa/gAa	10/17	0.268273063226466	2	FACETS	1	0.986	1	0.671	0.617	0.728	CLONAL	1	TRUE	0	0.317197026688861	2		201	756	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55573419	55573419	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011395-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	73	225	0	ENST00000288135.5:c.1081G>T	p.Asp361Tyr	p.D361Y	ENST00000288135	NM_000222.2	361	Gat/Tat	6/21	1	2	FACETS	0.589	0.514	0.669	0.589	0.514	0.669	SUBCLONAL	1	TRUE	1	0.317197026688861	2		225	782	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67575554	67575554	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0011395-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	99	234	0	ENST00000274335.5:c.627A>T	p.Leu209Phe	p.L209F	ENST00000274335		209	ttA/ttT	4/15	0.250277189123321	1	FACETS	0.692	0.618	0.771	0.692	0.618	0.771	SUBCLONAL	1	TRUE	0	0.317197026688861	1		234	759	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472567	88472567	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1311977254	NA	P-0011395-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	195	440	0	ENST00000360948.2:c.1988T>A	p.Ile663Asn	p.I663N	ENST00000360948	NM_001012338.2	663	aTc/aAc	16/19	0.317197026688861	1	FACETS	0.979	0.905	1	0.979	0.905	1	CLONAL	1	TRUE	0	0.317197026688861	1		440	1057	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40979319	40979319	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011395-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	114	297	0	ENST00000373198.4:c.1814C>A	p.Thr605Lys	p.T605K	ENST00000373198	NM_133170.3	605	aCg/aAg	11/32	1	2	FACETS	0.787	0.708	0.871	0.787	0.708	0.871	SUBCLONAL	1	TRUE	1	0.317197026688861	2		297	913	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411882	116411902	+	splice_acceptor_variant,intron_variant	Splice_Site	DEL	TTTCTTTCTCTCTGTTTTAAG	TTTCTTTCTCTCTGTTTTAAG	-	novel	NA	P-0011395-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	226	146	0	ENST00000397752.3:c.2888-21_2888-1del		p.X963_splice	ENST00000397752	NM_000245.2	963			0.300486546234617	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	0	0.317197026688861	2		146	623	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	170	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.609044237291837	2		280	473	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10250929	10250929	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011423-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	215	314	0	ENST00000340748.4:c.3551C>T	p.Ser1184Phe	p.S1184F	ENST00000340748		1184	tCc/tTc	32/40	1	2	FACETS	0.814	0.758	0.872	0.814	0.758	0.872	CLONAL	1	TRUE	1	0.609044237291837	2		314	867	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	1203	280	0				ENST00000310581	NM_198253.2	-/1132			0.840089485754082	7	FACETS	0.997	0.981	1			1	CLONAL	6	TRUE	NA	0.840089485754082	7		280	1485	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782202	56782202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	188	453	0	ENST00000308159.5:c.43C>T	p.Gln15Ter	p.Q15*	ENST00000308159	NM_014669.4	15	Cag/Tag	2/22	0.840089485754082	3	FACETS	0.913	0.847	0.982	0.457	0.423	0.491	CLONAL	1	TRUE	1	0.840089485754082	3		453	696	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579418	7579418	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555526625	NA	P-0011440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	279	660	0	ENST00000269305.4:c.269C>T	p.Ser90Phe	p.S90F	ENST00000269305	NM_001126112.2	90	tCc/tTc	4/11	0.283511662649938	5	FACETS	0.773	0.727	0.82			1	INDETERMINATE	2	TRUE	NA	0.840089485754082	5		660	971	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786202962	NA	P-0011440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	505	567	0	ENST00000269305.4:c.527G>A	p.Cys176Tyr	p.C176Y	ENST00000269305	NM_001126112.2	176	tGc/tAc	5/11	0.283511662649938	5	FACETS	1	0.993	1			1	INDETERMINATE	3	TRUE	NA	0.840089485754082	5		567	825	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578449	7578449	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	330	685	0	ENST00000269305.4:c.481G>T	p.Ala161Ser	p.A161S	ENST00000269305	NM_001126112.2	161	Gcc/Tcc	5/11	0.283511662649938	5	FACETS	0.818	0.774	0.863			1	INDETERMINATE	2	TRUE	NA	0.840089485754082	5		685	1085	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	240515	240515	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	16	35	0	ENST00000264932.6:c.1475C>G	p.Ser492Cys	p.S492C	ENST00000264932	NM_004168.2	492	tCt/tGt	11/15	0.840089485754082	7	FACETS	0.952	0.711	1			1	CLONAL	1	TRUE	NA	0.840089485754082	7		35	124	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867469	35867469	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs191585195	NA	P-0011440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	153	391	0	ENST00000303115.3:c.283G>A	p.Glu95Lys	p.E95K	ENST00000303115	NM_002185.3	95	Gag/Aag	3/8	0.726727893012273	6	FACETS	0.969	0.886	1			1	CLONAL	1	TRUE	NA	0.840089485754082	6		391	1007	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255007	16255007	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs72649638	NA	P-0011440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	156	352	0	ENST00000375759.3:c.2272C>T	p.Arg758Ter	p.R758*	ENST00000375759	NM_015001.2	758	Cga/Tga	11/15	0.840089485754082	3	FACETS	1	0.953	1	0.523	0.482	0.565	CLONAL	1	TRUE	1	0.840089485754082	3		352	504	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849098	156849098	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	666	901	2	ENST00000524377.1:c.1990G>A	p.Val664Ile	p.V664I	ENST00000524377	NM_002529.3	664	Gtc/Atc	15/17	0.840089485754082	3	FACETS	0.902	0.873	0.931	0.902	0.873	0.931	CLONAL	2	TRUE	1	0.840089485754082	3		903	1248	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332706	70332706	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs781620810	NA	P-0011440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	203	544	0	ENST00000373644.4:c.611C>G	p.Pro204Arg	p.P204R	ENST00000373644	NM_030625.2	204	cCt/cGt	2/12	0.840089485754082	2	FACETS	0.946	0.885	1	0.473	0.442	0.504	CLONAL	1	TRUE	0	0.840089485754082	2		544	511	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659865	88659865	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs781286980	NA	P-0011440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	124	290	0	ENST00000372037.3:c.512C>G	p.Ser171Cys	p.S171C	ENST00000372037	NM_004329.2	171	tCc/tGc	7/13	0.840089485754082	2	FACETS	0.917	0.841	0.994	0.458	0.42	0.497	CLONAL	1	TRUE	0	0.840089485754082	2		290	322	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514296	69514296	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	270	647	0	ENST00000294312.3:c.385G>A	p.Asp129Asn	p.D129N	ENST00000294312	NM_005117.2	129	Gat/Aat	3/3	0.840089485754082	3	FACETS	1	0.957	1	0.511	0.48	0.543	CLONAL	1	TRUE	1	0.840089485754082	3		647	893	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102076628	102076628	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	123	278	0	ENST00000282441.5:c.807G>A	p.Met269Ile	p.M269I	ENST00000282441	NM_001130145.2	269	atG/atA	5/9	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.840089485754082	2		278	276	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376250	118376250	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	219	446	0	ENST00000534358.1:c.9643G>T	p.Ala3215Ser	p.A3215S	ENST00000534358	NM_005933.3	3215	Gcc/Tcc	27/36	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.840089485754082	2		446	506	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448464	49448464	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	562	672	1	ENST00000301067.7:c.247C>G	p.Arg83Gly	p.R83G	ENST00000301067	NM_003482.3	83	Cgg/Ggg	3/54	0.840089485754082	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.840089485754082	3		673	941	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49047515	49047515	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	63	152	351	0	ENST00000267163.4:c.2509G>T	p.Glu837Ter	p.E837*	ENST00000267163	NM_000321.2	837	Gaa/Taa	24/27	0.829528131722034	1	FACETS	0.976	0.924	1	0.976	0.924	1	CLONAL	1	TRUE	0	0.840089485754082	1		351	215	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630742	90630742	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	208	545	0	ENST00000330062.3:c.744G>C	p.Met248Ile	p.M248I	ENST00000330062	NM_002168.2	248	atG/atC	6/11	0.840089485754082	3	FACETS	0.898	0.836	0.962	0.449	0.418	0.481	CLONAL	1	TRUE	1	0.840089485754082	3		545	783	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129453	30129453	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1449756762	NA	P-0011440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	312	604	0	ENST00000263025.4:c.575A>T	p.Asp192Val	p.D192V	ENST00000263025	NM_002746.2	192	gAt/gTt	4/9	0.840089485754082	3	FACETS	1	0.976	1	0.528	0.499	0.558	CLONAL	1	TRUE	1	0.840089485754082	3		604	998	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618701	37618701	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	541	633	0	ENST00000447079.4:c.377A>G	p.Lys126Arg	p.K126R	ENST00000447079	NM_015083.1	126	aAa/aGa	1/14	0.820248447458472	4	FACETS	0.974	0.937	1	0.974	0.937	1	CLONAL	2	TRUE	2	0.840089485754082	4		633	1216	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10292716	10292716	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0011440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	493	506	0	ENST00000340748.4:c.117+1G>A		p.X39_splice	ENST00000340748		39			0.820248447458472	4	FACETS	0.956	0.917	0.994	0.956	0.917	0.994	CLONAL	2	TRUE	2	0.840089485754082	4		506	1130	SUCCESS
CALR	811	MSKCC	GRCh37	19	13054656	13054656	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	215	436	1	ENST00000316448.5:c.1183G>T	p.Glu395Ter	p.E395*	ENST00000316448	NM_004343.3	395	Gag/Tag	9/9	0.820248447458472	4	FACETS	1	0.943	1	0.507	0.472	0.544	CLONAL	1	TRUE	2	0.840089485754082	4		437	928	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215593477	215593477	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	138	317	0	ENST00000260947.4:c.2257G>C	p.Gly753Arg	p.G753R	ENST00000260947	NM_000465.2	753	Ggc/Cgc	11/11	1	2	FACETS	0.939	0.866	1	0.939	0.866	1	CLONAL	1	TRUE	1	0.840089485754082	2		317	350	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514578	44514578	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	rs765300587	NA	P-0011440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	157	389	0	ENST00000291552.4:c.575+3G>A		p.X192_splice	ENST00000291552	NM_006758.2	192			1	2	FACETS	0.875	0.81	0.942	0.875	0.81	0.942	CLONAL	1	TRUE	1	0.840089485754082	2		389	427	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158185	47158185	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	588	526	0	ENST00000409792.3:c.4514C>G	p.Ser1505Cys	p.S1505C	ENST00000409792	NM_014159.6	1505	tCt/tGt	4/21	0.820248447458472	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	2	0.840089485754082	4		526	1201	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247435	71247435	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587780339	NA	P-0011440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	214	495	1	ENST00000318789.4:c.98G>T	p.Arg33Leu	p.R33L	ENST00000318789	NM_032682.5	33	cGg/cTg	6/21	0.840089485754082	3	FACETS	1	0.951	1	0.512	0.477	0.547	CLONAL	1	TRUE	1	0.840089485754082	3		496	707	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71247458	71247458	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	223	507	0	ENST00000318789.4:c.75C>G	p.His25Gln	p.H25Q	ENST00000318789	NM_032682.5	25	caC/caG	6/21	0.840089485754082	3	FACETS	0.951	0.888	1	0.475	0.444	0.508	CLONAL	1	TRUE	1	0.840089485754082	3		507	793	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524864	187524864	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	254	543	0	ENST00000441802.2:c.10816G>C	p.Asp3606His	p.D3606H	ENST00000441802	NM_005245.3	3606	Gac/Cac	19/27	0.840089485754082	3	FACETS	1	0.98	1	0.55	0.517	0.585	CLONAL	1	TRUE	1	0.840089485754082	3		543	780	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527590	157527590	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	502	571	1	ENST00000346085.5:c.5315C>A	p.Ala1772Glu	p.A1772E	ENST00000346085	NM_020732.3	1772	gCa/gAa	20/20	0.840089485754082	3	FACETS	0.946	0.912	0.979	0.946	0.912	0.979	CLONAL	2	TRUE	1	0.840089485754082	3		572	897	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850880	128850880	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0011440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	813	661	0	ENST00000249373.3:c.1727G>C	p.Arg576Pro	p.R576P	ENST00000249373	NM_005631.4	576	cGg/cCg	10/12	0.840089485754082	5	FACETS	0.96	0.932	0.987	0.96	0.932	0.987	CLONAL	3	TRUE	2	0.840089485754082	5		661	1519	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396721	139396721	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0011440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	258	655	1	ENST00000277541.6:c.5384+3G>A		p.X1795_splice	ENST00000277541	NM_017617.3	1795			0.840089485754082	3	FACETS	1	0.975	1	0.536	0.503	0.569	CLONAL	1	TRUE	1	0.840089485754082	3		656	814	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966783	44966783	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0011440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	40	676	308	1	ENST00000377967.4:c.4005+2T>C		p.X1335_splice	ENST00000377967	NM_021140.2	1335			0.840089485754082	3	FACETS	1	0.998	1			1	CLONAL	3	TRUE	NA	0.840089485754082	3		309	716	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424722	47424722	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011440-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	247	325	0	ENST00000377045.4:c.530A>G	p.Asn177Ser	p.N177S	ENST00000377045	NM_001654.4	177	aAt/aGt	6/16	0.75870819256648	2	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.840089485754082	2		325	545	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	232	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.932189948167717	2		280	466	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0011486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	434	511	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.932189948167717	2		512	917	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794072	42794072	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0011486-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	55	329	378	0	ENST00000575354.2:c.1433del	p.Asp478AlafsTer21	p.D478Afs*21	ENST00000575354	NM_015125.3	478	gAc/gc	9/20	0.932189948167717	1	FACETS	0.981	0.956	1	0.981	0.956	1	CLONAL	1	TRUE	0	0.932189948167717	1		378	384	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0011503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	140	464	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.959	0.88	1			1	INDETERMINATE	1	FALSE	NA	0.619992393431185	2		464	471	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs139236063	NA	P-0011503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	1948	340	0	ENST00000275493.2:c.1793G>C	p.Gly598Ala	p.G598A	ENST00000275493	NM_005228.3	598	gGa/gCa	15/28	0.619992393431185	10	FACETS	1	0.995	1			1	CLONAL	7	FALSE	NA	0.619992393431185	10		340	3032	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120830	115120830	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011503-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	125	273	0	ENST00000257566.3:c.176C>A	p.Ala59Asp	p.A59D	ENST00000257566	NM_016569.3	59	gCc/gAc	1/8	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	FALSE	1	0.619992393431185	2		273	402	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0011519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	273	464	0				ENST00000310581	NM_198253.2	-/1132			0.320036700922569	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	1	0.320036700922569	4		464	683	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577113	7577113	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1555525279	NA	P-0011519-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	350	554	0	ENST00000269305.4:c.825T>G	p.Cys275Trp	p.C275W	ENST00000269305	NM_001126112.2	275	tgT/tgG	8/11	0.317776872280752	2	FACETS	0.989	0.937	1	0.989	0.937	1	CLONAL	2	TRUE	0	0.320036700922569	2		554	1106	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0011521-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	169	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.948	0.88	1	0.948	0.88	1	CLONAL	1	TRUE	1	0.760206258705661	2		280	469	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0011521-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	33	145	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	0.214	0.174	0.259	0.214	0.174	0.259	SUBCLONAL	1	TRUE	1	0.760206258705661	2		145	406	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0011521-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1118	420	1211	0	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	1	2	FACETS	0.718	0.683	0.754	0.718	0.683	0.754	SUBCLONAL	1	TRUE	1	0.760206258705661	2		1211	1538	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144148	55144148	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519700	NA	P-0011521-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	243	775	0	ENST00000257290.5:c.1977C>G	p.Asn659Lys	p.N659K	ENST00000257290	NM_006206.4	659	aaC/aaG	14/23	1	2	FACETS	0.762	0.714	0.812	0.762	0.714	0.812	SUBCLONAL	1	TRUE	1	0.760206258705661	2		775	839	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888199	112888199	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121918454	NA	P-0011521-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	80	1044	0	ENST00000351677.2:c.215C>G	p.Ala72Gly	p.A72G	ENST00000351677	NM_002834.3	72	gCc/gGc	3/16	1	2	FACETS	0.191	0.167	0.216	0.191	0.167	0.216	SUBCLONAL	1	TRUE	1	0.760206258705661	2		1044	1103	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888198	112888198	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121918453	NA	P-0011521-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	319	1057	0	ENST00000351677.2:c.214G>T	p.Ala72Ser	p.A72S	ENST00000351677	NM_002834.3	72	Gcc/Tcc	3/16	1	2	FACETS	0.758	0.716	0.801	0.758	0.716	0.801	SUBCLONAL	1	TRUE	1	0.760206258705661	2		1057	1107	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29586066	29586066	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011521-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	132	614	1	ENST00000356175.3:c.4286C>T	p.Ala1429Val	p.A1429V	ENST00000356175	NM_000267.3	1429	gCc/gTc	32/57	1	2	FACETS	0.515	0.469	0.564	0.515	0.469	0.564	SUBCLONAL	1	TRUE	1	0.760206258705661	2		615	674	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922867	39922867	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011521-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	457	581	0	ENST00000378444.4:c.3841G>T	p.Glu1281Ter	p.E1281*	ENST00000378444	NM_001123385.1	1281	Gaa/Taa	8/15	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.760206258705661	1		581	608	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0011568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	90	145	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.462615793803599	2		145	372	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579355	7579355	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1057519997	NA	P-0011568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	201	494	0	ENST00000269305.4:c.332T>C	p.Leu111Pro	p.L111P	ENST00000269305	NM_001126112.2	111	cTg/cCg	4/11	0.462615793803599	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.462615793803599	1		494	640	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913385	NA	P-0011568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	33	181	0	ENST00000304494.5:c.247C>G	p.His83Asp	p.H83D	ENST00000304494	NM_000077.4	83	Cac/Gac	2/3	0.203325210833455	1	FACETS	0.277	0.225	0.335	0.277	0.225	0.335	INDETERMINATE	1	TRUE	0	0.462615793803599	1		181	396	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521483	46521483	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs968243629	NA	P-0011568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	61	624	2	ENST00000262741.5:c.925C>T	p.Arg309Ter	p.R309*	ENST00000262741	NM_003629.3	309	Cga/Tga	7/10	0.203325210833455	1	FACETS	0.179	0.154	0.207	0.179	0.154	0.207	INDETERMINATE	1	TRUE	0	0.462615793803599	1		626	1132	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971125	21971126	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GAGTGGCGGGGTC	novel	NA	P-0011568-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	23	233	0	ENST00000304494.5:c.220_232dup	p.Leu78ArgfsTer46	p.L78Rfs*46	ENST00000304494	NM_000077.4	78	ctc/cGACCCCGCCACTCtc	2/3	0.203325210833455	1	FACETS	0.204	0.159	0.257	0.204	0.159	0.257	INDETERMINATE	1	TRUE	0	0.462615793803599	1		233	374	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	45	351	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.333	0.279	0.394	0.333	0.279	0.394	SUBCLONAL	1	TRUE	1	0.36	2		351	750	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	181	593	1	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.36	2		594	921	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570366	87570366	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1210	68	613	1	ENST00000277120.3:c.2106G>T	p.Glu702Asp	p.E702D	ENST00000277120		702	gaG/gaT	17/19	1	2	FACETS	0.296	0.256	0.339	0.296	0.256	0.339	SUBCLONAL	1	TRUE	1	0.36	2		614	1278	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464916	120464916	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587737953	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	47	302	0	ENST00000256646.2:c.5156G>A	p.Arg1719Gln	p.R1719Q	ENST00000256646	NM_024408.3	1719	cGa/cAa	28/34	1	2	FACETS	0.434	0.366	0.51	0.434	0.366	0.51	SUBCLONAL	1	TRUE	1	0.36	2		302	601	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543829	212543829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs771154734	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	55	347	0	ENST00000342788.4:c.1570C>T	p.Arg524Cys	p.R524C	ENST00000342788	NM_005235.2	524	Cgc/Tgc	13/28	1	2	FACETS	0.421	0.36	0.489	0.421	0.36	0.489	SUBCLONAL	1	TRUE	1	0.36	2		347	725	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	80	243	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	0.956	0.844	1	0.956	0.844	1	CLONAL	1	TRUE	1	0.36	2		243	465	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419920	152419920	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	137	337	0	ENST00000206249.3:c.1607T>A	p.Leu536His	p.L536H	ENST00000206249	NM_000125.3	536	cTc/cAc	8/8	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.36	2		337	753	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719472	61719472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520009	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	67	269	0	ENST00000401558.2:c.1711G>A	p.Glu571Lys	p.E571K	ENST00000401558	NM_003400.3	571	Gaa/Aaa	15/25	1	2	FACETS	0.753	0.656	0.859	0.753	0.656	0.859	SUBCLONAL	1	TRUE	1	0.36	2		269	494	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936103	178936103	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519699	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	56	185	0	ENST00000263967.3:c.1645G>A	p.Asp549Asn	p.D549N	ENST00000263967	NM_006218.2	549	Gat/Aat	10/21	1	2	FACETS	0.81	0.697	0.933	0.81	0.697	0.933	CLONAL	1	TRUE	1	0.36	2		185	384	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244185	153244185	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	207	547	1	ENST00000281708.4:c.1972C>T	p.Arg658Ter	p.R658*	ENST00000281708	NM_033632.3	658	Cga/Tga	12/12	1	2	FACETS	0.898	0.831	0.967	0.898	0.831	0.967	CLONAL	1	TRUE	1	0.36	2		548	1281	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26911760	26911760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	40	416	0	ENST00000381527.3:c.185C>T	p.Ser62Leu	p.S62L	ENST00000381527	NM_001260.1	62	tCg/tTg	2/13	1	2	FACETS	0.307	0.254	0.367	0.307	0.254	0.367	SUBCLONAL	1	TRUE	1	0.36	2		416	723	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909629	76909629	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs919106518	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1329	76	808	0	ENST00000373344.5:c.4276C>T	p.Arg1426Ter	p.R1426*	ENST00000373344	NM_000489.3	1426	Cga/Tga	14/35	1	2	FACETS	0.301	0.262	0.342	0.301	0.262	0.342	SUBCLONAL	1	TRUE	1	0.36	2		808	1405	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045676	47045676	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	109	382	0	ENST00000377604.3:c.2557C>T	p.Arg853Trp	p.R853W	ENST00000377604	NM_001204468.1	853	Cgg/Tgg	23/24	1	2	FACETS	0.945	0.85	1	0.945	0.85	1	CLONAL	1	TRUE	1	0.36	2		382	641	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417596	139417596	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372660483	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	61	522	0	ENST00000277541.6:c.448G>A	p.Ala150Thr	p.A150T	ENST00000277541	NM_017617.3	150	Gcc/Acc	4/34	1	2	FACETS	0.35	0.301	0.404	0.35	0.301	0.404	SUBCLONAL	1	TRUE	1	0.36	2		522	968	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172385	108172385	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764389018	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	90	319	1	ENST00000278616.4:c.5188C>T	p.Arg1730Ter	p.R1730*	ENST00000278616	NM_000051.3	1730	Cga/Tga	35/63	1	2	FACETS	0.791	0.703	0.885	0.791	0.703	0.885	SUBCLONAL	1	TRUE	1	0.36	2		320	632	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539951	187539951	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs777631605	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	106	380	0	ENST00000441802.2:c.7789C>T	p.Arg2597Ter	p.R2597*	ENST00000441802	NM_005245.3	2597	Cga/Tga	10/27	1	2	FACETS	0.9	0.808	0.998	0.9	0.808	0.998	CLONAL	1	TRUE	1	0.36	2		380	654	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12013719	12013719	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	101	291	0	ENST00000353533.5:c.661G>T	p.Glu221Ter	p.E221*	ENST00000353533	NM_003010.3	221	Gaa/Taa	6/11	1	2	FACETS	0.945	0.846	1	0.945	0.846	1	CLONAL	1	TRUE	1	0.36	2		291	594	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42021428	42021428	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	256	743	1	ENST00000219905.7:c.3724C>T	p.Arg1242Ter	p.R1242*	ENST00000219905	NM_001164273.1	1242	Cga/Tga	11/24	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.36	2		744	1417	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181765	56181765	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1287268127	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	46	326	1	ENST00000399503.3:c.3989C>T	p.Ser1330Leu	p.S1330L	ENST00000399503	NM_005921.1	1330	tCg/tTg	17/20	1	2	FACETS	0.413	0.347	0.486	0.413	0.347	0.486	SUBCLONAL	1	TRUE	1	0.36	2		327	619	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112412	115112412	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	36	315	0	ENST00000257566.3:c.1328C>T	p.Ser443Leu	p.S443L	ENST00000257566	NM_016569.3	443	tCg/tTg	7/8	1	2	FACETS	0.359	0.294	0.432	0.359	0.294	0.432	SUBCLONAL	1	TRUE	1	0.36	2		315	557	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912007	32912007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80358600	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1422	106	785	0	ENST00000380152.3:c.3515C>T	p.Ser1172Leu	p.S1172L	ENST00000380152		1172	tCg/tTg	11/27	1	2	FACETS	0.385	0.344	0.43	0.385	0.344	0.43	SUBCLONAL	1	TRUE	1	0.36	2		785	1528	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098533	108098533	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs55861249	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	63	197	0	ENST00000278616.4:c.103C>T	p.Arg35Ter	p.R35*	ENST00000278616	NM_000051.3	35	Cga/Tga	3/63	1	2	FACETS	0.884	0.768	1	0.884	0.768	1	CLONAL	1	TRUE	1	0.36	2		197	396	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828552	72828552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1530	167	842	2	ENST00000268489.5:c.8029G>A	p.Glu2677Lys	p.E2677K	ENST00000268489	NM_006885.3	2677	Gag/Aag	9/10	1	2	FACETS	0.547	0.5	0.596	0.547	0.5	0.596	SUBCLONAL	1	TRUE	1	0.36	2		844	1697	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151167676	151167676	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	86	358	0	ENST00000262187.5:c.443C>A	p.Ser148Tyr	p.S148Y	ENST00000262187	NM_005614.3	148	tCt/tAt	7/8	1	2	FACETS	0.586	0.518	0.66	0.586	0.518	0.66	SUBCLONAL	1	TRUE	1	0.36	2		358	815	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94224031	94224031	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs116679717	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	60	448	0	ENST00000323929.3:c.121G>A	p.Asp41Asn	p.D41N	ENST00000323929	NM_005591.3	41	Gat/Aat	3/20	1	2	FACETS	0.371	0.319	0.429	0.371	0.319	0.429	SUBCLONAL	1	TRUE	1	0.36	2		448	898	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136804	55136804	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	118	334	1	ENST00000257290.5:c.1126C>T	p.Arg376Ter	p.R376*	ENST00000257290	NM_006206.4	376	Cga/Tga	8/23	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.36	2		335	596	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527462	29527462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs76015786	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	90	312	0	ENST00000356175.3:c.911G>A	p.Arg304Gln	p.R304Q	ENST00000356175	NM_000267.3	304	cGa/cAa	9/57	1	2	FACETS	0.921	0.819	1	0.921	0.819	1	CLONAL	1	TRUE	1	0.36	2		312	543	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740668	58740668	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs759850701	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1210	374	843	0	ENST00000305921.3:c.1573G>T	p.Glu525Ter	p.E525*	ENST00000305921	NM_003620.3	525	Gaa/Taa	6/6	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.36	2		843	1584	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48941654	48941654	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776534331	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	29	291	0	ENST00000267163.4:c.964G>A	p.Glu322Lys	p.E322K	ENST00000267163	NM_000321.2	322	Gaa/Aaa	10/27	1	2	FACETS	0.303	0.243	0.373	0.303	0.243	0.373	SUBCLONAL	1	TRUE	1	0.36	2		291	531	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261766	16261766	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs777176191	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	134	319	0	ENST00000375759.3:c.9031C>T	p.Arg3011Ter	p.R3011*	ENST00000375759	NM_015001.2	3011	Cga/Tga	11/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.36	2		319	665	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65300295	65300295	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	42	254	0	ENST00000342505.4:c.3415C>T	p.Arg1139Trp	p.R1139W	ENST00000342505	NM_002227.2	1139	Cgg/Tgg	25/25	1	2	FACETS	0.444	0.371	0.527	0.444	0.371	0.527	SUBCLONAL	1	TRUE	1	0.36	2		254	525	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65300313	65300313	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	25	245	0	ENST00000342505.4:c.3397G>T	p.Glu1133Ter	p.E1133*	ENST00000342505	NM_002227.2	1133	Gaa/Taa	25/25	1	2	FACETS	0.282	0.221	0.352	0.282	0.221	0.352	SUBCLONAL	1	TRUE	1	0.36	2		245	493	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65344804	65344804	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	64	359	0	ENST00000342505.4:c.233T>C	p.Phe78Ser	p.F78S	ENST00000342505	NM_002227.2	78	tTt/tCt	4/25	1	2	FACETS	0.525	0.454	0.602	0.525	0.454	0.602	SUBCLONAL	1	TRUE	1	0.36	2		359	677	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176145073	176145073	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	54	502	0	ENST00000367669.3:c.538A>G	p.Ile180Val	p.I180V	ENST00000367669	NM_022457.5	180	Att/Gtt	3/20	1	2	FACETS	0.367	0.313	0.427	0.367	0.313	0.427	SUBCLONAL	1	TRUE	1	0.36	2		502	817	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612764	228612764	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1482262254	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1660	92	952	1	ENST00000366696.1:c.263C>T	p.Ser88Leu	p.S88L	ENST00000366696	NM_003493.2	88	tCg/tTg	1/1	1	2	FACETS	0.292	0.258	0.328	0.292	0.258	0.328	SUBCLONAL	1	TRUE	1	0.36	2		953	1752	SUCCESS
FH	2271	MSKCC	GRCh37	1	241669390	241669390	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772190176	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	49	410	0	ENST00000366560.3:c.817G>A	p.Ala273Thr	p.A273T	ENST00000366560	NM_000143.3	273	Gca/Aca	6/10	1	2	FACETS	0.327	0.276	0.383	0.327	0.276	0.383	SUBCLONAL	1	TRUE	1	0.36	2		410	833	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243828129	243828129	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	54	472	0	ENST00000263826.5:c.229C>A	p.Leu77Ile	p.L77I	ENST00000263826	NM_005465.4	77	Ctc/Atc	3/13	1	2	FACETS	0.352	0.299	0.409	0.352	0.299	0.409	SUBCLONAL	1	TRUE	1	0.36	2		472	853	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47607082	47607082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	125	527	0	ENST00000263735.4:c.832G>A	p.Ala278Thr	p.A278T	ENST00000263735	NM_002354.2	278	Gca/Aca	7/9	1	2	FACETS	0.585	0.528	0.646	0.585	0.528	0.646	SUBCLONAL	1	TRUE	1	0.36	2		527	1187	SUCCESS
REL	5966	MSKCC	GRCh37	2	61128173	61128173	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	26	234	0	ENST00000295025.8:c.349G>A	p.Glu117Lys	p.E117K	ENST00000295025	NM_002908.2	117	Gaa/Aaa	4/11	1	2	FACETS	0.313	0.247	0.389	0.313	0.247	0.389	SUBCLONAL	1	TRUE	1	0.36	2		234	461	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193602	99193602	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1271977013	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	64	228	0	ENST00000074304.5:c.2797C>T	p.Arg933Cys	p.R933C	ENST00000074304	NM_001134224.1	933	Cgc/Tgc	25/26	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.36	2		228	314	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99203950	99203950	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755469992	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	116	317	0	ENST00000074304.5:c.2813G>A	p.Arg938Gln	p.R938Q	ENST00000074304	NM_001134224.1	938	cGa/cAa	26/26	1	2	FACETS	0.923	0.833	1	0.923	0.833	1	CLONAL	1	TRUE	1	0.36	2		317	698	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713506	30713506	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs886038794	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	35	264	0	ENST00000295754.5:c.831G>T	p.Lys277Asn	p.K277N	ENST00000295754	NM_003242.5	277	aaG/aaT	4/7	1	2	FACETS	0.37	0.302	0.445	0.37	0.302	0.445	SUBCLONAL	1	TRUE	1	0.36	2		264	526	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41277225	41277225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760837728	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	53	376	1	ENST00000349496.5:c.1694G>A	p.Arg565His	p.R565H	ENST00000349496	NM_001904.3	565	cGc/cAc	11/15	1	2	FACETS	0.415	0.353	0.483	0.415	0.353	0.483	SUBCLONAL	1	TRUE	1	0.36	2		377	710	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125370	47125370	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143991928	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1273	69	642	1	ENST00000409792.3:c.5900G>A	p.Gly1967Asp	p.G1967D	ENST00000409792	NM_014159.6	1967	gGc/gAc	12/21	1	2	FACETS	0.286	0.247	0.327	0.286	0.247	0.327	SUBCLONAL	1	TRUE	1	0.36	2		643	1342	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119634999	119634999	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756003147	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	53	339	0	ENST00000316626.5:c.500G>A	p.Arg167Gln	p.R167Q	ENST00000316626		167	cGa/cAa	5/12	1	2	FACETS	0.65	0.555	0.754	0.65	0.555	0.754	SUBCLONAL	1	TRUE	1	0.36	2		339	453	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205733	128205733	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	105	623	0	ENST00000341105.2:c.142T>G	p.Phe48Val	p.F48V	ENST00000341105	NM_032638.4	48	Ttc/Gtc	2/6	1	2	FACETS	0.54	0.482	0.601	0.54	0.482	0.601	SUBCLONAL	1	TRUE	1	0.36	2		623	1081	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916861	178916861	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1560137208	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1329	315	937	0	ENST00000263967.3:c.248T>C	p.Phe83Ser	p.F83S	ENST00000263967	NM_006218.2	83	tTt/tCt	2/21	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.36	2		937	1644	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921533	178921533	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1428379257	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	72	325	1	ENST00000263967.3:c.1015C>A	p.Leu339Ile	p.L339I	ENST00000263967	NM_006218.2	339	Ctt/Att	5/21	1	2	FACETS	0.737	0.644	0.836	0.737	0.644	0.836	SUBCLONAL	1	TRUE	1	0.36	2		326	543	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185169106	185169106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775670152	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	238	579	3	ENST00000265026.3:c.1201C>T	p.Arg401Trp	p.R401W	ENST00000265026	NM_004721.4	401	Cgg/Tgg	7/14	1	2	FACETS	0.988	0.921	1	0.988	0.921	1	CLONAL	1	TRUE	1	0.36	2		582	1338	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955592	55955592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560674167	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	102	637	0	ENST00000263923.4:c.3353G>A	p.Arg1118Gln	p.R1118Q	ENST00000263923	NM_002253.2	1118	cGa/cAa	25/30	1	2	FACETS	0.512	0.457	0.572	0.512	0.457	0.572	SUBCLONAL	1	TRUE	1	0.36	2		637	1106	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356309	66356309	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	50	359	0	ENST00000273854.3:c.1188G>T	p.Lys396Asn	p.K396N	ENST00000273854	NM_004439.5	396	aaG/aaT	5/18	1	2	FACETS	0.403	0.341	0.471	0.403	0.341	0.471	SUBCLONAL	1	TRUE	1	0.36	2		359	690	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467575	66467575	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1276193993	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	131	404	1	ENST00000273854.3:c.694A>G	p.Lys232Glu	p.K232E	ENST00000273854	NM_004439.5	232	Aaa/Gaa	3/18	1	2	FACETS	0.898	0.816	0.986	0.898	0.816	0.986	CLONAL	1	TRUE	1	0.36	2		405	810	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157539	106157539	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs192553789	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	111	404	0	ENST00000380013.4:c.2440C>T	p.Arg814Cys	p.R814C	ENST00000380013	NM_001127208.2	814	Cgt/Tgt	3/11	1	2	FACETS	0.998	0.899	1	0.998	0.899	1	CLONAL	1	TRUE	1	0.36	2		404	618	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143003277	143003277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369778611	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	63	379	0	ENST00000262992.4:c.2549C>T	p.Ser850Leu	p.S850L	ENST00000262992	NM_001101669.1	850	tCg/tTg	23/24	1	2	FACETS	0.395	0.341	0.455	0.395	0.341	0.455	SUBCLONAL	1	TRUE	1	0.36	2		379	885	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007319	143007319	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	108	309	1	ENST00000262992.4:c.2465A>G	p.Glu822Gly	p.E822G	ENST00000262992	NM_001101669.1	822	gAa/gGa	22/24	1	2	FACETS	0.916	0.823	1	0.916	0.823	1	CLONAL	1	TRUE	1	0.36	2		310	655	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143043280	143043280	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	138	407	0	ENST00000262992.4:c.2135+1G>A		p.X712_splice	ENST00000262992	NM_001101669.1	712			1	2	FACETS	0.843	0.767	0.924	0.843	0.767	0.924	CLONAL	1	TRUE	1	0.36	2		407	909	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539097	187539097	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	61	438	0	ENST00000441802.2:c.8643C>A	p.Asp2881Glu	p.D2881E	ENST00000441802	NM_005245.3	2881	gaC/gaA	10/27	1	2	FACETS	0.425	0.365	0.489	0.425	0.365	0.489	SUBCLONAL	1	TRUE	1	0.36	2		438	798	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628440	187628440	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs890035208	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	153	362	1	ENST00000441802.2:c.2542G>A	p.Asp848Asn	p.D848N	ENST00000441802	NM_005245.3	848	Gat/Aat	2/27	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.36	2		363	717	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86670124	86670124	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	96	332	0	ENST00000274376.6:c.1921G>T	p.Glu641Ter	p.E641*	ENST00000274376	NM_002890.2	641	Gag/Tag	14/25	1	2	FACETS	0.909	0.811	1	0.909	0.811	1	CLONAL	1	TRUE	1	0.36	2		332	587	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86675635	86675635	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	26	235	0	ENST00000274376.6:c.2571G>T	p.Glu857Asp	p.E857D	ENST00000274376	NM_002890.2	857	gaG/gaT	19/25	1	2	FACETS	0.311	0.246	0.387	0.311	0.246	0.387	SUBCLONAL	1	TRUE	1	0.36	2		235	464	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131894980	131894980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs786202168	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	103	245	0	ENST00000265335.6:c.134T>C	p.Ile45Thr	p.I45T	ENST00000265335		45	aTc/aCc	2/25	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.36	2		245	455	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636744	176636744	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	152	450	2	ENST00000439151.2:c.1344G>T	p.Lys448Asn	p.K448N	ENST00000439151	NM_022455.4	448	aaG/aaT	5/23	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.36	2		452	793	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066648	94066648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371089003	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1221	272	778	1	ENST00000369303.4:c.1111C>T	p.Arg371Trp	p.R371W	ENST00000369303	NM_004440.3	371	Cgg/Tgg	5/17	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.36	2		779	1493	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642470	117642470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765146445	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	247	733	1	ENST00000368508.3:c.5729G>A	p.Arg1910Gln	p.R1910Q	ENST00000368508	NM_002944.2	1910	cGa/cAa	35/43	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.36	2		734	1319	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117679091	117679091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	39	312	0	ENST00000368508.3:c.3730G>A	p.Glu1244Lys	p.E1244K	ENST00000368508	NM_002944.2	1244	Gaa/Aaa	24/43	1	2	FACETS	0.4	0.331	0.477	0.4	0.331	0.477	SUBCLONAL	1	TRUE	1	0.36	2		312	542	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81331962	81331962	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs201768315	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	39	425	0	ENST00000222390.5:c.2122C>T	p.Arg708Ter	p.R708*	ENST00000222390	NM_000601.4	708	Cga/Tga	18/18	1	2	FACETS	0.29	0.24	0.347	0.29	0.24	0.347	SUBCLONAL	1	TRUE	1	0.36	2		425	746	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334816	81334816	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs779267373	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	31	346	0	ENST00000222390.5:c.1900C>A	p.Leu634Ile	p.L634I	ENST00000222390	NM_000601.4	634	Ctc/Atc	17/18	1	2	FACETS	0.334	0.269	0.407	0.334	0.269	0.407	SUBCLONAL	1	TRUE	1	0.36	2		346	516	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81374415	81374415	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	38	365	1	ENST00000222390.5:c.647G>T	p.Gly216Val	p.G216V	ENST00000222390	NM_000601.4	216	gGg/gTg	6/18	1	2	FACETS	0.34	0.28	0.407	0.34	0.28	0.407	SUBCLONAL	1	TRUE	1	0.36	2		366	621	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512615	148512615	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	103	263	0	ENST00000320356.2:c.1529A>C	p.Lys510Thr	p.K510T	ENST00000320356	NM_004456.4	510	aAg/aCg	13/20	1	2	FACETS	0.889	0.796	0.986	0.889	0.796	0.986	CLONAL	1	TRUE	1	0.36	2		263	644	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151848562	151848562	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367652375	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	983	60	494	1	ENST00000262189.6:c.12631C>T	p.Arg4211Trp	p.R4211W	ENST00000262189	NM_170606.2	4211	Cgg/Tgg	50/59	1	2	FACETS	0.32	0.274	0.369	0.32	0.274	0.369	SUBCLONAL	1	TRUE	1	0.36	2		495	1043	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849886	151849886	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	144	443	2	ENST00000262189.6:c.12430C>A	p.Leu4144Ile	p.L4144I	ENST00000262189	NM_170606.2	4144	Ctc/Atc	49/59	1	2	FACETS	0.957	0.873	1	0.957	0.873	1	CLONAL	1	TRUE	1	0.36	2		445	836	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879166	151879166	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	50	531	0	ENST00000262189.6:c.5779A>G	p.Thr1927Ala	p.T1927A	ENST00000262189	NM_170606.2	1927	Aca/Gca	36/59	1	2	FACETS	0.302	0.255	0.354	0.302	0.255	0.354	SUBCLONAL	1	TRUE	1	0.36	2		531	920	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884870	151884870	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	129	361	0	ENST00000262189.6:c.4723A>C	p.Asn1575His	p.N1575H	ENST00000262189	NM_170606.2	1575	Aat/Cat	32/59	1	2	FACETS	0.98	0.89	1	0.98	0.89	1	CLONAL	1	TRUE	1	0.36	2		361	731	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597849	43597849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564490056	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	282	765	2	ENST00000355710.3:c.397C>T	p.Arg133Cys	p.R133C	ENST00000355710	NM_020975.4	133	Cgt/Tgt	3/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.36	2		767	1415	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850777	63850777	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	206	486	2	ENST00000279873.7:c.1555G>T	p.Glu519Ter	p.E519*	ENST00000279873	NM_032199.2	519	Gaa/Taa	10/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.36	2		488	1084	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851773	63851773	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	156	488	0	ENST00000279873.7:c.2551G>T	p.Glu851Ter	p.E851*	ENST00000279873	NM_032199.2	851	Gaa/Taa	10/10	1	2	FACETS	0.882	0.807	0.96	0.882	0.807	0.96	CLONAL	1	TRUE	1	0.36	2		488	983	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653824	89653824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	82	342	0	ENST00000371953.3:c.122G>A	p.Arg41Lys	p.R41K	ENST00000371953	NM_000314.4	41	aGa/aAa	2/9	1	2	FACETS	0.913	0.807	1	0.913	0.807	1	CLONAL	1	TRUE	1	0.36	2		342	499	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588164	69588164	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1212	279	780	2	ENST00000168712.1:c.534C>A	p.Phe178Leu	p.F178L	ENST00000168712	NM_002007.2	178	ttC/ttA	3/3	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.36	2		782	1491	SUCCESS
ATM	472	MSKCC	GRCh37	11	108150330	108150330	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	43	231	0	ENST00000278616.4:c.3397G>T	p.Glu1133Ter	p.E1133*	ENST00000278616	NM_000051.3	1133	Gaa/Taa	23/63	1	2	FACETS	0.539	0.451	0.636	0.539	0.451	0.636	SUBCLONAL	1	TRUE	1	0.36	2		231	443	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372512	118372512	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	257	639	0	ENST00000534358.1:c.6445C>T	p.Arg2149Ter	p.R2149*	ENST00000534358	NM_005933.3	2149	Cga/Tga	26/36	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.36	2		639	1288	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46287441	46287441	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	96	316	0	ENST00000334344.6:c.5300A>G	p.His1767Arg	p.H1767R	ENST00000334344	NM_152641.2	1767	cAc/cGc	20/21	1	2	FACETS	0.837	0.747	0.933	0.837	0.747	0.933	CLONAL	1	TRUE	1	0.36	2		316	637	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428709	49428709	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	94	453	0	ENST00000301067.7:c.10241A>C	p.Lys3414Thr	p.K3414T	ENST00000301067	NM_003482.3	3414	aAa/aCa	35/54	1	2	FACETS	0.644	0.572	0.72	0.644	0.572	0.72	SUBCLONAL	1	TRUE	1	0.36	2		453	811	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	159	536	1	ENST00000267101.3:c.273G>T	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atT	3/28	1	2	FACETS	0.881	0.807	0.958	0.881	0.807	0.958	CLONAL	1	TRUE	1	0.36	2		537	1003	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493772	56493772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370221639	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	60	460	5	ENST00000267101.3:c.3088G>A	p.Ala1030Thr	p.A1030T	ENST00000267101	NM_001982.3	1030	Gcc/Acc	25/28	1	2	FACETS	0.326	0.28	0.377	0.326	0.28	0.377	SUBCLONAL	1	TRUE	1	0.36	2		465	1022	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864432	57864432	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	200	692	0	ENST00000228682.2:c.1909C>G	p.Arg637Gly	p.R637G	ENST00000228682	NM_005269.2	637	Cgg/Ggg	12/12	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.36	2		692	1103	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133212495	133212495	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs879254168	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	67	388	1	ENST00000320574.5:c.5794C>T	p.Arg1932Cys	p.R1932C	ENST00000320574	NM_006231.2	1932	Cgt/Tgt	42/49	1	2	FACETS	0.453	0.393	0.519	0.453	0.393	0.519	SUBCLONAL	1	TRUE	1	0.36	2		389	821	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623876	28623876	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	96	343	0	ENST00000241453.7:c.778T>G	p.Leu260Val	p.L260V	ENST00000241453	NM_004119.2	260	Tta/Gta	7/24	1	2	FACETS	0.975	0.871	1	0.975	0.871	1	CLONAL	1	TRUE	1	0.36	2		343	547	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28883012	28883012	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	203	539	0	ENST00000282397.4:c.3688G>T	p.Glu1230Ter	p.E1230*	ENST00000282397	NM_002019.4	1230	Gaa/Taa	28/30	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.36	2		539	1073	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73347911	73347911	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146500302	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	130	362	0	ENST00000377767.4:c.1150C>T	p.Arg384Cys	p.R384C	ENST00000377767	NM_014953.3	384	Cgc/Tgc	8/21	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.36	2		362	689	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582053	95582053	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	52	482	1	ENST00000393063.1:c.1858G>A	p.Asp620Asn	p.D620N	ENST00000393063	NM_030621.3	620	Gat/Aat	12/28	1	2	FACETS	0.341	0.289	0.398	0.341	0.289	0.398	SUBCLONAL	1	TRUE	1	0.36	2		483	847	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14024709	14024709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	42	339	0	ENST00000311895.7:c.935C>T	p.Ser312Phe	p.S312F	ENST00000311895	NM_005236.2	312	tCt/tTt	5/11	1	2	FACETS	0.324	0.269	0.384	0.324	0.269	0.384	SUBCLONAL	1	TRUE	1	0.36	2		339	721	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67100694	67100694	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	164	491	0	ENST00000412916.2:c.392G>A	p.Arg131Gln	p.R131Q	ENST00000412916		131	cGa/cAa	4/6	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.36	2		491	863	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645255	67645255	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	178	446	0	ENST00000264010.4:c.520G>A	p.Glu174Lys	p.E174K	ENST00000264010	NM_006565.3	174	Gag/Aag	3/12	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.36	2		446	977	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992936	72992936	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774852976	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1451	136	843	1	ENST00000268489.5:c.1109G>A	p.Gly370Asp	p.G370D	ENST00000268489	NM_006885.3	370	gGc/gAc	2/10	1	2	FACETS	0.476	0.431	0.524	0.476	0.431	0.524	SUBCLONAL	1	TRUE	1	0.36	2		844	1587	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349058	89349058	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555528234	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1533	106	864	2	ENST00000301030.4:c.3892G>A	p.Asp1298Asn	p.D1298N	ENST00000301030	NM_001256183.1	1298	Gat/Aat	9/13	1	2	FACETS	0.359	0.32	0.401	0.359	0.32	0.401	SUBCLONAL	1	TRUE	1	0.36	2		866	1639	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357135	89357135	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1540	91	814	0	ENST00000301030.4:c.499C>T	p.Arg167Cys	p.R167C	ENST00000301030	NM_001256183.1	167	Cgt/Tgt	6/13	1	2	FACETS	0.31	0.274	0.349	0.31	0.274	0.349	SUBCLONAL	1	TRUE	1	0.36	2		814	1631	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983233	7983233	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	87	585	0	ENST00000319144.4:c.781G>A	p.Asp261Asn	p.D261N	ENST00000319144	NM_001139.2	261	Gac/Aac	7/15	1	2	FACETS	0.523	0.462	0.589	0.523	0.462	0.589	SUBCLONAL	1	TRUE	1	0.36	2		585	924	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40368066	40368066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1432	95	753	0	ENST00000293328.3:c.1439C>T	p.Ala480Val	p.A480V	ENST00000293328	NM_012448.3	480	gCc/gTc	12/19	1	2	FACETS	0.346	0.306	0.388	0.346	0.306	0.388	SUBCLONAL	1	TRUE	1	0.36	2		753	1527	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45368218	45368218	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	81	478	2	ENST00000262160.6:c.1384C>T	p.Arg462Cys	p.R462C	ENST00000262160	NM_005901.5	462	Cgt/Tgt	11/11	1	2	FACETS	0.489	0.429	0.552	0.489	0.429	0.552	SUBCLONAL	1	TRUE	1	0.36	2		480	921	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625592	1625592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1280061503	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1288	75	717	0	ENST00000344749.5:c.482C>T	p.Ala161Val	p.A161V	ENST00000344749	NM_001136139.2	161	gCg/gTg	7/19	1	2	FACETS	0.306	0.266	0.348	0.306	0.266	0.348	SUBCLONAL	1	TRUE	1	0.36	2		717	1363	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138509	11138509	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	174	527	0	ENST00000358026.2:c.3265C>A	p.Leu1089Ile	p.L1089I	ENST00000358026	NM_001128849.1	1089	Ctt/Att	24/36	1	2	FACETS	0.892	0.82	0.967	0.892	0.82	0.967	CLONAL	1	TRUE	1	0.36	2		527	1084	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302801	15302801	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756520455	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	39	262	0	ENST00000263388.2:c.649G>A	p.Asp217Asn	p.D217N	ENST00000263388	NM_000435.2	217	Gac/Aac	4/33	1	2	FACETS	0.476	0.395	0.567	0.476	0.395	0.567	SUBCLONAL	1	TRUE	1	0.36	2		262	455	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797910	42797910	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367735541	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	107	529	2	ENST00000575354.2:c.3962G>A	p.Arg1321His	p.R1321H	ENST00000575354	NM_015125.3	1321	cGc/cAc	16/20	1	2	FACETS	0.63	0.564	0.701	0.63	0.564	0.701	SUBCLONAL	1	TRUE	1	0.36	2		531	943	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281219	46281219	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1294	81	771	0	ENST00000371998.3:c.4016G>T	p.Arg1339Ile	p.R1339I	ENST00000371998		1339	aGa/aTa	21/23	1	2	FACETS	0.327	0.287	0.371	0.327	0.287	0.371	SUBCLONAL	1	TRUE	1	0.36	2		771	1375	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22123600	22123600	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	76	446	0	ENST00000215832.6:c.976G>A	p.Glu326Lys	p.E326K	ENST00000215832	NM_002745.4	326	Gaa/Aaa	8/9	1	2	FACETS	0.412	0.36	0.468	0.412	0.36	0.468	SUBCLONAL	1	TRUE	1	0.36	2		446	1026	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317499	1317499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764008924	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1250	105	779	0	ENST00000400841.2:c.566C>T	p.Ala189Val	p.A189V	ENST00000400841		189	gCt/gTt	5/6	1	2	FACETS	0.431	0.384	0.48	0.431	0.384	0.48	SUBCLONAL	1	TRUE	1	0.36	2		779	1355	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932948	39932948	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372463512	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	61	505	2	ENST00000378444.4:c.1651G>A	p.Asp551Asn	p.D551N	ENST00000378444	NM_001123385.1	551	Gat/Aat	4/15	1	2	FACETS	0.356	0.306	0.411	0.356	0.306	0.411	SUBCLONAL	1	TRUE	1	0.36	2		507	951	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411980	63411980	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1308	76	923	1	ENST00000330258.3:c.1187A>T	p.Glu396Val	p.E396V	ENST00000330258	NM_152424.3	396	gAg/gTg	2/2	1	2	FACETS	0.305	0.266	0.347	0.305	0.266	0.347	SUBCLONAL	1	TRUE	1	0.36	2		924	1384	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345910	70345910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	126	622	0	ENST00000374080.3:c.2447G>A	p.Arg816Gln	p.R816Q	ENST00000374080		816	cGa/cAa	18/45	1	2	FACETS	0.621	0.561	0.685	0.621	0.561	0.685	SUBCLONAL	1	TRUE	1	0.36	2		622	1127	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346191	70346191	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1309	108	779	1	ENST00000374080.3:c.2542G>A	p.Val848Ile	p.V848I	ENST00000374080		848	Gtc/Atc	19/45	1	2	FACETS	0.423	0.378	0.472	0.423	0.378	0.472	SUBCLONAL	1	TRUE	1	0.36	2		780	1417	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829806	76829806	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	66	572	1	ENST00000373344.5:c.6235C>T	p.Arg2079Ter	p.R2079*	ENST00000373344	NM_000489.3	2079	Cga/Tga	28/35	1	2	FACETS	0.33	0.285	0.379	0.33	0.285	0.379	SUBCLONAL	1	TRUE	1	0.36	2		573	1112	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918943	76918943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782726588	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1423	95	768	0	ENST00000373344.5:c.4048G>A	p.Gly1350Arg	p.G1350R	ENST00000373344	NM_000489.3	1350	Gga/Aga	12/35	1	2	FACETS	0.348	0.308	0.39	0.348	0.308	0.39	SUBCLONAL	1	TRUE	1	0.36	2		768	1518	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938065	76938065	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	166	503	1	ENST00000373344.5:c.2683G>A	p.Val895Ile	p.V895I	ENST00000373344	NM_000489.3	895	Gtt/Att	9/35	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.36	2		504	914	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617634	100617634	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1555978891	NA	P-0011570-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	186	602	1	ENST00000308731.7:c.435C>A	p.Cys145Ter	p.C145*	ENST00000308731	NM_000061.2	145	tgC/tgA	6/19	1	2	FACETS	0.975	0.9	1	0.975	0.9	1	CLONAL	1	TRUE	1	0.36	2		603	1060	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0011580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	214	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.648323273497794	2		464	501	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0011580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	120	631	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	1	2	FACETS	0.37	0.333	0.409	0.37	0.333	0.409	SUBCLONAL	1	TRUE	1	0.648323273497794	2		631	1001	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279531	1279531	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372140951	NA	P-0011580-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	171	437	1	ENST00000310581.5:c.2005C>T	p.Arg669Trp	p.R669W	ENST00000310581	NM_198253.2	669	Cgg/Tgg	5/16	1	2	FACETS	0.855	0.79	0.922	0.855	0.79	0.922	CLONAL	1	TRUE	1	0.648323273497794	2		438	617	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	29	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.923	0.748	1	0.923	0.748	1	CLONAL	1	TRUE	1	0.355093347902023	2		280	177	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273946	10273946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012060-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	94	469	1	ENST00000330684.3:c.323C>T	p.Ala108Val	p.A108V	ENST00000330684	NM_001134407.1	108	gCc/gTc	2/13	1	2	FACETS	0.905	0.807	1	0.905	0.807	1	CLONAL	1	TRUE	1	0.355093347902023	2		470	585	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	51	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.87	0.745	1	0.87	0.745	1	CLONAL	1	TRUE	1	0.424933543004589	2		280	276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579311	7579311	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1567555445	NA	P-0012077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	79	367	0	ENST00000269305.4:c.375+1G>A		p.X125_splice	ENST00000269305	NM_001126112.2	125			1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.424933543004589	2		367	306	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955547	48955549	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	novel	NA	P-0012077-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	102	421	0	ENST00000267163.4:c.1664_1666del	p.His555del	p.H555del	ENST00000267163	NM_000321.2	555	CAT/-	17/27	0.424933543004589	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.424933543004589	1		421	361	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	224	280	0				ENST00000310581	NM_198253.2	-/1132			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		280	618	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0012080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	587	524	0	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		524	926	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0012080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	541	511	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		511	1233	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528644	89528644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147992008	NA	P-0012080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	335	233	0	ENST00000336596.2:c.2944C>T	p.Pro982Ser	p.P982S	ENST00000336596	NM_005233.5	982	Ccc/Tcc	17/17	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		233	844	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949069	151949069	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776295921	NA	P-0012080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	229	333	0	ENST00000262189.6:c.1576C>T	p.Arg526Cys	p.R526C	ENST00000262189	NM_170606.2	526	Cgt/Tgt	11/59	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		333	1074	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434664	49434664	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748334191	NA	P-0012080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	200	389	1	ENST00000301067.7:c.6889C>T	p.Pro2297Ser	p.P2297S	ENST00000301067	NM_003482.3	2297	Cct/Tct	31/54	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		390	778	SUCCESS
BTK	695	MSKCC	GRCh37	X	100611144	100611144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	266	214	0	ENST00000308731.7:c.1462G>A	p.Glu488Lys	p.E488K	ENST00000308731	NM_000061.2	488	Gag/Aag	15/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		214	435	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56486824	56486824	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1023742896	NA	P-0012080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	630	498	0	ENST00000267101.3:c.1238C>T	p.Ser413Phe	p.S413F	ENST00000267101	NM_001982.3	413	tCc/tTc	11/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		498	1007	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474038	29474038	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	279	500	1	ENST00000389048.3:c.2137G>A	p.Glu713Lys	p.E713K	ENST00000389048	NM_004304.4	713	Gag/Aag	12/29	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		501	1161	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537974	212537974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777013174	NA	P-0012080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	336	297	0	ENST00000342788.4:c.1631G>A	p.Arg544Gln	p.R544Q	ENST00000342788	NM_005235.2	544	cGg/cAg	14/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		297	758	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212568872	212568872	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	210	357	0	ENST00000342788.4:c.1246G>T	p.Val416Phe	p.V416F	ENST00000342788	NM_005235.2	416	Gtt/Ttt	11/28	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		357	963	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455576	189455576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754361670	NA	P-0012080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	188	283	0	ENST00000264731.3:c.110G>A	p.Arg37Gln	p.R37Q	ENST00000264731	NM_003722.4	37	cGa/cAa	2/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		283	874	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163672	32163672	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	289	212	0	ENST00000375023.3:c.5554C>T	p.Pro1852Ser	p.P1852S	ENST00000375023	NM_004557.3	1852	Ccg/Tcg	30/30	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		212	418	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335602	81335602	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0012080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	349	291	0	ENST00000222390.5:c.1757+1G>A		p.X586_splice	ENST00000222390	NM_000601.4	586			NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		291	876	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38277071	38277071	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	186	315	0	ENST00000425967.3:c.1357C>T	p.Pro453Ser	p.P453S	ENST00000425967	NM_001174067.1	453	Cct/Tct	10/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		315	565	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370799	55370799	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	206	221	0	ENST00000297316.4:c.101A>G	p.Glu34Gly	p.E34G	ENST00000297316	NM_022454.3	34	gAg/gGg	1/2	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		221	384	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87366935	87366935	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1153	331	583	1	ENST00000277120.3:c.1331G>A	p.Gly444Glu	p.G444E	ENST00000277120		444	gGa/gAa	12/19	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		584	1484	SUCCESS
RET	5979	MSKCC	GRCh37	10	43612046	43612046	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1218	351	657	0	ENST00000355710.3:c.2151G>A	p.Trp717Ter	p.W717*	ENST00000355710	NM_020975.4	717	tgG/tgA	12/20	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		657	1569	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342715	118342715	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	405	307	0	ENST00000534358.1:c.841C>T	p.Leu281Phe	p.L281F	ENST00000534358	NM_005933.3	281	Ctc/Ttc	3/36	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		307	666	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466994	18466994	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773615749	NA	P-0012080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	351	276	2	ENST00000266497.5:c.1133G>A	p.Arg378Gln	p.R378Q	ENST00000266497		378	cGa/cAa	5/31	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		278	811	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622446	28622446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	377	303	0	ENST00000241453.7:c.1171C>T	p.Pro391Ser	p.P391S	ENST00000241453	NM_004119.2	391	Cct/Tct	9/24	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		303	893	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284946	15284946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	351	334	0	ENST00000263388.2:c.4669C>T	p.Pro1557Ser	p.P1557S	ENST00000263388	NM_000435.2	1557	Cct/Tct	25/33	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		334	721	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303192	11303193	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	403	350	0	ENST00000361445.4:c.1390_1391delinsTT	p.Pro464Phe	p.P464F	ENST00000361445	NM_004958.3	464	CCc/TTc	9/58	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		350	992	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40747932	40747933	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	247	391	0	ENST00000392038.2:c.485_486delinsTT	p.Thr162Ile	p.T162I	ENST00000392038	NM_001626.4	162	aCC/aTT	6/14	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		391	1106	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518724	176518725	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	323	290	1	ENST00000292408.4:c.642_643delinsAA	p.Val215Met	p.V215M	ENST00000292408	NM_213647.1	214	gtGGtg/gtAAtg	6/18	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		291	518	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845482	151845484	+	missense_variant	Missense_Mutation	TNP	TCC	TCC	CCT	novel	NA	P-0012080-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	177	375	1	ENST00000262189.6:c.13528_13530delinsAGG	p.Gly4510Arg	p.G4510R	ENST00000262189	NM_170606.2	4510	GGA/AGG	52/59	NA		FACETS		NA	NA				NA	NA	NA	NA	NA	NA		376	924	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378561	25378561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519725	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	104	365	0	ENST00000311936.3:c.437C>T	p.Ala146Val	p.A146V	ENST00000311936	NM_004985.3	146	gCa/gTa	4/5	0.78802667480544	3	FACETS	0.405	0.362	0.451	0.203	0.181	0.226	SUBCLONAL	1	TRUE	1	0.801808410997827	3		365	897	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579525	7579525	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	99	425	483	2	ENST00000269305.4:c.162del	p.Phe54LeufsTer69	p.F54Lfs*69	ENST00000269305	NM_001126112.2	54	ttC/tt	4/11	0.801808410997827	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.801808410997827	2		485	524	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027168	49027168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913305	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	165	326	492	3	ENST00000267163.4:c.1735C>T	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	579	Cga/Tga	18/27	0.782093730109424	1	FACETS	0.992	0.954	1	0.992	0.954	1	CLONAL	1	TRUE	0	0.801808410997827	1		495	491	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729610	162729610	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	313	329	0	ENST00000367921.3:c.696G>C	p.Leu232Phe	p.L232F	ENST00000367921	NM_006182.2	232	ttG/ttC	8/18	0.801808410997827	7	FACETS	0.956	0.901	1			1	CLONAL	2	TRUE	NA	0.801808410997827	7		329	1227	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220437275	220437275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370513243	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	687	755	0	ENST00000243786.2:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000243786	NM_002191.3	60	cGa/cAa	1/2	0.444852879761742	3	FACETS	1	0.997	1			1	INDETERMINATE	2	TRUE	NA	0.801808410997827	3		755	983	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9783346	9783346	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	250	473	2	ENST00000377346.4:c.2590C>A	p.Pro864Thr	p.P864T	ENST00000377346	NM_005026.3	864	Ccg/Acg	20/24	1	2	FACETS	0.99	0.932	1	0.99	0.932	1	CLONAL	1	TRUE	1	0.801808410997827	2		475	630	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464459	25464459	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	439	456	0	ENST00000264709.3:c.2054G>T	p.Gly685Val	p.G685V	ENST00000264709	NM_175629.2	685	gGg/gTg	17/23	0.78802667480544	3	FACETS	0.978	0.941	1	0.978	0.941	1	CLONAL	2	TRUE	1	0.801808410997827	3		456	784	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977915	134977915	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	300	578	0	ENST00000398015.3:c.2908C>A	p.His970Asn	p.H970N	ENST00000398015	NM_004441.4	970	Cat/Aat	16/16	0.789353442332283	3	FACETS	1	0.959	1	0.51	0.481	0.54	CLONAL	1	TRUE	1	0.801808410997827	3		578	1027	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197692	66197692	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	165	301	0	ENST00000273854.3:c.3007G>T	p.Glu1003Ter	p.E1003*	ENST00000273854	NM_004439.5	1003	Gag/Tag	17/18	1	2	FACETS	0.925	0.858	0.993	0.925	0.858	0.993	CLONAL	1	TRUE	1	0.801808410997827	2		301	445	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457755	149457755	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	154	401	0	ENST00000286301.3:c.649G>T	p.Gly217Trp	p.G217W	ENST00000286301	NM_005211.3	217	Ggg/Tgg	5/22	0.769666345837942	3	FACETS	0.892	0.82	0.967	0.446	0.41	0.484	CLONAL	1	TRUE	1	0.801808410997827	3		401	603	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729696	41729696	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	656	856	1	ENST00000242208.4:c.833G>T	p.Gly278Val	p.G278V	ENST00000242208	NM_002192.2	278	gGg/gTg	3/3	0.78802667480544	3	FACETS	0.999	0.969	1	0.999	0.969	1	CLONAL	2	TRUE	1	0.801808410997827	3		857	1147	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845547	128845547	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	251	472	0	ENST00000249373.3:c.844C>A	p.Leu282Met	p.L282M	ENST00000249373	NM_005631.4	282	Ctg/Atg	4/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.801808410997827	2		472	571	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851482	128851482	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	269	509	0	ENST00000249373.3:c.1807T>A	p.Leu603Met	p.L603M	ENST00000249373	NM_005631.4	603	Ttg/Atg	11/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.801808410997827	2		509	618	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389333	8389333	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	590	631	0	ENST00000356435.5:c.4285C>A	p.Gln1429Lys	p.Q1429K	ENST00000356435		1429	Cag/Aag	26/35	0.78802667480544	3	FACETS	0.99	0.958	1	0.99	0.958	1	CLONAL	2	TRUE	1	0.801808410997827	3		631	1041	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507336	8507336	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	312	565	0	ENST00000356435.5:c.1642G>A	p.Glu548Lys	p.E548K	ENST00000356435		548	Gaa/Aaa	11/35	0.78802667480544	3	FACETS	1	0.976	1	0.53	0.501	0.561	CLONAL	1	TRUE	1	0.801808410997827	3		565	1028	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528755	8528755	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	405	407	0	ENST00000356435.5:c.377C>A	p.Pro126His	p.P126H	ENST00000356435		126	cCt/cAt	4/35	0.78802667480544	3	FACETS	1	0.98	1	1	0.98	1	CLONAL	2	TRUE	1	0.801808410997827	3		407	687	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636758	8636758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	209	334	0	ENST00000356435.5:c.151C>T	p.Pro51Ser	p.P51S	ENST00000356435		51	Cca/Tca	2/35	0.78802667480544	3	FACETS	0.976	0.909	1	0.488	0.454	0.523	CLONAL	1	TRUE	1	0.801808410997827	3		334	748	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882067	36882067	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	229	522	0	ENST00000358127.4:c.946C>A	p.Pro316Thr	p.P316T	ENST00000358127	NM_001280556.1	316	Cct/Act	8/10	0.78802667480544	3	FACETS	0.972	0.908	1	0.486	0.454	0.519	CLONAL	1	TRUE	1	0.801808410997827	3		522	823	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332949	70332949	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	337	634	0	ENST00000373644.4:c.854C>G	p.Ser285Cys	p.S285C	ENST00000373644	NM_030625.2	285	tCt/tGt	2/12	0.801808410997827	2	FACETS	1	0.971	1	0.515	0.489	0.541	CLONAL	1	TRUE	0	0.801808410997827	2		634	816	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127755	64127755	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	133	267	0	ENST00000334205.4:c.248G>T	p.Arg83Leu	p.R83L	ENST00000334205	NM_003942.2	83	cGc/cTc	3/17	0.769666345837942	3	FACETS	1	0.945	1	0.521	0.477	0.567	CLONAL	1	TRUE	1	0.801808410997827	3		267	446	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861159	57861159	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	305	704	0	ENST00000228682.2:c.956A>G	p.Lys319Arg	p.K319R	ENST00000228682	NM_005269.2	319	aAg/aGg	9/12	0.251072734475124	3	FACETS	0.869	0.818	0.921			1	INDETERMINATE	1	TRUE	NA	0.801808410997827	3		704	1227	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436473	110436473	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	233	497	0	ENST00000375856.3:c.1928C>G	p.Ser643Cys	p.S643C	ENST00000375856	NM_003749.2	643	tCc/tGc	1/2	0.801808410997827	4	FACETS	1	0.963	1	0.349	0.326	0.374	CLONAL	1	TRUE	1	0.801808410997827	4		497	999	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678622	88678622	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	170	174	0	ENST00000360948.2:c.914C>A	p.Pro305Gln	p.P305Q	ENST00000360948	NM_001012338.2	305	cCa/cAa	9/19	0.801808410997827	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.801808410997827	2		174	198	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992463	72992463	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	331	852	2	ENST00000268489.5:c.1582C>T	p.Gln528Ter	p.Q528*	ENST00000268489	NM_006885.3	528	Caa/Taa	2/10	0.334106641137003	1	FACETS	0.534	0.506	0.563	0.534	0.506	0.563	INDETERMINATE	1	TRUE	0	0.801808410997827	1		854	926	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857888	89857888	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1026686587	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	167	380	1	ENST00000389301.3:c.1282G>T	p.Val428Phe	p.V428F	ENST00000389301	NM_000135.2	428	Gtc/Ttc	14/43	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.801808410997827	NA		381	508	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47679227	47679227	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	818	358	0	ENST00000347630.2:c.980A>T	p.Tyr327Phe	p.Y327F	ENST00000347630	NM_001007230.1	327	tAt/tTt	10/11	0.801808410997827	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	4	TRUE	0	0.801808410997827	4		358	908	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602520	10602520	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	97	328	345	0	ENST00000171111.5:c.1058T>C	p.Leu353Pro	p.L353P	ENST00000171111	NM_203500.1	353	cTc/cCc	3/6	0.801808410997827	2	FACETS	0.963	0.931	0.992	0.963	0.931	0.992	CLONAL	2	TRUE	0	0.801808410997827	2		345	425	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11105646	11105646	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	436	340	0	ENST00000358026.2:c.1562G>T	p.Arg521Leu	p.R521L	ENST00000358026	NM_001128849.1	521	cGg/cTg	9/36	0.801808410997827	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.801808410997827	2		340	510	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152033	11152033	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1384070535	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	354	269	1	ENST00000358026.2:c.4317G>T	p.Lys1439Asn	p.K1439N	ENST00000358026	NM_001128849.1	1439	aaG/aaT	31/36	0.801808410997827	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	0	0.801808410997827	2		270	438	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546751	9546751	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	285	285	0	ENST00000353224.5:c.1271C>A	p.Pro424His	p.P424H	ENST00000353224	NM_177990.2	424	cCc/cAc	5/10	0.789353442332283	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.801808410997827	3		285	468	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076889	41076889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	259	535	1	ENST00000373198.4:c.1531G>A	p.Glu511Lys	p.E511K	ENST00000373198	NM_133170.3	511	Gag/Aag	9/32	0.544085985350548	3	FACETS	1	0.951	1	0.507	0.476	0.539	CLONAL	1	TRUE	1	0.801808410997827	3		536	892	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30000025	30000025	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	215	504	0	ENST00000338641.4:c.38C>A	p.Ser13Tyr	p.S13Y	ENST00000338641	NM_000268.3	13	tCt/tAt	1/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.801808410997827	2		504	506	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41537133	41537133	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	240	423	0	ENST00000263253.7:c.1960A>T	p.Lys654Ter	p.K654*	ENST00000263253	NM_001429.3	654	Aag/Tag	10/31	1	2	FACETS	0.985	0.926	1	0.985	0.926	1	CLONAL	1	TRUE	1	0.801808410997827	2		423	608	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918349	44918349	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	242	424	0	ENST00000377967.4:c.974G>T	p.Gly325Val	p.G325V	ENST00000377967	NM_021140.2	325	gGt/gTt	11/29	0.554913088061615	6	FACETS	1	0.989	1			1	CLONAL	1	TRUE	NA	0.801808410997827	6		424	1208	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006764	47006764	+	5_prime_UTR_variant	5'UTR	SNP	C	C	A	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	816	545	1	ENST00000377604.3:c.-117C>A		p.*39*	ENST00000377604	NM_001204468.1	-/852		2/24	0.554913088061615	6	FACETS	1	0.996	1			1	CLONAL	4	TRUE	NA	0.801808410997827	6		546	1187	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035965	47035965	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1358	300	648	0	ENST00000377604.3:c.643G>A	p.Glu215Lys	p.E215K	ENST00000377604	NM_001204468.1	215	Gag/Aag	7/24	0.582441947388053	5	FACETS	0.994	0.933	1			1	CLONAL	1	TRUE	NA	0.801808410997827	5		648	1658	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76875944	76875944	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	397	628	0	ENST00000373344.5:c.5191G>T	p.Val1731Phe	p.V1731F	ENST00000373344	NM_000489.3	1731	Gtt/Ttt	20/35	0.801808410997827	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.801808410997827	1		628	535	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937284	76937284	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	292	474	0	ENST00000373344.5:c.3464C>T	p.Ser1155Leu	p.S1155L	ENST00000373344	NM_000489.3	1155	tCa/tTa	9/35	0.801808410997827	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.801808410997827	1		474	383	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535432	66535432	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	92	219	0	ENST00000273854.3:c.29del	p.Gly10AspfsTer52	p.G10Dfs*52	ENST00000273854	NM_004439.5	10	gGa/ga	1/18	1	2	FACETS	0.859	0.775	0.947	0.859	0.775	0.947	CLONAL	1	TRUE	1	0.801808410997827	2		219	267	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280094	66280095	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0012082-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	232	406	0	ENST00000273854.3:c.1594_1595delinsAA	p.Pro532Lys	p.P532K	ENST00000273854	NM_004439.5	532	CCa/AAa	7/18	1	2	FACETS	0.989	0.93	1	0.989	0.93	1	CLONAL	1	TRUE	1	0.801808410997827	2		406	585	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478854	56478854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519893	NA	P-0012140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	26	960	0	ENST00000267101.3:c.310G>A	p.Val104Met	p.V104M	ENST00000267101	NM_001982.3	104	Gtg/Atg	3/28	1	2	FACETS	0.412	0.325	0.514	0.412	0.325	0.514	SUBCLONAL	1	TRUE	1	0.14	2		960	901	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0012140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	20	463	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.702	0.536	0.897	0.702	0.536	0.897	SUBCLONAL	1	TRUE	1	0.14	2		463	407	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717770	89717770	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913289	NA	P-0012140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	12	274	1	ENST00000371953.3:c.800del	p.Lys267ArgfsTer9	p.K267Rfs*9	ENST00000371953	NM_000314.4	265	ctA/ct	7/9	1	2	FACETS	1	0.813	1	1	0.813	1	CLONAL	1	TRUE	1	0.14	2		275	140	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249384	153249384	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519895	NA	P-0012140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	15	563	0	ENST00000281708.4:c.1394G>A	p.Arg465His	p.R465H	ENST00000281708	NM_033632.3	465	cGt/cAt	9/12	0.110195699650176	3	FACETS	0.503	0.366	0.668	0.251	0.183	0.334	SUBCLONAL	1	TRUE	1	0.14	3		563	456	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106917	27106917	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	29	583	0	ENST00000324856.7:c.6532del	p.Asp2178ThrfsTer22	p.D2178Tfs*22	ENST00000324856	NM_006015.4	2176	caG/ca	20/20	1	2	FACETS	0.819	0.656	1	0.819	0.656	1	CLONAL	1	TRUE	1	0.14	2		583	506	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171593	36171596	+	splice_donor_variant,intron_variant	Splice_Site	DEL	CTTA	CTTA	-	novel	NA	P-0012140-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	14	269	0	ENST00000300305.3:c.967+2_967+5del		p.X323_splice	ENST00000300305		323			1	2	FACETS	0.87	0.629	1	0.87	0.629	1	CLONAL	1	TRUE	1	0.14	2		269	230	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	179	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.862651494460869	2		280	397	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0012183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	105	263	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.915	0.834	0.998	0.915	0.834	0.998	CLONAL	1	TRUE	1	0.862651494460869	2		263	266	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1803568	1803568	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913483	NA	P-0012183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	224	595	0	ENST00000260795.2:c.746C>G	p.Ser249Cys	p.S249C	ENST00000260795		249	tCc/tGc	6/17	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.862651494460869	2		595	515	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480320	56480320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	293	656	0	ENST00000267101.3:c.427C>A	p.Leu143Met	p.L143M	ENST00000267101	NM_001982.3	143	Ctg/Atg	4/28	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.862651494460869	2		656	621	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100093	27100093	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	364	971	0	ENST00000324856.7:c.3889G>C	p.Glu1297Gln	p.E1297Q	ENST00000324856	NM_006015.4	1297	Gag/Cag	16/20	1	2	FACETS	0.981	0.935	1	0.981	0.935	1	CLONAL	1	TRUE	1	0.862651494460869	2		971	860	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287404	33287404	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	324	716	0	ENST00000374542.5:c.1693C>T	p.Gln565Ter	p.Q565*	ENST00000374542	NM_001141970.1	565	Cag/Tag	6/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.862651494460869	2		716	728	SUCCESS
ATM	472	MSKCC	GRCh37	11	108106537	108106537	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	187	447	0	ENST00000278616.4:c.472G>A	p.Glu158Lys	p.E158K	ENST00000278616	NM_000051.3	158	Gaa/Aaa	5/63	1	2	FACETS	0.983	0.919	1	0.983	0.919	1	CLONAL	1	TRUE	1	0.862651494460869	2		447	441	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44969496	44969496	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0012183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	21	298	475	0	ENST00000377967.4:c.4176+2T>G		p.X1392_splice	ENST00000377967	NM_021140.2	1392			1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.862651494460869	1		475	319	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123195076	123195076	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012183-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	263	274	0	ENST00000218089.9:c.1419del	p.Leu473PhefsTer20	p.L473Ffs*20	ENST00000218089	NM_001042749.1	473	ttA/tt	16/35	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.862651494460869	1		274	308	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	27	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.805	1	1	0.805	1	CLONAL	1	TRUE	1	0.21	2		280	255	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0012191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	14	467	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.368	0.265	0.494	0.368	0.265	0.494	SUBCLONAL	1	TRUE	1	0.21	2		467	362	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577095	7577095	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519984	NA	P-0012191-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	11	682	0	ENST00000269305.4:c.843C>A	p.Asp281Glu	p.D281E	ENST00000269305	NM_001126112.2	281	gaC/gaA	8/11	1	2	FACETS	0.212	0.145	0.296	0.212	0.145	0.296	SUBCLONAL	1	TRUE	1	0.21	2		682	494	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	76	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.954	0.843	1	0.954	0.843	1	CLONAL	1	TRUE	1	0.462054005651116	2		280	345	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0012202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	148	383	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.462054005651116	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.462054005651116	1		383	416	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578532	7578532	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	290	575	0	ENST00000269305.4:c.398T>G	p.Met133Arg	p.M133R	ENST00000269305	NM_001126112.2	133	aTg/aGg	5/11	NA	2	FACETS	0.958	0.908	1			1	INDETERMINATE	2	TRUE	NA	0.462054005651116	2		575	655	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060574	38060574	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	294	1007	2	ENST00000250448.2:c.1415C>T	p.Ser472Phe	p.S472F	ENST00000250448	NM_004496.3	472	tCc/tTc	2/2	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.462054005651116	2		1009	1168	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78426086	78426086	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	180	669	0	ENST00000370768.2:c.1439C>T	p.Pro480Leu	p.P480L	ENST00000370768	NM_003902.3	480	cCa/cTa	15/20	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.462054005651116	2		669	748	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658359	206658359	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	104	393	0	ENST00000367120.3:c.1453G>T	p.Glu485Ter	p.E485*	ENST00000367120	NM_014002.3	485	Gag/Tag	14/22	1	2	FACETS	0.897	0.806	0.992	0.897	0.806	0.992	CLONAL	1	TRUE	1	0.462054005651116	2		393	502	SUCCESS
ATR	545	MSKCC	GRCh37	3	142212108	142212108	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	297	558	0	ENST00000350721.4:c.5944T>A	p.Leu1982Ile	p.L1982I	ENST00000350721	NM_001184.3	1982	Tta/Ata	35/47	0.425490906083705	3	FACETS	0.977	0.924	1	0.977	0.924	1	CLONAL	2	TRUE	1	0.462054005651116	3		558	810	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964399	93964399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs568334270	NA	P-0012202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	210	917	0	ENST00000369303.4:c.2498G>A	p.Gly833Glu	p.G833E	ENST00000369303	NM_004440.3	833	gGa/gAa	14/17	0.409313758225295	1	FACETS	0.71	0.659	0.762	0.71	0.659	0.762	SUBCLONAL	1	TRUE	0	0.462054005651116	1		917	985	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686799	117686799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs917101052	NA	P-0012202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	157	593	1	ENST00000368508.3:c.2918C>T	p.Pro973Leu	p.P973L	ENST00000368508	NM_002944.2	973	cCt/cTt	19/43	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.462054005651116	2		594	667	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335657	81335657	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	310	609	1	ENST00000222390.5:c.1703C>T	p.Ser568Phe	p.S568F	ENST00000222390	NM_000601.4	568	tCc/tTc	15/18	0.462054005651116	3	FACETS	0.994	0.941	1	0.994	0.941	1	CLONAL	2	TRUE	1	0.462054005651116	3		610	831	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139408960	139408960	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0012202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	258	368	1	ENST00000277541.6:c.2207+2T>A		p.X736_splice	ENST00000277541	NM_017617.3	736			0.455155870838353	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	0	0.462054005651116	3		369	442	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596088	43596088	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	153	588	0	ENST00000355710.3:c.255G>A	p.Trp85Ter	p.W85*	ENST00000355710	NM_020975.4	85	tgG/tgA	2/20	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.462054005651116	2		588	657	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619187	43619187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1259087541	NA	P-0012202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	143	753	1	ENST00000355710.3:c.2870C>T	p.Pro957Leu	p.P957L	ENST00000355710	NM_020975.4	957	cCt/cTt	17/20	1	2	FACETS	0.86	0.785	0.938	0.86	0.785	0.938	CLONAL	1	TRUE	1	0.462054005651116	2		754	720	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852673	63852673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	160	528	0	ENST00000279873.7:c.3451G>A	p.Gly1151Arg	p.G1151R	ENST00000279873	NM_032199.2	1151	Gga/Aga	10/10	1	2	FACETS	0.954	0.877	1	0.954	0.877	1	CLONAL	1	TRUE	1	0.462054005651116	2		528	726	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432086	121432086	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760640415	NA	P-0012202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	196	737	0	ENST00000257555.6:c.833G>A	p.Arg278Gln	p.R278Q	ENST00000257555		278	cGg/cAg	4/10	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.462054005651116	2		737	753	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89352046	89352046	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	255	1047	0	ENST00000301030.4:c.904G>A	p.Glu302Lys	p.E302K	ENST00000301030	NM_001256183.1	302	Gag/Aag	9/13	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.462054005651116	2		1047	1058	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40491346	40491346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs869312890	NA	P-0012202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	196	707	0	ENST00000264657.5:c.454C>T	p.Arg152Trp	p.R152W	ENST00000264657	NM_139276.2	152	Cgg/Tgg	5/24	1	2	FACETS	0.917	0.849	0.987	0.917	0.849	0.987	CLONAL	1	TRUE	1	0.462054005651116	2		707	925	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78599536	78599536	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	97	672	0	ENST00000306801.3:c.208G>C	p.Val70Leu	p.V70L	ENST00000306801	NM_020761.2	70	Gtg/Ctg	2/34	1	2	FACETS	0.552	0.492	0.617	0.552	0.492	0.617	SUBCLONAL	1	TRUE	1	0.462054005651116	2		672	760	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400191	41400191	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0012202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	106	398	0	ENST00000373198.4:c.569-1G>A		p.X190_splice	ENST00000373198	NM_133170.3	190			1	2	FACETS	0.972	0.876	1	0.972	0.876	1	CLONAL	1	TRUE	1	0.462054005651116	2		398	472	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30054212	30054212	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	366	716	1	ENST00000338641.4:c.634C>T	p.Gln212Ter	p.Q212*	ENST00000338641	NM_000268.3	212	Cag/Tag	7/16	0.461863726020395	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	0	0.462054005651116	2		717	774	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021671	31021671	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	75	312	0	ENST00000375687.4:c.1671del	p.Glu558LysfsTer145	p.E558Kfs*145	ENST00000375687	NM_015338.5	557	aCc/ac	12/13	1	2	FACETS	0.782	0.689	0.882	0.782	0.689	0.882	SUBCLONAL	1	TRUE	1	0.462054005651116	2		312	415	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510150	149510150	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	175	652	0	ENST00000261799.4:c.1319del	p.Gly440AlafsTer41	p.G440Afs*41	ENST00000261799	NM_002609.3	440	gGc/gc	9/23	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.462054005651116	2		652	735	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468033	120468033	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	163	796	0	ENST00000256646.2:c.4406del	p.Pro1469HisfsTer84	p.P1469Hfs*84	ENST00000256646	NM_024408.3	1469	cCa/ca	25/34	1	2	FACETS	0.855	0.786	0.928	0.855	0.786	0.928	CLONAL	1	TRUE	1	0.462054005651116	2		796	825	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157521998	157521999	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0012202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	125	610	0	ENST00000346085.5:c.4270_4271delinsTT	p.Pro1424Leu	p.P1424L	ENST00000346085	NM_020732.3	1424	CCg/TTg	18/20	1	2	FACETS	0.917	0.833	1	0.917	0.833	1	CLONAL	1	TRUE	1	0.462054005651116	2		610	590	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553707	106553708	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	121	438	0	ENST00000369096.4:c.1672_1673delinsAA	p.Gly558Asn	p.G558N	ENST00000369096	NM_001198.3	558	GGc/AAc	5/7	1	2	FACETS	0.838	0.759	0.921	0.838	0.759	0.921	CLONAL	1	TRUE	1	0.462054005651116	2		438	625	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948767	55948768	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012202-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	111	472	0	ENST00000263923.4:c.3697_3698delinsTT	p.Pro1233Phe	p.P1233F	ENST00000263923	NM_002253.2	1233	CCt/TTt	28/30	1	2	FACETS	0.809	0.729	0.893	0.809	0.729	0.893	CLONAL	1	TRUE	1	0.462054005651116	2		472	594	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	141	280	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.928	0.857	1			1	INDETERMINATE	1	FALSE	NA	0.878118230855605	2		280	346	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0012225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	410	463	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.878118230855605	2		463	846	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579358	7579358	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs11540654	NA	P-0012225-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	438	566	0	ENST00000269305.4:c.329G>C	p.Arg110Pro	p.R110P	ENST00000269305	NM_001126112.2	110	cGt/cCt	4/11	0.855260159420603	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	0	0.878118230855605	1		566	536	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137785	64137785	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779751342	NA	P-0012241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	160	774	2	ENST00000334205.4:c.1886G>A	p.Arg629His	p.R629H	ENST00000334205	NM_003942.2	629	cGc/cAc	15/17	0.155328781421295	5	FACETS	1	0.969	1	0.28	0.256	0.306	INDETERMINATE	1	FALSE	1	0.453432071043951	5		776	1057	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574021	7574021	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	378	711	0	ENST00000269305.4:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000269305	NM_001126112.2	336	Gag/Tag	10/11	0.355276796067577	2	FACETS	0.815	0.775	0.855	0.815	0.775	0.855	CLONAL	2	FALSE	0	0.453432071043951	2		711	1023	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735579	204735579	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	91	379	0	ENST00000302823.3:c.380A>G	p.Tyr127Cys	p.Y127C	ENST00000302823	NM_005214.4	127	tAc/tGc	2/4	1	2	FACETS	0.703	0.625	0.785	0.703	0.625	0.785	SUBCLONAL	1	FALSE	1	0.453432071043951	2		379	571	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012207	16012207	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	62	418	0	ENST00000268712.3:c.2075A>T	p.Glu692Val	p.E692V	ENST00000268712	NM_006311.3	692	gAa/gTa	19/46	0.355276796067577	2	FACETS	0.415	0.358	0.477	0.207	0.179	0.239	SUBCLONAL	1	FALSE	0	0.453432071043951	2		418	659	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66525112	66525112	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	127	287	0	ENST00000358598.2:c.871G>T	p.Glu291Ter	p.E291*	ENST00000358598	NM_212471.2	291	Gag/Tag	9/11	0.453432071043951	3	FACETS	1	0.971	1	0.582	0.529	0.638	CLONAL	1	FALSE	1	0.453432071043951	3		287	590	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42843850	42843850	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	114	607	0	ENST00000398585.3:c.1069A>C	p.Met357Leu	p.M357L	ENST00000398585	NM_001135099.1	357	Atg/Ctg	10/14	0.155328781421295	5	FACETS	0.801	0.719	0.887	0.2	0.179	0.222	INDETERMINATE	1	FALSE	1	0.453432071043951	5		607	1055	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971067	21971074	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCACCA	CAGCACCA	-	novel	NA	P-0012241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	145	362	0	ENST00000304494.5:c.284_291del	p.Val95AlafsTer22	p.V95Afs*22	ENST00000304494	NM_000077.4	95	gTGGTGCTG/g	2/3	0.362480385571981	2	FACETS	0.786	0.724	0.849	0.786	0.724	0.849	SUBCLONAL	2	FALSE	0	0.453432071043951	2		362	407	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098943	178098948	+	inframe_deletion	In_Frame_Del	DEL	TCGACT	TCGACT	-	novel	NA	P-0012241-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	42	489	0	ENST00000397062.3:c.97_102del	p.Ser33_Arg34del	p.S33_R34del	ENST00000397062	NM_006164.4	33	AGTCGA/-	2/5	1	2	FACETS	0.238	0.198	0.283	0.238	0.198	0.283	SUBCLONAL	1	FALSE	1	0.453432071043951	2		489	779	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	29	280	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.873	1			1	INDETERMINATE	1	TRUE	NA	0.255311207464196	2		280	205	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	58	383	0	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.255311207464196	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.255311207464196	1		383	321	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827964	72827964	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768307205	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	102	998	1	ENST00000268489.5:c.8617G>A	p.Glu2873Lys	p.E2873K	ENST00000268489	NM_006885.3	2873	Gaa/Aaa	9/10	1	2	FACETS	0.716	0.639	0.799	0.716	0.639	0.799	SUBCLONAL	1	TRUE	1	0.255311207464196	2		999	1116	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076812	72076812	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	79	462	0	ENST00000357731.5:c.685G>A	p.Glu229Lys	p.E229K	ENST00000357731	NM_173808.2	229	Gaa/Aaa	5/7	1	2	FACETS	0.887	0.78	1	0.887	0.78	1	CLONAL	1	TRUE	1	0.255311207464196	2		462	698	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55946137	55946137	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	79	538	0	ENST00000263923.4:c.4042G>A	p.Gly1348Arg	p.G1348R	ENST00000263923	NM_002253.2	1348	Ggg/Agg	30/30	0.189939022258035	1	FACETS	0.746	0.655	0.843	0.746	0.655	0.843	SUBCLONAL	1	TRUE	0	0.255311207464196	1		538	724	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	46	408	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	1	2	FACETS	0.705	0.594	0.828	0.705	0.594	0.828	SUBCLONAL	1	TRUE	1	0.255311207464196	2		408	511	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426738	212426738	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	40	487	0	ENST00000342788.4:c.2377C>T	p.Gln793Ter	p.Q793*	ENST00000342788	NM_005235.2	793	Cag/Tag	20/28	0.189939022258035	1	FACETS	0.475	0.394	0.566	0.475	0.394	0.566	SUBCLONAL	1	TRUE	0	0.255311207464196	1		487	575	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15302860	15302860	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	47	371	0	ENST00000263388.2:c.590C>T	p.Pro197Leu	p.P197L	ENST00000263388	NM_000435.2	197	cCc/cTc	4/33	0.189939022258035	1	FACETS	0.799	0.676	0.934	0.799	0.676	0.934	CLONAL	1	TRUE	0	0.255311207464196	1		371	402	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446273	187446273	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1466913399	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	99	396	0	ENST00000232014.4:c.1415C>T	p.Pro472Leu	p.P472L	ENST00000232014	NM_001130845.1	472	cCc/cTc	6/10	0.187328861992361	3	FACETS	0.805	0.721	0.894	0.805	0.721	0.894	CLONAL	2	TRUE	1	0.255311207464196	3		396	543	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508631	106508631	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	41	377	0	ENST00000359195.3:c.625G>A	p.Glu209Lys	p.E209K	ENST00000359195	NM_002649.2	209	Gag/Aag	2/11	1	2	FACETS	0.759	0.633	0.899	0.759	0.633	0.899	SUBCLONAL	1	TRUE	1	0.255311207464196	2		377	423	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11168271	11168271	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	81	564	0	ENST00000361445.4:c.7601C>T	p.Ser2534Phe	p.S2534F	ENST00000361445	NM_004958.3	2534	tCc/tTc	57/58	0.189939022258035	1	FACETS	0.896	0.79	1	0.896	0.79	1	CLONAL	1	TRUE	0	0.255311207464196	1		564	618	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190649	11190649	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	89	604	1	ENST00000361445.4:c.5550G>T	p.Glu1850Asp	p.E1850D	ENST00000361445	NM_004958.3	1850	gaG/gaT	39/58	0.189939022258035	1	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	0	0.255311207464196	1		605	603	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733342	85733342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	180	905	0	ENST00000370580.1:c.670C>T	p.Pro224Ser	p.P224S	ENST00000370580	NM_003921.4	224	Ccc/Tcc	3/3	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.255311207464196	2		905	1295	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510712	120510712	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	78	538	0	ENST00000256646.2:c.1252G>A	p.Glu418Lys	p.E418K	ENST00000256646	NM_024408.3	418	Gaa/Aaa	7/34	1	2	FACETS	0.674	0.591	0.763	0.674	0.591	0.763	SUBCLONAL	1	TRUE	1	0.255311207464196	2		538	907	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731104	162731104	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	109	781	0	ENST00000367921.3:c.959T>C	p.Phe320Ser	p.F320S	ENST00000367921	NM_006182.2	320	tTc/tCc	9/18	1	2	FACETS	0.988	0.887	1	0.988	0.887	1	CLONAL	1	TRUE	1	0.255311207464196	2		781	864	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206944290	206944290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	82	544	0	ENST00000423557.1:c.340G>A	p.Glu114Lys	p.E114K	ENST00000423557	NM_000572.2	114	Gag/Aag	3/5	1	2	FACETS	0.854	0.753	0.963	0.854	0.753	0.963	CLONAL	1	TRUE	1	0.255311207464196	2		544	752	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243800946	243800946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	78	537	0	ENST00000263826.5:c.528G>A	p.Met176Ile	p.M176I	ENST00000263826	NM_005465.4	176	atG/atA	5/13	1	2	FACETS	0.909	0.799	1	0.909	0.799	1	CLONAL	1	TRUE	1	0.255311207464196	2		537	672	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25978936	25978936	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	66	447	0	ENST00000435504.4:c.987T>A	p.Asn329Lys	p.N329K	ENST00000435504		329	aaT/aaA	10/13	0.189939022258035	1	FACETS	0.733	0.636	0.838	0.733	0.636	0.838	SUBCLONAL	1	TRUE	0	0.255311207464196	1		447	615	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158634710	158634710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1063	67	830	1	ENST00000263640.3:c.476C>T	p.Pro159Leu	p.P159L	ENST00000263640	NM_001105.4	159	cCc/cTc	5/11	0.189939022258035	1	FACETS	0.405	0.351	0.465	0.405	0.351	0.465	SUBCLONAL	1	TRUE	0	0.255311207464196	1		831	1130	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137456	202137456	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	32	451	0	ENST00000358485.4:c.684G>C	p.Lys228Asn	p.K228N	ENST00000358485	NM_001080125.1	228	aaG/aaC	4/9	0.189939022258035	1	FACETS	0.398	0.322	0.483	0.398	0.322	0.483	SUBCLONAL	1	TRUE	0	0.255311207464196	1		451	550	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227663031	227663031	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	32	439	0	ENST00000305123.5:c.424C>T	p.Leu142Phe	p.L142F	ENST00000305123	NM_005544.2	142	Ctt/Ttt	1/2	0.189939022258035	1	FACETS	0.555	0.45	0.673	0.555	0.45	0.673	SUBCLONAL	1	TRUE	0	0.255311207464196	1		439	394	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468516	89468516	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1453560937	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	78	356	0	ENST00000336596.2:c.2050C>T	p.Arg684Ter	p.R684*	ENST00000336596	NM_005233.5	684	Cga/Tga	11/17	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.255311207464196	2		356	444	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528591	89528591	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	70	422	0	ENST00000336596.2:c.2891A>T	p.Lys964Met	p.K964M	ENST00000336596	NM_005233.5	964	aAg/aTg	17/17	1	2	FACETS	0.902	0.787	1	0.902	0.787	1	CLONAL	1	TRUE	1	0.255311207464196	2		422	608	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968180	134968180	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	117	580	0	ENST00000398015.3:c.2693C>A	p.Pro898His	p.P898H	ENST00000398015	NM_004441.4	898	cCt/cAt	15/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.255311207464196	2		580	617	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182665083	182665083	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	56	600	0	ENST00000292782.4:c.643C>T	p.Leu215Phe	p.L215F	ENST00000292782	NM_020640.2	215	Ctt/Ttt	6/7	0.187328861992361	3	FACETS	0.605	0.517	0.702	0.303	0.258	0.351	SUBCLONAL	1	TRUE	1	0.255311207464196	3		600	817	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981166	55981166	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	58	580	0	ENST00000263923.4:c.533C>T	p.Ser178Phe	p.S178F	ENST00000263923	NM_002253.2	178	tCc/tTc	5/30	0.189939022258035	1	FACETS	0.686	0.589	0.791	0.686	0.589	0.791	SUBCLONAL	1	TRUE	0	0.255311207464196	1		580	578	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286179	66286179	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	87	544	0	ENST00000273854.3:c.1507G>A	p.Glu503Lys	p.E503K	ENST00000273854	NM_004439.5	503	Gaa/Aaa	6/18	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.255311207464196	2		544	660	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007331	143007331	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	38	350	0	ENST00000262992.4:c.2453G>A	p.Arg818Lys	p.R818K	ENST00000262992	NM_001101669.1	818	aGa/aAa	22/24	1	2	FACETS	0.597	0.493	0.713	0.597	0.493	0.713	SUBCLONAL	1	TRUE	1	0.255311207464196	2		350	499	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114250	143114250	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	50	537	1	ENST00000262992.4:c.1171G>A	p.Glu391Lys	p.E391K	ENST00000262992	NM_001101669.1	391	Gaa/Aaa	13/24	1	2	FACETS	0.574	0.486	0.671	0.574	0.486	0.671	SUBCLONAL	1	TRUE	1	0.255311207464196	2		538	682	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540784	187540784	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867550264	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	62	446	0	ENST00000441802.2:c.6956C>T	p.Ser2319Leu	p.S2319L	ENST00000441802	NM_005245.3	2319	tCa/tTa	10/27	1	2	FACETS	0.934	0.808	1	0.934	0.808	1	CLONAL	1	TRUE	1	0.255311207464196	2		446	520	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38982010	38982010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	57	399	0	ENST00000357387.3:c.712C>T	p.Pro238Ser	p.P238S	ENST00000357387	NM_152756.3	238	Cca/Tca	8/38	0.187328861992361	3	FACETS	0.883	0.758	1	0.442	0.379	0.51	CLONAL	1	TRUE	1	0.255311207464196	3		399	570	SUCCESS
APC	324	MSKCC	GRCh37	5	112175925	112175925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	42	275	0	ENST00000257430.4:c.4634C>T	p.Ser1545Leu	p.S1545L	ENST00000257430	NM_000038.5	1545	tCa/tTa	16/16	1	2	FACETS	0.762	0.636	0.9	0.762	0.636	0.9	SUBCLONAL	1	TRUE	1	0.255311207464196	2		275	432	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180058731	180058731	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	45	500	1	ENST00000261937.6:c.106G>A	p.Glu36Lys	p.E36K	ENST00000261937	NM_182925.4	36	Gag/Aag	2/30	0.232255783452594	0	FACETS	0.634	0.534	0.745			1	SUBCLONAL	1	TRUE	0	0.255311207464196	0		501	414	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288203	33288203	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	79	438	0	ENST00000374542.5:c.1205C>T	p.Ser402Phe	p.S402F	ENST00000374542	NM_001141970.1	402	tCt/tTt	4/8	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.255311207464196	2		438	556	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120701	94120701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	168	923	1	ENST00000369303.4:c.350G>A	p.Gly117Glu	p.G117E	ENST00000369303	NM_004440.3	117	gGa/gAa	3/17	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.255311207464196	2		924	1101	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117658372	117658372	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	144	794	1	ENST00000368508.3:c.5211A>T	p.Glu1737Asp	p.E1737D	ENST00000368508	NM_002944.2	1737	gaA/gaT	31/43	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.255311207464196	2		795	863	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686839	117686839	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866331955	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	33	494	0	ENST00000368508.3:c.2878G>A	p.Gly960Arg	p.G960R	ENST00000368508	NM_002944.2	960	Gga/Aga	19/43	1	2	FACETS	0.42	0.341	0.51	0.42	0.341	0.51	SUBCLONAL	1	TRUE	1	0.255311207464196	2		494	615	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710834	117710834	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	126	608	0	ENST00000368508.3:c.1438A>G	p.Thr480Ala	p.T480A	ENST00000368508	NM_002944.2	480	Aca/Gca	12/43	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.255311207464196	2		608	850	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959220	2959220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	103	563	0	ENST00000396946.4:c.2296G>A	p.Glu766Lys	p.E766K	ENST00000396946	NM_032415.4	766	Gag/Aag	18/25	0.207009377246683	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.255311207464196	1		563	604	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6031637	6031637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1248142939	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	52	345	0	ENST00000265849.7:c.955C>T	p.Pro319Ser	p.P319S	ENST00000265849	NM_000535.5	319	Cca/Tca	9/15	0.187328861992361	3	FACETS	0.947	0.807	1	0.474	0.403	0.55	CLONAL	1	TRUE	1	0.255311207464196	3		345	485	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55272964	55272964	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	49	434	0	ENST00000275493.2:c.3287C>T	p.Ser1096Phe	p.S1096F	ENST00000275493	NM_005228.3	1096	tCc/tTc	28/28	1	2	FACETS	0.71	0.601	0.829	0.71	0.601	0.829	SUBCLONAL	1	TRUE	1	0.255311207464196	2		434	541	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81388011	81388011	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	70	572	0	ENST00000222390.5:c.364A>G	p.Lys122Glu	p.K122E	ENST00000222390	NM_000601.4	122	Aaa/Gaa	3/18	1	2	FACETS	0.893	0.779	1	0.893	0.779	1	CLONAL	1	TRUE	1	0.255311207464196	2		572	614	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403149	116403150	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	40	348	1	ENST00000397752.3:c.2410_2411delinsTT	p.Pro804Phe	p.P804F	ENST00000397752	NM_000245.2	804	CCt/TTt	11/21	1	2	FACETS	0.696	0.579	0.827	0.696	0.579	0.827	SUBCLONAL	1	TRUE	1	0.255311207464196	2		349	450	SUCCESS
MET	4233	MSKCC	GRCh37	7	116418866	116418867	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	53	441	0	ENST00000397752.3:c.3377_3378delinsTT	p.Thr1126Ile	p.T1126I	ENST00000397752	NM_000245.2	1126	aCC/aTT	17/21	1	2	FACETS	0.712	0.607	0.828	0.712	0.607	0.828	SUBCLONAL	1	TRUE	1	0.255311207464196	2		441	583	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876952	151876952	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	49	465	0	ENST00000262189.6:c.7409T>C	p.Val2470Ala	p.V2470A	ENST00000262189	NM_170606.2	2470	gTt/gCt	37/59	1	2	FACETS	0.851	0.722	0.993	0.851	0.722	0.993	CLONAL	1	TRUE	1	0.255311207464196	2		465	451	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372491	55372491	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780271052	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	80	594	1	ENST00000297316.4:c.1181C>T	p.Ala394Val	p.A394V	ENST00000297316	NM_022454.3	394	gCc/gTc	2/2	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.255311207464196	2		595	575	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8504281	8504281	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1455551669	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	60	384	0	ENST00000356435.5:c.1802C>T	p.Ser601Leu	p.S601L	ENST00000356435		601	tCa/tTa	12/35	0.255311207464196	1	FACETS	0.702	0.605	0.808	0.702	0.605	0.808	SUBCLONAL	1	TRUE	0	0.255311207464196	1		384	584	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98244479	98244480	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	39	303	0	ENST00000331920.6:c.590_591delinsAA	p.Trp197Ter	p.W197*	ENST00000331920	NM_000264.3	197	tGG/tAA	4/24	0.255311207464196	1	FACETS	0.888	0.74	1	0.888	0.74	1	CLONAL	1	TRUE	0	0.255311207464196	1		303	300	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912061	127912061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1481246558	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	125	781	1	ENST00000373547.4:c.809C>T	p.Ser270Leu	p.S270L	ENST00000373547	NM_002721.4	270	tCg/tTg	7/7	0.255311207464196	1	FACETS	0.878	0.794	0.967	0.878	0.794	0.967	CLONAL	1	TRUE	0	0.255311207464196	1		782	973	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870826	12870826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	43	202	0	ENST00000228872.4:c.53C>T	p.Ala18Val	p.A18V	ENST00000228872	NM_004064.3	18	gCc/gTc	1/3	0.187328861992361	3	FACETS	1	0.925	1	0.59	0.495	0.693	CLONAL	1	TRUE	1	0.255311207464196	3		202	322	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432459	49432459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	81	734	1	ENST00000301067.7:c.8680C>T	p.Pro2894Ser	p.P2894S	ENST00000301067	NM_003482.3	2894	Ccg/Tcg	34/54	1	2	FACETS	0.891	0.785	1	0.891	0.785	1	CLONAL	1	TRUE	1	0.255311207464196	2		735	712	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481857	56481857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	80	643	0	ENST00000267101.3:c.785C>T	p.Pro262Leu	p.P262L	ENST00000267101	NM_001982.3	262	cCt/cTt	7/28	1	2	FACETS	0.866	0.762	0.977	0.866	0.762	0.977	CLONAL	1	TRUE	1	0.255311207464196	2		643	724	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856190	111856190	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	27	368	0	ENST00000341259.2:c.241G>A	p.Asp81Asn	p.D81N	ENST00000341259	NM_005475.2	81	Gac/Aac	2/8	0.253548209645393	3	FACETS	0.507	0.403	0.627			1	SUBCLONAL	1	TRUE	NA	0.255311207464196	3		368	470	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133220545	133220545	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768504121	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	28	323	0	ENST00000320574.5:c.4168C>T	p.Arg1390Cys	p.R1390C	ENST00000320574	NM_006231.2	1390	Cgc/Tgc	33/49	0.255311207464196	1	FACETS	0.667	0.534	0.817	0.667	0.534	0.817	SUBCLONAL	1	TRUE	0	0.255311207464196	1		323	287	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557570	21557570	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756702960	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	83	608	1	ENST00000382592.4:c.2275C>T	p.Arg759Trp	p.R759W	ENST00000382592	NM_014572.2	759	Cgg/Tgg	5/8	1	2	FACETS	0.924	0.815	1	0.924	0.815	1	CLONAL	1	TRUE	1	0.255311207464196	2		609	704	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557740	21557740	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	107	621	1	ENST00000382592.4:c.2105A>T	p.Lys702Met	p.K702M	ENST00000382592	NM_014572.2	702	aAg/aTg	5/8	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.255311207464196	2		622	757	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950923	32950923	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	58	384	0	ENST00000380152.3:c.8749C>T	p.Leu2917Phe	p.L2917F	ENST00000380152		2917	Ctt/Ttt	21/27	1	2	FACETS	0.852	0.733	0.983	0.852	0.733	0.983	CLONAL	1	TRUE	1	0.255311207464196	2		384	533	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122905	2122905	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	73	638	0	ENST00000219476.3:c.2276G>A	p.Arg759Lys	p.R759K	ENST00000219476	NM_000548.3	759	aGa/aAa	21/42	0.189939022258035	1	FACETS	0.834	0.73	0.946	0.834	0.73	0.946	CLONAL	1	TRUE	0	0.255311207464196	1		638	598	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857865	9857865	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	91	590	0	ENST00000330684.3:c.3536C>T	p.Ser1179Phe	p.S1179F	ENST00000330684	NM_001134407.1	1179	tCc/tTc	13/13	0.189939022258035	1	FACETS	0.906	0.805	1	0.906	0.805	1	CLONAL	1	TRUE	0	0.255311207464196	1		590	686	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858097	9858097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770546037	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	119	671	0	ENST00000330684.3:c.3304G>A	p.Glu1102Lys	p.E1102K	ENST00000330684	NM_001134407.1	1102	Gag/Aag	13/13	0.189939022258035	1	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	0	0.255311207464196	1		671	745	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858428	9858429	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	61	584	0	ENST00000330684.3:c.2972_2973delinsTT	p.Ser991Phe	p.S991F	ENST00000330684	NM_001134407.1	991	tCC/tTT	13/13	0.189939022258035	1	FACETS	0.739	0.638	0.849	0.739	0.638	0.849	SUBCLONAL	1	TRUE	0	0.255311207464196	1		584	564	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641169	23641169	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	63	459	0	ENST00000261584.4:c.2306T>C	p.Leu769Pro	p.L769P	ENST00000261584	NM_024675.3	769	cTt/cCt	5/13	1	2	FACETS	0.904	0.782	1	0.904	0.782	1	CLONAL	1	TRUE	1	0.255311207464196	2		459	546	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641758	23641758	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	45	392	1	ENST00000261584.4:c.1717C>T	p.Leu573Phe	p.L573F	ENST00000261584	NM_024675.3	573	Ctt/Ttt	5/13	1	2	FACETS	0.711	0.597	0.836	0.711	0.597	0.836	SUBCLONAL	1	TRUE	1	0.255311207464196	2		393	496	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829383	72829383	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	113	919	1	ENST00000268489.5:c.7198A>T	p.Asn2400Tyr	p.N2400Y	ENST00000268489	NM_006885.3	2400	Aat/Tat	9/10	1	2	FACETS	0.87	0.781	0.964	0.87	0.781	0.964	CLONAL	1	TRUE	1	0.255311207464196	2		920	1018	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831852	72831853	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	133	1061	1	ENST00000268489.5:c.4728_4729delinsTT	p.Leu1577Phe	p.L1577F	ENST00000268489	NM_006885.3	1576	gcCCtt/gcTTtt	9/10	1	2	FACETS	0.943	0.855	1	0.943	0.855	1	CLONAL	1	TRUE	1	0.255311207464196	2		1062	1105	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577142	7577143	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	56	648	0	ENST00000269305.4:c.795_796delinsAA	p.Gly266Arg	p.G266R	ENST00000269305	NM_001126112.2	265	ctGGga/ctAAga	8/11	1	2	FACETS	0.675	0.577	0.782	0.675	0.577	0.782	SUBCLONAL	1	TRUE	1	0.255311207464196	2		648	650	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980495	7980495	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	57	448	0	ENST00000319144.4:c.1088G>A	p.Gly363Glu	p.G363E	ENST00000319144	NM_001139.2	363	gGg/gAg	9/15	1	2	FACETS	0.946	0.813	1	0.946	0.813	1	CLONAL	1	TRUE	1	0.255311207464196	2		448	472	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16056660	16056660	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	45	579	0	ENST00000268712.3:c.782T>C	p.Val261Ala	p.V261A	ENST00000268712	NM_006311.3	261	gTt/gCt	7/46	1	2	FACETS	0.473	0.396	0.558	0.473	0.396	0.558	SUBCLONAL	1	TRUE	1	0.255311207464196	2		579	745	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17124889	17124889	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748031634	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	43	499	0	ENST00000285071.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000285071	NM_144997.5	278	cCg/cTg	8/14	1	2	FACETS	0.653	0.546	0.771	0.653	0.546	0.771	SUBCLONAL	1	TRUE	1	0.255311207464196	2		499	516	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30302675	30302675	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778990935	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	21	215	0	ENST00000322652.5:c.766C>T	p.Arg256Cys	p.R256C	ENST00000322652	NM_015355.2	256	Cgt/Tgt	7/16	1	2	FACETS	0.514	0.396	0.652	0.514	0.396	0.652	SUBCLONAL	1	TRUE	1	0.255311207464196	2		215	320	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41228592	41228592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	48	562	0	ENST00000357654.3:c.4397G>T	p.Ser1466Ile	p.S1466I	ENST00000357654	NM_007294.3	1466	aGc/aTc	13/23	1	2	FACETS	0.633	0.534	0.742	0.633	0.534	0.742	SUBCLONAL	1	TRUE	1	0.255311207464196	2		562	594	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56440903	56440903	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151209912	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	89	559	1	ENST00000407977.2:c.434G>A	p.Arg145Gln	p.R145Q	ENST00000407977		145	cGa/cAa	4/10	1	2	FACETS	0.968	0.858	1	0.968	0.858	1	CLONAL	1	TRUE	1	0.255311207464196	2		560	720	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936356	78936356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	63	506	0	ENST00000306801.3:c.3788C>T	p.Pro1263Leu	p.P1263L	ENST00000306801	NM_020761.2	1263	cCc/cTc	32/34	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.255311207464196	2		506	463	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1632377	1632377	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1312155259	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	84	696	0	ENST00000344749.5:c.173C>T	p.Ser58Phe	p.S58F	ENST00000344749	NM_001136139.2	58	tCc/tTc	4/19	0.255311207464196	1	FACETS	0.962	0.85	1	0.962	0.85	1	CLONAL	1	TRUE	0	0.255311207464196	1		696	597	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5221165	5221165	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	73	555	0	ENST00000357368.4:c.3301A>C	p.Asn1101His	p.N1101H	ENST00000357368	NM_002850.3	1101	Aat/Cat	20/38	0.255311207464196	1	FACETS	0.994	0.871	1	0.994	0.871	1	CLONAL	1	TRUE	0	0.255311207464196	1		555	502	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7120695	7120695	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	82	684	0	ENST00000302850.5:c.3595C>T	p.Pro1199Ser	p.P1199S	ENST00000302850	NM_000208.2	1199	Cct/Tct	20/22	0.255311207464196	1	FACETS	0.764	0.674	0.862	0.764	0.674	0.862	SUBCLONAL	1	TRUE	0	0.255311207464196	1		684	733	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145605	11145605	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	36	314	0	ENST00000358026.2:c.3967C>T	p.Arg1323Cys	p.R1323C	ENST00000358026	NM_001128849.1	1323	Cgc/Tgc	29/36	0.189939022258035	1	FACETS	0.872	0.72	1	0.872	0.72	1	CLONAL	1	TRUE	0	0.255311207464196	1		314	282	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18273811	18273811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	91	677	1	ENST00000222254.8:c.1144C>T	p.His382Tyr	p.H382Y	ENST00000222254	NM_005027.3	382	Cac/Tac	10/16	0.189939022258035	1	FACETS	0.781	0.693	0.876	0.781	0.693	0.876	SUBCLONAL	1	TRUE	0	0.255311207464196	1		678	796	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31021250	31021250	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs375215583	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	43	413	0	ENST00000375687.4:c.1249C>T	p.Arg417Ter	p.R417*	ENST00000375687	NM_015338.5	417	Cga/Tga	12/13	1	2	FACETS	0.685	0.573	0.809	0.685	0.573	0.809	SUBCLONAL	1	TRUE	1	0.255311207464196	2		413	492	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485823	57485823	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	101	485	0	ENST00000371085.3:c.1124T>G	p.Val375Gly	p.V375G	ENST00000371085	NM_000516.4	375	gTg/gGg	13/13	NA	2	FACETS	1	0.932	1			1	INDETERMINATE	1	TRUE	NA	0.255311207464196	2		485	749	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860422	42860422	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs142988104	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	34	481	0	ENST00000398585.3:c.455A>G	p.Asn152Ser	p.N152S	ENST00000398585	NM_001135099.1	152	aAc/aGc	5/14	1	2	FACETS	0.547	0.446	0.66	0.547	0.446	0.66	SUBCLONAL	1	TRUE	1	0.255311207464196	2		481	487	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41533689	41533690	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0012262-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	76	557	0	ENST00000263253.7:c.1655_1656delinsTT	p.Ser552Phe	p.S552F	ENST00000263253	NM_001429.3	552	tCC/tTT	8/31	1	2	FACETS	0.938	0.823	1	0.938	0.823	1	CLONAL	1	TRUE	1	0.255311207464196	2		557	635	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	136	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.830665623517809	2		280	319	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385108	41385108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776607737	NA	P-0012303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	492	554	0	ENST00000373198.4:c.853G>A	p.Val285Met	p.V285M	ENST00000373198	NM_133170.3	285	Gtg/Atg	6/32	0.629466480548334	3	FACETS	0.977	0.943	1	0.977	0.943	1	CLONAL	2	TRUE	1	0.830665623517809	3		554	858	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304394	91304397	+	frameshift_variant	Frame_Shift_Del	DEL	AGAA	AGAA	-	novel	NA	P-0012303-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	107	424	0	ENST00000355112.3:c.1794_1797del	p.Glu598AspfsTer19	p.E598Dfs*19	ENST00000355112	NM_000057.2	597	tcAGAA/tc	7/22	1	2	FACETS	0.369	0.331	0.409	0.369	0.331	0.409	SUBCLONAL	1	TRUE	1	0.830665623517809	2		424	698	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	187	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.664530210261732	2		280	495	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0012315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	533	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.649725829259458	3	FACETS	0.983	0.947	1	0.983	0.947	1	CLONAL	2	TRUE	1	0.664530210261732	3		490	1087	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2493144	2493144	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753377213	NA	P-0012315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	303	692	0	ENST00000355716.4:c.584G>A	p.Gly195Glu	p.G195E	ENST00000355716	NM_003820.2	195	gGg/gAg	6/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.664530210261732	2		692	866	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49725304	49725304	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	200	497	0	ENST00000449682.2:c.121C>T	p.Gln41Ter	p.Q41*	ENST00000449682	NM_020998.3	41	Caa/Taa	2/18	1	2	FACETS	0.988	0.921	1	0.988	0.921	1	CLONAL	1	TRUE	1	0.664530210261732	2		497	609	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859812	117859812	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1402700421	NA	P-0012315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	962	1011	0	ENST00000297338.2:c.1823C>G	p.Ala608Gly	p.A608G	ENST00000297338	NM_006265.2	608	gCt/gGt	14/14	0.664530210261732	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.664530210261732	3		1011	1897	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850952	63850952	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	302	634	0	ENST00000279873.7:c.1730C>T	p.Ser577Phe	p.S577F	ENST00000279873	NM_032199.2	577	tCc/tTc	10/10	0.664530210261732	1	FACETS	0.976	0.928	1	0.976	0.928	1	CLONAL	1	TRUE	0	0.664530210261732	1		634	622	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964193	28964193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	242	583	0	ENST00000282397.4:c.1709G>A	p.Gly570Glu	p.G570E	ENST00000282397	NM_002019.4	570	gGa/gAa	13/30	1	2	FACETS	0.883	0.827	0.94	0.883	0.827	0.94	CLONAL	1	TRUE	1	0.664530210261732	2		583	825	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351092	89351092	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1210410309	NA	P-0012315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	465	1088	1	ENST00000301030.4:c.1858C>T	p.Pro620Ser	p.P620S	ENST00000301030	NM_001256183.1	620	Ccc/Tcc	9/13	1	2	FACETS	0.922	0.88	0.965	0.922	0.88	0.965	CLONAL	1	TRUE	1	0.664530210261732	2		1089	1518	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40447644	40447644	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	461	950	0	ENST00000345506.4:c.383C>T	p.Ser128Phe	p.S128F	ENST00000345506	NM_003152.3	128	tCt/tTt	6/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.664530210261732	2		950	1315	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41226479	41226479	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs398122688	NA	P-0012315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	369	787	1	ENST00000357654.3:c.4544G>A	p.Gly1515Glu	p.G1515E	ENST00000357654	NM_007294.3	1515	gGg/gAg	14/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.664530210261732	2		788	1080	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373502	118373537	+	inframe_deletion	In_Frame_Del	DEL	TTGGTGTCCAAGAGCTCCTCTTTAAAGGGAGAGAAG	TTGGTGTCCAAGAGCTCCTCTTTAAAGGGAGAGAAG	-	novel	NA	P-0012315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	51	640	0	ENST00000534358.1:c.6895_6930del	p.Leu2299_Lys2310del	p.L2299_K2310del	ENST00000534358	NM_005933.3	2299	TTGGTGTCCAAGAGCTCCTCTTTAAAGGGAGAGAAG/-	27/36	0.57703427507772	1	FACETS	0.149	0.126	0.174	0.149	0.126	0.174	SUBCLONAL	1	TRUE	0	0.664530210261732	1		640	689	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373541	118373541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0012315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	46	659	0	ENST00000534358.1:c.6936del	p.Val2313CysfsTer2	p.V2313Cfs*2	ENST00000534358	NM_005933.3	2312	Aaa/aa	27/36	0.57703427507772	1	FACETS	0.136	0.114	0.161	0.136	0.114	0.161	SUBCLONAL	1	TRUE	0	0.664530210261732	1		659	678	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852273	63852274	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	216	522	0	ENST00000279873.7:c.3051_3052delinsAA	p.Asp1018Asn	p.D1018N	ENST00000279873	NM_032199.2	1017	gaGGat/gaAAat	10/10	0.664530210261732	1	FACETS	0.912	0.858	0.967	0.912	0.858	0.967	CLONAL	1	TRUE	0	0.664530210261732	1		522	476	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9770535	9770536	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0012315-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	331	813	0	ENST00000377346.4:c.22_23delinsTT	p.Pro8Phe	p.P8F	ENST00000377346	NM_005026.3	8	CCc/TTc	3/24	1	2	FACETS	0.971	0.919	1	0.971	0.919	1	CLONAL	1	TRUE	1	0.664530210261732	2		813	1026	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577094	7577094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs28934574	NA	P-0012333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	106	616	0	ENST00000269305.4:c.844C>T	p.Arg282Trp	p.R282W	ENST00000269305	NM_001126112.2	282	Cgg/Tgg	8/11	1	2	FACETS	0.924	0.826	1	0.924	0.826	1	CLONAL	1	TRUE	1	0.21	2		616	1093	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259262	89259262	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770780950	NA	P-0012333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	83	441	1	ENST00000336596.2:c.406C>T	p.Arg136Ter	p.R136*	ENST00000336596	NM_005233.5	136	Cga/Tga	3/17	1	2	FACETS	0.966	0.852	1	0.966	0.852	1	CLONAL	1	TRUE	1	0.21	2		442	818	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017196	31017196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	85	519	0	ENST00000375687.4:c.527C>T	p.Pro176Leu	p.P176L	ENST00000375687	NM_015338.5	176	cCt/cTt	7/13	1	2	FACETS	0.824	0.727	0.929	0.824	0.727	0.929	CLONAL	1	TRUE	1	0.21	2		519	982	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812293	212812293	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569995088	NA	P-0012333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	67	452	3	ENST00000342788.4:c.283C>T	p.Arg95Cys	p.R95C	ENST00000342788	NM_005235.2	95	Cgt/Tgt	3/28	1	2	FACETS	0.713	0.618	0.816	0.713	0.618	0.816	SUBCLONAL	1	TRUE	1	0.21	2		455	895	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576891	7576891	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0012333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	83	451	1	ENST00000269305.4:c.955A>T	p.Lys319Ter	p.K319*	ENST00000269305	NM_001126112.2	319	Aag/Tag	9/11	1	2	FACETS	0.926	0.816	1	0.926	0.816	1	CLONAL	1	TRUE	1	0.21	2		452	854	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211536	46211536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	63	544	0	ENST00000334344.6:c.502G>A	p.Gly168Arg	p.G168R	ENST00000334344	NM_152641.2	168	Gga/Aga	5/21	1	2	FACETS	0.65	0.561	0.748	0.65	0.561	0.748	SUBCLONAL	1	TRUE	1	0.21	2		544	923	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120478229	120478229	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0012333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	56	309	0	ENST00000256646.2:c.3523-2A>T		p.X1175_splice	ENST00000256646	NM_024408.3	1175			1	2	FACETS	0.909	0.778	1	0.909	0.778	1	CLONAL	1	TRUE	1	0.21	2		309	587	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938922	178938922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	23	192	0	ENST00000263967.3:c.2164G>A	p.Glu722Lys	p.E722K	ENST00000263967	NM_006218.2	722	Gag/Aag	14/21	1	2	FACETS	0.61	0.475	0.766	0.61	0.475	0.766	SUBCLONAL	1	TRUE	1	0.21	2		192	359	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182681834	182681834	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763048538	NA	P-0012333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	57	360	0	ENST00000292782.4:c.224C>T	p.Pro75Leu	p.P75L	ENST00000292782	NM_020640.2	75	cCt/cTt	3/7	1	2	FACETS	0.813	0.696	0.94	0.813	0.696	0.94	CLONAL	1	TRUE	1	0.21	2		360	668	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630852	187630852	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	123	598	1	ENST00000441802.2:c.130C>T	p.Gln44Ter	p.Q44*	ENST00000441802	NM_005245.3	44	Cag/Tag	2/27	1	2	FACETS	0.974	0.878	1	0.974	0.878	1	CLONAL	1	TRUE	1	0.21	2		599	1203	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157502208	157502208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	91	374	0	ENST00000346085.5:c.3241G>A	p.Glu1081Lys	p.E1081K	ENST00000346085	NM_020732.3	1081	Gaa/Aaa	12/20	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.21	2		374	747	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739828	41739828	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	126	754	0	ENST00000242208.4:c.145A>G	p.Asn49Asp	p.N49D	ENST00000242208	NM_002192.2	49	Aac/Gac	2/3	1	2	FACETS	0.952	0.859	1	0.952	0.859	1	CLONAL	1	TRUE	1	0.21	2		754	1261	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845727	151845727	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	100	585	0	ENST00000262189.6:c.13285C>T	p.His4429Tyr	p.H4429Y	ENST00000262189	NM_170606.2	4429	Cac/Tac	52/59	1	2	FACETS	0.935	0.833	1	0.935	0.833	1	CLONAL	1	TRUE	1	0.21	2		585	1019	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139402743	139402743	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1554728428	NA	P-0012333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	78	370	0	ENST00000277541.6:c.3266G>A	p.Trp1089Ter	p.W1089*	ENST00000277541	NM_017617.3	1089	tGg/tAg	20/34	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.21	2		370	730	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518116	69518116	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	100	536	0	ENST00000294312.3:c.249G>T	p.Lys83Asn	p.K83N	ENST00000294312	NM_005117.2	83	aaG/aaT	2/3	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.21	2		536	848	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518124	69518124	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	100	498	0	ENST00000294312.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000294312	NM_005117.2	81	Gag/Aag	2/3	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.21	2		498	810	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562634	21562634	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	23	141	0	ENST00000382592.4:c.1285C>T	p.Pro429Ser	p.P429S	ENST00000382592	NM_014572.2	429	Ccc/Tcc	4/8	0.3	2	FACETS	1	0.826	1			1	CLONAL	1	TRUE	NA	0.21	2		141	206	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66679692	66679692	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0012333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	100	549	1	ENST00000307102.5:c.7A>T	p.Lys3Ter	p.K3*	ENST00000307102	NM_002755.3	3	Aag/Tag	1/11	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.21	2		550	907	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486244	99486244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	74	479	0	ENST00000268035.6:c.3550C>T	p.Leu1184Phe	p.L1184F	ENST00000268035	NM_000875.3	1184	Ctc/Ttc	19/21	1	2	FACETS	0.862	0.753	0.979	0.862	0.753	0.979	CLONAL	1	TRUE	1	0.21	2		479	818	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858163	9858163	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	114	645	0	ENST00000330684.3:c.3238C>A	p.His1080Asn	p.H1080N	ENST00000330684	NM_001134407.1	1080	Cac/Aac	13/13	1	2	FACETS	0.93	0.835	1	0.93	0.835	1	CLONAL	1	TRUE	1	0.21	2		645	1168	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993368	72993368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1250	131	843	1	ENST00000268489.5:c.677C>T	p.Pro226Leu	p.P226L	ENST00000268489	NM_006885.3	226	cCc/cTc	2/10	1	2	FACETS	0.903	0.817	0.995	0.903	0.817	0.995	CLONAL	1	TRUE	1	0.21	2		844	1381	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462598	40462598	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1306	130	761	2	ENST00000345506.4:c.2296G>A	p.Glu766Lys	p.E766K	ENST00000345506	NM_003152.3	766	Gaa/Aaa	20/20	1	2	FACETS	0.862	0.779	0.95	0.862	0.779	0.95	CLONAL	1	TRUE	1	0.21	2		763	1436	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696381	47696381	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	67	453	1	ENST00000347630.2:c.442G>A	p.Gly148Arg	p.G148R	ENST00000347630	NM_001007230.1	148	Ggg/Agg	6/11	1	2	FACETS	0.844	0.732	0.965	0.844	0.732	0.965	CLONAL	1	TRUE	1	0.21	2		454	756	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017764	31017764	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	74	413	0	ENST00000375687.4:c.626C>T	p.Ser209Phe	p.S209F	ENST00000375687	NM_015338.5	209	tCt/tTt	8/13	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.21	2		413	673	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510216	187510217	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTCGATGTCGTAGCCTCCAGGGTAATAGTCCG	novel	NA	P-0012333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	55	508	0	ENST00000441802.2:c.13265_13296dup	p.Ser4433ArgfsTer65	p.S4433Rfs*65	ENST00000441802	NM_005245.3	4432	-/CGGACTATTACCCTGGAGGCTACGACATCGAA	27/27	1	2	FACETS	0.5	0.426	0.582	0.5	0.426	0.582	SUBCLONAL	1	TRUE	1	0.21	2		508	1047	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870972	12870973	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0012333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	68	375	0	ENST00000228872.4:c.201_202del	p.His67GlnfsTer57	p.H67Qfs*57	ENST00000228872	NM_004064.3	67	CAc/c	1/3	1	2	FACETS	0.815	0.707	0.931	0.815	0.707	0.931	CLONAL	1	TRUE	1	0.21	2		375	795	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46123836	46123837	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0012333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	45	218	0	ENST00000334344.6:c.109dup	p.Ile37AsnfsTer29	p.I37Nfs*29	ENST00000334344	NM_152641.2	34	-/A	2/21	1	2	FACETS	0.889	0.747	1	0.889	0.747	1	CLONAL	1	TRUE	1	0.21	2		218	482	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288503	15288504	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0012333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	35	123	0	ENST00000263388.2:c.4235_4236delinsAA	p.Trp1412Ter	p.W1412*	ENST00000263388	NM_000435.2	1412	tGG/tAA	24/33	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.21	2		123	231	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89347968	89347969	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1399	127	844	0	ENST00000301030.4:c.4981_4982delinsTT	p.Pro1661Leu	p.P1661L	ENST00000301030	NM_001256183.1	1661	CCa/TTa	9/13	1	2	FACETS	0.793	0.715	0.875	0.793	0.715	0.875	SUBCLONAL	1	TRUE	1	0.21	2		844	1526	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139413064	139413066	+	frameshift_variant	Frame_Shift_Del	DEL	CGC	CGC	TG	novel	NA	P-0012333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	61	476	0	ENST00000277541.6:c.1076_1078delinsCA	p.Cys359SerfsTer272	p.C359Sfs*272	ENST00000277541	NM_017617.3	359	tGCGag/tCAag	6/34	0.3	2	FACETS	0.723	0.622	0.832			1	SUBCLONAL	1	TRUE	NA	0.21	2		476	804	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971179	21971181	+	missense_variant	Missense_Mutation	TNP	GCC	GCC	TTT	novel	NA	P-0012333-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	19	133	1	ENST00000304494.5:c.177_179delinsAAA	p.Ala60Lys	p.A60K	ENST00000304494	NM_000077.4	59	gtGGCg/gtAAAg	2/3	0.0818400157465726	0	FACETS	0.598	0.455	0.766			1	INDETERMINATE	1	TRUE	0	0.21	0		134	239	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012336-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	47	280	0				ENST00000310581	NM_198253.2	-/1132			0.18858540937156	1	FACETS	0.719	0.608	0.839	0.719	0.608	0.839	SUBCLONAL	1	TRUE	0	0.306781722775926	1		280	361	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0012336-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	334	660	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	0.306781722775926	2	FACETS	0.843	0.8	0.886	1	0.993	1	CLONAL	3	TRUE	0	0.306781722775926	2		660	861	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577144	7577144	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs879253942	NA	P-0012336-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	247	850	0	ENST00000269305.4:c.794T>C	p.Leu265Pro	p.L265P	ENST00000269305	NM_001126112.2	265	cTg/cCg	8/11	0.306781722775926	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.306781722775926	1		850	1016	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971026	21971026	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012336-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	126	360	0	ENST00000304494.5:c.332del	p.Gly111AlafsTer35	p.G111Afs*35	ENST00000304494	NM_000077.4	111	gGc/gc	2/3	0.306781722775926	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.306781722775926	1		360	479	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10248677	10248677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1259943763	NA	P-0012336-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	47	452	1	ENST00000340748.4:c.4076C>T	p.Ser1359Leu	p.S1359L	ENST00000340748		1359	tCg/tTg	35/40	0.18858540937156	1	FACETS	0.429	0.361	0.504	0.429	0.361	0.504	SUBCLONAL	1	TRUE	0	0.306781722775926	1		453	605	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513437	41513437	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012336-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	93	766	0	ENST00000263253.7:c.341G>C	p.Gly114Ala	p.G114A	ENST00000263253	NM_001429.3	114	gGa/gCa	2/31	0.193123566937926	2	FACETS	0.56	0.497	0.629	0.28	0.248	0.315	SUBCLONAL	1	TRUE	0	0.306781722775926	2		766	1082	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352735	70352735	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012336-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1100	275	1139	0	ENST00000374080.3:c.4456C>G	p.Leu1486Val	p.L1486V	ENST00000374080		1486	Cta/Gta	32/45	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.306781722775926	2		1139	1375	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28597507	28597507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	86	693	0	ENST00000241453.7:c.2398G>A	p.Glu800Lys	p.E800K	ENST00000241453	NM_004119.2	800	Gaa/Aaa	19/24	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.19	2		693	870	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133250289	133250289	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519945	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	77	593	1	ENST00000320574.5:c.1231G>T	p.Val411Leu	p.V411L	ENST00000320574	NM_006231.2	411	Gtg/Ttg	13/49	1	2	FACETS	0.806	0.706	0.915	0.806	0.706	0.915	CLONAL	1	TRUE	1	0.19	2		594	1005	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528141	29528141	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	110	713	0	ENST00000356175.3:c.1149C>A	p.Cys383Ter	p.C383*	ENST00000356175	NM_000267.3	383	tgC/tgA	10/57	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.19	2		713	1002	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132552	11132552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	81	646	1	ENST00000358026.2:c.2768C>T	p.Ala923Val	p.A923V	ENST00000358026	NM_001128849.1	923	gCg/gTg	19/36	1	2	FACETS	0.809	0.711	0.915	0.809	0.711	0.915	CLONAL	1	TRUE	1	0.19	2		647	1054	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164440	36164440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	27	135	0	ENST00000300305.3:c.1435C>T	p.Pro479Ser	p.P479S	ENST00000300305		479	Ccc/Tcc	8/8	1	2	FACETS	1	0.804	1	1	0.804	1	CLONAL	1	TRUE	1	0.19	2		135	282	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916876	178916876	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913287	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1261	145	1089	1	ENST00000263967.3:c.263G>A	p.Arg88Gln	p.R88Q	ENST00000263967	NM_006218.2	88	cGa/cAa	2/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.19	2		1090	1406	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028632	12028632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753665559	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	70	624	1	ENST00000353533.5:c.835G>A	p.Ala279Thr	p.A279T	ENST00000353533	NM_003010.3	279	Gca/Aca	8/11	1	2	FACETS	0.733	0.637	0.837	0.733	0.637	0.837	SUBCLONAL	1	TRUE	1	0.19	2		625	1005	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16247377	16247377	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748683309	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	47	357	1	ENST00000375759.3:c.1648C>T	p.Arg550Cys	p.R550C	ENST00000375759	NM_015001.2	550	Cgc/Tgc	9/15	1	2	FACETS	0.782	0.658	0.918	0.782	0.658	0.918	CLONAL	1	TRUE	1	0.19	2		358	633	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952007	178952007	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913288	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	71	589	0	ENST00000263967.3:c.3062A>G	p.Tyr1021Cys	p.Y1021C	ENST00000263967	NM_006218.2	1021	tAc/tGc	21/21	1	2	FACETS	0.854	0.744	0.974	0.854	0.744	0.974	CLONAL	1	TRUE	1	0.19	2		589	875	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25470573	25470573	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553414070	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	74	651	1	ENST00000264709.3:c.901C>T	p.Arg301Trp	p.R301W	ENST00000264709	NM_175629.2	301	Cgg/Tgg	8/23	1	2	FACETS	0.786	0.686	0.894	0.786	0.686	0.894	SUBCLONAL	1	TRUE	1	0.19	2		652	991	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321697	30321697	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	87	688	0	ENST00000322652.5:c.1552G>A	p.Gly518Arg	p.G518R	ENST00000322652	NM_015355.2	518	Gga/Aga	13/16	1	2	FACETS	0.874	0.772	0.984	0.874	0.772	0.984	CLONAL	1	TRUE	1	0.19	2		688	1048	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552891	106552891	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771056895	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1240	96	903	4	ENST00000369096.4:c.856C>T	p.Arg286Cys	p.R286C	ENST00000369096	NM_001198.3	286	Cgt/Tgt	5/7	1	2	FACETS	0.756	0.671	0.848	0.756	0.671	0.848	SUBCLONAL	1	TRUE	1	0.19	2		907	1336	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317111	87317111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	80	529	0	ENST00000277120.3:c.250G>A	p.Glu84Lys	p.E84K	ENST00000277120		84	Gaa/Aaa	3/19	1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.19	2		529	811	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157132	106157132	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	58	564	1	ENST00000380013.4:c.2033G>A	p.Gly678Asp	p.G678D	ENST00000380013	NM_001127208.2	678	gGc/gAc	3/11	1	2	FACETS	0.636	0.545	0.736	0.636	0.545	0.736	SUBCLONAL	1	TRUE	1	0.19	2		565	960	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175528	108175528	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs376603775	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	71	552	1	ENST00000278616.4:c.5623C>T	p.Arg1875Ter	p.R1875*	ENST00000278616	NM_000051.3	1875	Cga/Tga	37/63	1	2	FACETS	0.836	0.728	0.953	0.836	0.728	0.953	CLONAL	1	TRUE	1	0.19	2		553	894	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247366	153247366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866987936	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	48	371	0	ENST00000281708.4:c.1436G>A	p.Arg479Gln	p.R479Q	ENST00000281708	NM_033632.3	479	cGa/cAa	10/12	1	2	FACETS	0.864	0.73	1	0.864	0.73	1	CLONAL	1	TRUE	1	0.19	2		371	585	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2126157	2126157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1319146226	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	98	648	2	ENST00000219476.3:c.2728C>T	p.Pro910Ser	p.P910S	ENST00000219476	NM_000548.3	910	Cct/Tct	24/42	1	2	FACETS	0.932	0.829	1	0.932	0.829	1	CLONAL	1	TRUE	1	0.19	2		650	1107	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432068	121432068	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137853238	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	71	705	1	ENST00000257555.6:c.815G>A	p.Arg272His	p.R272H	ENST00000257555		272	cGc/cAc	4/10	1	2	FACETS	0.677	0.589	0.773	0.677	0.589	0.773	SUBCLONAL	1	TRUE	1	0.19	2		706	1104	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743883	41743883	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374699228	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	104	791	3	ENST00000301178.4:c.818C>T	p.Ala273Val	p.A273V	ENST00000301178	NM_021913.4	273	gCg/gTg	7/20	1	2	FACETS	0.881	0.786	0.982	0.881	0.786	0.982	CLONAL	1	TRUE	1	0.19	2		794	1243	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15303028	15303028	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773630799	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	52	411	1	ENST00000263388.2:c.422G>A	p.Arg141His	p.R141H	ENST00000263388	NM_000435.2	141	cGc/cAc	4/33	1	2	FACETS	0.851	0.724	0.991	0.851	0.724	0.991	CLONAL	1	TRUE	1	0.19	2		412	643	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11121076	11121076	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1131691371	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	70	657	1	ENST00000358026.2:c.2143G>A	p.Asp715Asn	p.D715N	ENST00000358026	NM_001128849.1	715	Gat/Aat	15/36	1	2	FACETS	0.669	0.581	0.765	0.669	0.581	0.765	SUBCLONAL	1	TRUE	1	0.19	2		658	1101	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289271	33289271	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1303387799	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	59	463	1	ENST00000374542.5:c.281G>A	p.Arg94His	p.R94H	ENST00000374542	NM_001141970.1	94	cGt/cAt	3/8	1	2	FACETS	0.742	0.637	0.857	0.742	0.637	0.857	SUBCLONAL	1	TRUE	1	0.19	2		464	837	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950396	15950396	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201721277	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	65	645	0	ENST00000268712.3:c.6548G>A	p.Arg2183His	p.R2183H	ENST00000268712	NM_006311.3	2183	cGc/cAc	42/46	1	2	FACETS	0.744	0.643	0.853	0.744	0.643	0.853	SUBCLONAL	1	TRUE	1	0.19	2		645	920	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587118	189587118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761885185	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	74	605	0	ENST00000264731.3:c.1135C>T	p.Arg379Cys	p.R379C	ENST00000264731	NM_003722.4	379	Cgt/Tgt	9/14	1	2	FACETS	0.931	0.813	1	0.931	0.813	1	CLONAL	1	TRUE	1	0.19	2		605	837	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001366	29001366	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779189056	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	73	529	1	ENST00000282397.4:c.1366G>A	p.Ala456Thr	p.A456T	ENST00000282397	NM_002019.4	456	Gca/Aca	10/30	1	2	FACETS	0.889	0.776	1	0.889	0.776	1	CLONAL	1	TRUE	1	0.19	2		530	864	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933151	39933151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587778096	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	62	699	0	ENST00000378444.4:c.1448C>T	p.Pro483Leu	p.P483L	ENST00000378444	NM_001123385.1	483	cCg/cTg	4/15	1	2	FACETS	0.563	0.484	0.649	0.563	0.484	0.649	SUBCLONAL	1	TRUE	1	0.19	2		699	1160	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162740215	162740215	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771675675	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	60	581	0	ENST00000367921.3:c.1417C>T	p.Arg473Cys	p.R473C	ENST00000367921	NM_006182.2	473	Cgc/Tgc	12/18	1	2	FACETS	0.604	0.518	0.698	0.604	0.518	0.698	SUBCLONAL	1	TRUE	1	0.19	2		581	1046	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430668	80430668	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	43	361	0	ENST00000286548.4:c.340C>T	p.Arg114Ter	p.R114*	ENST00000286548	NM_002072.3	114	Cga/Tga	3/7	1	2	FACETS	1	0.856	1	1	0.856	1	CLONAL	1	TRUE	1	0.19	2		361	442	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45797890	45797890	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146044717	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	54	646	1	ENST00000450313.1:c.881G>A	p.Arg294His	p.R294H	ENST00000450313	NM_012222.2	294	cGc/cAc	10/16	1	2	FACETS	0.564	0.48	0.657	0.564	0.48	0.657	SUBCLONAL	1	TRUE	1	0.19	2		647	1008	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876230	35876230	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	55	563	3	ENST00000303115.3:c.1022G>T	p.Gly341Val	p.G341V	ENST00000303115	NM_002185.3	341	gGa/gTa	8/8	1	2	FACETS	0.682	0.582	0.792	0.682	0.582	0.792	SUBCLONAL	1	TRUE	1	0.19	2		566	849	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566522	41566522	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	101	730	0	ENST00000263253.7:c.4399T>C	p.Tyr1467His	p.Y1467H	ENST00000263253	NM_001429.3	1467	Tac/Cac	27/31	1	2	FACETS	0.945	0.842	1	0.945	0.842	1	CLONAL	1	TRUE	1	0.19	2		730	1125	SUCCESS
AR	367	MSKCC	GRCh37	X	66937326	66937326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137852593	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	80	740	4	ENST00000374690.3:c.2180G>A	p.Arg727His	p.R727H	ENST00000374690	NM_000044.3	727	cGc/cAc	5/8	1	2	FACETS	0.783	0.687	0.887	0.783	0.687	0.887	SUBCLONAL	1	TRUE	1	0.19	2		744	1075	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101353	27101353	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	82	666	0	ENST00000324856.7:c.4635G>A	p.Trp1545Ter	p.W1545*	ENST00000324856	NM_006015.4	1545	tgG/tgA	18/20	1	2	FACETS	0.895	0.788	1	0.895	0.788	1	CLONAL	1	TRUE	1	0.19	2		666	964	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280068	66280068	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	56	631	0	ENST00000273854.3:c.1621C>T	p.Arg541Ter	p.R541*	ENST00000273854	NM_004439.5	541	Cga/Tga	7/18	1	2	FACETS	0.62	0.529	0.719	0.62	0.529	0.719	SUBCLONAL	1	TRUE	1	0.19	2		631	951	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157405905	157405905	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774701560	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	58	515	0	ENST00000346085.5:c.2147C>T	p.Ala716Val	p.A716V	ENST00000346085	NM_020732.3	716	gCg/gTg	6/20	1	2	FACETS	0.779	0.668	0.9	0.779	0.668	0.9	SUBCLONAL	1	TRUE	1	0.19	2		515	784	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520087	106520087	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774448553	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	55	395	0	ENST00000359195.3:c.2515C>T	p.Arg839Cys	p.R839C	ENST00000359195	NM_002649.2	839	Cgc/Tgc	6/11	1	2	FACETS	1	0.882	1	1	0.882	1	CLONAL	1	TRUE	1	0.19	2		395	559	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393357	393357	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	54	449	1	ENST00000380956.4:c.205G>A	p.Ala69Thr	p.A69T	ENST00000380956	NM_001195286.1	69	Gcg/Acg	2/9	1	2	FACETS	0.801	0.683	0.93	0.801	0.683	0.93	CLONAL	1	TRUE	1	0.19	2		450	710	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350291	15350291	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1233820799	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	81	664	1	ENST00000263377.2:c.3488G>A	p.Arg1163Gln	p.R1163Q	ENST00000263377	NM_058243.2	1163	cGg/cAg	17/20	1	2	FACETS	0.781	0.686	0.883	0.781	0.686	0.883	SUBCLONAL	1	TRUE	1	0.19	2		665	1092	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29654553	29654553	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs876657714	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	71	587	2	ENST00000356175.3:c.5242C>T	p.Arg1748Ter	p.R1748*	ENST00000356175	NM_000267.3	1748	Cga/Tga	37/57	1	2	FACETS	0.764	0.665	0.872	0.764	0.665	0.872	SUBCLONAL	1	TRUE	1	0.19	2		589	978	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123182928	123182928	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	75	631	0	ENST00000218089.9:c.893G>A	p.Arg298His	p.R298H	ENST00000218089	NM_001042749.1	298	cGt/cAt	10/35	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.19	2		631	752	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022390	12022390	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142603082	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1280	78	914	1	ENST00000396373.4:c.496G>A	p.Val166Met	p.V166M	ENST00000396373	NM_001987.4	166	Gtg/Atg	5/8	1	2	FACETS	0.605	0.529	0.687	0.605	0.529	0.687	SUBCLONAL	1	TRUE	1	0.19	2		915	1358	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671451	30671451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	97	753	0	ENST00000376406.3:c.5509G>A	p.Val1837Met	p.V1837M	ENST00000376406	NM_014641.2	1837	Gtg/Atg	10/15	1	2	FACETS	0.857	0.762	0.959	0.857	0.762	0.959	CLONAL	1	TRUE	1	0.19	2		753	1191	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674234	86674234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	40	384	0	ENST00000274376.6:c.2366G>A	p.Arg789Gln	p.R789Q	ENST00000274376	NM_002890.2	789	cGa/cAa	18/25	1	2	FACETS	0.735	0.61	0.875	0.735	0.61	0.875	SUBCLONAL	1	TRUE	1	0.19	2		384	573	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435777	56435777	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1055597951	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	36	340	1	ENST00000407977.2:c.1360C>T	p.Arg454Cys	p.R454C	ENST00000407977		454	Cgc/Tgc	9/10	1	2	FACETS	0.714	0.586	0.857	0.714	0.586	0.857	SUBCLONAL	1	TRUE	1	0.19	2		341	531	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81939042	81939042	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1204	96	981	0	ENST00000359376.3:c.1397T>C	p.Val466Ala	p.V466A	ENST00000359376	NM_002661.3	466	gTc/gCc	15/33	1	2	FACETS	0.777	0.69	0.871	0.777	0.69	0.871	SUBCLONAL	1	TRUE	1	0.19	2		981	1300	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289660	33289660	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758327720	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	50	508	0	ENST00000374542.5:c.43G>A	p.Glu15Lys	p.E15K	ENST00000374542	NM_001141970.1	15	Gaa/Aaa	2/8	1	2	FACETS	0.686	0.581	0.803	0.686	0.581	0.803	SUBCLONAL	1	TRUE	1	0.19	2		508	767	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156729	106156729	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1440692352	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	64	555	0	ENST00000380013.4:c.1630C>T	p.Arg544Ter	p.R544*	ENST00000380013	NM_001127208.2	544	Cga/Tga	3/11	1	2	FACETS	0.748	0.646	0.859	0.748	0.646	0.859	SUBCLONAL	1	TRUE	1	0.19	2		555	901	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346918	89346918	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775544970	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	40	481	0	ENST00000301030.4:c.6032C>T	p.Ser2011Leu	p.S2011L	ENST00000301030	NM_001256183.1	2011	tCg/tTg	9/13	1	2	FACETS	0.608	0.503	0.724	0.608	0.503	0.724	SUBCLONAL	1	TRUE	1	0.19	2		481	693	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760559	133760559	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs557879885	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	104	754	4	ENST00000318560.5:c.2882C>T	p.Pro961Leu	p.P961L	ENST00000318560	NM_005157.4	961	cCg/cTg	11/11	1	2	FACETS	0.911	0.813	1	0.911	0.813	1	CLONAL	1	TRUE	1	0.19	2		758	1202	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185181425	185181425	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1435276633	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	58	668	1	ENST00000265026.3:c.1366C>T	p.Arg456Ter	p.R456*	ENST00000265026	NM_004721.4	456	Cga/Tga	8/14	1	2	FACETS	0.612	0.524	0.709	0.612	0.524	0.709	SUBCLONAL	1	TRUE	1	0.19	2		669	997	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9775729	9775729	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	74	578	0	ENST00000377346.4:c.272A>G	p.Asp91Gly	p.D91G	ENST00000377346	NM_005026.3	91	gAc/gGc	4/24	1	2	FACETS	0.852	0.744	0.969	0.852	0.744	0.969	CLONAL	1	TRUE	1	0.19	2		578	914	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9780939	9780939	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	65	611	0	ENST00000377346.4:c.1661A>G	p.Lys554Arg	p.K554R	ENST00000377346	NM_005026.3	554	aAg/aGg	13/24	1	2	FACETS	0.74	0.64	0.85	0.74	0.64	0.85	SUBCLONAL	1	TRUE	1	0.19	2		611	924	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11190608	11190608	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750903815	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	61	569	0	ENST00000361445.4:c.5591C>T	p.Pro1864Leu	p.P1864L	ENST00000361445	NM_004958.3	1864	cCg/cTg	39/58	1	2	FACETS	0.662	0.569	0.763	0.662	0.569	0.763	SUBCLONAL	1	TRUE	1	0.19	2		569	970	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11307730	11307730	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1087	75	606	2	ENST00000361445.4:c.1177C>A	p.Leu393Ile	p.L393I	ENST00000361445	NM_004958.3	393	Ctt/Att	8/58	1	2	FACETS	0.679	0.593	0.773	0.679	0.593	0.773	SUBCLONAL	1	TRUE	1	0.19	2		608	1162	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202870	16202870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	977	94	650	0	ENST00000375759.3:c.578G>A	p.Arg193His	p.R193H	ENST00000375759	NM_015001.2	193	cGc/cAc	3/15	1	2	FACETS	0.924	0.82	1	0.924	0.82	1	CLONAL	1	TRUE	1	0.19	2		650	1071	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255940	16255940	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	35	371	0	ENST00000375759.3:c.3205C>A	p.Leu1069Ile	p.L1069I	ENST00000375759	NM_015001.2	1069	Ctt/Att	11/15	1	2	FACETS	0.646	0.529	0.779	0.646	0.529	0.779	SUBCLONAL	1	TRUE	1	0.19	2		371	570	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885861	23885861	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	96	755	0	ENST00000374561.5:c.57A>C	p.Glu19Asp	p.E19D	ENST00000374561	NM_002167.4	19	gaA/gaC	1/3	1	2	FACETS	0.896	0.796	1	0.896	0.796	1	CLONAL	1	TRUE	1	0.19	2		755	1128	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089641	27089641	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775126641	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	73	612	0	ENST00000324856.7:c.2597G>A	p.Arg866Gln	p.R866Q	ENST00000324856	NM_006015.4	866	cGg/cAg	8/20	1	2	FACETS	0.774	0.675	0.881	0.774	0.675	0.881	SUBCLONAL	1	TRUE	1	0.19	2		612	993	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156837904	156837904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs41267427	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	71	618	0	ENST00000524377.1:c.437C>T	p.Ser146Leu	p.S146L	ENST00000524377	NM_002529.3	146	tCg/tTg	5/17	1	2	FACETS	0.699	0.608	0.798	0.699	0.608	0.798	SUBCLONAL	1	TRUE	1	0.19	2		618	1069	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226552710	226552710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	87	429	0	ENST00000366794.5:c.2651C>T	p.Ala884Val	p.A884V	ENST00000366794	NM_001618.3	884	gCg/gTg	19/23	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.19	2		429	808	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675374	241675374	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	74	770	0	ENST00000366560.3:c.448A>C	p.Asn150His	p.N150H	ENST00000366560	NM_000143.3	150	Aat/Cat	4/10	1	2	FACETS	0.935	0.817	1	0.935	0.817	1	CLONAL	1	TRUE	1	0.19	2		770	833	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675399	241675399	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	66	698	2	ENST00000366560.3:c.423G>A	p.Trp141Ter	p.W141*	ENST00000366560	NM_000143.3	141	tgG/tgA	4/10	1	2	FACETS	0.9	0.78	1	0.9	0.78	1	CLONAL	1	TRUE	1	0.19	2		700	772	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716177	243716177	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	78	648	1	ENST00000263826.5:c.1017G>T	p.Met339Ile	p.M339I	ENST00000263826	NM_005465.4	339	atG/atT	10/13	1	2	FACETS	0.833	0.73	0.944	0.833	0.73	0.944	CLONAL	1	TRUE	1	0.19	2		649	986	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25462062	25462062	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	66	543	0	ENST00000264709.3:c.2345C>T	p.Ala782Val	p.A782V	ENST00000264709	NM_175629.2	782	gCc/gTc	20/23	1	2	FACETS	0.713	0.617	0.817	0.713	0.617	0.817	SUBCLONAL	1	TRUE	1	0.19	2		543	975	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25463209	25463209	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1167559489	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	88	653	1	ENST00000264709.3:c.2284G>A	p.Gly762Ser	p.G762S	ENST00000264709	NM_175629.2	762	Ggc/Agc	19/23	1	2	FACETS	0.85	0.751	0.956	0.85	0.751	0.956	CLONAL	1	TRUE	1	0.19	2		654	1090	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523072	25523072	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369618387	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	92	637	0	ENST00000264709.3:c.113G>A	p.Arg38His	p.R38H	ENST00000264709	NM_175629.2	38	cGc/cAc	3/23	1	2	FACETS	0.899	0.797	1	0.899	0.797	1	CLONAL	1	TRUE	1	0.19	2		637	1077	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026437	48026437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	85	664	1	ENST00000234420.5:c.1315G>A	p.Asp439Asn	p.D439N	ENST00000234420	NM_000179.2	439	Gat/Aat	4/10	1	2	FACETS	0.959	0.846	1	0.959	0.846	1	CLONAL	1	TRUE	1	0.19	2		665	933	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027511	48027511	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	62	367	0	ENST00000234420.5:c.2389G>T	p.Asp797Tyr	p.D797Y	ENST00000234420	NM_000179.2	797	Gac/Tac	4/10	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.19	2		367	646	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719525	61719525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	78	614	2	ENST00000401558.2:c.1658G>A	p.Arg553His	p.R553H	ENST00000401558	NM_003400.3	553	cGt/cAt	15/25	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.19	2		616	767	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907726	111907726	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	101	734	0	ENST00000393256.3:c.498+2T>C		p.X166_splice	ENST00000393256	NM_006538.4	166			1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.19	2		734	949	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128050319	128050319	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	75	623	0	ENST00000285398.2:c.338T>C	p.Val113Ala	p.V113A	ENST00000285398	NM_000122.1	113	gTg/gCg	3/15	1	2	FACETS	0.801	0.7	0.911	0.801	0.7	0.911	CLONAL	1	TRUE	1	0.19	2		623	985	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158627021	158627021	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	95	758	0	ENST00000263640.3:c.649G>T	p.Gly217Cys	p.G217C	ENST00000263640	NM_001105.4	217	Ggc/Tgc	7/11	1	2	FACETS	0.88	0.782	0.986	0.88	0.782	0.986	CLONAL	1	TRUE	1	0.19	2		758	1136	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136245	202136245	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	73	636	0	ENST00000358485.4:c.489G>A	p.Met163Ile	p.M163I	ENST00000358485	NM_001080125.1	163	atG/atA	3/9	1	2	FACETS	0.858	0.748	0.976	0.858	0.748	0.976	CLONAL	1	TRUE	1	0.19	2		636	896	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137422	202137422	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	43	500	0	ENST00000358485.4:c.650A>G	p.Asp217Gly	p.D217G	ENST00000358485	NM_001080125.1	217	gAc/gGc	4/9	1	2	FACETS	0.604	0.504	0.716	0.604	0.504	0.716	SUBCLONAL	1	TRUE	1	0.19	2		500	749	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149658	202149658	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	65	651	2	ENST00000358485.4:c.1099G>T	p.Asp367Tyr	p.D367Y	ENST00000358485	NM_001080125.1	367	Gac/Tac	8/9	1	2	FACETS	0.7	0.605	0.803	0.7	0.605	0.803	SUBCLONAL	1	TRUE	1	0.19	2		653	978	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212495213	212495213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	60	591	0	ENST00000342788.4:c.2053G>A	p.Ala685Thr	p.A685T	ENST00000342788	NM_005235.2	685	Gcc/Acc	17/28	1	2	FACETS	0.73	0.627	0.843	0.73	0.627	0.843	SUBCLONAL	1	TRUE	1	0.19	2		591	865	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645780	215645780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	69	668	1	ENST00000260947.4:c.818G>A	p.Gly273Glu	p.G273E	ENST00000260947	NM_000465.2	273	gGa/gAa	4/11	1	2	FACETS	0.828	0.72	0.946	0.828	0.72	0.946	CLONAL	1	TRUE	1	0.19	2		669	877	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275669	41275669	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764576683	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	70	593	4	ENST00000349496.5:c.1564G>A	p.Ala522Thr	p.A522T	ENST00000349496	NM_001904.3	522	Gca/Aca	10/15	1	2	FACETS	0.772	0.671	0.881	0.772	0.671	0.881	SUBCLONAL	1	TRUE	1	0.19	2		597	955	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723149	49723149	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780890872	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	97	700	2	ENST00000449682.2:c.1267G>A	p.Glu423Lys	p.E423K	ENST00000449682	NM_020998.3	423	Gaa/Aaa	11/18	1	2	FACETS	0.919	0.817	1	0.919	0.817	1	CLONAL	1	TRUE	1	0.19	2		702	1111	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438525	52438525	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	74	598	0	ENST00000460680.1:c.1194G>T	p.Glu398Asp	p.E398D	ENST00000460680	NM_004656.3	398	gaG/gaT	12/17	1	2	FACETS	0.736	0.642	0.837	0.736	0.642	0.837	SUBCLONAL	1	TRUE	1	0.19	2		598	1059	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021790	71021790	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	77	628	0	ENST00000318789.4:c.1568T>G	p.Phe523Cys	p.F523C	ENST00000318789	NM_032682.5	523	tTt/tGt	18/21	1	2	FACETS	0.878	0.769	0.996	0.878	0.769	0.996	CLONAL	1	TRUE	1	0.19	2		628	923	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259089	89259089	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	43	475	0	ENST00000336596.2:c.233A>G	p.Gln78Arg	p.Q78R	ENST00000336596	NM_005233.5	78	cAa/cGa	3/17	1	2	FACETS	0.594	0.496	0.704	0.594	0.496	0.704	SUBCLONAL	1	TRUE	1	0.19	2		475	762	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390072	89390072	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765502894	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	56	530	1	ENST00000336596.2:c.821G>A	p.Arg274Gln	p.R274Q	ENST00000336596	NM_005233.5	274	cGa/cAa	4/17	1	2	FACETS	0.854	0.731	0.99	0.854	0.731	0.99	CLONAL	1	TRUE	1	0.19	2		531	690	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462305	89462305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	43	439	1	ENST00000336596.2:c.1777C>T	p.Leu593Phe	p.L593F	ENST00000336596	NM_005233.5	593	Ctc/Ttc	10/17	1	2	FACETS	0.706	0.59	0.836	0.706	0.59	0.836	SUBCLONAL	1	TRUE	1	0.19	2		440	641	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498447	89498447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	66	606	0	ENST00000336596.2:c.2419G>A	p.Val807Ile	p.V807I	ENST00000336596	NM_005233.5	807	Gta/Ata	14/17	1	2	FACETS	0.769	0.666	0.882	0.769	0.666	0.882	SUBCLONAL	1	TRUE	1	0.19	2		606	903	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205721	128205721	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	79	751	0	ENST00000341105.2:c.154C>A	p.Leu52Ile	p.L52I	ENST00000341105	NM_032638.4	52	Ctc/Atc	2/6	1	2	FACETS	0.724	0.634	0.82	0.724	0.634	0.82	SUBCLONAL	1	TRUE	1	0.19	2		751	1149	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977925	134977925	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	92	779	2	ENST00000398015.3:c.2918G>T	p.Arg973Met	p.R973M	ENST00000398015	NM_004441.4	973	aGg/aTg	16/16	1	2	FACETS	0.987	0.875	1	0.987	0.875	1	CLONAL	1	TRUE	1	0.19	2		781	981	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456643	138456643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	87	814	2	ENST00000289153.2:c.707G>A	p.Gly236Glu	p.G236E	ENST00000289153	NM_006219.2	236	gGg/gAg	4/22	1	2	FACETS	0.949	0.838	1	0.949	0.838	1	CLONAL	1	TRUE	1	0.19	2		816	965	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947119	178947119	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199943173	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	81	548	1	ENST00000263967.3:c.2555G>A	p.Arg852Gln	p.R852Q	ENST00000263967	NM_006218.2	852	cGa/cAa	18/21	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.19	2		549	815	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183609	185183609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	79	601	0	ENST00000265026.3:c.1463C>T	p.Ala488Val	p.A488V	ENST00000265026	NM_004721.4	488	gCc/gTc	9/14	1	2	FACETS	0.869	0.762	0.984	0.869	0.762	0.984	CLONAL	1	TRUE	1	0.19	2		601	957	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801473	1801473	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	58	575	0	ENST00000260795.2:c.380-1G>A		p.X127_splice	ENST00000260795		127			1	2	FACETS	0.786	0.674	0.908	0.786	0.674	0.908	CLONAL	1	TRUE	1	0.19	2		575	777	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55589771	55589771	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	84	577	0	ENST00000288135.5:c.1253A>G	p.Tyr418Cys	p.Y418C	ENST00000288135	NM_000222.2	418	tAc/tGc	8/21	1	2	FACETS	0.984	0.867	1	0.984	0.867	1	CLONAL	1	TRUE	1	0.19	2		577	899	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391389	84391389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760079258	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	83	540	2	ENST00000321945.7:c.443G>A	p.Arg148Gln	p.R148Q	ENST00000321945	NM_139076.2	148	cGa/cAa	5/9	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.19	2		542	714	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244119	153244119	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	60	647	0	ENST00000281708.4:c.2038A>G	p.Thr680Ala	p.T680A	ENST00000281708	NM_033632.3	680	Aca/Gca	12/12	1	2	FACETS	0.601	0.516	0.694	0.601	0.516	0.694	SUBCLONAL	1	TRUE	1	0.19	2		647	1051	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509963	187509963	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	65	544	1	ENST00000441802.2:c.13550C>T	p.Ala4517Val	p.A4517V	ENST00000441802	NM_005245.3	4517	gCc/gTc	27/27	1	2	FACETS	0.82	0.71	0.941	0.82	0.71	0.941	CLONAL	1	TRUE	1	0.19	2		545	834	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187558040	187558040	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746739063	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	40	435	0	ENST00000441802.2:c.3671C>T	p.Pro1224Leu	p.P1224L	ENST00000441802	NM_005245.3	1224	cCc/cTc	5/27	1	2	FACETS	0.799	0.663	0.95	0.799	0.663	0.95	CLONAL	1	TRUE	1	0.19	2		435	527	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187558064	187558064	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	31	371	0	ENST00000441802.2:c.3647C>A	p.Thr1216Asn	p.T1216N	ENST00000441802	NM_005245.3	1216	aCt/aAt	5/27	1	2	FACETS	0.794	0.642	0.966	0.794	0.642	0.966	CLONAL	1	TRUE	1	0.19	2		371	411	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628206	187628206	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	67	510	0	ENST00000441802.2:c.2776A>G	p.Thr926Ala	p.T926A	ENST00000441802	NM_005245.3	926	Aca/Gca	2/27	1	2	FACETS	0.914	0.793	1	0.914	0.793	1	CLONAL	1	TRUE	1	0.19	2		510	772	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628323	187628323	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	43	336	0	ENST00000441802.2:c.2659C>A	p.Leu887Met	p.L887M	ENST00000441802	NM_005245.3	887	Ctg/Atg	2/27	1	2	FACETS	0.724	0.605	0.857	0.724	0.605	0.857	SUBCLONAL	1	TRUE	1	0.19	2		336	625	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224586	224586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	52	534	0	ENST00000264932.6:c.262G>A	p.Ala88Thr	p.A88T	ENST00000264932	NM_004168.2	88	Gca/Aca	3/15	1	2	FACETS	0.588	0.499	0.686	0.588	0.499	0.686	SUBCLONAL	1	TRUE	1	0.19	2		534	931	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1282656	1282656	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749051614	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	76	628	0	ENST00000310581.5:c.1657G>A	p.Val553Ile	p.V553I	ENST00000310581	NM_198253.2	553	Gtc/Atc	3/16	1	2	FACETS	0.768	0.671	0.872	0.768	0.671	0.872	SUBCLONAL	1	TRUE	1	0.19	2		628	1042	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38946647	38946647	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs867802066	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	41	386	0	ENST00000357387.3:c.4322A>G	p.Asp1441Gly	p.D1441G	ENST00000357387	NM_152756.3	1441	gAt/gGt	33/38	1	2	FACETS	0.814	0.678	0.966	0.814	0.678	0.966	CLONAL	1	TRUE	1	0.19	2		386	530	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189422	56189422	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	74	668	0	ENST00000399503.3:c.4454C>T	p.Ala1485Val	p.A1485V	ENST00000399503	NM_005921.1	1485	gCt/gTt	20/20	1	2	FACETS	0.776	0.677	0.883	0.776	0.677	0.883	SUBCLONAL	1	TRUE	1	0.19	2		668	1004	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57750426	57750426	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	64	638	0	ENST00000274289.3:c.2042T>C	p.Leu681Ser	p.L681S	ENST00000274289	NM_006622.3	681	tTa/tCa	14/14	1	2	FACETS	0.735	0.635	0.845	0.735	0.635	0.845	SUBCLONAL	1	TRUE	1	0.19	2		638	916	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590445	67590445	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	70	497	2	ENST00000274335.5:c.1507C>T	p.Arg503Trp	p.R503W	ENST00000274335		503	Cgg/Tgg	11/15	1	2	FACETS	0.928	0.808	1	0.928	0.808	1	CLONAL	1	TRUE	1	0.19	2		499	794	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86628365	86628365	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	56	529	0	ENST00000274376.6:c.734G>A	p.Arg245His	p.R245H	ENST00000274376	NM_002890.2	245	cGt/cAt	3/25	1	2	FACETS	1	0.863	1	1	0.863	1	CLONAL	1	TRUE	1	0.19	2		529	585	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633825	86633825	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	68	628	1	ENST00000274376.6:c.934G>T	p.Glu312Ter	p.E312*	ENST00000274376	NM_002890.2	312	Gaa/Taa	5/25	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.19	2		629	622	SUCCESS
APC	324	MSKCC	GRCh37	5	112177045	112177045	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1294277674	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	113	886	0	ENST00000257430.4:c.5754A>G	p.Ile1918Met	p.I1918M	ENST00000257430	NM_000038.5	1918	atA/atG	16/16	1	2	FACETS	0.962	0.863	1	0.962	0.863	1	CLONAL	1	TRUE	1	0.19	2		886	1236	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131939138	131939138	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754508700	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	68	582	1	ENST00000265335.6:c.2354C>T	p.Ala785Val	p.A785V	ENST00000265335		785	gCc/gTc	14/25	1	2	FACETS	0.858	0.745	0.981	0.858	0.745	0.981	CLONAL	1	TRUE	1	0.19	2		583	834	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520201	176520201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368558499	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	57	607	2	ENST00000292408.4:c.1120G>A	p.Ala374Thr	p.A374T	ENST00000292408	NM_213647.1	374	Gcg/Acg	9/18	1	2	FACETS	0.685	0.586	0.794	0.685	0.586	0.794	SUBCLONAL	1	TRUE	1	0.19	2		609	876	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707645	176707645	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	57	504	0	ENST00000439151.2:c.5702A>G	p.Asp1901Gly	p.D1901G	ENST00000439151	NM_022455.4	1901	gAt/gGt	18/23	1	2	FACETS	0.715	0.612	0.828	0.715	0.612	0.828	SUBCLONAL	1	TRUE	1	0.19	2		504	839	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41908248	41908248	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	64	529	2	ENST00000372991.4:c.274G>A	p.Val92Ile	p.V92I	ENST00000372991	NM_001760.3	92	Gtc/Atc	2/5	1	2	FACETS	0.749	0.647	0.861	0.749	0.647	0.861	SUBCLONAL	1	TRUE	1	0.19	2		531	899	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793605	89793605	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	72	472	0	ENST00000336032.3:c.674T>C	p.Ile225Thr	p.I225T	ENST00000336032	NM_006813.2	225	aTc/aCc	2/2	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.19	2		472	651	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106547235	106547235	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	34	386	0	ENST00000369096.4:c.472T>G	p.Trp158Gly	p.W158G	ENST00000369096	NM_001198.3	158	Tgg/Ggg	4/7	1	2	FACETS	0.561	0.457	0.679	0.561	0.457	0.679	SUBCLONAL	1	TRUE	1	0.19	2		386	638	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715794	117715794	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	65	563	0	ENST00000368508.3:c.964T>C	p.Tyr322His	p.Y322H	ENST00000368508	NM_002944.2	322	Tac/Cac	9/43	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.19	2		563	605	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137525500	137525500	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	853	109	765	0	ENST00000367739.4:c.515A>G	p.Tyr172Cys	p.Y172C	ENST00000367739	NM_000416.2	172	tAc/tGc	4/7	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.19	2		765	962	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975484	13975484	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	29	345	0	ENST00000405192.2:c.403T>C	p.Ser135Pro	p.S135P	ENST00000405192	NM_001163147.1	135	Tcc/Ccc	7/12	1	2	FACETS	0.539	0.432	0.662	0.539	0.432	0.662	SUBCLONAL	1	TRUE	1	0.19	2		345	566	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494170	140494170	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	86	688	3	ENST00000288602.6:c.1078C>T	p.Arg360Ter	p.R360*	ENST00000288602	NM_004333.4	360	Cga/Tga	8/18	1	2	FACETS	0.946	0.835	1	0.946	0.835	1	CLONAL	1	TRUE	1	0.19	2		691	957	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836296	151836296	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771641625	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	58	392	1	ENST00000262189.6:c.14509G>A	p.Ala4837Thr	p.A4837T	ENST00000262189	NM_170606.2	4837	Gcg/Acg	57/59	1	2	FACETS	0.855	0.734	0.988	0.855	0.734	0.988	CLONAL	1	TRUE	1	0.19	2		393	714	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845355	151845355	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	61	503	0	ENST00000262189.6:c.13657C>T	p.Leu4553Phe	p.L4553F	ENST00000262189	NM_170606.2	4553	Ctc/Ttc	52/59	1	2	FACETS	0.809	0.696	0.932	0.809	0.696	0.932	CLONAL	1	TRUE	1	0.19	2		503	794	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152132842	152132842	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	37	552	0	ENST00000262189.6:c.30G>T	p.Glu10Asp	p.E10D	ENST00000262189	NM_170606.2	10	gaG/gaT	1/59	1	2	FACETS	0.537	0.441	0.645	0.537	0.441	0.645	SUBCLONAL	1	TRUE	1	0.19	2		552	725	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341730	8341730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41281783	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	96	713	3	ENST00000356435.5:c.4910C>T	p.Thr1637Met	p.T1637M	ENST00000356435		1637	aCg/aTg	29/35	1	2	FACETS	0.905	0.805	1	0.905	0.805	1	CLONAL	1	TRUE	1	0.19	2		716	1116	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376624	8376624	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	85	648	0	ENST00000356435.5:c.4489A>G	p.Thr1497Ala	p.T1497A	ENST00000356435		1497	Aca/Gca	27/35	1	2	FACETS	0.932	0.822	1	0.932	0.822	1	CLONAL	1	TRUE	1	0.19	2		648	960	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239048	98239048	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	86	519	0	ENST00000331920.6:c.1595C>T	p.Pro532Leu	p.P532L	ENST00000331920	NM_000264.3	532	cCt/cTt	11/24	1	2	FACETS	0.973	0.859	1	0.973	0.859	1	CLONAL	1	TRUE	1	0.19	2		519	930	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400035	139400035	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61751541	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	60	598	0	ENST00000277541.6:c.4313G>A	p.Arg1438His	p.R1438H	ENST00000277541	NM_017617.3	1438	cGc/cAc	25/34	1	2	FACETS	0.632	0.542	0.729	0.632	0.542	0.729	SUBCLONAL	1	TRUE	1	0.19	2		598	1000	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400303	139400303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs553328686	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	26	205	0	ENST00000277541.6:c.4045G>A	p.Ala1349Thr	p.A1349T	ENST00000277541	NM_017617.3	1349	Gct/Act	25/34	1	2	FACETS	0.999	0.793	1	0.999	0.793	1	CLONAL	1	TRUE	1	0.19	2		205	274	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405624	139405624	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	56	701	1	ENST00000277541.6:c.2567T>C	p.Val856Ala	p.V856A	ENST00000277541	NM_017617.3	856	gTc/gCc	16/34	1	2	FACETS	0.57	0.487	0.662	0.57	0.487	0.662	SUBCLONAL	1	TRUE	1	0.19	2		702	1034	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411801	139411801	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	94	707	0	ENST00000277541.6:c.1478A>G	p.Glu493Gly	p.E493G	ENST00000277541	NM_017617.3	493	gAg/gGg	9/34	1	2	FACETS	0.834	0.74	0.935	0.834	0.74	0.935	CLONAL	1	TRUE	1	0.19	2		707	1186	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106003	8106003	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	44	481	1	ENST00000346208.3:c.823C>T	p.Arg275Trp	p.R275W	ENST00000346208		275	Cgg/Tgg	4/6	1	2	FACETS	0.609	0.509	0.72	0.609	0.509	0.72	SUBCLONAL	1	TRUE	1	0.19	2		482	761	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333885	70333885	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	56	462	0	ENST00000373644.4:c.1790G>A	p.Cys597Tyr	p.C597Y	ENST00000373644	NM_030625.2	597	tGc/tAc	2/12	1	2	FACETS	0.863	0.738	1	0.863	0.738	1	CLONAL	1	TRUE	1	0.19	2		462	683	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910798	114910798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs951950988	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1443	84	1074	2	ENST00000543371.1:c.917C>T	p.Thr306Met	p.T306M	ENST00000543371	NM_001198531.1	306	aCg/aTg	9/14	1	2	FACETS	0.579	0.509	0.655	0.579	0.509	0.655	SUBCLONAL	1	TRUE	1	0.19	2		1076	1527	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123274752	123274752	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1329578117	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	72	685	2	ENST00000358487.5:c.1166C>T	p.Ala389Val	p.A389V	ENST00000358487	NM_000141.4	389	gCc/gTc	9/18	1	2	FACETS	0.756	0.659	0.862	0.756	0.659	0.862	SUBCLONAL	1	TRUE	1	0.19	2		687	1002	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69458697	69458697	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1373641771	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	123	678	1	ENST00000227507.2:c.512C>T	p.Ala171Val	p.A171V	ENST00000227507	NM_053056.2	171	gCg/gTg	3/5	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.19	2		679	1206	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588824	69588824	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781699363	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	83	708	2	ENST00000168712.1:c.412G>A	p.Ala138Thr	p.A138T	ENST00000168712	NM_002007.2	138	Gcc/Acc	2/3	1	2	FACETS	0.902	0.794	1	0.902	0.794	1	CLONAL	1	TRUE	1	0.19	2		710	969	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115753	108115753	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	38	265	0	ENST00000278616.4:c.901G>T	p.Gly301Cys	p.G301C	ENST00000278616	NM_000051.3	301	Ggt/Tgt	7/63	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.19	2		265	301	SUCCESS
ATM	472	MSKCC	GRCh37	11	108196951	108196951	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs200940211	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	50	377	0	ENST00000278616.4:c.6974C>T	p.Ala2325Val	p.A2325V	ENST00000278616	NM_000051.3	2325	gCg/gTg	47/63	1	2	FACETS	0.813	0.689	0.95	0.813	0.689	0.95	CLONAL	1	TRUE	1	0.19	2		377	647	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374394	118374394	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs781809969	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	74	643	0	ENST00000534358.1:c.7787T>C	p.Val2596Ala	p.V2596A	ENST00000534358	NM_005933.3	2596	gTa/gCa	27/36	1	2	FACETS	0.895	0.782	1	0.895	0.782	1	CLONAL	1	TRUE	1	0.19	2		643	870	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374740	118374740	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	65	626	0	ENST00000534358.1:c.8133G>T	p.Gln2711His	p.Q2711H	ENST00000534358	NM_005933.3	2711	caG/caT	27/36	1	2	FACETS	0.71	0.614	0.816	0.71	0.614	0.816	SUBCLONAL	1	TRUE	1	0.19	2		626	963	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375201	118375201	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	49	571	0	ENST00000534358.1:c.8594C>T	p.Ala2865Val	p.A2865V	ENST00000534358	NM_005933.3	2865	gCt/gTt	27/36	1	2	FACETS	0.647	0.547	0.758	0.647	0.547	0.758	SUBCLONAL	1	TRUE	1	0.19	2		571	797	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125497566	125497566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771939046	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	48	260	0	ENST00000428830.2:c.130C>T	p.Arg44Cys	p.R44C	ENST00000428830	NM_001114121.2	44	Cgt/Tgt	3/14	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.19	2		260	377	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11992143	11992143	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	55	525	0	ENST00000396373.4:c.233C>T	p.Ser78Phe	p.S78F	ENST00000396373	NM_001987.4	78	tCt/tTt	3/8	1	2	FACETS	0.629	0.536	0.731	0.629	0.536	0.731	SUBCLONAL	1	TRUE	1	0.19	2		525	921	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230719	46230719	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	71	652	0	ENST00000334344.6:c.968A>G	p.His323Arg	p.H323R	ENST00000334344	NM_152641.2	323	cAt/cGt	8/21	1	2	FACETS	0.875	0.762	0.997	0.875	0.762	0.997	CLONAL	1	TRUE	1	0.19	2		652	854	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242652	46242652	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	51	418	0	ENST00000334344.6:c.1614T>G	p.Cys538Trp	p.C538W	ENST00000334344	NM_152641.2	538	tgT/tgG	13/21	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.19	2		418	476	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425454	49425454	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	77	865	0	ENST00000301067.7:c.13034A>C	p.Lys4345Thr	p.K4345T	ENST00000301067	NM_003482.3	4345	aAa/aCa	39/54	1	2	FACETS	0.73	0.638	0.828	0.73	0.638	0.828	SUBCLONAL	1	TRUE	1	0.19	2		865	1111	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425534	49425534	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1306	90	1009	0	ENST00000301067.7:c.12954G>T	p.Lys4318Asn	p.K4318N	ENST00000301067	NM_003482.3	4318	aaG/aaT	39/54	1	2	FACETS	0.679	0.6	0.764	0.679	0.6	0.764	SUBCLONAL	1	TRUE	1	0.19	2		1009	1396	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431915	49431915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	51	596	0	ENST00000301067.7:c.9224C>T	p.Ser3075Leu	p.S3075L	ENST00000301067	NM_003482.3	3075	tCg/tTg	34/54	1	2	FACETS	0.643	0.545	0.751	0.643	0.545	0.751	SUBCLONAL	1	TRUE	1	0.19	2		596	835	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447304	49447304	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201231484	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	57	589	2	ENST00000301067.7:c.794G>A	p.Arg265His	p.R265H	ENST00000301067	NM_003482.3	265	cGt/cAt	6/54	1	2	FACETS	0.585	0.5	0.678	0.585	0.5	0.678	SUBCLONAL	1	TRUE	1	0.19	2		591	1026	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863395	57863395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775171324	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	102	933	3	ENST00000228682.2:c.1490G>A	p.Arg497His	p.R497H	ENST00000228682	NM_005269.2	497	cGc/cAc	11/12	1	2	FACETS	0.887	0.791	0.99	0.887	0.791	0.99	CLONAL	1	TRUE	1	0.19	2		936	1210	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869493	102869493	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	44	348	0	ENST00000307046.8:c.148C>T	p.Pro50Ser	p.P50S	ENST00000307046	NM_001111285.1	50	Ccg/Tcg	2/4	1	2	FACETS	0.859	0.72	1	0.859	0.72	1	CLONAL	1	TRUE	1	0.19	2		348	539	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891064	112891064	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	57	476	1	ENST00000351677.2:c.398G>A	p.Gly133Asp	p.G133D	ENST00000351677	NM_002834.3	133	gGt/gAt	4/16	1	2	FACETS	0.832	0.713	0.963	0.832	0.713	0.963	CLONAL	1	TRUE	1	0.19	2		477	721	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115115419	115115419	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	64	795	0	ENST00000257566.3:c.907T>G	p.Phe303Val	p.F303V	ENST00000257566	NM_016569.3	303	Ttc/Gtc	5/8	1	2	FACETS	0.543	0.468	0.625	0.543	0.468	0.625	SUBCLONAL	1	TRUE	1	0.19	2		795	1240	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117745	115117745	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	51	674	2	ENST00000257566.3:c.690G>A	p.Trp230Ter	p.W230*	ENST00000257566	NM_016569.3	230	tgG/tgA	3/8	1	2	FACETS	0.553	0.469	0.647	0.553	0.469	0.647	SUBCLONAL	1	TRUE	1	0.19	2		676	970	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120536842	120536842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751790181	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	89	793	2	ENST00000229340.5:c.344G>A	p.Arg115Gln	p.R115Q	ENST00000229340	NM_006861.6	115	cGa/cAa	4/6	1	2	FACETS	0.795	0.703	0.895	0.795	0.703	0.895	SUBCLONAL	1	TRUE	1	0.19	2		795	1178	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218828	133218828	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs961736994	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	63	623	0	ENST00000320574.5:c.5108G>A	p.Cys1703Tyr	p.C1703Y	ENST00000320574	NM_006231.2	1703	tGt/tAt	38/49	1	2	FACETS	0.661	0.57	0.761	0.661	0.57	0.761	SUBCLONAL	1	TRUE	1	0.19	2		623	1003	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226444	133226444	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772686048	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	71	536	0	ENST00000320574.5:c.3614C>T	p.Pro1205Leu	p.P1205L	ENST00000320574	NM_006231.2	1205	cCg/cTg	30/49	1	2	FACETS	0.847	0.738	0.966	0.847	0.738	0.966	CLONAL	1	TRUE	1	0.19	2		536	882	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26923286	26923286	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	89	685	0	ENST00000381527.3:c.282G>A	p.Trp94Ter	p.W94*	ENST00000381527	NM_001260.1	94	tgG/tgA	3/13	1	2	FACETS	0.88	0.779	0.99	0.88	0.779	0.99	CLONAL	1	TRUE	1	0.19	2		685	1064	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28626733	28626733	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	80	682	1	ENST00000241453.7:c.563G>T	p.Ser188Ile	p.S188I	ENST00000241453	NM_004119.2	188	aGc/aTc	5/24	1	2	FACETS	0.752	0.66	0.851	0.752	0.66	0.851	SUBCLONAL	1	TRUE	1	0.19	2		683	1120	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911312	32911312	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1080	87	1028	0	ENST00000380152.3:c.2820A>C	p.Gln940His	p.Q940H	ENST00000380152		940	caA/caC	11/27	1	2	FACETS	0.785	0.692	0.884	0.785	0.692	0.884	SUBCLONAL	1	TRUE	1	0.19	2		1028	1167	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436081	110436081	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	54	589	0	ENST00000375856.3:c.2320G>A	p.Ala774Thr	p.A774T	ENST00000375856	NM_003749.2	774	Gcg/Acg	1/2	1	2	FACETS	0.585	0.498	0.681	0.585	0.498	0.681	SUBCLONAL	1	TRUE	1	0.19	2		589	972	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610002	81610002	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150602845	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	58	384	3	ENST00000298171.2:c.1600C>T	p.Arg534Cys	p.R534C	ENST00000298171	NM_000369.2	534	Cgc/Tgc	10/10	1	2	FACETS	0.949	0.815	1	0.949	0.815	1	CLONAL	1	TRUE	1	0.19	2		387	643	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95574047	95574047	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	56	412	0	ENST00000393063.1:c.2702A>T	p.Glu901Val	p.E901V	ENST00000393063	NM_030621.3	901	gAg/gTg	18/28	1	2	FACETS	0.982	0.841	1	0.982	0.841	1	CLONAL	1	TRUE	1	0.19	2		412	600	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961741	41961741	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1294	115	1003	2	ENST00000219905.7:c.649C>T	p.Gln217Ter	p.Q217*	ENST00000219905	NM_001164273.1	217	Caa/Taa	2/24	1	2	FACETS	0.859	0.771	0.953	0.859	0.771	0.953	CLONAL	1	TRUE	1	0.19	2		1005	1409	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988517	41988517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1334889318	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1322	93	1011	1	ENST00000219905.7:c.1309G>A	p.Glu437Lys	p.E437K	ENST00000219905	NM_001164273.1	437	Gaa/Aaa	3/24	1	2	FACETS	0.692	0.613	0.777	0.692	0.613	0.777	SUBCLONAL	1	TRUE	1	0.19	2		1012	1415	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477106	67477106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1348033858	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	68	659	1	ENST00000327367.4:c.913G>A	p.Ala305Thr	p.A305T	ENST00000327367	NM_005902.3	305	Gca/Aca	7/9	1	2	FACETS	0.654	0.567	0.749	0.654	0.567	0.749	SUBCLONAL	1	TRUE	1	0.19	2		660	1094	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88690572	88690572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs546426782	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	50	581	0	ENST00000360948.2:c.458G>A	p.Arg153Gln	p.R153Q	ENST00000360948	NM_001012338.2	153	cGg/cAg	5/19	1	2	FACETS	0.551	0.466	0.646	0.551	0.466	0.646	SUBCLONAL	1	TRUE	1	0.19	2		581	955	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900734	3900734	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	35	352	0	ENST00000262367.5:c.362G>T	p.Ser121Ile	p.S121I	ENST00000262367	NM_004380.2	121	aGc/aTc	2/31	1	2	FACETS	0.686	0.561	0.826	0.686	0.561	0.826	SUBCLONAL	1	TRUE	1	0.19	2		352	537	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032000	10032000	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1131	108	866	1	ENST00000330684.3:c.823G>A	p.Gly275Arg	p.G275R	ENST00000330684	NM_001134407.1	275	Gga/Aga	3/13	1	2	FACETS	0.918	0.821	1	0.918	0.821	1	CLONAL	1	TRUE	1	0.19	2		867	1239	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273944	10273944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	86	806	0	ENST00000330684.3:c.325G>A	p.Val109Ile	p.V109I	ENST00000330684	NM_001134407.1	109	Gta/Ata	2/13	1	2	FACETS	0.734	0.647	0.828	0.734	0.647	0.828	SUBCLONAL	1	TRUE	1	0.19	2		806	1233	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14020496	14020496	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	89	639	0	ENST00000311895.7:c.467A>G	p.Asn156Ser	p.N156S	ENST00000311895	NM_005236.2	156	aAc/aGc	3/11	1	2	FACETS	0.9	0.796	1	0.9	0.796	1	CLONAL	1	TRUE	1	0.19	2		639	1041	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81902892	81902892	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1288	86	844	0	ENST00000359376.3:c.553G>T	p.Asp185Tyr	p.D185Y	ENST00000359376	NM_002661.3	185	Gat/Tat	6/33	1	2	FACETS	0.659	0.58	0.743	0.659	0.58	0.743	SUBCLONAL	1	TRUE	1	0.19	2		844	1374	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81968073	81968073	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1336	73	928	3	ENST00000359376.3:c.2779G>A	p.Ala927Thr	p.A927T	ENST00000359376	NM_002661.3	927	Gcc/Acc	26/33	1	2	FACETS	0.545	0.475	0.622	0.545	0.475	0.622	SUBCLONAL	1	TRUE	1	0.19	2		931	1409	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942780	15942780	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1110	74	842	1	ENST00000268712.3:c.6922C>T	p.Arg2308Ter	p.R2308*	ENST00000268712	NM_006311.3	2308	Cga/Tga	44/46	1	2	FACETS	0.658	0.574	0.749	0.658	0.574	0.749	SUBCLONAL	1	TRUE	1	0.19	2		843	1184	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15950263	15950263	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	93	724	0	ENST00000268712.3:c.6679+2T>C		p.X2227_splice	ENST00000268712	NM_006311.3	2227			1	2	FACETS	0.964	0.855	1	0.964	0.855	1	CLONAL	1	TRUE	1	0.19	2		724	1016	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435252	56435252	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs538022572	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	30	258	1	ENST00000407977.2:c.1885G>A	p.Ala629Thr	p.A629T	ENST00000407977		629	Gcc/Acc	9/10	1	2	FACETS	0.831	0.67	1	0.831	0.67	1	CLONAL	1	TRUE	1	0.19	2		259	380	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438142	56438142	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	79	783	0	ENST00000407977.2:c.849+2T>C		p.X283_splice	ENST00000407977		283			1	2	FACETS	0.785	0.689	0.89	0.785	0.689	0.89	SUBCLONAL	1	TRUE	1	0.19	2		783	1059	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876485	59876485	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753214212	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	84	562	0	ENST00000259008.2:c.1316G>A	p.Arg439Gln	p.R439Q	ENST00000259008	NM_032043.2	439	cGa/cAa	9/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.19	2		562	767	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59926510	59926510	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064795902	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	62	627	0	ENST00000259008.2:c.487C>T	p.Pro163Ser	p.P163S	ENST00000259008	NM_032043.2	163	Ccc/Tcc	5/20	1	2	FACETS	0.758	0.653	0.873	0.758	0.653	0.873	SUBCLONAL	1	TRUE	1	0.19	2		627	861	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007580	62007580	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778771873	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	95	789	1	ENST00000392795.3:c.287G>A	p.Arg96His	p.R96H	ENST00000392795	NM_001039933.1	96	cGc/cAc	3/6	1	2	FACETS	0.926	0.822	1	0.926	0.822	1	CLONAL	1	TRUE	1	0.19	2		790	1080	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39647367	39647367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373107502	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	67	671	0	ENST00000262039.4:c.2539C>T	p.Arg847Cys	p.R847C	ENST00000262039	NM_002647.2	847	Cgc/Tgc	24/25	1	2	FACETS	0.702	0.609	0.805	0.702	0.609	0.805	SUBCLONAL	1	TRUE	1	0.19	2		671	1004	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604809	48604809	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	60	541	2	ENST00000342988.3:c.1631C>T	p.Pro544Leu	p.P544L	ENST00000342988	NM_005359.5	544	cCg/cTg	12/12	1	2	FACETS	0.766	0.658	0.883	0.766	0.658	0.883	SUBCLONAL	1	TRUE	1	0.19	2		543	825	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56376660	56376660	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs748542076	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1261	107	926	0	ENST00000348428.3:c.700A>G	p.Thr234Ala	p.T234A	ENST00000348428	NM_006785.3	234	Act/Gct	5/17	1	2	FACETS	0.823	0.736	0.917	0.823	0.736	0.917	CLONAL	1	TRUE	1	0.19	2		926	1368	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220595	1220595	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881981	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	59	593	0	ENST00000326873.7:c.613G>A	p.Ala205Thr	p.A205T	ENST00000326873	NM_000455.4	205	Gcg/Acg	5/10	1	2	FACETS	0.711	0.61	0.821	0.711	0.61	0.821	SUBCLONAL	1	TRUE	1	0.19	2		593	874	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132181	7132181	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753371466	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1019	72	643	2	ENST00000302850.5:c.2830G>A	p.Val944Met	p.V944M	ENST00000302850	NM_000208.2	944	Gtg/Atg	14/22	1	2	FACETS	0.695	0.605	0.792	0.695	0.605	0.792	SUBCLONAL	1	TRUE	1	0.19	2		645	1091	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184559	7184559	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773115239	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	37	283	0	ENST00000302850.5:c.742G>A	p.Asp248Asn	p.D248N	ENST00000302850	NM_000208.2	248	Gac/Aac	3/22	1	2	FACETS	0.711	0.585	0.852	0.711	0.585	0.852	SUBCLONAL	1	TRUE	1	0.19	2		283	548	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267491	7267491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	87	674	3	ENST00000302850.5:c.517G>A	p.Val173Met	p.V173M	ENST00000302850	NM_000208.2	173	Gtg/Atg	2/22	1	2	FACETS	0.757	0.668	0.853	0.757	0.668	0.853	SUBCLONAL	1	TRUE	1	0.19	2		677	1210	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265723	10265723	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	87	726	0	ENST00000340748.4:c.1454A>G	p.Glu485Gly	p.E485G	ENST00000340748		485	gAa/gGa	19/40	1	2	FACETS	0.823	0.726	0.927	0.823	0.726	0.927	CLONAL	1	TRUE	1	0.19	2		726	1113	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145690	11145690	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	88	612	0	ENST00000358026.2:c.4052A>G	p.Asp1351Gly	p.D1351G	ENST00000358026	NM_001128849.1	1351	gAc/gGc	29/36	1	2	FACETS	0.906	0.801	1	0.906	0.801	1	CLONAL	1	TRUE	1	0.19	2		612	1022	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051453	13051453	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1362	101	980	1	ENST00000316448.5:c.801G>T	p.Gln267His	p.Q267H	ENST00000316448	NM_004343.3	267	caG/caT	6/9	1	2	FACETS	0.727	0.647	0.812	0.727	0.647	0.812	SUBCLONAL	1	TRUE	1	0.19	2		981	1463	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14628999	14628999	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	105	789	1	ENST00000254322.2:c.163C>A	p.Leu55Ile	p.L55I	ENST00000254322	NM_006145.1	55	Ctc/Atc	1/3	1	2	FACETS	0.913	0.815	1	0.913	0.815	1	CLONAL	1	TRUE	1	0.19	2		790	1211	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308375	15308375	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142031490	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	69	622	0	ENST00000263388.2:c.133G>A	p.Asp45Asn	p.D45N	ENST00000263388	NM_000435.2	45	Gac/Aac	2/33	1	2	FACETS	0.725	0.629	0.829	0.725	0.629	0.829	SUBCLONAL	1	TRUE	1	0.19	2		622	1002	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349933	15349933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	43	448	0	ENST00000263377.2:c.3719C>T	p.Ala1240Val	p.A1240V	ENST00000263377	NM_058243.2	1240	gCc/gTc	18/20	1	2	FACETS	0.586	0.489	0.695	0.586	0.489	0.695	SUBCLONAL	1	TRUE	1	0.19	2		448	772	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17941356	17941356	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1407021823	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	60	481	0	ENST00000458235.1:c.3052T>C	p.Tyr1018His	p.Y1018H	ENST00000458235	NM_000215.3	1018	Tac/Cac	22/24	1	2	FACETS	0.788	0.678	0.909	0.788	0.678	0.909	CLONAL	1	TRUE	1	0.19	2		481	801	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18278092	18278092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	76	610	0	ENST00000222254.8:c.1712G>A	p.Arg571His	p.R571H	ENST00000222254	NM_005027.3	571	cGc/cAc	13/16	1	2	FACETS	0.804	0.703	0.913	0.804	0.703	0.913	CLONAL	1	TRUE	1	0.19	2		610	995	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260070	19260070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	83	552	1	ENST00000162023.5:c.223C>T	p.Pro75Ser	p.P75S	ENST00000162023		75	Ccc/Tcc	7/13	1	2	FACETS	0.815	0.717	0.921	0.815	0.717	0.921	CLONAL	1	TRUE	1	0.19	2		553	1072	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872372	45872372	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1360631927	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	78	715	2	ENST00000391945.4:c.139G>A	p.Gly47Arg	p.G47R	ENST00000391945	NM_000400.3	47	Ggg/Agg	3/23	1	2	FACETS	0.764	0.669	0.866	0.764	0.669	0.866	SUBCLONAL	1	TRUE	1	0.19	2		717	1075	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905951	50905951	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1060501823	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1133	107	837	1	ENST00000440232.2:c.923C>T	p.Ala308Val	p.A308V	ENST00000440232	NM_002691.3	308	gCg/gTg	8/27	1	2	FACETS	0.908	0.812	1	0.908	0.812	1	CLONAL	1	TRUE	1	0.19	2		838	1240	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520141	9520141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560752200	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	71	576	1	ENST00000353224.5:c.2128G>A	p.Val710Ile	p.V710I	ENST00000353224	NM_177990.2	710	Gtc/Atc	10/10	1	2	FACETS	0.788	0.686	0.899	0.788	0.686	0.899	SUBCLONAL	1	TRUE	1	0.19	2		577	948	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022547	31022547	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	51	493	0	ENST00000375687.4:c.2032A>G	p.Arg678Gly	p.R678G	ENST00000375687	NM_015338.5	678	Agg/Ggg	13/13	1	2	FACETS	0.759	0.644	0.886	0.759	0.644	0.886	SUBCLONAL	1	TRUE	1	0.19	2		493	707	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742763	39742763	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	84	753	1	ENST00000361337.2:c.1606A>G	p.Arg536Gly	p.R536G	ENST00000361337	NM_003286.2	536	Aga/Gga	15/21	1	2	FACETS	0.749	0.659	0.845	0.749	0.659	0.845	SUBCLONAL	1	TRUE	1	0.19	2		754	1181	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710554	40710554	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746059787	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	65	558	1	ENST00000373198.4:c.4297C>T	p.Arg1433Cys	p.R1433C	ENST00000373198	NM_133170.3	1433	Cgt/Tgt	31/32	1	2	FACETS	0.863	0.747	0.989	0.863	0.747	0.989	CLONAL	1	TRUE	1	0.19	2		559	793	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385222	41385222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	74	645	0	ENST00000373198.4:c.739C>T	p.Arg247Cys	p.R247C	ENST00000373198	NM_133170.3	247	Cgc/Tgc	6/32	1	2	FACETS	0.761	0.665	0.866	0.761	0.665	0.866	SUBCLONAL	1	TRUE	1	0.19	2		645	1023	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41400186	41400186	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	36	463	0	ENST00000373198.4:c.573A>C	p.Lys191Asn	p.K191N	ENST00000373198	NM_133170.3	191	aaA/aaC	5/32	1	2	FACETS	0.574	0.471	0.691	0.574	0.471	0.691	SUBCLONAL	1	TRUE	1	0.19	2		463	660	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256409	46256409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754382773	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1200	124	940	1	ENST00000371998.3:c.637G>A	p.Ala213Thr	p.A213T	ENST00000371998		213	Gcc/Acc	7/23	1	2	FACETS	0.986	0.889	1	0.986	0.889	1	CLONAL	1	TRUE	1	0.19	2		941	1324	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945543	54945543	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs774552788	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	83	659	0	ENST00000312783.6:c.1027C>T	p.Arg343Trp	p.R343W	ENST00000312783	NM_198436.1	343	Cgg/Tgg	9/10	1	2	FACETS	0.88	0.775	0.993	0.88	0.775	0.993	CLONAL	1	TRUE	1	0.19	2		659	993	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948585	54948585	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	59	595	0	ENST00000312783.6:c.733T>C	p.Ser245Pro	p.S245P	ENST00000312783	NM_198436.1	245	Tct/Cct	8/10	1	2	FACETS	0.89	0.765	1	0.89	0.765	1	CLONAL	1	TRUE	1	0.19	2		595	698	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54961466	54961466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375420005	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	35	256	0	ENST00000312783.6:c.166C>T	p.Arg56Cys	p.R56C	ENST00000312783	NM_198436.1	56	Cgc/Tgc	4/10	1	2	FACETS	0.711	0.582	0.857	0.711	0.582	0.857	SUBCLONAL	1	TRUE	1	0.19	2		256	518	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42848513	42848513	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762108701	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	80	762	1	ENST00000398585.3:c.829C>T	p.Arg277Cys	p.R277C	ENST00000398585	NM_001135099.1	277	Cgc/Tgc	8/14	1	2	FACETS	0.807	0.708	0.913	0.807	0.708	0.913	CLONAL	1	TRUE	1	0.19	2		763	1044	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922175	39922175	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1427	125	889	2	ENST00000378444.4:c.3997C>A	p.Leu1333Met	p.L1333M	ENST00000378444	NM_001123385.1	1333	Ctg/Atg	9/15	1	2	FACETS	0.848	0.764	0.937	0.848	0.764	0.937	CLONAL	1	TRUE	1	0.19	2		891	1552	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030475	47030475	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782595848	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1208	79	718	3	ENST00000377604.3:c.250C>T	p.Arg84Trp	p.R84W	ENST00000377604	NM_001204468.1	84	Cgg/Tgg	4/24	1	2	FACETS	0.646	0.566	0.733	0.646	0.566	0.733	SUBCLONAL	1	TRUE	1	0.19	2		721	1287	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045552	47045552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	70	447	0	ENST00000377604.3:c.2519G>A	p.Gly840Asp	p.G840D	ENST00000377604	NM_001204468.1	840	gGc/gAc	22/24	1	2	FACETS	0.975	0.849	1	0.975	0.849	1	CLONAL	1	TRUE	1	0.19	2		447	756	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428973	47428973	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1282	176	879	2	ENST00000377045.4:c.1336G>A	p.Gly446Ser	p.G446S	ENST00000377045	NM_001654.4	446	Ggt/Agt	13/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.19	2		881	1458	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222456	53222456	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	137	644	0	ENST00000375401.3:c.4376G>A	p.Arg1459Gln	p.R1459Q	ENST00000375401	NM_004187.3	1459	cGg/cAg	26/26	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.19	2		644	986	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223601	53223601	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	100	428	0	ENST00000375401.3:c.3758C>T	p.Pro1253Leu	p.P1253L	ENST00000375401	NM_004187.3	1253	cCg/cTg	23/26	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.19	2		428	765	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230914	53230914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	46	518	0	ENST00000375401.3:c.1879C>T	p.Arg627Cys	p.R627C	ENST00000375401	NM_004187.3	627	Cgc/Tgc	14/26	1	2	FACETS	0.579	0.486	0.683	0.579	0.486	0.683	SUBCLONAL	1	TRUE	1	0.19	2		518	836	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53244991	53244991	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1372	108	910	0	ENST00000375401.3:c.949A>C	p.Ser317Arg	p.S317R	ENST00000375401	NM_004187.3	317	Agc/Cgc	7/26	1	2	FACETS	0.768	0.687	0.855	0.768	0.687	0.855	SUBCLONAL	1	TRUE	1	0.19	2		910	1480	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345283	70345283	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	111	738	2	ENST00000374080.3:c.2309C>T	p.Ala770Val	p.A770V	ENST00000374080		770	gCc/gTc	16/45	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.19	2		740	1152	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829740	76829740	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	98	897	0	ENST00000373344.5:c.6301G>T	p.Glu2101Ter	p.E2101*	ENST00000373344	NM_000489.3	2101	Gaa/Taa	28/35	1	2	FACETS	0.984	0.876	1	0.984	0.876	1	CLONAL	1	TRUE	1	0.19	2		897	1048	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76874395	76874395	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	75	812	1	ENST00000373344.5:c.5327T>A	p.Phe1776Tyr	p.F1776Y	ENST00000373344	NM_000489.3	1776	tTc/tAc	21/35	1	2	FACETS	0.959	0.839	1	0.959	0.839	1	CLONAL	1	TRUE	1	0.19	2		813	823	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889062	76889062	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	86	833	0	ENST00000373344.5:c.4948A>G	p.Lys1650Glu	p.K1650E	ENST00000373344	NM_000489.3	1650	Aag/Gag	18/35	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.19	2		833	878	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938830	76938830	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	92	819	2	ENST00000373344.5:c.1918G>A	p.Val640Ile	p.V640I	ENST00000373344	NM_000489.3	640	Gtt/Att	9/35	1	2	FACETS	0.867	0.768	0.973	0.867	0.768	0.973	CLONAL	1	TRUE	1	0.19	2		821	1117	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938967	76938967	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782774889	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	106	972	0	ENST00000373344.5:c.1781C>T	p.Ser594Phe	p.S594F	ENST00000373344	NM_000489.3	594	tCc/tTc	9/35	1	2	FACETS	0.892	0.797	0.993	0.892	0.797	0.993	CLONAL	1	TRUE	1	0.19	2		972	1251	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615101	100615101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	106	921	1	ENST00000308731.7:c.814G>A	p.Ala272Thr	p.A272T	ENST00000308731	NM_000061.2	272	Gca/Aca	9/19	1	2	FACETS	0.986	0.881	1	0.986	0.881	1	CLONAL	1	TRUE	1	0.19	2		922	1132	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215302	123215302	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	132	896	3	ENST00000218089.9:c.2848G>T	p.Glu950Ter	p.E950*	ENST00000218089	NM_001042749.1	950	Gaa/Taa	28/35	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.19	2		899	1137	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217323	123217323	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012397-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	78	828	0	ENST00000218089.9:c.2977C>G	p.Pro993Ala	p.P993A	ENST00000218089	NM_001042749.1	993	Cca/Gca	29/35	1	2	FACETS	0.914	0.802	1	0.914	0.802	1	CLONAL	1	TRUE	1	0.19	2		828	898	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508361	106508361	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	32	185	0	ENST00000359195.3:c.355C>A	p.Leu119Met	p.L119M	ENST00000359195	NM_002649.2	119	Ctg/Atg	2/11	0.250554098341949	6	FACETS	0.762	0.618	0.926	0.152	0.123	0.186	CLONAL	1	TRUE	1	0.250554098341949	6		185	503	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578492	7578492	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1131691026	NA	P-0012400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	191	524	0	ENST00000269305.4:c.438G>A	p.Trp146Ter	p.W146*	ENST00000269305	NM_001126112.2	146	tgG/tgA	5/11	0.181514810488292	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.250554098341949	1		524	1037	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494306	2494306	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs756119640	NA	P-0012400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	231	607	1	ENST00000355716.4:c.697G>A	p.Asp233Asn	p.D233N	ENST00000355716	NM_003820.2	233	Gat/Aat	7/8	0.162911664542751	3	FACETS	0.804	0.748	0.862			1	CLONAL	2	TRUE	NA	0.250554098341949	3		608	1291	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518496	204518496	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	56	426	0	ENST00000367182.3:c.1159G>C	p.Asp387His	p.D387H	ENST00000367182	NM_001278516.1	387	Gat/Cat	11/11	0.24697566736113	3	FACETS	0.5	0.427	0.581	0.25	0.213	0.291	SUBCLONAL	1	TRUE	1	0.250554098341949	3		426	1006	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518731	204518731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	59	411	0	ENST00000367182.3:c.1394G>A	p.Arg465Lys	p.R465K	ENST00000367182	NM_001278516.1	465	aGa/aAa	11/11	0.24697566736113	3	FACETS	0.521	0.447	0.603	0.261	0.223	0.302	SUBCLONAL	1	TRUE	1	0.250554098341949	3		411	1017	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149399	61149399	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1039331587	NA	P-0012400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	230	563	0	ENST00000295025.8:c.1589C>A	p.Pro530Gln	p.P530Q	ENST00000295025	NM_002908.2	530	cCa/cAa	11/11	0.166440443457605	2	FACETS	0.859	0.8	0.919	0.859	0.8	0.919	CLONAL	2	TRUE	0	0.250554098341949	2		563	1069	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977861	134977861	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	99	472	1	ENST00000398015.3:c.2854C>A	p.Leu952Met	p.L952M	ENST00000398015	NM_004441.4	952	Ctg/Atg	16/16	1	2	FACETS	0.9	0.802	1	0.9	0.802	1	CLONAL	1	TRUE	1	0.250554098341949	2		473	878	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189608590	189608590	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	173	605	0	ENST00000264731.3:c.1665G>T	p.Arg555Ser	p.R555S	ENST00000264731	NM_003722.4	555	agG/agT	13/14	0.230180144040271	3	FACETS	1	0.986	1	0.665	0.611	0.722	CLONAL	1	TRUE	1	0.250554098341949	3		605	1168	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612133	189612133	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	134	574	1	ENST00000264731.3:c.1885G>T	p.Gly629Cys	p.G629C	ENST00000264731	NM_003722.4	629	Ggc/Tgc	14/14	0.230180144040271	3	FACETS	0.982	0.89	1	0.491	0.445	0.54	CLONAL	1	TRUE	1	0.250554098341949	3		575	1226	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141031	55141031	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	109	511	0	ENST00000257290.5:c.1677G>T	p.Trp559Cys	p.W559C	ENST00000257290	NM_006206.4	559	tgG/tgT	12/23	0.181514810488292	1	FACETS	0.819	0.735	0.909	0.819	0.735	0.909	CLONAL	1	TRUE	0	0.250554098341949	1		511	929	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968064	55968064	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	69	347	1	ENST00000263923.4:c.2266G>A	p.Gly756Ser	p.G756S	ENST00000263923	NM_002253.2	756	Ggt/Agt	15/30	0.181514810488292	1	FACETS	0.761	0.663	0.867	0.761	0.663	0.867	SUBCLONAL	1	TRUE	0	0.250554098341949	1		348	633	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66230794	66230794	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	65	575	0	ENST00000273854.3:c.2177G>T	p.Ser726Ile	p.S726I	ENST00000273854	NM_004439.5	726	aGt/aTt	12/18	0.181514810488292	1	FACETS	0.397	0.342	0.456	0.397	0.342	0.456	SUBCLONAL	1	TRUE	0	0.250554098341949	1		575	1144	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540407	187540407	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	71	325	0	ENST00000441802.2:c.7333G>C	p.Gly2445Arg	p.G2445R	ENST00000441802	NM_005245.3	2445	Ggg/Cgg	10/27	0.181514810488292	1	FACETS	0.846	0.739	0.961	0.846	0.739	0.961	CLONAL	1	TRUE	0	0.250554098341949	1		325	586	SUCCESS
APC	324	MSKCC	GRCh37	5	112177784	112177784	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	98	315	0	ENST00000257430.4:c.6493C>G	p.Pro2165Ala	p.P2165A	ENST00000257430	NM_000038.5	2165	Cca/Gca	16/16	0.250554098341949	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.250554098341949	1		315	644	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694713	176694713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1008	63	687	0	ENST00000439151.2:c.5297G>A	p.Arg1766Gln	p.R1766Q	ENST00000439151	NM_022455.4	1766	cGa/cAa	15/23	0.250554098341949	1	FACETS	0.411	0.354	0.473	0.411	0.354	0.473	SUBCLONAL	1	TRUE	0	0.250554098341949	1		687	1071	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169072	32169072	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	167	604	0	ENST00000375023.3:c.3961C>A	p.Leu1321Met	p.L1321M	ENST00000375023	NM_004557.3	1321	Ctg/Atg	22/30	0.250554098341949	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.250554098341949	1		604	977	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528747	157528747	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	92	516	0	ENST00000346085.5:c.6472A>T	p.Asn2158Tyr	p.N2158Y	ENST00000346085	NM_020732.3	2158	Aac/Tac	20/20	1	2	FACETS	0.715	0.634	0.802	0.715	0.634	0.802	SUBCLONAL	1	TRUE	1	0.250554098341949	2		516	1027	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518366	8518366	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754478667	NA	P-0012400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	78	267	1	ENST00000356435.5:c.1025C>T	p.Thr342Met	p.T342M	ENST00000356435		342	aCg/aTg	10/35	0.250554098341949	1	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	0	0.250554098341949	1		268	538	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923375	36923375	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	209	532	0	ENST00000358127.4:c.887C>G	p.Pro296Arg	p.P296R	ENST00000358127	NM_001280556.1	296	cCg/cGg	7/10	0.250554098341949	1	FACETS	0.795	0.738	0.853	1	0.992	1	SUBCLONAL	2	TRUE	0	0.250554098341949	1		532	918	SUCCESS
EED	8726	MSKCC	GRCh37	11	85963262	85963262	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	138	482	0	ENST00000263360.6:c.340G>T	p.Ala114Ser	p.A114S	ENST00000263360	NM_003797.3	114	Gca/Tca	3/12	0.24697566736113	3	FACETS	1	0.984	1	0.687	0.625	0.753	CLONAL	1	TRUE	1	0.250554098341949	3		482	902	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102201946	102201946	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1234	137	785	0	ENST00000263464.3:c.1298A>T	p.Glu433Val	p.E433V	ENST00000263464	NM_001165.4	433	gAa/gTa	6/9	0.24697566736113	3	FACETS	0.898	0.814	0.986	0.449	0.407	0.493	CLONAL	1	TRUE	1	0.250554098341949	3		785	1371	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472427	88472427	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	135	523	0	ENST00000360948.2:c.2128T>C	p.Tyr710His	p.Y710H	ENST00000360948	NM_001012338.2	710	Tac/Cac	16/19	0.230180144040271	3	FACETS	1	0.976	1	0.612	0.555	0.671	CLONAL	1	TRUE	1	0.250554098341949	3		523	991	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900443	3900443	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1165	83	613	0	ENST00000262367.5:c.653G>C	p.Arg218Thr	p.R218T	ENST00000262367	NM_004380.2	218	aGa/aCa	2/31	0.211421941566499	2	FACETS	0.531	0.467	0.6	0.265	0.233	0.3	SUBCLONAL	1	TRUE	0	0.250554098341949	2		613	1248	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3900455	3900455	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	87	649	0	ENST00000262367.5:c.641G>T	p.Gly214Val	p.G214V	ENST00000262367	NM_004380.2	214	gGg/gTg	2/31	0.211421941566499	2	FACETS	0.55	0.485	0.62	0.275	0.242	0.31	SUBCLONAL	1	TRUE	0	0.250554098341949	2		649	1262	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969851	81969851	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1239554317	NA	P-0012400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1222	309	757	1	ENST00000359376.3:c.2920C>T	p.Leu974Phe	p.L974F	ENST00000359376	NM_002661.3	974	Ctc/Ttc	27/33	0.211421941566499	2	FACETS	0.806	0.758	0.855	0.806	0.758	0.855	CLONAL	2	TRUE	0	0.250554098341949	2		758	1531	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805924	46805924	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	151	676	0	ENST00000290295.7:c.32G>A	p.Gly11Glu	p.G11E	ENST00000290295	NM_006361.5	11	gGa/gAa	1/2	0.186231607634213	1	FACETS	0.899	0.82	0.982	0.899	0.82	0.982	CLONAL	1	TRUE	0	0.250554098341949	1		676	1173	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47699321	47699321	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1028	96	541	0	ENST00000347630.2:c.187G>C	p.Asp63His	p.D63H	ENST00000347630	NM_001007230.1	63	Gat/Cat	4/11	1	2	FACETS	0.682	0.606	0.763	0.682	0.606	0.763	SUBCLONAL	1	TRUE	1	0.250554098341949	2		541	1124	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245051	53245051	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1144	251	832	1	ENST00000375401.3:c.889G>T	p.Glu297Ter	p.E297*	ENST00000375401	NM_004187.3	297	Gag/Tag	7/26	0.250554098341949	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.250554098341949	1		833	1395	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245127	53245127	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1034	225	735	0	ENST00000375401.3:c.813del	p.Val272TrpfsTer2	p.V272Wfs*2	ENST00000375401	NM_004187.3	271	gtA/gt	7/26	0.250554098341949	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.250554098341949	1		735	1259	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971153	21971154	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0012400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	61	221	0	ENST00000304494.5:c.204_205delinsTT	p.Glu69Ter	p.E69*	ENST00000304494	NM_000077.4	68	gcGGag/gcTTag	2/3	0.250554098341949	1	FACETS	1	0.89	1	1	0.89	1	CLONAL	1	TRUE	0	0.250554098341949	1		221	413	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602487	10602488	+	missense_variant	Missense_Mutation	DNP	CC	CC	AA	novel	NA	P-0012400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	232	444	0	ENST00000171111.5:c.1090_1091delinsTT	p.Gly364Phe	p.G364F	ENST00000171111	NM_203500.1	364	GGc/TTc	3/6	0.211421941566499	2	FACETS	0.985	0.919	1	0.985	0.919	1	CLONAL	2	TRUE	0	0.250554098341949	2		444	940	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128845597	128845598	+	missense_variant	Missense_Mutation	DNP	TG	TG	AT	novel	NA	P-0012400-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1103	310	444	0	ENST00000249373.3:c.894_895delinsAT	p.Asp298_Gly299delinsGluCys	p.D298_G299delinsEC	ENST00000249373	NM_005631.4	298	gaTGgc/gaATgc	4/12	0.250554098341949	6	FACETS	0.876	0.825	0.929	0.526	0.495	0.558	CLONAL	3	TRUE	1	0.250554098341949	6		444	1413	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	109	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.505495136700301	2		280	330	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0012417-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	250	558	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.841	0.793	0.889	1	0.994	1	CLONAL	2	TRUE	1	0.505495136700301	2		558	588	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	49	12	280	0				ENST00000310581	NM_198253.2	-/1132			0.242157408105007	0	FACETS	0.619	0.445	0.821			1	SUBCLONAL	1	FALSE	0	0.388768398220409	0		280	61	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578526	7578526	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781991	NA	P-0012421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	114	518	0	ENST00000269305.4:c.404G>A	p.Cys135Tyr	p.C135Y	ENST00000269305	NM_001126112.2	135	tGc/tAc	5/11	0.331563701131809	3	FACETS	0.858	0.779	0.941	0.858	0.779	0.941	CLONAL	2	FALSE	1	0.388768398220409	3		518	408	SUCCESS
APC	324	MSKCC	GRCh37	5	112174886	112174886	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1561586087	NA	P-0012421-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	67	488	0	ENST00000257430.4:c.3595A>G	p.Lys1199Glu	p.K1199E	ENST00000257430	NM_000038.5	1199	Aag/Gag	16/16	0.331563701131809	3	FACETS	0.814	0.716	0.917	0.814	0.716	0.917	CLONAL	2	FALSE	1	0.388768398220409	3		488	253	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	69	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	FALSE	1	0.204381583305782	2		280	580	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0012446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	191	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.204381583305782	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	2	FALSE	0	0.204381583305782	2		490	917	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321372	1321372	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1319865856	NA	P-0012446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	98	549	0	ENST00000400841.2:c.383C>T	p.Ser128Leu	p.S128L	ENST00000400841		128	tCg/tTg	4/6	1	2	FACETS	0.902	0.803	1	0.902	0.803	1	CLONAL	1	FALSE	1	0.204381583305782	2		549	1063	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53226187	53226187	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376775932	NA	P-0012446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	182	516	3	ENST00000375401.3:c.2662C>T	p.Arg888Cys	p.R888C	ENST00000375401	NM_004187.3	888	Cgt/Tgt	19/26	1	2	FACETS	0.868	0.8	0.939	1	0.992	1	CLONAL	2	FALSE	1	0.204381583305782	2		519	1026	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467669	50467669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	154	473	0	ENST00000331340.3:c.904G>A	p.Glu302Lys	p.E302K	ENST00000331340	NM_006060.4	302	Gag/Aag	8/8	0.204381583305782	2	FACETS	0.861	0.788	0.937	0.861	0.788	0.937	CLONAL	2	FALSE	0	0.204381583305782	2		473	875	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560902	9560902	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756198440	NA	P-0012446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	172	638	0	ENST00000353224.5:c.880G>A	p.Glu294Lys	p.E294K	ENST00000353224	NM_177990.2	294	Gaa/Aaa	4/10	0.204381583305782	3	FACETS	0.795	0.73	0.863	0.795	0.73	0.863	SUBCLONAL	2	FALSE	1	0.204381583305782	3		638	1167	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693886	47693886	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750029	NA	P-0012446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1143	198	695	0	ENST00000233146.2:c.1600C>T	p.Arg534Cys	p.R534C	ENST00000233146	NM_000251.2	534	Cgt/Tgt	10/16	0.204381583305782	3	FACETS	0.796	0.736	0.86	0.796	0.736	0.86	SUBCLONAL	2	FALSE	1	0.204381583305782	3		695	1341	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376322	118376322	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1482	187	944	0	ENST00000534358.1:c.9715C>T	p.Pro3239Ser	p.P3239S	ENST00000534358	NM_005933.3	3239	Ccc/Tcc	27/36	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.204381583305782	2		944	1669	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72076784	72076784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	171	776	0	ENST00000357731.5:c.713G>A	p.Gly238Glu	p.G238E	ENST00000357731	NM_173808.2	238	gGa/gAa	5/7	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.204381583305782	2		776	1209	SUCCESS
ATM	472	MSKCC	GRCh37	11	108163486	108163486	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770590652	NA	P-0012446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	147	565	0	ENST00000278616.4:c.4577C>T	p.Pro1526Leu	p.P1526L	ENST00000278616	NM_000051.3	1526	cCc/cTc	30/63	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.204381583305782	2		565	1093	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665379	176665379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	186	504	1	ENST00000439151.2:c.4063C>T	p.Pro1355Ser	p.P1355S	ENST00000439151	NM_022455.4	1355	Ccc/Tcc	7/23	0.17975356974226	2	FACETS	0.897	0.828	0.969	0.897	0.828	0.969	CLONAL	2	FALSE	0	0.204381583305782	2		505	1014	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	397187	397187	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1121	156	566	1	ENST00000380956.4:c.572C>T	p.Pro191Leu	p.P191L	ENST00000380956	NM_001195286.1	191	cCg/cTg	5/9	0.11948672030968	4	FACETS	1	0.986	1	0.72	0.657	0.786	INDETERMINATE	1	FALSE	2	0.204381583305782	4		567	1277	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124437	94124437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1224	101	832	0	ENST00000369303.4:c.146C>T	p.Ser49Phe	p.S49F	ENST00000369303	NM_004440.3	49	tCc/tTc	2/17	0.191179779056056	1	FACETS	0.67	0.596	0.748	0.67	0.596	0.748	SUBCLONAL	1	FALSE	0	0.204381583305782	1		832	1325	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260456	16260456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201347979	NA	P-0012446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	88	325	0	ENST00000375759.3:c.7721C>T	p.Pro2574Leu	p.P2574L	ENST00000375759	NM_015001.2	2574	cCg/cTg	11/15	1	2	FACETS	0.873	0.777	0.976	1	0.983	1	CLONAL	2	FALSE	1	0.204381583305782	2		325	493	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570880	226570880	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0012446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	61	239	0	ENST00000366794.5:c.1016T>G	p.Phe339Cys	p.F339C	ENST00000366794	NM_001618.3	339	tTc/tGc	8/23	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	FALSE	1	0.204381583305782	2		239	545	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439922	220439922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	265	781	0	ENST00000243786.2:c.775C>T	p.His259Tyr	p.H259Y	ENST00000243786	NM_002191.3	259	Cat/Tat	2/2	0.204381583305782	3	FACETS	0.997	0.933	1	0.997	0.933	1	CLONAL	2	FALSE	1	0.204381583305782	3		781	1433	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55970899	55970899	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1112	145	636	0	ENST00000263923.4:c.1898C>T	p.Ser633Phe	p.S633F	ENST00000263923	NM_002253.2	633	tCc/tTc	13/30	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	FALSE	1	0.204381583305782	2		636	1257	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250770	26250770	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1443	267	950	4	ENST00000446824.2:c.64G>A	p.Ala22Thr	p.A22T	ENST00000446824	NM_021018.2	22	Gcc/Acc	1/1	0.11948672030968	4	FACETS	0.92	0.86	0.983	0.92	0.86	0.983	INDETERMINATE	2	FALSE	2	0.204381583305782	4		954	1710	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178701	32178701	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1337439880	NA	P-0012446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	170	474	0	ENST00000375023.3:c.2693C>T	p.Ser898Phe	p.S898F	ENST00000375023	NM_004557.3	898	tCt/tTt	18/30	0.11948672030968	4	FACETS	1	0.971	1	1	0.971	1	INDETERMINATE	2	FALSE	2	0.204381583305782	4		474	897	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741491	145741491	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754299237	NA	P-0012446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1234	164	725	0	ENST00000428558.2:c.1012C>T	p.Pro338Ser	p.P338S	ENST00000428558	NM_004260.3	338	Ccc/Tcc	5/22	0.204381583305782	3	FACETS	1	0.982	1	0.633	0.579	0.689	CLONAL	1	FALSE	1	0.204381583305782	3		725	1398	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342852	87342852	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	63	348	0	ENST00000277120.3:c.1137G>A	p.Met379Ile	p.M379I	ENST00000277120		379	atG/atA	9/19	1	2	FACETS	0.985	0.852	1	0.985	0.852	1	CLONAL	1	FALSE	1	0.204381583305782	2		348	626	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692892	89692892	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554898129	NA	P-0012446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	71	322	1	ENST00000371953.3:c.376G>A	p.Ala126Thr	p.A126T	ENST00000371953	NM_000314.4	126	Gct/Act	5/9	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	FALSE	1	0.204381583305782	2		323	558	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993785	72993785	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1353571938	NA	P-0012446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	118	709	2	ENST00000268489.5:c.260C>T	p.Ser87Phe	p.S87F	ENST00000268489	NM_006885.3	87	tCc/tTc	2/10	1	2	FACETS	0.989	0.89	1	0.989	0.89	1	CLONAL	1	FALSE	1	0.204381583305782	2		711	1167	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889146	76889146	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1333	236	754	0	ENST00000373344.5:c.4864G>A	p.Ala1622Thr	p.A1622T	ENST00000373344	NM_000489.3	1622	Gcg/Acg	18/35	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.204381583305782	2		754	1569	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937453	76937453	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	151	579	0	ENST00000373344.5:c.3295A>C	p.Lys1099Gln	p.K1099Q	ENST00000373344	NM_000489.3	1099	Aag/Cag	9/35	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.204381583305782	2		579	1148	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78681752	78681753	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	114	583	0	ENST00000306801.3:c.460_461delinsAA	p.Gly154Lys	p.G154K	ENST00000306801	NM_020761.2	154	GGg/AAg	4/34	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	FALSE	1	0.204381583305782	2		583	1062	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40730905	40730906	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0012446-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	87	336	1	ENST00000373198.4:c.3629_3630delinsTT	p.Pro1210Leu	p.P1210L	ENST00000373198	NM_133170.3	1210	cCC/cTT	27/32	0.204381583305782	3	FACETS	0.762	0.675	0.854	0.762	0.675	0.854	SUBCLONAL	2	FALSE	1	0.204381583305782	3		337	616	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012536-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	146	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.866522259941479	2		280	286	SUCCESS
CDKN2C	1031	MSKCC	GRCh37	1	51436044	51436044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012536-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	278	342	2	ENST00000262662.1:c.4G>A	p.Ala2Thr	p.A2T	ENST00000262662		2	Gcc/Acc	3/4	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.866522259941479	2		344	611	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133839	55133839	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012536-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	332	519	0	ENST00000257290.5:c.1052A>G	p.Lys351Arg	p.K351R	ENST00000257290	NM_006206.4	351	aAa/aGa	7/23	NA	2	FACETS	0.966	0.918	1			1	INDETERMINATE	1	TRUE	NA	0.866522259941479	2		519	793	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	74	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.809	0.709	0.916	0.809	0.709	0.916	CLONAL	1	TRUE	1	0.34	2		280	538	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259515	55259515	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121434568	NA	P-0012595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	178	265	0	ENST00000275493.2:c.2573T>G	p.Leu858Arg	p.L858R	ENST00000275493	NM_005228.3	858	cTg/cGg	21/28	0.295968483788914	3	FACETS	1	0.967	1	0.547	0.504	0.593	CLONAL	1	TRUE	1	0.34	3		265	1119	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47032529	47032529	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012595-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1009	165	419	0	ENST00000377604.3:c.436del	p.Arg146ValfsTer16	p.R146Vfs*16	ENST00000377604	NM_001204468.1	145	atC/at	5/24	1	2	FACETS	0.827	0.758	0.899	0.827	0.758	0.899	CLONAL	1	TRUE	1	0.34	2		419	1174	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0012681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	117	464	0				ENST00000310581	NM_198253.2	-/1132			0.221961271610693	1	FACETS	0.458	0.414	0.503	0.458	0.414	0.503	INDETERMINATE	1	TRUE	0	0.6524047571151	1		464	528	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578222	7578223	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	-	rs1057517840	NA	P-0012681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	380	642	0	ENST00000269305.4:c.626_627del	p.Arg209LysfsTer6	p.R209Kfs*6	ENST00000269305	NM_001126112.2	209	aGA/a	6/11	0.396991532623246	1	FACETS	0.994	0.95	1	0.994	0.95	1	CLONAL	1	TRUE	0	0.6524047571151	1		642	790	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591258	67591258	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012681-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	311	425	0	ENST00000274335.5:c.1756C>T	p.Gln586Ter	p.Q586*	ENST00000274335		586	Caa/Taa	13/15	0.221961271610693	1	FACETS	0.792	0.75	0.834	0.792	0.75	0.834	INDETERMINATE	1	TRUE	0	0.6524047571151	1		425	811	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971204	21971208	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	TGACC	TGACC	-	novel	NA	P-0012694-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	25	147	0	ENST00000304494.5:c.151-1_154del		p.X51_splice	ENST00000304494	NM_000077.4	51		2/3	NA		FACETS		NA	NA				NA	NA	TRUE	NA	NA	NA		147	319	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	232	280	0				ENST00000310581	NM_198253.2	-/1132			0.391828933834523	4	FACETS	0.983	0.925	1	1	0.993	1	CLONAL	3	TRUE	2	0.391828933834523	4		280	559	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604775	48604775	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377767381	NA	P-0012696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	278	568	0	ENST00000342988.3:c.1597C>T	p.Leu533Phe	p.L533F	ENST00000342988	NM_005359.5	533	Ctc/Ttc	12/12	0.384101746810272	2	FACETS	0.999	0.944	1	0.999	0.944	1	CLONAL	2	TRUE	0	0.391828933834523	2		568	710	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971202	21971608	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CATGACCTGCCAGAGAGAACAGAATGGTCAGAGCCAGGGTGGGGGCCGGCATGACGGAAAGGAAGCTTGTGTAGAGCCCCCTCACCGCCAAGCAGACCCCCACACAAGCCCCAGGTGTCTAATTACCCCTACATTTGCTTCCAGTTTCCAATTTCCTTCTTGAGTTCTCTATCCATTCTTCAGTACACAATGAATTCCATTATATCCTCCGAACTTCTGCGGAGCTGTCGTCACAGGCAGAGAGCACTGTGAGGCACGGGCAAAATAGCAAAGGGGCAGGGACAGACTGACTTTTACTCCAGGCTAACTTCCTGTATTTCCCCTGAGATACAACTACTGAAATTTCTTCCTGAAATTATGTTAGGCCTGGAGATTTTTTTTTTTTTTTTTGTTCACTGCTGTATATC	CATGACCTGCCAGAGAGAACAGAATGGTCAGAGCCAGGGTGGGGGCCGGCATGACGGAAAGGAAGCTTGTGTAGAGCCCCCTCACCGCCAAGCAGACCCCCACACAAGCCCCAGGTGTCTAATTACCCCTACATTTGCTTCCAGTTTCCAATTTCCTTCTTGAGTTCTCTATCCATTCTTCAGTACACAATGAATTCCATTATATCCTCCGAACTTCTGCGGAGCTGTCGTCACAGGCAGAGAGCACTGTGAGGCACGGGCAAAATAGCAAAGGGGCAGGGACAGACTGACTTTTACTCCAGGCTAACTTCCTGTATTTCCCCTGAGATACAACTACTGAAATTTCTTCCTGAAATTATGTTAGGCCTGGAGATTTTTTTTTTTTTTTTTGTTCACTGCTGTATATC	-	novel	NA	P-0012696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	45	205	0	ENST00000304494.5:c.151-401_156del		p.X51_splice	ENST00000304494	NM_000077.4	51		2/3	0.391828933834523	5	FACETS	1	0.958	1			1	CLONAL	1	TRUE	NA	0.391828933834523	5		205	252	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621035	1621035	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	144	862	2	ENST00000344749.5:c.1025del	p.Pro342ArgfsTer52	p.P342Rfs*52	ENST00000344749	NM_001136139.2	342	cCg/cg	13/19	0.391828933834523	4	FACETS	0.806	0.733	0.883	0.269	0.244	0.295	CLONAL	1	TRUE	1	0.391828933834523	4		864	1269	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578165	7578188	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TGCAAACCAGACCTCAGGCGGCTC	TGCAAACCAGACCTCAGGCGGCTC	-	novel	NA	P-0012696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	400	647	0	ENST00000269305.4:c.661_672+12del		p.X221_splice	ENST00000269305	NM_001126112.2	221		6/11	0.391828933834523	4	FACETS	0.923	0.884	0.961	0.923	0.884	0.961	CLONAL	4	TRUE	0	0.391828933834523	4		647	770	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411658	116411662	+	protein_altering_variant	In_Frame_Del	DEL	TATTA	TATTA	AT	novel	NA	P-0012696-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	626	543	0	ENST00000397752.3:c.2837_2841delinsAT	p.Leu946_Leu947delinsTyr	p.L946_L947delinsY	ENST00000397752	NM_000245.2	946	tTATTA/tAT	13/21	0.391828933834523	4	FACETS	1	0.994	1	1	0.994	1	CLONAL	3	TRUE	1	0.391828933834523	4		543	1315	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0012705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	37	511	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.829	0.683	0.992	0.829	0.683	0.992	CLONAL	1	TRUE	1	0.19	2		512	470	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645683	12645683	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs397516829	NA	P-0012705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	60	588	0	ENST00000251849.4:c.786T>A	p.Asn262Lys	p.N262K	ENST00000251849	NM_002880.3	262	aaT/aaA	7/17	1	2	FACETS	0.887	0.763	1	0.887	0.763	1	CLONAL	1	TRUE	1	0.19	2		588	712	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037402	12037402	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765031845	NA	P-0012705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	74	1101	3	ENST00000396373.4:c.1033G>A	p.Val345Ile	p.V345I	ENST00000396373	NM_001987.4	345	Gtc/Atc	6/8	0.15361347581939	3	FACETS	0.871	0.761	0.991	0.436	0.38	0.496	CLONAL	1	TRUE	1	0.19	3		1104	979	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430361	78430361	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012705-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	61	935	1	ENST00000370768.2:c.807del	p.Ser270GlnfsTer3	p.S270Qfs*3	ENST00000370768	NM_003902.3	269	ggG/gg	10/20	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.19	2		936	630	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	77	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.933	0.824	1	0.933	0.824	1	CLONAL	1	TRUE	1	0.438027322837871	2		280	377	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69998274	69998274	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	212	524	0	ENST00000394351.3:c.514A>G	p.Asn172Asp	p.N172D	ENST00000394351	NM_000248.3	172	Aac/Gac	5/9	0.438027322837871	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.438027322837871	1		524	725	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023151	150023151	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	220	666	0	ENST00000253339.5:c.112C>G	p.Leu38Val	p.L38V	ENST00000253339		38	Ctt/Gtt	1/7	1	2	FACETS	0.899	0.836	0.965	0.899	0.836	0.965	CLONAL	1	TRUE	1	0.438027322837871	2		666	1117	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520029	106520029	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	181	522	0	ENST00000359195.3:c.2457T>A	p.Asp819Glu	p.D819E	ENST00000359195	NM_002649.2	819	gaT/gaA	6/11	1	2	FACETS	0.933	0.861	1	0.933	0.861	1	CLONAL	1	TRUE	1	0.438027322837871	2		522	886	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864057	97864057	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	91	640	2	ENST00000289081.3:c.1609G>A	p.Gly537Ser	p.G537S	ENST00000289081	NM_000136.2	537	Ggc/Agc	15/15	0.356587527092526	1	FACETS	0.399	0.354	0.448	0.399	0.354	0.448	SUBCLONAL	1	TRUE	0	0.438027322837871	1		642	813	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40368064	40368064	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	220	806	0	ENST00000293328.3:c.1441A>G	p.Thr481Ala	p.T481A	ENST00000293328	NM_012448.3	481	Act/Gct	12/19	1	2	FACETS	0.878	0.816	0.942	0.878	0.816	0.942	CLONAL	1	TRUE	1	0.438027322837871	2		806	1144	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602767	10602767	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	148	488	0	ENST00000171111.5:c.811G>C	p.Val271Leu	p.V271L	ENST00000171111	NM_203500.1	271	Gtg/Ctg	3/6	0.438027322837871	1	FACETS	0.931	0.854	1	0.931	0.854	1	CLONAL	1	TRUE	0	0.438027322837871	1		488	567	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67482736	67482757	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	CCCTATTTCTTACAGGAGACAG	CCCTATTTCTTACAGGAGACAG	-	novel	NA	P-0012709-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	140	527	0	ENST00000327367.4:c.1155-15_1161del		p.X385_splice	ENST00000327367	NM_005902.3	385		9/9	1	2	FACETS	0.903	0.824	0.986	0.903	0.824	0.986	CLONAL	1	TRUE	1	0.438027322837871	2		527	708	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012770-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	213	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.998	0.936	1	0.998	0.936	1	CLONAL	1	TRUE	1	0.802294419999549	2		280	532	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924843	49924843	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012770-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	52	856	0	ENST00000296474.3:c.4100C>A	p.Thr1367Asn	p.T1367N	ENST00000296474	NM_002447.2	1367	aCc/aAc	20/20	0.802294419999549	1	FACETS	0.082	0.069	0.096	0.082	0.069	0.096	SUBCLONAL	1	TRUE	0	0.802294419999549	1		856	948	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012789-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	63	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.867	0.759	0.982	1	0.978	1	CLONAL	2	TRUE	1	0.294077592144966	2		280	247	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0012789-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	182	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.767	0.709	0.827	1	0.99	1	SUBCLONAL	2	TRUE	1	0.294077592144966	2		490	807	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	102	280	0				ENST00000310581	NM_198253.2	-/1132			0.190985752308733	5	FACETS	0.86	0.776	0.949	0.86	0.776	0.949	CLONAL	3	TRUE	2	0.287966297408759	5		280	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0012790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	196	592	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	1	2	FACETS	0.791	0.733	0.851	1	0.991	1	SUBCLONAL	2	TRUE	1	0.287966297408759	2		592	860	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0012790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	74	589	0	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.491	0.429	0.559	0.491	0.429	0.559	SUBCLONAL	1	TRUE	1	0.287966297408759	2		589	1046	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0012790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	153	599	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.287966297408759	3	FACETS	1	0.914	1	0.501	0.457	0.547	CLONAL	1	TRUE	1	0.287966297408759	3		599	1214	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916728	178916728	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1527	123	893	0	ENST00000263967.3:c.115G>A	p.Glu39Lys	p.E39K	ENST00000263967	NM_006218.2	39	Gag/Aag	2/21	0.287966297408759	3	FACETS	0.592	0.533	0.655	0.296	0.266	0.328	SUBCLONAL	1	TRUE	1	0.287966297408759	3		893	1650	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288194	33288194	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs375524506	NA	P-0012790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	73	432	0	ENST00000374542.5:c.1214C>G	p.Ser405Cys	p.S405C	ENST00000374542	NM_001141970.1	405	tCt/tGt	4/8	1	2	FACETS	0.719	0.628	0.817	0.719	0.628	0.817	SUBCLONAL	1	TRUE	1	0.287966297408759	2		432	705	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850981	63850981	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	40	507	0	ENST00000279873.7:c.1759G>T	p.Glu587Ter	p.E587*	ENST00000279873	NM_032199.2	587	Gaa/Taa	10/10	1	2	FACETS	0.414	0.343	0.493	0.414	0.343	0.493	SUBCLONAL	1	TRUE	1	0.287966297408759	2		507	671	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67198863	67198863	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	43	514	0	ENST00000312629.5:c.334G>C	p.Asp112His	p.D112H	ENST00000312629	NM_003952.2	112	Gac/Cac	5/15	1	2	FACETS	0.353	0.294	0.419	0.353	0.294	0.419	SUBCLONAL	1	TRUE	1	0.287966297408759	2		514	845	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374271	118374271	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0012790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	55	691	0	ENST00000534358.1:c.7664C>G	p.Ser2555Ter	p.S2555*	ENST00000534358	NM_005933.3	2555	tCa/tGa	27/36	1	2	FACETS	0.353	0.301	0.411	0.353	0.301	0.411	SUBCLONAL	1	TRUE	1	0.287966297408759	2		691	1081	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448360	49448360	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	897	56	659	0	ENST00000301067.7:c.351G>C	p.Gln117His	p.Q117H	ENST00000301067	NM_003482.3	117	caG/caC	3/54	1	2	FACETS	0.408	0.348	0.474	0.408	0.348	0.474	SUBCLONAL	1	TRUE	1	0.287966297408759	2		659	953	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562625	21562625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1381166851	NA	P-0012790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	24	142	1	ENST00000382592.4:c.1294G>A	p.Val432Met	p.V432M	ENST00000382592	NM_014572.2	432	Gtg/Atg	4/8	0.11421568097441	4	FACETS	0.665	0.521	0.83	0.332	0.26	0.415	INDETERMINATE	1	TRUE	2	0.287966297408759	4		143	323	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89838163	89838163	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	85	699	0	ENST00000389301.3:c.2074G>T	p.Glu692Ter	p.E692*	ENST00000389301	NM_000135.2	692	Gag/Tag	23/43	1	2	FACETS	0.58	0.511	0.654	0.58	0.511	0.654	SUBCLONAL	1	TRUE	1	0.287966297408759	2		699	1018	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121063	3121063	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0012790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	81	680	0	ENST00000078429.4:c.966G>C	p.Lys322Asn	p.K322N	ENST00000078429	NM_002067.2	322	aaG/aaC	7/7	0.200073667022267	2	FACETS	0.556	0.489	0.629	0.278	0.244	0.315	SUBCLONAL	1	TRUE	0	0.287966297408759	2		680	1011	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039379	49039379	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0012790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	312	798	0	ENST00000267163.4:c.2366del	p.Pro789LeufsTer21	p.P789Lfs*21	ENST00000267163	NM_000321.2	788	agC/ag	23/27	NA	2	FACETS	0.923	0.87	0.977			1	INDETERMINATE	2	TRUE	NA	0.287966297408759	2		798	1174	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105668	27105669	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0012790-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	176	611	0	ENST00000324856.7:c.5282dup	p.Gly1762TrpfsTer11	p.G1762Wfs*11	ENST00000324856	NM_006015.4	1760	gag/gaGg	20/20	0.200073667022267	2	FACETS	1	0.988	1	0.691	0.637	0.748	CLONAL	1	TRUE	0	0.287966297408759	2		611	884	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266113	41266113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913403	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	46	614	0	ENST00000349496.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000349496	NM_001904.3	37	tCt/tTt	3/15	1	2	FACETS	0.491	0.412	0.579	0.491	0.412	0.579	SUBCLONAL	1	TRUE	1	0.193212600115304	2		614	970	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188865	32188865	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138205668	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	140	588	1	ENST00000375023.3:c.689G>A	p.Arg230His	p.R230H	ENST00000375023	NM_004557.3	230	cGt/cAt	4/30	0.170759400555897	4	FACETS	0.939	0.854	1	0.939	0.854	1	CLONAL	2	TRUE	2	0.193212600115304	4		589	921	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980345	55980345	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1172	66	826	0	ENST00000263923.4:c.746G>T	p.Arg249Ile	p.R249I	ENST00000263923	NM_002253.2	249	aGa/aTa	6/30	1	2	FACETS	0.552	0.477	0.634	0.552	0.477	0.634	SUBCLONAL	1	TRUE	1	0.193212600115304	2		826	1238	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970966	21970966	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	86	558	0	ENST00000304494.5:c.392G>C	p.Arg131Pro	p.R131P	ENST00000304494	NM_000077.4	131	cGc/cCc	2/3	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.193212600115304	2		558	755	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578478	7578478	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057520000	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	200	578	0	ENST00000269305.4:c.452C>G	p.Pro151Arg	p.P151R	ENST00000269305	NM_001126112.2	151	cCc/cGc	5/11	0.193212600115304	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	2	TRUE	0	0.193212600115304	2		578	1025	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458630	120458630	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	90	490	0	ENST00000256646.2:c.6715G>C	p.Gly2239Arg	p.G2239R	ENST00000256646	NM_024408.3	2239	Gga/Cga	34/34	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.193212600115304	2		490	776	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510838	120510838	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	61	436	0	ENST00000256646.2:c.1126G>C	p.Asp376His	p.D376H	ENST00000256646	NM_024408.3	376	Gat/Cat	7/34	1	2	FACETS	0.883	0.761	1	0.883	0.761	1	CLONAL	1	TRUE	1	0.193212600115304	2		436	715	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612754	228612754	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1382	286	1238	1	ENST00000366696.1:c.273G>T	p.Met91Ile	p.M91I	ENST00000366696	NM_003493.2	91	atG/atT	1/1	0.193212600115304	3	FACETS	0.973	0.912	1	0.973	0.912	1	CLONAL	2	TRUE	1	0.193212600115304	3		1239	1668	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645996	215645996	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	151	638	2	ENST00000260947.4:c.602G>T	p.Arg201Ile	p.R201I	ENST00000260947	NM_000465.2	201	aGa/aTa	4/11	0.183012139062475	2	FACETS	0.808	0.738	0.882	0.808	0.738	0.882	CLONAL	2	TRUE	0	0.193212600115304	2		640	967	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204752	128204752	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1363	155	1005	2	ENST00000341105.2:c.689G>T	p.Arg230Leu	p.R230L	ENST00000341105	NM_032638.4	230	cGc/cTc	3/6	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.193212600115304	2		1007	1518	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134880952	134880952	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	90	605	1	ENST00000398015.3:c.1515G>T	p.Gln505His	p.Q505H	ENST00000398015	NM_004441.4	505	caG/caT	7/16	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.193212600115304	2		606	887	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295322	1295322	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	108	502	0				ENST00000310581	NM_198253.2	-/1132			0.193212600115304	5	FACETS	1	0.982	1	0.494	0.442	0.549	CLONAL	1	TRUE	2	0.193212600115304	5		502	973	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754599	57754599	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	778	91	677	0	ENST00000274289.3:c.448G>A	p.Glu150Lys	p.E150K	ENST00000274289	NM_006622.3	150	Gag/Aag	3/14	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.193212600115304	2		677	869	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162475134	162475134	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	109	792	0	ENST00000366898.1:c.607G>T	p.Gly203Trp	p.G203W	ENST00000366898	NM_004562.2	203	Ggg/Tgg	5/12	1	2	FACETS	0.982	0.879	1	0.982	0.879	1	CLONAL	1	TRUE	1	0.193212600115304	2		792	1149	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878107	151878107	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	125	508	0	ENST00000262189.6:c.6838G>C	p.Gly2280Arg	p.G2280R	ENST00000262189	NM_170606.2	2280	Gga/Cga	36/59	0.193212600115304	3	FACETS	0.851	0.77	0.936	0.851	0.77	0.936	CLONAL	2	TRUE	1	0.193212600115304	3		508	834	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36840597	36840597	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	81	606	0	ENST00000358127.4:c.1136C>A	p.Ala379Asp	p.A379D	ENST00000358127	NM_001280556.1	379	gCc/gAc	10/10	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.193212600115304	2		606	832	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32450138	32450138	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	74	551	0	ENST00000332351.3:c.674C>A	p.Thr225Lys	p.T225K	ENST00000332351	NM_024426.4	225	aCg/aAg	2/10	1	2	FACETS	0.892	0.779	1	0.892	0.779	1	CLONAL	1	TRUE	1	0.193212600115304	2		551	859	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69518619	69518619	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs376666157	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	44	260	0	ENST00000294312.3:c.26A>T	p.His9Leu	p.H9L	ENST00000294312	NM_005117.2	9	cAc/cTc	1/3	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.193212600115304	2		260	426	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100922228	100922228	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	150	941	0	ENST00000325455.5:c.2284G>T	p.Gly762Cys	p.G762C	ENST00000325455	NM_001202474.3	762	Ggt/Tgt	5/8	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.193212600115304	2		941	1306	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999530	100999530	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1376	170	1000	1	ENST00000325455.5:c.272A>T	p.Glu91Val	p.E91V	ENST00000325455	NM_001202474.3	91	gAa/gTa	1/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.193212600115304	2		1001	1546	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342614	118342614	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	999	152	817	0	ENST00000534358.1:c.740G>A	p.Gly247Glu	p.G247E	ENST00000534358	NM_005933.3	247	gGa/gAa	3/36	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.193212600115304	2		817	1151	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109812	115109812	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	41	531	0	ENST00000257566.3:c.2066G>T	p.Gly689Val	p.G689V	ENST00000257566	NM_016569.3	689	gGc/gTc	8/8	0.1869418969593	2	FACETS	0.563	0.467	0.67	0.281	0.233	0.335	SUBCLONAL	1	TRUE	0	0.193212600115304	2		531	754	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112113	115112113	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	202	712	0	ENST00000257566.3:c.1627C>A	p.Leu543Met	p.L543M	ENST00000257566	NM_016569.3	543	Ctg/Atg	7/8	0.1869418969593	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	0	0.193212600115304	2		712	1033	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120752	115120752	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs777208877	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	53	643	0	ENST00000257566.3:c.254C>A	p.Ala85Glu	p.A85E	ENST00000257566	NM_016569.3	85	gCg/gAg	1/8	0.1869418969593	2	FACETS	0.523	0.445	0.611	0.262	0.222	0.306	SUBCLONAL	1	TRUE	0	0.193212600115304	2		643	1048	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28624281	28624281	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	105	815	1	ENST00000241453.7:c.693C>A	p.Cys231Ter	p.C231*	ENST00000241453	NM_004119.2	231	tgC/tgA	6/24	1	2	FACETS	0.923	0.825	1	0.923	0.825	1	CLONAL	1	TRUE	1	0.193212600115304	2		816	1177	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38060976	38060976	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	70	347	0	ENST00000250448.2:c.1013G>T	p.Ser338Ile	p.S338I	ENST00000250448	NM_004496.3	338	aGt/aTt	2/2	0.183012139062475	2	FACETS	1	0.971	1	0.709	0.619	0.806	CLONAL	1	TRUE	0	0.193212600115304	2		347	511	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572537	95572537	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	101	387	0	ENST00000393063.1:c.2828A>C	p.His943Pro	p.H943P	ENST00000393063	NM_030621.3	943	cAt/cCt	19/28	0.193212600115304	3	FACETS	0.865	0.774	0.961	0.576	0.516	0.641	CLONAL	2	TRUE	0	0.193212600115304	3		387	663	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007815	45007815	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	120	558	2	ENST00000558401.1:c.262A>T	p.Thr88Ser	p.T88S	ENST00000558401	NM_004048.2	88	Act/Tct	2/4	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.193212600115304	2		560	855	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476354	88476354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	270	679	0	ENST00000360948.2:c.1778C>T	p.Thr593Ile	p.T593I	ENST00000360948	NM_001012338.2	593	aCc/aTc	15/19	0.193212600115304	5	FACETS	1	0.967	1			1	CLONAL	3	TRUE	NA	0.193212600115304	5		679	1147	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442834	99442834	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	72	546	0	ENST00000268035.6:c.1231G>T	p.Glu411Ter	p.E411*	ENST00000268035	NM_000875.3	411	Gag/Tag	5/21	0.175749238230183	3	FACETS	0.981	0.856	1			1	CLONAL	1	TRUE	NA	0.193212600115304	3		546	833	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	347721	347721	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	133	458	0	ENST00000262320.3:c.1784+1G>T		p.X595_splice	ENST00000262320	NM_003502.3	595			0.1869418969593	2	FACETS	0.87	0.791	0.954	0.87	0.791	0.954	CLONAL	2	TRUE	0	0.193212600115304	2		458	791	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31016052	31016052	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1302	134	848	0	ENST00000375687.4:c.373+1G>T		p.X125_splice	ENST00000375687	NM_015338.5	125			0.170759400555897	4	FACETS	1	0.967	1	0.576	0.522	0.634	CLONAL	1	TRUE	2	0.193212600115304	4		848	1436	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218442	1218442	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	206	701	0	ENST00000326873.7:c.318del	p.His107ThrfsTer22	p.H107Tfs*22	ENST00000326873	NM_000455.4	106	cGg/cg	2/10	0.1869418969593	2	FACETS	0.964	0.894	1	0.964	0.894	1	CLONAL	2	TRUE	0	0.193212600115304	2		701	1106	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230669	46230670	+	missense_variant	Missense_Mutation	DNP	GG	GG	CT	novel	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	229	788	0	ENST00000334344.6:c.918_919delinsCT	p.Leu306_Ala307delinsPheSer	p.L306_A307delinsFS	ENST00000334344	NM_152641.2	306	ttGGca/ttCTca	8/21	0.1869418969593	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	2	TRUE	0	0.193212600115304	2		788	1157	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483272	120483273	+	synonymous_variant	Silent	DNP	CT	CT	GA	novel	NA	P-0012817-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	75	508	0	ENST00000256646.2:c.3088_3089delinsTC	p.Ser1030=	p.S1030=	ENST00000256646	NM_024408.3	1030	AGc/TCc	19/34	1	2	FACETS	0.829	0.724	0.941	0.829	0.724	0.941	CLONAL	1	TRUE	1	0.193212600115304	2		508	937	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0012829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	134	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.365868359763073	2		464	620	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860349	151860349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	212	736	1	ENST00000262189.6:c.10313G>A	p.Gly3438Asp	p.G3438D	ENST00000262189	NM_170606.2	3438	gGc/gAc	43/59	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.365868359763073	2		737	1139	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858517	9858517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765370528	NA	P-0012829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	197	752	0	ENST00000330684.3:c.2884G>A	p.Glu962Lys	p.E962K	ENST00000330684	NM_001134407.1	962	Gaa/Aaa	13/13	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.365868359763073	2		752	1046	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	11905391	11905391	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781494988	NA	P-0012829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	166	448	1	ENST00000396373.4:c.41G>A	p.Arg14Gln	p.R14Q	ENST00000396373	NM_001987.4	14	cGa/cAa	2/8	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.365868359763073	2		449	816	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148504782	148504782	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	102	524	2	ENST00000320356.2:c.2212G>A	p.Ala738Thr	p.A738T	ENST00000320356	NM_004456.4	738	Gcc/Acc	20/20	1	2	FACETS	0.631	0.563	0.703	0.631	0.563	0.703	SUBCLONAL	1	TRUE	1	0.365868359763073	2		526	884	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554086	63554086	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0012829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	206	798	0	ENST00000307078.5:c.653T>C	p.Leu218Pro	p.L218P	ENST00000307078	NM_004655.3	218	cTa/cCa	2/11	1	2	FACETS	0.938	0.869	1	0.938	0.869	1	CLONAL	1	TRUE	1	0.365868359763073	2		798	1200	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575065	48575065	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	175	578	0	ENST00000342988.3:c.259C>T	p.Arg87Trp	p.R87W	ENST00000342988	NM_005359.5	87	Cgg/Tgg	3/12	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.365868359763073	2		578	936	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220404	98220404	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0012829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	201	672	0	ENST00000331920.6:c.3059del	p.Gln1020ArgfsTer29	p.Q1020Rfs*29	ENST00000331920	NM_000264.3	1020	cAg/cg	18/24	0.365868359763073	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	0	0.365868359763073	1		672	790	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	78	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.625631513958669	2		280	214	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748308	41748308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0012835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	134	461	1	ENST00000226382.2:c.461G>A	p.Arg154His	p.R154H	ENST00000226382	NM_003924.3	154	cGc/cAc	3/3	NA	2	FACETS	0.76	0.693	0.829			1	INDETERMINATE	1	TRUE	NA	0.625631513958669	2		462	564	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164875	36164875	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	75	353	0	ENST00000300305.3:c.1000C>T	p.Arg334Cys	p.R334C	ENST00000300305		334	Cgc/Tgc	8/8	1	2	FACETS	0.518	0.455	0.585	0.518	0.455	0.585	SUBCLONAL	1	TRUE	1	0.625631513958669	2		353	463	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55981483	55981483	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781709766	NA	P-0012835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	81	633	1	ENST00000263923.4:c.454G>A	p.Gly152Arg	p.G152R	ENST00000263923	NM_002253.2	152	Ggg/Agg	4/30	1	2	FACETS	0.3	0.264	0.339	0.3	0.264	0.339	SUBCLONAL	1	TRUE	1	0.625631513958669	2		634	863	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29662020	29662020	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	122	311	0	ENST00000356175.3:c.5914C>T	p.Gln1972Ter	p.Q1972*	ENST00000356175	NM_000267.3	1972	Caa/Taa	39/57	1	2	FACETS	0.929	0.846	1	0.929	0.846	1	CLONAL	1	TRUE	1	0.625631513958669	2		311	420	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118865	70118865	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0012835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	128	517	0	ENST00000245479.2:c.437T>C	p.Leu146Pro	p.L146P	ENST00000245479	NM_000346.3	146	cTg/cCg	2/3	1	2	FACETS	0.674	0.613	0.738	0.674	0.613	0.738	SUBCLONAL	1	TRUE	1	0.625631513958669	2		517	607	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70118874	70118874	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0012835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	141	546	2	ENST00000245479.2:c.446G>A	p.Ser149Asn	p.S149N	ENST00000245479	NM_000346.3	149	aGc/aAc	2/3	1	2	FACETS	0.695	0.634	0.757	0.695	0.634	0.757	SUBCLONAL	1	TRUE	1	0.625631513958669	2		548	649	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720803	89720817	+	inframe_deletion	In_Frame_Del	DEL	TACTTTAACAAAAAA	TACTTTAACAAAAAA	-	novel	NA	P-0012835-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	51	60	116	0	ENST00000371953.3:c.955_969del	p.Thr319_Asn323del	p.T319_N323del	ENST00000371953	NM_000314.4	318	ctTACTTTAACAAAAAAt/ctt	8/9	0.625631513958669	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.625631513958669	1		116	111	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	53	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.999	0.876	1	0.999	0.876	1	CLONAL	1	TRUE	1	0.81	2		280	131	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0012839-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	128	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	0.735	0.672	0.801	0.735	0.672	0.801	SUBCLONAL	1	TRUE	1	0.81	2		490	430	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012884-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	247	280	0				ENST00000310581	NM_198253.2	-/1132			0.317117817147842	3	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	1	0.317117817147842	3		280	872	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99149885	99149885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1443462676	NA	P-0012884-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	173	541	0	ENST00000074304.5:c.197G>A	p.Ser66Asn	p.S66N	ENST00000074304	NM_001134224.1	66	aGt/aAt	5/26	1	2	FACETS	0.972	0.893	1	0.972	0.893	1	CLONAL	1	TRUE	1	0.317117817147842	2		541	1123	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0012947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	203	354	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.715817859539375	2		354	538	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44524456	44524456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371769427	NA	P-0012947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	308	497	0	ENST00000291552.4:c.101C>T	p.Ser34Phe	p.S34F	ENST00000291552	NM_006758.2	34	tCt/tTt	2/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.715817859539375	2		497	812	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0012947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	301	554	0	ENST00000397062.3:c.101G>C	p.Arg34Pro	p.R34P	ENST00000397062	NM_006164.4	34	cGa/cCa	2/5	1	2	FACETS	0.987	0.933	1	0.987	0.933	1	CLONAL	1	TRUE	1	0.715817859539375	2		554	852	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023895	27023895	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0012947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	180	263	2	ENST00000324856.7:c.1001C>A	p.Ser334Ter	p.S334*	ENST00000324856	NM_006015.4	334	tCg/tAg	1/20	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.715817859539375	2		265	471	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27100201	27100201	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	235	504	0	ENST00000324856.7:c.3997C>T	p.Gln1333Ter	p.Q1333*	ENST00000324856	NM_006015.4	1333	Cag/Tag	16/20	1	2	FACETS	0.943	0.885	1	0.943	0.885	1	CLONAL	1	TRUE	1	0.715817859539375	2		504	696	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251725	212251725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs144311212	NA	P-0012947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	255	621	1	ENST00000342788.4:c.3334C>T	p.Arg1112Cys	p.R1112C	ENST00000342788	NM_005235.2	1112	Cgc/Tgc	27/28	NA	2	FACETS	0.886	0.832	0.941			1	INDETERMINATE	1	TRUE	NA	0.715817859539375	2		622	804	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64127727	64127727	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0012947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	217	428	0	ENST00000334205.4:c.220C>T	p.Gln74Ter	p.Q74*	ENST00000334205	NM_003942.2	74	Cag/Tag	3/17	0.688347781308271	3	FACETS	1	0.959	1	0.52	0.484	0.556	CLONAL	1	TRUE	1	0.715817859539375	3		428	792	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134260	11134260	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0012947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	344	698	0	ENST00000358026.2:c.2926T>A	p.Leu976Met	p.L976M	ENST00000358026	NM_001128849.1	976	Ttg/Atg	20/36	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.715817859539375	2		698	948	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317428	1317428	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200254974	NA	P-0012947-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	376	855	0	ENST00000400841.2:c.637G>A	p.Glu213Lys	p.E213K	ENST00000400841		213	Gag/Aag	5/6	1	1	FACETS	0.533	0.505	0.561	0.533	0.505	0.561	SUBCLONAL	1	TRUE	0	0.715817859539375	1		855	1266	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0012997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	70	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.814	0.717	0.917	0.814	0.717	0.917	CLONAL	1	TRUE	1	0.597125008276492	2		280	288	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0012997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	139	511	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.986	0.905	1	0.986	0.905	1	CLONAL	1	TRUE	1	0.597125008276492	2		512	472	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791757	42791757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568504941	NA	P-0012997-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	128	671	0	ENST00000575354.2:c.643C>T	p.Arg215Trp	p.R215W	ENST00000575354	NM_015125.3	215	Cgg/Tgg	5/20	0.597125008276492	1	FACETS	0.605	0.551	0.661	0.605	0.551	0.661	SUBCLONAL	1	TRUE	0	0.597125008276492	1		671	497	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	60	463	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.992	0.859	1	0.992	0.859	1	CLONAL	1	TRUE	1	0.327812418729421	2		463	369	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	79	447	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.327812418729421	2		447	414	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	27	263	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.952	0.765	1	0.952	0.765	1	CLONAL	1	TRUE	1	0.327812418729421	2		263	173	SUCCESS
APC	324	MSKCC	GRCh37	5	112175639	112175639	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913332	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	122	703	2	ENST00000257430.4:c.4348C>T	p.Arg1450Ter	p.R1450*	ENST00000257430	NM_000038.5	1450	Cga/Tga	16/16	1	2	FACETS	0.979	0.886	1	0.979	0.886	1	CLONAL	1	TRUE	1	0.327812418729421	2		705	760	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268144	153268144	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs920052554	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	145	604	1	ENST00000281708.4:c.664C>T	p.Arg222Ter	p.R222*	ENST00000281708	NM_033632.3	222	Cga/Tga	4/12	1	2	FACETS	0.932	0.85	1	0.932	0.85	1	CLONAL	1	TRUE	1	0.327812418729421	2		605	949	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	49	469	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	0.842	0.716	0.98	0.842	0.716	0.98	CLONAL	1	TRUE	1	0.327812418729421	2		469	355	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225379350	225379350	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	77	595	1	ENST00000264414.4:c.518G>A	p.Arg173Gln	p.R173Q	ENST00000264414	NM_003590.4	173	cGg/cAg	4/16	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.327812418729421	2		596	426	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145644	11145644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555785374	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	132	439	1	ENST00000358026.2:c.4006C>T	p.Arg1336Cys	p.R1336C	ENST00000358026	NM_001128849.1	1336	Cgc/Tgc	29/36	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.327812418729421	2		440	701	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133561	55133561	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs958381664	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	112	580	0	ENST00000257290.5:c.865G>A	p.Glu289Lys	p.E289K	ENST00000257290	NM_006206.4	289	Gaa/Aaa	6/23	1	2	FACETS	0.866	0.779	0.958	0.866	0.779	0.958	CLONAL	1	TRUE	1	0.327812418729421	2		580	789	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220275	55220275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751295137	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	159	639	1	ENST00000275493.2:c.665G>A	p.Arg222His	p.R222H	ENST00000275493	NM_005228.3	222	cGc/cAc	6/28	0.327812418729421	3	FACETS	0.914	0.836	0.996	0.457	0.418	0.498	CLONAL	1	TRUE	1	0.327812418729421	3		640	1235	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139397768	139397768	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	91	411	0	ENST00000277541.6:c.5033T>C	p.Leu1678Pro	p.L1678P	ENST00000277541	NM_017617.3	1678	cTg/cCg	27/34	1	2	FACETS	0.957	0.852	1	0.957	0.852	1	CLONAL	1	TRUE	1	0.327812418729421	2		411	580	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098419	108098419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587779858	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	53	285	0	ENST00000278616.4:c.68G>A	p.Arg23Gln	p.R23Q	ENST00000278616	NM_000051.3	23	cGa/cAa	2/63	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.327812418729421	2		285	299	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111921737	111921737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1170116948	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	131	643	0	ENST00000393256.3:c.526G>A	p.Glu176Lys	p.E176K	ENST00000393256	NM_006538.4	176	Gaa/Aaa	4/4	1	2	FACETS	0.918	0.832	1	0.918	0.832	1	CLONAL	1	TRUE	1	0.327812418729421	2		643	871	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732970	30732970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104893815	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	150	430	1	ENST00000295754.5:c.1583G>A	p.Arg528His	p.R528H	ENST00000295754	NM_003242.5	528	cGt/cAt	7/7	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.327812418729421	2		431	766	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52439834	52439834	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777664260	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	177	614	0	ENST00000460680.1:c.878C>T	p.Pro293Leu	p.P293L	ENST00000460680	NM_004656.3	293	cCg/cTg	10/17	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.327812418729421	2		614	994	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412922	49412922	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	209	867	0	ENST00000418115.1:c.101A>G	p.Tyr34Cys	p.Y34C	ENST00000418115	NM_001664.2	34	tAt/tGt	2/5	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.327812418729421	2		867	1103	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11300570	11300570	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764486955	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	165	650	1	ENST00000361445.4:c.1576C>T	p.Arg526Cys	p.R526C	ENST00000361445	NM_004958.3	526	Cgt/Tgt	11/58	1	2	FACETS	0.995	0.913	1	0.995	0.913	1	CLONAL	1	TRUE	1	0.327812418729421	2		651	1012	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397700	49397700	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	164	721	1	ENST00000418115.1:c.524C>T	p.Thr175Met	p.T175M	ENST00000418115	NM_001664.2	175	aCg/aTg	5/5	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.327812418729421	2		722	1001	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198193	185198193	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544421900	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	155	613	1	ENST00000265026.3:c.2675C>T	p.Thr892Met	p.T892M	ENST00000265026	NM_004721.4	892	aCg/aTg	13/14	1	2	FACETS	0.99	0.906	1	0.99	0.906	1	CLONAL	1	TRUE	1	0.327812418729421	2		614	955	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411276	63411276	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	200	403	0	ENST00000330258.3:c.1891C>T	p.Arg631Ter	p.R631*	ENST00000330258	NM_152424.3	631	Cga/Tga	2/2	1	1	FACETS	0.873	0.815	0.934	1	0.993	1	CLONAL	2	TRUE	0	0.327812418729421	1		403	584	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121438954	121438954	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1316999782	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	219	879	1	ENST00000257555.6:c.1855G>A	p.Glu619Lys	p.E619K	ENST00000257555		619	Gag/Aag	10/10	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.327812418729421	2		880	1334	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264985	46264985	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1040	217	1140	0	ENST00000371998.3:c.1860del	p.Lys620AsnfsTer18	p.K620Nfs*18	ENST00000371998		619	Aaa/aa	12/23	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.327812418729421	2		1140	1257	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321351	1321351	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763354527	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	164	650	1	ENST00000400841.2:c.404C>T	p.Thr135Met	p.T135M	ENST00000400841		135	aCg/aTg	4/6	1	1	FACETS	0.879	0.806	0.954	0.879	0.806	0.954	CLONAL	1	TRUE	0	0.327812418729421	1		651	952	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274018	10274018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1354238435	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	206	676	1	ENST00000330684.3:c.251C>T	p.Thr84Met	p.T84M	ENST00000330684	NM_001134407.1	84	aCg/aTg	2/13	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.327812418729421	2		677	1197	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120541651	120541651	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752816549	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1380	254	1019	2	ENST00000229340.5:c.206G>A	p.Arg69His	p.R69H	ENST00000229340	NM_006861.6	69	cGc/cAc	3/6	1	2	FACETS	0.948	0.885	1	0.948	0.885	1	CLONAL	1	TRUE	1	0.327812418729421	2		1021	1634	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120468186	120468186	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749662461	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	122	450	0	ENST00000256646.2:c.4253C>T	p.Pro1418Leu	p.P1418L	ENST00000256646	NM_024408.3	1418	cCc/cTc	25/34	1	2	FACETS	0.916	0.828	1	0.916	0.828	1	CLONAL	1	TRUE	1	0.327812418729421	2		450	813	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525838	148525838	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554498830	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	79	464	0	ENST00000320356.2:c.619C>T	p.Arg207Ter	p.R207*	ENST00000320356	NM_004456.4	207	Cga/Tga	6/20	0.327812418729421	3	FACETS	1	0.883	1	0.501	0.441	0.565	CLONAL	1	TRUE	1	0.327812418729421	3		464	560	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317043	11317043	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	171	683	0	ENST00000361445.4:c.451C>T	p.Arg151Ter	p.R151*	ENST00000361445	NM_004958.3	151	Cga/Tga	4/58	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.327812418729421	2		683	996	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056142	27056142	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	rs747034279	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	109	359	0	ENST00000324856.7:c.1138C>A	p.Pro380Thr	p.P380T	ENST00000324856	NM_006015.4	380	Cca/Aca	2/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.327812418729421	2		359	539	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46736387	46736387	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	158	590	3	ENST00000371975.4:c.1099G>A	p.Ala367Thr	p.A367T	ENST00000371975	NM_003579.3	367	Gct/Act	10/18	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.327812418729421	2		593	911	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65330624	65330624	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	147	605	0	ENST00000342505.4:c.1022T>G	p.Leu341Arg	p.L341R	ENST00000342505	NM_002227.2	341	cTg/cGg	8/25	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.327812418729421	2		605	739	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166512	118166512	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	142	553	0	ENST00000369448.3:c.1022T>C	p.Leu341Pro	p.L341P	ENST00000369448	NM_017709.3	341	cTg/cCg	2/2	1	2	FACETS	0.998	0.91	1	0.998	0.91	1	CLONAL	1	TRUE	1	0.327812418729421	2		553	868	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204512028	204512028	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	65	477	0	ENST00000367182.3:c.628T>C	p.Tyr210His	p.Y210H	ENST00000367182	NM_001278516.1	210	Tat/Cat	8/11	1	2	FACETS	0.994	0.865	1	0.994	0.865	1	CLONAL	1	TRUE	1	0.327812418729421	2		477	399	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649643	206649643	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1344445148	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	114	473	0	ENST00000367120.3:c.478G>A	p.Ala160Thr	p.A160T	ENST00000367120	NM_014002.3	160	Gct/Act	6/22	1	2	FACETS	0.865	0.779	0.956	0.865	0.779	0.956	CLONAL	1	TRUE	1	0.327812418729421	2		473	804	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594066	158594066	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769751827	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	178	863	1	ENST00000263640.3:c.1507G>A	p.Asp503Asn	p.D503N	ENST00000263640	NM_001105.4	503	Gac/Aac	11/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.327812418729421	2		864	1008	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131422	202131422	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	103	495	0	ENST00000358485.4:c.390A>T	p.Arg130Ser	p.R130S	ENST00000358485	NM_001080125.1	130	agA/agT	2/9	1	2	FACETS	0.952	0.853	1	0.952	0.853	1	CLONAL	1	TRUE	1	0.327812418729421	2		495	660	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202151298	202151298	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1382820779	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	182	713	0	ENST00000358485.4:c.1598T>G	p.Leu533Arg	p.L533R	ENST00000358485	NM_001080125.1	533	cTt/cGt	9/9	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.327812418729421	2		713	1089	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251788	212251788	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	43	438	0	ENST00000342788.4:c.3271G>A	p.Ala1091Thr	p.A1091T	ENST00000342788	NM_005235.2	1091	Gct/Act	27/28	1	2	FACETS	0.394	0.329	0.467	0.394	0.329	0.467	SUBCLONAL	1	TRUE	1	0.327812418729421	2		438	666	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339038	225339038	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	123	631	1	ENST00000264414.4:c.2231G>A	p.Arg744His	p.R744H	ENST00000264414	NM_003590.4	744	cGt/cAt	16/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.327812418729421	2		632	604	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346713	225346713	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	103	599	0	ENST00000264414.4:c.1925G>A	p.Arg642Gln	p.R642Q	ENST00000264414	NM_003590.4	642	cGg/cAg	14/16	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.327812418729421	2		599	492	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41278079	41278079	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1031583127	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	109	700	0	ENST00000349496.5:c.1955C>T	p.Ala652Val	p.A652V	ENST00000349496	NM_001904.3	652	gCg/gTg	13/15	1	2	FACETS	0.999	0.898	1	0.999	0.898	1	CLONAL	1	TRUE	1	0.327812418729421	2		700	666	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49928015	49928015	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs780224945	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1259	269	953	0	ENST00000296474.3:c.3713A>G	p.Tyr1238Cys	p.Y1238C	ENST00000296474	NM_002447.2	1238	tAc/tGc	18/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.327812418729421	2		953	1528	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56181825	56181825	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	127	532	0	ENST00000399503.3:c.4049C>T	p.Thr1350Ile	p.T1350I	ENST00000399503	NM_005921.1	1350	aCt/aTt	17/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.327812418729421	2		532	597	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753945	57753945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	63	565	0	ENST00000274289.3:c.679G>A	p.Ala227Thr	p.A227T	ENST00000274289	NM_006622.3	227	Gca/Aca	5/14	1	2	FACETS	0.752	0.651	0.861	0.752	0.651	0.861	SUBCLONAL	1	TRUE	1	0.327812418729421	2		565	511	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520205	176520205	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766563138	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	135	545	0	ENST00000292408.4:c.1124C>T	p.Ser375Leu	p.S375L	ENST00000292408	NM_213647.1	375	tCg/tTg	9/18	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.327812418729421	2		545	802	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225591	26225591	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1757	319	1395	1	ENST00000360408.1:c.209G>A	p.Arg70His	p.R70H	ENST00000360408	NM_003532.2	70	cGc/cAc	1/1	1	2	FACETS	0.937	0.881	0.996	0.937	0.881	0.996	CLONAL	1	TRUE	1	0.327812418729421	2		1396	2076	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29913029	29913029	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	179	634	0	ENST00000376809.5:c.1064G>A	p.Gly355Asp	p.G355D	ENST00000376809	NM_002116.7	355	gGc/gAc	7/8	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.327812418729421	2		634	1036	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112025267	112025267	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	194	942	1	ENST00000368678.4:c.482G>A	p.Arg161Gln	p.R161Q	ENST00000368678		161	cGa/cAa	6/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.327812418729421	2		943	942	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725529	117725529	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs374639065	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	103	575	0	ENST00000368508.3:c.352C>T	p.Arg118Ter	p.R118*	ENST00000368508	NM_002944.2	118	Cga/Tga	5/43	1	2	FACETS	0.993	0.89	1	0.993	0.89	1	CLONAL	1	TRUE	1	0.327812418729421	2		575	633	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517428	157517428	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1229105280	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	134	516	0	ENST00000346085.5:c.3992A>G	p.Tyr1331Cys	p.Y1331C	ENST00000346085	NM_020732.3	1331	tAt/tGt	16/20	1	2	FACETS	0.991	0.901	1	0.991	0.901	1	CLONAL	1	TRUE	1	0.327812418729421	2		516	825	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339463	81339463	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	175	636	1	ENST00000222390.5:c.1541G>A	p.Arg514Lys	p.R514K	ENST00000222390	NM_000601.4	514	aGa/aAa	13/18	0.327812418729421	3	FACETS	0.982	0.908	1	0.982	0.908	1	CLONAL	2	TRUE	1	0.327812418729421	3		637	633	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879276	151879276	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146455116	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	246	543	0	ENST00000262189.6:c.5669G>A	p.Arg1890Gln	p.R1890Q	ENST00000262189	NM_170606.2	1890	cGa/cAa	36/59	0.327812418729421	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.327812418729421	3		543	832	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891099	151891099	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs753232315	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	73	392	0	ENST00000262189.6:c.4655A>G	p.Asn1552Ser	p.N1552S	ENST00000262189	NM_170606.2	1552	aAt/aGt	31/59	0.327812418729421	3	FACETS	1	0.947	1	0.575	0.504	0.65	CLONAL	1	TRUE	1	0.327812418729421	3		392	451	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64128672	64128672	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	181	604	0	ENST00000334205.4:c.529C>A	p.Leu177Ile	p.L177I	ENST00000334205	NM_003942.2	177	Ctc/Atc	5/17	1	2	FACETS	0.972	0.895	1	0.972	0.895	1	CLONAL	1	TRUE	1	0.327812418729421	2		604	1136	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129418	64129418	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	147	609	1	ENST00000334205.4:c.850C>T	p.Arg284Ter	p.R284*	ENST00000334205	NM_003942.2	284	Cga/Tga	8/17	1	2	FACETS	0.884	0.807	0.966	0.884	0.807	0.966	CLONAL	1	TRUE	1	0.327812418729421	2		610	1014	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416066	49416066	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	241	867	0	ENST00000301067.7:c.16409C>A	p.Ala5470Asp	p.A5470D	ENST00000301067	NM_003482.3	5470	gCc/gAc	52/54	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.327812418729421	2		867	1428	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481841	56481841	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	195	646	0	ENST00000267101.3:c.769C>T	p.Pro257Ser	p.P257S	ENST00000267101	NM_001982.3	257	Cct/Tct	7/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.327812418729421	2		646	996	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133233742	133233742	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	191	652	2	ENST00000320574.5:c.3562A>G	p.Thr1188Ala	p.T1188A	ENST00000320574	NM_006231.2	1188	Acc/Gcc	29/49	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.327812418729421	2		654	1033	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134490	41134490	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1489	294	1210	0	ENST00000379561.5:c.1138C>A	p.Leu380Ile	p.L380I	ENST00000379561	NM_002015.3	380	Ctt/Att	2/3	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.327812418729421	2		1210	1783	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435297	110435297	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	60	156	0	ENST00000375856.3:c.3104C>T	p.Pro1035Leu	p.P1035L	ENST00000375856	NM_003749.2	1035	cCg/cTg	1/2	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.327812418729421	2		156	295	SUCCESS
BLM	641	MSKCC	GRCh37	15	91333922	91333922	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs962069708	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	107	568	1	ENST00000355112.3:c.2867C>T	p.Pro956Leu	p.P956L	ENST00000355112	NM_000057.2	956	cCg/cTg	15/22	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.327812418729421	2		569	513	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	364637	364637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774810442	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	149	593	0	ENST00000262320.3:c.925G>A	p.Gly309Ser	p.G309S	ENST00000262320	NM_003502.3	309	Ggc/Agc	3/11	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	1	0.327812418729421	2		593	895	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641058	23641058	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs45464991	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	169	646	0	ENST00000261584.4:c.2417C>T	p.Pro806Leu	p.P806L	ENST00000261584	NM_024675.3	806	cCg/cTg	5/13	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.327812418729421	2		646	955	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1612344	1612344	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1320707074	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1349	198	918	1	ENST00000344749.5:c.1675G>A	p.Val559Met	p.V559M	ENST00000344749	NM_001136139.2	559	Gtg/Atg	18/19	1	2	FACETS	0.781	0.721	0.844	0.781	0.721	0.844	SUBCLONAL	1	TRUE	1	0.327812418729421	2		919	1547	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11101853	11101853	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	157	565	0	ENST00000358026.2:c.1273C>T	p.Arg425Trp	p.R425W	ENST00000358026	NM_001128849.1	425	Cgg/Tgg	8/36	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.327812418729421	2		565	903	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11118686	11118686	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781539973	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1141	205	766	0	ENST00000358026.2:c.2110C>T	p.Arg704Trp	p.R704W	ENST00000358026	NM_001128849.1	704	Cgg/Tgg	14/36	1	2	FACETS	0.929	0.86	1	0.929	0.86	1	CLONAL	1	TRUE	1	0.327812418729421	2		766	1346	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15379801	15379801	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	209	711	1	ENST00000263377.2:c.338G>A	p.Arg113His	p.R113H	ENST00000263377	NM_058243.2	113	cGc/cAc	3/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.327812418729421	2		712	1119	SUCCESS
AXL	558	MSKCC	GRCh37	19	41725365	41725365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754135882	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	86	600	0	ENST00000301178.4:c.68C>T	p.Ala23Val	p.A23V	ENST00000301178	NM_021913.4	23	gCg/gTg	1/20	1	2	FACETS	0.484	0.427	0.546	0.484	0.427	0.546	SUBCLONAL	1	TRUE	1	0.327812418729421	2		600	1083	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762430	41762430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781426924	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	230	696	1	ENST00000301178.4:c.2110C>T	p.Arg704Cys	p.R704C	ENST00000301178	NM_021913.4	704	Cgc/Tgc	18/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.327812418729421	2		697	1197	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52722957	52722957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	159	545	0	ENST00000322088.6:c.1142G>A	p.Arg381Gln	p.R381Q	ENST00000322088	NM_014225.5	381	cGg/cAg	10/15	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.327812418729421	2		545	891	SUCCESS
BCL2L1	598	MSKCC	GRCh37	20	30253759	30253759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1388146136	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	146	721	2	ENST00000307677.4:c.695G>A	p.Arg232Gln	p.R232Q	ENST00000307677	NM_138578.1	232	cGg/cAg	3/3	1	2	FACETS	0.839	0.764	0.917	0.839	0.764	0.917	CLONAL	1	TRUE	1	0.327812418729421	2		723	1062	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727085	40727085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	156	581	3	ENST00000373198.4:c.3879G>A	p.Met1293Ile	p.M1293I	ENST00000373198	NM_133170.3	1293	atG/atA	28/32	1	2	FACETS	0.977	0.894	1	0.977	0.894	1	CLONAL	1	TRUE	1	0.327812418729421	2		584	974	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485136	57485136	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	62	420	0	ENST00000371085.3:c.970G>T	p.Ala324Ser	p.A324S	ENST00000371085	NM_000516.4	324	Gct/Tct	11/13	1	2	FACETS	0.672	0.581	0.771	0.672	0.581	0.771	SUBCLONAL	1	TRUE	1	0.327812418729421	2		420	563	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574436	41574436	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	129	587	0	ENST00000263253.7:c.6721C>T	p.Gln2241Ter	p.Q2241*	ENST00000263253	NM_001429.3	2241	Cag/Tag	31/31	1	2	FACETS	0.97	0.88	1	0.97	0.88	1	CLONAL	1	TRUE	1	0.327812418729421	2		587	811	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222450	53222450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782525435	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	169	354	0	ENST00000375401.3:c.4382G>A	p.Arg1461Gln	p.R1461Q	ENST00000375401	NM_004187.3	1461	cGg/cAg	26/26	1	1	FACETS	0.818	0.757	0.88	1	0.991	1	CLONAL	2	TRUE	0	0.327812418729421	1		354	527	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412408	63412408	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	39	538	2	ENST00000330258.3:c.759G>A	p.Met253Ile	p.M253I	ENST00000330258	NM_152424.3	253	atG/atA	2/2	1	1	FACETS	0.272	0.224	0.325	0.272	0.224	0.325	SUBCLONAL	1	TRUE	0	0.327812418729421	1		540	732	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412628	63412628	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755983037	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	144	342	2	ENST00000330258.3:c.539G>A	p.Arg180Gln	p.R180Q	ENST00000330258	NM_152424.3	180	cGg/cAg	2/2	1	1	FACETS	0.767	0.704	0.831	1	0.989	1	SUBCLONAL	2	TRUE	0	0.327812418729421	1		344	479	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339230	70339230	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	238	420	0	ENST00000374080.3:c.107T>C	p.Leu36Pro	p.L36P	ENST00000374080		36	cTg/cCg	2/45	1	1	FACETS	0.901	0.845	0.957	1	0.994	1	CLONAL	2	TRUE	0	0.327812418729421	1		420	674	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931825	39931826	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	179	354	0	ENST00000378444.4:c.2773dup	p.Cys925LeufsTer21	p.C925Lfs*21	ENST00000378444	NM_001123385.1	925	tgt/tTgt	4/15	1	1	FACETS	0.883	0.82	0.947	1	0.992	1	CLONAL	2	TRUE	0	0.327812418729421	1		354	517	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29580009	29580010	+	intron_variant	Intron	INS	-	-	A	novel	NA	P-0013010-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	36	298	0	ENST00000356175.3:c.4110+3878dup		p.*1370*	ENST00000356175	NM_000267.3	1388-1389/2839			1	2	FACETS	0.805	0.665	0.96	0.805	0.665	0.96	CLONAL	1	TRUE	1	0.327812418729421	2		298	273	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0013025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	113	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.355628581842273	2		464	544	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0013025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	272	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.355628581842273	5	FACETS	0.969	0.913	1	0.969	0.913	1	CLONAL	3	TRUE	2	0.355628581842273	5		490	807	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	322	514	1	ENST00000394830.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000394830	NM_018313.4	710	Cga/Tga	17/30	0.319333650353274	3	FACETS	1	0.984	1	1	0.996	1	CLONAL	3	TRUE	1	0.355628581842273	3		515	661	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578406	7578406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934578	NA	P-0013025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	181	414	0	ENST00000269305.4:c.524G>A	p.Arg175His	p.R175H	ENST00000269305	NM_001126112.2	175	cGc/cAc	5/11	0.329397331155218	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	0	0.355628581842273	2		414	505	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858016	9858016	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	163	762	0	ENST00000330684.3:c.3385C>T	p.His1129Tyr	p.H1129Y	ENST00000330684	NM_001134407.1	1129	Cac/Tac	13/13	0.321086105164279	3	FACETS	0.971	0.89	1	0.485	0.445	0.528	CLONAL	1	TRUE	1	0.355628581842273	3		762	1112	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486082	8486082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	236	820	0	ENST00000356435.5:c.2735C>T	p.Ser912Phe	p.S912F	ENST00000356435		912	tCc/tTc	17/35	0.355628581842273	3	FACETS	0.946	0.885	1	0.946	0.885	1	CLONAL	2	TRUE	1	0.355628581842273	3		820	826	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225449690	225449690	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	935	381	691	1	ENST00000264414.4:c.37G>A	p.Asp13Asn	p.D13N	ENST00000264414	NM_003590.4	13	Gac/Aac	1/16	0.288063792339433	4	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	2	0.355628581842273	4		692	1316	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47158132	47158132	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	342	702	2	ENST00000409792.3:c.4567C>T	p.Arg1523Cys	p.R1523C	ENST00000409792	NM_014159.6	1523	Cgt/Tgt	4/21	0.319333650353274	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.355628581842273	3		704	1045	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89858388	89858388	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	187	729	0	ENST00000389301.3:c.1172C>T	p.Ser391Phe	p.S391F	ENST00000389301	NM_000135.2	391	tCc/tTc	13/43	0.321086105164279	3	FACETS	1	0.981	1	0.598	0.552	0.646	CLONAL	1	TRUE	1	0.355628581842273	3		729	1036	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533874	63533874	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1309062534	NA	P-0013025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	215	472	0	ENST00000307078.5:c.1280C>T	p.Pro427Leu	p.P427L	ENST00000307078	NM_004655.3	427	cCc/cTc	6/11	0.329397331155218	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	0	0.355628581842273	2		472	595	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2220202	2220202	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	126	721	0	ENST00000398665.3:c.2787C>G	p.Ser929Arg	p.S929R	ENST00000398665	NM_032482.2	929	agC/agG	23/28	0.355628581842273	2	FACETS	0.83	0.751	0.913	0.415	0.375	0.457	CLONAL	1	TRUE	0	0.355628581842273	2		721	854	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271810	15271810	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	151	377	0	ENST00000263388.2:c.6629C>T	p.Pro2210Leu	p.P2210L	ENST00000263388	NM_000435.2	2210	cCt/cTt	33/33	0.288063792339433	4	FACETS	0.948	0.871	1	0.948	0.871	1	CLONAL	2	TRUE	2	0.355628581842273	4		377	607	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46281227	46281227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1174	349	982	0	ENST00000371998.3:c.4024C>T	p.Pro1342Ser	p.P1342S	ENST00000371998		1342	Ccc/Tcc	21/23	0.288063792339433	4	FACETS	0.874	0.825	0.923	0.874	0.825	0.923	CLONAL	2	TRUE	2	0.355628581842273	4		982	1523	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166570	118166571	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0013025-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	230	401	0	ENST00000369448.3:c.1080_1081delinsTT	p.Pro361Ser	p.P361S	ENST00000369448	NM_017709.3	360	gcCCct/gcTTct	2/2	0.341763488841896	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.355628581842273	4		401	791	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	37	280	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.951	0.791	1			1	INDETERMINATE	1	TRUE	NA	0.36536319817452	2		280	213	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579389	7579389	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1567555994	NA	P-0013044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	74	456	1	ENST00000269305.4:c.298C>T	p.Gln100Ter	p.Q100*	ENST00000269305	NM_001126112.2	100	Cag/Tag	4/11	0.36536319817452	1	FACETS	1	0.891	1	1	0.891	1	CLONAL	1	TRUE	0	0.36536319817452	1		457	328	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692995	89692995	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554898225	NA	P-0013044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	47	186	0	ENST00000371953.3:c.479C>T	p.Thr160Ile	p.T160I	ENST00000371953	NM_000314.4	160	aCc/aTc	5/9	0.36536319817452	1	FACETS	0.93	0.793	1	0.93	0.793	1	CLONAL	1	TRUE	0	0.36536319817452	1		186	226	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164703	36164703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	97	608	1	ENST00000300305.3:c.1172C>T	p.Ala391Val	p.A391V	ENST00000300305		391	gCg/gTg	8/8	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.36536319817452	2		609	490	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888199	112888199	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121918454	NA	P-0013044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	31	529	0	ENST00000351677.2:c.215C>A	p.Ala72Asp	p.A72D	ENST00000351677	NM_002834.3	72	gCc/gAc	3/16	1	2	FACETS	0.29	0.233	0.354	0.29	0.233	0.354	SUBCLONAL	1	TRUE	1	0.36536319817452	2		529	586	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46252677	46252677	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145292442	NA	P-0013044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	104	739	1	ENST00000371998.3:c.106C>T	p.Arg36Trp	p.R36W	ENST00000371998		36	Cgg/Tgg	4/23	0.36536319817452	1	FACETS	0.741	0.665	0.822	0.741	0.665	0.822	SUBCLONAL	1	TRUE	0	0.36536319817452	1		740	628	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36171648	36171648	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139336358	NA	P-0013044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	85	306	1	ENST00000300305.3:c.917G>A	p.Arg306His	p.R306H	ENST00000300305		306	cGt/cAt	7/8	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.36536319817452	2		307	373	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120529655	120529655	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0013044-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	164	554	0	ENST00000256646.2:c.802del	p.Arg268GlyfsTer128	p.R268Gfs*128	ENST00000256646	NM_024408.3	268	Agg/gg	5/34	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.36536319817452	2		554	646	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013052-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	85	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.651	0.578	0.729	0.651	0.578	0.729	SUBCLONAL	1	TRUE	1	0.594390017026619	2		280	439	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578475	7578514	+	frameshift_variant	Frame_Shift_Del	DEL	GGGGGTGTGGAATCAACCCACAGCTGCACAGGGCAGGTCT	GGGGGTGTGGAATCAACCCACAGCTGCACAGGGCAGGTCT	-	novel	NA	P-0013052-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	64	474	0	ENST00000269305.4:c.416_455del	p.Lys139SerfsTer18	p.K139Sfs*18	ENST00000269305	NM_001126112.2	139	aAGACCTGCCCTGTGCAGCTGTGGGTTGATTCCACACCCCCg/ag	5/11	0.502617534292178	3	FACETS	0.61	0.529	0.697	0.203	0.176	0.233	SUBCLONAL	1	TRUE	0	0.594390017026619	3		474	458	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	111	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.60427640603515	2		280	333	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149456863	149456863	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	222	576	0	ENST00000286301.3:c.865A>G	p.Thr289Ala	p.T289A	ENST00000286301	NM_005211.3	289	Acc/Gcc	6/22	1	2	FACETS	0.997	0.931	1	0.997	0.931	1	CLONAL	1	TRUE	1	0.60427640603515	2		576	737	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144819	58144819	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150281463	NA	P-0013057-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	44	620	0	ENST00000257904.6:c.409G>A	p.Val137Ile	p.V137I	ENST00000257904	NM_000075.3	137	Gtt/Att	4/8	1	2	FACETS	0.181	0.151	0.215	0.181	0.151	0.215	SUBCLONAL	1	TRUE	1	0.60427640603515	2		620	803	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	58	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.995	0.855	1	0.995	0.855	1	CLONAL	1	TRUE	1	0.21	2		280	555	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15818003	15818003	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013075-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	67	225	1	ENST00000307771.7:c.130C>T	p.Gln44Ter	p.Q44*	ENST00000307771	NM_005089.3	44	Cag/Tag	3/11	1	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	0	0.21	1		226	437	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	40	280	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.372133479682066	2		280	157	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233033	55233033	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013104-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	2583	600	2	ENST00000275493.2:c.1783T>A	p.Cys595Ser	p.C595S	ENST00000275493	NM_005228.3	595	Tgc/Agc	15/28	0.372133479682066	32	FACETS	0.986	0.976	0.996			1	CLONAL	30	TRUE	NA	0.372133479682066	32		602	3089	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0013111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	260	558	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	1	2	FACETS	0.922	0.864	0.982	0.922	0.864	0.982	CLONAL	1	TRUE	1	0.530886798967736	2		558	1062	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0013111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	54	300	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.873	0.754	1	0.873	0.754	1	CLONAL	1	TRUE	1	0.530886798967736	2		300	233	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276902	123276902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	230	758	0	ENST00000358487.5:c.1015G>A	p.Glu339Lys	p.E339K	ENST00000358487	NM_000141.4	339	Gaa/Aaa	8/18	NA	2	FACETS	0.912	0.851	0.975			1	INDETERMINATE	1	TRUE	NA	0.530886798967736	2		758	950	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985561	2985561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	142	596	0	ENST00000396946.4:c.250G>A	p.Gly84Arg	p.G84R	ENST00000396946	NM_032415.4	84	Ggg/Agg	4/25	NA	2	FACETS	0.748	0.683	0.816			1	INDETERMINATE	1	TRUE	NA	0.530886798967736	2		596	715	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16263844	16263844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	214	853	0	ENST00000375759.3:c.10213C>T	p.Pro3405Ser	p.P3405S	ENST00000375759	NM_015001.2	3405	Cca/Tca	12/15	1	2	FACETS	0.913	0.85	0.978	0.913	0.85	0.978	CLONAL	1	TRUE	1	0.530886798967736	2		853	883	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225376109	225376109	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	301	785	1	ENST00000264414.4:c.845C>A	p.Ser282Tyr	p.S282Y	ENST00000264414	NM_003590.4	282	tCt/tAt	6/16	1	2	FACETS	0.986	0.929	1	0.986	0.929	1	CLONAL	1	TRUE	1	0.530886798967736	2		786	1150	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430576	181430576	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	44	347	0	ENST00000325404.1:c.428T>C	p.Val143Ala	p.V143A	ENST00000325404	NM_003106.3	143	gTc/gCc	1/1	1	2	FACETS	0.513	0.432	0.602	0.513	0.432	0.602	SUBCLONAL	1	TRUE	1	0.530886798967736	2		347	323	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967957	93967957	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	306	1098	0	ENST00000369303.4:c.1970A>T	p.Lys657Ile	p.K657I	ENST00000369303	NM_004440.3	657	aAa/aTa	11/17	0.465072748154985	1	FACETS	0.619	0.582	0.657	0.619	0.582	0.657	SUBCLONAL	1	TRUE	0	0.530886798967736	1		1098	1368	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162475143	162475143	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	250	787	2	ENST00000366898.1:c.598C>T	p.His200Tyr	p.H200Y	ENST00000366898	NM_004562.2	200	Cac/Tac	5/12	0.530886798967736	1	FACETS	0.913	0.857	0.969	0.913	0.857	0.969	CLONAL	1	TRUE	0	0.530886798967736	1		789	758	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2949718	2949718	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	142	875	0	ENST00000396946.4:c.3226A>C	p.Ile1076Leu	p.I1076L	ENST00000396946	NM_032415.4	1076	Atc/Ctc	24/25	NA	2	FACETS	0.708	0.646	0.773			1	INDETERMINATE	1	TRUE	NA	0.530886798967736	2		875	756	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482879	140482879	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	251	694	0	ENST00000288602.6:c.1256C>T	p.Ser419Phe	p.S419F	ENST00000288602	NM_004333.4	419	tCt/tTt	10/18	1	2	FACETS	0.917	0.858	0.978	0.917	0.858	0.978	CLONAL	1	TRUE	1	0.530886798967736	2		694	1031	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097635	8097635	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	57	296	0	ENST00000346208.3:c.17A>C	p.Asp6Ala	p.D6A	ENST00000346208		6	gAc/gCc	2/6	1	2	FACETS	0.866	0.751	0.989	0.866	0.751	0.989	CLONAL	1	TRUE	1	0.530886798967736	2		296	248	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343150	118343150	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	209	722	0	ENST00000534358.1:c.1276C>G	p.Arg426Gly	p.R426G	ENST00000534358	NM_005933.3	426	Cgg/Ggg	3/36	1	2	FACETS	0.912	0.848	0.979	0.912	0.848	0.979	CLONAL	1	TRUE	1	0.530886798967736	2		722	863	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534795	18534795	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	176	667	0	ENST00000266497.5:c.1853C>T	p.Pro618Leu	p.P618L	ENST00000266497		618	cCa/cTa	12/31	NA	2	FACETS	0.779	0.718	0.842			1	INDETERMINATE	1	TRUE	NA	0.530886798967736	2		667	851	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66777494	66777494	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	132	522	0	ENST00000307102.5:c.860C>T	p.Pro287Leu	p.P287L	ENST00000307102	NM_002755.3	287	cCa/cTa	7/11	1	2	FACETS	0.862	0.785	0.942	0.862	0.785	0.942	CLONAL	1	TRUE	1	0.530886798967736	2		522	577	SUCCESS
BLM	641	MSKCC	GRCh37	15	91337577	91337577	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	139	352	0	ENST00000355112.3:c.3200G>T	p.Cys1067Phe	p.C1067F	ENST00000355112	NM_000057.2	1067	tGt/tTt	16/22	1	2	FACETS	0.829	0.757	0.904	0.829	0.757	0.904	CLONAL	1	TRUE	1	0.530886798967736	2		352	632	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897363	78897363	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	196	799	0	ENST00000306801.3:c.2698G>A	p.Asp900Asn	p.D900N	ENST00000306801	NM_020761.2	900	Gac/Aac	23/34	0.530886798967736	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.530886798967736	1		799	524	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122625	7122625	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	147	512	0	ENST00000302850.5:c.3529G>A	p.Asp1177Asn	p.D1177N	ENST00000302850	NM_000208.2	1177	Gac/Aac	19/22	1	2	FACETS	0.917	0.84	0.996	0.917	0.84	0.996	CLONAL	1	TRUE	1	0.530886798967736	2		512	604	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383312	42383312	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	275	977	0	ENST00000221972.3:c.332G>A	p.Gly111Asp	p.G111D	ENST00000221972	NM_021601.3	111	gGc/gAc	2/5	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.530886798967736	NA		977	1005	SUCCESS
AR	367	MSKCC	GRCh37	X	66863199	66863199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	193	487	1	ENST00000374690.3:c.1718G>A	p.Gly573Glu	p.G573E	ENST00000374690	NM_000044.3	573	gGa/gAa	2/8	1	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.530886798967736	1		488	454	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106261	27106261	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013111-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	178	577	0	ENST00000324856.7:c.5872del	p.Glu1958AsnfsTer57	p.E1958Nfs*57	ENST00000324856	NM_006015.4	1958	Gaa/aa	20/20	1	2	FACETS	0.804	0.742	0.869	0.804	0.742	0.869	CLONAL	1	TRUE	1	0.530886798967736	2		577	834	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	39	280	0				ENST00000310581	NM_198253.2	-/1132			0.402284707755523	1	FACETS	1	0.919	1	1	0.919	1	INDETERMINATE	1	FALSE	0	0.683231219884759	1		280	70	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660532	227660532	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013161-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	106	331	0	ENST00000305123.5:c.2923A>G	p.Ile975Val	p.I975V	ENST00000305123	NM_005544.2	975	Att/Gtt	1/2	0.557570700899529	6	FACETS	1	0.951	1			1	CLONAL	3	FALSE	NA	0.683231219884759	6		331	232	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	61	280	0				ENST00000310581	NM_198253.2	-/1132			0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		280	521	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2220642	2220642	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780287797	NA	P-0013168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1343	91	664	2	ENST00000326181.6:c.259G>A	p.Asp87Asn	p.D87N	ENST00000326181	NM_032271.2	87	Gac/Aac	5/21	0.110497456015181	3	FACETS		NA	1			1	NA	NA	FALSE	1	NA	3		666	1434	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506159	103506160	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0013168-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	43	331	0	ENST00000355739.4:c.318dup	p.Glu107ArgfsTer23	p.E107Rfs*23	ENST00000355739	NM_000123.3	106	aca/acAa	3/15	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		331	592	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0013180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	173	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.641731076687537	2		464	479	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0013180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	351	511	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.641731076687537	2		511	852	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0013180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	302	490	0	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.641731076687537	2		490	805	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162050	47162050	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	239	485	1	ENST00000409792.3:c.4076C>T	p.Ser1359Phe	p.S1359F	ENST00000409792	NM_014159.6	1359	tCc/tTc	3/21	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.641731076687537	2		486	634	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65348960	65348960	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs762318572	NA	P-0013180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	134	261	0	ENST00000342505.4:c.205C>T	p.Arg69Cys	p.R69C	ENST00000342505	NM_002227.2	69	Cgt/Tgt	3/25	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.641731076687537	2		261	405	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518061	103518061	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	503	428	0	ENST00000355739.4:c.1999C>T	p.Gln667Ter	p.Q667*	ENST00000355739	NM_000123.3	667	Caa/Taa	9/15	0.641731076687537	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	1	0.641731076687537	3		428	876	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248617	212248617	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765120252	NA	P-0013180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	356	611	0	ENST00000342788.4:c.3650G>A	p.Gly1217Glu	p.G1217E	ENST00000342788	NM_005235.2	1217	gGa/gAa	28/28	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.641731076687537	2		611	877	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627202	12627202	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	295	522	0	ENST00000251849.4:c.1514C>A	p.Pro505His	p.P505H	ENST00000251849	NM_002880.3	505	cCt/cAt	14/17	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.641731076687537	2		522	834	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442536	52442536	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	228	344	0	ENST00000460680.1:c.209C>T	p.Ser70Phe	p.S70F	ENST00000460680	NM_004656.3	70	tCc/tTc	4/17	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.641731076687537	2		344	631	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801157	1801157	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1181504082	NA	P-0013180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	238	484	0	ENST00000260795.2:c.286G>A	p.Val96Met	p.V96M	ENST00000260795		96	Gtg/Atg	2/17	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.641731076687537	2		484	584	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729478	41729478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	482	988	0	ENST00000242208.4:c.1051G>A	p.Glu351Lys	p.E351K	ENST00000242208	NM_002192.2	351	Gag/Aag	3/3	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.641731076687537	2		988	1346	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508553	106508553	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752518004	NA	P-0013180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	64	168	0	ENST00000359195.3:c.547C>T	p.Pro183Ser	p.P183S	ENST00000359195	NM_002649.2	183	Ccg/Tcg	2/11	0.641731076687537	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.641731076687537	1		168	112	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024150	31024150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs542568224	NA	P-0013180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	315	521	1	ENST00000375687.4:c.3635C>T	p.Ser1212Phe	p.S1212F	ENST00000375687	NM_015338.5	1212	tCc/tTc	13/13	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.641731076687537	2		522	739	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156741	20156741	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1449534841	NA	P-0013180-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	220	259	0	ENST00000379607.5:c.17-1G>A		p.X6_splice	ENST00000379607	NM_001412.3	6			1	1	FACETS	0.763	0.73	0.795	1	0.995	1	SUBCLONAL	2	TRUE	0	0.641731076687537	1		259	305	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013183-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	43	521	1	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		522	976	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121913385	NA	P-0013183-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	14	181	0	ENST00000304494.5:c.247C>G	p.His83Asp	p.H83D	ENST00000304494	NM_000077.4	83	Cac/Gac	2/3	1	2	FACETS		NA	1			1	NA	NA	FALSE	1	NA	2		181	280	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013204-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	151	280	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.656854411059906	2		280	348	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264459	30264459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013204-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	299	722	0	ENST00000322652.5:c.194G>A	p.Gly65Glu	p.G65E	ENST00000322652	NM_015355.2	65	gGg/gAg	1/16	0.656854411059906	1	FACETS	0.986	0.937	1	0.986	0.937	1	CLONAL	1	TRUE	0	0.656854411059906	1		722	620	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888189	112888189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507511	NA	P-0013204-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	232	741	0	ENST00000351677.2:c.205G>A	p.Glu69Lys	p.E69K	ENST00000351677	NM_002834.3	69	Gag/Aag	3/16	1	2	FACETS	0.925	0.865	0.985	0.925	0.865	0.985	CLONAL	1	TRUE	1	0.656854411059906	2		741	764	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29588828	29588828	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs137854555	NA	P-0013204-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	244	759	1	ENST00000356175.3:c.4614G>A	p.Trp1538Ter	p.W1538*	ENST00000356175	NM_000267.3	1538	tgG/tgA	34/57	0.656854411059906	1	FACETS	0.904	0.853	0.955	0.904	0.853	0.955	CLONAL	1	TRUE	0	0.656854411059906	1		760	552	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317568	1317568	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013204-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	218	644	1	ENST00000400841.2:c.497A>T	p.Asn166Ile	p.N166I	ENST00000400841		166	aAt/aTt	5/6	1	1	FACETS	0.726	0.679	0.773	0.726	0.679	0.773	SUBCLONAL	1	TRUE	0	0.656854411059906	1		645	614	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341914	8341914	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	296	739	1	ENST00000356435.5:c.4726G>A	p.Glu1576Lys	p.E1576K	ENST00000356435		1576	Gaa/Aaa	29/35	0.160781911047227	4	FACETS	0.999	0.941	1			1	CLONAL	4	TRUE	NA	0.165262767820111	4		740	1045	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	26	75	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.725	0.573	0.899	0.725	0.573	0.899	SUBCLONAL	1	TRUE	1	0.165262767820111	2		75	434	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212537918	212537918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146197533	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	74	693	1	ENST00000342788.4:c.1687G>A	p.Glu563Lys	p.E563K	ENST00000342788	NM_005235.2	563	Gaa/Aaa	14/28	1	2	FACETS	1	0.887	1	1	0.887	1	CLONAL	1	TRUE	1	0.165262767820111	2		694	881	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724328	117724328	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	64	776	0	ENST00000368508.3:c.551C>T	p.Pro184Leu	p.P184L	ENST00000368508	NM_002944.2	184	cCc/cTc	6/43	0.165262767820111	1	FACETS	0.705	0.608	0.81	0.705	0.608	0.81	SUBCLONAL	1	TRUE	0	0.165262767820111	1		776	1008	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	54	672	2	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.165262767820111	1	FACETS	0.717	0.611	0.834	0.717	0.611	0.834	SUBCLONAL	1	TRUE	0	0.165262767820111	1		674	836	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993828	72993828	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371922710	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	967	96	927	0	ENST00000268489.5:c.217G>A	p.Glu73Lys	p.E73K	ENST00000268489	NM_006885.3	73	Gag/Aag	2/10	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.165262767820111	2		927	1063	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412203	139412204	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	62	686	0	ENST00000277541.6:c.1441_1441+1delinsAA		p.X481_splice	ENST00000277541	NM_017617.3	481		8/34	1	2	FACETS	0.779	0.671	0.897	0.779	0.671	0.897	SUBCLONAL	1	TRUE	1	0.165262767820111	2		686	963	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162107	22162107	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	63	535	0	ENST00000215832.6:c.148C>T	p.Arg50Ter	p.R50*	ENST00000215832	NM_002745.4	50	Cga/Tga	2/9	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.165262767820111	2		535	748	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11297959	11297959	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1468487695	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1072	99	760	5	ENST00000361445.4:c.2149C>T	p.Arg717Ter	p.R717*	ENST00000361445	NM_004958.3	717	Cga/Tga	13/58	0.159086888925981	3	FACETS	1	0.947	1			1	CLONAL	1	TRUE	NA	0.165262767820111	3		765	1171	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099843	27099843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	67	586	0	ENST00000324856.7:c.3722G>A	p.Gly1241Glu	p.G1241E	ENST00000324856	NM_006015.4	1241	gGg/gAg	15/20	1	2	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	1	0.165262767820111	2		586	792	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	71873250	71873250	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747740530	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	84	1002	2	ENST00000357731.5:c.944C>T	p.Pro315Leu	p.P315L	ENST00000357731	NM_173808.2	315	cCa/cTa	7/7	1	2	FACETS	0.852	0.75	0.962	0.852	0.75	0.962	CLONAL	1	TRUE	1	0.165262767820111	2		1004	1193	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162688856	162688856	+	start_lost	Translation_Start_Site	SNP	G	G	A	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	146	692	0	ENST00000367921.3:c.3G>A	p.Met1?	p.M1?	ENST00000367921	NM_006182.2	1	atG/atA	3/18	0.165262767820111	3	FACETS	0.964	0.879	1	0.964	0.879	1	CLONAL	2	TRUE	1	0.165262767820111	3		692	992	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193091415	193091415	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	67	852	1	ENST00000367435.3:c.85G>A	p.Glu29Lys	p.E29K	ENST00000367435	NM_024529.4	29	Gag/Aag	1/17	0.165262767820111	3	FACETS	0.774	0.67	0.887	0.387	0.335	0.444	SUBCLONAL	1	TRUE	1	0.165262767820111	3		853	1134	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226570772	226570772	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1401471013	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	116	489	0	ENST00000366794.5:c.1124C>T	p.Ser375Leu	p.S375L	ENST00000366794	NM_001618.3	375	tCg/tTg	8/23	0.165262767820111	3	FACETS	0.997	0.899	1	0.997	0.899	1	CLONAL	2	TRUE	1	0.165262767820111	3		489	762	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25991682	25991682	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	58	636	0	ENST00000435504.4:c.560C>T	p.Ser187Phe	p.S187F	ENST00000435504		187	tCc/tTc	7/13	1	2	FACETS	0.755	0.646	0.874	0.755	0.646	0.874	SUBCLONAL	1	TRUE	1	0.165262767820111	2		636	930	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630700	158630700	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	111	857	1	ENST00000263640.3:c.544-1G>T		p.X182_splice	ENST00000263640	NM_001105.4	182			1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.165262767820111	2		858	1165	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209116178	209116178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	48	903	2	ENST00000345146.2:c.98C>T	p.Pro33Leu	p.P33L	ENST00000345146	NM_005896.2	33	cCc/cTc	3/10	1	2	FACETS	0.476	0.4	0.56	0.476	0.4	0.56	SUBCLONAL	1	TRUE	1	0.165262767820111	2		905	1221	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164526	47164526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	111	769	1	ENST00000409792.3:c.1600C>T	p.Pro534Ser	p.P534S	ENST00000409792	NM_014159.6	534	Cct/Tct	3/21	0.165262767820111	2	FACETS	1	0.981	1	0.717	0.643	0.795	CLONAL	1	TRUE	0	0.165262767820111	2		770	937	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138402603	138402603	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	79	856	0	ENST00000289153.2:c.2342C>T	p.Ser781Phe	p.S781F	ENST00000289153	NM_006219.2	781	tCc/tTc	16/22	0.165262767820111	3	FACETS	0.905	0.793	1	0.452	0.396	0.513	CLONAL	1	TRUE	1	0.165262767820111	3		856	1144	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524902	187524902	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1213260736	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1051	90	908	0	ENST00000441802.2:c.10778C>T	p.Ser3593Phe	p.S3593F	ENST00000441802	NM_005245.3	3593	tCc/tTc	19/27	1	2	FACETS	0.955	0.844	1	0.955	0.844	1	CLONAL	1	TRUE	1	0.165262767820111	2		908	1141	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534412	187534412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776487441	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	67	808	0	ENST00000441802.2:c.9314G>A	p.Arg3105Lys	p.R3105K	ENST00000441802	NM_005245.3	3105	aGa/aAa	13/27	1	2	FACETS	0.891	0.772	1	0.891	0.772	1	CLONAL	1	TRUE	1	0.165262767820111	2		808	910	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295198	1295198	+	upstream_gene_variant	5'Flank	SNP	A	A	C	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	24	358	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.752	0.589	0.941	0.752	0.589	0.941	CLONAL	1	TRUE	1	0.165262767820111	2		358	386	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047966	180047966	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	91	770	0	ENST00000261937.6:c.2209C>G	p.Arg737Gly	p.R737G	ENST00000261937	NM_182925.4	737	Cgc/Ggc	15/30	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.165262767820111	2		770	969	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041043	112041043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1423	129	1308	0	ENST00000368678.4:c.212C>T	p.Ser71Phe	p.S71F	ENST00000368678		71	tCt/tTt	3/13	0.165262767820111	1	FACETS	0.923	0.833	1	0.923	0.833	1	CLONAL	1	TRUE	0	0.165262767820111	1		1308	1552	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704548	117704548	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1136	69	910	0	ENST00000368508.3:c.2428G>A	p.Glu810Lys	p.E810K	ENST00000368508	NM_002944.2	810	Gaa/Aaa	16/43	0.165262767820111	1	FACETS	0.636	0.551	0.727	0.636	0.551	0.727	SUBCLONAL	1	TRUE	0	0.165262767820111	1		910	1205	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891655	151891655	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	40	365	0	ENST00000262189.6:c.4379-2A>G		p.X1460_splice	ENST00000262189	NM_170606.2	1460			1	2	FACETS	0.98	0.814	1	0.98	0.814	1	CLONAL	1	TRUE	1	0.165262767820111	2		365	494	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401303	139401303	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1085	97	836	0	ENST00000277541.6:c.3766C>T	p.Pro1256Ser	p.P1256S	ENST00000277541	NM_017617.3	1256	Ccg/Tcg	23/34	1	2	FACETS	0.993	0.883	1	0.993	0.883	1	CLONAL	1	TRUE	1	0.165262767820111	2		836	1182	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793298	139793298	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1410	116	1110	0	ENST00000247668.2:c.106G>C	p.Ala36Pro	p.A36P	ENST00000247668	NM_021138.3	36	Gcc/Ccc	2/11	1	2	FACETS	0.92	0.826	1	0.92	0.826	1	CLONAL	1	TRUE	1	0.165262767820111	2		1110	1526	SUCCESS
RET	5979	MSKCC	GRCh37	10	43619154	43619154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs794728687	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	99	874	0	ENST00000355710.3:c.2837C>T	p.Thr946Ile	p.T946I	ENST00000355710	NM_020975.4	946	aCc/aTc	17/20	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.165262767820111	2		874	1018	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32438045	32438045	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1407234143	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	1714	733	2	ENST00000332351.3:c.992G>A	p.Gly331Glu	p.G331E	ENST00000332351	NM_024426.4	331	gGg/gAg	5/10	0.165262767820111	21	FACETS	0.999	0.981	1			1	CLONAL	20	TRUE	NA	0.165262767820111	21		735	2669	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933369	100933369	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1377	101	1253	0	ENST00000325455.5:c.2021C>T	p.Thr674Ile	p.T674I	ENST00000325455	NM_001202474.3	674	aCt/aTt	4/8	1	2	FACETS	0.827	0.736	0.924	0.827	0.736	0.924	CLONAL	1	TRUE	1	0.165262767820111	2		1253	1478	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46245162	46245162	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	57	676	0	ENST00000334344.6:c.3256C>T	p.Pro1086Ser	p.P1086S	ENST00000334344	NM_152641.2	1086	Ccc/Tcc	15/21	1	2	FACETS	0.811	0.694	0.939	0.811	0.694	0.939	CLONAL	1	TRUE	1	0.165262767820111	2		676	851	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285566	46285566	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	84	489	0	ENST00000334344.6:c.4926G>A	p.Trp1642Ter	p.W1642*	ENST00000334344	NM_152641.2	1642	tgG/tgA	17/21	0.165262767820111	2	FACETS	0.878	0.777	0.986	0.878	0.777	0.986	CLONAL	2	TRUE	0	0.165262767820111	2		489	579	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49428255	49428255	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371223664	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	176	699	3	ENST00000301067.7:c.10445G>A	p.Arg3482Gln	p.R3482Q	ENST00000301067	NM_003482.3	3482	cGg/cAg	37/54	0.165262767820111	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	0	0.165262767820111	2		702	1014	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28896448	28896448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1044	88	775	0	ENST00000282397.4:c.3002C>T	p.Ser1001Phe	p.S1001F	ENST00000282397	NM_002019.4	1001	tCt/tTt	22/30	1	2	FACETS	0.941	0.831	1	0.941	0.831	1	CLONAL	1	TRUE	1	0.165262767820111	2		775	1132	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434766	110434766	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs923486089	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	98	700	0	ENST00000375856.3:c.3635C>T	p.Pro1212Leu	p.P1212L	ENST00000375856	NM_003749.2	1212	cCt/cTt	1/2	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.165262767820111	2		700	939	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961687	41961687	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1529	86	1350	3	ENST00000219905.7:c.595C>T	p.Arg199Cys	p.R199C	ENST00000219905	NM_001164273.1	199	Cgt/Tgt	2/24	1	2	FACETS	0.644	0.567	0.728	0.644	0.567	0.728	SUBCLONAL	1	TRUE	1	0.165262767820111	2		1353	1615	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500553	99500553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	39	672	0	ENST00000268035.6:c.3986C>T	p.Pro1329Leu	p.P1329L	ENST00000268035	NM_000875.3	1329	cCc/cTc	21/21	1	2	FACETS	0.607	0.501	0.725	0.607	0.501	0.725	SUBCLONAL	1	TRUE	1	0.165262767820111	2		672	778	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222541	2222541	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1271645823	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	217	971	0	ENST00000326181.6:c.735G>A	p.Met245Ile	p.M245I	ENST00000326181	NM_032271.2	245	atG/atA	9/21	0.0201510528049398	3	FACETS	1	0.979	1			1	INDETERMINATE	2	TRUE	NA	0.165262767820111	3		971	1244	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858186	9858186	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377746289	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	211	998	0	ENST00000330684.3:c.3215G>A	p.Arg1072Lys	p.R1072K	ENST00000330684	NM_001134407.1	1072	aGg/aAg	13/13	0.165262767820111	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	0	0.165262767820111	2		998	1263	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56872940	56872940	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1515	117	1205	0	ENST00000308159.5:c.2095T>C	p.Phe699Leu	p.F699L	ENST00000308159	NM_014669.4	699	Ttt/Ctt	19/22	1	2	FACETS	0.868	0.779	0.962	0.868	0.779	0.962	CLONAL	1	TRUE	1	0.165262767820111	2		1205	1632	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81941318	81941318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	104	1018	1	ENST00000359376.3:c.1496C>T	p.Ala499Val	p.A499V	ENST00000359376	NM_002661.3	499	gCc/gTc	16/33	1	2	FACETS	0.988	0.882	1	0.988	0.882	1	CLONAL	1	TRUE	1	0.165262767820111	2		1019	1274	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877132	89877132	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs372691338	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	64	617	0	ENST00000389301.3:c.505G>C	p.Glu169Gln	p.E169Q	ENST00000389301	NM_000135.2	169	Gaa/Caa	5/43	0.095999167932348	3	FACETS	0.903	0.78	1	0.451	0.39	0.519	INDETERMINATE	1	TRUE	1	0.165262767820111	3		617	929	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548880	29548880	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	62	572	0	ENST00000356175.3:c.1654C>G	p.Leu552Val	p.L552V	ENST00000356175	NM_000267.3	552	Ctt/Gtt	15/57	0.165262767820111	2	FACETS	1	0.937	1	0.575	0.497	0.661	CLONAL	1	TRUE	0	0.165262767820111	2		572	652	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267503	7267503	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	139	883	0	ENST00000302850.5:c.505G>C	p.Asp169His	p.D169H	ENST00000302850	NM_000208.2	169	Gat/Cat	2/22	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.165262767820111	2		883	1229	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145629	11145629	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	50	566	0	ENST00000358026.2:c.3991C>T	p.Pro1331Ser	p.P1331S	ENST00000358026	NM_001128849.1	1331	Ccc/Tcc	29/36	1	2	FACETS	0.808	0.684	0.945	0.808	0.684	0.945	CLONAL	1	TRUE	1	0.165262767820111	2		566	749	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860333	42860333	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758778273	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1096	102	928	1	ENST00000398585.3:c.544G>A	p.Glu182Lys	p.E182K	ENST00000398585	NM_001135099.1	182	Gag/Aag	5/14	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.165262767820111	2		929	1198	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41572841	41572841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	93	920	0	ENST00000263253.7:c.5126G>A	p.Gly1709Asp	p.G1709D	ENST00000263253	NM_001429.3	1709	gGc/gAc	31/31	1	2	FACETS	0.882	0.782	0.99	0.882	0.782	0.99	CLONAL	1	TRUE	1	0.165262767820111	2		920	1276	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938082	76938082	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	94	418	0	ENST00000373344.5:c.2666C>G	p.Ser889Cys	p.S889C	ENST00000373344	NM_000489.3	889	tCt/tGt	9/35	1	1	FACETS	1	0.896	1	1	0.986	1	CLONAL	2	TRUE	0	0.165262767820111	1		418	520	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042169	6042170	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1120	266	881	0	ENST00000265849.7:c.451dup	p.Arg151ProfsTer21	p.R151Pfs*21	ENST00000265849	NM_000535.5	151	cgc/cCgc	5/15	0.165262767820111	4	FACETS	0.902	0.844	0.962	0.902	0.844	0.962	CLONAL	3	TRUE	1	0.165262767820111	4		881	1386	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562633	21562634	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	42	250	0	ENST00000382592.4:c.1285_1286delinsTT	p.Pro429Phe	p.P429F	ENST00000382592	NM_014572.2	429	CCc/TTc	4/8	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.165262767820111	2		250	415	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534429	63534430	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	134	613	1	ENST00000307078.5:c.1091_1092delinsTT	p.Pro364Leu	p.P364L	ENST00000307078	NM_004655.3	364	cCC/cTT	5/11	0.165262767820111	2	FACETS	0.931	0.846	1	0.931	0.846	1	CLONAL	2	TRUE	0	0.165262767820111	2		614	871	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308147	30308148	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	61	719	0	ENST00000262643.3:c.284_285delinsAA	p.Arg95Gln	p.R95Q	ENST00000262643	NM_001238.2	95	cGG/cAA	5/12	1	2	FACETS	0.749	0.644	0.864	0.749	0.644	0.864	SUBCLONAL	1	TRUE	1	0.165262767820111	2		719	985	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671744	67671745	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	53	605	1	ENST00000264010.4:c.2153_2154delinsTT	p.Pro718Leu	p.P718L	ENST00000264010	NM_006565.3	718	cCC/cTT	12/12	1	2	FACETS	0.726	0.618	0.846	0.726	0.618	0.846	SUBCLONAL	1	TRUE	1	0.165262767820111	2		606	883	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56111496	56111497	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	20	181	1	ENST00000399503.3:c.96_97delinsAA	p.Ala33Thr	p.A33T	ENST00000399503	NM_005921.1	32	aaGGcg/aaAAcg	1/20	1	2	FACETS	0.938	0.719	1	0.938	0.719	1	CLONAL	1	TRUE	1	0.165262767820111	2		182	258	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15942917	15942918	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	53	780	0	ENST00000268712.3:c.6784_6785delinsAA	p.Gly2262Lys	p.G2262K	ENST00000268712	NM_006311.3	2262	GGg/AAg	44/46	0.165262767820111	1	FACETS	0.695	0.591	0.809	0.695	0.591	0.809	SUBCLONAL	1	TRUE	0	0.165262767820111	1		780	847	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784030	9784031	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0013218-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1210	66	914	0	ENST00000377346.4:c.2598_2599delinsAA	p.Ala867Thr	p.A867T	ENST00000377346	NM_005026.3	866	gaGGcc/gaAAcc	21/24	0.159086888925981	3	FACETS	0.678	0.586	0.778			1	SUBCLONAL	1	TRUE	NA	0.165262767820111	3		914	1276	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578398	7578398	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1064795203	NA	P-0013260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	380	381	0	ENST00000269305.4:c.532C>G	p.His178Asp	p.H178D	ENST00000269305	NM_001126112.2	178	Cac/Gac	5/11	0.676687875833703	2	FACETS	0.948	0.914	0.98	0.948	0.914	0.98	CLONAL	2	TRUE	0	0.713422274266695	2		381	562	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55241707	55241707	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs28929495	NA	P-0013260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	865	575	1	ENST00000275493.2:c.2155G>T	p.Gly719Cys	p.G719C	ENST00000275493	NM_005228.3	719	Ggc/Tgc	18/28	0.588510971373986	5	FACETS	0.944	0.917	0.972			1	CLONAL	3	TRUE	NA	0.713422274266695	5		576	1772	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249005	55249005	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913465	NA	P-0013260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	743	536	0	ENST00000275493.2:c.2303G>T	p.Ser768Ile	p.S768I	ENST00000275493	NM_005228.3	768	aGc/aTc	20/28	0.588510971373986	5	FACETS	0.969	0.938	0.999			1	CLONAL	3	TRUE	NA	0.713422274266695	5		536	1484	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793298	242793298	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0013260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	262	573	0	ENST00000334409.5:c.779C>G	p.Ser260Ter	p.S260*	ENST00000334409	NM_005018.2	260	tCa/tGa	5/5	0.699955092182405	3	FACETS	1	0.968	1	0.524	0.491	0.557	CLONAL	1	TRUE	1	0.713422274266695	3		573	951	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66535408	66535408	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1163511215	NA	P-0013260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	151	177	2	ENST00000273854.3:c.53G>T	p.Gly18Val	p.G18V	ENST00000273854	NM_004439.5	18	gGc/gTc	1/18	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.713422274266695	2		179	310	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295226	1295226	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0013260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	292	198	0				ENST00000310581	NM_198253.2	-/1132			0.673751362552454	5	FACETS	1	0.98	1	1	0.98	1	CLONAL	3	TRUE	2	0.713422274266695	5		198	536	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562585	176562585	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	219	331	0	ENST00000439151.2:c.481G>T	p.Asp161Tyr	p.D161Y	ENST00000439151	NM_022455.4	161	Gat/Tat	2/23	0.673751362552454	5	FACETS	1	0.96	1	0.35	0.324	0.376	CLONAL	1	TRUE	2	0.713422274266695	5		331	1212	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342647	70342647	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013260-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1303	420	818	2	ENST00000374080.3:c.1408C>T	p.Arg470Cys	p.R470C	ENST00000374080		470	Cgc/Tgc	10/45	0.700414729072414	3	FACETS	0.927	0.881	0.974	0.464	0.44	0.487	CLONAL	1	TRUE	1	0.713422274266695	3		820	1723	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0013274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	112	229	0				ENST00000310581	NM_198253.2	-/1132			0.30457261141677	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	0	0.33	2		229	318	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0013274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	283	511	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.30457261141677	3	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	1	0.33	3		511	987	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145430	58145430	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs104894340	NA	P-0013274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	248	573	0	ENST00000257904.6:c.71G>T	p.Arg24Leu	p.R24L	ENST00000257904	NM_000075.3	24	cGt/cTt	2/8	0.24163349240542	3	FACETS	1	0.985	1	0.771	0.724	0.819	CLONAL	2	TRUE	0	0.33	3		573	757	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486082	8486082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	258	820	0	ENST00000356435.5:c.2735C>T	p.Ser912Phe	p.S912F	ENST00000356435		912	tCc/tTc	17/35	0.280262708084657	2	FACETS	0.853	0.8	0.907	0.853	0.8	0.907	CLONAL	2	TRUE	0	0.33	2		820	917	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151949698	151949698	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	300	772	1	ENST00000262189.6:c.1402C>T	p.Pro468Ser	p.P468S	ENST00000262189	NM_170606.2	468	Ccc/Tcc	10/59	0.17046298912273	5	FACETS	1	0.977	1	0.717	0.675	0.761	INDETERMINATE	2	TRUE	2	0.33	5		773	1263	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48881523	48881523	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755704180	NA	P-0013274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	163	619	0	ENST00000267163.4:c.245C>T	p.Ser82Leu	p.S82L	ENST00000267163	NM_000321.2	82	tCa/tTa	2/27	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.33	2		619	827	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520156	9520156	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	268	653	0	ENST00000353224.5:c.2113C>T	p.Pro705Ser	p.P705S	ENST00000353224	NM_177990.2	705	Cca/Tca	10/10	0.178206154818227	5	FACETS	1	0.976	1	0.721	0.676	0.767	INDETERMINATE	2	TRUE	2	0.33	5		653	1123	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579408	7579414	+	frameshift_variant	Frame_Shift_Del	DEL	CAGGGGC	CAGGGGC	-	rs1064796124	NA	P-0013274-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	183	548	2	ENST00000269305.4:c.273_279del	p.Trp91CysfsTer30	p.W91Cfs*30	ENST00000269305	NM_001126112.2	91	tgGCCCCTG/tg	4/11	0.273778259690539	2	FACETS	0.818	0.758	0.88	0.818	0.758	0.88	CLONAL	2	TRUE	0	0.33	2		550	678	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013318-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	57	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.257883259486475	2		280	362	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0013318-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	287	511	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.240634706164309	2	FACETS	0.997	0.938	1	0.997	0.938	1	CLONAL	2	TRUE	0	0.257883259486475	2		511	1116	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47161957	47161957	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0013318-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	97	406	0	ENST00000409792.3:c.4169C>A	p.Ser1390Ter	p.S1390*	ENST00000409792	NM_014159.6	1390	tCa/tAa	3/21	1	2	FACETS	0.928	0.826	1	0.928	0.826	1	CLONAL	1	TRUE	1	0.257883259486475	2		406	811	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876359	35876359	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013318-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	79	406	0	ENST00000303115.3:c.1151C>A	p.Ser384Tyr	p.S384Y	ENST00000303115	NM_002185.3	384	tCt/tAt	8/8	1	2	FACETS	0.88	0.774	0.995	0.88	0.774	0.995	CLONAL	1	TRUE	1	0.257883259486475	2		406	696	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046367	180046367	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013318-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	56	404	0	ENST00000261937.6:c.2648-1G>A		p.X883_splice	ENST00000261937	NM_182925.4	883			0.257883259486475	1	FACETS	0.88	0.756	1	0.88	0.756	1	CLONAL	1	TRUE	0	0.257883259486475	1		404	430	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32414251	32414251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121907910	NA	P-0013318-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	143	535	0	ENST00000332351.3:c.1300C>T	p.Arg434Cys	p.R434C	ENST00000332351	NM_024426.4	434	Cgt/Tgt	8/10	1	2	FACETS	0.882	0.802	0.967	0.882	0.802	0.967	CLONAL	1	TRUE	1	0.257883259486475	2		535	1257	SUCCESS
ATM	472	MSKCC	GRCh37	11	108137897	108137897	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0013318-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	105	403	1	ENST00000278616.4:c.2467-1G>T		p.X823_splice	ENST00000278616	NM_000051.3	823			0.257883259486475	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.257883259486475	1		404	663	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81902827	81902827	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013318-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1471	191	738	0	ENST00000359376.3:c.488T>A	p.Leu163His	p.L163H	ENST00000359376	NM_002661.3	163	cTc/cAc	6/33	1	2	FACETS	0.891	0.821	0.965	0.891	0.821	0.965	CLONAL	1	TRUE	1	0.257883259486475	2		738	1662	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	29	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.476	0.381	0.583	0.476	0.381	0.583	SUBCLONAL	1	TRUE	1	0.285535578197908	2		280	427	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0013343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	217	489	1	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.27522027941313	3	FACETS	0.884	0.823	0.948	0.884	0.823	0.948	CLONAL	2	TRUE	1	0.285535578197908	3		490	982	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0013343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	42	157	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.285535578197908	1	FACETS	0.981	0.825	1	0.981	0.825	1	CLONAL	1	TRUE	0	0.285535578197908	1		157	257	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971187	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0013343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	43	164	0	ENST00000304494.5:c.171_172delinsTT	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	57	gcCCga/gcTTga	2/3	0.285535578197908	1	FACETS	0.978	0.824	1	0.978	0.824	1	CLONAL	1	TRUE	0	0.285535578197908	1		164	264	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244997	46244997	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs868082376	NA	P-0013343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	152	739	0	ENST00000334344.6:c.3091C>T	p.Gln1031Ter	p.Q1031*	ENST00000334344	NM_152641.2	1031	Cag/Tag	15/21	1	2	FACETS	0.796	0.726	0.87	0.796	0.726	0.87	SUBCLONAL	1	TRUE	1	0.285535578197908	2		739	1338	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266134	41266136	+	inframe_deletion	In_Frame_Del	DEL	CTT	CTT	-	rs587776850	NA	P-0013343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	106	502	0	ENST00000349496.5:c.133_135del	p.Ser45del	p.S45del	ENST00000349496	NM_001904.3	44	cCTTct/cct	3/15	1	2	FACETS	0.869	0.779	0.966	0.869	0.779	0.966	CLONAL	1	TRUE	1	0.285535578197908	2		502	854	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412470	63412470	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1285	156	931	0	ENST00000330258.3:c.697G>A	p.Asp233Asn	p.D233N	ENST00000330258	NM_152424.3	233	Gat/Aat	2/2	1	2	FACETS	0.758	0.692	0.828	0.758	0.692	0.828	SUBCLONAL	1	TRUE	1	0.285535578197908	2		931	1441	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713470	40713470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318044562	NA	P-0013343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	82	424	0	ENST00000373198.4:c.4045C>T	p.Arg1349Cys	p.R1349C	ENST00000373198	NM_133170.3	1349	Cgt/Tgt	30/32	1	2	FACETS	0.859	0.757	0.967	0.859	0.757	0.967	CLONAL	1	TRUE	1	0.285535578197908	2		424	669	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856664	111856664	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1188274508	NA	P-0013343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	120	404	0	ENST00000341259.2:c.715C>T	p.Leu239Phe	p.L239F	ENST00000341259	NM_005475.2	239	Ctc/Ttc	2/8	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.285535578197908	2		404	782	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55141020	55141020	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	46	537	0	ENST00000257290.5:c.1666G>A	p.Glu556Lys	p.E556K	ENST00000257290	NM_006206.4	556	Gaa/Aaa	12/23	1	2	FACETS	0.435	0.365	0.512	0.435	0.365	0.512	SUBCLONAL	1	TRUE	1	0.285535578197908	2		537	741	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143518	30143518	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	27	106	0	ENST00000389048.3:c.8C>T	p.Ala3Val	p.A3V	ENST00000389048	NM_004304.4	3	gCc/gTc	1/29	1	2	FACETS	0.965	0.773	1	0.965	0.773	1	CLONAL	1	TRUE	1	0.285535578197908	2		106	196	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106162534	106162534	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	61	448	1	ENST00000380013.4:c.3448C>T	p.His1150Tyr	p.H1150Y	ENST00000380013	NM_001127208.2	1150	Cat/Tat	4/11	1	2	FACETS	0.763	0.658	0.877	0.763	0.658	0.877	SUBCLONAL	1	TRUE	1	0.285535578197908	2		449	560	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549391	187549391	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	95	656	0	ENST00000441802.2:c.4727C>T	p.Ala1576Val	p.A1576V	ENST00000441802	NM_005245.3	1576	gCc/gTc	9/27	1	2	FACETS	0.591	0.525	0.663	0.591	0.525	0.663	SUBCLONAL	1	TRUE	1	0.285535578197908	2		656	1125	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876461	35876461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	44	492	0	ENST00000303115.3:c.1253C>T	p.Pro418Leu	p.P418L	ENST00000303115	NM_002185.3	418	cCa/cTa	8/8	1	2	FACETS	0.39	0.326	0.462	0.39	0.326	0.462	SUBCLONAL	1	TRUE	1	0.285535578197908	2		492	790	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123260433	123260433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	87	500	0	ENST00000358487.5:c.1468G>A	p.Gly490Ser	p.G490S	ENST00000358487	NM_000141.4	490	Ggt/Agt	11/18	1	2	FACETS	0.828	0.733	0.93	0.828	0.733	0.93	CLONAL	1	TRUE	1	0.285535578197908	2		500	736	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625223	69625223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369547972	NA	P-0013343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	138	605	1	ENST00000334134.2:c.570G>A	p.Met190Ile	p.M190I	ENST00000334134	NM_005247.2	190	atG/atA	3/3	1	2	FACETS	0.916	0.832	1	0.916	0.832	1	CLONAL	1	TRUE	1	0.285535578197908	2		606	1055	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552663	18552663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	104	694	0	ENST00000266497.5:c.2074C>T	p.Pro692Ser	p.P692S	ENST00000266497		692	Cct/Tct	14/31	1	2	FACETS	0.72	0.643	0.802	0.72	0.643	0.802	SUBCLONAL	1	TRUE	1	0.285535578197908	2		694	1012	SUCCESS
AR	367	MSKCC	GRCh37	X	66937413	66937413	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	140	730	0	ENST00000374690.3:c.2267C>T	p.Thr756Ile	p.T756I	ENST00000374690	NM_000044.3	756	aCc/aTc	5/8	1	2	FACETS	0.805	0.731	0.883	0.805	0.731	0.883	CLONAL	1	TRUE	1	0.285535578197908	2		730	1218	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020155	123020155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778612322	NA	P-0013343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	175	744	0	ENST00000355640.3:c.643C>T	p.Arg215Cys	p.R215C	ENST00000355640		215	Cgt/Tgt	2/7	1	2	FACETS	0.944	0.867	1	0.944	0.867	1	CLONAL	1	TRUE	1	0.285535578197908	2		744	1299	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007643	45007799	+	frameshift_variant	Frame_Shift_Del	DEL	CTCACGTCATCCAGCAGAGAATGGAAAGTCAAATTTCCTGAATTGCTATGTGTCTGGGTTTCATCCATCCGACATTGAAGTTGACTTACTGAAGAATGGAGAGAGAATTGAAAAAGTGGAGCATTCAGACTTGTCTTTCAGCAAGGACTGGTCTTTC	CTCACGTCATCCAGCAGAGAATGGAAAGTCAAATTTCCTGAATTGCTATGTGTCTGGGTTTCATCCATCCGACATTGAAGTTGACTTACTGAAGAATGGAGAGAGAATTGAAAAAGTGGAGCATTCAGACTTGTCTTTCAGCAAGGACTGGTCTTTC	-	novel	NA	P-0013343-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	62	357	0	ENST00000558401.1:c.90_246del	p.Ser31IlefsTer20	p.S31Ifs*20	ENST00000558401	NM_004048.2	30	taCTCACGTCATCCAGCAGAGAATGGAAAGTCAAATTTCCTGAATTGCTATGTGTCTGGGTTTCATCCATCCGACATTGAAGTTGACTTACTGAAGAATGGAGAGAGAATTGAAAAAGTGGAGCATTCAGACTTGTCTTTCAGCAAGGACTGGTCTTTC/ta	2/4	0.285535578197908	1	FACETS	0.666	0.575	0.764	0.666	0.575	0.764	SUBCLONAL	1	TRUE	0	0.285535578197908	1		357	559	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0013347-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	61	464	0				ENST00000310581	NM_198253.2	-/1132			0.22884487719476	3	FACETS	0.814	0.724	0.904	0.814	0.724	0.904	INDETERMINATE	2	TRUE	1	0.793080989067386	3		464	132	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0013347-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	145	769	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	0.22884487719476	3	FACETS	1	0.989	1	0.723	0.669	0.778	INDETERMINATE	1	TRUE	1	0.793080989067386	3		769	353	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006218	22006218	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1204549439	NA	P-0013347-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	87	366	0	ENST00000276925.6:c.185C>T	p.Ala62Val	p.A62V	ENST00000276925	NM_004936.3	62	gCg/gTg	2/2	0.208532490736729	4	FACETS	0.902	0.815	0.992	0.902	0.815	0.992	INDETERMINATE	2	TRUE	2	0.793080989067386	4		366	218	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606334	93606334	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs796052158	NA	P-0013347-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	101	578	2	ENST00000375746.1:c.154G>A	p.Ala52Thr	p.A52T	ENST00000375746	NM_001174167.1	52	Gcc/Acc	2/14	0.208532490736729	4	FACETS	0.948	0.863	1	0.948	0.863	1	INDETERMINATE	2	TRUE	2	0.793080989067386	4		580	241	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578439	7578439	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013347-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	151	104	579	1	ENST00000269305.4:c.491A>G	p.Lys164Arg	p.K164R	ENST00000269305	NM_001126112.2	164	aAg/aGg	5/11	0.22884487719476	3	FACETS	1	0.984	1	0.718	0.655	0.783	INDETERMINATE	1	TRUE	1	0.793080989067386	3		580	255	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819709	81819709	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013347-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	48	876	0	ENST00000359376.3:c.115G>A	p.Glu39Lys	p.E39K	ENST00000359376	NM_002661.3	39	Gag/Aag	2/33	0.136747304259447	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.793080989067386	0		876	318	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131160	55131160	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013347-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7807	2862	820	0	ENST00000257290.5:c.703T>A	p.Cys235Ser	p.C235S	ENST00000257290	NM_006206.4	235	Tgt/Agt	5/23	0.793080989067386	57	FACETS	1	0.994	1			1	CLONAL	15	TRUE	NA	0.793080989067386	57		820	10669	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045957	26045957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013347-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	79	1130	0	ENST00000540144.1:c.319G>A	p.Asp107Asn	p.D107N	ENST00000540144	NM_003531.2	107	Gac/Aac	1/1	0.217975905074787	5	FACETS	0.95	0.839	1	0.317	0.279	0.357	INDETERMINATE	1	TRUE	2	0.793080989067386	5		1130	459	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	142	280	0				ENST00000310581	NM_198253.2	-/1132			0.3	4	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	4		280	292	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39775601	39775601	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146705250	NA	P-0013380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	186	410	0	ENST00000288319.7:c.419G>A	p.Arg140Gln	p.R140Q	ENST00000288319	NM_182918.3	140	cGg/cAg	4/10	0.3	2	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	2		410	420	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89725050	89725064	+	inframe_deletion	In_Frame_Del	DEL	CTGTACTTCACAAAA	CTGTACTTCACAAAA	-	novel	NA	P-0013380-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	277	434	0	ENST00000371953.3:c.1033_1047del	p.Leu345_Lys349del	p.L345_K349del	ENST00000371953	NM_000314.4	345	CTGTACTTCACAAAA/-	9/9	0.3	3	FACETS		NA	1			1	NA	NA	FALSE	NA	NA	3		434	361	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	61	280	0				ENST00000310581	NM_198253.2	-/1132			0.273624807057154	2	FACETS	0.789	0.694	0.888	0.395	0.347	0.444	INDETERMINATE	1	FALSE	0	0.86331819537957	2		280	179	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256530	115256530	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs121913254	NA	P-0013413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	448	558	0	ENST00000369535.4:c.181C>A	p.Gln61Lys	p.Q61K	ENST00000369535	NM_002524.4	61	Caa/Aaa	3/7	0.86331819537957	3	FACETS	1	0.984	1	0.689	0.665	0.713	CLONAL	2	FALSE	0	0.86331819537957	3		558	719	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467675	50467675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759124417	NA	P-0013413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	99	499	0	ENST00000331340.3:c.910G>A	p.Glu304Lys	p.E304K	ENST00000331340	NM_006060.4	304	Gaa/Aaa	8/8	0.0357538978572984	3	FACETS	0.587	0.526	0.653			1	INDETERMINATE	1	FALSE	NA	0.86331819537957	3		499	559	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0013413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	154	157	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.86331819537957	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	FALSE	0	0.86331819537957	2		157	168	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434663	49434663	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778904794	NA	P-0013413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	369	567	0	ENST00000301067.7:c.6890C>T	p.Pro2297Leu	p.P2297L	ENST00000301067	NM_003482.3	2297	cCt/cTt	31/54	0.85232373873575	3	FACETS	0.998	0.959	1	0.998	0.959	1	CLONAL	2	FALSE	1	0.86331819537957	3		567	613	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0013413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	62	75	0				ENST00000310581	NM_198253.2	-/1132			0.273624807057154	2	FACETS	0.84	0.741	0.942	0.42	0.37	0.471	INDETERMINATE	1	FALSE	0	0.86331819537957	2		75	171	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	240484	240484	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1205384855	NA	P-0013413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	40	181	0	ENST00000264932.6:c.1444C>T	p.Pro482Ser	p.P482S	ENST00000264932	NM_004168.2	482	Cct/Tct	11/15	0.273624807057154	2	FACETS	0.53	0.446	0.62	0.265	0.223	0.31	INDETERMINATE	1	FALSE	0	0.86331819537957	2		181	175	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027081	71027081	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	391	421	0	ENST00000318789.4:c.1246C>T	p.Pro416Ser	p.P416S	ENST00000318789	NM_032682.5	416	Ccc/Tcc	15/21	0.86331819537957	3	FACETS	0.981	0.943	1	0.981	0.943	1	CLONAL	2	FALSE	1	0.86331819537957	3		421	661	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149241	119149241	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867564832	NA	P-0013413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	87	503	704	0	ENST00000264033.4:c.1249C>T	p.Pro417Ser	p.P417S	ENST00000264033	NM_005188.3	417	Cct/Tct	9/16	0.86331819537957	2	FACETS	0.988	0.966	1	0.988	0.966	1	CLONAL	2	FALSE	0	0.86331819537957	2		704	590	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445530	49445530	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	627	453	0	ENST00000301067.7:c.1936C>T	p.Pro646Ser	p.P646S	ENST00000301067	NM_003482.3	646	Ccc/Tcc	10/54	0.85232373873575	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	FALSE	1	0.86331819537957	3		453	920	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971187	21971188	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0013413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	12	157	167	0	ENST00000304494.5:c.170_171delinsTT	p.Ala57Val	p.A57V	ENST00000304494	NM_000077.4	57	gCC/gTT	2/3	0.86331819537957	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	FALSE	0	0.86331819537957	2		167	169	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261061	16261061	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0013413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	254	325	0	ENST00000375759.3:c.8326A>T	p.Arg2776Ter	p.R2776*	ENST00000375759	NM_015001.2	2776	Aga/Tga	11/15	0.772950309802456	3	FACETS	0.91	0.864	0.955	0.606	0.576	0.637	CLONAL	2	FALSE	0	0.86331819537957	3		325	463	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182744	38182744	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	452	582	1	ENST00000396334.3:c.897G>A	p.Trp299Ter	p.W299*	ENST00000396334	NM_002468.4	299	tgG/tgA	5/5	0.86331819537957	3	FACETS	0.995	0.96	1	0.995	0.96	1	CLONAL	2	FALSE	1	0.86331819537957	3		583	753	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643923	52643923	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	108	378	0	ENST00000394830.3:c.1973T>C	p.Met658Thr	p.M658T	ENST00000394830	NM_018313.4	658	aTg/aCg	17/30	0.86331819537957	3	FACETS	0.82	0.74	0.902	0.41	0.37	0.451	CLONAL	1	FALSE	1	0.86331819537957	3		378	437	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33289058	33289058	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	564	601	0	ENST00000374542.5:c.494C>T	p.Ser165Phe	p.S165F	ENST00000374542	NM_001141970.1	165	tCc/tTc	3/8	0.713994714011026	4	FACETS	0.985	0.948	1	0.985	0.948	1	CLONAL	2	FALSE	2	0.86331819537957	4		601	1236	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514332	69514332	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1376908325	NA	P-0013413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1525	141	421	0	ENST00000294312.3:c.349G>A	p.Glu117Lys	p.E117K	ENST00000294312	NM_005117.2	117	Gag/Aag	3/3	0.86331819537957	6	FACETS	0.535	0.485	0.587			1	SUBCLONAL	1	FALSE	NA	0.86331819537957	6		421	1666	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573933	18573933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	63	455	0	ENST00000266497.5:c.2251G>A	p.Asp751Asn	p.D751N	ENST00000266497		751	Gat/Aat	15/31	NA	2	FACETS	0.502	0.437	0.57			1	INDETERMINATE	1	FALSE	NA	0.86331819537957	2		455	291	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610525	81610525	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	216	553	0	ENST00000298171.2:c.2123G>A	p.Gly708Glu	p.G708E	ENST00000298171	NM_000369.2	708	gGg/gAg	10/10	0.422630346347834	4	FACETS	0.956	0.889	1			1	INDETERMINATE	1	FALSE	NA	0.86331819537957	4		553	975	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969953	81969953	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	438	810	1	ENST00000359376.3:c.3022C>T	p.Gln1008Ter	p.Q1008*	ENST00000359376	NM_002661.3	1008	Cag/Tag	27/33	0.627736841241268	1	FACETS	0.8	0.771	0.828	0.8	0.771	0.828	SUBCLONAL	1	FALSE	0	0.86331819537957	1		811	721	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10257168	10257168	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	195	294	337	0	ENST00000340748.4:c.2705T>G	p.Met902Arg	p.M902R	ENST00000340748		902	aTg/aGg	27/40	0.244550101930973	3	FACETS	0.997	0.953	1	0.665	0.635	0.694	INDETERMINATE	2	FALSE	0	0.86331819537957	3		337	489	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10277330	10277330	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	254	756	0	ENST00000340748.4:c.787G>T	p.Asp263Tyr	p.D263Y	ENST00000340748		263	Gac/Tac	10/40	0.86331819537957	3	FACETS	1	0.969	1	0.525	0.492	0.557	CLONAL	1	FALSE	1	0.86331819537957	3		756	803	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141561	11141561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	182	531	1	ENST00000358026.2:c.3538C>T	p.Pro1180Ser	p.P1180S	ENST00000358026	NM_001128849.1	1180	Cct/Tct	25/36	0.86331819537957	3	FACETS	0.986	0.915	1	0.493	0.457	0.53	CLONAL	1	FALSE	1	0.86331819537957	3		532	612	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017770	31017770	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1265899855	NA	P-0013413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	126	461	1	ENST00000375687.4:c.632C>T	p.Ala211Val	p.A211V	ENST00000375687	NM_015338.5	211	gCc/gTc	8/13	0.786573559748962	3	FACETS	0.884	0.805	0.965	0.442	0.402	0.483	CLONAL	1	FALSE	1	0.86331819537957	3		462	473	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980730	40980730	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	39	351	0	ENST00000373198.4:c.1756A>G	p.Ile586Val	p.I586V	ENST00000373198	NM_133170.3	586	Att/Gtt	10/32	NA	2	FACETS	0.218	0.181	0.26			1	INDETERMINATE	1	FALSE	NA	0.86331819537957	2		351	414	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923819	39923819	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	268	435	3	ENST00000378444.4:c.3272C>T	p.Pro1091Leu	p.P1091L	ENST00000378444	NM_001123385.1	1091	cCc/cTc	7/15	0.765102057807751	2	FACETS	0.998	0.944	1			1	CLONAL	1	FALSE	NA	0.86331819537957	2		438	622	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974373	93974373	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013413-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	186	866	0	ENST00000369303.4:c.1681del	p.Val561LeufsTer3	p.V561Lfs*3	ENST00000369303	NM_004440.3	561	Gtt/tt	8/17	0.728111366143852	1	FACETS	0.381	0.354	0.41	0.381	0.354	0.41	SUBCLONAL	1	FALSE	0	0.86331819537957	1		866	642	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0013448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	104	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.486790211991045	2		464	369	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0013448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	190	631	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	1	2	FACETS	0.742	0.685	0.801	0.742	0.685	0.801	SUBCLONAL	1	TRUE	1	0.486790211991045	2		631	1052	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0013448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	723	528	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	0.94	0.909	0.971	1	0.998	1	CLONAL	2	TRUE	1	0.486790211991045	2		528	1580	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935280	36935280	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	311	842	2	ENST00000361632.4:c.1447G>A	p.Gly483Arg	p.G483R	ENST00000361632		483	Ggg/Agg	10/16	1	2	FACETS	0.867	0.816	0.92	0.867	0.816	0.92	CLONAL	1	TRUE	1	0.486790211991045	2		844	1474	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675205	30675205	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	219	564	1	ENST00000376406.3:c.3040G>T	p.Ala1014Ser	p.A1014S	ENST00000376406	NM_014641.2	1014	Gct/Tct	9/15	1	2	FACETS	0.794	0.738	0.852	0.794	0.738	0.852	SUBCLONAL	1	TRUE	1	0.486790211991045	2		565	1133	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647515	117647515	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1256569613	NA	P-0013448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	230	586	0	ENST00000368508.3:c.5429C>T	p.Ser1810Phe	p.S1810F	ENST00000368508	NM_002944.2	1810	tCc/tTc	33/43	NA	2	FACETS	0.971	0.906	1			1	INDETERMINATE	1	TRUE	NA	0.486790211991045	2		586	973	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970906	21970906	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501275	NA	P-0013448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	189	452	0	ENST00000304494.5:c.452C>T	p.Pro151Leu	p.P151L	ENST00000304494	NM_000077.4	151	cCc/cTc	2/3	1	2	FACETS	0.841	0.778	0.907	0.841	0.778	0.907	CLONAL	1	TRUE	1	0.486790211991045	2		452	923	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971106	21971106	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	92	144	0	ENST00000304494.5:c.252C>A	p.Asp84Glu	p.D84E	ENST00000304494	NM_000077.4	84	gaC/gaA	2/3	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.486790211991045	2		144	323	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971163	21971163	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	117	137	0	ENST00000579755.1:c.238C>T	p.Pro80Ser	p.P80S	ENST00000579755		80	Cca/Tca	2/3	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.486790211991045	2		137	351	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77054863	77054863	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	219	629	0	ENST00000356341.3:c.998+1G>A		p.X333_splice	ENST00000356341	NM_002576.4	333			1	2	FACETS	0.812	0.755	0.871	0.812	0.755	0.871	CLONAL	1	TRUE	1	0.486790211991045	2		629	1108	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422152	81422152	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	218	416	0	ENST00000298171.2:c.128A>G	p.Asp43Gly	p.D43G	ENST00000298171	NM_000369.2	43	gAt/gGt	1/10	1	2	FACETS	0.964	0.897	1	0.964	0.897	1	CLONAL	1	TRUE	1	0.486790211991045	2		416	929	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472433	88472433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	162	454	0	ENST00000360948.2:c.2122G>A	p.Asp708Asn	p.D708N	ENST00000360948	NM_001012338.2	708	Gat/Aat	16/19	1	2	FACETS	0.948	0.872	1	0.948	0.872	1	CLONAL	1	TRUE	1	0.486790211991045	2		454	702	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21968235	21968237	+	missense_variant	Missense_Mutation	TNP	GGG	GGG	AGA	novel	NA	P-0013448-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	128	318	0	ENST00000304494.5:c.462_464delinsTCT	p.Pro155Leu	p.P155L	ENST00000304494	NM_000077.4	154	atCCCc/atTCTc	3/3	1	2	FACETS	0.781	0.71	0.857	0.781	0.71	0.857	SUBCLONAL	1	TRUE	1	0.486790211991045	2		318	673	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0013455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	190	464	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.913	0.851	0.976	0.913	0.851	0.976	CLONAL	1	TRUE	1	0.812791562910856	2		464	512	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0013455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	58	511	1	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.767	0.671	0.868	0.767	0.671	0.868	SUBCLONAL	1	TRUE	1	0.812791562910856	2		512	186	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562657	29562660	+	frameshift_variant	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs1064794276	NA	P-0013455-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	46	880	2	ENST00000356175.3:c.3739_3742del	p.Phe1247IlefsTer18	p.F1247Ifs*18	ENST00000356175	NM_000267.3	1246	cTGTTt/ct	28/57	1	2	FACETS	0.219	0.184	0.257	0.219	0.184	0.257	SUBCLONAL	1	TRUE	1	0.812791562910856	2		882	518	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	86	280	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.869	0.776	0.965	0.869	0.776	0.965	CLONAL	1	TRUE	1	0.622675698971018	2		280	318	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1174	16102	910	2	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.622675698971018	37	FACETS	0.989	0.986	0.992	0.963	0.96	0.965	CLONAL	36	TRUE	0	0.622675698971018	37		912	17276	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985534	2985534	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	198	645	1	ENST00000396946.4:c.277G>A	p.Glu93Lys	p.E93K	ENST00000396946	NM_032415.4	93	Gag/Aag	4/25	1	2	FACETS	0.738	0.684	0.793	0.738	0.684	0.793	SUBCLONAL	1	TRUE	1	0.622675698971018	2		646	862	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89624293	89624293	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs876661244	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	158	382	0	ENST00000371953.3:c.67T>G	p.Leu23Val	p.L23V	ENST00000371953	NM_000314.4	23	Tta/Gta	1/9	0.622675698971018	1	FACETS	0.96	0.892	1	0.96	0.892	1	CLONAL	1	TRUE	0	0.622675698971018	1		382	364	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061762	38061762	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	186	455	2	ENST00000250448.2:c.227G>A	p.Gly76Asp	p.G76D	ENST00000250448	NM_004496.3	76	gGc/gAc	2/2	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.622675698971018	2		457	523	SUCCESS
ATR	545	MSKCC	GRCh37	3	142186844	142186845	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	54	527	1	ENST00000350721.4:c.6618dup	p.Ser2207IlefsTer15	p.S2207Ifs*15	ENST00000350721	NM_001184.3	2206	-/A	39/47	0.622675698971018	3	FACETS	0.232	0.197	0.27	0.116	0.098	0.135	SUBCLONAL	1	TRUE	1	0.622675698971018	3		528	982	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885947	59885947	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs865910081	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	247	688	0	ENST00000259008.2:c.799G>A	p.Ala267Thr	p.A267T	ENST00000259008	NM_032043.2	267	Gca/Aca	7/20	1	2	FACETS	0.92	0.862	0.98	0.92	0.862	0.98	CLONAL	1	TRUE	1	0.622675698971018	2		688	862	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033352	48033352	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750949	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	223	579	2	ENST00000234420.5:c.3656C>T	p.Thr1219Ile	p.T1219I	ENST00000234420	NM_000179.2	1219	aCt/aTt	8/10	1	2	FACETS	0.977	0.913	1	0.977	0.913	1	CLONAL	1	TRUE	1	0.622675698971018	2		581	733	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11188944	11188944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	297	784	1	ENST00000361445.4:c.5779G>A	p.Val1927Met	p.V1927M	ENST00000361445	NM_004958.3	1927	Gtg/Atg	41/58	0.622675698971018	3	FACETS	1	0.955	1	0.509	0.478	0.54	CLONAL	1	TRUE	1	0.622675698971018	3		785	1230	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260203	16260203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	92	300	0	ENST00000375759.3:c.7468C>T	p.Pro2490Ser	p.P2490S	ENST00000375759	NM_015001.2	2490	Cca/Tca	11/15	0.622675698971018	3	FACETS	0.929	0.831	1	0.465	0.415	0.517	CLONAL	1	TRUE	1	0.622675698971018	3		300	417	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798079	45798079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	185	429	0	ENST00000450313.1:c.772G>A	p.Val258Ile	p.V258I	ENST00000450313	NM_012222.2	258	Gtt/Att	9/16	0.529120063430575	3	FACETS	1	0.98	1			1	CLONAL	1	TRUE	NA	0.622675698971018	3		429	670	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65313228	65313228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	342	822	0	ENST00000342505.4:c.1886G>A	p.Arg629Lys	p.R629K	ENST00000342505	NM_002227.2	629	aGg/aAg	13/25	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.622675698971018	2		822	950	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880462	155880462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	205	577	0	ENST00000368323.3:c.91G>A	p.Gly31Ser	p.G31S	ENST00000368323	NM_006912.5	31	Ggt/Agt	2/6	1	2	FACETS	0.891	0.829	0.955	0.891	0.829	0.955	CLONAL	1	TRUE	1	0.622675698971018	2		577	739	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612627	228612627	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1487311934	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	298	864	0	ENST00000366696.1:c.400G>A	p.Glu134Lys	p.E134K	ENST00000366696	NM_003493.2	134	Gag/Aag	1/1	1	2	FACETS	0.939	0.886	0.994	0.939	0.886	0.994	CLONAL	1	TRUE	1	0.622675698971018	2		864	1019	SUCCESS
ALK	238	MSKCC	GRCh37	2	29436917	29436917	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	239	655	0	ENST00000389048.3:c.3676C>T	p.Leu1226Phe	p.L1226F	ENST00000389048	NM_004304.4	1226	Ctt/Ttt	24/29	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.622675698971018	2		655	653	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48018232	48018232	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876661110	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	190	430	0	ENST00000234420.5:c.427G>A	p.Val143Ile	p.V143I	ENST00000234420	NM_000179.2	143	Gtt/Att	2/10	1	2	FACETS	0.981	0.912	1	0.981	0.912	1	CLONAL	1	TRUE	1	0.622675698971018	2		430	622	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660669	227660669	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	213	574	0	ENST00000305123.5:c.2786C>T	p.Pro929Leu	p.P929L	ENST00000305123	NM_005544.2	929	cCa/cTa	1/2	1	2	FACETS	0.982	0.916	1	0.982	0.916	1	CLONAL	1	TRUE	1	0.622675698971018	2		574	697	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162434	47162434	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	234	650	1	ENST00000409792.3:c.3692G>A	p.Gly1231Glu	p.G1231E	ENST00000409792	NM_014159.6	1231	gGa/gAa	3/21	1	2	FACETS	0.912	0.853	0.973	0.912	0.853	0.973	CLONAL	1	TRUE	1	0.622675698971018	2		651	824	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027029	71027029	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	188	421	0	ENST00000318789.4:c.1298G>A	p.Gly433Glu	p.G433E	ENST00000318789	NM_032682.5	433	gGa/gAa	15/21	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.622675698971018	2		421	535	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181431004	181431004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	243	496	0	ENST00000325404.1:c.856C>T	p.Pro286Ser	p.P286S	ENST00000325404	NM_003106.3	286	Ccc/Tcc	1/1	0.622675698971018	3	FACETS	1	0.957	1	0.515	0.482	0.55	CLONAL	1	TRUE	1	0.622675698971018	3		496	993	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187444635	187444635	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	204	473	0	ENST00000232014.4:c.1592C>T	p.Ala531Val	p.A531V	ENST00000232014	NM_001130845.1	531	gCc/gTc	7/10	0.622675698971018	3	FACETS	1	0.962	1	0.526	0.489	0.565	CLONAL	1	TRUE	1	0.622675698971018	3		473	816	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584767	187584767	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	159	356	2	ENST00000441802.2:c.3266G>A	p.Gly1089Asp	p.G1089D	ENST00000441802	NM_005245.3	1089	gGt/gAt	3/27	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.622675698971018	2		358	446	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140918	37140918	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	243	611	0	ENST00000373509.5:c.754C>T	p.Gln252Ter	p.Q252*	ENST00000373509	NM_002648.3	252	Cag/Tag	5/6	1	2	FACETS	0.984	0.923	1	0.984	0.923	1	CLONAL	1	TRUE	1	0.622675698971018	2		611	793	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467918	50467918	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	126	329	1	ENST00000331340.3:c.1153G>A	p.Glu385Lys	p.E385K	ENST00000331340	NM_006060.4	385	Gag/Aag	8/8	NA	2	FACETS	0.961	0.878	1			1	INDETERMINATE	1	TRUE	NA	0.622675698971018	2		330	421	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151843692	151843692	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395146799	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	184	420	0	ENST00000262189.6:c.14023G>A	p.Ala4675Thr	p.A4675T	ENST00000262189	NM_170606.2	4675	Gcg/Acg	53/59	0.622675698971018	4	FACETS	1	0.942	1	0.341	0.315	0.369	CLONAL	1	TRUE	1	0.622675698971018	4		420	937	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846238	151846238	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	170	381	0	ENST00000262189.6:c.12775-1G>A		p.X4259_splice	ENST00000262189	NM_170606.2	4259			0.622675698971018	4	FACETS	1	0.946	1	0.345	0.318	0.374	CLONAL	1	TRUE	1	0.622675698971018	4		381	855	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742009	145742009	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	206	449	0	ENST00000428558.2:c.494C>T	p.Pro165Leu	p.P165L	ENST00000428558	NM_004260.3	165	cCc/cTc	5/22	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.622675698971018	2		449	614	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80412497	80412497	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	270	749	1	ENST00000286548.4:c.544G>A	p.Val182Ile	p.V182I	ENST00000286548	NM_002072.3	182	Gtt/Att	4/7	1	2	FACETS	0.988	0.929	1	0.988	0.929	1	CLONAL	1	TRUE	1	0.622675698971018	2		750	878	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589789	69589789	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1201213049	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	100	49	94	0	ENST00000168712.1:c.64C>T	p.Pro22Ser	p.P22S	ENST00000168712	NM_002007.2	22	Ccc/Tcc	1/3	1	2	FACETS	1	0.904	1	1	0.904	1	CLONAL	1	TRUE	1	0.622675698971018	2		94	149	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49418404	49418404	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	174	447	0	ENST00000301067.7:c.16009G>A	p.Gly5337Ser	p.G5337S	ENST00000301067	NM_003482.3	5337	Ggc/Agc	50/54	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.622675698971018	2		447	554	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50482382	50482382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	253	655	0	ENST00000394963.4:c.733G>A	p.Asp245Asn	p.D245N	ENST00000394963	NM_003076.4	245	Gac/Aac	6/13	1	2	FACETS	0.998	0.937	1	0.998	0.937	1	CLONAL	1	TRUE	1	0.622675698971018	2		655	814	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69222647	69222647	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	250	802	0	ENST00000462284.1:c.620T>C	p.Val207Ala	p.V207A	ENST00000462284	NM_002392.5	207	gTa/gCa	8/11	1	2	FACETS	0.91	0.853	0.969	0.91	0.853	0.969	CLONAL	1	TRUE	1	0.622675698971018	2		802	882	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133988	41133988	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1419978485	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	382	1061	1	ENST00000379561.5:c.1640C>T	p.Pro547Leu	p.P547L	ENST00000379561	NM_002015.3	547	cCc/cTc	2/3	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.622675698971018	2		1062	1218	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039437	49039437	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	282	655	0	ENST00000267163.4:c.2422C>T	p.Pro808Ser	p.P808S	ENST00000267163	NM_000321.2	808	Ccc/Tcc	23/27	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.622675698971018	2		655	862	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103520538	103520538	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	312	751	0	ENST00000355739.4:c.2609G>A	p.Gly870Asp	p.G870D	ENST00000355739	NM_000123.3	870	gGt/gAt	12/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.622675698971018	2		751	943	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422079	81422079	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	195	479	0	ENST00000298171.2:c.55C>G	p.Leu19Val	p.L19V	ENST00000298171	NM_000369.2	19	Ctg/Gtg	1/10	1	2	FACETS	0.988	0.919	1	0.988	0.919	1	CLONAL	1	TRUE	1	0.622675698971018	2		479	634	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67457276	67457276	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	224	550	0	ENST00000327367.4:c.250C>T	p.Pro84Ser	p.P84S	ENST00000327367	NM_005902.3	84	Cct/Tct	2/9	0.622675698971018	3	FACETS	1	0.974	1	0.543	0.506	0.581	CLONAL	1	TRUE	1	0.622675698971018	3		550	869	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73992053	73992053	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	274	692	0	ENST00000318443.5:c.73C>T	p.Leu25Phe	p.L25F	ENST00000318443	NM_001024736.1	25	Ctc/Ttc	2/10	0.622675698971018	3	FACETS	1	0.945	1	0.504	0.472	0.536	CLONAL	1	TRUE	1	0.622675698971018	3		692	1146	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81942172	81942172	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	319	896	0	ENST00000359376.3:c.1709C>T	p.Pro570Leu	p.P570L	ENST00000359376	NM_002661.3	570	cCc/cTc	17/33	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.622675698971018	2		896	998	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89355004	89355004	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	377	910	0	ENST00000301030.4:c.676G>A	p.Glu226Lys	p.E226K	ENST00000301030	NM_001256183.1	226	Gag/Aag	7/13	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.622675698971018	2		910	1210	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971291	15971291	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	206	534	0	ENST00000268712.3:c.4658G>A	p.Gly1553Asp	p.G1553D	ENST00000268712	NM_006311.3	1553	gGc/gAc	32/46	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.622675698971018	2		534	656	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29560064	29560064	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	285	633	2	ENST00000356175.3:c.3541G>A	p.Glu1181Lys	p.E1181K	ENST00000356175	NM_000267.3	1181	Gaa/Aaa	27/57	1	2	FACETS	0.998	0.941	1	0.998	0.941	1	CLONAL	1	TRUE	1	0.622675698971018	2		635	917	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40462673	40462673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	372	923	2	ENST00000345506.4:c.2371G>A	p.Gly791Ser	p.G791S	ENST00000345506	NM_003152.3	791	Ggc/Agc	20/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.622675698971018	2		925	1124	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244999	41244999	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	329	770	0	ENST00000357654.3:c.2549G>A	p.Ser850Asn	p.S850N	ENST00000357654	NM_007294.3	850	aGt/aAt	10/23	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.622675698971018	2		770	950	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57567443	57567443	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1256397073	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	208	427	0	ENST00000316660.6:c.34C>T	p.Pro12Ser	p.P12S	ENST00000316660	NM_021127.2	12	Ccg/Tcg	1/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.622675698971018	2		427	620	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2214506	2214506	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	229	525	0	ENST00000398665.3:c.1834G>A	p.Ala612Thr	p.A612T	ENST00000398665	NM_032482.2	612	Gcc/Acc	19/28	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.622675698971018	2		525	661	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166335	7166335	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	259	762	0	ENST00000302850.5:c.1691C>T	p.Pro564Leu	p.P564L	ENST00000302850	NM_000208.2	564	cCc/cTc	8/22	1	2	FACETS	0.955	0.897	1	0.955	0.897	1	CLONAL	1	TRUE	1	0.622675698971018	2		762	871	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132480	11132480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1401056652	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	232	691	0	ENST00000358026.2:c.2696C>T	p.Thr899Met	p.T899M	ENST00000358026	NM_001128849.1	899	aCg/aTg	19/36	1	2	FACETS	0.927	0.867	0.989	0.927	0.867	0.989	CLONAL	1	TRUE	1	0.622675698971018	2		691	804	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296308	15296308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	223	649	0	ENST00000263388.2:c.2134G>A	p.Ala712Thr	p.A712T	ENST00000263388	NM_000435.2	712	Gca/Aca	13/33	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.622675698971018	2		649	660	SUCCESS
AXL	558	MSKCC	GRCh37	19	41762357	41762357	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1466691509	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	253	707	0	ENST00000301178.4:c.2037G>A	p.Met679Ile	p.M679I	ENST00000301178	NM_021913.4	679	atG/atA	18/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.622675698971018	2		707	795	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791055	42791055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	137	320	0	ENST00000575354.2:c.200C>T	p.Ala67Val	p.A67V	ENST00000575354	NM_015125.3	67	gCc/gTc	2/20	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.622675698971018	2		320	394	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31374425	31374425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	204	705	1	ENST00000328111.2:c.424G>A	p.Ala142Thr	p.A142T	ENST00000328111	NM_006892.3	142	Gct/Act	5/23	1	2	FACETS	0.876	0.815	0.939	0.876	0.815	0.939	CLONAL	1	TRUE	1	0.622675698971018	2		706	748	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41522030	41522030	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755143118	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	253	522	0	ENST00000263253.7:c.892G>A	p.Gly298Arg	p.G298R	ENST00000263253	NM_001429.3	298	Gga/Aga	3/31	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.622675698971018	2		522	743	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41522037	41522037	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756328815	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	239	473	2	ENST00000263253.7:c.899C>T	p.Pro300Leu	p.P300L	ENST00000263253	NM_001429.3	300	cCc/cTc	3/31	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.622675698971018	2		475	718	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44942803	44942803	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	371	992	0	ENST00000377967.4:c.3383G>A	p.Gly1128Asp	p.G1128D	ENST00000377967	NM_021140.2	1128	gGc/gAc	23/29	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.622675698971018	2		992	1176	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44970652	44970652	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	301	815	0	ENST00000377967.4:c.4202C>T	p.Ser1401Phe	p.S1401F	ENST00000377967	NM_021140.2	1401	tCt/tTt	29/29	1	2	FACETS	0.986	0.93	1	0.986	0.93	1	CLONAL	1	TRUE	1	0.622675698971018	2		815	981	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426048	47426048	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	327	810	3	ENST00000377045.4:c.568C>T	p.Gln190Ter	p.Q190*	ENST00000377045	NM_001654.4	190	Cag/Tag	7/16	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.622675698971018	2		813	928	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185186	123185186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013506-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	266	689	0	ENST00000218089.9:c.1138C>T	p.Leu380Phe	p.L380F	ENST00000218089	NM_001042749.1	380	Ctt/Ttt	13/35	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.622675698971018	2		689	822	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0013522-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	45	354	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.201	0.168	0.238	0.201	0.168	0.238	SUBCLONAL	1	TRUE	1	0.55	2		354	814	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0013522-T03-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	25	429	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	1	2	FACETS	0.203	0.16	0.254	0.203	0.16	0.254	SUBCLONAL	1	TRUE	1	0.55	2		429	447	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	132	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.966	0.889	1	0.966	0.889	1	CLONAL	1	TRUE	1	0.801071805503615	2		215	341	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369269	40369269	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757544937	NA	P-0013529-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	486	933	1	ENST00000293328.3:c.1289G>A	p.Arg430His	p.R430H	ENST00000293328	NM_012448.3	430	cGt/cAt	11/19	1	2	FACETS	0.887	0.849	0.926	0.887	0.849	0.926	CLONAL	1	TRUE	1	0.801071805503615	2		934	1368	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	29	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.404	0.323	0.496	0.404	0.323	0.496	SUBCLONAL	1	FALSE	1	0.270610984623634	2		215	531	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577580	7577580	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs587780073	NA	P-0013557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	63	689	0	ENST00000269305.4:c.701A>G	p.Tyr234Cys	p.Y234C	ENST00000269305	NM_001126112.2	234	tAc/tGc	7/11	0.176753003351363	1	FACETS	0.501	0.433	0.576	0.501	0.433	0.576	SUBCLONAL	1	FALSE	0	0.270610984623634	1		689	803	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478851	56478851	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	109	1313	0	ENST00000267101.3:c.307C>G	p.Arg103Gly	p.R103G	ENST00000267101	NM_001982.3	103	Cgc/Ggc	3/28	1	2	FACETS	0.637	0.57	0.709	0.637	0.57	0.709	SUBCLONAL	1	FALSE	1	0.270610984623634	2		1313	1264	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156625	2156625	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1111	85	947	0	ENST00000434045.2:c.297C>A	p.Phe99Leu	p.F99L	ENST00000434045	NM_001127598.1	99	ttC/ttA	3/5	1	2	FACETS	0.525	0.463	0.593	0.525	0.463	0.593	SUBCLONAL	1	FALSE	1	0.270610984623634	2		947	1196	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742837	17742837	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	72	636	0	ENST00000250003.3:c.745C>A	p.Leu249Ile	p.L249I	ENST00000250003	NM_002478.4	249	Cta/Ata	3/3	1	2	FACETS	0.683	0.596	0.777	0.683	0.596	0.777	SUBCLONAL	1	FALSE	1	0.270610984623634	2		636	779	SUCCESS
EED	8726	MSKCC	GRCh37	11	85975293	85975293	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	61	847	0	ENST00000263360.6:c.714A>C	p.Glu238Asp	p.E238D	ENST00000263360	NM_003797.3	238	gaA/gaC	7/12	1	2	FACETS	0.499	0.429	0.575	0.499	0.429	0.575	SUBCLONAL	1	FALSE	1	0.270610984623634	2		847	904	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94192683	94192683	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	69	933	1	ENST00000323929.3:c.1391A>T	p.Lys464Met	p.K464M	ENST00000323929	NM_005591.3	464	aAg/aTg	13/20	1	2	FACETS	0.557	0.484	0.636	0.557	0.484	0.636	SUBCLONAL	1	FALSE	1	0.270610984623634	2		934	916	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139278	108139278	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	63	779	0	ENST00000278616.4:c.2780T>C	p.Leu927Ser	p.L927S	ENST00000278616	NM_000051.3	927	tTg/tCg	18/63	1	2	FACETS	0.559	0.482	0.643	0.559	0.482	0.643	SUBCLONAL	1	FALSE	1	0.270610984623634	2		779	833	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42019597	42019597	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1014	109	1190	0	ENST00000219905.7:c.3650A>T	p.Asn1217Ile	p.N1217I	ENST00000219905	NM_001164273.1	1217	aAt/aTt	10/24	1	2	FACETS	0.717	0.642	0.797	0.717	0.642	0.797	SUBCLONAL	1	FALSE	1	0.270610984623634	2		1190	1123	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23614787	23614787	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	50	577	0	ENST00000261584.4:c.3554A>T	p.Tyr1185Phe	p.Y1185F	ENST00000261584	NM_024675.3	1185	tAt/tTt	13/13	1	2	FACETS	0.525	0.444	0.614	0.525	0.444	0.614	SUBCLONAL	1	FALSE	1	0.270610984623634	2		577	704	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89828379	89828379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	129	862	1	ENST00000389301.3:c.2830G>A	p.Asp944Asn	p.D944N	ENST00000389301	NM_000135.2	944	Gat/Aat	29/43	1	2	FACETS	0.933	0.844	1	0.933	0.844	1	CLONAL	1	FALSE	1	0.270610984623634	2		863	1022	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29528427	29528427	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	rs1373365576	NA	P-0013557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	63	457	4	ENST00000356175.3:c.1186-2A>T		p.X396_splice	ENST00000356175	NM_000267.3	396			0.16286014600099	3	FACETS	0.742	0.641	0.853			1	SUBCLONAL	1	FALSE	NA	0.270610984623634	3		461	712	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29587386	29587386	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0013557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	92	663	1	ENST00000356175.3:c.4368-1G>T		p.X1456_splice	ENST00000356175	NM_000267.3	1456			0.16286014600099	3	FACETS	1	0.913	1			1	CLONAL	1	FALSE	NA	0.270610984623634	3		664	748	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29657435	29657435	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs146523293	NA	P-0013557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	61	764	0	ENST00000356175.3:c.5668A>G	p.Ile1890Val	p.I1890V	ENST00000356175	NM_000267.3	1890	Att/Gtt	38/57	0.16286014600099	3	FACETS	0.531	0.457	0.613			1	SUBCLONAL	1	FALSE	NA	0.270610984623634	3		764	963	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40486030	40486030	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1258	144	1191	0	ENST00000264657.5:c.835C>G	p.Gln279Glu	p.Q279E	ENST00000264657	NM_139276.2	279	Caa/Gaa	9/24	1	2	FACETS	0.759	0.69	0.832	0.759	0.69	0.832	SUBCLONAL	1	FALSE	1	0.270610984623634	2		1191	1402	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551342	29551342	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	46	724	0	ENST00000389048.3:c.1288T>C	p.Ser430Pro	p.S430P	ENST00000389048	NM_004304.4	430	Tcc/Ccc	6/29	1	2	FACETS	0.46	0.386	0.542	0.46	0.386	0.542	SUBCLONAL	1	FALSE	1	0.270610984623634	2		724	739	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30035098	30035098	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0013557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	175	906	1	ENST00000338641.4:c.260C>G	p.Ser87Ter	p.S87*	ENST00000338641	NM_000268.3	87	tCa/tGa	3/16	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.270610984623634	2		907	961	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259251	89259251	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	72	785	2	ENST00000336596.2:c.395G>T	p.Gly132Val	p.G132V	ENST00000336596	NM_005233.5	132	gGg/gTg	3/17	1	2	FACETS	0.697	0.608	0.793	0.697	0.608	0.793	SUBCLONAL	1	FALSE	1	0.270610984623634	2		787	764	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89480395	89480396	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AT	novel	NA	P-0013557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	63	880	7	ENST00000336596.2:c.2232_2233delinsAT	p.His744_Arg745delinsGlnTer	p.H744_R745delinsQ*	ENST00000336596	NM_005233.5	744	caCCga/caATga	13/17	1	2	FACETS	0.539	0.465	0.62	0.539	0.465	0.62	SUBCLONAL	1	FALSE	1	0.270610984623634	2		887	864	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539390	187539390	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	69	880	1	ENST00000441802.2:c.8350C>A	p.Gln2784Lys	p.Q2784K	ENST00000441802	NM_005245.3	2784	Caa/Aaa	10/27	1	2	FACETS	0.609	0.529	0.696	0.609	0.529	0.696	SUBCLONAL	1	FALSE	1	0.270610984623634	2		881	837	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672813	86672813	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	48	602	0	ENST00000274376.6:c.2300C>A	p.Ser767Ter	p.S767*	ENST00000274376	NM_002890.2	767	tCg/tAg	17/25	1	2	FACETS	0.56	0.473	0.657	0.56	0.473	0.657	SUBCLONAL	1	FALSE	1	0.270610984623634	2		602	633	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152163889	152163889	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	62	739	0	ENST00000206249.3:c.610G>T	p.Gly204Cys	p.G204C	ENST00000206249	NM_000125.3	204	Ggc/Tgc	2/8	1	2	FACETS	0.535	0.461	0.616	0.535	0.461	0.616	SUBCLONAL	1	FALSE	1	0.270610984623634	2		739	857	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81339560	81339560	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0013557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	78	764	0	ENST00000222390.5:c.1445-1G>T		p.X482_splice	ENST00000222390	NM_000601.4	482			0.150970517839352	3	FACETS	0.774	0.679	0.876	0.387	0.339	0.438	INDETERMINATE	1	FALSE	1	0.270610984623634	3		764	846	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485843	8485843	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	49	904	0	ENST00000356435.5:c.2974G>T	p.Val992Leu	p.V992L	ENST00000356435		992	Gta/Tta	17/35	0.270610984623634	1	FACETS	0.322	0.271	0.377	0.322	0.271	0.377	SUBCLONAL	1	FALSE	0	0.270610984623634	1		904	974	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518388	8518388	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	32	307	0	ENST00000356435.5:c.1003A>G	p.Thr335Ala	p.T335A	ENST00000356435		335	Aca/Gca	10/35	0.270610984623634	1	FACETS	0.522	0.423	0.633	0.522	0.423	0.633	SUBCLONAL	1	FALSE	0	0.270610984623634	1		307	392	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039906	47039906	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0013557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	49	525	0	ENST00000377604.3:c.1248+1G>T		p.X416_splice	ENST00000377604	NM_001204468.1	416			0.176753003351363	1	FACETS	0.595	0.504	0.696	0.595	0.504	0.696	SUBCLONAL	1	FALSE	0	0.270610984623634	1		525	526	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48649734	48649734	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013557-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	94	1058	1	ENST00000376670.3:c.218C>A	p.Pro73Gln	p.P73Q	ENST00000376670	NM_002049.3	73	cCa/cAa	2/6	0.176753003351363	1	FACETS	0.526	0.466	0.59	0.526	0.466	0.59	SUBCLONAL	1	FALSE	0	0.270610984623634	1		1059	1142	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0013559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	164	282	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.92	0.852	0.99	0.92	0.852	0.99	CLONAL	1	TRUE	1	0.756719755294455	2		282	471	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984226	7984226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	315	711	0	ENST00000319144.4:c.503G>A	p.Arg168Lys	p.R168K	ENST00000319144	NM_001139.2	168	aGg/aAg	4/15	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.756719755294455	2		711	814	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527593	29527593	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs864622064	NA	P-0013559-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	144	739	1	ENST00000356175.3:c.1042T>C	p.Ser348Pro	p.S348P	ENST00000356175	NM_000267.3	348	Tcc/Ccc	9/57	1	2	FACETS	0.748	0.686	0.811	0.748	0.686	0.811	SUBCLONAL	1	TRUE	1	0.756719755294455	2		740	509	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464961	120464961	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	37	653	1	ENST00000256646.2:c.5111G>T	p.Arg1704Leu	p.R1704L	ENST00000256646	NM_024408.3	1704	cGt/cTt	28/34	0.505365038240535	5	FACETS	1	0.932	1	1	0.932	1	CLONAL	3	TRUE	2	0.505365038240535	5		654	75	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506251	120506251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781827529	NA	P-0013563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	16	470	0	ENST00000256646.2:c.1861C>T	p.Arg621Cys	p.R621C	ENST00000256646	NM_024408.3	621	Cgc/Tgc	11/34	0.505365038240535	5	FACETS	0.752	0.569	0.96	0.501	0.379	0.64	CLONAL	2	TRUE	2	0.505365038240535	5		470	74	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99442770	99442770	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	44	32	1162	0	ENST00000268035.6:c.1167G>T	p.Lys389Asn	p.K389N	ENST00000268035	NM_000875.3	389	aaG/aaT	5/21	0.304526211450387	3	FACETS	1	0.876	1	1	0.876	1	CLONAL	2	TRUE	1	0.505365038240535	3		1162	76	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786748	3786748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	48	1428	2	ENST00000262367.5:c.4463C>T	p.Pro1488Leu	p.P1488L	ENST00000262367	NM_004380.2	1488	cCa/cTa	27/31	0.180728182978312	3	FACETS	0.881	0.778	0.983	0.881	0.778	0.983	INDETERMINATE	3	TRUE	0	0.505365038240535	3		1430	90	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577106	7577106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs17849781	NA	P-0013563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	69	590	0	ENST00000269305.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000269305	NM_001126112.2	278	Cct/Tct	8/11	0.393731699166566	4	FACETS	0.918	0.835	0.997	0.918	0.835	0.997	CLONAL	4	TRUE	0	0.505365038240535	4		590	112	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38506128	38506128	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	11	1038	2	ENST00000254066.5:c.420C>A	p.Cys140Ter	p.C140*	ENST00000254066	NM_000964.3	140	tgC/tgA	4/9	0.304526211450387	3	FACETS	0.58	0.405	0.792	0.29	0.202	0.396	SUBCLONAL	1	TRUE	1	0.505365038240535	3		1040	94	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622120	1622120	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	12	1171	0	ENST00000344749.5:c.755G>T	p.Gly252Val	p.G252V	ENST00000344749	NM_001136139.2	252	gGt/gTt	10/19	1	2	FACETS	0.5	0.355	0.673	0.5	0.355	0.673	SUBCLONAL	1	TRUE	1	0.505365038240535	2		1171	95	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426747	212426747	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	47	35	903	1	ENST00000342788.4:c.2368C>A	p.Pro790Thr	p.P790T	ENST00000342788	NM_005235.2	790	Cca/Aca	20/28	0.180728182978312	3	FACETS	1	0.891	1	0.705	0.6	0.813	INDETERMINATE	2	TRUE	0	0.505365038240535	3		904	82	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628218	187628218	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	29	745	0	ENST00000441802.2:c.2764G>T	p.Asp922Tyr	p.D922Y	ENST00000441802	NM_005245.3	922	Gac/Tac	2/27	0.503926661906214	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	2	TRUE	0	0.505365038240535	2		745	48	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515181	149515181	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	13	1170	0	ENST00000261799.4:c.301A>T	p.Thr101Ser	p.T101S	ENST00000261799	NM_002609.3	101	Acc/Tcc	3/23	0.168986216077993	0	FACETS	0.353	0.257	0.466			1	INDETERMINATE	1	TRUE	0	0.505365038240535	0		1170	72	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176631141	176631141	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748311206	NA	P-0013563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	25	969	0	ENST00000439151.2:c.1084C>T	p.Arg362Trp	p.R362W	ENST00000439151	NM_022455.4	362	Cgg/Tgg	4/23	0.180728182978312	3	FACETS	1	0.822	1	0.666	0.548	0.79	INDETERMINATE	2	TRUE	0	0.505365038240535	3		969	62	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265355	152265356	+	missense_variant	Missense_Mutation	DNP	CA	CA	TG	novel	NA	P-0013563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	39	23	934	2	ENST00000206249.3:c.808_809inv	p.Gln270Trp	p.Q270W	ENST00000206249	NM_000125.3	270	CAg/TGg	4/8	0.375394674460559	3	FACETS	0.92	0.746	1	0.613	0.497	0.735	CLONAL	2	TRUE	0	0.505365038240535	3		936	62	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465513	8465513	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	30	1133	0	ENST00000356435.5:c.3667C>A	p.Gln1223Lys	p.Q1223K	ENST00000356435		1223	Caa/Aaa	21/35	0.505365038240535	1	FACETS	0.822	0.703	0.938	1	0.962	1	CLONAL	2	TRUE	0	0.505365038240535	1		1133	54	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013563-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	25	40	650	0	ENST00000304494.5:c.322del	p.Asp108MetfsTer38	p.D108Mfs*38	ENST00000304494	NM_000077.4	108	Gat/at	2/3	0.391735801540219	3	FACETS	1	0.896	1	1	0.896	1	CLONAL	3	TRUE	0	0.505365038240535	3		650	65	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013578-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	277	215	0				ENST00000310581	NM_198253.2	-/1132			0.633280171758199	3	FACETS	1	0.994	1			1	CLONAL	1	TRUE	NA	0.810317362419263	3		215	660	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619849	1619849	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758087547	NA	P-0013578-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	818	961	1	ENST00000344749.5:c.1097C>T	p.Thr366Met	p.T366M	ENST00000344749	NM_001136139.2	366	aCg/aTg	14/19	0.753588712252017	3	FACETS	1	0.998	1	0.496	0.48	0.512	CLONAL	1	TRUE	0	0.810317362419263	3		962	1908	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916851	178916853	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0013578-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1293	844	939	0	ENST00000263967.3:c.241_243del	p.Glu81del	p.E81del	ENST00000263967	NM_006218.2	80	GAA/-	2/21	0.364366276486975	4	FACETS	0.882	0.854	0.911	0.882	0.854	0.911	INDETERMINATE	2	TRUE	2	0.810317362419263	4		939	2137	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0013593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	274	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.759323619178547	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.796692893294804	2		458	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578537	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs879254214	NA	P-0013593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	1100	893	4	ENST00000269305.4:c.393_395del	p.Asn131del	p.N131del	ENST00000269305	NM_001126112.2	131	aaCAAg/aag	5/11	0.349658104973529	6	FACETS	1	0.998	1			1	INDETERMINATE	5	TRUE	NA	0.796692893294804	6		897	1312	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937711	36937711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752325760	NA	P-0013593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	438	803	2	ENST00000361632.4:c.1027C>T	p.Arg343Trp	p.R343W	ENST00000361632		343	Cgg/Tgg	8/16	NA	2	FACETS	1	0.99	1			1	INDETERMINATE	1	TRUE	NA	0.796692893294804	2		805	1000	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986514	36986514	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	282	684	0	ENST00000354822.5:c.1175G>T	p.Cys392Phe	p.C392F	ENST00000354822	NM_001079668.2	392	tGc/tTc	3/3	0.415242450277791	5	FACETS	1	0.984	1	0.381	0.357	0.405	INDETERMINATE	1	TRUE	2	0.796692893294804	5		684	1361	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615769	1615769	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1439	461	1031	4	ENST00000344749.5:c.1502A>T	p.Glu501Val	p.E501V	ENST00000344749	NM_001136139.2	501	gAg/gTg	17/19	0.289899843487079	5	FACETS	1	0.995	1	0.446	0.424	0.468	INDETERMINATE	1	TRUE	2	0.796692893294804	5		1035	1900	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794699	42794699	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	311	593	0	ENST00000575354.2:c.1779G>A	p.Met593Ile	p.M593I	ENST00000575354	NM_015125.3	593	atG/atA	10/20	0.343585572332938	5	FACETS	1	0.993	1	0.475	0.447	0.503	INDETERMINATE	1	TRUE	2	0.796692893294804	5		593	1203	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1279465	1279465	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866767063	NA	P-0013593-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1394	339	525	2	ENST00000310581.5:c.2071C>T	p.Arg691Cys	p.R691C	ENST00000310581	NM_198253.2	691	Cgc/Tgc	5/16	0.796692893294804	6	FACETS	1	0.992	1			1	CLONAL	1	TRUE	NA	0.796692893294804	6		527	1733	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0013605-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	37	282	0				ENST00000310581	NM_198253.2	-/1132			0.223234439656793	4	FACETS	0.86	0.709	1	0.43	0.354	0.515	CLONAL	1	TRUE	2	0.228379956886476	4		282	463	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916614	178916614	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0013605-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1201	111	432	0	ENST00000263967.3:c.1A>G	p.Met1?	p.M1?	ENST00000263967	NM_006218.2	1	Atg/Gtg	2/21	1	2	FACETS	0.741	0.664	0.823	0.741	0.664	0.823	SUBCLONAL	1	TRUE	1	0.228379956886476	2		432	1312	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143181659	143181659	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013605-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1108	106	669	1	ENST00000262992.4:c.674del	p.Pro225LeufsTer3	p.P225Lfs*3	ENST00000262992	NM_001101669.1	225	cCt/ct	9/24	0.201625887392895	3	FACETS	0.852	0.761	0.949	0.426	0.38	0.475	CLONAL	1	TRUE	1	0.228379956886476	3		670	1214	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	152	124	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.753946802405903	2		215	276	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0013634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	265	351	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.753946802405903	2		351	671	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573747	64573747	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	251	496	0	ENST00000312049.6:c.1006G>T	p.Glu336Ter	p.E336*	ENST00000312049	NM_130799.2	336	Gaa/Taa	7/10	0.753946802405903	1	FACETS	0.976	0.929	1	0.976	0.929	1	CLONAL	1	TRUE	0	0.753946802405903	1		496	425	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013653-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	79	215	0				ENST00000310581	NM_198253.2	-/1132			0.150759235956637	3	FACETS	0.779	0.687	0.876	0.779	0.687	0.876	SUBCLONAL	2	TRUE	1	0.245466586712489	3		215	464	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562324	21562324	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013653-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	34	349	0	ENST00000382592.4:c.1595A>T	p.Asp532Val	p.D532V	ENST00000382592	NM_014572.2	532	gAc/gTc	4/8	1	2	FACETS	0.471	0.384	0.57	0.471	0.384	0.57	SUBCLONAL	1	TRUE	1	0.245466586712489	2		349	588	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554551	63554551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013653-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	64	400	0	ENST00000307078.5:c.188G>A	p.Gly63Glu	p.G63E	ENST00000307078	NM_004655.3	63	gGg/gAg	2/11	0.245466586712489	3	FACETS	0.632	0.546	0.726	0.316	0.273	0.363	SUBCLONAL	1	TRUE	1	0.245466586712489	3		400	926	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107001	11107001	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1050237	NA	P-0013653-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	85	474	1	ENST00000358026.2:c.1706G>A	p.Arg569Gln	p.R569Q	ENST00000358026	NM_001128849.1	569	cGg/cAg	10/36	1	2	FACETS	0.741	0.654	0.836	0.741	0.654	0.836	SUBCLONAL	1	TRUE	1	0.245466586712489	2		475	934	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267710	198267710	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013653-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	124	418	1	ENST00000335508.6:c.1769G>T	p.Arg590Ile	p.R590I	ENST00000335508	NM_012433.2	590	aGa/aTa	13/25	0.150759235956637	3	FACETS	1	0.977	1	0.629	0.569	0.693	CLONAL	1	TRUE	1	0.245466586712489	3		419	901	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225608	26225608	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013653-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1892	278	1207	1	ENST00000360408.1:c.226G>T	p.Ala76Ser	p.A76S	ENST00000360408	NM_003532.2	76	Gct/Tct	1/1	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.245466586712489	2		1208	2170	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486028	8486028	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013653-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	201	638	1	ENST00000356435.5:c.2789C>A	p.Thr930Asn	p.T930N	ENST00000356435		930	aCc/aAc	17/35	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.245466586712489	2		639	1246	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045190	47045190	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0013653-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	166	518	1	ENST00000377604.3:c.2430+1G>T		p.X810_splice	ENST00000377604	NM_001204468.1	810			1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.245466586712489	2		519	1006	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55961109	55961110	+	frameshift_variant	Frame_Shift_Del	DEL	CG	CG	T	novel	NA	P-0013653-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	147	507	0	ENST00000263923.4:c.2830_2831delinsA	p.Arg944AsnfsTer16	p.R944Nfs*16	ENST00000263923	NM_002253.2	944	CGa/Aa	21/30	NA	2	FACETS	1	0.967	1			1	INDETERMINATE	1	TRUE	NA	0.245466586712489	2		507	1067	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013664-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	80	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.436840784439531	2		215	355	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476265	88476265	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013664-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	142	776	0	ENST00000360948.2:c.1867G>C	p.Gly623Arg	p.G623R	ENST00000360948	NM_001012338.2	623	Gga/Cga	15/19	1	2	FACETS	0.879	0.802	0.959	0.879	0.802	0.959	CLONAL	1	TRUE	1	0.436840784439531	2		776	740	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971191	21971192	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013664-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	48	318	0	ENST00000304494.5:c.166dup	p.Ser56LysfsTer64	p.S56Kfs*64	ENST00000304494	NM_000077.4	56	agc/aAgc	2/3	1	2	FACETS	1	0.873	1	1	0.873	1	CLONAL	1	TRUE	1	0.436840784439531	2		318	215	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411818	139411818	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013664-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	221	853	0	ENST00000277541.6:c.1461C>G	p.Cys487Trp	p.C487W	ENST00000277541	NM_017617.3	487	tgC/tgG	9/34	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.436840784439531	2		853	854	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630157	100630157	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013664-T02-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	957	203	541	0	ENST00000308731.7:c.116A>T	p.Tyr39Phe	p.Y39F	ENST00000308731	NM_000061.2	39	tAc/tTc	2/19	1	2	FACETS	0.801	0.742	0.863	0.801	0.742	0.863	CLONAL	1	TRUE	1	0.436840784439531	2		541	1160	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013664-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	43	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.721	0.614	0.834	0.721	0.614	0.834	SUBCLONAL	1	TRUE	1	0.780084751478752	2		215	153	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476265	88476265	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013664-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	114	776	0	ENST00000360948.2:c.1867G>C	p.Gly623Arg	p.G623R	ENST00000360948	NM_001012338.2	623	Gga/Cga	15/19	0.780084751478752	3	FACETS	0.913	0.828	1	0.456	0.414	0.501	CLONAL	1	TRUE	1	0.780084751478752	3		776	445	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971191	21971192	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0013664-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	61	143	318	0	ENST00000304494.5:c.166dup	p.Ser56LysfsTer64	p.S56Kfs*64	ENST00000304494	NM_000077.4	56	agc/aAgc	2/3	0.780084751478752	2	FACETS	0.899	0.849	0.946	0.899	0.849	0.946	CLONAL	2	TRUE	0	0.780084751478752	2		318	204	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139411818	139411818	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013664-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	383	853	0	ENST00000277541.6:c.1461C>G	p.Cys487Trp	p.C487W	ENST00000277541	NM_017617.3	487	tgC/tgG	9/34	0.780084751478752	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.780084751478752	2		853	463	SUCCESS
BTK	695	MSKCC	GRCh37	X	100630157	100630157	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013664-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	127	541	0	ENST00000308731.7:c.116A>T	p.Tyr39Phe	p.Y39F	ENST00000308731	NM_000061.2	39	tAc/tTc	2/19	1	2	FACETS	0.91	0.834	0.987	0.91	0.834	0.987	CLONAL	1	TRUE	1	0.780084751478752	2		541	358	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391163	139391163	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013664-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	116	754	0	ENST00000277541.6:c.7028A>G	p.Gln2343Arg	p.Q2343R	ENST00000277541	NM_017617.3	2343	cAg/cGg	34/34	0.780084751478752	2	FACETS	0.944	0.863	1	0.472	0.431	0.514	CLONAL	1	TRUE	0	0.780084751478752	2		754	315	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472499	88472499	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013664-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	156	640	0	ENST00000360948.2:c.2056C>A	p.Leu686Met	p.L686M	ENST00000360948	NM_001012338.2	686	Ctg/Atg	16/19	0.780084751478752	3	FACETS	1	0.948	1	0.519	0.478	0.561	CLONAL	1	TRUE	1	0.780084751478752	3		640	536	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48575072	48575072	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013664-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	81	434	1	ENST00000342988.3:c.266G>A	p.Gly89Glu	p.G89E	ENST00000342988	NM_005359.5	89	gGa/gAa	3/12	1	2	FACETS	0.869	0.778	0.963	0.869	0.778	0.963	CLONAL	1	TRUE	1	0.780084751478752	2		435	239	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	35	22	215	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.811	1			1	INDETERMINATE	1	TRUE	NA	0.769820946854365	2		215	57	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113112	209113112	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913500	NA	P-0013678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	70	316	0	ENST00000345146.2:c.395G>A	p.Arg132His	p.R132H	ENST00000345146	NM_005896.2	132	cGt/cAt	4/10	1	2	FACETS	0.973	0.866	1	0.973	0.866	1	CLONAL	1	TRUE	1	0.769820946854365	2		316	187	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791718	42791718	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1344635105	NA	P-0013678-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	42	89	472	0	ENST00000575354.2:c.604C>T	p.Arg202Trp	p.R202W	ENST00000575354	NM_015125.3	202	Cgg/Tgg	5/20	0.769820946854365	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.769820946854365	1		472	131	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220629	1220629	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057520017	NA	P-0013716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	317	479	1	ENST00000326873.7:c.647C>T	p.Ser216Phe	p.S216F	ENST00000326873	NM_000455.4	216	tCc/tTc	5/10	0.523043751294248	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.523043751294248	2		480	576	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0013716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	207	693	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	NA	2	FACETS	0.97	0.914	1			1	INDETERMINATE	2	TRUE	NA	0.523043751294248	2		693	408	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168613	32168613	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	125	382	0	ENST00000375023.3:c.4310G>A	p.Gly1437Glu	p.G1437E	ENST00000375023	NM_004557.3	1437	gGg/gAg	23/30	0.523043751294248	3	FACETS	0.971	0.881	1	0.324	0.293	0.355	CLONAL	1	TRUE	0	0.523043751294248	3		382	621	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885884	23885884	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765906626	NA	P-0013716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	427	674	0	ENST00000374561.5:c.34G>A	p.Glu12Lys	p.E12K	ENST00000374561	NM_002167.4	12	Gag/Aag	1/3	0.523043751294248	3	FACETS	1	0.978	1	1	0.978	1	CLONAL	2	TRUE	1	0.523043751294248	3		674	995	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094347	27094347	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	77	380	0	ENST00000324856.7:c.3055G>C	p.Glu1019Gln	p.E1019Q	ENST00000324856	NM_006015.4	1019	Gag/Cag	11/20	0.523043751294248	3	FACETS	0.65	0.572	0.735	0.325	0.286	0.368	SUBCLONAL	1	TRUE	1	0.523043751294248	3		380	571	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123624	11123624	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0013716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	327	441	4	ENST00000358026.2:c.2275-1G>T		p.X759_splice	ENST00000358026	NM_001128849.1	759			0.523043751294248	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.523043751294248	2		445	565	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182505	99182505	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	247	507	3	ENST00000074304.5:c.2308G>T	p.Val770Leu	p.V770L	ENST00000074304	NM_001134224.1	770	Gtg/Ttg	22/26	0.523043751294248	3	FACETS	0.903	0.849	0.957	0.903	0.849	0.957	CLONAL	2	TRUE	1	0.523043751294248	3		510	660	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714472	40714472	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	111	361	0	ENST00000373198.4:c.3925G>A	p.Glu1309Lys	p.E1309K	ENST00000373198	NM_133170.3	1309	Gag/Aag	29/32	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.523043751294248	2		361	388	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390130	89390130	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	165	503	0	ENST00000336596.2:c.879C>A	p.His293Gln	p.H293Q	ENST00000336596	NM_005233.5	293	caC/caA	4/17	0.523043751294248	3	FACETS	1	0.972	1	0.56	0.515	0.606	CLONAL	1	TRUE	1	0.523043751294248	3		503	711	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448529	89448529	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	152	552	0	ENST00000336596.2:c.1493G>T	p.Ser498Ile	p.S498I	ENST00000336596	NM_005233.5	498	aGc/aTc	7/17	0.523043751294248	3	FACETS	1	0.927	1	0.506	0.464	0.551	CLONAL	1	TRUE	1	0.523043751294248	3		552	724	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920344	134920344	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	526	623	0	ENST00000398015.3:c.2159A>G	p.Gln720Arg	p.Q720R	ENST00000398015	NM_004441.4	720	cAg/cGg	12/16	0.441439120939667	4	FACETS	0.952	0.916	0.987	0.952	0.916	0.987	CLONAL	3	TRUE	1	0.523043751294248	4		623	1073	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845145	151845145	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	366	674	0	ENST00000262189.6:c.13867del	p.Leu4623TrpfsTer3	p.L4623Wfs*3	ENST00000262189	NM_170606.2	4623	Ctg/tg	52/59	0.523043751294248	3	FACETS	0.931	0.886	0.977	0.931	0.886	0.977	CLONAL	2	TRUE	1	0.523043751294248	3		674	948	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636763	8636763	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	286	443	2	ENST00000356435.5:c.146del	p.Gly49GlufsTer23	p.G49Efs*23	ENST00000356435		49	gGa/ga	2/35	0.523043751294248	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.523043751294248	2		445	517	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971023	21971023	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013716-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	166	624	0	ENST00000304494.5:c.335del	p.Arg112LeufsTer34	p.R112Lfs*34	ENST00000304494	NM_000077.4	112	cGt/ct	2/3	0.523043751294248	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	0	0.523043751294248	2		624	283	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	58	215	0				ENST00000310581	NM_198253.2	-/1132			0.177378521674884	3	FACETS	1	0.923	1	1	0.923	1	INDETERMINATE	2	TRUE	1	0.359795061659057	3		215	177	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0013718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	152	886	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	1	2	FACETS	0.862	0.788	0.94	0.862	0.788	0.94	CLONAL	1	TRUE	1	0.359795061659057	2		886	980	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900209	101900209	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	287	572	0	ENST00000374994.4:c.643C>T	p.Arg215Ter	p.R215*	ENST00000374994	NM_004612.2	215	Cga/Tga	4/9	0.329499304486914	2	FACETS	0.921	0.869	0.974	0.921	0.869	0.974	CLONAL	2	TRUE	0	0.359795061659057	2		572	866	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955096	17955096	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201650430	NA	P-0013718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	99	438	0	ENST00000458235.1:c.131C>T	p.Ser44Phe	p.S44F	ENST00000458235	NM_000215.3	44	tCc/tTc	2/24	1	2	FACETS	0.872	0.78	0.97	0.872	0.78	0.97	CLONAL	1	TRUE	1	0.359795061659057	2		438	631	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955863	55955863	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868047715	NA	P-0013718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	43	437	0	ENST00000263923.4:c.3299C>T	p.Ser1100Phe	p.S1100F	ENST00000263923	NM_002253.2	1100	tCc/tTc	24/30	1	2	FACETS	0.432	0.361	0.511	0.432	0.361	0.511	SUBCLONAL	1	TRUE	1	0.359795061659057	2		437	553	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601918	43601918	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	79	610	0	ENST00000355710.3:c.962G>A	p.Gly321Glu	p.G321E	ENST00000355710	NM_020975.4	321	gGg/gAg	5/20	0.303792263177378	3	FACETS	0.718	0.631	0.811	0.359	0.315	0.406	SUBCLONAL	1	TRUE	1	0.359795061659057	3		610	722	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	394745	394745	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	142	548	0	ENST00000399788.2:c.4950T>G	p.Asn1650Lys	p.N1650K	ENST00000399788	NM_001042603.1	1650	aaT/aaG	28/28	0.254275539566981	4	FACETS	1	0.985	1	0.705	0.643	0.77	CLONAL	1	TRUE	2	0.359795061659057	4		548	761	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103524576	103524576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	86	284	0	ENST00000355739.4:c.2707C>T	p.Pro903Ser	p.P903S	ENST00000355739	NM_000123.3	903	Cca/Tca	13/15	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.359795061659057	2		284	434	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875699	56875699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	133	787	0	ENST00000308159.5:c.2303C>T	p.Pro768Leu	p.P768L	ENST00000308159	NM_014669.4	768	cCa/cTa	21/22	0.131932104567177	3	FACETS	0.736	0.667	0.809	0.245	0.222	0.27	INDETERMINATE	1	TRUE	0	0.359795061659057	3		787	1185	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654663	67654663	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0013718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	101	586	0	ENST00000264010.4:c.1150T>G	p.Cys384Gly	p.C384G	ENST00000264010	NM_006565.3	384	Tgc/Ggc	6/12	0.131932104567177	3	FACETS	0.761	0.679	0.847	0.254	0.226	0.283	INDETERMINATE	1	TRUE	0	0.359795061659057	3		586	871	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830862	72830862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1230	182	1062	1	ENST00000268489.5:c.5719G>A	p.Glu1907Lys	p.E1907K	ENST00000268489	NM_006885.3	1907	Gaa/Aaa	9/10	0.131932104567177	3	FACETS	0.845	0.778	0.916	0.282	0.259	0.306	INDETERMINATE	1	TRUE	0	0.359795061659057	3		1063	1412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578476	7578477	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0013718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	213	451	1	ENST00000269305.4:c.453_454delinsTT	p.Pro152Ser	p.P152S	ENST00000269305	NM_001126112.2	151	ccCCcg/ccTTcg	5/11	0.348682439659881	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	2	TRUE	0	0.359795061659057	2		452	586	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289857	15289857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	108	368	2	ENST00000263388.2:c.3697C>T	p.Leu1233Phe	p.L1233F	ENST00000263388	NM_000435.2	1233	Ctt/Ttt	22/33	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.359795061659057	2		370	486	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295208	15295208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	126	646	0	ENST00000263388.2:c.2464C>T	p.Pro822Ser	p.P822S	ENST00000263388	NM_000435.2	822	Cct/Tct	16/33	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.359795061659057	2		646	699	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99137149	99137149	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0013718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	168	418	0	ENST00000074304.5:c.107-1G>A		p.X36_splice	ENST00000074304	NM_001134224.1	36			1	2	FACETS	0.886	0.82	0.954	1	0.992	1	CLONAL	2	TRUE	1	0.359795061659057	2		418	527	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39741455	39741455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	57	391	0	ENST00000361337.2:c.1342C>T	p.Arg448Trp	p.R448W	ENST00000361337	NM_003286.2	448	Cgg/Tgg	14/21	0.359795061659057	3	FACETS	0.539	0.462	0.624	0.27	0.231	0.312	SUBCLONAL	1	TRUE	1	0.359795061659057	3		391	693	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860342	42860342	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779659161	NA	P-0013718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	217	651	0	ENST00000398585.3:c.535G>A	p.Gly179Arg	p.G179R	ENST00000398585	NM_001135099.1	179	Ggg/Agg	5/14	1	2	FACETS	0.787	0.734	0.842	1	0.992	1	SUBCLONAL	2	TRUE	1	0.359795061659057	2		651	766	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266607	142266607	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	81	450	0	ENST00000350721.4:c.3317C>T	p.Pro1106Leu	p.P1106L	ENST00000350721	NM_001184.3	1106	cCa/cTa	16/47	1	2	FACETS	0.883	0.78	0.993	0.883	0.78	0.993	CLONAL	1	TRUE	1	0.359795061659057	2		450	510	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55561701	55561701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	51	272	0	ENST00000288135.5:c.91C>T	p.Pro31Ser	p.P31S	ENST00000288135	NM_000222.2	31	Cca/Tca	2/21	1	2	FACETS	0.649	0.552	0.754	0.649	0.552	0.754	SUBCLONAL	1	TRUE	1	0.359795061659057	2		272	437	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876133	35876133	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867328876	NA	P-0013718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	75	425	0	ENST00000303115.3:c.925C>T	p.His309Tyr	p.H309Y	ENST00000303115	NM_002185.3	309	Cat/Tat	8/8	0.177378521674884	3	FACETS	0.937	0.823	1	0.468	0.411	0.53	INDETERMINATE	1	TRUE	1	0.359795061659057	3		425	525	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515268	149515268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	99	571	0	ENST00000261799.4:c.214G>A	p.Glu72Lys	p.E72K	ENST00000261799	NM_002609.3	72	Gaa/Aaa	3/23	1	2	FACETS	0.964	0.863	1	0.964	0.863	1	CLONAL	1	TRUE	1	0.359795061659057	2		571	571	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622298	117622298	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	114	408	0	ENST00000368508.3:c.6572G>A	p.Trp2191Ter	p.W2191*	ENST00000368508	NM_002944.2	2191	tGg/tAg	42/43	0.359795061659057	1	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	0	0.359795061659057	1		408	434	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681507	117681507	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	156	392	0	ENST00000368508.3:c.3443C>T	p.Ser1148Leu	p.S1148L	ENST00000368508	NM_002944.2	1148	tCa/tTa	22/43	0.359795061659057	1	FACETS	0.766	0.708	0.826	1	0.99	1	SUBCLONAL	2	TRUE	0	0.359795061659057	1		392	464	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509477	106509477	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376127490	NA	P-0013718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	50	463	0	ENST00000359195.3:c.1471G>A	p.Gly491Arg	p.G491R	ENST00000359195	NM_002649.2	491	Gga/Aga	2/11	1	2	FACETS	0.6	0.51	0.7	0.6	0.51	0.7	SUBCLONAL	1	TRUE	1	0.359795061659057	2		463	463	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242779	98242779	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	263	532	0	ENST00000331920.6:c.838G>T	p.Glu280Ter	p.E280*	ENST00000331920	NM_000264.3	280	Gaa/Taa	6/24	0.329499304486914	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.359795061659057	2		532	622	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349251	70349251	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	201	841	0	ENST00000374080.3:c.3663T>A	p.Phe1221Leu	p.F1221L	ENST00000374080		1221	ttT/ttA	26/45	0.359795061659057	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.359795061659057	1		841	914	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939279	76939279	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013718-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	84	573	1	ENST00000373344.5:c.1469G>T	p.Gly490Val	p.G490V	ENST00000373344	NM_000489.3	490	gGt/gTt	9/35	0.359795061659057	1	FACETS	0.7	0.62	0.786	0.7	0.62	0.786	SUBCLONAL	1	TRUE	0	0.359795061659057	1		574	547	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	140	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.887	0.811	0.965	0.887	0.811	0.965	CLONAL	1	TRUE	1	0.539897120082977	2		215	585	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0013765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	362	351	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.539897120082977	3	FACETS	0.97	0.924	1	0.97	0.924	1	CLONAL	2	TRUE	1	0.539897120082977	3		351	878	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0013765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	138	281	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.742	0.676	0.81	0.742	0.676	0.81	SUBCLONAL	1	TRUE	1	0.539897120082977	2		281	689	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692904	89692904	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909224	NA	P-0013765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	275	156	374	1	ENST00000371953.3:c.388C>T	p.Arg130Ter	p.R130*	ENST00000371953	NM_000314.4	130	Cga/Tga	5/9	0.539897120082977	1	FACETS	0.979	0.906	1	0.979	0.906	1	CLONAL	1	TRUE	0	0.539897120082977	1		375	431	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40877330	40877330	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750253646	NA	P-0013765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	139	366	0	ENST00000373198.4:c.2366G>A	p.Arg789Lys	p.R789K	ENST00000373198	NM_133170.3	789	aGg/aAg	15/32	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.539897120082977	2		366	502	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029554	14029554	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147105770	NA	P-0013765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	98	285	0	ENST00000311895.7:c.1765C>T	p.Arg589Trp	p.R589W	ENST00000311895	NM_005236.2	589	Cgg/Tgg	8/11	1	2	FACETS	1	0.903	1	1	0.903	1	CLONAL	1	TRUE	1	0.539897120082977	2		285	362	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546655	9546655	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	300	810	0	ENST00000353224.5:c.1367G>A	p.Gly456Glu	p.G456E	ENST00000353224	NM_177990.2	456	gGg/gAg	5/10	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.539897120082977	2		810	1111	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2949781	2949781	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013765-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	215	588	0	ENST00000396946.4:c.3163G>A	p.Glu1055Lys	p.E1055K	ENST00000396946	NM_032415.4	1055	Gag/Aag	24/25	1	2	FACETS	0.95	0.885	1	0.95	0.885	1	CLONAL	1	TRUE	1	0.539897120082977	2		588	838	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587782144	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	259	745	0	ENST00000269305.4:c.473G>T	p.Arg158Leu	p.R158L	ENST00000269305	NM_001126112.2	158	cGc/cTc	5/11	0.34523385291314	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.37036830409774	2		745	606	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948558	54948558	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	108	542	0	ENST00000312783.6:c.760C>T	p.His254Tyr	p.H254Y	ENST00000312783	NM_198436.1	254	Cat/Tat	8/10	0.291852013337115	4	FACETS	0.665	0.595	0.74	0.333	0.297	0.37	SUBCLONAL	1	TRUE	2	0.37036830409774	4		542	1201	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175826	176175826	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	19	221	0	ENST00000367669.3:c.289G>T	p.Ala97Ser	p.A97S	ENST00000367669	NM_022457.5	97	Gcc/Tcc	1/20	0.37036830409774	3	FACETS	0.38	0.288	0.488	0.19	0.144	0.244	SUBCLONAL	1	TRUE	1	0.37036830409774	3		221	320	SUCCESS
CHEK1	1111	MSKCC	GRCh37	11	125514457	125514457	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	62	489	0	ENST00000428830.2:c.1152G>T	p.Leu384Phe	p.L384F	ENST00000428830	NM_001114121.2	384	ttG/ttT	11/14	1	2	FACETS	0.467	0.403	0.537	0.467	0.403	0.537	SUBCLONAL	1	TRUE	1	0.37036830409774	2		489	717	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971003	21971003	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	50	484	0	ENST00000304494.5:c.355G>T	p.Glu119Ter	p.E119*	ENST00000304494	NM_000077.4	119	Gag/Tag	2/3	0.278819592311067	0	FACETS	0.442	0.376	0.514			1	SUBCLONAL	1	TRUE	0	0.37036830409774	0		484	385	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567800	226567800	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1389888337	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	74	550	0	ENST00000366794.5:c.1366G>A	p.Glu456Lys	p.E456K	ENST00000366794	NM_001618.3	456	Gag/Aag	10/23	0.37036830409774	3	FACETS	0.564	0.493	0.641	0.282	0.246	0.321	SUBCLONAL	1	TRUE	1	0.37036830409774	3		550	840	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55953864	55953864	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	91	582	0	ENST00000263923.4:c.3572G>A	p.Gly1191Glu	p.G1191E	ENST00000263923	NM_002253.2	1191	gGa/gAa	27/30	0.37036830409774	6	FACETS	0.676	0.598	0.759	0.135	0.119	0.152	SUBCLONAL	1	TRUE	1	0.37036830409774	6		582	1266	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36808989	36808989	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	75	688	0	ENST00000373129.3:c.1065G>C	p.Met355Ile	p.M355I	ENST00000373129	NM_032017.1	355	atG/atC	11/12	0.37036830409774	3	FACETS	0.532	0.465	0.605	0.266	0.232	0.303	SUBCLONAL	1	TRUE	1	0.37036830409774	3		688	902	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102811604	102811604	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1197	163	808	0	ENST00000307046.8:c.580G>T	p.Gly194Ter	p.G194*	ENST00000307046	NM_001111285.1	194	Gga/Tga	4/4	0.256472682867511	3	FACETS	0.767	0.702	0.836	0.384	0.351	0.418	SUBCLONAL	1	TRUE	1	0.37036830409774	3		808	1360	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977861	134977861	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	129	510	0	ENST00000398015.3:c.2854C>A	p.Leu952Met	p.L952M	ENST00000398015	NM_004441.4	952	Ctg/Atg	16/16	0.256472682867511	3	FACETS	1	0.946	1	0.53	0.481	0.582	CLONAL	1	TRUE	1	0.37036830409774	3		510	779	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781644	9781644	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	rs765392990	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	193	427	0	ENST00000377346.4:c.1954C>G	p.Arg652Gly	p.R652G	ENST00000377346	NM_005026.3	652	Cgc/Ggc	15/24	0.37036830409774	3	FACETS	0.973	0.904	1	0.973	0.904	1	CLONAL	2	TRUE	1	0.37036830409774	3		427	635	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106741	27106741	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	235	560	0	ENST00000324856.7:c.6352G>C	p.Val2118Leu	p.V2118L	ENST00000324856	NM_006015.4	2118	Gtc/Ctc	20/20	0.37036830409774	3	FACETS	0.979	0.917	1	0.979	0.917	1	CLONAL	2	TRUE	1	0.37036830409774	3		560	768	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366634	40366634	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	113	475	0	ENST00000397332.2:c.563G>T	p.Gly188Val	p.G188V	ENST00000397332	NM_001033082.2	188	gGg/gTg	2/3	0.37036830409774	3	FACETS	1	0.917	1	0.51	0.459	0.564	CLONAL	1	TRUE	1	0.37036830409774	3		475	709	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46597608	46597608	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	50	576	0	ENST00000262741.5:c.17G>T	p.Trp6Leu	p.W6L	ENST00000262741	NM_003629.3	6	tGg/tTg	1/10	0.37036830409774	3	FACETS	0.355	0.3	0.416	0.177	0.15	0.208	SUBCLONAL	1	TRUE	1	0.37036830409774	3		576	902	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72400952	72400952	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	608	889	1	ENST00000357731.5:c.219C>A	p.Asn73Lys	p.N73K	ENST00000357731	NM_173808.2	73	aaC/aaA	2/7	0.37036830409774	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	1	0.37036830409774	3		890	1625	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462998	120462998	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	56	552	0	ENST00000256646.2:c.5333C>G	p.Ser1778Ter	p.S1778*	ENST00000256646	NM_024408.3	1778	tCa/tGa	30/34	0.37036830409774	3	FACETS	0.425	0.363	0.493	0.212	0.181	0.247	SUBCLONAL	1	TRUE	1	0.37036830409774	3		552	844	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120464978	120464978	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	43	389	0	ENST00000256646.2:c.5094C>G	p.Ile1698Met	p.I1698M	ENST00000256646	NM_024408.3	1698	atC/atG	28/34	0.37036830409774	3	FACETS	0.407	0.339	0.481	0.203	0.169	0.241	SUBCLONAL	1	TRUE	1	0.37036830409774	3		389	677	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120483192	120483192	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	89	419	0	ENST00000256646.2:c.3169G>T	p.Gly1057Trp	p.G1057W	ENST00000256646	NM_024408.3	1057	Ggg/Tgg	19/34	0.37036830409774	3	FACETS	0.844	0.748	0.946	0.422	0.374	0.473	CLONAL	1	TRUE	1	0.37036830409774	3		419	675	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745946	162745946	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	50	605	0	ENST00000367921.3:c.2069T>C	p.Met690Thr	p.M690T	ENST00000367921	NM_006182.2	690	aTg/aCg	16/18	0.37036830409774	3	FACETS	0.329	0.278	0.386	0.165	0.139	0.193	SUBCLONAL	1	TRUE	1	0.37036830409774	3		605	972	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651522	206651522	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	50	384	0	ENST00000367120.3:c.832G>T	p.Val278Leu	p.V278L	ENST00000367120	NM_014002.3	278	Gtg/Ttg	9/22	0.37036830409774	3	FACETS	0.64	0.543	0.746	0.32	0.271	0.373	SUBCLONAL	1	TRUE	1	0.37036830409774	3		384	500	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612810	228612810	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs148579172	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1270	263	986	0	ENST00000366696.1:c.217C>G	p.Arg73Gly	p.R73G	ENST00000366696	NM_003493.2	73	Cgc/Ggc	1/1	0.37036830409774	3	FACETS	1	0.977	1	0.549	0.513	0.586	CLONAL	1	TRUE	1	0.37036830409774	3		986	1533	SUCCESS
FH	2271	MSKCC	GRCh37	1	241671907	241671907	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	93	454	0	ENST00000366560.3:c.734G>T	p.Gly245Val	p.G245V	ENST00000366560	NM_000143.3	245	gGg/gTg	5/10	0.37036830409774	3	FACETS	0.658	0.584	0.738	0.329	0.292	0.369	SUBCLONAL	1	TRUE	1	0.37036830409774	3		454	904	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727087	243727087	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	137	559	0	ENST00000263826.5:c.883G>A	p.Glu295Lys	p.E295K	ENST00000263826	NM_005465.4	295	Gaa/Aaa	9/13	0.37036830409774	3	FACETS	0.921	0.837	1	0.461	0.418	0.505	CLONAL	1	TRUE	1	0.37036830409774	3		559	952	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106098	8106098	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	57	329	0	ENST00000346208.3:c.918G>T	p.Arg306Ser	p.R306S	ENST00000346208		306	agG/agT	4/6	1	2	FACETS	0.709	0.61	0.817	0.709	0.61	0.817	SUBCLONAL	1	TRUE	1	0.37036830409774	2		329	434	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111484	8111484	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs757598199	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	49	639	0	ENST00000346208.3:c.970A>G	p.Thr324Ala	p.T324A	ENST00000346208		324	Aca/Gca	5/6	1	2	FACETS	0.302	0.254	0.354	0.302	0.254	0.354	SUBCLONAL	1	TRUE	1	0.37036830409774	2		639	877	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70441155	70441155	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	130	438	0	ENST00000373644.4:c.4825-1G>T		p.X1609_splice	ENST00000373644	NM_030625.2	1609			0.256472682867511	3	FACETS	1	0.923	1	0.51	0.462	0.56	CLONAL	1	TRUE	1	0.37036830409774	3		438	816	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711933	89711933	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	77	461	0	ENST00000371953.3:c.551A>G	p.Asn184Ser	p.N184S	ENST00000371953	NM_000314.4	184	aAt/aGt	6/9	0.256472682867511	3	FACETS	0.705	0.619	0.798	0.353	0.309	0.399	SUBCLONAL	1	TRUE	1	0.37036830409774	3		461	699	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741834	17741834	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	20	165	0	ENST00000250003.3:c.505G>C	p.Ala169Pro	p.A169P	ENST00000250003	NM_002478.4	169	Gcc/Ccc	1/3	NA	2	FACETS	0.54	0.415	0.685			1	INDETERMINATE	1	TRUE	NA	0.37036830409774	2		165	200	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742458	17742458	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	62	557	0	ENST00000250003.3:c.640A>T	p.Ser214Cys	p.S214C	ENST00000250003	NM_002478.4	214	Agc/Tgc	2/3	NA	2	FACETS	0.508	0.438	0.584			1	INDETERMINATE	1	TRUE	NA	0.37036830409774	2		557	659	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17743018	17743018	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	105	416	0	ENST00000250003.3:c.926C>G	p.Ala309Gly	p.A309G	ENST00000250003	NM_002478.4	309	gCg/gGg	3/3	NA	2	FACETS	1	0.957	1			1	INDETERMINATE	1	TRUE	NA	0.37036830409774	2		416	507	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32438071	32438071	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	133	522	0	ENST00000332351.3:c.966C>A	p.Ser322Arg	p.S322R	ENST00000332351	NM_024426.4	322	agC/agA	5/10	0.321649966970652	3	FACETS	0.965	0.876	1	0.483	0.438	0.53	CLONAL	1	TRUE	1	0.37036830409774	3		522	882	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912834	100912834	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	93	548	0	ENST00000325455.5:c.2489-1G>T		p.X830_splice	ENST00000325455	NM_001202474.3	830			0.321649966970652	3	FACETS	0.606	0.538	0.679	0.303	0.269	0.34	SUBCLONAL	1	TRUE	1	0.37036830409774	3		548	982	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374220	118374220	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	80	651	0	ENST00000534358.1:c.7613C>T	p.Ser2538Phe	p.S2538F	ENST00000534358	NM_005933.3	2538	tCc/tTc	27/36	1	2	FACETS	0.497	0.436	0.562	0.497	0.436	0.562	SUBCLONAL	1	TRUE	1	0.37036830409774	2		651	870	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715720	18715720	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	149	567	0	ENST00000266497.5:c.3551C>G	p.Pro1184Arg	p.P1184R	ENST00000266497		1184	cCt/cGt	25/31	0.34523385291314	2	FACETS	0.904	0.826	0.986	0.452	0.413	0.493	CLONAL	1	TRUE	0	0.37036830409774	2		567	890	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427080	49427080	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	70	423	0	ENST00000301067.7:c.11408G>T	p.Gly3803Val	p.G3803V	ENST00000301067	NM_003482.3	3803	gGc/gTc	39/54	0.256472682867511	3	FACETS	0.765	0.667	0.87	0.382	0.333	0.435	SUBCLONAL	1	TRUE	1	0.37036830409774	3		423	586	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434883	49434883	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	126	568	0	ENST00000301067.7:c.6670G>T	p.Gly2224Trp	p.G2224W	ENST00000301067	NM_003482.3	2224	Ggg/Tgg	31/54	0.256472682867511	3	FACETS	1	0.95	1	0.536	0.486	0.589	CLONAL	1	TRUE	1	0.37036830409774	3		568	752	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864253	57864253	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	63	796	0	ENST00000228682.2:c.1730C>G	p.Ser577Cys	p.S577C	ENST00000228682	NM_005269.2	577	tCc/tGc	12/12	0.256472682867511	3	FACETS	0.4	0.345	0.461	0.2	0.172	0.231	SUBCLONAL	1	TRUE	1	0.37036830409774	3		796	1008	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112919909	112919909	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	70	215	0	ENST00000351677.2:c.1124A>T	p.Tyr375Phe	p.Y375F	ENST00000351677	NM_002834.3	375	tAt/tTt	10/16	0.256472682867511	3	FACETS	1	0.963	1	0.636	0.558	0.719	CLONAL	1	TRUE	1	0.37036830409774	3		215	352	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112490	115112490	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	74	439	0	ENST00000257566.3:c.1250del	p.Phe417SerfsTer215	p.F417Sfs*215	ENST00000257566	NM_016569.3	417	tTc/tc	7/8	1	2	FACETS	0.685	0.6	0.777	0.685	0.6	0.777	SUBCLONAL	1	TRUE	1	0.37036830409774	2		439	583	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431442	121431442	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	122	508	0	ENST00000257555.6:c.646C>A	p.Gln216Lys	p.Q216K	ENST00000257555		216	Cag/Aag	3/10	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.37036830409774	2		508	638	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432181	121432181	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	29	457	0	ENST00000257555.6:c.928C>A	p.Pro310Thr	p.P310T	ENST00000257555		310	Cct/Act	4/10	1	2	FACETS	0.282	0.225	0.346	0.282	0.225	0.346	SUBCLONAL	1	TRUE	1	0.37036830409774	2		457	556	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563047	21563047	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	60	488	2	ENST00000382592.4:c.872C>T	p.Thr291Met	p.T291M	ENST00000382592	NM_014572.2	291	aCg/aTg	4/8	1	2	FACETS	0.518	0.445	0.596	0.518	0.445	0.596	SUBCLONAL	1	TRUE	1	0.37036830409774	2		490	626	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28963941	28963941	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	61	683	1	ENST00000282397.4:c.1961C>A	p.Thr654Lys	p.T654K	ENST00000282397	NM_002019.4	654	aCa/aAa	13/30	1	2	FACETS	0.337	0.289	0.389	0.337	0.289	0.389	SUBCLONAL	1	TRUE	1	0.37036830409774	2		684	978	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32890647	32890647	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	59	356	1	ENST00000380152.3:c.50C>G	p.Thr17Arg	p.T17R	ENST00000380152		17	aCa/aGa	2/27	1	2	FACETS	0.458	0.394	0.529	0.458	0.394	0.529	SUBCLONAL	1	TRUE	1	0.37036830409774	2		357	695	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041335	42041335	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1106	258	878	0	ENST00000219905.7:c.5530G>T	p.Ala1844Ser	p.A1844S	ENST00000219905	NM_001164273.1	1844	Gct/Tct	17/24	0.213201395235403	3	FACETS	1	0.987	1	0.605	0.566	0.646	INDETERMINATE	1	TRUE	1	0.37036830409774	3		878	1364	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041984	42041984	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	195	848	0	ENST00000219905.7:c.6179A>C	p.Gln2060Pro	p.Q2060P	ENST00000219905	NM_001164273.1	2060	cAa/cCa	17/24	0.213201395235403	3	FACETS	1	0.975	1	0.561	0.519	0.605	INDETERMINATE	1	TRUE	1	0.37036830409774	3		848	1112	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472574	88472574	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	139	541	0	ENST00000360948.2:c.1981A>T	p.Ser661Cys	p.S661C	ENST00000360948	NM_001012338.2	661	Agt/Tgt	16/19	0.213201395235403	3	FACETS	1	0.973	1	0.587	0.535	0.641	INDETERMINATE	1	TRUE	1	0.37036830409774	3		541	758	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472667	88472667	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	16	262	0	ENST00000360948.2:c.1890-2A>T		p.X630_splice	ENST00000360948	NM_001012338.2	630			0.213201395235403	3	FACETS	0.339	0.25	0.446	0.17	0.125	0.223	INDETERMINATE	1	TRUE	1	0.37036830409774	3		262	302	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670433	88670433	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	51	604	1	ENST00000360948.2:c.1253C>A	p.Pro418His	p.P418H	ENST00000360948	NM_001012338.2	418	cCt/cAt	11/19	0.213201395235403	3	FACETS	0.397	0.336	0.464	0.198	0.168	0.232	INDETERMINATE	1	TRUE	1	0.37036830409774	3		605	823	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88799332	88799332	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	57	620	0	ENST00000360948.2:c.53T>A	p.Leu18Gln	p.L18Q	ENST00000360948	NM_001012338.2	18	cTg/cAg	2/19	0.213201395235403	3	FACETS	0.481	0.411	0.557	0.24	0.205	0.279	INDETERMINATE	1	TRUE	1	0.37036830409774	3		620	759	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434796	99434796	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	114	448	0	ENST00000268035.6:c.883G>T	p.Gly295Trp	p.G295W	ENST00000268035	NM_000875.3	295	Ggg/Tgg	3/21	0.213201395235403	3	FACETS	1	0.955	1	0.552	0.498	0.609	INDETERMINATE	1	TRUE	1	0.37036830409774	3		448	661	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857591	9857591	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	92	582	0	ENST00000330684.3:c.3810C>G	p.Asp1270Glu	p.D1270E	ENST00000330684	NM_001134407.1	1270	gaC/gaG	13/13	1	2	FACETS	0.787	0.7	0.88	0.787	0.7	0.88	SUBCLONAL	1	TRUE	1	0.37036830409774	2		582	631	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934820	9934820	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	972	79	796	0	ENST00000330684.3:c.1470C>A	p.Asn490Lys	p.N490K	ENST00000330684	NM_001134407.1	490	aaC/aaA	6/13	1	2	FACETS	0.406	0.356	0.46	0.406	0.356	0.46	SUBCLONAL	1	TRUE	1	0.37036830409774	2		796	1051	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934900	9934900	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	73	527	0	ENST00000330684.3:c.1390C>G	p.Leu464Val	p.L464V	ENST00000330684	NM_001134407.1	464	Ctg/Gtg	6/13	1	2	FACETS	0.533	0.466	0.606	0.533	0.466	0.606	SUBCLONAL	1	TRUE	1	0.37036830409774	2		527	739	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646791	23646791	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	167	722	0	ENST00000261584.4:c.1076G>T	p.Ser359Ile	p.S359I	ENST00000261584	NM_024675.3	359	aGt/aTt	4/13	1	2	FACETS	0.901	0.827	0.978	0.901	0.827	0.978	CLONAL	1	TRUE	1	0.37036830409774	2		722	1001	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67654599	67654599	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	120	623	3	ENST00000264010.4:c.1087-1G>T		p.X363_splice	ENST00000264010	NM_006565.3	363			1	2	FACETS	0.655	0.591	0.724	0.655	0.591	0.724	SUBCLONAL	1	TRUE	1	0.37036830409774	2		626	989	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81929422	81929422	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	178	777	1	ENST00000359376.3:c.1083G>T	p.Trp361Cys	p.W361C	ENST00000359376	NM_002661.3	361	tgG/tgT	13/33	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.37036830409774	2		778	938	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346628	89346628	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	144	590	0	ENST00000301030.4:c.6322G>T	p.Gly2108Cys	p.G2108C	ENST00000301030	NM_001256183.1	2108	Ggc/Tgc	9/13	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.37036830409774	2		590	674	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7980312	7980312	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	30	339	0	ENST00000319144.4:c.1271A>G	p.Tyr424Cys	p.Y424C	ENST00000319144	NM_001139.2	424	tAc/tGc	9/15	0.34523385291314	2	FACETS	0.393	0.316	0.48	0.197	0.158	0.24	SUBCLONAL	1	TRUE	0	0.37036830409774	2		339	412	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984214	7984214	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	149	602	0	ENST00000319144.4:c.515C>A	p.Pro172His	p.P172H	ENST00000319144	NM_001139.2	172	cCc/cAc	4/15	0.34523385291314	2	FACETS	1	0.965	1	0.55	0.504	0.599	CLONAL	1	TRUE	0	0.37036830409774	2		602	731	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983722	15983722	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	74	389	0	ENST00000268712.3:c.3400G>T	p.Gly1134Cys	p.G1134C	ENST00000268712	NM_006311.3	1134	Ggt/Tgt	25/46	0.34523385291314	2	FACETS	0.71	0.622	0.804	0.355	0.311	0.402	SUBCLONAL	1	TRUE	0	0.37036830409774	2		389	563	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40379606	40379606	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1579	102	1005	2	ENST00000293328.3:c.226G>T	p.Val76Leu	p.V76L	ENST00000293328	NM_012448.3	76	Gtg/Ttg	3/19	0.166487058641333	6	FACETS	0.57	0.508	0.638	0.19	0.169	0.213	INDETERMINATE	1	TRUE	3	0.37036830409774	6		1007	1681	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804398	46804398	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	67	508	0	ENST00000290295.7:c.609C>G	p.Ser203Arg	p.S203R	ENST00000290295	NM_006361.5	203	agC/agG	2/2	0.166487058641333	6	FACETS	0.789	0.685	0.903	0.263	0.228	0.301	INDETERMINATE	1	TRUE	3	0.37036830409774	6		508	798	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58725428	58725428	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1328	148	670	0	ENST00000305921.3:c.1002G>T	p.Glu334Asp	p.E334D	ENST00000305921	NM_003620.3	334	gaG/gaT	4/6	0.166487058641333	6	FACETS	0.943	0.858	1	0.314	0.286	0.344	INDETERMINATE	1	TRUE	3	0.37036830409774	6		670	1476	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876658	59876658	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	112	282	0	ENST00000259008.2:c.1143G>C	p.Met381Ile	p.M381I	ENST00000259008	NM_032043.2	381	atG/atC	9/20	0.166487058641333	6	FACETS	0.756	0.681	0.836	0.504	0.454	0.557	INDETERMINATE	2	TRUE	3	0.37036830409774	6		282	696	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885986	59885986	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	116	511	1	ENST00000259008.2:c.760A>T	p.Lys254Ter	p.K254*	ENST00000259008	NM_032043.2	254	Aag/Tag	7/20	0.166487058641333	6	FACETS	1	0.909	1	0.337	0.303	0.374	INDETERMINATE	1	TRUE	3	0.37036830409774	6		512	1078	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007249	62007249	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	50	462	0	ENST00000392795.3:c.434-1G>T		p.X145_splice	ENST00000392795	NM_001039933.1	145			0.166487058641333	6	FACETS	0.591	0.5	0.692	0.197	0.166	0.231	INDETERMINATE	1	TRUE	3	0.37036830409774	6		462	795	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533913	63533913	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs758255310	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	63	285	0	ENST00000307078.5:c.1241G>T	p.Arg414Leu	p.R414L	ENST00000307078	NM_004655.3	414	cGg/cTg	6/11	0.166487058641333	6	FACETS	1	0.91	1	0.356	0.308	0.408	INDETERMINATE	1	TRUE	3	0.37036830409774	6		285	555	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119034	70119035	+	missense_variant	Missense_Mutation	DNP	CA	CA	AT	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	71	471	0	ENST00000245479.2:c.606_607delinsAT	p.Ile203Phe	p.I203F	ENST00000245479	NM_000346.3	202	gcCAtc/gcATtc	2/3	0.166487058641333	6	FACETS	1	0.877	1	0.335	0.292	0.381	INDETERMINATE	1	TRUE	3	0.37036830409774	6		471	664	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119697	70119697	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1190	75	654	0	ENST00000245479.2:c.701del	p.Pro234HisfsTer19	p.P234Hfs*19	ENST00000245479	NM_000346.3	233	ggC/gg	3/3	0.166487058641333	6	FACETS	0.557	0.486	0.634	0.186	0.162	0.212	INDETERMINATE	1	TRUE	3	0.37036830409774	6		654	1265	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74733239	74733239	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	74	416	0	ENST00000359995.5:c.4A>T	p.Ser2Cys	p.S2C	ENST00000359995	NM_001195427.1	2	Agc/Tgc	1/3	0.166487058641333	6	FACETS	0.826	0.722	0.939	0.275	0.24	0.313	INDETERMINATE	1	TRUE	3	0.37036830409774	6		416	842	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39576695	39576695	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	111	339	0	ENST00000262039.4:c.984+1G>T		p.X328_splice	ENST00000262039	NM_002647.2	328			0.37036830409774	3	FACETS	1	0.964	1	0.574	0.517	0.634	CLONAL	1	TRUE	1	0.37036830409774	3		339	619	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39607485	39607485	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	128	592	0	ENST00000262039.4:c.1563G>T	p.Met521Ile	p.M521I	ENST00000262039	NM_002647.2	521	atG/atT	14/25	0.37036830409774	3	FACETS	0.891	0.807	0.98	0.446	0.403	0.49	CLONAL	1	TRUE	1	0.37036830409774	3		592	919	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222937	5222937	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564427160	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	64	389	1	ENST00000357368.4:c.2866G>A	p.Ala956Thr	p.A956T	ENST00000357368	NM_002850.3	956	Gcc/Acc	18/38	0.213201395235403	3	FACETS	0.894	0.776	1	0.447	0.388	0.511	INDETERMINATE	1	TRUE	1	0.37036830409774	3		390	458	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117192	7117192	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	111	644	1	ENST00000302850.5:c.4024G>T	p.Gly1342Cys	p.G1342C	ENST00000302850	NM_000208.2	1342	Ggc/Tgc	22/22	0.213201395235403	3	FACETS	0.863	0.776	0.956	0.432	0.388	0.478	INDETERMINATE	1	TRUE	1	0.37036830409774	3		645	823	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7141781	7141781	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	132	696	0	ENST00000302850.5:c.2589G>T	p.Glu863Asp	p.E863D	ENST00000302850	NM_000208.2	863	gaG/gaT	13/22	0.213201395235403	3	FACETS	0.798	0.723	0.877	0.399	0.361	0.439	INDETERMINATE	1	TRUE	1	0.37036830409774	3		696	1059	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142937	7142937	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	97	602	2	ENST00000302850.5:c.2432G>T	p.Gly811Val	p.G811V	ENST00000302850	NM_000208.2	811	gGc/gTc	12/22	0.213201395235403	3	FACETS	0.713	0.635	0.796	0.356	0.317	0.398	INDETERMINATE	1	TRUE	1	0.37036830409774	3		604	871	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272206	15272206	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	98	283	0	ENST00000263388.2:c.6233G>T	p.Arg2078Leu	p.R2078L	ENST00000263388	NM_000435.2	2078	cGg/cTg	33/33	0.213201395235403	3	FACETS	1	0.944	1	1	0.944	1	INDETERMINATE	2	TRUE	1	0.37036830409774	3		283	295	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278138	15278138	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	155	683	2	ENST00000263388.2:c.5284G>T	p.Val1762Leu	p.V1762L	ENST00000263388	NM_000435.2	1762	Gtg/Ttg	29/33	0.213201395235403	3	FACETS	1	0.978	1	0.601	0.551	0.654	INDETERMINATE	1	TRUE	1	0.37036830409774	3		685	825	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30303465	30303465	+	start_lost	Translation_Start_Site	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	39	148	0	ENST00000262643.3:c.3G>T	p.Met1?	p.M1?	ENST00000262643	NM_001238.2	1	atG/atT	2/12	0.213201395235403	3	FACETS	0.987	0.823	1	0.493	0.411	0.583	INDETERMINATE	1	TRUE	1	0.37036830409774	3		148	253	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765760	41765760	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	75	375	0	ENST00000301178.4:c.2636C>A	p.Pro879His	p.P879H	ENST00000301178	NM_021913.4	879	cCt/cAt	20/20	0.213201395235403	3	FACETS	0.994	0.873	1	0.497	0.436	0.562	INDETERMINATE	1	TRUE	1	0.37036830409774	3		375	483	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905378	50905378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	70	873	0	ENST00000440232.2:c.586G>A	p.Glu196Lys	p.E196K	ENST00000440232	NM_002691.3	196	Gag/Aag	5/27	0.213201395235403	3	FACETS	0.461	0.401	0.527	0.231	0.2	0.264	INDETERMINATE	1	TRUE	1	0.37036830409774	3		873	971	SUCCESS
ALK	238	MSKCC	GRCh37	2	29420448	29420448	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	171	668	0	ENST00000389048.3:c.4033G>C	p.Gly1345Arg	p.G1345R	ENST00000389048	NM_004304.4	1345	Gga/Cga	27/29	0.37036830409774	3	FACETS	1	0.956	1	0.53	0.487	0.575	CLONAL	1	TRUE	1	0.37036830409774	3		668	1032	SUCCESS
ALK	238	MSKCC	GRCh37	2	29430115	29430115	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	124	581	1	ENST00000389048.3:c.3860G>T	p.Gly1287Val	p.G1287V	ENST00000389048	NM_004304.4	1287	gGc/gTc	26/29	0.37036830409774	3	FACETS	0.924	0.835	1	0.462	0.417	0.509	CLONAL	1	TRUE	1	0.37036830409774	3		582	859	SUCCESS
ALK	238	MSKCC	GRCh37	2	29551338	29551338	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	59	486	0	ENST00000389048.3:c.1292C>A	p.Pro431Gln	p.P431Q	ENST00000389048	NM_004304.4	431	cCa/cAa	6/29	0.37036830409774	3	FACETS	0.583	0.501	0.672	0.291	0.25	0.336	SUBCLONAL	1	TRUE	1	0.37036830409774	3		486	648	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99156092	99156092	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	62	540	0	ENST00000074304.5:c.772G>T	p.Val258Leu	p.V258L	ENST00000074304	NM_001134224.1	258	Gtg/Ttg	10/26	0.37036830409774	3	FACETS	0.459	0.396	0.529	0.23	0.198	0.265	SUBCLONAL	1	TRUE	1	0.37036830409774	3		540	864	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735327	204735327	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	74	260	0	ENST00000302823.3:c.128C>T	p.Pro43Leu	p.P43L	ENST00000302823	NM_005214.4	43	cCt/cTt	2/4	0.37036830409774	3	FACETS	1	0.965	1	0.633	0.557	0.714	CLONAL	1	TRUE	1	0.37036830409774	3		260	374	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661203	227661203	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1479479676	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	125	580	0	ENST00000305123.5:c.2252A>G	p.Tyr751Cys	p.Y751C	ENST00000305123	NM_005544.2	751	tAc/tGc	1/2	0.37036830409774	3	FACETS	0.932	0.844	1	0.466	0.422	0.513	CLONAL	1	TRUE	1	0.37036830409774	3		580	858	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561133	9561133	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	170	578	0	ENST00000353224.5:c.649T>A	p.Trp217Arg	p.W217R	ENST00000353224	NM_177990.2	217	Tgg/Agg	4/10	NA	2	FACETS	1	0.988	1			1	INDETERMINATE	1	TRUE	NA	0.37036830409774	2		578	667	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368200	31368200	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	100	567	0	ENST00000328111.2:c.71A>C	p.Asn24Thr	p.N24T	ENST00000328111	NM_006892.3	24	aAc/aCc	2/23	0.291852013337115	4	FACETS	0.718	0.64	0.801	0.359	0.32	0.401	SUBCLONAL	1	TRUE	2	0.37036830409774	4		567	1031	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376663	31376663	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	40	430	0	ENST00000328111.2:c.658G>T	p.Gly220Trp	p.G220W	ENST00000328111	NM_006892.3	220	Ggg/Tgg	7/23	0.291852013337115	4	FACETS	0.381	0.315	0.454	0.19	0.157	0.228	SUBCLONAL	1	TRUE	2	0.37036830409774	4		430	777	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743858	40743858	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	295	563	0	ENST00000373198.4:c.3137del	p.Arg1046ProfsTer54	p.R1046Pfs*54	ENST00000373198	NM_133170.3	1046	cGc/cc	23/32	0.291852013337115	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	2	0.37036830409774	4		563	1053	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40743887	40743887	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	103	626	0	ENST00000373198.4:c.3108A>T	p.Glu1036Asp	p.E1036D	ENST00000373198	NM_133170.3	1036	gaA/gaT	23/32	0.291852013337115	4	FACETS	0.643	0.574	0.717	0.322	0.287	0.359	SUBCLONAL	1	TRUE	2	0.37036830409774	4		626	1185	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40944384	40944384	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	995	56	665	1	ENST00000373198.4:c.2118G>T	p.Gln706His	p.Q706H	ENST00000373198	NM_133170.3	706	caG/caT	12/32	0.291852013337115	4	FACETS	0.394	0.336	0.458	0.197	0.168	0.229	SUBCLONAL	1	TRUE	2	0.37036830409774	4		666	1051	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076937	41076937	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	86	633	1	ENST00000373198.4:c.1483G>T	p.Gly495Trp	p.G495W	ENST00000373198	NM_133170.3	495	Ggg/Tgg	9/32	0.291852013337115	4	FACETS	0.655	0.578	0.738	0.328	0.289	0.369	SUBCLONAL	1	TRUE	2	0.37036830409774	4		634	971	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46262333	46262333	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1385	118	818	2	ENST00000371998.3:c.917G>T	p.Ser306Ile	p.S306I	ENST00000371998		306	aGt/aTt	9/23	0.291852013337115	4	FACETS	0.581	0.522	0.644	0.29	0.261	0.322	SUBCLONAL	1	TRUE	2	0.37036830409774	4		820	1503	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755614	39755614	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	88	615	0	ENST00000288319.7:c.1151A>G	p.Lys384Arg	p.K384R	ENST00000288319	NM_182918.3	384	aAg/aGg	10/10	0.37036830409774	3	FACETS	0.587	0.519	0.661	0.196	0.173	0.221	SUBCLONAL	1	TRUE	0	0.37036830409774	3		615	959	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42840434	42840434	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	81	492	0	ENST00000398585.3:c.1314G>C	p.Lys438Asn	p.K438N	ENST00000398585	NM_001135099.1	438	aaG/aaC	12/14	0.37036830409774	3	FACETS	0.735	0.648	0.83	0.245	0.216	0.277	SUBCLONAL	1	TRUE	0	0.37036830409774	3		492	705	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41562664	41562664	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	67	377	0	ENST00000263253.7:c.3868G>T	p.Ala1290Ser	p.A1290S	ENST00000263253	NM_001429.3	1290	Gct/Tct	23/31	0.37036830409774	3	FACETS	0.705	0.613	0.805	0.353	0.306	0.403	SUBCLONAL	1	TRUE	1	0.37036830409774	3		377	608	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641226	12641226	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	84	750	0	ENST00000251849.4:c.1072G>T	p.Gly358Cys	p.G358C	ENST00000251849	NM_002880.3	358	Ggc/Tgc	10/17	0.256472682867511	3	FACETS	0.473	0.416	0.534	0.236	0.208	0.267	SUBCLONAL	1	TRUE	1	0.37036830409774	3		750	1137	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30664712	30664712	+	intron_variant	Intron	SNP	A	A	G	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	81	393	0	ENST00000295754.5:c.94+16243A>G		p.*32*	ENST00000295754	NM_003242.5	39/592			0.256472682867511	3	FACETS	0.737	0.649	0.832	0.369	0.324	0.416	SUBCLONAL	1	TRUE	1	0.37036830409774	3		393	703	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713423	30713423	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	108	431	0	ENST00000295754.5:c.748G>C	p.Val250Leu	p.V250L	ENST00000295754	NM_003242.5	250	Gtg/Ctg	4/7	0.256472682867511	3	FACETS	1	0.909	1	0.506	0.454	0.561	CLONAL	1	TRUE	1	0.37036830409774	3		431	683	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729969	30729969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200958264	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	63	389	0	ENST00000295754.5:c.1490G>A	p.Arg497Gln	p.R497Q	ENST00000295754	NM_003242.5	497	cGa/cAa	6/7	0.256472682867511	3	FACETS	0.586	0.506	0.673	0.293	0.253	0.337	SUBCLONAL	1	TRUE	1	0.37036830409774	3		389	688	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164121	47164121	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	46	359	1	ENST00000409792.3:c.2005A>T	p.Ile669Leu	p.I669L	ENST00000409792	NM_014159.6	669	Ata/Tta	3/21	0.256472682867511	3	FACETS	0.456	0.383	0.536	0.228	0.191	0.268	SUBCLONAL	1	TRUE	1	0.37036830409774	3		360	646	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643881	52643881	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	98	483	0	ENST00000394830.3:c.2015A>T	p.Tyr672Phe	p.Y672F	ENST00000394830	NM_018313.4	672	tAt/tTt	17/30	0.256472682867511	3	FACETS	0.808	0.721	0.901	0.404	0.36	0.451	CLONAL	1	TRUE	1	0.37036830409774	3		483	776	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134644668	134644669	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	115	389	1	ENST00000398015.3:c.69_70delinsTT	p.Met23_Asp24delinsIleTyr	p.M23_D24delinsIY	ENST00000398015	NM_004441.4	23	atGGac/atTTac	2/16	0.256472682867511	3	FACETS	1	0.916	1	0.509	0.459	0.562	CLONAL	1	TRUE	1	0.37036830409774	3		390	723	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670492	134670492	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	111	516	0	ENST00000398015.3:c.403C>T	p.Leu135Phe	p.L135F	ENST00000398015	NM_004441.4	135	Ctc/Ttc	3/16	0.256472682867511	3	FACETS	0.911	0.819	1	0.455	0.409	0.504	CLONAL	1	TRUE	1	0.37036830409774	3		516	780	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134851693	134851693	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1042789	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	94	464	0	ENST00000398015.3:c.1099C>A	p.Arg367Ser	p.R367S	ENST00000398015	NM_004441.4	367	Cgc/Agc	5/16	0.256472682867511	3	FACETS	0.829	0.737	0.926	0.414	0.368	0.463	CLONAL	1	TRUE	1	0.37036830409774	3		464	726	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134881021	134881021	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	53	348	0	ENST00000398015.3:c.1584C>A	p.Asp528Glu	p.D528E	ENST00000398015	NM_004441.4	528	gaC/gaA	7/16	0.256472682867511	3	FACETS	0.699	0.597	0.811	0.35	0.298	0.406	SUBCLONAL	1	TRUE	1	0.37036830409774	3		348	485	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134884836	134884836	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	45	580	0	ENST00000398015.3:c.1612C>A	p.Gln538Lys	p.Q538K	ENST00000398015	NM_004441.4	538	Cag/Aag	8/16	0.256472682867511	3	FACETS	0.34	0.285	0.402	0.17	0.142	0.201	SUBCLONAL	1	TRUE	1	0.37036830409774	3		580	846	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134977881	134977881	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	47	562	0	ENST00000398015.3:c.2875del	p.Ala959GlnfsTer8	p.A959Qfs*8	ENST00000398015	NM_004441.4	958	ttG/tt	16/16	0.256472682867511	3	FACETS	0.336	0.283	0.396	0.168	0.141	0.198	SUBCLONAL	1	TRUE	1	0.37036830409774	3		562	894	SUCCESS
ATR	545	MSKCC	GRCh37	3	142184020	142184020	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	135	591	0	ENST00000350721.4:c.6960G>T	p.Lys2320Asn	p.K2320N	ENST00000350721	NM_001184.3	2320	aaG/aaT	41/47	0.256472682867511	3	FACETS	0.771	0.699	0.846	0.385	0.349	0.423	SUBCLONAL	1	TRUE	1	0.37036830409774	3		591	1121	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430989	181430989	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	285	515	0	ENST00000325404.1:c.841G>C	p.Ala281Pro	p.A281P	ENST00000325404	NM_003106.3	281	Gcc/Ccc	1/1	0.307408871772995	4	FACETS	0.932	0.881	0.984	0.932	0.881	0.984	CLONAL	3	TRUE	1	0.37036830409774	4		515	754	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446986	187446986	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	158	660	0	ENST00000232014.4:c.1207C>T	p.Leu403Phe	p.L403F	ENST00000232014	NM_001130845.1	403	Ctt/Ttt	5/10	0.307408871772995	4	FACETS	1	0.933	1	0.341	0.312	0.372	CLONAL	1	TRUE	1	0.37036830409774	4		660	1142	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447002	187447002	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	159	676	0	ENST00000232014.4:c.1191G>T	p.Gln397His	p.Q397H	ENST00000232014	NM_001130845.1	397	caG/caT	5/10	0.307408871772995	4	FACETS	1	0.945	1	0.347	0.318	0.379	CLONAL	1	TRUE	1	0.37036830409774	4		676	1129	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187447175	187447175	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	121	487	0	ENST00000232014.4:c.1018C>T	p.Gln340Ter	p.Q340*	ENST00000232014	NM_001130845.1	340	Cag/Tag	5/10	0.307408871772995	4	FACETS	1	0.94	1	0.352	0.317	0.388	CLONAL	1	TRUE	1	0.37036830409774	4		487	849	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590764	189590764	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	194	533	1	ENST00000264731.3:c.1329C>A	p.His443Gln	p.H443Q	ENST00000264731	NM_003722.4	443	caC/caA	10/14	0.307408871772995	4	FACETS	1	0.987	1	0.443	0.409	0.478	CLONAL	1	TRUE	1	0.37036830409774	4		534	1081	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806204	1806204	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	69	621	0	ENST00000260795.2:c.1223C>G	p.Ser408Cys	p.S408C	ENST00000260795		408	tCc/tGc	8/17	NA	2	FACETS	0.52	0.453	0.594			1	INDETERMINATE	1	TRUE	NA	0.37036830409774	2		621	716	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55129889	55129889	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1187957560	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	720	707	0	ENST00000257290.5:c.423G>T	p.Glu141Asp	p.E141D	ENST00000257290	NM_006206.4	141	gaG/gaT	4/23	0.37036830409774	6	FACETS	0.939	0.909	0.968	0.939	0.909	0.968	CLONAL	5	TRUE	1	0.37036830409774	6		707	1442	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955115	55955115	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	140	542	2	ENST00000263923.4:c.3430C>A	p.His1144Asn	p.H1144N	ENST00000263923	NM_002253.2	1144	Cac/Aac	26/30	0.37036830409774	6	FACETS	1	0.933	1	0.207	0.187	0.227	CLONAL	1	TRUE	1	0.37036830409774	6		544	1274	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968166	55968167	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	799	642	2	ENST00000263923.4:c.2163_2164delinsAT	p.Asn721_Leu722delinsLysPhe	p.N721_L722delinsKF	ENST00000263923	NM_002253.2	721	aaCCtc/aaATtc	15/30	0.37036830409774	6	FACETS	0.953	0.925	0.981	0.953	0.925	0.981	CLONAL	5	TRUE	1	0.37036830409774	6		644	1576	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976822	55976822	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1235	132	542	0	ENST00000263923.4:c.1090T>C	p.Trp364Arg	p.W364R	ENST00000263923	NM_002253.2	364	Tgg/Cgg	8/30	0.37036830409774	6	FACETS	0.908	0.821	0.999	0.182	0.164	0.2	CLONAL	1	TRUE	1	0.37036830409774	6		542	1367	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143045914	143045914	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	44	383	0	ENST00000262992.4:c.1721-1G>C		p.X574_splice	ENST00000262992	NM_001101669.1	574			1	2	FACETS	0.447	0.374	0.527	0.447	0.374	0.527	SUBCLONAL	1	TRUE	1	0.37036830409774	2		383	532	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293710	1293710	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	41	308	1	ENST00000310581.5:c.1291C>A	p.Pro431Thr	p.P431T	ENST00000310581	NM_198253.2	431	Ccc/Acc	2/16	0.37036830409774	4	FACETS	0.639	0.532	0.757	0.213	0.177	0.253	SUBCLONAL	1	TRUE	1	0.37036830409774	4		309	475	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35874550	35874550	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	71	714	0	ENST00000303115.3:c.707-1G>T		p.X236_splice	ENST00000303115	NM_002185.3	236			0.37036830409774	4	FACETS	0.456	0.396	0.521	0.152	0.132	0.174	SUBCLONAL	1	TRUE	1	0.37036830409774	4		714	1152	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876335	35876335	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs751674240	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	142	432	1	ENST00000303115.3:c.1127C>A	p.Ala376Glu	p.A376E	ENST00000303115	NM_002185.3	376	gCa/gAa	8/8	0.37036830409774	4	FACETS	1	0.985	1	0.465	0.424	0.507	CLONAL	1	TRUE	1	0.37036830409774	4		433	754	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950170	38950170	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs1373844080	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	54	468	0	ENST00000357387.3:c.3780T>A	p.Ser1260Arg	p.S1260R	ENST00000357387	NM_152756.3	1260	agT/agA	31/38	0.37036830409774	4	FACETS	0.415	0.353	0.483	0.138	0.117	0.161	SUBCLONAL	1	TRUE	1	0.37036830409774	4		468	964	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449755	149449755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	89	407	0	ENST00000286301.3:c.1309C>T	p.His437Tyr	p.H437Y	ENST00000286301	NM_005211.3	437	Cac/Tac	9/22	0.213201395235403	3	FACETS	1	0.969	1	0.627	0.559	0.7	INDETERMINATE	1	TRUE	1	0.37036830409774	3		407	454	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460427	149460427	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	189	749	1	ENST00000286301.3:c.210C>A	p.Ser70Arg	p.S70R	ENST00000286301	NM_005211.3	70	agC/agA	3/22	0.213201395235403	3	FACETS	1	0.988	1	0.69	0.638	0.743	INDETERMINATE	1	TRUE	1	0.37036830409774	3		750	877	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170832307	170832307	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	120	661	0	ENST00000296930.5:c.671G>T	p.Gly224Val	p.G224V	ENST00000296930	NM_002520.6	224	gGa/gTa	9/11	0.213201395235403	3	FACETS	0.674	0.607	0.745	0.337	0.303	0.373	INDETERMINATE	1	TRUE	1	0.37036830409774	3		661	1140	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20481448	20481448	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	98	400	0	ENST00000346618.3:c.517C>G	p.Pro173Ala	p.P173A	ENST00000346618	NM_001949.4	173	Ccc/Gcc	3/7	0.37036830409774	5	FACETS	0.922	0.821	1	0.23	0.205	0.258	CLONAL	1	TRUE	1	0.37036830409774	5		400	893	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158413	26158413	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	60	452	0	ENST00000289316.2:c.16A>T	p.Lys6Ter	p.K6*	ENST00000289316	NM_138720.2	6	Aag/Tag	1/2	0.37036830409774	5	FACETS	0.513	0.441	0.593	0.128	0.11	0.149	SUBCLONAL	1	TRUE	1	0.37036830409774	5		452	982	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197206	26197206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2168	134	1146	0	ENST00000356476.2:c.273G>A	p.Met91Ile	p.M91I	ENST00000356476		91	atG/atA	1/1	0.37036830409774	5	FACETS	0.489	0.442	0.539	0.122	0.11	0.135	SUBCLONAL	1	TRUE	1	0.37036830409774	5		1146	2302	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778180	27778180	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1921	270	1316	0	ENST00000369163.2:c.329T>A	p.Leu110Gln	p.L110Q	ENST00000369163	NM_003536.2	110	cTg/cAg	1/1	0.37036830409774	5	FACETS	1	0.958	1	0.259	0.241	0.277	CLONAL	1	TRUE	1	0.37036830409774	5		1316	2191	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178643	32178643	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	97	567	0	ENST00000375023.3:c.2751C>G	p.His917Gln	p.H917Q	ENST00000375023	NM_004557.3	917	caC/caG	18/30	0.37036830409774	5	FACETS	0.764	0.679	0.854	0.191	0.169	0.214	SUBCLONAL	1	TRUE	1	0.37036830409774	5		567	1067	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183037	32183037	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	120	593	1	ENST00000375023.3:c.1987G>T	p.Asp663Tyr	p.D663Y	ENST00000375023	NM_004557.3	663	Gac/Tac	12/30	0.37036830409774	5	FACETS	1	0.912	1	0.253	0.228	0.28	CLONAL	1	TRUE	1	0.37036830409774	5		594	996	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183123	32183123	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	93	626	0	ENST00000375023.3:c.1901G>T	p.Cys634Phe	p.C634F	ENST00000375023	NM_004557.3	634	tGc/tTc	12/30	0.37036830409774	5	FACETS	0.656	0.581	0.736	0.164	0.145	0.184	SUBCLONAL	1	TRUE	1	0.37036830409774	5		626	1191	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287163	33287163	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	55	465	0	ENST00000374542.5:c.1934G>T	p.Gly645Val	p.G645V	ENST00000374542	NM_001141970.1	645	gGa/gTa	6/8	0.37036830409774	5	FACETS	0.443	0.377	0.515	0.111	0.094	0.129	SUBCLONAL	1	TRUE	1	0.37036830409774	5		465	1043	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149997777	149997777	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	59	524	0	ENST00000253339.5:c.2690G>T	p.Arg897Ile	p.R897I	ENST00000253339		897	aGa/aTa	5/7	1	2	FACETS	0.507	0.436	0.585	0.507	0.436	0.585	SUBCLONAL	1	TRUE	1	0.37036830409774	2		524	628	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005729	150005729	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	54	229	0	ENST00000253339.5:c.497-1G>A		p.X166_splice	ENST00000253339		166			1	2	FACETS	0.828	0.711	0.956	0.828	0.711	0.956	CLONAL	1	TRUE	1	0.37036830409774	2		229	352	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959038	2959038	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	137	427	1	ENST00000396946.4:c.2478C>A	p.Asp826Glu	p.D826E	ENST00000396946	NM_032415.4	826	gaC/gaA	18/25	0.37036830409774	3	FACETS	1	0.98	1	0.631	0.575	0.689	CLONAL	1	TRUE	1	0.37036830409774	3		428	695	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962825	2962825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	119	520	0	ENST00000396946.4:c.2083del	p.Val695SerfsTer21	p.V695Sfs*21	ENST00000396946	NM_032415.4	695	Gtc/tc	16/25	0.37036830409774	3	FACETS	1	0.933	1	0.521	0.47	0.574	CLONAL	1	TRUE	1	0.37036830409774	3		520	731	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729898	41729898	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1309408013	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	201	820	1	ENST00000242208.4:c.631G>A	p.Val211Ile	p.V211I	ENST00000242208	NM_002192.2	211	Gta/Ata	3/3	0.37036830409774	3	FACETS	0.972	0.898	1	0.486	0.449	0.524	CLONAL	1	TRUE	1	0.37036830409774	3		821	1324	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334974	81334974	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs771594786	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	85	515	0	ENST00000222390.5:c.1853G>T	p.Gly618Val	p.G618V	ENST00000222390	NM_000601.4	618	gGc/gTc	16/18	0.37036830409774	3	FACETS	0.608	0.536	0.685	0.304	0.268	0.343	SUBCLONAL	1	TRUE	1	0.37036830409774	3		515	895	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81355224	81355224	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	134	593	0	ENST00000222390.5:c.1150G>T	p.Asp384Tyr	p.D384Y	ENST00000222390	NM_000601.4	384	Gat/Tat	9/18	0.37036830409774	3	FACETS	0.932	0.846	1	0.466	0.423	0.512	CLONAL	1	TRUE	1	0.37036830409774	3		593	920	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372688	81372688	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	286	575	0	ENST00000222390.5:c.846C>G	p.Tyr282Ter	p.Y282*	ENST00000222390	NM_000601.4	282	taC/taG	7/18	0.37036830409774	3	FACETS	0.934	0.879	0.99	0.934	0.879	0.99	CLONAL	2	TRUE	1	0.37036830409774	3		575	980	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508232	106508232	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	30	243	0	ENST00000359195.3:c.226C>G	p.Leu76Val	p.L76V	ENST00000359195	NM_002649.2	76	Ctg/Gtg	2/11	0.37036830409774	3	FACETS	0.539	0.435	0.658	0.27	0.217	0.329	SUBCLONAL	1	TRUE	1	0.37036830409774	3		243	356	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508730	106508730	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	41	474	0	ENST00000359195.3:c.724G>T	p.Gly242Cys	p.G242C	ENST00000359195	NM_002649.2	242	Ggc/Tgc	2/11	0.37036830409774	3	FACETS	0.326	0.27	0.388	0.163	0.135	0.194	SUBCLONAL	1	TRUE	1	0.37036830409774	3		474	805	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140449179	140449179	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	26	220	0	ENST00000288602.6:c.1900A>T	p.Ser634Cys	p.S634C	ENST00000288602	NM_004333.4	634	Agc/Tgc	16/18	0.37036830409774	3	FACETS	0.475	0.376	0.589	0.238	0.188	0.295	SUBCLONAL	1	TRUE	1	0.37036830409774	3		220	350	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140550008	140550008	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	140	461	0	ENST00000288602.6:c.143G>A	p.Trp48Ter	p.W48*	ENST00000288602	NM_004333.4	48	tGg/tAg	2/18	0.37036830409774	3	FACETS	1	0.97	1	0.573	0.522	0.626	CLONAL	1	TRUE	1	0.37036830409774	3		461	782	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859850	151859850	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	51	529	0	ENST00000262189.6:c.10812G>C	p.Lys3604Asn	p.K3604N	ENST00000262189	NM_170606.2	3604	aaG/aaC	43/59	0.37036830409774	3	FACETS	0.399	0.338	0.466	0.2	0.169	0.233	SUBCLONAL	1	TRUE	1	0.37036830409774	3		529	818	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55371914	55371914	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1379706162	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	16	160	0	ENST00000297316.4:c.604C>A	p.His202Asn	p.H202N	ENST00000297316	NM_022454.3	202	Cac/Aac	2/2	0.37036830409774	4	FACETS	0.401	0.296	0.527	0.201	0.148	0.264	SUBCLONAL	1	TRUE	2	0.37036830409774	4		160	295	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74868154	74868154	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	10	74	0	ENST00000284811.8:c.140G>T	p.Ser47Ile	p.S47I	ENST00000284811		47	aGt/aTt	3/4	0.37036830409774	4	FACETS	0.536	0.364	0.75	0.268	0.182	0.375	SUBCLONAL	1	TRUE	2	0.37036830409774	4		74	138	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965495	90965495	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	94	537	0	ENST00000265433.3:c.1822G>T	p.Val608Leu	p.V608L	ENST00000265433	NM_002485.4	608	Gta/Tta	11/16	0.37036830409774	4	FACETS	0.689	0.612	0.772	0.345	0.306	0.386	SUBCLONAL	1	TRUE	2	0.37036830409774	4		537	1009	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128751253	128751253	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	47	212	0	ENST00000377970.2:c.790A>C	p.Ser264Arg	p.S264R	ENST00000377970	NM_002467.4	264	Agc/Cgc	2/3	0.37036830409774	4	FACETS	1	0.884	1	0.525	0.445	0.613	CLONAL	1	TRUE	2	0.37036830409774	4		212	331	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8340344	8340344	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	59	500	0	ENST00000356435.5:c.5252G>T	p.Arg1751Ile	p.R1751I	ENST00000356435		1751	aGa/aTa	31/35	0.34523385291314	2	FACETS	0.473	0.406	0.545	0.236	0.203	0.273	SUBCLONAL	1	TRUE	0	0.37036830409774	2		500	674	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8436679	8436679	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs761845336	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	210	444	0	ENST00000356435.5:c.3999C>A	p.Ser1333Arg	p.S1333R	ENST00000356435		1333	agC/agA	24/35	0.34523385291314	2	FACETS	0.853	0.796	0.911	0.853	0.796	0.911	CLONAL	2	TRUE	0	0.37036830409774	2		444	665	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528611	8528611	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	92	734	0	ENST00000356435.5:c.521G>T	p.Arg174Leu	p.R174L	ENST00000356435		174	cGt/cTt	4/35	0.34523385291314	2	FACETS	0.486	0.43	0.545	0.243	0.215	0.273	SUBCLONAL	1	TRUE	0	0.37036830409774	2		734	1023	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015121	37015121	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	118	699	0	ENST00000358127.4:c.283G>T	p.Val95Leu	p.V95L	ENST00000358127	NM_001280556.1	95	Gtg/Ttg	3/10	0.37036830409774	3	FACETS	0.925	0.835	1	0.308	0.278	0.341	CLONAL	1	TRUE	0	0.37036830409774	3		699	816	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215871	98215871	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143781513	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	98	411	0	ENST00000331920.6:c.3338G>A	p.Arg1113His	p.R1113H	ENST00000331920	NM_000264.3	1113	cGc/cAc	20/24	0.37036830409774	3	FACETS	0.963	0.861	1	0.321	0.287	0.358	CLONAL	1	TRUE	0	0.37036830409774	3		411	651	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759456	133759456	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	201	765	1	ENST00000318560.5:c.1779A>T	p.Lys593Asn	p.K593N	ENST00000318560	NM_005157.4	593	aaA/aaT	11/11	0.37036830409774	3	FACETS	1	0.984	1	0.408	0.377	0.439	CLONAL	1	TRUE	0	0.37036830409774	3		766	1052	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815572	139815572	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	943	72	775	0	ENST00000247668.2:c.1043C>G	p.Ser348Cys	p.S348C	ENST00000247668	NM_021138.3	348	tCc/tGc	9/11	0.37036830409774	3	FACETS	0.454	0.395	0.518	0.151	0.131	0.173	SUBCLONAL	1	TRUE	0	0.37036830409774	3		775	1015	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317481	1317481	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	74	832	0	ENST00000400841.2:c.584G>C	p.Gly195Ala	p.G195A	ENST00000400841		195	gGg/gCg	5/6	0.213887613810528	2	FACETS	0.386	0.337	0.44	0.193	0.168	0.22	INDETERMINATE	1	TRUE	0	0.37036830409774	2		832	1035	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650286	48650286	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	235	637	1	ENST00000376670.3:c.256G>T	p.Gly86Trp	p.G86W	ENST00000376670	NM_002049.3	86	Ggg/Tgg	3/6	0.213887613810528	2	FACETS	0.851	0.797	0.906	0.851	0.797	0.906	INDETERMINATE	2	TRUE	0	0.37036830409774	2		638	746	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652543	48652543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	47	350	0	ENST00000376670.3:c.1214C>T	p.Thr405Ile	p.T405I	ENST00000376670	NM_002049.3	405	aCt/aTt	6/6	0.213887613810528	2	FACETS	0.703	0.595	0.821	0.352	0.297	0.411	INDETERMINATE	1	TRUE	0	0.37036830409774	2		350	361	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411818	63411818	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	102	909	0	ENST00000330258.3:c.1349C>A	p.Pro450His	p.P450H	ENST00000330258	NM_152424.3	450	cCt/cAt	2/2	0.213887613810528	2	FACETS	0.495	0.442	0.553	0.248	0.221	0.277	INDETERMINATE	1	TRUE	0	0.37036830409774	2		909	1112	SUCCESS
AR	367	MSKCC	GRCh37	X	66765529	66765529	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1158367061	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	113	643	1	ENST00000374690.3:c.541C>A	p.Leu181Ile	p.L181I	ENST00000374690	NM_000044.3	181	Ctt/Att	1/8	0.213887613810528	2	FACETS	0.853	0.769	0.943	0.427	0.384	0.472	INDETERMINATE	1	TRUE	0	0.37036830409774	2		644	715	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344011	70344011	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	97	780	2	ENST00000374080.3:c.1747G>A	p.Asp583Asn	p.D583N	ENST00000374080		583	Gac/Aac	13/45	0.213887613810528	2	FACETS	0.522	0.464	0.583	0.261	0.232	0.292	INDETERMINATE	1	TRUE	0	0.37036830409774	2		782	1004	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346243	70346243	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	84	776	0	ENST00000374080.3:c.2594A>T	p.Tyr865Phe	p.Y865F	ENST00000374080		865	tAc/tTc	19/45	0.213887613810528	2	FACETS	0.462	0.407	0.521	0.231	0.203	0.261	INDETERMINATE	1	TRUE	0	0.37036830409774	2		776	982	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347811	70347811	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	273	791	0	ENST00000374080.3:c.3050G>T	p.Trp1017Leu	p.W1017L	ENST00000374080		1017	tGg/tTg	22/45	0.213887613810528	2	FACETS	0.801	0.753	0.85	0.801	0.753	0.85	INDETERMINATE	2	TRUE	0	0.37036830409774	2		791	920	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352041	70352041	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs759532414	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	75	753	0	ENST00000374080.3:c.4238C>A	p.Thr1413Asn	p.T1413N	ENST00000374080		1413	aCc/aAc	30/45	0.213887613810528	2	FACETS	0.47	0.411	0.534	0.235	0.205	0.267	INDETERMINATE	1	TRUE	0	0.37036830409774	2		753	861	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123020041	123020041	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	801	65	677	4	ENST00000355640.3:c.529G>T	p.Ala177Ser	p.A177S	ENST00000355640		177	Gct/Tct	2/7	0.213887613810528	2	FACETS	0.405	0.35	0.465	0.203	0.175	0.233	INDETERMINATE	1	TRUE	0	0.37036830409774	2		681	866	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123022475	123022475	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013768-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	231	837	0	ENST00000355640.3:c.884G>T	p.Gly295Val	p.G295V	ENST00000355640		295	gGt/gTt	3/7	0.213887613810528	2	FACETS	1	0.979	1	0.562	0.524	0.602	INDETERMINATE	1	TRUE	0	0.37036830409774	2		837	1109	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013770-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	120	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.615741912500355	2		215	372	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166547	118166547	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs74114325	NA	P-0013770-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	245	613	1	ENST00000369448.3:c.1057G>A	p.Val353Ile	p.V353I	ENST00000369448	NM_017709.3	353	Gtc/Atc	2/2	1	2	FACETS	0.905	0.848	0.964	0.905	0.848	0.964	CLONAL	1	TRUE	1	0.615741912500355	2		614	879	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95572031	95572031	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013770-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	390	791	0	ENST00000393063.1:c.3077G>C	p.Ser1026Thr	p.S1026T	ENST00000393063	NM_030621.3	1026	aGt/aCt	20/28	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.615741912500355	2		791	1250	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0013770-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	391	662	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.615741912500355	2		662	984	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290007	15290007	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs10408676	NA	P-0013770-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	47	873	0	ENST00000263388.2:c.3547G>A	p.Val1183Met	p.V1183M	ENST00000263388	NM_000435.2	1183	Gtg/Atg	22/33	0.321354143079439	1	FACETS	0.119	0.1	0.14	0.119	0.1	0.14	INDETERMINATE	1	TRUE	0	0.615741912500355	1		873	889	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291848	15291848	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1419024906	NA	P-0013770-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	181	741	0	ENST00000263388.2:c.2918A>G	p.His973Arg	p.H973R	ENST00000263388	NM_000435.2	973	cAc/cGc	18/33	0.321354143079439	1	FACETS	0.669	0.62	0.72	0.669	0.62	0.72	INDETERMINATE	1	TRUE	0	0.615741912500355	1		741	608	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589586	67589591	+	inframe_deletion	In_Frame_Del	DEL	ATGAAT	ATGAAT	-	novel	NA	P-0013770-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	199	404	0	ENST00000274335.5:c.1351_1356del	p.Glu451_Tyr452del	p.E451_Y452del	ENST00000274335		450	cATGAATat/cat	10/15	1	2	FACETS	0.922	0.857	0.989	0.922	0.857	0.989	CLONAL	1	TRUE	1	0.615741912500355	2		404	701	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563476	87563476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200399260	NA	P-0013770-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	220	621	0	ENST00000277120.3:c.1864G>A	p.Val622Ile	p.V622I	ENST00000277120		622	Gtc/Atc	16/19	1	2	FACETS	0.906	0.845	0.968	0.906	0.845	0.968	CLONAL	1	TRUE	1	0.615741912500355	2		621	789	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0013771-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	91	390	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.995	0.884	1	0.995	0.884	1	CLONAL	1	TRUE	1	0.268281971546498	2		390	682	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419926	152419926	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013771-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	57	548	0	ENST00000206249.3:c.1613A>G	p.Asp538Gly	p.D538G	ENST00000206249	NM_000125.3	538	gAc/gGc	8/8	0.268281971546498	1	FACETS	0.545	0.467	0.631	0.545	0.467	0.631	SUBCLONAL	1	TRUE	0	0.268281971546498	1		548	675	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178938934	178938934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867262025	NA	P-0013771-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	34	503	0	ENST00000263967.3:c.2176G>A	p.Glu726Lys	p.E726K	ENST00000263967	NM_006218.2	726	Gaa/Aaa	14/21	1	2	FACETS	0.77	0.631	0.926	0.77	0.631	0.926	CLONAL	1	TRUE	1	0.268281971546498	2		503	329	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152332832	152332832	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1057519827	NA	P-0013771-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	59	706	0	ENST00000206249.3:c.1138G>C	p.Glu380Gln	p.E380Q	ENST00000206249	NM_000125.3	380	Gaa/Caa	5/8	0.268281971546498	1	FACETS	0.381	0.326	0.441	0.381	0.326	0.441	SUBCLONAL	1	TRUE	0	0.268281971546498	1		706	1000	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295168	1295168	+	upstream_gene_variant	5'Flank	SNP	C	C	G	novel	NA	P-0013771-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	45	290	0				ENST00000310581	NM_198253.2	-/1132			0.170926804833572	4	FACETS	0.992	0.835	1	0.496	0.417	0.583	CLONAL	1	TRUE	2	0.268281971546498	4		290	429	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923350	131923350	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013771-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	50	430	0	ENST00000265335.6:c.853G>C	p.Asp285His	p.D285H	ENST00000265335		285	Gat/Cat	6/25	0.170926804833572	4	FACETS	0.959	0.814	1	0.479	0.407	0.559	CLONAL	1	TRUE	2	0.268281971546498	4		430	493	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638420	117638420	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013771-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	71	496	0	ENST00000368508.3:c.6021del	p.Asn2008ThrfsTer3	p.N2008Tfs*3	ENST00000368508	NM_002944.2	2007	ccC/cc	38/43	0.268281971546498	1	FACETS	0.807	0.705	0.917	0.807	0.705	0.917	CLONAL	1	TRUE	0	0.268281971546498	1		496	568	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945634	151945634	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0013771-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	91	238	0	ENST00000262189.6:c.1885A>T	p.Lys629Ter	p.K629*	ENST00000262189	NM_170606.2	629	Aaa/Taa	14/59	0.234272544845309	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.268281971546498	2		238	300	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245323	53245323	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0013771-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	172	824	0	ENST00000375401.3:c.714C>G	p.Ile238Met	p.I238M	ENST00000375401	NM_004187.3	238	atC/atG	6/26	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.268281971546498	2		824	1250	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0013782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	97	282	0				ENST00000310581	NM_198253.2	-/1132			0.517275887533441	1	FACETS	0.7	0.631	0.771	0.7	0.631	0.771	SUBCLONAL	1	TRUE	0	0.620832715656107	1		282	308	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0013782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	258	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.620832715656107	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	0	0.620832715656107	2		458	407	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0013782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	261	662	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.620832715656107	2		662	742	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs28934575	NA	P-0013782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	226	600	0	ENST00000269305.4:c.733G>C	p.Gly245Arg	p.G245R	ENST00000269305	NM_001126112.2	245	Ggc/Cgc	7/11	1	2	FACETS	0.981	0.917	1	0.981	0.917	1	CLONAL	1	TRUE	1	0.620832715656107	2		600	742	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750518	128750518	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0013782-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	198	679	0	ENST00000377970.2:c.55A>G	p.Asn19Asp	p.N19D	ENST00000377970	NM_002467.4	19	Aac/Gac	2/3	1	2	FACETS	0.873	0.811	0.936	0.873	0.811	0.936	CLONAL	1	TRUE	1	0.620832715656107	2		679	731	SUCCESS
AR	367	MSKCC	GRCh37	X	66931463	66931463	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs864622007	NA	P-0013808-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	449	327	0	ENST00000374690.3:c.2105T>A	p.Leu702His	p.L702H	ENST00000374690	NM_000044.3	702	cTc/cAc	4/8	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.76115488586878	1		327	566	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258207	16258207	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0013808-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	381	792	0	ENST00000375759.3:c.5474del	p.Lys1825ArgfsTer9	p.K1825Rfs*9	ENST00000375759	NM_015001.2	1824	tcA/tc	11/15	1	2	FACETS	0.895	0.851	0.94	0.895	0.851	0.94	CLONAL	1	TRUE	1	0.76115488586878	2		792	1118	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44945173	44945173	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0013808-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	348	351	0	ENST00000377967.4:c.3497G>A	p.Trp1166Ter	p.W1166*	ENST00000377967	NM_021140.2	1166	tGg/tAg	24/29	1	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.76115488586878	1		351	454	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0013829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	47	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.88	1	1	0.975	1	CLONAL	2	TRUE	1	0.29	2		458	158	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0013829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	85	446	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	1	2	FACETS	0.916	0.81	1	0.916	0.81	1	CLONAL	1	TRUE	1	0.29	2		446	640	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913530	NA	P-0013829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	54	583	0	ENST00000311936.3:c.34G>C	p.Gly12Arg	p.G12R	ENST00000311936	NM_004985.3	12	Ggt/Cgt	2/5	1	2	FACETS	0.583	0.497	0.677	0.583	0.497	0.677	SUBCLONAL	1	TRUE	1	0.29	2		583	639	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0013829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	43	491	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	NA	2	FACETS	0.499	0.417	0.591			1	INDETERMINATE	1	TRUE	NA	0.29	2		492	594	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604764	48604765	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs377767376	NA	P-0013829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	96	862	2	ENST00000342988.3:c.1587dup	p.His530ThrfsTer47	p.H530Tfs*47	ENST00000342988	NM_005359.5	529	tta/ttAa	12/12	0.3	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.29	1		864	543	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357060	89357060	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	33	1089	0	ENST00000301030.4:c.574del	p.Ala192GlnfsTer36	p.A192Qfs*36	ENST00000301030	NM_001256183.1	192	Gca/ca	6/13	0.3	1	FACETS	0.346	0.281	0.419	0.346	0.281	0.419	SUBCLONAL	1	TRUE	0	0.29	1		1089	563	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983210	149983210	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0013829-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	60	721	0	ENST00000253339.5:c.3048del	p.Ser1017ValfsTer3	p.S1017Vfs*3	ENST00000253339		1016	tcC/tc	7/7	0.3	1	FACETS	0.743	0.641	0.854	0.743	0.641	0.854	SUBCLONAL	1	TRUE	0	0.29	1		721	476	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577058	7577058	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	142	545	0	ENST00000269305.4:c.880del	p.Glu294SerfsTer51	p.E294Sfs*51	ENST00000269305	NM_001126112.2	294	Gag/ag	8/11	0.148684066621165	2	FACETS	1	0.986	1	0.717	0.654	0.783	CLONAL	1	TRUE	0	0.241551502266583	2		545	820	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0013833-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	16	188	2	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	NA	2	FACETS	0.599	0.444	0.785			1	INDETERMINATE	1	TRUE	NA	0.241551502266583	2		190	221	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	31	215	0				ENST00000310581	NM_198253.2	-/1132			0.198770017992208	3	FACETS	1	0.913	1	0.61	0.497	0.736	CLONAL	1	TRUE	1	0.281217971802259	3		215	206	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0013920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	143	598	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	1	2	FACETS	0.846	0.774	0.921	1	0.989	1	CLONAL	2	TRUE	1	0.281217971802259	2		598	601	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0013920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	48	492	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.281217971802259	2		492	272	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141427	11141427	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	51	588	2	ENST00000358026.2:c.3404G>T	p.Arg1135Leu	p.R1135L	ENST00000358026	NM_001128849.1	1135	cGg/cTg	25/36	0.103606135044421	0	FACETS	0.644	0.548	0.748			1	INDETERMINATE	1	TRUE	0	0.281217971802259	0		590	405	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795333	42795333	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0013920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	21	567	0	ENST00000575354.2:c.2414del	p.Pro805GlnfsTer119	p.P805Qfs*119	ENST00000575354	NM_015125.3	805	Cca/ca	10/20	1	2	FACETS	0.528	0.407	0.669	0.528	0.407	0.669	SUBCLONAL	1	TRUE	1	0.281217971802259	2		567	283	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691952	30691961	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTGAGTTTT	GGTGAGTTTT	-	novel	NA	P-0013920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	19	355	0	ENST00000295754.5:c.454_454+9del		p.X152_splice	ENST00000295754	NM_003242.5	152		3/7	1	2	FACETS	0.422	0.32	0.542	0.422	0.32	0.542	SUBCLONAL	1	TRUE	1	0.281217971802259	2		355	320	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748339	41748339	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	42	642	0	ENST00000226382.2:c.430G>A	p.Val144Met	p.V144M	ENST00000226382	NM_003924.3	144	Gtg/Atg	3/3	0.281217971802259	1	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	0	0.281217971802259	1		642	214	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013920-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	24	288	0	ENST00000304494.5:c.151-1G>A		p.X51_splice	ENST00000304494	NM_000077.4	51			0.281217971802259	1	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	0	0.281217971802259	1		288	133	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013920-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	83	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.9	0.799	1	0.9	0.799	1	CLONAL	1	TRUE	1	0.466791471649185	2		215	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574003	7574003	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs730882029	NA	P-0013920-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	430	598	0	ENST00000269305.4:c.1024C>T	p.Arg342Ter	p.R342*	ENST00000269305	NM_001126112.2	342	Cga/Tga	10/11	0.466791471649185	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.466791471649185	1		598	1124	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921549	178921549	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519941	NA	P-0013920-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	327	492	0	ENST00000263967.3:c.1031T>G	p.Val344Gly	p.V344G	ENST00000263967	NM_006218.2	344	gTg/gGg	5/21	0.466791471649185	3	FACETS	0.874	0.827	0.921	0.874	0.827	0.921	CLONAL	2	TRUE	1	0.466791471649185	3		492	989	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141427	11141427	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0013920-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	263	588	2	ENST00000358026.2:c.3404G>T	p.Arg1135Leu	p.R1135L	ENST00000358026	NM_001128849.1	1135	cGg/cTg	25/36	1	2	FACETS	0.967	0.906	1	0.967	0.906	1	CLONAL	1	TRUE	1	0.466791471649185	2		590	1165	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691952	30691961	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	GGTGAGTTTT	GGTGAGTTTT	-	novel	NA	P-0013920-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	127	355	0	ENST00000295754.5:c.454_454+9del		p.X152_splice	ENST00000295754	NM_003242.5	152		3/7	0.46307823079793	1	FACETS	0.875	0.797	0.955	0.875	0.797	0.955	CLONAL	1	TRUE	0	0.466791471649185	1		355	477	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748339	41748339	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013920-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	520	642	0	ENST00000226382.2:c.430G>A	p.Val144Met	p.V144M	ENST00000226382	NM_003924.3	144	Gtg/Atg	3/3	0.466791471649185	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.466791471649185	2		642	1060	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0013920-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	276	288	0	ENST00000304494.5:c.151-1G>A		p.X51_splice	ENST00000304494	NM_000077.4	51			0.466791471649185	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	0	0.466791471649185	2		288	540	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38962977	38962977	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0013920-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	94	236	0	ENST00000357387.3:c.1566+1G>T		p.X522_splice	ENST00000357387	NM_152756.3	522			1	2	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	1	0.466791471649185	2		236	388	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013926-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	42	215	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.759	0.638	0.891			1	INDETERMINATE	1	TRUE	NA	0.439029624128495	2		215	252	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795353	39795353	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs187337793	NA	P-0013926-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	154	790	0	ENST00000288319.7:c.367C>T	p.Arg123Cys	p.R123C	ENST00000288319	NM_182918.3	123	Cgc/Tgc	3/10	1	2	FACETS	0.93	0.853	1	0.93	0.853	1	CLONAL	1	TRUE	1	0.439029624128495	2		790	754	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279667	18279667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0013926-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	102	428	2	ENST00000222254.8:c.1940G>A	p.Arg647His	p.R647H	ENST00000222254	NM_005027.3	647	cGc/cAc	15/16	0.121355154129805	3	FACETS	0.94	0.842	1	0.313	0.28	0.348	INDETERMINATE	1	TRUE	0	0.439029624128495	3		430	603	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0013938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	92	282	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.953	0.85	1			1	INDETERMINATE	1	TRUE	NA	0.397310227560878	2		282	486	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586470	189586470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147148566	NA	P-0013938-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	102	363	0	ENST00000264731.3:c.1094C>T	p.Ser365Leu	p.S365L	ENST00000264731	NM_003722.4	365	tCg/tTg	8/14	0.387888749468329	3	FACETS	0.838	0.75	0.932	0.419	0.375	0.466	CLONAL	1	TRUE	1	0.397310227560878	3		363	734	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0013961-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	38	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.931	0.771	1	0.931	0.771	1	CLONAL	1	TRUE	1	0.2	2		215	408	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916938	178916940	+	inframe_deletion	In_Frame_Del	DEL	GAA	GAA	-	novel	NA	P-0013961-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1052	142	936	0	ENST00000263967.3:c.328_330del	p.Glu110del	p.E110del	ENST00000263967	NM_006218.2	109	GAA/-	2/21	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.2	2		936	1194	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942541	17942541	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013961-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	41	462	0	ENST00000458235.1:c.2747G>T	p.Arg916Leu	p.R916L	ENST00000458235	NM_000215.3	916	cGg/cTg	20/24	1	2	FACETS	0.745	0.62	0.885	0.745	0.62	0.885	SUBCLONAL	1	TRUE	1	0.2	2		462	550	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0013995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	536	625	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.655814245197391	5	FACETS	1	0.994	1			1	CLONAL	2	TRUE	NA	0.710295742763791	5		625	1309	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934576	NA	P-0013995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	321	555	0	ENST00000269305.4:c.818G>T	p.Arg273Leu	p.R273L	ENST00000269305	NM_001126112.2	273	cGt/cTt	8/11	0.710364555670096	3	FACETS	1	0.991	1	0.611	0.577	0.644	CLONAL	1	TRUE	1	0.710295742763791	3		555	1003	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971138	21971138	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs760640852	NA	P-0013995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	28	266	0	ENST00000304494.5:c.220G>T	p.Asp74Tyr	p.D74Y	ENST00000304494	NM_000077.4	74	Gac/Tac	2/3	1	2	FACETS	0.335	0.269	0.41	0.335	0.269	0.41	SUBCLONAL	1	TRUE	1	0.710295742763791	2		266	235	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729606	41729606	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1239	337	977	2	ENST00000242208.4:c.923G>A	p.Arg308His	p.R308H	ENST00000242208	NM_002192.2	308	cGt/cAt	3/3	0.568044527245892	4	FACETS	1	0.965	1	0.515	0.486	0.545	CLONAL	1	TRUE	2	0.710295742763791	4		979	1576	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16199373	16199373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0013995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	78	805	1	ENST00000375759.3:c.146C>T	p.Ala49Val	p.A49V	ENST00000375759	NM_015001.2	49	gCc/gTc	2/15	0.341762656505435	4	FACETS	0.361	0.316	0.41	0.181	0.158	0.205	INDETERMINATE	1	TRUE	2	0.710295742763791	4		806	1040	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432182	121432182	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0013995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	82	530	1	ENST00000257555.6:c.929C>A	p.Pro310His	p.P310H	ENST00000257555		310	cCt/cAt	4/10	0.710364555670096	3	FACETS	0.673	0.595	0.755	0.336	0.297	0.378	SUBCLONAL	1	TRUE	1	0.710295742763791	3		531	465	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120311	94120311	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0013995-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	234	913	0	ENST00000369303.4:c.740G>C	p.Arg247Thr	p.R247T	ENST00000369303	NM_004440.3	247	aGg/aCg	3/17	0.489525578486848	4	FACETS	0.871	0.811	0.933	0.435	0.405	0.467	CLONAL	1	TRUE	2	0.710295742763791	4		913	1294	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014006-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	192	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.947	0.884	1	0.947	0.884	1	CLONAL	1	TRUE	1	0.838211313061028	2		215	484	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55221822	55221822	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149840192	NA	P-0014006-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7982	17290	1152	2	ENST00000275493.2:c.866C>T	p.Ala289Val	p.A289V	ENST00000275493	NM_005228.3	289	gCc/gTc	7/28	0.838211313061028	27	FACETS	0.986	0.981	0.992	0.694	0.69	0.698	CLONAL	19	TRUE	0	0.838211313061028	27		1154	25272	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249385	153249385	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867384286	NA	P-0014021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	189	463	0	ENST00000281708.4:c.1393C>T	p.Arg465Cys	p.R465C	ENST00000281708	NM_033632.3	465	Cgt/Tgt	9/12	1	2	FACETS	0.98	0.91	1	0.98	0.91	1	CLONAL	1	TRUE	1	0.582595761348797	2		463	662	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134670358	134670358	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1449079060	NA	P-0014021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	296	509	2	ENST00000398015.3:c.269G>A	p.Arg90His	p.R90H	ENST00000398015	NM_004441.4	90	cGc/cAc	3/16	0.561329750359568	3	FACETS	0.924	0.876	0.973	0.924	0.876	0.973	CLONAL	2	TRUE	1	0.582595761348797	3		511	710	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11186829	11186829	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	157	485	1	ENST00000361445.4:c.6376G>T	p.Val2126Phe	p.V2126F	ENST00000361445	NM_004958.3	2126	Gtt/Ttt	46/58	0.468061793822558	3	FACETS	0.89	0.816	0.967			1	CLONAL	1	TRUE	NA	0.582595761348797	3		486	782	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578369	7578369	+	splice_donor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0014021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	252	363	0	ENST00000269305.4:c.559+2T>G		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.565746858964291	2	FACETS	0.905	0.858	0.951	0.905	0.858	0.951	CLONAL	2	TRUE	0	0.582595761348797	2		363	478	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7990714	7990714	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147784568	NA	P-0014021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	442	661	1	ENST00000319144.4:c.47C>T	p.Ser16Leu	p.S16L	ENST00000319144	NM_001139.2	16	tCg/tTg	1/15	0.565746858964291	2	FACETS	0.987	0.95	1	0.987	0.95	1	CLONAL	2	TRUE	0	0.582595761348797	2		662	769	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023324	31023324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	511	457	0	ENST00000375687.4:c.2809C>T	p.Pro937Ser	p.P937S	ENST00000375687	NM_015338.5	937	Cct/Tct	13/13	0.338194967759584	5	FACETS	1	0.986	1	0.826	0.799	0.852	INDETERMINATE	4	TRUE	0	0.582595761348797	5		457	796	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467875	66467875	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	173	588	0	ENST00000273854.3:c.394T>G	p.Phe132Val	p.F132V	ENST00000273854	NM_004439.5	132	Ttt/Gtt	3/18	0.561329750359568	3	FACETS	0.812	0.748	0.88	0.406	0.374	0.44	CLONAL	1	TRUE	1	0.582595761348797	3		588	944	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971203	21971209	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DEL	ATGACCT	ATGACCT	-	novel	NA	P-0014021-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	56	142	0	ENST00000304494.5:c.151-2_155del		p.X51_splice	ENST00000304494	NM_000077.4	51		2/3	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.582595761348797	2		142	157	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	231	215	0				ENST00000310581	NM_198253.2	-/1132			0.158059691448975	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.833266690787128	0		215	493	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0014059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2027	52	566	1	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.740289858520302	4	FACETS	0.11	0.093	0.129			1	SUBCLONAL	1	TRUE	NA	0.833266690787128	4		567	2079	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589147	67589147	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014059-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	373	381	0	ENST00000274335.5:c.1135A>G	p.Lys379Glu	p.K379E	ENST00000274335		379	Aaa/Gaa	9/15	0.10589318415077	3	FACETS	1	0.995	1	0.695	0.662	0.729	INDETERMINATE	1	TRUE	1	0.833266690787128	3		381	912	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0014137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	41	282	0				ENST00000310581	NM_198253.2	-/1132			0.356709866019178	1	FACETS	0.812	0.682	0.952	0.812	0.682	0.952	CLONAL	1	TRUE	0	0.373430152072048	1		282	220	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0014137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	129	598	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	0.93	0.844	1	0.93	0.844	1	CLONAL	1	TRUE	1	0.373430152072048	2		598	743	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444514	49444514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	93	371	0	ENST00000301067.7:c.2857C>T	p.Pro953Ser	p.P953S	ENST00000301067	NM_003482.3	953	Cct/Tct	11/54	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.373430152072048	2		371	397	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123298174	123298174	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	93	567	1	ENST00000358487.5:c.680G>A	p.Gly227Glu	p.G227E	ENST00000358487	NM_000141.4	227	gGa/gAa	6/18	1	2	FACETS	0.917	0.818	1	0.917	0.818	1	CLONAL	1	TRUE	1	0.373430152072048	2		568	543	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9547004	9547004	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	50	233	0	ENST00000353224.5:c.1018C>T	p.Leu340Phe	p.L340F	ENST00000353224	NM_177990.2	340	Ctc/Ttc	5/10	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.373430152072048	2		233	237	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499706	8499706	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	107	665	0	ENST00000356435.5:c.2263G>A	p.Glu755Lys	p.E755K	ENST00000356435		755	Gaa/Aaa	14/35	1	2	FACETS	0.936	0.842	1	0.936	0.842	1	CLONAL	1	TRUE	1	0.373430152072048	2		665	612	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729162	66729162	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519732	NA	P-0014137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	131	668	0	ENST00000307102.5:c.370C>T	p.Pro124Ser	p.P124S	ENST00000307102	NM_002755.3	124	Ccg/Tcg	3/11	1	2	FACETS	0.949	0.862	1	0.949	0.862	1	CLONAL	1	TRUE	1	0.373430152072048	2		668	739	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162394367	162394367	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144032774	NA	P-0014137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	126	659	0	ENST00000366898.1:c.701G>A	p.Arg234Gln	p.R234Q	ENST00000366898	NM_004562.2	234	cGg/cAg	6/12	1	2	FACETS	0.979	0.888	1	0.979	0.888	1	CLONAL	1	TRUE	1	0.373430152072048	2		659	689	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11317148	11317148	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	139	696	0	ENST00000361445.4:c.346C>T	p.Pro116Ser	p.P116S	ENST00000361445	NM_004958.3	116	Ccc/Tcc	4/58	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.373430152072048	2		696	685	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206649538	206649538	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	127	332	2	ENST00000367120.3:c.373C>T	p.His125Tyr	p.H125Y	ENST00000367120	NM_014002.3	125	Cac/Tac	6/22	0.373430152072048	3	FACETS	0.893	0.815	0.974	0.893	0.815	0.974	CLONAL	2	TRUE	1	0.373430152072048	3		334	452	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604659	43604659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	79	465	0	ENST00000355710.3:c.1244G>A	p.Arg415Lys	p.R415K	ENST00000355710	NM_020975.4	415	aGg/aAg	6/20	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.373430152072048	2		465	395	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371862	118371862	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	87	454	1	ENST00000534358.1:c.6319G>A	p.Glu2107Lys	p.E2107K	ENST00000534358	NM_005933.3	2107	Gaa/Aaa	25/36	1	2	FACETS	0.993	0.883	1	0.993	0.883	1	CLONAL	1	TRUE	1	0.373430152072048	2		455	469	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377246	118377246	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	142	645	0	ENST00000534358.1:c.10639C>T	p.Gln3547Ter	p.Q3547*	ENST00000534358	NM_005933.3	3547	Cag/Tag	27/36	1	2	FACETS	0.902	0.822	0.986	0.902	0.822	0.986	CLONAL	1	TRUE	1	0.373430152072048	2		645	843	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48916840	48916840	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	92	331	0	ENST00000267163.4:c.370A>T	p.Ile124Leu	p.I124L	ENST00000267163	NM_000321.2	124	Ata/Tta	3/27	1	2	FACETS	0.957	0.853	1	0.957	0.853	1	CLONAL	1	TRUE	1	0.373430152072048	2		331	515	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034932	42034932	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	225	895	0	ENST00000219905.7:c.4774C>T	p.Pro1592Ser	p.P1592S	ENST00000219905	NM_001164273.1	1592	Cct/Tct	15/24	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.373430152072048	2		895	1061	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349267	89349267	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	277	1325	0	ENST00000301030.4:c.3683C>A	p.Ser1228Tyr	p.S1228Y	ENST00000301030	NM_001256183.1	1228	tCc/tAc	9/13	NA	2	FACETS	1	0.987	1			1	INDETERMINATE	1	TRUE	NA	0.373430152072048	2		1325	1259	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37676303	37676303	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	149	700	1	ENST00000447079.4:c.3058C>T	p.Leu1020Phe	p.L1020F	ENST00000447079	NM_015083.1	1020	Ctt/Ttt	11/14	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.373430152072048	2		701	780	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40458440	40458440	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	124	571	0	ENST00000345506.4:c.1655C>T	p.Ser552Phe	p.S552F	ENST00000345506	NM_003152.3	552	tCc/tTc	14/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.373430152072048	2		571	487	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1623954	1623954	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370431685	NA	P-0014137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	116	892	3	ENST00000344749.5:c.545C>T	p.Ser182Phe	p.S182F	ENST00000344749	NM_001136139.2	182	tCc/tTc	8/19	1	2	FACETS	0.989	0.894	1	0.989	0.894	1	CLONAL	1	TRUE	1	0.373430152072048	2		895	628	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158594128	158594128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	200	826	1	ENST00000263640.3:c.1445C>T	p.Pro482Leu	p.P482L	ENST00000263640	NM_001105.4	482	cCa/cTa	11/11	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.373430152072048	2		827	1017	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385215	41385215	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	79	601	0	ENST00000373198.4:c.746C>T	p.Ser249Leu	p.S249L	ENST00000373198	NM_133170.3	249	tCa/tTa	6/32	0.373430152072048	1	FACETS	0.751	0.663	0.845	0.751	0.663	0.845	SUBCLONAL	1	TRUE	0	0.373430152072048	1		601	458	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755685	39755685	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	86	475	0	ENST00000288319.7:c.1080G>A	p.Met360Ile	p.M360I	ENST00000288319	NM_182918.3	360	atG/atA	10/10	1	2	FACETS	0.763	0.675	0.856	0.763	0.675	0.856	SUBCLONAL	1	TRUE	1	0.373430152072048	2		475	604	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55960978	55960978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	76	388	0	ENST00000263923.4:c.2962G>A	p.Glu988Lys	p.E988K	ENST00000263923	NM_002253.2	988	Gaa/Aaa	21/30	1	2	FACETS	0.844	0.743	0.953	0.844	0.743	0.953	CLONAL	1	TRUE	1	0.373430152072048	2		388	482	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176687067	176687067	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	131	608	0	ENST00000439151.2:c.5044C>T	p.Leu1682Phe	p.L1682F	ENST00000439151	NM_022455.4	1682	Ctt/Ttt	14/23	1	2	FACETS	0.915	0.831	1	0.915	0.831	1	CLONAL	1	TRUE	1	0.373430152072048	2		608	767	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725524	117725524	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1388562198	NA	P-0014137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	125	607	0	ENST00000368508.3:c.357G>A	p.Trp119Ter	p.W119*	ENST00000368508	NM_002944.2	119	tgG/tgA	5/43	0.373430152072048	1	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	0	0.373430152072048	1		607	492	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845547	151845547	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014137-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	105	557	0	ENST00000262189.6:c.13465A>G	p.Ile4489Val	p.I4489V	ENST00000262189	NM_170606.2	4489	Att/Gtt	52/59	1	2	FACETS	0.9	0.808	0.997	0.9	0.808	0.997	CLONAL	1	TRUE	1	0.373430152072048	2		557	625	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0014159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	289	282	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.999	0.946	1	0.999	0.946	1	CLONAL	1	TRUE	1	0.833366895990521	2		282	694	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0014159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	245	351	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	0.819888406594083	3	FACETS	0.885	0.828	0.944	0.443	0.414	0.472	CLONAL	1	TRUE	1	0.833366895990521	3		351	941	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812335	212812335	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	120	285	0	ENST00000342788.4:c.241C>T	p.Arg81Ter	p.R81*	ENST00000342788	NM_005235.2	81	Cga/Tga	3/28	0.433563173756788	1	FACETS	0.352	0.32	0.386	0.352	0.32	0.386	INDETERMINATE	1	TRUE	0	0.833366895990521	1		285	477	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59924472	59924472	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs565458815	NA	P-0014159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	404	637	1	ENST00000259008.2:c.617C>T	p.Ser206Leu	p.S206L	ENST00000259008	NM_032043.2	206	tCg/tTg	6/20	1	2	FACETS	0.93	0.887	0.973	0.93	0.887	0.973	CLONAL	1	TRUE	1	0.833366895990521	2		638	1043	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440145	220440145	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	659	1026	0	ENST00000243786.2:c.998G>A	p.Gly333Glu	p.G333E	ENST00000243786	NM_002191.3	333	gGg/gAg	2/2	0.433563173756788	1	FACETS	0.757	0.733	0.781	0.757	0.733	0.781	INDETERMINATE	1	TRUE	0	0.833366895990521	1		1026	1218	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720851	89720852	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0014159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	48	133	196	0	ENST00000371953.3:c.1002_1003delinsTT	p.Arg335Ter	p.R335*	ENST00000371953	NM_000314.4	334	aaCCga/aaTTga	8/9	0.833366895990521	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.833366895990521	1		196	181	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100580	102100580	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	155	486	0	ENST00000282441.5:c.1424A>T	p.Gln475Leu	p.Q475L	ENST00000282441	NM_001130145.2	475	cAg/cTg	9/9	0.433563173756788	1	FACETS	0.368	0.339	0.399	0.368	0.339	0.399	INDETERMINATE	1	TRUE	0	0.833366895990521	1		486	589	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054479	42054479	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	533	859	1	ENST00000219905.7:c.7663T>C	p.Ser2555Pro	p.S2555P	ENST00000219905	NM_001164273.1	2555	Tct/Cct	22/24	0.833366895990521	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.833366895990521	1		860	714	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858319	9858319	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	112	388	0	ENST00000330684.3:c.3082C>A	p.Gln1028Lys	p.Q1028K	ENST00000330684	NM_001134407.1	1028	Cag/Aag	13/13	0.51612465486266	4	FACETS	0.431	0.387	0.479			1	SUBCLONAL	1	TRUE	NA	0.833366895990521	4		388	1143	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100057	11100057	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	526	653	1	ENST00000358026.2:c.1183G>A	p.Asp395Asn	p.D395N	ENST00000358026	NM_001128849.1	395	Gat/Aat	7/36	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.833366895990521	2		654	1150	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45856063	45856063	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1309347920	NA	P-0014159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	415	505	0	ENST00000391945.4:c.1843G>A	p.Gly615Arg	p.G615R	ENST00000391945	NM_000400.3	615	Ggg/Agg	20/23	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.833366895990521	2		505	905	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909451	50909451	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	661	991	0	ENST00000440232.2:c.1255C>T	p.Pro419Ser	p.P419S	ENST00000440232	NM_002691.3	419	Cct/Tct	11/27	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.833366895990521	2		991	1475	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9543656	9543656	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs140682624	NA	P-0014159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	340	481	0	ENST00000353224.5:c.1498G>A	p.Asp500Asn	p.D500N	ENST00000353224	NM_177990.2	500	Gat/Aat	6/10	1	2	FACETS	0.944	0.897	0.992	0.944	0.897	0.992	CLONAL	1	TRUE	1	0.833366895990521	2		481	864	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755755	39755755	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	228	304	0	ENST00000288319.7:c.1010G>A	p.Gly337Glu	p.G337E	ENST00000288319	NM_182918.3	337	gGg/gAg	10/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.833366895990521	2		304	475	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138382857	138382857	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142933486	NA	P-0014159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	337	452	0	ENST00000289153.2:c.2687G>A	p.Arg896Gln	p.R896Q	ENST00000289153	NM_006219.2	896	cGa/cAa	19/22	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.833366895990521	2		452	761	SUCCESS
H3C4	8968	MSKCC	GRCh37	6	26197121	26197121	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	1838	1597	0	ENST00000356476.2:c.358A>T	p.Ile120Phe	p.I120F	ENST00000356476		120	Atc/Ttc	1/1	0.819888406594083	3	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	1	0.833366895990521	3		1597	3083	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508506	106508506	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	84	122	0	ENST00000359195.3:c.500A>G	p.Asn167Ser	p.N167S	ENST00000359195	NM_002649.2	167	aAc/aGc	2/11	0.819888406594083	3	FACETS	0.958	0.856	1	0.479	0.428	0.533	CLONAL	1	TRUE	1	0.833366895990521	3		122	298	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145742552	145742552	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1173220801	NA	P-0014159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	632	375	1	ENST00000428558.2:c.236G>T	p.Gly79Val	p.G79V	ENST00000428558	NM_004260.3	79	gGg/gTg	4/22	0.64009319061362	4	FACETS	0.944	0.917	0.971	0.944	0.917	0.971	CLONAL	3	TRUE	1	0.833366895990521	4		376	982	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971153	21971154	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AT	novel	NA	P-0014159-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	266	256	0	ENST00000304494.5:c.204_205delinsAT	p.Glu69Ter	p.E69*	ENST00000304494	NM_000077.4	68	gcGGag/gcATag	2/3	0.806815245857896	2	FACETS	0.988	0.957	1	0.988	0.957	1	CLONAL	2	TRUE	0	0.833366895990521	2		256	323	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0014166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	282	693	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.329799368494308	2	FACETS	0.991	0.937	1	0.991	0.937	1	CLONAL	2	TRUE	0	0.400032365537076	2		693	711	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098944	178098944	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	348	396	0	ENST00000397062.3:c.101G>C	p.Arg34Pro	p.R34P	ENST00000397062	NM_006164.4	34	cGa/cCa	2/5	0.400032365537076	1	FACETS	0.848	0.807	0.889	1	0.996	1	CLONAL	2	TRUE	0	0.400032365537076	1		396	821	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0014166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	110	635	0	ENST00000304494.5:c.172del	p.Arg58GlufsTer88	p.R58Efs*88	ENST00000304494	NM_000077.4	58	Cga/ga	2/3	0.329543229217811	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.400032365537076	1		635	359	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246382	41246382	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	100	650	0	ENST00000357654.3:c.1166G>C	p.Ser389Thr	p.S389T	ENST00000357654	NM_007294.3	389	aGt/aCt	10/23	0.284959689141894	1	FACETS	0.414	0.369	0.462	0.414	0.369	0.462	SUBCLONAL	1	TRUE	0	0.400032365537076	1		650	967	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259089	153259089	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0014166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	268	58	374	0	ENST00000281708.4:c.727-1G>A		p.X243_splice	ENST00000281708	NM_033632.3	243			0.378159200901779	1	FACETS	0.712	0.615	0.815	0.712	0.615	0.815	SUBCLONAL	1	TRUE	0	0.400032365537076	1		374	326	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179357	56179357	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	123	338	0	ENST00000399503.3:c.3670C>G	p.Pro1224Ala	p.P1224A	ENST00000399503	NM_005921.1	1224	Cca/Gca	15/20	0.400032365537076	1	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	0	0.400032365537076	1		338	457	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411734	63411734	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs751544083	NA	P-0014166-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	278	773	0	ENST00000330258.3:c.1433G>T	p.Gly478Val	p.G478V	ENST00000330258	NM_152424.3	478	gGa/gTa	2/2	1	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.400032365537076	1		773	750	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0014171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	425	446	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.302813467384193	4	FACETS	0.95	0.91	0.991	0.95	0.91	0.991	CLONAL	4	TRUE	0	0.317026161836325	4		446	929	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578442	7578442	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs148924904	NA	P-0014171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	175	997	0	ENST00000269305.4:c.488A>G	p.Tyr163Cys	p.Y163C	ENST00000269305	NM_001126112.2	163	tAc/tGc	5/11	0.283428552158237	2	FACETS	0.96	0.889	1	0.96	0.889	1	CLONAL	2	TRUE	0	0.317026161836325	2		997	575	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0014171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	100	380	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.189832800246371	4	FACETS	1	0.935	1	1	0.985	1	INDETERMINATE	3	TRUE	2	0.317026161836325	4		380	267	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0014171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	192	364	1	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.300198790649021	3	FACETS	0.959	0.889	1	0.959	0.889	1	CLONAL	2	TRUE	1	0.317026161836325	3		365	732	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999566	100999566	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745363836	NA	P-0014171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	428	1256	1	ENST00000325455.5:c.236C>T	p.Ser79Leu	p.S79L	ENST00000325455	NM_001202474.3	79	tCg/tTg	1/8	0.302386026706452	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	0	0.317026161836325	2		1257	1270	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63553951	63553951	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1567	142	663	0	ENST00000307078.5:c.788C>G	p.Ser263Cys	p.S263C	ENST00000307078	NM_004655.3	263	tCc/tGc	2/11	0.317026161836325	6	FACETS	0.857	0.777	0.94			1	CLONAL	1	TRUE	NA	0.317026161836325	6		663	1709	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63553987	63553987	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1490	116	641	0	ENST00000307078.5:c.752C>G	p.Ser251Cys	p.S251C	ENST00000307078	NM_004655.3	251	tCc/tGc	2/11	0.317026161836325	6	FACETS	0.745	0.668	0.826			1	SUBCLONAL	1	TRUE	NA	0.317026161836325	6		641	1606	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038803	47038804	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0014171-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	54	162	0	ENST00000377604.3:c.814dup	p.Leu272ProfsTer29	p.L272Pfs*29	ENST00000377604	NM_001204468.1	270	-/C	9/24	1	1	FACETS	0.779	0.676	0.887	1	0.971	1	SUBCLONAL	2	TRUE	0	0.317026161836325	1		162	184	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	111	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.86	0.772	0.952	0.86	0.772	0.952	CLONAL	1	TRUE	1	0.309321631930079	2		215	835	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711872	89711873	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	AGGG	novel	NA	P-0014180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	88	396	0	ENST00000371953.3:c.493_496dup		p.X165_splice	ENST00000371953	NM_000314.4	165			0.309321631930079	1	FACETS	0.879	0.781	0.984	0.879	0.781	0.984	CLONAL	1	TRUE	0	0.309321631930079	1		396	547	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213255	39213255	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014180-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1224	205	850	0	ENST00000402219.2:c.3712T>G	p.Leu1238Val	p.L1238V	ENST00000402219	NM_005633.3	1238	Ttg/Gtg	23/23	1	2	FACETS	0.928	0.858	1	0.928	0.858	1	CLONAL	1	TRUE	1	0.309321631930079	2		850	1429	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	477	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.810959747757979	2		215	1123	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0014206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	436	598	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	0.98	0.937	1	0.98	0.937	1	CLONAL	1	TRUE	1	0.810959747757979	2		598	1097	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0014206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	274	316	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.810959747757979	2		316	641	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916193	9916193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	322	620	0	ENST00000330684.3:c.2096C>T	p.Pro699Leu	p.P699L	ENST00000330684	NM_001134407.1	699	cCc/cTc	10/13	1	2	FACETS	0.899	0.852	0.947	0.899	0.852	0.947	CLONAL	1	TRUE	1	0.810959747757979	2		620	883	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10267111	10267111	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	445	629	0	ENST00000340748.4:c.1307C>T	p.Ser436Phe	p.S436F	ENST00000340748		436	tCt/tTt	17/40	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.810959747757979	2		629	1069	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623625	28623625	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1279372452	NA	P-0014206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	845	519	0	ENST00000241453.7:c.932G>A	p.Arg311Gln	p.R311Q	ENST00000241453	NM_004119.2	311	cGg/cAg	8/24	0.810959747757979	4	FACETS	0.914	0.891	0.938	0.914	0.891	0.938	CLONAL	3	TRUE	1	0.810959747757979	4		519	1376	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11316127	11316151	+	frameshift_variant	Frame_Shift_Del	DEL	AGCTCCCTCACGGATGGCCTGTTTG	AGCTCCCTCACGGATGGCCTGTTTG	-	novel	NA	P-0014206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	342	684	0	ENST00000361445.4:c.603_627del	p.Lys202Ter	p.K202*	ENST00000361445	NM_004958.3	201	ccCAAACAGGCCATCCGTGAGGGAGCT/cc	5/58	1	2	FACETS	0.839	0.796	0.883	0.839	0.796	0.883	CLONAL	1	TRUE	1	0.810959747757979	2		684	1005	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260726	16260726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1347933435	NA	P-0014206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	349	599	2	ENST00000375759.3:c.7991C>T	p.Pro2664Leu	p.P2664L	ENST00000375759	NM_015001.2	2664	cCg/cTg	11/15	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.810959747757979	2		601	831	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939474	36939474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	557	940	0	ENST00000361632.4:c.376C>T	p.Pro126Ser	p.P126S	ENST00000361632		126	Ccc/Tcc	4/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.810959747757979	2		940	1345	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279680	123279680	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	323	308	0	ENST00000358487.5:c.752G>A	p.Arg251Gln	p.R251Q	ENST00000358487	NM_000141.4	251	cGa/cAa	7/18	0.810959747757979	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	2	TRUE	0	0.810959747757979	2		308	393	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99251243	99251243	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	793	708	0	ENST00000268035.6:c.547C>T	p.Pro183Ser	p.P183S	ENST00000268035	NM_000875.3	183	Cca/Tca	2/21	0.810959747757979	3	FACETS	0.953	0.926	0.98	0.953	0.926	0.98	CLONAL	2	TRUE	1	0.810959747757979	3		708	1442	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99467150	99467150	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	267	454	1	ENST00000268035.6:c.2531C>T	p.Pro844Leu	p.P844L	ENST00000268035	NM_000875.3	844	cCt/cTt	12/21	0.810959747757979	3	FACETS	0.885	0.83	0.941	0.442	0.415	0.471	CLONAL	1	TRUE	1	0.810959747757979	3		455	1046	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781459	3781459	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1041379163	NA	P-0014206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	193	443	1	ENST00000262367.5:c.4906C>T	p.His1636Tyr	p.H1636Y	ENST00000262367	NM_004380.2	1636	Cac/Tac	30/31	1	2	FACETS	0.903	0.842	0.965	0.903	0.842	0.965	CLONAL	1	TRUE	1	0.810959747757979	2		444	527	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89833560	89833561	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0014206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	467	514	0	ENST00000389301.3:c.2589_2590delinsTT	p.Leu864Phe	p.L864F	ENST00000389301	NM_000135.2	863	ggCCtt/ggTTtt	27/43	0.775753673428071	3	FACETS	0.882	0.857	0.905	0.882	0.857	0.905	CLONAL	3	TRUE	0	0.810959747757979	3		514	612	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622332	1622332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs551790548	NA	P-0014206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	720	917	0	ENST00000344749.5:c.632C>T	p.Pro211Leu	p.P211L	ENST00000344749	NM_001136139.2	211	cCc/cTc	9/19	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.810959747757979	2		917	1767	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379682	17379683	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0014206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	374	755	0	ENST00000359435.4:c.67_68delinsTT	p.Pro23Phe	p.P23F	ENST00000359435	NM_001033549.1	23	CCt/TTt	2/9	1	2	FACETS	0.919	0.874	0.964	0.919	0.874	0.964	CLONAL	1	TRUE	1	0.810959747757979	2		755	1004	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797756	42797756	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	576	1038	0	ENST00000575354.2:c.3808C>T	p.Pro1270Ser	p.P1270S	ENST00000575354	NM_015125.3	1270	Ccc/Tcc	16/20	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.810959747757979	2		1038	1399	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48028189	48028189	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	265	405	0	ENST00000234420.5:c.3067G>A	p.Glu1023Lys	p.E1023K	ENST00000234420	NM_000179.2	1023	Gaa/Aaa	4/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.810959747757979	2		405	594	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99204001	99204001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	235	409	0	ENST00000074304.5:c.2864C>T	p.Ser955Phe	p.S955F	ENST00000074304	NM_001134224.1	955	tCc/tTc	26/26	1	2	FACETS	0.952	0.894	1	0.952	0.894	1	CLONAL	1	TRUE	1	0.810959747757979	2		409	609	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546670	9546670	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	192	360	0	ENST00000353224.5:c.1352A>G	p.Asn451Ser	p.N451S	ENST00000353224	NM_177990.2	451	aAc/aGc	5/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.810959747757979	2		360	452	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419978	41419978	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	302	647	0	ENST00000373198.4:c.343T>G	p.Ser115Ala	p.S115A	ENST00000373198	NM_133170.3	115	Tcc/Gcc	3/32	1	2	FACETS	0.979	0.927	1	0.979	0.927	1	CLONAL	1	TRUE	1	0.810959747757979	2		647	761	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55130049	55130049	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	418	783	1	ENST00000257290.5:c.583G>A	p.Gly195Arg	p.G195R	ENST00000257290	NM_006206.4	195	Gga/Aga	4/23	1	2	FACETS	0.973	0.929	1	0.973	0.929	1	CLONAL	1	TRUE	1	0.810959747757979	2		784	1060	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871196	35871196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773491081	NA	P-0014206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	186	380	0	ENST00000303115.3:c.418C>T	p.Arg140Trp	p.R140W	ENST00000303115	NM_002185.3	140	Cgg/Tgg	4/8	1	2	FACETS	0.972	0.907	1	0.972	0.907	1	CLONAL	1	TRUE	1	0.810959747757979	2		380	472	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940160	31940160	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1697	662	1126	1	ENST00000375333.2:c.302C>T	p.Pro101Leu	p.P101L	ENST00000375333	NM_032454.1	101	cCc/cTc	2/8	0.768324850413824	3	FACETS	0.973	0.935	1	0.486	0.467	0.506	CLONAL	1	TRUE	1	0.810959747757979	3		1127	2359	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979393	2979393	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	361	553	0	ENST00000396946.4:c.854C>T	p.Ser285Phe	p.S285F	ENST00000396946	NM_032415.4	285	tCc/tTc	6/25	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.810959747757979	2		553	829	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739609	41739609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	343	626	1	ENST00000242208.4:c.364G>A	p.Glu122Lys	p.E122K	ENST00000242208	NM_002192.2	122	Gag/Aag	2/3	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.810959747757979	2		627	830	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317520	1317520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	469	746	0	ENST00000400841.2:c.545C>T	p.Ser182Phe	p.S182F	ENST00000400841		182	tCt/tTt	5/6	0.810959747757979	0	FACETS		NA	1			1	NA	1	TRUE	NA	0.810959747757979	0		746	706	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211270	36211270	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014206-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1442	1051	894	0	ENST00000222270.7:c.1021C>T	p.Gln341Ter	p.Q341*	ENST00000222270	NM_014727.1	341	Caa/Taa	3/37	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.810959747757979	2		894	2493	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	73	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.858	0.748	0.977	0.858	0.748	0.977	CLONAL	1	TRUE	1	0.16	2		215	1064	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578263	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516435	NA	P-0014392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1328	116	720	2	ENST00000269305.4:c.586C>T	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	196	Cga/Tga	6/11	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.16	2		722	1444	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743897	41743897	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748294158	NA	P-0014392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1828	148	923	2	ENST00000301178.4:c.832C>T	p.Pro278Ser	p.P278S	ENST00000301178	NM_021913.4	278	Ccc/Tcc	7/20	1	2	FACETS	0.936	0.851	1	0.936	0.851	1	CLONAL	1	TRUE	1	0.16	2		925	1976	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562746	29562746	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs199474742	NA	P-0014392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	77	355	0	ENST00000356175.3:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000356175	NM_000267.3	1276	Cga/Tga	28/57	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.16	2		355	961	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518755	204518755	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	36	222	0	ENST00000367182.3:c.1418C>T	p.Ser473Leu	p.S473L	ENST00000367182	NM_001278516.1	473	tCa/tTa	11/11	1	2	FACETS	0.679	0.556	0.817	0.679	0.556	0.817	SUBCLONAL	1	TRUE	1	0.16	2		222	663	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375132	104375132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1398	77	590	1	ENST00000369902.3:c.1130C>T	p.Ser377Phe	p.S377F	ENST00000369902	NM_016169.3	377	tCc/tTc	9/12	1	2	FACETS	0.653	0.57	0.742	0.653	0.57	0.742	SUBCLONAL	1	TRUE	1	0.16	2		591	1475	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453399	40453399	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1509	109	663	0	ENST00000345506.4:c.1096C>T	p.Pro366Ser	p.P366S	ENST00000345506	NM_003152.3	366	Ccc/Tcc	10/20	1	2	FACETS	0.842	0.753	0.937	0.842	0.753	0.937	CLONAL	1	TRUE	1	0.16	2		663	1618	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381520	81381520	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	50	315	1	ENST00000222390.5:c.541C>T	p.Arg181Ter	p.R181*	ENST00000222390	NM_000601.4	181	Cga/Tga	5/18	1	2	FACETS	0.767	0.649	0.897	0.767	0.649	0.897	SUBCLONAL	1	TRUE	1	0.16	2		316	815	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9778780	9778780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1129	81	411	0	ENST00000377346.4:c.1049G>A	p.Gly350Asp	p.G350D	ENST00000377346	NM_005026.3	350	gGc/gAc	9/24	1	2	FACETS	0.837	0.735	0.947	0.837	0.735	0.947	CLONAL	1	TRUE	1	0.16	2		411	1210	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163315501	163315501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	56	416	0	ENST00000271452.3:c.841G>A	p.Asp281Asn	p.D281N	ENST00000271452	NM_145697.2	281	Gac/Aac	11/14	1	2	FACETS	0.913	0.78	1	0.913	0.78	1	CLONAL	1	TRUE	1	0.16	2		416	767	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204779	94204779	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776912688	NA	P-0014392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	41	366	2	ENST00000323929.3:c.806C>T	p.Ser269Leu	p.S269L	ENST00000323929	NM_005591.3	269	tCa/tTa	8/20	1	2	FACETS	0.751	0.624	0.893	0.751	0.624	0.893	SUBCLONAL	1	TRUE	1	0.16	2		368	682	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155953	119155953	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs764340189	NA	P-0014392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1510	125	923	0	ENST00000264033.4:c.1618C>T	p.Arg540Ter	p.R540*	ENST00000264033	NM_005188.3	540	Cga/Tga	11/16	1	2	FACETS	0.956	0.861	1	0.956	0.861	1	CLONAL	1	TRUE	1	0.16	2		923	1635	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926882	112926882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507543	NA	P-0014392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1281	108	541	0	ENST00000351677.2:c.1502G>A	p.Arg501Lys	p.R501K	ENST00000351677	NM_002834.3	501	aGg/aAg	13/16	1	2	FACETS	0.972	0.869	1	0.972	0.869	1	CLONAL	1	TRUE	1	0.16	2		541	1389	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965173	81965173	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1321	84	564	1	ENST00000359376.3:c.2653C>T	p.Pro885Ser	p.P885S	ENST00000359376	NM_002661.3	885	Ccg/Tcg	25/33	1	2	FACETS	0.747	0.657	0.845	0.747	0.657	0.845	SUBCLONAL	1	TRUE	1	0.16	2		565	1405	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29661976	29661976	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	63	450	0	ENST00000356175.3:c.5870T>G	p.Leu1957Arg	p.L1957R	ENST00000356175	NM_000267.3	1957	cTg/cGg	39/57	1	2	FACETS	0.751	0.648	0.865	0.751	0.648	0.865	SUBCLONAL	1	TRUE	1	0.16	2		450	1048	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732314	74732314	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	63	296	0	ENST00000359995.5:c.595G>T	p.Glu199Ter	p.E199*	ENST00000359995	NM_001195427.1	199	Gaa/Taa	2/3	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.16	2		296	715	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7120662	7120662	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1660	118	722	0	ENST00000302850.5:c.3628G>A	p.Asp1210Asn	p.D1210N	ENST00000302850	NM_000208.2	1210	Gat/Aat	20/22	1	2	FACETS	0.83	0.745	0.92	0.83	0.745	0.92	CLONAL	1	TRUE	1	0.16	2		722	1778	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375340	15375340	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1226	102	484	0	ENST00000263377.2:c.1087G>A	p.Glu363Lys	p.E363K	ENST00000263377	NM_058243.2	363	Gag/Aag	6/20	1	2	FACETS	0.96	0.856	1	0.96	0.856	1	CLONAL	1	TRUE	1	0.16	2		484	1328	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18277956	18277956	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1291125379	NA	P-0014392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	93	524	0	ENST00000222254.8:c.1576G>A	p.Glu526Lys	p.E526K	ENST00000222254	NM_005027.3	526	Gag/Aag	13/16	1	2	FACETS	0.915	0.811	1	0.915	0.811	1	CLONAL	1	TRUE	1	0.16	2		524	1270	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383644	42383644	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs148797987	NA	P-0014392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1253	81	580	0	ENST00000221972.3:c.419C>T	p.Thr140Ile	p.T140I	ENST00000221972	NM_021601.3	140	aCc/aTc	3/5	1	2	FACETS	0.759	0.666	0.86	0.759	0.666	0.86	SUBCLONAL	1	TRUE	1	0.16	2		580	1334	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966381	25966381	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1182809842	NA	P-0014392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1630	124	693	0	ENST00000435504.4:c.2825C>T	p.Pro942Leu	p.P942L	ENST00000435504		942	cCa/cTa	13/13	1	2	FACETS	0.884	0.796	0.977	0.884	0.796	0.977	CLONAL	1	TRUE	1	0.16	2		693	1754	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213365	39213365	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1422169849	NA	P-0014392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1614	146	678	1	ENST00000402219.2:c.3602G>A	p.Arg1201Gln	p.R1201Q	ENST00000402219	NM_005633.3	1201	cGg/cAg	23/23	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.16	2		679	1760	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42866409	42866409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762928261	NA	P-0014392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1662	121	821	0	ENST00000398585.3:c.223G>A	p.Glu75Lys	p.E75K	ENST00000398585	NM_001135099.1	75	Gag/Aag	3/14	1	2	FACETS	0.848	0.763	0.939	0.848	0.763	0.939	CLONAL	1	TRUE	1	0.16	2		821	1783	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185167723	185167723	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749369724	NA	P-0014392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1183	74	491	0	ENST00000265026.3:c.1046G>A	p.Gly349Glu	p.G349E	ENST00000265026	NM_004721.4	349	gGa/gAa	6/14	1	2	FACETS	0.736	0.642	0.838	0.736	0.642	0.838	SUBCLONAL	1	TRUE	1	0.16	2		491	1257	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157165	106157165	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750088604	NA	P-0014392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	87	390	0	ENST00000380013.4:c.2066C>T	p.Ser689Phe	p.S689F	ENST00000380013	NM_001127208.2	689	tCc/tTc	3/11	1	2	FACETS	0.909	0.802	1	0.909	0.802	1	CLONAL	1	TRUE	1	0.16	2		390	1196	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33290672	33290672	+	5_prime_UTR_variant	5'UTR	SNP	C	C	G	rs202133870	NA	P-0014392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1540	117	570	0	ENST00000374542.5:c.-86G>C		p.*29*	ENST00000374542	NM_001141970.1	-/740		1/8	1	2	FACETS	0.883	0.792	0.979	0.883	0.792	0.979	CLONAL	1	TRUE	1	0.16	2		570	1657	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117737444	117737444	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	66	380	0	ENST00000368508.3:c.205C>T	p.Gln69Ter	p.Q69*	ENST00000368508	NM_002944.2	69	Cag/Tag	3/43	1	2	FACETS	0.805	0.696	0.923	0.805	0.696	0.923	CLONAL	1	TRUE	1	0.16	2		380	1025	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151859804	151859804	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0014392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	50	241	0	ENST00000262189.6:c.10858A>T	p.Lys3620Ter	p.K3620*	ENST00000262189	NM_170606.2	3620	Aag/Tag	43/59	1	2	FACETS	0.87	0.737	1	0.87	0.737	1	CLONAL	1	TRUE	1	0.16	2		241	718	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641056	93641056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	48	437	0	ENST00000375746.1:c.1402G>A	p.Asp468Asn	p.D468N	ENST00000375746	NM_001174167.1	468	Gat/Aat	11/14	1	2	FACETS	0.802	0.676	0.941	0.802	0.676	0.941	CLONAL	1	TRUE	1	0.16	2		437	748	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123197800	123197800	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	48	227	1	ENST00000218089.9:c.1924G>A	p.Glu642Lys	p.E642K	ENST00000218089	NM_001042749.1	642	Gaa/Aaa	20/35	1	1	FACETS	1	0.924	1	1	0.924	1	CLONAL	1	TRUE	0	0.16	1		228	477	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204760	94204761	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0014392-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	26	322	0	ENST00000323929.3:c.824_825delinsTT	p.Ser275Phe	p.S275F	ENST00000323929	NM_005591.3	275	tCC/tTT	8/20	1	2	FACETS	0.554	0.437	0.688	0.554	0.437	0.688	SUBCLONAL	1	TRUE	1	0.16	2		322	587	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0014418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	50	215	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.703	0.607	0.804			1	INDETERMINATE	1	TRUE	NA	0.831909376440549	2		215	171	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0014418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	652	625	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.831909376440549	6	FACETS	1	0.993	1			1	CLONAL	3	TRUE	NA	0.831909376440549	6		625	1281	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0014418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	81	322	380	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.146915432421463	6	FACETS	1	0.984	1			1	INDETERMINATE	5	TRUE	NA	0.831909376440549	6		380	403	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16029456	16029457	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	38	290	0	ENST00000268712.3:c.1573dup	p.Thr525AsnfsTer11	p.T525Nfs*11	ENST00000268712	NM_006311.3	525	aca/aAca	15/46	0.343680647800658	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.831909376440549	0		290	386	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554840	187554840	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	443	309	0	ENST00000441802.2:c.4321C>T	p.Gln1441Ter	p.Q1441*	ENST00000441802	NM_005245.3	1441	Cag/Tag	7/27	0.795268555782012	3	FACETS	0.963	0.941	0.984	0.963	0.941	0.984	CLONAL	3	TRUE	0	0.831909376440549	3		309	522	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577121	7577121	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913343	NA	P-0014418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	101	287	738	0	ENST00000269305.4:c.817C>T	p.Arg273Cys	p.R273C	ENST00000269305	NM_001126112.2	273	Cgt/Tgt	8/11	0.775915550840127	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.831909376440549	1		738	388	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433896	49433896	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0014418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	139	690	1	ENST00000301067.7:c.7657C>T	p.Gln2553Ter	p.Q2553*	ENST00000301067	NM_003482.3	2553	Cag/Tag	31/54	0.669541365606284	3	FACETS	0.814	0.744	0.887	0.271	0.248	0.296	CLONAL	1	TRUE	0	0.831909376440549	3		691	581	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057874	27057874	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	175	794	0	ENST00000324856.7:c.1582C>T	p.Gln528Ter	p.Q528*	ENST00000324856	NM_006015.4	528	Cag/Tag	3/20	0.407876903740186	4	FACETS	0.662	0.608	0.718			1	INDETERMINATE	1	TRUE	NA	0.831909376440549	4		794	1165	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433827	49433827	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs761581210	NA	P-0014418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	126	781	0	ENST00000301067.7:c.7726C>G	p.Gln2576Glu	p.Q2576E	ENST00000301067	NM_003482.3	2576	Caa/Gaa	31/54	0.669541365606284	3	FACETS	0.616	0.559	0.677	0.205	0.186	0.226	SUBCLONAL	1	TRUE	0	0.831909376440549	3		781	696	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49446052	49446052	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	165	986	0	ENST00000301067.7:c.1414G>T	p.Glu472Ter	p.E472*	ENST00000301067	NM_003482.3	472	Gag/Tag	10/54	0.669541365606284	3	FACETS	0.556	0.51	0.604	0.185	0.17	0.202	SUBCLONAL	1	TRUE	0	0.831909376440549	3		986	1011	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448143	49448144	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0014418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	96	431	1	ENST00000301067.7:c.456_457delinsAA	p.Glu153Lys	p.E153K	ENST00000301067	NM_003482.3	152	caGGag/caAAag	4/54	0.669541365606284	3	FACETS	0.473	0.421	0.528	0.158	0.14	0.176	SUBCLONAL	1	TRUE	0	0.831909376440549	3		432	691	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448455	49448455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	105	522	1	ENST00000301067.7:c.256G>A	p.Glu86Lys	p.E86K	ENST00000301067	NM_003482.3	86	Gag/Aag	3/54	0.669541365606284	3	FACETS	0.521	0.467	0.578	0.174	0.155	0.193	SUBCLONAL	1	TRUE	0	0.831909376440549	3		523	686	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86669981	86669981	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	50	243	0	ENST00000274376.6:c.1778T>C	p.Val593Ala	p.V593A	ENST00000274376	NM_002890.2	593	gTc/gCc	14/25	0.831909376440549	1	FACETS	0.253	0.216	0.294	0.253	0.216	0.294	SUBCLONAL	1	TRUE	0	0.831909376440549	1		243	277	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68999979	68999979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	102	458	0	ENST00000288368.4:c.2048C>T	p.Ser683Leu	p.S683L	ENST00000288368	NM_024870.2	683	tCa/tTa	19/40	1	2	FACETS	0.307	0.274	0.341	0.307	0.274	0.341	SUBCLONAL	1	TRUE	1	0.831909376440549	2		458	800	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123210293	123210294	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	50	248	181	0	ENST00000218089.9:c.2646dup	p.Ala883CysfsTer12	p.A883Cfs*12	ENST00000218089	NM_001042749.1	882	gct/gcTt	26/35	0.5498845099004	2	FACETS	1	0.968	1			1	CLONAL	2	TRUE	NA	0.831909376440549	2		181	298	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8111461	8111462	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0014529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	364	465	0	ENST00000346208.3:c.947_948delinsAT	p.Ser316Tyr	p.S316Y	ENST00000346208		316	tCC/tAT	5/6	NA	2	FACETS	0.844	0.801	0.888			1	INDETERMINATE	1	TRUE	NA	0.73863682889081	2		465	1168	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717687	89717687	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	295	428	0	ENST00000371953.3:c.713del	p.Phe238SerfsTer18	p.F238Sfs*18	ENST00000371953	NM_000314.4	238	Ttc/tc	7/9	0.73863682889081	1	FACETS	0.805	0.764	0.845	0.805	0.764	0.845	CLONAL	1	TRUE	0	0.73863682889081	1		428	626	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417917	32417917	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	458	509	0	ENST00000332351.3:c.1135G>T	p.Val379Leu	p.V379L	ENST00000332351	NM_024426.4	379	Gta/Tta	7/10	1	2	FACETS	0.977	0.934	1	0.977	0.934	1	CLONAL	1	TRUE	1	0.73863682889081	2		509	1269	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827327	72827327	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	578	603	0	ENST00000268489.5:c.9254A>C	p.Lys3085Thr	p.K3085T	ENST00000268489	NM_006885.3	3085	aAa/aCa	9/10	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.73863682889081	2		603	1559	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578403	7578403	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs786202962	NA	P-0014529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	533	489	0	ENST00000269305.4:c.527G>T	p.Cys176Phe	p.C176F	ENST00000269305	NM_001126112.2	176	tGc/tTc	5/11	0.738570159002453	1	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	0	0.73863682889081	1		489	861	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	10982593	10982593	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	129	154	0	ENST00000327064.4:c.215A>G	p.Tyr72Cys	p.Y72C	ENST00000327064	NM_199141.1	72	tAc/tGc	1/16	1	2	FACETS	0.987	0.906	1	0.987	0.906	1	CLONAL	1	TRUE	1	0.73863682889081	2		154	354	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276654	15276654	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	620	609	0	ENST00000263388.2:c.5611T>C	p.Ser1871Pro	p.S1871P	ENST00000263388	NM_000435.2	1871	Tca/Cca	30/33	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.73863682889081	2		609	1593	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288874	15288874	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	314	322	0	ENST00000263388.2:c.3865G>T	p.Val1289Leu	p.V1289L	ENST00000263388	NM_000435.2	1289	Gtg/Ttg	24/33	1	2	FACETS	0.944	0.893	0.995	0.944	0.893	0.995	CLONAL	1	TRUE	1	0.73863682889081	2		322	901	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17942536	17942536	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs371883879	NA	P-0014529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	570	581	0	ENST00000458235.1:c.2752C>A	p.Arg918Ser	p.R918S	ENST00000458235	NM_000215.3	918	Cgc/Agc	20/24	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.73863682889081	2		581	1439	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25965748	25965748	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1790	673	605	2	ENST00000435504.4:c.3458G>A	p.Ser1153Asn	p.S1153N	ENST00000435504		1153	aGc/aAc	13/13	0.73863682889081	3	FACETS	1	0.972	1	0.507	0.487	0.527	CLONAL	1	TRUE	1	0.73863682889081	3		607	2463	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519920	NA	P-0014529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	215	283	0	ENST00000397062.3:c.85G>T	p.Asp29Tyr	p.D29Y	ENST00000397062	NM_006164.4	29	Gat/Tat	2/5	0.21334716477232	3	FACETS	1	0.974	1	0.542	0.506	0.58	INDETERMINATE	1	TRUE	1	0.73863682889081	3		283	735	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259428	89259428	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	693	454	1	ENST00000336596.2:c.572C>T	p.Ala191Val	p.A191V	ENST00000336596	NM_005233.5	191	gCc/gTc	3/17	0.728029745617101	3	FACETS	0.948	0.918	0.978	0.632	0.612	0.652	CLONAL	2	TRUE	0	0.73863682889081	3		455	1355	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259462	89259463	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	AA	novel	NA	P-0014529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	610	437	0	ENST00000336596.2:c.606_607delinsAA	p.Cys202_Pro203delinsTer	p.C202_P203delins*	ENST00000336596	NM_005233.5	202	tgCCca/tgAAca	3/17	0.728029745617101	3	FACETS	0.916	0.884	0.947	0.61	0.589	0.632	CLONAL	2	TRUE	0	0.73863682889081	3		437	1235	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189389	56189389	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	450	464	0	ENST00000399503.3:c.4421C>T	p.Pro1474Leu	p.P1474L	ENST00000399503	NM_005921.1	1474	cCt/cTt	20/20	1	2	FACETS	0.972	0.928	1	0.972	0.928	1	CLONAL	1	TRUE	1	0.73863682889081	2		464	1254	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149505107	149505107	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1656	578	602	0	ENST00000261799.4:c.1708G>T	p.Glu570Ter	p.E570*	ENST00000261799	NM_002609.3	570	Gag/Tag	12/23	0.73863682889081	3	FACETS	0.959	0.919	1	0.48	0.459	0.501	CLONAL	1	TRUE	1	0.73863682889081	3		602	2234	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798510	32798510	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	608	571	0	ENST00000374899.4:c.1346G>T	p.Arg449Leu	p.R449L	ENST00000374899	NM_018833.2	449	cGa/cTa	8/12	0.738570159002453	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.73863682889081	1		571	1007	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068124	94068124	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	242	259	0	ENST00000369303.4:c.838G>T	p.Gly280Cys	p.G280C	ENST00000369303	NM_004440.3	280	Ggc/Tgc	4/17	1	2	FACETS	0.914	0.858	0.971	0.914	0.858	0.971	CLONAL	1	TRUE	1	0.73863682889081	2		259	717	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453088	140453088	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	645	388	0	ENST00000288602.6:c.1847C>A	p.Ser616Tyr	p.S616Y	ENST00000288602	NM_004333.4	616	tCc/tAc	15/18	0.151087801188905	5	FACETS	0.946	0.915	0.978			1	INDETERMINATE	3	TRUE	NA	0.73863682889081	5		388	1297	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970988	21970988	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs34170727	NA	P-0014529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	1161	539	0	ENST00000304494.5:c.370C>G	p.Arg124Gly	p.R124G	ENST00000304494	NM_000077.4	124	Cgc/Ggc	2/3	0.724356632405644	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.73863682889081	2		539	1535	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971194	21971194	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	750	413	0	ENST00000304494.5:c.164del	p.Gly55AlafsTer91	p.G55Afs*91	ENST00000304494	NM_000077.4	55	gGc/gc	2/3	0.724356632405644	2	FACETS	0.967	0.944	0.989	0.967	0.944	0.989	CLONAL	2	TRUE	0	0.73863682889081	2		413	1050	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971199	21971199	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104894095	NA	P-0014529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	786	315	0	ENST00000304494.5:c.159G>A	p.Met53Ile	p.M53I	ENST00000304494	NM_000077.4	53	atG/atA	2/3	0.724356632405644	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	0	0.73863682889081	2		315	1042	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045189	47045189	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014529-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	487	474	0	ENST00000377604.3:c.2430G>T	p.Glu810Asp	p.E810D	ENST00000377604	NM_001204468.1	810	gaG/gaT	21/24	0.73863682889081	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.73863682889081	1		474	788	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	510	778	1	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.60081885834197	2	FACETS	0.919	0.886	0.951	0.919	0.886	0.951	CLONAL	2	TRUE	0	0.608783365845698	2		779	912	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1222986	1222986	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	rs864622488	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	421	365	0	ENST00000326873.7:c.923G>T	p.Trp308Leu	p.W308L	ENST00000326873	NM_000455.4	308	tGg/tTg	8/10	0.60081885834197	2	FACETS	0.982	0.946	1	0.982	0.946	1	CLONAL	2	TRUE	0	0.608783365845698	2		365	704	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs11552822	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	207	563	0	ENST00000304494.5:c.250G>T	p.Asp84Tyr	p.D84Y	ENST00000304494	NM_000077.4	84	Gac/Tac	2/3	0.608307321815938	1	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	0	0.608783365845698	1		563	401	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933810	36933811	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	224	363	0	ENST00000361632.4:c.1588_1589insA	p.Ala530AspfsTer21	p.A530Dfs*21	ENST00000361632		530	gcc/gAcc	12/16	1	2	FACETS	0.973	0.91	1	0.973	0.91	1	CLONAL	1	TRUE	1	0.608783365845698	2		363	756	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651162	206651162	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1162	244	488	0	ENST00000367120.3:c.772G>T	p.Glu258Ter	p.E258*	ENST00000367120	NM_014002.3	258	Gag/Tag	8/22	0.608856936982572	4	FACETS	0.917	0.855	0.982	0.306	0.285	0.328	CLONAL	1	TRUE	1	0.608783365845698	4		488	1406	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563066	21563066	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	534	491	0	ENST00000382592.4:c.853G>T	p.Gly285Cys	p.G285C	ENST00000382592	NM_014572.2	285	Ggt/Tgt	4/8	0.60081885834197	2	FACETS	0.98	0.948	1	0.98	0.948	1	CLONAL	2	TRUE	0	0.608783365845698	2		491	895	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43720363	43720363	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	271	392	0	ENST00000382044.4:c.3679G>C	p.Glu1227Gln	p.E1227Q	ENST00000382044	NM_001141980.1	1227	Gaa/Caa	18/28	0.355190341227494	3	FACETS	1	0.986	1	0.577	0.542	0.613	INDETERMINATE	1	TRUE	1	0.608783365845698	3		392	1006	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867632	78867632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1196323454	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	288	510	0	ENST00000306801.3:c.2368G>A	p.Ala790Thr	p.A790T	ENST00000306801	NM_020761.2	790	Gcc/Acc	20/34	0.608856936982572	3	FACETS	0.98	0.921	1	0.49	0.46	0.521	CLONAL	1	TRUE	1	0.608783365845698	3		510	1259	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11130265	11130265	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	402	290	1	ENST00000358026.2:c.2506-2A>T		p.X836_splice	ENST00000358026	NM_001128849.1	836			0.60081885834197	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.608783365845698	2		291	582	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143206	30143206	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	348	392	0	ENST00000389048.3:c.320G>C	p.Gly107Ala	p.G107A	ENST00000389048	NM_004304.4	107	gGg/gCg	1/29	0.608856936982572	3	FACETS	0.98	0.934	1	0.98	0.934	1	CLONAL	2	TRUE	1	0.608783365845698	3		392	761	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225362561	225362561	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	198	370	0	ENST00000264414.4:c.1616A>G	p.Tyr539Cys	p.Y539C	ENST00000264414	NM_003590.4	539	tAc/tGc	12/16	0.608856936982572	3	FACETS	0.925	0.857	0.996	0.463	0.428	0.498	CLONAL	1	TRUE	1	0.608783365845698	3		370	917	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023899	31023899	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	523	457	0	ENST00000375687.4:c.3384C>G	p.Asp1128Glu	p.D1128E	ENST00000375687	NM_015338.5	1128	gaC/gaG	13/13	0.608856936982572	3	FACETS	0.935	0.898	0.971	0.935	0.898	0.971	CLONAL	2	TRUE	1	0.608783365845698	3		457	1199	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401639	401639	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	582	324	0	ENST00000380956.4:c.961C>A	p.Pro321Thr	p.P321T	ENST00000380956	NM_001195286.1	321	Ccc/Acc	7/9	0.608856936982572	3	FACETS	1	0.996	1	0.832	0.805	0.859	CLONAL	2	TRUE	0	0.608783365845698	3		324	999	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681847	30681847	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	764	439	0	ENST00000376406.3:c.250del	p.Asp84ThrfsTer18	p.D84Tfs*18	ENST00000376406	NM_014641.2	84	Gac/ac	3/15	0.608856936982572	4	FACETS	0.927	0.899	0.955	0.927	0.899	0.955	CLONAL	3	TRUE	1	0.608783365845698	4		439	1452	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120835	94120835	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	659	442	0	ENST00000369303.4:c.216G>C	p.Gln72His	p.Q72H	ENST00000369303	NM_004440.3	72	caG/caC	3/17	0.588089975174293	3	FACETS	0.929	0.903	0.955	0.929	0.903	0.955	CLONAL	3	TRUE	0	0.608783365845698	3		442	1013	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552997	106552997	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	841	504	0	ENST00000369096.4:c.962C>A	p.Pro321His	p.P321H	ENST00000369096	NM_001198.3	321	cCc/cAc	5/7	0.588089975174293	3	FACETS	0.949	0.926	0.972	0.949	0.926	0.972	CLONAL	3	TRUE	0	0.608783365845698	3		504	1266	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199916	138199916	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	316	327	2	ENST00000237289.4:c.1334C>T	p.Pro445Leu	p.P445L	ENST00000237289	NM_001270507.1	445	cCc/cTc	7/9	0.588089975174293	3	FACETS	0.97	0.922	1	0.647	0.615	0.679	CLONAL	2	TRUE	0	0.608783365845698	3		329	698	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148525832	148525832	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	158	288	0	ENST00000320356.2:c.625G>C	p.Asp209His	p.D209H	ENST00000320356	NM_004456.4	209	Gat/Cat	6/20	0.368068889164592	5	FACETS	1	0.965	1	0.367	0.336	0.399	CLONAL	1	TRUE	2	0.608783365845698	5		288	903	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44870262	44870262	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	468	192	0	ENST00000377967.4:c.441G>T	p.Gln147His	p.Q147H	ENST00000377967	NM_021140.2	147	caG/caT	5/29	0.369898956610294	2	FACETS	1	0.996	1			1	CLONAL	2	TRUE	NA	0.608783365845698	2		192	646	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226567334	226567334	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	328	309	0	ENST00000366794.5:c.1552A>C	p.Lys518Gln	p.K518Q	ENST00000366794	NM_001618.3	518	Aaa/Caa	11/23	0.550042496547244	4	FACETS	0.846	0.801	0.893	0.846	0.801	0.893	CLONAL	2	TRUE	2	0.608783365845698	4		309	1024	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195635	102195635	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1205	157	416	1	ENST00000263464.3:c.395G>T	p.Gly132Val	p.G132V	ENST00000263464	NM_001165.4	132	gGa/gTa	2/9	0.368068889164592	5	FACETS	0.725	0.662	0.791	0.242	0.22	0.264	SUBCLONAL	1	TRUE	2	0.608783365845698	5		417	1362	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404739	404739	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	168	268	0	ENST00000399788.2:c.4455G>T	p.Glu1485Asp	p.E1485D	ENST00000399788	NM_001042603.1	1485	gaG/gaT	26/28	0.379853656881067	3	FACETS	1	0.984	1	0.415	0.383	0.448	CLONAL	1	TRUE	0	0.608783365845698	3		268	578	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18446832	18446832	+	splice_region_variant,intron_variant	Splice_Region	SNP	T	T	A	novel	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	27	250	0	ENST00000266497.5:c.920-3T>A		p.X307_splice	ENST00000266497		307			0.379853656881067	3	FACETS	0.223	0.177	0.276	0.074	0.059	0.092	SUBCLONAL	1	TRUE	0	0.608783365845698	3		250	519	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656266	18656266	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs979866570	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	70	452	0	ENST00000266497.5:c.2945A>G	p.His982Arg	p.H982R	ENST00000266497		982	cAt/cGt	21/31	0.379853656881067	3	FACETS	0.3	0.26	0.343	0.1	0.086	0.115	SUBCLONAL	1	TRUE	0	0.608783365845698	3		452	1000	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121435399	121435399	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1383989627	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	246	484	0	ENST00000257555.6:c.1432C>A	p.Pro478Thr	p.P478T	ENST00000257555		478	Cca/Aca	7/10	0.608856936982572	3	FACETS	1	0.948	1	0.508	0.475	0.542	CLONAL	1	TRUE	1	0.608783365845698	3		484	1038	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281411	49281411	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	270	481	0	ENST00000282018.3:c.458G>T	p.Arg153Met	p.R153M	ENST00000282018	NM_020377.2	153	aGg/aTg	1/1	NA	2	FACETS	1	0.972	1			1	INDETERMINATE	1	TRUE	NA	0.608783365845698	2		481	841	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727531	88727531	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	186	263	0	ENST00000360948.2:c.249-1G>T		p.X83_splice	ENST00000360948	NM_001012338.2	83			0.608856936982572	3	FACETS	1	0.973	1	0.551	0.51	0.593	CLONAL	1	TRUE	1	0.608783365845698	3		263	723	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81819748	81819748	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	119	278	0	ENST00000359376.3:c.154G>A	p.Val52Met	p.V52M	ENST00000359376	NM_002661.3	52	Gtg/Atg	2/33	0.550042496547244	4	FACETS	0.781	0.705	0.862	0.391	0.352	0.431	SUBCLONAL	1	TRUE	2	0.608783365845698	4		278	805	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006649	62006649	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	235	465	0	ENST00000392795.3:c.630C>G	p.Asp210Glu	p.D210E	ENST00000392795	NM_001039933.1	210	gaC/gaG	6/6	0.608856936982572	3	FACETS	0.965	0.9	1	0.482	0.45	0.516	CLONAL	1	TRUE	1	0.608783365845698	3		465	1044	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223949	36223949	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	281	551	0	ENST00000222270.7:c.6499C>G	p.Pro2167Ala	p.P2167A	ENST00000222270	NM_014727.1	2167	Cca/Gca	28/37	0.608856936982572	3	FACETS	0.878	0.824	0.935	0.439	0.412	0.468	CLONAL	1	TRUE	1	0.608783365845698	3		551	1371	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42793162	42793162	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1246	73	503	0	ENST00000575354.2:c.1054C>A	p.Pro352Thr	p.P352T	ENST00000575354	NM_015125.3	352	Ccc/Acc	7/20	0.608856936982572	3	FACETS	0.237	0.206	0.271	0.119	0.103	0.136	SUBCLONAL	1	TRUE	1	0.608783365845698	3		503	1319	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606678	29606678	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	257	447	0	ENST00000389048.3:c.1202G>T	p.Arg401Leu	p.R401L	ENST00000389048	NM_004304.4	401	cGa/cTa	5/29	0.608856936982572	3	FACETS	0.955	0.894	1	0.478	0.447	0.509	CLONAL	1	TRUE	1	0.608783365845698	3		447	1153	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40827928	40827928	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773152433	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	251	345	0	ENST00000373198.4:c.2500C>T	p.Arg834Cys	p.R834C	ENST00000373198	NM_133170.3	834	Cgc/Tgc	17/32	0.608856936982572	3	FACETS	1	0.964	1	0.522	0.488	0.556	CLONAL	1	TRUE	1	0.608783365845698	3		345	1031	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566452	41566486	+	frameshift_variant	Frame_Shift_Del	DEL	AGATGATTATATCTTCCATTGCCATCCTCCTGACC	AGATGATTATATCTTCCATTGCCATCCTCCTGACC	-	novel	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	201	344	0	ENST00000263253.7:c.4332_4366del	p.Asp1444GlufsTer17	p.D1444Efs*17	ENST00000263253	NM_001429.3	1443	ggAGATGATTATATCTTCCATTGCCATCCTCCTGACCag/ggag	27/31	0.608856936982572	3	FACETS	0.847	0.785	0.912	0.423	0.392	0.456	CLONAL	1	TRUE	1	0.608783365845698	3		344	1017	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713322	30713322	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	166	293	0	ENST00000295754.5:c.647G>C	p.Cys216Ser	p.C216S	ENST00000295754	NM_003242.5	216	tGt/tCt	4/7	1	2	FACETS	0.849	0.783	0.918	0.849	0.783	0.918	CLONAL	1	TRUE	1	0.608783365845698	2		293	642	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37083769	37083769	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	571	210	344	0	ENST00000231790.2:c.1678T>A	p.Phe560Ile	p.F560I	ENST00000231790	NM_000249.3	560	Ttc/Atc	15/19	1	2	FACETS	0.883	0.822	0.946	0.883	0.822	0.946	CLONAL	1	TRUE	1	0.608783365845698	2		344	781	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259119	89259119	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1244334822	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	200	316	0	ENST00000336596.2:c.263C>T	p.Pro88Leu	p.P88L	ENST00000336596	NM_005233.5	88	cCc/cTc	3/17	0.203973829056248	1	FACETS	0.729	0.679	0.78	0.729	0.679	0.78	INDETERMINATE	1	TRUE	0	0.608783365845698	1		316	627	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920530	134920530	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	412	331	0	ENST00000398015.3:c.2345T>C	p.Leu782Ser	p.L782S	ENST00000398015	NM_004441.4	782	tTg/tCg	12/16	0.608856936982572	3	FACETS	0.997	0.955	1	0.997	0.955	1	CLONAL	2	TRUE	1	0.608783365845698	3		331	885	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964430	55964430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs564385300	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	220	370	0	ENST00000263923.4:c.2383G>A	p.Gly795Arg	p.G795R	ENST00000263923	NM_002253.2	795	Ggg/Agg	17/30	0.608856936982572	4	FACETS	0.851	0.79	0.915			1	CLONAL	1	TRUE	NA	0.608783365845698	4		370	1366	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149514535	149514535	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	180	328	0	ENST00000261799.4:c.409A>G	p.Ile137Val	p.I137V	ENST00000261799	NM_002609.3	137	Atc/Gtc	4/23	0.608856936982572	2	FACETS	0.958	0.888	1	0.479	0.444	0.516	CLONAL	1	TRUE	0	0.608783365845698	2		328	617	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858327	27858327	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014639-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	57	352	0	ENST00000359303.2:c.244G>T	p.Asp82Tyr	p.D82Y	ENST00000359303	NM_003535.2	82	Gac/Tac	1/1	0.608856936982572	3	FACETS	0.26	0.222	0.301	0.087	0.074	0.101	SUBCLONAL	1	TRUE	0	0.608783365845698	3		352	940	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0014656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1054	208	282	0				ENST00000310581	NM_198253.2	-/1132			0.366391109257509	3	FACETS	1	0.956	1	0.523	0.484	0.563	CLONAL	1	TRUE	1	0.374454830870192	3		282	1262	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578535	7578537	+	inframe_deletion	In_Frame_Del	DEL	TTG	TTG	-	rs879254214	NA	P-0014656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	535	893	4	ENST00000269305.4:c.393_395del	p.Asn131del	p.N131del	ENST00000269305	NM_001126112.2	131	aaCAAg/aag	5/11	0.368636135431299	2	FACETS	0.973	0.933	1	0.973	0.933	1	CLONAL	2	TRUE	0	0.374454830870192	2		897	1469	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0014656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	95	499	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.341056822045368	4	FACETS	0.772	0.687	0.864	0.386	0.343	0.432	SUBCLONAL	1	TRUE	2	0.374454830870192	4		499	903	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153268144	153268144	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs920052554	NA	P-0014656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	132	467	0	ENST00000281708.4:c.664C>T	p.Arg222Ter	p.R222*	ENST00000281708	NM_033632.3	222	Cga/Tga	4/12	0.368636135431299	2	FACETS	1	0.949	1	0.531	0.483	0.581	CLONAL	1	TRUE	0	0.374454830870192	2		467	664	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782199	56782199	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528073782	NA	P-0014656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	142	376	0	ENST00000308159.5:c.40G>A	p.Glu14Lys	p.E14K	ENST00000308159	NM_014669.4	14	Gaa/Aaa	2/22	0.368636135431299	2	FACETS	1	0.943	1	0.522	0.476	0.569	CLONAL	1	TRUE	0	0.374454830870192	2		376	727	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466809	57466809	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs200163406	NA	P-0014656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	164	374	0	ENST00000371085.3:c.28G>C	p.Glu10Gln	p.E10Q	ENST00000371085	NM_000516.4	10	Gag/Cag	1/13	0.341056822045368	4	FACETS	1	0.984	1	0.642	0.589	0.697	CLONAL	1	TRUE	2	0.374454830870192	4		374	938	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11205055	11205055	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	195	714	0	ENST00000361445.4:c.4734G>A	p.Met1578Ile	p.M1578I	ENST00000361445	NM_004958.3	1578	atG/atA	33/58	0.366391109257509	3	FACETS	0.916	0.846	0.989	0.458	0.423	0.495	CLONAL	1	TRUE	1	0.374454830870192	3		714	1350	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430819	78430819	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1003	146	620	0	ENST00000370768.2:c.570C>G	p.Ile190Met	p.I190M	ENST00000370768	NM_003902.3	190	atC/atG	8/20	0.366391109257509	3	FACETS	0.806	0.734	0.881	0.403	0.367	0.441	CLONAL	1	TRUE	1	0.374454830870192	3		620	1149	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120493434	120493434	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	133	490	0	ENST00000256646.2:c.2392G>C	p.Glu798Gln	p.E798Q	ENST00000256646	NM_024408.3	798	Gaa/Caa	15/34	0.338172239432418	4	FACETS	0.922	0.836	1			1	CLONAL	1	TRUE	NA	0.374454830870192	4		490	1059	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156844195	156844195	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	novel	NA	P-0014656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	187	672	1	ENST00000524377.1:c.1195+3G>A		p.X399_splice	ENST00000524377	NM_002529.3	399			0.338172239432418	4	FACETS	1	0.932	1			1	CLONAL	1	TRUE	NA	0.374454830870192	4		673	1356	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333350	70333350	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2153	227	837	0	ENST00000373644.4:c.1255C>G	p.Leu419Val	p.L419V	ENST00000373644	NM_030625.2	419	Ctt/Gtt	2/12	0.374454830870192	7	FACETS	0.986	0.914	1			1	CLONAL	1	TRUE	NA	0.374454830870192	7		837	2380	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94209462	94209462	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	78	404	0	ENST00000323929.3:c.652C>G	p.Gln218Glu	p.Q218E	ENST00000323929	NM_005591.3	218	Cag/Gag	7/20	0.341056822045368	4	FACETS	0.743	0.652	0.841	0.371	0.326	0.421	SUBCLONAL	1	TRUE	2	0.374454830870192	4		404	771	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406224	406224	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1343841537	NA	P-0014656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	130	431	0	ENST00000399788.2:c.4217C>T	p.Ser1406Phe	p.S1406F	ENST00000399788	NM_001042603.1	1406	tCt/tTt	25/28	0.366391109257509	3	FACETS	0.977	0.886	1	0.488	0.443	0.536	CLONAL	1	TRUE	1	0.374454830870192	3		431	844	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936959	48936960	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0014656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	98	427	0	ENST00000267163.4:c.729dup	p.Ile244TyrfsTer4	p.I244Yfs*4	ENST00000267163	NM_000321.2	243	gtt/gTtt	8/27	0.368636135431299	2	FACETS	0.823	0.735	0.916	0.411	0.367	0.458	CLONAL	1	TRUE	0	0.374454830870192	2		427	636	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937091	48937091	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	45	234	0	ENST00000267163.4:c.859G>C	p.Glu287Gln	p.E287Q	ENST00000267163	NM_000321.2	287	Gag/Cag	8/27	0.368636135431299	2	FACETS	0.621	0.523	0.729	0.311	0.261	0.365	SUBCLONAL	1	TRUE	0	0.374454830870192	2		234	387	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103518208	103518208	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	172	301	0	ENST00000355739.4:c.2146G>C	p.Glu716Gln	p.E716Q	ENST00000355739	NM_000123.3	716	Gaa/Caa	9/15	0.374454830870192	3	FACETS	0.948	0.878	1	0.632	0.585	0.681	CLONAL	2	TRUE	0	0.374454830870192	3		301	575	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81891870	81891870	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	122	499	0	ENST00000359376.3:c.340G>A	p.Asp114Asn	p.D114N	ENST00000359376	NM_002661.3	114	Gac/Aac	4/33	0.368636135431299	2	FACETS	0.884	0.8	0.973	0.442	0.4	0.487	CLONAL	1	TRUE	0	0.374454830870192	2		499	737	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912654	NA	P-0014656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	247	704	0	ENST00000269305.4:c.469G>A	p.Val157Ile	p.V157I	ENST00000269305	NM_001126112.2	157	Gtc/Atc	5/11	0.368636135431299	2	FACETS	1	0.964	1	0.525	0.49	0.561	CLONAL	1	TRUE	0	0.374454830870192	2		704	1257	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578488	7578488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1131691007	NA	P-0014656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1094	281	800	0	ENST00000269305.4:c.442G>A	p.Asp148Asn	p.D148N	ENST00000269305	NM_001126112.2	148	Gat/Aat	5/11	0.368636135431299	2	FACETS	1	0.978	1	0.546	0.512	0.581	CLONAL	1	TRUE	0	0.374454830870192	2		800	1375	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089884	16089884	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	70	373	0	ENST00000268712.3:c.226C>T	p.His76Tyr	p.H76Y	ENST00000268712	NM_006311.3	76	Cac/Tac	3/46	0.368636135431299	2	FACETS	0.665	0.58	0.757	0.333	0.29	0.379	SUBCLONAL	1	TRUE	0	0.374454830870192	2		373	562	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576091	29576091	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1843	184	726	0	ENST00000356175.3:c.4064C>T	p.Ser1355Leu	p.S1355L	ENST00000356175	NM_000267.3	1355	tCa/tTa	30/57	0.374454830870192	7	FACETS	0.939	0.862	1			1	CLONAL	1	TRUE	NA	0.374454830870192	7		726	2027	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55754356	55754356	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0014656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1354	216	695	2	ENST00000284073.2:c.954G>T	p.Leu318Phe	p.L318F	ENST00000284073	NM_138962.2	318	ttG/ttT	13/14	0.363255646299005	4	FACETS	1	0.935	1	0.252	0.234	0.272	CLONAL	1	TRUE	0	0.374454830870192	4		697	1570	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190738302	190738302	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	84	395	0	ENST00000441310.2:c.2554G>C	p.Glu852Gln	p.E852Q	ENST00000441310	NM_000534.4	852	Gaa/Caa	12/13	0.341056822045368	4	FACETS	0.782	0.69	0.88	0.391	0.345	0.44	SUBCLONAL	1	TRUE	2	0.374454830870192	4		395	789	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546620	9546620	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	167	549	0	ENST00000353224.5:c.1402G>C	p.Glu468Gln	p.E468Q	ENST00000353224	NM_177990.2	468	Gag/Cag	5/10	0.341056822045368	4	FACETS	1	0.983	1	0.629	0.577	0.682	CLONAL	1	TRUE	2	0.374454830870192	4		549	975	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54959353	54959353	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0014656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	73	409	0	ENST00000312783.6:c.347C>G	p.Ser116Ter	p.S116*	ENST00000312783	NM_198436.1	116	tCa/tGa	5/10	0.341056822045368	4	FACETS	0.755	0.66	0.858	0.377	0.33	0.429	SUBCLONAL	1	TRUE	2	0.374454830870192	4		409	710	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42840421	42840421	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0014656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1154	144	486	0	ENST00000398585.3:c.1327G>C	p.Glu443Gln	p.E443Q	ENST00000398585	NM_001135099.1	443	Gag/Cag	12/14	0.374454830870192	5	FACETS	0.925	0.842	1	0.308	0.28	0.338	CLONAL	1	TRUE	2	0.374454830870192	5		486	1298	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163682	47163682	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	112	371	0	ENST00000409792.3:c.2444C>T	p.Ser815Leu	p.S815L	ENST00000409792	NM_014159.6	815	tCa/tTa	3/21	0.366391109257509	3	FACETS	1	0.947	1	0.539	0.485	0.595	CLONAL	1	TRUE	1	0.374454830870192	3		371	659	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178919233	178919233	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	79	312	0	ENST00000263967.3:c.718A>C	p.Lys240Gln	p.K240Q	ENST00000263967	NM_006218.2	240	Aaa/Caa	4/21	0.341056822045368	4	FACETS	0.887	0.78	1	0.443	0.39	0.501	CLONAL	1	TRUE	2	0.374454830870192	4		312	654	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745332	43745332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762664023	NA	P-0014656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1206	429	743	0	ENST00000523873.1:c.245G>A	p.Arg82Gln	p.R82Q	ENST00000523873		82	cGa/cAa	3/8	0.355553416989834	5	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.374454830870192	5		743	1635	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527943	157527943	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1554237567	NA	P-0014656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	188	648	1	ENST00000346085.5:c.5668G>T	p.Glu1890Ter	p.E1890*	ENST00000346085	NM_020732.3	1890	Gaa/Taa	20/20	0.366391109257509	3	FACETS	0.951	0.877	1	0.476	0.438	0.515	CLONAL	1	TRUE	1	0.374454830870192	3		649	1253	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467966	50467966	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	141	479	0	ENST00000331340.3:c.1201G>A	p.Glu401Lys	p.E401K	ENST00000331340	NM_006060.4	401	Gag/Aag	8/8	0.325258452992616	5	FACETS	1	0.923	1	0.339	0.308	0.372	CLONAL	1	TRUE	2	0.374454830870192	5		479	1157	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145738338	145738338	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0014656-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1531	261	786	0	ENST00000428558.2:c.2647G>T	p.Glu883Ter	p.E883*	ENST00000428558	NM_004260.3	883	Gag/Tag	16/22	0.325258452992616	5	FACETS	1	0.987	1	0.405	0.378	0.433	CLONAL	1	TRUE	2	0.374454830870192	5		786	1792	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0014671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	58	282	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.19	2		282	537	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0014671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	105	616	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	1	2	FACETS	0.981	0.876	1	0.981	0.876	1	CLONAL	1	TRUE	1	0.19	2		617	1127	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717769	89717770	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0014671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	43	331	0	ENST00000371953.3:c.800dup	p.Asp268GlyfsTer30	p.D268Gfs*30	ENST00000371953	NM_000314.4	265	cta/ctAa	7/9	1	2	FACETS	0.712	0.594	0.842	0.712	0.594	0.842	SUBCLONAL	1	TRUE	1	0.19	2		331	636	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152009026	152009026	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0014671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	55	307	0	ENST00000262189.6:c.596del	p.Arg199HisfsTer7	p.R199Hfs*7	ENST00000262189	NM_170606.2	199	cGa/ca	5/59	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.19	2		307	498	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149593	202149593	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	54	443	0	ENST00000358485.4:c.1034A>G	p.Asp345Gly	p.D345G	ENST00000358485	NM_001080125.1	345	gAc/gGc	8/9	1	2	FACETS	0.798	0.681	0.928	0.798	0.681	0.928	CLONAL	1	TRUE	1	0.19	2		443	712	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712899	43712899	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	83	633	1	ENST00000382044.4:c.4285G>T	p.Asp1429Tyr	p.D1429Y	ENST00000382044	NM_001141980.1	1429	Gac/Tac	21/28	1	2	FACETS	0.924	0.813	1	0.924	0.813	1	CLONAL	1	TRUE	1	0.19	2		634	946	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7217607	7217607	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0014671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	62	377	0	ENST00000380728.2:c.317+3G>A		p.X106_splice	ENST00000380728		106			1	2	FACETS	1	0.908	1	1	0.908	1	CLONAL	1	TRUE	1	0.19	2		377	612	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121057	3121071	+	inframe_deletion	In_Frame_Del	DEL	CGACAAGATCATCTA	CGACAAGATCATCTA	-	novel	NA	P-0014671-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	91	815	0	ENST00000078429.4:c.961_975del	p.Asp321_Tyr325del	p.D321_Y325del	ENST00000078429	NM_002067.2	320	agCGACAAGATCATCTAc/agc	7/7	1	2	FACETS	0.982	0.871	1	0.982	0.871	1	CLONAL	1	TRUE	1	0.19	2		815	975	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0014789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	803	655	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.407239947168783	4	FACETS	1	0.989	1	1	0.989	1	CLONAL	4	TRUE	0	0.432701915338281	4		655	1295	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119789	70119789	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0014789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	328	595	0	ENST00000245479.2:c.791G>C	p.Arg264Thr	p.R264T	ENST00000245479	NM_000346.3	264	aGa/aCa	3/3	0.42241902652087	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	0	0.432701915338281	2		595	740	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29683977	29683977	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0014789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	378	490	0	ENST00000356175.3:c.7676-1G>A		p.X2559_splice	ENST00000356175	NM_000267.3	2559			0.421899908716965	3	FACETS	0.947	0.906	0.988	0.947	0.906	0.988	CLONAL	3	TRUE	0	0.432701915338281	3		490	748	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642470	117642470	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765146445	NA	P-0014789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	322	538	0	ENST00000368508.3:c.5729G>A	p.Arg1910Gln	p.R1910Q	ENST00000368508	NM_002944.2	1910	cGa/cAa	35/43	0.432701915338281	5	FACETS	0.849	0.8	0.9			1	CLONAL	2	TRUE	NA	0.432701915338281	5		538	1445	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123324013	123324013	+	splice_region_variant,intron_variant	Splice_Region	SNP	T	T	C	rs768823111	NA	P-0014789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	312	492	0	ENST00000358487.5:c.454+3A>G		p.X152_splice	ENST00000358487	NM_000141.4	152			0.396131302766251	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	0	0.432701915338281	2		492	714	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48936978	48936978	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	859	468	0	ENST00000267163.4:c.746C>T	p.Ser249Leu	p.S249L	ENST00000267163	NM_000321.2	249	tCa/tTa	8/27	0.432701915338281	8	FACETS	1	0.995	1	0.925	0.904	0.946	CLONAL	7	TRUE	0	0.432701915338281	8		468	1233	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37866662	37866662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	595	675	0	ENST00000269571.5:c.829G>A	p.Asp277Asn	p.D277N	ENST00000269571		277	Gac/Aac	7/27	0.421899908716965	3	FACETS	1	0.969	1	1	0.969	1	CLONAL	3	TRUE	0	0.432701915338281	3		675	1112	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622378	1622378	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0014789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	364	708	1	ENST00000344749.5:c.586G>T	p.Asp196Tyr	p.D196Y	ENST00000344749	NM_001136139.2	196	Gat/Tat	9/19	0.402224943280466	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.432701915338281	4		709	1164	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86645036	86645036	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	133	270	0	ENST00000274376.6:c.1108C>T	p.Gln370Ter	p.Q370*	ENST00000274376	NM_002890.2	370	Caa/Taa	8/25	0.408597752902293	2	FACETS	0.861	0.792	0.932	0.861	0.792	0.932	CLONAL	2	TRUE	0	0.432701915338281	2		270	357	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172076	32172076	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0014789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	349	662	0	ENST00000375023.3:c.2956A>C	p.Lys986Gln	p.K986Q	ENST00000375023	NM_004557.3	986	Aaa/Caa	19/30	0.402224943280466	4	FACETS	0.919	0.87	0.97	0.919	0.87	0.97	CLONAL	2	TRUE	2	0.432701915338281	4		662	1257	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117650519	117650519	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	273	573	1	ENST00000368508.3:c.5339G>A	p.Arg1780Lys	p.R1780K	ENST00000368508	NM_002944.2	1780	aGa/aAa	32/43	0.432701915338281	5	FACETS	0.791	0.741	0.843			1	SUBCLONAL	2	TRUE	NA	0.432701915338281	5		574	1315	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390600	139390600	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749355748	NA	P-0014789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	483	832	1	ENST00000277541.6:c.7591G>A	p.Asp2531Asn	p.D2531N	ENST00000277541	NM_017617.3	2531	Gac/Aac	34/34	0.402224943280466	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.432701915338281	4		833	1515	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030650	47030650	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	295	678	0	ENST00000377604.3:c.425A>T	p.Glu142Val	p.E142V	ENST00000377604	NM_001204468.1	142	gAg/gTg	4/24	0.287098808744409	4	FACETS	1	0.946	1	1	0.946	1	CLONAL	2	TRUE	2	0.432701915338281	4		678	973	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426390	47426390	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014789-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	305	547	1	ENST00000377045.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000377045	NM_001654.4	245	Ggt/Agt	9/16	0.287098808744409	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.432701915338281	4		548	977	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	66	282	0				ENST00000310581	NM_198253.2	-/1132			0.342158957654613	0	FACETS	0.598	0.529	0.67			1	SUBCLONAL	1	FALSE	0	0.532193151958687	0		282	194	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	152	598	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	0.888	0.815	0.964	0.888	0.815	0.964	CLONAL	1	FALSE	1	0.532193151958687	2		598	643	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333555	70333555	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs150689919	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	193	566	1	ENST00000373644.4:c.1460C>T	p.Ser487Leu	p.S487L	ENST00000373644	NM_030625.2	487	tCa/tTa	2/12	0.346934556597335	0	FACETS		NA	1			1	NA	2	FALSE	0	0.532193151958687	0		567	347	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495394	149495394	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	99	852	0	ENST00000261799.4:c.3253G>A	p.Glu1085Lys	p.E1085K	ENST00000261799	NM_002609.3	1085	Gag/Aag	23/23	1	2	FACETS	0.877	0.788	0.971	0.877	0.788	0.971	CLONAL	1	FALSE	1	0.532193151958687	2		852	424	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609861	117609861	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	126	719	0	ENST00000368508.3:c.6838G>A	p.Glu2280Lys	p.E2280K	ENST00000368508	NM_002944.2	2280	Gaa/Aaa	43/43	0.488878552391747	0	FACETS	0.759	0.699	0.819			1	SUBCLONAL	1	FALSE	0	0.532193151958687	0		719	292	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120506379	120506379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553199314	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	278	596	0	ENST00000256646.2:c.1733C>T	p.Pro578Leu	p.P578L	ENST00000256646	NM_024408.3	578	cCt/cTt	11/34	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.532193151958687	2		596	848	SUCCESS
RET	5979	MSKCC	GRCh37	10	43597840	43597840	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	96	1009	0	ENST00000355710.3:c.388A>C	p.Thr130Pro	p.T130P	ENST00000355710	NM_020975.4	130	Aca/Cca	3/20	0.488878552391747	0	FACETS	0.734	0.667	0.802			1	SUBCLONAL	1	FALSE	0	0.532193151958687	0		1009	230	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426330	49426330	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1268361839	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	274	1150	0	ENST00000301067.7:c.12158C>T	p.Thr4053Ile	p.T4053I	ENST00000301067	NM_003482.3	4053	aCt/aTt	39/54	0.143344233909372	6	FACETS	1	0.989	1	0.809	0.761	0.858	INDETERMINATE	2	FALSE	3	0.532193151958687	6		1150	876	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133201326	133201326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779145729	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	90	838	0	ENST00000320574.5:c.6818C>T	p.Thr2273Ile	p.T2273I	ENST00000320574	NM_006231.2	2273	aCc/aTc	49/49	0.369126753060204	1	FACETS	0.713	0.638	0.792	0.713	0.638	0.792	SUBCLONAL	1	FALSE	0	0.532193151958687	1		838	348	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28919608	28919608	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	145	792	0	ENST00000282397.4:c.2329del	p.Thr777ProfsTer7	p.T777Pfs*7	ENST00000282397	NM_002019.4	777	Acc/cc	16/30	0.532193151958687	1	FACETS	0.709	0.65	0.77	0.709	0.65	0.77	SUBCLONAL	1	FALSE	0	0.532193151958687	1		792	564	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914800	32914800	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	196	545	1	ENST00000380152.3:c.6308C>T	p.Ser2103Leu	p.S2103L	ENST00000380152		2103	tCa/tTa	11/27	0.190731275942494	5	FACETS	0.816	0.756	0.877			1	INDETERMINATE	2	FALSE	NA	0.532193151958687	5		546	812	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36989255	36989255	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	74	692	3	ENST00000354822.5:c.77+3G>A		p.X26_splice	ENST00000354822	NM_001079668.2	26			1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.532193151958687	2		695	242	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609780	81609780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	73	360	1	ENST00000298171.2:c.1378G>A	p.Asp460Asn	p.D460N	ENST00000298171	NM_000369.2	460	Gat/Aat	10/10	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	1	0.532193151958687	2		361	243	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67358500	67358500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	52	259	0	ENST00000327367.4:c.8C>T	p.Ser3Phe	p.S3F	ENST00000327367	NM_005902.3	3	tCc/tTc	1/9	0.121117945910379	4	FACETS	0.776	0.67	0.887	0.776	0.67	0.887	INDETERMINATE	2	FALSE	2	0.532193151958687	4		259	193	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476309	88476309	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	148	817	2	ENST00000360948.2:c.1823G>A	p.Gly608Asp	p.G608D	ENST00000360948	NM_001012338.2	608	gGc/gAc	15/19	NA	2	FACETS	1	0.978	1			1	INDETERMINATE	1	FALSE	NA	0.532193151958687	2		819	475	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679272	88679272	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	132	585	0	ENST00000360948.2:c.766-1G>A		p.X256_splice	ENST00000360948	NM_001012338.2	256			NA	2	FACETS	1	0.984	1			1	INDETERMINATE	1	FALSE	NA	0.532193151958687	2		585	376	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50783806	50783806	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	185	731	0	ENST00000398568.2:c.197A>T	p.Lys66Met	p.K66M	ENST00000398568	NM_001042412.1	66	aAg/aTg	3/18	1	2	FACETS	0.964	0.893	1	0.964	0.893	1	CLONAL	1	FALSE	1	0.532193151958687	2		731	721	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829181	72829181	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	84	714	1	ENST00000268489.5:c.7400C>T	p.Pro2467Leu	p.P2467L	ENST00000268489	NM_006885.3	2467	cCc/cTc	9/10	0.33667068583755	0	FACETS	0.479	0.428	0.534			1	SUBCLONAL	1	FALSE	0	0.532193151958687	0		715	308	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991678	72991679	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	52	342	2	ENST00000268489.5:c.2366_2367delinsTT	p.Ser789Phe	p.S789F	ENST00000268489	NM_006885.3	789	tCC/tTT	2/10	0.33667068583755	0	FACETS	0.528	0.458	0.603			1	SUBCLONAL	1	FALSE	0	0.532193151958687	0		344	173	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357102	89357102	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1286864966	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	102	733	0	ENST00000301030.4:c.532C>T	p.Arg178Cys	p.R178C	ENST00000301030	NM_001256183.1	178	Cgc/Tgc	6/13	NA	2	FACETS	0.682	0.612	0.756			1	INDETERMINATE	1	FALSE	NA	0.532193151958687	2		733	562	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836660	89836660	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1475950375	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	246	983	0	ENST00000389301.3:c.2230C>T	p.Pro744Ser	p.P744S	ENST00000389301	NM_000135.2	744	Ccc/Tcc	25/43	NA	2	FACETS	1	0.942	1			1	INDETERMINATE	1	FALSE	NA	0.532193151958687	2		983	918	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604760	48604760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	185	570	0	ENST00000342988.3:c.1582C>T	p.His528Tyr	p.H528Y	ENST00000342988	NM_005359.5	528	Cac/Tac	12/12	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.532193151958687	2		570	551	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7166225	7166225	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	154	737	0	ENST00000302850.5:c.1801G>A	p.Asp601Asn	p.D601N	ENST00000302850	NM_000208.2	601	Gat/Aat	8/22	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	FALSE	1	0.532193151958687	2		737	557	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744494	41744494	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	112	918	0	ENST00000301178.4:c.1114C>T	p.Gln372Ter	p.Q372*	ENST00000301178	NM_021913.4	372	Caa/Taa	8/20	0.462147083346795	0	FACETS	0.396	0.358	0.436			1	SUBCLONAL	1	FALSE	0	0.532193151958687	0		918	497	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449788	29449788	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs756986057	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	220	1181	2	ENST00000389048.3:c.3067G>A	p.Val1023Met	p.V1023M	ENST00000389048	NM_004304.4	1023	Gtg/Atg	18/29	0.121117945910379	4	FACETS	0.882	0.824	0.942	0.882	0.824	0.942	INDETERMINATE	2	FALSE	2	0.532193151958687	4		1183	718	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560824	9560824	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376118527	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	65	667	0	ENST00000353224.5:c.958C>T	p.Arg320Cys	p.R320C	ENST00000353224	NM_177990.2	320	Cgc/Tgc	4/10	1	2	FACETS	0.812	0.709	0.92	0.812	0.709	0.92	CLONAL	1	FALSE	1	0.532193151958687	2		667	301	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22123602	22123602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	173	528	0	ENST00000215832.6:c.974C>T	p.Ala325Val	p.A325V	ENST00000215832	NM_002745.4	325	gCc/gTc	8/9	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.532193151958687	2		528	588	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12633256	12633256	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	238	705	0	ENST00000251849.4:c.1144C>T	p.Pro382Ser	p.P382S	ENST00000251849	NM_002880.3	382	Cca/Tca	11/17	0.109057423715011	5	FACETS	1	0.977	1	0.725	0.679	0.771	INDETERMINATE	2	FALSE	2	0.532193151958687	5		705	740	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52692222	52692222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	169	432	0	ENST00000394830.3:c.638C>T	p.Ser213Phe	p.S213F	ENST00000394830	NM_018313.4	213	tCt/tTt	6/30	0.109057423715011	5	FACETS	1	0.925	1	0.667	0.616	0.719	INDETERMINATE	2	FALSE	2	0.532193151958687	5		432	571	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446947	187446947	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	148	785	1	ENST00000232014.4:c.1246C>T	p.Pro416Ser	p.P416S	ENST00000232014	NM_001130845.1	416	Cca/Tca	5/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.532193151958687	2		786	449	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149510181	149510181	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762918648	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	155	742	2	ENST00000261799.4:c.1288G>A	p.Gly430Arg	p.G430R	ENST00000261799	NM_002609.3	430	Ggg/Agg	9/23	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	FALSE	1	0.532193151958687	2		744	572	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803044	32803044	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	240	807	0	ENST00000374899.4:c.832G>A	p.Val278Met	p.V278M	ENST00000374899	NM_018833.2	278	Gtg/Atg	5/12	0.109057423715011	5	FACETS	0.969	0.907	1	0.646	0.605	0.688	INDETERMINATE	2	FALSE	2	0.532193151958687	5		807	837	SUCCESS
MET	4233	MSKCC	GRCh37	7	116403208	116403208	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	286	672	0	ENST00000397752.3:c.2469A>C	p.Leu823Phe	p.L823F	ENST00000397752	NM_000245.2	823	ttA/ttC	11/21	0.532193151958687	5	FACETS	0.858	0.807	0.911	0.572	0.538	0.608	CLONAL	2	FALSE	2	0.532193151958687	5		672	1126	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874131	151874131	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	161	420	0	ENST00000262189.6:c.8407A>T	p.Thr2803Ser	p.T2803S	ENST00000262189	NM_170606.2	2803	Act/Tct	38/59	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	FALSE	1	0.532193151958687	2		420	554	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90970983	90970983	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	140	402	0	ENST00000265433.3:c.1094C>T	p.Ala365Val	p.A365V	ENST00000265433	NM_002485.4	365	gCt/gTt	9/16	0.532193151958687	3	FACETS	0.925	0.844	1	0.463	0.422	0.505	CLONAL	1	FALSE	1	0.532193151958687	3		402	720	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486104	8486104	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1369780691	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	83	581	0	ENST00000356435.5:c.2713G>A	p.Glu905Lys	p.E905K	ENST00000356435		905	Gag/Aag	17/35	0.504490758341381	0	FACETS	0.611	0.547	0.676			1	SUBCLONAL	1	FALSE	0	0.532193151958687	0		581	239	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87475970	87475970	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	266	1089	0	ENST00000277120.3:c.1412G>A	p.Gly471Glu	p.G471E	ENST00000277120		471	gGa/gAa	13/19	0.303148060952359	0	FACETS	0.522	0.49	0.554			1	INDETERMINATE	1	FALSE	0	0.532193151958687	0		1089	896	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137325995	137325995	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	147	1051	2	ENST00000481739.1:c.1183A>G	p.Lys395Glu	p.K395E	ENST00000481739	NM_002957.4	395	Aag/Gag	9/10	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	1	0.532193151958687	2		1053	466	SUCCESS
AR	367	MSKCC	GRCh37	X	66765332	66765333	+	missense_variant	Missense_Mutation	DNP	AA	AA	TC	novel	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	69	524	0	ENST00000374690.3:c.344_345delinsTC	p.Gln115Leu	p.Q115L	ENST00000374690	NM_000044.3	115	cAA/cTC	1/8	0.341692754467953	0	FACETS	0.899	0.809	0.988			1	CLONAL	1	FALSE	NA	0.532193151958687	0		524	135	SUCCESS
AR	367	MSKCC	GRCh37	X	66765332	66765332	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	69	524	0	ENST00000374690.3:c.344A>T	p.Gln115Leu	p.Q115L	ENST00000374690	NM_000044.3	115	cAa/cTa	1/8	0.341692754467953	0	FACETS	0.912	0.822	1			1	CLONAL	1	FALSE	NA	0.532193151958687	0		524	133	SUCCESS
AR	367	MSKCC	GRCh37	X	66765333	66765333	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0014910-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	69	519	0	ENST00000374690.3:c.345A>C	p.Gln115His	p.Q115H	ENST00000374690	NM_000044.3	115	caA/caC	1/8	0.341692754467953	0	FACETS	0.899	0.809	0.988			1	CLONAL	1	FALSE	NA	0.532193151958687	0		519	135	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	236	215	0				ENST00000310581	NM_198253.2	-/1132			0.275481115511759	5	FACETS	1	0.96	1	1	0.96	1	CLONAL	3	TRUE	2	0.275481115511759	5		215	780	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0015067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	108	531	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.275481115511759	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.275481115511759	1		531	537	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248409	59248409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184098204	NA	P-0015067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	76	189	1	ENST00000371222.2:c.334G>A	p.Glu112Lys	p.E112K	ENST00000371222	NM_002228.3	112	Gag/Aag	1/1	1	2	FACETS	0.982	0.862	1	0.982	0.862	1	CLONAL	1	TRUE	1	0.275481115511759	2		190	562	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0015067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	64	595	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.275481115511759	1	FACETS	0.736	0.638	0.843	0.736	0.638	0.843	SUBCLONAL	1	TRUE	0	0.275481115511759	1		595	544	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59770854	59770854	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	103	432	0	ENST00000259008.2:c.2512G>A	p.Asp838Asn	p.D838N	ENST00000259008	NM_032043.2	838	Gat/Aat	18/20	0.172578727236922	3	FACETS	1	0.948	1	0.549	0.491	0.61	CLONAL	1	TRUE	1	0.275481115511759	3		432	775	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652035	36652035	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	760	310	906	0	ENST00000244741.5:c.159del	p.Phe53LeufsTer95	p.F53Lfs*95	ENST00000244741	NM_000389.4	53	Ttt/tt	2/3	0.275481115511759	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.275481115511759	2		906	1070	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983222	149983223	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	98	387	0	ENST00000253339.5:c.3035dup	p.Ile1013AsnfsTer2	p.I1013Nfs*2	ENST00000253339		1012	aca/acCa	7/7	0.275481115511759	1	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	0	0.275481115511759	1		387	523	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983350	149983350	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	71	391	0	ENST00000253339.5:c.2908C>A	p.His970Asn	p.H970N	ENST00000253339		970	Cac/Aac	7/7	0.275481115511759	1	FACETS	0.885	0.774	1	0.885	0.774	1	CLONAL	1	TRUE	0	0.275481115511759	1		391	502	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346188	70346188	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	G	novel	NA	P-0015067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	91	369	0	ENST00000374080.3:c.2542-3C>G		p.X848_splice	ENST00000374080		848			1	1	FACETS	0.943	0.847	1	1	0.986	1	CLONAL	2	TRUE	0	0.275481115511759	1		369	302	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889108	76889108	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015067-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	106	243	0	ENST00000373344.5:c.4902G>T	p.Trp1634Cys	p.W1634C	ENST00000373344	NM_000489.3	1634	tgG/tgT	18/35	1	1	FACETS	0.869	0.785	0.955	1	0.987	1	CLONAL	2	TRUE	0	0.275481115511759	1		243	382	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015067-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	390	215	0				ENST00000310581	NM_198253.2	-/1132			0.595123811694932	5	FACETS	1	0.977	1	1	0.977	1	CLONAL	3	TRUE	2	0.595123811694932	5		215	801	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717708	89717708	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202918	NA	P-0015067-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	173	531	0	ENST00000371953.3:c.733C>T	p.Gln245Ter	p.Q245*	ENST00000371953	NM_000314.4	245	Cag/Tag	7/9	0.595123811694932	1	FACETS	0.999	0.931	1	0.999	0.931	1	CLONAL	1	TRUE	0	0.595123811694932	1		531	409	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248409	59248409	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1184098204	NA	P-0015067-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	97	189	1	ENST00000371222.2:c.334G>A	p.Glu112Lys	p.E112K	ENST00000371222	NM_002228.3	112	Gag/Aag	1/1	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.595123811694932	2		190	326	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0015067-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	186	595	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.595123811694932	1	FACETS	0.991	0.926	1	0.991	0.926	1	CLONAL	1	TRUE	0	0.595123811694932	1		595	443	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652035	36652035	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015067-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	494	906	0	ENST00000244741.5:c.159del	p.Phe53LeufsTer95	p.F53Lfs*95	ENST00000244741	NM_000389.4	53	Ttt/tt	2/3	0.595123811694932	2	FACETS	0.994	0.96	1	0.994	0.96	1	CLONAL	2	TRUE	0	0.595123811694932	2		906	835	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983222	149983223	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015067-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	151	387	0	ENST00000253339.5:c.3035dup	p.Ile1013AsnfsTer2	p.I1013Nfs*2	ENST00000253339		1012	aca/acCa	7/7	0.595123811694932	1	FACETS	0.887	0.82	0.955	0.887	0.82	0.955	CLONAL	1	TRUE	0	0.595123811694932	1		387	402	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983350	149983350	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015067-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	194	391	0	ENST00000253339.5:c.2908C>A	p.His970Asn	p.H970N	ENST00000253339		970	Cac/Aac	7/7	0.595123811694932	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.595123811694932	1		391	398	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346188	70346188	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	G	novel	NA	P-0015067-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	173	369	0	ENST00000374080.3:c.2542-3C>G		p.X848_splice	ENST00000374080		848			1	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.595123811694932	1		369	323	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889108	76889108	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015067-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	225	243	0	ENST00000373344.5:c.4902G>T	p.Trp1634Cys	p.W1634C	ENST00000373344	NM_000489.3	1634	tgG/tgT	18/35	1	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.595123811694932	1		243	388	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712614	52712614	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0015067-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	140	257	0	ENST00000394830.3:c.139-1G>A		p.X47_splice	ENST00000394830	NM_018313.4	47			0.580414224875609	3	FACETS	0.933	0.852	1	0.467	0.426	0.509	CLONAL	1	TRUE	1	0.595123811694932	3		257	654	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0015137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	159	282	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.915	0.853	0.979			1	INDETERMINATE	2	TRUE	NA	0.50636209025918	2		282	343	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16203058	16203058	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	147	471	1	ENST00000375759.3:c.766C>G	p.Gln256Glu	p.Q256E	ENST00000375759	NM_015001.2	256	Cag/Gag	3/15	1	2	FACETS	0.808	0.739	0.879	0.808	0.739	0.879	CLONAL	1	TRUE	1	0.50636209025918	2		472	719	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16248783	16248783	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	47	423	0	ENST00000375759.3:c.1789C>T	p.His597Tyr	p.H597Y	ENST00000375759	NM_015001.2	597	Cac/Tac	10/15	1	2	FACETS	0.248	0.208	0.292	0.248	0.208	0.292	SUBCLONAL	1	TRUE	1	0.50636209025918	2		423	749	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16248818	16248818	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs774187030	NA	P-0015137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	48	450	0	ENST00000375759.3:c.1824C>G	p.Asp608Glu	p.D608E	ENST00000375759	NM_015001.2	608	gaC/gaG	10/15	1	2	FACETS	0.236	0.198	0.277	0.236	0.198	0.277	SUBCLONAL	1	TRUE	1	0.50636209025918	2		450	804	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106395	27106415	+	inframe_deletion	In_Frame_Del	DEL	CAAACACCCAGGGCTGCTGCT	CAAACACCCAGGGCTGCTGCT	-	novel	NA	P-0015137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	180	460	0	ENST00000324856.7:c.6008_6028del	p.Lys2003_Leu2009del	p.K2003_L2009del	ENST00000324856	NM_006015.4	2002	tcCAAACACCCAGGGCTGCTGCTc/tcc	20/20	NA	2	FACETS	1	0.989	1			1	INDETERMINATE	1	TRUE	NA	0.50636209025918	2		460	525	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70450687	70450687	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	140	442	0	ENST00000373644.4:c.5527G>C	p.Glu1843Gln	p.E1843Q	ENST00000373644	NM_030625.2	1843	Gag/Cag	12/12	NA	2	FACETS	0.853	0.779	0.931			1	INDETERMINATE	1	TRUE	NA	0.50636209025918	2		442	648	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56487175	56487175	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	104	435	0	ENST00000267101.3:c.1321C>G	p.Leu441Val	p.L441V	ENST00000267101	NM_001982.3	441	Ctg/Gtg	12/28	0.265459317865344	3	FACETS	0.575	0.514	0.64	0.192	0.171	0.214	INDETERMINATE	1	TRUE	0	0.50636209025918	3		435	895	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622409	28622409	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0015137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	56	371	0	ENST00000241453.7:c.1205+3G>A		p.X402_splice	ENST00000241453	NM_004119.2	402			0.265459317865344	3	FACETS	0.451	0.386	0.523	0.15	0.128	0.175	INDETERMINATE	1	TRUE	0	0.50636209025918	3		371	614	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991718	72991718	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs544025035	NA	P-0015137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	27	191	0	ENST00000268489.5:c.2327C>T	p.Ala776Val	p.A776V	ENST00000268489	NM_006885.3	776	gCg/gTg	2/10	0.50636209025918	3	FACETS	0.438	0.349	0.54	0.219	0.174	0.27	SUBCLONAL	1	TRUE	1	0.50636209025918	3		191	305	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0015137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	291	685	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.50636209025918	3	FACETS	0.826	0.779	0.873			1	CLONAL	2	TRUE	NA	0.50636209025918	3		685	872	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265583	10265583	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs865891586	NA	P-0015137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	44	371	0	ENST00000340748.4:c.1594G>A	p.Glu532Lys	p.E532K	ENST00000340748		532	Gag/Aag	19/40	0.176267935345432	0	FACETS	0.196	0.164	0.231			1	INDETERMINATE	1	TRUE	0	0.50636209025918	0		371	438	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909491	50909491	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	59	656	1	ENST00000440232.2:c.1295G>T	p.Arg432Leu	p.R432L	ENST00000440232	NM_002691.3	432	cGg/cTg	11/27	0.249616239764328	2	FACETS	0.348	0.299	0.402	0.174	0.149	0.201	INDETERMINATE	1	TRUE	0	0.50636209025918	2		657	669	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626459	12626459	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	45	405	0	ENST00000251849.4:c.1690G>C	p.Gly564Arg	p.G564R	ENST00000251849	NM_002880.3	564	Gga/Cga	16/17	0.438373682043491	3	FACETS	0.353	0.296	0.416	0.176	0.148	0.208	SUBCLONAL	1	TRUE	1	0.50636209025918	3		405	631	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80537190	80537190	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	42	336	1	ENST00000286548.4:c.208G>T	p.Glu70Ter	p.E70*	ENST00000286548	NM_002072.3	70	Gaa/Taa	2/7	0.389309090458433	3	FACETS	0.407	0.339	0.482			1	SUBCLONAL	1	TRUE	NA	0.50636209025918	3		337	511	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040908	47040909	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	CC	CC	-	novel	NA	P-0015137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	158	222	352	0	ENST00000377604.3:c.1439_1440del	p.Pro480ArgfsTer37	p.P480Rfs*37	ENST00000377604	NM_001204468.1	480	CCc/c	14/24	0.389309090458433	2	FACETS	1	0.988	1			1	CLONAL	2	TRUE	NA	0.50636209025918	2		352	380	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521315	187521316	+	frameshift_variant	Frame_Shift_Del	DEL	TC	TC	A	novel	NA	P-0015137-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	103	504	0	ENST00000441802.2:c.11839_11840delinsT	p.Asp3947LeufsTer36	p.D3947Lfs*36	ENST00000441802	NM_005245.3	3947	GAt/Tt	22/27	0.265035329609982	3	FACETS	0.653	0.584	0.726			1	INDETERMINATE	1	TRUE	NA	0.50636209025918	3		504	781	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577046	7577046	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs201744589	NA	P-0015195-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	139	655	0	ENST00000269305.4:c.892G>T	p.Glu298Ter	p.E298*	ENST00000269305	NM_001126112.2	298	Gag/Tag	8/11	0.255279465865378	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.23	1		655	759	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30098286	30098287	+	frameshift_variant	Frame_Shift_Del	DEL	CA	CA	-	novel	NA	P-0015195-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	460	496	0	ENST00000331968.5:c.1685_1686del	p.Val562GlufsTer24	p.V562Efs*24	ENST00000331968	NM_002742.2	562	gTG/g	11/18	0.298347562572642	5	FACETS	1	0.987	1	1	0.987	1	CLONAL	4	TRUE	1	0.23	5		496	1250	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50827578	50827578	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	novel	NA	P-0015195-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	105	400	0	ENST00000398568.2:c.2460+3G>A		p.X820_splice	ENST00000398568	NM_001042412.1	820			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.23	2		400	745	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945399	54945399	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	C	novel	NA	P-0015195-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	136	564	0	ENST00000312783.6:c.1030-3C>G		p.X344_splice	ENST00000312783	NM_198436.1	344			0.298347562572642	3	FACETS	1	0.976	1			1	CLONAL	1	TRUE	NA	0.23	3		564	1076	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158657	26158657	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1166967098	NA	P-0015195-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	64	30	51	0	ENST00000289316.2:c.260G>C	p.Arg87Pro	p.R87P	ENST00000289316	NM_138720.2	87	cGc/cCc	1/2	0.250859395304432	3	FACETS	1	0.852	1	1	0.951	1	CLONAL	3	TRUE	1	0.23	3		51	94	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55249062	55249062	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs1458440474	NA	P-0015195-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	50	543	0	ENST00000275493.2:c.2360A>C	p.Gln787Pro	p.Q787P	ENST00000275493	NM_005228.3	787	cAg/cCg	20/28	1	2	FACETS	0.532	0.45	0.623	0.532	0.45	0.623	SUBCLONAL	1	TRUE	1	0.23	2		543	817	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3788618	3788618	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs398124146	NA	P-0015205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	80	546	1	ENST00000262367.5:c.4336C>T	p.Arg1446Cys	p.R1446C	ENST00000262367	NM_004380.2	1446	Cgc/Tgc	26/31	1	2	FACETS	0.286	0.251	0.324	0.286	0.251	0.324	SUBCLONAL	1	TRUE	1	0.64	2		547	873	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0015205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	134	430	0				ENST00000310581	NM_198253.2	-/1132			0.3	1	FACETS	0.732	0.672	0.794	0.732	0.672	0.794	INDETERMINATE	1	TRUE	0	0.64	1		430	389	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101908873	101908873	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs200595614	NA	P-0015205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	65	442	1	ENST00000374994.4:c.1237C>T	p.Arg413Ter	p.R413*	ENST00000374994	NM_004612.2	413	Cga/Tga	7/9	0.3	0	FACETS	0.136	0.117	0.155			1	INDETERMINATE	1	TRUE	0	0.64	0		443	539	SUCCESS
APC	324	MSKCC	GRCh37	5	112128185	112128185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779805	NA	P-0015205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	232	326	1	ENST00000257430.4:c.688C>T	p.Arg230Cys	p.R230C	ENST00000257430	NM_000038.5	230	Cgt/Tgt	7/16	1	2	FACETS	0.697	0.65	0.746	0.697	0.65	0.746	SUBCLONAL	1	TRUE	1	0.64	2		327	1040	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376026	118376026	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	251	536	0	ENST00000534358.1:c.9419C>T	p.Pro3140Leu	p.P3140L	ENST00000534358	NM_005933.3	3140	cCa/cTa	27/36	1	2	FACETS	0.998	0.937	1	0.998	0.937	1	CLONAL	1	TRUE	1	0.64	2		536	786	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481899	56481899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	380	779	0	ENST00000267101.3:c.827C>T	p.Pro276Leu	p.P276L	ENST00000267101	NM_001982.3	276	cCc/cTc	7/28	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.64	2		779	1142	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3794892	3794892	+	splice_region_variant,intron_variant	Splice_Region	SNP	T	T	A	novel	NA	P-0015205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	294	487	0	ENST00000262367.5:c.3982+3A>T		p.X1328_splice	ENST00000262367	NM_004380.2	1328			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.64	2		487	874	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134255	11134255	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	82	691	1	ENST00000358026.2:c.2921C>T	p.Pro974Leu	p.P974L	ENST00000358026	NM_001128849.1	974	cCc/cTc	20/36	0.0973859760384226	0	FACETS	0.107	0.094	0.121			1	INDETERMINATE	1	TRUE	0	0.64	0		692	864	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180050946	180050946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	50	815	0	ENST00000261937.6:c.1537G>A	p.Gly513Arg	p.G513R	ENST00000261937	NM_182925.4	513	Gga/Aga	11/30	0.3	1	FACETS	0.138	0.116	0.162	0.138	0.116	0.162	INDETERMINATE	1	TRUE	0	0.64	1		815	771	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117737471	117737471	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	89	496	0	ENST00000368508.3:c.178G>A	p.Gly60Arg	p.G60R	ENST00000368508	NM_002944.2	60	Gga/Aga	3/43	1	2	FACETS	0.276	0.243	0.31	0.276	0.243	0.31	SUBCLONAL	1	TRUE	1	0.64	2		496	1009	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239860	98239863	+	frameshift_variant	Frame_Shift_Del	DEL	ATCA	ATCA	-	novel	NA	P-0015205-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	396	658	0	ENST00000331920.6:c.1469_1472del	p.Leu490SerfsTer51	p.L490Sfs*51	ENST00000331920	NM_000264.3	490	tTGATc/tc	10/24	0.3	0	FACETS	0.639	0.614	0.664			1	INDETERMINATE	1	TRUE	0	0.64	0		658	697	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	496	430	0				ENST00000310581	NM_198253.2	-/1132			0.793418120731719	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.793418120731719	2		430	572	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577105	7577105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876659802	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	1126	596	1	ENST00000269305.4:c.833C>T	p.Pro278Leu	p.P278L	ENST00000269305	NM_001126112.2	278	cCt/cTt	8/11	0.793418120731719	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.793418120731719	2		597	1257	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5240314	5240314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777007079	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	1027	1060	2	ENST00000357368.4:c.1600G>A	p.Glu534Lys	p.E534K	ENST00000357368	NM_002850.3	534	Gag/Aag	12/38	0.793418120731719	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.793418120731719	2		1062	1171	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317422	1317422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759127718	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	661	585	0	ENST00000400841.2:c.643C>T	p.Arg215Trp	p.R215W	ENST00000400841		215	Cgg/Tgg	5/6	1	1	FACETS	1	0.998	1	1	0.998	1	CLONAL	1	TRUE	0	0.793418120731719	1		585	767	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	CT	rs121913227	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	544	446	0	ENST00000288602.6:c.1798_1799delinsAG	p.Val600Arg	p.V600R	ENST00000288602	NM_004333.4	600	GTg/AGg	15/18	0.793418120731719	6	FACETS	0.905	0.874	0.936			1	CLONAL	4	TRUE	NA	0.793418120731719	6		446	980	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254623	16254623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749814808	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	273	564	0	ENST00000375759.3:c.1888C>T	p.Arg630Cys	p.R630C	ENST00000375759	NM_015001.2	630	Cgt/Tgt	11/15	0.793418120731719	3	FACETS	0.97	0.911	1	0.485	0.455	0.515	CLONAL	1	TRUE	1	0.793418120731719	3		564	991	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131301	202131301	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748087575	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	446	762	0	ENST00000358485.4:c.269C>T	p.Pro90Leu	p.P90L	ENST00000358485	NM_001080125.1	90	cCg/cTg	2/9	0.793418120731719	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.793418120731719	3		762	757	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242749	66242749	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	300	260	0	ENST00000273854.3:c.1823C>T	p.Ser608Phe	p.S608F	ENST00000273854	NM_004439.5	608	tCc/tTc	9/18	0.793418120731719	3	FACETS	1	0.966	1	0.517	0.488	0.548	CLONAL	1	TRUE	1	0.793418120731719	3		260	1021	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085995	16085995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	334	766	2	ENST00000281043.3:c.1171C>T	p.Arg391Cys	p.R391C	ENST00000281043	NM_005378.4	391	Cgc/Tgc	3/3	0.793418120731719	3	FACETS	1	0.988	1	0.568	0.537	0.598	CLONAL	1	TRUE	1	0.793418120731719	3		768	1036	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203609	108203609	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	196	422	0	ENST00000278616.4:c.7909C>T	p.Gln2637Ter	p.Q2637*	ENST00000278616	NM_000051.3	2637	Cag/Tag	53/63	0.793418120731719	3	FACETS	0.997	0.941	1	0.997	0.941	1	CLONAL	2	TRUE	1	0.793418120731719	3		422	346	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638349	117638349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	185	767	2	ENST00000368508.3:c.6092G>A	p.Gly2031Glu	p.G2031E	ENST00000368508	NM_002944.2	2031	gGa/gAa	38/43	1	2	FACETS	0.938	0.874	1	0.938	0.874	1	CLONAL	1	TRUE	1	0.793418120731719	2		769	497	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453127	140453127	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372569965	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	621	774	0	ENST00000288602.6:c.1808G>A	p.Arg603Gln	p.R603Q	ENST00000288602	NM_004333.4	603	cGa/cAa	15/18	0.793418120731719	6	FACETS	0.956	0.926	0.985			1	CLONAL	4	TRUE	NA	0.793418120731719	6		774	1059	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98009731	98009731	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	288	679	0	ENST00000289081.3:c.233C>T	p.Pro78Leu	p.P78L	ENST00000289081	NM_000136.2	78	cCt/cTt	3/15	0.714622819420125	4	FACETS	0.926	0.876	0.976	0.926	0.876	0.976	CLONAL	2	TRUE	2	0.793418120731719	4		679	703	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68939478	68939478	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139157434	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	258	654	2	ENST00000288368.4:c.463C>T	p.Arg155Trp	p.R155W	ENST00000288368	NM_024870.2	155	Cgg/Tgg	5/40	0.793418120731719	3	FACETS	0.921	0.874	0.968	0.921	0.874	0.968	CLONAL	2	TRUE	1	0.793418120731719	3		656	493	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934283	68934283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773476490	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	175	557	0	ENST00000288368.4:c.349C>T	p.Arg117Cys	p.R117C	ENST00000288368	NM_024870.2	117	Cgt/Tgt	4/40	0.793418120731719	3	FACETS	0.966	0.893	1	0.483	0.446	0.521	CLONAL	1	TRUE	1	0.793418120731719	3		557	638	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261553	16261553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	375	785	1	ENST00000375759.3:c.8818C>T	p.Pro2940Ser	p.P2940S	ENST00000375759	NM_015001.2	2940	Cct/Tct	11/15	0.793418120731719	3	FACETS	1	0.978	1	0.526	0.499	0.554	CLONAL	1	TRUE	1	0.793418120731719	3		786	1255	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246498712	246498712	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1257689530	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	269	818	0	ENST00000388985.4:c.293C>T	p.Pro98Leu	p.P98L	ENST00000388985		98	cCt/cTt	3/12	0.742107960398341	3	FACETS	0.973	0.914	1	0.487	0.457	0.517	CLONAL	1	TRUE	1	0.793418120731719	3		818	973	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100355	8100355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	853	1005	0	ENST00000346208.3:c.329C>T	p.Ser110Phe	p.S110F	ENST00000346208		110	tCc/tTc	3/6	0.793418120731719	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.793418120731719	2		1005	1006	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123279657	123279657	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	62	376	486	0	ENST00000358487.5:c.775C>T	p.Gln259Ter	p.Q259*	ENST00000358487	NM_000141.4	259	Caa/Taa	7/18	0.793418120731719	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	0	0.793418120731719	2		486	438	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310941	123310941	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	397	515	0	ENST00000358487.5:c.487G>A	p.Glu163Lys	p.E163K	ENST00000358487	NM_000141.4	163	Gaa/Aaa	5/18	0.793418120731719	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	TRUE	0	0.793418120731719	2		515	451	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948385	71948385	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138023922	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	1044	1180	2	ENST00000298229.2:c.3097C>T	p.Arg1033Cys	p.R1033C	ENST00000298229	NM_001567.3	1033	Cgt/Tgt	26/28	0.793418120731719	3	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	1	0.793418120731719	3		1182	1746	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715780	18715780	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745816756	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	128	552	1	ENST00000266497.5:c.3611C>T	p.Ser1204Leu	p.S1204L	ENST00000266497		1204	tCg/tTg	25/31	0.190457401522302	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.793418120731719	0		553	314	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243824	46243824	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	336	358	0	ENST00000334344.6:c.1918C>T	p.Pro640Ser	p.P640S	ENST00000334344	NM_152641.2	640	Cct/Tct	15/21	0.647816514479185	5	FACETS	1	0.978	1			1	CLONAL	4	TRUE	NA	0.793418120731719	5		358	456	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433904	49433904	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368698254	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	537	1095	0	ENST00000301067.7:c.7649C>T	p.Pro2550Leu	p.P2550L	ENST00000301067	NM_003482.3	2550	cCt/cTt	31/54	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.793418120731719	2		1095	1217	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444737	49444737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	562	1208	1	ENST00000301067.7:c.2729C>T	p.Pro910Leu	p.P910L	ENST00000301067	NM_003482.3	910	cCt/cTt	10/54	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.793418120731719	2		1209	1247	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444809	49444809	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587783709	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	618	1145	0	ENST00000301067.7:c.2657C>T	p.Pro886Leu	p.P886L	ENST00000301067	NM_003482.3	886	cCt/cTt	10/54	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.793418120731719	2		1145	1291	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445613	49445613	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	736	1421	3	ENST00000301067.7:c.1853C>T	p.Ser618Phe	p.S618F	ENST00000301067	NM_003482.3	618	tCc/tTc	10/54	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.793418120731719	2		1424	1691	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856455	111856455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	364	519	0	ENST00000341259.2:c.506C>T	p.Ala169Val	p.A169V	ENST00000341259	NM_005475.2	169	gCt/gTt	2/8	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.793418120731719	2		519	776	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28609637	28609637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	299	594	0	ENST00000241453.7:c.1592C>T	p.Ser531Phe	p.S531F	ENST00000241453	NM_004119.2	531	tCt/tTt	12/24	0.226424064851313	5	FACETS	0.869	0.826	0.913	0.869	0.826	0.913	INDETERMINATE	3	TRUE	2	0.793418120731719	5		594	633	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675103	40675103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	360	1002	1	ENST00000249776.8:c.67G>A	p.Asp23Asn	p.D23N	ENST00000249776	NM_033286.3	23	Gat/Aat	1/9	0.793418120731719	3	FACETS	0.947	0.897	0.999	0.474	0.448	0.5	CLONAL	1	TRUE	1	0.793418120731719	3		1003	1338	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729162	66729163	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	328	828	1	ENST00000307102.5:c.370_371delinsTT	p.Pro124Leu	p.P124L	ENST00000307102	NM_002755.3	124	CCg/TTg	3/11	0.793418120731719	3	FACETS	0.855	0.807	0.905	0.428	0.403	0.453	CLONAL	1	TRUE	1	0.793418120731719	3		829	1350	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2133719	2133719	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1422874936	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	744	858	0	ENST00000219476.3:c.3907G>A	p.Gly1303Arg	p.G1303R	ENST00000219476	NM_000548.3	1303	Gga/Aga	33/42	0.403297090984015	3	FACETS	1	0.997	1	0.79	0.77	0.81	INDETERMINATE	2	TRUE	0	0.793418120731719	3		858	1105	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857368	9857368	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	424	774	3	ENST00000330684.3:c.4033C>T	p.Pro1345Ser	p.P1345S	ENST00000330684	NM_001134407.1	1345	Ccc/Tcc	13/13	NA	2	FACETS	0.851	0.822	0.879			1	INDETERMINATE	2	TRUE	NA	0.793418120731719	2		777	628	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857725	9857725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	426	521	0	ENST00000330684.3:c.3676G>A	p.Gly1226Ser	p.G1226S	ENST00000330684	NM_001134407.1	1226	Ggc/Agc	13/13	NA	2	FACETS	0.924	0.896	0.951			1	INDETERMINATE	2	TRUE	NA	0.793418120731719	2		521	581	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68835740	68835740	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	850	857	0	ENST00000261769.5:c.331T>C	p.Ser111Pro	p.S111P	ENST00000261769	NM_004360.3	111	Tcc/Ccc	3/16	0.793418120731719	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.793418120731719	2		857	1003	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346895	89346895	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1165374364	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	256	310	1	ENST00000301030.4:c.6055C>T	p.Pro2019Ser	p.P2019S	ENST00000301030	NM_001256183.1	2019	Ccc/Tcc	9/13	0.793418120731719	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.793418120731719	2		311	301	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118919	3118919	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	rs374438586	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	116	842	876	2	ENST00000078429.4:c.606-3C>T		p.X202_splice	ENST00000078429	NM_002067.2	202			0.793418120731719	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.793418120731719	2		878	958	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416472	29416472	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368484630	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	968	991	2	ENST00000389048.3:c.4481G>A	p.Gly1494Glu	p.G1494E	ENST00000389048	NM_004304.4	1494	gGa/gAa	29/29	0.793418120731719	3	FACETS	1	0.995	1	1	0.995	1	CLONAL	2	TRUE	1	0.793418120731719	3		993	1594	SUCCESS
REL	5966	MSKCC	GRCh37	2	61144086	61144086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867470560	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	177	916	2	ENST00000295025.8:c.469C>T	p.Pro157Ser	p.P157S	ENST00000295025	NM_002908.2	157	Cct/Tct	5/11	0.793418120731719	3	FACETS	0.907	0.839	0.978	0.454	0.419	0.489	CLONAL	1	TRUE	1	0.793418120731719	3		918	687	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198265501	198265501	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	267	876	0	ENST00000335508.6:c.2656C>T	p.His886Tyr	p.H886Y	ENST00000335508	NM_012433.2	886	Cat/Tat	18/25	0.793418120731719	3	FACETS	1	0.985	1	0.569	0.535	0.604	CLONAL	1	TRUE	1	0.793418120731719	3		876	826	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131228	202131228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	410	611	0	ENST00000358485.4:c.196C>T	p.Leu66Phe	p.L66F	ENST00000358485	NM_001080125.1	66	Ctt/Ttt	2/9	0.793418120731719	3	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	1	0.793418120731719	3		611	668	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543860	212543860	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	322	755	0	ENST00000342788.4:c.1539G>A	p.Trp513Ter	p.W513*	ENST00000342788	NM_005235.2	513	tgG/tgA	13/28	0.793418120731719	3	FACETS	1	0.987	1	0.566	0.535	0.598	CLONAL	1	TRUE	1	0.793418120731719	3		755	1001	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561325	9561325	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	537	446	1	ENST00000353224.5:c.457G>A	p.Gly153Arg	p.G153R	ENST00000353224	NM_177990.2	153	Gga/Aga	4/10	0.763655884210919	5	FACETS	0.95	0.916	0.984	0.95	0.916	0.984	CLONAL	3	TRUE	2	0.793418120731719	5		447	1040	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41385227	41385227	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	895	740	1	ENST00000373198.4:c.734A>T	p.His245Leu	p.H245L	ENST00000373198	NM_133170.3	245	cAc/cTc	6/32	0.763655884210919	5	FACETS	0.981	0.954	1	0.981	0.954	1	CLONAL	3	TRUE	2	0.793418120731719	5		741	1679	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149243843	149243844	+	missense_variant	Missense_Mutation	DNP	TG	TG	GT	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	1188	896	3	ENST00000360632.3:c.974_975delinsAC	p.Thr325Asn	p.T325N	ENST00000360632	NM_015472.4	325	aCA/aAC	6/7	0.788317939771498	3	FACETS	1	0.998	1	1	0.998	1	CLONAL	3	TRUE	0	0.793418120731719	3		899	1328	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955547	55955547	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	173	832	0	ENST00000263923.4:c.3398C>T	p.Pro1133Leu	p.P1133L	ENST00000263923	NM_002253.2	1133	cCa/cTa	25/30	0.793418120731719	3	FACETS	0.913	0.844	0.985	0.457	0.422	0.493	CLONAL	1	TRUE	1	0.793418120731719	3		832	667	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540046	187540046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1390713115	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	190	603	0	ENST00000441802.2:c.7694C>T	p.Ser2565Leu	p.S2565L	ENST00000441802	NM_005245.3	2565	tCa/tTa	10/27	0.793418120731719	3	FACETS	0.982	0.912	1	0.491	0.456	0.528	CLONAL	1	TRUE	1	0.793418120731719	3		603	681	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106552813	106552813	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	395	1150	0	ENST00000369096.4:c.778C>T	p.Pro260Ser	p.P260S	ENST00000369096	NM_001198.3	260	Ccc/Tcc	5/7	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.793418120731719	2		1150	965	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609828	117609828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	264	433	0	ENST00000368508.3:c.6871C>T	p.Pro2291Ser	p.P2291S	ENST00000368508	NM_002944.2	2291	Cct/Tct	43/43	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.793418120731719	2		433	623	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851528	151851528	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	269	398	0	ENST00000262189.6:c.11963T>A	p.Ile3988Lys	p.I3988K	ENST00000262189	NM_170606.2	3988	aTa/aAa	47/59	0.672183131801095	4	FACETS	0.976	0.923	1	0.976	0.923	1	CLONAL	2	TRUE	2	0.793418120731719	4		398	623	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151853320	151853320	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	394	634	2	ENST00000262189.6:c.11782G>A	p.Gly3928Arg	p.G3928R	ENST00000262189	NM_170606.2	3928	Gga/Aga	45/59	0.672183131801095	4	FACETS	0.955	0.911	0.998	0.955	0.911	0.998	CLONAL	2	TRUE	2	0.793418120731719	4		636	933	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860563	151860563	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199597064	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	554	710	0	ENST00000262189.6:c.10099C>T	p.Pro3367Ser	p.P3367S	ENST00000262189	NM_170606.2	3367	Cca/Tca	43/59	0.672183131801095	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	2	0.793418120731719	4		710	1154	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38279347	38279347	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	454	1126	0	ENST00000425967.3:c.1142C>T	p.Ser381Phe	p.S381F	ENST00000425967	NM_001174067.1	381	tCc/tTc	9/19	0.793418120731719	3	FACETS	1	0.975	1	0.517	0.492	0.541	CLONAL	1	TRUE	1	0.793418120731719	3		1126	1547	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68968173	68968173	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	263	993	0	ENST00000288368.4:c.1202G>A	p.Arg401Lys	p.R401K	ENST00000288368	NM_024870.2	401	aGa/aAa	10/40	0.793418120731719	3	FACETS	1	0.983	1	0.561	0.527	0.596	CLONAL	1	TRUE	1	0.793418120731719	3		993	825	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128753098	128753098	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	265	627	0	ENST00000377970.2:c.1259C>T	p.Ser420Phe	p.S420F	ENST00000377970	NM_002467.4	420	tCc/tTc	3/3	0.793418120731719	3	FACETS	1	0.943	1	0.502	0.471	0.534	CLONAL	1	TRUE	1	0.793418120731719	3		627	929	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98209632	98209633	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	529	677	0	ENST00000331920.6:c.3905_3906delinsTT	p.Pro1302Leu	p.P1302L	ENST00000331920	NM_000264.3	1302	cCC/cTT	23/24	0.714622819420125	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.793418120731719	4		677	1181	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98215901	98215901	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	764	886	0	ENST00000331920.6:c.3308C>T	p.Ala1103Val	p.A1103V	ENST00000331920	NM_000264.3	1103	gCc/gTc	20/24	0.714622819420125	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	2	0.793418120731719	4		886	1637	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250158	110250158	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	746	871	0	ENST00000374672.4:c.517T>A	p.Tyr173Asn	p.Y173N	ENST00000374672	NM_004235.4	173	Tat/Aat	3/5	0.714622819420125	4	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	2	0.793418120731719	4		871	1548	SUCCESS
RET	5979	MSKCC	GRCh37	10	43595967	43595968	+	missense_variant	Missense_Mutation	DNP	CA	CA	GG	novel	NA	P-0015261-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	795	963	0	ENST00000355710.3:c.134_135delinsGG	p.Ala45Gly	p.A45G	ENST00000355710	NM_020975.4	45	gCA/gGG	2/20	0.793418120731719	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	2	TRUE	0	0.793418120731719	2		963	941	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	76	215	0				ENST00000310581	NM_198253.2	-/1132			0.211957081430457	1	FACETS	0.739	0.648	0.836	0.739	0.648	0.836	SUBCLONAL	1	TRUE	0	0.28	1		215	632	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	942	102	427	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.698	0.623	0.778	0.698	0.623	0.778	SUBCLONAL	1	TRUE	1	0.28	2		427	1044	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	97	654	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	1	2	FACETS	0.717	0.638	0.802	0.717	0.638	0.802	SUBCLONAL	1	TRUE	1	0.28	2		654	966	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18271969	18271969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1418268495	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	67	319	0	ENST00000222254.8:c.572C>T	p.Ser191Leu	p.S191L	ENST00000222254	NM_005027.3	191	tCg/tTg	5/16	1	2	FACETS	0.886	0.771	1	0.886	0.771	1	CLONAL	1	TRUE	1	0.28	2		319	540	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430425	181430425	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1156	125	653	1	ENST00000325404.1:c.277G>A	p.Glu93Lys	p.E93K	ENST00000325404	NM_003106.3	93	Gag/Aag	1/1	1	2	FACETS	0.697	0.629	0.769	0.697	0.629	0.769	SUBCLONAL	1	TRUE	1	0.28	2		654	1281	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6431634	6431634	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	93	423	0	ENST00000356142.4:c.187G>A	p.Asp63Asn	p.D63N	ENST00000356142	NM_018890.3	63	Gat/Aat	3/7	1	2	FACETS	0.89	0.792	0.996	0.89	0.792	0.996	CLONAL	1	TRUE	1	0.28	2		423	746	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16203058	16203058	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	101	395	0	ENST00000375759.3:c.766C>T	p.Gln256Ter	p.Q256*	ENST00000375759	NM_015001.2	256	Cag/Tag	3/15	1	2	FACETS	0.768	0.686	0.857	0.768	0.686	0.857	SUBCLONAL	1	TRUE	1	0.28	2		395	939	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023214	27023226	+	frameshift_variant	Frame_Shift_Del	DEL	CGGGCCCTAGGCC	CGGGCCCTAGGCC	-	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	45	411	0	ENST00000324856.7:c.322_334del	p.Gly108ProfsTer2	p.G108Pfs*2	ENST00000324856	NM_006015.4	107	gCGGGCCCTAGGCCc/gc	1/20	1	2	FACETS	0.439	0.367	0.518	0.439	0.367	0.518	SUBCLONAL	1	TRUE	1	0.28	2		411	733	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27094360	27094360	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	90	400	0	ENST00000324856.7:c.3068G>A	p.Trp1023Ter	p.W1023*	ENST00000324856	NM_006015.4	1023	tGg/tAg	11/20	1	2	FACETS	0.678	0.6	0.762	0.678	0.6	0.762	SUBCLONAL	1	TRUE	1	0.28	2		400	948	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46743805	46743806	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	79	508	0	ENST00000371975.4:c.2095_2096del	p.Cys699HisfsTer12	p.C699Hfs*12	ENST00000371975	NM_003579.3	699	TGc/c	18/18	1	2	FACETS	0.623	0.547	0.705	0.623	0.547	0.705	SUBCLONAL	1	TRUE	1	0.28	2		508	906	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78433858	78433858	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	667	45	300	0	ENST00000370768.2:c.241C>T	p.Gln81Ter	p.Q81*	ENST00000370768	NM_003902.3	81	Caa/Taa	3/20	1	2	FACETS	0.451	0.378	0.533	0.451	0.378	0.533	SUBCLONAL	1	TRUE	1	0.28	2		300	712	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262243	115262243	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1030	114	490	1	ENST00000438362.2:c.2311C>T	p.Gln771Ter	p.Q771*	ENST00000438362	NM_001242891.1	771	Cag/Tag	18/20	1	2	FACETS	0.712	0.639	0.789	0.712	0.639	0.789	SUBCLONAL	1	TRUE	1	0.28	2		491	1144	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150550890	150550890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	99	353	0	ENST00000369026.2:c.766G>A	p.Asp256Asn	p.D256N	ENST00000369026	NM_021960.4	256	Gac/Aac	2/3	1	2	FACETS	0.768	0.684	0.857	0.768	0.684	0.857	SUBCLONAL	1	TRUE	1	0.28	2		353	921	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981761	101981761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748301282	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	122	542	0	ENST00000282441.5:c.182C>T	p.Ser61Leu	p.S61L	ENST00000282441	NM_001130145.2	61	tCg/tTg	1/9	1	2	FACETS	0.862	0.778	0.951	0.862	0.778	0.951	CLONAL	1	TRUE	1	0.28	2		542	1011	SUCCESS
ATM	472	MSKCC	GRCh37	11	108225575	108225575	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	81	353	0	ENST00000278616.4:c.8824C>T	p.Gln2942Ter	p.Q2942*	ENST00000278616	NM_000051.3	2942	Cag/Tag	61/63	1	2	FACETS	0.709	0.624	0.801	0.709	0.624	0.801	SUBCLONAL	1	TRUE	1	0.28	2		353	816	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118371719	118371719	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	43	196	1	ENST00000534358.1:c.6176G>A	p.Trp2059Ter	p.W2059*	ENST00000534358	NM_005933.3	2059	tGg/tAg	25/36	1	2	FACETS	0.684	0.573	0.807	0.684	0.573	0.807	SUBCLONAL	1	TRUE	1	0.28	2		197	449	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49415878	49415878	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	66	346	0	ENST00000301067.7:c.16469A>G	p.Lys5490Arg	p.K5490R	ENST00000301067	NM_003482.3	5490	aAa/aGa	53/54	1	2	FACETS	0.704	0.61	0.805	0.704	0.61	0.805	SUBCLONAL	1	TRUE	1	0.28	2		346	670	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56477621	56477621	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	105	473	0	ENST00000267101.3:c.169G>A	p.Glu57Lys	p.E57K	ENST00000267101	NM_001982.3	57	Gag/Aag	2/28	1	2	FACETS	0.68	0.608	0.757	0.68	0.608	0.757	SUBCLONAL	1	TRUE	1	0.28	2		473	1103	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495496	56495496	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217262342	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	88	498	0	ENST00000267101.3:c.3686C>T	p.Ser1229Leu	p.S1229L	ENST00000267101	NM_001982.3	1229	tCa/tTa	28/28	1	2	FACETS	0.694	0.613	0.78	0.694	0.613	0.78	SUBCLONAL	1	TRUE	1	0.28	2		498	906	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133215887	133215887	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	rs1415497701	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	40	259	0	ENST00000320574.5:c.5379-3C>T		p.X1793_splice	ENST00000320574	NM_006231.2	1793			1	2	FACETS	0.738	0.614	0.876	0.738	0.614	0.876	SUBCLONAL	1	TRUE	1	0.28	2		259	387	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226101	133226101	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs984562653	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	69	463	0	ENST00000320574.5:c.3796G>A	p.Glu1266Lys	p.E1266K	ENST00000320574	NM_006231.2	1266	Gag/Aag	31/49	1	2	FACETS	0.612	0.532	0.699	0.612	0.532	0.699	SUBCLONAL	1	TRUE	1	0.28	2		463	805	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912262	32912262	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782581	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	86	442	0	ENST00000380152.3:c.3770C>T	p.Pro1257Leu	p.P1257L	ENST00000380152		1257	cCa/cTa	11/27	1	2	FACETS	0.673	0.594	0.758	0.673	0.594	0.758	SUBCLONAL	1	TRUE	1	0.28	2		442	913	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506193	103506193	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	100	430	0	ENST00000355739.4:c.351A>C	p.Gln117His	p.Q117H	ENST00000355739	NM_000123.3	117	caA/caC	3/15	1	2	FACETS	0.712	0.635	0.795	0.712	0.635	0.795	SUBCLONAL	1	TRUE	1	0.28	2		430	1003	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90645507	90645507	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	10	52	0	ENST00000330062.3:c.115+1G>A		p.X39_splice	ENST00000330062	NM_002168.2	39			1	2	FACETS	0.585	0.399	0.817	0.585	0.399	0.817	SUBCLONAL	1	TRUE	1	0.28	2		52	122	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098710	2098710	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	79	578	0	ENST00000219476.3:c.94G>A	p.Glu32Lys	p.E32K	ENST00000219476	NM_000548.3	32	Gag/Aag	2/42	1	2	FACETS	0.525	0.46	0.595	0.525	0.46	0.595	SUBCLONAL	1	TRUE	1	0.28	2		578	1075	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29559158	29559158	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs9907627	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	113	370	0	ENST00000356175.3:c.3265G>A	p.Glu1089Lys	p.E1089K	ENST00000356175	NM_000267.3	1089	Gaa/Aaa	25/57	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.28	2		370	799	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37864665	37864665	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	97	566	0	ENST00000269571.5:c.317A>G	p.Gln106Arg	p.Q106R	ENST00000269571		106	cAg/cGg	3/27	1	2	FACETS	0.649	0.577	0.726	0.649	0.577	0.726	SUBCLONAL	1	TRUE	1	0.28	2		566	1068	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096885	11096885	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1146	127	812	0	ENST00000358026.2:c.376G>C	p.Gly126Arg	p.G126R	ENST00000358026	NM_001128849.1	126	Ggc/Cgc	4/36	1	2	FACETS	0.713	0.644	0.786	0.713	0.644	0.786	SUBCLONAL	1	TRUE	1	0.28	2		812	1273	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860620	45860620	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	112	684	0	ENST00000391945.4:c.1387C>T	p.Pro463Ser	p.P463S	ENST00000391945	NM_000400.3	463	Ccg/Tcg	15/23	1	2	FACETS	0.677	0.607	0.751	0.677	0.607	0.751	SUBCLONAL	1	TRUE	1	0.28	2		684	1182	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52442569	52442569	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	89	427	1	ENST00000460680.1:c.176G>C	p.Arg59Pro	p.R59P	ENST00000460680	NM_004656.3	59	cGg/cCg	4/17	1	2	FACETS	0.686	0.607	0.771	0.686	0.607	0.771	SUBCLONAL	1	TRUE	1	0.28	2		428	927	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72861879	72861879	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746829352	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	118	511	0	ENST00000325599.8:c.1003C>T	p.Arg335Cys	p.R335C	ENST00000325599	NM_018130.2	335	Cgc/Tgc	9/11	1	2	FACETS	0.727	0.654	0.804	0.727	0.654	0.804	SUBCLONAL	1	TRUE	1	0.28	2		511	1160	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430778	181430778	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	130	687	0	ENST00000325404.1:c.630G>A	p.Met210Ile	p.M210I	ENST00000325404	NM_003106.3	210	atG/atA	1/1	1	2	FACETS	0.734	0.664	0.808	0.734	0.664	0.808	SUBCLONAL	1	TRUE	1	0.28	2		687	1265	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186502386	186502386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs953593626	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	68	268	0	ENST00000323963.5:c.109G>A	p.Asp37Asn	p.D37N	ENST00000323963		37	Gat/Aat	3/11	1	2	FACETS	0.639	0.555	0.73	0.639	0.555	0.73	SUBCLONAL	1	TRUE	1	0.28	2		268	760	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1953841	1953841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	84	543	0	ENST00000382891.5:c.2020G>A	p.Glu674Lys	p.E674K	ENST00000382891	NM_133335.3	674	Gag/Aag	11/22	NA	2	FACETS	0.706	0.622	0.796			1	INDETERMINATE	1	TRUE	NA	0.28	2		543	850	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384656	84384656	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	94	435	0	ENST00000321945.7:c.787C>T	p.Gln263Ter	p.Q263*	ENST00000321945	NM_139076.2	263	Cag/Tag	8/9	1	2	FACETS	0.607	0.539	0.681	0.607	0.539	0.681	SUBCLONAL	1	TRUE	1	0.28	2		435	1106	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081670	143081670	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	86	292	0	ENST00000262992.4:c.1404T>G	p.Ser468Arg	p.S468R	ENST00000262992	NM_001101669.1	468	agT/agG	15/24	1	2	FACETS	0.878	0.776	0.986	0.878	0.776	0.986	CLONAL	1	TRUE	1	0.28	2		292	700	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526232	31526232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	120	683	0	ENST00000344624.3:c.808G>A	p.Asp270Asn	p.D270N	ENST00000344624		270	Gac/Aac	2/33	0.211957081430457	1	FACETS	0.569	0.512	0.629	0.569	0.512	0.629	SUBCLONAL	1	TRUE	0	0.28	1		683	1296	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131925500	131925500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	74	323	0	ENST00000265335.6:c.1423C>T	p.Leu475Phe	p.L475F	ENST00000265335		475	Ctt/Ttt	9/25	1	2	FACETS	0.718	0.628	0.815	0.718	0.628	0.815	SUBCLONAL	1	TRUE	1	0.28	2		323	736	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562378	176562378	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1216848793	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	102	513	0	ENST00000439151.2:c.274G>A	p.Asp92Asn	p.D92N	ENST00000439151	NM_022455.4	92	Gat/Aat	2/23	1	2	FACETS	0.683	0.61	0.762	0.683	0.61	0.762	SUBCLONAL	1	TRUE	1	0.28	2		513	1066	SUCCESS
FYN	2534	MSKCC	GRCh37	6	111983048	111983048	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	94	692	1	ENST00000368678.4:c.1499G>A	p.Trp500Ter	p.W500*	ENST00000368678		500	tGg/tAg	13/13	1	2	FACETS	0.659	0.585	0.738	0.659	0.585	0.738	SUBCLONAL	1	TRUE	1	0.28	2		693	1019	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335614	81335614	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201395847	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	65	374	0	ENST00000222390.5:c.1746G>A	p.Met582Ile	p.M582I	ENST00000222390	NM_000601.4	582	atG/atA	15/18	1	2	FACETS	0.505	0.436	0.579	0.505	0.436	0.579	SUBCLONAL	1	TRUE	1	0.28	2		374	920	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189089	38189089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	168	414	0	ENST00000317025.8:c.925C>T	p.His309Tyr	p.H309Y	ENST00000317025	NM_023034.1	309	Cat/Tat	5/24	0.173769366847039	3	FACETS	1	0.988	1	0.724	0.665	0.785	CLONAL	1	TRUE	1	0.28	3		414	945	SUCCESS
MYC	4609	MSKCC	GRCh37	8	128750937	128750937	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	152	356	3	ENST00000377970.2:c.474G>T	p.Lys158Asn	p.K158N	ENST00000377970	NM_002467.4	158	aaG/aaT	2/3	0.187674068726701	5	FACETS	0.891	0.815	0.971	0.594	0.543	0.647	CLONAL	2	TRUE	2	0.28	5		359	865	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141582921	141582921	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1226	99	561	4	ENST00000220592.5:c.326G>A	p.Gly109Glu	p.G109E	ENST00000220592	NM_012154.3	109	gGg/gAg	3/19	0.161319199205147	4	FACETS	0.683	0.608	0.764	0.342	0.304	0.382	INDETERMINATE	1	TRUE	2	0.28	4		565	1325	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36923484	36923484	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	83	573	0	ENST00000358127.4:c.781-3C>T		p.X261_splice	ENST00000358127	NM_001280556.1	261			1	2	FACETS	0.612	0.539	0.691	0.612	0.539	0.691	SUBCLONAL	1	TRUE	1	0.28	2		573	969	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915831	127915831	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	79	343	1	ENST00000373547.4:c.650G>A	p.Gly217Glu	p.G217E	ENST00000373547	NM_002721.4	217	gGa/gAa	6/7	1	2	FACETS	0.739	0.649	0.835	0.739	0.649	0.835	SUBCLONAL	1	TRUE	1	0.28	2		344	764	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782757	135782757	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	57	258	0	ENST00000298552.3:c.1264G>A	p.Glu422Lys	p.E422K	ENST00000298552	NM_001162426.1	422	Gaa/Aaa	13/23	1	2	FACETS	0.768	0.659	0.887	0.768	0.659	0.887	SUBCLONAL	1	TRUE	1	0.28	2		258	530	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922704	44922704	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	77	162	0	ENST00000377967.4:c.1565G>A	p.Gly522Glu	p.G522E	ENST00000377967	NM_021140.2	522	gGa/gAa	16/29	1	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.28	1		162	393	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939951	76939951	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015267-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	110	248	0	ENST00000373344.5:c.797A>T	p.Tyr266Phe	p.Y266F	ENST00000373344	NM_000489.3	266	tAc/tTc	9/35	1	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.28	1		248	602	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	47	354	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.385	0.324	0.453	0.385	0.324	0.453	SUBCLONAL	1	TRUE	1	0.358890140934267	2		354	680	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	98	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.864	0.772	0.962	0.864	0.772	0.962	CLONAL	1	TRUE	1	0.358890140934267	2		215	632	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873756	35873756	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28933100	NA	P-0015271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1036	71	596	0	ENST00000216797.5:c.95G>A	p.Ser32Asn	p.S32N	ENST00000216797	NM_020529.2	32	aGc/aAc	1/6	1	2	FACETS	0.357	0.311	0.408	0.357	0.311	0.408	SUBCLONAL	1	TRUE	1	0.358890140934267	2		596	1107	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207009	1207009	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	63	567	0	ENST00000326873.7:c.97G>T	p.Glu33Ter	p.E33*	ENST00000326873	NM_000455.4	33	Gag/Tag	1/10	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.358890140934267	NA		567	885	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023439	27023448	+	frameshift_variant	Frame_Shift_Del	DEL	CAGCGCTGCA	CAGCGCTGCA	-	novel	NA	P-0015271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	50	571	0	ENST00000324856.7:c.545_554del	p.Ala182GlyfsTer47	p.A182Gfs*47	ENST00000324856	NM_006015.4	182	gCAGCGCTGCAg/gg	1/20	1	2	FACETS	0.332	0.28	0.388	0.332	0.28	0.388	SUBCLONAL	1	TRUE	1	0.358890140934267	2		571	840	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41256258	41256259	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	35	281	0	ENST00000357654.3:c.321dup	p.Ala108CysfsTer6	p.A108Cfs*6	ENST00000357654	NM_007294.3	107	-/T	6/23	1	2	FACETS	0.436	0.357	0.525	0.436	0.357	0.525	SUBCLONAL	1	TRUE	1	0.358890140934267	2		281	447	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225346798	225346798	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	T	novel	NA	P-0015271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	29	236	0	ENST00000264414.4:c.1843-3C>A		p.X615_splice	ENST00000264414	NM_003590.4	615			1	2	FACETS	0.455	0.365	0.557	0.455	0.365	0.557	SUBCLONAL	1	TRUE	1	0.358890140934267	2		236	355	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434139	12434139	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	30	300	0	ENST00000287820.6:c.507G>T	p.Leu169Phe	p.L169F	ENST00000287820	NM_015869.4	169	ttG/ttT	4/7	1	2	FACETS	0.296	0.238	0.363	0.296	0.238	0.363	SUBCLONAL	1	TRUE	1	0.358890140934267	2		300	564	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434148	12434148	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	31	337	0	ENST00000287820.6:c.516C>G	p.Ile172Met	p.I172M	ENST00000287820	NM_015869.4	172	atC/atG	4/7	1	2	FACETS	0.291	0.234	0.355	0.291	0.234	0.355	SUBCLONAL	1	TRUE	1	0.358890140934267	2		337	594	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591142	67591154	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	CAATACTTGATGT	CAATACTTGATGT	-	novel	NA	P-0015271-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	42	237	0	ENST00000274335.5:c.1735_1745+2del		p.X579_splice	ENST00000274335		579		12/15	0.188619488516324	3	FACETS	0.548	0.457	0.649	0.274	0.228	0.325	INDETERMINATE	1	TRUE	1	0.358890140934267	3		237	504	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0015292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	149	282	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.321728028695388	2		282	666	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0015292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	308	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.321728028695388	2	FACETS	0.922	0.876	0.969	1	0.994	1	CLONAL	3	TRUE	0	0.321728028695388	2		458	692	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0015292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	206	390	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	0.321728028695388	3	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	1	0.321728028695388	3		390	647	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158626	26158626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772836222	NA	P-0015292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	58	305	0	ENST00000289316.2:c.229G>A	p.Glu77Lys	p.E77K	ENST00000289316	NM_138720.2	77	Gag/Aag	1/2	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.321728028695388	2		305	291	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892299	9892299	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs796052549	NA	P-0015292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	113	475	0	ENST00000330684.3:c.2191G>A	p.Asp731Asn	p.D731N	ENST00000330684	NM_001134407.1	731	Gat/Aat	11/13	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.321728028695388	2		475	698	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576927	7576927	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs587781702	NA	P-0015292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	176	883	0	ENST00000269305.4:c.920-1G>A		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.321728028695388	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.321728028695388	1		883	687	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426094	49426094	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	158	947	0	ENST00000301067.7:c.12394del	p.His4132ThrfsTer10	p.H4132Tfs*10	ENST00000301067	NM_003482.3	4132	Cac/ac	39/54	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.321728028695388	2		947	829	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858165	152858165	+	synonymous_variant	Silent	SNP	G	G	T	novel	NA	P-0015292-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	283	1224	2	ENST00000406277.2:c.450C>A	p.Leu150=	p.L150=	ENST00000406277	NM_152274.4	150	ctC/ctA	6/7	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	1	0.321728028695388	2		1226	1258	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913529	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	157	597	0	ENST00000311936.3:c.35G>C	p.Gly12Ala	p.G12A	ENST00000311936	NM_004985.3	12	gGt/gCt	2/5	0.138200018966015	4	FACETS	0.905	0.83	0.982	0.905	0.83	0.982	INDETERMINATE	2	FALSE	2	0.291023846550566	4		597	770	SUCCESS
APC	324	MSKCC	GRCh37	5	112175951	112175952	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587783031	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	168	290	0	ENST00000257430.4:c.4666dup	p.Thr1556AsnfsTer3	p.T1556Nfs*3	ENST00000257430	NM_000038.5	1554	gaa/gAaa	16/16	1	2	FACETS	1	0.934	1	1	0.994	1	CLONAL	3	FALSE	1	0.291023846550566	2		290	384	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965666	90965666	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	92	746	0	ENST00000265433.3:c.1651del	p.Arg551GlyfsTer8	p.R551Gfs*8	ENST00000265433	NM_002485.4	551	Agg/gg	11/16	0.291023846550566	5	FACETS	0.776	0.691	0.867			1	SUBCLONAL	2	FALSE	NA	0.291023846550566	5		746	585	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	75	426	0	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	1	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	FALSE	1	0.291023846550566	2		426	479	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968323	2968323	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762770988	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	85	529	3	ENST00000396946.4:c.1663del	p.Arg555GlyfsTer45	p.R555Gfs*45	ENST00000396946	NM_032415.4	555	Cgg/gg	13/25	0.291023846550566	1	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	FALSE	0	0.291023846550566	1		532	477	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242795103	242795104	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs768249210	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	118	908	2	ENST00000334409.5:c.105dup	p.Thr36HisfsTer70	p.T36Hfs*70	ENST00000334409	NM_005018.2	35	-/C	2/5	0.291023846550566	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	0	0.291023846550566	1		910	538	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936092	178936092	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913274	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	35	627	0	ENST00000263967.3:c.1634A>G	p.Glu545Gly	p.E545G	ENST00000263967	NM_006218.2	545	gAg/gGg	10/21	1	2	FACETS	0.503	0.412	0.606	0.503	0.412	0.606	SUBCLONAL	1	FALSE	1	0.291023846550566	2		627	478	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991758	72991758	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	86	244	2	ENST00000268489.5:c.2287del	p.Glu763SerfsTer61	p.E763Sfs*61	ENST00000268489	NM_006885.3	763	Gag/ag	2/10	1	2	FACETS	1	0.911	1	1	0.986	1	CLONAL	2	FALSE	1	0.291023846550566	2		246	290	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17119708	17119709	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs80338682	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	139	445	9	ENST00000285071.4:c.1285dup	p.His429ProfsTer27	p.H429Pfs*27	ENST00000285071	NM_144997.5	429	cac/cCac	11/14	1	2	FACETS	0.836	0.77	0.903	1	0.992	1	CLONAL	3	FALSE	1	0.291023846550566	2		454	381	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687471	37687472	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs760014508	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	59	385	2	ENST00000447079.4:c.4382dup	p.Thr1463AsnfsTer50	p.T1463Nfs*50	ENST00000447079	NM_015083.1	1459	tgg/tGgg	14/14	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	1	0.291023846550566	2		387	360	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905055	50905055	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	39	520	0	ENST00000440232.2:c.342del	p.Pro116HisfsTer53	p.P116Hfs*53	ENST00000440232	NM_002691.3	113	Ggg/gg	4/27	0.288955267588527	0	FACETS	0.551	0.458	0.654			1	SUBCLONAL	1	FALSE	0	0.291023846550566	0		520	345	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90993676	90993676	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	107	540	0	ENST00000265433.3:c.247del	p.Met83CysfsTer9	p.M83Cfs*9	ENST00000265433	NM_002485.4	83	Atg/tg	3/16	0.291023846550566	5	FACETS	1	0.961	1			1	CLONAL	1	FALSE	NA	0.291023846550566	5		540	915	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444378	49444378	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	143	732	1	ENST00000301067.7:c.2993del	p.Pro998LeufsTer2	p.P998Lfs*2	ENST00000301067	NM_003482.3	998	cCt/ct	11/54	0.138200018966015	4	FACETS	1	0.925	1	1	0.925	1	INDETERMINATE	2	FALSE	2	0.291023846550566	4		733	627	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806569	1806569	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs182935140	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	44	670	0	ENST00000260795.2:c.1285G>A	p.Ala429Thr	p.A429T	ENST00000260795		429	Gcg/Acg	9/17	0.291023846550566	1	FACETS	0.568	0.476	0.669	0.568	0.476	0.669	SUBCLONAL	1	FALSE	0	0.291023846550566	1		670	455	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630704	90630704	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs118101777	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	152	656	0	ENST00000330062.3:c.782G>A	p.Arg261His	p.R261H	ENST00000330062	NM_002168.2	261	cGt/cAt	6/11	0.12572196539848	4	FACETS	0.95	0.87	1	0.95	0.87	1	INDETERMINATE	2	FALSE	2	0.291023846550566	4		656	710	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59760684	59760685	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	120	586	0	ENST00000259008.2:c.3722dup	p.Asn1241LysfsTer2	p.N1241Kfs*2	ENST00000259008	NM_032043.2	1241	aat/aaAt	20/20	1	2	FACETS	0.755	0.685	0.829	1	0.985	1	SUBCLONAL	2	FALSE	1	0.291023846550566	2		586	546	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119909	70119910	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	168	670	0	ENST00000245479.2:c.916dup	p.Val306GlyfsTer272	p.V306Gfs*272	ENST00000245479	NM_000346.3	304	ccg/ccGg	3/3	1	2	FACETS	0.918	0.847	0.991	1	0.992	1	CLONAL	2	FALSE	1	0.291023846550566	2		670	629	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5207953	5207953	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	125	834	1	ENST00000357368.4:c.5758C>T	p.Pro1920Ser	p.P1920S	ENST00000357368	NM_002850.3	1920	Ccg/Tcg	37/38	1	2	FACETS	0.837	0.762	0.916	1	0.988	1	CLONAL	2	FALSE	1	0.291023846550566	2		835	513	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023535	27023535	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	198	861	3	ENST00000324856.7:c.641C>A	p.Ser214Tyr	p.S214Y	ENST00000324856	NM_006015.4	214	tCc/tAc	1/20	0.0518383438204191	4	FACETS	0.994	0.921	1	0.994	0.921	1	INDETERMINATE	2	FALSE	2	0.291023846550566	4		864	884	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739048	46739049	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GT	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	89	496	0	ENST00000371975.4:c.1403_1404dup	p.Glu469TrpfsTer40	p.E469Wfs*40	ENST00000371975	NM_003579.3	466	aag/aaGTg	13/18	0.0518383438204191	4	FACETS	0.925	0.824	1	0.925	0.824	1	INDETERMINATE	2	FALSE	2	0.291023846550566	4		496	427	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243727081	243727081	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	123	655	0	ENST00000263826.5:c.889A>G	p.Ile297Val	p.I297V	ENST00000263826	NM_005465.4	297	Atc/Gtc	9/13	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.291023846550566	2		655	621	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852536	63852536	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	93	500	0	ENST00000279873.7:c.3314A>G	p.Tyr1105Cys	p.Y1105C	ENST00000279873	NM_032199.2	1105	tAc/tGc	10/10	0.291023846550566	6	FACETS	1	0.93	1			1	CLONAL	2	FALSE	NA	0.291023846550566	6		500	479	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944549	71944549	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	110	546	0	ENST00000298229.2:c.2105T>C	p.Ile702Thr	p.I702T	ENST00000298229	NM_001567.3	702	aTc/aCc	18/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.291023846550566	2		546	524	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499574	18499574	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	86	471	0	ENST00000266497.5:c.1430-1G>C		p.X477_splice	ENST00000266497		477			NA	2	FACETS	1	0.979	1			1	INDETERMINATE	1	FALSE	NA	0.291023846550566	2		471	398	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656344	18656344	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	108	544	1	ENST00000266497.5:c.3023A>G	p.Tyr1008Cys	p.Y1008C	ENST00000266497		1008	tAt/tGt	21/31	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	FALSE	NA	0.291023846550566	2		545	506	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120832	115120838	+	frameshift_variant	Frame_Shift_Del	DEL	GCCCGGC	GCCCGGC	CACGGG	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	81	460	2	ENST00000257566.3:c.168_174delinsCCCGTG	p.Gly58TrpfsTer30	p.G58Wfs*30	ENST00000257566	NM_016569.3	56	ctGCCGGGC/ctCCCGTG	1/8	0.291023846550566	1	FACETS	0.871	0.777	0.969	1	0.983	1	CLONAL	2	FALSE	0	0.291023846550566	1		462	273	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911148	32911148	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	130	597	0	ENST00000380152.3:c.2656A>G	p.Asn886Asp	p.N886D	ENST00000380152		886	Aat/Gat	11/27	1	2	FACETS	0.841	0.767	0.919	1	0.988	1	CLONAL	2	FALSE	1	0.291023846550566	2		597	531	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913836	32913837	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs80359507	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	89	612	3	ENST00000380152.3:c.5351dup	p.Asn1784LysfsTer3	p.N1784Kfs*3	ENST00000380152		1782	caa/cAaa	11/27	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	FALSE	1	0.291023846550566	2		615	572	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972843	32972843	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs374275215	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	91	563	0	ENST00000380152.3:c.10193A>G	p.Gln3398Arg	p.Q3398R	ENST00000380152		3398	cAg/cGg	27/27	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	1	0.291023846550566	2		563	525	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103520549	103520549	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121434576	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	96	480	2	ENST00000355739.4:c.2620G>A	p.Ala874Thr	p.A874T	ENST00000355739	NM_000123.3	874	Gcc/Acc	12/15	1	2	FACETS	0.892	0.801	0.986	1	0.986	1	CLONAL	2	FALSE	1	0.291023846550566	2		482	370	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436171	110436171	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs558236298	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	133	897	2	ENST00000375856.3:c.2230C>T	p.Arg744Cys	p.R744C	ENST00000375856	NM_003749.2	744	Cgc/Tgc	1/2	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.291023846550566	2		899	671	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3929877	3929878	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	144	733	0	ENST00000262367.5:c.40dup	p.Arg14LysfsTer13	p.R14Kfs*13	ENST00000262367	NM_004380.2	14	aga/aAga	1/31	1	2	FACETS	0.867	0.794	0.942	1	0.99	1	CLONAL	2	FALSE	1	0.291023846550566	2		733	571	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049852	16049853	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	81	318	0	ENST00000268712.3:c.919dup	p.Ile307AsnfsTer6	p.I307Nfs*6	ENST00000268712	NM_006311.3	307	atc/aAtc	10/46	1	2	FACETS	0.823	0.732	0.92	1	0.981	1	CLONAL	2	FALSE	1	0.291023846550566	2		318	338	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687298	37687298	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	136	594	0	ENST00000447079.4:c.4202A>G	p.Gln1401Arg	p.Q1401R	ENST00000447079	NM_015083.1	1401	cAg/cGg	14/14	1	2	FACETS	0.757	0.691	0.827	1	0.987	1	SUBCLONAL	2	FALSE	1	0.291023846550566	2		594	617	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740438	58740439	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs758630849	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	153	672	0	ENST00000305921.3:c.1349dup	p.Leu450PhefsTer6	p.L450Ffs*6	ENST00000305921	NM_003620.3	448	aat/aaTt	6/6	1	2	FACETS	0.899	0.826	0.974	1	0.991	1	CLONAL	2	FALSE	1	0.291023846550566	2		672	585	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36229220	36229220	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	110	650	1	ENST00000222270.7:c.7910A>T	p.Asp2637Val	p.D2637V	ENST00000222270	NM_014727.1	2637	gAt/gTt	37/37	0.291023846550566	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	FALSE	0	0.291023846550566	1		651	583	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794553	42794553	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	125	847	0	ENST00000575354.2:c.1633T>C	p.Ser545Pro	p.S545P	ENST00000575354	NM_015125.3	545	Tcg/Ccg	10/20	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.291023846550566	2		847	643	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42798379	42798379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749470261	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	137	769	1	ENST00000575354.2:c.4250G>A	p.Arg1417His	p.R1417H	ENST00000575354	NM_015125.3	1417	cGc/cAc	18/20	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.291023846550566	2		770	657	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46609673	46609673	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	99	693	0	ENST00000263734.3:c.2402del	p.Pro801HisfsTer39	p.P801Hfs*39	ENST00000263734	NM_001430.4	799	ttC/tt	15/16	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.291023846550566	2		693	541	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198262832	198262832	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	82	360	0	ENST00000335508.6:c.3143A>G	p.Glu1048Gly	p.E1048G	ENST00000335508	NM_012433.2	1048	gAa/gGa	22/25	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.291023846550566	2		360	391	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57470742	57470742	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	G	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	84	362	0	ENST00000371085.3:c.212+3A>G		p.X71_splice	ENST00000371085	NM_000516.4	71			0.291023846550566	1	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	FALSE	0	0.291023846550566	1		362	334	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146717	185146717	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs755931976	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	150	632	0	ENST00000265026.3:c.348A>G	p.Ile116Met	p.I116M	ENST00000265026	NM_004721.4	116	atA/atG	2/14	1	2	FACETS	0.772	0.707	0.839	1	0.988	1	SUBCLONAL	2	FALSE	1	0.291023846550566	2		632	668	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38946656	38946657	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	A	rs1458580558	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	71	379	0	ENST00000357387.3:c.4315-3dup		p.X1439_splice	ENST00000357387	NM_152756.3	1439			1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.291023846550566	2		379	342	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970914	79970915	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587776701	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	264	825	11	ENST00000265081.6:c.1148dup	p.Asn385GlnfsTer19	p.N385Qfs*19	ENST00000265081	NM_002439.4	380	-/A	7/24	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	FALSE	1	0.291023846550566	2		836	749	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633806	86633806	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	65	325	0	ENST00000274376.6:c.915T>G	p.Asp305Glu	p.D305E	ENST00000274376	NM_002890.2	305	gaT/gaG	5/25	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	FALSE	1	0.291023846550566	2		325	366	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86633814	86633814	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	74	361	0	ENST00000274376.6:c.923T>A	p.Ile308Asn	p.I308N	ENST00000274376	NM_002890.2	308	aTt/aAt	5/25	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	FALSE	1	0.291023846550566	2		361	432	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86686673	86686673	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	115	521	0	ENST00000274376.6:c.3117G>C	p.Gln1039His	p.Q1039H	ENST00000274376	NM_002890.2	1039	caG/caC	25/25	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.291023846550566	2		521	623	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519641	176519641	+	splice_region_variant,intron_variant	Splice_Region	DEL	C	C	-	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	33	619	0	ENST00000292408.4:c.919-3del		p.X307_splice	ENST00000292408	NM_213647.1	307			1	2	FACETS	0.657	0.536	0.793	0.657	0.536	0.793	SUBCLONAL	1	FALSE	1	0.291023846550566	2		619	345	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948469	31948469	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	84	495	0	ENST00000375333.2:c.952T>C	p.Tyr318His	p.Y318H	ENST00000375333	NM_032454.1	318	Tac/Cac	7/8	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	FALSE	1	0.291023846550566	2		495	430	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93964414	93964414	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	102	613	0	ENST00000369303.4:c.2483A>G	p.Glu828Gly	p.E828G	ENST00000369303	NM_004440.3	828	gAa/gGa	14/17	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.291023846550566	2		613	562	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397808	116397808	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	123	696	0	ENST00000397752.3:c.2086del	p.Thr696HisfsTer4	p.T696Hfs*4	ENST00000397752	NM_000245.2	694	ggA/gg	8/21	0.12572196539848	4	FACETS	0.822	0.744	0.903	0.822	0.744	0.903	INDETERMINATE	2	FALSE	2	0.291023846550566	4		696	664	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151174416	151174416	+	splice_region_variant,intron_variant	Splice_Region	SNP	T	T	A	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	111	610	0	ENST00000262187.5:c.275+3A>T		p.X92_splice	ENST00000262187	NM_005614.3	92			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	FALSE	1	0.291023846550566	2		610	587	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90958386	90958387	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	87	408	0	ENST00000265433.3:c.2051dup	p.Asn684LysfsTer58	p.N684Kfs*58	ENST00000265433	NM_002485.4	684	aat/aaAt	13/16	0.291023846550566	5	FACETS	1	0.978	1			1	CLONAL	1	FALSE	NA	0.291023846550566	5		408	585	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929061	44929061	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015322-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	117	319	0	ENST00000377967.4:c.2161T>C	p.Ser721Pro	p.S721P	ENST00000377967	NM_021140.2	721	Tca/Cca	17/29	1	1	FACETS	1	0.978	1	1	0.991	1	CLONAL	2	FALSE	0	0.291023846550566	1		319	283	SUCCESS
APC	324	MSKCC	GRCh37	5	112175303	112175303	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121913327	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	203	340	0	ENST00000257430.4:c.4012C>T	p.Gln1338Ter	p.Q1338*	ENST00000257430	NM_000038.5	1338	Cag/Tag	16/16	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.63187812659068	2		340	515	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106648	27106648	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1553153748	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	426	684	2	ENST00000324856.7:c.6259G>A	p.Gly2087Arg	p.G2087R	ENST00000324856	NM_006015.4	2087	Gga/Aga	20/20	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	FALSE	1	0.63187812659068	2		686	1027	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138413637	138413637	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780387670	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	309	579	0	ENST00000289153.2:c.1883G>A	p.Arg628Gln	p.R628Q	ENST00000289153	NM_006219.2	628	cGa/cAa	12/22	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.63187812659068	2		579	858	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325832	65325833	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs755650243	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	91	420	2	ENST00000342505.4:c.1289dup	p.Leu431ValfsTer22	p.L431Vfs*22	ENST00000342505	NM_002227.2	430	ccg/ccCg	9/25	1	2	FACETS	0.336	0.298	0.378	0.336	0.298	0.378	SUBCLONAL	1	FALSE	1	0.63187812659068	2		422	856	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15308383	15308383	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	690	797	4	ENST00000263388.2:c.125del	p.Pro42LeufsTer194	p.P42Lfs*194	ENST00000263388	NM_000435.2	42	cCt/ct	2/33	0.63187812659068	3	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	FALSE	1	0.63187812659068	3		801	1393	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132513	11132513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238758086	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	420	774	3	ENST00000358026.2:c.2729C>T	p.Thr910Met	p.T910M	ENST00000358026	NM_001128849.1	910	aCg/aTg	19/36	0.63187812659068	3	FACETS	1	0.994	1			1	CLONAL	1	FALSE	NA	0.63187812659068	3		777	1351	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088682	27088682	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	468	958	0	ENST00000324856.7:c.2296del	p.Gln766SerfsTer67	p.Q766Sfs*67	ENST00000324856	NM_006015.4	764	tCc/tc	7/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.63187812659068	2		958	1346	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5126730	5126730	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1437629509	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	304	613	0	ENST00000381652.3:c.3338G>A	p.Arg1113His	p.R1113H	ENST00000381652	NM_004972.3	1113	cGc/cAc	25/25	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.63187812659068	2		613	828	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176675269	176675269	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	215	304	1	ENST00000439151.2:c.4591del	p.Met1531CysfsTer43	p.M1531Cfs*43	ENST00000439151	NM_022455.4	1529	Aaa/aa	11/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	FALSE	1	0.63187812659068	2		305	639	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157511329	157511329	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	230	428	0	ENST00000346085.5:c.3851del	p.Gly1284GlufsTer2	p.G1284Efs*2	ENST00000346085	NM_020732.3	1283	Ggg/gg	15/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.63187812659068	2		428	643	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52643768	52643768	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	408	678	1	ENST00000394830.3:c.2128C>T	p.Arg710Ter	p.R710*	ENST00000394830	NM_018313.4	710	Cga/Tga	17/30	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	FALSE	1	0.63187812659068	2		679	1053	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52712580	52712580	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	371	668	1	ENST00000394830.3:c.172C>T	p.Arg58Ter	p.R58*	ENST00000394830	NM_018313.4	58	Cga/Tga	3/30	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.63187812659068	2		669	1100	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40370236	40370236	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs761761205	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	215	832	15	ENST00000293328.3:c.1102del	p.Gln368ArgfsTer2	p.Q368Rfs*2	ENST00000293328	NM_012448.3	368	Cag/ag	9/19	1	2	FACETS	0.742	0.69	0.796	0.742	0.69	0.796	SUBCLONAL	1	FALSE	1	0.63187812659068	2		847	917	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2210837	2210837	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753115153	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	545	473	0	ENST00000398665.3:c.1334C>T	p.Ala445Val	p.A445V	ENST00000398665	NM_032482.2	445	gCg/gTg	14/28	0.63187812659068	3	FACETS	1	0.996	1	1	0.996	1	CLONAL	2	FALSE	1	0.63187812659068	3		473	939	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115600	108115600	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs772821016	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	387	681	0	ENST00000278616.4:c.748C>T	p.Arg250Ter	p.R250*	ENST00000278616	NM_000051.3	250	Cga/Tga	7/63	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	FALSE	1	0.63187812659068	2		681	961	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306638	41306638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	347	772	2	ENST00000373198.4:c.1021G>A	p.Asp341Asn	p.D341N	ENST00000373198	NM_133170.3	341	Gac/Aac	7/32	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.63187812659068	2		774	946	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390736	139390736	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	388	798	0	ENST00000277541.6:c.7455del	p.Ser2486ArgfsTer103	p.S2486Rfs*103	ENST00000277541	NM_017617.3	2485	ccC/cc	34/34	1	2	FACETS	0.993	0.944	1	0.993	0.944	1	CLONAL	1	FALSE	1	0.63187812659068	2		798	1237	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729603	41729603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	280	538	1	ENST00000242208.4:c.926G>A	p.Arg309Gln	p.R309Q	ENST00000242208	NM_002192.2	309	cGg/cAg	3/3	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.63187812659068	2		539	748	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49723126	49723128	+	inframe_deletion	In_Frame_Del	DEL	CTC	CTC	-	rs751306787	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	395	702	0	ENST00000449682.2:c.1288_1290del	p.Glu430del	p.E430del	ENST00000449682	NM_020998.3	430	GAG/-	11/18	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	FALSE	1	0.63187812659068	2		702	896	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71027087	71027087	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	338	643	1	ENST00000318789.4:c.1240del	p.Leu414Ter	p.L414*	ENST00000318789	NM_032682.5	414	Ctg/tg	15/21	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	FALSE	1	0.63187812659068	2		644	1000	SUCCESS
ATR	545	MSKCC	GRCh37	3	142232477	142232477	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs754602382	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	279	417	0	ENST00000350721.4:c.4507C>T	p.Arg1503Ter	p.R1503*	ENST00000350721	NM_001184.3	1503	Cga/Tga	26/47	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	FALSE	1	0.63187812659068	2		417	762	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438211	49438211	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	428	435	0	ENST00000301067.7:c.5058del	p.Lys1686AsnfsTer36	p.K1686Nfs*36	ENST00000301067	NM_003482.3	1686	aaA/aa	20/54	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	1	0.63187812659068	2		435	1155	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143191881	143191881	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs184155869	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	303	641	1	ENST00000262992.4:c.550G>A	p.Val184Met	p.V184M	ENST00000262992	NM_001101669.1	184	Gtg/Atg	8/24	1	2	FACETS	0.972	0.917	1	0.972	0.917	1	CLONAL	1	FALSE	1	0.63187812659068	2		642	987	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	527	519	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.63187812659068	2		524	1496	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2493111	2493111	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	198	399	0	ENST00000355716.4:c.552-1G>A		p.X184_splice	ENST00000355716	NM_003820.2	184			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	FALSE	1	0.63187812659068	2		399	538	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599234	28599234	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	428	801	2	ENST00000253063.3:c.685del	p.Gln229ArgfsTer18	p.Q229Rfs*18	ENST00000253063	NM_031459.4	227	gCc/gc	5/10	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	1	0.63187812659068	2		803	1148	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461100	120461100	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs312262797	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	283	648	0	ENST00000256646.2:c.5858G>A	p.Arg1953His	p.R1953H	ENST00000256646	NM_024408.3	1953	cGc/cAc	32/34	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	FALSE	1	0.63187812659068	2		648	848	SUCCESS
FH	2271	MSKCC	GRCh37	1	241671943	241671943	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913123	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	120	747	1	ENST00000366560.3:c.698G>A	p.Arg233His	p.R233H	ENST00000366560	NM_000143.3	233	cGt/cAt	5/10	1	2	FACETS	0.373	0.336	0.412	0.373	0.336	0.412	SUBCLONAL	1	FALSE	1	0.63187812659068	2		748	1019	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606856	43606856	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs9282834	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1135	376	876	5	ENST00000355710.3:c.1465G>A	p.Asp489Asn	p.D489N	ENST00000355710	NM_020975.4	489	Gac/Aac	7/20	0.63187812659068	3	FACETS	1	0.971	1	0.518	0.491	0.546	CLONAL	1	FALSE	1	0.63187812659068	3		881	1511	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941430	71941430	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755089930	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1093	132	870	1	ENST00000298229.2:c.1115G>A	p.Arg372His	p.R372H	ENST00000298229	NM_001567.3	372	cGt/cAt	10/28	1	2	FACETS	0.341	0.308	0.376	0.341	0.308	0.376	SUBCLONAL	1	FALSE	1	0.63187812659068	2		871	1225	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434811	49434811	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371402071	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	568	947	3	ENST00000301067.7:c.6742C>T	p.Arg2248Cys	p.R2248C	ENST00000301067	NM_003482.3	2248	Cgc/Tgc	31/54	1	2	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	FALSE	1	0.63187812659068	2		950	1448	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435706	49435706	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	349	668	0	ENST00000301067.7:c.6177del	p.Tyr2060ThrfsTer34	p.Y2060Tfs*34	ENST00000301067	NM_003482.3	2059	ccC/cc	29/54	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.63187812659068	2		668	945	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49436109	49436109	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755573725	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	135	303	1	ENST00000301067.7:c.5872C>T	p.Arg1958Cys	p.R1958C	ENST00000301067	NM_003482.3	1958	Cgc/Tgc	28/54	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	FALSE	1	0.63187812659068	2		304	381	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445673	49445673	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377761041	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	984	558	1126	3	ENST00000301067.7:c.1793G>A	p.Arg598His	p.R598H	ENST00000301067	NM_003482.3	598	cGt/cAt	10/54	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	FALSE	1	0.63187812659068	2		1129	1542	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50492742	50492742	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	341	636	0	ENST00000394963.4:c.1507C>T	p.Arg503Ter	p.R503*	ENST00000394963	NM_003076.4	503	Cga/Tga	13/13	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.63187812659068	2		636	970	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864195	57864195	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371089900	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	264	494	0	ENST00000228682.2:c.1672C>T	p.Arg558Cys	p.R558C	ENST00000228682	NM_005269.2	558	Cgc/Tgc	12/12	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.63187812659068	2		494	782	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869534	102869534	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775312813	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	315	687	1	ENST00000307046.8:c.107C>T	p.Ala36Val	p.A36V	ENST00000307046	NM_001111285.1	36	gCg/gTg	2/4	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.63187812659068	2		688	864	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123889576	123889576	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374294423	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	182	262	2	ENST00000330479.4:c.803C>T	p.Thr268Met	p.T268M	ENST00000330479	NM_020382.3	268	aCg/aTg	7/9	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.63187812659068	2		264	422	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99472873	99472873	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1320984804	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	310	640	0	ENST00000268035.6:c.2869G>A	p.Val957Ile	p.V957I	ENST00000268035	NM_000875.3	957	Gtc/Atc	14/21	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.63187812659068	2		640	832	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2125838	2125838	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759837836	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	448	940	3	ENST00000219476.3:c.2584G>A	p.Ala862Thr	p.A862T	ENST00000219476	NM_000548.3	862	Gcg/Acg	23/42	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.63187812659068	2		943	1238	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2127694	2127694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660733	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	307	588	2	ENST00000219476.3:c.2933G>A	p.Arg978His	p.R978H	ENST00000219476	NM_000548.3	978	cGc/cAc	26/42	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.63187812659068	2		590	854	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779773	3779773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	354	751	0	ENST00000262367.5:c.5275C>T	p.Pro1759Ser	p.P1759S	ENST00000262367	NM_004380.2	1759	Cca/Tca	31/31	1	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	FALSE	1	0.63187812659068	2		751	929	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3842075	3842075	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1302427305	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	289	511	0	ENST00000262367.5:c.1237C>T	p.Arg413Ter	p.R413*	ENST00000262367	NM_004380.2	413	Cga/Tga	5/31	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	FALSE	1	0.63187812659068	2		511	839	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622383	1622383	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1435	109	881	2	ENST00000344749.5:c.581G>A	p.Gly194Asp	p.G194D	ENST00000344749	NM_001136139.2	194	gGc/gAc	9/19	0.63187812659068	3	FACETS	0.294	0.263	0.328	0.147	0.131	0.164	SUBCLONAL	1	FALSE	1	0.63187812659068	3		883	1544	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11019828	11019828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	833	739	0	ENST00000327064.4:c.503G>A	p.Arg168Gln	p.R168Q	ENST00000327064	NM_199141.1	168	cGg/cAg	4/16	0.63187812659068	3	FACETS	1	0.996	1			1	CLONAL	2	FALSE	NA	0.63187812659068	3		739	1523	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272527	15272528	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	G	rs763699925	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	84	570	0	ENST00000263388.2:c.5914-3dup		p.X1972_splice	ENST00000263388	NM_000435.2	1972			0.63187812659068	3	FACETS	0.394	0.347	0.444	0.197	0.173	0.222	SUBCLONAL	1	FALSE	1	0.63187812659068	3		570	889	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39233665	39233665	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	61	490	0	ENST00000402219.2:c.2679A>G	p.Ile893Met	p.I893M	ENST00000402219	NM_005633.3	893	atA/atG	17/23	1	2	FACETS	0.257	0.221	0.296	0.257	0.221	0.296	SUBCLONAL	1	FALSE	1	0.63187812659068	2		490	752	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705600	47705606	+	frameshift_variant	Frame_Shift_Del	DEL	ACATGTC	ACATGTC	-	novel	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	281	526	0	ENST00000233146.2:c.2403_2409del	p.His801GlnfsTer9	p.H801Qfs*9	ENST00000233146	NM_000251.2	800	ctACATGTC/ct	14/16	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.63187812659068	2		526	823	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026524	48026524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369456858	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	311	512	0	ENST00000234420.5:c.1402C>T	p.Arg468Cys	p.R468C	ENST00000234420	NM_000179.2	468	Cgt/Tgt	4/10	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.63187812659068	2		512	843	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46279991	46279991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376614401	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	144	910	1	ENST00000371998.3:c.3917C>T	p.Pro1306Leu	p.P1306L	ENST00000371998		1306	cCg/cTg	20/23	1	2	FACETS	0.353	0.321	0.387	0.353	0.321	0.387	SUBCLONAL	1	FALSE	1	0.63187812659068	2		911	1292	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620706	52620707	+	splice_region_variant,intron_variant	Splice_Region	INS	-	-	G	rs1236693676	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	99	299	0	ENST00000394830.3:c.3049-3dup		p.X1017_splice	ENST00000394830	NM_018313.4	1017			1	2	FACETS	0.661	0.593	0.733	0.661	0.593	0.733	SUBCLONAL	1	FALSE	1	0.63187812659068	2		299	474	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71021784	71021784	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1553663084	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	257	427	0	ENST00000318789.4:c.1574G>A	p.Arg525Gln	p.R525Q	ENST00000318789	NM_032682.5	525	cGa/cAa	18/21	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	FALSE	1	0.63187812659068	2		427	693	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73113216	73113216	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	44	126	0	ENST00000356692.5:c.561del	p.Met188Ter	p.M188*	ENST00000356692		186	gCc/gc	7/9	1	2	FACETS	0.765	0.651	0.888	0.765	0.651	0.888	SUBCLONAL	1	FALSE	1	0.63187812659068	2		126	182	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260150	149260150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761556137	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	278	565	0	ENST00000360632.3:c.743G>A	p.Arg248Gln	p.R248Q	ENST00000360632	NM_015472.4	248	cGa/cAa	4/7	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.63187812659068	2		565	732	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99806134	99806134	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	112	161	0	ENST00000280892.6:c.538G>T	p.Gly180Cys	p.G180C	ENST00000280892	NM_001130678.1	180	Ggt/Tgt	6/7	1	2	FACETS	0.813	0.75	0.876	1	0.989	1	CLONAL	2	FALSE	1	0.63187812659068	2		161	218	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673702	176673702	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	301	497	1	ENST00000439151.2:c.4402C>T	p.Pro1468Ser	p.P1468S	ENST00000439151	NM_022455.4	1468	Cca/Tca	10/23	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	FALSE	1	0.63187812659068	2		498	813	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176673711	176673711	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs570278338	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	321	517	0	ENST00000439151.2:c.4411C>T	p.Arg1471Ter	p.R1471*	ENST00000439151	NM_022455.4	1471	Cga/Tga	10/23	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	FALSE	1	0.63187812659068	2		517	855	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553441	106553441	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746535819	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	180	320	0	ENST00000369096.4:c.1406C>T	p.Ser469Leu	p.S469L	ENST00000369096	NM_001198.3	469	tCg/tTg	5/7	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.63187812659068	2		320	497	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100172	157100172	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1235492881	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	109	161	0	ENST00000346085.5:c.1114del	p.Arg372GlyfsTer7	p.R372Gfs*7	ENST00000346085	NM_020732.3	370	tCc/tc	1/20	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	FALSE	1	0.63187812659068	2		161	271	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851508	151851508	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1005725533	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	231	475	2	ENST00000262189.6:c.11983C>T	p.Arg3995Ter	p.R3995*	ENST00000262189	NM_170606.2	3995	Cga/Tga	47/59	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.63187812659068	2		477	626	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050833	5050833	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	383	639	0	ENST00000381652.3:c.614+2T>C		p.X205_splice	ENST00000381652	NM_004972.3	205			1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	FALSE	1	0.63187812659068	2		639	967	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8465603	8465603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	372	735	0	ENST00000356435.5:c.3577G>A	p.Ala1193Thr	p.A1193T	ENST00000356435		1193	Gcc/Acc	21/35	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	FALSE	1	0.63187812659068	2		735	995	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250034	110250034	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769135101	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	258	609	0	ENST00000374672.4:c.641C>T	p.Pro214Leu	p.P214L	ENST00000374672	NM_004235.4	214	cCg/cTg	3/5	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	FALSE	1	0.63187812659068	2		609	763	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127911968	127911968	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768855518	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	318	541	0	ENST00000373547.4:c.902C>T	p.Thr301Met	p.T301M	ENST00000373547	NM_002721.4	301	aCg/aTg	7/7	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	FALSE	1	0.63187812659068	2		541	901	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652464	48652464	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	470	458	0	ENST00000376670.3:c.1135C>A	p.Leu379Ile	p.L379I	ENST00000376670	NM_002049.3	379	Ctc/Atc	6/6	1	1	FACETS	0.806	0.783	0.829	1	0.997	1	CLONAL	2	FALSE	0	0.63187812659068	1		458	631	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223340	53223340	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781964479	NA	P-0015344-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	444	362	0	ENST00000375401.3:c.4019G>A	p.Ser1340Asn	p.S1340N	ENST00000375401	NM_004187.3	1340	aGt/aAt	23/26	1	1	FACETS	0.851	0.828	0.873	1	0.997	1	CLONAL	2	FALSE	0	0.63187812659068	1		362	565	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	62	282	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.802	0.71	0.897			1	INDETERMINATE	2	TRUE	NA	0.501761843368094	2		282	154	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	204	351	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	NA	2	FACETS	1	0.991	1			1	INDETERMINATE	1	TRUE	NA	0.501761843368094	2		351	571	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971177	21971177	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913382	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	112	298	0	ENST00000304494.5:c.181G>T	p.Glu61Ter	p.E61*	ENST00000304494	NM_000077.4	61	Gag/Tag	2/3	0.464440993366587	5	FACETS	1	0.968	1			1	CLONAL	2	TRUE	NA	0.501761843368094	5		298	342	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032038	10032038	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	114	541	0	ENST00000330684.3:c.785C>T	p.Ser262Phe	p.S262F	ENST00000330684	NM_001134407.1	262	tCt/tTt	3/13	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.501761843368094	NA		541	346	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101867538	101867546	+	inframe_deletion	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs11466445	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	11	24	0	ENST00000374994.4:c.70_78del	p.Ala24_Ala26del	p.A24_A26del	ENST00000374994	NM_004612.2	17	ctGGCGGCGGCg/ctg	1/9	0.17692602848849	4	FACETS	1	0.789	1	1	0.789	1	INDETERMINATE	2	TRUE	2	0.501761843368094	4		24	30	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295253	1295253	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1232074117	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	126	35	279	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.867	0.72	1			1	INDETERMINATE	1	TRUE	NA	0.501761843368094	2		279	161	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001438	29001438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1473309404	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	90	256	0	ENST00000282397.4:c.1294G>A	p.Glu432Lys	p.E432K	ENST00000282397	NM_002019.4	432	Gaa/Aaa	10/30	0.329578010687463	4	FACETS	0.804	0.72	0.892	0.804	0.72	0.892	CLONAL	2	TRUE	2	0.501761843368094	4		256	335	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974715	21974732	+	inframe_deletion	In_Frame_Del	DEL	GCAGCGCCCCCGCCTCCA	GCAGCGCCCCCGCCTCCA	-	novel	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	73	347	0	ENST00000304494.5:c.95_112del	p.Leu32_Leu37del	p.L32_L37del	ENST00000304494	NM_000077.4	32	cTGGAGGCGGGGGCGCTGCcc/ccc	1/3	0.464440993366587	5	FACETS	0.861	0.761	0.968			1	CLONAL	2	TRUE	NA	0.501761843368094	5		347	296	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11174420	11174420	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587777900	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	226	578	0	ENST00000361445.4:c.7255G>A	p.Glu2419Lys	p.E2419K	ENST00000361445	NM_004958.3	2419	Gaa/Aaa	53/58	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	2	TRUE	NA	0.501761843368094	2		578	433	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151876977	151876977	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	50	369	0	ENST00000262189.6:c.7384C>T	p.Gln2462Ter	p.Q2462*	ENST00000262189	NM_170606.2	2462	Cag/Tag	37/59	0.281828497672418	4	FACETS	0.777	0.662	0.904	0.389	0.331	0.452	INDETERMINATE	1	TRUE	2	0.501761843368094	4		369	385	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319902	8319902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	132	354	0	ENST00000356435.5:c.5599G>A	p.Glu1867Lys	p.E1867K	ENST00000356435		1867	Gaa/Aaa	34/35	0.196026669406549	5	FACETS	1	0.95	1			1	INDETERMINATE	2	TRUE	NA	0.501761843368094	5		354	438	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405491	70405491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	108	538	0	ENST00000373644.4:c.3005C>T	p.Ser1002Leu	p.S1002L	ENST00000373644	NM_030625.2	1002	tCa/tTa	4/12	0.237497320317577	4	FACETS	1	0.966	1	0.585	0.526	0.646	INDETERMINATE	1	TRUE	2	0.501761843368094	4		538	553	SUCCESS
ATM	472	MSKCC	GRCh37	11	108155094	108155094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	148	445	0	ENST00000278616.4:c.3887C>T	p.Pro1296Leu	p.P1296L	ENST00000278616	NM_000051.3	1296	cCt/cTt	26/63	0.237497320317577	4	FACETS	0.877	0.806	0.95	0.877	0.806	0.95	INDETERMINATE	2	TRUE	2	0.501761843368094	4		445	505	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210860	133210861	+	missense_variant	Missense_Mutation	DNP	CA	CA	AT	novel	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	113	526	0	ENST00000320574.5:c.5915_5916delinsAT	p.Val1972Asp	p.V1972D	ENST00000320574	NM_006231.2	1972	gTG/gAT	43/49	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.501761843368094	2		526	338	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95582133	95582133	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752424727	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	136	289	0	ENST00000393063.1:c.1778C>T	p.Ser593Leu	p.S593L	ENST00000393063	NM_030621.3	593	tCg/tTg	12/28	0.329578010687463	4	FACETS	0.951	0.872	1	0.951	0.872	1	CLONAL	2	TRUE	2	0.501761843368094	4		289	428	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246552	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	28	394	0	ENST00000349310.3:c.48_49delinsAA	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	16	ggGGag/ggAAag	4/15	0.329578010687463	4	FACETS	0.974	0.787	1	0.487	0.393	0.592	CLONAL	1	TRUE	2	0.501761843368094	4		394	172	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805399	46805399	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1483360509	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	108	659	0	ENST00000290295.7:c.557G>A	p.Gly186Glu	p.G186E	ENST00000290295	NM_006361.5	186	gGa/gAa	1/2	0.163227216850817	2	FACETS	1	0.985	1	0.745	0.678	0.813	INDETERMINATE	1	TRUE	0	0.501761843368094	2		659	289	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15383840	15383840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1229502583	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	88	488	0	ENST00000263377.2:c.71C>T	p.Ser24Phe	p.S24F	ENST00000263377	NM_058243.2	24	tCc/tTc	2/20	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.501761843368094	2		488	280	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99172227	99172227	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	56	505	0	ENST00000074304.5:c.1793C>T	p.Pro598Leu	p.P598L	ENST00000074304	NM_001134224.1	598	cCc/cTc	17/26	0.281828497672418	4	FACETS	0.926	0.797	1	0.463	0.398	0.533	INDETERMINATE	1	TRUE	2	0.501761843368094	4		505	362	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793268	242793268	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	52	544	1	ENST00000334409.5:c.809G>A	p.Gly270Asp	p.G270D	ENST00000334409	NM_005018.2	270	gGc/gAc	5/5	0.281828497672418	4	FACETS	1	0.968	1	0.748	0.645	0.858	INDETERMINATE	1	TRUE	2	0.501761843368094	4		545	208	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40828008	40828008	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	85	286	0	ENST00000373198.4:c.2420A>C	p.Lys807Thr	p.K807T	ENST00000373198	NM_133170.3	807	aAg/aCg	17/32	0.17692602848849	4	FACETS	0.808	0.721	0.898	0.808	0.721	0.898	INDETERMINATE	2	TRUE	2	0.501761843368094	4		286	315	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41514558	41514558	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	113	517	1	ENST00000373198.4:c.103G>A	p.Asp35Asn	p.D35N	ENST00000373198	NM_133170.3	35	Gat/Aat	2/32	0.17692602848849	4	FACETS	0.927	0.842	1	0.927	0.842	1	INDETERMINATE	2	TRUE	2	0.501761843368094	4		518	365	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526275	189526275	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	165	445	1	ENST00000264731.3:c.539C>T	p.Ser180Phe	p.S180F	ENST00000264731	NM_003722.4	180	tCc/tTc	4/14	0.237497320317577	4	FACETS	1	0.955	1	1	0.955	1	INDETERMINATE	2	TRUE	2	0.501761843368094	4		446	474	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38964910	38964910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	49	254	0	ENST00000357387.3:c.1384C>T	p.Pro462Ser	p.P462S	ENST00000357387	NM_152756.3	462	Ccc/Tcc	16/38	0.37635644907934	4	FACETS	0.838	0.713	0.975	0.419	0.356	0.488	CLONAL	1	TRUE	2	0.501761843368094	4		254	350	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974318	93974318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	125	440	0	ENST00000369303.4:c.1736G>A	p.Gly579Glu	p.G579E	ENST00000369303	NM_004440.3	579	gGg/gAg	8/17	0.329578010687463	4	FACETS	0.794	0.724	0.868	0.794	0.724	0.868	SUBCLONAL	2	TRUE	2	0.501761843368094	4		440	471	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150016251	150016251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426631850	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	65	426	0	ENST00000253339.5:c.455C>T	p.Ala152Val	p.A152V	ENST00000253339		152	gCt/gTt	2/7	0.329578010687463	4	FACETS	0.84	0.73	0.959	0.42	0.365	0.48	CLONAL	1	TRUE	2	0.501761843368094	4		426	463	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771213	161771213	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	151	452	1	ENST00000366898.1:c.1316C>T	p.Pro439Leu	p.P439L	ENST00000366898	NM_004562.2	439	cCc/cTc	12/12	0.329578010687463	4	FACETS	1	0.942	1	1	0.942	1	CLONAL	2	TRUE	2	0.501761843368094	4		453	441	SUCCESS
MET	4233	MSKCC	GRCh37	7	116397711	116397711	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	190	452	0	ENST00000397752.3:c.1985T>A	p.Ile662Asn	p.I662N	ENST00000397752	NM_000245.2	662	aTt/aAt	8/21	0.329578010687463	4	FACETS	1	0.97	1	1	0.97	1	CLONAL	2	TRUE	2	0.501761843368094	4		452	530	SUCCESS
MET	4233	MSKCC	GRCh37	7	116435749	116435749	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	183	426	0	ENST00000397752.3:c.3839G>A	p.Gly1280Glu	p.G1280E	ENST00000397752	NM_000245.2	1280	gGa/gAa	20/21	0.329578010687463	4	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	2	0.501761843368094	4		426	513	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436044	116436044	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	154	456	1	ENST00000397752.3:c.4039G>A	p.Glu1347Lys	p.E1347K	ENST00000397752	NM_000245.2	1347	Gag/Aag	21/21	0.329578010687463	4	FACETS	0.858	0.79	0.929	0.858	0.79	0.929	CLONAL	2	TRUE	2	0.501761843368094	4		457	537	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436096	116436096	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752791731	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	195	358	0	ENST00000397752.3:c.4091C>T	p.Pro1364Leu	p.P1364L	ENST00000397752	NM_000245.2	1364	cCg/cTg	21/21	0.329578010687463	4	FACETS	1	0.982	1	1	0.982	1	CLONAL	2	TRUE	2	0.501761843368094	4		358	509	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148523680	148523680	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	66	302	0	ENST00000320356.2:c.773C>T	p.Pro258Leu	p.P258L	ENST00000320356	NM_004456.4	258	cCt/cTt	8/20	0.281828497672418	4	FACETS	0.938	0.818	1	0.469	0.409	0.534	INDETERMINATE	1	TRUE	2	0.501761843368094	4		302	421	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68931862	68931862	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200600940	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	215	670	0	ENST00000288368.4:c.292G>A	p.Glu98Lys	p.E98K	ENST00000288368	NM_024870.2	98	Gaa/Aaa	3/40	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.501761843368094	NA		670	701	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939021	76939021	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015373-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	143	265	0	ENST00000373344.5:c.1727C>T	p.Ser576Leu	p.S576L	ENST00000373344	NM_000489.3	576	tCa/tTa	9/35	1	1	FACETS	0.815	0.76	0.869	1	0.991	1	CLONAL	2	TRUE	0	0.501761843368094	1		265	262	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435667	18435667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	59	313	2	ENST00000266497.5:c.652G>A	p.Glu218Lys	p.E218K	ENST00000266497		218	Gaa/Aaa	1/31	0.911706787743697	1	FACETS	0.377	0.33	0.426	0.377	0.33	0.426	SUBCLONAL	1	TRUE	0	0.911706787743697	1		315	187	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	295	817	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	0.911706787743697	1	FACETS	0.91	0.878	0.94	0.91	0.878	0.94	CLONAL	1	TRUE	0	0.911706787743697	1		817	387	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189526119	189526119	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	200	506	0	ENST00000264731.3:c.383C>T	p.Ser128Phe	p.S128F	ENST00000264731	NM_003722.4	128	tCc/tTc	4/14	0.475649734288951	2	FACETS	0.464	0.43	0.499	0.232	0.215	0.25	INDETERMINATE	1	TRUE	0	0.911706787743697	2		506	946	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587118	189587118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761885185	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	109	271	0	ENST00000264731.3:c.1135C>T	p.Arg379Cys	p.R379C	ENST00000264731	NM_003722.4	379	Cgt/Tgt	9/14	0.475649734288951	2	FACETS	0.51	0.46	0.562	0.255	0.23	0.281	INDETERMINATE	1	TRUE	0	0.911706787743697	2		271	469	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636143	28636143	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371663652	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	1181	399	0	ENST00000241453.7:c.229G>A	p.Glu77Lys	p.E77K	ENST00000241453	NM_004119.2	77	Gaa/Aaa	3/24	0.525006893514365	4	FACETS	1	0.998	1	0.847	0.833	0.86	INDETERMINATE	3	TRUE	0	0.911706787743697	4		399	1462	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984848	9984848	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	158	359	1	ENST00000330684.3:c.1117G>A	p.Glu373Lys	p.E373K	ENST00000330684	NM_001134407.1	373	Gaa/Aaa	4/13	0.503756558968929	1	FACETS	0.299	0.275	0.325	0.299	0.275	0.325	INDETERMINATE	1	TRUE	0	0.911706787743697	1		360	630	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22221708	22221709	+	inframe_insertion	In_Frame_Ins	INS	-	-	CCG	rs751880548	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	10	85	0	ENST00000215832.6:c.20_22dup	p.Ala7dup	p.A7dup	ENST00000215832	NM_002745.4	7	ggc/gCGGgc	1/9	1	2	FACETS	0.12	0.081	0.169	0.12	0.081	0.169	SUBCLONAL	1	TRUE	1	0.911706787743697	2		85	183	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	600	179	0				ENST00000310581	NM_198253.2	-/1132			0.911706787743697	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.911706787743697	2		179	657	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677227	29677227	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs786202457	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	24	294	261	1	ENST00000356175.3:c.7285C>T	p.Arg2429Ter	p.R2429*	ENST00000356175	NM_000267.3	2429	Cga/Tga	49/57	0.911706787743697	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	2	TRUE	0	0.911706787743697	2		262	318	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111907674	111907674	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	41	771	282	0	ENST00000393256.3:c.448C>T	p.Gln150Ter	p.Q150*	ENST00000393256	NM_006538.4	150	Caa/Taa	3/4	0.911706787743697	2	FACETS	1	0.998	1	1	0.998	1	CLONAL	2	TRUE	0	0.911706787743697	2		282	812	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8507308	8507308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	201	256	1	ENST00000356435.5:c.1670G>A	p.Gly557Glu	p.G557E	ENST00000356435		557	gGa/gAa	11/35	0.911706787743697	1	FACETS	0.738	0.7	0.776	0.738	0.7	0.776	SUBCLONAL	1	TRUE	0	0.911706787743697	1		257	325	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867256	45867256	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780129241	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	308	589	0	ENST00000391945.4:c.937G>A	p.Glu313Lys	p.E313K	ENST00000391945	NM_000400.3	313	Gaa/Aaa	10/23	1	2	FACETS	0.571	0.538	0.604	0.571	0.538	0.604	SUBCLONAL	1	TRUE	1	0.911706787743697	2		589	1184	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664880	138664880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757038357	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	115	92	0	ENST00000330315.3:c.685G>A	p.Ala229Thr	p.A229T	ENST00000330315	NM_023067.3	229	Gct/Act	1/1	0.475649734288951	2	FACETS	1	0.93	1	0.507	0.465	0.548	INDETERMINATE	1	TRUE	0	0.911706787743697	2		92	249	SUCCESS
CBL	867	MSKCC	GRCh37	11	119148875	119148876	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	205	269	0	ENST00000264033.4:c.1096-1_1096delinsAA		p.X366_splice	ENST00000264033	NM_005188.3	366		8/16	0.911706787743697	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.911706787743697	1		269	235	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679835	88679835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	131	256	0	ENST00000360948.2:c.628C>T	p.Pro210Ser	p.P210S	ENST00000360948	NM_001012338.2	210	Cct/Tct	7/19	0.503756558968929	1	FACETS	0.332	0.303	0.362	0.332	0.303	0.362	INDETERMINATE	1	TRUE	0	0.911706787743697	1		256	471	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164691	36164691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868527382	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	314	595	2	ENST00000300305.3:c.1184C>T	p.Pro395Leu	p.P395L	ENST00000300305		395	cCg/cTg	8/8	0.52564441122993	1	FACETS	0.361	0.341	0.382	0.361	0.341	0.382	INDETERMINATE	1	TRUE	0	0.911706787743697	1		597	1037	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255076	16255076	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1283954838	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	289	395	0	ENST00000375759.3:c.2341C>T	p.Arg781Cys	p.R781C	ENST00000375759	NM_015001.2	781	Cgt/Tgt	11/15	0.898233954435887	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.911706787743697	1		395	326	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099457	27099457	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769227665	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	28	283	322	0	ENST00000324856.7:c.3694C>T	p.Pro1232Ser	p.P1232S	ENST00000324856	NM_006015.4	1232	Cct/Tct	14/20	0.911706787743697	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.911706787743697	1		322	311	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156846300	156846300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150579345	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	895	565	0	ENST00000524377.1:c.1741G>A	p.Glu581Lys	p.E581K	ENST00000524377	NM_002529.3	581	Gag/Aag	14/17	0.25504742231113	5	FACETS	0.839	0.815	0.864	0.839	0.815	0.864	INDETERMINATE	3	TRUE	2	0.911706787743697	5		565	1846	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46242654	46242654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	146	138	254	1	ENST00000334344.6:c.1616C>T	p.Ser539Phe	p.S539F	ENST00000334344	NM_152641.2	539	tCt/tTt	13/21	0.911706787743697	2	FACETS	1	0.965	1	0.533	0.494	0.572	CLONAL	1	TRUE	0	0.911706787743697	2		255	284	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133254204	133254204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060500784	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	414	383	1	ENST00000320574.5:c.680C>T	p.Pro227Leu	p.P227L	ENST00000320574	NM_006231.2	227	cCc/cTc	7/49	0.911706787743697	2	FACETS	1	0.985	1	0.53	0.508	0.553	CLONAL	1	TRUE	0	0.911706787743697	2		384	856	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32893351	32893351	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	763	490	0	ENST00000380152.3:c.205C>T	p.Pro69Ser	p.P69S	ENST00000380152		69	Cca/Tca	3/27	0.525006893514365	4	FACETS	1	0.997	1	0.849	0.833	0.865	INDETERMINATE	3	TRUE	0	0.911706787743697	4		490	942	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41239911	41239911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	76	119	0	ENST00000379561.5:c.439G>A	p.Gly147Arg	p.G147R	ENST00000379561	NM_002015.3	147	Ggg/Agg	1/3	0.525006893514365	4	FACETS	0.663	0.583	0.748	0.166	0.145	0.187	INDETERMINATE	1	TRUE	0	0.911706787743697	4		119	481	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2222591	2222592	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	208	449	1	ENST00000326181.6:c.785_786delinsTT	p.Ser262Phe	p.S262F	ENST00000326181	NM_032271.2	262	tCC/tTT	9/21	0.503756558968929	1	FACETS	0.318	0.295	0.341	0.318	0.295	0.341	INDETERMINATE	1	TRUE	0	0.911706787743697	1		450	782	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30133232	30133232	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	206	420	0	ENST00000263025.4:c.266T>A	p.Ile89Asn	p.I89N	ENST00000263025	NM_002746.2	89	aTc/aAc	2/9	0.503756558968929	1	FACETS	0.345	0.321	0.37	0.345	0.321	0.37	INDETERMINATE	1	TRUE	0	0.911706787743697	1		420	713	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89837041	89837041	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	550	574	0	ENST00000389301.3:c.2153C>T	p.Ala718Val	p.A718V	ENST00000389301	NM_000135.2	718	gCt/gTt	24/43	0.503756558968929	1	FACETS	0.797	0.773	0.82	0.797	0.773	0.82	INDETERMINATE	1	TRUE	0	0.911706787743697	1		574	824	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15964858	15964858	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	38	494	403	0	ENST00000268712.3:c.5738C>T	p.Ser1913Phe	p.S1913F	ENST00000268712	NM_006311.3	1913	tCc/tTc	37/46	0.911706787743697	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.911706787743697	1		403	532	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097222	11097222	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	238	484	0	ENST00000358026.2:c.713C>T	p.Pro238Leu	p.P238L	ENST00000358026	NM_001128849.1	238	cCc/cTc	4/36	0.503756558968929	1	FACETS	0.358	0.335	0.381	0.358	0.335	0.381	INDETERMINATE	1	TRUE	0	0.911706787743697	1		484	794	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725011	47725011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1342443339	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	669	916	1	ENST00000449228.1:c.733C>T	p.Leu245Phe	p.L245F	ENST00000449228	NM_001127240.2	245	Ctc/Ttc	4/4	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.911706787743697	2		917	1454	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917772	29917772	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	36	1255	496	0	ENST00000389048.3:c.896C>T	p.Ser299Phe	p.S299F	ENST00000389048	NM_004304.4	299	tCc/tTc	3/29	0.911706787743697	3	FACETS	1	0.999	1	1	0.999	1	CLONAL	3	TRUE	0	0.911706787743697	3		496	1291	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198269819	198269819	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	528	461	0	ENST00000335508.6:c.1520G>A	p.Gly507Glu	p.G507E	ENST00000335508	NM_012433.2	507	gGa/gAa	11/25	0.911706787743697	2	FACETS	1	0.995	1	0.595	0.573	0.616	CLONAL	1	TRUE	0	0.911706787743697	2		461	974	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286822	212286822	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	219	307	0	ENST00000342788.4:c.2874G>A	p.Met958Ile	p.M958I	ENST00000342788	NM_005235.2	958	atG/atA	24/28	0.911706787743697	2	FACETS	1	0.986	1	0.571	0.539	0.602	CLONAL	1	TRUE	0	0.911706787743697	2		307	421	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624780	9624780	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	112	294	0	ENST00000353224.5:c.197C>T	p.Pro66Leu	p.P66L	ENST00000353224	NM_177990.2	66	cCt/cTt	3/10	0.453749780178019	2	FACETS	0.469	0.423	0.517	0.234	0.211	0.259	INDETERMINATE	1	TRUE	0	0.911706787743697	2		294	524	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36030956	36030956	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	222	510	0	ENST00000358208.4:c.1235G>A	p.Arg412Gln	p.R412Q	ENST00000358208		412	cGg/cAg	10/12	0.453749780178019	2	FACETS	0.482	0.449	0.517	0.241	0.224	0.259	INDETERMINATE	1	TRUE	0	0.911706787743697	2		510	1010	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100905	41100905	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	144	373	1	ENST00000373198.4:c.1450+1G>A		p.X484_splice	ENST00000373198	NM_133170.3	484			0.453749780178019	2	FACETS	0.479	0.438	0.522	0.24	0.219	0.261	INDETERMINATE	1	TRUE	0	0.911706787743697	2		374	659	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47125739	47125739	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	152	267	0	ENST00000409792.3:c.5531C>T	p.Ser1844Phe	p.S1844F	ENST00000409792	NM_014159.6	1844	tCt/tTt	12/21	0.475649734288951	2	FACETS	0.57	0.524	0.618	0.285	0.262	0.309	INDETERMINATE	1	TRUE	0	0.911706787743697	2		267	585	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163935	47163935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	82	204	194	0	ENST00000409792.3:c.2191G>A	p.Asp731Asn	p.D731N	ENST00000409792	NM_014159.6	731	Gac/Aac	3/21	0.475649734288951	2	FACETS	0.782	0.747	0.817	0.782	0.747	0.817	INDETERMINATE	2	TRUE	0	0.911706787743697	2		194	286	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231286	142231287	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	220	407	376	0	ENST00000350721.4:c.4667dup	p.His1558AlafsTer2	p.H1558Afs*2	ENST00000350721	NM_001184.3	1556	cta/ctTa	27/47	0.475649734288951	2	FACETS	1	0.996	1	0.712	0.687	0.737	INDETERMINATE	1	TRUE	0	0.911706787743697	2		376	627	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139822	55139822	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868384918	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	191	377	0	ENST00000257290.5:c.1483G>A	p.Glu495Lys	p.E495K	ENST00000257290	NM_006206.4	495	Gag/Aag	10/23	0.503756558968929	1	FACETS	0.36	0.334	0.386	0.36	0.334	0.386	INDETERMINATE	1	TRUE	0	0.911706787743697	1		377	634	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143114327	143114328	+	missense_variant	Missense_Mutation	DNP	GT	GT	AA	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	211	301	0	ENST00000262992.4:c.1093_1094delinsTT	p.Thr365Phe	p.T365F	ENST00000262992	NM_001101669.1	365	ACt/TTt	13/24	0.503756558968929	1	FACETS	0.686	0.649	0.723	0.686	0.649	0.723	INDETERMINATE	1	TRUE	0	0.911706787743697	1		301	367	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332745	153332745	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	151	334	0	ENST00000281708.4:c.211G>A	p.Asp71Asn	p.D71N	ENST00000281708	NM_033632.3	71	Gat/Aat	2/12	0.503756558968929	1	FACETS	0.381	0.351	0.412	0.381	0.351	0.412	INDETERMINATE	1	TRUE	0	0.911706787743697	1		334	473	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965575	93965575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	109	346	0	ENST00000369303.4:c.2353G>A	p.Asp785Asn	p.D785N	ENST00000369303	NM_004440.3	785	Gat/Aat	13/17	0.482607203884725	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.911706787743697	0		346	263	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041061	112041061	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	202	351	0	ENST00000368678.4:c.194G>A	p.Gly65Glu	p.G65E	ENST00000368678		65	gGa/gAa	3/13	0.482607203884725	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.911706787743697	0		351	457	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631443	117631443	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	109	80	328	0	ENST00000368508.3:c.6235G>A	p.Asp2079Asn	p.D2079N	ENST00000368508	NM_002944.2	2079	Gat/Aat	40/43	0.482607203884725	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.911706787743697	0		328	189	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150005032	150005032	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750553952	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	104	302	0	ENST00000253339.5:c.1193C>T	p.Ser398Leu	p.S398L	ENST00000253339		398	tCg/tTg	3/7	0.482607203884725	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.911706787743697	0		302	232	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505553	157505554	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	59	54	173	2	ENST00000346085.5:c.3534_3535delinsTT	p.Gln1179Ter	p.Q1179*	ENST00000346085	NM_020732.3	1178	ctCCag/ctTTag	13/20	0.482607203884725	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.911706787743697	0		175	113	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522553	157522553	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	297	686	0	ENST00000346085.5:c.4825C>T	p.Pro1609Ser	p.P1609S	ENST00000346085	NM_020732.3	1609	Cct/Tct	18/20	0.482607203884725	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.911706787743697	0		686	674	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878231	151878231	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	597	486	0	ENST00000262189.6:c.6714G>A	p.Met2238Ile	p.M2238I	ENST00000262189	NM_170606.2	2238	atG/atA	36/59	0.25504742231113	5	FACETS	0.846	0.817	0.876	0.846	0.817	0.876	INDETERMINATE	3	TRUE	2	0.911706787743697	5		486	1221	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972943	68972943	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	125	344	0	ENST00000288368.4:c.1268G>A	p.Gly423Glu	p.G423E	ENST00000288368	NM_024870.2	423	gGa/gAa	11/40	0.60609905956874	1	FACETS	0.341	0.311	0.373	0.341	0.311	0.373	SUBCLONAL	1	TRUE	0	0.911706787743697	1		344	437	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971114	21971115	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	GGGTCGGGTGAGAGTGGCG	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	221	306	0	ENST00000304494.5:c.225_243dup	p.Val82ArgfsTer44	p.V82Rfs*44	ENST00000304494	NM_000077.4	81	-/CGCCACTCTCACCCGACCC	2/3	0.911706787743697	1	FACETS	0.399	0.373	0.426	0.399	0.373	0.426	SUBCLONAL	1	TRUE	0	0.911706787743697	1		306	661	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802645	139802645	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762052203	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	686	444	0	ENST00000247668.2:c.490C>T	p.Arg164Trp	p.R164W	ENST00000247668	NM_021138.3	164	Cgg/Tgg	5/11	0.465111429647038	2	FACETS	0.755	0.735	0.774	0.755	0.735	0.774	INDETERMINATE	2	TRUE	0	0.911706787743697	2		444	997	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39913140	39913141	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	134	106	147	2	ENST00000378444.4:c.4974_4975delinsAA	p.Gly1659Arg	p.G1659R	ENST00000378444	NM_001123385.1	1658	caGGgg/caAAgg	14/15	1	1	FACETS	0.527	0.482	0.573	0.527	0.482	0.573	SUBCLONAL	1	TRUE	0	0.911706787743697	1		149	240	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829748	76829748	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	134	292	0	ENST00000373344.5:c.6293G>A	p.Trp2098Ter	p.W2098*	ENST00000373344	NM_000489.3	2098	tGg/tAg	28/35	1	1	FACETS	0.542	0.501	0.584	0.542	0.501	0.584	SUBCLONAL	1	TRUE	0	0.911706787743697	1		292	295	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49726078	49726078	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015386-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	10	28	12	0	ENST00000449682.2:c.47G>A	p.Gly16Glu	p.G16E	ENST00000449682	NM_020998.3	16	gGg/gAg	1/18	0.475649734288951	2	FACETS	0.808	0.71	0.894	0.808	0.71	0.894	INDETERMINATE	2	TRUE	0	0.911706787743697	2		12	38	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	408	282	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.868046783662762	2		282	798	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123310896	123310896	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs974173968	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	178	425	0	ENST00000358487.5:c.532C>T	p.Arg178Cys	p.R178C	ENST00000358487	NM_000141.4	178	Cgc/Tgc	5/18	0.488133388583447	1	FACETS	0.333	0.307	0.359	0.333	0.307	0.359	INDETERMINATE	1	TRUE	0	0.868046783662762	1		425	698	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453193	140453193	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs121913370	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	130	328	0	ENST00000288602.6:c.1742A>G	p.Asn581Ser	p.N581S	ENST00000288602	NM_004333.4	581	aAt/aGt	15/18	1	2	FACETS	0.453	0.412	0.497	0.453	0.412	0.497	SUBCLONAL	1	TRUE	1	0.868046783662762	2		328	661	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542356	187542356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs56790426	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	292	335	1	ENST00000441802.2:c.5384G>A	p.Arg1795Gln	p.R1795Q	ENST00000441802	NM_005245.3	1795	cGa/cAa	10/27	1	2	FACETS	0.984	0.932	1	0.984	0.932	1	CLONAL	1	TRUE	1	0.868046783662762	2		336	684	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926248	112926248	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs121918468	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	371	481	0	ENST00000351677.2:c.1381G>A	p.Ala461Thr	p.A461T	ENST00000351677	NM_002834.3	461	Gct/Act	12/16	0.184060183339632	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.868046783662762	0		481	848	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189427	56189427	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	504	627	0	ENST00000399503.3:c.4459C>T	p.Arg1487Cys	p.R1487C	ENST00000399503	NM_005921.1	1487	Cgt/Tgt	20/20	1	2	FACETS	0.971	0.932	1	0.971	0.932	1	CLONAL	1	TRUE	1	0.868046783662762	2		627	1196	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455576	189455576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754361670	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	450	648	1	ENST00000264731.3:c.110G>A	p.Arg37Gln	p.R37Q	ENST00000264731	NM_003722.4	37	cGa/cAa	2/14	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.868046783662762	2		649	1030	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477859	140477859	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs727504375	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	482	604	0	ENST00000288602.6:c.1449A>C	p.Lys483Asn	p.K483N	ENST00000288602	NM_004333.4	483	aaA/aaC	12/18	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.868046783662762	2		604	1033	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799165	45799165	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	546	744	0	ENST00000450313.1:c.268G>C	p.Val90Leu	p.V90L	ENST00000450313	NM_012222.2	90	Gta/Cta	3/16	1	2	FACETS	0.969	0.932	1	0.969	0.932	1	CLONAL	1	TRUE	1	0.868046783662762	2		744	1298	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120510247	120510247	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	novel	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	309	350	0	ENST00000256646.2:c.1265-3C>T		p.X422_splice	ENST00000256646	NM_024408.3	422			1	2	FACETS	0.937	0.888	0.986	0.937	0.888	0.986	CLONAL	1	TRUE	1	0.868046783662762	2		350	760	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404656	70404656	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	601	752	0	ENST00000373644.4:c.2170G>A	p.Gly724Arg	p.G724R	ENST00000373644	NM_030625.2	724	Gga/Aga	4/12	0.488133388583447	1	FACETS	0.756	0.732	0.78	0.756	0.732	0.78	INDETERMINATE	1	TRUE	0	0.868046783662762	1		752	1036	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769526	112769526	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	254	760	0	ENST00000369452.4:c.1478T>C	p.Leu493Pro	p.L493P	ENST00000369452	NM_007373.3	493	cTt/cCt	8/9	0.488133388583447	1	FACETS	0.335	0.313	0.357	0.335	0.313	0.357	INDETERMINATE	1	TRUE	0	0.868046783662762	1		760	989	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49425559	49425559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	676	1003	0	ENST00000301067.7:c.12929C>T	p.Pro4310Leu	p.P4310L	ENST00000301067	NM_003482.3	4310	cCa/cTa	39/54	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.868046783662762	2		1003	1497	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891115	112891115	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	419	727	0	ENST00000351677.2:c.449del	p.Ser150LeufsTer18	p.S150Lfs*18	ENST00000351677	NM_002834.3	150	tCt/tt	4/16	1	2	FACETS	0.816	0.778	0.855	0.816	0.778	0.855	CLONAL	1	TRUE	1	0.868046783662762	2		727	1183	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435883	110435883	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	402	599	0	ENST00000375856.3:c.2518G>T	p.Glu840Ter	p.E840*	ENST00000375856	NM_003749.2	840	Gag/Tag	1/2	1	2	FACETS	0.882	0.841	0.924	0.882	0.841	0.924	CLONAL	1	TRUE	1	0.868046783662762	2		599	1050	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105239911	105239911	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	410	624	0	ENST00000349310.3:c.709T>C	p.Phe237Leu	p.F237L	ENST00000349310	NM_001014432.1	237	Ttc/Ctc	10/15	1	2	FACETS	0.956	0.913	0.999	0.956	0.913	0.999	CLONAL	1	TRUE	1	0.868046783662762	2		624	988	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643498	38643498	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	544	606	0	ENST00000299084.4:c.968C>A	p.Ser323Ter	p.S323*	ENST00000299084	NM_152594.2	323	tCa/tAa	7/7	0.868046783662762	1	FACETS	0.969	0.943	0.994	0.969	0.943	0.994	CLONAL	1	TRUE	0	0.868046783662762	1		606	732	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781423	3781423	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	449	555	0	ENST00000262367.5:c.4942C>T	p.Pro1648Ser	p.P1648S	ENST00000262367	NM_004380.2	1648	Ccc/Tcc	30/31	0.559426207428952	1	FACETS	0.754	0.726	0.781	0.754	0.726	0.781	SUBCLONAL	1	TRUE	0	0.868046783662762	1		555	777	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59934498	59934498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	397	398	0	ENST00000259008.2:c.300G>A	p.Met100Ile	p.M100I	ENST00000259008	NM_032043.2	100	atG/atA	4/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.868046783662762	2		398	882	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66520180	66520180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568696484	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	418	486	0	ENST00000358598.2:c.464C>T	p.Ser155Leu	p.S155L	ENST00000358598	NM_212471.2	155	tCg/tTg	5/11	1	2	FACETS	0.886	0.846	0.927	0.886	0.846	0.927	CLONAL	1	TRUE	1	0.868046783662762	2		486	1087	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226749	2226749	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781442735	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	811	835	0	ENST00000398665.3:c.4229C>T	p.Ala1410Val	p.A1410V	ENST00000398665	NM_032482.2	1410	gCc/gTc	27/28	1	2	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	1	0.868046783662762	2		835	1529	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211154	36211154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	710	1202	4	ENST00000222270.7:c.905C>T	p.Pro302Leu	p.P302L	ENST00000222270	NM_014727.1	302	cCc/cTc	3/37	0.148571836013378	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.868046783662762	0		1206	1787	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198260837	198260837	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	409	598	0	ENST00000335508.6:c.3482T>G	p.Met1161Arg	p.M1161R	ENST00000335508	NM_012433.2	1161	aTg/aGg	23/25	0.390162654284938	1	FACETS	0.675	0.647	0.703	0.675	0.647	0.703	INDETERMINATE	1	TRUE	0	0.868046783662762	1		598	790	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30077591	30077591	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	755	518	0	ENST00000338641.4:c.1737+1G>A		p.X579_splice	ENST00000338641	NM_000268.3	579			0.866849391390785	2	FACETS	0.994	0.977	1	0.994	0.977	1	CLONAL	2	TRUE	0	0.868046783662762	2		518	875	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620532	52620532	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	471	575	0	ENST00000394830.3:c.3221C>G	p.Ser1074Cys	p.S1074C	ENST00000394830	NM_018313.4	1074	tCt/tGt	21/30	NA	2	FACETS	0.979	0.939	1			1	INDETERMINATE	1	TRUE	NA	0.868046783662762	2		575	1108	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106180912	106180912	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	300	378	0	ENST00000380013.4:c.3940G>A	p.Asp1314Asn	p.D1314N	ENST00000380013	NM_001127208.2	1314	Gat/Aat	7/11	1	2	FACETS	0.875	0.828	0.923	0.875	0.828	0.923	CLONAL	1	TRUE	1	0.868046783662762	2		378	790	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294063	1294064	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	645	1096	1	ENST00000310581.5:c.937_938delinsTT	p.Pro313Leu	p.P313L	ENST00000310581	NM_198253.2	313	CCa/TTa	2/16	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.868046783662762	2		1097	1417	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80160645	80160645	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	453	684	0	ENST00000265081.6:c.3014C>T	p.Thr1005Ile	p.T1005I	ENST00000265081	NM_002439.4	1005	aCc/aTc	22/24	1	2	FACETS	0.931	0.891	0.971	0.931	0.891	0.971	CLONAL	1	TRUE	1	0.868046783662762	2		684	1121	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86665638	86665638	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137853217	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	98	306	0	ENST00000274376.6:c.1619G>A	p.Cys540Tyr	p.C540Y	ENST00000274376	NM_002890.2	540	tGt/tAt	12/25	1	2	FACETS	0.427	0.382	0.474	0.427	0.382	0.474	SUBCLONAL	1	TRUE	1	0.868046783662762	2		306	529	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940145	31940145	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779960597	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1672	712	382	1	ENST00000375333.2:c.287C>T	p.Ser96Phe	p.S96F	ENST00000375333	NM_032454.1	96	tCc/tTc	2/8	0.868046783662762	3	FACETS	0.987	0.95	1	0.493	0.475	0.512	CLONAL	1	TRUE	1	0.868046783662762	3		383	2384	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066683	94066683	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759223701	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	436	618	3	ENST00000369303.4:c.1076G>A	p.Gly359Glu	p.G359E	ENST00000369303	NM_004440.3	359	gGa/gAa	5/17	0.868046783662762	1	FACETS	0.941	0.912	0.969	0.941	0.912	0.969	CLONAL	1	TRUE	0	0.868046783662762	1		621	604	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120269	94120269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	238	296	1	ENST00000369303.4:c.782G>A	p.Gly261Glu	p.G261E	ENST00000369303	NM_004440.3	261	gGa/gAa	3/17	0.868046783662762	1	FACETS	0.94	0.901	0.978	0.94	0.901	0.978	CLONAL	1	TRUE	0	0.868046783662762	1		297	330	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450240	50450240	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	347	387	0	ENST00000331340.3:c.424G>A	p.Glu142Lys	p.E142K	ENST00000331340	NM_006060.4	142	Gaa/Aaa	5/8	NA	2	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.868046783662762	2		387	766	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211104	55211104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	406	573	2	ENST00000275493.2:c.347C>T	p.Ser116Phe	p.S116F	ENST00000275493	NM_005228.3	116	tCc/tTc	3/28	NA	2	FACETS	0.906	0.865	0.948			1	INDETERMINATE	1	TRUE	NA	0.868046783662762	2		575	1032	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55242415	55242415	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	379	523	0	ENST00000275493.2:c.2185G>A	p.Gly729Arg	p.G729R	ENST00000275493	NM_005228.3	729	Gga/Aga	19/28	NA	2	FACETS	0.942	0.898	0.986			1	INDETERMINATE	1	TRUE	NA	0.868046783662762	2		523	927	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38189043	38189043	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	641	754	2	ENST00000317025.8:c.971A>T	p.Glu324Val	p.E324V	ENST00000317025	NM_023034.1	324	gAa/gTa	5/24	0.488133388583447	1	FACETS	0.722	0.699	0.745	0.722	0.699	0.745	INDETERMINATE	1	TRUE	0	0.868046783662762	1		756	1158	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69129903	69129903	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752113779	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	683	365	1	ENST00000288368.4:c.4657G>A	p.Gly1553Arg	p.G1553R	ENST00000288368	NM_024870.2	1553	Gga/Aga	38/40	0.291003090293312	5	FACETS	1	0.994	1	0.653	0.634	0.672	INDETERMINATE	3	TRUE	0	0.868046783662762	5		366	1109	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228211	53228211	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199422234	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	594	362	0	ENST00000375401.3:c.2191C>T	p.Leu731Phe	p.L731F	ENST00000375401	NM_004187.3	731	Ctt/Ttt	15/26	1	1	FACETS	1	0.997	1	1	0.997	1	CLONAL	1	TRUE	0	0.868046783662762	1		362	682	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939662	76939663	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	414	357	0	ENST00000373344.5:c.1085_1086delinsTT	p.Thr362Ile	p.T362I	ENST00000373344	NM_000489.3	362	aCC/aTT	9/35	1	1	FACETS	1	0.995	1	1	0.995	1	CLONAL	1	TRUE	0	0.868046783662762	1		357	488	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968282	18968284	+	missense_variant	Missense_Mutation	TNP	CTC	CTC	TTT	novel	NA	P-0015407-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	679	832	1	ENST00000262803.5:c.2122_2124delinsTTT	p.Leu708Phe	p.L708F	ENST00000262803	NM_002911.3	708	CTC/TTT	15/24	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.868046783662762	2		833	1489	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	290	282	0				ENST00000310581	NM_198253.2	-/1132			0.673400322664386	3	FACETS	0.939	0.893	0.985	0.939	0.893	0.985	CLONAL	2	TRUE	1	0.72747606435266	3		282	579	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	633	316	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.72747606435266	8	FACETS	1	0.973	1			1	CLONAL	4	TRUE	NA	0.72747606435266	8		316	1372	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16203032	16203032	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	369	658	0	ENST00000375759.3:c.740C>T	p.Ser247Leu	p.S247L	ENST00000375759	NM_015001.2	247	tCa/tTa	3/15	0.72747606435266	4	FACETS	0.948	0.903	0.994	0.948	0.903	0.994	CLONAL	2	TRUE	2	0.72747606435266	4		658	924	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933436	36933436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	350	751	0	ENST00000361632.4:c.1851G>A	p.Met617Ile	p.M617I	ENST00000361632		617	atG/atA	13/16	0.72747606435266	4	FACETS	0.956	0.91	1	0.956	0.91	1	CLONAL	2	TRUE	2	0.72747606435266	4		751	869	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256556	115256556	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	293	685	0	ENST00000369535.4:c.155T>G	p.Leu52Trp	p.L52W	ENST00000369535	NM_002524.4	52	tTg/tGg	3/7	0.72747606435266	4	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	2	0.72747606435266	4		685	695	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258682	115258682	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	212	406	0	ENST00000369535.4:c.100C>T	p.Pro34Ser	p.P34S	ENST00000369535	NM_002524.4	34	Ccc/Tcc	2/7	0.72747606435266	4	FACETS	0.991	0.93	1	0.991	0.93	1	CLONAL	2	TRUE	2	0.72747606435266	4		406	508	SUCCESS
FH	2271	MSKCC	GRCh37	1	241675412	241675412	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	175	471	0	ENST00000366560.3:c.410C>T	p.Pro137Leu	p.P137L	ENST00000366560	NM_000143.3	137	cCt/cTt	4/10	0.72747606435266	4	FACETS	1	0.948	1	1	0.948	1	CLONAL	2	TRUE	2	0.72747606435266	4		471	408	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70441204	70441204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	200	665	0	ENST00000373644.4:c.4873C>T	p.Pro1625Ser	p.P1625S	ENST00000373644	NM_030625.2	1625	Cca/Tca	9/12	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.72747606435266	2		665	472	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70441243	70441243	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs866146478	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	136	513	0	ENST00000373644.4:c.4912C>T	p.Gln1638Ter	p.Q1638*	ENST00000373644	NM_030625.2	1638	Cag/Tag	9/12	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.72747606435266	2		513	353	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123256129	123256129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	203	742	0	ENST00000358487.5:c.1780C>T	p.Pro594Ser	p.P594S	ENST00000358487	NM_000141.4	594	Cct/Tct	13/18	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.72747606435266	2		742	558	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948253	71948253	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	513	1029	0	ENST00000298229.2:c.2965C>T	p.Leu989Phe	p.L989F	ENST00000298229	NM_001567.3	989	Ctt/Ttt	26/28	0.54149631375248	3	FACETS	0.957	0.922	0.992	0.957	0.922	0.992	CLONAL	2	TRUE	1	0.72747606435266	3		1029	1005	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	101981755	101981756	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	298	653	2	ENST00000282441.5:c.176_177delinsAA	p.Gly59Glu	p.G59E	ENST00000282441	NM_001130145.2	59	gGG/gAA	1/9	0.54149631375248	3	FACETS	0.947	0.901	0.993	0.947	0.901	0.993	CLONAL	2	TRUE	1	0.72747606435266	3		655	590	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344563	118344564	+	missense_variant	Missense_Mutation	DNP	TC	TC	GT	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	111	591	2	ENST00000534358.1:c.2689_2690delinsGT	p.Ser897Val	p.S897V	ENST00000534358	NM_005933.3	897	TCa/GTa	3/36	0.54149631375248	3	FACETS	0.848	0.766	0.933	0.424	0.383	0.467	CLONAL	1	TRUE	1	0.72747606435266	3		593	491	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373125	118373125	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	186	161	405	0	ENST00000534358.1:c.6518C>T	p.Pro2173Leu	p.P2173L	ENST00000534358	NM_005933.3	2173	cCa/cTa	27/36	0.54149631375248	3	FACETS	0.87	0.81	0.929	0.87	0.81	0.929	CLONAL	2	TRUE	1	0.72747606435266	3		405	347	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865281	57865281	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368469814	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	357	773	4	ENST00000228682.2:c.2758G>A	p.Ala920Thr	p.A920T	ENST00000228682	NM_005269.2	920	Gcc/Acc	12/12	0.667830160367963	4	FACETS	0.883	0.839	0.927	0.883	0.839	0.927	CLONAL	2	TRUE	2	0.72747606435266	4		777	960	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109876	115109876	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768590444	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	440	712	1	ENST00000257566.3:c.2002G>A	p.Gly668Arg	p.G668R	ENST00000257566	NM_016569.3	668	Ggg/Agg	8/8	0.72747606435266	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.72747606435266	2		713	569	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601298	28601298	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	230	669	1	ENST00000241453.7:c.2134A>T	p.Arg712Trp	p.R712W	ENST00000241453	NM_004119.2	712	Agg/Tgg	17/24	0.423773480192486	4	FACETS	0.768	0.719	0.818	0.768	0.719	0.818	INDETERMINATE	2	TRUE	2	0.72747606435266	4		670	711	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041266	29041267	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	154	466	1	ENST00000282397.4:c.162-1_162delinsAA		p.X54_splice	ENST00000282397	NM_002019.4	54		3/30	0.423773480192486	4	FACETS	1	0.947	1	1	0.947	1	INDETERMINATE	2	TRUE	2	0.72747606435266	4		467	357	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32920978	32920978	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs80358920	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	145	500	2	ENST00000380152.3:c.6952C>T	p.Arg2318Ter	p.R2318*	ENST00000380152		2318	Cga/Tga	13/27	0.423773480192486	4	FACETS	0.959	0.887	1	0.959	0.887	1	INDETERMINATE	2	TRUE	2	0.72747606435266	4		502	359	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609774	81609774	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	136	416	0	ENST00000298171.2:c.1372T>C	p.Phe458Leu	p.F458L	ENST00000298171	NM_000369.2	458	Ttt/Ctt	10/10	1	2	FACETS	0.981	0.902	1	0.981	0.902	1	CLONAL	1	TRUE	1	0.72747606435266	2		416	381	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042616	42042616	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	144	626	0	ENST00000219905.7:c.6811C>T	p.Gln2271Ter	p.Q2271*	ENST00000219905	NM_001164273.1	2271	Cag/Tag	17/24	0.220344253747321	4	FACETS	0.866	0.798	0.935	0.866	0.798	0.935	INDETERMINATE	2	TRUE	2	0.72747606435266	4		626	395	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472466	88472466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	191	685	0	ENST00000360948.2:c.2089G>A	p.Asp697Asn	p.D697N	ENST00000360948	NM_001012338.2	697	Gac/Aac	16/19	0.220344253747321	4	FACETS	1	0.991	1	0.735	0.683	0.788	INDETERMINATE	1	TRUE	2	0.72747606435266	4		685	617	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130373	2130373	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	334	647	0	ENST00000219476.3:c.3605C>T	p.Pro1202Leu	p.P1202L	ENST00000219476	NM_000548.3	1202	cCc/cTc	30/42	0.667830160367963	4	FACETS	0.993	0.944	1	0.993	0.944	1	CLONAL	2	TRUE	2	0.72747606435266	4		647	799	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778852	3778852	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479729612	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	162	710	2	ENST00000262367.5:c.6196G>A	p.Ala2066Thr	p.A2066T	ENST00000262367	NM_004380.2	2066	Gct/Act	31/31	0.667830160367963	4	FACETS	0.881	0.809	0.957	0.441	0.404	0.479	CLONAL	1	TRUE	2	0.72747606435266	4		712	873	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857097	9857097	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	156	340	0	ENST00000330684.3:c.4304A>G	p.Lys1435Arg	p.K1435R	ENST00000330684	NM_001134407.1	1435	aAg/aGg	13/13	0.667830160367963	4	FACETS	0.863	0.799	0.93	0.863	0.799	0.93	CLONAL	2	TRUE	2	0.72747606435266	4		340	429	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857788	9857788	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs918332999	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	283	494	1	ENST00000330684.3:c.3613G>A	p.Glu1205Lys	p.E1205K	ENST00000330684	NM_001134407.1	1205	Gag/Aag	13/13	0.667830160367963	4	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	2	0.72747606435266	4		495	662	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943643	9943643	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	370	610	1	ENST00000330684.3:c.1298C>T	p.Thr433Ile	p.T433I	ENST00000330684	NM_001134407.1	433	aCc/aTc	5/13	0.667830160367963	4	FACETS	0.974	0.928	1	0.974	0.928	1	CLONAL	2	TRUE	2	0.72747606435266	4		611	902	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984911	9984911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	343	683	0	ENST00000330684.3:c.1054G>A	p.Glu352Lys	p.E352K	ENST00000330684	NM_001134407.1	352	Gag/Aag	4/13	0.667830160367963	4	FACETS	0.993	0.945	1	0.993	0.945	1	CLONAL	2	TRUE	2	0.72747606435266	4		683	820	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10273921	10273921	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1373259478	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	390	881	0	ENST00000330684.3:c.348C>G	p.Ile116Met	p.I116M	ENST00000330684	NM_001134407.1	116	atC/atG	2/13	0.667830160367963	4	FACETS	0.906	0.863	0.949	0.906	0.863	0.949	CLONAL	2	TRUE	2	0.72747606435266	4		881	1022	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029456	14029456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1229724657	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	281	507	0	ENST00000311895.7:c.1667C>T	p.Pro556Leu	p.P556L	ENST00000311895	NM_005236.2	556	cCg/cTg	8/11	0.667830160367963	4	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	2	0.72747606435266	4		507	652	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23647500	23647500	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	273	661	1	ENST00000261584.4:c.367G>A	p.Asp123Asn	p.D123N	ENST00000261584	NM_024675.3	123	Gac/Aac	4/13	0.667830160367963	4	FACETS	0.931	0.88	0.984	0.931	0.88	0.984	CLONAL	2	TRUE	2	0.72747606435266	4		662	696	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845688	68845688	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	480	811	0	ENST00000261769.5:c.934C>T	p.Pro312Ser	p.P312S	ENST00000261769	NM_004360.3	312	Cct/Tct	7/16	0.667830160367963	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.72747606435266	4		811	1106	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346963	89346963	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768652993	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	206	409	0	ENST00000301030.4:c.5987C>T	p.Pro1996Leu	p.P1996L	ENST00000301030	NM_001256183.1	1996	cCc/cTc	9/13	0.667830160367963	4	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	2	0.72747606435266	4		409	489	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577539	7577539	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs121912651	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	144	385	601	0	ENST00000269305.4:c.742C>G	p.Arg248Gly	p.R248G	ENST00000269305	NM_001126112.2	248	Cgg/Ggg	7/11	NA	2	FACETS	1	0.968	1			1	INDETERMINATE	2	TRUE	NA	0.72747606435266	2		601	529	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576010	29576010	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	248	458	1	ENST00000356175.3:c.3983C>T	p.Pro1328Leu	p.P1328L	ENST00000356175	NM_000267.3	1328	cCa/cTa	30/57	0.430044079353475	6	FACETS	0.946	0.892	1	0.946	0.892	1	INDETERMINATE	3	TRUE	3	0.72747606435266	6		459	590	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29592318	29592318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	197	488	0	ENST00000356175.3:c.4733C>T	p.Ser1578Phe	p.S1578F	ENST00000356175	NM_000267.3	1578	tCc/tTc	35/57	0.72747606435266	3	FACETS	0.914	0.859	0.97	0.914	0.859	0.97	CLONAL	2	TRUE	1	0.72747606435266	3		488	404	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62006651	62006651	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	203	725	1	ENST00000392795.3:c.628G>A	p.Asp210Asn	p.D210N	ENST00000392795	NM_001039933.1	210	Gac/Aac	6/6	0.72747606435266	3	FACETS	0.996	0.926	1	0.498	0.463	0.534	CLONAL	1	TRUE	1	0.72747606435266	3		726	764	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48604750	48604750	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1568211588	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	178	592	1	ENST00000342988.3:c.1572G>A	p.Trp524Ter	p.W524*	ENST00000342988	NM_005359.5	524	tgG/tgA	12/12	0.673400322664386	3	FACETS	1	0.953	1	0.52	0.481	0.56	CLONAL	1	TRUE	1	0.72747606435266	3		593	642	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4090613	4090613	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	345	540	0	ENST00000262948.5:c.1186A>T	p.Thr396Ser	p.T396S	ENST00000262948	NM_030662.3	396	Acg/Tcg	11/11	0.60600710690967	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	2	0.72747606435266	4		540	790	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271823	15271823	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778006941	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	392	667	0	ENST00000263388.2:c.6616G>A	p.Glu2206Lys	p.E2206K	ENST00000263388	NM_000435.2	2206	Gag/Aag	33/33	0.60600710690967	4	FACETS	0.993	0.948	1	0.993	0.948	1	CLONAL	2	TRUE	2	0.72747606435266	4		667	937	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353893	15353893	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1347891450	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	302	654	1	ENST00000263377.2:c.2987C>T	p.Pro996Leu	p.P996L	ENST00000263377	NM_058243.2	996	cCc/cTc	14/20	0.60600710690967	4	FACETS	0.857	0.81	0.904	0.857	0.81	0.904	CLONAL	2	TRUE	2	0.72747606435266	4		655	837	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375489	15375489	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	470	827	0	ENST00000263377.2:c.938C>T	p.Pro313Leu	p.P313L	ENST00000263377	NM_058243.2	313	cCc/cTc	6/20	0.60600710690967	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.72747606435266	4		827	1062	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36224250	36224250	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	380	710	0	ENST00000222270.7:c.6800G>A	p.Gly2267Glu	p.G2267E	ENST00000222270	NM_014727.1	2267	gGg/gAg	28/37	0.60600710690967	4	FACETS	1	0.967	1	1	0.967	1	CLONAL	2	TRUE	2	0.72747606435266	4		710	888	SUCCESS
ALK	238	MSKCC	GRCh37	2	29449925	29449925	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	587	1106	1	ENST00000389048.3:c.2930G>A	p.Gly977Glu	p.G977E	ENST00000389048	NM_004304.4	977	gGg/gAg	18/29	0.667830160367963	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	2	TRUE	2	0.72747606435266	4		1107	1303	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47596663	47596663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	255	474	0	ENST00000263735.4:c.19C>T	p.Leu7Phe	p.L7F	ENST00000263735	NM_002354.2	7	Ctc/Ttc	1/9	0.667830160367963	4	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	2	0.72747606435266	4		474	550	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033348	48033348	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776407427	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	197	510	0	ENST00000234420.5:c.3652G>A	p.Gly1218Ser	p.G1218S	ENST00000234420	NM_000179.2	1218	Ggt/Agt	8/10	0.667830160367963	4	FACETS	0.901	0.842	0.962	0.901	0.842	0.962	CLONAL	2	TRUE	2	0.72747606435266	4		510	519	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190708778	190708778	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	268	603	0	ENST00000441310.2:c.671C>T	p.Ser224Phe	p.S224F	ENST00000441310	NM_000534.4	224	tCc/tTc	6/13	0.667830160367963	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.72747606435266	4		603	610	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212285273	212285273	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	199	605	0	ENST00000342788.4:c.3028G>A	p.Glu1010Lys	p.E1010K	ENST00000342788	NM_005235.2	1010	Gaa/Aaa	25/28	0.667830160367963	4	FACETS	1	0.952	1	1	0.952	1	CLONAL	2	TRUE	2	0.72747606435266	4		605	464	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212295732	212295732	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	259	644	0	ENST00000342788.4:c.2581G>A	p.Asp861Asn	p.D861N	ENST00000342788	NM_005235.2	861	Gat/Aat	21/28	0.667830160367963	4	FACETS	1	0.985	1	1	0.985	1	CLONAL	2	TRUE	2	0.72747606435266	4		644	554	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566827	212566827	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202247795	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	185	365	0	ENST00000342788.4:c.1354G>A	p.Glu452Lys	p.E452K	ENST00000342788	NM_005235.2	452	Gaa/Aaa	12/28	0.667830160367963	4	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	2	0.72747606435266	4		365	428	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561085	9561085	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	182	378	0	ENST00000353224.5:c.697C>T	p.Gln233Ter	p.Q233*	ENST00000353224	NM_177990.2	233	Caa/Taa	4/10	0.667830160367963	4	FACETS	0.937	0.874	1	0.937	0.874	1	CLONAL	2	TRUE	2	0.72747606435266	4		378	461	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561504	9561504	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542553062	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	315	570	0	ENST00000353224.5:c.278C>T	p.Ser93Leu	p.S93L	ENST00000353224	NM_177990.2	93	tCg/tTg	4/10	0.667830160367963	4	FACETS	0.954	0.905	1	0.954	0.905	1	CLONAL	2	TRUE	2	0.72747606435266	4		570	784	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076868	41076868	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	206	538	0	ENST00000373198.4:c.1552C>T	p.Leu518Phe	p.L518F	ENST00000373198	NM_133170.3	518	Ctc/Ttc	9/32	0.667830160367963	4	FACETS	0.854	0.798	0.911	0.854	0.798	0.911	CLONAL	2	TRUE	2	0.72747606435266	4		538	573	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100959	41100959	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	280	274	0	ENST00000373198.4:c.1397A>G	p.Asn466Ser	p.N466S	ENST00000373198	NM_133170.3	466	aAc/aGc	8/32	0.667830160367963	4	FACETS	0.879	0.83	0.929	0.879	0.83	0.929	CLONAL	2	TRUE	2	0.72747606435266	4		274	756	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44514870	44514870	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	292	546	0	ENST00000291552.4:c.377C>T	p.Ala126Val	p.A126V	ENST00000291552	NM_006758.2	126	gCt/gTt	6/8	0.60600710690967	4	FACETS	0.892	0.844	0.942	0.892	0.844	0.942	CLONAL	2	TRUE	2	0.72747606435266	4		546	777	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37042498	37042498	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	290	466	0	ENST00000231790.2:c.260C>T	p.Ser87Phe	p.S87F	ENST00000231790	NM_000249.3	87	tCc/tTc	3/19	0.667830160367963	4	FACETS	0.912	0.862	0.962	0.912	0.862	0.962	CLONAL	2	TRUE	2	0.72747606435266	4		466	755	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275658	41275658	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	298	512	0	ENST00000349496.5:c.1553C>T	p.Ala518Val	p.A518V	ENST00000349496	NM_001904.3	518	gCc/gTc	10/15	0.667830160367963	4	FACETS	0.915	0.866	0.965	0.915	0.866	0.965	CLONAL	2	TRUE	2	0.72747606435266	4		512	773	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164529	47164529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1301833521	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	175	503	0	ENST00000409792.3:c.1597C>T	p.Pro533Ser	p.P533S	ENST00000409792	NM_014159.6	533	Ccc/Tcc	3/21	0.667830160367963	4	FACETS	0.834	0.775	0.895	0.834	0.775	0.895	CLONAL	2	TRUE	2	0.72747606435266	4		503	498	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164823	47164823	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	204	390	2	ENST00000409792.3:c.1303C>T	p.His435Tyr	p.H435Y	ENST00000409792	NM_014159.6	435	Cat/Tat	3/21	0.667830160367963	4	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	2	0.72747606435266	4		392	442	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134898764	134898764	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs185655852	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	216	432	0	ENST00000398015.3:c.1822C>T	p.Arg608Trp	p.R608W	ENST00000398015	NM_004441.4	608	Cgg/Tgg	10/16	0.667830160367963	4	FACETS	1	0.953	1	1	0.953	1	CLONAL	2	TRUE	2	0.72747606435266	4		432	504	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189455608	189455608	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	321	758	2	ENST00000264731.3:c.142G>A	p.Glu48Lys	p.E48K	ENST00000264731	NM_003722.4	48	Gaa/Aaa	2/14	0.667830160367963	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.72747606435266	4		760	738	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902463	1902463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	413	706	0	ENST00000382891.5:c.82C>T	p.Leu28Phe	p.L28F	ENST00000382891	NM_133335.3	28	Ctc/Ttc	2/22	0.667830160367963	4	FACETS	0.905	0.863	0.947	0.905	0.863	0.947	CLONAL	2	TRUE	2	0.72747606435266	4		706	1084	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902725	1902725	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	458	897	0	ENST00000382891.5:c.344C>T	p.Thr115Ile	p.T115I	ENST00000382891	NM_133335.3	115	aCc/aTc	2/22	0.667830160367963	4	FACETS	0.94	0.9	0.981	0.94	0.9	0.981	CLONAL	2	TRUE	2	0.72747606435266	4		897	1157	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139853	55139853	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	302	440	0	ENST00000257290.5:c.1514A>G	p.Asn505Ser	p.N505S	ENST00000257290	NM_006206.4	505	aAt/aGt	10/23	0.667830160367963	4	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	2	0.72747606435266	4		440	701	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964429	55964429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747827262	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	212	547	0	ENST00000263923.4:c.2384G>A	p.Gly795Glu	p.G795E	ENST00000263923	NM_002253.2	795	gGg/gAg	17/30	0.667830160367963	4	FACETS	0.869	0.814	0.926	0.869	0.814	0.926	CLONAL	2	TRUE	2	0.72747606435266	4		547	579	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	224614	224615	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	134	394	3	ENST00000264932.6:c.290_291delinsAA	p.Arg97Lys	p.R97K	ENST00000264932	NM_004168.2	97	aGG/aAA	3/15	0.673400322664386	3	FACETS	1	0.983	1	0.647	0.594	0.702	CLONAL	1	TRUE	1	0.72747606435266	3		397	388	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293875	1293875	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	512	1031	0	ENST00000310581.5:c.1126C>T	p.Pro376Ser	p.P376S	ENST00000310581	NM_198253.2	376	Ccc/Tcc	2/16	0.673400322664386	3	FACETS	0.958	0.923	0.993	0.958	0.923	0.993	CLONAL	2	TRUE	1	0.72747606435266	3		1031	1002	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295230	1295230	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs796516131	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	159	262	1				ENST00000310581	NM_198253.2	-/1132			0.673400322664386	3	FACETS	1	0.975	1	0.568	0.524	0.613	CLONAL	1	TRUE	1	0.72747606435266	3		263	525	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873748	35873748	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs766555082	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	120	399	0	ENST00000303115.3:c.704C>T	p.Ser235Leu	p.S235L	ENST00000303115	NM_002185.3	235	tCa/tTa	5/8	0.673400322664386	3	FACETS	0.752	0.69	0.816	0.752	0.69	0.816	SUBCLONAL	2	TRUE	1	0.72747606435266	3		399	299	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38959932	38959932	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	85	354	0	ENST00000357387.3:c.2000C>T	p.Ser667Phe	p.S667F	ENST00000357387	NM_152756.3	667	tCt/tTt	21/38	0.673400322664386	3	FACETS	1	0.936	1	0.533	0.476	0.592	CLONAL	1	TRUE	1	0.72747606435266	3		354	299	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176720994	176720994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	149	598	2	ENST00000439151.2:c.6625G>A	p.Gly2209Arg	p.G2209R	ENST00000439151	NM_022455.4	2209	Ggg/Agg	23/23	0.54149631375248	3	FACETS	0.98	0.9	1	0.49	0.45	0.532	CLONAL	1	TRUE	1	0.72747606435266	3		600	570	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180057759	180057759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	297	536	0	ENST00000261937.6:c.196G>A	p.Glu66Lys	p.E66K	ENST00000261937	NM_182925.4	66	Gag/Aag	3/30	0.54149631375248	3	FACETS	0.994	0.947	1	0.994	0.947	1	CLONAL	2	TRUE	1	0.72747606435266	3		536	560	SUCCESS
H3C10	8968	MSKCC	GRCh37	6	27778167	27778167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	246	549	0	ENST00000369163.2:c.316G>A	p.Glu106Lys	p.E106K	ENST00000369163	NM_003536.2	106	Gag/Aag	1/1	0.72747606435266	6	FACETS	0.859	0.804	0.916	0.43	0.402	0.458	CLONAL	2	TRUE	2	0.72747606435266	6		549	966	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940127	31940127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	471	937	0	ENST00000375333.2:c.269C>T	p.Pro90Leu	p.P90L	ENST00000375333	NM_032454.1	90	cCt/cTt	2/8	0.72747606435266	6	FACETS	0.982	0.937	1	0.491	0.468	0.514	CLONAL	2	TRUE	2	0.72747606435266	6		937	1618	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31948532	31948532	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180131726	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	89	162	0	ENST00000375333.2:c.1015C>T	p.Leu339Phe	p.L339F	ENST00000375333	NM_032454.1	339	Ctc/Ttc	7/8	0.72747606435266	6	FACETS	0.878	0.786	0.975	0.439	0.393	0.488	CLONAL	2	TRUE	2	0.72747606435266	6		162	342	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169171	32169171	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	391	714	0	ENST00000375023.3:c.3862G>A	p.Asp1288Asn	p.D1288N	ENST00000375023	NM_004557.3	1288	Gat/Aat	22/30	0.72747606435266	6	FACETS	0.998	0.948	1	0.499	0.474	0.525	CLONAL	2	TRUE	2	0.72747606435266	6		714	1322	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553473	106553473	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	80	223	320	0	ENST00000369096.4:c.1438C>A	p.Gln480Lys	p.Q480K	ENST00000369096	NM_001198.3	480	Cag/Aag	5/7	NA	2	FACETS	1	0.968	1			1	INDETERMINATE	2	TRUE	NA	0.72747606435266	2		320	303	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152415701	152415701	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1455484428	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	235	453	0	ENST00000206249.3:c.1551G>A	p.Met517Ile	p.M517I	ENST00000206249	NM_000125.3	517	atG/atA	7/8	0.72747606435266	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.72747606435266	2		453	313	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522622	157522623	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DNP	GG	GG	AA	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	333	708	2	ENST00000346085.5:c.4894_4894+1delinsAA		p.X1632_splice	ENST00000346085	NM_020732.3	1632		18/20	0.72747606435266	2	FACETS	0.928	0.893	0.963	0.928	0.893	0.963	CLONAL	2	TRUE	0	0.72747606435266	2		710	493	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979468	2979468	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	340	766	2	ENST00000396946.4:c.779G>A	p.Arg260Gln	p.R260Q	ENST00000396946	NM_032415.4	260	cGg/cAg	6/25	0.667830160367963	4	FACETS	0.816	0.774	0.859	0.816	0.774	0.859	CLONAL	2	TRUE	2	0.72747606435266	4		768	989	SUCCESS
STAG3L2	442582	MSKCC	GRCh37	7	74133216	74133216	+	intron_variant,non_coding_transcript_variant	Intron	SNP	C	C	T	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	252	461	1	ENST00000380775.3:n.1218+4368G>A		p.*406*	ENST00000380775		300/998			0.667830160367963	4	FACETS	1	0.951	1	1	0.951	1	CLONAL	2	TRUE	2	0.72747606435266	4		462	593	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545813	106545813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1344211812	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	177	509	1	ENST00000359195.3:c.3290G>A	p.Gly1097Glu	p.G1097E	ENST00000359195	NM_002649.2	1097	gGa/gAa	11/11	0.667830160367963	4	FACETS	0.953	0.888	1	0.953	0.888	1	CLONAL	2	TRUE	2	0.72747606435266	4		510	441	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90983463	90983463	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	91	249	0	ENST00000265433.3:c.640G>A	p.Gly214Arg	p.G214R	ENST00000265433	NM_002485.4	214	Gga/Aga	6/16	0.72747606435266	5	FACETS	0.896	0.797	1	0.299	0.265	0.334	CLONAL	1	TRUE	2	0.72747606435266	5		249	584	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737543	145737543	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	343	698	0	ENST00000428558.2:c.3220T>G	p.Phe1074Val	p.F1074V	ENST00000428558	NM_004260.3	1074	Ttc/Gtc	19/22	0.72747606435266	5	FACETS	0.928	0.88	0.978	0.619	0.586	0.652	CLONAL	2	TRUE	2	0.72747606435266	5		698	1062	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8497265	8497265	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1270795879	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	221	581	0	ENST00000356435.5:c.2326G>A	p.Glu776Lys	p.E776K	ENST00000356435		776	Gaa/Aaa	15/35	0.196912461887942	5	FACETS	1	0.983	1			1	INDETERMINATE	3	TRUE	NA	0.72747606435266	5		581	387	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971089	21971089	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	90	172	563	0	ENST00000304494.5:c.269T>C	p.Phe90Ser	p.F90S	ENST00000304494	NM_000077.4	90	tTc/tCc	2/3	0.72747606435266	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.72747606435266	1		563	262	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624600	93624600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	185	721	1	ENST00000375746.1:c.691G>A	p.Gly231Arg	p.G231R	ENST00000375746	NM_001174167.1	231	Gga/Aga	4/14	0.673400322664386	3	FACETS	0.976	0.904	1	0.488	0.452	0.525	CLONAL	1	TRUE	1	0.72747606435266	3		722	711	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39914651	39914651	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	387	339	0	ENST00000378444.4:c.4711C>T	p.His1571Tyr	p.H1571Y	ENST00000378444	NM_001123385.1	1571	Cac/Tac	12/15	0.647818960011528	2	FACETS	1	0.997	1			1	CLONAL	2	TRUE	NA	0.72747606435266	2		339	445	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928957	44928957	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	354	327	0	ENST00000377967.4:c.2057C>T	p.Pro686Leu	p.P686L	ENST00000377967	NM_021140.2	686	cCt/cTt	17/29	0.647818960011528	2	FACETS	1	0.995	1			1	CLONAL	2	TRUE	NA	0.72747606435266	2		327	432	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982038	70982038	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	399	870	0	ENST00000276594.2:c.58G>A	p.Glu20Lys	p.E20K	ENST00000276594	NM_024504.3	20	Gag/Aag	2/8	0.667830160367963	4	FACETS	0.871	0.83	0.912	0.871	0.83	0.912	CLONAL	2	TRUE	2	0.72747606435266	4		870	1088	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62322295	62322295	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015415-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	394	828	4	ENST00000360203.5:c.2551G>T	p.Glu851Ter	p.E851*	ENST00000360203	NM_001283009.1	851	Gag/Tag	27/35	0.667830160367963	4	FACETS	0.911	0.868	0.954	0.911	0.868	0.954	CLONAL	2	TRUE	2	0.72747606435266	4		832	1027	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913529	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	131	354	0	ENST00000311936.3:c.35G>A	p.Gly12Asp	p.G12D	ENST00000311936	NM_004985.3	12	gGt/gAt	2/5	1	2	FACETS	0.92	0.834	1	0.92	0.834	1	CLONAL	1	TRUE	1	0.282212158196593	2		354	1009	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	149	390	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.282212158196593	2		390	781	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16262669	16262669	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs138432235	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	124	365	0	ENST00000375759.3:c.9934C>T	p.Arg3312Cys	p.R3312C	ENST00000375759	NM_015001.2	3312	Cgc/Tgc	11/15	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.282212158196593	2		365	676	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023135	27023135	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	50	122	0	ENST00000324856.7:c.245del	p.Gly82ValfsTer19	p.G82Vfs*19	ENST00000324856	NM_006015.4	81	Ggg/gg	1/20	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.282212158196593	2		122	273	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	144	530	7	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.282212158196593	2		537	873	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	89	341	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.917	0.813	1	0.917	0.813	1	CLONAL	1	TRUE	1	0.282212158196593	2		341	688	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65325833	65325833	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs755650243	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	117	490	2	ENST00000342505.4:c.1289del	p.Pro430ArgfsTer2	p.P430Rfs*2	ENST00000342505	NM_002227.2	430	cCg/cg	9/25	1	2	FACETS	0.92	0.829	1	0.92	0.829	1	CLONAL	1	TRUE	1	0.282212158196593	2		492	901	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156830874	156830874	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	173	619	0	ENST00000524377.1:c.148T>C	p.Cys50Arg	p.C50R	ENST00000524377	NM_002529.3	50	Tgc/Cgc	1/17	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.282212158196593	2		619	1009	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193117069	193117069	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	172	417	1	ENST00000367435.3:c.802C>T	p.Arg268Ter	p.R268*	ENST00000367435	NM_024529.4	268	Cga/Tga	8/17	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.282212158196593	2		418	905	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982373	201982373	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1398134258	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1217	167	681	1	ENST00000359651.3:c.752G>A	p.Arg251Gln	p.R251Q	ENST00000359651		251	cGa/cAa	6/8	1	2	FACETS	0.855	0.783	0.93	0.855	0.783	0.93	CLONAL	1	TRUE	1	0.282212158196593	2		682	1384	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982989	201982989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	248	791	4	ENST00000359651.3:c.838C>T	p.Arg280Trp	p.R280W	ENST00000359651		280	Cgg/Tgg	7/8	1	2	FACETS	0.758	0.708	0.809	1	0.993	1	SUBCLONAL	2	TRUE	1	0.282212158196593	2		795	1160	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206652386	206652386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781784265	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	247	627	0	ENST00000367120.3:c.1093G>A	p.Val365Ile	p.V365I	ENST00000367120	NM_014002.3	365	Gtc/Atc	10/22	1	2	FACETS	0.777	0.726	0.83	1	0.993	1	SUBCLONAL	2	TRUE	1	0.282212158196593	2		627	1126	SUCCESS
FH	2271	MSKCC	GRCh37	1	241676971	241676971	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1303488878	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	171	564	0	ENST00000366560.3:c.310G>A	p.Ala104Thr	p.A104T	ENST00000366560	NM_000143.3	104	Gct/Act	3/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.282212158196593	2		564	987	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850705	63850705	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs201178069	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	116	409	1	ENST00000279873.7:c.1489del	p.Ile497Ter	p.I497*	ENST00000279873	NM_032199.2	495	Aaa/aa	10/10	1	2	FACETS	0.955	0.86	1	0.955	0.86	1	CLONAL	1	TRUE	1	0.282212158196593	2		410	861	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717745	89717745	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	179	406	0	ENST00000371953.3:c.770T>C	p.Phe257Ser	p.F257S	ENST00000371953	NM_000314.4	257	tTc/tCc	7/9	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.282212158196593	2		406	881	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104263973	104263974	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs587776579	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	56	360	0	ENST00000369902.3:c.71dup	p.Ala25GlyfsTer23	p.A25Gfs*23	ENST00000369902	NM_016169.3	22	gcc/gCcc	1/12	1	2	FACETS	0.69	0.591	0.798	0.69	0.591	0.798	SUBCLONAL	1	TRUE	1	0.282212158196593	2		360	575	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417879	32417880	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	142	624	1	ENST00000332351.3:c.1172dup	p.Met392HisfsTer9	p.M392Hfs*9	ENST00000332351	NM_024426.4	391	ttc/ttTc	7/10	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.282212158196593	2		625	985	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948209	71948209	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1265	213	953	7	ENST00000298229.2:c.2927del	p.Pro976HisfsTer155	p.P976Hfs*155	ENST00000298229	NM_001567.3	974	gCc/gc	26/28	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.282212158196593	2		960	1478	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098609	108098609	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	89	237	0	ENST00000278616.4:c.183del	p.Phe61LeufsTer15	p.F61Lfs*15	ENST00000278616	NM_000051.3	60	gTt/gt	3/63	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.282212158196593	2		237	520	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118391551	118391551	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	97	414	0	ENST00000534358.1:c.11464C>T	p.Arg3822Cys	p.R3822C	ENST00000534358	NM_005933.3	3822	Cgc/Tgc	34/36	1	2	FACETS	0.933	0.832	1	0.933	0.832	1	CLONAL	1	TRUE	1	0.282212158196593	2		414	737	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	419038	419042	+	frameshift_variant	Frame_Shift_Del	DEL	CTTTT	CTTTT	-	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	138	659	0	ENST00000399788.2:c.3305_3309del	p.Glu1102GlyfsTer9	p.E1102Gfs*9	ENST00000399788	NM_001042603.1	1102	gAAAAG/g	22/28	1	2	FACETS	0.81	0.735	0.889	0.81	0.735	0.889	CLONAL	1	TRUE	1	0.282212158196593	2		659	1208	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12043918	12043918	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1264117662	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	123	509	0	ENST00000396373.4:c.1297C>T	p.Arg433Cys	p.R433C	ENST00000396373	NM_001987.4	433	Cgt/Tgt	8/8	1	2	FACETS	0.95	0.858	1	0.95	0.858	1	CLONAL	1	TRUE	1	0.282212158196593	2		509	918	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380283	25380283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913528	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	187	605	0	ENST00000311936.3:c.175G>A	p.Ala59Thr	p.A59T	ENST00000311936	NM_004985.3	59	Gca/Aca	3/5	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.282212158196593	2		605	1027	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243382	46243382	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	30	300	0	ENST00000334344.6:c.1735A>G	p.Thr579Ala	p.T579A	ENST00000334344	NM_152641.2	579	Aca/Gca	14/21	1	2	FACETS	0.38	0.305	0.466	0.38	0.305	0.466	SUBCLONAL	1	TRUE	1	0.282212158196593	2		300	559	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434492	49434492	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	244	630	1	ENST00000301067.7:c.7061del	p.Pro2354LeufsTer30	p.P2354Lfs*30	ENST00000301067	NM_003482.3	2354	cCt/ct	31/54	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.282212158196593	2		631	1240	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	141	417	0	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.973	0.885	1	0.973	0.885	1	CLONAL	1	TRUE	1	0.282212158196593	2		417	1027	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863293	57863293	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200730656	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	124	569	1	ENST00000228682.2:c.1388G>A	p.Ser463Asn	p.S463N	ENST00000228682	NM_005269.2	463	aGt/aAt	11/12	1	2	FACETS	0.853	0.77	0.941	0.853	0.77	0.941	CLONAL	1	TRUE	1	0.282212158196593	2		570	1030	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856166	111856166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1446024614	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	117	540	1	ENST00000341259.2:c.217C>T	p.Arg73Cys	p.R73C	ENST00000341259	NM_005475.2	73	Cgc/Tgc	2/8	1	2	FACETS	0.929	0.837	1	0.929	0.837	1	CLONAL	1	TRUE	1	0.282212158196593	2		541	893	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111885286	111885286	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770836648	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	147	429	2	ENST00000341259.2:c.1174C>T	p.Arg392Trp	p.R392W	ENST00000341259	NM_005475.2	392	Cgg/Tgg	6/8	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.282212158196593	2		431	778	SUCCESS
RAB35	11021	MSKCC	GRCh37	12	120535147	120535147	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs771876856	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	166	278	0	ENST00000229340.5:c.508C>T	p.Arg170Ter	p.R170*	ENST00000229340	NM_006861.6	170	Cga/Tga	6/6	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.282212158196593	2		278	802	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21557912	21557912	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757472527	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	178	414	1	ENST00000382592.4:c.1933C>T	p.Arg645Trp	p.R645W	ENST00000382592	NM_014572.2	645	Cgg/Tgg	5/8	0.282212158196593	5	FACETS	0.77	0.708	0.834	0.385	0.354	0.417	SUBCLONAL	2	TRUE	1	0.282212158196593	5		415	1166	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134628	41134628	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759316607	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	391	382	1	ENST00000379561.5:c.1000G>A	p.Glu334Lys	p.E334K	ENST00000379561	NM_002015.3	334	Gaa/Aaa	2/3	0.282212158196593	5	FACETS	1	0.955	1	1	0.955	1	CLONAL	4	TRUE	1	0.282212158196593	5		383	984	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068315	30068315	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141649026	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	83	331	0	ENST00000331968.5:c.2084G>A	p.Arg695Gln	p.R695Q	ENST00000331968	NM_002742.2	695	cGg/cAg	15/18	1	2	FACETS	0.958	0.846	1	0.958	0.846	1	CLONAL	1	TRUE	1	0.282212158196593	2		331	614	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30396643	30396643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	206	36	147	0	ENST00000331968.5:c.76G>A	p.Ala26Thr	p.A26T	ENST00000331968	NM_002742.2	26	Gca/Aca	1/18	1	2	FACETS	1	0.866	1	1	0.866	1	CLONAL	1	TRUE	1	0.282212158196593	2		147	242	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81610503	81610503	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs137908024	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	77	397	0	ENST00000298171.2:c.2101C>T	p.Arg701Cys	p.R701C	ENST00000298171	NM_000369.2	701	Cgc/Tgc	10/10	1	2	FACETS	0.761	0.668	0.862	0.761	0.668	0.862	SUBCLONAL	1	TRUE	1	0.282212158196593	2		397	717	SUCCESS
GREM1	26585	MSKCC	GRCh37	15	33022990	33022990	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	152	458	1	ENST00000300177.4:c.104del	p.Pro35ArgfsTer49	p.P35Rfs*49	ENST00000300177	NM_001191322.1	33	atC/at	2/2	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.282212158196593	2		459	746	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631917	90631918	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs747216375	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1060	149	729	5	ENST00000330062.3:c.435dup	p.Thr146AspfsTer126	p.T146Dfs*126	ENST00000330062	NM_002168.2	145	-/G	4/11	1	2	FACETS	0.873	0.796	0.955	0.873	0.796	0.955	CLONAL	1	TRUE	1	0.282212158196593	2		734	1209	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99478614	99478614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1277066179	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	131	506	0	ENST00000268035.6:c.3256G>A	p.Asp1086Asn	p.D1086N	ENST00000268035	NM_000875.3	1086	Gat/Aat	17/21	1	2	FACETS	0.987	0.894	1	0.987	0.894	1	CLONAL	1	TRUE	1	0.282212158196593	2		506	941	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	338166	338166	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376835130	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	194	711	0	ENST00000262320.3:c.2545G>A	p.Val849Ile	p.V849I	ENST00000262320	NM_003502.3	849	Gtc/Atc	11/11	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.282212158196593	2		711	1160	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	354437	354437	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs538987269	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	127	623	0	ENST00000262320.3:c.1121C>T	p.Thr374Met	p.T374M	ENST00000262320	NM_003502.3	374	aCg/aTg	5/11	1	2	FACETS	0.936	0.847	1	0.936	0.847	1	CLONAL	1	TRUE	1	0.282212158196593	2		623	962	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129377	2129377	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs78956195	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	149	598	1	ENST00000219476.3:c.3232C>T	p.Arg1078Trp	p.R1078W	ENST00000219476	NM_000548.3	1078	Cgg/Tgg	28/42	1	2	FACETS	0.96	0.876	1	0.96	0.876	1	CLONAL	1	TRUE	1	0.282212158196593	2		599	1100	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3646322	3646322	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764210911	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	240	772	0	ENST00000294008.3:c.1756G>A	p.Ala586Thr	p.A586T	ENST00000294008	NM_032444.2	586	Gct/Act	8/15	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.282212158196593	2		772	1231	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14014191	14014191	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	124	369	0	ENST00000311895.7:c.169T>A	p.Cys57Ser	p.C57S	ENST00000311895	NM_005236.2	57	Tgc/Agc	1/11	1	2	FACETS	0.762	0.691	0.835	1	0.986	1	SUBCLONAL	2	TRUE	1	0.282212158196593	2		369	577	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649272	23649272	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs202194596	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	103	309	0	ENST00000261584.4:c.110G>A	p.Arg37His	p.R37H	ENST00000261584	NM_024675.3	37	cGt/cAt	3/13	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.282212158196593	2		309	628	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992437	72992437	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1168	230	828	1	ENST00000268489.5:c.1608G>A	p.Met536Ile	p.M536I	ENST00000268489	NM_006885.3	536	atG/atA	2/10	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.282212158196593	2		829	1398	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993143	72993143	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375991410	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1088	252	723	1	ENST00000268489.5:c.902C>T	p.Ala301Val	p.A301V	ENST00000268489	NM_006885.3	301	gCg/gTg	2/10	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.282212158196593	2		724	1340	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81891957	81891957	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768646306	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	104	429	0	ENST00000359376.3:c.427G>A	p.Glu143Lys	p.E143K	ENST00000359376	NM_002661.3	143	Gag/Aag	4/33	1	2	FACETS	0.898	0.803	0.998	0.898	0.803	0.998	CLONAL	1	TRUE	1	0.282212158196593	2		429	821	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346792	89346792	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765013102	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	117	314	1	ENST00000301030.4:c.6158C>T	p.Ala2053Val	p.A2053V	ENST00000301030	NM_001256183.1	2053	gCg/gTg	9/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.282212158196593	2		315	578	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321689	30321689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	220	712	0	ENST00000322652.5:c.1544G>A	p.Ser515Asn	p.S515N	ENST00000322652	NM_015355.2	515	aGt/aAt	13/16	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.282212158196593	2		712	1298	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880220	37880220	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913470	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1181	166	740	0	ENST00000269571.5:c.2264T>C	p.Leu755Ser	p.L755S	ENST00000269571		755	tTg/tCg	19/27	1	2	FACETS	0.873	0.8	0.95	0.873	0.8	0.95	CLONAL	1	TRUE	1	0.282212158196593	2		740	1347	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40489466	40489466	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	200	515	1	ENST00000264657.5:c.784C>T	p.Arg262Trp	p.R262W	ENST00000264657	NM_139276.2	262	Cgg/Tgg	8/24	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.282212158196593	2		516	952	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40497641	40497641	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1417279405	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	215	553	0	ENST00000264657.5:c.308G>A	p.Arg103Gln	p.R103Q	ENST00000264657	NM_139276.2	103	cGg/cAg	4/24	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.282212158196593	2		553	1083	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	478	736	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.993	1	1	0.998	1	CLONAL	3	TRUE	1	0.282212158196593	2		741	989	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007455	62007455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912424	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	95	409	0	ENST00000392795.3:c.412G>A	p.Gly138Ser	p.G138S	ENST00000392795	NM_001039933.1	138	Ggc/Agc	3/6	1	2	FACETS	0.921	0.82	1	0.921	0.82	1	CLONAL	1	TRUE	1	0.282212158196593	2		409	731	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11132522	11132522	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778175819	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	918	201	616	1	ENST00000358026.2:c.2738C>T	p.Pro913Leu	p.P913L	ENST00000358026	NM_001128849.1	913	cCg/cTg	19/36	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.282212158196593	2		617	1119	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11135088	11135088	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	232	752	0	ENST00000358026.2:c.3055A>G	p.Thr1019Ala	p.T1019A	ENST00000358026	NM_001128849.1	1019	Act/Gct	21/36	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.282212158196593	2		752	1211	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349666	15349666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200976853	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	164	491	0	ENST00000263377.2:c.3908C>T	p.Ala1303Val	p.A1303V	ENST00000263377	NM_058243.2	1303	gCg/gTg	19/20	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.282212158196593	2		491	871	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971636	18971636	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	193	548	0	ENST00000262803.5:c.2302A>G	p.Thr768Ala	p.T768A	ENST00000262803	NM_002911.3	768	Acc/Gcc	17/24	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.282212158196593	2		548	1036	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19258521	19258521	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1053	213	751	0	ENST00000162023.5:c.379C>T	p.Arg127Ter	p.R127*	ENST00000162023		127	Cga/Tga	8/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.282212158196593	2		751	1266	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211460	36211460	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1021849113	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1209	278	897	2	ENST00000222270.7:c.1211C>T	p.Pro404Leu	p.P404L	ENST00000222270	NM_014727.1	404	cCg/cTg	3/37	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.282212158196593	2		899	1487	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36222828	36222828	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1090	234	752	4	ENST00000222270.7:c.5462del	p.Pro1821HisfsTer74	p.P1821Hfs*74	ENST00000222270	NM_014727.1	1819	gaC/ga	27/37	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.282212158196593	2		756	1324	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42752691	42752691	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	223	600	1	ENST00000222329.4:c.1573C>A	p.Leu525Ile	p.L525I	ENST00000222329	NM_006494.2	525	Ctc/Atc	4/4	1	2	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	1	0.282212158196593	2		601	1077	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754595	42754595	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	176	646	2	ENST00000222329.4:c.145C>T	p.Gln49Ter	p.Q49*	ENST00000222329	NM_006494.2	49	Cag/Tag	2/4	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.282212158196593	2		648	1069	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791513	42791513	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754063822	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	137	626	3	ENST00000575354.2:c.494C>T	p.Pro165Leu	p.P165L	ENST00000575354	NM_015125.3	165	cCg/cTg	4/20	1	2	FACETS	0.846	0.768	0.929	0.846	0.768	0.929	CLONAL	1	TRUE	1	0.282212158196593	2		629	1147	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792047	42792047	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1432205915	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	123	566	0	ENST00000575354.2:c.851C>T	p.Thr284Met	p.T284M	ENST00000575354	NM_015125.3	284	aCg/aTg	6/20	1	2	FACETS	0.953	0.861	1	0.953	0.861	1	CLONAL	1	TRUE	1	0.282212158196593	2		566	915	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868341	45868341	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	228	767	0	ENST00000391945.4:c.436T>C	p.Tyr146His	p.Y146H	ENST00000391945	NM_000400.3	146	Tac/Cac	6/23	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.282212158196593	2		767	1254	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50910264	50910264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs878854523	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	207	665	2	ENST00000440232.2:c.1519C>T	p.Arg507Cys	p.R507C	ENST00000440232	NM_002691.3	507	Cgc/Tgc	13/27	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.282212158196593	2		667	1105	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52715982	52715982	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519946	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	167	775	0	ENST00000322088.6:c.547C>T	p.Arg183Trp	p.R183W	ENST00000322088	NM_014225.5	183	Cgg/Tgg	5/15	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.282212158196593	2		775	891	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082314	16082314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1210	233	469	3	ENST00000281043.3:c.134del	p.Pro45ArgfsTer86	p.P45Rfs*86	ENST00000281043	NM_005378.4	43	aCc/ac	2/3	0.282212158196593	2	FACETS	1	0.981	1	0.572	0.532	0.614	CLONAL	1	TRUE	0	0.282212158196593	2		472	1443	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25536799	25536799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs959218576	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	226	623	3	ENST00000264709.3:c.55C>T	p.Arg19Trp	p.R19W	ENST00000264709	NM_175629.2	19	Cgg/Tgg	2/23	0.282212158196593	2	FACETS	0.753	0.701	0.806	0.753	0.701	0.806	SUBCLONAL	2	TRUE	0	0.282212158196593	2		626	1064	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143052	30143052	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1244823020	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	221	785	1	ENST00000389048.3:c.474del	p.Glu160ArgfsTer26	p.E160Rfs*26	ENST00000389048	NM_004304.4	158	ccC/cc	1/29	0.282212158196593	2	FACETS	1	0.985	1	0.61	0.567	0.656	CLONAL	1	TRUE	0	0.282212158196593	2		786	1283	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46602891	46602891	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762258398	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	214	630	1	ENST00000263734.3:c.949G>A	p.Val317Met	p.V317M	ENST00000263734	NM_001430.4	317	Gtg/Atg	8/16	0.282212158196593	2	FACETS	1	0.989	1	0.672	0.623	0.722	CLONAL	1	TRUE	0	0.282212158196593	2		631	1129	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47703653	47703653	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	139	475	0	ENST00000233146.2:c.2154del	p.Gln718HisfsTer2	p.Q718Hfs*2	ENST00000233146	NM_000251.2	718	cAa/ca	13/16	0.282212158196593	2	FACETS	1	0.957	1	0.543	0.494	0.595	CLONAL	1	TRUE	0	0.282212158196593	2		475	907	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026020	48026020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779858670	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	179	436	1	ENST00000234420.5:c.898C>T	p.Arg300Trp	p.R300W	ENST00000234420	NM_000179.2	300	Cgg/Tgg	4/10	0.282212158196593	2	FACETS	0.795	0.734	0.858	0.795	0.734	0.858	SUBCLONAL	2	TRUE	0	0.282212158196593	2		437	798	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030639	48030640	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs267608078	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	110	495	2	ENST00000234420.5:c.3261dup	p.Phe1088LeufsTer5	p.F1088Lfs*5	ENST00000234420	NM_000179.2	1085	acc/aCcc	5/10	0.282212158196593	2	FACETS	0.815	0.731	0.905	0.408	0.365	0.453	CLONAL	1	TRUE	0	0.282212158196593	2		497	956	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202149799	202149799	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	48	582	0	ENST00000358485.4:c.1245del	p.Phe415LeufsTer26	p.F415Lfs*26	ENST00000358485	NM_001080125.1	414	Ttt/tt	8/9	0.157219207021293	2	FACETS	0.37	0.311	0.435	0.185	0.155	0.218	INDETERMINATE	1	TRUE	0	0.282212158196593	2		582	920	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812259	212812259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs991337964	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	143	423	2	ENST00000342788.4:c.317G>A	p.Arg106His	p.R106H	ENST00000342788	NM_005235.2	106	cGt/cAt	3/28	0.157219207021293	2	FACETS	1	0.983	1	0.668	0.61	0.73	INDETERMINATE	1	TRUE	0	0.282212158196593	2		425	758	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306584	41306584	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	121	654	1	ENST00000373198.4:c.1075C>T	p.Arg359Ter	p.R359*	ENST00000373198	NM_133170.3	359	Cga/Tga	7/32	1	2	FACETS	0.808	0.729	0.893	0.808	0.729	0.893	CLONAL	1	TRUE	1	0.282212158196593	2		655	1061	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264985	46264985	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	197	294	0	ENST00000371998.3:c.1860del	p.Lys620AsnfsTer18	p.K620Nfs*18	ENST00000371998		619	Aaa/aa	12/23	1	2	FACETS	0.772	0.715	0.831	1	0.991	1	SUBCLONAL	2	TRUE	1	0.282212158196593	2		294	904	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42851212	42851212	+	splice_region_variant,intron_variant	Splice_Region	DEL	A	A	-	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	131	368	0	ENST00000398585.3:c.684-3del		p.X228_splice	ENST00000398585	NM_001135099.1	228			1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.282212158196593	2		368	736	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37627348	37627348	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1250	309	969	0	ENST00000249071.6:c.371A>C	p.Asp124Ala	p.D124A	ENST00000249071	NM_002872.4	124	gAc/gCc	5/7	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.282212158196593	2		969	1559	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421349	12421349	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	269	749	0	ENST00000287820.6:c.229C>T	p.His77Tyr	p.H77Y	ENST00000287820	NM_015869.4	77	Cat/Tat	2/7	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.282212158196593	2		749	1447	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12434182	12434182	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776687	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	153	509	2	ENST00000287820.6:c.556del	p.Ser186ValfsTer47	p.S186Vfs*47	ENST00000287820	NM_015869.4	184	Aaa/aa	4/7	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.282212158196593	2		511	996	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12632469	12632469	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	127	500	0	ENST00000251849.4:c.1198A>G	p.Thr400Ala	p.T400A	ENST00000251849	NM_002880.3	400	Aca/Gca	12/17	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.282212158196593	2		500	873	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30732996	30732996	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs104893809	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	140	319	0	ENST00000295754.5:c.1609C>T	p.Arg537Cys	p.R537C	ENST00000295754	NM_003242.5	537	Cgc/Tgc	7/7	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.282212158196593	2		319	734	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49935036	49935036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1309171612	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	157	693	2	ENST00000296474.3:c.1963G>A	p.Val655Ile	p.V655I	ENST00000296474	NM_002447.2	655	Gtc/Atc	6/20	1	2	FACETS	0.958	0.876	1	0.958	0.876	1	CLONAL	1	TRUE	1	0.282212158196593	2		695	1161	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69928380	69928380	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	106	321	0	ENST00000352241.4:c.200A>G	p.Gln67Arg	p.Q67R	ENST00000352241	NM_198159.2	67	cAg/cGg	2/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.282212158196593	2		321	599	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73108281	73108281	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	43	151	0	ENST00000356692.5:c.381G>T	p.Lys127Asn	p.K127N	ENST00000356692		127	aaG/aaT	4/9	1	2	FACETS	1	0.877	1	1	0.877	1	CLONAL	1	TRUE	1	0.282212158196593	2		151	290	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170009727	170009727	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	78	265	0	ENST00000295797.4:c.1289A>G	p.Tyr430Cys	p.Y430C	ENST00000295797	NM_002740.5	430	tAt/tGt	13/18	1	2	FACETS	0.814	0.715	0.92	0.814	0.715	0.92	CLONAL	1	TRUE	1	0.282212158196593	2		265	679	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430901	181430901	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	973	164	383	0	ENST00000325404.1:c.758del	p.Pro253LeufsTer21	p.P253Lfs*21	ENST00000325404	NM_003106.3	251	agC/ag	1/1	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.282212158196593	2		383	1137	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156664	55156664	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	147	449	0	ENST00000257290.5:c.3065T>C	p.Leu1022Pro	p.L1022P	ENST00000257290	NM_006206.4	1022	cTg/cCg	22/23	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.282212158196593	2		449	851	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467573	66467573	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	99	321	0	ENST00000273854.3:c.696del	p.Lys232AsnfsTer36	p.K232Nfs*36	ENST00000273854	NM_004439.5	232	aaA/aa	3/18	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.282212158196593	2		321	692	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	173	616	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.282212158196593	2		617	989	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534439	187534441	+	inframe_deletion	In_Frame_Del	DEL	AGA	AGA	-	rs1560934316	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	797	92	431	0	ENST00000441802.2:c.9285_9287del	p.Leu3096del	p.L3096del	ENST00000441802	NM_005245.3	3095	ctTCTc/ctc	13/27	1	2	FACETS	0.733	0.651	0.822	0.733	0.651	0.822	SUBCLONAL	1	TRUE	1	0.282212158196593	2		431	889	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630266	187630266	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	78	535	0	ENST00000441802.2:c.716G>A	p.Ser239Asn	p.S239N	ENST00000441802	NM_005245.3	239	aGc/aAc	2/27	1	2	FACETS	0.548	0.48	0.621	0.548	0.48	0.621	SUBCLONAL	1	TRUE	1	0.282212158196593	2		535	1009	SUCCESS
APC	324	MSKCC	GRCh37	5	112128191	112128191	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs397515734	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	243	467	0	ENST00000257430.4:c.694C>T	p.Arg232Ter	p.R232*	ENST00000257430	NM_000038.5	232	Cga/Tga	7/16	1	2	FACETS	0.762	0.711	0.814	1	0.992	1	SUBCLONAL	2	TRUE	1	0.282212158196593	2		467	1130	SUCCESS
APC	324	MSKCC	GRCh37	5	112175510	112175510	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	95	353	0	ENST00000257430.4:c.4219A>G	p.Ser1407Gly	p.S1407G	ENST00000257430	NM_000038.5	1407	Agt/Ggt	16/16	1	2	FACETS	1	0.895	1	1	0.895	1	CLONAL	1	TRUE	1	0.282212158196593	2		353	670	SUCCESS
APC	324	MSKCC	GRCh37	5	112175952	112175952	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587783031	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	97	209	1	ENST00000257430.4:c.4666del	p.Thr1556LeufsTer9	p.T1556Lfs*9	ENST00000257430	NM_000038.5	1554	gAa/ga	16/16	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.282212158196593	2		210	585	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048668	180048668	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1158883745	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	206	571	3	ENST00000261937.6:c.1894C>T	p.Arg632Cys	p.R632C	ENST00000261937	NM_182925.4	632	Cgc/Tgc	13/30	1	2	FACETS	0.787	0.73	0.845	1	0.992	1	SUBCLONAL	2	TRUE	1	0.282212158196593	2		574	928	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800564	32800564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148663600	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	156	708	1	ENST00000374899.4:c.983C>T	p.Ala328Val	p.A328V	ENST00000374899	NM_018833.2	328	gCg/gTg	6/12	1	2	FACETS	0.935	0.855	1	0.935	0.855	1	CLONAL	1	TRUE	1	0.282212158196593	2		709	1182	SUCCESS
CCND3	896	MSKCC	GRCh37	6	41903706	41903706	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	132	576	0	ENST00000372991.4:c.851C>T	p.Pro284Leu	p.P284L	ENST00000372991	NM_001760.3	284	cCt/cTt	5/5	1	2	FACETS	0.934	0.846	1	0.934	0.846	1	CLONAL	1	TRUE	1	0.282212158196593	2		576	1002	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967244	93967244	+	splice_region_variant,intron_variant	Splice_Region	DEL	A	A	-	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	47	284	0	ENST00000369303.4:c.2111-3del		p.X704_splice	ENST00000369303	NM_004440.3	704			1	2	FACETS	0.643	0.542	0.754	0.643	0.542	0.754	SUBCLONAL	1	TRUE	1	0.282212158196593	2		284	518	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117706974	117706974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776027945	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	164	589	0	ENST00000368508.3:c.2176G>A	p.Val726Ile	p.V726I	ENST00000368508	NM_002944.2	726	Gtt/Att	15/43	1	2	FACETS	0.995	0.912	1	0.995	0.912	1	CLONAL	1	TRUE	1	0.282212158196593	2		589	1168	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152129201	152129201	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	213	653	0	ENST00000206249.3:c.154T>C	p.Tyr52His	p.Y52H	ENST00000206249	NM_000125.3	52	Tac/Cac	1/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.282212158196593	2		653	1209	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157510806	157510806	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	129	392	1	ENST00000346085.5:c.3586del	p.Gln1196SerfsTer15	p.Q1196Sfs*15	ENST00000346085	NM_020732.3	1194	aCc/ac	14/20	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.282212158196593	2		393	836	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	121	225	1	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	0.27978759274145	3	FACETS	1	0.983	1	0.712	0.644	0.784	CLONAL	1	TRUE	1	0.282212158196593	3		226	687	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851987	128851987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1245615022	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1097	124	660	1	ENST00000249373.3:c.2059C>T	p.Pro687Ser	p.P687S	ENST00000249373	NM_005631.4	687	Ccg/Tcg	12/12	0.27978759274145	3	FACETS	0.821	0.741	0.907	0.411	0.37	0.454	CLONAL	1	TRUE	1	0.282212158196593	3		661	1221	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151168649	151168649	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1130	194	516	0	ENST00000262187.5:c.318G>T	p.Met106Ile	p.M106I	ENST00000262187	NM_005614.3	106	atG/atT	5/8	0.27978759274145	3	FACETS	1	0.981	1	0.592	0.547	0.64	CLONAL	1	TRUE	1	0.282212158196593	3		516	1324	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38285869	38285869	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs515726222	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	195	646	0	ENST00000425967.3:c.541+1G>A		p.X181_splice	ENST00000425967	NM_001174067.1	181			1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.282212158196593	2		646	1091	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70982031	70982031	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	207	717	0	ENST00000276594.2:c.65G>C	p.Ser22Thr	p.S22T	ENST00000276594	NM_024504.3	22	aGc/aCc	2/8	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.282212158196593	2		717	1285	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878926	117878926	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	127	422	0	ENST00000297338.2:c.43G>C	p.Ala15Pro	p.A15P	ENST00000297338	NM_006265.2	15	Gcc/Ccc	2/14	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.282212158196593	2		422	843	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737415	145737415	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	170	616	0	ENST00000428558.2:c.3272A>G	p.Gln1091Arg	p.Q1091R	ENST00000428558	NM_004260.3	1091	cAg/cGg	20/22	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.282212158196593	2		616	970	SUCCESS
CDKN2B	1030	MSKCC	GRCh37	9	22006224	22006224	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	151	508	0	ENST00000276925.6:c.179G>A	p.Arg60His	p.R60H	ENST00000276925	NM_004936.3	60	cGc/cAc	2/2	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.282212158196593	2		508	932	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87322805	87322805	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749146781	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	103	477	2	ENST00000277120.3:c.406C>T	p.Arg136Cys	p.R136C	ENST00000277120		136	Cgt/Tgt	5/19	1	2	FACETS	0.74	0.66	0.824	0.74	0.66	0.824	SUBCLONAL	1	TRUE	1	0.282212158196593	2		479	987	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624552	93624552	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	144	623	0	ENST00000375746.1:c.643C>T	p.His215Tyr	p.H215Y	ENST00000375746	NM_001174167.1	215	Cac/Tac	4/14	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.282212158196593	2		623	986	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624623	93624623	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	138	434	2	ENST00000375746.1:c.714G>A	p.Trp238Ter	p.W238*	ENST00000375746	NM_001174167.1	238	tgG/tgA	4/14	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.282212158196593	2		436	771	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900239	101900239	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1564161544	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	132	492	0	ENST00000374994.4:c.673C>T	p.Arg225Trp	p.R225W	ENST00000374994	NM_004612.2	225	Cgg/Tgg	4/9	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.282212158196593	2		492	834	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293514	137293514	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs55836231	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1095	203	773	0	ENST00000481739.1:c.65C>T	p.Pro22Leu	p.P22L	ENST00000481739	NM_002957.4	22	cCg/cTg	2/10	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.282212158196593	2		773	1298	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426415	47426415	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	180	306	0	ENST00000377045.4:c.763del	p.Arg255GlyfsTer37	p.R255Gfs*37	ENST00000377045	NM_001654.4	253	aCc/ac	9/16	1	1	FACETS	1	0.968	1	1	0.993	1	CLONAL	2	TRUE	0	0.282212158196593	1		306	511	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228063	53228063	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015416-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	200	320	0	ENST00000375401.3:c.2251T>C	p.Tyr751His	p.Y751H	ENST00000375401	NM_004187.3	751	Tat/Cat	16/26	1	1	FACETS	1	0.974	1	1	0.994	1	CLONAL	2	TRUE	0	0.282212158196593	1		320	560	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426885	70426885	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	33	402	0	ENST00000373644.4:c.4545G>A	p.Met1515Ile	p.M1515I	ENST00000373644	NM_030625.2	1515	atG/atA	7/12	0.225088609283307	1	FACETS	0.488	0.397	0.592	0.488	0.397	0.592	SUBCLONAL	1	FALSE	0	0.225088609283307	1		402	533	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154778	2154778	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	100	873	0	ENST00000434045.2:c.443G>C	p.Arg148Thr	p.R148T	ENST00000434045	NM_001127598.1	148	aGg/aCg	4/5	0.225088609283307	0	FACETS	0.856	0.765	0.954			1	CLONAL	1	FALSE	0	0.225088609283307	0		873	804	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25380275	25380275	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs17851045	NA	P-0015420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	97	599	1	ENST00000311936.3:c.183A>T	p.Gln61His	p.Q61H	ENST00000311936	NM_004985.3	61	caA/caT	3/5	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	FALSE	1	0.225088609283307	2		600	813	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115118770	115118770	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	91	570	0	ENST00000257566.3:c.571C>A	p.Pro191Thr	p.P191T	ENST00000257566	NM_016569.3	191	Ccc/Acc	2/8	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	FALSE	1	0.225088609283307	2		570	618	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054051	42054051	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	T	novel	NA	P-0015420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	28	333	0	ENST00000219905.7:c.7510+3G>T		p.X2504_splice	ENST00000219905	NM_001164273.1	2504			0.225088609283307	1	FACETS	0.679	0.544	0.834	0.679	0.544	0.834	SUBCLONAL	1	FALSE	0	0.225088609283307	1		333	325	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88472460	88472460	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	87	593	0	ENST00000360948.2:c.2095G>T	p.Gly699Cys	p.G699C	ENST00000360948	NM_001012338.2	699	Ggc/Tgc	16/19	0.225088609283307	1	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	FALSE	0	0.225088609283307	1		593	647	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30128306	30128306	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1019644388	NA	P-0015420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	115	692	0	ENST00000263025.4:c.926G>T	p.Arg309Leu	p.R309L	ENST00000263025	NM_002746.2	309	cGg/cTg	7/9	0.225088609283307	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	FALSE	0	0.225088609283307	1		692	871	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991512	72991512	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	78	766	0	ENST00000268489.5:c.2533A>T	p.Asn845Tyr	p.N845Y	ENST00000268489	NM_006885.3	845	Aac/Tac	2/10	0.225088609283307	1	FACETS	0.843	0.74	0.953	0.843	0.74	0.953	CLONAL	1	FALSE	0	0.225088609283307	1		766	730	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38512429	38512429	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	62	745	1	ENST00000254066.5:c.1340G>T	p.Ser447Ile	p.S447I	ENST00000254066	NM_000964.3	447	aGc/aTc	9/9	1	2	FACETS	0.619	0.533	0.713	0.619	0.533	0.713	SUBCLONAL	1	FALSE	1	0.225088609283307	2		746	890	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40359635	40359635	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	54	616	1	ENST00000293328.3:c.2018G>T	p.Arg673Leu	p.R673L	ENST00000293328	NM_012448.3	673	cGg/cTg	16/19	1	2	FACETS	0.522	0.444	0.608	0.522	0.444	0.608	SUBCLONAL	1	FALSE	1	0.225088609283307	2		617	919	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740747	58740747	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	57	760	0	ENST00000305921.3:c.1652G>C	p.Arg551Thr	p.R551T	ENST00000305921	NM_003620.3	551	aGa/aCa	6/6	1	2	FACETS	0.561	0.48	0.651	0.561	0.48	0.651	SUBCLONAL	1	FALSE	1	0.225088609283307	2		760	902	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63553994	63554025	+	frameshift_variant	Frame_Shift_Del	DEL	CAACCACGGTTGGCGAAAGTTTGCACTTGAAG	CAACCACGGTTGGCGAAAGTTTGCACTTGAAG	-	novel	NA	P-0015420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	40	529	0	ENST00000307078.5:c.714_745del	p.Asp238GlufsTer20	p.D238Efs*20	ENST00000307078	NM_004655.3	238	gaCTTCAAGTGCAAACTTTCGCCAACCGTGGTTGgc/gagc	2/11	1	2	FACETS	0.581	0.482	0.692	0.581	0.482	0.692	SUBCLONAL	1	FALSE	1	0.225088609283307	2		529	612	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1207162	1207162	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	rs137853076	NA	P-0015420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	121	850	1	ENST00000326873.7:c.250A>T	p.Lys84Ter	p.K84*	ENST00000326873	NM_000455.4	84	Aag/Tag	1/10	0.225088609283307	1	FACETS	0.947	0.854	1	0.947	0.854	1	CLONAL	1	FALSE	0	0.225088609283307	1		851	1008	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602662	10602662	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs1457377196	NA	P-0015420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	96	694	1	ENST00000171111.5:c.916G>T	p.Glu306Ter	p.E306*	ENST00000171111	NM_203500.1	306	Gag/Tag	3/6	0.225088609283307	1	FACETS	0.955	0.85	1	0.955	0.85	1	CLONAL	1	FALSE	0	0.225088609283307	1		695	793	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11123685	11123685	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	104	592	0	ENST00000358026.2:c.2335G>C	p.Asp779His	p.D779H	ENST00000358026	NM_001128849.1	779	Gac/Cac	16/36	0.225088609283307	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	FALSE	0	0.225088609283307	1		592	756	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921347	178921347	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	49	514	0	ENST00000263967.3:c.829A>T	p.Ile277Leu	p.I277L	ENST00000263967	NM_006218.2	277	Ata/Tta	5/21	1	2	FACETS	0.744	0.63	0.87	0.744	0.63	0.87	SUBCLONAL	1	FALSE	1	0.225088609283307	2		514	585	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964872	55964872	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374386254	NA	P-0015420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	30	433	0	ENST00000263923.4:c.2365G>A	p.Val789Ile	p.V789I	ENST00000263923	NM_002253.2	789	Gtt/Att	16/30	0.225088609283307	1	FACETS	0.494	0.397	0.604	0.494	0.397	0.604	SUBCLONAL	1	FALSE	0	0.225088609283307	1		433	479	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176519486	176519486	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776720644	NA	P-0015420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	53	842	1	ENST00000292408.4:c.892G>A	p.Gly298Ser	p.G298S	ENST00000292408	NM_213647.1	298	Ggt/Agt	7/18	1	2	FACETS	0.55	0.468	0.641	0.55	0.468	0.641	SUBCLONAL	1	FALSE	1	0.225088609283307	2		843	856	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32178685	32178685	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	78	759	0	ENST00000375023.3:c.2709T>A	p.Asn903Lys	p.N903K	ENST00000375023	NM_004557.3	903	aaT/aaA	18/30	1	2	FACETS	0.703	0.616	0.797	0.703	0.616	0.797	SUBCLONAL	1	FALSE	1	0.225088609283307	2		759	986	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468097	50468097	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	58	366	0	ENST00000331340.3:c.1332C>A	p.Asn444Lys	p.N444K	ENST00000331340	NM_006060.4	444	aaC/aaA	8/8	1	2	FACETS	1	0.897	1	1	0.897	1	CLONAL	1	FALSE	1	0.225088609283307	2		366	490	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140534668	140534668	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	52	338	0	ENST00000288602.6:c.245A>T	p.Tyr82Phe	p.Y82F	ENST00000288602	NM_004333.4	82	tAt/tTt	3/18	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	FALSE	1	0.225088609283307	2		338	365	SUCCESS
RHEB	6009	MSKCC	GRCh37	7	151216557	151216557	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	35	304	0	ENST00000262187.5:c.41A>T	p.Tyr14Phe	p.Y14F	ENST00000262187	NM_005614.3	14	tAc/tTc	1/8	1	2	FACETS	0.755	0.619	0.907	0.755	0.619	0.907	CLONAL	1	FALSE	1	0.225088609283307	2		304	412	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69009311	69009311	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	73	479	0	ENST00000288368.4:c.2428C>A	p.Leu810Met	p.L810M	ENST00000288368	NM_024870.2	810	Ctg/Atg	22/40	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	FALSE	1	0.225088609283307	2		479	544	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87636327	87636327	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770827440	NA	P-0015420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	93	663	1	ENST00000277120.3:c.2492C>T	p.Pro831Leu	p.P831L	ENST00000277120		831	cCg/cTg	19/19	0.225088609283307	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	FALSE	0	0.225088609283307	1		664	676	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317468	1317468	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	45	818	0	ENST00000400841.2:c.597C>A	p.Tyr199Ter	p.Y199*	ENST00000400841		199	taC/taA	5/6	0.225088609283307	1	FACETS	0.404	0.338	0.477	0.404	0.338	0.477	SUBCLONAL	1	FALSE	0	0.225088609283307	1		818	879	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361100	70361100	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015420-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	45	462	0	ENST00000374080.3:c.6288G>C	p.Gln2096His	p.Q2096H	ENST00000374080		2096	caG/caC	43/45	0.225088609283307	1	FACETS	0.839	0.706	0.985	0.839	0.706	0.985	CLONAL	1	FALSE	0	0.225088609283307	1		462	423	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	170	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.937	0.868	1	0.937	0.868	1	CLONAL	1	TRUE	1	0.698993872182364	2		215	519	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805076	43805076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	300	787	1	ENST00000372470.3:c.526C>T	p.Pro176Ser	p.P176S	ENST00000372470	NM_005373.2	176	Ccc/Tcc	4/12	0.698993872182364	3	FACETS	0.919	0.864	0.974	0.459	0.432	0.487	CLONAL	1	TRUE	1	0.698993872182364	3		788	1261	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115258744	115258744	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121434596	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	520	477	0	ENST00000369535.4:c.38G>A	p.Gly13Asp	p.G13D	ENST00000369535	NM_002524.4	13	gGt/gAt	2/7	0.698993872182364	3	FACETS	0.981	0.945	1	0.981	0.945	1	CLONAL	2	TRUE	1	0.698993872182364	3		477	1023	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63850751	63850751	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	223	538	0	ENST00000279873.7:c.1529C>T	p.Ser510Phe	p.S510F	ENST00000279873	NM_032199.2	510	tCc/tTc	10/10	0.698993872182364	3	FACETS	0.868	0.808	0.93	0.434	0.404	0.465	CLONAL	1	TRUE	1	0.698993872182364	3		538	992	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421568	32421568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267602851	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	250	290	0	ENST00000332351.3:c.1024G>A	p.Asp342Asn	p.D342N	ENST00000332351	NM_024426.4	342	Gat/Aat	6/10	1	2	FACETS	0.899	0.843	0.955	0.899	0.843	0.955	CLONAL	1	TRUE	1	0.698993872182364	2		290	796	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137784	64137784	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	922	982	0	ENST00000334205.4:c.1885C>T	p.Arg629Cys	p.R629C	ENST00000334205	NM_003942.2	629	Cgc/Tgc	15/17	0.580440225875257	4	FACETS	0.908	0.884	0.931	0.908	0.884	0.931	CLONAL	3	TRUE	1	0.698993872182364	4		982	1646	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572003	64572003	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	852	822	1	ENST00000312049.6:c.1636C>T	p.Pro546Ser	p.P546S	ENST00000312049	NM_130799.2	546	Ccg/Tcg	10/10	0.580440225875257	4	FACETS	0.978	0.952	1	0.978	0.952	1	CLONAL	3	TRUE	1	0.698993872182364	4		823	1412	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999777	100999777	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	47	673	0	ENST00000325455.5:c.25C>T	p.Pro9Ser	p.P9S	ENST00000325455	NM_001202474.3	9	Ccc/Tcc	1/8	0.599894444284563	1	FACETS	0.165	0.139	0.194	0.165	0.139	0.194	SUBCLONAL	1	TRUE	0	0.698993872182364	1		673	529	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945093	31945093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	334	650	0	ENST00000340398.3:c.8G>A	p.Arg3Gln	p.R3Q	ENST00000340398	NM_001013699.2	3	cGa/cAa	1/1	0.698993872182364	2	FACETS	0.908	0.872	0.944	0.908	0.872	0.944	CLONAL	2	TRUE	0	0.698993872182364	2		650	526	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211590	46211590	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	363	330	0	ENST00000334344.6:c.556G>A	p.Glu186Lys	p.E186K	ENST00000334344	NM_152641.2	186	Gaa/Aaa	5/21	0.698993872182364	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.698993872182364	2		330	510	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959151	28959151	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1418663249	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	303	263	0	ENST00000282397.4:c.1987C>T	p.Leu663Phe	p.L663F	ENST00000282397	NM_002019.4	663	Ctc/Ttc	14/30	0.698993872182364	2	FACETS	0.92	0.882	0.958	0.92	0.882	0.958	CLONAL	2	TRUE	0	0.698993872182364	2		263	471	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133907	41133907	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	298	274	0	ENST00000379561.5:c.1721C>T	p.Ala574Val	p.A574V	ENST00000379561	NM_002015.3	574	gCc/gTc	2/3	0.698993872182364	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.698993872182364	2		274	390	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857020	9857020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1555481892	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	160	258	0	ENST00000330684.3:c.4381G>A	p.Glu1461Lys	p.E1461K	ENST00000330684	NM_001134407.1	1461	Gaa/Aaa	13/13	0.698993872182364	3	FACETS	0.928	0.865	0.99	0.928	0.865	0.99	CLONAL	2	TRUE	1	0.698993872182364	3		258	333	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992340	72992340	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148894513	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1254	384	1021	0	ENST00000268489.5:c.1705C>T	p.Arg569Cys	p.R569C	ENST00000268489	NM_006885.3	569	Cgt/Tgt	2/10	0.698993872182364	3	FACETS	0.905	0.858	0.954	0.453	0.429	0.477	CLONAL	1	TRUE	1	0.698993872182364	3		1021	1638	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81939102	81939102	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	409	517	0	ENST00000359376.3:c.1457C>T	p.Ser486Phe	p.S486F	ENST00000359376	NM_002661.3	486	tCc/tTc	15/33	0.698993872182364	3	FACETS	0.907	0.868	0.946	0.907	0.868	0.946	CLONAL	2	TRUE	1	0.698993872182364	3		517	871	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577052	7577055	+	stop_gained,frameshift_variant	Nonsense_Mutation	DEL	GAGG	GAGG	TA	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	659	726	2	ENST00000269305.4:c.883_886delinsTA	p.Pro295Ter	p.P295*	ENST00000269305	NM_001126112.2	295	CCTCac/TAac	8/11	NA	2	FACETS	0.99	0.964	1			1	INDETERMINATE	2	TRUE	NA	0.698993872182364	2		728	952	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556463	29556463	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs1567849208	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	186	329	0	ENST00000356175.3:c.2835del	p.Phe945LeufsTer9	p.F945Lfs*9	ENST00000356175	NM_000267.3	944	Ttt/tt	21/57	0.698993872182364	3	FACETS	0.958	0.887	1	0.479	0.443	0.516	CLONAL	1	TRUE	1	0.698993872182364	3		329	750	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	458	510	1	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	0.698993872182364	3	FACETS	0.926	0.889	0.963	0.926	0.889	0.963	CLONAL	2	TRUE	1	0.698993872182364	3		511	955	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677308	29677308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	243	358	0	ENST00000356175.3:c.7366C>T	p.Pro2456Ser	p.P2456S	ENST00000356175	NM_000267.3	2456	Ccc/Tcc	49/57	0.698993872182364	3	FACETS	0.807	0.761	0.855	0.807	0.761	0.855	CLONAL	2	TRUE	1	0.698993872182364	3		358	581	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37686902	37686902	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	481	536	0	ENST00000447079.4:c.3806C>T	p.Pro1269Leu	p.P1269L	ENST00000447079	NM_015083.1	1269	cCc/cTc	14/14	0.698993872182364	3	FACETS	1	0.984	1	1	0.984	1	CLONAL	2	TRUE	1	0.698993872182364	3		536	894	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936856	78936856	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	320	412	0	ENST00000306801.3:c.3938G>A	p.Trp1313Ter	p.W1313*	ENST00000306801	NM_020761.2	1313	tGg/tAg	33/34	0.698993872182364	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.698993872182364	3		412	615	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219479	5219479	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs1453369741	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	434	656	0	ENST00000357368.4:c.3766-1G>A		p.X1256_splice	ENST00000357368	NM_002850.3	1256			0.646375614011148	3	FACETS	0.922	0.884	0.96	0.922	0.884	0.96	CLONAL	2	TRUE	1	0.698993872182364	3		656	909	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5222732	5222732	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772912033	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	595	717	0	ENST00000357368.4:c.3071C>T	p.Pro1024Leu	p.P1024L	ENST00000357368	NM_002850.3	1024	cCc/cTc	18/38	0.646375614011148	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	1	0.698993872182364	3		717	1120	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184562	7184562	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770690301	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	418	502	2	ENST00000302850.5:c.739G>A	p.Asp247Asn	p.D247N	ENST00000302850	NM_000208.2	247	Gac/Aac	3/22	0.646375614011148	3	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	1	0.698993872182364	3		504	792	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145669	11145669	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	588	848	0	ENST00000358026.2:c.4031C>T	p.Pro1344Leu	p.P1344L	ENST00000358026	NM_001128849.1	1344	cCc/cTc	29/36	0.646375614011148	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.698993872182364	3		848	1122	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741243	40741243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	569	689	1	ENST00000392038.2:c.1190C>T	p.Pro397Leu	p.P397L	ENST00000392038	NM_001626.4	397	cCc/cTc	12/14	0.698993872182364	3	FACETS	0.991	0.956	1	0.991	0.956	1	CLONAL	2	TRUE	1	0.698993872182364	3		690	1109	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966664	25966664	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	492	508	0	ENST00000435504.4:c.2542C>T	p.His848Tyr	p.H848Y	ENST00000435504		848	Cat/Tat	13/13	0.179592521149363	6	FACETS	0.916	0.883	0.95			1	INDETERMINATE	4	TRUE	NA	0.698993872182364	6		508	921	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416689	29416689	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	330	397	0	ENST00000389048.3:c.4264C>T	p.Pro1422Ser	p.P1422S	ENST00000389048	NM_004304.4	1422	Cct/Tct	29/29	0.526073407422336	3	FACETS	0.988	0.943	1	0.988	0.943	1	CLONAL	2	TRUE	1	0.698993872182364	3		397	645	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158626984	158626985	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	363	517	1	ENST00000263640.3:c.685_686delinsAA	p.Gly229Lys	p.G229K	ENST00000263640	NM_001105.4	229	GGg/AAg	7/11	0.698993872182364	3	FACETS	0.839	0.8	0.879	0.839	0.8	0.879	CLONAL	2	TRUE	1	0.698993872182364	3		518	835	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190660562	190660562	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	348	389	0	ENST00000441310.2:c.200C>T	p.Pro67Leu	p.P67L	ENST00000441310	NM_000534.4	67	cCt/cTt	3/13	0.698993872182364	3	FACETS	0.91	0.868	0.953	0.91	0.868	0.953	CLONAL	2	TRUE	1	0.698993872182364	3		389	738	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190732614	190732614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	427	494	0	ENST00000441310.2:c.2432C>T	p.Pro811Leu	p.P811L	ENST00000441310	NM_000534.4	811	cCt/cTt	11/13	0.698993872182364	3	FACETS	0.937	0.898	0.976	0.937	0.898	0.976	CLONAL	2	TRUE	1	0.698993872182364	3		494	880	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251853	212251854	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	230	335	0	ENST00000342788.4:c.3205_3206delinsAA	p.Gly1069Lys	p.G1069K	ENST00000342788	NM_005235.2	1069	GGa/AAa	27/28	0.698993872182364	3	FACETS	0.866	0.815	0.916	0.866	0.815	0.916	CLONAL	2	TRUE	1	0.698993872182364	3		335	513	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566709	212566709	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	129	345	1	ENST00000342788.4:c.1472G>A	p.Arg491Lys	p.R491K	ENST00000342788	NM_005235.2	491	aGa/aAa	12/28	0.698993872182364	3	FACETS	0.874	0.795	0.956	0.437	0.397	0.478	CLONAL	1	TRUE	1	0.698993872182364	3		346	570	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439805	220439805	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs368930117	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	516	616	0	ENST00000243786.2:c.658C>T	p.Arg220Trp	p.R220W	ENST00000243786	NM_002191.3	220	Cgg/Tgg	2/2	0.698993872182364	3	FACETS	0.953	0.918	0.989	0.953	0.918	0.989	CLONAL	2	TRUE	1	0.698993872182364	3		616	1045	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793371	242793372	+	missense_variant	Missense_Mutation	DNP	CC	CC	GT	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	623	952	1	ENST00000334409.5:c.705_706delinsAC	p.Glu236Gln	p.E236Q	ENST00000334409	NM_005018.2	235	ccGGag/ccACag	5/5	0.698993872182364	3	FACETS	0.975	0.942	1	0.975	0.942	1	CLONAL	2	TRUE	1	0.698993872182364	3		953	1234	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710603	40710603	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	269	688	1	ENST00000373198.4:c.4248G>A	p.Met1416Ile	p.M1416I	ENST00000373198	NM_133170.3	1416	atG/atA	31/32	0.333035431493062	3	FACETS	0.988	0.927	1			1	INDETERMINATE	1	TRUE	NA	0.698993872182364	3		689	1051	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39795392	39795392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	295	742	0	ENST00000288319.7:c.328G>A	p.Glu110Lys	p.E110K	ENST00000288319	NM_182918.3	110	Gag/Aag	3/10	1	2	FACETS	0.935	0.882	0.988	0.935	0.882	0.988	CLONAL	1	TRUE	1	0.698993872182364	2		742	903	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656750	45656750	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	229	583	0	ENST00000407780.3:c.406G>A	p.Ala136Thr	p.A136T	ENST00000407780	NM_001283052.1	136	Gca/Aca	3/7	1	2	FACETS	0.943	0.883	1	0.943	0.883	1	CLONAL	1	TRUE	1	0.698993872182364	2		583	695	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52610608	52610609	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	TTTTCAGAAATACTTT	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	118	452	0	ENST00000394830.3:c.3564_3565insAAAGTATTTCTGAAAA	p.Glu1189LysfsTer11	p.E1189Kfs*11	ENST00000394830	NM_018313.4	1188	-/AAAGTATTTCTGAAAA	23/30	1	2	FACETS	0.537	0.485	0.591	0.537	0.485	0.591	SUBCLONAL	1	TRUE	1	0.698993872182364	2		452	629	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52676009	52676009	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	297	787	0	ENST00000394830.3:c.1048C>T	p.Gln350Ter	p.Q350*	ENST00000394830	NM_018313.4	350	Caa/Taa	11/30	1	2	FACETS	0.899	0.848	0.951	0.899	0.848	0.951	CLONAL	1	TRUE	1	0.698993872182364	2		787	945	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119721033	119721033	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	269	514	0	ENST00000316626.5:c.142C>T	p.Pro48Ser	p.P48S	ENST00000316626		48	Cca/Tca	2/12	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.698993872182364	2		514	767	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178921563	178921563	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	115	262	0	ENST00000263967.3:c.1045C>T	p.Arg349Ter	p.R349*	ENST00000263967	NM_006218.2	349	Cga/Tga	5/21	0.698993872182364	3	FACETS	0.866	0.783	0.952	0.433	0.391	0.476	CLONAL	1	TRUE	1	0.698993872182364	3		262	513	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185198228	185198228	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	249	534	1	ENST00000265026.3:c.2710G>A	p.Asp904Asn	p.D904N	ENST00000265026	NM_004721.4	904	Gat/Aat	13/14	NA	2	FACETS	0.999	0.939	1			1	INDETERMINATE	1	TRUE	NA	0.698993872182364	2		535	713	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612176	189612176	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	260	560	1	ENST00000264731.3:c.1928G>A	p.Arg643Gln	p.R643Q	ENST00000264731	NM_003722.4	643	cGa/cAa	14/14	NA	2	FACETS	1	0.944	1			1	INDETERMINATE	1	TRUE	NA	0.698993872182364	2		561	742	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902520	1902520	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	263	662	0	ENST00000382891.5:c.139T>C	p.Phe47Leu	p.F47L	ENST00000382891	NM_133335.3	47	Ttc/Ctc	2/22	1	2	FACETS	0.854	0.802	0.907	0.854	0.802	0.907	CLONAL	1	TRUE	1	0.698993872182364	2		662	881	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961207	1961207	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	189	463	0	ENST00000382891.5:c.2995C>T	p.Pro999Ser	p.P999S	ENST00000382891	NM_133335.3	999	Cct/Tct	17/22	1	2	FACETS	0.853	0.792	0.915	0.853	0.792	0.915	CLONAL	1	TRUE	1	0.698993872182364	2		463	634	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139865	55139865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	179	421	0	ENST00000257290.5:c.1526C>T	p.Ala509Val	p.A509V	ENST00000257290	NM_006206.4	509	gCt/gTt	10/23	1	2	FACETS	0.991	0.92	1	0.991	0.92	1	CLONAL	1	TRUE	1	0.698993872182364	2		421	517	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55153692	55153692	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	206	486	1	ENST00000257290.5:c.2658G>A	p.Trp886Ter	p.W886*	ENST00000257290	NM_006206.4	886	tgG/tgA	19/23	1	2	FACETS	0.955	0.892	1	0.955	0.892	1	CLONAL	1	TRUE	1	0.698993872182364	2		487	617	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161408	55161410	+	missense_variant	Missense_Mutation	TNP	CTT	CTT	TTC	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	188	493	0	ENST00000257290.5:c.3239_3241delinsTTC	p.Ser1080_Ser1081delinsPhePro	p.S1080_S1081delinsFP	ENST00000257290	NM_006206.4	1080	tCTTca/tTTCca	23/23	1	2	FACETS	0.828	0.768	0.889	0.828	0.768	0.889	CLONAL	1	TRUE	1	0.698993872182364	2		493	650	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106193820	106193820	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	159	421	0	ENST00000380013.4:c.4282G>A	p.Glu1428Lys	p.E1428K	ENST00000380013	NM_001127208.2	1428	Gag/Aag	10/11	1	2	FACETS	0.946	0.874	1	0.946	0.874	1	CLONAL	1	TRUE	1	0.698993872182364	2		421	481	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245341	153245341	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	201	487	1	ENST00000281708.4:c.1850T>A	p.Leu617Ter	p.L617*	ENST00000281708	NM_033632.3	617	tTg/tAg	11/12	1	2	FACETS	0.954	0.889	1	0.954	0.889	1	CLONAL	1	TRUE	1	0.698993872182364	2		488	603	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521300	187521300	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	597	280	724	0	ENST00000441802.2:c.11855T>G	p.Phe3952Cys	p.F3952C	ENST00000441802	NM_005245.3	3952	tTt/tGt	22/27	1	2	FACETS	0.914	0.861	0.968	0.914	0.861	0.968	CLONAL	1	TRUE	1	0.698993872182364	2		724	877	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260656	1260656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	292	785	1	ENST00000310581.5:c.2903G>A	p.Arg968Lys	p.R968K	ENST00000310581	NM_198253.2	968	aGg/aAg	12/16	1	2	FACETS	0.903	0.852	0.956	0.903	0.852	0.956	CLONAL	1	TRUE	1	0.698993872182364	2		786	925	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295204	1295204	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs2735943	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	146	586	2				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.954	0.878	1	0.954	0.878	1	CLONAL	1	TRUE	1	0.698993872182364	2		588	438	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876352	35876352	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	243	557	0	ENST00000303115.3:c.1144C>T	p.Leu382Phe	p.L382F	ENST00000303115	NM_002185.3	382	Ctc/Ttc	8/8	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.698993872182364	2		557	654	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576482	67576482	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768144572	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	186	413	0	ENST00000274335.5:c.761C>T	p.Ser254Phe	p.S254F	ENST00000274335		254	tCc/tTc	5/15	1	2	FACETS	0.986	0.917	1	0.986	0.917	1	CLONAL	1	TRUE	1	0.698993872182364	2		413	540	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515196	149515197	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	292	779	2	ENST00000261799.4:c.285_286delinsAA	p.Gly96Arg	p.G96R	ENST00000261799	NM_002609.3	95	acGGga/acAAga	3/23	1	2	FACETS	0.895	0.843	0.947	0.895	0.843	0.947	CLONAL	1	TRUE	1	0.698993872182364	2		781	934	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176518103	176518103	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs866476239	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	213	617	0	ENST00000292408.4:c.601C>T	p.Arg201Trp	p.R201W	ENST00000292408	NM_213647.1	201	Cgg/Tgg	5/18	1	2	FACETS	0.895	0.835	0.956	0.895	0.835	0.956	CLONAL	1	TRUE	1	0.698993872182364	2		617	681	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176665454	176665454	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	185	399	1	ENST00000439151.2:c.4138G>A	p.Glu1380Lys	p.E1380K	ENST00000439151	NM_022455.4	1380	Gaa/Aaa	7/23	1	2	FACETS	0.932	0.866	0.999	0.932	0.866	0.999	CLONAL	1	TRUE	1	0.698993872182364	2		400	568	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176715855	176715855	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	267	604	0	ENST00000439151.2:c.6187C>T	p.Leu2063Phe	p.L2063F	ENST00000439151	NM_022455.4	2063	Ctt/Ttt	21/23	1	2	FACETS	0.871	0.819	0.925	0.871	0.819	0.925	CLONAL	1	TRUE	1	0.698993872182364	2		604	877	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721567	176721567	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777713632	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	245	682	0	ENST00000439151.2:c.7198C>T	p.Pro2400Ser	p.P2400S	ENST00000439151	NM_022455.4	2400	Ccc/Tcc	23/23	1	2	FACETS	0.816	0.764	0.869	0.816	0.764	0.869	CLONAL	1	TRUE	1	0.698993872182364	2		682	859	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056796	180056796	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	327	757	3	ENST00000261937.6:c.716C>T	p.Ser239Leu	p.S239L	ENST00000261937	NM_182925.4	239	tCg/tTg	6/30	1	2	FACETS	0.991	0.939	1	0.991	0.939	1	CLONAL	1	TRUE	1	0.698993872182364	2		760	944	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271372	26271372	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	365	372	0	ENST00000305910.3:c.241A>C	p.Thr81Pro	p.T81P	ENST00000305910	NM_003534.2	81	Aca/Cca	1/1	0.698993872182364	4	FACETS	1	0.983	1	1	0.983	1	CLONAL	2	TRUE	2	0.698993872182364	4		372	834	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672381	30672381	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	358	423	0	ENST00000376406.3:c.4579C>T	p.Pro1527Ser	p.P1527S	ENST00000376406	NM_014641.2	1527	Cct/Tct	10/15	0.698993872182364	4	FACETS	0.933	0.887	0.979	0.933	0.887	0.979	CLONAL	2	TRUE	2	0.698993872182364	4		423	933	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32180376	32180376	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1348206760	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1073	287	701	0	ENST00000375023.3:c.2555C>T	p.Pro852Leu	p.P852L	ENST00000375023	NM_004557.3	852	cCc/cTc	17/30	0.612698391260297	4	FACETS	1	0.958	1	0.513	0.481	0.546	CLONAL	1	TRUE	2	0.698993872182364	4		701	1360	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32185817	32185817	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1170	281	776	0	ENST00000375023.3:c.1579G>A	p.Asp527Asn	p.D527N	ENST00000375023	NM_004557.3	527	Gat/Aat	9/30	0.612698391260297	4	FACETS	0.941	0.883	1	0.471	0.441	0.501	CLONAL	1	TRUE	2	0.698993872182364	4		776	1451	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106536140	106536140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	342	306	0	ENST00000369096.4:c.107C>T	p.Thr36Ile	p.T36I	ENST00000369096	NM_001198.3	36	aCc/aTc	2/7	0.698993872182364	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.698993872182364	3		306	642	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609906	117609906	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	500	544	0	ENST00000368508.3:c.6793G>A	p.Glu2265Lys	p.E2265K	ENST00000368508	NM_002944.2	2265	Gaa/Aaa	43/43	0.698993872182364	3	FACETS	0.954	0.918	0.99	0.954	0.918	0.99	CLONAL	2	TRUE	1	0.698993872182364	3		544	1012	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117641177	117641177	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773843792	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	927	268	736	0	ENST00000368508.3:c.5794G>A	p.Glu1932Lys	p.E1932K	ENST00000368508	NM_002944.2	1932	Gag/Aag	36/43	0.698993872182364	3	FACETS	0.866	0.811	0.922	0.433	0.405	0.461	CLONAL	1	TRUE	1	0.698993872182364	3		736	1195	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662759	117662759	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141448347	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	280	294	0	ENST00000368508.3:c.4706G>A	p.Arg1569Gln	p.R1569Q	ENST00000368508	NM_002944.2	1569	cGg/cAg	29/43	0.698993872182364	3	FACETS	0.983	0.934	1	0.983	0.934	1	CLONAL	2	TRUE	1	0.698993872182364	3		294	550	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677934	117677934	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	470	455	1	ENST00000368508.3:c.3999A>T	p.Glu1333Asp	p.E1333D	ENST00000368508	NM_002944.2	1333	gaA/gaT	25/43	0.698993872182364	3	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	1	0.698993872182364	3		456	848	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467675	50467675	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759124417	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1059	507	668	0	ENST00000331340.3:c.910G>A	p.Glu304Lys	p.E304K	ENST00000331340	NM_006060.4	304	Gaa/Aaa	8/8	0.691507742731368	5	FACETS	0.949	0.908	0.99	0.633	0.605	0.66	CLONAL	2	TRUE	2	0.698993872182364	5		668	1566	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468099	50468099	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	341	415	1	ENST00000331340.3:c.1334C>T	p.Ser445Leu	p.S445L	ENST00000331340	NM_006060.4	445	tCg/tTg	8/8	0.691507742731368	5	FACETS	1	0.967	1	0.684	0.649	0.72	CLONAL	2	TRUE	2	0.698993872182364	5		416	974	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515195	106515195	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	440	548	0	ENST00000359195.3:c.2338C>T	p.Pro780Ser	p.P780S	ENST00000359195	NM_002649.2	780	Ccc/Tcc	5/11	0.691507742731368	5	FACETS	0.87	0.829	0.912	0.58	0.553	0.608	CLONAL	2	TRUE	2	0.698993872182364	5		548	1482	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106523546	106523546	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	540	451	0	ENST00000359195.3:c.2698G>A	p.Gly900Arg	p.G900R	ENST00000359195	NM_002649.2	900	Gga/Aga	8/11	0.691507742731368	5	FACETS	0.941	0.906	0.976	0.941	0.906	0.976	CLONAL	3	TRUE	2	0.698993872182364	5		451	1121	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436159	116436159	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	411	360	0	ENST00000397752.3:c.4154C>T	p.Ser1385Phe	p.S1385F	ENST00000397752	NM_000245.2	1385	tCc/tTc	21/21	0.691507742731368	5	FACETS	1	0.966	1	0.678	0.646	0.71	CLONAL	2	TRUE	2	0.698993872182364	5		360	1185	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56863023	56863023	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	216	497	0	ENST00000519728.1:c.290G>A	p.Gly97Glu	p.G97E	ENST00000519728	NM_002350.3	97	gGa/gAa	5/13	0.646375614011148	3	FACETS	1	0.935	1	0.502	0.467	0.537	CLONAL	1	TRUE	1	0.698993872182364	3		497	831	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8486242	8486242	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	317	387	0	ENST00000356435.5:c.2575A>C	p.Lys859Gln	p.K859Q	ENST00000356435		859	Aaa/Caa	17/35	0.698993872182364	2	FACETS	0.961	0.923	0.997	0.961	0.923	0.997	CLONAL	2	TRUE	0	0.698993872182364	2		387	472	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912316	97912316	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776991402	NA	P-0015438-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	476	563	0	ENST00000289081.3:c.575C>T	p.Thr192Ile	p.T192I	ENST00000289081	NM_000136.2	192	aCc/aTc	7/15	0.698993872182364	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	0	0.698993872182364	2		563	676	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	217	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.629037988939908	2		215	602	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653805	89653805	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659443	NA	P-0015449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	100	426	0	ENST00000371953.3:c.103A>G	p.Met35Val	p.M35V	ENST00000371953	NM_000314.4	35	Atg/Gtg	2/9	0.629037988939908	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.629037988939908	1		426	198	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971122	21971123	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	208	538	0	ENST00000304494.5:c.235dup	p.Thr79AsnfsTer41	p.T79Nfs*41	ENST00000304494	NM_000077.4	79	acc/aAcc	2/3	0.629037988939908	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.629037988939908	1		538	399	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55131161	55131162	+	missense_variant	Missense_Mutation	DNP	GT	GT	TG	novel	NA	P-0015449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	5996	3891	493	1	ENST00000257290.5:c.704_705delinsTG	p.Cys235Leu	p.C235L	ENST00000257290	NM_006206.4	235	tGT/tTG	5/23	0.629037988939908	36	FACETS	0.975	0.961	0.99			1	CLONAL	15	TRUE	NA	0.629037988939908	36		494	9887	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55133624	55133897	+	splice_donor_variant,splice_acceptor_variant,stop_lost,inframe_deletion,intron_variant	Splice_Site	DEL	CATGGTACATTCCGCTTTCTAAAATGTCAGTTGTCCATGCTGCTCGGGATCCATATGTGGTAATCATTATTTAATGGAAACTCTTCCCTGTACAGAGAAAGGTTTCATTGAAATCAAACCCACCTTCAGCCAGTTGGAAGCTGTCAACCTGCATGAAGTCAAACATTTTGTTGTAGAGGTGCGGGCCTACCCACCTCCCAGGATATCCTGGCTGAAAAACAATCTGACTCTGATTGAAAATCTCACTGAGATCACCACTGATGTGGAAAAGATT	CATGGTACATTCCGCTTTCTAAAATGTCAGTTGTCCATGCTGCTCGGGATCCATATGTGGTAATCATTATTTAATGGAAACTCTTCCCTGTACAGAGAAAGGTTTCATTGAAATCAAACCCACCTTCAGCCAGTTGGAAGCTGTCAACCTGCATGAAGTCAAACATTTTGTTGTAGAGGTGCGGGCCTACCCACCTCCCAGGATATCCTGGCTGAAAAACAATCTGACTCTGATTGAAAATCTCACTGAGATCACCACTGATGTGGAAAAGATT	-	novel	NA	P-0015449-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	7830	418	410	0	ENST00000257290.5:c.930_1112del		p.X310_splice	ENST00000257290	NM_006206.4	310	CATGGTACATTCCGCTTTCTAAAATGTCAGTTGTCCATGCTGCTCGGGATCCATATGTGGTAATCATTATTTAATGGAAACTCTTCCCTGTACAGAGAAAGGTTTCATTGAAATCAAACCCACCTTCAGCCAGTTGGAAGCTGTCAACCTGCATGAAGTCAAACATTTTGTTGTAGAGGTGCGGGCCTACCCACCTCCCAGGATATCCTGGCTGAAAAACAATCTGACTCTGATTGAAAATCTCACTGAGATCACCACTGATGTGGAAAAGATT/-	6-7/23	0.629037988939908	36	FACETS	0.942	0.89	0.996			1	CLONAL	2	TRUE	NA	0.629037988939908	36		410	8248	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398285	25398285	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913530	NA	P-0015454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	116	515	0	ENST00000311936.3:c.34G>T	p.Gly12Cys	p.G12C	ENST00000311936	NM_004985.3	12	Ggt/Tgt	2/5	0.16708665874741	4	FACETS	0.848	0.764	0.937	0.848	0.764	0.937	CLONAL	2	TRUE	2	0.204677114930446	4		515	805	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030585	47030585	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs377667483	NA	P-0015454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	180	754	1	ENST00000377604.3:c.360T>G	p.Asp120Glu	p.D120E	ENST00000377604	NM_001204468.1	120	gaT/gaG	4/24	0.152126387807385	2	FACETS	0.896	0.83	0.965			1	CLONAL	3	TRUE	NA	0.204677114930446	2		755	654	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52440379	52440379	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	180	320	1	ENST00000460680.1:c.673G>A	p.Asp225Asn	p.D225N	ENST00000460680	NM_004656.3	225	Gac/Aac	9/17	0.204677114930446	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	0	0.204677114930446	2		321	760	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66270177	66270177	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	36	322	0	ENST00000273854.3:c.1705C>T	p.Gln569Ter	p.Q569*	ENST00000273854	NM_004439.5	569	Caa/Taa	8/18	0.169343471134915	3	FACETS	0.609	0.499	0.732	0.304	0.249	0.366	SUBCLONAL	1	TRUE	1	0.204677114930446	3		322	637	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262336	115262336	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	88	402	0	ENST00000438362.2:c.2218G>A	p.Asp740Asn	p.D740N	ENST00000438362	NM_001242891.1	740	Gat/Aat	18/20	0.204677114930446	2	FACETS	1	0.92	1	0.525	0.464	0.59	CLONAL	1	TRUE	0	0.204677114930446	2		402	819	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206651642	206651642	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1521	130	742	0	ENST00000367120.3:c.952C>A	p.Gln318Lys	p.Q318K	ENST00000367120	NM_014002.3	318	Cag/Aag	9/22	0.16708665874741	4	FACETS	0.927	0.837	1	0.463	0.418	0.511	CLONAL	1	TRUE	2	0.204677114930446	4		742	1651	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741925	17741925	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765066996	NA	P-0015454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	46	185	0	ENST00000250003.3:c.596C>T	p.Ala199Val	p.A199V	ENST00000250003	NM_002478.4	199	gCg/gTg	1/3	0.204677114930446	3	FACETS	1	0.94	1	0.624	0.527	0.731	CLONAL	1	TRUE	1	0.204677114930446	3		185	397	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132921	64132922	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0015454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	223	575	0	ENST00000334205.4:c.1060dup	p.Arg354ProfsTer16	p.R354Pfs*16	ENST00000334205	NM_003942.2	352	gac/gaCc	9/17	0.204677114930446	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.204677114930446	3		575	1092	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120784063	120784064	+	missense_variant	Missense_Mutation	DNP	GG	GG	TT	novel	NA	P-0015454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	133	771	3	ENST00000257552.2:c.921_922delinsAA	p.Phe307_Leu308delinsLeuMet	p.F307_L308delinsLM	ENST00000257552	NM_002442.3	307	ttCCtg/ttAAtg	13/15	1	2	FACETS	0.98	0.887	1	0.98	0.887	1	CLONAL	1	TRUE	1	0.204677114930446	2		774	1326	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218415	1218415	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	rs112675807	NA	P-0015454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	236	524	0	ENST00000326873.7:c.291-1G>C		p.X97_splice	ENST00000326873	NM_000455.4	97			0.204677114930446	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.204677114930446	2		524	1049	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610081	10610081	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	248	605	0	ENST00000171111.5:c.629A>T	p.His210Leu	p.H210L	ENST00000171111	NM_203500.1	210	cAt/cTt	2/6	0.204677114930446	2	FACETS	0.999	0.933	1	0.999	0.933	1	CLONAL	2	TRUE	0	0.204677114930446	2		605	1213	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145811	11145811	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	G	novel	NA	P-0015454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	178	474	0	ENST00000358026.2:c.4170+3A>G		p.X1390_splice	ENST00000358026	NM_001128849.1	1390			0.204677114930446	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	2	TRUE	0	0.204677114930446	2		474	809	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225360680	225360680	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	35	261	0	ENST00000264414.4:c.1711G>C	p.Asp571His	p.D571H	ENST00000264414	NM_003590.4	571	Gat/Cat	13/16	1	2	FACETS	0.784	0.643	0.943	0.784	0.643	0.943	CLONAL	1	TRUE	1	0.204677114930446	2		261	436	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55599361	55599361	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	novel	NA	P-0015454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	78	341	0	ENST00000288135.5:c.2484+3G>A		p.X828_splice	ENST00000288135	NM_000222.2	828			0.169343471134915	3	FACETS	0.866	0.763	0.976	0.866	0.763	0.976	CLONAL	2	TRUE	1	0.204677114930446	3		341	485	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55991459	55991459	+	start_lost	Translation_Start_Site	SNP	A	A	G	novel	NA	P-0015454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	78	510	0	ENST00000263923.4:c.2T>C	p.Met1?	p.M1?	ENST00000263923	NM_002253.2	1	aTg/aCg	1/30	0.169343471134915	3	FACETS	0.895	0.784	1	0.447	0.392	0.507	CLONAL	1	TRUE	1	0.204677114930446	3		510	939	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512455	149512455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	177	380	1	ENST00000261799.4:c.985G>A	p.Glu329Lys	p.E329K	ENST00000261799	NM_002609.3	329	Gag/Aag	7/23	0.204677114930446	2	FACETS	0.978	0.902	1	0.978	0.902	1	CLONAL	2	TRUE	0	0.204677114930446	2		381	884	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509275	106509275	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	177	437	0	ENST00000359195.3:c.1269G>T	p.Leu423Phe	p.L423F	ENST00000359195	NM_002649.2	423	ttG/ttT	2/11	0.204677114930446	2	FACETS	0.966	0.891	1	0.966	0.891	1	CLONAL	2	TRUE	0	0.204677114930446	2		437	895	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106520081	106520081	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015454-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	78	259	0	ENST00000359195.3:c.2509G>C	p.Asp837His	p.D837H	ENST00000359195	NM_002649.2	837	Gat/Cat	6/11	0.204677114930446	2	FACETS	0.982	0.868	1	0.982	0.868	1	CLONAL	2	TRUE	0	0.204677114930446	2		259	388	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	163	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.373965884270532	2		215	828	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66242749	66242749	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	123	260	0	ENST00000273854.3:c.1823C>T	p.Ser608Phe	p.S608F	ENST00000273854	NM_004439.5	608	tCc/tTc	9/18	1	2	FACETS	0.764	0.69	0.842	0.764	0.69	0.842	SUBCLONAL	1	TRUE	1	0.373965884270532	2		260	861	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41100959	41100959	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	158	274	0	ENST00000373198.4:c.1397A>G	p.Asn466Ser	p.N466S	ENST00000373198	NM_133170.3	466	aAc/aGc	8/32	1	2	FACETS	0.944	0.865	1	0.944	0.865	1	CLONAL	1	TRUE	1	0.373965884270532	2		274	895	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32421568	32421568	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs267602851	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	166	290	0	ENST00000332351.3:c.1024G>A	p.Asp342Asn	p.D342N	ENST00000332351	NM_024426.4	342	Gat/Aat	6/10	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.373965884270532	2		290	875	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105511	27105511	+	splice_region_variant,intron_variant	Splice_Region	SNP	T	T	C	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	134	197	0	ENST00000324856.7:c.5125-3T>C		p.X1709_splice	ENST00000324856	NM_006015.4	1709			1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.373965884270532	2		197	601	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43804298	43804298	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs760631916	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	201	296	0	ENST00000372470.3:c.298G>A	p.Glu100Lys	p.E100K	ENST00000372470	NM_005373.2	100	Gaa/Aaa	3/12	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.373965884270532	2		296	940	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100321	8100321	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768583935	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	188	424	1	ENST00000346208.3:c.295G>A	p.Gly99Ser	p.G99S	ENST00000346208		99	Ggc/Agc	3/6	1	2	FACETS	0.887	0.819	0.959	0.887	0.819	0.959	CLONAL	1	TRUE	1	0.373965884270532	2		425	1133	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8106097	8106097	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	183	293	1	ENST00000346208.3:c.917G>A	p.Arg306Lys	p.R306K	ENST00000346208		306	aGg/aAg	4/6	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.373965884270532	2		294	875	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606880	43606880	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	264	485	0	ENST00000355710.3:c.1489C>T	p.Gln497Ter	p.Q497*	ENST00000355710	NM_020975.4	497	Cag/Tag	7/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.373965884270532	2		485	1387	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112769112	112769112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	126	305	0	ENST00000369452.4:c.1391C>T	p.Pro464Leu	p.P464L	ENST00000369452	NM_007373.3	464	cCa/cTa	7/9	1	2	FACETS	0.882	0.799	0.969	0.882	0.799	0.969	CLONAL	1	TRUE	1	0.373965884270532	2		305	764	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123246896	123246896	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	172	303	0	ENST00000358487.5:c.2029G>A	p.Asp677Asn	p.D677N	ENST00000358487	NM_000141.4	677	Gat/Aat	15/18	1	2	FACETS	0.901	0.828	0.977	0.901	0.828	0.977	CLONAL	1	TRUE	1	0.373965884270532	2		303	1021	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933358	100933358	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	171	284	0	ENST00000325455.5:c.2032G>A	p.Gly678Ser	p.G678S	ENST00000325455	NM_001202474.3	678	Ggt/Agt	4/8	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.373965884270532	2		284	891	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344908	118344908	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1565280934	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	108	155	0	ENST00000534358.1:c.3034C>T	p.Gln1012Ter	p.Q1012*	ENST00000534358	NM_005933.3	1012	Cag/Tag	3/36	0.373965884270532	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.373965884270532	1		155	450	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352643	118352643	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	140	315	0	ENST00000534358.1:c.3848C>T	p.Ser1283Phe	p.S1283F	ENST00000534358	NM_005933.3	1283	tCc/tTc	7/36	0.373965884270532	1	FACETS	0.854	0.779	0.932	0.854	0.779	0.932	CLONAL	1	TRUE	0	0.373965884270532	1		315	713	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118390479	118390479	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	153	267	0	ENST00000534358.1:c.11293G>T	p.Gly3765Cys	p.G3765C	ENST00000534358	NM_005933.3	3765	Ggc/Tgc	32/36	0.373965884270532	1	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	0	0.373965884270532	1		267	619	SUCCESS
CBL	867	MSKCC	GRCh37	11	119103248	119103248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs147438359	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	148	296	0	ENST00000264033.4:c.286C>T	p.Arg96Cys	p.R96C	ENST00000264033	NM_005188.3	96	Cgt/Tgt	2/16	0.373965884270532	1	FACETS	0.883	0.808	0.961	0.883	0.808	0.961	CLONAL	1	TRUE	0	0.373965884270532	1		296	729	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491450	18491450	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	125	279	0	ENST00000266497.5:c.1363G>A	p.Glu455Lys	p.E455K	ENST00000266497		455	Gaa/Aaa	8/31	1	2	FACETS	0.894	0.81	0.982	0.894	0.81	0.982	CLONAL	1	TRUE	1	0.373965884270532	2		279	748	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650671	18650671	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	84	181	1	ENST00000266497.5:c.2882G>A	p.Gly961Glu	p.G961E	ENST00000266497		961	gGa/gAa	20/31	1	2	FACETS	0.93	0.824	1	0.93	0.824	1	CLONAL	1	TRUE	1	0.373965884270532	2		182	483	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650676	18650676	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	84	181	0	ENST00000266497.5:c.2887G>A	p.Asp963Asn	p.D963N	ENST00000266497		963	Gac/Aac	20/31	1	2	FACETS	0.948	0.84	1	0.948	0.84	1	CLONAL	1	TRUE	1	0.373965884270532	2		181	474	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246513	46246513	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	99	155	0	ENST00000334344.6:c.4607T>G	p.Val1536Gly	p.V1536G	ENST00000334344	NM_152641.2	1536	gTt/gGt	15/21	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.373965884270532	2		155	492	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120777	115120777	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	188	335	0	ENST00000257566.3:c.229C>T	p.Pro77Ser	p.P77S	ENST00000257566	NM_016569.3	77	Ccg/Tcg	1/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.373965884270532	2		335	835	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120789189	120789189	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	147	326	0	ENST00000257552.2:c.748C>T	p.Arg250Trp	p.R250W	ENST00000257552	NM_002442.3	250	Cgg/Tgg	11/15	1	2	FACETS	0.873	0.796	0.952	0.873	0.796	0.952	CLONAL	1	TRUE	1	0.373965884270532	2		326	901	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28959144	28959144	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767259336	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	100	182	0	ENST00000282397.4:c.1994G>A	p.Arg665Gln	p.R665Q	ENST00000282397	NM_002019.4	665	cGa/cAa	14/30	0.373965884270532	1	FACETS	0.811	0.727	0.9	0.811	0.727	0.9	CLONAL	1	TRUE	0	0.373965884270532	1		182	536	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675107	40675107	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868438023	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	614	779	1	ENST00000249776.8:c.71C>T	p.Ser24Phe	p.S24F	ENST00000249776	NM_033286.3	24	tCc/tTc	1/9	0.321560311878101	3	FACETS	0.939	0.905	0.973	1	0.997	1	CLONAL	3	TRUE	1	0.373965884270532	3		780	1384	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005558	42005558	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	337	377	0	ENST00000219905.7:c.3294T>A	p.His1098Gln	p.H1098Q	ENST00000219905	NM_001164273.1	1098	caT/caA	9/24	0.321560311878101	3	FACETS	0.91	0.86	0.96	0.91	0.86	0.96	CLONAL	2	TRUE	1	0.373965884270532	3		377	1176	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43766957	43766957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	178	158	2	ENST00000382044.4:c.1094C>T	p.Ser365Leu	p.S365L	ENST00000382044	NM_001141980.1	365	tCa/tTa	10/28	0.321560311878101	3	FACETS	0.842	0.779	0.907	0.842	0.779	0.907	CLONAL	2	TRUE	1	0.373965884270532	3		160	671	SUCCESS
BLM	641	MSKCC	GRCh37	15	91312682	91312682	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	138	149	0	ENST00000355112.3:c.2421T>A	p.Phe807Leu	p.F807L	ENST00000355112	NM_000057.2	807	ttT/ttA	12/22	0.321560311878101	3	FACETS	0.873	0.799	0.949	0.873	0.799	0.949	CLONAL	2	TRUE	1	0.373965884270532	3		149	502	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99459204	99459204	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1235	232	420	1	ENST00000268035.6:c.1840C>T	p.Pro614Ser	p.P614S	ENST00000268035	NM_000875.3	614	Ccc/Tcc	9/21	0.321560311878101	3	FACETS	1	0.933	1	0.502	0.467	0.539	CLONAL	1	TRUE	1	0.373965884270532	3		421	1467	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396238	396239	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	182	361	0	ENST00000262320.3:c.787_788delinsTT	p.Pro263Phe	p.P263F	ENST00000262320	NM_003502.3	263	CCc/TTc	2/11	1	2	FACETS	0.911	0.839	0.985	0.911	0.839	0.985	CLONAL	1	TRUE	1	0.373965884270532	2		361	1069	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857454	9857454	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	132	257	0	ENST00000330684.3:c.3947G>A	p.Arg1316Lys	p.R1316K	ENST00000330684	NM_001134407.1	1316	aGg/aAg	13/13	1	2	FACETS	0.907	0.824	0.995	0.907	0.824	0.995	CLONAL	1	TRUE	1	0.373965884270532	2		257	778	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857878	9857878	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867464241	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	122	298	1	ENST00000330684.3:c.3523G>A	p.Glu1175Lys	p.E1175K	ENST00000330684	NM_001134407.1	1175	Gaa/Aaa	13/13	1	2	FACETS	0.787	0.711	0.867	0.787	0.711	0.867	SUBCLONAL	1	TRUE	1	0.373965884270532	2		299	829	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892205	9892205	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	177	335	0	ENST00000330684.3:c.2285G>A	p.Gly762Glu	p.G762E	ENST00000330684	NM_001134407.1	762	gGa/gAa	11/13	1	2	FACETS	0.931	0.857	1	0.931	0.857	1	CLONAL	1	TRUE	1	0.373965884270532	2		335	1017	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943730	9943730	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs773990289	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	791	143	336	0	ENST00000330684.3:c.1211A>G	p.Asn404Ser	p.N404S	ENST00000330684	NM_001134407.1	404	aAc/aGc	5/13	1	2	FACETS	0.819	0.746	0.895	0.819	0.746	0.895	CLONAL	1	TRUE	1	0.373965884270532	2		336	934	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029000	14029000	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	45	85	0	ENST00000311895.7:c.1214-3C>T		p.X405_splice	ENST00000311895	NM_005236.2	405			1	2	FACETS	0.805	0.68	0.941	0.805	0.68	0.941	CLONAL	1	TRUE	1	0.373965884270532	2		85	299	SUCCESS
MAPK3	5595	MSKCC	GRCh37	16	30129794	30129794	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs921399991	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	164	315	0	ENST00000263025.4:c.419A>G	p.Asn140Ser	p.N140S	ENST00000263025	NM_002746.2	140	aAt/aGt	3/9	1	2	FACETS	0.951	0.873	1	0.951	0.873	1	CLONAL	1	TRUE	1	0.373965884270532	2		315	922	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50784085	50784085	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	158	353	0	ENST00000398568.2:c.476C>T	p.Ser159Phe	p.S159F	ENST00000398568	NM_001042412.1	159	tCc/tTc	3/18	1	2	FACETS	0.815	0.746	0.887	0.815	0.746	0.887	CLONAL	1	TRUE	1	0.373965884270532	2		353	1037	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67663412	67663412	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	124	221	0	ENST00000264010.4:c.1813A>G	p.Lys605Glu	p.K605E	ENST00000264010	NM_006565.3	605	Aag/Gag	10/12	1	2	FACETS	0.848	0.767	0.933	0.848	0.767	0.933	CLONAL	1	TRUE	1	0.373965884270532	2		221	782	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81962179	81962179	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	163	321	0	ENST00000359376.3:c.2531C>T	p.Pro844Leu	p.P844L	ENST00000359376	NM_002661.3	844	cCc/cTc	24/33	1	2	FACETS	0.85	0.779	0.924	0.85	0.779	0.924	CLONAL	1	TRUE	1	0.373965884270532	2		321	1026	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	456	593	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	0.321937984065556	2	FACETS	0.886	0.845	0.926	0.886	0.845	0.926	CLONAL	2	TRUE	0	0.373965884270532	2		593	1377	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576001	29576001	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	204	197	0	ENST00000356175.3:c.3975-1G>A		p.X1325_splice	ENST00000356175	NM_000267.3	1325			0.321937984065556	2	FACETS	0.884	0.825	0.945	0.884	0.825	0.945	CLONAL	2	TRUE	0	0.373965884270532	2		197	617	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30264440	30264440	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	327	395	0	ENST00000322652.5:c.175T>A	p.Ser59Thr	p.S59T	ENST00000322652	NM_015355.2	59	Tcc/Acc	1/16	0.321937984065556	2	FACETS	0.866	0.819	0.913	0.866	0.819	0.913	CLONAL	2	TRUE	0	0.373965884270532	2		395	1010	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46805762	46805762	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	292	357	0	ENST00000290295.7:c.194C>T	p.Pro65Leu	p.P65L	ENST00000290295	NM_006361.5	65	cCa/cTa	1/2	0.321937984065556	2	FACETS	0.868	0.818	0.918	0.868	0.818	0.918	CLONAL	2	TRUE	0	0.373965884270532	2		357	900	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55693370	55693370	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	448	426	0	ENST00000284073.2:c.577C>T	p.Pro193Ser	p.P193S	ENST00000284073	NM_138962.2	193	Cca/Tca	9/14	0.321937984065556	2	FACETS	0.964	0.921	1	0.964	0.921	1	CLONAL	2	TRUE	0	0.373965884270532	2		426	1243	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435556	56435557	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	279	377	0	ENST00000407977.2:c.1580_1581delinsTT	p.Thr527Ile	p.T527I	ENST00000407977		527	aCC/aTT	9/10	0.321937984065556	2	FACETS	0.804	0.757	0.852	0.804	0.757	0.852	CLONAL	2	TRUE	0	0.373965884270532	2		377	928	SUCCESS
CD79B	974	MSKCC	GRCh37	17	62007576	62007576	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	342	416	1	ENST00000392795.3:c.291G>A	p.Met97Ile	p.M97I	ENST00000392795	NM_001039933.1	97	atG/atA	3/6	0.246850743248852	3	FACETS	0.803	0.759	0.848	0.803	0.759	0.848	CLONAL	2	TRUE	1	0.373965884270532	3		417	1352	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796989	78796989	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	251	221	0	ENST00000306801.3:c.1102C>T	p.Pro368Ser	p.P368S	ENST00000306801	NM_020761.2	368	Ccg/Tcg	9/34	0.246850743248852	3	FACETS	0.827	0.775	0.881	0.827	0.775	0.881	CLONAL	2	TRUE	1	0.373965884270532	3		221	963	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231585	5231585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779378586	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	101	167	3	ENST00000357368.4:c.1891C>T	p.Arg631Cys	p.R631C	ENST00000357368	NM_002850.3	631	Cgc/Tgc	14/38	1	2	FACETS	0.956	0.857	1	0.956	0.857	1	CLONAL	1	TRUE	1	0.373965884270532	2		170	565	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218449	36218449	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs267605436	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	155	346	0	ENST00000222270.7:c.4228C>T	p.Gln1410Ter	p.Q1410*	ENST00000222270	NM_014727.1	1410	Cag/Tag	16/37	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.373965884270532	2		346	815	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223013	36223013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1201	268	515	0	ENST00000222270.7:c.5642C>T	p.Ser1881Phe	p.S1881F	ENST00000222270	NM_014727.1	1881	tCc/tTc	27/37	1	2	FACETS	0.976	0.913	1	0.976	0.913	1	CLONAL	1	TRUE	1	0.373965884270532	2		515	1469	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796979	42796979	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145102151	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1376	273	535	1	ENST00000575354.2:c.3437C>T	p.Pro1146Leu	p.P1146L	ENST00000575354	NM_015125.3	1146	cCa/cTa	14/20	1	2	FACETS	0.885	0.828	0.945	0.885	0.828	0.945	CLONAL	1	TRUE	1	0.373965884270532	2		536	1649	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858059	45858059	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1185	238	507	1	ENST00000391945.4:c.1594C>T	p.Pro532Ser	p.P532S	ENST00000391945	NM_000400.3	532	Cct/Tct	17/23	1	2	FACETS	0.894	0.833	0.958	0.894	0.833	0.958	CLONAL	1	TRUE	1	0.373965884270532	2		508	1423	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505478	25505478	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	156	272	0	ENST00000264709.3:c.280G>A	p.Glu94Lys	p.E94K	ENST00000264709	NM_175629.2	94	Gag/Aag	4/23	NA	2	FACETS	0.992	0.909	1			1	INDETERMINATE	1	TRUE	NA	0.373965884270532	2		272	841	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570097	212570097	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	242	246	0	ENST00000342788.4:c.1144G>A	p.Glu382Lys	p.E382K	ENST00000342788	NM_005235.2	382	Gaa/Aaa	10/28	0.194268534817197	5	FACETS	1	0.955	1	0.685	0.64	0.731	INDETERMINATE	2	TRUE	2	0.373965884270532	5		246	983	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525080	9525080	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	158	327	0	ENST00000353224.5:c.1805C>T	p.Ser602Leu	p.S602L	ENST00000353224	NM_177990.2	602	tCa/tTa	8/10	1	2	FACETS	0.887	0.812	0.965	0.887	0.812	0.965	CLONAL	1	TRUE	1	0.373965884270532	2		327	953	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546608	9546608	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763093827	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	190	269	0	ENST00000353224.5:c.1414G>A	p.Gly472Arg	p.G472R	ENST00000353224	NM_177990.2	472	Ggg/Agg	5/10	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.373965884270532	2		269	921	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40864896	40864896	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	119	278	0	ENST00000373198.4:c.2372G>A	p.Arg791Lys	p.R791K	ENST00000373198	NM_133170.3	791	aGa/aAa	16/32	1	2	FACETS	0.808	0.729	0.891	0.808	0.729	0.891	CLONAL	1	TRUE	1	0.373965884270532	2		278	788	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41408905	41408905	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	149	260	0	ENST00000373198.4:c.521C>T	p.Pro174Leu	p.P174L	ENST00000373198	NM_133170.3	174	cCt/cTt	4/32	1	2	FACETS	0.999	0.913	1	0.999	0.913	1	CLONAL	1	TRUE	1	0.373965884270532	2		260	798	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319954	62319954	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	118	301	0	ENST00000360203.5:c.1796C>T	p.Ser599Phe	p.S599F	ENST00000360203	NM_001283009.1	599	tCc/tTc	21/35	1	2	FACETS	0.66	0.595	0.73	0.66	0.595	0.73	SUBCLONAL	1	TRUE	1	0.373965884270532	2		301	956	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546048	41546048	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1297	240	415	0	ENST00000263253.7:c.2663C>T	p.Pro888Leu	p.P888L	ENST00000263253	NM_001429.3	888	cCa/cTa	14/31	0.246850743248852	3	FACETS	0.991	0.923	1	0.496	0.461	0.531	CLONAL	1	TRUE	1	0.373965884270532	3		415	1537	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932624	49932624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs889230721	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	940	202	358	0	ENST00000296474.3:c.3247C>T	p.His1083Tyr	p.H1083Y	ENST00000296474	NM_002447.2	1083	Cac/Tac	14/20	1	2	FACETS	0.946	0.876	1	0.946	0.876	1	CLONAL	1	TRUE	1	0.373965884270532	2		358	1142	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52443756	52443756	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	159	346	0	ENST00000460680.1:c.41T>C	p.Leu14Pro	p.L14P	ENST00000460680	NM_004656.3	14	cTc/cCc	2/17	1	2	FACETS	0.818	0.749	0.891	0.818	0.749	0.891	CLONAL	1	TRUE	1	0.373965884270532	2		346	1039	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71102882	71102882	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	113	314	0	ENST00000318789.4:c.325C>T	p.Pro109Ser	p.P109S	ENST00000318789	NM_032682.5	109	Ccc/Tcc	8/21	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.373965884270532	2		314	559	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138461413	138461413	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	76	171	0	ENST00000289153.2:c.608T>G	p.Phe203Cys	p.F203C	ENST00000289153	NM_006219.2	203	tTt/tGt	3/22	1	2	FACETS	0.732	0.643	0.828	0.732	0.643	0.828	SUBCLONAL	1	TRUE	1	0.373965884270532	2		171	555	SUCCESS
ATR	545	MSKCC	GRCh37	3	142238575	142238575	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	85	143	0	ENST00000350721.4:c.4318C>T	p.His1440Tyr	p.H1440Y	ENST00000350721	NM_001184.3	1440	Cac/Tac	24/47	1	2	FACETS	0.918	0.814	1	0.918	0.814	1	CLONAL	1	TRUE	1	0.373965884270532	2		143	495	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs121913279	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	106	232	0	ENST00000263967.3:c.3140A>T	p.His1047Leu	p.H1047L	ENST00000263967	NM_006218.2	1047	cAt/cTt	21/21	1	2	FACETS	0.82	0.736	0.91	0.82	0.736	0.91	CLONAL	1	TRUE	1	0.373965884270532	2		232	691	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189582106	189582106	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	170	332	0	ENST00000264731.3:c.665G>A	p.Gly222Glu	p.G222E	ENST00000264731	NM_003722.4	222	gGa/gAa	5/14	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.373965884270532	2		332	903	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612028	189612028	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs900140738	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	110	475	0	ENST00000264731.3:c.1780C>T	p.Arg594Ter	p.R594*	ENST00000264731	NM_003722.4	594	Cga/Tga	14/14	1	2	FACETS	0.791	0.711	0.875	0.791	0.711	0.875	SUBCLONAL	1	TRUE	1	0.373965884270532	2		475	744	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41748170	41748170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs964285984	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	159	329	0	ENST00000226382.2:c.599C>T	p.Pro200Leu	p.P200L	ENST00000226382	NM_003924.3	200	cCc/cTc	3/3	1	2	FACETS	0.855	0.783	0.931	0.855	0.783	0.931	CLONAL	1	TRUE	1	0.373965884270532	2		329	994	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155180	55155180	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600187	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	160	516	0	ENST00000257290.5:c.2779G>A	p.Glu927Lys	p.E927K	ENST00000257290	NM_006206.4	927	Gag/Aag	21/23	1	2	FACETS	0.997	0.915	1	0.997	0.915	1	CLONAL	1	TRUE	1	0.373965884270532	2		516	858	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979597	55979597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	186	327	0	ENST00000263923.4:c.850G>A	p.Glu284Lys	p.E284K	ENST00000263923	NM_002253.2	284	Gag/Aag	7/30	1	2	FACETS	0.932	0.86	1	0.932	0.86	1	CLONAL	1	TRUE	1	0.373965884270532	2		327	1067	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156493	106156493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	161	374	0	ENST00000380013.4:c.1394C>T	p.Pro465Leu	p.P465L	ENST00000380013	NM_001127208.2	465	cCa/cTa	3/11	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.373965884270532	2		374	730	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143350355	143350355	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	78	196	0	ENST00000262992.4:c.107C>T	p.Pro36Leu	p.P36L	ENST00000262992	NM_001101669.1	36	cCa/cTa	3/24	1	2	FACETS	0.853	0.752	0.961	0.853	0.752	0.961	CLONAL	1	TRUE	1	0.373965884270532	2		196	489	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	225663	225665	+	frameshift_variant	Frame_Shift_Del	DEL	GCC	GCC	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1210	85	484	0	ENST00000264932.6:c.442_444delinsT	p.Ala148CysfsTer13	p.A148Cfs*13	ENST00000264932	NM_004168.2	148	GCC/T	4/15	1	2	FACETS	0.351	0.309	0.397	0.351	0.309	0.397	SUBCLONAL	1	TRUE	1	0.373965884270532	2		484	1295	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1254587	1254587	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs886059831	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	238	361	0	ENST00000310581.5:c.3191C>T	p.Pro1064Leu	p.P1064L	ENST00000310581	NM_198253.2	1064	cCt/cTt	15/16	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.373965884270532	2		361	1097	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260660	1260660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	226	373	0	ENST00000310581.5:c.2899G>A	p.Gly967Arg	p.G967R	ENST00000310581	NM_198253.2	967	Ggg/Agg	12/16	1	2	FACETS	0.997	0.928	1	0.997	0.928	1	CLONAL	1	TRUE	1	0.373965884270532	2		373	1212	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	153	173	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.373965884270532	2		174	758	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753379	57753379	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	118	219	0	ENST00000274289.3:c.745C>T	p.Pro249Ser	p.P249S	ENST00000274289	NM_006622.3	249	Cct/Tct	6/14	1	2	FACETS	0.893	0.806	0.984	0.893	0.806	0.984	CLONAL	1	TRUE	1	0.373965884270532	2		219	707	SUCCESS
APC	324	MSKCC	GRCh37	5	112177484	112177485	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	100	205	0	ENST00000257430.4:c.6193_6194delinsTT	p.Pro2065Phe	p.P2065F	ENST00000257430	NM_000038.5	2065	CCc/TTc	16/16	1	2	FACETS	0.88	0.787	0.977	0.88	0.787	0.977	CLONAL	1	TRUE	1	0.373965884270532	2		205	608	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149511632	149511632	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167658274	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	144	267	0	ENST00000261799.4:c.1153C>T	p.Arg385Cys	p.R385C	ENST00000261799	NM_002609.3	385	Cgc/Tgc	8/23	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.373965884270532	2		267	747	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052995	180052995	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	238	607	0	ENST00000261937.6:c.1295C>T	p.Pro432Leu	p.P432L	ENST00000261937	NM_182925.4	432	cCc/cTc	10/30	1	2	FACETS	0.886	0.825	0.949	0.886	0.825	0.949	CLONAL	1	TRUE	1	0.373965884270532	2		607	1437	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056403	180056403	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149373386	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	160	316	0	ENST00000261937.6:c.841G>A	p.Glu281Lys	p.E281K	ENST00000261937	NM_182925.4	281	Gag/Aag	7/30	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.373965884270532	2		316	806	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1079	257	705	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.373965884270532	2		705	1336	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32184737	32184737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	919	222	626	1	ENST00000375023.3:c.1846C>T	p.Pro616Ser	p.P616S	ENST00000375023	NM_004557.3	616	Ccc/Tcc	11/30	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.373965884270532	2		627	1141	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800433	32800433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1352	300	549	0	ENST00000374899.4:c.1114G>A	p.Glu372Lys	p.E372K	ENST00000374899	NM_018833.2	372	Gaa/Aaa	6/12	1	2	FACETS	0.971	0.912	1	0.971	0.912	1	CLONAL	1	TRUE	1	0.373965884270532	2		549	1652	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956509	93956509	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	84	124	0	ENST00000369303.4:c.2726+1G>A		p.X909_splice	ENST00000369303	NM_004440.3	909			1	2	FACETS	0.99	0.878	1	0.99	0.878	1	CLONAL	1	TRUE	1	0.373965884270532	2		124	454	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979219	93979219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1009626356	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	81	193	0	ENST00000369303.4:c.1609G>A	p.Glu537Lys	p.E537K	ENST00000369303	NM_004440.3	537	Gaa/Aaa	7/17	1	2	FACETS	0.808	0.714	0.909	0.808	0.714	0.909	CLONAL	1	TRUE	1	0.373965884270532	2		193	536	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068003	94068003	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757798599	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	118	175	0	ENST00000369303.4:c.959C>T	p.Pro320Leu	p.P320L	ENST00000369303	NM_004440.3	320	cCa/cTa	4/17	1	2	FACETS	0.88	0.795	0.97	0.88	0.795	0.97	CLONAL	1	TRUE	1	0.373965884270532	2		175	717	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112017478	112017478	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	121	182	0	ENST00000368678.4:c.1033+2T>C		p.X345_splice	ENST00000368678		345			1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.373965884270532	2		182	612	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117630069	117630069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	94	218	0	ENST00000368508.3:c.6457G>A	p.Glu2153Lys	p.E2153K	ENST00000368508	NM_002944.2	2153	Gag/Aag	41/43	1	2	FACETS	0.815	0.726	0.909	0.815	0.726	0.909	CLONAL	1	TRUE	1	0.373965884270532	2		218	617	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117645530	117645530	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	129	253	0	ENST00000368508.3:c.5606G>A	p.Gly1869Glu	p.G1869E	ENST00000368508	NM_002944.2	1869	gGa/gAa	34/43	1	2	FACETS	0.895	0.812	0.982	0.895	0.812	0.982	CLONAL	1	TRUE	1	0.373965884270532	2		253	771	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662625	117662625	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	160	644	1	ENST00000368508.3:c.4840C>T	p.Pro1614Ser	p.P1614S	ENST00000368508	NM_002944.2	1614	Cca/Tca	29/43	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.373965884270532	2		645	848	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681046	117681046	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	169	284	0	ENST00000368508.3:c.3574G>A	p.Asp1192Asn	p.D1192N	ENST00000368508	NM_002944.2	1192	Gat/Aat	23/43	1	2	FACETS	0.888	0.816	0.963	0.888	0.816	0.963	CLONAL	1	TRUE	1	0.373965884270532	2		284	1018	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117724305	117724305	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	149	296	0	ENST00000368508.3:c.574G>A	p.Gly192Arg	p.G192R	ENST00000368508	NM_002944.2	192	Gga/Aga	6/43	1	2	FACETS	0.889	0.812	0.97	0.889	0.812	0.97	CLONAL	1	TRUE	1	0.373965884270532	2		296	896	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265323	152265323	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866869178	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	131	335	0	ENST00000206249.3:c.776G>A	p.Arg259Gln	p.R259Q	ENST00000206249	NM_000125.3	259	cGa/cAa	4/8	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.373965884270532	2		335	638	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157522148	157522148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	169	438	0	ENST00000346085.5:c.4420C>T	p.Pro1474Ser	p.P1474S	ENST00000346085	NM_020732.3	1474	Ccc/Tcc	18/20	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.373965884270532	2		438	865	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976791	2976791	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	623	437	0	ENST00000396946.4:c.1221C>G	p.Ile407Met	p.I407M	ENST00000396946	NM_032415.4	407	atC/atG	9/25	0.373965884270532	3	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	1	0.373965884270532	3		437	1786	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729952	41729952	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1007889051	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1124	144	330	1	ENST00000242208.4:c.577G>A	p.Glu193Lys	p.E193K	ENST00000242208	NM_002192.2	193	Gag/Aag	3/3	0.373965884270532	3	FACETS	0.721	0.656	0.79	0.36	0.328	0.395	SUBCLONAL	1	TRUE	1	0.373965884270532	3		331	1268	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381466	81381466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	104	431	1	ENST00000222390.5:c.595G>A	p.Glu199Lys	p.E199K	ENST00000222390	NM_000601.4	199	Gaa/Aaa	5/18	1	2	FACETS	0.946	0.849	1	0.946	0.849	1	CLONAL	1	TRUE	1	0.373965884270532	2		432	588	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508609	106508609	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	109	260	0	ENST00000359195.3:c.603G>A	p.Trp201Ter	p.W201*	ENST00000359195	NM_002649.2	201	tgG/tgA	2/11	1	2	FACETS	0.799	0.717	0.884	0.799	0.717	0.884	SUBCLONAL	1	TRUE	1	0.373965884270532	2		260	730	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509015	106509015	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	143	263	0	ENST00000359195.3:c.1009G>A	p.Glu337Lys	p.E337K	ENST00000359195	NM_002649.2	337	Gag/Aag	2/11	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.373965884270532	2		263	744	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106515145	106515145	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	163	261	0	ENST00000359195.3:c.2288T>G	p.Val763Gly	p.V763G	ENST00000359195	NM_002649.2	763	gTt/gGt	5/11	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.373965884270532	2		261	814	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395557	116395557	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1481812764	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	122	235	0	ENST00000397752.3:c.1850G>A	p.Ser617Asn	p.S617N	ENST00000397752	NM_000245.2	617	aGc/aAc	6/21	1	2	FACETS	0.847	0.766	0.933	0.847	0.766	0.933	CLONAL	1	TRUE	1	0.373965884270532	2		235	770	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860052	151860052	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	94	177	0	ENST00000262189.6:c.10610G>A	p.Gly3537Glu	p.G3537E	ENST00000262189	NM_170606.2	3537	gGa/gAa	43/59	1	2	FACETS	0.821	0.732	0.916	0.821	0.732	0.916	CLONAL	1	TRUE	1	0.373965884270532	2		177	612	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874538	151874538	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753762683	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	132	178	0	ENST00000262189.6:c.8000C>T	p.Pro2667Leu	p.P2667L	ENST00000262189	NM_170606.2	2667	cCg/cTg	38/59	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.373965884270532	2		178	618	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29197680	29197680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779380098	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	986	195	483	2	ENST00000240100.2:c.514C>T	p.Pro172Ser	p.P172S	ENST00000240100	NM_001394.6	172	Ccc/Tcc	2/4	1	2	FACETS	0.883	0.816	0.953	0.883	0.816	0.953	CLONAL	1	TRUE	1	0.373965884270532	2		485	1181	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56882275	56882275	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	134	278	0	ENST00000519728.1:c.974-1G>A		p.X325_splice	ENST00000519728	NM_002350.3	325			1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.373965884270532	2		278	711	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046410	69046410	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868582467	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	152	314	0	ENST00000288368.4:c.3883G>A	p.Glu1295Lys	p.E1295K	ENST00000288368	NM_024870.2	1295	Gaa/Aaa	32/40	1	2	FACETS	0.842	0.77	0.918	0.842	0.77	0.918	CLONAL	1	TRUE	1	0.373965884270532	2		314	965	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5065040	5065040	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs267602253	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	134	213	0	ENST00000381652.3:c.1214C>T	p.Ser405Leu	p.S405L	ENST00000381652	NM_004972.3	405	tCg/tTg	9/25	0.321937984065556	2	FACETS	1	0.986	1	0.71	0.648	0.773	CLONAL	1	TRUE	0	0.373965884270532	2		213	505	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27158095	27158095	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	344	378	0	ENST00000380036.4:c.319C>T	p.Arg107Ter	p.R107*	ENST00000380036	NM_000459.3	107	Cga/Tga	2/23	0.370946405234145	0	FACETS	0.882	0.834	0.931			1	CLONAL	1	TRUE	0	0.373965884270532	0		378	1306	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27169586	27169586	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1102	221	406	1	ENST00000380036.4:c.587G>A	p.Gly196Glu	p.G196E	ENST00000380036	NM_000459.3	196	gGa/gAa	4/23	0.321560311878101	3	FACETS	1	0.964	1	0.53	0.492	0.57	CLONAL	1	TRUE	1	0.373965884270532	3		407	1323	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27209131	27209131	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	184	316	0	ENST00000380036.4:c.2588A>T	p.Lys863Ile	p.K863I	ENST00000380036	NM_000459.3	863	aAa/aTa	16/23	0.321560311878101	3	FACETS	1	0.972	1	0.558	0.514	0.603	CLONAL	1	TRUE	1	0.373965884270532	3		316	1047	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932584	39932584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	264	232	0	ENST00000378444.4:c.2015C>T	p.Ser672Phe	p.S672F	ENST00000378444	NM_001123385.1	672	tCc/tTc	4/15	1	1	FACETS	0.774	0.728	0.819	1	0.994	1	SUBCLONAL	2	TRUE	0	0.373965884270532	1		232	742	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615568	100615568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	143	150	0	ENST00000308731.7:c.764G>A	p.Arg255Gln	p.R255Q	ENST00000308731	NM_000061.2	255	cGa/cAa	8/19	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.373965884270532	1		150	438	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110032	115110032	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015512-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1290	251	457	0	ENST00000257566.3:c.1846T>G	p.Ser616Ala	p.S616A	ENST00000257566	NM_016569.3	616	Tct/Gct	8/8	1	2	FACETS	0.871	0.812	0.932	0.871	0.812	0.932	CLONAL	1	TRUE	1	0.373965884270532	2		457	1541	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0015521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	171	282	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.472193887727936	2		282	675	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0015521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	205	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.472193887727936	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.472193887727936	1		458	552	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs11554290	NA	P-0015521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	200	598	0	ENST00000369535.4:c.182A>T	p.Gln61Leu	p.Q61L	ENST00000369535	NM_002524.4	61	cAa/cTa	3/7	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.472193887727936	2		598	818	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0015521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	298	316	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	0.409049365571138	3	FACETS	0.97	0.918	1	0.97	0.918	1	CLONAL	2	TRUE	1	0.472193887727936	3		316	804	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261757	16261757	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	185	342	0	ENST00000375759.3:c.9022C>T	p.Pro3008Ser	p.P3008S	ENST00000375759	NM_015001.2	3008	Cca/Tca	11/15	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.472193887727936	2		342	641	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193107257	193107257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	91	171	0	ENST00000367435.3:c.466C>T	p.Arg156Cys	p.R156C	ENST00000367435	NM_024529.4	156	Cgt/Tgt	6/17	0.472193887727936	4	FACETS	0.784	0.696	0.878	0.261	0.232	0.293	SUBCLONAL	1	TRUE	1	0.472193887727936	4		171	724	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573894	18573894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759658584	NA	P-0015521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	128	416	0	ENST00000266497.5:c.2212C>T	p.Arg738Cys	p.R738C	ENST00000266497		738	Cgt/Tgt	15/31	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.472193887727936	2		416	436	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416713	121416713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772222326	NA	P-0015521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	242	488	0	ENST00000257555.6:c.142G>A	p.Glu48Lys	p.E48K	ENST00000257555		48	Gag/Aag	1/10	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.472193887727936	2		488	965	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28964193	28964193	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	95	213	0	ENST00000282397.4:c.1709G>A	p.Gly570Glu	p.G570E	ENST00000282397	NM_002019.4	570	gGa/gAa	13/30	1	2	FACETS	0.925	0.828	1	0.925	0.828	1	CLONAL	1	TRUE	1	0.472193887727936	2		213	435	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281662	49281662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	288	459	2	ENST00000282018.3:c.709G>A	p.Gly237Arg	p.G237R	ENST00000282018	NM_020377.2	237	Ggg/Agg	1/1	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.472193887727936	2		461	1105	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853251	68853251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780115	NA	P-0015521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	228	396	0	ENST00000261769.5:c.1634G>A	p.Arg545Gln	p.R545Q	ENST00000261769	NM_004360.3	545	cGg/cAg	11/16	0.472193887727936	1	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	0	0.472193887727936	1		396	727	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828347	72828347	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760790924	NA	P-0015521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	173	305	0	ENST00000268489.5:c.8234T>C	p.Leu2745Pro	p.L2745P	ENST00000268489	NM_006885.3	2745	cTa/cCa	9/10	0.472193887727936	1	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	0	0.472193887727936	1		305	451	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45868409	45868409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747619345	NA	P-0015521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	266	519	0	ENST00000391945.4:c.368C>T	p.Pro123Leu	p.P123L	ENST00000391945	NM_000400.3	123	cCc/cTc	6/23	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.472193887727936	2		519	1053	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42860440	42860440	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	146	306	0	ENST00000398585.3:c.437T>A	p.Met146Lys	p.M146K	ENST00000398585	NM_001135099.1	146	aTg/aAg	5/14	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.472193887727936	2		306	605	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163813	47163814	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	108	236	0	ENST00000409792.3:c.2312_2313delinsTT	p.Ser771Phe	p.S771F	ENST00000409792	NM_014159.6	771	tCC/tTT	3/21	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.472193887727936	2		236	449	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509084	66509085	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0015521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	69	231	0	ENST00000273854.3:c.242dup	p.Asn81LysfsTer8	p.N81Kfs*8	ENST00000273854	NM_004439.5	81	aat/aaAt	2/18	1	2	FACETS	0.67	0.586	0.761	0.67	0.586	0.761	SUBCLONAL	1	TRUE	1	0.472193887727936	2		231	436	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31407023	31407023	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	110	411	0	ENST00000344624.3:c.3884C>G	p.Ala1295Gly	p.A1295G	ENST00000344624		1295	gCc/gGc	31/33	1	2	FACETS	0.518	0.465	0.575	0.518	0.465	0.575	SUBCLONAL	1	TRUE	1	0.472193887727936	2		411	899	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968229	2968229	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0015521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	474	530	1	ENST00000396946.4:c.1754+3G>A		p.X585_splice	ENST00000396946	NM_032415.4	585			0.409049365571138	3	FACETS	0.993	0.951	1	0.993	0.951	1	CLONAL	2	TRUE	1	0.472193887727936	3		531	1249	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518175	8518175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1354824749	NA	P-0015521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	136	453	1	ENST00000356435.5:c.1216G>A	p.Glu406Lys	p.E406K	ENST00000356435		406	Gaa/Aaa	10/35	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.472193887727936	2		454	506	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889178	76889178	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	223	202	0	ENST00000373344.5:c.4832T>C	p.Val1611Ala	p.V1611A	ENST00000373344	NM_000489.3	1611	gTt/gCt	18/35	1	1	FACETS	0.843	0.796	0.889	1	0.994	1	CLONAL	2	TRUE	0	0.472193887727936	1		202	428	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47163814	47163814	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015521-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	103	236	0	ENST00000409792.3:c.2312C>T	p.Ser771Phe	p.S771F	ENST00000409792	NM_014159.6	771	tCc/tTc	3/21	1	2	FACETS	0.992	0.893	1	0.992	0.893	1	CLONAL	1	TRUE	1	0.472193887727936	2		236	440	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295242	1295243	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	292	430	0				ENST00000310581	NM_198253.2	-/1132			0.537801369808628	3	FACETS	0.812	0.767	0.859	0.812	0.767	0.859	CLONAL	2	TRUE	1	0.537801369808628	3		430	848	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	337	510	1	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	0.507885263219978	2	FACETS	0.979	0.935	1	0.979	0.935	1	CLONAL	2	TRUE	0	0.537801369808628	2		511	640	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857974	9857974	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61758996	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	223	436	0	ENST00000330684.3:c.3427G>A	p.Glu1143Lys	p.E1143K	ENST00000330684	NM_001134407.1	1143	Gag/Aag	13/13	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.537801369808628	2		436	783	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419837	41419837	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	rs267605939	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	151	449	0	ENST00000373198.4:c.484C>T	p.Gln162Ter	p.Q162*	ENST00000373198	NM_133170.3	162	Cag/Tag	3/32	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.537801369808628	2		449	538	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873724	35873724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148165103	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	121	254	0	ENST00000303115.3:c.680G>A	p.Arg227Lys	p.R227K	ENST00000303115	NM_002185.3	227	aGa/aAa	5/8	1	2	FACETS	0.976	0.888	1	0.976	0.888	1	CLONAL	1	TRUE	1	0.537801369808628	2		254	461	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248683	212248683	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	119	290	0	ENST00000342788.4:c.3584C>T	p.Pro1195Leu	p.P1195L	ENST00000342788	NM_005235.2	1195	cCa/cTa	28/28	1	2	FACETS	0.911	0.827	0.998	0.911	0.827	0.998	CLONAL	1	TRUE	1	0.537801369808628	2		290	486	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41521893	41521893	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	230	592	0	ENST00000263253.7:c.755C>T	p.Pro252Leu	p.P252L	ENST00000263253	NM_001429.3	252	cCt/cTt	3/31	1	2	FACETS	0.95	0.887	1	0.95	0.887	1	CLONAL	1	TRUE	1	0.537801369808628	2		592	900	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417602	139417602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1074	360	763	0	ENST00000277541.6:c.442C>T	p.Pro148Ser	p.P148S	ENST00000277541	NM_017617.3	148	Ccc/Tcc	4/34	1	2	FACETS	0.934	0.884	0.985	0.934	0.884	0.985	CLONAL	1	TRUE	1	0.537801369808628	2		763	1434	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930595	131930595	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	91	262	0	ENST00000265335.6:c.1828C>T	p.His610Tyr	p.H610Y	ENST00000265335		610	Cat/Tat	12/25	1	2	FACETS	0.842	0.752	0.936	0.842	0.752	0.936	CLONAL	1	TRUE	1	0.537801369808628	2		262	402	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94163118	94163119	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	279	131	385	0	ENST00000323929.3:c.2028_2029delinsTT	p.Gln677Ter	p.Q677*	ENST00000323929	NM_005591.3	676	tcCCag/tcTTag	19/20	0.537801369808628	1	FACETS	0.869	0.796	0.944	0.869	0.796	0.944	CLONAL	1	TRUE	0	0.537801369808628	1		385	410	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40364030	40364030	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	997	483	561	0	ENST00000293328.3:c.1652T>C	p.Leu551Pro	p.L551P	ENST00000293328	NM_012448.3	551	cTg/cCg	13/19	0.478250493928227	4	FACETS	0.933	0.892	0.975	0.933	0.892	0.975	CLONAL	2	TRUE	2	0.537801369808628	4		561	1480	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087515	27087516	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	205	545	1	ENST00000324856.7:c.2089_2090delinsTT	p.Pro697Leu	p.P697L	ENST00000324856	NM_006015.4	697	CCg/TTg	5/20	1	2	FACETS	0.812	0.753	0.872	0.812	0.753	0.872	CLONAL	1	TRUE	1	0.537801369808628	2		546	939	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087519	27087519	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758974480	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	277	544	1	ENST00000324856.7:c.2093C>T	p.Ser698Phe	p.S698F	ENST00000324856	NM_006015.4	698	tCc/tTc	5/20	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.537801369808628	2		545	948	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599278	28599278	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	341	684	0	ENST00000253063.3:c.724A>C	p.Ser242Arg	p.S242R	ENST00000253063	NM_031459.4	242	Agc/Cgc	5/10	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.537801369808628	2		684	1236	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339094	65339094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	183	377	0	ENST00000342505.4:c.442C>T	p.Pro148Ser	p.P148S	ENST00000342505	NM_002227.2	148	Cct/Tct	5/25	1	2	FACETS	0.886	0.82	0.955	0.886	0.82	0.955	CLONAL	1	TRUE	1	0.537801369808628	2		377	768	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745609	162745609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	960	182	474	0	ENST00000367921.3:c.2024C>T	p.Ser675Phe	p.S675F	ENST00000367921	NM_006182.2	675	tCc/tTc	15/18	0.537801369808628	4	FACETS	0.911	0.84	0.986	0.304	0.28	0.329	CLONAL	1	TRUE	1	0.537801369808628	4		474	1142	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573174	64573174	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	689	276	559	0	ENST00000312049.6:c.1118C>A	p.Pro373His	p.P373H	ENST00000312049	NM_130799.2	373	cCc/cAc	8/10	1	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	1	TRUE	1	0.537801369808628	2		559	965	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	432368	432368	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1362895739	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	81	134	0	ENST00000399788.2:c.2155C>T	p.Arg719Cys	p.R719C	ENST00000399788	NM_001042603.1	719	Cgc/Tgc	16/28	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.537801369808628	2		134	271	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69230464	69230464	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	136	336	0	ENST00000462284.1:c.853A>G	p.Thr285Ala	p.T285A	ENST00000462284	NM_002392.5	285	Act/Gct	10/11	1	2	FACETS	0.908	0.829	0.99	0.908	0.829	0.99	CLONAL	1	TRUE	1	0.537801369808628	2		336	557	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120984	115120984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	205	689	0	ENST00000257566.3:c.22C>T	p.Pro8Ser	p.P8S	ENST00000257566	NM_016569.3	8	Ccg/Tcg	1/8	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.537801369808628	2		689	742	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29005342	29005342	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	155	465	0	ENST00000282397.4:c.919G>A	p.Gly307Arg	p.G307R	ENST00000282397	NM_002019.4	307	Gga/Aga	7/30	1	2	FACETS	0.987	0.908	1	0.987	0.908	1	CLONAL	1	TRUE	1	0.537801369808628	2		465	584	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3119008	3119009	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	237	569	1	ENST00000078429.4:c.692_693delinsTT	p.Ala231Val	p.A231V	ENST00000078429	NM_002067.2	231	gCC/gTT	5/7	1	2	FACETS	0.902	0.842	0.964	0.902	0.842	0.964	CLONAL	1	TRUE	1	0.537801369808628	2		570	977	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11015753	11015753	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	138	301	0	ENST00000327064.4:c.346+1G>A		p.X116_splice	ENST00000327064	NM_199141.1	116			1	2	FACETS	0.978	0.895	1	0.978	0.895	1	CLONAL	1	TRUE	1	0.537801369808628	2		301	525	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271975	15271976	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	202	566	1	ENST00000263388.2:c.6463_6464delinsAA	p.Gly2155Lys	p.G2155K	ENST00000263388	NM_000435.2	2155	GGa/AAa	33/33	1	2	FACETS	0.88	0.817	0.945	0.88	0.817	0.945	CLONAL	1	TRUE	1	0.537801369808628	2		567	854	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945785	17945785	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	191	499	0	ENST00000458235.1:c.2075C>T	p.Ala692Val	p.A692V	ENST00000458235	NM_000215.3	692	gCc/gTc	16/24	1	2	FACETS	0.9	0.834	0.969	0.9	0.834	0.969	CLONAL	1	TRUE	1	0.537801369808628	2		499	789	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219686	36219686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	283	565	0	ENST00000222270.7:c.4583C>T	p.Pro1528Leu	p.P1528L	ENST00000222270	NM_014727.1	1528	cCc/cTc	20/37	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.537801369808628	2		565	956	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212589823	212589823	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	182	352	0	ENST00000342788.4:c.719G>A	p.Gly240Glu	p.G240E	ENST00000342788	NM_005235.2	240	gGa/gAa	6/28	1	2	FACETS	0.953	0.882	1	0.953	0.882	1	CLONAL	1	TRUE	1	0.537801369808628	2		352	710	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46276009	46276009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369514609	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	251	667	0	ENST00000371998.3:c.3445C>T	p.Pro1149Ser	p.P1149S	ENST00000371998		1149	Cct/Tct	18/23	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.537801369808628	2		667	874	SUCCESS
RAC2	5880	MSKCC	GRCh37	22	37628034	37628034	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	215	417	0	ENST00000249071.6:c.226G>A	p.Asp76Asn	p.D76N	ENST00000249071	NM_002872.4	76	Gac/Aac	4/7	1	2	FACETS	0.996	0.928	1	0.996	0.928	1	CLONAL	1	TRUE	1	0.537801369808628	2		417	803	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295274	1295274	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	263	558	0				ENST00000310581	NM_198253.2	-/1132			0.537801369808628	3	FACETS	1	0.985	1	0.576	0.539	0.613	CLONAL	1	TRUE	1	0.537801369808628	3		558	1078	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271349	26271350	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	159	326	0	ENST00000305910.3:c.263_264delinsTT	p.Ser88Phe	p.S88F	ENST00000305910	NM_003534.2	88	tCC/tTT	1/1	0.376103995245241	3	FACETS	1	0.955	1	0.529	0.486	0.574	CLONAL	1	TRUE	1	0.537801369808628	3		326	709	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674155	117674155	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs765733079	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	202	377	0	ENST00000368508.3:c.4319C>T	p.Pro1440Leu	p.P1440L	ENST00000368508	NM_002944.2	1440	cCa/cTa	26/43	0.463483109181754	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.537801369808628	1		377	515	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946418	2946418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	303	636	0	ENST00000396946.4:c.3319G>A	p.Glu1107Lys	p.E1107K	ENST00000396946	NM_032415.4	1107	Gag/Aag	25/25	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.537801369808628	2		636	1101	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976769	2976769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1402987893	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	236	606	0	ENST00000396946.4:c.1243G>A	p.Asp415Asn	p.D415N	ENST00000396946	NM_032415.4	415	Gac/Aac	9/25	1	2	FACETS	0.909	0.849	0.971	0.909	0.849	0.971	CLONAL	1	TRUE	1	0.537801369808628	2		606	965	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729673	41729673	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	179	400	0	ENST00000242208.4:c.856G>A	p.Glu286Lys	p.E286K	ENST00000242208	NM_002192.2	286	Gag/Aag	3/3	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.537801369808628	2		400	660	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68972936	68972936	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	161	507	0	ENST00000288368.4:c.1261G>A	p.Glu421Lys	p.E421K	ENST00000288368	NM_024870.2	421	Gaa/Aaa	11/40	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.537801369808628	2		507	591	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69028013	69028013	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs533278837	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	126	363	0	ENST00000288368.4:c.3172C>T	p.Pro1058Ser	p.P1058S	ENST00000288368	NM_024870.2	1058	Cct/Tct	26/40	1	2	FACETS	0.928	0.845	1	0.928	0.845	1	CLONAL	1	TRUE	1	0.537801369808628	2		363	505	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213479	27213479	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	101	251	0	ENST00000380036.4:c.2878-3C>T		p.X960_splice	ENST00000380036	NM_000459.3	960			NA	2	FACETS	0.951	0.856	1			1	INDETERMINATE	1	TRUE	NA	0.537801369808628	2		251	395	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259054	153259056	+	missense_variant	Missense_Mutation	TNP	TCT	TCT	ACA	novel	NA	P-0015526-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	160	55	166	0	ENST00000281708.4:c.759_761delinsTGT	p.Leu253_Asp254delinsPheVal	p.L253_D254delinsFV	ENST00000281708	NM_033632.3	253	ttAGAt/ttTGTt	5/12	1	2	FACETS	0.951	0.825	1	0.951	0.825	1	CLONAL	1	TRUE	1	0.537801369808628	2		166	215	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578395	7578395	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780070	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	321	693	0	ENST00000269305.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000269305	NM_001126112.2	179	Cat/Tat	5/11	0.305020663823876	4	FACETS	1	0.968	1	0.765	0.729	0.8	INDETERMINATE	3	TRUE	0	0.509366332916471	4		693	622	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55155180	55155180	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600187	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	106	516	0	ENST00000257290.5:c.2779G>A	p.Glu927Lys	p.E927K	ENST00000257290	NM_006206.4	927	Gag/Aag	21/23	NA	2	FACETS	0.929	0.838	1			1	INDETERMINATE	1	TRUE	NA	0.509366332916471	2		516	448	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295205	1295205	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	154	173	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.785	0.728	0.844	1	0.99	1	SUBCLONAL	2	TRUE	1	0.509366332916471	2		174	385	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858517	9858517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765370528	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	76	595	0	ENST00000330684.3:c.2884G>A	p.Glu962Lys	p.E962K	ENST00000330684	NM_001134407.1	962	Gaa/Aaa	13/13	0.509366332916471	1	FACETS	0.637	0.563	0.716	0.637	0.563	0.716	SUBCLONAL	1	TRUE	0	0.509366332916471	1		595	349	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971017	21971017	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913386	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	195	623	1	ENST00000304494.5:c.341C>T	p.Pro114Leu	p.P114L	ENST00000304494	NM_000077.4	114	cCc/cTc	2/3	0.509366332916471	1	FACETS	1	0.991	1	1	0.991	1	CLONAL	1	TRUE	0	0.509366332916471	1		624	408	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3807367	3807367	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	81	428	0	ENST00000262367.5:c.3620C>T	p.Ser1207Phe	p.S1207F	ENST00000262367	NM_004380.2	1207	tCc/tTc	19/31	1	2	FACETS	0.561	0.495	0.632	0.561	0.495	0.632	SUBCLONAL	1	TRUE	1	0.509366332916471	2		428	567	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912737	100912737	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	140	589	2	ENST00000325455.5:c.2585G>A	p.Gly862Glu	p.G862E	ENST00000325455	NM_001202474.3	862	gGa/gAa	7/8	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.509366332916471	2		591	429	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857127	9857127	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs976259560	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	56	391	1	ENST00000330684.3:c.4274C>T	p.Ser1425Leu	p.S1425L	ENST00000330684	NM_001134407.1	1425	tCg/tTg	13/13	0.509366332916471	1	FACETS	0.683	0.591	0.78	0.683	0.591	0.78	SUBCLONAL	1	TRUE	0	0.509366332916471	1		392	240	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435061	18435061	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603400	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	115	402	1	ENST00000266497.5:c.46G>A	p.Glu16Lys	p.E16K	ENST00000266497		16	Gaa/Aaa	1/31	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.509366332916471	2		403	401	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40748610	40748610	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	133	480	0	ENST00000373198.4:c.2906G>A	p.Gly969Glu	p.G969E	ENST00000373198	NM_133170.3	969	gGa/gAa	21/32	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.509366332916471	2		480	436	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707785	176707785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886041941	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	305	488	0	ENST00000439151.2:c.5842C>T	p.Arg1948Cys	p.R1948C	ENST00000439151	NM_022455.4	1948	Cgc/Tgc	18/23	0.496798581231678	2	FACETS	0.96	0.913	1	0.96	0.913	1	CLONAL	2	TRUE	0	0.509366332916471	2		488	624	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50484057	50484057	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	201	703	1	ENST00000394963.4:c.907C>T	p.Arg303Ter	p.R303*	ENST00000394963	NM_003076.4	303	Cga/Tga	8/13	0.363295309146282	3	FACETS	1	0.978	1	0.565	0.524	0.607	CLONAL	1	TRUE	1	0.509366332916471	3		704	877	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346771	89346771	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	45	346	3	ENST00000301030.4:c.6179C>T	p.Ser2060Phe	p.S2060F	ENST00000301030	NM_001256183.1	2060	tCc/tTc	9/13	0.258362672877648	3	FACETS	0.827	0.7	0.966	0.414	0.35	0.483	INDETERMINATE	1	TRUE	1	0.509366332916471	3		349	268	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533390	29533390	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs267604791	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	179	214	0	ENST00000356175.3:c.1392+1G>A		p.X464_splice	ENST00000356175	NM_000267.3	464			0.33961730754733	6	FACETS	1	0.963	1			1	CLONAL	4	TRUE	NA	0.509366332916471	6		214	342	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89528553	89528553	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	97	293	0	ENST00000336596.2:c.2853G>A	p.Met951Ile	p.M951I	ENST00000336596	NM_005233.5	951	atG/atA	17/17	0.363295309146282	3	FACETS	1	0.982	1	0.731	0.658	0.806	CLONAL	1	TRUE	1	0.509366332916471	3		293	327	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88669600	88669600	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	138	431	0	ENST00000360948.2:c.1298C>T	p.Ser433Phe	p.S433F	ENST00000360948	NM_001012338.2	433	tCc/tTc	12/19	NA	2	FACETS	1	0.946	1			1	INDETERMINATE	1	TRUE	NA	0.509366332916471	2		431	519	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117715868	117715868	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	85	401	0	ENST00000368508.3:c.890G>A	p.Arg297Lys	p.R297K	ENST00000368508	NM_002944.2	297	aGa/aAa	9/43	NA	2	FACETS	1	0.904	1			1	INDETERMINATE	1	TRUE	NA	0.509366332916471	2		401	329	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925397	114925397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773530340	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	162	768	1	ENST00000543371.1:c.1475C>T	p.Ser492Leu	p.S492L	ENST00000543371	NM_001198531.1	492	tCg/tTg	14/14	0.187773192501372	0	FACETS	0.499	0.459	0.539			1	INDETERMINATE	1	TRUE	0	0.509366332916471	0		769	626	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88428957	88428957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	69	533	0	ENST00000360948.2:c.2143C>T	p.Pro715Ser	p.P715S	ENST00000360948	NM_001012338.2	715	Cca/Tca	17/19	NA	2	FACETS	0.868	0.763	0.981			1	INDETERMINATE	1	TRUE	NA	0.509366332916471	2		533	312	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162688867	162688867	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	110	506	1	ENST00000367921.3:c.14C>T	p.Pro5Leu	p.P5L	ENST00000367921	NM_006182.2	5	cCc/cTc	3/18	1	2	FACETS	0.866	0.781	0.954	0.866	0.781	0.954	CLONAL	1	TRUE	1	0.509366332916471	2		507	499	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956676	93956676	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465960814	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	44	385	0	ENST00000369303.4:c.2560C>T	p.Arg854Cys	p.R854C	ENST00000369303	NM_004440.3	854	Cgt/Tgt	15/17	NA	2	FACETS	0.522	0.439	0.613			1	INDETERMINATE	1	TRUE	NA	0.509366332916471	2		385	331	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124437	94124437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	116	516	2	ENST00000369303.4:c.146C>T	p.Ser49Phe	p.S49F	ENST00000369303	NM_004440.3	49	tCc/tTc	2/17	NA	2	FACETS	1	0.973	1			1	INDETERMINATE	1	TRUE	NA	0.509366332916471	2		518	386	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436012	116436012	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369312680	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	193	643	0	ENST00000397752.3:c.4007G>A	p.Arg1336Gln	p.R1336Q	ENST00000397752	NM_000245.2	1336	cGg/cAg	21/21	0.24002258557666	4	FACETS	0.782	0.726	0.841	0.782	0.726	0.841	INDETERMINATE	2	TRUE	2	0.509366332916471	4		643	731	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2954957	2954957	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	238	676	0	ENST00000396946.4:c.2753G>A	p.Arg918Gln	p.R918Q	ENST00000396946	NM_032415.4	918	cGg/cAg	21/25	0.363295309146282	3	FACETS	0.891	0.837	0.946	0.891	0.837	0.946	CLONAL	2	TRUE	1	0.509366332916471	3		676	658	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271813	15271813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs541716070	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	178	749	1	ENST00000263388.2:c.6626C>T	p.Pro2209Leu	p.P2209L	ENST00000263388	NM_000435.2	2209	cCg/cTg	33/33	0.169384122445364	1	FACETS	0.873	0.808	0.938	0.873	0.808	0.938	INDETERMINATE	1	TRUE	0	0.509366332916471	1		750	597	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141595332	141595332	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	176	781	0	ENST00000220592.5:c.101C>T	p.Ser34Phe	p.S34F	ENST00000220592	NM_012154.3	34	tCc/tTc	2/19	0.258362672877648	3	FACETS	1	0.979	1	0.581	0.536	0.628	INDETERMINATE	1	TRUE	1	0.509366332916471	3		781	746	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476387	88476387	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202056599	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	109	550	0	ENST00000360948.2:c.1745G>A	p.Arg582Gln	p.R582Q	ENST00000360948	NM_001012338.2	582	cGg/cAg	15/19	NA	2	FACETS	0.743	0.669	0.821			1	INDETERMINATE	1	TRUE	NA	0.509366332916471	2		550	576	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005919	69005919	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	112	655	0	ENST00000288368.4:c.2330G>A	p.Gly777Glu	p.G777E	ENST00000288368	NM_024870.2	777	gGa/gAa	21/40	0.273867007699568	0	FACETS	0.529	0.479	0.58			1	INDETERMINATE	1	TRUE	0	0.509366332916471	0		655	408	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805735	43805735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	137	688	0	ENST00000372470.3:c.791C>T	p.Ser264Phe	p.S264F	ENST00000372470	NM_005373.2	264	tCc/tTc	5/12	0.24002258557666	4	FACETS	1	0.983	1	0.671	0.612	0.732	INDETERMINATE	1	TRUE	2	0.509366332916471	4		688	605	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120478179	120478179	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	203	469	0	ENST00000256646.2:c.3571T>C	p.Cys1191Arg	p.C1191R	ENST00000256646	NM_024408.3	1191	Tgc/Cgc	22/34	0.24002258557666	4	FACETS	0.969	0.903	1	0.969	0.903	1	INDETERMINATE	2	TRUE	2	0.509366332916471	4		469	621	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156849056	156849056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	120	806	0	ENST00000524377.1:c.1948G>A	p.Asp650Asn	p.D650N	ENST00000524377	NM_002529.3	650	Gac/Aac	15/17	1	2	FACETS	0.754	0.682	0.829	0.754	0.682	0.829	SUBCLONAL	1	TRUE	1	0.509366332916471	2		806	625	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609939	43609939	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767406	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	130	757	2	ENST00000355710.3:c.1891G>A	p.Asp631Asn	p.D631N	ENST00000355710	NM_020975.4	631	Gac/Aac	11/20	0.187773192501372	0	FACETS	0.482	0.439	0.526			1	INDETERMINATE	1	TRUE	0	0.509366332916471	0		759	520	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332867	70332867	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	108	660	0	ENST00000373644.4:c.772C>G	p.Pro258Ala	p.P258A	ENST00000373644	NM_030625.2	258	Ccc/Gcc	2/12	NA	2	FACETS	0.88	0.794	0.97			1	INDETERMINATE	1	TRUE	NA	0.509366332916471	2		660	482	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123239436	123239436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	72	524	2	ENST00000358487.5:c.2401G>A	p.Asp801Asn	p.D801N	ENST00000358487	NM_000141.4	801	Gac/Aac	18/18	0.187773192501372	0	FACETS	0.422	0.371	0.475			1	INDETERMINATE	1	TRUE	0	0.509366332916471	0		526	329	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137036	64137036	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	353	774	0	ENST00000334205.4:c.1547C>T	p.Ala516Val	p.A516V	ENST00000334205	NM_003942.2	516	gCc/gTc	13/17	0.409419515003366	6	FACETS	1	0.975	1			1	CLONAL	3	TRUE	NA	0.509366332916471	6		774	898	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100933314	100933314	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143150313	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	75	587	0	ENST00000325455.5:c.2076G>A	p.Met692Ile	p.M692I	ENST00000325455	NM_001202474.3	692	atG/atA	4/8	1	2	FACETS	0.787	0.694	0.886	0.787	0.694	0.886	SUBCLONAL	1	TRUE	1	0.509366332916471	2		587	374	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998556	100998556	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1474172577	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	87	574	0	ENST00000325455.5:c.1246G>A	p.Asp416Asn	p.D416N	ENST00000325455	NM_001202474.3	416	Gat/Aat	1/8	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.509366332916471	2		574	309	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18534763	18534763	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	109	515	0	ENST00000266497.5:c.1821G>A	p.Met607Ile	p.M607I	ENST00000266497		607	atG/atA	12/31	1	2	FACETS	0.955	0.863	1	0.955	0.863	1	CLONAL	1	TRUE	1	0.509366332916471	2		515	448	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18544088	18544088	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	78	321	0	ENST00000266497.5:c.1905G>A	p.Met635Ile	p.M635I	ENST00000266497		635	atG/atA	13/31	1	2	FACETS	0.939	0.833	1	0.939	0.833	1	CLONAL	1	TRUE	1	0.509366332916471	2		321	326	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641480	18641480	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	69	386	0	ENST00000266497.5:c.2479G>A	p.Glu827Lys	p.E827K	ENST00000266497		827	Gag/Aag	17/31	1	2	FACETS	0.79	0.693	0.894	0.79	0.693	0.894	SUBCLONAL	1	TRUE	1	0.509366332916471	2		386	343	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18650562	18650562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	77	476	0	ENST00000266497.5:c.2773G>A	p.Asp925Asn	p.D925N	ENST00000266497		925	Gat/Aat	20/31	1	2	FACETS	0.978	0.867	1	0.978	0.867	1	CLONAL	1	TRUE	1	0.509366332916471	2		476	309	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859006	57859006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	123	692	1	ENST00000228682.2:c.502C>T	p.Pro168Ser	p.P168S	ENST00000228682	NM_005269.2	168	Cct/Tct	5/12	1	2	FACETS	0.687	0.622	0.755	0.687	0.622	0.755	SUBCLONAL	1	TRUE	1	0.509366332916471	2		693	703	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865705	57865705	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	144	907	1	ENST00000228682.2:c.3182C>T	p.Pro1061Leu	p.P1061L	ENST00000228682	NM_005269.2	1061	cCt/cTt	12/12	1	2	FACETS	0.814	0.744	0.887	0.814	0.744	0.887	CLONAL	1	TRUE	1	0.509366332916471	2		908	695	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58145413	58145413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750707985	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	145	474	1	ENST00000257904.6:c.88C>T	p.His30Tyr	p.H30Y	ENST00000257904	NM_000075.3	30	Cac/Tac	2/8	1	2	FACETS	0.921	0.844	1	0.921	0.844	1	CLONAL	1	TRUE	1	0.509366332916471	2		475	618	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112888241	112888241	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	66	516	0	ENST00000351677.2:c.257G>C	p.Gly86Ala	p.G86A	ENST00000351677	NM_002834.3	86	gGg/gCg	3/16	1	2	FACETS	0.573	0.499	0.653	0.573	0.499	0.653	SUBCLONAL	1	TRUE	1	0.509366332916471	2		516	452	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120783942	120783943	+	missense_variant	Missense_Mutation	DNP	AG	AG	GA	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	126	567	4	ENST00000257552.2:c.1042_1043delinsTC	p.Leu348Ser	p.L348S	ENST00000257552	NM_002442.3	348	CTt/TCt	13/15	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.509366332916471	2		571	465	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133240690	133240690	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	135	649	0	ENST00000320574.5:c.2606C>T	p.Pro869Leu	p.P869L	ENST00000320574	NM_006231.2	869	cCc/cTc	23/49	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.509366332916471	2		649	521	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929071	32929071	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs786203493	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	179	572	0	ENST00000380152.3:c.7081C>T	p.His2361Tyr	p.H2361Y	ENST00000380152		2361	Cat/Tat	14/27	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.509366332916471	2		572	553	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281459	49281459	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	105	518	0	ENST00000282018.3:c.506C>T	p.Ser169Phe	p.S169F	ENST00000282018	NM_020377.2	169	tCc/tTc	1/1	0.509366332916471	1	FACETS	0.912	0.826	1	0.912	0.826	1	CLONAL	1	TRUE	0	0.509366332916471	1		518	337	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061887	38061887	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	128	873	0	ENST00000250448.2:c.102G>A	p.Met34Ile	p.M34I	ENST00000250448	NM_004496.3	34	atG/atA	2/2	NA	2	FACETS	0.995	0.907	1			1	INDETERMINATE	1	TRUE	NA	0.509366332916471	2		873	505	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988937	41988937	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	167	683	0	ENST00000219905.7:c.1729C>T	p.Leu577Phe	p.L577F	ENST00000219905	NM_001164273.1	577	Ctt/Ttt	3/24	0.509366332916471	3	FACETS	1	0.966	1	0.545	0.501	0.59	CLONAL	1	TRUE	1	0.509366332916471	3		683	755	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88483985	88483985	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	105	490	0	ENST00000360948.2:c.1586-1G>A		p.X529_splice	ENST00000360948	NM_001012338.2	529			NA	2	FACETS	0.85	0.765	0.939			1	INDETERMINATE	1	TRUE	NA	0.509366332916471	2		490	485	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	359998	359999	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	193	784	0	ENST00000262320.3:c.1090_1091delinsAA	p.Gly364Lys	p.G364K	ENST00000262320	NM_003502.3	364	GGg/AAg	4/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.509366332916471	2		784	649	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779208	3779208	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	60	292	0	ENST00000262367.5:c.5840C>T	p.Pro1947Leu	p.P1947L	ENST00000262367	NM_004380.2	1947	cCc/cTc	31/31	1	2	FACETS	0.847	0.737	0.966	0.847	0.737	0.966	CLONAL	1	TRUE	1	0.509366332916471	2		292	278	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3832745	3832745	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	105	498	0	ENST00000262367.5:c.1513C>T	p.Pro505Ser	p.P505S	ENST00000262367	NM_004380.2	505	Cct/Tct	6/31	1	2	FACETS	0.779	0.701	0.862	0.779	0.701	0.862	SUBCLONAL	1	TRUE	1	0.509366332916471	2		498	529	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857154	9857154	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377712891	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	114	474	0	ENST00000330684.3:c.4247G>A	p.Ser1416Asn	p.S1416N	ENST00000330684	NM_001134407.1	1416	aGt/aAt	13/13	0.509366332916471	1	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	0	0.509366332916471	1		474	324	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857374	9857374	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	84	435	0	ENST00000330684.3:c.4027C>T	p.Leu1343Phe	p.L1343F	ENST00000330684	NM_001134407.1	1343	Ctt/Ttt	13/13	0.509366332916471	1	FACETS	0.654	0.581	0.73	0.654	0.581	0.73	SUBCLONAL	1	TRUE	0	0.509366332916471	1		435	376	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031984	10031984	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs185993125	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	137	732	1	ENST00000330684.3:c.839C>T	p.Ser280Phe	p.S280F	ENST00000330684	NM_001134407.1	280	tCc/tTc	3/13	0.509366332916471	1	FACETS	0.943	0.866	1	0.943	0.866	1	CLONAL	1	TRUE	0	0.509366332916471	1		733	425	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827754	72827754	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773228518	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	163	482	4	ENST00000268489.5:c.8827C>T	p.Arg2943Trp	p.R2943W	ENST00000268489	NM_006885.3	2943	Cgg/Tgg	9/10	0.372110685003224	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.509366332916471	1		486	412	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984367	72984367	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	42	345	0	ENST00000268489.5:c.3216+1G>A		p.X1072_splice	ENST00000268489	NM_006885.3	1072			0.372110685003224	1	FACETS	0.372	0.312	0.439	0.372	0.312	0.439	SUBCLONAL	1	TRUE	0	0.509366332916471	1		345	330	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992184	72992184	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	156	572	1	ENST00000268489.5:c.1861C>T	p.Gln621Ter	p.Q621*	ENST00000268489	NM_006885.3	621	Cag/Tag	2/10	0.372110685003224	1	FACETS	0.982	0.907	1	0.982	0.907	1	CLONAL	1	TRUE	0	0.509366332916471	1		573	465	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944304	81944304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	134	622	0	ENST00000359376.3:c.1913C>T	p.Pro638Leu	p.P638L	ENST00000359376	NM_002661.3	638	cCc/cTc	18/33	0.372110685003224	1	FACETS	0.956	0.877	1	0.956	0.877	1	CLONAL	1	TRUE	0	0.509366332916471	1		622	410	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7983579	7983579	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	390	635	0	ENST00000319144.4:c.728T>A	p.Phe243Tyr	p.F243Y	ENST00000319144	NM_001139.2	243	tTc/tAc	6/15	0.305020663823876	4	FACETS	1	0.987	1	0.799	0.766	0.832	INDETERMINATE	3	TRUE	0	0.509366332916471	4		635	723	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39550400	39550400	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	104	335	0	ENST00000262039.4:c.511C>T	p.Gln171Ter	p.Q171*	ENST00000262039	NM_002647.2	171	Cag/Tag	4/25	0.258362672877648	3	FACETS	1	0.98	1	0.685	0.619	0.754	INDETERMINATE	1	TRUE	1	0.509366332916471	3		335	374	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5225764	5225764	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	210	765	0	ENST00000357368.4:c.2468C>T	p.Pro823Leu	p.P823L	ENST00000357368	NM_002850.3	823	cCc/cTc	17/38	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.509366332916471	2		765	660	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231624	5231624	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	32	83	2	ENST00000357368.4:c.1852C>T	p.Pro618Ser	p.P618S	ENST00000357368	NM_002850.3	618	Ccg/Tcg	14/38	1	2	FACETS	0.917	0.757	1	0.917	0.757	1	CLONAL	1	TRUE	1	0.509366332916471	2		85	137	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5265129	5265129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1423947612	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	197	810	0	ENST00000357368.4:c.458C>T	p.Thr153Ile	p.T153I	ENST00000357368	NM_002850.3	153	aCc/aTc	5/38	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.509366332916471	2		810	671	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17950466	17950466	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267605359	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	147	614	2	ENST00000458235.1:c.1261C>T	p.Leu421Phe	p.L421F	ENST00000458235	NM_000215.3	421	Ctt/Ttt	10/24	0.363295309146282	3	FACETS	0.927	0.847	1	0.464	0.423	0.506	CLONAL	1	TRUE	1	0.509366332916471	3		616	781	SUCCESS
CCNE1	898	MSKCC	GRCh37	19	30308081	30308081	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762615251	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	147	623	1	ENST00000262643.3:c.218C>T	p.Ser73Phe	p.S73F	ENST00000262643	NM_001238.2	73	tCc/tTc	5/12	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.509366332916471	2		624	541	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211507	36211507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	176	681	0	ENST00000222270.7:c.1258C>T	p.Pro420Ser	p.P420S	ENST00000222270	NM_014727.1	420	Cct/Tct	3/37	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.509366332916471	2		681	607	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211972	36211972	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1179025944	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	195	1165	1	ENST00000222270.7:c.1723C>T	p.Gln575Ter	p.Q575*	ENST00000222270	NM_014727.1	575	Cag/Tag	3/37	1	2	FACETS	0.959	0.89	1	0.959	0.89	1	CLONAL	1	TRUE	1	0.509366332916471	2		1166	798	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223196	36223196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	241	1106	0	ENST00000222270.7:c.5746C>T	p.Pro1916Ser	p.P1916S	ENST00000222270	NM_014727.1	1916	Ccc/Tcc	28/37	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.509366332916471	2		1106	916	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16085991	16085992	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	104	576	2	ENST00000281043.3:c.1167_1168delinsAA	p.Glu390Lys	p.E390K	ENST00000281043	NM_005378.4	389	ctGGag/ctAAag	3/3	NA	2	FACETS	1	0.953	1			1	INDETERMINATE	1	TRUE	NA	0.509366332916471	2		578	374	SUCCESS
ALK	238	MSKCC	GRCh37	2	29474032	29474032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1252096909	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	178	745	0	ENST00000389048.3:c.2143G>A	p.Gly715Arg	p.G715R	ENST00000389048	NM_004304.4	715	Ggg/Agg	12/29	0.509366332916471	1	FACETS	0.985	0.914	1	0.985	0.914	1	CLONAL	1	TRUE	0	0.509366332916471	1		745	529	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917832	29917832	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	206	899	0	ENST00000389048.3:c.836C>T	p.Pro279Leu	p.P279L	ENST00000389048	NM_004304.4	279	cCa/cTa	3/29	0.509366332916471	1	FACETS	0.982	0.916	1	0.982	0.916	1	CLONAL	1	TRUE	0	0.509366332916471	1		899	614	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99175961	99175961	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	G	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	185	483	0	ENST00000074304.5:c.1870+3A>G		p.X624_splice	ENST00000074304	NM_001134224.1	624			1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.509366332916471	2		483	627	SUCCESS
ACVR1	90	MSKCC	GRCh37	2	158630627	158630627	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	61	367	0	ENST00000263640.3:c.616C>T	p.Arg206Cys	p.R206C	ENST00000263640	NM_001105.4	206	Cgc/Tgc	6/11	NA	2	FACETS	0.663	0.575	0.758			1	INDETERMINATE	1	TRUE	NA	0.509366332916471	2		367	361	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024104	31024104	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753491851	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	162	532	0	ENST00000375687.4:c.3589C>T	p.Pro1197Ser	p.P1197S	ENST00000375687	NM_015338.5	1197	Cct/Tct	13/13	0.363295309146282	3	FACETS	1	0.987	1	0.69	0.637	0.746	CLONAL	1	TRUE	1	0.509366332916471	3		532	578	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739001	40739001	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	156	542	0	ENST00000373198.4:c.3283G>A	p.Glu1095Lys	p.E1095K	ENST00000373198	NM_133170.3	1095	Gaa/Aaa	24/32	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.509366332916471	2		542	469	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755769	39755769	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	64	408	0	ENST00000288319.7:c.996G>A	p.Trp332Ter	p.W332*	ENST00000288319	NM_182918.3	332	tgG/tgA	10/10	0.169384122445364	1	FACETS	0.497	0.432	0.566	0.497	0.432	0.566	INDETERMINATE	1	TRUE	0	0.509366332916471	1		408	377	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41551103	41551103	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1461863256	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	200	591	1	ENST00000263253.7:c.3247C>T	p.Leu1083Phe	p.L1083F	ENST00000263253	NM_001429.3	1083	Ctt/Ttt	17/31	0.407994472820628	4	FACETS	1	0.987	1			1	CLONAL	1	TRUE	NA	0.509366332916471	4		592	916	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49934225	49934225	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868140197	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	224	835	1	ENST00000296474.3:c.2282C>T	p.Ser761Phe	p.S761F	ENST00000296474	NM_002447.2	761	tCc/tTc	8/20	0.235774275273548	5	FACETS	0.948	0.885	1	0.632	0.59	0.676	INDETERMINATE	2	TRUE	2	0.509366332916471	5		836	818	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902538	1902538	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	286	729	0	ENST00000382891.5:c.157C>T	p.Leu53Phe	p.L53F	ENST00000382891	NM_133335.3	53	Ctc/Ttc	2/22	NA	2	FACETS	1	0.992	1			1	INDETERMINATE	1	TRUE	NA	0.509366332916471	2		729	858	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41749455	41749455	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	108	393	1	ENST00000226382.2:c.340G>A	p.Glu114Lys	p.E114K	ENST00000226382	NM_003924.3	114	Gaa/Aaa	2/3	NA	2	FACETS	1	0.978	1			1	INDETERMINATE	1	TRUE	NA	0.509366332916471	2		394	334	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955959	55955960	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	77	490	2	ENST00000263923.4:c.3202_3203delinsTT	p.Pro1068Phe	p.P1068F	ENST00000263923	NM_002253.2	1068	CCt/TTt	24/30	NA	2	FACETS	0.777	0.686	0.874			1	INDETERMINATE	1	TRUE	NA	0.509366332916471	2		492	389	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979561	55979561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	134	642	2	ENST00000263923.4:c.886G>A	p.Gly296Ser	p.G296S	ENST00000263923	NM_002253.2	296	Ggt/Agt	7/30	NA	2	FACETS	1	0.954	1			1	INDETERMINATE	1	TRUE	NA	0.509366332916471	2		644	494	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156222	106156222	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	72	336	0	ENST00000380013.4:c.1123G>A	p.Glu375Lys	p.E375K	ENST00000380013	NM_001127208.2	375	Gaa/Aaa	3/11	1	2	FACETS	0.812	0.715	0.916	0.812	0.715	0.916	CLONAL	1	TRUE	1	0.509366332916471	2		336	348	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149498390	149498390	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	381	720	0	ENST00000261799.4:c.2824G>A	p.Glu942Lys	p.E942K	ENST00000261799	NM_002609.3	942	Gaa/Aaa	21/23	0.496798581231678	2	FACETS	0.953	0.911	0.995	0.953	0.911	0.995	CLONAL	2	TRUE	0	0.509366332916471	2		720	785	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520206	176520207	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	225	853	4	ENST00000292408.4:c.1125_1126delinsAA	p.Gly376Ser	p.G376S	ENST00000292408	NM_213647.1	375	tcGGgc/tcAAgc	9/18	0.496798581231678	2	FACETS	0.863	0.812	0.914	0.863	0.812	0.914	CLONAL	2	TRUE	0	0.509366332916471	2		857	512	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056970	180056970	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	234	842	2	ENST00000261937.6:c.649T>A	p.Ser217Thr	p.S217T	ENST00000261937	NM_182925.4	217	Tcc/Acc	5/30	0.509366332916471	1	FACETS	0.865	0.821	0.907	1	0.995	1	CLONAL	2	TRUE	0	0.509366332916471	1		844	396	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940082	31940082	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	233	716	0	ENST00000375333.2:c.224G>A	p.Gly75Glu	p.G75E	ENST00000375333	NM_032454.1	75	gGg/gAg	2/8	0.509366332916471	4	FACETS	0.824	0.77	0.879	0.824	0.77	0.879	CLONAL	2	TRUE	2	0.509366332916471	4		716	838	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800150	32800150	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	169	373	0	ENST00000374899.4:c.1232C>T	p.Ser411Phe	p.S411F	ENST00000374899	NM_018833.2	411	tCc/tTc	7/12	0.33961730754733	6	FACETS	1	0.926	1			1	CLONAL	2	TRUE	NA	0.509366332916471	6		373	667	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803029	32803035	+	frameshift_variant	Frame_Shift_Del	DEL	CATACAG	CATACAG	-	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	234	653	0	ENST00000374899.4:c.841_847del	p.Leu281AlafsTer22	p.L281Afs*22	ENST00000374899	NM_018833.2	281	CTGTATGgc/gc	5/12	0.33961730754733	6	FACETS	0.897	0.837	0.959			1	CLONAL	2	TRUE	NA	0.509366332916471	6		653	1034	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969189	93969189	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs868510824	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	47	288	0	ENST00000369303.4:c.1807C>T	p.Pro603Ser	p.P603S	ENST00000369303	NM_004440.3	603	Cca/Tca	10/17	NA	2	FACETS	0.648	0.55	0.754			1	INDETERMINATE	1	TRUE	NA	0.509366332916471	2		288	285	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109308830	109308830	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	78	253	0	ENST00000436639.2:c.1573C>T	p.His525Tyr	p.H525Y	ENST00000436639	NM_014454.2	525	Cat/Tat	10/10	0.249908140274734	5	FACETS	0.806	0.714	0.903			1	INDETERMINATE	2	TRUE	NA	0.509366332916471	5		253	335	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206935	162206935	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	84	310	0	ENST00000366898.1:c.740C>T	p.Pro247Leu	p.P247L	ENST00000366898	NM_004562.2	247	cCc/cTc	7/12	NA	2	FACETS	0.959	0.854	1			1	INDETERMINATE	1	TRUE	NA	0.509366332916471	2		310	344	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2968248	2968248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762612040	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	162	846	2	ENST00000396946.4:c.1738G>A	p.Asp580Asn	p.D580N	ENST00000396946	NM_032415.4	580	Gac/Aac	13/25	0.363295309146282	3	FACETS	1	0.975	1	0.574	0.528	0.622	CLONAL	1	TRUE	1	0.509366332916471	3		848	695	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729429	41729429	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	109	509	0	ENST00000242208.4:c.1100C>T	p.Ser367Phe	p.S367F	ENST00000242208	NM_002192.2	367	tCc/tTc	3/3	0.363295309146282	3	FACETS	1	0.962	1	0.565	0.51	0.623	CLONAL	1	TRUE	1	0.509366332916471	3		509	475	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508167	106508167	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	40	185	0	ENST00000359195.3:c.161C>T	p.Pro54Leu	p.P54L	ENST00000359195	NM_002649.2	54	cCc/cTc	2/11	0.24002258557666	4	FACETS	1	0.886	1	0.536	0.45	0.631	INDETERMINATE	1	TRUE	2	0.509366332916471	4		185	221	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508728	106508728	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	79	536	0	ENST00000359195.3:c.722C>T	p.Pro241Leu	p.P241L	ENST00000359195	NM_002649.2	241	cCc/cTc	2/11	0.24002258557666	4	FACETS	0.786	0.692	0.886	0.393	0.346	0.443	INDETERMINATE	1	TRUE	2	0.509366332916471	4		536	596	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372152	55372152	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	79	713	0	ENST00000297316.4:c.842C>T	p.Pro281Leu	p.P281L	ENST00000297316	NM_022454.3	281	cCc/cTc	2/2	1	2	FACETS	0.855	0.757	0.958	0.855	0.757	0.958	CLONAL	1	TRUE	1	0.509366332916471	2		713	363	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058566	69058566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866534903	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	96	819	0	ENST00000288368.4:c.4210C>T	p.His1404Tyr	p.H1404Y	ENST00000288368	NM_024870.2	1404	Cat/Tat	34/40	0.273867007699568	0	FACETS	0.39	0.349	0.434			1	INDETERMINATE	1	TRUE	0	0.509366332916471	0		819	474	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978503	70978503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	73	461	0	ENST00000276594.2:c.1150G>A	p.Glu384Lys	p.E384K	ENST00000276594	NM_024504.3	384	Gag/Aag	5/8	0.273867007699568	0	FACETS	0.411	0.362	0.463			1	INDETERMINATE	1	TRUE	0	0.509366332916471	0		461	342	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117878899	117878899	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	115	426	0	ENST00000297338.2:c.70G>A	p.Asp24Asn	p.D24N	ENST00000297338	NM_006265.2	24	Gat/Aat	2/14	0.258362672877648	3	FACETS	1	0.958	1	0.552	0.5	0.607	INDETERMINATE	1	TRUE	1	0.509366332916471	3		426	513	SUCCESS
CD274	29126	MSKCC	GRCh37	9	5457198	5457198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	167	376	1	ENST00000381577.3:c.172G>A	p.Glu58Lys	p.E58K	ENST00000381577	NM_014143.3	58	Gaa/Aaa	3/7	NA	2	FACETS	0.75	0.697	0.805			1	INDETERMINATE	2	TRUE	NA	0.509366332916471	2		377	437	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197390	27197390	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	217	800	0	ENST00000380036.4:c.1702C>T	p.Pro568Ser	p.P568S	ENST00000380036	NM_000459.3	568	Cca/Tca	12/23	0.509366332916471	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.509366332916471	1		800	464	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37002648	37002648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	97	404	0	ENST00000358127.4:c.601G>A	p.Glu201Lys	p.E201K	ENST00000358127	NM_001280556.1	201	Gaa/Aaa	5/10	0.509366332916471	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.509366332916471	1		404	246	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93626952	93626952	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	67	491	0	ENST00000375746.1:c.796+3G>A		p.X266_splice	ENST00000375746	NM_001174167.1	266			0.509366332916471	1	FACETS	0.484	0.422	0.55	0.484	0.422	0.55	SUBCLONAL	1	TRUE	0	0.509366332916471	1		491	405	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760610	133760610	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	170	978	4	ENST00000318560.5:c.2933C>T	p.Pro978Leu	p.P978L	ENST00000318560	NM_005157.4	978	cCa/cTa	11/11	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.509366332916471	2		982	664	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391808	139391808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770713134	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	100	560	0	ENST00000277541.6:c.6383C>T	p.Pro2128Leu	p.P2128L	ENST00000277541	NM_017617.3	2128	cCg/cTg	34/34	1	2	FACETS	0.89	0.8	0.985	0.89	0.8	0.985	CLONAL	1	TRUE	1	0.509366332916471	2		560	441	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139793257	139793257	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771594805	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	187	766	1	ENST00000247668.2:c.65C>T	p.Thr22Ile	p.T22I	ENST00000247668	NM_021138.3	22	aCc/aTc	2/11	1	2	FACETS	0.983	0.91	1	0.983	0.91	1	CLONAL	1	TRUE	1	0.509366332916471	2		767	747	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53245080	53245080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1428740468	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	336	682	0	ENST00000375401.3:c.860C>T	p.Ser287Leu	p.S287L	ENST00000375401	NM_004187.3	287	tCg/tTg	7/26	0.509366332916471	1	FACETS	0.935	0.898	0.971	1	0.997	1	CLONAL	2	TRUE	0	0.509366332916471	1		682	526	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295230	+	upstream_gene_variant	5'Flank	TNP	GGG	GGG	AGA	novel	NA	P-0015532-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	155	646	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.838	0.778	0.899	1	0.991	1	CLONAL	2	TRUE	1	0.509366332916471	2		646	363	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	137	118	215	0				ENST00000310581	NM_198253.2	-/1132			0.419145856819025	5	FACETS	0.899	0.827	0.971	1	0.979	1	CLONAL	4	TRUE	2	0.419145856819025	5		215	255	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88428957	88428957	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	62	533	0	ENST00000360948.2:c.2143C>T	p.Pro715Ser	p.P715S	ENST00000360948	NM_001012338.2	715	Cca/Tca	17/19	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.419145856819025	2		533	229	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66729163	66729163	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs397516792	NA	P-0015544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	12	835	0	ENST00000307102.5:c.371C>G	p.Pro124Arg	p.P124R	ENST00000307102	NM_002755.3	124	cCg/cGg	3/11	1	2	FACETS	0.128	0.089	0.177	0.128	0.089	0.177	SUBCLONAL	1	TRUE	1	0.419145856819025	2		835	446	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0015544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	176	392	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.419145856819025	2	FACETS	1	0.974	1	1	0.974	1	CLONAL	2	TRUE	0	0.419145856819025	2		392	388	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25378647	25378647	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs770248150	NA	P-0015544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	16	665	0	ENST00000311936.3:c.351A>C	p.Lys117Asn	p.K117N	ENST00000311936	NM_004985.3	117	aaA/aaC	4/5	1	2	FACETS	0.256	0.189	0.337	0.256	0.189	0.337	SUBCLONAL	1	TRUE	1	0.419145856819025	2		665	298	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0015544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	295	156	500	2	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	NA	2	FACETS	0.825	0.763	0.889			1	INDETERMINATE	2	TRUE	NA	0.419145856819025	2		502	451	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46726977	46726977	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	181	690	0	ENST00000371975.4:c.811C>T	p.Leu271Phe	p.L271F	ENST00000371975	NM_003579.3	271	Ctc/Ttc	8/18	0.412768050616286	2	FACETS	0.957	0.893	1	0.957	0.893	1	CLONAL	2	TRUE	0	0.419145856819025	2		690	451	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3781326	3781326	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1445723787	NA	P-0015544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	116	928	0	ENST00000262367.5:c.5039C>T	p.Ser1680Phe	p.S1680F	ENST00000262367	NM_004380.2	1680	tCc/tTc	30/31	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.419145856819025	2		928	433	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892206	9892206	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	50	700	0	ENST00000330684.3:c.2284G>A	p.Gly762Arg	p.G762R	ENST00000330684	NM_001134407.1	762	Gga/Aga	11/13	1	2	FACETS	0.736	0.628	0.854	0.736	0.628	0.854	SUBCLONAL	1	TRUE	1	0.419145856819025	2		700	324	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554006	63554006	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs62640028	NA	P-0015544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	58	613	1	ENST00000307078.5:c.733C>T	p.Pro245Ser	p.P245S	ENST00000307078	NM_004655.3	245	Cca/Tca	2/11	1	2	FACETS	0.824	0.712	0.944	0.824	0.712	0.944	CLONAL	1	TRUE	1	0.419145856819025	2		614	336	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591143	67591151	+	inframe_deletion,splice_region_variant	In_Frame_Del	DEL	AATACTTGA	AATACTTGA	-	novel	NA	P-0015544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	68	534	0	ENST00000274335.5:c.1736_1744del	p.Gln579_Met582delinsLeu	p.Q579_M582delinsL	ENST00000274335		579	cAATACTTGAtg/ctg	12/15	1	2	FACETS	1	0.893	1	1	0.893	1	CLONAL	1	TRUE	1	0.419145856819025	2		534	318	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523709	176523709	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761135791	NA	P-0015544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	75	713	3	ENST00000292408.4:c.2120G>A	p.Arg707Gln	p.R707Q	ENST00000292408	NM_213647.1	707	cGg/cAg	16/18	1	2	FACETS	0.89	0.784	1	0.89	0.784	1	CLONAL	1	TRUE	1	0.419145856819025	2		716	402	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638416	176638416	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758553569	NA	P-0015544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	107	833	1	ENST00000439151.2:c.3016C>T	p.Pro1006Ser	p.P1006S	ENST00000439151	NM_022455.4	1006	Cct/Tct	5/23	1	2	FACETS	0.999	0.9	1	0.999	0.9	1	CLONAL	1	TRUE	1	0.419145856819025	2		834	511	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671967	30671967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	76	908	0	ENST00000376406.3:c.4993C>T	p.Pro1665Ser	p.P1665S	ENST00000376406	NM_014641.2	1665	Ccc/Tcc	10/15	1	2	FACETS	0.739	0.65	0.834	0.739	0.65	0.834	SUBCLONAL	1	TRUE	1	0.419145856819025	2		908	491	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681955	30681955	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	54	287	0	ENST00000376406.3:c.142C>T	p.Pro48Ser	p.P48S	ENST00000376406	NM_014641.2	48	Cca/Tca	3/15	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.419145856819025	2		287	203	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969090	93969090	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1188528023	NA	P-0015544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	55	366	0	ENST00000369303.4:c.1906G>A	p.Glu636Lys	p.E636K	ENST00000369303	NM_004440.3	636	Gag/Aag	10/17	1	2	FACETS	0.937	0.808	1	0.937	0.808	1	CLONAL	1	TRUE	1	0.419145856819025	2		366	280	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971060	21971063	+	frameshift_variant	Frame_Shift_Ins	INS	CCCG	CCCG	TCCCC	novel	NA	P-0015544-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	112	244	0	ENST00000304494.5:c.295_298delinsGGGGA	p.Arg99GlyfsTer21	p.R99Gfs*21	ENST00000304494	NM_000077.4	99	CGGGcc/GGGGAcc	2/3	0.419145856819025	2	FACETS	0.848	0.783	0.913	1	0.983	1	CLONAL	3	TRUE	0	0.419145856819025	2		244	210	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70346188	70346188	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	G	novel	NA	P-0015590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	371	369	0	ENST00000374080.3:c.2542-3C>G		p.X848_splice	ENST00000374080		848			0.373571215403925	4	FACETS	0.961	0.912	1	0.961	0.912	1	CLONAL	2	TRUE	2	0.4933372525601	4		369	1169	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266101	41266101	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121913400	NA	P-0015590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	66	238	0	ENST00000349496.5:c.98C>G	p.Ser33Cys	p.S33C	ENST00000349496	NM_001904.3	33	tCt/tGt	3/15	1	2	FACETS	0.437	0.379	0.5	0.437	0.379	0.5	SUBCLONAL	1	TRUE	1	0.4933372525601	2		238	612	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885731	23885731	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	110	392	0	ENST00000374561.5:c.187C>G	p.Gln63Glu	p.Q63E	ENST00000374561	NM_002167.4	63	Cag/Gag	1/3	0.208577166976172	4	FACETS	0.562	0.503	0.624	0.281	0.251	0.312	INDETERMINATE	1	TRUE	2	0.4933372525601	4		392	1185	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392792	118392792	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	62	358	0	ENST00000534358.1:c.11824G>A	p.Glu3942Lys	p.E3942K	ENST00000534358	NM_005933.3	3942	Gaa/Aaa	36/36	0.144342636432512	5	FACETS	0.424	0.365	0.489			1	INDETERMINATE	1	TRUE	NA	0.4933372525601	5		358	1032	SUCCESS
CBL	867	MSKCC	GRCh37	11	119145657	119145657	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	71	226	0	ENST00000264033.4:c.863C>G	p.Pro288Arg	p.P288R	ENST00000264033	NM_005188.3	288	cCt/cGt	5/16	0.144342636432512	5	FACETS	0.778	0.679	0.885			1	INDETERMINATE	1	TRUE	NA	0.4933372525601	5		226	644	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32968900	32968900	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs397508047	NA	P-0015590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	61	258	3	ENST00000380152.3:c.9331G>T	p.Glu3111Ter	p.E3111*	ENST00000380152		3111	Gag/Tag	25/27	0.456116142798518	2	FACETS	0.488	0.421	0.56	0.244	0.21	0.28	SUBCLONAL	1	TRUE	0	0.4933372525601	2		261	507	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476251	88476251	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	126	406	0	ENST00000360948.2:c.1881G>T	p.Lys627Asn	p.K627N	ENST00000360948	NM_001012338.2	627	aaG/aaT	15/19	NA	2	FACETS	0.463	0.418	0.51			1	INDETERMINATE	1	TRUE	NA	0.4933372525601	2		406	1104	SUCCESS
RAD51C	5889	MSKCC	GRCh37	17	56770022	56770022	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs774685897	NA	P-0015590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	58	294	0	ENST00000337432.4:c.18C>A	p.Phe6Leu	p.F6L	ENST00000337432	NM_058216.2	6	ttC/ttA	1/9	0.288486559309519	5	FACETS	0.417	0.357	0.483	0.139	0.119	0.161	INDETERMINATE	1	TRUE	2	0.4933372525601	5		294	981	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735501	40735501	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	65	418	0	ENST00000373198.4:c.3372G>C	p.Glu1124Asp	p.E1124D	ENST00000373198	NM_133170.3	1124	gaG/gaC	25/32	NA	2	FACETS	0.281	0.243	0.323			1	INDETERMINATE	1	TRUE	NA	0.4933372525601	2		418	937	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151877802	151877802	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	70	164	0	ENST00000262189.6:c.7143G>C	p.Leu2381Phe	p.L2381F	ENST00000262189	NM_170606.2	2381	ttG/ttC	36/59	0.424394596729365	3	FACETS	1	0.941	1	0.373	0.328	0.421	CLONAL	1	TRUE	0	0.4933372525601	3		164	316	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56910902	56910902	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0015590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	813	68	284	0	ENST00000519728.1:c.1051-3C>T		p.X351_splice	ENST00000519728	NM_002350.3	351			0.429583720850193	3	FACETS	0.39	0.338	0.446	0.195	0.169	0.223	SUBCLONAL	1	TRUE	1	0.4933372525601	3		284	881	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412033	116412046	+	splice_donor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TTTTCCAGAAGGTA	TTTTCCAGAAGGTA	G	novel	NA	P-0015590-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	443	480	0	ENST00000397752.3:c.3018_3028+3delinsG		p.X1006_splice	ENST00000397752	NM_000245.2	1006		14/21	0.424394596729365	3	FACETS	1	0.994	1	0.792	0.76	0.825	CLONAL	2	TRUE	0	0.4933372525601	3		480	942	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	130	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.776	0.705	0.851	1	0.986	1	SUBCLONAL	2	TRUE	1	0.226075230487648	2		215	741	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	228	616	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.18546838002374	2	FACETS	0.807	0.75	0.865	0.807	0.75	0.865	CLONAL	2	TRUE	0	0.226075230487648	2		617	1250	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	177	512	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	0.109124865446093	3	FACETS	0.915	0.843	0.99	0.61	0.562	0.66	INDETERMINATE	2	TRUE	0	0.226075230487648	3		512	952	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46246147	46246147	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	94	510	0	ENST00000334344.6:c.4241G>C	p.Arg1414Thr	p.R1414T	ENST00000334344	NM_152641.2	1414	aGa/aCa	15/21	0.182278210248093	3	FACETS	1	0.959	1	0.582	0.517	0.651	CLONAL	1	TRUE	1	0.226075230487648	3		510	795	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806099	1806099	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913485	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	294	738	0	ENST00000260795.2:c.1118A>G	p.Tyr373Cys	p.Y373C	ENST00000260795		373	tAt/tGt	8/17	0.18546838002374	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	2	TRUE	0	0.226075230487648	2		738	1207	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189585728	189585728	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	58	486	0	ENST00000264731.3:c.989G>C	p.Arg330Thr	p.R330T	ENST00000264731	NM_003722.4	330	aGa/aCa	7/14	0.109124865446093	3	FACETS	0.829	0.711	0.958	0.276	0.237	0.32	INDETERMINATE	1	TRUE	0	0.226075230487648	3		486	689	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81334798	81334798	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	190	535	0	ENST00000222390.5:c.1918G>A	p.Glu640Lys	p.E640K	ENST00000222390	NM_000601.4	640	Gag/Aag	17/18	0.109124865446093	3	FACETS	1	0.967	1	0.72	0.666	0.776	INDETERMINATE	2	TRUE	0	0.226075230487648	3		535	866	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074397	8074397	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	153	396	0	ENST00000377482.5:c.262C>G	p.Gln88Glu	p.Q88E	ENST00000377482	NM_018948.3	88	Caa/Gaa	4/4	0.105768257010506	3	FACETS	1	0.969	1			1	INDETERMINATE	2	TRUE	NA	0.226075230487648	3		396	674	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36934817	36934817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	70	667	0	ENST00000361632.4:c.1516C>T	p.Pro506Ser	p.P506S	ENST00000361632		506	Ccc/Tcc	11/16	0.226357894193262	2	FACETS	0.568	0.493	0.649	0.284	0.246	0.325	SUBCLONAL	1	TRUE	0	0.226075230487648	2		667	1091	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59247951	59247951	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1410	121	743	0	ENST00000371222.2:c.792C>G	p.Ile264Met	p.I264M	ENST00000371222	NM_002228.3	264	atC/atG	1/1	0.182278210248093	3	FACETS	0.778	0.7	0.861	0.389	0.35	0.431	SUBCLONAL	1	TRUE	1	0.226075230487648	3		743	1531	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166148	118166148	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	159	445	0	ENST00000369448.3:c.658G>C	p.Glu220Gln	p.E220Q	ENST00000369448	NM_017709.3	220	Gag/Cag	2/2	0.182278210248093	3	FACETS	1	0.966	1	1	0.966	1	CLONAL	2	TRUE	1	0.226075230487648	3		445	715	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156841532	156841532	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs368040165	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1181	120	723	2	ENST00000524377.1:c.835C>T	p.Gln279Ter	p.Q279*	ENST00000524377	NM_002529.3	279	Cag/Tag	7/17	0.198974127102798	2	FACETS	0.816	0.734	0.903	0.408	0.367	0.452	CLONAL	1	TRUE	0	0.226075230487648	2		725	1301	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156845869	156845869	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	G	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	351	908	0	ENST00000524377.1:c.1502-3C>G		p.X501_splice	ENST00000524377	NM_002529.3	501			0.198974127102798	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.226075230487648	2		908	1333	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724598	162724598	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	143	558	0	ENST00000367921.3:c.370C>T	p.Arg124Trp	p.R124W	ENST00000367921	NM_006182.2	124	Cgg/Tgg	5/18	0.198974127102798	2	FACETS	1	0.985	1	0.698	0.636	0.763	CLONAL	1	TRUE	0	0.226075230487648	2		558	906	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64137800	64137800	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1426	150	1172	2	ENST00000334205.4:c.1901C>A	p.Ser634Tyr	p.S634Y	ENST00000334205	NM_003942.2	634	tCc/tAc	15/17	NA	2	FACETS	0.842	0.767	0.922			1	INDETERMINATE	1	TRUE	NA	0.226075230487648	2		1174	1576	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575368	64575368	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	78	626	0	ENST00000312049.6:c.649G>C	p.Glu217Gln	p.E217Q	ENST00000312049	NM_130799.2	217	Gag/Cag	3/10	NA	2	FACETS	0.737	0.646	0.835			1	INDETERMINATE	1	TRUE	NA	0.226075230487648	2		626	936	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589848	69589848	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	19	121	0	ENST00000168712.1:c.5C>T	p.Ser2Leu	p.S2L	ENST00000168712	NM_002007.2	2	tCg/tTg	1/3	0.226357894193262	0	FACETS	0.711	0.542	0.907			1	CLONAL	1	TRUE	0	0.226075230487648	0		121	183	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941013	71941013	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1310	131	963	0	ENST00000298229.2:c.889C>T	p.Pro297Ser	p.P297S	ENST00000298229	NM_001567.3	297	Ccg/Tcg	8/28	1	2	FACETS	0.804	0.727	0.886	0.804	0.727	0.886	CLONAL	1	TRUE	1	0.226075230487648	2		963	1441	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71941916	71941916	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1077	115	917	0	ENST00000298229.2:c.1274C>G	p.Ser425Ter	p.S425*	ENST00000298229	NM_001567.3	425	tCa/tGa	11/28	1	2	FACETS	0.853	0.767	0.946	0.853	0.767	0.946	CLONAL	1	TRUE	1	0.226075230487648	2		917	1192	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416691	416691	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	141	339	0	ENST00000399788.2:c.3859G>A	p.Ala1287Thr	p.A1287T	ENST00000399788	NM_001042603.1	1287	Gcg/Acg	23/28	0.170994890013747	4	FACETS	1	0.969	1	1	0.969	1	CLONAL	2	TRUE	2	0.226075230487648	4		339	674	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115111972	115111972	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	92	724	0	ENST00000257566.3:c.1768C>G	p.Gln590Glu	p.Q590E	ENST00000257566	NM_016569.3	590	Cag/Gag	7/8	1	2	FACETS	0.781	0.692	0.876	0.781	0.692	0.876	SUBCLONAL	1	TRUE	1	0.226075230487648	2		724	1042	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929257	32929257	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1393996926	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	47	652	0	ENST00000380152.3:c.7267G>A	p.Val2423Ile	p.V2423I	ENST00000380152		2423	Gtt/Att	14/27	1	2	FACETS	0.443	0.372	0.522	0.443	0.372	0.522	SUBCLONAL	1	TRUE	1	0.226075230487648	2		652	938	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027219	49027219	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	54	556	0	ENST00000267163.4:c.1786C>T	p.Leu596Phe	p.L596F	ENST00000267163	NM_000321.2	596	Ctc/Ttc	18/27	0.226357894193262	3	FACETS	0.55	0.468	0.641			1	SUBCLONAL	1	TRUE	NA	0.226075230487648	3		556	966	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437166	110437166	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	135	16	60	0	ENST00000375856.3:c.1235G>A	p.Arg412His	p.R412H	ENST00000375856	NM_003749.2	412	cGc/cAc	1/2	1	2	FACETS	0.937	0.697	1	0.937	0.697	1	CLONAL	1	TRUE	1	0.226075230487648	2		60	151	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110438004	110438005	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	90	475	1	ENST00000375856.3:c.396_397delinsAA	p.Glu133Lys	p.E133K	ENST00000375856	NM_003749.2	132	caGGag/caAAag	1/2	1	2	FACETS	0.816	0.722	0.916	0.816	0.722	0.916	CLONAL	1	TRUE	1	0.226075230487648	2		476	976	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41001231	41001231	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	141	526	0	ENST00000267868.3:c.352G>C	p.Glu118Gln	p.E118Q	ENST00000267868	NM_002875.4	118	Gag/Cag	5/10	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.226075230487648	2		526	856	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	338217	338217	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	263	849	0	ENST00000262320.3:c.2494G>C	p.Asp832His	p.D832H	ENST00000262320	NM_003502.3	832	Gac/Cac	11/11	0.18546838002374	2	FACETS	0.929	0.87	0.991	0.929	0.87	0.991	CLONAL	2	TRUE	0	0.226075230487648	2		849	1252	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790461	3790461	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	100	629	0	ENST00000262367.5:c.4072T>A	p.Phe1358Ile	p.F1358I	ENST00000262367	NM_004380.2	1358	Ttt/Att	24/31	1	2	FACETS	0.864	0.77	0.964	0.864	0.77	0.964	CLONAL	1	TRUE	1	0.226075230487648	2		629	1024	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3790476	3790476	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	993	98	656	0	ENST00000262367.5:c.4057G>A	p.Glu1353Lys	p.E1353K	ENST00000262367	NM_004380.2	1353	Gaa/Aaa	24/31	1	2	FACETS	0.795	0.707	0.888	0.795	0.707	0.888	SUBCLONAL	1	TRUE	1	0.226075230487648	2		656	1091	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89874715	89874715	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	124	942	0	ENST00000389301.3:c.583G>C	p.Glu195Gln	p.E195Q	ENST00000389301	NM_000135.2	195	Gag/Cag	6/43	0.170352684443809	0	FACETS	0.7	0.631	0.773			1	SUBCLONAL	1	TRUE	0	0.226075230487648	0		942	1213	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122479	17122479	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1238	93	885	0	ENST00000285071.4:c.916G>C	p.Glu306Gln	p.E306Q	ENST00000285071	NM_144997.5	306	Gag/Cag	9/14	0.18546838002374	2	FACETS	0.618	0.547	0.694	0.309	0.273	0.347	SUBCLONAL	1	TRUE	0	0.226075230487648	2		885	1331	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29684380	29684380	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587781791	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	109	473	0	ENST00000356175.3:c.7900C>G	p.Pro2634Ala	p.P2634A	ENST00000356175	NM_000267.3	2634	Cct/Gct	53/57	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.226075230487648	2		473	745	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11032381	11032381	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	251	826	4	ENST00000327064.4:c.1775C>T	p.Ser592Phe	p.S592F	ENST00000327064	NM_199141.1	592	tCc/tTc	16/16	1	2	FACETS	0.846	0.79	0.904	1	0.994	1	CLONAL	2	TRUE	1	0.226075230487648	2		830	1312	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14629110	14629110	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs768130288	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	177	399	0	ENST00000254322.2:c.52G>T	p.Glu18Ter	p.E18*	ENST00000254322	NM_006145.1	18	Gag/Tag	1/3	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.226075230487648	2		399	1050	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272050	15272050	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	115	790	0	ENST00000263388.2:c.6389C>G	p.Ala2130Gly	p.A2130G	ENST00000263388	NM_000435.2	2130	gCc/gGc	33/33	1	2	FACETS	0.849	0.763	0.941	0.849	0.763	0.941	CLONAL	1	TRUE	1	0.226075230487648	2		790	1198	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50909489	50909489	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1223	260	975	0	ENST00000440232.2:c.1293C>G	p.Ile431Met	p.I431M	ENST00000440232	NM_002691.3	431	atC/atG	11/27	1	2	FACETS	0.775	0.724	0.828	1	0.993	1	SUBCLONAL	2	TRUE	1	0.226075230487648	2		975	1483	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966600	25966600	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	85	563	0	ENST00000435504.4:c.2606C>G	p.Ser869Ter	p.S869*	ENST00000435504		869	tCa/tGa	13/13	0.114325493324064	3	FACETS	0.898	0.792	1			1	INDETERMINATE	1	TRUE	NA	0.226075230487648	3		563	932	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25967348	25967348	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	C	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	62	357	0	ENST00000435504.4:c.1861-3C>G		p.X621_splice	ENST00000435504		621			0.114325493324064	3	FACETS	0.951	0.821	1			1	INDETERMINATE	1	TRUE	NA	0.226075230487648	3		357	642	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976438	25976438	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	130	556	2	ENST00000435504.4:c.1107G>A	p.Trp369Ter	p.W369*	ENST00000435504		369	tgG/tgA	11/13	0.114325493324064	3	FACETS	1	0.985	1			1	INDETERMINATE	1	TRUE	NA	0.226075230487648	3		558	875	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656896	45656896	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1162	123	665	0	ENST00000407780.3:c.260C>T	p.Ser87Leu	p.S87L	ENST00000407780	NM_001283052.1	87	tCa/tTa	3/7	1	2	FACETS	0.847	0.763	0.935	0.847	0.763	0.935	CLONAL	1	TRUE	1	0.226075230487648	2		665	1285	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30067863	30067863	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778412102	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	87	589	0	ENST00000338641.4:c.1048G>A	p.Glu350Lys	p.E350K	ENST00000338641	NM_000268.3	350	Gaa/Aaa	11/16	0.226075230487648	1	FACETS	0.891	0.788	1	0.891	0.788	1	CLONAL	1	TRUE	0	0.226075230487648	1		589	766	SUCCESS
PPP4R2	151987	MSKCC	GRCh37	3	73114682	73114682	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747658097	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	62	637	1	ENST00000356692.5:c.1063G>A	p.Glu355Lys	p.E355K	ENST00000356692		355	Gag/Aag	9/9	1	2	FACETS	0.683	0.589	0.786	0.683	0.589	0.786	SUBCLONAL	1	TRUE	1	0.226075230487648	2		638	803	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259340	89259340	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	174	407	0	ENST00000336596.2:c.484C>G	p.Leu162Val	p.L162V	ENST00000336596	NM_005233.5	162	Ctg/Gtg	3/17	0.109124865446093	3	FACETS	1	0.962	1	0.714	0.658	0.772	INDETERMINATE	2	TRUE	0	0.226075230487648	3		407	800	SUCCESS
ATR	545	MSKCC	GRCh37	3	142188386	142188386	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	113	501	0	ENST00000350721.4:c.6345G>C	p.Met2115Ile	p.M2115I	ENST00000350721	NM_001184.3	2115	atG/atC	38/47	0.109124865446093	3	FACETS	0.811	0.731	0.896	0.541	0.487	0.597	INDETERMINATE	2	TRUE	0	0.226075230487648	3		501	686	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26032284	26032284	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779303049	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	32	236	0	ENST00000244661.2:c.5C>T	p.Ala2Val	p.A2V	ENST00000244661	NM_003537.3	2	gCt/gTt	1/1	0.213622975423834	4	FACETS	0.674	0.546	0.819	0.337	0.273	0.41	SUBCLONAL	1	TRUE	2	0.226075230487648	4		236	515	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32815776	32815776	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1265	127	761	0	ENST00000354258.4:c.1840C>G	p.Leu614Val	p.L614V	ENST00000354258	NM_000593.5	614	Ctg/Gtg	8/11	1	2	FACETS	0.807	0.729	0.89	0.807	0.729	0.89	CLONAL	1	TRUE	1	0.226075230487648	2		761	1392	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020865	112020865	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	66	420	0	ENST00000368678.4:c.706G>A	p.Asp236Asn	p.D236N	ENST00000368678		236	Gat/Aat	8/13	1	2	FACETS	0.836	0.725	0.957	0.836	0.725	0.957	CLONAL	1	TRUE	1	0.226075230487648	2		420	698	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90970981	90970981	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1554560367	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	57	348	1	ENST00000265433.3:c.1096G>A	p.Asp366Asn	p.D366N	ENST00000265433	NM_002485.4	366	Gac/Aac	9/16	0.182278210248093	3	FACETS	0.783	0.67	0.906	0.391	0.335	0.453	CLONAL	1	TRUE	1	0.226075230487648	3		349	717	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80409473	80409473	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	58	528	0	ENST00000286548.4:c.641G>C	p.Arg214Thr	p.R214T	ENST00000286548	NM_002072.3	214	aGa/aCa	5/7	1	2	FACETS	0.66	0.566	0.764	0.66	0.566	0.764	SUBCLONAL	1	TRUE	1	0.226075230487648	2		528	777	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80430545	80430545	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	52	708	0	ENST00000286548.4:c.463G>C	p.Asp155His	p.D155H	ENST00000286548	NM_002072.3	155	Gac/Cac	3/7	1	2	FACETS	0.528	0.448	0.616	0.528	0.448	0.616	SUBCLONAL	1	TRUE	1	0.226075230487648	2		708	871	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156699	20156699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	175	320	1	ENST00000379607.5:c.58G>A	p.Glu20Lys	p.E20K	ENST00000379607	NM_001412.3	20	Gaa/Aaa	2/7	0.114325493324064	2	FACETS	0.857	0.793	0.923			1	INDETERMINATE	3	TRUE	NA	0.226075230487648	2		321	602	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44922731	44922731	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	160	257	0	ENST00000377967.4:c.1592C>G	p.Ser531Ter	p.S531*	ENST00000377967	NM_021140.2	531	tCa/tGa	16/29	0.114325493324064	2	FACETS	0.965	0.892	1			1	INDETERMINATE	3	TRUE	NA	0.226075230487648	2		257	489	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76937950	76937950	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015649-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	124	244	0	ENST00000373344.5:c.2798C>G	p.Ser933Cys	p.S933C	ENST00000373344	NM_000489.3	933	tCt/tGt	9/35	0.114325493324064	2	FACETS	0.862	0.787	0.941			1	INDETERMINATE	3	TRUE	NA	0.226075230487648	2		244	424	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	188	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.334594852982042	2		215	1113	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880257	37880257	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1224	279	592	0	ENST00000269571.5:c.2301C>G	p.Ile767Met	p.I767M	ENST00000269571		767	atC/atG	19/27	0.197148749722609	1	FACETS	0.924	0.866	0.984	0.924	0.866	0.984	INDETERMINATE	1	TRUE	0	0.334594852982042	1		592	1503	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137620	202137620	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0015660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	279	457	0	ENST00000358485.4:c.728-1G>C		p.X243_splice	ENST00000358485	NM_001080125.1	243			0.275169537461395	2	FACETS	1	0.993	1	0.715	0.671	0.76	CLONAL	1	TRUE	0	0.334594852982042	2		457	1166	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81953195	81953195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs187454354	NA	P-0015660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	130	337	0	ENST00000359376.3:c.2161G>A	p.Glu721Lys	p.E721K	ENST00000359376	NM_002661.3	721	Gag/Aag	20/33	1	2	FACETS	0.869	0.788	0.955	0.869	0.788	0.955	CLONAL	1	TRUE	1	0.334594852982042	2		337	894	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809854	36809854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749198474	NA	P-0015660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1274	257	534	0	ENST00000373129.3:c.751C>T	p.Arg251Cys	p.R251C	ENST00000373129	NM_032017.1	251	Cgt/Tgt	9/12	0.162233572723708	2	FACETS	1	0.937	1	0.502	0.468	0.536	INDETERMINATE	1	TRUE	0	0.334594852982042	2		534	1531	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724943	162724943	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	G	novel	NA	P-0015660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	52	271	0	ENST00000367921.3:c.418-3C>G		p.X140_splice	ENST00000367921	NM_006182.2	140			0.162233572723708	2	FACETS	0.428	0.364	0.499	0.214	0.182	0.25	INDETERMINATE	1	TRUE	0	0.334594852982042	2		271	726	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72923773	72923773	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs776321338	NA	P-0015660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1248	210	501	0	ENST00000268489.5:c.3305A>G	p.Asn1102Ser	p.N1102S	ENST00000268489	NM_006885.3	1102	aAc/aGc	4/10	1	2	FACETS	0.861	0.797	0.927	0.861	0.797	0.927	CLONAL	1	TRUE	1	0.334594852982042	2		501	1458	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527726	29528203	+	splice_donor_variant,splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	ATAAGTTCATAGGACTTGCTTTTGTTGTTACTGTGTTCATCAGCCTAAATGGACTGAGAATATGAAGAAAACACCATTTTCTTAAATAAGCATAAATATACAGACTTGGGTTTAAAATAATGTGGCAATTAGGGCCTGAAATGAACCTATATATGGTATAGGAAGAATTGTATCAGACTGATGAACCACAGTATGGGTGCTTTGTGCTTCTTCTGGCAGCTGGATTTTACTGCCATTTGTGTGGGTAATGTGTTGATGTTATTACATGTTAGTAAAGAAATACTGCATGGGTATTTAAAGGCTTTTGTTTTCTGTTGGGGTTTTTATAGAACCTGCTTTTTAATCCAAGTAAGCCATTCTCAAGAGGCAGTCAGCCTGCAGATGTGGATCTAATGATTGACTGCCTTGTTTCTTGCTTTCGTATAAGCCCTCACAACAACCAACACTTTAAGGTGAGAGCATTGGTTTTTATCTAACT	ATAAGTTCATAGGACTTGCTTTTGTTGTTACTGTGTTCATCAGCCTAAATGGACTGAGAATATGAAGAAAACACCATTTTCTTAAATAAGCATAAATATACAGACTTGGGTTTAAAATAATGTGGCAATTAGGGCCTGAAATGAACCTATATATGGTATAGGAAGAATTGTATCAGACTGATGAACCACAGTATGGGTGCTTTGTGCTTCTTCTGGCAGCTGGATTTTACTGCCATTTGTGTGGGTAATGTGTTGATGTTATTACATGTTAGTAAAGAAATACTGCATGGGTATTTAAAGGCTTTTGTTTTCTGTTGGGGTTTTTATAGAACCTGCTTTTTAATCCAAGTAAGCCATTCTCAAGAGGCAGTCAGCCTGCAGATGTGGATCTAATGATTGACTGCCTTGTTTCTTGCTTTCGTATAAGCCCTCACAACAACCAACACTTTAAGGTGAGAGCATTGGTTTTTATCTAACT	-	novel	NA	P-0015660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	13	61	0	ENST00000356175.3:c.1062+116_1185+29del		p.X354_splice	ENST00000356175	NM_000267.3	354		10/57	0.193872763333807	0	FACETS	0.427	0.307	0.571			1	INDETERMINATE	1	TRUE	0	0.334594852982042	0		61	121	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29554305	29554305	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1544	141	744	0	ENST00000356175.3:c.2321C>G	p.Thr774Ser	p.T774S	ENST00000356175	NM_000267.3	774	aCt/aGt	19/57	0.193872763333807	0	FACETS	0.333	0.302	0.366			1	INDETERMINATE	1	TRUE	0	0.334594852982042	0		744	1685	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412958	49412958	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1571	524	695	0	ENST00000418115.1:c.65T>C	p.Leu22Pro	p.L22P	ENST00000418115	NM_001664.2	22	cTc/cCc	2/5	0.172620911453617	3	FACETS	0.873	0.834	0.912	0.873	0.834	0.912	INDETERMINATE	2	TRUE	1	0.334594852982042	3		695	2095	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612198	189612198	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1023563516	NA	P-0015660-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	377	521	0	ENST00000264731.3:c.1950C>G	p.Ile650Met	p.I650M	ENST00000264731	NM_003722.4	650	atC/atG	14/14	0.172620911453617	3	FACETS	0.877	0.831	0.924	0.877	0.831	0.924	INDETERMINATE	2	TRUE	1	0.334594852982042	3		521	1500	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295229	+	upstream_gene_variant	5'Flank	DNP	GG	GG	AA	novel	NA	P-0015694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	189	511	179	0				ENST00000310581	NM_198253.2	-/1132			0.742574788898684	2	FACETS	0.939	0.913	0.965	0.939	0.913	0.965	CLONAL	2	TRUE	0	0.777053953088403	2		179	700	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0015694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	662	586	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.271668597235761	3	FACETS	0.985	0.954	1	0.657	0.636	0.677	INDETERMINATE	2	TRUE	0	0.777053953088403	3		586	1201	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576897	7576897	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs764735889	NA	P-0015694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	441	636	0	ENST00000269305.4:c.949C>T	p.Gln317Ter	p.Q317*	ENST00000269305	NM_001126112.2	317	Cag/Tag	9/11	0.777053953088403	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.777053953088403	1		636	679	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39930238	39930238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs202065982	NA	P-0015694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	221	549	0	ENST00000378444.4:c.3226G>A	p.Glu1076Lys	p.E1076K	ENST00000378444	NM_001123385.1	1076	Gaa/Aaa	6/15	0.541202703494151	1	FACETS	0.449	0.419	0.48	0.449	0.419	0.48	SUBCLONAL	1	TRUE	0	0.777053953088403	1		549	775	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170256	119170256	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374672276	NA	P-0015694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	117	168	269	0	ENST00000264033.4:c.2486G>A	p.Arg829Gln	p.R829Q	ENST00000264033	NM_005188.3	829	cGg/cAg	16/16	0.777053953088403	1	FACETS	0.928	0.873	0.982	0.928	0.873	0.982	CLONAL	1	TRUE	0	0.777053953088403	1		269	285	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288834	11288834	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766640389	NA	P-0015694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	342	486	0	ENST00000361445.4:c.2921C>T	p.Ala974Val	p.A974V	ENST00000361445	NM_004958.3	974	gCc/gTc	19/58	NA	2	FACETS	0.98	0.931	1			1	INDETERMINATE	1	TRUE	NA	0.777053953088403	2		486	898	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305335	39305335	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370745456	NA	P-0015694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	686	730	0	ENST00000373001.3:c.1090C>T	p.His364Tyr	p.H364Y	ENST00000373001	NM_022157.3	364	Cat/Tat	7/7	0.414484555043202	2	FACETS	1	0.997	1	0.716	0.694	0.738	INDETERMINATE	1	TRUE	0	0.777053953088403	2		730	1233	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156838378	156838378	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1075	397	805	0	ENST00000524377.1:c.656G>A	p.Gly219Glu	p.G219E	ENST00000524377	NM_002529.3	219	gGg/gAg	6/17	0.777053953088403	2	FACETS	0.694	0.659	0.73	0.347	0.329	0.365	SUBCLONAL	1	TRUE	0	0.777053953088403	2		805	1472	SUCCESS
H3-4	8290	MSKCC	GRCh37	1	228612627	228612627	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	210	722	493	0	ENST00000366696.1:c.400G>T	p.Glu134Ter	p.E134*	ENST00000366696	NM_003493.2	134	Gag/Tag	1/1	0.777053953088403	2	FACETS	0.997	0.975	1	0.997	0.975	1	CLONAL	2	TRUE	0	0.777053953088403	2		493	932	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89871799	89871799	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1217239476	NA	P-0015694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	378	597	0	ENST00000389301.3:c.598C>T	p.His200Tyr	p.H200Y	ENST00000389301	NM_000135.2	200	Cat/Tat	7/43	1	2	FACETS	0.959	0.912	1	0.959	0.912	1	CLONAL	1	TRUE	1	0.777053953088403	2		597	1015	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533660	63533661	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	381	574	1	ENST00000307078.5:c.1493_1494delinsTT	p.Pro498Leu	p.P498L	ENST00000307078	NM_004655.3	498	cCC/cTT	6/11	0.384954354404134	1	FACETS	0.707	0.675	0.739	0.707	0.675	0.739	INDETERMINATE	1	TRUE	0	0.777053953088403	1		575	848	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219891	36219891	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	331	615	1	ENST00000222270.7:c.4693C>T	p.Gln1565Ter	p.Q1565*	ENST00000222270	NM_014727.1	1565	Cag/Tag	21/37	0.262699270940706	1	FACETS	0.506	0.479	0.534	0.506	0.479	0.534	INDETERMINATE	1	TRUE	0	0.777053953088403	1		616	1029	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528649	157528649	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	444	721	0	ENST00000346085.5:c.6374C>T	p.Pro2125Leu	p.P2125L	ENST00000346085	NM_020732.3	2125	cCa/cTa	20/20	0.384954354404134	1	FACETS	0.7	0.671	0.73	0.7	0.671	0.73	INDETERMINATE	1	TRUE	0	0.777053953088403	1		721	998	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992737	68992737	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200411060	NA	P-0015694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	493	678	0	ENST00000288368.4:c.1702G>A	p.Glu568Lys	p.E568K	ENST00000288368	NM_024870.2	568	Gaa/Aaa	16/40	0.384954354404134	1	FACETS	0.763	0.733	0.792	0.763	0.733	0.792	INDETERMINATE	1	TRUE	0	0.777053953088403	1		678	1017	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971099	21971099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749714198	NA	P-0015694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	402	606	0	ENST00000304494.5:c.259C>T	p.Arg87Trp	p.R87W	ENST00000304494	NM_000077.4	87	Cgg/Tgg	2/3	0.777053953088403	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.777053953088403	1		606	558	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76764050	76764050	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	319	655	0	ENST00000373344.5:c.7258C>T	p.Gln2420Ter	p.Q2420*	ENST00000373344	NM_000489.3	2420	Cag/Tag	35/35	0.541202703494151	1	FACETS	0.639	0.606	0.672	0.639	0.606	0.672	SUBCLONAL	1	TRUE	0	0.777053953088403	1		655	786	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217276	123217276	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015694-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	151	458	0	ENST00000218089.9:c.2930G>A	p.Gly977Asp	p.G977D	ENST00000218089	NM_001042749.1	977	gGc/gAc	29/35	0.541202703494151	1	FACETS	0.399	0.366	0.434	0.399	0.366	0.434	SUBCLONAL	1	TRUE	0	0.777053953088403	1		458	595	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	241	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.643093369626759	2		215	727	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0015696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	597	586	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	0.32244425817441	5	FACETS	1	0.995	1	0.797	0.767	0.828	INDETERMINATE	2	TRUE	2	0.643093369626759	5		586	1525	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255703	16255703	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	379	474	0	ENST00000375759.3:c.2968G>C	p.Asp990His	p.D990H	ENST00000375759	NM_015001.2	990	Gat/Cat	11/15	0.32244425817441	5	FACETS	1	0.991	1	0.784	0.746	0.822	INDETERMINATE	2	TRUE	2	0.643093369626759	5		474	985	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087379	27087379	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	461	576	0	ENST00000324856.7:c.1953G>A	p.Met651Ile	p.M651I	ENST00000324856	NM_006015.4	651	atG/atA	5/20	0.32244425817441	5	FACETS	0.857	0.821	0.894	0.857	0.821	0.894	INDETERMINATE	3	TRUE	2	0.643093369626759	5		576	1095	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193219803	193219803	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0015696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	159	273	1	ENST00000367435.3:c.1560-3C>T		p.X520_splice	ENST00000367435	NM_024529.4	520			0.32244425817441	5	FACETS	1	0.983	1	0.802	0.743	0.861	INDETERMINATE	2	TRUE	2	0.643093369626759	5		274	404	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149501461	149501461	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751904503	NA	P-0015696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	325	813	1	ENST00000261799.4:c.2326G>A	p.Asp776Asn	p.D776N	ENST00000261799	NM_002609.3	776	Gat/Aat	16/23	1	2	FACETS	0.968	0.916	1	0.968	0.916	1	CLONAL	1	TRUE	1	0.643093369626759	2		814	1044	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971204	13971204	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	421	476	0	ENST00000405192.2:c.725T>C	p.Val242Ala	p.V242A	ENST00000405192	NM_001163147.1	242	gTt/gCt	8/12	0.614902514514199	5	FACETS	0.853	0.816	0.891	0.853	0.816	0.891	CLONAL	3	TRUE	2	0.643093369626759	5		476	1005	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127915849	127915849	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015696-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	614	539	0	ENST00000373547.4:c.632G>A	p.Gly211Glu	p.G211E	ENST00000373547	NM_002721.4	211	gGa/gAa	6/7	0.643093369626759	3	FACETS	0.944	0.918	0.969	0.944	0.918	0.969	CLONAL	3	TRUE	0	0.643093369626759	3		539	891	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971111	21971111	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913385	NA	P-0015724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	176	429	0	ENST00000304494.5:c.247C>T	p.His83Tyr	p.H83Y	ENST00000304494	NM_000077.4	83	Cac/Tac	2/3	0.311000140442087	4	FACETS	1	0.969	1	0.798	0.745	0.852	CLONAL	3	TRUE	0	0.387106741044507	4		429	395	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577570	7577570	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782664	NA	P-0015724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	134	670	0	ENST00000269305.4:c.711G>A	p.Met237Ile	p.M237I	ENST00000269305	NM_001126112.2	237	atG/atA	7/11	0.234412613044422	3	FACETS	1	0.959	1	0.714	0.655	0.773	CLONAL	2	TRUE	0	0.387106741044507	3		670	386	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656969	47656969	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779075	NA	P-0015724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	39	443	0	ENST00000233146.2:c.1165C>T	p.Arg389Ter	p.R389*	ENST00000233146	NM_000251.2	389	Cga/Tga	7/16	0.30508377638387	4	FACETS	0.739	0.614	0.879	0.246	0.204	0.293	SUBCLONAL	1	TRUE	1	0.387106741044507	4		443	378	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88649939	88649939	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	32	806	1	ENST00000372037.3:c.188G>T	p.Cys63Phe	p.C63F	ENST00000372037	NM_004329.2	63	tGc/tTc	4/13	0.374609024935054	1	FACETS	0.332	0.269	0.402	0.332	0.269	0.402	SUBCLONAL	1	TRUE	0	0.387106741044507	1		807	402	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120806883	120806883	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	11	114	0	ENST00000257552.2:c.12C>A	p.Asp4Glu	p.D4E	ENST00000257552	NM_002442.3	4	gaC/gaA	1/15	0.390158633712954	2	FACETS	0.874	0.616	1	0.437	0.308	0.591	CLONAL	1	TRUE	0	0.387106741044507	2		114	65	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467430	25467430	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	46	582	0	ENST00000264709.3:c.1646G>T	p.Cys549Phe	p.C549F	ENST00000264709	NM_175629.2	549	tGc/tTc	14/23	0.30508377638387	4	FACETS	0.911	0.769	1	0.304	0.256	0.356	CLONAL	1	TRUE	1	0.387106741044507	4		582	362	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5054887	5054887	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	C	novel	NA	P-0015724-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	56	473	0	ENST00000381652.3:c.936+3A>C		p.X312_splice	ENST00000381652	NM_004972.3	312			0.311000140442087	4	FACETS	0.776	0.665	0.897	0.194	0.166	0.225	SUBCLONAL	1	TRUE	0	0.387106741044507	4		473	517	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	30	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.541	0.437	0.659	0.541	0.437	0.659	SUBCLONAL	1	TRUE	1	0.349617253687525	2		215	317	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0015773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	243	685	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.27483768006557	4	FACETS	0.994	0.935	1	0.994	0.935	1	CLONAL	3	TRUE	1	0.349617253687525	4		685	629	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044357	128044357	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	67	567	0	ENST00000285398.2:c.1264G>A	p.Glu422Lys	p.E422K	ENST00000285398	NM_000122.1	422	Gag/Aag	8/15	0.349617253687525	1	FACETS	0.995	0.871	1	0.995	0.871	1	CLONAL	1	TRUE	0	0.349617253687525	1		567	318	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039365	49039365	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	40	813	0	ENST00000267163.4:c.2350C>T	p.His784Tyr	p.H784Y	ENST00000267163	NM_000321.2	784	Cac/Tac	23/27	0.263309152265642	2	FACETS	0.8	0.677	0.931	0.8	0.677	0.931	CLONAL	2	TRUE	0	0.349617253687525	2		813	143	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs121912660	NA	P-0015773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	43	691	2	ENST00000269305.4:c.839G>C	p.Arg280Thr	p.R280T	ENST00000269305	NM_001126112.2	280	aGa/aCa	8/11	0.313394691160897	1	FACETS	0.569	0.477	0.669	0.569	0.477	0.669	SUBCLONAL	1	TRUE	0	0.349617253687525	1		693	357	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039501	49039501	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0015773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	34	558	0	ENST00000267163.4:c.2486C>G	p.Ser829Ter	p.S829*	ENST00000267163	NM_000321.2	829	tCa/tGa	23/27	0.263309152265642	2	FACETS	1	0.923	1	0.612	0.507	0.726	CLONAL	1	TRUE	0	0.349617253687525	2		558	159	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106159	27106159	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0015773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	38	568	2	ENST00000324856.7:c.5770G>T	p.Glu1924Ter	p.E1924*	ENST00000324856	NM_006015.4	1924	Gag/Tag	20/20	1	2	FACETS	0.706	0.586	0.839	0.706	0.586	0.839	SUBCLONAL	1	TRUE	1	0.349617253687525	2		570	308	SUCCESS
SUFU	51684	MSKCC	GRCh37	10	104375101	104375101	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	37	656	0	ENST00000369902.3:c.1099G>C	p.Glu367Gln	p.E367Q	ENST00000369902	NM_016169.3	367	Gag/Cag	9/12	1	2	FACETS	0.459	0.378	0.55	0.459	0.378	0.55	SUBCLONAL	1	TRUE	1	0.349617253687525	2		656	461	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911652	32911652	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555283071	NA	P-0015773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	22	478	0	ENST00000380152.3:c.3160G>C	p.Asp1054His	p.D1054H	ENST00000380152		1054	Gat/Cat	11/27	0.313394691160897	1	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	0	0.349617253687525	1		478	90	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49039131	49039131	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	G	novel	NA	P-0015773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	26	21	234	0	ENST00000267163.4:c.2212-3C>G		p.X738_splice	ENST00000267163	NM_000321.2	738			0.263309152265642	2	FACETS	0.852	0.692	1	1	0.916	1	CLONAL	3	TRUE	0	0.349617253687525	2		234	47	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670427	88670427	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	28	468	2	ENST00000360948.2:c.1259C>T	p.Thr420Ile	p.T420I	ENST00000360948	NM_001012338.2	420	aCt/aTt	11/19	1	2	FACETS	0.774	0.623	0.944	0.774	0.623	0.944	CLONAL	1	TRUE	1	0.349617253687525	2		470	207	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45858001	45858001	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	89	675	0	ENST00000391945.4:c.1652C>T	p.Ser551Phe	p.S551F	ENST00000391945	NM_000400.3	551	tCc/tTc	17/23	0.204979225811774	3	FACETS	1	0.972	1			1	INDETERMINATE	1	TRUE	NA	0.349617253687525	3		675	462	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739099	145739099	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	C	novel	NA	P-0015773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	16	452	0	ENST00000428558.2:c.2059-3C>G		p.X687_splice	ENST00000428558	NM_004260.3	687			0.313394691160897	1	FACETS	0.27	0.199	0.354	0.27	0.199	0.354	SUBCLONAL	1	TRUE	0	0.349617253687525	1		452	280	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98218654	98218654	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	31	483	0	ENST00000331920.6:c.3210G>A	p.Met1070Ile	p.M1070I	ENST00000331920	NM_000264.3	1070	atG/atA	19/24	1	2	FACETS	0.5	0.404	0.607	0.5	0.404	0.607	SUBCLONAL	1	TRUE	1	0.349617253687525	2		483	355	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928935	44928935	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	104	38	275	1	ENST00000377967.4:c.2035C>T	p.Gln679Ter	p.Q679*	ENST00000377967	NM_021140.2	679	Cag/Tag	17/29	0.204979225811774	2	FACETS	0.765	0.644	0.895			1	INDETERMINATE	2	TRUE	NA	0.349617253687525	2		276	142	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36651923	36651928	+	frameshift_variant	Frame_Shift_Del	DEL	CAAGGC	CAAGGC	TG	novel	NA	P-0015773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	42	553	0	ENST00000244741.5:c.45_50delinsTG	p.Lys16AlafsTer14	p.K16Afs*14	ENST00000244741	NM_000389.4	15	agCAAGGCc/agTGc	2/3	0.132560564393843	3	FACETS	0.753	0.63	0.888	0.376	0.315	0.444	INDETERMINATE	1	TRUE	1	0.349617253687525	3		553	375	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	202	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.585110642139241	2		215	608	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211154	36211154	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1375	498	1202	4	ENST00000222270.7:c.905C>T	p.Pro302Leu	p.P302L	ENST00000222270	NM_014727.1	302	cCc/cTc	3/37	1	2	FACETS	0.909	0.868	0.951	0.909	0.868	0.951	CLONAL	1	TRUE	1	0.585110642139241	2		1206	1873	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16245968	16245968	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	222	513	0	ENST00000375759.3:c.1591C>T	p.Gln531Ter	p.Q531*	ENST00000375759	NM_015001.2	531	Cag/Tag	8/15	1	2	FACETS	0.988	0.923	1	0.988	0.923	1	CLONAL	1	TRUE	1	0.585110642139241	2		513	768	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163724	72163724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	209	789	0	ENST00000357731.5:c.634C>T	p.Pro212Ser	p.P212S	ENST00000357731	NM_173808.2	212	Cca/Tca	4/7	1	2	FACETS	0.935	0.871	1	0.935	0.871	1	CLONAL	1	TRUE	1	0.585110642139241	2		789	764	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205125	61205125	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	312	739	0	ENST00000301761.2:c.65T>C	p.Leu22Ser	p.L22S	ENST00000301761	NM_017841.2	22	tTg/tCg	2/4	0.585110642139241	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.585110642139241	1		739	754	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64577204	64577204	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1555166365	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	355	869	0	ENST00000312049.6:c.378G>A	p.Trp126Ter	p.W126*	ENST00000312049	NM_130799.2	126	tgG/tgA	2/10	0.585110642139241	1	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	0	0.585110642139241	1		869	835	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588235	69588235	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2062	208	457	0	ENST00000168712.1:c.463T>C	p.Cys155Arg	p.C155R	ENST00000168712	NM_002007.2	155	Tgc/Cgc	3/3	0.585110642139241	8	FACETS	0.863	0.797	0.932			1	CLONAL	1	TRUE	NA	0.585110642139241	8		457	2270	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589776	69589776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747109892	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	48	61	0	ENST00000168712.1:c.77G>A	p.Arg26Gln	p.R26Q	ENST00000168712	NM_002007.2	26	cGa/cAa	1/3	0.585110642139241	8	FACETS	0.948	0.802	1			1	CLONAL	1	TRUE	NA	0.585110642139241	8		61	477	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66735666	66735666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	180	606	0	ENST00000307102.5:c.487G>A	p.Glu163Lys	p.E163K	ENST00000307102	NM_002755.3	163	Gaa/Aaa	4/11	1	2	FACETS	0.768	0.709	0.829	0.768	0.709	0.829	SUBCLONAL	1	TRUE	1	0.585110642139241	2		606	801	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857296	9857296	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1567275428	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	268	559	0	ENST00000330684.3:c.4105C>T	p.His1369Tyr	p.H1369Y	ENST00000330684	NM_001134407.1	1369	Cac/Tac	13/13	1	2	FACETS	0.912	0.856	0.969	0.912	0.856	0.969	CLONAL	1	TRUE	1	0.585110642139241	2		559	1005	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858456	9858456	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768295624	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	211	575	0	ENST00000330684.3:c.2945G>A	p.Gly982Glu	p.G982E	ENST00000330684	NM_001134407.1	982	gGa/gAa	13/13	1	2	FACETS	0.945	0.881	1	0.945	0.881	1	CLONAL	1	TRUE	1	0.585110642139241	2		575	763	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923375	9923375	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	277	647	0	ENST00000330684.3:c.1912G>A	p.Ala638Thr	p.A638T	ENST00000330684	NM_001134407.1	638	Gct/Act	9/13	1	2	FACETS	0.927	0.872	0.985	0.927	0.872	0.985	CLONAL	1	TRUE	1	0.585110642139241	2		647	1021	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9934887	9934887	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	243	707	1	ENST00000330684.3:c.1403C>T	p.Ser468Phe	p.S468F	ENST00000330684	NM_001134407.1	468	tCc/tTc	6/13	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.585110642139241	2		708	828	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12032534	12032534	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	171	498	0	ENST00000353533.5:c.970G>A	p.Asp324Asn	p.D324N	ENST00000353533	NM_003010.3	324	Gat/Aat	9/11	1	2	FACETS	0.982	0.908	1	0.982	0.908	1	CLONAL	1	TRUE	1	0.585110642139241	2		498	595	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66511589	66511589	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	246	505	0	ENST00000358598.2:c.49G>A	p.Glu17Lys	p.E17K	ENST00000358598	NM_212471.2	17	Gaa/Aaa	2/11	0.217651228421256	3	FACETS	1	0.983	1	0.569	0.532	0.607	INDETERMINATE	1	TRUE	1	0.585110642139241	3		505	955	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39584480	39584480	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	271	396	0	ENST00000262039.4:c.1147del	p.Arg383GlyfsTer11	p.R383Gfs*11	ENST00000262039	NM_002647.2	382	gCc/gc	10/25	0.217651228421256	3	FACETS	0.797	0.751	0.844	0.797	0.751	0.844	INDETERMINATE	2	TRUE	1	0.585110642139241	3		396	751	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2199896	2199896	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	874	350	864	0	ENST00000398665.3:c.665A>G	p.Asp222Gly	p.D222G	ENST00000398665	NM_032482.2	222	gAt/gGt	8/28	1	2	FACETS	0.977	0.925	1	0.977	0.925	1	CLONAL	1	TRUE	1	0.585110642139241	2		864	1224	SUCCESS
ALK	238	MSKCC	GRCh37	2	29432704	29432704	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774360880	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	286	653	0	ENST00000389048.3:c.3784C>T	p.Pro1262Ser	p.P1262S	ENST00000389048	NM_004304.4	1262	Cct/Tct	25/29	1	2	FACETS	0.957	0.9	1	0.957	0.9	1	CLONAL	1	TRUE	1	0.585110642139241	2		653	1022	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40714462	40714462	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1167887381	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	287	631	1	ENST00000373198.4:c.3935C>T	p.Ser1312Phe	p.S1312F	ENST00000373198	NM_133170.3	1312	tCc/tTc	29/32	1	2	FACETS	0.971	0.914	1	0.971	0.914	1	CLONAL	1	TRUE	1	0.585110642139241	2		632	1010	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41076940	41076940	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	210	658	1	ENST00000373198.4:c.1480C>T	p.Gln494Ter	p.Q494*	ENST00000373198	NM_133170.3	494	Caa/Taa	9/32	1	2	FACETS	0.815	0.757	0.874	0.815	0.757	0.874	CLONAL	1	TRUE	1	0.585110642139241	2		659	881	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12645693	12645693	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397516827	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	154	318	0	ENST00000251849.4:c.776C>T	p.Ser259Phe	p.S259F	ENST00000251849	NM_002880.3	259	tCc/tTc	7/17	1	2	FACETS	0.848	0.779	0.919	0.848	0.779	0.919	CLONAL	1	TRUE	1	0.585110642139241	2		318	621	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52613071	52613071	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	218	467	0	ENST00000394830.3:c.3457A>G	p.Arg1153Gly	p.R1153G	ENST00000394830	NM_018313.4	1153	Aga/Gga	22/30	1	2	FACETS	0.9	0.839	0.963	0.9	0.839	0.963	CLONAL	1	TRUE	1	0.585110642139241	2		467	828	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69998265	69998265	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	380	769	0	ENST00000394351.3:c.505A>G	p.Thr169Ala	p.T169A	ENST00000394351	NM_000248.3	169	Acc/Gcc	5/9	1	2	FACETS	0.969	0.919	1	0.969	0.919	1	CLONAL	1	TRUE	1	0.585110642139241	2		769	1341	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593661	55593661	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913513	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	209	435	0	ENST00000288135.5:c.1727T>C	p.Leu576Pro	p.L576P	ENST00000288135	NM_000222.2	576	cTt/cCt	11/21	1	2	FACETS	0.954	0.888	1	0.954	0.888	1	CLONAL	1	TRUE	1	0.585110642139241	2		435	749	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964973	55964973	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	novel	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	118	328	0	ENST00000263923.4:c.2267-3C>T		p.X756_splice	ENST00000263923	NM_002253.2	756			1	2	FACETS	0.945	0.859	1	0.945	0.859	1	CLONAL	1	TRUE	1	0.585110642139241	2		328	427	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35875648	35875648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	207	266	0	ENST00000303115.3:c.835C>T	p.His279Tyr	p.H279Y	ENST00000303115	NM_002185.3	279	Cat/Tat	7/8	1	2	FACETS	0.929	0.864	0.995	0.929	0.864	0.995	CLONAL	1	TRUE	1	0.585110642139241	2		266	762	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67522522	67522522	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs999932649	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	93	254	0	ENST00000274335.5:c.19C>T	p.Gln7Ter	p.Q7*	ENST00000274335		7	Cag/Tag	1/15	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.585110642139241	2		254	312	SUCCESS
APC	324	MSKCC	GRCh37	5	112173580	112173581	+	frameshift_variant	Frame_Shift_Del	DEL	AT	AT	C	novel	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	120	469	0	ENST00000257430.4:c.2289_2290delinsC	p.Glu763AspfsTer2	p.E763Dfs*2	ENST00000257430	NM_000038.5	763	gaATta/gaCta	16/16	1	2	FACETS	0.875	0.795	0.958	0.875	0.795	0.958	CLONAL	1	TRUE	1	0.585110642139241	2		469	469	SUCCESS
APC	324	MSKCC	GRCh37	5	112174437	112174439	+	stop_gained	Nonsense_Mutation	TNP	GGG	GGG	AGA	novel	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	104	368	0	ENST00000257430.4:c.3146_3148delinsAGA	p.Trp1049_Ala1050delinsTer	p.W1049_A1050delins*	ENST00000257430	NM_000038.5	1049	tGGGca/tAGAca	16/16	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.585110642139241	2		368	326	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805518	32805518	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1117	404	1085	0	ENST00000374899.4:c.493G>A	p.Gly165Ser	p.G165S	ENST00000374899	NM_018833.2	165	Ggt/Agt	2/12	1	2	FACETS	0.908	0.862	0.954	0.908	0.862	0.954	CLONAL	1	TRUE	1	0.585110642139241	2		1085	1521	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287962	33287962	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	210	481	0	ENST00000374542.5:c.1291T>G	p.Ser431Ala	p.S431A	ENST00000374542	NM_001141970.1	431	Tcc/Gcc	5/8	1	2	FACETS	0.935	0.87	1	0.935	0.87	1	CLONAL	1	TRUE	1	0.585110642139241	2		481	768	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117663590	117663590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	162	804	0	ENST00000368508.3:c.4642G>A	p.Glu1548Lys	p.E1548K	ENST00000368508	NM_002944.2	1548	Gag/Aag	28/43	1	2	FACETS	0.702	0.645	0.761	0.702	0.645	0.761	SUBCLONAL	1	TRUE	1	0.585110642139241	2		804	789	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963922	2963922	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	358	856	1	ENST00000396946.4:c.1885G>A	p.Asp629Asn	p.D629N	ENST00000396946	NM_032415.4	629	Gat/Aat	15/25	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.585110642139241	2		857	1197	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509648	106509648	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	351	672	2	ENST00000359195.3:c.1642C>T	p.Pro548Ser	p.P548S	ENST00000359195	NM_002649.2	548	Ccc/Tcc	2/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.585110642139241	2		674	1062	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412739	116412739	+	intron_variant	Intron	SNP	C	C	T	novel	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	276	1145	0	ENST00000397752.3:c.3028+696C>T		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.929	0.873	0.987	0.929	0.873	0.987	CLONAL	1	TRUE	1	0.585110642139241	2		1145	1015	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879365	151879366	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	239	546	2	ENST00000262189.6:c.5579_5580delinsTT	p.Ser1860Phe	p.S1860F	ENST00000262189	NM_170606.2	1860	tCC/tTT	36/59	1	2	FACETS	0.965	0.903	1	0.965	0.903	1	CLONAL	1	TRUE	1	0.585110642139241	2		548	847	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484306	8484306	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	249	718	0	ENST00000356435.5:c.3226A>G	p.Lys1076Glu	p.K1076E	ENST00000356435		1076	Aag/Gag	19/35	1	2	FACETS	0.866	0.81	0.923	0.866	0.81	0.923	CLONAL	1	TRUE	1	0.585110642139241	2		718	983	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517893	8517893	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200333683	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	121	434	0	ENST00000356435.5:c.1498G>A	p.Asp500Asn	p.D500N	ENST00000356435		500	Gat/Aat	10/35	1	2	FACETS	0.782	0.71	0.857	0.782	0.71	0.857	SUBCLONAL	1	TRUE	1	0.585110642139241	2		434	529	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21970896	21970896	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	rs866937105	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	452	931	0	ENST00000304494.5:c.457+5G>A		p.X153_splice	ENST00000304494	NM_000077.4	153			1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.585110642139241	2		931	1399	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27172691	27172692	+	missense_variant	Missense_Mutation	DNP	GA	GA	AT	novel	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	293	785	3	ENST00000380036.4:c.706_707delinsAT	p.Asp236Ile	p.D236I	ENST00000380036	NM_000459.3	236	GAt/ATt	5/23	1	2	FACETS	0.938	0.883	0.994	0.938	0.883	0.994	CLONAL	1	TRUE	1	0.585110642139241	2		788	1068	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135776157	135776157	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	861	352	701	0	ENST00000298552.3:c.2570A>T	p.Glu857Val	p.E857V	ENST00000298552	NM_001162426.1	857	gAg/gTg	20/23	1	2	FACETS	0.992	0.94	1	0.992	0.94	1	CLONAL	1	TRUE	1	0.585110642139241	2		701	1213	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47006782	47006782	+	5_prime_UTR_variant	5'UTR	SNP	C	C	A	novel	NA	P-0015827-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	307	701	0	ENST00000377604.3:c.-99C>A		p.*33*	ENST00000377604	NM_001204468.1	-/852		2/24	1	2	FACETS	0.936	0.883	0.991	0.936	0.883	0.991	CLONAL	1	TRUE	1	0.585110642139241	2		701	1121	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	48	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.76	0.642	0.89	0.76	0.642	0.89	SUBCLONAL	1	TRUE	1	0.231859185726081	2		215	545	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001438	29001438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1473309404	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	54	256	0	ENST00000282397.4:c.1294G>A	p.Glu432Lys	p.E432K	ENST00000282397	NM_002019.4	432	Gaa/Aaa	10/30	1	2	FACETS	0.897	0.767	1	0.897	0.767	1	CLONAL	1	TRUE	1	0.231859185726081	2		256	519	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561418	9561418	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	86	456	0	ENST00000353224.5:c.364G>A	p.Glu122Lys	p.E122K	ENST00000353224	NM_177990.2	122	Gaa/Aaa	4/10	1	2	FACETS	0.923	0.815	1	0.923	0.815	1	CLONAL	1	TRUE	1	0.231859185726081	2		456	804	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980844	40980844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	113	548	0	ENST00000373198.4:c.1642G>A	p.Glu548Lys	p.E548K	ENST00000373198	NM_133170.3	548	Gaa/Aaa	10/32	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.231859185726081	2		548	944	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	149983275	149983275	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	88	434	0	ENST00000253339.5:c.2983C>T	p.Arg995Cys	p.R995C	ENST00000253339		995	Cgc/Tgc	7/7	1	2	FACETS	0.919	0.813	1	0.919	0.813	1	CLONAL	1	TRUE	1	0.231859185726081	2		434	826	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11169376	11169376	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	165	588	0	ENST00000361445.4:c.7499T>A	p.Ile2500Asn	p.I2500N	ENST00000361445	NM_004958.3	2500	aTt/aAt	56/58	0.203108766647191	3	FACETS	0.947	0.87	1	0.947	0.87	1	CLONAL	2	TRUE	1	0.231859185726081	3		588	839	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149241	119149241	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867564832	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	90	596	0	ENST00000264033.4:c.1249C>T	p.Pro417Ser	p.P417S	ENST00000264033	NM_005188.3	417	Cct/Tct	9/16	0.231859185726081	1	FACETS	0.925	0.82	1	0.925	0.82	1	CLONAL	1	TRUE	0	0.231859185726081	1		596	742	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206945657	206945657	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1274280163	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	91	567	0	ENST00000423557.1:c.124C>T	p.Arg42Ter	p.R42*	ENST00000423557	NM_000572.2	42	Cga/Tga	1/5	1	2	FACETS	0.962	0.853	1	0.962	0.853	1	CLONAL	1	TRUE	1	0.231859185726081	2		567	816	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8338945	8338945	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	71	530	0	ENST00000356435.5:c.5356G>A	p.Glu1786Lys	p.E1786K	ENST00000356435		1786	Gaa/Aaa	32/35	1	2	FACETS	0.925	0.807	1	0.925	0.807	1	CLONAL	1	TRUE	1	0.231859185726081	2		530	662	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451917	29451917	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	950	103	664	0	ENST00000389048.3:c.2648G>A	p.Trp883Ter	p.W883*	ENST00000389048	NM_004304.4	883	tGg/tAg	16/29	1	2	FACETS	0.844	0.753	0.94	0.844	0.753	0.94	CLONAL	1	TRUE	1	0.231859185726081	2		664	1053	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32166769	32166769	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs527962523	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	132	727	0	ENST00000375023.3:c.4469G>A	p.Arg1490Gln	p.R1490Q	ENST00000375023	NM_004557.3	1490	cGg/cAg	24/30	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.231859185726081	2		727	1122	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857436	9857436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	90	514	0	ENST00000330684.3:c.3965G>A	p.Gly1322Glu	p.G1322E	ENST00000330684	NM_001134407.1	1322	gGa/gAa	13/13	1	2	FACETS	0.977	0.866	1	0.977	0.866	1	CLONAL	1	TRUE	1	0.231859185726081	2		514	795	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560970	9560970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781706438	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	55	452	1	ENST00000353224.5:c.812C>T	p.Ser271Leu	p.S271L	ENST00000353224	NM_177990.2	271	tCg/tTg	4/10	1	2	FACETS	0.799	0.683	0.925	0.799	0.683	0.925	CLONAL	1	TRUE	1	0.231859185726081	2		453	594	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306560	41306560	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	106	549	0	ENST00000373198.4:c.1099G>A	p.Glu367Lys	p.E367K	ENST00000373198	NM_133170.3	367	Gag/Aag	7/32	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.231859185726081	2		549	912	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18641528	18641528	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	77	504	0	ENST00000266497.5:c.2527G>A	p.Glu843Lys	p.E843K	ENST00000266497		843	Gaa/Aaa	17/31	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.231859185726081	2		504	579	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754929	29754929	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	95	580	0	ENST00000389048.3:c.1006C>T	p.Pro336Ser	p.P336S	ENST00000389048	NM_004304.4	336	Ccg/Tcg	4/29	1	2	FACETS	0.981	0.873	1	0.981	0.873	1	CLONAL	1	TRUE	1	0.231859185726081	2		580	835	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805779	43805779	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	214	658	0	ENST00000372470.3:c.835G>A	p.Asp279Asn	p.D279N	ENST00000372470	NM_005373.2	279	Gac/Aac	5/12	0.203108766647191	3	FACETS	0.943	0.876	1	0.943	0.876	1	CLONAL	2	TRUE	1	0.231859185726081	3		658	1092	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165834	118165834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780049033	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	62	388	1	ENST00000369448.3:c.344C>T	p.Ser115Phe	p.S115F	ENST00000369448	NM_017709.3	115	tCc/tTc	2/2	0.203108766647191	3	FACETS	0.844	0.728	0.97	0.422	0.364	0.485	CLONAL	1	TRUE	1	0.231859185726081	3		389	707	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462171	120462171	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1296823228	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	172	557	0	ENST00000256646.2:c.5545G>A	p.Glu1849Lys	p.E1849K	ENST00000256646	NM_024408.3	1849	Gaa/Aaa	31/34	0.203108766647191	3	FACETS	0.94	0.865	1	0.94	0.865	1	CLONAL	2	TRUE	1	0.231859185726081	3		557	881	SUCCESS
RET	5979	MSKCC	GRCh37	10	43604647	43604648	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	96	571	2	ENST00000355710.3:c.1232_1233delinsTT	p.Ser411Phe	p.S411F	ENST00000355710	NM_020975.4	411	tCC/tTT	6/20	1	2	FACETS	0.827	0.735	0.925	0.827	0.735	0.925	CLONAL	1	TRUE	1	0.231859185726081	2		573	1001	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851834	63851834	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs865814457	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	118	671	0	ENST00000279873.7:c.2612C>T	p.Pro871Leu	p.P871L	ENST00000279873	NM_032199.2	871	cCt/cTt	10/10	1	2	FACETS	0.952	0.857	1	0.952	0.857	1	CLONAL	1	TRUE	1	0.231859185726081	2		671	1069	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771428	112771428	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	110	743	0	ENST00000369452.4:c.1601C>T	p.Pro534Leu	p.P534L	ENST00000369452	NM_007373.3	534	cCc/cTc	9/9	1	2	FACETS	0.919	0.824	1	0.919	0.824	1	CLONAL	1	TRUE	1	0.231859185726081	2		743	1032	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18473955	18473955	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	42	380	0	ENST00000266497.5:c.1197G>A	p.Trp399Ter	p.W399*	ENST00000266497		399	tgG/tgA	6/31	1	2	FACETS	0.843	0.704	0.996	0.843	0.704	0.996	CLONAL	1	TRUE	1	0.231859185726081	2		380	430	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46285845	46285845	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	100	524	0	ENST00000334344.6:c.5113C>G	p.Pro1705Ala	p.P1705A	ENST00000334344	NM_152641.2	1705	Cca/Gca	18/21	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.231859185726081	2		524	788	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431588	49431588	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1305161243	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	115	554	0	ENST00000301067.7:c.9551C>T	p.Ser3184Phe	p.S3184F	ENST00000301067	NM_003482.3	3184	tCc/tTc	34/54	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.231859185726081	2		554	863	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434841	49434841	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1174	171	889	2	ENST00000301067.7:c.6712C>T	p.Pro2238Ser	p.P2238S	ENST00000301067	NM_003482.3	2238	Ccc/Tcc	31/54	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.231859185726081	2		891	1345	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623860	28623860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	76	557	0	ENST00000241453.7:c.794G>A	p.Gly265Glu	p.G265E	ENST00000241453	NM_004119.2	265	gGg/gAg	7/24	1	2	FACETS	0.931	0.816	1	0.931	0.816	1	CLONAL	1	TRUE	1	0.231859185726081	2		557	704	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042365	42042365	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	114	705	0	ENST00000219905.7:c.6560T>C	p.Val2187Ala	p.V2187A	ENST00000219905	NM_001164273.1	2187	gTt/gCt	17/24	1	2	FACETS	0.932	0.837	1	0.932	0.837	1	CLONAL	1	TRUE	1	0.231859185726081	2		705	1055	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680737	88680737	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	132	613	0	ENST00000360948.2:c.520T>C	p.Trp174Arg	p.W174R	ENST00000360948	NM_001012338.2	174	Tgg/Cgg	6/19	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.231859185726081	2		613	1070	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826538	50826538	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121908388	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	51	342	0	ENST00000398568.2:c.2263C>T	p.Arg755Ter	p.R755*	ENST00000398568	NM_001042412.1	755	Cga/Tga	15/18	1	2	FACETS	0.779	0.661	0.907	0.779	0.661	0.907	CLONAL	1	TRUE	1	0.231859185726081	2		342	565	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576928	7576928	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	108	623	0	ENST00000269305.4:c.920-2A>T		p.X307_splice	ENST00000269305	NM_001126112.2	307			0.231859185726081	1	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	0	0.231859185726081	1		623	778	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667658	29667658	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	69	431	0	ENST00000356175.3:c.6994G>A	p.Asp2332Asn	p.D2332N	ENST00000356175	NM_000267.3	2332	Gac/Aac	46/57	0.231859185726081	1	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	0	0.231859185726081	1		431	495	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5225776	5225776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1158	145	665	0	ENST00000357368.4:c.2456C>T	p.Ala819Val	p.A819V	ENST00000357368	NM_002850.3	819	gCt/gTt	17/38	1	2	FACETS	0.96	0.873	1	0.96	0.873	1	CLONAL	1	TRUE	1	0.231859185726081	2		665	1303	SUCCESS
AXL	558	MSKCC	GRCh37	19	41726639	41726640	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	962	130	733	1	ENST00000301178.4:c.184_185delinsAA	p.Gly62Lys	p.G62K	ENST00000301178	NM_021913.4	62	GGa/AAa	2/20	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.231859185726081	2		734	1092	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25505403	25505403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	69	485	0	ENST00000264709.3:c.355G>A	p.Glu119Lys	p.E119K	ENST00000264709	NM_175629.2	119	Gag/Aag	4/23	1	2	FACETS	0.823	0.716	0.939	0.823	0.716	0.939	CLONAL	1	TRUE	1	0.231859185726081	2		485	723	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39216420	39216420	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762576997	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	75	570	1	ENST00000402219.2:c.3382C>T	p.His1128Tyr	p.H1128Y	ENST00000402219	NM_005633.3	1128	Cat/Tat	21/23	1	2	FACETS	0.947	0.83	1	0.947	0.83	1	CLONAL	1	TRUE	1	0.231859185726081	2		571	683	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202136259	202136259	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	170	545	0	ENST00000358485.4:c.503C>G	p.Ser168Ter	p.S168*	ENST00000358485	NM_001080125.1	168	tCa/tGa	3/9	0.203108766647191	3	FACETS	0.868	0.798	0.941	0.868	0.798	0.941	CLONAL	2	TRUE	1	0.231859185726081	3		545	943	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9520166	9520166	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	96	498	0	ENST00000353224.5:c.2103A>T	p.Lys701Asn	p.K701N	ENST00000353224	NM_177990.2	701	aaA/aaT	10/10	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.231859185726081	2		498	686	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546774	9546774	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	52	238	0	ENST00000353224.5:c.1248G>A	p.Trp416Ter	p.W416*	ENST00000353224	NM_177990.2	416	tgG/tgA	5/10	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.231859185726081	2		238	380	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46251019	46251019	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	72	488	0	ENST00000371998.3:c.28C>T	p.Pro10Ser	p.P10S	ENST00000371998		10	Cca/Tca	3/23	1	2	FACETS	0.859	0.75	0.977	0.859	0.75	0.977	CLONAL	1	TRUE	1	0.231859185726081	2		488	723	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52668757	52668757	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	69	579	0	ENST00000394830.3:c.1162C>T	p.Gln388Ter	p.Q388*	ENST00000394830	NM_018313.4	388	Cag/Tag	12/30	1	2	FACETS	0.797	0.693	0.909	0.797	0.693	0.909	CLONAL	1	TRUE	1	0.231859185726081	2		579	747	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190828	185190828	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	120	768	1	ENST00000265026.3:c.1709C>T	p.Ser570Phe	p.S570F	ENST00000265026	NM_004721.4	570	tCc/tTc	11/14	1	2	FACETS	0.889	0.8	0.982	0.889	0.8	0.982	CLONAL	1	TRUE	1	0.231859185726081	2		769	1165	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144682	55144682	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	52	470	1	ENST00000257290.5:c.2156G>A	p.Ser719Asn	p.S719N	ENST00000257290	NM_006206.4	719	aGc/aAc	15/23	1	2	FACETS	0.808	0.688	0.94	0.808	0.688	0.94	CLONAL	1	TRUE	1	0.231859185726081	2		471	555	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55146590	55146590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139465754	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	86	545	0	ENST00000257290.5:c.2264C>T	p.Ser755Phe	p.S755F	ENST00000257290	NM_006206.4	755	tCc/tTc	16/23	1	2	FACETS	0.937	0.828	1	0.937	0.828	1	CLONAL	1	TRUE	1	0.231859185726081	2		545	792	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540950	187540950	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	54	359	1	ENST00000441802.2:c.6790C>A	p.His2264Asn	p.H2264N	ENST00000441802	NM_005245.3	2264	Cat/Aat	10/27	1	2	FACETS	0.915	0.782	1	0.915	0.782	1	CLONAL	1	TRUE	1	0.231859185726081	2		360	509	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515295	31515295	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756537138	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	95	629	0	ENST00000344624.3:c.1090C>T	p.Arg364Cys	p.R364C	ENST00000344624		364	Cgt/Tgt	5/33	1	2	FACETS	0.951	0.845	1	0.951	0.845	1	CLONAL	1	TRUE	1	0.231859185726081	2		629	862	SUCCESS
APC	324	MSKCC	GRCh37	5	112173699	112173699	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	53	400	0	ENST00000257430.4:c.2408C>A	p.Thr803Asn	p.T803N	ENST00000257430	NM_000038.5	803	aCc/aAc	16/16	1	2	FACETS	0.856	0.73	0.994	0.856	0.73	0.994	CLONAL	1	TRUE	1	0.231859185726081	2		400	534	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048652	180048652	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772355537	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	127	589	0	ENST00000261937.6:c.1910G>A	p.Ser637Asn	p.S637N	ENST00000261937	NM_182925.4	637	aGc/aAc	13/30	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.231859185726081	2		589	1017	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	398937	398937	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	79	345	0	ENST00000380956.4:c.745+2T>G		p.X249_splice	ENST00000380956	NM_001195286.1	249			1	2	FACETS	1	0.9	1	1	0.9	1	CLONAL	1	TRUE	1	0.231859185726081	2		345	664	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32169853	32169853	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	rs751390609	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	876	122	602	0	ENST00000375023.3:c.3755C>G	p.Thr1252Ser	p.T1252S	ENST00000375023	NM_004557.3	1252	aCt/aGt	21/30	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.231859185726081	2		602	998	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43748581	43748581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs139206878	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	72	219	0	ENST00000523873.1:c.535C>T	p.Pro179Ser	p.P179S	ENST00000523873		179	Cct/Tct	6/8	1	2	FACETS	0.909	0.794	1	0.909	0.794	1	CLONAL	1	TRUE	1	0.231859185726081	2		219	683	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117686811	117686811	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	63	590	0	ENST00000368508.3:c.2906G>A	p.Trp969Ter	p.W969*	ENST00000368508	NM_002944.2	969	tGg/tAg	19/43	1	2	FACETS	0.674	0.582	0.775	0.674	0.582	0.775	SUBCLONAL	1	TRUE	1	0.231859185726081	2		590	806	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55227888	55227889	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	82	492	1	ENST00000275493.2:c.1355_1356delinsTT	p.Ser452Phe	p.S452F	ENST00000275493	NM_005228.3	452	tCC/tTT	12/28	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.231859185726081	2		493	682	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69103983	69103983	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	96	714	0	ENST00000288368.4:c.4373C>T	p.Ser1458Leu	p.S1458L	ENST00000288368	NM_024870.2	1458	tCa/tTa	36/40	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.231859185726081	2		714	783	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319884	8319884	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	59	453	0	ENST00000356435.5:c.5617T>A	p.Phe1873Ile	p.F1873I	ENST00000356435		1873	Ttc/Atc	34/35	1	2	FACETS	0.805	0.692	0.928	0.805	0.692	0.928	CLONAL	1	TRUE	1	0.231859185726081	2		453	632	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484354	8484354	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145574906	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	52	446	0	ENST00000356435.5:c.3178G>A	p.Val1060Ile	p.V1060I	ENST00000356435		1060	Gta/Ata	19/35	1	2	FACETS	0.777	0.661	0.905	0.777	0.661	0.905	CLONAL	1	TRUE	1	0.231859185726081	2		446	577	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499699	8499699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	80	570	2	ENST00000356435.5:c.2270G>A	p.Gly757Asp	p.G757D	ENST00000356435		757	gGt/gAt	14/35	1	2	FACETS	0.859	0.756	0.971	0.859	0.756	0.971	CLONAL	1	TRUE	1	0.231859185726081	2		572	803	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27209116	27209116	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	rs1440193984	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	68	508	1	ENST00000380036.4:c.2576-3C>T		p.X859_splice	ENST00000380036	NM_000459.3	859			1	2	FACETS	0.856	0.744	0.977	0.856	0.744	0.977	CLONAL	1	TRUE	1	0.231859185726081	2		509	685	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325398	1325398	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754961260	NA	P-0015830-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	85	579	2	ENST00000400841.2:c.277G>A	p.Asp93Asn	p.D93N	ENST00000400841		93	Gac/Aac	3/6	1	1	FACETS	0.713	0.629	0.803	0.713	0.629	0.803	SUBCLONAL	1	TRUE	0	0.231859185726081	1		581	909	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	83	282	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.391979205631009	2		282	374	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099947	27099947	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	248	433	0	ENST00000324856.7:c.3826C>T	p.Arg1276Ter	p.R1276*	ENST00000324856	NM_006015.4	1276	Cga/Tga	15/20	1	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	1	0.391979205631009	2		433	991	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774131	66774131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519733	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1006	281	995	0	ENST00000307102.5:c.607G>A	p.Glu203Lys	p.E203K	ENST00000307102	NM_002755.3	203	Gag/Aag	6/11	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.391979205631009	2		995	1287	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49932747	49932747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144684048	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	233	997	4	ENST00000296474.3:c.3124G>A	p.Asp1042Asn	p.D1042N	ENST00000296474	NM_002447.2	1042	Gat/Aat	14/20	1	2	FACETS	0.952	0.886	1	0.952	0.886	1	CLONAL	1	TRUE	1	0.391979205631009	2		1001	1249	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743903	41743903	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	199	935	0	ENST00000301178.4:c.838G>A	p.Glu280Lys	p.E280K	ENST00000301178	NM_021913.4	280	Gag/Aag	7/20	1	2	FACETS	0.897	0.83	0.967	0.897	0.83	0.967	CLONAL	1	TRUE	1	0.391979205631009	2		935	1132	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261338	16261338	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	225	664	0	ENST00000375759.3:c.8603C>T	p.Ser2868Phe	p.S2868F	ENST00000375759	NM_015001.2	2868	tCc/tTc	11/15	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.391979205631009	2		664	1029	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29556367	29556367	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	245	456	1	ENST00000356175.3:c.2734C>T	p.Gln912Ter	p.Q912*	ENST00000356175	NM_000267.3	912	Caa/Taa	21/57	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.391979205631009	2		457	1030	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357483	89357483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	203	774	0	ENST00000301030.4:c.335C>T	p.Ser112Phe	p.S112F	ENST00000301030	NM_001256183.1	112	tCc/tTc	5/13	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.391979205631009	2		774	901	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429758	78429758	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	111	331	0	ENST00000370768.2:c.1030C>T	p.Arg344Ter	p.R344*	ENST00000370768	NM_003902.3	344	Cga/Tga	12/20	1	2	FACETS	0.893	0.805	0.987	0.893	0.805	0.987	CLONAL	1	TRUE	1	0.391979205631009	2		331	634	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534288	534289	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	160	674	3	ENST00000451590.1:c.34_35delinsAA	p.Gly12Asn	p.G12N	ENST00000451590	NM_001130442.1	12	GGc/AAc	2/5	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.391979205631009	2		677	799	SUCCESS
ATM	472	MSKCC	GRCh37	11	108115630	108115631	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	205	556	0	ENST00000278616.4:c.778_779delinsTT	p.Pro260Phe	p.P260F	ENST00000278616	NM_000051.3	260	CCc/TTc	7/63	1	2	FACETS	0.947	0.878	1	0.947	0.878	1	CLONAL	1	TRUE	1	0.391979205631009	2		556	1104	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481358	56481358	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	212	720	1	ENST00000267101.3:c.548-3C>T		p.X183_splice	ENST00000267101	NM_001982.3	183			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.391979205631009	2		721	969	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863247	57863247	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	82	636	0	ENST00000228682.2:c.1342T>C	p.Cys448Arg	p.C448R	ENST00000228682	NM_005269.2	448	Tgc/Cgc	11/12	1	2	FACETS	0.511	0.45	0.577	0.511	0.45	0.577	SUBCLONAL	1	TRUE	1	0.391979205631009	2		636	818	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863415	57863415	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	217	823	0	ENST00000228682.2:c.1510G>A	p.Asp504Asn	p.D504N	ENST00000228682	NM_005269.2	504	Gac/Aac	11/12	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.391979205631009	2		823	1061	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864879	57864879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	206	793	0	ENST00000228682.2:c.2356C>T	p.His786Tyr	p.H786Y	ENST00000228682	NM_005269.2	786	Cac/Tac	12/12	1	2	FACETS	0.989	0.917	1	0.989	0.917	1	CLONAL	1	TRUE	1	0.391979205631009	2		793	1063	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592623	28592623	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	124	660	0	ENST00000241453.7:c.2522A>G	p.Asn841Ser	p.N841S	ENST00000241453	NM_004119.2	841	aAc/aGc	20/24	NA	2	FACETS	0.765	0.692	0.842			1	INDETERMINATE	1	TRUE	NA	0.391979205631009	2		660	827	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95597967	95597967	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	142	394	0	ENST00000393063.1:c.317T>C	p.Val106Ala	p.V106A	ENST00000393063	NM_030621.3	106	gTt/gCt	5/28	1	2	FACETS	0.994	0.907	1	0.994	0.907	1	CLONAL	1	TRUE	1	0.391979205631009	2		394	729	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028727	42028727	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1242451475	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	208	609	0	ENST00000219905.7:c.4265C>T	p.Ser1422Phe	p.S1422F	ENST00000219905	NM_001164273.1	1422	tCc/tTc	13/24	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.391979205631009	2		609	905	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707915	43707915	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	230	937	1	ENST00000382044.4:c.4966C>T	p.Arg1656Ter	p.R1656*	ENST00000382044	NM_001141980.1	1656	Cga/Tga	23/28	1	2	FACETS	0.944	0.879	1	0.944	0.879	1	CLONAL	1	TRUE	1	0.391979205631009	2		938	1243	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89836386	89836386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746098172	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	145	538	0	ENST00000389301.3:c.2363C>T	p.Ala788Val	p.A788V	ENST00000389301	NM_000135.2	788	gCc/gTc	26/43	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.391979205631009	2		538	705	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562745	29562746	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	155	562	1	ENST00000356175.3:c.3825_3826delinsTT	p.Arg1276Ter	p.R1276*	ENST00000356175	NM_000267.3	1275	ttCCga/ttTTga	28/57	1	2	FACETS	0.924	0.846	1	0.924	0.846	1	CLONAL	1	TRUE	1	0.391979205631009	2		563	856	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78617569	78617570	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	183	557	1	ENST00000306801.3:c.307_308delinsAA	p.Gly103Asn	p.G103N	ENST00000306801	NM_020761.2	103	GGt/AAt	3/34	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.391979205631009	2		558	893	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257606	19257606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764313266	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	212	773	7	ENST00000162023.5:c.620G>A	p.Arg207Gln	p.R207Q	ENST00000162023		207	cGg/cAg	10/13	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.391979205631009	2		780	893	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140324	50140324	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	244	661	0	ENST00000246792.3:c.217G>A	p.Asp73Asn	p.D73N	ENST00000246792	NM_006270.3	73	Gat/Aat	2/6	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.391979205631009	2		661	1005	SUCCESS
ALK	238	MSKCC	GRCh37	2	29456476	29456476	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	221	820	0	ENST00000389048.3:c.2442G>A	p.Trp814Ter	p.W814*	ENST00000389048	NM_004304.4	814	tgG/tgA	14/29	1	2	FACETS	0.95	0.883	1	0.95	0.883	1	CLONAL	1	TRUE	1	0.391979205631009	2		820	1187	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143460	30143461	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	53	197	1	ENST00000389048.3:c.65_66delinsAA	p.Gly22Glu	p.G22E	ENST00000389048	NM_004304.4	22	gGG/gAA	1/29	1	2	FACETS	1	0.885	1	1	0.885	1	CLONAL	1	TRUE	1	0.391979205631009	2		198	262	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39751885	39751885	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs56111014	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	800	239	687	1	ENST00000361337.2:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000361337	NM_003286.2	749	cGg/cAg	21/21	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.391979205631009	2		688	1039	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445070	89445070	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	50	658	0	ENST00000336596.2:c.1390A>C	p.Asn464His	p.N464H	ENST00000336596	NM_005233.5	464	Aat/Cat	6/17	1	2	FACETS	0.299	0.253	0.35	0.299	0.253	0.35	SUBCLONAL	1	TRUE	1	0.391979205631009	2		658	853	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509949	187509949	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	87	472	0	ENST00000441802.2:c.13564G>T	p.Gly4522Trp	p.G4522W	ENST00000441802	NM_005245.3	4522	Ggg/Tgg	27/27	1	2	FACETS	0.838	0.743	0.938	0.838	0.743	0.938	CLONAL	1	TRUE	1	0.391979205631009	2		472	530	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56177939	56177939	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369084439	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	164	638	0	ENST00000399503.3:c.2912C>T	p.Pro971Leu	p.P971L	ENST00000399503	NM_005921.1	971	cCt/cTt	14/20	1	2	FACETS	0.844	0.774	0.916	0.844	0.774	0.916	CLONAL	1	TRUE	1	0.391979205631009	2		638	992	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149460576	149460576	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757795589	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	196	687	1	ENST00000286301.3:c.61C>T	p.Pro21Ser	p.P21S	ENST00000286301	NM_005211.3	21	Cca/Tca	3/22	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.391979205631009	2		688	868	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672302	30672302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	198	745	0	ENST00000376406.3:c.4658C>T	p.Ser1553Phe	p.S1553F	ENST00000376406	NM_014641.2	1553	tCt/tTt	10/15	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.391979205631009	2		745	869	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453155	140453156	+	missense_variant	Missense_Mutation	DNP	CA	CA	TT	novel	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	152	596	1	ENST00000288602.6:c.1779_1780delinsAA	p.Asp594Asn	p.D594N	ENST00000288602	NM_004333.4	593	ggTGat/ggAAat	15/18	1	2	FACETS	0.885	0.81	0.964	0.885	0.81	0.964	CLONAL	1	TRUE	1	0.391979205631009	2		597	876	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860518	151860518	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375738474	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	166	619	0	ENST00000262189.6:c.10144C>T	p.Arg3382Trp	p.R3382W	ENST00000262189	NM_170606.2	3382	Cgg/Tgg	43/59	1	2	FACETS	0.899	0.826	0.976	0.899	0.826	0.976	CLONAL	1	TRUE	1	0.391979205631009	2		619	942	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046421	69046421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	176	400	0	ENST00000288368.4:c.3894G>A	p.Met1298Ile	p.M1298I	ENST00000288368	NM_024870.2	1298	atG/atA	32/40	1	2	FACETS	0.751	0.69	0.814	0.751	0.69	0.814	SUBCLONAL	1	TRUE	1	0.391979205631009	2		400	1196	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978703	70978703	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	345	755	0	ENST00000276594.2:c.950G>A	p.Gly317Glu	p.G317E	ENST00000276594	NM_024504.3	317	gGa/gAa	5/8	1	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	1	0.391979205631009	2		755	1207	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341139	8341139	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	340	698	0	ENST00000356435.5:c.5077G>A	p.Gly1693Arg	p.G1693R	ENST00000356435		1693	Gga/Aga	30/35	0.381737425190903	2	FACETS	0.962	0.913	1	0.962	0.913	1	CLONAL	2	TRUE	0	0.391979205631009	2		698	902	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87339172	87339172	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	460	575	0	ENST00000277120.3:c.754A>G	p.Ile252Val	p.I252V	ENST00000277120		252	Ata/Gta	8/19	0.391979205631009	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.391979205631009	2		575	1022	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93637010	93637010	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	212	587	2	ENST00000375746.1:c.1060G>A	p.Asp354Asn	p.D354N	ENST00000375746	NM_001174167.1	354	Gac/Aac	9/14	0.391979205631009	2	FACETS	0.766	0.714	0.819	0.766	0.714	0.819	SUBCLONAL	2	TRUE	0	0.391979205631009	2		589	706	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401796	139401796	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554728268	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	443	825	1	ENST00000277541.6:c.3604C>T	p.Pro1202Ser	p.P1202S	ENST00000277541	NM_017617.3	1202	Ccc/Tcc	22/34	0.391979205631009	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.391979205631009	2		826	998	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858164	152858164	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	261	506	0	ENST00000406277.2:c.451C>T	p.Gln151Ter	p.Q151*	ENST00000406277	NM_152274.4	151	Cag/Tag	6/7	1	1	FACETS	0.833	0.786	0.88	1	0.994	1	CLONAL	2	TRUE	0	0.391979205631009	1		506	643	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149238709	149238711	+	missense_variant	Missense_Mutation	TNP	GTC	GTC	TTT	novel	NA	P-0015832-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	276	869	2	ENST00000360632.3:c.1084_1086delinsAAA	p.Asp362Lys	p.D362K	ENST00000360632	NM_015472.4	362	GAC/AAA	7/7	1	2	FACETS	0.989	0.927	1	0.989	0.927	1	CLONAL	1	TRUE	1	0.391979205631009	2		871	1424	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015881-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	26	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.527	0.417	0.652	0.527	0.417	0.652	SUBCLONAL	1	TRUE	1	0.281326765347901	2		215	351	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0015881-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	130	662	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	0.281326765347901	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.281326765347901	1		662	775	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317520	1317520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015881-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	151	746	0	ENST00000400841.2:c.545C>T	p.Ser182Phe	p.S182F	ENST00000400841		182	tCt/tTt	5/6	1	1	FACETS	0.79	0.721	0.863	0.79	0.721	0.863	SUBCLONAL	1	TRUE	0	0.281326765347901	1		746	1167	SUCCESS
APC	324	MSKCC	GRCh37	5	112128185	112128185	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587779805	NA	P-0015881-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	920	121	326	1	ENST00000257430.4:c.688C>T	p.Arg230Cys	p.R230C	ENST00000257430	NM_000038.5	230	Cgt/Tgt	7/16	1	2	FACETS	0.826	0.745	0.912	0.826	0.745	0.912	CLONAL	1	TRUE	1	0.281326765347901	2		327	1041	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124437	94124437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015881-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	69	516	2	ENST00000369303.4:c.146C>T	p.Ser49Phe	p.S49F	ENST00000369303	NM_004440.3	49	tCc/tTc	2/17	1	2	FACETS	0.67	0.583	0.765	0.67	0.583	0.765	SUBCLONAL	1	TRUE	1	0.281326765347901	2		518	732	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221981	1221981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015881-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	134	634	0	ENST00000326873.7:c.896C>T	p.Ser299Phe	p.S299F	ENST00000326873	NM_000455.4	299	tCc/tTc	7/10	1	2	FACETS	0.893	0.81	0.981	0.893	0.81	0.981	CLONAL	1	TRUE	1	0.281326765347901	2		634	1067	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95556921	95556921	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015881-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	120	555	0	ENST00000393063.1:c.5683C>T	p.Arg1895Ter	p.R1895*	ENST00000393063	NM_030621.3	1895	Cga/Tga	28/28	1	2	FACETS	0.845	0.762	0.934	0.845	0.762	0.934	CLONAL	1	TRUE	1	0.281326765347901	2		555	1009	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800928	120800928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1337094477	NA	P-0015881-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	177	667	0	ENST00000257552.2:c.320G>A	p.Arg107Gln	p.R107Q	ENST00000257552	NM_002442.3	107	cGa/cAa	6/15	0.281326765347901	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.281326765347901	1		667	909	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881009	37881009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1419499014	NA	P-0015881-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	151	742	0	ENST00000269571.5:c.2338C>T	p.Pro780Ser	p.P780S	ENST00000269571		780	Cca/Tca	20/27	0.281326765347901	1	FACETS	0.988	0.903	1	0.988	0.903	1	CLONAL	1	TRUE	0	0.281326765347901	1		742	934	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966462	25966462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015881-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	100	581	0	ENST00000435504.4:c.2744C>T	p.Pro915Leu	p.P915L	ENST00000435504		915	cCa/cTa	13/13	1	2	FACETS	0.735	0.655	0.82	0.735	0.655	0.82	SUBCLONAL	1	TRUE	1	0.281326765347901	2		581	967	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561234	9561234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015881-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	133	448	0	ENST00000353224.5:c.548C>T	p.Ser183Phe	p.S183F	ENST00000353224	NM_177990.2	183	tCt/tTt	4/10	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.281326765347901	2		448	853	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62320915	62320915	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015881-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	164	847	0	ENST00000360203.5:c.1939C>T	p.Pro647Ser	p.P647S	ENST00000360203	NM_001283009.1	647	Ccg/Tcg	23/35	1	2	FACETS	0.912	0.835	0.992	0.912	0.835	0.992	CLONAL	1	TRUE	1	0.281326765347901	2		847	1279	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656786	45656786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015881-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	123	629	1	ENST00000407780.3:c.370G>A	p.Glu124Lys	p.E124K	ENST00000407780	NM_001283052.1	124	Gag/Aag	3/7	1	2	FACETS	0.92	0.831	1	0.92	0.831	1	CLONAL	1	TRUE	1	0.281326765347901	2		630	950	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546089	41546089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015881-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	134	603	0	ENST00000263253.7:c.2704C>T	p.Pro902Ser	p.P902S	ENST00000263253	NM_001429.3	902	Cct/Tct	14/31	1	2	FACETS	0.907	0.823	0.996	0.907	0.823	0.996	CLONAL	1	TRUE	1	0.281326765347901	2		603	1050	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485307	8485307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015881-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	115	574	1	ENST00000356435.5:c.3073C>T	p.His1025Tyr	p.H1025Y	ENST00000356435		1025	Cat/Tat	18/35	1	2	FACETS	0.919	0.827	1	0.919	0.827	1	CLONAL	1	TRUE	1	0.281326765347901	2		575	890	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907743	76907743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015881-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	139	294	0	ENST00000373344.5:c.4418C>T	p.Pro1473Leu	p.P1473L	ENST00000373344	NM_000489.3	1473	cCt/cTt	15/35	1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.281326765347901	1		294	577	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562791	29562791	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1131691075	NA	P-0015881-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	75	356	0	ENST00000356175.3:c.3870+1G>A		p.X1290_splice	ENST00000356175	NM_000267.3	1290			0.281326765347901	1	FACETS	0.805	0.706	0.911	0.805	0.706	0.911	CLONAL	1	TRUE	0	0.281326765347901	1		356	569	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56400679	56400679	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015881-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	87	429	0	ENST00000348428.3:c.1273A>G	p.Met425Val	p.M425V	ENST00000348428	NM_006785.3	425	Atg/Gtg	11/17	1	2	FACETS	0.877	0.777	0.985	0.877	0.777	0.985	CLONAL	1	TRUE	1	0.281326765347901	2		429	705	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50906474	50906474	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	rs1064794926	NA	P-0015881-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	958	123	752	0	ENST00000440232.2:c.1135C>T	p.Gln379Ter	p.Q379*	ENST00000440232	NM_002691.3	379	Cag/Tag	9/27	1	2	FACETS	0.809	0.73	0.893	0.809	0.73	0.893	CLONAL	1	TRUE	1	0.281326765347901	2		752	1081	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525024	9525024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015881-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	109	519	0	ENST00000353224.5:c.1861G>A	p.Gly621Arg	p.G621R	ENST00000353224	NM_177990.2	621	Ggg/Agg	8/10	1	2	FACETS	0.884	0.793	0.98	0.884	0.793	0.98	CLONAL	1	TRUE	1	0.281326765347901	2		519	877	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624897	9624897	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015881-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	117	541	1	ENST00000353224.5:c.80C>T	p.Pro27Leu	p.P27L	ENST00000353224	NM_177990.2	27	cCa/cTa	3/10	1	2	FACETS	0.942	0.849	1	0.942	0.849	1	CLONAL	1	TRUE	1	0.281326765347901	2		542	883	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131953835	131953835	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015881-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	118	495	0	ENST00000265335.6:c.3238G>A	p.Gly1080Ser	p.G1080S	ENST00000265335		1080	Ggt/Agt	21/25	1	2	FACETS	0.954	0.86	1	0.954	0.86	1	CLONAL	1	TRUE	1	0.281326765347901	2		495	879	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93974312	93974312	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015881-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	116	534	0	ENST00000369303.4:c.1742G>A	p.Arg581Lys	p.R581K	ENST00000369303	NM_004440.3	581	aGg/aAg	8/17	1	2	FACETS	0.985	0.888	1	0.985	0.888	1	CLONAL	1	TRUE	1	0.281326765347901	2		534	837	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152265590	152265590	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1462204859	NA	P-0015881-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	93	457	0	ENST00000206249.3:c.1043A>G	p.Asn348Ser	p.N348S	ENST00000206249	NM_000125.3	348	aAc/aGc	4/8	1	2	FACETS	0.954	0.849	1	0.954	0.849	1	CLONAL	1	TRUE	1	0.281326765347901	2		457	693	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528477	157528477	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015881-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	112	511	1	ENST00000346085.5:c.6202C>T	p.Pro2068Ser	p.P2068S	ENST00000346085	NM_020732.3	2068	Cca/Tca	20/20	1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.281326765347901	2		512	789	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98248125	98248125	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0015881-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	116	556	0	ENST00000331920.6:c.426T>A	p.Tyr142Ter	p.Y142*	ENST00000331920	NM_000264.3	142	taT/taA	3/24	1	2	FACETS	0.82	0.737	0.907	0.82	0.737	0.907	CLONAL	1	TRUE	1	0.281326765347901	2		556	1006	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015881-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	19	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.767	1	1	0.767	1	CLONAL	1	TRUE	1	0.15	2		215	251	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0015881-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	39	662	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.677	0.559	0.809	0.677	0.559	0.809	SUBCLONAL	1	TRUE	1	0.15	2		662	768	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317520	1317520	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015881-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	48	746	0	ENST00000400841.2:c.545C>T	p.Ser182Phe	p.S182F	ENST00000400841		182	tCt/tTt	5/6	1	1	FACETS	0.665	0.56	0.781	0.665	0.56	0.781	SUBCLONAL	1	TRUE	0	0.15	1		746	890	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221981	1221981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015881-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	54	634	0	ENST00000326873.7:c.896C>T	p.Ser299Phe	p.S299F	ENST00000326873	NM_000455.4	299	tCc/tTc	7/10	1	2	FACETS	0.86	0.733	1	0.86	0.733	1	CLONAL	1	TRUE	1	0.15	2		634	837	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800928	120800928	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1337094477	NA	P-0015881-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	88	667	0	ENST00000257552.2:c.320G>A	p.Arg107Gln	p.R107Q	ENST00000257552	NM_002442.3	107	cGa/cAa	6/15	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.15	2		667	937	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37881009	37881009	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1419499014	NA	P-0015881-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	61	742	0	ENST00000269571.5:c.2338C>T	p.Pro780Ser	p.P780S	ENST00000269571		780	Cca/Tca	20/27	1	2	FACETS	1	0.878	1	1	0.878	1	CLONAL	1	TRUE	1	0.15	2		742	796	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966462	25966462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015881-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	41	581	0	ENST00000435504.4:c.2744C>T	p.Pro915Leu	p.P915L	ENST00000435504		915	cCa/cTa	13/13	1	2	FACETS	0.777	0.645	0.923	0.777	0.645	0.923	CLONAL	1	TRUE	1	0.15	2		581	704	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561234	9561234	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015881-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	42	448	0	ENST00000353224.5:c.548C>T	p.Ser183Phe	p.S183F	ENST00000353224	NM_177990.2	183	tCt/tTt	4/10	1	2	FACETS	0.795	0.662	0.944	0.795	0.662	0.944	CLONAL	1	TRUE	1	0.15	2		448	704	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62320915	62320915	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015881-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	66	847	0	ENST00000360203.5:c.1939C>T	p.Pro647Ser	p.P647S	ENST00000360203	NM_001283009.1	647	Ccg/Tcg	23/35	1	2	FACETS	0.81	0.701	0.93	0.81	0.701	0.93	CLONAL	1	TRUE	1	0.15	2		847	1086	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656786	45656786	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015881-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	53	629	1	ENST00000407780.3:c.370G>A	p.Glu124Lys	p.E124K	ENST00000407780	NM_001283052.1	124	Gag/Aag	3/7	1	2	FACETS	0.9	0.766	1	0.9	0.766	1	CLONAL	1	TRUE	1	0.15	2		630	785	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546089	41546089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015881-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	840	46	603	0	ENST00000263253.7:c.2704C>T	p.Pro902Ser	p.P902S	ENST00000263253	NM_001429.3	902	Cct/Tct	14/31	1	2	FACETS	0.692	0.581	0.816	0.692	0.581	0.816	SUBCLONAL	1	TRUE	1	0.15	2		603	886	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485307	8485307	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015881-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	52	574	1	ENST00000356435.5:c.3073C>T	p.His1025Tyr	p.H1025Y	ENST00000356435		1025	Cat/Tat	18/35	1	2	FACETS	0.958	0.814	1	0.958	0.814	1	CLONAL	1	TRUE	1	0.15	2		575	724	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76907743	76907743	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015881-T04-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	57	294	0	ENST00000373344.5:c.4418C>T	p.Pro1473Leu	p.P1473L	ENST00000373344	NM_000489.3	1473	cCt/cTt	15/35	1	1	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	0	0.15	1		294	558	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	148	215	0				ENST00000310581	NM_198253.2	-/1132			0.490024282935689	3	FACETS	1	0.949	1	0.525	0.48	0.572	CLONAL	1	TRUE	1	0.490024282935689	3		215	716	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579369	7579369	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1555526581	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	213	549	0	ENST00000269305.4:c.318C>G	p.Ser106Arg	p.S106R	ENST00000269305	NM_001126112.2	106	agC/agG	4/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.490024282935689	2		549	857	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562459	95562459	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	94	331	0	ENST00000393063.1:c.4798G>A	p.Glu1600Lys	p.E1600K	ENST00000393063	NM_030621.3	1600	Gaa/Aaa	24/28	1	2	FACETS	0.766	0.684	0.852	0.766	0.684	0.852	SUBCLONAL	1	TRUE	1	0.490024282935689	2		331	501	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15295180	15295180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	340	757	1	ENST00000263388.2:c.2492G>A	p.Gly831Glu	p.G831E	ENST00000263388	NM_000435.2	831	gGg/gAg	16/33	0.175700173094825	3	FACETS	0.787	0.746	0.83	0.787	0.746	0.83	INDETERMINATE	2	TRUE	1	0.490024282935689	3		758	1097	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971121	21971121	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	172	423	0	ENST00000579755.1:c.280C>T	p.Pro94Ser	p.P94S	ENST00000579755		94	Ccg/Tcg	2/3	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.490024282935689	2		423	670	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986544	36986544	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	201	680	0	ENST00000354822.5:c.1145C>T	p.Ser382Phe	p.S382F	ENST00000354822	NM_001079668.2	382	tCc/tTc	3/3	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.490024282935689	2		680	810	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100912815	100912815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1000609240	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	132	579	0	ENST00000325455.5:c.2507G>A	p.Arg836Gln	p.R836Q	ENST00000325455	NM_001202474.3	836	cGa/cAa	7/8	0.490024282935689	1	FACETS	0.971	0.889	1	0.971	0.889	1	CLONAL	1	TRUE	0	0.490024282935689	1		579	419	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431425	121431425	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	182	546	1	ENST00000257555.6:c.629C>T	p.Ser210Phe	p.S210F	ENST00000257555		210	tCc/tTc	3/10	1	2	FACETS	0.937	0.866	1	0.937	0.866	1	CLONAL	1	TRUE	1	0.490024282935689	2		547	793	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267773	7267773	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	263	550	0	ENST00000302850.5:c.235C>T	p.Pro79Ser	p.P79S	ENST00000302850	NM_000208.2	79	Ccc/Tcc	2/22	0.175700173094825	3	FACETS	0.756	0.71	0.803	0.756	0.71	0.803	INDETERMINATE	2	TRUE	1	0.490024282935689	3		550	884	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979257	93979257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	117	499	0	ENST00000369303.4:c.1571G>A	p.Gly524Glu	p.G524E	ENST00000369303	NM_004440.3	524	gGa/gAa	7/17	1	2	FACETS	0.946	0.857	1	0.946	0.857	1	CLONAL	1	TRUE	1	0.490024282935689	2		499	505	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683748	162683748	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	154	508	1	ENST00000366898.1:c.221G>A	p.Trp74Ter	p.W74*	ENST00000366898	NM_004562.2	74	tGg/tAg	3/12	1	2	FACETS	0.91	0.835	0.988	0.91	0.835	0.988	CLONAL	1	TRUE	1	0.490024282935689	2		509	691	SUCCESS
AXL	558	MSKCC	GRCh37	19	41736934	41736934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768702995	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	72	543	0	ENST00000301178.4:c.649C>T	p.Arg217Cys	p.R217C	ENST00000301178	NM_021913.4	217	Cgc/Tgc	5/20	0.303634801449185	1	FACETS	0.306	0.267	0.349	0.306	0.267	0.349	SUBCLONAL	1	TRUE	0	0.490024282935689	1		543	724	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49027167	49027168	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	114	415	1	ENST00000267163.4:c.1734_1735delinsTT	p.Arg579Ter	p.R579*	ENST00000267163	NM_000321.2	578	gaCCga/gaTTga	18/27	0.490024282935689	1	FACETS	0.832	0.755	0.913	0.832	0.755	0.913	CLONAL	1	TRUE	0	0.490024282935689	1		416	422	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143226689	143226689	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs149208667	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	99	274	0	ENST00000262992.4:c.425G>A	p.Arg142Gln	p.R142Q	ENST00000262992	NM_001101669.1	142	cGa/cAa	7/24	1	2	FACETS	0.923	0.828	1	0.923	0.828	1	CLONAL	1	TRUE	1	0.490024282935689	2		274	438	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754979	29754979	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	132	475	1	ENST00000389048.3:c.956C>T	p.Ser319Phe	p.S319F	ENST00000389048	NM_004304.4	319	tCc/tTc	4/29	1	2	FACETS	0.913	0.832	0.998	0.913	0.832	0.998	CLONAL	1	TRUE	1	0.490024282935689	2		476	590	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27087521	27087521	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	186	527	1	ENST00000324856.7:c.2095C>T	p.Pro699Ser	p.P699S	ENST00000324856	NM_006015.4	699	Cct/Tct	5/20	1	2	FACETS	0.966	0.894	1	0.966	0.894	1	CLONAL	1	TRUE	1	0.490024282935689	2		528	786	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120465361	120465361	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	154	390	0	ENST00000256646.2:c.4900C>T	p.Gln1634Ter	p.Q1634*	ENST00000256646	NM_024408.3	1634	Caa/Taa	27/34	1	2	FACETS	0.926	0.85	1	0.926	0.85	1	CLONAL	1	TRUE	1	0.490024282935689	2		390	679	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8074204	8074205	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	81	338	2	ENST00000377482.5:c.454_455delinsTT	p.Pro152Phe	p.P152F	ENST00000377482	NM_018948.3	152	CCt/TTt	4/4	1	2	FACETS	0.629	0.555	0.707	0.629	0.555	0.707	SUBCLONAL	1	TRUE	1	0.490024282935689	2		340	526	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261476	16261477	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	162	450	0	ENST00000375759.3:c.8741_8742delinsTT	p.Pro2914Leu	p.P2914L	ENST00000375759	NM_015001.2	2914	cCC/cTT	11/15	1	2	FACETS	0.978	0.9	1	0.978	0.9	1	CLONAL	1	TRUE	1	0.490024282935689	2		450	676	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28599091	28599091	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	163	526	0	ENST00000253063.3:c.538-1G>A		p.X180_splice	ENST00000253063	NM_031459.4	180			1	2	FACETS	0.858	0.789	0.931	0.858	0.789	0.931	CLONAL	1	TRUE	1	0.490024282935689	2		526	775	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36938134	36938134	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	206	528	0	ENST00000361632.4:c.827A>T	p.Glu276Val	p.E276V	ENST00000361632		276	gAa/gTa	6/16	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.490024282935689	2		528	779	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695860	117695860	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	241	581	0	ENST00000369458.3:c.577G>A	p.Glu193Lys	p.E193K	ENST00000369458	NM_024626.3	193	Gaa/Aaa	4/6	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.490024282935689	2		581	841	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695889	117695889	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	160	557	1	ENST00000369458.3:c.548C>T	p.Ser183Phe	p.S183F	ENST00000369458	NM_024626.3	183	tCc/tTc	4/6	1	2	FACETS	0.783	0.718	0.85	0.783	0.718	0.85	SUBCLONAL	1	TRUE	1	0.490024282935689	2		558	834	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699409	117699409	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	168	509	0	ENST00000369458.3:c.232G>A	p.Gly78Ser	p.G78S	ENST00000369458	NM_024626.3	78	Ggc/Agc	3/6	1	2	FACETS	0.914	0.842	0.989	0.914	0.842	0.989	CLONAL	1	TRUE	1	0.490024282935689	2		509	750	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204507356	204507356	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	152	462	0	ENST00000367182.3:c.431C>T	p.Ser144Phe	p.S144F	ENST00000367182	NM_001278516.1	144	tCc/tTc	7/11	1	2	FACETS	0.902	0.827	0.98	0.902	0.827	0.98	CLONAL	1	TRUE	1	0.490024282935689	2		462	688	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226555928	226555929	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	161	476	1	ENST00000366794.5:c.2248_2249delinsTT	p.Pro750Leu	p.P750L	ENST00000366794	NM_001618.3	750	CCg/TTg	16/23	1	2	FACETS	0.906	0.833	0.982	0.906	0.833	0.982	CLONAL	1	TRUE	1	0.490024282935689	2		477	725	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667524	241667524	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756528378	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	95	214	1	ENST00000366560.3:c.926C>T	p.Pro309Leu	p.P309L	ENST00000366560	NM_000143.3	309	cCg/cTg	7/10	1	2	FACETS	1	0.906	1	1	0.906	1	CLONAL	1	TRUE	1	0.490024282935689	2		215	384	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243675628	243675628	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	284	102	262	0	ENST00000263826.5:c.1352A>T	p.Lys451Ile	p.K451I	ENST00000263826	NM_005465.4	451	aAa/aTa	12/13	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.490024282935689	2		262	386	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89653834	89653836	+	frameshift_variant	Frame_Shift_Del	DEL	CGT	CGT	TG	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	103	399	1	ENST00000371953.3:c.132_134delinsTG	p.Val45AspfsTer9	p.V45Dfs*9	ENST00000371953	NM_000314.4	44	ggCGTa/ggTGa	2/9	1	2	FACETS	0.777	0.698	0.861	0.777	0.698	0.861	SUBCLONAL	1	TRUE	1	0.490024282935689	2		400	541	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114910755	114910755	+	splice_acceptor_variant	Splice_Site	SNP	A	A	C	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	146	404	0	ENST00000543371.1:c.876-2A>C		p.X292_splice	ENST00000543371	NM_001198531.1	292			1	2	FACETS	0.974	0.892	1	0.974	0.892	1	CLONAL	1	TRUE	1	0.490024282935689	2		404	612	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102100657	102100657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	92	202	0	ENST00000282441.5:c.1501C>T	p.Leu501Phe	p.L501F	ENST00000282441	NM_001130145.2	501	Ctt/Ttt	9/9	0.490024282935689	1	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	0	0.490024282935689	1		202	265	SUCCESS
ATM	472	MSKCC	GRCh37	11	108142079	108142079	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	170	460	0	ENST00000278616.4:c.3023C>T	p.Ser1008Phe	p.S1008F	ENST00000278616	NM_000051.3	1008	tCt/tTt	20/63	0.490024282935689	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.490024282935689	1		460	513	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149405	119149406	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	111	366	0	ENST00000264033.4:c.1413_1414delinsAA	p.Glu472Lys	p.E472K	ENST00000264033	NM_005188.3	471	aaGGaa/aaAAaa	9/16	0.490024282935689	1	FACETS	0.87	0.789	0.955	0.87	0.789	0.955	CLONAL	1	TRUE	0	0.490024282935689	1		366	393	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21629845	21629845	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	128	468	0	ENST00000421138.2:c.949G>T	p.Gly317Ter	p.G317*	ENST00000421138		317	Gga/Tga	9/16	1	2	FACETS	0.892	0.811	0.976	0.892	0.811	0.976	CLONAL	1	TRUE	1	0.490024282935689	2		468	586	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46243466	46243467	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	126	403	0	ENST00000334344.6:c.1819_1820delinsTT	p.Pro607Phe	p.P607F	ENST00000334344	NM_152641.2	607	CCc/TTc	14/21	1	2	FACETS	0.89	0.809	0.975	0.89	0.809	0.975	CLONAL	1	TRUE	1	0.490024282935689	2		403	578	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434564	49434564	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748336779	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	200	485	0	ENST00000301067.7:c.6989C>T	p.Pro2330Leu	p.P2330L	ENST00000301067	NM_003482.3	2330	cCc/cTc	31/54	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.490024282935689	2		485	805	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444070	49444070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	145	383	2	ENST00000301067.7:c.3301C>T	p.Leu1101Phe	p.L1101F	ENST00000301067	NM_003482.3	1101	Ctt/Ttt	11/54	1	2	FACETS	0.981	0.899	1	0.981	0.899	1	CLONAL	1	TRUE	1	0.490024282935689	2		385	603	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865536	57865537	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	201	558	1	ENST00000228682.2:c.3013_3014delinsAA	p.Gly1005Lys	p.G1005K	ENST00000228682	NM_005269.2	1005	GGa/AAa	12/12	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.490024282935689	2		559	806	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115110013	115110013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	192	766	1	ENST00000257566.3:c.1865C>T	p.Ser622Leu	p.S622L	ENST00000257566	NM_016569.3	622	tCg/tTg	8/8	1	2	FACETS	0.913	0.846	0.983	0.913	0.846	0.983	CLONAL	1	TRUE	1	0.490024282935689	2		767	858	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879672	123879673	+	missense_variant	Missense_Mutation	DNP	CC	CC	GA	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	17	159	0	ENST00000330479.4:c.368_369delinsGA	p.Pro123Arg	p.P123R	ENST00000330479	NM_020382.3	123	cCC/cGA	4/9	1	2	FACETS	0.329	0.246	0.427	0.329	0.246	0.427	SUBCLONAL	1	TRUE	1	0.490024282935689	2		159	211	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336239	73336240	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	72	235	0	ENST00000377767.4:c.2163_2164delinsAA	p.Ala722Thr	p.A722T	ENST00000377767	NM_014953.3	721	ttGGct/ttAAct	17/21	1	2	FACETS	0.794	0.698	0.897	0.794	0.698	0.897	SUBCLONAL	1	TRUE	1	0.490024282935689	2		235	370	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81422150	81422151	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	123	466	2	ENST00000298171.2:c.126_127delinsAA	p.Asp43Asn	p.D43N	ENST00000298171	NM_000369.2	42	aaGGat/aaAAat	1/10	1	2	FACETS	0.77	0.698	0.846	0.77	0.698	0.846	SUBCLONAL	1	TRUE	1	0.490024282935689	2		468	652	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562638	95562638	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	124	329	0	ENST00000393063.1:c.4619G>A	p.Gly1540Glu	p.G1540E	ENST00000393063	NM_030621.3	1540	gGa/gAa	24/28	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.490024282935689	2		329	453	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105242038	105242038	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	198	628	0	ENST00000349310.3:c.386C>T	p.Ser129Leu	p.S129L	ENST00000349310	NM_001014432.1	129	tCa/tTa	6/15	1	2	FACETS	0.974	0.903	1	0.974	0.903	1	CLONAL	1	TRUE	1	0.490024282935689	2		628	830	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67479850	67479850	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	174	388	0	ENST00000327367.4:c.1154+3C>T		p.X385_splice	ENST00000327367	NM_005902.3	385			0.490024282935689	1	FACETS	0.982	0.91	1	0.982	0.91	1	CLONAL	1	TRUE	0	0.490024282935689	1		388	546	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476403	88476403	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	142	336	1	ENST00000360948.2:c.1729C>T	p.Pro577Ser	p.P577S	ENST00000360948	NM_001012338.2	577	Ccc/Tcc	15/19	0.490024282935689	1	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	0	0.490024282935689	1		337	420	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786816	3786817	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	78	277	0	ENST00000262367.5:c.4395-1_4395delinsAA		p.X1465_splice	ENST00000262367	NM_004380.2	1465		27/31	1	2	FACETS	0.776	0.686	0.873	0.776	0.686	0.873	SUBCLONAL	1	TRUE	1	0.490024282935689	2		277	410	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50784103	50784103	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	133	411	0	ENST00000398568.2:c.494T>C	p.Val165Ala	p.V165A	ENST00000398568	NM_001042412.1	165	gTt/gCt	3/18	1	2	FACETS	0.88	0.802	0.962	0.88	0.802	0.962	CLONAL	1	TRUE	1	0.490024282935689	2		411	617	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50813663	50813663	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	195	569	0	ENST00000398568.2:c.1217C>T	p.Ser406Leu	p.S406L	ENST00000398568	NM_001042412.1	406	tCa/tTa	8/18	1	2	FACETS	0.991	0.919	1	0.991	0.919	1	CLONAL	1	TRUE	1	0.490024282935689	2		569	803	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829095	72829095	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	170	394	0	ENST00000268489.5:c.7486C>T	p.Gln2496Ter	p.Q2496*	ENST00000268489	NM_006885.3	2496	Cag/Tag	9/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.490024282935689	2		394	649	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89805962	89805962	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	123	390	0	ENST00000389301.3:c.3935-1G>A		p.X1312_splice	ENST00000389301	NM_000135.2	1312			1	2	FACETS	0.87	0.79	0.954	0.87	0.79	0.954	CLONAL	1	TRUE	1	0.490024282935689	2		390	577	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89816244	89816244	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	173	558	0	ENST00000389301.3:c.3133G>A	p.Glu1045Lys	p.E1045K	ENST00000389301	NM_000135.2	1045	Gag/Aag	32/43	1	2	FACETS	0.823	0.758	0.891	0.823	0.758	0.891	CLONAL	1	TRUE	1	0.490024282935689	2		558	858	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577146	7577170	+	splice_acceptor_variant,coding_sequence_variant,intron_variant	Splice_Site	DEL	TAGATTACCACTACTCAGGATAGGA	TAGATTACCACTACTCAGGATAGGA	-	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	177	522	0	ENST00000269305.4:c.783-15_792del		p.X261_splice	ENST00000269305	NM_001126112.2	261		8/11	1	2	FACETS	0.941	0.868	1	0.941	0.868	1	CLONAL	1	TRUE	1	0.490024282935689	2		522	768	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968969	15968969	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs904210912	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	112	371	0	ENST00000268712.3:c.4781C>T	p.Thr1594Ile	p.T1594I	ENST00000268712	NM_006311.3	1594	aCt/aTt	33/46	1	2	FACETS	0.85	0.767	0.936	0.85	0.767	0.936	CLONAL	1	TRUE	1	0.490024282935689	2		371	538	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40369203	40369203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	189	495	0	ENST00000293328.3:c.1355G>A	p.Gly452Glu	p.G452E	ENST00000293328	NM_012448.3	452	gGa/gAa	11/19	1	2	FACETS	0.993	0.92	1	0.993	0.92	1	CLONAL	1	TRUE	1	0.490024282935689	2		495	777	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985422	60985423	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	199	566	2	ENST00000333681.4:c.477_478delinsAA	p.Glu160Lys	p.E160K	ENST00000333681		159	gtGGag/gtAAag	2/3	1	2	FACETS	0.888	0.823	0.955	0.888	0.823	0.955	CLONAL	1	TRUE	1	0.490024282935689	2		568	915	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226549	1226549	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	261	649	0	ENST00000326873.7:c.1205C>T	p.Thr402Ile	p.T402I	ENST00000326873	NM_000455.4	402	aCc/aTc	9/10	0.175700173094825	3	FACETS	1	0.992	1	0.705	0.662	0.75	INDETERMINATE	1	TRUE	1	0.490024282935689	3		649	940	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5219985	5219986	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	230	606	1	ENST00000357368.4:c.3729_3730delinsTT	p.Leu1244Phe	p.L1244F	ENST00000357368	NM_002850.3	1243	gtCCtc/gtTTtc	22/38	0.175700173094825	3	FACETS	1	0.98	1	0.564	0.525	0.603	INDETERMINATE	1	TRUE	1	0.490024282935689	3		607	1037	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15292550	15292550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1428777171	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	354	655	0	ENST00000263388.2:c.2629C>T	p.Pro877Ser	p.P877S	ENST00000263388	NM_000435.2	877	Cct/Tct	17/33	0.175700173094825	3	FACETS	0.818	0.776	0.861	0.818	0.776	0.861	INDETERMINATE	2	TRUE	1	0.490024282935689	3		655	1099	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212363	36212363	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	191	585	1	ENST00000222270.7:c.2114C>T	p.Pro705Leu	p.P705L	ENST00000222270	NM_014727.1	705	cCt/cTt	3/37	0.303634801449185	1	FACETS	0.797	0.739	0.857	0.797	0.739	0.857	SUBCLONAL	1	TRUE	0	0.490024282935689	1		586	738	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765671	41765672	+	missense_variant	Missense_Mutation	DNP	GG	GG	TA	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	163	586	1	ENST00000301178.4:c.2547_2548delinsTA	p.Lys849_Asp850delinsAsnAsn	p.K849_D850delinsNN	ENST00000301178	NM_021913.4	849	aaGGat/aaTAat	20/20	0.303634801449185	1	FACETS	0.736	0.678	0.797	0.736	0.678	0.797	SUBCLONAL	1	TRUE	0	0.490024282935689	1		587	682	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25497937	25497937	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	175	403	1	ENST00000264709.3:c.512G>A	p.Arg171Gln	p.R171Q	ENST00000264709	NM_175629.2	171	cGg/cAg	6/23	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.490024282935689	2		404	652	SUCCESS
TMEM127	55654	MSKCC	GRCh37	2	96919762	96919763	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	153	462	2	ENST00000258439.3:c.500_501delinsTT	p.Ser167Phe	p.S167F	ENST00000258439	NM_001193304.2	167	tCC/tTT	4/4	1	2	FACETS	0.914	0.839	0.993	0.914	0.839	0.993	CLONAL	1	TRUE	1	0.490024282935689	2		464	683	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202137382	202137382	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	91	288	0	ENST00000358485.4:c.610G>A	p.Glu204Lys	p.E204K	ENST00000358485	NM_001080125.1	204	Gag/Aag	4/9	1	2	FACETS	0.833	0.743	0.927	0.833	0.743	0.927	CLONAL	1	TRUE	1	0.490024282935689	2		288	446	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212426789	212426789	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	139	318	0	ENST00000342788.4:c.2326G>A	p.Asp776Asn	p.D776N	ENST00000342788	NM_005235.2	776	Gat/Aat	20/28	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.490024282935689	2		318	557	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660482	227660483	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	102	353	0	ENST00000305123.5:c.2972_2973delinsTT	p.Thr991Ile	p.T991I	ENST00000305123	NM_005544.2	991	aCC/aTT	1/2	1	2	FACETS	0.718	0.643	0.796	0.718	0.643	0.796	SUBCLONAL	1	TRUE	1	0.490024282935689	2		353	580	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660999	227660999	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	133	350	0	ENST00000305123.5:c.2456G>A	p.Gly819Glu	p.G819E	ENST00000305123	NM_005544.2	819	gGa/gAa	1/2	1	2	FACETS	0.894	0.815	0.977	0.894	0.815	0.977	CLONAL	1	TRUE	1	0.490024282935689	2		350	607	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41489064	41489064	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	420	139	414	0	ENST00000263253.7:c.56C>G	p.Ser19Ter	p.S19*	ENST00000263253	NM_001429.3	19	tCa/tGa	1/31	0.186421101734756	1	FACETS	0.766	0.701	0.834	0.766	0.701	0.834	INDETERMINATE	1	TRUE	0	0.490024282935689	1		414	559	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566485	41566486	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	80	460	2	ENST00000263253.7:c.4362_4363delinsTT	p.Gln1455Ter	p.Q1455*	ENST00000263253	NM_001429.3	1454	gaCCag/gaTTag	27/31	0.186421101734756	1	FACETS	0.412	0.363	0.465	0.412	0.363	0.465	INDETERMINATE	1	TRUE	0	0.490024282935689	1		462	598	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280636	41280636	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768012106	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	273	453	1	ENST00000349496.5:c.2149C>T	p.Arg717Cys	p.R717C	ENST00000349496	NM_001904.3	717	Cgt/Tgt	15/15	0.439518904998264	2	FACETS	0.864	0.817	0.911	0.864	0.817	0.911	CLONAL	2	TRUE	0	0.490024282935689	2		454	645	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52588805	52588805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	292	504	0	ENST00000394830.3:c.4223C>T	p.Pro1408Leu	p.P1408L	ENST00000394830	NM_018313.4	1408	cCt/cTt	27/30	0.439518904998264	2	FACETS	0.857	0.812	0.903	0.857	0.812	0.903	CLONAL	2	TRUE	0	0.490024282935689	2		504	695	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037150	71037150	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	167	260	0	ENST00000318789.4:c.1141C>T	p.Gln381Ter	p.Q381*	ENST00000318789	NM_032682.5	381	Cag/Tag	14/21	0.172276540271725	5	FACETS	1	0.978	1	0.767	0.71	0.826	INDETERMINATE	2	TRUE	2	0.490024282935689	5		260	514	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259078	89259079	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	167	279	1	ENST00000336596.2:c.222_223delinsAA	p.Met74_Asp75delinsIleAsn	p.M74_D75delinsIN	ENST00000336596	NM_005233.5	74	atGGac/atAAac	3/17	0.172276540271725	5	FACETS	1	0.977	1	0.758	0.701	0.816	INDETERMINATE	2	TRUE	2	0.490024282935689	5		280	520	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807135	1807135	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	208	631	0	ENST00000260795.2:c.1466C>G	p.Ala489Gly	p.A489G	ENST00000260795		489	gCg/gGg	10/17	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.490024282935689	2		631	841	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139861	55139861	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770129304	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	113	311	1	ENST00000257290.5:c.1522G>A	p.Gly508Arg	p.G508R	ENST00000257290	NM_006206.4	508	Gga/Aga	10/23	1	2	FACETS	0.896	0.81	0.986	0.896	0.81	0.986	CLONAL	1	TRUE	1	0.490024282935689	2		312	515	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187530473	187530473	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	71	267	0	ENST00000441802.2:c.10070T>G	p.Val3357Gly	p.V3357G	ENST00000441802	NM_005245.3	3357	gTt/gGt	16/27	1	2	FACETS	0.812	0.713	0.917	0.812	0.713	0.917	CLONAL	1	TRUE	1	0.490024282935689	2		267	357	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80169042	80169043	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	144	501	3	ENST00000265081.6:c.3238_3239delinsAA	p.Gly1080Lys	p.G1080K	ENST00000265081	NM_002439.4	1080	GGa/AAa	23/24	1	2	FACETS	0.829	0.757	0.904	0.829	0.757	0.904	CLONAL	1	TRUE	1	0.490024282935689	2		504	709	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86659171	86659171	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	44	117	0	ENST00000274376.6:c.1460G>A	p.Gly487Glu	p.G487E	ENST00000274376	NM_002890.2	487	gGa/gAa	11/25	1	2	FACETS	0.998	0.849	1	0.998	0.849	1	CLONAL	1	TRUE	1	0.490024282935689	2		117	180	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138197274	138197274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	105	220	0	ENST00000237289.4:c.776C>T	p.Pro259Leu	p.P259L	ENST00000237289	NM_001270507.1	259	cCc/cTc	5/9	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.490024282935689	2		220	410	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202323	138202324	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	149	471	0	ENST00000237289.4:c.2240_2241delinsTT	p.Ala747Val	p.A747V	ENST00000237289	NM_001270507.1	747	gCC/gTT	9/9	1	2	FACETS	0.894	0.819	0.973	0.894	0.819	0.973	CLONAL	1	TRUE	1	0.490024282935689	2		471	680	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508970	106508970	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774900026	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	119	337	0	ENST00000359195.3:c.964G>A	p.Glu322Lys	p.E322K	ENST00000359195	NM_002649.2	322	Gag/Aag	2/11	1	2	FACETS	0.943	0.855	1	0.943	0.855	1	CLONAL	1	TRUE	1	0.490024282935689	2		337	515	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106513383	106513383	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	101	261	0	ENST00000359195.3:c.2287G>A	p.Val763Ile	p.V763I	ENST00000359195	NM_002649.2	763	Gtt/Att	4/11	1	2	FACETS	0.885	0.795	0.979	0.885	0.795	0.979	CLONAL	1	TRUE	1	0.490024282935689	2		261	466	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151874719	151874719	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	116	363	0	ENST00000262189.6:c.7819C>T	p.Pro2607Ser	p.P2607S	ENST00000262189	NM_170606.2	2607	Ccc/Tcc	38/59	1	2	FACETS	0.885	0.801	0.973	0.885	0.801	0.973	CLONAL	1	TRUE	1	0.490024282935689	2		363	535	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271782	38271782	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs876661335	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	311	506	0	ENST00000425967.3:c.2167G>A	p.Glu723Lys	p.E723K	ENST00000425967	NM_001174067.1	723	Gag/Aag	17/19	0.479074063669735	3	FACETS	0.883	0.835	0.931	0.883	0.835	0.931	CLONAL	2	TRUE	1	0.490024282935689	3		506	895	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8499843	8499844	+	splice_region_variant,intron_variant	Splice_Region	DNP	GG	GG	AA	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	104	350	3	ENST00000356435.5:c.2129-4_2129-3delinsTT		p.X710_splice	ENST00000356435		710			1	2	FACETS	0.834	0.75	0.922	0.834	0.75	0.922	CLONAL	1	TRUE	1	0.490024282935689	2		353	509	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500913	8500913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	147	392	0	ENST00000356435.5:c.1969G>A	p.Asp657Asn	p.D657N	ENST00000356435		657	Gac/Aac	13/35	1	2	FACETS	0.932	0.853	1	0.932	0.853	1	CLONAL	1	TRUE	1	0.490024282935689	2		392	644	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8518043	8518043	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	120	355	0	ENST00000356435.5:c.1348G>A	p.Gly450Arg	p.G450R	ENST00000356435		450	Gga/Aga	10/35	1	2	FACETS	1	0.915	1	1	0.915	1	CLONAL	1	TRUE	1	0.490024282935689	2		355	486	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8633459	8633459	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	91	273	0	ENST00000356435.5:c.211-1G>A		p.X71_splice	ENST00000356435		71			1	2	FACETS	0.938	0.838	1	0.938	0.838	1	CLONAL	1	TRUE	1	0.490024282935689	2		273	396	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133750355	133750355	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	211	476	0	ENST00000318560.5:c.1186C>T	p.His396Tyr	p.H396Y	ENST00000318560	NM_005157.4	396	Cat/Tat	7/11	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.490024282935689	2		476	758	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391285	139391286	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	253	747	1	ENST00000277541.6:c.6905_6906delinsAT	p.Thr2302Asn	p.T2302N	ENST00000277541	NM_017617.3	2302	aCC/aAT	34/34	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.490024282935689	2		748	1025	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139418372	139418373	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	210	692	3	ENST00000277541.6:c.199_200delinsTT	p.Pro67Phe	p.P67F	ENST00000277541	NM_017617.3	67	CCc/TTc	3/34	1	2	FACETS	0.921	0.855	0.988	0.921	0.855	0.988	CLONAL	1	TRUE	1	0.490024282935689	2		695	931	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932645	39932645	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	279	343	1	ENST00000378444.4:c.1954C>T	p.Pro652Ser	p.P652S	ENST00000378444	NM_001123385.1	652	Ccc/Tcc	4/15	0.187888624157391	2	FACETS	1	0.982	1			1	INDETERMINATE	2	TRUE	NA	0.490024282935689	2		344	533	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76776282	76776282	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015894-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	226	226	295	0	ENST00000373344.5:c.7184T>G	p.Leu2395Trp	p.L2395W	ENST00000373344	NM_000489.3	2395	tTg/tGg	34/35	0.187888624157391	2	FACETS	1	0.96	1			1	INDETERMINATE	2	TRUE	NA	0.490024282935689	2		295	452	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	171	215	0				ENST00000310581	NM_198253.2	-/1132			0.334780885254364	1	FACETS	0.698	0.647	0.75	0.698	0.647	0.75	INDETERMINATE	1	TRUE	0	0.650843425361538	1		215	508	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18573894	18573894	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759658584	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	72	416	0	ENST00000266497.5:c.2212C>T	p.Arg738Cys	p.R738C	ENST00000266497		738	Cgt/Tgt	15/31	0.334780885254364	1	FACETS	0.356	0.312	0.403	0.356	0.312	0.403	INDETERMINATE	1	TRUE	0	0.650843425361538	1		416	419	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858517	9858517	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs765370528	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	216	595	0	ENST00000330684.3:c.2884G>A	p.Glu962Lys	p.E962K	ENST00000330684	NM_001134407.1	962	Gaa/Aaa	13/13	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.650843425361538	2		595	663	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124437	94124437	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	143	516	2	ENST00000369303.4:c.146C>T	p.Ser49Phe	p.S49F	ENST00000369303	NM_004440.3	49	tCc/tTc	2/17	0.334780885254364	1	FACETS	0.776	0.716	0.838	0.776	0.716	0.838	INDETERMINATE	1	TRUE	0	0.650843425361538	1		518	382	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857436	9857436	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	211	514	0	ENST00000330684.3:c.3965G>A	p.Gly1322Glu	p.G1322E	ENST00000330684	NM_001134407.1	1322	gGa/gAa	13/13	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.650843425361538	2		514	636	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979257	93979257	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	145	499	0	ENST00000369303.4:c.1571G>A	p.Gly524Glu	p.G524E	ENST00000369303	NM_004440.3	524	gGa/gAa	7/17	0.334780885254364	1	FACETS	0.761	0.702	0.821	0.761	0.702	0.821	INDETERMINATE	1	TRUE	0	0.650843425361538	1		499	395	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374293	138374293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	283	606	0	ENST00000289153.2:c.3151G>A	p.Glu1051Lys	p.E1051K	ENST00000289153	NM_006219.2	1051	Gaa/Aaa	22/22	0.334780885254364	1	FACETS	0.843	0.797	0.889	0.843	0.797	0.889	INDETERMINATE	1	TRUE	0	0.650843425361538	1		606	696	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170021	32170021	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1070	162	679	0	ENST00000375023.3:c.3587G>A	p.Gly1196Glu	p.G1196E	ENST00000375023	NM_004557.3	1196	gGa/gAa	21/30	0.309547047684579	3	FACETS	0.536	0.49	0.583	0.179	0.163	0.195	INDETERMINATE	1	TRUE	0	0.650843425361538	3		679	1232	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89498379	89498379	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866959883	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	46	243	0	ENST00000336596.2:c.2351G>A	p.Gly784Glu	p.G784E	ENST00000336596	NM_005233.5	784	gGg/gAg	14/17	0.334780885254364	1	FACETS	0.386	0.328	0.449	0.386	0.328	0.449	INDETERMINATE	1	TRUE	0	0.650843425361538	1		243	247	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256528	115256528	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs121913255	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	247	476	0	ENST00000369535.4:c.183A>C	p.Gln61His	p.Q61H	ENST00000369535	NM_002524.4	61	caA/caC	3/7	1	2	FACETS	0.945	0.887	1	0.945	0.887	1	CLONAL	1	TRUE	1	0.650843425361538	2		476	803	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185146499	185146499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35266179	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	216	512	0	ENST00000265026.3:c.130G>A	p.Glu44Lys	p.E44K	ENST00000265026	NM_004721.4	44	Gag/Aag	2/14	0.334780885254364	1	FACETS	0.79	0.74	0.84	0.79	0.74	0.84	INDETERMINATE	1	TRUE	0	0.650843425361538	1		512	567	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372669	81372669	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs764746019	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	58	273	1	ENST00000222390.5:c.865G>A	p.Ala289Thr	p.A289T	ENST00000222390	NM_000601.4	289	Gct/Act	7/18	0.334780885254364	1	FACETS	0.368	0.318	0.422	0.368	0.318	0.422	INDETERMINATE	1	TRUE	0	0.650843425361538	1		274	327	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43805052	43805052	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs6088	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	297	674	4	ENST00000372470.3:c.502G>A	p.Glu168Lys	p.E168K	ENST00000372470	NM_005373.2	168	Gaa/Aaa	4/12	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.650843425361538	2		678	888	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149440464	149440464	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371692872	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	241	681	1	ENST00000286301.3:c.1930G>A	p.Glu644Lys	p.E644K	ENST00000286301	NM_005211.3	644	Gag/Aag	14/22	0.334780885254364	1	FACETS	0.74	0.695	0.786	0.74	0.695	0.786	INDETERMINATE	1	TRUE	0	0.650843425361538	1		682	675	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939191	36939191	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	273	668	0	ENST00000361632.4:c.518C>T	p.Ser173Phe	p.S173F	ENST00000361632		173	tCc/tTc	5/16	1	2	FACETS	0.99	0.932	1	0.99	0.932	1	CLONAL	1	TRUE	1	0.650843425361538	2		668	847	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948777	71948778	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	286	783	3	ENST00000298229.2:c.3489_3490delinsTT	p.Arg1164Trp	p.R1164W	ENST00000298229	NM_001567.3	1163	ggCCgg/ggTTgg	26/28	0.334780885254364	1	FACETS	0.789	0.746	0.833	0.789	0.746	0.833	INDETERMINATE	1	TRUE	0	0.650843425361538	1		786	751	SUCCESS
ATM	472	MSKCC	GRCh37	11	108117818	108117818	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	97	537	1	ENST00000278616.4:c.1029A>T	p.Glu343Asp	p.E343D	ENST00000278616	NM_000051.3	343	gaA/gaT	8/63	0.334780885254364	1	FACETS	0.448	0.401	0.497	0.448	0.401	0.497	INDETERMINATE	1	TRUE	0	0.650843425361538	1		538	449	SUCCESS
ATM	472	MSKCC	GRCh37	11	108151894	108151894	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	52	345	0	ENST00000278616.4:c.3575A>C	p.Lys1192Thr	p.K1192T	ENST00000278616	NM_000051.3	1192	aAg/aCg	24/63	0.334780885254364	1	FACETS	0.374	0.321	0.432	0.374	0.321	0.432	INDETERMINATE	1	TRUE	0	0.650843425361538	1		345	288	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444933	49444933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746841307	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	242	616	1	ENST00000301067.7:c.2533C>T	p.Arg845Trp	p.R845W	ENST00000301067	NM_003482.3	845	Cgg/Tgg	10/54	0.334780885254364	1	FACETS	0.799	0.751	0.847	0.799	0.751	0.847	INDETERMINATE	1	TRUE	0	0.650843425361538	1		617	628	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495418	56495419	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	140	692	2	ENST00000267101.3:c.3608_3609delinsAA	p.Arg1203Lys	p.R1203K	ENST00000267101	NM_001982.3	1203	aGG/aAA	28/28	0.334780885254364	1	FACETS	0.423	0.386	0.462	0.423	0.386	0.462	INDETERMINATE	1	TRUE	0	0.650843425361538	1		694	686	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437349	110437350	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	TA	novel	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	92	150	2	ENST00000375856.3:c.1051_1052delinsTA	p.Pro351Ter	p.P351*	ENST00000375856	NM_003749.2	351	CCg/TAg	1/2	0.322510152650108	3	FACETS	1	0.981	1	0.718	0.648	0.79	INDETERMINATE	1	TRUE	1	0.650843425361538	3		152	261	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989144	41989144	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	222	590	1	ENST00000219905.7:c.1936C>T	p.Pro646Ser	p.P646S	ENST00000219905	NM_001164273.1	646	Cct/Tct	3/24	0.334780885254364	1	FACETS	0.749	0.702	0.798	0.749	0.702	0.798	INDETERMINATE	1	TRUE	0	0.650843425361538	1		591	614	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003311	42003311	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	232	601	0	ENST00000219905.7:c.2848C>T	p.Gln950Ter	p.Q950*	ENST00000219905	NM_001164273.1	950	Cag/Tag	8/24	0.334780885254364	1	FACETS	0.747	0.701	0.794	0.747	0.701	0.794	INDETERMINATE	1	TRUE	0	0.650843425361538	1		601	644	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828995	72828995	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	287	724	0	ENST00000268489.5:c.7586C>G	p.Pro2529Arg	p.P2529R	ENST00000268489	NM_006885.3	2529	cCc/cGc	9/10	1	2	FACETS	0.964	0.908	1	0.964	0.908	1	CLONAL	1	TRUE	1	0.650843425361538	2		724	915	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37649074	37649074	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	112	553	0	ENST00000447079.4:c.2179T>C	p.Phe727Leu	p.F727L	ENST00000447079	NM_015083.1	727	Ttt/Ctt	4/14	0.334780885254364	1	FACETS	0.381	0.343	0.421	0.381	0.343	0.421	INDETERMINATE	1	TRUE	0	0.650843425361538	1		553	609	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231358	5231359	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	262	641	1	ENST00000357368.4:c.2117_2118delinsTT	p.Pro706Leu	p.P706L	ENST00000357368	NM_002850.3	706	cCC/cTT	14/38	1	2	FACETS	0.985	0.927	1	0.985	0.927	1	CLONAL	1	TRUE	1	0.650843425361538	2		642	817	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31019202	31019202	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	248	600	0	ENST00000375687.4:c.797C>T	p.Ala266Val	p.A266V	ENST00000375687	NM_015338.5	266	gCc/gTc	9/13	1	2	FACETS	0.981	0.92	1	0.981	0.92	1	CLONAL	1	TRUE	1	0.650843425361538	2		600	777	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713891	30713891	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	103	526	0	ENST00000295754.5:c.1216C>T	p.Pro406Ser	p.P406S	ENST00000295754	NM_003242.5	406	Cct/Tct	4/7	0.334780885254364	1	FACETS	0.38	0.341	0.421	0.38	0.341	0.421	INDETERMINATE	1	TRUE	0	0.650843425361538	1		526	562	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259233	89259233	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	97	450	0	ENST00000336596.2:c.377A>T	p.Glu126Val	p.E126V	ENST00000336596	NM_005233.5	126	gAg/gTg	3/17	0.334780885254364	1	FACETS	0.459	0.411	0.509	0.459	0.411	0.509	INDETERMINATE	1	TRUE	0	0.650843425361538	1		450	438	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134968279	134968279	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	141	606	1	ENST00000398015.3:c.2792G>A	p.Ser931Asn	p.S931N	ENST00000398015	NM_004441.4	931	aGc/aAc	15/16	0.334780885254364	1	FACETS	0.406	0.37	0.443	0.406	0.37	0.443	INDETERMINATE	1	TRUE	0	0.650843425361538	1		607	720	SUCCESS
ATR	545	MSKCC	GRCh37	3	142268354	142268354	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	297	53	437	0	ENST00000350721.4:c.3138del	p.Asp1047MetfsTer3	p.D1047Mfs*3	ENST00000350721	NM_001184.3	1046	aaA/aa	15/47	0.334780885254364	1	FACETS	0.314	0.269	0.363	0.314	0.269	0.363	INDETERMINATE	1	TRUE	0	0.650843425361538	1		437	350	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587139	189587139	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	107	525	0	ENST00000264731.3:c.1156C>T	p.Gln386Ter	p.Q386*	ENST00000264731	NM_003722.4	386	Cag/Tag	9/14	0.334780885254364	1	FACETS	0.414	0.372	0.458	0.414	0.372	0.458	INDETERMINATE	1	TRUE	0	0.650843425361538	1		525	536	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55598145	55598146	+	missense_variant	Missense_Mutation	DNP	CT	CT	TA	novel	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	156	485	0	ENST00000288135.5:c.2342_2343delinsTA	p.Ala781Val	p.A781V	ENST00000288135	NM_000222.2	781	gCT/gTA	16/21	0.334780885254364	1	FACETS	0.701	0.648	0.756	0.701	0.648	0.756	INDETERMINATE	1	TRUE	0	0.650843425361538	1		485	461	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153258970	153258970	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	72	279	0	ENST00000281708.4:c.845C>T	p.Ser282Leu	p.S282L	ENST00000281708	NM_033632.3	282	tCa/tTa	5/12	0.334780885254364	1	FACETS	0.672	0.597	0.751	0.672	0.597	0.751	INDETERMINATE	1	TRUE	0	0.650843425361538	1		279	222	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867441	35867441	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	62	417	0	ENST00000303115.3:c.255C>G	p.Phe85Leu	p.F85L	ENST00000303115	NM_002185.3	85	ttC/ttG	3/8	0.334780885254364	1	FACETS	0.374	0.324	0.426	0.374	0.324	0.426	INDETERMINATE	1	TRUE	0	0.650843425361538	1		417	344	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57753370	57753370	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	75	465	0	ENST00000274289.3:c.754C>T	p.Leu252Phe	p.L252F	ENST00000274289	NM_006622.3	252	Ctc/Ttc	6/14	0.334780885254364	1	FACETS	0.319	0.28	0.36	0.319	0.28	0.36	INDETERMINATE	1	TRUE	0	0.650843425361538	1		465	488	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176721024	176721024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	391	89	445	0	ENST00000439151.2:c.6655C>T	p.Arg2219Cys	p.R2219C	ENST00000439151	NM_022455.4	2219	Cgt/Tgt	23/23	0.334780885254364	1	FACETS	0.384	0.342	0.429	0.384	0.342	0.429	INDETERMINATE	1	TRUE	0	0.650843425361538	1		445	480	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31946722	31946722	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	281	672	0	ENST00000375333.2:c.610G>A	p.Gly204Ser	p.G204S	ENST00000375333	NM_032454.1	204	Ggc/Agc	4/8	0.309547047684579	3	FACETS	1	0.983	1	0.373	0.35	0.396	INDETERMINATE	1	TRUE	0	0.650843425361538	3		672	1023	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798412	32798412	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	295	630	2	ENST00000374899.4:c.1444G>A	p.Asp482Asn	p.D482N	ENST00000374899	NM_018833.2	482	Gac/Aac	8/12	0.309547047684579	3	FACETS	1	0.992	1	0.432	0.407	0.457	INDETERMINATE	1	TRUE	0	0.650843425361538	3		632	927	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662624	117662624	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755766404	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	198	542	0	ENST00000368508.3:c.4841C>T	p.Pro1614Leu	p.P1614L	ENST00000368508	NM_002944.2	1614	cCa/cTa	29/43	0.650843425361538	1	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	0	0.650843425361538	1		542	396	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81332037	81332037	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	139	412	1	ENST00000222390.5:c.2047A>G	p.Lys683Glu	p.K683E	ENST00000222390	NM_000601.4	683	Aaa/Gaa	18/18	0.334780885254364	1	FACETS	0.785	0.724	0.848	0.785	0.724	0.848	INDETERMINATE	1	TRUE	0	0.650843425361538	1		413	367	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140500166	140500166	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs775040765	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	195	836	0	ENST00000288602.6:c.976A>G	p.Ile326Val	p.I326V	ENST00000288602	NM_004333.4	326	Att/Gtt	7/18	0.340724978443968	2	FACETS	0.536	0.496	0.579	0.268	0.248	0.29	INDETERMINATE	1	TRUE	0	0.650843425361538	2		836	1117	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845196	151845196	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	216	518	0	ENST00000262189.6:c.13816G>A	p.Asp4606Asn	p.D4606N	ENST00000262189	NM_170606.2	4606	Gat/Aat	52/59	0.340724978443968	2	FACETS	0.963	0.9	1	0.482	0.45	0.515	INDETERMINATE	1	TRUE	0	0.650843425361538	2		518	689	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69032438	69032438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866494601	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	175	678	1	ENST00000288368.4:c.3512C>T	p.Ser1171Leu	p.S1171L	ENST00000288368	NM_024870.2	1171	tCa/tTa	29/40	0.391173998852018	1	FACETS	0.707	0.656	0.759	0.707	0.656	0.759	SUBCLONAL	1	TRUE	0	0.650843425361538	1		679	513	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971187	21971194	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGCTGC	GGCGCTGC	-	novel	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	191	438	0	ENST00000304494.5:c.164_171del	p.Gly55AlafsTer62	p.G55Afs*62	ENST00000304494	NM_000077.4	55	gGCAGCGCC/g	2/3	0.650843425361538	1	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	0	0.650843425361538	1		438	395	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93636502	93636502	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199612745	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	124	465	0	ENST00000375746.1:c.932G>A	p.Gly311Glu	p.G311E	ENST00000375746	NM_001174167.1	311	gGg/gAg	8/14	0.391173998852018	1	FACETS	0.507	0.461	0.555	0.507	0.461	0.555	SUBCLONAL	1	TRUE	0	0.650843425361538	1		465	507	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249666	110249666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140990946	NA	P-0015917-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	162	903	1	ENST00000374672.4:c.1009C>T	p.Pro337Ser	p.P337S	ENST00000374672	NM_004235.4	337	Cct/Tct	3/5	0.391173998852018	1	FACETS	0.394	0.362	0.428	0.394	0.362	0.428	SUBCLONAL	1	TRUE	0	0.650843425361538	1		904	852	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	345	215	0				ENST00000310581	NM_198253.2	-/1132			0.438916040331254	6	FACETS	0.987	0.936	1			1	CLONAL	3	TRUE	NA	0.438916040331254	6		215	997	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971108	21971108	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552822	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	163	188	2	ENST00000304494.5:c.250G>A	p.Asp84Asn	p.D84N	ENST00000304494	NM_000077.4	84	Gac/Aac	2/3	0.438916040331254	1	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	0	0.438916040331254	1		190	461	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560947	9560947	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	92	340	0	ENST00000353224.5:c.835C>A	p.Gln279Lys	p.Q279K	ENST00000353224	NM_177990.2	279	Cag/Aag	4/10	0.405642567441471	4	FACETS	0.995	0.886	1	0.498	0.443	0.556	CLONAL	1	TRUE	2	0.438916040331254	4		340	606	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56480320	56480320	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	136	341	0	ENST00000267101.3:c.427C>A	p.Leu143Met	p.L143M	ENST00000267101	NM_001982.3	143	Ctg/Atg	4/28	0.272231241008483	5	FACETS	1	0.983	1	0.451	0.411	0.494	CLONAL	1	TRUE	2	0.438916040331254	5		341	759	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577506	7577506	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	292	473	0	ENST00000269305.4:c.775G>C	p.Asp259His	p.D259H	ENST00000269305	NM_001126112.2	259	Gac/Cac	7/11	0.438916040331254	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	2	TRUE	0	0.438916040331254	2		473	606	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2120523	2120523	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs45517199	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	417	734	1	ENST00000219476.3:c.1783C>T	p.Gln595Ter	p.Q595*	ENST00000219476	NM_000548.3	595	Cag/Tag	17/42	NA	2	FACETS	1	0.986	1			1	INDETERMINATE	2	TRUE	NA	0.438916040331254	2		735	892	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1807335	1807335	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1448843898	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	329	740	0	ENST00000260795.2:c.1584G>A	p.Met528Ile	p.M528I	ENST00000260795		528	atG/atA	11/17	0.318724354645223	3	FACETS	0.924	0.875	0.974			1	CLONAL	2	TRUE	NA	0.438916040331254	3		740	989	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397710	49397710	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	182	574	1	ENST00000418115.1:c.514G>A	p.Glu172Lys	p.E172K	ENST00000418115	NM_001664.2	172	Gaa/Aaa	5/5	0.280425467818213	3	FACETS	1	0.937	1	0.509	0.469	0.55	CLONAL	1	TRUE	1	0.438916040331254	3		575	994	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61721082	61721082	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	626	424	0	ENST00000401558.2:c.1192C>G	p.Gln398Glu	p.Q398E	ENST00000401558	NM_003400.3	398	Caa/Gaa	12/25	0.438916040331254	9	FACETS	1	0.992	1			1	CLONAL	4	TRUE	NA	0.438916040331254	9		424	1647	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52722950	52722950	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	144	453	0	ENST00000322088.6:c.1135G>C	p.Glu379Gln	p.E379Q	ENST00000322088	NM_014225.5	379	Gag/Cag	10/15	0.223388782774227	3	FACETS	1	0.951	1			1	INDETERMINATE	1	TRUE	NA	0.438916040331254	3		453	755	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004922	150004922	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	59	372	0	ENST00000253339.5:c.1303C>G	p.Gln435Glu	p.Q435E	ENST00000253339		435	Cag/Gag	3/7	0.244859801294874	1	FACETS	0.458	0.395	0.527	0.458	0.395	0.527	INDETERMINATE	1	TRUE	0	0.438916040331254	1		372	458	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16235913	16235913	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	139	443	0	ENST00000375759.3:c.979G>C	p.Glu327Gln	p.E327Q	ENST00000375759	NM_015001.2	327	Gaa/Caa	4/15	0.354997764889203	2	FACETS	0.845	0.77	0.923	0.422	0.385	0.462	CLONAL	1	TRUE	0	0.438916040331254	2		443	750	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437694	49437694	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	281	688	0	ENST00000301067.7:c.5276G>C	p.Arg1759Pro	p.R1759P	ENST00000301067	NM_003482.3	1759	cGc/cCc	22/54	0.272231241008483	5	FACETS	0.914	0.859	0.972	0.61	0.572	0.648	CLONAL	2	TRUE	2	0.438916040331254	5		688	1161	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121426823	121426823	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1041132609	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	51	441	0	ENST00000257555.6:c.514G>C	p.Glu172Gln	p.E172Q	ENST00000257555		172	Gag/Cag	2/10	0.214397163079111	3	FACETS	0.402	0.341	0.469	0.134	0.113	0.157	INDETERMINATE	1	TRUE	0	0.438916040331254	3		441	705	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81558955	81558955	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	117	380	1	ENST00000298171.2:c.545+3G>A		p.X182_splice	ENST00000298171	NM_000369.2	182			1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.438916040331254	2		381	524	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42054409	42054409	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	63	420	0	ENST00000219905.7:c.7593G>C	p.Lys2531Asn	p.K2531N	ENST00000219905	NM_001164273.1	2531	aaG/aaC	22/24	0.240929635947327	2	FACETS	0.494	0.427	0.567	0.247	0.213	0.284	INDETERMINATE	1	TRUE	0	0.438916040331254	2		420	581	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2124305	2124305	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	358	718	0	ENST00000219476.3:c.2460C>G	p.Ile820Met	p.I820M	ENST00000219476	NM_000548.3	820	atC/atG	22/42	NA	2	FACETS	0.958	0.913	1			1	INDETERMINATE	2	TRUE	NA	0.438916040331254	2		718	851	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2130277	2130277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs45517296	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	400	628	0	ENST00000219476.3:c.3509C>T	p.Ser1170Leu	p.S1170L	ENST00000219476	NM_000548.3	1170	tCa/tTa	30/42	NA	2	FACETS	1	0.977	1			1	INDETERMINATE	2	TRUE	NA	0.438916040331254	2		628	883	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646399	23646399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs878855101	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	65	512	0	ENST00000261584.4:c.1468C>T	p.Pro490Ser	p.P490S	ENST00000261584	NM_024675.3	490	Ccc/Tcc	4/13	0.318724354645223	3	FACETS	0.494	0.428	0.566			1	SUBCLONAL	1	TRUE	NA	0.438916040331254	3		512	731	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646419	23646419	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057520736	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	64	533	1	ENST00000261584.4:c.1448C>T	p.Ser483Leu	p.S483L	ENST00000261584	NM_024675.3	483	tCa/tTa	4/13	0.318724354645223	3	FACETS	0.491	0.425	0.564			1	SUBCLONAL	1	TRUE	NA	0.438916040331254	3		534	724	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991329	72991329	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs143561313	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	58	416	0	ENST00000268489.5:c.2716C>G	p.Leu906Val	p.L906V	ENST00000268489	NM_006885.3	906	Cta/Gta	2/10	0.280425467818213	3	FACETS	0.468	0.401	0.541	0.234	0.2	0.271	SUBCLONAL	1	TRUE	1	0.438916040331254	3		416	689	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89348371	89348371	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs777979146	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	617	634	3	ENST00000301030.4:c.4579G>A	p.Asp1527Asn	p.D1527N	ENST00000301030	NM_001256183.1	1527	Gat/Aat	9/13	0.438916040331254	5	FACETS	1	0.993	1			1	CLONAL	3	TRUE	NA	0.438916040331254	5		637	1391	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12016580	12016580	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	218	350	0	ENST00000353533.5:c.716G>C	p.Arg239Thr	p.R239T	ENST00000353533	NM_003010.3	239	aGa/aCa	7/11	0.438916040331254	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	2	TRUE	0	0.438916040331254	2		350	472	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244746	41244746	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	80	588	0	ENST00000357654.3:c.2802G>C	p.Gln934His	p.Q934H	ENST00000357654	NM_007294.3	934	caG/caC	10/23	0.284836121973618	3	FACETS	0.486	0.427	0.55	0.243	0.213	0.275	SUBCLONAL	1	TRUE	1	0.438916040331254	3		588	915	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58725336	58725336	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	244	498	0	ENST00000305921.3:c.910C>T	p.Gln304Ter	p.Q304*	ENST00000305921	NM_003620.3	304	Cag/Tag	4/6	0.284836121973618	3	FACETS	0.875	0.82	0.93	0.875	0.82	0.93	CLONAL	2	TRUE	1	0.438916040331254	3		498	775	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732993	74732993	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	174	381	0	ENST00000359995.5:c.250G>T	p.Glu84Ter	p.E84*	ENST00000359995	NM_001195427.1	84	Gag/Tag	1/3	0.284836121973618	3	FACETS	0.835	0.773	0.899	0.835	0.773	0.899	CLONAL	2	TRUE	1	0.438916040331254	3		381	579	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2207606	2207606	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754413497	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	166	565	1	ENST00000398665.3:c.890C>T	p.Ser297Leu	p.S297L	ENST00000398665	NM_032482.2	297	tCg/tTg	11/28	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.438916040331254	2		566	736	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152004	11152004	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	145	478	0	ENST00000358026.2:c.4288G>A	p.Glu1430Lys	p.E1430K	ENST00000358026	NM_001128849.1	1430	Gag/Aag	31/36	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.438916040331254	2		478	615	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11152030	11152030	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	165	517	0	ENST00000358026.2:c.4314G>C	p.Gln1438His	p.Q1438H	ENST00000358026	NM_001128849.1	1438	caG/caC	31/36	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.438916040331254	2		517	695	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61753572	61753572	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	484	435	0	ENST00000401558.2:c.211C>T	p.Gln71Ter	p.Q71*	ENST00000401558	NM_003400.3	71	Cag/Tag	3/25	0.438916040331254	9	FACETS	0.945	0.903	0.987			1	CLONAL	4	TRUE	NA	0.438916040331254	9		435	1480	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209104608	209104609	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	122	448	1	ENST00000345146.2:c.969_970delinsAA	p.Glu324Lys	p.E324K	ENST00000345146	NM_005896.2	323	caGGag/caAAag	8/10	0.223388782774227	3	FACETS	0.862	0.78	0.95			1	INDETERMINATE	1	TRUE	NA	0.438916040331254	3		449	786	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024332	31024332	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778060	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	264	461	0	ENST00000375687.4:c.3817C>T	p.Arg1273Cys	p.R1273C	ENST00000375687	NM_015338.5	1273	Cgt/Tgt	13/13	0.405642567441471	4	FACETS	0.955	0.897	1	0.955	0.897	1	CLONAL	2	TRUE	2	0.438916040331254	4		461	906	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164885	36164885	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	156	595	0	ENST00000300305.3:c.990C>A	p.Phe330Leu	p.F330L	ENST00000300305		330	ttC/ttA	8/8	0.438389586342927	3	FACETS	0.942	0.863	1	0.471	0.431	0.513	CLONAL	1	TRUE	1	0.438916040331254	3		595	920	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41560083	41560083	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	118	405	0	ENST00000263253.7:c.3755G>C	p.Arg1252Thr	p.R1252T	ENST00000263253	NM_001429.3	1252	aGa/aCa	22/31	0.244859801294874	1	FACETS	0.841	0.763	0.923	0.841	0.763	0.923	INDETERMINATE	1	TRUE	0	0.438916040331254	1		405	499	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10183655	10183655	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	161	650	0	ENST00000256474.2:c.124G>C	p.Glu42Gln	p.E42Q	ENST00000256474	NM_000551.3	42	Gag/Cag	1/3	0.280425467818213	3	FACETS	1	0.928	1	0.506	0.464	0.55	CLONAL	1	TRUE	1	0.438916040331254	3		650	884	SUCCESS
ATR	545	MSKCC	GRCh37	3	142185282	142185282	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	270	446	0	ENST00000350721.4:c.6781C>A	p.Pro2261Thr	p.P2261T	ENST00000350721	NM_001184.3	2261	Cct/Act	40/47	0.405642567441471	4	FACETS	0.959	0.901	1	0.959	0.901	1	CLONAL	2	TRUE	2	0.438916040331254	4		446	923	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170016856	170016856	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	165	502	0	ENST00000295797.4:c.1661C>G	p.Ser554Cys	p.S554C	ENST00000295797	NM_002740.5	554	tCt/tGt	17/18	0.438389586342927	3	FACETS	0.986	0.905	1	0.493	0.452	0.535	CLONAL	1	TRUE	1	0.438916040331254	3		502	930	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178947127	178947127	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	87	362	0	ENST00000263967.3:c.2563C>T	p.His855Tyr	p.H855Y	ENST00000263967	NM_006218.2	855	Cac/Tac	18/21	0.438389586342927	3	FACETS	0.781	0.692	0.876	0.39	0.346	0.438	SUBCLONAL	1	TRUE	1	0.438916040331254	3		362	619	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539822	187539822	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	127	349	0	ENST00000441802.2:c.7918G>A	p.Glu2640Lys	p.E2640K	ENST00000441802	NM_005245.3	2640	Gaa/Aaa	10/27	NA	2	FACETS	1	0.97	1			1	INDETERMINATE	1	TRUE	NA	0.438916040331254	2		349	503	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045858	26045858	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs774188493	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	291	312	0	ENST00000540144.1:c.220G>T	p.Glu74Ter	p.E74*	ENST00000540144	NM_003531.2	74	Gaa/Taa	1/1	0.438916040331254	6	FACETS	0.944	0.891	0.999	0.708	0.668	0.749	CLONAL	3	TRUE	2	0.438916040331254	6		312	879	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94067976	94067976	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	25	267	0	ENST00000369303.4:c.986C>T	p.Thr329Ile	p.T329I	ENST00000369303	NM_004440.3	329	aCa/aTa	4/17	0.244859801294874	1	FACETS	0.313	0.247	0.389	0.313	0.247	0.389	INDETERMINATE	1	TRUE	0	0.438916040331254	1		267	284	SUCCESS
ESR1	2099	MSKCC	GRCh37	6	152419954	152419954	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	67	450	0	ENST00000206249.3:c.1641C>A	p.His547Gln	p.H547Q	ENST00000206249	NM_000125.3	547	caC/caA	8/8	0.244859801294874	1	FACETS	0.425	0.369	0.485	0.425	0.369	0.485	INDETERMINATE	1	TRUE	0	0.438916040331254	1		450	561	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884514	151884514	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	52	425	0	ENST00000262189.6:c.4841C>G	p.Ser1614Cys	p.S1614C	ENST00000262189	NM_170606.2	1614	tCt/tGt	33/59	0.403560447586046	2	FACETS	0.452	0.385	0.526	0.226	0.192	0.263	SUBCLONAL	1	TRUE	0	0.438916040331254	2		425	524	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370951	55370951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	356	649	0	ENST00000297316.4:c.253C>T	p.Arg85Trp	p.R85W	ENST00000297316	NM_022454.3	85	Cgg/Tgg	1/2	0.438389586342927	3	FACETS	0.953	0.905	1	0.953	0.905	1	CLONAL	2	TRUE	1	0.438916040331254	3		649	1038	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69136801	69136801	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	127	421	0	ENST00000288368.4:c.4715G>C	p.Arg1572Thr	p.R1572T	ENST00000288368	NM_024870.2	1572	aGa/aCa	39/40	0.438389586342927	3	FACETS	1	0.926	1	0.511	0.464	0.561	CLONAL	1	TRUE	1	0.438916040331254	3		421	690	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97873849	97873849	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	152	687	0	ENST00000289081.3:c.1225G>C	p.Glu409Gln	p.E409Q	ENST00000289081	NM_000136.2	409	Gag/Cag	13/15	0.438916040331254	2	FACETS	0.776	0.71	0.846	0.388	0.355	0.423	SUBCLONAL	1	TRUE	0	0.438916040331254	2		687	892	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179180	123179180	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015920-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	124	211	0	ENST00000218089.9:c.629C>T	p.Ser210Leu	p.S210L	ENST00000218089	NM_001042749.1	210	tCa/tTa	8/35	1	1	FACETS	0.758	0.697	0.819	1	0.988	1	SUBCLONAL	2	TRUE	0	0.438916040331254	1		211	291	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	98	215	0				ENST00000310581	NM_198253.2	-/1132			0.377233835789085	3	FACETS	0.96	0.867	1	0.96	0.867	1	CLONAL	2	TRUE	1	0.383605583654354	3		215	317	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971036	21971036	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913381	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	151	441	0	ENST00000304494.5:c.322G>A	p.Asp108Asn	p.D108N	ENST00000304494	NM_000077.4	108	Gat/Aat	2/3	0.334258144101339	2	FACETS	1	0.927	1	1	0.927	1	CLONAL	2	TRUE	0	0.383605583654354	2		441	393	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578275	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866380588	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	162	597	0	ENST00000269305.4:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000269305	NM_001126112.2	192	Cag/Tag	6/11	0.334258144101339	2	FACETS	0.882	0.816	0.949	0.882	0.816	0.949	CLONAL	2	TRUE	0	0.383605583654354	2		597	479	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37619289	37619289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	164	293	0	ENST00000447079.4:c.965G>A	p.Arg322Gln	p.R322Q	ENST00000447079	NM_015083.1	322	cGa/cAa	1/14	0.383605583654354	6	FACETS	1	0.983	1			1	CLONAL	2	TRUE	NA	0.383605583654354	6		293	614	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872380	45872380	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	108	680	1	ENST00000391945.4:c.131C>T	p.Ser44Leu	p.S44L	ENST00000391945	NM_000400.3	44	tCa/tTa	3/23	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.383605583654354	2		681	537	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178098960	178098960	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1057519920	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	62	233	0	ENST00000397062.3:c.85G>C	p.Asp29His	p.D29H	ENST00000397062	NM_006164.4	29	Gat/Cat	2/5	0.383605583654354	3	FACETS	0.928	0.805	1	0.309	0.268	0.354	CLONAL	1	TRUE	0	0.383605583654354	3		233	415	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37681036	37681036	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	83	424	0	ENST00000447079.4:c.3205G>C	p.Glu1069Gln	p.E1069Q	ENST00000447079	NM_015083.1	1069	Gaa/Caa	12/14	0.383605583654354	6	FACETS	0.902	0.795	1			1	CLONAL	1	TRUE	NA	0.383605583654354	6		424	848	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134920499	134920499	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	76	447	0	ENST00000398015.3:c.2314G>A	p.Asp772Asn	p.D772N	ENST00000398015	NM_004441.4	772	Gac/Aac	12/16	0.383605583654354	5	FACETS	0.845	0.74	0.957	0.282	0.246	0.319	CLONAL	1	TRUE	2	0.383605583654354	5		447	739	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237593	16237593	+	splice_region_variant,intron_variant	Splice_Region	SNP	T	T	C	novel	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	54	237	0	ENST00000375759.3:c.1043-3T>C		p.X348_splice	ENST00000375759	NM_015001.2	348			0.383605583654354	1	FACETS	0.903	0.779	1	0.903	0.779	1	CLONAL	1	TRUE	0	0.383605583654354	1		237	252	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27093043	27093043	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	52	355	1	ENST00000324856.7:c.2974G>A	p.Glu992Lys	p.E992K	ENST00000324856	NM_006015.4	992	Gaa/Aaa	10/20	1	2	FACETS	0.786	0.672	0.909	0.786	0.672	0.909	CLONAL	1	TRUE	1	0.383605583654354	2		356	345	SUCCESS
MCL1	4170	MSKCC	GRCh37	1	150551448	150551448	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	260	602	0	ENST00000369026.2:c.559C>T	p.Arg187Trp	p.R187W	ENST00000369026	NM_021960.4	187	Cgg/Tgg	1/3	0.344345120865204	3	FACETS	0.842	0.79	0.896	0.842	0.79	0.896	CLONAL	2	TRUE	1	0.383605583654354	3		602	959	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70405049	70405049	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	85	513	0	ENST00000373644.4:c.2563C>T	p.Gln855Ter	p.Q855*	ENST00000373644	NM_030625.2	855	Caa/Taa	4/12	0.334258144101339	2	FACETS	0.767	0.679	0.861	0.383	0.339	0.431	SUBCLONAL	1	TRUE	0	0.383605583654354	2		513	578	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589577	69589577	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	40	281	0	ENST00000168712.1:c.276C>G	p.Ile92Met	p.I92M	ENST00000168712	NM_002007.2	92	atC/atG	1/3	0.235965043820104	3	FACETS	0.642	0.534	0.762			1	SUBCLONAL	1	TRUE	NA	0.383605583654354	3		281	387	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376505	118376505	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	49	338	0	ENST00000534358.1:c.9898G>A	p.Glu3300Lys	p.E3300K	ENST00000534358	NM_005933.3	3300	Gaa/Aaa	27/36	0.383605583654354	3	FACETS	0.805	0.684	0.938	0.268	0.228	0.313	CLONAL	1	TRUE	0	0.383605583654354	3		338	378	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49421012	49421012	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	151	417	0	ENST00000301067.7:c.14737G>A	p.Glu4913Lys	p.E4913K	ENST00000301067	NM_003482.3	4913	Gaa/Aaa	48/54	0.304991432752238	5	FACETS	1	0.971	1			1	CLONAL	2	TRUE	NA	0.383605583654354	5		417	553	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427974	49427974	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	180	703	1	ENST00000301067.7:c.10616G>A	p.Arg3539Gln	p.R3539Q	ENST00000301067	NM_003482.3	3539	cGg/cAg	38/54	0.304991432752238	5	FACETS	1	0.976	1			1	CLONAL	2	TRUE	NA	0.383605583654354	5		704	655	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35871269	35871269	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	rs1458968522	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	85	398	2	ENST00000216797.5:c.907-3C>T		p.X303_splice	ENST00000216797	NM_020529.2	303			0.290128535063359	3	FACETS	0.984	0.872	1	0.328	0.29	0.368	CLONAL	1	TRUE	0	0.383605583654354	3		400	537	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50818362	50818362	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs773205473	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	109	307	0	ENST00000398568.2:c.1940T>C	p.Ile647Thr	p.I647T	ENST00000398568	NM_001042412.1	647	aTa/aCa	11/18	0.377233835789085	3	FACETS	0.806	0.729	0.887	0.806	0.729	0.887	CLONAL	2	TRUE	1	0.383605583654354	3		307	420	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216980	7216980	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	152	421	0	ENST00000380728.2:c.541C>T	p.Gln181Ter	p.Q181*	ENST00000380728		181	Caa/Taa	7/11	0.334258144101339	2	FACETS	0.901	0.831	0.971	0.901	0.831	0.971	CLONAL	2	TRUE	0	0.383605583654354	2		421	440	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15965470	15965470	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs373678242	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	136	381	0	ENST00000268712.3:c.5336A>G	p.Asn1779Ser	p.N1779S	ENST00000268712	NM_006311.3	1779	aAt/aGt	36/46	0.334258144101339	2	FACETS	0.875	0.804	0.949	0.875	0.804	0.949	CLONAL	2	TRUE	0	0.383605583654354	2		381	405	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16049835	16049835	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	55	263	0	ENST00000268712.3:c.937C>T	p.Gln313Ter	p.Q313*	ENST00000268712	NM_006311.3	313	Cag/Tag	10/46	0.334258144101339	2	FACETS	0.905	0.779	1	0.452	0.389	0.521	CLONAL	1	TRUE	0	0.383605583654354	2		263	317	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320962	30320962	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs372771855	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	259	540	0	ENST00000322652.5:c.1372C>T	p.Arg458Cys	p.R458C	ENST00000322652	NM_015355.2	458	Cgc/Tgc	12/16	0.383605583654354	6	FACETS	1	0.986	1			1	CLONAL	2	TRUE	NA	0.383605583654354	6		540	1018	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121269	29121269	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1555927222	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	239	630	1	ENST00000328354.6:c.406T>C	p.Tyr136His	p.Y136H	ENST00000328354	NM_007194.3	136	Tac/Cac	3/15	0.320966861279926	2	FACETS	0.953	0.895	1	0.953	0.895	1	CLONAL	2	TRUE	0	0.383605583654354	2		631	654	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12447507	12447507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	196	406	1	ENST00000287820.6:c.746C>T	p.Ser249Leu	p.S249L	ENST00000287820	NM_015869.4	249	tCa/tTa	5/7	0.150206655939225	5	FACETS	1	0.986	1	0.819	0.762	0.878	INDETERMINATE	2	TRUE	2	0.383605583654354	5		407	655	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187557948	187557948	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	74	341	0	ENST00000441802.2:c.3763C>A	p.Pro1255Thr	p.P1255T	ENST00000441802	NM_005245.3	1255	Cct/Act	5/27	1	2	FACETS	0.8	0.703	0.905	0.8	0.703	0.905	CLONAL	1	TRUE	1	0.383605583654354	2		341	482	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56179468	56179468	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	46	327	0	ENST00000399503.3:c.3781C>G	p.Gln1261Glu	p.Q1261E	ENST00000399503	NM_005921.1	1261	Caa/Gaa	15/20	0.334258144101339	2	FACETS	0.575	0.485	0.674	0.288	0.242	0.337	SUBCLONAL	1	TRUE	0	0.383605583654354	2		327	417	SUCCESS
APC	324	MSKCC	GRCh37	5	112175864	112175864	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	99	237	0	ENST00000257430.4:c.4573A>G	p.Met1525Val	p.M1525V	ENST00000257430	NM_000038.5	1525	Atg/Gtg	16/16	0.334258144101339	2	FACETS	0.875	0.791	0.961	0.875	0.791	0.961	CLONAL	2	TRUE	0	0.383605583654354	2		237	295	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26021077	26021077	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	37	288	0	ENST00000357647.3:c.360C>G	p.Ile120Met	p.I120M	ENST00000357647	NM_003529.2	120	atC/atG	1/1	0.344345120865204	3	FACETS	0.562	0.464	0.672	0.281	0.232	0.336	SUBCLONAL	1	TRUE	1	0.383605583654354	3		288	409	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971178	13971178	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	60	273	1	ENST00000405192.2:c.751C>A	p.Pro251Thr	p.P251T	ENST00000405192	NM_001163147.1	251	Ccc/Acc	8/12	0.383605583654354	5	FACETS	0.953	0.822	1	0.318	0.274	0.366	CLONAL	1	TRUE	2	0.383605583654354	5		274	517	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509483	106509483	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	187	475	0	ENST00000359195.3:c.1477G>A	p.Asp493Asn	p.D493N	ENST00000359195	NM_002649.2	493	Gac/Aac	2/11	0.34135016786829	4	FACETS	0.889	0.823	0.957			1	CLONAL	2	TRUE	NA	0.383605583654354	4		475	759	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106524684	106524684	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	150	260	0	ENST00000359195.3:c.2845A>T	p.Asn949Tyr	p.N949Y	ENST00000359195	NM_002649.2	949	Aat/Tat	9/11	0.34135016786829	4	FACETS	1	0.975	1			1	CLONAL	2	TRUE	NA	0.383605583654354	4		260	475	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205049	38205049	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	216	569	0	ENST00000317025.8:c.641A>G	p.His214Arg	p.H214R	ENST00000317025	NM_023034.1	214	cAc/cGc	2/24	0.150206655939225	5	FACETS	1	0.981	1	0.762	0.71	0.815	INDETERMINATE	2	TRUE	2	0.383605583654354	5		569	776	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1325399	1325399	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1176524694	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	132	283	0	ENST00000400841.2:c.276C>G	p.Asp92Glu	p.D92E	ENST00000400841		92	gaC/gaG	3/6	0.304991432752238	2	FACETS	1	0.985	1			1	CLONAL	1	TRUE	NA	0.383605583654354	2		283	491	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44966654	44966654	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	95	149	0	ENST00000377967.4:c.3879-1G>C		p.X1293_splice	ENST00000377967	NM_021140.2	1293			0.304991432752238	2	FACETS	0.912	0.836	0.988			1	CLONAL	3	TRUE	NA	0.383605583654354	2		149	181	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224445	123224448	+	frameshift_variant	Frame_Shift_Del	DEL	GACA	GACA	-	novel	NA	P-0015923-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	167	234	0	ENST00000218089.9:c.3299_3302del	p.Asp1100ValfsTer4	p.D1100Vfs*4	ENST00000218089	NM_001042749.1	1100	GACAgt/gt	31/35	0.304991432752238	2	FACETS	1	0.984	1			1	CLONAL	2	TRUE	NA	0.383605583654354	2		234	367	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0015966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	111	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.27	2		215	732	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578212	7578212	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs397516436	NA	P-0015966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	136	593	0	ENST00000269305.4:c.637C>T	p.Arg213Ter	p.R213*	ENST00000269305	NM_001126112.2	213	Cga/Tga	6/11	1	2	FACETS	0.906	0.822	0.994	0.906	0.822	0.994	CLONAL	1	TRUE	1	0.27	2		593	1112	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44918502	44918502	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0015966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	178	28	145	0	ENST00000377967.4:c.985C>T	p.Gln329Ter	p.Q329*	ENST00000377967	NM_021140.2	329	Cag/Tag	12/29	1	1	FACETS	0.871	0.701	1	0.871	0.701	1	CLONAL	1	TRUE	0	0.27	1		145	206	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478817	56478817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	117	561	1	ENST00000267101.3:c.273G>A	p.Met91Ile	p.M91I	ENST00000267101	NM_001982.3	91	atG/atA	3/28	1	2	FACETS	0.94	0.847	1	0.94	0.847	1	CLONAL	1	TRUE	1	0.27	2		562	922	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58740727	58740727	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	75	526	0	ENST00000305921.3:c.1636del	p.Leu546Ter	p.L546*	ENST00000305921	NM_003620.3	544	ggC/gg	6/6	1	2	FACETS	0.574	0.501	0.652	0.574	0.501	0.652	SUBCLONAL	1	TRUE	1	0.27	2		526	968	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916929	178916929	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	94	417	0	ENST00000263967.3:c.316G>T	p.Gly106Cys	p.G106C	ENST00000263967	NM_006218.2	106	Ggc/Tgc	2/21	0.212676688049024	3	FACETS	0.988	0.878	1	0.494	0.439	0.553	CLONAL	1	TRUE	1	0.27	3		417	800	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7122904	7122904	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1229730671	NA	P-0015966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	71	581	1	ENST00000302850.5:c.3355C>T	p.Arg1119Trp	p.R1119W	ENST00000302850	NM_000208.2	1119	Cgg/Tgg	18/22	1	2	FACETS	0.631	0.549	0.719	0.631	0.549	0.719	SUBCLONAL	1	TRUE	1	0.27	2		582	834	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777098	9777098	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs917453045	NA	P-0015966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	782	152	667	0	ENST00000377346.4:c.862G>A	p.Glu288Lys	p.E288K	ENST00000377346	NM_005026.3	288	Gag/Aag	7/24	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.27	2		667	934	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112764462	112764462	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	72	471	0	ENST00000369452.4:c.1071C>G	p.Ile357Met	p.I357M	ENST00000369452	NM_007373.3	357	atC/atG	5/9	1	2	FACETS	0.614	0.536	0.7	0.614	0.536	0.7	SUBCLONAL	1	TRUE	1	0.27	2		471	868	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64135716	64135716	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	60	546	0	ENST00000334205.4:c.1184G>A	p.Arg395Lys	p.R395K	ENST00000334205	NM_003942.2	395	aGg/aAg	10/17	1	2	FACETS	0.497	0.426	0.573	0.497	0.426	0.573	SUBCLONAL	1	TRUE	1	0.27	2		546	895	SUCCESS
ATM	472	MSKCC	GRCh37	11	108123635	108123635	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	38	269	0	ENST00000278616.4:c.1894G>C	p.Glu632Gln	p.E632Q	ENST00000278616	NM_000051.3	632	Gaa/Caa	12/63	1	2	FACETS	0.543	0.449	0.649	0.543	0.449	0.649	SUBCLONAL	1	TRUE	1	0.27	2		269	518	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133238273	133238273	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	rs1555226069	NA	P-0015966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	64	306	0	ENST00000320574.5:c.2707-3C>T		p.X903_splice	ENST00000320574	NM_006231.2	903			NA	2	FACETS	0.998	0.866	1			1	INDETERMINATE	1	TRUE	NA	0.27	2		306	475	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549277	21549277	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777989771	NA	P-0015966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	73	677	0	ENST00000382592.4:c.2999C>T	p.Ser1000Leu	p.S1000L	ENST00000382592	NM_014572.2	1000	tCg/tTg	8/8	1	2	FACETS	0.573	0.5	0.653	0.573	0.5	0.653	SUBCLONAL	1	TRUE	1	0.27	2		677	943	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32950806	32950806	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0015966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	38	316	0	ENST00000380152.3:c.8633-1G>C		p.X2878_splice	ENST00000380152		2878			1	2	FACETS	0.611	0.505	0.729	0.611	0.505	0.729	SUBCLONAL	1	TRUE	1	0.27	2		316	461	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2098753	2098753	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	105	452	0	ENST00000219476.3:c.137G>A	p.Arg46Lys	p.R46K	ENST00000219476	NM_000548.3	46	aGa/aAa	2/42	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.27	2		452	762	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640873	3640873	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	58	635	0	ENST00000294008.3:c.2766G>C	p.Lys922Asn	p.K922N	ENST00000294008	NM_032444.2	922	aaG/aaC	12/15	1	2	FACETS	0.413	0.353	0.479	0.413	0.353	0.479	SUBCLONAL	1	TRUE	1	0.27	2		635	1040	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349032	11349033	+	missense_variant	Missense_Mutation	DNP	GG	GG	AT	novel	NA	P-0015966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	53	479	0	ENST00000332029.2:c.303_304delinsAT	p.Phe101Leu	p.F101L	ENST00000332029	NM_003745.1	101	ttCCtg/ttATtg	2/2	1	2	FACETS	0.482	0.41	0.562	0.482	0.41	0.562	SUBCLONAL	1	TRUE	1	0.27	2		479	814	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16021315	16021315	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	48	233	0	ENST00000268712.3:c.1942del	p.Ala648GlnfsTer120	p.A648Qfs*120	ENST00000268712	NM_006311.3	648	Gca/ca	18/46	1	2	FACETS	0.855	0.724	0.998	0.855	0.724	0.998	CLONAL	1	TRUE	1	0.27	2		233	416	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29550464	29550464	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs915463951	NA	P-0015966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	50	211	0	ENST00000356175.3:c.1724C>T	p.Ser575Leu	p.S575L	ENST00000356175	NM_000267.3	575	tCa/tTa	16/57	1	2	FACETS	0.993	0.845	1	0.993	0.845	1	CLONAL	1	TRUE	1	0.27	2		211	373	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7132319	7132319	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	44	336	0	ENST00000302850.5:c.2692C>G	p.Leu898Val	p.L898V	ENST00000302850	NM_000208.2	898	Ctc/Gtc	14/22	1	2	FACETS	0.583	0.488	0.688	0.583	0.488	0.688	SUBCLONAL	1	TRUE	1	0.27	2		336	559	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11138571	11138571	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	147	671	0	ENST00000358026.2:c.3327G>C	p.Met1109Ile	p.M1109I	ENST00000358026	NM_001128849.1	1109	atG/atC	24/36	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.27	2		671	968	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15289922	15289922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	153	664	0	ENST00000263388.2:c.3632C>T	p.Ser1211Leu	p.S1211L	ENST00000263388	NM_000435.2	1211	tCa/tTa	22/33	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.27	2		664	1087	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18967070	18967070	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0015966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	50	651	0	ENST00000262803.5:c.1785C>G	p.Tyr595Ter	p.Y595*	ENST00000262803	NM_002911.3	595	taC/taG	13/24	1	2	FACETS	0.431	0.364	0.505	0.431	0.364	0.505	SUBCLONAL	1	TRUE	1	0.27	2		651	859	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794572	42794572	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	162	693	0	ENST00000575354.2:c.1652C>T	p.Ser551Leu	p.S551L	ENST00000575354	NM_015125.3	551	tCa/tTa	10/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.27	2		693	1033	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744019	39744019	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	35	315	1	ENST00000361337.2:c.1647G>T	p.Lys549Asn	p.K549N	ENST00000361337	NM_003286.2	549	aaG/aaT	16/21	1	2	FACETS	0.49	0.401	0.59	0.49	0.401	0.59	SUBCLONAL	1	TRUE	1	0.27	2		316	529	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417896	138417896	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	69	437	0	ENST00000289153.2:c.1623C>G	p.Ile541Met	p.I541M	ENST00000289153	NM_006219.2	541	atC/atG	11/22	0.212676688049024	3	FACETS	0.714	0.62	0.815	0.357	0.31	0.408	SUBCLONAL	1	TRUE	1	0.27	3		437	813	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652126	36652136	+	frameshift_variant	Frame_Shift_Del	DEL	GGCGAGGCCGG	GGCGAGGCCGG	-	novel	NA	P-0015966-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	118	526	0	ENST00000244741.5:c.249_259del	p.Arg84Ter	p.R84*	ENST00000244741	NM_000389.4	83	cGGCGAGGCCGG/c	2/3	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.27	2		526	730	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578461	7578461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912654	NA	P-0015978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	246	756	0	ENST00000269305.4:c.469G>T	p.Val157Phe	p.V157F	ENST00000269305	NM_001126112.2	157	Gtc/Ttc	5/11	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	2	TRUE	NA	0.257013850816602	2		756	899	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17350526	17350526	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	91	578	0	ENST00000375499.3:c.584G>A	p.Ser195Asn	p.S195N	ENST00000375499	NM_003000.2	195	aGc/aAc	6/8	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.257013850816602	2		578	634	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27088813	27088813	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	G	rs766313779	NA	P-0015978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	63	486	0	ENST00000324856.7:c.2419+3C>G		p.X807_splice	ENST00000324856	NM_006015.4	807			1	2	FACETS	0.937	0.812	1	0.937	0.812	1	CLONAL	1	TRUE	1	0.257013850816602	2		486	523	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78430918	78430918	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	rs201322936	NA	P-0015978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	151	450	1	ENST00000370768.2:c.474-3C>T		p.X158_splice	ENST00000370768	NM_003902.3	158			0.257013850816602	5	FACETS	0.923	0.848	1	0.923	0.848	1	CLONAL	3	TRUE	2	0.257013850816602	5		451	588	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243716174	243716174	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	961	83	937	1	ENST00000263826.5:c.1020G>T	p.Met340Ile	p.M340I	ENST00000263826	NM_005465.4	340	atG/atT	10/13	0.257013850816602	6	FACETS	0.937	0.824	1	0.234	0.206	0.265	CLONAL	1	TRUE	2	0.257013850816602	6		938	1044	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69588868	69588868	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	149	638	0	ENST00000168712.1:c.368G>A	p.Arg123Gln	p.R123Q	ENST00000168712	NM_002007.2	123	cGg/cAg	2/3	0.257013850816602	3	FACETS	0.987	0.904	1	0.987	0.904	1	CLONAL	2	TRUE	1	0.257013850816602	3		638	663	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94911069	94911069	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0015978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	46	640	0	ENST00000536441.1:c.1061A>C	p.Tyr354Ser	p.Y354S	ENST00000536441	NM_144665.3	354	tAt/tCt	8/10	0.257013850816602	3	FACETS	0.636	0.535	0.748	0.318	0.267	0.374	SUBCLONAL	1	TRUE	1	0.257013850816602	3		640	635	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12028614	12028614	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	46	375	0	ENST00000353533.5:c.817G>A	p.Glu273Lys	p.E273K	ENST00000353533	NM_003010.3	273	Gaa/Aaa	8/11	NA	2	FACETS	0.952	0.804	1			1	INDETERMINATE	1	TRUE	NA	0.257013850816602	2		375	376	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45872404	45872404	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	89	550	0	ENST00000391945.4:c.107G>T	p.Gly36Val	p.G36V	ENST00000391945	NM_000400.3	36	gGt/gTt	3/23	0.257013850816602	3	FACETS	1	0.961	1	0.597	0.529	0.669	CLONAL	1	TRUE	1	0.257013850816602	3		550	655	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215634015	215634015	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0015978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	51	671	0	ENST00000260947.4:c.1336T>A	p.Tyr446Asn	p.Y446N	ENST00000260947	NM_000465.2	446	Tac/Aac	5/11	0.236093856456525	3	FACETS	0.701	0.595	0.818	0.35	0.297	0.409	SUBCLONAL	1	TRUE	1	0.257013850816602	3		671	639	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220439938	220439938	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs928419389	NA	P-0015978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	100	934	0	ENST00000243786.2:c.791G>C	p.Arg264Thr	p.R264T	ENST00000243786	NM_002191.3	264	aGa/aCa	2/2	0.236093856456525	3	FACETS	0.983	0.877	1	0.492	0.438	0.549	CLONAL	1	TRUE	1	0.257013850816602	3		934	893	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47103816	47103816	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	53	416	0	ENST00000409792.3:c.6130G>C	p.Ala2044Pro	p.A2044P	ENST00000409792	NM_014159.6	2044	Gct/Cct	14/21	0.257013850816602	3	FACETS	0.913	0.779	1	0.456	0.389	0.53	CLONAL	1	TRUE	1	0.257013850816602	3		416	510	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168678	32168678	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775488332	NA	P-0015978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	72	658	0	ENST00000375023.3:c.4245G>A	p.Met1415Ile	p.M1415I	ENST00000375023	NM_004557.3	1415	atG/atA	23/30	0.252817265843546	3	FACETS	0.905	0.79	1	0.302	0.263	0.343	CLONAL	1	TRUE	0	0.257013850816602	3		658	699	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372740	81372740	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs775564237	NA	P-0015978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	67	446	0	ENST00000222390.5:c.794G>C	p.Gly265Ala	p.G265A	ENST00000222390	NM_000601.4	265	gGc/gCc	7/18	0.257013850816602	5	FACETS	1	0.9	1	0.348	0.302	0.398	CLONAL	1	TRUE	2	0.257013850816602	5		446	692	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69011970	69011970	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	172	924	0	ENST00000288368.4:c.2607C>G	p.Ser869Arg	p.S869R	ENST00000288368	NM_024870.2	869	agC/agG	23/40	0.248589906098951	4	FACETS	0.913	0.84	0.989	0.609	0.56	0.66	CLONAL	2	TRUE	1	0.257013850816602	4		924	921	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606252	93606252	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	172	636	0	ENST00000375746.1:c.72G>T	p.Glu24Asp	p.E24D	ENST00000375746	NM_001174167.1	24	gaG/gaT	2/14	0.257013850816602	3	FACETS	0.986	0.909	1	0.986	0.909	1	CLONAL	2	TRUE	1	0.257013850816602	3		636	766	SUCCESS
AR	367	MSKCC	GRCh37	X	66941807	66941807	+	splice_donor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0015978-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	70	257	1	ENST00000374690.3:c.2449+2T>A		p.X817_splice	ENST00000374690	NM_000044.3	817			1	1	FACETS	0.889	0.784	1	1	0.981	1	CLONAL	2	TRUE	0	0.257013850816602	1		258	267	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577141	7577141	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs193920774	NA	P-0015984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	413	654	2	ENST00000269305.4:c.797G>T	p.Gly266Val	p.G266V	ENST00000269305	NM_001126112.2	266	gGa/gTa	8/11	0.482772412986549	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	2	TRUE	0	0.482772412986549	2		656	803	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41543904	41543904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs910443361	NA	P-0015984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	321	604	1	ENST00000263253.7:c.2195C>T	p.Pro732Leu	p.P732L	ENST00000263253	NM_001429.3	732	cCt/cTt	12/31	0.313060048238118	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.482772412986549	3		605	812	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72241861	72241861	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	133	297	0	ENST00000357731.5:c.529C>A	p.Pro177Thr	p.P177T	ENST00000357731	NM_173808.2	177	Cca/Aca	3/7	0.482772412986549	3	FACETS	1	0.987	1	0.737	0.674	0.802	CLONAL	1	TRUE	1	0.482772412986549	3		297	464	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120471694	120471694	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	133	406	0	ENST00000256646.2:c.3797A>T	p.Asn1266Ile	p.N1266I	ENST00000256646	NM_024408.3	1266	aAc/aTc	23/34	0.482772412986549	3	FACETS	1	0.918	1	0.504	0.459	0.552	CLONAL	1	TRUE	1	0.482772412986549	3		406	678	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720663	89720663	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0015984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	147	220	0	ENST00000371953.3:c.814del	p.His272ThrfsTer4	p.H272Tfs*4	ENST00000371953	NM_000314.4	272	Cac/ac	8/9	0.482772412986549	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	2	TRUE	0	0.482772412986549	2		220	292	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94201062	94201062	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	G	novel	NA	P-0015984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	39	268	0	ENST00000323929.3:c.1018-3G>C		p.X340_splice	ENST00000323929	NM_005591.3	340			0.482772412986549	3	FACETS	0.386	0.32	0.461	0.193	0.16	0.231	SUBCLONAL	1	TRUE	1	0.482772412986549	3		268	519	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443821	49443821	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0015984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	836	95	621	0	ENST00000301067.7:c.3550G>T	p.Glu1184Ter	p.E1184*	ENST00000301067	NM_003482.3	1184	Gaa/Taa	11/54	0.482772412986549	3	FACETS	0.525	0.466	0.587	0.262	0.233	0.294	SUBCLONAL	1	TRUE	1	0.482772412986549	3		621	931	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918784	32918784	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	134	415	0	ENST00000380152.3:c.6931C>G	p.Pro2311Ala	p.P2311A	ENST00000380152		2311	Cca/Gca	12/27	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.482772412986549	2		415	544	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3777863	3777863	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1300659854	NA	P-0015984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	494	819	0	ENST00000262367.5:c.7185A>G	p.Ile2395Met	p.I2395M	ENST00000262367	NM_004380.2	2395	atA/atG	31/31	0.110598602859556	6	FACETS	1	0.989	1			1	INDETERMINATE	3	TRUE	NA	0.482772412986549	6		819	1235	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778671	3778671	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	141	510	0	ENST00000262367.5:c.6377G>A	p.Gly2126Asp	p.G2126D	ENST00000262367	NM_004380.2	2126	gGc/gAc	31/31	0.110598602859556	6	FACETS	0.824	0.752	0.899			1	INDETERMINATE	2	TRUE	NA	0.482772412986549	6		510	697	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3801796	3801796	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0015984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	300	483	0	ENST00000262367.5:c.3710G>A	p.Cys1237Tyr	p.C1237Y	ENST00000262367	NM_004380.2	1237	tGt/tAt	20/31	0.110598602859556	6	FACETS	1	0.972	1			1	INDETERMINATE	3	TRUE	NA	0.482772412986549	6		483	783	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051704	13051704	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	novel	NA	P-0015984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	241	392	0	ENST00000316448.5:c.960+3G>A		p.X320_splice	ENST00000316448	NM_004343.3	320			0.482772412986549	2	FACETS	0.971	0.917	1	0.971	0.917	1	CLONAL	2	TRUE	0	0.482772412986549	2		392	514	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145544	61145544	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	34	352	0	ENST00000295025.8:c.656G>A	p.Arg219His	p.R219H	ENST00000295025	NM_002908.2	219	cGt/cAt	7/11	0.482772412986549	3	FACETS	0.29	0.236	0.351	0.145	0.118	0.176	SUBCLONAL	1	TRUE	1	0.482772412986549	3		352	603	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99136407	99136407	+	splice_acceptor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0015984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	91	72	126	0	ENST00000074304.5:c.-103-2A>T		p.X35_splice	ENST00000074304	NM_001134224.1	35			0.482772412986549	3	FACETS	1	0.957	1	1	0.957	1	CLONAL	2	TRUE	1	0.482772412986549	3		126	163	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872474	136872474	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	130	193	0	ENST00000241393.3:c.1024A>T	p.Thr342Ser	p.T342S	ENST00000241393	NM_003467.2	342	Act/Tct	2/2	NA	2	FACETS	0.895	0.825	0.965			1	INDETERMINATE	2	TRUE	NA	0.482772412986549	2		193	301	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54948528	54948528	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	169	471	0	ENST00000312783.6:c.790C>G	p.Leu264Val	p.L264V	ENST00000312783	NM_198436.1	264	Ctt/Gtt	8/10	0.384915580776324	4	FACETS	1	0.97	1	0.556	0.511	0.603	CLONAL	1	TRUE	2	0.482772412986549	4		471	933	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319369	62319369	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774688252	NA	P-0015984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	226	681	0	ENST00000360203.5:c.1561G>A	p.Asp521Asn	p.D521N	ENST00000360203	NM_001283009.1	521	Gat/Aat	18/35	0.384915580776324	4	FACETS	1	0.973	1	0.545	0.506	0.585	CLONAL	1	TRUE	2	0.482772412986549	4		681	1274	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556729	41556729	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	T	novel	NA	P-0015984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	187	355	0	ENST00000263253.7:c.3671+3A>T		p.X1224_splice	ENST00000263253	NM_001429.3	1224			0.313060048238118	3	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	TRUE	1	0.482772412986549	3		355	479	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52597510	52597510	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0015984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	190	297	0	ENST00000394830.3:c.3801-1G>A		p.X1267_splice	ENST00000394830	NM_018313.4	1267			0.482772412986549	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	0	0.482772412986549	2		297	371	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134825421	134825421	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	187	506	0	ENST00000398015.3:c.937G>T	p.Asp313Tyr	p.D313Y	ENST00000398015	NM_004441.4	313	Gac/Tac	4/16	0.2276848852142	5	FACETS	0.874	0.809	0.941	0.583	0.539	0.628	INDETERMINATE	2	TRUE	2	0.482772412986549	5		506	764	SUCCESS
SOX2	6657	MSKCC	GRCh37	3	181430401	181430401	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0015984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	282	677	0	ENST00000325404.1:c.253A>G	p.Thr85Ala	p.T85A	ENST00000325404	NM_003106.3	85	Acg/Gcg	1/1	0.2276848852142	5	FACETS	0.959	0.902	1	0.639	0.601	0.679	INDETERMINATE	2	TRUE	2	0.482772412986549	5		677	1050	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55139821	55139821	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0015984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	238	412	0	ENST00000257290.5:c.1482G>T	p.Glu494Asp	p.E494D	ENST00000257290	NM_006206.4	494	gaG/gaT	10/23	0.362670229553727	3	FACETS	0.929	0.872	0.986			1	CLONAL	2	TRUE	NA	0.482772412986549	3		412	659	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873615	35873615	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0015984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	318	283	0	ENST00000303115.3:c.571C>A	p.Leu191Met	p.L191M	ENST00000303115	NM_002185.3	191	Ctg/Atg	5/8	0.482772412986549	5	FACETS	1	0.985	1	1	0.985	1	CLONAL	3	TRUE	2	0.482772412986549	5		283	694	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	393345	393345	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0015984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	227	396	1	ENST00000380956.4:c.193G>A	p.Glu65Lys	p.E65K	ENST00000380956	NM_001195286.1	65	Gag/Aag	2/9	0.482772412986549	4	FACETS	0.905	0.846	0.966	0.905	0.846	0.966	CLONAL	2	TRUE	2	0.482772412986549	4		397	770	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162206801	162206801	+	splice_region_variant,intron_variant	Splice_Region	SNP	T	T	A	novel	NA	P-0015984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	277	435	0	ENST00000366898.1:c.871+3A>T		p.X291_splice	ENST00000366898	NM_004562.2	291			0.482772412986549	4	FACETS	1	0.944	1	1	0.944	1	CLONAL	2	TRUE	2	0.482772412986549	4		435	849	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8339019	8339019	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0015984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	98	381	1	ENST00000356435.5:c.5282A>T	p.Glu1761Val	p.E1761V	ENST00000356435		1761	gAa/gTa	32/35	NA	2	FACETS	0.778	0.696	0.864			1	INDETERMINATE	1	TRUE	NA	0.482772412986549	2		382	522	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27213569	27213569	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0015984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	296	498	0	ENST00000380036.4:c.2965C>G	p.Gln989Glu	p.Q989E	ENST00000380036	NM_000459.3	989	Caa/Gaa	18/23	0.482772412986549	2	FACETS	0.926	0.879	0.974	0.926	0.879	0.974	CLONAL	2	TRUE	0	0.482772412986549	2		498	662	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399932	139399932	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0015984-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	414	713	0	ENST00000277541.6:c.4416C>G	p.Cys1472Trp	p.C1472W	ENST00000277541	NM_017617.3	1472	tgC/tgG	25/34	0.482772412986549	2	FACETS	0.991	0.95	1	0.991	0.95	1	CLONAL	2	TRUE	0	0.482772412986549	2		713	865	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105246551	105246551	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs121434592	NA	P-0016001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	418	563	0	ENST00000349310.3:c.49G>A	p.Glu17Lys	p.E17K	ENST00000349310	NM_001014432.1	17	Gag/Aag	4/15	0.325912141378254	5	FACETS	1	0.965	1			1	CLONAL	4	TRUE	NA	0.325912141378254	5		563	945	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288996	212288996	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	159	463	0	ENST00000342788.4:c.2750G>A	p.Gly917Glu	p.G917E	ENST00000342788	NM_005235.2	917	gGa/gAa	23/28	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.325912141378254	2		463	877	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77043802	77043802	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	156	567	0	ENST00000356341.3:c.1524G>C	p.Lys508Asn	p.K508N	ENST00000356341	NM_002576.4	508	aaG/aaC	14/15	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.325912141378254	2		567	883	SUCCESS
H2BC5	3017	MSKCC	GRCh37	6	26158610	26158610	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	82	294	0	ENST00000289316.2:c.213C>G	p.Phe71Leu	p.F71L	ENST00000289316	NM_138720.2	71	ttC/ttG	1/2	1	2	FACETS	0.991	0.876	1	0.991	0.876	1	CLONAL	1	TRUE	1	0.325912141378254	2		294	508	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608264	28608264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1312380044	NA	P-0016001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	154	560	1	ENST00000241453.7:c.1792G>A	p.Glu598Lys	p.E598K	ENST00000241453	NM_004119.2	598	Gaa/Aaa	14/24	0.325912141378254	1	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	0	0.325912141378254	1		561	783	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2225391	2225391	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	149	585	0	ENST00000398665.3:c.3601G>C	p.Glu1201Gln	p.E1201Q	ENST00000398665	NM_032482.2	1201	Gag/Cag	26/28	1	2	FACETS	0.915	0.835	0.999	0.915	0.835	0.999	CLONAL	1	TRUE	1	0.325912141378254	2		585	999	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1131691042	NA	P-0016001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	119	420	1	ENST00000269305.4:c.559+1G>A		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.325912141378254	1	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	0	0.325912141378254	1		421	521	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176104152	176104152	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	110	382	0	ENST00000367669.3:c.962C>T	p.Ser321Leu	p.S321L	ENST00000367669	NM_022457.5	321	tCa/tTa	8/20	0.325912141378254	3	FACETS	1	0.935	1	0.527	0.473	0.584	CLONAL	1	TRUE	1	0.325912141378254	3		382	745	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879631	123879631	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	139	442	0	ENST00000330479.4:c.327G>A	p.Met109Ile	p.M109I	ENST00000330479	NM_020382.3	109	atG/atA	4/9	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.325912141378254	2		442	759	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354497	91354497	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	121	482	0	ENST00000355112.3:c.3937G>A	p.Glu1313Lys	p.E1313K	ENST00000355112	NM_000057.2	1313	Gag/Aag	21/22	1	2	FACETS	0.927	0.838	1	0.927	0.838	1	CLONAL	1	TRUE	1	0.325912141378254	2		482	801	SUCCESS
BLM	641	MSKCC	GRCh37	15	91354565	91354565	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	905	153	630	0	ENST00000355112.3:c.4005G>C	p.Lys1335Asn	p.K1335N	ENST00000355112	NM_000057.2	1335	aaG/aaC	21/22	1	2	FACETS	0.887	0.811	0.968	0.887	0.811	0.968	CLONAL	1	TRUE	1	0.325912141378254	2		630	1058	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56782341	56782341	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	novel	NA	P-0016001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	108	385	0	ENST00000308159.5:c.179+3G>A		p.X60_splice	ENST00000308159	NM_014669.4	60			0.325912141378254	1	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	0	0.325912141378254	1		385	541	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68845718	68845719	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	ACAC	novel	NA	P-0016001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	133	599	0	ENST00000261769.5:c.966_969dup	p.Gly324HisfsTer27	p.G324Hfs*27	ENST00000261769	NM_004360.3	322	aac/aACACac	7/16	0.325912141378254	1	FACETS	0.898	0.816	0.983	0.898	0.816	0.983	CLONAL	1	TRUE	0	0.325912141378254	1		599	761	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40453318	40453318	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	156	544	0	ENST00000345506.4:c.1015C>G	p.Pro339Ala	p.P339A	ENST00000345506	NM_003152.3	339	Cct/Gct	10/20	0.325912141378254	1	FACETS	0.984	0.902	1	0.984	0.902	1	CLONAL	1	TRUE	0	0.325912141378254	1		544	814	SUCCESS
SMAD4	4089	MSKCC	GRCh37	18	48591925	48591925	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876660556	NA	P-0016001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	75	345	0	ENST00000342988.3:c.1088G>C	p.Cys363Ser	p.C363S	ENST00000342988	NM_005359.5	363	tGt/tCt	9/12	0.325912141378254	1	FACETS	0.872	0.767	0.984	0.872	0.767	0.984	CLONAL	1	TRUE	0	0.325912141378254	1		345	442	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753362	42753362	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	189	803	1	ENST00000222329.4:c.902C>T	p.Ser301Phe	p.S301F	ENST00000222329	NM_006494.2	301	tCc/tTc	4/4	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.325912141378254	2		804	1112	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187440274	187440274	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	81	321	0	ENST00000232014.4:c.2093T>C	p.Leu698Pro	p.L698P	ENST00000232014	NM_001130845.1	698	cTg/cCg	10/10	1	2	FACETS	0.984	0.87	1	0.984	0.87	1	CLONAL	1	TRUE	1	0.325912141378254	2		321	505	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20490396	20490396	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	G	novel	NA	P-0016001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	115	347	0	ENST00000346618.3:c.1136-3C>G		p.X379_splice	ENST00000346618	NM_001949.4	379			1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.325912141378254	2		347	663	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339605	116339605	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	86	245	0	ENST00000397752.3:c.467C>G	p.Ser156Trp	p.S156W	ENST00000397752	NM_000245.2	156	tCg/tGg	2/21	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.325912141378254	2		245	419	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945114	151945114	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	40	335	0	ENST00000262189.6:c.2405del	p.Ser802Ter	p.S802*	ENST00000262189	NM_170606.2	802	tCa/ta	14/59	1	2	FACETS	0.515	0.427	0.612	0.515	0.427	0.612	SUBCLONAL	1	TRUE	1	0.325912141378254	2		335	477	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920586	127920586	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016001-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	187	653	0	ENST00000373547.4:c.313G>A	p.Asp105Asn	p.D105N	ENST00000373547	NM_002721.4	105	Gat/Aat	4/7	1	2	FACETS	0.973	0.898	1	0.973	0.898	1	CLONAL	1	TRUE	1	0.325912141378254	2		653	1179	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0016025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	43	282	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.892	1	1	0.892	1	CLONAL	1	TRUE	1	0.19	2		282	417	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0016025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	108	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.187298224492821	2	FACETS	0.9	0.814	0.99	1	0.98	1	CLONAL	3	TRUE	0	0.19	2		458	421	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577545	7577545	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs483352695	NA	P-0016025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	97	563	0	ENST00000269305.4:c.736A>G	p.Met246Val	p.M246V	ENST00000269305	NM_001126112.2	246	Atg/Gtg	7/11	1	2	FACETS	0.755	0.674	0.842	1	0.981	1	SUBCLONAL	2	TRUE	1	0.19	2		563	676	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205070	128205070	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs569301892	NA	P-0016025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	55	647	0	ENST00000341105.2:c.371C>T	p.Thr124Met	p.T124M	ENST00000341105	NM_032638.4	124	aCg/aTg	3/6	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.19	2		647	567	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131498	202131498	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	45	403	0	ENST00000358485.4:c.466C>G	p.Gln156Glu	p.Q156E	ENST00000358485	NM_001080125.1	156	Caa/Gaa	2/9	1	2	FACETS	0.913	0.767	1	0.913	0.767	1	CLONAL	1	TRUE	1	0.19	2		403	519	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41545855	41545855	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs867077693	NA	P-0016025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	67	890	0	ENST00000263253.7:c.2470C>T	p.Gln824Ter	p.Q824*	ENST00000263253	NM_001429.3	824	Caa/Taa	14/31	1	2	FACETS	0.823	0.714	0.942	0.823	0.714	0.942	CLONAL	1	TRUE	1	0.19	2		890	857	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84391389	84391389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760079258	NA	P-0016025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	69	584	0	ENST00000321945.7:c.443G>A	p.Arg148Gln	p.R148Q	ENST00000321945	NM_139076.2	148	cGa/cAa	5/9	1	2	FACETS	0.972	0.846	1	0.972	0.846	1	CLONAL	1	TRUE	1	0.19	2		584	747	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41556727	41556727	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0016025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	28	327	0	ENST00000263253.7:c.3671+1G>A		p.X1224_splice	ENST00000263253	NM_001429.3	1224			1	2	FACETS	0.752	0.601	0.924	0.752	0.601	0.924	CLONAL	1	TRUE	1	0.19	2		327	392	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120512171	120512172	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	44	358	0	ENST00000256646.2:c.1070dup	p.Ala358GlyfsTer20	p.A358Gfs*20	ENST00000256646	NM_024408.3	357	gtg/gtTg	6/34	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.19	2		358	406	SUCCESS
RET	5979	MSKCC	GRCh37	10	43615038	43615038	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377767420	NA	P-0016025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	37	573	2	ENST00000355710.3:c.2452G>A	p.Glu818Lys	p.E818K	ENST00000355710	NM_020975.4	818	Gag/Aag	14/20	1	2	FACETS	0.838	0.69	1	0.838	0.69	1	CLONAL	1	TRUE	1	0.19	2		575	465	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058783	42058783	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	236	14	228	0	ENST00000219905.7:c.8503C>G	p.Gln2835Glu	p.Q2835E	ENST00000219905	NM_001164273.1	2835	Caa/Gaa	24/24	1	2	FACETS	0.589	0.426	0.788	0.589	0.426	0.788	SUBCLONAL	1	TRUE	1	0.19	2		228	250	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303846	91303846	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	24	262	0	ENST00000355112.3:c.1243G>C	p.Asp415His	p.D415H	ENST00000355112	NM_000057.2	415	Gat/Cat	7/22	1	2	FACETS	0.724	0.567	0.904	0.724	0.567	0.904	CLONAL	1	TRUE	1	0.19	2		262	349	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304278	91304278	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	37	386	0	ENST00000355112.3:c.1675G>A	p.Asp559Asn	p.D559N	ENST00000355112	NM_000057.2	559	Gat/Aat	7/22	1	2	FACETS	0.862	0.71	1	0.862	0.71	1	CLONAL	1	TRUE	1	0.19	2		386	452	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3651097	3651097	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	49	748	0	ENST00000294008.3:c.1046G>C	p.Arg349Thr	p.R349T	ENST00000294008	NM_032444.2	349	aGa/aCa	5/15	1	2	FACETS	0.632	0.534	0.741	0.632	0.534	0.741	SUBCLONAL	1	TRUE	1	0.19	2		748	816	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66518894	66518894	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	rs745980273	NA	P-0016025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	21	314	0	ENST00000358598.2:c.178-3C>T		p.X60_splice	ENST00000358598	NM_212471.2	60			1	2	FACETS	0.648	0.499	0.823	0.648	0.499	0.823	SUBCLONAL	1	TRUE	1	0.19	2		314	341	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11098450	11098450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886054151	NA	P-0016025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	47	444	0	ENST00000358026.2:c.968C>T	p.Ser323Leu	p.S323L	ENST00000358026	NM_001128849.1	323	tCg/tTg	6/36	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.19	2		444	436	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11172481	11172481	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1261182514	NA	P-0016025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	85	643	2	ENST00000358026.2:c.5029G>A	p.Glu1677Lys	p.E1677K	ENST00000358026	NM_001128849.1	1677	Gaa/Aaa	36/36	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.19	2		645	712	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213005	39213005	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	64	730	1	ENST00000402219.2:c.3962G>A	p.Arg1321Lys	p.R1321K	ENST00000402219	NM_005633.3	1321	aGa/aAa	23/23	1	2	FACETS	0.889	0.768	1	0.889	0.768	1	CLONAL	1	TRUE	1	0.19	2		731	758	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017186	31017186	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	48	422	0	ENST00000375687.4:c.517G>T	p.Val173Phe	p.V173F	ENST00000375687	NM_015338.5	173	Gtc/Ttc	7/13	1	2	FACETS	0.944	0.798	1	0.944	0.798	1	CLONAL	1	TRUE	1	0.19	2		422	535	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048626	180048626	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	40	561	0	ENST00000261937.6:c.1936G>C	p.Glu646Gln	p.E646Q	ENST00000261937	NM_182925.4	646	Gag/Cag	13/30	1	2	FACETS	0.79	0.656	0.94	0.79	0.656	0.94	CLONAL	1	TRUE	1	0.19	2		561	533	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324156	31324156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151341237	NA	P-0016025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	37	449	0	ENST00000412585.2:c.407G>A	p.Gly136Glu	p.G136E	ENST00000412585	NM_005514.6	136	gGg/gAg	3/8	1	2	FACETS	0.856	0.706	1	0.856	0.706	1	CLONAL	1	TRUE	1	0.19	2		449	455	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2963907	2963907	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	50	617	0	ENST00000396946.4:c.1900G>T	p.Glu634Ter	p.E634*	ENST00000396946	NM_032415.4	634	Gag/Tag	15/25	1	2	FACETS	0.831	0.705	0.971	0.831	0.705	0.971	CLONAL	1	TRUE	1	0.19	2		617	633	SUCCESS
MET	4233	MSKCC	GRCh37	7	116436122	116436122	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	54	418	0	ENST00000397752.3:c.4117G>T	p.Asp1373Tyr	p.D1373Y	ENST00000397752	NM_000245.2	1373	Gat/Tat	21/21	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.19	2		418	491	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845538	151845538	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	41	638	0	ENST00000262189.6:c.13474C>T	p.Gln4492Ter	p.Q4492*	ENST00000262189	NM_170606.2	4492	Caa/Taa	52/59	1	2	FACETS	0.617	0.512	0.733	0.617	0.512	0.733	SUBCLONAL	1	TRUE	1	0.19	2		638	700	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	152009018	152009018	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	30	305	0	ENST00000262189.6:c.604C>T	p.Gln202Ter	p.Q202*	ENST00000262189	NM_170606.2	202	Cag/Tag	5/59	1	2	FACETS	0.789	0.636	0.964	0.789	0.636	0.964	CLONAL	1	TRUE	1	0.19	2		305	400	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90960111	90960111	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016025-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	23	209	0	ENST00000265433.3:c.1855G>A	p.Glu619Lys	p.E619K	ENST00000265433	NM_002485.4	619	Gaa/Aaa	12/16	1	2	FACETS	0.796	0.621	0.998	0.796	0.621	0.998	CLONAL	1	TRUE	1	0.19	2		209	304	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	126	215	0				ENST00000310581	NM_198253.2	-/1132			0.400454880912087	7	FACETS	1	0.91	1	0.401	0.364	0.44	CLONAL	2	TRUE	2	0.400454880912087	7		215	628	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0016095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	272	288	0	ENST00000304494.5:c.151-1G>A		p.X51_splice	ENST00000304494	NM_000077.4	51			0.400454880912087	3	FACETS	1	0.983	1	1	0.983	1	CLONAL	3	TRUE	0	0.400454880912087	3		288	505	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0016095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	98	701	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.247019303770635	3	FACETS	0.984	0.88	1			1	CLONAL	1	TRUE	NA	0.400454880912087	3		701	597	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361249	66361249	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1430800927	NA	P-0016095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	259	38	394	0	ENST00000273854.3:c.923G>T	p.Gly308Val	p.G308V	ENST00000273854	NM_004439.5	308	gGg/gTg	4/18	1	2	FACETS	0.639	0.53	0.759	0.639	0.53	0.759	SUBCLONAL	1	TRUE	1	0.400454880912087	2		394	297	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88659854	88659854	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	137	405	0	ENST00000372037.3:c.501G>A	p.Met167Ile	p.M167I	ENST00000372037	NM_004329.2	167	atG/atA	7/13	0.221893960675819	3	FACETS	1	0.964	1	0.722	0.664	0.781	INDETERMINATE	2	TRUE	0	0.400454880912087	3		405	379	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49438067	49438067	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs886043414	NA	P-0016095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	101	705	1	ENST00000301067.7:c.5104C>T	p.Arg1702Ter	p.R1702*	ENST00000301067	NM_003482.3	1702	Cga/Tga	21/54	0.298215611869941	3	FACETS	0.949	0.849	1	0.474	0.424	0.527	CLONAL	1	TRUE	1	0.400454880912087	3		706	638	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966270	25966270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759268577	NA	P-0016095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	39	598	0	ENST00000435504.4:c.2936C>T	p.Thr979Met	p.T979M	ENST00000435504		979	aCg/aTg	13/13	1	2	FACETS	0.455	0.377	0.542	0.455	0.377	0.542	SUBCLONAL	1	TRUE	1	0.400454880912087	2		598	428	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248358	212248358	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	19	294	1	ENST00000342788.4:c.3909C>A	p.His1303Gln	p.H1303Q	ENST00000342788	NM_005235.2	1303	caC/caA	28/28	0.400454880912087	3	FACETS	0.553	0.421	0.707	0.276	0.21	0.354	SUBCLONAL	1	TRUE	1	0.400454880912087	3		295	206	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212286767	212286767	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	136	612	0	ENST00000342788.4:c.2929A>G	p.Met977Val	p.M977V	ENST00000342788	NM_005235.2	977	Atg/Gtg	24/28	0.400454880912087	3	FACETS	0.91	0.834	0.988	0.91	0.834	0.988	CLONAL	2	TRUE	1	0.400454880912087	3		612	448	SUCCESS
EIF4A2	1974	MSKCC	GRCh37	3	186505638	186505649	+	inframe_deletion	In_Frame_Del	DEL	ATCTACCTACCA	ATCTACCTACCA	-	novel	NA	P-0016095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	77	432	0	ENST00000323963.5:c.1049_1060del	p.Leu350_Asn353del	p.L350_N353del	ENST00000323963		349	gATCTACCTACCAat/gat	10/11	0.298215611869941	3	FACETS	1	0.916	1	0.525	0.462	0.591	CLONAL	1	TRUE	1	0.400454880912087	3		432	440	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156642	106156642	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	62	562	0	ENST00000380013.4:c.1543A>G	p.Asn515Asp	p.N515D	ENST00000380013	NM_001127208.2	515	Aac/Gac	3/11	1	2	FACETS	0.75	0.65	0.857	0.75	0.65	0.857	SUBCLONAL	1	TRUE	1	0.400454880912087	2		562	413	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554872	187554872	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	48	493	0	ENST00000441802.2:c.4289A>G	p.Glu1430Gly	p.E1430G	ENST00000441802	NM_005245.3	1430	gAg/gGg	7/27	0.400454880912087	1	FACETS	0.551	0.467	0.642	0.551	0.467	0.642	SUBCLONAL	1	TRUE	0	0.400454880912087	1		493	348	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180040017	180040017	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	169	906	2	ENST00000261937.6:c.3425C>A	p.Pro1142His	p.P1142H	ENST00000261937	NM_182925.4	1142	cCc/cAc	25/30	0.367462938136147	2	FACETS	0.804	0.744	0.865	0.804	0.744	0.865	CLONAL	2	TRUE	0	0.400454880912087	2		908	525	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982022	93982022	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0016095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	97	371	0	ENST00000369303.4:c.1443C>G	p.Tyr481Ter	p.Y481*	ENST00000369303	NM_004440.3	481	taC/taG	6/17	NA	2	FACETS	0.859	0.777	0.944			1	INDETERMINATE	2	TRUE	NA	0.400454880912087	2		371	282	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94068033	94068033	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	127	513	0	ENST00000369303.4:c.929G>C	p.Cys310Ser	p.C310S	ENST00000369303	NM_004440.3	310	tGt/tCt	4/17	NA	2	FACETS	0.828	0.758	0.9			1	INDETERMINATE	2	TRUE	NA	0.400454880912087	2		513	383	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117674206	117674206	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1418282255	NA	P-0016095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	213	765	0	ENST00000368508.3:c.4268C>G	p.Ala1423Gly	p.A1423G	ENST00000368508	NM_002944.2	1423	gCc/gGc	26/43	0.400454880912087	3	FACETS	0.954	0.891	1	0.954	0.891	1	CLONAL	2	TRUE	1	0.400454880912087	3		765	669	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922118	39922118	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	113	885	0	ENST00000378444.4:c.4054G>T	p.Asp1352Tyr	p.D1352Y	ENST00000378444	NM_001123385.1	1352	Gac/Tac	9/15	0.258101190461358	4	FACETS	1	0.956	1			1	CLONAL	1	TRUE	NA	0.400454880912087	4		885	711	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76813032	76813032	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	96	719	0	ENST00000373344.5:c.6589C>G	p.Arg2197Gly	p.R2197G	ENST00000373344	NM_000489.3	2197	Cgt/Ggt	30/35	0.101709712323255	5	FACETS	1	0.973	1	0.323	0.288	0.36	INDETERMINATE	1	TRUE	1	0.400454880912087	5		719	594	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76888770	76888770	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0016095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	92	673	0	ENST00000373344.5:c.5059A>T	p.Arg1687Ter	p.R1687*	ENST00000373344	NM_000489.3	1687	Aga/Tga	19/35	0.101709712323255	5	FACETS	1	0.979	1	0.361	0.322	0.403	INDETERMINATE	1	TRUE	1	0.400454880912087	5		673	509	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939306	76939306	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016095-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	92	672	0	ENST00000373344.5:c.1442A>T	p.Glu481Val	p.E481V	ENST00000373344	NM_000489.3	481	gAg/gTg	9/35	0.101709712323255	5	FACETS	1	0.972	1	0.321	0.286	0.359	INDETERMINATE	1	TRUE	1	0.400454880912087	5		672	572	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	53	281	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.793	0.687	0.905	0.793	0.687	0.905	CLONAL	1	TRUE	1	0.7	2		281	191	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212812335	212812335	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	90	285	0	ENST00000342788.4:c.241C>T	p.Arg81Ter	p.R81*	ENST00000342788	NM_005235.2	81	Cga/Tga	3/28	1	2	FACETS	0.978	0.881	1	0.978	0.881	1	CLONAL	1	TRUE	1	0.7	2		285	263	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35871196	35871196	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773491081	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	80	380	0	ENST00000303115.3:c.418C>T	p.Arg140Trp	p.R140W	ENST00000303115	NM_002185.3	140	Cgg/Tgg	4/8	1	2	FACETS	0.752	0.669	0.839	0.752	0.669	0.839	SUBCLONAL	1	TRUE	1	0.7	2		380	304	SUCCESS
ERRFI1	54206	MSKCC	GRCh37	1	8073899	8073899	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	110	359	0	ENST00000377482.5:c.760G>T	p.Ala254Ser	p.A254S	ENST00000377482	NM_018948.3	254	Gct/Tct	4/4	1	2	FACETS	0.93	0.845	1	0.93	0.845	1	CLONAL	1	TRUE	1	0.7	2		359	338	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11189004	11189004	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	148	437	0	ENST00000361445.4:c.5719C>A	p.Leu1907Ile	p.L1907I	ENST00000361445	NM_004958.3	1907	Ctc/Atc	41/58	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.7	2		437	405	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272449	11272449	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	188	492	0	ENST00000361445.4:c.3481C>T	p.Arg1161Ter	p.R1161*	ENST00000361445	NM_004958.3	1161	Cga/Tga	23/58	1	2	FACETS	0.906	0.842	0.971	0.906	0.842	0.971	CLONAL	1	TRUE	1	0.7	2		492	593	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11293466	11293466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	145	546	1	ENST00000361445.4:c.2410G>A	p.Glu804Lys	p.E804K	ENST00000361445	NM_004958.3	804	Gaa/Aaa	15/58	1	2	FACETS	0.881	0.81	0.955	0.881	0.81	0.955	CLONAL	1	TRUE	1	0.7	2		547	470	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242643	16242643	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	154	536	0	ENST00000375759.3:c.1264T>G	p.Phe422Val	p.F422V	ENST00000375759	NM_015001.2	422	Ttt/Gtt	6/15	1	2	FACETS	0.965	0.891	1	0.965	0.891	1	CLONAL	1	TRUE	1	0.7	2		536	456	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257551	16257551	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	146	421	0	ENST00000375759.3:c.4816G>T	p.Glu1606Ter	p.E1606*	ENST00000375759	NM_015001.2	1606	Gag/Tag	11/15	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.7	2		421	410	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17354250	17354250	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	85	363	0	ENST00000375499.3:c.534G>T	p.Glu178Asp	p.E178D	ENST00000375499	NM_003000.2	178	gaG/gaT	5/8	1	2	FACETS	0.736	0.656	0.819	0.736	0.656	0.819	SUBCLONAL	1	TRUE	1	0.7	2		363	330	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099430	27099430	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1227227387	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	148	566	1	ENST00000324856.7:c.3667C>T	p.Arg1223Cys	p.R1223C	ENST00000324856	NM_006015.4	1223	Cgc/Tgc	14/20	1	2	FACETS	0.913	0.841	0.988	0.913	0.841	0.988	CLONAL	1	TRUE	1	0.7	2		567	463	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	148	327	548	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.983	0.947	1	1	0.997	1	CLONAL	2	TRUE	1	0.7	2		548	475	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807474	36807474	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	187	573	0	ENST00000373129.3:c.1190G>T	p.Ser397Ile	p.S397I	ENST00000373129	NM_032017.1	397	aGc/aTc	12/12	1	2	FACETS	0.87	0.808	0.934	0.87	0.808	0.934	CLONAL	1	TRUE	1	0.7	2		573	614	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39322565	39322565	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	147	532	0	ENST00000373001.3:c.427G>T	p.Val143Phe	p.V143F	ENST00000373001	NM_022157.3	143	Gtc/Ttc	2/7	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.7	2		532	404	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40367484	40367484	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	52	35	47	0	ENST00000397332.2:c.77G>A	p.Ser26Asn	p.S26N	ENST00000397332	NM_001033082.2	26	aGc/aAc	1/3	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.7	2		47	87	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46531777	46531777	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	102	412	0	ENST00000262741.5:c.570G>T	p.Glu190Asp	p.E190D	ENST00000262741	NM_003629.3	190	gaG/gaT	5/10	1	2	FACETS	0.867	0.784	0.954	0.867	0.784	0.954	CLONAL	1	TRUE	1	0.7	2		412	336	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303660	65303660	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	180	568	0	ENST00000342505.4:c.3095A>C	p.Lys1032Thr	p.K1032T	ENST00000342505	NM_002227.2	1032	aAg/aCg	22/25	1	2	FACETS	0.933	0.867	1	0.933	0.867	1	CLONAL	1	TRUE	1	0.7	2		568	551	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65304240	65304240	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	261	119	417	0	ENST00000342505.4:c.2875C>A	p.Leu959Met	p.L959M	ENST00000342505	NM_002227.2	959	Ctg/Atg	21/25	1	2	FACETS	0.895	0.816	0.977	0.895	0.816	0.977	CLONAL	1	TRUE	1	0.7	2		417	380	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65311309	65311309	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	113	400	0	ENST00000342505.4:c.2002G>T	p.Glu668Ter	p.E668*	ENST00000342505	NM_002227.2	668	Gag/Tag	15/25	1	2	FACETS	0.892	0.811	0.976	0.892	0.811	0.976	CLONAL	1	TRUE	1	0.7	2		400	362	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65352023	65352023	+	splice_region_variant,5_prime_UTR_variant	Splice_Region	SNP	C	C	T	rs991262307	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	51	209	0	ENST00000342505.4:c.-76G>A		p.X26_splice	ENST00000342505	NM_002227.2	26		2/25	1	2	FACETS	0.771	0.665	0.883	0.771	0.665	0.883	SUBCLONAL	1	TRUE	1	0.7	2		209	189	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72058499	72058499	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	118	394	3	ENST00000357731.5:c.940+1G>A		p.X314_splice	ENST00000357731	NM_173808.2	314			1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.7	2		397	334	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78429757	78429757	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755419864	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	136	59	285	0	ENST00000370768.2:c.1031G>A	p.Arg344Gln	p.R344Q	ENST00000370768	NM_003902.3	344	cGa/cAa	12/20	1	2	FACETS	0.864	0.756	0.978	0.864	0.756	0.978	CLONAL	1	TRUE	1	0.7	2		285	195	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736573	85736573	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1281752374	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	108	70	206	0	ENST00000370580.1:c.74G>A	p.Arg25His	p.R25H	ENST00000370580	NM_003921.4	25	cGt/cAt	2/3	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.7	2		206	178	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256514	115256514	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	36	561	1	ENST00000369535.4:c.197C>T	p.Ala66Val	p.A66V	ENST00000369535	NM_002524.4	66	gCc/gTc	3/7	1	2	FACETS	0.175	0.143	0.211	0.175	0.143	0.211	SUBCLONAL	1	TRUE	1	0.7	2		562	587	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263192	115263192	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	172	528	0	ENST00000438362.2:c.2158C>T	p.Arg720Cys	p.R720C	ENST00000438362	NM_001242891.1	720	Cgc/Tgc	17/20	1	2	FACETS	0.925	0.858	0.995	0.925	0.858	0.995	CLONAL	1	TRUE	1	0.7	2		528	531	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699453	117699453	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	34	459	0	ENST00000369458.3:c.188A>G	p.Lys63Arg	p.K63R	ENST00000369458	NM_024626.3	63	aAa/aGa	3/6	1	2	FACETS	0.191	0.156	0.231	0.191	0.156	0.231	SUBCLONAL	1	TRUE	1	0.7	2		459	508	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120466499	120466499	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	138	620	0	ENST00000256646.2:c.4620G>T	p.Glu1540Asp	p.E1540D	ENST00000256646	NM_024408.3	1540	gaG/gaT	26/34	1	2	FACETS	0.564	0.514	0.616	0.564	0.514	0.616	SUBCLONAL	1	TRUE	1	0.7	2		620	699	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120508112	120508112	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	126	398	2	ENST00000256646.2:c.1645G>A	p.Asp549Asn	p.D549N	ENST00000256646	NM_024408.3	549	Gat/Aat	10/34	1	2	FACETS	0.95	0.869	1	0.95	0.869	1	CLONAL	1	TRUE	1	0.7	2		400	379	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874539	155874539	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	219	680	0	ENST00000368323.3:c.220T>A	p.Leu74Met	p.L74M	ENST00000368323	NM_006912.5	74	Ttg/Atg	4/6	1	2	FACETS	0.981	0.918	1	0.981	0.918	1	CLONAL	1	TRUE	1	0.7	2		680	638	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156848943	156848943	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	171	615	0	ENST00000524377.1:c.1835C>G	p.Ala612Gly	p.A612G	ENST00000524377	NM_002529.3	612	gCt/gGt	15/17	1	2	FACETS	0.903	0.836	0.972	0.903	0.836	0.972	CLONAL	1	TRUE	1	0.7	2		615	541	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724610	162724610	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs778566598	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	163	465	0	ENST00000367921.3:c.382C>T	p.Arg128Cys	p.R128C	ENST00000367921	NM_006182.2	128	Cgc/Tgc	5/18	1	2	FACETS	0.993	0.919	1	0.993	0.919	1	CLONAL	1	TRUE	1	0.7	2		465	469	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745503	162745503	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	113	485	0	ENST00000367921.3:c.1918C>A	p.Leu640Ile	p.L640I	ENST00000367921	NM_006182.2	640	Cta/Ata	15/18	1	2	FACETS	0.912	0.83	0.997	0.912	0.83	0.997	CLONAL	1	TRUE	1	0.7	2		485	354	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175723	176175723	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	290	763	1	ENST00000367669.3:c.392G>T	p.Ser131Ile	p.S131I	ENST00000367669	NM_022457.5	131	aGc/aTc	1/20	1	2	FACETS	0.968	0.914	1	0.968	0.914	1	CLONAL	1	TRUE	1	0.7	2		764	856	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193181526	193181526	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	110	454	0	ENST00000367435.3:c.1073G>A	p.Arg358Gln	p.R358Q	ENST00000367435	NM_024529.4	358	cGa/cAa	13/17	1	2	FACETS	0.859	0.779	0.941	0.859	0.779	0.941	CLONAL	1	TRUE	1	0.7	2		454	366	SUCCESS
FH	2271	MSKCC	GRCh37	1	241661231	241661231	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	153	580	0	ENST00000366560.3:c.1430A>C	p.Lys477Thr	p.K477T	ENST00000366560	NM_000143.3	477	aAa/aCa	10/10	1	2	FACETS	0.957	0.883	1	0.957	0.883	1	CLONAL	1	TRUE	1	0.7	2		580	457	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680541	241680541	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782207	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	132	492	0	ENST00000366560.3:c.208G>A	p.Ala70Thr	p.A70T	ENST00000366560	NM_000143.3	70	Gcc/Acc	2/10	1	2	FACETS	0.855	0.783	0.93	0.855	0.783	0.93	CLONAL	1	TRUE	1	0.7	2		492	441	SUCCESS
FH	2271	MSKCC	GRCh37	1	241680598	241680598	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778678782	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	118	373	0	ENST00000366560.3:c.151C>T	p.Arg51Trp	p.R51W	ENST00000366560	NM_000143.3	51	Cgg/Tgg	2/10	1	2	FACETS	1	0.916	1	1	0.916	1	CLONAL	1	TRUE	1	0.7	2		373	336	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	246518379	246518379	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773483378	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	133	357	0	ENST00000388985.4:c.182G>A	p.Arg61Gln	p.R61Q	ENST00000388985		61	cGa/cAa	2/12	1	2	FACETS	0.943	0.865	1	0.943	0.865	1	CLONAL	1	TRUE	1	0.7	2		357	403	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100283	8100283	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	141	538	1	ENST00000346208.3:c.257G>A	p.Arg86His	p.R86H	ENST00000346208		86	cGc/cAc	3/6	1	2	FACETS	0.838	0.768	0.909	0.838	0.768	0.909	CLONAL	1	TRUE	1	0.7	2		539	481	SUCCESS
RET	5979	MSKCC	GRCh37	10	43596057	43596057	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142641173	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	40	651	0	ENST00000355710.3:c.224C>T	p.Thr75Met	p.T75M	ENST00000355710	NM_020975.4	75	aCg/aTg	2/20	1	2	FACETS	0.19	0.157	0.227	0.19	0.157	0.227	SUBCLONAL	1	TRUE	1	0.7	2		651	601	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63829541	63829541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	121	376	0	ENST00000279873.7:c.1184G>A	p.Arg395His	p.R395H	ENST00000279873	NM_032199.2	395	cGc/cAc	8/10	1	2	FACETS	0.893	0.815	0.974	0.893	0.815	0.974	CLONAL	1	TRUE	1	0.7	2		376	387	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404865	70404865	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	95	467	0	ENST00000373644.4:c.2379C>A	p.Phe793Leu	p.F793L	ENST00000373644	NM_030625.2	793	ttC/ttA	4/12	1	2	FACETS	0.939	0.847	1	0.939	0.847	1	CLONAL	1	TRUE	1	0.7	2		467	289	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70432730	70432730	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	36	544	0	ENST00000373644.4:c.4752C>A	p.Tyr1584Ter	p.Y1584*	ENST00000373644	NM_030625.2	1584	taC/taA	8/12	1	2	FACETS	0.247	0.203	0.296	0.247	0.203	0.296	SUBCLONAL	1	TRUE	1	0.7	2		544	417	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681437	88681437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs35619497	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	197	628	0	ENST00000372037.3:c.1327C>T	p.Arg443Cys	p.R443C	ENST00000372037	NM_004329.2	443	Cgt/Tgt	11/13	1	2	FACETS	0.849	0.79	0.91	0.849	0.79	0.91	CLONAL	1	TRUE	1	0.7	2		628	663	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692905	89692905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121909229	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	145	548	0	ENST00000371953.3:c.389G>A	p.Arg130Gln	p.R130Q	ENST00000371953	NM_000314.4	130	cGa/cAa	5/9	1	2	FACETS	1	0.964	1	1	0.964	1	CLONAL	1	TRUE	1	0.7	2		548	385	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692920	89692920	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	128	557	0	ENST00000371953.3:c.404T>G	p.Ile135Arg	p.I135R	ENST00000371953	NM_000314.4	135	aTa/aGa	5/9	1	2	FACETS	0.881	0.806	0.959	0.881	0.806	0.959	CLONAL	1	TRUE	1	0.7	2		557	415	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710629	114710629	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	174	542	0	ENST00000543371.1:c.114G>T	p.Glu38Asp	p.E38D	ENST00000543371	NM_001198531.1	38	gaG/gaT	1/14	1	2	FACETS	0.922	0.855	0.991	0.922	0.855	0.991	CLONAL	1	TRUE	1	0.7	2		542	539	SUCCESS
LMO1	4004	MSKCC	GRCh37	11	8246189	8246189	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	156	522	1	ENST00000335790.3:c.445G>T	p.Gly149Cys	p.G149C	ENST00000335790	NM_002315.2	149	Ggc/Tgc	4/4	1	2	FACETS	0.851	0.784	0.919	0.851	0.784	0.919	CLONAL	1	TRUE	1	0.7	2		523	524	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32456866	32456866	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	120	525	0	ENST00000332351.3:c.26T>C	p.Val9Ala	p.V9A	ENST00000332351	NM_024426.4	9	gTc/gCc	1/10	1	2	FACETS	0.79	0.719	0.864	0.79	0.719	0.864	SUBCLONAL	1	TRUE	1	0.7	2		525	434	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67197051	67197051	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	131	470	0	ENST00000312629.5:c.294G>A	p.Met98Ile	p.M98I	ENST00000312629	NM_003952.2	98	atG/atA	4/15	1	2	FACETS	0.81	0.74	0.882	0.81	0.74	0.882	CLONAL	1	TRUE	1	0.7	2		470	462	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202604	67202604	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	187	537	0	ENST00000312629.5:c.1413G>T	p.Lys471Asn	p.K471N	ENST00000312629	NM_003952.2	471	aaG/aaT	15/15	1	2	FACETS	0.929	0.864	0.996	0.929	0.864	0.996	CLONAL	1	TRUE	1	0.7	2		537	575	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94170395	94170395	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	77	277	0	ENST00000323929.3:c.1874A>C	p.Lys625Thr	p.K625T	ENST00000323929	NM_005591.3	625	aAa/aCa	17/20	1	2	FACETS	0.728	0.646	0.815	0.728	0.646	0.815	SUBCLONAL	1	TRUE	1	0.7	2		277	302	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94189473	94189473	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs757691558	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	101	457	0	ENST00000323929.3:c.1532del	p.Asn511IlefsTer13	p.N511Ifs*13	ENST00000323929	NM_005591.3	511	aAt/at	14/20	1	2	FACETS	0.77	0.694	0.849	0.77	0.694	0.849	SUBCLONAL	1	TRUE	1	0.7	2		457	375	SUCCESS
YAP1	10413	MSKCC	GRCh37	11	102080254	102080254	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs193100333	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	145	445	0	ENST00000282441.5:c.991C>T	p.Arg331Trp	p.R331W	ENST00000282441	NM_001130145.2	331	Cgg/Tgg	6/9	1	2	FACETS	0.963	0.887	1	0.963	0.887	1	CLONAL	1	TRUE	1	0.7	2		445	430	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114842	108114842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs145355104	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	92	412	0	ENST00000278616.4:c.659C>T	p.Ala220Val	p.A220V	ENST00000278616	NM_000051.3	220	gCg/gTg	6/63	1	2	FACETS	0.862	0.775	0.952	0.862	0.775	0.952	CLONAL	1	TRUE	1	0.7	2		412	305	SUCCESS
ATM	472	MSKCC	GRCh37	11	108159816	108159816	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	69	29	124	0	ENST00000278616.4:c.4222C>A	p.Leu1408Ile	p.L1408I	ENST00000278616	NM_000051.3	1408	Ctt/Att	28/63	1	2	FACETS	0.845	0.696	1	0.845	0.696	1	CLONAL	1	TRUE	1	0.7	2		124	98	SUCCESS
ATM	472	MSKCC	GRCh37	11	108190753	108190753	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587780635	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	104	496	0	ENST00000278616.4:c.6420C>A	p.Phe2140Leu	p.F2140L	ENST00000278616	NM_000051.3	2140	ttC/ttA	44/63	1	2	FACETS	0.849	0.768	0.933	0.849	0.768	0.933	CLONAL	1	TRUE	1	0.7	2		496	350	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342507	118342507	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	87	252	0	ENST00000534358.1:c.633G>T	p.Lys211Asn	p.K211N	ENST00000534358	NM_005933.3	211	aaG/aaT	3/36	1	2	FACETS	0.956	0.859	1	0.956	0.859	1	CLONAL	1	TRUE	1	0.7	2		252	260	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118342641	118342641	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	93	335	0	ENST00000534358.1:c.767T>G	p.Ile256Ser	p.I256S	ENST00000534358	NM_005933.3	256	aTt/aGt	3/36	1	2	FACETS	0.973	0.878	1	0.973	0.878	1	CLONAL	1	TRUE	1	0.7	2		335	273	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343093	118343093	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs868934108	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	109	344	1	ENST00000534358.1:c.1219C>T	p.Arg407Ter	p.R407*	ENST00000534358	NM_005933.3	407	Cga/Tga	3/36	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.7	2		345	292	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343805	118343805	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	144	481	3	ENST00000534358.1:c.1931G>A	p.Arg644His	p.R644H	ENST00000534358	NM_005933.3	644	cGc/cAc	3/36	1	2	FACETS	0.857	0.787	0.929	0.857	0.787	0.929	CLONAL	1	TRUE	1	0.7	2		484	480	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343933	118343933	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	94	338	0	ENST00000534358.1:c.2059A>T	p.Arg687Trp	p.R687W	ENST00000534358	NM_005933.3	687	Agg/Tgg	3/36	1	2	FACETS	0.939	0.847	1	0.939	0.847	1	CLONAL	1	TRUE	1	0.7	2		338	286	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118347602	118347602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	154	537	1	ENST00000534358.1:c.3239G>A	p.Gly1080Asp	p.G1080D	ENST00000534358	NM_005933.3	1080	gGc/gAc	4/36	1	2	FACETS	0.882	0.813	0.953	0.882	0.813	0.953	CLONAL	1	TRUE	1	0.7	2		538	499	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118372512	118372512	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	176	631	2	ENST00000534358.1:c.6445C>T	p.Arg2149Ter	p.R2149*	ENST00000534358	NM_005933.3	2149	Cga/Tga	26/36	1	2	FACETS	0.837	0.775	0.901	0.837	0.775	0.901	CLONAL	1	TRUE	1	0.7	2		633	601	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118377160	118377160	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	223	131	425	0	ENST00000534358.1:c.10553C>A	p.Ser3518Tyr	p.S3518Y	ENST00000534358	NM_005933.3	3518	tCt/tAt	27/36	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.7	2		425	354	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118380810	118380810	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	179	83	331	0	ENST00000534358.1:c.11048A>C	p.Gln3683Pro	p.Q3683P	ENST00000534358	NM_005933.3	3683	cAg/cCg	30/36	1	2	FACETS	0.905	0.81	1	0.905	0.81	1	CLONAL	1	TRUE	1	0.7	2		331	262	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144724	119144724	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1253824253	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	85	427	0	ENST00000264033.4:c.737G>A	p.Arg246Gln	p.R246Q	ENST00000264033	NM_005188.3	246	cGa/cAa	4/16	1	2	FACETS	0.804	0.719	0.894	0.804	0.719	0.894	CLONAL	1	TRUE	1	0.7	2		427	302	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170354	119170354	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507498	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	159	114	351	0	ENST00000264033.4:c.2584G>A	p.Glu862Lys	p.E862K	ENST00000264033	NM_005188.3	862	Gag/Aag	16/16	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.7	2		351	273	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402275	402275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751548422	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	179	630	1	ENST00000399788.2:c.4516C>T	p.Arg1506Trp	p.R1506W	ENST00000399788	NM_001042603.1	1506	Cgg/Tgg	27/28	1	2	FACETS	0.908	0.843	0.976	0.908	0.843	0.976	CLONAL	1	TRUE	1	0.7	2		631	563	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406212	406212	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	80	343	0	ENST00000399788.2:c.4229C>A	p.Ser1410Tyr	p.S1410Y	ENST00000399788	NM_001042603.1	1410	tCt/tAt	25/28	1	2	FACETS	0.843	0.752	0.939	0.843	0.752	0.939	CLONAL	1	TRUE	1	0.7	2		343	271	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	418983	418983	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	166	740	1	ENST00000399788.2:c.3364G>T	p.Asp1122Tyr	p.D1122Y	ENST00000399788	NM_001042603.1	1122	Gat/Tat	22/28	1	2	FACETS	0.848	0.784	0.915	0.848	0.784	0.915	CLONAL	1	TRUE	1	0.7	2		741	559	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	464374	464374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1225548195	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	150	538	1	ENST00000399788.2:c.820G>A	p.Ala274Thr	p.A274T	ENST00000399788	NM_001042603.1	274	Gca/Aca	7/28	1	2	FACETS	0.938	0.864	1	0.938	0.864	1	CLONAL	1	TRUE	1	0.7	2		539	457	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18466940	18466940	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	156	526	0	ENST00000266497.5:c.1079C>A	p.Ser360Tyr	p.S360Y	ENST00000266497		360	tCt/tAt	5/31	1	2	FACETS	0.969	0.895	1	0.969	0.895	1	CLONAL	1	TRUE	1	0.7	2		526	460	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793366	18793366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	73	355	0	ENST00000266497.5:c.4063C>A	p.Leu1355Ile	p.L1355I	ENST00000266497		1355	Ctc/Atc	30/31	1	2	FACETS	0.851	0.755	0.952	0.851	0.755	0.952	CLONAL	1	TRUE	1	0.7	2		355	245	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21630748	21630748	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	180	92	372	0	ENST00000421138.2:c.856C>A	p.Leu286Ile	p.L286I	ENST00000421138		286	Cta/Ata	8/16	1	2	FACETS	0.966	0.871	1	0.966	0.871	1	CLONAL	1	TRUE	1	0.7	2		372	272	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427369	49427369	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1565779294	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	189	600	1	ENST00000301067.7:c.11119C>T	p.Arg3707Ter	p.R3707*	ENST00000301067	NM_003482.3	3707	Cga/Tga	39/54	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.7	2		601	533	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435243	49435243	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	183	685	2	ENST00000301067.7:c.6310C>A	p.Leu2104Ile	p.L2104I	ENST00000301067	NM_003482.3	2104	Ctc/Atc	31/54	1	2	FACETS	0.901	0.837	0.968	0.901	0.837	0.968	CLONAL	1	TRUE	1	0.7	2		687	580	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480629	50480629	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	143	427	0	ENST00000394963.4:c.499G>T	p.Asp167Tyr	p.D167Y	ENST00000394963	NM_003076.4	167	Gat/Tat	4/13	1	2	FACETS	0.985	0.907	1	0.985	0.907	1	CLONAL	1	TRUE	1	0.7	2		427	415	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56481660	56481660	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	234	627	0	ENST00000267101.3:c.695C>T	p.Ala232Val	p.A232V	ENST00000267101	NM_001982.3	232	gCc/gTc	6/28	1	2	FACETS	0.992	0.93	1	0.992	0.93	1	CLONAL	1	TRUE	1	0.7	2		627	674	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143065	58143065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531817742	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	212	622	0	ENST00000257904.6:c.719G>A	p.Arg240Gln	p.R240Q	ENST00000257904	NM_000075.3	240	cGa/cAa	7/8	1	2	FACETS	0.945	0.883	1	0.945	0.883	1	CLONAL	1	TRUE	1	0.7	2		622	641	SUCCESS
IGF1	3479	MSKCC	GRCh37	12	102869539	102869539	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	202	502	0	ENST00000307046.8:c.102C>A	p.Tyr34Ter	p.Y34*	ENST00000307046	NM_001111285.1	34	taC/taA	2/4	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.7	2		502	550	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112891035	112891035	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs755619262	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	90	323	0	ENST00000351677.2:c.369G>T	p.Glu123Asp	p.E123D	ENST00000351677	NM_002834.3	123	gaG/gaT	4/16	1	2	FACETS	0.863	0.775	0.955	0.863	0.775	0.955	CLONAL	1	TRUE	1	0.7	2		323	298	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120640	115120640	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	225	789	0	ENST00000257566.3:c.366G>T	p.Glu122Asp	p.E122D	ENST00000257566	NM_016569.3	122	gaG/gaT	1/8	1	2	FACETS	0.888	0.83	0.947	0.888	0.83	0.947	CLONAL	1	TRUE	1	0.7	2		789	724	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115120675	115120675	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	59	750	1	ENST00000257566.3:c.331G>T	p.Glu111Ter	p.E111*	ENST00000257566	NM_016569.3	111	Gaa/Taa	1/8	1	2	FACETS	0.243	0.208	0.28	0.243	0.208	0.28	SUBCLONAL	1	TRUE	1	0.7	2		751	695	SUCCESS
KMT5A	387893	MSKCC	GRCh37	12	123879656	123879656	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	100	286	0	ENST00000330479.4:c.352G>T	p.Asp118Tyr	p.D118Y	ENST00000330479	NM_020382.3	118	Gac/Tac	4/9	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.7	2		286	274	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249847	133249847	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	145	475	0	ENST00000320574.5:c.1376C>A	p.Ser459Tyr	p.S459Y	ENST00000320574	NM_006231.2	459	tCt/tAt	14/49	1	2	FACETS	0.939	0.865	1	0.939	0.865	1	CLONAL	1	TRUE	1	0.7	2		475	441	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133257255	133257255	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	151	497	1	ENST00000320574.5:c.223G>T	p.Asp75Tyr	p.D75Y	ENST00000320574	NM_006231.2	75	Gat/Tat	3/49	1	2	FACETS	0.836	0.769	0.905	0.836	0.769	0.905	CLONAL	1	TRUE	1	0.7	2		498	516	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563383	21563383	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	275	814	2	ENST00000382592.4:c.536C>T	p.Ser179Leu	p.S179L	ENST00000382592	NM_014572.2	179	tCg/tTg	4/8	1	2	FACETS	0.955	0.899	1	0.955	0.899	1	CLONAL	1	TRUE	1	0.7	2		816	823	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622526	28622526	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1231097306	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	102	424	0	ENST00000241453.7:c.1091A>G	p.Tyr364Cys	p.Y364C	ENST00000241453	NM_004119.2	364	tAt/tGt	9/24	1	2	FACETS	0.814	0.735	0.896	0.814	0.735	0.896	CLONAL	1	TRUE	1	0.7	2		424	358	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623571	28623571	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762424747	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	152	404	0	ENST00000241453.7:c.986C>T	p.Thr329Ile	p.T329I	ENST00000241453	NM_004119.2	329	aCt/aTt	8/24	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.7	2		404	419	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28636086	28636086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1044875315	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	133	539	1	ENST00000241453.7:c.286G>A	p.Asp96Asn	p.D96N	ENST00000241453	NM_004119.2	96	Gac/Aac	3/24	1	2	FACETS	0.752	0.687	0.82	0.752	0.687	0.82	SUBCLONAL	1	TRUE	1	0.7	2		540	505	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32899248	32899248	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375125172	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	95	368	0	ENST00000380152.3:c.352C>T	p.Arg118Cys	p.R118C	ENST00000380152		118	Cgc/Tgc	4/27	1	2	FACETS	0.722	0.648	0.799	0.722	0.648	0.799	SUBCLONAL	1	TRUE	1	0.7	2		368	376	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32903598	32903598	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	168	100	392	0	ENST00000380152.3:c.650C>T	p.Ser217Phe	p.S217F	ENST00000380152		217	tCt/tTt	8/27	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.7	2		392	268	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906750	32906750	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	154	627	1	ENST00000380152.3:c.1135G>T	p.Gly379Ter	p.G379*	ENST00000380152		379	Gga/Tga	10/27	1	2	FACETS	0.987	0.911	1	0.987	0.911	1	CLONAL	1	TRUE	1	0.7	2		628	446	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32907384	32907384	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs80358459	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	96	392	0	ENST00000380152.3:c.1769T>G	p.Phe590Cys	p.F590C	ENST00000380152		590	tTt/tGt	10/27	1	2	FACETS	0.983	0.889	1	0.983	0.889	1	CLONAL	1	TRUE	1	0.7	2		392	279	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911909	32911909	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs145625991	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	125	539	0	ENST00000380152.3:c.3417G>T	p.Lys1139Asn	p.K1139N	ENST00000380152		1139	aaG/aaT	11/27	1	2	FACETS	0.932	0.853	1	0.932	0.853	1	CLONAL	1	TRUE	1	0.7	2		539	383	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912750	32912753	+	missense_variant	Missense_Mutation	ONP	GATT	GATT	TATG	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	83	334	0	ENST00000380152.3:c.4258_4261delinsTATG	p.Asp1420_Phe1421delinsTyrVal	p.D1420_F1421delinsYV	ENST00000380152		1420	GATTtt/TATGtt	11/27	1	2	FACETS	0.815	0.727	0.906	0.815	0.727	0.906	CLONAL	1	TRUE	1	0.7	2		334	291	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918761	32918761	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1239798218	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	79	310	0	ENST00000380152.3:c.6908C>T	p.Ser2303Phe	p.S2303F	ENST00000380152		2303	tCc/tTc	12/27	1	2	FACETS	0.83	0.739	0.925	0.83	0.739	0.925	CLONAL	1	TRUE	1	0.7	2		310	272	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32920979	32920979	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358921	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	109	436	1	ENST00000380152.3:c.6953G>A	p.Arg2318Gln	p.R2318Q	ENST00000380152		2318	cGa/cAa	13/27	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.7	2		437	293	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972900	32972900	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs730881600	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	150	70	303	0	ENST00000380152.3:c.10250A>G	p.Tyr3417Cys	p.Y3417C	ENST00000380152		3417	tAt/tGt	27/27	1	2	FACETS	0.909	0.805	1	0.909	0.805	1	CLONAL	1	TRUE	1	0.7	2		303	220	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133773	41133773	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1164031879	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	85	346	0	ENST00000379561.5:c.1855C>T	p.Arg619Trp	p.R619W	ENST00000379561	NM_002015.3	619	Cgg/Tgg	2/3	1	2	FACETS	0.849	0.76	0.942	0.849	0.76	0.942	CLONAL	1	TRUE	1	0.7	2		346	286	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41133851	41133851	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	79	286	0	ENST00000379561.5:c.1777C>A	p.Leu593Ile	p.L593I	ENST00000379561	NM_002015.3	593	Ctc/Atc	2/3	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.7	2		286	211	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281497	49281497	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201906229	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	133	574	0	ENST00000282018.3:c.544G>A	p.Gly182Ser	p.G182S	ENST00000282018	NM_020377.2	182	Ggc/Agc	1/1	1	2	FACETS	0.856	0.783	0.931	0.856	0.783	0.931	CLONAL	1	TRUE	1	0.7	2		574	444	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73336276	73336276	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	93	44	183	0	ENST00000377767.4:c.2128-1G>T		p.X710_splice	ENST00000377767	NM_014953.3	710			1	2	FACETS	0.918	0.787	1	0.918	0.787	1	CLONAL	1	TRUE	1	0.7	2		183	137	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103504542	103504542	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	101	313	0	ENST00000355739.4:c.163C>A	p.Leu55Ile	p.L55I	ENST00000355739	NM_000123.3	55	Ctt/Att	2/15	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.7	2		313	273	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514775	103514775	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603745	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	124	416	0	ENST00000355739.4:c.1276G>A	p.Glu426Lys	p.E426K	ENST00000355739	NM_000123.3	426	Gag/Aag	8/15	1	2	FACETS	0.789	0.719	0.862	0.789	0.719	0.862	SUBCLONAL	1	TRUE	1	0.7	2		416	449	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103525652	103525652	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	122	417	0	ENST00000355739.4:c.2923G>T	p.Glu975Ter	p.E975*	ENST00000355739	NM_000123.3	975	Gaa/Taa	14/15	1	2	FACETS	0.92	0.84	1	0.92	0.84	1	CLONAL	1	TRUE	1	0.7	2		417	379	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609390	81609390	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	155	420	0	ENST00000298171.2:c.988C>A	p.Leu330Met	p.L330M	ENST00000298171	NM_000369.2	330	Ctg/Atg	10/10	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.7	2		420	436	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95562618	95562618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	133	356	1	ENST00000393063.1:c.4639G>A	p.Asp1547Asn	p.D1547N	ENST00000393063	NM_030621.3	1547	Gac/Aac	24/28	1	2	FACETS	0.995	0.913	1	0.995	0.913	1	CLONAL	1	TRUE	1	0.7	2		357	382	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95563044	95563044	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	64	217	0	ENST00000393063.1:c.4213G>T	p.Asp1405Tyr	p.D1405Y	ENST00000393063	NM_030621.3	1405	Gac/Tac	24/28	1	2	FACETS	0.947	0.835	1	0.947	0.835	1	CLONAL	1	TRUE	1	0.7	2		217	193	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643599	38643599	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	161	490	0	ENST00000299084.4:c.1069G>T	p.Asp357Tyr	p.D357Y	ENST00000299084	NM_152594.2	357	Gac/Tac	7/7	1	2	FACETS	0.915	0.845	0.986	0.915	0.845	0.986	CLONAL	1	TRUE	1	0.7	2		490	503	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40998435	40998435	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1013168760	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	173	671	4	ENST00000267868.3:c.286C>T	p.Arg96Trp	p.R96W	ENST00000267868	NM_002875.4	96	Cgg/Tgg	4/10	1	2	FACETS	0.81	0.749	0.873	0.81	0.749	0.873	CLONAL	1	TRUE	1	0.7	2		675	610	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41988654	41988654	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs765283602	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	266	103	383	0	ENST00000219905.7:c.1446G>T	p.Lys482Asn	p.K482N	ENST00000219905	NM_001164273.1	482	aaG/aaT	3/24	1	2	FACETS	0.798	0.72	0.878	0.798	0.72	0.878	SUBCLONAL	1	TRUE	1	0.7	2		383	369	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42050032	42050032	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	191	83	325	0	ENST00000219905.7:c.7186C>T	p.Arg2396Ter	p.R2396*	ENST00000219905	NM_001164273.1	2396	Cga/Tga	19/24	1	2	FACETS	0.865	0.774	0.961	0.865	0.774	0.961	CLONAL	1	TRUE	1	0.7	2		325	274	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42053997	42053997	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	99	603	1	ENST00000219905.7:c.7459C>A	p.Leu2487Ile	p.L2487I	ENST00000219905	NM_001164273.1	2487	Ctc/Atc	21/24	1	2	FACETS	0.818	0.737	0.901	0.818	0.737	0.901	CLONAL	1	TRUE	1	0.7	2		604	346	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701231	43701231	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	230	622	0	ENST00000382044.4:c.5464C>A	p.Leu1822Met	p.L1822M	ENST00000382044	NM_001141980.1	1822	Ctg/Atg	26/28	1	2	FACETS	0.968	0.907	1	0.968	0.907	1	CLONAL	1	TRUE	1	0.7	2		622	679	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43724594	43724594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	253	766	0	ENST00000382044.4:c.3473G>A	p.Gly1158Glu	p.G1158E	ENST00000382044	NM_001141980.1	1158	gGa/gAa	17/28	1	2	FACETS	0.946	0.889	1	0.946	0.889	1	CLONAL	1	TRUE	1	0.7	2		766	764	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66777506	66777506	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	29	530	2	ENST00000307102.5:c.872G>T	p.Arg291Met	p.R291M	ENST00000307102	NM_002755.3	291	aGg/aTg	7/11	1	2	FACETS	0.163	0.131	0.201	0.163	0.131	0.201	SUBCLONAL	1	TRUE	1	0.7	2		532	507	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67477106	67477106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1348033858	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	170	552	2	ENST00000327367.4:c.913G>A	p.Ala305Thr	p.A305T	ENST00000327367	NM_005902.3	305	Gca/Aca	7/9	1	2	FACETS	0.969	0.899	1	0.969	0.899	1	CLONAL	1	TRUE	1	0.7	2		554	501	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680783	88680783	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	201	562	0	ENST00000360948.2:c.474G>T	p.Glu158Asp	p.E158D	ENST00000360948	NM_001012338.2	158	gaG/gaT	6/19	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.7	2		562	541	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631934	90631934	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913502	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	29	650	1	ENST00000330062.3:c.419G>T	p.Arg140Leu	p.R140L	ENST00000330062	NM_002168.2	140	cGg/cTg	4/11	1	2	FACETS	0.129	0.103	0.16	0.129	0.103	0.16	SUBCLONAL	1	TRUE	1	0.7	2		651	640	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99486166	99486166	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1287599859	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	131	392	0	ENST00000268035.6:c.3472C>T	p.Arg1158Ter	p.R1158*	ENST00000268035	NM_000875.3	1158	Cga/Tga	19/21	1	2	FACETS	0.866	0.793	0.942	0.866	0.793	0.942	CLONAL	1	TRUE	1	0.7	2		392	432	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2104303	2104303	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1256047792	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	149	421	0	ENST00000219476.3:c.343C>T	p.Arg115Cys	p.R115C	ENST00000219476	NM_000548.3	115	Cgt/Tgt	5/42	1	2	FACETS	0.94	0.866	1	0.94	0.866	1	CLONAL	1	TRUE	1	0.7	2		421	453	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2122887	2122887	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	223	621	0	ENST00000219476.3:c.2258C>T	p.Ala753Val	p.A753V	ENST00000219476	NM_000548.3	753	gCc/gTc	21/42	1	2	FACETS	0.948	0.887	1	0.948	0.887	1	CLONAL	1	TRUE	1	0.7	2		621	672	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2225841	2225841	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1211399252	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	156	587	1	ENST00000326181.6:c.1633G>A	p.Asp545Asn	p.D545N	ENST00000326181	NM_032271.2	545	Gac/Aac	18/21	1	2	FACETS	0.917	0.846	0.99	0.917	0.846	0.99	CLONAL	1	TRUE	1	0.7	2		588	486	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639116	3639116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs112694849	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	222	688	1	ENST00000294008.3:c.4523C>T	p.Ser1508Leu	p.S1508L	ENST00000294008	NM_032444.2	1508	tCg/tTg	12/15	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.7	2		689	628	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641146	3641146	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	348	893	2	ENST00000294008.3:c.2493G>T	p.Glu831Asp	p.E831D	ENST00000294008	NM_032444.2	831	gaG/gaT	12/15	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.7	2		895	982	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858688	9858688	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	231	121	384	0	ENST00000330684.3:c.2713T>A	p.Ser905Thr	p.S905T	ENST00000330684	NM_001134407.1	905	Tcc/Acc	13/13	1	2	FACETS	0.982	0.898	1	0.982	0.898	1	CLONAL	1	TRUE	1	0.7	2		384	352	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9984919	9984919	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	177	607	0	ENST00000330684.3:c.1046C>T	p.Ser349Phe	p.S349F	ENST00000330684	NM_001134407.1	349	tCc/tTc	4/13	1	2	FACETS	0.919	0.853	0.988	0.919	0.853	0.988	CLONAL	1	TRUE	1	0.7	2		607	550	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10274136	10274136	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	149	500	1	ENST00000330684.3:c.133G>T	p.Asp45Tyr	p.D45Y	ENST00000330684	NM_001134407.1	45	Gac/Tac	2/13	1	2	FACETS	0.985	0.909	1	0.985	0.909	1	CLONAL	1	TRUE	1	0.7	2		501	432	SUCCESS
SOCS1	8651	MSKCC	GRCh37	16	11349128	11349128	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1394282648	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	229	129	347	0	ENST00000332029.2:c.208G>A	p.Ala70Thr	p.A70T	ENST00000332029	NM_003745.1	70	Gcc/Acc	2/2	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.7	2		347	358	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14029225	14029225	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	225	105	311	1	ENST00000311895.7:c.1436C>A	p.Ser479Tyr	p.S479Y	ENST00000311895	NM_005236.2	479	tCt/tAt	8/11	1	2	FACETS	0.909	0.824	0.997	0.909	0.824	0.997	CLONAL	1	TRUE	1	0.7	2		312	330	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041557	14041557	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180030515	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	151	473	0	ENST00000311895.7:c.2104C>T	p.Arg702Trp	p.R702W	ENST00000311895	NM_005236.2	702	Cgg/Tgg	11/11	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.7	2		473	413	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23637624	23637624	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	260	661	0	ENST00000261584.4:c.2681T>C	p.Val894Ala	p.V894A	ENST00000261584	NM_024675.3	894	gTa/gCa	7/13	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.7	2		661	672	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646338	23646338	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	166	576	0	ENST00000261584.4:c.1529G>T	p.Arg510Ile	p.R510I	ENST00000261584	NM_024675.3	510	aGa/aTa	4/13	1	2	FACETS	0.888	0.821	0.957	0.888	0.821	0.957	CLONAL	1	TRUE	1	0.7	2		576	534	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68857512	68857512	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	117	373	0	ENST00000261769.5:c.2147G>T	p.Gly716Val	p.G716V	ENST00000261769	NM_004360.3	716	gGa/gTa	13/16	1	2	FACETS	0.842	0.766	0.921	0.842	0.766	0.921	CLONAL	1	TRUE	1	0.7	2		373	397	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821530	72821530	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773606987	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	229	396	0	ENST00000268489.5:c.10645G>A	p.Glu3549Lys	p.E3549K	ENST00000268489	NM_006885.3	3549	Gag/Aag	10/10	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.7	2		396	578	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828204	72828204	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs953508094	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	165	550	0	ENST00000268489.5:c.8377G>A	p.Glu2793Lys	p.E2793K	ENST00000268489	NM_006885.3	2793	Gaa/Aaa	9/10	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.7	2		550	461	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828503	72828503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	188	519	0	ENST00000268489.5:c.8078G>A	p.Arg2693Gln	p.R2693Q	ENST00000268489	NM_006885.3	2693	cGa/cAa	9/10	1	2	FACETS	0.961	0.894	1	0.961	0.894	1	CLONAL	1	TRUE	1	0.7	2		519	559	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993335	72993335	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773329700	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	276	690	0	ENST00000268489.5:c.710G>A	p.Arg237Gln	p.R237Q	ENST00000268489	NM_006885.3	237	cGa/cAa	2/10	1	2	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	1	0.7	2		690	690	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81954827	81954827	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	118	616	0	ENST00000359376.3:c.2260G>A	p.Asp754Asn	p.D754N	ENST00000359376	NM_002661.3	754	Gac/Aac	21/33	1	2	FACETS	0.664	0.602	0.729	0.664	0.602	0.729	SUBCLONAL	1	TRUE	1	0.7	2		616	508	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81960742	81960742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768839912	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	166	639	1	ENST00000359376.3:c.2473G>A	p.Glu825Lys	p.E825K	ENST00000359376	NM_002661.3	825	Gag/Aag	23/33	1	2	FACETS	0.805	0.743	0.869	0.805	0.743	0.869	CLONAL	1	TRUE	1	0.7	2		640	589	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990351	81990351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	208	575	0	ENST00000359376.3:c.3622G>A	p.Glu1208Lys	p.E1208K	ENST00000359376	NM_002661.3	1208	Gaa/Aaa	32/33	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.7	2		575	592	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990429	81990429	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	175	588	0	ENST00000359376.3:c.3700G>T	p.Glu1234Ter	p.E1234*	ENST00000359376	NM_002661.3	1234	Gag/Tag	32/33	1	2	FACETS	0.924	0.857	0.993	0.924	0.857	0.993	CLONAL	1	TRUE	1	0.7	2		588	541	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89857912	89857912	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760352719	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	203	547	1	ENST00000389301.3:c.1258G>A	p.Glu420Lys	p.E420K	ENST00000389301	NM_000135.2	420	Gag/Aag	14/43	0.239069935637397	1	FACETS	0.731	0.683	0.778	0.731	0.683	0.778	INDETERMINATE	1	TRUE	0	0.7	1		548	516	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7976219	7976219	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779729947	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	138	459	0	ENST00000319144.4:c.1976G>A	p.Arg659Gln	p.R659Q	ENST00000319144	NM_001139.2	659	cGg/cAg	15/15	1	2	FACETS	0.886	0.813	0.961	0.886	0.813	0.961	CLONAL	1	TRUE	1	0.7	2		459	445	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984460	7984460	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	224	567	0	ENST00000319144.4:c.398G>T	p.Arg133Ile	p.R133I	ENST00000319144	NM_001139.2	133	aGa/aTa	3/15	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.7	2		567	637	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16024417	16024417	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771531803	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	107	284	1	ENST00000268712.3:c.1801G>A	p.Ala601Thr	p.A601T	ENST00000268712	NM_006311.3	601	Gca/Aca	16/46	1	2	FACETS	0.932	0.846	1	0.932	0.846	1	CLONAL	1	TRUE	1	0.7	2		285	328	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16089913	16089913	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	134	353	1	ENST00000268712.3:c.197G>A	p.Arg66Gln	p.R66Q	ENST00000268712	NM_006311.3	66	cGa/cAa	3/46	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.7	2		354	382	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29497004	29497004	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587781670	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	155	77	255	0	ENST00000356175.3:c.575G>A	p.Arg192Gln	p.R192Q	ENST00000356175	NM_000267.3	192	cGa/cAa	5/57	1	2	FACETS	0.948	0.846	1	0.948	0.846	1	CLONAL	1	TRUE	1	0.7	2		255	232	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29533315	29533315	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs778405030	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	107	449	0	ENST00000356175.3:c.1318C>T	p.Arg440Ter	p.R440*	ENST00000356175	NM_000267.3	440	Cga/Tga	12/57	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.7	2		449	291	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29548950	29548950	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	G	rs1057518904	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	33	228	0	ENST00000356175.3:c.1721+3A>G		p.X574_splice	ENST00000356175	NM_000267.3	574			1	2	FACETS	0.597	0.492	0.711	0.597	0.492	0.711	SUBCLONAL	1	TRUE	1	0.7	2		228	158	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29653028	29653028	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756450772	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	120	384	0	ENST00000356175.3:c.4963G>A	p.Ala1655Thr	p.A1655T	ENST00000356175	NM_000267.3	1655	Gca/Aca	36/57	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.7	2		384	335	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29663686	29663686	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	132	477	0	ENST00000356175.3:c.6118A>G	p.Thr2040Ala	p.T2040A	ENST00000356175	NM_000267.3	2040	Aca/Gca	41/57	1	2	FACETS	0.9	0.824	0.978	0.9	0.824	0.978	CLONAL	1	TRUE	1	0.7	2		477	419	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29677216	29677216	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	85	360	0	ENST00000356175.3:c.7274C>A	p.Ser2425Tyr	p.S2425Y	ENST00000356175	NM_000267.3	2425	tCt/tAt	49/57	1	2	FACETS	0.829	0.741	0.92	0.829	0.741	0.92	CLONAL	1	TRUE	1	0.7	2		360	293	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30302690	30302690	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	96	571	0	ENST00000322652.5:c.781G>T	p.Glu261Ter	p.E261*	ENST00000322652	NM_015355.2	261	Gag/Tag	7/16	1	2	FACETS	0.636	0.57	0.706	0.636	0.57	0.706	SUBCLONAL	1	TRUE	1	0.7	2		571	431	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30321677	30321677	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	147	674	0	ENST00000322652.5:c.1532G>A	p.Gly511Glu	p.G511E	ENST00000322652	NM_015355.2	511	gGa/gAa	13/16	1	2	FACETS	0.854	0.785	0.925	0.854	0.785	0.925	CLONAL	1	TRUE	1	0.7	2		674	492	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30325762	30325762	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs771704089	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	133	68	298	0	ENST00000322652.5:c.1960C>T	p.Arg654Ter	p.R654*	ENST00000322652	NM_015355.2	654	Cga/Tga	16/16	1	2	FACETS	0.967	0.856	1	0.967	0.856	1	CLONAL	1	TRUE	1	0.7	2		298	201	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37657655	37657655	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	28	553	1	ENST00000447079.4:c.2572C>T	p.Arg858Trp	p.R858W	ENST00000447079	NM_015083.1	858	Cgg/Tgg	6/14	1	2	FACETS	0.166	0.132	0.204	0.166	0.132	0.204	SUBCLONAL	1	TRUE	1	0.7	2		554	483	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37865694	37865694	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763371007	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	182	553	2	ENST00000269571.5:c.563G>A	p.Arg188His	p.R188H	ENST00000269571		188	cGc/cAc	4/27	1	2	FACETS	0.889	0.825	0.955	0.889	0.825	0.955	CLONAL	1	TRUE	1	0.7	2		555	585	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40481459	40481459	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	164	563	1	ENST00000264657.5:c.1250G>T	p.Arg417Ile	p.R417I	ENST00000264657	NM_139276.2	417	aGa/aTa	14/24	1	2	FACETS	0.891	0.823	0.96	0.891	0.823	0.96	CLONAL	1	TRUE	1	0.7	2		564	526	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40498636	40498636	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	177	468	0	ENST00000264657.5:c.224C>T	p.Ser75Leu	p.S75L	ENST00000264657	NM_139276.2	75	tCg/tTg	3/24	1	2	FACETS	0.988	0.917	1	0.988	0.917	1	CLONAL	1	TRUE	1	0.7	2		468	512	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40859995	40859995	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	150	438	0	ENST00000428826.2:c.1641C>A	p.Phe547Leu	p.F547L	ENST00000428826		547	ttC/ttA	15/21	1	2	FACETS	0.873	0.804	0.944	0.873	0.804	0.944	CLONAL	1	TRUE	1	0.7	2		438	491	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40880886	40880886	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	197	661	0	ENST00000428826.2:c.74G>A	p.Arg25Gln	p.R25Q	ENST00000428826		25	cGa/cAa	3/21	1	2	FACETS	0.888	0.826	0.951	0.888	0.826	0.951	CLONAL	1	TRUE	1	0.7	2		661	634	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41245260	41245260	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	186	585	1	ENST00000357654.3:c.2288C>A	p.Ser763Tyr	p.S763Y	ENST00000357654	NM_007294.3	763	tCt/tAt	10/23	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.7	2		586	528	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58711228	58711228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	132	537	0	ENST00000305921.3:c.716C>T	p.Ser239Phe	p.S239F	ENST00000305921	NM_003620.3	239	tCt/tTt	3/6	1	2	FACETS	0.801	0.732	0.872	0.801	0.732	0.872	CLONAL	1	TRUE	1	0.7	2		537	471	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761021	59761021	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	112	757	0	ENST00000259008.2:c.3386C>T	p.Ser1129Phe	p.S1129F	ENST00000259008	NM_032043.2	1129	tCt/tTt	20/20	1	2	FACETS	0.872	0.792	0.955	0.872	0.792	0.955	CLONAL	1	TRUE	1	0.7	2		757	367	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63532456	63532456	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs587780123	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	188	548	4	ENST00000307078.5:c.2123C>T	p.Ser708Leu	p.S708L	ENST00000307078	NM_004655.3	708	tCg/tTg	8/11	1	2	FACETS	0.97	0.902	1	0.97	0.902	1	CLONAL	1	TRUE	1	0.7	2		552	554	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78931486	78931486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	370	191	506	0	ENST00000306801.3:c.3433C>T	p.Arg1145Trp	p.R1145W	ENST00000306801	NM_020761.2	1145	Cgg/Tgg	29/34	1	2	FACETS	0.973	0.906	1	0.973	0.906	1	CLONAL	1	TRUE	1	0.7	2		506	561	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78936277	78936277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1476697249	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	171	574	0	ENST00000306801.3:c.3709C>T	p.Arg1237Cys	p.R1237C	ENST00000306801	NM_020761.2	1237	Cgc/Tgc	32/34	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.7	2		574	476	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743327	743327	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	149	560	0	ENST00000314574.4:c.813A>C	p.Glu271Asp	p.E271D	ENST00000314574	NM_005433.3	271	gaA/gaC	7/12	1	2	FACETS	0.845	0.777	0.915	0.845	0.777	0.915	CLONAL	1	TRUE	1	0.7	2		560	504	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39609394	39609394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1360571803	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	120	421	0	ENST00000262039.4:c.1696C>T	p.Arg566Cys	p.R566C	ENST00000262039	NM_002647.2	566	Cgt/Tgt	15/25	1	2	FACETS	0.749	0.68	0.82	0.749	0.68	0.82	SUBCLONAL	1	TRUE	1	0.7	2		421	458	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56401549	56401549	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	253	143	447	0	ENST00000348428.3:c.1411G>A	p.Asp471Asn	p.D471N	ENST00000348428	NM_006785.3	471	Gat/Aat	12/17	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.7	2		447	396	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60985760	60985760	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1448547701	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	80	236	0	ENST00000333681.4:c.140G>T	p.Gly47Val	p.G47V	ENST00000333681		47	gGc/gTc	2/3	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.7	2		236	194	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1621011	1621011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs963433488	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	275	822	1	ENST00000344749.5:c.1049C>T	p.Ser350Leu	p.S350L	ENST00000344749	NM_001136139.2	350	tCg/tTg	13/19	1	2	FACETS	0.977	0.921	1	0.977	0.921	1	CLONAL	1	TRUE	1	0.7	2		823	804	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622223	1622223	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	35	518	0	ENST00000344749.5:c.653-1G>T		p.X218_splice	ENST00000344749	NM_001136139.2	218			1	2	FACETS	0.228	0.187	0.275	0.228	0.187	0.275	SUBCLONAL	1	TRUE	1	0.7	2		518	438	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222136	2222136	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	235	703	1	ENST00000398665.3:c.2968C>A	p.Leu990Met	p.L990M	ENST00000398665	NM_032482.2	990	Ctg/Atg	24/28	1	2	FACETS	0.959	0.899	1	0.959	0.899	1	CLONAL	1	TRUE	1	0.7	2		704	700	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3110150	3110150	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	97	358	0	ENST00000078429.4:c.140C>A	p.Thr47Lys	p.T47K	ENST00000078429	NM_002067.2	47	aCg/aAg	2/7	1	2	FACETS	0.921	0.831	1	0.921	0.831	1	CLONAL	1	TRUE	1	0.7	2		358	301	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121094	3121094	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs776555145	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	224	638	0	ENST00000078429.4:c.997G>A	p.Asp333Asn	p.D333N	ENST00000078429	NM_002067.2	333	Gac/Aac	7/7	1	2	FACETS	0.928	0.868	0.989	0.928	0.868	0.989	CLONAL	1	TRUE	1	0.7	2		638	690	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208367	5208367	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	216	537	0	ENST00000357368.4:c.5523C>A	p.Phe1841Leu	p.F1841L	ENST00000357368	NM_002850.3	1841	ttC/ttA	36/38	1	2	FACETS	0.976	0.913	1	0.976	0.913	1	CLONAL	1	TRUE	1	0.7	2		537	632	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5210733	5210733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779302415	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	222	617	0	ENST00000357368.4:c.5318C>T	p.Ser1773Leu	p.S1773L	ENST00000357368	NM_002850.3	1773	tCg/tTg	34/38	1	2	FACETS	0.971	0.909	1	0.971	0.909	1	CLONAL	1	TRUE	1	0.7	2		617	653	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7125350	7125350	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762687424	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	203	636	0	ENST00000302850.5:c.3202C>T	p.Arg1068Trp	p.R1068W	ENST00000302850	NM_000208.2	1068	Cgg/Tgg	17/22	1	2	FACETS	0.927	0.864	0.991	0.927	0.864	0.991	CLONAL	1	TRUE	1	0.7	2		636	626	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7143088	7143088	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	191	454	0	ENST00000302850.5:c.2281C>T	p.Arg761Cys	p.R761C	ENST00000302850	NM_000208.2	761	Cgc/Tgc	12/22	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.7	2		454	523	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7184622	7184622	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1331227306	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	79	240	0	ENST00000302850.5:c.679G>A	p.Gly227Ser	p.G227S	ENST00000302850	NM_000208.2	227	Ggc/Agc	3/22	1	2	FACETS	0.899	0.802	1	0.899	0.802	1	CLONAL	1	TRUE	1	0.7	2		240	251	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267569	7267569	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	239	608	4	ENST00000302850.5:c.439G>A	p.Glu147Lys	p.E147K	ENST00000302850	NM_000208.2	147	Gag/Aag	2/22	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.7	2		612	657	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10265322	10265322	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	175	490	0	ENST00000340748.4:c.1724T>C	p.Ile575Thr	p.I575T	ENST00000340748		575	aTc/aCc	20/40	1	2	FACETS	0.988	0.917	1	0.988	0.917	1	CLONAL	1	TRUE	1	0.7	2		490	506	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10283787	10283787	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	234	598	1	ENST00000340748.4:c.699G>T	p.Lys233Asn	p.K233N	ENST00000340748		233	aaG/aaT	8/40	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.7	2		599	630	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15281566	15281566	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	261	744	3	ENST00000263388.2:c.4807G>A	p.Asp1603Asn	p.D1603N	ENST00000263388	NM_000435.2	1603	Gat/Aat	26/33	1	2	FACETS	0.98	0.922	1	0.98	0.922	1	CLONAL	1	TRUE	1	0.7	2		747	761	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15298083	15298083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs544145401	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	266	773	0	ENST00000263388.2:c.1673G>A	p.Arg558His	p.R558H	ENST00000263388	NM_000435.2	558	cGc/cAc	11/33	1	2	FACETS	0.96	0.903	1	0.96	0.903	1	CLONAL	1	TRUE	1	0.7	2		773	792	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349733	15349733	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754054879	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	152	653	1	ENST00000263377.2:c.3841C>T	p.Arg1281Trp	p.R1281W	ENST00000263377	NM_058243.2	1281	Cgg/Tgg	19/20	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.7	2		654	425	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379758	17379758	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754145226	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	211	695	4	ENST00000359435.4:c.143G>A	p.Arg48His	p.R48H	ENST00000359435	NM_001033549.1	48	cGc/cAc	2/9	1	2	FACETS	0.724	0.673	0.776	0.724	0.673	0.776	SUBCLONAL	1	TRUE	1	0.7	2		699	833	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17948774	17948774	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	248	743	0	ENST00000458235.1:c.1668G>T	p.Lys556Asn	p.K556N	ENST00000458235	NM_000215.3	556	aaG/aaT	12/24	1	2	FACETS	0.963	0.904	1	0.963	0.904	1	CLONAL	1	TRUE	1	0.7	2		743	736	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955169	17955169	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	228	704	0	ENST00000458235.1:c.58T>C	p.Ser20Pro	p.S20P	ENST00000458235	NM_000215.3	20	Tcc/Ccc	2/24	1	2	FACETS	0.955	0.895	1	0.955	0.895	1	CLONAL	1	TRUE	1	0.7	2		704	682	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36227680	36227680	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1389394920	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	234	679	1	ENST00000222270.7:c.7249G>A	p.Glu2417Lys	p.E2417K	ENST00000222270	NM_014727.1	2417	Gag/Aag	31/37	1	2	FACETS	0.905	0.847	0.963	0.905	0.847	0.963	CLONAL	1	TRUE	1	0.7	2		680	739	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36228145	36228145	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	215	655	1	ENST00000222270.7:c.7531C>T	p.Arg2511Trp	p.R2511W	ENST00000222270	NM_014727.1	2511	Cgg/Tgg	33/37	1	2	FACETS	0.969	0.906	1	0.969	0.906	1	CLONAL	1	TRUE	1	0.7	2		656	634	SUCCESS
AXL	558	MSKCC	GRCh37	19	41765733	41765733	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1400226430	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	141	472	0	ENST00000301178.4:c.2609C>A	p.Pro870His	p.P870H	ENST00000301178	NM_021913.4	870	cCt/cAt	20/20	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.7	2		472	390	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42384741	42384741	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1355355628	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	140	441	0	ENST00000221972.3:c.503G>A	p.Arg168Gln	p.R168Q	ENST00000221972	NM_021601.3	168	cGa/cAa	4/5	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.7	2		441	383	SUCCESS
ALK	238	MSKCC	GRCh37	2	29462691	29462691	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs368581969	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	188	548	1	ENST00000389048.3:c.2210C>T	p.Ser737Leu	p.S737L	ENST00000389048	NM_004304.4	737	tCg/tTg	13/29	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.7	2		549	537	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47600653	47600653	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	174	609	0	ENST00000263735.4:c.128A>C	p.Asn43Thr	p.N43T	ENST00000263735	NM_002354.2	43	aAt/aCt	2/9	0.3	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.7	0		609	359	SUCCESS
EPCAM	4072	MSKCC	GRCh37	2	47602407	47602407	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	128	457	0	ENST00000263735.4:c.460G>T	p.Glu154Ter	p.E154*	ENST00000263735	NM_002354.2	154	Gaa/Taa	4/9	0.3	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.7	0		457	256	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47639687	47639687	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	121	83	482	0	ENST00000233146.2:c.780A>C	p.Glu260Asp	p.E260D	ENST00000233146	NM_000251.2	260	gaA/gaC	4/16	0.3	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.7	0		482	204	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47693898	47693898	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1553366615	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	121	410	0	ENST00000233146.2:c.1612A>G	p.Asn538Asp	p.N538D	ENST00000233146	NM_000251.2	538	Aac/Gac	10/16	0.3	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.7	0		410	235	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719851	61719851	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	119	526	0	ENST00000401558.2:c.1417G>T	p.Glu473Ter	p.E473*	ENST00000401558	NM_003400.3	473	Gaa/Taa	14/25	1	2	FACETS	0.955	0.872	1	0.955	0.872	1	CLONAL	1	TRUE	1	0.7	2		526	356	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719862	61719862	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	114	497	0	ENST00000401558.2:c.1406A>G	p.Tyr469Cys	p.Y469C	ENST00000401558	NM_003400.3	469	tAt/tGt	14/25	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.7	2		497	318	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61720080	61720080	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	103	422	0	ENST00000401558.2:c.1354A>C	p.Asn452His	p.N452H	ENST00000401558	NM_003400.3	452	Aat/Cat	13/25	1	2	FACETS	0.831	0.751	0.915	0.831	0.751	0.915	CLONAL	1	TRUE	1	0.7	2		422	354	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99163060	99163060	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1180664445	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	142	418	0	ENST00000074304.5:c.1066G>A	p.Asp356Asn	p.D356N	ENST00000074304	NM_001134224.1	356	Gac/Aac	13/26	1	2	FACETS	0.88	0.808	0.954	0.88	0.808	0.954	CLONAL	1	TRUE	1	0.7	2		418	461	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182172	99182172	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	223	527	0	ENST00000074304.5:c.2237T>C	p.Val746Ala	p.V746A	ENST00000074304	NM_001134224.1	746	gTc/gCc	21/26	1	2	FACETS	0.996	0.932	1	0.996	0.932	1	CLONAL	1	TRUE	1	0.7	2		527	640	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128036890	128036890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	181	576	0	ENST00000285398.2:c.1589G>A	p.Arg530Gln	p.R530Q	ENST00000285398	NM_000122.1	530	cGa/cAa	10/15	1	2	FACETS	0.927	0.86	0.995	0.927	0.86	0.995	CLONAL	1	TRUE	1	0.7	2		576	558	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257155	198257155	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1228443616	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	110	400	0	ENST00000335508.6:c.3787G>A	p.Asp1263Asn	p.D1263N	ENST00000335508	NM_012433.2	1263	Gat/Aat	25/25	1	2	FACETS	0.911	0.828	0.997	0.911	0.828	0.997	CLONAL	1	TRUE	1	0.7	2		400	345	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198267698	198267698	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	218	115	417	3	ENST00000335508.6:c.1781G>A	p.Arg594Gln	p.R594Q	ENST00000335508	NM_012433.2	594	cGa/cAa	13/25	1	2	FACETS	0.987	0.9	1	0.987	0.9	1	CLONAL	1	TRUE	1	0.7	2		420	333	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209106814	209106814	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs752130008	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	159	577	0	ENST00000345146.2:c.754G>A	p.Asp252Asn	p.D252N	ENST00000345146	NM_005896.2	252	Gac/Aac	7/10	1	2	FACETS	0.958	0.886	1	0.958	0.886	1	CLONAL	1	TRUE	1	0.7	2		577	474	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212543838	212543838	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	192	470	0	ENST00000342788.4:c.1561C>A	p.Leu521Met	p.L521M	ENST00000342788	NM_005235.2	521	Ctg/Atg	13/28	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.7	2		470	544	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212570063	212570063	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746784831	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	103	494	0	ENST00000342788.4:c.1178G>A	p.Arg393Gln	p.R393Q	ENST00000342788	NM_005235.2	393	cGg/cAg	10/28	1	2	FACETS	0.654	0.588	0.723	0.654	0.588	0.723	SUBCLONAL	1	TRUE	1	0.7	2		494	450	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225339038	225339038	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	123	471	0	ENST00000264414.4:c.2231G>A	p.Arg744His	p.R744H	ENST00000264414	NM_003590.4	744	cGt/cAt	16/16	1	2	FACETS	0.942	0.861	1	0.942	0.861	1	CLONAL	1	TRUE	1	0.7	2		471	373	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242793242	242793242	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	216	685	0	ENST00000334409.5:c.835C>T	p.Pro279Ser	p.P279S	ENST00000334409	NM_005018.2	279	Cct/Tct	5/5	1	2	FACETS	0.928	0.867	0.99	0.928	0.867	0.99	CLONAL	1	TRUE	1	0.7	2		685	665	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9561147	9561147	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	196	91	349	0	ENST00000353224.5:c.635A>G	p.Tyr212Cys	p.Y212C	ENST00000353224	NM_177990.2	212	tAc/tGc	4/10	1	2	FACETS	0.906	0.815	1	0.906	0.815	1	CLONAL	1	TRUE	1	0.7	2		349	287	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022586	31022586	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	185	564	0	ENST00000375687.4:c.2071C>A	p.Leu691Ile	p.L691I	ENST00000375687	NM_015338.5	691	Cta/Ata	13/13	1	2	FACETS	0.999	0.93	1	0.999	0.93	1	CLONAL	1	TRUE	1	0.7	2		564	529	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024220	31024220	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	165	547	0	ENST00000375687.4:c.3705C>A	p.Phe1235Leu	p.F1235L	ENST00000375687	NM_015338.5	1235	ttC/ttA	13/13	1	2	FACETS	0.947	0.876	1	0.947	0.876	1	CLONAL	1	TRUE	1	0.7	2		547	498	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024239	31024239	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	28	491	0	ENST00000375687.4:c.3724G>A	p.Asp1242Asn	p.D1242N	ENST00000375687	NM_015338.5	1242	Gat/Aat	13/13	1	2	FACETS	0.181	0.144	0.223	0.181	0.144	0.223	SUBCLONAL	1	TRUE	1	0.7	2		491	443	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31388006	31388006	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121908943	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	155	409	0	ENST00000328111.2:c.1807G>A	p.Ala603Thr	p.A603T	ENST00000328111	NM_006892.3	603	Gct/Act	17/23	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.7	2		409	438	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36031262	36031262	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	150	547	0	ENST00000358208.4:c.1381A>T	p.Lys461Ter	p.K461*	ENST00000358208		461	Aag/Tag	11/12	1	2	FACETS	0.875	0.805	0.946	0.875	0.805	0.946	CLONAL	1	TRUE	1	0.7	2		547	490	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39704821	39704821	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	119	48	237	0	ENST00000361337.2:c.166G>T	p.Asp56Tyr	p.D56Y	ENST00000361337	NM_003286.2	56	Gat/Tat	4/21	1	2	FACETS	0.821	0.706	0.943	0.821	0.706	0.943	CLONAL	1	TRUE	1	0.7	2		237	167	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39708808	39708808	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs183058581	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	63	279	0	ENST00000361337.2:c.419G>A	p.Arg140Gln	p.R140Q	ENST00000361337	NM_003286.2	140	cGa/cAa	6/21	1	2	FACETS	0.756	0.662	0.855	0.756	0.662	0.855	SUBCLONAL	1	TRUE	1	0.7	2		279	238	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39725915	39725915	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	132	403	0	ENST00000361337.2:c.786A>T	p.Lys262Asn	p.K262N	ENST00000361337	NM_003286.2	262	aaA/aaT	10/21	1	2	FACETS	0.97	0.889	1	0.97	0.889	1	CLONAL	1	TRUE	1	0.7	2		403	389	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39744072	39744072	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	130	343	0	ENST00000361337.2:c.1700G>T	p.Arg567Ile	p.R567I	ENST00000361337	NM_003286.2	567	aGa/aTa	16/21	1	2	FACETS	0.929	0.851	1	0.929	0.851	1	CLONAL	1	TRUE	1	0.7	2		343	400	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46265181	46265181	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	102	386	0	ENST00000371998.3:c.2051T>A	p.Ile684Asn	p.I684N	ENST00000371998		684	aTt/aAt	12/23	1	2	FACETS	0.94	0.851	1	0.94	0.851	1	CLONAL	1	TRUE	1	0.7	2		386	310	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62309650	62309650	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753838163	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	157	487	0	ENST00000360203.5:c.988G>A	p.Asp330Asn	p.D330N	ENST00000360203	NM_001283009.1	330	Gat/Aat	12/35	1	2	FACETS	0.931	0.859	1	0.931	0.859	1	CLONAL	1	TRUE	1	0.7	2		487	482	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62319887	62319887	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371161995	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	192	588	0	ENST00000360203.5:c.1729G>A	p.Asp577Asn	p.D577N	ENST00000360203	NM_001283009.1	577	Gac/Aac	21/35	1	2	FACETS	0.973	0.906	1	0.973	0.906	1	CLONAL	1	TRUE	1	0.7	2		588	564	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42843782	42843782	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	199	538	0	ENST00000398585.3:c.1137G>T	p.Lys379Asn	p.K379N	ENST00000398585	NM_001135099.1	379	aaG/aaT	10/14	1	2	FACETS	0.996	0.929	1	0.996	0.929	1	CLONAL	1	TRUE	1	0.7	2		538	571	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21288474	21288474	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749456958	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	40	576	0	ENST00000354336.3:c.719C>T	p.Ala240Val	p.A240V	ENST00000354336	NM_005207.3	240	gCg/gTg	2/3	1	2	FACETS	0.176	0.146	0.21	0.176	0.146	0.21	SUBCLONAL	1	TRUE	1	0.7	2		576	649	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24159001	24159001	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768379745	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	226	640	1	ENST00000263121.7:c.673G>A	p.Asp225Asn	p.D225N	ENST00000263121	NM_003073.3	225	Gat/Aat	6/9	1	2	FACETS	0.924	0.864	0.984	0.924	0.864	0.984	CLONAL	1	TRUE	1	0.7	2		641	699	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29106023	29106023	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs587782152	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	233	93	346	0	ENST00000328354.6:c.817G>T	p.Glu273Ter	p.E273*	ENST00000328354	NM_007194.3	273	Gaa/Taa	7/15	1	2	FACETS	0.815	0.732	0.901	0.815	0.732	0.901	CLONAL	1	TRUE	1	0.7	2		346	326	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41525996	41525996	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	121	457	1	ENST00000263253.7:c.1271G>A	p.Arg424Lys	p.R424K	ENST00000263253	NM_001429.3	424	aGa/aAa	5/31	1	2	FACETS	0.817	0.744	0.893	0.817	0.744	0.893	CLONAL	1	TRUE	1	0.7	2		458	423	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573597	41573597	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	195	625	2	ENST00000263253.7:c.5882C>T	p.Pro1961Leu	p.P1961L	ENST00000263253	NM_001429.3	1961	cCc/cTc	31/31	1	2	FACETS	0.941	0.876	1	0.941	0.876	1	CLONAL	1	TRUE	1	0.7	2		627	592	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574832	41574832	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	206	577	0	ENST00000263253.7:c.7117C>A	p.Leu2373Ile	p.L2373I	ENST00000263253	NM_001429.3	2373	Ctt/Att	31/31	1	2	FACETS	0.991	0.925	1	0.991	0.925	1	CLONAL	1	TRUE	1	0.7	2		577	594	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12632321	12632321	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	172	539	0	ENST00000251849.4:c.1346C>T	p.Ala449Val	p.A449V	ENST00000251849	NM_002880.3	449	gCc/gTc	12/17	1	2	FACETS	0.989	0.917	1	0.989	0.917	1	CLONAL	1	TRUE	1	0.7	2		539	497	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713543	30713543	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	177	442	0	ENST00000295754.5:c.868G>T	p.Glu290Ter	p.E290*	ENST00000295754	NM_003242.5	290	Gag/Tag	4/7	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.7	2		442	497	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30729875	30729875	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	85	273	0	ENST00000295754.5:c.1397-1G>T		p.X466_splice	ENST00000295754	NM_003242.5	466			1	2	FACETS	0.956	0.858	1	0.956	0.858	1	CLONAL	1	TRUE	1	0.7	2		273	254	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37058999	37058999	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs63751194	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	33	673	4	ENST00000231790.2:c.793C>T	p.Arg265Cys	p.R265C	ENST00000231790	NM_000249.3	265	Cgt/Tgt	10/19	1	2	FACETS	0.213	0.173	0.258	0.213	0.173	0.258	SUBCLONAL	1	TRUE	1	0.7	2		677	442	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147533	47147533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	277	125	502	1	ENST00000409792.3:c.4793G>A	p.Arg1598Gln	p.R1598Q	ENST00000409792	NM_014159.6	1598	cGa/cAa	6/21	1	2	FACETS	0.888	0.812	0.968	0.888	0.812	0.968	CLONAL	1	TRUE	1	0.7	2		503	402	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165078	47165078	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	54	237	0	ENST00000409792.3:c.1048G>T	p.Asp350Tyr	p.D350Y	ENST00000409792	NM_014159.6	350	Gat/Tat	3/21	1	2	FACETS	0.804	0.697	0.916	0.804	0.697	0.916	CLONAL	1	TRUE	1	0.7	2		237	192	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799799	72799799	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779590242	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	145	465	1	ENST00000325599.8:c.1370C>T	p.Ser457Leu	p.S457L	ENST00000325599	NM_018130.2	457	tCg/tTg	11/11	1	2	FACETS	0.952	0.877	1	0.952	0.877	1	CLONAL	1	TRUE	1	0.7	2		466	435	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259357	89259357	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	120	404	0	ENST00000336596.2:c.501G>T	p.Glu167Asp	p.E167D	ENST00000336596	NM_005233.5	167	gaG/gaT	3/17	1	2	FACETS	0.95	0.867	1	0.95	0.867	1	CLONAL	1	TRUE	1	0.7	2		404	361	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89390935	89390935	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	131	422	0	ENST00000336596.2:c.1001C>A	p.Ser334Tyr	p.S334Y	ENST00000336596	NM_005233.5	334	tCt/tAt	5/17	1	2	FACETS	0.898	0.822	0.976	0.898	0.822	0.976	CLONAL	1	TRUE	1	0.7	2		422	417	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462293	89462293	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	162	90	384	0	ENST00000336596.2:c.1765A>C	p.Lys589Gln	p.K589Q	ENST00000336596	NM_005233.5	589	Aaa/Caa	10/17	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.7	2		384	252	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468381	89468381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754102338	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	79	213	0	ENST00000336596.2:c.1915C>T	p.Arg639Cys	p.R639C	ENST00000336596	NM_005233.5	639	Cgc/Tgc	11/17	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.7	2		213	207	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468457	89468457	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	184	88	384	0	ENST00000336596.2:c.1991G>T	p.Arg664Met	p.R664M	ENST00000336596	NM_005233.5	664	aGg/aTg	11/17	1	2	FACETS	0.924	0.83	1	0.924	0.83	1	CLONAL	1	TRUE	1	0.7	2		384	272	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89499433	89499433	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	148	452	0	ENST00000336596.2:c.2603G>T	p.Arg868Ile	p.R868I	ENST00000336596	NM_005233.5	868	aGa/aTa	15/17	1	2	FACETS	0.766	0.703	0.831	0.766	0.703	0.831	SUBCLONAL	1	TRUE	1	0.7	2		452	552	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138456592	138456592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	148	548	0	ENST00000289153.2:c.758G>T	p.Arg253Ile	p.R253I	ENST00000289153	NM_006219.2	253	aGa/aTa	4/22	1	2	FACETS	0.921	0.848	0.996	0.921	0.848	0.996	CLONAL	1	TRUE	1	0.7	2		548	459	SUCCESS
ATR	545	MSKCC	GRCh37	3	142226801	142226801	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	242	61	342	0	ENST00000350721.4:c.5003A>C	p.Asn1668Thr	p.N1668T	ENST00000350721	NM_001184.3	1668	aAt/aCt	28/47	1	2	FACETS	0.575	0.5	0.656	0.575	0.5	0.656	SUBCLONAL	1	TRUE	1	0.7	2		342	303	SUCCESS
ATR	545	MSKCC	GRCh37	3	142269003	142269003	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs537845660	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	121	418	0	ENST00000350721.4:c.2947G>A	p.Asp983Asn	p.D983N	ENST00000350721	NM_001184.3	983	Gac/Aac	14/47	1	2	FACETS	0.81	0.737	0.885	0.81	0.737	0.885	CLONAL	1	TRUE	1	0.7	2		418	427	SUCCESS
ATR	545	MSKCC	GRCh37	3	142274725	142274725	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	69	235	0	ENST00000350721.4:c.2335A>C	p.Lys779Gln	p.K779Q	ENST00000350721	NM_001184.3	779	Aaa/Caa	10/47	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.7	2		235	181	SUCCESS
ATR	545	MSKCC	GRCh37	3	142275369	142275369	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	204	107	497	2	ENST00000350721.4:c.1934G>T	p.Arg645Ile	p.R645I	ENST00000350721	NM_001184.3	645	aGa/aTa	9/47	1	2	FACETS	0.983	0.893	1	0.983	0.893	1	CLONAL	1	TRUE	1	0.7	2		499	311	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149260177	149260177	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	154	483	0	ENST00000360632.3:c.716G>T	p.Arg239Ile	p.R239I	ENST00000360632	NM_015472.4	239	aGa/aTa	4/7	1	2	FACETS	0.922	0.851	0.996	0.922	0.851	0.996	CLONAL	1	TRUE	1	0.7	2		483	477	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178922324	178922324	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793732	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	379	149	305	0	ENST00000263967.3:c.1093G>A	p.Glu365Lys	p.E365K	ENST00000263967	NM_006218.2	365	Gaa/Aaa	6/21	1	2	FACETS	0.806	0.741	0.874	0.806	0.741	0.874	CLONAL	1	TRUE	1	0.7	2		305	528	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178951949	178951949	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	135	422	0	ENST00000263967.3:c.3004T>G	p.Phe1002Val	p.F1002V	ENST00000263967	NM_006218.2	1002	Ttc/Gtc	21/21	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.7	2		422	379	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187451339	187451339	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200263685	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	86	389	0	ENST00000232014.4:c.143C>T	p.Thr48Met	p.T48M	ENST00000232014	NM_001130845.1	48	aCg/aTg	3/10	1	2	FACETS	0.611	0.544	0.682	0.611	0.544	0.682	SUBCLONAL	1	TRUE	1	0.7	2		389	402	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189590683	189590683	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	187	514	0	ENST00000264731.3:c.1248G>T	p.Lys416Asn	p.K416N	ENST00000264731	NM_003722.4	416	aaG/aaT	10/14	1	2	FACETS	0.982	0.914	1	0.982	0.914	1	CLONAL	1	TRUE	1	0.7	2		514	544	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1919931	1919931	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	206	538	1	ENST00000382891.5:c.991G>T	p.Glu331Ter	p.E331*	ENST00000382891	NM_133335.3	331	Gaa/Taa	5/22	1	2	FACETS	0.908	0.847	0.971	0.908	0.847	0.971	CLONAL	1	TRUE	1	0.7	2		539	648	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1955068	1955068	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	184	561	0	ENST00000382891.5:c.2155G>A	p.Val719Met	p.V719M	ENST00000382891	NM_133335.3	719	Gtg/Atg	12/22	1	2	FACETS	0.811	0.752	0.872	0.811	0.752	0.872	CLONAL	1	TRUE	1	0.7	2		561	648	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564615	55564615	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs149092990	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	145	498	0	ENST00000288135.5:c.503C>T	p.Ala168Val	p.A168V	ENST00000288135	NM_000222.2	168	gCg/gTg	3/21	1	2	FACETS	0.861	0.792	0.933	0.861	0.792	0.933	CLONAL	1	TRUE	1	0.7	2		498	481	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55948714	55948714	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	123	497	1	ENST00000263923.4:c.3751G>A	p.Val1251Ile	p.V1251I	ENST00000263923	NM_002253.2	1251	Gta/Ata	28/30	1	2	FACETS	0.908	0.829	0.989	0.908	0.829	0.989	CLONAL	1	TRUE	1	0.7	2		498	387	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55960978	55960978	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	112	350	0	ENST00000263923.4:c.2962G>T	p.Glu988Ter	p.E988*	ENST00000263923	NM_002253.2	988	Gaa/Taa	21/30	1	2	FACETS	0.988	0.9	1	0.988	0.9	1	CLONAL	1	TRUE	1	0.7	2		350	324	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467464	66467464	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773032839	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	140	80	246	0	ENST00000273854.3:c.805G>A	p.Asp269Asn	p.D269N	ENST00000273854	NM_004439.5	269	Gat/Aat	3/18	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.7	2		246	220	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467565	66467565	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	129	325	0	ENST00000273854.3:c.704C>A	p.Ser235Tyr	p.S235Y	ENST00000273854	NM_004439.5	235	tCt/tAt	3/18	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.7	2		325	351	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84383972	84383972	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	126	486	1	ENST00000321945.7:c.880C>A	p.Leu294Ile	p.L294I	ENST00000321945	NM_139076.2	294	Ctt/Att	9/9	1	2	FACETS	0.909	0.831	0.989	0.909	0.831	0.989	CLONAL	1	TRUE	1	0.7	2		487	396	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106196283	106196283	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	139	70	218	0	ENST00000380013.4:c.4616A>T	p.Gln1539Leu	p.Q1539L	ENST00000380013	NM_001127208.2	1539	cAg/cTg	11/11	1	2	FACETS	0.957	0.849	1	0.957	0.849	1	CLONAL	1	TRUE	1	0.7	2		218	209	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153251891	153251891	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	102	381	0	ENST00000281708.4:c.1115C>A	p.Ser372Tyr	p.S372Y	ENST00000281708	NM_033632.3	372	tCt/tAt	7/12	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.7	2		381	277	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518260	187518260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	174	78	210	0	ENST00000441802.2:c.12434C>T	p.Thr4145Met	p.T4145M	ENST00000441802	NM_005245.3	4145	aCg/aTg	25/27	1	2	FACETS	0.884	0.788	0.985	0.884	0.788	0.985	CLONAL	1	TRUE	1	0.7	2		210	252	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532732	187532732	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	290	165	507	0	ENST00000441802.2:c.9661C>A	p.Leu3221Ile	p.L3221I	ENST00000441802	NM_005245.3	3221	Ctt/Att	14/27	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.7	2		507	455	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540815	187540815	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1221788415	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	203	84	317	0	ENST00000441802.2:c.6925G>A	p.Asp2309Asn	p.D2309N	ENST00000441802	NM_005245.3	2309	Gat/Aat	10/27	1	2	FACETS	0.836	0.747	0.929	0.836	0.747	0.929	CLONAL	1	TRUE	1	0.7	2		317	287	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554954	187554954	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs560351512	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	190	79	367	0	ENST00000441802.2:c.4207G>A	p.Asp1403Asn	p.D1403N	ENST00000441802	NM_005245.3	1403	Gat/Aat	7/27	1	2	FACETS	0.839	0.747	0.935	0.839	0.747	0.935	CLONAL	1	TRUE	1	0.7	2		367	269	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584696	187584696	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144526682	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	153	551	1	ENST00000441802.2:c.3337G>A	p.Asp1113Asn	p.D1113N	ENST00000441802	NM_005245.3	1113	Gat/Aat	3/27	1	2	FACETS	0.854	0.786	0.923	0.854	0.786	0.923	CLONAL	1	TRUE	1	0.7	2		552	512	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	223684	223684	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs1057523165	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	101	343	1	ENST00000264932.6:c.150+1G>A		p.X50_splice	ENST00000264932	NM_004168.2	50			1	2	FACETS	0.877	0.793	0.965	0.877	0.793	0.965	CLONAL	1	TRUE	1	0.7	2		344	329	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950622	38950622	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748585755	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	76	420	0	ENST00000357387.3:c.3328C>T	p.Arg1110Cys	p.R1110C	ENST00000357387	NM_152756.3	1110	Cgt/Tgt	31/38	1	2	FACETS	0.674	0.596	0.757	0.674	0.596	0.757	SUBCLONAL	1	TRUE	1	0.7	2		420	322	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950726	38950726	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370517295	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	128	65	270	0	ENST00000357387.3:c.3224G>A	p.Arg1075Gln	p.R1075Q	ENST00000357387	NM_152756.3	1075	cGa/cAa	31/38	1	2	FACETS	0.962	0.85	1	0.962	0.85	1	CLONAL	1	TRUE	1	0.7	2		270	193	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38964916	38964916	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	138	55	267	0	ENST00000357387.3:c.1378G>T	p.Asp460Tyr	p.D460Y	ENST00000357387	NM_152756.3	460	Gat/Tat	16/38	1	2	FACETS	0.814	0.708	0.927	0.814	0.708	0.927	CLONAL	1	TRUE	1	0.7	2		267	193	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160589	56160589	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761217931	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	95	331	1	ENST00000399503.3:c.863G>A	p.Arg288Gln	p.R288Q	ENST00000399503	NM_005921.1	288	cGa/cAa	4/20	1	2	FACETS	0.914	0.824	1	0.914	0.824	1	CLONAL	1	TRUE	1	0.7	2		332	297	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189415	56189415	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	172	571	1	ENST00000399503.3:c.4447G>T	p.Asp1483Tyr	p.D1483Y	ENST00000399503	NM_005921.1	1483	Gat/Tat	20/20	1	2	FACETS	0.905	0.838	0.974	0.905	0.838	0.974	CLONAL	1	TRUE	1	0.7	2		572	543	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86648973	86648973	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	104	325	0	ENST00000274376.6:c.1254-1G>A		p.X418_splice	ENST00000274376	NM_002890.2	418			1	2	FACETS	0.955	0.866	1	0.955	0.866	1	CLONAL	1	TRUE	1	0.7	2		325	311	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672366	86672366	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	81	319	0	ENST00000274376.6:c.2168A>G	p.Tyr723Cys	p.Y723C	ENST00000274376	NM_002890.2	723	tAc/tGc	16/25	1	2	FACETS	0.751	0.669	0.838	0.751	0.669	0.838	SUBCLONAL	1	TRUE	1	0.7	2		319	308	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672759	86672759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	83	391	0	ENST00000274376.6:c.2246G>A	p.Arg749Gln	p.R749Q	ENST00000274376	NM_002890.2	749	cGa/cAa	17/25	1	2	FACETS	0.835	0.746	0.928	0.835	0.746	0.928	CLONAL	1	TRUE	1	0.7	2		391	284	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672800	86672800	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764802465	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	208	89	320	2	ENST00000274376.6:c.2287G>A	p.Glu763Lys	p.E763K	ENST00000274376	NM_002890.2	763	Gaa/Aaa	17/25	1	2	FACETS	0.856	0.768	0.948	0.856	0.768	0.948	CLONAL	1	TRUE	1	0.7	2		322	297	SUCCESS
APC	324	MSKCC	GRCh37	5	112090657	112090657	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs145945630	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	87	474	0	ENST00000257430.4:c.70C>T	p.Arg24Ter	p.R24*	ENST00000257430	NM_000038.5	24	Cga/Tga	2/16	1	2	FACETS	0.869	0.779	0.963	0.869	0.779	0.963	CLONAL	1	TRUE	1	0.7	2		474	286	SUCCESS
APC	324	MSKCC	GRCh37	5	112154771	112154771	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1314843920	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	124	414	0	ENST00000257430.4:c.1042C>T	p.Arg348Ter	p.R348*	ENST00000257430	NM_000038.5	348	Cga/Tga	10/16	1	2	FACETS	0.945	0.864	1	0.945	0.864	1	CLONAL	1	TRUE	1	0.7	2		414	375	SUCCESS
APC	324	MSKCC	GRCh37	5	112173303	112173303	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	74	242	0	ENST00000257430.4:c.2012C>A	p.Ser671Tyr	p.S671Y	ENST00000257430	NM_000038.5	671	tCt/tAt	16/16	1	2	FACETS	0.856	0.76	0.957	0.856	0.76	0.957	CLONAL	1	TRUE	1	0.7	2		242	247	SUCCESS
APC	324	MSKCC	GRCh37	5	112173704	112173704	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs587779783	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	198	120	352	0	ENST00000257430.4:c.2413C>T	p.Arg805Ter	p.R805*	ENST00000257430	NM_000038.5	805	Cga/Tga	16/16	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.7	2		352	318	SUCCESS
APC	324	MSKCC	GRCh37	5	112176411	112176411	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	171	12	281	0	ENST00000257430.4:c.5120C>A	p.Ser1707Tyr	p.S1707Y	ENST00000257430	NM_000038.5	1707	tCt/tAt	16/16	1	2	FACETS	0.187	0.132	0.256	0.187	0.132	0.256	SUBCLONAL	1	TRUE	1	0.7	2		281	183	SUCCESS
APC	324	MSKCC	GRCh37	5	112176873	112176873	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	111	370	0	ENST00000257430.4:c.5582C>T	p.Ser1861Phe	p.S1861F	ENST00000257430	NM_000038.5	1861	tCt/tTt	16/16	1	2	FACETS	0.991	0.902	1	0.991	0.902	1	CLONAL	1	TRUE	1	0.7	2		370	320	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131923334	131923334	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1561638972	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	87	354	0	ENST00000265335.6:c.837G>T	p.Lys279Asn	p.K279N	ENST00000265335		279	aaG/aaT	6/25	1	2	FACETS	0.789	0.706	0.876	0.789	0.706	0.876	SUBCLONAL	1	TRUE	1	0.7	2		354	315	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502666	149502666	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749226501	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	155	434	0	ENST00000261799.4:c.2122C>T	p.Arg708Cys	p.R708C	ENST00000261799	NM_002609.3	708	Cgc/Tgc	15/23	1	2	FACETS	0.959	0.885	1	0.959	0.885	1	CLONAL	1	TRUE	1	0.7	2		434	462	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562545	176562545	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	139	574	0	ENST00000439151.2:c.441G>T	p.Lys147Asn	p.K147N	ENST00000439151	NM_022455.4	147	aaG/aaT	2/23	1	2	FACETS	0.852	0.782	0.925	0.852	0.782	0.925	CLONAL	1	TRUE	1	0.7	2		574	466	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562806	176562806	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	220	559	0	ENST00000439151.2:c.702A>T	p.Glu234Asp	p.E234D	ENST00000439151	NM_022455.4	234	gaA/gaT	2/23	1	2	FACETS	0.975	0.912	1	0.975	0.912	1	CLONAL	1	TRUE	1	0.7	2		559	645	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176636899	176636899	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs867877508	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	147	505	0	ENST00000439151.2:c.1499G>T	p.Arg500Ile	p.R500I	ENST00000439151	NM_022455.4	500	aGa/aTa	5/23	1	2	FACETS	0.993	0.916	1	0.993	0.916	1	CLONAL	1	TRUE	1	0.7	2		505	423	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176700781	176700781	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	102	425	0	ENST00000439151.2:c.5618T>A	p.Ile1873Lys	p.I1873K	ENST00000439151	NM_022455.4	1873	aTa/aAa	17/23	1	2	FACETS	0.79	0.713	0.87	0.79	0.713	0.87	SUBCLONAL	1	TRUE	1	0.7	2		425	369	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407593	407593	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	247	116	375	2	ENST00000380956.4:c.1351G>A	p.Glu451Lys	p.E451K	ENST00000380956	NM_001195286.1	451	Gaa/Aaa	9/9	1	2	FACETS	0.913	0.832	0.997	0.913	0.832	0.997	CLONAL	1	TRUE	1	0.7	2		377	363	SUCCESS
E2F3	1871	MSKCC	GRCh37	6	20486948	20486948	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs773975473	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	101	369	0	ENST00000346618.3:c.913C>T	p.Arg305Ter	p.R305*	ENST00000346618	NM_001949.4	305	Cga/Tga	5/7	1	2	FACETS	0.943	0.854	1	0.943	0.854	1	CLONAL	1	TRUE	1	0.7	2		369	306	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271369	26271369	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	72	354	0	ENST00000305910.3:c.244G>T	p.Asp82Tyr	p.D82Y	ENST00000305910	NM_003534.2	82	Gat/Tat	1/1	1	2	FACETS	0.595	0.523	0.671	0.595	0.523	0.671	SUBCLONAL	1	TRUE	1	0.7	2		354	346	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672385	30672385	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	143	378	0	ENST00000376406.3:c.4575G>T	p.Lys1525Asn	p.K1525N	ENST00000376406	NM_014641.2	1525	aaG/aaT	10/15	1	2	FACETS	0.877	0.806	0.95	0.877	0.806	0.95	CLONAL	1	TRUE	1	0.7	2		378	466	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675778	30675778	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	54	691	0	ENST00000376406.3:c.2578G>T	p.Glu860Ter	p.E860*	ENST00000376406	NM_014641.2	860	Gaa/Taa	8/15	1	2	FACETS	0.194	0.165	0.226	0.194	0.165	0.226	SUBCLONAL	1	TRUE	1	0.7	2		691	795	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30681043	30681043	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	129	403	0	ENST00000376406.3:c.676C>A	p.Gln226Lys	p.Q226K	ENST00000376406	NM_014641.2	226	Cag/Aag	5/15	1	2	FACETS	0.901	0.825	0.98	0.901	0.825	0.98	CLONAL	1	TRUE	1	0.7	2		403	409	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805417	32805417	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	60	687	0	ENST00000374899.4:c.505A>C	p.Ile169Leu	p.I169L	ENST00000374899	NM_018833.2	169	Atc/Ctc	3/12	1	2	FACETS	0.227	0.195	0.262	0.227	0.195	0.262	SUBCLONAL	1	TRUE	1	0.7	2		687	755	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33288180	33288180	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772037578	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	142	330	1	ENST00000374542.5:c.1228G>A	p.Glu410Lys	p.E410K	ENST00000374542	NM_001141970.1	410	Gaa/Aaa	4/8	1	2	FACETS	0.957	0.88	1	0.957	0.88	1	CLONAL	1	TRUE	1	0.7	2		331	424	SUCCESS
PTP4A1	7803	MSKCC	GRCh37	6	64290057	64290057	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	127	479	0	ENST00000370651.3:c.500G>T	p.Arg167Ile	p.R167I	ENST00000370651	NM_003463.4	167	aGa/aTa	6/6	1	2	FACETS	0.85	0.776	0.926	0.85	0.776	0.926	CLONAL	1	TRUE	1	0.7	2		479	427	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94124422	94124422	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	183	73	374	0	ENST00000369303.4:c.161G>A	p.Gly54Glu	p.G54E	ENST00000369303	NM_004440.3	54	gGg/gAg	2/17	1	2	FACETS	0.815	0.722	0.912	0.815	0.722	0.912	CLONAL	1	TRUE	1	0.7	2		374	256	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106555141	106555141	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	191	572	0	ENST00000369096.4:c.2258C>A	p.Ser753Tyr	p.S753Y	ENST00000369096	NM_001198.3	753	tCt/tAt	7/7	1	2	FACETS	0.905	0.842	0.97	0.905	0.842	0.97	CLONAL	1	TRUE	1	0.7	2		572	603	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112041037	112041037	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761032788	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	122	411	0	ENST00000368678.4:c.218C>T	p.Thr73Met	p.T73M	ENST00000368678		73	aCg/aTg	3/13	1	2	FACETS	0.932	0.851	1	0.932	0.851	1	CLONAL	1	TRUE	1	0.7	2		411	374	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117622241	117622241	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs148104006	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	98	245	398	1	ENST00000368508.3:c.6629G>T	p.Arg2210Ile	p.R2210I	ENST00000368508	NM_002944.2	2210	aGa/aTa	42/43	1	2	FACETS	1	0.973	1	1	0.996	1	CLONAL	2	TRUE	1	0.7	2		399	343	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117665253	117665253	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	90	274	0	ENST00000368508.3:c.4494A>C	p.Lys1498Asn	p.K1498N	ENST00000368508	NM_002944.2	1498	aaA/aaC	27/43	1	2	FACETS	0.909	0.817	1	0.909	0.817	1	CLONAL	1	TRUE	1	0.7	2		274	283	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710971	117710971	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	66	250	0	ENST00000368508.3:c.1301C>G	p.Ala434Gly	p.A434G	ENST00000368508	NM_002944.2	434	gCa/gGa	12/43	1	2	FACETS	0.671	0.588	0.759	0.671	0.588	0.759	SUBCLONAL	1	TRUE	1	0.7	2		250	281	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199638	138199638	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	130	472	0	ENST00000237289.4:c.1056G>T	p.Glu352Asp	p.E352D	ENST00000237289	NM_001270507.1	352	gaG/gaT	7/9	1	2	FACETS	0.842	0.77	0.917	0.842	0.77	0.917	CLONAL	1	TRUE	1	0.7	2		472	441	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138202346	138202346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780709741	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	179	543	1	ENST00000237289.4:c.2263G>A	p.Glu755Lys	p.E755K	ENST00000237289	NM_001270507.1	755	Gaa/Aaa	9/9	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.7	2		544	507	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527796	157527796	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	145	382	1	ENST00000346085.5:c.5521C>A	p.Pro1841Thr	p.P1841T	ENST00000346085	NM_020732.3	1841	Cct/Act	20/20	1	2	FACETS	0.984	0.907	1	0.984	0.907	1	CLONAL	1	TRUE	1	0.7	2		383	421	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528094	157528094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	172	425	0	ENST00000346085.5:c.5819C>T	p.Ser1940Leu	p.S1940L	ENST00000346085	NM_020732.3	1940	tCg/tTg	20/20	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.7	2		425	415	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162475207	162475207	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	95	370	0	ENST00000366898.1:c.535-1G>T		p.X179_splice	ENST00000366898	NM_004562.2	179			1	2	FACETS	0.808	0.726	0.893	0.808	0.726	0.893	CLONAL	1	TRUE	1	0.7	2		370	336	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13949266	13949266	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	161	52	353	0	ENST00000405192.2:c.862A>C	p.Lys288Gln	p.K288Q	ENST00000405192	NM_001163147.1	288	Aaa/Caa	9/12	1	2	FACETS	0.698	0.601	0.8	0.698	0.601	0.8	SUBCLONAL	1	TRUE	1	0.7	2		353	213	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468032	50468032	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs757907717	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	114	366	0	ENST00000331340.3:c.1267C>T	p.Arg423Cys	p.R423C	ENST00000331340	NM_006060.4	423	Cgc/Tgc	8/8	1	2	FACETS	0.862	0.783	0.943	0.862	0.783	0.943	CLONAL	1	TRUE	1	0.7	2		366	378	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223604	55223604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758748662	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	158	413	2	ENST00000275493.2:c.971G>A	p.Arg324His	p.R324H	ENST00000275493	NM_005228.3	324	cGc/cAc	8/28	1	2	FACETS	0.944	0.873	1	0.944	0.873	1	CLONAL	1	TRUE	1	0.7	2		415	478	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412972	116412972	+	intron_variant	Intron	SNP	G	G	A	rs1039629132	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	206	759	1	ENST00000397752.3:c.3028+929G>A		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.819	0.762	0.877	0.819	0.762	0.877	CLONAL	1	TRUE	1	0.7	2		760	719	SUCCESS
MET	4233	MSKCC	GRCh37	7	116413119	116413119	+	intron_variant	Intron	SNP	T	T	G	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	149	495	0	ENST00000397752.3:c.3028+1076T>G		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.846	0.778	0.916	0.846	0.778	0.916	CLONAL	1	TRUE	1	0.7	2		495	503	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423392	116423392	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	102	354	0	ENST00000397752.3:c.3667T>G	p.Phe1223Val	p.F1223V	ENST00000397752	NM_000245.2	1223	Ttt/Gtt	19/21	1	2	FACETS	0.922	0.835	1	0.922	0.835	1	CLONAL	1	TRUE	1	0.7	2		354	316	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128850898	128850898	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	199	640	0	ENST00000249373.3:c.1745A>C	p.Asn582Thr	p.N582T	ENST00000249373	NM_005631.4	582	aAc/aCc	10/12	1	2	FACETS	0.897	0.835	0.96	0.897	0.835	0.96	CLONAL	1	TRUE	1	0.7	2		640	634	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140487360	140487360	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs397507472	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	190	602	1	ENST00000288602.6:c.1165C>T	p.Arg389Cys	p.R389C	ENST00000288602	NM_004333.4	389	Cgt/Tgt	9/18	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.7	2		603	510	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836764	151836764	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	129	376	0	ENST00000262189.6:c.14456C>A	p.Ser4819Tyr	p.S4819Y	ENST00000262189	NM_170606.2	4819	tCt/tAt	56/59	1	2	FACETS	0.895	0.818	0.973	0.895	0.818	0.973	CLONAL	1	TRUE	1	0.7	2		376	412	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151846227	151846227	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	136	445	0	ENST00000262189.6:c.12785C>A	p.Pro4262His	p.P4262H	ENST00000262189	NM_170606.2	4262	cCt/cAt	52/59	1	2	FACETS	0.996	0.916	1	0.996	0.916	1	CLONAL	1	TRUE	1	0.7	2		445	390	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878694	151878694	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	193	91	326	0	ENST00000262189.6:c.6251A>C	p.Asn2084Thr	p.N2084T	ENST00000262189	NM_170606.2	2084	aAt/aCt	36/59	1	2	FACETS	0.915	0.824	1	0.915	0.824	1	CLONAL	1	TRUE	1	0.7	2		326	284	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151891322	151891322	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	117	402	0	ENST00000262189.6:c.4532A>C	p.Lys1511Thr	p.K1511T	ENST00000262189	NM_170606.2	1511	aAa/aCa	30/59	1	2	FACETS	0.819	0.745	0.896	0.819	0.745	0.896	CLONAL	1	TRUE	1	0.7	2		402	408	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151945054	151945054	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs778616260	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	48	585	0	ENST00000262189.6:c.2465A>C	p.Lys822Thr	p.K822T	ENST00000262189	NM_170606.2	822	aAa/aCa	14/59	1	2	FACETS	0.247	0.208	0.29	0.247	0.208	0.29	SUBCLONAL	1	TRUE	1	0.7	2		585	555	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538990	23538990	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775943527	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	156	543	0	ENST00000380871.4:c.449C>T	p.Ser150Leu	p.S150L	ENST00000380871	NM_006167.3	150	tCg/tTg	2/2	1	2	FACETS	0.936	0.865	1	0.936	0.865	1	CLONAL	1	TRUE	1	0.7	2		543	476	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29207369	29207369	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	77	265	0	ENST00000240100.2:c.427C>A	p.Leu143Ile	p.L143I	ENST00000240100	NM_001394.6	143	Ctc/Atc	1/4	1	2	FACETS	0.94	0.838	1	0.94	0.838	1	CLONAL	1	TRUE	1	0.7	2		265	234	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38157028	38157028	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	157	646	0	ENST00000317025.8:c.2692C>T	p.Arg898Cys	p.R898C	ENST00000317025	NM_023034.1	898	Cgt/Tgt	15/24	1	2	FACETS	0.81	0.746	0.876	0.81	0.746	0.876	CLONAL	1	TRUE	1	0.7	2		646	554	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38314972	38314972	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1175350192	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	222	752	1	ENST00000425967.3:c.92G>T	p.Arg31Ile	p.R31I	ENST00000425967	NM_001174067.1	31	aGa/aTa	3/19	1	2	FACETS	0.891	0.833	0.95	0.891	0.833	0.95	CLONAL	1	TRUE	1	0.7	2		753	712	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370819	55370819	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	159	518	1	ENST00000297316.4:c.121G>T	p.Asp41Tyr	p.D41Y	ENST00000297316	NM_022454.3	41	Gac/Tac	1/2	1	2	FACETS	0.931	0.86	1	0.931	0.86	1	CLONAL	1	TRUE	1	0.7	2		519	488	SUCCESS
LYN	4067	MSKCC	GRCh37	8	56866516	56866516	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376329765	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	299	680	0	ENST00000519728.1:c.763G>A	p.Ala255Thr	p.A255T	ENST00000519728	NM_002350.3	255	Gct/Act	8/13	1	2	FACETS	0.992	0.938	1	0.992	0.938	1	CLONAL	1	TRUE	1	0.7	2		680	861	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68942833	68942833	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	215	666	0	ENST00000288368.4:c.645G>T	p.Lys215Asn	p.K215N	ENST00000288368	NM_024870.2	215	aaG/aaT	6/40	1	2	FACETS	0.975	0.912	1	0.975	0.912	1	CLONAL	1	TRUE	1	0.7	2		666	630	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69005843	69005843	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	87	392	0	ENST00000288368.4:c.2254G>A	p.Asp752Asn	p.D752N	ENST00000288368	NM_024870.2	752	Gat/Aat	21/40	1	2	FACETS	0.831	0.744	0.922	0.831	0.744	0.922	CLONAL	1	TRUE	1	0.7	2		392	299	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69021782	69021782	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	198	684	1	ENST00000288368.4:c.3070G>T	p.Asp1024Tyr	p.D1024Y	ENST00000288368	NM_024870.2	1024	Gac/Tac	25/40	1	2	FACETS	0.912	0.85	0.977	0.912	0.85	0.977	CLONAL	1	TRUE	1	0.7	2		685	620	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964530	70964530	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	129	564	0	ENST00000276594.2:c.1498G>T	p.Ala500Ser	p.A500S	ENST00000276594	NM_024504.3	500	Gcc/Tcc	8/8	1	2	FACETS	0.769	0.702	0.839	0.769	0.702	0.839	SUBCLONAL	1	TRUE	1	0.7	2		564	479	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980604	70980604	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1036596459	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	189	566	0	ENST00000276594.2:c.773C>T	p.Thr258Met	p.T258M	ENST00000276594	NM_024504.3	258	aCg/aTg	4/8	1	2	FACETS	0.959	0.893	1	0.959	0.893	1	CLONAL	1	TRUE	1	0.7	2		566	563	SUCCESS
ELOC	6921	MSKCC	GRCh37	8	74858992	74858992	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	77	220	0	ENST00000284811.8:c.212C>T	p.Ser71Leu	p.S71L	ENST00000284811		71	tCg/tTg	4/4	1	2	FACETS	0.797	0.708	0.89	0.797	0.708	0.89	SUBCLONAL	1	TRUE	1	0.7	2		220	276	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145737123	145737123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs35346077	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	197	588	0	ENST00000428558.2:c.3443C>T	p.Ser1148Phe	p.S1148F	ENST00000428558	NM_004260.3	1148	tCc/tTc	21/22	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.7	2		588	557	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5021963	5021963	+	splice_region_variant,5_prime_UTR_variant	Splice_Region	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	72	262	0	ENST00000381652.3:c.-25G>A		p.X9_splice	ENST00000381652	NM_004972.3	9		3/25	1	2	FACETS	1	0.901	1	1	0.901	1	CLONAL	1	TRUE	1	0.7	2		262	203	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050746	5050746	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	271	122	500	0	ENST00000381652.3:c.529G>T	p.Glu177Ter	p.E177*	ENST00000381652	NM_004972.3	177	Gaa/Taa	6/25	1	2	FACETS	0.887	0.809	0.967	0.887	0.809	0.967	CLONAL	1	TRUE	1	0.7	2		500	393	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5050780	5050780	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	128	542	0	ENST00000381652.3:c.563G>T	p.Arg188Ile	p.R188I	ENST00000381652	NM_004972.3	188	aGa/aTa	6/25	1	2	FACETS	0.896	0.82	0.975	0.896	0.82	0.975	CLONAL	1	TRUE	1	0.7	2		542	408	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5066739	5066739	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1340580425	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	99	405	0	ENST00000381652.3:c.1276C>T	p.Arg426Ter	p.R426*	ENST00000381652	NM_004972.3	426	Cga/Tga	10/25	1	2	FACETS	0.907	0.819	0.997	0.907	0.819	0.997	CLONAL	1	TRUE	1	0.7	2		405	312	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341849	8341849	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	118	584	0	ENST00000356435.5:c.4791A>C	p.Gln1597His	p.Q1597H	ENST00000356435		1597	caA/caC	29/35	1	2	FACETS	0.869	0.791	0.949	0.869	0.791	0.949	CLONAL	1	TRUE	1	0.7	2		584	388	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8389318	8389318	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	138	596	1	ENST00000356435.5:c.4300G>A	p.Glu1434Lys	p.E1434K	ENST00000356435		1434	Gaa/Aaa	26/35	1	2	FACETS	0.93	0.854	1	0.93	0.854	1	CLONAL	1	TRUE	1	0.7	2		597	424	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404587	8404587	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	74	307	0	ENST00000356435.5:c.4160C>T	p.Ala1387Val	p.A1387V	ENST00000356435		1387	gCg/gTg	25/35	1	2	FACETS	0.881	0.782	0.984	0.881	0.782	0.984	CLONAL	1	TRUE	1	0.7	2		307	240	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8484270	8484270	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs867884876	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	151	497	0	ENST00000356435.5:c.3262C>T	p.Arg1088Cys	p.R1088C	ENST00000356435		1088	Cgt/Tgt	19/35	1	2	FACETS	0.92	0.848	0.994	0.92	0.848	0.994	CLONAL	1	TRUE	1	0.7	2		497	469	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8485311	8485311	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	114	455	0	ENST00000356435.5:c.3069T>A	p.Asn1023Lys	p.N1023K	ENST00000356435		1023	aaT/aaA	18/35	1	2	FACETS	0.947	0.862	1	0.947	0.862	1	CLONAL	1	TRUE	1	0.7	2		455	344	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8528626	8528626	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	263	110	391	0	ENST00000356435.5:c.506G>A	p.Ser169Asn	p.S169N	ENST00000356435		169	aGc/aAc	4/35	1	2	FACETS	0.843	0.764	0.924	0.843	0.764	0.924	CLONAL	1	TRUE	1	0.7	2		391	373	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197433	27197433	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	407	239	619	0	ENST00000380036.4:c.1745C>A	p.Ser582Tyr	p.S582Y	ENST00000380036	NM_000459.3	582	tCt/tAt	12/23	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.7	2		619	646	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87356842	87356842	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	83	403	0	ENST00000277120.3:c.1195G>T	p.Asp399Tyr	p.D399Y	ENST00000277120		399	Gat/Tat	10/19	1	2	FACETS	0.736	0.656	0.821	0.736	0.656	0.821	SUBCLONAL	1	TRUE	1	0.7	2		403	322	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87570334	87570334	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	200	517	0	ENST00000277120.3:c.2074G>A	p.Asp692Asn	p.D692N	ENST00000277120		692	Gat/Aat	17/19	1	2	FACETS	0.972	0.906	1	0.972	0.906	1	CLONAL	1	TRUE	1	0.7	2		517	588	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98009794	98009794	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	207	67	329	0	ENST00000289081.3:c.170C>A	p.Ser57Tyr	p.S57Y	ENST00000289081	NM_000136.2	57	tCt/tAt	3/15	1	2	FACETS	0.699	0.613	0.789	0.699	0.613	0.789	SUBCLONAL	1	TRUE	1	0.7	2		329	274	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231113	98231113	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144501989	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	173	388	1	ENST00000331920.6:c.2170G>A	p.Glu724Lys	p.E724K	ENST00000331920	NM_000264.3	724	Gag/Aag	14/24	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.7	2		389	464	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128246746	128246746	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	156	517	0	ENST00000265960.3:c.1183C>T	p.Arg395Ter	p.R395*	ENST00000265960	NM_001006617.1	395	Cga/Tga	9/12	1	2	FACETS	0.744	0.684	0.806	0.744	0.684	0.806	SUBCLONAL	1	TRUE	1	0.7	2		517	599	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781388	135781388	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	192	490	0	ENST00000298552.3:c.1577C>A	p.Ser526Tyr	p.S526Y	ENST00000298552	NM_001162426.1	526	tCt/tAt	15/23	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.7	2		490	519	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404312	139404312	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	226	653	1	ENST00000277541.6:c.2842G>A	p.Glu948Lys	p.E948K	ENST00000277541	NM_017617.3	948	Gag/Aag	18/34	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.7	2		654	636	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139564688	139564688	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	269	846	0	ENST00000308874.7:c.477C>A	p.Tyr159Ter	p.Y159*	ENST00000308874		159	taC/taA	7/10	1	2	FACETS	0.989	0.932	1	0.989	0.932	1	CLONAL	1	TRUE	1	0.7	2		846	777	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15833871	15833871	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	205	67	294	0	ENST00000307771.7:c.629G>A	p.Gly210Glu	p.G210E	ENST00000307771	NM_005089.3	210	gGa/gAa	8/11	1	2	FACETS	0.704	0.618	0.795	0.704	0.618	0.795	SUBCLONAL	1	TRUE	1	0.7	2		294	272	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15834005	15834005	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	332	712	0	ENST00000307771.7:c.763C>A	p.Gln255Lys	p.Q255K	ENST00000307771	NM_005089.3	255	Cag/Aag	8/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.7	2		712	912	SUCCESS
EIF1AX	1964	MSKCC	GRCh37	X	20156690	20156690	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	139	591	0	ENST00000379607.5:c.67A>G	p.Lys23Glu	p.K23E	ENST00000379607	NM_001412.3	23	Aaa/Gaa	2/7	1	2	FACETS	0.754	0.69	0.82	0.754	0.69	0.82	SUBCLONAL	1	TRUE	1	0.7	2		591	527	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923796	39923796	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs779083606	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	242	737	0	ENST00000378444.4:c.3295G>T	p.Asp1099Tyr	p.D1099Y	ENST00000378444	NM_001123385.1	1099	Gat/Tat	7/15	1	2	FACETS	0.921	0.863	0.979	0.921	0.863	0.979	CLONAL	1	TRUE	1	0.7	2		737	751	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932447	39932447	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	178	575	0	ENST00000378444.4:c.2152G>T	p.Asp718Tyr	p.D718Y	ENST00000378444	NM_001123385.1	718	Gat/Tat	4/15	1	2	FACETS	0.868	0.804	0.933	0.868	0.804	0.933	CLONAL	1	TRUE	1	0.7	2		575	586	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933872	39933872	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1274186244	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	53	664	1	ENST00000378444.4:c.727C>T	p.Arg243Cys	p.R243C	ENST00000378444	NM_001123385.1	243	Cgc/Tgc	4/15	1	2	FACETS	0.226	0.192	0.263	0.226	0.192	0.263	SUBCLONAL	1	TRUE	1	0.7	2		665	670	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44936066	44936066	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	141	563	0	ENST00000377967.4:c.2827A>G	p.Ile943Val	p.I943V	ENST00000377967	NM_021140.2	943	Att/Gtt	18/29	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.7	2		563	403	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028882	47028882	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	148	510	0	ENST00000377604.3:c.186G>T	p.Glu62Asp	p.E62D	ENST00000377604	NM_001204468.1	62	gaG/gaT	3/24	1	2	FACETS	0.952	0.878	1	0.952	0.878	1	CLONAL	1	TRUE	1	0.7	2		510	444	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426737	47426737	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200106543	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	213	635	2	ENST00000377045.4:c.982C>T	p.Arg328Trp	p.R328W	ENST00000377045	NM_001654.4	328	Cgg/Tgg	10/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.7	2		637	597	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411267	63411267	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866313799	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	210	574	1	ENST00000330258.3:c.1900C>T	p.Arg634Cys	p.R634C	ENST00000330258	NM_152424.3	634	Cgt/Tgt	2/2	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.7	2		575	570	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411888	63411888	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	54	935	0	ENST00000330258.3:c.1279C>T	p.Pro427Ser	p.P427S	ENST00000330258	NM_152424.3	427	Ccc/Tcc	2/2	1	2	FACETS	0.18	0.153	0.21	0.18	0.153	0.21	SUBCLONAL	1	TRUE	1	0.7	2		935	858	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339654	70339654	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	260	711	0	ENST00000374080.3:c.323G>A	p.Arg108Gln	p.R108Q	ENST00000374080		108	cGa/cAa	3/45	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.7	2		711	698	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344018	70344018	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747113641	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	185	1004	2	ENST00000374080.3:c.1754G>A	p.Arg585Gln	p.R585Q	ENST00000374080		585	cGa/cAa	13/45	1	2	FACETS	0.781	0.724	0.84	0.781	0.724	0.84	SUBCLONAL	1	TRUE	1	0.7	2		1006	677	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70348502	70348502	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1317457286	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	183	526	0	ENST00000374080.3:c.3409G>A	p.Ala1137Thr	p.A1137T	ENST00000374080		1137	Gct/Act	24/45	1	2	FACETS	0.927	0.861	0.995	0.927	0.861	0.995	CLONAL	1	TRUE	1	0.7	2		526	564	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349577	70349577	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	199	642	1	ENST00000374080.3:c.3739G>T	p.Glu1247Ter	p.E1247*	ENST00000374080		1247	Gaa/Taa	27/45	1	2	FACETS	0.931	0.867	0.996	0.931	0.867	0.996	CLONAL	1	TRUE	1	0.7	2		643	611	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352366	70352366	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	226	562	0	ENST00000374080.3:c.4393C>T	p.Arg1465Cys	p.R1465C	ENST00000374080		1465	Cgt/Tgt	31/45	1	2	FACETS	0.911	0.852	0.971	0.911	0.852	0.971	CLONAL	1	TRUE	1	0.7	2		562	709	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76891498	76891498	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	147	483	0	ENST00000373344.5:c.4607A>C	p.Lys1536Thr	p.K1536T	ENST00000373344	NM_000489.3	1536	aAg/aCg	16/35	1	2	FACETS	0.85	0.782	0.921	0.85	0.782	0.921	CLONAL	1	TRUE	1	0.7	2		483	494	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76909588	76909588	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	115	440	0	ENST00000373344.5:c.4317G>T	p.Lys1439Asn	p.K1439N	ENST00000373344	NM_000489.3	1439	aaG/aaT	14/35	1	2	FACETS	0.969	0.884	1	0.969	0.884	1	CLONAL	1	TRUE	1	0.7	2		440	339	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938854	76938854	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1557140572	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	285	138	612	0	ENST00000373344.5:c.1894G>A	p.Glu632Lys	p.E632K	ENST00000373344	NM_000489.3	632	Gaa/Aaa	9/35	1	2	FACETS	0.932	0.856	1	0.932	0.856	1	CLONAL	1	TRUE	1	0.7	2		612	423	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939266	76939266	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	140	577	1	ENST00000373344.5:c.1482G>T	p.Lys494Asn	p.K494N	ENST00000373344	NM_000489.3	494	aaG/aaT	9/35	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.7	2		578	380	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76940499	76940499	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	201	84	455	0	ENST00000373344.5:c.595-1G>T		p.X199_splice	ENST00000373344	NM_000489.3	199			1	2	FACETS	0.842	0.753	0.935	0.842	0.753	0.935	CLONAL	1	TRUE	1	0.7	2		455	285	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76949323	76949323	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	173	108	376	0	ENST00000373344.5:c.474A>C	p.Lys158Asn	p.K158N	ENST00000373344	NM_000489.3	158	aaA/aaC	6/35	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.7	2		376	281	SUCCESS
BTK	695	MSKCC	GRCh37	X	100625040	100625040	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	99	509	0	ENST00000308731.7:c.337G>A	p.Val113Ile	p.V113I	ENST00000308731	NM_000061.2	113	Gtc/Atc	5/19	1	2	FACETS	0.847	0.764	0.933	0.847	0.764	0.933	CLONAL	1	TRUE	1	0.7	2		509	334	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123185178	123185178	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	95	431	0	ENST00000218089.9:c.1130C>A	p.Ser377Tyr	p.S377Y	ENST00000218089	NM_001042749.1	377	tCt/tAt	13/35	1	2	FACETS	0.776	0.697	0.858	0.776	0.697	0.858	SUBCLONAL	1	TRUE	1	0.7	2		431	350	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123189977	123189977	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	296	128	516	0	ENST00000218089.9:c.1197-1G>T		p.X399_splice	ENST00000218089	NM_001042749.1	399			1	2	FACETS	0.863	0.788	0.939	0.863	0.788	0.939	CLONAL	1	TRUE	1	0.7	2		516	424	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123189988	123189988	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	148	565	1	ENST00000218089.9:c.1207G>T	p.Glu403Ter	p.E403*	ENST00000218089	NM_001042749.1	403	Gaa/Taa	14/35	1	2	FACETS	0.909	0.837	0.984	0.909	0.837	0.984	CLONAL	1	TRUE	1	0.7	2		566	465	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123200027	123200027	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	56	223	0	ENST00000218089.9:c.2099C>T	p.Ala700Val	p.A700V	ENST00000218089	NM_001042749.1	700	gCc/gTc	22/35	1	2	FACETS	0.947	0.827	1	0.947	0.827	1	CLONAL	1	TRUE	1	0.7	2		223	169	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224539	123224539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016099-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	183	675	0	ENST00000218089.9:c.3392G>T	p.Arg1131Ile	p.R1131I	ENST00000218089	NM_001042749.1	1131	aGa/aTa	31/35	1	2	FACETS	0.929	0.863	0.996	0.929	0.863	0.996	CLONAL	1	TRUE	1	0.7	2		675	563	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	292	164	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.710872325525308	2		215	456	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480092	120480092	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	T	novel	NA	P-0016142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	254	380	0	ENST00000256646.2:c.3338-3C>A		p.X1113_splice	ENST00000256646	NM_024408.3	1113			1	2	FACETS	0.978	0.919	1	0.978	0.919	1	CLONAL	1	TRUE	1	0.710872325525308	2		380	731	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	170016828	170016828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016142-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	319	479	0	ENST00000295797.4:c.1633G>A	p.Gly545Arg	p.G545R	ENST00000295797	NM_002740.5	545	Ggg/Agg	17/18	1	2	FACETS	0.944	0.893	0.995	0.944	0.893	0.995	CLONAL	1	TRUE	1	0.710872325525308	2		479	951	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	138	215	0				ENST00000310581	NM_198253.2	-/1132			0.315530199759155	4	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	2	0.330099239007045	4		215	511	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880981	37880982	+	inframe_insertion	In_Frame_Ins	INS	-	-	GCATACGTGATG	rs397516975	NA	P-0016174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	353	625	0	ENST00000269571.5:c.2313_2324dup	p.Tyr772_Ala775dup	p.Y772_A775dup	ENST00000269571		772	-/GCATACGTGATG	20/27	0.330099239007045	4	FACETS	1	0.99	1			1	CLONAL	2	TRUE	NA	0.330099239007045	4		625	1209	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928079	178928079	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519925	NA	P-0016174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	110	427	0	ENST00000263967.3:c.1357G>A	p.Glu453Lys	p.E453K	ENST00000263967	NM_006218.2	453	Gaa/Aaa	8/21	1	2	FACETS	0.679	0.609	0.754	0.679	0.609	0.754	SUBCLONAL	1	TRUE	1	0.330099239007045	2		427	981	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs28934575	NA	P-0016174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	46	701	0	ENST00000269305.4:c.733G>T	p.Gly245Cys	p.G245C	ENST00000269305	NM_001126112.2	245	Ggc/Tgc	7/11	0.330099239007045	1	FACETS	0.354	0.297	0.416	0.354	0.297	0.416	SUBCLONAL	1	TRUE	0	0.330099239007045	1		701	658	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576855	7576855	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	101	517	0	ENST00000269305.4:c.991C>T	p.Gln331Ter	p.Q331*	ENST00000269305	NM_001126112.2	331	Cag/Tag	9/11	0.330099239007045	1	FACETS	0.747	0.668	0.831	0.747	0.668	0.831	SUBCLONAL	1	TRUE	0	0.330099239007045	1		517	684	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495384	56495384	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	50	665	0	ENST00000267101.3:c.3574G>C	p.Asp1192His	p.D1192H	ENST00000267101	NM_001982.3	1192	Gat/Cat	28/28	1	2	FACETS	0.373	0.315	0.437	0.373	0.315	0.437	SUBCLONAL	1	TRUE	1	0.330099239007045	2		665	812	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307261	118307261	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	14	152	0	ENST00000534358.1:c.34C>G	p.Arg12Gly	p.R12G	ENST00000534358	NM_005933.3	12	Cga/Gga	1/36	1	2	FACETS	0.364	0.263	0.486	0.364	0.263	0.486	SUBCLONAL	1	TRUE	1	0.330099239007045	2		152	233	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022677	12022677	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	34	520	0	ENST00000396373.4:c.783G>C	p.Glu261Asp	p.E261D	ENST00000396373	NM_001987.4	261	gaG/gaC	5/8	1	2	FACETS	0.311	0.253	0.376	0.311	0.253	0.376	SUBCLONAL	1	TRUE	1	0.330099239007045	2		520	663	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628639	21628639	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	57	728	0	ENST00000421138.2:c.1069C>G	p.His357Asp	p.H357D	ENST00000421138		357	Cat/Gat	10/16	1	2	FACETS	0.35	0.299	0.405	0.35	0.299	0.405	SUBCLONAL	1	TRUE	1	0.330099239007045	2		728	988	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701862	43701862	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	42	426	0	ENST00000382044.4:c.5383G>A	p.Asp1795Asn	p.D1795N	ENST00000382044	NM_001141980.1	1795	Gat/Aat	25/28	1	2	FACETS	0.384	0.319	0.456	0.384	0.319	0.456	SUBCLONAL	1	TRUE	1	0.330099239007045	2		426	663	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68856017	68856017	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1567512385	NA	P-0016174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	58	740	0	ENST00000261769.5:c.1825C>T	p.Pro609Ser	p.P609S	ENST00000261769	NM_004360.3	609	Cct/Tct	12/16	1	2	FACETS	0.335	0.287	0.388	0.335	0.287	0.388	SUBCLONAL	1	TRUE	1	0.330099239007045	2		740	1049	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821576	72821619	+	frameshift_variant	Frame_Shift_Del	DEL	CGCCAGGCAGTGGTACGAGCCGCCGCCGCCGCCGCCGCCGCCAC	CGCCAGGCAGTGGTACGAGCCGCCGCCGCCGCCGCCGCCGCCAC	-	novel	NA	P-0016174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	211	69	171	0	ENST00000268489.5:c.10556_10599del	p.Gly3519ValfsTer37	p.G3519Vfs*37	ENST00000268489	NM_006885.3	3519	gGTGGCGGCGGCGGCGGCGGCGGCGGCTCGTACCACTGCCTGGCG/g	10/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.330099239007045	2		171	280	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221756	36221756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs377420237	NA	P-0016174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	938	70	358	0	ENST00000222270.7:c.5425G>A	p.Ala1809Thr	p.A1809T	ENST00000222270	NM_014727.1	1809	Gcc/Acc	26/37	1	2	FACETS	0.421	0.366	0.481	0.421	0.366	0.481	SUBCLONAL	1	TRUE	1	0.330099239007045	2		358	1008	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52661374	52661374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1031229949	NA	P-0016174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	27	405	0	ENST00000394830.3:c.1456G>A	p.Glu486Lys	p.E486K	ENST00000394830	NM_018313.4	486	Gag/Aag	14/30	0.19060848446229	1	FACETS	0.265	0.21	0.328	0.265	0.21	0.328	INDETERMINATE	1	TRUE	0	0.330099239007045	1		405	516	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176523745	176523745	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	C	novel	NA	P-0016174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	41	481	0	ENST00000292408.4:c.2153+3G>C		p.X718_splice	ENST00000292408	NM_213647.1	718			1	2	FACETS	0.403	0.335	0.479	0.403	0.335	0.479	SUBCLONAL	1	TRUE	1	0.330099239007045	2		481	616	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123199793	123199793	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016174-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	106	363	0	ENST00000218089.9:c.2093A>T	p.His698Leu	p.H698L	ENST00000218089	NM_001042749.1	698	cAt/cTt	21/35	0.330099239007045	3	FACETS	0.927	0.831	1	0.464	0.415	0.515	CLONAL	1	TRUE	1	0.330099239007045	3		363	807	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	218	215	0				ENST00000310581	NM_198253.2	-/1132			0.423917119444437	4	FACETS	0.809	0.755	0.864	0.809	0.755	0.864	CLONAL	2	TRUE	2	0.56240705097476	4		215	749	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	485	446	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.512401269329577	4	FACETS	0.941	0.9	0.983	0.941	0.9	0.983	CLONAL	2	TRUE	2	0.56240705097476	4		446	1432	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0016188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	832	456	778	1	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	0.512401269329577	4	FACETS	0.984	0.94	1	0.984	0.94	1	CLONAL	2	TRUE	2	0.56240705097476	4		779	1288	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578280	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs876660825	NA	P-0016188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	372	745	1	ENST00000269305.4:c.569C>T	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	190	cCt/cTt	6/11	0.512401269329577	4	FACETS	0.898	0.853	0.944	0.898	0.853	0.944	CLONAL	2	TRUE	2	0.56240705097476	4		746	1151	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971187	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0016188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	228	650	418	0	ENST00000304494.5:c.171_172delinsTT	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	57	gcCCga/gcTTga	2/3	0.558984609479	4	FACETS	1	0.99	1	1	0.99	1	CLONAL	4	TRUE	0	0.56240705097476	4		418	878	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162107	22162107	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	170	442	0	ENST00000215832.6:c.148C>T	p.Arg50Ter	p.R50*	ENST00000215832	NM_002745.4	50	Cga/Tga	2/9	0.557823278961849	3	FACETS	1	0.956	1	0.527	0.485	0.57	CLONAL	1	TRUE	1	0.56240705097476	3		442	735	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163811	72163811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	335	444	0	ENST00000357731.5:c.547G>A	p.Glu183Lys	p.E183K	ENST00000357731	NM_173808.2	183	Gaa/Aaa	4/7	0.557823278961849	3	FACETS	0.947	0.9	0.994	0.947	0.9	0.994	CLONAL	2	TRUE	1	0.56240705097476	3		444	806	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132049	176132049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774336303	NA	P-0016188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	974	524	664	0	ENST00000367669.3:c.718C>T	p.Leu240Phe	p.L240F	ENST00000367669	NM_022457.5	240	Ctt/Ttt	5/20	0.512401269329577	4	FACETS	0.972	0.931	1	0.972	0.931	1	CLONAL	2	TRUE	2	0.56240705097476	4		664	1498	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549787	226549787	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	novel	NA	P-0016188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	368	541	0	ENST00000366794.5:c.2849-3C>T		p.X950_splice	ENST00000366794	NM_001618.3	950			0.551440900035048	2	FACETS	0.948	0.908	0.988	0.948	0.908	0.988	CLONAL	2	TRUE	0	0.56240705097476	2		541	690	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066712	30066712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751618424	NA	P-0016188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	252	395	0	ENST00000331968.5:c.2419G>A	p.Glu807Lys	p.E807K	ENST00000331968	NM_002742.2	807	Gaa/Aaa	16/18	NA	2	FACETS	0.93	0.881	0.978			1	INDETERMINATE	2	TRUE	NA	0.56240705097476	2		395	482	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675156	40675157	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0016188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	988	229	827	3	ENST00000249776.8:c.120_121delinsAA	p.Ala41Thr	p.A41T	ENST00000249776	NM_033286.3	40	gcGGcc/gcAAcc	1/9	0.557823278961849	3	FACETS	0.857	0.798	0.919	0.429	0.399	0.46	CLONAL	1	TRUE	1	0.56240705097476	3		830	1217	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420210	88420210	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	167	585	1	ENST00000360948.2:c.2476G>A	p.Ala826Thr	p.A826T	ENST00000360948	NM_001012338.2	826	Gct/Act	19/19	0.512401269329577	4	FACETS	0.916	0.841	0.994	0.458	0.42	0.497	CLONAL	1	TRUE	2	0.56240705097476	4		586	1013	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679798	88679798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774739739	NA	P-0016188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	135	605	2	ENST00000360948.2:c.665G>A	p.Arg222Gln	p.R222Q	ENST00000360948	NM_001012338.2	222	cGa/cAa	7/19	0.512401269329577	4	FACETS	0.789	0.716	0.865	0.394	0.358	0.433	SUBCLONAL	1	TRUE	2	0.56240705097476	4		607	951	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075146	16075146	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	339	350	0	ENST00000268712.3:c.406G>T	p.Gly136Trp	p.G136W	ENST00000268712	NM_006311.3	136	Ggg/Tgg	4/46	0.512401269329577	4	FACETS	1	0.949	1	1	0.949	1	CLONAL	2	TRUE	2	0.56240705097476	4		350	942	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858290	59858290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	495	640	0	ENST00000259008.2:c.1705G>A	p.Gly569Arg	p.G569R	ENST00000259008	NM_032043.2	569	Ggg/Agg	12/20	0.512401269329577	4	FACETS	0.927	0.886	0.967	0.927	0.886	0.967	CLONAL	2	TRUE	2	0.56240705097476	4		640	1484	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18966000	18966001	+	missense_variant	Missense_Mutation	DNP	AG	AG	CA	novel	NA	P-0016188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	178	700	2	ENST00000262803.5:c.1493_1494delinsCA	p.Lys498Thr	p.K498T	ENST00000262803	NM_002911.3	498	aAG/aCA	11/24	0.56240705097476	3	FACETS	0.916	0.845	0.991	0.458	0.422	0.496	CLONAL	1	TRUE	1	0.56240705097476	3		702	885	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293195	212293195	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	333	467	0	ENST00000342788.4:c.2657G>A	p.Trp886Ter	p.W886*	ENST00000342788	NM_005235.2	886	tGg/tAg	22/28	0.273867760184066	3	FACETS	0.955	0.908	1			1	INDETERMINATE	2	TRUE	NA	0.56240705097476	3		467	794	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022916	31022916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	197	562	1	ENST00000375687.4:c.2401G>A	p.Glu801Lys	p.E801K	ENST00000375687	NM_015338.5	801	Gag/Aag	13/13	0.557823278961849	3	FACETS	1	0.97	1	0.543	0.504	0.584	CLONAL	1	TRUE	1	0.56240705097476	3		563	826	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397764	49397764	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	515	601	735	0	ENST00000418115.1:c.460T>A	p.Phe154Ile	p.F154I	ENST00000418115	NM_001664.2	154	Ttt/Att	5/5	0.551440900035048	2	FACETS	0.958	0.926	0.989	0.958	0.926	0.989	CLONAL	2	TRUE	0	0.56240705097476	2		735	1116	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468457	89468457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	332	418	0	ENST00000336596.2:c.1991G>A	p.Arg664Lys	p.R664K	ENST00000336596	NM_005233.5	664	aGg/aAg	11/17	0.551440900035048	2	FACETS	0.922	0.88	0.964	0.922	0.88	0.964	CLONAL	2	TRUE	0	0.56240705097476	2		418	640	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259023	153259023	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	150	343	0	ENST00000281708.4:c.792A>T	p.Gln264His	p.Q264H	ENST00000281708	NM_033632.3	264	caA/caT	5/12	0.557823278961849	3	FACETS	0.873	0.799	0.95	0.436	0.399	0.475	CLONAL	1	TRUE	1	0.56240705097476	3		343	783	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180049838	180049838	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	404	847	0	ENST00000261937.6:c.1550C>T	p.Thr517Ile	p.T517I	ENST00000261937	NM_182925.4	517	aCt/aTt	12/30	0.423917119444437	4	FACETS	0.904	0.86	0.948	0.904	0.86	0.948	CLONAL	2	TRUE	2	0.56240705097476	4		847	1242	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672300	30672300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140008669	NA	P-0016188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	457	708	2	ENST00000376406.3:c.4660C>T	p.Arg1554Trp	p.R1554W	ENST00000376406	NM_014641.2	1554	Cgg/Tgg	10/15	0.56240705097476	4	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	2	0.56240705097476	4		710	1266	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172033	32172033	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	371	593	0	ENST00000375023.3:c.2999G>C	p.Gly1000Ala	p.G1000A	ENST00000375023	NM_004557.3	1000	gGg/gCg	19/30	0.56240705097476	4	FACETS	0.94	0.893	0.987	0.94	0.893	0.987	CLONAL	2	TRUE	2	0.56240705097476	4		593	1097	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023153	150023153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	431	643	1	ENST00000253339.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000253339		37	tCc/tTc	1/7	0.56240705097476	2	FACETS	0.954	0.917	0.992	0.954	0.917	0.992	CLONAL	2	TRUE	0	0.56240705097476	2		644	803	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983998	2983998	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	390	733	1	ENST00000396946.4:c.532G>T	p.Glu178Ter	p.E178*	ENST00000396946	NM_032415.4	178	Gag/Tag	5/25	0.423917119444437	4	FACETS	0.898	0.854	0.943	0.898	0.854	0.943	CLONAL	2	TRUE	2	0.56240705097476	4		734	1206	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512099	148512099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	316	532	0	ENST00000320356.2:c.1579C>T	p.Pro527Ser	p.P527S	ENST00000320356	NM_004456.4	527	Ccc/Tcc	14/20	0.423917119444437	4	FACETS	0.752	0.71	0.796	0.752	0.71	0.796	SUBCLONAL	2	TRUE	2	0.56240705097476	4		532	1167	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878200	151878200	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016188-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	275	531	0	ENST00000262189.6:c.6745C>T	p.Pro2249Ser	p.P2249S	ENST00000262189	NM_170606.2	2249	Cct/Tct	36/59	0.423917119444437	4	FACETS	0.807	0.759	0.856	0.807	0.759	0.856	CLONAL	2	TRUE	2	0.56240705097476	4		531	947	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016188-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	269	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.817063666810445	2		215	633	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398284	25398284	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121913529	NA	P-0016188-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	366	446	0	ENST00000311936.3:c.35G>T	p.Gly12Val	p.G12V	ENST00000311936	NM_004985.3	12	gGt/gTt	2/5	0.156617622321519	1	FACETS	0.531	0.505	0.558	0.531	0.505	0.558	INDETERMINATE	1	TRUE	0	0.817063666810445	1		446	997	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574017	7574017	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs121912664	NA	P-0016188-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	480	778	1	ENST00000269305.4:c.1010G>T	p.Arg337Leu	p.R337L	ENST00000269305	NM_001126112.2	337	cGc/cTc	10/11	1	2	FACETS	0.951	0.911	0.992	0.951	0.911	0.992	CLONAL	1	TRUE	1	0.817063666810445	2		779	1235	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971187	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0016188-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	120	639	418	0	ENST00000304494.5:c.171_172delinsTT	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	57	gcCCga/gcTTga	2/3	0.817063666810445	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	2	TRUE	0	0.817063666810445	2		418	759	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22162107	22162107	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016188-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	268	442	0	ENST00000215832.6:c.148C>T	p.Arg50Ter	p.R50*	ENST00000215832	NM_002745.4	50	Cga/Tga	2/9	1	2	FACETS	0.909	0.857	0.961	0.909	0.857	0.961	CLONAL	1	TRUE	1	0.817063666810445	2		442	722	SUCCESS
NEGR1	257194	MSKCC	GRCh37	1	72163811	72163811	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016188-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	239	444	0	ENST00000357731.5:c.547G>A	p.Glu183Lys	p.E183K	ENST00000357731	NM_173808.2	183	Gaa/Aaa	4/7	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.817063666810445	2		444	565	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176132049	176132049	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs774336303	NA	P-0016188-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	400	664	0	ENST00000367669.3:c.718C>T	p.Leu240Phe	p.L240F	ENST00000367669	NM_022457.5	240	Ctt/Ttt	5/20	1	2	FACETS	0.912	0.869	0.955	0.912	0.869	0.955	CLONAL	1	TRUE	1	0.817063666810445	2		664	1074	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226549787	226549787	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	novel	NA	P-0016188-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	288	541	0	ENST00000366794.5:c.2849-3C>T		p.X950_splice	ENST00000366794	NM_001618.3	950			0.817063666810445	1	FACETS	0.937	0.897	0.976	0.937	0.897	0.976	CLONAL	1	TRUE	0	0.817063666810445	1		541	445	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30066712	30066712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751618424	NA	P-0016188-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	215	395	0	ENST00000331968.5:c.2419G>A	p.Glu807Lys	p.E807K	ENST00000331968	NM_002742.2	807	Gaa/Aaa	16/18	0.817063666810445	1	FACETS	0.979	0.933	1	0.979	0.933	1	CLONAL	1	TRUE	0	0.817063666810445	1		395	318	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675156	40675157	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0016188-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	489	827	3	ENST00000249776.8:c.120_121delinsAA	p.Ala41Thr	p.A41T	ENST00000249776	NM_033286.3	40	gcGGcc/gcAAcc	1/9	1	2	FACETS	0.857	0.82	0.895	0.857	0.82	0.895	CLONAL	1	TRUE	1	0.817063666810445	2		830	1396	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420210	88420210	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016188-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	363	585	1	ENST00000360948.2:c.2476G>A	p.Ala826Thr	p.A826T	ENST00000360948	NM_001012338.2	826	Gct/Act	19/19	0.477817282203348	3	FACETS	1	0.959	1			1	INDETERMINATE	1	TRUE	NA	0.817063666810445	3		586	1235	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679798	88679798	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774739739	NA	P-0016188-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	380	605	2	ENST00000360948.2:c.665G>A	p.Arg222Gln	p.R222Q	ENST00000360948	NM_001012338.2	222	cGa/cAa	7/19	0.477817282203348	3	FACETS	0.963	0.914	1			1	INDETERMINATE	1	TRUE	NA	0.817063666810445	3		607	1360	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075146	16075146	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016188-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	277	350	0	ENST00000268712.3:c.406G>T	p.Gly136Trp	p.G136W	ENST00000268712	NM_006311.3	136	Ggg/Tgg	4/46	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.817063666810445	2		350	649	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59858290	59858290	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016188-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	746	640	0	ENST00000259008.2:c.1705G>A	p.Gly569Arg	p.G569R	ENST00000259008	NM_032043.2	569	Ggg/Agg	12/20	0.781792133072862	3	FACETS	0.929	0.901	0.957	0.929	0.901	0.957	CLONAL	2	TRUE	1	0.817063666810445	3		640	1384	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212293195	212293195	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016188-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	280	467	0	ENST00000342788.4:c.2657G>A	p.Trp886Ter	p.W886*	ENST00000342788	NM_005235.2	886	tGg/tAg	22/28	0.817063666810445	1	FACETS	0.934	0.894	0.973	0.934	0.894	0.973	CLONAL	1	TRUE	0	0.817063666810445	1		467	434	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022916	31022916	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016188-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	329	562	1	ENST00000375687.4:c.2401G>A	p.Glu801Lys	p.E801K	ENST00000375687	NM_015338.5	801	Gag/Aag	13/13	1	2	FACETS	0.915	0.868	0.963	0.915	0.868	0.963	CLONAL	1	TRUE	1	0.817063666810445	2		563	880	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49397764	49397764	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016188-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	508	735	0	ENST00000418115.1:c.460T>A	p.Phe154Ile	p.F154I	ENST00000418115	NM_001664.2	154	Ttt/Att	5/5	0.817063666810445	1	FACETS	0.975	0.946	1	0.975	0.946	1	CLONAL	1	TRUE	0	0.817063666810445	1		735	754	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89468457	89468457	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016188-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	114	282	418	0	ENST00000336596.2:c.1991G>A	p.Arg664Lys	p.R664K	ENST00000336596	NM_005233.5	664	aGg/aAg	11/17	0.817063666810445	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.817063666810445	1		418	396	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153259023	153259023	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016188-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	299	212	343	0	ENST00000281708.4:c.792A>T	p.Gln264His	p.Q264H	ENST00000281708	NM_033632.3	264	caA/caT	5/12	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.817063666810445	2		343	511	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180049838	180049838	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016188-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	483	847	0	ENST00000261937.6:c.1550C>T	p.Thr517Ile	p.T517I	ENST00000261937	NM_182925.4	517	aCt/aTt	12/30	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	1	TRUE	NA	0.817063666810445	2		847	1132	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672300	30672300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140008669	NA	P-0016188-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	474	708	2	ENST00000376406.3:c.4660C>T	p.Arg1554Trp	p.R1554W	ENST00000376406	NM_014641.2	1554	Cgg/Tgg	10/15	1	2	FACETS	0.919	0.879	0.959	0.919	0.879	0.959	CLONAL	1	TRUE	1	0.817063666810445	2		710	1263	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32172033	32172033	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016188-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	393	593	0	ENST00000375023.3:c.2999G>C	p.Gly1000Ala	p.G1000A	ENST00000375023	NM_004557.3	1000	gGg/gCg	19/30	1	2	FACETS	0.985	0.939	1	0.985	0.939	1	CLONAL	1	TRUE	1	0.817063666810445	2		593	977	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150023153	150023153	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016188-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	202	413	643	1	ENST00000253339.5:c.110C>T	p.Ser37Phe	p.S37F	ENST00000253339		37	tCc/tTc	1/7	0.817063666810445	1	FACETS	0.972	0.939	1	0.972	0.939	1	CLONAL	1	TRUE	0	0.817063666810445	1		644	615	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2983998	2983998	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016188-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	405	733	1	ENST00000396946.4:c.532G>T	p.Glu178Ter	p.E178*	ENST00000396946	NM_032415.4	178	Gag/Tag	5/25	1	2	FACETS	0.905	0.862	0.947	0.905	0.862	0.947	CLONAL	1	TRUE	1	0.817063666810445	2		734	1096	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148512099	148512099	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016188-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	290	532	0	ENST00000320356.2:c.1579C>T	p.Pro527Ser	p.P527S	ENST00000320356	NM_004456.4	527	Ccc/Tcc	14/20	1	2	FACETS	0.825	0.779	0.873	0.825	0.779	0.873	CLONAL	1	TRUE	1	0.817063666810445	2		532	860	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878200	151878200	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016188-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	335	531	0	ENST00000262189.6:c.6745C>T	p.Pro2249Ser	p.P2249S	ENST00000262189	NM_170606.2	2249	Cct/Tct	36/59	1	2	FACETS	0.95	0.902	0.999	0.95	0.902	0.999	CLONAL	1	TRUE	1	0.817063666810445	2		531	863	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477861	140477861	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs397507474	NA	P-0016188-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	378	603	0	ENST00000288602.6:c.1447A>G	p.Lys483Glu	p.K483E	ENST00000288602	NM_004333.4	483	Aaa/Gaa	12/18	1	2	FACETS	0.932	0.887	0.977	0.932	0.887	0.977	CLONAL	1	TRUE	1	0.817063666810445	2		603	993	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578280	7578282	+	missense_variant	Missense_Mutation	TNP	GGG	GGG	AGT	novel	NA	P-0016188-T03-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	389	742	0	ENST00000269305.4:c.567_569delinsACT	p.Pro190Leu	p.P190L	ENST00000269305	NM_001126112.2	189	gcCCCt/gcACTt	6/11	1	2	FACETS	0.946	0.901	0.991	0.946	0.901	0.991	CLONAL	1	TRUE	1	0.817063666810445	2		742	1007	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	137	215	0				ENST00000310581	NM_198253.2	-/1132			0.186926522263178	7	FACETS	1	0.937	1	1	0.988	1	CLONAL	7	TRUE	2	0.186926522263178	7		215	303	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0016208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	25	685	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.186926522263178	7	FACETS	0.406	0.318	0.508	0.102	0.079	0.127	SUBCLONAL	1	TRUE	3	0.186926522263178	7		685	966	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519816	NA	P-0016208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	135	654	0	ENST00000269571.5:c.929C>T	p.Ser310Phe	p.S310F	ENST00000269571		310	tCc/tTc	8/27	0.186926522263178	7	FACETS	1	0.958	1	0.549	0.498	0.602	CLONAL	2	TRUE	3	0.186926522263178	7		654	966	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435317	56435317	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200066146	NA	P-0016208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	81	327	0	ENST00000407977.2:c.1820C>T	p.Ser607Leu	p.S607L	ENST00000407977		607	tCg/tTg	9/10	0.186926522263178	7	FACETS	0.988	0.875	1	0.741	0.656	0.831	CLONAL	3	TRUE	3	0.186926522263178	7		327	429	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0016208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	616	679	1	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.186926522263178	5	FACETS	1	0.978	1			1	CLONAL	9	TRUE	NA	0.186926522263178	5		680	930	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577127	7577127	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	283	599	676	0	ENST00000269305.4:c.811G>C	p.Glu271Gln	p.E271Q	ENST00000269305	NM_001126112.2	271	Gag/Cag	8/11	0.186926522263178	5	FACETS	1	0.989	1			1	CLONAL	9	TRUE	NA	0.186926522263178	5		676	882	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874261	155874261	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352822	NA	P-0016208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	29	440	1	ENST00000368323.3:c.270G>A	p.Met90Ile	p.M90I	ENST00000368323	NM_006912.5	90	atG/atA	5/6	0.186926522263178	11	FACETS	0.63	0.503	0.775	0.09	0.071	0.111	SUBCLONAL	1	TRUE	4	0.186926522263178	11		441	907	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577079	7577079	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	584	605	0	ENST00000269305.4:c.859G>C	p.Glu287Gln	p.E287Q	ENST00000269305	NM_001126112.2	287	Gag/Cag	8/11	0.186926522263178	5	FACETS	0.993	0.964	1			1	CLONAL	9	TRUE	NA	0.186926522263178	5		605	895	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579894	7579894	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782646	NA	P-0016208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	98	501	0	ENST00000269305.4:c.19G>C	p.Asp7His	p.D7H	ENST00000269305	NM_001126112.2	7	Gat/Cat	2/11	0.186926522263178	5	FACETS	0.932	0.832	1			1	CLONAL	2	TRUE	NA	0.186926522263178	5		501	720	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044457	128044457	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	79	455	0	ENST00000285398.2:c.1164G>C	p.Gln388His	p.Q388H	ENST00000285398	NM_000122.1	388	caG/caC	8/15	0.278272658802542	4	FACETS	0.936	0.825	1	0.624	0.55	0.703	CLONAL	2	TRUE	1	0.186926522263178	4		455	536	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40789994	40789994	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs746391800	NA	P-0016208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	69	329	0	ENST00000373198.4:c.2737G>A	p.Glu913Lys	p.E913K	ENST00000373198	NM_133170.3	913	Gag/Aag	18/32	0.186926522263178	8	FACETS	1	0.929	1	0.439	0.383	0.5	CLONAL	2	TRUE	3	0.186926522263178	8		329	525	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1264516	1264516	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	rs1224148602	NA	P-0016208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	64	260	0	ENST00000310581.5:c.2843+3G>A		p.X948_splice	ENST00000310581	NM_198253.2	948			0.186926522263178	7	FACETS	0.985	0.858	1	0.591	0.515	0.673	CLONAL	3	TRUE	2	0.186926522263178	7		260	340	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192409	138192409	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	65	235	0	ENST00000237289.4:c.45G>A	p.Met15Ile	p.M15I	ENST00000237289	NM_001270507.1	15	atG/atA	2/9	0.278272658802542	3	FACETS	1	0.954	1	1	0.954	1	CLONAL	2	TRUE	1	0.186926522263178	3		235	314	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1031	264	390	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	0.575	0.538	0.614	0.575	0.538	0.614	SUBCLONAL	1	TRUE	1	0.708774437451504	2		390	1295	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484421	57484421	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913495	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1201	190	491	1	ENST00000371085.3:c.602G>A	p.Arg201His	p.R201H	ENST00000371085	NM_000516.4	201	cGt/cAt	8/13	1	2	FACETS	0.385	0.355	0.417	0.385	0.355	0.417	SUBCLONAL	1	TRUE	1	0.708774437451504	2		492	1391	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41266136	41266136	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913407	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	689	364	1	ENST00000349496.5:c.133T>C	p.Ser45Pro	p.S45P	ENST00000349496	NM_001904.3	45	Tct/Cct	3/15	0.708009242465465	2	FACETS	0.979	0.954	1	0.979	0.954	1	CLONAL	2	TRUE	0	0.708774437451504	2		365	993	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1233	786	519	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	1	0.708774437451504	2		524	2019	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003781	45003782	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	125	817	0	ENST00000558401.1:c.43_44del	p.Leu15PhefsTer41	p.L15Ffs*41	ENST00000558401	NM_004048.2	13	CTc/c	1/4	1	2	FACETS	0.319	0.288	0.352	0.319	0.288	0.352	SUBCLONAL	1	TRUE	1	0.708774437451504	2		817	1106	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577566	7577566	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs876660807	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1612	37	670	0	ENST00000269305.4:c.715A>G	p.Asn239Asp	p.N239D	ENST00000269305	NM_001126112.2	239	Aac/Gac	7/11	1	2	FACETS	0.063	0.051	0.077	0.063	0.051	0.077	SUBCLONAL	1	TRUE	1	0.708774437451504	2		670	1649	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577517	7577517	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs876659675	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1396	138	635	0	ENST00000269305.4:c.764T>C	p.Ile255Thr	p.I255T	ENST00000269305	NM_001126112.2	255	aTc/aCc	7/11	1	2	FACETS	0.254	0.23	0.279	0.254	0.23	0.279	SUBCLONAL	1	TRUE	1	0.708774437451504	2		635	1534	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15971325	15971325	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs377505818	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1177	202	544	0	ENST00000268712.3:c.4624G>A	p.Val1542Met	p.V1542M	ENST00000268712	NM_006311.3	1542	Gtg/Atg	32/46	1	2	FACETS	0.413	0.382	0.446	0.413	0.382	0.446	SUBCLONAL	1	TRUE	1	0.708774437451504	2		544	1379	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927980	178927980	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs121913272	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	110	395	0	ENST00000263967.3:c.1258T>C	p.Cys420Arg	p.C420R	ENST00000263967	NM_006218.2	420	Tgt/Cgt	8/21	1	2	FACETS	0.426	0.382	0.472	0.426	0.382	0.472	SUBCLONAL	1	TRUE	1	0.708774437451504	2		395	729	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56495023	56495023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs2271188	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1271	206	586	0	ENST00000267101.3:c.3380G>A	p.Arg1127His	p.R1127H	ENST00000267101	NM_001982.3	1127	cGc/cAc	27/28	1	2	FACETS	0.394	0.364	0.425	0.394	0.364	0.425	SUBCLONAL	1	TRUE	1	0.708774437451504	2		586	1477	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	965	438	320	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	0.708009242465465	2	FACETS	0.881	0.84	0.923	0.44	0.42	0.462	CLONAL	1	TRUE	0	0.708774437451504	2		321	1403	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432115	121432115	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs762703502	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1197	512	484	8	ENST00000257555.6:c.864del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		288	Ggg/gg	4/10	1	2	FACETS	0.845	0.808	0.883	0.845	0.808	0.883	CLONAL	1	TRUE	1	0.708774437451504	2		492	1709	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578206	7578206	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1450	689	968	0	ENST00000269305.4:c.643A>T	p.Ser215Cys	p.S215C	ENST00000269305	NM_001126112.2	215	Agt/Tgt	6/11	1	2	FACETS	0.909	0.875	0.943	0.909	0.875	0.943	CLONAL	1	TRUE	1	0.708774437451504	2		968	2139	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671655	67671655	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs1400980130	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1150	274	444	2	ENST00000264010.4:c.2070del	p.Glu691SerfsTer30	p.E691Sfs*30	ENST00000264010	NM_006565.3	688	gtA/gt	12/12	1	2	FACETS	0.543	0.508	0.579	0.543	0.508	0.579	SUBCLONAL	1	TRUE	1	0.708774437451504	2		446	1424	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138941	64138941	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	939	428	304	1	ENST00000334205.4:c.2313del	p.Ser772ProfsTer12	p.S772Pfs*12	ENST00000334205	NM_003942.2	770	Ccc/cc	17/17	1	2	FACETS	0.883	0.842	0.926	0.883	0.842	0.926	CLONAL	1	TRUE	1	0.708774437451504	2		305	1367	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030479	49030479	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	852	398	644	2	ENST00000267163.4:c.1959del	p.Val654CysfsTer4	p.V654Cfs*4	ENST00000267163	NM_000321.2	652	Aaa/aa	19/27	1	2	FACETS	0.898	0.855	0.943	0.898	0.855	0.943	CLONAL	1	TRUE	1	0.708774437451504	2		646	1250	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857380	9857380	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	201	216	0	ENST00000330684.3:c.4021del	p.Ser1341AlafsTer56	p.S1341Afs*56	ENST00000330684	NM_001134407.1	1341	Agc/gc	13/13	1	2	FACETS	0.484	0.448	0.522	0.484	0.448	0.522	SUBCLONAL	1	TRUE	1	0.708774437451504	2		216	1171	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1017	478	354	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	1	2	FACETS	0.902	0.862	0.943	0.902	0.862	0.943	CLONAL	1	TRUE	1	0.708774437451504	2		354	1495	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1005	497	513	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	0.934	0.893	0.975	0.934	0.893	0.975	CLONAL	1	TRUE	1	0.708774437451504	2		513	1502	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50919866	50919866	+	splice_acceptor_variant	Splice_Site	DEL	G	G	-	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1057	524	701	5	ENST00000440232.2:c.2959del		p.X987_splice	ENST00000440232	NM_002691.3	987			1	2	FACETS	0.935	0.896	0.975	0.935	0.896	0.975	CLONAL	1	TRUE	1	0.708774437451504	2		706	1581	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1595	342	430	2	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.498	0.469	0.528	0.498	0.469	0.528	SUBCLONAL	1	TRUE	1	0.708774437451504	2		432	1937	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416953	416953	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs771545848	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	423	417	2	ENST00000399788.2:c.3597del	p.Gly1200AspfsTer9	p.G1200Dfs*9	ENST00000399788	NM_001042603.1	1199	aaA/aa	23/28	1	2	FACETS	0.861	0.819	0.903	0.861	0.819	0.903	CLONAL	1	TRUE	1	0.708774437451504	2		419	1387	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70119781	70119781	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1274036689	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1105	593	709	4	ENST00000245479.2:c.788del	p.Gly263AlafsTer16	p.G263Afs*16	ENST00000245479	NM_000346.3	261	gaG/ga	3/3	1	2	FACETS	0.985	0.947	1	0.985	0.947	1	CLONAL	1	TRUE	1	0.708774437451504	2		713	1698	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288934	212288934	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	239	575	2	ENST00000342788.4:c.2812C>T	p.Arg938Cys	p.R938C	ENST00000342788	NM_005235.2	938	Cgt/Tgt	23/28	1	2	FACETS	0.855	0.801	0.91	0.855	0.801	0.91	CLONAL	1	TRUE	1	0.708774437451504	2		577	789	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007824	45007825	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	482	651	0	ENST00000558401.1:c.276dup	p.Thr93HisfsTer2	p.T93Hfs*2	ENST00000558401	NM_004048.2	91	acc/aCcc	2/4	1	2	FACETS	0.938	0.897	0.98	0.938	0.897	0.98	CLONAL	1	TRUE	1	0.708774437451504	2		651	1450	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148514998	148515000	+	inframe_deletion	In_Frame_Del	DEL	TCT	TCT	-	rs775039041	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1291	280	636	0	ENST00000320356.2:c.1209_1211del	p.Glu404del	p.E404del	ENST00000320356	NM_004456.4	403	gaAGAg/gag	10/20	1	2	FACETS	0.503	0.471	0.536	0.503	0.471	0.536	SUBCLONAL	1	TRUE	1	0.708774437451504	2		636	1571	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	696	391	1	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	1	2	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	1	0.708774437451504	2		392	1561	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39937104	39937104	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	611	725	2	ENST00000378444.4:c.79G>A	p.Glu27Lys	p.E27K	ENST00000378444	NM_001123385.1	27	Gaa/Aaa	2/15	1	2	FACETS	0.964	0.926	1	0.964	0.926	1	CLONAL	1	TRUE	1	0.708774437451504	2		727	1789	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645339	67645339	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1245	344	487	1	ENST00000264010.4:c.610del	p.Thr204GlnfsTer18	p.T204Qfs*18	ENST00000264010	NM_006565.3	202	Aaa/aa	3/12	1	2	FACETS	0.611	0.577	0.646	0.611	0.577	0.646	SUBCLONAL	1	TRUE	1	0.708774437451504	2		488	1589	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64132927	64132927	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs145356210	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1237	169	628	0	ENST00000334205.4:c.1061G>A	p.Arg354Gln	p.R354Q	ENST00000334205	NM_003942.2	354	cGa/cAa	9/17	1	2	FACETS	0.339	0.311	0.369	0.339	0.311	0.369	SUBCLONAL	1	TRUE	1	0.708774437451504	2		628	1406	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922238	39922238	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs888552486	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	130	394	0	ENST00000378444.4:c.3934G>A	p.Ala1312Thr	p.A1312T	ENST00000378444	NM_001123385.1	1312	Gca/Aca	9/15	1	2	FACETS	0.347	0.314	0.382	0.347	0.314	0.382	SUBCLONAL	1	TRUE	1	0.708774437451504	2		394	1056	SUCCESS
AR	367	MSKCC	GRCh37	X	66765826	66765826	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1786	432	1009	3	ENST00000374690.3:c.838C>T	p.Arg280Cys	p.R280C	ENST00000374690	NM_000044.3	280	Cgt/Tgt	1/8	1	2	FACETS	0.55	0.522	0.578	0.55	0.522	0.578	SUBCLONAL	1	TRUE	1	0.708774437451504	2		1012	2218	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157100302	157100302	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1417035592	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	275	455	0	ENST00000346085.5:c.1243del	p.Ala415ProfsTer15	p.A415Pfs*15	ENST00000346085	NM_020732.3	413	tcG/tc	1/20	1	2	FACETS	0.937	0.883	0.993	0.937	0.883	0.993	CLONAL	1	TRUE	1	0.708774437451504	2		455	828	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37045935	37045935	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs63750781	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	1020	689	2	ENST00000231790.2:c.350C>T	p.Thr117Met	p.T117M	ENST00000231790	NM_000249.3	117	aCg/aTg	4/19	0.708009242465465	2	FACETS	0.988	0.967	1	0.988	0.967	1	CLONAL	2	TRUE	0	0.708774437451504	2		691	1457	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396482	139396482	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1633	148	728	1	ENST00000277541.6:c.5443del	p.Asp1815ThrfsTer72	p.D1815Tfs*72	ENST00000277541	NM_017617.3	1815	Gac/ac	29/34	1	2	FACETS	0.234	0.213	0.257	0.234	0.213	0.257	SUBCLONAL	1	TRUE	1	0.708774437451504	2		729	1781	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36164781	36164781	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1306	319	757	0	ENST00000300305.3:c.1094G>A	p.Gly365Asp	p.G365D	ENST00000300305		365	gGc/gAc	8/8	1	2	FACETS	0.554	0.521	0.588	0.554	0.521	0.588	SUBCLONAL	1	TRUE	1	0.708774437451504	2		757	1625	SUCCESS
B2M	567	MSKCC	GRCh37	15	45003782	45003782	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs752758095	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	236	457	0	ENST00000558401.1:c.38T>C	p.Leu13Pro	p.L13P	ENST00000558401	NM_004048.2	13	cTc/cCc	1/4	1	2	FACETS	0.603	0.562	0.645	0.603	0.562	0.645	SUBCLONAL	1	TRUE	1	0.708774437451504	2		457	1104	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61726051	61726052	+	splice_region_variant,intron_variant	Splice_Region	DEL	AA	AA	-	rs372688892	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1043	536	485	1	ENST00000401558.2:c.591-4_591-3del		p.X197_splice	ENST00000401558	NM_003400.3	197			1	2	FACETS	0.958	0.918	0.998	0.958	0.918	0.998	CLONAL	1	TRUE	1	0.708774437451504	2		486	1579	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948748	71948748	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs760925109	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1047	477	930	3	ENST00000298229.2:c.3466del	p.Arg1156GlyfsTer46	p.R1156Gfs*46	ENST00000298229	NM_001567.3	1154	Ccc/cc	26/28	1	2	FACETS	0.883	0.844	0.923	0.883	0.844	0.923	CLONAL	1	TRUE	1	0.708774437451504	2		933	1524	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71939260	71939260	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1293	310	747	0	ENST00000298229.2:c.209G>A	p.Arg70His	p.R70H	ENST00000298229	NM_001567.3	70	cGc/cAc	2/28	1	2	FACETS	0.546	0.513	0.579	0.546	0.513	0.579	SUBCLONAL	1	TRUE	1	0.708774437451504	2		747	1603	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21644547	21644547	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	rs745659712	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1193	483	504	7	ENST00000421138.2:c.120del	p.Val41SerfsTer2	p.V41Sfs*2	ENST00000421138		40	aaA/aa	4/16	1	2	FACETS	0.813	0.776	0.851	0.813	0.776	0.851	CLONAL	1	TRUE	1	0.708774437451504	2		511	1676	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223002	36223002	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1599	414	797	3	ENST00000222270.7:c.5636del	p.Gly1879ValfsTer16	p.G1879Vfs*16	ENST00000222270	NM_014727.1	1877	ttG/tt	27/37	1	2	FACETS	0.58	0.55	0.611	0.58	0.55	0.611	SUBCLONAL	1	TRUE	1	0.708774437451504	2		800	2013	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9781599	9781599	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1591	234	793	0	ENST00000377346.4:c.1909G>A	p.Ala637Thr	p.A637T	ENST00000377346	NM_005026.3	637	Gcc/Acc	15/24	1	2	FACETS	0.362	0.336	0.389	0.362	0.336	0.389	SUBCLONAL	1	TRUE	1	0.708774437451504	2		793	1825	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937220	36937220	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs563493972	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1113	527	737	1	ENST00000361632.4:c.1099C>T	p.Arg367Trp	p.R367W	ENST00000361632		367	Cgg/Tgg	9/16	1	2	FACETS	0.907	0.868	0.946	0.907	0.868	0.946	CLONAL	1	TRUE	1	0.708774437451504	2		738	1640	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812216	43812216	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1798	215	862	0	ENST00000372470.3:c.1081A>G	p.Ile361Val	p.I361V	ENST00000372470	NM_005373.2	361	Att/Gtt	7/12	1	2	FACETS	0.301	0.279	0.325	0.301	0.279	0.325	SUBCLONAL	1	TRUE	1	0.708774437451504	2		862	2013	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812531	43812531	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1337	359	664	1	ENST00000372470.3:c.1234C>T	p.His412Tyr	p.H412Y	ENST00000372470	NM_005373.2	412	Cac/Tac	8/12	1	2	FACETS	0.597	0.564	0.631	0.597	0.564	0.631	SUBCLONAL	1	TRUE	1	0.708774437451504	2		665	1696	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85733668	85733668	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	T	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	81	517	0	ENST00000370580.1:c.347-3T>A		p.X116_splice	ENST00000370580	NM_003921.4	116			1	2	FACETS	0.212	0.186	0.24	0.212	0.186	0.24	SUBCLONAL	1	TRUE	1	0.708774437451504	2		517	1077	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162729588	162729588	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs921329017	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	356	545	0	ENST00000367921.3:c.674T>C	p.Met225Thr	p.M225T	ENST00000367921	NM_006182.2	225	aTg/aCg	8/18	1	2	FACETS	0.855	0.81	0.9	0.855	0.81	0.9	CLONAL	1	TRUE	1	0.708774437451504	2		545	1175	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176153831	176153831	+	splice_region_variant,intron_variant	Splice_Region	DEL	A	A	-	rs760923753	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	125	417	2	ENST00000367669.3:c.408-3del		p.X136_splice	ENST00000367669	NM_022457.5	136			1	2	FACETS	0.46	0.417	0.506	0.46	0.417	0.506	SUBCLONAL	1	TRUE	1	0.708774437451504	2		419	766	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175799	176175799	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1115	272	586	0	ENST00000367669.3:c.316C>A	p.Leu106Ile	p.L106I	ENST00000367669	NM_022457.5	106	Cta/Ata	1/20	1	2	FACETS	0.553	0.518	0.59	0.553	0.518	0.59	SUBCLONAL	1	TRUE	1	0.708774437451504	2		586	1387	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193205393	193205393	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	210	480	0	ENST00000367435.3:c.1324G>A	p.Val442Ile	p.V442I	ENST00000367435	NM_024529.4	442	Gtt/Att	15/17	1	2	FACETS	0.509	0.472	0.548	0.509	0.472	0.548	SUBCLONAL	1	TRUE	1	0.708774437451504	2		480	1164	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206646659	206646659	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1652	88	743	0	ENST00000367120.3:c.87+2T>C		p.X29_splice	ENST00000367120	NM_014002.3	29			1	2	FACETS	0.143	0.125	0.161	0.143	0.125	0.161	SUBCLONAL	1	TRUE	1	0.708774437451504	2		743	1740	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609063	43609063	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	524	729	0	ENST00000355710.3:c.1819G>T	p.Gly607Cys	p.G607C	ENST00000355710	NM_020975.4	607	Ggc/Tgc	10/20	1	2	FACETS	0.924	0.885	0.964	0.924	0.885	0.964	CLONAL	1	TRUE	1	0.708774437451504	2		729	1600	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67197056	67197056	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1348	110	630	1	ENST00000312629.5:c.299T>A	p.Val100Asp	p.V100D	ENST00000312629	NM_003952.2	100	gTc/gAc	4/15	1	2	FACETS	0.213	0.19	0.237	0.213	0.19	0.237	SUBCLONAL	1	TRUE	1	0.708774437451504	2		631	1458	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	404743	404743	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1283571546	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1001	132	387	0	ENST00000399788.2:c.4451T>C	p.Met1484Thr	p.M1484T	ENST00000399788	NM_001042603.1	1484	aTg/aCg	26/28	1	2	FACETS	0.329	0.297	0.362	0.329	0.297	0.362	SUBCLONAL	1	TRUE	1	0.708774437451504	2		387	1133	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211671	46211671	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	281	378	0	ENST00000334344.6:c.637A>G	p.Thr213Ala	p.T213A	ENST00000334344	NM_152641.2	213	Act/Gct	5/21	1	2	FACETS	0.956	0.902	1	0.956	0.902	1	CLONAL	1	TRUE	1	0.708774437451504	2		378	829	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420661	49420661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1555185875	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1248	184	571	2	ENST00000301067.7:c.15088C>T	p.Arg5030Cys	p.R5030C	ENST00000301067	NM_003482.3	5030	Cgt/Tgt	48/54	1	2	FACETS	0.363	0.333	0.393	0.363	0.333	0.393	SUBCLONAL	1	TRUE	1	0.708774437451504	2		573	1432	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432462	49432462	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1710	128	821	0	ENST00000301067.7:c.8677A>G	p.Thr2893Ala	p.T2893A	ENST00000301067	NM_003482.3	2893	Act/Gct	34/54	1	2	FACETS	0.197	0.177	0.217	0.197	0.177	0.217	SUBCLONAL	1	TRUE	1	0.708774437451504	2		821	1838	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445526	49445526	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs770315135	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1325	388	695	3	ENST00000301067.7:c.1940del	p.Pro647HisfsTer283	p.P647Hfs*283	ENST00000301067	NM_003482.3	647	cCa/ca	10/54	1	2	FACETS	0.639	0.605	0.674	0.639	0.605	0.674	SUBCLONAL	1	TRUE	1	0.708774437451504	2		698	1713	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49448480	49448480	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1240	356	665	0	ENST00000301067.7:c.231del	p.His77GlnfsTer53	p.H77Qfs*53	ENST00000301067	NM_003482.3	77	caC/ca	3/54	1	2	FACETS	0.629	0.595	0.665	0.629	0.595	0.665	SUBCLONAL	1	TRUE	1	0.708774437451504	2		665	1596	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856322	111856323	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	46	131	0	ENST00000341259.2:c.377dup	p.Pro127AlafsTer45	p.P127Afs*45	ENST00000341259	NM_005475.2	125	gcc/gCcc	2/8	1	2	FACETS	0.475	0.403	0.554	0.475	0.403	0.554	SUBCLONAL	1	TRUE	1	0.708774437451504	2		131	273	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48937095	48937095	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	143	329	0	ENST00000267163.4:c.861+2T>C		p.X287_splice	ENST00000267163	NM_000321.2	287			1	2	FACETS	0.54	0.493	0.59	0.54	0.493	0.59	SUBCLONAL	1	TRUE	1	0.708774437451504	2		329	747	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281749	49281750	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1691	458	856	0	ENST00000282018.3:c.796_797del	p.Leu266GlufsTer19	p.L266Efs*19	ENST00000282018	NM_020377.2	266	CTg/g	1/1	1	2	FACETS	0.601	0.572	0.632	0.601	0.572	0.632	SUBCLONAL	1	TRUE	1	0.708774437451504	2		856	2149	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647657	3647657	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs774532876	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1876	429	1014	10	ENST00000294008.3:c.1406del	p.Pro469HisfsTer4	p.P469Hfs*4	ENST00000294008	NM_032444.2	469	cCa/ca	7/15	1	2	FACETS	0.525	0.498	0.553	0.525	0.498	0.553	SUBCLONAL	1	TRUE	1	0.708774437451504	2		1024	2305	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830517	72830517	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1527	120	661	0	ENST00000268489.5:c.6064T>C	p.Tyr2022His	p.Y2022H	ENST00000268489	NM_006885.3	2022	Tac/Cac	9/10	1	2	FACETS	0.206	0.184	0.228	0.206	0.184	0.228	SUBCLONAL	1	TRUE	1	0.708774437451504	2		661	1647	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351595	89351595	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1519	646	848	0	ENST00000301030.4:c.1355del	p.Asn452IlefsTer3	p.N452Ifs*3	ENST00000301030	NM_001256183.1	452	aAt/at	9/13	1	2	FACETS	0.842	0.809	0.875	0.842	0.809	0.875	CLONAL	1	TRUE	1	0.708774437451504	2		848	2165	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7574035	7574035	+	splice_acceptor_variant	Splice_Site	SNP	T	T	A	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1416	77	701	0	ENST00000269305.4:c.994-2A>T		p.X332_splice	ENST00000269305	NM_001126112.2	332			1	2	FACETS	0.146	0.127	0.166	0.146	0.127	0.166	SUBCLONAL	1	TRUE	1	0.708774437451504	2		701	1493	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974932	15974932	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769380838	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1104	236	559	0	ENST00000268712.3:c.3943C>T	p.Pro1315Ser	p.P1315S	ENST00000268712	NM_006311.3	1315	Ccc/Tcc	30/46	1	2	FACETS	0.497	0.463	0.533	0.497	0.463	0.533	SUBCLONAL	1	TRUE	1	0.708774437451504	2		559	1340	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682480	37682480	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1423552280	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	476	627	1	ENST00000447079.4:c.3671C>T	p.Ala1224Val	p.A1224V	ENST00000447079	NM_015083.1	1224	gCa/gTa	13/14	1	2	FACETS	0.93	0.888	0.971	0.93	0.888	0.971	CLONAL	1	TRUE	1	0.708774437451504	2		628	1445	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40865396	40865396	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1495	407	820	0	ENST00000428826.2:c.1035G>T	p.Lys345Asn	p.K345N	ENST00000428826		345	aaG/aaT	11/21	1	2	FACETS	0.604	0.572	0.636	0.604	0.572	0.636	SUBCLONAL	1	TRUE	1	0.708774437451504	2		820	1902	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78858829	78858829	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs769317295	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1259	346	698	1	ENST00000306801.3:c.1864G>A	p.Ala622Thr	p.A622T	ENST00000306801	NM_020761.2	622	Gcc/Acc	17/34	1	2	FACETS	0.608	0.574	0.643	0.608	0.574	0.643	SUBCLONAL	1	TRUE	1	0.708774437451504	2		699	1605	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45395764	45395764	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	450	533	0	ENST00000262160.6:c.370C>T	p.Pro124Ser	p.P124S	ENST00000262160	NM_005901.5	124	Cca/Tca	4/11	1	2	FACETS	0.942	0.899	0.985	0.942	0.899	0.985	CLONAL	1	TRUE	1	0.708774437451504	2		533	1348	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56367783	56367783	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs753744537	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1291	122	630	0	ENST00000348428.3:c.609G>A	p.Trp203Ter	p.W203*	ENST00000348428	NM_006785.3	203	tgG/tgA	4/17	1	2	FACETS	0.244	0.219	0.27	0.244	0.219	0.27	SUBCLONAL	1	TRUE	1	0.708774437451504	2		630	1413	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1226528	1226528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770011294	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1317	645	866	1	ENST00000326873.7:c.1184C>T	p.Thr395Ile	p.T395I	ENST00000326873	NM_000455.4	395	aCa/aTa	9/10	1	2	FACETS	0.928	0.892	0.964	0.928	0.892	0.964	CLONAL	1	TRUE	1	0.708774437451504	2		867	1962	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1622138	1622138	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs370087169	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1046	259	575	0	ENST00000344749.5:c.737C>A	p.Pro246Gln	p.P246Q	ENST00000344749	NM_001136139.2	246	cCg/cAg	10/19	1	2	FACETS	0.56	0.523	0.598	0.56	0.523	0.598	SUBCLONAL	1	TRUE	1	0.708774437451504	2		575	1305	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5244322	5244322	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1908	137	880	0	ENST00000357368.4:c.1160A>G	p.Tyr387Cys	p.Y387C	ENST00000357368	NM_002850.3	387	tAc/tGc	11/38	1	2	FACETS	0.189	0.171	0.208	0.189	0.171	0.208	SUBCLONAL	1	TRUE	1	0.708774437451504	2		880	2045	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602329	10602329	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1753	94	807	1	ENST00000171111.5:c.1249G>A	p.Gly417Arg	p.G417R	ENST00000171111	NM_203500.1	417	Ggg/Agg	3/6	1	2	FACETS	0.144	0.127	0.162	0.144	0.127	0.162	SUBCLONAL	1	TRUE	1	0.708774437451504	2		808	1847	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271583	15271583	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1535	806	1044	0	ENST00000263388.2:c.6856G>A	p.Ala2286Thr	p.A2286T	ENST00000263388	NM_000435.2	2286	Gca/Aca	33/33	1	2	FACETS	0.972	0.939	1	0.972	0.939	1	CLONAL	1	TRUE	1	0.708774437451504	2		1044	2341	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15276615	15276615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	515	651	2	ENST00000263388.2:c.5650G>A	p.Ala1884Thr	p.A1884T	ENST00000263388	NM_000435.2	1884	Gcc/Acc	30/33	1	2	FACETS	0.944	0.903	0.984	0.944	0.903	0.984	CLONAL	1	TRUE	1	0.708774437451504	2		653	1540	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216443	36216443	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1932	248	891	0	ENST00000222270.7:c.3706C>T	p.Pro1236Ser	p.P1236S	ENST00000222270	NM_014727.1	1236	Ccc/Tcc	12/37	1	2	FACETS	0.321	0.298	0.345	0.321	0.298	0.345	SUBCLONAL	1	TRUE	1	0.708774437451504	2		891	2180	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218414	36218414	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1393	115	650	0	ENST00000222270.7:c.4193A>G	p.Gln1398Arg	p.Q1398R	ENST00000222270	NM_014727.1	1398	cAg/cGg	16/37	1	2	FACETS	0.215	0.193	0.239	0.215	0.193	0.239	SUBCLONAL	1	TRUE	1	0.708774437451504	2		650	1508	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40739798	40739798	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766596535	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1526	399	842	1	ENST00000392038.2:c.1427C>T	p.Ser476Leu	p.S476L	ENST00000392038	NM_001626.4	476	tCg/tTg	14/14	1	2	FACETS	0.585	0.554	0.616	0.585	0.554	0.616	SUBCLONAL	1	TRUE	1	0.708774437451504	2		843	1925	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40741986	40741986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1382	355	808	0	ENST00000392038.2:c.986G>A	p.Arg329Gln	p.R329Q	ENST00000392038	NM_001626.4	329	cGg/cAg	11/14	1	2	FACETS	0.577	0.545	0.61	0.577	0.545	0.61	SUBCLONAL	1	TRUE	1	0.708774437451504	2		808	1737	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52724307	52724307	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	484	675	0	ENST00000322088.6:c.1439C>G	p.Ala480Gly	p.A480G	ENST00000322088	NM_014225.5	480	gCc/gGc	12/15	1	2	FACETS	0.904	0.864	0.945	0.904	0.864	0.945	CLONAL	1	TRUE	1	0.708774437451504	2		675	1510	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16086157	16086158	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1441	151	699	0	ENST00000281043.3:c.1338dup	p.Leu447IlefsTer13	p.L447Ifs*13	ENST00000281043	NM_005378.4	445	gaa/gAaa	3/3	1	2	FACETS	0.268	0.243	0.293	0.268	0.243	0.293	SUBCLONAL	1	TRUE	1	0.708774437451504	2		699	1592	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467088	25467088	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1293	287	686	0	ENST00000264709.3:c.1787G>T	p.Arg596Leu	p.R596L	ENST00000264709	NM_175629.2	596	cGg/cTg	15/23	1	2	FACETS	0.513	0.48	0.546	0.513	0.48	0.546	SUBCLONAL	1	TRUE	1	0.708774437451504	2		686	1580	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523088	25523088	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758534627	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1056	251	521	4	ENST00000264709.3:c.97C>T	p.Arg33Cys	p.R33C	ENST00000264709	NM_175629.2	33	Cgt/Tgt	3/23	1	2	FACETS	0.542	0.506	0.579	0.542	0.506	0.579	SUBCLONAL	1	TRUE	1	0.708774437451504	2		525	1307	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212248630	212248631	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	AA	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1139	108	554	0	ENST00000342788.4:c.3635_3636dup	p.Ala1213LeufsTer11	p.A1213Lfs*11	ENST00000342788	NM_005235.2	1212	-/TT	28/28	1	2	FACETS	0.244	0.218	0.272	0.244	0.218	0.272	SUBCLONAL	1	TRUE	1	0.708774437451504	2		554	1247	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212576842	212576842	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs921053875	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1032	120	666	0	ENST00000342788.4:c.1057A>G	p.Ile353Val	p.I353V	ENST00000342788	NM_005235.2	353	Att/Gtt	9/28	1	2	FACETS	0.294	0.264	0.325	0.294	0.264	0.325	SUBCLONAL	1	TRUE	1	0.708774437451504	2		666	1152	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31386409	31386409	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs572676072	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1430	190	706	0	ENST00000328111.2:c.1634G>A	p.Arg545His	p.R545H	ENST00000328111	NM_006892.3	545	cGc/cAc	15/23	1	2	FACETS	0.331	0.305	0.359	0.331	0.305	0.359	SUBCLONAL	1	TRUE	1	0.708774437451504	2		706	1620	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57485116	57485116	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1369025856	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	200	472	0	ENST00000371085.3:c.950G>A	p.Arg317His	p.R317H	ENST00000371085	NM_000516.4	317	cGc/cAc	11/13	1	2	FACETS	0.491	0.454	0.53	0.491	0.454	0.53	SUBCLONAL	1	TRUE	1	0.708774437451504	2		472	1149	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026106	71026106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs759521321	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	131	502	0	ENST00000318789.4:c.1516G>A	p.Ala506Thr	p.A506T	ENST00000318789	NM_032682.5	506	Gcg/Acg	17/21	1	2	FACETS	0.29	0.262	0.319	0.29	0.262	0.319	SUBCLONAL	1	TRUE	1	0.708774437451504	2		502	1276	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71090497	71090497	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	86	373	0	ENST00000318789.4:c.851A>G	p.His284Arg	p.H284R	ENST00000318789	NM_032682.5	284	cAc/cGc	11/21	1	2	FACETS	0.289	0.255	0.326	0.289	0.255	0.326	SUBCLONAL	1	TRUE	1	0.708774437451504	2		373	839	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1980581	1980581	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370127436	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1187	268	576	0	ENST00000382891.5:c.4043C>T	p.Pro1348Leu	p.P1348L	ENST00000382891	NM_133335.3	1348	cCg/cTg	22/22	1	2	FACETS	0.52	0.486	0.555	0.52	0.486	0.555	SUBCLONAL	1	TRUE	1	0.708774437451504	2		576	1455	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509119	66509119	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	168	712	0	ENST00000273854.3:c.208A>G	p.Met70Val	p.M70V	ENST00000273854	NM_004439.5	70	Atg/Gtg	2/18	1	2	FACETS	0.486	0.446	0.528	0.486	0.446	0.528	SUBCLONAL	1	TRUE	1	0.708774437451504	2		712	975	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143081558	143081558	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	409	574	1	ENST00000262992.4:c.1516G>T	p.Gly506Trp	p.G506W	ENST00000262992	NM_001101669.1	506	Ggg/Tgg	15/24	1	2	FACETS	0.995	0.948	1	0.995	0.948	1	CLONAL	1	TRUE	1	0.708774437451504	2		575	1160	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187510170	187510170	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1303	98	512	0	ENST00000441802.2:c.13343T>C	p.Leu4448Pro	p.L4448P	ENST00000441802	NM_005245.3	4448	cTa/cCa	27/27	1	2	FACETS	0.197	0.175	0.221	0.197	0.175	0.221	SUBCLONAL	1	TRUE	1	0.708774437451504	2		512	1401	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187518869	187518869	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs759213300	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1520	410	833	0	ENST00000441802.2:c.12335T>C	p.Val4112Ala	p.V4112A	ENST00000441802	NM_005245.3	4112	gTt/gCt	24/27	1	2	FACETS	0.599	0.568	0.631	0.599	0.568	0.631	SUBCLONAL	1	TRUE	1	0.708774437451504	2		833	1930	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187628739	187628739	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1966	107	866	0	ENST00000441802.2:c.2243T>C	p.Phe748Ser	p.F748S	ENST00000441802	NM_005245.3	748	tTc/tCc	2/27	1	2	FACETS	0.146	0.13	0.163	0.146	0.13	0.163	SUBCLONAL	1	TRUE	1	0.708774437451504	2		866	2073	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295233	1295233	+	upstream_gene_variant	5'Flank	SNP	C	C	T	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	211	420	1				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.646	0.6	0.693	0.646	0.6	0.693	SUBCLONAL	1	TRUE	1	0.708774437451504	2		421	922	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67591289	67591289	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	211	517	0	ENST00000274335.5:c.1787A>G	p.Glu596Gly	p.E596G	ENST00000274335		596	gAg/gGg	13/15	1	2	FACETS	0.504	0.467	0.542	0.504	0.467	0.542	SUBCLONAL	1	TRUE	1	0.708774437451504	2		517	1181	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131930737	131930737	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs587782078	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	323	435	0	ENST00000265335.6:c.1969+1G>A		p.X657_splice	ENST00000265335		657			1	2	FACETS	0.971	0.919	1	0.971	0.919	1	CLONAL	1	TRUE	1	0.708774437451504	2		435	939	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524398	176524398	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1301	163	602	0	ENST00000292408.4:c.2259G>T	p.Glu753Asp	p.E753D	ENST00000292408	NM_213647.1	753	gaG/gaT	17/18	1	2	FACETS	0.314	0.287	0.343	0.314	0.287	0.343	SUBCLONAL	1	TRUE	1	0.708774437451504	2		602	1464	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180046076	180046076	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	854	234	514	0	ENST00000261937.6:c.2795A>G	p.Tyr932Cys	p.Y932C	ENST00000261937	NM_182925.4	932	tAc/tGc	20/30	1	2	FACETS	0.607	0.566	0.649	0.607	0.566	0.649	SUBCLONAL	1	TRUE	1	0.708774437451504	2		514	1088	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324917	31324917	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	131	373	0	ENST00000412585.2:c.19del	p.Arg7GlufsTer13	p.R7Efs*13	ENST00000412585	NM_005514.6	7	Cga/ga	1/8	1	2	FACETS	0.397	0.36	0.437	0.397	0.36	0.437	SUBCLONAL	1	TRUE	1	0.708774437451504	2		373	930	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32163217	32163217	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1250	655	907	1	ENST00000375023.3:c.6009del	p.Lys2003AsnfsTer13	p.K2003Nfs*13	ENST00000375023	NM_004557.3	2003	aaA/aa	30/30	1	2	FACETS	0.97	0.934	1	0.97	0.934	1	CLONAL	1	TRUE	1	0.708774437451504	2		908	1905	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32164180	32164180	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	131	409	0	ENST00000375023.3:c.5219G>T	p.Trp1740Leu	p.W1740L	ENST00000375023	NM_004557.3	1740	tGg/tTg	29/30	1	2	FACETS	0.377	0.342	0.415	0.377	0.342	0.415	SUBCLONAL	1	TRUE	1	0.708774437451504	2		409	980	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797187	32797187	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1562324327	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1409	181	634	2	ENST00000374899.4:c.1922G>A	p.Cys641Tyr	p.C641Y	ENST00000374899	NM_018833.2	641	tGc/tAc	11/12	1	2	FACETS	0.321	0.295	0.349	0.321	0.295	0.349	SUBCLONAL	1	TRUE	1	0.708774437451504	2		636	1590	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	162683604	162683604	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1041	216	515	0	ENST00000366898.1:c.365T>G	p.Ile122Ser	p.I122S	ENST00000366898	NM_004562.2	122	aTt/aGt	3/12	1	2	FACETS	0.485	0.45	0.521	0.485	0.45	0.521	SUBCLONAL	1	TRUE	1	0.708774437451504	2		515	1257	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2958141	2958141	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1430102723	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1290	256	692	1	ENST00000396946.4:c.2591C>T	p.Thr864Ile	p.T864I	ENST00000396946	NM_032415.4	864	aCc/aTc	19/25	1	2	FACETS	0.467	0.436	0.5	0.467	0.436	0.5	SUBCLONAL	1	TRUE	1	0.708774437451504	2		693	1546	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2977669	2977669	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1337	288	693	2	ENST00000396946.4:c.1018-3C>T		p.X340_splice	ENST00000396946	NM_032415.4	340			1	2	FACETS	0.5	0.469	0.533	0.5	0.469	0.533	SUBCLONAL	1	TRUE	1	0.708774437451504	2		695	1625	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979478	2979478	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1758	150	766	0	ENST00000396946.4:c.769A>G	p.Ile257Val	p.I257V	ENST00000396946	NM_032415.4	257	Att/Gtt	6/25	1	2	FACETS	0.222	0.201	0.243	0.222	0.201	0.243	SUBCLONAL	1	TRUE	1	0.708774437451504	2		766	1908	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6042145	6042145	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	149	450	0	ENST00000265849.7:c.476T>C	p.Val159Ala	p.V159A	ENST00000265849	NM_000535.5	159	gTg/gCg	5/15	1	2	FACETS	0.362	0.33	0.396	0.362	0.33	0.396	SUBCLONAL	1	TRUE	1	0.708774437451504	2		450	1162	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70980471	70980471	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1547	341	833	3	ENST00000276594.2:c.906G>A	p.Met302Ile	p.M302I	ENST00000276594	NM_024504.3	302	atG/atA	4/8	1	2	FACETS	0.51	0.48	0.54	0.51	0.48	0.54	SUBCLONAL	1	TRUE	1	0.708774437451504	2		836	1888	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069193	5069193	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	391	745	0	ENST00000381652.3:c.1502del	p.Pro501GlnfsTer10	p.P501Qfs*10	ENST00000381652	NM_004972.3	500	Ccc/cc	11/25	1	2	FACETS	0.823	0.782	0.866	0.823	0.782	0.866	CLONAL	1	TRUE	1	0.708774437451504	2		745	1340	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971039	21971039	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554654024	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	446	481	1	ENST00000304494.5:c.319C>T	p.Arg107Cys	p.R107C	ENST00000304494	NM_000077.4	107	Cgc/Tgc	2/3	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.708774437451504	2		482	1240	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563419	87563419	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1327	352	747	0	ENST00000277120.3:c.1807C>T	p.Arg603Cys	p.R603C	ENST00000277120		603	Cgt/Tgt	16/19	1	2	FACETS	0.592	0.559	0.626	0.592	0.559	0.626	SUBCLONAL	1	TRUE	1	0.708774437451504	2		747	1679	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93626948	93626948	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1238	267	673	2	ENST00000375746.1:c.795G>T	p.Gln265His	p.Q265H	ENST00000375746	NM_001174167.1	265	caG/caT	5/14	1	2	FACETS	0.501	0.468	0.534	0.501	0.468	0.534	SUBCLONAL	1	TRUE	1	0.708774437451504	2		675	1505	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293634	137293634	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564527735	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1468	682	949	2	ENST00000481739.1:c.185G>A	p.Gly62Asp	p.G62D	ENST00000481739	NM_002957.4	62	gGc/gAc	2/10	1	2	FACETS	0.895	0.861	0.929	0.895	0.861	0.929	CLONAL	1	TRUE	1	0.708774437451504	2		951	2150	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802649	139802649	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1123	84	511	0	ENST00000247668.2:c.494A>G	p.His165Arg	p.H165R	ENST00000247668	NM_021138.3	165	cAt/cGt	5/11	1	2	FACETS	0.196	0.172	0.222	0.196	0.172	0.222	SUBCLONAL	1	TRUE	1	0.708774437451504	2		511	1207	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39923680	39923681	+	frameshift_variant	Frame_Shift_Del	DEL	TT	TT	-	rs1555915763	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1438	179	648	0	ENST00000378444.4:c.3410_3411del	p.Lys1137SerfsTer4	p.K1137Sfs*4	ENST00000378444	NM_001123385.1	1137	aAA/a	7/15	1	2	FACETS	0.312	0.287	0.339	0.312	0.287	0.339	SUBCLONAL	1	TRUE	1	0.708774437451504	2		648	1617	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652554	48652554	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	326	434	0	ENST00000376670.3:c.1225G>A	p.Ala409Thr	p.A409T	ENST00000376670	NM_002049.3	409	Gct/Act	6/6	1	2	FACETS	0.921	0.872	0.971	0.921	0.872	0.971	CLONAL	1	TRUE	1	0.708774437451504	2		434	999	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53225186	53225186	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1403	301	806	0	ENST00000375401.3:c.3032del	p.Asn1011ThrfsTer44	p.N1011Tfs*44	ENST00000375401	NM_004187.3	1011	aAc/ac	20/26	1	2	FACETS	0.498	0.468	0.53	0.498	0.468	0.53	SUBCLONAL	1	TRUE	1	0.708774437451504	2		806	1704	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70339584	70339584	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1675	140	825	0	ENST00000374080.3:c.253A>G	p.Thr85Ala	p.T85A	ENST00000374080		85	Acc/Gcc	3/45	1	2	FACETS	0.218	0.197	0.24	0.218	0.197	0.24	SUBCLONAL	1	TRUE	1	0.708774437451504	2		825	1815	SUCCESS
BTK	695	MSKCC	GRCh37	X	100608978	100608978	+	splice_acceptor_variant	Splice_Site	SNP	T	T	C	rs886039555	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1283	96	588	0	ENST00000308731.7:c.1632-2A>G		p.X544_splice	ENST00000308731	NM_000061.2	544			1	2	FACETS	0.196	0.174	0.221	0.196	0.174	0.221	SUBCLONAL	1	TRUE	1	0.708774437451504	2		588	1379	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089628	27089633	+	frameshift_variant	Frame_Shift_Ins	INS	TCCATG	TCCATG	GGCCTTATGA	novel	NA	P-0016314-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1354	333	664	0	ENST00000324856.7:c.2584_2589delinsGGCCTTATGA	p.Ser862GlyfsTer11	p.S862Gfs*11	ENST00000324856	NM_006015.4	862	TCCATG/GGCCTTATGA	8/20	1	2	FACETS	0.557	0.525	0.59	0.557	0.525	0.59	SUBCLONAL	1	TRUE	1	0.708774437451504	2		664	1687	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0016347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	37	282	0				ENST00000310581	NM_198253.2	-/1132			0.265782404453179	0	FACETS	0.807	0.672	0.956			1	CLONAL	1	TRUE	0	0.31	0		282	204	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31940123	31940123	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267600971	NA	P-0016347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	88	705	0	ENST00000375333.2:c.265G>A	p.Asp89Asn	p.D89N	ENST00000375333	NM_032454.1	89	Gac/Aac	2/8	0.123233361153376	4	FACETS	1	0.976	1	0.698	0.62	0.781	INDETERMINATE	1	TRUE	2	0.31	4		705	533	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81381466	81381466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	79	431	1	ENST00000222390.5:c.595G>A	p.Glu199Lys	p.E199K	ENST00000222390	NM_000601.4	199	Gaa/Aaa	5/18	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.31	2		432	439	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31944812	31944812	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866971809	NA	P-0016347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	67	668	0	ENST00000340398.3:c.289G>A	p.Glu97Lys	p.E97K	ENST00000340398	NM_001013699.2	97	Gaa/Aaa	1/1	0.187414149707402	2	FACETS	0.982	0.857	1	0.491	0.428	0.559	CLONAL	1	TRUE	0	0.31	2		668	440	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89345484	89345484	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	142	26	307	0	ENST00000301030.4:c.7466C>T	p.Pro2489Leu	p.P2489L	ENST00000301030	NM_001256183.1	2489	cCc/cTc	9/13	0.300931770625407	1	FACETS	0.844	0.675	1	0.844	0.675	1	CLONAL	1	TRUE	0	0.31	1		307	168	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974684	21974684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	265	58	525	0	ENST00000304494.5:c.143C>T	p.Pro48Leu	p.P48L	ENST00000304494	NM_000077.4	48	cCg/cTg	1/3	0.300931770625407	1	FACETS	0.979	0.846	1	0.979	0.846	1	CLONAL	1	TRUE	0	0.31	1		525	323	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923482	9923482	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	50	703	0	ENST00000330684.3:c.1805G>A	p.Gly602Glu	p.G602E	ENST00000330684	NM_001134407.1	602	gGa/gAa	9/13	0.147938722040421	1	FACETS	0.714	0.607	0.83	0.714	0.607	0.83	INDETERMINATE	1	TRUE	0	0.31	1		703	382	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68956771	68956771	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774302685	NA	P-0016347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	506	74	644	2	ENST00000288368.4:c.889C>T	p.Arg297Cys	p.R297C	ENST00000288368	NM_024870.2	297	Cgt/Tgt	8/40	1	2	FACETS	0.823	0.721	0.933	0.823	0.721	0.933	CLONAL	1	TRUE	1	0.31	2		646	580	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2154240	2154241	+	missense_variant	Missense_Mutation	DNP	CT	CT	TA	novel	NA	P-0016347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	197	29	663	1	ENST00000434045.2:c.687_688delinsTA	p.Glu230Lys	p.E230K	ENST00000434045	NM_001127598.1	229	ccAGag/ccTAag	5/5	0.300931770625407	1	FACETS	0.7	0.565	0.851	0.7	0.565	0.851	SUBCLONAL	1	TRUE	0	0.31	1		664	226	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67200234	67200234	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	65	711	0	ENST00000312629.5:c.542C>T	p.Ala181Val	p.A181V	ENST00000312629	NM_003952.2	181	gCc/gTc	7/15	0.300931770625407	1	FACETS	0.866	0.754	0.987	0.866	0.754	0.987	CLONAL	1	TRUE	0	0.31	1		711	409	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29012477	29012477	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	35	536	0	ENST00000282397.4:c.394G>A	p.Gly132Ser	p.G132S	ENST00000282397	NM_002019.4	132	Ggt/Agt	4/30	0.103709642208988	0	FACETS	0.421	0.345	0.506			1	INDETERMINATE	1	TRUE	0	0.31	0		536	370	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32972298	32972298	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0016347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	48	476	0	ENST00000380152.3:c.9649-1G>A		p.X3217_splice	ENST00000380152		3217			NA	2	FACETS	0.69	0.584	0.806			1	INDETERMINATE	1	TRUE	NA	0.31	2		476	449	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670460	88670460	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	novel	NA	P-0016347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	214	59	427	0	ENST00000360948.2:c.1229-3C>T		p.X410_splice	ENST00000360948	NM_001012338.2	410			0.235347350709002	0	FACETS	0.962	0.835	1			1	CLONAL	1	TRUE	0	0.31	0		427	273	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221243	1221243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	79	804	3	ENST00000326873.7:c.766G>A	p.Glu256Lys	p.E256K	ENST00000326873	NM_000455.4	256	Gaa/Aaa	6/10	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.31	2		807	491	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19257911	19257911	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	59	840	1	ENST00000162023.5:c.475G>A	p.Glu159Lys	p.E159K	ENST00000162023		159	Gaa/Aaa	9/13	0.147938722040421	1	FACETS	0.8	0.691	0.918	0.8	0.691	0.918	INDETERMINATE	1	TRUE	0	0.31	1		841	402	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525066	9525066	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	41	753	0	ENST00000353224.5:c.1819C>T	p.Pro607Ser	p.P607S	ENST00000353224	NM_177990.2	607	Ccc/Tcc	8/10	1	2	FACETS	0.57	0.475	0.676	0.57	0.475	0.676	SUBCLONAL	1	TRUE	1	0.31	2		753	464	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31368259	31368260	+	missense_variant	Missense_Mutation	DNP	CC	CC	AT	novel	NA	P-0016347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	34	564	0	ENST00000328111.2:c.130_131delinsAT	p.Pro44Met	p.P44M	ENST00000328111	NM_006892.3	44	CCg/ATg	2/23	1	2	FACETS	0.715	0.586	0.859	0.715	0.586	0.859	SUBCLONAL	1	TRUE	1	0.31	2		564	307	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41306547	41306547	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	61	569	0	ENST00000373198.4:c.1112G>A	p.Gly371Glu	p.G371E	ENST00000373198	NM_133170.3	371	gGa/gAa	7/32	0.235347350709002	0	FACETS	0.707	0.613	0.809			1	SUBCLONAL	1	TRUE	0	0.31	0		569	384	SUCCESS
TMPRSS2	7113	MSKCC	GRCh37	21	42852428	42852428	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	52	629	0	ENST00000398585.3:c.658G>T	p.Ala220Ser	p.A220S	ENST00000398585	NM_001135099.1	220	Gcg/Tcg	6/14	1	2	FACETS	0.751	0.64	0.871	0.751	0.64	0.871	SUBCLONAL	1	TRUE	1	0.31	2		629	447	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12627284	12627284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	70	601	0	ENST00000251849.4:c.1432G>A	p.Glu478Lys	p.E478K	ENST00000251849	NM_002880.3	478	Gaa/Aaa	14/17	1	2	FACETS	0.99	0.866	1	0.99	0.866	1	CLONAL	1	TRUE	1	0.31	2		601	456	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437181	52437182	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0016347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	49	652	1	ENST00000460680.1:c.1862_1863delinsTT	p.Pro621Leu	p.P621L	ENST00000460680	NM_004656.3	621	cCC/cTT	14/17	1	2	FACETS	0.737	0.625	0.859	0.737	0.625	0.859	SUBCLONAL	1	TRUE	1	0.31	2		653	429	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72427591	72427591	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	217	49	272	0	ENST00000477973.2:c.899C>A	p.Ser300Tyr	p.S300Y	ENST00000477973	NM_012234.5	300	tCc/tAc	4/4	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.31	2		272	266	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259099	89259099	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	69	477	0	ENST00000336596.2:c.243G>C	p.Trp81Cys	p.W81C	ENST00000336596	NM_005233.5	81	tgG/tgC	3/17	1	2	FACETS	0.996	0.87	1	0.996	0.87	1	CLONAL	1	TRUE	1	0.31	2		477	447	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156585	55156585	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779173667	NA	P-0016347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	63	641	0	ENST00000257290.5:c.2986G>A	p.Glu996Lys	p.E996K	ENST00000257290	NM_006206.4	996	Gag/Aag	22/23	1	2	FACETS	0.934	0.811	1	0.934	0.811	1	CLONAL	1	TRUE	1	0.31	2		641	435	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31515277	31515277	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	95	752	0	ENST00000344624.3:c.1108G>A	p.Asp370Asn	p.D370N	ENST00000344624		370	Gac/Aac	5/33	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.31	2		752	568	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170814963	170814963	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1363897984	NA	P-0016347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	26	179	0	ENST00000296930.5:c.11C>T	p.Ser4Leu	p.S4L	ENST00000296930	NM_002520.6	4	tCg/tTg	1/11	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.31	2		179	139	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81350155	81350155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758567520	NA	P-0016347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	61	490	1	ENST00000222390.5:c.1177C>T	p.Arg393Cys	p.R393C	ENST00000222390	NM_000601.4	393	Cgt/Tgt	10/18	1	2	FACETS	0.797	0.688	0.914	0.797	0.688	0.914	CLONAL	1	TRUE	1	0.31	2		491	494	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339236	116339236	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	92	516	1	ENST00000397752.3:c.98C>T	p.Ser33Phe	p.S33F	ENST00000397752	NM_000245.2	33	tCc/tTc	2/21	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.31	2		517	518	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417462	139417463	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0016347-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	56	878	1	ENST00000277541.6:c.581_582delinsTT	p.Thr194Ile	p.T194I	ENST00000277541	NM_017617.3	194	aCC/aTT	4/34	0.147938722040421	1	FACETS	0.783	0.673	0.902	0.783	0.673	0.902	INDETERMINATE	1	TRUE	0	0.31	1		879	390	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	40	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.638	0.529	0.759	0.638	0.529	0.759	SUBCLONAL	1	TRUE	1	0.238905599460325	2		215	525	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0016351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	52	380	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	1	2	FACETS	0.924	0.788	1	0.924	0.788	1	CLONAL	1	TRUE	1	0.238905599460325	2		380	471	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0016351-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1228	54	633	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	0.353	0.3	0.411	0.353	0.3	0.411	SUBCLONAL	1	TRUE	1	0.238905599460325	2		633	1282	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	884	282	215	0				ENST00000310581	NM_198253.2	-/1132			0.532929644115871	6	FACETS	0.938	0.881	0.996	0.469	0.44	0.498	CLONAL	2	TRUE	2	0.532929644115871	6		215	1166	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577509	7577509	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912652	NA	P-0016356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	388	428	823	0	ENST00000269305.4:c.772G>A	p.Glu258Lys	p.E258K	ENST00000269305	NM_001126112.2	258	Gaa/Aaa	7/11	0.532929644115871	2	FACETS	0.984	0.945	1	0.984	0.945	1	CLONAL	2	TRUE	0	0.532929644115871	2		823	816	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026813	48026813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs864622153	NA	P-0016356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	438	527	0	ENST00000234420.5:c.1691C>T	p.Ser564Leu	p.S564L	ENST00000234420	NM_000179.2	564	tCa/tTa	4/10	0.532929644115871	3	FACETS	1	0.975	1	1	0.975	1	CLONAL	2	TRUE	1	0.532929644115871	3		527	1015	SUCCESS
MST1	4485	MSKCC	GRCh37	3	49722761	49722761	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs62262682	NA	P-0016356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	17	12	34	0	ENST00000449682.2:c.1478G>T	p.Arg493Leu	p.R493L	ENST00000449682	NM_020998.3	493	cGt/cTt	13/18	0.532929644115871	2	FACETS	0.776	0.581	0.982	0.776	0.581	0.982	CLONAL	2	TRUE	0	0.532929644115871	2		34	29	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18496258	18496258	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0016356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	493	489	1	ENST00000266497.5:c.1396-3C>T		p.X466_splice	ENST00000266497		466			0.525393710205479	3	FACETS	0.93	0.897	0.962	0.93	0.897	0.962	CLONAL	3	TRUE	0	0.532929644115871	3		490	840	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17946822	17946822	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	212	728	0	ENST00000458235.1:c.1825G>A	p.Asp609Asn	p.D609N	ENST00000458235	NM_000215.3	609	Gac/Aac	14/24	1	2	FACETS	0.837	0.778	0.899	0.837	0.778	0.899	CLONAL	1	TRUE	1	0.532929644115871	2		728	950	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57466824	57466824	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	179	432	0	ENST00000371085.3:c.43G>A	p.Glu15Lys	p.E15K	ENST00000371085	NM_000516.4	15	Gag/Aag	1/13	0.526726139423651	3	FACETS	0.982	0.906	1			1	CLONAL	1	TRUE	NA	0.532929644115871	3		432	866	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70005680	70005680	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	415	584	0	ENST00000394351.3:c.709C>T	p.Pro237Ser	p.P237S	ENST00000394351	NM_000248.3	237	Cca/Tca	7/9	0.532929644115871	2	FACETS	0.924	0.885	0.962	0.924	0.885	0.962	CLONAL	2	TRUE	0	0.532929644115871	2		584	843	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178928013	178928013	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	914	363	562	1	ENST00000263967.3:c.1291G>A	p.Asp431Asn	p.D431N	ENST00000263967	NM_006218.2	431	Gat/Aat	8/21	0.512438416636981	5	FACETS	0.96	0.91	1	0.64	0.606	0.674	CLONAL	2	TRUE	2	0.532929644115871	5		563	1277	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128851900	128851900	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016356-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	949	466	784	0	ENST00000249373.3:c.1972G>A	p.Glu658Lys	p.E658K	ENST00000249373	NM_005631.4	658	Gag/Aag	12/12	0.522836949932548	4	FACETS	0.947	0.905	0.99	0.947	0.905	0.99	CLONAL	2	TRUE	2	0.532929644115871	4		784	1415	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1389	205	519	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	0.944	0.873	1	0.944	0.873	1	CLONAL	1	TRUE	1	0.272376159531599	2		524	1594	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27105931	27105931	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	129	530	7	ENST00000324856.7:c.5548del	p.Asp1850ThrfsTer33	p.D1850Tfs*33	ENST00000324856	NM_006015.4	1848	Ggg/gg	20/20	0.272376159531599	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.272376159531599	1		537	777	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	281	736	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.979	1	1	0.996	1	CLONAL	2	TRUE	1	0.272376159531599	2		741	954	SUCCESS
COP1	64326	MSKCC	GRCh37	1	176175760	176175760	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1368	307	735	0	ENST00000367669.3:c.355del	p.Leu119SerfsTer24	p.L119Sfs*24	ENST00000367669	NM_022457.5	119	Ctc/tc	1/20	0.244061699149694	3	FACETS	0.765	0.718	0.812	0.765	0.718	0.812	SUBCLONAL	2	TRUE	1	0.272376159531599	3		735	1675	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201983151	201983151	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1166	181	626	0	ENST00000359651.3:c.1000A>G	p.Arg334Gly	p.R334G	ENST00000359651		334	Agg/Ggg	7/8	0.244061699149694	3	FACETS	1	0.972	1	0.561	0.515	0.608	CLONAL	1	TRUE	1	0.272376159531599	3		626	1347	SUCCESS
RPS6KB2	6199	MSKCC	GRCh37	11	67202488	67202488	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1396	207	824	0	ENST00000312629.5:c.1297T>C	p.Phe433Leu	p.F433L	ENST00000312629	NM_003952.2	433	Ttt/Ctt	15/15	1	2	FACETS	0.948	0.877	1	0.948	0.877	1	CLONAL	1	TRUE	1	0.272376159531599	2		824	1603	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118361928	118361929	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	30	194	1	ENST00000534358.1:c.4716_4717del	p.Cys1572Ter	p.C1572*	ENST00000534358	NM_005933.3	1572	TGt/t	14/36	1	2	FACETS	0.456	0.367	0.558	0.456	0.367	0.558	SUBCLONAL	1	TRUE	1	0.272376159531599	2		195	483	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022436	12022436	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150089916	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1845	223	955	1	ENST00000396373.4:c.542G>A	p.Arg181His	p.R181H	ENST00000396373	NM_001987.4	181	cGc/cAc	5/8	0.158468221479051	2	FACETS	0.792	0.734	0.853	0.396	0.367	0.427	INDETERMINATE	1	TRUE	0	0.272376159531599	2		956	2068	SUCCESS
H3-5	440093	MSKCC	GRCh37	12	31945049	31945049	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs754427138	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1207	116	598	3	ENST00000340398.3:c.52del	p.Arg18AlafsTer19	p.R18Afs*19	ENST00000340398	NM_001013699.2	18	Cgc/gc	1/1	0.248250091669642	3	FACETS	0.731	0.657	0.811	0.366	0.328	0.406	SUBCLONAL	1	TRUE	1	0.272376159531599	3		601	1323	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433060	49433060	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1251778848	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1163	321	691	2	ENST00000301067.7:c.8311C>T	p.Arg2771Ter	p.R2771*	ENST00000301067	NM_003482.3	2771	Cga/Tga	33/54	0.248250091669642	3	FACETS	0.902	0.85	0.956	0.902	0.85	0.956	CLONAL	2	TRUE	1	0.272376159531599	3		693	1484	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49449095	49449095	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	158	613	0	ENST00000301067.7:c.13A>G	p.Lys5Glu	p.K5E	ENST00000301067	NM_003482.3	5	Aag/Gag	1/54	0.248250091669642	3	FACETS	0.971	0.888	1	0.486	0.444	0.53	CLONAL	1	TRUE	1	0.272376159531599	3		613	1357	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609934	81609934	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369995834	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	102	257	0	ENST00000298171.2:c.1532C>T	p.Thr511Met	p.T511M	ENST00000298171	NM_000369.2	511	aCg/aTg	10/10	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.272376159531599	2		257	575	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748660	43748661	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1498	231	908	1	ENST00000382044.4:c.2145dup	p.Glu716ArgfsTer9	p.E716Rfs*9	ENST00000382044	NM_001141980.1	715	-/A	12/28	1	2	FACETS	0.981	0.911	1	0.981	0.911	1	CLONAL	1	TRUE	1	0.272376159531599	2		909	1729	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89357226	89357228	+	inframe_deletion	In_Frame_Del	DEL	TGT	TGT	-	novel	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	112	430	0	ENST00000301030.4:c.406_408del	p.Thr136del	p.T136del	ENST00000301030	NM_001256183.1	136	ACA/-	6/13	1	2	FACETS	0.876	0.787	0.97	0.876	0.787	0.97	CLONAL	1	TRUE	1	0.272376159531599	2		430	939	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15983322	15983322	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	152	500	0	ENST00000268712.3:c.3457del	p.Ile1153PhefsTer31	p.I1153Ffs*31	ENST00000268712	NM_006311.3	1153	Att/tt	26/46	1	2	FACETS	0.949	0.866	1	0.949	0.866	1	CLONAL	1	TRUE	1	0.272376159531599	2		500	1176	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29490318	29490318	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775191883	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	155	576	0	ENST00000356175.3:c.403C>T	p.Arg135Trp	p.R135W	ENST00000356175	NM_000267.3	135	Cgg/Tgg	4/57	1	2	FACETS	0.931	0.851	1	0.931	0.851	1	CLONAL	1	TRUE	1	0.272376159531599	2		576	1222	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37879658	37879658	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519862	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1027	187	683	2	ENST00000269571.5:c.2033G>A	p.Arg678Gln	p.R678Q	ENST00000269571		678	cGg/cAg	17/27	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.272376159531599	2		685	1214	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47677790	47677790	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762651623	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	166	532	2	ENST00000347630.2:c.1075G>A	p.Ala359Thr	p.A359T	ENST00000347630	NM_001007230.1	359	Gca/Aca	11/11	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.272376159531599	2		534	1066	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78796918	78796918	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1033	142	514	2	ENST00000306801.3:c.1031C>T	p.Ala344Val	p.A344V	ENST00000306801	NM_020761.2	344	gCt/gTt	9/34	1	2	FACETS	0.887	0.807	0.972	0.887	0.807	0.972	CLONAL	1	TRUE	1	0.272376159531599	2		516	1175	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2217851	2217851	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1298	242	733	2	ENST00000398665.3:c.2625G>T	p.Gln875His	p.Q875H	ENST00000398665	NM_032482.2	875	caG/caT	22/28	1	2	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	1	0.272376159531599	2		735	1540	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3121083	3121083	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1298964952	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1367	242	779	8	ENST00000078429.4:c.986C>T	p.Thr329Met	p.T329M	ENST00000078429	NM_002067.2	329	aCg/aTg	7/7	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.272376159531599	2		787	1609	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7117224	7117224	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1370871210	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1274	185	720	0	ENST00000302850.5:c.3992G>A	p.Arg1331His	p.R1331H	ENST00000302850	NM_000208.2	1331	cGt/cAt	22/22	1	2	FACETS	0.931	0.857	1	0.931	0.857	1	CLONAL	1	TRUE	1	0.272376159531599	2		720	1459	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284985	15284985	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1025	234	627	5	ENST00000263388.2:c.4630C>T	p.Arg1544Cys	p.R1544C	ENST00000263388	NM_000435.2	1544	Cgc/Tgc	25/33	1	2	FACETS	1	0.99	1	1	0.99	1	CLONAL	1	TRUE	1	0.272376159531599	2		632	1259	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260066	19260067	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1147	201	628	1	ENST00000162023.5:c.226dup	p.His76ProfsTer8	p.H76Pfs*8	ENST00000162023		76	cac/cCac	7/13	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.272376159531599	2		629	1348	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1622	186	1190	1	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.755	0.695	0.819	0.755	0.695	0.819	SUBCLONAL	1	TRUE	1	0.272376159531599	2		1191	1808	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45867291	45867291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199863965	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1037	199	593	4	ENST00000391945.4:c.902C>T	p.Thr301Met	p.T301M	ENST00000391945	NM_000400.3	301	aCg/aTg	10/23	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.272376159531599	2		597	1236	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140309	50140309	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755565332	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	159	465	1	ENST00000246792.3:c.232C>T	p.Arg78Trp	p.R78W	ENST00000246792	NM_006270.3	78	Cgg/Tgg	2/6	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.272376159531599	2		466	990	SUCCESS
REL	5966	MSKCC	GRCh37	2	61145637	61145637	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	212	575	1	ENST00000295025.8:c.749G>A	p.Cys250Tyr	p.C250Y	ENST00000295025	NM_002908.2	250	tGc/tAc	7/11	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.272376159531599	2		576	1357	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212578261	212578261	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1055	147	598	0	ENST00000342788.4:c.996del	p.Ala333LeufsTer10	p.A333Lfs*10	ENST00000342788	NM_005235.2	332	aaA/aa	8/28	1	2	FACETS	0.898	0.818	0.982	0.898	0.818	0.982	CLONAL	1	TRUE	1	0.272376159531599	2		598	1202	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39750746	39750746	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1042	304	558	0	ENST00000361337.2:c.2146C>A	p.Leu716Met	p.L716M	ENST00000361337	NM_003286.2	716	Ctg/Atg	20/21	0.244061699149694	3	FACETS	0.942	0.886	0.999	0.942	0.886	0.999	CLONAL	2	TRUE	1	0.272376159531599	3		558	1346	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30713457	30713457	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	161	455	0	ENST00000295754.5:c.782C>A	p.Ala261Asp	p.A261D	ENST00000295754	NM_003242.5	261	gCc/gAc	4/7	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.272376159531599	2		455	1116	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52620438	52620438	+	splice_region_variant,intron_variant	Splice_Region	SNP	T	T	A	novel	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	128	453	0	ENST00000394830.3:c.3312+3A>T		p.X1104_splice	ENST00000394830	NM_018313.4	1104			0.272376159531599	1	FACETS	0.882	0.799	0.97	0.882	0.799	0.97	CLONAL	1	TRUE	0	0.272376159531599	1		453	920	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71026792	71026792	+	splice_donor_variant	Splice_Site	SNP	A	A	T	novel	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	86	257	0	ENST00000318789.4:c.1428+2T>A		p.X476_splice	ENST00000318789	NM_032682.5	476			0.272376159531599	1	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	0	0.272376159531599	1		257	497	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524869	187524869	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	966	143	519	0	ENST00000441802.2:c.10811del	p.Lys3604SerfsTer2	p.K3604Sfs*2	ENST00000441802	NM_005245.3	3604	aAg/ag	19/27	1	2	FACETS	0.947	0.862	1	0.947	0.862	1	CLONAL	1	TRUE	1	0.272376159531599	2		519	1109	SUCCESS
H3C2	8968	MSKCC	GRCh37	6	26031880	26031880	+	stop_lost	Nonstop_Mutation	SNP	A	A	G	novel	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	53	161	0	ENST00000244661.2:c.409T>C	p.Ter137GlnextTer2	p.*137Qext*2	ENST00000244661	NM_003537.3	137	Taa/Caa	1/1	0.248250091669642	3	FACETS	1	0.944	1	0.609	0.521	0.704	CLONAL	1	TRUE	1	0.272376159531599	3		161	363	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099877	157099877	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	134	609	0	ENST00000346085.5:c.814G>T	p.Ala272Ser	p.A272S	ENST00000346085	NM_020732.3	272	Gcc/Tcc	1/20	1	2	FACETS	0.813	0.737	0.894	0.813	0.737	0.894	CLONAL	1	TRUE	1	0.272376159531599	2		609	1210	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528825	157528825	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	117	446	1	ENST00000346085.5:c.6554del	p.Pro2185ArgfsTer8	p.P2185Rfs*8	ENST00000346085	NM_020732.3	2184	Ccc/cc	20/20	1	2	FACETS	0.884	0.796	0.977	0.884	0.796	0.977	CLONAL	1	TRUE	1	0.272376159531599	2		447	972	SUCCESS
MET	4233	MSKCC	GRCh37	7	116414866	116414866	+	intron_variant	Intron	SNP	C	C	A	rs760935013	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1930	186	924	0	ENST00000397752.3:c.3029-69C>A		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.645	0.593	0.7	0.645	0.593	0.7	SUBCLONAL	1	TRUE	1	0.272376159531599	2		924	2116	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140481401	140481409	+	inframe_deletion	In_Frame_Del	DEL	TCCAAATGA	TCCAAATGA	-	novel	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	392	459	0	ENST00000288602.6:c.1399_1407del	p.Ser467_Gly469del	p.S467_G469del	ENST00000288602	NM_004333.4	467	TCATTTGGA/-	11/18	0.272376159531599	2	FACETS	1	0.989	1	1	0.989	1	CLONAL	2	TRUE	0	0.272376159531599	2		459	1263	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089758	5089758	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	116	298	0	ENST00000381652.3:c.2656C>T	p.His886Tyr	p.H886Y	ENST00000381652	NM_004972.3	886	Cat/Tat	20/25	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.272376159531599	2		298	776	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36882050	36882050	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs780753361	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1339	212	663	7	ENST00000358127.4:c.963del	p.Ala322LeufsTer11	p.A322Lfs*11	ENST00000358127	NM_001280556.1	321	ccC/cc	8/10	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.272376159531599	2		670	1551	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98239124	98239124	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745669155	NA	P-0016413-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1277	172	631	1	ENST00000331920.6:c.1519G>A	p.Ala507Thr	p.A507T	ENST00000331920	NM_000264.3	507	Gct/Act	11/24	1	2	FACETS	0.872	0.799	0.947	0.872	0.799	0.947	CLONAL	1	TRUE	1	0.272376159531599	2		632	1449	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	588	215	0				ENST00000310581	NM_198253.2	-/1132			0.277762287940125	6	FACETS	1	0.976	1			1	INDETERMINATE	5	TRUE	NA	0.656734769937815	6		215	826	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs11575997	NA	P-0016418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	291	595	0	ENST00000269305.4:c.993+1G>A		p.X331_splice	ENST00000269305	NM_001126112.2	331			0.656734769937815	1	FACETS	0.942	0.894	0.99	0.942	0.894	0.99	CLONAL	1	TRUE	0	0.656734769937815	1		595	632	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0016418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1140	3852	685	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	0.656734769937815	8	FACETS	0.997	0.987	1			1	CLONAL	7	TRUE	NA	0.656734769937815	8		685	4992	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916854	178916854	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519929	NA	P-0016418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	268	932	2	ENST00000263967.3:c.241G>A	p.Glu81Lys	p.E81K	ENST00000263967	NM_006218.2	81	Gaa/Aaa	2/21	1	2	FACETS	0.816	0.766	0.868	0.816	0.766	0.868	CLONAL	1	TRUE	1	0.656734769937815	2		934	1000	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63851517	63851517	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1318622103	NA	P-0016418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	468	751	2	ENST00000279873.7:c.2295G>C	p.Glu765Asp	p.E765D	ENST00000279873	NM_032199.2	765	gaG/gaC	10/10	0.391991424075623	1	FACETS	0.833	0.798	0.869	0.833	0.798	0.869	INDETERMINATE	1	TRUE	0	0.656734769937815	1		753	1149	SUCCESS
FGF19	9965	MSKCC	GRCh37	11	69514284	69514284	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	903	275	703	0	ENST00000294312.3:c.397G>A	p.Val133Met	p.V133M	ENST00000294312	NM_005117.2	133	Gtg/Atg	3/3	0.284906506354224	1	FACETS	0.477	0.448	0.508	0.477	0.448	0.508	INDETERMINATE	1	TRUE	0	0.656734769937815	1		703	1178	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118374069	118374069	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	243	549	1	ENST00000534358.1:c.7462G>A	p.Asp2488Asn	p.D2488N	ENST00000534358	NM_005933.3	2488	Gat/Aat	27/36	0.284906506354224	1	FACETS	0.674	0.633	0.717	0.674	0.633	0.717	INDETERMINATE	1	TRUE	0	0.656734769937815	1		550	737	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65569033	65569033	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs201743423	NA	P-0016418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	304	556	2	ENST00000358664.4:c.25G>T	p.Val9Leu	p.V9L	ENST00000358664	NM_002382.4	9	Gtg/Ttg	1/5	1	2	FACETS	0.918	0.867	0.971	0.918	0.867	0.971	CLONAL	1	TRUE	1	0.656734769937815	2		558	1008	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56832405	56832405	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	131	420	0	ENST00000308159.5:c.315G>C	p.Glu105Asp	p.E105D	ENST00000308159	NM_014669.4	105	gaG/gaC	4/22	0.634386798096216	1	FACETS	0.527	0.481	0.576	0.527	0.481	0.576	SUBCLONAL	1	TRUE	0	0.656734769937815	1		420	508	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41234590	41234590	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	143	503	0	ENST00000357654.3:c.4188G>C	p.Gln1396His	p.Q1396H	ENST00000357654	NM_007294.3	1396	caG/caC	12/23	1	2	FACETS	0.551	0.503	0.602	0.551	0.503	0.602	SUBCLONAL	1	TRUE	1	0.656734769937815	2		503	790	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735408	204735408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	71	330	1	ENST00000302823.3:c.209G>A	p.Arg70Gln	p.R70Q	ENST00000302823	NM_005214.4	70	cGg/cAg	2/4	0.656734769937815	1	FACETS	0.29	0.254	0.33	0.29	0.254	0.33	SUBCLONAL	1	TRUE	0	0.656734769937815	1		331	500	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161362	55161362	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369389595	NA	P-0016418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	339	688	0	ENST00000257290.5:c.3193G>A	p.Glu1065Lys	p.E1065K	ENST00000257290	NM_006206.4	1065	Gag/Aag	23/23	0.284906506354224	1	FACETS	0.771	0.732	0.811	0.771	0.732	0.811	INDETERMINATE	1	TRUE	0	0.656734769937815	1		688	899	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845301	76845301	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	A	novel	NA	P-0016418-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	159	291	0	ENST00000373344.5:c.6217+3G>T		p.X2073_splice	ENST00000373344	NM_000489.3	2073			1	1	FACETS	1	0.987	1	1	0.987	1	CLONAL	1	TRUE	0	0.656734769937815	1		291	269	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673804	30673805	+	missense_variant	Missense_Mutation	DNP	GG	GG	TA	novel	NA	P-0016453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	64	318	1	ENST00000376406.3:c.3155_3156delinsTA	p.Pro1052Leu	p.P1052L	ENST00000376406	NM_014641.2	1052	cCC/cTA	10/15	1	2	FACETS	0.774	0.672	0.883	1	0.973	1	SUBCLONAL	2	TRUE	1	0.190114298356475	2		319	435	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70964479	70964479	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	53	494	0	ENST00000276594.2:c.1549T>C	p.Phe517Leu	p.F517L	ENST00000276594	NM_024504.3	517	Ttc/Ctc	8/8	1	2	FACETS	0.85	0.724	0.988	0.85	0.724	0.988	CLONAL	1	TRUE	1	0.190114298356475	2		494	656	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971210	21971210	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	C	novel	NA	P-0016453-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	44	346	0	ENST00000304494.5:c.151-3C>G		p.X51_splice	ENST00000304494	NM_000077.4	51			0.190114298356475	1	FACETS	1	0.848	1	1	0.848	1	CLONAL	1	TRUE	0	0.190114298356475	1		346	415	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10602646	10602646	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	119	472	0	ENST00000171111.5:c.932A>G	p.His311Arg	p.H311R	ENST00000171111	NM_203500.1	311	cAc/cGc	3/6	0.282750156120014	1	FACETS	0.96	0.867	1	0.96	0.867	1	CLONAL	1	TRUE	0	0.282750156120014	1		472	753	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1221314	1221314	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs121913321	NA	P-0016471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	113	488	1	ENST00000326873.7:c.842del	p.Pro281ArgfsTer6	p.P281Rfs*6	ENST00000326873	NM_000455.4	279	ggC/gg	6/10	0.282750156120014	1	FACETS	0.821	0.738	0.908	0.821	0.738	0.908	CLONAL	1	TRUE	0	0.282750156120014	1		489	836	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198268383	198268383	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1172363633	NA	P-0016471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1175	104	497	0	ENST00000335508.6:c.1645C>T	p.Arg549Cys	p.R549C	ENST00000335508	NM_012433.2	549	Cgt/Tgt	12/25	1	2	FACETS	0.575	0.513	0.641	0.575	0.513	0.641	SUBCLONAL	1	TRUE	1	0.282750156120014	2		497	1279	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332105	70332105	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1297376295	NA	P-0016471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	30	161	0	ENST00000373644.4:c.10T>A	p.Ser4Thr	p.S4T	ENST00000373644	NM_030625.2	4	Tcc/Acc	2/12	1	2	FACETS	0.608	0.49	0.741	0.608	0.49	0.741	SUBCLONAL	1	TRUE	1	0.282750156120014	2		161	349	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600420	10600420	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	189	669	0	ENST00000171111.5:c.1435G>A	p.Asp479Asn	p.D479N	ENST00000171111	NM_203500.1	479	Gac/Aac	4/6	0.282750156120014	1	FACETS	1	0.927	1	1	0.927	1	CLONAL	1	TRUE	0	0.282750156120014	1		669	1142	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101118	41101118	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	116	461	0	ENST00000373198.4:c.1238C>G	p.Ala413Gly	p.A413G	ENST00000373198	NM_133170.3	413	gCg/gGg	8/32	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.282750156120014	2		461	748	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232214	98232214	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0016471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	764	111	402	0	ENST00000331920.6:c.1729-1G>C		p.X577_splice	ENST00000331920	NM_000264.3	577			1	2	FACETS	0.897	0.806	0.994	0.897	0.806	0.994	CLONAL	1	TRUE	1	0.282750156120014	2		402	875	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039815	47039815	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	G	novel	NA	P-0016471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1084	126	415	0	ENST00000377604.3:c.1161-3C>G		p.X387_splice	ENST00000377604	NM_001204468.1	387			1	2	FACETS	0.737	0.665	0.812	0.737	0.665	0.812	SUBCLONAL	1	TRUE	1	0.282750156120014	2		415	1210	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040611	47040611	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	G	novel	NA	P-0016471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	56	315	0	ENST00000377604.3:c.1249-3C>G		p.X417_splice	ENST00000377604	NM_001204468.1	417			1	2	FACETS	0.719	0.616	0.831	0.719	0.616	0.831	SUBCLONAL	1	TRUE	1	0.282750156120014	2		315	551	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	122	215	0				ENST00000310581	NM_198253.2	-/1132			0.125343272560263	4	FACETS	1	0.984	1	0.734	0.664	0.808	INDETERMINATE	1	TRUE	2	0.28	4		215	760	SUCCESS
APC	324	MSKCC	GRCh37	5	112090657	112090657	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs145945630	NA	P-0016546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	91	474	0	ENST00000257430.4:c.70C>T	p.Arg24Ter	p.R24*	ENST00000257430	NM_000038.5	24	Cga/Tga	2/16	1	2	FACETS	0.7	0.62	0.785	0.7	0.62	0.785	SUBCLONAL	1	TRUE	1	0.28	2		474	929	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135801105	135801105	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	95	380	0	ENST00000298552.3:c.232G>T	p.Glu78Ter	p.E78*	ENST00000298552	NM_001162426.1	78	Gaa/Taa	5/23	1	2	FACETS	0.9	0.801	1	0.9	0.801	1	CLONAL	1	TRUE	1	0.28	2		380	754	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023449	27023449	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	115	475	0	ENST00000324856.7:c.555G>C	p.Gln185His	p.Q185H	ENST00000324856	NM_006015.4	185	caG/caC	1/20	1	2	FACETS	0.773	0.695	0.857	0.773	0.695	0.857	SUBCLONAL	1	TRUE	1	0.28	2		475	1062	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138201355	138201355	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	833	89	497	0	ENST00000237289.4:c.2054G>A	p.Arg685Lys	p.R685K	ENST00000237289	NM_001270507.1	685	aGa/aAa	8/9	1	2	FACETS	0.689	0.61	0.775	0.689	0.61	0.775	SUBCLONAL	1	TRUE	1	0.28	2		497	922	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141449	11141449	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	155	613	1	ENST00000358026.2:c.3426C>G	p.Phe1142Leu	p.F1142L	ENST00000358026	NM_001128849.1	1142	ttC/ttG	25/36	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.28	2		614	1089	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7216899	7216899	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	126	399	0	ENST00000380728.2:c.622C>T	p.Gln208Ter	p.Q208*	ENST00000380728		208	Cag/Tag	7/11	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.28	2		399	794	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31495482	31495482	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	C	novel	NA	P-0016546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	906	152	459	0	ENST00000344624.3:c.1669-3C>G		p.X557_splice	ENST00000344624		557			0.125343272560263	4	FACETS	1	0.983	1	0.657	0.6	0.717	INDETERMINATE	1	TRUE	2	0.28	4		459	1058	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27059260	27059260	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	53	492	0	ENST00000324856.7:c.1897C>A	p.Gln633Lys	p.Q633K	ENST00000324856	NM_006015.4	633	Cag/Aag	4/20	1	2	FACETS	0.359	0.305	0.419	0.359	0.305	0.419	SUBCLONAL	1	TRUE	1	0.28	2		492	1055	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163298673	163298673	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1186	113	654	0	ENST00000271452.3:c.313G>A	p.Glu105Lys	p.E105K	ENST00000271452	NM_145697.2	105	Gag/Aag	5/14	1	2	FACETS	0.621	0.557	0.69	0.621	0.557	0.69	SUBCLONAL	1	TRUE	1	0.28	2		654	1299	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195313	102195313	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370738985	NA	P-0016546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	96	456	1	ENST00000263464.3:c.73G>A	p.Asp25Asn	p.D25N	ENST00000263464	NM_001165.4	25	Gac/Aac	2/9	1	2	FACETS	0.668	0.593	0.747	0.668	0.593	0.747	SUBCLONAL	1	TRUE	1	0.28	2		457	1027	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49422915	49422915	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0016546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	978	119	468	0	ENST00000301067.7:c.14180C>G	p.Ser4727Ter	p.S4727*	ENST00000301067	NM_003482.3	4727	tCa/tGa	44/54	1	2	FACETS	0.775	0.698	0.857	0.775	0.698	0.857	SUBCLONAL	1	TRUE	1	0.28	2		468	1097	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431898	49431898	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1189	130	712	0	ENST00000301067.7:c.9241G>A	p.Glu3081Lys	p.E3081K	ENST00000301067	NM_003482.3	3081	Gaa/Aaa	34/54	1	2	FACETS	0.704	0.636	0.776	0.704	0.636	0.776	SUBCLONAL	1	TRUE	1	0.28	2		712	1319	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906637	32906637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80358403	NA	P-0016546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1048	107	548	0	ENST00000380152.3:c.1022G>A	p.Cys341Tyr	p.C341Y	ENST00000380152		341	tGt/tAt	10/27	1	2	FACETS	0.662	0.592	0.736	0.662	0.592	0.736	SUBCLONAL	1	TRUE	1	0.28	2		548	1155	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914736	32914736	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	154	643	0	ENST00000380152.3:c.6244G>A	p.Glu2082Lys	p.E2082K	ENST00000380152		2082	Gaa/Aaa	11/27	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.28	2		643	1076	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914752	32914752	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	964	162	648	0	ENST00000380152.3:c.6260G>C	p.Arg2087Thr	p.R2087T	ENST00000380152		2087	aGa/aCa	11/27	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.28	2		648	1126	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32915015	32915015	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs876658412	NA	P-0016546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1099	180	626	0	ENST00000380152.3:c.6523G>C	p.Glu2175Gln	p.E2175Q	ENST00000380152		2175	Gag/Cag	11/27	1	2	FACETS	1	0.925	1	1	0.925	1	CLONAL	1	TRUE	1	0.28	2		626	1279	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578290	7578290	+	splice_acceptor_variant	Splice_Site	SNP	C	C	G	rs1202793339	NA	P-0016546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	145	523	0	ENST00000269305.4:c.560-1G>C		p.X187_splice	ENST00000269305	NM_001126112.2	187			1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.28	2		523	970	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2211115	2211115	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1137	150	582	1	ENST00000398665.3:c.1369C>T	p.His457Tyr	p.H457Y	ENST00000398665	NM_032482.2	457	Cac/Tac	15/28	1	2	FACETS	0.833	0.759	0.91	0.833	0.759	0.91	CLONAL	1	TRUE	1	0.28	2		583	1287	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5212101	5212101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	953	142	549	0	ENST00000357368.4:c.4930G>A	p.Ala1644Thr	p.A1644T	ENST00000357368	NM_002850.3	1644	Gcc/Acc	32/38	1	2	FACETS	0.926	0.843	1	0.926	0.843	1	CLONAL	1	TRUE	1	0.28	2		549	1095	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051659	13051659	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0016546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1161	78	570	1	ENST00000316448.5:c.918T>A	p.Tyr306Ter	p.Y306*	ENST00000316448	NM_004343.3	306	taT/taA	7/9	0.184149546678595	3	FACETS	0.513	0.449	0.582			1	SUBCLONAL	1	TRUE	NA	0.28	3		571	1239	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17955076	17955076	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	73	561	1	ENST00000458235.1:c.151G>A	p.Glu51Lys	p.E51K	ENST00000458235	NM_000215.3	51	Gag/Aag	2/24	1	2	FACETS	0.496	0.432	0.565	0.496	0.432	0.565	SUBCLONAL	1	TRUE	1	0.28	2		562	1052	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30664690	30664690	+	intron_variant	Intron	SNP	G	G	A	novel	NA	P-0016546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	98	412	0	ENST00000295754.5:c.94+16221G>A		p.*32*	ENST00000295754	NM_003242.5	32/592			1	2	FACETS	0.749	0.667	0.836	0.749	0.667	0.836	SUBCLONAL	1	TRUE	1	0.28	2		412	935	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045714	26045714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	92	262	0	ENST00000540144.1:c.76G>A	p.Ala26Thr	p.A26T	ENST00000540144	NM_003531.2	26	Gcc/Acc	1/1	0.3	3	FACETS	0.847	0.757	0.943	0.565	0.504	0.629	CLONAL	2	TRUE	0	0.28	3		262	442	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878464	151878464	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	130	600	0	ENST00000262189.6:c.6481C>T	p.Gln2161Ter	p.Q2161*	ENST00000262189	NM_170606.2	2161	Caa/Taa	36/59	1	2	FACETS	0.93	0.842	1	0.93	0.842	1	CLONAL	1	TRUE	1	0.28	2		600	999	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69032434	69032434	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1232	79	597	0	ENST00000288368.4:c.3508G>C	p.Asp1170His	p.D1170H	ENST00000288368	NM_024870.2	1170	Gat/Cat	29/40	1	2	FACETS	0.43	0.377	0.488	0.43	0.377	0.488	SUBCLONAL	1	TRUE	1	0.28	2		597	1311	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135772880	135772880	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016546-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	968	144	562	1	ENST00000298552.3:c.2743C>T	p.His915Tyr	p.H915Y	ENST00000298552	NM_001162426.1	915	Cac/Tac	21/23	1	2	FACETS	0.925	0.842	1	0.925	0.842	1	CLONAL	1	TRUE	1	0.28	2		563	1112	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0016624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	944	227	282	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.698	0.65	0.749	0.698	0.65	0.749	SUBCLONAL	1	TRUE	1	0.555051459965131	2		282	1171	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0016624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	987	646	616	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.555051459965131	1	FACETS	1	0.982	1	1	0.982	1	CLONAL	1	TRUE	0	0.555051459965131	1		617	1633	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41021749	41021749	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	293	395	0	ENST00000267868.3:c.691G>C	p.Asp231His	p.D231H	ENST00000267868	NM_002875.4	231	Gac/Cac	8/10	1	2	FACETS	0.916	0.861	0.971	0.916	0.861	0.971	CLONAL	1	TRUE	1	0.555051459965131	2		395	1153	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849436	89849436	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	274	489	0	ENST00000389301.3:c.1545G>C	p.Lys515Asn	p.K515N	ENST00000389301	NM_000135.2	515	aaG/aaC	16/43	0.555051459965131	1	FACETS	0.871	0.82	0.922	0.871	0.82	0.922	CLONAL	1	TRUE	0	0.555051459965131	1		489	819	SUCCESS
STAT5B	6777	MSKCC	GRCh37	17	40371858	40371858	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1732	688	1162	0	ENST00000293328.3:c.553C>G	p.Gln185Glu	p.Q185E	ENST00000293328	NM_012448.3	185	Cag/Gag	6/19	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.555051459965131	2		1162	2420	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5208319	5208319	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1236	611	863	0	ENST00000357368.4:c.5571C>G	p.Ile1857Met	p.I1857M	ENST00000357368	NM_002850.3	1857	atC/atG	36/38	0.295119784329711	1	FACETS	0.861	0.827	0.895	0.861	0.827	0.895	INDETERMINATE	1	TRUE	0	0.555051459965131	1		863	1847	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475555	12475555	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	933	614	0	ENST00000287820.6:c.1429C>G	p.His477Asp	p.H477D	ENST00000287820	NM_015869.4	477	Cac/Gac	7/7	0.555051459965131	2	FACETS	1	0.994	1	1	0.994	1	CLONAL	2	TRUE	0	0.555051459965131	2		614	1577	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	240568	240568	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	36	53	0	ENST00000264932.6:c.1528G>T	p.Glu510Ter	p.E510*	ENST00000264932	NM_004168.2	510	Gaa/Taa	11/15	1	2	FACETS	1	0.92	1	1	0.92	1	CLONAL	1	TRUE	1	0.555051459965131	2		53	112	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295181	1295181	+	upstream_gene_variant	5'Flank	SNP	G	G	C	novel	NA	P-0016624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	116	308	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.632	0.571	0.697	0.632	0.571	0.697	SUBCLONAL	1	TRUE	1	0.555051459965131	2		308	661	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295411	1295411	+	upstream_gene_variant	5'Flank	SNP	G	G	A	novel	NA	P-0016624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	68	170	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.747	0.655	0.845	0.747	0.655	0.845	SUBCLONAL	1	TRUE	1	0.555051459965131	2		170	328	SUCCESS
APC	324	MSKCC	GRCh37	5	112154907	112154907	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs1114167545	NA	P-0016624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	447	512	0	ENST00000257430.4:c.1178C>G	p.Ser393Ter	p.S393*	ENST00000257430	NM_000038.5	393	tCa/tGa	10/16	0.555051459965131	1	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	0	0.555051459965131	1		512	1130	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566315	141566315	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	268	406	0	ENST00000220592.5:c.1097G>A	p.Arg366Lys	p.R366K	ENST00000220592	NM_012154.3	366	aGa/aAa	9/19	NA	2	FACETS	1	0.98	1			1	INDETERMINATE	1	TRUE	NA	0.555051459965131	2		406	883	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141566332	141566332	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016624-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	252	403	0	ENST00000220592.5:c.1080G>C	p.Gln360His	p.Q360H	ENST00000220592	NM_012154.3	360	caG/caC	9/19	NA	2	FACETS	1	0.966	1			1	INDETERMINATE	1	TRUE	NA	0.555051459965131	2		403	869	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	293	215	0				ENST00000310581	NM_198253.2	-/1132			0.264297891787693	4	FACETS	1	0.972	1	1	0.972	1	CLONAL	2	TRUE	2	0.328727525741753	4		215	1124	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69046421	69046421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1119	175	400	0	ENST00000288368.4:c.3894G>A	p.Met1298Ile	p.M1298I	ENST00000288368	NM_024870.2	1298	atG/atA	32/40	0.212415773960098	3	FACETS	0.958	0.88	1	0.479	0.44	0.52	CLONAL	1	TRUE	1	0.328727525741753	3		400	1294	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49050864	49050864	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs886042935	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	371	413	0	ENST00000267163.4:c.2548C>T	p.Gln850Ter	p.Q850*	ENST00000267163	NM_000321.2	850	Cag/Tag	25/27	0.135409882791234	4	FACETS	0.895	0.85	0.941	0.671	0.638	0.706	INDETERMINATE	3	TRUE	0	0.328727525741753	4		413	1117	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911598	39911598	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765528893	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1199	218	576	0	ENST00000378444.4:c.5032C>T	p.Arg1678Cys	p.R1678C	ENST00000378444	NM_001123385.1	1678	Cgc/Tgc	15/15	1	2	FACETS	0.936	0.868	1	0.936	0.868	1	CLONAL	1	TRUE	1	0.328727525741753	2		576	1417	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578457	7578457	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs587782144	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1235	393	673	0	ENST00000269305.4:c.473G>C	p.Arg158Pro	p.R158P	ENST00000269305	NM_001126112.2	158	cGc/cCc	5/11	0.212415773960098	3	FACETS	0.855	0.811	0.9	0.855	0.811	0.9	CLONAL	2	TRUE	1	0.328727525741753	3		673	1628	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045688	26045688	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1350355423	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	71	159	0	ENST00000540144.1:c.50C>T	p.Pro17Leu	p.P17L	ENST00000540144	NM_003531.2	17	cCg/cTg	1/1	0.212415773960098	3	FACETS	1	0.94	1	0.561	0.491	0.636	CLONAL	1	TRUE	1	0.328727525741753	3		159	448	SUCCESS
IGF2	3481	MSKCC	GRCh37	11	2156615	2156615	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	241	522	0	ENST00000434045.2:c.307G>A	p.Asp103Asn	p.D103N	ENST00000434045	NM_001127598.1	103	Gac/Aac	3/5	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.328727525741753	2		522	1322	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81372699	81372699	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs756224070	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	601	114	282	0	ENST00000222390.5:c.835C>T	p.Arg279Cys	p.R279C	ENST00000222390	NM_000601.4	279	Cgc/Tgc	7/18	1	2	FACETS	0.97	0.874	1	0.97	0.874	1	CLONAL	1	TRUE	1	0.328727525741753	2		282	715	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57863272	57863272	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1305707895	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	138	471	0	ENST00000228682.2:c.1367G>A	p.Gly456Glu	p.G456E	ENST00000228682	NM_005269.2	456	gGg/gAg	11/12	1	2	FACETS	0.834	0.758	0.914	0.834	0.758	0.914	CLONAL	1	TRUE	1	0.328727525741753	2		471	1007	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117755	70117755	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1173	269	668	1	ENST00000245479.2:c.223G>A	p.Glu75Lys	p.E75K	ENST00000245479	NM_000346.3	75	Gag/Aag	1/3	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.328727525741753	2		669	1442	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43812606	43812606	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	862	333	566	0	ENST00000372470.3:c.1308+1G>A		p.X436_splice	ENST00000372470	NM_005373.2	436			0.242647329617933	2	FACETS	0.848	0.801	0.895	0.848	0.801	0.895	CLONAL	2	TRUE	0	0.328727525741753	2		566	1195	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117695923	117695924	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	299	544	2	ENST00000369458.3:c.513_514delinsTT	p.Arg172Ter	p.R172*	ENST00000369458	NM_024626.3	171	ccCCga/ccTTga	4/6	0.242647329617933	2	FACETS	0.785	0.739	0.832	0.785	0.739	0.832	SUBCLONAL	2	TRUE	0	0.328727525741753	2		546	1159	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458450	120458450	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	222	374	0	ENST00000256646.2:c.6895G>A	p.Glu2299Lys	p.E2299K	ENST00000256646	NM_024408.3	2299	Gag/Aag	34/34	0.242647329617933	2	FACETS	0.848	0.792	0.907	0.848	0.792	0.907	CLONAL	2	TRUE	0	0.328727525741753	2		374	796	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642737	3642737	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	890	236	553	0	ENST00000294008.3:c.2290C>T	p.Pro764Ser	p.P764S	ENST00000294008	NM_032444.2	764	Cct/Tct	11/15	0.328727525741753	1	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	0	0.328727525741753	1		553	1126	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3644465	3644465	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	248	595	0	ENST00000294008.3:c.2149C>T	p.Leu717Phe	p.L717F	ENST00000294008	NM_032444.2	717	Ctc/Ttc	10/15	0.328727525741753	1	FACETS	0.957	0.893	1	0.957	0.893	1	CLONAL	1	TRUE	0	0.328727525741753	1		595	1317	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30322749	30322749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1325577906	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	131	433	0	ENST00000322652.5:c.1762G>A	p.Asp588Asn	p.D588N	ENST00000322652	NM_015355.2	588	Gat/Aat	14/16	1	2	FACETS	0.766	0.694	0.842	0.766	0.694	0.842	SUBCLONAL	1	TRUE	1	0.328727525741753	2		433	1041	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40483508	40483508	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1109	241	498	0	ENST00000264657.5:c.1091T>A	p.Ile364Asn	p.I364N	ENST00000264657	NM_139276.2	364	aTt/aAt	11/24	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.328727525741753	2		498	1350	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78938099	78938099	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1410	189	750	1	ENST00000306801.3:c.3977C>T	p.Ser1326Phe	p.S1326F	ENST00000306801	NM_020761.2	1326	tCc/tTc	34/34	1	2	FACETS	0.719	0.662	0.779	0.719	0.662	0.779	SUBCLONAL	1	TRUE	1	0.328727525741753	2		751	1599	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10610558	10610558	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1348405716	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	201	499	0	ENST00000171111.5:c.152C>T	p.Thr51Ile	p.T51I	ENST00000171111	NM_203500.1	51	aCc/aTc	2/6	0.162882072604795	1	FACETS	1	0.95	1	1	0.95	1	INDETERMINATE	1	TRUE	0	0.328727525741753	1		499	991	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024559	11024559	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	144	367	0	ENST00000327064.4:c.676G>T	p.Val226Leu	p.V226L	ENST00000327064	NM_199141.1	226	Gtg/Ttg	6/16	0.162882072604795	1	FACETS	0.841	0.767	0.918	0.841	0.767	0.918	INDETERMINATE	1	TRUE	0	0.328727525741753	1		367	871	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107187	11107187	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	175	411	0	ENST00000358026.2:c.1779A>C	p.Glu593Asp	p.E593D	ENST00000358026	NM_001128849.1	593	gaA/gaC	11/36	0.162882072604795	1	FACETS	0.864	0.795	0.936	0.864	0.795	0.936	INDETERMINATE	1	TRUE	0	0.328727525741753	1		411	1030	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18960966	18960966	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	156	551	0	ENST00000262803.5:c.544G>A	p.Glu182Lys	p.E182K	ENST00000262803	NM_002911.3	182	Gag/Aag	4/24	0.162882072604795	1	FACETS	0.643	0.587	0.701	0.643	0.587	0.701	INDETERMINATE	1	TRUE	0	0.328727525741753	1		551	1234	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794394	42794394	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373584239	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1670	312	984	2	ENST00000575354.2:c.1474C>T	p.Arg492Trp	p.R492W	ENST00000575354	NM_015125.3	492	Cgg/Tgg	10/20	0.162882072604795	1	FACETS	0.8	0.752	0.851	0.8	0.752	0.851	INDETERMINATE	1	TRUE	0	0.328727525741753	1		986	1982	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095694	178095694	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	170	390	0	ENST00000397062.3:c.1637A>G	p.Asn546Ser	p.N546S	ENST00000397062	NM_006164.4	546	aAt/aGt	5/5	1	2	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	1	0.328727525741753	2		390	808	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131410	202131411	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	209	478	0	ENST00000358485.4:c.378_379delinsTT	p.Arg127Ter	p.R127*	ENST00000358485	NM_001080125.1	126	ttCCga/ttTTga	2/9	1	2	FACETS	1	0.985	1	1	0.985	1	CLONAL	1	TRUE	1	0.328727525741753	2		478	1037	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31376715	31376716	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	70	249	1	ENST00000328111.2:c.710_711delinsTT	p.Ser237Phe	p.S237F	ENST00000328111	NM_006892.3	237	tCC/tTT	7/23	0.328727525741753	3	FACETS	0.74	0.645	0.843	0.37	0.322	0.422	SUBCLONAL	1	TRUE	1	0.328727525741753	3		250	670	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57484798	57484798	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1092	399	467	0	ENST00000371085.3:c.778G>A	p.Asp260Asn	p.D260N	ENST00000371085	NM_000516.4	260	Gac/Aac	10/13	0.328727525741753	3	FACETS	0.948	0.9	0.997	0.948	0.9	0.997	CLONAL	2	TRUE	1	0.328727525741753	3		467	1491	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41568569	41568569	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1148	284	545	0	ENST00000263253.7:c.4519G>A	p.Asp1507Asn	p.D1507N	ENST00000263253	NM_001429.3	1507	Gat/Aat	28/31	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.328727525741753	2		545	1432	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155288	185155288	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	124	329	0	ENST00000265026.3:c.529G>A	p.Gly177Arg	p.G177R	ENST00000265026	NM_004721.4	177	Gga/Aga	3/14	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.328727525741753	2		329	743	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525728	187525729	+	splice_acceptor_variant,coding_sequence_variant	Splice_Site	DNP	CC	CC	TT	novel	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	96	237	1	ENST00000441802.2:c.10351-1_10351delinsAA		p.X3451_splice	ENST00000441802	NM_005245.3	3451		18/27	0.328727525741753	1	FACETS	0.864	0.772	0.962	0.864	0.772	0.962	CLONAL	1	TRUE	0	0.328727525741753	1		238	565	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526265	31526265	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1758	306	759	0	ENST00000344624.3:c.775A>G	p.Arg259Gly	p.R259G	ENST00000344624		259	Aga/Gga	2/33	0.264297891787693	4	FACETS	1	0.988	1	0.599	0.562	0.638	CLONAL	1	TRUE	2	0.328727525741753	4		759	2064	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38947506	38947506	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	306	289	0	ENST00000357387.3:c.4174G>A	p.Glu1392Lys	p.E1392K	ENST00000357387	NM_152756.3	1392	Gaa/Aaa	32/38	0.264297891787693	4	FACETS	1	0.991	1	1	0.991	1	CLONAL	2	TRUE	2	0.328727525741753	4		289	994	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37139121	37139121	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	197	332	0	ENST00000373509.5:c.461C>T	p.Ala154Val	p.A154V	ENST00000373509	NM_002648.3	154	gCc/gTc	4/6	0.212415773960098	3	FACETS	0.839	0.778	0.902	0.839	0.778	0.902	CLONAL	2	TRUE	1	0.328727525741753	3		332	832	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066630	94066630	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	100	477	0	ENST00000369303.4:c.1129G>A	p.Gly377Ser	p.G377S	ENST00000369303	NM_004440.3	377	Ggc/Agc	5/17	0.162882072604795	1	FACETS	0.424	0.378	0.474	0.424	0.378	0.474	INDETERMINATE	1	TRUE	0	0.328727525741753	1		477	1198	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004625	150004625	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	136	384	0	ENST00000253339.5:c.1600G>C	p.Glu534Gln	p.E534Q	ENST00000253339		534	Gag/Cag	3/7	0.162882072604795	1	FACETS	0.711	0.645	0.779	0.711	0.645	0.779	INDETERMINATE	1	TRUE	0	0.328727525741753	1		384	973	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509438	106509438	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs748511834	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	227	530	0	ENST00000359195.3:c.1432G>A	p.Gly478Arg	p.G478R	ENST00000359195	NM_002649.2	478	Gga/Aga	2/11	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.328727525741753	2		530	1247	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151841835	151841835	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	103	264	0	ENST00000262189.6:c.14306G>A	p.Trp4769Ter	p.W4769*	ENST00000262189	NM_170606.2	4769	tGg/tAg	55/59	1	2	FACETS	0.819	0.733	0.911	0.819	0.733	0.911	CLONAL	1	TRUE	1	0.328727525741753	2		264	765	SUCCESS
XRCC2	7516	MSKCC	GRCh37	7	152345901	152345901	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	846	141	410	0	ENST00000359321.1:c.669C>A	p.Tyr223Ter	p.Y223*	ENST00000359321	NM_005431.1	223	taC/taA	3/3	1	2	FACETS	0.869	0.791	0.951	0.869	0.791	0.951	CLONAL	1	TRUE	1	0.328727525741753	2		410	987	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020539	69020539	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1234	179	467	0	ENST00000288368.4:c.2911G>A	p.Asp971Asn	p.D971N	ENST00000288368	NM_024870.2	971	Gat/Aat	24/40	0.212415773960098	3	FACETS	0.897	0.825	0.973	0.449	0.412	0.487	CLONAL	1	TRUE	1	0.328727525741753	3		467	1413	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27203119	27203119	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	971	210	427	0	ENST00000380036.4:c.2209+2T>C		p.X737_splice	ENST00000380036	NM_000459.3	737			0.142017807653668	3	FACETS	1	0.986	1	0.63	0.584	0.678	INDETERMINATE	1	TRUE	1	0.328727525741753	3		427	1181	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249837	110249837	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	990	197	487	1	ENST00000374672.4:c.838G>C	p.Glu280Gln	p.E280Q	ENST00000374672	NM_004235.4	280	Gag/Cag	3/5	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.328727525741753	2		488	1187	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345348	70345348	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	novel	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1228	218	601	1	ENST00000374080.3:c.2371+3G>A		p.X791_splice	ENST00000374080		791			1	2	FACETS	0.917	0.851	0.986	0.917	0.851	0.986	CLONAL	1	TRUE	1	0.328727525741753	2		602	1446	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938988	76938988	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016633-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1298	311	658	0	ENST00000373344.5:c.1760A>C	p.Tyr587Ser	p.Y587S	ENST00000373344	NM_000489.3	587	tAt/tCt	9/35	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.328727525741753	2		658	1609	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66518894	66518894	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	rs745980273	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	95	314	0	ENST00000358598.2:c.178-3C>T		p.X60_splice	ENST00000358598	NM_212471.2	60			1	2	FACETS	0.915	0.817	1	0.915	0.817	1	CLONAL	1	TRUE	1	0.37	2		314	561	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58143065	58143065	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs531817742	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	882	139	622	0	ENST00000257904.6:c.719G>A	p.Arg240Gln	p.R240Q	ENST00000257904	NM_000075.3	240	cGa/cAa	7/8	0.165807479755987	3	FACETS	0.872	0.793	0.956	0.436	0.396	0.478	INDETERMINATE	1	TRUE	1	0.37	3		622	1021	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47147533	47147533	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	90	502	1	ENST00000409792.3:c.4793G>A	p.Arg1598Gln	p.R1598Q	ENST00000409792	NM_014159.6	1598	cGa/cAa	6/21	1	2	FACETS	0.628	0.556	0.704	0.628	0.556	0.704	SUBCLONAL	1	TRUE	1	0.37	2		503	775	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867516	35867516	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	86	526	0	ENST00000303115.3:c.330G>T	p.Lys110Asn	p.K110N	ENST00000303115	NM_002185.3	110	aaG/aaT	3/8	1	2	FACETS	0.655	0.579	0.736	0.655	0.579	0.736	SUBCLONAL	1	TRUE	1	0.37	2		526	710	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743993	41743993	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	194	758	1	ENST00000301178.4:c.928G>A	p.Ala310Thr	p.A310T	ENST00000301178	NM_021913.4	310	Gca/Aca	7/20	1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.37	2		759	919	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18491483	18491483	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	66	413	0	ENST00000266497.5:c.1395+1G>C		p.X465_splice	ENST00000266497		465			0.3	1	FACETS	0.471	0.409	0.539	0.471	0.409	0.539	SUBCLONAL	1	TRUE	0	0.37	1		413	617	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916930	178916930	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519930	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	116	572	1	ENST00000263967.3:c.317G>T	p.Gly106Val	p.G106V	ENST00000263967	NM_006218.2	106	gGc/gTc	2/21	1	2	FACETS	0.692	0.623	0.765	0.692	0.623	0.765	SUBCLONAL	1	TRUE	1	0.37	2		573	906	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89790793	89790793	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	141	743	0	ENST00000336032.3:c.180C>A	p.Phe60Leu	p.F60L	ENST00000336032	NM_006813.2	60	ttC/ttA	1/2	0.165807479755987	3	FACETS	0.967	0.88	1	0.483	0.44	0.529	INDETERMINATE	1	TRUE	1	0.37	3		743	934	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66509103	66509103	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs759127824	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	114	511	1	ENST00000273854.3:c.224G>A	p.Trp75Ter	p.W75*	ENST00000273854	NM_004439.5	75	tGg/tAg	2/18	1	2	FACETS	0.931	0.839	1	0.931	0.839	1	CLONAL	1	TRUE	1	0.37	2		512	662	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1293661	1293661	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	146	633	2	ENST00000310581.5:c.1340G>A	p.Arg447His	p.R447H	ENST00000310581	NM_198253.2	447	cGc/cAc	2/16	0.130923951212186	1	FACETS	0.957	0.876	1	0.957	0.876	1	INDETERMINATE	1	TRUE	0	0.37	1		635	672	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178685	56178685	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	49	173	0	ENST00000399503.3:c.3658C>T	p.Gln1220Ter	p.Q1220*	ENST00000399503	NM_005921.1	1220	Caa/Taa	14/20	1	2	FACETS	0.898	0.765	1	0.898	0.765	1	CLONAL	1	TRUE	1	0.37	2		173	295	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803818	43803818	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147938568	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	139	549	0	ENST00000372470.3:c.128G>A	p.Arg43Gln	p.R43Q	ENST00000372470	NM_005373.2	43	cGa/cAa	2/12	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.37	2		549	730	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101909971	101909971	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	60	241	0	ENST00000374994.4:c.1291C>A	p.Leu431Ile	p.L431I	ENST00000374994	NM_004612.2	431	Ctt/Att	8/9	1	2	FACETS	0.891	0.771	1	0.891	0.771	1	CLONAL	1	TRUE	1	0.37	2		241	364	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936096	178936096	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1057519940	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	136	643	4	ENST00000263967.3:c.1638G>T	p.Gln546His	p.Q546H	ENST00000263967	NM_006218.2	546	caG/caT	10/21	1	2	FACETS	0.824	0.749	0.903	0.824	0.749	0.903	CLONAL	1	TRUE	1	0.37	2		647	892	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180043386	180043386	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	127	571	0	ENST00000261937.6:c.3200A>T	p.Asp1067Val	p.D1067V	ENST00000261937	NM_182925.4	1067	gAc/gTc	23/30	0.3	1	FACETS	0.87	0.79	0.954	0.87	0.79	0.954	CLONAL	1	TRUE	0	0.37	1		571	643	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16254749	16254749	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	158	545	2	ENST00000375759.3:c.2014C>T	p.Arg672Ter	p.R672*	ENST00000375759	NM_015001.2	672	Cga/Tga	11/15	0.3	3	FACETS	1	0.966	1			1	CLONAL	1	TRUE	NA	0.37	3		547	916	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600447	10600447	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1081	26	684	1	ENST00000171111.5:c.1408C>T	p.Arg470Cys	p.R470C	ENST00000171111	NM_203500.1	470	Cgt/Tgt	4/6	1	2	FACETS	0.127	0.1	0.159	0.127	0.1	0.159	SUBCLONAL	1	TRUE	1	0.37	2		685	1107	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395162	139395162	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199652954	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	110	587	0	ENST00000277541.6:c.5776C>T	p.Arg1926Cys	p.R1926C	ENST00000277541	NM_017617.3	1926	Cgc/Tgc	31/34	1	2	FACETS	0.826	0.742	0.914	0.826	0.742	0.914	CLONAL	1	TRUE	1	0.37	2		587	720	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921170	50921170	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs375328523	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	129	645	2	ENST00000440232.2:c.3290G>A	p.Arg1097Gln	p.R1097Q	ENST00000440232	NM_002691.3	1097	cGg/cAg	27/27	1	2	FACETS	0.908	0.824	0.996	0.908	0.824	0.996	CLONAL	1	TRUE	1	0.37	2		647	768	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729907	41729907	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	108	493	0	ENST00000242208.4:c.622G>A	p.Glu208Lys	p.E208K	ENST00000242208	NM_002192.2	208	Gaa/Aaa	3/3	1	2	FACETS	0.827	0.743	0.916	0.827	0.743	0.916	CLONAL	1	TRUE	1	0.37	2		493	706	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335719	81335719	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	94	413	1	ENST00000222390.5:c.1641G>T	p.Trp547Cys	p.W547C	ENST00000222390	NM_000601.4	547	tgG/tgT	15/18	1	2	FACETS	0.837	0.746	0.934	0.837	0.746	0.934	CLONAL	1	TRUE	1	0.37	2		414	607	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852251	63852251	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137983907	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	101	412	1	ENST00000279873.7:c.3029G>A	p.Arg1010Gln	p.R1010Q	ENST00000279873	NM_032199.2	1010	cGg/cAg	10/10	0.3	5	FACETS	1	0.961	1			1	CLONAL	1	TRUE	NA	0.37	5		413	733	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467548	66467548	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	75	341	0	ENST00000273854.3:c.721G>T	p.Ala241Ser	p.A241S	ENST00000273854	NM_004439.5	241	Gct/Tct	3/18	1	2	FACETS	0.737	0.647	0.834	0.737	0.647	0.834	SUBCLONAL	1	TRUE	1	0.37	2		341	550	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44513309	44513309	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1568949835	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	907	186	700	0	ENST00000291552.4:c.626G>A	p.Arg209His	p.R209H	ENST00000291552	NM_006758.2	209	cGt/cAt	8/8	0.130923951212186	1	FACETS	0.75	0.691	0.81	0.75	0.691	0.81	INDETERMINATE	1	TRUE	0	0.37	1		700	1093	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66356251	66356251	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	128	500	1	ENST00000273854.3:c.1246C>T	p.Pro416Ser	p.P416S	ENST00000273854	NM_004439.5	416	Ccc/Tcc	5/18	1	2	FACETS	0.848	0.769	0.932	0.848	0.769	0.932	CLONAL	1	TRUE	1	0.37	2		501	816	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332272	70332272	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	48	538	0	ENST00000373644.4:c.177G>T	p.Lys59Asn	p.K59N	ENST00000373644	NM_030625.2	59	aaG/aaT	2/12	1	2	FACETS	0.316	0.266	0.371	0.316	0.266	0.371	SUBCLONAL	1	TRUE	1	0.37	2		538	821	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81969848	81969848	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs568724894	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	149	612	0	ENST00000359376.3:c.2917G>A	p.Asp973Asn	p.D973N	ENST00000359376	NM_002661.3	973	Gac/Aac	27/33	1	2	FACETS	0.854	0.78	0.932	0.854	0.78	0.932	CLONAL	1	TRUE	1	0.37	2		612	943	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841178	15841178	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs753128407	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	127	538	2	ENST00000307771.7:c.1262G>A	p.Arg421Gln	p.R421Q	ENST00000307771	NM_005089.3	421	cGa/cAa	11/11	0.130923951212186	0	FACETS	0.602	0.546	0.661			1	INDETERMINATE	1	TRUE	0	0.37	0		540	718	SUCCESS
VEGFA	7422	MSKCC	GRCh37	6	43745248	43745248	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	113	616	0	ENST00000523873.1:c.161C>T	p.Pro54Leu	p.P54L	ENST00000523873		54	cCa/cTa	3/8	0.165807479755987	3	FACETS	0.952	0.857	1	0.476	0.428	0.527	INDETERMINATE	1	TRUE	1	0.37	3		616	760	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40710643	40710643	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs151076965	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	105	493	0	ENST00000373198.4:c.4208G>A	p.Arg1403His	p.R1403H	ENST00000373198	NM_133170.3	1403	cGt/cAt	31/32	0.3	1	FACETS	0.74	0.664	0.82	0.74	0.664	0.82	SUBCLONAL	1	TRUE	0	0.37	1		493	625	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70411602	70411602	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	84	495	1	ENST00000373644.4:c.4277-1G>T		p.X1426_splice	ENST00000373644	NM_030625.2	1426			1	2	FACETS	0.666	0.588	0.749	0.666	0.588	0.749	SUBCLONAL	1	TRUE	1	0.37	2		496	682	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333864	70333864	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528233201	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	91	428	2	ENST00000373644.4:c.1769G>A	p.Arg590Gln	p.R590Q	ENST00000373644	NM_030625.2	590	cGa/cAa	2/12	1	2	FACETS	0.937	0.834	1	0.937	0.834	1	CLONAL	1	TRUE	1	0.37	2		430	525	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13946150	13946150	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	142	599	0	ENST00000405192.2:c.946C>T	p.Gln316Ter	p.Q316*	ENST00000405192	NM_001163147.1	316	Cag/Tag	10/12	1	2	FACETS	0.819	0.746	0.896	0.819	0.746	0.896	CLONAL	1	TRUE	1	0.37	2		599	937	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562336	21562336	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765917652	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	139	599	0	ENST00000382592.4:c.1583C>T	p.Ser528Leu	p.S528L	ENST00000382592	NM_014572.2	528	tCg/tTg	4/8	1	2	FACETS	1	0.979	1	1	0.979	1	CLONAL	1	TRUE	1	0.37	2		599	607	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412303	139412303	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs869025494	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	89	591	0	ENST00000277541.6:c.1342C>T	p.Arg448Ter	p.R448*	ENST00000277541	NM_017617.3	448	Cga/Tga	8/34	1	2	FACETS	0.604	0.535	0.678	0.604	0.535	0.678	SUBCLONAL	1	TRUE	1	0.37	2		591	797	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81973613	81973613	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	119	659	0	ENST00000359376.3:c.3430G>A	p.Asp1144Asn	p.D1144N	ENST00000359376	NM_002661.3	1144	Gat/Aat	30/33	1	2	FACETS	0.757	0.683	0.835	0.757	0.683	0.835	SUBCLONAL	1	TRUE	1	0.37	2		659	850	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178104	56178104	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	72	376	0	ENST00000399503.3:c.3077C>A	p.Ser1026Tyr	p.S1026Y	ENST00000399503	NM_005921.1	1026	tCt/tAt	14/20	1	2	FACETS	0.625	0.546	0.71	0.625	0.546	0.71	SUBCLONAL	1	TRUE	1	0.37	2		376	623	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63852488	63852488	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1170860237	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	98	405	1	ENST00000279873.7:c.3266C>T	p.Ser1089Leu	p.S1089L	ENST00000279873	NM_032199.2	1089	tCg/tTg	10/10	0.3	5	FACETS	1	0.958	1			1	CLONAL	1	TRUE	NA	0.37	5		406	716	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190728826	190728826	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	99	420	0	ENST00000441310.2:c.2214G>T	p.Met738Ile	p.M738I	ENST00000441310	NM_000534.4	738	atG/atT	10/13	1	2	FACETS	0.805	0.719	0.896	0.805	0.719	0.896	CLONAL	1	TRUE	1	0.37	2		420	665	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39772519	39772519	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	103	425	0	ENST00000288319.7:c.722C>T	p.Thr241Met	p.T241M	ENST00000288319	NM_182918.3	241	aCg/aTg	6/10	0.130923951212186	1	FACETS	0.684	0.613	0.76	0.684	0.613	0.76	INDETERMINATE	1	TRUE	0	0.37	1		425	663	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38315007	38315007	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	187	664	1	ENST00000425967.3:c.57G>T	p.Trp19Cys	p.W19C	ENST00000425967	NM_001174067.1	19	tgG/tgT	3/19	1	2	FACETS	1	0.969	1	1	0.969	1	CLONAL	1	TRUE	1	0.37	2		665	926	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979201	93979201	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	60	278	0	ENST00000369303.4:c.1627T>G	p.Phe543Val	p.F543V	ENST00000369303	NM_004440.3	543	Ttt/Gtt	7/17	0.165807479755987	3	FACETS	0.935	0.808	1	0.468	0.404	0.536	INDETERMINATE	1	TRUE	1	0.37	3		278	411	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	343506	343506	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs141807086	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	100	613	1	ENST00000262320.3:c.2168G>A	p.Arg723Gln	p.R723Q	ENST00000262320	NM_003502.3	723	cGa/cAa	8/11	0.3	2	FACETS	0.699	0.624	0.779			1	SUBCLONAL	1	TRUE	NA	0.37	2		614	773	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521544	8521544	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	406	102	514	1	ENST00000356435.5:c.694C>T	p.Arg232Cys	p.R232C	ENST00000356435		232	Cgc/Tgc	9/35	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.37	2		515	508	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139818343	139818343	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	898	161	612	0	ENST00000247668.2:c.1178G>A	p.Arg393His	p.R393H	ENST00000247668	NM_021138.3	393	cGt/cAt	10/11	1	2	FACETS	0.822	0.753	0.894	0.822	0.753	0.894	CLONAL	1	TRUE	1	0.37	2		612	1059	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519874	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	109	479	1	ENST00000356142.4:c.85C>A	p.Pro29Thr	p.P29T	ENST00000356142	NM_018890.3	29	Cct/Act	2/7	1	2	FACETS	0.786	0.706	0.87	0.786	0.706	0.87	SUBCLONAL	1	TRUE	1	0.37	2		480	750	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275649	41275649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	104	374	0	ENST00000349496.5:c.1544G>A	p.Arg515Gln	p.R515Q	ENST00000349496	NM_001904.3	515	cGa/cAa	10/15	1	2	FACETS	0.914	0.82	1	0.914	0.82	1	CLONAL	1	TRUE	1	0.37	2		374	615	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226564924	226564924	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	113	457	0	ENST00000366794.5:c.1826A>G	p.Asp609Gly	p.D609G	ENST00000366794	NM_001618.3	609	gAt/gGt	13/23	1	2	FACETS	0.894	0.806	0.988	0.894	0.806	0.988	CLONAL	1	TRUE	1	0.37	2		457	683	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5215356	5215356	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1420232605	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	43	420	1	ENST00000357368.4:c.4262G>A	p.Arg1421His	p.R1421H	ENST00000357368	NM_002850.3	1421	cGc/cAc	28/38	0.213959579355727	0	FACETS	0.299	0.25	0.353			1	INDETERMINATE	1	TRUE	0	0.37	0		421	490	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341142	8341142	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	94	541	2	ENST00000356435.5:c.5074C>T	p.Arg1692Cys	p.R1692C	ENST00000356435		1692	Cgt/Tgt	30/35	1	2	FACETS	0.779	0.694	0.87	0.779	0.694	0.87	SUBCLONAL	1	TRUE	1	0.37	2		543	652	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41275291	41275291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750554859	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	131	338	0	ENST00000349496.5:c.1457G>A	p.Arg486His	p.R486H	ENST00000349496	NM_001904.3	486	cGc/cAc	9/15	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.37	2		338	673	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128201212	128201212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs374025668	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	105	594	0	ENST00000265960.3:c.1523G>A	p.Arg508His	p.R508H	ENST00000265960	NM_001006617.1	508	cGt/cAt	12/12	1	2	FACETS	0.744	0.666	0.826	0.744	0.666	0.826	SUBCLONAL	1	TRUE	1	0.37	2		594	763	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66774133	66774133	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	130	790	1	ENST00000307102.5:c.609G>T	p.Glu203Asp	p.E203D	ENST00000307102	NM_002755.3	203	gaG/gaT	6/11	1	2	FACETS	0.633	0.573	0.697	0.633	0.573	0.697	SUBCLONAL	1	TRUE	1	0.37	2		791	1110	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681073	117681073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	135	614	0	ENST00000368508.3:c.3547G>A	p.Val1183Ile	p.V1183I	ENST00000368508	NM_002944.2	1183	Gtt/Att	23/43	1	2	FACETS	0.824	0.748	0.903	0.824	0.748	0.903	CLONAL	1	TRUE	1	0.37	2		614	886	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874167	155874167	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	163	656	1	ENST00000368323.3:c.364C>T	p.Arg122Ter	p.R122*	ENST00000368323	NM_006912.5	122	Cga/Tga	5/6	1	2	FACETS	0.743	0.68	0.809	0.743	0.68	0.809	SUBCLONAL	1	TRUE	1	0.37	2		657	1186	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2489172	2489172	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	130	540	0	ENST00000355716.4:c.77A>T	p.Tyr26Phe	p.Y26F	ENST00000355716	NM_003820.2	26	tAt/tTt	2/8	0.3	1	FACETS	0.792	0.719	0.868	0.792	0.719	0.868	SUBCLONAL	1	TRUE	0	0.37	1		540	723	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9777122	9777122	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	165	810	1	ENST00000377346.4:c.886G>T	p.Val296Phe	p.V296F	ENST00000377346	NM_005026.3	296	Gtc/Ttc	7/24	0.3	1	FACETS	0.711	0.652	0.773	0.711	0.652	0.773	SUBCLONAL	1	TRUE	0	0.37	1		811	1022	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784394	9784394	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	187	738	1	ENST00000377346.4:c.2779C>A	p.Arg927Ser	p.R927S	ENST00000377346	NM_005026.3	927	Cgc/Agc	22/24	0.3	1	FACETS	0.825	0.761	0.89	0.825	0.761	0.89	CLONAL	1	TRUE	0	0.37	1		739	999	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784442	9784442	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	647	134	558	0	ENST00000377346.4:c.2827C>T	p.Gln943Ter	p.Q943*	ENST00000377346	NM_005026.3	943	Cag/Tag	22/24	0.3	1	FACETS	0.756	0.687	0.828	0.756	0.687	0.828	SUBCLONAL	1	TRUE	0	0.37	1		558	781	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11184646	11184646	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	122	374	1	ENST00000361445.4:c.6571G>T	p.Asp2191Tyr	p.D2191Y	ENST00000361445	NM_004958.3	2191	Gat/Tat	47/58	0.3	1	FACETS	0.797	0.722	0.877	0.797	0.722	0.877	SUBCLONAL	1	TRUE	0	0.37	1		375	674	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11205060	11205060	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1271789662	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	176	597	1	ENST00000361445.4:c.4729G>A	p.Ala1577Thr	p.A1577T	ENST00000361445	NM_004958.3	1577	Gcg/Acg	33/58	0.3	1	FACETS	0.898	0.828	0.971	0.898	0.828	0.971	CLONAL	1	TRUE	0	0.37	1		598	863	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11272940	11272940	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	117	417	1	ENST00000361445.4:c.3311G>T	p.Gly1104Val	p.G1104V	ENST00000361445	NM_004958.3	1104	gGc/gTc	22/58	0.3	1	FACETS	0.833	0.753	0.917	0.833	0.753	0.917	CLONAL	1	TRUE	0	0.37	1		418	619	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16246014	16246014	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	74	241	0	ENST00000375759.3:c.1635+2T>C		p.X545_splice	ENST00000375759	NM_015001.2	545			0.3	3	FACETS	1	0.913	1			1	CLONAL	1	TRUE	NA	0.37	3		241	452	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16255263	16255263	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	163	563	0	ENST00000375759.3:c.2528A>T	p.Glu843Val	p.E843V	ENST00000375759	NM_015001.2	843	gAg/gTg	11/15	0.3	3	FACETS	1	0.945	1			1	CLONAL	1	TRUE	NA	0.37	3		563	1005	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259024	16259024	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	124	461	0	ENST00000375759.3:c.6289G>T	p.Asp2097Tyr	p.D2097Y	ENST00000375759	NM_015001.2	2097	Gat/Tat	11/15	0.3	3	FACETS	1	0.962	1			1	CLONAL	1	TRUE	NA	0.37	3		461	708	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259489	16259489	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	72	420	0	ENST00000375759.3:c.6754G>T	p.Gly2252Cys	p.G2252C	ENST00000375759	NM_015001.2	2252	Ggt/Tgt	11/15	0.3	3	FACETS	0.761	0.665	0.864			1	SUBCLONAL	1	TRUE	NA	0.37	3		420	606	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260789	16260789	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	104	392	0	ENST00000375759.3:c.8054C>G	p.Thr2685Ser	p.T2685S	ENST00000375759	NM_015001.2	2685	aCc/aGc	11/15	0.3	3	FACETS	1	0.937	1			1	CLONAL	1	TRUE	NA	0.37	3		392	627	SUCCESS
CDC42	998	MSKCC	GRCh37	1	22405042	22405042	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	88	271	0	ENST00000344548.3:c.71C>A	p.Thr24Lys	p.T24K	ENST00000344548	NM_001039802.1	24	aCa/aAa	3/7	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.37	2		271	394	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106104	27106104	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	125	485	0	ENST00000324856.7:c.5715A>T	p.Lys1905Asn	p.K1905N	ENST00000324856	NM_006015.4	1905	aaA/aaT	20/20	1	2	FACETS	0.979	0.888	1	0.979	0.888	1	CLONAL	1	TRUE	1	0.37	2		485	690	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40366705	40366705	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	85	344	0	ENST00000397332.2:c.492C>A	p.Ser164Arg	p.S164R	ENST00000397332	NM_001033082.2	164	agC/agA	2/3	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.37	2		344	399	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248046	59248046	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	60	293	0	ENST00000371222.2:c.697C>T	p.Pro233Ser	p.P233S	ENST00000371222	NM_002228.3	233	Ccc/Tcc	1/1	1	2	FACETS	0.891	0.771	1	0.891	0.771	1	CLONAL	1	TRUE	1	0.37	2		293	364	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65300330	65300330	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	80	308	0	ENST00000342505.4:c.3380T>G	p.Leu1127Arg	p.L1127R	ENST00000342505	NM_002227.2	1127	cTt/cGt	25/25	1	2	FACETS	0.886	0.782	0.997	0.886	0.782	0.997	CLONAL	1	TRUE	1	0.37	2		308	488	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65309869	65309869	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	78	425	1	ENST00000342505.4:c.2281C>A	p.Pro761Thr	p.P761T	ENST00000342505	NM_002227.2	761	Cct/Act	17/25	1	2	FACETS	0.633	0.556	0.716	0.633	0.556	0.716	SUBCLONAL	1	TRUE	1	0.37	2		426	666	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65335069	65335069	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	630	64	413	1	ENST00000342505.4:c.572G>A	p.Gly191Glu	p.G191E	ENST00000342505	NM_002227.2	191	gGg/gAg	6/25	1	2	FACETS	0.498	0.431	0.572	0.498	0.431	0.572	SUBCLONAL	1	TRUE	1	0.37	2		414	694	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117690338	117690338	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	116	393	0	ENST00000369458.3:c.791C>T	p.Ser264Phe	p.S264F	ENST00000369458	NM_024626.3	264	tCt/tTt	5/6	1	2	FACETS	0.953	0.86	1	0.953	0.86	1	CLONAL	1	TRUE	1	0.37	2		393	658	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165686	118165686	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	79	248	0	ENST00000369448.3:c.196G>C	p.Val66Leu	p.V66L	ENST00000369448	NM_017709.3	66	Gtg/Ctg	2/2	1	2	FACETS	0.995	0.88	1	0.995	0.88	1	CLONAL	1	TRUE	1	0.37	2		248	429	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118166428	118166428	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	70	334	0	ENST00000369448.3:c.938T>C	p.Val313Ala	p.V313A	ENST00000369448	NM_017709.3	313	gTg/gCg	2/2	1	2	FACETS	0.735	0.642	0.835	0.735	0.642	0.835	SUBCLONAL	1	TRUE	1	0.37	2		334	515	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120462857	120462857	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	215	43	178	0	ENST00000256646.2:c.5474G>A	p.Gly1825Asp	p.G1825D	ENST00000256646	NM_024408.3	1825	gGc/gAc	30/34	1	2	FACETS	0.901	0.759	1	0.901	0.759	1	CLONAL	1	TRUE	1	0.37	2		178	258	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193181198	193181198	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	87	382	1	ENST00000367435.3:c.1034C>T	p.Ser345Phe	p.S345F	ENST00000367435	NM_024529.4	345	tCt/tTt	12/17	1	2	FACETS	0.826	0.733	0.926	0.826	0.733	0.926	CLONAL	1	TRUE	1	0.37	2		383	569	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201982429	201982429	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	168	583	0	ENST00000359651.3:c.805+3G>T		p.X269_splice	ENST00000359651		269			1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.37	2		583	785	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609087	43609087	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	121	711	1	ENST00000355710.3:c.1843G>A	p.Glu615Lys	p.E615K	ENST00000355710	NM_020975.4	615	Gag/Aag	10/20	1	2	FACETS	0.897	0.811	0.988	0.897	0.811	0.988	CLONAL	1	TRUE	1	0.37	2		712	729	SUCCESS
RET	5979	MSKCC	GRCh37	10	43609106	43609106	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	107	747	0	ENST00000355710.3:c.1862A>C	p.Glu621Ala	p.E621A	ENST00000355710	NM_020975.4	621	gAg/gCg	10/20	1	2	FACETS	0.725	0.65	0.804	0.725	0.65	0.804	SUBCLONAL	1	TRUE	1	0.37	2		747	798	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446129	70446129	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1333809107	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	60	412	2	ENST00000373644.4:c.5069G>A	p.Arg1690Gln	p.R1690Q	ENST00000373644	NM_030625.2	1690	cGa/cAa	11/12	1	2	FACETS	0.707	0.61	0.811	0.707	0.61	0.811	SUBCLONAL	1	TRUE	1	0.37	2		414	459	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451141	70451141	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	123	558	0	ENST00000373644.4:c.5981G>A	p.Trp1994Ter	p.W1994*	ENST00000373644	NM_030625.2	1994	tGg/tAg	12/12	1	2	FACETS	0.87	0.787	0.958	0.87	0.787	0.958	CLONAL	1	TRUE	1	0.37	2		558	764	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70451516	70451516	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	174	618	1	ENST00000373644.4:c.6356C>T	p.Thr2119Ile	p.T2119I	ENST00000373644	NM_030625.2	2119	aCc/aTc	12/12	1	2	FACETS	0.898	0.826	0.974	0.898	0.826	0.974	CLONAL	1	TRUE	1	0.37	2		619	1047	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88672125	88672125	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	136	584	0	ENST00000372037.3:c.659C>A	p.Ser220Tyr	p.S220Y	ENST00000372037	NM_004329.2	220	tCt/tAt	8/13	1	2	FACETS	1	0.931	1	1	0.931	1	CLONAL	1	TRUE	1	0.37	2		584	717	SUCCESS
BMPR1A	657	MSKCC	GRCh37	10	88681276	88681276	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	115	435	0	ENST00000372037.3:c.1167-1G>C		p.X389_splice	ENST00000372037	NM_004329.2	389			1	2	FACETS	0.913	0.823	1	0.913	0.823	1	CLONAL	1	TRUE	1	0.37	2		435	681	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720839	89720839	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	136	436	0	ENST00000371953.3:c.990A>T	p.Lys330Asn	p.K330N	ENST00000371953	NM_000314.4	330	aaA/aaT	8/9	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.37	2		436	705	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64575511	64575511	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	123	545	1	ENST00000312049.6:c.506G>C	p.Gly169Ala	p.G169A	ENST00000312049	NM_130799.2	169	gGt/gCt	3/10	1	2	FACETS	0.815	0.737	0.897	0.815	0.737	0.897	CLONAL	1	TRUE	1	0.37	2		546	816	SUCCESS
FGF4	2249	MSKCC	GRCh37	11	69589750	69589750	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	26	79	0	ENST00000168712.1:c.103C>G	p.Pro35Ala	p.P35A	ENST00000168712	NM_002007.2	35	Ccc/Gcc	1/3	1	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	1	TRUE	1	0.37	2		79	111	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943958	71943958	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	151	697	0	ENST00000298229.2:c.1891C>T	p.Leu631Phe	p.L631F	ENST00000298229	NM_001567.3	631	Ctc/Ttc	16/28	1	2	FACETS	0.951	0.87	1	0.951	0.87	1	CLONAL	1	TRUE	1	0.37	2		697	858	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71943962	71943962	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	153	688	1	ENST00000298229.2:c.1895T>A	p.Leu632His	p.L632H	ENST00000298229	NM_001567.3	632	cTc/cAc	16/28	1	2	FACETS	0.981	0.898	1	0.981	0.898	1	CLONAL	1	TRUE	1	0.37	2		689	843	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77091039	77091039	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	74	303	0	ENST00000356341.3:c.191C>G	p.Thr64Arg	p.T64R	ENST00000356341	NM_002576.4	64	aCa/aGa	3/15	1	2	FACETS	0.928	0.816	1	0.928	0.816	1	CLONAL	1	TRUE	1	0.37	2		303	431	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989443	85989443	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	57	300	0	ENST00000263360.6:c.1202G>T	p.Cys401Phe	p.C401F	ENST00000263360	NM_003797.3	401	tGt/tTt	12/12	1	2	FACETS	0.68	0.585	0.784	0.68	0.585	0.784	SUBCLONAL	1	TRUE	1	0.37	2		300	453	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94204874	94204874	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	78	393	2	ENST00000323929.3:c.711C>A	p.Phe237Leu	p.F237L	ENST00000323929	NM_005591.3	237	ttC/ttA	8/20	1	2	FACETS	0.737	0.648	0.832	0.737	0.648	0.832	SUBCLONAL	1	TRUE	1	0.37	2		395	572	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998456	100998456	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs369471546	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	83	423	0	ENST00000325455.5:c.1346C>A	p.Ser449Ter	p.S449*	ENST00000325455	NM_001202474.3	449	tCg/tAg	1/8	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.37	2		423	396	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998903	100998903	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	92	543	0	ENST00000325455.5:c.899T>A	p.Val300Glu	p.V300E	ENST00000325455	NM_001202474.3	300	gTg/gAg	1/8	1	2	FACETS	0.991	0.883	1	0.991	0.883	1	CLONAL	1	TRUE	1	0.37	2		543	502	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102206781	102206781	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	142	556	0	ENST00000263464.3:c.1409C>G	p.Thr470Ser	p.T470S	ENST00000263464	NM_001165.4	470	aCt/aGt	7/9	1	2	FACETS	0.827	0.753	0.905	0.827	0.753	0.905	CLONAL	1	TRUE	1	0.37	2		556	928	SUCCESS
ATM	472	MSKCC	GRCh37	11	108114793	108114793	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147915571	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	137	556	1	ENST00000278616.4:c.610G>A	p.Gly204Arg	p.G204R	ENST00000278616	NM_000051.3	204	Gga/Aga	6/63	1	2	FACETS	0.851	0.774	0.932	0.851	0.774	0.932	CLONAL	1	TRUE	1	0.37	2		557	870	SUCCESS
ATM	472	MSKCC	GRCh37	11	108192126	108192126	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	117	517	2	ENST00000278616.4:c.6551G>A	p.Ser2184Asn	p.S2184N	ENST00000278616	NM_000051.3	2184	aGc/aAc	45/63	1	2	FACETS	0.848	0.765	0.935	0.848	0.765	0.935	CLONAL	1	TRUE	1	0.37	2		519	746	SUCCESS
ATM	472	MSKCC	GRCh37	11	108203625	108203625	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	274	39	180	0	ENST00000278616.4:c.7925G>A	p.Arg2642Lys	p.R2642K	ENST00000278616	NM_000051.3	2642	aGa/aAa	53/63	1	2	FACETS	0.674	0.56	0.799	0.674	0.56	0.799	SUBCLONAL	1	TRUE	1	0.37	2		180	313	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118307396	118307396	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1244598071	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	19	13	25	0	ENST00000534358.1:c.169C>T	p.Pro57Ser	p.P57S	ENST00000534358	NM_005933.3	57	Ccc/Tcc	1/36	1	2	FACETS	1	0.816	1	1	0.924	1	CLONAL	2	TRUE	1	0.37	2		25	32	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118352612	118352612	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	144	567	0	ENST00000534358.1:c.3817G>T	p.Glu1273Ter	p.E1273*	ENST00000534358	NM_005933.3	1273	Gaa/Taa	7/36	1	2	FACETS	0.915	0.834	0.999	0.915	0.834	0.999	CLONAL	1	TRUE	1	0.37	2		567	851	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373119	118373119	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	80	287	0	ENST00000534358.1:c.6512C>A	p.Pro2171His	p.P2171H	ENST00000534358	NM_005933.3	2171	cCt/cAt	27/36	1	2	FACETS	0.932	0.823	1	0.932	0.823	1	CLONAL	1	TRUE	1	0.37	2		287	464	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	402193	402193	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	182	675	1	ENST00000399788.2:c.4598C>A	p.Pro1533His	p.P1533H	ENST00000399788	NM_001042603.1	1533	cCt/cAt	27/28	0.3	2	FACETS	0.984	0.907	1			1	CLONAL	1	TRUE	NA	0.37	2		676	1000	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	406356	406356	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	139	561	0	ENST00000399788.2:c.4085G>C	p.Ser1362Thr	p.S1362T	ENST00000399788	NM_001042603.1	1362	aGt/aCt	25/28	0.3	2	FACETS	0.967	0.881	1			1	CLONAL	1	TRUE	NA	0.37	2		561	777	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442721	442721	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	668	125	531	1	ENST00000399788.2:c.1585C>T	p.Gln529Ter	p.Q529*	ENST00000399788	NM_001042603.1	529	Cag/Tag	12/28	0.3	2	FACETS	0.852	0.771	0.937			1	CLONAL	1	TRUE	NA	0.37	2		532	793	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	459888	459888	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	183	797	0	ENST00000399788.2:c.1207G>C	p.Glu403Gln	p.E403Q	ENST00000399788	NM_001042603.1	403	Gaa/Caa	10/28	0.3	2	FACETS	0.914	0.843	0.989			1	CLONAL	1	TRUE	NA	0.37	2		797	1082	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12870962	12870962	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	75	299	0	ENST00000228872.4:c.189T>A	p.Asp63Glu	p.D63E	ENST00000228872	NM_004064.3	63	gaT/gaA	1/3	0.130923951212186	3	FACETS	0.763	0.668	0.864	0.381	0.334	0.432	INDETERMINATE	1	TRUE	1	0.37	3		299	630	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18439787	18439787	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs867581120	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	75	373	0	ENST00000266497.5:c.685G>T	p.Gly229Cys	p.G229C	ENST00000266497		229	Ggt/Tgt	2/31	0.130923951212186	3	FACETS	0.825	0.724	0.934	0.413	0.362	0.467	INDETERMINATE	1	TRUE	1	0.37	3		373	582	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18478024	18478024	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	144	636	0	ENST00000266497.5:c.1264A>T	p.Lys422Ter	p.K422*	ENST00000266497		422	Aaa/Taa	7/31	0.3	1	FACETS	0.678	0.618	0.741	0.678	0.618	0.741	SUBCLONAL	1	TRUE	0	0.37	1		636	936	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800935	18800935	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	70	481	0	ENST00000266497.5:c.4311G>C	p.Trp1437Cys	p.W1437C	ENST00000266497		1437	tgG/tgC	31/31	0.3	1	FACETS	0.542	0.473	0.617	0.542	0.473	0.617	SUBCLONAL	1	TRUE	0	0.37	1		481	569	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49424212	49424212	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	45	149	0	ENST00000301067.7:c.13850G>T	p.Ser4617Ile	p.S4617I	ENST00000301067	NM_003482.3	4617	aGt/aTt	42/54	0.165807479755987	3	FACETS	1	0.913	1	0.559	0.473	0.652	INDETERMINATE	1	TRUE	1	0.37	3		149	258	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431434	49431434	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	139	568	0	ENST00000301067.7:c.9705G>T	p.Lys3235Asn	p.K3235N	ENST00000301067	NM_003482.3	3235	aaG/aaT	34/54	0.165807479755987	3	FACETS	1	0.963	1	0.554	0.505	0.606	INDETERMINATE	1	TRUE	1	0.37	3		568	803	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433051	49433051	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs779166504	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	133	535	0	ENST00000301067.7:c.8320C>T	p.Arg2774Trp	p.R2774W	ENST00000301067	NM_003482.3	2774	Cgg/Tgg	33/54	0.165807479755987	3	FACETS	1	0.957	1	0.545	0.495	0.598	INDETERMINATE	1	TRUE	1	0.37	3		535	781	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49437498	49437498	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	94	513	0	ENST00000301067.7:c.5387G>T	p.Arg1796Leu	p.R1796L	ENST00000301067	NM_003482.3	1796	cGg/cTg	23/54	0.165807479755987	3	FACETS	0.683	0.606	0.764	0.341	0.303	0.382	INDETERMINATE	1	TRUE	1	0.37	3		513	882	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444138	49444138	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	128	648	1	ENST00000301067.7:c.3233T>A	p.Val1078Asp	p.V1078D	ENST00000301067	NM_003482.3	1078	gTt/gAt	11/54	0.165807479755987	3	FACETS	1	0.928	1	0.514	0.466	0.564	INDETERMINATE	1	TRUE	1	0.37	3		649	798	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56490901	56490901	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	142	498	1	ENST00000267101.3:c.2347C>A	p.Leu783Met	p.L783M	ENST00000267101	NM_001982.3	783	Ctg/Atg	20/28	0.165807479755987	3	FACETS	1	0.962	1	0.55	0.501	0.601	INDETERMINATE	1	TRUE	1	0.37	3		499	827	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57861928	57861928	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	105	412	0	ENST00000228682.2:c.1229C>A	p.Ser410Tyr	p.S410Y	ENST00000228682	NM_005269.2	410	tCt/tAt	10/12	0.165807479755987	3	FACETS	1	0.937	1	0.53	0.476	0.588	INDETERMINATE	1	TRUE	1	0.37	3		412	634	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112884105	112884105	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	527	71	440	0	ENST00000351677.2:c.40G>A	p.Val14Met	p.V14M	ENST00000351677	NM_002834.3	14	Gtg/Atg	2/16	1	2	FACETS	0.642	0.56	0.73	0.642	0.56	0.73	SUBCLONAL	1	TRUE	1	0.37	2		440	598	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112611	115112611	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs780968472	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	174	839	0	ENST00000257566.3:c.1129G>A	p.Ala377Thr	p.A377T	ENST00000257566	NM_016569.3	377	Gcc/Acc	7/8	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.37	2		839	889	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115112629	115112629	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	212	894	0	ENST00000257566.3:c.1111A>T	p.Ser371Cys	p.S371C	ENST00000257566	NM_016569.3	371	Agc/Tgc	7/8	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.37	2		894	933	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120783963	120783963	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	119	542	0	ENST00000257552.2:c.1022G>T	p.Ser341Ile	p.S341I	ENST00000257552	NM_002442.3	341	aGc/aTc	13/15	1	2	FACETS	0.953	0.862	1	0.953	0.862	1	CLONAL	1	TRUE	1	0.37	2		542	675	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120783993	120783993	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	108	636	0	ENST00000257552.2:c.992G>A	p.Ser331Asn	p.S331N	ENST00000257552	NM_002442.3	331	aGt/aAt	13/15	1	2	FACETS	0.723	0.649	0.802	0.723	0.649	0.802	SUBCLONAL	1	TRUE	1	0.37	2		636	807	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121431456	121431456	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	122	550	0	ENST00000257555.6:c.660G>C	p.Arg220Ser	p.R220S	ENST00000257555		220	agG/agC	3/10	1	2	FACETS	0.873	0.79	0.961	0.873	0.79	0.961	CLONAL	1	TRUE	1	0.37	2		550	755	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432004	121432004	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	132	691	0	ENST00000257555.6:c.751G>A	p.Ala251Thr	p.A251T	ENST00000257555		251	Gca/Aca	4/10	1	2	FACETS	0.855	0.776	0.937	0.855	0.776	0.937	CLONAL	1	TRUE	1	0.37	2		691	835	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249311	133249311	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	165	676	0	ENST00000320574.5:c.1588G>T	p.Asp530Tyr	p.D530Y	ENST00000320574	NM_006231.2	530	Gac/Tac	15/49	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.37	2		676	876	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21562946	21562946	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	95	523	0	ENST00000382592.4:c.973G>C	p.Ala325Pro	p.A325P	ENST00000382592	NM_014572.2	325	Gcc/Ccc	4/8	1	2	FACETS	0.939	0.838	1	0.939	0.838	1	CLONAL	1	TRUE	1	0.37	2		523	547	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21565438	21565438	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	104	572	0	ENST00000382592.4:c.448G>C	p.Val150Leu	p.V150L	ENST00000382592	NM_014572.2	150	Gtg/Ctg	3/8	1	2	FACETS	0.834	0.748	0.926	0.834	0.748	0.926	CLONAL	1	TRUE	1	0.37	2		572	674	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26967644	26967644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	99	429	0	ENST00000381527.3:c.787G>A	p.Ala263Thr	p.A263T	ENST00000381527	NM_001260.1	263	Gca/Aca	7/13	1	2	FACETS	0.947	0.848	1	0.947	0.848	1	CLONAL	1	TRUE	1	0.37	2		429	565	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28886206	28886206	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	98	560	0	ENST00000282397.4:c.3416G>T	p.Arg1139Ile	p.R1139I	ENST00000282397	NM_002019.4	1139	aGa/aTa	26/30	1	2	FACETS	0.768	0.685	0.855	0.768	0.685	0.855	SUBCLONAL	1	TRUE	1	0.37	2		560	690	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32890607	32890607	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs397507571	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	635	115	433	2	ENST00000380152.3:c.10G>T	p.Gly4Ter	p.G4*	ENST00000380152		4	Gga/Tga	2/27	1	2	FACETS	0.829	0.747	0.915	0.829	0.747	0.915	CLONAL	1	TRUE	1	0.37	2		435	750	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906773	32906773	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	148	756	0	ENST00000380152.3:c.1158A>T	p.Glu386Asp	p.E386D	ENST00000380152		386	gaA/gaT	10/27	1	2	FACETS	0.716	0.653	0.783	0.716	0.653	0.783	SUBCLONAL	1	TRUE	1	0.37	2		756	1117	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911439	32911439	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs587781848	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	86	494	1	ENST00000380152.3:c.2947C>A	p.Pro983Thr	p.P983T	ENST00000380152		983	Cca/Aca	11/27	1	2	FACETS	0.646	0.571	0.726	0.646	0.571	0.726	SUBCLONAL	1	TRUE	1	0.37	2		495	720	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32911646	32911646	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881520	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	85	451	1	ENST00000380152.3:c.3154G>A	p.Ala1052Thr	p.A1052T	ENST00000380152		1052	Gca/Aca	11/27	1	2	FACETS	0.689	0.609	0.774	0.689	0.609	0.774	SUBCLONAL	1	TRUE	1	0.37	2		452	667	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914347	32914347	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	rs375064902	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	99	442	0	ENST00000380152.3:c.5855T>A	p.Leu1952Ter	p.L1952*	ENST00000380152		1952	tTg/tAg	11/27	1	2	FACETS	0.796	0.711	0.886	0.796	0.711	0.886	SUBCLONAL	1	TRUE	1	0.37	2		442	672	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32929183	32929183	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	175	703	0	ENST00000380152.3:c.7193C>A	p.Thr2398Asn	p.T2398N	ENST00000380152		2398	aCt/aAt	14/27	1	2	FACETS	0.86	0.791	0.932	0.86	0.791	0.932	CLONAL	1	TRUE	1	0.37	2		703	1100	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32945215	32945215	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	124	559	0	ENST00000380152.3:c.8610G>T	p.Gln2870His	p.Q2870H	ENST00000380152		2870	caG/caT	20/27	1	2	FACETS	0.82	0.742	0.903	0.82	0.742	0.903	CLONAL	1	TRUE	1	0.37	2		559	817	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32971182	32971182	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs730881573	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	108	516	0	ENST00000380152.3:c.9648+1G>A		p.X3216_splice	ENST00000380152		3216			1	2	FACETS	0.811	0.728	0.898	0.811	0.728	0.898	CLONAL	1	TRUE	1	0.37	2		516	720	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134339	41134339	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	66	304	0	ENST00000379561.5:c.1289G>T	p.Ser430Ile	p.S430I	ENST00000379561	NM_002015.3	430	aGc/aTc	2/3	1	2	FACETS	0.74	0.644	0.844	0.74	0.644	0.844	SUBCLONAL	1	TRUE	1	0.37	2		304	482	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134405	41134405	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772929365	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	79	370	0	ENST00000379561.5:c.1223C>T	p.Ala408Val	p.A408V	ENST00000379561	NM_002015.3	408	gCg/gTg	2/3	1	2	FACETS	0.741	0.653	0.836	0.741	0.653	0.836	SUBCLONAL	1	TRUE	1	0.37	2		370	576	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281926	49281926	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	147	649	0	ENST00000282018.3:c.973C>A	p.Pro325Thr	p.P325T	ENST00000282018	NM_020377.2	325	Cca/Aca	1/1	1	2	FACETS	0.82	0.748	0.896	0.82	0.748	0.896	CLONAL	1	TRUE	1	0.37	2		649	969	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514380	103514380	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	53	214	0	ENST00000355739.4:c.881G>C	p.Gly294Ala	p.G294A	ENST00000355739	NM_000123.3	294	gGt/gCt	8/15	1	2	FACETS	0.978	0.84	1	0.978	0.84	1	CLONAL	1	TRUE	1	0.37	2		214	293	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514691	103514691	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	91	356	0	ENST00000355739.4:c.1192G>T	p.Asp398Tyr	p.D398Y	ENST00000355739	NM_000123.3	398	Gac/Tac	8/15	1	2	FACETS	0.933	0.831	1	0.933	0.831	1	CLONAL	1	TRUE	1	0.37	2		356	527	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435622	110435622	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	61	556	0	ENST00000375856.3:c.2779C>T	p.Pro927Ser	p.P927S	ENST00000375856	NM_003749.2	927	Ccc/Tcc	1/2	0.3	2	FACETS	0.534	0.461	0.615			1	SUBCLONAL	1	TRUE	NA	0.37	2		556	617	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061185	38061185	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1449268552	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	245	84	307	1	ENST00000250448.2:c.804C>A	p.Cys268Ter	p.C268*	ENST00000250448	NM_004496.3	268	tgC/tgA	2/2	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.37	2		308	329	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061616	38061616	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	92	28	154	0	ENST00000250448.2:c.373A>T	p.Asn125Tyr	p.N125Y	ENST00000250448	NM_004496.3	125	Aat/Tat	2/2	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.37	2		154	120	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68352614	68352614	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	111	420	0	ENST00000487270.1:c.481C>T	p.Pro161Ser	p.P161S	ENST00000487270	NM_133509.3	161	Ccc/Tcc	6/11	1	2	FACETS	0.801	0.72	0.887	0.801	0.72	0.887	CLONAL	1	TRUE	1	0.37	2		420	749	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81554299	81554299	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	134	582	0	ENST00000298171.2:c.319G>A	p.Glu107Lys	p.E107K	ENST00000298171	NM_000369.2	107	Gaa/Aaa	4/10	1	2	FACETS	0.962	0.875	1	0.962	0.875	1	CLONAL	1	TRUE	1	0.37	2		582	753	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81574766	81574766	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	123	463	0	ENST00000298171.2:c.662T>G	p.Phe221Cys	p.F221C	ENST00000298171	NM_000369.2	221	tTt/tGt	8/10	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.37	2		463	634	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95571537	95571537	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	73	437	0	ENST00000393063.1:c.3140T>G	p.Leu1047Arg	p.L1047R	ENST00000393063	NM_030621.3	1047	cTg/cGg	21/28	1	2	FACETS	0.646	0.565	0.733	0.646	0.565	0.733	SUBCLONAL	1	TRUE	1	0.37	2		437	611	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675119	40675119	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	135	721	1	ENST00000249776.8:c.83C>A	p.Pro28Gln	p.P28Q	ENST00000249776	NM_033286.3	28	cCg/cAg	1/9	1	2	FACETS	0.674	0.611	0.74	0.674	0.611	0.74	SUBCLONAL	1	TRUE	1	0.37	2		722	1083	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40993383	40993383	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	83	369	0	ENST00000267868.3:c.209A>T	p.Lys70Ile	p.K70I	ENST00000267868	NM_002875.4	70	aAa/aTa	3/10	1	2	FACETS	0.728	0.643	0.819	0.728	0.643	0.819	SUBCLONAL	1	TRUE	1	0.37	2		369	616	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41962157	41962157	+	splice_donor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	43	250	0	ENST00000219905.7:c.1064+1G>C		p.X355_splice	ENST00000219905	NM_001164273.1	355			1	2	FACETS	0.646	0.542	0.76	0.646	0.542	0.76	SUBCLONAL	1	TRUE	1	0.37	2		250	360	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42005557	42005557	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs774416143	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	119	547	0	ENST00000219905.7:c.3293A>G	p.His1098Arg	p.H1098R	ENST00000219905	NM_001164273.1	1098	cAt/cGt	9/24	1	2	FACETS	0.76	0.686	0.839	0.76	0.686	0.839	SUBCLONAL	1	TRUE	1	0.37	2		547	846	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42034999	42034999	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	143	557	0	ENST00000219905.7:c.4841C>A	p.Pro1614His	p.P1614H	ENST00000219905	NM_001164273.1	1614	cCt/cAt	15/24	1	2	FACETS	0.833	0.759	0.911	0.833	0.759	0.911	CLONAL	1	TRUE	1	0.37	2		557	928	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42042175	42042175	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	143	682	1	ENST00000219905.7:c.6370G>T	p.Glu2124Ter	p.E2124*	ENST00000219905	NM_001164273.1	2124	Gaa/Taa	17/24	1	2	FACETS	0.869	0.792	0.95	0.869	0.792	0.95	CLONAL	1	TRUE	1	0.37	2		683	889	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42057152	42057152	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	178	616	1	ENST00000219905.7:c.7813C>A	p.Leu2605Ile	p.L2605I	ENST00000219905	NM_001164273.1	2605	Ctc/Atc	23/24	1	2	FACETS	0.935	0.861	1	0.935	0.861	1	CLONAL	1	TRUE	1	0.37	2		617	1029	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058491	42058491	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	73	473	0	ENST00000219905.7:c.8211G>T	p.Gln2737His	p.Q2737H	ENST00000219905	NM_001164273.1	2737	caG/caT	24/24	1	2	FACETS	0.555	0.485	0.631	0.555	0.485	0.631	SUBCLONAL	1	TRUE	1	0.37	2		473	711	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43713327	43713327	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs199673175	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	994	198	880	0	ENST00000382044.4:c.4146G>T	p.Glu1382Asp	p.E1382D	ENST00000382044	NM_001141980.1	1382	gaG/gaT	20/28	1	2	FACETS	0.898	0.83	0.968	0.898	0.83	0.968	CLONAL	1	TRUE	1	0.37	2		880	1192	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43784526	43784526	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	174	534	2	ENST00000382044.4:c.148C>T	p.Arg50Ter	p.R50*	ENST00000382044	NM_001141980.1	50	Cga/Tga	2/28	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.37	2		536	923	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007758	45007758	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	76	340	0	ENST00000558401.1:c.205G>C	p.Val69Leu	p.V69L	ENST00000558401	NM_004048.2	69	Gtg/Ctg	2/4	1	2	FACETS	0.564	0.494	0.64	0.564	0.494	0.64	SUBCLONAL	1	TRUE	1	0.37	2		340	728	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996138	73996138	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	172	750	0	ENST00000318443.5:c.872A>C	p.Lys291Thr	p.K291T	ENST00000318443	NM_001024736.1	291	aAa/aCa	5/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.37	2		750	873	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88670449	88670449	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1460680404	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	58	370	0	ENST00000360948.2:c.1237G>A	p.Val413Met	p.V413M	ENST00000360948	NM_001012338.2	413	Gtg/Atg	11/19	1	2	FACETS	0.67	0.577	0.771	0.67	0.577	0.771	SUBCLONAL	1	TRUE	1	0.37	2		370	468	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680726	88680726	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	110	504	0	ENST00000360948.2:c.531G>T	p.Gln177His	p.Q177H	ENST00000360948	NM_001012338.2	177	caG/caT	6/19	1	2	FACETS	0.953	0.858	1	0.953	0.858	1	CLONAL	1	TRUE	1	0.37	2		504	624	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88727456	88727456	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	65	384	0	ENST00000360948.2:c.323T>G	p.Leu108Arg	p.L108R	ENST00000360948	NM_001012338.2	108	cTg/cGg	3/19	1	2	FACETS	0.729	0.633	0.832	0.729	0.633	0.832	SUBCLONAL	1	TRUE	1	0.37	2		384	482	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90631917	90631917	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	750	146	639	0	ENST00000330062.3:c.436A>T	p.Thr146Ser	p.T146S	ENST00000330062	NM_002168.2	146	Act/Tct	4/11	1	2	FACETS	0.881	0.804	0.962	0.881	0.804	0.962	CLONAL	1	TRUE	1	0.37	2		639	896	SUCCESS
BLM	641	MSKCC	GRCh37	15	91303937	91303937	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	122	553	1	ENST00000355112.3:c.1334C>T	p.Pro445Leu	p.P445L	ENST00000355112	NM_000057.2	445	cCt/cTt	7/22	1	2	FACETS	0.804	0.727	0.886	0.804	0.727	0.886	CLONAL	1	TRUE	1	0.37	2		554	820	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99482590	99482590	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	106	343	0	ENST00000268035.6:c.3457+1G>T		p.X1153_splice	ENST00000268035	NM_000875.3	1153			1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.37	2		343	537	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99491892	99491892	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1261830079	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	124	536	0	ENST00000268035.6:c.3677T>C	p.Met1226Thr	p.M1226T	ENST00000268035	NM_000875.3	1226	aTg/aCg	20/21	1	2	FACETS	0.903	0.818	0.993	0.903	0.818	0.993	CLONAL	1	TRUE	1	0.37	2		536	742	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	396746	396746	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	99	442	2	ENST00000262320.3:c.280G>A	p.Asp94Asn	p.D94N	ENST00000262320	NM_003502.3	94	Gat/Aat	2/11	0.3	2	FACETS	0.91	0.814	1			1	CLONAL	1	TRUE	NA	0.37	2		444	588	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2112592	2112592	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	76	496	0	ENST00000219476.3:c.1352G>T	p.Arg451Ile	p.R451I	ENST00000219476	NM_000548.3	451	aGa/aTa	13/42	0.3	2	FACETS	0.638	0.559	0.722			1	SUBCLONAL	1	TRUE	NA	0.37	2		496	644	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633323	3633323	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	144	580	2	ENST00000294008.3:c.4928C>T	p.Ala1643Val	p.A1643V	ENST00000294008	NM_032444.2	1643	gCc/gTc	14/15	1	2	FACETS	0.99	0.904	1	0.99	0.904	1	CLONAL	1	TRUE	1	0.37	2		582	786	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3650995	3650995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	89	277	1	ENST00000294008.3:c.1148G>A	p.Ser383Asn	p.S383N	ENST00000294008	NM_032444.2	383	aGc/aAc	5/15	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.37	2		278	464	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3786170	3786170	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	148	620	0	ENST00000262367.5:c.4595C>T	p.Thr1532Ile	p.T1532I	ENST00000262367	NM_004380.2	1532	aCc/aTc	28/31	1	2	FACETS	0.928	0.848	1	0.928	0.848	1	CLONAL	1	TRUE	1	0.37	2		620	862	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858514	9858514	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1395645259	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	78	470	0	ENST00000330684.3:c.2887C>T	p.Leu963Phe	p.L963F	ENST00000330684	NM_001134407.1	963	Ctc/Ttc	13/13	1	2	FACETS	0.848	0.747	0.956	0.848	0.747	0.956	CLONAL	1	TRUE	1	0.37	2		470	497	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9892199	9892199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	114	617	0	ENST00000330684.3:c.2291C>T	p.Ala764Val	p.A764V	ENST00000330684	NM_001134407.1	764	gCc/gTc	11/13	1	2	FACETS	0.898	0.81	0.992	0.898	0.81	0.992	CLONAL	1	TRUE	1	0.37	2		617	686	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9916271	9916271	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	354	71	370	0	ENST00000330684.3:c.2018C>A	p.Pro673His	p.P673H	ENST00000330684	NM_001134407.1	673	cCt/cAt	10/13	1	2	FACETS	0.903	0.791	1	0.903	0.791	1	CLONAL	1	TRUE	1	0.37	2		370	425	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943740	9943740	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	119	439	1	ENST00000330684.3:c.1201C>T	p.Pro401Ser	p.P401S	ENST00000330684	NM_001134407.1	401	Ccg/Tcg	5/13	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.37	2		440	608	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14026061	14026061	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	59	290	1	ENST00000311895.7:c.1021G>T	p.Ala341Ser	p.A341S	ENST00000311895	NM_005236.2	341	Gca/Tca	6/11	1	2	FACETS	0.72	0.621	0.827	0.72	0.621	0.827	SUBCLONAL	1	TRUE	1	0.37	2		291	443	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23641476	23641476	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	136	693	2	ENST00000261584.4:c.1999G>T	p.Glu667Ter	p.E667*	ENST00000261584	NM_024675.3	667	Gaa/Taa	5/13	1	2	FACETS	0.848	0.771	0.929	0.848	0.771	0.929	CLONAL	1	TRUE	1	0.37	2		695	867	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56868166	56868166	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	95	495	0	ENST00000308159.5:c.1664G>T	p.Arg555Met	p.R555M	ENST00000308159	NM_014669.4	555	aGg/aTg	14/22	1	2	FACETS	0.721	0.642	0.805	0.721	0.642	0.805	SUBCLONAL	1	TRUE	1	0.37	2		495	712	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67671731	67671731	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	119	388	1	ENST00000264010.4:c.2140G>T	p.Gly714Ter	p.G714*	ENST00000264010	NM_006565.3	714	Gga/Tga	12/12	1	2	FACETS	0.909	0.821	1	0.909	0.821	1	CLONAL	1	TRUE	1	0.37	2		389	708	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822584	72822584	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	71	280	1	ENST00000268489.5:c.9591G>T	p.Gln3197His	p.Q3197H	ENST00000268489	NM_006885.3	3197	caG/caT	10/10	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.37	2		281	338	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72827462	72827462	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs143909254	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	137	585	0	ENST00000268489.5:c.9119G>A	p.Arg3040His	p.R3040H	ENST00000268489	NM_006885.3	3040	cGt/cAt	9/10	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.37	2		585	730	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828360	72828360	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	102	388	0	ENST00000268489.5:c.8221G>C	p.Ala2741Pro	p.A2741P	ENST00000268489	NM_006885.3	2741	Gct/Cct	9/10	1	2	FACETS	1	0.91	1	1	0.91	1	CLONAL	1	TRUE	1	0.37	2		388	543	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828736	72828736	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	365	69	399	1	ENST00000268489.5:c.7845G>T	p.Lys2615Asn	p.K2615N	ENST00000268489	NM_006885.3	2615	aaG/aaT	9/10	1	2	FACETS	0.859	0.751	0.975	0.859	0.751	0.975	CLONAL	1	TRUE	1	0.37	2		400	434	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829368	72829368	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201280219	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	329	83	330	0	ENST00000268489.5:c.7213G>A	p.Ala2405Thr	p.A2405T	ENST00000268489	NM_006885.3	2405	Gct/Act	9/10	1	2	FACETS	1	0.939	1	1	0.939	1	CLONAL	1	TRUE	1	0.37	2		330	412	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81891936	81891936	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	149	545	0	ENST00000359376.3:c.406G>T	p.Ala136Ser	p.A136S	ENST00000359376	NM_002661.3	136	Gcg/Tcg	4/33	1	2	FACETS	0.951	0.869	1	0.951	0.869	1	CLONAL	1	TRUE	1	0.37	2		545	847	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944200	81944200	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	158	704	0	ENST00000359376.3:c.1809C>G	p.Asp603Glu	p.D603E	ENST00000359376	NM_002661.3	603	gaC/gaG	18/33	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.37	2		704	837	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944297	81944297	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	110	456	0	ENST00000359376.3:c.1906C>A	p.Pro636Thr	p.P636T	ENST00000359376	NM_002661.3	636	Ccc/Acc	18/33	1	2	FACETS	0.885	0.796	0.979	0.885	0.796	0.979	CLONAL	1	TRUE	1	0.37	2		456	672	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944315	81944315	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs367884906	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	91	419	0	ENST00000359376.3:c.1924G>A	p.Glu642Lys	p.E642K	ENST00000359376	NM_002661.3	642	Gag/Aag	18/33	1	2	FACETS	0.858	0.764	0.959	0.858	0.764	0.959	CLONAL	1	TRUE	1	0.37	2		419	573	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81979795	81979795	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	44	336	0	ENST00000359376.3:c.3497C>A	p.Pro1166His	p.P1166H	ENST00000359376	NM_002661.3	1166	cCt/cAt	31/33	1	2	FACETS	0.505	0.423	0.595	0.505	0.423	0.595	SUBCLONAL	1	TRUE	1	0.37	2		336	471	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89337240	89337240	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	123	489	0	ENST00000301030.4:c.7791G>T	p.Lys2597Asn	p.K2597N	ENST00000301030	NM_001256183.1	2597	aaG/aaT	12/13	1	2	FACETS	0.935	0.847	1	0.935	0.847	1	CLONAL	1	TRUE	1	0.37	2		489	711	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89346909	89346909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs773948438	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	12	110	1	ENST00000301030.4:c.6041C>T	p.Pro2014Leu	p.P2014L	ENST00000301030	NM_001256183.1	2014	cCg/cTg	9/13	1	2	FACETS	0.564	0.399	0.763	0.564	0.399	0.763	SUBCLONAL	1	TRUE	1	0.37	2		111	115	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349424	89349424	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	174	708	1	ENST00000301030.4:c.3526C>T	p.Gln1176Ter	p.Q1176*	ENST00000301030	NM_001256183.1	1176	Cag/Tag	9/13	1	2	FACETS	0.968	0.891	1	0.968	0.891	1	CLONAL	1	TRUE	1	0.37	2		709	972	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89811473	89811473	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	126	502	2	ENST00000389301.3:c.3520T>C	p.Trp1174Arg	p.W1174R	ENST00000389301	NM_000135.2	1174	Tgg/Cgg	36/43	1	2	FACETS	0.88	0.797	0.967	0.88	0.797	0.967	CLONAL	1	TRUE	1	0.37	2		504	774	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579360	7579360	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	174	603	0	ENST00000269305.4:c.327C>A	p.Phe109Leu	p.F109L	ENST00000269305	NM_001126112.2	109	ttC/ttA	4/11	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.37	2		603	873	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968237	15968237	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	81	291	0	ENST00000268712.3:c.5048G>C	p.Gly1683Ala	p.G1683A	ENST00000268712	NM_006311.3	1683	gGt/gCt	34/46	1	2	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	1	0.37	2		291	402	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509630	29509630	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	95	618	0	ENST00000356175.3:c.835G>T	p.Glu279Ter	p.E279*	ENST00000356175	NM_000267.3	279	Gaa/Taa	8/57	1	2	FACETS	0.59	0.525	0.66	0.59	0.525	0.66	SUBCLONAL	1	TRUE	1	0.37	2		618	870	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29562745	29562745	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	116	449	1	ENST00000356175.3:c.3825C>A	p.Phe1275Leu	p.F1275L	ENST00000356175	NM_000267.3	1275	ttC/ttA	28/57	1	2	FACETS	0.953	0.86	1	0.953	0.86	1	CLONAL	1	TRUE	1	0.37	2		450	658	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29670036	29670036	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	61	343	0	ENST00000356175.3:c.7009G>T	p.Glu2337Ter	p.E2337*	ENST00000356175	NM_000267.3	2337	Gaa/Taa	47/57	1	2	FACETS	0.687	0.594	0.788	0.687	0.594	0.788	SUBCLONAL	1	TRUE	1	0.37	2		343	480	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33446622	33446622	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	82	422	0	ENST00000345365.6:c.11T>A	p.Leu4His	p.L4H	ENST00000345365	NM_002878.3	4	cTc/cAc	1/10	1	2	FACETS	0.878	0.776	0.986	0.878	0.776	0.986	CLONAL	1	TRUE	1	0.37	2		422	505	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627445	37627445	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	193	714	0	ENST00000447079.4:c.1360G>A	p.Glu454Lys	p.E454K	ENST00000447079	NM_015083.1	454	Gaa/Aaa	2/14	1	2	FACETS	0.892	0.824	0.963	0.892	0.824	0.963	CLONAL	1	TRUE	1	0.37	2		714	1169	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37682543	37682543	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	102	436	0	ENST00000447079.4:c.3734C>A	p.Pro1245His	p.P1245H	ENST00000447079	NM_015083.1	1245	cCc/cAc	13/14	1	2	FACETS	0.881	0.789	0.978	0.881	0.789	0.978	CLONAL	1	TRUE	1	0.37	2		436	626	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40874858	40874858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	180	708	2	ENST00000428826.2:c.442G>A	p.Glu148Lys	p.E148K	ENST00000428826		148	Gag/Aag	6/21	1	2	FACETS	0.959	0.883	1	0.959	0.883	1	CLONAL	1	TRUE	1	0.37	2		710	1015	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41243890	41243890	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	146	571	0	ENST00000357654.3:c.3658G>A	p.Asp1220Asn	p.D1220N	ENST00000357654	NM_007294.3	1220	Gat/Aat	10/23	1	2	FACETS	0.92	0.84	1	0.92	0.84	1	CLONAL	1	TRUE	1	0.37	2		571	858	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55478811	55478811	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	135	474	1	ENST00000284073.2:c.384A>T	p.Gln128His	p.Q128H	ENST00000284073	NM_138962.2	128	caA/caT	6/14	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.37	2		475	672	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56438259	56438259	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	437	94	421	1	ENST00000407977.2:c.734C>A	p.Thr245Asn	p.T245N	ENST00000407977		245	aCc/aAc	7/10	1	2	FACETS	0.957	0.854	1	0.957	0.854	1	CLONAL	1	TRUE	1	0.37	2		422	531	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58678227	58678227	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	127	638	0	ENST00000305921.3:c.452T>A	p.Leu151His	p.L151H	ENST00000305921	NM_003620.3	151	cTt/cAt	1/6	1	2	FACETS	0.688	0.622	0.757	0.688	0.622	0.757	SUBCLONAL	1	TRUE	1	0.37	2		638	998	SUCCESS
PPM1D	8493	MSKCC	GRCh37	17	58734029	58734029	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	142	439	0	ENST00000305921.3:c.1087C>A	p.Leu363Ile	p.L363I	ENST00000305921	NM_003620.3	363	Ctc/Atc	5/6	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.37	2		439	748	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59761044	59761044	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	64	475	0	ENST00000259008.2:c.3363T>A	p.Phe1121Leu	p.F1121L	ENST00000259008	NM_032043.2	1121	ttT/ttA	20/20	1	2	FACETS	0.599	0.518	0.685	0.599	0.518	0.685	SUBCLONAL	1	TRUE	1	0.37	2		475	578	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59763377	59763377	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs587781853	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	126	628	0	ENST00000259008.2:c.2725C>G	p.Leu909Val	p.L909V	ENST00000259008	NM_032043.2	909	Ctt/Gtt	19/20	1	2	FACETS	0.83	0.751	0.912	0.83	0.751	0.912	CLONAL	1	TRUE	1	0.37	2		628	821	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59820420	59820420	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	115	520	0	ENST00000259008.2:c.2333C>T	p.Ala778Val	p.A778V	ENST00000259008	NM_032043.2	778	gCt/gTt	16/20	1	2	FACETS	0.821	0.74	0.907	0.821	0.74	0.907	CLONAL	1	TRUE	1	0.37	2		520	757	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66526498	66526498	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	115	398	0	ENST00000358598.2:c.1054C>T	p.Arg352Ter	p.R352*	ENST00000358598	NM_212471.2	352	Cga/Tga	11/11	1	2	FACETS	0.893	0.805	0.986	0.893	0.805	0.986	CLONAL	1	TRUE	1	0.37	2		398	696	SUCCESS
SOX9	6662	MSKCC	GRCh37	17	70117794	70117794	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	84	505	0	ENST00000245479.2:c.262C>G	p.Leu88Val	p.L88V	ENST00000245479	NM_000346.3	88	Ctg/Gtg	1/3	1	2	FACETS	0.912	0.808	1	0.912	0.808	1	CLONAL	1	TRUE	1	0.37	2		505	498	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78867515	78867515	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371707022	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	100	379	0	ENST00000306801.3:c.2251G>A	p.Ala751Thr	p.A751T	ENST00000306801	NM_020761.2	751	Gcg/Acg	20/34	1	2	FACETS	0.967	0.866	1	0.967	0.866	1	CLONAL	1	TRUE	1	0.37	2		379	559	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78896542	78896542	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	187	807	1	ENST00000306801.3:c.2539C>T	p.Pro847Ser	p.P847S	ENST00000306801	NM_020761.2	847	Ccg/Tcg	22/34	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.37	2		808	1004	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45372100	45372100	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	744	144	645	0	ENST00000262160.6:c.1069G>C	p.Val357Leu	p.V357L	ENST00000262160	NM_005901.5	357	Gtg/Ctg	9/11	1	2	FACETS	0.877	0.799	0.958	0.877	0.799	0.958	CLONAL	1	TRUE	1	0.37	2		645	888	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1206962	1206962	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	522	80	383	0	ENST00000326873.7:c.50T>G	p.Leu17Arg	p.L17R	ENST00000326873	NM_000455.4	17	cTg/cGg	1/10	0.3	2	FACETS	0.718	0.633	0.81			1	SUBCLONAL	1	TRUE	NA	0.37	2		383	602	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619151	1619151	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1469002739	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	136	511	2	ENST00000344749.5:c.1409G>A	p.Gly470Asp	p.G470D	ENST00000344749	NM_001136139.2	470	gGc/gAc	16/19	0.3	2	FACETS	0.933	0.849	1			1	CLONAL	1	TRUE	NA	0.37	2		513	788	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1619835	1619835	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	662	135	625	1	ENST00000344749.5:c.1111C>T	p.Arg371Ter	p.R371*	ENST00000344749	NM_001136139.2	371	Cga/Tga	14/19	0.3	2	FACETS	0.916	0.833	1			1	CLONAL	1	TRUE	NA	0.37	2		626	797	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2185859	2185859	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1016	186	736	0	ENST00000398665.3:c.131T>A	p.Val44Asp	p.V44D	ENST00000398665	NM_032482.2	44	gTc/gAc	3/28	0.3	2	FACETS	0.836	0.771	0.905			1	CLONAL	1	TRUE	NA	0.37	2		736	1202	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4123839	4123839	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	65	380	0	ENST00000262948.5:c.34C>G	p.Leu12Val	p.L12V	ENST00000262948	NM_030662.3	12	Ctc/Gtc	1/11	0.213959579355727	0	FACETS	0.504	0.438	0.575			1	INDETERMINATE	1	TRUE	0	0.37	0		380	439	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231329	5231329	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	272	83	383	0	ENST00000357368.4:c.2147A>C	p.Asp716Ala	p.D716A	ENST00000357368	NM_002850.3	716	gAc/gCc	14/38	0.213959579355727	0	FACETS	0.796	0.708	0.889			1	INDETERMINATE	1	TRUE	0	0.37	0		383	355	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5274259	5274259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs569886681	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	165	693	0	ENST00000357368.4:c.188G>A	p.Arg63Gln	p.R63Q	ENST00000357368	NM_002850.3	63	cGa/cAa	3/38	0.213959579355727	0	FACETS	0.705	0.648	0.764			1	INDETERMINATE	1	TRUE	0	0.37	0		693	797	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10246927	10246927	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	119	403	0	ENST00000340748.4:c.4478A>T	p.Asn1493Ile	p.N1493I	ENST00000340748		1493	aAc/aTc	37/40	1	2	FACETS	0.952	0.86	1	0.952	0.86	1	CLONAL	1	TRUE	1	0.37	2		403	676	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11097632	11097632	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	142	714	1	ENST00000358026.2:c.812G>A	p.Gly271Glu	p.G271E	ENST00000358026	NM_001128849.1	271	gGg/gAg	5/36	1	2	FACETS	0.923	0.841	1	0.923	0.841	1	CLONAL	1	TRUE	1	0.37	2		715	832	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11168930	11168930	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	rs766881255	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	50	355	0	ENST00000358026.2:c.4521-1G>A		p.X1507_splice	ENST00000358026	NM_001128849.1	1507			1	2	FACETS	0.676	0.575	0.786	0.676	0.575	0.786	SUBCLONAL	1	TRUE	1	0.37	2		355	400	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627434	14627434	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	162	682	0	ENST00000254322.2:c.636G>A	p.Trp212Ter	p.W212*	ENST00000254322	NM_006145.1	212	tgG/tgA	2/3	1	2	FACETS	0.809	0.741	0.88	0.809	0.741	0.88	CLONAL	1	TRUE	1	0.37	2		682	1083	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272332	15272332	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	125	750	1	ENST00000263388.2:c.6107C>A	p.Pro2036His	p.P2036H	ENST00000263388	NM_000435.2	2036	cCc/cAc	33/33	1	2	FACETS	0.856	0.775	0.942	0.856	0.775	0.942	CLONAL	1	TRUE	1	0.37	2		751	789	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349208	15349208	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	119	515	1	ENST00000263377.2:c.4069T>A	p.Phe1357Ile	p.F1357I	ENST00000263377	NM_058243.2	1357	Ttt/Att	20/20	1	2	FACETS	0.901	0.814	0.992	0.901	0.814	0.992	CLONAL	1	TRUE	1	0.37	2		516	714	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366923	15366923	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	173	778	1	ENST00000263377.2:c.1703C>A	p.Pro568His	p.P568H	ENST00000263377	NM_058243.2	568	cCt/cAt	9/20	1	2	FACETS	0.872	0.802	0.946	0.872	0.802	0.946	CLONAL	1	TRUE	1	0.37	2		779	1072	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18274188	18274188	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146112354	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	872	143	589	3	ENST00000222254.8:c.1406G>A	p.Arg469Gln	p.R469Q	ENST00000222254	NM_005027.3	469	cGg/cAg	11/16	1	2	FACETS	0.762	0.693	0.833	0.762	0.693	0.833	SUBCLONAL	1	TRUE	1	0.37	2		592	1015	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18962977	18962977	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	162	754	0	ENST00000262803.5:c.844A>G	p.Lys282Glu	p.K282E	ENST00000262803	NM_002911.3	282	Aag/Gag	6/24	1	2	FACETS	0.907	0.832	0.986	0.907	0.832	0.986	CLONAL	1	TRUE	1	0.37	2		754	965	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256796	19256796	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	86	365	0	ENST00000162023.5:c.917C>G	p.Thr306Ser	p.T306S	ENST00000162023		306	aCc/aGc	13/13	1	2	FACETS	0.96	0.853	1	0.96	0.853	1	CLONAL	1	TRUE	1	0.37	2		365	484	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210973	36210973	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	180	886	3	ENST00000222270.7:c.724G>T	p.Glu242Ter	p.E242*	ENST00000222270	NM_014727.1	242	Gaa/Taa	3/37	1	2	FACETS	0.933	0.859	1	0.933	0.859	1	CLONAL	1	TRUE	1	0.37	2		889	1043	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211649	36211649	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	56	365	0	ENST00000222270.7:c.1400G>A	p.Arg467Lys	p.R467K	ENST00000222270	NM_014727.1	467	aGg/aAg	3/37	1	2	FACETS	0.784	0.674	0.903	0.784	0.674	0.903	CLONAL	1	TRUE	1	0.37	2		365	386	SUCCESS
AXL	558	MSKCC	GRCh37	19	41727818	41727818	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	201	777	2	ENST00000301178.4:c.443G>A	p.Arg148Lys	p.R148K	ENST00000301178	NM_021913.4	148	aGg/aAg	4/20	1	2	FACETS	1	0.96	1	1	0.96	1	CLONAL	1	TRUE	1	0.37	2		779	1031	SUCCESS
AXL	558	MSKCC	GRCh37	19	41754692	41754692	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs774738552	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	140	564	0	ENST00000301178.4:c.1678T>G	p.Ser560Ala	p.S560A	ENST00000301178	NM_021913.4	560	Tcc/Gcc	14/20	1	2	FACETS	0.925	0.843	1	0.925	0.843	1	CLONAL	1	TRUE	1	0.37	2		564	818	SUCCESS
AXL	558	MSKCC	GRCh37	19	41758331	41758331	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	113	486	1	ENST00000301178.4:c.1787A>T	p.Asn596Ile	p.N596I	ENST00000301178	NM_021913.4	596	aAc/aTc	15/20	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.37	2		487	596	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383133	42383133	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	137	632	0	ENST00000221972.3:c.153C>G	p.His51Gln	p.H51Q	ENST00000221972	NM_021601.3	51	caC/caG	2/5	1	2	FACETS	0.759	0.689	0.832	0.759	0.689	0.832	SUBCLONAL	1	TRUE	1	0.37	2		632	976	SUCCESS
CD79A	973	MSKCC	GRCh37	19	42383300	42383300	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs143511203	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	102	497	3	ENST00000221972.3:c.320G>A	p.Arg107Gln	p.R107Q	ENST00000221972	NM_021601.3	107	cGg/cAg	2/5	1	2	FACETS	0.746	0.667	0.83	0.746	0.667	0.83	SUBCLONAL	1	TRUE	1	0.37	2		500	739	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42797748	42797748	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	138	607	1	ENST00000575354.2:c.3800G>T	p.Ser1267Ile	p.S1267I	ENST00000575354	NM_015125.3	1267	aGc/aTc	16/20	1	2	FACETS	0.851	0.774	0.931	0.851	0.774	0.931	CLONAL	1	TRUE	1	0.37	2		608	877	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47731458	47731458	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	123	27	60	0	ENST00000449228.1:c.334G>T	p.Ala112Ser	p.A112S	ENST00000449228	NM_001127240.2	112	Gcc/Tcc	2/4	1	2	FACETS	0.973	0.784	1	0.973	0.784	1	CLONAL	1	TRUE	1	0.37	2		60	150	SUCCESS
RRAS	6237	MSKCC	GRCh37	19	50140169	50140169	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	98	402	1	ENST00000246792.3:c.256G>A	p.Gly86Ser	p.G86S	ENST00000246792	NM_006270.3	86	Ggc/Agc	3/6	1	2	FACETS	0.889	0.795	0.989	0.889	0.795	0.989	CLONAL	1	TRUE	1	0.37	2		403	596	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905479	50905479	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369896998	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	138	738	2	ENST00000440232.2:c.607G>A	p.Gly203Arg	p.G203R	ENST00000440232	NM_002691.3	203	Ggg/Agg	6/27	1	2	FACETS	0.938	0.854	1	0.938	0.854	1	CLONAL	1	TRUE	1	0.37	2		740	795	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082244	16082244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	189	854	1	ENST00000281043.3:c.58G>A	p.Glu20Lys	p.E20K	ENST00000281043	NM_005378.4	20	Gag/Aag	2/3	0.3	2	FACETS	1	0.966	1			1	CLONAL	1	TRUE	NA	0.37	2		855	948	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25464549	25464549	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	152	663	0	ENST00000264709.3:c.1964T>C	p.Ile655Thr	p.I655T	ENST00000264709	NM_175629.2	655	aTt/aCt	17/23	0.3	2	FACETS	0.943	0.863	1			1	CLONAL	1	TRUE	NA	0.37	2		663	871	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25523007	25523007	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	129	476	0	ENST00000264709.3:c.177+1G>A		p.X59_splice	ENST00000264709	NM_175629.2	59			0.3	2	FACETS	0.809	0.733	0.889			1	CLONAL	1	TRUE	NA	0.37	2		476	862	SUCCESS
CENPA	1058	MSKCC	GRCh37	2	27015094	27015094	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	75	410	0	ENST00000335756.4:c.196C>T	p.Pro66Ser	p.P66S	ENST00000335756	NM_001809.3	66	Ccc/Tcc	2/5	0.3	2	FACETS	0.614	0.538	0.696			1	SUBCLONAL	1	TRUE	NA	0.37	2		410	660	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416152	29416152	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs376702277	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	95	422	0	ENST00000389048.3:c.4801G>A	p.Ala1601Thr	p.A1601T	ENST00000389048	NM_004304.4	1601	Gct/Act	29/29	0.3	2	FACETS	0.969	0.865	1			1	CLONAL	1	TRUE	NA	0.37	2		422	530	SUCCESS
ALK	238	MSKCC	GRCh37	2	29420486	29420486	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	145	452	0	ENST00000389048.3:c.3995G>A	p.Ser1332Asn	p.S1332N	ENST00000389048	NM_004304.4	1332	aGc/aAc	27/29	1	2	FACETS	1	0.955	1	1	0.955	1	CLONAL	1	TRUE	1	0.37	2		452	733	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455251	29455251	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	503	111	476	0	ENST00000389048.3:c.2551G>A	p.Ala851Thr	p.A851T	ENST00000389048	NM_004304.4	851	Gcc/Acc	15/29	1	2	FACETS	0.977	0.88	1	0.977	0.88	1	CLONAL	1	TRUE	1	0.37	2		476	614	SUCCESS
ALK	238	MSKCC	GRCh37	2	29497965	29497965	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	70	337	0	ENST00000389048.3:c.2041G>T	p.Val681Phe	p.V681F	ENST00000389048	NM_004304.4	681	Gtt/Ttt	11/29	1	2	FACETS	0.848	0.742	0.962	0.848	0.742	0.962	CLONAL	1	TRUE	1	0.37	2		337	446	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142930	30142930	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	158	742	0	ENST00000389048.3:c.596G>C	p.Gly199Ala	p.G199A	ENST00000389048	NM_004304.4	199	gGc/gCc	1/29	1	2	FACETS	0.955	0.875	1	0.955	0.875	1	CLONAL	1	TRUE	1	0.37	2		742	894	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39240630	39240630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs483352826	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	119	493	1	ENST00000402219.2:c.2138G>A	p.Arg713Gln	p.R713Q	ENST00000402219	NM_005633.3	713	cGa/cAa	13/23	1	2	FACETS	0.785	0.709	0.866	0.785	0.709	0.866	SUBCLONAL	1	TRUE	1	0.37	2		494	819	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47656901	47656901	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	80	292	0	ENST00000233146.2:c.1097T>G	p.Phe366Cys	p.F366C	ENST00000233146	NM_000251.2	366	tTt/tGt	7/16	1	2	FACETS	0.948	0.838	1	0.948	0.838	1	CLONAL	1	TRUE	1	0.37	2		292	456	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47702229	47702229	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs150980616	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	134	480	0	ENST00000233146.2:c.1825G>C	p.Ala609Pro	p.A609P	ENST00000233146	NM_000251.2	609	Gct/Cct	12/16	1	2	FACETS	0.922	0.838	1	0.922	0.838	1	CLONAL	1	TRUE	1	0.37	2		480	786	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026861	48026861	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	101	348	0	ENST00000234420.5:c.1739C>A	p.Ser580Ter	p.S580*	ENST00000234420	NM_000179.2	580	tCg/tAg	4/10	1	2	FACETS	0.918	0.822	1	0.918	0.822	1	CLONAL	1	TRUE	1	0.37	2		348	595	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61724118	61724118	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	113	377	0	ENST00000401558.2:c.784A>C	p.Asn262His	p.N262H	ENST00000401558	NM_003400.3	262	Aat/Cat	10/25	1	2	FACETS	0.95	0.856	1	0.95	0.856	1	CLONAL	1	TRUE	1	0.37	2		377	643	SUCCESS
BCL2L11	10018	MSKCC	GRCh37	2	111881495	111881495	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	72	440	0	ENST00000393256.3:c.173G>T	p.Gly58Val	p.G58V	ENST00000393256	NM_006538.4	58	gGc/gTc	2/4	1	2	FACETS	0.747	0.654	0.847	0.747	0.654	0.847	SUBCLONAL	1	TRUE	1	0.37	2		440	521	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872599	136872599	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	82	319	0	ENST00000241393.3:c.899T>A	p.Ile300Asn	p.I300N	ENST00000241393	NM_003467.2	300	aTc/aAc	2/2	1	2	FACETS	0.707	0.624	0.796	0.707	0.624	0.796	SUBCLONAL	1	TRUE	1	0.37	2		319	627	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136873334	136873334	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	65	329	0	ENST00000241393.3:c.164G>A	p.Gly55Asp	p.G55D	ENST00000241393	NM_003467.2	55	gGc/gAc	2/2	1	2	FACETS	0.581	0.503	0.665	0.581	0.503	0.665	SUBCLONAL	1	TRUE	1	0.37	2		329	605	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178096151	178096151	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	79	371	0	ENST00000397062.3:c.1180A>C	p.Lys394Gln	p.K394Q	ENST00000397062	NM_006164.4	394	Aaa/Caa	5/5	1	2	FACETS	0.7	0.616	0.79	0.7	0.616	0.79	SUBCLONAL	1	TRUE	1	0.37	2		371	610	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190682785	190682785	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	106	435	1	ENST00000441310.2:c.461T>C	p.Val154Ala	p.V154A	ENST00000441310	NM_000534.4	154	gTa/gCa	5/13	1	2	FACETS	0.798	0.716	0.885	0.798	0.716	0.885	SUBCLONAL	1	TRUE	1	0.37	2		436	718	SUCCESS
CTLA4	1493	MSKCC	GRCh37	2	204735636	204735636	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	64	318	0	ENST00000302823.3:c.437G>T	p.Gly146Val	p.G146V	ENST00000302823	NM_005214.4	146	gGa/gTa	2/4	1	2	FACETS	0.62	0.537	0.71	0.62	0.537	0.71	SUBCLONAL	1	TRUE	1	0.37	2		318	558	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212251784	212251784	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs372258619	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	86	291	0	ENST00000342788.4:c.3275C>A	p.Pro1092His	p.P1092H	ENST00000342788	NM_005235.2	1092	cCt/cAt	27/28	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.37	2		291	431	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212566709	212566709	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	84	221	0	ENST00000342788.4:c.1472G>T	p.Arg491Ile	p.R491I	ENST00000342788	NM_005235.2	491	aGa/aTa	12/28	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.37	2		221	435	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215609863	215609863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	143	451	0	ENST00000260947.4:c.1831G>A	p.Gly611Ser	p.G611S	ENST00000260947	NM_000465.2	611	Ggt/Agt	9/11	1	2	FACETS	0.997	0.91	1	0.997	0.91	1	CLONAL	1	TRUE	1	0.37	2		451	775	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660640	227660640	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1254174874	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	69	432	1	ENST00000305123.5:c.2815G>A	p.Glu939Lys	p.E939K	ENST00000305123	NM_005544.2	939	Gag/Aag	1/2	1	2	FACETS	0.716	0.624	0.814	0.716	0.624	0.814	SUBCLONAL	1	TRUE	1	0.37	2		433	521	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9624877	9624877	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	89	425	0	ENST00000353224.5:c.100G>T	p.Gly34Cys	p.G34C	ENST00000353224	NM_177990.2	34	Ggc/Tgc	3/10	1	2	FACETS	0.758	0.672	0.849	0.758	0.672	0.849	SUBCLONAL	1	TRUE	1	0.37	2		425	635	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31375226	31375226	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	118	555	0	ENST00000328111.2:c.623A>T	p.Asp208Val	p.D208V	ENST00000328111	NM_006892.3	208	gAc/gTc	6/23	1	2	FACETS	0.972	0.879	1	0.972	0.879	1	CLONAL	1	TRUE	1	0.37	2		555	656	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36022671	36022671	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	136	511	0	ENST00000358208.4:c.544A>T	p.Thr182Ser	p.T182S	ENST00000358208		182	Acc/Tcc	5/12	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.37	2		511	694	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713398	40713398	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	119	489	0	ENST00000373198.4:c.4117C>G	p.Leu1373Val	p.L1373V	ENST00000373198	NM_133170.3	1373	Ctc/Gtc	30/32	0.3	1	FACETS	0.892	0.807	0.98	0.892	0.807	0.98	CLONAL	1	TRUE	0	0.37	1		489	588	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735434	40735434	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	438	101	481	0	ENST00000373198.4:c.3439C>T	p.Gln1147Ter	p.Q1147*	ENST00000373198	NM_133170.3	1147	Cag/Tag	25/32	0.3	1	FACETS	0.826	0.74	0.916	0.826	0.74	0.916	CLONAL	1	TRUE	0	0.37	1		481	539	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40738976	40738976	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	72	337	0	ENST00000373198.4:c.3308G>T	p.Cys1103Phe	p.C1103F	ENST00000373198	NM_133170.3	1103	tGc/tTc	24/32	0.3	1	FACETS	0.973	0.857	1	0.973	0.857	1	CLONAL	1	TRUE	0	0.37	1		337	326	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40739084	40739084	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	454	88	500	0	ENST00000373198.4:c.3200C>G	p.Thr1067Ser	p.T1067S	ENST00000373198	NM_133170.3	1067	aCc/aGc	24/32	0.3	1	FACETS	0.715	0.635	0.8	0.715	0.635	0.8	SUBCLONAL	1	TRUE	0	0.37	1		500	542	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264725	46264725	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	79	418	0	ENST00000371998.3:c.1595G>C	p.Gly532Ala	p.G532A	ENST00000371998		532	gGt/gCt	12/23	1	2	FACETS	0.681	0.599	0.769	0.681	0.599	0.769	SUBCLONAL	1	TRUE	1	0.37	2		418	627	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321546	62321546	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	134	584	0	ENST00000360203.5:c.2248C>A	p.Arg750Ser	p.R750S	ENST00000360203	NM_001283009.1	750	Cgt/Agt	25/35	1	2	FACETS	0.925	0.841	1	0.925	0.841	1	CLONAL	1	TRUE	1	0.37	2		584	783	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259140	36259140	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	89	445	0	ENST00000300305.3:c.351G>T	p.Lys117Asn	p.K117N	ENST00000300305		117	aaG/aaT	3/8	0.130923951212186	1	FACETS	0.628	0.558	0.704	0.628	0.558	0.704	INDETERMINATE	1	TRUE	0	0.37	1		445	624	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45655170	45655170	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	69	323	0	ENST00000407780.3:c.682G>T	p.Val228Phe	p.V228F	ENST00000407780	NM_001283052.1	228	Gtc/Ttc	4/7	0.130923951212186	1	FACETS	0.664	0.58	0.754	0.664	0.58	0.754	INDETERMINATE	1	TRUE	0	0.37	1		323	458	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24167470	24167470	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	99	561	0	ENST00000263121.7:c.854A>T	p.Glu285Val	p.E285V	ENST00000263121	NM_003073.3	285	gAg/gTg	7/9	1	2	FACETS	0.653	0.583	0.729	0.653	0.583	0.729	SUBCLONAL	1	TRUE	1	0.37	2		561	819	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29092950	29092950	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	118	529	0	ENST00000328354.6:c.1034A>G	p.His345Arg	p.H345R	ENST00000328354	NM_007194.3	345	cAc/cGc	10/15	1	2	FACETS	0.896	0.809	0.987	0.896	0.809	0.987	CLONAL	1	TRUE	1	0.37	2		529	712	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513536	41513536	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	140	492	0	ENST00000263253.7:c.440C>A	p.Pro147His	p.P147H	ENST00000263253	NM_001429.3	147	cCt/cAt	2/31	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.37	2		492	757	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41569755	41569755	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	118	514	0	ENST00000263253.7:c.4746G>T	p.Gln1582His	p.Q1582H	ENST00000263253	NM_001429.3	1582	caG/caT	29/31	1	2	FACETS	0.831	0.749	0.916	0.831	0.749	0.916	CLONAL	1	TRUE	1	0.37	2		514	768	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191581	10191581	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	124	469	0	ENST00000256474.2:c.574C>A	p.Pro192Thr	p.P192T	ENST00000256474	NM_000551.3	192	Cca/Aca	3/3	1	2	FACETS	0.897	0.812	0.987	0.897	0.812	0.987	CLONAL	1	TRUE	1	0.37	2		469	747	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182741	38182741	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	156	478	0	ENST00000396334.3:c.894C>A	p.Phe298Leu	p.F298L	ENST00000396334	NM_002468.4	298	ttC/ttA	5/5	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.37	2		478	762	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47139539	47139539	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	101	361	0	ENST00000409792.3:c.5048C>A	p.Ala1683Asp	p.A1683D	ENST00000409792	NM_014159.6	1683	gCc/gAc	9/21	1	2	FACETS	0.895	0.801	0.994	0.895	0.801	0.994	CLONAL	1	TRUE	1	0.37	2		361	610	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47162942	47162942	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	109	420	2	ENST00000409792.3:c.3184C>T	p.Pro1062Ser	p.P1062S	ENST00000409792	NM_014159.6	1062	Cca/Tca	3/21	1	2	FACETS	0.848	0.762	0.938	0.848	0.762	0.938	CLONAL	1	TRUE	1	0.37	2		422	695	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47164456	47164456	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	56	329	0	ENST00000409792.3:c.1670C>A	p.Ser557Tyr	p.S557Y	ENST00000409792	NM_014159.6	557	tCt/tAt	3/21	1	2	FACETS	0.629	0.54	0.727	0.629	0.54	0.727	SUBCLONAL	1	TRUE	1	0.37	2		329	481	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52437158	52437158	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	142	482	0	ENST00000460680.1:c.1886C>A	p.Pro629His	p.P629H	ENST00000460680	NM_004656.3	629	cCc/cAc	14/17	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.37	2		482	649	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52678778	52678778	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	87	409	0	ENST00000394830.3:c.841T>A	p.Tyr281Asn	p.Y281N	ENST00000394830	NM_018313.4	281	Tat/Aat	9/30	1	2	FACETS	0.63	0.558	0.708	0.63	0.558	0.708	SUBCLONAL	1	TRUE	1	0.37	2		409	746	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52702552	52702552	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	117	614	0	ENST00000394830.3:c.346T>A	p.Phe116Ile	p.F116I	ENST00000394830	NM_018313.4	116	Ttc/Atc	4/30	1	2	FACETS	0.672	0.605	0.743	0.672	0.605	0.743	SUBCLONAL	1	TRUE	1	0.37	2		614	941	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69987002	69987002	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	166	668	0	ENST00000394351.3:c.63G>C	p.Lys21Asn	p.K21N	ENST00000394351	NM_000248.3	21	aaG/aaC	2/9	1	2	FACETS	0.877	0.805	0.953	0.877	0.805	0.953	CLONAL	1	TRUE	1	0.37	2		668	1023	SUCCESS
FOXP1	27086	MSKCC	GRCh37	3	71037168	71037168	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	89	318	0	ENST00000318789.4:c.1123G>T	p.Glu375Ter	p.E375*	ENST00000318789	NM_032682.5	375	Gaa/Taa	14/21	1	2	FACETS	0.898	0.798	1	0.898	0.798	1	CLONAL	1	TRUE	1	0.37	2		318	536	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89456423	89456423	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	62	195	0	ENST00000336596.2:c.1599C>A	p.Phe533Leu	p.F533L	ENST00000336596	NM_005233.5	533	ttC/ttA	8/17	1	2	FACETS	0.882	0.765	1	0.882	0.765	1	CLONAL	1	TRUE	1	0.37	2		195	380	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89462377	89462377	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs374235660	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	147	622	0	ENST00000336596.2:c.1849G>A	p.Asp617Asn	p.D617N	ENST00000336596	NM_005233.5	617	Gat/Aat	10/17	1	2	FACETS	0.994	0.909	1	0.994	0.909	1	CLONAL	1	TRUE	1	0.37	2		622	799	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119585457	119585457	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	104	525	0	ENST00000316626.5:c.928C>G	p.His310Asp	p.H310D	ENST00000316626		310	Cat/Gat	9/12	1	2	FACETS	0.84	0.753	0.933	0.84	0.753	0.933	CLONAL	1	TRUE	1	0.37	2		525	669	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128202736	128202736	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	95	571	1	ENST00000341105.2:c.984G>T	p.Gln328His	p.Q328H	ENST00000341105	NM_032638.4	328	caG/caT	4/6	1	2	FACETS	0.785	0.7	0.876	0.785	0.7	0.876	SUBCLONAL	1	TRUE	1	0.37	2		572	654	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205191	128205191	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	76	339	0	ENST00000341105.2:c.250A>T	p.Met84Leu	p.M84L	ENST00000341105	NM_032638.4	84	Atg/Ttg	3/6	1	2	FACETS	0.929	0.818	1	0.929	0.818	1	CLONAL	1	TRUE	1	0.37	2		339	442	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205715	128205715	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	153	639	1	ENST00000341105.2:c.160T>A	p.Ser54Thr	p.S54T	ENST00000341105	NM_032638.4	54	Tcg/Acg	2/6	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.37	2		640	801	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374250	138374250	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1384758874	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	144	506	0	ENST00000289153.2:c.3194G>A	p.Arg1065Gln	p.R1065Q	ENST00000289153	NM_006219.2	1065	cGg/cAg	22/22	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.37	2		506	702	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138417759	138417759	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs774931559	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	568	64	408	0	ENST00000289153.2:c.1760A>T	p.Asp587Val	p.D587V	ENST00000289153	NM_006219.2	587	gAt/gTt	11/22	1	2	FACETS	0.547	0.474	0.627	0.547	0.474	0.627	SUBCLONAL	1	TRUE	1	0.37	2		408	632	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138478044	138478044	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs545189148	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	656	95	556	0	ENST00000289153.2:c.142C>T	p.Arg48Trp	p.R48W	ENST00000289153	NM_006219.2	48	Cgg/Tgg	1/22	1	2	FACETS	0.684	0.609	0.764	0.684	0.609	0.764	SUBCLONAL	1	TRUE	1	0.37	2		556	751	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664511	138664511	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	53	372	1	ENST00000330315.3:c.1054G>A	p.Glu352Lys	p.E352K	ENST00000330315	NM_023067.3	352	Gag/Aag	1/1	1	2	FACETS	0.613	0.524	0.711	0.613	0.524	0.711	SUBCLONAL	1	TRUE	1	0.37	2		373	467	SUCCESS
ATR	545	MSKCC	GRCh37	3	142231145	142231145	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	76	440	0	ENST00000350721.4:c.4809A>C	p.Lys1603Asn	p.K1603N	ENST00000350721	NM_001184.3	1603	aaA/aaC	27/47	1	2	FACETS	0.616	0.54	0.698	0.616	0.54	0.698	SUBCLONAL	1	TRUE	1	0.37	2		440	667	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281073	142281073	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	99	435	0	ENST00000350721.4:c.1170+1G>T		p.X390_splice	ENST00000350721	NM_001184.3	390			1	2	FACETS	0.731	0.653	0.814	0.731	0.653	0.814	SUBCLONAL	1	TRUE	1	0.37	2		435	732	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185155333	185155333	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	97	404	0	ENST00000265026.3:c.574G>T	p.Val192Leu	p.V192L	ENST00000265026	NM_004721.4	192	Gtg/Ttg	3/14	1	2	FACETS	0.809	0.722	0.902	0.809	0.722	0.902	CLONAL	1	TRUE	1	0.37	2		404	648	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55127273	55127273	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	478	116	463	0	ENST00000257290.5:c.61A>T	p.Ile21Phe	p.I21F	ENST00000257290	NM_006206.4	21	Atc/Ttc	3/23	0.130923951212186	1	FACETS	0.86	0.778	0.947	0.86	0.778	0.947	INDETERMINATE	1	TRUE	0	0.37	1		463	594	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55130031	55130031	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	121	593	0	ENST00000257290.5:c.565T>C	p.Cys189Arg	p.C189R	ENST00000257290	NM_006206.4	189	Tgt/Cgt	4/23	0.130923951212186	1	FACETS	0.695	0.628	0.766	0.695	0.628	0.766	INDETERMINATE	1	TRUE	0	0.37	1		593	767	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955592	55955592	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	722	116	671	1	ENST00000263923.4:c.3353G>T	p.Arg1118Leu	p.R1118L	ENST00000263923	NM_002253.2	1118	cGa/cTa	25/30	0.130923951212186	1	FACETS	0.61	0.549	0.674	0.61	0.549	0.674	INDETERMINATE	1	TRUE	0	0.37	1		672	838	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55962480	55962480	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	70	415	0	ENST00000263923.4:c.2644C>A	p.Leu882Ile	p.L882I	ENST00000263923	NM_002253.2	882	Ctc/Atc	19/30	0.130923951212186	1	FACETS	0.541	0.472	0.615	0.541	0.472	0.615	INDETERMINATE	1	TRUE	0	0.37	1		415	570	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968123	55968123	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	129	541	0	ENST00000263923.4:c.2207C>T	p.Thr736Ile	p.T736I	ENST00000263923	NM_002253.2	736	aCc/aTc	15/30	0.130923951212186	1	FACETS	0.756	0.686	0.829	0.756	0.686	0.829	INDETERMINATE	1	TRUE	0	0.37	1		541	752	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979582	55979582	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	124	553	0	ENST00000263923.4:c.865T>G	p.Leu289Val	p.L289V	ENST00000263923	NM_002253.2	289	Ttg/Gtg	7/30	0.130923951212186	1	FACETS	0.721	0.652	0.793	0.721	0.652	0.793	INDETERMINATE	1	TRUE	0	0.37	1		553	758	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980315	55980315	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	104	551	0	ENST00000263923.4:c.776A>T	p.Asn259Ile	p.N259I	ENST00000263923	NM_002253.2	259	aAc/aTc	6/30	0.130923951212186	1	FACETS	0.63	0.564	0.7	0.63	0.564	0.7	INDETERMINATE	1	TRUE	0	0.37	1		551	727	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467563	66467563	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	88	381	0	ENST00000273854.3:c.706G>T	p.Val236Leu	p.V236L	ENST00000273854	NM_004439.5	236	Gtg/Ttg	3/18	1	2	FACETS	0.786	0.697	0.881	0.786	0.697	0.881	SUBCLONAL	1	TRUE	1	0.37	2		381	605	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384048	84384048	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	138	467	0	ENST00000321945.7:c.804G>T	p.Lys268Asn	p.K268N	ENST00000321945	NM_139076.2	268	aaG/aaT	9/9	1	2	FACETS	0.895	0.815	0.98	0.895	0.815	0.98	CLONAL	1	TRUE	1	0.37	2		467	833	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384051	84384051	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	121	454	0	ENST00000321945.7:c.801G>T	p.Glu267Asp	p.E267D	ENST00000321945	NM_139076.2	267	gaG/gaT	9/9	1	2	FACETS	0.801	0.723	0.882	0.801	0.723	0.882	CLONAL	1	TRUE	1	0.37	2		454	817	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99850069	99850069	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1409744121	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	117	588	0	ENST00000280892.6:c.55G>T	p.Ala19Ser	p.A19S	ENST00000280892	NM_001130678.1	19	Gcg/Tcg	1/7	1	2	FACETS	0.821	0.741	0.906	0.821	0.741	0.906	CLONAL	1	TRUE	1	0.37	2		588	770	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244264	153244264	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	104	282	0	ENST00000281708.4:c.1893G>C	p.Gln631His	p.Q631H	ENST00000281708	NM_033632.3	631	caG/caC	12/12	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.37	2		282	526	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524828	187524828	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	99	483	0	ENST00000441802.2:c.10852G>T	p.Asp3618Tyr	p.D3618Y	ENST00000441802	NM_005245.3	3618	Gat/Tat	19/27	1	2	FACETS	0.851	0.761	0.946	0.851	0.761	0.946	CLONAL	1	TRUE	1	0.37	2		483	629	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187525016	187525016	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	112	490	0	ENST00000441802.2:c.10664C>A	p.Ser3555Tyr	p.S3555Y	ENST00000441802	NM_005245.3	3555	tCt/tAt	19/27	1	2	FACETS	0.898	0.809	0.992	0.898	0.809	0.992	CLONAL	1	TRUE	1	0.37	2		490	674	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187535414	187535414	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	134	504	0	ENST00000441802.2:c.9160T>G	p.Ser3054Ala	p.S3054A	ENST00000441802	NM_005245.3	3054	Tct/Gct	12/27	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.37	2		504	645	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542188	187542188	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	87	381	0	ENST00000441802.2:c.5552A>T	p.Asp1851Val	p.D1851V	ENST00000441802	NM_005245.3	1851	gAc/gTc	10/27	1	2	FACETS	0.894	0.794	1	0.894	0.794	1	CLONAL	1	TRUE	1	0.37	2		381	526	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542543	187542543	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	113	507	0	ENST00000441802.2:c.5197T>A	p.Tyr1733Asn	p.Y1733N	ENST00000441802	NM_005245.3	1733	Tac/Aac	10/27	1	2	FACETS	0.935	0.843	1	0.935	0.843	1	CLONAL	1	TRUE	1	0.37	2		507	653	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549437	187549437	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	123	470	0	ENST00000441802.2:c.4681T>C	p.Trp1561Arg	p.W1561R	ENST00000441802	NM_005245.3	1561	Tgg/Cgg	9/27	1	2	FACETS	0.939	0.85	1	0.939	0.85	1	CLONAL	1	TRUE	1	0.37	2		470	708	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187584578	187584578	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	76	463	0	ENST00000441802.2:c.3455C>A	p.Ser1152Tyr	p.S1152Y	ENST00000441802	NM_005245.3	1152	tCt/tAt	3/27	1	2	FACETS	0.845	0.744	0.954	0.845	0.744	0.954	CLONAL	1	TRUE	1	0.37	2		463	486	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31429599	31429599	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	183	682	0	ENST00000344624.3:c.3199T>G	p.Leu1067Val	p.L1067V	ENST00000344624		1067	Ttg/Gtg	24/33	0.130923951212186	1	FACETS	0.848	0.782	0.916	0.848	0.782	0.916	INDETERMINATE	1	TRUE	0	0.37	1		682	951	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56160562	56160562	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	96	283	0	ENST00000399503.3:c.836T>A	p.Phe279Tyr	p.F279Y	ENST00000399503	NM_005921.1	279	tTt/tAt	4/20	1	2	FACETS	0.895	0.799	0.996	0.895	0.799	0.996	CLONAL	1	TRUE	1	0.37	2		283	580	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754823	57754823	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	48	284	0	ENST00000274289.3:c.367C>A	p.Gln123Lys	p.Q123K	ENST00000274289	NM_006622.3	123	Caa/Aaa	2/14	1	2	FACETS	0.67	0.568	0.782	0.67	0.568	0.782	SUBCLONAL	1	TRUE	1	0.37	2		284	387	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57755538	57755538	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	432	118	409	0	ENST00000274289.3:c.249C>G	p.Cys83Trp	p.C83W	ENST00000274289	NM_006622.3	83	tgC/tgG	1/14	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.37	2		409	550	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79966028	79966028	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201748817	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	144	692	0	ENST00000265081.6:c.692C>T	p.Pro231Leu	p.P231L	ENST00000265081	NM_002439.4	231	cCg/cTg	4/24	1	2	FACETS	0.802	0.731	0.877	0.802	0.731	0.877	CLONAL	1	TRUE	1	0.37	2		692	970	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80024726	80024726	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	114	664	0	ENST00000265081.6:c.1510G>C	p.Ala504Pro	p.A504P	ENST00000265081	NM_002439.4	504	Gct/Cct	10/24	1	2	FACETS	0.649	0.584	0.719	0.649	0.584	0.719	SUBCLONAL	1	TRUE	1	0.37	2		664	949	SUCCESS
APC	324	MSKCC	GRCh37	5	112170734	112170734	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	86	463	0	ENST00000257430.4:c.1830T>A	p.Asp610Glu	p.D610E	ENST00000257430	NM_000038.5	610	gaT/gaA	15/16	1	2	FACETS	0.648	0.573	0.729	0.648	0.573	0.729	SUBCLONAL	1	TRUE	1	0.37	2		463	717	SUCCESS
APC	324	MSKCC	GRCh37	5	112170770	112170770	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs876658355	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	130	491	0	ENST00000257430.4:c.1866C>G	p.Tyr622Ter	p.Y622*	ENST00000257430	NM_000038.5	622	taC/taG	15/16	1	2	FACETS	0.938	0.852	1	0.938	0.852	1	CLONAL	1	TRUE	1	0.37	2		491	749	SUCCESS
APC	324	MSKCC	GRCh37	5	112170823	112170823	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1273594465	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	123	486	0	ENST00000257430.4:c.1919G>A	p.Arg640Gln	p.R640Q	ENST00000257430	NM_000038.5	640	cGg/cAg	15/16	1	2	FACETS	0.882	0.798	0.97	0.882	0.798	0.97	CLONAL	1	TRUE	1	0.37	2		486	754	SUCCESS
APC	324	MSKCC	GRCh37	5	112176305	112176305	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	102	427	0	ENST00000257430.4:c.5014G>A	p.Gly1672Arg	p.G1672R	ENST00000257430	NM_000038.5	1672	Gga/Aga	16/16	1	2	FACETS	0.902	0.809	1	0.902	0.809	1	CLONAL	1	TRUE	1	0.37	2		427	611	SUCCESS
APC	324	MSKCC	GRCh37	5	112178094	112178094	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	99	445	0	ENST00000257430.4:c.6803C>G	p.Thr2268Ser	p.T2268S	ENST00000257430	NM_000038.5	2268	aCc/aGc	16/16	1	2	FACETS	0.932	0.834	1	0.932	0.834	1	CLONAL	1	TRUE	1	0.37	2		445	574	SUCCESS
APC	324	MSKCC	GRCh37	5	112179567	112179567	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs538289470	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	67	394	1	ENST00000257430.4:c.8276G>A	p.Arg2759His	p.R2759H	ENST00000257430	NM_000038.5	2759	cGt/cAt	16/16	1	2	FACETS	0.646	0.561	0.737	0.646	0.561	0.737	SUBCLONAL	1	TRUE	1	0.37	2		395	561	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149515373	149515373	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs748906060	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	113	454	0	ENST00000261799.4:c.109C>G	p.Pro37Ala	p.P37A	ENST00000261799	NM_002609.3	37	Ccc/Gcc	3/23	1	2	FACETS	1	0.905	1	1	0.905	1	CLONAL	1	TRUE	1	0.37	2		454	609	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176517960	176517960	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs777012486	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	75	553	0	ENST00000292408.4:c.458A>C	p.Gln153Pro	p.Q153P	ENST00000292408	NM_213647.1	153	cAg/cCg	5/18	1	2	FACETS	0.585	0.512	0.663	0.585	0.512	0.663	SUBCLONAL	1	TRUE	1	0.37	2		553	693	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176637649	176637649	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	186	656	0	ENST00000439151.2:c.2249C>A	p.Ala750Asp	p.A750D	ENST00000439151	NM_022455.4	750	gCt/gAt	5/23	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.37	2		656	970	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176666826	176666826	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	114	596	0	ENST00000439151.2:c.4262G>A	p.Gly1421Glu	p.G1421E	ENST00000439151	NM_022455.4	1421	gGa/gAa	8/23	1	2	FACETS	0.752	0.677	0.832	0.752	0.677	0.832	SUBCLONAL	1	TRUE	1	0.37	2		596	819	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707728	176707728	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	128	459	1	ENST00000439151.2:c.5785G>T	p.Gly1929Trp	p.G1929W	ENST00000439151	NM_022455.4	1929	Ggg/Tgg	18/23	1	2	FACETS	0.991	0.9	1	0.991	0.9	1	CLONAL	1	TRUE	1	0.37	2		460	698	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176722430	176722430	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	111	480	0	ENST00000439151.2:c.8061T>A	p.Ser2687Arg	p.S2687R	ENST00000439151	NM_022455.4	2687	agT/agA	23/23	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.37	NA		480	756	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180056421	180056421	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	66	301	0	ENST00000261937.6:c.823C>T	p.Arg275Trp	p.R275W	ENST00000261937	NM_182925.4	275	Cgg/Tgg	7/30	0.3	1	FACETS	0.826	0.721	0.938	0.826	0.721	0.938	CLONAL	1	TRUE	0	0.37	1		301	352	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401679	401679	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	82	429	0	ENST00000380956.4:c.1001T>A	p.Ile334Asn	p.I334N	ENST00000380956	NM_001195286.1	334	aTc/aAc	7/9	0.3	2	FACETS	0.755	0.667	0.85			1	SUBCLONAL	1	TRUE	NA	0.37	2		429	587	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671194	30671194	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	140	616	0	ENST00000376406.3:c.5682+1G>C		p.X1894_splice	ENST00000376406	NM_014641.2	1894			0.165807479755987	3	FACETS	0.894	0.813	0.979	0.447	0.406	0.49	INDETERMINATE	1	TRUE	1	0.37	3		616	1003	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671679	30671679	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	106	487	0	ENST00000376406.3:c.5281G>C	p.Val1761Leu	p.V1761L	ENST00000376406	NM_014641.2	1761	Gtg/Ctg	10/15	0.165807479755987	3	FACETS	0.993	0.891	1	0.496	0.445	0.55	INDETERMINATE	1	TRUE	1	0.37	3		487	684	SUCCESS
WHR1	8859	MSKCC	GRCh37	6	31947323	31947323	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	96	412	0	ENST00000375333.2:c.808G>T	p.Glu270Ter	p.E270*	ENST00000375333	NM_032454.1	270	Gaa/Taa	5/8	0.165807479755987	3	FACETS	0.846	0.754	0.944	0.423	0.377	0.472	INDETERMINATE	1	TRUE	1	0.37	3		412	727	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32183003	32183003	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	66	398	0	ENST00000375023.3:c.2021G>T	p.Arg674Ile	p.R674I	ENST00000375023	NM_004557.3	674	aGa/aTa	12/30	0.165807479755987	3	FACETS	1	0.922	1	0.541	0.471	0.615	INDETERMINATE	1	TRUE	1	0.37	3		398	391	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32188347	32188347	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	147	588	0	ENST00000375023.3:c.994T>A	p.Cys332Ser	p.C332S	ENST00000375023	NM_004557.3	332	Tgc/Agc	6/30	0.165807479755987	3	FACETS	1	0.968	1	0.562	0.513	0.613	INDETERMINATE	1	TRUE	1	0.37	3		588	838	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32800585	32800585	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	929	158	671	0	ENST00000374899.4:c.962T>A	p.Ile321Asn	p.I321N	ENST00000374899	NM_018833.2	321	aTc/aAc	6/12	0.165807479755987	3	FACETS	0.931	0.852	1	0.466	0.426	0.507	INDETERMINATE	1	TRUE	1	0.37	3		671	1087	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818159	32818159	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	945	165	641	0	ENST00000354258.4:c.1366G>T	p.Glu456Ter	p.E456*	ENST00000354258	NM_000593.5	456	Gaa/Taa	5/11	0.165807479755987	3	FACETS	0.952	0.873	1	0.476	0.436	0.518	INDETERMINATE	1	TRUE	1	0.37	3		641	1110	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32821071	32821071	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	176	823	2	ENST00000354258.4:c.523G>T	p.Glu175Ter	p.E175*	ENST00000354258	NM_000593.5	175	Gag/Tag	1/11	0.165807479755987	3	FACETS	0.957	0.88	1	0.479	0.44	0.519	INDETERMINATE	1	TRUE	1	0.37	3		825	1178	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652067	36652067	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs4986867	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	139	550	0	ENST00000244741.5:c.189C>A	p.Phe63Leu	p.F63L	ENST00000244741	NM_000389.4	63	ttC/ttA	2/3	0.165807479755987	3	FACETS	0.991	0.902	1	0.496	0.451	0.543	INDETERMINATE	1	TRUE	1	0.37	3		550	898	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120705	94120705	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	87	394	0	ENST00000369303.4:c.346C>G	p.Leu116Val	p.L116V	ENST00000369303	NM_004440.3	116	Ctg/Gtg	3/17	0.165807479755987	3	FACETS	0.992	0.88	1	0.496	0.44	0.556	INDETERMINATE	1	TRUE	1	0.37	3		394	562	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112029198	112029198	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	138	428	0	ENST00000368678.4:c.370T>A	p.Ser124Thr	p.S124T	ENST00000368678		124	Tcc/Acc	5/13	0.165807479755987	3	FACETS	1	0.91	1	0.5	0.455	0.548	INDETERMINATE	1	TRUE	1	0.37	3		428	884	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117647406	117647406	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	110	671	2	ENST00000368508.3:c.5538G>T	p.Glu1846Asp	p.E1846D	ENST00000368508	NM_002944.2	1846	gaG/gaT	33/43	1	2	FACETS	0.752	0.675	0.833	0.752	0.675	0.833	SUBCLONAL	1	TRUE	1	0.37	2		673	791	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710660	117710660	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	76	393	0	ENST00000368508.3:c.1612G>T	p.Glu538Ter	p.E538*	ENST00000368508	NM_002944.2	538	Gaa/Taa	12/43	1	2	FACETS	0.758	0.666	0.857	0.758	0.666	0.857	SUBCLONAL	1	TRUE	1	0.37	2		393	542	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117717392	117717392	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	107	500	0	ENST00000368508.3:c.815G>A	p.Gly272Asp	p.G272D	ENST00000368508	NM_002944.2	272	gGt/gAt	8/43	1	2	FACETS	0.772	0.693	0.856	0.772	0.693	0.856	SUBCLONAL	1	TRUE	1	0.37	2		500	749	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519293	137519293	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	544	106	434	0	ENST00000367739.4:c.1345A>T	p.Ile449Leu	p.I449L	ENST00000367739	NM_000416.2	449	Ata/Tta	7/7	1	2	FACETS	0.881	0.791	0.977	0.881	0.791	0.977	CLONAL	1	TRUE	1	0.37	2		434	650	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138192607	138192607	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	115	441	2	ENST00000237289.4:c.243G>T	p.Lys81Asn	p.K81N	ENST00000237289	NM_001270507.1	81	aaG/aaT	2/9	1	2	FACETS	0.738	0.665	0.816	0.738	0.665	0.816	SUBCLONAL	1	TRUE	1	0.37	2		443	842	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200300	138200300	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	47	342	0	ENST00000237289.4:c.1718G>A	p.Ser573Asn	p.S573N	ENST00000237289	NM_001270507.1	573	aGc/aAc	7/9	1	2	FACETS	0.464	0.391	0.544	0.464	0.391	0.544	SUBCLONAL	1	TRUE	1	0.37	2		342	548	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157406041	157406041	+	splice_donor_variant	Splice_Site	SNP	T	T	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	58	324	0	ENST00000346085.5:c.2281+2T>G		p.X761_splice	ENST00000346085	NM_020732.3	761			1	2	FACETS	0.604	0.519	0.696	0.604	0.519	0.696	SUBCLONAL	1	TRUE	1	0.37	2		324	519	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469914	157469914	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	105	479	1	ENST00000346085.5:c.2708G>A	p.Gly903Glu	p.G903E	ENST00000346085	NM_020732.3	903	gGg/gAg	9/20	1	2	FACETS	0.949	0.852	1	0.949	0.852	1	CLONAL	1	TRUE	1	0.37	2		480	598	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157505364	157505364	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	108	375	1	ENST00000346085.5:c.3346-1G>T		p.X1116_splice	ENST00000346085	NM_020732.3	1116			1	2	FACETS	0.875	0.787	0.969	0.875	0.787	0.969	CLONAL	1	TRUE	1	0.37	2		376	667	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527508	157527508	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs528801298	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	125	382	1	ENST00000346085.5:c.5233G>A	p.Glu1745Lys	p.E1745K	ENST00000346085	NM_020732.3	1745	Gag/Aag	20/20	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.37	2		383	654	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528426	157528426	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	117	400	1	ENST00000346085.5:c.6151G>A	p.Gly2051Ser	p.G2051S	ENST00000346085	NM_020732.3	2051	Ggc/Agc	20/20	1	2	FACETS	0.994	0.899	1	0.994	0.899	1	CLONAL	1	TRUE	1	0.37	2		401	636	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739819	41739819	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	108	419	0	ENST00000242208.4:c.154C>A	p.Pro52Thr	p.P52T	ENST00000242208	NM_002192.2	52	Cca/Aca	2/3	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.37	2		419	541	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220353	55220353	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	86	383	0	ENST00000275493.2:c.743G>A	p.Cys248Tyr	p.C248Y	ENST00000275493	NM_005228.3	248	tGc/tAc	6/28	0.165807479755987	0	FACETS	0.55	0.488	0.617			1	INDETERMINATE	1	TRUE	0	0.37	0		383	532	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55270264	55270264	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs768226783	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	116	649	0	ENST00000275493.2:c.3217C>A	p.Pro1073Thr	p.P1073T	ENST00000275493	NM_005228.3	1073	Ccc/Acc	27/28	0.165807479755987	0	FACETS	0.56	0.505	0.617			1	INDETERMINATE	1	TRUE	0	0.37	0		649	706	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509897	106509897	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	98	434	1	ENST00000359195.3:c.1891C>A	p.Leu631Met	p.L631M	ENST00000359195	NM_002649.2	631	Ctg/Atg	2/11	1	2	FACETS	0.701	0.625	0.781	0.701	0.625	0.781	SUBCLONAL	1	TRUE	1	0.37	2		435	756	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339478	116339478	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	76	259	0	ENST00000397752.3:c.340G>A	p.Asp114Asn	p.D114N	ENST00000397752	NM_000245.2	114	Gat/Aat	2/21	1	2	FACETS	0.919	0.809	1	0.919	0.809	1	CLONAL	1	TRUE	1	0.37	2		259	447	SUCCESS
MET	4233	MSKCC	GRCh37	7	116339946	116339946	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	113	453	0	ENST00000397752.3:c.808G>T	p.Asp270Tyr	p.D270Y	ENST00000397752	NM_000245.2	270	Gat/Tat	2/21	1	2	FACETS	0.971	0.876	1	0.971	0.876	1	CLONAL	1	TRUE	1	0.37	2		453	629	SUCCESS
MET	4233	MSKCC	GRCh37	7	116423402	116423402	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	76	297	0	ENST00000397752.3:c.3677C>A	p.Ala1226Asp	p.A1226D	ENST00000397752	NM_000245.2	1226	gCc/gAc	19/21	1	2	FACETS	0.915	0.806	1	0.915	0.806	1	CLONAL	1	TRUE	1	0.37	2		297	449	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151842256	151842256	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	473	121	335	0	ENST00000262189.6:c.14156T>A	p.Val4719Asp	p.V4719D	ENST00000262189	NM_170606.2	4719	gTc/gAc	54/59	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.37	2		335	594	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845234	151845234	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs199858308	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	90	326	0	ENST00000262189.6:c.13778A>G	p.Asn4593Ser	p.N4593S	ENST00000262189	NM_170606.2	4593	aAt/aGt	52/59	1	2	FACETS	0.999	0.89	1	0.999	0.89	1	CLONAL	1	TRUE	1	0.37	2		326	487	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23540330	23540330	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	104	457	0	ENST00000380871.4:c.73C>A	p.Pro25Thr	p.P25T	ENST00000380871	NM_006167.3	25	Ccg/Acg	1/2	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.37	2		457	455	SUCCESS
DUSP4	1846	MSKCC	GRCh37	8	29194674	29194674	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	137	593	2	ENST00000240100.2:c.1054G>T	p.Glu352Ter	p.E352*	ENST00000240100	NM_001394.6	352	Gag/Tag	4/4	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.37	2		595	730	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38186915	38186915	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	162	678	0	ENST00000317025.8:c.1562A>G	p.Gln521Arg	p.Q521R	ENST00000317025	NM_023034.1	521	cAa/cGa	6/24	1	2	FACETS	0.833	0.763	0.906	0.833	0.763	0.906	CLONAL	1	TRUE	1	0.37	2		678	1051	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38205214	38205214	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	165	646	0	ENST00000317025.8:c.476A>T	p.Lys159Ile	p.K159I	ENST00000317025	NM_023034.1	159	aAa/aTa	2/24	1	2	FACETS	0.791	0.725	0.86	0.791	0.725	0.86	SUBCLONAL	1	TRUE	1	0.37	2		646	1128	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69058479	69058479	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	114	510	0	ENST00000288368.4:c.4123C>T	p.Gln1375Ter	p.Q1375*	ENST00000288368	NM_024870.2	1375	Caa/Taa	34/40	1	2	FACETS	0.85	0.766	0.939	0.85	0.766	0.939	CLONAL	1	TRUE	1	0.37	2		510	725	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69069654	69069654	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs762727483	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	102	549	0	ENST00000288368.4:c.4329G>T	p.Gln1443His	p.Q1443H	ENST00000288368	NM_024870.2	1443	caG/caT	35/40	1	2	FACETS	0.673	0.602	0.749	0.673	0.602	0.749	SUBCLONAL	1	TRUE	1	0.37	2		549	819	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70978472	70978472	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	246	51	270	0	ENST00000276594.2:c.1181A>G	p.Glu394Gly	p.E394G	ENST00000276594	NM_024504.3	394	gAa/gGa	5/8	1	2	FACETS	0.928	0.794	1	0.928	0.794	1	CLONAL	1	TRUE	1	0.37	2		270	297	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90965883	90965883	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	64	213	0	ENST00000265433.3:c.1434C>G	p.Cys478Trp	p.C478W	ENST00000265433	NM_002485.4	478	tgC/tgG	11/16	1	2	FACETS	0.945	0.823	1	0.945	0.823	1	CLONAL	1	TRUE	1	0.37	2		213	366	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90967727	90967727	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	43	218	0	ENST00000265433.3:c.1181G>T	p.Arg394Ile	p.R394I	ENST00000265433	NM_002485.4	394	aGa/aTa	10/16	1	2	FACETS	0.602	0.505	0.71	0.602	0.505	0.71	SUBCLONAL	1	TRUE	1	0.37	2		218	386	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869549	117869549	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	118	554	0	ENST00000297338.2:c.645T>A	p.Tyr215Ter	p.Y215*	ENST00000297338	NM_006265.2	215	taT/taA	6/14	1	2	FACETS	0.85	0.768	0.938	0.85	0.768	0.938	CLONAL	1	TRUE	1	0.37	2		554	750	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145741506	145741506	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	93	603	1	ENST00000428558.2:c.997G>T	p.Ala333Ser	p.A333S	ENST00000428558	NM_004260.3	333	Gct/Tct	5/22	1	2	FACETS	0.655	0.582	0.733	0.655	0.582	0.733	SUBCLONAL	1	TRUE	1	0.37	2		604	767	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5089825	5089825	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	66	347	0	ENST00000381652.3:c.2723A>T	p.Asp908Val	p.D908V	ENST00000381652	NM_004972.3	908	gAc/gTc	20/25	1	2	FACETS	0.705	0.613	0.804	0.705	0.613	0.804	SUBCLONAL	1	TRUE	1	0.37	2		347	506	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8317943	8317943	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	51	341	0	ENST00000356435.5:c.5671-1G>A		p.X1891_splice	ENST00000356435		1891			1	2	FACETS	0.709	0.604	0.823	0.709	0.604	0.823	SUBCLONAL	1	TRUE	1	0.37	2		341	389	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319833	8319833	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	86	309	0	ENST00000356435.5:c.5668G>T	p.Glu1890Ter	p.E1890*	ENST00000356435		1890	Gag/Tag	34/35	1	2	FACETS	0.884	0.784	0.99	0.884	0.784	0.99	CLONAL	1	TRUE	1	0.37	2		309	526	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8500886	8500886	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	136	519	0	ENST00000356435.5:c.1996C>A	p.Pro666Thr	p.P666T	ENST00000356435		666	Cct/Act	13/35	1	2	FACETS	0.957	0.871	1	0.957	0.871	1	CLONAL	1	TRUE	1	0.37	2		519	768	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21974714	21974714	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1563892591	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	51	323	0	ENST00000304494.5:c.113C>T	p.Pro38Leu	p.P38L	ENST00000304494	NM_000077.4	38	cCc/cTc	1/3	1	2	FACETS	0.72	0.614	0.835	0.72	0.614	0.835	SUBCLONAL	1	TRUE	1	0.37	2		323	383	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27185619	27185619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1217204389	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	155	611	0	ENST00000380036.4:c.1319C>T	p.Ser440Phe	p.S440F	ENST00000380036	NM_000459.3	440	tCt/tTt	9/23	1	2	FACETS	1	0.926	1	1	0.926	1	CLONAL	1	TRUE	1	0.37	2		611	828	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197357	27197357	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	142	707	0	ENST00000380036.4:c.1669A>G	p.Thr557Ala	p.T557A	ENST00000380036	NM_000459.3	557	Acc/Gcc	12/23	1	2	FACETS	0.899	0.819	0.982	0.899	0.819	0.982	CLONAL	1	TRUE	1	0.37	2		707	854	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212754	27212754	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	143	626	0	ENST00000380036.4:c.2736C>G	p.Asp912Glu	p.D912E	ENST00000380036	NM_000459.3	912	gaC/gaG	17/23	1	2	FACETS	0.971	0.886	1	0.971	0.886	1	CLONAL	1	TRUE	1	0.37	2		626	796	SUCCESS
GNAQ	2776	MSKCC	GRCh37	9	80336327	80336327	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	89	330	0	ENST00000286548.4:c.992C>A	p.Ala331Asp	p.A331D	ENST00000286548	NM_002072.3	331	gCc/gAc	7/7	1	2	FACETS	0.82	0.728	0.917	0.82	0.728	0.917	CLONAL	1	TRUE	1	0.37	2		330	587	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87317121	87317121	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	558	98	418	0	ENST00000277120.3:c.260T>A	p.Val87Asp	p.V87D	ENST00000277120		87	gTt/gAt	3/19	1	2	FACETS	0.808	0.721	0.899	0.808	0.721	0.899	CLONAL	1	TRUE	1	0.37	2		418	656	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87482164	87482164	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	137	549	0	ENST00000277120.3:c.1451C>G	p.Ala484Gly	p.A484G	ENST00000277120		484	gCc/gGc	14/19	1	2	FACETS	1	0.95	1	1	0.95	1	CLONAL	1	TRUE	1	0.37	2		549	697	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641074	93641074	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	122	461	0	ENST00000375746.1:c.1420C>G	p.Leu474Val	p.L474V	ENST00000375746	NM_001174167.1	474	Ctg/Gtg	11/14	1	2	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	1	0.37	2		461	603	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231231	98231231	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	99	414	0	ENST00000331920.6:c.2052G>T	p.Glu684Asp	p.E684D	ENST00000331920	NM_000264.3	684	gaG/gaT	14/24	1	2	FACETS	1	0.923	1	1	0.923	1	CLONAL	1	TRUE	1	0.37	2		414	516	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98231356	98231356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	86	397	0	ENST00000331920.6:c.1927C>T	p.Pro643Ser	p.P643S	ENST00000331920	NM_000264.3	643	Cct/Tct	14/24	1	2	FACETS	0.845	0.749	0.947	0.845	0.749	0.947	CLONAL	1	TRUE	1	0.37	2		397	550	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98238404	98238404	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	84	302	0	ENST00000331920.6:c.1640G>A	p.Ser547Asn	p.S547N	ENST00000331920	NM_000264.3	547	aGc/aAc	12/24	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.37	2		302	409	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98268715	98268715	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	104	404	0	ENST00000331920.6:c.368C>T	p.Thr123Ile	p.T123I	ENST00000331920	NM_000264.3	123	aCc/aTc	2/24	1	2	FACETS	0.979	0.879	1	0.979	0.879	1	CLONAL	1	TRUE	1	0.37	2		404	574	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249447	110249447	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	767	189	892	0	ENST00000374672.4:c.1126C>G	p.Pro376Ala	p.P376A	ENST00000374672	NM_004235.4	376	Cca/Gca	4/5	1	2	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	TRUE	1	0.37	2		892	956	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912107	127912107	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	91	394	0	ENST00000373547.4:c.763G>T	p.Val255Leu	p.V255L	ENST00000373547	NM_002721.4	255	Gta/Tta	7/7	1	2	FACETS	0.901	0.802	1	0.901	0.802	1	CLONAL	1	TRUE	1	0.37	2		394	546	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128420058	128420058	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	139	603	0	ENST00000265960.3:c.370T>A	p.Phe124Ile	p.F124I	ENST00000265960	NM_001006617.1	124	Ttt/Att	4/12	1	2	FACETS	0.903	0.822	0.988	0.903	0.822	0.988	CLONAL	1	TRUE	1	0.37	2		603	832	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135778118	135778118	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	103	517	0	ENST00000298552.3:c.2265G>T	p.Gln755His	p.Q755H	ENST00000298552	NM_001162426.1	755	caG/caT	18/23	1	2	FACETS	0.854	0.765	0.948	0.854	0.765	0.948	CLONAL	1	TRUE	1	0.37	2		517	652	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782706	135782706	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	106	522	1	ENST00000298552.3:c.1315C>A	p.Leu439Met	p.L439M	ENST00000298552	NM_001162426.1	439	Ctg/Atg	13/23	1	2	FACETS	0.933	0.838	1	0.933	0.838	1	CLONAL	1	TRUE	1	0.37	2		523	614	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137293594	137293594	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	780	168	891	0	ENST00000481739.1:c.145T>G	p.Ser49Ala	p.S49A	ENST00000481739	NM_002957.4	49	Tct/Gct	2/10	1	2	FACETS	0.958	0.88	1	0.958	0.88	1	CLONAL	1	TRUE	1	0.37	2		891	948	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309172	137309172	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs145832863	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	109	574	0	ENST00000481739.1:c.779C>T	p.Ser260Leu	p.S260L	ENST00000481739	NM_002957.4	260	tCg/tTg	5/10	1	2	FACETS	0.928	0.835	1	0.928	0.835	1	CLONAL	1	TRUE	1	0.37	2		574	635	SUCCESS
EGFL7	51162	MSKCC	GRCh37	9	139565414	139565414	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	138	583	2	ENST00000308874.7:c.584C>T	p.Ala195Val	p.A195V	ENST00000308874		195	gCa/gTa	8/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.37	2		585	702	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139815490	139815490	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	472	78	402	1	ENST00000247668.2:c.961G>C	p.Val321Leu	p.V321L	ENST00000247668	NM_021138.3	321	Gtg/Ctg	9/11	1	2	FACETS	0.767	0.675	0.865	0.767	0.675	0.865	SUBCLONAL	1	TRUE	1	0.37	2		403	550	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317557	1317557	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775246045	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	101	473	1	ENST00000400841.2:c.508G>A	p.Val170Ile	p.V170I	ENST00000400841		170	Gtc/Atc	5/6	0.130923951212186	0	FACETS	0.608	0.544	0.674			1	INDETERMINATE	1	TRUE	0	0.37	0		474	566	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15822262	15822262	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1216810013	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	120	409	0	ENST00000307771.7:c.341A>G	p.Gln114Arg	p.Q114R	ENST00000307771	NM_005089.3	114	cAg/cGg	5/11	0.130923951212186	0	FACETS	0.615	0.556	0.676			1	INDETERMINATE	1	TRUE	0	0.37	0		409	665	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841306	15841306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1196200389	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	188	568	1	ENST00000307771.7:c.1390C>T	p.Arg464Cys	p.R464C	ENST00000307771	NM_005089.3	464	Cgt/Tgt	11/11	0.130923951212186	0	FACETS	0.694	0.642	0.749			1	INDETERMINATE	1	TRUE	0	0.37	0		569	922	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39922964	39922964	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	458	109	459	0	ENST00000378444.4:c.3744G>T	p.Gln1248His	p.Q1248H	ENST00000378444	NM_001123385.1	1248	caG/caT	8/15	0.130923951212186	0	FACETS	0.655	0.59	0.723			1	INDETERMINATE	1	TRUE	0	0.37	0		459	567	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932495	39932495	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	166	676	0	ENST00000378444.4:c.2104C>A	p.Leu702Met	p.L702M	ENST00000378444	NM_001123385.1	702	Ctg/Atg	4/15	0.130923951212186	0	FACETS	0.759	0.698	0.822			1	INDETERMINATE	1	TRUE	0	0.37	0		676	745	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934115	39934115	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	107	473	0	ENST00000378444.4:c.484A>T	p.Thr162Ser	p.T162S	ENST00000378444	NM_001123385.1	162	Aca/Tca	4/15	0.130923951212186	0	FACETS	0.627	0.564	0.694			1	INDETERMINATE	1	TRUE	0	0.37	0		473	581	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44911035	44911035	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	103	497	0	ENST00000377967.4:c.736T>G	p.Leu246Val	p.L246V	ENST00000377967	NM_021140.2	246	Tta/Gta	9/29	0.130923951212186	0	FACETS	0.511	0.457	0.567			1	INDETERMINATE	1	TRUE	0	0.37	0		497	687	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44919275	44919275	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	33	260	0	ENST00000377967.4:c.1203G>C	p.Leu401Phe	p.L401F	ENST00000377967	NM_021140.2	401	ttG/ttC	13/29	0.130923951212186	0	FACETS	0.482	0.395	0.579			1	INDETERMINATE	1	TRUE	0	0.37	0		260	233	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44929103	44929103	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	143	486	0	ENST00000377967.4:c.2203G>A	p.Gly735Arg	p.G735R	ENST00000377967	NM_021140.2	735	Gga/Aga	17/29	0.130923951212186	0	FACETS	0.669	0.611	0.73			1	INDETERMINATE	1	TRUE	0	0.37	0		486	728	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44938515	44938515	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	161	587	1	ENST00000377967.4:c.3063G>A	p.Trp1021Ter	p.W1021*	ENST00000377967	NM_021140.2	1021	tgG/tgA	20/29	0.130923951212186	0	FACETS	0.677	0.621	0.735			1	INDETERMINATE	1	TRUE	0	0.37	0		588	810	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47035926	47035926	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	111	684	0	ENST00000377604.3:c.604G>A	p.Val202Met	p.V202M	ENST00000377604	NM_001204468.1	202	Gtg/Atg	7/24	0.130923951212186	0	FACETS	0.48	0.432	0.532			1	INDETERMINATE	1	TRUE	0	0.37	0		684	787	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038889	47038889	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	100	542	0	ENST00000377604.3:c.896A>T	p.Asn299Ile	p.N299I	ENST00000377604	NM_001204468.1	299	aAt/aTt	9/24	0.130923951212186	0	FACETS	0.536	0.48	0.596			1	INDETERMINATE	1	TRUE	0	0.37	0		542	635	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47041661	47041661	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	139	688	2	ENST00000377604.3:c.1886C>T	p.Thr629Ile	p.T629I	ENST00000377604	NM_001204468.1	629	aCa/aTa	17/24	0.130923951212186	0	FACETS	0.59	0.537	0.646			1	INDETERMINATE	1	TRUE	0	0.37	0		690	802	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48650616	48650616	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	159	631	0	ENST00000376670.3:c.586C>A	p.Leu196Met	p.L196M	ENST00000376670	NM_002049.3	196	Ctg/Atg	3/6	0.130923951212186	0	FACETS	0.741	0.68	0.804			1	INDETERMINATE	1	TRUE	0	0.37	0		631	731	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53253994	53253994	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	123	585	0	ENST00000375401.3:c.78C>A	p.Asp26Glu	p.D26E	ENST00000375401	NM_004187.3	26	gaC/gaA	1/26	0.130923951212186	0	FACETS	0.65	0.589	0.715			1	INDETERMINATE	1	TRUE	0	0.37	0		585	644	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410526	63410526	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs750449400	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	77	469	0	ENST00000330258.3:c.2641C>T	p.Arg881Ter	p.R881*	ENST00000330258	NM_152424.3	881	Cga/Tga	2/2	0.130923951212186	0	FACETS	0.456	0.401	0.515			1	INDETERMINATE	1	TRUE	0	0.37	0		469	575	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411472	63411472	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	669	77	769	0	ENST00000330258.3:c.1695G>T	p.Gln565His	p.Q565H	ENST00000330258	NM_152424.3	565	caG/caT	2/2	0.130923951212186	0	FACETS	0.351	0.308	0.398			1	INDETERMINATE	1	TRUE	0	0.37	0		769	746	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413082	63413082	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	81	643	0	ENST00000330258.3:c.85G>C	p.Ala29Pro	p.A29P	ENST00000330258	NM_152424.3	29	Gcc/Ccc	2/2	0.130923951212186	0	FACETS	0.347	0.305	0.392			1	INDETERMINATE	1	TRUE	0	0.37	0		643	796	SUCCESS
AR	367	MSKCC	GRCh37	X	66766562	66766562	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	724	208	818	0	ENST00000374690.3:c.1574G>C	p.Gly525Ala	p.G525A	ENST00000374690	NM_000044.3	525	gGc/gCc	1/8	0.130923951212186	0	FACETS	0.76	0.706	0.816			1	INDETERMINATE	1	TRUE	0	0.37	0		818	932	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70342192	70342192	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	83	423	0	ENST00000374080.3:c.1244A>C	p.Gln415Pro	p.Q415P	ENST00000374080		415	cAg/cCg	8/45	0.130923951212186	0	FACETS	0.473	0.418	0.533			1	INDETERMINATE	1	TRUE	0	0.37	0		423	597	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70349020	70349020	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	135	601	0	ENST00000374080.3:c.3532C>T	p.His1178Tyr	p.H1178Y	ENST00000374080		1178	Cac/Tac	25/45	0.130923951212186	0	FACETS	0.53	0.481	0.581			1	INDETERMINATE	1	TRUE	0	0.37	0		601	868	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70352336	70352336	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	111	567	0	ENST00000374080.3:c.4363C>T	p.Gln1455Ter	p.Q1455*	ENST00000374080		1455	Cag/Tag	31/45	0.130923951212186	0	FACETS	0.541	0.486	0.598			1	INDETERMINATE	1	TRUE	0	0.37	0		567	699	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70354956	70354956	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	562	34	481	1	ENST00000374080.3:c.4878G>T	p.Glu1626Asp	p.E1626D	ENST00000374080		1626	gaG/gaT	36/45	0.130923951212186	0	FACETS	0.194	0.158	0.235			1	INDETERMINATE	1	TRUE	0	0.37	0		482	596	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76889090	76889090	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	128	638	0	ENST00000373344.5:c.4920G>C	p.Lys1640Asn	p.K1640N	ENST00000373344	NM_000489.3	1640	aaG/aaC	18/35	0.130923951212186	0	FACETS	0.579	0.525	0.636			1	INDETERMINATE	1	TRUE	0	0.37	0		638	753	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76918876	76918876	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	93	642	0	ENST00000373344.5:c.4115G>T	p.Arg1372Ile	p.R1372I	ENST00000373344	NM_000489.3	1372	aGa/aTa	12/35	0.130923951212186	0	FACETS	0.368	0.326	0.412			1	INDETERMINATE	1	TRUE	0	0.37	0		642	861	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938313	76938313	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	102	538	0	ENST00000373344.5:c.2435C>A	p.Ser812Tyr	p.S812Y	ENST00000373344	NM_000489.3	812	tCt/tAt	9/35	0.130923951212186	0	FACETS	0.489	0.438	0.544			1	INDETERMINATE	1	TRUE	0	0.37	0		538	710	SUCCESS
BTK	695	MSKCC	GRCh37	X	100617594	100617594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	142	679	1	ENST00000308731.7:c.475G>A	p.Ala159Thr	p.A159T	ENST00000308731	NM_000061.2	159	Gcc/Acc	6/19	0.130923951212186	0	FACETS	0.565	0.515	0.618			1	INDETERMINATE	1	TRUE	0	0.37	0		680	856	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123171438	123171438	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	87	545	0	ENST00000218089.9:c.350T>A	p.Leu117His	p.L117H	ENST00000218089	NM_001042749.1	117	cTt/cAt	6/35	0.130923951212186	0	FACETS	0.359	0.317	0.404			1	INDETERMINATE	1	TRUE	0	0.37	0		545	825	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179018	123179018	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	75	414	0	ENST00000218089.9:c.467G>C	p.Ser156Thr	p.S156T	ENST00000218089	NM_001042749.1	156	aGt/aCt	8/35	0.130923951212186	0	FACETS	0.491	0.431	0.556			1	INDETERMINATE	1	TRUE	0	0.37	0		414	520	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123191727	123191727	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777167759	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	61	410	0	ENST00000218089.9:c.1316G>A	p.Arg439His	p.R439H	ENST00000218089	NM_001042749.1	439	cGt/cAt	15/35	0.130923951212186	0	FACETS	0.39	0.337	0.449			1	INDETERMINATE	1	TRUE	0	0.37	0		410	532	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123217366	123217366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	740	100	582	0	ENST00000218089.9:c.3020C>A	p.Ser1007Tyr	p.S1007Y	ENST00000218089	NM_001042749.1	1007	tCt/tAt	29/35	0.130923951212186	0	FACETS	0.405	0.362	0.452			1	INDETERMINATE	1	TRUE	0	0.37	0		582	840	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123224422	123224422	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	109	438	1	ENST00000218089.9:c.3278-3C>T		p.X1093_splice	ENST00000218089	NM_001042749.1	1093			0.130923951212186	0	FACETS	0.52	0.467	0.576			1	INDETERMINATE	1	TRUE	0	0.37	0		439	714	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860071	152860071	+	synonymous_variant	Silent	SNP	G	G	A	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	48	615	0	ENST00000406277.2:c.357C>T	p.Ile119=	p.I119=	ENST00000406277	NM_152274.4	119	atC/atT	5/7	0.130923951212186		FACETS		0.199	0.278				INDETERMINATE	1	TRUE	0	0.37	0		615	691	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50918845	50918847	+	missense_variant,splice_region_variant	Missense_Mutation	TNP	GAG	GAG	TAA	novel	NA	P-0016773-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	86	587	0	ENST00000440232.2:c.2715_2717delinsTAA	p.Glu905_Arg906delinsAspLys	p.E905_R906delinsDK	ENST00000440232	NM_002691.3	905	gaGAGg/gaTAAg	21/27	1	2	FACETS	0.8	0.709	0.897	0.8	0.709	0.897	SUBCLONAL	1	TRUE	1	0.37	2		587	581	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453136	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs113488022	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	101	351	0	ENST00000288602.6:c.1799T>A	p.Val600Glu	p.V600E	ENST00000288602	NM_004333.4	600	gTg/gAg	15/18	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.22	2		351	866	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	65	736	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.22	2		741	508	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247289	153247289	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149680468	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	101	616	1	ENST00000281708.4:c.1513C>T	p.Arg505Cys	p.R505C	ENST00000281708	NM_033632.3	505	Cgc/Tgc	10/12	1	2	FACETS	1	0.909	1	1	0.909	1	CLONAL	1	TRUE	1	0.22	2		617	900	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13975473	13975473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	342	23	225	1	ENST00000405192.2:c.414del	p.Thr139HisfsTer116	p.T139Hfs*116	ENST00000405192	NM_001163147.1	138	ccC/cc	7/12	1	2	FACETS	0.573	0.446	0.72	0.573	0.446	0.72	SUBCLONAL	1	TRUE	1	0.22	2		226	365	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30691872	30691873	+	frameshift_variant	Frame_Shift_Del	DEL	AA	AA	-	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	103	320	1	ENST00000295754.5:c.382_383del	p.Lys128AlafsTer3	p.K128Afs*3	ENST00000295754	NM_003242.5	125	gAA/g	3/7	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.22	2		321	719	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	752	169	430	2	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	0.834	0.767	0.904	1	0.99	1	CLONAL	2	TRUE	1	0.22	2		432	921	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16242646	16242646	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1068	57	638	3	ENST00000375759.3:c.1267C>T	p.Arg423Cys	p.R423C	ENST00000375759	NM_015001.2	423	Cgc/Tgc	6/15	1	2	FACETS	0.461	0.393	0.534	0.461	0.393	0.534	SUBCLONAL	1	TRUE	1	0.22	2		641	1125	SUCCESS
SESN2	83667	MSKCC	GRCh37	1	28605660	28605660	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	932	55	719	0	ENST00000253063.3:c.1264A>G	p.Lys422Glu	p.K422E	ENST00000253063	NM_031459.4	422	Aag/Gag	9/10	1	2	FACETS	0.507	0.432	0.589	0.507	0.432	0.589	SUBCLONAL	1	TRUE	1	0.22	2		719	987	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115262276	115262276	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	60	715	0	ENST00000438362.2:c.2278G>T	p.Gly760Ter	p.G760*	ENST00000438362	NM_001242891.1	760	Gga/Tga	18/20	1	2	FACETS	0.509	0.437	0.588	0.509	0.437	0.588	SUBCLONAL	1	TRUE	1	0.22	2		715	1072	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115275364	115275364	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs542388231	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	52	677	1	ENST00000438362.2:c.1049C>T	p.Thr350Met	p.T350M	ENST00000438362	NM_001242891.1	350	aCg/aTg	10/20	1	2	FACETS	0.473	0.401	0.552	0.473	0.401	0.552	SUBCLONAL	1	TRUE	1	0.22	2		678	1000	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480570	120480571	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	rs1553195973	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	49	519	0	ENST00000256646.2:c.3246dup	p.Ala1083SerfsTer17	p.A1083Sfs*17	ENST00000256646	NM_024408.3	1082	-/A	20/34	1	2	FACETS	0.513	0.433	0.601	0.513	0.433	0.601	SUBCLONAL	1	TRUE	1	0.22	2		519	869	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243668583	243668583	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	49	490	1	ENST00000263826.5:c.1408C>T	p.Gln470Ter	p.Q470*	ENST00000263826	NM_005465.4	470	Caa/Taa	13/13	1	2	FACETS	0.549	0.463	0.643	0.549	0.463	0.643	SUBCLONAL	1	TRUE	1	0.22	2		491	812	SUCCESS
RET	5979	MSKCC	GRCh37	10	43608301	43608301	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	119	774	3	ENST00000355710.3:c.1649G>T	p.Gly550Val	p.G550V	ENST00000355710	NM_020975.4	550	gGg/gTg	9/20	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.22	2		777	861	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89720812	89720812	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs121913291	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	34	341	0	ENST00000371953.3:c.968del	p.Asn323MetfsTer21	p.N323Mfs*21	ENST00000371953	NM_000314.4	321	acA/ac	8/9	1	2	FACETS	0.691	0.565	0.834	0.691	0.565	0.834	SUBCLONAL	1	TRUE	1	0.22	2		341	447	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175495	108175495	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1240167425	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	91	537	0	ENST00000278616.4:c.5590A>G	p.Thr1864Ala	p.T1864A	ENST00000278616	NM_000051.3	1864	Aca/Gca	37/63	1	2	FACETS	1	0.922	1	1	0.922	1	CLONAL	1	TRUE	1	0.22	2		537	789	SUCCESS
CBL	867	MSKCC	GRCh37	11	119170370	119170370	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	35	447	0	ENST00000264033.4:c.2600del	p.Gln867ArgfsTer38	p.Q867Rfs*38	ENST00000264033	NM_005188.3	867	cAg/cg	16/16	1	2	FACETS	0.567	0.464	0.684	0.567	0.464	0.684	SUBCLONAL	1	TRUE	1	0.22	2		447	561	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	442737	442737	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	47	582	0	ENST00000399788.2:c.1569del	p.Glu524SerfsTer13	p.E524Sfs*13	ENST00000399788	NM_001042603.1	523	ccC/cc	12/28	0.3	2	FACETS	0.528	0.444	0.621			1	SUBCLONAL	1	TRUE	NA	0.22	2		582	809	SUCCESS
CDKN1B	1027	MSKCC	GRCh37	12	12871053	12871053	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	45	325	0	ENST00000228872.4:c.285del	p.Gly97ValfsTer22	p.G97Vfs*22	ENST00000228872	NM_004064.3	94	Ccc/cc	1/3	0.3	2	FACETS	1	0.869	1			1	CLONAL	1	TRUE	NA	0.22	2		325	395	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18499650	18499650	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs752464101	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	55	707	0	ENST00000266497.5:c.1505A>G	p.Tyr502Cys	p.Y502C	ENST00000266497		502	tAt/tGt	10/31	1	2	FACETS	0.493	0.42	0.573	0.493	0.42	0.573	SUBCLONAL	1	TRUE	1	0.22	2		707	1014	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21629929	21629929	+	splice_region_variant,intron_variant	Splice_Region	DEL	A	A	-	rs762736004	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	68	422	3	ENST00000421138.2:c.868-3del		p.X290_splice	ENST00000421138		290			1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.22	2		425	581	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49423188	49423188	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762462902	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	49	626	1	ENST00000301067.7:c.14071G>A	p.Val4691Ile	p.V4691I	ENST00000301067	NM_003482.3	4691	Gtc/Atc	43/54	1	2	FACETS	0.56	0.473	0.656	0.56	0.473	0.656	SUBCLONAL	1	TRUE	1	0.22	2		627	796	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494882	56494882	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376234145	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	51	485	0	ENST00000267101.3:c.3239G>A	p.Arg1080His	p.R1080H	ENST00000267101	NM_001982.3	1080	cGt/cAt	27/28	1	2	FACETS	0.63	0.534	0.736	0.63	0.534	0.736	SUBCLONAL	1	TRUE	1	0.22	2		485	736	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21565435	21565435	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1217575272	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	46	636	5	ENST00000382592.4:c.451C>T	p.Arg151Trp	p.R151W	ENST00000382592	NM_014572.2	151	Cgg/Tgg	3/8	1	2	FACETS	0.521	0.437	0.614	0.521	0.437	0.614	SUBCLONAL	1	TRUE	1	0.22	2		641	803	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29041262	29041262	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	62	473	2	ENST00000282397.4:c.166del	p.Glu56LysfsTer12	p.E56Kfs*12	ENST00000282397	NM_002019.4	56	Gaa/aa	3/30	1	2	FACETS	0.816	0.704	0.938	0.816	0.704	0.938	CLONAL	1	TRUE	1	0.22	2		475	691	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	41001215	41001215	+	splice_region_variant,intron_variant	Splice_Region	DEL	T	T	-	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	40	404	2	ENST00000267868.3:c.344-3del		p.X115_splice	ENST00000267868	NM_002875.4	115			1	2	FACETS	0.58	0.481	0.691	0.58	0.481	0.691	SUBCLONAL	1	TRUE	1	0.22	2		406	627	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90630711	90630711	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1339259178	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	51	651	1	ENST00000330062.3:c.775G>A	p.Asp259Asn	p.D259N	ENST00000330062	NM_002168.2	259	Gat/Aat	6/11	1	2	FACETS	0.499	0.422	0.583	0.499	0.422	0.583	SUBCLONAL	1	TRUE	1	0.22	2		652	930	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9943625	9943625	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	55	616	0	ENST00000330684.3:c.1316T>C	p.Phe439Ser	p.F439S	ENST00000330684	NM_001134407.1	439	tTc/tCc	5/13	1	2	FACETS	0.603	0.514	0.701	0.603	0.514	0.701	SUBCLONAL	1	TRUE	1	0.22	2		616	829	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72831056	72831056	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	46	262	0	ENST00000268489.5:c.5525C>T	p.Pro1842Leu	p.P1842L	ENST00000268489	NM_006885.3	1842	cCa/cTa	9/10	1	2	FACETS	1	0.854	1	1	0.854	1	CLONAL	1	TRUE	1	0.22	2		262	413	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15974899	15974899	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	75	476	0	ENST00000268712.3:c.3976C>T	p.Arg1326Ter	p.R1326*	ENST00000268712	NM_006311.3	1326	Cga/Tga	30/46	1	2	FACETS	1	0.889	1	1	0.889	1	CLONAL	1	TRUE	1	0.22	2		476	671	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627688	37627688	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1083	151	924	2	ENST00000447079.4:c.1607del	p.Pro536HisfsTer74	p.P536Hfs*74	ENST00000447079	NM_015083.1	535	Ccc/cc	2/14	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.22	2		926	1234	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56437569	56437569	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	81	628	1	ENST00000407977.2:c.893del	p.Cys298LeufsTer121	p.C298Lfs*121	ENST00000407977		298	tGt/tt	8/10	1	2	FACETS	0.85	0.748	0.961	0.85	0.748	0.961	CLONAL	1	TRUE	1	0.22	2		629	866	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897444	78897444	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746953724	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	94	651	0	ENST00000306801.3:c.2779C>T	p.Arg927Trp	p.R927W	ENST00000306801	NM_020761.2	927	Cgg/Tgg	23/34	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.22	2		651	740	SUCCESS
PMAIP1	5366	MSKCC	GRCh37	18	57569908	57569910	+	inframe_deletion	In_Frame_Del	DEL	AGG	AGG	-	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	33	321	0	ENST00000316660.6:c.90_92del	p.Arg31del	p.R31del	ENST00000316660	NM_021127.2	30	AGG/-	2/2	1	2	FACETS	0.519	0.422	0.629	0.519	0.422	0.629	SUBCLONAL	1	TRUE	1	0.22	2		321	578	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5225740	5225740	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs1015526594	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	72	576	0	ENST00000357368.4:c.2492C>T	p.Ala831Val	p.A831V	ENST00000357368	NM_002850.3	831	gCa/gTa	17/38	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.22	2		576	614	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355254	15355254	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	26	327	1	ENST00000263377.2:c.2369C>T	p.Ala790Val	p.A790V	ENST00000263377	NM_058243.2	790	gCc/gTc	13/20	1	2	FACETS	0.608	0.481	0.753	0.608	0.481	0.753	SUBCLONAL	1	TRUE	1	0.22	2		328	389	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279905	18279905	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	59	637	0	ENST00000222254.8:c.1988G>A	p.Gly663Asp	p.G663D	ENST00000222254	NM_005027.3	663	gGc/gAc	16/16	1	2	FACETS	0.658	0.565	0.76	0.658	0.565	0.76	SUBCLONAL	1	TRUE	1	0.22	2		637	815	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210764	36210764	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs763183959	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	948	55	924	1	ENST00000222270.7:c.521del	p.Pro174GlnfsTer20	p.P174Qfs*20	ENST00000222270	NM_014727.1	172	aCc/ac	3/37	1	2	FACETS	0.499	0.425	0.58	0.499	0.425	0.58	SUBCLONAL	1	TRUE	1	0.22	2		925	1003	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210863	36210890	+	frameshift_variant	Frame_Shift_Del	DEL	CACCCCGGAGCCGGGCATGTGAGCCCTC	CACCCCGGAGCCGGGCATGTGAGCCCTC	-	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	88	745	0	ENST00000222270.7:c.620_647del	p.Arg207ProfsTer23	p.R207Pfs*23	ENST00000222270	NM_014727.1	205	gCACCCCGGAGCCGGGCATGTGAGCCCTCc/gc	3/37	1	2	FACETS	0.986	0.873	1	0.986	0.873	1	CLONAL	1	TRUE	1	0.22	2		745	811	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36213358	36213359	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	917	56	827	0	ENST00000222270.7:c.2561_2562del	p.Glu854AlafsTer34	p.E854Afs*34	ENST00000222270	NM_014727.1	852	aAG/a	4/37	1	2	FACETS	0.523	0.447	0.607	0.523	0.447	0.607	SUBCLONAL	1	TRUE	1	0.22	2		827	973	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25966267	25966267	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	39	374	0	ENST00000435504.4:c.2939T>C	p.Val980Ala	p.V980A	ENST00000435504		980	gTt/gCt	13/13	1	2	FACETS	0.562	0.465	0.671	0.562	0.465	0.671	SUBCLONAL	1	TRUE	1	0.22	2		374	631	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26101046	26101046	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	43	560	2	ENST00000435504.4:c.46G>A	p.Ala16Thr	p.A16T	ENST00000435504		16	Gcc/Acc	1/13	1	2	FACETS	0.565	0.471	0.669	0.565	0.471	0.669	SUBCLONAL	1	TRUE	1	0.22	2		562	692	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99193586	99193586	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	426	28	367	0	ENST00000074304.5:c.2781G>T	p.Gln927His	p.Q927H	ENST00000074304	NM_001134224.1	927	caG/caT	25/26	1	2	FACETS	0.561	0.447	0.69	0.561	0.447	0.69	SUBCLONAL	1	TRUE	1	0.22	2		367	454	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198285158	198285158	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	48	454	2	ENST00000335508.6:c.409G>A	p.Ala137Thr	p.A137T	ENST00000335508	NM_012433.2	137	Gca/Aca	4/25	1	2	FACETS	0.622	0.524	0.729	0.622	0.524	0.729	SUBCLONAL	1	TRUE	1	0.22	2		456	702	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204810	128204810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	72	886	0	ENST00000341105.2:c.631G>A	p.Val211Ile	p.V211I	ENST00000341105	NM_032638.4	211	Gtc/Atc	3/6	1	2	FACETS	0.697	0.607	0.794	0.697	0.607	0.794	SUBCLONAL	1	TRUE	1	0.22	2		886	939	SUCCESS
ATR	545	MSKCC	GRCh37	3	142266679	142266679	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146504354	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	877	48	661	0	ENST00000350721.4:c.3245G>A	p.Arg1082His	p.R1082H	ENST00000350721	NM_001184.3	1082	cGt/cAt	16/47	1	2	FACETS	0.472	0.397	0.554	0.472	0.397	0.554	SUBCLONAL	1	TRUE	1	0.22	2		661	925	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169953085	169953085	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	47	561	0	ENST00000295797.4:c.169A>G	p.Met57Val	p.M57V	ENST00000295797	NM_002740.5	57	Atg/Gtg	2/18	1	2	FACETS	0.493	0.414	0.58	0.493	0.414	0.58	SUBCLONAL	1	TRUE	1	0.22	2		561	867	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55604677	55604677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761339150	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	61	427	0	ENST00000288135.5:c.2885G>A	p.Ser962Asn	p.S962N	ENST00000288135	NM_000222.2	962	aGc/aAc	21/21	1	2	FACETS	0.756	0.651	0.87	0.756	0.651	0.87	SUBCLONAL	1	TRUE	1	0.22	2		427	734	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153245344	153245344	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	43	548	0	ENST00000281708.4:c.1847C>T	p.Thr616Ile	p.T616I	ENST00000281708	NM_033632.3	616	aCa/aTa	11/12	1	2	FACETS	0.477	0.398	0.566	0.477	0.398	0.566	SUBCLONAL	1	TRUE	1	0.22	2		548	819	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38945757	38945757	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1032272899	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	49	300	0	ENST00000357387.3:c.4469C>T	p.Thr1490Met	p.T1490M	ENST00000357387	NM_152756.3	1490	aCg/aTg	34/38	1	2	FACETS	0.884	0.749	1	0.884	0.749	1	CLONAL	1	TRUE	1	0.22	2		300	504	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38950366	38950366	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	38	424	0	ENST00000357387.3:c.3584G>T	p.Arg1195Ile	p.R1195I	ENST00000357387	NM_152756.3	1195	aGa/aTa	31/38	1	2	FACETS	0.476	0.392	0.57	0.476	0.392	0.57	SUBCLONAL	1	TRUE	1	0.22	2		424	726	SUCCESS
APC	324	MSKCC	GRCh37	5	112177434	112177435	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	58	472	0	ENST00000257430.4:c.6149dup	p.Lys2051GlufsTer9	p.K2051Efs*9	ENST00000257430	NM_000038.5	2048	cca/ccAa	16/16	1	2	FACETS	0.686	0.588	0.793	0.686	0.588	0.793	SUBCLONAL	1	TRUE	1	0.22	2		472	769	SUCCESS
APC	324	MSKCC	GRCh37	5	112178369	112178369	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	49	558	0	ENST00000257430.4:c.7078G>T	p.Gly2360Cys	p.G2360C	ENST00000257430	NM_000038.5	2360	Ggt/Tgt	16/16	1	2	FACETS	0.497	0.419	0.583	0.497	0.419	0.583	SUBCLONAL	1	TRUE	1	0.22	2		558	897	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131977937	131977937	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501978	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	54	445	0	ENST00000265335.6:c.3820G>A	p.Val1274Met	p.V1274M	ENST00000265335		1274	Gtg/Atg	25/25	1	2	FACETS	0.699	0.596	0.813	0.699	0.596	0.813	SUBCLONAL	1	TRUE	1	0.22	2		445	702	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287346	33287346	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371054058	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	40	489	0	ENST00000374542.5:c.1751C>T	p.Thr584Met	p.T584M	ENST00000374542	NM_001141970.1	584	aCg/aTg	6/8	1	2	FACETS	0.531	0.44	0.633	0.531	0.44	0.633	SUBCLONAL	1	TRUE	1	0.22	2		489	685	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141545617	141545617	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	955	66	820	0	ENST00000220592.5:c.2221A>G	p.Thr741Ala	p.T741A	ENST00000220592	NM_012154.3	741	Acc/Gcc	17/19	1	2	FACETS	0.588	0.508	0.674	0.588	0.508	0.674	SUBCLONAL	1	TRUE	1	0.22	2		820	1021	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139404302	139404302	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	98	700	0	ENST00000277541.6:c.2852G>A	p.Ser951Asn	p.S951N	ENST00000277541	NM_017617.3	951	aGt/aAt	18/34	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.22	2		700	795	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39933593	39933594	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	16	183	0	ENST00000378444.4:c.1005dup	p.Ser336LeufsTer45	p.S336Lfs*45	ENST00000378444	NM_001123385.1	335	-/C	4/15	1	1	FACETS	0.526	0.389	0.69	0.526	0.389	0.69	SUBCLONAL	1	TRUE	0	0.22	1		183	246	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53223345	53223345	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	58	308	0	ENST00000375401.3:c.4014G>T	p.Glu1338Asp	p.E1338D	ENST00000375401	NM_004187.3	1338	gaG/gaT	23/26	1	1	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	0	0.22	1		308	392	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63411530	63411530	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016890-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	51	445	0	ENST00000330258.3:c.1637del	p.Leu546CysfsTer16	p.L546Cfs*16	ENST00000330258	NM_152424.3	546	tTg/tg	2/2	1	1	FACETS	0.792	0.673	0.922	0.792	0.673	0.922	CLONAL	1	TRUE	0	0.22	1		445	521	SUCCESS
VHL	7428	MSKCC	GRCh37	3	10191501	10191501	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0016902-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	453	65	731	1	ENST00000256474.2:c.494T>A	p.Val165Asp	p.V165D	ENST00000256474	NM_000551.3	165	gTt/gAt	3/3	0.259540382308424	1	FACETS	0.841	0.731	0.961	0.841	0.731	0.961	CLONAL	1	TRUE	0	0.259540382308424	1		732	518	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562535	176562535	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016902-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	81	908	0	ENST00000439151.2:c.431A>C	p.Lys144Thr	p.K144T	ENST00000439151	NM_022455.4	144	aAg/aCg	2/23	0.259540382308424	3	FACETS	0.925	0.815	1	0.463	0.407	0.523	CLONAL	1	TRUE	1	0.259540382308424	3		908	762	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123179150	123179154	+	frameshift_variant	Frame_Shift_Del	DEL	TCATT	TCATT	-	novel	NA	P-0016902-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	200	59	357	0	ENST00000218089.9:c.602_606del	p.Ile201ThrfsTer7	p.I201Tfs*7	ENST00000218089	NM_001042749.1	200	gTCATT/g	8/35	1	1	FACETS	0.764	0.664	0.87	1	0.972	1	SUBCLONAL	2	TRUE	0	0.259540382308424	1		357	259	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	102	222	215	0				ENST00000310581	NM_198253.2	-/1132			0.547767454301797	4	FACETS	1	0.975	1	1	0.975	1	CLONAL	3	TRUE	1	0.79282285131373	4		215	324	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577085	7577085	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112431538	NA	P-0016925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	30	616	1	ENST00000269305.4:c.853G>A	p.Glu285Lys	p.E285K	ENST00000269305	NM_001126112.2	285	Gag/Aag	8/11	0.659220468874061	3	FACETS	0.13	0.104	0.159	0.065	0.052	0.08	SUBCLONAL	1	TRUE	1	0.79282285131373	3		617	815	SUCCESS
APC	324	MSKCC	GRCh37	5	112175162	112175162	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1561588104	NA	P-0016925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	54	239	244	0	ENST00000257430.4:c.3871C>T	p.Gln1291Ter	p.Q1291*	ENST00000257430	NM_000038.5	1291	Cag/Tag	16/16	0.79282285131373	3	FACETS	0.958	0.925	0.988	0.958	0.925	0.988	CLONAL	3	TRUE	0	0.79282285131373	3		244	293	SUCCESS
MYCL	4610	MSKCC	GRCh37	1	40363243	40363243	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	279	402	0	ENST00000397332.2:c.986C>T	p.Ser329Leu	p.S329L	ENST00000397332	NM_001033082.2	329	tCg/tTg	3/3	0.344903762997325	3	FACETS	0.912	0.867	0.957	0.912	0.867	0.957	INDETERMINATE	2	TRUE	1	0.79282285131373	3		402	539	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314981	1314981	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1255	189	611	0	ENST00000400841.2:c.680C>G	p.Pro227Arg	p.P227R	ENST00000400841		227	cCa/cGa	6/6	0.778800063789135	2	FACETS	0.33	0.304	0.358			1	SUBCLONAL	1	TRUE	NA	0.79282285131373	2		611	1444	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27056160	27056160	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	167	431	0	ENST00000324856.7:c.1156C>T	p.Gln386Ter	p.Q386*	ENST00000324856	NM_006015.4	386	Cag/Tag	2/20	0.344903762997325	3	FACETS	1	0.934	1	0.506	0.467	0.546	INDETERMINATE	1	TRUE	1	0.79282285131373	3		431	581	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971367	13971367	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs755892534	NA	P-0016925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	89	295	0	ENST00000405192.2:c.562C>T	p.Arg188Cys	p.R188C	ENST00000405192	NM_001163147.1	188	Cgc/Tgc	8/12	0.632792631379984	4	FACETS	0.643	0.571	0.72	0.214	0.19	0.24	SUBCLONAL	1	TRUE	1	0.79282285131373	4		295	626	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137328351	137328351	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519958	NA	P-0016925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	58	628	0	ENST00000481739.1:c.1280C>T	p.Ser427Phe	p.S427F	ENST00000481739	NM_002957.4	427	tCc/tTc	10/10	0.496841187731496	3	FACETS	0.233	0.199	0.27	0.117	0.099	0.135	SUBCLONAL	1	TRUE	1	0.79282285131373	3		628	876	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46739397	46739397	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	100	393	0	ENST00000371975.4:c.1588G>C	p.Glu530Gln	p.E530Q	ENST00000371975	NM_003579.3	530	Gag/Cag	14/18	0.344903762997325	3	FACETS	0.618	0.553	0.686	0.309	0.276	0.343	INDETERMINATE	1	TRUE	1	0.79282285131373	3		393	570	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118375038	118375038	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782078199	NA	P-0016925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	59	502	2	ENST00000534358.1:c.8431C>T	p.Arg2811Cys	p.R2811C	ENST00000534358	NM_005933.3	2811	Cgc/Tgc	27/36	0.78098918640339	3	FACETS	0.25	0.214	0.289	0.125	0.107	0.145	SUBCLONAL	1	TRUE	1	0.79282285131373	3		504	833	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623646	28623646	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	89	517	0	ENST00000241453.7:c.911C>T	p.Ser304Leu	p.S304L	ENST00000241453	NM_004119.2	304	tCa/tTa	8/24	0.271878423647248	4	FACETS	0.568	0.503	0.637	0.284	0.251	0.319	INDETERMINATE	1	TRUE	2	0.79282285131373	4		517	709	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95599654	95599654	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	19	245	0	ENST00000393063.1:c.142C>T	p.Gln48Ter	p.Q48*	ENST00000393063	NM_030621.3	48	Cag/Tag	3/28	1	2	FACETS	0.157	0.118	0.201	0.157	0.118	0.201	SUBCLONAL	1	TRUE	1	0.79282285131373	2		245	306	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618622	37618622	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	776	529	0	ENST00000447079.4:c.298C>T	p.Arg100Cys	p.R100C	ENST00000447079	NM_015083.1	100	Cgt/Tgt	1/14	0.79282285131373	5	FACETS	1	0.992	1	1	0.992	1	CLONAL	3	TRUE	2	0.79282285131373	5		529	1355	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267639	7267639	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	322	618	0	ENST00000302850.5:c.369C>G	p.Phe123Leu	p.F123L	ENST00000302850	NM_000208.2	123	ttC/ttG	2/22	0.324027864161276	5	FACETS	0.884	0.836	0.933	0.589	0.557	0.622	INDETERMINATE	2	TRUE	2	0.79282285131373	5		618	1006	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7267673	7267751	+	stop_gained,protein_altering_variant	Nonsense_Mutation	DEL	GATCCCCGGATGACCGTGAGGTTGGGGAACAGGTCCTTCAGGCTCTCGAGCCCATAGACCCGGAAGAGCAGCAAGTAAT	GATCCCCGGATGACCGTGAGGTTGGGGAACAGGTCCTTCAGGCTCTCGAGCCCATAGACCCGGAAGAGCAGCAAGTAAT	CATC	novel	NA	P-0016925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	321	538	2	ENST00000302850.5:c.257_335delinsGATG	p.Asp86_Ser112delinsGlyTer	p.D86_S112delinsG*	ENST00000302850	NM_000208.2	86	gATTACTTGCTGCTCTTCCGGGTCTATGGGCTCGAGAGCCTGAAGGACCTGTTCCCCAACCTCACGGTCATCCGGGGATCa/gGATGa	2/22	0.324027864161276	5	FACETS	0.904	0.855	0.953	0.602	0.57	0.636	INDETERMINATE	2	TRUE	2	0.79282285131373	5		540	981	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11024691	11024691	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0016925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	70	354	0	ENST00000327064.4:c.808G>T	p.Glu270Ter	p.E270*	ENST00000327064	NM_199141.1	270	Gag/Tag	6/16	0.324027864161276	5	FACETS	0.673	0.588	0.766	0.224	0.196	0.256	INDETERMINATE	1	TRUE	2	0.79282285131373	5		354	574	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662873	227662873	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	127	502	2	ENST00000305123.5:c.582C>A	p.Phe194Leu	p.F194L	ENST00000305123	NM_005544.2	194	ttC/ttA	1/2	0.781633763137034	3	FACETS	0.706	0.641	0.774	0.235	0.213	0.258	SUBCLONAL	1	TRUE	0	0.79282285131373	3		504	634	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41546084	41546084	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	787	44	595	1	ENST00000263253.7:c.2699C>A	p.Ser900Ter	p.S900*	ENST00000263253	NM_001429.3	900	tCa/tAa	14/31	0.496841187731496	3	FACETS	0.187	0.156	0.221	0.093	0.078	0.111	SUBCLONAL	1	TRUE	1	0.79282285131373	3		596	831	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12475550	12475550	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1479145908	NA	P-0016925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	113	519	2	ENST00000287820.6:c.1424C>T	p.Thr475Met	p.T475M	ENST00000287820	NM_015869.4	475	aCg/aTg	7/7	0.547767454301797	4	FACETS	0.576	0.517	0.637	0.192	0.172	0.213	SUBCLONAL	1	TRUE	1	0.79282285131373	4		521	888	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89445078	89445078	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	698	96	468	0	ENST00000336596.2:c.1398C>G	p.Ile466Met	p.I466M	ENST00000336596	NM_005233.5	466	atC/atG	6/17	0.547767454301797	4	FACETS	0.547	0.487	0.611	0.182	0.162	0.204	SUBCLONAL	1	TRUE	1	0.79282285131373	4		468	794	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215981	142215981	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	213	419	0	ENST00000350721.4:c.5612C>G	p.Ser1871Cys	p.S1871C	ENST00000350721	NM_001184.3	1871	tCt/tGt	33/47	0.547767454301797	4	FACETS	1	0.99	1	0.461	0.43	0.493	CLONAL	1	TRUE	1	0.79282285131373	4		419	697	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1801122	1801122	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121913116	NA	P-0016925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	45	663	0	ENST00000260795.2:c.251C>T	p.Ser84Leu	p.S84L	ENST00000260795		84	tCg/tTg	2/17	0.496841187731496	3	FACETS	0.199	0.166	0.235	0.099	0.083	0.118	SUBCLONAL	1	TRUE	1	0.79282285131373	3		663	798	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187554969	187554969	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs760550311	NA	P-0016925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	314	49	285	0	ENST00000441802.2:c.4192T>C	p.Tyr1398His	p.Y1398H	ENST00000441802	NM_005245.3	1398	Tac/Cac	7/27	0.496841187731496	3	FACETS	0.476	0.404	0.554	0.238	0.202	0.277	SUBCLONAL	1	TRUE	1	0.79282285131373	3		285	363	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674233	86674233	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	71	328	421	0	ENST00000274376.6:c.2365C>G	p.Arg789Gly	p.R789G	ENST00000274376	NM_002890.2	789	Cga/Gga	18/25	0.79282285131373	3	FACETS	0.965	0.937	0.991	0.965	0.937	0.991	CLONAL	3	TRUE	0	0.79282285131373	3		421	399	SUCCESS
APC	324	MSKCC	GRCh37	5	112102976	112102976	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	rs74953290	NA	P-0016925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	385	404	0	ENST00000257430.4:c.311C>G	p.Ser104Ter	p.S104*	ENST00000257430	NM_000038.5	104	tCa/tGa	4/16	0.79282285131373	3	FACETS	0.974	0.949	0.998	0.974	0.949	0.998	CLONAL	3	TRUE	0	0.79282285131373	3		404	464	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638363	176638363	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	518	550	0	ENST00000439151.2:c.2963C>G	p.Ser988Cys	p.S988C	ENST00000439151	NM_022455.4	988	tCt/tGt	5/23	0.79282285131373	2	FACETS	1	0.992	1	1	0.992	1	CLONAL	2	TRUE	0	0.79282285131373	2		550	630	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638471	176638471	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0016925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	164	586	657	0	ENST00000439151.2:c.3071C>G	p.Ser1024Ter	p.S1024*	ENST00000439151	NM_022455.4	1024	tCa/tGa	5/23	0.79282285131373	2	FACETS	0.986	0.962	1	0.986	0.962	1	CLONAL	2	TRUE	0	0.79282285131373	2		657	750	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370902	55370902	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	57	458	0	ENST00000297316.4:c.204C>G	p.Ile68Met	p.I68M	ENST00000297316	NM_022454.3	68	atC/atG	1/2	0.470505844504436	5	FACETS	0.314	0.268	0.364	0.105	0.089	0.122	INDETERMINATE	1	TRUE	2	0.79282285131373	5		458	1004	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76944367	76944367	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0016925-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	140	269	0	ENST00000373344.5:c.538C>G	p.His180Asp	p.H180D	ENST00000373344	NM_000489.3	180	Cat/Gat	7/35	0.79282285131373	2	FACETS	0.621	0.568	0.676			1	SUBCLONAL	1	TRUE	NA	0.79282285131373	2		269	569	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	213	19	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.712	0.542	0.911	0.712	0.542	0.911	CLONAL	1	TRUE	1	0.23	2		215	232	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	355	62	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.273363813127356	1	FACETS	1	0.938	1	1	0.938	1	CLONAL	1	TRUE	0	0.23	1		458	417	SUCCESS
RAC1	5879	MSKCC	GRCh37	7	6426892	6426892	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1057519874	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	82	316	0	ENST00000356142.4:c.85C>T	p.Pro29Ser	p.P29S	ENST00000356142	NM_018890.3	29	Cct/Tct	2/7	1	2	FACETS	0.773	0.68	0.872	0.773	0.68	0.872	SUBCLONAL	1	TRUE	1	0.23	2		316	923	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1317422	1317422	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759127718	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	87	585	0	ENST00000400841.2:c.643C>T	p.Arg215Trp	p.R215W	ENST00000400841		215	Cgg/Tgg	5/6	1	1	FACETS	0.876	0.775	0.985	0.876	0.775	0.985	CLONAL	1	TRUE	0	0.23	1		585	764	SUCCESS
ATR	545	MSKCC	GRCh37	3	142232477	142232477	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs754602382	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	66	417	0	ENST00000350721.4:c.4507C>T	p.Arg1503Ter	p.R1503*	ENST00000350721	NM_001184.3	1503	Cga/Tga	26/47	1	2	FACETS	0.797	0.691	0.912	0.797	0.691	0.912	CLONAL	1	TRUE	1	0.23	2		417	720	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	rs121913227	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1050	221	500	2	ENST00000288602.6:c.1798_1799delinsAA	p.Val600Lys	p.V600K	ENST00000288602	NM_004333.4	600	GTg/AAg	15/18	0.194123930138003	3	FACETS	0.843	0.783	0.905	0.843	0.783	0.905	CLONAL	2	TRUE	1	0.23	3		502	1271	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980844	40980844	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	94	548	0	ENST00000373198.4:c.1642G>A	p.Glu548Lys	p.E548K	ENST00000373198	NM_133170.3	548	Gaa/Aaa	10/32	1	2	FACETS	1	0.913	1	1	0.913	1	CLONAL	1	TRUE	1	0.23	2		548	793	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18266990	18266990	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs187640248	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	110	20	90	0	ENST00000222254.8:c.301C>T	p.Arg101Cys	p.R101C	ENST00000222254	NM_005027.3	101	Cgt/Tgt	2/16	1	2	FACETS	1	0.899	1	1	0.899	1	CLONAL	1	TRUE	1	0.23	2		90	130	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552630	18552630	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200787716	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	63	492	2	ENST00000266497.5:c.2041C>T	p.Arg681Cys	p.R681C	ENST00000266497		681	Cgc/Tgc	14/31	1	2	FACETS	0.594	0.512	0.684	0.594	0.512	0.684	SUBCLONAL	1	TRUE	1	0.23	2		494	922	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36931998	36931998	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	76	527	0	ENST00000361632.4:c.2471G>A	p.Gly824Glu	p.G824E	ENST00000361632		824	gGg/gAg	16/16	1	2	FACETS	0.917	0.803	1	0.917	0.803	1	CLONAL	1	TRUE	1	0.23	2		527	721	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139802543	139802543	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1042886761	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	125	650	0	ENST00000247668.2:c.388C>T	p.Pro130Ser	p.P130S	ENST00000247668	NM_021138.3	130	Ccg/Tcg	5/11	0.273363813127356	1	FACETS	1	0.956	1	1	0.956	1	CLONAL	1	TRUE	0	0.23	1		650	876	SUCCESS
ALK	238	MSKCC	GRCh37	2	29606667	29606667	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs4363989	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	88	598	1	ENST00000389048.3:c.1213G>A	p.Glu405Lys	p.E405K	ENST00000389048	NM_004304.4	405	Gaa/Aaa	5/29	1	2	FACETS	0.86	0.76	0.966	0.86	0.76	0.966	CLONAL	1	TRUE	1	0.23	2		599	890	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70344985	70344985	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1365839691	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	78	145	0	ENST00000374080.3:c.2215C>T	p.Pro739Ser	p.P739S	ENST00000374080		739	Ccc/Tcc	15/45	1	1	FACETS	0.818	0.723	0.918	1	0.98	1	CLONAL	2	TRUE	0	0.23	1		145	367	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138384011	138384011	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759151757	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	104	574	0	ENST00000289153.2:c.2539C>T	p.Arg847Cys	p.R847C	ENST00000289153	NM_006219.2	847	Cgc/Tgc	18/22	1	2	FACETS	0.905	0.809	1	0.905	0.809	1	CLONAL	1	TRUE	1	0.23	2		574	999	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73351584	73351584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	912	80	386	0	ENST00000377767.4:c.628C>T	p.Arg210Cys	p.R210C	ENST00000377767	NM_014953.3	210	Cgt/Tgt	4/21	1	2	FACETS	0.701	0.616	0.794	0.701	0.616	0.794	SUBCLONAL	1	TRUE	1	0.23	2		386	992	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88476406	88476406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1395756451	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	57	355	0	ENST00000360948.2:c.1726G>A	p.Asp576Asn	p.D576N	ENST00000360948	NM_001012338.2	576	Gat/Aat	15/19	1	2	FACETS	0.974	0.836	1	0.974	0.836	1	CLONAL	1	TRUE	1	0.23	2		355	509	SUCCESS
RAD51B	5890	MSKCC	GRCh37	14	68331729	68331729	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	44	203	0	ENST00000487270.1:c.325C>T	p.Pro109Ser	p.P109S	ENST00000487270	NM_133509.3	109	Cca/Tca	5/11	1	2	FACETS	1	0.857	1	1	0.857	1	CLONAL	1	TRUE	1	0.23	2		203	375	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123164869	123164869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	326	106	258	0	ENST00000218089.9:c.182G>A	p.Gly61Glu	p.G61E	ENST00000218089	NM_001042749.1	61	gGa/gAa	5/35	1	1	FACETS	0.944	0.852	1	1	0.988	1	CLONAL	2	TRUE	0	0.23	1		258	432	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50450261	50450261	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	65	423	1	ENST00000331340.3:c.445C>T	p.Gln149Ter	p.Q149*	ENST00000331340	NM_006060.4	149	Cag/Tag	5/8	1	2	FACETS	0.909	0.788	1	0.909	0.788	1	CLONAL	1	TRUE	1	0.23	2		424	622	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15284946	15284946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	75	783	0	ENST00000263388.2:c.4669C>T	p.Pro1557Ser	p.P1557S	ENST00000263388	NM_000435.2	1557	Cct/Tct	25/33	1	2	FACETS	0.78	0.682	0.886	0.78	0.682	0.886	SUBCLONAL	1	TRUE	1	0.23	2		783	836	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115117749	115117749	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs554364556	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	105	552	0	ENST00000257566.3:c.686C>T	p.Thr229Met	p.T229M	ENST00000257566	NM_016569.3	229	aCg/aTg	3/8	1	2	FACETS	0.917	0.82	1	0.917	0.82	1	CLONAL	1	TRUE	1	0.23	2		552	996	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99434685	99434685	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs543792941	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	114	562	1	ENST00000268035.6:c.772G>A	p.Gly258Ser	p.G258S	ENST00000268035	NM_000875.3	258	Ggt/Agt	3/21	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.23	2		563	964	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933751	36933751	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1438427534	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	703	83	543	1	ENST00000361632.4:c.1648G>A	p.Glu550Lys	p.E550K	ENST00000361632		550	Gag/Aag	12/16	1	2	FACETS	0.918	0.81	1	0.918	0.81	1	CLONAL	1	TRUE	1	0.23	2		544	786	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625303	69625303	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1335560620	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	71	599	0	ENST00000334134.2:c.490C>T	p.Arg164Cys	p.R164C	ENST00000334134	NM_005247.2	164	Cgc/Tgc	3/3	1	2	FACETS	0.895	0.78	1	0.895	0.78	1	CLONAL	1	TRUE	1	0.23	2		599	690	SUCCESS
MRE11	4361	MSKCC	GRCh37	11	94212922	94212922	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	652	78	398	1	ENST00000323929.3:c.320C>T	p.Pro107Leu	p.P107L	ENST00000323929	NM_005591.3	107	cCa/cTa	5/20	1	2	FACETS	0.929	0.816	1	0.929	0.816	1	CLONAL	1	TRUE	1	0.23	2		399	730	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18552733	18552733	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	899	77	531	2	ENST00000266497.5:c.2144G>A	p.Arg715Lys	p.R715K	ENST00000266497		715	aGa/aAa	14/31	1	2	FACETS	0.686	0.601	0.778	0.686	0.601	0.778	SUBCLONAL	1	TRUE	1	0.23	2		533	976	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914527	32914527	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1169	147	709	0	ENST00000380152.3:c.6035C>T	p.Ser2012Phe	p.S2012F	ENST00000380152		2012	tCc/tTc	11/27	1	2	FACETS	0.971	0.884	1	0.971	0.884	1	CLONAL	1	TRUE	1	0.23	2		709	1316	SUCCESS
KNSTRN	90417	MSKCC	GRCh37	15	40675092	40675092	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1089	100	763	1	ENST00000249776.8:c.56C>T	p.Ser19Phe	p.S19F	ENST00000249776	NM_033286.3	19	tCt/tTt	1/9	1	2	FACETS	0.731	0.651	0.817	0.731	0.651	0.817	SUBCLONAL	1	TRUE	1	0.23	2		764	1189	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43783915	43783915	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	131	639	1	ENST00000382044.4:c.323C>T	p.Ser108Phe	p.S108F	ENST00000382044	NM_001141980.1	108	tCc/tTc	4/28	1	2	FACETS	0.948	0.858	1	0.948	0.858	1	CLONAL	1	TRUE	1	0.23	2		640	1202	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3641007	3641007	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	930	116	783	0	ENST00000294008.3:c.2632G>T	p.Asp878Tyr	p.D878Y	ENST00000294008	NM_032444.2	878	Gac/Tac	12/15	1	2	FACETS	0.964	0.867	1	0.964	0.867	1	CLONAL	1	TRUE	1	0.23	2		783	1046	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3642724	3642724	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	84	574	0	ENST00000294008.3:c.2303C>T	p.Ser768Phe	p.S768F	ENST00000294008	NM_032444.2	768	tCt/tTt	11/15	1	2	FACETS	0.983	0.868	1	0.983	0.868	1	CLONAL	1	TRUE	1	0.23	2		574	743	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9862935	9862935	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	77	431	0	ENST00000330684.3:c.2368G>A	p.Glu790Lys	p.E790K	ENST00000330684	NM_001134407.1	790	Gag/Aag	12/13	1	2	FACETS	1	0.902	1	1	0.902	1	CLONAL	1	TRUE	1	0.23	2		431	649	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16075158	16075158	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	74	362	0	ENST00000268712.3:c.394C>T	p.Pro132Ser	p.P132S	ENST00000268712	NM_006311.3	132	Ccg/Tcg	4/46	1	2	FACETS	0.991	0.868	1	0.991	0.868	1	CLONAL	1	TRUE	1	0.23	2		362	649	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56448274	56448274	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	60	427	0	ENST00000407977.2:c.373A>G	p.Lys125Glu	p.K125E	ENST00000407977		125	Aag/Gag	3/10	1	2	FACETS	0.736	0.633	0.848	0.736	0.633	0.848	SUBCLONAL	1	TRUE	1	0.23	2		427	709	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349700	15349701	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	32	435	0	ENST00000263377.2:c.3873_3874delinsAA	p.Glu1292Lys	p.E1292K	ENST00000263377	NM_058243.2	1291	caGGag/caAAag	19/20	1	2	FACETS	0.575	0.466	0.698	0.575	0.466	0.698	SUBCLONAL	1	TRUE	1	0.23	2		435	484	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15349701	15349702	+	inframe_insertion	In_Frame_Ins	INS	-	-	TGGCGCTGCTGCTGCTGTTGCTTT	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	32	446	0	ENST00000263377.2:c.3872_3873insAAAGCAACAGCAGCAGCAGCGCCA	p.Gln1291_Glu1292insLysGlnGlnGlnGlnGlnArgGln	p.Q1291_E1292insKQQQQQRQ	ENST00000263377	NM_058243.2	1291	cag/caAAAGCAACAGCAGCAGCAGCGCCAg	19/20	1	2	FACETS	0.586	0.475	0.711	0.586	0.475	0.711	SUBCLONAL	1	TRUE	1	0.23	2		446	475	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354010	15354010	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1458261626	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	175	11	173	0	ENST00000263377.2:c.2870C>T	p.Pro957Leu	p.P957L	ENST00000263377	NM_058243.2	957	cCc/cTc	14/20	1	2	FACETS	0.514	0.355	0.711	0.514	0.355	0.711	SUBCLONAL	1	TRUE	1	0.23	2		173	186	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17945686	17945686	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	87	692	0	ENST00000458235.1:c.2174C>T	p.Pro725Leu	p.P725L	ENST00000458235	NM_000215.3	725	cCc/cTc	16/24	1	2	FACETS	0.872	0.77	0.98	0.872	0.77	0.98	CLONAL	1	TRUE	1	0.23	2		692	868	SUCCESS
CXCR4	7852	MSKCC	GRCh37	2	136872591	136872591	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	52	366	1	ENST00000241393.3:c.907G>A	p.Ala303Thr	p.A303T	ENST00000241393	NM_003467.2	303	Gct/Act	2/2	1	2	FACETS	0.708	0.602	0.824	0.708	0.602	0.824	SUBCLONAL	1	TRUE	1	0.23	2		367	639	SUCCESS
PDCD1	5133	MSKCC	GRCh37	2	242794815	242794816	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	369	42	320	1	ENST00000334409.5:c.393_394delinsAA	p.Ala132Thr	p.A132T	ENST00000334409	NM_005018.2	131	aaGGcg/aaAAcg	2/5	1	2	FACETS	0.889	0.743	1	0.889	0.743	1	CLONAL	1	TRUE	1	0.23	2		321	411	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790129	40790129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	70	515	0	ENST00000373198.4:c.2602C>T	p.Pro868Ser	p.P868S	ENST00000373198	NM_133170.3	868	Ccc/Tcc	18/32	1	2	FACETS	1	0.879	1	1	0.879	1	CLONAL	1	TRUE	1	0.23	2		515	604	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46264656	46264656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	364	44	276	0	ENST00000371998.3:c.1526C>T	p.Ser509Phe	p.S509F	ENST00000371998		509	tCt/tTt	12/23	1	2	FACETS	0.938	0.788	1	0.938	0.788	1	CLONAL	1	TRUE	1	0.23	2		276	408	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41548313	41548313	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	831	90	555	0	ENST00000263253.7:c.3101C>G	p.Ala1034Gly	p.A1034G	ENST00000263253	NM_001429.3	1034	gCt/gGt	16/31	1	2	FACETS	0.85	0.753	0.954	0.85	0.753	0.954	CLONAL	1	TRUE	1	0.23	2		555	921	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128205089	128205089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	66	512	0	ENST00000341105.2:c.352G>A	p.Val118Met	p.V118M	ENST00000341105	NM_032638.4	118	Gtg/Atg	3/6	1	2	FACETS	0.897	0.778	1	0.897	0.778	1	CLONAL	1	TRUE	1	0.23	2		512	640	SUCCESS
ATR	545	MSKCC	GRCh37	3	142254994	142254994	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	76	371	0	ENST00000350721.4:c.3775C>T	p.Pro1259Ser	p.P1259S	ENST00000350721	NM_001184.3	1259	Cca/Tca	20/47	1	2	FACETS	0.767	0.671	0.87	0.767	0.671	0.87	SUBCLONAL	1	TRUE	1	0.23	2		371	862	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185183598	185183598	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	60	407	0	ENST00000265026.3:c.1452G>A	p.Met484Ile	p.M484I	ENST00000265026	NM_004721.4	484	atG/atA	9/14	1	2	FACETS	0.749	0.644	0.863	0.749	0.644	0.863	SUBCLONAL	1	TRUE	1	0.23	2		407	697	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55964308	55964308	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	82	392	0	ENST00000263923.4:c.2505G>T	p.Lys835Asn	p.K835N	ENST00000263923	NM_002253.2	835	aaG/aaT	17/30	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.23	2		392	586	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55968178	55968178	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	110	557	0	ENST00000263923.4:c.2152G>A	p.Gly718Arg	p.G718R	ENST00000263923	NM_002253.2	718	Ggg/Agg	15/30	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.23	2		557	939	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31449462	31449462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	99	492	0	ENST00000344624.3:c.2747C>T	p.Ser916Leu	p.S916L	ENST00000344624		916	tCa/tTa	19/33	1	2	FACETS	0.909	0.81	1	0.909	0.81	1	CLONAL	1	TRUE	1	0.23	2		492	947	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31526631	31526631	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1269978298	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	63	393	0	ENST00000344624.3:c.409C>T	p.Pro137Ser	p.P137S	ENST00000344624		137	Cct/Tct	2/33	1	2	FACETS	0.915	0.791	1	0.915	0.791	1	CLONAL	1	TRUE	1	0.23	2		393	599	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520143	176520144	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	76	652	2	ENST00000292408.4:c.1062_1063delinsAA	p.Asp355Asn	p.D355N	ENST00000292408	NM_213647.1	354	gaGGac/gaAAac	9/18	1	2	FACETS	0.849	0.744	0.963	0.849	0.744	0.963	CLONAL	1	TRUE	1	0.23	2		654	778	SUCCESS
PRDM1	639	MSKCC	GRCh37	6	106553185	106553185	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1361893897	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	68	469	0	ENST00000369096.4:c.1150G>A	p.Glu384Lys	p.E384K	ENST00000369096	NM_001198.3	384	Gaa/Aaa	5/7	1	2	FACETS	0.799	0.694	0.913	0.799	0.694	0.913	CLONAL	1	TRUE	1	0.23	2		469	740	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687304	117687304	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	62	357	0	ENST00000368508.3:c.2747C>T	p.Ser916Phe	p.S916F	ENST00000368508	NM_002944.2	916	tCt/tTt	18/43	1	2	FACETS	0.742	0.64	0.853	0.742	0.64	0.853	SUBCLONAL	1	TRUE	1	0.23	2		357	727	SUCCESS
PRKN	5071	MSKCC	GRCh37	6	161771244	161771244	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	51	401	0	ENST00000366898.1:c.1286-1G>A		p.X429_splice	ENST00000366898	NM_004562.2	429			1	2	FACETS	0.686	0.583	0.801	0.686	0.583	0.801	SUBCLONAL	1	TRUE	1	0.23	2		401	646	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508790	106508790	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	76	576	1	ENST00000359195.3:c.784C>T	p.Pro262Ser	p.P262S	ENST00000359195	NM_002649.2	262	Ccc/Tcc	2/11	0.194123930138003	3	FACETS	0.873	0.764	0.99	0.437	0.382	0.495	CLONAL	1	TRUE	1	0.23	3		577	844	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69033198	69033198	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1012	104	433	0	ENST00000288368.4:c.3638G>A	p.Arg1213Lys	p.R1213K	ENST00000288368	NM_024870.2	1213	aGg/aAg	30/40	1	2	FACETS	0.81	0.724	0.903	0.81	0.724	0.903	CLONAL	1	TRUE	1	0.23	2		433	1116	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36846926	36846926	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1165827105	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	35	401	0	ENST00000358127.4:c.1013G>A	p.Gly338Glu	p.G338E	ENST00000358127	NM_001280556.1	338	gGg/gAg	9/10	1	2	FACETS	0.698	0.572	0.84	0.698	0.572	0.84	SUBCLONAL	1	TRUE	1	0.23	2		401	436	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98212128	98212128	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	67	463	0	ENST00000331920.6:c.3544C>T	p.Pro1182Ser	p.P1182S	ENST00000331920	NM_000264.3	1182	Cct/Tct	21/24	1	2	FACETS	0.802	0.697	0.917	0.802	0.697	0.917	CLONAL	1	TRUE	1	0.23	2		463	726	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920559	127920559	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	142	643	0	ENST00000373547.4:c.340C>T	p.His114Tyr	p.H114Y	ENST00000373547	NM_002721.4	114	Cat/Tat	4/7	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.23	2		643	1164	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911436	39911436	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1437936868	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	381	104	463	0	ENST00000378444.4:c.5194G>A	p.Glu1732Lys	p.E1732K	ENST00000378444	NM_001123385.1	1732	Gaa/Aaa	15/15	1	1	FACETS	0.825	0.742	0.912	1	0.985	1	CLONAL	2	TRUE	0	0.23	1		463	485	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44919285	44919285	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	185	41	139	0	ENST00000377967.4:c.1213C>T	p.Pro405Ser	p.P405S	ENST00000377967	NM_021140.2	405	Cca/Tca	13/29	1	1	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	0	0.23	1		139	226	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247523	53247523	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	128	332	0	ENST00000375401.3:c.286C>T	p.Gln96Ter	p.Q96*	ENST00000375401	NM_004187.3	96	Cag/Tag	3/26	1	1	FACETS	0.875	0.796	0.957	1	0.989	1	CLONAL	2	TRUE	0	0.23	1		332	563	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152860138	152860138	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	93	280	0	ENST00000406277.2:c.291-1G>A		p.X97_splice	ENST00000406277	NM_152274.4	97			1		FACETS		0.762	0.947				CLONAL	2	TRUE	0	0.23	1		280	420	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494641	2494641	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016928-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	72	572	0	ENST00000355716.4:c.781C>G	p.Pro261Ala	p.P261A	ENST00000355716	NM_003820.2	261	Cct/Gct	8/8	1	2	FACETS	0.879	0.768	1	0.879	0.768	1	CLONAL	1	TRUE	1	0.23	2		572	712	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36211270	36211270	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1227	338	894	0	ENST00000222270.7:c.1021C>T	p.Gln341Ter	p.Q341*	ENST00000222270	NM_014727.1	341	Caa/Taa	3/37	1	2	FACETS	0.931	0.878	0.985	0.931	0.878	0.985	CLONAL	1	TRUE	1	0.463993858425059	2		894	1565	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295204	1295204	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs2735943	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	163	67	586	2				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.964	1			1	INDETERMINATE	1	TRUE	NA	0.463993858425059	2		588	230	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295230	+	upstream_gene_variant	5'Flank	TNP	GGG	GGG	AGA	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	172	81	646	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.977	1			1	INDETERMINATE	1	TRUE	NA	0.463993858425059	2		646	253	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727111	40727111	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779663880	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	186	505	0	ENST00000373198.4:c.3853G>A	p.Asp1285Asn	p.D1285N	ENST00000373198	NM_133170.3	1285	Gat/Aat	28/32	1	2	FACETS	1	0.941	1	1	0.941	1	CLONAL	1	TRUE	1	0.463993858425059	2		505	786	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953135	17953135	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587778420	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	207	510	0	ENST00000458235.1:c.851G>A	p.Gly284Glu	p.G284E	ENST00000458235	NM_000215.3	284	gGa/gAa	6/24	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.463993858425059	2		510	828	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448564	89448564	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1184230536	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	183	482	0	ENST00000336596.2:c.1528C>T	p.Arg510Ter	p.R510*	ENST00000336596	NM_005233.5	510	Cga/Tga	7/17	1	2	FACETS	0.886	0.818	0.957	0.886	0.818	0.957	CLONAL	1	TRUE	1	0.463993858425059	2		482	890	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50358686	50358686	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	77	244	0	ENST00000331340.3:c.29C>T	p.Ser10Phe	p.S10F	ENST00000331340	NM_006060.4	10	tCc/tTc	2/8	1	2	FACETS	0.785	0.692	0.883	0.785	0.692	0.883	SUBCLONAL	1	TRUE	1	0.463993858425059	2		244	423	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16256750	16256750	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760134992	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	170	514	1	ENST00000375759.3:c.4015C>T	p.Arg1339Cys	p.R1339C	ENST00000375759	NM_015001.2	1339	Cgt/Tgt	11/15	1	2	FACETS	0.886	0.816	0.959	0.886	0.816	0.959	CLONAL	1	TRUE	1	0.463993858425059	2		515	827	SUCCESS
ATR	545	MSKCC	GRCh37	3	142261583	142261583	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	131	493	0	ENST00000350721.4:c.3374C>T	p.Pro1125Leu	p.P1125L	ENST00000350721	NM_001184.3	1125	cCc/cTc	17/47	1	2	FACETS	0.905	0.824	0.99	0.905	0.824	0.99	CLONAL	1	TRUE	1	0.463993858425059	2		493	624	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495732	72495732	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	199	449	0	ENST00000477973.2:c.340T>G	p.Trp114Gly	p.W114G	ENST00000477973	NM_012234.5	114	Tgg/Ggg	1/4	1	2	FACETS	0.995	0.923	1	0.995	0.923	1	CLONAL	1	TRUE	1	0.463993858425059	2		449	862	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157099341	157099341	+	missense_variant	Missense_Mutation	SNP	A	A	T	rs587779741	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	216	35	242	0	ENST00000346085.5:c.278A>T	p.His93Leu	p.H93L	ENST00000346085	NM_020732.3	93	cAc/cTc	1/20	0.463993858425059	1	FACETS	0.462	0.38	0.552	0.462	0.38	0.552	SUBCLONAL	1	TRUE	0	0.463993858425059	1		242	251	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76912075	76912075	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs782228142	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	164	547	1	ENST00000373344.5:c.4189G>A	p.Glu1397Lys	p.E1397K	ENST00000373344	NM_000489.3	1397	Gaa/Aaa	13/35	1	2	FACETS	0.971	0.893	1	0.971	0.893	1	CLONAL	1	TRUE	1	0.463993858425059	2		548	728	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795276	42795276	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1212762678	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	116	414	0	ENST00000575354.2:c.2356C>T	p.Pro786Ser	p.P786S	ENST00000575354	NM_015125.3	786	Cct/Tct	10/20	1	2	FACETS	0.921	0.833	1	0.921	0.833	1	CLONAL	1	TRUE	1	0.463993858425059	2		414	543	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52651519	52651519	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	210	496	0	ENST00000394830.3:c.1577T>C	p.Leu526Ser	p.L526S	ENST00000394830	NM_018313.4	526	tTa/tCa	15/30	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.463993858425059	2		496	773	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16202863	16202863	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	205	481	0	ENST00000375759.3:c.571C>T	p.Pro191Ser	p.P191S	ENST00000375759	NM_015001.2	191	Cca/Tca	3/15	1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.463993858425059	2		481	846	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259708	16259708	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	937	288	585	0	ENST00000375759.3:c.6973C>T	p.Leu2325Phe	p.L2325F	ENST00000375759	NM_015001.2	2325	Ctt/Ttt	11/15	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.463993858425059	2		585	1225	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27089769	27089769	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	190	466	0	ENST00000324856.7:c.2725C>T	p.Gln909Ter	p.Q909*	ENST00000324856	NM_006015.4	909	Caa/Taa	8/20	1	2	FACETS	0.927	0.858	0.999	0.927	0.858	0.999	CLONAL	1	TRUE	1	0.463993858425059	2		466	883	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834575	156834575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	199	601	0	ENST00000524377.1:c.343C>T	p.Pro115Ser	p.P115S	ENST00000524377	NM_002529.3	115	Cct/Tct	3/17	1	2	FACETS	0.917	0.85	0.987	0.917	0.85	0.987	CLONAL	1	TRUE	1	0.463993858425059	2		601	935	SUCCESS
RET	5979	MSKCC	GRCh37	10	43622128	43622128	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	168	518	2	ENST00000355710.3:c.3145C>T	p.Pro1049Ser	p.P1049S	ENST00000355710	NM_020975.4	1049	Cct/Tct	19/20	0.270946530579647	1	FACETS	0.71	0.654	0.769	0.71	0.654	0.769	INDETERMINATE	1	TRUE	0	0.463993858425059	1		520	783	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332438	70332438	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1426634332	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	228	658	0	ENST00000373644.4:c.343C>T	p.Leu115Phe	p.L115F	ENST00000373644	NM_030625.2	115	Ctc/Ttc	2/12	0.270946530579647	1	FACETS	0.7	0.652	0.75	0.7	0.652	0.75	INDETERMINATE	1	TRUE	0	0.463993858425059	1		658	1078	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332469	70332469	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs866518744	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	212	666	0	ENST00000373644.4:c.374C>T	p.Ser125Phe	p.S125F	ENST00000373644	NM_030625.2	125	tCc/tTc	2/12	0.270946530579647	1	FACETS	0.698	0.648	0.749	0.698	0.648	0.749	INDETERMINATE	1	TRUE	0	0.463993858425059	1		666	1006	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741860	17741861	+	missense_variant	Missense_Mutation	DNP	CT	CT	TG	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	105	13	107	0	ENST00000250003.3:c.531_532delinsTG	p.Phe178Val	p.F178V	ENST00000250003	NM_002478.4	177	gcCTtc/gcTGtc	1/3	0.327973714622261	1	FACETS	0.365	0.262	0.488	0.365	0.262	0.488	SUBCLONAL	1	TRUE	0	0.463993858425059	1		107	118	SUCCESS
PAK1	5058	MSKCC	GRCh37	11	77085386	77085386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1276198531	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	98	672	2	ENST00000356341.3:c.464C>T	p.Ser155Phe	p.S155F	ENST00000356341	NM_002576.4	155	tCt/tTt	5/15	NA	2	FACETS	0.494	0.44	0.552			1	INDETERMINATE	1	TRUE	NA	0.463993858425059	2		674	855	SUCCESS
ATM	472	MSKCC	GRCh37	11	108098407	108098407	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1064793029	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	142	436	0	ENST00000278616.4:c.56G>A	p.Arg19Lys	p.R19K	ENST00000278616	NM_000051.3	19	aGa/aAa	2/63	0.463993858425059	1	FACETS	0.992	0.911	1	0.992	0.911	1	CLONAL	1	TRUE	0	0.463993858425059	1		436	474	SUCCESS
CBL	867	MSKCC	GRCh37	11	119149244	119149244	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs745896960	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	255	465	0	ENST00000264033.4:c.1252T>C	p.Phe418Leu	p.F418L	ENST00000264033	NM_005188.3	418	Ttc/Ctc	9/16	NA	2	FACETS	0.836	0.788	0.886			1	INDETERMINATE	2	TRUE	NA	0.463993858425059	2		465	657	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435253	18435253	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	58	258	0	ENST00000266497.5:c.238G>A	p.Glu80Lys	p.E80K	ENST00000266497		80	Gaa/Aaa	1/31	0.270946530579647	1	FACETS	0.416	0.358	0.479	0.416	0.358	0.479	INDETERMINATE	1	TRUE	0	0.463993858425059	1		258	462	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18800885	18800885	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	81	504	0	ENST00000266497.5:c.4261G>A	p.Gly1421Arg	p.G1421R	ENST00000266497		1421	Gga/Aga	31/31	0.270946530579647	1	FACETS	0.533	0.471	0.599	0.533	0.471	0.599	INDETERMINATE	1	TRUE	0	0.463993858425059	1		504	503	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111884933	111884933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	84	429	0	ENST00000341259.2:c.931G>A	p.Glu311Lys	p.E311K	ENST00000341259	NM_005475.2	311	Gag/Aag	5/8	0.270946530579647	1	FACETS	0.394	0.348	0.444	0.394	0.348	0.444	INDETERMINATE	1	TRUE	0	0.463993858425059	1		429	705	SUCCESS
TBX3	6926	MSKCC	GRCh37	12	115109653	115109653	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	154	605	0	ENST00000257566.3:c.2225C>T	p.Ser742Phe	p.S742F	ENST00000257566	NM_016569.3	742	tCc/tTc	8/8	0.270946530579647	1	FACETS	0.473	0.432	0.516	0.473	0.432	0.516	INDETERMINATE	1	TRUE	0	0.463993858425059	1		605	1078	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28601228	28601228	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772146579	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	91	407	0	ENST00000241453.7:c.2204C>T	p.Ser735Phe	p.S735F	ENST00000241453	NM_004119.2	735	tCc/tTc	17/24	0.327973714622261	1	FACETS	0.574	0.511	0.641	0.574	0.511	0.641	SUBCLONAL	1	TRUE	0	0.463993858425059	1		407	525	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346005	73346005	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	145	504	0	ENST00000377767.4:c.1533T>A	p.His511Gln	p.H511Q	ENST00000377767	NM_014953.3	511	caT/caA	11/21	0.327973714622261	1	FACETS	0.884	0.811	0.96	0.884	0.811	0.96	CLONAL	1	TRUE	0	0.463993858425059	1		504	543	SUCCESS
FOXA1	3169	MSKCC	GRCh37	14	38061283	38061283	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	619	232	539	2	ENST00000250448.2:c.706G>T	p.Asp236Tyr	p.D236Y	ENST00000250448	NM_004496.3	236	Gac/Tac	2/2	0.270946530579647	1	FACETS	0.902	0.843	0.963	0.902	0.843	0.963	INDETERMINATE	1	TRUE	0	0.463993858425059	1		541	851	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38632094	38632094	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	313	118	468	0	ENST00000299084.4:c.580C>T	p.Gln194Ter	p.Q194*	ENST00000299084	NM_152594.2	194	Cag/Tag	5/7	0.463993858425059	1	FACETS	0.906	0.824	0.992	0.906	0.824	0.992	CLONAL	1	TRUE	0	0.463993858425059	1		468	431	SUCCESS
B2M	567	MSKCC	GRCh37	15	45007752	45007753	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	115	371	0	ENST00000558401.1:c.204dup	p.Val69SerfsTer21	p.V69Sfs*21	ENST00000558401	NM_004048.2	67	gaa/gAaa	2/4	0.463993858425059	1	FACETS	0.873	0.792	0.958	0.873	0.792	0.958	CLONAL	1	TRUE	0	0.463993858425059	1		371	436	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826577	50826577	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	87	348	0	ENST00000398568.2:c.2302C>T	p.Pro768Ser	p.P768S	ENST00000398568	NM_001042412.1	768	Cct/Tct	15/18	1	2	FACETS	0.808	0.718	0.903	0.808	0.718	0.903	CLONAL	1	TRUE	1	0.463993858425059	2		348	464	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992838	72992838	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758176150	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	135	587	0	ENST00000268489.5:c.1207C>T	p.Leu403Phe	p.L403F	ENST00000268489	NM_006885.3	403	Ctt/Ttt	2/10	1	2	FACETS	0.853	0.777	0.933	0.853	0.777	0.933	CLONAL	1	TRUE	1	0.463993858425059	2		587	682	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89831392	89831392	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1234246540	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	216	518	0	ENST00000389301.3:c.2684C>T	p.Pro895Leu	p.P895L	ENST00000389301	NM_000135.2	895	cCc/cTc	28/43	1	2	FACETS	0.971	0.903	1	0.971	0.903	1	CLONAL	1	TRUE	1	0.463993858425059	2		518	959	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37627242	37627242	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	185	575	0	ENST00000447079.4:c.1157C>T	p.Pro386Leu	p.P386L	ENST00000447079	NM_015083.1	386	cCt/cTt	2/14	0.270946530579647	1	FACETS	0.778	0.72	0.839	0.778	0.72	0.839	INDETERMINATE	1	TRUE	0	0.463993858425059	1		575	787	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884092	37884092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	909	152	625	0	ENST00000269571.5:c.3563G>A	p.Gly1188Glu	p.G1188E	ENST00000269571		1188	gGg/gAg	27/27	0.270946530579647	1	FACETS	0.474	0.433	0.518	0.474	0.433	0.518	INDETERMINATE	1	TRUE	0	0.463993858425059	1		625	1061	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897295	78897295	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs768404459	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	543	217	432	0	ENST00000306801.3:c.2630C>T	p.Ser877Phe	p.S877F	ENST00000306801	NM_020761.2	877	tCc/tTc	23/34	0.463993858425059	2	FACETS	1	0.987	1	0.615	0.574	0.658	CLONAL	1	TRUE	0	0.463993858425059	2		432	760	SUCCESS
YES1	7525	MSKCC	GRCh37	18	756700	756700	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765855267	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	186	483	0	ENST00000314574.4:c.128C>T	p.Pro43Leu	p.P43L	ENST00000314574	NM_005433.3	43	cCg/cTg	2/12	0.327973714622261	1	FACETS	0.883	0.819	0.95	0.883	0.819	0.95	CLONAL	1	TRUE	0	0.463993858425059	1		483	697	SUCCESS
GNA11	2767	MSKCC	GRCh37	19	3118968	3118968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	821	238	616	0	ENST00000078429.4:c.652C>T	p.His218Tyr	p.H218Y	ENST00000078429	NM_002067.2	218	Cac/Tac	5/7	1	2	FACETS	0.969	0.904	1	0.969	0.904	1	CLONAL	1	TRUE	1	0.463993858425059	2		616	1059	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5231410	5231410	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs770401761	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	221	492	0	ENST00000357368.4:c.2066G>A	p.Trp689Ter	p.W689*	ENST00000357368	NM_002850.3	689	tGg/tAg	14/38	1	2	FACETS	0.938	0.873	1	0.938	0.873	1	CLONAL	1	TRUE	1	0.463993858425059	2		492	1016	SUCCESS
CARM1	10498	MSKCC	GRCh37	19	11015696	11015696	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	746	232	513	0	ENST00000327064.4:c.290C>T	p.Ser97Phe	p.S97F	ENST00000327064	NM_199141.1	97	tCc/tTc	2/16	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.463993858425059	2		513	978	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271901	15271901	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	657	232	539	1	ENST00000263388.2:c.6538C>T	p.Pro2180Ser	p.P2180S	ENST00000263388	NM_000435.2	2180	Cct/Tct	33/33	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.463993858425059	2		540	889	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15367944	15367945	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	190	536	0	ENST00000263377.2:c.1381_1382delinsTT	p.Pro461Phe	p.P461F	ENST00000263377	NM_058243.2	461	CCt/TTt	8/20	1	2	FACETS	0.821	0.759	0.886	0.821	0.759	0.886	CLONAL	1	TRUE	1	0.463993858425059	2		536	997	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18968315	18968315	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	880	244	654	0	ENST00000262803.5:c.2155G>A	p.Gly719Ser	p.G719S	ENST00000262803	NM_002911.3	719	Ggc/Agc	15/24	1	2	FACETS	0.936	0.874	1	0.936	0.874	1	CLONAL	1	TRUE	1	0.463993858425059	2		654	1124	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36218428	36218451	+	inframe_deletion	In_Frame_Del	DEL	GAGGCCCTGAGCGGGGCCCTCCAG	GAGGCCCTGAGCGGGGCCCTCCAG	-	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	191	414	0	ENST00000222270.7:c.4208_4231del	p.Glu1403_Gln1410del	p.E1403_Q1410del	ENST00000222270	NM_014727.1	1403	GAGGCCCTGAGCGGGGCCCTCCAG/-	16/37	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.463993858425059	2		414	765	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223176	36223176	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1114	374	800	2	ENST00000222270.7:c.5726C>T	p.Pro1909Leu	p.P1909L	ENST00000222270	NM_014727.1	1909	cCc/cTc	28/37	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.463993858425059	2		802	1488	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52714679	52714679	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	205	473	0	ENST00000322088.6:c.437C>T	p.Ser146Leu	p.S146L	ENST00000322088	NM_014225.5	146	tCg/tTg	4/15	1	2	FACETS	0.963	0.894	1	0.963	0.894	1	CLONAL	1	TRUE	1	0.463993858425059	2		473	918	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25994406	25994406	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs781524282	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	85	215	0	ENST00000435504.4:c.407C>T	p.Ser136Leu	p.S136L	ENST00000435504		136	tCg/tTg	6/13	1	2	FACETS	0.87	0.773	0.973	0.87	0.773	0.973	CLONAL	1	TRUE	1	0.463993858425059	2		215	421	SUCCESS
ALK	238	MSKCC	GRCh37	2	29451797	29451797	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs79530637	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	274	649	1	ENST00000389048.3:c.2768G>A	p.Gly923Glu	p.G923E	ENST00000389048	NM_004304.4	923	gGg/gAg	16/29	1	2	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	1	0.463993858425059	2		650	1070	SUCCESS
ALK	238	MSKCC	GRCh37	2	29498304	29498304	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	193	492	0	ENST00000389048.3:c.1876G>A	p.Asp626Asn	p.D626N	ENST00000389048	NM_004304.4	626	Gac/Aac	10/29	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.463993858425059	2		492	779	SUCCESS
ALK	238	MSKCC	GRCh37	2	29754793	29754793	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	104	455	1	ENST00000389048.3:c.1142C>T	p.Pro381Leu	p.P381L	ENST00000389048	NM_004304.4	381	cCa/cTa	4/29	1	2	FACETS	0.954	0.859	1	0.954	0.859	1	CLONAL	1	TRUE	1	0.463993858425059	2		456	470	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212288997	212288997	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	124	505	0	ENST00000342788.4:c.2749G>A	p.Gly917Arg	p.G917R	ENST00000342788	NM_005235.2	917	Gga/Aga	23/28	1	2	FACETS	0.883	0.802	0.969	0.883	0.802	0.969	CLONAL	1	TRUE	1	0.463993858425059	2		505	605	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023882	31023882	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	248	630	0	ENST00000375687.4:c.3367C>T	p.Pro1123Ser	p.P1123S	ENST00000375687	NM_015338.5	1123	Cca/Tca	13/13	1	2	FACETS	1	0.965	1	1	0.965	1	CLONAL	1	TRUE	1	0.463993858425059	2		630	1022	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790000	40790000	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs724159843	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	492	125	500	0	ENST00000373198.4:c.2731G>A	p.Glu911Lys	p.E911K	ENST00000373198	NM_133170.3	911	Gaa/Aaa	18/32	1	2	FACETS	0.873	0.793	0.958	0.873	0.793	0.958	CLONAL	1	TRUE	1	0.463993858425059	2		500	617	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40980862	40980862	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	180	453	0	ENST00000373198.4:c.1624G>C	p.Val542Leu	p.V542L	ENST00000373198	NM_133170.3	542	Gtg/Ctg	10/32	1	2	FACETS	0.965	0.891	1	0.965	0.891	1	CLONAL	1	TRUE	1	0.463993858425059	2		453	804	SUCCESS
U2AF1	7307	MSKCC	GRCh37	21	44520582	44520582	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	97	366	0	ENST00000291552.4:c.180G>C	p.Gln60His	p.Q60H	ENST00000291552	NM_006758.2	60	caG/caC	3/8	0.327973714622261	1	FACETS	0.544	0.486	0.606	0.544	0.486	0.606	SUBCLONAL	1	TRUE	0	0.463993858425059	1		366	590	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12422910	12422910	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	198	614	2	ENST00000287820.6:c.400C>T	p.Leu134Phe	p.L134F	ENST00000287820	NM_015869.4	134	Ctc/Ttc	3/7	1	2	FACETS	0.885	0.82	0.953	0.885	0.82	0.953	CLONAL	1	TRUE	1	0.463993858425059	2		616	964	SUCCESS
GSK3B	2932	MSKCC	GRCh37	3	119642288	119642288	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	139	545	0	ENST00000316626.5:c.409G>T	p.Glu137Ter	p.E137*	ENST00000316626		137	Gaa/Taa	4/12	1	2	FACETS	0.846	0.772	0.924	0.846	0.772	0.924	CLONAL	1	TRUE	1	0.463993858425059	2		545	708	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178927429	178927429	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1401795892	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	107	482	1	ENST00000263967.3:c.1192C>T	p.Arg398Cys	p.R398C	ENST00000263967	NM_006218.2	398	Cgt/Tgt	7/21	1	2	FACETS	0.842	0.757	0.93	0.842	0.757	0.93	CLONAL	1	TRUE	1	0.463993858425059	2		483	548	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189607171	189607171	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	893	251	653	0	ENST00000264731.3:c.1550A>G	p.Asn517Ser	p.N517S	ENST00000264731	NM_003722.4	517	aAt/aGt	12/14	1	2	FACETS	0.946	0.884	1	0.946	0.884	1	CLONAL	1	TRUE	1	0.463993858425059	2		653	1144	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55156684	55156685	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	103	327	0	ENST00000257290.5:c.3085_3086delinsTT	p.Pro1029Phe	p.P1029F	ENST00000257290	NM_006206.4	1029	CCt/TTt	22/23	1	2	FACETS	0.79	0.709	0.876	0.79	0.709	0.876	SUBCLONAL	1	TRUE	1	0.463993858425059	2		327	562	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873716	35873716	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	149	443	0	ENST00000303115.3:c.672T>A	p.Tyr224Ter	p.Y224*	ENST00000303115	NM_002185.3	224	taT/taA	5/8	0.327973714622261	1	FACETS	0.975	0.897	1	0.975	0.897	1	CLONAL	1	TRUE	0	0.463993858425059	1		443	506	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178300	56178300	+	stop_gained	Nonsense_Mutation	SNP	T	T	A	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	65	373	1	ENST00000399503.3:c.3273T>A	p.Cys1091Ter	p.C1091*	ENST00000399503	NM_005921.1	1091	tgT/tgA	14/20	0.327973714622261	1	FACETS	0.488	0.424	0.557	0.488	0.424	0.557	SUBCLONAL	1	TRUE	0	0.463993858425059	1		374	441	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67569232	67569232	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	166	416	0	ENST00000274335.5:c.349G>A	p.Asp117Asn	p.D117N	ENST00000274335		117	Gat/Aat	2/15	1	2	FACETS	0.915	0.842	0.991	0.915	0.842	0.991	CLONAL	1	TRUE	1	0.463993858425059	2		416	782	SUCCESS
APC	324	MSKCC	GRCh37	5	112178978	112178978	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	140	398	1	ENST00000257430.4:c.7687A>T	p.Thr2563Ser	p.T2563S	ENST00000257430	NM_000038.5	2563	Act/Tct	16/16	1	2	FACETS	0.993	0.907	1	0.993	0.907	1	CLONAL	1	TRUE	1	0.463993858425059	2		399	608	SUCCESS
NPM1	4869	MSKCC	GRCh37	5	170832354	170832354	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	119	288	1	ENST00000296930.5:c.718G>A	p.Gly240Arg	p.G240R	ENST00000296930	NM_002520.6	240	Gga/Aga	9/11	1	2	FACETS	0.99	0.898	1	0.99	0.898	1	CLONAL	1	TRUE	1	0.463993858425059	2		289	518	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176524337	176524338	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	195	570	1	ENST00000292408.4:c.2198_2199delinsAA	p.Arg733Lys	p.R733K	ENST00000292408	NM_213647.1	733	aGG/aAA	17/18	1	2	FACETS	0.836	0.774	0.901	0.836	0.774	0.901	CLONAL	1	TRUE	1	0.463993858425059	2		571	1005	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180041089	180041089	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	952	308	733	0	ENST00000261937.6:c.3310C>T	p.Leu1104Phe	p.L1104F	ENST00000261937	NM_182925.4	1104	Ctc/Ttc	24/30	1	2	FACETS	1	0.973	1	1	0.973	1	CLONAL	1	TRUE	1	0.463993858425059	2		733	1260	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056247	26056247	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs777384681	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	539	161	370	0	ENST00000343677.2:c.410A>C	p.Lys137Thr	p.K137T	ENST00000343677	NM_005319.3	137	aAg/aCg	1/1	1	2	FACETS	0.991	0.912	1	0.991	0.912	1	CLONAL	1	TRUE	1	0.463993858425059	2		370	700	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30675440	30675441	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	136	348	1	ENST00000376406.3:c.2915_2916delinsAA	p.Gly972Glu	p.G972E	ENST00000376406	NM_014641.2	972	gGG/gAA	8/15	1	2	FACETS	0.915	0.834	0.999	0.915	0.834	0.999	CLONAL	1	TRUE	1	0.463993858425059	2		349	641	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6026828	6026828	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	188	421	0	ENST00000265849.7:c.1568C>T	p.Ser523Phe	p.S523F	ENST00000265849	NM_000535.5	523	tCc/tTc	11/15	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.463993858425059	2		421	780	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55224296	55224296	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	177	558	1	ENST00000275493.2:c.1077C>A	p.Phe359Leu	p.F359L	ENST00000275493	NM_005228.3	359	ttC/ttA	9/28	1	2	FACETS	0.826	0.761	0.893	0.826	0.761	0.893	CLONAL	1	TRUE	1	0.463993858425059	2		559	924	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845906	151845906	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	963	203	609	0	ENST00000262189.6:c.13106G>A	p.Gly4369Glu	p.G4369E	ENST00000262189	NM_170606.2	4369	gGg/gAg	52/59	0.154754797343548	5	FACETS	1	0.986	1			1	INDETERMINATE	1	TRUE	NA	0.463993858425059	5		609	1166	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23538750	23538750	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	192	97	237	0	ENST00000380871.4:c.689G>C	p.Ser230Thr	p.S230T	ENST00000380871	NM_006167.3	230	aGc/aCc	2/2	0.463993858425059	1	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	0	0.463993858425059	1		237	289	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38287286	38287286	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	222	594	0	ENST00000425967.3:c.371C>T	p.Ser124Phe	p.S124F	ENST00000425967	NM_001174067.1	124	tCc/tTc	4/19	0.463993858425059	1	FACETS	0.9	0.839	0.962	0.9	0.839	0.962	CLONAL	1	TRUE	0	0.463993858425059	1		594	817	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69020465	69020465	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	189	551	1	ENST00000288368.4:c.2837C>T	p.Ser946Phe	p.S946F	ENST00000288368	NM_024870.2	946	tCt/tTt	24/40	0.422679325104346	3	FACETS	0.9	0.831	0.972	0.45	0.415	0.486	CLONAL	1	TRUE	1	0.463993858425059	3		552	1115	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869002	117869002	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	127	493	0	ENST00000297338.2:c.697C>T	p.Leu233Phe	p.L233F	ENST00000297338	NM_006265.2	233	Ctt/Ttt	7/14	0.422679325104346	3	FACETS	0.798	0.723	0.878	0.399	0.361	0.439	SUBCLONAL	1	TRUE	1	0.463993858425059	3		493	845	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27228239	27228239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	201	548	1	ENST00000380036.4:c.3236C>T	p.Pro1079Leu	p.P1079L	ENST00000380036	NM_000459.3	1079	cCt/cTt	22/23	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.463993858425059	2		549	808	SUCCESS
RXRA	6256	MSKCC	GRCh37	9	137309090	137309090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	701	285	803	2	ENST00000481739.1:c.697G>A	p.Glu233Lys	p.E233K	ENST00000481739	NM_002957.4	233	Gag/Aag	5/10	0.463993858425059	1	FACETS	0.957	0.901	1	0.957	0.901	1	CLONAL	1	TRUE	0	0.463993858425059	1		805	986	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321306	1321306	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	135	454	0	ENST00000400841.2:c.449T>C	p.Val150Ala	p.V150A	ENST00000400841		150	gTt/gCt	4/6	1	2	FACETS	0.759	0.69	0.831	0.759	0.69	0.831	SUBCLONAL	1	TRUE	1	0.463993858425059	2		454	767	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1327717	1327717	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	176	499	0	ENST00000400841.2:c.164A>G	p.Asn55Ser	p.N55S	ENST00000400841		55	aAc/aGc	2/6	1	2	FACETS	0.96	0.886	1	0.96	0.886	1	CLONAL	1	TRUE	1	0.463993858425059	2		499	790	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63412226	63412226	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	307	772	0	ENST00000330258.3:c.941G>A	p.Gly314Glu	p.G314E	ENST00000330258	NM_152424.3	314	gGg/gAg	2/2	1	2	FACETS	1	0.966	1	1	0.966	1	CLONAL	1	TRUE	1	0.463993858425059	2		772	1277	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939973	76939973	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	155	606	1	ENST00000373344.5:c.775G>A	p.Glu259Lys	p.E259K	ENST00000373344	NM_000489.3	259	Gaa/Aaa	9/35	1	2	FACETS	0.86	0.788	0.935	0.86	0.788	0.935	CLONAL	1	TRUE	1	0.463993858425059	2		607	777	SUCCESS
BTK	695	MSKCC	GRCh37	X	100615617	100615617	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	705	201	550	3	ENST00000308731.7:c.715G>A	p.Asp239Asn	p.D239N	ENST00000308731	NM_000061.2	239	Gat/Aat	8/19	1	2	FACETS	0.956	0.887	1	0.956	0.887	1	CLONAL	1	TRUE	1	0.463993858425059	2		553	906	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791247	42791247	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771946862	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	708	180	519	0	ENST00000575354.2:c.307C>T	p.Pro103Ser	p.P103S	ENST00000575354	NM_015125.3	103	Cct/Tct	3/20	1	2	FACETS	0.874	0.806	0.944	0.874	0.806	0.944	CLONAL	1	TRUE	1	0.463993858425059	2		519	888	SUCCESS
PBRM1	55193	MSKCC	GRCh37	3	52623206	52623206	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	156	415	0	ENST00000394830.3:c.2845C>T	p.Gln949Ter	p.Q949*	ENST00000394830	NM_018313.4	949	Cag/Tag	19/30	1	2	FACETS	0.99	0.909	1	0.99	0.909	1	CLONAL	1	TRUE	1	0.463993858425059	2		415	679	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522689	176522689	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1453935269	NA	P-0016935-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	736	182	610	0	ENST00000292408.4:c.1786G>A	p.Val596Met	p.V596M	ENST00000292408	NM_213647.1	596	Gtg/Atg	13/18	1	2	FACETS	0.855	0.789	0.923	0.855	0.789	0.923	CLONAL	1	TRUE	1	0.463993858425059	2		610	918	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0016954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	89	215	0				ENST00000310581	NM_198253.2	-/1132			0.268274557461059	1	FACETS	0.886	0.79	0.988	0.886	0.79	0.988	CLONAL	1	TRUE	0	0.385886062417625	1		215	420	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578275	7578277	+	inframe_deletion	In_Frame_Del	DEL	GAG	GAG	-	rs1555525902	NA	P-0016954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	110	985	0	ENST00000269305.4:c.572_574del	p.Pro191del	p.P191del	ENST00000269305	NM_001126112.2	191	cCTCag/cag	6/11	0.357065360113966	1	FACETS	0.931	0.841	1	0.931	0.841	1	CLONAL	1	TRUE	0	0.385886062417625	1		985	494	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89711984	89711984	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0016954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	54	544	0	ENST00000371953.3:c.604del	p.Thr202LeufsTer19	p.T202Lfs*19	ENST00000371953	NM_000314.4	201	gAa/ga	6/9	0.385886062417625	1	FACETS	1	0.886	1	1	0.886	1	CLONAL	1	TRUE	0	0.385886062417625	1		544	220	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41566488	41566488	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0016954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	108	835	1	ENST00000263253.7:c.4365G>T	p.Gln1455His	p.Q1455H	ENST00000263253	NM_001429.3	1455	caG/caT	27/31	1	2	FACETS	1	0.936	1	1	0.936	1	CLONAL	1	TRUE	1	0.385886062417625	2		836	532	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295183	1295183	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0016954-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	287	75	411	0				ENST00000310581	NM_198253.2	-/1132			0.268274557461059	1	FACETS	0.867	0.764	0.975	0.867	0.764	0.975	CLONAL	1	TRUE	0	0.385886062417625	1		411	362	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	435	127	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.686	0.624	0.751	0.686	0.624	0.751	SUBCLONAL	1	TRUE	1	0.65904997152504	2		215	562	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0017006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	81	281	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	1	2	FACETS	0.52	0.459	0.584	0.52	0.459	0.584	SUBCLONAL	1	TRUE	1	0.65904997152504	2		281	473	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0017006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	285	586	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.717	0.674	0.762	0.717	0.674	0.762	SUBCLONAL	1	TRUE	1	0.65904997152504	2		586	1206	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106354	27106354	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs879255270	NA	P-0017006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	200	548	0	ENST00000324856.7:c.5965C>T	p.Arg1989Ter	p.R1989*	ENST00000324856	NM_006015.4	1989	Cga/Tga	20/20	1	2	FACETS	0.652	0.604	0.701	0.652	0.604	0.701	SUBCLONAL	1	TRUE	1	0.65904997152504	2		548	931	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73351584	73351584	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	47	386	0	ENST00000377767.4:c.628C>T	p.Arg210Cys	p.R210C	ENST00000377767	NM_014953.3	210	Cgt/Tgt	4/21	1	2	FACETS	0.173	0.145	0.203	0.173	0.145	0.203	SUBCLONAL	1	TRUE	1	0.65904997152504	2		386	826	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9538374	9538374	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868564987	NA	P-0017006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	134	517	0	ENST00000353224.5:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000353224	NM_177990.2	542	Gaa/Aaa	7/10	1	2	FACETS	0.652	0.594	0.712	0.652	0.594	0.712	SUBCLONAL	1	TRUE	1	0.65904997152504	2		517	624	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18716344	18716344	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778895247	NA	P-0017006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	214	300	0	ENST00000266497.5:c.3691G>A	p.Glu1231Lys	p.E1231K	ENST00000266497		1231	Gaa/Aaa	26/31	1	2	FACETS	0.722	0.672	0.774	0.722	0.672	0.774	SUBCLONAL	1	TRUE	1	0.65904997152504	2		300	899	SUCCESS
DAXX	1616	MSKCC	GRCh37	6	33287871	33287871	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1237131098	NA	P-0017006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1011	249	651	0	ENST00000374542.5:c.1382C>T	p.Ser461Phe	p.S461F	ENST00000374542	NM_001141970.1	461	tCt/tTt	5/8	0.49172774026445	3	FACETS	0.797	0.744	0.852	0.399	0.372	0.426	SUBCLONAL	1	TRUE	1	0.65904997152504	3		651	1260	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587167	189587167	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1209841422	NA	P-0017006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	825	49	325	0	ENST00000264731.3:c.1184C>T	p.Ser395Phe	p.S395F	ENST00000264731	NM_003722.4	395	tCc/tTc	9/14	1	2	FACETS	0.17	0.143	0.2	0.17	0.143	0.2	SUBCLONAL	1	TRUE	1	0.65904997152504	2		325	874	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189587161	189587161	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173679499	NA	P-0017006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	184	522	0	ENST00000264731.3:c.1178G>A	p.Arg393Gln	p.R393Q	ENST00000264731	NM_003722.4	393	cGa/cAa	9/14	1	2	FACETS	0.623	0.575	0.673	0.623	0.575	0.673	SUBCLONAL	1	TRUE	1	0.65904997152504	2		522	896	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589618	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519838	NA	P-0017006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	901	54	494	1	ENST00000274335.5:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000274335		461	Cga/Tga	10/15	1	2	FACETS	0.172	0.146	0.2	0.172	0.146	0.2	SUBCLONAL	1	TRUE	1	0.65904997152504	2		495	955	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12421355	12421355	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777334819	NA	P-0017006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1486	89	823	0	ENST00000287820.6:c.235G>A	p.Glu79Lys	p.E79K	ENST00000287820	NM_015869.4	79	Gaa/Aaa	2/7	1	2	FACETS	0.171	0.151	0.194	0.171	0.151	0.194	SUBCLONAL	1	TRUE	1	0.65904997152504	2		823	1575	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248558	59248558	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	734	212	554	0	ENST00000371222.2:c.185C>T	p.Thr62Ile	p.T62I	ENST00000371222	NM_002228.3	62	aCc/aTc	1/1	1	2	FACETS	0.68	0.632	0.73	0.68	0.632	0.73	SUBCLONAL	1	TRUE	1	0.65904997152504	2		554	946	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144675	119144675	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	201	500	0	ENST00000264033.4:c.688C>A	p.Leu230Met	p.L230M	ENST00000264033	NM_005188.3	230	Ctg/Atg	4/16	1	2	FACETS	0.687	0.637	0.738	0.687	0.637	0.738	SUBCLONAL	1	TRUE	1	0.65904997152504	2		500	888	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46211519	46211519	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	146	365	0	ENST00000334344.6:c.485T>G	p.Val162Gly	p.V162G	ENST00000334344	NM_152641.2	162	gTg/gGg	5/21	1	2	FACETS	0.638	0.584	0.695	0.638	0.584	0.695	SUBCLONAL	1	TRUE	1	0.65904997152504	2		365	694	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32918751	32918751	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	238	506	0	ENST00000380152.3:c.6898C>T	p.Gln2300Ter	p.Q2300*	ENST00000380152		2300	Caa/Taa	12/27	1	2	FACETS	0.733	0.684	0.782	0.733	0.684	0.782	SUBCLONAL	1	TRUE	1	0.65904997152504	2		506	986	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639677	3639677	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs778781581	NA	P-0017006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1132	312	1018	0	ENST00000294008.3:c.3962C>T	p.Pro1321Leu	p.P1321L	ENST00000294008	NM_032444.2	1321	cCg/cTg	12/15	1	2	FACETS	0.656	0.617	0.695	0.656	0.617	0.695	SUBCLONAL	1	TRUE	1	0.65904997152504	2		1018	1444	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16021282	16021282	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0017006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	166	381	0	ENST00000268712.3:c.1975G>T	p.Glu659Ter	p.E659*	ENST00000268712	NM_006311.3	659	Gaa/Taa	18/46	1	2	FACETS	0.668	0.615	0.724	0.668	0.615	0.724	SUBCLONAL	1	TRUE	1	0.65904997152504	2		381	754	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37618575	37618575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	226	566	0	ENST00000447079.4:c.251C>T	p.Ser84Phe	p.S84F	ENST00000447079	NM_015083.1	84	tCc/tTc	1/14	1	2	FACETS	0.653	0.608	0.7	0.653	0.608	0.7	SUBCLONAL	1	TRUE	1	0.65904997152504	2		566	1050	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11134266	11134266	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1064796254	NA	P-0017006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	264	620	0	ENST00000358026.2:c.2932C>T	p.Arg978Ter	p.R978*	ENST00000358026	NM_001128849.1	978	Cga/Tga	20/36	1	2	FACETS	0.818	0.768	0.87	0.818	0.768	0.87	CLONAL	1	TRUE	1	0.65904997152504	2		620	979	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61709635	61709635	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	126	309	0	ENST00000401558.2:c.2852A>C	p.Asn951Thr	p.N951T	ENST00000401558	NM_003400.3	951	aAt/aCt	23/25	1	2	FACETS	0.61	0.554	0.669	0.61	0.554	0.669	SUBCLONAL	1	TRUE	1	0.65904997152504	2		309	627	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020744	112020744	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	834	243	526	0	ENST00000368678.4:c.827A>G	p.Gln276Arg	p.Q276R	ENST00000368678		276	cAg/cGg	8/13	1	2	FACETS	0.685	0.639	0.731	0.685	0.639	0.731	SUBCLONAL	1	TRUE	1	0.65904997152504	2		526	1077	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117700256	117700256	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs1460047377	NA	P-0017006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1026	290	708	0	ENST00000368508.3:c.2563A>T	p.Ile855Phe	p.I855F	ENST00000368508	NM_002944.2	855	Att/Ttt	17/43	1	2	FACETS	0.669	0.628	0.711	0.669	0.628	0.711	SUBCLONAL	1	TRUE	1	0.65904997152504	2		708	1316	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55273238	55273238	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0017006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	272	604	0	ENST00000275493.2:c.3561T>A	p.Phe1187Leu	p.F1187L	ENST00000275493	NM_005228.3	1187	ttT/ttA	28/28	1	2	FACETS	0.754	0.707	0.802	0.754	0.707	0.802	SUBCLONAL	1	TRUE	1	0.65904997152504	2		604	1095	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69031666	69031666	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0017006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	154	460	0	ENST00000288368.4:c.3422-1G>A		p.X1141_splice	ENST00000288368	NM_024870.2	1141			1	2	FACETS	0.563	0.515	0.613	0.563	0.515	0.613	SUBCLONAL	1	TRUE	1	0.65904997152504	2		460	830	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8339017	8339017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	197	492	1	ENST00000356435.5:c.5284C>T	p.Arg1762Trp	p.R1762W	ENST00000356435		1762	Cgg/Tgg	32/35	0.472002591644449	1	FACETS	0.595	0.553	0.638	0.595	0.553	0.638	SUBCLONAL	1	TRUE	0	0.65904997152504	1		493	674	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971073	21971086	+	frameshift_variant	Frame_Shift_Del	DEL	CACCAGCGTGTCCA	CACCAGCGTGTCCA	-	novel	NA	P-0017006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	101	433	0	ENST00000304494.5:c.272_285del	p.Leu91ArgfsTer24	p.L91Rfs*24	ENST00000304494	NM_000077.4	91	cTGGACACGCTGGTG/c	2/3	0.472002591644449	1	FACETS	0.447	0.401	0.495	0.447	0.401	0.495	SUBCLONAL	1	TRUE	0	0.65904997152504	1		433	460	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27157952	27157952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017006-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	235	618	0	ENST00000380036.4:c.176G>A	p.Arg59Lys	p.R59K	ENST00000380036	NM_000459.3	59	aGg/aAg	2/23	0.472002591644449	1	FACETS	0.591	0.553	0.63	0.591	0.553	0.63	SUBCLONAL	1	TRUE	0	0.65904997152504	1		618	809	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	74	124	215	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.974	1			1	INDETERMINATE	2	TRUE	NA	0.574857254811673	2		215	198	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412973	49412973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs11552761	NA	P-0017208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	992	137	886	0	ENST00000418115.1:c.50G>A	p.Gly17Glu	p.G17E	ENST00000418115	NM_001664.2	17	gGa/gAa	2/5	0.554586662722928	2	FACETS	0.422	0.383	0.464	0.211	0.191	0.232	SUBCLONAL	1	TRUE	0	0.574857254811673	2		886	1129	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37868208	37868208	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1057519816	NA	P-0017208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	125	685	0	ENST00000269571.5:c.929C>A	p.Ser310Tyr	p.S310Y	ENST00000269571		310	tCc/tAc	8/27	1	2	FACETS	0.489	0.442	0.538	0.489	0.442	0.538	SUBCLONAL	1	TRUE	1	0.574857254811673	2		685	890	SUCCESS
MYD88	4615	MSKCC	GRCh37	3	38182641	38182641	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs387907272	NA	P-0017208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	11	368	0	ENST00000396334.3:c.794T>C	p.Leu265Pro	p.L265P	ENST00000396334	NM_002468.4	265	cTg/cCg	5/5	0.554586662722928	2	FACETS	0.079	0.054	0.11	0.039	0.027	0.055	SUBCLONAL	1	TRUE	0	0.574857254811673	2		368	485	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056021	26056021	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs987043105	NA	P-0017208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	341	55	239	0	ENST00000343677.2:c.636G>C	p.Lys212Asn	p.K212N	ENST00000343677	NM_005319.3	212	aaG/aaC	1/1	1	2	FACETS	0.483	0.414	0.558	0.483	0.414	0.558	SUBCLONAL	1	TRUE	1	0.574857254811673	2		239	396	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141507	11141507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	256	265	689	2	ENST00000358026.2:c.3484G>A	p.Gly1162Ser	p.G1162S	ENST00000358026	NM_001128849.1	1162	Ggc/Agc	25/36	0.574857254811673	1	FACETS	1	0.992	1	1	0.992	1	CLONAL	1	TRUE	0	0.574857254811673	1		691	521	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857275	9857275	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1426934537	NA	P-0017208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	63	509	1	ENST00000330684.3:c.4126C>T	p.Arg1376Cys	p.R1376C	ENST00000330684	NM_001134407.1	1376	Cgc/Tgc	13/13	0.574857254811673	1	FACETS	0.348	0.301	0.398	0.348	0.301	0.398	SUBCLONAL	1	TRUE	0	0.574857254811673	1		510	449	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495709	72495709	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	90	564	1	ENST00000477973.2:c.363C>A	p.Phe121Leu	p.F121L	ENST00000477973	NM_012234.5	121	ttC/ttA	1/4	0.554586662722928	2	FACETS	0.375	0.332	0.421	0.187	0.166	0.211	SUBCLONAL	1	TRUE	0	0.574857254811673	2		565	835	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46543213	46543213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1128	136	809	0	ENST00000262741.5:c.288G>A	p.Met96Ile	p.M96I	ENST00000262741	NM_003629.3	96	atG/atA	3/10	0.240160628433003	3	FACETS	0.482	0.437	0.53	0.241	0.218	0.265	INDETERMINATE	1	TRUE	1	0.574857254811673	3		809	1264	SUCCESS
ELF3	1999	MSKCC	GRCh37	1	201981506	201981506	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1398893368	NA	P-0017208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	356	666	0	ENST00000359651.3:c.420T>G	p.Ile140Met	p.I140M	ENST00000359651		140	atT/atG	3/8	0.302516743329337	3	FACETS	0.916	0.872	0.961	0.916	0.872	0.961	INDETERMINATE	2	TRUE	1	0.574857254811673	3		666	870	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420846	49420846	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1310451207	NA	P-0017208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	152	495	0	ENST00000301067.7:c.14903C>T	p.Pro4968Leu	p.P4968L	ENST00000301067	NM_003482.3	4968	cCt/cTt	48/54	0.574857254811673	3	FACETS	1	0.972	1	0.566	0.52	0.614	CLONAL	1	TRUE	1	0.574857254811673	3		495	601	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81922855	81922855	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1022	75	483	0	ENST00000359376.3:c.844G>C	p.Glu282Gln	p.E282Q	ENST00000359376	NM_002661.3	282	Gag/Cag	10/33	0.574857254811673	4	FACETS	0.375	0.327	0.426	0.125	0.109	0.142	SUBCLONAL	1	TRUE	1	0.574857254811673	4		483	1097	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89849513	89849513	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	C	rs1291307989	NA	P-0017208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	42	368	0	ENST00000389301.3:c.1471-3C>G		p.X491_splice	ENST00000389301	NM_000135.2	491			0.574857254811673	3	FACETS	0.368	0.307	0.436	0.184	0.153	0.218	SUBCLONAL	1	TRUE	1	0.574857254811673	3		368	511	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41246581	41246581	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	258	784	1	ENST00000357654.3:c.967G>A	p.Gly323Arg	p.G323R	ENST00000357654	NM_007294.3	323	Gga/Aga	10/23	1	2	FACETS	0.885	0.829	0.943	0.885	0.829	0.943	CLONAL	1	TRUE	1	0.574857254811673	2		785	1014	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25976494	25976494	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	599	83	523	0	ENST00000435504.4:c.1051G>C	p.Glu351Gln	p.E351Q	ENST00000435504		351	Gag/Cag	11/13	0.240160628433003	3	FACETS	0.545	0.481	0.614	0.273	0.24	0.307	INDETERMINATE	1	TRUE	1	0.574857254811673	3		523	682	SUCCESS
ATR	545	MSKCC	GRCh37	3	142278247	142278247	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	125	662	0	ENST00000350721.4:c.1578G>C	p.Lys526Asn	p.K526N	ENST00000350721	NM_001184.3	526	aaG/aaC	7/47	0.554586662722928	2	FACETS	0.419	0.378	0.462	0.209	0.189	0.231	SUBCLONAL	1	TRUE	0	0.574857254811673	2		662	1038	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120386	94120386	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	82	387	0	ENST00000369303.4:c.665C>T	p.Ser222Leu	p.S222L	ENST00000369303	NM_004440.3	222	tCa/tTa	3/17	1	2	FACETS	0.511	0.451	0.575	0.511	0.451	0.575	SUBCLONAL	1	TRUE	1	0.574857254811673	2		387	558	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109321813	109321813	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs773524051	NA	P-0017208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1020	184	869	0	ENST00000436639.2:c.610G>C	p.Gly204Arg	p.G204R	ENST00000436639	NM_014454.2	204	Ggt/Cgt	4/10	1	2	FACETS	0.532	0.49	0.576	0.532	0.49	0.576	SUBCLONAL	1	TRUE	1	0.574857254811673	2		869	1204	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2985525	2985525	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	120	666	0	ENST00000396946.4:c.286G>C	p.Glu96Gln	p.E96Q	ENST00000396946	NM_032415.4	96	Gaa/Caa	4/25	NA	2	FACETS	0.468	0.422	0.516			1	INDETERMINATE	1	TRUE	NA	0.574857254811673	2		666	893	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836846	151836846	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017208-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	126	693	0	ENST00000262189.6:c.14374G>C	p.Glu4792Gln	p.E4792Q	ENST00000262189	NM_170606.2	4792	Gag/Cag	56/59	1	2	FACETS	0.476	0.43	0.524	0.476	0.43	0.524	SUBCLONAL	1	TRUE	1	0.574857254811673	2		693	921	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49412898	49412898	+	missense_variant	Missense_Mutation	SNP	T	T	G	rs1057519954	NA	P-0017217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	822	247	817	0	ENST00000418115.1:c.125A>C	p.Tyr42Ser	p.Y42S	ENST00000418115	NM_001664.2	42	tAt/tCt	2/5	1	2	FACETS	0.66	0.617	0.705	0.66	0.617	0.705	SUBCLONAL	1	TRUE	1	0.699924978479035	2		817	1069	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971024	21971024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	68	611	1	ENST00000304494.5:c.334C>T	p.Arg112Cys	p.R112C	ENST00000304494	NM_000077.4	112	Cgt/Tgt	2/3	1	2	FACETS	0.463	0.404	0.526	0.463	0.404	0.526	SUBCLONAL	1	TRUE	1	0.699924978479035	2		612	420	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71946237	71946248	+	splice_donor_variant,coding_sequence_variant	Splice_Site	DEL	TGAATCCTATGG	TGAATCCTATGG	-	novel	NA	P-0017217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	311	724	0	ENST00000298229.2:c.2496_2503+4del		p.X832_splice	ENST00000298229	NM_001567.3	832		22/28	0.699924978479035	3	FACETS	1	0.962	1	0.513	0.484	0.543	CLONAL	1	TRUE	1	0.699924978479035	3		724	1169	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18478035	18478035	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	G	novel	NA	P-0017217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	168	755	0	ENST00000266497.5:c.1272+3A>G		p.X424_splice	ENST00000266497		424			1	2	FACETS	0.476	0.437	0.517	0.476	0.437	0.517	SUBCLONAL	1	TRUE	1	0.699924978479035	2		755	1009	SUCCESS
AKT1	207	MSKCC	GRCh37	14	105236758	105237081	+	splice_donor_variant,splice_acceptor_variant,intron_variant	Splice_Site	DEL	CTGTGGGTGTAGACAGCTCAGACCCCGGTGCCCCACCTCCCTGCCACCTCCACCCACCCACAGCTCCAGTAGGAAGCCAACCTCTTAAAGCACGGCCAGCACGCTGCCATACTGCCAGGAAACTGAGACAGGGCCCCACAGATTGACACAGGGACCTGGGCCCTCAGAGCACTGCCTCCCACCCTGATCATTGGCACTCTCCAAAAGGAACCTTTTTAAATATTTAGATTTTAAAACATCTGAAGCCAAAAAAGCTGAACACTGCAGGCCTCTCTGAGTGTGGAGAGAAAAGGGAGTGGGCGGGGGCAGGCAGTGGCCCCTCAC	CTGTGGGTGTAGACAGCTCAGACCCCGGTGCCCCACCTCCCTGCCACCTCCACCCACCCACAGCTCCAGTAGGAAGCCAACCTCTTAAAGCACGGCCAGCACGCTGCCATACTGCCAGGAAACTGAGACAGGGCCCCACAGATTGACACAGGGACCTGGGCCCTCAGAGCACTGCCTCCCACCCTGATCATTGGCACTCTCCAAAAGGAACCTTTTTAAATATTTAGATTTTAAAACATCTGAAGCCAAAAAAGCTGAACACTGCAGGCCTCTCTGAGTGTGGAGAGAAAAGGGAGTGGGCGGGGGCAGGCAGTGGCCCCTCAC	-	novel	NA	P-0017217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	926	70	546	1	ENST00000349310.3:c.1363+1_1364-1del		p.X455_splice	ENST00000349310	NM_001014432.1	455			NA	2	FACETS	0.201	0.174	0.23			1	INDETERMINATE	1	TRUE	NA	0.699924978479035	2		547	996	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223538	2223538	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762161612	NA	P-0017217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	286	731	0	ENST00000326181.6:c.1069G>A	p.Asp357Asn	p.D357N	ENST00000326181	NM_032271.2	357	Gac/Aac	11/21	0.699924978479035	3	FACETS	1	0.952	1	0.507	0.477	0.538	CLONAL	1	TRUE	1	0.699924978479035	3		731	1088	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853266	68853270	+	frameshift_variant	Frame_Shift_Del	DEL	GGGAG	GGGAG	-	novel	NA	P-0017217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	239	585	680	0	ENST00000261769.5:c.1650_1654del	p.Glu551PhefsTer2	p.E551Ffs*2	ENST00000261769	NM_004360.3	550	aGGGAG/a	11/16	NA	2	FACETS	1	0.983	1			1	INDETERMINATE	2	TRUE	NA	0.699924978479035	2		680	824	SUCCESS
AXL	558	MSKCC	GRCh37	19	41744376	41744383	+	frameshift_variant,splice_region_variant	Frame_Shift_Del	DEL	GCCCCTGG	GCCCCTGG	-	novel	NA	P-0017217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	35	549	0	ENST00000301178.4:c.1001_1008del	p.Leu334ProfsTer2	p.L334Pfs*2	ENST00000301178	NM_021913.4	332	gtGCCCCTGGgc/gtgc	8/20	0.102148607318219	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.699924978479035	0		549	651	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082307	16082307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1191742873	NA	P-0017217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	50	918	3	ENST00000281043.3:c.121G>A	p.Asp41Asn	p.D41N	ENST00000281043	NM_005378.4	41	Gac/Aac	2/3	0.699924978479035	1	FACETS	0.135	0.114	0.158	0.135	0.114	0.158	SUBCLONAL	1	TRUE	0	0.699924978479035	1		921	690	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55564569	55564569	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017217-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	915	55	643	0	ENST00000288135.5:c.457G>T	p.Gly153Trp	p.G153W	ENST00000288135	NM_000222.2	153	Ggg/Tgg	3/21	1	2	FACETS	0.162	0.138	0.189	0.162	0.138	0.189	SUBCLONAL	1	TRUE	1	0.699924978479035	2		643	970	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	409	81	215	0				ENST00000310581	NM_198253.2	-/1132			0.506271114990499	4	FACETS	0.984	0.869	1	0.328	0.289	0.369	CLONAL	1	TRUE	1	0.506271114990499	4		215	490	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578550	7578550	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881999	NA	P-0017381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	606	521	676	2	ENST00000269305.4:c.380C>T	p.Ser127Phe	p.S127F	ENST00000269305	NM_001126112.2	127	tCc/tTc	5/11	0.48381653108527	2	FACETS	0.913	0.878	0.948	0.913	0.878	0.948	CLONAL	2	TRUE	0	0.506271114990499	2		678	1127	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18793483	18793483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267603405	NA	P-0017381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	129	315	0	ENST00000266497.5:c.4180G>A	p.Glu1394Lys	p.E1394K	ENST00000266497		1394	Gaa/Aaa	30/31	1	2	FACETS	0.963	0.878	1	0.963	0.878	1	CLONAL	1	TRUE	1	0.506271114990499	2		315	529	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846037	68846037	+	splice_acceptor_variant	Splice_Site	SNP	G	G	C	novel	NA	P-0017381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	219	422	0	ENST00000261769.5:c.1009-1G>C		p.X337_splice	ENST00000261769	NM_004360.3	337			0.484363910566293	1	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	0	0.506271114990499	1		422	641	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325092	39325092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	428	133	431	0	ENST00000373001.3:c.227C>T	p.Ser76Phe	p.S76F	ENST00000373001	NM_022157.3	76	tCc/tTc	1/7	0.493991373059221	2	FACETS	0.937	0.854	1	0.468	0.427	0.511	CLONAL	1	TRUE	0	0.506271114990499	2		431	561	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133210937	133210937	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1382652919	NA	P-0017381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	126	452	0	ENST00000320574.5:c.5839G>A	p.Glu1947Lys	p.E1947K	ENST00000320574	NM_006231.2	1947	Gag/Aag	43/49	1	2	FACETS	0.759	0.688	0.833	0.759	0.688	0.833	SUBCLONAL	1	TRUE	1	0.506271114990499	2		452	656	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133252409	133252409	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	C	novel	NA	P-0017381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	273	85	222	0	ENST00000320574.5:c.1021-3C>G		p.X341_splice	ENST00000320574	NM_006231.2	341			1	2	FACETS	0.938	0.836	1	0.938	0.836	1	CLONAL	1	TRUE	1	0.506271114990499	2		222	358	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	11984678	11984678	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	88	291	0	ENST00000353533.5:c.224G>A	p.Arg75Lys	p.R75K	ENST00000353533	NM_003010.3	75	aGa/aAa	3/11	0.48381653108527	2	FACETS	0.776	0.691	0.866	0.388	0.345	0.433	SUBCLONAL	1	TRUE	0	0.506271114990499	2		291	448	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37883246	37883246	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199905364	NA	P-0017381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	131	634	0	ENST00000269571.5:c.3149C>T	p.Ser1050Leu	p.S1050L	ENST00000269571		1050	tCa/tTa	25/27	1	2	FACETS	0.863	0.785	0.943	0.863	0.785	0.943	CLONAL	1	TRUE	1	0.506271114990499	2		634	600	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37884145	37884145	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	185	544	0	ENST00000269571.5:c.3616C>T	p.Gln1206Ter	p.Q1206*	ENST00000269571		1206	Cag/Tag	27/27	1	2	FACETS	0.955	0.884	1	0.955	0.884	1	CLONAL	1	TRUE	1	0.506271114990499	2		544	765	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15288349	15288349	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1442573031	NA	P-0017381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	276	729	0	ENST00000263388.2:c.4390G>A	p.Glu1464Lys	p.E1464K	ENST00000263388	NM_000435.2	1464	Gag/Aag	24/33	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.506271114990499	2		729	1037	SUCCESS
ERCC2	2068	MSKCC	GRCh37	19	45860777	45860777	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	138	401	0	ENST00000391945.4:c.1332C>G	p.Ile444Met	p.I444M	ENST00000391945	NM_000400.3	444	atC/atG	14/23	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.506271114990499	2		401	516	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972633	25972633	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1304291937	NA	P-0017381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	166	179	0	ENST00000435504.4:c.1792C>G	p.Gln598Glu	p.Q598E	ENST00000435504		598	Cag/Gag	12/13	0.346008685389249	3	FACETS	0.99	0.92	1			1	CLONAL	2	TRUE	NA	0.506271114990499	3		179	415	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973181	25973181	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0017381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	300	186	225	0	ENST00000435504.4:c.1244C>G	p.Ser415Ter	p.S415*	ENST00000435504		415	tCa/tGa	12/13	0.346008685389249	3	FACETS	0.947	0.883	1			1	CLONAL	2	TRUE	NA	0.506271114990499	3		225	486	SUCCESS
RYBP	23429	MSKCC	GRCh37	3	72495709	72495709	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	198	392	0	ENST00000477973.2:c.363C>G	p.Phe121Leu	p.F121L	ENST00000477973	NM_012234.5	121	ttC/ttG	1/4	0.506271114990499	3	FACETS	1	0.955	1	0.521	0.483	0.561	CLONAL	1	TRUE	1	0.506271114990499	3		392	940	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138403604	138403604	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	863	195	463	0	ENST00000289153.2:c.2178C>G	p.Ile726Met	p.I726M	ENST00000289153	NM_006219.2	726	atC/atG	15/22	0.506271114990499	3	FACETS	0.912	0.844	0.984	0.456	0.422	0.492	CLONAL	1	TRUE	1	0.506271114990499	3		463	1058	SUCCESS
ATR	545	MSKCC	GRCh37	3	142254038	142254038	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017381-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	128	305	0	ENST00000350721.4:c.3829G>A	p.Glu1277Lys	p.E1277K	ENST00000350721	NM_001184.3	1277	Gag/Aag	21/47	0.506271114990499	3	FACETS	0.995	0.904	1	0.497	0.452	0.545	CLONAL	1	TRUE	1	0.506271114990499	3		305	637	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	129	87	215	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	1	0.911	1			1	INDETERMINATE	1	TRUE	NA	0.797933502624796	2		215	216	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0017471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	19	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.752492080083715	0	FACETS		NA	1			1	NA	1	TRUE	0	0.797933502624796	0		458	95	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55211080	55211080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519828	NA	P-0017471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1218	12622	566	1	ENST00000275493.2:c.323G>A	p.Arg108Lys	p.R108K	ENST00000275493	NM_005228.3	108	aGa/aAa	3/28	0.797933502624796	23	FACETS	1	0.999	1			1	CLONAL	21	TRUE	NA	0.797933502624796	23		567	13840	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690805	89690805	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	124	255	541	1	ENST00000371953.3:c.212G>A	p.Cys71Tyr	p.C71Y	ENST00000371953	NM_000314.4	71	tGt/tAt	4/9	0.797933502624796	1	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	0	0.797933502624796	1		542	379	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106538	27106538	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	788	260	922	1	ENST00000324856.7:c.6149G>A	p.Trp2050Ter	p.W2050*	ENST00000324856	NM_006015.4	2050	tGg/tAg	20/20	0.531909979787323	3	FACETS	0.87	0.815	0.926	0.435	0.407	0.463	CLONAL	1	TRUE	1	0.797933502624796	3		923	1048	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493977	56493979	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	rs768349544	NA	P-0017471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	250	711	0	ENST00000267101.3:c.3153_3155del	p.Ser1052del	p.S1052del	ENST00000267101	NM_001982.3	1050	cCATca/cca	26/28	1	2	FACETS	0.931	0.876	0.987	0.931	0.876	0.987	CLONAL	1	TRUE	1	0.797933502624796	2		711	673	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825539	50825539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762650238	NA	P-0017471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	242	702	0	ENST00000398568.2:c.2170G>A	p.Val724Ile	p.V724I	ENST00000398568	NM_001042412.1	724	Gtt/Att	14/18	1	2	FACETS	0.897	0.843	0.953	0.897	0.843	0.953	CLONAL	1	TRUE	1	0.797933502624796	2		702	676	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718711	190718711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs183717609	NA	P-0017471-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	320	695	1	ENST00000441310.2:c.869G>A	p.Arg290His	p.R290H	ENST00000441310	NM_000534.4	290	cGt/cAt	8/13	1	2	FACETS	0.868	0.822	0.915	0.868	0.822	0.915	CLONAL	1	TRUE	1	0.797933502624796	2		696	924	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017471-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	40	215	0				ENST00000310581	NM_198253.2	-/1132			NA	2	FACETS	0.755	0.634	0.887			1	INDETERMINATE	1	TRUE	NA	0.506820899584296	2		215	209	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0017471-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	14	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	0.42220352470856	1	FACETS	0.266	0.193	0.354	0.266	0.193	0.354	SUBCLONAL	1	TRUE	0	0.506820899584296	1		458	155	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89690805	89690805	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017471-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	139	541	1	ENST00000371953.3:c.212G>A	p.Cys71Tyr	p.C71Y	ENST00000371953	NM_000314.4	71	tGt/tAt	4/9	0.506820899584296	1	FACETS	0.857	0.785	0.93	0.857	0.785	0.93	CLONAL	1	TRUE	0	0.506820899584296	1		542	478	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27106538	27106538	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017471-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	679	122	922	1	ENST00000324856.7:c.6149G>A	p.Trp2050Ter	p.W2050*	ENST00000324856	NM_006015.4	2050	tGg/tAg	20/20	0.228225423453709	3	FACETS	0.753	0.681	0.83	0.377	0.34	0.415	INDETERMINATE	1	TRUE	1	0.506820899584296	3		923	801	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56493977	56493979	+	inframe_deletion	In_Frame_Del	DEL	CAT	CAT	-	rs768349544	NA	P-0017471-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	136	711	0	ENST00000267101.3:c.3153_3155del	p.Ser1052del	p.S1052del	ENST00000267101	NM_001982.3	1050	cCATca/cca	26/28	1	2	FACETS	0.819	0.747	0.895	0.819	0.747	0.895	CLONAL	1	TRUE	1	0.506820899584296	2		711	655	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50825539	50825539	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs762650238	NA	P-0017471-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	158	702	0	ENST00000398568.2:c.2170G>A	p.Val724Ile	p.V724I	ENST00000398568	NM_001042412.1	724	Gtt/Att	14/18	1	2	FACETS	0.877	0.805	0.951	0.877	0.805	0.951	CLONAL	1	TRUE	1	0.506820899584296	2		702	711	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190718711	190718711	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs183717609	NA	P-0017471-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	179	695	1	ENST00000441310.2:c.869G>A	p.Arg290His	p.R290H	ENST00000441310	NM_000534.4	290	cGt/cAt	8/13	1	2	FACETS	0.861	0.795	0.93	0.861	0.795	0.93	CLONAL	1	TRUE	1	0.506820899584296	2		696	820	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55223543	55223543	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017471-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	2540	2059	744	2	ENST00000275493.2:c.910C>T	p.His304Tyr	p.H304Y	ENST00000275493	NM_005228.3	304	Cac/Tac	8/28	0.506820899584296	25	FACETS	1	0.985	1			1	CLONAL	12	TRUE	NA	0.506820899584296	25		746	4599	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233043	55233043	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs139236063	NA	P-0017471-T02-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	4601	159	664	1	ENST00000275493.2:c.1793G>T	p.Gly598Val	p.G598V	ENST00000275493	NM_005228.3	598	gGa/gTa	15/28	0.506820899584296	25	FACETS	0.9	0.819	0.986			1	CLONAL	1	TRUE	NA	0.506820899584296	25		665	4760	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	72	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.958	1	1	0.958	1	CLONAL	1	TRUE	1	0.367939434097421	2		215	326	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717615	89717615	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs121909227	NA	P-0017544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	82	241	0	ENST00000371953.3:c.640C>T	p.Gln214Ter	p.Q214*	ENST00000371953	NM_000314.4	214	Cag/Tag	7/9	0.363779123929662	1	FACETS	0.983	0.873	1	0.983	0.873	1	CLONAL	1	TRUE	0	0.367939434097421	1		241	370	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579547	7579547	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1567557016	NA	P-0017544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	132	922	0	ENST00000269305.4:c.140del	p.Pro47ArgfsTer76	p.P47Rfs*76	ENST00000269305	NM_001126112.2	47	cCg/cg	4/11	1	2	FACETS	0.998	0.907	1	0.998	0.907	1	CLONAL	1	TRUE	1	0.367939434097421	2		922	719	SUCCESS
MAP2K4	6416	MSKCC	GRCh37	17	12011128	12011128	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0017544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	55	235	0	ENST00000353533.5:c.535G>T	p.Glu179Ter	p.E179*	ENST00000353533	NM_003010.3	179	Gaa/Taa	5/11	1	2	FACETS	0.783	0.672	0.903	0.783	0.672	0.903	CLONAL	1	TRUE	1	0.367939434097421	2		235	382	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10597402	10597402	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	168	477	0	ENST00000171111.5:c.1801C>G	p.Arg601Gly	p.R601G	ENST00000171111	NM_203500.1	601	Cgg/Ggg	6/6	0.347275027216633	1	FACETS	0.787	0.723	0.854	0.787	0.723	0.854	SUBCLONAL	1	TRUE	0	0.367939434097421	1		477	947	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66197718	66197718	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0017544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	81	324	0	ENST00000273854.3:c.2981T>A	p.Met994Lys	p.M994K	ENST00000273854	NM_004439.5	994	aTg/aAg	17/18	1	2	FACETS	0.758	0.668	0.853	0.758	0.668	0.853	SUBCLONAL	1	TRUE	1	0.367939434097421	2		324	581	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153249359	153249359	+	splice_donor_variant	Splice_Site	SNP	C	C	T	rs1371675972	NA	P-0017544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	413	95	232	0	ENST00000281708.4:c.1418+1G>A		p.X473_splice	ENST00000281708	NM_033632.3	473			1	2	FACETS	1	0.907	1	1	0.907	1	CLONAL	1	TRUE	1	0.367939434097421	2		232	508	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589588	67589598	+	protein_altering_variant	In_Frame_Del	DEL	GAATATAACAC	GAATATAACAC	AT	novel	NA	P-0017544-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	35	150	1	ENST00000274335.5:c.1351_1361delinsAT	p.Glu451_Thr454delinsIle	p.E451_T454delinsI	ENST00000274335		451	GAATATAACACt/ATt	10/15	1	2	FACETS	0.668	0.549	0.799	0.668	0.549	0.799	SUBCLONAL	1	TRUE	1	0.367939434097421	2		151	285	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	138	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.896	0.822	0.972	0.896	0.822	0.972	CLONAL	1	FALSE	1	0.688949587853005	2		215	447	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565535	41565535	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	257	473	0	ENST00000263253.7:c.4201G>T	p.Val1401Phe	p.V1401F	ENST00000263253	NM_001429.3	1401	Gtt/Ttt	26/31	1	2	FACETS	0.827	0.776	0.88	0.827	0.776	0.88	CLONAL	1	FALSE	1	0.688949587853005	2		473	902	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55960981	55960981	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017600-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	273	409	0	ENST00000263923.4:c.2959G>C	p.Glu987Gln	p.E987Q	ENST00000263923	NM_002253.2	987	Gaa/Caa	21/30	1	2	FACETS	0.974	0.917	1	0.974	0.917	1	CLONAL	1	FALSE	1	0.688949587853005	2		409	814	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017633-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	29	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.939	0.753	1	0.939	0.753	1	CLONAL	1	TRUE	1	0.14	2		215	441	SUCCESS
ERBB2	2064	MSKCC	GRCh37	17	37880997	37880998	+	protein_altering_variant	In_Frame_Ins	INS	-	-	TCT	rs397516979	NA	P-0017633-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1098	252	572	0	ENST00000269571.5:c.2326_2327insTCT	p.Gly776delinsValCys	p.G776delinsVC	ENST00000269571		776	ggt/gTCTgt	20/27	0.203205345080435	3	FACETS	0.951	0.888	1	1	0.992	1	CLONAL	3	TRUE	1	0.14	3		572	1350	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0017634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	235	282	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.768603552351941	2		282	582	SUCCESS
FGF3	2248	MSKCC	GRCh37	11	69625389	69625389	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs199801193	NA	P-0017634-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	677	280	608	1	ENST00000334134.2:c.404G>A	p.Arg135Gln	p.R135Q	ENST00000334134	NM_005247.2	135	cGg/cAg	3/3	0.259889571957004	1	FACETS	0.469	0.441	0.497	0.469	0.441	0.497	INDETERMINATE	1	TRUE	0	0.768603552351941	1		609	957	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0017635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	234	282	0				ENST00000310581	NM_198253.2	-/1132			0.371265750816256	4	FACETS	1	0.938	1	1	0.938	1	CLONAL	2	TRUE	2	0.398644231975404	4		282	819	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140453136	140453137	+	missense_variant	Missense_Mutation	DNP	AC	AC	CT	rs121913227	NA	P-0017635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	417	161	446	0	ENST00000288602.6:c.1798_1799delinsAG	p.Val600Arg	p.V600R	ENST00000288602	NM_004333.4	600	GTg/AGg	15/18	0.37421061428122	3	FACETS	0.838	0.773	0.906	0.838	0.773	0.906	CLONAL	2	TRUE	1	0.398644231975404	3		446	578	SUCCESS
EED	8726	MSKCC	GRCh37	11	85989481	85989481	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	126	296	0	ENST00000263360.6:c.1240C>T	p.Arg414Ter	p.R414*	ENST00000263360	NM_003797.3	414	Cga/Tga	12/12	0.37421061428122	3	FACETS	0.922	0.835	1	0.461	0.417	0.507	CLONAL	1	TRUE	1	0.398644231975404	3		296	822	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55962438	55962438	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	528	333	650	0	ENST00000263923.4:c.2686C>T	p.Leu896Phe	p.L896F	ENST00000263923	NM_002253.2	896	Ctc/Ttc	19/30	0.389642450675669	2	FACETS	0.97	0.921	1	0.97	0.921	1	CLONAL	2	TRUE	0	0.398644231975404	2		650	861	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40713470	40713470	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1318044562	NA	P-0017635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	466	100	428	0	ENST00000373198.4:c.4045C>T	p.Arg1349Cys	p.R1349C	ENST00000373198	NM_133170.3	1349	Cgt/Tgt	30/32	1	2	FACETS	0.886	0.794	0.984	0.886	0.794	0.984	CLONAL	1	TRUE	1	0.398644231975404	2		428	566	SUCCESS
JUN	3725	MSKCC	GRCh37	1	59248432	59248432	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	252	445	0	ENST00000371222.2:c.311C>T	p.Thr104Ile	p.T104I	ENST00000371222	NM_002228.3	104	aCa/aTa	1/1	0.371265750816256	4	FACETS	0.911	0.854	0.971	0.911	0.854	0.971	CLONAL	2	TRUE	2	0.398644231975404	4		445	970	SUCCESS
ATR	545	MSKCC	GRCh37	3	142277562	142277562	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	85	465	1	ENST00000350721.4:c.1789C>T	p.Pro597Ser	p.P597S	ENST00000350721	NM_001184.3	597	Cca/Tca	8/47	0.37421061428122	3	FACETS	0.76	0.672	0.854	0.38	0.336	0.427	SUBCLONAL	1	TRUE	1	0.398644231975404	3		466	673	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247243	153247243	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0017635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	459	769	0	ENST00000281708.4:c.1559A>C	p.Asp520Ala	p.D520A	ENST00000281708	NM_033632.3	520	gAt/gCt	10/12	0.389642450675669	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	2	TRUE	0	0.398644231975404	2		769	1146	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127920628	127920628	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017635-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	951	727	975	1	ENST00000373547.4:c.271G>A	p.Glu91Lys	p.E91K	ENST00000373547	NM_002721.4	91	Gag/Aag	4/7	0.398644231975404	3	FACETS	0.869	0.84	0.898	0.869	0.84	0.898	CLONAL	3	TRUE	0	0.398644231975404	3		976	1678	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017669-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	85	48	215	0				ENST00000310581	NM_198253.2	-/1132			0.252810805076098	4	FACETS	1	0.892	1	1	0.892	1	INDETERMINATE	2	TRUE	2	0.535927424712036	4		215	133	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577099	7577099	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs121912660	NA	P-0017669-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	269	220	679	1	ENST00000269305.4:c.839G>A	p.Arg280Lys	p.R280K	ENST00000269305	NM_001126112.2	280	aGa/aAa	8/11	0.535927424712036	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.535927424712036	1		680	489	SUCCESS
KRAS	3845	MSKCC	GRCh37	12	25398281	25398281	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs112445441	NA	P-0017669-T01-IM5	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	445	354	0	ENST00000311936.3:c.38G>A	p.Gly13Asp	p.G13D	ENST00000311936	NM_004985.3	13	gGc/gAc	2/5	0.535927424712036	8	FACETS	0.956	0.921	0.99			1	CLONAL	6	TRUE	NA	0.535927424712036	8		354	755	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	106	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.978	1	1	0.978	1	CLONAL	1	TRUE	1	0.480056777422187	2		215	343	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725524	117725524	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1388562198	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	161	607	0	ENST00000368508.3:c.357G>A	p.Trp119Ter	p.W119*	ENST00000368508	NM_002944.2	119	tgG/tgA	5/43	0.480056777422187	1	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	0	0.480056777422187	1		607	481	SUCCESS
PPP6C	5537	MSKCC	GRCh37	9	127912080	127912080	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763733111	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	221	106	392	0	ENST00000373547.4:c.790C>T	p.Arg264Cys	p.R264C	ENST00000373547	NM_002721.4	264	Cgt/Tgt	7/7	0.480056777422187	1	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	0	0.480056777422187	1		392	327	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40790129	40790129	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	110	515	0	ENST00000373198.4:c.2602C>T	p.Pro868Ser	p.P868S	ENST00000373198	NM_133170.3	868	Ccc/Tcc	18/32	1	2	FACETS	0.821	0.74	0.906	0.821	0.74	0.906	CLONAL	1	TRUE	1	0.480056777422187	2		515	558	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11288751	11288751	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs770601118	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	499	178	549	0	ENST00000361445.4:c.3004C>T	p.Arg1002Ter	p.R1002*	ENST00000361445	NM_004958.3	1002	Cga/Tga	19/58	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.480056777422187	2		549	677	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932111	36932112	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	94	428	2	ENST00000361632.4:c.2357_2358delinsTT	p.Ser786Phe	p.S786F	ENST00000361632		786	tCC/tTT	16/16	1	2	FACETS	0.911	0.815	1	0.911	0.815	1	CLONAL	1	TRUE	1	0.480056777422187	2		430	430	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692791	89692791	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1114167623	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	252	120	427	0	ENST00000371953.3:c.275A>G	p.Asp92Gly	p.D92G	ENST00000371953	NM_000314.4	92	gAc/gGc	5/9	0.480056777422187	1	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	0	0.480056777422187	1		427	372	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123244913	123244913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1224606327	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	199	831	2	ENST00000358487.5:c.2191G>A	p.Glu731Lys	p.E731K	ENST00000358487	NM_000141.4	731	Gaa/Aaa	16/18	0.480056777422187	1	FACETS	0.927	0.862	0.993	0.927	0.862	0.993	CLONAL	1	TRUE	0	0.480056777422187	1		833	680	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32410618	32410618	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs866837692	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	140	499	0	ENST00000332351.3:c.1540C>T	p.Gln514Ter	p.Q514*	ENST00000332351	NM_024426.4	514	Cag/Tag	10/10	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.480056777422187	2		499	541	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998991	100998991	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1270021730	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	73	474	1	ENST00000325455.5:c.811G>A	p.Glu271Lys	p.E271K	ENST00000325455	NM_001202474.3	271	Gaa/Aaa	1/8	1	2	FACETS	0.753	0.661	0.85	0.753	0.661	0.85	SUBCLONAL	1	TRUE	1	0.480056777422187	2		475	404	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18435289	18435289	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	360	83	437	0	ENST00000266497.5:c.277del	p.Ser93AlafsTer38	p.S93Afs*38	ENST00000266497		92	Aaa/aa	1/31	1	2	FACETS	0.781	0.692	0.875	0.781	0.692	0.875	SUBCLONAL	1	TRUE	1	0.480056777422187	2		437	443	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230641	46230641	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	129	464	0	ENST00000334344.6:c.890C>T	p.Ser297Phe	p.S297F	ENST00000334344	NM_152641.2	297	tCc/tTc	8/21	1	2	FACETS	0.983	0.895	1	0.983	0.895	1	CLONAL	1	TRUE	1	0.480056777422187	2		464	547	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46230691	46230691	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1424958105	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	94	320	0	ENST00000334344.6:c.940C>T	p.Arg314Cys	p.R314C	ENST00000334344	NM_152641.2	314	Cgt/Tgt	8/21	1	2	FACETS	0.857	0.766	0.953	0.857	0.766	0.953	CLONAL	1	TRUE	1	0.480056777422187	2		320	457	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431691	49431692	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	158	712	0	ENST00000301067.7:c.9447_9448delinsTT	p.Leu3150Phe	p.L3150F	ENST00000301067	NM_003482.3	3149	tcCCtt/tcTTtt	34/54	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.480056777422187	2		712	588	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28588626	28588626	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs548609046	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	165	596	0	ENST00000241453.7:c.2822C>T	p.Ser941Leu	p.S941L	ENST00000241453	NM_004119.2	941	tCg/tTg	23/24	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.480056777422187	2		596	663	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28963969	28963969	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770598745	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	270	77	360	0	ENST00000282397.4:c.1933G>A	p.Glu645Lys	p.E645K	ENST00000282397	NM_002019.4	645	Gaa/Aaa	13/30	1	2	FACETS	0.924	0.818	1	0.924	0.818	1	CLONAL	1	TRUE	1	0.480056777422187	2		360	347	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614575	38614575	+	frameshift_variant	Frame_Shift_Ins	INS	G	G	AA	novel	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	157	707	0	ENST00000299084.4:c.341delinsAA	p.Arg114LysfsTer20	p.R114Kfs*20	ENST00000299084	NM_152594.2	114	aGa/aAAa	3/7	0.480056777422187	1	FACETS	0.963	0.888	1	0.963	0.888	1	CLONAL	1	TRUE	0	0.480056777422187	1		707	516	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778638	3778638	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	91	545	0	ENST00000262367.5:c.6410C>T	p.Pro2137Leu	p.P2137L	ENST00000262367	NM_004380.2	2137	cCc/cTc	31/31	1	2	FACETS	1	0.912	1	1	0.912	1	CLONAL	1	TRUE	1	0.480056777422187	2		545	371	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10031979	10031979	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	167	657	1	ENST00000330684.3:c.844G>A	p.Asp282Asn	p.D282N	ENST00000330684	NM_001134407.1	282	Gat/Aat	3/13	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.480056777422187	2		658	631	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59876539	59876539	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	150	569	0	ENST00000259008.2:c.1262A>G	p.Glu421Gly	p.E421G	ENST00000259008	NM_032043.2	421	gAa/gGa	9/20	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.480056777422187	2		569	612	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39537632	39537636	+	stop_gained	Nonsense_Mutation	ONP	GATCT	GATCT	TAACC	novel	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	293	79	354	0	ENST00000262039.4:c.166_170delinsTAACC	p.Asp56_Leu57delinsTer	p.D56_L57delins*	ENST00000262039	NM_002647.2	56	GATCTt/TAACCt	2/25	1	2	FACETS	0.885	0.783	0.992	0.885	0.783	0.992	CLONAL	1	TRUE	1	0.480056777422187	2		354	372	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2222530	2222530	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs760394488	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	170	654	1	ENST00000398665.3:c.3362C>T	p.Ser1121Leu	p.S1121L	ENST00000398665	NM_032482.2	1121	tCg/tTg	24/28	1	2	FACETS	0.882	0.812	0.955	0.882	0.812	0.955	CLONAL	1	TRUE	1	0.480056777422187	2		655	803	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4110574	4110574	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267607230	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	535	194	608	3	ENST00000262948.5:c.383C>T	p.Pro128Leu	p.P128L	ENST00000262948	NM_030662.3	128	cCg/cTg	3/11	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.480056777422187	2		611	729	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17954587	17954587	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs761583890	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	169	739	0	ENST00000458235.1:c.307C>T	p.Arg103Cys	p.R103C	ENST00000458235	NM_000215.3	103	Cgc/Tgc	3/24	1	2	FACETS	0.943	0.868	1	0.943	0.868	1	CLONAL	1	TRUE	1	0.480056777422187	2		739	747	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25972788	25972788	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs746907412	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	358	81	413	0	ENST00000435504.4:c.1637C>T	p.Pro546Leu	p.P546L	ENST00000435504		546	cCa/cTa	12/13	1	2	FACETS	0.769	0.68	0.863	0.769	0.68	0.863	SUBCLONAL	1	TRUE	1	0.480056777422187	2		413	439	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41101200	41101200	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	89	542	0	ENST00000373198.4:c.1156C>T	p.Pro386Ser	p.P386S	ENST00000373198	NM_133170.3	386	Ccg/Tcg	8/32	1	2	FACETS	0.702	0.624	0.785	0.702	0.624	0.785	SUBCLONAL	1	TRUE	1	0.480056777422187	2		542	528	SUCCESS
PPARG	5468	MSKCC	GRCh37	3	12458537	12458537	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs140204299	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	190	728	2	ENST00000287820.6:c.1154G>A	p.Arg385Gln	p.R385Q	ENST00000287820	NM_015869.4	385	cGa/cAa	6/7	1	2	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	1	0.480056777422187	2		730	753	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72799578	72799578	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	125	485	1	ENST00000325599.8:c.1591C>T	p.Pro531Ser	p.P531S	ENST00000325599	NM_018130.2	531	Cct/Tct	11/11	1	2	FACETS	1	0.911	1	1	0.911	1	CLONAL	1	TRUE	1	0.480056777422187	2		486	520	SUCCESS
PRKCI	5584	MSKCC	GRCh37	3	169988293	169988293	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	159	512	0	ENST00000295797.4:c.535C>T	p.His179Tyr	p.H179Y	ENST00000295797	NM_002740.5	179	Cat/Tat	6/18	1	2	FACETS	0.959	0.881	1	0.959	0.881	1	CLONAL	1	TRUE	1	0.480056777422187	2		512	691	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41750524	41750524	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	137	596	0	ENST00000226382.2:c.104C>T	p.Ser35Phe	p.S35F	ENST00000226382	NM_003924.3	35	tCc/tTc	1/3	1	2	FACETS	1	0.954	1	1	0.954	1	CLONAL	1	TRUE	1	0.480056777422187	2		596	536	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260659	1260659	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	611	195	645	0	ENST00000310581.5:c.2900G>A	p.Gly967Glu	p.G967E	ENST00000310581	NM_198253.2	967	gGg/gAg	12/16	1	2	FACETS	1	0.934	1	1	0.934	1	CLONAL	1	TRUE	1	0.480056777422187	2		645	806	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35873661	35873661	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs193922644	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	87	389	0	ENST00000303115.3:c.617G>A	p.Arg206Gln	p.R206Q	ENST00000303115	NM_002185.3	206	cGa/cAa	5/8	1	2	FACETS	0.776	0.69	0.868	0.776	0.69	0.868	SUBCLONAL	1	TRUE	1	0.480056777422187	2		389	467	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876467	35876467	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	109	660	0	ENST00000303115.3:c.1259C>T	p.Ser420Phe	p.S420F	ENST00000303115	NM_002185.3	420	tCt/tTt	8/8	1	2	FACETS	0.722	0.649	0.798	0.722	0.649	0.798	SUBCLONAL	1	TRUE	1	0.480056777422187	2		660	629	SUCCESS
H3C8	8968	MSKCC	GRCh37	6	26271447	26271447	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1453083205	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	111	326	1	ENST00000305910.3:c.166C>T	p.Gln56Ter	p.Q56*	ENST00000305910	NM_003534.2	56	Cag/Tag	1/1	0.480056777422187	2	FACETS	1	0.969	1	0.582	0.528	0.639	CLONAL	1	TRUE	0	0.480056777422187	2		327	397	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31324166	31324166	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs41558819	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	167	14	374	5	ENST00000412585.2:c.397C>T	p.Leu133Phe	p.L133F	ENST00000412585	NM_005514.6	133	Ctc/Ttc	3/8	0.480056777422187	2	FACETS	0.322	0.233	0.429	0.161	0.116	0.215	SUBCLONAL	1	TRUE	0	0.480056777422187	2		379	181	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979258	93979258	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	123	500	0	ENST00000369303.4:c.1570G>A	p.Gly524Arg	p.G524R	ENST00000369303	NM_004440.3	524	Gga/Aga	7/17	0.480056777422187	1	FACETS	0.879	0.801	0.96	0.879	0.801	0.96	CLONAL	1	TRUE	0	0.480056777422187	1		500	443	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117662429	117662429	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	249	150	527	0	ENST00000368508.3:c.4948C>T	p.Pro1650Ser	p.P1650S	ENST00000368508	NM_002944.2	1650	Cct/Tct	30/43	0.480056777422187	1	FACETS	1	0.981	1	1	0.981	1	CLONAL	1	TRUE	0	0.480056777422187	1		527	399	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2962334	2962334	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	342	655	0	ENST00000396946.4:c.2203G>A	p.Glu735Lys	p.E735K	ENST00000396946	NM_032415.4	735	Gaa/Aaa	17/25	0.480056777422187	3	FACETS	1	0.976	1	1	0.976	1	CLONAL	2	TRUE	1	0.480056777422187	3		655	846	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935523	13935523	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	331	200	350	0	ENST00000405192.2:c.1333C>T	p.Pro445Ser	p.P445S	ENST00000405192	NM_001163147.1	445	Ccc/Tcc	12/12	0.480056777422187	3	FACETS	0.973	0.909	1	0.973	0.909	1	CLONAL	2	TRUE	1	0.480056777422187	3		350	531	SUCCESS
MET	4233	MSKCC	GRCh37	7	116399527	116399527	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	351	243	452	0	ENST00000397752.3:c.2347G>A	p.Gly783Arg	p.G783R	ENST00000397752	NM_000245.2	783	Gga/Aga	10/21	0.480056777422187	3	FACETS	1	0.973	1	1	0.973	1	CLONAL	2	TRUE	1	0.480056777422187	3		452	594	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477854	140477854	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	325	760	0	ENST00000288602.6:c.1454T>G	p.Leu485Trp	p.L485W	ENST00000288602	NM_004333.4	485	tTg/tGg	12/18	0.480056777422187	3	FACETS	0.963	0.913	1	0.963	0.913	1	CLONAL	2	TRUE	1	0.480056777422187	3		760	872	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140494149	140494149	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	440	836	0	ENST00000288602.6:c.1099C>T	p.Pro367Ser	p.P367S	ENST00000288602	NM_004333.4	367	Ccc/Tcc	8/18	0.480056777422187	3	FACETS	1	0.968	1	1	0.968	1	CLONAL	2	TRUE	1	0.480056777422187	3		836	1120	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860104	151860104	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	265	512	3	ENST00000262189.6:c.10558C>T	p.Pro3520Ser	p.P3520S	ENST00000262189	NM_170606.2	3520	Cca/Tca	43/59	0.480056777422187	3	FACETS	1	0.965	1	1	0.965	1	CLONAL	2	TRUE	1	0.480056777422187	3		515	664	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878329	151878329	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	274	530	0	ENST00000262189.6:c.6616C>T	p.Pro2206Ser	p.P2206S	ENST00000262189	NM_170606.2	2206	Cct/Tct	36/59	0.480056777422187	3	FACETS	1	0.979	1	1	0.979	1	CLONAL	2	TRUE	1	0.480056777422187	3		530	660	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69011995	69011995	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	197	806	0	ENST00000288368.4:c.2632C>T	p.Pro878Ser	p.P878S	ENST00000288368	NM_024870.2	878	Cct/Tct	23/40	1	2	FACETS	0.934	0.865	1	0.934	0.865	1	CLONAL	1	TRUE	1	0.480056777422187	2		806	879	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069952	5069952	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	96	393	0	ENST00000381652.3:c.1541C>G	p.Thr514Arg	p.T514R	ENST00000381652	NM_004972.3	514	aCg/aGg	12/25	0.480056777422187	1	FACETS	0.804	0.722	0.89	0.804	0.722	0.89	CLONAL	1	TRUE	0	0.480056777422187	1		393	378	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8341785	8341785	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776356704	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	363	148	732	0	ENST00000356435.5:c.4855G>A	p.Glu1619Lys	p.E1619K	ENST00000356435		1619	Gaa/Aaa	29/35	0.480056777422187	1	FACETS	0.917	0.843	0.993	0.917	0.843	0.993	CLONAL	1	TRUE	0	0.480056777422187	1		732	511	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971096	21971096	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	rs121913384	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	187	94	322	0	ENST00000304494.5:c.262G>T	p.Glu88Ter	p.E88*	ENST00000304494	NM_000077.4	88	Gag/Tag	2/3	0.480056777422187	1	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	0	0.480056777422187	1		322	281	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202881	27202881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	151	603	0	ENST00000380036.4:c.1973C>T	p.Ser658Phe	p.S658F	ENST00000380036	NM_000459.3	658	tCt/tTt	13/23	0.480056777422187	1	FACETS	0.974	0.897	1	0.974	0.897	1	CLONAL	1	TRUE	0	0.480056777422187	1		603	491	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27212890	27212890	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	163	621	0	ENST00000380036.4:c.2872A>T	p.Lys958Ter	p.K958*	ENST00000380036	NM_000459.3	958	Aaa/Taa	17/23	0.480056777422187	1	FACETS	0.95	0.878	1	0.95	0.878	1	CLONAL	1	TRUE	0	0.480056777422187	1		621	543	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93624541	93624541	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	140	693	0	ENST00000375746.1:c.632G>A	p.Gly211Glu	p.G211E	ENST00000375746	NM_001174167.1	211	gGg/gAg	4/14	0.480056777422187	1	FACETS	0.989	0.909	1	0.989	0.909	1	CLONAL	1	TRUE	0	0.480056777422187	1		693	448	SUCCESS
CCNQ	92002	MSKCC	GRCh37	X	152858079	152858105	+	inframe_deletion	In_Frame_Del	DEL	GCCCCATGGTAGCTGTCCCGCAGCAGG	GCCCCATGGTAGCTGTCCCGCAGCAGG	-	novel	NA	P-0017683-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	143	137	300	0	ENST00000406277.2:c.510_536del	p.Leu172_Leu180del	p.L172_L180del	ENST00000406277	NM_152274.4	170	gcCCTGCTGCGGGACAGCTACCATGGGGCg/gcg	6/7	1	1	FACETS	0.775	0.719	0.831	1	0.99	1	SUBCLONAL	2	TRUE	0	0.480056777422187	1		300	280	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0017721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	402	100	282	0				ENST00000310581	NM_198253.2	-/1132			0.2050409518029	3	FACETS	0.921	0.826	1	0.921	0.826	1	CLONAL	2	TRUE	1	0.242553047315758	3		282	502	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971120	21971120	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913388	NA	P-0017721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	302	64	458	0	ENST00000304494.5:c.238C>T	p.Arg80Ter	p.R80*	ENST00000304494	NM_000077.4	80	Cga/Tga	2/3	1	2	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	1	0.242553047315758	2		458	366	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187521298	187521299	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0017721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	77	840	0	ENST00000441802.2:c.11856dup	p.Gly3953TrpfsTer19	p.G3953Wfs*19	ENST00000441802	NM_005245.3	3952	-/T	22/27	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.242553047315758	2		840	554	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578181	7578181	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138983188	NA	P-0017721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	92	924	2	ENST00000269305.4:c.668C>T	p.Pro223Leu	p.P223L	ENST00000269305	NM_001126112.2	223	cCt/cTt	6/11	0.242553047315758	1	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	0	0.242553047315758	1		926	626	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023247	27023259	+	frameshift_variant	Frame_Shift_Del	DEL	CGGAGCCGCCCGG	CGGAGCCGCCCGG	-	novel	NA	P-0017721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	41	501	1	ENST00000324856.7:c.356_368del	p.Glu119AlafsTer109	p.E119Afs*109	ENST00000324856	NM_006015.4	118	aCGGAGCCGCCCGGc/ac	1/20	1	2	FACETS	0.958	0.8	1	0.958	0.8	1	CLONAL	1	TRUE	1	0.242553047315758	2		502	353	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858308	27858308	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	28	622	1	ENST00000359303.2:c.263C>T	p.Ser88Leu	p.S88L	ENST00000359303	NM_003535.2	88	tCg/tTg	1/1	1	2	FACETS	0.494	0.394	0.609	0.494	0.394	0.609	SUBCLONAL	1	TRUE	1	0.242553047315758	2		623	467	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69456182	69456182	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	78	779	2	ENST00000227507.2:c.101C>T	p.Ala34Val	p.A34V	ENST00000227507	NM_053056.2	34	gCg/gTg	1/5	0.242553047315758	3	FACETS	1	0.936	1	0.551	0.484	0.623	CLONAL	1	TRUE	1	0.242553047315758	3		781	654	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577505	7577505	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs745425759	NA	P-0017721-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	443	65	772	0	ENST00000269305.4:c.776A>G	p.Asp259Gly	p.D259G	ENST00000269305	NM_001126112.2	259	gAc/gGc	7/11	0.242553047315758	1	FACETS	0.927	0.805	1	0.927	0.805	1	CLONAL	1	TRUE	0	0.242553047315758	1		772	508	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	45	40	215	0				ENST00000310581	NM_198253.2	-/1132			0.43709641084005	0	FACETS	0.575	0.497	0.653			1	SUBCLONAL	2	FALSE	0	0.45018562081789	0		215	85	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134823	41134823	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	149	56	259	0	ENST00000379561.5:c.805C>T	p.Arg269Ter	p.R269*	ENST00000379561	NM_002015.3	269	Cga/Tga	2/3	0.194507809754559	6	FACETS	1	0.941	1	0.769	0.668	0.875	INDETERMINATE	2	FALSE	3	0.45018562081789	6		259	205	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212289026	212289026	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	106	30	395	0	ENST00000342788.4:c.2720G>A	p.Gly907Glu	p.G907E	ENST00000342788	NM_005235.2	907	gGa/gAa	23/28	1	2	FACETS	0.98	0.802	1	0.98	0.802	1	CLONAL	1	FALSE	1	0.45018562081789	2		395	136	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42028834	42028834	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	209	110	455	0	ENST00000219905.7:c.4372C>T	p.Pro1458Ser	p.P1458S	ENST00000219905	NM_001164273.1	1458	Cct/Tct	13/24	0.277460591690955	5	FACETS	0.855	0.778	0.935	0.855	0.778	0.935	CLONAL	3	FALSE	2	0.45018562081789	5		455	319	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149495372	149495372	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs146614144	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	170	77	556	0	ENST00000261799.4:c.3275C>T	p.Ser1092Leu	p.S1092L	ENST00000261799	NM_002609.3	1092	tCg/tTg	23/23	0.225937193805886	4	FACETS	1	0.894	1	1	0.894	1	INDETERMINATE	2	FALSE	2	0.45018562081789	4		556	247	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056437	26056437	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781281855	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	83	102	249	0	ENST00000343677.2:c.220G>A	p.Glu74Lys	p.E74K	ENST00000343677	NM_005319.3	74	Gag/Aag	1/1	0.45018562081789	7	FACETS	1	0.949	1			1	CLONAL	5	FALSE	NA	0.45018562081789	7		249	185	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57865093	57865093	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	156	766	0	ENST00000228682.2:c.2570C>T	p.Pro857Leu	p.P857L	ENST00000228682	NM_005269.2	857	cCc/cTc	12/12	0.452108719410779	4	FACETS	1	0.945	1			1	CLONAL	2	FALSE	NA	0.45018562081789	4		766	488	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939473	36939473	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	177	92	356	0	ENST00000361632.4:c.377C>T	p.Pro126Leu	p.P126L	ENST00000361632		126	cCc/cTc	4/16	0.194507809754559	6	FACETS	0.962	0.868	1	0.962	0.868	1	INDETERMINATE	3	FALSE	3	0.45018562081789	6		356	269	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256496	115256496	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	318	131	525	0	ENST00000369535.4:c.215T>C	p.Met72Thr	p.M72T	ENST00000369535	NM_002524.4	72	aTg/aCg	3/7	0.194507809754559	6	FACETS	1	0.979	1	0.821	0.751	0.894	INDETERMINATE	2	FALSE	3	0.45018562081789	6		525	449	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115282405	115282405	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	96	416	1	ENST00000438362.2:c.245C>T	p.Ser82Phe	p.S82F	ENST00000438362	NM_001242891.1	82	tCt/tTt	3/20	0.194507809754559	6	FACETS	1	0.934	1	0.702	0.63	0.777	INDETERMINATE	2	FALSE	3	0.45018562081789	6		417	385	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243809220	243809220	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	147	39	453	1	ENST00000263826.5:c.404C>T	p.Ala135Val	p.A135V	ENST00000263826	NM_005465.4	135	gCc/gTc	4/13	NA	2	FACETS	0.932	0.782	1			1	INDETERMINATE	1	FALSE	NA	0.45018562081789	2		454	186	SUCCESS
RET	5979	MSKCC	GRCh37	10	43601944	43601944	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1172318035	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	135	723	0	ENST00000355710.3:c.988C>T	p.Arg330Trp	p.R330W	ENST00000355710	NM_020975.4	330	Cgg/Tgg	5/20	1	2	FACETS	0.986	0.912	1	1	0.991	1	CLONAL	2	FALSE	1	0.45018562081789	2		723	304	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134147	41134147	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	36	233	0	ENST00000379561.5:c.1481A>G	p.Gln494Arg	p.Q494R	ENST00000379561	NM_002015.3	494	cAg/cGg	2/3	0.194507809754559	6	FACETS	0.859	0.714	1	0.572	0.476	0.677	INDETERMINATE	2	FALSE	3	0.45018562081789	6		233	177	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779206	3779207	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	76	15	191	0	ENST00000262367.5:c.5841_5842delinsTT	p.Pro1948Ser	p.P1948S	ENST00000262367	NM_004380.2	1947	ccCCcg/ccTTcg	31/31	0.449995208162206	3	FACETS	0.897	0.666	1			1	CLONAL	1	FALSE	NA	0.45018562081789	3		191	91	SUCCESS
ERCC4	2072	MSKCC	GRCh37	16	14041854	14041854	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	194	110	344	0	ENST00000311895.7:c.2401C>T	p.Leu801Phe	p.L801F	ENST00000311895	NM_005236.2	801	Ctc/Ttc	11/11	0.45018562081789	6	FACETS	1	0.926	1			1	CLONAL	3	FALSE	NA	0.45018562081789	6		344	304	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578370	7578370	+	splice_donor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	84	125	351	0	ENST00000269305.4:c.559+1G>T		p.X187_splice	ENST00000269305	NM_001126112.2	187			0.397827692320627	4	FACETS	0.963	0.898	1	0.963	0.898	1	CLONAL	4	FALSE	0	0.45018562081789	4		351	209	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37687561	37687561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	157	78	341	0	ENST00000447079.4:c.4465C>T	p.Pro1489Ser	p.P1489S	ENST00000447079	NM_015083.1	1489	Cct/Tct	14/14	0.443674940848135	4	FACETS	1	0.936	1	1	0.936	1	CLONAL	2	FALSE	2	0.45018562081789	4		341	235	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40870595	40870595	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	280	118	523	0	ENST00000428826.2:c.808C>T	p.Pro270Ser	p.P270S	ENST00000428826		270	Ccc/Tcc	9/21	0.443674940848135	4	FACETS	0.955	0.869	1	0.955	0.869	1	CLONAL	2	FALSE	2	0.45018562081789	4		523	398	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15350825	15350825	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs768141679	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	111	492	0	ENST00000263377.2:c.3178C>T	p.Arg1060Cys	p.R1060C	ENST00000263377	NM_058243.2	1060	Cgc/Tgc	15/20	0.452108719410779	1	FACETS	0.79	0.724	0.855	1	0.988	1	SUBCLONAL	2	FALSE	0	0.45018562081789	1		492	242	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15354040	15354040	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	88	54	225	0	ENST00000263377.2:c.2840C>T	p.Ser947Phe	p.S947F	ENST00000263377	NM_058243.2	947	tCc/tTc	14/20	0.452108719410779	1	FACETS	1	0.963	1	1	0.963	1	CLONAL	1	FALSE	0	0.45018562081789	1		225	142	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17953944	17953944	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	122	47	535	1	ENST00000458235.1:c.458G>A	p.Gly153Asp	p.G153D	ENST00000458235	NM_000215.3	153	gGc/gAc	5/24	0.452108719410779	1	FACETS	0.957	0.822	1	0.957	0.822	1	CLONAL	1	FALSE	0	0.45018562081789	1		536	169	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25973046	25973046	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750947456	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	58	255	0	ENST00000435504.4:c.1379C>T	p.Ser460Phe	p.S460F	ENST00000435504		460	tCt/tTt	12/13	0.111713684338886	6	FACETS	1	0.943	1	0.77	0.671	0.874	INDETERMINATE	2	FALSE	3	0.45018562081789	6		255	212	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12626707	12626707	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	95	483	0	ENST00000251849.4:c.1582C>T	p.Gln528Ter	p.Q528*	ENST00000251849	NM_002880.3	528	Cag/Tag	15/17	0.452108719410779	1	FACETS	0.79	0.72	0.861	1	0.986	1	SUBCLONAL	2	FALSE	0	0.45018562081789	1		483	207	SUCCESS
MITF	4286	MSKCC	GRCh37	3	69990386	69990386	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	40	213	0	ENST00000394351.3:c.346-1G>A		p.X116_splice	ENST00000394351	NM_000248.3	116			0.373176155042688	2	FACETS	0.759	0.647	0.877	0.759	0.647	0.877	SUBCLONAL	2	FALSE	0	0.45018562081789	2		213	117	SUCCESS
DCUN1D1	54165	MSKCC	GRCh37	3	182662920	182662920	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	244	116	445	0	ENST00000292782.4:c.742C>G	p.Arg248Gly	p.R248G	ENST00000292782	NM_020640.2	248	Cgc/Ggc	7/7	0.268959619221958	4	FACETS	1	0.938	1			1	INDETERMINATE	2	FALSE	NA	0.45018562081789	4		445	360	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955596	55955596	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs999160762	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	44	596	0	ENST00000263923.4:c.3349A>G	p.Arg1117Gly	p.R1117G	ENST00000263923	NM_002253.2	1117	Agg/Ggg	25/30	0.452108719410779	1	FACETS	0.769	0.653	0.894	0.769	0.653	0.894	SUBCLONAL	1	FALSE	0	0.45018562081789	1		596	197	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187519220	187519220	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	188	78	463	0	ENST00000441802.2:c.12163C>T	p.Pro4055Ser	p.P4055S	ENST00000441802	NM_005245.3	4055	Ccg/Tcg	23/27	NA	2	FACETS	1	0.971	1			1	INDETERMINATE	1	FALSE	NA	0.45018562081789	2		463	266	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176522581	176522581	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	131	77	501	1	ENST00000292408.4:c.1678G>A	p.Glu560Lys	p.E560K	ENST00000292408	NM_213647.1	560	Gag/Aag	13/18	0.225937193805886	4	FACETS	1	0.965	1	1	0.965	1	INDETERMINATE	2	FALSE	2	0.45018562081789	4		502	208	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93969150	93969150	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1562049937	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	113	43	333	0	ENST00000369303.4:c.1846G>A	p.Asp616Asn	p.D616N	ENST00000369303	NM_004440.3	616	Gac/Aac	10/17	0.452108719410779	1	FACETS	0.949	0.808	1	0.949	0.808	1	CLONAL	1	FALSE	0	0.45018562081789	1		333	156	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93982042	93982042	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762787694	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	130	31	335	0	ENST00000369303.4:c.1423G>A	p.Glu475Lys	p.E475K	ENST00000369303	NM_004440.3	475	Gaa/Aaa	6/17	0.452108719410779	1	FACETS	0.663	0.543	0.795	0.663	0.543	0.795	SUBCLONAL	1	FALSE	0	0.45018562081789	1		335	161	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066464	94066464	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	86	27	290	0	ENST00000369303.4:c.1295C>T	p.Ala432Val	p.A432V	ENST00000369303	NM_004440.3	432	gCt/gTt	5/17	0.452108719410779	1	FACETS	0.823	0.667	0.993	0.823	0.667	0.993	CLONAL	1	FALSE	0	0.45018562081789	1		290	113	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527391	157527391	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	71	343	0	ENST00000346085.5:c.5116C>T	p.Pro1706Ser	p.P1706S	ENST00000346085	NM_020732.3	1706	Ccc/Tcc	20/20	0.443674940848135	4	FACETS	1	0.974	1	0.728	0.641	0.821	CLONAL	1	FALSE	2	0.45018562081789	4		343	314	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38271210	38271210	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	56	355	0	ENST00000425967.3:c.2498C>T	p.Pro833Leu	p.P833L	ENST00000425967	NM_001174067.1	833	cCc/cTc	19/19	1	2	FACETS	0.935	0.824	1	1	0.979	1	CLONAL	2	FALSE	1	0.45018562081789	2		355	133	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98242783	98242783	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	239	463	0	ENST00000331920.6:c.834G>A	p.Trp278Ter	p.W278*	ENST00000331920	NM_000264.3	278	tgG/tgA	6/24	0.449995208162206	3	FACETS	0.893	0.853	0.933			1	CLONAL	4	FALSE	NA	0.45018562081789	3		463	364	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101891251	101891251	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	111	87	431	0	ENST00000374994.4:c.212G>T	p.Cys71Phe	p.C71F	ENST00000374994	NM_004612.2	71	tGt/tTt	2/9	0.452108719410779	1	FACETS	0.756	0.685	0.829	1	0.983	1	SUBCLONAL	2	FALSE	0	0.45018562081789	1		431	198	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934176	39934177	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	57	77	260	1	ENST00000378444.4:c.422_423delinsTT	p.Pro141Leu	p.P141L	ENST00000378444	NM_001123385.1	141	cCC/cTT	4/15	0.313832319073339	2	FACETS	0.851	0.775	0.925			1	CLONAL	3	FALSE	NA	0.45018562081789	2		261	134	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030445	47030445	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs967857316	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	65	71	303	0	ENST00000377604.3:c.220C>T	p.Pro74Ser	p.P74S	ENST00000377604	NM_001204468.1	74	Ccg/Tcg	4/24	0.449995208162206	2	FACETS	1	0.964	1			1	CLONAL	2	FALSE	NA	0.45018562081789	2		303	136	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53254046	53254046	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0017788-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	98	201	0	ENST00000375401.3:c.26T>C	p.Leu9Pro	p.L9P	ENST00000375401	NM_004187.3	9	cTa/cCa	1/26	0.449995208162206	2	FACETS	0.93	0.861	0.997			1	CLONAL	3	FALSE	NA	0.45018562081789	2		201	156	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0017916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	339	51	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.902	0.769	1	0.902	0.769	1	CLONAL	1	TRUE	1	0.289877641815305	2		215	390	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577548	7577548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934575	NA	P-0017916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	642	106	662	0	ENST00000269305.4:c.733G>A	p.Gly245Ser	p.G245S	ENST00000269305	NM_001126112.2	245	Ggc/Agc	7/11	1	2	FACETS	0.978	0.877	1	0.978	0.877	1	CLONAL	1	TRUE	1	0.289877641815305	2		662	748	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178952085	178952085	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs121913279	NA	P-0017916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	62	390	0	ENST00000263967.3:c.3140A>G	p.His1047Arg	p.H1047R	ENST00000263967	NM_006218.2	1047	cAt/cGt	21/21	1	2	FACETS	1	0.874	1	1	0.874	1	CLONAL	1	TRUE	1	0.289877641815305	2		390	424	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0017916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	320	115	288	0	ENST00000304494.5:c.151-1G>A		p.X51_splice	ENST00000304494	NM_000077.4	51			0.289877641815305	2	FACETS	0.912	0.827	1	0.912	0.827	1	CLONAL	2	TRUE	0	0.289877641815305	2		288	435	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187534473	187534473	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0017916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	66	535	0	ENST00000441802.2:c.9253del	p.Asp3086IlefsTer30	p.D3086Ifs*30	ENST00000441802	NM_005245.3	3085	Ctt/tt	13/27	1	2	FACETS	0.911	0.792	1	0.911	0.792	1	CLONAL	1	TRUE	1	0.289877641815305	2		535	500	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178646	56178646	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0017916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	301	44	401	0	ENST00000399503.3:c.3619C>T	p.Gln1207Ter	p.Q1207*	ENST00000399503	NM_005921.1	1207	Cag/Tag	14/20	1	2	FACETS	0.88	0.74	1	0.88	0.74	1	CLONAL	1	TRUE	1	0.289877641815305	2		401	345	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	534226	534226	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0017916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	107	849	1	ENST00000451590.1:c.97G>T	p.Asp33Tyr	p.D33Y	ENST00000451590	NM_001130442.1	33	Gac/Tac	2/5	1	2	FACETS	0.896	0.803	0.994	0.896	0.803	0.994	CLONAL	1	TRUE	1	0.289877641815305	2		850	824	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187532590	187532590	+	stop_gained	Nonsense_Mutation	SNP	G	G	C	novel	NA	P-0017916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	63	517	0	ENST00000441802.2:c.9803C>G	p.Ser3268Ter	p.S3268*	ENST00000441802	NM_005245.3	3268	tCa/tGa	14/27	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.289877641815305	2		517	375	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70333446	70333446	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0017916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	94	782	0	ENST00000373644.4:c.1351G>A	p.Glu451Lys	p.E451K	ENST00000373644	NM_030625.2	451	Gag/Aag	2/12	1	2	FACETS	0.971	0.865	1	0.971	0.865	1	CLONAL	1	TRUE	1	0.289877641815305	2		782	668	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131218	202131218	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	144	533	0	ENST00000358485.4:c.186del	p.Phe62LeufsTer23	p.F62Lfs*23	ENST00000358485	NM_001080125.1	62	ttC/tt	2/9	0.289877641815305	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	2	TRUE	0	0.289877641815305	2		533	489	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139403410	139403411	+	frameshift_variant	Frame_Shift_Del	DEL	TG	TG	-	novel	NA	P-0017916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	89	765	0	ENST00000277541.6:c.3082_3083del	p.Gln1028AlafsTer36	p.Q1028Afs*36	ENST00000277541	NM_017617.3	1028	CAg/g	19/34	1	2	FACETS	0.767	0.679	0.86	0.767	0.679	0.86	SUBCLONAL	1	TRUE	1	0.289877641815305	2		765	801	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139417492	139417492	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0017916-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	95	880	0	ENST00000277541.6:c.552del	p.Lys185SerfsTer92	p.K185Sfs*92	ENST00000277541	NM_017617.3	184	caG/ca	4/34	1	2	FACETS	0.75	0.667	0.839	0.75	0.667	0.839	SUBCLONAL	1	TRUE	1	0.289877641815305	2		880	874	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0018031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	254	282	0				ENST00000310581	NM_198253.2	-/1132			0.124313161845796	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.911063595361028	0		282	573	SUCCESS
IDH1	3417	MSKCC	GRCh37	2	209113113	209113113	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913499	NA	P-0018031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	323	192	281	0	ENST00000345146.2:c.394C>T	p.Arg132Cys	p.R132C	ENST00000345146	NM_005896.2	132	Cgt/Tgt	4/10	0.124313161845796	0	FACETS		NA	1			1	INDETERMINATE	1	TRUE	0	0.911063595361028	0		281	515	SUCCESS
NRAS	4893	MSKCC	GRCh37	1	115256529	115256529	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs11554290	NA	P-0018031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	674	548	586	0	ENST00000369535.4:c.182A>G	p.Gln61Arg	p.Q61R	ENST00000369535	NM_002524.4	61	cAa/cGa	3/7	1	2	FACETS	0.984	0.947	1	0.984	0.947	1	CLONAL	1	TRUE	1	0.911063595361028	2		586	1222	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18576957	18576957	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1323833536	NA	P-0018031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	383	451	1	ENST00000266497.5:c.2365G>T	p.Ala789Ser	p.A789S	ENST00000266497		789	Gcc/Tcc	16/31	1	2	FACETS	0.974	0.93	1	0.974	0.93	1	CLONAL	1	TRUE	1	0.911063595361028	2		452	863	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432321	49432322	+	missense_variant	Missense_Mutation	DNP	GG	GG	TA	novel	NA	P-0018031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	728	543	508	0	ENST00000301067.7:c.8817_8818delinsTA	p.Pro2940Thr	p.P2940T	ENST00000301067	NM_003482.3	2939	gcCCct/gcTAct	34/54	0.347397540431514	3	FACETS	1	0.996	1	0.683	0.656	0.709	INDETERMINATE	1	TRUE	1	0.911063595361028	3		508	1271	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88420203	88420203	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	306	429	1	ENST00000360948.2:c.2483G>A	p.Gly828Glu	p.G828E	ENST00000360948	NM_001012338.2	828	gGg/gAg	19/19	NA	2	FACETS	0.953	0.904	1			1	INDETERMINATE	1	TRUE	NA	0.911063595361028	2		430	705	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2226968	2226968	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	494	400	3	ENST00000398665.3:c.4448C>T	p.Ala1483Val	p.A1483V	ENST00000398665	NM_032482.2	1483	gCc/gTc	27/28	NA	2	FACETS	1	0.982	1			1	INDETERMINATE	1	TRUE	NA	0.911063595361028	2		403	1046	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62293867	62293867	+	intron_variant	Intron	SNP	C	C	T	novel	NA	P-0018031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	463	403	0	ENST00000360203.5:c.396-32C>T		p.*132*	ENST00000360203	NM_001283009.1	146/1243			NA	2	FACETS	0.995	0.954	1			1	INDETERMINATE	1	TRUE	NA	0.911063595361028	2		403	1022	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49940060	49940060	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	476	448	0	ENST00000296474.3:c.983C>T	p.Pro328Leu	p.P328L	ENST00000296474	NM_002447.2	328	cCa/cTa	1/20	1	2	FACETS	0.977	0.937	1	0.977	0.937	1	CLONAL	1	TRUE	1	0.911063595361028	2		448	1070	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80063845	80063845	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	445	579	0	ENST00000265081.6:c.1990C>T	p.Gln664Ter	p.Q664*	ENST00000265081	NM_002439.4	664	Cag/Tag	14/24	1	2	FACETS	0.868	0.83	0.907	0.868	0.83	0.907	CLONAL	1	TRUE	1	0.911063595361028	2		579	1125	SUCCESS
HGF	3082	MSKCC	GRCh37	7	81335072	81335072	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	novel	NA	P-0018031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	542	426	392	1	ENST00000222390.5:c.1758-3C>T		p.X586_splice	ENST00000222390	NM_000601.4	586			1	2	FACETS	0.966	0.924	1	0.966	0.924	1	CLONAL	1	TRUE	1	0.911063595361028	2		393	968	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151849915	151849915	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777060178	NA	P-0018031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	350	330	0	ENST00000262189.6:c.12401C>T	p.Pro4134Leu	p.P4134L	ENST00000262189	NM_170606.2	4134	cCg/cTg	49/59	0.706512585523004	3	FACETS	1	0.957	1			1	CLONAL	1	TRUE	NA	0.911063595361028	3		330	1107	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934375	68934375	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1145	480	464	2	ENST00000288368.4:c.441G>T	p.Leu147Phe	p.L147F	ENST00000288368	NM_024870.2	147	ttG/ttT	4/40	0.814248972227394	3	FACETS	0.944	0.901	0.987	0.472	0.45	0.494	CLONAL	1	TRUE	1	0.911063595361028	3		466	1625	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5123122	5123122	+	splice_donor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0018031-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	56	277	309	0	ENST00000381652.3:c.3177+1G>T		p.X1059_splice	ENST00000381652	NM_004972.3	1059			0.911063595361028	1	FACETS	0.994	0.964	1	0.994	0.964	1	CLONAL	1	TRUE	0	0.911063595361028	1		309	333	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35867541	35867541	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	145	426	0	ENST00000303115.3:c.361del	p.Ile121Ter	p.I121*	ENST00000303115	NM_002185.3	119	Aaa/aa	3/8	1	2	FACETS	0.935	0.854	1	0.935	0.854	1	CLONAL	1	TRUE	1	0.414591988376653	2		426	748	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944549	71944549	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	805	148	546	0	ENST00000298229.2:c.2105T>C	p.Ile702Thr	p.I702T	ENST00000298229	NM_001567.3	702	aTc/aCc	18/28	1	2	FACETS	0.749	0.684	0.818	0.749	0.684	0.818	SUBCLONAL	1	TRUE	1	0.414591988376653	2		546	953	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	210	341	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.82	0.766	0.875	1	0.993	1	CLONAL	2	TRUE	1	0.414591988376653	2		341	618	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49443667	49443667	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs1364500207	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	143	417	0	ENST00000301067.7:c.3704del	p.Gly1235ValfsTer95	p.G1235Vfs*95	ENST00000301067	NM_003482.3	1235	gGt/gt	11/54	1	2	FACETS	0.864	0.789	0.944	0.864	0.789	0.944	CLONAL	1	TRUE	1	0.414591988376653	2		417	798	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	173	736	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.414591988376653	2		741	703	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57860075	57860075	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs759448855	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	234	430	2	ENST00000228682.2:c.821del	p.Gly274AlafsTer6	p.G274Afs*6	ENST00000228682	NM_005269.2	272	tGg/tg	8/12	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.414591988376653	2		432	1107	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633323	3633323	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	197	580	2	ENST00000294008.3:c.4928C>T	p.Ala1643Val	p.A1643V	ENST00000294008	NM_032444.2	1643	gCc/gTc	14/15	1	2	FACETS	0.909	0.842	0.98	0.909	0.842	0.98	CLONAL	1	TRUE	1	0.414591988376653	2		582	1045	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938952	76938952	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	133	571	0	ENST00000373344.5:c.1796C>A	p.Pro599Gln	p.P599Q	ENST00000373344	NM_000489.3	599	cCa/cAa	9/35	1	2	FACETS	0.7	0.636	0.769	0.7	0.636	0.769	SUBCLONAL	1	TRUE	1	0.414591988376653	2		571	916	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89448592	89448592	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs543425684	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	208	440	0	ENST00000336596.2:c.1556C>T	p.Thr519Met	p.T519M	ENST00000336596	NM_005233.5	519	aCg/aTg	7/17	1	2	FACETS	1	0.972	1	1	0.972	1	CLONAL	1	TRUE	1	0.414591988376653	2		440	922	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579471	7579471	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs730882018	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	85	474	0	ENST00000269305.4:c.216del	p.Val73TrpfsTer50	p.V73Wfs*50	ENST00000269305	NM_001126112.2	72	ccC/cc	4/11	1	2	FACETS	0.436	0.385	0.492	0.436	0.385	0.492	SUBCLONAL	1	TRUE	1	0.414591988376653	2		474	940	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27023716	27023716	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	193	400	0	ENST00000324856.7:c.827del	p.Gly276GlufsTer87	p.G276Efs*87	ENST00000324856	NM_006015.4	274	atG/at	1/20	0.414591988376653	2	FACETS	1	0.973	1	0.553	0.512	0.595	CLONAL	1	TRUE	0	0.414591988376653	2		400	842	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577097	7577097	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs764146326	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1078	252	660	1	ENST00000269305.4:c.841G>A	p.Asp281Asn	p.D281N	ENST00000269305	NM_001126112.2	281	Gac/Aac	8/11	1	2	FACETS	0.914	0.854	0.977	0.914	0.854	0.977	CLONAL	1	TRUE	1	0.414591988376653	2		661	1330	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45394805	45394805	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	69	259	0	ENST00000262160.6:c.544C>T	p.Arg182Ter	p.R182*	ENST00000262160	NM_005901.5	182	Cga/Tga	5/11	1	2	FACETS	0.781	0.683	0.887	0.781	0.683	0.887	SUBCLONAL	1	TRUE	1	0.414591988376653	2		259	426	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162724560	162724560	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	564	132	322	1	ENST00000367921.3:c.332G>A	p.Gly111Asp	p.G111D	ENST00000367921	NM_006182.2	111	gGc/gAc	5/18	1	2	FACETS	0.915	0.832	1	0.915	0.832	1	CLONAL	1	TRUE	1	0.414591988376653	2		323	696	SUCCESS
KIT	3815	MSKCC	GRCh37	4	55593616	55593616	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	116	364	0	ENST00000288135.5:c.1682A>C	p.Glu561Ala	p.E561A	ENST00000288135	NM_000222.2	561	gAg/gCg	11/21	1	2	FACETS	0.901	0.814	0.993	0.901	0.814	0.993	CLONAL	1	TRUE	1	0.414591988376653	2		364	621	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204714	128204714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	185	604	0	ENST00000341105.2:c.727C>T	p.His243Tyr	p.H243Y	ENST00000341105	NM_032638.4	243	Cac/Tac	3/6	1	2	FACETS	0.991	0.915	1	0.991	0.915	1	CLONAL	1	TRUE	1	0.414591988376653	2		604	901	SUCCESS
MET	4233	MSKCC	GRCh37	7	116395560	116395560	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs753407699	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	81	362	0	ENST00000397752.3:c.1853C>T	p.Thr618Met	p.T618M	ENST00000397752	NM_000245.2	618	aCg/aTg	6/21	1	2	FACETS	0.689	0.608	0.776	0.689	0.608	0.776	SUBCLONAL	1	TRUE	1	0.414591988376653	2		362	567	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81965260	81965260	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	434	97	292	0	ENST00000359376.3:c.2739+1G>A		p.X913_splice	ENST00000359376	NM_002661.3	913			1	2	FACETS	0.881	0.788	0.98	0.881	0.788	0.98	CLONAL	1	TRUE	1	0.414591988376653	2		292	531	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11137009	11137009	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765857427	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	187	528	0	ENST00000358026.2:c.3202G>A	p.Gly1068Ser	p.G1068S	ENST00000358026	NM_001128849.1	1068	Ggc/Agc	23/36	1	2	FACETS	0.896	0.827	0.967	0.896	0.827	0.967	CLONAL	1	TRUE	1	0.414591988376653	2		528	1007	SUCCESS
RHOA	387	MSKCC	GRCh37	3	49405964	49405964	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	885	227	600	0	ENST00000418115.1:c.174G>T	p.Trp58Cys	p.W58C	ENST00000418115	NM_001664.2	58	tgG/tgT	3/5	1	2	FACETS	0.985	0.917	1	0.985	0.917	1	CLONAL	1	TRUE	1	0.414591988376653	2		600	1112	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133759443	133759443	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs376925416	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	205	575	0	ENST00000318560.5:c.1766G>A	p.Arg589His	p.R589H	ENST00000318560	NM_005157.4	589	cGc/cAc	11/11	1	2	FACETS	0.951	0.882	1	0.951	0.882	1	CLONAL	1	TRUE	1	0.414591988376653	2		575	1040	SUCCESS
BCL6	604	MSKCC	GRCh37	3	187446270	187446270	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	138	364	1	ENST00000232014.4:c.1418del	p.Pro473ArgfsTer117	p.P473Rfs*117	ENST00000232014	NM_001130845.1	473	cCg/cg	6/10	1	2	FACETS	0.844	0.768	0.923	0.844	0.768	0.923	CLONAL	1	TRUE	1	0.414591988376653	2		365	789	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	407527	407527	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs908661692	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	235	571	0	ENST00000380956.4:c.1285G>A	p.Asp429Asn	p.D429N	ENST00000380956	NM_001195286.1	429	Gat/Aat	9/9	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.414591988376653	2		571	984	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65339175	65339175	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1180823763	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	110	291	0	ENST00000342505.4:c.361G>A	p.Asp121Asn	p.D121N	ENST00000342505	NM_002227.2	121	Gac/Aac	5/25	1	2	FACETS	0.92	0.829	1	0.92	0.829	1	CLONAL	1	TRUE	1	0.414591988376653	2		291	577	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52441457	52441457	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	171	418	1	ENST00000460680.1:c.395G>A	p.Gly132Asp	p.G132D	ENST00000460680	NM_004656.3	132	gGc/gAc	6/17	1	2	FACETS	1	0.93	1	1	0.93	1	CLONAL	1	TRUE	1	0.414591988376653	2		419	816	SUCCESS
ATM	472	MSKCC	GRCh37	11	108158382	108158382	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587781785	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	50	431	3	ENST00000278616.4:c.4049C>T	p.Thr1350Met	p.T1350M	ENST00000278616	NM_000051.3	1350	aCg/aTg	27/63	1	2	FACETS	0.35	0.296	0.409	0.35	0.296	0.409	SUBCLONAL	1	TRUE	1	0.414591988376653	2		434	690	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609883	81609883	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	87	231	0	ENST00000298171.2:c.1481G>A	p.Cys494Tyr	p.C494Y	ENST00000298171	NM_000369.2	494	tGc/tAc	10/10	1	2	FACETS	0.903	0.802	1	0.903	0.802	1	CLONAL	1	TRUE	1	0.414591988376653	2		231	465	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99163121	99163121	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	925	181	520	0	ENST00000074304.5:c.1127G>T	p.Arg376Leu	p.R376L	ENST00000074304	NM_001134224.1	376	cGc/cTc	13/26	1	2	FACETS	0.789	0.727	0.854	0.789	0.727	0.854	SUBCLONAL	1	TRUE	1	0.414591988376653	2		520	1106	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72829529	72829529	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	682	147	439	0	ENST00000268489.5:c.7052G>A	p.Cys2351Tyr	p.C2351Y	ENST00000268489	NM_006885.3	2351	tGt/tAt	9/10	1	2	FACETS	0.855	0.781	0.933	0.855	0.781	0.933	CLONAL	1	TRUE	1	0.414591988376653	2		439	829	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2213905	2213905	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs750798710	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	252	976	6	ENST00000398665.3:c.1717G>A	p.Ala573Thr	p.A573T	ENST00000398665	NM_032482.2	573	Gcc/Acc	18/28	1	2	FACETS	0.995	0.93	1	0.995	0.93	1	CLONAL	1	TRUE	1	0.414591988376653	2		982	1222	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225422567	225422567	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	55	217	0	ENST00000264414.4:c.73A>G	p.Met25Val	p.M25V	ENST00000264414	NM_003590.4	25	Atg/Gtg	2/16	1	2	FACETS	0.771	0.663	0.888	0.771	0.663	0.888	SUBCLONAL	1	TRUE	1	0.414591988376653	2		217	344	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	37015106	37015106	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1313118042	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	817	169	571	0	ENST00000358127.4:c.298G>A	p.Ala100Thr	p.A100T	ENST00000358127	NM_001280556.1	100	Gct/Act	3/10	1	2	FACETS	0.827	0.76	0.897	0.827	0.76	0.897	CLONAL	1	TRUE	1	0.414591988376653	2		571	986	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46521525	46521525	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	160	469	3	ENST00000262741.5:c.883del	p.Met295Ter	p.M295*	ENST00000262741	NM_003629.3	295	Atg/tg	7/10	0.414591988376653	2	FACETS	0.788	0.722	0.858	0.394	0.361	0.429	SUBCLONAL	1	TRUE	0	0.414591988376653	2		472	979	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36935355	36935355	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	186	469	1	ENST00000361632.4:c.1372G>T	p.Gly458Cys	p.G458C	ENST00000361632		458	Ggc/Tgc	10/16	0.414591988376653	2	FACETS	0.993	0.917	1	0.496	0.458	0.536	CLONAL	1	TRUE	0	0.414591988376653	2		470	904	SUCCESS
ZRSR2	8233	MSKCC	GRCh37	X	15841231	15841236	+	inframe_deletion	In_Frame_Del	DEL	AGCCGG	AGCCGG	-	rs752736259	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	93	303	1	ENST00000307771.7:c.1338_1343del	p.Ser447_Arg448del	p.S447_R448del	ENST00000307771	NM_005089.3	439	AGCCGG/-	11/11	1	2	FACETS	0.751	0.669	0.839	0.751	0.669	0.839	SUBCLONAL	1	TRUE	1	0.414591988376653	2		304	597	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778264	3778264	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766219870	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	422	113	344	0	ENST00000262367.5:c.6784G>A	p.Gly2262Ser	p.G2262S	ENST00000262367	NM_004380.2	2262	Ggc/Agc	31/31	1	2	FACETS	1	0.919	1	1	0.919	1	CLONAL	1	TRUE	1	0.414591988376653	2		344	535	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971208	21971208	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	rs730881677	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	78	465	0	ENST00000304494.5:c.151-1G>T		p.X51_splice	ENST00000304494	NM_000077.4	51			1	2	FACETS	0.768	0.677	0.865	0.768	0.677	0.865	SUBCLONAL	1	TRUE	1	0.414591988376653	2		465	490	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839886	27839886	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1027454605	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	156	355	1	ENST00000328488.2:c.208C>T	p.Arg70Cys	p.R70C	ENST00000328488	NM_003533.2	70	Cgc/Tgc	1/1	1	2	FACETS	0.995	0.913	1	0.995	0.913	1	CLONAL	1	TRUE	1	0.414591988376653	2		356	756	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21563212	21563212	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	204	584	1	ENST00000382592.4:c.707G>T	p.Gly236Val	p.G236V	ENST00000382592	NM_014572.2	236	gGt/gTt	4/8	1	2	FACETS	0.941	0.872	1	0.941	0.872	1	CLONAL	1	TRUE	1	0.414591988376653	2		585	1046	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27099017	27099017	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	191	509	2	ENST00000324856.7:c.3433C>T	p.Gln1145Ter	p.Q1145*	ENST00000324856	NM_006015.4	1145	Cag/Tag	13/20	0.414591988376653	2	FACETS	0.92	0.851	0.993	0.46	0.425	0.497	CLONAL	1	TRUE	0	0.414591988376653	2		511	1001	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436431	110436431	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	220	596	0	ENST00000375856.3:c.1970C>T	p.Thr657Met	p.T657M	ENST00000375856	NM_003749.2	657	aCg/aTg	1/2	1	2	FACETS	0.922	0.857	0.99	0.922	0.857	0.99	CLONAL	1	TRUE	1	0.414591988376653	2		596	1151	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14626892	14626892	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	922	142	436	1	ENST00000254322.2:c.883C>T	p.Arg295Ter	p.R295*	ENST00000254322	NM_006145.1	295	Cga/Tga	3/3	1	2	FACETS	0.644	0.586	0.705	0.644	0.586	0.705	SUBCLONAL	1	TRUE	1	0.414591988376653	2		437	1064	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100998193	100998193	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1293482599	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	131	341	1	ENST00000325455.5:c.1609G>A	p.Val537Ile	p.V537I	ENST00000325455	NM_001202474.3	537	Gtc/Atc	1/8	1	2	FACETS	0.995	0.906	1	0.995	0.906	1	CLONAL	1	TRUE	1	0.414591988376653	2		342	635	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151836879	151836879	+	splice_region_variant,intron_variant	Splice_Region	DEL	A	A	-	rs369965395	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	134	409	3	ENST00000262189.6:c.14344-3del		p.X4782_splice	ENST00000262189	NM_170606.2	4782			1	2	FACETS	0.863	0.785	0.945	0.863	0.785	0.945	CLONAL	1	TRUE	1	0.414591988376653	2		412	749	SUCCESS
TNFRSF14	8764	MSKCC	GRCh37	1	2494618	2494618	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779526358	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	175	451	0	ENST00000355716.4:c.758C>T	p.Thr253Ile	p.T253I	ENST00000355716	NM_003820.2	253	aCa/aTa	8/8	0.414591988376653	2	FACETS	0.91	0.838	0.985	0.455	0.419	0.493	CLONAL	1	TRUE	0	0.414591988376653	2		451	928	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11205041	11205041	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	860	187	600	0	ENST00000361445.4:c.4748A>G	p.Tyr1583Cys	p.Y1583C	ENST00000361445	NM_004958.3	1583	tAc/tGc	33/58	0.414591988376653	2	FACETS	0.862	0.795	0.931	0.431	0.397	0.466	CLONAL	1	TRUE	0	0.414591988376653	2		600	1047	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11206849	11206849	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	115	371	0	ENST00000361445.4:c.4571-1G>T		p.X1524_splice	ENST00000361445	NM_004958.3	1524			0.414591988376653	2	FACETS	0.79	0.713	0.872	0.395	0.356	0.436	SUBCLONAL	1	TRUE	0	0.414591988376653	2		371	702	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303222	11303222	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747412972	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	188	514	1	ENST00000361445.4:c.1361G>A	p.Arg454His	p.R454H	ENST00000361445	NM_004958.3	454	cGc/cAc	9/58	0.414591988376653	2	FACETS	0.912	0.843	0.985	0.456	0.421	0.493	CLONAL	1	TRUE	0	0.414591988376653	2		515	994	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16258350	16258350	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs756861745	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	175	507	0	ENST00000375759.3:c.5615C>T	p.Ala1872Val	p.A1872V	ENST00000375759	NM_015001.2	1872	gCa/gTa	11/15	0.414591988376653	2	FACETS	0.816	0.751	0.885	0.408	0.375	0.443	CLONAL	1	TRUE	0	0.414591988376653	2		507	1034	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16259861	16259861	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	785	173	512	0	ENST00000375759.3:c.7126C>T	p.Gln2376Ter	p.Q2376*	ENST00000375759	NM_015001.2	2376	Cag/Tag	11/15	0.414591988376653	2	FACETS	0.871	0.802	0.944	0.436	0.401	0.472	CLONAL	1	TRUE	0	0.414591988376653	2		512	958	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260426	16260426	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	140	346	0	ENST00000375759.3:c.7691C>T	p.Ala2564Val	p.A2564V	ENST00000375759	NM_015001.2	2564	gCt/gTt	11/15	0.414591988376653	2	FACETS	0.863	0.786	0.943	0.431	0.393	0.472	CLONAL	1	TRUE	0	0.414591988376653	2		346	783	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16260978	16260978	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774527727	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	105	272	0	ENST00000375759.3:c.8243C>T	p.Ala2748Val	p.A2748V	ENST00000375759	NM_015001.2	2748	gCt/gTt	11/15	0.414591988376653	2	FACETS	0.896	0.806	0.992	0.448	0.403	0.496	CLONAL	1	TRUE	0	0.414591988376653	2		272	565	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261007	16261007	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	116	330	0	ENST00000375759.3:c.8272G>T	p.Gly2758Cys	p.G2758C	ENST00000375759	NM_015001.2	2758	Ggc/Tgc	11/15	0.414591988376653	2	FACETS	0.816	0.736	0.9	0.408	0.368	0.45	CLONAL	1	TRUE	0	0.414591988376653	2		330	686	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261481	16261481	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	148	446	0	ENST00000375759.3:c.8746C>T	p.His2916Tyr	p.H2916Y	ENST00000375759	NM_015001.2	2916	Cac/Tac	11/15	0.414591988376653	2	FACETS	0.907	0.829	0.989	0.454	0.414	0.495	CLONAL	1	TRUE	0	0.414591988376653	2		446	787	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16261924	16261925	+	missense_variant	Missense_Mutation	DNP	AG	AG	GA	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	638	112	369	2	ENST00000375759.3:c.9189_9190delinsGA	p.Val3064Met	p.V3064M	ENST00000375759	NM_015001.2	3063	ccAGtg/ccGAtg	11/15	0.414591988376653	2	FACETS	0.72	0.648	0.797	0.36	0.324	0.399	SUBCLONAL	1	TRUE	0	0.414591988376653	2		371	750	SUCCESS
SDHB	6390	MSKCC	GRCh37	1	17355108	17355108	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	131	384	0	ENST00000375499.3:c.410A>C	p.Lys137Thr	p.K137T	ENST00000375499	NM_003000.2	137	aAg/aCg	4/8	0.414591988376653	2	FACETS	0.932	0.847	1	0.466	0.423	0.511	CLONAL	1	TRUE	0	0.414591988376653	2		384	678	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36820902	36820902	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	161	432	0	ENST00000373129.3:c.475C>A	p.Leu159Met	p.L159M	ENST00000373129	NM_032017.1	159	Ctg/Atg	6/12	0.414591988376653	2	FACETS	0.931	0.855	1	0.466	0.427	0.506	CLONAL	1	TRUE	0	0.414591988376653	2		432	834	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36823964	36823964	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs761856633	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1061	217	584	0	ENST00000373129.3:c.218G>T	p.Arg73Met	p.R73M	ENST00000373129	NM_032017.1	73	aGg/aTg	5/12	0.414591988376653	2	FACETS	0.819	0.76	0.88	0.41	0.38	0.44	CLONAL	1	TRUE	0	0.414591988376653	2		584	1278	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36933235	36933235	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	153	425	0	ENST00000361632.4:c.1882A>C	p.Ile628Leu	p.I628L	ENST00000361632		628	Atc/Ctc	14/16	0.414591988376653	2	FACETS	0.919	0.842	1	0.46	0.421	0.5	CLONAL	1	TRUE	0	0.414591988376653	2		425	803	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305292	39305292	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	208	585	1	ENST00000373001.3:c.1133G>A	p.Gly378Asp	p.G378D	ENST00000373001	NM_022157.3	378	gGt/gAt	7/7	0.414591988376653	2	FACETS	0.911	0.844	0.979	0.455	0.422	0.49	CLONAL	1	TRUE	0	0.414591988376653	2		586	1102	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803829	43803829	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	212	519	0	ENST00000372470.3:c.139G>A	p.Asp47Asn	p.D47N	ENST00000372470	NM_005373.2	47	Gac/Aac	2/12	0.414591988376653	2	FACETS	1	0.971	1	0.542	0.503	0.581	CLONAL	1	TRUE	0	0.414591988376653	2		519	944	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45798434	45798434	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	770	174	534	0	ENST00000450313.1:c.576+1G>A		p.X192_splice	ENST00000450313	NM_012222.2	192			0.414591988376653	2	FACETS	0.889	0.819	0.963	0.445	0.409	0.482	CLONAL	1	TRUE	0	0.414591988376653	2		534	944	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45799192	45799192	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	132	455	0	ENST00000450313.1:c.241G>A	p.Val81Ile	p.V81I	ENST00000450313	NM_012222.2	81	Gtc/Atc	3/16	0.414591988376653	2	FACETS	0.902	0.82	0.988	0.451	0.41	0.494	CLONAL	1	TRUE	0	0.414591988376653	2		455	706	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46532618	46532618	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	82	273	1	ENST00000262741.5:c.460G>A	p.Val154Met	p.V154M	ENST00000262741	NM_003629.3	154	Gtg/Atg	4/10	0.414591988376653	2	FACETS	0.821	0.726	0.921	0.41	0.363	0.461	CLONAL	1	TRUE	0	0.414591988376653	2		274	482	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65301089	65301089	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	19	182	0	ENST00000342505.4:c.3359G>A	p.Cys1120Tyr	p.C1120Y	ENST00000342505	NM_002227.2	1120	tGt/tAt	24/25	1	2	FACETS	0.25	0.189	0.321	0.25	0.189	0.321	SUBCLONAL	1	TRUE	1	0.414591988376653	2		182	367	SUCCESS
CSDE1	7812	MSKCC	GRCh37	1	115263187	115263187	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	175	460	0	ENST00000438362.2:c.2163G>T	p.Arg721Ser	p.R721S	ENST00000438362	NM_001242891.1	721	agG/agT	17/20	1	2	FACETS	0.99	0.912	1	0.99	0.912	1	CLONAL	1	TRUE	1	0.414591988376653	2		460	853	SUCCESS
TENT5C	54855	MSKCC	GRCh37	1	118165984	118165984	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	119	348	0	ENST00000369448.3:c.494T>C	p.Val165Ala	p.V165A	ENST00000369448	NM_017709.3	165	gTg/gCg	2/2	1	2	FACETS	0.812	0.734	0.894	0.812	0.734	0.894	CLONAL	1	TRUE	1	0.414591988376653	2		348	707	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120480017	120480017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	169	403	0	ENST00000256646.2:c.3410G>A	p.Cys1137Tyr	p.C1137Y	ENST00000256646	NM_024408.3	1137	tGc/tAc	21/34	1	2	FACETS	0.896	0.824	0.971	0.896	0.824	0.971	CLONAL	1	TRUE	1	0.414591988376653	2		403	910	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155874281	155874281	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	103	415	0	ENST00000368323.3:c.250G>T	p.Ala84Ser	p.A84S	ENST00000368323	NM_006912.5	84	Gcc/Tcc	5/6	1	2	FACETS	0.663	0.594	0.737	0.663	0.594	0.737	SUBCLONAL	1	TRUE	1	0.414591988376653	2		415	749	SUCCESS
RIT1	6016	MSKCC	GRCh37	1	155880471	155880471	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	867	80	439	0	ENST00000368323.3:c.82G>T	p.Gly28Cys	p.G28C	ENST00000368323	NM_006912.5	28	Ggt/Tgt	2/6	1	2	FACETS	0.408	0.358	0.461	0.408	0.358	0.461	SUBCLONAL	1	TRUE	1	0.414591988376653	2		439	947	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162722910	162722910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	732	141	444	0	ENST00000367921.3:c.108G>A	p.Met36Ile	p.M36I	ENST00000367921	NM_006182.2	36	atG/atA	4/18	1	2	FACETS	0.779	0.71	0.852	0.779	0.71	0.852	SUBCLONAL	1	TRUE	1	0.414591988376653	2		444	873	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193104717	193104717	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	74	345	0	ENST00000367435.3:c.421G>A	p.Glu141Lys	p.E141K	ENST00000367435	NM_024529.4	141	Gag/Aag	5/17	1	2	FACETS	0.614	0.538	0.696	0.614	0.538	0.696	SUBCLONAL	1	TRUE	1	0.414591988376653	2		345	581	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206653434	206653434	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	678	147	429	0	ENST00000367120.3:c.1320del	p.Arg441GlyfsTer49	p.R441Gfs*49	ENST00000367120	NM_014002.3	440	Ttt/tt	12/22	1	2	FACETS	0.86	0.785	0.937	0.86	0.785	0.937	CLONAL	1	TRUE	1	0.414591988376653	2		429	825	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206664154	206664154	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1553390134	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	108	358	0	ENST00000367120.3:c.1696C>T	p.Leu566Phe	p.L566F	ENST00000367120	NM_014002.3	566	Ctt/Ttt	17/22	1	2	FACETS	0.675	0.606	0.748	0.675	0.606	0.748	SUBCLONAL	1	TRUE	1	0.414591988376653	2		358	772	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226578328	226578328	+	splice_region_variant,intron_variant	Splice_Region	SNP	G	G	A	rs776284379	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	129	353	1	ENST00000366794.5:c.403-3C>T		p.X135_splice	ENST00000366794	NM_001618.3	135			1	2	FACETS	0.963	0.876	1	0.963	0.876	1	CLONAL	1	TRUE	1	0.414591988376653	2		354	646	SUCCESS
AKT3	10000	MSKCC	GRCh37	1	243736302	243736302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	141	459	1	ENST00000263826.5:c.745C>T	p.Arg249Cys	p.R249C	ENST00000263826	NM_005465.4	249	Cgt/Tgt	8/13	1	2	FACETS	0.731	0.665	0.799	0.731	0.665	0.799	SUBCLONAL	1	TRUE	1	0.414591988376653	2		460	931	SUCCESS
SMYD3	64754	MSKCC	GRCh37	1	245927438	245927438	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	888	176	562	0	ENST00000388985.4:c.1090G>T	p.Gly364Ter	p.G364*	ENST00000388985		364	Gga/Tga	11/12	1	2	FACETS	0.798	0.734	0.865	0.798	0.734	0.865	SUBCLONAL	1	TRUE	1	0.414591988376653	2		562	1064	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8097667	8097667	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	63	219	2	ENST00000346208.3:c.49G>A	p.Ala17Thr	p.A17T	ENST00000346208		17	Gcc/Acc	2/6	1	2	FACETS	0.749	0.65	0.855	0.749	0.65	0.855	SUBCLONAL	1	TRUE	1	0.414591988376653	2		221	406	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63817050	63817050	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	58	272	0	ENST00000279873.7:c.1021C>T	p.Arg341Ter	p.R341*	ENST00000279873	NM_032199.2	341	Cga/Tga	6/10	1	2	FACETS	0.48	0.412	0.554	0.48	0.412	0.554	SUBCLONAL	1	TRUE	1	0.414591988376653	2		272	583	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70426966	70426966	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1474170533	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	695	117	479	0	ENST00000373644.4:c.4626G>T	p.Lys1542Asn	p.K1542N	ENST00000373644	NM_030625.2	1542	aaG/aaT	7/12	0.414591988376653	2	FACETS	0.695	0.627	0.768	0.348	0.313	0.384	SUBCLONAL	1	TRUE	0	0.414591988376653	2		479	812	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717777	89717777	+	splice_donor_variant	Splice_Site	SNP	G	G	A	rs786204873	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	267	167	269	0	ENST00000371953.3:c.801+1G>A		p.X267_splice	ENST00000371953	NM_000314.4	267			0.414591988376653	2	FACETS	0.928	0.862	0.995	0.928	0.862	0.995	CLONAL	2	TRUE	0	0.414591988376653	2		269	434	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114710979	114710979	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	627	135	412	0	ENST00000543371.1:c.203C>A	p.Pro68His	p.P68H	ENST00000543371	NM_001198531.1	68	cCt/cAt	2/14	0.414591988376653	2	FACETS	0.855	0.777	0.936	0.427	0.388	0.468	CLONAL	1	TRUE	0	0.414591988376653	2		412	762	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925621	114925621	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763934346	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	848	162	510	0	ENST00000543371.1:c.1699G>A	p.Ala567Thr	p.A567T	ENST00000543371	NM_001198531.1	567	Gcc/Acc	14/14	0.414591988376653	2	FACETS	0.774	0.709	0.841	0.387	0.354	0.421	SUBCLONAL	1	TRUE	0	0.414591988376653	2		510	1010	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123243286	123243286	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	169	629	0	ENST00000358487.5:c.2227G>A	p.Val743Met	p.V743M	ENST00000358487	NM_000141.4	743	Gtg/Atg	17/18	0.414591988376653	2	FACETS	0.802	0.737	0.871	0.401	0.368	0.436	CLONAL	1	TRUE	0	0.414591988376653	2		629	1016	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533563	533563	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1163968308	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	931	213	546	0	ENST00000451590.1:c.340G>T	p.Val114Leu	p.V114L	ENST00000451590	NM_001130442.1	114	Gtg/Ttg	4/5	1	2	FACETS	0.898	0.834	0.965	0.898	0.834	0.965	CLONAL	1	TRUE	1	0.414591988376653	2		546	1144	SUCCESS
HRAS	3265	MSKCC	GRCh37	11	533839	533839	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749674880	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	998	243	556	0	ENST00000451590.1:c.217C>T	p.Arg73Cys	p.R73C	ENST00000451590	NM_001130442.1	73	Cgc/Tgc	3/5	1	2	FACETS	0.945	0.881	1	0.945	0.881	1	CLONAL	1	TRUE	1	0.414591988376653	2		556	1241	SUCCESS
RRAS2	22800	MSKCC	GRCh37	11	14317373	14317373	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	144	492	2	ENST00000256196.4:c.137C>A	p.Thr46Asn	p.T46N	ENST00000256196		46	aCc/aAc	2/6	1	2	FACETS	0.829	0.756	0.905	0.829	0.756	0.905	CLONAL	1	TRUE	1	0.414591988376653	2		494	838	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742459	17742459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	118	388	0	ENST00000250003.3:c.641G>A	p.Ser214Asn	p.S214N	ENST00000250003	NM_002478.4	214	aGc/aAc	2/3	1	2	FACETS	0.845	0.763	0.93	0.845	0.763	0.93	CLONAL	1	TRUE	1	0.414591988376653	2		388	674	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17742493	17742493	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	676	156	475	1	ENST00000250003.3:c.675C>A	p.Cys225Ter	p.C225*	ENST00000250003	NM_002478.4	225	tgC/tgA	2/3	1	2	FACETS	0.905	0.829	0.984	0.905	0.829	0.984	CLONAL	1	TRUE	1	0.414591988376653	2		476	832	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32413581	32413581	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	101	329	1	ENST00000332351.3:c.1369C>T	p.Gln457Ter	p.Q457*	ENST00000332351	NM_024426.4	457	Cag/Tag	9/10	1	2	FACETS	0.754	0.675	0.838	0.754	0.675	0.838	SUBCLONAL	1	TRUE	1	0.414591988376653	2		330	646	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64129165	64129165	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs905501710	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	191	544	0	ENST00000334205.4:c.703G>A	p.Ala235Thr	p.A235T	ENST00000334205	NM_003942.2	235	Gcc/Acc	7/17	1	2	FACETS	1	0.947	1	1	0.947	1	CLONAL	1	TRUE	1	0.414591988376653	2		544	895	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138096	64138096	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	167	505	1	ENST00000334205.4:c.2019G>A	p.Trp673Ter	p.W673*	ENST00000334205	NM_003942.2	673	tgG/tgA	16/17	1	2	FACETS	0.874	0.803	0.948	0.874	0.803	0.948	CLONAL	1	TRUE	1	0.414591988376653	2		506	922	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572111	64572111	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1248279049	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	157	390	0	ENST00000312049.6:c.1528G>A	p.Ala510Thr	p.A510T	ENST00000312049	NM_130799.2	510	Gca/Aca	10/10	1	2	FACETS	0.944	0.866	1	0.944	0.866	1	CLONAL	1	TRUE	1	0.414591988376653	2		390	802	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64573729	64573729	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776561706	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	158	337	1	ENST00000312049.6:c.1024G>A	p.Ala342Thr	p.A342T	ENST00000312049	NM_130799.2	342	Gcg/Acg	7/10	1	2	FACETS	1	0.962	1	1	0.962	1	CLONAL	1	TRUE	1	0.414591988376653	2		338	705	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948397	71948397	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1069	249	753	0	ENST00000298229.2:c.3109G>T	p.Gly1037Trp	p.G1037W	ENST00000298229	NM_001567.3	1037	Ggg/Tgg	26/28	1	2	FACETS	0.911	0.851	0.974	0.911	0.851	0.974	CLONAL	1	TRUE	1	0.414591988376653	2		753	1318	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71948674	71948674	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776092159	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	111	482	0	ENST00000298229.2:c.3386C>T	p.Thr1129Met	p.T1129M	ENST00000298229	NM_001567.3	1129	aCg/aTg	26/28	1	2	FACETS	0.695	0.625	0.77	0.695	0.625	0.77	SUBCLONAL	1	TRUE	1	0.414591988376653	2		482	770	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195643	102195643	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	761	152	478	0	ENST00000263464.3:c.403C>A	p.Arg135Ser	p.R135S	ENST00000263464	NM_001165.4	135	Cgt/Agt	2/9	1	2	FACETS	0.803	0.734	0.875	0.803	0.734	0.875	CLONAL	1	TRUE	1	0.414591988376653	2		478	913	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195706	102195706	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	631	97	378	0	ENST00000263464.3:c.466G>A	p.Ala156Thr	p.A156T	ENST00000263464	NM_001165.4	156	Gcc/Acc	2/9	1	2	FACETS	0.643	0.573	0.717	0.643	0.573	0.717	SUBCLONAL	1	TRUE	1	0.414591988376653	2		378	728	SUCCESS
ATM	472	MSKCC	GRCh37	11	108172433	108172433	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1060501571	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	143	479	0	ENST00000278616.4:c.5236G>A	p.Gly1746Arg	p.G1746R	ENST00000278616	NM_000051.3	1746	Gga/Aga	35/63	1	2	FACETS	0.944	0.862	1	0.944	0.862	1	CLONAL	1	TRUE	1	0.414591988376653	2		479	731	SUCCESS
ATM	472	MSKCC	GRCh37	11	108175564	108175564	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	97	426	0	ENST00000278616.4:c.5659G>A	p.Ala1887Thr	p.A1887T	ENST00000278616	NM_000051.3	1887	Gca/Aca	37/63	1	2	FACETS	0.606	0.54	0.677	0.606	0.54	0.677	SUBCLONAL	1	TRUE	1	0.414591988376653	2		426	772	SUCCESS
ATM	472	MSKCC	GRCh37	11	108183190	108183190	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs786203404	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	90	416	2	ENST00000278616.4:c.5971G>T	p.Glu1991Ter	p.E1991*	ENST00000278616	NM_000051.3	1991	Gaa/Taa	40/63	1	2	FACETS	0.654	0.58	0.732	0.654	0.58	0.732	SUBCLONAL	1	TRUE	1	0.414591988376653	2		418	664	SUCCESS
SDHD	6392	MSKCC	GRCh37	11	111959590	111959590	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1038	88	573	0	ENST00000375549.3:c.170-1G>A		p.X57_splice	ENST00000375549	NM_003002.3	57			1	2	FACETS	0.377	0.333	0.425	0.377	0.333	0.425	SUBCLONAL	1	TRUE	1	0.414591988376653	2		573	1126	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118376788	118376788	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	94	295	2	ENST00000534358.1:c.10181G>T	p.Gly3394Val	p.G3394V	ENST00000534358	NM_005933.3	3394	gGg/gTg	27/36	1	2	FACETS	0.804	0.717	0.896	0.804	0.717	0.896	CLONAL	1	TRUE	1	0.414591988376653	2		297	564	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118378271	118378271	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	151	383	2	ENST00000534358.1:c.10782G>T	p.Gln3594His	p.Q3594H	ENST00000534358	NM_005933.3	3594	caG/caT	28/36	1	2	FACETS	0.87	0.796	0.948	0.87	0.796	0.948	CLONAL	1	TRUE	1	0.414591988376653	2		385	837	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118392125	118392125	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	129	324	0	ENST00000534358.1:c.11636A>T	p.Asp3879Val	p.D3879V	ENST00000534358	NM_005933.3	3879	gAc/gTc	35/36	1	2	FACETS	0.94	0.854	1	0.94	0.854	1	CLONAL	1	TRUE	1	0.414591988376653	2		324	662	SUCCESS
CBL	867	MSKCC	GRCh37	11	119144676	119144676	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	128	366	0	ENST00000264033.4:c.689T>C	p.Leu230Pro	p.L230P	ENST00000264033	NM_005188.3	230	cTg/cCg	4/16	1	2	FACETS	0.826	0.749	0.906	0.826	0.749	0.906	CLONAL	1	TRUE	1	0.414591988376653	2		366	748	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18656280	18656280	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	715	122	449	1	ENST00000266497.5:c.2959G>T	p.Gly987Ter	p.G987*	ENST00000266497		987	Gga/Tga	21/31	1	2	FACETS	0.703	0.635	0.775	0.703	0.635	0.775	SUBCLONAL	1	TRUE	1	0.414591988376653	2		450	837	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18715747	18715747	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1448964458	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	78	351	0	ENST00000266497.5:c.3578C>T	p.Pro1193Leu	p.P1193L	ENST00000266497		1193	cCt/cTt	25/31	1	2	FACETS	0.671	0.59	0.757	0.671	0.59	0.757	SUBCLONAL	1	TRUE	1	0.414591988376653	2		351	561	SUCCESS
RECQL	5965	MSKCC	GRCh37	12	21628471	21628471	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750555750	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	132	657	0	ENST00000421138.2:c.1147G>A	p.Val383Met	p.V383M	ENST00000421138		383	Gtg/Atg	11/16	1	2	FACETS	0.694	0.629	0.762	0.694	0.629	0.762	SUBCLONAL	1	TRUE	1	0.414591988376653	2		657	918	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49416378	49416378	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	114	315	0	ENST00000301067.7:c.16333G>T	p.Glu5445Ter	p.E5445*	ENST00000301067	NM_003482.3	5445	Gag/Tag	51/54	1	2	FACETS	0.878	0.793	0.969	0.878	0.793	0.969	CLONAL	1	TRUE	1	0.414591988376653	2		315	626	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49432459	49432459	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	991	58	572	0	ENST00000301067.7:c.8680C>T	p.Pro2894Ser	p.P2894S	ENST00000301067	NM_003482.3	2894	Ccg/Tcg	34/54	1	2	FACETS	0.267	0.228	0.309	0.267	0.228	0.309	SUBCLONAL	1	TRUE	1	0.414591988376653	2		572	1049	SUCCESS
SMARCD1	6602	MSKCC	GRCh37	12	50480062	50480062	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	773	175	513	0	ENST00000394963.4:c.296C>A	p.Ser99Tyr	p.S99Y	ENST00000394963	NM_003076.4	99	tCc/tAc	2/13	1	2	FACETS	0.891	0.82	0.964	0.891	0.82	0.964	CLONAL	1	TRUE	1	0.414591988376653	2		513	948	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864315	57864315	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs758888293	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	125	429	1	ENST00000228682.2:c.1796del	p.Gly599ValfsTer14	p.G599Vfs*14	ENST00000228682	NM_005269.2	598	Ggg/gg	12/12	1	2	FACETS	0.803	0.727	0.883	0.803	0.727	0.883	CLONAL	1	TRUE	1	0.414591988376653	2		430	751	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57864423	57864423	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	178	401	1	ENST00000228682.2:c.1900G>T	p.Gly634Trp	p.G634W	ENST00000228682	NM_005269.2	634	Ggg/Tgg	12/12	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.414591988376653	2		402	792	SUCCESS
CDK4	1019	MSKCC	GRCh37	12	58144849	58144850	+	frameshift_variant	Frame_Shift_Del	DEL	CT	CT	-	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	92	346	0	ENST00000257904.6:c.378_379del	p.Gly127ProfsTer31	p.G127Pfs*31	ENST00000257904	NM_000075.3	126	agAGgc/aggc	4/8	1	2	FACETS	0.67	0.596	0.75	0.67	0.596	0.75	SUBCLONAL	1	TRUE	1	0.414591988376653	2		346	662	SUCCESS
SH2B3	10019	MSKCC	GRCh37	12	111856416	111856416	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	59	199	0	ENST00000341259.2:c.467C>T	p.Ala156Val	p.A156V	ENST00000341259	NM_005475.2	156	gCg/gTg	2/8	1	2	FACETS	0.66	0.57	0.759	0.66	0.57	0.759	SUBCLONAL	1	TRUE	1	0.414591988376653	2		199	431	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112892399	112892399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764663951	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	94	406	0	ENST00000351677.2:c.557G>A	p.Arg186Gln	p.R186Q	ENST00000351677	NM_002834.3	186	cGg/cAg	5/16	1	2	FACETS	0.597	0.531	0.667	0.597	0.531	0.667	SUBCLONAL	1	TRUE	1	0.414591988376653	2		406	760	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120783951	120783951	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	161	421	0	ENST00000257552.2:c.1034G>A	p.Gly345Asp	p.G345D	ENST00000257552	NM_002442.3	345	gGc/gAc	13/15	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.414591988376653	2		421	738	SUCCESS
MSI1	4440	MSKCC	GRCh37	12	120800851	120800851	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1155	284	657	1	ENST00000257552.2:c.397G>A	p.Gly133Arg	p.G133R	ENST00000257552	NM_002442.3	133	Ggg/Agg	6/15	1	2	FACETS	0.952	0.893	1	0.952	0.893	1	CLONAL	1	TRUE	1	0.414591988376653	2		658	1439	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21555659	21555659	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	137	503	0	ENST00000382592.4:c.2611C>T	p.His871Tyr	p.H871Y	ENST00000382592	NM_014572.2	871	Cat/Tat	6/8	1	2	FACETS	0.755	0.687	0.827	0.755	0.687	0.827	SUBCLONAL	1	TRUE	1	0.414591988376653	2		503	875	SUCCESS
CDK8	1024	MSKCC	GRCh37	13	26978179	26978179	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	136	492	1	ENST00000381527.3:c.1356G>T	p.Gln452His	p.Q452H	ENST00000381527	NM_001260.1	452	caG/caT	13/13	1	2	FACETS	0.77	0.7	0.844	0.77	0.7	0.844	SUBCLONAL	1	TRUE	1	0.414591988376653	2		493	852	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28622442	28622442	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	103	427	1	ENST00000241453.7:c.1175G>A	p.Cys392Tyr	p.C392Y	ENST00000241453	NM_004119.2	392	tGt/tAt	9/24	1	2	FACETS	0.699	0.626	0.777	0.699	0.626	0.777	SUBCLONAL	1	TRUE	1	0.414591988376653	2		428	711	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32912360	32912360	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	75	356	0	ENST00000380152.3:c.3868T>C	p.Cys1290Arg	p.C1290R	ENST00000380152		1290	Tgc/Cgc	11/27	1	2	FACETS	0.658	0.577	0.744	0.658	0.577	0.744	SUBCLONAL	1	TRUE	1	0.414591988376653	2		356	550	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914512	32914512	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	745	134	528	3	ENST00000380152.3:c.6020C>T	p.Thr2007Ile	p.T2007I	ENST00000380152		2007	aCc/aTc	11/27	1	2	FACETS	0.735	0.668	0.807	0.735	0.668	0.807	SUBCLONAL	1	TRUE	1	0.414591988376653	2		531	879	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954016	32954016	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	175	616	1	ENST00000380152.3:c.9083C>T	p.Ala3028Val	p.A3028V	ENST00000380152		3028	gCa/gTa	23/27	1	2	FACETS	0.84	0.773	0.91	0.84	0.773	0.91	CLONAL	1	TRUE	1	0.414591988376653	2		617	1005	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281470	49281470	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	105	398	0	ENST00000282018.3:c.517C>T	p.Leu173Phe	p.L173F	ENST00000282018	NM_020377.2	173	Ctc/Ttc	1/1	1	2	FACETS	0.745	0.668	0.826	0.745	0.668	0.826	SUBCLONAL	1	TRUE	1	0.414591988376653	2		398	680	SUCCESS
DIS3	22894	MSKCC	GRCh37	13	73346373	73346373	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1413423633	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	115	376	0	ENST00000377767.4:c.1427G>A	p.Cys476Tyr	p.C476Y	ENST00000377767	NM_014953.3	476	tGt/tAt	10/21	1	2	FACETS	0.942	0.851	1	0.942	0.851	1	CLONAL	1	TRUE	1	0.414591988376653	2		376	589	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103510763	103510763	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	109	426	0	ENST00000355739.4:c.667C>T	p.Pro223Ser	p.P223S	ENST00000355739	NM_000123.3	223	Cca/Tca	6/15	1	2	FACETS	0.8	0.72	0.886	0.8	0.72	0.886	SUBCLONAL	1	TRUE	1	0.414591988376653	2		426	657	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103519094	103519094	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	155	456	0	ENST00000355739.4:c.2432G>A	p.Ser811Asn	p.S811N	ENST00000355739	NM_000123.3	811	aGt/aAt	11/15	1	2	FACETS	0.889	0.814	0.967	0.889	0.814	0.967	CLONAL	1	TRUE	1	0.414591988376653	2		456	841	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436748	110436748	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	985	208	706	0	ENST00000375856.3:c.1653C>A	p.His551Gln	p.H551Q	ENST00000375856	NM_003749.2	551	caC/caA	1/2	1	2	FACETS	0.841	0.779	0.905	0.841	0.779	0.905	CLONAL	1	TRUE	1	0.414591988376653	2		706	1193	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436990	110436990	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	112	32	73	0	ENST00000375856.3:c.1411C>T	p.His471Tyr	p.H471Y	ENST00000375856	NM_003749.2	471	Cat/Tat	1/2	1	2	FACETS	1	0.872	1	1	0.872	1	CLONAL	1	TRUE	1	0.414591988376653	2		73	144	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110437563	110437563	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	970	249	650	0	ENST00000375856.3:c.838G>A	p.Ala280Thr	p.A280T	ENST00000375856	NM_003749.2	280	Gcg/Acg	1/2	1	2	FACETS	0.985	0.92	1	0.985	0.92	1	CLONAL	1	TRUE	1	0.414591988376653	2		650	1219	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30093359	30093359	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	125	466	0	ENST00000331968.5:c.1904A>G	p.Gln635Arg	p.Q635R	ENST00000331968	NM_002742.2	635	cAg/cGg	13/18	1	2	FACETS	0.813	0.736	0.893	0.813	0.736	0.893	CLONAL	1	TRUE	1	0.414591988376653	2		466	742	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81609427	81609427	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	145	486	0	ENST00000298171.2:c.1025A>G	p.Lys342Arg	p.K342R	ENST00000298171	NM_000369.2	342	aAg/aGg	10/10	1	2	FACETS	0.775	0.706	0.846	0.775	0.706	0.846	SUBCLONAL	1	TRUE	1	0.414591988376653	2		486	903	SUCCESS
DICER1	23405	MSKCC	GRCh37	14	95560349	95560349	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	88	366	0	ENST00000393063.1:c.5240C>A	p.Ser1747Ter	p.S1747*	ENST00000393063	NM_030621.3	1747	tCg/tAg	25/28	1	2	FACETS	0.622	0.551	0.698	0.622	0.551	0.698	SUBCLONAL	1	TRUE	1	0.414591988376653	2		366	682	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961633	41961633	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	83	385	0	ENST00000219905.7:c.541C>A	p.Leu181Ile	p.L181I	ENST00000219905	NM_001164273.1	181	Ctt/Att	2/24	1	2	FACETS	0.694	0.613	0.78	0.694	0.613	0.78	SUBCLONAL	1	TRUE	1	0.414591988376653	2		385	577	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41961727	41961727	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	592	113	407	0	ENST00000219905.7:c.635C>T	p.Ala212Val	p.A212V	ENST00000219905	NM_001164273.1	212	gCt/gTt	2/24	1	2	FACETS	0.773	0.696	0.854	0.773	0.696	0.854	SUBCLONAL	1	TRUE	1	0.414591988376653	2		407	705	SUCCESS
MGA	23269	MSKCC	GRCh37	15	41989085	41989085	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1430724265	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	921	72	544	0	ENST00000219905.7:c.1877G>A	p.Gly626Glu	p.G626E	ENST00000219905	NM_001164273.1	626	gGa/gAa	3/24	1	2	FACETS	0.35	0.304	0.399	0.35	0.304	0.399	SUBCLONAL	1	TRUE	1	0.414591988376653	2		544	993	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42003074	42003074	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	89	673	0	ENST00000219905.7:c.2611G>A	p.Val871Ile	p.V871I	ENST00000219905	NM_001164273.1	871	Gta/Ata	8/24	1	2	FACETS	0.41	0.362	0.461	0.41	0.362	0.461	SUBCLONAL	1	TRUE	1	0.414591988376653	2		673	1048	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42032291	42032291	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745655618	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	194	620	0	ENST00000219905.7:c.4475G>A	p.Arg1492His	p.R1492H	ENST00000219905	NM_001164273.1	1492	cGt/cAt	14/24	1	2	FACETS	0.812	0.75	0.876	0.812	0.75	0.876	CLONAL	1	TRUE	1	0.414591988376653	2		620	1153	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041435	42041435	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	639	155	486	0	ENST00000219905.7:c.5630T>C	p.Val1877Ala	p.V1877A	ENST00000219905	NM_001164273.1	1877	gTg/gCg	17/24	1	2	FACETS	0.942	0.863	1	0.942	0.863	1	CLONAL	1	TRUE	1	0.414591988376653	2		486	794	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42058673	42058673	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	250	48	228	0	ENST00000219905.7:c.8393C>A	p.Ala2798Asp	p.A2798D	ENST00000219905	NM_001164273.1	2798	gCt/gAt	24/24	1	2	FACETS	0.777	0.661	0.903	0.777	0.661	0.903	CLONAL	1	TRUE	1	0.414591988376653	2		228	298	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43708429	43708429	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	124	399	0	ENST00000382044.4:c.4867A>T	p.Ser1623Cys	p.S1623C	ENST00000382044	NM_001141980.1	1623	Agc/Tgc	22/28	1	2	FACETS	0.844	0.764	0.927	0.844	0.764	0.927	CLONAL	1	TRUE	1	0.414591988376653	2		399	709	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43748312	43748312	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	183	672	0	ENST00000382044.4:c.2494G>T	p.Glu832Ter	p.E832*	ENST00000382044	NM_001141980.1	832	Gag/Tag	12/28	1	2	FACETS	0.803	0.74	0.869	0.803	0.74	0.869	CLONAL	1	TRUE	1	0.414591988376653	2		672	1099	SUCCESS
CD276	80381	MSKCC	GRCh37	15	73996311	73996311	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	103	16	74	0	ENST00000318443.5:c.1045A>G	p.Ser349Gly	p.S349G	ENST00000318443	NM_001024736.1	349	Agc/Ggc	5/10	1	2	FACETS	0.649	0.484	0.84	0.649	0.484	0.84	SUBCLONAL	1	TRUE	1	0.414591988376653	2		74	119	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358447	91358447	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	895	187	576	0	ENST00000355112.3:c.4192A>G	p.Ile1398Val	p.I1398V	ENST00000355112	NM_000057.2	1398	Att/Gtt	22/22	1	2	FACETS	0.834	0.769	0.901	0.834	0.769	0.901	CLONAL	1	TRUE	1	0.414591988376653	2		576	1082	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99465464	99465464	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	163	450	0	ENST00000268035.6:c.2289C>G	p.Tyr763Ter	p.Y763*	ENST00000268035	NM_000875.3	763	taC/taG	11/21	1	2	FACETS	0.847	0.777	0.92	0.847	0.777	0.92	CLONAL	1	TRUE	1	0.414591988376653	2		450	928	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99500304	99500304	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	124	419	0	ENST00000268035.6:c.3737G>T	p.Arg1246Leu	p.R1246L	ENST00000268035	NM_000875.3	1246	cGc/cTc	21/21	1	2	FACETS	0.741	0.671	0.816	0.741	0.671	0.816	SUBCLONAL	1	TRUE	1	0.414591988376653	2		419	807	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	360058	360058	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	106	405	0	ENST00000262320.3:c.1031C>A	p.Pro344His	p.P344H	ENST00000262320	NM_003502.3	344	cCc/cAc	4/11	1	2	FACETS	0.748	0.671	0.829	0.748	0.671	0.829	SUBCLONAL	1	TRUE	1	0.414591988376653	2		405	684	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136231	2136231	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs45517364	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	127	511	0	ENST00000219476.3:c.4700G>T	p.Gly1567Val	p.G1567V	ENST00000219476	NM_000548.3	1567	gGc/gTc	37/42	1	2	FACETS	0.805	0.73	0.884	0.805	0.73	0.884	CLONAL	1	TRUE	1	0.414591988376653	2		511	761	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3647470	3647470	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	188	521	0	ENST00000294008.3:c.1593G>T	p.Trp531Cys	p.W531C	ENST00000294008	NM_032444.2	531	tgG/tgT	7/15	1	2	FACETS	0.959	0.886	1	0.959	0.886	1	CLONAL	1	TRUE	1	0.414591988376653	2		521	946	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778309	3778309	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	111	329	0	ENST00000262367.5:c.6739C>A	p.Gln2247Lys	p.Q2247K	ENST00000262367	NM_004380.2	2247	Cag/Aag	31/31	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.414591988376653	2		329	501	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50826509	50826509	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	40	341	0	ENST00000398568.2:c.2234C>T	p.Ala745Val	p.A745V	ENST00000398568	NM_001042412.1	745	gCa/gTa	15/18	1	2	FACETS	0.304	0.252	0.362	0.304	0.252	0.362	SUBCLONAL	1	TRUE	1	0.414591988376653	2		341	635	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56864572	56864572	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	114	350	0	ENST00000308159.5:c.1060G>T	p.Glu354Ter	p.E354*	ENST00000308159	NM_014669.4	354	Gag/Tag	10/22	1	2	FACETS	0.777	0.7	0.858	0.777	0.7	0.858	SUBCLONAL	1	TRUE	1	0.414591988376653	2		350	708	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67644874	67644874	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	157	341	0	ENST00000264010.4:c.143del	p.Gly48ValfsTer14	p.G48Vfs*14	ENST00000264010	NM_006565.3	47	Ggg/gg	3/12	1	2	FACETS	1	0.945	1	1	0.945	1	CLONAL	1	TRUE	1	0.414591988376653	2		341	730	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645275	67645276	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	816	196	579	0	ENST00000264010.4:c.544dup	p.Glu182GlyfsTer9	p.E182Gfs*9	ENST00000264010	NM_006565.3	180	-/G	3/12	1	2	FACETS	0.934	0.865	1	0.934	0.865	1	CLONAL	1	TRUE	1	0.414591988376653	2		579	1012	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67645902	67645902	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	158	416	0	ENST00000264010.4:c.830G>T	p.Arg277Leu	p.R277L	ENST00000264010	NM_006565.3	277	cGg/cTg	4/12	1	2	FACETS	0.809	0.741	0.88	0.809	0.741	0.88	CLONAL	1	TRUE	1	0.414591988376653	2		416	942	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68846044	68846044	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	203	534	0	ENST00000261769.5:c.1015C>A	p.Pro339Thr	p.P339T	ENST00000261769	NM_004360.3	339	Cct/Act	8/16	1	2	FACETS	1	0.949	1	1	0.949	1	CLONAL	1	TRUE	1	0.414591988376653	2		534	952	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72830230	72830230	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	181	36	198	0	ENST00000268489.5:c.6351G>C	p.Gln2117His	p.Q2117H	ENST00000268489	NM_006885.3	2117	caG/caC	9/10	1	2	FACETS	0.8	0.663	0.951	0.8	0.663	0.951	CLONAL	1	TRUE	1	0.414591988376653	2		198	217	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991464	72991464	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	194	491	0	ENST00000268489.5:c.2581C>A	p.Leu861Ile	p.L861I	ENST00000268489	NM_006885.3	861	Ctc/Atc	2/10	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.414591988376653	2		491	904	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81939035	81939035	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777539665	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	566	99	359	0	ENST00000359376.3:c.1390G>A	p.Val464Met	p.V464M	ENST00000359376	NM_002661.3	464	Gtg/Atg	15/33	1	2	FACETS	0.718	0.642	0.799	0.718	0.642	0.799	SUBCLONAL	1	TRUE	1	0.414591988376653	2		359	665	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350707	89350707	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1062	231	648	0	ENST00000301030.4:c.2243T>C	p.Leu748Pro	p.L748P	ENST00000301030	NM_001256183.1	748	cTg/cCg	9/13	1	2	FACETS	0.862	0.802	0.924	0.862	0.802	0.924	CLONAL	1	TRUE	1	0.414591988376653	2		648	1293	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89811409	89811409	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs138013482	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1010	230	636	0	ENST00000389301.3:c.3584G>T	p.Arg1195Leu	p.R1195L	ENST00000389301	NM_000135.2	1195	cGg/cTg	36/43	1	2	FACETS	0.895	0.833	0.959	0.895	0.833	0.959	CLONAL	1	TRUE	1	0.414591988376653	2		636	1240	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89825104	89825104	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	167	409	0	ENST00000389301.3:c.2862C>A	p.Phe954Leu	p.F954L	ENST00000389301	NM_000135.2	954	ttC/ttA	30/43	1	2	FACETS	0.962	0.885	1	0.962	0.885	1	CLONAL	1	TRUE	1	0.414591988376653	2		409	837	SUCCESS
GPS2	2874	MSKCC	GRCh37	17	7218317	7218317	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	126	458	0	ENST00000380728.2:c.55C>T	p.His19Tyr	p.H19Y	ENST00000380728		19	Cac/Tac	2/11	1	2	FACETS	0.844	0.765	0.927	0.844	0.765	0.927	CLONAL	1	TRUE	1	0.414591988376653	2		458	720	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7572941	7572941	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	103	370	0	ENST00000269305.4:c.1168C>T	p.Pro390Ser	p.P390S	ENST00000269305	NM_001126112.2	390	Cct/Tct	11/11	1	2	FACETS	0.709	0.635	0.787	0.709	0.635	0.787	SUBCLONAL	1	TRUE	1	0.414591988376653	2		370	701	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15968877	15968877	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	147	391	0	ENST00000268712.3:c.4873G>C	p.Val1625Leu	p.V1625L	ENST00000268712	NM_006311.3	1625	Gtg/Ctg	33/46	1	2	FACETS	0.982	0.898	1	0.982	0.898	1	CLONAL	1	TRUE	1	0.414591988376653	2		391	722	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17118577	17118577	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763920904	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	205	523	1	ENST00000285071.4:c.1354G>A	p.Val452Met	p.V452M	ENST00000285071	NM_144997.5	452	Gtg/Atg	12/14	1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.414591988376653	2		524	940	SUCCESS
CDK12	51755	MSKCC	GRCh37	17	37650831	37650831	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	946	225	630	1	ENST00000447079.4:c.2303C>A	p.Pro768Gln	p.P768Q	ENST00000447079	NM_015083.1	768	cCa/cAa	5/14	1	2	FACETS	0.927	0.862	0.994	0.927	0.862	0.994	CLONAL	1	TRUE	1	0.414591988376653	2		631	1171	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40475359	40475359	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	89	373	0	ENST00000264657.5:c.1667G>A	p.Gly556Asp	p.G556D	ENST00000264657	NM_139276.2	556	gGc/gAc	19/24	1	2	FACETS	0.639	0.567	0.716	0.639	0.567	0.716	SUBCLONAL	1	TRUE	1	0.414591988376653	2		373	672	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40871147	40871147	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	116	378	0	ENST00000428826.2:c.743G>T	p.Gly248Val	p.G248V	ENST00000428826		248	gGt/gTt	8/21	1	2	FACETS	0.807	0.729	0.891	0.807	0.729	0.891	CLONAL	1	TRUE	1	0.414591988376653	2		378	693	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41244783	41244783	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs80357460	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	759	143	655	0	ENST00000357654.3:c.2765C>T	p.Thr922Ile	p.T922I	ENST00000357654	NM_007294.3	922	aCa/aTa	10/23	1	2	FACETS	0.765	0.697	0.836	0.765	0.697	0.836	SUBCLONAL	1	TRUE	1	0.414591988376653	2		655	902	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47679300	47679300	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	151	445	0	ENST00000347630.2:c.907G>A	p.Ala303Thr	p.A303T	ENST00000347630	NM_001007230.1	303	Gca/Aca	10/11	1	2	FACETS	0.795	0.727	0.867	0.795	0.727	0.867	SUBCLONAL	1	TRUE	1	0.414591988376653	2		445	916	SUCCESS
MSI2	124540	MSKCC	GRCh37	17	55752428	55752428	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1076	290	696	1	ENST00000284073.2:c.886G>T	p.Gly296Trp	p.G296W	ENST00000284073	NM_138962.2	296	Ggg/Tgg	12/14	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.414591988376653	2		697	1366	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435750	56435750	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	386	101	306	0	ENST00000407977.2:c.1387G>A	p.Ala463Thr	p.A463T	ENST00000407977		463	Gcc/Acc	9/10	1	2	FACETS	1	0.898	1	1	0.898	1	CLONAL	1	TRUE	1	0.414591988376653	2		306	487	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59885886	59885886	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	696	144	458	0	ENST00000259008.2:c.860A>G	p.Glu287Gly	p.E287G	ENST00000259008	NM_032043.2	287	gAg/gGg	7/20	1	2	FACETS	0.827	0.754	0.903	0.827	0.754	0.903	CLONAL	1	TRUE	1	0.414591988376653	2		458	840	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533078	63533078	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	161	438	2	ENST00000307078.5:c.1816C>A	p.Leu606Met	p.L606M	ENST00000307078	NM_004655.3	606	Ctg/Atg	7/11	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.414591988376653	2		440	746	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78866595	78866595	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	859	179	518	0	ENST00000306801.3:c.2168A>G	p.Tyr723Cys	p.Y723C	ENST00000306801	NM_020761.2	723	tAt/tGt	19/34	1	2	FACETS	0.832	0.766	0.9	0.832	0.766	0.9	CLONAL	1	TRUE	1	0.414591988376653	2		518	1038	SUCCESS
RPTOR	57521	MSKCC	GRCh37	17	78897381	78897381	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762582186	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	160	568	0	ENST00000306801.3:c.2716C>T	p.Pro906Ser	p.P906S	ENST00000306801	NM_020761.2	906	Ccg/Tcg	23/34	1	2	FACETS	0.87	0.798	0.946	0.87	0.798	0.946	CLONAL	1	TRUE	1	0.414591988376653	2		568	887	SUCCESS
YES1	7525	MSKCC	GRCh37	18	743376	743376	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1275516375	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	119	384	0	ENST00000314574.4:c.764G>A	p.Cys255Tyr	p.C255Y	ENST00000314574	NM_005433.3	255	tGt/tAt	7/12	1	2	FACETS	0.891	0.806	0.981	0.891	0.806	0.981	CLONAL	1	TRUE	1	0.414591988376653	2		384	644	SUCCESS
SMAD2	4087	MSKCC	GRCh37	18	45391457	45391457	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	561	99	379	0	ENST00000262160.6:c.703C>T	p.Gln235Ter	p.Q235*	ENST00000262160	NM_005901.5	235	Caa/Taa	6/11	1	2	FACETS	0.724	0.647	0.805	0.724	0.647	0.805	SUBCLONAL	1	TRUE	1	0.414591988376653	2		379	660	SUCCESS
BCL2	596	MSKCC	GRCh37	18	60795881	60795881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	683	113	400	2	ENST00000333681.4:c.697G>A	p.Gly233Ser	p.G233S	ENST00000333681		233	Ggt/Agt	3/3	1	2	FACETS	0.685	0.616	0.758	0.685	0.616	0.758	SUBCLONAL	1	TRUE	1	0.414591988376653	2		402	796	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7163181	7163181	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1220855203	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	153	476	0	ENST00000302850.5:c.1891G>A	p.Val631Met	p.V631M	ENST00000302850	NM_000208.2	631	Gtg/Atg	9/22	1	2	FACETS	0.827	0.757	0.901	0.827	0.757	0.901	CLONAL	1	TRUE	1	0.414591988376653	2		476	892	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10244964	10244964	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1248265917	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	133	461	0	ENST00000340748.4:c.4745C>T	p.Pro1582Leu	p.P1582L	ENST00000340748		1582	cCg/cTg	39/40	1	2	FACETS	0.846	0.769	0.927	0.846	0.769	0.927	CLONAL	1	TRUE	1	0.414591988376653	2		461	758	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11096004	11096004	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	223	676	0	ENST00000358026.2:c.278T>C	p.Met93Thr	p.M93T	ENST00000358026	NM_001128849.1	93	aTg/aCg	3/36	1	2	FACETS	0.949	0.882	1	0.949	0.882	1	CLONAL	1	TRUE	1	0.414591988376653	2		676	1134	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285170	15285170	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	285	660	0	ENST00000263388.2:c.4445G>A	p.Gly1482Asp	p.G1482D	ENST00000263388	NM_000435.2	1482	gGc/gAc	25/33	1	2	FACETS	1	0.944	1	1	0.944	1	CLONAL	1	TRUE	1	0.414591988376653	2		660	1367	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15353918	15353918	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	91	283	0	ENST00000263377.2:c.2962C>T	p.Gln988Ter	p.Q988*	ENST00000263377	NM_058243.2	988	Cag/Tag	14/20	1	2	FACETS	0.892	0.795	0.995	0.892	0.795	0.995	CLONAL	1	TRUE	1	0.414591988376653	2		283	492	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15375468	15375468	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	202	493	0	ENST00000263377.2:c.959A>T	p.Gln320Leu	p.Q320L	ENST00000263377	NM_058243.2	320	cAg/cTg	6/20	1	2	FACETS	0.925	0.857	0.996	0.925	0.857	0.996	CLONAL	1	TRUE	1	0.414591988376653	2		493	1053	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17387368	17387368	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754753033	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1125	319	756	1	ENST00000359435.4:c.634C>T	p.Arg212Cys	p.R212C	ENST00000359435	NM_001033549.1	212	Cgc/Tgc	7/9	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.414591988376653	2		757	1444	SUCCESS
PIK3R2	5296	MSKCC	GRCh37	19	18279310	18279310	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	204	440	0	ENST00000222254.8:c.1762C>T	p.Gln588Ter	p.Q588*	ENST00000222254	NM_005027.3	588	Cag/Tag	14/16	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.414591988376653	2		440	952	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18972962	18972962	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	87	399	0	ENST00000262803.5:c.2600+1G>A		p.X867_splice	ENST00000262803	NM_002911.3	867			1	2	FACETS	0.508	0.449	0.571	0.508	0.449	0.571	SUBCLONAL	1	TRUE	1	0.414591988376653	2		399	826	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214040	36214040	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1002	224	635	1	ENST00000222270.7:c.2866C>A	p.His956Asn	p.H956N	ENST00000222270	NM_014727.1	956	Cat/Aat	6/37	1	2	FACETS	0.881	0.819	0.946	0.881	0.819	0.946	CLONAL	1	TRUE	1	0.414591988376653	2		636	1226	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223145	36223145	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1249	264	731	0	ENST00000222270.7:c.5695C>A	p.Pro1899Thr	p.P1899T	ENST00000222270	NM_014727.1	1899	Ccc/Acc	28/37	1	2	FACETS	0.842	0.787	0.899	0.842	0.787	0.899	CLONAL	1	TRUE	1	0.414591988376653	2		731	1513	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36223858	36223858	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	891	228	663	4	ENST00000222270.7:c.6413del	p.Pro2138ArgfsTer15	p.P2138Rfs*15	ENST00000222270	NM_014727.1	2136	ctC/ct	28/37	1	2	FACETS	0.983	0.915	1	0.983	0.915	1	CLONAL	1	TRUE	1	0.414591988376653	2		667	1119	SUCCESS
AXL	558	MSKCC	GRCh37	19	41743987	41743987	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1306116384	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1023	196	654	0	ENST00000301178.4:c.922C>T	p.Arg308Cys	p.R308C	ENST00000301178	NM_021913.4	308	Cgc/Tgc	7/20	1	2	FACETS	0.776	0.717	0.837	0.776	0.717	0.837	SUBCLONAL	1	TRUE	1	0.414591988376653	2		654	1219	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791767	42791767	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	182	506	0	ENST00000575354.2:c.653T>A	p.Val218Asp	p.V218D	ENST00000575354	NM_015125.3	218	gTc/gAc	5/20	1	2	FACETS	0.944	0.871	1	0.944	0.871	1	CLONAL	1	TRUE	1	0.414591988376653	2		506	930	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42792032	42792032	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	729	149	424	0	ENST00000575354.2:c.836C>A	p.Ser279Ter	p.S279*	ENST00000575354	NM_015125.3	279	tCa/tAa	6/20	1	2	FACETS	0.819	0.748	0.893	0.819	0.748	0.893	CLONAL	1	TRUE	1	0.414591988376653	2		424	878	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42795271	42795271	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	508	137	433	0	ENST00000575354.2:c.2351G>T	p.Gly784Val	p.G784V	ENST00000575354	NM_015125.3	784	gGg/gTg	10/20	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.414591988376653	2		433	645	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905485	50905485	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs914238978	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	975	264	633	0	ENST00000440232.2:c.613G>A	p.Gly205Ser	p.G205S	ENST00000440232	NM_002691.3	205	Ggc/Agc	6/27	1	2	FACETS	1	0.957	1	1	0.957	1	CLONAL	1	TRUE	1	0.414591988376653	2		633	1239	SUCCESS
DNMT3A	1788	MSKCC	GRCh37	2	25467172	25467172	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	135	398	0	ENST00000264709.3:c.1703G>T	p.Gly568Val	p.G568V	ENST00000264709	NM_175629.2	568	gGg/gTg	15/23	1	2	FACETS	0.839	0.763	0.919	0.839	0.763	0.919	CLONAL	1	TRUE	1	0.414591988376653	2		398	776	SUCCESS
ALK	238	MSKCC	GRCh37	2	29416551	29416551	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	641	146	402	0	ENST00000389048.3:c.4402G>T	p.Gly1468Trp	p.G1468W	ENST00000389048	NM_004304.4	1468	Ggg/Tgg	29/29	1	2	FACETS	0.895	0.818	0.976	0.895	0.818	0.976	CLONAL	1	TRUE	1	0.414591988376653	2		402	787	SUCCESS
ALK	238	MSKCC	GRCh37	2	29455170	29455170	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	133	309	0	ENST00000389048.3:c.2632G>T	p.Gly878Cys	p.G878C	ENST00000389048	NM_004304.4	878	Ggt/Tgt	15/29	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.414591988376653	2		309	628	SUCCESS
ALK	238	MSKCC	GRCh37	2	30143282	30143282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1322397265	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	224	478	0	ENST00000389048.3:c.244G>A	p.Ala82Thr	p.A82T	ENST00000389048	NM_004304.4	82	Gct/Act	1/29	1	2	FACETS	1	0.976	1	1	0.976	1	CLONAL	1	TRUE	1	0.414591988376653	2		478	982	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39213027	39213027	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	873	183	608	0	ENST00000402219.2:c.3940C>T	p.His1314Tyr	p.H1314Y	ENST00000402219	NM_005633.3	1314	Cac/Tac	23/23	1	2	FACETS	0.836	0.771	0.904	0.836	0.771	0.904	CLONAL	1	TRUE	1	0.414591988376653	2		608	1056	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224123	39224123	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	875	119	550	0	ENST00000402219.2:c.3021T>A	p.Asp1007Glu	p.D1007E	ENST00000402219	NM_005633.3	1007	gaT/gaA	19/23	1	2	FACETS	0.578	0.52	0.638	0.578	0.52	0.638	SUBCLONAL	1	TRUE	1	0.414591988376653	2		550	994	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47635563	47635563	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	100	323	0	ENST00000233146.2:c.235G>A	p.Val79Met	p.V79M	ENST00000233146	NM_000251.2	79	Gtg/Atg	2/16	1	2	FACETS	0.723	0.647	0.805	0.723	0.647	0.805	SUBCLONAL	1	TRUE	1	0.414591988376653	2		323	667	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026461	48026461	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs369709529	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	521	97	317	0	ENST00000234420.5:c.1339C>A	p.Leu447Met	p.L447M	ENST00000234420	NM_000179.2	447	Ctg/Atg	4/10	1	2	FACETS	0.757	0.676	0.843	0.757	0.676	0.843	SUBCLONAL	1	TRUE	1	0.414591988376653	2		317	618	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027503	48027503	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	411	86	313	0	ENST00000234420.5:c.2381C>T	p.Ala794Val	p.A794V	ENST00000234420	NM_000179.2	794	gCc/gTc	4/10	1	2	FACETS	0.835	0.741	0.935	0.835	0.741	0.935	CLONAL	1	TRUE	1	0.414591988376653	2		313	497	SUCCESS
REL	5966	MSKCC	GRCh37	2	61149159	61149159	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	90	355	2	ENST00000295025.8:c.1349C>A	p.Pro450His	p.P450H	ENST00000295025	NM_002908.2	450	cCt/cAt	11/11	1	2	FACETS	0.722	0.642	0.808	0.722	0.642	0.808	SUBCLONAL	1	TRUE	1	0.414591988376653	2		357	601	SUCCESS
INPP4A	3631	MSKCC	GRCh37	2	99182222	99182222	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	181	432	0	ENST00000074304.5:c.2287G>T	p.Gly763Ter	p.G763*	ENST00000074304	NM_001134224.1	763	Gga/Tga	21/26	1	2	FACETS	0.892	0.822	0.964	0.892	0.822	0.964	CLONAL	1	TRUE	1	0.414591988376653	2		432	979	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128036768	128036768	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	137	484	0	ENST00000285398.2:c.1711T>C	p.Tyr571His	p.Y571H	ENST00000285398	NM_000122.1	571	Tat/Cat	10/15	1	2	FACETS	0.751	0.683	0.823	0.751	0.683	0.823	SUBCLONAL	1	TRUE	1	0.414591988376653	2		484	880	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128044389	128044389	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	688	152	449	1	ENST00000285398.2:c.1232C>A	p.Ser411Tyr	p.S411Y	ENST00000285398	NM_000122.1	411	tCc/tAc	8/15	1	2	FACETS	0.873	0.799	0.951	0.873	0.799	0.951	CLONAL	1	TRUE	1	0.414591988376653	2		450	840	SUCCESS
PMS1	5378	MSKCC	GRCh37	2	190670375	190670375	+	splice_region_variant,intron_variant	Splice_Region	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	474	85	324	0	ENST00000441310.2:c.316-3C>T		p.X106_splice	ENST00000441310	NM_000534.4	106			1	2	FACETS	0.734	0.65	0.823	0.734	0.65	0.823	SUBCLONAL	1	TRUE	1	0.414591988376653	2		324	559	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198257776	198257776	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	136	486	0	ENST00000335508.6:c.3676G>A	p.Val1226Ile	p.V1226I	ENST00000335508	NM_012433.2	1226	Gta/Ata	24/25	1	2	FACETS	0.738	0.671	0.809	0.738	0.671	0.809	SUBCLONAL	1	TRUE	1	0.414591988376653	2		486	889	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198270118	198270118	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1238024065	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	124	494	0	ENST00000335508.6:c.1318G>A	p.Gly440Ser	p.G440S	ENST00000335508	NM_012433.2	440	Ggt/Agt	10/25	1	2	FACETS	0.71	0.642	0.781	0.71	0.642	0.781	SUBCLONAL	1	TRUE	1	0.414591988376653	2		494	843	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202131288	202131288	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	133	466	0	ENST00000358485.4:c.256C>A	p.Leu86Met	p.L86M	ENST00000358485	NM_001080125.1	86	Ctg/Atg	2/9	1	2	FACETS	0.859	0.781	0.941	0.859	0.781	0.941	CLONAL	1	TRUE	1	0.414591988376653	2		466	747	SUCCESS
INHA	3623	MSKCC	GRCh37	2	220440213	220440213	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	923	181	649	0	ENST00000243786.2:c.1066C>T	p.Pro356Ser	p.P356S	ENST00000243786	NM_002191.3	356	Ccc/Tcc	2/2	1	2	FACETS	0.791	0.728	0.856	0.791	0.728	0.856	SUBCLONAL	1	TRUE	1	0.414591988376653	2		649	1104	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225449680	225449680	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	115	335	0	ENST00000264414.4:c.47T>C	p.Met16Thr	p.M16T	ENST00000264414	NM_003590.4	16	aTg/aCg	1/16	1	2	FACETS	0.865	0.781	0.954	0.865	0.781	0.954	CLONAL	1	TRUE	1	0.414591988376653	2		335	641	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227660775	227660775	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	136	466	0	ENST00000305123.5:c.2680G>A	p.Gly894Arg	p.G894R	ENST00000305123	NM_005544.2	894	Ggg/Agg	1/2	1	2	FACETS	0.736	0.668	0.806	0.736	0.668	0.806	SUBCLONAL	1	TRUE	1	0.414591988376653	2		466	892	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9525075	9525075	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	771	158	544	0	ENST00000353224.5:c.1810G>A	p.Val604Ile	p.V604I	ENST00000353224	NM_177990.2	604	Gtt/Att	8/10	1	2	FACETS	0.82	0.752	0.893	0.82	0.752	0.893	CLONAL	1	TRUE	1	0.414591988376653	2		544	929	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9546891	9546891	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	106	269	0	ENST00000353224.5:c.1131C>A	p.Tyr377Ter	p.Y377*	ENST00000353224	NM_177990.2	377	taC/taA	5/10	1	2	FACETS	0.908	0.817	1	0.908	0.817	1	CLONAL	1	TRUE	1	0.414591988376653	2		269	563	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31017752	31017752	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	115	382	0	ENST00000375687.4:c.614G>A	p.Ser205Asn	p.S205N	ENST00000375687	NM_015338.5	205	aGc/aAc	8/13	1	2	FACETS	0.926	0.837	1	0.926	0.837	1	CLONAL	1	TRUE	1	0.414591988376653	2		382	599	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31024131	31024131	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757978318	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	172	557	0	ENST00000375687.4:c.3616G>A	p.Ala1206Thr	p.A1206T	ENST00000375687	NM_015338.5	1206	Gca/Aca	13/13	1	2	FACETS	0.842	0.774	0.912	0.842	0.774	0.912	CLONAL	1	TRUE	1	0.414591988376653	2		557	986	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31385096	31385096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	101	288	0	ENST00000328111.2:c.1481G>A	p.Ser494Asn	p.S494N	ENST00000328111	NM_006892.3	494	aGc/aAc	14/23	1	2	FACETS	0.819	0.733	0.909	0.819	0.733	0.909	CLONAL	1	TRUE	1	0.414591988376653	2		288	595	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62321753	62321753	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	716	152	470	0	ENST00000360203.5:c.2372G>A	p.Ser791Asn	p.S791N	ENST00000360203	NM_001283009.1	791	aGt/aAt	26/35	1	2	FACETS	0.845	0.773	0.92	0.845	0.773	0.92	CLONAL	1	TRUE	1	0.414591988376653	2		470	868	SUCCESS
RUNX1	861	MSKCC	GRCh37	21	36259256	36259256	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1267412169	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	498	111	340	0	ENST00000300305.3:c.235G>A	p.Val79Met	p.V79M	ENST00000300305		79	Gtg/Atg	3/8	1	2	FACETS	0.879	0.792	0.971	0.879	0.792	0.971	CLONAL	1	TRUE	1	0.414591988376653	2		340	609	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22127184	22127184	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	706	90	434	0	ENST00000215832.6:c.944A>G	p.Gln315Arg	p.Q315R	ENST00000215832	NM_002745.4	315	cAg/cGg	7/9	1	2	FACETS	0.545	0.483	0.612	0.545	0.483	0.612	SUBCLONAL	1	TRUE	1	0.414591988376653	2		434	796	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41513478	41513478	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	151	500	1	ENST00000263253.7:c.382C>T	p.Gln128Ter	p.Q128*	ENST00000263253	NM_001429.3	128	Cag/Tag	2/31	1	2	FACETS	0.783	0.716	0.854	0.783	0.716	0.854	SUBCLONAL	1	TRUE	1	0.414591988376653	2		501	930	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41554433	41554433	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	603	94	300	2	ENST00000263253.7:c.3519G>T	p.Gln1173His	p.Q1173H	ENST00000263253	NM_001429.3	1173	caG/caT	19/31	1	2	FACETS	0.651	0.579	0.727	0.651	0.579	0.727	SUBCLONAL	1	TRUE	1	0.414591988376653	2		302	697	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573393	41573393	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	911	206	538	0	ENST00000263253.7:c.5678C>T	p.Ala1893Val	p.A1893V	ENST00000263253	NM_001429.3	1893	gCt/gTt	31/31	1	2	FACETS	0.89	0.825	0.957	0.89	0.825	0.957	CLONAL	1	TRUE	1	0.414591988376653	2		538	1117	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574595	41574595	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1045	248	774	1	ENST00000263253.7:c.6880C>A	p.Leu2294Ile	p.L2294I	ENST00000263253	NM_001429.3	2294	Cta/Ata	31/31	1	2	FACETS	0.925	0.864	0.989	0.925	0.864	0.989	CLONAL	1	TRUE	1	0.414591988376653	2		775	1293	SUCCESS
RAF1	5894	MSKCC	GRCh37	3	12641703	12641703	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	160	359	0	ENST00000251849.4:c.938C>T	p.Pro313Leu	p.P313L	ENST00000251849	NM_002880.3	313	cCa/cTa	9/17	1	2	FACETS	0.94	0.863	1	0.94	0.863	1	CLONAL	1	TRUE	1	0.414591988376653	2		359	821	SUCCESS
SETD2	29072	MSKCC	GRCh37	3	47165574	47165574	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	86	257	0	ENST00000409792.3:c.552C>A	p.Asp184Glu	p.D184E	ENST00000409792	NM_014159.6	184	gaC/gaA	3/21	1	2	FACETS	0.748	0.663	0.838	0.748	0.663	0.838	SUBCLONAL	1	TRUE	1	0.414591988376653	2		257	555	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49936543	49936543	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs139493185	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	779	171	537	1	ENST00000296474.3:c.1384G>T	p.Ala462Ser	p.A462S	ENST00000296474	NM_002447.2	462	Gca/Tca	2/20	1	2	FACETS	0.868	0.799	0.941	0.868	0.799	0.941	CLONAL	1	TRUE	1	0.414591988376653	2		538	950	SUCCESS
SHQ1	55164	MSKCC	GRCh37	3	72842086	72842086	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs776668832	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	120	338	0	ENST00000325599.8:c.1162G>A	p.Val388Met	p.V388M	ENST00000325599	NM_018130.2	388	Gtg/Atg	10/11	1	2	FACETS	0.885	0.801	0.974	0.885	0.801	0.974	CLONAL	1	TRUE	1	0.414591988376653	2		338	654	SUCCESS
EPHB1	2047	MSKCC	GRCh37	3	134967232	134967232	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	136	460	0	ENST00000398015.3:c.2571G>A	p.Met857Ile	p.M857I	ENST00000398015	NM_004441.4	857	atG/atA	14/16	1	2	FACETS	0.863	0.786	0.945	0.863	0.786	0.945	CLONAL	1	TRUE	1	0.414591988376653	2		460	760	SUCCESS
PIK3CB	5291	MSKCC	GRCh37	3	138374298	138374298	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	144	482	0	ENST00000289153.2:c.3146T>G	p.Leu1049Arg	p.L1049R	ENST00000289153	NM_006219.2	1049	cTc/cGc	22/22	1	2	FACETS	0.767	0.699	0.838	0.767	0.699	0.838	SUBCLONAL	1	TRUE	1	0.414591988376653	2		482	906	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215329	142215329	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	605	143	421	1	ENST00000350721.4:c.5772G>A	p.Trp1924Ter	p.W1924*	ENST00000350721	NM_001184.3	1924	tgG/tgA	34/47	1	2	FACETS	0.922	0.842	1	0.922	0.842	1	CLONAL	1	TRUE	1	0.414591988376653	2		422	748	SUCCESS
ATR	545	MSKCC	GRCh37	3	142222210	142222210	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	165	423	0	ENST00000350721.4:c.5282C>T	p.Ala1761Val	p.A1761V	ENST00000350721	NM_001184.3	1761	gCt/gTt	30/47	1	2	FACETS	1	0.948	1	1	0.948	1	CLONAL	1	TRUE	1	0.414591988376653	2		423	765	SUCCESS
ATR	545	MSKCC	GRCh37	3	142281239	142281239	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	115	483	1	ENST00000350721.4:c.1005G>A	p.Met335Ile	p.M335I	ENST00000350721	NM_001184.3	335	atG/atA	4/47	1	2	FACETS	0.799	0.721	0.882	0.799	0.721	0.882	SUBCLONAL	1	TRUE	1	0.414591988376653	2		484	694	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149245623	149245623	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	796	195	490	0	ENST00000360632.3:c.905G>T	p.Gly302Val	p.G302V	ENST00000360632	NM_015472.4	302	gGa/gTa	5/7	1	2	FACETS	0.949	0.878	1	0.949	0.878	1	CLONAL	1	TRUE	1	0.414591988376653	2		490	991	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185190816	185190816	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	193	625	0	ENST00000265026.3:c.1697C>T	p.Ala566Val	p.A566V	ENST00000265026	NM_004721.4	566	gCa/gTa	11/14	1	2	FACETS	0.834	0.77	0.9	0.834	0.77	0.9	CLONAL	1	TRUE	1	0.414591988376653	2		625	1117	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185191400	185191400	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1004	228	590	0	ENST00000265026.3:c.2281C>T	p.Pro761Ser	p.P761S	ENST00000265026	NM_004721.4	761	Cca/Tca	11/14	1	2	FACETS	0.893	0.831	0.957	0.893	0.831	0.957	CLONAL	1	TRUE	1	0.414591988376653	2		590	1232	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189586416	189586416	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	92	326	1	ENST00000264731.3:c.1040G>A	p.Cys347Tyr	p.C347Y	ENST00000264731	NM_003722.4	347	tGc/tAc	8/14	1	2	FACETS	0.684	0.608	0.765	0.684	0.608	0.765	SUBCLONAL	1	TRUE	1	0.414591988376653	2		327	649	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1956990	1956990	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	133	416	0	ENST00000382891.5:c.2441C>T	p.Thr814Ile	p.T814I	ENST00000382891	NM_133335.3	814	aCt/aTt	13/22	1	2	FACETS	0.796	0.723	0.873	0.796	0.723	0.873	SUBCLONAL	1	TRUE	1	0.414591988376653	2		416	806	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1961301	1961301	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	762	180	539	1	ENST00000382891.5:c.3089C>A	p.Ser1030Ter	p.S1030*	ENST00000382891	NM_133335.3	1030	tCg/tAg	17/22	1	2	FACETS	0.922	0.85	0.996	0.922	0.85	0.996	CLONAL	1	TRUE	1	0.414591988376653	2		540	942	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55136840	55136840	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1227372630	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	132	422	0	ENST00000257290.5:c.1162G>A	p.Asp388Asn	p.D388N	ENST00000257290	NM_006206.4	388	Gac/Aac	8/23	1	2	FACETS	0.922	0.838	1	0.922	0.838	1	CLONAL	1	TRUE	1	0.414591988376653	2		422	691	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55152033	55152033	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs763325080	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	118	385	0	ENST00000257290.5:c.2465G>A	p.Arg822His	p.R822H	ENST00000257290	NM_006206.4	822	cGc/cAc	18/23	1	2	FACETS	0.784	0.708	0.864	0.784	0.708	0.864	SUBCLONAL	1	TRUE	1	0.414591988376653	2		385	726	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55976858	55976858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	883	134	581	0	ENST00000263923.4:c.1054G>A	p.Ala352Thr	p.A352T	ENST00000263923	NM_002253.2	352	Gcg/Acg	8/30	1	2	FACETS	0.636	0.576	0.698	0.636	0.576	0.698	SUBCLONAL	1	TRUE	1	0.414591988376653	2		581	1017	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66361120	66361120	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	78	354	0	ENST00000273854.3:c.1052C>T	p.Thr351Ile	p.T351I	ENST00000273854	NM_004439.5	351	aCa/aTa	4/18	1	2	FACETS	0.806	0.71	0.907	0.806	0.71	0.907	CLONAL	1	TRUE	1	0.414591988376653	2		354	467	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153247186	153247186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	533	62	339	0	ENST00000281708.4:c.1616G>A	p.Gly539Glu	p.G539E	ENST00000281708	NM_033632.3	539	gGg/gAg	10/12	1	2	FACETS	0.503	0.434	0.577	0.503	0.434	0.577	SUBCLONAL	1	TRUE	1	0.414591988376653	2		339	595	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187509952	187509952	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	418	90	274	1	ENST00000441802.2:c.13561C>T	p.Pro4521Ser	p.P4521S	ENST00000441802	NM_005245.3	4521	Cca/Tca	27/27	1	2	FACETS	0.855	0.761	0.954	0.855	0.761	0.954	CLONAL	1	TRUE	1	0.414591988376653	2		275	508	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524080	187524080	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	147	528	0	ENST00000441802.2:c.11459G>A	p.Ser3820Asn	p.S3820N	ENST00000441802	NM_005245.3	3820	aGc/aAc	20/27	1	2	FACETS	0.712	0.649	0.778	0.712	0.649	0.778	SUBCLONAL	1	TRUE	1	0.414591988376653	2		528	996	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187540946	187540946	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	382	84	253	1	ENST00000441802.2:c.6794C>T	p.Ala2265Val	p.A2265V	ENST00000441802	NM_005245.3	2265	gCt/gTt	10/27	1	2	FACETS	0.87	0.771	0.974	0.87	0.771	0.974	CLONAL	1	TRUE	1	0.414591988376653	2		254	466	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	235266	235266	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	471	129	342	0	ENST00000264932.6:c.1072G>A	p.Gly358Ser	p.G358S	ENST00000264932	NM_004168.2	358	Ggc/Agc	9/15	1	2	FACETS	1	0.937	1	1	0.937	1	CLONAL	1	TRUE	1	0.414591988376653	2		342	600	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1294470	1294470	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	205	505	0	ENST00000310581.5:c.531G>C	p.Gln177His	p.Q177H	ENST00000310581	NM_198253.2	177	caG/caC	2/16	1	2	FACETS	1	0.967	1	1	0.967	1	CLONAL	1	TRUE	1	0.414591988376653	2		505	922	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31424566	31424566	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1169731112	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	845	181	543	0	ENST00000344624.3:c.3229G>A	p.Val1077Ile	p.V1077I	ENST00000344624		1077	Gtc/Atc	25/33	1	2	FACETS	0.851	0.784	0.921	0.851	0.784	0.921	CLONAL	1	TRUE	1	0.414591988376653	2		543	1026	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31431746	31431746	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	823	127	477	0	ENST00000344624.3:c.3082C>G	p.Pro1028Ala	p.P1028A	ENST00000344624		1028	Cct/Gct	23/33	1	2	FACETS	0.645	0.583	0.71	0.645	0.583	0.71	SUBCLONAL	1	TRUE	1	0.414591988376653	2		477	950	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38946570	38946570	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	64	347	0	ENST00000357387.3:c.4399G>T	p.Gly1467Cys	p.G1467C	ENST00000357387	NM_152756.3	1467	Ggt/Tgt	33/38	1	2	FACETS	0.748	0.65	0.853	0.748	0.65	0.853	SUBCLONAL	1	TRUE	1	0.414591988376653	2		347	413	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178673	56178675	+	inframe_deletion	In_Frame_Del	DEL	ATC	ATC	-	rs758576258	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	51	178	0	ENST00000399503.3:c.3651_3653del	p.Ile1219del	p.I1219del	ENST00000399503	NM_005921.1	1216	ATC/-	14/20	1	2	FACETS	0.68	0.58	0.788	0.68	0.58	0.788	SUBCLONAL	1	TRUE	1	0.414591988376653	2		178	362	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56184096	56184096	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	116	387	0	ENST00000399503.3:c.4301G>A	p.Ser1434Asn	p.S1434N	ENST00000399503	NM_005921.1	1434	aGt/aAt	19/20	1	2	FACETS	0.901	0.814	0.993	0.901	0.814	0.993	CLONAL	1	TRUE	1	0.414591988376653	2		387	621	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67576831	67576831	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs371778244	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	518	112	351	0	ENST00000274335.5:c.913C>T	p.Pro305Ser	p.P305S	ENST00000274335		305	Cca/Tca	6/15	1	2	FACETS	0.858	0.773	0.947	0.858	0.773	0.947	CLONAL	1	TRUE	1	0.414591988376653	2		351	630	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80024730	80024730	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	829	124	632	0	ENST00000265081.6:c.1514C>A	p.Ala505Asp	p.A505D	ENST00000265081	NM_002439.4	505	gCc/gAc	10/24	1	2	FACETS	0.628	0.567	0.692	0.628	0.567	0.692	SUBCLONAL	1	TRUE	1	0.414591988376653	2		632	953	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685247	86685247	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	91	216	0	ENST00000274376.6:c.2963G>A	p.Arg988Lys	p.R988K	ENST00000274376	NM_002890.2	988	aGa/aAa	24/25	1	2	FACETS	0.817	0.728	0.913	0.817	0.728	0.913	CLONAL	1	TRUE	1	0.414591988376653	2		216	537	SUCCESS
APC	324	MSKCC	GRCh37	5	112177040	112177040	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	976	87	637	0	ENST00000257430.4:c.5749C>T	p.Pro1917Ser	p.P1917S	ENST00000257430	NM_000038.5	1917	Cca/Tca	16/16	1	2	FACETS	0.395	0.348	0.445	0.395	0.348	0.445	SUBCLONAL	1	TRUE	1	0.414591988376653	2		637	1063	SUCCESS
APC	324	MSKCC	GRCh37	5	112177853	112177853	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	140	385	0	ENST00000257430.4:c.6562A>G	p.Ile2188Val	p.I2188V	ENST00000257430	NM_000038.5	2188	Atc/Gtc	16/16	1	2	FACETS	0.9	0.821	0.984	0.9	0.821	0.984	CLONAL	1	TRUE	1	0.414591988376653	2		385	750	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433735	149433735	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	763	108	433	0	ENST00000286301.3:c.2816G>T	p.Ser939Ile	p.S939I	ENST00000286301	NM_005211.3	939	aGc/aTc	22/22	1	2	FACETS	0.598	0.536	0.664	0.598	0.536	0.664	SUBCLONAL	1	TRUE	1	0.414591988376653	2		433	871	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149449511	149449511	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	733	150	459	0	ENST00000286301.3:c.1435C>T	p.His479Tyr	p.H479Y	ENST00000286301	NM_005211.3	479	Cac/Tac	10/22	1	2	FACETS	0.819	0.749	0.893	0.819	0.749	0.893	CLONAL	1	TRUE	1	0.414591988376653	2		459	883	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149457745	149457745	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs752816265	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	157	428	0	ENST00000286301.3:c.659C>T	p.Ala220Val	p.A220V	ENST00000286301	NM_005211.3	220	gCc/gTc	5/22	1	2	FACETS	0.79	0.723	0.86	0.79	0.723	0.86	SUBCLONAL	1	TRUE	1	0.414591988376653	2		428	959	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176638222	176638222	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs189716582	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	889	217	530	0	ENST00000439151.2:c.2822G>A	p.Arg941His	p.R941H	ENST00000439151	NM_022455.4	941	cGt/cAt	5/23	1	2	FACETS	0.946	0.879	1	0.946	0.879	1	CLONAL	1	TRUE	1	0.414591988376653	2		530	1106	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176694568	176694568	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	90	260	0	ENST00000439151.2:c.5152A>G	p.Ser1718Gly	p.S1718G	ENST00000439151	NM_022455.4	1718	Agc/Ggc	15/23	1	2	FACETS	0.807	0.718	0.902	0.807	0.718	0.902	CLONAL	1	TRUE	1	0.414591988376653	2		260	538	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176707684	176707684	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	185	404	1	ENST00000439151.2:c.5741G>A	p.Arg1914His	p.R1914H	ENST00000439151	NM_022455.4	1914	cGc/cAc	18/23	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.414591988376653	2		405	821	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176709483	176709483	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1554204594	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	91	280	0	ENST00000439151.2:c.5910G>C	p.Glu1970Asp	p.E1970D	ENST00000439151	NM_022455.4	1970	gaG/gaC	19/23	1	2	FACETS	0.892	0.795	0.995	0.892	0.795	0.995	CLONAL	1	TRUE	1	0.414591988376653	2		280	492	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180047875	180047875	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	858	176	574	1	ENST00000261937.6:c.2299+1G>A		p.X767_splice	ENST00000261937	NM_182925.4	767			1	2	FACETS	0.821	0.756	0.889	0.821	0.756	0.889	CLONAL	1	TRUE	1	0.414591988376653	2		575	1034	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180048886	180048886	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1212875216	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	842	186	535	0	ENST00000261937.6:c.1676C>T	p.Thr559Ile	p.T559I	ENST00000261937	NM_182925.4	559	aCc/aTc	13/30	1	2	FACETS	0.873	0.806	0.943	0.873	0.806	0.943	CLONAL	1	TRUE	1	0.414591988376653	2		535	1028	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180052877	180052877	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	163	572	0	ENST00000261937.6:c.1413G>T	p.Gln471His	p.Q471H	ENST00000261937	NM_182925.4	471	caG/caT	10/30	1	2	FACETS	0.761	0.698	0.828	0.761	0.698	0.828	SUBCLONAL	1	TRUE	1	0.414591988376653	2		572	1033	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	394879	394879	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	645	132	392	0	ENST00000380956.4:c.275C>T	p.Thr92Ile	p.T92I	ENST00000380956	NM_001195286.1	92	aCc/aTc	3/9	1	2	FACETS	0.82	0.744	0.898	0.82	0.744	0.898	CLONAL	1	TRUE	1	0.414591988376653	2		392	777	SUCCESS
H3C1	8968	MSKCC	GRCh37	6	26020901	26020901	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1026102996	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	25	219	0	ENST00000357647.3:c.184C>T	p.Leu62Phe	p.L62F	ENST00000357647	NM_003529.2	62	Ctt/Ttt	1/1	1	2	FACETS	0.259	0.204	0.324	0.259	0.204	0.324	SUBCLONAL	1	TRUE	1	0.414591988376653	2		219	465	SUCCESS
H3C11	8968	MSKCC	GRCh37	6	27839760	27839760	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	122	372	1	ENST00000328488.2:c.334G>A	p.Ala112Thr	p.A112T	ENST00000328488	NM_003533.2	112	Gcc/Acc	1/1	1	2	FACETS	0.878	0.795	0.966	0.878	0.795	0.966	CLONAL	1	TRUE	1	0.414591988376653	2		373	670	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858228	27858228	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1344759679	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	153	337	0	ENST00000359303.2:c.343G>A	p.Ala115Thr	p.A115T	ENST00000359303	NM_003535.2	115	Gcc/Acc	1/1	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.414591988376653	2		337	701	SUCCESS
HLA-A	3105	MSKCC	GRCh37	6	29912369	29912369	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	108	379	0	ENST00000376809.5:c.988G>T	p.Val330Leu	p.V330L	ENST00000376809	NM_002116.7	330	Gtg/Ttg	5/8	1	2	FACETS	0.759	0.682	0.841	0.759	0.682	0.841	SUBCLONAL	1	TRUE	1	0.414591988376653	2		379	686	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672837	30672837	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	719	178	487	0	ENST00000376406.3:c.4123C>T	p.Pro1375Ser	p.P1375S	ENST00000376406	NM_014641.2	1375	Cct/Tct	10/15	1	2	FACETS	0.957	0.883	1	0.957	0.883	1	CLONAL	1	TRUE	1	0.414591988376653	2		487	897	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32187552	32187552	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	150	359	1	ENST00000375023.3:c.1327C>A	p.Pro443Thr	p.P443T	ENST00000375023	NM_004557.3	443	Cca/Aca	8/30	1	2	FACETS	1	0.953	1	1	0.953	1	CLONAL	1	TRUE	1	0.414591988376653	2		360	684	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32189048	32189048	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	636	131	460	0	ENST00000375023.3:c.506G>T	p.Gly169Val	p.G169V	ENST00000375023	NM_004557.3	169	gGg/gTg	4/30	1	2	FACETS	0.824	0.748	0.903	0.824	0.748	0.903	CLONAL	1	TRUE	1	0.414591988376653	2		460	767	SUCCESS
TAP1	6890	MSKCC	GRCh37	6	32818728	32818728	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	684	142	429	0	ENST00000354258.4:c.1223G>A	p.Trp408Ter	p.W408*	ENST00000354258	NM_000593.5	408	tGg/tAg	4/11	1	2	FACETS	0.829	0.756	0.906	0.829	0.756	0.906	CLONAL	1	TRUE	1	0.414591988376653	2		429	826	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793577	89793577	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1226228262	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	93	385	0	ENST00000336032.3:c.646A>G	p.Ser216Gly	p.S216G	ENST00000336032	NM_006813.2	216	Agc/Ggc	2/2	1	2	FACETS	0.629	0.559	0.704	0.629	0.559	0.704	SUBCLONAL	1	TRUE	1	0.414591988376653	2		385	713	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93973636	93973636	+	splice_region_variant,intron_variant	Splice_Region	SNP	T	T	C	rs1327243437	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	115	370	0	ENST00000369303.4:c.1743-3A>G		p.X581_splice	ENST00000369303	NM_004440.3	581			1	2	FACETS	0.939	0.848	1	0.939	0.848	1	CLONAL	1	TRUE	1	0.414591988376653	2		370	591	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120398	94120398	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	497	29	327	0	ENST00000369303.4:c.653C>T	p.Thr218Ile	p.T218I	ENST00000369303	NM_004440.3	218	aCa/aTa	3/17	1	2	FACETS	0.266	0.213	0.327	0.266	0.213	0.327	SUBCLONAL	1	TRUE	1	0.414591988376653	2		327	526	SUCCESS
FYN	2534	MSKCC	GRCh37	6	112020732	112020732	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	838	175	424	0	ENST00000368678.4:c.839C>T	p.Ala280Val	p.A280V	ENST00000368678		280	gCt/gTt	8/13	1	2	FACETS	0.833	0.767	0.903	0.833	0.767	0.903	CLONAL	1	TRUE	1	0.414591988376653	2		424	1013	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117631445	117631445	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	rs190667369	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	71	291	0	ENST00000368508.3:c.6234-1G>A		p.X2078_splice	ENST00000368508	NM_002944.2	2078			1	2	FACETS	0.768	0.673	0.87	0.768	0.673	0.87	SUBCLONAL	1	TRUE	1	0.414591988376653	2		291	446	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117677989	117677989	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	116	404	0	ENST00000368508.3:c.3944C>A	p.Pro1315His	p.P1315H	ENST00000368508	NM_002944.2	1315	cCc/cAc	25/43	1	2	FACETS	0.903	0.815	0.994	0.903	0.815	0.994	CLONAL	1	TRUE	1	0.414591988376653	2		404	620	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117681024	117681024	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	485	99	438	0	ENST00000368508.3:c.3596C>A	p.Ala1199Asp	p.A1199D	ENST00000368508	NM_002944.2	1199	gCt/gAt	23/43	1	2	FACETS	0.818	0.732	0.909	0.818	0.732	0.909	CLONAL	1	TRUE	1	0.414591988376653	2		438	584	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117708967	117708967	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	131	401	0	ENST00000368508.3:c.1990T>C	p.Ser664Pro	p.S664P	ENST00000368508	NM_002944.2	664	Tca/Cca	13/43	1	2	FACETS	0.88	0.8	0.964	0.88	0.8	0.964	CLONAL	1	TRUE	1	0.414591988376653	2		401	718	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117710605	117710605	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	95	266	0	ENST00000368508.3:c.1667C>T	p.Pro556Leu	p.P556L	ENST00000368508	NM_002944.2	556	cCt/cTt	12/43	1	2	FACETS	0.885	0.79	0.984	0.885	0.79	0.984	CLONAL	1	TRUE	1	0.414591988376653	2		266	518	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138196058	138196058	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	105	237	0	ENST00000237289.4:c.372G>T	p.Lys124Asn	p.K124N	ENST00000237289	NM_001270507.1	124	aaG/aaT	3/9	1	2	FACETS	0.893	0.803	0.989	0.893	0.803	0.989	CLONAL	1	TRUE	1	0.414591988376653	2		237	567	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138199967	138199967	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1430533454	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	112	277	1	ENST00000237289.4:c.1385C>T	p.Pro462Leu	p.P462L	ENST00000237289	NM_001270507.1	462	cCg/cTg	7/9	1	2	FACETS	0.91	0.82	1	0.91	0.82	1	CLONAL	1	TRUE	1	0.414591988376653	2		278	594	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157517417	157517417	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	718	156	456	0	ENST00000346085.5:c.3981G>T	p.Gln1327His	p.Q1327H	ENST00000346085	NM_020732.3	1327	caG/caT	16/20	1	2	FACETS	0.861	0.789	0.937	0.861	0.789	0.937	CLONAL	1	TRUE	1	0.414591988376653	2		456	874	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2959220	2959220	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	947	69	468	1	ENST00000396946.4:c.2296G>T	p.Glu766Ter	p.E766*	ENST00000396946	NM_032415.4	766	Gag/Tag	18/25	1	2	FACETS	0.328	0.284	0.375	0.328	0.284	0.375	SUBCLONAL	1	TRUE	1	0.414591988376653	2		469	1016	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50367326	50367326	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	121	257	0	ENST00000331340.3:c.133C>T	p.Gln45Ter	p.Q45*	ENST00000331340	NM_006060.4	45	Caa/Taa	3/8	1	2	FACETS	0.888	0.804	0.977	0.888	0.804	0.977	CLONAL	1	TRUE	1	0.414591988376653	2		257	657	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50468320	50468320	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	622	163	428	0	ENST00000331340.3:c.1555A>T	p.Ser519Cys	p.S519C	ENST00000331340	NM_006060.4	519	Agc/Tgc	8/8	1	2	FACETS	1	0.921	1	1	0.921	1	CLONAL	1	TRUE	1	0.414591988376653	2		428	785	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55219028	55219028	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	119	321	0	ENST00000275493.2:c.601G>T	p.Gly201Cys	p.G201C	ENST00000275493	NM_005228.3	201	Ggt/Tgt	5/28	1	2	FACETS	0.91	0.823	1	0.91	0.823	1	CLONAL	1	TRUE	1	0.414591988376653	2		321	631	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508456	106508456	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	154	36	115	0	ENST00000359195.3:c.450C>A	p.Phe150Leu	p.F150L	ENST00000359195	NM_002649.2	150	ttC/ttA	2/11	1	2	FACETS	0.914	0.76	1	0.914	0.76	1	CLONAL	1	TRUE	1	0.414591988376653	2		115	190	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106545781	106545781	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1346203324	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	83	478	2	ENST00000359195.3:c.3258G>A	p.Trp1086Ter	p.W1086*	ENST00000359195	NM_002649.2	1086	tgG/tgA	11/11	1	2	FACETS	0.638	0.563	0.717	0.638	0.563	0.717	SUBCLONAL	1	TRUE	1	0.414591988376653	2		480	628	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128829156	128829156	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1363551380	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	153	46	99	1	ENST00000249373.3:c.164C>T	p.Thr55Ile	p.T55I	ENST00000249373	NM_005631.4	55	aCt/aTt	1/12	1	2	FACETS	1	0.917	1	1	0.917	1	CLONAL	1	TRUE	1	0.414591988376653	2		100	199	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140439654	140439654	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	72	311	0	ENST00000288602.6:c.2085G>T	p.Glu695Asp	p.E695D	ENST00000288602	NM_004333.4	695	gaG/gaT	17/18	1	2	FACETS	0.731	0.641	0.828	0.731	0.641	0.828	SUBCLONAL	1	TRUE	1	0.414591988376653	2		311	475	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140476857	140476857	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	596	107	417	0	ENST00000288602.6:c.1549A>G	p.Met517Val	p.M517V	ENST00000288602	NM_004333.4	517	Atg/Gtg	13/18	1	2	FACETS	0.734	0.659	0.814	0.734	0.659	0.814	SUBCLONAL	1	TRUE	1	0.414591988376653	2		417	703	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845739	151845739	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	739	177	495	0	ENST00000262189.6:c.13273G>A	p.Asp4425Asn	p.D4425N	ENST00000262189	NM_170606.2	4425	Gat/Aat	52/59	1	2	FACETS	0.932	0.859	1	0.932	0.859	1	CLONAL	1	TRUE	1	0.414591988376653	2		495	916	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151851105	151851105	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1470835588	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	258	51	225	0	ENST00000262189.6:c.12266C>T	p.Thr4089Ile	p.T4089I	ENST00000262189	NM_170606.2	4089	aCa/aTa	48/59	1	2	FACETS	0.796	0.681	0.921	0.796	0.681	0.921	CLONAL	1	TRUE	1	0.414591988376653	2		225	309	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878491	151878491	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	150	396	0	ENST00000262189.6:c.6454G>A	p.Ala2152Thr	p.A2152T	ENST00000262189	NM_170606.2	2152	Gct/Act	36/59	1	2	FACETS	0.973	0.89	1	0.973	0.89	1	CLONAL	1	TRUE	1	0.414591988376653	2		396	744	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151879310	151879310	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	90	305	0	ENST00000262189.6:c.5635C>G	p.Pro1879Ala	p.P1879A	ENST00000262189	NM_170606.2	1879	Ccg/Gcg	36/59	1	2	FACETS	0.895	0.797	0.999	0.895	0.797	0.999	CLONAL	1	TRUE	1	0.414591988376653	2		305	485	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151884523	151884523	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs746430166	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	80	298	0	ENST00000262189.6:c.4832C>A	p.Pro1611His	p.P1611H	ENST00000262189	NM_170606.2	1611	cCt/cAt	33/59	1	2	FACETS	0.711	0.627	0.8	0.711	0.627	0.8	SUBCLONAL	1	TRUE	1	0.414591988376653	2		298	543	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38146217	38146217	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	934	154	531	0	ENST00000317025.8:c.3289C>A	p.Arg1097Ser	p.R1097S	ENST00000317025	NM_023034.1	1097	Cgc/Agc	19/24	1	2	FACETS	0.683	0.624	0.745	0.683	0.624	0.745	SUBCLONAL	1	TRUE	1	0.414591988376653	2		531	1088	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55370899	55370900	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	253	575	0	ENST00000297316.4:c.202dup	p.Ile68AsnfsTer13	p.I68Nfs*13	ENST00000297316	NM_022454.3	67	-/A	1/2	1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.414591988376653	2		575	1068	SUCCESS
SOX17	64321	MSKCC	GRCh37	8	55372239	55372239	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs745596528	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	484	133	371	1	ENST00000297316.4:c.929G>A	p.Gly310Asp	p.G310D	ENST00000297316	NM_022454.3	310	gGc/gAc	2/2	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.414591988376653	2		372	617	SUCCESS
NBN	4683	MSKCC	GRCh37	8	90990458	90990458	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1554566613	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	86	396	0	ENST00000265433.3:c.574C>T	p.Gln192Ter	p.Q192*	ENST00000265433	NM_002485.4	192	Caa/Taa	5/16	1	2	FACETS	0.63	0.557	0.707	0.63	0.557	0.707	SUBCLONAL	1	TRUE	1	0.414591988376653	2		396	659	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117869656	117869656	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	711	121	564	0	ENST00000297338.2:c.538G>A	p.Asp180Asn	p.D180N	ENST00000297338	NM_006265.2	180	Gac/Aac	6/14	1	2	FACETS	0.702	0.634	0.773	0.702	0.634	0.773	SUBCLONAL	1	TRUE	1	0.414591988376653	2		564	832	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559398	141559398	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	155	404	0	ENST00000220592.5:c.1404-1G>T		p.X468_splice	ENST00000220592	NM_012154.3	468			1	2	FACETS	0.901	0.825	0.98	0.901	0.825	0.98	CLONAL	1	TRUE	1	0.414591988376653	2		404	830	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404545	8404545	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	232	53	206	0	ENST00000356435.5:c.4202C>T	p.Ala1401Val	p.A1401V	ENST00000356435		1401	gCt/gTt	25/35	1	2	FACETS	0.897	0.771	1	0.897	0.771	1	CLONAL	1	TRUE	1	0.414591988376653	2		206	285	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8404619	8404619	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	23	253	0	ENST00000356435.5:c.4128C>G	p.Asn1376Lys	p.N1376K	ENST00000356435		1376	aaC/aaG	25/35	1	2	FACETS	0.269	0.209	0.339	0.269	0.209	0.339	SUBCLONAL	1	TRUE	1	0.414591988376653	2		253	412	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8517851	8517851	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	340	62	239	0	ENST00000356435.5:c.1540G>T	p.Gly514Ter	p.G514*	ENST00000356435		514	Gga/Tga	10/35	1	2	FACETS	0.744	0.645	0.851	0.744	0.645	0.851	SUBCLONAL	1	TRUE	1	0.414591988376653	2		239	402	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27197433	27197433	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	928	166	658	0	ENST00000380036.4:c.1745C>T	p.Ser582Phe	p.S582F	ENST00000380036	NM_000459.3	582	tCt/tTt	12/23	1	2	FACETS	0.732	0.671	0.795	0.732	0.671	0.795	SUBCLONAL	1	TRUE	1	0.414591988376653	2		658	1094	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27220142	27220142	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	rs763579590	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	573	117	376	0	ENST00000380036.4:c.3199G>A	p.Val1067Met	p.V1067M	ENST00000380036	NM_000459.3	1067	Gtg/Atg	21/23	1	2	FACETS	0.818	0.739	0.902	0.818	0.739	0.902	CLONAL	1	TRUE	1	0.414591988376653	2		376	690	SUCCESS
PAX5	5079	MSKCC	GRCh37	9	36966553	36966553	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	119	371	1	ENST00000358127.4:c.773C>A	p.Pro258His	p.P258H	ENST00000358127	NM_001280556.1	258	cCc/cAc	6/10	1	2	FACETS	0.879	0.795	0.968	0.879	0.795	0.968	CLONAL	1	TRUE	1	0.414591988376653	2		372	653	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87342574	87342574	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	116	382	0	ENST00000277120.3:c.859C>A	p.Pro287Thr	p.P287T	ENST00000277120		287	Cca/Aca	9/19	1	2	FACETS	0.895	0.809	0.986	0.895	0.809	0.986	CLONAL	1	TRUE	1	0.414591988376653	2		382	625	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93606368	93606368	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs1388733927	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	108	464	0	ENST00000375746.1:c.188A>G	p.His63Arg	p.H63R	ENST00000375746	NM_001174167.1	63	cAc/cGc	2/14	1	2	FACETS	0.674	0.605	0.747	0.674	0.605	0.747	SUBCLONAL	1	TRUE	1	0.414591988376653	2		464	773	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110249442	110249442	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1134	266	710	0	ENST00000374672.4:c.1131G>T	p.Glu377Asp	p.E377D	ENST00000374672	NM_004235.4	377	gaG/gaT	4/5	1	2	FACETS	0.917	0.858	0.978	0.917	0.858	0.978	CLONAL	1	TRUE	1	0.414591988376653	2		710	1400	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250097	110250097	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	157	458	0	ENST00000374672.4:c.578T>C	p.Val193Ala	p.V193A	ENST00000374672	NM_004235.4	193	gTg/gCg	3/5	1	2	FACETS	0.971	0.891	1	0.971	0.891	1	CLONAL	1	TRUE	1	0.414591988376653	2		458	780	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128201209	128201209	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1369730858	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	775	150	459	2	ENST00000265960.3:c.1526C>T	p.Thr509Met	p.T509M	ENST00000265960	NM_001006617.1	509	aCg/aTg	12/12	1	2	FACETS	0.782	0.715	0.853	0.782	0.715	0.853	SUBCLONAL	1	TRUE	1	0.414591988376653	2		461	925	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781182	135781182	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	169	474	0	ENST00000298552.3:c.1783G>T	p.Gly595Cys	p.G595C	ENST00000298552	NM_001162426.1	595	Ggc/Tgc	15/23	1	2	FACETS	0.899	0.826	0.974	0.899	0.826	0.974	CLONAL	1	TRUE	1	0.414591988376653	2		474	907	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139391802	139391802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	143	393	0	ENST00000277541.6:c.6389G>A	p.Gly2130Glu	p.G2130E	ENST00000277541	NM_017617.3	2130	gGg/gAg	34/34	1	2	FACETS	0.953	0.87	1	0.953	0.87	1	CLONAL	1	TRUE	1	0.414591988376653	2		393	724	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395300	139395300	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	58	368	0	ENST00000277541.6:c.5639-1G>T		p.X1880_splice	ENST00000277541	NM_017617.3	1880			1	2	FACETS	0.458	0.393	0.529	0.458	0.393	0.529	SUBCLONAL	1	TRUE	1	0.414591988376653	2		368	611	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139399168	139399168	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	165	437	2	ENST00000277541.6:c.4975G>T	p.Gly1659Cys	p.G1659C	ENST00000277541	NM_017617.3	1659	Ggt/Tgt	26/34	1	2	FACETS	0.911	0.837	0.988	0.911	0.837	0.988	CLONAL	1	TRUE	1	0.414591988376653	2		439	874	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139400101	139400101	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1024	206	664	0	ENST00000277541.6:c.4247G>A	p.Cys1416Tyr	p.C1416Y	ENST00000277541	NM_017617.3	1416	tGc/tAc	25/34	1	2	FACETS	0.808	0.748	0.87	0.808	0.748	0.87	CLONAL	1	TRUE	1	0.414591988376653	2		664	1230	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139401020	139401020	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs767910007	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	828	203	486	3	ENST00000277541.6:c.3973G>A	p.Ala1325Thr	p.A1325T	ENST00000277541	NM_017617.3	1325	Gcc/Acc	24/34	1	2	FACETS	0.95	0.88	1	0.95	0.88	1	CLONAL	1	TRUE	1	0.414591988376653	2		489	1031	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412280	139412280	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	969	183	538	0	ENST00000277541.6:c.1365G>C	p.Glu455Asp	p.E455D	ENST00000277541	NM_017617.3	455	gaG/gaC	8/34	1	2	FACETS	0.766	0.706	0.829	0.766	0.706	0.829	SUBCLONAL	1	TRUE	1	0.414591988376653	2		538	1152	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44928905	44928905	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	612	98	377	0	ENST00000377967.4:c.2005C>T	p.Leu669Phe	p.L669F	ENST00000377967	NM_021140.2	669	Ctc/Ttc	17/29	1	2	FACETS	0.666	0.594	0.742	0.666	0.594	0.742	SUBCLONAL	1	TRUE	1	0.414591988376653	2		377	710	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228321	53228321	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1556840281	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	139	540	0	ENST00000375401.3:c.2081G>A	p.Arg694Gln	p.R694Q	ENST00000375401	NM_004187.3	694	cGa/cAa	15/26	1	2	FACETS	0.71	0.645	0.777	0.71	0.645	0.777	SUBCLONAL	1	TRUE	1	0.414591988376653	2		540	945	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53230894	53230894	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	150	456	0	ENST00000375401.3:c.1899C>A	p.Tyr633Ter	p.Y633*	ENST00000375401	NM_004187.3	633	taC/taA	14/26	1	2	FACETS	0.811	0.741	0.884	0.811	0.741	0.884	CLONAL	1	TRUE	1	0.414591988376653	2		456	892	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53253984	53253984	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	152	485	0	ENST00000375401.3:c.88T>C	p.Tyr30His	p.Y30H	ENST00000375401	NM_004187.3	30	Tac/Cac	1/26	1	2	FACETS	0.819	0.749	0.893	0.819	0.749	0.893	CLONAL	1	TRUE	1	0.414591988376653	2		485	895	SUCCESS
AR	367	MSKCC	GRCh37	X	66765836	66765836	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1176	212	750	0	ENST00000374690.3:c.848C>A	p.Pro283His	p.P283H	ENST00000374690	NM_000044.3	283	cCt/cAt	1/8	1	2	FACETS	0.737	0.683	0.793	0.737	0.683	0.793	SUBCLONAL	1	TRUE	1	0.414591988376653	2		750	1388	SUCCESS
AR	367	MSKCC	GRCh37	X	66931342	66931342	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	142	477	0	ENST00000374690.3:c.1984G>T	p.Val662Leu	p.V662L	ENST00000374690	NM_000044.3	662	Gtg/Ttg	4/8	1	2	FACETS	0.815	0.742	0.89	0.815	0.742	0.89	CLONAL	1	TRUE	1	0.414591988376653	2		477	841	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70340924	70340924	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	625	152	396	0	ENST00000374080.3:c.657A>G	p.Ile219Met	p.I219M	ENST00000374080		219	atA/atG	5/45	1	2	FACETS	0.944	0.864	1	0.944	0.864	1	CLONAL	1	TRUE	1	0.414591988376653	2		396	777	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76829719	76829719	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	116	507	0	ENST00000373344.5:c.6322G>A	p.Val2108Met	p.V2108M	ENST00000373344	NM_000489.3	2108	Gtg/Atg	28/35	1	2	FACETS	0.72	0.649	0.795	0.72	0.649	0.795	SUBCLONAL	1	TRUE	1	0.414591988376653	2		507	777	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972719	76972719	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	76	363	0	ENST00000373344.5:c.22G>A	p.Glu8Lys	p.E8K	ENST00000373344	NM_000489.3	8	Gaa/Aaa	2/35	1	2	FACETS	0.564	0.495	0.639	0.564	0.495	0.639	SUBCLONAL	1	TRUE	1	0.414591988376653	2		363	650	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123196759	123196759	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018100-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	414	79	356	0	ENST00000218089.9:c.1646C>T	p.Thr549Ile	p.T549I	ENST00000218089	NM_001042749.1	549	aCa/aTa	18/35	1	2	FACETS	0.773	0.682	0.87	0.773	0.682	0.87	SUBCLONAL	1	TRUE	1	0.414591988376653	2		356	493	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	69	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.961	1	1	0.961	1	CLONAL	1	TRUE	1	0.260615560275889	2		215	418	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936082	178936082	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs121913273	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	142	499	0	ENST00000263967.3:c.1624G>A	p.Glu542Lys	p.E542K	ENST00000263967	NM_006218.2	542	Gaa/Aaa	10/21	0.254876588018056	3	FACETS	0.896	0.819	0.978	0.896	0.819	0.978	CLONAL	2	TRUE	1	0.260615560275889	3		499	687	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180050946	180050946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	851	109	815	0	ENST00000261937.6:c.1537G>A	p.Gly513Arg	p.G513R	ENST00000261937	NM_182925.4	513	Gga/Aga	11/30	1	2	FACETS	0.871	0.781	0.967	0.871	0.781	0.967	CLONAL	1	TRUE	1	0.260615560275889	2		815	960	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41565529	41565529	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1057519889	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	649	96	586	0	ENST00000263253.7:c.4195G>A	p.Asp1399Asn	p.D1399N	ENST00000263253	NM_001429.3	1399	Gat/Aat	26/31	1	2	FACETS	0.989	0.881	1	0.989	0.881	1	CLONAL	1	TRUE	1	0.260615560275889	2		586	745	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549725	187549725	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs199516712	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	64	457	0	ENST00000441802.2:c.4516C>T	p.Arg1506Cys	p.R1506C	ENST00000441802	NM_005245.3	1506	Cgt/Tgt	8/27	0.260615560275889	1	FACETS	0.742	0.642	0.849	0.742	0.642	0.849	SUBCLONAL	1	TRUE	0	0.260615560275889	1		457	576	SUCCESS
ATR	545	MSKCC	GRCh37	3	142176561	142176561	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	76	788	0	ENST00000350721.4:c.7540C>T	p.Arg2514Cys	p.R2514C	ENST00000350721	NM_001184.3	2514	Cgc/Tgc	45/47	0.254876588018056	3	FACETS	0.717	0.627	0.813	0.358	0.313	0.407	SUBCLONAL	1	TRUE	1	0.260615560275889	3		788	920	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106157845	106157845	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs780710758	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	578	71	546	0	ENST00000380013.4:c.2746C>T	p.Gln916Ter	p.Q916*	ENST00000380013	NM_001127208.2	916	Cag/Tag	3/11	1	2	FACETS	0.84	0.733	0.955	0.84	0.733	0.955	CLONAL	1	TRUE	1	0.260615560275889	2		546	649	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162731101	162731101	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761991484	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	102	638	0	ENST00000367921.3:c.956C>T	p.Ser319Phe	p.S319F	ENST00000367921	NM_006182.2	319	tCc/tTc	9/18	1	2	FACETS	0.971	0.868	1	0.971	0.868	1	CLONAL	1	TRUE	1	0.260615560275889	2		638	806	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106519967	106519967	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	30	391	0	ENST00000359195.3:c.2395G>A	p.Glu799Lys	p.E799K	ENST00000359195	NM_002649.2	799	Gaa/Aaa	6/11	1	2	FACETS	0.438	0.352	0.536	0.438	0.352	0.536	SUBCLONAL	1	TRUE	1	0.260615560275889	2		391	526	SUCCESS
ATM	472	MSKCC	GRCh37	11	108235849	108235849	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	82	620	0	ENST00000278616.4:c.8891C>T	p.Pro2964Leu	p.P2964L	ENST00000278616	NM_000051.3	2964	cCt/cTt	62/63	0.260615560275889	1	FACETS	0.883	0.779	0.994	0.883	0.779	0.994	CLONAL	1	TRUE	0	0.260615560275889	1		620	620	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138198228	138198228	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	37	347	0	ENST00000237289.4:c.821C>T	p.Pro274Leu	p.P274L	ENST00000237289	NM_001270507.1	274	cCa/cTa	6/9	1	2	FACETS	0.569	0.469	0.682	0.569	0.469	0.682	SUBCLONAL	1	TRUE	1	0.260615560275889	2		347	499	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120497748	120497748	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs782035658	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	685	114	670	0	ENST00000256646.2:c.2134C>T	p.Pro712Ser	p.P712S	ENST00000256646	NM_024408.3	712	Ccc/Tcc	13/34	1	2	FACETS	1	0.952	1	1	0.952	1	CLONAL	1	TRUE	1	0.260615560275889	2		670	799	SUCCESS
NTRK1	4914	MSKCC	GRCh37	1	156834561	156834561	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	850	119	796	1	ENST00000524377.1:c.329C>T	p.Ala110Val	p.A110V	ENST00000524377	NM_002529.3	110	gCc/gTc	3/17	1	2	FACETS	0.942	0.849	1	0.942	0.849	1	CLONAL	1	TRUE	1	0.260615560275889	2		797	969	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100370	8100370	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	837	90	946	1	ENST00000346208.3:c.344G>A	p.Ser115Asn	p.S115N	ENST00000346208		115	aGc/aAc	3/6	1	2	FACETS	0.745	0.66	0.837	0.745	0.66	0.837	SUBCLONAL	1	TRUE	1	0.260615560275889	2		947	927	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64574491	64574491	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	95	662	0	ENST00000312049.6:c.904T>A	p.Tyr302Asn	p.Y302N	ENST00000312049	NM_130799.2	302	Tac/Aac	6/10	1	2	FACETS	0.912	0.812	1	0.912	0.812	1	CLONAL	1	TRUE	1	0.260615560275889	2		662	799	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	416661	416663	+	inframe_deletion	In_Frame_Del	DEL	TGA	TGA	-	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	77	433	0	ENST00000399788.2:c.3887_3889del	p.Ile1296del	p.I1296del	ENST00000399788	NM_001042603.1	1296	aTCAgt/agt	23/28	NA	2	FACETS	1	0.936	1			1	INDETERMINATE	1	TRUE	NA	0.260615560275889	2		433	538	SUCCESS
RAD52	5893	MSKCC	GRCh37	12	1025944	1025944	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	89	682	1	ENST00000358495.3:c.586C>T	p.Leu196Phe	p.L196F	ENST00000358495	NM_134424.2	196	Ctt/Ttt	8/12	NA	2	FACETS	0.782	0.693	0.879			1	INDETERMINATE	1	TRUE	NA	0.260615560275889	2		683	873	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46244344	46244344	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	793	81	678	0	ENST00000334344.6:c.2438C>T	p.Ser813Phe	p.S813F	ENST00000334344	NM_152641.2	813	tCt/tTt	15/21	0.254876588018056	3	FACETS	0.804	0.707	0.908	0.402	0.353	0.454	CLONAL	1	TRUE	1	0.260615560275889	3		678	874	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49445252	49445253	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1013	126	896	3	ENST00000301067.7:c.2213_2214delinsTT	p.Ser738Phe	p.S738F	ENST00000301067	NM_003482.3	738	tCC/tTT	10/54	0.254876588018056	3	FACETS	0.96	0.867	1	0.48	0.433	0.529	CLONAL	1	TRUE	1	0.260615560275889	3		899	1139	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133218404	133218404	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	110	710	0	ENST00000320574.5:c.5207T>A	p.Val1736Asp	p.V1736D	ENST00000320574	NM_006231.2	1736	gTc/gAc	39/49	1	2	FACETS	0.901	0.808	0.999	0.901	0.808	0.999	CLONAL	1	TRUE	1	0.260615560275889	2		710	937	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	28895618	28895618	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	900	96	775	1	ENST00000282397.4:c.3156T>A	p.Asp1052Glu	p.D1052E	ENST00000282397	NM_002019.4	1052	gaT/gaA	23/30	0.260615560275889	2	FACETS	0.74	0.658	0.828	0.37	0.329	0.414	SUBCLONAL	1	TRUE	0	0.260615560275889	2		776	996	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29007984	29007984	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	384	124	378	0	ENST00000282397.4:c.785T>C	p.Val262Ala	p.V262A	ENST00000282397	NM_002019.4	262	gTt/gCt	6/30	0.260615560275889	2	FACETS	0.937	0.852	1	0.937	0.852	1	CLONAL	2	TRUE	0	0.260615560275889	2		378	508	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32913783	32913783	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	189	709	0	ENST00000380152.3:c.5291C>A	p.Ser1764Ter	p.S1764*	ENST00000380152		1764	tCa/tAa	11/27	0.260615560275889	2	FACETS	0.892	0.826	0.961	0.892	0.826	0.961	CLONAL	2	TRUE	0	0.260615560275889	2		709	813	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955331	48955379	+	splice_region_variant,intron_variant	Splice_Region	DEL	TAGCTCAAGGGTTAATATTTCATAAATAGTTACTTTTTTTTTTCATTTT	TAGCTCAAGGGTTAATATTTCATAAATAGTTACTTTTTTTTTTCATTTT	-	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	75	34	88	0	ENST00000267163.4:c.1499-49_1499-1del		p.X500_splice	ENST00000267163	NM_000321.2	500			0.260615560275889	1	FACETS	1	0.867	1	1	0.967	1	CLONAL	2	TRUE	0	0.260615560275889	1		88	109	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42041876	42041877	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	83	685	1	ENST00000219905.7:c.6071_6072delinsTT	p.Ser2024Phe	p.S2024F	ENST00000219905	NM_001164273.1	2024	tCC/tTT	17/24	0.260615560275889	1	FACETS	0.792	0.699	0.892	0.792	0.699	0.892	SUBCLONAL	1	TRUE	0	0.260615560275889	1		686	699	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	341199	341199	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	830	128	843	0	ENST00000262320.3:c.2285C>T	p.Ser762Phe	p.S762F	ENST00000262320	NM_003502.3	762	tCc/tTc	9/11	0.226733970023471	1	FACETS	0.892	0.807	0.981	0.892	0.807	0.981	CLONAL	1	TRUE	0	0.260615560275889	1		843	958	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89839704	89839705	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	90	672	1	ENST00000389301.3:c.1988_1989delinsTT	p.Ser663Phe	p.S663F	ENST00000389301	NM_000135.2	663	tCC/tTT	22/43	0.260615560275889	1	FACETS	0.901	0.8	1	0.901	0.8	1	CLONAL	1	TRUE	0	0.260615560275889	1		673	667	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7578263	7578264	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	887	112	766	1	ENST00000269305.4:c.585_586delinsTT	p.Arg196Ter	p.R196*	ENST00000269305	NM_001126112.2	195	atCCga/atTTga	6/11	1	2	FACETS	0.86	0.772	0.954	0.86	0.772	0.954	CLONAL	1	TRUE	1	0.260615560275889	2		767	999	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7579528	7579529	+	stop_gained	Nonsense_Mutation	DNP	CC	CC	TT	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	913	104	838	0	ENST00000269305.4:c.158_159delinsAA	p.Trp53Ter	p.W53*	ENST00000269305	NM_001126112.2	53	tGG/tAA	4/11	1	2	FACETS	0.785	0.701	0.874	0.785	0.701	0.874	SUBCLONAL	1	TRUE	1	0.260615560275889	2		838	1017	SUCCESS
H3-3B	3021	MSKCC	GRCh37	17	73774955	73774955	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	523	80	404	0	ENST00000254810.4:c.218G>A	p.Arg73Lys	p.R73K	ENST00000254810	NM_005324.3	73	aGg/aAg	3/4	1	2	FACETS	1	0.896	1	1	0.896	1	CLONAL	1	TRUE	1	0.260615560275889	2		404	603	SUCCESS
SRSF2	6427	MSKCC	GRCh37	17	74732259	74732259	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1470066389	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	54	340	0	ENST00000359995.5:c.650G>A	p.Gly217Glu	p.G217E	ENST00000359995	NM_001195427.1	217	gGa/gAa	2/3	1	2	FACETS	0.917	0.784	1	0.917	0.784	1	CLONAL	1	TRUE	1	0.260615560275889	2		340	452	SUCCESS
DOT1L	84444	MSKCC	GRCh37	19	2220181	2220182	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	878	119	787	1	ENST00000398665.3:c.2766_2767delinsTT	p.His923Tyr	p.H923Y	ENST00000398665	NM_032482.2	922	gcCCac/gcTTac	23/28	1	2	FACETS	0.916	0.825	1	0.916	0.825	1	CLONAL	1	TRUE	1	0.260615560275889	2		788	997	SUCCESS
MAP2K2	5605	MSKCC	GRCh37	19	4099223	4099223	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	579	73	631	1	ENST00000262948.5:c.895A>G	p.Arg299Gly	p.R299G	ENST00000262948	NM_030662.3	299	Agg/Ggg	7/11	1	2	FACETS	0.859	0.751	0.975	0.859	0.751	0.975	CLONAL	1	TRUE	1	0.260615560275889	2		632	652	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10273408	10273408	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	806	104	737	0	ENST00000340748.4:c.895C>T	p.Pro299Ser	p.P299S	ENST00000340748		299	Ccc/Tcc	12/40	1	2	FACETS	0.877	0.784	0.976	0.877	0.784	0.976	CLONAL	1	TRUE	1	0.260615560275889	2		737	910	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290043	15290044	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	116	867	1	ENST00000263388.2:c.3510_3511delinsAA	p.Asp1171Asn	p.D1171N	ENST00000263388	NM_000435.2	1170	ctGGac/ctAAac	22/33	1	2	FACETS	0.924	0.832	1	0.924	0.832	1	CLONAL	1	TRUE	1	0.260615560275889	2		868	963	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15355167	15355167	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	98	971	1	ENST00000263377.2:c.2456C>T	p.Pro819Leu	p.P819L	ENST00000263377	NM_058243.2	819	cCc/cTc	13/20	1	2	FACETS	0.796	0.709	0.889	0.796	0.709	0.889	SUBCLONAL	1	TRUE	1	0.260615560275889	2		972	945	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15366239	15366239	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	123	719	0	ENST00000263377.2:c.1916C>T	p.Ser639Leu	p.S639L	ENST00000263377	NM_058243.2	639	tCa/tTa	10/20	1	2	FACETS	1	0.935	1	1	0.935	1	CLONAL	1	TRUE	1	0.260615560275889	2		719	904	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379701	17379701	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	86	698	2	ENST00000359435.4:c.86C>T	p.Ser29Phe	p.S29F	ENST00000359435	NM_001033549.1	29	tCc/tTc	2/9	1	2	FACETS	0.829	0.733	0.933	0.829	0.733	0.933	CLONAL	1	TRUE	1	0.260615560275889	2		700	796	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379853	17379853	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	136	959	0	ENST00000359435.4:c.238C>T	p.Pro80Ser	p.P80S	ENST00000359435	NM_001033549.1	80	Cct/Tct	2/9	1	2	FACETS	0.857	0.777	0.941	0.857	0.777	0.941	CLONAL	1	TRUE	1	0.260615560275889	2		959	1218	SUCCESS
JAK3	3718	MSKCC	GRCh37	19	17951106	17951106	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs149047410	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	138	808	0	ENST00000458235.1:c.1187C>T	p.Pro396Leu	p.P396L	ENST00000458235	NM_000215.3	396	cCt/cTt	9/24	1	2	FACETS	1	0.929	1	1	0.929	1	CLONAL	1	TRUE	1	0.260615560275889	2		808	1032	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19256713	19256713	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	116	786	1	ENST00000162023.5:c.1000C>T	p.Pro334Ser	p.P334S	ENST00000162023		334	Cct/Tct	13/13	1	2	FACETS	0.945	0.851	1	0.945	0.851	1	CLONAL	1	TRUE	1	0.260615560275889	2		787	942	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753467	42753467	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1436649291	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	99	704	2	ENST00000222329.4:c.797C>T	p.Pro266Leu	p.P266L	ENST00000222329	NM_006494.2	266	cCg/cTg	4/4	1	2	FACETS	0.952	0.849	1	0.952	0.849	1	CLONAL	1	TRUE	1	0.260615560275889	2		706	798	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42794830	42794830	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	50	593	0	ENST00000575354.2:c.1910A>T	p.Lys637Met	p.K637M	ENST00000575354	NM_015125.3	637	aAg/aTg	10/20	1	2	FACETS	0.668	0.567	0.78	0.668	0.567	0.78	SUBCLONAL	1	TRUE	1	0.260615560275889	2		593	574	SUCCESS
ALK	238	MSKCC	GRCh37	2	29419727	29419727	+	splice_acceptor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	536	62	506	0	ENST00000389048.3:c.4074-1G>A		p.X1358_splice	ENST00000389048	NM_004304.4	1358			1	2	FACETS	0.796	0.687	0.913	0.796	0.687	0.913	CLONAL	1	TRUE	1	0.260615560275889	2		506	598	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46588155	46588155	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs866478982	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	871	122	865	2	ENST00000263734.3:c.705G>A	p.Met235Ile	p.M235I	ENST00000263734	NM_001430.4	235	atG/atA	6/16	1	2	FACETS	0.943	0.851	1	0.943	0.851	1	CLONAL	1	TRUE	1	0.260615560275889	2		867	993	SUCCESS
CASP8	841	MSKCC	GRCh37	2	202141634	202141634	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	809	111	737	1	ENST00000358485.4:c.922G>A	p.Glu308Lys	p.E308K	ENST00000358485	NM_001080125.1	308	Gag/Aag	7/9	1	2	FACETS	0.926	0.831	1	0.926	0.831	1	CLONAL	1	TRUE	1	0.260615560275889	2		738	920	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29120966	29120966	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	646	108	577	0	ENST00000328354.6:c.591A>T	p.Lys197Asn	p.K197N	ENST00000328354	NM_007194.3	197	aaA/aaT	4/15	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.260615560275889	2		577	754	SUCCESS
NF2	4771	MSKCC	GRCh37	22	30090763	30090763	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761191666	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	807	105	762	2	ENST00000338641.4:c.1760C>T	p.Ser587Phe	p.S587F	ENST00000338641	NM_000268.3	587	tCc/tTc	16/16	1	2	FACETS	0.884	0.791	0.983	0.884	0.791	0.983	CLONAL	1	TRUE	1	0.260615560275889	2		764	912	SUCCESS
WWTR1	25937	MSKCC	GRCh37	3	149374688	149374689	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	777	181	723	1	ENST00000360632.3:c.405_406delinsAA	p.Ala136Thr	p.A136T	ENST00000360632	NM_015472.4	135	acGGcc/acAAcc	2/7	0.254876588018056	3	FACETS	0.819	0.756	0.886	0.819	0.756	0.886	CLONAL	2	TRUE	1	0.260615560275889	3		724	958	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66217251	66217251	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1281456118	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	490	61	547	0	ENST00000273854.3:c.2364G>A	p.Met788Ile	p.M788I	ENST00000273854	NM_004439.5	788	atG/atA	14/18	1	2	FACETS	0.85	0.733	0.976	0.85	0.733	0.976	CLONAL	1	TRUE	1	0.260615560275889	2		547	551	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56178575	56178575	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	440	60	367	2	ENST00000399503.3:c.3548C>T	p.Ala1183Val	p.A1183V	ENST00000399503	NM_005921.1	1183	gCt/gTt	14/20	1	2	FACETS	0.921	0.795	1	0.921	0.795	1	CLONAL	1	TRUE	1	0.260615560275889	2		369	500	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149502618	149502618	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	264	39	324	0	ENST00000261799.4:c.2170C>T	p.Leu724Phe	p.L724F	ENST00000261799	NM_002609.3	724	Ctc/Ttc	15/23	1	2	FACETS	0.988	0.822	1	0.988	0.822	1	CLONAL	1	TRUE	1	0.260615560275889	2		324	303	SUCCESS
H3C7	8968	MSKCC	GRCh37	6	26250542	26250542	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	67	508	0	ENST00000446824.2:c.292G>A	p.Glu98Lys	p.E98K	ENST00000446824	NM_021018.2	98	Gag/Aag	1/1	1	2	FACETS	0.882	0.767	1	0.882	0.767	1	CLONAL	1	TRUE	1	0.260615560275889	2		508	583	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117609905	117609905	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	107	846	0	ENST00000368508.3:c.6794A>G	p.Glu2265Gly	p.E2265G	ENST00000368508	NM_002944.2	2265	gAa/gGa	43/43	1	2	FACETS	0.831	0.744	0.924	0.831	0.744	0.924	CLONAL	1	TRUE	1	0.260615560275889	2		846	988	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157527929	157527929	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	827	106	755	0	ENST00000346085.5:c.5654C>T	p.Pro1885Leu	p.P1885L	ENST00000346085	NM_020732.3	1885	cCa/cTa	20/20	1	2	FACETS	0.872	0.78	0.969	0.872	0.78	0.969	CLONAL	1	TRUE	1	0.260615560275889	2		755	933	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509536	106509536	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	941	125	799	2	ENST00000359195.3:c.1530G>T	p.Lys510Asn	p.K510N	ENST00000359195	NM_002649.2	510	aaG/aaT	2/11	1	2	FACETS	0.9	0.813	0.992	0.9	0.813	0.992	CLONAL	1	TRUE	1	0.260615560275889	2		801	1066	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395192	139395192	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	124	841	0	ENST00000277541.6:c.5746C>T	p.Gln1916Ter	p.Q1916*	ENST00000277541	NM_017617.3	1916	Cag/Tag	31/34	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.260615560275889	2		841	935	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139396735	139396736	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	94	695	3	ENST00000277541.6:c.5372_5373delinsTT	p.Ser1791Phe	p.S1791F	ENST00000277541	NM_017617.3	1791	tCC/tTT	28/34	1	2	FACETS	0.88	0.782	0.984	0.88	0.782	0.984	CLONAL	1	TRUE	1	0.260615560275889	2		698	820	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412240	139412240	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	808	105	743	0	ENST00000277541.6:c.1405G>T	p.Asp469Tyr	p.D469Y	ENST00000277541	NM_017617.3	469	Gac/Tac	8/34	1	2	FACETS	0.883	0.79	0.981	0.883	0.79	0.981	CLONAL	1	TRUE	1	0.260615560275889	2		743	913	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1321339	1321339	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018172-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	110	775	0	ENST00000400841.2:c.416C>T	p.Ser139Phe	p.S139F	ENST00000400841		139	tCt/tTt	4/6	1	1	FACETS	0.839	0.753	0.93	0.839	0.753	0.93	CLONAL	1	TRUE	0	0.260615560275889	1		775	875	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971186	21971186	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs121913387	NA	P-0018177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	25	380	0	ENST00000304494.5:c.172C>T	p.Arg58Ter	p.R58*	ENST00000304494	NM_000077.4	58	Cga/Tga	2/3	0.3	1	FACETS	0.489	0.386	0.608	0.489	0.386	0.608	SUBCLONAL	1	TRUE	0	0.28	1		380	314	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7577120	7577120	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs28934576	NA	P-0018177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	154	633	0	ENST00000269305.4:c.818G>A	p.Arg273His	p.R273H	ENST00000269305	NM_001126112.2	273	cGt/cAt	8/11	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.28	2		633	747	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	T	novel	NA	P-0018177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	282	28	230	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.645	0.516	0.791	0.645	0.516	0.791	SUBCLONAL	1	TRUE	1	0.28	2		230	310	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149439282	149439282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766586864	NA	P-0018177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	546	51	671	1	ENST00000286301.3:c.2113G>A	p.Glu705Lys	p.E705K	ENST00000286301	NM_005211.3	705	Gag/Aag	15/22	1	2	FACETS	0.61	0.518	0.711	0.61	0.518	0.711	SUBCLONAL	1	TRUE	1	0.28	2		672	597	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139412372	139412372	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018177-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	42	492	3	ENST00000277541.6:c.1273C>T	p.His425Tyr	p.H425Y	ENST00000277541	NM_017617.3	425	Cat/Tat	8/34	0.3	1	FACETS	0.729	0.61	0.86	0.729	0.61	0.86	SUBCLONAL	1	TRUE	0	0.28	1		495	354	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	212	53	215	0				ENST00000310581	NM_198253.2	-/1132			0.259119642179414	1	FACETS	1	0.959	1	1	0.959	1	CLONAL	1	TRUE	0	0.259119642179414	1		215	265	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21971099	21971099	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749714198	NA	P-0018185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	304	108	606	0	ENST00000304494.5:c.259C>T	p.Arg87Trp	p.R87W	ENST00000304494	NM_000077.4	87	Cgg/Tgg	2/3	0.259119642179414	2	FACETS	1	0.914	1	1	0.914	1	CLONAL	2	TRUE	0	0.259119642179414	2		606	412	SUCCESS
TP53	7157	MSKCC	GRCh37	17	7576852	7576852	+	splice_donor_variant	Splice_Site	SNP	C	C	G	rs11575997	NA	P-0018185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	191	807	0	ENST00000269305.4:c.993+1G>C		p.X331_splice	ENST00000269305	NM_001126112.2	331			NA	2	FACETS	1	0.981	1			1	INDETERMINATE	2	TRUE	NA	0.259119642179414	2		807	639	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66286244	66286244	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018185-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	48	716	2	ENST00000273854.3:c.1442C>T	p.Ala481Val	p.A481V	ENST00000273854	NM_004439.5	481	gCa/gTa	6/18	1	2	FACETS	0.684	0.578	0.8	0.684	0.578	0.8	SUBCLONAL	1	TRUE	1	0.259119642179414	2		718	542	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55161362	55161362	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs369389595	NA	P-0018187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	46	688	0	ENST00000257290.5:c.3193G>A	p.Glu1065Lys	p.E1065K	ENST00000257290	NM_006206.4	1065	Gag/Aag	23/23	1	2	FACETS	0.79	0.664	0.931	0.79	0.664	0.931	CLONAL	1	TRUE	1	0.15	2		688	776	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140477854	140477854	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	94	760	0	ENST00000288602.6:c.1454T>G	p.Leu485Trp	p.L485W	ENST00000288602	NM_004333.4	485	tTg/tGg	12/18	1	2	FACETS	1	0.977	1	1	0.977	1	CLONAL	1	TRUE	1	0.15	2		760	886	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106509637	106509637	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766453335	NA	P-0018187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	774	52	700	3	ENST00000359195.3:c.1631G>A	p.Arg544Gln	p.R544Q	ENST00000359195	NM_002649.2	544	cGa/cAa	2/11	1	2	FACETS	0.839	0.713	0.979	0.839	0.713	0.979	CLONAL	1	TRUE	1	0.15	2		703	826	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55979551	55979551	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs375035755	NA	P-0018187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	881	49	757	2	ENST00000263923.4:c.896G>A	p.Arg299Gln	p.R299Q	ENST00000263923	NM_002253.2	299	cGg/cAg	7/30	1	2	FACETS	0.703	0.593	0.824	0.703	0.593	0.824	SUBCLONAL	1	TRUE	1	0.15	2		759	930	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7979527	7979527	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1064796312	NA	P-0018187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	727	39	831	2	ENST00000319144.4:c.1498G>A	p.Asp500Asn	p.D500N	ENST00000319144	NM_001139.2	500	Gat/Aat	11/15	1	2	FACETS	0.679	0.561	0.811	0.679	0.561	0.811	SUBCLONAL	1	TRUE	1	0.15	2		833	766	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15272132	15272132	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	799	51	816	0	ENST00000263388.2:c.6307G>A	p.Asp2103Asn	p.D2103N	ENST00000263388	NM_000435.2	2103	Gac/Aac	33/33	1	2	FACETS	0.8	0.678	0.935	0.8	0.678	0.935	CLONAL	1	TRUE	1	0.15	2		816	850	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435093	56435093	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1304658474	NA	P-0018187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	687	46	640	0	ENST00000407977.2:c.2044C>T	p.Pro682Ser	p.P682S	ENST00000407977		682	Ccc/Tcc	9/10	1	2	FACETS	0.837	0.703	0.985	0.837	0.703	0.985	CLONAL	1	TRUE	1	0.15	2		640	733	SUCCESS
AKT2	208	MSKCC	GRCh37	19	40762857	40762857	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	40	724	0	ENST00000392038.2:c.151C>T	p.Pro51Ser	p.P51S	ENST00000392038	NM_001626.4	51	Ccc/Tcc	3/14	1	2	FACETS	0.709	0.588	0.846	0.709	0.588	0.846	SUBCLONAL	1	TRUE	1	0.15	2		724	752	SUCCESS
AXL	558	MSKCC	GRCh37	19	41763447	41763447	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	41	734	1	ENST00000301178.4:c.2246C>T	p.Pro749Leu	p.P749L	ENST00000301178	NM_021913.4	749	cCa/cTa	19/20	1	2	FACETS	0.745	0.619	0.886	0.745	0.619	0.886	SUBCLONAL	1	TRUE	1	0.15	2		735	734	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31022350	31022351	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0018187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	46	402	1	ENST00000375687.4:c.1835_1836delinsAA	p.Arg612Lys	p.R612K	ENST00000375687	NM_015338.5	612	aGG/aAA	13/13	1	2	FACETS	1	0.932	1	1	0.932	1	CLONAL	1	TRUE	1	0.15	2		403	507	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444289	50444289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	34	361	1	ENST00000331340.3:c.219G>A	p.Met73Ile	p.M73I	ENST00000331340	NM_006060.4	73	atG/atA	4/8	1	2	FACETS	0.877	0.716	1	0.877	0.716	1	CLONAL	1	TRUE	1	0.15	2		362	517	SUCCESS
MET	4233	MSKCC	GRCh37	7	116413663	116413663	+	intron_variant	Intron	SNP	G	G	A	novel	NA	P-0018187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1082	165	1031	1	ENST00000397752.3:c.3029-1272G>A		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.882	0.808	0.96	1	0.991	1	CLONAL	2	TRUE	1	0.15	2		1032	1247	SUCCESS
MET	4233	MSKCC	GRCh37	7	116413672	116413672	+	intron_variant	Intron	SNP	G	G	A	novel	NA	P-0018187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1235	47	1043	1	ENST00000397752.3:c.3029-1263G>A		p.*1010*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	0.489	0.41	0.576	0.489	0.41	0.576	SUBCLONAL	1	TRUE	1	0.15	2		1044	1282	SUCCESS
CRLF2	64109	MSKCC	GRCh37	X	1314972	1314972	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372481844	NA	P-0018187-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	868	52	755	0	ENST00000400841.2:c.689C>T	p.Ser230Phe	p.S230F	ENST00000400841		230	tCc/tTc	6/6	1	1	FACETS	0.697	0.592	0.814	0.697	0.592	0.814	SUBCLONAL	1	TRUE	0	0.15	1		755	920	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244092	153244092	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	553	212	513	0	ENST00000281708.4:c.2065C>T	p.Arg689Trp	p.R689W	ENST00000281708	NM_033632.3	689	Cgg/Tgg	12/12	1	2	FACETS	1	0.97	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		513	765	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589618	67589618	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1057519838	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	405	136	494	1	ENST00000274335.5:c.1381C>T	p.Arg461Ter	p.R461*	ENST00000274335		461	Cga/Tga	10/15	1	2	FACETS	0.972	0.888	1	1	0.99	1	CLONAL	2	TRUE	1	0.258652869545824	2		495	541	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11141507	11141507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	241	689	2	ENST00000358026.2:c.3484G>A	p.Gly1162Ser	p.G1162S	ENST00000358026	NM_001128849.1	1162	Ggc/Agc	25/36	1	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		691	804	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600407	10600407	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867398451	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	378	803	4	ENST00000171111.5:c.1448G>A	p.Arg483His	p.R483H	ENST00000171111	NM_203500.1	483	cGc/cAc	4/6	1	2	FACETS	0.837	0.795	0.88	1	0.997	1	CLONAL	3	TRUE	1	0.258652869545824	2		807	1164	SUCCESS
MPL	4352	MSKCC	GRCh37	1	43803899	43803899	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61754776	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	157	472	0	ENST00000372470.3:c.209C>T	p.Pro70Leu	p.P70L	ENST00000372470	NM_005373.2	70	cCg/cTg	2/12	1	2	FACETS	1	0.978	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		472	523	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589168	67589168	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	349	105	352	0	ENST00000274335.5:c.1156C>T	p.Arg386Ter	p.R386*	ENST00000274335		386	Cga/Tga	9/15	1	2	FACETS	0.894	0.806	0.987	1	0.987	1	CLONAL	2	TRUE	1	0.258652869545824	2		352	454	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187549764	187549764	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	160	398	0	ENST00000441802.2:c.4477C>G	p.Leu1493Val	p.L1493V	ENST00000441802	NM_005245.3	1493	Ctg/Gtg	8/27	1	2	FACETS	1	0.971	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		398	557	SUCCESS
AURKB	9212	MSKCC	GRCh37	17	8110524	8110524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1322292985	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	175	441	0	ENST00000585124.1:c.368G>A	p.Arg123His	p.R123H	ENST00000585124	NM_004217.3	123	cGc/cAc	5/9	1	2	FACETS	1	0.972	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		441	614	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67660469	67660469	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	136	361	0	ENST00000264010.4:c.1369C>T	p.Arg457Ter	p.R457*	ENST00000264010	NM_006565.3	457	Cga/Tga	8/12	1	2	FACETS	1	0.96	1	1	0.991	1	CLONAL	2	TRUE	1	0.258652869545824	2		361	486	SUCCESS
ARID2	196528	MSKCC	GRCh37	12	46205332	46205332	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	501	156	458	0	ENST00000334344.6:c.416C>T	p.Ser139Leu	p.S139L	ENST00000334344	NM_152641.2	139	tCg/tTg	4/21	1	2	FACETS	0.918	0.843	0.995	1	0.991	1	CLONAL	2	TRUE	1	0.258652869545824	2		458	657	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47039641	47039641	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	726	278	798	0	ENST00000377604.3:c.1093G>A	p.Ala365Thr	p.A365T	ENST00000377604	NM_001204468.1	365	Gcc/Acc	11/24	1	2	FACETS	1	0.976	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		798	1004	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38967279	38967279	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs746828213	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	231	502	0	ENST00000357387.3:c.1202G>A	p.Arg401His	p.R401H	ENST00000357387	NM_152756.3	401	cGt/cAt	14/38	1	2	FACETS	1	0.98	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		502	801	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	26068357	26068357	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	560	190	551	0	ENST00000435504.4:c.133G>T	p.Glu45Ter	p.E45*	ENST00000435504		45	Gaa/Taa	2/13	1	2	FACETS	0.979	0.908	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		551	750	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32914483	32914483	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	90	712	0	ENST00000380152.3:c.5991A>C	p.Arg1997Ser	p.R1997S	ENST00000380152		1997	agA/agC	11/27	1	2	FACETS	0.862	0.764	0.967	0.862	0.764	0.967	CLONAL	1	TRUE	1	0.258652869545824	2		712	807	SUCCESS
GNAS	2778	MSKCC	GRCh37	20	57478633	57478633	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1131691999	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	248	619	1	ENST00000371085.3:c.305C>T	p.Ala102Val	p.A102V	ENST00000371085	NM_000516.4	102	gCg/gTg	4/13	1	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		620	828	SUCCESS
AXIN1	8312	MSKCC	GRCh37	16	339599	339599	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs138816818	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	245	551	2	ENST00000262320.3:c.2303C>T	p.Ser768Leu	p.S768L	ENST00000262320	NM_003502.3	768	tCg/tTg	10/11	1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		553	800	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31383307	31383307	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs148646143	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	629	260	627	0	ENST00000328111.2:c.1219G>A	p.Gly407Ser	p.G407S	ENST00000328111	NM_006892.3	407	Ggc/Agc	11/23	1	2	FACETS	1	0.983	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		627	889	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28608039	28608039	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762198688	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	545	225	640	2	ENST00000241453.7:c.1927G>A	p.Val643Ile	p.V643I	ENST00000241453	NM_004119.2	643	Gtc/Atc	15/24	1	2	FACETS	1	0.981	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		642	770	SUCCESS
NKX3-1	4824	MSKCC	GRCh37	8	23539105	23539105	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	163	458	3	ENST00000380871.4:c.334G>A	p.Ala112Thr	p.A112T	ENST00000380871	NM_006167.3	112	Gcc/Acc	2/2	1	2	FACETS	1	0.965	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		461	584	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345913	70345913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749801457	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	200	555	0	ENST00000374080.3:c.2450G>A	p.Arg817His	p.R817H	ENST00000374080		817	cGc/cAc	18/45	1	2	FACETS	1	0.978	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		555	689	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52725412	52725412	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs770194852	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	585	214	624	1	ENST00000322088.6:c.1579C>T	p.Arg527Cys	p.R527C	ENST00000322088	NM_014225.5	527	Cgc/Tgc	13/15	1	2	FACETS	1	0.957	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		625	799	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8636818	8636818	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146973770	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	158	513	1	ENST00000356435.5:c.91G>A	p.Val31Ile	p.V31I	ENST00000356435		31	Gtt/Att	2/35	1	2	FACETS	1	0.931	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		514	603	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155972	119155972	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs751274314	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	300	801	3	ENST00000264033.4:c.1637C>T	p.Pro546Leu	p.P546L	ENST00000264033	NM_005188.3	546	cCg/cTg	11/16	1	2	FACETS	1	0.968	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		804	1114	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9858403	9858403	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	141	406	0	ENST00000330684.3:c.2998G>A	p.Val1000Met	p.V1000M	ENST00000330684	NM_001134407.1	1000	Gtg/Atg	13/13	1	2	FACETS	1	0.963	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		406	500	SUCCESS
RB1	5925	MSKCC	GRCh37	13	49030456	49030456	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	660	272	650	2	ENST00000267163.4:c.1931C>A	p.Ser644Tyr	p.S644Y	ENST00000267163	NM_000321.2	644	tCt/tAt	19/27	1	2	FACETS	1	0.984	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		652	932	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1218483	1218483	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775595174	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	707	308	692	2	ENST00000326873.7:c.358G>A	p.Glu120Lys	p.E120K	ENST00000326873	NM_000455.4	120	Gaa/Aaa	2/10	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		694	1015	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944264	81944264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1009796025	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	290	599	0	ENST00000359376.3:c.1873G>A	p.Ala625Thr	p.A625T	ENST00000359376	NM_002661.3	625	Gcc/Acc	18/33	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		599	940	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133226041	133226041	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373170535	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	227	631	3	ENST00000320574.5:c.3856C>T	p.Arg1286Cys	p.R1286C	ENST00000320574	NM_006231.2	1286	Cgc/Tgc	31/49	1	2	FACETS	1	0.953	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		634	855	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98232138	98232138	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs863224650	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	666	236	674	2	ENST00000331920.6:c.1804C>T	p.Arg602Ter	p.R602*	ENST00000331920	NM_000264.3	602	Cga/Tga	13/24	1	2	FACETS	1	0.944	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		676	902	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	15938195	15938195	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	171	531	0	ENST00000268712.3:c.7019C>A	p.Pro2340His	p.P2340H	ENST00000268712	NM_006311.3	2340	cCt/cAt	45/46	1	2	FACETS	0.978	0.903	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		531	676	SUCCESS
GATA3	2625	MSKCC	GRCh37	10	8100727	8100728	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs771019738	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	187	728	2	ENST00000346208.3:c.708dup	p.Ser237GlnfsTer66	p.S237Qfs*66	ENST00000346208		234	ttc/ttCc	3/6	1	2	FACETS	0.815	0.753	0.879	1	0.991	1	CLONAL	2	TRUE	1	0.258652869545824	2		730	887	SUCCESS
SDHAF2	54949	MSKCC	GRCh37	11	61205157	61205157	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs144867876	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	278	792	3	ENST00000301761.2:c.97C>T	p.Arg33Cys	p.R33C	ENST00000301761	NM_017841.2	33	Cgc/Tgc	2/4	1	2	FACETS	1	0.971	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		795	1019	SUCCESS
PAK5	57144	MSKCC	GRCh37	20	9560913	9560913	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559720359	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	182	334	0	ENST00000353224.5:c.869C>T	p.Ser290Leu	p.S290L	ENST00000353224	NM_177990.2	290	tCg/tTg	4/10	1	2	FACETS	0.847	0.786	0.909	1	0.994	1	CLONAL	3	TRUE	1	0.258652869545824	2		334	554	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39911441	39911441	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	613	242	613	1	ENST00000378444.4:c.5189C>T	p.Thr1730Met	p.T1730M	ENST00000378444	NM_001123385.1	1730	aCg/aTg	15/15	1	2	FACETS	1	0.978	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		614	855	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29486112	29486112	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	126	445	0	ENST00000356175.3:c.288+1G>A		p.X96_splice	ENST00000356175	NM_000267.3	96			1	2	FACETS	1	0.939	1	1	0.99	1	CLONAL	2	TRUE	1	0.258652869545824	2		445	469	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7989406	7989406	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs8077661	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	615	290	686	2	ENST00000319144.4:c.280G>A	p.Gly94Ser	p.G94S	ENST00000319144	NM_001139.2	94	Ggc/Agc	2/15	1	2	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		688	905	SUCCESS
H3C12	8968	MSKCC	GRCh37	6	27858476	27858476	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs766861086	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	237	76	250	1	ENST00000359303.2:c.95C>T	p.Ala32Val	p.A32V	ENST00000359303	NM_003535.2	32	gCg/gTg	1/1	1	2	FACETS	0.939	0.831	1	1	0.983	1	CLONAL	2	TRUE	1	0.258652869545824	2		251	313	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133249847	133249847	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	444	184	514	0	ENST00000320574.5:c.1376C>T	p.Ser459Phe	p.S459F	ENST00000320574	NM_006231.2	459	tCt/tTt	14/49	1	2	FACETS	1	0.978	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		514	628	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72993740	72993740	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371536462	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	390	59	349	1	ENST00000268489.5:c.305C>T	p.Ala102Val	p.A102V	ENST00000268489	NM_006885.3	102	gCg/gTg	2/10	1	2	FACETS	1	0.875	1	1	0.875	1	CLONAL	1	TRUE	1	0.258652869545824	2		350	449	SUCCESS
SDHA	6389	MSKCC	GRCh37	5	251542	251542	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs200397144	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	186	504	2	ENST00000264932.6:c.1753C>T	p.Arg585Trp	p.R585W	ENST00000264932	NM_004168.2	585	Cgg/Tgg	13/15	1	2	FACETS	1	0.973	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		506	654	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48027043	48027043	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1553413305	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	145	375	0	ENST00000234420.5:c.1921G>T	p.Glu641Ter	p.E641*	ENST00000234420	NM_000179.2	641	Gaa/Taa	4/10	1	2	FACETS	1	0.97	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		375	501	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48033753	48033753	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	rs1553333707	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	159	233	0	ENST00000234420.5:c.3964G>T	p.Glu1322Ter	p.E1322*	ENST00000234420	NM_000179.2	1322	Gaa/Taa	9/10	1	2	FACETS	0.97	0.892	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		233	634	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70446203	70446203	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	154	535	0	ENST00000373644.4:c.5143G>T	p.Asp1715Tyr	p.D1715Y	ENST00000373644	NM_030625.2	1715	Gac/Tac	11/12	1	2	FACETS	0.954	0.877	1	1	0.991	1	CLONAL	2	TRUE	1	0.258652869545824	2		535	624	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30670957	30670957	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs868678495	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	285	767	2	ENST00000376406.3:c.5789G>A	p.Arg1930His	p.R1930H	ENST00000376406	NM_014641.2	1930	cGc/cAc	12/15	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		769	935	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674233	86674233	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs1463885690	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	395	139	468	0	ENST00000274376.6:c.2365C>T	p.Arg789Ter	p.R789*	ENST00000274376	NM_002890.2	789	Cga/Tga	18/25	1	2	FACETS	1	0.921	1	1	0.991	1	CLONAL	2	TRUE	1	0.258652869545824	2		468	534	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66280061	66280061	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1254027522	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	97	367	1	ENST00000273854.3:c.1628G>A	p.Arg543His	p.R543H	ENST00000273854	NM_004439.5	543	cGt/cAt	7/18	1	2	FACETS	0.826	0.74	0.916	1	0.984	1	CLONAL	2	TRUE	1	0.258652869545824	2		368	454	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98240450	98240450	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs370354759	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	142	371	0	ENST00000331920.6:c.1234G>A	p.Ala412Thr	p.A412T	ENST00000331920	NM_000264.3	412	Gca/Aca	9/24	1	2	FACETS	0.972	0.89	1	1	0.991	1	CLONAL	2	TRUE	1	0.258652869545824	2		371	565	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30672423	30672423	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs370120921	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	146	482	0	ENST00000376406.3:c.4537C>T	p.Arg1513Trp	p.R1513W	ENST00000376406	NM_014641.2	1513	Cgg/Tgg	10/15	1	2	FACETS	0.897	0.822	0.976	1	0.99	1	CLONAL	2	TRUE	1	0.258652869545824	2		482	629	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76972711	76972711	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	524	152	487	0	ENST00000373344.5:c.30G>C	p.Lys10Asn	p.K10N	ENST00000373344	NM_000489.3	10	aaG/aaC	2/35	1	2	FACETS	0.869	0.797	0.944	1	0.99	1	CLONAL	2	TRUE	1	0.258652869545824	2		487	676	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117638353	117638353	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	192	543	1	ENST00000368508.3:c.6088G>T	p.Glu2030Ter	p.E2030*	ENST00000368508	NM_002944.2	2030	Gag/Tag	38/43	1	2	FACETS	1	0.959	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		544	709	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755470	39755470	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	134	379	2	ENST00000288319.7:c.1295C>T	p.Ala432Val	p.A432V	ENST00000288319	NM_182918.3	432	gCg/gTg	10/10	1	2	FACETS	1	0.97	1	1	0.991	1	CLONAL	2	TRUE	1	0.258652869545824	2		381	459	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53247070	53247070	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	236	776	0	ENST00000375401.3:c.430C>T	p.Pro144Ser	p.P144S	ENST00000375401	NM_004187.3	144	Cca/Tca	4/26	1	2	FACETS	1	0.969	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		776	860	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86685312	86685312	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	145	76	150	0	ENST00000274376.6:c.3028C>T	p.Arg1010Ter	p.R1010*	ENST00000274376	NM_002890.2	1010	Cga/Tga	24/25	1	2	FACETS	0.886	0.791	0.985	1	0.987	1	CLONAL	3	TRUE	1	0.258652869545824	2		150	221	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508517	106508517	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs549157001	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	166	70	156	0	ENST00000359195.3:c.511G>A	p.Asp171Asn	p.D171N	ENST00000359195	NM_002649.2	171	Gat/Aat	2/11	1	2	FACETS	1	0.951	1	1	0.984	1	CLONAL	2	TRUE	1	0.258652869545824	2		156	236	SUCCESS
ATM	472	MSKCC	GRCh37	11	108186742	108186742	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs532480170	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	529	218	663	1	ENST00000278616.4:c.6100C>T	p.Arg2034Ter	p.R2034*	ENST00000278616	NM_000051.3	2034	Cga/Tga	42/63	1	2	FACETS	1	0.98	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		664	747	SUCCESS
ABL1	25	MSKCC	GRCh37	9	133760066	133760066	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1459798133	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	979	66	796	0	ENST00000318560.5:c.2389G>A	p.Val797Ile	p.V797I	ENST00000318560	NM_005157.4	797	Gtc/Atc	11/11	1	2	FACETS	0.488	0.422	0.56	0.488	0.422	0.56	SUBCLONAL	1	TRUE	1	0.258652869545824	2		796	1045	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11303193	11303193	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	179	519	0	ENST00000361445.4:c.1390C>T	p.Pro464Ser	p.P464S	ENST00000361445	NM_004958.3	464	Ccc/Tcc	9/58	1	2	FACETS	1	0.925	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		519	692	SUCCESS
NCOA3	8202	MSKCC	GRCh37	20	46256425	46256425	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1200320359	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	186	566	0	ENST00000371998.3:c.653G>A	p.Arg218His	p.R218H	ENST00000371998		218	cGc/cAc	7/23	1	2	FACETS	1	0.95	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		566	697	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139405696	139405696	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs559917218	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	894	349	966	8	ENST00000277541.6:c.2495C>T	p.Pro832Leu	p.P832L	ENST00000277541	NM_017617.3	832	cCg/cTg	16/34	1	2	FACETS	1	0.983	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		974	1243	SUCCESS
ASXL2	55252	MSKCC	GRCh37	2	25982386	25982386	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	143	299	0	ENST00000435504.4:c.904C>T	p.Arg302Ter	p.R302*	ENST00000435504		302	Cga/Tga	9/13	1	2	FACETS	1	0.975	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		299	478	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32168933	32168933	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs979783685	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	217	744	0	ENST00000375023.3:c.4100C>T	p.Thr1367Met	p.T1367M	ENST00000375023	NM_004557.3	1367	aCg/aTg	22/30	1	2	FACETS	0.841	0.782	0.902	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		744	998	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106190858	106190858	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	158	460	3	ENST00000380013.4:c.4136C>T	p.Ala1379Val	p.A1379V	ENST00000380013	NM_001127208.2	1379	gCt/gTt	9/11	1	2	FACETS	1	0.948	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		463	588	SUCCESS
BCL10	8915	MSKCC	GRCh37	1	85736474	85736474	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	465	227	488	0	ENST00000370580.1:c.173G>A	p.Arg58Gln	p.R58Q	ENST00000370580	NM_003921.4	58	cGa/cAa	2/3	1	2	FACETS	0.845	0.791	0.901	1	0.995	1	CLONAL	3	TRUE	1	0.258652869545824	2		488	692	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15280904	15280904	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1251693132	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	634	246	759	2	ENST00000263388.2:c.5192G>A	p.Arg1731Gln	p.R1731Q	ENST00000263388	NM_000435.2	1731	cGg/cAg	28/33	1	2	FACETS	1	0.975	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		761	880	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67589017	67589017	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	241	95	285	0	ENST00000274335.5:c.1108C>T	p.Leu370Phe	p.L370F	ENST00000274335		370	Ctt/Ttt	8/15	1	2	FACETS	1	0.95	1	1	0.988	1	CLONAL	2	TRUE	1	0.258652869545824	2		285	336	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163307846	163307846	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61747498	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	184	569	0	ENST00000271452.3:c.472G>A	p.Ala158Thr	p.A158T	ENST00000271452	NM_145697.2	158	Gca/Aca	7/14	0.258652869545824	1	FACETS	1	0.975	1	1	0.994	1	CLONAL	2	TRUE	0	0.258652869545824	1		569	559	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101213	27101213	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	204	649	2	ENST00000324856.7:c.4495C>T	p.Gln1499Ter	p.Q1499*	ENST00000324856	NM_006015.4	1499	Cag/Tag	18/20	1	2	FACETS	1	0.96	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		651	754	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30673271	30673271	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	188	529	2	ENST00000376406.3:c.3689G>A	p.Gly1230Glu	p.G1230E	ENST00000376406	NM_014641.2	1230	gGa/gAa	10/15	1	2	FACETS	0.98	0.908	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		531	742	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23634308	23634308	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs61756146	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	810	329	875	0	ENST00000261584.4:c.2978C>T	p.Thr993Met	p.T993M	ENST00000261584	NM_024675.3	993	aCg/aTg	9/13	1	2	FACETS	1	0.985	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		875	1139	SUCCESS
PARP1	142	MSKCC	GRCh37	1	226574031	226574031	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201975538	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	84	340	0	ENST00000366794.5:c.830C>T	p.Ser277Leu	p.S277L	ENST00000366794	NM_001618.3	277	tCg/tTg	6/23	0.258652869545824	1	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	0	0.258652869545824	1		340	411	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1615742	1615742	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs201649703	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	591	311	675	2	ENST00000344749.5:c.1529C>T	p.Ala510Val	p.A510V	ENST00000344749	NM_001136139.2	510	gCg/gTg	17/19	1	2	FACETS	0.889	0.841	0.938	1	0.996	1	CLONAL	3	TRUE	1	0.258652869545824	2		677	902	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717712	89717712	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs587782350	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	246	533	2	ENST00000371953.3:c.737C>T	p.Pro246Leu	p.P246L	ENST00000371953	NM_000314.4	246	cCg/cTg	7/9	1	2	FACETS	0.904	0.85	0.96	1	0.996	1	CLONAL	3	TRUE	1	0.258652869545824	2		535	701	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110436696	110436696	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1297955422	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	841	327	958	2	ENST00000375856.3:c.1705C>T	p.Arg569Ter	p.R569*	ENST00000375856	NM_003749.2	569	Cga/Tga	1/2	1	2	FACETS	1	0.981	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		960	1168	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992764	68992764	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs769067107	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	670	237	864	2	ENST00000288368.4:c.1729C>T	p.Arg577Ter	p.R577*	ENST00000288368	NM_024870.2	577	Cga/Tga	16/40	1	2	FACETS	1	0.944	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		866	907	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212215	36212215	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1010777622	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	717	292	787	0	ENST00000222270.7:c.1966G>A	p.Glu656Lys	p.E656K	ENST00000222270	NM_014727.1	656	Gaa/Aaa	3/37	1	2	FACETS	1	0.984	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		787	1009	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411778	116411778	+	intron_variant	Intron	SNP	G	G	A	rs6978257	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1178	457	1186	1	ENST00000397752.3:c.2887+70G>A		p.*963*	ENST00000397752	NM_000245.2	-/1390			1	2	FACETS	1	0.986	1	1	0.997	1	CLONAL	2	TRUE	1	0.258652869545824	2		1187	1635	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8319934	8319934	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs764537367	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	157	403	0	ENST00000356435.5:c.5567C>T	p.Thr1856Met	p.T1856M	ENST00000356435		1856	aCg/aTg	34/35	1	2	FACETS	1	0.978	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		403	519	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112926960	112926960	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770363146	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	447	178	464	0	ENST00000351677.2:c.1580G>A	p.Arg527His	p.R527H	ENST00000351677	NM_002834.3	527	cGc/cAc	13/16	1	2	FACETS	1	0.972	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		464	625	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187630604	187630605	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	663	269	728	1	ENST00000441802.2:c.377dup	p.Asn126LysfsTer3	p.N126Kfs*3	ENST00000441802	NM_005245.3	126	aat/aaAt	2/27	1	2	FACETS	1	0.982	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		729	932	SUCCESS
PIK3CD	5293	MSKCC	GRCh37	1	9784478	9784478	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs1414657892	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	399	185	413	0	ENST00000377346.4:c.2863C>T	p.Arg955Trp	p.R955W	ENST00000377346	NM_005026.3	955	Cgg/Tgg	22/24	1	2	FACETS	1	0.985	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		413	584	SUCCESS
MTOR	2475	MSKCC	GRCh37	1	11175457	11175457	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	204	643	0	ENST00000361445.4:c.7085T>G	p.Phe2362Cys	p.F2362C	ENST00000361445	NM_004958.3	2362	tTt/tGt	51/58	1	2	FACETS	0.998	0.928	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		643	790	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16257360	16257360	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	624	283	629	0	ENST00000375759.3:c.4625G>A	p.Arg1542Gln	p.R1542Q	ENST00000375759	NM_015001.2	1542	cGa/cAa	11/15	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		629	907	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16264331	16264331	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	482	216	517	0	ENST00000375759.3:c.10534C>A	p.Leu3512Met	p.L3512M	ENST00000375759	NM_015001.2	3512	Ctg/Atg	13/15	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		517	698	SUCCESS
ID3	3399	MSKCC	GRCh37	1	23885881	23885881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	330	21	333	1	ENST00000374561.5:c.37G>A	p.Ala13Thr	p.A13T	ENST00000374561	NM_002167.4	13	Gcg/Acg	1/3	1	2	FACETS	0.463	0.356	0.587	0.463	0.356	0.587	SUBCLONAL	1	TRUE	1	0.258652869545824	2		334	351	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27057894	27057894	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	908	103	779	0	ENST00000324856.7:c.1602C>G	p.Tyr534Ter	p.Y534*	ENST00000324856	NM_006015.4	534	taC/taG	3/20	1	2	FACETS	0.788	0.703	0.878	0.788	0.703	0.878	SUBCLONAL	1	TRUE	1	0.258652869545824	2		779	1011	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36807433	36807433	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	195	607	1	ENST00000373129.3:c.1231C>T	p.Arg411Ter	p.R411*	ENST00000373129	NM_032017.1	411	Cga/Tga	12/12	1	2	FACETS	1	0.938	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		608	745	SUCCESS
STK40	83931	MSKCC	GRCh37	1	36809829	36809829	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	242	695	0	ENST00000373129.3:c.776C>T	p.Ala259Val	p.A259V	ENST00000373129	NM_032017.1	259	gCc/gTc	9/12	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		695	814	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36932272	36932272	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	540	225	609	0	ENST00000361632.4:c.2197C>T	p.Pro733Ser	p.P733S	ENST00000361632		733	Cca/Tca	16/16	1	2	FACETS	1	0.982	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		609	765	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36934819	36934819	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	512	206	558	1	ENST00000361632.4:c.1514C>G	p.Thr505Ser	p.T505S	ENST00000361632		505	aCt/aGt	11/16	1	2	FACETS	1	0.977	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		559	718	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36937160	36937160	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	242	628	1	ENST00000361632.4:c.1159C>A	p.Leu387Ile	p.L387I	ENST00000361632		387	Ctc/Atc	9/16	1	2	FACETS	1	0.983	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		629	824	SUCCESS
CSF3R	1441	MSKCC	GRCh37	1	36939401	36939401	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	547	178	592	0	ENST00000361632.4:c.449C>T	p.Thr150Ile	p.T150I	ENST00000361632		150	aCc/aTc	4/16	1	2	FACETS	0.949	0.877	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		592	725	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305298	39305298	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	755	331	845	0	ENST00000373001.3:c.1127G>C	p.Ser376Thr	p.S376T	ENST00000373001	NM_022157.3	376	aGc/aCc	7/7	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		845	1086	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39325282	39325282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1266744229	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	425	206	554	2	ENST00000373001.3:c.37G>A	p.Ala13Thr	p.A13T	ENST00000373001	NM_022157.3	13	Gcc/Acc	1/7	1	2	FACETS	0.841	0.785	0.899	1	0.995	1	CLONAL	3	TRUE	1	0.258652869545824	2		556	631	SUCCESS
MUTYH	4595	MSKCC	GRCh37	1	45796880	45796880	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1441591597	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	90	570	0	ENST00000450313.1:c.1450G>A	p.Ala484Thr	p.A484T	ENST00000450313	NM_012222.2	484	Gca/Aca	14/16	1	2	FACETS	0.849	0.752	0.952	0.849	0.752	0.952	CLONAL	1	TRUE	1	0.258652869545824	2		570	820	SUCCESS
PIK3R3	8503	MSKCC	GRCh37	1	46509413	46509413	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs772733484	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	194	485	0	ENST00000262741.5:c.1318C>T	p.His440Tyr	p.H440Y	ENST00000262741	NM_003629.3	440	Cac/Tac	10/10	1	2	FACETS	1	0.961	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		485	713	SUCCESS
RAD54L	8438	MSKCC	GRCh37	1	46727002	46727002	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1363172157	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	552	171	529	1	ENST00000371975.4:c.836G>A	p.Arg279His	p.R279H	ENST00000371975	NM_003579.3	279	cGc/cAc	8/18	1	2	FACETS	0.914	0.843	0.988	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		530	723	SUCCESS
FUBP1	8880	MSKCC	GRCh37	1	78432573	78432573	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	140	528	0	ENST00000370768.2:c.410C>A	p.Ala137Asp	p.A137D	ENST00000370768	NM_003902.3	137	gCt/gAt	6/20	1	2	FACETS	0.872	0.796	0.95	1	0.989	1	CLONAL	2	TRUE	1	0.258652869545824	2		528	621	SUCCESS
VTCN1	79679	MSKCC	GRCh37	1	117699442	117699442	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	232	632	0	ENST00000369458.3:c.199A>G	p.Ile67Val	p.I67V	ENST00000369458	NM_024626.3	67	Atc/Gtc	3/6	1	2	FACETS	1	0.98	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		632	801	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120458131	120458131	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1399142103	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	367	159	431	0	ENST00000256646.2:c.7214G>C	p.Ser2405Thr	p.S2405T	ENST00000256646	NM_024408.3	2405	aGt/aCt	34/34	1	2	FACETS	1	0.979	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		431	526	SUCCESS
NOTCH2	4853	MSKCC	GRCh37	1	120461945	120461945	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	262	97	278	0	ENST00000256646.2:c.5771G>C	p.Gly1924Ala	p.G1924A	ENST00000256646	NM_024408.3	1924	gGt/gCt	31/34	1	2	FACETS	1	0.931	1	1	0.988	1	CLONAL	2	TRUE	1	0.258652869545824	2		278	359	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162748474	162748474	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	332	176	357	0	ENST00000367921.3:c.2388G>C	p.Gln796His	p.Q796H	ENST00000367921	NM_006182.2	796	caG/caC	17/18	0.258652869545824	1	FACETS	1	0.981	1	1	0.994	1	CLONAL	2	TRUE	0	0.258652869545824	1		357	508	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163317623	163317623	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747173543	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	174	628	0	ENST00000271452.3:c.1019C>T	p.Ser340Leu	p.S340L	ENST00000271452	NM_145697.2	340	tCg/tTg	12/14	0.258652869545824	1	FACETS	1	0.964	1	1	0.993	1	CLONAL	2	TRUE	0	0.258652869545824	1		628	549	SUCCESS
NUF2	83540	MSKCC	GRCh37	1	163318778	163318778	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs375173490	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	146	871	2	ENST00000271452.3:c.1168C>T	p.Arg390Ter	p.R390*	ENST00000271452	NM_145697.2	390	Cga/Tga	13/14	0.258652869545824	1	FACETS	1	0.984	1	1	0.984	1	CLONAL	1	TRUE	0	0.258652869545824	1		873	736	SUCCESS
CDC73	79577	MSKCC	GRCh37	1	193111134	193111134	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	344	82	464	0	ENST00000367435.3:c.667G>T	p.Asp223Tyr	p.D223Y	ENST00000367435	NM_024529.4	223	Gat/Tat	7/17	0.258652869545824	1	FACETS	1	0.97	1	1	0.97	1	CLONAL	1	TRUE	0	0.258652869545824	1		464	426	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204495525	204495525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	481	29	383	0	ENST00000367182.3:c.116C>T	p.Ala39Val	p.A39V	ENST00000367182	NM_001278516.1	39	gCa/gTa	3/11	0.258652869545824	1	FACETS	0.383	0.306	0.47	0.383	0.306	0.47	SUBCLONAL	1	TRUE	0	0.258652869545824	1		383	510	SUCCESS
MDM4	4194	MSKCC	GRCh37	1	204518482	204518482	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	350	154	398	0	ENST00000367182.3:c.1145A>G	p.Asn382Ser	p.N382S	ENST00000367182	NM_001278516.1	382	aAc/aGc	11/11	0.258652869545824	1	FACETS	1	0.943	1	1	0.992	1	CLONAL	2	TRUE	0	0.258652869545824	1		398	504	SUCCESS
IKBKE	9641	MSKCC	GRCh37	1	206658395	206658395	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	127	420	0	ENST00000367120.3:c.1489T>C	p.Ser497Pro	p.S497P	ENST00000367120	NM_014002.3	497	Tcc/Ccc	14/22	0.258652869545824	1	FACETS	0.919	0.839	1	1	0.989	1	CLONAL	2	TRUE	0	0.258652869545824	1		420	465	SUCCESS
IL10	3586	MSKCC	GRCh37	1	206943236	206943236	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs766492258	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	366	98	328	0	ENST00000423557.1:c.382C>T	p.Arg128Ter	p.R128*	ENST00000423557	NM_000572.2	128	Cga/Tga	4/5	0.258652869545824	1	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	0	0.258652869545824	1		328	464	SUCCESS
FH	2271	MSKCC	GRCh37	1	241667492	241667492	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766441385	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	281	88	275	1	ENST00000366560.3:c.958G>A	p.Ala320Thr	p.A320T	ENST00000366560	NM_000143.3	320	Gct/Act	7/10	0.258652869545824	1	FACETS	0.803	0.717	0.893	1	0.982	1	CLONAL	2	TRUE	0	0.258652869545824	1		276	369	SUCCESS
RET	5979	MSKCC	GRCh37	10	43606871	43606871	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	795	235	835	0	ENST00000355710.3:c.1480A>G	p.Arg494Gly	p.R494G	ENST00000355710	NM_020975.4	494	Agg/Ggg	7/20	1	2	FACETS	0.882	0.823	0.943	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		835	1030	SUCCESS
RET	5979	MSKCC	GRCh37	10	43614996	43614996	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs79658334	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	532	174	561	1	ENST00000355710.3:c.2410G>A	p.Val804Met	p.V804M	ENST00000355710	NM_020975.4	804	Gtg/Atg	14/20	1	2	FACETS	0.953	0.88	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		562	706	SUCCESS
ARID5B	84159	MSKCC	GRCh37	10	63829472	63829472	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	412	166	432	1	ENST00000279873.7:c.1115G>A	p.Arg372His	p.R372H	ENST00000279873	NM_032199.2	372	cGt/cAt	8/10	1	2	FACETS	1	0.972	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		433	578	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70332774	70332774	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	216	624	0	ENST00000373644.4:c.679C>G	p.Leu227Val	p.L227V	ENST00000373644	NM_030625.2	227	Cta/Gta	2/12	1	2	FACETS	1	0.955	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		624	809	SUCCESS
TET1	80312	MSKCC	GRCh37	10	70404513	70404513	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	274	582	3	ENST00000373644.4:c.2027G>T	p.Arg676Ile	p.R676I	ENST00000373644	NM_030625.2	676	aGa/aTa	4/12	1	2	FACETS	0.902	0.85	0.955	1	0.996	1	CLONAL	3	TRUE	1	0.258652869545824	2		585	783	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717666	89717666	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	183	647	0	ENST00000371953.3:c.691C>T	p.Pro231Ser	p.P231S	ENST00000371953	NM_000314.4	231	Ccc/Tcc	7/9	1	2	FACETS	0.906	0.838	0.977	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		647	781	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123263318	123263318	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	368	159	423	0	ENST00000358487.5:c.1425G>C	p.Glu475Asp	p.E475D	ENST00000358487	NM_000141.4	475	gaG/gaC	10/18	1	2	FACETS	1	0.978	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		423	527	SUCCESS
FGFR2	2263	MSKCC	GRCh37	10	123276961	123276961	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	152	397	0	ENST00000358487.5:c.956C>T	p.Thr319Ile	p.T319I	ENST00000358487	NM_000141.4	319	aCc/aTc	8/18	1	2	FACETS	1	0.945	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		397	567	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741552	17741552	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	254	152	279	1	ENST00000250003.3:c.223G>A	p.Ala75Thr	p.A75T	ENST00000250003	NM_002478.4	75	Gca/Aca	1/3	1	2	FACETS	0.965	0.892	1	1	0.993	1	CLONAL	3	TRUE	1	0.258652869545824	2		280	406	SUCCESS
MYOD1	4654	MSKCC	GRCh37	11	17741780	17741780	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	216	620	0	ENST00000250003.3:c.451C>T	p.Arg151Cys	p.R151C	ENST00000250003	NM_002478.4	151	Cgc/Tgc	1/3	1	2	FACETS	0.971	0.904	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		620	860	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32439189	32439189	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	419	175	557	0	ENST00000332351.3:c.884A>G	p.Tyr295Cys	p.Y295C	ENST00000332351	NM_024426.4	295	tAc/tGc	4/10	1	2	FACETS	1	0.977	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		557	594	SUCCESS
RPS6KA4	8986	MSKCC	GRCh37	11	64138845	64138845	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs761843231	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	217	463	3	ENST00000334205.4:c.2212G>A	p.Ala738Thr	p.A738T	ENST00000334205	NM_003942.2	738	Gcc/Acc	17/17	1	2	FACETS	0.917	0.858	0.977	1	0.995	1	CLONAL	3	TRUE	1	0.258652869545824	2		466	610	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572024	64572024	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	588	263	643	0	ENST00000312049.6:c.1615G>A	p.Ala539Thr	p.A539T	ENST00000312049	NM_130799.2	539	Gca/Aca	10/10	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		643	851	SUCCESS
INPPL1	3636	MSKCC	GRCh37	11	71944160	71944160	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs201836862	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	301	720	1	ENST00000298229.2:c.1993C>T	p.Arg665Trp	p.R665W	ENST00000298229	NM_001567.3	665	Cgg/Tgg	17/28	1	2	FACETS	0.84	0.793	0.887	1	0.996	1	CLONAL	3	TRUE	1	0.258652869545824	2		721	924	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100962516	100962516	+	stop_gained	Nonsense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	201	568	0	ENST00000325455.5:c.1881C>A	p.Cys627Ter	p.C627*	ENST00000325455	NM_001202474.3	627	tgC/tgA	3/8	1	2	FACETS	1	0.95	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		568	757	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999011	100999011	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	168	460	0	ENST00000325455.5:c.791G>A	p.Gly264Asp	p.G264D	ENST00000325455	NM_001202474.3	264	gGc/gAc	1/8	1	2	FACETS	1	0.981	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		460	546	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100999464	100999464	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1021	68	838	0	ENST00000325455.5:c.338G>C	p.Ser113Thr	p.S113T	ENST00000325455	NM_001202474.3	113	aGt/aCt	1/8	1	2	FACETS	0.483	0.418	0.553	0.483	0.418	0.553	SUBCLONAL	1	TRUE	1	0.258652869545824	2		838	1089	SUCCESS
BIRC3	330	MSKCC	GRCh37	11	102195472	102195472	+	stop_gained	Nonsense_Mutation	SNP	A	A	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	175	429	0	ENST00000263464.3:c.232A>T	p.Arg78Ter	p.R78*	ENST00000263464	NM_001165.4	78	Aga/Tga	2/9	1	2	FACETS	1	0.965	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		429	631	SUCCESS
ATM	472	MSKCC	GRCh37	11	108139178	108139178	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	191	658	1	ENST00000278616.4:c.2680G>A	p.Asp894Asn	p.D894N	ENST00000278616	NM_000051.3	894	Gat/Aat	18/63	1	2	FACETS	1	0.938	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		659	729	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118344582	118344582	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	160	526	0	ENST00000534358.1:c.2708C>T	p.Ser903Phe	p.S903F	ENST00000534358	NM_005933.3	903	tCt/tTt	3/36	1	2	FACETS	0.865	0.795	0.938	1	0.991	1	CLONAL	2	TRUE	1	0.258652869545824	2		526	715	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118373662	118373662	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	213	607	0	ENST00000534358.1:c.7055G>A	p.Gly2352Asp	p.G2352D	ENST00000534358	NM_005933.3	2352	gGc/gAc	27/36	1	2	FACETS	0.975	0.907	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		607	845	SUCCESS
CBL	867	MSKCC	GRCh37	11	119155954	119155954	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs980503623	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	820	314	785	4	ENST00000264033.4:c.1619G>A	p.Arg540Gln	p.R540Q	ENST00000264033	NM_005188.3	540	cGa/cAa	11/16	1	2	FACETS	1	0.978	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		789	1134	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	422269	422269	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	618	267	694	1	ENST00000399788.2:c.2989G>T	p.Ala997Ser	p.A997S	ENST00000399788	NM_001042603.1	997	Gcc/Tcc	20/28	1	2	FACETS	1	0.987	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		695	885	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	461462	461462	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	769	270	720	0	ENST00000399788.2:c.1058G>A	p.Gly353Glu	p.G353E	ENST00000399788	NM_001042603.1	353	gGa/gAa	9/28	1	2	FACETS	1	0.943	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		720	1039	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	463352	463352	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	721	311	672	0	ENST00000399788.2:c.919A>G	p.Lys307Glu	p.K307E	ENST00000399788	NM_001042603.1	307	Aaa/Gaa	8/28	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		672	1032	SUCCESS
KDM5A	5927	MSKCC	GRCh37	12	475156	475156	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	271	796	0	ENST00000399788.2:c.481C>T	p.His161Tyr	p.H161Y	ENST00000399788	NM_001042603.1	161	Cat/Tat	4/28	1	2	FACETS	0.966	0.906	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		796	1085	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49420460	49420460	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	520	224	489	1	ENST00000301067.7:c.15289C>T	p.Arg5097Ter	p.R5097*	ENST00000301067	NM_003482.3	5097	Cga/Tga	48/54	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		490	744	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49426223	49426223	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	509	200	629	0	ENST00000301067.7:c.12265C>A	p.Leu4089Met	p.L4089M	ENST00000301067	NM_003482.3	4089	Ctg/Atg	39/54	1	2	FACETS	1	0.973	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		629	709	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49427521	49427521	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1232636989	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	393	186	457	0	ENST00000301067.7:c.10967G>A	p.Arg3656His	p.R3656H	ENST00000301067	NM_003482.3	3656	cGc/cAc	39/54	1	2	FACETS	1	0.986	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		457	579	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49431493	49431493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1288465936	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	737	314	756	1	ENST00000301067.7:c.9646G>A	p.Glu3216Lys	p.E3216K	ENST00000301067	NM_003482.3	3216	Gag/Aag	34/54	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		757	1051	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49433351	49433351	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	222	735	0	ENST00000301067.7:c.8096C>T	p.Thr2699Ile	p.T2699I	ENST00000301067	NM_003482.3	2699	aCc/aTc	32/54	1	2	FACETS	0.937	0.873	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		735	916	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435147	49435147	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	305	127	402	0	ENST00000301067.7:c.6406T>G	p.Ser2136Ala	p.S2136A	ENST00000301067	NM_003482.3	2136	Tct/Gct	31/54	1	2	FACETS	1	0.969	1	1	0.991	1	CLONAL	2	TRUE	1	0.258652869545824	2		402	432	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435204	49435204	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs758476128	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	460	48	431	0	ENST00000301067.7:c.6349C>T	p.Pro2117Ser	p.P2117S	ENST00000301067	NM_003482.3	2117	Ccc/Tcc	31/54	1	2	FACETS	0.731	0.618	0.855	0.731	0.618	0.855	SUBCLONAL	1	TRUE	1	0.258652869545824	2		431	508	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444073	49444073	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	445	205	542	0	ENST00000301067.7:c.3298G>A	p.Asp1100Asn	p.D1100N	ENST00000301067	NM_003482.3	1100	Gac/Aac	11/54	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		542	650	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444574	49444574	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	431	168	527	2	ENST00000301067.7:c.2798-1G>T		p.X933_splice	ENST00000301067	NM_003482.3	933			1	2	FACETS	1	0.967	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		529	599	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49447842	49447842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1280814073	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	169	559	2	ENST00000301067.7:c.592G>A	p.Ala198Thr	p.A198T	ENST00000301067	NM_003482.3	198	Gcg/Acg	5/54	1	2	FACETS	0.962	0.888	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		561	679	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56478899	56478899	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759113437	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	287	813	3	ENST00000267101.3:c.355G>A	p.Val119Ile	p.V119I	ENST00000267101	NM_001982.3	119	Gtc/Atc	3/28	1	2	FACETS	1	0.972	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		816	1052	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57858584	57858584	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765007750	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	255	752	0	ENST00000228682.2:c.322G>A	p.Ala108Thr	p.A108T	ENST00000228682	NM_005269.2	108	Gct/Act	4/12	1	2	FACETS	0.984	0.922	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		752	1002	SUCCESS
GLI1	2735	MSKCC	GRCh37	12	57859621	57859621	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	461	177	512	0	ENST00000228682.2:c.675G>T	p.Glu225Asp	p.E225D	ENST00000228682	NM_005269.2	225	gaG/gaT	7/12	1	2	FACETS	1	0.965	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		512	638	SUCCESS
MDM2	4193	MSKCC	GRCh37	12	69218161	69218161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1320937462	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	197	480	0	ENST00000462284.1:c.377C>T	p.Thr126Ile	p.T126I	ENST00000462284	NM_002392.5	126	aCa/aTa	6/11	1	2	FACETS	1	0.982	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		480	656	SUCCESS
PTPN11	5781	MSKCC	GRCh37	12	112893770	112893770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs780911423	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	167	479	1	ENST00000351677.2:c.659G>A	p.Arg220His	p.R220H	ENST00000351677	NM_002834.3	220	cGt/cAt	6/16	1	2	FACETS	1	0.969	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		480	590	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121416620	121416620	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	205	589	1	ENST00000257555.6:c.49C>T	p.Leu17Phe	p.L17F	ENST00000257555		17	Ctc/Ttc	1/10	1	2	FACETS	1	0.981	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		590	694	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133209008	133209008	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1326812680	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	580	202	598	0	ENST00000320574.5:c.6223A>G	p.Thr2075Ala	p.T2075A	ENST00000320574	NM_006231.2	2075	Aca/Gca	45/49	1	2	FACETS	0.999	0.928	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		598	782	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133219881	133219881	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	470	190	503	0	ENST00000320574.5:c.4480C>T	p.Gln1494Ter	p.Q1494*	ENST00000320574	NM_006231.2	1494	Cag/Tag	35/49	1	2	FACETS	1	0.976	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		503	660	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21619864	21619864	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1235573411	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	141	399	1	ENST00000382592.4:c.302G>A	p.Arg101Gln	p.R101Q	ENST00000382592	NM_014572.2	101	cGg/cAg	2/8	1	2	FACETS	1	0.938	1	1	0.991	1	CLONAL	2	TRUE	1	0.258652869545824	2		400	530	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28592608	28592608	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	574	185	562	1	ENST00000241453.7:c.2537G>A	p.Gly846Asp	p.G846D	ENST00000241453	NM_004119.2	846	gGc/gAc	20/24	1	2	FACETS	0.942	0.872	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		563	759	SUCCESS
FLT3	2322	MSKCC	GRCh37	13	28623568	28623568	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	463	168	548	0	ENST00000241453.7:c.989G>A	p.Cys330Tyr	p.C330Y	ENST00000241453	NM_004119.2	330	tGt/tAt	8/24	1	2	FACETS	1	0.945	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		548	631	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32899231	32899231	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	397	146	392	0	ENST00000380152.3:c.335G>T	p.Ser112Ile	p.S112I	ENST00000380152		112	aGt/aTt	4/27	1	2	FACETS	1	0.946	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		392	543	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32906879	32906879	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	587	188	679	0	ENST00000380152.3:c.1264A>C	p.Asn422His	p.N422H	ENST00000380152		422	Aat/Cat	10/27	1	2	FACETS	0.938	0.868	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		679	775	SUCCESS
BRCA2	675	MSKCC	GRCh37	13	32954053	32954053	+	splice_region_variant,intron_variant	Splice_Region	SNP	A	A	G	rs1555288517	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	187	729	0	ENST00000380152.3:c.9117+3A>G		p.X3039_splice	ENST00000380152		3039			1	2	FACETS	1	0.96	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		729	687	SUCCESS
FOXO1	2308	MSKCC	GRCh37	13	41134604	41134630	+	inframe_deletion	In_Frame_Del	DEL	CCCCTTCTCCAAGATCATCCTGTTCGG	CCCCTTCTCCAAGATCATCCTGTTCGG	-	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	102	434	0	ENST00000379561.5:c.998_1024del	p.Thr333_Asp342delinsAsn	p.T333_D342delinsN	ENST00000379561	NM_002015.3	333	aCCGAACAGGATGATCTTGGAGAAGGGGat/aat	2/3	1	2	FACETS	0.784	0.704	0.868	1	0.984	1	SUBCLONAL	2	TRUE	1	0.258652869545824	2		434	503	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48934203	48934203	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	500	206	634	0	ENST00000267163.4:c.658C>A	p.Leu220Ile	p.L220I	ENST00000267163	NM_000321.2	220	Cta/Ata	7/27	1	2	FACETS	1	0.979	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		634	706	SUCCESS
RB1	5925	MSKCC	GRCh37	13	48955522	48955529	+	frameshift_variant	Frame_Shift_Del	DEL	GATAAAAC	GATAAAAC	-	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	177	568	0	ENST00000267163.4:c.1638_1645del	p.Met546IlefsTer6	p.M546Ifs*6	ENST00000267163	NM_000321.2	546	atGATAAAACat/atat	17/27	1	2	FACETS	0.987	0.913	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		568	693	SUCCESS
CYSLTR2	57105	MSKCC	GRCh37	13	49281953	49281953	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	766	274	781	0	ENST00000282018.3:c.1000T>C	p.Phe334Leu	p.F334L	ENST00000282018	NM_020377.2	334	Ttc/Ctc	1/1	1	2	FACETS	1	0.954	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		781	1040	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103506141	103506141	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	86	509	0	ENST00000355739.4:c.299G>A	p.Ser100Asn	p.S100N	ENST00000355739	NM_000123.3	100	aGt/aAt	3/15	1	2	FACETS	0.997	0.882	1	0.997	0.882	1	CLONAL	1	TRUE	1	0.258652869545824	2		509	667	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103514756	103514756	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs371251823	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	147	418	1	ENST00000355739.4:c.1257G>A	p.Met419Ile	p.M419I	ENST00000355739	NM_000123.3	419	atG/atA	8/15	1	2	FACETS	1	0.964	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		419	523	SUCCESS
ERCC5	2073	MSKCC	GRCh37	13	103527783	103527783	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1279336454	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	442	182	527	1	ENST00000355739.4:c.3091G>A	p.Ala1031Thr	p.A1031T	ENST00000355739	NM_000123.3	1031	Gcc/Acc	15/15	1	2	FACETS	1	0.977	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		528	624	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435181	110435181	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1357518676	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	316	841	1	ENST00000375856.3:c.3220G>A	p.Glu1074Lys	p.E1074K	ENST00000375856	NM_003749.2	1074	Gag/Aag	1/2	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		842	1036	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110435619	110435619	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1248526870	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	199	427	1	ENST00000375856.3:c.2782G>A	p.Gly928Arg	p.G928R	ENST00000375856	NM_003749.2	928	Ggg/Agg	1/2	1	2	FACETS	0.845	0.787	0.904	1	0.995	1	CLONAL	3	TRUE	1	0.258652869545824	2		428	607	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30068887	30068887	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	924	139	891	0	ENST00000331968.5:c.2042A>G	p.His681Arg	p.H681R	ENST00000331968	NM_002742.2	681	cAc/cGc	14/18	1	2	FACETS	1	0.918	1	1	0.918	1	CLONAL	1	TRUE	1	0.258652869545824	2		891	1063	SUCCESS
PRKD1	5587	MSKCC	GRCh37	14	30105614	30105614	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	839	385	884	1	ENST00000331968.5:c.1072G>T	p.Asp358Tyr	p.D358Y	ENST00000331968	NM_002742.2	358	Gat/Tat	7/18	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	1	0.258652869545824	2		885	1224	SUCCESS
NFKBIA	4792	MSKCC	GRCh37	14	35873816	35873816	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	125	315	0	ENST00000216797.5:c.35C>G	p.Ala12Gly	p.A12G	ENST00000216797	NM_020529.2	12	gCc/gGc	1/6	1	2	FACETS	1	0.952	1	1	0.99	1	CLONAL	2	TRUE	1	0.258652869545824	2		315	453	SUCCESS
NKX2-1	7080	MSKCC	GRCh37	14	36986670	36986670	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	14	10	11	0	ENST00000354822.5:c.1019G>A	p.Gly340Asp	p.G340D	ENST00000354822	NM_001079668.2	340	gGc/gAc	3/3	1	2	FACETS	1	0.772	1	1	0.917	1	CLONAL	3	TRUE	1	0.258652869545824	2		11	24	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81563048	81563048	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	343	177	404	0	ENST00000298171.2:c.611C>G	p.Ala204Gly	p.A204G	ENST00000298171	NM_000369.2	204	gCt/gGt	7/10	1	2	FACETS	0.877	0.815	0.942	1	0.994	1	CLONAL	3	TRUE	1	0.258652869545824	2		404	520	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38614612	38614612	+	splice_donor_variant	Splice_Site	SNP	T	T	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	311	144	367	0	ENST00000299084.4:c.376+2T>C		p.X126_splice	ENST00000299084	NM_152594.2	126			1	2	FACETS	1	0.981	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		367	455	SUCCESS
SPRED1	161742	MSKCC	GRCh37	15	38643412	38643412	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	633	274	689	0	ENST00000299084.4:c.882C>A	p.Tyr294Ter	p.Y294*	ENST00000299084	NM_152594.2	294	taC/taA	7/7	1	2	FACETS	1	0.987	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		689	907	SUCCESS
MGA	23269	MSKCC	GRCh37	15	42059276	42059276	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	146	389	0	ENST00000219905.7:c.8996C>A	p.Pro2999His	p.P2999H	ENST00000219905	NM_001164273.1	2999	cCt/cAt	24/24	1	2	FACETS	1	0.977	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		389	481	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712934	43712934	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	223	526	0	ENST00000382044.4:c.4251-1G>T		p.X1417_splice	ENST00000382044	NM_001141980.1	1417			1	2	FACETS	0.893	0.836	0.95	1	0.995	1	CLONAL	3	TRUE	1	0.258652869545824	2		526	644	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43769919	43769919	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	212	540	1	ENST00000382044.4:c.827C>T	p.Ala276Val	p.A276V	ENST00000382044	NM_001141980.1	276	gCt/gTt	8/28	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		541	680	SUCCESS
SMAD3	4088	MSKCC	GRCh37	15	67462943	67462943	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	702	207	594	0	ENST00000327367.4:c.658+1G>A		p.X220_splice	ENST00000327367	NM_005902.3	220			0.258652869545824	3	FACETS	0.994	0.924	1	0.994	0.924	1	CLONAL	2	TRUE	1	0.258652869545824	3		594	909	SUCCESS
CD276	80381	MSKCC	GRCh37	15	74000721	74000721	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs150498569	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	593	319	636	1	ENST00000318443.5:c.1411G>A	p.Val471Met	p.V471M	ENST00000318443	NM_001024736.1	471	Gtg/Atg	7/10	0.258652869545824	3	FACETS	1	0.961	1	1	0.995	1	CLONAL	3	TRUE	1	0.258652869545824	3		637	912	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88679186	88679186	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	786	242	649	1	ENST00000360948.2:c.851G>A	p.Cys284Tyr	p.C284Y	ENST00000360948	NM_001012338.2	284	tGc/tAc	8/19	0.258652869545824	3	FACETS	1	0.955	1	1	0.955	1	CLONAL	2	TRUE	1	0.258652869545824	3		650	1028	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88680718	88680718	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	315	686	0	ENST00000360948.2:c.539C>T	p.Ala180Val	p.A180V	ENST00000360948	NM_001012338.2	180	gCc/gTc	6/19	0.258652869545824	3	FACETS	1	0.96	1	1	0.995	1	CLONAL	3	TRUE	1	0.258652869545824	3		686	901	SUCCESS
IDH2	3418	MSKCC	GRCh37	15	90628590	90628590	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs61733005	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	847	261	758	0	ENST00000330062.3:c.997G>A	p.Val333Ile	p.V333I	ENST00000330062	NM_002168.2	333	Gtc/Atc	8/11	0.258652869545824	3	FACETS	1	0.958	1	1	0.958	1	CLONAL	2	TRUE	1	0.258652869545824	3		758	1108	SUCCESS
BLM	641	MSKCC	GRCh37	15	91293297	91293297	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	328	170	340	1	ENST00000355112.3:c.799G>A	p.Asp267Asn	p.D267N	ENST00000355112	NM_000057.2	267	Gat/Aat	3/22	0.258652869545824	3	FACETS	0.994	0.921	1	1	0.99	1	CLONAL	3	TRUE	1	0.258652869545824	3		341	498	SUCCESS
BLM	641	MSKCC	GRCh37	15	91306259	91306259	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	192	545	1	ENST00000355112.3:c.1946T>A	p.Phe649Tyr	p.F649Y	ENST00000355112	NM_000057.2	649	tTt/tAt	8/22	0.258652869545824	3	FACETS	1	0.96	1	1	0.96	1	CLONAL	2	TRUE	1	0.258652869545824	3		546	796	SUCCESS
BLM	641	MSKCC	GRCh37	15	91347477	91347477	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	383	719	2	ENST00000355112.3:c.3639G>T	p.Glu1213Asp	p.E1213D	ENST00000355112	NM_000057.2	1213	gaG/gaT	19/22	0.258652869545824	3	FACETS	1	0.978	1	1	0.996	1	CLONAL	3	TRUE	1	0.258652869545824	3		721	1064	SUCCESS
BLM	641	MSKCC	GRCh37	15	91358397	91358397	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1277229461	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	269	759	0	ENST00000355112.3:c.4142C>T	p.Ser1381Leu	p.S1381L	ENST00000355112	NM_000057.2	1381	tCa/tTa	22/22	0.258652869545824	3	FACETS	1	0.962	1	1	0.962	1	CLONAL	2	TRUE	1	0.258652869545824	3		759	1134	SUCCESS
IGF1R	3480	MSKCC	GRCh37	15	99472832	99472832	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	554	289	545	0	ENST00000268035.6:c.2828C>A	p.Ala943Asp	p.A943D	ENST00000268035	NM_000875.3	943	gCt/gAt	14/21	0.258652869545824	3	FACETS	0.998	0.942	1	1	0.994	1	CLONAL	3	TRUE	1	0.258652869545824	3		545	843	SUCCESS
NTHL1	4913	MSKCC	GRCh37	16	2094682	2094682	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	655	265	763	0	ENST00000219066.1:c.498G>T	p.Gln166His	p.Q166H	ENST00000219066	NM_002528.5	166	caG/caT	3/6	1	2	FACETS	1	0.982	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		763	920	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2129412	2129412	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	494	154	545	0	ENST00000219476.3:c.3267G>C	p.Gln1089His	p.Q1089H	ENST00000219476	NM_000548.3	1089	caG/caC	28/42	1	2	FACETS	0.919	0.844	0.997	1	0.991	1	CLONAL	2	TRUE	1	0.258652869545824	2		545	648	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2134655	2134655	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	270	873	0	ENST00000219476.3:c.4432G>T	p.Asp1478Tyr	p.D1478Y	ENST00000219476	NM_000548.3	1478	Gac/Tac	34/42	1	2	FACETS	1	0.957	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		873	1019	SUCCESS
TSC2	7249	MSKCC	GRCh37	16	2136813	2136813	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs137853999	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	369	903	1	ENST00000219476.3:c.4930G>A	p.Asp1644Asn	p.D1644N	ENST00000219476	NM_000548.3	1644	Gac/Aac	38/42	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	1	0.258652869545824	2		904	1150	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2223277	2223277	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs745725943	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	754	192	656	0	ENST00000326181.6:c.889C>T	p.Arg297Cys	p.R297C	ENST00000326181	NM_032271.2	297	Cgc/Tgc	10/21	1	2	FACETS	0.785	0.726	0.846	1	0.991	1	SUBCLONAL	2	TRUE	1	0.258652869545824	2		656	946	SUCCESS
TRAF7	84231	MSKCC	GRCh37	16	2226149	2226149	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	720	283	822	0	ENST00000326181.6:c.1846G>T	p.Val616Phe	p.V616F	ENST00000326181	NM_032271.2	616	Gtc/Ttc	19/21	1	2	FACETS	1	0.98	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		822	1003	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3633215	3633215	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	954	310	1045	0	ENST00000294008.3:c.5036G>C	p.Ser1679Thr	p.S1679T	ENST00000294008	NM_032444.2	1679	aGc/aCc	14/15	1	2	FACETS	0.948	0.893	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		1045	1264	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3639723	3639723	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	981	357	974	0	ENST00000294008.3:c.3916C>T	p.Gln1306Ter	p.Q1306*	ENST00000294008	NM_032444.2	1306	Cag/Tag	12/15	1	2	FACETS	1	0.968	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		974	1338	SUCCESS
SLX4	84464	MSKCC	GRCh37	16	3640332	3640332	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200708159	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	790	336	883	3	ENST00000294008.3:c.3307C>T	p.Arg1103Cys	p.R1103C	ENST00000294008	NM_032444.2	1103	Cgt/Tgt	12/15	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		886	1126	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857614	9857614	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs142113044	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	123	336	1	ENST00000330684.3:c.3787G>A	p.Gly1263Arg	p.G1263R	ENST00000330684	NM_001134407.1	1263	Ggg/Agg	13/13	1	2	FACETS	1	0.97	1	1	0.991	1	CLONAL	2	TRUE	1	0.258652869545824	2		337	414	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9857694	9857694	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	260	113	316	0	ENST00000330684.3:c.3707G>A	p.Cys1236Tyr	p.C1236Y	ENST00000330684	NM_001134407.1	1236	tGc/tAc	13/13	1	2	FACETS	1	0.971	1	1	0.99	1	CLONAL	2	TRUE	1	0.258652869545824	2		316	373	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	9923440	9923440	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	216	625	0	ENST00000330684.3:c.1847C>T	p.Ser616Phe	p.S616F	ENST00000330684	NM_001134407.1	616	tCc/tTc	9/13	1	2	FACETS	1	0.944	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		625	823	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032024	10032024	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	196	677	1	ENST00000330684.3:c.799C>T	p.Leu267Phe	p.L267F	ENST00000330684	NM_001134407.1	267	Ctc/Ttc	3/13	1	2	FACETS	0.92	0.853	0.989	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		678	824	SUCCESS
GRIN2A	2903	MSKCC	GRCh37	16	10032223	10032223	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs762233114	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	168	649	6	ENST00000330684.3:c.600G>A	p.Met200Ile	p.M200I	ENST00000330684	NM_001134407.1	200	atG/atA	3/13	1	2	FACETS	0.77	0.709	0.835	1	0.989	1	SUBCLONAL	2	TRUE	1	0.258652869545824	2		655	843	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23646528	23646528	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	193	532	1	ENST00000261584.4:c.1339G>A	p.Ala447Thr	p.A447T	ENST00000261584	NM_024675.3	447	Gca/Aca	4/13	1	2	FACETS	1	0.971	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		533	686	SUCCESS
CYLD	1540	MSKCC	GRCh37	16	50784011	50784011	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	250	675	1	ENST00000398568.2:c.402G>T	p.Gln134His	p.Q134H	ENST00000398568	NM_001042412.1	134	caG/caT	3/18	1	2	FACETS	1	0.978	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		676	882	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56855464	56855464	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	180	533	0	ENST00000308159.5:c.613C>A	p.Leu205Met	p.L205M	ENST00000308159	NM_014669.4	205	Ctg/Atg	7/22	1	2	FACETS	0.986	0.912	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		533	706	SUCCESS
NUP93	9688	MSKCC	GRCh37	16	56875742	56875742	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	56	464	0	ENST00000308159.5:c.2346C>G	p.Asp782Glu	p.D782E	ENST00000308159	NM_014669.4	782	gaC/gaG	21/22	1	2	FACETS	0.738	0.632	0.853	0.738	0.632	0.853	SUBCLONAL	1	TRUE	1	0.258652869545824	2		464	587	SUCCESS
CTCF	10664	MSKCC	GRCh37	16	67650654	67650654	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	167	436	0	ENST00000264010.4:c.959G>A	p.Arg320His	p.R320H	ENST00000264010	NM_006565.3	320	cGt/cAt	5/12	1	2	FACETS	1	0.966	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		436	596	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68853316	68853316	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	221	635	0	ENST00000261769.5:c.1699G>A	p.Ala567Thr	p.A567T	ENST00000261769	NM_004360.3	567	Gct/Act	11/16	1	2	FACETS	0.988	0.921	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		635	865	SUCCESS
CDH1	999	MSKCC	GRCh37	16	68867244	68867244	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	637	243	600	0	ENST00000261769.5:c.2491C>G	p.Leu831Val	p.L831V	ENST00000261769	NM_004360.3	831	Ctc/Gtc	16/16	1	2	FACETS	1	0.972	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		600	880	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821232	72821232	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	589	149	614	1	ENST00000268489.5:c.10943C>T	p.Thr3648Ile	p.T3648I	ENST00000268489	NM_006885.3	3648	aCc/aTc	10/10	1	2	FACETS	0.781	0.714	0.85	1	0.988	1	SUBCLONAL	2	TRUE	1	0.258652869545824	2		615	738	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72821607	72821607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	37	23	53	0	ENST00000268489.5:c.10568G>A	p.Gly3523Asp	p.G3523D	ENST00000268489	NM_006885.3	3523	gGc/gAc	10/10	1	2	FACETS	0.988	0.803	1	1	0.961	1	CLONAL	3	TRUE	1	0.258652869545824	2		53	60	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72828011	72828011	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1372314790	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	757	361	790	0	ENST00000268489.5:c.8570G>A	p.Ser2857Asn	p.S2857N	ENST00000268489	NM_006885.3	2857	aGt/aAt	9/10	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	1	0.258652869545824	2		790	1118	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72832577	72832577	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1230922721	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	347	106	281	0	ENST00000268489.5:c.4004C>T	p.Ser1335Phe	p.S1335F	ENST00000268489	NM_006885.3	1335	tCc/tTc	9/10	1	2	FACETS	0.905	0.816	0.998	1	0.987	1	CLONAL	2	TRUE	1	0.258652869545824	2		281	453	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72863693	72863693	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	262	737	0	ENST00000268489.5:c.3514G>A	p.Asp1172Asn	p.D1172N	ENST00000268489	NM_006885.3	1172	Gac/Aac	5/10	1	2	FACETS	1	0.979	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		737	927	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72984514	72984514	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	247	640	2	ENST00000268489.5:c.3070G>A	p.Ala1024Thr	p.A1024T	ENST00000268489	NM_006885.3	1024	Gcc/Acc	3/10	1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		642	795	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72991476	72991476	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs146607776	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	608	262	662	1	ENST00000268489.5:c.2569G>A	p.Ala857Thr	p.A857T	ENST00000268489	NM_006885.3	857	Gcc/Acc	2/10	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		663	870	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992247	72992247	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	798	284	849	1	ENST00000268489.5:c.1798G>A	p.Ala600Thr	p.A600T	ENST00000268489	NM_006885.3	600	Gcc/Acc	2/10	1	2	FACETS	1	0.952	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		850	1082	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992768	72992768	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	74	553	1	ENST00000268489.5:c.1277G>A	p.Ser426Asn	p.S426N	ENST00000268489	NM_006885.3	426	aGt/aAt	2/10	1	2	FACETS	0.985	0.863	1	0.985	0.863	1	CLONAL	1	TRUE	1	0.258652869545824	2		554	581	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72992829	72992829	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	455	155	525	1	ENST00000268489.5:c.1216C>A	p.Leu406Ile	p.L406I	ENST00000268489	NM_006885.3	406	Ctc/Atc	2/10	1	2	FACETS	0.982	0.903	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		526	610	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81946227	81946227	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1295648437	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	423	169	562	1	ENST00000359376.3:c.1960G>A	p.Gly654Arg	p.G654R	ENST00000359376	NM_002661.3	654	Gga/Aga	19/33	1	2	FACETS	1	0.971	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		563	592	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81990299	81990299	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	385	155	368	2	ENST00000359376.3:c.3571-1G>T		p.X1191_splice	ENST00000359376	NM_002661.3	1191			1	2	FACETS	1	0.97	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		370	540	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89349426	89349426	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	298	823	0	ENST00000301030.4:c.3524G>C	p.Arg1175Thr	p.R1175T	ENST00000301030	NM_001256183.1	1175	aGg/aCg	9/13	1	2	FACETS	1	0.984	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		823	1029	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89350217	89350217	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs938858138	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	252	824	0	ENST00000301030.4:c.2733C>G	p.Asp911Glu	p.D911E	ENST00000301030	NM_001256183.1	911	gaC/gaG	9/13	1	2	FACETS	0.991	0.928	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		824	983	SUCCESS
ANKRD11	29123	MSKCC	GRCh37	16	89351811	89351811	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	879	437	932	1	ENST00000301030.4:c.1139T>C	p.Phe380Ser	p.F380S	ENST00000301030	NM_001256183.1	380	tTt/tCt	9/13	1	2	FACETS	0.856	0.816	0.896	1	0.997	1	CLONAL	3	TRUE	1	0.258652869545824	2		933	1316	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89862370	89862370	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	270	678	0	ENST00000389301.3:c.950A>C	p.Lys317Thr	p.K317T	ENST00000389301	NM_000135.2	317	aAg/aCg	11/43	1	2	FACETS	1	0.979	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		678	956	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89877137	89877137	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	665	211	711	0	ENST00000389301.3:c.500G>C	p.Cys167Ser	p.C167S	ENST00000389301	NM_000135.2	167	tGt/tCt	5/43	1	2	FACETS	0.931	0.866	0.999	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		711	876	SUCCESS
ALOX12B	242	MSKCC	GRCh37	17	7984025	7984025	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	396	146	757	0	ENST00000319144.4:c.601C>T	p.Arg201Cys	p.R201C	ENST00000319144	NM_001139.2	201	Cgc/Tgc	5/15	1	2	FACETS	1	0.947	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		757	542	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16001680	16001680	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	404	52	295	0	ENST00000268712.3:c.2820+1G>A		p.X940_splice	ENST00000268712	NM_006311.3	940			1	2	FACETS	0.882	0.752	1	0.882	0.752	1	CLONAL	1	TRUE	1	0.258652869545824	2		295	456	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16012099	16012099	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	441	131	452	0	ENST00000268712.3:c.2182+1G>C		p.X728_splice	ENST00000268712	NM_006311.3	728			1	2	FACETS	0.885	0.807	0.968	1	0.989	1	CLONAL	2	TRUE	1	0.258652869545824	2		452	572	SUCCESS
NCOR1	9611	MSKCC	GRCh37	17	16042403	16042403	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	824	103	800	0	ENST00000268712.3:c.1271T>C	p.Met424Thr	p.M424T	ENST00000268712	NM_006311.3	424	aTg/aCg	12/46	1	2	FACETS	0.859	0.768	0.957	0.859	0.768	0.957	CLONAL	1	TRUE	1	0.258652869545824	2		800	927	SUCCESS
FLCN	201163	MSKCC	GRCh37	17	17122332	17122332	+	splice_donor_variant	Splice_Site	SNP	C	C	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	240	116	301	0	ENST00000285071.4:c.1062+1G>C		p.X354_splice	ENST00000285071	NM_144997.5	354			1	2	FACETS	0.84	0.765	0.917	1	0.991	1	CLONAL	3	TRUE	1	0.258652869545824	2		301	356	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29509543	29509543	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	168	513	0	ENST00000356175.3:c.748T>C	p.Phe250Leu	p.F250L	ENST00000356175	NM_000267.3	250	Ttt/Ctt	8/57	1	2	FACETS	1	0.955	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		513	620	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29667625	29667625	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	604	261	684	1	ENST00000356175.3:c.6961C>A	p.Leu2321Met	p.L2321M	ENST00000356175	NM_000267.3	2321	Ctg/Atg	46/57	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		685	865	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29685597	29685597	+	stop_gained	Nonsense_Mutation	SNP	C	C	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	671	307	787	0	ENST00000356175.3:c.8007C>G	p.Tyr2669Ter	p.Y2669*	ENST00000356175	NM_000267.3	2669	taC/taG	54/57	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		787	978	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320282	30320282	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs748955039	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	700	248	692	0	ENST00000322652.5:c.1223C>T	p.Thr408Ile	p.T408I	ENST00000322652	NM_015355.2	408	aCa/aTa	11/16	1	2	FACETS	1	0.946	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		692	948	SUCCESS
SUZ12	23512	MSKCC	GRCh37	17	30320986	30320986	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	255	608	0	ENST00000322652.5:c.1396C>T	p.His466Tyr	p.H466Y	ENST00000322652	NM_015355.2	466	Cat/Tat	12/16	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		608	845	SUCCESS
RAD51D	5892	MSKCC	GRCh37	17	33446555	33446555	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	511	190	552	0	ENST00000345365.6:c.78G>T	p.Lys26Asn	p.K26N	ENST00000345365	NM_002878.3	26	aaG/aaT	1/10	1	2	FACETS	1	0.959	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		552	701	SUCCESS
STAT5A	6776	MSKCC	GRCh37	17	40459621	40459621	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	541	242	545	1	ENST00000345506.4:c.1786G>T	p.Gly596Cys	p.G596C	ENST00000345506	NM_003152.3	596	Ggt/Tgt	16/20	1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		546	783	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40498609	40498609	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	176	456	0	ENST00000264657.5:c.251G>A	p.Arg84Gln	p.R84Q	ENST00000264657	NM_139276.2	84	cGa/cAa	3/24	1	2	FACETS	1	0.977	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		456	600	SUCCESS
STAT3	6774	MSKCC	GRCh37	17	40500461	40500461	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	548	233	543	0	ENST00000264657.5:c.74G>A	p.Ser25Asn	p.S25N	ENST00000264657	NM_139276.2	25	aGc/aAc	2/24	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		543	781	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40872291	40872291	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	628	261	655	1	ENST00000428826.2:c.664G>T	p.Gly222Cys	p.G222C	ENST00000428826		222	Ggc/Tgc	7/21	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		656	889	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41249270	41249270	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1065	129	863	0	ENST00000357654.3:c.584C>T	p.Thr195Ile	p.T195I	ENST00000357654	NM_007294.3	195	aCt/aTt	8/23	1	2	FACETS	0.835	0.755	0.92	0.835	0.755	0.92	CLONAL	1	TRUE	1	0.258652869545824	2		863	1194	SUCCESS
BRCA1	672	MSKCC	GRCh37	17	41276043	41276043	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs80357198	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	244	665	0	ENST00000357654.3:c.71G>A	p.Cys24Tyr	p.C24Y	ENST00000357654	NM_007294.3	24	tGt/tAt	2/23	1	2	FACETS	0.987	0.923	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		665	956	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804211	46804211	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	870	66	731	0	ENST00000290295.7:c.796A>G	p.Asn266Asp	p.N266D	ENST00000290295	NM_006361.5	266	Aac/Gac	2/2	1	2	FACETS	0.545	0.472	0.625	0.545	0.472	0.625	SUBCLONAL	1	TRUE	1	0.258652869545824	2		731	936	SUCCESS
HOXB13	10481	MSKCC	GRCh37	17	46804322	46804322	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs529100627	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	205	516	0	ENST00000290295.7:c.685C>T	p.Arg229Trp	p.R229W	ENST00000290295	NM_006361.5	229	Cgg/Tgg	2/2	1	2	FACETS	1	0.98	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		516	700	SUCCESS
BRIP1	83990	MSKCC	GRCh37	17	59853889	59853889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	175	709	0	ENST00000259008.2:c.1970G>A	p.Gly657Asp	p.G657D	ENST00000259008	NM_032043.2	657	gGt/gAt	14/20	1	2	FACETS	0.798	0.735	0.863	1	0.99	1	SUBCLONAL	2	TRUE	1	0.258652869545824	2		709	848	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63533713	63533713	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1345875693	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	243	109	336	0	ENST00000307078.5:c.1441C>T	p.Leu481Phe	p.L481F	ENST00000307078	NM_004655.3	481	Ctc/Ttc	6/11	1	2	FACETS	1	0.973	1	1	0.99	1	CLONAL	2	TRUE	1	0.258652869545824	2		336	352	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63534374	63534374	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	297	781	1	ENST00000307078.5:c.1147C>A	p.Leu383Met	p.L383M	ENST00000307078	NM_004655.3	383	Ctg/Atg	5/11	1	2	FACETS	1	0.987	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		782	991	SUCCESS
AXIN2	8313	MSKCC	GRCh37	17	63554012	63554012	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs1060502152	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	516	232	524	0	ENST00000307078.5:c.727C>G	p.Leu243Val	p.L243V	ENST00000307078	NM_004655.3	243	Ctt/Gtt	2/11	1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		524	748	SUCCESS
PRKAR1A	5573	MSKCC	GRCh37	17	66521100	66521100	+	splice_donor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	276	113	274	0	ENST00000358598.2:c.549+1G>A		p.X183_splice	ENST00000358598	NM_212471.2	183			1	2	FACETS	1	0.964	1	1	0.99	1	CLONAL	2	TRUE	1	0.258652869545824	2		274	389	SUCCESS
PIK3C3	5289	MSKCC	GRCh37	18	39542493	39542493	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	58	440	0	ENST00000262039.4:c.297C>G	p.Asp99Glu	p.D99E	ENST00000262039	NM_002647.2	99	gaC/gaG	3/25	1	2	FACETS	0.777	0.668	0.897	0.777	0.668	0.897	SUBCLONAL	1	TRUE	1	0.258652869545824	2		440	577	SUCCESS
MALT1	10892	MSKCC	GRCh37	18	56412950	56412950	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	609	236	660	0	ENST00000348428.3:c.1964G>A	p.Gly655Asp	p.G655D	ENST00000348428	NM_006785.3	655	gGc/gAc	16/17	1	2	FACETS	1	0.974	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		660	845	SUCCESS
STK11	6794	MSKCC	GRCh37	19	1220614	1220614	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs730881982	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	288	688	0	ENST00000326873.7:c.632G>A	p.Arg211Gln	p.R211Q	ENST00000326873	NM_000455.4	211	cGg/cAg	5/10	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		688	911	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1611717	1611717	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs755856969	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	758	110	653	2	ENST00000344749.5:c.1945G>A	p.Gly649Arg	p.G649R	ENST00000344749	NM_001136139.2	649	Ggg/Agg	19/19	1	2	FACETS	0.98	0.88	1	0.98	0.88	1	CLONAL	1	TRUE	1	0.258652869545824	2		655	868	SUCCESS
TCF3	6929	MSKCC	GRCh37	19	1625706	1625706	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	251	649	0	ENST00000344749.5:c.368C>A	p.Ala123Asp	p.A123D	ENST00000344749	NM_001136139.2	123	gCt/gAt	7/19	1	2	FACETS	1	0.98	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		649	877	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5206810	5206810	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	710	278	742	0	ENST00000357368.4:c.5822G>T	p.Gly1941Val	p.G1941V	ENST00000357368	NM_002850.3	1941	gGa/gTa	38/38	1	2	FACETS	1	0.979	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		742	988	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5211607	5211607	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	333	159	396	1	ENST00000357368.4:c.5228G>A	p.Gly1743Asp	p.G1743D	ENST00000357368	NM_002850.3	1743	gGc/gAc	33/38	1	2	FACETS	1	0.984	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		397	492	SUCCESS
PTPRS	5802	MSKCC	GRCh37	19	5223179	5223179	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	783	338	808	2	ENST00000357368.4:c.2624C>T	p.Ser875Leu	p.S875L	ENST00000357368	NM_002850.3	875	tCg/tTg	18/38	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		810	1121	SUCCESS
INSR	3643	MSKCC	GRCh37	19	7142888	7142888	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	457	206	517	0	ENST00000302850.5:c.2481G>T	p.Gln827His	p.Q827H	ENST00000302850	NM_000208.2	827	caG/caT	12/22	1	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		517	663	SUCCESS
DNMT1	1786	MSKCC	GRCh37	19	10254597	10254597	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	190	552	0	ENST00000340748.4:c.2913G>T	p.Glu971Asp	p.E971D	ENST00000340748		971	gaG/gaT	28/40	1	2	FACETS	1	0.97	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		552	677	SUCCESS
KEAP1	9817	MSKCC	GRCh37	19	10600396	10600396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1067	147	806	0	ENST00000171111.5:c.1459G>A	p.Ala487Thr	p.A487T	ENST00000171111	NM_203500.1	487	Gct/Act	4/6	1	2	FACETS	0.936	0.853	1	0.936	0.853	1	CLONAL	1	TRUE	1	0.258652869545824	2		806	1214	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100042	11100042	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1568430508	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	287	846	0	ENST00000358026.2:c.1168G>A	p.Gly390Arg	p.G390R	ENST00000358026	NM_001128849.1	390	Ggg/Agg	7/36	1	2	FACETS	1	0.965	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		846	1071	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051232	13051232	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	446	199	477	0	ENST00000316448.5:c.668C>T	p.Ala223Val	p.A223V	ENST00000316448	NM_004343.3	223	gCc/gTc	5/9	1	2	FACETS	1	0.984	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		477	645	SUCCESS
CALR	811	MSKCC	GRCh37	19	13051462	13051462	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs777096782	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	346	101	401	0	ENST00000316448.5:c.810G>C	p.Glu270Asp	p.E270D	ENST00000316448	NM_004343.3	270	gaG/gaC	6/9	1	2	FACETS	0.874	0.785	0.966	1	0.986	1	CLONAL	2	TRUE	1	0.258652869545824	2		401	447	SUCCESS
DNAJB1	3337	MSKCC	GRCh37	19	14627755	14627755	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	582	260	645	1	ENST00000254322.2:c.315C>A	p.Phe105Leu	p.F105L	ENST00000254322	NM_006145.1	105	ttC/ttA	2/3	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		646	842	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15271700	15271700	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	849	381	962	3	ENST00000263388.2:c.6739C>A	p.Pro2247Thr	p.P2247T	ENST00000263388	NM_000435.2	2247	Cca/Aca	33/33	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	1	0.258652869545824	2		965	1230	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15278175	15278175	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	996	65	827	0	ENST00000263388.2:c.5247G>C	p.Gln1749His	p.Q1749H	ENST00000263388	NM_000435.2	1749	caG/caC	29/33	1	2	FACETS	0.474	0.409	0.544	0.474	0.409	0.544	SUBCLONAL	1	TRUE	1	0.258652869545824	2		827	1061	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15285006	15285006	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	526	211	606	2	ENST00000263388.2:c.4609G>A	p.Ala1537Thr	p.A1537T	ENST00000263388	NM_000435.2	1537	Gcc/Acc	25/33	1	2	FACETS	1	0.977	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		608	737	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15290889	15290889	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	886	247	995	1	ENST00000263388.2:c.3321G>A	p.Met1107Ile	p.M1107I	ENST00000263388	NM_000435.2	1107	atG/atA	20/33	1	2	FACETS	0.843	0.787	0.9	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		996	1133	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15296160	15296160	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs772203584	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	713	213	693	5	ENST00000263388.2:c.2204G>A	p.Arg735Gln	p.R735Q	ENST00000263388	NM_000435.2	735	cGa/cAa	14/33	1	2	FACETS	0.889	0.827	0.954	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		698	926	SUCCESS
BABAM1	29086	MSKCC	GRCh37	19	17379802	17379802	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	980	386	966	0	ENST00000359435.4:c.187C>T	p.Leu63Phe	p.L63F	ENST00000359435	NM_001033549.1	63	Ctc/Ttc	2/9	1	2	FACETS	1	0.985	1	1	0.997	1	CLONAL	2	TRUE	1	0.258652869545824	2		966	1366	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18958623	18958623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	254	606	0	ENST00000262803.5:c.442C>T	p.Arg148Cys	p.R148C	ENST00000262803	NM_002911.3	148	Cgt/Tgt	3/24	1	2	FACETS	1	0.975	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		606	912	SUCCESS
UPF1	5976	MSKCC	GRCh37	19	18971765	18971765	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs775965911	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	575	204	627	1	ENST00000262803.5:c.2431G>A	p.Gly811Ser	p.G811S	ENST00000262803	NM_002911.3	811	Ggc/Agc	17/24	1	2	FACETS	1	0.94	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		628	779	SUCCESS
MEF2B	1.00271849E8	MSKCC	GRCh37	19	19260084	19260084	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	731	206	697	2	ENST00000162023.5:c.209C>T	p.Thr70Ile	p.T70I	ENST00000162023		70	aCa/aTa	7/13	1	2	FACETS	0.85	0.789	0.913	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		699	937	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210898	36210898	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747219825	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	691	261	782	1	ENST00000222270.7:c.649C>T	p.Arg217Trp	p.R217W	ENST00000222270	NM_014727.1	217	Cgg/Tgg	3/37	1	2	FACETS	1	0.972	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		783	952	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36212575	36212575	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs769208559	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	349	862	4	ENST00000222270.7:c.2326C>T	p.Arg776Trp	p.R776W	ENST00000222270	NM_014727.1	776	Cgg/Tgg	3/37	1	2	FACETS	1	0.986	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		866	1206	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214397	36214398	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	768	303	798	1	ENST00000222270.7:c.3057dup	p.Gly1020ArgfsTer15	p.G1020Rfs*15	ENST00000222270	NM_014727.1	1017	-/A	7/37	1	2	FACETS	1	0.982	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		799	1071	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214821	36214821	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	730	260	798	1	ENST00000222270.7:c.3247C>T	p.Arg1083Ter	p.R1083*	ENST00000222270	NM_014727.1	1083	Cga/Tga	8/37	1	2	FACETS	1	0.95	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		799	990	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36214849	36214849	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775845065	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	802	317	849	1	ENST00000222270.7:c.3275C>T	p.Ser1092Leu	p.S1092L	ENST00000222270	NM_014727.1	1092	tCg/tTg	8/37	1	2	FACETS	1	0.982	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		850	1119	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36215971	36215971	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	217	721	0	ENST00000222270.7:c.3511G>A	p.Val1171Ile	p.V1171I	ENST00000222270	NM_014727.1	1171	Gtc/Atc	10/37	1	2	FACETS	0.923	0.859	0.989	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		721	909	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36216148	36216148	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	433	168	487	0	ENST00000222270.7:c.3556C>A	p.Leu1186Met	p.L1186M	ENST00000222270	NM_014727.1	1186	Ctg/Atg	11/37	1	2	FACETS	1	0.966	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		487	601	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36219712	36219712	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	869	278	834	0	ENST00000222270.7:c.4609G>A	p.Asp1537Asn	p.D1537N	ENST00000222270	NM_014727.1	1537	Gat/Aat	20/37	1	2	FACETS	0.937	0.88	0.996	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		834	1147	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36221301	36221301	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1049	80	812	1	ENST00000222270.7:c.5135G>A	p.Gly1712Asp	p.G1712D	ENST00000222270	NM_014727.1	1712	gGc/gAc	24/37	1	2	FACETS	0.548	0.481	0.621	0.548	0.481	0.621	SUBCLONAL	1	TRUE	1	0.258652869545824	2		813	1129	SUCCESS
AXL	558	MSKCC	GRCh37	19	41749592	41749592	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1162584880	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	738	310	817	1	ENST00000301178.4:c.1517G>A	p.Arg506His	p.R506H	ENST00000301178	NM_021913.4	506	cGt/cAt	12/20	1	2	FACETS	1	0.987	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		818	1048	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753026	42753026	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs915295153	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	241	620	0	ENST00000222329.4:c.1238C>T	p.Ala413Val	p.A413V	ENST00000222329	NM_006494.2	413	gCa/gTa	4/4	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		620	810	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42753735	42753735	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	672	190	713	0	ENST00000222329.4:c.529G>A	p.Val177Met	p.V177M	ENST00000222329	NM_006494.2	177	Gtg/Atg	4/4	1	2	FACETS	0.852	0.789	0.918	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		713	862	SUCCESS
ERF	2077	MSKCC	GRCh37	19	42754650	42754650	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	534	210	574	0	ENST00000222329.4:c.90G>A	p.Trp30Ter	p.W30*	ENST00000222329	NM_006494.2	30	tgG/tgA	2/4	1	2	FACETS	1	0.974	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		574	744	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47725019	47725019	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs774280756	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	892	159	802	3	ENST00000449228.1:c.725G>A	p.Gly242Asp	p.G242D	ENST00000449228	NM_001127240.2	242	gGc/gAc	4/4	1	2	FACETS	1	0.975	1	1	0.975	1	CLONAL	1	TRUE	1	0.258652869545824	2		805	1051	SUCCESS
BBC3	27113	MSKCC	GRCh37	19	47730003	47730003	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	86	280	0	ENST00000449228.1:c.386C>T	p.Ala129Val	p.A129V	ENST00000449228	NM_001127240.2	129	gCc/gTc	3/4	1	2	FACETS	0.969	0.865	1	1	0.985	1	CLONAL	2	TRUE	1	0.258652869545824	2		280	343	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50905097	50905097	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372299975	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	323	861	0	ENST00000440232.2:c.379G>A	p.Ala127Thr	p.A127T	ENST00000440232	NM_002691.3	127	Gcc/Acc	4/27	1	2	FACETS	1	0.991	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		861	1009	SUCCESS
PPP2R1A	5518	MSKCC	GRCh37	19	52705201	52705201	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1372727039	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	157	411	0	ENST00000322088.6:c.83G>A	p.Arg28His	p.R28H	ENST00000322088	NM_014225.5	28	cGc/cAc	2/15	1	2	FACETS	1	0.974	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		411	535	SUCCESS
ALK	238	MSKCC	GRCh37	2	29917769	29917769	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	653	259	701	0	ENST00000389048.3:c.899A>G	p.Gln300Arg	p.Q300R	ENST00000389048	NM_004304.4	300	cAg/cGg	3/29	1	2	FACETS	1	0.979	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		701	912	SUCCESS
ALK	238	MSKCC	GRCh37	2	30142976	30142976	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs1379890469	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	792	380	902	1	ENST00000389048.3:c.550C>T	p.Arg184Ter	p.R184*	ENST00000389048	NM_004304.4	184	Cga/Tga	1/29	1	2	FACETS	0.836	0.794	0.878	1	0.997	1	CLONAL	3	TRUE	1	0.258652869545824	2		903	1172	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39224165	39224165	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	219	526	2	ENST00000402219.2:c.2979C>A	p.Asn993Lys	p.N993K	ENST00000402219	NM_005633.3	993	aaC/aaA	19/23	1	2	FACETS	0.871	0.815	0.929	1	0.995	1	CLONAL	3	TRUE	1	0.258652869545824	2		528	648	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39278325	39278325	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	632	256	807	0	ENST00000402219.2:c.824C>T	p.Pro275Leu	p.P275L	ENST00000402219	NM_005633.3	275	cCc/cTc	6/23	1	2	FACETS	1	0.982	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		807	888	SUCCESS
EPAS1	2034	MSKCC	GRCh37	2	46602913	46602913	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs766854881	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	741	107	639	2	ENST00000263734.3:c.971C>T	p.Thr324Met	p.T324M	ENST00000263734	NM_001430.4	324	aCg/aTg	8/16	1	2	FACETS	0.976	0.875	1	0.976	0.875	1	CLONAL	1	TRUE	1	0.258652869545824	2		641	848	SUCCESS
MSH2	4436	MSKCC	GRCh37	2	47705610	47705610	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	452	172	435	1	ENST00000233146.2:c.2410G>T	p.Ala804Ser	p.A804S	ENST00000233146	NM_000251.2	804	Gca/Tca	14/16	1	2	FACETS	1	0.962	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		436	624	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48026708	48026708	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs786201964	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	180	421	0	ENST00000234420.5:c.1586G>A	p.Gly529Asp	p.G529D	ENST00000234420	NM_000179.2	529	gGt/gAt	4/10	1	2	FACETS	1	0.978	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		421	610	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030746	48030746	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	309	134	302	0	ENST00000234420.5:c.3360G>T	p.Glu1120Asp	p.E1120D	ENST00000234420	NM_000179.2	1120	gaG/gaT	5/10	1	2	FACETS	1	0.975	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		302	443	SUCCESS
REL	5966	MSKCC	GRCh37	2	61144065	61144065	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	531	200	627	0	ENST00000295025.8:c.448C>A	p.Leu150Met	p.L150M	ENST00000295025	NM_002908.2	150	Ctg/Atg	5/11	1	2	FACETS	1	0.964	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		627	731	SUCCESS
ERCC3	2071	MSKCC	GRCh37	2	128016922	128016922	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	233	687	0	ENST00000285398.2:c.2167G>T	p.Asp723Tyr	p.D723Y	ENST00000285398	NM_000122.1	723	Gat/Tat	14/15	1	2	FACETS	1	0.955	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		687	877	SUCCESS
SF3B1	23451	MSKCC	GRCh37	2	198264978	198264978	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	153	317	0	ENST00000335508.6:c.2899G>A	p.Glu967Lys	p.E967K	ENST00000335508	NM_012433.2	967	Gag/Aag	19/25	1	2	FACETS	0.865	0.798	0.933	1	0.993	1	CLONAL	3	TRUE	1	0.258652869545824	2		317	456	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212989601	212989601	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	156	388	0	ENST00000342788.4:c.110G>C	p.Ser37Thr	p.S37T	ENST00000342788	NM_005235.2	37	aGc/aCc	2/28	1	2	FACETS	0.836	0.772	0.902	1	0.993	1	CLONAL	3	TRUE	1	0.258652869545824	2		388	481	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645295	215645295	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	193	418	0	ENST00000260947.4:c.1303G>T	p.Ala435Ser	p.A435S	ENST00000260947	NM_000465.2	435	Gct/Tct	4/11	1	2	FACETS	1	0.974	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		418	676	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645717	215645717	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	493	219	630	0	ENST00000260947.4:c.881G>A	p.Arg294Lys	p.R294K	ENST00000260947	NM_000465.2	294	aGg/aAg	4/11	1	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		630	712	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215657162	215657162	+	missense_variant	Missense_Mutation	SNP	C	C	G	rs1559437285	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	303	134	327	0	ENST00000260947.4:c.223G>C	p.Val75Leu	p.V75L	ENST00000260947	NM_000465.2	75	Gta/Cta	3/11	1	2	FACETS	1	0.977	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		327	437	SUCCESS
CUL3	8452	MSKCC	GRCh37	2	225342971	225342971	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1375147112	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	610	270	664	0	ENST00000264414.4:c.2121A>G	p.Ile707Met	p.I707M	ENST00000264414	NM_003590.4	707	atA/atG	15/16	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		664	880	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661054	227661054	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	496	39	428	1	ENST00000305123.5:c.2401G>A	p.Ala801Thr	p.A801T	ENST00000305123	NM_005544.2	801	Gct/Act	1/2	1	2	FACETS	0.564	0.467	0.672	0.564	0.467	0.672	SUBCLONAL	1	TRUE	1	0.258652869545824	2		429	535	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227661623	227661623	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	131	477	0	ENST00000305123.5:c.1832G>A	p.Gly611Asp	p.G611D	ENST00000305123	NM_005544.2	611	gGc/gAc	1/2	1	2	FACETS	0.918	0.836	1	1	0.989	1	CLONAL	2	TRUE	1	0.258652869545824	2		477	552	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662046	227662046	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	448	181	522	0	ENST00000305123.5:c.1409G>A	p.Gly470Asp	p.G470D	ENST00000305123	NM_005544.2	470	gGc/gAc	1/2	1	2	FACETS	1	0.974	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		522	629	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662466	227662466	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	40	368	1	ENST00000305123.5:c.989G>A	p.Ser330Asn	p.S330N	ENST00000305123	NM_005544.2	330	aGt/aAt	1/2	1	2	FACETS	0.779	0.648	0.924	0.779	0.648	0.924	CLONAL	1	TRUE	1	0.258652869545824	2		369	397	SUCCESS
IRS1	3667	MSKCC	GRCh37	2	227662968	227662968	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	654	288	715	0	ENST00000305123.5:c.487G>C	p.Val163Leu	p.V163L	ENST00000305123	NM_005544.2	163	Gtc/Ctc	1/2	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		715	942	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023441	31023441	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs776868653	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	177	481	1	ENST00000375687.4:c.2926C>T	p.Gln976Ter	p.Q976*	ENST00000375687	NM_015338.5	976	Caa/Taa	13/13	1	2	FACETS	1	0.968	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		482	633	SUCCESS
ASXL1	171023	MSKCC	GRCh37	20	31023697	31023697	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	291	649	0	ENST00000375687.4:c.3182C>T	p.Ala1061Val	p.A1061V	ENST00000375687	NM_015338.5	1061	gCt/gTt	13/13	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		649	912	SUCCESS
DNMT3B	1789	MSKCC	GRCh37	20	31380475	31380475	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777499803	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	258	527	1	ENST00000328111.2:c.965G>A	p.Gly322Glu	p.G322E	ENST00000328111	NM_006892.3	322	gGa/gAa	9/23	1	2	FACETS	0.869	0.817	0.922	1	0.996	1	CLONAL	3	TRUE	1	0.258652869545824	2		528	765	SUCCESS
SRC	6714	MSKCC	GRCh37	20	36012657	36012657	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	132	79	154	0	ENST00000358208.4:c.101C>T	p.Ala34Val	p.A34V	ENST00000358208		34	gCc/gTc	2/12	1	2	FACETS	0.965	0.865	1	1	0.988	1	CLONAL	3	TRUE	1	0.258652869545824	2		154	211	SUCCESS
TOP1	7150	MSKCC	GRCh37	20	39742739	39742739	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	559	246	557	0	ENST00000361337.2:c.1582G>A	p.Asp528Asn	p.D528N	ENST00000361337	NM_003286.2	528	Gac/Aac	15/21	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		557	805	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	41419842	41419842	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	451	197	503	0	ENST00000373198.4:c.479T>G	p.Phe160Cys	p.F160C	ENST00000373198	NM_133170.3	160	tTc/tGc	3/32	1	2	FACETS	1	0.983	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		503	648	SUCCESS
AURKA	6790	MSKCC	GRCh37	20	54945214	54945214	+	stop_lost	Nonstop_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	584	213	616	0	ENST00000312783.6:c.1212G>T	p.Ter404TyrextTer9	p.*404Yext*9	ENST00000312783	NM_198436.1	404	taG/taT	10/10	1	2	FACETS	1	0.955	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		616	797	SUCCESS
RTEL1	51750	MSKCC	GRCh37	20	62298895	62298895	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	658	292	740	0	ENST00000360203.5:c.688T>G	p.Leu230Val	p.L230V	ENST00000360203	NM_001283009.1	230	Ttg/Gtg	8/35	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		740	950	SUCCESS
ERG	2078	MSKCC	GRCh37	21	39755726	39755726	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	166	414	1	ENST00000288319.7:c.1039G>A	p.Val347Met	p.V347M	ENST00000288319	NM_182918.3	347	Gtg/Atg	10/10	1	2	FACETS	1	0.973	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		415	576	SUCCESS
ICOSLG	23308	MSKCC	GRCh37	21	45656861	45656861	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs200561939	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	507	237	543	1	ENST00000407780.3:c.295C>T	p.Arg99Cys	p.R99C	ENST00000407780	NM_001283052.1	99	Cgc/Tgc	3/7	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		544	744	SUCCESS
CRKL	1399	MSKCC	GRCh37	22	21304024	21304024	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	189	563	1	ENST00000354336.3:c.803G>T	p.Arg268Met	p.R268M	ENST00000354336	NM_005207.3	268	aGg/aTg	3/3	1	2	FACETS	0.981	0.909	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		564	745	SUCCESS
MAPK1	5594	MSKCC	GRCh37	22	22143090	22143090	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	557	180	540	0	ENST00000215832.6:c.617C>T	p.Thr206Ile	p.T206I	ENST00000215832	NM_002745.4	206	aCc/aTc	5/9	1	2	FACETS	0.944	0.873	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		540	737	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29091723	29091723	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	118	46	134	0	ENST00000328354.6:c.1234A>T	p.Ser412Cys	p.S412C	ENST00000328354	NM_007194.3	412	Agt/Tgt	11/15	1	2	FACETS	1	0.909	1	1	0.976	1	CLONAL	2	TRUE	1	0.258652869545824	2		134	164	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29121256	29121256	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	310	708	0	ENST00000328354.6:c.419G>T	p.Ser140Ile	p.S140I	ENST00000328354	NM_007194.3	140	aGc/aTc	3/15	1	2	FACETS	1	0.989	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		708	1009	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41523499	41523499	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs1432040176	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	356	154	354	0	ENST00000263253.7:c.915G>T	p.Gln305His	p.Q305H	ENST00000263253	NM_001429.3	305	caG/caT	4/31	1	2	FACETS	1	0.978	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		354	510	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41573470	41573470	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	709	293	762	1	ENST00000263253.7:c.5755C>T	p.Pro1919Ser	p.P1919S	ENST00000263253	NM_001429.3	1919	Cca/Tca	31/31	1	2	FACETS	1	0.985	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		763	1002	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574650	41574650	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	856	393	925	0	ENST00000263253.7:c.6935C>A	p.Pro2312His	p.P2312H	ENST00000263253	NM_001429.3	2312	cCt/cAt	31/31	1	2	FACETS	1	0.992	1	1	0.997	1	CLONAL	2	TRUE	1	0.258652869545824	2		925	1249	SUCCESS
TGFBR2	7048	MSKCC	GRCh37	3	30715707	30715707	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	125	289	0	ENST00000295754.5:c.1365G>A	p.Trp455Ter	p.W455*	ENST00000295754	NM_003242.5	455	tgG/tgA	5/7	1	2	FACETS	1	0.976	1	1	0.991	1	CLONAL	2	TRUE	1	0.258652869545824	2		289	403	SUCCESS
MLH1	4292	MSKCC	GRCh37	3	37053563	37053563	+	missense_variant	Missense_Mutation	SNP	G	G	C	rs762099920	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	804	91	714	0	ENST00000231790.2:c.650G>C	p.Arg217Pro	p.R217P	ENST00000231790	NM_000249.3	217	cGc/cCc	8/19	1	2	FACETS	0.786	0.697	0.882	0.786	0.697	0.882	SUBCLONAL	1	TRUE	1	0.258652869545824	2		714	895	SUCCESS
CTNNB1	1499	MSKCC	GRCh37	3	41280657	41280657	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	602	208	589	0	ENST00000349496.5:c.2170T>C	p.Tyr724His	p.Y724H	ENST00000349496	NM_001904.3	724	Tat/Cat	15/15	1	2	FACETS	0.993	0.924	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		589	810	SUCCESS
MST1R	4486	MSKCC	GRCh37	3	49924805	49924805	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	753	316	835	0	ENST00000296474.3:c.4138T>G	p.Phe1380Val	p.F1380V	ENST00000296474	NM_002447.2	1380	Ttc/Gtc	20/20	1	2	FACETS	1	0.987	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		835	1069	SUCCESS
BAP1	8314	MSKCC	GRCh37	3	52438467	52438467	+	splice_donor_variant	Splice_Site	SNP	A	A	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	164	540	0	ENST00000460680.1:c.1250+2T>C		p.X417_splice	ENST00000460680	NM_004656.3	417			1	2	FACETS	1	0.946	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		540	614	SUCCESS
MITF	4286	MSKCC	GRCh37	3	70005630	70005630	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	502	210	692	0	ENST00000394351.3:c.659T>C	p.Ile220Thr	p.I220T	ENST00000394351	NM_000248.3	220	aTa/aCa	7/9	1	2	FACETS	1	0.981	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		692	712	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89521648	89521648	+	missense_variant	Missense_Mutation	SNP	G	G	T	rs374961385	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	198	569	1	ENST00000336596.2:c.2725G>T	p.Asp909Tyr	p.D909Y	ENST00000336596	NM_005233.5	909	Gat/Tat	16/17	1	2	FACETS	1	0.981	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		570	667	SUCCESS
GATA2	2624	MSKCC	GRCh37	3	128204590	128204590	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	462	157	535	2	ENST00000341105.2:c.851G>A	p.Ser284Asn	p.S284N	ENST00000341105	NM_032638.4	284	aGc/aAc	3/6	1	2	FACETS	0.981	0.902	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		537	619	SUCCESS
FOXL2	668	MSKCC	GRCh37	3	138664936	138664936	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	307	147	362	0	ENST00000330315.3:c.629C>A	p.Pro210His	p.P210H	ENST00000330315	NM_023067.3	210	cCc/cAc	1/1	1	2	FACETS	0.835	0.768	0.903	1	0.993	1	CLONAL	3	TRUE	1	0.258652869545824	2		362	454	SUCCESS
ATR	545	MSKCC	GRCh37	3	142168300	142168300	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	362	192	448	0	ENST00000350721.4:c.7906A>T	p.Met2636Leu	p.M2636L	ENST00000350721	NM_001184.3	2636	Atg/Ttg	47/47	1	2	FACETS	0.893	0.832	0.956	1	0.995	1	CLONAL	3	TRUE	1	0.258652869545824	2		448	554	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215216	142215216	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	374	134	419	0	ENST00000350721.4:c.5885G>A	p.Trp1962Ter	p.W1962*	ENST00000350721	NM_001184.3	1962	tGg/tAg	34/47	1	2	FACETS	1	0.93	1	1	0.991	1	CLONAL	2	TRUE	1	0.258652869545824	2		419	508	SUCCESS
ATR	545	MSKCC	GRCh37	3	142215313	142215313	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	704	81	536	0	ENST00000350721.4:c.5788G>A	p.Val1930Ile	p.V1930I	ENST00000350721	NM_001184.3	1930	Gta/Ata	34/47	1	2	FACETS	0.798	0.702	0.901	0.798	0.702	0.901	CLONAL	1	TRUE	1	0.258652869545824	2		536	785	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178916540	178916540	+	splice_region_variant,5_prime_UTR_variant	Splice_Region	SNP	T	T	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	222	91	288	0	ENST00000263967.3:c.-74T>G		p.X25_splice	ENST00000263967	NM_006218.2	25		2/21	1	2	FACETS	1	0.957	1	1	0.988	1	CLONAL	2	TRUE	1	0.258652869545824	2		288	313	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185165665	185165665	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	211	500	0	ENST00000265026.3:c.940G>A	p.Ala314Thr	p.A314T	ENST00000265026	NM_004721.4	314	Gct/Act	5/14	1	2	FACETS	1	0.984	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		500	690	SUCCESS
FGFR3	2261	MSKCC	GRCh37	4	1806071	1806071	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	75	669	0	ENST00000260795.2:c.1090G>C	p.Val364Leu	p.V364L	ENST00000260795		364	Gtg/Ctg	8/17	1	2	FACETS	0.704	0.616	0.799	0.704	0.616	0.799	SUBCLONAL	1	TRUE	1	0.258652869545824	2		669	824	SUCCESS
NSD2	7468	MSKCC	GRCh37	4	1902833	1902833	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs754468750	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	723	323	714	0	ENST00000382891.5:c.452T>C	p.Val151Ala	p.V151A	ENST00000382891	NM_133335.3	151	gTg/gCg	2/22	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		714	1046	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66218770	66218770	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs747762296	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	449	159	552	0	ENST00000273854.3:c.2288C>T	p.Thr763Ile	p.T763I	ENST00000273854	NM_004439.5	763	aCa/aTa	13/18	1	2	FACETS	1	0.93	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		552	608	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66233078	66233079	+	missense_variant	Missense_Mutation	DNP	GC	GC	AT	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	117	485	0	ENST00000273854.3:c.1920_1921delinsAT	p.His641Tyr	p.H641Y	ENST00000273854	NM_004439.5	640	ggGCac/ggATac	10/18	1	2	FACETS	0.858	0.777	0.943	1	0.987	1	CLONAL	2	TRUE	1	0.258652869545824	2		485	527	SUCCESS
EPHA5	2044	MSKCC	GRCh37	4	66467438	66467438	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	87	260	0	ENST00000273854.3:c.831C>A	p.Ser277Arg	p.S277R	ENST00000273854	NM_004439.5	277	agC/agA	3/18	1	2	FACETS	1	0.943	1	1	0.987	1	CLONAL	2	TRUE	1	0.258652869545824	2		260	311	SUCCESS
ABRAXAS1	84142	MSKCC	GRCh37	4	84384014	84384015	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	278	697	0	ENST00000321945.7:c.837dup	p.Leu280SerfsTer13	p.L280Sfs*13	ENST00000321945	NM_139076.2	279	-/T	9/9	1	2	FACETS	1	0.986	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		697	939	SUCCESS
EIF4E	1977	MSKCC	GRCh37	4	99808298	99808298	+	stop_gained	Nonsense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	141	420	0	ENST00000280892.6:c.391G>T	p.Gly131Ter	p.G131*	ENST00000280892	NM_001130678.1	131	Gga/Tga	5/7	1	2	FACETS	1	0.951	1	1	0.991	1	CLONAL	2	TRUE	1	0.258652869545824	2		420	518	SUCCESS
INPP4B	8821	MSKCC	GRCh37	4	143007302	143007302	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs548378688	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	128	436	0	ENST00000262992.4:c.2482G>A	p.Ala828Thr	p.A828T	ENST00000262992	NM_001101669.1	828	Gca/Aca	22/24	1	2	FACETS	0.91	0.828	0.995	1	0.989	1	CLONAL	2	TRUE	1	0.258652869545824	2		436	544	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153244065	153244065	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	576	72	539	0	ENST00000281708.4:c.2092C>G	p.Leu698Val	p.L698V	ENST00000281708	NM_033632.3	698	Ctg/Gtg	12/12	1	2	FACETS	0.859	0.751	0.976	0.859	0.751	0.976	CLONAL	1	TRUE	1	0.258652869545824	2		539	648	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187524776	187524776	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	51	589	1	ENST00000441802.2:c.10904C>T	p.Thr3635Ile	p.T3635I	ENST00000441802	NM_005245.3	3635	aCa/aTa	19/27	1	2	FACETS	0.53	0.449	0.619	0.53	0.449	0.619	SUBCLONAL	1	TRUE	1	0.258652869545824	2		590	744	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187539323	187539323	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	155	392	2	ENST00000441802.2:c.8417G>T	p.Ser2806Ile	p.S2806I	ENST00000441802	NM_005245.3	2806	aGc/aTc	10/27	1	2	FACETS	1	0.979	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		394	508	SUCCESS
FAT1	2195	MSKCC	GRCh37	4	187542779	187542779	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs369592206	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	436	203	507	1	ENST00000441802.2:c.4961G>A	p.Arg1654His	p.R1654H	ENST00000441802	NM_005245.3	1654	cGt/cAt	10/27	1	2	FACETS	1	0.986	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		508	639	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1260641	1260641	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	866	117	786	0	ENST00000310581.5:c.2918A>G	p.Lys973Arg	p.K973R	ENST00000310581	NM_198253.2	973	aAa/aGa	12/16	1	2	FACETS	0.92	0.829	1	0.92	0.829	1	CLONAL	1	TRUE	1	0.258652869545824	2		786	983	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31410992	31410992	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	781	100	671	0	ENST00000344624.3:c.3528G>C	p.Leu1176Phe	p.L1176F	ENST00000344624		1176	ttG/ttC	28/33	1	2	FACETS	0.878	0.783	0.979	0.878	0.783	0.979	CLONAL	1	TRUE	1	0.258652869545824	2		671	881	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31431691	31431691	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	551	176	532	0	ENST00000344624.3:c.3137C>T	p.Ala1046Val	p.A1046V	ENST00000344624		1046	gCg/gTg	23/33	1	2	FACETS	0.936	0.864	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		532	727	SUCCESS
DROSHA	29102	MSKCC	GRCh37	5	31468160	31468160	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	567	243	634	0	ENST00000344624.3:c.2252C>T	p.Ser751Phe	p.S751F	ENST00000344624		751	tCt/tTt	15/33	1	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		634	810	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38960074	38960074	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	124	359	1	ENST00000357387.3:c.1858C>T	p.Gln620Ter	p.Q620*	ENST00000357387	NM_152756.3	620	Caa/Taa	21/38	1	2	FACETS	0.89	0.815	0.968	1	0.992	1	CLONAL	3	TRUE	1	0.258652869545824	2		360	359	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189422	56189422	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	651	218	768	1	ENST00000399503.3:c.4454C>A	p.Ala1485Asp	p.A1485D	ENST00000399503	NM_005921.1	1485	gCt/gAt	20/20	1	2	FACETS	0.97	0.903	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		769	869	SUCCESS
MAP3K1	4214	MSKCC	GRCh37	5	56189487	56189487	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs759161230	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	488	169	551	1	ENST00000399503.3:c.4519G>A	p.Val1507Ile	p.V1507I	ENST00000399503	NM_005921.1	1507	Gtc/Atc	20/20	1	2	FACETS	0.994	0.918	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		552	657	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57751396	57751396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	116	306	0	ENST00000274289.3:c.1595G>A	p.Gly532Asp	p.G532D	ENST00000274289	NM_006622.3	532	gGt/gAt	11/14	1	2	FACETS	1	0.931	1	1	0.989	1	CLONAL	2	TRUE	1	0.258652869545824	2		306	435	SUCCESS
PIK3R1	5295	MSKCC	GRCh37	5	67590429	67590429	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	371	142	409	3	ENST00000274335.5:c.1491G>T	p.Gln497His	p.Q497H	ENST00000274335		497	caG/caT	11/15	1	2	FACETS	1	0.958	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		412	513	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	80171577	80171577	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	483	206	596	0	ENST00000265081.6:c.3310C>A	p.Leu1104Ile	p.L1104I	ENST00000265081	NM_002439.4	1104	Ctc/Atc	24/24	1	2	FACETS	1	0.982	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		596	689	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86669984	86669984	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	427	57	449	0	ENST00000274376.6:c.1781G>A	p.Ser594Asn	p.S594N	ENST00000274376	NM_002890.2	594	aGc/aAc	14/25	1	2	FACETS	0.911	0.782	1	0.911	0.782	1	CLONAL	1	TRUE	1	0.258652869545824	2		449	484	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86672849	86672849	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	16	249	0	ENST00000274376.6:c.2336G>C	p.Ser779Thr	p.S779T	ENST00000274376	NM_002890.2	779	aGc/aCc	17/25	1	2	FACETS	0.41	0.302	0.538	0.41	0.302	0.538	SUBCLONAL	1	TRUE	1	0.258652869545824	2		249	302	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86682692	86682692	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs757298110	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	286	88	284	0	ENST00000274376.6:c.2897G>A	p.Arg966His	p.R966H	ENST00000274376	NM_002890.2	966	cGt/cAt	23/25	1	2	FACETS	0.91	0.812	1	1	0.985	1	CLONAL	2	TRUE	1	0.258652869545824	2		284	374	SUCCESS
APC	324	MSKCC	GRCh37	5	112175262	112175262	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	106	319	0	ENST00000257430.4:c.3971C>A	p.Pro1324Gln	p.P1324Q	ENST00000257430	NM_000038.5	1324	cCa/cAa	16/16	1	2	FACETS	0.969	0.875	1	1	0.988	1	CLONAL	2	TRUE	1	0.258652869545824	2		319	423	SUCCESS
APC	324	MSKCC	GRCh37	5	112175364	112175364	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs730881249	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	248	95	326	0	ENST00000257430.4:c.4073C>T	p.Ala1358Val	p.A1358V	ENST00000257430	NM_000038.5	1358	gCg/gTg	16/16	1	2	FACETS	1	0.942	1	1	0.988	1	CLONAL	2	TRUE	1	0.258652869545824	2		326	343	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131915585	131915585	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	352	98	434	0	ENST00000265335.6:c.583G>C	p.Val195Leu	p.V195L	ENST00000265335		195	Gta/Cta	5/25	1	2	FACETS	0.842	0.755	0.933	1	0.985	1	CLONAL	2	TRUE	1	0.258652869545824	2		434	450	SUCCESS
RAD50	10111	MSKCC	GRCh37	5	131924462	131924462	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	486	192	584	0	ENST00000265335.6:c.1135G>A	p.Glu379Lys	p.E379K	ENST00000265335		379	Gaa/Aaa	8/25	1	2	FACETS	1	0.973	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		584	678	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433721	149433721	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs761835712	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	693	39	620	0	ENST00000286301.3:c.2830G>A	p.Glu944Lys	p.E944K	ENST00000286301	NM_005211.3	944	Gag/Aag	22/22	1	2	FACETS	0.412	0.34	0.492	0.412	0.34	0.492	SUBCLONAL	1	TRUE	1	0.258652869545824	2		620	732	SUCCESS
CSF1R	1436	MSKCC	GRCh37	5	149433780	149433780	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1417120408	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	165	579	0	ENST00000286301.3:c.2771C>T	p.Thr924Ile	p.T924I	ENST00000286301	NM_005211.3	924	aCc/aTc	22/22	1	2	FACETS	0.909	0.837	0.983	1	0.991	1	CLONAL	2	TRUE	1	0.258652869545824	2		579	702	SUCCESS
PDGFRB	5159	MSKCC	GRCh37	5	149512400	149512400	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	818	81	682	0	ENST00000261799.4:c.1040C>T	p.Thr347Ile	p.T347I	ENST00000261799	NM_002609.3	347	aCt/aTt	7/23	1	2	FACETS	0.697	0.613	0.787	0.697	0.613	0.787	SUBCLONAL	1	TRUE	1	0.258652869545824	2		682	899	SUCCESS
FGFR4	2264	MSKCC	GRCh37	5	176520693	176520693	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	643	226	634	0	ENST00000292408.4:c.1436G>A	p.Gly479Asp	p.G479D	ENST00000292408	NM_213647.1	479	gGc/gAc	11/18	1	2	FACETS	1	0.938	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		634	869	SUCCESS
NSD1	64324	MSKCC	GRCh37	5	176562909	176562909	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs751787444	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	826	327	748	2	ENST00000439151.2:c.805G>A	p.Glu269Lys	p.E269K	ENST00000439151	NM_022455.4	269	Gag/Aag	2/23	1	2	FACETS	1	0.983	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		750	1153	SUCCESS
FLT4	2324	MSKCC	GRCh37	5	180036949	180036949	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	699	312	718	1	ENST00000261937.6:c.3763T>G	p.Phe1255Val	p.F1255V	ENST00000261937	NM_182925.4	1255	Ttt/Gtt	28/30	1	2	FACETS	1	0.99	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		719	1011	SUCCESS
H3C3	8968	MSKCC	GRCh37	6	26045981	26045981	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1377734473	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	376	151	350	2	ENST00000540144.1:c.343G>A	p.Ala115Thr	p.A115T	ENST00000540144	NM_003531.2	115	Gct/Act	1/1	1	2	FACETS	1	0.969	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		352	527	SUCCESS
H1-2	3006	MSKCC	GRCh37	6	26056478	26056478	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs564431683	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	64	188	0	ENST00000343677.2:c.179C>T	p.Ala60Val	p.A60V	ENST00000343677	NM_005319.3	60	gCt/gTt	1/1	1	2	FACETS	0.941	0.823	1	1	0.98	1	CLONAL	2	TRUE	1	0.258652869545824	2		188	263	SUCCESS
H3C6	8968	MSKCC	GRCh37	6	26225776	26225776	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1186783518	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	421	120	384	0	ENST00000360408.1:c.394C>T	p.Arg132Cys	p.R132C	ENST00000360408	NM_003532.2	132	Cgt/Tgt	1/1	1	2	FACETS	0.858	0.778	0.941	1	0.988	1	CLONAL	2	TRUE	1	0.258652869545824	2		384	541	SUCCESS
MDC1	9656	MSKCC	GRCh37	6	30671519	30671519	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	260	695	0	ENST00000376406.3:c.5441C>A	p.Ser1814Tyr	p.S1814Y	ENST00000376406	NM_014641.2	1814	tCt/tAt	10/15	1	2	FACETS	1	0.975	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		695	935	SUCCESS
HLA-B	3106	MSKCC	GRCh37	6	31323133	31323133	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	510	209	516	2	ENST00000412585.2:c.856C>T	p.Gln286Ter	p.Q286*	ENST00000412585	NM_005514.6	286	Cag/Tag	4/8	1	2	FACETS	1	0.979	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		518	719	SUCCESS
NOTCH4	4855	MSKCC	GRCh37	6	32170273	32170273	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs770685356	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	248	644	0	ENST00000375023.3:c.3335C>T	p.Pro1112Leu	p.P1112L	ENST00000375023	NM_004557.3	1112	cCa/cTa	21/30	1	2	FACETS	1	0.98	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		644	864	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32797287	32797287	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	742	368	727	0	ENST00000374899.4:c.1822G>A	p.Ala608Thr	p.A608T	ENST00000374899	NM_018833.2	608	Gct/Act	11/12	1	2	FACETS	0.855	0.811	0.898	1	0.997	1	CLONAL	3	TRUE	1	0.258652869545824	2		727	1110	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32798169	32798169	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	725	284	716	1	ENST00000374899.4:c.1510C>T	p.Pro504Ser	p.P504S	ENST00000374899	NM_018833.2	504	Ccc/Tcc	9/12	1	2	FACETS	1	0.98	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		717	1009	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32803419	32803419	+	splice_donor_variant	Splice_Site	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	253	677	0	ENST00000374899.4:c.739+1G>A		p.X247_splice	ENST00000374899	NM_018833.2	247			1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		677	825	SUCCESS
TAP2	6891	MSKCC	GRCh37	6	32805548	32805548	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs763454543	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	391	935	2	ENST00000374899.4:c.463G>A	p.Ala155Thr	p.A155T	ENST00000374899	NM_018833.2	155	Gcc/Acc	2/12	1	2	FACETS	1	0.991	1	1	0.997	1	CLONAL	2	TRUE	1	0.258652869545824	2		937	1287	SUCCESS
CDKN1A	1026	MSKCC	GRCh37	6	36652205	36652205	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	644	81	553	1	ENST00000244741.5:c.327C>A	p.Asp109Glu	p.D109E	ENST00000244741	NM_000389.4	109	gaC/gaA	2/3	1	2	FACETS	0.864	0.761	0.975	0.864	0.761	0.975	CLONAL	1	TRUE	1	0.258652869545824	2		554	725	SUCCESS
PIM1	5292	MSKCC	GRCh37	6	37140869	37140869	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	487	178	543	1	ENST00000373509.5:c.705G>A	p.Met235Ile	p.M235I	ENST00000373509	NM_002648.3	235	atG/atA	5/6	1	2	FACETS	1	0.95	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		544	665	SUCCESS
PNRC1	10957	MSKCC	GRCh37	6	89793877	89793877	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	43	517	0	ENST00000336032.3:c.946G>A	p.Ala316Thr	p.A316T	ENST00000336032	NM_006813.2	316	Gca/Aca	2/2	1	2	FACETS	0.533	0.445	0.631	0.533	0.445	0.631	SUBCLONAL	1	TRUE	1	0.258652869545824	2		517	624	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93956704	93956704	+	splice_acceptor_variant	Splice_Site	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	143	348	0	ENST00000369303.4:c.2533-1G>T		p.X845_splice	ENST00000369303	NM_004440.3	845			1	2	FACETS	1	0.979	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		348	459	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93965644	93965644	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	220	691	1	ENST00000369303.4:c.2284C>T	p.Arg762Cys	p.R762C	ENST00000369303	NM_004440.3	762	Cgc/Tgc	13/17	1	2	FACETS	1	0.972	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		692	790	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93967946	93967946	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	598	187	601	0	ENST00000369303.4:c.1981G>A	p.Ala661Thr	p.A661T	ENST00000369303	NM_004440.3	661	Gca/Aca	11/17	1	2	FACETS	0.921	0.852	0.992	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		601	785	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	93979293	93979293	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	415	133	554	0	ENST00000369303.4:c.1535T>C	p.Val512Ala	p.V512A	ENST00000369303	NM_004440.3	512	gTt/gCt	7/17	1	2	FACETS	0.938	0.856	1	1	0.99	1	CLONAL	2	TRUE	1	0.258652869545824	2		554	548	SUCCESS
SESN1	27244	MSKCC	GRCh37	6	109323507	109323507	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	815	302	892	2	ENST00000436639.2:c.319C>T	p.Pro107Ser	p.P107S	ENST00000436639	NM_014454.2	107	Cca/Tca	2/10	1	2	FACETS	1	0.97	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		894	1117	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117642507	117642507	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	268	786	2	ENST00000368508.3:c.5692G>A	p.Val1898Met	p.V1898M	ENST00000368508	NM_002944.2	1898	Gtg/Atg	35/43	1	2	FACETS	1	0.971	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		788	982	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117687424	117687424	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	345	134	381	1	ENST00000368508.3:c.2627C>T	p.Ala876Val	p.A876V	ENST00000368508	NM_002944.2	876	gCa/gTa	18/43	1	2	FACETS	1	0.959	1	1	0.991	1	CLONAL	2	TRUE	1	0.258652869545824	2		382	479	SUCCESS
IFNGR1	3459	MSKCC	GRCh37	6	137519506	137519506	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	35	371	0	ENST00000367739.4:c.1132A>C	p.Ser378Arg	p.S378R	ENST00000367739	NM_000416.2	378	Agt/Cgt	7/7	1	2	FACETS	0.53	0.433	0.638	0.53	0.433	0.638	SUBCLONAL	1	TRUE	1	0.258652869545824	2		371	511	SUCCESS
LATS1	9113	MSKCC	GRCh37	6	150004486	150004486	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	37	503	0	ENST00000253339.5:c.1739G>C	p.Ser580Thr	p.S580T	ENST00000253339		580	aGc/aCc	3/7	1	2	FACETS	0.39	0.32	0.468	0.39	0.32	0.468	SUBCLONAL	1	TRUE	1	0.258652869545824	2		503	734	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157469919	157469919	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	214	518	1	ENST00000346085.5:c.2713C>T	p.Gln905Ter	p.Q905*	ENST00000346085	NM_020732.3	905	Cag/Tag	9/20	1	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		519	694	SUCCESS
ARID1B	57492	MSKCC	GRCh37	6	157528598	157528598	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	735	309	768	0	ENST00000346085.5:c.6323A>G	p.Gln2108Arg	p.Q2108R	ENST00000346085	NM_020732.3	2108	cAg/cGg	20/20	1	2	FACETS	1	0.987	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		768	1044	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2946306	2946306	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs573740263	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	756	309	837	2	ENST00000396946.4:c.3431G>A	p.Arg1144His	p.R1144H	ENST00000396946	NM_032415.4	1144	cGc/cAc	25/25	1	2	FACETS	1	0.985	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		839	1065	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2976846	2976846	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	217	616	1	ENST00000396946.4:c.1166C>A	p.Ala389Asp	p.A389D	ENST00000396946	NM_032415.4	389	gCt/gAt	9/25	1	2	FACETS	1	0.956	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		617	811	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2978455	2978455	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs747972220	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	491	188	573	2	ENST00000396946.4:c.875G>A	p.Arg292His	p.R292H	ENST00000396946	NM_032415.4	292	cGc/cAc	7/25	1	2	FACETS	1	0.966	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		575	679	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2987343	2987343	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	680	277	740	1	ENST00000396946.4:c.86A>G	p.Asn29Ser	p.N29S	ENST00000396946	NM_032415.4	29	aAc/aGc	3/25	1	2	FACETS	1	0.983	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		741	957	SUCCESS
PMS2	5395	MSKCC	GRCh37	7	6038813	6038813	+	stop_gained	Nonsense_Mutation	SNP	G	G	A	rs760228510	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	784	351	820	0	ENST00000265849.7:c.631C>T	p.Arg211Ter	p.R211*	ENST00000265849	NM_000535.5	211	Cga/Tga	6/15	1	2	FACETS	1	0.991	1	1	0.997	1	CLONAL	2	TRUE	1	0.258652869545824	2		820	1135	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13935528	13935528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781723736	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	298	110	306	0	ENST00000405192.2:c.1328G>A	p.Cys443Tyr	p.C443Y	ENST00000405192	NM_001163147.1	443	tGc/tAc	12/12	1	2	FACETS	1	0.936	1	1	0.989	1	CLONAL	2	TRUE	1	0.258652869545824	2		306	408	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41729766	41729766	+	missense_variant	Missense_Mutation	SNP	C	C	A	rs1163090037	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	325	131	331	0	ENST00000242208.4:c.763G>T	p.Val255Phe	p.V255F	ENST00000242208	NM_002192.2	255	Gtt/Ttt	3/3	1	2	FACETS	1	0.966	1	1	0.991	1	CLONAL	2	TRUE	1	0.258652869545824	2		331	456	SUCCESS
INHBA	3624	MSKCC	GRCh37	7	41739699	41739699	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	352	821	0	ENST00000242208.4:c.274G>A	p.Val92Met	p.V92M	ENST00000242208	NM_002192.2	92	Gtg/Atg	2/3	1	2	FACETS	0.874	0.829	0.919	1	0.997	1	CLONAL	3	TRUE	1	0.258652869545824	2		821	1038	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55259420	55259420	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	324	148	348	0	ENST00000275493.2:c.2478C>G	p.Asn826Lys	p.N826K	ENST00000275493	NM_005228.3	826	aaC/aaG	21/28	1	2	FACETS	1	0.981	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		348	472	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106519993	106519994	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs770069386	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	429	154	460	0	ENST00000359195.3:c.2427dup	p.Pro810ThrfsTer5	p.P810Tfs*5	ENST00000359195	NM_002649.2	807	-/A	6/11	1	2	FACETS	1	0.937	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		460	583	SUCCESS
MET	4233	MSKCC	GRCh37	7	116411561	116411561	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	99	296	0	ENST00000397752.3:c.2740G>T	p.Ala914Ser	p.A914S	ENST00000397752	NM_000245.2	914	Gca/Tca	13/21	1	2	FACETS	0.916	0.823	1	1	0.986	1	CLONAL	2	TRUE	1	0.258652869545824	2		296	418	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128843302	128843302	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	765	269	734	2	ENST00000249373.3:c.409G>A	p.Asp137Asn	p.D137N	ENST00000249373	NM_005631.4	137	Gac/Aac	2/12	1	2	FACETS	1	0.944	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		736	1034	SUCCESS
SMO	6608	MSKCC	GRCh37	7	128846363	128846363	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs754146515	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	772	87	652	2	ENST00000249373.3:c.1199G>A	p.Arg400His	p.R400H	ENST00000249373	NM_005631.4	400	cGt/cAt	6/12	1	2	FACETS	0.783	0.692	0.881	0.783	0.692	0.881	SUBCLONAL	1	TRUE	1	0.258652869545824	2		654	859	SUCCESS
BRAF	673	MSKCC	GRCh37	7	140482928	140482928	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs749792302	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	675	228	712	2	ENST00000288602.6:c.1207C>T	p.Pro403Ser	p.P403S	ENST00000288602	NM_004333.4	403	Cct/Tct	10/18	1	2	FACETS	0.976	0.911	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		714	903	SUCCESS
EZH2	2146	MSKCC	GRCh37	7	148506223	148506223	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	621	238	663	0	ENST00000320356.2:c.2135G>T	p.Arg712Met	p.R712M	ENST00000320356	NM_004456.4	712	aGg/aTg	19/20	1	2	FACETS	1	0.972	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		663	859	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151845282	151845282	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	110	398	0	ENST00000262189.6:c.13730C>A	p.Pro4577His	p.P4577H	ENST00000262189	NM_170606.2	4577	cCt/cAt	52/59	1	2	FACETS	0.984	0.891	1	1	0.988	1	CLONAL	2	TRUE	1	0.258652869545824	2		398	432	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151860842	151860842	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs781376139	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	353	141	363	0	ENST00000262189.6:c.9820G>A	p.Ala3274Thr	p.A3274T	ENST00000262189	NM_170606.2	3274	Gca/Aca	43/59	1	2	FACETS	1	0.966	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		363	494	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151932973	151932973	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1366232611	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	43	36	38	1	ENST00000262189.6:c.2698G>A	p.Gly900Arg	p.G900R	ENST00000262189	NM_170606.2	900	Gga/Aga	16/59	1	2	FACETS	0.881	0.754	1	1	0.976	1	CLONAL	4	TRUE	1	0.258652869545824	2		39	79	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38133928	38133928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	959	352	960	1	ENST00000317025.8:c.3958C>T	p.His1320Tyr	p.H1320Y	ENST00000317025	NM_023034.1	1320	Cat/Tat	23/24	1	2	FACETS	1	0.971	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		961	1311	SUCCESS
NSD3	54904	MSKCC	GRCh37	8	38162817	38162817	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	661	195	655	0	ENST00000317025.8:c.2389C>T	p.His797Tyr	p.H797Y	ENST00000317025	NM_023034.1	797	Cac/Tac	13/24	1	2	FACETS	0.881	0.816	0.948	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		655	856	SUCCESS
FGFR1	2260	MSKCC	GRCh37	8	38273544	38273544	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	348	167	436	1	ENST00000425967.3:c.1791G>T	p.Lys597Asn	p.K597N	ENST00000425967	NM_001174067.1	597	aaG/aaT	14/19	1	2	FACETS	0.836	0.774	0.9	1	0.994	1	CLONAL	3	TRUE	1	0.258652869545824	2		437	515	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68992718	68992718	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	659	257	811	0	ENST00000288368.4:c.1683C>A	p.Phe561Leu	p.F561L	ENST00000288368	NM_024870.2	561	ttC/ttA	16/40	1	2	FACETS	1	0.977	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		811	916	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	69002932	69002932	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	316	99	358	0	ENST00000288368.4:c.2232G>C	p.Lys744Asn	p.K744N	ENST00000288368	NM_024870.2	744	aaG/aaC	20/40	1	2	FACETS	0.922	0.829	1	1	0.986	1	CLONAL	2	TRUE	1	0.258652869545824	2		358	415	SUCCESS
PRDM14	63978	MSKCC	GRCh37	8	70970918	70970918	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	586	245	662	0	ENST00000276594.2:c.1343G>T	p.Arg448Leu	p.R448L	ENST00000276594	NM_024504.3	448	cGg/cTg	6/8	1	2	FACETS	1	0.983	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		662	831	SUCCESS
RAD21	5885	MSKCC	GRCh37	8	117859788	117859788	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	306	81	329	0	ENST00000297338.2:c.1847C>T	p.Pro616Leu	p.P616L	ENST00000297338	NM_006265.2	616	cCg/cTg	14/14	1	2	FACETS	0.809	0.717	0.906	1	0.98	1	CLONAL	2	TRUE	1	0.258652869545824	2		329	387	SUCCESS
AGO2	27161	MSKCC	GRCh37	8	141559317	141559317	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	475	224	529	0	ENST00000220592.5:c.1484C>T	p.Ala495Val	p.A495V	ENST00000220592	NM_012154.3	495	gCg/gTg	12/19	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		529	699	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739000	145739000	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	513	194	509	1	ENST00000428558.2:c.2155C>A	p.Leu719Ile	p.L719I	ENST00000428558	NM_004260.3	719	Ctc/Atc	13/22	1	2	FACETS	1	0.964	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		510	707	SUCCESS
RECQL4	9401	MSKCC	GRCh37	8	145739017	145739017	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	743	85	586	0	ENST00000428558.2:c.2138C>T	p.Thr713Ile	p.T713I	ENST00000428558	NM_004260.3	713	aCa/aTa	13/22	1	2	FACETS	0.794	0.701	0.894	0.794	0.701	0.894	SUBCLONAL	1	TRUE	1	0.258652869545824	2		586	828	SUCCESS
JAK2	3717	MSKCC	GRCh37	9	5069981	5069981	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	187	592	1	ENST00000381652.3:c.1570C>T	p.Pro524Ser	p.P524S	ENST00000381652	NM_004972.3	524	Cca/Tca	12/25	1	2	FACETS	0.974	0.903	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		593	742	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8376044	8376044	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs147319681	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	308	134	384	1	ENST00000356435.5:c.4553C>T	p.Ala1518Val	p.A1518V	ENST00000356435		1518	gCc/gTc	28/35	1	2	FACETS	1	0.975	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		385	442	SUCCESS
PTPRD	5789	MSKCC	GRCh37	9	8521290	8521290	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	278	96	273	0	ENST00000356435.5:c.948G>T	p.Gln316His	p.Q316H	ENST00000356435		316	caG/caT	9/35	1	2	FACETS	0.992	0.891	1	1	0.987	1	CLONAL	2	TRUE	1	0.258652869545824	2		273	374	SUCCESS
CDKN2A	1029	MSKCC	GRCh37	9	21994279	21994279	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	489	193	599	0	ENST00000579755.1:c.52C>T	p.Pro18Ser	p.P18S	ENST00000579755		18	Ccg/Tcg	1/3	1				0.973	1				CLONAL	2	TRUE	1	0.258652869545824	2		599	682	SUCCESS
NTRK2	4915	MSKCC	GRCh37	9	87563474	87563474	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	570	233	598	0	ENST00000277120.3:c.1862G>A	p.Gly621Asp	p.G621D	ENST00000277120		621	gGc/gAc	16/19	1	2	FACETS	1	0.981	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		598	803	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93641165	93641165	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	590	244	636	0	ENST00000375746.1:c.1511C>T	p.Thr504Ile	p.T504I	ENST00000375746	NM_001174167.1	504	aCc/aTc	11/14	1	2	FACETS	1	0.983	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		636	834	SUCCESS
SYK	6850	MSKCC	GRCh37	9	93650821	93650821	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	317	155	399	0	ENST00000375746.1:c.1747G>T	p.Ala583Ser	p.A583S	ENST00000375746	NM_001174167.1	583	Gct/Tct	13/14	1	2	FACETS	0.846	0.781	0.913	1	0.993	1	CLONAL	3	TRUE	1	0.258652869545824	2		399	472	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97864128	97864128	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	456	168	513	0	ENST00000289081.3:c.1538C>A	p.Ala513Asp	p.A513D	ENST00000289081	NM_000136.2	513	gCt/gAt	15/15	1	2	FACETS	1	0.951	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		513	624	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	97912214	97912214	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	583	177	622	0	ENST00000289081.3:c.677C>A	p.Ala226Asp	p.A226D	ENST00000289081	NM_000136.2	226	gCc/gAc	7/15	1	2	FACETS	0.9	0.831	0.972	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		622	760	SUCCESS
FANCC	2176	MSKCC	GRCh37	9	98009785	98009785	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	519	31	491	0	ENST00000289081.3:c.179T>A	p.Val60Asp	p.V60D	ENST00000289081	NM_000136.2	60	gTc/gAc	3/15	1	2	FACETS	0.436	0.352	0.532	0.436	0.352	0.532	SUBCLONAL	1	TRUE	1	0.258652869545824	2		491	550	SUCCESS
PTCH1	5727	MSKCC	GRCh37	9	98220342	98220342	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	400	178	389	1	ENST00000331920.6:c.3121C>T	p.Leu1041Phe	p.L1041F	ENST00000331920	NM_000264.3	1041	Ctc/Ttc	18/24	1	2	FACETS	1	0.982	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		390	578	SUCCESS
TGFBR1	7046	MSKCC	GRCh37	9	101900284	101900284	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs775429965	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	387	154	372	1	ENST00000374994.4:c.718C>T	p.Arg240Cys	p.R240C	ENST00000374994	NM_004612.2	240	Cgt/Tgt	4/9	1	2	FACETS	1	0.968	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		373	541	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110248159	110248159	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	131	452	2	ENST00000374672.4:c.1313C>T	p.Ala438Val	p.A438V	ENST00000374672	NM_004235.4	438	gCc/gTc	5/5	1	2	FACETS	0.926	0.844	1	1	0.99	1	CLONAL	2	TRUE	1	0.258652869545824	2		454	547	SUCCESS
KLF4	9314	MSKCC	GRCh37	9	110250244	110250244	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1471124290	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	459	193	516	1	ENST00000374672.4:c.431C>T	p.Ala144Val	p.A144V	ENST00000374672	NM_004235.4	144	gCg/gTg	3/5	1	2	FACETS	1	0.98	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		517	652	SUCCESS
MAPKAP1	79109	MSKCC	GRCh37	9	128347861	128347861	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	563	179	671	0	ENST00000265960.3:c.644C>G	p.Thr215Arg	p.T215R	ENST00000265960	NM_001006617.1	215	aCa/aGa	5/12	1	2	FACETS	0.933	0.862	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		671	742	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135781439	135781439	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs118203543	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	359	152	407	0	ENST00000298552.3:c.1526G>A	p.Arg509Gln	p.R509Q	ENST00000298552	NM_001162426.1	509	cGa/cAa	15/23	1	2	FACETS	1	0.976	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		407	511	SUCCESS
TSC1	7248	MSKCC	GRCh37	9	135782738	135782738	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1554816420	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	480	173	481	0	ENST00000298552.3:c.1283C>T	p.Ala428Val	p.A428V	ENST00000298552	NM_001162426.1	428	gCa/gTa	13/23	1	2	FACETS	1	0.943	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		481	653	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395074	139395074	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	530	178	578	1	ENST00000277541.6:c.5864A>G	p.Asn1955Ser	p.N1955S	ENST00000277541	NM_017617.3	1955	aAc/aGc	31/34	1	2	FACETS	0.972	0.899	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		579	708	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139395161	139395161	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771407924	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	640	280	663	2	ENST00000277541.6:c.5777G>A	p.Arg1926His	p.R1926H	ENST00000277541	NM_017617.3	1926	cGc/cAc	31/34	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		665	920	SUCCESS
TRAF2	7186	MSKCC	GRCh37	9	139820243	139820243	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1465825300	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	620	274	673	1	ENST00000247668.2:c.1396G>A	p.Ala466Thr	p.A466T	ENST00000247668	NM_021138.3	466	Gca/Aca	11/11	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		674	894	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39931759	39931759	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	692	274	706	0	ENST00000378444.4:c.2840C>T	p.Ala947Val	p.A947V	ENST00000378444	NM_001123385.1	947	gCt/gTt	4/15	1	2	FACETS	1	0.98	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		706	966	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39932463	39932463	+	missense_variant	Missense_Mutation	SNP	C	C	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	47	640	0	ENST00000378444.4:c.2136G>C	p.Glu712Asp	p.E712D	ENST00000378444	NM_001123385.1	712	gaG/gaC	4/15	1	2	FACETS	0.428	0.359	0.503	0.428	0.359	0.503	SUBCLONAL	1	TRUE	1	0.258652869545824	2		640	850	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934322	39934322	+	missense_variant	Missense_Mutation	SNP	A	A	C	rs780311291	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	616	208	705	1	ENST00000378444.4:c.277T>G	p.Leu93Val	p.L93V	ENST00000378444	NM_001123385.1	93	Ttg/Gtg	4/15	1	2	FACETS	0.976	0.908	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		706	824	SUCCESS
BCOR	54880	MSKCC	GRCh37	X	39934334	39934334	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs754807742	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	600	208	663	3	ENST00000378444.4:c.265G>A	p.Val89Ile	p.V89I	ENST00000378444	NM_001123385.1	89	Gtc/Atc	4/15	1	2	FACETS	0.995	0.926	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		666	808	SUCCESS
KDM6A	7403	MSKCC	GRCh37	X	44950012	44950012	+	missense_variant	Missense_Mutation	SNP	T	T	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	505	236	623	0	ENST00000377967.4:c.3781T>A	p.Leu1261Met	p.L1261M	ENST00000377967	NM_021140.2	1261	Ttg/Atg	26/29	1	2	FACETS	1	0.988	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		623	741	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47030499	47030499	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs372162654	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	714	265	787	1	ENST00000377604.3:c.274G>A	p.Gly92Ser	p.G92S	ENST00000377604	NM_001204468.1	92	Ggc/Agc	4/24	1	2	FACETS	1	0.967	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		788	979	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47038881	47038881	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	614	240	679	0	ENST00000377604.3:c.888G>C	p.Glu296Asp	p.E296D	ENST00000377604	NM_001204468.1	296	gaG/gaC	9/24	1	2	FACETS	1	0.976	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		679	854	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47040945	47040945	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1447493714	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	242	853	2	ENST00000377604.3:c.1475C>T	p.Ser492Leu	p.S492L	ENST00000377604	NM_001204468.1	492	tCg/tTg	14/24	1	2	FACETS	0.981	0.917	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		855	954	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47045140	47045140	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	712	244	778	1	ENST00000377604.3:c.2381C>T	p.Ala794Val	p.A794V	ENST00000377604	NM_001204468.1	794	gCc/gTc	21/24	1	2	FACETS	0.987	0.923	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		779	956	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47424438	47424438	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	686	294	659	0	ENST00000377045.4:c.358T>G	p.Phe120Val	p.F120V	ENST00000377045	NM_001654.4	120	Ttc/Gtc	5/16	1	2	FACETS	1	0.987	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		659	980	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47426476	47426476	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	812	65	695	0	ENST00000377045.4:c.819G>C	p.Lys273Asn	p.K273N	ENST00000377045	NM_001654.4	273	aaG/aaC	9/16	1	2	FACETS	0.573	0.496	0.658	0.573	0.496	0.658	SUBCLONAL	1	TRUE	1	0.258652869545824	2		695	877	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47428962	47428962	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	623	221	662	0	ENST00000377045.4:c.1325C>T	p.Thr442Met	p.T442M	ENST00000377045	NM_001654.4	442	aCg/aTg	13/16	1	2	FACETS	1	0.943	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		662	844	SUCCESS
ARAF	369	MSKCC	GRCh37	X	47430308	47430308	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	319	810	0	ENST00000377045.4:c.1583C>T	p.Ser528Phe	p.S528F	ENST00000377045	NM_001654.4	528	tCc/tTc	15/16	1	2	FACETS	1	0.985	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		810	1108	SUCCESS
GATA1	2623	MSKCC	GRCh37	X	48652201	48652201	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	581	214	681	0	ENST00000376670.3:c.872T>C	p.Val291Ala	p.V291A	ENST00000376670	NM_002049.3	291	gTg/gCg	6/6	1	2	FACETS	1	0.959	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		681	795	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53222420	53222420	+	missense_variant	Missense_Mutation	SNP	T	T	C	rs1556832481	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	803	337	962	1	ENST00000375401.3:c.4412A>G	p.Asp1471Gly	p.D1471G	ENST00000375401	NM_004187.3	1471	gAc/gGc	26/26	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		963	1140	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53228211	53228211	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	555	227	637	1	ENST00000375401.3:c.2191C>A	p.Leu731Ile	p.L731I	ENST00000375401	NM_004187.3	731	Ctt/Att	15/26	1	2	FACETS	1	0.98	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		638	782	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53231148	53231148	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	477	175	476	0	ENST00000375401.3:c.1754G>A	p.Arg585His	p.R585H	ENST00000375401	NM_004187.3	585	cGc/cAc	13/26	1	2	FACETS	1	0.951	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		476	652	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53240679	53240679	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	514	209	574	0	ENST00000375401.3:c.1401G>T	p.Glu467Asp	p.E467D	ENST00000375401	NM_004187.3	467	gaG/gaT	10/26	1	2	FACETS	1	0.978	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		574	723	SUCCESS
KDM5C	8242	MSKCC	GRCh37	X	53243978	53243978	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	794	325	819	1	ENST00000375401.3:c.1015C>T	p.Leu339Phe	p.L339F	ENST00000375401	NM_004187.3	339	Ctc/Ttc	8/26	1	2	FACETS	1	0.986	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		820	1119	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63410516	63410516	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	479	205	637	0	ENST00000330258.3:c.2651C>A	p.Pro884His	p.P884H	ENST00000330258	NM_152424.3	884	cCt/cAt	2/2	1	2	FACETS	1	0.982	1	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		637	684	SUCCESS
AMER1	139285	MSKCC	GRCh37	X	63413019	63413019	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	819	345	876	1	ENST00000330258.3:c.148G>T	p.Gly50Cys	p.G50C	ENST00000330258	NM_152424.3	50	Ggt/Tgt	2/2	1	2	FACETS	1	0.988	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		877	1164	SUCCESS
AR	367	MSKCC	GRCh37	X	66766255	66766255	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1202977049	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	389	112	355	0	ENST00000374690.3:c.1267G>A	p.Gly423Ser	p.G423S	ENST00000374690	NM_000044.3	423	Ggt/Agt	1/8	1	2	FACETS	0.864	0.781	0.951	1	0.987	1	CLONAL	2	TRUE	1	0.258652869545824	2		355	501	SUCCESS
AR	367	MSKCC	GRCh37	X	66766541	66766541	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	855	347	920	1	ENST00000374690.3:c.1553C>T	p.Thr518Ile	p.T518I	ENST00000374690	NM_000044.3	518	aCt/aTt	1/8	1	2	FACETS	1	0.986	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		921	1202	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70338697	70338697	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	549	222	659	0	ENST00000374080.3:c.93G>T	p.Gln31His	p.Q31H	ENST00000374080		31	caG/caT	1/45	1	2	FACETS	1	0.979	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		659	771	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70345203	70345203	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	403	153	398	1	ENST00000374080.3:c.2229G>T	p.Glu743Asp	p.E743D	ENST00000374080		743	gaG/gaT	16/45	1	2	FACETS	1	0.958	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		399	556	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70347742	70347742	+	splice_acceptor_variant	Splice_Site	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	408	151	436	2	ENST00000374080.3:c.2982-1G>T		p.X994_splice	ENST00000374080		994			1	2	FACETS	1	0.949	1	1	0.992	1	CLONAL	2	TRUE	1	0.258652869545824	2		438	559	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70356269	70356269	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	577	254	737	1	ENST00000374080.3:c.5164C>T	p.Arg1722Trp	p.R1722W	ENST00000374080		1722	Cgg/Tgg	37/45	1	2	FACETS	1	0.987	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		738	831	SUCCESS
MED12	9968	MSKCC	GRCh37	X	70361807	70361807	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	751	290	824	0	ENST00000374080.3:c.6483G>T	p.Gln2161His	p.Q2161H	ENST00000374080		2161	caG/caT	44/45	1	2	FACETS	1	0.978	1	1	0.996	1	CLONAL	2	TRUE	1	0.258652869545824	2		824	1041	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76812972	76812972	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	468	177	596	0	ENST00000373344.5:c.6649G>A	p.Asp2217Asn	p.D2217N	ENST00000373344	NM_000489.3	2217	Gac/Aac	30/35	1	2	FACETS	1	0.961	1	1	0.993	1	CLONAL	2	TRUE	1	0.258652869545824	2		596	645	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76938056	76938056	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	517	225	679	0	ENST00000373344.5:c.2692G>T	p.Asp898Tyr	p.D898Y	ENST00000373344	NM_000489.3	898	Gac/Tac	9/35	1	2	FACETS	1	0.985	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		679	742	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76939893	76939893	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	673	248	667	0	ENST00000373344.5:c.855G>T	p.Glu285Asp	p.E285D	ENST00000373344	NM_000489.3	285	gaG/gaT	9/35	1	2	FACETS	1	0.963	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		667	921	SUCCESS
XIAP	331	MSKCC	GRCh37	X	123040865	123040865	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1173411245	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	902	250	1022	0	ENST00000355640.3:c.1328G>A	p.Arg443His	p.R443H	ENST00000355640		443	cGc/cAc	7/7	1	2	FACETS	0.839	0.784	0.896	1	0.994	1	CLONAL	2	TRUE	1	0.258652869545824	2		1022	1152	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123211806	123211806	+	splice_acceptor_variant	Splice_Site	SNP	G	G	A	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	338	101	445	0	ENST00000218089.9:c.2674-1G>A		p.X892_splice	ENST00000218089	NM_001042749.1	892			1	2	FACETS	0.889	0.8	0.984	1	0.986	1	CLONAL	2	TRUE	1	0.258652869545824	2		445	439	SUCCESS
STAG2	10735	MSKCC	GRCh37	X	123215287	123215287	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018334-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	594	242	591	0	ENST00000218089.9:c.2833T>G	p.Phe945Val	p.F945V	ENST00000218089	NM_001042749.1	945	Ttt/Gtt	28/35	1	2	FACETS	1	0.981	1	1	0.995	1	CLONAL	2	TRUE	1	0.258652869545824	2		591	836	SUCCESS
MSH3	4437	MSKCC	GRCh37	5	79970915	79970915	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs587776701	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	439	242	519	5	ENST00000265081.6:c.1148del	p.Lys383ArgfsTer32	p.K383Rfs*32	ENST00000265081	NM_002439.4	381	Aaa/aa	7/24	1	2	FACETS	1	0.942	1	1	0.942	1	CLONAL	1	TRUE	1	0.708958041759045	2		524	681	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65306997	65306997	+	frameshift_variant	Frame_Shift_Del	DEL	T	T	-	novel	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	98	341	0	ENST00000342505.4:c.2580del	p.Lys860AsnfsTer16	p.K860Nfs*16	ENST00000342505	NM_002227.2	860	aaA/aa	19/25	1	2	FACETS	0.833	0.751	0.918	0.833	0.751	0.918	CLONAL	1	TRUE	1	0.708958041759045	2		341	332	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56435161	56435161	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs755128667	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	125	248	736	5	ENST00000407977.2:c.1976del	p.Gly659ValfsTer41	p.G659Vfs*41	ENST00000407977		659	gGt/gt	9/10	1	2	FACETS	0.938	0.896	0.978	1	0.996	1	CLONAL	2	TRUE	1	0.708958041759045	2		741	373	SUCCESS
PIK3CA	5290	MSKCC	GRCh37	3	178936091	178936091	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs104886003	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	321	169	512	0	ENST00000263967.3:c.1633G>A	p.Glu545Lys	p.E545K	ENST00000263967	NM_006218.2	545	Gag/Aag	10/21	1	2	FACETS	0.973	0.902	1	0.973	0.902	1	CLONAL	1	TRUE	1	0.708958041759045	2		512	490	SUCCESS
TCF7L2	6934	MSKCC	GRCh37	10	114925317	114925317	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs745872748	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	289	172	391	1	ENST00000543371.1:c.1403del	p.Lys468SerfsTer23	p.K468Sfs*23	ENST00000543371	NM_001198531.1	465	agA/ag	14/14	0.69941427242178	2	FACETS	1	0.962	1	0.526	0.489	0.565	CLONAL	1	TRUE	0	0.708958041759045	2		392	461	SUCCESS
KMT2B	9757	MSKCC	GRCh37	19	36210763	36210764	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs763183959	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	241	1190	1	ENST00000222270.7:c.521dup	p.Thr176AspfsTer8	p.T176Dfs*8	ENST00000222270	NM_014727.1	172	acc/aCcc	3/37	1	2	FACETS	0.874	0.819	0.93	0.874	0.819	0.93	CLONAL	1	TRUE	1	0.708958041759045	2		1191	778	SUCCESS
EP300	2033	MSKCC	GRCh37	22	41574678	41574679	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	C	rs754418509	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	525	221	1180	4	ENST00000263253.7:c.6970dup	p.His2324ProfsTer55	p.H2324Pfs*55	ENST00000263253	NM_001429.3	2321	-/C	31/31	1	2	FACETS	0.836	0.78	0.892	0.836	0.78	0.892	CLONAL	1	TRUE	1	0.708958041759045	2		1184	746	SUCCESS
MAX	4149	MSKCC	GRCh37	14	65544747	65544747	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	392	40	557	0	ENST00000358664.4:c.179G>A	p.Arg60Gln	p.R60Q	ENST00000358664	NM_002382.4	60	cGg/cAg	4/5	1	2	FACETS	0.261	0.217	0.31	0.261	0.217	0.31	SUBCLONAL	1	TRUE	1	0.708958041759045	2		557	432	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89717715	89717716	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	A	rs587782341	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	141	289	653	1	ENST00000371953.3:c.741dup	p.Pro248ThrfsTer5	p.P248Tfs*5	ENST00000371953	NM_000314.4	247	tta/ttAa	7/9	0.69941427242178	2	FACETS	0.948	0.909	0.986	0.948	0.909	0.986	CLONAL	2	TRUE	0	0.708958041759045	2		654	430	SUCCESS
HNF1A	6927	MSKCC	GRCh37	12	121432118	121432118	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs587776825	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	357	196	472	4	ENST00000257555.6:c.872del	p.Pro291GlnfsTer51	p.P291Qfs*51	ENST00000257555		289	Ccc/cc	4/10	1	2	FACETS	1	0.933	1	1	0.933	1	CLONAL	1	TRUE	1	0.708958041759045	2		476	553	SUCCESS
MSH6	2956	MSKCC	GRCh37	2	48030640	48030640	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs267608078	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	319	173	508	12	ENST00000234420.5:c.3261del	p.Phe1088SerfsTer2	p.F1088Sfs*2	ENST00000234420	NM_000179.2	1085	aCc/ac	5/10	1	2	FACETS	0.992	0.921	1	0.992	0.921	1	CLONAL	1	TRUE	1	0.708958041759045	2		520	492	SUCCESS
ZFHX3	463	MSKCC	GRCh37	16	72822585	72822586	+	frameshift_variant	Frame_Shift_Ins	INS	-	-	G	rs764626362	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	83	487	0	ENST00000268489.5:c.9589dup	p.Gln3197ProfsTer42	p.Q3197Pfs*42	ENST00000268489	NM_006885.3	3197	cag/cCag	10/10	1	2	FACETS	0.775	0.692	0.863	0.775	0.692	0.863	SUBCLONAL	1	TRUE	1	0.708958041759045	2		487	302	SUCCESS
BLM	641	MSKCC	GRCh37	15	91304139	91304139	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	rs367543043	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	380	200	402	7	ENST00000355112.3:c.1544del	p.Asn515MetfsTer16	p.N515Mfs*16	ENST00000355112	NM_000057.2	512	ggA/gg	7/22	1	2	FACETS	0.973	0.907	1	0.973	0.907	1	CLONAL	1	TRUE	1	0.708958041759045	2		409	580	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94120396	94120396	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	230	99	501	0	ENST00000369303.4:c.655G>A	p.Val219Met	p.V219M	ENST00000369303	NM_004440.3	219	Gtg/Atg	3/17	1	2	FACETS	0.849	0.766	0.935	0.849	0.766	0.935	CLONAL	1	TRUE	1	0.708958041759045	2		501	329	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101375	27101375	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	novel	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	312	228	690	3	ENST00000324856.7:c.4661del	p.Pro1554HisfsTer11	p.P1554Hfs*11	ENST00000324856	NM_006015.4	1553	Ccc/cc	18/20	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.708958041759045	2		693	540	SUCCESS
XPO1	7514	MSKCC	GRCh37	2	61719525	61719525	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	450	60	738	0	ENST00000401558.2:c.1658G>A	p.Arg553His	p.R553H	ENST00000401558	NM_003400.3	553	cGt/cAt	15/25	1	2	FACETS	0.332	0.286	0.382	0.332	0.286	0.382	SUBCLONAL	1	TRUE	1	0.708958041759045	2		738	510	SUCCESS
ATRX	546	MSKCC	GRCh37	X	76845413	76845413	+	splice_region_variant,intron_variant	Splice_Region	DEL	A	A	-	novel	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	310	46	578	3	ENST00000373344.5:c.6111-3del		p.X2037_splice	ENST00000373344	NM_000489.3	2037			1	2	FACETS	0.365	0.308	0.427	0.365	0.308	0.427	SUBCLONAL	1	TRUE	1	0.708958041759045	2		581	356	SUCCESS
CCND1	595	MSKCC	GRCh37	11	69466022	69466022	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	195	444	2	ENST00000227507.2:c.860C>A	p.Pro287His	p.P287H	ENST00000227507	NM_053056.2	287	cCc/cAc	5/5	1	2	FACETS	0.968	0.903	1	0.968	0.903	1	CLONAL	1	TRUE	1	0.708958041759045	2		446	568	SUCCESS
IRS2	8660	MSKCC	GRCh37	13	110434454	110434454	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	137	696	1	ENST00000375856.3:c.3947del	p.Pro1316LeufsTer15	p.P1316Lfs*15	ENST00000375856	NM_003749.2	1316	cCt/ct	1/2	1	2	FACETS	0.815	0.747	0.886	0.815	0.747	0.886	CLONAL	1	TRUE	1	0.708958041759045	2		697	474	SUCCESS
MAP2K1	5604	MSKCC	GRCh37	15	66782074	66782075	+	frameshift_variant	Frame_Shift_Del	DEL	AG	AG	-	novel	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	219	127	517	0	ENST00000307102.5:c.1047_1048del	p.Arg349SerfsTer16	p.R349Sfs*16	ENST00000307102	NM_002755.3	347	gcAGag/gcag	10/11	1	2	FACETS	1	0.943	1	1	0.943	1	CLONAL	1	TRUE	1	0.708958041759045	2		517	346	SUCCESS
ARID1A	8289	MSKCC	GRCh37	1	27101037	27101037	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	467	211	955	2	ENST00000324856.7:c.4319C>T	p.Thr1440Ile	p.T1440I	ENST00000324856	NM_006015.4	1440	aCa/aTa	18/20	1	2	FACETS	0.878	0.819	0.938	0.878	0.819	0.938	CLONAL	1	TRUE	1	0.708958041759045	2		957	678	SUCCESS
RRAGC	64121	MSKCC	GRCh37	1	39305365	39305365	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	378	174	721	0	ENST00000373001.3:c.1060T>C	p.Tyr354His	p.Y354H	ENST00000373001	NM_022157.3	354	Tac/Cac	7/7	1	2	FACETS	0.889	0.824	0.956	0.889	0.824	0.956	CLONAL	1	TRUE	1	0.708958041759045	2		721	552	SUCCESS
JAK1	3716	MSKCC	GRCh37	1	65303615	65303616	+	frameshift_variant,splice_region_variant	Frame_Shift_Ins	INS	-	-	A	novel	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	294	148	594	0	ENST00000342505.4:c.3139dup	p.Trp1047LeufsTer11	p.W1047Lfs*11	ENST00000342505	NM_002227.2	1047	tgg/tTgg	22/25	1	2	FACETS	0.945	0.871	1	0.945	0.871	1	CLONAL	1	TRUE	1	0.708958041759045	2		594	442	SUCCESS
DDR2	4921	MSKCC	GRCh37	1	162745570	162745573	+	frameshift_variant	Frame_Shift_Del	DEL	TCAA	TCAA	-	novel	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	322	169	721	0	ENST00000367921.3:c.1988_1991del	p.Asn663SerfsTer24	p.N663Sfs*24	ENST00000367921	NM_006182.2	662	cTCAAt/ct	15/18	1	2	FACETS	0.971	0.9	1	0.971	0.9	1	CLONAL	1	TRUE	1	0.708958041759045	2		721	491	SUCCESS
SESN3	143686	MSKCC	GRCh37	11	94908705	94908705	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs547426358	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	569	58	894	1	ENST00000536441.1:c.1349G>A	p.Arg450His	p.R450H	ENST00000536441	NM_144665.3	450	cGc/cAc	9/10	1	2	FACETS	0.261	0.224	0.302	0.261	0.224	0.302	SUBCLONAL	1	TRUE	1	0.708958041759045	2		895	627	SUCCESS
ATM	472	MSKCC	GRCh37	11	108159757	108159757	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	155	827	0	ENST00000278616.4:c.4163C>T	p.Ala1388Val	p.A1388V	ENST00000278616	NM_000051.3	1388	gCa/gTa	28/63	1	2	FACETS	0.907	0.837	0.979	0.907	0.837	0.979	CLONAL	1	TRUE	1	0.708958041759045	2		827	482	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49434959	49434959	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	rs1555192751	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	169	97	437	2	ENST00000301067.7:c.6594del	p.Tyr2199IlefsTer65	p.Y2199Ifs*65	ENST00000301067	NM_003482.3	2198	ccC/cc	31/54	1	2	FACETS	1	0.928	1	1	0.928	1	CLONAL	1	TRUE	1	0.708958041759045	2		439	266	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49435199	49435199	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	235	103	490	0	ENST00000301067.7:c.6354del	p.Ala2119LeufsTer25	p.A2119Lfs*25	ENST00000301067	NM_003482.3	2118	ccC/cc	31/54	1	2	FACETS	0.86	0.778	0.945	0.86	0.778	0.945	CLONAL	1	TRUE	1	0.708958041759045	2		490	338	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3778452	3778452	+	missense_variant	Missense_Mutation	SNP	T	T	A	rs765821935	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	361	146	782	2	ENST00000262367.5:c.6596A>T	p.Gln2199Leu	p.Q2199L	ENST00000262367	NM_004380.2	2199	cAg/cTg	31/31	1	2	FACETS	0.812	0.746	0.881	0.812	0.746	0.881	CLONAL	1	TRUE	1	0.708958041759045	2		784	507	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29527602	29527602	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	257	91	584	0	ENST00000356175.3:c.1051G>A	p.Val351Ile	p.V351I	ENST00000356175	NM_000267.3	351	Gtt/Att	9/57	1	2	FACETS	0.738	0.661	0.818	0.738	0.661	0.818	SUBCLONAL	1	TRUE	1	0.708958041759045	2		584	348	SUCCESS
SPOP	8405	MSKCC	GRCh37	17	47696730	47696730	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	255	113	507	0	ENST00000347630.2:c.218C>T	p.Pro73Leu	p.P73L	ENST00000347630	NM_001007230.1	73	cCc/cTc	5/11	1	2	FACETS	0.866	0.787	0.948	0.866	0.787	0.948	CLONAL	1	TRUE	1	0.708958041759045	2		507	368	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11107182	11107182	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1257518561	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	327	167	721	1	ENST00000358026.2:c.1774G>A	p.Ala592Thr	p.A592T	ENST00000358026	NM_001128849.1	592	Gca/Aca	11/36	1	2	FACETS	0.954	0.883	1	0.954	0.883	1	CLONAL	1	TRUE	1	0.708958041759045	2		722	494	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15273288	15273288	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs373866355	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	410	221	916	1	ENST00000263388.2:c.5901G>A	p.Met1967Ile	p.M1967I	ENST00000263388	NM_000435.2	1967	atG/atA	32/33	1	2	FACETS	0.988	0.925	1	0.988	0.925	1	CLONAL	1	TRUE	1	0.708958041759045	2		917	631	SUCCESS
BRD4	23476	MSKCC	GRCh37	19	15376212	15376212	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs551722840	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	176	81	417	0	ENST00000263377.2:c.802G>A	p.Val268Ile	p.V268I	ENST00000263377	NM_058243.2	268	Gta/Ata	5/20	1	2	FACETS	0.889	0.794	0.988	0.889	0.794	0.988	CLONAL	1	TRUE	1	0.708958041759045	2		417	257	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42796266	42796266	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	424	217	857	0	ENST00000575354.2:c.2915G>A	p.Ser972Asn	p.S972N	ENST00000575354	NM_015125.3	972	aGc/aAc	12/20	1	2	FACETS	0.955	0.893	1	0.955	0.893	1	CLONAL	1	TRUE	1	0.708958041759045	2		857	641	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50921125	50921125	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	377	150	858	2	ENST00000440232.2:c.3245G>A	p.Arg1082His	p.R1082H	ENST00000440232	NM_002691.3	1082	cGc/cAc	27/27	1	2	FACETS	0.803	0.738	0.87	0.803	0.738	0.87	CLONAL	1	TRUE	1	0.708958041759045	2		860	527	SUCCESS
NFE2L2	4780	MSKCC	GRCh37	2	178095716	178095716	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	234	134	423	0	ENST00000397062.3:c.1615T>A	p.Leu539Met	p.L539M	ENST00000397062	NM_006164.4	539	Ttg/Atg	5/5	1	2	FACETS	1	0.94	1	1	0.94	1	CLONAL	1	TRUE	1	0.708958041759045	2		423	368	SUCCESS
CHEK2	11200	MSKCC	GRCh37	22	29095914	29095914	+	frameshift_variant	Frame_Shift_Del	DEL	C	C	-	rs786203053	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	430	239	981	0	ENST00000328354.6:c.920del	p.Gly307GlufsTer13	p.G307Efs*13	ENST00000328354	NM_007194.3	307	gGa/ga	9/15	1	2	FACETS	1	0.946	1	1	0.946	1	CLONAL	1	TRUE	1	0.708958041759045	2		981	669	SUCCESS
FBXW7	55294	MSKCC	GRCh37	4	153332735	153332735	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	291	122	644	0	ENST00000281708.4:c.221A>G	p.Gln74Arg	p.Q74R	ENST00000281708	NM_033632.3	74	cAa/cGa	2/12	1	2	FACETS	0.833	0.76	0.91	0.833	0.76	0.91	CLONAL	1	TRUE	1	0.708958041759045	2		644	413	SUCCESS
IL7R	3575	MSKCC	GRCh37	5	35876118	35876118	+	missense_variant	Missense_Mutation	SNP	C	C	A	novel	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	315	22	527	0	ENST00000303115.3:c.910C>A	p.Leu304Met	p.L304M	ENST00000303115	NM_002185.3	304	Ctg/Atg	8/8	1	2	FACETS	0.184	0.142	0.233	0.184	0.142	0.233	SUBCLONAL	1	TRUE	1	0.708958041759045	2		527	337	SUCCESS
RICTOR	253260	MSKCC	GRCh37	5	38946657	38946657	+	splice_region_variant,intron_variant	Splice_Region	DEL	A	A	-	novel	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	156	59	352	2	ENST00000357387.3:c.4315-3del		p.X1439_splice	ENST00000357387	NM_152756.3	1439			1	2	FACETS	0.774	0.675	0.878	0.774	0.675	0.878	SUBCLONAL	1	TRUE	1	0.708958041759045	2		354	215	SUCCESS
PLK2	10769	MSKCC	GRCh37	5	57754313	57754313	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	251	104	549	0	ENST00000274289.3:c.538C>T	p.Pro180Ser	p.P180S	ENST00000274289	NM_006622.3	180	Cca/Tca	4/14	1	2	FACETS	0.826	0.747	0.909	0.826	0.747	0.909	CLONAL	1	TRUE	1	0.708958041759045	2		549	355	SUCCESS
RASA1	5921	MSKCC	GRCh37	5	86674319	86674320	+	frameshift_variant	Frame_Shift_Del	DEL	TA	TA	-	novel	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	199	96	517	0	ENST00000274376.6:c.2452_2453del	p.Ile818PhefsTer11	p.I818Ffs*11	ENST00000274376	NM_002890.2	817	tcTAtt/tctt	18/25	1	2	FACETS	0.918	0.829	1	0.918	0.829	1	CLONAL	1	TRUE	1	0.708958041759045	2		517	295	SUCCESS
IRF4	3662	MSKCC	GRCh37	6	401601	401601	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	238	121	616	0	ENST00000380956.4:c.923T>C	p.Leu308Pro	p.L308P	ENST00000380956	NM_001195286.1	308	cTg/cCg	7/9	1	2	FACETS	0.951	0.869	1	0.951	0.869	1	CLONAL	1	TRUE	1	0.708958041759045	2		616	359	SUCCESS
TNFAIP3	7128	MSKCC	GRCh37	6	138200413	138200413	+	missense_variant	Missense_Mutation	SNP	G	G	C	novel	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	372	181	621	1	ENST00000237289.4:c.1831G>C	p.Gly611Arg	p.G611R	ENST00000237289	NM_001270507.1	611	Ggc/Cgc	7/9	1	2	FACETS	0.923	0.857	0.991	0.923	0.857	0.991	CLONAL	1	TRUE	1	0.708958041759045	2		622	553	SUCCESS
KMT2C	58508	MSKCC	GRCh37	7	151878596	151878596	+	frameshift_variant	Frame_Shift_Del	DEL	A	A	-	novel	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	394	39	540	4	ENST00000262189.6:c.6349del	p.Ser2117ProfsTer26	p.S2117Pfs*26	ENST00000262189	NM_170606.2	2117	Tcc/cc	36/59	1	2	FACETS	0.254	0.21	0.303	0.254	0.21	0.303	SUBCLONAL	1	TRUE	1	0.708958041759045	2		544	433	SUCCESS
NOTCH1	4851	MSKCC	GRCh37	9	139390786	139390786	+	missense_variant	Missense_Mutation	SNP	G	G	T	novel	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	373	181	883	1	ENST00000277541.6:c.7405C>A	p.Pro2469Thr	p.P2469T	ENST00000277541	NM_017617.3	2469	Cca/Aca	34/34	1	2	FACETS	0.922	0.856	0.989	0.922	0.856	0.989	CLONAL	1	TRUE	1	0.708958041759045	2		884	554	SUCCESS
RBM10	8241	MSKCC	GRCh37	X	47028896	47028896	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018350-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	224	77	497	0	ENST00000377604.3:c.200A>G	p.Glu67Gly	p.E67G	ENST00000377604	NM_001204468.1	67	gAg/gGg	3/24	1	2	FACETS	0.722	0.64	0.808	0.722	0.64	0.808	SUBCLONAL	1	TRUE	1	0.708958041759045	2		497	301	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295228	1295228	+	upstream_gene_variant	5'Flank	SNP	G	G	A	rs1242535815	NA	P-0018441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	227	207	215	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	1	0.983	1	1	0.983	1	CLONAL	1	TRUE	1	0.848790747087322	2		215	434	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55220274	55220274	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	18904	1352	459	0	ENST00000275493.2:c.664C>T	p.Arg222Cys	p.R222C	ENST00000275493	NM_005228.3	222	Cgc/Tgc	6/28	0.848790747087322	24	FACETS	0.813	0.787	0.839			1	CLONAL	2	TRUE	NA	0.848790747087322	24		459	20256	SUCCESS
FANCA	2175	MSKCC	GRCh37	16	89813023	89813023	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs142833057	NA	P-0018441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	464	320	389	0	ENST00000389301.3:c.3482C>T	p.Thr1161Met	p.T1161M	ENST00000389301	NM_000135.2	1161	aCg/aTg	35/43	1	2	FACETS	0.962	0.913	1	0.962	0.913	1	CLONAL	1	TRUE	1	0.848790747087322	2		389	784	SUCCESS
PIK3CG	5294	MSKCC	GRCh37	7	106508260	106508260	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	334	164	201	0	ENST00000359195.3:c.254C>T	p.Ala85Val	p.A85V	ENST00000359195	NM_002649.2	85	gCg/gTg	2/11	0.829401375323842	3	FACETS	1	0.972	1	0.553	0.511	0.595	CLONAL	1	TRUE	1	0.848790747087322	3		201	498	SUCCESS
PTEN	5728	MSKCC	GRCh37	10	89692913	89692913	+	frameshift_variant	Frame_Shift_Del	DEL	G	G	-	novel	NA	P-0018441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	78	14	345	0	ENST00000371953.3:c.397del	p.Val133Ter	p.V133*	ENST00000371953	NM_000314.4	133	Gta/ta	5/9	0.848790747087322	1	FACETS	0.206	0.151	0.271	0.206	0.151	0.271	SUBCLONAL	1	TRUE	0	0.848790747087322	1		345	92	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39239348	39239348	+	missense_variant	Missense_Mutation	SNP	T	T	C	novel	NA	P-0018441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	295	463	0	ENST00000402219.2:c.2309A>G	p.His770Arg	p.H770R	ENST00000402219	NM_005633.3	770	cAc/cGc	14/23	1	2	FACETS	1	0.951	1	1	0.951	1	CLONAL	1	TRUE	1	0.848790747087322	2		463	693	SUCCESS
EGFR	1956	MSKCC	GRCh37	7	55233099	55233099	+	missense_variant	Missense_Mutation	SNP	T	T	G	novel	NA	P-0018441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	20077	1628	463	0	ENST00000275493.2:c.1849T>G	p.Cys617Gly	p.C617G	ENST00000275493	NM_005228.3	617	Tgc/Ggc	15/28	0.848790747087322	24	FACETS	0.913	0.888	0.94			1	CLONAL	2	TRUE	NA	0.848790747087322	24		463	21705	SUCCESS
MET	4233	MSKCC	GRCh37	7	116412582	116412584	+	intron_variant	Intron	DEL	ATC	ATC	-	novel	NA	P-0018441-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	843	312	555	0	ENST00000397752.3:c.3028+543_3028+545del		p.*1010*	ENST00000397752	NM_000245.2	-/1390			0.829401375323842	3	FACETS	0.907	0.855	0.959	0.453	0.427	0.48	CLONAL	1	TRUE	1	0.848790747087322	3		555	1155	SUCCESS
TERT	7015	MSKCC	GRCh37	5	1295250	1295254	+	upstream_gene_variant	5'Flank	ONP	GAGGG	GAGGG	AAGGA	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	565	508	282	0				ENST00000310581	NM_198253.2	-/1132			1	2	FACETS	0.996	0.958	1	0.996	0.958	1	CLONAL	1	TRUE	1	0.950734814351431	2		282	1073	SUCCESS
PREX2	80243	MSKCC	GRCh37	8	68934283	68934283	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs773476490	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	835	807	557	0	ENST00000288368.4:c.349C>T	p.Arg117Cys	p.R117C	ENST00000288368	NM_024870.2	117	Cgt/Tgt	4/40	1	2	FACETS	1	0.988	1	1	0.988	1	CLONAL	1	TRUE	1	0.950734814351431	2		557	1642	SUCCESS
NF1	4763	MSKCC	GRCh37	17	29576111	29576111	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	rs137854560	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	79	737	510	1	ENST00000356175.3:c.4084C>T	p.Arg1362Ter	p.R1362*	ENST00000356175	NM_000267.3	1362	Cga/Tga	30/57	0.910601992417252	1	FACETS	0.997	0.982	1	0.997	0.982	1	CLONAL	1	TRUE	0	0.950734814351431	1		511	816	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40727111	40727111	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs779663880	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	586	505	0	ENST00000373198.4:c.3853G>A	p.Asp1285Asn	p.D1285N	ENST00000373198	NM_133170.3	1285	Gat/Aat	28/32	1	2	FACETS	0.966	0.931	1	0.966	0.931	1	CLONAL	1	TRUE	1	0.950734814351431	2		505	1276	SUCCESS
TEK	7010	MSKCC	GRCh37	9	27202881	27202881	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	77	716	603	0	ENST00000380036.4:c.1973C>T	p.Ser658Phe	p.S658F	ENST00000380036	NM_000459.3	658	tCt/tTt	13/23	0.950734814351431	1	FACETS	0.996	0.982	1	0.996	0.982	1	CLONAL	1	TRUE	0	0.950734814351431	1		603	793	SUCCESS
PLCG2	5336	MSKCC	GRCh37	16	81944264	81944264	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1009796025	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	68	756	599	0	ENST00000359376.3:c.1873G>A	p.Ala625Thr	p.A625T	ENST00000359376	NM_002661.3	625	Gcc/Acc	18/33	0.950734814351431	1	FACETS	1	0.994	1	1	0.994	1	CLONAL	1	TRUE	0	0.950734814351431	1		599	824	SUCCESS
SPEN	23013	MSKCC	GRCh37	1	16237793	16237794	+	missense_variant,splice_region_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	617	447	388	1	ENST00000375759.3:c.1240_1241delinsTT	p.Pro414Leu	p.P414L	ENST00000375759	NM_015001.2	414	CCa/TTa	5/15	1	2	FACETS	0.884	0.846	0.922	0.884	0.846	0.922	CLONAL	1	TRUE	1	0.950734814351431	2		389	1064	SUCCESS
SHOC2	8036	MSKCC	GRCh37	10	112771483	112771484	+	missense_variant	Missense_Mutation	DNP	AC	AC	TT	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	865	655	586	1	ENST00000369452.4:c.1656_1657delinsTT	p.Leu553Phe	p.L553F	ENST00000369452	NM_007373.3	552	ccACtc/ccTTtc	9/9	1	2	FACETS	0.907	0.875	0.939	0.907	0.875	0.939	CLONAL	1	TRUE	1	0.950734814351431	2		587	1520	SUCCESS
WT1	7490	MSKCC	GRCh37	11	32417910	32417910	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	747	678	522	0	ENST00000332351.3:c.1142C>T	p.Ser381Leu	p.S381L	ENST00000332351	NM_024426.4	381	tCg/tTg	7/10	1	2	FACETS	1	0.968	1	1	0.968	1	CLONAL	1	TRUE	1	0.950734814351431	2		522	1425	SUCCESS
MEN1	4221	MSKCC	GRCh37	11	64572666	64572666	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	595	450	373	1	ENST00000312049.6:c.1190C>T	p.Thr397Ile	p.T397I	ENST00000312049	NM_130799.2	397	aCc/aTc	9/10	1	2	FACETS	0.906	0.868	0.944	0.906	0.868	0.944	CLONAL	1	TRUE	1	0.950734814351431	2		374	1045	SUCCESS
PGR	5241	MSKCC	GRCh37	11	100996810	100996810	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	66	723	577	0	ENST00000325455.5:c.1717G>A	p.Glu573Lys	p.E573K	ENST00000325455	NM_001202474.3	573	Gaa/Aaa	2/8	0.950734814351431	1	FACETS	1	0.993	1	1	0.993	1	CLONAL	1	TRUE	0	0.950734814351431	1		577	789	SUCCESS
KMT2A	4297	MSKCC	GRCh37	11	118343372	118343372	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	30	466	353	0	ENST00000534358.1:c.1498C>T	p.Pro500Ser	p.P500S	ENST00000534358	NM_005933.3	500	Cct/Tct	3/36	0.950734814351431	1	FACETS	1	0.996	1	1	0.996	1	CLONAL	1	TRUE	0	0.950734814351431	1		353	496	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12022493	12022493	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	469	694	725	0	ENST00000396373.4:c.599C>T	p.Pro200Leu	p.P200L	ENST00000396373	NM_001987.4	200	cCc/cTc	5/8	0.550116625749163	1	FACETS	0.659	0.639	0.678	0.659	0.639	0.678	INDETERMINATE	1	TRUE	0	0.950734814351431	1		725	1163	SUCCESS
ETV6	2120	MSKCC	GRCh37	12	12037394	12037395	+	stop_gained	Nonsense_Mutation	DNP	GG	GG	AA	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	910	364	622	1	ENST00000396373.4:c.1025_1026delinsAA	p.Trp342Ter	p.W342*	ENST00000396373	NM_001987.4	342	tGG/tAA	6/8	NA		FACETS		NA	1			1	INDETERMINATE	NA	TRUE	NA	0.950734814351431	NA		623	1274	SUCCESS
PIK3C2G	5288	MSKCC	GRCh37	12	18658386	18658386	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs765894008	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	288	431	355	0	ENST00000266497.5:c.3191G>A	p.Gly1064Glu	p.G1064E	ENST00000266497		1064	gGg/gAg	22/31	0.476553022551747	1	FACETS	0.662	0.637	0.686	0.662	0.637	0.686	INDETERMINATE	1	TRUE	0	0.950734814351431	1		355	719	SUCCESS
KMT2D	8085	MSKCC	GRCh37	12	49444881	49444881	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	476	786	559	0	ENST00000301067.7:c.2585C>T	p.Pro862Leu	p.P862L	ENST00000301067	NM_003482.3	862	cCt/cTt	10/54	0.476553022551747	1	FACETS	0.687	0.669	0.705	0.687	0.669	0.705	INDETERMINATE	1	TRUE	0	0.950734814351431	1		559	1262	SUCCESS
ERBB3	2065	MSKCC	GRCh37	12	56494935	56494935	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	337	580	417	2	ENST00000267101.3:c.3292G>A	p.Glu1098Lys	p.E1098K	ENST00000267101	NM_001982.3	1098	Gag/Aag	27/28	0.476553022551747	1	FACETS	0.698	0.677	0.719	0.698	0.677	0.719	INDETERMINATE	1	TRUE	0	0.950734814351431	1		419	917	SUCCESS
POLE	5426	MSKCC	GRCh37	12	133241038	133241038	+	missense_variant	Missense_Mutation	SNP	A	A	C	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	336	579	433	2	ENST00000320574.5:c.2479T>G	p.Tyr827Asp	p.Y827D	ENST00000320574	NM_006231.2	827	Tac/Gac	22/49	0.550116625749163	1	FACETS	0.698	0.677	0.719	0.698	0.677	0.719	INDETERMINATE	1	TRUE	0	0.950734814351431	1		435	915	SUCCESS
LATS2	26524	MSKCC	GRCh37	13	21549364	21549364	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	70	451	369	0	ENST00000382592.4:c.2912C>T	p.Pro971Leu	p.P971L	ENST00000382592	NM_014572.2	971	cCc/cTc	8/8	0.950734814351431	1	FACETS	0.955	0.935	0.975	0.955	0.935	0.975	CLONAL	1	TRUE	0	0.950734814351431	1		369	521	SUCCESS
FLT1	2321	MSKCC	GRCh37	13	29001360	29001360	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	58	478	368	1	ENST00000282397.4:c.1372G>A	p.Gly458Ser	p.G458S	ENST00000282397	NM_002019.4	458	Ggt/Agt	10/30	0.950734814351431	1	FACETS	0.984	0.966	1	0.984	0.966	1	CLONAL	1	TRUE	0	0.950734814351431	1		369	536	SUCCESS
TSHR	7253	MSKCC	GRCh37	14	81558928	81558928	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	776	599	511	1	ENST00000298171.2:c.521G>A	p.Gly174Glu	p.G174E	ENST00000298171	NM_000369.2	174	gGa/gAa	6/10	1	2	FACETS	0.916	0.883	0.95	0.916	0.883	0.95	CLONAL	1	TRUE	1	0.950734814351431	2		512	1375	SUCCESS
RAD51	5888	MSKCC	GRCh37	15	40998433	40998434	+	missense_variant	Missense_Mutation	DNP	GG	GG	AA	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	989	746	683	3	ENST00000267868.3:c.284_285delinsAA	p.Arg95Lys	p.R95K	ENST00000267868	NM_002875.4	95	aGG/aAA	4/10	1	2	FACETS	0.905	0.875	0.935	0.905	0.875	0.935	CLONAL	1	TRUE	1	0.950734814351431	2		686	1735	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43701930	43701931	+	missense_variant	Missense_Mutation	DNP	TC	TC	GT	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	375	284	239	0	ENST00000382044.4:c.5314_5315delinsAC	p.Glu1772Thr	p.E1772T	ENST00000382044	NM_001141980.1	1772	GAa/ACa	25/28	1	2	FACETS	0.907	0.859	0.955	0.907	0.859	0.955	CLONAL	1	TRUE	1	0.950734814351431	2		239	659	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43707876	43707876	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	916	769	622	0	ENST00000382044.4:c.5005C>T	p.Leu1669Phe	p.L1669F	ENST00000382044	NM_001141980.1	1669	Ctc/Ttc	23/28	1	2	FACETS	0.96	0.93	0.991	0.96	0.93	0.991	CLONAL	1	TRUE	1	0.950734814351431	2		622	1685	SUCCESS
TP53BP1	7158	MSKCC	GRCh37	15	43712773	43712773	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs267604218	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	844	713	676	0	ENST00000382044.4:c.4411C>T	p.Pro1471Ser	p.P1471S	ENST00000382044	NM_001141980.1	1471	Cct/Tct	21/28	1	2	FACETS	0.963	0.932	0.995	0.963	0.932	0.995	CLONAL	1	TRUE	1	0.950734814351431	2		676	1557	SUCCESS
NTRK3	4916	MSKCC	GRCh37	15	88678572	88678572	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1161765368	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	398	340	275	1	ENST00000360948.2:c.964G>A	p.Glu322Lys	p.E322K	ENST00000360948	NM_001012338.2	322	Gag/Aag	9/19	1	2	FACETS	0.969	0.923	1	0.969	0.923	1	CLONAL	1	TRUE	1	0.950734814351431	2		276	738	SUCCESS
BLM	641	MSKCC	GRCh37	15	91290720	91290720	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	C	C	T	rs139282091	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	626	520	291	0	ENST00000355112.3:c.98C>T	p.Ser33Leu	p.S33L	ENST00000355112	NM_000057.2	33	tCa/tTa	2/22	1	2	FACETS	0.955	0.918	0.992	0.955	0.918	0.992	CLONAL	1	TRUE	1	0.950734814351431	2		291	1146	SUCCESS
CREBBP	1387	MSKCC	GRCh37	16	3779163	3779163	+	missense_variant	Missense_Mutation	SNP	A	A	G	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	538	409	362	0	ENST00000262367.5:c.5885T>C	p.Ile1962Thr	p.I1962T	ENST00000262367	NM_004380.2	1962	aTc/aCc	31/31	1	2	FACETS	0.909	0.868	0.949	0.909	0.868	0.949	CLONAL	1	TRUE	1	0.950734814351431	2		362	947	SUCCESS
PALB2	79728	MSKCC	GRCh37	16	23649399	23649399	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs373483056	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	664	524	377	1	ENST00000261584.4:c.100C>T	p.Arg34Cys	p.R34C	ENST00000261584	NM_024675.3	34	Cgc/Tgc	2/13	1	2	FACETS	0.928	0.892	0.964	0.928	0.892	0.964	CLONAL	1	TRUE	1	0.950734814351431	2		378	1188	SUCCESS
CBFB	865	MSKCC	GRCh37	16	67063356	67063356	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	607	542	358	0	ENST00000412916.2:c.46G>A	p.Glu16Lys	p.E16K	ENST00000412916		16	Gag/Aag	1/6	1	2	FACETS	0.992	0.955	1	0.992	0.955	1	CLONAL	1	TRUE	1	0.950734814351431	2		358	1149	SUCCESS
RARA	5914	MSKCC	GRCh37	17	38510600	38510601	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1507	671	597	0	ENST00000254066.5:c.854_855delinsTT	p.Thr285Ile	p.T285I	ENST00000254066	NM_000964.3	285	aCC/aTT	7/9	0.698512055369843	3	FACETS	0.956	0.92	0.993			1	CLONAL	1	TRUE	NA	0.950734814351431	3		597	2178	SUCCESS
EZH1	2145	MSKCC	GRCh37	17	40858195	40858195	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs777686988	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1574	672	555	1	ENST00000428826.2:c.1669C>T	p.Arg557Cys	p.R557C	ENST00000428826		557	Cgt/Tgt	16/21	0.897972895808122	3	FACETS	0.929	0.893	0.965	0.464	0.446	0.483	CLONAL	1	TRUE	1	0.950734814351431	3		556	2246	SUCCESS
RNF43	54894	MSKCC	GRCh37	17	56436055	56436055	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1348903060	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	416	717	245	0	ENST00000407977.2:c.1082C>T	p.Pro361Leu	p.P361L	ENST00000407977		361	cCt/cTt	9/10	0.897972895808122	3	FACETS	0.982	0.955	1	0.982	0.955	1	CLONAL	2	TRUE	1	0.950734814351431	3		245	1133	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11100046	11100046	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	933	797	700	0	ENST00000358026.2:c.1172C>T	p.Ser391Phe	p.S391F	ENST00000358026	NM_001128849.1	391	tCc/tTc	7/36	1	2	FACETS	0.969	0.939	0.999	0.969	0.939	0.999	CLONAL	1	TRUE	1	0.950734814351431	2		700	1730	SUCCESS
SMARCA4	6597	MSKCC	GRCh37	19	11145668	11145668	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	694	653	548	0	ENST00000358026.2:c.4030C>T	p.Pro1344Ser	p.P1344S	ENST00000358026	NM_001128849.1	1344	Ccc/Tcc	29/36	1	2	FACETS	1	0.98	1	1	0.98	1	CLONAL	1	TRUE	1	0.950734814351431	2		548	1347	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15291524	15291524	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs982964988	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	789	680	506	0	ENST00000263388.2:c.3110G>A	p.Ser1037Asn	p.S1037N	ENST00000263388	NM_000435.2	1037	aGc/aAc	19/33	1	2	FACETS	0.974	0.941	1	0.974	0.941	1	CLONAL	1	TRUE	1	0.950734814351431	2		506	1469	SUCCESS
NOTCH3	4854	MSKCC	GRCh37	19	15297757	15297757	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	982	865	692	0	ENST00000263388.2:c.1883C>T	p.Pro628Leu	p.P628L	ENST00000263388	NM_000435.2	628	cCc/cTc	12/33	1	2	FACETS	0.985	0.956	1	0.985	0.956	1	CLONAL	1	TRUE	1	0.950734814351431	2		692	1847	SUCCESS
CIC	23152	MSKCC	GRCh37	19	42791984	42791985	+	missense_variant	Missense_Mutation	DNP	CC	CC	TT	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	857	681	627	2	ENST00000575354.2:c.788_789delinsTT	p.Ala263Val	p.A263V	ENST00000575354	NM_015125.3	263	gCC/gTT	6/20	1	2	FACETS	0.931	0.9	0.963	0.931	0.9	0.963	CLONAL	1	TRUE	1	0.950734814351431	2		629	1538	SUCCESS
POLD1	5424	MSKCC	GRCh37	19	50912813	50912813	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs758260006	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	814	692	639	0	ENST00000440232.2:c.2044C>T	p.Arg682Trp	p.R682W	ENST00000440232	NM_002691.3	682	Cgg/Tgg	17/27	1	2	FACETS	0.967	0.934	0.999	0.967	0.934	0.999	CLONAL	1	TRUE	1	0.950734814351431	2		639	1506	SUCCESS
MYCN	4613	MSKCC	GRCh37	2	16082322	16082322	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1071	855	748	0	ENST00000281043.3:c.136G>A	p.Gly46Arg	p.G46R	ENST00000281043	NM_005378.4	46	Ggg/Agg	2/3	1	2	FACETS	0.934	0.905	0.962	0.934	0.905	0.962	CLONAL	1	TRUE	1	0.950734814351431	2		748	1926	SUCCESS
SOS1	6654	MSKCC	GRCh37	2	39214714	39214714	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	495	427	379	2	ENST00000402219.2:c.3410C>T	p.Ser1137Phe	p.S1137F	ENST00000402219	NM_005633.3	1137	tCt/tTt	22/23	1	2	FACETS	0.974	0.933	1	0.974	0.933	1	CLONAL	1	TRUE	1	0.950734814351431	2		381	922	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212483982	212483982	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	572	515	431	0	ENST00000342788.4:c.2221G>A	p.Gly741Arg	p.G741R	ENST00000342788	NM_005235.2	741	Gga/Aga	19/28	1	2	FACETS	0.997	0.959	1	0.997	0.959	1	CLONAL	1	TRUE	1	0.950734814351431	2		431	1087	SUCCESS
ERBB4	2066	MSKCC	GRCh37	2	212488678	212488678	+	missense_variant	Missense_Mutation	SNP	A	A	T	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	749	720	568	0	ENST00000342788.4:c.2171T>A	p.Leu724His	p.L724H	ENST00000342788	NM_005235.2	724	cTt/cAt	18/28	1	2	FACETS	1	0.986	1	1	0.986	1	CLONAL	1	TRUE	1	0.950734814351431	2		568	1469	SUCCESS
BARD1	580	MSKCC	GRCh37	2	215645966	215645966	+	missense_variant	Missense_Mutation	SNP	A	A	G	rs762171436	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	648	580	436	0	ENST00000260947.4:c.632T>C	p.Leu211Ser	p.L211S	ENST00000260947	NM_000465.2	211	tTa/tCa	4/11	1	2	FACETS	0.994	0.958	1	0.994	0.958	1	CLONAL	1	TRUE	1	0.950734814351431	2		436	1228	SUCCESS
PTPRT	11122	MSKCC	GRCh37	20	40735493	40735493	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs750916964	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	811	644	567	1	ENST00000373198.4:c.3380G>A	p.Gly1127Glu	p.G1127E	ENST00000373198	NM_133170.3	1127	gGg/gAg	25/32	1	2	FACETS	0.931	0.898	0.964	0.931	0.898	0.964	CLONAL	1	TRUE	1	0.950734814351431	2		568	1455	SUCCESS
SMARCB1	6598	MSKCC	GRCh37	22	24175868	24175868	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs886039520	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	697	604	366	0	ENST00000263121.7:c.1096C>T	p.Arg366Cys	p.R366C	ENST00000263121	NM_003073.3	366	Cgc/Tgc	8/9	1	2	FACETS	0.977	0.942	1	0.977	0.942	1	CLONAL	1	TRUE	1	0.950734814351431	2		366	1301	SUCCESS
EPHA3	2042	MSKCC	GRCh37	3	89259565	89259565	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs139652107	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	504	385	281	0	ENST00000336596.2:c.709G>A	p.Glu237Lys	p.E237K	ENST00000336596	NM_005233.5	237	Gaa/Aaa	3/17	1	2	FACETS	0.911	0.87	0.953	0.911	0.87	0.953	CLONAL	1	TRUE	1	0.950734814351431	2		281	889	SUCCESS
MAP3K13	9175	MSKCC	GRCh37	3	185161289	185161289	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	896	808	560	0	ENST00000265026.3:c.716G>A	p.Gly239Glu	p.G239E	ENST00000265026	NM_004721.4	239	gGa/gAa	4/14	1	2	FACETS	0.997	0.967	1	0.997	0.967	1	CLONAL	1	TRUE	1	0.950734814351431	2		560	1704	SUCCESS
TP63	8626	MSKCC	GRCh37	3	189612016	189612016	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs1560310917	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	690	510	480	1	ENST00000264731.3:c.1768C>T	p.Pro590Ser	p.P590S	ENST00000264731	NM_003722.4	590	Cct/Tct	14/14	1	2	FACETS	0.894	0.858	0.93	0.894	0.858	0.93	CLONAL	1	TRUE	1	0.950734814351431	2		481	1200	SUCCESS
PHOX2B	8929	MSKCC	GRCh37	4	41747933	41747933	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	556	253	391	0	ENST00000226382.2:c.836C>T	p.Pro279Leu	p.P279L	ENST00000226382	NM_003924.3	279	cCc/cTc	3/3	0.476553022551747	1	FACETS	0.345	0.324	0.367	0.345	0.324	0.367	INDETERMINATE	1	TRUE	0	0.950734814351431	1		391	809	SUCCESS
PDGFRA	5156	MSKCC	GRCh37	4	55144564	55144564	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	383	639	493	0	ENST00000257290.5:c.2038G>A	p.Gly680Arg	p.G680R	ENST00000257290	NM_006206.4	680	Gga/Aga	15/23	0.476553022551747	1	FACETS	0.69	0.67	0.71	0.69	0.67	0.71	INDETERMINATE	1	TRUE	0	0.950734814351431	1		493	1022	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55955874	55955874	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	748	358	560	2	ENST00000263923.4:c.3288G>A	p.Trp1096Ter	p.W1096*	ENST00000263923	NM_002253.2	1096	tgG/tgA	24/30	0.476553022551747	1	FACETS	0.357	0.339	0.376	0.357	0.339	0.376	INDETERMINATE	1	TRUE	0	0.950734814351431	1		562	1106	SUCCESS
KDR	3791	MSKCC	GRCh37	4	55980303	55980303	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	401	711	534	0	ENST00000263923.4:c.788C>T	p.Pro263Leu	p.P263L	ENST00000263923	NM_002253.2	263	cCt/cTt	6/30	0.476553022551747	1	FACETS	0.706	0.686	0.725	0.706	0.686	0.725	INDETERMINATE	1	TRUE	0	0.950734814351431	1		534	1112	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106155202	106155202	+	stop_gained	Nonsense_Mutation	SNP	C	C	T	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	335	559	435	0	ENST00000380013.4:c.103C>T	p.Gln35Ter	p.Q35*	ENST00000380013	NM_001127208.2	35	Cag/Tag	3/11	0.476553022551747	1	FACETS	0.69	0.668	0.711	0.69	0.668	0.711	INDETERMINATE	1	TRUE	0	0.950734814351431	1		435	894	SUCCESS
TET2	54790	MSKCC	GRCh37	4	106156594	106156594	+	missense_variant	Missense_Mutation	SNP	C	C	T	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	550	263	377	0	ENST00000380013.4:c.1495C>T	p.Pro499Ser	p.P499S	ENST00000380013	NM_001127208.2	499	Cca/Tca	3/11	0.476553022551747	1	FACETS	0.357	0.335	0.379	0.357	0.335	0.379	INDETERMINATE	1	TRUE	0	0.950734814351431	1		377	813	SUCCESS
APC	324	MSKCC	GRCh37	5	112177379	112177379	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs749725391	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	537	461	393	0	ENST00000257430.4:c.6088C>T	p.Leu2030Phe	p.L2030F	ENST00000257430	NM_000038.5	2030	Ctt/Ttt	16/16	1	2	FACETS	0.972	0.932	1	0.972	0.932	1	CLONAL	1	TRUE	1	0.950734814351431	2		393	998	SUCCESS
EPHA7	2045	MSKCC	GRCh37	6	94066701	94066701	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	681	624	542	0	ENST00000369303.4:c.1058C>T	p.Pro353Leu	p.P353L	ENST00000369303	NM_004440.3	353	cCt/cTt	5/17	1	2	FACETS	1	0.971	1	1	0.971	1	CLONAL	1	TRUE	1	0.950734814351431	2		542	1305	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117704482	117704482	+	missense_variant,splice_region_variant	Missense_Mutation	SNP	T	T	C	rs1374573342	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	31	347	338	0	ENST00000368508.3:c.2494A>G	p.Lys832Glu	p.K832E	ENST00000368508	NM_002944.2	832	Aag/Gag	16/43	0.950734814351431	1	FACETS	1	0.989	1	1	0.989	1	CLONAL	1	TRUE	0	0.950734814351431	1		338	378	SUCCESS
ROS1	6098	MSKCC	GRCh37	6	117725528	117725528	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs867759865	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	67	625	482	1	ENST00000368508.3:c.353G>A	p.Arg118Gln	p.R118Q	ENST00000368508	NM_002944.2	118	cGa/cAa	5/43	0.950734814351431	1	FACETS	0.997	0.981	1	0.997	0.981	1	CLONAL	1	TRUE	0	0.950734814351431	1		483	692	SUCCESS
CARD11	84433	MSKCC	GRCh37	7	2979385	2979385	+	stop_gained,splice_region_variant	Nonsense_Mutation	SNP	G	G	A	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	1149	280	472	0	ENST00000396946.4:c.862C>T	p.Gln288Ter	p.Q288*	ENST00000396946	NM_032415.4	288	Cag/Tag	6/25	0.469991508980283	3	FACETS	0.608	0.57	0.648	0.203	0.19	0.216	INDETERMINATE	1	TRUE	0	0.950734814351431	3		472	1429	SUCCESS
ETV1	2115	MSKCC	GRCh37	7	13971210	13971210	+	missense_variant	Missense_Mutation	SNP	G	G	A	novel	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	864	210	359	0	ENST00000405192.2:c.719C>T	p.Thr240Ile	p.T240I	ENST00000405192	NM_001163147.1	240	aCc/aTc	8/12	0.469991508980283	3	FACETS	0.607	0.563	0.652	0.202	0.187	0.218	INDETERMINATE	1	TRUE	0	0.950734814351431	3		359	1074	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50444318	50444318	+	missense_variant	Missense_Mutation	SNP	G	G	A	rs1427077431	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	650	389	260	0	ENST00000331340.3:c.248G>A	p.Arg83Gln	p.R83Q	ENST00000331340	NM_006060.4	83	cGa/cAa	4/8	0.469991508980283	3	FACETS	1	0.991	1	0.387	0.369	0.406	INDETERMINATE	1	TRUE	0	0.950734814351431	3		260	1039	SUCCESS
IKZF1	10320	MSKCC	GRCh37	7	50467856	50467856	+	missense_variant	Missense_Mutation	SNP	C	C	T	rs771544454	NA	P-0018561-T01-IM6	NA	NA	NA	NA	NA	NA	NA	NA	Unknown	SOMATIC	NA	NA	NA	MSK-IMPACT	NA	NA	182	653	308	1	ENST00000331340.3:c.1091C>T	p.Se